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|254781167|ref|YP_003065580.1| tRNA-dihydrouridine synthase A
[Candidatus Liberibacter asiaticus str. psy62]
         (322 letters)

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

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


Results from round 1


>gi|254781167|ref|YP_003065580.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254040844|gb|ACT57640.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 322

 Score =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/322 (100%), Positives = 322/322 (100%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS
Sbjct: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT
Sbjct: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY
Sbjct: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS
Sbjct: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE
Sbjct: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300

Query: 301 AGASTATHHIIETAFNLMIESL 322
           AGASTATHHIIETAFNLMIESL
Sbjct: 301 AGASTATHHIIETAFNLMIESL 322


>gi|315122552|ref|YP_004063041.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313495954|gb|ADR52553.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 352

 Score =  556 bits (1434), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 258/322 (80%), Positives = 292/322 (90%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVDWTDRHYRFFARLLTNNA+LYTEMIVADAIL G+++NILGFST+EKPLALQIGG+DI+
Sbjct: 29  MVDWTDRHYRFFARLLTNNAILYTEMIVADAILYGNRQNILGFSTEEKPLALQIGGSDIA 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KLVE+AKIVEDFGYNEIN NVGCPS  VH GSFGACLML P+ VGDCIAAM  ALSIPVT
Sbjct: 89  KLVESAKIVEDFGYNEINFNVGCPSPNVHAGSFGACLMLTPESVGDCIAAMQNALSIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+QIPA+ALRNL+KSIK+SGV GIWIHARKAIL GLSPKDNRKIP LDYDI+Y
Sbjct: 149 VKCRIGVDNQIPAIALRNLIKSIKQSGVKGIWIHARKAILGGLSPKDNRKIPKLDYDIIY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKKENPDLFIGLNGGL++M Q L++LP VDGVM+GR+AY+NS +L +VDEYF NPLTGS
Sbjct: 209 EIKKENPDLFIGLNGGLDNMQQILQVLPHVDGVMVGRSAYQNSIILASVDEYFMNPLTGS 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P K  +DKDFW++IS SM+ YA RH+ +GGKL  ITRHMIGLFHGFP++RRCRHILTVE
Sbjct: 269 APKKKTIDKDFWKQISDSMSKYADRHIKAGGKLSHITRHMIGLFHGFPHARRCRHILTVE 328

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A A TATH +I+TAFNLMIESL
Sbjct: 329 ANAPTATHQLIKTAFNLMIESL 350


>gi|307321239|ref|ZP_07600641.1| dihydrouridine synthase DuS [Sinorhizobium meliloti AK83]
 gi|306893141|gb|EFN23925.1| dihydrouridine synthase DuS [Sinorhizobium meliloti AK83]
          Length = 385

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/352 (54%), Positives = 249/352 (70%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 27  MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 87  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALK-----ILPS---------------VDGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL       LP+               +DGVM+GRAAY
Sbjct: 207 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK----------DFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 267 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+ EA    A   +I  AF+ + E++
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQILSTEATRKDAGPQVIHAAFDAVFEAV 378


>gi|307315973|ref|ZP_07595462.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
 gi|306898376|gb|EFN29074.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
          Length = 361

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/352 (54%), Positives = 249/352 (70%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 3   MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 63  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 123 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 182

Query: 181 EIKKENPDLFIGLNGGLEDMSQALK-----ILPS---------------VDGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL       LP+               +DGVM+GRAAY
Sbjct: 183 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 242

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK----------DFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 243 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 302

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+ EA    A   +I  AF+ + E++
Sbjct: 303 GRLIHVTRHMVGLFQGWPGARRYRQILSTEATRKDAGPQVIHAAFDAVFEAV 354


>gi|15965658|ref|NP_386011.1| tRNA-dihydrouridine synthase A [Sinorhizobium meliloti 1021]
 gi|15074839|emb|CAC46484.1| Conserved hypothetical protein [Sinorhizobium meliloti 1021]
          Length = 359

 Score =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/352 (54%), Positives = 249/352 (70%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 1   MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 61  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 121 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALK-----ILPS---------------VDGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL       LP+               +DGVM+GRAAY
Sbjct: 181 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 240

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK----------DFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 241 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 300

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+ EA    A   +I  AF+ + E++
Sbjct: 301 GRLIHVTRHMVGLFQGWPGARRYRQILSTEATRKDAGPQVIHAAFDAVFEAV 352


>gi|150396830|ref|YP_001327297.1| tRNA-dihydrouridine synthase A [Sinorhizobium medicae WSM419]
 gi|150028345|gb|ABR60462.1| dihydrouridine synthase DuS [Sinorhizobium medicae WSM419]
          Length = 385

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 187/352 (53%), Positives = 244/352 (69%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR+L+ +ALLYTEMIVADA+LRGD+  +LG    E P+ALQ+GG D  
Sbjct: 27  MIDWTDRHYRFFARVLSRHALLYTEMIVADAVLRGDRAKLLGHDASEHPVALQLGGNDPV 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E +GY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 87  KMAEAARIGEAYGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVEIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LVK  K +G +G+W+HARKA L+GLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRDLVKCAKDAGTDGVWVHARKAWLQGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL-----KILPS---------------VDGVMIGRAAY 220
            +K EN  LFIG+NGGL+ + QAL     + LP+               +DGVM+GRAAY
Sbjct: 207 RLKAENESLFIGINGGLQGLDQALSHLDPRSLPAGEAMKAATEIKSGAPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK----------DFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG++ + T  D           +FW  +   M DYAA H+ +G
Sbjct: 267 HDSGLLTAADGYFRHPLTGAAAVPTDPDGFSDRDHNLSLEFWSGVRDVMEDYAAAHIENG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+  A    A   +I TAF+ + ++ 
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQILSTRATRKDAGPEVIHTAFDAVFQAF 378


>gi|307310192|ref|ZP_07589841.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
 gi|306899744|gb|EFN30369.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
          Length = 353

 Score =  389 bits (998), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/327 (56%), Positives = 236/327 (72%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 27  MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 87  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALK-----ILPS---------------VDGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL       LP+               +DGVM+GRAAY
Sbjct: 207 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK----------DFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 267 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHIL 297
           G+L  +TRHM+GLF G+P +RR R IL
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQIL 353


>gi|227822301|ref|YP_002826272.1| tRNA-dihydrouridine synthase A [Sinorhizobium fredii NGR234]
 gi|227341301|gb|ACP25519.1| putative tRNA-dihydrouridine synthase A [Sinorhizobium fredii
           NGR234]
          Length = 385

 Score =  375 bits (964), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 183/346 (52%), Positives = 241/346 (69%), Gaps = 30/346 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+ +ALLYTEMIVADAILRGD+  +LG    E P+ALQ+GG D +
Sbjct: 27  MIDWTDRHYRFFARQLSRHALLYTEMIVADAILRGDRDRLLGHDAAEHPVALQLGGNDPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V +C+AAM +A++IPVT
Sbjct: 87  KMAEAARIAEAFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVAECVAAMKEAVTIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR LV  +K +G + +W+HARKA L+GLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRALVARVKSAGADAVWVHARKAWLQGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL-----KILPS---------------VDGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL     ++LP+               +DGVM+GRAAY
Sbjct: 207 RLKSENKNLFIGLNGGLQTLDQALAHLDPRLLPAHAPKLAVAEAEHEVPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK----------DFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF++PLTG+ P+    D            FW  +  +M  YAA H+ +G
Sbjct: 267 HDSGLLTAADGYFAHPLTGAPPVPLDPDSFSERGHCLSLTFWADVRDAMAAYAAAHIDNG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           G+L  +TRHM+GLF G+P +RR R +L+ +A    A   +I  AF 
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQMLSADATRKGAGPEVIHAAFE 372


>gi|209549798|ref|YP_002281715.1| tRNA-dihydrouridine synthase A [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209535554|gb|ACI55489.1| TIM-barrel protein, yjbN family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 333

 Score =  365 bits (937), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 172/315 (54%), Positives = 219/315 (69%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D S
Sbjct: 13  MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E +GY+EINLNVGCPS RV  G+FGACLML P+ V DCIAAM K  ++PVT
Sbjct: 73  KLAEAVKISEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVADCIAAMKKVATVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEQALPELITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD+ F     G 
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAAAHLAHVDGVMLGRAAYQNAAILAEVDQRFFGAPAGE 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+ SGG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 253 PD---------WEGLRDRMMAYAERHIASGGRLQHVARHMVGLFTGLPGARRYRQILSTD 303

Query: 301 AGASTATHHIIETAF 315
           A  S A   ++  AF
Sbjct: 304 AAKSGAGPEVLAAAF 318


>gi|116252712|ref|YP_768550.1| tRNA-dihydrouridine synthase A [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115257360|emb|CAK08455.1| putative tRNA-dihydrouridine synthase A [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 333

 Score =  357 bits (917), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 169/316 (53%), Positives = 221/316 (69%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G +  +LG    E PLALQ+GG+D +
Sbjct: 13  MIDWTDRHCRYFHRQISREALLYTEMVVADAIIHGPRDRLLGHDAAEHPLALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E + Y+EINLNVGCPS RV  G+FGACLML P++V +CIAAM +  ++PVT
Sbjct: 73  KLAEAVKIAEPYFYDEINLNVGCPSDRVQSGTFGACLMLTPEMVAECIAAMKRVATVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEQALPELITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  +D+ +F  P   
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAATHLAHVDGVMLGRAAYQNAAILADIDQRFFGAP--A 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S P         W  +   M  YA RH+ SGG+LQ + RHM+GLF G P +RR R IL+ 
Sbjct: 251 SEPD--------WEALRDRMMAYAERHIASGGRLQHVARHMVGLFTGLPGARRYRQILST 302

Query: 300 EAGASTATHHIIETAF 315
           +A  S A   ++  AF
Sbjct: 303 DAAKSGAGPEVLAAAF 318


>gi|241205218|ref|YP_002976314.1| tRNA-dihydrouridine synthase A [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859108|gb|ACS56775.1| TIM-barrel protein, yjbN family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 333

 Score =  353 bits (906), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 165/316 (52%), Positives = 217/316 (68%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G +  +LG    E PLALQ+GG+D +
Sbjct: 13  MIDWTDRHCRYFHRQISREALLYTEMVVADAIIHGPRDRLLGHDAAEHPLALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI + +GY+EINLNVGCPS RV  G+FGACLML P+ V +CIAAM +  + PVT
Sbjct: 73  KLTEAVKIAQPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAECIAAMKRVATAPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEQALPELISRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  +D+ +F  P   
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAAVHLEHVDGVMLGRAAYQNAAILADIDQRFFGAPAAE 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                       W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ 
Sbjct: 253 PD----------WEALCNRMMAYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILST 302

Query: 300 EAGASTATHHIIETAF 315
           +A  + A   ++  AF
Sbjct: 303 DAAKTGAGPEVLAAAF 318


>gi|218463688|ref|ZP_03503779.1| tRNA-dihydrouridine synthase A [Rhizobium etli Kim 5]
          Length = 333

 Score =  351 bits (900), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 165/316 (52%), Positives = 214/316 (67%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D  
Sbjct: 13  MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDVAEHPLALQLGGSDPG 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 73  KLAEAVKIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAACVAAMKAVATAPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+I Y
Sbjct: 133 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIAY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  +F  P   
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAASHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                       W  +   M  YA RH+ +GG+LQ + RHM+GLF G P +RR R IL+ 
Sbjct: 253 PD----------WPALCERMMTYAERHIAAGGRLQHVARHMVGLFTGLPGARRYRQILST 302

Query: 300 EAGASTATHHIIETAF 315
           +A  + A   ++  AF
Sbjct: 303 DAAKTGAGPEVLAAAF 318


>gi|163759729|ref|ZP_02166814.1| tRNA-dihydrouridine synthase A [Hoeflea phototrophica DFL-43]
 gi|162283326|gb|EDQ33612.1| tRNA-dihydrouridine synthase A [Hoeflea phototrophica DFL-43]
          Length = 336

 Score =  349 bits (895), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 174/318 (54%), Positives = 223/318 (70%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RF  R LT +ALLYTEM+VADA + GD++ +LGF   E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRFLHRQLTRHALLYTEMVVADAAIHGDRERLLGFDAVEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
           KL EA +I   FGY+EINLNVGCPS RV  G+FGACLM  PD+V  CIAAM KA S  +P
Sbjct: 78  KLAEAVRIAGGFGYDEINLNVGCPSDRVQSGTFGACLMREPDLVARCIAAM-KAASGDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVKCRIGVD+Q P +AL  L +++ + G + IW+HARKA L+GLSPK+NR +P LDYD 
Sbjct: 137 VTVKCRIGVDEQDPEIALSALTEAVIQVGADAIWVHARKAWLEGLSPKENRDVPPLDYDR 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ P++FIGLNGG+ED++QAL+ L  VDGVMIGRAAY N+ MLT VD        
Sbjct: 197 VYRLKQDYPNVFIGLNGGVEDLNQALEHLNHVDGVMIGRAAYHNAQMLTGVDRLIYGDDV 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +      VD   WR +  +M  +A  H+ SGG+L  +TRHM+GLF G   +RR R IL+
Sbjct: 257 AA------VD---WRAVCEAMMAHADAHVASGGRLNHVTRHMVGLFQGVRGARRFRQILS 307

Query: 299 VEAGASTATHHIIETAFN 316
            E+    A   +I  AF+
Sbjct: 308 TESTKPGAGPDVIARAFD 325


>gi|13470773|ref|NP_102342.1| tRNA-dihydrouridine synthase A [Mesorhizobium loti MAFF303099]
 gi|14021516|dbj|BAB48128.1| mll0566 [Mesorhizobium loti MAFF303099]
          Length = 332

 Score =  347 bits (891), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 169/315 (53%), Positives = 219/315 (69%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT+ ALLYTEM+VADA++ G ++ +LGF   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRFFHRQLTSRALLYTEMVVADAVIHGARERLLGFDDAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E FGY+E+NLNVGCPS RV  G+FGACLM  PD+V  C+ AM  A++IPVT
Sbjct: 74  KLAEAARIGEAFGYDEVNLNVGCPSDRVQSGTFGACLMKVPDLVAGCVTAMKAAVAIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L   +  +G + +W+HARKA L+GLSPK+NR IP LDY+ VY
Sbjct: 134 VKCRIGVDEQNPEPALDALADGVFNAGADALWVHARKAWLEGLSPKENRDIPPLDYNRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P+ FIG+NGG++ + +A   L  VDG M+GRAAY    +L  VD  F     G+
Sbjct: 194 RLKAKKPNEFIGINGGIQSLEEARAHLDHVDGAMLGRAAYHTPGILAGVDAGF----YGA 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P       DF   I A M DYAARH+  GG+L  +TRHM+GLFHG P +RR R IL+ +
Sbjct: 250 KPEAF----DFAALIDA-MADYAARHIEQGGRLGHVTRHMVGLFHGLPGARRYRQILSTD 304

Query: 301 AGASTATHHIIETAF 315
           A    A   +++TAF
Sbjct: 305 ANRPGAGPDVLKTAF 319


>gi|86358178|ref|YP_470070.1| tRNA-dihydrouridine synthase A [Rhizobium etli CFN 42]
 gi|86282280|gb|ABC91343.1| putative tRNA-dihydrouridine synthase (nifR3-like) protein
           [Rhizobium etli CFN 42]
          Length = 321

 Score =  347 bits (891), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 165/316 (52%), Positives = 215/316 (68%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 1   MIDWTDRHCRYFHRQISREALLYTEMVVADAIIHGPRERLLGHDATEHPLALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E + Y+EINLNVGCPS RV  G+FGACLML P+ V +C+AAM    + PVT
Sbjct: 61  KLAEAVKIAEPYRYDEINLNVGCPSDRVQSGTFGACLMLTPETVAECVAAMKAVATAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 121 VKCRIGVDEQEPEEALPELITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  +F  P   
Sbjct: 181 RMKQRWPDVFIGINGGIRTLDEAASHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                       W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ 
Sbjct: 241 PD----------WEALRDRMMVYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSS 290

Query: 300 EAGASTATHHIIETAF 315
           +A  + A   ++  AF
Sbjct: 291 DAVKNGAGPEVLAAAF 306


>gi|190892270|ref|YP_001978812.1| tRNA-dihydrouridine synthase [Rhizobium etli CIAT 652]
 gi|190697549|gb|ACE91634.1| putative tRNA-dihydrouridine synthase protein [Rhizobium etli CIAT
           652]
          Length = 321

 Score =  347 bits (889), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 164/307 (53%), Positives = 211/307 (68%), Gaps = 11/307 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 1   MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 61  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAGCVAAMKAVSTAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 121 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  +F  P   
Sbjct: 181 RMKQRWPDVFIGINGGIRTLDEAADHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                       W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ 
Sbjct: 241 PD----------WPALCERMMAYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILST 290

Query: 300 EAGASTA 306
           +A  S A
Sbjct: 291 DAAKSGA 297


>gi|218510078|ref|ZP_03507956.1| tRNA-dihydrouridine synthase A [Rhizobium etli Brasil 5]
          Length = 301

 Score =  346 bits (888), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 164/307 (53%), Positives = 211/307 (68%), Gaps = 11/307 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 1   MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 61  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAGCVAAMKAVSTAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 121 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  +F  P   
Sbjct: 181 RMKQRWPDVFIGINGGIRTLDEAADHLARVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                       W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ 
Sbjct: 241 PD----------WPALCERMMAYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILST 290

Query: 300 EAGASTA 306
           +A  S A
Sbjct: 291 DAAKSGA 297


>gi|260459398|ref|ZP_05807653.1| TIM-barrel protein, yjbN family [Mesorhizobium opportunistum
           WSM2075]
 gi|259034952|gb|EEW36208.1| TIM-barrel protein, yjbN family [Mesorhizobium opportunistum
           WSM2075]
          Length = 332

 Score =  345 bits (885), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 169/313 (53%), Positives = 216/313 (69%), Gaps = 9/313 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT  ALLYTEM+VADA+++G +  +LGF   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRFFHRQLTTCALLYTEMVVADAVIQGARDRLLGFDQAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E FGY+EINLNVGCPS RV  G+FGACLM  PD+V DC+AAM   + IPVT
Sbjct: 74  KLAEAARIGEAFGYDEINLNVGCPSDRVQSGTFGACLMKVPDLVADCVAAMKATVKIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L   + ++G + +W+HARKA L+GLSPK+NR IP LDY+ VY
Sbjct: 134 VKCRIGVDEQDPEPALDALANGVFEAGTDALWVHARKAWLEGLSPKENRDIPPLDYNRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+ FIG+NGG++ + +A   L  VDG M+GRAAY    +L  VD  F     G+
Sbjct: 194 RLKAGKPNKFIGINGGIQSLDEARGHLDHVDGAMLGRAAYHTPGILAGVDAAF----YGT 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P       DF   I A M DYAARH+  GG+L  +TRHM+GLFHG P +RR R IL+ +
Sbjct: 250 EPAAF----DFAALIDA-MADYAARHIEQGGRLGHVTRHMVGLFHGLPGARRYRQILSTD 304

Query: 301 AGASTATHHIIET 313
           A    A   +++T
Sbjct: 305 ATRPGAGPDVLKT 317


>gi|15888840|ref|NP_354521.1| tRNA-dihydrouridine synthase A [Agrobacterium tumefaciens str. C58]
 gi|15156601|gb|AAK87306.1| conserved hypothetical protein [Agrobacterium tumefaciens str. C58]
          Length = 336

 Score =  344 bits (883), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 159/315 (50%), Positives = 221/315 (70%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   RF  R L+  ALL+TEMIVADAI+ G ++ +LG+  QE P+ALQ+GG++ +
Sbjct: 18  MIDWTDTRCRFLHRQLSKRALLFTEMIVADAIIHGQREKLLGYHPQEHPVALQLGGSNPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  D+GY+EINLNVGCPS RV  G+FGACLM  P++V  CI+AM    ++PVT
Sbjct: 78  KLAEAVRIAGDYGYDEINLNVGCPSDRVQSGTFGACLMREPEVVAQCISAMKAVAAVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  +  +G + +W+HARKA L+GLSPK+NR++P LDYD+VY
Sbjct: 138 VKCRIGVDDQEPETVLPDFLARVVAAGADAVWVHARKAWLQGLSPKENREVPPLDYDLVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++NPD+FIG+NGG+ D+ QA + L  VDGVM+GRAAY N+++L  VD    + + G 
Sbjct: 198 RMKRDNPDVFIGINGGIADLDQAGEHLKYVDGVMLGRAAYHNTSILADVD----HRIHGE 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             ++       W  +  +M  YAA ++ +GG+L  +TRHM+GLF G P +RR R IL+ +
Sbjct: 254 EALQYD-----WMALRDTMMAYAADYIATGGRLNHVTRHMVGLFQGMPGARRFRQILSSD 308

Query: 301 AGASTATHHIIETAF 315
           A    A   +IE AF
Sbjct: 309 ATRPGAGPEVIEAAF 323


>gi|222086273|ref|YP_002544805.1| tRNA-dihydrouridine synthase (nifR3-like) protein [Agrobacterium
           radiobacter K84]
 gi|221723721|gb|ACM26877.1| tRNA-dihydrouridine synthase (nifR3-like) protein [Agrobacterium
           radiobacter K84]
          Length = 337

 Score =  343 bits (880), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 165/315 (52%), Positives = 213/315 (67%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  R ++ +ALLYTEM+VADAI+ G +  +LG    E P+ALQ+GG+D +
Sbjct: 18  MIDWTDRHCRYLHRQISRHALLYTEMVVADAIIHGPRDRLLGHDVSEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL  A +I E + Y+EINLNVGCPS RV  G+FGACLML P+ V +CIAAM      PVT
Sbjct: 78  KLSNALQIAEAYNYDEINLNVGCPSDRVQSGTFGACLMLTPETVAECIAAMKAVSKAPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDYDIVY
Sbjct: 138 VKCRIGVDEQEPEQALPELIARVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYDIVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG++ + QA   L  VDGVM+GRAAY+N+A+L  VD  F       
Sbjct: 198 RMKQRWPDVFIGINGGIQTLDQAEAHLAHVDGVMLGRAAYQNAAILADVDHRFFG----- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              +  V+ D W  +   M  Y  RH+ SGG++  + RHM+GLF G P SRR R IL+ +
Sbjct: 253 ---EAAVEPD-WNDLRDRMMAYTERHIASGGRVHHVARHMVGLFTGLPGSRRYRQILSTD 308

Query: 301 AGASTATHHIIETAF 315
           A    A   +I  AF
Sbjct: 309 ANKPGAEPEVIAAAF 323


>gi|222106594|ref|YP_002547385.1| hypothetical protein Avi_5568 [Agrobacterium vitis S4]
 gi|221737773|gb|ACM38669.1| conserved hypothetical protein [Agrobacterium vitis S4]
          Length = 341

 Score =  342 bits (878), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 172/316 (54%), Positives = 214/316 (67%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   R F RLLT +ALLYTEMIVADAIL G +  +L F   E PLALQ+GG+D  
Sbjct: 23  MIDWTDTFCRRFHRLLTRHALLYTEMIVADAILHGKRDRLLAFDASEHPLALQLGGSDPH 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  D+GY+EINLNVGCPS RV  G+FGACLM  P  V  CI AM  A ++PVT
Sbjct: 83  KLAEAVRIANDWGYDEINLNVGCPSDRVQAGTFGACLMREPQTVEACIQAMKAASTVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +K +  +G + +WIHARKA L+GLSPK+NR IP LDY +V+
Sbjct: 143 VKCRIGVDDQEPGDVLPDFIKRMIGAGADALWIHARKAWLQGLSPKENRDIPPLDYPLVH 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+ENPD+FIG+NGG+ D+ QA   L  +DGVM+GRAAY N+ MLT VD   +  PL  
Sbjct: 203 LMKQENPDIFIGINGGVTDLDQASAHLQVMDGVMVGRAAYNNATMLTEVDARIYGEPLQA 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +    R DK         M DYAARH+  GG+L  +TRHM+GLF G+  +RR R IL+ 
Sbjct: 263 QNMDIVR-DK---------MMDYAARHIAEGGRLVHLTRHMVGLFQGYAGARRFRQILSA 312

Query: 300 EAGASTATHHIIETAF 315
           +A    A   +I  AF
Sbjct: 313 DAPKPGAGPDVIAAAF 328


>gi|325292867|ref|YP_004278731.1| tRNA-dihydrouridine synthase A [Agrobacterium sp. H13-3]
 gi|325060720|gb|ADY64411.1| tRNA-dihydrouridine synthase A [Agrobacterium sp. H13-3]
          Length = 319

 Score =  342 bits (877), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 161/315 (51%), Positives = 212/315 (67%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   RF  R L+  ALLYTEMIVADAI+ G +  +L + TQE P+ALQ+GG+D  
Sbjct: 1   MIDWTDTRCRFLHRQLSKRALLYTEMIVADAIIHGQRDRLLNYHTQEHPVALQLGGSDPV 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  D+GY+EINLNVGCPS RV  G+FGACLM  P+IV  C+AAM     +PVT
Sbjct: 61  KLSEAVRIASDYGYDEINLNVGCPSDRVQSGTFGACLMREPEIVAQCVAAMKAVAKVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  +  +G + +WIHARKA L+GLSPK+NR++P LDYD+VY
Sbjct: 121 VKCRIGVDDQEPEAVLPDFLSRVVAAGADAVWIHARKAWLQGLSPKENREVPPLDYDLVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ NPD+FIG+NGG+ D+ QA   L  +DGVM+GRAAY N+++L  VD          
Sbjct: 181 RMKRANPDIFIGINGGISDLDQASLHLHHMDGVMLGRAAYHNTSILADVDHRIYG----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +  W  +  +M  YAA ++ +GG+L  +TRHM+GLF G P +RR R IL+ +
Sbjct: 236 ----EEARQADWMGLRDAMMAYAADYIAAGGRLNHVTRHMVGLFQGMPGARRFRQILSSD 291

Query: 301 AGASTATHHIIETAF 315
           A    A   +IE AF
Sbjct: 292 ATRPGAGTEVIEAAF 306


>gi|163868285|ref|YP_001609494.1| tRNA-dihydrouridine synthase A [Bartonella tribocorum CIP 105476]
 gi|161017941|emb|CAK01499.1| tRNA-dihydrouridine synthase A [Bartonella tribocorum CIP 105476]
          Length = 327

 Score =  341 bits (875), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 172/323 (53%), Positives = 223/323 (69%), Gaps = 17/323 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VADAI+ G ++ +L FS +E P+ALQ+GGAD  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMMVADAIIHGVREQLLAFSHKECPVALQLGGADPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGYNEINLNVGCPS RV  G FGACLML+PDIV + + +M KA++IPVT
Sbjct: 77  KLAEAARIAEDFGYNEINLNVGCPSNRVQAGVFGACLMLHPDIVANAVESMKKAVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q   +AL  L   +  +G + +WIHARKA LKGLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRIGVDEQDEELALDLLADKVWDAGCDALWIHARKAWLKGLSPKENRNIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SNP 236
           ++K++ P  FIG+NGG++ + +  + L   D  M+GR  Y +  +L  +D  F     N 
Sbjct: 197 KLKRKYPHKFIGINGGIKSIDEIKEHLVFCDATMVGRQVYHDPTLLKHIDFEFYGESQNN 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           L+ S  I+T             M DYAARH+ SGG+L  +TRHMIGLFHG   +RR R I
Sbjct: 257 LSESDLIET-------------MCDYAARHIASGGRLSHVTRHMIGLFHGRSGARRWRQI 303

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           L+ +A  S A  +I+  AF+ +I
Sbjct: 304 LSNDATKSNADIYILREAFSALI 326


>gi|90418092|ref|ZP_01226004.1| tRNA-dihydrouridine synthase A [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90337764|gb|EAS51415.1| tRNA-dihydrouridine synthase A [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 351

 Score =  341 bits (874), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 174/315 (55%), Positives = 219/315 (69%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT +ALLYTEM+VADAIL GD+  +LG    E PLALQIGG++  
Sbjct: 33  MIDWTDRHCRFFHRQLTWHALLYTEMVVADAILHGDRDRLLGHDAVESPLALQIGGSEPQ 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  DFGY+EINLNVGCPS RV  G+FGACLM  PD+VG C+AAM +A  +PVT
Sbjct: 93  KLAEACRIAADFGYDEINLNVGCPSDRVQSGAFGACLMREPDLVGRCLAAMAEASDVPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL +L  +   +GV  IW+HARKA L+GLSPK+NR IP LDYD V+
Sbjct: 153 VKCRIGVDEQDPEPALDDLADAAIAAGVTTIWVHARKAWLQGLSPKENRDIPPLDYDRVH 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+ F+GLNGGL  +  A++ L  VDGVM+GRAAY+    L  VD      + G+
Sbjct: 213 RLKQRLPEAFVGLNGGLTTLDAAVEELDRVDGVMMGRAAYQTPDRLAEVDAR----VFGA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P    VD   +  +  +M DYAARHL  GG+L Q+TRHM+GLF+G P +RR R IL+  
Sbjct: 269 APRP--VD---YAALIDTMADYAARHLERGGRLGQVTRHMLGLFNGMPGARRWRQILSDG 323

Query: 301 AGASTATHHIIETAF 315
           A    A   ++  AF
Sbjct: 324 AVRPNAGPQLLREAF 338


>gi|319783627|ref|YP_004143103.1| TIM-barrel protein, yjbN family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169515|gb|ADV13053.1| TIM-barrel protein, yjbN family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 332

 Score =  341 bits (874), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 167/315 (53%), Positives = 216/315 (68%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+++ALLYTEM+VADA++ G ++ +LGF   E P+ALQ+GG+D  
Sbjct: 14  MMDWTDRHCRFFHRQLSSHALLYTEMVVADAVIHGARERLLGFDASEHPVALQLGGSDRE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E FGY+EINLNVGCPS RV  G+FGACLM  PD+V  C+AAM  A++IPVT
Sbjct: 74  KLAEAARIGEAFGYDEINLNVGCPSDRVQSGTFGACLMKVPDLVAGCVAAMKAAVTIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L   +  +G + +W+HARKA L+GLSPK+NR IP LDY+ VY
Sbjct: 134 VKCRIGVDEQDPEPALDALADGVFDAGADALWVHARKAWLEGLSPKENRDIPPLDYNRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K    + FIG+NGG++ + +AL  L  VDG M+GRAAY    +L  VD  F      S
Sbjct: 194 RLKARKHNEFIGINGGIQTIEEALAHLDHVDGAMLGRAAYHTPGILAGVDAAFYG--VQS 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P       DF   I  +M DYAARH+  GG+L  +TRHM+GLFHG   +RR R IL+ +
Sbjct: 252 EPF------DFAALID-TMADYAARHIEQGGRLGHVTRHMVGLFHGLSGARRYRQILSTD 304

Query: 301 AGASTATHHIIETAF 315
           A    A   +++ AF
Sbjct: 305 ATKPGAGPDVLKAAF 319


>gi|17987386|ref|NP_540020.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str. 16M]
 gi|225852375|ref|YP_002732608.1| tRNA-dihydrouridine synthase A [Brucella melitensis ATCC 23457]
 gi|256044537|ref|ZP_05447441.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256113397|ref|ZP_05454251.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|256264126|ref|ZP_05466658.1| TIM-barrel protein [Brucella melitensis bv. 2 str. 63/9]
 gi|260563890|ref|ZP_05834376.1| TIM-barrel protein [Brucella melitensis bv. 1 str. 16M]
 gi|265990962|ref|ZP_06103519.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265994799|ref|ZP_06107356.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|17983074|gb|AAL52284.1| nifr3-like protein [Brucella melitensis bv. 1 str. 16M]
 gi|225640740|gb|ACO00654.1| TIM-barrel protein, yjbN family protein [Brucella melitensis ATCC
           23457]
 gi|260153906|gb|EEW88998.1| TIM-barrel protein [Brucella melitensis bv. 1 str. 16M]
 gi|262765912|gb|EEZ11701.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|263001746|gb|EEZ14321.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263094345|gb|EEZ18190.1| TIM-barrel protein [Brucella melitensis bv. 2 str. 63/9]
          Length = 340

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKACLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|326408882|gb|ADZ65947.1| tRNA-dihydrouridine synthase A [Brucella melitensis M28]
          Length = 329

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 13  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 73  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 133 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKACLKGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 193 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 251 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 304 ATKPGATSDVVRQAYATVVEA 324


>gi|256369291|ref|YP_003106799.1| TIM-barrel protein, yjbN family [Brucella microti CCM 4915]
 gi|255999451|gb|ACU47850.1| TIM-barrel protein, yjbN family [Brucella microti CCM 4915]
          Length = 340

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|254701628|ref|ZP_05163456.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|261752180|ref|ZP_05995889.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|261741933|gb|EEY29859.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 5 str. 513]
          Length = 340

 Score =  340 bits (871), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|23501749|ref|NP_697876.1| tRNA-dihydrouridine synthase A [Brucella suis 1330]
 gi|62289809|ref|YP_221602.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 1 str. 9-941]
 gi|82699735|ref|YP_414309.1| tRNA-dihydrouridine synthase A [Brucella melitensis biovar Abortus
           2308]
 gi|148560730|ref|YP_001258838.1| tRNA-dihydrouridine synthase A [Brucella ovis ATCC 25840]
 gi|161618824|ref|YP_001592711.1| tRNA-dihydrouridine synthase A [Brucella canis ATCC 23365]
 gi|163843134|ref|YP_001627538.1| tRNA-dihydrouridine synthase A [Brucella suis ATCC 23445]
 gi|189024050|ref|YP_001934818.1| tRNA-dihydrouridine synthase A [Brucella abortus S19]
 gi|225627352|ref|ZP_03785389.1| TIM-barrel protein, yjbN family protein [Brucella ceti str. Cudo]
 gi|237815294|ref|ZP_04594292.1| TIM-barrel protein, yjbN family [Brucella abortus str. 2308 A]
 gi|254689114|ref|ZP_05152368.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|254693597|ref|ZP_05155425.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|254697247|ref|ZP_05159075.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254704172|ref|ZP_05166000.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|254706926|ref|ZP_05168754.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|254709966|ref|ZP_05171777.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis B2/94]
 gi|254713966|ref|ZP_05175777.1| tRNA-dihydrouridine synthase A [Brucella ceti M644/93/1]
 gi|254716976|ref|ZP_05178787.1| tRNA-dihydrouridine synthase A [Brucella ceti M13/05/1]
 gi|254730146|ref|ZP_05188724.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|256031459|ref|ZP_05445073.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|256060968|ref|ZP_05451126.1| tRNA-dihydrouridine synthase A [Brucella neotomae 5K33]
 gi|256159585|ref|ZP_05457347.1| tRNA-dihydrouridine synthase A [Brucella ceti M490/95/1]
 gi|256254865|ref|ZP_05460401.1| tRNA-dihydrouridine synthase A [Brucella ceti B1/94]
 gi|256257363|ref|ZP_05462899.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|260168593|ref|ZP_05755404.1| tRNA-dihydrouridine synthase A [Brucella sp. F5/99]
 gi|260545444|ref|ZP_05821185.1| TIM-barrel protein [Brucella abortus NCTC 8038]
 gi|260566579|ref|ZP_05837049.1| TIM-barrel protein [Brucella suis bv. 4 str. 40]
 gi|260754612|ref|ZP_05866960.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|260757835|ref|ZP_05870183.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|260761658|ref|ZP_05874001.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260883639|ref|ZP_05895253.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|261213862|ref|ZP_05928143.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|261218781|ref|ZP_05933062.1| tRNA-dihydrouridine synthase A [Brucella ceti M13/05/1]
 gi|261222048|ref|ZP_05936329.1| tRNA-dihydrouridine synthase A [Brucella ceti B1/94]
 gi|261314391|ref|ZP_05953588.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|261317513|ref|ZP_05956710.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis B2/94]
 gi|261321720|ref|ZP_05960917.1| tRNA-dihydrouridine synthase A [Brucella ceti M644/93/1]
 gi|261324970|ref|ZP_05964167.1| tRNA-dihydrouridine synthase A [Brucella neotomae 5K33]
 gi|261754840|ref|ZP_05998549.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|261758066|ref|ZP_06001775.1| TIM-barrel protein [Brucella sp. F5/99]
 gi|265988548|ref|ZP_06101105.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|265998013|ref|ZP_06110570.1| tRNA-dihydrouridine synthase A [Brucella ceti M490/95/1]
 gi|297248212|ref|ZP_06931930.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 5 str. B3196]
 gi|23347676|gb|AAN29791.1| TIM-barrel protein, yjbN family [Brucella suis 1330]
 gi|62195941|gb|AAX74241.1| TIM-barrel protein, yjbN family [Brucella abortus bv. 1 str. 9-941]
 gi|82615836|emb|CAJ10838.1| Protein of unknown function UPF0034:TIM-barrel protein yjbN family
           [Brucella melitensis biovar Abortus 2308]
 gi|148371987|gb|ABQ61966.1| TIM-barrel protein, yjbN family [Brucella ovis ATCC 25840]
 gi|161335635|gb|ABX61940.1| TIM-barrel protein, yjbN family [Brucella canis ATCC 23365]
 gi|163673857|gb|ABY37968.1| TIM-barrel protein, yjbN family [Brucella suis ATCC 23445]
 gi|189019622|gb|ACD72344.1| TIM-barrel protein, yjbN family [Brucella abortus S19]
 gi|225617357|gb|EEH14402.1| TIM-barrel protein, yjbN family protein [Brucella ceti str. Cudo]
 gi|237790131|gb|EEP64341.1| TIM-barrel protein, yjbN family [Brucella abortus str. 2308 A]
 gi|260096851|gb|EEW80726.1| TIM-barrel protein [Brucella abortus NCTC 8038]
 gi|260156097|gb|EEW91177.1| TIM-barrel protein [Brucella suis bv. 4 str. 40]
 gi|260668153|gb|EEX55093.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|260672090|gb|EEX58911.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260674720|gb|EEX61541.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|260873167|gb|EEX80236.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|260915469|gb|EEX82330.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|260920632|gb|EEX87285.1| tRNA-dihydrouridine synthase A [Brucella ceti B1/94]
 gi|260923870|gb|EEX90438.1| tRNA-dihydrouridine synthase A [Brucella ceti M13/05/1]
 gi|261294410|gb|EEX97906.1| tRNA-dihydrouridine synthase A [Brucella ceti M644/93/1]
 gi|261296736|gb|EEY00233.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis B2/94]
 gi|261300950|gb|EEY04447.1| tRNA-dihydrouridine synthase A [Brucella neotomae 5K33]
 gi|261303417|gb|EEY06914.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|261738050|gb|EEY26046.1| TIM-barrel protein [Brucella sp. F5/99]
 gi|261744593|gb|EEY32519.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|262552481|gb|EEZ08471.1| tRNA-dihydrouridine synthase A [Brucella ceti M490/95/1]
 gi|264660745|gb|EEZ31006.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|297175381|gb|EFH34728.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 5 str. B3196]
          Length = 340

 Score =  340 bits (871), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|326538599|gb|ADZ86814.1| TIM-barrel protein, yjbN family protein [Brucella melitensis M5-90]
          Length = 317

 Score =  340 bits (871), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 1   MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 61  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 121 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKACLKGLSPKENREIPPLDYERVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 181 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 239 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 291

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 292 ATKPGATSDVVRQAYATVVEA 312


>gi|294852216|ref|ZP_06792889.1| tRNA-dihydrouridine synthase A [Brucella sp. NVSL 07-0026]
 gi|294820805|gb|EFG37804.1| tRNA-dihydrouridine synthase A [Brucella sp. NVSL 07-0026]
          Length = 329

 Score =  340 bits (871), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 13  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 73  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 133 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 193 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 251 EPLAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 304 ATKPGATSDVVRQAYATVVEA 324


>gi|254718967|ref|ZP_05180778.1| tRNA-dihydrouridine synthase A [Brucella sp. 83/13]
 gi|306838802|ref|ZP_07471633.1| TIM-barrel protein, yjbN family [Brucella sp. NF 2653]
 gi|306406086|gb|EFM62334.1| TIM-barrel protein, yjbN family [Brucella sp. NF 2653]
          Length = 340

 Score =  336 bits (862), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 161/321 (50%), Positives = 216/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETVSIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            KCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 AKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P           +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPPAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|265983957|ref|ZP_06096692.1| tRNA-dihydrouridine synthase A [Brucella sp. 83/13]
 gi|264662549|gb|EEZ32810.1| tRNA-dihydrouridine synthase A [Brucella sp. 83/13]
          Length = 329

 Score =  336 bits (861), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 161/321 (50%), Positives = 216/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 13  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 73  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            KCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 133 AKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 193 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P           +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 251 EPPAM-------PEIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 304 ATKPGATSDVVRQAYATVVEA 324


>gi|306844081|ref|ZP_07476675.1| TIM-barrel protein, yjbN family [Brucella sp. BO1]
 gi|306275524|gb|EFM57256.1| TIM-barrel protein, yjbN family [Brucella sp. BO1]
          Length = 340

 Score =  335 bits (859), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 161/321 (50%), Positives = 217/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML+PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLSPDVVARCVAAMKETVSIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYG--EGQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P           +I  +M  Y  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPPAM-------PEIIDAMCAYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYAAVVEA 335


>gi|153009692|ref|YP_001370907.1| tRNA-dihydrouridine synthase A [Ochrobactrum anthropi ATCC 49188]
 gi|151561580|gb|ABS15078.1| TIM-barrel protein, yjbN family [Ochrobactrum anthropi ATCC 49188]
          Length = 337

 Score =  333 bits (855), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 160/315 (50%), Positives = 211/315 (66%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADAI+ G +  +LGF T E P+ALQ+GG+D  
Sbjct: 21  MIDWSDRHCRYFHRLFSKQALLYTEMVVADAIIHGPRDRLLGFDTAEHPVALQLGGSDPV 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAAKI  D+GY+EINLNVGCPS RV  G+FGACLM  PD+V  C++AM +A+S+PVT
Sbjct: 81  KLKEAAKIGADYGYDEINLNVGCPSDRVQSGTFGACLMQTPDVVARCVSAMKEAVSVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   VAL  L      +G + +W+HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 141 VKCRIGVDDQDVEVALDTLADLTLDAGADALWVHARKAWLKGLSPKENREIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K    D+F+G+NGG+  + +A + L +VD VM+GRAAY N  +L  VD          
Sbjct: 201 RLKARLGDVFVGINGGINTLDEAEQHLQTVDAVMLGRAAYHNPEILAEVDARLYGGDQAD 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + I   +D          M  Y  RH+ +GG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 261 TSIADIID---------DMCAYTDRHIATGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 311

Query: 301 AGASTATHHIIETAF 315
           A    A   ++  A+
Sbjct: 312 ATKPGANSDVLRQAY 326


>gi|240850670|ref|YP_002972070.1| tRNA-dihydrouridine synthase A [Bartonella grahamii as4aup]
 gi|240267793|gb|ACS51381.1| tRNA-dihydrouridine synthase A [Bartonella grahamii as4aup]
          Length = 326

 Score =  333 bits (854), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 167/323 (51%), Positives = 222/323 (68%), Gaps = 17/323 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VAD+++ G ++ +L FS +E+P+ALQ+GGAD  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMMVADSVIHGVREQLLAFSDKERPVALQLGGADPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGYNEINLNVGCPS RV  G FGACLM +PDIV + + AM + ++IPVT
Sbjct: 77  KLAEAARIAEDFGYNEINLNVGCPSNRVQAGVFGACLMRHPDIVANAVEAMKREVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q   +AL  L   +  +G + +WIHARKA L+GLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRIGVDEQDEELALDLLANQVWNAGCDALWIHARKAWLQGLSPKENRNIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD----EYFSNP 236
           ++K++ P  FIG+NGG++ + +  + L   D VM+GR  Y + A+L  +D    +   N 
Sbjct: 197 KLKRKYPHKFIGINGGIKSIDEIKEHLTFCDAVMLGRQVYHDPALLKHIDFELYDEARNN 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           L+ S  I+              M DYAARH+ SGG+L  +TRHMIGLFHG   +RR R I
Sbjct: 257 LSESDLIEV-------------MCDYAARHIASGGRLSHVTRHMIGLFHGRGGARRWRQI 303

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           L+ +A  S A   I++ AF  +I
Sbjct: 304 LSNDATKSNADICILKEAFYALI 326


>gi|121602008|ref|YP_989139.1| tRNA-dihydrouridine synthase A [Bartonella bacilliformis KC583]
 gi|120614185|gb|ABM44786.1| tRNA-dihydrouridine synthase A [Bartonella bacilliformis KC583]
          Length = 326

 Score =  329 bits (844), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 166/319 (52%), Positives = 219/319 (68%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VADAI+ G ++++L F+ QE P+ALQIGG+D  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMVVADAIIHGIRESLLAFNDQEHPVALQIGGSDPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G+FGACLMLNPDIV + + AM + ++IPVT
Sbjct: 77  KLAEAAQIAEDFGYDEINLNVGCPSNRVQSGTFGACLMLNPDIVANAVEAMKRVVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 137 VKCRIGVDEQDEELALDFLADRVWNAGCDALWVHARKAWLKGLSPKENRDIPQLNYKRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K +  + FIG+NGG++ + +  + L   D VM+GR  Y N ++L  +D  F       
Sbjct: 197 KLKNKFYNKFIGINGGIKSIYEMKEHLKLCDAVMVGRQVYYNPSLLQLID--FEIYSESQ 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +K   D D    +   M DYAA+H+ SGG L  +TRHMI  FHG   +RR R IL+ +
Sbjct: 255 SNLK---DCD----VIDIMCDYAAKHIASGGHLSHVTRHMISFFHGRDGARRWRQILSND 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   I++ AF+ +I
Sbjct: 308 ARGKDADVRILKEAFSALI 326


>gi|239831743|ref|ZP_04680072.1| TIM-barrel protein, yjbN family [Ochrobactrum intermedium LMG 3301]
 gi|239824010|gb|EEQ95578.1| TIM-barrel protein, yjbN family [Ochrobactrum intermedium LMG 3301]
          Length = 337

 Score =  329 bits (843), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 158/314 (50%), Positives = 213/314 (67%), Gaps = 9/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +++ALLYTEM+VADAI+ G +  +LGF   E P+ALQ+GG+D +
Sbjct: 21  MIDWSDRHCRYFHRLFSSHALLYTEMVVADAIIHGPRDRLLGFDAAEHPVALQLGGSDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAAKI  D+GY+EINLNVGCPS RV  G+FGACLM  PD+V  C++AM +A+S+PVT
Sbjct: 81  KLKEAAKIGADYGYDEINLNVGCPSDRVQSGTFGACLMQTPDVVARCVSAMKEAVSVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR GVDDQ   VAL  L      +G + +W+HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 141 VKCRTGVDDQDVEVALDTLADMTLDAGADALWVHARKAWLKGLSPKENREIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K    D+F+G+NGG+  + +A + L +VD VM+GRAAY N  +L  VD          
Sbjct: 201 RLKARLGDVFVGINGGITTLDEAEQHLQTVDAVMLGRAAYHNPELLAEVDVRLYGGEQRD 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +   +D+         M  Y  RH+ +GG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 261 TSMAGIIDE---------MCAYIDRHIAAGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 311

Query: 301 AGASTATHHIIETA 314
           A    AT  ++  A
Sbjct: 312 ATRPGATSDVLRQA 325


>gi|254473354|ref|ZP_05086751.1| tRNA-dihydrouridine synthase A [Pseudovibrio sp. JE062]
 gi|211957470|gb|EEA92673.1| tRNA-dihydrouridine synthase A [Pseudovibrio sp. JE062]
          Length = 348

 Score =  328 bits (842), Expect = 5e-88,   Method: Compositional matrix adjust.
 Identities = 158/316 (50%), Positives = 210/316 (66%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+ N+LLYTEM+   A++ GD+   L FS QE+P+A Q+GG+D  
Sbjct: 21  MLDWTDRHCRAFHRVLSKNSLLYTEMVTTGALIHGDRDRHLNFSRQEQPVACQLGGSDPK 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AK+VED+GY+E+NLNVGCPS RV  G FGACLML PD+V +CIAAM   +SIPVT
Sbjct: 81  ALAECAKMVEDWGYDEVNLNVGCPSDRVQSGKFGACLMLEPDLVAECIAAMKDVVSIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            KCRIGVDDQ P  AL  L   +  +G + +W+HARKA LKGLSPK+NR +P LDYD+VY
Sbjct: 141 TKCRIGVDDQEPEEALNALADKVIAAGTDALWVHARKAWLKGLSPKENRDVPPLDYDLVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K+  PD+FIG+NGG+  + +    L  +DGVM+GRAAY+N  +L  VD   +    T 
Sbjct: 201 RLKQRLPDVFIGINGGVATLEETSAHLEKLDGVMMGRAAYQNPMLLAEVDRVVYGEDGTA 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P++     D +R        Y    L +G KL  ITRH++G + G P +R  R I+TV
Sbjct: 261 ITPVEA---MDVYR-------GYIENELTAGTKLASITRHILGTYQGVPGARHFRRIMTV 310

Query: 300 EAGASTATHHIIETAF 315
           EA  + A   ++E A 
Sbjct: 311 EANKTGAGIEVLEEAL 326


>gi|319408524|emb|CBI82177.1| tRNA-dihydrouridine synthase A [Bartonella schoenbuchensis R1]
          Length = 326

 Score =  328 bits (841), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 163/320 (50%), Positives = 218/320 (68%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VADA + G ++ +LGFS +E P+ALQ+GG+D  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMVVADAAIHGIRERLLGFSDEEHPIALQLGGSDSQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML+PDIV   + AM +A++I VT
Sbjct: 77  KLAEAARIAEDFGYDEINLNVGCPSNRVQAGMFGACLMLHPDIVARAVEAMKQAVTISVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD Q   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRIGVDKQDEELALDILADQVWNAGCDALWVHARKAWLKGLSPKENRGIPELNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K++ P  FIG+NGG++ + +  + L   D  M+GR  Y N A+L ++D + +  P + 
Sbjct: 197 RLKRKYPHKFIGINGGIQSIDEVKEHLKLCDATMVGRQVYHNPALLMSIDSKIYGQPHSD 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S      D D    +  +M DYAA+H+ SGG+L  +TRHMI LFHG   +RR R IL+ 
Sbjct: 257 LS------DCD----LIDAMCDYAAKHIASGGRLSHVTRHMINLFHGRNGARRWRQILSN 306

Query: 300 EAGASTATHHIIETAFNLMI 319
           +A    A   +++ AF   +
Sbjct: 307 DATRRDADVSVLKEAFAAFV 326


>gi|328544451|ref|YP_004304560.1| TRNA-dihydrouridine synthase A [polymorphum gilvum SL003B-26A1]
 gi|326414193|gb|ADZ71256.1| TRNA-dihydrouridine synthase A [Polymorphum gilvum SL003B-26A1]
          Length = 320

 Score =  327 bits (839), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 160/315 (50%), Positives = 210/315 (66%), Gaps = 9/315 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F R  T+ ALLYTEM+   A+L GD++ +LGFS  E PLA Q+GGA+ + 
Sbjct: 1   MDWTDRHCRAFHRQFTHRALLYTEMVTTGAVLHGDRERLLGFSAVEHPLACQLGGAEPAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L +AA+IVE FGY+E+NLNVGCPS RV  G FGACLM  P +VGDC+AAM  A++IPVTV
Sbjct: 61  LAQAARIVEAFGYDEVNLNVGCPSDRVQSGRFGACLMHEPQLVGDCVAAMKAAVAIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIGVDDQ   +AL  L  ++  +GV+G+W+HARKA L+GLSPK+NR +P LDY  V  
Sbjct: 121 KCRIGVDDQDAEIALDTLADAVVAAGVDGLWVHARKAWLQGLSPKENRDVPPLDYGRVIR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K+  PDLF+G+NGG+ D+ QA  +L  +DGVM+GRAAY +  +L  VD          +
Sbjct: 181 LKRRLPDLFVGVNGGIADLDQAETLLADLDGVMLGRAAYHDPGLLGAVDRRLYG---DEA 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P +T V+         +   Y A  L  G +L  +TRHM+G FHG P +R  R ILTVEA
Sbjct: 238 PDRTPVEA------VEAFLPYVADRLAEGVRLSHMTRHMLGAFHGRPGARAFRRILTVEA 291

Query: 302 GASTATHHIIETAFN 316
               A   ++  A +
Sbjct: 292 VRPGAGIEVVHRALD 306


>gi|110633902|ref|YP_674110.1| tRNA-dihydrouridine synthase A [Mesorhizobium sp. BNC1]
 gi|110284886|gb|ABG62945.1| tRNA-U16,U17-dihydrouridine synthase [Chelativorans sp. BNC1]
          Length = 342

 Score =  326 bits (836), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 153/301 (50%), Positives = 208/301 (69%), Gaps = 9/301 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEMIVADAI+ G ++ +L +   E P+ALQ+GG++  
Sbjct: 25  MMDWTDRHCRFFHRQLSKDALLYTEMIVADAIIHGSRERLLAYDPAEHPVALQLGGSEPG 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I   FGY+EINLNVGCPS RV  G+FGACLM  P++V  C+AAM + + +PVT
Sbjct: 85  KLGEAARIAASFGYDEINLNVGCPSDRVQSGTFGACLMKTPELVSACVAAMKECVDVPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  + + +  +G + +W+HARKA L+GLSP++NR+IP LDYD VY
Sbjct: 145 VKCRIGVDDQDPEEALDRIAELVFAAGADALWVHARKAWLQGLSPRENREIPPLDYDRVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P  F+G+NGG++ + +A+  L  +DGVM+GRAAY    +L  VD         +
Sbjct: 205 RLKKKYPGKFVGINGGIQTIDEAVNHLAHMDGVMLGRAAYHTPGILAEVDSRIYG--GQN 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+        + ++  +M  YA RH+  GG+L  +TRHM GLFHG   +RR R IL+ E
Sbjct: 263 EPVS-------FAEVVEAMAAYAQRHIERGGRLAHVTRHMTGLFHGRAGARRFRQILSTE 315

Query: 301 A 301
           A
Sbjct: 316 A 316


>gi|319405737|emb|CBI79360.1| tRNA-dihydrouridine synthase A [Bartonella sp. AR 15-3]
          Length = 331

 Score =  324 bits (830), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 163/316 (51%), Positives = 213/316 (67%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEM VAD ++ G +K +L FS +E P+ALQ+GG+D  
Sbjct: 22  MLGWTDRHCRFFYRLLTKKALLYTEMFVADTVIHGIRKKLLAFSDEEHPIALQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML+PD+V   + AM + ++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGACLMLHPDVVAQLVEAMKRTVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEELALDFLADRVWNAGCDALWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K++  + FIGLNGG++ +S+  + L S D VM+GR  Y N   L  +D E +  P   
Sbjct: 202 NLKRKYENNFIGLNGGIKSISEIKEHLRSCDAVMVGRQVYHNPIWLCLIDSEIYGEPQNN 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S      D D    +  +M +Y+A+H+ SGG+L  ITRHM+GLF G   +RR R IL+ 
Sbjct: 262 LS------DYD----LINAMCEYSAKHIASGGRLSHITRHMLGLFQGRDGARRWRQILSH 311

Query: 300 EAGASTATHHIIETAF 315
            A  + A  HI++ AF
Sbjct: 312 NATKTDANTHILKEAF 327


>gi|319898967|ref|YP_004159060.1| tRNA-dihydrouridine synthase A [Bartonella clarridgeiae 73]
 gi|319402931|emb|CBI76482.1| tRNA-dihydrouridine synthase A [Bartonella clarridgeiae 73]
          Length = 331

 Score =  323 bits (828), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 164/316 (51%), Positives = 212/316 (67%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEM +AD ++ G ++ +L FS +E P+ALQ+GG+D  
Sbjct: 22  MLGWTDRHCRFFYRLLTKKALLYTEMFIADTVIHGVRERLLAFSNEEHPIALQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML PDIV   + AM +A++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGACLMLYPDIVAQAVEAMKRAVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   +  +G +G+W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEELALDFLADRVWNAGCDGLWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K +  + FIGLNGG+  +S+  + L S D VM+GR  Y N  +L  +D    + + G 
Sbjct: 202 NLKHKYENNFIGLNGGIRSISEIKEHLRSCDAVMVGRQVYNNPVLLCLID----SEIYGE 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S      D D    +  +M DY A+H+ SGG+L  +TRHMIGLF G   +RR R IL+  
Sbjct: 258 SGYNLS-DCD----LINAMCDYTAKHIASGGRLSHVTRHMIGLFQGRDGARRWRQILSHN 312

Query: 301 AGASTATHHIIETAFN 316
           A    A  HI++ AF+
Sbjct: 313 ATRRDANVHILKEAFS 328


>gi|319407299|emb|CBI80940.1| tRNA-dihydrouridine synthase A [Bartonella sp. 1-1C]
          Length = 331

 Score =  318 bits (815), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 164/316 (51%), Positives = 210/316 (66%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEM VAD ++ G +K +L FS +E P+A+Q+GG+D  
Sbjct: 22  MLGWTDRHCRFFYRLLTKRALLYTEMFVADTVIYGIRKKLLAFSDEEHPIAIQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGA LML+PDIV   + AM + ++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGAYLMLHPDIVARAVEAMKRTVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   I   G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEELALDFLADRIWNVGCDALWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K++  + FIGLNGG++ +S+  + L S D VM+GR  Y N   L  +D E +  P   
Sbjct: 202 NLKRKYENNFIGLNGGIKSISEIKEHLRSCDAVMVGRQVYHNPIWLRLIDSEIYGEPQNN 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S      D D    +  +M DY A+H+ SGG+L  ITRHMIGLF G   +RR R IL+ 
Sbjct: 262 LS------DYD----LINAMCDYTAKHIASGGRLSHITRHMIGLFQGRDGARRWRQILSH 311

Query: 300 EAGASTATHHIIETAF 315
           +A  + A  H ++ AF
Sbjct: 312 DATKTDANVHTLKEAF 327


>gi|118590253|ref|ZP_01547656.1| tRNA-dihydrouridine synthase A [Stappia aggregata IAM 12614]
 gi|118437225|gb|EAV43863.1| tRNA-dihydrouridine synthase A [Stappia aggregata IAM 12614]
          Length = 351

 Score =  317 bits (813), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 158/315 (50%), Positives = 205/315 (65%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R LT +ALLYTEM+   A++ GD++ +LGFS  E P+A Q+GG+D  
Sbjct: 32  MMEWTDRHCRAFHRQLTRHALLYTEMVTTGAVIHGDREYLLGFSDIEHPVACQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+IV +FGY+E+N+NVGCPS RV  G FGACLM  P +V  C+ AM  A+ IPVT
Sbjct: 92  DMAEAARIVAEFGYDEVNINVGCPSDRVQSGRFGACLMEEPALVAACVEAMKAAVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P VAL  +  ++  +G + +W+HARKA LKGLSPK+NR IP LDY+ V 
Sbjct: 152 VKCRIGVDEQDPEVALDTMADAVFAAGADALWVHARKAWLKGLSPKENRDIPPLDYERVL 211

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD FIGLNGGL+ + QA   L ++DG+M GRAAY    ++  VD         S
Sbjct: 212 RLKQRLPDRFIGLNGGLQTLDQAEPFLETLDGLMFGRAAYHTPQIMGEVDRRLYG---AS 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P     D   W  + A M  Y    L +G KL  +TRHM+GLFHG P +R  R ILTVE
Sbjct: 269 GP-----DITPWDAVKAHMP-YLEAQLTNGVKLAHMTRHMLGLFHGRPGARSWRRILTVE 322

Query: 301 AGASTATHHIIETAF 315
           A    A   ++E A 
Sbjct: 323 AIKPGAGLEVVEKAL 337


>gi|329849777|ref|ZP_08264623.1| tRNA-dihydrouridine synthase A [Asticcacaulis biprosthecum C19]
 gi|328841688|gb|EGF91258.1| tRNA-dihydrouridine synthase A [Asticcacaulis biprosthecum C19]
          Length = 340

 Score =  317 bits (811), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 159/314 (50%), Positives = 210/314 (66%), Gaps = 10/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+   A++ GD++ ++GFS  E P+ALQ+GG+D +
Sbjct: 13  MMDWTDRHCRAFHRALTKRALLYTEMVTTKAVIHGDRERLIGFSDIEHPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AKI ED+GY+EINLN GCPS RV  G+FGACLM +P +V D + AM +A  +P T
Sbjct: 73  ELAQCAKIAEDWGYDEINLNCGCPSDRVQSGAFGACLMRDPQLVADGMQAMIEASKLPAT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  LV++ +K+GV    +HARKA LKGLSPK+NR IP LDY++VY
Sbjct: 133 VKCRIGVDDQDPRDALFTLVEACRKAGVTTFIVHARKAWLKGLSPKENRDIPPLDYELVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+ +PDLFI +NGG+ ++  A + L  VDGVM+GRAAY   A+L  VD   ++   GS
Sbjct: 193 ELKRSHPDLFISINGGIANLDDAQRHLQHVDGVMLGRAAYHEPALLGQVD---TSVFGGS 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +      D +R        Y A  L  G  L  +TRH++GL HG P +R  R ILTVE
Sbjct: 250 KDVAPFEALDAYRP-------YIAARLDEGVPLTHMTRHILGLMHGLPGARAFRRILTVE 302

Query: 301 AGASTATHHIIETA 314
           +    A   +I+ A
Sbjct: 303 SIVPGAGTEVIDRA 316


>gi|254501102|ref|ZP_05113253.1| TIM-barrel protein, yjbN family [Labrenzia alexandrii DFL-11]
 gi|222437173|gb|EEE43852.1| TIM-barrel protein, yjbN family [Labrenzia alexandrii DFL-11]
          Length = 327

 Score =  317 bits (811), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 159/317 (50%), Positives = 206/317 (64%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R L+ +ALLYTEM+   A++ GD+++ILGFS  E P+A Q+GG+D  
Sbjct: 8   MMEWTDRHCRAFHRHLSAHALLYTEMVTTGAVIHGDREHILGFSDLEHPVACQLGGSDPQ 67

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+IVE FGY+E+N+NVGCPS RV  G FGACLM  P +V DC++AM  A++IPVT
Sbjct: 68  AMAEAAQIVEGFGYDEVNINVGCPSDRVQSGRFGACLMEEPQLVADCVSAMKAAVAIPVT 127

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  +      +G + +W+HARKA L+GLSPK+NR +P LDYD V 
Sbjct: 128 VKCRIGVDDQDPEPALDAVADLTFAAGSDALWVHARKAWLQGLSPKENRDVPPLDYDRVV 187

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD FIGLNGGL+ + Q    L  +DG+M GRAAY +  +L  VD       T +
Sbjct: 188 RLKQRLPDKFIGLNGGLDTLEQGEPYLKPLDGLMYGRAAYHSPEILGEVDARLYGAETET 247

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SP         W  +   MT Y    L  G KL  +TRHM+GLFHG P +R  R ILTV
Sbjct: 248 ISP---------WDAVRGHMT-YLEDQLSQGVKLAHMTRHMLGLFHGRPGARSWRRILTV 297

Query: 300 EAGASTATHHIIETAFN 316
           EA    A   ++E A +
Sbjct: 298 EAIKPGAGLEVVEKALD 314


>gi|307945371|ref|ZP_07660707.1| tRNA-dihydrouridine synthase A [Roseibium sp. TrichSKD4]
 gi|307771244|gb|EFO30469.1| tRNA-dihydrouridine synthase A [Roseibium sp. TrichSKD4]
          Length = 353

 Score =  316 bits (810), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 155/317 (48%), Positives = 209/317 (65%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R L++ ALLYTEM+   A++ GD++ +LGFS  E P+A Q+GG+D +
Sbjct: 20  MMEWTDRNCRAFHRQLSSRALLYTEMVTTGAVIHGDREKLLGFSDLEHPIACQLGGSDPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +  +AKIVED+GY+E+N+NVGCPS RV  GSFGACLM  PD+V +C+AAM  A+SIPVT
Sbjct: 80  DMATSAKIVEDWGYDEVNINVGCPSDRVQSGSFGACLMREPDLVAECVAAMKAAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  +   +  +G + +W+HARKA L+GLSPK NR +P LDYD V 
Sbjct: 140 VKCRIGVDDQDPEEALDAVADKVFAAGSDALWVHARKAWLQGLSPKQNRDVPPLDYDRVL 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K   P+ FIGLNGGL D+ QA   L ++DGVM+GRAAY N  ++  VD   +   +  
Sbjct: 200 RLKARFPEKFIGLNGGLADLDQAEPFLDTLDGVMLGRAAYHNPGLMGEVDRRLYGEDVED 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SP         W+ +   +  Y    L  G +L  +TRHM+GLFHG P ++  R ILTV
Sbjct: 260 VSP---------WQAVGKYIP-YIEDGLARGVRLPHMTRHMLGLFHGRPGAKAWRRILTV 309

Query: 300 EAGASTATHHIIETAFN 316
           EA    A   +++ A  
Sbjct: 310 EAIKPEAGIEVVQKALE 326


>gi|319404295|emb|CBI77888.1| tRNA-dihydrouridine synthase A [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 331

 Score =  316 bits (809), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 161/316 (50%), Positives = 209/316 (66%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTD+H RFF RLLT  ALLYTEM VAD ++ G +K +L FS +E P+A+Q+GG+D  
Sbjct: 22  MLGWTDQHCRFFYRLLTKKALLYTEMFVADTVIYGIRKKLLAFSDEEHPIAIQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML+PDIV   +  M + ++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGACLMLHPDIVARAVEEMKRTVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEKLALDFLADRVWNAGCDALWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K++  + FIGLNGG++ +S+  + L S D  M+GR  Y N   L  +D E +  P   
Sbjct: 202 NLKRKYKNNFIGLNGGIKSISEIKEHLRSCDAAMVGRQVYHNPIWLNLIDSEIYGEPQNN 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S      D D    +  +M DY A+H+ SGG+L  ITRHMIGLF G   +RR R IL+ 
Sbjct: 262 LS------DYD----LINAMCDYTAKHIASGGRLSHITRHMIGLFQGRDGARRWRQILSH 311

Query: 300 EAGASTATHHIIETAF 315
            A  + A   I++ AF
Sbjct: 312 NATKTDANVRILKEAF 327


>gi|49475574|ref|YP_033615.1| tRNA-dihydrouridine synthase A [Bartonella henselae str. Houston-1]
 gi|49238381|emb|CAF27608.1| hypothetical protein BH08090 [Bartonella henselae str. Houston-1]
          Length = 326

 Score =  316 bits (809), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 158/323 (48%), Positives = 215/323 (66%), Gaps = 17/323 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEMIVADA++ G ++ +L  + +E P+ALQ+GG+D  
Sbjct: 17  MLGWTDRHCRFFYRLLTKKALLYTEMIVADAVIHGVREQLLALNHKEHPIALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G+FGACLML PDIV   + A+ K +++ VT
Sbjct: 77  KLAEAARIAEDFGYDEINLNVGCPSNRVQSGAFGACLMLYPDIVASAVEAIKKVVTLSVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRVGVDDQDEELALDLLADKVWNAGCDALWVHARKAWLKGLSPKENRDIPPLNYNRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SNP 236
           ++K++  + FIG+NGG++ + +  + L   D  M+GR  Y +  +L  +D        N 
Sbjct: 197 KLKRKYHNKFIGINGGIKSIYEIKEHLILCDAAMVGRQVYHDPTLLKYIDSEIYGEQQNN 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           L+ S  I+             +M DYAA+H+ SGG L  +TRHMIGLFHG   +RR R I
Sbjct: 257 LSDSDLIE-------------AMCDYAAQHIASGGLLSHVTRHMIGLFHGRNGARRWRQI 303

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           L+  A    A  H+++ AF+ +I
Sbjct: 304 LSNNARGRDAGIHVLKEAFSALI 326


>gi|49474253|ref|YP_032295.1| tRNA-dihydrouridine synthase A [Bartonella quintana str. Toulouse]
 gi|49239757|emb|CAF26141.1| hypothetical protein BQ06500 [Bartonella quintana str. Toulouse]
          Length = 326

 Score =  315 bits (806), Expect = 8e-84,   Method: Compositional matrix adjust.
 Identities = 153/320 (47%), Positives = 217/320 (67%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTD+H RFF RLLT  ALLYTEMIVADA++ G ++ +L  + +E P+ALQ+GG+D  
Sbjct: 17  MLGWTDQHCRFFHRLLTKKALLYTEMIVADAVIHGVRERVLALNHKEHPIALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G+FGACLML PDIV + + A+ + +++ VT
Sbjct: 77  KLAEAARIAEDFGYDEINLNVGCPSNRVQSGAFGACLMLQPDIVANAVEAIKQVVTLSVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIGVD+Q   +AL  L + +  +G + +W+HARKA LKGLSPK+NR IP ++Y+ VY
Sbjct: 137 IKCRIGVDEQDEELALDFLAEKVWNAGCDALWVHARKAWLKGLSPKENRDIPPINYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++  + FIG+NG ++ + +  + L   D  M+GR  Y N  +L  +D E +  P + 
Sbjct: 197 KLKRKYYNKFIGINGEIKSLDEIKEHLTLCDAAMVGRQVYHNPTLLKHIDSEIYGEPQSN 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + +           +  SM DYAA+H+ SGG L  +TRHMIGLF+G   +RR R IL+ 
Sbjct: 257 LNDV----------DLIESMCDYAAQHIASGGLLSHVTRHMIGLFNGRNGARRWRQILSN 306

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A  H+I+ AF+ +I
Sbjct: 307 NASRRDADVHVIKEAFSALI 326


>gi|304391898|ref|ZP_07373840.1| tRNA-dihydrouridine synthase A [Ahrensia sp. R2A130]
 gi|303296127|gb|EFL90485.1| tRNA-dihydrouridine synthase A [Ahrensia sp. R2A130]
          Length = 349

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 163/318 (51%), Positives = 215/318 (67%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT +ALLYTEM+VADA++ GD +  L F   E PLALQ+GG++  
Sbjct: 34  MMDWTDRHCRYFHRQLTRHALLYTEMVVADALIHGDIERHLRFHADEHPLALQLGGSEPE 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL+ AAK+ +D+GY+E+NLNVGCPS RV  G+FGACLM  P++V  C+ AM   +  PVT
Sbjct: 94  KLIFAAKLAQDWGYDEVNLNVGCPSDRVQSGTFGACLMREPELVARCVEAMKSVVDSPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L   +  +G +G+W+HARKA LKGLSPK+NR IP LDY+IV 
Sbjct: 154 VKCRIGVDDQEPRDALFKLAADVFAAGADGLWVHARKAWLKGLSPKENRDIPPLDYEIVR 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+   D FIGLNGGL  + QA      +DGVM+GRAAY +S  L  VD+ F      S
Sbjct: 214 ELKRSYSDRFIGLNGGLATLEQAQHEGQGLDGVMLGRAAYHDSDQLRAVDKLFYGDDADS 273

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D      +  +M ++AA H+ +GG+L  +TRHM+GLF G P +RR R++L+V 
Sbjct: 274 ------IDD---TALCEAMMEHAAAHIAAGGRLHHVTRHMLGLFSGRPGARRYRNVLSVG 324

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  AF++M
Sbjct: 325 AVPRDAGPEVIADAFSVM 342


>gi|114569505|ref|YP_756185.1| tRNA-dihydrouridine synthase A [Maricaulis maris MCS10]
 gi|114339967|gb|ABI65247.1| tRNA-U16,U17-dihydrouridine synthase [Maricaulis maris MCS10]
          Length = 353

 Score =  313 bits (802), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 159/314 (50%), Positives = 204/314 (64%), Gaps = 9/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+LT  ALLYTEM V  AI+ GD   ++GF   E P+A+Q+GG+D  
Sbjct: 38  MMDWTDRHCRAFHRVLTRRALLYTEMAVDKAIIHGDTARLIGFDAAEHPVAIQLGGSDPG 97

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A+K  E FGY EINLNVGCPS RV  G FGACLM  PD+V DC+AAM  A+S+PVT
Sbjct: 98  ELAQASKTAEGFGYCEINLNVGCPSDRVQSGRFGACLMQEPDLVADCVAAMQDAVSVPVT 157

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  LV ++   GV    +HARKA LKGLSPK+NR +P LDY +V+
Sbjct: 158 VKCRIGVDDQEPEQALFTLVDTVAARGVTSFAVHARKAWLKGLSPKENRSVPPLDYALVH 217

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L I LNGGL+D+  A+     +DG MIGRAAY    +L  VD   S     +
Sbjct: 218 RLKAERPELEIILNGGLQDLDHAISESTGLDGAMIGRAAYHTPWILARVD---SAVFGET 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ TR       +  A+   Y A  L  GG+L  ITRHM+GL+ G P +R+ R IL+ +
Sbjct: 275 DPVATR------SQALAAFRPYIAACLDEGGRLHDITRHMMGLYAGEPGARQWRRILSEK 328

Query: 301 AGASTATHHIIETA 314
           A  + A   +++ A
Sbjct: 329 ATRAGAGLDVLDEA 342


>gi|300023380|ref|YP_003755991.1| TIM-barrel protein, yjbN family [Hyphomicrobium denitrificans ATCC
           51888]
 gi|299525201|gb|ADJ23670.1| TIM-barrel protein, yjbN family [Hyphomicrobium denitrificans ATCC
           51888]
          Length = 335

 Score =  311 bits (798), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 154/318 (48%), Positives = 206/318 (64%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+ ADA++ GD+  +LG+S  E P+ALQ+GG+D +
Sbjct: 13  MMDWTDRHCRVFHRQLTTRALLYTEMVTADAVIHGDRARLLGYSEVEHPIALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I  + GY+EINLNVGCPS RV EG FGACLM  P++V  C+AAM     +PVT
Sbjct: 73  KLAEAARIGAELGYDEINLNVGCPSDRVQEGRFGACLMSEPELVAACVAAMRAHQPVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ     LR  +  +  +G     +HARKA LKGLSPK+NR++P LDY+ VY
Sbjct: 133 VKCRIGIDDQDAEEDLRRFIDVVADAGCTRFVVHARKAWLKGLSPKENREVPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   PDL I +NGG+E + +A   L  VDGVM+GRAAY+N A+L  VD    +  T  
Sbjct: 193 RLKAARPDLEIVINGGIETIEEARAHLDHVDGVMLGRAAYQNPAILADVDRLIFDADT-E 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SP +             +M  Y  +HL  GG+L  +TRH++GL+HG P  +  R  L+  
Sbjct: 252 SPTRA--------AALEAMLPYIEQHLKRGGRLSNVTRHVLGLYHGQPRGKTFRRHLSEG 303

Query: 301 AGASTATHHIIETAFNLM 318
           A ++ AT  ++  A  ++
Sbjct: 304 ATSADATADVLREAIAIV 321


>gi|114707271|ref|ZP_01440168.1| hypothetical protein FP2506_03595 [Fulvimarina pelagi HTCC2506]
 gi|114537152|gb|EAU40279.1| hypothetical protein FP2506_03595 [Fulvimarina pelagi HTCC2506]
          Length = 346

 Score =  310 bits (794), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 159/320 (49%), Positives = 212/320 (66%), Gaps = 14/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT  ALLYTEM+VADAIL G ++ +L     E P+ALQ+GG+D  
Sbjct: 26  MIDWTDRHCRFFHRQLTAKALLYTEMVVADAILHGPQEKLLDHDAAEHPVALQLGGSDPE 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
           KL  A  +  ++GY+E NLNVGCPS RV  G+FGACLM  P+ VGDC+ AM  A +  PV
Sbjct: 86  KLGAAVTVAREWGYDEFNLNVGCPSDRVQSGTFGACLMREPERVGDCLQAMRDAANETPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCR+GVDDQ    +L  L     ++GV+ IW+HARKA L+GLSPK+NR IP LDYD V
Sbjct: 146 TVKCRLGVDDQDIEESLDRLADEAIRAGVSVIWVHARKAWLEGLSPKENRDIPPLDYDRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE-YFSNP 236
             +K+  P++F+GLNGGL  ++ A + +    +DG+M GRAAY+   +L+ VD   +  P
Sbjct: 206 GRLKRRLPNVFVGLNGGLRSVAVANETIADLELDGMMFGRAAYQTPDLLSEVDHCIYGEP 265

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                  +  +D   +  + A M DYAARH+  GG+L  ITRHM+GLF+G P +RR R +
Sbjct: 266 -------ERAID---YPALIAVMEDYAARHIALGGRLNHITRHMVGLFNGLPGARRWRQV 315

Query: 297 LTVEAGASTATHHIIETAFN 316
           L+ ++  S A   II  AF+
Sbjct: 316 LSTKSTGSEAKPAIIREAFS 335


>gi|220923671|ref|YP_002498973.1| tRNA-dihydrouridine synthase A [Methylobacterium nodulans ORS 2060]
 gi|219948278|gb|ACL58670.1| TIM-barrel protein, yjbN family [Methylobacterium nodulans ORS
           2060]
          Length = 337

 Score =  308 bits (789), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 154/319 (48%), Positives = 209/319 (65%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+  A LYTEM+   A+L G ++ ++GF   E P+A+Q+GG+D  
Sbjct: 21  MMDWTDRHCRAFHRVLSARARLYTEMVTTGAVLHGPRERLIGFDPAEHPVAIQLGGSDPG 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  +A+I E +GY E+NLNVGCPS RV +G FGACLM  P +VG+C+AAM  A++IPVT
Sbjct: 81  ELAASARIAEGYGYAEVNLNVGCPSDRVQDGRFGACLMREPALVGECVAAMKAAVAIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  S++ +GV+G+ +HARKA L+GLSPK+NR IP LDY  V+
Sbjct: 141 VKCRIGVDDQDPEAALDALTASVRAAGVDGLVVHARKAWLQGLSPKENRDIPPLDYPRVH 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K  +PDL I +NGGL  ++QA   L  VDGVM+GRAAY   A+L  VD E+F  P   
Sbjct: 201 RLKAAHPDLPIAINGGLNSLAQAQAQLAHVDGVMLGRAAYAEPALLLGVDPEFFGTPAPV 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P            + A +   AAR L  G +L  +TRHM+GLF+G P +R  R  L+ 
Sbjct: 261 AGPFAA---------VEAYLPYIAAR-LGEGIRLHAMTRHMLGLFNGRPGARAFRRHLST 310

Query: 300 EAGASTATHHIIETAFNLM 318
           E   + A   ++  A + +
Sbjct: 311 EGLRANAGLGVLREAVSFV 329


>gi|315497697|ref|YP_004086501.1| tim-barrel protein, yjbn family [Asticcacaulis excentricus CB 48]
 gi|315415709|gb|ADU12350.1| TIM-barrel protein, yjbN family [Asticcacaulis excentricus CB 48]
          Length = 343

 Score =  305 bits (782), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 151/299 (50%), Positives = 196/299 (65%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+ + AI+ GD++ +LGFS  E P+ALQ+GG++  
Sbjct: 14  MMDWTDRHCRAFHRTLTKGALLYTEMVTSRAIINGDRQKLLGFSEVEHPVALQLGGSEPD 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+E+NLN GCPS RV  GSFGACLM  P +V DC+ AM +A  +PVT
Sbjct: 74  ELAACAKIAEDWGYDEVNLNCGCPSDRVQSGSFGACLMREPQLVADCMQAMGEATRLPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  LV++ +++GV    +HARKA LKGLSPK+NR IP L+Y++VY
Sbjct: 134 VKCRIGVDDQDEETALFALVEACRQAGVRTFIVHARKAWLKGLSPKENRDIPPLNYELVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ +PDL I +NGG+  + +A   L  VDGVM+GRAAY   A+L  VD    +     
Sbjct: 194 ALKRAHPDLTISINGGIGTLQEAETHLKHVDGVMLGRAAYHEPALLGQVDRRIFSGEADV 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            P +             + + Y    L +G  L  ITRHM+GL HG P +R  R ILTV
Sbjct: 254 GPFEAL----------EAYSPYVQAQLAAGVHLPAITRHMLGLMHGLPGARAFRRILTV 302


>gi|224588182|gb|ACN58806.1| tRNA dihydrouridine synthase A [uncultured bacterium BLR9]
          Length = 334

 Score =  305 bits (781), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 154/304 (50%), Positives = 203/304 (66%), Gaps = 17/304 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R   RLL+ +ALLYTEM+ A+A++RGD+  +LGFS  E P+ALQ+GGA+ +
Sbjct: 20  MMDCTDRHCRVLHRLLSRHALLYTEMVTAEAVIRGDRARLLGFSPAEHPVALQLGGAEPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAKI  DFGY+EINLNVGCPS RV  G FGA LM  P  VGDC+AAM  A+S+PVT
Sbjct: 80  RLAEAAKIGADFGYDEINLNVGCPSDRVQSGCFGAALMKEPLRVGDCVAAMRAAVSVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+++  ++GV    +HARKA L GLSPK+NR++P LDY +VY
Sbjct: 140 VKCRIGVDEQEPREALPALIEACTRAGVTAFAVHARKAWLSGLSPKENREVPPLDYSLVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG+  + +A   LP VDGVM+GRAAY+  A+L  VD  F       
Sbjct: 200 ALKRARPELTIVINGGIGSLDEAEAHLPHVDGVMLGRAAYQTPAILAEVDSRFFG----- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAA---RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                    +  R I  ++  YAA     L  G  L  +T+HM+GLF+G P +R+ R  L
Sbjct: 255 ---------EGARDIGEAVEAYAAYIGARLAEGVPLNAMTKHMLGLFNGIPGARQFRRHL 305

Query: 298 TVEA 301
           +  A
Sbjct: 306 SENA 309


>gi|295689004|ref|YP_003592697.1| YjbN family TIM-barrel protein [Caulobacter segnis ATCC 21756]
 gi|295430907|gb|ADG10079.1| TIM-barrel protein, yjbN family [Caulobacter segnis ATCC 21756]
          Length = 339

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 152/323 (47%), Positives = 211/323 (65%), Gaps = 10/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+L++ ALLYTEM+ + A++ GD++ +LGF   + P+ALQ+GG+D +
Sbjct: 15  MMDWTDRHCRSLHRVLSSRALLYTEMVTSGAVVHGDREKLLGFDAGQHPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I ED+GY+EINLNVGCPS RV  G FGACLM  P++V +C+AA+  A+ +P T
Sbjct: 75  DLAQAARIGEDWGYDEINLNVGCPSDRVQSGRFGACLMREPNLVAECMAAIKDAVKVPAT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV     +G++   +HARKA L+GLSPK+NR IP LDY++VY
Sbjct: 135 VKCRIGVDDQDPEESLFTLVDRCAAAGIDNFIVHARKAWLQGLSPKENRDIPPLDYELVY 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+E P+L I +NGG+  +  AL+ L + VDGVM+GRAAY  + +L  VD         
Sbjct: 195 RLKRERPNLTIAINGGVPSVDAALEHLANGVDGVMLGRAAYHEAGLLGEVDRRVFG---- 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                   D D +  +      Y AR L +G  L  +TRHM+GLFHG P +R  R ILTV
Sbjct: 251 ----LDVADVDSFEAVE-RYRPYLARELAAGTHLAAMTRHMLGLFHGLPGARAWRRILTV 305

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           E     A   +++ A + +  +L
Sbjct: 306 EGVKPGAGLDVVDRALDAVRAAL 328


>gi|154248170|ref|YP_001419128.1| tRNA-dihydrouridine synthase A [Xanthobacter autotrophicus Py2]
 gi|154162255|gb|ABS69471.1| TIM-barrel protein, yjbN family [Xanthobacter autotrophicus Py2]
          Length = 330

 Score =  303 bits (776), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 154/316 (48%), Positives = 207/316 (65%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  A LYTEM+ A AIL GD+  +LGFS +E P+A+Q+GG+D +
Sbjct: 14  MMDWTDRHCRAFHRTLSRRARLYTEMVTAPAILHGDRARLLGFSPEEHPVAVQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I  D+GY+EINLNVGCPS RV  G+FGACLM  PD+V DC+AAM   ++IPVT
Sbjct: 74  ELAQAARICADYGYDEINLNVGCPSDRVQGGNFGACLMREPDLVADCVAAMKAVVAIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  ++  +G + + +HARKA LKGLSP++NR IP LDYD V 
Sbjct: 134 VKCRIGVDDQDPEEALDRLADAVVAAGTDALIVHARKAWLKGLSPRENRDIPPLDYDRVR 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + I +NGG+  ++Q L+    +DG+M+GRAAY++  +L  VD     PL   
Sbjct: 194 RLKARLPHVPIAVNGGIASIAQGLEEARGLDGMMLGRAAYQDPELLLGVD-----PLLFG 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P       D +  + A    Y A HL +GG+L  ITRHM+GLF G   +R  R  L+ E
Sbjct: 249 TPAP---HADGFAAVEA-FEPYVAHHLEAGGRLSDITRHMLGLFTGRKGARIFRRHLSTE 304

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++  A +
Sbjct: 305 AIRPGAGLDVLRAAVD 320


>gi|167646006|ref|YP_001683669.1| tRNA-dihydrouridine synthase A [Caulobacter sp. K31]
 gi|167348436|gb|ABZ71171.1| TIM-barrel protein, yjbN family [Caulobacter sp. K31]
          Length = 325

 Score =  302 bits (774), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 153/315 (48%), Positives = 202/315 (64%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R   R+L+  ALLY+EM+ + A+L GD + +LGF   + P+ALQ+GG++ +
Sbjct: 1   MMDWSDRHCRSLHRVLSRRALLYSEMVTSGAVLHGDCEKLLGFDAGQHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I EDFGY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM  A+S+PVT
Sbjct: 61  DLAAAARIGEDFGYDEINLNVGCPSDRVQSGRFGACLMREPKLVADCMAAMTAAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV    ++GV    +HARKA LKGLSPK+NR +P LDY +V+
Sbjct: 121 VKCRIGVDDQDPEQSLFELVDLSAQAGVTHFVVHARKAWLKGLSPKENRDVPPLDYPLVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG+ D+  +L  L  VDGVM+GRAAY    +L  VD          
Sbjct: 181 RLKAERPALTIVINGGIPDLDASLVQLAHVDGVMLGRAAYHEPGLLGQVDRRV------- 233

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D D +  +    + Y A  L +G  L  ++RHM+GLFHG P +R  R ILTVE
Sbjct: 234 --FGEGRDVDAFEAVELYKS-YMASQLAAGVHLTAMSRHMLGLFHGMPGARAWRRILTVE 290

Query: 301 AGASTATHHIIETAF 315
             A+ A   +++ A 
Sbjct: 291 GVAAGAGLEVVDRAL 305


>gi|126461351|ref|YP_001042465.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides ATCC 17029]
 gi|126103015|gb|ABN75693.1| TIM-barrel protein, yjbN family [Rhodobacter sphaeroides ATCC
           17029]
          Length = 331

 Score =  301 bits (772), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 202/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRDRLLGFSEAEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 79  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPSLVADCVAAMIAESPVPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 139 VKCRIGVDEQEPSEVLPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D      L G
Sbjct: 199 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADR-----LWG 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 254 EEPPRDLA------AVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 307

Query: 300 EAGASTATHHIIETAFN 316
            A    A   + + A  
Sbjct: 308 GASRPGAGLALFDEALE 324


>gi|77462473|ref|YP_351977.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides 2.4.1]
 gi|77386891|gb|ABA78076.1| tRNA-Dihydrouridine synthase [Rhodobacter sphaeroides 2.4.1]
          Length = 313

 Score =  301 bits (772), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 202/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRDRLLGFSEAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 61  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPSLVADCVAAMIAESPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 121 VKCRIGVDEQEPSEVLPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D      L G
Sbjct: 181 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADR-----LWG 235

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 236 EEPPRDLA------AVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 289

Query: 300 EAGASTATHHIIETAFN 316
            A    A   + + A  
Sbjct: 290 GAARPGAGLALFDEALE 306


>gi|221638336|ref|YP_002524598.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides KD131]
 gi|221159117|gb|ACM00097.1| TIM-barrel protein, yjbN family [Rhodobacter sphaeroides KD131]
          Length = 313

 Score =  301 bits (771), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 202/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGQRDRLLGFSEAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 61  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPSLVADCVAAMIAESPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 121 VKCRIGVDEQEPSEVLPAFLETLAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D      L G
Sbjct: 181 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADR-----LWG 235

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 236 EEPPRDLA------AVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 289

Query: 300 EAGASTATHHIIETAFN 316
            A    A   + + A  
Sbjct: 290 GASRPGAGLALFDEALE 306


>gi|332560358|ref|ZP_08414680.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides WS8N]
 gi|332278070|gb|EGJ23385.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides WS8N]
          Length = 313

 Score =  300 bits (769), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 202/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRDRLLGFSEAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 61  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPALVADCVAAMIAESPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 121 VKCRIGVDEQEPSEVLPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D      L G
Sbjct: 181 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADR-----LWG 235

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 236 EEPPRDLA------AVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 289

Query: 300 EAGASTATHHIIETAFN 316
            A    A   + + A  
Sbjct: 290 GASRPGAGLALFDEALE 306


>gi|146276373|ref|YP_001166532.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides ATCC 17025]
 gi|145554614|gb|ABP69227.1| TIM-barrel protein, yjbN family [Rhodobacter sphaeroides ATCC
           17025]
          Length = 335

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 153/317 (48%), Positives = 206/317 (64%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G ++ +LGFS  E P+ALQ+GG+D +
Sbjct: 23  MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRERLLGFSPAEHPVALQLGGSDPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++    G++EINLNVGCPS RV  G FGA LM  P ++ DC+AAM     +PVT
Sbjct: 83  ELAQAVRVAAPHGHDEINLNVGCPSDRVQSGCFGAVLMERPALLADCVAAMIAESPVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q PA  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 143 VKCRIGVDEQEPAEILPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  +SQA ++L   +DGVMIGRAAY    +L   D      L G
Sbjct: 203 AMKRRFPELTICLNGGVATLSQAEELLAQGLDGVMIGRAAYNEPELLLGADR-----LWG 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +   D D   ++ A M  Y A HL +GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 258 CEPPR---DLD---RVLADMRPYIAEHLAAGGRLHQITRHMLGLFSGRPGARHWRRILSE 311

Query: 300 EAGASTATHHIIETAFN 316
            A    A   + + A  
Sbjct: 312 GASRPGAGLDLFDEALE 328


>gi|16125555|ref|NP_420119.1| tRNA-dihydrouridine synthase A [Caulobacter crescentus CB15]
 gi|221234301|ref|YP_002516737.1| tRNA-dihydrouridine synthase A [Caulobacter crescentus NA1000]
 gi|13422645|gb|AAK23287.1| TIM-barrel protein, yjbN family [Caulobacter crescentus CB15]
 gi|220963473|gb|ACL94829.1| NIFR3-like protein [Caulobacter crescentus NA1000]
          Length = 341

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 150/323 (46%), Positives = 209/323 (64%), Gaps = 10/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R L++ ALLYTEM+ + A++ GD+  +LG+   + P+A+Q+GG+D +
Sbjct: 17  MMDWTDRHCRSLHRGLSSRALLYTEMVTSGAVVHGDRNKLLGYDPGQHPVAVQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I ED+GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+AA+  A+ +P T
Sbjct: 77  ELAQAARIAEDYGYDEVNLNVGCPSDRVQSGRFGACLMREPDLVAECMAAIKNAVRVPAT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV     +G++   +HARKA L+GLSPK+NR IP LDY +VY
Sbjct: 137 VKCRIGVDDQDPEESLFTLVDRCAAAGIDTFVVHARKAWLQGLSPKENRDIPPLDYALVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+E P L I +NGG+  +  AL+ L + VDGVM+GRAAY  + +L  VD         
Sbjct: 197 RLKRERPALTIAINGGVPSVDAALEHLANGVDGVMLGRAAYHEAGLLGEVDRRVFG---- 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                   D D +  +      Y AR L +G  L  ++RHM+GLFHG P +R  R ILTV
Sbjct: 253 ----LDVADVDSFEAVE-RYRPYLARELAAGTHLAAMSRHMLGLFHGLPGARAWRRILTV 307

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           E   S A   +++ A + +  +L
Sbjct: 308 EGVKSGAGLDVVDRALDAVRAAL 330


>gi|323137432|ref|ZP_08072510.1| TIM-barrel protein, yjbN family [Methylocystis sp. ATCC 49242]
 gi|322397419|gb|EFX99942.1| TIM-barrel protein, yjbN family [Methylocystis sp. ATCC 49242]
          Length = 358

 Score =  300 bits (767), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 148/302 (49%), Positives = 204/302 (67%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  A LYTEM+   A++ GD+  ++GF   E+P+A Q+GG++ +
Sbjct: 36  MMDWTDRHCRYFHRLLSRRARLYTEMLTTGAVIHGDRLRLMGFDAFEQPVAFQLGGSEPA 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+IVE+FGY E+NLNVGCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 96  DLGRAARIVEEFGYAEVNLNVGCPSDRVQNGAFGACLMQCPALVADCVKAMKDAVALPVT 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL ++ +   ++GV+ + +HARKA L+GLSPK+NR IP LDY +V+
Sbjct: 156 VKCRIGVDDQEPERALFDIAERCVEAGVDALIVHARKAWLQGLSPKENRDIPPLDYALVH 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  P   I +NGG+  ++Q  + L  VDGVM+GRAAY + A+L  VD E F  P   
Sbjct: 216 RLKRALPATPIAINGGIATLAQMREQLTEVDGVMVGRAAYHDPALLLQVDAELFDAP--- 272

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SP+      D ++ + A +  Y  R L  G +L  ITRH++GLF G P +R  R  L +
Sbjct: 273 -SPL-----ADCFQAVEAFLP-YIERELSKGERLSSITRHLLGLFAGLPGARSYRRRLAL 325

Query: 300 EA 301
           EA
Sbjct: 326 EA 327


>gi|83945621|ref|ZP_00957967.1| TIM-barrel protein, yjbN family protein [Oceanicaulis alexandrii
           HTCC2633]
 gi|83850987|gb|EAP88846.1| TIM-barrel protein, yjbN family protein [Oceanicaulis alexandrii
           HTCC2633]
          Length = 332

 Score =  299 bits (766), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 151/316 (47%), Positives = 197/316 (62%), Gaps = 8/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+LT  A+LYTEM V  A++ GD   ++GF   E P+A+Q+GG+D  
Sbjct: 17  MMDWTDRHCRAFHRVLTRRAVLYTEMAVDQALIHGDVPRLIGFDASEHPVAIQLGGSDPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  A+KI E FGY EINLNVGCPS RV  G FGACLM  P++V DC+ AM +A+S+PVT
Sbjct: 77  ILARASKIAEGFGYLEINLNVGCPSDRVQSGKFGACLMREPELVRDCLTAMREAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+GVDDQ P   L   V+++++SGV    +HARKA LKGLSPK+NR +P LDYD+V 
Sbjct: 137 VKHRLGVDDQDPEKTLFGFVETVRESGVKTFIVHARKAWLKGLSPKENRDVPPLDYDLVR 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E+PDL + LNGGLE +   +  +   DG+M+GRAAY     L  VD         S
Sbjct: 197 RMKAEHPDLEVLLNGGLETLEHGMAEIHGADGIMLGRAAYHTPWTLAEVDTRIYG--EAS 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  T  +         +   Y  R L  G KL  ITRHM+GLF G P +R+ R +L+  
Sbjct: 255 DPCATPFEA------VEAYRPYVERQLDQGVKLHAITRHMLGLFAGRPGARKWRQVLSER 308

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A +
Sbjct: 309 ANRPGAGWEVLEDALD 324


>gi|237809463|ref|YP_002893903.1| TIM-barrel protein, yjbN family [Tolumonas auensis DSM 9187]
 gi|237501724|gb|ACQ94317.1| TIM-barrel protein, yjbN family [Tolumonas auensis DSM 9187]
          Length = 338

 Score =  299 bits (766), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 155/321 (48%), Positives = 207/321 (64%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AIL G K + L +ST+E P+ALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAILFG-KGDYLQYSTEEHPIALQLGGSDPV 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I ED GY+EINLNVGCPS RV  G FGACLM +  +V DC+AAM   + IPVT
Sbjct: 83  DLAKCARIAEDRGYDEINLNVGCPSDRVQNGRFGACLMASAQLVADCVAAMRAEVQIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + +++++++G N   +HARKA L GLSPK+NR IP LDY+ VY
Sbjct: 143 VKTRIGIDELDSYAFLCDFIETVQQTGCNTFIVHARKAWLSGLSPKENRDIPPLDYERVY 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ P L I +NGG+ D++QA   L  VDGVM+GR AY+N  ML  VD + F++P   
Sbjct: 203 QLKRDYPHLTIAINGGITDLAQAKHHLQYVDGVMVGREAYQNPYMLAQVDAQLFADP--- 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+ +R       +    M  Y   HL +GG L  ITRHM+GLF G P +R  R  L+ 
Sbjct: 260 -HPVLSR------HETVMQMLPYIDAHLQAGGYLSHITRHMLGLFQGVPGARAWRRHLSE 312

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A    A   I+  A + + E
Sbjct: 313 NATRKGADTKIVLDALSHVQE 333


>gi|296444599|ref|ZP_06886563.1| TIM-barrel protein, yjbN family [Methylosinus trichosporium OB3b]
 gi|296257867|gb|EFH04930.1| TIM-barrel protein, yjbN family [Methylosinus trichosporium OB3b]
          Length = 351

 Score =  299 bits (765), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 148/290 (51%), Positives = 194/290 (66%), Gaps = 11/290 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL++  A LYTEM+   A++ GD++ +LGF   E+PLALQ+GG+D  
Sbjct: 30  MMDWTDRHCRFFHRLMSRRARLYTEMLTTGAVIFGDRQRLLGFDPAERPLALQLGGSDPL 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +A +I E FGY+EINLNVGCPS RV  G+FGACLML PD+V DC++AM  A+ +PVT
Sbjct: 90  DLAKATRIAEPFGYDEINLNVGCPSDRVQNGAFGACLMLRPDLVADCVSAMKDAVDLPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L + +  +G + + +HARKA L GLSPK+NR +P LDY +V+
Sbjct: 150 VKCRIGVDDQDPRTALFALCERVVAAGCDALVVHARKAWLAGLSPKENRDVPPLDYALVH 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           E+K+  P L I +NGG+E + Q    L  VDGVMIGRAAY N  +L  VD + F  P   
Sbjct: 210 ELKRAFPTLPIAINGGIETIEQMRAQLEHVDGVMIGRAAYHNPELLLAVDPQLFGEP--- 266

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            +P+      D +  + A +  Y    L  G +L  +TRHM+GLF G P 
Sbjct: 267 -APL-----PDGFAAVEAFIP-YVEAQLRRGERLASMTRHMLGLFAGRPG 309


>gi|117919170|ref|YP_868362.1| tRNA-dihydrouridine synthase A [Shewanella sp. ANA-3]
 gi|117611502|gb|ABK46956.1| TIM-barrel protein, yjbN family [Shewanella sp. ANA-3]
          Length = 334

 Score =  299 bits (765), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 148/316 (46%), Positives = 208/316 (65%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++ +
Sbjct: 21  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM +A+ IPVT
Sbjct: 80  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQAVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 140 VKTRIGIDEQDSYEFLTHFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 200 QLKRDYPTLNISINGGITSLEQAKTHLQHLDGVMVGREAYQNPYILAQVDQL----LCGS 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  + ++    +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 256 Q--KAVMSRE---AVIETMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 310

Query: 301 AGASTATHHIIETAFN 316
           A  + A   +++ A+ 
Sbjct: 311 AHKNGAGIEVVKQAYQ 326


>gi|152999313|ref|YP_001364994.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS185]
 gi|151363931|gb|ABS06931.1| TIM-barrel protein, yjbN family [Shewanella baltica OS185]
          Length = 339

 Score =  298 bits (764), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 204/317 (64%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 205 QLKRDYPTLNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQV----LCGS 260

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 261 QKAVISRED------VIEAMLPYIEAHLQSGGRLNHITRHMIGLFQGLPGARAWRRYLSE 314

Query: 300 EAGASTATHHIIETAFN 316
            A  + A   +++ AF 
Sbjct: 315 NAHKNGAGIEVVKQAFQ 331


>gi|217978983|ref|YP_002363130.1| TIM-barrel protein, yjbN family [Methylocella silvestris BL2]
 gi|217504359|gb|ACK51768.1| TIM-barrel protein, yjbN family [Methylocella silvestris BL2]
          Length = 335

 Score =  298 bits (763), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 151/318 (47%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT  A LYTEM+   A+L G +  +LGF   E PLA Q+GG+D +
Sbjct: 14  MMDWTDRHCRSFHRLLTRRARLYTEMVTTGAVLHGQRDRLLGFDAAEHPLAAQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY+EINLN GCPS RV  G+FGACLM  P++VGDC+AAM  A+S PVT
Sbjct: 74  DLAAAARICADFGYDEINLNAGCPSKRVQNGAFGACLMREPELVGDCVAAMKAAVSAPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL    +++  +G + + +HARKA L+GLSPKDNR IP LDY +V+
Sbjct: 134 VKCRIGVDEQEPREALFAFAETVLGAGADALIVHARKAWLEGLSPKDNRHIPPLDYALVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+  PD  I +NGGL+ +      L  VDGVMIGRAAY++ A+L  VD  F       
Sbjct: 194 ELKRRFPDTPIAINGGLDTIDAMRAQLDHVDGVMIGRAAYQDPALLLEVDPVFFGEDAPF 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +   ++         + T Y A  L  G  L  + RH++G F+G P +R  R  L  E
Sbjct: 254 SEMAQAIE---------AFTPYIAARLTEGVPLNAMVRHLLGAFNGRPGARAFRRHLATE 304

Query: 301 AGASTATHHIIETAFNLM 318
           +    A   ++  A  L+
Sbjct: 305 SVKPGAGLEVLRAALALI 322


>gi|160873928|ref|YP_001553244.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS195]
 gi|160859450|gb|ABX47984.1| TIM-barrel protein, yjbN family [Shewanella baltica OS195]
 gi|315266160|gb|ADT93013.1| TIM-barrel protein, yjbN family [Shewanella baltica OS678]
          Length = 339

 Score =  298 bits (763), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 204/317 (64%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 205 QLKRDYPTLNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQV----LCGS 260

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 261 QKAVISRED------VIEAMLPYIEAHLQSGGRLNHITRHMIGLFQGLPGARAWRRYLSE 314

Query: 300 EAGASTATHHIIETAFN 316
            A  + A   +++ AF 
Sbjct: 315 NAHKNGAGIEVVKQAFQ 331


>gi|260575169|ref|ZP_05843170.1| TIM-barrel protein, yjbN family [Rhodobacter sp. SW2]
 gi|259022791|gb|EEW26086.1| TIM-barrel protein, yjbN family [Rhodobacter sp. SW2]
          Length = 325

 Score =  298 bits (762), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 152/317 (47%), Positives = 206/317 (64%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R +T  A+LYTEM+ A A++ G +  +LG+   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRYFHRAMTARAMLYTEMVTALAVIHGPRDRLLGYDLAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++   +GY+EINLNVGCPS RV  G+FGA LML P +V  C+AAM  A  +PVT
Sbjct: 74  ELAQAVRLAAPWGYDEINLNVGCPSDRVQSGAFGAVLMLQPALVAACVAAMQDASPVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ+P   L   ++ ++  GV  + IHARKA L+GLSPK+NR+IP LDY +V 
Sbjct: 134 VKCRIGVDDQVPEDVLPAFLEMLRGVGVGHVIIHARKAWLQGLSPKENREIPPLDYPLVL 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
            +K+E PDL I +NGG+  + QA  +L   +DGVMIGRAAY +  A L   D  + +P  
Sbjct: 194 RMKREFPDLTISINGGVATLDQARGLLAQGLDGVMIGRAAYHDPGATLIGADTLWGDP-- 251

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                     +D +  I A M  Y A HL  GGKL QITRHM+GLF G P +R  R +L+
Sbjct: 252 --------PGRDAFGVIEA-MQPYIAAHLAQGGKLHQITRHMLGLFAGRPGARGWRRVLS 302

Query: 299 VEAGASTATHHIIETAF 315
            +A    A   +++ A 
Sbjct: 303 EQAVRDGAGLQVLDAAL 319


>gi|148254870|ref|YP_001239455.1| tRNA-dihydrouridine synthase A [Bradyrhizobium sp. BTAi1]
 gi|146407043|gb|ABQ35549.1| tRNA-U16,U17-dihydrouridine synthase [Bradyrhizobium sp. BTAi1]
          Length = 318

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 149/319 (46%), Positives = 201/319 (63%), Gaps = 9/319 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F RLL+  ALLYTEM+   A++ GD+K +LGF   E P+ALQ+GG+D + 
Sbjct: 1   MDWTDRHCRVFHRLLSRRALLYTEMVTTGAVIHGDRKRLLGFDASEHPVALQLGGSDPAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  +A+I EDFGY+EINLNVGCPS RV +G FGACLM  P++V  C+AAM +A+ IPVTV
Sbjct: 61  LATSARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPELVAACVAAMKRAVRIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIG+DDQ P +AL  L  ++  +G + + +HARKA L GLSPK+NR+IP LDYD VY 
Sbjct: 121 KCRIGIDDQDPELALDTLADAVVDAGADALIVHARKAWLNGLSPKENREIPPLDYDRVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K   P++ + +NGG+  ++ A   L  VDGVM+GRAAY+    L  VD     P+    
Sbjct: 181 LKARLPNVPVIINGGITSIAAAQAHLAHVDGVMLGRAAYQEPWQLLDVD-----PMLFGD 235

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
               R  KD      A++  Y  R L  G +L  ITRH++G +H  P +R  R  L    
Sbjct: 236 AAPHRSMKDAL----AALEPYIERQLREGSRLHAITRHLVGAYHAVPGARAFRRHLAERG 291

Query: 302 GASTATHHIIETAFNLMIE 320
               A   ++  A  ++ E
Sbjct: 292 VKPDAGIEVLREAVAMVEE 310


>gi|329888317|ref|ZP_08266915.1| tRNA-dihydrouridine synthase A [Brevundimonas diminuta ATCC 11568]
 gi|328846873|gb|EGF96435.1| tRNA-dihydrouridine synthase A [Brevundimonas diminuta ATCC 11568]
          Length = 323

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 205/326 (62%), Gaps = 14/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR+ R F R L+  ALLYTEM+ A A++ GD+  +LGF   E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRNCRAFHRALSTRALLYTEMVTAPAVIHGDRDRLLGFDVVEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAKI E +GY+EINLNVGCPS RV  G FGACLM  P++V DC+AA+ +A+S+P T
Sbjct: 61  QLAEAAKIGEAYGYDEINLNVGCPSDRVQSGKFGACLMREPELVADCMAAIKEAVSVPAT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P ++L   V +    G++   IHARKA LKGLSPK+NR +P LDY +V 
Sbjct: 121 VKCRIGVDDQDPEISLFATVDASAAVGIDSFIIHARKAWLKGLSPKENRDVPPLDYALVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-----VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +K+E P L I +NGG+ D+ QA   L +     +DGVM+GRAAY   A++  VD     
Sbjct: 181 RLKRERPHLSISINGGIGDLDQAEAHLRADDGVQLDGVMLGRAAYHEPALMGQVDRRIFG 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   +T  D D +  +      Y A  L  G  L  +TRHM+GL HG   +R  R 
Sbjct: 241 --------ETTPDVDVFEALE-RYRPYMAARLEEGANLAGMTRHMLGLMHGRAGARAFRR 291

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ILTVE     A   +++ A   + E+
Sbjct: 292 ILTVEGVKPGAGLEVVDRAVEAVREA 317


>gi|304411176|ref|ZP_07392791.1| TIM-barrel protein, yjbN family [Shewanella baltica OS183]
 gi|307306471|ref|ZP_07586214.1| TIM-barrel protein, yjbN family [Shewanella baltica BA175]
 gi|304350369|gb|EFM14772.1| TIM-barrel protein, yjbN family [Shewanella baltica OS183]
 gi|306910762|gb|EFN41190.1| TIM-barrel protein, yjbN family [Shewanella baltica BA175]
          Length = 339

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 204/317 (64%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVIDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 205 QLKRDYPTLNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQV----LCGS 260

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 261 QKAVISRED------VIEAMLPYIEAHLLSGGRLNHITRHMIGLFQGLPGARAWRRYLSE 314

Query: 300 EAGASTATHHIIETAFN 316
            A  + A   +++ AF 
Sbjct: 315 NAHKNGAGIEVVKQAFQ 331


>gi|126175780|ref|YP_001051929.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS155]
 gi|125998985|gb|ABN63060.1| TIM-barrel protein, yjbN family [Shewanella baltica OS155]
          Length = 339

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 204/317 (64%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 205 QLKRDYPALNIGINGGITTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQV----LCGS 260

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 261 QKAVISRED------VIEAMLPYIEAHLLSGGRLNHITRHMIGLFQGLPGARAWRRYLSE 314

Query: 300 EAGASTATHHIIETAFN 316
            A  + A   +++ AF 
Sbjct: 315 NAHKNGAGIEVVKQAFQ 331


>gi|254418914|ref|ZP_05032638.1| TIM-barrel protein, yjbN family [Brevundimonas sp. BAL3]
 gi|196185091|gb|EDX80067.1| TIM-barrel protein, yjbN family [Brevundimonas sp. BAL3]
          Length = 338

 Score =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 153/306 (50%), Positives = 197/306 (64%), Gaps = 14/306 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+LT  ALLYTEM+ A A+L GD+  +LGF   E P+ALQ+GG++  
Sbjct: 14  MMDWTDRHCRAFHRVLTARALLYTEMVTAPAVLHGDRDYLLGFDAVEHPVALQLGGSNPM 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAK+ E +GY+EINLNVGCPS RV  G FGACLM  P++V DC+AA+  A+SIP T
Sbjct: 74  ELAEAAKVGEAYGYDEINLNVGCPSDRVQSGKFGACLMREPELVADCMAAIRSAVSIPAT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PA +L   V +    G+    +HARKA L+GLSPK+NR +P LDYD+V 
Sbjct: 134 VKCRIGVDDQEPATSLFATVDACAAVGIEVFIVHARKAWLQGLSPKENRDVPPLDYDLVR 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-----VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +K+E P L I +NGG+ ++ +A   L       +DGVM+GRAAY   A+L   D     
Sbjct: 194 RLKRERPHLNISINGGIANLDEAEAHLAETDGVRLDGVMMGRAAYHEPAILGQADRRLYG 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T        +D+  +R        Y A  L  G +L  ITRHM+GL HG P +R  R 
Sbjct: 254 ADTADVDAFAALDR--YRP-------YIAARLEEGVRLPAITRHMLGLMHGRPGARAFRR 304

Query: 296 ILTVEA 301
           ILTVE+
Sbjct: 305 ILTVES 310


>gi|260428471|ref|ZP_05782450.1| tRNA-dihydrouridine synthase A [Citreicella sp. SE45]
 gi|260422963|gb|EEX16214.1| tRNA-dihydrouridine synthase A [Citreicella sp. SE45]
          Length = 372

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 151/319 (47%), Positives = 205/319 (64%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ NALLYTEM+ A A++RG   ++L F+ +E P+ALQ+GG+D  
Sbjct: 58  MMDWTDRHCRYLHRLLSRNALLYTEMVTAPALVRGGAVHLLDFNPEEHPVALQLGGSDPD 117

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AAK+    GY++I+LN GCPS RV  G+FGA LM  P++V DC+AAM +A ++ VT
Sbjct: 118 ELAQAAKLGGAAGYDQIDLNCGCPSDRVQSGTFGAVLMKTPELVADCVAAMQEATAVEVT 177

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  ++ +G   I IHARKA L+GLSPK+NR+IP LDY IV+
Sbjct: 178 VKCRIGVDDQKPREVLPAFIDKVRGAGCRRIAIHARKAWLQGLSPKENREIPPLDYAIVH 237

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVD-EYFSNPL 237
           E+K   PDL + LNGG+E ++   K+L   +DGVM+GRAAY     +L   D   +    
Sbjct: 238 EMKAAFPDLHVSLNGGVESLATVEKLLDEGLDGVMVGRAAYHQPWDILAEADARIWGEER 297

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              SP           +I+ +M  Y  RHL  GGKL Q+TRHM+GLF G P +R  R +L
Sbjct: 298 ETPSP----------EEIARAMLPYIERHLSDGGKLHQVTRHMLGLFAGRPGARGWRRVL 347

Query: 298 TVEAGASTATHHIIETAFN 316
           +  A    A   ++E A  
Sbjct: 348 SERATRDGAGPEVVEAALE 366


>gi|119776187|ref|YP_928927.1| tRNA-dihydrouridine synthase A [Shewanella amazonensis SB2B]
 gi|119768687|gb|ABM01258.1| TIM-barrel protein, yjbN family [Shewanella amazonensis SB2B]
          Length = 326

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 148/319 (46%), Positives = 203/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G K + L ++ +E PLALQ+GG+D  
Sbjct: 14  MLDWTDRHYRYFARLMSKEALLYTEMVTTGAILHG-KGDYLAYNQEEHPLALQLGGSDPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+N+NVGCPS RV  G FGACLM  P +V +C+ AM + +S+PVT
Sbjct: 73  DLATCAKLAEARGYDEVNINVGCPSDRVQNGRFGACLMAEPKLVAECVDAMRQQVSVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + V+++  +G +   IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 133 VKTRIGIDEQDSYGFLTDFVETVSAAGCDTFIIHARKAWLQGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L +VD E    P   
Sbjct: 193 QLKRDYPQLSISINGGVTSIEQAKTHLAQLDGVMVGREAYQNPYILASVDTELCGKPAVV 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           SS            ++   +  Y  +HL  GG+L  I+RH+IGL+ G P SR  R  L+ 
Sbjct: 253 SS----------REEVIGKLLPYIGKHLADGGRLNHISRHIIGLYQGLPGSRAWRRHLSE 302

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   +IE A   M
Sbjct: 303 NAHKPGAGIEVIENAIKAM 321


>gi|24375400|ref|NP_719443.1| tRNA-dihydrouridine synthase A [Shewanella oneidensis MR-1]
 gi|38604868|sp|Q8EAJ0|DUSA_SHEON RecName: Full=tRNA-dihydrouridine synthase A
 gi|24350234|gb|AAN56887.1|AE015823_9 TIM-barrel protein, yjbN family [Shewanella oneidensis MR-1]
          Length = 335

 Score =  295 bits (755), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 148/316 (46%), Positives = 206/316 (65%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 21  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLTYNQEEHPLALQLGGSNPV 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 80  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 140 VKTRIGIDEQDSYEFLTHFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  ML  VD+     L GS
Sbjct: 200 QLKRDYPALNISINGGITSLEQAQTHLQHLDGVMVGREAYQNPYMLAQVDQV----LCGS 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +  K  + ++    +  +M  Y   HL  GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 256 T--KAVMSRE---AVIEAMLPYIEAHLQVGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 310

Query: 301 AGASTATHHIIETAFN 316
           A  + A   +++ A+ 
Sbjct: 311 AHKNGAGIEVVKLAYQ 326


>gi|217971989|ref|YP_002356740.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS223]
 gi|217497124|gb|ACK45317.1| TIM-barrel protein, yjbN family [Shewanella baltica OS223]
          Length = 339

 Score =  295 bits (755), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 150/317 (47%), Positives = 203/317 (64%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 205 QLKRDYPALNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQV----LCGS 260

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +   M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 261 QKAVISRED------VIEVMLPYIEAHLLSGGRLNHITRHMIGLFQGLPGARAWRRYLSE 314

Query: 300 EAGASTATHHIIETAFN 316
            A  + A   +++ AF 
Sbjct: 315 NAHKNGAGIEVVKQAFQ 331


>gi|27378845|ref|NP_770374.1| tRNA-dihydrouridine synthase A [Bradyrhizobium japonicum USDA 110]
 gi|27351994|dbj|BAC48999.1| blr3734 [Bradyrhizobium japonicum USDA 110]
          Length = 331

 Score =  295 bits (754), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 147/298 (49%), Positives = 196/298 (65%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+   AI+ GD++ +LGF   E P+ALQ+GG+D S
Sbjct: 13  MMDWTDRHCRVFHRQLTRRALLYTEMLTTGAIIHGDRERLLGFDACENPVALQLGGSDPS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I E FGY+EINLNVGCPS RV +G FGACLM  P++V  C+ AM +A+++PVT
Sbjct: 73  ELAQAARIGEAFGYDEINLNVGCPSDRVKDGRFGACLMAEPELVARCVDAMKRAVAVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDY+ VY
Sbjct: 133 VKCRIGIDDQDPEVALDTLARAVVAAGCDALIVHARKAWLNGLSPKENRDIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+ + +NGG+  + +A   L  VDGVM+GRAAY+    L +VD   S+    +
Sbjct: 193 RLKRAMPDVPVIINGGIPGIDEAKAHLEHVDGVMLGRAAYQEPWRLLSVD---SDIFGET 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  T  D         +M  Y    L  G +L  ITRH +G FH  P +R  R  L 
Sbjct: 250 APHATMQDA------LEAMMPYIEAQLARGTRLHAITRHFVGAFHAVPGARAFRRHLA 301


>gi|254293797|ref|YP_003059820.1| TIM-barrel protein, yjbN family [Hirschia baltica ATCC 49814]
 gi|254042328|gb|ACT59123.1| TIM-barrel protein, yjbN family [Hirschia baltica ATCC 49814]
          Length = 327

 Score =  295 bits (754), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 151/310 (48%), Positives = 196/310 (63%), Gaps = 9/310 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R  T  ALLYTEM+ ADA+L GD + ++GF+  E+PLALQ+GG+D  
Sbjct: 14  MMDWTDRHCRMFHRAFTKRALLYTEMVTADALLHGDLEYLIGFNPDEQPLALQLGGSDPI 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +A+K+ ED+GY+EINLN GCPS RV  G+FGACLM  P+ V +CI+AM  A+ IPVT
Sbjct: 74  KLAQASKVGEDYGYSEINLNCGCPSDRVQSGAFGACLMAQPERVAECISAMQNAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DD  P   L + V ++  +G     +HARKA LKGLSPK+NR IP LDYD+V 
Sbjct: 134 VKCRIGIDDDDPNERLFSFVNTVADAGCQVFIVHARKAWLKGLSPKENRDIPPLDYDLVV 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK  PDL I LNGGL DM  +L  L  +DGVM+GRAAY    +L  VD         +
Sbjct: 194 RLKKARPDLTISLNGGLVDMEASLDQLSCLDGVMLGRAAYHTPHILGQVDRLV---FGET 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +        +  A+   Y    L  G  L  ITRHM+GLF+G   +++ R  L+  
Sbjct: 251 TPDVSE------HQALATYRPYIKAQLEKGTHLHAITRHMMGLFNGKRGAKKWRRYLSEN 304

Query: 301 AGASTATHHI 310
           A  +     I
Sbjct: 305 APGAKGVEAI 314


>gi|209885665|ref|YP_002289522.1| tRNA-dihydrouridine synthase A [Oligotropha carboxidovorans OM5]
 gi|209873861|gb|ACI93657.1| tRNA-dihydrouridine synthase A [Oligotropha carboxidovorans OM5]
          Length = 332

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 145/299 (48%), Positives = 191/299 (63%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+   A++ G ++ +LGF   E P+ALQ+GG++  
Sbjct: 14  MMDWTDRHCRVFHRALTRRALLYTEMVTTGAVIHGSRERLLGFDACEHPVALQLGGSNPR 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+AKI E FGY+EINLNVGCPS RV +G FGACLM  P +VG+C+ AM  A+ +PVT
Sbjct: 74  DLAESAKIGEGFGYDEINLNVGCPSDRVQDGRFGACLMAEPQLVGECVVAMKAAVRVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL +L +S+  +G + + +HARKA L+GLSPK+NR +P LDYD VY
Sbjct: 134 VKCRIGIDDQDPERALDDLARSVVTAGADALIVHARKAWLQGLSPKENRNVPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K   PD+ I +NGG+  + +A   L  VDGVM+GRAAY+    L  VD E F  P   
Sbjct: 194 RLKAAMPDMTIAINGGIASIEEARGHLQHVDGVMLGRAAYQEPWRLLAVDPELFDAPPPH 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +S            +   ++  Y  +    G +L  ITRHM+G FHG   +R  R  L 
Sbjct: 254 AS----------MHEAIETLFPYIEKERARGTRLHSITRHMVGAFHGVAGARAFRRALA 302


>gi|114046253|ref|YP_736803.1| tRNA-dihydrouridine synthase A [Shewanella sp. MR-7]
 gi|113887695|gb|ABI41746.1| TIM-barrel protein, yjbN family [Shewanella sp. MR-7]
          Length = 340

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 206/316 (65%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++ +
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 145 VKTRIGIDEQDSYEFLTHFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++   L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 205 QLKRDYSTLNISINGGITSLEQAKTHLQHLDGVMVGREAYQNPYILAQVDQL----LCGS 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  + ++    +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 261 Q--KAVISRE---AVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFN 316
           A  + A   +++ A+ 
Sbjct: 316 AHKNGAGIEVVKQAYQ 331


>gi|126735535|ref|ZP_01751280.1| TIM-barrel protein, yjbN family [Roseobacter sp. CCS2]
 gi|126714722|gb|EBA11588.1| TIM-barrel protein, yjbN family [Roseobacter sp. CCS2]
          Length = 331

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 149/319 (46%), Positives = 206/319 (64%), Gaps = 14/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL++ + LLYTEM+ A A++ GD+  +LGF   E+PLALQ+GG+D +
Sbjct: 17  MMDWTDRHCRYLHRLMSRHTLLYTEMVTAPAVIHGDRDRLLGFHVDEQPLALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I E +GY EINLN GCPS RV  G FGA LM +P +V DC+AAM  A+ +PVT
Sbjct: 77  QLAEAARIAEGYGYAEINLNCGCPSDRVQSGHFGAVLMESPVLVADCVAAMIAAVRVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P V L + +  +  +GV+   +HARKA L+GLSPK+NR++P L+YD+V 
Sbjct: 137 VKCRIGVDDQDPHVILPDFLARVSAAGVDRFSVHARKAWLQGLSPKENREVPPLNYDLVM 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA--MLTTVDEYFSNPL 237
           ++K   P L + +NGG+  + QA   L   +DGVMIGRAAY   A  +L      + +P 
Sbjct: 197 KMKGLFPHLHVSINGGIATLDQAEDFLARGLDGVMIGRAAYHTPADILLQADARIYGDP- 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                 + R  +D    +   M  Y A H+  GG+L Q+TRHM+GLF G P +R  R  L
Sbjct: 256 ------RERTAED----VVHLMLPYIADHIAQGGRLGQVTRHMLGLFQGRPGARGWRRHL 305

Query: 298 TVEAGASTATHHIIETAFN 316
           +  A A  A   ++ +A +
Sbjct: 306 SENAHADGAGPAVVLSALD 324


>gi|91976520|ref|YP_569179.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris BisB5]
 gi|91682976|gb|ABE39278.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris BisB5]
          Length = 317

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 150/299 (50%), Positives = 196/299 (65%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD   R F RLLT    LYTEM+   A++RGD++ +LGF   E P+ALQ+GG++ +
Sbjct: 1   MMEWTDTRCRVFHRLLTRRGRLYTEMLTCGAVIRGDRQRLLGFDASEHPVALQLGGSNPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA I EDFGY+EINLNVGCPS RV EG FGACLM  P +V DC+AAM +A++IPVT
Sbjct: 61  DLATAATIGEDFGYDEINLNVGCPSDRVKEGRFGACLMAEPMLVADCVAAMKRAVTIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL NL +S+  +GV+ + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 121 VKCRIGIDDQDPETALDNLAQSVVAAGVDALIVHARKAWLNGLSPKENRDIPPLDYDRVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  P + I +NGG+  ++QA + L  VDGVM+GRAAY+    L  VD E F      
Sbjct: 181 RLKRAMPAVPIIINGGITSIAQAKQHLAYVDGVMLGRAAYQEPWRLLDVDPELFGE---- 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           ++P  T  D         ++  Y    L  G +L  ITRH+IG + G P +R  R  L+
Sbjct: 237 AAPHATMKDA------LEALMPYIEDQLAQGVRLHAITRHLIGAYQGVPGARAFRRYLS 289


>gi|86750510|ref|YP_487006.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris HaA2]
 gi|86573538|gb|ABD08095.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris HaA2]
          Length = 332

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 149/299 (49%), Positives = 194/299 (64%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD   R F RLLT  A LYTEM+   A++ GD++ +LGF   E P+ALQ+GG+D +
Sbjct: 16  MMEWTDSRCRVFHRLLTKRARLYTEMVTTGAVIHGDRQRLLGFDASEHPVALQLGGSDPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAKI EDFGY+EINLNVGCPS RV EG FGACLM  P++V D +AAM +A+ IPVT
Sbjct: 76  ALATAAKIGEDFGYDEINLNVGCPSDRVKEGRFGACLMAEPELVADGVAAMKRAVEIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL  L + +  +GV+ + +HARKA L GLSPK+NR +P LDYD VY
Sbjct: 136 VKCRIGIDDQDPEAALDTLARGVVAAGVDALIVHARKAWLNGLSPKENRHVPPLDYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  PDL I +NGG+  +++A   L  VDGVM+GRAAY+    L  VD E F      
Sbjct: 196 RLKRALPDLPIVINGGIGSIAEAKLHLAHVDGVMLGRAAYQEPWRLLEVDPELFGE---- 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           ++P  T  D         ++  Y    L  G +L  ITRH+IG + G P +R  R  L+
Sbjct: 252 AAPYATMKDA------LEALMPYIEDQLAQGVRLHAITRHLIGAYQGVPGARAFRRYLS 304


>gi|297624812|ref|YP_003706246.1| TIM-barrel protein, yjbN family [Truepera radiovictrix DSM 17093]
 gi|297165992|gb|ADI15703.1| TIM-barrel protein, yjbN family [Truepera radiovictrix DSM 17093]
          Length = 354

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 205/322 (63%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR F R +T   LLYTEM+  +A+LRGD++ +LGFS  EKPLALQ+GG D  
Sbjct: 15  MMDWTDRHYRAFMRGVTRRTLLYTEMVHVNAVLRGDRERVLGFSEFEKPLALQLGGDDPR 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL   A++ ED+GY+E+NLNVGCPS RV  G+FGACLM  P+ V  C+AAM +A ++PVT
Sbjct: 75  KLAACARVAEDWGYSELNLNVGCPSPRVQRGNFGACLMAQPERVAACVAAMREATTLPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L + V+ + ++      +HARKA L GLSPK+NR +P L Y+ VY
Sbjct: 135 VKHRIGIDDRDRFDDLAHFVEVVAQAAPARFTVHARKAWLSGLSPKENRTVPPLRYEEVY 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+ +P+L I LNGG+  +  A   L  VD VMIGRAAY++   L   D  F     G+
Sbjct: 195 QLKRLHPELEIELNGGVRSLEAAAAHLGRVDAVMIGRAAYEDPYALARADALF----YGA 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + TR      R++  +   YA+R L  G  L  +TRH++GLF G P +R  R +L+ +
Sbjct: 251 PHVPTR------REVVEAFLPYASRQLERGVPLASLTRHLLGLFTGAPGARAWRRLLSEQ 304

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A    A   ++E A   + + +
Sbjct: 305 AHQPGAGVEVLERALGALPDEV 326


>gi|302382184|ref|YP_003818007.1| hypothetical protein Bresu_1072 [Brevundimonas subvibrioides ATCC
           15264]
 gi|302192812|gb|ADL00384.1| TIM-barrel protein, yjbN family [Brevundimonas subvibrioides ATCC
           15264]
          Length = 341

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 156/326 (47%), Positives = 201/326 (61%), Gaps = 14/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  ALLYTEM+ A A+L GD++ +LGF   E P+ALQ+GG+D  
Sbjct: 14  MMDWTDRHCRAFHRALSTRALLYTEMVTAPAVLHGDRERLLGFDPVEHPVALQLGGSDPE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I    GY+EINLNVGCPS RV  G FGACLM  P++V DC+AA+  A+ IP T
Sbjct: 74  QLAQAARIGAAMGYDEINLNVGCPSDRVQSGRFGACLMKEPELVADCMAAIKGAVDIPAT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PAV+L   V +    GV    +HARKA L GLSPK+NR +P LDY +V 
Sbjct: 134 VKCRIGVDDQDPAVSLFATVDASAAVGVTTFIVHARKAWLSGLSPKENRDVPPLDYGLVR 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +K+E P L I +NGG+  +  A   L      ++DGVM+GRAAY   A+L  VD     
Sbjct: 194 RLKRERPHLTICINGGIASLDAAEAHLDDTDGVALDGVMLGRAAYHEPALLGQVDRRLFG 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG        D D +  +      Y A  L  G  L  +TRHM+GL HG P +R  R 
Sbjct: 254 EGTG--------DVDPFAAVE-RYKPYLAARLSEGWGLHAMTRHMLGLMHGRPGARAFRR 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ILTVEA    A   +++ A + + E+
Sbjct: 305 ILTVEAIRPGAGLEVVDRALDAVREA 330


>gi|197105805|ref|YP_002131182.1| tRNA-dihydrouridine synthase [Phenylobacterium zucineum HLK1]
 gi|196479225|gb|ACG78753.1| tRNA-dihydrouridine synthase [Phenylobacterium zucineum HLK1]
          Length = 343

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 150/320 (46%), Positives = 198/320 (61%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R L++ ALLYTEM+   A+L GD++ +L +   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDRHCRVLHRTLSSRALLYTEMLTTGAVLHGDRERLLAYDPVEHPVALQLGGSEPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA+I E  GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM  A+ +PVT
Sbjct: 74  ELAAAARIGEAEGYDEINLNVGCPSDRVQSGRFGACLMREPELVAECMAAMGAAVKVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV    ++GV    +HARKA LKGLSPK+NR +P LDY +V+
Sbjct: 134 VKCRIGVDDQDPEESLFTLVDLCAEAGVTSFVVHARKAWLKGLSPKENRDVPPLDYPLVW 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E PDL I +NGG+  + +A   L  VDGVM+GRAAY    +L   D          
Sbjct: 194 RLKAERPDLTIVINGGIGSLDEAEDHLRHVDGVMLGRAAYHTPDLLGQADARIFGEDRRV 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SP +             +   Y A  L  G  L  +TRHM+GLFHG P +R  R ILTV+
Sbjct: 254 SPFEA----------VEAFRPYVAGQLARGTHLAAMTRHMLGLFHGVPGARAWRRILTVD 303

Query: 301 AGASTATHHIIETAFNLMIE 320
              + A   +I+ A   + E
Sbjct: 304 GVKAGAGLEVIDRALAAVSE 323


>gi|299133589|ref|ZP_07026783.1| TIM-barrel protein, yjbN family [Afipia sp. 1NLS2]
 gi|298591425|gb|EFI51626.1| TIM-barrel protein, yjbN family [Afipia sp. 1NLS2]
          Length = 316

 Score =  293 bits (749), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 154/321 (47%), Positives = 198/321 (61%), Gaps = 11/321 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F R LT  A LYTEM+   A++RGD++ +LGF   E P+ALQ+GG++   
Sbjct: 1   MDWTDRHCRVFHRALTRRAWLYTEMLTTGAVIRGDRERLLGFDACEHPVALQLGGSNPHD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L E+AKI E FGY+EINLNVGCPS RV +G FGACLM  P +VGDC+AAM  A+ +PVTV
Sbjct: 61  LAESAKIGEGFGYDEINLNVGCPSDRVQDGRFGACLMTVPQLVGDCVAAMKAAVRVPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIGVD Q P  AL  L +++  +G + + +HARKA L+GLSPK+NR IP LDYD VY 
Sbjct: 121 KCRIGVDKQDPEQALDALAQNVVTAGADALIVHARKAWLEGLSPKENRDIPPLDYDRVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGS 240
           +K   PD+ I +NGG+  + QA   L  VDGVM+GRAAY     L  VD E F      S
Sbjct: 181 LKAAMPDVTISINGGVTSIEQAKAHLQHVDGVMLGRAAYHEPWRLLAVDPELFG----AS 236

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SP  +        +   S+  Y  R    G +L  ITRHM+G FHG   +R  R  L   
Sbjct: 237 SPHAS------MHEAIESLFPYIERQRARGMRLHSITRHMVGAFHGVAGARAFRRALAEN 290

Query: 301 AGASTATHHIIETAFNLMIES 321
              + A    +  A  L++ +
Sbjct: 291 CVKADAGVEQLRDALRLVVPA 311


>gi|182677984|ref|YP_001832130.1| YjbN family TIM-barrel protein [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182633867|gb|ACB94641.1| TIM-barrel protein, yjbN family [Beijerinckia indica subsp. indica
           ATCC 9039]
          Length = 336

 Score =  292 bits (748), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 153/317 (48%), Positives = 202/317 (63%), Gaps = 15/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F RLL+  ALLYTEMI   A+L G    +LGF   E P+A+Q+GG++  
Sbjct: 14  MMEWTDRHCRVFHRLLSRRALLYTEMITTAALLHGHVDRLLGFDDVEHPVAVQLGGSEPR 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY+EINLN+GCPS RV  G+FGACLML P++VGDC+AA+  ++S+PVT
Sbjct: 74  DLAAAARICADFGYDEINLNIGCPSERVQNGAFGACLMLEPELVGDCVAAIKASVSLPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  +I  +GV+GI +HARKA LKGLSP+ NR +P LDY +V+
Sbjct: 134 VKCRIGVDDQDPEEALGTLSAAIIAAGVDGIIVHARKAWLKGLSPRQNRDVPPLDYPLVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF---SNPL 237
            +K+  P++ I +NGGL       + L  VDGVM+GR AY+  AML +VD  F     PL
Sbjct: 194 ALKRTYPEIPIMINGGLVTHESMQEQLRHVDGVMVGRQAYQEPAMLLSVDPLFFGEEAPL 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           T +    T V + F   + A   +        G  L  +TRH++GLF+G P +R  R  L
Sbjct: 254 TDA----TDVVEAFIPYVEARRAE--------GVPLHSMTRHILGLFNGRPGARAFRRHL 301

Query: 298 TVEAGASTATHHIIETA 314
             E  A  A   ++  A
Sbjct: 302 ATEGLARDAGADVLRAA 318


>gi|115523989|ref|YP_780900.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris BisA53]
 gi|115517936|gb|ABJ05920.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris BisA53]
          Length = 332

 Score =  292 bits (747), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 151/317 (47%), Positives = 201/317 (63%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+  ALLYTEM+   A++ GD++ +LGF   E P+ALQ+GG+   
Sbjct: 14  MMDWTDRHCRVFHRVLSRRALLYTEMVTTGAVIHGDRQRLLGFHDSEHPVALQLGGSAPR 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA I E+FGY+EINLNVGCPS RV +G FGACLM  P++V + +AAM  A+ +PVT
Sbjct: 74  DLASAAAIGEEFGYDEINLNVGCPSDRVKDGRFGACLMAEPELVAEGVAAMKHAVRVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P +AL  L +++  +GV+ + +HARKA L+GLSPK NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPELALDTLARALVDAGVDLLIVHARKAWLQGLSPKQNRDIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K   P L I +NGG+  +++A   L  VDGVM+GRAAY+    L  VD E F  P   
Sbjct: 194 RLKASLPRLPIVINGGISGIAEAKPHLDHVDGVMLGRAAYQEPWRLLAVDPELFGEPAPH 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +S +K  ++         +MT Y A  L  G +L  ITRH +G FH  P +R  R  L  
Sbjct: 254 AS-MKAALE---------AMTPYIAEELARGTRLHAITRHFVGAFHAVPGARAFRRHLAE 303

Query: 300 EAGASTATHHIIETAFN 316
              A  A   ++  A +
Sbjct: 304 HGVAPDAGIAVLREAID 320


>gi|197334068|ref|YP_002155065.1| tRNA-dihydrouridine synthase A [Vibrio fischeri MJ11]
 gi|197315558|gb|ACH65005.1| tRNA-dihydrouridine synthase A [Vibrio fischeri MJ11]
          Length = 328

 Score =  291 bits (746), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 151/317 (47%), Positives = 204/317 (64%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +ALLYTEM+   AI+ G K + L ++ +E P+ALQ+GG+++ 
Sbjct: 14  MLDWTDRHCRYFHRQLSEHALLYTEMVTTGAIIHG-KGDFLAYNEEEHPVALQLGGSNVK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV  AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+A M   + IPVT
Sbjct: 73  DLVHCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAECVAEMKAVVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 133 VKTRIGIDDQDSYEFLTKFVSTVHEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ +++A + L  +DGVMIGR AY++  +L  VD+     L G
Sbjct: 193 YQIKKDFPQLIIAVNGGIKTLAEAKEHLAHLDGVMIGREAYQSPYLLAEVDQQ----LFG 248

Query: 240 S-SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  PIK R      R+I  SM  Y  R L +G  L  ITRHM+GLF   P +R+ R  ++
Sbjct: 249 SDKPIKKR------REIVESMYPYIERQLENGAYLGHITRHMLGLFQSMPGARQWRRYIS 302

Query: 299 VEAGASTATHHIIETAF 315
             A    A   ++ETA 
Sbjct: 303 ENAHKPGAGIEVVETAL 319


>gi|59710914|ref|YP_203690.1| tRNA-dihydrouridine synthase A [Vibrio fischeri ES114]
 gi|59479015|gb|AAW84802.1| NifR3/Smm1 family protein [Vibrio fischeri ES114]
          Length = 328

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/317 (47%), Positives = 204/317 (64%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +ALLYTEM+   AI+ G K + L ++ +E P+ALQ+GG+++ 
Sbjct: 14  MLDWTDRHCRYFHRQLSEHALLYTEMVTTGAIIHG-KGDFLAYNEEEHPVALQLGGSNVK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV  AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+A M   + IPVT
Sbjct: 73  DLVHCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAECVAEMKAVVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 133 VKTRIGIDDQDSYEFLTKFVSTVHEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ +S+A + L  +DGVMIGR AY++  +L  VD+     L G
Sbjct: 193 YQIKKDFPQLIIAVNGGIKTLSEAKEHLEHLDGVMIGREAYQSPYLLAEVDQQ----LFG 248

Query: 240 S-SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  PIK R      R+I  SM  Y  R L +G  L  ITRHM+GLF   P +R+ R  ++
Sbjct: 249 SDKPIKKR------REIVESMYPYIERQLENGAYLGHITRHMLGLFQSMPGARQWRRYIS 302

Query: 299 VEAGASTATHHIIETAF 315
             A    A   +++TA 
Sbjct: 303 ENAHKPGAGIEVVKTAL 319


>gi|90423563|ref|YP_531933.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris BisB18]
 gi|90105577|gb|ABD87614.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris BisB18]
          Length = 330

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 148/299 (49%), Positives = 194/299 (64%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  A LY+EM+   A++ GD++ +LGF   E PLALQ+GG+D +
Sbjct: 14  MMDWTDRHCRVFHRRLSRRARLYSEMLTTGAVIHGDRQRLLGFDASEHPLALQLGGSDSA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAKI EDFGY+EINLNVGCPS RV +G FGACLM  P +V + IAAM +A+S+PVT
Sbjct: 74  DLATAAKIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPALVAEGIAAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P +AL +L +++  +G + + +HARKA L GLSPK+NR +P LDYD VY
Sbjct: 134 VKCRIGIDDQDPELALDSLARAVVAAGADLLVVHARKAWLNGLSPKENRDVPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K   P + I +NGG+  +++A   L  VDGVM+GRAAY+    L  VD E F  P   
Sbjct: 194 RLKAALPAVPIVINGGIAGIAEAKPHLGHVDGVMLGRAAYQEPWRLLAVDPELFGEP--A 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             P  T   +        +MT Y    L  G +L  ITRH +G +HG P +R  R  L 
Sbjct: 252 PYPSMTAALQ--------AMTPYIEAQLAQGTRLHSITRHFVGAYHGVPGARAFRRHLA 302


>gi|146291866|ref|YP_001182290.1| tRNA-dihydrouridine synthase A [Shewanella putrefaciens CN-32]
 gi|145563556|gb|ABP74491.1| TIM-barrel protein, yjbN family [Shewanella putrefaciens CN-32]
          Length = 343

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 148/317 (46%), Positives = 200/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 30  MLDWTDRHYRYFARLMSAKALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+ AM + + IPVT
Sbjct: 89  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAECVDAMKQVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 149 VKTRIGIDEQDSYEFLTYFIDIVNAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 209 QLKRDYPVLNISINGGVTTLEQAQGHLAQLDGVMMGREAYQNPYILARVDQV----LCGS 264

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 265 QRAVISRED------VIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSE 318

Query: 300 EAGASTATHHIIETAFN 316
            A  + A    +  AF 
Sbjct: 319 NAHKNGAGIETVRQAFQ 335


>gi|126725475|ref|ZP_01741317.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2150]
 gi|126704679|gb|EBA03770.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2150]
          Length = 337

 Score =  290 bits (741), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 152/322 (47%), Positives = 200/322 (62%), Gaps = 12/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ N+LLYTEM+ A AI+ GD++ +LGF   E P+A+Q+GG++ +
Sbjct: 22  MMDWTDRHCRYFHRQLSKNSLLYTEMVTAPAIINGDRERLLGFDATEHPVAVQLGGSNPA 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A  I  DFGY+E+NLN GCPS RV  G FGA LM  PD+V +C++ M  A ++ +T
Sbjct: 82  QLQQATAISCDFGYDEVNLNCGCPSDRVQSGYFGAVLMAKPDLVAECVSEMKAAANVEIT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L N +  +  +GV    IHARKA L+GLSPK+NR IP LDYDIV+
Sbjct: 142 VKCRIGVDDQDPQTVLPNFLAKVSAAGVTRFTIHARKAWLQGLSPKENRDIPPLDYDIVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K E P L I +NGG+  + QA  ++   +DGVMIGRAAY   A +L   DE   +   
Sbjct: 202 QMKAEFPHLHISINGGVTTLEQASGLIEQGLDGVMIGRAAYHQPADILCDADELIFSDEK 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G       VD         +M  Y   HL  GG+L QITRHM+G F G P +RR R  L+
Sbjct: 262 GQG-----VDAAI-----QTMLPYIENHLLKGGRLNQITRHMLGAFAGKPGARRWRRHLS 311

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A    +  A   M E
Sbjct: 312 EFAHKDGAGPETVLEALAKMRE 333


>gi|146341642|ref|YP_001206690.1| tRNA-dihydrouridine synthase A [Bradyrhizobium sp. ORS278]
 gi|146194448|emb|CAL78473.1| tRNA-dihydrouridine synthase A [Bradyrhizobium sp. ORS278]
          Length = 339

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 148/320 (46%), Positives = 197/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+  ALLYTEM+   A++ GD+  +LGF   E P+ALQ+GG+D +
Sbjct: 21  MMDWTDRHCRVFHRLLSRRALLYTEMVTTGAVIHGDRTRLLGFDRSEHPVALQLGGSDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A+I EDFGY+EINLNVGCPS RV +G FGACLM  P +V  C+AAM + ++IPVT
Sbjct: 81  DLATSARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPALVAACVAAMKRVVTIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L  ++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 141 VKCRIGIDDQDPEVALDALADAVVDAGADALIVHARKAWLNGLSPKENRDIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + + +NGG+  +  A   L  VDGVM+GRAAY+    L  VD     P+   
Sbjct: 201 RLKARLPRVPVIINGGITSIEAAQDHLAHVDGVMLGRAAYQEPWRLLDVD-----PVLFG 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                R  KD      A++  Y  R +  G +L  ITRH++G +H  P +R  R  L   
Sbjct: 256 EAGPQRSMKDAL----AALEPYIERQVAQGMRLHAITRHLVGAYHAVPGARAFRRHLAER 311

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A  ++ E
Sbjct: 312 GVKPDAGIEVLREAVAMIEE 331


>gi|294677314|ref|YP_003577929.1| tRNA-dihydrouridine synthase A [Rhodobacter capsulatus SB 1003]
 gi|294476134|gb|ADE85522.1| tRNA-dihydrouridine synthase A [Rhodobacter capsulatus SB 1003]
          Length = 346

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 145/299 (48%), Positives = 201/299 (67%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+++  ALLYTEM+ A A++ G +  +L FS  E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRVFHRMMSRQALLYTEMVTAPAVIHGKRAQLLDFSPVEHPVALQLGGSDPA 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EA +I  D+GY+EINLNVGCPS RV  G+FGA LM  PD+V  C+AAM  A ++ VT
Sbjct: 93  ELAEATRIARDWGYDEINLNVGCPSDRVQSGAFGAVLMKTPDLVARCVAAMQAAAAVEVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +K++ ++GV    +HARKA L+GLSPK+NR+IP LDY +V+
Sbjct: 153 VKCRIGVDDQSPEEVLPAFLKTVSEAGVTRFILHARKAWLQGLSPKENREIPPLDYPLVH 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+E P L + LNGG+  + Q    L + +DGVM+GRAAY+    +    +     L G
Sbjct: 213 AMKREFPHLHLSLNGGVATLDQVETHLAAGMDGVMVGRAAYQEPMQVLAGADVA---LWG 269

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              + + V+      ++ +M  Y A HL +GG+L QITRHM+GLFHG P +R  R +L+
Sbjct: 270 RGEVLSAVE------VAEAMKPYIADHLAAGGRLHQITRHMLGLFHGRPGARGWRRVLS 322


>gi|260433272|ref|ZP_05787243.1| tRNA-dihydrouridine synthase A [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417100|gb|EEX10359.1| tRNA-dihydrouridine synthase A [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 345

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 147/318 (46%), Positives = 205/318 (64%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL++NALLYTEM+ A A++RG   ++L FS +E P+ALQ+GG+D  
Sbjct: 26  MMDWTDRHCRYLHRLLSSNALLYTEMVTAPALVRGGALHLLEFSPEEHPVALQLGGSDPE 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM +P  V DC+AA   A+ + VT
Sbjct: 86  ELAQAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMKDPARVADCVAATRAAVRVEVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L + +  I+ +G   + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 146 VKCRIGVDEQTPEEVLPDFLDKIRAAGCQRVTIHARKAWLQGLSPKENRDIPPLDYDLVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAY-KNSAMLTTVDEYFSNPLT 238
            +K   PD+ I +NGG+  +++A   L + +DGVMIGRAAY + + +L   D       T
Sbjct: 206 RMKAAFPDMHISINGGIASLAEARAHLEAGLDGVMIGRAAYHQPTDILAEADPLIFGTGT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y  RHL +GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 266 AADPV----------DVVHQMLPYIDRHLAAGGRLHQITRHMLGLFAGRPGARGWRRVLS 315

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++  A +
Sbjct: 316 EGAVRDNAGPEVVLEALD 333


>gi|16329480|ref|NP_440208.1| tRNA-dihydrouridine synthase A [Synechocystis sp. PCC 6803]
 gi|2829606|sp|P72872|DUS2_SYNY3 RecName: Full=Probable tRNA-dihydrouridine synthase 2
 gi|1651962|dbj|BAA16888.1| sll0926 [Synechocystis sp. PCC 6803]
          Length = 334

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 148/318 (46%), Positives = 199/318 (62%), Gaps = 13/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R LT + LLYTEMI A AIL GD++ +L FS +EKP+ALQ+GG D  
Sbjct: 18  MMDHTDRHFRYFLRQLTRHTLLYTEMITAQAILHGDRQRLLNFSPEEKPVALQLGGDDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I +D+GY+EINLNVGCPS RV  G+FGACLM  PD+V  C++AM KA+ IPVT
Sbjct: 78  LLAECARIGQDWGYDEINLNVGCPSDRVQSGNFGACLMAQPDLVAQCVSAMQKAVEIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     L + V+ +  +G     +HARKA L+GLSPK+NR IP L Y+ VY
Sbjct: 138 VKHRIGIDHRDSYEDLVHFVEIVANAGCQRFTVHARKAWLQGLSPKENRTIPPLRYEDVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPLT 238
           ++KK+ P L I +NGG+    Q  + L  VD VM+GRAAY+N  +  TVD   Y    L 
Sbjct: 198 QLKKDFPQLLIEINGGITQTEQIQQHLSHVDAVMVGRAAYENPYLFATVDRDIYHKTNLV 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S             +I   M  Y    L  G +L QITRH++ LF+G P ++  R  L+
Sbjct: 258 PSRA-----------EIIERMLPYVEERLRHGDRLNQITRHLLSLFNGQPRAKFWRRTLS 306

Query: 299 VEAGASTATHHIIETAFN 316
                ++A   +++TA  
Sbjct: 307 DSTLLASAGPELLQTALQ 324


>gi|154251505|ref|YP_001412329.1| tRNA-dihydrouridine synthase A [Parvibaculum lavamentivorans DS-1]
 gi|154155455|gb|ABS62672.1| TIM-barrel protein, yjbN family [Parvibaculum lavamentivorans DS-1]
          Length = 335

 Score =  288 bits (738), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 144/318 (45%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T  +LLYTEM+   AIL G ++ +L F   E P+A+Q+GG++ +
Sbjct: 13  MMDWTDRHDRYFLRLITRRSLLYTEMVTTGAILHGPRERLLKFDLSEHPVAVQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+A+I  DFGY+EINLNVGCPS RV  G FGACLM  PD+V  C+ AM  A+S+PVT
Sbjct: 73  DLAESARIAADFGYDEINLNVGCPSDRVQSGRFGACLMREPDLVARCVEAMKNAVSVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  + K+++ +G   + +HARKA L+GLSPK+NR +P LDY +VY
Sbjct: 133 VKCRIGVDEQEPEEALPAMAKAVRGAGCETLIVHARKAWLEGLSPKENRDVPPLDYPLVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+ I +NGG+  + +A   L  VDGVM+GRAAY++  +L   D  F       
Sbjct: 193 RLKQAMPDMEIIINGGIATLDEAEAHLAHVDGVMLGRAAYQHPYILAEADRRFYGD-GHD 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +  V + F   +   M          G  L  +TRH++GLF G P +R  R  ++  
Sbjct: 252 VPSRHEVLEGFVLYVQEEMA--------HGTHLHAMTRHILGLFQGCPGARAFRRHISEN 303

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  A  L+
Sbjct: 304 APRPGAGAEVIREAMALV 321


>gi|120600206|ref|YP_964780.1| tRNA-dihydrouridine synthase A [Shewanella sp. W3-18-1]
 gi|120560299|gb|ABM26226.1| TIM-barrel protein, yjbN family [Shewanella sp. W3-18-1]
          Length = 343

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 147/317 (46%), Positives = 200/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 30  MLDWTDRHYRYFARLMSAKALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 89  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 149 VKTRIGIDEQDSYEFLTYFIDIVNAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 209 QLKRDYPVLNISINGGVTTLEQAQGHLAQLDGVMMGREAYQNPYILARVDQV----LCGS 264

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 265 QRAVISRED------VIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSE 318

Query: 300 EAGASTATHHIIETAFN 316
            A  + A    +  AF 
Sbjct: 319 NAHKNGAGIETVRQAFQ 335


>gi|319425100|gb|ADV53174.1| TIM-barrel protein, yjbN family [Shewanella putrefaciens 200]
          Length = 343

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 147/317 (46%), Positives = 200/317 (63%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 30  MLDWTDRHYRYFARLMSAKALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 89  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 149 VKTRIGIDEQDSYEFLTYFIDIVNAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 209 QLKRDYPVLNISINGGVTTLEQAQGHLSQLDGVMMGREAYQNPYILARVDQV----LCGS 264

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              + +R D      +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+ 
Sbjct: 265 QRAVISRED------VIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSE 318

Query: 300 EAGASTATHHIIETAFN 316
            A  + A    +  AF 
Sbjct: 319 NAHKNGAGIETVRQAFQ 335


>gi|271501941|ref|YP_003334967.1| yjbN family TIM-barrel protein [Dickeya dadantii Ech586]
 gi|270345496|gb|ACZ78261.1| TIM-barrel protein, yjbN family [Dickeya dadantii Ech586]
          Length = 344

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 149/319 (46%), Positives = 205/319 (64%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AIL G K + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRLLSHNALLYTEMVTTGAILHG-KGDYLAYSDEEHPLALQLGGSDPT 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM + +SIPVT
Sbjct: 92  ALAQCAVLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAQLVADCVTAMRERVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIRTVSEQGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A + L  VDGVM+GR AY+N  ML  VD    +  T 
Sbjct: 212 YQLKRDFPSLTLAINGGIKTLAEAKQHLEHVDGVMVGREAYQNPGMLAQVDRDLFD-ATS 270

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  V +        +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 271 VVPNQAAVVQ--------AMYPYIERELSGGAALGHITRHMLGLFQGIPGARQWRRYLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A +L+
Sbjct: 323 NAHKPGADASVVEHALSLV 341


>gi|307132468|ref|YP_003884484.1| tRNA dihydrouridine synthase A [Dickeya dadantii 3937]
 gi|306529997|gb|ADM99927.1| tRNA dihydrouridine synthase A [Dickeya dadantii 3937]
          Length = 346

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 149/320 (46%), Positives = 206/320 (64%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AIL G K + L +S +E PLALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFHRLLSHNALLYTEMVTTGAILHG-KGDYLAYSDEEHPLALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM + + IPVT
Sbjct: 94  ALAQCAVLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAQLVADCVTAMRERVDIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYAFLCDFIRTVSEQGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A + L  VDGVM+GR AY+N  ML  VD E F     
Sbjct: 214 YQLKRDFPSLTLAINGGVKTLAEARQHLQHVDGVMVGREAYQNPGMLAQVDRELFGA--D 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P +  V +        +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 SAAPDQADVVR--------AMYPYIERELSAGASLGHITRHMLGLFQGLPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 324 ENAHKPGADAAVVERALALV 343


>gi|113971575|ref|YP_735368.1| tRNA-dihydrouridine synthase A [Shewanella sp. MR-4]
 gi|113886259|gb|ABI40311.1| TIM-barrel protein, yjbN family [Shewanella sp. MR-4]
          Length = 335

 Score =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 145/316 (45%), Positives = 204/316 (64%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRHYR+FARL++ NALLYTEM+   AIL G + + L ++ +E PLALQ+GG++ +
Sbjct: 21  MLDLTDRHYRYFARLMSANALLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 80  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 140 VKTRIGIDEQDSYEFLTYFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+     L G 
Sbjct: 200 QLKRDYPMLNISINGGITSLEQAKTHLQYLDGVMVGREAYQNPYILAQVDQL----LCGC 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  + ++    +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 256 E--KAVISRE---AVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 310

Query: 301 AGASTATHHIIETAFN 316
           A  + A   +++ A+ 
Sbjct: 311 AHKNGAGIEVVKQAYQ 326


>gi|330721563|gb|EGG99595.1| tRNA dihydrouridine synthase A [gamma proteobacterium IMCC2047]
          Length = 351

 Score =  288 bits (736), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 145/317 (45%), Positives = 200/317 (63%), Gaps = 9/317 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRHYR+F RL++ +ALLY+EM+   AI+ GD+ ++LGF   E+P+ALQ+GG+  S
Sbjct: 42  MLDWSDRHYRYFMRLISQHALLYSEMVTTGAIIHGDRDHLLGFDNHEQPVALQLGGSSPS 101

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E +KI ED GYNEINLNVGCPS RV  G+FGACLM  P++V  C+ +M +A++IPVT
Sbjct: 102 DLAECSKIGEDRGYNEINLNVGCPSDRVQNGAFGACLMAKPELVAACLESMQRAVNIPVT 161

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L+  ++ +  SG +   IHARKA L+GLSPK+NR IP L YD VY
Sbjct: 162 VKHRIGIDDLDSYELLQRFIEIVSHSGCSTFIIHARKAFLQGLSPKENRDIPPLKYDWVY 221

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P L I +NGG++ ++++ K L  VDGVMIGR AY N   L   D          
Sbjct: 222 QIKEQFPHLEIIINGGIKSLTESQKHLEQVDGVMIGREAYHNPYSLAQADAQL---FDDH 278

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R D      I      Y  + L    +L  I++H++GLFHG P  R+ R  ++  
Sbjct: 279 HQIASRHD------ILQQFLPYIEQQLTQDVRLTHISKHILGLFHGQPGGRKFRQYISEN 332

Query: 301 AGASTATHHIIETAFNL 317
           A    A   ++E A  L
Sbjct: 333 AYKPGAGIEVLENAAKL 349


>gi|127511470|ref|YP_001092667.1| tRNA-dihydrouridine synthase A [Shewanella loihica PV-4]
 gi|126636765|gb|ABO22408.1| TIM-barrel protein, yjbN family [Shewanella loihica PV-4]
          Length = 329

 Score =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 148/321 (46%), Positives = 202/321 (62%), Gaps = 15/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++  LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 19  MLDWTDRHYRYFARLMSSELLLYTEMVTTGAIIHG-KGDYLAYNQEEHPLALQLGGSNPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V  C+AAM + + IPVT
Sbjct: 78  DLAKCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAQCVAAMNEVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   V  +  +G +   IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 138 VKTRIGIDEQDSYEFLTEFVDKVSAAGCDTFIIHARKAWLQGLSPKENREIPELDYDRVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG- 239
            +K++ P L I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+     L G 
Sbjct: 198 RLKQDYPQLSISINGGVKTLEECGEHLKQLDGVMVGREAYQNPYLLAQVDQ----QLCGL 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+ +R        +  +M  Y  +HL SGG+L  ITRHM GL+ G   SR  R  L+ 
Sbjct: 254 DKPVLSR------DAVLENMIPYIEKHLVSGGRLNHITRHMTGLYQGEAGSRAWRRYLSE 307

Query: 300 EA---GASTATHHIIETAFNL 317
            A   GA  A  H    +  L
Sbjct: 308 NAHKPGAGIAVVHEARASMEL 328


>gi|157373905|ref|YP_001472505.1| tRNA-dihydrouridine synthase A [Shewanella sediminis HAW-EB3]
 gi|157316279|gb|ABV35377.1| TIM-barrel protein, YjbN family [Shewanella sediminis HAW-EB3]
          Length = 327

 Score =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 146/315 (46%), Positives = 201/315 (63%), Gaps = 12/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ ARL++   LLYTEM+   AI+ G K + L ++++E  LALQ+GG++  
Sbjct: 18  MLDWTDRHYRYMARLMSAELLLYTEMVTTGAIIHG-KGDYLAYNSEEHALALQLGGSNAH 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  D GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM + + IPVT
Sbjct: 77  DLAICAKLAADRGYDEINLNVGCPSDRVQNGRFGACLMAEPKLVAECVTAMREVVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   V++++ +G +   +HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 137 VKTRIGIDEQDSYPFLTEFVETVRDAGCDTFIVHARKAWLKGLSPKENREIPPLDYDRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I +NGG++ + +    L  +DGVM+GR AY+N  ML  VD+     L GS
Sbjct: 197 QLKQDYPELSISINGGVKSLDECRTHLTKLDGVMVGREAYQNPYMLAEVDQ----QLCGS 252

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+ +R        +      Y  +HL SGG+L  I+RHM GLF G P SR  R  ++ 
Sbjct: 253 DRPVLSR------DAVLEKFIPYIEKHLQSGGRLNHISRHMTGLFQGEPGSRVWRRYISE 306

Query: 300 EAGASTATHHIIETA 314
            A    A   +IE A
Sbjct: 307 NAHKPGAGIEVIEQA 321


>gi|114765460|ref|ZP_01444570.1| tRNA-dihydrouridine synthase A [Pelagibaca bermudensis HTCC2601]
 gi|114542170|gb|EAU45201.1| tRNA-dihydrouridine synthase A [Roseovarius sp. HTCC2601]
          Length = 315

 Score =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 147/318 (46%), Positives = 203/318 (63%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLY+EM+ A A++RG   ++L ++ +E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSRRALLYSEMVTAPALVRGGALHLLDYNPEEHPVALQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA + E  GY++I+LN GCPS RV  G+FGA LM +P++V DC+AAM +A+ I VT
Sbjct: 61  ELARAATLGEQAGYDQIDLNCGCPSDRVQSGTFGAVLMRSPELVADCVAAMREAVKIDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L + ++ I  +G   + IHARKA L+GLSPK+NR IP LDY+IV 
Sbjct: 121 VKCRIGVDEQEPRDVLPDFLQKISGAGCERVVIHARKAWLQGLSPKENRDIPPLDYEIVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
           E+K+  P L + +NGG+ D+  A  +L   +DGVMIGRAAY     +L   D        
Sbjct: 181 EMKRAFPQLHVSINGGITDLDTAEALLADGLDGVMIGRAAYHQPWDILANADARIYGEAA 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G    +  V          +M  Y  RHL SGG+L QITRHM+GLF G P +R+ R +L+
Sbjct: 241 GPVSPEEAVQ---------AMLPYIGRHLASGGRLHQITRHMLGLFAGRPGARQWRRVLS 291

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++E A +
Sbjct: 292 EGATRDGAGPELVEEALS 309


>gi|91794580|ref|YP_564231.1| tRNA-dihydrouridine synthase A [Shewanella denitrificans OS217]
 gi|91716582|gb|ABE56508.1| TIM-barrel protein, yjbN family [Shewanella denitrificans OS217]
          Length = 327

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 203/316 (64%), Gaps = 14/316 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+HYR+FAR+++  ALLYTEM+   AIL G + + L ++T+E PLALQ+GG++  
Sbjct: 11  MLDWTDKHYRYFARIMSTKALLYTEMVTTGAILHG-RGDYLAYNTEEHPLALQLGGSNPV 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 70  DLAACAKLAFERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   ++++   G +   IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 130 VKTRIGIDEQDSYEFLTKFIETVAAKGCDDFTIHARKAWLQGLSPKENREIPLLDYDRVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG++ +++A   L  +DGVM+GR AY+N  +L  VD      L G 
Sbjct: 190 QLKRDFPKLNIGINGGIKTLAEAKLHLTQLDGVMVGREAYQNPYLLAEVD----TQLYG- 244

Query: 241 SPIKTRVDKDF--WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                 V +D     ++   M  Y   HL +GG+L  ITRHMIGLF G   SR+ R  L+
Sbjct: 245 ------VKRDIISREQVIEKMLPYIEAHLKTGGRLNHITRHMIGLFQGLAGSRQWRRHLS 298

Query: 299 VEAGASTATHHIIETA 314
             A    A   ++  A
Sbjct: 299 ENAHKPNAGIEVVREA 314


>gi|308051003|ref|YP_003914569.1| tRNA-U16,U17-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
 gi|307633193|gb|ADN77495.1| tRNA-U16,U17-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
          Length = 324

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 142/321 (44%), Positives = 199/321 (61%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AI+ G K + LGF+ +E P+ALQ+GG++ +
Sbjct: 10  MLDWTDRHYRYFARLISRQALLYTEMVTTGAIIHG-KGDYLGFNEEEHPVALQLGGSNPA 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV  G FGACLM  P +V DC+ AM   +SIPVT
Sbjct: 69  DLAHCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVKAMQDVVSIPVT 128

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++  +G +   IHARKA L+GLSPK+NR+IP L YD  Y
Sbjct: 129 VKTRIGIDEQDSYEFLTRFIDTVASAGCDIFTIHARKAWLQGLSPKENREIPELIYDRAY 188

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++   L I +NGG+  + Q    L  +DGVM+GR AY+N  M+  VD+         
Sbjct: 189 QVKRDFAHLNISVNGGITTLEQCEAHLQHLDGVMVGREAYQNPYMMAEVDQRLYG---DD 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R +      +   M  Y  RH+ +GG+   +TRHM+GLF+G P +R+ R  L   
Sbjct: 246 RPVLSRAE------VVEQMIPYLERHISNGGRANHVTRHMLGLFNGMPGARQWRRYLAQN 299

Query: 301 AGASTATHHIIETAFNLMIES 321
           A        ++  A   M E+
Sbjct: 300 AHLPGMGAELLADALASMPEA 320


>gi|163743186|ref|ZP_02150568.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis 2.10]
 gi|161383603|gb|EDQ07990.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis 2.10]
          Length = 390

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 148/318 (46%), Positives = 201/318 (63%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL++  LLYTEM+ A A++RG   ++L  S QE P+ALQ+GG+D +
Sbjct: 76  MMDWTDRHCRYLHRLLSHETLLYTEMVTAPALVRGGALHLLDHSPQEHPVALQLGGSDPA 135

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+   + GY+EINLN GCPS RV  G+FGA LM +PD+V +C+AAM   + + VT
Sbjct: 136 ELAQAAEFGAEAGYDEINLNCGCPSDRVQSGAFGAVLMKSPDLVAECVAAMQAKVDVEVT 195

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I  +G   + IHARKA LKGLSPK+NR IP LDY+IV+
Sbjct: 196 VKCRIGVDDQDPQEVLPVFLERIAAAGCERVTIHARKAWLKGLSPKENRDIPPLDYEIVH 255

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY-KNSAMLTTVDEYFSNPLT 238
           ++K E P L I LNGG+  + +AL  L   +DGVMIGRAAY + S +L+  D       +
Sbjct: 256 QMKAEFPQLHISLNGGVASLDEALPHLERGLDGVMIGRAAYHQPSDILSQADPLIFGTGS 315

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 316 ATDPV----------AVVGHMLGYIDDQMAQGARLHQITRHMLGLFAGRPGARNWRRVLS 365

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++ETA  
Sbjct: 366 EGASRPGADTRLVETALE 383


>gi|82546382|ref|YP_410329.1| tRNA-dihydrouridine synthase A [Shigella boydii Sb227]
 gi|81247793|gb|ABB68501.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|332087840|gb|EGI92966.1| tRNA-dihydrouridine synthase A [Shigella boydii 3594-74]
          Length = 345

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 205/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G  G++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECGMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DAYPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|293417553|ref|ZP_06660175.1| tRNA-dihydrouridine synthase A [Escherichia coli B185]
 gi|291430271|gb|EFF03269.1| tRNA-dihydrouridine synthase A [Escherichia coli B185]
          Length = 345

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 205/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E+ GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSYT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|312114498|ref|YP_004012094.1| TIM-barrel protein, yjbN family [Rhodomicrobium vannielii ATCC
           17100]
 gi|311219627|gb|ADP70995.1| TIM-barrel protein, yjbN family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 343

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 151/318 (47%), Positives = 198/318 (62%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+  A LYTEM+ + AI+ GD++ +LGF   E P+ALQ+GG+D  
Sbjct: 22  MMDWTDRHCRFFHRQLSRRARLYTEMVTSGAIMFGDRERLLGFDASEHPVALQLGGSDPV 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP 118
           +L  AA+I   FGY+EINLN GCPS RV  G FGACLM  P++V  C+AA+  A+   IP
Sbjct: 82  ELARAAEIGAGFGYDEINLNCGCPSDRVQSGRFGACLMAEPELVASCVAAIKSAVGGQIP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG+D+Q     L   ++++  SG     +HARKA LKGLSP++NR +P LDY+ 
Sbjct: 142 VTVKNRIGIDEQDSEADLTRFIETVAASGCEIFIVHARKAWLKGLSPRENRDVPPLDYER 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K   P+L I +NGG+E ++Q+ K L  VDGVM+GRAAYKN A+L  VD      L 
Sbjct: 202 VYRLKAAFPELTIIINGGIETIAQSAKHLEMVDGVMLGRAAYKNPALLLEVD----AALY 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G +    R  +   R     M  Y  R L  G +L  I RHM+GL +G P +R  R +LT
Sbjct: 258 GETAAPLRPHEALER-----MLPYIERELERGTRLSAIARHMLGLVNGRPGARPFRRLLT 312

Query: 299 VEAGASTATHHIIETAFN 316
            E+    A   II  A  
Sbjct: 313 EESVKPGAGLDIIHAAIE 330


>gi|187731116|ref|YP_001882727.1| tRNA-dihydrouridine synthase A [Shigella boydii CDC 3083-94]
 gi|187428108|gb|ACD07382.1| tRNA-dihydrouridine synthase A [Shigella boydii CDC 3083-94]
          Length = 347

 Score =  286 bits (733), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 205/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G  G++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECGMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DAYPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 324 ENAHKAGADINVLEHALKLVAD 345


>gi|320174478|gb|EFW49618.1| tRNA dihydrouridine synthase A [Shigella dysenteriae CDC 74-1112]
 gi|320185261|gb|EFW60037.1| tRNA dihydrouridine synthase A [Shigella flexneri CDC 796-83]
          Length = 339

 Score =  286 bits (733), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 205/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G  G++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECGMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DAYPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|209694000|ref|YP_002261928.1| tRNA-dihydrouridine synthase A [Aliivibrio salmonicida LFI1238]
 gi|208007951|emb|CAQ78084.1| tRNA-dihydrouridine synthase A [Aliivibrio salmonicida LFI1238]
          Length = 338

 Score =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/316 (46%), Positives = 198/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +ALLY+EMI   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 24  MLDWTDRHCRYFHRQLSEHALLYSEMITTGAIIHG-KGDFLAYNEEEHPLALQLGGSNAK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  D GY+EINLNVGCPS RV  G FGACLM +P++V +CIA M   + IPVT
Sbjct: 83  DLAHCAKLAADRGYDEINLNVGCPSDRVQNGRFGACLMADPELVAECIAEMKAVVDIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 143 VKTRIGIDDQDSYEFLTKFVSTVHEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ + +A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 203 YQIKKDFPQLIIAVNGGIKTLEEAKEHLAHLDGVMIGREAYQSPYLLAEVDQQL---FGS 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R      R+I  SM  Y  R L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 260 DKPIKKR------REIVESMYPYIERQLENGAHLGHITRHMLGLFQSMPGARQWRRYISE 313

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 314 NAHKPGSGIEVVQAAL 329


>gi|262277019|ref|ZP_06054812.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HIMB114]
 gi|262224122|gb|EEY74581.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HIMB114]
          Length = 330

 Score =  286 bits (731), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 147/319 (46%), Positives = 204/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RL++ N  LY+EMI   AIL GDKK IL FS  EKP+ALQ+GG++  
Sbjct: 13  MMDCTDRHDRYFLRLISKNIFLYSEMIATGAILNGDKKKILEFSEFEKPVALQLGGSNKK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +LVE  KIVEDFGY+EINLN+GCPS +V +  FGACL+  PD+V DC++AM ++  +PVT
Sbjct: 73  ELVECCKIVEDFGYDEINLNLGCPSKKVQKNKFGACLIKEPDLVADCLSAMAQSTKLPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG DD      L + V+ IK +GV  I +HARKAILKGLSPK+N +IP L+Y++VY
Sbjct: 133 AKTRIGYDDVEDFDYLNSFVEKIKNTGVKTIILHARKAILKGLSPKENLRIPKLNYNMVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           EIKK NP++ I +NG + D +Q    L  VDGVMIGRA Y++   L  ++ + F N    
Sbjct: 193 EIKKSNPEIEIIINGAVTDTNQIKSHLEKVDGVMIGRAIYQSPYFLADIEKDVFKN---- 248

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              I TR       +I   + +Y    ++ G ++ QI RH +GL+HG   + R +  L+ 
Sbjct: 249 -DDILTR------EQIVEKLVEYVDTEVNKGTRVNQIMRHTVGLYHGQRGAGRWKRYLSD 301

Query: 300 EAGASTATHHIIETAFNLM 318
              A  +    ++   N++
Sbjct: 302 NMMARDSDFQKVKHILNVV 320


>gi|56697231|ref|YP_167596.1| tRNA-dihydrouridine synthase A [Ruegeria pomeroyi DSS-3]
 gi|56678968|gb|AAV95634.1| tRNA-dihydrouridine synthase A [Ruegeria pomeroyi DSS-3]
          Length = 344

 Score =  286 bits (731), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 146/318 (45%), Positives = 201/318 (63%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L +S +E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRYLHRLLSRQTLLYTEMVTAPALVRGGALHLLEYSVEEHPVALQLGGSDPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM +P +V DC+ AM +A+ + VT
Sbjct: 78  ELAQAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMKHPGLVADCVTAMREAVDVEVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I  +G   + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 138 VKCRIGVDDQDPETVLPEFLEQIAGAGCQRVIIHARKAWLQGLSPKENRDIPPLDYDLVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P + I +NGG++ ++ A   L + +DGVMIGRAAY   A +L   D       T
Sbjct: 198 RMKARFPGMHISINGGIDTLAAARAHLDAGLDGVMIGRAAYHQPADILCKADPLIYGTGT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+              +M  Y   HL +GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 258 ASDPVTA----------VRAMLPYIEAHLATGGRLHQITRHMLGLFAGRPGARGWRRMLS 307

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++E A +
Sbjct: 308 EGAVRPGAGPELVEAALD 325


>gi|309704516|emb|CBJ03865.1| tRNA-dihydrouridine synthase A [Escherichia coli ETEC H10407]
          Length = 345

 Score =  285 bits (730), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L N + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCNFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|255264528|ref|ZP_05343870.1| tRNA-dihydrouridine synthase A [Thalassiobium sp. R2A62]
 gi|255106863|gb|EET49537.1| tRNA-dihydrouridine synthase A [Thalassiobium sp. R2A62]
          Length = 330

 Score =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 144/302 (47%), Positives = 196/302 (64%), Gaps = 12/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R  ++ ALLYTEM+ A AI+RGD +++L F   E+P+ALQ+GGAD  
Sbjct: 18  MMDWTDRHCRYFHRQFSSQALLYTEMVTAPAIVRGDARHLLAFDPAEQPVALQLGGADPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I  D GY E+NLN GCPS RV  G+FGA  M  PD+V +  +AM  A    +T
Sbjct: 78  QLAQAARIGADEGYPEVNLNCGCPSDRVQSGAFGAIHMTTPDLVAEICSAMIAASHAEIT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I+ +GV  + IHARKA L+GLSPK+NR IP LDY +V+
Sbjct: 138 VKCRIGVDDQDPHEVLPTFLTKIRAAGVRRVTIHARKAWLQGLSPKENRDIPPLDYPLVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
           ++K E PDL I +NGG+  + +A + +   +DGVMIGRAAY   +A+LT  D+      T
Sbjct: 198 QMKAEFPDLHISINGGIASLDEAKIHLNQGLDGVMIGRAAYHTPAAILTDADQMIWGQGT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             S  +  VD+         M  Y A H+  GG++  +TRHM+GLF G P +R  R +L+
Sbjct: 258 TRSSFEV-VDR---------MKPYIADHIAGGGRMHHVTRHMLGLFSGQPGARGWRQVLS 307

Query: 299 VE 300
            +
Sbjct: 308 TQ 309


>gi|254475974|ref|ZP_05089360.1| tRNA-dihydrouridine synthase A [Ruegeria sp. R11]
 gi|214030217|gb|EEB71052.1| tRNA-dihydrouridine synthase A [Ruegeria sp. R11]
          Length = 320

 Score =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 150/318 (47%), Positives = 202/318 (63%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ A A++RG   ++L  S +E P+ALQ+GG+D +
Sbjct: 6   MMDWTDRHCRYLHRLLSREALLYTEMVTAPALVRGGALHLLDHSVEEHPVALQLGGSDPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLN GCPS RV  G+FGA LM +PD+V +C+AAM   + + VT
Sbjct: 66  ELAEAARLGGQAGYDEINLNCGCPSDRVQSGAFGAVLMKSPDLVAECVAAMQAKVDVEVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   + +I  +G   + IHARKA LKGLSPK+NR IP LDYDIV+
Sbjct: 126 VKCRIGVDDQDPQEVLPGFIAAIAAAGCKRVTIHARKAWLKGLSPKENRDIPPLDYDIVH 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY-KNSAMLTTVDEYFSNPLT 238
           ++K E P L I +NGG+  + QA++ L   +DGVM+GRAAY + S +L   D        
Sbjct: 186 QMKAEFPALHISINGGITSLDQAVEHLDRGLDGVMVGRAAYHQPSDILCAADPRIFGTGE 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+          ++ A M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 246 VSDPV----------EVVAQMLGYIDDEMAKGARLHQITRHMLGLFAGRPGARNWRRVLS 295

Query: 299 VEAGASTATHHIIETAFN 316
             A  S A   ++E A  
Sbjct: 296 EGASRSGAGTELVEAALQ 313


>gi|53804232|ref|YP_114112.1| tRNA-dihydrouridine synthase A [Methylococcus capsulatus str. Bath]
 gi|53757993|gb|AAU92284.1| TIM-barrel protein, yjbN family [Methylococcus capsulatus str.
           Bath]
          Length = 360

 Score =  285 bits (729), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 141/307 (45%), Positives = 193/307 (62%), Gaps = 8/307 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL++ + LLYTEM+   AIL GD++ +LGF   E PLA+Q+GG+D  
Sbjct: 35  MMDWTDRHCRFFLRLISRHTLLYTEMVTTAAILHGDRERLLGFHPAEHPLAIQLGGSDPE 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AKI E  G++E+NLNVGCPS RV  G FGACLM  P+ V DC+ AMC+A+S+PVT
Sbjct: 95  ALAECAKIAEFRGFDEVNLNVGCPSPRVQTGRFGACLMAEPERVADCVRAMCEAVSVPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L + V  + ++G     +HARKA L+GLSPK+NR+ P L YD+V 
Sbjct: 155 VKTRIGIDDRDSYEDLLHFVTIVAEAGCRTFIVHARKAWLQGLSPKENRQTPPLRYDVVR 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L I LNGG++ + +A + L   DGVMIGRAAY N  +L   D        G 
Sbjct: 215 RLKSELPELAIVLNGGIQTLDEAERHLSWCDGVMIGRAAYHNPYLLAEADRR----CYGH 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S ++ R  ++    +      Y    L  G +L  +TRH++GL+H  P  +R R  ++  
Sbjct: 271 SDVRPRTREE----VIEDFMPYVRNELSKGSRLHALTRHILGLYHATPGGKRWRRHISEG 326

Query: 301 AGASTAT 307
           A    A+
Sbjct: 327 ASRRGAS 333


>gi|16762924|ref|NP_458541.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29144411|ref|NP_807753.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213051927|ref|ZP_03344805.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213424511|ref|ZP_03357308.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213582871|ref|ZP_03364697.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
 gi|213614451|ref|ZP_03371277.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213647516|ref|ZP_03377569.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|289824651|ref|ZP_06544178.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|38604946|sp|Q8Z1T1|DUSA_SALTI RecName: Full=tRNA-dihydrouridine synthase A
 gi|25329941|pir||AB1016 conserved hypothetical protein STY4439 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16505231|emb|CAD09227.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29140049|gb|AAO71613.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
          Length = 332

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DTDPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADAAVLEQALKLIAD 330


>gi|99080805|ref|YP_612959.1| tRNA-dihydrouridine synthase A [Ruegeria sp. TM1040]
 gi|99037085|gb|ABF63697.1| TIM-barrel protein yjbN family [Ruegeria sp. TM1040]
          Length = 336

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 144/321 (44%), Positives = 203/321 (63%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R  R+  RLL+   LLYTEM+ A A++RG   ++L     E P+ALQ+GG+D  
Sbjct: 22  MMDWTTRECRYLHRLLSRETLLYTEMVTAPALVRGGALHLLDHDPSEHPVALQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++  + GY+EINLN GCPS RV  G+FGA LM  P++V DC+AAM +A+S+ VT
Sbjct: 82  ELAEAARLGAEAGYDEINLNCGCPSDRVQSGAFGAVLMQTPELVADCVAAMAEAVSVEVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  I+ +GV  + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 142 VKCRIGVDDQTPDEILPDFLDKIRAAGVKRVTIHARKAWLQGLSPKENRDIPPLDYELVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K    D+ I LNGG+  + +A  ++   +DGVM+GRAAY   A +L   D       T
Sbjct: 202 AMKSAFADMHISLNGGITSLDEAQAQLARGLDGVMVGRAAYHQPADVLCAADPRIYGTGT 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+          ++   M  Y  + + SG +L QITRHM+GLF G P +R+ R  L+
Sbjct: 262 ASDPL----------EVVRQMLPYIEQQMQSGSRLHQITRHMLGLFAGRPGARQWRRHLS 311

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A  + A   ++E A +L++
Sbjct: 312 EGAHRTGAGPELVEEALSLVL 332


>gi|114564502|ref|YP_752016.1| tRNA-dihydrouridine synthase A [Shewanella frigidimarina NCIMB 400]
 gi|114335795|gb|ABI73177.1| TIM-barrel protein, yjbN family protein [Shewanella frigidimarina
           NCIMB 400]
          Length = 349

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 142/301 (47%), Positives = 195/301 (64%), Gaps = 10/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++ ALLYTEMI   AIL+G K + L ++ QE P+ALQ+GG++  
Sbjct: 29  MLDWTDRHYRYFARLMSSKALLYTEMITTGAILQG-KGDYLAYNEQEHPVALQLGGSNAV 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P +V  C+ AM +   IP+T
Sbjct: 88  DLAACAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPALVAQCVDAMKQVTDIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + ++++   G +   IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 148 VKTRIGIDEQDSYQFLTDFIETVSAQGCSAFTIHARKAWLQGLSPKENREIPPLDYDRVY 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++   L I +NGG++ + ++   L  +DGVM+GR AY+N  +L  VD+      T  
Sbjct: 208 QLKRDYQHLNISINGGIKTLEESKLHLALLDGVMVGREAYQNPYILAQVDQQLCGLDTA- 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + TR      +++   M  Y   HL  GG+L  ITRHMIGLF G P SR  R  L+  
Sbjct: 267 --VITR------QQVIEQMLPYIEAHLAQGGRLNHITRHMIGLFQGLPGSRGWRRHLSEN 318

Query: 301 A 301
           A
Sbjct: 319 A 319


>gi|114799763|ref|YP_759023.1| tRNA-dihydrouridine synthase A [Hyphomonas neptunium ATCC 15444]
 gi|114739937|gb|ABI78062.1| tRNA-dihydrouridine synthase A [Hyphomonas neptunium ATCC 15444]
          Length = 328

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 195/316 (61%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALL+TEM+ ADA++ GD++ ++GFS  E PL LQ+GG++  
Sbjct: 14  MMDWTDRHCRAFHRTLTKRALLWTEMVTADAVIHGDRQRLIGFSDVEHPLVLQLGGSEPG 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E +GY+E+NLN GCPS RV  G+FGACLM  PD+V DC+AAM  A+SIPVT
Sbjct: 74  KLAEAARIAEGYGYDEVNLNCGCPSERVQSGAFGACLMAEPDLVADCVAAMRAAVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +DD      L   ++ +  +G +   +HARKA LKGLSPK+NR++P LDY +V 
Sbjct: 134 VKNRIAIDDLPARETLFTFIEKVSVAGCSVFTVHARKAWLKGLSPKENREVPPLDYGLVA 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K   PDL I LNGG+  + Q    +   DGVM+GRAAY+   +L  VD    + L G 
Sbjct: 194 ELKTARPDLTIILNGGIATIDQCRDHIGVFDGVMLGRAAYQTPGLLGQVD----SDLFGE 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +    D         +   Y A  L  G  L  +TRHM+GLF G P +R+ R IL+ +
Sbjct: 250 GAMIAAGDA------VRAYEPYIAARLAEGSNLHAMTRHMLGLFAGQPGARQWRRILSEQ 303

Query: 301 AGASTATHHIIETAFN 316
                A   ++  A  
Sbjct: 304 GVKKGAGLDVLRAALG 319


>gi|158423257|ref|YP_001524549.1| tRNA-dihydrouridine synthase A [Azorhizobium caulinodans ORS 571]
 gi|158330146|dbj|BAF87631.1| dihydrouridine synthase TIM-barrel protein [Azorhizobium
           caulinodans ORS 571]
          Length = 338

 Score =  285 bits (728), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 152/301 (50%), Positives = 198/301 (65%), Gaps = 9/301 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R L+  A LYTEM+ A AI+ GD+  +LG+S  E P+ +Q+GG++ +
Sbjct: 14  MMEWTDRHCRAFHRTLSRRAWLYTEMVTAPAIIHGDRARLLGYSQAEHPVVVQLGGSNPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I  DFGY+EINLNVGCPS RV  G+FGACLM +P +V +C+AAM  A+SIPVT
Sbjct: 74  LLAEAARICADFGYDEINLNVGCPSDRVKGGNFGACLMRDPALVAECVAAMRAAVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L  ++  +G   + +HARKA LKGLSPK+NR+IP LDYD V+
Sbjct: 134 VKCRIGVDDQDVEEALDALADAVLAAGCARLIVHARKAWLKGLSPKENREIPPLDYDRVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + I LNGGL  +  A      +DGVM+GRAAY++  +L  VD      + G 
Sbjct: 194 RLKARLPHVPIELNGGLVTLEDARAAGAGLDGVMLGRAAYQDPDLLLEVDAQ----VHGE 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P       D +  I A+   Y A HL +GG+L  ITRHM+GLF G P +R  R  L  E
Sbjct: 250 TPPHA----DAFEAI-AAFEPYIAAHLEAGGRLHDITRHMLGLFGGRPGARTYRRTLATE 304

Query: 301 A 301
           A
Sbjct: 305 A 305


>gi|194426795|ref|ZP_03059348.1| tRNA-dihydrouridine synthase A [Escherichia coli B171]
 gi|194415131|gb|EDX31400.1| tRNA-dihydrouridine synthase A [Escherichia coli B171]
 gi|195183268|dbj|BAG66809.1| tRNA-dihydrouridine synthase A [Escherichia coli O111:H-]
          Length = 345

 Score =  285 bits (728), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEAHGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|323965711|gb|EGB61163.1| tRNA dihydrouridine synthase A [Escherichia coli M863]
 gi|327250393|gb|EGE62106.1| tRNA-dihydrouridine synthase A [Escherichia coli STEC_7v]
          Length = 345

 Score =  285 bits (728), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAETRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|157157144|ref|YP_001465549.1| tRNA-dihydrouridine synthase A [Escherichia coli E24377A]
 gi|157163519|ref|YP_001460837.1| tRNA-dihydrouridine synthase A [Escherichia coli HS]
 gi|254037046|ref|ZP_04871123.1| tRNA-dihydrouridine synthase A [Escherichia sp. 1_1_43]
 gi|157069199|gb|ABV08454.1| tRNA-dihydrouridine synthase A [Escherichia coli HS]
 gi|157079174|gb|ABV18882.1| tRNA-dihydrouridine synthase A [Escherichia coli E24377A]
 gi|226840152|gb|EEH72154.1| tRNA-dihydrouridine synthase A [Escherichia sp. 1_1_43]
          Length = 347

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 324 ENAHKAGADINVLEHALKLVAD 345


>gi|323155612|gb|EFZ41787.1| tRNA-dihydrouridine synthase A [Escherichia coli EPECa14]
          Length = 347

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 324 ENAHKAGADINVLEHALKLVAD 345


>gi|331650053|ref|ZP_08351126.1| tRNA-dihydrouridine synthase A [Escherichia coli M605]
 gi|331040998|gb|EGI13155.1| tRNA-dihydrouridine synthase A [Escherichia coli M605]
          Length = 345

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|83645166|ref|YP_433601.1| tRNA-dihydrouridine synthase A [Hahella chejuensis KCTC 2396]
 gi|83633209|gb|ABC29176.1| tRNA-dihydrouridine synthase [Hahella chejuensis KCTC 2396]
          Length = 349

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/319 (46%), Positives = 200/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ ARLL+ +  LYTEM+   AI+ GD+   L F+ +E P+A+Q+GG++  
Sbjct: 25  MMDWTDRHYRYLARLLSRHTYLYTEMVTTGAIIHGDRNRFLDFNAEEHPIAVQLGGSNPD 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E AKI ED+GY+EINLNVGCPS RV     GACLM  P+ V +C+AAMC A+SIPVT
Sbjct: 85  ELKECAKICEDWGYDEINLNVGCPSDRVQNNMIGACLMGYPERVAECVAAMCSAVSIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L N V+++K +G +   IHARKAILKGLSPK+NR+IP L Y   Y
Sbjct: 145 VKHRIGIDDQDSEEFLLNFVRTVKAAGCSTFIIHARKAILKGLSPKENREIPPLIYPRAY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            IK+  P+L I +NGG++ M ++   L  VDGVMIGR AY+   ML  VD   F  P   
Sbjct: 205 LIKQTFPELEIIINGGIKTMDESESHLQEVDGVMIGREAYQRPWMLADVDHRLFHCP--- 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P  +  D      I     +Y  R+  +G  +  + RH +GLFHG    ++ R  L+ 
Sbjct: 262 -PPSFSATD------IGYQFLEYIERNYQNGVAVWHMARHALGLFHGQKGGKQFRRYLSE 314

Query: 300 EAGASTATHHIIETAFNLM 318
            A   TA+  +   A +++
Sbjct: 315 NAIKRTASPTVFRDALDIV 333


>gi|168263436|ref|ZP_02685409.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205348025|gb|EDZ34656.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 332

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L +VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILASVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DTDPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|15834285|ref|NP_313058.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           Sakai]
 gi|74314543|ref|YP_312962.1| tRNA-dihydrouridine synthase A [Shigella sonnei Ss046]
 gi|89110770|ref|AP_004550.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           W3110]
 gi|170083506|ref|YP_001732826.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           DH10B]
 gi|193063063|ref|ZP_03044155.1| tRNA-dihydrouridine synthase A [Escherichia coli E22]
 gi|218556606|ref|YP_002389520.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI1]
 gi|218697757|ref|YP_002405424.1| tRNA-dihydrouridine synthase A [Escherichia coli 55989]
 gi|218707670|ref|YP_002415189.1| tRNA -dihydrouridine synthase A [Escherichia coli UMN026]
 gi|254163985|ref|YP_003047093.1| tRNA-dihydrouridine synthase A [Escherichia coli B str. REL606]
 gi|260846843|ref|YP_003224621.1| tRNA-dihydrouridine synthase A [Escherichia coli O103:H2 str.
           12009]
 gi|291285465|ref|YP_003502283.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str.
           CB9615]
 gi|300817967|ref|ZP_07098180.1| tRNA dihydrouridine synthase A [Escherichia coli MS 107-1]
 gi|300823590|ref|ZP_07103718.1| tRNA dihydrouridine synthase A [Escherichia coli MS 119-7]
 gi|300899835|ref|ZP_07118049.1| tRNA dihydrouridine synthase A [Escherichia coli MS 198-1]
 gi|300906360|ref|ZP_07124058.1| tRNA dihydrouridine synthase A [Escherichia coli MS 84-1]
 gi|300917303|ref|ZP_07133976.1| tRNA dihydrouridine synthase A [Escherichia coli MS 115-1]
 gi|300924312|ref|ZP_07140291.1| tRNA dihydrouridine synthase A [Escherichia coli MS 182-1]
 gi|300938186|ref|ZP_07152956.1| tRNA dihydrouridine synthase A [Escherichia coli MS 21-1]
 gi|300946621|ref|ZP_07160880.1| tRNA dihydrouridine synthase A [Escherichia coli MS 116-1]
 gi|300957541|ref|ZP_07169748.1| tRNA dihydrouridine synthase A [Escherichia coli MS 175-1]
 gi|301021575|ref|ZP_07185575.1| tRNA dihydrouridine synthase A [Escherichia coli MS 69-1]
 gi|301302728|ref|ZP_07208857.1| tRNA dihydrouridine synthase A [Escherichia coli MS 124-1]
 gi|301330578|ref|ZP_07223186.1| tRNA dihydrouridine synthase A [Escherichia coli MS 78-1]
 gi|301645037|ref|ZP_07245000.1| tRNA dihydrouridine synthase A [Escherichia coli MS 146-1]
 gi|307312109|ref|ZP_07591746.1| TIM-barrel protein, yjbN family [Escherichia coli W]
 gi|309795855|ref|ZP_07690269.1| tRNA dihydrouridine synthase A [Escherichia coli MS 145-7]
 gi|331644790|ref|ZP_08345907.1| tRNA-dihydrouridine synthase A [Escherichia coli H736]
 gi|331665718|ref|ZP_08366612.1| tRNA-dihydrouridine synthase A [Escherichia coli TA143]
 gi|331670912|ref|ZP_08371746.1| tRNA-dihydrouridine synthase A [Escherichia coli TA271]
 gi|331680179|ref|ZP_08380838.1| tRNA-dihydrouridine synthase A [Escherichia coli H591]
 gi|13364508|dbj|BAB38454.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|73858020|gb|AAZ90727.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|85676801|dbj|BAE78051.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K12 substr.
           W3110]
 gi|169891341|gb|ACB05048.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           DH10B]
 gi|192931322|gb|EDV83924.1| tRNA-dihydrouridine synthase A [Escherichia coli E22]
 gi|218354489|emb|CAV01337.1| tRNA-dihydrouridine synthase A [Escherichia coli 55989]
 gi|218363375|emb|CAR01028.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI1]
 gi|218434767|emb|CAR15700.1| tRNA-dihydrouridine synthase A [Escherichia coli UMN026]
 gi|253975886|gb|ACT41557.1| tRNA-dihydrouridine synthase A [Escherichia coli B str. REL606]
 gi|257761990|dbj|BAI33487.1| tRNA-dihydrouridine synthase A [Escherichia coli O103:H2 str.
           12009]
 gi|260451122|gb|ACX41544.1| TIM-barrel protein, yjbN family [Escherichia coli DH1]
 gi|290765338|gb|ADD59299.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str.
           CB9615]
 gi|300315715|gb|EFJ65499.1| tRNA dihydrouridine synthase A [Escherichia coli MS 175-1]
 gi|300356606|gb|EFJ72476.1| tRNA dihydrouridine synthase A [Escherichia coli MS 198-1]
 gi|300397973|gb|EFJ81511.1| tRNA dihydrouridine synthase A [Escherichia coli MS 69-1]
 gi|300401808|gb|EFJ85346.1| tRNA dihydrouridine synthase A [Escherichia coli MS 84-1]
 gi|300415447|gb|EFJ98757.1| tRNA dihydrouridine synthase A [Escherichia coli MS 115-1]
 gi|300419477|gb|EFK02788.1| tRNA dihydrouridine synthase A [Escherichia coli MS 182-1]
 gi|300453720|gb|EFK17340.1| tRNA dihydrouridine synthase A [Escherichia coli MS 116-1]
 gi|300456844|gb|EFK20337.1| tRNA dihydrouridine synthase A [Escherichia coli MS 21-1]
 gi|300523922|gb|EFK44991.1| tRNA dihydrouridine synthase A [Escherichia coli MS 119-7]
 gi|300529377|gb|EFK50439.1| tRNA dihydrouridine synthase A [Escherichia coli MS 107-1]
 gi|300841948|gb|EFK69708.1| tRNA dihydrouridine synthase A [Escherichia coli MS 124-1]
 gi|300843456|gb|EFK71216.1| tRNA dihydrouridine synthase A [Escherichia coli MS 78-1]
 gi|301076659|gb|EFK91465.1| tRNA dihydrouridine synthase A [Escherichia coli MS 146-1]
 gi|306907916|gb|EFN38417.1| TIM-barrel protein, yjbN family [Escherichia coli W]
 gi|308120516|gb|EFO57778.1| tRNA dihydrouridine synthase A [Escherichia coli MS 145-7]
 gi|315063373|gb|ADT77700.1| tRNA-dihydrouridine synthase A [Escherichia coli W]
 gi|315138603|dbj|BAJ45762.1| tRNA-dihydrouridine synthase A [Escherichia coli DH1]
 gi|315254721|gb|EFU34689.1| tRNA dihydrouridine synthase A [Escherichia coli MS 85-1]
 gi|315617417|gb|EFU98023.1| tRNA-dihydrouridine synthase A [Escherichia coli 3431]
 gi|323164554|gb|EFZ50355.1| tRNA-dihydrouridine synthase A [Shigella sonnei 53G]
 gi|323182152|gb|EFZ67562.1| tRNA-dihydrouridine synthase A [Escherichia coli 1357]
 gi|323380563|gb|ADX52831.1| TIM-barrel protein, yjbN family [Escherichia coli KO11]
 gi|323946182|gb|EGB42216.1| tRNA dihydrouridine synthase A [Escherichia coli H120]
 gi|324017108|gb|EGB86327.1| tRNA dihydrouridine synthase A [Escherichia coli MS 117-3]
 gi|331035765|gb|EGI08003.1| tRNA-dihydrouridine synthase A [Escherichia coli H736]
 gi|331056769|gb|EGI28763.1| tRNA-dihydrouridine synthase A [Escherichia coli TA143]
 gi|331061826|gb|EGI33751.1| tRNA-dihydrouridine synthase A [Escherichia coli TA271]
 gi|331071642|gb|EGI42978.1| tRNA-dihydrouridine synthase A [Escherichia coli H591]
          Length = 345

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|168760895|ref|ZP_02785902.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4501]
 gi|170682797|ref|YP_001746438.1| tRNA-dihydrouridine synthase A [Escherichia coli SMS-3-5]
 gi|191167463|ref|ZP_03029277.1| tRNA-dihydrouridine synthase A [Escherichia coli B7A]
 gi|209921533|ref|YP_002295617.1| tRNA-dihydrouridine synthase A [Escherichia coli SE11]
 gi|217325395|ref|ZP_03441479.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14588]
 gi|256024922|ref|ZP_05438787.1| tRNA-dihydrouridine synthase A [Escherichia sp. 4_1_40B]
 gi|301019187|ref|ZP_07183385.1| tRNA dihydrouridine synthase A [Escherichia coli MS 196-1]
 gi|307140739|ref|ZP_07500095.1| tRNA-dihydrouridine synthase A [Escherichia coli H736]
 gi|170520515|gb|ACB18693.1| tRNA-dihydrouridine synthase A [Escherichia coli SMS-3-5]
 gi|189368570|gb|EDU86986.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4501]
 gi|190902505|gb|EDV62240.1| tRNA-dihydrouridine synthase A [Escherichia coli B7A]
 gi|209914792|dbj|BAG79866.1| conserved hypothetical protein [Escherichia coli SE11]
 gi|217321616|gb|EEC30040.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14588]
 gi|299882344|gb|EFI90555.1| tRNA dihydrouridine synthase A [Escherichia coli MS 196-1]
 gi|320200820|gb|EFW75406.1| tRNA dihydrouridine synthase A [Escherichia coli EC4100B]
 gi|320654888|gb|EFX22849.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320660736|gb|EFX28193.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str. USDA
           5905]
 gi|323940232|gb|EGB36425.1| tRNA dihydrouridine synthase A [Escherichia coli E482]
 gi|324118621|gb|EGC12513.1| tRNA dihydrouridine synthase A [Escherichia coli E1167]
 gi|326346520|gb|EGD70254.1| tRNA dihydrouridine synthase A [Escherichia coli O157:H7 str. 1044]
          Length = 339

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|260858159|ref|YP_003232050.1| tRNA-dihydrouridine synthase A [Escherichia coli O26:H11 str.
           11368]
 gi|257756808|dbj|BAI28310.1| tRNA-dihydrouridine synthase A [Escherichia coli O26:H11 str.
           11368]
          Length = 345

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|170769561|ref|ZP_02904014.1| tRNA-dihydrouridine synthase A [Escherichia albertii TW07627]
 gi|170121618|gb|EDS90549.1| tRNA-dihydrouridine synthase A [Escherichia albertii TW07627]
          Length = 331

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 198 YQLKRDFPHLTMAINGGIKSLEEAKAHLQYMDGVMVGREAYQNPGILAAVDREIFGSSDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 308 ENAHKAGADINVLEHALRLVAD 329


>gi|197263333|ref|ZP_03163407.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197241588|gb|EDY24208.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
          Length = 332

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------TVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|256019697|ref|ZP_05433562.1| tRNA-dihydrouridine synthase A [Shigella sp. D9]
 gi|332280828|ref|ZP_08393241.1| tRNA-dihydrouridine synthase A [Shigella sp. D9]
 gi|323171192|gb|EFZ56840.1| tRNA-dihydrouridine synthase A [Escherichia coli LT-68]
 gi|324014847|gb|EGB84066.1| tRNA dihydrouridine synthase A [Escherichia coli MS 60-1]
 gi|332103180|gb|EGJ06526.1| tRNA-dihydrouridine synthase A [Shigella sp. D9]
          Length = 345

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|320644173|gb|EFX13238.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H- str.
           493-89]
 gi|320665665|gb|EFX32702.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 339

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|320638805|gb|EFX08451.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           G5101]
          Length = 339

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|56416043|ref|YP_153118.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|161617371|ref|YP_001591336.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167552533|ref|ZP_02346286.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|197364970|ref|YP_002144607.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56130300|gb|AAV79806.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|161366735|gb|ABX70503.1| hypothetical protein SPAB_05226 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|197096447|emb|CAR62053.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|205322837|gb|EDZ10676.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|322615399|gb|EFY12319.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322618459|gb|EFY15348.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322622129|gb|EFY18979.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322627200|gb|EFY23992.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322631160|gb|EFY27924.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322637622|gb|EFY34323.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643604|gb|EFY40159.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322648339|gb|EFY44798.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322654648|gb|EFY50968.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659608|gb|EFY55851.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322662183|gb|EFY58399.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322666071|gb|EFY62249.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322672491|gb|EFY68602.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675920|gb|EFY71991.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322680405|gb|EFY76443.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322684701|gb|EFY80705.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323195965|gb|EFZ81131.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323197105|gb|EFZ82246.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323201777|gb|EFZ86841.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323206291|gb|EFZ91253.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323213302|gb|EFZ98104.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323215672|gb|EGA00416.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222095|gb|EGA06481.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323226506|gb|EGA10712.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323229131|gb|EGA13260.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323236259|gb|EGA20335.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237621|gb|EGA21682.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323241713|gb|EGA25742.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323248140|gb|EGA32077.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323254530|gb|EGA38341.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323258410|gb|EGA42087.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323259690|gb|EGA43324.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323265963|gb|EGA49459.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323270405|gb|EGA53853.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
          Length = 332

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|288957792|ref|YP_003448133.1| tRNA-dihydrouridine synthase A [Azospirillum sp. B510]
 gi|288910100|dbj|BAI71589.1| tRNA-dihydrouridine synthase A [Azospirillum sp. B510]
          Length = 335

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 144/318 (45%), Positives = 196/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   A+L GD++ +LGF   E P+ALQ+GG+D +
Sbjct: 11  MMDWTDRHCRYFHRLLSASTLLYTEMVTTGAVLHGDRERLLGFDAAEHPVALQLGGSDPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A+I E++GY+E+NLNVGCPS RV  G FGACLM  PD+V   + AM  A++IPVT
Sbjct: 71  DLAACARIAEEWGYDEVNLNVGCPSDRVQSGRFGACLMAEPDLVARLVGAMRDAVAIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +D+      L + V+++  +G     +HARKA LKGLSPK+NR IP L YD+V+
Sbjct: 131 VKSRIAIDEMEEWPTLDHFVRTVSAAGCTHFIVHARKAWLKGLSPKENRDIPPLRYDLVH 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K ENP L I +NGG+  + +A + L  VD VMIGRAAY+   +L   D      LTG 
Sbjct: 191 RLKAENPHLTIAINGGIRTLDEAEEHLGKVDSVMIGRAAYETPYLLADADRR----LTGG 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R        + A+M  +    +  G  L  ITRHM+GLF G P +R  R  +   
Sbjct: 247 APGPDR------HAVIAAMLPFIEARMALGTPLSAITRHMLGLFQGLPGARAYRRHIAEN 300

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A  L+
Sbjct: 301 AHRPGAGPEVLECAAALV 318


>gi|26250830|ref|NP_756870.1| tRNA-dihydrouridine synthase A [Escherichia coli CFT073]
 gi|91213570|ref|YP_543556.1| tRNA-dihydrouridine synthase A [Escherichia coli UTI89]
 gi|110644384|ref|YP_672114.1| tRNA-dihydrouridine synthase A [Escherichia coli 536]
 gi|117626314|ref|YP_859637.1| tRNA-dihydrouridine synthase A [Escherichia coli APEC O1]
 gi|191172024|ref|ZP_03033569.1| tRNA-dihydrouridine synthase A [Escherichia coli F11]
 gi|215489385|ref|YP_002331816.1| tRNA-dihydrouridine synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218561117|ref|YP_002394030.1| tRNA-dihydrouridine synthase A [Escherichia coli S88]
 gi|218692332|ref|YP_002400544.1| tRNA-dihydrouridine synthase A [Escherichia coli ED1a]
 gi|227886947|ref|ZP_04004752.1| tRNA-dihydrouridine synthase A [Escherichia coli 83972]
 gi|237703603|ref|ZP_04534084.1| tRNA-dihydrouridine synthase A [Escherichia sp. 3_2_53FAA]
 gi|306815840|ref|ZP_07449985.1| tRNA-dihydrouridine synthase A [Escherichia coli NC101]
 gi|331660615|ref|ZP_08361547.1| tRNA-dihydrouridine synthase A [Escherichia coli TA206]
 gi|38604877|sp|Q8FB30|DUSA_ECOL6 RecName: Full=tRNA-dihydrouridine synthase A
 gi|26111261|gb|AAN83444.1|AE016770_244 Hypothetical protein yjbN [Escherichia coli CFT073]
 gi|91075144|gb|ABE10025.1| hypothetical protein YjbN [Escherichia coli UTI89]
 gi|110345976|gb|ABG72213.1| hypothetical protein YjbN (putative tRNA-dihydrouridine synthase)
           [Escherichia coli 536]
 gi|115515438|gb|ABJ03513.1| tRNA-dihydrouridine synthase A [Escherichia coli APEC O1]
 gi|190907789|gb|EDV67383.1| tRNA-dihydrouridine synthase A [Escherichia coli F11]
 gi|215267457|emb|CAS11910.1| tRNA-dihydrouridine synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218367886|emb|CAR05681.1| tRNA-dihydrouridine synthase A [Escherichia coli S88]
 gi|218429896|emb|CAR10723.1| tRNA-dihydrouridine synthase A [Escherichia coli ED1a]
 gi|222035761|emb|CAP78506.1| tRNA-dihydrouridine synthase A [Escherichia coli LF82]
 gi|226901515|gb|EEH87774.1| tRNA-dihydrouridine synthase A [Escherichia sp. 3_2_53FAA]
 gi|227836088|gb|EEJ46554.1| tRNA-dihydrouridine synthase A [Escherichia coli 83972]
 gi|281181113|dbj|BAI57443.1| conserved hypothetical protein [Escherichia coli SE15]
 gi|294489479|gb|ADE88235.1| tRNA-dihydrouridine synthase A [Escherichia coli IHE3034]
 gi|305850815|gb|EFM51271.1| tRNA-dihydrouridine synthase A [Escherichia coli NC101]
 gi|307556192|gb|ADN48967.1| tRNA-dihydrouridine synthase A [Escherichia coli ABU 83972]
 gi|307629096|gb|ADN73400.1| tRNA-dihydrouridine synthase A [Escherichia coli UM146]
 gi|312948626|gb|ADR29453.1| tRNA-dihydrouridine synthase A [Escherichia coli O83:H1 str. NRG
           857C]
 gi|323950409|gb|EGB46290.1| tRNA dihydrouridine synthase A [Escherichia coli H252]
 gi|323954491|gb|EGB50275.1| tRNA dihydrouridine synthase A [Escherichia coli H263]
 gi|330908368|gb|EGH36887.1| tRNA dihydrouridine synthase A [Escherichia coli AA86]
 gi|331051657|gb|EGI23696.1| tRNA-dihydrouridine synthase A [Escherichia coli TA206]
          Length = 331

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 308 ENAHKAGADINVLEHALKLVAD 329


>gi|301046994|ref|ZP_07194104.1| tRNA dihydrouridine synthase A [Escherichia coli MS 185-1]
 gi|300301082|gb|EFJ57467.1| tRNA dihydrouridine synthase A [Escherichia coli MS 185-1]
 gi|323190088|gb|EFZ75366.1| tRNA-dihydrouridine synthase A [Escherichia coli RN587/1]
          Length = 313

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 180 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 290 ENAHKAGADINVLEHALKLVAD 311


>gi|260870808|ref|YP_003237210.1| tRNA-dihydrouridine synthase A [Escherichia coli O111:H- str.
           11128]
 gi|257767164|dbj|BAI38659.1| tRNA-dihydrouridine synthase A [Escherichia coli O111:H- str.
           11128]
 gi|323175935|gb|EFZ61527.1| tRNA-dihydrouridine synthase A [Escherichia coli 1180]
          Length = 345

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|218702713|ref|YP_002410342.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI39]
 gi|218372699|emb|CAR20575.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI39]
          Length = 345

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGVPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|323162189|gb|EFZ48052.1| tRNA-dihydrouridine synthase A [Escherichia coli E128010]
          Length = 330

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 307 ENAHKAGADINVLEHALKLVAD 328


>gi|168784662|ref|ZP_02809669.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC869]
 gi|168798291|ref|ZP_02823298.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC508]
 gi|261225167|ref|ZP_05939448.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261255581|ref|ZP_05948114.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           FRIK966]
 gi|189375043|gb|EDU93459.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC869]
 gi|189379226|gb|EDU97642.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC508]
 gi|320190826|gb|EFW65476.1| tRNA dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC1212]
 gi|326341906|gb|EGD65689.1| tRNA dihydrouridine synthase A [Escherichia coli O157:H7 str. 1125]
          Length = 345

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|168236934|ref|ZP_02661992.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194736682|ref|YP_002117177.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194712184|gb|ACF91405.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197289961|gb|EDY29320.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 345

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------TVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 322 ENAHKAGADVAVLEQALKLVAD 343


>gi|312965642|ref|ZP_07779871.1| tRNA-dihydrouridine synthase A [Escherichia coli 2362-75]
 gi|312289616|gb|EFR17507.1| tRNA-dihydrouridine synthase A [Escherichia coli 2362-75]
          Length = 345

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|197247584|ref|YP_002149157.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197211287|gb|ACH48684.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
          Length = 332

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|145698340|ref|NP_418473.2| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           MG1655]
 gi|238903158|ref|YP_002928954.1| tRNA-dihydrouridine synthase A [Escherichia coli BW2952]
 gi|293402687|ref|ZP_06646784.1| tRNA dihydrouridine synthase A [Escherichia coli FVEC1412]
 gi|293407781|ref|ZP_06651621.1| tRNA-dihydrouridine synthase A [Escherichia coli B354]
 gi|293476353|ref|ZP_06664761.1| tRNA-dihydrouridine synthase A [Escherichia coli B088]
 gi|298378215|ref|ZP_06988099.1| tRNA-dihydrouridine synthase A [Escherichia coli FVEC1302]
 gi|3183570|sp|P32695|DUSA_ECOLI RecName: Full=tRNA-dihydrouridine synthase A
 gi|38604936|sp|Q8X5V6|DUSA_ECO57 RecName: Full=tRNA-dihydrouridine synthase A
 gi|145693211|gb|AAC77019.2| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           MG1655]
 gi|238863713|gb|ACR65711.1| tRNA-dihydrouridine synthase A [Escherichia coli BW2952]
 gi|284924142|emb|CBG37241.1| tRNA-dihydrouridine synthase A [Escherichia coli 042]
 gi|291320806|gb|EFE60248.1| tRNA-dihydrouridine synthase A [Escherichia coli B088]
 gi|291429602|gb|EFF02616.1| tRNA dihydrouridine synthase A [Escherichia coli FVEC1412]
 gi|291472032|gb|EFF14514.1| tRNA-dihydrouridine synthase A [Escherichia coli B354]
 gi|298280549|gb|EFI22050.1| tRNA-dihydrouridine synthase A [Escherichia coli FVEC1302]
          Length = 330

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 307 ENAHKAGADINVLEHALKLVAD 328


>gi|204927346|ref|ZP_03218548.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|204324011|gb|EDZ09206.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
          Length = 332

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------TVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|312884652|ref|ZP_07744353.1| tRNA-dihydrouridine synthase A [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367565|gb|EFP95116.1| tRNA-dihydrouridine synthase A [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 333

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/323 (45%), Positives = 199/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLTN ALLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRFFHRLLTNEALLYTEMVTTGAIIHG-KGDFLAYNQEEHPVALQLGGSNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + IPVT
Sbjct: 78  DLAQCAKLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMREVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYQFLTDFVSIVAEKGGCEQFTIHARKAWLSGLSPKQNREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + ++ + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLNIAINGGVKTLQESQEHLVHLDGVMMGREAYQNPYILAQVDQLI---FGA 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SPIK R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 255 DSPIKKR------SQVVEEMYPYIEQQLSQGAYLGHITRHMLGLFQNMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++TA   + + L
Sbjct: 309 NAHKPGSGIEVVQTALAKIPQEL 331


>gi|168243640|ref|ZP_02668572.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194448858|ref|YP_002048234.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194407162|gb|ACF67381.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205337347|gb|EDZ24111.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 332

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|218551359|ref|YP_002385151.1| tRNA-dihydrouridine synthase A [Escherichia fergusonii ATCC 35469]
 gi|218358901|emb|CAQ91560.1| tRNA-dihydrouridine synthase A [Escherichia fergusonii ATCC 35469]
          Length = 331

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/323 (45%), Positives = 205/323 (63%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F++  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKMHLQHMDGVMVGREAYQNPGILAAVDREIFASTDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A  +++E A  L+ ++
Sbjct: 308 ENAHKPGADINVLEHALKLVADN 330


>gi|89054629|ref|YP_510080.1| tRNA-dihydrouridine synthase A [Jannaschia sp. CCS1]
 gi|88864178|gb|ABD55055.1| tRNA-U16,U17-dihydrouridine synthase [Jannaschia sp. CCS1]
          Length = 329

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +ALLYTEM+ + A++ GD+  +L F   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRYFHRLMSRDALLYTEMVTSAAVINGDRNRLLRFDPAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  A +IV D+GY+E+NLNVGCPS RV  G FGA LM  PD+V +C+ AM     + VT
Sbjct: 74  ELAHAVRIVRDWGYDEVNLNVGCPSDRVQSGCFGAVLMRQPDLVAECVRAMRDECPVDVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL   ++++  +GV  + IHARKA L+GLSPK NR +P LDY +V+
Sbjct: 134 VKCRIGVDDQDPEDALPRFLEAMVTAGVTRVTIHARKAWLQGLSPKQNRDVPPLDYPLVF 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA--MLTTVDEYFSNPL 237
            +K+  P L I LNGG+  + +A   L   +DGVMIGRAAY   A  +L      F +  
Sbjct: 194 RMKQMFPQLHISLNGGIATLEEAGAHLEDGLDGVMIGRAAYHTPAEVLLQADQRIFGH-- 251

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             ++P ++        +++  M  Y   HL  GG+L QITRH++GLF G P +R  + IL
Sbjct: 252 --ATPARSA------EEVALLMLPYIDAHLTDGGRLNQITRHILGLFAGRPGARGWKRIL 303

Query: 298 TVEAGASTATHHIIETAFNLMI 319
           +  A    A   ++E A   +I
Sbjct: 304 SEGAHQDGAGPELVERALQEVI 325


>gi|306840355|ref|ZP_07473124.1| tRNA-dihydrouridine synthase A [Brucella sp. BO2]
 gi|306289676|gb|EFM60872.1| tRNA-dihydrouridine synthase A [Brucella sp. BO2]
          Length = 278

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 139/282 (49%), Positives = 187/282 (66%), Gaps = 9/282 (3%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           +LGF   E P+ALQ+GG+D +KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML
Sbjct: 1   MLGFDPAENPVALQLGGSDPAKLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLML 60

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            PD+V  C+AAM + +SIPVTVKCRIGVDDQ    AL  L   + ++G + +W+HARKA 
Sbjct: 61  TPDVVARCVAAMKETVSIPVTVKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAW 120

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
           LKGLSPK+NR+IP LDY+ VY +K+   + F+G+NGG+  + +A   L  VD VM+GRAA
Sbjct: 121 LKGLSPKENREIPPLDYERVYRLKQRLGETFVGINGGIATLEEAEVHLQKVDAVMLGRAA 180

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
           Y N A+L  VD        G  P           +I  +M  Y  RH+ SGG+L  ++RH
Sbjct: 181 YHNPALLADVDARLYG--DGQEPPAM-------PEIIDAMCAYIDRHIASGGRLSHVSRH 231

Query: 280 MIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           M+GLF G P +RR R IL+ +A    AT  ++  A+  ++E+
Sbjct: 232 MVGLFTGQPGARRWRQILSTDATKPGATSDVVRQAYATVVEA 273


>gi|237728132|ref|ZP_04558613.1| tRNA-dihydrouridine synthase A [Citrobacter sp. 30_2]
 gi|226910143|gb|EEH96061.1| tRNA-dihydrouridine synthase A [Citrobacter sp. 30_2]
          Length = 331

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 205/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSSQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDYD V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYDRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F+    
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKIHLQHMDGVMVGREAYQNPGILASVDREIFAATTE 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 258 DTDPV----------AVVRAMYPYIERELSKGTYLGHVTRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 308 ENAHKAGADINVLEHALKLVAD 329


>gi|325499627|gb|EGC97486.1| tRNA-dihydrouridine synthase A [Escherichia fergusonii ECD227]
          Length = 331

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNMLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYSRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F++  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKMHLQHMDGVMVGREAYQNPGILAAVDREIFASTDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A  +++E A  L+ +
Sbjct: 308 ENAHKPGADINVLEHALKLVAD 329


>gi|200388599|ref|ZP_03215211.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|199605697|gb|EDZ04242.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
          Length = 332

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|82779541|ref|YP_405890.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae Sd197]
 gi|81243689|gb|ABB64399.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
          Length = 345

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCGFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|320193408|gb|EFW68045.1| tRNA dihydrouridine synthase A [Escherichia coli WV_060327]
          Length = 331

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLGEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 308 ENAHKAGADINVLEHALKLVAD 329


>gi|15804641|ref|NP_290682.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 EDL933]
 gi|12519000|gb|AAG59247.1|AE005638_1 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
          Length = 345

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFXGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|259418773|ref|ZP_05742690.1| tRNA-dihydrouridine synthase A [Silicibacter sp. TrichCH4B]
 gi|259344995|gb|EEW56849.1| tRNA-dihydrouridine synthase A [Silicibacter sp. TrichCH4B]
          Length = 336

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 145/321 (45%), Positives = 201/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R  R+  RLL+   LLYTEM+ A A++RG   ++L     E P+ALQ+GG+D  
Sbjct: 22  MMDWTTRECRYLHRLLSKETLLYTEMVTAPALVRGRALHLLDHDVSEHPVALQLGGSDPD 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAK+  + GY+EINLN GCPS RV  G+FGA LM +P++V DC+AAM +A+ + VT
Sbjct: 82  ELAEAAKLGAEAGYDEINLNCGCPSDRVQSGAFGAILMQSPELVADCMAAMAQAVDVEVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I+ +GV+ + IHARKA LKGLSPK+NR IP LDY++V+
Sbjct: 142 VKCRIGVDDQNPQDVLPEFLEKIRAAGVDRVTIHARKAWLKGLSPKENRDIPPLDYELVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K   PD+ I +NGG+  +  A  ++   +DGVMIGRAAY   A +L   D        
Sbjct: 202 QMKASFPDMHISINGGIATLEDAQAQLARGLDGVMIGRAAYHQPADVLCAADPRIFGTGE 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+    D          M  Y  R +  G +L QI+RHM+GLF G P +R+ R  L+
Sbjct: 262 VTDPVSVVQD----------MLPYIEREMQQGARLHQISRHMLGLFAGRPGARQWRRHLS 311

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   ++E A +L+I
Sbjct: 312 EGASRKGAGPELVEEALDLVI 332


>gi|332346048|gb|AEE59382.1| tRNA-dihydrouridine synthase A DusA [Escherichia coli UMNK88]
          Length = 339

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L N + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCNFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|309787535|ref|ZP_07682147.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1617]
 gi|308925113|gb|EFP70608.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1617]
          Length = 339

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCGFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|194446261|ref|YP_002043494.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194404924|gb|ACF65146.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
          Length = 332

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------TVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|84687027|ref|ZP_01014910.1| tRNA-dihydrouridine synthase A [Maritimibacter alkaliphilus
           HTCC2654]
 gi|84665001|gb|EAQ11482.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2654]
          Length = 313

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/318 (46%), Positives = 204/318 (64%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R F R+++   LLYTEM+ A A++RG   ++L F   E P+ALQ+GG+D  
Sbjct: 1   MMDWTDSHCRVFHRMMSRETLLYTEMVTAPALVRGGVTHLLDFDPSEHPVALQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
           +L EA ++  D GY+E+NLNVGCPS RV  G+FGA L+ +PD+V  C AAM +A   + V
Sbjct: 61  ELAEATRMAVDRGYDEVNLNVGCPSDRVQSGTFGAVLLKDPDLVARCTAAMIRAAGPVEV 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIGVDDQ     L + +  +  +GV    IHARKA L+GLSPK+NR IP LDY +V
Sbjct: 121 TVKCRIGVDDQDAEAVLPDFLDRVSDAGVRRFTIHARKAWLQGLSPKENRDIPPLDYPLV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPL 237
           + +K E PDL + +NGG+  ++QA + L + +DGVMIGRAAY+  A +L T D   S   
Sbjct: 181 HRMKAEWPDLHLSINGGITSLTQAEEHLAAGMDGVMIGRAAYQQPADILLTAD---SRIF 237

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             + P++         +++ +M  +  RHL +GGKL Q+TRHM+GLF G P +R  R +L
Sbjct: 238 GAADPMRDP------GEVALAMIPHIERHLSNGGKLSQVTRHMLGLFAGRPGARHWRRVL 291

Query: 298 TVEAGASTATHHIIETAF 315
           +  A    A   +IE A 
Sbjct: 292 SENAHRPDADARLIEDAM 309


>gi|332084336|gb|EGI89539.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 155-74]
          Length = 345

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+VE  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLVEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIEHELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|198244614|ref|YP_002218138.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|207859397|ref|YP_002246048.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|197939130|gb|ACH76463.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|206711200|emb|CAR35576.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|326625935|gb|EGE32280.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
          Length = 332

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|92119109|ref|YP_578838.1| tRNA-dihydrouridine synthase A [Nitrobacter hamburgensis X14]
 gi|91802003|gb|ABE64378.1| tRNA-U16,U17-dihydrouridine synthase [Nitrobacter hamburgensis X14]
          Length = 336

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 151/320 (47%), Positives = 197/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT  A LYTEM+   AI+ G +  +LGFS  E P+ALQ+GG+   
Sbjct: 18  MMDWTDRHCRLFHRLLTRKARLYTEMLTTGAIIHGARDRLLGFSDIEHPVALQLGGSHPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I EDFGY+EINLNVGCPS RV +G FGACLM  PDIV + + AM +A+S+PVT
Sbjct: 78  DLAAAARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPDIVAEGVHAMKRAVSVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P   L +  + +  +GV+ + +HARKA L+GLSPKDNR IP LDYD VY
Sbjct: 138 VKCRIGIDDQDPEAGLDSFARKVVAAGVDALIVHARKAWLQGLSPKDNRNIPPLDYDRVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L + +NGG+  +S+A   L  VDGVM+GRAAY++   L  VD          
Sbjct: 198 RLKALLPALPVIINGGIGGISEAKNHLAHVDGVMLGRAAYQDPWRLLKVDSELFGEAAPH 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +K  ++         +M  Y    L  G +L  ITRH++G FHG P +R  R  L   
Sbjct: 258 ATMKCALE---------AMIPYIEDQLAGGARLHSITRHLVGAFHGVPGARAFRRYLAEN 308

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     I+  A  L+ E
Sbjct: 309 GVKAGVGADILREAIALVEE 328


>gi|149190495|ref|ZP_01868765.1| NifR3/Smm1 family protein [Vibrio shilonii AK1]
 gi|148835619|gb|EDL52586.1| NifR3/Smm1 family protein [Vibrio shilonii AK1]
          Length = 315

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 144/316 (45%), Positives = 201/316 (63%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-KGDFLAYNEEEHPVALQLGGSNPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM + + +PVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMKEVVDVPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V  + +K+G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTRFVSLVSEKAGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ + ++L+ L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 180 YQIKKDFPHLQIAVNGGVKTLEESLEHLKHLDGVMIGREAYQNPYILAQVDQLI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R      +++   M  Y  R L +G  L  I+RHMIGLF   P +R+ R  ++ 
Sbjct: 237 DTPVKKR------KQVVEEMYPYIERQLANGSYLGHISRHMIGLFQAMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++ETA 
Sbjct: 291 NAHKKGAGIEVLETAL 306


>gi|194432327|ref|ZP_03064615.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1012]
 gi|194419530|gb|EDX35611.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1012]
 gi|320179045|gb|EFW54004.1| tRNA dihydrouridine synthase A [Shigella boydii ATCC 9905]
 gi|332083541|gb|EGI88761.1| tRNA-dihydrouridine synthase A [Shigella boydii 5216-82]
          Length = 339

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 204/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+VE  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLVEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIEHELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|161505294|ref|YP_001572406.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160866641|gb|ABX23264.1| hypothetical protein SARI_03435 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 345

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPLALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  QLTHCAKLAEVRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 212 YQLKRDFPHLNMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 322 ENAHKAGADIGVLEQALKLVAD 343


>gi|168466925|ref|ZP_02700773.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|195630652|gb|EDX49264.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
          Length = 332

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQMLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------TVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|331675581|ref|ZP_08376328.1| tRNA-dihydrouridine synthase A [Escherichia coli TA280]
 gi|331067189|gb|EGI38597.1| tRNA-dihydrouridine synthase A [Escherichia coli TA280]
          Length = 345

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DVDPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|62182692|ref|YP_219109.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|168821313|ref|ZP_02833313.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|224586008|ref|YP_002639807.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|62130325|gb|AAX68028.1| putative TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|205342153|gb|EDZ28917.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|224470536|gb|ACN48366.1| hypothetical protein SPC_4304 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|320088651|emb|CBY98409.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|322717191|gb|EFZ08762.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 332

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSCQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|168231239|ref|ZP_02656297.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|194470364|ref|ZP_03076348.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194456728|gb|EDX45567.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|205334267|gb|EDZ21031.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
          Length = 332

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSCQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|119384161|ref|YP_915217.1| tRNA-dihydrouridine synthase A [Paracoccus denitrificans PD1222]
 gi|119373928|gb|ABL69521.1| tRNA-U16,U17-dihydrouridine synthase [Paracoccus denitrificans
           PD1222]
          Length = 329

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 141/307 (45%), Positives = 197/307 (64%), Gaps = 13/307 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   R   RLL+  ALLYTEM+ A A++ GD+  +L F   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDSLCRRIHRLLSRRALLYTEMVTAPALVYGDRAKLLDFDAGEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I  D+GY+EINLNVGCPS RV  G FGA LM  P++V +C+AAM  A  + VT
Sbjct: 74  QLAEAARIGADWGYDEINLNVGCPSDRVQSGCFGAVLMTRPELVAECVAAMIAASPVEVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L + +  ++++GV  + +HARKA L+GLSP++NR++P LDY +V+
Sbjct: 134 VKCRIGVDEQDPEAVLPDFIARMREAGVRRMTVHARKAWLQGLSPRENREVPPLDYPLVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTG 239
            +K+  PDL + +NGG+  +      L ++DGVMIGRAAY     ML   D  +      
Sbjct: 194 RMKQAFPDLHLSINGGIASLDAVRDHLAAMDGVMIGRAAYHQPWDMLGQADRLWGEEPRF 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P++           + ++ D    HL +GG+L Q TRHM+GLFHG P +R  R  L+ 
Sbjct: 254 ADPLEA----------ARALRDLVEAHLATGGRLHQATRHMLGLFHGRPGARGWRRQLS- 302

Query: 300 EAGASTA 306
             GAS A
Sbjct: 303 -EGASRA 308


>gi|269468879|gb|EEZ80471.1| tRNA-dihydrouridine synthase [uncultured SUP05 cluster bacterium]
          Length = 310

 Score =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 139/311 (44%), Positives = 196/311 (63%), Gaps = 12/311 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+F RL++ +  LYTEMI   AIL GD+  +L +   E PL LQ+GG++  +
Sbjct: 1   MDWTDRHCRYFYRLMSKHTQLYTEMITTKAILHGDQARLLDYHQDEHPLTLQLGGSNTDE 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +   AKI +D+GY+E+N+N GCPS RV  GSFGACLM  P +V DC+ AM +  ++ +TV
Sbjct: 61  MARCAKIAQDWGYDEVNINAGCPSDRVQSGSFGACLMNTPQVVADCVDAMKQVSNLSITV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIGVDD      L N +  ++KSG +   IHARKA LKGLSPK+NR +P L+YD VY+
Sbjct: 121 KSRIGVDDMESYDELTNFISLVEKSGCDTFIIHARKAWLKGLSPKENRTVPPLNYDWVYQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           IK++ P L IG+NGG+  +  A K L  VD VM+GRA Y    +LT VDE   +    SS
Sbjct: 181 IKQDFPSLTIGINGGINHLEDACKHLEKVDSVMLGRAVYHQPYLLTDVDEIIYHQ---SS 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
            I +R       ++  S  DY       G  ++ +TRH++GL+HG  N+++ + +L   +
Sbjct: 238 SITSR------EQVLLSFIDYMKVQSQQGVPIRAMTRHILGLYHGQKNAKKFKRLL---S 288

Query: 302 GASTATHHIIE 312
           G+S    H+ E
Sbjct: 289 GSSVTLDHLYE 299


>gi|114771777|ref|ZP_01449170.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HTCC2255]
 gi|114547593|gb|EAU50484.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HTCC2255]
          Length = 318

 Score =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+  RL++ N LLYTEM+ A A++ GD   +L F+  E P+ALQIGG+  ++
Sbjct: 1   MDWTDRHCRYLHRLISKNVLLYTEMVTAPALIHGDADRLLEFNQSEHPIALQIGGSHPNQ 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVT 120
           L +A ++  + GY+EIN+N+GCPS RV  G FGACLM  P++V +C+ AM +A +   +T
Sbjct: 61  LAQATRLGCEAGYDEININIGCPSDRVQFGRFGACLMKEPELVSECVTAMKEASTGAEIT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  + ++GV+   IHARKA L GLSPK NR +P LDY++V+
Sbjct: 121 VKCRIGVDDQEPKRILPDFIDKVSQNGVSSFTIHARKAWLSGLSPKQNRDVPPLDYELVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
           EIKKE P+L I LNGGL+   QA+ +I   +DG MIGR AY N   +L   D  F     
Sbjct: 181 EIKKERPELEIILNGGLQTFDQAVHEINKGLDGAMIGRTAYHNPMEILANADSLF----- 235

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                +T  +K    KI   M  Y   HL +GG+L QITRHM+GLF G   ++  +  L+
Sbjct: 236 -----ETNTNKKSVNKIIDEMLPYIQNHLDTGGRLNQITRHMLGLFSGQSGAKIWKRTLS 290

Query: 299 VEAGASTATHHIIETAFNLMIE 320
            EA    A   +++ A   ++E
Sbjct: 291 DEAHKKDAGVEVVQNALRNVLE 312


>gi|396384|gb|AAC43143.1| ORF_o345 [Escherichia coli str. K-12 substr. MG1655]
          Length = 345

 Score =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N   V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAXXVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|163739977|ref|ZP_02147382.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis BS107]
 gi|161386722|gb|EDQ11086.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis BS107]
          Length = 315

 Score =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 149/318 (46%), Positives = 201/318 (63%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+N ALLYTEM+ + A++RG   ++L  S QE P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLLSNEALLYTEMVTSPALVRGGALHLLDHSPQEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA    + GY+EINLN GCPS RV  G+FGA LM +PD+V +C+AAM   + + VT
Sbjct: 61  ELAQAAAFGAEAGYDEINLNCGCPSDRVQSGAFGAVLMKSPDLVAECVAAMRAKVDVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I  +G   + IHARKA LKGLSPK+NR IP LDY+IV+
Sbjct: 121 VKCRIGVDDQDPQEVLPVFLERIAAAGCERVTIHARKAWLKGLSPKENRDIPPLDYEIVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY-KNSAMLTTVDEYFSNPLT 238
           ++K E P L I LNGG+  + +AL  L   +DGVMIGRAAY + S +L+  D       +
Sbjct: 181 QMKAEFPQLHISLNGGVASLDEALPHLERGLDGVMIGRAAYHQPSDILSQADPLIFGTGS 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 241 ATDPV----------AVVGHMLGYIDDQMAQGARLHQITRHMLGLFAGRPGARNWRRVLS 290

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++ETA  
Sbjct: 291 EGASRPGADTRLVETALE 308


>gi|193067849|ref|ZP_03048815.1| tRNA-dihydrouridine synthase A [Escherichia coli E110019]
 gi|192958824|gb|EDV89261.1| tRNA-dihydrouridine synthase A [Escherichia coli E110019]
          Length = 339

 Score =  282 bits (721), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ LQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVVLQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|226940607|ref|YP_002795681.1| tRNA-dihydrouridine synthase A [Laribacter hongkongensis HLHK9]
 gi|226715534|gb|ACO74672.1| Dihydrouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 339

 Score =  282 bits (721), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 138/298 (46%), Positives = 192/298 (64%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARLL+ +  LYTEM+   A++ GD    L F   E P+ALQ+GG++ +
Sbjct: 26  MLDWTDRHYRYFARLLSRHTWLYTEMVTTGALIHGDVPRHLTFHETEHPIALQLGGSEPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A++ E +GY+E+NLNVGCPS RV +G+FGACLM  P +V DC+ AM    ++PVT
Sbjct: 86  ELAQCARLAESWGYDEVNLNVGCPSERVQKGAFGACLMKEPGLVADCVRAMRDVTTLPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVDD      + + V  +  +G +   +HAR AILKGLSPK+NR+IP L YD  +
Sbjct: 146 VKHRIGVDDVEAFGFVSDFVGEVAAAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAW 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E PDL I +NGG+  + +A + L  VDGVMIGR AY N  +L  VD  F       
Sbjct: 206 RLKAEFPDLEILVNGGIRTLDEAAEQLGHVDGVMIGREAYHNPYLLAGVDARFYG---DE 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P+ TR +      +   +  Y   HL +GGK++ I RH++GL +G P +RR R +L+
Sbjct: 263 HPVPTRAE------VIERLIPYVDAHLAAGGKVRDIARHVLGLVNGVPGARRFRQMLS 314


>gi|22124488|ref|NP_667911.1| tRNA-dihydrouridine synthase A [Yersinia pestis KIM 10]
 gi|45440326|ref|NP_991865.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108809958|ref|YP_653874.1| tRNA-dihydrouridine synthase A [Yersinia pestis Antiqua]
 gi|108813513|ref|YP_649280.1| tRNA-dihydrouridine synthase A [Yersinia pestis Nepal516]
 gi|145600902|ref|YP_001164978.1| tRNA-dihydrouridine synthase A [Yersinia pestis Pestoides F]
 gi|150260637|ref|ZP_01917365.1| tRNA-dihydrouridine synthase A [Yersinia pestis CA88-4125]
 gi|162420841|ref|YP_001605835.1| tRNA-dihydrouridine synthase A [Yersinia pestis Angola]
 gi|165926732|ref|ZP_02222564.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165936521|ref|ZP_02225089.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166010496|ref|ZP_02231394.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166213918|ref|ZP_02239953.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167402469|ref|ZP_02307926.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167418732|ref|ZP_02310485.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167426194|ref|ZP_02317947.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167467147|ref|ZP_02331851.1| tRNA-dihydrouridine synthase A [Yersinia pestis FV-1]
 gi|218927522|ref|YP_002345397.1| tRNA-dihydrouridine synthase A [Yersinia pestis CO92]
 gi|229836573|ref|ZP_04456739.1| tRNA-dihydrouridine synthase A [Yersinia pestis Pestoides A]
 gi|229840181|ref|ZP_04460340.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229842263|ref|ZP_04462418.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229903999|ref|ZP_04519112.1| tRNA-dihydrouridine synthase A [Yersinia pestis Nepal516]
 gi|270489016|ref|ZP_06206090.1| tRNA dihydrouridine synthase A [Yersinia pestis KIM D27]
 gi|294502383|ref|YP_003566445.1| hypothetical protein YPZ3_0273 [Yersinia pestis Z176003]
 gi|38604954|sp|Q8ZJ14|DUSA_YERPE RecName: Full=tRNA-dihydrouridine synthase A
 gi|21957280|gb|AAM84162.1|AE013659_6 hypothetical protein y0574 [Yersinia pestis KIM 10]
 gi|45435182|gb|AAS60742.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Yersinia pestis biovar Microtus str. 91001]
 gi|108777161|gb|ABG19680.1| hypothetical protein YPN_3353 [Yersinia pestis Nepal516]
 gi|108781871|gb|ABG15929.1| hypothetical protein YPA_3968 [Yersinia pestis Antiqua]
 gi|115346133|emb|CAL19001.1| conserved hypothetical protein [Yersinia pestis CO92]
 gi|145212598|gb|ABP42005.1| hypothetical protein YPDSF_3655 [Yersinia pestis Pestoides F]
 gi|149290045|gb|EDM40122.1| tRNA-dihydrouridine synthase A [Yersinia pestis CA88-4125]
 gi|162353656|gb|ABX87604.1| tRNA-dihydrouridine synthase A [Yersinia pestis Angola]
 gi|165915637|gb|EDR34246.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165921355|gb|EDR38579.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165990586|gb|EDR42887.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166204893|gb|EDR49373.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962726|gb|EDR58747.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167048157|gb|EDR59565.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167054905|gb|EDR64707.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|229679769|gb|EEO75872.1| tRNA-dihydrouridine synthase A [Yersinia pestis Nepal516]
 gi|229690573|gb|EEO82627.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229696547|gb|EEO86594.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229706257|gb|EEO92265.1| tRNA-dihydrouridine synthase A [Yersinia pestis Pestoides A]
 gi|262360466|gb|ACY57187.1| hypothetical protein YPD4_0278 [Yersinia pestis D106004]
 gi|262364412|gb|ACY60969.1| hypothetical protein YPD8_0279 [Yersinia pestis D182038]
 gi|270337520|gb|EFA48297.1| tRNA dihydrouridine synthase A [Yersinia pestis KIM D27]
 gi|294352842|gb|ADE63183.1| hypothetical protein YPZ3_0273 [Yersinia pestis Z176003]
 gi|320013820|gb|ADV97391.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 345

 Score =  282 bits (721), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 204/322 (63%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|157963384|ref|YP_001503418.1| tRNA-dihydrouridine synthase A [Shewanella pealeana ATCC 700345]
 gi|157848384|gb|ABV88883.1| TIM-barrel protein, yjbN family [Shewanella pealeana ATCC 700345]
          Length = 328

 Score =  282 bits (721), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 141/315 (44%), Positives = 201/315 (63%), Gaps = 12/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++  LLYTEM+   AIL G + + L ++ +E PLALQ+GG++  
Sbjct: 15  MLDWTDRHYRYFARLMSSQTLLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPV 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 74  DLAACAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVTAMKQVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++K +G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKTRIGIDEQDSYEFLTQFIDTVKAAGCEEFIIHARKAWLQGLSPKENREIPPLDYERVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG- 239
           ++K++ P+L I +NGG++ + +    L  +DGVM+GR AY+N  +L  VD+     L G 
Sbjct: 194 QLKRDYPELNISINGGVKTLEECQTHLQHLDGVMVGREAYQNPYILAEVDQ----KLCGI 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R        +   +  Y  +HL  GG+L  I+RH+IGLF G   SR  R  ++ 
Sbjct: 250 DAPVMSR------DAVLEKLLPYIEKHLQQGGRLNHISRHIIGLFQGEVGSRVWRRYISE 303

Query: 300 EAGASTATHHIIETA 314
            A    A   +I  A
Sbjct: 304 NAHKQGAGIEVITQA 318


>gi|167625570|ref|YP_001675864.1| tRNA-dihydrouridine synthase A [Shewanella halifaxensis HAW-EB4]
 gi|167355592|gb|ABZ78205.1| TIM-barrel protein, yjbN family [Shewanella halifaxensis HAW-EB4]
          Length = 328

 Score =  282 bits (721), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 139/315 (44%), Positives = 202/315 (64%), Gaps = 12/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++  LLYTEM+   AIL G + + L ++ +E PLALQ+GG++ +
Sbjct: 15  MLDWTDRHYRYFARLMSSQVLLYTEMVTTGAILHG-RGDYLAYNQEEHPLALQLGGSNPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C++AM + + IP+T
Sbjct: 74  DLAACAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVSAMKQVVDIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++K +G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKTRIGIDEQDSYEFLTQFIDTVKAAGCEEFTIHARKAWLQGLSPKENREIPPLDYERVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG- 239
           ++K++ P L I +NGG++ + +    L  +DGVM+GR AY+N  +L  VD+     L G 
Sbjct: 194 QLKRDYPQLNISINGGIKTLEECQTHLQHLDGVMVGREAYQNPYILAEVDQ----KLCGI 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R        +   +  Y  +HL  GG+L  ITRH+IGL+ G   SR  R  L+ 
Sbjct: 250 DTPVISR------DAVLEKLLPYIEKHLQQGGRLNHITRHIIGLYQGEVGSRVWRRYLSE 303

Query: 300 EAGASTATHHIIETA 314
            A    A   ++  A
Sbjct: 304 NAHKQGAGIEVVTQA 318


>gi|86148209|ref|ZP_01066506.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
 gi|218708347|ref|YP_002415968.1| tRNA-dihydrouridine synthase A [Vibrio splendidus LGP32]
 gi|85833979|gb|EAQ52140.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
 gi|218321366|emb|CAV17316.1| tRNA-dihydrouridine synthase A [Vibrio splendidus LGP32]
          Length = 333

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AIL G K + L ++ QE PLALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLSQQTLLYTEMVTTGAILHG-KGDFLEYNEQEHPLALQLGGSNPV 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V DC++AM +   IP+T
Sbjct: 78  DLAACAKLAGERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVADCVSAMKEVTDIPIT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G     IHARKA L GLSPK+NR+IP LDYD  
Sbjct: 138 VKTRIGIDDQDSYEFLTKFVSTVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYDRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+  DL I +NGG+  + Q  + L  +DGVMIGR AY +  +L  VD+        
Sbjct: 198 YQIKKDFSDLVIAVNGGITTLEQTKEHLQHLDGVMIGREAYHSPFILAEVDQQI---FGL 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PIK R       ++   M  Y  R L +G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 255 DTPIKKR------SQVVEEMYPYIERQLSNGASLGHISRHMLGLFQSMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAF 315
            A    A   +I+TA 
Sbjct: 309 NAHKKGAGIEVIQTAL 324


>gi|294139225|ref|YP_003555203.1| tRNA-dihydrouridine synthase A [Shewanella violacea DSS12]
 gi|293325694|dbj|BAJ00425.1| tRNA-dihydrouridine synthase A [Shewanella violacea DSS12]
          Length = 329

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 143/315 (45%), Positives = 197/315 (62%), Gaps = 12/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR+++   LLYTEM+   AI+ G K + L ++++E PLALQ+GG++  
Sbjct: 20  MLDWTDRHYRYLARIMSTELLLYTEMVTTGAIIHG-KGDYLAYNSEENPLALQLGGSNHH 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM + + IPVT
Sbjct: 79  DLATCAKLAAERGYDEINLNVGCPSDRVQSGRFGACLMAEPKLVAECVTAMKQVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V ++   G +   +HARKA L+GLSPK NR+IP LDY  VY
Sbjct: 139 VKTRIGIDDQDSYEFLSEFVDTVSDVGCDTFIVHARKAWLQGLSPKQNREIPPLDYQRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ PDL I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 199 RLKKDYPDLHISINGGVKTLDECHEHLQHIDGVMVGREAYQNPYILAEVDQR----LCGS 254

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P+ +R        +      Y  +HL  GG+L  ITRHM G++ G P SR  R  ++ 
Sbjct: 255 NKPVLSR------DAVLDKFIPYIEKHLMDGGRLNHITRHMTGMYQGEPGSRAWRRYISE 308

Query: 300 EAGASTATHHIIETA 314
            A    A   +IE A
Sbjct: 309 NAHKPGAGIEVIEQA 323


>gi|331680980|ref|ZP_08381617.1| tRNA-dihydrouridine synthase A [Escherichia coli H299]
 gi|331081201|gb|EGI52362.1| tRNA-dihydrouridine synthase A [Escherichia coli H299]
          Length = 345

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|300115485|ref|YP_003762060.1| TIM-barrel protein [Nitrosococcus watsonii C-113]
 gi|299541422|gb|ADJ29739.1| TIM-barrel protein, yjbN family [Nitrosococcus watsonii C-113]
          Length = 325

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 142/319 (44%), Positives = 199/319 (62%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++++ALLYTEM+   A++ GD+   L   + E PLALQ+GG+   
Sbjct: 15  MMDWTDRHCRYFLRLISHHALLYTEMVTTGALVHGDRIRFLAHHSSEHPLALQLGGSHPE 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A+I ED+G++E+NLNVGCPS RV  G FGACLM  P +V +C+AAM +A  IPVT
Sbjct: 75  ELALCAQIAEDYGFDEVNLNVGCPSNRVQSGRFGACLMAEPQLVAECVAAMAQATQIPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q    AL + + ++ ++G     IHARKA L+GLSPK+NR+ P L YD+V 
Sbjct: 135 VKTRIGIDEQDSYEALSSFISTVAQAGCRTFIIHARKAWLQGLSPKENREKPPLRYDVVR 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK++ P L + +NGG+  + +  + L  +DGVMIGRAAY N  +L  VD+ F       
Sbjct: 195 AIKRDFPQLEVMINGGITTLKEVSEHLELLDGVMIGRAAYHNPYLLAPVDQRFYGDFRA- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + TR       +I  +   YAA  L  G  L ++TRH++GLF G P +R  R  L+  
Sbjct: 254 --LPTR------HEIIEAFLPYAAEQLARGVYLSRMTRHILGLFQGQPGARAWRRYLSEN 305

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   II  A   ++
Sbjct: 306 AHRPGAGIEIIREALQRVL 324


>gi|149907717|ref|ZP_01896464.1| TIM-barrel protein, yjbN family [Moritella sp. PE36]
 gi|149809387|gb|EDM69316.1| TIM-barrel protein, yjbN family [Moritella sp. PE36]
          Length = 330

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 202/321 (62%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AI+ G + + L ++ +E P++LQ+GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAIIHG-RGDYLAYNKEEHPVSLQLGGSNPI 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+ AM   + IP+T
Sbjct: 79  DLAQSAKLAQERGYDEINLNVGCPSDRVQSGKFGACLMAEPTLVADCVKAMQDVVDIPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  + ++  +G     +HARKA L GLSPK+NR+IP L+Y  VY
Sbjct: 139 VKTRIGIDDQDSYEFLQTFIDTVAATGCKDFTLHARKAWLSGLSPKENREIPELNYQRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P LFI +NGG++ +++    L +VDGVM+GR AY N  +L+ +DE       G 
Sbjct: 199 DIKQDFPALFIAINGGVKTLAETQLHLGNVDGVMMGREAYHNPFLLSQIDELVYG---GE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R D       +  M  Y   H+ +GG L  I RHM+GLF G P +R  +  L+ +
Sbjct: 256 KSIHSRHD------YAEMMLPYIDNHIRNGGSLTHIYRHMLGLFLGLPGARAWKRHLSEQ 309

Query: 301 AGASTATHHIIETAFNLMIES 321
                A   ++E A  L+ +S
Sbjct: 310 GHKKGAGVEVVEAALLLVPKS 330


>gi|39935038|ref|NP_947314.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris CGA009]
 gi|39648889|emb|CAE27410.1| NifR3/Smm1 family protein [Rhodopseudomonas palustris CGA009]
          Length = 331

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 143/298 (47%), Positives = 195/298 (65%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R F RLLT   LLYTEM+   A++ GD++ +LGF   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDSHCRVFHRLLTRRGLLYTEMVTTGAVIHGDRQRLLGFDASEHPVALQLGGSNPN 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EIN+NVGCPS RV EG FGACLM  P++V + +AAM +A+S+PVT
Sbjct: 74  DLATSAKIGEDFGYDEININVGCPSDRVKEGRFGACLMAEPELVAEGVAAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPEVALDALARAVVAAGADALIVHARKAWLNGLSPKENRHIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  +++A + L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKQAMPQVPIIINGGIGSIAEAKRHLEHVDGVMLGRAAYQEPWRLLEVDPELYGETAPY 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +K  ++         ++  Y  R L  G +L  ITRH+IG + G P +R  R  L+
Sbjct: 254 PSMKEALE---------ALIPYIERQLAQGLRLHAITRHVIGAYQGVPGARAFRRYLS 302


>gi|194437343|ref|ZP_03069441.1| tRNA-dihydrouridine synthase A [Escherichia coli 101-1]
 gi|194423899|gb|EDX39888.1| tRNA-dihydrouridine synthase A [Escherichia coli 101-1]
          Length = 345

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|170021953|ref|YP_001726907.1| tRNA-dihydrouridine synthase A [Escherichia coli ATCC 8739]
 gi|253775323|ref|YP_003038154.1| tRNA-dihydrouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|300929788|ref|ZP_07145240.1| tRNA dihydrouridine synthase A [Escherichia coli MS 187-1]
 gi|312974158|ref|ZP_07788329.1| tRNA-dihydrouridine synthase A [Escherichia coli 1827-70]
 gi|169756881|gb|ACA79580.1| TIM-barrel protein, yjbN family [Escherichia coli ATCC 8739]
 gi|242379577|emb|CAQ34398.1| tRNA-dihydrouridine synthase A [Escherichia coli BL21(DE3)]
 gi|253326367|gb|ACT30969.1| TIM-barrel protein, yjbN family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253980042|gb|ACT45712.1| tRNA-dihydrouridine synthase A [Escherichia coli BL21(DE3)]
 gi|300462294|gb|EFK25787.1| tRNA dihydrouridine synthase A [Escherichia coli MS 187-1]
 gi|310331692|gb|EFP98948.1| tRNA-dihydrouridine synthase A [Escherichia coli 1827-70]
 gi|323935538|gb|EGB31869.1| tRNA dihydrouridine synthase A [Escherichia coli E1520]
 gi|323960455|gb|EGB56088.1| tRNA dihydrouridine synthase A [Escherichia coli H489]
 gi|323969817|gb|EGB65098.1| tRNA dihydrouridine synthase A [Escherichia coli TA007]
          Length = 345

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|316934857|ref|YP_004109839.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris DX-1]
 gi|315602571|gb|ADU45106.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris DX-1]
          Length = 331

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 146/299 (48%), Positives = 197/299 (65%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD   R F RLLT  ALLYTEM+   A++ GD++ +LGF   E PLALQ+GG++ +
Sbjct: 14  MMEWTDSPCRVFHRLLTKRALLYTEMVTTGAVIHGDRQRLLGFDASEHPLALQLGGSNPN 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EIN+NVGCPS RV EG FGACLM  P++V + +AAM +A+S+PVT
Sbjct: 74  DLATSAKIGEDFGYDEININVGCPSDRVKEGRFGACLMAEPELVAEGVAAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPEVALDALARAVVAAGADALIVHARKAWLNGLSPKENRDIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  P + I +NGG+  +++A + L  VDGVM+GRAAY+    L  VD E F  P   
Sbjct: 194 RLKQAMPQVPIIINGGIGSIAEAKRHLDHVDGVMLGRAAYQEPWRLLEVDPELFGEPAPY 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S           ++   ++  Y  R L  G +L  ITRH+IG + G P +R  R  L+
Sbjct: 254 PS----------MKEALEALIPYIERQLAQGLRLHAITRHVIGAYQGVPGARAFRRYLS 302


>gi|254282686|ref|ZP_04957654.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR51-B]
 gi|219678889|gb|EED35238.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR51-B]
          Length = 311

 Score =  281 bits (720), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 142/316 (44%), Positives = 199/316 (62%), Gaps = 11/316 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+F RLLT  A LYTEM+   A+L GD    L F+  E P+ALQ+GG++  +
Sbjct: 1   MDWTDRHCRYFWRLLTRRARLYTEMVTTGALLHGDVARHLQFNDCEHPIALQLGGSNPEE 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L   A++ ED+GY+E+NLN GCPS RV  G FGACLM   ++V DC+AAMC A ++PVTV
Sbjct: 61  LASCARMAEDWGYDEVNLNCGCPSDRVQNGRFGACLMAEAELVRDCVAAMCDASALPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D Q     LR+ V ++   G     +HARKA L+GLSPK+NR+IP L+Y  VY 
Sbjct: 121 KHRIGIDHQESYNELRDFVGTVASGGARVFIVHARKAWLQGLSPKENREIPPLNYPWVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P L I LNGG+ D+      L  VDGVM+GRAAY+N  +L +VD+     L G +
Sbjct: 181 LKQDFPHLTIVLNGGVTDIPACESHLGKVDGVMLGRAAYQNPWLLASVDQ----ALFGDA 236

Query: 242 PI-KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           P  ++R        +  ++  Y  R L  GG+L  +TRH++GL+ G P  +R R +++  
Sbjct: 237 PRGQSRA------SVLEALMPYIDRELARGGRLNHVTRHVLGLYQGIPGGKRFRRVISEN 290

Query: 301 AGASTATHHIIETAFN 316
           A    AT  ++  A +
Sbjct: 291 AHLPNATSDVLRAAMD 306


>gi|188494852|ref|ZP_03002122.1| tRNA-dihydrouridine synthase A [Escherichia coli 53638]
 gi|188490051|gb|EDU65154.1| tRNA-dihydrouridine synthase A [Escherichia coli 53638]
          Length = 347

 Score =  281 bits (720), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 324 ENAHKAGADINVLEHALKLVAD 345


>gi|51594726|ref|YP_068917.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186893729|ref|YP_001870841.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis PB1/+]
 gi|51588008|emb|CAH19612.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|186696755|gb|ACC87384.1| TIM-barrel protein, yjbN family [Yersinia pseudotuberculosis PB1/+]
          Length = 345

 Score =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 203/322 (63%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 HAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|212633607|ref|YP_002310132.1| tRNA-dihydrouridine synthase A [Shewanella piezotolerans WP3]
 gi|212555091|gb|ACJ27545.1| TIM-barrel protein, yjbN family [Shewanella piezotolerans WP3]
          Length = 370

 Score =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 142/319 (44%), Positives = 201/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++   LLYTEM+   AI+ G + + L ++ +E P+ALQ+GG++  
Sbjct: 57  MLDWTDRHYRYFARLMSAEVLLYTEMVTTGAIIHG-RGDYLAYNQEEHPVALQLGGSNAV 115

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM + + IPVT
Sbjct: 116 DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPTLVAECVDAMKQVVDIPVT 175

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++K  G N   IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 176 VKTRIGIDEQDSYEFLTEFIDTVKAVGCNDFIIHARKAWLQGLSPKENREIPELDYERVY 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG- 239
           ++K++  DL I +NGG++ +++    L  +DGVM+GR AY+N  +L  VD+     L G 
Sbjct: 236 QLKRDYADLSISINGGVKTLAECKTHLQQLDGVMVGREAYQNPYILAEVDQ----QLCGI 291

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+ +R        +   +  Y  +HL +GGKL  +TRH+IGLF G   SR  R  ++ 
Sbjct: 292 DKPVMSR------DAVLEKLLPYIEKHLQAGGKLNHVTRHIIGLFQGEVGSRVWRRYISE 345

Query: 300 EAGASTATHHIIETAFNLM 318
            A  S A   ++  A   M
Sbjct: 346 NAHKSGAGIEVVTQARQEM 364


>gi|205355015|ref|YP_002228816.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205274796|emb|CAR39855.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|326630167|gb|EGE36510.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 332

 Score =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DG M+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGAMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|238754677|ref|ZP_04616030.1| tRNA-dihydrouridine synthase A [Yersinia ruckeri ATCC 29473]
 gi|238707136|gb|EEP99500.1| tRNA-dihydrouridine synthase A [Yersinia ruckeri ATCC 29473]
          Length = 343

 Score =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 148/319 (46%), Positives = 200/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKEALLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DC+ AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V+ + ++ G +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCEFVQKVAEQGGCDMFTIHARKAWLSGLSPKENREVPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 206 YQLKRDFPALTMAINGGVKTLEEAKEHLKYLDGVMMGREAYQNPSILTQVDRELFDPQA- 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                  V  D    I A +  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 265 -------VVTDSVAAIEA-LYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRYLSE 316

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A +L+
Sbjct: 317 NAHKPGAGVSVVEKALSLV 335


>gi|296100676|ref|YP_003610822.1| tRNA-dihydrouridine synthase A [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295055135|gb|ADF59873.1| tRNA-dihydrouridine synthase A [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 331

 Score =  281 bits (719), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 148/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAHCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVAGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +LTTVD E F     
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLDEAKTHLAHMDGVMVGREAYQNPGILTTVDREIFGVEGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DTDPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 308 ENAHKAGADIEVLEQALRLVAD 329


>gi|238913008|ref|ZP_04656845.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
          Length = 332

 Score =  281 bits (719), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 200/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++  +       IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQDECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|16767493|ref|NP_463108.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167991432|ref|ZP_02572531.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|38604955|sp|Q8ZKH4|DUSA_SALTY RecName: Full=tRNA-dihydrouridine synthase A
 gi|16422801|gb|AAL23067.1| putative TIM-barrel enzyme [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|205330107|gb|EDZ16871.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261249341|emb|CBG27204.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267996554|gb|ACY91439.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301160735|emb|CBW20266.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312915348|dbj|BAJ39322.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321223111|gb|EFX48181.1| tRNA dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. TN061786]
 gi|323132582|gb|ADX20012.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332991059|gb|AEF10042.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 332

 Score =  281 bits (719), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+    LYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTQLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADVAVLEQALKLVAD 330


>gi|84393138|ref|ZP_00991902.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
 gi|84376190|gb|EAP93074.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
          Length = 334

 Score =  281 bits (719), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 147/316 (46%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEMI   AIL G K + L ++ QE PLALQ+GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLSQQTLLYTEMITTGAILHG-KGDFLEYNEQEHPLALQLGGSNPV 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V DC++AM +   IP+T
Sbjct: 79  DLAACAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVADCVSAMKEVTDIPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G     IHARKA L GLSPK+NR+IP LDYD  
Sbjct: 139 VKTRIGIDDQDSYEFLTKFVSTVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYDRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+  DL I +NGG+  + Q  + L  +DGVMIGR AY +  +L  VD+        
Sbjct: 199 YQIKKDFSDLVIAVNGGVTTLEQTKEHLQHLDGVMIGREAYHSPFILAEVDQQI---FGL 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PIK R       ++   M  Y  R L +G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 256 DTPIKKR------SQVVEEMYPYIERELSNGASLGHISRHMLGLFQSMPGARQWRRYISE 309

Query: 300 EAGASTATHHIIETAF 315
            A    A   +++TA 
Sbjct: 310 NAHKKGAGIEVMQTAL 325


>gi|323975321|gb|EGB70424.1| tRNA dihydrouridine synthase A [Escherichia coli TW10509]
          Length = 345

 Score =  281 bits (719), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAETRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DD      L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDLDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|126658190|ref|ZP_01729341.1| tRNA-dihydrouridine synthase A [Cyanothece sp. CCY0110]
 gi|126620561|gb|EAZ91279.1| tRNA-dihydrouridine synthase A [Cyanothece sp. CCY0110]
          Length = 341

 Score =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 144/315 (45%), Positives = 193/315 (61%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R +T + LLYTEMIV  AI  GD+  +L FS +EKPL+LQ+GG    
Sbjct: 17  MMDYTDRHFRYFMRQITRHTLLYTEMIVTAAIKHGDRSKLLDFSPEEKPLSLQLGGDKPH 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I ED+GY+E+NLNVGCPS RV  G FGACLM NPD+V  C+  M KA++IPVT
Sbjct: 77  ELAECAIIAEDWGYDEVNLNVGCPSDRVQSGHFGACLMANPDLVAQCVEKMQKAVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     +   VK +  +G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 137 VKHRIGIDDQDSYENMAQFVKVVSDAGCQRFTVHARKAWLKGLSPKENRNIPPLRYEAVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P LFI +NGG+ ++ Q    L  VD VMIGRAAY N  +  TVD          
Sbjct: 197 RLKQEFPHLFIEINGGITNLEQVRNHLELVDAVMIGRAAYDNPYLFATVDRDIY-----Q 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I      +   K+   + D+ +R    G KL +I+RH++ +F G P ++  +  ++  
Sbjct: 252 DKIIQLTRHEIIEKMLPYIDDWVSR----GHKLHKISRHLLAIFSGIPGTKAWKRHISEN 307

Query: 301 AGASTATHHIIETAF 315
           A    A   +I  A 
Sbjct: 308 AHLPDADSKVIVEAL 322


>gi|331655869|ref|ZP_08356857.1| tRNA-dihydrouridine synthase A [Escherichia coli M718]
 gi|331046223|gb|EGI18313.1| tRNA-dihydrouridine synthase A [Escherichia coli M718]
          Length = 345

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPALDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIECELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|56752036|ref|YP_172737.1| tRNA-dihydrouridine synthase A [Synechococcus elongatus PCC 6301]
 gi|81300875|ref|YP_401083.1| tRNA-dihydrouridine synthase A [Synechococcus elongatus PCC 7942]
 gi|56686995|dbj|BAD80217.1| hypothetical protein [Synechococcus elongatus PCC 6301]
 gi|81169756|gb|ABB58096.1| TIM-barrel protein, yjbN family [Synechococcus elongatus PCC 7942]
          Length = 343

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 142/322 (44%), Positives = 199/322 (61%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F R ++   LLYTEMIVA AI  GD+  +L +  QE P+ALQ+GG +  
Sbjct: 24  MLDRTDRHCRYFLRQISRRTLLYTEMIVAQAIQYGDRARLLDYDPQEHPVALQVGGDNPQ 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I ED+GY+EINLNVGCPS RV +G FGACLM  P+ V  C+ AM  A ++PVT
Sbjct: 84  WLADCARIAEDWGYDEINLNVGCPSDRVQKGQFGACLMARPEQVAQCVEAMRSASTLPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L++ V+ + +SG +   +HARKA L+GL PK NR IP L YD+VY
Sbjct: 144 VKHRIGIDDRDSYEELQDFVRIVAESGCDRFSVHARKAWLQGLDPKQNRTIPPLRYDVVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ P L I +NGG+ D+ QA + L  VD VM+GRA Y N  +L   D + + + L  
Sbjct: 204 QLKQDFPQLVIEINGGILDLDQAQQHLQQVDAVMMGRAIYDNPYLLAAADAQLYGDHLEP 263

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S +          ++  +M  Y  + L  G +L  ITRH++ LFHG P SR  + +LT 
Sbjct: 264 RSRL----------QVVLAMMPYIEQQLSQGVRLHSITRHLLQLFHGCPGSRAWKRVLTE 313

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +     A   ++  A   + ES
Sbjct: 314 QGCKPGAGPEVLLAALEQVSES 335


>gi|292490501|ref|YP_003525940.1| TIM-barrel protein, yjbN family [Nitrosococcus halophilus Nc4]
 gi|291579096|gb|ADE13553.1| TIM-barrel protein, yjbN family [Nitrosococcus halophilus Nc4]
          Length = 340

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 136/316 (43%), Positives = 198/316 (62%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RL++++ALLYTEM+   A++ GD++  L +   E PLA+Q+GG++  
Sbjct: 27  MMEWTDRHCRYFLRLISHHALLYTEMVTTGALIHGDRERFLAYHPTEHPLAVQLGGSNPE 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ ED G++E+NLNVGCPS RV  G FGACLM+ P++V +C+AAM + + +PVT
Sbjct: 87  ELAFCARLAEDHGFDEVNLNVGCPSDRVQSGRFGACLMMEPELVAECVAAMAQTVQLPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+Q    AL   + ++ ++G     +HARKA L+GLSPK+NR+ P L Y++V 
Sbjct: 147 VKTRIGVDEQDSYEALTRFINTVSQAGCRTFILHARKAWLQGLSPKENREKPPLRYEVVR 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK++ P L + +NGG+  + +A + L  +DG+MIGRAAY N  +L  VD YF       
Sbjct: 207 AIKQDFPHLEVVINGGIATLEEAQEQLTLLDGIMIGRAAYHNPYLLAQVDRYFYGDF--- 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ TR        I  +   Y    L  G  L +ITRH++GLF G P +R  R  L+  
Sbjct: 264 HPLPTR------HGIMEAFLPYVEEQLAQGIYLSRITRHILGLFQGQPGARAWRRYLSEN 317

Query: 301 AGASTATHHIIETAFN 316
           A    A   +I  A  
Sbjct: 318 AHRPGAGIEVIREALR 333


>gi|163749318|ref|ZP_02156567.1| TIM-barrel protein, yjbN family [Shewanella benthica KT99]
 gi|161331037|gb|EDQ01963.1| TIM-barrel protein, yjbN family [Shewanella benthica KT99]
          Length = 310

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 143/318 (44%), Positives = 199/318 (62%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR+++   LLYTEM+   AI+ G K + L ++++E PLALQ+GG++  
Sbjct: 1   MLDWTDRHYRYLARIMSTELLLYTEMVTTGAIIHG-KGDYLAYNSEENPLALQLGGSNPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM +P +V +C+ AM + + IPVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQSGRFGACLMADPKLVAECVTAMKQVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V ++   G +   +HARKA L+GLSPK NR+IP LDY  VY
Sbjct: 120 VKTRIGIDDQDSYEFLTEFVDTVSDVGCDTFIVHARKAWLQGLSPKQNREIPPLDYQRVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+     L GS
Sbjct: 180 RLKQDYPKLHISINGGVKTLDECRQHLLHIDGVMVGREAYQNPYILAEVDQR----LCGS 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +  K+ + +D    +      Y  +HL  GG+L  ITRHM G+F G P SR  R  ++  
Sbjct: 236 N--KSVLSRD---AVLEKFIPYIEKHLVEGGRLNHITRHMTGMFQGEPGSRAWRRYISEN 290

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IE A   M
Sbjct: 291 AHKQGAGIEVIEQARKKM 308


>gi|283787222|ref|YP_003367087.1| tRNA-dihydrouridine synthase A [Citrobacter rodentium ICC168]
 gi|282950676|emb|CBG90350.1| putative tRNA-dihydrouridine synthase A [Citrobacter rodentium
           ICC168]
          Length = 345

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSGEEHPLALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  QLAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRNTVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIDTVSGHGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLAEAKAHLEHMDGVMVGREAYQNPGILASVDREIFGVDSP 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|310816167|ref|YP_003964131.1| tRNA-dihydrouridine synthase A [Ketogulonicigenium vulgare Y25]
 gi|308754902|gb|ADO42831.1| tRNA-dihydrouridine synthase A [Ketogulonicigenium vulgare Y25]
          Length = 329

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 150/327 (45%), Positives = 199/327 (60%), Gaps = 26/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD + R F R  + NALLYTEM+ A A++ G +  +LG+   E P+ALQ+GGAD +
Sbjct: 15  MIDWTDSNCRIFHRQFSRNALLYTEMVTAPAVIHGPRARLLGYRDAEHPVALQLGGADPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EA +I  D+ Y+EINLN GCPS RV  G+FGA LM  PD+V + ++ M  A  + VT
Sbjct: 75  QLREAVRIAADWNYDEINLNCGCPSDRVQSGAFGAVLMRQPDLVAEILSEMIAASPVEVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIGVDDQ P+  L   ++ +  SGV  + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 135 LKCRIGVDDQEPSDILPAFLEKVAASGVRRVIIHARKAWLQGLSPKENRDIPPLDYDLVF 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K   PDL I LNGG++ +++A  +L   +DGVMIGRAAY   A               
Sbjct: 195 AMKAAFPDLHISLNGGVKSLAEAQALLDRGLDGVMIGRAAYHEPA--------------- 239

Query: 240 SSPIKTRVDKDFW---RKISASMTDYA-----ARHLHSGGKLQQITRHMIGLFHGFPNSR 291
              I  + D   W     ISA    +A       HL +GG+L QITRHM+G F G P +R
Sbjct: 240 --DILGQADPLIWGEGHAISAEEAVHAMFPVIEDHLRAGGRLHQITRHMLGAFAGRPGAR 297

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
           + R IL+ EA    A  H +E A   M
Sbjct: 298 QWRRILSEEANRDGAGLHTVEKALAAM 324


>gi|85714507|ref|ZP_01045495.1| dihydrouridine synthase TIM-barrel protein yjbN [Nitrobacter sp.
           Nb-311A]
 gi|85698954|gb|EAQ36823.1| dihydrouridine synthase TIM-barrel protein yjbN [Nitrobacter sp.
           Nb-311A]
          Length = 341

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 151/321 (47%), Positives = 204/321 (63%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F RLL   A LYTEM+   A++ G++  +LGFS  E P+ALQ+GG++  
Sbjct: 8   MMEWTDRHCRVFHRLLARKARLYTEMLTTGAVIHGERDRLLGFSDVEHPVALQLGGSNPV 67

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EINLNVGCPS RV +G FGACLM  PD+V + + AM +A+S+PVT
Sbjct: 68  DLATSAKIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPDVVAETVNAMKRAVSVPVT 127

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ     L    + ++ +GV+ + +HARKA L+GLSPK+NR IP LDYD VY
Sbjct: 128 VKCRIGIDDQDTETELDIFARKVRAAGVDTLIVHARKAWLQGLSPKENRDIPPLDYDRVY 187

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L I +NGG+  +S+A + L  VDGVM+GRAAY+    L  VD   S     +
Sbjct: 188 RLKASLPGLPIVINGGIGGISEAKQHLAHVDGVMLGRAAYQEPWRLLEVD---SQLFGEA 244

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P KT       ++   +M  Y    L  G +L  I+RH+IG FHG P +R  R  L   
Sbjct: 245 APPKT------MKQALEAMMPYIEDQLADGARLHSISRHLIGAFHGVPGARAFRRYLAGN 298

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   +++ A  L+ ES
Sbjct: 299 AVKAGAGIDVLQEAIALVDES 319


>gi|192290571|ref|YP_001991176.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris TIE-1]
 gi|192284320|gb|ACF00701.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris TIE-1]
          Length = 330

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 143/299 (47%), Positives = 197/299 (65%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD H R F RLLT   LLYTEM+   A++ GD++ +LGF   E P+ALQ+GG++ +
Sbjct: 14  MMEWTDSHCRVFHRLLTRRGLLYTEMVTTGAVIHGDRQRLLGFDASEHPVALQLGGSNPN 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EIN+NVGCPS RV EG FGACLM  P++V + +AAM +A+++PVT
Sbjct: 74  DLATSAKIGEDFGYDEININVGCPSDRVKEGRFGACLMAEPELVAEGVAAMERAVAVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPEVALDALARAVVAAGADALIVHARKAWLNGLSPKENRHIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  P + I +NGG+  +++A + L  VDGVM+GRAAY+    L  VD E +  P   
Sbjct: 194 RLKQAMPQVPIIINGGIGSIAEAKRHLEHVDGVMLGRAAYQEPWRLLEVDPELYGEPAPY 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S           ++   ++  Y  R L  G +L  ITRH+IG + G P +R  R  L+
Sbjct: 254 PS----------MKEALEALIPYIERQLAQGLRLHAITRHVIGAYQGVPGARAFRRYLS 302


>gi|188025481|ref|ZP_02958806.2| hypothetical protein PROSTU_00565 [Providencia stuartii ATCC 25827]
 gi|188023335|gb|EDU61375.1| hypothetical protein PROSTU_00565 [Providencia stuartii ATCC 25827]
          Length = 336

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 146/317 (46%), Positives = 201/317 (63%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L FS +E+P+ALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRLLSKNTLLYTEMVTTGAIIHG-KGDYLAFSEEEQPVALQLGGSDPE 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   +SIPVT
Sbjct: 83  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMADAQLVADCVKAMQDVVSIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++  K G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 143 VKTRIGIDEQDSYEFLCDFIDTVSTKGGCEMFIIHARKAWLSGLSPKENREIPPLDYPRV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD + F + L 
Sbjct: 203 YQLKRDFPHLTMAINGGIKTLEEAKEHLRHLDGVMVGREAYQNPSILTAVDNQLFDSQL- 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+   VD          M  Y  + L  G  L  ITRHM+G+F G P +R+ R  L+
Sbjct: 262 ---PVVNAVDA------VRQMFPYIEKELSQGTYLGHITRHMLGIFQGIPGARQWRRYLS 312

Query: 299 VEAGASTATHHIIETAF 315
             A    A   ++E A 
Sbjct: 313 ENAHKKGADLAVVEQAL 329


>gi|242238196|ref|YP_002986377.1| TIM-barrel protein, yjbN family [Dickeya dadantii Ech703]
 gi|242130253|gb|ACS84555.1| TIM-barrel protein, yjbN family [Dickeya dadantii Ech703]
          Length = 335

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 145/317 (45%), Positives = 201/317 (63%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AIL G + + L ++ +E PLALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRLLSHNALLYTEMVTTGAILHG-RGDYLAYNDEEHPLALQLGGSDPQ 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I E  GY+EINLNVGCPS RV  G FGACLM   ++V DC+ AM   + +PVT
Sbjct: 83  ALAQCAEIAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAELVADCVDAMRGRVRLPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 143 VKTRIGIDDQDSYDFLCAFIRTVAERGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + QA + L  +DGVM+GR AY+N  +L  VD   S     
Sbjct: 203 YQLKRDFPALTIAINGGIKTLEQAQQHLQHLDGVMVGREAYQNPGVLAQVD---SQLFGV 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+      D +  +   M  Y  R L  G +L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 260 TAPV-----PDLF-AVVEGMYPYIERELSRGAQLGHITRHMLGLFQGLPGARQWRRFLSE 313

Query: 300 EAGASTATHHIIETAFN 316
            A    A   ++E A  
Sbjct: 314 NAHRPGADVSVVEQALT 330


>gi|310818800|ref|YP_003951158.1| tRNA-dihydrouridine synthase a [Stigmatella aurantiaca DW4/3-1]
 gi|309391872|gb|ADO69331.1| tRNA-dihydrouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 344

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 146/318 (45%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD+  +LGF   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDRHCRFFHRQLSRHTLLYTEMLTTGAVLHGDRDRLLGFEPAEHPVALQLGGSEPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E +GY+EINLNVGCPS RV  G FGACLM  P++V   +AAM +A+ IPVT
Sbjct: 74  ALAEAARIGEAWGYDEINLNVGCPSDRVQSGRFGACLMAEPELVARLVAAMREAVRIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +DD      L   V+ I   G +   +HARKA L+GLSPK+NR IP L Y++VY
Sbjct: 134 VKSRIAIDDMEEWPTLERFVRLISAEGCSRFIVHARKAWLQGLSPKENRDIPPLRYELVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG++ +  A + L  VDGVMIGRAAY+N  +L   D   S     S
Sbjct: 194 RLKAEFPSLDISINGGIKTLEAAAEHLRHVDGVMIGRAAYENPYLLAEAD---SRLFGAS 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + R D      +  +M  Y       G  L  ITRHM+GLF G P +R  R  L+  
Sbjct: 251 EAPRDRHD------VVEAMLPYMEARRSQGAPLNAITRHMLGLFQGLPGARAWRRHLSEN 304

Query: 301 AGASTATHHIIETAFNLM 318
                A   ++  A  L+
Sbjct: 305 IHKPGAGPEVVTAALALV 322


>gi|192359553|ref|YP_001981977.1| tRNA-dihydrouridine synthase A [Cellvibrio japonicus Ueda107]
 gi|190685718|gb|ACE83396.1| tRNA-dihydrouridine synthase A [Cellvibrio japonicus Ueda107]
          Length = 341

 Score =  280 bits (717), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 140/320 (43%), Positives = 198/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++W+    R F R+LT  A+LY+EM+   A+L GD+K  L ++  E PLALQ+GG+D  
Sbjct: 22  MMEWSTSDCRTFWRILTQRAVLYSEMVTTGALLYGDRKRFLDYNACEHPLALQLGGSDPR 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I E +GY+E+NLN GCPS RV  G  GACLM  P +V +CIAAM +A+SIPVT
Sbjct: 82  ALAECARIAEGWGYDEVNLNCGCPSDRVQNGMIGACLMAEPQLVAECIAAMQQAVSIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V++I  +G N   +HARKA LKGLSPK+NR+IP L YD VY
Sbjct: 142 VKHRIGIDDMDDYEGLETFVRTIAATGCNTFIVHARKAWLKGLSPKENREIPPLQYDKVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + Q+  +L  VDGVM+GR AY N  +L  VD+        S
Sbjct: 202 QLKQDFPHLNIIINGGITTLEQSQALLEHVDGVMVGREAYSNPYLLAQVDQTLYGE---S 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       +++ +   Y    L  G +L  +TRH++GL+ G P +R+ R +++  
Sbjct: 259 RPVISR------DQVTQAFIAYCEEQLAKGARLNHLTRHILGLYQGQPGARQFRRVISEH 312

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   +IE A   + E
Sbjct: 313 AHKPGAGIEVIERALAALNE 332


>gi|311281407|ref|YP_003943638.1| TIM-barrel protein, yjbN family [Enterobacter cloacae SCF1]
 gi|308750602|gb|ADO50354.1| TIM-barrel protein, yjbN family [Enterobacter cloacae SCF1]
          Length = 332

 Score =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 201/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ +  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM  A SIPVT
Sbjct: 79  ALAQCAKLAQARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDAASIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCEFINTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR  Y+N  +L TVD E F     
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLAEAKAHLQHMDGVMVGREVYQNPGILATVDREIFGASAA 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + PI           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPI----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLM 318
             A  + A  +++E A  L+
Sbjct: 309 ENAHKAGADINVLEQALQLV 328


>gi|148981615|ref|ZP_01816472.1| tRNA-dihydrouridine synthase A [Vibrionales bacterium SWAT-3]
 gi|145960800|gb|EDK26135.1| tRNA-dihydrouridine synthase A [Vibrionales bacterium SWAT-3]
          Length = 315

 Score =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 145/316 (45%), Positives = 192/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AIL G K + L +S QE PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSQQTLLYTEMVTTGAILHG-KGDFLEYSEQEHPLALQLGGSNPV 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V DC+ AM +   IP+T
Sbjct: 60  DLAACAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVADCVLAMKEVTDIPIT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDYD  
Sbjct: 120 VKTRIGIDDQDSYEFLTKFISTVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYDRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+  DL I +NGG+  + Q  + L  +DGVMIGR AY +  +L  VD+        
Sbjct: 180 YQIKKDFSDLVIAVNGGITTLEQTKEHLQHLDGVMIGREAYHSPFILAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PIK R       ++   M  Y  R L  G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 237 DTPIKKR------SQVVEEMYPYIERELSKGASLGHISRHMLGLFQSMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    A   +++TA 
Sbjct: 291 NAHKKGAGIEVMQTAL 306


>gi|260773671|ref|ZP_05882587.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
 gi|260612810|gb|EEX38013.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
          Length = 335

 Score =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 196/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT+  LLYTEM+   AI+ G K + L ++ +E P++LQ+GG++ +
Sbjct: 20  MLDWTDRHCRYFHRLLTSQTLLYTEMVTTGAIIHG-KGDFLTYNQEEHPVSLQLGGSNPT 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ +D GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + IPVT
Sbjct: 79  DLAHCAKLAQDRGYDEINLNVGCPSDRVQNGKFGACLMAEPQLVADCVAAMREVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V+ + ++ G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 139 VKTRIGIDDQDSYEFLTRFVQLVSEQGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++ L  L  +DGVM+GR AY+N  +L   D+        
Sbjct: 199 YQLKQDFPHLTIAINGGVKSLTEVLDHLQHLDGVMVGREAYQNPYLLAEADQQI---FGL 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 256 DKPIKKR------SQVVQEMYPYIEQQLTQGAYLGHITRHMLGLFQSMPGARQWRRYISE 309

Query: 300 EAGASTATHHIIETAF 315
            A    +   ++ETA 
Sbjct: 310 NAHKPGSGVEVVETAL 325


>gi|258625982|ref|ZP_05720847.1| NifR3/Smm1 family protein [Vibrio mimicus VM603]
 gi|258581730|gb|EEW06614.1| NifR3/Smm1 family protein [Vibrio mimicus VM603]
          Length = 339

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 142/316 (44%), Positives = 196/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 24  MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 83  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 143 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 203 YQIKRDFPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQI---FGL 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 260 DTPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 313

Query: 300 EAGASTATHHIIETAF 315
            A  S A   ++E A 
Sbjct: 314 NAHKSGAGLEVVEQAL 329


>gi|220935021|ref|YP_002513920.1| tRNA-dihydrouridine synthase A [Thioalkalivibrio sp. HL-EbGR7]
 gi|219996331|gb|ACL72933.1| tRNA-dihydrouridine synthase A [Thioalkalivibrio sp. HL-EbGR7]
          Length = 336

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 138/314 (43%), Positives = 193/314 (61%), Gaps = 9/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + LLYTEM+   A+L GD++  L F   E PLALQ+GG++  
Sbjct: 26  MMDWTDRHCRYFLRLISRHTLLYTEMVTTGALLHGDRERFLAFHPDEHPLALQLGGSEPG 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ ED GY+E+NLNVGCPS RV  G FGACLM  P +V DC+ AM  A  +PVT
Sbjct: 86  ELAACARMAEDHGYDEVNLNVGCPSDRVQSGRFGACLMAEPQLVADCVEAMRSACGLPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L   + ++++SG     IHARKA L+GLSP++NR++P L +D VY
Sbjct: 146 VKTRIGIDDRDSYPELTAFIDTVQRSGCRTFIIHARKAWLQGLSPRENREVPPLRHDWVY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I LNGG++D+      L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 206 RLKQDFPALEIILNGGVKDLDTVSDALRQVDGVMLGREAYHNPYVLAQVDARFYG---DA 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       ++      Y    L  G  LQ +TRH++GLF G P +R  R  ++  
Sbjct: 263 HPVPSR------HQVVERFLPYVEARLAQGVPLQAMTRHILGLFQGVPGARAWRRTISEN 316

Query: 301 AGASTATHHIIETA 314
           A  + A   +I+ A
Sbjct: 317 AHRAGAGVEVIQAA 330


>gi|307822581|ref|ZP_07652812.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
 gi|307826605|ref|ZP_07656722.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
 gi|307732393|gb|EFO03309.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
 gi|307736185|gb|EFO07031.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
          Length = 312

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 143/321 (44%), Positives = 196/321 (61%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +A LYTEM+   A++ GD    L FS  E+P+A Q+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLISQHAFLYTEMVTTGALIHGDHHRFLQFSAAERPVAFQLGGSNPR 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK++ED+GY+E+NLNVGCPS RV  G FGACLM  P++V +C+AAM +A+SIPVT
Sbjct: 61  ELAICAKMIEDYGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMAQAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     L + V ++  +G     IHARKA L GLSPK NR +P L YD+ Y
Sbjct: 121 VKSRIGIDERDSYEELVHFVSTVADAGCETFIIHARKAWLSGLSPKQNRDVPPLRYDVAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P L I LNGG+  + QA  +L  VDGVM+GR AY N  +L  VD  F       
Sbjct: 181 QIKQDFPQLEIILNGGITTLDQAEAVLAHVDGVMVGREAYHNPYLLAEVDRRFYG--ESK 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P    +  D        +  Y  +   L+ G +L  I+RH++GLFHG P +R  R  L+
Sbjct: 239 EPRSREMIMDL-------LIPYIQQQLELNDGVRLNNISRHILGLFHGEPGARGWRRHLS 291

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   +I  A    I
Sbjct: 292 ENACKPGADIKVILEALPTRI 312


>gi|238789911|ref|ZP_04633691.1| tRNA-dihydrouridine synthase A [Yersinia frederiksenii ATCC 33641]
 gi|238721984|gb|EEQ13644.1| tRNA-dihydrouridine synthase A [Yersinia frederiksenii ATCC 33641]
          Length = 343

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 146/319 (45%), Positives = 202/319 (63%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNE+NLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEVNLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKYLDGVMMGREAYQNPSILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 317 NAHKPGADVSVVEQALALV 335


>gi|126739044|ref|ZP_01754738.1| tRNA-dihydrouridine synthase A [Roseobacter sp. SK209-2-6]
 gi|126719661|gb|EBA16369.1| tRNA-dihydrouridine synthase A [Roseobacter sp. SK209-2-6]
          Length = 319

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 147/314 (46%), Positives = 196/314 (62%), Gaps = 12/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL + ALLYTEM+ A A++RG   ++L  + +E PLALQ+GGAD  
Sbjct: 1   MMDWTDRHCRFFHRLLCHEALLYTEMVTAPALVRGGALHLLDHNAEEHPLALQLGGADPV 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+   + GY+EINLN GCPS RV  G+FGA LM +PD+V DC+AAM   +++ VT
Sbjct: 61  ELAQAARHGAEAGYDEINLNCGCPSDRVQSGAFGAILMKSPDLVADCVAAMQAKVAVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I+ +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 121 VKCRIGVDDQEPREVLPRFLEKIRAAGCQRVTIHARKAWLQGLSPKENRDIPPLDYELVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           E+K+  PDL I LNGG+  + +AL  L   +DGVM+GRAAY   A +L   D        
Sbjct: 181 EMKQAFPDLHISLNGGIASLLEALPHLERGLDGVMVGRAAYHQPADILAEADPLVFGTGE 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+    D          M  Y    +  G +L QITRHM+G F G P +R  R  L+
Sbjct: 241 VTDPVAAVRD----------MLPYIEAEMSKGARLHQITRHMLGAFAGRPGARAWRRQLS 290

Query: 299 VEAGASTATHHIIE 312
                  A   ++E
Sbjct: 291 EGVSRKGAGPELVE 304


>gi|262163875|ref|ZP_06031615.1| tRNA-dihydrouridine synthase [Vibrio mimicus VM223]
 gi|262027855|gb|EEY46520.1| tRNA-dihydrouridine synthase [Vibrio mimicus VM223]
          Length = 335

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 142/316 (44%), Positives = 196/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++ ALLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLSSQALLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 79  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 139 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 199 YQIKRDLPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQI---FGL 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 256 DTPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 309

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 310 NAHKPGAGLEVVEQAL 325


>gi|168748106|ref|ZP_02773128.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755216|ref|ZP_02780223.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4401]
 gi|168766306|ref|ZP_02791313.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4486]
 gi|168774404|ref|ZP_02799411.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4196]
 gi|168780459|ref|ZP_02805466.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4076]
 gi|195935832|ref|ZP_03081214.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807897|ref|ZP_03250234.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814168|ref|ZP_03255497.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821033|ref|ZP_03261353.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4042]
 gi|209398005|ref|YP_002273589.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4115]
 gi|187769933|gb|EDU33777.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4196]
 gi|188017450|gb|EDU55572.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4113]
 gi|189001854|gb|EDU70840.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357455|gb|EDU75874.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4401]
 gi|189364132|gb|EDU82551.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4486]
 gi|208727698|gb|EDZ77299.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735445|gb|EDZ84132.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741156|gb|EDZ88838.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4042]
 gi|209159405|gb|ACI36838.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4115]
          Length = 345

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++   L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFLHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|170026071|ref|YP_001722576.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis YPIII]
 gi|169752605|gb|ACA70123.1| TIM-barrel protein, yjbN family [Yersinia pseudotuberculosis YPIII]
          Length = 345

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 202/322 (62%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K + P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKCDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 HAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|257059573|ref|YP_003137461.1| tRNA-dihydrouridine synthase A [Cyanothece sp. PCC 8802]
 gi|256589739|gb|ACV00626.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 8802]
          Length = 331

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 146/317 (46%), Positives = 201/317 (63%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+F R +T++ LLYTEMIV  AI  GD+  +LGFS +EKPL+LQ+GG D  
Sbjct: 14  MMERTDRHFRYFMRQITHHTLLYTEMIVTQAIRYGDRTKLLGFSPEEKPLSLQLGGDDPL 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I EDFGY+E+NLNVGCPS RV  G+FGACLML P++V  C+ AM K ++IP+T
Sbjct: 74  ELAECAIIAEDFGYDEVNLNVGCPSDRVQSGNFGACLMLQPELVARCVEAMQKRVNIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIGVD++     L N VK + ++G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 134 IKHRIGVDERDRYEDLVNFVKIVSEAGCQRFTVHARKAWLKGLSPKENRTIPPLRYEEVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPLT 238
           ++KK+ P LFI +NGG+  + Q    L  VDGVMIGRAAY N  +  TVD   Y  N + 
Sbjct: 194 QLKKDFPQLFIEINGGIITLDQIEHHLQFVDGVMIGRAAYDNPYLFATVDRDIYGQNIIP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +             ++   M  Y    +++G KL  I+RH++ +F G P ++  +  ++
Sbjct: 254 PTR-----------HQVVEKMLPYIDYWVNNGLKLHAISRHILAIFGGVPGTKAWKRHIS 302

Query: 299 VEAGASTATHHIIETAF 315
             A    A   +IE A 
Sbjct: 303 ENAHLPGAGVKVIEEAL 319


>gi|254796068|ref|YP_003080905.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14359]
 gi|254595468|gb|ACT74829.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14359]
          Length = 330

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++   L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFLHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 307 ENAHKAGADINVLEHALKLVAD 328


>gi|110807934|ref|YP_691454.1| tRNA-dihydrouridine synthase A [Shigella flexneri 5 str. 8401]
 gi|110617482|gb|ABF06149.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|281603466|gb|ADA76450.1| TIM-barrel protein, yjbN family [Shigella flexneri 2002017]
 gi|332998117|gb|EGK17721.1| tRNA-dihydrouridine synthase A [Shigella flexneri VA-6]
          Length = 347

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 324 ENAHKAGADINVLEHALKLVAD 345


>gi|313648753|gb|EFS13193.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2a str. 2457T]
 gi|332751993|gb|EGJ82386.1| tRNA-dihydrouridine synthase A [Shigella flexneri 4343-70]
 gi|332752162|gb|EGJ82554.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-671]
 gi|332753251|gb|EGJ83632.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2747-71]
 gi|332764755|gb|EGJ94984.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2930-71]
 gi|332999047|gb|EGK18636.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-272]
 gi|332999143|gb|EGK18730.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-218]
 gi|333014208|gb|EGK33564.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-304]
 gi|333014419|gb|EGK33770.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-227]
          Length = 345

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|322642507|gb|EFY39107.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
          Length = 310

 Score =  279 bits (714), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 145/319 (45%), Positives = 199/319 (62%), Gaps = 13/319 (4%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           WTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D ++L 
Sbjct: 1   WTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPAQLA 59

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
             AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVTVK 
Sbjct: 60  HCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKT 119

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  VY++
Sbjct: 120 RIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQL 179

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSS 241
           K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T + 
Sbjct: 180 KRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTTDAD 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+  A
Sbjct: 240 PV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLSENA 289

Query: 302 GASTATHHIIETAFNLMIE 320
             + A   ++E A  L+ +
Sbjct: 290 HKAGADVAVLEQALKLVAD 308


>gi|30064638|ref|NP_838809.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2a str. 2457T]
 gi|56480527|ref|NP_709871.2| tRNA-dihydrouridine synthase A [Shigella flexneri 2a str. 301]
 gi|30042897|gb|AAP18620.1| hypothetical protein S3574 [Shigella flexneri 2a str. 2457T]
 gi|56384078|gb|AAN45578.2| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
          Length = 339

 Score =  279 bits (714), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|188535214|ref|YP_001909011.1| tRNA-dihydrouridine synthase A [Erwinia tasmaniensis Et1/99]
 gi|188030256|emb|CAO98143.1| tRNA-dihydrouridine synthase A [Erwinia tasmaniensis Et1/99]
          Length = 332

 Score =  279 bits (714), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 147/324 (45%), Positives = 200/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLYTEM+   AI+ G K + L FS +E+P+ALQ+GG+D +
Sbjct: 16  MLDWTDRHCRYFHRQLTRQTLLYTEMVTTGAIIHG-KGDYLAFSREEQPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM    S+PVT
Sbjct: 75  ALAQCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEARLVADGIKAMRDVTSLPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 135 VKTRIGIDDQDSYAFLCDFIRTVSEQGGCEMFIIHARKAWLSGLSPKENREIPPLDYPRV 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + LNGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F   L 
Sbjct: 195 YQLKRDFPHLTLSLNGGVKTLEEAKVHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTLP 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  SM  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 255 DTDPV----------AVVRSMYPYIERELAKGTYLGHVTRHMLGLFQGVPGARQWRRYLS 304

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +L+ + +
Sbjct: 305 ENAHKAGAGVEVVEKALSLVADKV 328


>gi|54310405|ref|YP_131425.1| tRNA-dihydrouridine synthase A [Photobacterium profundum SS9]
 gi|46914846|emb|CAG21623.1| putative NifR3/Smm1 family protein [Photobacterium profundum SS9]
          Length = 346

 Score =  279 bits (714), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 204/316 (64%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AI+ G K + L F+ +E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRLLSDNALLYTEMVTTGAIIHG-KGDFLTFNEEENPVALQLGGSNPV 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   D+V  C+++M + + IPVT
Sbjct: 91  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEADLVALCVSSMREVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ +KSG +   +HARKA LKGLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDEQDSYQFLVDFIGTVNEKSGCDNFTVHARKAWLKGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P++ + +NGG++   +  + L  +DGVM+GR AY+N  ++  VD+        
Sbjct: 211 YQLKRDFPNIIMAINGGIKTFDEMEEHLKHMDGVMVGREAYQNPYLMAEVDQRL---FGS 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S PI  R      R+ + +M  Y  R L +G KL  ITRHM+GLF G P  R+ R  ++ 
Sbjct: 268 SKPIIKR------REAAEAMFPYIERQLANGSKLGHITRHMLGLFQGIPGGRQWRRYISE 321

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 322 NAHKPGSGIEVVQRAL 337


>gi|38604722|sp|Q7UBC5|DUSA_SHIFL RecName: Full=tRNA-dihydrouridine synthase A
          Length = 330

 Score =  279 bits (714), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 307 ENAHKAGADINVLEHALKLVAD 328


>gi|324112315|gb|EGC06293.1| tRNA dihydrouridine synthase A [Escherichia fergusonii B253]
          Length = 333

 Score =  279 bits (714), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 149/322 (46%), Positives = 204/322 (63%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GL+PK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLNPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L+ VD E F++   
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKMHLQHMDGVMVGREAYQNPGILSAVDREIFAS--- 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                 T  D D    + A M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 255 ----TDTDTDADPVAVVRA-MYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 309

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A  +++E A  L+ +
Sbjct: 310 ENAHKPGADINVLEHALKLVAD 331


>gi|254466832|ref|ZP_05080243.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium Y4I]
 gi|206687740|gb|EDZ48222.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium Y4I]
          Length = 316

 Score =  279 bits (713), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 142/317 (44%), Positives = 199/317 (62%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L F+ +E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSRETLLYTEMVTAPALVRGGALHLLEFNAEEHPVALQLGGSDPG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++  + GY+EINLN GCPS RV  G+FGA LM  P++V DC+AAM + + + VT
Sbjct: 61  ELAEAARLGAEAGYDEINLNCGCPSDRVQSGAFGAVLMQTPELVADCVAAMRETVDVDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L   ++ I+ +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 121 VKCRIGVDEQEPEEVLPEFLEKIRAAGCGRVTIHARKAWLQGLSPKENRDIPPLDYELVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   PDL + +NGG+  +++A   L   +DGVM+GRAAY   A +L   D       T
Sbjct: 181 RMKAAFPDLHVSINGGIATLAEAKAHLDRGLDGVMVGRAAYHQPADVLCAADPEIYGTGT 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P +              M  Y    L  G +L QITRHM+GLF G P +R+ R +L+
Sbjct: 241 VSDPAEA----------VRQMLPYIEARLSEGARLNQITRHMLGLFAGKPGARQWRRMLS 290

Query: 299 VEAGASTATHHIIETAF 315
             A  + A   +++ A 
Sbjct: 291 EGACRAGAGPELVQEAL 307


>gi|90414453|ref|ZP_01222429.1| putative NifR3/Smm1 family protein [Photobacterium profundum 3TCK]
 gi|90324458|gb|EAS41017.1| putative NifR3/Smm1 family protein [Photobacterium profundum 3TCK]
          Length = 346

 Score =  279 bits (713), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 141/317 (44%), Positives = 205/317 (64%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AI+ G K + L F+ +E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRLLSDNALLYTEMVTTGAIIHG-KGDFLTFNEEENPVALQLGGSNPV 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   D+V  C+++M + + IPVT
Sbjct: 91  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEADLVALCVSSMREVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ +KSG +   +HARKA LKGLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDEQDSYQFLVDFIGTVNEKSGCDNFTVHARKAWLKGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P+L + +NGG++   +  + L  +DGVM+GR AY+N  ++  VD+        
Sbjct: 211 YQLKRDFPNLIMAINGGIKTFDEMEEHLNHMDGVMVGREAYQNPYLMAEVDQRL---FGC 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S PI  R      R+ + +M  Y  R L +G KL  ITRHM+GLF G P  R+ R  ++ 
Sbjct: 268 SKPIIKR------REAAEAMFPYIERQLANGSKLGHITRHMLGLFQGIPGGRQWRRYISE 321

Query: 300 EAGASTATHHIIETAFN 316
            A    +   +++ A +
Sbjct: 322 NAHKPGSGIEVVQYALD 338


>gi|320649492|gb|EFX18016.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H- str. H
           2687]
          Length = 339

 Score =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDRTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|77166407|ref|YP_344932.1| tRNA-dihydrouridine synthase A [Nitrosococcus oceani ATCC 19707]
 gi|254435191|ref|ZP_05048698.1| TIM-barrel protein, yjbN family [Nitrosococcus oceani AFC27]
 gi|76884721|gb|ABA59402.1| tRNA-U16,U17-dihydrouridine synthase [Nitrosococcus oceani ATCC
           19707]
 gi|207088302|gb|EDZ65574.1| TIM-barrel protein, yjbN family [Nitrosococcus oceani AFC27]
          Length = 337

 Score =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 145/321 (45%), Positives = 200/321 (62%), Gaps = 15/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RL+++ ALLYTEM+ A A++ G++   L +   E PLALQ+GG+   
Sbjct: 27  MMEWTDRHCRYFLRLISHRALLYTEMVTAGALIHGNRARFLAYHKSEHPLALQLGGSHPE 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ ED+G++E+NLNVGCPS RV  G FGACLM  P++V +C+AAM +A  IPVT
Sbjct: 87  ELALCAQMAEDYGFDEVNLNVGCPSNRVQSGRFGACLMAEPELVAECVAAMAQATQIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q    AL + + ++ ++G     IHARKA L+GLSPK+NR+ P L YD+V 
Sbjct: 147 VKTRIGIDEQDSYEALDHFISTVAQAGCRTFIIHARKAWLQGLSPKENREKPPLRYDVVR 206

Query: 181 EIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            IK++ P L + +NGG   LE++S+ L++L   DGVMIGRAAY N  +L  VD  F    
Sbjct: 207 TIKQDFPQLTVIINGGITTLEEISEHLELL---DGVMIGRAAYHNPYLLAQVDRNFYGDF 263

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P  TR       +I  +   Y A  L  G  L  +TRH++GLF G P +R  R  L
Sbjct: 264 ---HPFLTR------HEIIEAFLPYVAEQLVQGVYLNHMTRHILGLFQGQPGARAWRRHL 314

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +  A    A   II  A   M
Sbjct: 315 SENAHRPGAGIEIIREALRQM 335


>gi|218246535|ref|YP_002371906.1| tRNA-dihydrouridine synthase A [Cyanothece sp. PCC 8801]
 gi|218167013|gb|ACK65750.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 8801]
          Length = 331

 Score =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 145/317 (45%), Positives = 198/317 (62%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+F R +T + LLYTEMIV  AI  GD+  +LGFS +EKPL+LQ+GG D  
Sbjct: 14  MMERTDRHFRYFMRQITQDTLLYTEMIVTQAIRYGDRTKLLGFSPEEKPLSLQLGGDDPQ 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I EDFGY+E+NLNVGCPS RV  G+FGACLML P++V  C+ AM K ++IP+T
Sbjct: 74  ELAECAMIAEDFGYDEVNLNVGCPSDRVQSGNFGACLMLQPELVARCVEAMQKKVNIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIGVD++     L N VK +  +G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 134 IKHRIGVDERDRYEDLANFVKIVSDAGCQRFTVHARKAWLKGLSPKENRTIPPLKYEEVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPLT 238
           ++K+E   LFI +NGG+  + Q    L  VDGVMIGRAAY N  +  TVD   Y  N + 
Sbjct: 194 QLKQEFSQLFIEINGGIITLDQIEHHLQFVDGVMIGRAAYDNPYLFATVDRDIYGQNIIP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +             ++   M  Y    +++G KL  I+RH++ +F G P ++  +  ++
Sbjct: 254 PTR-----------HQVVEKMLPYIDYWVNNGLKLHAISRHILAIFGGVPGTKAWKRHIS 302

Query: 299 VEAGASTATHHIIETAF 315
             A    A   +IE A 
Sbjct: 303 ENAHLPGAGVKVIEEAL 319


>gi|330954517|gb|EGH54777.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae Cit 7]
          Length = 312

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 137/300 (45%), Positives = 192/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSKAA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 61  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 121 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L S DGVM+GR AY N  +L  VD+        +
Sbjct: 181 QLKSDFPDLEIVLNGGIKTLEQCSEHLQSFDGVMLGREAYHNPYLLAHVDQQL---FGST 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 238 APVISRYDA------LESMRPYIAEHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 291


>gi|262380225|ref|ZP_06073380.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SH164]
 gi|262298419|gb|EEY86333.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SH164]
          Length = 335

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 194/316 (61%), Gaps = 15/316 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRFFARL   N +LYTEM+   AIL GD    L ++ +E P+ LQ+GG+   
Sbjct: 16  MMDWTTRDYRFFARLFNPNMILYTEMVTTGAILFGDAGRHLNYNQEEHPVVLQLGGSSPK 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ ED+GYNE+NLNVGCPS RV     GACLM  P++V +CI+AM +A++IPVT
Sbjct: 76  DLATCTKMAEDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPELVAECISAMRQAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G N   +HAR A+L+GLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAKTGCNNFIVHARIALLQGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++ +++  + L  VDGVMIGR AY N  +L  + E ++ P+   
Sbjct: 196 RLKQERPDLTIEINGGVKTLAETQEHLKHVDGVMIGREAYHNPYLLAELGELWNLPMPDR 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        +I   M  Y A+ L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 256 F------------EIMEQMLPYIAKRLEEGAPLSVITRHILGLFQYLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFN 316
            G +  T+  +E A  
Sbjct: 302 -GGNAKTYADVENAIQ 316


>gi|115372138|ref|ZP_01459449.1| tRNA-dihydrouridine synthase A [Stigmatella aurantiaca DW4/3-1]
 gi|115370840|gb|EAU69764.1| tRNA-dihydrouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 330

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 145/317 (45%), Positives = 190/317 (59%), Gaps = 9/317 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH RFF R L+ + LLYTEM+   A+L GD+  +LGF   E P+ALQ+GG++ + 
Sbjct: 1   MDWTDRHCRFFHRQLSRHTLLYTEMLTTGAVLHGDRDRLLGFEPAEHPVALQLGGSEPAA 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA+I E +GY+EINLNVGCPS RV  G FGACLM  P++V   +AAM +A+ IPVTV
Sbjct: 61  LAEAARIGEAWGYDEINLNVGCPSDRVQSGRFGACLMAEPELVARLVAAMREAVRIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RI +DD      L   V+ I   G +   +HARKA L+GLSPK+NR IP L Y++VY 
Sbjct: 121 KSRIAIDDMEEWPTLERFVRLISAEGCSRFIVHARKAWLQGLSPKENRDIPPLRYELVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K E P L I +NGG++ +  A + L  VDGVMIGRAAY+N  +L   D   S     S 
Sbjct: 181 LKAEFPSLDISINGGIKTLEAAAEHLRHVDGVMIGRAAYENPYLLAEAD---SRLFGASE 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
             + R D      +  +M  Y       G  L  ITRHM+GLF G P +R  R  L+   
Sbjct: 238 APRDRHD------VVEAMLPYMEARRSQGAPLNAITRHMLGLFQGLPGARAWRRHLSENI 291

Query: 302 GASTATHHIIETAFNLM 318
               A   ++  A  L+
Sbjct: 292 HKPGAGPEVVTAALALV 308


>gi|255320921|ref|ZP_05362095.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SK82]
 gi|255302090|gb|EET81333.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SK82]
          Length = 340

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 194/316 (61%), Gaps = 15/316 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRFFARL   N +LYTEM+   AIL GD    L ++ +E P+ LQ+GG+   
Sbjct: 21  MMDWTTRDYRFFARLFNPNMILYTEMVTTGAILFGDAGRHLNYNQEEHPVVLQLGGSSPK 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ ED+GYNE+NLNVGCPS RV     GACLM  P++V +CI+AM +A++IPVT
Sbjct: 81  DLATCTKMAEDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPELVAECISAMRQAVNIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G N   +HAR A+L+GLSPK+NR++P L Y+ VY
Sbjct: 141 VKHRIGIDDMQSYEEMLHFVDTVAKTGCNNFIVHARIALLQGLSPKENREVPPLRYEDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++ +++  + L  VDGVMIGR AY N  +L  + E ++ P+   
Sbjct: 201 RLKQERPDLTIEINGGVKTLAETQEHLKHVDGVMIGREAYHNPYLLAELGELWNLPMPDR 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        +I   M  Y A+ L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 261 F------------EIMEQMLPYIAKRLEEGAPLSVITRHILGLFQYLPGARKWRQALS-- 306

Query: 301 AGASTATHHIIETAFN 316
            G +  T+  +E A  
Sbjct: 307 -GGNAKTYADVENAIQ 321


>gi|289208454|ref|YP_003460520.1| TIM-barrel protein, yjbN family [Thioalkalivibrio sp. K90mix]
 gi|288944085|gb|ADC71784.1| TIM-barrel protein, yjbN family [Thioalkalivibrio sp. K90mix]
          Length = 329

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 148/314 (47%), Positives = 194/314 (61%), Gaps = 10/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   R F RLLT  ALLYTEM+ A+A++ GD+  +LG    E PLALQ+GG+D  
Sbjct: 17  MMDWTDSWCRRFHRLLTRRALLYTEMVHANAVIHGDRDRLLGHVAAEHPLALQLGGSDPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  + G++EINLNVGCPS RV  G+FGACLM  P+ V   + AM  A+ +PVT
Sbjct: 77  TLAQAARIAAERGFDEINLNVGCPSDRVQSGTFGACLMAQPEQVARMVRAMQDAVDVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     LRN V+++ + G     +HARKA L+GLSPKDNR +P LDY+ V+
Sbjct: 137 VKHRIGIDEQDSEADLRNFVETVARGGCRHFIVHARKAWLQGLSPKDNRDVPPLDYERVF 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L I LNGGL+D+  A   L  VDGVM GR AY    +L  VD  F +   G 
Sbjct: 197 RLKAEFPELTIVLNGGLDDVRVAHGYLERVDGVMFGRLAYHQPWVLAEVDRLFFDETGGV 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               TR        +   + D A      G  L ++TRH++GLFHG P +R+ R ILT  
Sbjct: 257 ----TR------EAVLQGLIDMAREMRAKGVPLARLTRHVLGLFHGEPGARQWRRILTEG 306

Query: 301 AGASTATHHIIETA 314
           A  + A   +IE A
Sbjct: 307 AHRADAGPELIERA 320


>gi|298486443|ref|ZP_07004503.1| tRNA dihydrouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298158920|gb|EFH99980.1| tRNA dihydrouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 339

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 193/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|289627280|ref|ZP_06460234.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289650430|ref|ZP_06481773.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330869475|gb|EGH04184.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 339

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 191/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|320329184|gb|EFW85181.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 339

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 193/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|262377397|ref|ZP_06070620.1| tRNA-dihydrouridine synthase A [Acinetobacter lwoffii SH145]
 gi|262307627|gb|EEY88767.1| tRNA-dihydrouridine synthase A [Acinetobacter lwoffii SH145]
          Length = 341

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 143/318 (44%), Positives = 198/318 (62%), Gaps = 16/318 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N ++YTEM+   AI+ GD K  L F+ +E+P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVIMYTEMVTTGAIIYGDAKRHLDFNAEEQPIVLQLGGSNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ +D+GYNE+NLNVGCPS RV     GACLM  PD+V +CIA M  A+ IPVT
Sbjct: 80  DLAICTKMAQDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIAEMRHAVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G N   +HAR A+LKGLSPK+NR +P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAKTGCNNFIVHARIALLKGLSPKENRDVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++  ++ LK L  VDGVMIGR AY N  +L  + + ++     +
Sbjct: 200 RLKQERPDLLIEINGGIKTYAETLKHLKHVDGVMIGREAYHNPYLLAELGQLWN----LN 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y A+ +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 256 AP--DRFD------IMQQMLPYIAQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETA-FNL 317
            G +  T   +ETA FN+
Sbjct: 306 -GGNAKTLKDVETALFNI 322


>gi|295095415|emb|CBK84505.1| tRNA-U16,U17-dihydrouridine synthase [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 331

 Score =  278 bits (711), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E+ GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGNAHLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG+  + +A   L  +DGVM+GR AY+N  +L TVD E F     
Sbjct: 198 YQLKRDFPHLTMSINGGITSLDEAKAHLEHMDGVMVGREAYQNPGILATVDREIFGVDGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DTDPV----------AVVRAMYPYIERELSHGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 308 ENAHKAGADIEVLEHALRLVAD 329


>gi|251788352|ref|YP_003003073.1| TIM-barrel protein, yjbN family [Dickeya zeae Ech1591]
 gi|247536973|gb|ACT05594.1| TIM-barrel protein, yjbN family [Dickeya zeae Ech1591]
          Length = 344

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 148/319 (46%), Positives = 202/319 (63%), Gaps = 17/319 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   AIL G K + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRLLSQHALLYTEMVTTGAILHG-KGDYLAYSDEEHPLALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+AAM + + IPVT
Sbjct: 92  ALAQCALLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAQLVADCVAAMRERVGIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIRTVSEQGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ ++ A + L  VDGVM+GR AY+N  ML  VD E F     
Sbjct: 212 YQLKRDFPSLTVAINGGIKTLADAQQHLQHVDGVMVGREAYQNPGMLAQVDSELFG---- 267

Query: 239 GSSPIKTRVDKDFWRKISA--SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   VD+    +++   +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  
Sbjct: 268 --------VDRAVPDQVAVVQAMYPYIERELSGGASLGHITRHMLGLFQGIPGARQWRRY 319

Query: 297 LTVEAGASTATHHIIETAF 315
           L+  A    A   ++E A 
Sbjct: 320 LSENAHKPGADAAVVERAL 338


>gi|238764115|ref|ZP_04625069.1| tRNA-dihydrouridine synthase A [Yersinia kristensenii ATCC 33638]
 gi|238697652|gb|EEP90415.1| tRNA-dihydrouridine synthase A [Yersinia kristensenii ATCC 33638]
          Length = 343

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 146/319 (45%), Positives = 202/319 (63%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHG-KGDYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMAEANLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L   V+++   G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDELDSYEFLCEFVQTVAGRGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 317 NAHKPGADVSVVEQALALV 335


>gi|330989295|gb|EGH87398.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 339

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 191/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCGEHLQTFDGVMLGREAYHNPYLLAQVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|166365548|ref|YP_001657821.1| tRNA-dihydrouridine synthase A [Microcystis aeruginosa NIES-843]
 gi|166087921|dbj|BAG02629.1| dihydrouridine synthase TIM-barrel protein [Microcystis aeruginosa
           NIES-843]
          Length = 342

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 147/316 (46%), Positives = 197/316 (62%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R ++   LLYTEMI   AI  GD+  +LGFS  EKPLALQ+GG +  
Sbjct: 21  MMDYTDRHFRYFWRQISLRPLLYTEMITTMAIKHGDRYKLLGFSLAEKPLALQLGGDNPY 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AKI ED GY+E+NLNVGCPS+RV EG+FGACLM NP++V   I+AM +A+SIPVT
Sbjct: 81  LLAECAKIAEDMGYDEVNLNVGCPSSRVKEGNFGACLMANPELVARGISAMNQAVSIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D Q     + N V+ +  +G     IHARKA L+GLSPK+NR +P L YD VY
Sbjct: 141 VKQRIGIDHQDSYENMANFVRIVADAGCQRFTIHARKAWLQGLSPKENRTVPPLRYDDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P LFI +NGG+ ++ QA + L  VD VMIGRAAY N  +  TVD  F    + +
Sbjct: 201 RLKNQFPHLFIEINGGIINLEQARQHLQLVDAVMIGRAAYDNPYLFATVDRDFYGE-SVT 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +  V K         M  Y    +  G KL QI++H++ LF G P ++  +  ++  
Sbjct: 260 PPTREEVIK--------KMLPYIDEWVSKGYKLHQISKHLLQLFAGQPGTKAWKRYISEN 311

Query: 301 AGASTATHHIIETAFN 316
           +    A   +I  A  
Sbjct: 312 SHFPGADSGVIWQALQ 327


>gi|302184838|ref|ZP_07261511.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. syringae
           642]
          Length = 312

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 193/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 61  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 121 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 181 QLKSDFPDLEIVLNGGIKTLEQCSEHLQAFDGVMLGREAYHNPYLLAHVDQQL---FGST 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 238 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 291


>gi|258622397|ref|ZP_05717420.1| NifR3/Smm1 family protein [Vibrio mimicus VM573]
 gi|258585311|gb|EEW10037.1| NifR3/Smm1 family protein [Vibrio mimicus VM573]
          Length = 339

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 195/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 24  MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 83  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 143 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 203 YQIKRDFPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQI---FGL 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 260 DTPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 313

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 314 NAHKPGAGLEVVEQAL 329


>gi|170748394|ref|YP_001754654.1| tRNA-dihydrouridine synthase A [Methylobacterium radiotolerans JCM
           2831]
 gi|170654916|gb|ACB23971.1| dihydrouridine synthase DuS [Methylobacterium radiotolerans JCM
           2831]
          Length = 319

 Score =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 148/299 (49%), Positives = 193/299 (64%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  A LYTEM+   A+L G ++ +LGF+  E P+A+Q+GG+D  
Sbjct: 1   MMDWTDRHCRAFHRSLSARARLYTEMVTTGAVLHGPRERLLGFAAVEHPVAVQLGGSDPG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I  D GY+E+NLNVGCPS RV EG FGACLM  P +VGDC+AAM  A+ +PVT
Sbjct: 61  ELAQAARIAADLGYDEVNLNVGCPSDRVQEGRFGACLMREPALVGDCVAAMKAAVPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  ++  +GV+G+ +HARKA L+GLSPK+NR +P LDY    
Sbjct: 121 VKCRIGVDDQDPEAALDALADAVVAAGVDGLIVHARKAWLQGLSPKENRDVPPLDYGRAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  P L I +NGGL D+  A   L  VDGVM+GRAAY   A+L  VD + F  P   
Sbjct: 181 RLKRRLPGLPIAVNGGLRDLDSARARLAEVDGVMVGRAAYTEPALLLGVDPDLFGVPAPA 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                     D +  + A    Y A  L  G +L  +TRHM+GLF+G P +R  R  L+
Sbjct: 241 P---------DVFAAV-AMFEPYIAACLARGERLHAVTRHMLGLFNGRPGARAFRRHLS 289


>gi|159029932|emb|CAO90311.1| dus2 [Microcystis aeruginosa PCC 7806]
          Length = 352

 Score =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 197/316 (62%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R ++   LLYTEMI   AI  GD+  +LGFS  EKPLALQ+GG +  
Sbjct: 34  MMDYTDRHFRYFLRQISRRPLLYTEMITTMAIKHGDRYKLLGFSLAEKPLALQLGGDNPY 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AKI E  GY+E+NLNVGCPS+RV EG+FGACLM NP++V   I+AM +A+SIPVT
Sbjct: 94  LLAECAKIAEYMGYDEVNLNVGCPSSRVKEGNFGACLMANPELVARGISAMNQAVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     + N V+ +  +G     IHARKA L+GLSPK+NR +P L YD VY
Sbjct: 154 VKQRIGIDDQDSYENMANFVRIVADAGCQRFTIHARKAWLQGLSPKENRTVPPLRYDDVY 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P LFI +NGG+ ++ QA + L  VD VMIGRAAY N  +  TVD  F    + +
Sbjct: 214 RLKNQFPHLFIEINGGIINLEQARQHLQLVDAVMIGRAAYDNPYLFATVDRDFYGE-SVT 272

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +  + K         M  Y    +  G KL QI++H++ LF G P ++  +  ++  
Sbjct: 273 PPTREEIIK--------KMLPYIDEWVSKGYKLHQISKHLLQLFAGQPGTKAWKRYISEN 324

Query: 301 AGASTATHHIIETAFN 316
           +    A   +I  A  
Sbjct: 325 SHFPGADSGVIWQALQ 340


>gi|123444030|ref|YP_001008000.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090991|emb|CAL13874.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 342

 Score =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 147/319 (46%), Positives = 201/319 (63%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  +LLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQSLLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAELRGYNEINLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY  V
Sbjct: 146 VKTRIGIDELDSYEFLCEFVQTVAERGECDIFTIHARKAWLSGLSPKENREVPPLDYARV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  VDGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKRDFPTLTIAINGGVKTLAEAKEHLKYVDGVMMGREAYQNPTILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALFPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 317 NAHKPGADVSVVEQALALV 335


>gi|37528192|ref|NP_931537.1| tRNA-dihydrouridine synthase A [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787629|emb|CAE16736.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 345

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 200/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S QE P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEQEHPIALQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AKI ++ GY+EINLNVGCPS RV  G FGACLM   ++V DC+ AM   +++PVT
Sbjct: 92  ALAHCAKIAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAELVADCVKAMQDVVNVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVK-SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + +   ++ SG N   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDEQDSYQFLCDFIDIVVQHSGCNIFTMHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L I +NGG++ + +A + L  VDG+MIGR AY+N ++L  VD         
Sbjct: 212 YQLKKDFPQLTIAINGGIKSLEEAKQHLQHVDGIMIGREAYQNPSILAQVDHEL---FDA 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S P+   V       +  ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 SMPVVNTV------AVVKALYPYIEQELSKGTYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  ++ E +
Sbjct: 323 NAHKPGADISVVEQALAMVTERM 345


>gi|330967777|gb|EGH68037.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 336

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 139/301 (46%), Positives = 195/301 (64%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 85  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++ ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 145 VKHRIGINGRDSYAELCDFVGTVHEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 205 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQ----LFGS 260

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R       +   SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V
Sbjct: 261 VAPVISR------HEALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSV 314

Query: 300 E 300
           +
Sbjct: 315 D 315


>gi|330878546|gb|EGH12695.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 339

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 139/301 (46%), Positives = 195/301 (64%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++ ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVHEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 208 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQ----LFGS 263

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R       +   SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V
Sbjct: 264 VAPVISR------HEALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSV 317

Query: 300 E 300
           +
Sbjct: 318 D 318


>gi|289679765|ref|ZP_06500655.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. syringae
           FF5]
          Length = 339

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/300 (45%), Positives = 193/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDESEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ ++ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FGST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|153949073|ref|YP_001402722.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
 gi|152960568|gb|ABS48029.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
          Length = 345

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 150/323 (46%), Positives = 204/323 (63%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K + P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD E F +   
Sbjct: 206 YQLKCDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDS--- 262

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+
Sbjct: 263 -NAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHVLGIFQGIPGARQWRRHLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++E A  L+  S
Sbjct: 316 ENAHKPGAGVSVVEEALALVSPS 338


>gi|300724718|ref|YP_003714043.1| tRNA -dihydrouridine synthase A [Xenorhabdus nematophila ATCC
           19061]
 gi|297631260|emb|CBJ91955.1| tRNA-dihydrouridine synthase A [Xenorhabdus nematophila ATCC 19061]
          Length = 342

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 202/323 (62%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  ALLYTEM+   AI+ G K + L ++ QE PLALQ+GG++  
Sbjct: 30  MLDWTDRHCRYFHRLLSKEALLYTEMVTTGAIIHG-KGDYLAYNEQEHPLALQLGGSEPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I ++ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   + IPVT
Sbjct: 89  ALAQCARIAQEKGYDEINLNVGCPSDRVQNGRFGACLMGDAALVADCVKAMQDVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + +++ +K S  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 149 VKTRIGIDEQDSYEFLCDFIETVVKNSDCDNFVIHARKAWLSGLSPKENREIPPLDYPRV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K + P L   +NGG++ + +A + L  VDGVMIGR AY+N +ML  VD    N    
Sbjct: 209 YQLKNDFPQLTFSINGGIKSLEEAKQHLQYVDGVMIGREAYQNPSMLAHVDRELFN---Q 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +SP+   V+         ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 266 TSPVTNTVEA------VQALYPYIEQELSKGTYLGHITRHILGIFQGIPGARQWRRHLSE 319

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   ++E A  ++ E +
Sbjct: 320 NAHKPGSDIRVVEKALEMVTERI 342


>gi|227326002|ref|ZP_03830026.1| tRNA-dihydrouridine synthase A [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 340

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 146/320 (45%), Positives = 200/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G K + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHG-KGDYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + G  +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCDFIQTVAERGECDTFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F   + 
Sbjct: 208 YQLKRDFPALTLAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFG--ID 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P    V +        +M  Y  R L SG  L  ITRHM+G+F G P +R+ R  L+
Sbjct: 266 AATPDLAGVVR--------AMYPYIERELSSGASLGHITRHMLGMFQGIPGARQWRRYLS 317

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 318 ENAHKPGADAAVVERALALV 337


>gi|145300509|ref|YP_001143350.1| tRNA-dihydrouridine synthase A [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853281|gb|ABO91602.1| tRNA-dihydrouridine synthase A [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 331

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 140/311 (45%), Positives = 193/311 (62%), Gaps = 10/311 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + LG+S QE+P++LQ+GG++ +
Sbjct: 14  MLDWTDRHCRYFHRLMTRQTLLYTEMVTTGAIIHG-KGDYLGYSEQERPVSLQLGGSNPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+ AM   + IPVT
Sbjct: 73  DLAHCAKLARERGYDEINLNVGCPSDRVQNGRFGACLMGEPALVADCVKAMRDVVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  ++ ++ +G +   +HARKA L GLSP++NR+IP LDY  VY
Sbjct: 133 VKTRIGIDDQDSYEFLQTFIEQVRDAGCDTFIVHARKAWLSGLSPRENREIPPLDYPRVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I LNGG+  + Q L+ L  VDGVM+GR AY+N  +L  VD   S     +
Sbjct: 193 RVKQDYPELTIALNGGVTSLEQTLEHLQQVDGVMMGREAYQNPYILAQVD---SQLFGLA 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S I +R       ++   M  Y  + L  G  L  +TRHM+GLF     +R  R  L+  
Sbjct: 250 SEIPSR------HEVVRMMLPYMEQELAKGNYLSHMTRHMLGLFQNMQGARAWRRHLSEN 303

Query: 301 AGASTATHHII 311
           A    A   ++
Sbjct: 304 ACKQGAGIQVV 314


>gi|254508997|ref|ZP_05121103.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus 16]
 gi|219548101|gb|EED25120.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus 16]
          Length = 315

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 147/323 (45%), Positives = 194/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIYG-KGDFLAYNEEEHPVALQLGGSNPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMRDVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +  +L  L  VDGVM+GR AY+N  +L  VD+        
Sbjct: 180 YQLKKDFAHLNIAVNGGVKTLGDSLSHLEHVDGVMVGREAYQNPYLLAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y    L  G  L  ITRHMIGLF   P +R+ R  ++ 
Sbjct: 237 DKPIKKR------SQVVKEMYPYIEAQLSKGAYLGHITRHMIGLFQAMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A   + + L
Sbjct: 291 NAHKPGAGIEVVEAALAKIPQEL 313


>gi|332163190|ref|YP_004299767.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318603925|emb|CBY25423.1| tRNA dihydrouridine synthase A [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325667420|gb|ADZ44064.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330861940|emb|CBX72109.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica W22703]
          Length = 348

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 146/319 (45%), Positives = 201/319 (63%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 92  ALAHCAKLAELRGYNEINLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L   V+++ + G   I+ IHARKA L GLSPK+NR++P L+Y+ V
Sbjct: 152 VKTRIGIDELDSYEFLCEFVQTVAERGECDIFTIHARKAWLSGLSPKENREVPPLNYERV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  VDGVM+GR AY+N  +LT VD    +P   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLAEAKEHLKHVDGVMMGREAYQNPTILTQVDRELFDP--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 NAPVVDSV------KAIETLFPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 323 NAHKPGADVSVVEQALALV 341


>gi|320324818|gb|EFW80890.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. glycinea
           str. B076]
          Length = 339

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 192/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPGLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|238752153|ref|ZP_04613635.1| tRNA-dihydrouridine synthase A [Yersinia rohdei ATCC 43380]
 gi|238709626|gb|EEQ01862.1| tRNA-dihydrouridine synthase A [Yersinia rohdei ATCC 43380]
          Length = 348

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 146/319 (45%), Positives = 203/319 (63%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KGDYLAYSEQDHPVALQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM    +V DCI AM  A++IPVT
Sbjct: 92  ALAHCAKLAELRGYNEINLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDAVTIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 152 VKTRIGIDQLDSYEFLCEFVQTVAEQGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDP--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      +   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 NAPVIDPV------QAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 323 NAHKPGADVSVVEQALALV 341


>gi|108761431|ref|YP_630504.1| tRNA-dihydrouridine synthase A [Myxococcus xanthus DK 1622]
 gi|108465311|gb|ABF90496.1| tRNA-dihydrouridine synthase A [Myxococcus xanthus DK 1622]
          Length = 332

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 137/315 (43%), Positives = 194/315 (61%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR+ R+F R L+ + LLYTEM+   AIL GD++ +LG+   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDRNCRYFHRQLSRHTLLYTEMVTTGAILHGDRERLLGYDAAEHPVALQLGGSEPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+A+I E +GY+EINLNVGCPS RV  G FGACLM  PD+V   + AM +A+SIPVT
Sbjct: 74  ALAESARIGEQWGYDEINLNVGCPSDRVQSGRFGACLMAEPDLVARLVGAMREAVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +D+      L   ++ +  +G     +HARKA L+GLSPK+NR +P L YD+V+
Sbjct: 134 VKSRIAIDELEEWPTLEGFIRKVSAAGCTRFIVHARKAWLQGLSPKENRDVPPLRYDLVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG++ +  A + L  VDGVM+GRA Y+N  +L   D  F      +
Sbjct: 194 RLKVEFPHLDISINGGIKTLDAAAEQLRHVDGVMMGRAPYENPYLLAEADRRF---FGAT 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+  R       ++  +M  Y  + +  G  L  ITRHM+GLF G P +R  R  L+  
Sbjct: 251 TPVPQR------HEVVEAMLPYIEKAMLRGAPLGAITRHMLGLFQGLPGARAWRRHLSEN 304

Query: 301 AGASTATHHIIETAF 315
           A    A   ++  A 
Sbjct: 305 AHKQGAGPEVVVAAL 319


>gi|288940773|ref|YP_003443013.1| TIM-barrel protein, yjbN family [Allochromatium vinosum DSM 180]
 gi|288896145|gb|ADC61981.1| TIM-barrel protein, yjbN family [Allochromatium vinosum DSM 180]
          Length = 310

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 193/301 (64%), Gaps = 9/301 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + LLYTEMI   A++ GD++  L +   E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRYFLRLISRHTLLYTEMITTGALIHGDRERFLRYDPAEHPVALQLGGSDSE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E++GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM  A+ +PVT
Sbjct: 61  DLARCARMAEEWGYDEINLNVGCPSDRVQNGRFGACLMAEPVLVAECVTAMRAAVRVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     L + V  + ++G + I +HARKA LKGLSPK+NR IP L Y+IV 
Sbjct: 121 VKHRIGIDERDSYAELVDFVGRLSEAGCDAIIVHARKAWLKGLSPKENRDIPPLRYEIVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+E +  A+  L  +DGVMIGRAAY N  +L   D         +
Sbjct: 181 DLKRDFPQLPIVINGGIETLDAAVDFLSDLDGVMIGRAAYHNPWILAEADRRV---FGDT 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  TR      R++  +   YA R L +G  L  ++RH++GLF G P +R  R  ++ +
Sbjct: 238 HPAPTR------RQVLEAFIPYAERQLAAGVPLNAMSRHLLGLFQGQPGARAWRRRISEQ 291

Query: 301 A 301
           A
Sbjct: 292 A 292


>gi|238892522|ref|YP_002917256.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae NTUH-K2044]
 gi|238544838|dbj|BAH61189.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 331

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D  
Sbjct: 19  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 198 WQLKRDFPHLTMAINGGIKSLDEARAQLEHMDGVMVGREAYQNPGILASVDREIFGVAGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 308 ENAHKAGADIAVLEHALKLVAD 329


>gi|254488703|ref|ZP_05101908.1| tRNA-dihydrouridine synthase A [Roseobacter sp. GAI101]
 gi|214045572|gb|EEB86210.1| tRNA-dihydrouridine synthase A [Roseobacter sp. GAI101]
          Length = 345

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 196/320 (61%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL++   LLYTEM+ + A++RG   ++L  S +E P+ALQ+GG+D +
Sbjct: 26  MMDWTDRHCRYLHRLMSKQTLLYTEMVTSPALVRGGALHLLDHSPEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLNVGCPS RV  GSFGA LM  P +V  C+AAM +A+ + VT
Sbjct: 86  ELAEAARLGAQAGYDEINLNVGCPSDRVQSGSFGAILMEQPALVAKCVAAMSRAVDVEVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA LKGLSPK+NR IP LDYD+V+
Sbjct: 146 VKCRIGVDDQAPETVLPEFLAHIVGAGCERVTIHARKAWLKGLSPKENRDIPPLDYDLVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K    +L I +NGG+  + QA + L   +DGVMIGR+AY + A +L   D       T
Sbjct: 206 RMKGLFSNLHISVNGGITSLDQAERFLDGGLDGVMIGRSAYHSPADILCQADRRIYG--T 263

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS        +         M  Y   H+  GG+L QITRHM+GLF G P +R  R  L+
Sbjct: 264 GSDTTAEDAVQ--------QMLPYIDAHIDGGGRLNQITRHMMGLFAGRPGARIWRRHLS 315

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++  A + M
Sbjct: 316 ENASGPAANRQVLLDALDAM 335


>gi|157148055|ref|YP_001455374.1| tRNA-dihydrouridine synthase A [Citrobacter koseri ATCC BAA-895]
 gi|157085260|gb|ABV14938.1| hypothetical protein CKO_03862 [Citrobacter koseri ATCC BAA-895]
          Length = 345

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 145/317 (45%), Positives = 197/317 (62%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ +  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAQARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVAGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG+  + +A   L  +DGVMIGR AY+N  +L +VD E F     
Sbjct: 212 YQLKRDFPHLTMSINGGITSLEEAKAHLEHMDGVMIGREAYQNPGILASVDREIFGATTA 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAF 315
             A  + A   ++E A 
Sbjct: 322 ENAHKAGADIDVLEHAL 338


>gi|84515494|ref|ZP_01002856.1| tRNA-dihydrouridine synthase A [Loktanella vestfoldensis SKA53]
 gi|84510777|gb|EAQ07232.1| tRNA-dihydrouridine synthase A [Loktanella vestfoldensis SKA53]
          Length = 315

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 138/304 (45%), Positives = 193/304 (63%), Gaps = 14/304 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL++ + L+Y+EM+ A A++ GD+  ++G+   E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLMSRHVLVYSEMVTAPAVIHGDRDRLIGYGPAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D GY+E+NLN GCPS RV  G FGA LM N  +V +C+AAM  A+ IPVT
Sbjct: 61  LLAQAARIAADMGYDEVNLNCGCPSDRVQSGFFGAVLMENAALVAECVAAMIAAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P+  L + +  +  +GV+   IHARKA L+GLSPK+NR IP LD+D+V 
Sbjct: 121 VKCRIGVDDQTPSDVLPDFIARVSAAGVDRFSIHARKAWLQGLSPKENRDIPPLDHDLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA--MLTTVDEYFSNPL 237
            +K   P L + +NGG+  + QA   L   +DGVMIGRAAY      +L      +++P 
Sbjct: 181 AMKALFPHLHLSVNGGITSLDQAQDFLDRGLDGVMIGRAAYHTPCDILLDADARIYADPS 240

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             S+             +   M  Y A HL +GG+L QITRHM+G+F G P ++  R  L
Sbjct: 241 GRSA-----------EDVVHLMLPYIAEHLQNGGRLGQITRHMLGMFQGRPGAKAWRRHL 289

Query: 298 TVEA 301
           +  A
Sbjct: 290 SEHA 293


>gi|149913943|ref|ZP_01902475.1| tRNA-dihydrouridine synthase A [Roseobacter sp. AzwK-3b]
 gi|149812227|gb|EDM72058.1| tRNA-dihydrouridine synthase A [Roseobacter sp. AzwK-3b]
          Length = 337

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 144/300 (48%), Positives = 190/300 (63%), Gaps = 11/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLY+EM+ A A++RG   ++L +S QE P+ALQ+GG+D  
Sbjct: 17  MMDWTDRHCRYLHRLLSRRALLYSEMVTAAALVRGGALHLLDYSPQEHPVALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLNVGCPS RV  G+FGA LM +P +V +C AAM +A ++ VT
Sbjct: 77  ELAQAARMGAEAGYDEINLNVGCPSDRVQSGTFGAVLMKDPGLVSECCAAMIEASAVEVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  +  +GV    IHARKA L+GLSPK NR IP LDYD+V 
Sbjct: 137 VKCRIGVDDQDPETVLPEFLARVSAAGVQRFTIHARKAWLQGLSPKQNRDIPPLDYDLVL 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P L + +NGG+  + Q    L + +DGVM+GRAAY   A +L   D      + 
Sbjct: 197 RMKALFPGLHLSINGGITTLDQVRDFLEAGLDGVMVGRAAYHQPADILCAADRL----IF 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G     T  D    +     M  Y   HL  GG+L QITRHM+GLF G P +R  R IL+
Sbjct: 253 GEEGPDTTPDDAVLK-----MLPYIEAHLAQGGRLHQITRHMLGLFAGRPGARAWRRILS 307


>gi|331013200|gb|EGH93256.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 339

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 190/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM  P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAYPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLDQCGEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|37681156|ref|NP_935765.1| tRNA-dihydrouridine synthase A [Vibrio vulnificus YJ016]
 gi|326423833|ref|NP_760320.2| tRNA dihydrouridine synthase A [Vibrio vulnificus CMCP6]
 gi|38604852|sp|Q8CWK7|DUSA_VIBVU RecName: Full=tRNA-dihydrouridine synthase A
 gi|37199907|dbj|BAC95736.1| NifR3/Smm1 family protein [Vibrio vulnificus YJ016]
 gi|319999203|gb|AAO09847.2| tRNA dihydrouridine synthase A [Vibrio vulnificus CMCP6]
          Length = 326

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 199/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEMI   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMITTGAIIHG-KGDFLAYNQEEHPVALQLGGSNPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P +V DC+AAM + + IPVT
Sbjct: 71  DLATCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A + L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKKDFSHLTIAINGGVKSLEEAKEHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SPIK R      R+I   M  Y  + L +G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 QSPIKKR------RQIVEEMYPYIEQQLANGAYLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGIEVLQQALAKIPQEL 324


>gi|253991388|ref|YP_003042744.1| tRNA -dihydrouridine synthase A [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782838|emb|CAQ86003.1| tRNA-dihydrouridine synthase A [Photorhabdus asymbiotica]
          Length = 341

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 145/323 (44%), Positives = 201/323 (62%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K N L ++ +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFHRLLSKQTLLYTEMVTTGAIIHG-KGNYLAYNEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AKI ++ GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +++PVT
Sbjct: 88  ALAHCAKIAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAKLVADCVKAMQDVVNVPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + + ++ SG N   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDEQDSYEFLCDFIDTVVQHSGCNIFTIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L I +NGG++ + +A + L  VDGVMIGR AY+N A+L  VD    + +  
Sbjct: 208 YQLKKDFPQLTIAINGGIKSLEEAKQHLQYVDGVMIGREAYQNPAILAQVDHELFDAVI- 266

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+   V       +  ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 267 --PVVDTV------AVIRALYPYIEQALSQGTYLGHITRHILGIFQGIPGARQWRRHLSE 318

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  ++ E +
Sbjct: 319 NAHKPGADISVVEQALAMVTERM 341


>gi|159045052|ref|YP_001533846.1| tRNA-dihydrouridine synthase A [Dinoroseobacter shibae DFL 12]
 gi|157912812|gb|ABV94245.1| tRNA-dihydrouridine synthase A [Dinoroseobacter shibae DFL 12]
          Length = 338

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 148/303 (48%), Positives = 189/303 (62%), Gaps = 13/303 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R  T +ALLYTEM+ A A++RGD   +L  +  E PLALQ+GG+D  
Sbjct: 20  MMDWTDRHCRMFHRQFTQHALLYTEMVTAPAVVRGDAGRLLEHAEAEHPLALQLGGSDPV 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-V 119
           +L EA +I    G++EINLNVGCPS RV  G FGA LM  P +V  C+AAM  A   P +
Sbjct: 80  ELAEAVRIACGHGFDEINLNVGCPSDRVQSGCFGAVLMEQPALVARCVAAMIAASDGPEI 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIGVDDQ P   L   ++++ ++GV    IHARKA L+GLSPK+NR IP LDY +V
Sbjct: 140 TVKCRIGVDDQQPEEMLPGFLRTVSEAGVRRFTIHARKAWLQGLSPKENRDIPPLDYPLV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPL 237
             +K+  P L + +NGG+ D+ QA   L S +DGVMIGRAAY   A +L   D  F    
Sbjct: 200 VRMKQAFPGLHLSINGGITDLDQAAAHLASGLDGVMIGRAAYHEPARVLGDADRRF---F 256

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            G+  +      +       +M  Y A HL  GGKL QITRHM+G F G P +R  R +L
Sbjct: 257 GGAETVSAETAVE-------AMRPYIADHLARGGKLAQITRHMLGAFAGRPGARGWRRVL 309

Query: 298 TVE 300
           + E
Sbjct: 310 SEE 312


>gi|291086669|ref|ZP_06356403.2| tRNA-dihydrouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291067402|gb|EFE05511.1| tRNA-dihydrouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 313

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 144/322 (44%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIVHG-KGDYLAYSEEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 60  ALAQCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DD      L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDLDSYEFLCDFINTVAGKGECEMFIIHARKAWLSGLSPKENREIPPLDYARV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F+    
Sbjct: 180 YQLKRDFPHLTMSINGGIKSLEEAKIHLQHMDGVMVGREAYQNPGILASVDREIFAAATH 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSQGTYLGHVTRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 290 ENAHKAGADINVLEHALKLVAD 311


>gi|213970480|ref|ZP_03398608.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           T1]
 gi|301383868|ref|ZP_07232286.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tomato
           Max13]
 gi|302060592|ref|ZP_07252133.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tomato
           K40]
 gi|213924798|gb|EEB58365.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           T1]
          Length = 339

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 139/301 (46%), Positives = 193/301 (64%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 208 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQ----LFGS 263

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V
Sbjct: 264 VAPVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSV 317

Query: 300 E 300
           +
Sbjct: 318 D 318


>gi|262045546|ref|ZP_06018567.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330004874|ref|ZP_08305056.1| tRNA dihydrouridine synthase A [Klebsiella sp. MS 92-3]
 gi|259037105|gb|EEW38355.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328536493|gb|EGF62835.1| tRNA dihydrouridine synthase A [Klebsiella sp. MS 92-3]
          Length = 313

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 180 WQLKRDFPHLTMAINGGIKSLDEARVQLEHMDGVMVGREAYQNPGILASVDREIFGVAGA 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 290 ENAHKAGADIAVLEHALKLVAD 311


>gi|288937656|ref|YP_003441715.1| TIM-barrel protein, yjbN family [Klebsiella variicola At-22]
 gi|288892365|gb|ADC60683.1| TIM-barrel protein, yjbN family [Klebsiella variicola At-22]
          Length = 331

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 203/322 (63%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D  
Sbjct: 19  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 198 WQLKRDFPHLTMAINGGIKSLDEARLQLEHMDGVMVGREAYQNPGILASVDREIFGIAGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 308 ENAHKAGADIAVLEHALKLVAD 329


>gi|152987423|ref|YP_001347729.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PA7]
 gi|150962581|gb|ABR84606.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PA7]
          Length = 334

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 139/319 (43%), Positives = 198/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 23  MMDWTDRHCRFFLRQLSRHALLYTEMVTTGALLHGDRQRFLRHDECEHPLALQLGGSVPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 83  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMRDAVEIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     LR+ V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 143 VKHRIGINGRDSYAELRDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 203 QLKKDFPDLEIVLNGGIKTLEDCREHLRTFDGVMLGREAYHNPYLLAAVD----SQLFGS 258

Query: 241 S-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P  +R +          +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V
Sbjct: 259 QVPPPSRSEALL------RLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSV 312

Query: 300 EAGASTATHHIIETAFNLM 318
           +   S     + + A  L+
Sbjct: 313 DVHKSADPLRVFDQALELL 331


>gi|254439812|ref|ZP_05053306.1| Dihydrouridine synthase superfamily [Octadecabacter antarcticus
           307]
 gi|198255258|gb|EDY79572.1| Dihydrouridine synthase superfamily [Octadecabacter antarcticus
           307]
          Length = 320

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 151/320 (47%), Positives = 196/320 (61%), Gaps = 8/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ + A++RG  +++L F   E+P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLLSKRALLYTEMVTSPALVRGQARHLLRFDPAEQPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA +  D GY EINLNVGCPS RV  G FGA LM  P +V  C AAM +A    VT
Sbjct: 61  ELAKAAVMGADAGYVEINLNVGCPSDRVQSGCFGAVLMERPALVAQCCAAMIQAQPSEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P V L   +  I  +GV  + IHARKA LKGLSPK+NR IP LDYD+V 
Sbjct: 121 VKCRIGVDDQDPEVVLPEFLARIVGAGVTRVAIHARKAWLKGLSPKENRDIPPLDYDLVL 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  +  A ++L   +DGVMIGRAAY N + +L   D        
Sbjct: 181 RMKGLFPNLHISINGGIASLEHAKELLDLGLDGVMIGRAAYHNPTDILQRADAVIWGDDV 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G  P+   +    +  I A M D        GGKL  +T+HM+GLF G P SR+ R  L+
Sbjct: 241 GPDPLDIVMQMRNY--IDAHMVD----QTRGGGKLAHVTKHMMGLFAGQPGSRQWRRYLS 294

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A   M
Sbjct: 295 ENAHRDGAGWAVVEDALAAM 314


>gi|170742500|ref|YP_001771155.1| tRNA-dihydrouridine synthase A [Methylobacterium sp. 4-46]
 gi|168196774|gb|ACA18721.1| TIM-barrel protein, yjbN family [Methylobacterium sp. 4-46]
          Length = 327

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 151/315 (47%), Positives = 207/315 (65%), Gaps = 11/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +A LYTEM+   A+L G ++ ++GF   E+P+A+Q+GG+D +
Sbjct: 11  MMDWTDRHCRAFHRTLTRHARLYTEMVTTGAVLHGPRERLIGFDPAEQPVAIQLGGSDPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I E  GY E+NLNVGCPS RV +G FGACLM  PD+VG+C+AAM  A+++PVT
Sbjct: 71  DLAAAARIAEAEGYAEVNLNVGCPSDRVQDGRFGACLMREPDLVGECVAAMKAAVAVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L +S+ ++GV+G+ +HARKA L+GLSPK+NR +P LDY  V+
Sbjct: 131 VKCRIGVDDQDPEAALDALARSVARAGVDGLVVHARKAWLQGLSPKENRDVPPLDYGRVH 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K  +PDL + +NGGL  + +A   L  VDG M+GRAAY   A+L  VD   F  P   
Sbjct: 191 RLKAAHPDLPVAINGGLRSLDEARAQLAHVDGAMLGRAAYAEPALLLAVDPVLFGAPAPV 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P +          + A +   +AR L  G +L  ITRHM+GLF+G P +R  R  L+ 
Sbjct: 251 ADPFEA---------VEAFLPYLSAR-LAEGVRLHAITRHMLGLFNGRPGARAFRRHLST 300

Query: 300 EAGASTATHHIIETA 314
           E   ++A   ++  A
Sbjct: 301 EGMRASAGTDVLRDA 315


>gi|259909942|ref|YP_002650298.1| tRNA-dihydrouridine synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224965564|emb|CAX57096.1| tRNA-dihydrouridine synthase A [Erwinia pyrifoliae Ep1/96]
          Length = 331

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 145/324 (44%), Positives = 201/324 (62%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLY+EM+   AI+ G K + L FS++E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTQQTLLYSEMVTTGAIIHG-KGDYLAFSSEEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 74  ALAHCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ + G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYEFLCDFIHTVSEQGGCEVFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPHLTLSINGGVKSLAEAKIHLQYLDGVMMGREAYQNPGLLAQVDRELFGCTSP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + PI           +  SM  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AADPI----------AVVRSMYPYIERELANGTYLGHVTRHMLGLFQGIPGARQWRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +++ E +
Sbjct: 304 ENAHKAGAGIEVVEKALSMVAEKV 327


>gi|300714901|ref|YP_003739704.1| tRNA-dihydrouridine synthase A [Erwinia billingiae Eb661]
 gi|299060737|emb|CAX57844.1| tRNA-dihydrouridine synthase A [Erwinia billingiae Eb661]
          Length = 331

 Score =  276 bits (705), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 147/324 (45%), Positives = 200/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT ++LLYTEM+   AI+ G K + L ++  E+P+ALQ+GG D +
Sbjct: 15  MLDWTDRHCRYFLRQLTRHSLLYTEMVTTGAIVHG-KGDYLAWNQAEQPVALQLGGYDAA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AK  E  GYNEINLNVGCPS RV  G FGACLM  P +V D I AM   +SIPVT
Sbjct: 74  ALAECAKQAEARGYNEINLNVGCPSDRVQNGRFGACLMGEPALVADGIKAMRDQVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L   ++ + ++ G +   IHARKA L GLSPK+NR+IP LDY+ V
Sbjct: 134 VKTRIGIDEQDSYEFLCEFIRQVSEQGGCDSFIIHARKAWLSGLSPKENREIPPLDYERV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  VDGVM+GR AY+N  +L  VD E F + L 
Sbjct: 194 YQLKRDFPHLTMSINGGIKSLAEAKVHLQHVDGVMMGREAYQNPGLLAQVDRELFGSELP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y    L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 254 APDPV----------AVVRAMYPYIEAELANGTYLGHITRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A    +E A  L+ + +
Sbjct: 304 ENAHKPGANIETVEQALALVADKI 327


>gi|206576636|ref|YP_002241010.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae 342]
 gi|206565694|gb|ACI07470.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae 342]
          Length = 332

 Score =  276 bits (705), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D  
Sbjct: 20  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPQ 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 79  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCEFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 199 WQLKRDFPHLTMAINGGIKSLDEARLQLEHMDGVMVGREAYQNPGILASVDREIFGIAGA 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 309 ENAHKAGADIAVLEHALKLVAD 330


>gi|283480036|emb|CAY75952.1| tRNA-dihydrouridine synthase A [Erwinia pyrifoliae DSM 12163]
          Length = 332

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 145/324 (44%), Positives = 201/324 (62%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLY+EM+   AI+ G K + L FS++E P+ALQ+GG+D +
Sbjct: 16  MLDWTDRHCRYFHRQLTQQTLLYSEMVTTGAIIHG-KGDYLAFSSEEHPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 75  ALAHCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ + G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 135 VKTRIGIDDQDSYEFLCDFIHTVSEQGGCEVFIIHARKAWLSGLSPKENREIPPLDYPRV 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 195 YQLKRDFPHLTLSINGGVKSLAEAKIHLQYLDGVMMGREAYQNPGLLAQVDRELFGCTSP 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + PI           +  SM  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 255 AADPI----------AVVRSMYPYIERELANGTYLGHVTRHMLGLFQGIPGARQWRRYLS 304

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +++ E +
Sbjct: 305 ENAHKAGAGIEVVEKALSMVAEKV 328


>gi|146306962|ref|YP_001187427.1| tRNA-dihydrouridine synthase A [Pseudomonas mendocina ymp]
 gi|145575163|gb|ABP84695.1| tRNA-U16,U17-dihydrouridine synthase [Pseudomonas mendocina ymp]
          Length = 331

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 137/301 (45%), Positives = 196/301 (65%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A++ GD++  L +S  E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRFFLRQLSRHALLYTEMVTTGALIHGDRERFLRYSECEHPIALQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 80  DLAACAKMAEQHGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 140 VKHRIGINGRDSYSELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG- 239
           ++K++ PDL I LNGG++ + +  + L + DGVM+GR AY N  +L  VD    N L G 
Sbjct: 200 QLKRDFPDLEIILNGGIKTLEECEQHLQTFDGVMLGREAYHNPYLLAQVD----NRLFGA 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P  +R+D         ++  Y  +HL  GG L  ++RH++GL  GFP +RR R +L+V
Sbjct: 256 AAPSISRMDALL------ALKPYVEQHLREGGTLHHVSRHVLGLAQGFPGARRFRQLLSV 309

Query: 300 E 300
           +
Sbjct: 310 D 310


>gi|227112414|ref|ZP_03826070.1| tRNA-dihydrouridine synthase A [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 340

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 199/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G K + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHG-KGDYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + G    +I HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCDFIQTVAERGECETFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F   + 
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFG--ID 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P    V +        +M  Y  R L  G  L  ITRHM+G+F G P +R+ R  L+
Sbjct: 266 AATPDLAGVVR--------AMYPYIERELSGGASLGHITRHMLGMFQGIPGARQWRRYLS 317

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 318 ENAHKPGADAAVVERALALV 337


>gi|170077369|ref|YP_001734007.1| dihydrouridine synthase A [Synechococcus sp. PCC 7002]
 gi|169885038|gb|ACA98751.1| Dihydrouridine synthase A [Synechococcus sp. PCC 7002]
          Length = 344

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 140/321 (43%), Positives = 196/321 (61%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+  R +T   LLYTEMI   AI+ GD+  +L F   E P++LQ+GG +  
Sbjct: 19  MMDRTDRHFRYLMRRITRRTLLYTEMITTQAIIHGDRPKLLDFDAAEHPISLQLGGDNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E AK+ ED+GY+EINLNVGCPS RV +G+FGACLM  P++V DC+AAM  A++IPVT
Sbjct: 79  ELAECAKVGEDWGYDEINLNVGCPSPRVQQGNFGACLMTQPELVADCVAAMQGAVNIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+Q     L   ++ +  +G +   +HARKA L+GLSPK+NR +P L Y  VY
Sbjct: 139 VKHRIGVDEQDSYADLCRFIEIVSATGCDRFSVHARKAWLQGLSPKENRTVPPLRYADVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L+I +NGG+  +      L  VD VM+GRAAY N  +  TVD      + G 
Sbjct: 199 RLKQDFPHLWIEINGGITTLEHIQTHLTQVDAVMVGRAAYDNPYLFATVD----RDIYGE 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     +      +I   M  Y  R   +G KL  I+RHM+ LF G P ++  +  +T E
Sbjct: 255 A-----IQPKSRHEIVEEMLPYIERATKAGVKLHSISRHMLSLFLGQPGTKAWKRFITEE 309

Query: 301 AGASTATHHIIETAFNLMIES 321
              +T    IIE A  L+ ++
Sbjct: 310 GRGTTVGREIIEQALALVSQT 330


>gi|290512395|ref|ZP_06551762.1| tRNA-dihydrouridine synthase A [Klebsiella sp. 1_1_55]
 gi|289775390|gb|EFD83391.1| tRNA-dihydrouridine synthase A [Klebsiella sp. 1_1_55]
          Length = 331

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D  
Sbjct: 19  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCEFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 198 WQLKRDFPHLTMAINGGIKSLDEARLQLEHMDGVMVGREAYQNPGILASVDREIFGIAGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 308 ENAHKAGADIAVLEHALKLVAD 329


>gi|262401531|ref|ZP_06078098.1| tRNA-dihydrouridine synthase [Vibrio sp. RC586]
 gi|262352246|gb|EEZ01375.1| tRNA-dihydrouridine synthase [Vibrio sp. RC586]
          Length = 316

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ +D GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQDRGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYSRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY++  +L  VD+        
Sbjct: 180 YQIKRDFPHLTIAVNGGVKTLEEAKLHLQHLDGVMIGREAYQSPYLLAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 237 DTPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 291 NAHKLGAGLEVVEQAL 306


>gi|152972912|ref|YP_001338058.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|150957761|gb|ABR79791.1| conserved protein, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 313

 Score =  275 bits (704), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 202/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNALLVADCIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 180 WQLKRDFPHLTMAINGGIKSLDEARVQLEHMDGVMVGREAYQNPGILASVDREIFGVAGA 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 290 ENAHKAGADIAVLEHALKLVAD 311


>gi|146309919|ref|YP_001174993.1| tRNA-dihydrouridine synthase A [Enterobacter sp. 638]
 gi|145316795|gb|ABP58942.1| tRNA-U16,U17-dihydrouridine synthase [Enterobacter sp. 638]
          Length = 331

 Score =  275 bits (704), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 147/322 (45%), Positives = 199/322 (61%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V D I AM   +SIPVT
Sbjct: 78  ALAECAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADGIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFIDTVAGKGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L TVD E F     
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKTHLQHMDGVMVGREAYQNPGILATVDREIFGIEGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+           +  +M  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 258 DSDPV----------AVVRAMYPYIERELSNGTYLGHVTRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 308 ENAHKAGADIEVLEHALRLVAD 329


>gi|323495575|ref|ZP_08100649.1| tRNA-dihydrouridine synthase A [Vibrio sinaloensis DSM 21326]
 gi|323319456|gb|EGA72393.1| tRNA-dihydrouridine synthase A [Vibrio sinaloensis DSM 21326]
          Length = 333

 Score =  275 bits (704), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 144/323 (44%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIHG-KGDFLAYNQEEHPVALQLGGSNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V  C+A+M + + IPVT
Sbjct: 78  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVASMREVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYEFLTDFVSIVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +  +L  L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLNIAVNGGVKTLEDSLVHLEHLDGVMVGREAYQNPYLLAQVDQQI---FGL 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y    L  G  L  ITRHMIGLF   P +R+ R  ++ 
Sbjct: 255 DKPVKKR------SQVVEEMYPYIEAQLSKGAYLGHITRHMIGLFQAMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++ETA   + + L
Sbjct: 309 NAHKPGAGIEVVETALAKIPQEL 331


>gi|172037930|ref|YP_001804431.1| tRNA-dihydrouridine synthase A [Cyanothece sp. ATCC 51142]
 gi|171699384|gb|ACB52365.1| putative dihydrouridine synthase TIM-barrel protein nifR3
           [Cyanothece sp. ATCC 51142]
          Length = 342

 Score =  275 bits (704), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 139/311 (44%), Positives = 194/311 (62%), Gaps = 9/311 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R +T + LLYTEMIV+ AI+ GD+  +L FS +EKPL+LQIGG +  
Sbjct: 22  MMDYTDRHFRYFMRQITRHTLLYTEMIVSAAIINGDRPKLLDFSPEEKPLSLQIGGDNPQ 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I ED+GY+E+NLNVGCPS RV  G FGACLM NP++V  C+  M + ++IPVT
Sbjct: 82  ELAECAIIGEDWGYDEVNLNVGCPSDRVQSGHFGACLMANPELVAQCVEKMQQGVTIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D Q     +   VK + ++G     +HARKA L+GLSPK+NR IP L Y  VY
Sbjct: 142 VKHRIGIDHQDSYEDMARFVKIVSEAGCQRFTVHARKAWLQGLSPKENRNIPPLRYQEVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P LFI +NGG+ ++ Q    L  VD VMIGR+AY N  +L TVD          
Sbjct: 202 RLKQEFPQLFIEINGGITNLEQVRNHLKLVDAVMIGRSAYDNPYLLATVDRDI------- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + +V +    +I   M  Y    +  G KL +I+RH++ +F G P ++  +  ++  
Sbjct: 255 --YRDKVTQLTRHQIIEKMLPYIDDWVSRGHKLHKISRHLLAIFSGIPGTKAWKRHISEN 312

Query: 301 AGASTATHHII 311
           A    A   +I
Sbjct: 313 AHLPGADSQVI 323


>gi|253689857|ref|YP_003019047.1| TIM-barrel protein, yjbN family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251756435|gb|ACT14511.1| TIM-barrel protein, yjbN family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 340

 Score =  275 bits (704), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 146/320 (45%), Positives = 199/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L++  LLYTEM+   AIL G K + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLSSQTLLYTEMVTTGAILHG-KGDYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEASLVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + G    +I HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYAFLCDFIQTVAELGECETFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F   + 
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFG--ID 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P    V +        +M  Y  R L  G  L  ITRHM+G+F G P +R+ R  L+
Sbjct: 266 AATPDLAGVVR--------TMYPYIERELSGGAALGHITRHMLGMFQGIPGARQWRRYLS 317

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 318 ENAHKPGADAAVVERALALV 337


>gi|238798490|ref|ZP_04641969.1| tRNA-dihydrouridine synthase A [Yersinia mollaretii ATCC 43969]
 gi|238717652|gb|EEQ09489.1| tRNA-dihydrouridine synthase A [Yersinia mollaretii ATCC 43969]
          Length = 343

 Score =  275 bits (703), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 203/320 (63%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHG-KGDYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK  E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAQCAKQAEFRGYNEINLNVGCPSDRVQNGRFGACLMAEANLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAEQGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD E F +   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDS--- 262

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+
Sbjct: 263 -NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLS 315

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 316 ENAHKPGADVSVVEQALALV 335


>gi|170728528|ref|YP_001762554.1| tRNA-dihydrouridine synthase A [Shewanella woodyi ATCC 51908]
 gi|169813875|gb|ACA88459.1| TIM-barrel protein, yjbN family [Shewanella woodyi ATCC 51908]
          Length = 331

 Score =  275 bits (703), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 142/315 (45%), Positives = 196/315 (62%), Gaps = 12/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ ARL++   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 22  MLDWTDRHYRYLARLMSAELLLYTEMVTTGAIIHG-KGDYLAYNEEEHPLALQLGGSNPH 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK   + GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM     IPVT
Sbjct: 81  DLAICAKQAVERGYDEINLNVGCPSDRVQSGRFGACLMAEPSLVAECVTAMRAVADIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   V++++ +G +   +HARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 141 VKTRIGIDEQDSYEFLTEFVETVRDAGCDTFIVHARKAWLQGLSPKENREIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG- 239
           ++K++ PDL I +NGG++ + +    L  +DGVM+GR AY+N  +L  VD+     L G 
Sbjct: 201 QLKRDYPDLSISINGGVKSLEECKVHLVKLDGVMVGREAYQNPYILAKVDQ----QLCGL 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+ +R        +      Y  +HL +GG+L  ITRHM GLF G   SR  R  ++ 
Sbjct: 257 DKPVLSR------DAVLEKFIPYIEKHLQAGGRLNHITRHMTGLFQGEVGSRIWRRYISE 310

Query: 300 EAGASTATHHIIETA 314
            A    +   +IE A
Sbjct: 311 NAHKPGSGIEVIEQA 325


>gi|254449979|ref|ZP_05063416.1| tRNA-dihydrouridine synthase A [Octadecabacter antarcticus 238]
 gi|198264385|gb|EDY88655.1| tRNA-dihydrouridine synthase A [Octadecabacter antarcticus 238]
          Length = 319

 Score =  275 bits (703), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 150/314 (47%), Positives = 196/314 (62%), Gaps = 8/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ + A++RG  +++L F   E+P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLLSKRALLYTEMVTSPALVRGQARHLLRFDPVEQPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++  D GY EINLNVGCPS RV  G FGA LM  P +V  C AAM +A    VT
Sbjct: 61  ELARAAEMGADEGYPEINLNVGCPSDRVQSGCFGAVLMEQPALVAACCAAMIRAQPSEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   + L   +  I  +GV  + IHARKA LKGLSPK+NR IP LDYD+V 
Sbjct: 121 VKCRIGVDDQDSEIVLPEFLAQIVGAGVTRVTIHARKAWLKGLSPKENRDIPPLDYDLVL 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  +  A ++L   +DGVMIGRAAY N A +L   D        
Sbjct: 181 RMKGLFPNLHISINGGVGSLEHAKELLDLGLDGVMIGRAAYHNPADILQRADAVIWGDDL 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G  P+   +    +  I A M+D       SGGKL  +T+HM+GLF G P SR+ R  L+
Sbjct: 241 GPDPLDVVLQMRSY--IEAHMSD----ETRSGGKLAHVTKHMMGLFAGQPGSRQWRRYLS 294

Query: 299 VEAGASTATHHIIE 312
             A  S A   ++E
Sbjct: 295 ENAYRSGAGWSVVE 308


>gi|237797725|ref|ZP_04586186.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|237806004|ref|ZP_04592708.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331020575|gb|EGI00632.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331027114|gb|EGI07169.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 339

 Score =  275 bits (703), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 139/301 (46%), Positives = 193/301 (64%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL+ +ALLYTEM+   A+L GD+   L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSRHALLYTEMVTTGALLHGDRDRFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVVIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V +++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L   DGVM+GR AY N  +L  VD+     L GS
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQVFDGVMLGREAYHNPYLLAQVDKQ----LFGS 263

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R           +M  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V
Sbjct: 264 MAPVISR------HAALEAMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSV 317

Query: 300 E 300
           +
Sbjct: 318 D 318


>gi|56461028|ref|YP_156309.1| tRNA-dihydrouridine synthase A [Idiomarina loihiensis L2TR]
 gi|56180038|gb|AAV82760.1| Predicted tRNA-dihydrouridine synthase [Idiomarina loihiensis L2TR]
          Length = 332

 Score =  275 bits (703), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 134/316 (42%), Positives = 200/316 (63%), Gaps = 13/316 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT + LLYTEM+   AI+ G +++ L F+ +E P+ALQ+GG++ +
Sbjct: 14  MLDWTDRHCRYFHRLLTRSTLLYTEMVTTGAIIFG-QQDFLAFNAEEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + E A++ ++ GY+E+N+NVGCPS RV  GSFGACLM  P+ V +C+ AM     IPVT
Sbjct: 73  AMAECARLAQERGYDEVNINVGCPSDRVQNGSFGACLMAQPEKVAECVKAMKAVTDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+Q     L  L  ++  +GV+ + +HARKA L+GLSPK+NR IP L Y+ VY
Sbjct: 133 VKTRLGIDEQDSDDFLYELTDAVVAAGVDQLTLHARKAWLQGLSPKENRDIPELQYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             +K  PD+ + +NGG+ ++ +  + L  V GVMIGRAAY+N  +LT +D      L+ +
Sbjct: 193 RAQKRYPDVPVAINGGIVELHEVKQHLNQVHGVMIGRAAYQNPWLLTQLDS-----LSET 247

Query: 241 SPIK-TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            P + TR        +  +M  Y   H+  GG+   + RHM+GLF G    +R R  L+V
Sbjct: 248 KPAELTR------EAVVTAMIPYIDNHIRQGGRAWHVARHMLGLFQGMTGGKRWRQYLSV 301

Query: 300 EAGASTATHHIIETAF 315
           +   +T+   ++  A 
Sbjct: 302 KGPRATSAEQLLYGAL 317


>gi|315181327|gb|ADT88241.1| tRNA-dihydrouridine synthase A [Vibrio furnissii NCTC 11218]
          Length = 319

 Score =  275 bits (703), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 197/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 4   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPV 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P++V  C+AAM   + IPVT
Sbjct: 63  DLARCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVAAMKAVVDIPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + ++ G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 123 VKTRIGIDDQDSYEFLTHFVTVVSEQGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 182

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 183 YQLKQDFPQLTIAVNGGVKSLAEAKEHLQHLDGVMIGREAYQSPYLLAEVDQQI---FGL 239

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 240 DTPVKKR------SQVVQEMYPYIEQQLAQGSYLGHITRHMLGLFQNMPGARQWRRHISE 293

Query: 300 EAGASTATHHIIETAF 315
            A  + A   ++E A 
Sbjct: 294 NAHKAGAGIEVVEQAL 309


>gi|260767137|ref|ZP_05876081.1| tRNA-dihydrouridine synthase [Vibrio furnissii CIP 102972]
 gi|260617858|gb|EEX43033.1| tRNA-dihydrouridine synthase [Vibrio furnissii CIP 102972]
          Length = 316

 Score =  275 bits (703), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 197/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPV 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P++V  C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVAAMKAVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + ++ G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTHFVTVVSEQGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 180 YQLKQDFPQLTIAVNGGVKSLAEAKEHLQHLDGVMIGREAYQSPYLLAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 DTPVKKR------SQVVQEMYPYIEQQLAQGSYLGHITRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAF 315
            A  + A   ++E A 
Sbjct: 291 NAHKAGAGIEVVEQAL 306


>gi|153803249|ref|ZP_01957835.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-3]
 gi|229519914|ref|ZP_04409345.1| tRNA dihydrouridine synthase A [Vibrio cholerae TM 11079-80]
 gi|124121229|gb|EAY39972.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-3]
 gi|229343042|gb|EEO08029.1| tRNA dihydrouridine synthase A [Vibrio cholerae TM 11079-80]
          Length = 327

 Score =  275 bits (703), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++ +
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPN 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGL 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 302 NAHKPGAGLEVVEQAL 317


>gi|255747176|ref|ZP_05421119.1| tRNA dihydrouridine synthase A [Vibrio cholera CIRS 101]
 gi|262147248|ref|ZP_06028049.1| tRNA dihydrouridine synthase A [Vibrio cholerae INDRE 91/1]
 gi|262166864|ref|ZP_06034586.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC27]
 gi|262190629|ref|ZP_06048865.1| tRNA dihydrouridine synthase A [Vibrio cholerae CT 5369-93]
 gi|255735225|gb|EET90627.1| tRNA dihydrouridine synthase A [Vibrio cholera CIRS 101]
 gi|262024694|gb|EEY43373.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC27]
 gi|262031308|gb|EEY49921.1| tRNA dihydrouridine synthase A [Vibrio cholerae INDRE 91/1]
 gi|262033494|gb|EEY51996.1| tRNA dihydrouridine synthase A [Vibrio cholerae CT 5369-93]
 gi|327483237|gb|AEA77644.1| tRNA dihydrouridine synthase A [Vibrio cholerae LMA3894-4]
          Length = 316

 Score =  275 bits (703), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 193/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 180 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 237 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 291 NAHKPGAGLEVVEQAL 306


>gi|254509778|ref|ZP_05121845.1| tRNA-dihydrouridine synthase A [Rhodobacteraceae bacterium KLH11]
 gi|221533489|gb|EEE36477.1| tRNA-dihydrouridine synthase A [Rhodobacteraceae bacterium KLH11]
          Length = 320

 Score =  275 bits (702), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 147/321 (45%), Positives = 200/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L  + QE P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSAQTLLYTEMVTAPALVRGGALHLLKHNPQEHPVALQLGGSDPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM  P  V DC+ AM +A+ + VT
Sbjct: 61  ELAKAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMREPTRVADCVRAMQEAVDVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L   ++ I  +G   + IHARKA L+GLSPK+NR IP LDY +V+
Sbjct: 121 VKCRIGVDEQEPHAVLPAFLEQISAAGCQRVTIHARKAWLQGLSPKENRDIPPLDYALVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAY-KNSAMLTTVDEYFSNPLT 238
            +K   P L I +NGG+  ++QA + L + +DGVMIGRAAY + + +L   D       T
Sbjct: 181 RMKAAFPALHISINGGITSLAQAQEQLEAGLDGVMIGRAAYHQPTDILAAADAQIFG--T 238

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G     T V ++        M  Y   HL  GG+L QITRHM+GLF G P +R  R IL+
Sbjct: 239 GRIVDPTEVVQE--------MLPYVEAHLTEGGRLHQITRHMLGLFAGRPGARHWRRILS 290

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   +I  A + ++
Sbjct: 291 EGAVRDQAGPEVILQALDAIM 311


>gi|320155187|ref|YP_004187566.1| tRNA dihydrouridine synthase A [Vibrio vulnificus MO6-24/O]
 gi|319930499|gb|ADV85363.1| tRNA dihydrouridine synthase A [Vibrio vulnificus MO6-24/O]
          Length = 326

 Score =  275 bits (702), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 142/323 (43%), Positives = 198/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEMI   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMITTGAIIHG-KGDFLSYNQEEHPVALQLGGSNPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P +V DC+A M + + IPVT
Sbjct: 71  DLATCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVATMKEVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A + L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKKDFSHLTIAINGGVKSLEEAKEHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SPIK R      R+I   M  Y  + L +G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 QSPIKKR------RQIVEEMYPYIEQQLANGAYLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGIEVLQQALAKIPQEL 324


>gi|238794664|ref|ZP_04638270.1| tRNA-dihydrouridine synthase A [Yersinia intermedia ATCC 29909]
 gi|238726053|gb|EEQ17601.1| tRNA-dihydrouridine synthase A [Yersinia intermedia ATCC 29909]
          Length = 343

 Score =  275 bits (702), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 145/319 (45%), Positives = 199/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHG-KADYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEAELVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++   G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVADRGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD         
Sbjct: 206 YQLKRDFPTLTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDREL---FDA 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 317 NAHKPGAGVAVVEQALALV 335


>gi|292489772|ref|YP_003532662.1| tRNA-dihydrouridine synthase A [Erwinia amylovora CFBP1430]
 gi|292898020|ref|YP_003537389.1| tRNA-dihydrouridine synthase A [Erwinia amylovora ATCC 49946]
 gi|291197868|emb|CBJ44967.1| tRNA-dihydrouridine synthase A [Erwinia amylovora ATCC 49946]
 gi|291555209|emb|CBA23447.1| tRNA-dihydrouridine synthase A [Erwinia amylovora CFBP1430]
          Length = 349

 Score =  275 bits (702), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 145/324 (44%), Positives = 200/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLYTEM+   AI+ G K + L FS++E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRQLTRQTLLYTEMVTTGAIIHG-KGDYLAFSSEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 92  ALAQCAKLAERRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G     IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFMRTVSEQGGCEMFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 212 YQLKRDFPHLTLSINGGVKSLAEAKIHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTSP 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              PI           +  SM  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 272 SIDPI----------AVVRSMYPYIERELAGGTYLGHVTRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +++ E +
Sbjct: 322 ENAHKAGAGIDVVEKALSMVAEKV 345


>gi|15640406|ref|NP_230033.1| tRNA-dihydrouridine synthase A [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590952|ref|ZP_01678272.1| TIM-barrel protein, yjbN family [Vibrio cholerae 2740-80]
 gi|121729744|ref|ZP_01682184.1| TIM-barrel protein, yjbN family [Vibrio cholerae V52]
 gi|147675235|ref|YP_001218647.1| tRNA-dihydrouridine synthase A [Vibrio cholerae O395]
 gi|153820423|ref|ZP_01973090.1| TIM-barrel protein, yjbN family [Vibrio cholerae NCTC 8457]
 gi|153823513|ref|ZP_01976180.1| TIM-barrel protein, yjbN family [Vibrio cholerae B33]
 gi|153827262|ref|ZP_01979929.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-2]
 gi|153830467|ref|ZP_01983134.1| TIM-barrel protein, yjbN family [Vibrio cholerae 623-39]
 gi|227080591|ref|YP_002809142.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|229504962|ref|ZP_04394473.1| tRNA dihydrouridine synthase A [Vibrio cholerae BX 330286]
 gi|229508600|ref|ZP_04398096.1| tRNA dihydrouridine synthase A [Vibrio cholerae B33]
 gi|229516011|ref|ZP_04405462.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC9]
 gi|229526966|ref|ZP_04416363.1| tRNA dihydrouridine synthase A [Vibrio cholerae 12129(1)]
 gi|229606339|ref|YP_002876987.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MJ-1236]
 gi|254286198|ref|ZP_04961157.1| TIM-barrel protein, yjbN family [Vibrio cholerae AM-19226]
 gi|254851689|ref|ZP_05241039.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MO10]
 gi|298501275|ref|ZP_07011073.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MAK 757]
 gi|38605061|sp|Q9KUX9|DUSA_VIBCH RecName: Full=tRNA-dihydrouridine synthase A
 gi|9654797|gb|AAF93552.1| NifR3/Smm1 family protein [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121547178|gb|EAX57305.1| TIM-barrel protein, yjbN family [Vibrio cholerae 2740-80]
 gi|121628529|gb|EAX61013.1| TIM-barrel protein, yjbN family [Vibrio cholerae V52]
 gi|126509034|gb|EAZ71628.1| TIM-barrel protein, yjbN family [Vibrio cholerae NCTC 8457]
 gi|126518958|gb|EAZ76181.1| TIM-barrel protein, yjbN family [Vibrio cholerae B33]
 gi|146317118|gb|ABQ21657.1| TIM-barrel protein, yjbN family [Vibrio cholerae O395]
 gi|148874069|gb|EDL72204.1| TIM-barrel protein, yjbN family [Vibrio cholerae 623-39]
 gi|149738810|gb|EDM53152.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-2]
 gi|150423613|gb|EDN15555.1| TIM-barrel protein, yjbN family [Vibrio cholerae AM-19226]
 gi|227008479|gb|ACP04691.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|227012235|gb|ACP08445.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|229335578|gb|EEO01058.1| tRNA dihydrouridine synthase A [Vibrio cholerae 12129(1)]
 gi|229346914|gb|EEO11881.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC9]
 gi|229354368|gb|EEO19295.1| tRNA dihydrouridine synthase A [Vibrio cholerae B33]
 gi|229358020|gb|EEO22936.1| tRNA dihydrouridine synthase A [Vibrio cholerae BX 330286]
 gi|229368994|gb|ACQ59417.1| tRNA dihydrouridine synthase A [Vibrio cholerae MJ-1236]
 gi|254847394|gb|EET25808.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MO10]
 gi|297540029|gb|EFH76092.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MAK 757]
          Length = 327

 Score =  275 bits (702), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 193/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGL 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 302 NAHKPGAGLEVVEQAL 317


>gi|78485554|ref|YP_391479.1| tRNA-dihydrouridine synthase A [Thiomicrospira crunogena XCL-2]
 gi|78363840|gb|ABB41805.1| tRNA-dihydrouridine synthase A [Thiomicrospira crunogena XCL-2]
          Length = 357

 Score =  275 bits (702), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 145/334 (43%), Positives = 205/334 (61%), Gaps = 21/334 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R F R LT +A LY+EM+   AI+ G+  +  LG S  + P+ LQ+GG++ 
Sbjct: 25  MLDWTDRHCRVFHRQLTKHAWLYSEMVTTGAIIYGNNLERFLGHSEMDSPVVLQLGGSNP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIP 118
            +L   AK+ E++GY+EINLNVGCPS RV     GACLM +P+IV D ++AM  A+  IP
Sbjct: 85  EELAHCAKLGEEWGYSEINLNVGCPSDRVQNNMIGACLMAHPNIVADAVSAMKTAVKEIP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG+D+Q     L   V +I+ +GV+G+ IHARKA L+GLSPK+NR +P L YD 
Sbjct: 145 VTVKSRIGIDEQEDFDTLVEFVSAIQTAGVDGVIIHARKAWLQGLSPKENRDVPPLKYDW 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI----------LPSVDGVMIGRAAYKNSAMLTT 228
           V +IK   P+L I +NGG++     L            LP+VDGVM+GRA Y+   +LT 
Sbjct: 205 VRQIKALFPELEIAINGGIQTPQAGLNFLEILKDDEQSLPAVDGVMLGRAVYEKPYLLTE 264

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           VD  + +    +SP+K+R        +  +M  Y   HL  GGKL Q++RHM+GLF G P
Sbjct: 265 VDALYYD---DASPVKSR------EAVLEAMYPYIENHLTQGGKLNQVSRHMLGLFAGLP 315

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
             R  R  ++  A  S A   +++ A+  ++  +
Sbjct: 316 GGRMWRRYISENAFKSGAGIDVLQEAYRRVVNEI 349


>gi|119492928|ref|ZP_01623958.1| hypothetical protein L8106_26412 [Lyngbya sp. PCC 8106]
 gi|119452854|gb|EAW34028.1| hypothetical protein L8106_26412 [Lyngbya sp. PCC 8106]
          Length = 338

 Score =  275 bits (702), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 141/315 (44%), Positives = 197/315 (62%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD++ +LGFS +EKPL LQIGG    
Sbjct: 25  MMDRTDRHFRYFMRQITKRTLLYTEMVTSAAIIHGDREKLLGFSPEEKPLVLQIGGDQPQ 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A+I ED GY+++NLNVGCPS+RV +G+FGACLM  P  V + ++ M + + IPVT
Sbjct: 85  ELAICAEIAEDMGYDQVNLNVGCPSSRVQDGNFGACLMAQPQRVAEAVSKMQQRVKIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD+     + N V+ + +SG     +HARKA L+GLSPKDNR IP L Y+ V+
Sbjct: 145 IKHRIGIDDRDRYEDMANFVEIVSQSGCQQFTVHARKAWLQGLSPKDNRNIPPLRYEDVH 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E P LFI +NGGL   SQ  + L SVD VM+GRAAY N  +  T D+ F    T  
Sbjct: 205 QLKQEFPHLFIEINGGLTIFSQVHEQLKSVDAVMLGRAAYDNPYLFATADQEFYGEKT-- 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ TR       ++  SM  Y    L  G KL  I RH++ LF G P ++  +  L+  
Sbjct: 263 TPL-TR------HQVVESMFPYLEYWLSRGVKLNSIMRHVLQLFSGQPGTKAWKRYLSEN 315

Query: 301 AGASTATHHIIETAF 315
              + A   ++  A 
Sbjct: 316 GYLAGAGVEVVREAL 330


>gi|71736634|ref|YP_274126.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557187|gb|AAZ36398.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 339

 Score =  275 bits (702), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 135/300 (45%), Positives = 193/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V +++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGNVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 ALVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|330973923|gb|EGH73989.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 339

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 192/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ ++ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPGLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FGST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|302134770|ref|ZP_07260760.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tomato
           NCPPB 1108]
          Length = 311

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 138/300 (46%), Positives = 192/300 (64%), Gaps = 11/300 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  + 
Sbjct: 1   MDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVTV
Sbjct: 61  LAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V +
Sbjct: 121 KHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVAQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS- 240
           +K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     L GS 
Sbjct: 181 LKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQ----LFGSV 236

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 237 APVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 290


>gi|66045176|ref|YP_235017.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. syringae
           B728a]
 gi|63255883|gb|AAY36979.1| Dihydrouridine synthase TIM-barrel protein yjbN [Pseudomonas
           syringae pv. syringae B728a]
          Length = 339

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 192/300 (64%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ ++ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPGLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FGST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318


>gi|157372686|ref|YP_001480675.1| tRNA-dihydrouridine synthase A [Serratia proteamaculans 568]
 gi|157324450|gb|ABV43547.1| TIM-barrel protein, yjbN family [Serratia proteamaculans 568]
          Length = 336

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 201/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFHRLLTKDTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 79  ALAHCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGQATLVADCIKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR++P LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCDFIATVAGRGECDMFTIHARKAWLSGLSPKENREVPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P+L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 199 YQLKRDFPELTLAINGGVKTLEEAKQHLQHLDGVMMGREAYQNPGILARVDSELFGR--- 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                +T V       I  S+  Y  R L +G  L  ITRH++GLF G P +R+ R  L+
Sbjct: 256 -----QTEVMDSV--AIIESLYPYIERELSNGTYLGHITRHILGLFQGVPGARQWRRHLS 308

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A +L+
Sbjct: 309 ENAHKPGADARVVEQALDLV 328


>gi|261210364|ref|ZP_05924658.1| tRNA-dihydrouridine synthase [Vibrio sp. RC341]
 gi|260840422|gb|EEX66988.1| tRNA-dihydrouridine synthase [Vibrio sp. RC341]
          Length = 335

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM   + IPVT
Sbjct: 79  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMRSVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 139 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYSRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY++  +L  VD+        
Sbjct: 199 YQIKRDFPHLTIAVNGGVKTLEEAKLHLQHLDGVMIGREAYQSPYLLAEVDQQI---FEL 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 256 DTPVKKR------SQVIHEMLPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 309

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 310 NAHKQGAGLEVVEQAL 325


>gi|307154453|ref|YP_003889837.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 7822]
 gi|306984681|gb|ADN16562.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 7822]
          Length = 329

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 145/316 (45%), Positives = 195/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+  R +T   LLYTEMI   AI+ GD+  +L FST+EKPLALQ+GG +  
Sbjct: 17  MMERTDRHFRYLMRQITRRTLLYTEMITTAAIIHGDRHKLLDFSTEEKPLALQLGGDNPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A I  D+GY+E+NLNVGCPS RV  G+FGACLM  P+ V  C+AAM KA++IPVT
Sbjct: 77  ELALCASIAADWGYDEVNLNVGCPSDRVQNGNFGACLMAQPEKVAHCVAAMQKAVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L N V+ + ++G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 137 VKHRIGIDDRDRYEDLANFVRIVSEAGCCRFSVHARKAWLKGLSPKENRTIPPLRYEDVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P LFI +NGG+  + Q  + L  VDGVMIGRAAY N  +  TVD      + G 
Sbjct: 197 RLKQEFPHLFIEINGGITTLEQVHQQLQWVDGVMIGRAAYDNPYLFATVD----RDIYGE 252

Query: 241 SPI-KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             I  TR       +++  M  Y    +  G KL  I+RH++ LF G P ++  +  ++ 
Sbjct: 253 ETIPPTR------HQVAEKMLPYIEDIVSQGIKLHAISRHLLQLFSGQPGTKAWKRYISE 306

Query: 300 EAGASTATHHIIETAF 315
                 A   +IE A 
Sbjct: 307 NVHHQAAGAEVIEAAL 322


>gi|288550133|ref|ZP_05969393.2| tRNA-dihydrouridine synthase A [Enterobacter cancerogenus ATCC
           35316]
 gi|288316334|gb|EFC55272.1| tRNA-dihydrouridine synthase A [Enterobacter cancerogenus ATCC
           35316]
          Length = 313

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 146/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHG-KGDYLAYSDEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V D I AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADSIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFIDTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L TVD E F     
Sbjct: 180 YQLKRDFPHLTMSINGGIKSLEEAKTHLAHMDGVMVGREAYQNPGILATVDREIFGVEGA 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DTDPV----------SVVRAMYPYIERELSNGTWLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  L+ +
Sbjct: 290 ENAHKAGADIDVLEHALRLVAD 311


>gi|323492300|ref|ZP_08097456.1| tRNA-dihydrouridine synthase A [Vibrio brasiliensis LMG 20546]
 gi|323313464|gb|EGA66572.1| tRNA-dihydrouridine synthase A [Vibrio brasiliensis LMG 20546]
          Length = 333

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 142/316 (44%), Positives = 192/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIHG-KGDFLAYNQEEHPVALQLGGSNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 78  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMGEPQLVADCVAAMRDVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLVIAVNGGVKTLQETKEHLQHLDGVMVGREAYQNPYILAEVDQQI---FGL 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PIK R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 255 DTPIKKR------SQVVEEMYPYIEQQLSKGAYLGHITRHMLGLFQNMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAF 315
            A    +   ++E A 
Sbjct: 309 NAHKPGSGIEVVEAAL 324


>gi|229525073|ref|ZP_04414478.1| tRNA dihydrouridine synthase A [Vibrio cholerae bv. albensis VL426]
 gi|229338654|gb|EEO03671.1| tRNA dihydrouridine synthase A [Vibrio cholerae bv. albensis VL426]
          Length = 327

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 192/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G + + L ++ +E P ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPAALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGL 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 302 NAHKPGAGLEVVEQAL 317


>gi|83952336|ref|ZP_00961067.1| tRNA-dihydrouridine synthase A [Roseovarius nubinhibens ISM]
 gi|83836009|gb|EAP75307.1| tRNA-dihydrouridine synthase A [Roseovarius nubinhibens ISM]
          Length = 343

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 147/324 (45%), Positives = 193/324 (59%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ A A++RG   ++L  + +E P+ALQ+GG+D  
Sbjct: 27  MMDWTDRHCRYLHRLLSREALLYTEMVTAPALVRGGAMHLLDHAPEEHPVALQLGGSDPE 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++  + GY+EINLN GCPS RV  G+FGA LM +P  V DC AAM  A  + VT
Sbjct: 87  ELAEAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMTDPGRVADCCAAMIAATDVEVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  +  +GV    IHARKA LKGLSPK+NR IP LDYD+  
Sbjct: 147 VKCRIGVDDQDPEEVLPEFLARVGAAGVGRFTIHARKAWLKGLSPKENRDIPPLDYDLAR 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +    P L + +NGG+  +  A+++L    DGVM+GRAAY   A +L   D        
Sbjct: 207 RMIGLFPSLHLSINGGIATLDHAVELLDQGFDGVMLGRAAYHQPADILCAADRRI---FG 263

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P  T  D         +M  Y   HL +GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 264 HDGPDSTAEDA------VQAMLPYIEAHLAAGGRLNQITRHMLGLFAGRPGARAWRRMLS 317

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A   +   L
Sbjct: 318 EGASRPGAGPELVEEALTQIAPDL 341


>gi|83943001|ref|ZP_00955461.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. EE-36]
 gi|83846009|gb|EAP83886.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. EE-36]
          Length = 337

 Score =  274 bits (700), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 145/320 (45%), Positives = 194/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL +   LLYTEM+ + A++RG   ++L   T E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRYMHRLFSKQTLLYTEMVTSPALVRGGALHLLDHDTSEHPVALQLGGSDPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I    GY+EINLNVGCPS RV  G FGA LM  P +V   +AAM +A+ + VT
Sbjct: 78  ELAEAARIGAQAGYDEINLNVGCPSDRVQSGCFGAVLMEQPALVAKSVAAMRRAVDVDVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PA  L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 138 VKCRIGVDDQNPAEVLPEFLAQIVGAGCERVTIHARKAWLQGLSPKENRDIPPLDYELVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  + QA   L + +DGVMIGR+AY N + +L   D        
Sbjct: 198 RMKGLFPNLHISINGGITSLDQAEAFLDAGLDGVMIGRSAYHNPTDILAQADRRIYGTGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P            + A M  Y   H+  GGKL QITRHM+GLF G   +R  R  L+
Sbjct: 258 DTTP----------EDVVAQMLPYIDAHIDGGGKLNQITRHMMGLFAGRTGARVWRRTLS 307

Query: 299 VEAGASTATHHIIETAFNLM 318
            +A    A   ++  A + M
Sbjct: 308 EQASRPGADRQVLLEALDTM 327


>gi|310765537|gb|ADP10487.1| tRNA-dihydrouridine synthase A [Erwinia sp. Ejp617]
          Length = 331

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 144/322 (44%), Positives = 199/322 (61%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLY+EM+   AI+ G K + L FS++E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTQQTLLYSEMVTTGAIIHG-KGDYLAFSSEEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 74  ALAHCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ + G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYEFLCDFIHTVSEQGGCEVFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPHLTLSINGGVKSLAEAKIHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTSP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + PI           +  SM  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AADPI----------AVVRSMYPYIERELANGTYLGHVTRHMLGLFQGIPGARQWRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIE 320
                + A   ++E A +L+ +
Sbjct: 304 ENTHKAGAGVEVVEKALSLVAD 325


>gi|107022641|ref|YP_620968.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia AU 1054]
 gi|116689590|ref|YP_835213.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia HI2424]
 gi|105892830|gb|ABF75995.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia cenocepacia AU
           1054]
 gi|116647679|gb|ABK08320.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia cenocepacia
           HI2424]
          Length = 365

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 138/298 (46%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 38  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 97

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 98  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVRAMRDAVSVPVT 157

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 158 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 217

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 218 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYGS-TAA 276

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P++   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 277 VPMREEAE--------AQLIEYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLS 326


>gi|117618436|ref|YP_858131.1| tRNA-dihydrouridine synthase A [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559843|gb|ABK36791.1| tRNA-dihydrouridine synthase A [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 328

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 137/311 (44%), Positives = 192/311 (61%), Gaps = 10/311 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + LG+S QE P++LQ+GG++ +
Sbjct: 11  MLDWTDRHCRYFHRLMTRQTLLYTEMVTTGAIIHG-KGDYLGYSEQEHPISLQLGGSNPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+E+N+NVGCPS RV  G FGACLM  P +V DC+ AM   + IPVT
Sbjct: 70  DLARCAKLAEERGYDEVNINVGCPSDRVQNGRFGACLMGEPALVADCVKAMRDVVDIPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  ++ ++ +G +   +HARKA L GLSPK+NR+IP LDY  VY
Sbjct: 130 VKTRIGIDDQDSYEFLQAFIEQVRDAGCDTFIVHARKAWLSGLSPKENREIPPLDYPRVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG+  M Q L+ L  +DGVM+GR AY+N  +L  VD         +
Sbjct: 190 RVKQDYPDLTIAINGGVTSMEQTLEHLQHLDGVMMGREAYQNPYILAQVDNLV---FGQN 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + +R       ++   M  Y  + L  G  L  +TRHM+GLF     +R  R  L+  
Sbjct: 247 NAVPSR------HEVVRMMLPYIEQELAKGNYLSHMTRHMLGLFQNMQGARAWRRHLSEN 300

Query: 301 AGASTATHHII 311
           A    A   ++
Sbjct: 301 ACKPGADIQVV 311


>gi|262172527|ref|ZP_06040205.1| tRNA-dihydrouridine synthase [Vibrio mimicus MB-451]
 gi|261893603|gb|EEY39589.1| tRNA-dihydrouridine synthase [Vibrio mimicus MB-451]
          Length = 316

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 139/317 (43%), Positives = 194/317 (61%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D Q     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDAQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 180 YQIKRDFPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRH++GLF   P +R+ R  ++ 
Sbjct: 237 DTPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHILGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFN 316
            A    A   ++E A  
Sbjct: 291 NAHKPGAGLEVVEQALT 307


>gi|315125488|ref|YP_004067491.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas sp. SM9913]
 gi|315014001|gb|ADT67339.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas sp. SM9913]
          Length = 310

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 142/320 (44%), Positives = 198/320 (61%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G + + L F+  E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFG-RGDYLHFNQHEGPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM   +SIPVT
Sbjct: 60  ALAQCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMKSEVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++  K G +   IHARKA LKGLSPK+NR++P L+Y  VY
Sbjct: 120 VKTRIGIDEQDSYEFLCALIEASHKVGCDDFIIHARKAWLKGLSPKENREVPELNYPRVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + +NGG++ + Q+L+ L  +DGVM+GR AY N  ML  VDE        +
Sbjct: 180 QLKKDYPQLDLSINGGVKTIEQSLEHLQYIDGVMVGREAYSNPFMLNEVDEKIYG---DA 236

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +  +TR D      +  SM DY    +  G     + RHM+G+F G P +R  R  L+  
Sbjct: 237 ANTQTRHD------VVRSMYDYIEEEMRLGANFWHVARHMLGIFQGQPGARGFRRHLSEN 290

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 291 GHGKQADLSVMDKALSYVPE 310


>gi|189350413|ref|YP_001946041.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans ATCC
           17616]
 gi|189334435|dbj|BAG43505.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans ATCC
           17616]
          Length = 344

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 139/298 (46%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 197 RLKREFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 256 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLS 305


>gi|297582262|ref|ZP_06944177.1| TIM-barrel protein [Vibrio cholerae RC385]
 gi|297533520|gb|EFH72366.1| TIM-barrel protein [Vibrio cholerae RC385]
          Length = 327

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 193/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGL 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+G+F   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGVFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 302 NAHKPGAGLEVVEQAL 317


>gi|83954176|ref|ZP_00962896.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. NAS-14.1]
 gi|83841213|gb|EAP80383.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. NAS-14.1]
          Length = 337

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 145/320 (45%), Positives = 194/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL +   LLYTEM+ + A++RG   ++L   T E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRYMHRLFSKQTLLYTEMVTSPALVRGGALHLLDHDTSEHPVALQLGGSDPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I    GY+EINLNVGCPS RV  G FGA LM  P +V   +AAM +A+ + VT
Sbjct: 78  ELAEAARIGAQAGYDEINLNVGCPSDRVQSGCFGAVLMEQPALVAKSVAAMRRAVDVDVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PA  L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 138 VKCRIGVDDQNPAEVLPEFLAQIVGAGCERVTIHARKAWLQGLSPKENRDIPPLDYELVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  + QA   L + +DGVMIGR+AY N + +L   D        
Sbjct: 198 RMKGLFPNLHISINGGITSLDQAEAFLDAGLDGVMIGRSAYHNPTDILAQADRRIYGTGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P            + A M  Y   H+  GGKL QITRHM+GLF G   +R  R  L+
Sbjct: 258 DTTP----------EDVVAQMLPYIDAHIDGGGKLNQITRHMMGLFAGRTGARVWRRTLS 307

Query: 299 VEAGASTATHHIIETAFNLM 318
            +A    A   ++  A + M
Sbjct: 308 EQASRPGADRQVLLEALDAM 327


>gi|270263331|ref|ZP_06191601.1| tRNA-dihydrouridine synthase A [Serratia odorifera 4Rx13]
 gi|270043019|gb|EFA16113.1| tRNA-dihydrouridine synthase A [Serratia odorifera 4Rx13]
          Length = 336

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 199/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFHRLLTKETLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 79  ALAHCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGQATLVADCIKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR++P LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCDFIATVAGRGECDMFTIHARKAWLSGLSPKENREVPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 199 YQLKRDFPQLTLAINGGVKTLEEAKQHLEHLDGVMMGREAYQNPGILARVDSELFGR--- 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                +T V       I  S+  Y  R L +G  L  ITRH++GLF G P +R+ R  L+
Sbjct: 256 -----QTEVMDSV--AIIESLYPYIERELSNGTYLGHITRHILGLFQGVPGARQWRRHLS 308

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A +L+
Sbjct: 309 ENAHKPGADARVVEAALDLV 328


>gi|212710291|ref|ZP_03318419.1| hypothetical protein PROVALCAL_01350 [Providencia alcalifaciens DSM
           30120]
 gi|212687098|gb|EEB46626.1| hypothetical protein PROVALCAL_01350 [Providencia alcalifaciens DSM
           30120]
          Length = 341

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 143/316 (45%), Positives = 197/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AI+ G K + L +S +E P++LQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAIIYG-KGDYLAYSEEEHPVSLQLGGSDPV 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E+ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   +SIPVT
Sbjct: 88  ALAQCAKLAEERGYDEINLNVGCPSDRVQNGRFGACLMADAQLVADCVKAMRDVVSIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L   + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDEQDSYEFLCEFIDTVSTKGDCEMFIIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 208 YQLKRDFPHLTMAINGGIKTLEEAKEHLKYLDGVMVGREAYQNPSILTAVDNQLFDE--- 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + PI   V          SM  Y    L  G  L  +TRHM+G+F G P +R+ R  L+ 
Sbjct: 265 NMPIVDSV------AAVRSMYPYIENELSKGAYLGHMTRHMLGIFQGIPGARQWRRHLSE 318

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 319 NAHKQGADLSVVEQAL 334


>gi|238782919|ref|ZP_04626947.1| tRNA-dihydrouridine synthase A [Yersinia bercovieri ATCC 43970]
 gi|238716122|gb|EEQ08106.1| tRNA-dihydrouridine synthase A [Yersinia bercovieri ATCC 43970]
          Length = 339

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 202/320 (63%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHG-KGDYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKQAELRGYNEINLNVGCPSDRVQNGRFGACLMAEANLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAEQGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD E F +   
Sbjct: 206 YQLKRDFPVLTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDS--- 262

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+
Sbjct: 263 -NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLS 315

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 316 ENAHKPGADVSVVEQALALV 335


>gi|153216666|ref|ZP_01950573.1| TIM-barrel protein, yjbN family [Vibrio cholerae 1587]
 gi|124114177|gb|EAY32997.1| TIM-barrel protein, yjbN family [Vibrio cholerae 1587]
          Length = 327

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 192/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+A M   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVATMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGL 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 302 NAHKPGAGLEVVEQAL 317


>gi|261346564|ref|ZP_05974208.1| tRNA-dihydrouridine synthase A [Providencia rustigianii DSM 4541]
 gi|282565268|gb|EFB70803.1| tRNA-dihydrouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 341

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 200/316 (63%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AI+ G K + L +S +E P++LQ+GG+D +
Sbjct: 29  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAIIFG-KGDYLAYSEEEHPVSLQLGGSDPA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   +SIPVT
Sbjct: 88  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMADAQLVADCVKAMRDVVSIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++   G  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDEQDSYEFLCDFIDTVSTKGDCDTFVIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 208 YQLKRDFPHLTMAINGGVKTLEEAKEHLKYLDGVMMGREAYQNPSILTAVDNQLFDE--- 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + PI   ++          M  Y  + L +G  L  +TRHM+G+F G P +R+ R  L+ 
Sbjct: 265 TMPIVDNIEA------VRRMYPYIEKELSNGAYLGHMTRHMLGIFQGIPGARQWRRHLSE 318

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 319 NAHKKGADLTVVEQAL 334


>gi|50122581|ref|YP_051748.1| tRNA-dihydrouridine synthase A [Pectobacterium atrosepticum
           SCRI1043]
 gi|49613107|emb|CAG76558.1| putative dihydrouridine synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 340

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 143/319 (44%), Positives = 193/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G K + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHG-KGDYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM +  +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGDAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++ + G  +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCEFIQTVAERGECDTFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKMHLQHLDGVMMGREAYQNPGILAQVDRELFGIDAA 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +  +   V          SM  Y  R L     L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 268 TQDLAGVV---------RSMYPYIERELSGDASLGHITRHMLGMFQGIPGARQWRRYLSE 318

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 319 NAHKPGADSAVVERALALV 337


>gi|251793819|ref|YP_003008551.1| tRNA-dihydrouridine synthase A [Aggregatibacter aphrophilus NJ8700]
 gi|247535218|gb|ACS98464.1| tRNA-dihydrouridine synthase A [Aggregatibacter aphrophilus NJ8700]
          Length = 327

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 141/320 (44%), Positives = 195/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + + LLYTEM+ A AI+   K + L F   E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRHTLLYTEMVTAQAIIHA-KYDHLDFDAAEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E  GY EINLNVGCPS RV  G FGACLM  P++V +C+  M  A+ IPVT
Sbjct: 77  QLKHCAQLAEQRGYQEINLNVGCPSDRVQNGMFGACLMAKPNLVAECVQQMQSAVQIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L N V+++K+ G     +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLYNFVQTVKQVGCREFIVHARKAWLSGLSPKQNREIPLLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPDLLISINGGIKTIEEIQQHLQHVDGVMVGREAYQNPSLLGHIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+  A M  Y    L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIITP------RQAVARMLPYIESQLSQGVYLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++ETA   + E
Sbjct: 308 AYKEGAGIEMVETALGFVEE 327


>gi|161524837|ref|YP_001579849.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans ATCC
           17616]
 gi|160342266|gb|ABX15352.1| TIM-barrel protein, yjbN family [Burkholderia multivorans ATCC
           17616]
          Length = 357

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 139/298 (46%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 30  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 90  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 210 RLKREFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 269 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLS 318


>gi|330503878|ref|YP_004380747.1| tRNA-dihydrouridine synthase A [Pseudomonas mendocina NK-01]
 gi|328918165|gb|AEB58996.1| tRNA-dihydrouridine synthase A [Pseudomonas mendocina NK-01]
          Length = 312

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 133/301 (44%), Positives = 193/301 (64%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A++ GD++  L +S  E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRFFLRQLSRHALLYTEMVTTGALIHGDRERFLRYSECEHPIALQLGGSNPQ 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 61  DLATCTKMAEEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMQDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR++P L YD+  
Sbjct: 121 VKHRIGINGRDSYAELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREVPPLRYDVAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ PDL I LNGG++ + +  + L S DGVM+GR AY N  +L  VD   F    TG
Sbjct: 181 QLKQDFPDLEIILNGGIKTIEECEQHLQSFDGVMLGREAYHNPYLLAQVDSRLFGTADTG 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + ++  +          ++  Y  +HL  GG L  ++RH++GL  GFP +RR R +L+V
Sbjct: 241 ITRMEALL----------ALKPYVEQHLREGGTLHHVSRHVLGLAQGFPGARRFRQLLSV 290

Query: 300 E 300
           +
Sbjct: 291 D 291


>gi|312173953|emb|CBX82207.1| tRNA-dihydrouridine synthase A [Erwinia amylovora ATCC BAA-2158]
          Length = 349

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 144/324 (44%), Positives = 199/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLYTEM+   AI+ G K + L F ++E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRQLTRQTLLYTEMVTTGAIIHG-KGDYLAFGSEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 92  ALAQCAKLAERRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G     IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFMRTVSEQGGCEMFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 212 YQLKRDFPHLTLSINGGVKSLAEAKIHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTSP 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              PI           +  SM  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 272 SIDPI----------AVVRSMYPYIERELAGGTYLGHVTRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +++ E +
Sbjct: 322 ENAHKAGAGIDVVEKALSMVAEKV 345


>gi|330828271|ref|YP_004391223.1| tRNA-dihydrouridine synthase A [Aeromonas veronii B565]
 gi|328803407|gb|AEB48606.1| tRNA-dihydrouridine synthase A [Aeromonas veronii B565]
          Length = 328

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 189/301 (62%), Gaps = 10/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++   LLYTEM+   AI+ G K + LG+S QE P++LQ+GG++ +
Sbjct: 11  MLDWTDRHCRYFHRLMSRQTLLYTEMVTTGAIIHG-KGDYLGYSEQEHPISLQLGGSNPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+E+N+NVGCPS RV  G FGACLM  P +V DC+ AM   + IPVT
Sbjct: 70  DLARCAKLAEERGYDEVNINVGCPSDRVQNGRFGACLMGEPALVADCVKAMRDVVDIPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  ++ ++ +G +   +HARKA L GLSPK+NR+IP LDY  VY
Sbjct: 130 VKTRIGIDDQDSYEFLQAFIEQVRDAGCDTFIVHARKAWLSGLSPKENREIPPLDYPRVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I LNGG+  M Q L+ L  VDGVM+GR AY+N  +L  VD         +
Sbjct: 190 RVKQDYPELTIALNGGVTSMEQTLEHLQHVDGVMMGREAYQNPYILAQVDNLV---FGQN 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + +R       ++   M  Y  + L  G  L  +TRHM+GLF     +R  R  L+  
Sbjct: 247 NAVPSR------HEVVRMMLPYIEQELAKGNYLSHMTRHMLGLFQNMQGARAWRRHLSEN 300

Query: 301 A 301
           A
Sbjct: 301 A 301


>gi|304313001|ref|YP_003812599.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HdN1]
 gi|301798734|emb|CBL46967.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HdN1]
          Length = 357

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 135/316 (42%), Positives = 192/316 (60%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  R ++   LLYTEM+   A+L  +    L +   E PLALQ+GG    
Sbjct: 47  MLDWTDRHARYMLRQISQRTLLYTEMVTTGALLHTNPARWLDYHHDEHPLALQLGGNQPH 106

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +  K+   + Y+E+NLNVGCPS RV EG+FGACLM  P+IV DC+ AM  A ++P+T
Sbjct: 107 ALAQCVKLAAQWQYDEVNLNVGCPSDRVQEGAFGACLMATPNIVADCVKAMQDASNLPIT 166

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ     L++ +++++ +G     +HARKA LKGLSPK+NR+IP L+Y  V+
Sbjct: 167 VKCRIGIDDQDEEQGLQDFIETVQAAGCKTFIVHARKAWLKGLSPKENREIPPLNYPRVH 226

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ PDL + +NGG + + +  + L  +DGVMIGR AY N  +L   D+        +
Sbjct: 227 RLKKDFPDLELIINGGFKTLDECAEQLAHLDGVMIGREAYHNPMVLADADQRIFG--ATN 284

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI           +   M  YA R    G  ++ ITRHM+GL HG P  RR R +L+ +
Sbjct: 285 APICREA-------LIHKMHAYAERQYRDGVAVKHITRHMLGLLHGIPGGRRWRRVLSEK 337

Query: 301 AGASTATHHIIETAFN 316
           A    AT  I+  A++
Sbjct: 338 APRDGATPDILLEAWH 353


>gi|110679742|ref|YP_682749.1| tRNA-dihydrouridine synthase A [Roseobacter denitrificans OCh 114]
 gi|109455858|gb|ABG32063.1| tRNA-dihydrouridine synthase A [Roseobacter denitrificans OCh 114]
          Length = 334

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 144/300 (48%), Positives = 192/300 (64%), Gaps = 12/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R LT+ +LLYTEM+ + A++RG   ++L FS  E P+ALQ+GG+D  
Sbjct: 14  MMDWTDRHCRMVHRQLTHQSLLYTEMVTSAALVRGGALHLLAFSPDEHPVALQLGGSDPK 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA + +  GY EINLNVGCPS RV  G FGA LM NP +V DC++AM +A+ IPVT
Sbjct: 74  ELAQAAMLGQTAGYREINLNVGCPSDRVQSGCFGAVLMENPGLVADCVSAMREAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY +V 
Sbjct: 134 VKCRIGVDDQNPDEVLPEFLARIVAAGCERVSIHARKAWLQGLSPKENRDIPPLDYPLVL 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K+  P+L I +NGG+  + QA+  L + +DGVMIGRAAY     +L  VD      + 
Sbjct: 194 RMKEYFPNLHISINGGITSLEQAVGFLEAGLDGVMIGRAAYHTPTDVLGAVDPV----IF 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G+  + T        +   +M  Y   H+  GG+L QITRHM+GLF   P +R  R +L+
Sbjct: 250 GTGKVVT------GEEAVHAMLPYIEAHVTGGGRLAQITRHMLGLFANRPGARVWRRMLS 303


>gi|85704298|ref|ZP_01035401.1| tRNA-dihydrouridine synthase A [Roseovarius sp. 217]
 gi|85671618|gb|EAQ26476.1| tRNA-dihydrouridine synthase A [Roseovarius sp. 217]
          Length = 321

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 148/317 (46%), Positives = 194/317 (61%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  R L+ +ALLYTEM+ A A++RG   ++L  S +E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRRLSRHALLYTEMVTAPALVRGGAVHLLEHSPEEYPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++    GY EINLN GCPS RV  G FGA LM  P +V +C AAM  A  + VT
Sbjct: 61  ELARAARMGAQAGYAEINLNCGCPSDRVQSGRFGAILMTEPALVAECCAAMIDAQPVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +GV  + IHARKA L GLSPK+NR IP L+YD+V 
Sbjct: 121 VKCRIGVDDQTPEEVLPEFLAQIIAAGVQRVQIHARKAWLDGLSPKENRDIPPLNYDLVQ 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  + QA+ +L   +DGVM+GRAAY   A +L   D      + 
Sbjct: 181 RMKMLFPNLHISINGGITSLDQAVSLLDQGLDGVMVGRAAYHQPADILCAADRR----IF 236

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS+   T  +         +M  Y   HL SGG+L QITRHM+GLF G P +R  R  L+
Sbjct: 237 GSTEPDTTPEGAV-----QAMLPYIETHLASGGRLNQITRHMLGLFAGRPGARAWRRHLS 291

Query: 299 VEAGASTATHHIIETAF 315
             A    A   ++E A 
Sbjct: 292 EGATRPGAGPELVERAL 308


>gi|332531883|ref|ZP_08407767.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038510|gb|EGI74953.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 313

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 144/320 (45%), Positives = 196/320 (61%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G + + L F+  E P+ALQ+GG+D  
Sbjct: 4   MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFG-RGDYLHFNKHEGPVALQLGGSDPK 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM   ++IPVT
Sbjct: 63  ALAQCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVAECVAAMKNEVNIPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++  K G +   IHARKA L GLSPK+NR++P LDY  VY
Sbjct: 123 VKTRIGIDEQDSYEFLCALIEASHKVGCDDFIIHARKAWLNGLSPKENREVPPLDYPRVY 182

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + LNGG++ + Q+L+ L  +DGVMIGR AY N  ML  VDE        S
Sbjct: 183 QLKKDYPQLDLSLNGGVKTIEQSLEHLQHIDGVMIGREAYSNPFMLNDVDEKIYG---DS 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +  ++R D      +  SM DY    +  G     I RHM+G+F G P +R  R  L+  
Sbjct: 240 ANTQSRHD------VVRSMYDYIEEEMRLGANFWHIARHMLGIFQGQPGARGFRRHLSES 293

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 294 GHGKQADLSVMDKALSFVPE 313


>gi|183221906|ref|YP_001839902.1| tRNA-dihydrouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189911975|ref|YP_001963530.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167776651|gb|ABZ94952.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167780328|gb|ABZ98626.1| tRNA-dihydrouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 323

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 144/314 (45%), Positives = 193/314 (61%), Gaps = 10/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH+R+F RL++ +ALLYTEM+   AILRG D    L FS +E P+ALQ+GG   
Sbjct: 15  MMDWTDRHFRYFIRLISKHALLYTEMVTTGAILRGKDNHRYLDFSKEEHPIALQLGGDSP 74

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L E AKI ED+GY+EINLNVGCPS RV  GSFGACLM  PD+V + +A     + IPV
Sbjct: 75  KALAECAKIGEDYGYDEINLNVGCPSDRVQSGSFGACLMKEPDLVAEMVAFCKSKVKIPV 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIGV+ +     L   V  I+K+GV+   +HAR AIL+GLSPK+NR IP L Y+ V
Sbjct: 135 TVKHRIGVNGKESYEDLHQFVSKIQKAGVDHCIVHARIAILEGLSPKENRTIPPLRYEDV 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K + P+L I +NGG++  ++    L   DGVM+GRAAY N  +   VD  +     G
Sbjct: 195 YRLKSDFPNLPITINGGIKTHAEIKTHLTKADGVMVGRAAYDNPFLFADVDSLYFGSKEG 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +   ++ + K         M  Y      SGGK+  I RH++GL+HG   +R  R   T 
Sbjct: 255 TITRESILQK---------MIPYVQSVRMSGGKVSHILRHILGLYHGEKGAREFRRYFTN 305

Query: 300 EAGASTATHHIIET 313
               ++AT  I+E+
Sbjct: 306 GMHLTSATESILES 319


>gi|261250374|ref|ZP_05942949.1| tRNA dihydrouridine synthase A [Vibrio orientalis CIP 102891]
 gi|260938943|gb|EEX94930.1| tRNA dihydrouridine synthase A [Vibrio orientalis CIP 102891]
          Length = 333

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 193/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIHG-KGDFLAYNQEEHPVALQLGGSNPK 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + +PVT
Sbjct: 78  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMGEPQLVADCVAAMRDVVDVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +++  + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLAIAVNGGVKTLAETKEHLQHLDGVMVGREAYQNPYILAEVDQQI---FGL 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 255 DKPVKKRT------QVVEEMYPYIEQQLSNGAYLGHITRHMLGLFQNMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAF 315
            A    +   ++E A 
Sbjct: 309 NAHKPGSGIEVVEAAL 324


>gi|325525397|gb|EGD03227.1| tRNA-dihydrouridine synthase A [Burkholderia sp. TJI49]
          Length = 328

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 138/298 (46%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L FS  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFSPNESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMNDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAEAGCATFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 RLKRDFPELEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TDA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 240 APTREEAE--------AKLIEYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLS 289


>gi|254449021|ref|ZP_05062475.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HTCC5015]
 gi|198261415|gb|EDY85706.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HTCC5015]
          Length = 315

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 136/314 (43%), Positives = 195/314 (62%), Gaps = 10/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A+L G+    L F + E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRYFHRLLSPHALLYTEMVTTGALLHGNVSRHLAFHSDEHPVALQLGGSEPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A++ E +GY+E+N+NVGCPS RV  G+FGACLM  PD V  C+AAM  A+SIPVT
Sbjct: 61  AMARCAELAERWGYDEVNINVGCPSDRVQSGAFGACLMAEPDTVASCVAAMKSAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L +    +  +  + + +HARKA LKGLSPK+NR IP L YD VY
Sbjct: 121 VKTRIGIDDMDDYQNLFDFTAKVIAANCDNLTVHARKAWLKGLSPKENRDIPPLMYDKVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L + +NGG+ D +   + L   DGVMIGRAAY+N   L  +++   + L   
Sbjct: 181 QLKRDYPELEVCINGGITDSASVSEHLRHTDGVMIGRAAYQNPWWLVELEQNLFDEL--H 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +         ++   M +Y    L +GG+L+ ITRHM+GLF   P +++ R  L+  
Sbjct: 239 RPTQ--------HEVVEGMLEYIEAELLAGGQLKHITRHMLGLFQAVPGAKQWRRHLSEN 290

Query: 301 AGASTATHHIIETA 314
           A    A   ++  A
Sbjct: 291 AHLPGAGPELLRAA 304


>gi|261822868|ref|YP_003260974.1| tRNA-dihydrouridine synthase A [Pectobacterium wasabiae WPP163]
 gi|261606881|gb|ACX89367.1| TIM-barrel protein, yjbN family [Pectobacterium wasabiae WPP163]
          Length = 340

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 147/320 (45%), Positives = 195/320 (60%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G K + L +S  E PLALQ+GG+D +
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHG-KGDYLAYSEDEHPLALQLGGSDPT 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEINLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++   G  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCEFIQTVAGRGECDTFIIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F   + 
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFG--ID 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P    V +        +M  Y  R L  G  L  ITRHM+G+F G   +R+ R  L+
Sbjct: 266 AAEPDLAGVVR--------AMYPYIERELSGGASLGHITRHMLGMFQGITGARQWRRYLS 317

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A  L+
Sbjct: 318 ENAHKPGADAAVVERALTLV 337


>gi|34496379|ref|NP_900594.1| tRNA-dihydrouridine synthase A [Chromobacterium violaceum ATCC
           12472]
 gi|34102232|gb|AAQ58598.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 347

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 134/298 (44%), Positives = 186/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FAR +T +  LYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 33  MLDWTDRHYRYFARQITRHTWLYTEMVTTGALLNGDVARHLRFDEAEHPVALQLGGSEPA 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ + +GY+E+NLNVGCPS RV +G+FGACLM  P +V DC+ AM  A+ I VT
Sbjct: 93  ELATCAKLAQQWGYDEVNLNVGCPSERVQKGAFGACLMAEPQLVSDCVKAMRDAVDIDVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       LR  V ++ ++G     +HAR AILKGLSPK+NR+IP L YD VY
Sbjct: 153 VKHRIGIDQIEHYDYLREFVDTVAEAGCRTFIVHARNAILKGLSPKENREIPPLKYDYVY 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++  ++  + L  VDGVM+GR AY N  ++   D  F    T +
Sbjct: 213 RLKRERPDLEILINGGVKTNAEIAEHLKHVDGVMVGREAYHNPWLMADWDALFYGDET-A 271

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P +          +  +M  Y    L  G  ++ I RH++GLF G P +R  R +L+
Sbjct: 272 RPERV--------AVVEAMMPYVTARLGDGSNVRHIARHILGLFQGLPGARNWRRMLS 321


>gi|167032718|ref|YP_001667949.1| tRNA-dihydrouridine synthase A [Pseudomonas putida GB-1]
 gi|166859206|gb|ABY97613.1| TIM-barrel protein, yjbN family [Pseudomonas putida GB-1]
          Length = 336

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 192/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D +  L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKQTLLYTEMVTTGALLHNDAQRFLRHDASEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ED GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 85  DLAACARLAEDAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + +  K L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKADFPDLEIVLNGGIKTLDECQKHLETFDGVMLGREAYHNPYLLAEVDQQL---FASD 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 262 APVVSRSEA------LAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKAAEPLAVFDQAMELL 333


>gi|332709415|ref|ZP_08429376.1| tRNA dihydrouridine synthase A [Lyngbya majuscula 3L]
 gi|332351674|gb|EGJ31253.1| tRNA dihydrouridine synthase A [Lyngbya majuscula 3L]
          Length = 340

 Score =  272 bits (695), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 141/299 (47%), Positives = 187/299 (62%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRHYR+F R +T   LLYTEM+ + AIL GD++ +LGFS QEKPL LQ+GG   S
Sbjct: 31  MMDRTDRHYRYFMRQITGRTLLYTEMVTSAAILHGDRERLLGFSPQEKPLVLQVGGDTPS 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I E   Y++INLNVGCPS+RV  G+FGACLM  PD V  C+  M K ++IPVT
Sbjct: 91  DLAECARIAEAMDYDQINLNVGCPSSRVQNGNFGACLMAQPDQVARCVEDMVKVVNIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + N V+ + ++G     +HARKA L+GLSPK+NR +P L Y  V+
Sbjct: 151 VKHRIGIDDLDRYEDMANFVRIVSEAGCQHFTVHARKAWLQGLSPKENRNVPPLRYSDVH 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+E PDLF+ +NGG   + Q  +    VDGVMIGRAAY N  +    D + +S+  T 
Sbjct: 211 RLKQELPDLFVEINGGFTSLEQVREQRKYVDGVMIGRAAYDNPYLFAKADCDIYSD--TV 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             P +         ++  +M  Y    +  G KL +ITRHM+ LF G P SR  +  LT
Sbjct: 269 IPPTR--------HQVVEAMFSYIDHWVGKGIKLNKITRHMLQLFAGQPGSRAWKRHLT 319


>gi|226945328|ref|YP_002800401.1| tRNA-dihydrouridine synthase A [Azotobacter vinelandii DJ]
 gi|226720255|gb|ACO79426.1| Dihydrouridine synthase yjbN family protein [Azotobacter vinelandii
           DJ]
          Length = 336

 Score =  272 bits (695), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 142/301 (47%), Positives = 190/301 (63%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L GD +  L     E PLALQ+GG+   
Sbjct: 25  MLDWTDRHCRFFLRQLSYHALLYTEMVTTGALLHGDARRFLRHERMEHPLALQLGGSVPG 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+EINLNVGCPS RV     GACLM +P  V DC+ AM  A++IPVT
Sbjct: 85  ELAACARLAEEAGYDEINLNVGCPSDRVQNNLIGACLMGDPARVADCVKAMRDAVTIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     LR+ V  + ++G     +HAR AIL GLSPK+NR+IP L Y+IV 
Sbjct: 145 VKHRIGIDGRDSYGELRDFVGQVCEAGCRSFIVHARIAILAGLSPKENREIPPLRYEIVA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ PDL I LNGG++ + +    L S DGVMIGR AY N  +L  VD E F +PL  
Sbjct: 205 QLKQDFPDLEIVLNGGIKTLEECRLHLRSFDGVMIGREAYHNPYLLAQVDRELFDSPLPA 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S            +    +  Y  ++L+ GG L  ITRH++GL  GFP +RR R +L+V
Sbjct: 265 LS----------RHEALKRLRPYIQQYLNEGGALHHITRHVLGLGQGFPGARRFRQLLSV 314

Query: 300 E 300
           +
Sbjct: 315 D 315


>gi|322834778|ref|YP_004214805.1| TIM-barrel protein, yjbN family [Rahnella sp. Y9602]
 gi|321169979|gb|ADW75678.1| TIM-barrel protein, yjbN family [Rahnella sp. Y9602]
          Length = 335

 Score =  272 bits (695), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 145/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RL+T   LLYTEM+   AI+ G K + LGF   E P++LQ+GG++ +
Sbjct: 17  MLDWTDRHCRHFHRLMTGQTLLYTEMVTTGAIIHG-KGDYLGFGDAEHPVSLQLGGSNPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 76  DLAHCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGQASLVADCIKAMRDVVSIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++ + ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 136 VKTRIGIDDQDSYEFLCDFIRQVSENGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 196 YQLKRDFPHLTLAINGGIKTLEEAKTHLQYMDGVMVGREAYQNPGLLLNVDRELFGS--- 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +P+KT  D      I  ++  Y    L  G  L  ITRH++GLF G P +R+ R  L+
Sbjct: 253 -DAPLKTGPD------IIRALYPYIEAELSKGTYLGHITRHILGLFQGVPGARQFRRHLS 305

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A   ++E A  ++ +
Sbjct: 306 ENAHKAGAGIDVVEQALQMVAQ 327


>gi|78066180|ref|YP_368949.1| tRNA-dihydrouridine synthase A [Burkholderia sp. 383]
 gi|77966925|gb|ABB08305.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia sp. 383]
          Length = 344

 Score =  272 bits (695), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 137/298 (45%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPSLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 QLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYG---ST 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             + TR + +      A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 254 EAVPTREEAE------AKLIEYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLS 305


>gi|269961484|ref|ZP_06175848.1| NifR3/Smm1 family protein [Vibrio harveyi 1DA3]
 gi|269833861|gb|EEZ87956.1| NifR3/Smm1 family protein [Vibrio harveyi 1DA3]
          Length = 369

 Score =  272 bits (695), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 143/317 (45%), Positives = 196/317 (61%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++ +
Sbjct: 55  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNAA 113

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 114 DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDIPVT 173

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 174 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 233

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+     L G
Sbjct: 234 YQLKKDFSHLTIAINGGVKSLEEAKDHLQHLDGVMIGREAYQSPYLLASVDQ----ELFG 289

Query: 240 S-SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S +P+K R +      I   M  Y    L  G  L  I+RHM+GLF   P +R+ R  ++
Sbjct: 290 SNAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHISRHMLGLFQNMPGARQWRRHIS 343

Query: 299 VEAGASTATHHIIETAF 315
             A    +   +++ A 
Sbjct: 344 ENAHKPGSGLEVLQDAL 360


>gi|254245521|ref|ZP_04938842.1| tRNA-dihydrouridine synthase [Burkholderia cenocepacia PC184]
 gi|124870297|gb|EAY62013.1| tRNA-dihydrouridine synthase [Burkholderia cenocepacia PC184]
          Length = 359

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 138/298 (46%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 92  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVRAMRDAVSVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 152 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 211

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 212 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYG---AT 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           + + TR + +      A +  Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 269 AAVPTREEAE------AQLIAYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLS 320


>gi|163735338|ref|ZP_02142772.1| tRNA-dihydrouridine synthase A [Roseobacter litoralis Och 149]
 gi|161391347|gb|EDQ15682.1| tRNA-dihydrouridine synthase A [Roseobacter litoralis Och 149]
          Length = 321

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 148/324 (45%), Positives = 199/324 (61%), Gaps = 19/324 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R LT   LLYTEM+ + A++RG   ++L FS  E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRMLHRQLTRQTLLYTEMVTSAALVRGGALHLLEFSPDEHPVALQLGGSDPK 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA + +  GY+EINLNVGCPS RV  G FGA LM +P +V DC+AAM  A+ +PVT
Sbjct: 61  ELAQAAVLGQTAGYDEINLNVGCPSDRVQSGCFGAVLMESPALVADCVAAMRDAVEVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY +V 
Sbjct: 121 VKCRIGVDDQNPEEVLPEFLARIVAAGCERVAIHARKAWLQGLSPKENRDIPPLDYPLVL 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K+  P+L I +NGG+  + +A   L + +DGVMIGRAAY     +L  VD      + 
Sbjct: 181 RMKEYFPNLHISVNGGITSLDEARAFLEAGLDGVMIGRAAYHTPTDILAAVDPV----IF 236

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G+  +    D         +M  Y   H+  GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 237 GTGEVVAAEDA------VHAMLPYIEGHVTGGGRLGQITRHMLGLFAGRPGARVWRRMLS 290

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A       H+     +L++E+L
Sbjct: 291 EGA-------HLPNAGSSLVLEAL 307


>gi|119469148|ref|ZP_01612132.1| tRNA-dihydrouridine synthase A [Alteromonadales bacterium TW-7]
 gi|119447400|gb|EAW28668.1| tRNA-dihydrouridine synthase A [Alteromonadales bacterium TW-7]
          Length = 329

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 142/320 (44%), Positives = 196/320 (61%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G + + L F+  E P+ALQ+GG+D  
Sbjct: 20  MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFG-RGDYLHFNQHEGPVALQLGGSDPE 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V  C+AAM   +SIPVT
Sbjct: 79  ALAKCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVAAMKNEVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++  K G +   IHARKA L GLSPK+NR++P LDY  VY
Sbjct: 139 VKTRIGIDEQDSYEFLCALIEASHKVGCDDFIIHARKAWLNGLSPKENREVPPLDYPRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + +NGG++ + Q+L+ L  +DGVM+GR AY N  ML  VDE        +
Sbjct: 199 QLKKDYPQLDLSINGGVKTVEQSLEHLQYIDGVMVGREAYSNPFMLNEVDEKIYG---DT 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +  +TR D      +  SM DY    +  G     + RHM+G+F G P +R  R  L+  
Sbjct: 256 ANTQTRHD------VVRSMYDYIEEEMRLGANFWHVARHMLGIFQGQPGARGFRRHLSEN 309

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 310 GHGKQADLSVMDKALSFVPE 329


>gi|156932320|ref|YP_001436236.1| tRNA-dihydrouridine synthase A [Cronobacter sakazakii ATCC BAA-894]
 gi|156530574|gb|ABU75400.1| hypothetical protein ESA_00095 [Cronobacter sakazakii ATCC BAA-894]
          Length = 313

 Score =  271 bits (694), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 143/322 (44%), Positives = 199/322 (61%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L++  LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRQLSSQVLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 60  ALAHCAKLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFVGTVAEQGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ +      L  +DGVM+GR AY+N  +L +VD E F   + 
Sbjct: 180 HQLKRDFPKLTMSINGGIKTLDDVKTHLEHMDGVMVGREAYQNPGILASVDREIFGLDVP 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELAKGTYLGHVTRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A  +++E A  L+ +
Sbjct: 290 ENAHKPGADINVLEQALKLVAD 311


>gi|325914535|ref|ZP_08176879.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
 gi|325539305|gb|EGD10957.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
          Length = 334

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 192/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRMRLIGFDPVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +D+GY+EINLN GCPS RV  G FGACLM  P +V +C+AAMC A ++P+T
Sbjct: 79  LLAQAATIAQDWGYDEINLNCGCPSDRVQAGRFGACLMREPTLVAECVAAMCAATALPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYAVFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +++E P L + LNGG+  +  AL  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLRQERPGLPVVLNGGIAAVDTALAHLQQTDGVMLGRAAYHDPYVLHQLDAALTQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  ++  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------EALLRALRPYVESQLEQGLALKHITRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALQ 323


>gi|254241250|ref|ZP_04934572.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|126194628|gb|EAZ58691.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
          Length = 332

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 135/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM NP +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGNPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFMVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVD----SQLFGS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   R     +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 257 EAPPLSRSEALLR-----LRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|91227265|ref|ZP_01261690.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
 gi|91188659|gb|EAS74948.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
          Length = 315

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++ +
Sbjct: 1   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 60  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 180 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 291 NAHKPGSGLEVLQDAL 306


>gi|104782703|ref|YP_609201.1| tRNA-dihydrouridine synthase A [Pseudomonas entomophila L48]
 gi|95111690|emb|CAK16414.1| tRNA-dihydrouridine synthase A [Pseudomonas entomophila L48]
          Length = 333

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 135/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ +ALLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 22  MMDWTDRHCRFFLRLLSKHALLYTEMVTTGALLHNDAHRFLRHDDSEHPLALQLGGSVPA 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 82  DLAACARLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMQDAVSIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 142 VKHRIGINGRDSYAELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL + LNGG++ + +    L + DGVM+GR AY N  +L  VD+        S
Sbjct: 202 QLKADFPDLELVLNGGIKTLEECRTHLETFDGVMLGREAYHNPYLLAEVDQQL---FGSS 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R +        A +  Y   H+ SGG +  ITRH++GL  GFP +RR R +L+ +
Sbjct: 259 EPVISRAEA------MAKLRPYIVAHMESGGAMHHITRHILGLGQGFPGARRFRQLLSAD 312

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 313 IHKTDTPLAVLDQAAELL 330


>gi|153839570|ref|ZP_01992237.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ3810]
 gi|149746903|gb|EDM57891.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ3810]
          Length = 326

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 195/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + +PVT
Sbjct: 71  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 248 NAPVKKRSE------IVEEMYPYIETQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 302 NAHKPGSGLEVLQDAL 317


>gi|170732894|ref|YP_001764841.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia MC0-3]
 gi|169816136|gb|ACA90719.1| TIM-barrel protein, yjbN family [Burkholderia cenocepacia MC0-3]
          Length = 328

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 138/298 (46%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVRAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 181 RLKHDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYG---ST 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           + + TR + +      A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 238 AAVPTREEAE------AQLIEYCAGELKRGTCLGAIVRHALGLYRGMPGARGWRRVLS 289


>gi|90021133|ref|YP_526960.1| tRNA-dihydrouridine synthase A [Saccharophagus degradans 2-40]
 gi|89950733|gb|ABD80748.1| TIM-barrel protein, yjbN family [Saccharophagus degradans 2-40]
          Length = 331

 Score =  271 bits (693), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 141/319 (44%), Positives = 198/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+D+H R+F R LT  + LYTEM+V  AI+ GD++  L F+  E P+ALQ+GG+D +
Sbjct: 20  MMDWSDKHCRYFWRQLTKKSRLYTEMVVTGAIIHGDRERFLQFNNAEHPIALQVGGSDPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I +D+GY+EINLN GCPS RV  G  GA LM  P++V +CI AM KA  IPVT
Sbjct: 80  ALAQCARIAQDWGYDEINLNCGCPSDRVQNGMIGAILMSKPELVAECIDAMQKACDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD     AL N V ++ ++G N   +HARKA LKGLSPK+NR+IP L YD+V 
Sbjct: 140 VKHRIGIDDMEDYEALSNFVTTVAQTGCNTFIVHARKAWLKGLSPKENREIPPLRYDLVV 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
           ++KK  P L I +NGG+  + QA  +L  +DGVMIGR AY N   L  VD+  F  P   
Sbjct: 200 QLKKAFPHLNIVINGGINCLEQAKTLLNDLDGVMIGREAYHNPFFLADVDQKLFGTP--- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P   R       ++      YA +   +G +L  ++RH++GL+ G   +R  R  +T+
Sbjct: 257 -NPSANR------HEVLDKFIHYAEQQNAAGTRLHHMSRHILGLYLGQKGARAFRRHITI 309

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A+  ++  A  L+
Sbjct: 310 HAANREASAVVLREAKQLV 328


>gi|308125855|ref|ZP_07663540.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus K5030]
 gi|308113305|gb|EFO50845.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus K5030]
          Length = 315

 Score =  271 bits (693), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 195/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + +PVT
Sbjct: 60  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDVPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 180 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 291 NAHKPGSGLEVLQDAL 306


>gi|28899501|ref|NP_799106.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260879420|ref|ZP_05891775.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AN-5034]
 gi|260894695|ref|ZP_05903191.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus Peru-466]
 gi|260902033|ref|ZP_05910428.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ4037]
 gi|38604768|sp|Q87L85|DUSA_VIBPA RecName: Full=tRNA-dihydrouridine synthase A
 gi|28807737|dbj|BAC60990.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|308087465|gb|EFO37160.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus Peru-466]
 gi|308089701|gb|EFO39396.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AN-5034]
 gi|308109416|gb|EFO46956.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ4037]
          Length = 326

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 195/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + +PVT
Sbjct: 71  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 248 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 302 NAHKPGSGLEVLQDAL 317


>gi|238760286|ref|ZP_04621429.1| tRNA-dihydrouridine synthase A [Yersinia aldovae ATCC 35236]
 gi|238701488|gb|EEP94062.1| tRNA-dihydrouridine synthase A [Yersinia aldovae ATCC 35236]
          Length = 349

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 144/319 (45%), Positives = 200/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G K + L +S Q+ P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHG-KGDYLAYSEQDHPVALQLGGSDPL 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 92  ALAHCAKSAELRGYNEINLNVGCPSDRVQNGRFGACLMGEAELVADCIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G   I+ IHARKA L GLSPK+NR++P L+Y+ V
Sbjct: 152 VKTRIGIDQLDSYEFLCEFVQTVAERGECNIFTIHARKAWLSGLSPKENREVPPLNYERV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N  +L  VD    +P   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPCILAQVDRELFDP--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 NAPVMDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGVPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  ++
Sbjct: 323 NAHKPGADVSVVEQALAMV 341


>gi|21233367|ref|NP_639284.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770330|ref|YP_245092.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|38604922|sp|Q8P3X4|DUSA_XANCP RecName: Full=tRNA-dihydrouridine synthase A
 gi|21115203|gb|AAM43166.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575662|gb|AAY51072.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. 8004]
          Length = 335

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 140/314 (44%), Positives = 193/314 (61%), Gaps = 11/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD++ ++GF   E PLALQ+GG+D +
Sbjct: 20  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRQRLIGFDAVEHPLALQLGGSDPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I + +GY+EINLN GCPS RV  G FGACLM  P +V DC+AAMC A ++PVT
Sbjct: 80  LLAQAAQIAQAWGYDEINLNCGCPSDRVQAGRFGACLMREPALVADCVAAMCAATALPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          +  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 140 VKCRLGVDDDDDYAVFAGFIDQVVGAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  +L  L   DGVM+GRAAY +  +L  ++   S      
Sbjct: 200 RLKQERPALPVVLNGGIASVEASLAHLQHTDGVMLGRAAYHDPYVLHQLEAALSG----- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R D      +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 255 RPERARAD------LLQAYQPYVQAQLDQGLALKHMTRHILGLFHGQPGGRVFRQVLSEG 308

Query: 301 AGASTATHHIIETA 314
           A    A   ++E A
Sbjct: 309 AHRPGAGWELVEQA 322


>gi|290476894|ref|YP_003469805.1| tRNA-dihydrouridine synthase A [Xenorhabdus bovienii SS-2004]
 gi|289176238|emb|CBJ83043.1| tRNA-dihydrouridine synthase A [Xenorhabdus bovienii SS-2004]
          Length = 345

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 146/323 (45%), Positives = 201/323 (62%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  ALLYTEM+   AI+ G K N L ++ +E PLALQ+GG++  
Sbjct: 33  MLDWTDRHCRYFHRLLSKEALLYTEMVTTGAIIHG-KGNYLTYNEEEHPLALQLGGSEPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AKI ++ GY+EINLNVGCPS RV  G FGACLM    +V D I AM   + IPVT
Sbjct: 92  ALAQCAKIAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAKLVADGIKAMQDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + + +K S  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDEQDSYEFLCDFIDTVVKNSDCDNFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L + +NGG++ + +A + L  VDGVMIGR AY+N ++L  VD    N    
Sbjct: 212 YQLKKDFPQLTLSINGGIKSLEEAKQHLQYVDGVMIGREAYQNPSILAHVDRELFN---- 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
               +T +  +    I A +  Y  R L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 268 ----ETALVVNTINAIKA-LYPYIERELSKGTYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A  + A   ++E A  ++ E +
Sbjct: 323 NAHKAGADIMVVEKALEMVTERM 345


>gi|206559989|ref|YP_002230753.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia J2315]
 gi|198036030|emb|CAR51923.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia J2315]
          Length = 353

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/298 (45%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 26  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPIALQLGGSERD 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 86  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVAVPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 146 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 206 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYG---ST 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           + + TR + +      A +  Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 263 AAVPTREEAE------AQLIAYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLS 314


>gi|118602457|ref|YP_903672.1| tRNA-dihydrouridine synthase A [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
 gi|118567396|gb|ABL02201.1| tRNA-U16,U17-dihydrouridine synthase [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 322

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 134/312 (42%), Positives = 196/312 (62%), Gaps = 12/312 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ N  L+TEM+ A AIL G+K  +L F+  E PL LQ+GG++  
Sbjct: 12  MMDWTDRHCRYFYRLISKNVQLWTEMVTARAILYGNKNRLLDFNVCEHPLVLQLGGSEPK 71

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ +AAKI +D+GYNEIN+NVGCPS RV   +FG CLM  P +V  C+ AM + + +P+T
Sbjct: 72  EMAQAAKIAQDWGYNEININVGCPSNRVQSSNFGVCLMQTPQVVAQCVDAMRQMVDVPIT 131

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      L N V +++ SG + + IHARKA LKGLSPK+NR +P L+Y+ VY
Sbjct: 132 VKSRIGVDNMDSYDELVNFVATVESSGCDNLVIHARKAWLKGLSPKENRSVPKLNYERVY 191

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P L IG+NGG+ DM  +L+ L  VD VM+GRA Y    +L  VD          
Sbjct: 192 QIKRDFPHLAIGINGGIMDMESSLQHLEHVDSVMLGRAVYHQPYLLRKVDGLI---YQKK 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S I +R       ++  +  +Y      +   ++ +TRH+ GL+HG  N+++ + +L+  
Sbjct: 249 SSILSR------EQVLLAFIEYMKVQHANSVLIRSMTRHIFGLYHGQKNAKKFKRLLS-- 300

Query: 301 AGASTATHHIIE 312
            G      H+ E
Sbjct: 301 -GKIVKFEHLYE 311


>gi|262393119|ref|YP_003284973.1| tRNA dihydrouridine synthase A [Vibrio sp. Ex25]
 gi|262336713|gb|ACY50508.1| tRNA dihydrouridine synthase A [Vibrio sp. Ex25]
          Length = 315

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+E+NLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 60  DLAKCAKLAQERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKGVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 180 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 291 NAHKPGSGLEVLQDAL 306


>gi|188993527|ref|YP_001905537.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           campestris str. B100]
 gi|167735287|emb|CAP53501.1| Putative dihydrouridine synthase [Xanthomonas campestris pv.
           campestris]
          Length = 366

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 140/314 (44%), Positives = 193/314 (61%), Gaps = 11/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD++ ++GF   E PLALQ+GG+D +
Sbjct: 51  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRQRLIGFDAVEHPLALQLGGSDPA 110

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I + +GY+EINLN GCPS RV  G FGACLM  P +V DC+AAMC A ++PVT
Sbjct: 111 LLAQAAQIAQAWGYDEINLNCGCPSDRVQAGRFGACLMREPALVADCVAAMCAATALPVT 170

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          +  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 171 VKCRLGVDDDDDYAVFAGFIDQVVGAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 230

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  +L  L   DGVM+GRAAY +  +L  ++   S      
Sbjct: 231 RLKQERPALPVVLNGGIASVEASLAHLQHTDGVMLGRAAYHDPYVLHQLEAALSG----- 285

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R D      +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 286 RPERARAD------LLQAYQPYVQAQLDQGLALKHMTRHILGLFHGQPGGRVFRQVLSEG 339

Query: 301 AGASTATHHIIETA 314
           A    A   ++E A
Sbjct: 340 AHRPGAGWELVEQA 353


>gi|88706546|ref|ZP_01104250.1| tRNA-dihydrouridine synthase A [Congregibacter litoralis KT71]
 gi|88699258|gb|EAQ96373.1| tRNA-dihydrouridine synthase A [Congregibacter litoralis KT71]
          Length = 359

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 195/316 (61%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RLL+  A LYTEM+   A++ GD++  L F  +E P+ALQ+GG++  
Sbjct: 46  MMDWSDRHCRYFWRLLSRRARLYTEMVTTGALIHGDRQRFLQFHEEEAPIALQLGGSNPG 105

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  ED+GY+E+NLN GCPS RV  G+FGACLM    +V DCI+AM  A +I VT
Sbjct: 106 DLARCAKWAEDWGYDEVNLNCGCPSDRVQNGAFGACLMGEASLVRDCISAMRSACAIDVT 165

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L + V ++ + G     +HARKA LKGLSPK+NR++P L+Y  VY
Sbjct: 166 VKHRIGIDHMESYEELCDFVGTVAEGGSEVFIVHARKAWLKGLSPKENREVPPLNYPWVY 225

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I +NGG+E +  +   L  VDGVM+GR+AY N  +L  VD      +   
Sbjct: 226 QLKEDFPELTIVMNGGIESLEDSQTHLGHVDGVMLGRSAYHNPWVLAEVDHRLFGDVK-- 283

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + R  +D    I  +M  Y  + L  G +L QITRH++GL+   P +RR R +L+ +
Sbjct: 284 ---QPRYRED----IIEAMLPYVEKELAHGARLNQITRHLLGLYQEVPGARRYRRLLSEQ 336

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++  A N
Sbjct: 337 AHRPGAGADVLRAAVN 352


>gi|269964431|ref|ZP_06178672.1| NifR3/Smm1 family protein [Vibrio alginolyticus 40B]
 gi|269830769|gb|EEZ84987.1| NifR3/Smm1 family protein [Vibrio alginolyticus 40B]
          Length = 354

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++ +
Sbjct: 40  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPA 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 99  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDIPVT 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 159 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 218

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 219 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 276 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 329

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 330 NAHKPGSGLEVLQDAL 345


>gi|260221113|emb|CBA29353.1| tRNA-dihydrouridine synthase A [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 370

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 187/300 (62%), Gaps = 12/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 53  MMDWTDRHCRYFHRLLSRHALLYTEMVTTGALIHGDVPRHLRFNVEEHPVALQLGGSEPA 112

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ +D+GY+EIN+N GCPS RV  G+FGACLM    +V DC+ +M  A+ +PVT
Sbjct: 113 DLARAAKLGQDWGYDEININCGCPSERVQRGAFGACLMNEAPLVADCVKSMVDAVDVPVT 172

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     +R+ V ++  +G N    HAR A LKGLSPK+NR+IP L Y++VY
Sbjct: 173 VKHRIGIDKEESYSFVRDFVGTVADAGCNVFIAHARNAWLKGLSPKENREIPPLRYELVY 232

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG+   ++    L  VDGVM+GR AY N   L   D  F       
Sbjct: 233 QLKKDFPHLTIAINGGITQTAEVAGHLEHVDGVMLGREAYHNPWWLAEWDSAFY-----G 287

Query: 241 SPIKTRVDKDFWRK-ISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P     D+D  R+ + A M  Y  R     G     I RHM+GL HG P +RR R + T
Sbjct: 288 AP-----DRDITREMVEAQMVAYMEREAAQHGTHWYSIARHMLGLRHGLPGARRWRQVWT 342


>gi|118497197|ref|YP_898247.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           novicida U112]
 gi|194323496|ref|ZP_03057273.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
 gi|118423103|gb|ABK89493.1| tRNA-dihydrouridine synthase [Francisella novicida U112]
 gi|194322351|gb|EDX19832.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
          Length = 327

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 138/325 (42%), Positives = 192/325 (59%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N P T 
Sbjct: 193 SIKKDFPNLELGINGGITTIQETQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            S +          +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISAL----------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
           +  A    A      TA  +    L
Sbjct: 303 SENATKKEANVDTFLTALEVFENKL 327


>gi|90416108|ref|ZP_01224041.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2207]
 gi|90332482|gb|EAS47679.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2207]
          Length = 322

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 195/316 (61%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + +LYTEM+   AI+ GD    L     E P+ALQ+GG+  +
Sbjct: 11  MLDWTDRHCRYFLRLISQHTMLYTEMLTTGAIIHGDSDYHLQMDAFEHPVALQLGGSSPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  A K+   + Y EINLN GCPS RV  G FGA +M + +I  +C++AM +A+ +P+T
Sbjct: 71  DLATACKMAAQYDYAEINLNCGCPSDRVQNGMFGAVMMKDAEITANCVSAMREAVDLPIT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      LR+ V  + +SG     +HARKA LKGLSPK NR+IP L+YD VY
Sbjct: 131 VKHRIGVDEYDSYEFLRDFVGRVTESGCEVFLVHARKAWLKGLSPKQNREIPELNYDRVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P L I +NGG+  + Q+ + L  +DGVM+GR  Y N  +L +VD+   +    S
Sbjct: 191 RLKKDFPQLEIIINGGVTTLEQSKEHLQHLDGVMVGREVYSNPYLLASVDQ---DIYGAS 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +KTR      R+I+     YA   L  G KL  +TRH++GLFHG P +R+ R  ++  
Sbjct: 248 HGVKTR------RQIAEEFLQYADNELSKGTKLNAMTRHILGLFHGMPGARQFRRHISEN 301

Query: 301 AGASTATHHIIETAFN 316
           A   +AT  ++ TA +
Sbjct: 302 AHKPSATIEVLSTALS 317


>gi|256821809|ref|YP_003145772.1| TIM-barrel protein, yjbN family [Kangiella koreensis DSM 16069]
 gi|256795348|gb|ACV26004.1| TIM-barrel protein, yjbN family [Kangiella koreensis DSM 16069]
          Length = 330

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 141/322 (43%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RL+T +A+LYTEMI   AI+ G  +  L F+ +E P+A+Q+GG+D  
Sbjct: 14  MLDWTDRHQRRFMRLITKHAVLYTEMITTGAIIHGGAERHLKFNQEEHPVAVQLGGSDPK 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AKI EDFGY+EINLNVGCPS RV  G FGACLM  P++V +C++AM   + +PVT
Sbjct: 74  DLAHCAKICEDFGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECMSAMANVVDVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + + +++ +GV    IHARKA L GLSPK NR+IP L YDI Y
Sbjct: 134 VKSRIGIDELDSYEHLHHFINTVQSAGVKTFIIHARKAWLSGLSPKQNREIPPLRYDIAY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P+L I +NGG+  + QA   +   DGVMIGR AY N   L  VD  F       
Sbjct: 194 QVKKDFPELEIIVNGGVNTLDQAEDHMKHADGVMIGREAYHNPYFLAEVDNRFYGK---D 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R++      I+     Y    L     L  +TRH++GLF   P  +  R  L+  
Sbjct: 251 YDIPSRIE------IAREYMVYIQSQLDQDVYLGHMTRHILGLFFAQPKGKLWRRYLSEN 304

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A    A   ++E A  +  E +
Sbjct: 305 AYQKGAGLEVLEGALAIYEEDI 326


>gi|240137455|ref|YP_002961926.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens AM1]
 gi|240007423|gb|ACS38649.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens AM1]
          Length = 340

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 155/311 (49%), Positives = 201/311 (64%), Gaps = 16/311 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 21  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DF Y EINLNVGCPS RV +G FGACLM  P +VG C+AAM  A+ +PVT
Sbjct: 81  DLAAAARIAADFSYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAAMKAAVPVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDYD V 
Sbjct: 141 VKCRLGVDDQDIEEALDAVADAVVAAGVDGLVVHARKAWLKGLSPRENRDVPPLDYDRVA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD E F  P   
Sbjct: 201 RLKRAHPDLPIAVNGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEP--- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-RHILT 298
            +P+      D +  I A     AA  L  G +L   TRHM+GLF+G P +R   RH+ T
Sbjct: 258 -APV-----ADAFAAIEAFEPIVAA-GLERGLRLHAYTRHMLGLFNGRPGARAYRRHLAT 310

Query: 299 V----EAGAST 305
                EAG +T
Sbjct: 311 AGMGPEAGLAT 321


>gi|254230410|ref|ZP_04923791.1| TIM-barrel protein, YjbN family [Vibrio sp. Ex25]
 gi|151937069|gb|EDN55946.1| TIM-barrel protein, YjbN family [Vibrio sp. Ex25]
          Length = 354

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 194/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 40  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+E+NLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 99  DLAKCAKLAQERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKGVVDIPVT 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 159 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 218

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 219 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 276 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 329

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 330 NAHKPGSGLEVLQDAL 345


>gi|293394136|ref|ZP_06638436.1| tRNA-dihydrouridine synthase A [Serratia odorifera DSM 4582]
 gi|291423114|gb|EFE96343.1| tRNA-dihydrouridine synthase A [Serratia odorifera DSM 4582]
          Length = 349

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 144/320 (45%), Positives = 201/320 (62%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRLLSKETLLYTEMVTTGAIVHG-KGDYLAYSEEEHPIALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 92  ALAHCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGQATLVADCIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + ++++   G   ++ IHARKA L GLSPK NR++P LDY  V
Sbjct: 152 VKTRIGIDEQDSYAFLCDFIETVAGRGECEMFTIHARKAWLSGLSPKQNREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLDEARQHLQHLDGVMMGREAYQNPGILLQVDRELFGS--- 268

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +P++  V          ++  Y  R L +G  L  ITRH++GLF G P +R+ R  L+
Sbjct: 269 -QAPLQDSV------AAIEALYPYIERELANGTYLGHITRHILGLFQGIPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A +L+
Sbjct: 322 ENAHKPGADVRVVEQALSLV 341


>gi|158336790|ref|YP_001517964.1| tRNA-dihydrouridine synthase A [Acaryochloris marina MBIC11017]
 gi|158307031|gb|ABW28648.1| tRNA-dihydrouridine synthase A [Acaryochloris marina MBIC11017]
          Length = 335

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 146/317 (46%), Positives = 191/317 (60%), Gaps = 10/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AIL GD+ ++L FS  EKPL LQ+GG +  
Sbjct: 18  MMDRTDRHFRYFMRQITQRTLLYTEMVTSAAILNGDRHHLLDFSPIEKPLVLQVGGDNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I  D+GY+EINLNVGCPS+RV  G FGACLM  PD V  C+ AM +A  +PV+
Sbjct: 78  DLAECARIATDWGYDEINLNVGCPSSRVQNGHFGACLMAQPDRVAACVEAMMQATHLPVS 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V+++  SG     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 138 VKHRIGIDDCDRYEDMAHFVQTVAASGCQIFSVHARKAWLKGLSPKENRDIPPLRYEDVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+    L+I +NGG   + Q    LP VD VMIGRAAY N  +  TVD  F +    S
Sbjct: 198 RLKQNFSHLWIEINGGFIQLFQVHNQLPKVDAVMIGRAAYDNPYLFATVDRDFYHE-DRS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +P +         K++ +M DY       G  K   ITRHM+ LF G P SR  + +LT 
Sbjct: 257 APSR--------HKVAQAMMDYLEEWKIKGLLKPHSITRHMLQLFSGQPGSRAWKRLLTE 308

Query: 300 EAGASTATHHIIETAFN 316
           +     A   II  A +
Sbjct: 309 QGCRPDAGPDIIHQALD 325


>gi|291296460|ref|YP_003507858.1| YjbN family TIM-barrel protein [Meiothermus ruber DSM 1279]
 gi|290471419|gb|ADD28838.1| TIM-barrel protein, yjbN family [Meiothermus ruber DSM 1279]
          Length = 339

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 192/316 (60%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+  RL++    LYTEM+V  +IL G++  +L FS +E P+ALQ+GG+   
Sbjct: 16  MLDWTDRHFRYLVRLISRRVRLYTEMVVDQSILLGNRPKLLDFSPEEHPVALQLGGSVPE 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E +GY+EINLN+GCPS RV  G FGACLML PD+V + +AAM +A+ IPVT
Sbjct: 76  KLAEAARIGEAWGYDEINLNLGCPSERVQGGGFGACLMLEPDLVAESMAAMRQAVKIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+GVD+      L   V+ +   GV    +HARKA LKGLSP +NR IP L YD VY
Sbjct: 136 AKHRLGVDEVEDYRYLARFVEKLAGVGVGVFIVHARKAYLKGLSPAENRTIPPLRYDWVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I LNGG+  + +    L  VDGVM+GRA Y++  +L   D      L G 
Sbjct: 196 RLKQDFPHLTIVLNGGVRTLEEVQAHLAKVDGVMLGRAVYEDPFVLEPADRR----LFGE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +   TR++      ++ +M  YA   L  G  L  + RHM+ LF G P  R  R +L+  
Sbjct: 252 AHATTRLE------VAQAMLRYAEAQLEQGTPLWAMARHMLNLFKGQPRGRLWRRVLSER 305

Query: 301 AGASTATHHIIETAFN 316
           A    A   +++ A  
Sbjct: 306 ACRRGAGVEVLQEALE 321


>gi|209527420|ref|ZP_03275926.1| TIM-barrel protein, yjbN family [Arthrospira maxima CS-328]
 gi|209492155|gb|EDZ92504.1| TIM-barrel protein, yjbN family [Arthrospira maxima CS-328]
          Length = 338

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 141/317 (44%), Positives = 190/317 (59%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +L FS +EKPLALQ+GG D +
Sbjct: 29  MMDRTDRHFRYFMRQITRRPLLYTEMVTSAAIINGDRHKLLDFSPEEKPLALQVGGDDPN 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+EINLNVGCPSARV  G+FGACLM  P+ V   I+AM KA++IPVT
Sbjct: 89  ELATCAKIAEDWGYDEINLNVGCPSARVQNGNFGACLMAEPERVAQAISAMKKAVNIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     +   V+ +  SG     +HARKA L+GLSPKDNR IP L Y  V+
Sbjct: 149 VKHRIGIDNRDRYEDMAAFVRVVAASGCQRFTVHARKAWLQGLSPKDNRNIPPLRYGDVH 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPLT 238
            +K E PDL I +NGG   + Q  + L  VD VMIGRAAY N  +    D   Y  N   
Sbjct: 209 RLKAEFPDLTIEINGGFTTLEQVKQQLTKVDAVMIGRAAYDNPYLFAIADREIYGEN--- 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                   ++     ++   M  Y    L  GG+L  + RH++ LF G P ++  +  L+
Sbjct: 266 --------INPPTRHQVVEQMLPYIENWLSQGGRLNSVVRHILQLFAGQPGTKAWKRYLS 317

Query: 299 VEAGASTATHHIIETAF 315
             A    A   +++ A 
Sbjct: 318 ENAHLPGAGVEVVKAAL 334


>gi|208778989|ref|ZP_03246335.1| RNA dihydrouridine synthase A [Francisella novicida FTG]
 gi|254372562|ref|ZP_04988051.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|254374021|ref|ZP_04989503.1| RNA dihydrouridine synthase A [Francisella novicida GA99-3548]
 gi|151570289|gb|EDN35943.1| RNA dihydrouridine synthase A [Francisella novicida GA99-3549]
 gi|151571741|gb|EDN37395.1| RNA dihydrouridine synthase A [Francisella novicida GA99-3548]
 gi|208744789|gb|EDZ91087.1| RNA dihydrouridine synthase A [Francisella novicida FTG]
          Length = 327

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 138/325 (42%), Positives = 192/325 (59%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N P T 
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            S +          +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISAL----------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
           +  A    A      TA  +    L
Sbjct: 303 SENATKKEANVDTFLTALEVFENKL 327


>gi|237746180|ref|ZP_04576660.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes HOxBLS]
 gi|229377531|gb|EEO27622.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes HOxBLS]
          Length = 328

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 142/302 (47%), Positives = 188/302 (62%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ N  LYTEM+   A+L GD    L FS +E P+ALQ+GG++ +
Sbjct: 13  MLDWTDRHCRYFHRLISRNTWLYTEMVTTGALLYGDVARHLDFSEEEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+ E +GY+EINLN GCPS RV +G+FGACLM    +V DC+ AM  A+SI VT
Sbjct: 73  ELAQCAKLGEKWGYDEINLNCGCPSERVQKGAFGACLMKESKLVADCVRAMKDAVSIDVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      +R+ +  I  +G     +HAR AILKGLSPK+NR+IP L YD+VY
Sbjct: 133 VKHRIGIDDMHTYDFVRDFIGEIAGAGCQTFIVHARNAILKGLSPKENREIPPLRYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I LNGG+E   Q  + L  VDGVMIGRAAY     +   D  F     G+
Sbjct: 193 QLKKDFPGLEILLNGGVETAGQVEEHLKHVDGVMIGRAAYHYPWRMAEFDARFYG--DGT 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL----HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            P            + A+M  Y  + L      G ++  ITRHM+GL  G P +RR R I
Sbjct: 251 VPENPSA-------VVAAMIPYIEKQLALYGEKGLRMHGITRHMLGLVTGMPGARRFRQI 303

Query: 297 LT 298
           L+
Sbjct: 304 LS 305


>gi|254490145|ref|ZP_05103336.1| TIM-barrel protein, yjbN family [Methylophaga thiooxidans DMS010]
 gi|224464631|gb|EEF80889.1| TIM-barrel protein, yjbN family [Methylophaga thiooxydans DMS010]
          Length = 327

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 136/318 (42%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R+  RL++ ++LLYTEM+   A++ GD+   L     E PLALQ+GG++ +
Sbjct: 18  MLDWTDRDCRYMLRLISRHSLLYTEMVTTGALIYGDRDRFLAHEALEYPLALQLGGSEPN 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ED GY+EINLNVGCPS RV  G FGACL+  PD+V + +AAM   +SIPVT
Sbjct: 78  DLAQCAKMGEDAGYDEINLNVGCPSDRVQSGRFGACLLAEPDVVAEGVAAMQNQVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L + +K +  +G +   +HARKA LKGLSPK+NR +P L+YD VY
Sbjct: 138 VKTRLGIDEHDSYEFLTDFIKKVSAAGCDTFILHARKAWLKGLSPKENRDVPPLNYDRVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + +A   L  VDGVM+GRA Y N  +L   DE         
Sbjct: 198 QVKQDFPHLHIDINGGINTLEEAQLHLQHVDGVMMGRAIYHNPFLLAQADEAI---FGHD 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + TR       ++  +M  Y  + +  G  L+ ITRHM+G+F G   +RR R  ++  
Sbjct: 255 ASVLTR------HQVVEAMLPYIEKRMAQGRPLKSITRHMLGVFQGQAGARRWRRHISEN 308

Query: 301 AGASTATHHIIETAFNLM 318
           A    A  HI++ A +L+
Sbjct: 309 AHLPGAGIHILQQALDLV 326


>gi|260779457|ref|ZP_05888347.1| tRNA dihydrouridine synthase A [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260604266|gb|EEX30570.1| tRNA dihydrouridine synthase A [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 315

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 140/323 (43%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT+  LLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLTSETLLYTEMVTTGAIIHG-KGDFLAYNQEEHPVALQLGGSNPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM   + +PVT
Sbjct: 60  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPLLVAECVAAMRDVVDVPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGSDQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +    + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 180 YQLKKDFAHLNIAINGGVKTLDDTKEHLTHLDGVMVGREAYQNPYILAEVDQQI---FGL 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 DKPVKKRT------QVVQEMYPYIESQLEKGAYLGHITRHMLGLFQNMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   ++ETA + + + L
Sbjct: 291 NAHKPGSGIEVVETALSKIPKEL 313


>gi|218528939|ref|YP_002419755.1| tRNA-dihydrouridine synthase A [Methylobacterium chloromethanicum
           CM4]
 gi|218521242|gb|ACK81827.1| dihydrouridine synthase DuS [Methylobacterium chloromethanicum CM4]
          Length = 340

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 155/311 (49%), Positives = 201/311 (64%), Gaps = 16/311 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 21  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY EINLNVGCPS RV +G FGACLM  P +VG C+AAM  A+ +PVT
Sbjct: 81  DLAAAARIAADFGYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAAMKAAVPVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 141 VKCRLGVDDQDIEEALDAVADAVVAAGVDGLVVHARKAWLKGLSPRENRDVPPLDYGRVA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD E F  P   
Sbjct: 201 RLKRAHPDLPIAINGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEP--- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-RHILT 298
            +P+      D +  I A     AA  L  G +L   TRHM+GLF+G P +R   RH+ T
Sbjct: 258 -APV-----ADAFAAIEAFEPIVAA-GLERGLRLHAYTRHMLGLFNGRPGARAYRRHLAT 310

Query: 299 V----EAGAST 305
                EAG +T
Sbjct: 311 AGMGPEAGLAT 321


>gi|163746890|ref|ZP_02154247.1| tRNA-dihydrouridine synthase A [Oceanibulbus indolifex HEL-45]
 gi|161380004|gb|EDQ04416.1| tRNA-dihydrouridine synthase A [Oceanibulbus indolifex HEL-45]
          Length = 335

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 141/300 (47%), Positives = 187/300 (62%), Gaps = 12/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L     E P+ALQ+GG+D +
Sbjct: 16  MMDWTDRHCRYLHRLLSRETLLYTEMVTAPALVRGGALHLLDHDPSEHPVALQLGGSDPT 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM  P +V DC+ AM  A  + VT
Sbjct: 76  ELAQAARLGAEAGYDEINLNCGCPSDRVQSGAFGAVLMQQPGLVADCVDAMRAACDVEVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 136 VKCRIGVDDQAPEEILPEFLARIVAAGCTRVTIHARKAWLQGLSPKENRDIPPLDYDLVH 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
           ++K   P+L I +NGG+  + QA   L + +DGVM+GR+AY   + +L   D        
Sbjct: 196 QMKGLFPNLHISVNGGITSLDQAEAFLDAGLDGVMVGRSAYHAPTDILAGADRRIYGQGA 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            SS                 M  Y   HL SGG+L QITRHM+GLF G P +R+ R IL+
Sbjct: 256 DSSA----------EAAVQGMLPYIETHLASGGRLGQITRHMLGLFAGRPGARQWRRILS 305


>gi|70729357|ref|YP_259094.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens Pf-5]
 gi|68343656|gb|AAY91262.1| TIM-barrel protein, yjbN family [Pseudomonas fluorescens Pf-5]
          Length = 336

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 133/300 (44%), Positives = 190/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ + LLYTEM+   A+L GD +  L +   E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKHTLLYTEMVTTGALLNGDHERFLRYHPSEHPLALQLGGSTPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 85  DLAACARMAQEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMRDAVSIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G +   +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAELCDFVGQVMEAGCSSFTVHARIAILEGLSPKENRDIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I LNGG++ +    + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 205 QLKADFPQLEIILNGGIKTLEACHEHLQTFDGVMLGREAYHNPYLLAEVDQQL---FGST 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R +        A +  Y A HL +GG +  ITRH++GL  GFP +R+ R +L+V+
Sbjct: 262 EPVISRAEA------LARLRPYIAEHLAAGGAMHHITRHVLGLGTGFPGARKFRQLLSVD 315


>gi|328472365|gb|EGF43235.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus 10329]
          Length = 326

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 195/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM + + +PVT
Sbjct: 71  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVAECVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQEL---FGS 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R +      I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 248 NAPVKKRSE------IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 302 NAHKPGSGLEVLQDAL 317


>gi|254559633|ref|YP_003066728.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens DM4]
 gi|254266911|emb|CAX22710.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens DM4]
          Length = 340

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 155/311 (49%), Positives = 201/311 (64%), Gaps = 16/311 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 21  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY EINLNVGCPS RV +G FGACLM  P +VG C+AAM  A+ +PVT
Sbjct: 81  DLAAAARIAADFGYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAAMKAAVPVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 141 VKCRLGVDDQDIEEALDAVADAVVAAGVDGLVVHARKAWLKGLSPRENRDVPPLDYGRVA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD E F  P   
Sbjct: 201 RLKRAHPDLPIAVNGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEP--- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-RHILT 298
            +P+      D +  I A     AA  L  G +L   TRHM+GLF+G P +R   RH+ T
Sbjct: 258 -APV-----ADAFAAIEAFEPIVAA-GLERGLRLHAYTRHMLGLFNGRPGARAYRRHLAT 310

Query: 299 V----EAGAST 305
                EAG +T
Sbjct: 311 AGMGPEAGLAT 321


>gi|56707647|ref|YP_169543.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670118|ref|YP_666675.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134302420|ref|YP_001122390.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|224456717|ref|ZP_03665190.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370162|ref|ZP_04986168.1| tRNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254874464|ref|ZP_05247174.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604139|emb|CAG45141.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320451|emb|CAL08524.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134050197|gb|ABO47268.1| dihydrouridine synthase [Francisella tularensis subsp. tularensis
           WY96-3418]
 gi|151568406|gb|EDN34060.1| tRNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254840463|gb|EET18899.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282158805|gb|ADA78196.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 327

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/325 (42%), Positives = 192/325 (59%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N P T 
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            S +          +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISAL----------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
           +  A    A      TA  +    L
Sbjct: 303 SENATKKEANVDTFLTALEVFENKL 327


>gi|325576762|ref|ZP_08147377.1| tRNA-dihydrouridine synthase A [Haemophilus parainfluenzae ATCC
           33392]
 gi|325160968|gb|EGC73086.1| tRNA-dihydrouridine synthase A [Haemophilus parainfluenzae ATCC
           33392]
          Length = 328

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 141/318 (44%), Positives = 195/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + NALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSKNALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V +CIA M + ++IPVT
Sbjct: 77  QLKHCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVAECIAEMQRVVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + +K +  +G     +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKTRIGIDDLDSYQFLCDFIKKVHHAGCQEFIVHARKAWLSGLSPKENREIPPLDYDRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  VD+        +
Sbjct: 197 QLKKDFPQLTIAINGGIKTIEEMKHHLQFVDGVMVGREAYQNPSLLGYVDQML---FDAN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + I T       ++   +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 ADIVTP------KQAVEAMFPYIEKQLSQGVYLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|163803123|ref|ZP_02197007.1| tRNA-dihydrouridine synthase A [Vibrio sp. AND4]
 gi|159173115|gb|EDP57947.1| tRNA-dihydrouridine synthase A [Vibrio sp. AND4]
          Length = 318

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 193/316 (61%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L  + +E PLALQ+GG++ +
Sbjct: 4   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAHNEEEHPLALQLGGSNPA 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + +PVT
Sbjct: 63  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDVPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DD      L + V  + +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 123 VKTRIGIDDHDSYQFLTDFVSIVSEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 182

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 183 YQLKKDFSHLTIAINGGVKSLEEAKEHLQHLDGVMIGREAYQSPYLLAFVDQEL---FGS 239

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 240 NAPVKKR------SQIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRYISE 293

Query: 300 EAGASTATHHIIETAF 315
            A    +   +++ A 
Sbjct: 294 NAHKPGSGLEVLQAAL 309


>gi|57339642|gb|AAW49808.1| hypothetical protein FTT0508 [synthetic construct]
          Length = 362

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/325 (42%), Positives = 192/325 (59%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 39  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 99  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 159 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 218

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N P T 
Sbjct: 219 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 278

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            S +          +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L
Sbjct: 279 ISAL----------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYL 328

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
           +  A    A      TA  +    L
Sbjct: 329 SENATKKEANVDTFLTALEVFENKL 353


>gi|304415193|ref|ZP_07395906.1| tRNA-dihydrouridine synthase A [Candidatus Regiella insecticola
           LSR1]
 gi|304282951|gb|EFL91401.1| tRNA-dihydrouridine synthase A [Candidatus Regiella insecticola
           LSR1]
          Length = 344

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 144/319 (45%), Positives = 195/319 (61%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLY+EM+   AI+ G K + L +S Q+ P+ LQ+GG+D  
Sbjct: 34  MLDWTDRHCRYFHRLLTKQTLLYSEMVTTGAIIHG-KADYLAYSEQDHPVVLQLGGSDPK 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ +  GYNEINLN+GCPS RV  G FGACLM   D+V DCI AM   +SIPVT
Sbjct: 93  ILADCAKLGQQRGYNEINLNIGCPSDRVQNGRFGACLMGEADLVADCIKAMNDGVSIPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L + V +I  K G +   IHARKA L GLSPK+NR++P L+Y  V
Sbjct: 153 VKTRIGIDSHDSYEFLCDFVDTIANKGGCHIFIIHARKAWLSGLSPKENREVPPLNYPRV 212

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG+  +  A   L  VDGVMIGR AY+N A+L  VD    +P   
Sbjct: 213 YQLKRDFPQLTIVINGGITTLEDAADHLKYVDGVMIGREAYQNPAILAEVDRKLFDP--- 269

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + I  +V       +  ++  Y  + L  G +L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 270 QAAITDKV------AVIKALYPYIEQELSRGARLGHITRHILGLFQGTPGARQWRRYLSE 323

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A + +
Sbjct: 324 HAHQPRADAAVVERALSFV 342


>gi|221213021|ref|ZP_03585997.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD1]
 gi|221167234|gb|EED99704.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD1]
          Length = 357

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/298 (45%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 30  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 90  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVAVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 210 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 269 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLS 318


>gi|313499712|gb|ADR61078.1| TRNA-dihydrouridine synthase A [Pseudomonas putida BIRD-1]
          Length = 312

 Score =  269 bits (688), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 136/319 (42%), Positives = 194/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDRHCRFFLRLLSRQTLLYTEMVTTGALLHNDAHRFLRHDASEHPLALQLGGSVPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 61  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YDI  
Sbjct: 121 VKHRIGINGRDSYAELSDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDIAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 181 QLKRDFPDLEIVLNGGIKSLDECQAHLETFDGVMLGREAYHNPYLLAEVDQQ----LFGS 236

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ 
Sbjct: 237 DAPVVSRSEA------LAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSA 290

Query: 300 EAGASTATHHIIETAFNLM 318
           +   +     + + A  L+
Sbjct: 291 DIHKAAEPLAVFDQAVELL 309


>gi|86138502|ref|ZP_01057076.1| tRNA-dihydrouridine synthase A [Roseobacter sp. MED193]
 gi|85825027|gb|EAQ45228.1| tRNA-dihydrouridine synthase A [Roseobacter sp. MED193]
          Length = 349

 Score =  269 bits (688), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 138/300 (46%), Positives = 197/300 (65%), Gaps = 12/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RLL+  ALLYTEM+ A A++RG   ++L ++ +E P+ALQ+GG+D  
Sbjct: 33  MMEWTDRHCRYFHRLLSQEALLYTEMVTAPALVRGQALHLLEYNAEEHPVALQLGGSDPQ 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++  + GY+EINLN GCPS RV  G+FGA LM +PD+V DCIA M   +++ VT
Sbjct: 93  ELGLAAQLGGEAGYDEINLNCGCPSDRVQSGAFGAVLMQSPDLVADCIAEMRAKVAVEVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L   ++ I+ +G   + IHARKA LKGLSPK+NR IP LDYD+V+
Sbjct: 153 VKCRIGVDEQEPREILPVFLEKIRAAGCQRVTIHARKAWLKGLSPKENRDIPPLDYDLVH 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAY-KNSAMLTTVDEYFSNPLT 238
           E+K+   D+ I +NGGL+ +  A+  L   +DGVM+GRAAY + + +L   D      + 
Sbjct: 213 EMKRAFCDMHISINGGLDTLDAAIAHLEQGLDGVMVGRAAYHQPTDILAAADVR----VF 268

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G+  ++   +      +   M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 269 GTGALRDPCE------VVLQMLPYIEAQMGQGARLHQITRHMLGLFAGRPGARAWRRMLS 322


>gi|26988893|ref|NP_744318.1| tRNA-dihydrouridine synthase A [Pseudomonas putida KT2440]
 gi|38604779|sp|Q88KX0|DUSA_PSEPK RecName: Full=tRNA-dihydrouridine synthase A
 gi|24983702|gb|AAN67782.1|AE016409_8 TIM-barrel protein, yjbN family [Pseudomonas putida KT2440]
          Length = 336

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 136/319 (42%), Positives = 194/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSRQTLLYTEMVTTGALLHNDAHRFLRHDASEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 85  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YDI  
Sbjct: 145 VKHRIGINGRDSYAELSDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDIAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 205 QLKRDFPDLEIVLNGGIKTLDECQAHLETFDGVMLGREAYHNPYLLAEVDQQ----LFGS 260

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ 
Sbjct: 261 DAPVVSRSEA------LAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSA 314

Query: 300 EAGASTATHHIIETAFNLM 318
           +   +     + + A  L+
Sbjct: 315 DIHKAAEPLAVFDQAVELL 333


>gi|15597991|ref|NP_251485.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PAO1]
 gi|218891014|ref|YP_002439880.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa LESB58]
 gi|38605052|sp|Q9I048|DUSA_PSEAE RecName: Full=tRNA-dihydrouridine synthase A
 gi|9948878|gb|AAG06183.1|AE004707_2 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|218771239|emb|CAW27004.1| putative TIM-barrel protein [Pseudomonas aeruginosa LESB58]
          Length = 332

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVD----SQLFGS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   R     +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 257 EAPPLSRSEALLR-----LRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|262275131|ref|ZP_06052942.1| tRNA dihydrouridine synthase A [Grimontia hollisae CIP 101886]
 gi|262221694|gb|EEY73008.1| tRNA dihydrouridine synthase A [Grimontia hollisae CIP 101886]
          Length = 315

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 197/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+L+ NALLYTEM+   AI+ G K + L F+ +E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHCRYFHRILSKNALLYTEMVTTGAIIHG-KGDFLAFNEEEHPVALQLGGSNPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM   ++V  C+AAM + + IPVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMGEAELVAQCVAAMKEVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V+++ +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLVDFVRTVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L + +NGG++ + +A   L  +DGVMIGR AY++  +L  VD   S     
Sbjct: 180 YQLKKDFPHLTMAINGGIKSLEEAEAHLKFMDGVMIGREAYQSPYLLAEVD---SRLFGS 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PI  R +         ++  Y    L  G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 237 DAPIIKRSEA------VRAIFPYIEAELSKGTYLNHISRHMLGLFQNMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    A   ++E A 
Sbjct: 291 NAHKPGAGTEVLEAAL 306


>gi|94499718|ref|ZP_01306255.1| Dihydrouridine synthase TIM-barrel protein yjbN [Oceanobacter sp.
           RED65]
 gi|94428472|gb|EAT13445.1| Dihydrouridine synthase TIM-barrel protein yjbN [Oceanobacter sp.
           RED65]
          Length = 330

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 143/320 (44%), Positives = 196/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M+DW+D H R F R L+ +A LYTEM+   A++ GD      + +  +E P+ALQ+GG++
Sbjct: 18  MMDWSDSHCRLFWRTLSKDAFLYTEMVTTGALIHGDGGPDRFIRYRDEEHPVALQLGGSN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L + AKI +DFGY+E+NLNVGCPS RV     GACLM +P +V DCI AM  A+ IP
Sbjct: 78  PKDLAQCAKIAQDFGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCIKAMQDAVEIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG+DDQ     L + V ++  +G     IH RKAIL GLSPK+NR+IP L Y++
Sbjct: 138 VTVKHRIGIDDQDSYEHLHHFVDTVAATGCETFIIHGRKAILDGLSPKENREIPPLRYEV 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           V +IK++ P L + LNGG++   +A + L   DGVM+GR AY N ++L  VD  +     
Sbjct: 198 VQQIKQDLPQLEVILNGGIKTHKEATEHLKWADGVMLGREAYHNPSVLMDVDALY----Y 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G  P +T+  KD  R +   + D    HL  G KL  +TRH++GLF+G P SR  R  L+
Sbjct: 254 GHEP-QTKDKKDCIRALYPHIED----HLSKGFKLSYVTRHILGLFNGQPGSRLFRRHLS 308

Query: 299 VEAGASTATHHIIETAFNLM 318
            +A    A+   IE A   M
Sbjct: 309 EQAFKKDASIQTIEDALAYM 328


>gi|49088070|gb|AAT51528.1| PA2795 [synthetic construct]
          Length = 333

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVD----SQLFGS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   R     +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 257 EAPPLSRSEALLR-----LRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|116050795|ref|YP_790384.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa UCBPP-PA14]
 gi|254235779|ref|ZP_04929102.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|115586016|gb|ABJ12031.1| putative TIM-barrel protein [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126167710|gb|EAZ53221.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
          Length = 332

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVD----SQLFGS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   R     +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 257 EAPPLSRSEALLR-----LRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|148548779|ref|YP_001268881.1| tRNA-dihydrouridine synthase A [Pseudomonas putida F1]
 gi|148512837|gb|ABQ79697.1| TIM-barrel protein, yjbN family [Pseudomonas putida F1]
          Length = 336

 Score =  269 bits (687), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 136/319 (42%), Positives = 194/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSRQTLLYTEMVTTGALLHNDAHRFLRHDASEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 85  DLAACARLAEETGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YDI  
Sbjct: 145 VKHRIGINGRDSYAELSDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDIAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 205 QLKRDFPDLEIVLNGGIKTLDECQAHLETFDGVMLGREAYHNPYLLAEVDQQ----LFGS 260

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ 
Sbjct: 261 DAPVVSRSEA------LAQLRPYIVTHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSA 314

Query: 300 EAGASTATHHIIETAFNLM 318
           +   +     + + A  L+
Sbjct: 315 DIHKAAEPLAVFDQAVELL 333


>gi|15603283|ref|NP_246357.1| tRNA-dihydrouridine synthase A [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|38605041|sp|Q9CL29|DUSA_PASMU RecName: Full=tRNA-dihydrouridine synthase A
 gi|12721794|gb|AAK03502.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 327

 Score =  269 bits (687), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 136/318 (42%), Positives = 195/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+   K + L FS  E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSQHALLYTEMVTTGAIIHA-KYDHLEFSPAENPVALQLGGSDPT 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AKI +  GY EINLNVGCPS RV  G FGACLM   D+V DC++AM   +SIPVT
Sbjct: 77  QLAQCAKIAQQRGYTEINLNVGCPSDRVQNGMFGACLMAKADLVADCVSAMQTEVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+ + ++G     IHARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDLDSYEFLCEFVQKVHEAGCQEFIIHARKAWLSGLSPKENREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG++ + +  + L  +DGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLLMSINGGIKTLEEMQQHLQYMDGVMVGREAYQNPSLLGYIDQALFDP---T 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y  + L  G  L  + RHM+G F     +R+ R  L+  
Sbjct: 254 CPVVTP------REAVEKMFPYIEQQLSQGVYLNHVVRHMLGAFQSCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++E A + +
Sbjct: 308 AHKAGAGLEVVEKALSFV 325


>gi|296388726|ref|ZP_06878201.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PAb1]
          Length = 332

 Score =  269 bits (687), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVD----SQLFGS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   R     +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 257 EAPPLSRSEALLR-----LRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|221197852|ref|ZP_03570898.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2M]
 gi|221204590|ref|ZP_03577607.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2]
 gi|221175447|gb|EEE07877.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2]
 gi|221181784|gb|EEE14185.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2M]
          Length = 357

 Score =  269 bits (687), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 137/298 (45%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 30  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 90  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVAVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 210 RLKHDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+
Sbjct: 269 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLS 318


>gi|134295639|ref|YP_001119374.1| tRNA-dihydrouridine synthase A [Burkholderia vietnamiensis G4]
 gi|134138796|gb|ABO54539.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia vietnamiensis
           G4]
          Length = 344

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 137/298 (45%), Positives = 186/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAQAGCDTFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPALEIVINGGIKTLDEVAEHLEHVDGVMLGREAYHNPYVLAGVDARFYG---ST 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR + +      A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTREEAE------AKLIEYCAAELKRGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|107102337|ref|ZP_01366255.1| hypothetical protein PaerPA_01003399 [Pseudomonas aeruginosa PACS2]
 gi|313107930|ref|ZP_07794099.1| hypothetical protein PA39016_001190015 [Pseudomonas aeruginosa
           39016]
 gi|310880601|gb|EFQ39195.1| hypothetical protein PA39016_001190015 [Pseudomonas aeruginosa
           39016]
          Length = 312

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 1   MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 61  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 121 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD    + L GS
Sbjct: 181 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVD----SQLFGS 236

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   R     +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 237 EAPPLSRSEALLR-----LRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 291

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 292 VHKAADPLRVFDQALELL 309


>gi|260599558|ref|YP_003212129.1| tRNA-dihydrouridine synthase A [Cronobacter turicensis z3032]
 gi|260218735|emb|CBA34083.1| tRNA-dihydrouridine synthase A [Cronobacter turicensis z3032]
          Length = 349

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 142/322 (44%), Positives = 196/322 (60%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L++ ALLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 37  MLDWTDRHCRYFLRQLSSQALLYTEMVTTGAIIHG-KGDYLAYSDEEHPVALQLGGSDPA 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 96  ALAHCAKLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 156 VKTRIGIDDQDSYEFLCDFVGTVAEQGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 215

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +      L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 216 YQLKRDFPQLTMSINGGIKTLDDVKAHLAHMDGVMVGREAYQNPGLLASVDREIFGLDTP 275

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y       G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 276 DADPV----------AVVRAMYPYIEGERAKGTYLGHVTRHMLGLFQGIPGARQWRRYLS 325

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A  L+ +
Sbjct: 326 ENAHKPGAGIDVLEQALKLVAD 347


>gi|330808532|ref|YP_004352994.1| tRNA-dihydrouridine synthase A [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327376640|gb|AEA67990.1| tRNA-dihydrouridine synthase A [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 312

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 190/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H RFF R+L+ +ALLYTEM+   A+L GD +  L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDAHCRFFLRILSKHALLYTEMVTTGALLNGDHERFLRHHESEHPLALQLGGSVPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAACARMAQEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPHLVADCVKAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L   V +++++G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 121 VKHRIGINGRDSYEQLCEFVGTVREAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P+L I LNGG++ +    + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 181 RLKADFPELEIVLNGGIKTLEACHEHLQTFDGVMLGREAYHNPYLLAEVDQQL---FGST 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ TR +        A +  Y A HL +GG +  ITRH++GL  GFP +RR R +L+V+
Sbjct: 238 APVITRAEA------LAQLRPYIADHLAAGGAMHHITRHVLGLGTGFPGARRFRQLLSVD 291


>gi|163850379|ref|YP_001638422.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens PA1]
 gi|163661984|gb|ABY29351.1| dihydrouridine synthase DuS [Methylobacterium extorquens PA1]
          Length = 354

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 153/311 (49%), Positives = 200/311 (64%), Gaps = 16/311 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 35  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY EINLNVGCPS RV +G FGACLM  P +VG C+AA+  A+ +PVT
Sbjct: 95  DLAAAARIAADFGYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAALKAAVPVPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +G +G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 155 VKCRLGVDDQDIEEALDAVADAVVAAGGDGLVVHARKAWLKGLSPRENRDVPPLDYGRVA 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD E F  P   
Sbjct: 215 RLKRAHPDLPIAVNGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEP--- 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-RHILT 298
            +P+      D +  I A     AA  L  G +L   TRHM+GLF+G P +R   RH+ T
Sbjct: 272 -APV-----ADAFAAIEAFEPIVAA-GLERGLRLHAYTRHMLGLFNGRPGARAYRRHLAT 324

Query: 299 V----EAGAST 305
                EAG +T
Sbjct: 325 AGMGPEAGLAT 335


>gi|329296553|ref|ZP_08253889.1| TIM-barrel protein, yjbN family [Plautia stali symbiont]
          Length = 331

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 145/322 (45%), Positives = 194/322 (60%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L  + LLYTEM+   AI+ G K + L +S  E PLALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLGGDTLLYTEMVTTGAIIHG-KGDYLAYSEAEHPLALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 74  ALATCAKLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMRDVVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+N +IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLCDFVGTVAQQGGCDTFIIHARKAWLSGLSPKENSEIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD + F     
Sbjct: 194 YQLKRDFPALTVAINGGIKTLDEAKAHLQHLDGVMMGREAYQNPGILAQVDRQLFGRETP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  SM  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 254 VADPV----------AVVRSMYPYIEVELAQGTYLGHITRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A  L+ +
Sbjct: 304 ENAHKPGADVRVLEAALALVAD 325


>gi|254456205|ref|ZP_05069634.1| tRNA-dihydrouridine synthase A [Candidatus Pelagibacter sp.
           HTCC7211]
 gi|207083207|gb|EDZ60633.1| tRNA-dihydrouridine synthase A [Candidatus Pelagibacter sp.
           HTCC7211]
          Length = 334

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 189/298 (63%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RL++ N +LY+EM+   + + GD+K IL +S +EKPLALQ+GG++  
Sbjct: 16  MMDCTDRHDRFFLRLMSKNVMLYSEMVATKSAIHGDRKKILSYSPEEKPLALQVGGSNKD 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E AKI ED GY+EIN+N+GCPS +V +  FGACLM  PD+V +CI +M  + +IPVT
Sbjct: 76  ELAEVAKIAEDMGYDEININLGCPSKKVQKNMFGACLMKEPDLVAECINSMVNSCNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG D       L N +  ++ +G     +HARKA+L GLSPK N  IP L+Y++VY
Sbjct: 136 AKTRIGFDQTEDFDYLNNFIHKMRDAGTKTFILHARKAMLTGLSPKQNLNIPKLNYNMVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKK+NP+L I +NGG+  +S+    L   DGVMIGR+ Y+N   L  ++    N  T +
Sbjct: 196 EIKKKNPELEIIINGGISKVSEIDNHLKFCDGVMIGRSIYQNPYSLIEIERDIFN--THN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P + +V           + +YA + +  G K+  I RH +GL+HG   S+  +  L+
Sbjct: 254 NPTREQV--------VEKLLEYADKEVKLGTKINHIMRHTVGLYHGQTGSKDWKRYLS 303


>gi|187932026|ref|YP_001892011.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712935|gb|ACD31232.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 327

 Score =  268 bits (685), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 136/325 (41%), Positives = 192/325 (59%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  + +  + L  VD VM+GR AY N  +    D  F N P T 
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMMGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            S +          +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISAL----------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
           +  A    A      TA  +    L
Sbjct: 303 SENATKKEAKVDTFLTALEVFKNKL 327


>gi|77460046|ref|YP_349553.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens Pf0-1]
 gi|77384049|gb|ABA75562.1| tRNA-U16,U17-dihydrouridine synthase [Pseudomonas fluorescens
           Pf0-1]
          Length = 331

 Score =  268 bits (685), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 190/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+L+ NALLYTEM+   A+L GD +  L  +  E PLALQ+GG+   
Sbjct: 20  MMDWTDRHCRYFLRILSKNALLYTEMVTTGALLNGDHERFLRHNEAEHPLALQLGGSVPL 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 80  DLAACARMAQEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V +++ +G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 140 VKHRIGINGRDSYEELCDFVGTVRDAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P+L   LNGG++ M    + L + DGVM+GR AY N  +L  VD+        S
Sbjct: 200 RLKADFPELEFILNGGIKTMEACHEHLQTFDGVMLGREAYHNPYLLAEVDQQL---FGSS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +        A +  Y A HL +GG +  ITRH++GL  GFP +R+ R +L+V+
Sbjct: 257 APVISRAEA------LAQLRPYIAEHLLAGGAMHHITRHVLGLGTGFPGARKFRQLLSVD 310


>gi|126729455|ref|ZP_01745269.1| tRNA-dihydrouridine synthase A [Sagittula stellata E-37]
 gi|126710445|gb|EBA09497.1| tRNA-dihydrouridine synthase A [Sagittula stellata E-37]
          Length = 339

 Score =  268 bits (685), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 148/318 (46%), Positives = 198/318 (62%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +ALLYTEM+ A A++RG   ++L     E P+ALQ+GG+D S
Sbjct: 24  MMDWTDRHCRVFHRFMSRHALLYTEMVTAPALVRGGALHLLDHDPGEHPVALQLGGSDPS 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLN GCPS RV  G+FGA LM NPD V  C+ AM  A+ + VT
Sbjct: 84  ELAEAARLGAAAGYDEINLNCGCPSDRVQSGTFGAVLMKNPDTVIRCVEAMQDAVDVDVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P V L   +  +  +G + I IHARKA L+GLSPK+NR IP LDYD+V 
Sbjct: 144 VKCRIGVDDQDPCVVLPEFLARLGAAGCSRISIHARKAWLQGLSPKENRDIPPLDYDLVM 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
           +++   P L + +NGG+  + QA+  L + +DGVM+GRAAY     +L   D        
Sbjct: 204 QMRGLFPHLHLSVNGGIGSLDQAVGFLDAGLDGVMVGRAAYHQPWDILGEADARIWG--- 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P   R  +D  R     M  Y  RHL  GG+L Q+TRHM+GLF G P +RR R +L+
Sbjct: 261 --DPQTRRGREDVVR----DMLPYIERHLTRGGRLHQVTRHMLGLFAGCPGARRWRQVLS 314

Query: 299 VEAGASTATHHIIETAFN 316
            +     A   ++E A +
Sbjct: 315 TDTTRDGAGPAVVERALS 332


>gi|184156887|ref|YP_001845226.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ACICU]
 gi|332874036|ref|ZP_08441971.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6014059]
 gi|183208481|gb|ACC55879.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|322506783|gb|ADX02237.1| dusA [Acinetobacter baumannii 1656-2]
 gi|323516652|gb|ADX91033.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332737777|gb|EGJ68669.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 334

 Score =  268 bits (685), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 192/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  LG++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLGYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M K ++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKVVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 302 -GGNAKTLTDVENAIHNM 318


>gi|163796265|ref|ZP_02190226.1| tRNA-dihydrouridine synthase A [alpha proteobacterium BAL199]
 gi|159178407|gb|EDP62949.1| tRNA-dihydrouridine synthase A [alpha proteobacterium BAL199]
          Length = 386

 Score =  268 bits (685), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 147/301 (48%), Positives = 193/301 (64%), Gaps = 13/301 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+ ADA+  GD+  ++GFST E P+ALQ+GG++ +
Sbjct: 68  MMDWTDRHCRMFHRHLTRRALLYTEMVTADAVRFGDRGRLIGFSTDEHPVALQLGGSEPA 127

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+I EDFGY+E+N+NVGCPS RV  G FGACLM  P +VG  + AM  A+SIPVT
Sbjct: 128 AMAEAARIAEDFGYDEVNINVGCPSDRVQSGRFGACLMREPVLVGRMVEAMRAAVSIPVT 187

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  ++  +G   + +HARKA L+GLSPK+NR +P LDYD V 
Sbjct: 188 VKCRIGVDDQDPGPALDALTAAVAAAGCRTLIVHARKAWLQGLSPKENRDVPPLDYDRVD 247

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY-FSNPLT 238
            +K  NPD+ + LNGGL D+      L   +DG M+GRAAY+   +L   D   F  P  
Sbjct: 248 ALKATNPDMVVVLNGGLLDLDAVEAALARGLDGGMVGRAAYQTPWVLADADRRIFGAP-- 305

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                 T +D+     +  +M +YA R     G  ++ + RHM+GLF G P +R  R  L
Sbjct: 306 -----STDIDR---HAVVEAMAEYAGRARRDLGTPVKSVVRHMLGLFQGLPGARAWRRYL 357

Query: 298 T 298
           +
Sbjct: 358 S 358


>gi|294634339|ref|ZP_06712877.1| tRNA dihydrouridine synthase A [Edwardsiella tarda ATCC 23685]
 gi|291092236|gb|EFE24797.1| tRNA dihydrouridine synthase A [Edwardsiella tarda ATCC 23685]
          Length = 345

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 142/319 (44%), Positives = 192/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S QE PLALQ+GG++ +
Sbjct: 32  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEQEHPLALQLGGSNPA 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 91  DLARCAALAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++   G  +   +HARKA L GLSPK+NR++P LDY  V
Sbjct: 151 VKTRIGIDEQDSYAFLCDFIGTVAGQGECDTFIVHARKAWLSGLSPKENREVPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P L I +NGG++ +++A   L  VDGVM+GR AY N  ML  VD    +  T 
Sbjct: 211 YRLKQDFPQLTIAINGGVKSLAEAQAHLCHVDGVMVGREAYHNPGMLAQVDRQLFD-ATA 269

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P    V +        ++  Y  R L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 270 AVPDSIAVVR--------ALYPYIERELAQGTYLGHITRHILGLFQGIPGARQWRRHLSE 321

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 322 NAHRPGADIAVVEQALRFV 340


>gi|170698688|ref|ZP_02889754.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria IOP40-10]
 gi|170136392|gb|EDT04654.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria IOP40-10]
          Length = 328

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 136/298 (45%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGKVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 QLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TAA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P +   +        A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 240 VPTREEAE--------AKLIEYCAAELKRGAYLGAIVRHALGLYRGVGGARGWRRVLS 289


>gi|146282034|ref|YP_001172187.1| tRNA-dihydrouridine synthase A [Pseudomonas stutzeri A1501]
 gi|145570239|gb|ABP79345.1| TIM-barrel protein, yjbN family [Pseudomonas stutzeri A1501]
          Length = 334

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 133/300 (44%), Positives = 189/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L GD    L +   E PLALQ+GG+   
Sbjct: 23  MMDWTDRHCRFFLRQLSKHALLYTEMVTTGALLHGDTARFLRYDESEHPLALQLGGSVPG 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ + VT
Sbjct: 83  DLAACAKLAEVAGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCVKAMRDAVGVEVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK NR++P L YD+  
Sbjct: 143 VKHRIGINGRDSYSQLCDFVGQVREAGCRSFTVHARIAILEGLSPKQNREVPPLRYDVAA 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +  + L + DGVM+GR AY N  +L  VD   S+    +
Sbjct: 203 QLKRDFPDLEIILNGGIKTLEECREHLQTFDGVMLGREAYHNPYLLAQVD---SSLFGNN 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   +M  Y  RHL  GG +  +TRH++GL  GFP +RR R +L+V+
Sbjct: 260 APVISRA------QALRNMRPYIERHLAEGGAMHHVTRHVLGLGQGFPGARRFRQLLSVD 313


>gi|312959660|ref|ZP_07774177.1| dihydrouridine synthase TIM-barrel protein YjbN [Pseudomonas
           fluorescens WH6]
 gi|311286377|gb|EFQ64941.1| dihydrouridine synthase TIM-barrel protein YjbN [Pseudomonas
           fluorescens WH6]
          Length = 328

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 139/300 (46%), Positives = 191/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ +ALLYTEM+   AIL GD    L  +  E PLALQ+GG+  +
Sbjct: 17  MMDWTDRHCRFFLRLLSKHALLYTEMVTTGAILHGDHDRFLRHNEAEHPLALQLGGSVPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GA LM +P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAACARMAEAAGYDEVNLNVGCPSDRVQNNMIGAILMAHPALVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++K +G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 137 VKHRIGINGRDSYAELCDFVGTVKDAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+         
Sbjct: 197 QLKRDFPELEIVLNGGIKTLEQCQEHLQTFDGVMLGREAYHNPYLLAEVDQRL---FGSE 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+  R       ++ A +  Y A HL SGG +  ITRH++GL  GFP +RR R +L+V+
Sbjct: 254 APVVGRA------QVLAQLRPYIAEHLASGGVMHHITRHVLGLGTGFPGARRFRQLLSVD 307


>gi|260914683|ref|ZP_05921149.1| tRNA-dihydrouridine synthase A [Pasteurella dagmatis ATCC 43325]
 gi|260631282|gb|EEX49467.1| tRNA-dihydrouridine synthase A [Pasteurella dagmatis ATCC 43325]
          Length = 328

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+   K + L FS +E P+ALQ+GG++ +
Sbjct: 18  MLDWTTRHCRYFHRQFSQHALLYTEMVTTGAIIHA-KYDHLAFSPEENPVALQLGGSNPT 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AKI E  GY EINLNVGCPS RV  G FGACLM   D+V +CI AM + + IPVT
Sbjct: 77  QLAQCAKIAEQRGYAEINLNVGCPSDRVQNGMFGACLMGKADLVAECINAMQEVVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V+ + ++G     IHARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDLDSYEFLCDFVQKVHQAGCQEFIIHARKAWLSGLSPKENREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG++ + +  + L  +DGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPQLIMSINGGIKTIEEMQQHLQYMDGVMVGREAYQNPSLLGYIDQALFDP---T 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SPI T       R+    M  Y  + L  G  L  + RHM+G F     +R+ R  L+  
Sbjct: 254 SPIVTP------REAVEKMFPYIEQQLTQGVYLNHMVRHMLGAFQSCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++E A + +
Sbjct: 308 AHKAGAGLEVVEQALSFI 325


>gi|45656544|ref|YP_000630.1| tRNA-dihydrouridine synthase A [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|294828345|ref|NP_713734.2| tRNA-dihydrouridine synthase A [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45599779|gb|AAS69267.1| conserved hypothetical protein [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|293386197|gb|AAN50752.2| tRNA-dihydrouridine synthase A [Leptospira interrogans serovar Lai
           str. 56601]
          Length = 347

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 187/300 (62%), Gaps = 11/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+F RL++ +  LYTEM+   A+L GD++ +L +S +E PLA+Q+GG+D  
Sbjct: 19  MMDWTDRHFRYFLRLISKHTFLYTEMVHTGAVLHGDRRKLLSYSPEELPLAIQLGGSDPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+ KI ED+GY EINLNVGCPS RV EG+FGACLM  P+ V +   AM  ++SIP+T
Sbjct: 79  ALAESCKIGEDYGYTEINLNVGCPSDRVREGNFGACLMETPEKVAELTFAMDTSVSIPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+  +     L   ++ ++++GV    +HAR AIL GL+P  NR++P L Y  V 
Sbjct: 139 VKCRIGIPGKETFEDLCKFIECVRQTGVQRFIVHARIAILGGLTPAQNRQVPPLHYTYVE 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PDL I +NGG+  ++   + L   DGVMIGRAAY+   + + VD  F      +
Sbjct: 199 SLKKEFPDLLIEINGGIRTITSIRERLEKNDGVMIGRAAYETPYLFSEVDSLF---FGEN 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P  +R      R+I   M DY    +     GK     RHM+GLFHG   +R  R ILT
Sbjct: 256 LPPLSR------REILLRMKDYIEEVILKEKNGKPHHALRHMLGLFHGEKGARSFRKILT 309


>gi|77359457|ref|YP_339032.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874368|emb|CAI85589.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 310

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 141/320 (44%), Positives = 195/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G + + L F+  E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFG-RGDYLHFNQHEGPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   ++IPVT
Sbjct: 60  ALAQCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMGEPQLVADCVAAMKAEVNIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++    G +   IHARKA LKGLSPK+NR++P LDY  VY
Sbjct: 120 VKTRIGIDEQDSYEFLCALIEASHNVGCDDFIIHARKAWLKGLSPKENREVPPLDYPRVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + LNGG++ + Q+L+ L  +DGVMIGR AY N  +L  VDE     +  +
Sbjct: 180 QLKKDYPQLDLSLNGGVKTIEQSLEHLQHIDGVMIGREAYSNPFILNEVDEKIYGDIANT 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              ++R D      +  SM  Y    +  G     + RHM+G+F G P +R  R  L+  
Sbjct: 240 ---QSRHD------VVRSMYSYIEDEMRLGANFWHVARHMLGIFQGQPGARGFRRHLSEN 290

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 291 GHGKQADLSVMDKALSFVPE 310


>gi|28869329|ref|NP_791948.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|38604776|sp|Q884G7|DUSA_PSESM RecName: Full=tRNA-dihydrouridine synthase A
 gi|28852570|gb|AAO55643.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 336

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 139/301 (46%), Positives = 192/301 (63%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 85  GLAACARLAEAAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 145 VKHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 205 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQ----LFGS 260

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V
Sbjct: 261 VAPVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSV 314

Query: 300 E 300
           +
Sbjct: 315 D 315


>gi|50086096|ref|YP_047606.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ADP1]
 gi|49532072|emb|CAG69784.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ADP1]
          Length = 341

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 137/315 (43%), Positives = 188/315 (59%), Gaps = 15/315 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L +S  E P+ LQ+GG++  
Sbjct: 23  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDTKRHLDYSHGEHPIVLQLGGSNPK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E  K+ +D+GY+E+NLNVGCPS RV     GACLM  PD+V +CIA M + + IPV 
Sbjct: 83  DLAECTKMAQDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIAKMQQVVDIPVH 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + N V ++ K+G +   +HAR A+LKGLSPK+NR+IP L Y+ VY
Sbjct: 143 VKHRIGIDDMQSYDEMLNFVDTVAKTGCHHFVVHARIALLKGLSPKENREIPPLRYEDVY 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+LFI +NGG++ +++    L  VDGVMIGR AY N  +L  + + ++  L   
Sbjct: 203 RLKQDRPELFIEINGGIKTVAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWNLDLPDR 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 263 F------------NIMQQMMPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 308

Query: 301 AGASTATHHIIETAF 315
            G +  T   IE A 
Sbjct: 309 -GGNAKTRSDIEHAL 322


>gi|167566497|ref|ZP_02359413.1| tRNA-dihydrouridine synthase A [Burkholderia oklahomensis EO147]
 gi|167570050|ref|ZP_02362924.1| tRNA-dihydrouridine synthase A [Burkholderia oklahomensis C6786]
          Length = 339

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 134/298 (44%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +  LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHTWLYTEMVTTGALVHGDVARHLAFTPGEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AMC A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMCDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKQDFPQLEIIVNGGITTLDEVERHLQHVDGVMLGREAYHNPYVLADVDARFYG---AA 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 TPAPTR------EAVEAQLVEYCATELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|331019219|gb|EGH99275.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 339

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 139/301 (46%), Positives = 192/301 (63%), Gaps = 11/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDEAEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEAAGYDEVNLNVGCPSDRVQNNMIGACLMAHPPLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     L GS
Sbjct: 208 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQ----LFGS 263

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V
Sbjct: 264 VAPVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSV 317

Query: 300 E 300
           +
Sbjct: 318 D 318


>gi|75677001|ref|YP_319422.1| tRNA-dihydrouridine synthase A [Nitrobacter winogradskyi Nb-255]
 gi|74421871|gb|ABA06070.1| tRNA-U16,U17-dihydrouridine synthase [Nitrobacter winogradskyi
           Nb-255]
          Length = 340

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 142/298 (47%), Positives = 193/298 (64%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F RLLT  A LY+EM+   A++ G +  +LGFS  E P+ALQ+GG++ +
Sbjct: 14  MMEWTDRHCRVFHRLLTRRAWLYSEMLTTGAVIHGARDRLLGFSDIEHPVALQLGGSNPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I EDFGY+EINLNVGCPS RV +G FGACLM  PDIV + + AM +A+S+PVT
Sbjct: 74  DLAIAARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPDIVAESVNAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ    AL   V+ +  +GV+ + +HARKA L+GLSPK+NR +P LD+  VY
Sbjct: 134 VKCRIGIDDQDMESALDIFVRKVVAAGVDALIVHARKAWLQGLSPKENRNVPPLDHGRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L I +NGG+  + +A + L  VDGVM+GRAAY+    L  VD    + L G 
Sbjct: 194 RLKASFPGLPIIINGGIGGIPEAKQHLAHVDGVMLGRAAYQEPWRLLEVD----SELFGE 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P    +     ++   +M  Y    L  G +L  I+RH++G FHG P +R  R  L 
Sbjct: 250 APPHPTM-----KQALEAMVPYIEEQLAGGARLHSISRHLVGAFHGVPGARGFRRYLA 302


>gi|148827810|ref|YP_001292563.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae PittGG]
 gi|148719052|gb|ABR00180.1| hypothetical protein CGSHiGG_06425 [Haemophilus influenzae PittGG]
          Length = 327

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKHCARLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYTRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T  +         SM  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTAYEA------VQSMLPYIEQQLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|115351522|ref|YP_773361.1| tRNA-dihydrouridine synthase A [Burkholderia ambifaria AMMD]
 gi|115281510|gb|ABI87027.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia ambifaria AMMD]
          Length = 344

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 136/298 (45%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGKVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 QLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYG---ST 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           + + TR + +      A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 AAVPTREEAE------AKLIEYCAAELKRGTYLGAIVRHALGLYRGVGGARGWRRVLS 305


>gi|94986095|ref|YP_605459.1| tRNA-dihydrouridine synthase A [Deinococcus geothermalis DSM 11300]
 gi|94556376|gb|ABF46290.1| tRNA-U16,U17-dihydrouridine synthase [Deinococcus geothermalis DSM
           11300]
          Length = 344

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/323 (43%), Positives = 193/323 (59%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT   LLYTEM+   AIL GD+   LGFS  E P+ALQ+GG+D +
Sbjct: 16  MMDWTDRHCRAFHRTLTRRTLLYTEMVTTGAILHGDRARHLGFSPAEHPVALQLGGSDPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I +D+GY+E+NLN GCPS RV  GSFGACLM  PD+V   + AM  A ++PVT
Sbjct: 76  ALAECARIAQDWGYDEVNLNCGCPSDRVQNGSFGACLMATPDVVARAVEAMRGATTLPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+++ ++G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 136 VKHRIGIDDLDSYEHLTRFVRTVAEAGCQTFIVHARKAWLSGLSPKENREIPPLRYEVVR 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K + P L + LNGG+  ++ A + L   DGVM+GRAAY++  +L   D + F   +T 
Sbjct: 196 QLKADFPHLTVVLNGGVLTLAAAQEHLAWADGVMVGRAAYQDPYLLAAADRDLFGEDVT- 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +        R+   +   Y A  L  G  L ++ RH +GLF G P +R  +  L+ 
Sbjct: 255 -PPTR--------REAIEAFLPYVAAQLAEGQPLHRMMRHTLGLFAGQPGARHWKRTLSE 305

Query: 300 EAGASTATHHIIETAFNLMIESL 322
                 A   ++  A   + ES+
Sbjct: 306 RGHRPGAGLEVVREALAGVPESV 328


>gi|145633883|ref|ZP_01789604.1| hypothetical protein CGSHi3655_08484 [Haemophilus influenzae 3655]
 gi|145635660|ref|ZP_01791356.1| hypothetical protein CGSHiAA_01434 [Haemophilus influenzae PittAA]
 gi|144985255|gb|EDJ92098.1| hypothetical protein CGSHi3655_08484 [Haemophilus influenzae 3655]
 gi|145267055|gb|EDK07063.1| hypothetical protein CGSHiAA_01434 [Haemophilus influenzae PittAA]
          Length = 329

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYTRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGVEVVETALSFV 325


>gi|262195064|ref|YP_003266273.1| hypothetical protein Hoch_1832 [Haliangium ochraceum DSM 14365]
 gi|262078411|gb|ACY14380.1| TIM-barrel protein, yjbN family [Haliangium ochraceum DSM 14365]
          Length = 376

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+F R ++ + LLYTEMIV   I+ GD+   L FS  E P+ALQ+GG D  
Sbjct: 47  MMECTDRHFRYFLRQISRHTLLYTEMIVTGTIIHGDRPRYLDFSEAEHPIALQLGGDDAE 106

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A+I ED+GY+E+NLNVGCPS+RV  GSFGACLM  P++V   + AM  A++IPVT
Sbjct: 107 ALATCARIAEDWGYDEVNLNVGCPSSRVSSGSFGACLMARPEVVARAVEAMRAAVAIPVT 166

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     +R  V+ + ++G +   +HARKA L GLSPK+NR++P L Y  V+
Sbjct: 167 VKHRIGIDDRDRYEDMREFVRVVAEAGADRFSVHARKAWLSGLSPKENREVPPLRYADVH 226

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG+ D+  A + L  VD VMIGRAAY    +    D  F   +   
Sbjct: 227 RLKREFPHLPIEINGGIVDLDSAQEQLAHVDAVMIGRAAYNTPWIFAEADARFFGSV-AP 285

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +T V +        +M DY       G  L +ITRHM  LF G   +R  R  LT +
Sbjct: 286 TPTQTAVVE--------AMIDYVEAQRGRGVPLHRITRHMFQLFAGQRGARGWRRYLTEQ 337

Query: 301 AGASTATHHIIETAFN 316
           A +  A   ++  A +
Sbjct: 338 AKSRDAGPEVLRVALD 353


>gi|260556088|ref|ZP_05828307.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 19606]
 gi|260410143|gb|EEX03442.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 19606]
          Length = 339

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 192/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 21  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 81  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 141 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 201 RLKQERPHLTIEINGGIKTFTETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 257 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 306

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 307 -GGNAKTLTDVENAIHNM 323


>gi|239500729|ref|ZP_04660039.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB900]
          Length = 334

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 192/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 302 -GGNAKTLTDVENAIHNM 318


>gi|171317498|ref|ZP_02906688.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria MEX-5]
 gi|172060541|ref|YP_001808193.1| tRNA-dihydrouridine synthase A [Burkholderia ambifaria MC40-6]
 gi|171097327|gb|EDT42172.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria MEX-5]
 gi|171993058|gb|ACB63977.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria MC40-6]
          Length = 328

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 136/298 (45%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGKVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 QLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TAA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P +   +        A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 240 VPTREEAE--------AKLIEYCAAELKRGTYLGAIVRHALGLYRGVGGARGWRRVLS 289


>gi|284006504|emb|CBA71765.1| tRNA-dihydrouridine synthase A [Arsenophonus nasoniae]
          Length = 344

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 146/320 (45%), Positives = 193/320 (60%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   A++ G K + L +S +E P+ALQ+GG + +
Sbjct: 33  MLDWTDRHCRYFHRLLTKEALLYTEMVTTGALIYG-KGDYLAYSEEEHPVALQLGGNEPT 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ +  GY+EINLN+GCPS RV  G FGACLM    +V DCI AM  A +IP+T
Sbjct: 92  ALAYCAKMAQQSGYDEINLNIGCPSDRVQNGRFGACLMREGGLVADCIKAMQDAATIPIT 151

Query: 121 VKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVDD      L + + K +  S      IHARKA L GLSPK NR+IP LDY  V
Sbjct: 152 VKTRIGVDDDDSYAFLTDFIDKIVTDSQCRLFIIHARKAWLSGLSPKQNREIPPLDYLRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++KK+ P L I +NGG++++ +A + L  +DGVMIGR AY+N A+LT VD E+F     
Sbjct: 212 YQLKKDFPQLTIVVNGGIKNIDEAKQHLHHLDGVMIGREAYQNPALLTQVDVEFFDQRSL 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              PI              +M  Y  R L  G  L  ITRHM+G+F   P +R+ R  L+
Sbjct: 272 VIDPIIA----------VQTMYPYIERELKQGTYLGHITRHMLGIFQAIPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   +++ A   +
Sbjct: 322 ENAHKKGADVTVVKQALEFI 341


>gi|299771563|ref|YP_003733589.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. DR1]
 gi|298701651|gb|ADI92216.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. DR1]
          Length = 334

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 140/322 (43%), Positives = 192/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L +S QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYSAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI  M KA+ IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHTMQKAVKIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTYFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAEMGQLWNL----E 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 AP--DRFD------IMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  +L
Sbjct: 302 -GGNAKTLGDVEQAISNMQAAL 322


>gi|89256833|ref|YP_514195.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115315219|ref|YP_763942.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|167009275|ref|ZP_02274206.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica FSC200]
 gi|169656701|ref|YP_001429066.2| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|254369716|ref|ZP_04985726.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|290954380|ref|ZP_06559001.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312201|ref|ZP_06803003.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144664|emb|CAJ79988.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115130118|gb|ABI83305.1| tRNA dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|157122675|gb|EDO66804.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|164551769|gb|ABU62110.2| tRNA dihydrouridine synthase [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 327

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 136/325 (41%), Positives = 191/325 (58%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+  YNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELDYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N P T 
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            S +          +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISAL----------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
           +  A    A      TA  +    L
Sbjct: 303 SENATKKEANVDTFLTALEVFENKL 327


>gi|169634371|ref|YP_001708107.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii SDF]
 gi|169153163|emb|CAP02248.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii]
          Length = 339

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 192/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 21  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 81  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 141 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 201 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 257 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 306

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 307 -GGNAKTLTDVENAIHNM 323


>gi|301155106|emb|CBW14569.1| tRNA-dihydrouridine synthase A [Haemophilus parainfluenzae T3T1]
          Length = 328

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + NALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSKNALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V +CIA M + ++IPVT
Sbjct: 77  QLKHCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVAECIAEMQRVVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ +   G     +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKTRIGIDDLDSYEFLCDFIEKVHHDGCQEFIVHARKAWLSGLSPKENREIPPLDYDRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D+        +
Sbjct: 197 QLKKDFPQLTIAINGGIKTIEEMKYHLQFVDGVMVGREAYQNPSLLGYIDQML---FDAN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + I T       ++   +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 ADIVTP------KQAVEAMFPYIEKQLSQGVYLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|237748250|ref|ZP_04578730.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes OXCC13]
 gi|229379612|gb|EEO29703.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes OXCC13]
          Length = 330

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 134/299 (44%), Positives = 192/299 (64%), Gaps = 7/299 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +  LYTEM+   A+L GD    L FS +E P+ALQ+GG++  
Sbjct: 16  MLDWTDRHCRYFHRLISRHTWLYTEMVTTGALLFGDVARHLDFSEEEHPIALQLGGSEPG 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A++ E +GY+EINLN GCPS RV +G+FGACLM    +V +C+ AM  A+SI VT
Sbjct: 76  DLAQCARLGEKWGYDEINLNCGCPSERVQKGAFGACLMSESTLVANCVKAMQDAVSIDVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ +  + ++G     +HAR AILKGLSP++NR+IP L Y++VY
Sbjct: 136 VKHRIGIDKNESYDFVRDFIGEVAEAGCKTFIVHARNAILKGLSPRENREIPPLRYEVVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++KK+ P+L I LNGG+E   +  + +  VDGVMIGRAAY     +   D  ++ +P T 
Sbjct: 196 QLKKDFPELEILLNGGIETADEVGEHIKHVDGVMIGRAAYHYPYRMAEFDARFYDDPTTA 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           ++P    V K     I   ++ Y ++    G K+  ITRHM+GL  G P +RR R IL+
Sbjct: 256 TTPAD--VVKAMMPYIEKQLSLYGSK----GLKMHGITRHMLGLMTGLPGARRFRQILS 308


>gi|88858983|ref|ZP_01133624.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas tunicata D2]
 gi|88819209|gb|EAR29023.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas tunicata D2]
          Length = 337

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 141/320 (44%), Positives = 189/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +A+LYTEMI   AI+ G + + L F   E+P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRTFHRKLTQHAVLYTEMITTGAIIYG-RGDYLHFGQHEQPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  ++ GY EINLNVGCPS RV  G FGACLM  P++V  C+AAM +  ++PVT
Sbjct: 86  ALALCAKQADERGYQEINLNVGCPSDRVQNGRFGACLMAEPNLVAQCVAAMKEQTNMPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L  L+ +      N   IHARKA L GLSPK+NR IP LDY+ VY
Sbjct: 146 VKTRIGIDDQDSYEFLCALIDACIAVDCNDFIIHARKAWLSGLSPKENRDIPPLDYERVY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P   I +NGG++ + Q+L  L  +DGVM+GR AY N  +LT VD         S
Sbjct: 206 QLKKDYPQTHISINGGVKTIEQSLAHLQFIDGVMMGREAYANPYLLTQVDSAIYG--DAS 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   +M DY    +  G     + RHM+G+F G P  R  R  L+  
Sbjct: 264 TPVLSR------HQAVRAMYDYFEAEMTGGASFWHVARHMLGIFQGVPGGRAFRRHLSEN 317

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++E A   + E
Sbjct: 318 GHKKDADISVMEQALGFVAE 337


>gi|326795079|ref|YP_004312899.1| TIM-barrel protein, yjbN family [Marinomonas mediterranea MMB-1]
 gi|326545843|gb|ADZ91063.1| TIM-barrel protein, yjbN family [Marinomonas mediterranea MMB-1]
          Length = 348

 Score =  266 bits (681), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/319 (43%), Positives = 191/319 (59%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWT R YR FAR LT + LLYTEM+   AIL+GD  +  L +   E P+ALQ+GG+D 
Sbjct: 29  MLDWTTRDYRVFARTLTKHTLLYTEMVTTGAILQGDNPERFLKYDDCEHPIALQLGGSDA 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   AKI E F Y+E+NLNVGCPS RV     GACLM  PD V D + AM  A SIPV
Sbjct: 89  VALATCAKIAETFHYDEVNLNVGCPSDRVQNSLIGACLMAYPDKVADILKAMQDATSIPV 148

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+DDQ     LR+ V ++  +G+    +HAR AIL+GLSPK+NR+IP L YD V
Sbjct: 149 TIKHRIGLDDQQEYSILRDFVGTVADTGIQTFIVHARNAILQGLSPKENREIPPLKYDYV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ PDL I +NGG++ + + +  L  VDGVM+GR AY N  +L+ +D   +     
Sbjct: 209 YQLKKDFPDLEIIINGGIKTIDETISHLDHVDGVMMGREAYNNPWILSDID---TKVYGA 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S+ +  R +             Y    L  G +L  +TRH++G+FHG P  ++ R  L+ 
Sbjct: 266 SACVNNRFEA------LERFVPYVEEQLAKGERLMHMTRHILGIFHGLPGGKQFRRYLSE 319

Query: 300 EAGASTATHHIIETAFNLM 318
               + A   I+  A  ++
Sbjct: 320 NGHKTDAKIDILLEAIEIV 338


>gi|67921570|ref|ZP_00515088.1| Dihydrouridine synthase TIM-barrel protein yjbN [Crocosphaera
           watsonii WH 8501]
 gi|67856682|gb|EAM51923.1| Dihydrouridine synthase TIM-barrel protein yjbN [Crocosphaera
           watsonii WH 8501]
          Length = 334

 Score =  266 bits (681), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 138/317 (43%), Positives = 190/317 (59%), Gaps = 13/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+  R +T + LLYTEMIV+ AI  GD+  +L FS +EKPL+LQ+GG +  
Sbjct: 9   MMDYTDRHFRYLMRQITRHTLLYTEMIVSAAIKHGDRPKLLDFSPEEKPLSLQLGGDNPQ 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I ED+GY+EINLNVGCPS RV  G FGACLM  P++V  C+  M + ++IPVT
Sbjct: 69  ELAECAIIAEDWGYDEINLNVGCPSDRVQSGHFGACLMAKPELVAQCVQKMQQGVNIPVT 128

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     +   V  + ++G     IHARKA LKGLSPK+NR IP L Y  VY
Sbjct: 129 VKQRIGIDDQDSYEEMARFVAIVAEAGCQRFTIHARKAWLKGLSPKENRNIPPLRYQDVY 188

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPLT 238
            +K++ P L I +NGG+ ++ Q    L  VD VMIGRAAY N  +  TVD   Y  + + 
Sbjct: 189 RLKQDFPHLLIEINGGITNLEQVDNHLKIVDAVMIGRAAYDNPYLFATVDRDIYQEDIIP 248

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +             +I   M  Y    +  G KL +I+RH++ +F G P ++  +  ++
Sbjct: 249 ATR-----------HEIIEKMLPYIDHWVSRGHKLHRISRHLLAMFAGIPGTKAWKRYIS 297

Query: 299 VEAGASTATHHIIETAF 315
             A    A   +I  A 
Sbjct: 298 ENAHLPGADSQVIIEAL 314


>gi|308188956|ref|YP_003933087.1| tRNA-dihydrouridine synthase A [Pantoea vagans C9-1]
 gi|308059466|gb|ADO11638.1| tRNA-dihydrouridine synthase A [Pantoea vagans C9-1]
          Length = 330

 Score =  266 bits (681), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 141/324 (43%), Positives = 196/324 (60%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G K + L +S  E P+ALQ+GG+D +
Sbjct: 14  MLDWTDRHCRYFHRQLTGDTLLYTEMVTTGAIIHG-KGDYLAYSEAEHPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM   ++V D I AM   +SIPVT
Sbjct: 73  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEANLVADAIKAMRDVVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 133 VKTRIGIDELDSYEFLTDFIGTVAGRGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLT 238
           Y++K++ P L I LNGG++ + +A   L  +DGVM+GR AY+N  +L  VD+  F     
Sbjct: 193 YQLKRDFPHLTIALNGGVKTLEEAQTHLQHLDGVMMGREAYQNPGILAQVDQTLFGRQHP 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P+          ++  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 253 AANPV----------EVVRAMYPYIEAELAKGTYLGHVTRHMLGLFQGIPGARQWRRHLS 302

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 303 ENAHKPGADVRVLEAALALVADKI 326


>gi|254424029|ref|ZP_05037747.1| TIM-barrel protein, yjbN family [Synechococcus sp. PCC 7335]
 gi|196191518|gb|EDX86482.1| TIM-barrel protein, yjbN family [Synechococcus sp. PCC 7335]
          Length = 355

 Score =  266 bits (681), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 141/301 (46%), Positives = 181/301 (60%), Gaps = 10/301 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +D TDRHYRFF R +T   LLYTEM+ A AI  GD   ++GF+  E PL LQ+GG D   
Sbjct: 1   MDRTDRHYRFFMRQITRRTLLYTEMVNAQAIYYGDLDRLIGFTPDENPLVLQVGGDDPKL 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  +A+   +FGY+EINLNVGCPS RV  G+FGACLM  P+ V DC++AM  A ++PV+V
Sbjct: 61  LANSARRAAEFGYSEINLNVGCPSDRVQSGNFGACLMAQPERVADCVSAMIAASALPVSV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+DDQ     + N V  +  +G     +HARKA L+GLSPKDNR IP L Y  V+ 
Sbjct: 121 KHRIGIDDQDSYEDMANFVTIVSATGCQRFSVHARKAWLQGLSPKDNRNIPPLRYADVHR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K+E P L I +NGG + ++Q    L +VD VMIGRAAY    +    D+      T   
Sbjct: 181 LKQEFPHLQIEINGGFKTLAQVKNQLRAVDAVMIGRAAYDIPFLFEKADQEIFGETTEP- 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +TR       ++  SM  Y   H    G +L  ITRHM+ LFHG P SR  +  LT E
Sbjct: 240 --QTRY------QVVESMLPYIDYHTQKLGTRLHSITRHMLHLFHGQPGSRIWKQTLTEE 291

Query: 301 A 301
           A
Sbjct: 292 A 292


>gi|169797208|ref|YP_001715001.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AYE]
 gi|213155999|ref|YP_002318044.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB0057]
 gi|301346115|ref|ZP_07226856.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB056]
 gi|301511827|ref|ZP_07237064.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB058]
 gi|301594892|ref|ZP_07239900.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB059]
 gi|332850773|ref|ZP_08433005.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332866157|ref|ZP_08436872.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013113]
 gi|169150135|emb|CAM88029.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AYE]
 gi|213055159|gb|ACJ40061.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB0057]
 gi|332730432|gb|EGJ61749.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332734798|gb|EGJ65892.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013113]
          Length = 338

 Score =  266 bits (681), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 192/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLN+GCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNIGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 256 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 306 -GGNAKTLTDVENAIHNM 322


>gi|227357643|ref|ZP_03841996.1| tRNA-dihydrouridine synthase A [Proteus mirabilis ATCC 29906]
 gi|227162353|gb|EEI47357.1| tRNA-dihydrouridine synthase A [Proteus mirabilis ATCC 29906]
          Length = 344

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 139/322 (43%), Positives = 197/322 (61%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT N LLYTEM+   AI+ G K + L +S +E P++LQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFFRQLTKNTLLYTEMVTTGAIIHG-KGDYLKYSNEEHPISLQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   + IPVT
Sbjct: 92  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ + +  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDNQDSYQFLCDFIDTVSRDNNCDTFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLT 238
           Y++K++   L + +NGG++ + +A + L  +DGVM+GR AY+N ++L  VD   F N L 
Sbjct: 212 YQLKRDFSHLTMAINGGIKSLEEAQEHLKYMDGVMVGREAYQNPSILAHVDHVLFDNQL- 270

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+   V          +M  Y  + L  G  L  ITRHM+G+F G P +R+ R  L+
Sbjct: 271 ---PVTNAV------AAVKAMYPYIEKELSQGTYLGHITRHMLGIFQGIPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A   + E
Sbjct: 322 ENAHKQGADLTVLENALKFVTE 343


>gi|317046530|ref|YP_004114178.1| TIM-barrel protein, yjbN family [Pantoea sp. At-9b]
 gi|316948147|gb|ADU67622.1| TIM-barrel protein, yjbN family [Pantoea sp. At-9b]
          Length = 331

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 145/324 (44%), Positives = 198/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G K + L FS  E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLSGDTLLYTEMVTTGAIIHG-KGDYLAFSEDEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A++ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 74  ALAQCAQLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMRDVVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLCDFVGTVAQQGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPQLTMAINGGIKSLAEAKVHLQHMDGVMMGREAYQNPGILAQVDRELFGRDTP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  SM  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AVDPV----------AVVRSMYPYIEAELAKGTYLGHVTRHMLGLFQGIPGARQWRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 304 ENAHKPGADVRVLEAALALVADKI 327


>gi|226326586|ref|ZP_03802104.1| hypothetical protein PROPEN_00436 [Proteus penneri ATCC 35198]
 gi|225205011|gb|EEG87365.1| hypothetical protein PROPEN_00436 [Proteus penneri ATCC 35198]
          Length = 344

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 138/322 (42%), Positives = 200/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ N LLYTEM+   AI+ G K + L +S +E P++LQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFFRQLSKNTLLYTEMVTTGAIIHG-KGDYLKYSEEEHPVSLQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM +  +V +C+ AM   + IPVT
Sbjct: 92  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGDAQLVANCVKAMRDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + +  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIETVSRDNNCDTFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++   L + +NGG++ + +A + L  +DGVM+GR AY+N ++L  VD E F N L 
Sbjct: 212 YQLKRDFSHLTMAINGGIKSLEEAKEHLKHMDGVMVGREAYQNPSILAHVDHELFDNQL- 270

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              PI   V          +M  Y  + L  G  L  +TRHM+G+F G P +R+ R  L+
Sbjct: 271 ---PIADAV------AAVRAMYPYIEKELSQGTYLGHVTRHMLGIFQGIPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A   + +
Sbjct: 322 ENAHKQGADLSVLENALKFVTD 343


>gi|215484648|ref|YP_002326883.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB307-0294]
 gi|213987851|gb|ACJ58150.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB307-0294]
          Length = 334

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 192/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLN+GCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNIGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 302 -GGNAKTLTDVENAIHNM 318


>gi|241668892|ref|ZP_04756470.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877424|ref|ZP_05250134.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843445|gb|EET21859.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 324

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 132/310 (42%), Positives = 186/310 (60%), Gaps = 13/310 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+HYR+  RL+T   +LYTEMI  +AI+ G+K  +L ++ +E P+ LQ+GG    
Sbjct: 13  MLDWTDKHYRYMMRLITKQTMLYTEMITLNAIIHGNKDFLLKYNPEENPVTLQLGGCVPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ ++ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L +P++
Sbjct: 73  DFITCGKLAQNLGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLDVPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVNKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  +    + L  VD VMIGR AY N  +    D  F N P+  
Sbjct: 193 NIKKDFPNLELGINGGVTTIEDTQEHLKYVDSVMIGREAYHNPMLFKDFDNLFYNQPIND 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHS--GGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            SP+          +++  M +Y    L+S    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISPL----------EVAYEMAEYIKIQLNSDPNMKLNNITKHTLNLFNGLPNAKVFRRYL 302

Query: 298 TVEAGASTAT 307
           +  A    A 
Sbjct: 303 SENATKKDAN 312


>gi|193076358|gb|ABO11015.2| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 17978]
          Length = 334

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 191/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG+   
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSTPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 AP--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A + M
Sbjct: 302 -GGNAKTLTDVENAIHNM 318


>gi|262280981|ref|ZP_06058764.1| tRNA-dihydrouridine synthase A [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257881|gb|EEY76616.1| tRNA-dihydrouridine synthase A [Acinetobacter calcoaceticus
           RUH2202]
          Length = 330

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 137/322 (42%), Positives = 191/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L +S QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYSAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY E+NLNVGCPS RV     GACLM  PD+V +CI  M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYGEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHTMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMHSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQTHLQHVDGVMIGREAYHNPYLLAEMGQLWN------ 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++     +I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 250 ------LEAPDRFEIMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  +L
Sbjct: 302 -GGNAKTLGDVEQAISNMQAAL 322


>gi|71279069|ref|YP_267111.1| tRNA-dihydrouridine synthase A [Colwellia psychrerythraea 34H]
 gi|71144809|gb|AAZ25282.1| TIM-barrel protein, yjbN family [Colwellia psychrerythraea 34H]
          Length = 335

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 189/316 (59%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RL+T + +LYTEM+   AILRG K + L ++  E PL LQ+GG+D+ 
Sbjct: 25  MLDWTDKHSRYFYRLMTQHTVLYTEMVTTGAILRG-KGDYLSYNDAEHPLVLQLGGSDVK 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + E AKI E +GY+E+N+NVGCPS RV  G FGACLM  P +V  C+  M  A +IPVT
Sbjct: 84  AMTECAKIAEQYGYDEVNINVGCPSDRVQNGRFGACLMAEPALVAQCVNQMQSATNIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   ++ + K+      IHARKA L GLSPK NR +P LDYD VY
Sbjct: 144 VKSRIGIDDLDSYEFLHTFIEEVSKADCRHFIIHARKAWLTGLSPKQNRDVPPLDYDRVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK +  DL + +NGG++  S+A + L  +DGVMIGR  Y +  ML   D    N +  S
Sbjct: 204 QIKNDFKDLEVSINGGIKTFSEANEHLQHIDGVMIGREIYNSPYMLADAD----NEIYQS 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             IK         ++   M  Y    + +GG+   + RHM+GL +G   +R+ R  L+  
Sbjct: 260 DTIKLSRS-----EVIDLMVPYIDETIANGGRAWHVLRHMLGLCNGLSGARKFRQHLSEC 314

Query: 301 AGASTATHHIIETAFN 316
           AG   A   ++  AFN
Sbjct: 315 AGKDGAGGQVLLDAFN 330


>gi|325124532|gb|ADY84055.1| tRNA-dihydrouridine synthase A [Acinetobacter calcoaceticus PHEA-2]
          Length = 334

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 191/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTYFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LK 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 AP--DRFD------IMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A   M
Sbjct: 302 -GGNAKTLADVENAIQNM 318


>gi|121605287|ref|YP_982616.1| tRNA-dihydrouridine synthase A [Polaromonas naphthalenivorans CJ2]
 gi|120594256|gb|ABM37695.1| tRNA-U16,U17-dihydrouridine synthase [Polaromonas naphthalenivorans
           CJ2]
          Length = 337

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 135/299 (45%), Positives = 186/299 (62%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RLL+ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 24  MMDWSDRHCRYFHRLLSRHALLYTEMVTTGALIHGDVGRHLRFNAEEHPVALQLGGSEPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EIN+N GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 84  DLAHCARLGEQWGYSEININCGCPSERVQRGAFGACLMAEPKLVADCVKAMVDAVSVPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     +R+ V ++ ++G +   +HAR A LKGLSPK+NR++P L Y++V+
Sbjct: 144 VKHRIGIDREERYEFVRDFVGTVSEAGCDTFIVHARNAWLKGLSPKENREVPPLRYELVH 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE   L I +NGG+    Q    L  +DGVMIGR AY N   L + D  F     G 
Sbjct: 204 RLKKEFAHLTICVNGGITTGEQVQGQLLELDGVMIGREAYHNPWWLASWDADFFG--AGG 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             I TR       ++ A M DY  R     G     I RHM+GL HG P SRR R + +
Sbjct: 262 ESI-TR------EQVEAQMCDYMVREAAGHGTPFSAIARHMLGLRHGLPGSRRWRQVWS 313


>gi|260549038|ref|ZP_05823259.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. RUH2624]
 gi|260407766|gb|EEX01238.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. RUH2624]
          Length = 338

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 191/318 (60%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 256 AP--DRFD------IMEQMLPYIEQRMAQGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A   M
Sbjct: 306 -GGNAKTLTDVENAIRNM 322


>gi|145639381|ref|ZP_01794986.1| hypothetical protein CGSHiII_04387 [Haemophilus influenzae PittII]
 gi|145271428|gb|EDK11340.1| hypothetical protein CGSHiII_04387 [Haemophilus influenzae PittII]
          Length = 327

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKHDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGVEVVETALSFV 325


>gi|304398443|ref|ZP_07380316.1| TIM-barrel protein, yjbN family [Pantoea sp. aB]
 gi|304353948|gb|EFM18322.1| TIM-barrel protein, yjbN family [Pantoea sp. aB]
          Length = 330

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 141/324 (43%), Positives = 195/324 (60%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G K + L +S  E P+ALQ+GG+D +
Sbjct: 14  MLDWTDRHCRYFHRQLTGDTLLYTEMVTTGAIIHG-KGDYLAYSEAEHPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM   ++V D I AM   +SIPVT
Sbjct: 73  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEANLVADAIKAMRDVVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 133 VKTRIGIDELDSYEFLTDFIGTVAGRGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLT 238
           Y++K++ P L I LNGG++ + +A   L  +DGVM+GR AY+N  +L  VD+  F     
Sbjct: 193 YQLKRDFPHLTIALNGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDQTLFGRQHP 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P+           +  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 253 AANPV----------DVVRAMYPYIEAELAKGTYLGHVTRHMLGLFQGIPGARQWRRHLS 302

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 303 ENAHKPGADVRVLEAALALVADKI 326


>gi|89093370|ref|ZP_01166319.1| NIFR3-like protein [Oceanospirillum sp. MED92]
 gi|89082349|gb|EAR61572.1| NIFR3-like protein [Oceanospirillum sp. MED92]
          Length = 328

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 131/302 (43%), Positives = 188/302 (62%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+L+ NA+LYTEM+   A++  +    L ++ +E+P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRYFHRILSQNAVLYTEMVTTGALIHAEADRFLRYNREEQPVALQLGGSNPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +  K+ ED+GYNE+NLNVGCPS RV     GACLM +P +V +C+  M  A+ IPVT
Sbjct: 77  DLAQCTKMAEDYGYNEVNLNVGCPSDRVQNNMIGACLMAHPQLVSECLEKMQAAVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G+DD      L   V ++++SG     IHARKAIL+GLSPK+NR IP L Y+ VY
Sbjct: 137 VKHRQGIDDMDSYEELVQFVDTVRQSGCKVFIIHARKAILQGLSPKENRDIPPLKYEWVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK+E P+L + +NGG++ + +    L  VDGVM+GR AY+N  +L  VD  F     G+
Sbjct: 197 QIKQEFPELEVHINGGIKTIDECHTHLQHVDGVMLGREAYQNPYLLADVDREF----YGA 252

Query: 241 SPIKTRVDKDFWRKISA-SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              K        RK +A +M  Y  + +  G  L  + RHM+GLFH     ++ R  ++ 
Sbjct: 253 DSEKIS------RKAAALAMVPYIEQQMEQGVPLNHVVRHMLGLFHAQRGGKQFRRFISE 306

Query: 300 EA 301
            A
Sbjct: 307 NA 308


>gi|293610334|ref|ZP_06692635.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827566|gb|EFF85930.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 338

 Score =  265 bits (678), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 190/318 (59%), Gaps = 15/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI  M KA++IPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHTMQKAVNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTYFVVHARIAILKGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R D      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 256 AP--DRFD------IMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLM 318
            G +  T   +E A   M
Sbjct: 306 -GGNAKTLADVENAIQNM 322


>gi|190572349|ref|YP_001970194.1| tRNA-dihydrouridine synthase A [Stenotrophomonas maltophilia K279a]
 gi|190010271|emb|CAQ43879.1| putative tRNA-dihydrouridine synthase A [Stenotrophomonas
           maltophilia K279a]
          Length = 334

 Score =  265 bits (678), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 140/315 (44%), Positives = 193/315 (61%), Gaps = 11/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L   A LYTEM+ A+A++ GD++ +LGF   E+PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRVLAPGARLYTEMVHANAVIHGDRERLLGFDRSEQPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM  A+ IPVT
Sbjct: 79  LLAQAARIAAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPVLVAECVAAMVDAVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD+        + V     +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDEDNDYDVFASFVDRQVAAGAAMVVVHARNAWLKGLSPKENREVPPLKYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGGL  +         VDGVM+GRAAY +  +L  ++      L   
Sbjct: 199 RLKQERPALPVVINGGLASIEAVQAQAAHVDGVMLGRAAYHDPYLLHQLEA-----LHTG 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++ R D      +  +M  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 254 APLQARGD------LLRAMRPYIEARLREGLALKHITRHLLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAF 315
           A    A   +IE A 
Sbjct: 308 AHRPGAGWSLIEQAL 322


>gi|186476399|ref|YP_001857869.1| YjbN family TIM-barrel protein [Burkholderia phymatum STM815]
 gi|184192858|gb|ACC70823.1| TIM-barrel protein, yjbN family [Burkholderia phymatum STM815]
          Length = 333

 Score =  265 bits (677), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 134/298 (44%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSFHRTLSRHAWLYTEMVTTGALIHGDVARHLAFTADEAPVALQLGGSERE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P++V DC+ AM  A+S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMKEPELVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVDD      +R+ V +I  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDDVEDYAFVRDFVGTIADAGCDVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 197 RLKRDFPQLEIIINGGIKTLDEVETHLQHVDGVMLGREAYHNPFVLADVDARFYGS-TDA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   +        A + +Y    L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 256 APTREEAE--------AQLIEYCRAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|149926267|ref|ZP_01914529.1| tRNA-dihydrouridine synthase A [Limnobacter sp. MED105]
 gi|149825085|gb|EDM84297.1| tRNA-dihydrouridine synthase A [Limnobacter sp. MED105]
          Length = 314

 Score =  265 bits (677), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 135/321 (42%), Positives = 186/321 (57%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +  LYTEMI   A++ GD+   L F+ +E P+A Q+GG+D  
Sbjct: 1   MIDWTDRHCRRFHRAISQHTWLYTEMITTGALVYGDRNRFLAFNDEEHPVAFQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   AK +E  GY+E+N+NVGCPS RV +G+FGACLM  P +V DC+ AM  A SI VT
Sbjct: 61  HMARCAKWIEQAGYDELNMNVGCPSERVQKGAFGACLMAEPGLVADCVKAMRDACSIDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L + V  + ++G N   +HAR A+LKGLSPK+NR IP L Y++V 
Sbjct: 121 VKHRIGLDYDESETMLFDFVGKVSEAGCNTFIVHARNAVLKGLSPKENRDIPPLRYEVVK 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P L I LNGG+  +      L   DG MIGR AY N  +L   DE    P T  
Sbjct: 181 RLKQHFPHLQIILNGGITTLEAIESHLQWADGCMIGREAYSNPWLLAGFDEVIGKPTTQ- 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              KTR+D      +   +  YA + L  G  ++ IT+  +GLFHG P  R  R +L+  
Sbjct: 240 ---KTRLD------VIDELRAYAEQELSRGESIRSITKSWLGLFHGQPGGRLYRQVLSDS 290

Query: 301 AGASTATHHIIETAFNLMIES 321
                    ++E A  +M++S
Sbjct: 291 TRLKANNWQVVEDALAMMVKS 311


>gi|241758541|ref|ZP_04756659.1| tRNA-dihydrouridine synthase A [Neisseria flavescens SK114]
 gi|241321314|gb|EER57468.1| tRNA-dihydrouridine synthase A [Neisseria flavescens SK114]
          Length = 334

 Score =  265 bits (677), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 137/301 (45%), Positives = 189/301 (62%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T NA LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 16  MLDWTDRHYRFMARQITRNAWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM   + IPVT
Sbjct: 76  DLAIAAKAAETYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDVVEIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR++P L Y+ V
Sbjct: 136 VKHRIGVDRQTEYQVVADFVGTLREKTACRTFIVHARNAWLDGLSPKENREVPPLKYEYV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 196 YRLKQEFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDALFYN--NT 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  ++A +  Y+   + SG    L+ I RH +GL HG  N+R  R +L
Sbjct: 254 HAPIQ-------YADLAAWLYAYSREQIASGRGTILRHIVRHALGLMHGLKNARTWRRML 306

Query: 298 T 298
           +
Sbjct: 307 S 307


>gi|254177532|ref|ZP_04884187.1| tRNA-dihydrouridine synthase A [Burkholderia mallei ATCC 10399]
 gi|160698571|gb|EDP88541.1| tRNA-dihydrouridine synthase A [Burkholderia mallei ATCC 10399]
          Length = 339

 Score =  265 bits (676), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 186/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F    + S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARF---YSAS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|71083884|ref|YP_266604.1| tRNA-dihydrouridine synthase A [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71062997|gb|AAZ22000.1| conserved hypothetical protein [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 330

 Score =  265 bits (676), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 133/286 (46%), Positives = 177/286 (61%), Gaps = 10/286 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RL++ N LLY+EM+V++AI RGDKK +L F+  EKP+ALQIGG+  +
Sbjct: 10  MMDCTDRHERFFLRLISKNTLLYSEMVVSEAIHRGDKKKLLEFNINEKPIALQIGGSSPT 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EA K+ EDFGY+EINLN+GCPS +V +  FGACLM  P++V DC++ M     +PVT
Sbjct: 70  LLAEATKVGEDFGYDEINLNLGCPSKKVEKNKFGACLMKEPNLVADCLSKMQSVTKLPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG DD      L   + ++K +GV    IHARKAIL   +PK N  IP L YD VY
Sbjct: 130 IKTRIGYDDTEDYENLHRFISTLKSTGVKTFIIHARKAILGKFTPKQNLNIPPLKYDFVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P+  I +NGG+    Q    L  VDGVMIGRAAY    +L  ++    N    +
Sbjct: 190 RLKKDFPNEEIIINGGITTTDQMKDHLDKVDGVMIGRAAYHTPYLLADIERDIFN----N 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             + +R D      +   +  Y    +  G +L QI RH +GLFHG
Sbjct: 246 ENVPSRQD------VIEQLLPYVREEIKKGTRLNQIMRHTLGLFHG 285


>gi|260583380|ref|ZP_05851150.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae NT127]
 gi|260093566|gb|EEW77484.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae NT127]
          Length = 327

 Score =  265 bits (676), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYTRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVRSMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|167836742|ref|ZP_02463625.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis MSMB43]
          Length = 339

 Score =  265 bits (676), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 135/298 (45%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHAAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDSVDDYAFVRDFVGTVAAAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPQLEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGVDARFYG---AT 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EAVEAKLVEYCATELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|254427220|ref|ZP_05040927.1| TIM-barrel protein, yjbN family [Alcanivorax sp. DG881]
 gi|196193389|gb|EDX88348.1| TIM-barrel protein, yjbN family [Alcanivorax sp. DG881]
          Length = 350

 Score =  265 bits (676), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 139/315 (44%), Positives = 184/315 (58%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRF ARL+T + LLYTEM+VA AIL GD+   L F+ +E P+ALQ+GG+D  
Sbjct: 41  MMDWTTRDYRFLARLITRHTLLYTEMVVAQAILHGDRDRFLSFNNEEHPVALQLGGSDPQ 100

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EA++I  D+GY+EINLNVGCPS RV +G  GA LM  P++V  C+ AM  A+ +PVT
Sbjct: 101 QLAEASRIAGDYGYDEINLNVGCPSDRVQQGKIGAILMAEPELVARCVEAMQAAVRVPVT 160

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V  ++ +G   + IHARKAIL GLSPK+NR IP L Y   Y
Sbjct: 161 VKTRIGIDDQDDYDFLYRFVGRMEAAGCTSLTIHARKAILSGLSPKENRDIPPLIYQRAY 220

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK+  P + I LNGG++ + Q  + +  VDGVMIGR AY+N   L   D          
Sbjct: 221 AIKQAFPHIEIILNGGVKTLDQVHEHMGEVDGVMIGREAYQNPYFLAEADRVV---FGDD 277

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R+       I+     Y  R    G   +   RH++ LF G P +RR R  L+  
Sbjct: 278 HAIPSRL------AIAEQFLPYVERRYALGHAPKHSLRHILNLFQGQPGARRFRRHLSEN 331

Query: 301 AGASTATHHIIETAF 315
                 T  ++  A 
Sbjct: 332 MHKPETTPQVLMDAL 346


>gi|320539402|ref|ZP_08039071.1| putative tRNA-dihydrouridine synthase A [Serratia symbiotica str.
           Tucson]
 gi|320030527|gb|EFW12537.1| putative tRNA-dihydrouridine synthase A [Serratia symbiotica str.
           Tucson]
          Length = 342

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 144/318 (45%), Positives = 195/318 (61%), Gaps = 13/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G K + L  + +E P+ALQ+G +D +
Sbjct: 33  MLDWTDRHCRYFHRLLTKETLLYTEMVTTGAIIHG-KGDYLAHNKEEHPVALQLGASDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V D I AM   +SIPVT
Sbjct: 92  ALAHCAKLAEQRGYDEINLNVGCPSGRVQNGMFGACLMAQAALVADGIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ +HARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFISTVAGRGECAMFTLHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD    N L G
Sbjct: 212 YQLKRDFPALTIAINGGVKTLEEAQQHLQHLDGVMMGREAYQNPGILARVD----NELFG 267

Query: 240 -SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
               +K  V       I  S+  Y  R L +G  L  ITRH++GLF G P +R+ R  L+
Sbjct: 268 VQGAVKDSV------AIIESLYPYIERELSNGTYLGHITRHILGLFQGVPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++E A +
Sbjct: 322 ENAHKPGADVQVVEQALD 339


>gi|291568895|dbj|BAI91167.1| hypothetical protein [Arthrospira platensis NIES-39]
          Length = 337

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +L FS  EKPLALQ+GG D  
Sbjct: 28  MMDRTDRHFRYFMRQITRRPLLYTEMVTSAAIINGDRHKLLDFSPVEKPLALQVGGDDPE 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+EINLNVGCPSARV  G+FGACLM  P+ V + I+AM KA++IPVT
Sbjct: 88  QLATCAKIAEDWGYDEINLNVGCPSARVQNGNFGACLMAEPERVAEAISAMKKAVNIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     +   V+ +  SG     +HARKA L+GLSPKDNR IP L Y  V+
Sbjct: 148 VKHRIGIDNRDRYEDMTAFVRVVAASGCQRFTVHARKAWLQGLSPKDNRNIPPLRYGDVH 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K E P L I +NGG   + Q  + L  VD VM+GRAAY N  +    D E + + +  
Sbjct: 208 RLKAEFPHLTIEINGGFTTLEQVKQQLKKVDAVMMGRAAYDNPYLFAIADREIYGDNI-- 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P +         ++   M  Y    L  GG+L  + RH++ LF G P ++  +  L+ 
Sbjct: 266 NPPTR--------HQVVEQMLPYIENWLSQGGRLNSVVRHILQLFAGQPGTKAWKRHLSE 317

Query: 300 EAGASTATHHIIETAF 315
            A    A   +++ A 
Sbjct: 318 NAHLPGAGVEVVKAAL 333


>gi|145642466|ref|ZP_01798016.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
 gi|145272834|gb|EDK12730.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 22.4-21]
          Length = 327

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|119476488|ref|ZP_01616839.1| Dihydrouridine synthase TIM-barrel protein yjbN [marine gamma
           proteobacterium HTCC2143]
 gi|119450352|gb|EAW31587.1| Dihydrouridine synthase TIM-barrel protein yjbN [marine gamma
           proteobacterium HTCC2143]
          Length = 341

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 137/321 (42%), Positives = 192/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ W+DRH R F R LT +A++YTEM+   AIL       L ++T E PLALQ+GG++  
Sbjct: 13  MMAWSDRHCRMFWRQLTQHAVMYTEMVTTGAILHAGADRFLTYNTGEHPLALQLGGSNPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    KI  DFGY+E+NLN GCPS RV  G FGACLM +P  V DCI+AM  A S+P+T
Sbjct: 73  DLASCTKIAADFGYDEVNLNCGCPSDRVQNGMFGACLMAHPQRVADCISAMQDASSLPIT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +   VK I  +G +   +HARKA L+GLSPK NR IP L YD+V+
Sbjct: 133 VKHRIGIDEMESYDEMLEFVKPIADTGCSTFIVHARKAWLQGLSPKQNRDIPPLHYDMVH 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG+  +   +  L  VDGVM+GRAAY+N  +L  VD    N     
Sbjct: 193 QLKQDFPSLNVIINGGITSIEHCVSHLQLVDGVMLGRAAYQNPYLLAEVDSLIYN---AP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + IKTR       ++      Y    L +   L  +TRH++GLF G P ++  R  ++ +
Sbjct: 250 TVIKTR------DQVLLDYIPYIEEQLQNNVALNHMTRHILGLFQGIPGAKLFRRHISEQ 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  S A  +++  A  LM+E+
Sbjct: 304 AHRSDAGINVVYQARELMLEA 324


>gi|148826732|ref|YP_001291485.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae PittEE]
 gi|229847414|ref|ZP_04467514.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 7P49H1]
 gi|148716892|gb|ABQ99102.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae PittEE]
 gi|229809652|gb|EEP45378.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 7P49H1]
 gi|309751771|gb|ADO81755.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R2866]
          Length = 327

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLS K+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSAKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L+ G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVQSMLPYIEQQLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IETA + +
Sbjct: 308 AFKQGAGVEVIETALSFV 325


>gi|68249213|ref|YP_248325.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 86-028NP]
 gi|68057412|gb|AAX87665.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 86-028NP]
          Length = 327

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + I T        +   SM  Y  + L+ G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 AAIVTA------HEAVQSMLPYIEQQLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IETA + +
Sbjct: 308 AFKQGAGVEVIETALSFV 325


>gi|145638041|ref|ZP_01793669.1| hypothetical protein CGSHiHH_03013 [Haemophilus influenzae PittHH]
 gi|145268759|gb|EDK08734.1| hypothetical protein CGSHiHH_03013 [Haemophilus influenzae PittHH]
          Length = 327

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGVEVVETALSFV 325


>gi|167586199|ref|ZP_02378587.1| tRNA-dihydrouridine synthase A [Burkholderia ubonensis Bu]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRHTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEEYAFVRDFVGTVAEAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGA-NDA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +   ++         + +Y A  L  G  L  + RH +GL+ G   +R  R +L+
Sbjct: 256 APTREEAEE--------RLIEYCAAELKRGTYLGAVVRHALGLYRGVAGARGWRRVLS 305


>gi|83592956|ref|YP_426708.1| tRNA-dihydrouridine synthase A [Rhodospirillum rubrum ATCC 11170]
 gi|83575870|gb|ABC22421.1| Dihydrouridine synthase TIM-barrel protein yjbN [Rhodospirillum
           rubrum ATCC 11170]
          Length = 349

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 140/309 (45%), Positives = 190/309 (61%), Gaps = 17/309 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R +T   LLYTEMI A A+L  D    L     E PLALQ+GG+D  
Sbjct: 26  MMDWTDRHDRWFLRQITKRTLLYTEMITAQALLHADPGRFLDHHPDEHPLALQLGGSDPR 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EA ++   FG+ EINLNVGCPS RV  G FGACLM +P +V +C++AM +A + PVT
Sbjct: 86  ALAEATRLAAPFGFAEINLNVGCPSDRVSSGRFGACLMADPALVAECLSAMAEASNAPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD      L   V  + +SG+  I +HARKA LKGLSPK+NR+IP L +D+V+
Sbjct: 146 IKHRIGIDDLDSYDQLVGFVDQVARSGIATIIVHARKAWLKGLSPKENREIPPLRHDVVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-------PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            +K + P L + LNGG+  ++QAL  L       P+VDGVMIGRAAY+   ML   D   
Sbjct: 206 RLKADFPGLEVILNGGITTLTQALDHLGSGDPAAPAVDGVMIGRAAYETPYMLAQADGLI 265

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P  +R       +++ ++  Y       G  ++++TRH++GLFHG P +R  
Sbjct: 266 ---FGEATPAPSR------HEVALALLPYLDAMTARGEPVKRLTRHILGLFHGQPGARAY 316

Query: 294 RHILTVEAG 302
           R  L  EAG
Sbjct: 317 RRHLG-EAG 324


>gi|298290876|ref|YP_003692815.1| TIM-barrel protein, yjbN family [Starkeya novella DSM 506]
 gi|296927387|gb|ADH88196.1| TIM-barrel protein, yjbN family [Starkeya novella DSM 506]
          Length = 337

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 205/316 (64%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L+  A LYTEM+ A+A++ GD++ ++GFS  E P+A+Q+GG+D +
Sbjct: 14  MMEWTDRNCRAFHRVLSRRARLYTEMVTANAVIFGDRERLIGFSDAEHPVAVQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I  D+GY E+NLNVGCPS RV  G+FGACLM +P +V DC+AAM   +SIPVT
Sbjct: 74  ALAKAAAICADWGYAEVNLNVGCPSDRVQGGNFGACLMRSPALVADCVAAMKAEVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L  ++  +G + + +HARKA L+GLSPK+NR IP LDY  V+
Sbjct: 134 VKCRIGVDEQDPEAALDALADAVLAAGADALIVHARKAWLEGLSPKENRDIPPLDYGRVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  + +A   L  VDGVM+GRAAY    +L  VD  F      +
Sbjct: 194 RLKQRLPHVPISINGGIASLEEAQAQLAHVDGVMLGRAAYHQPELLLRVDSLF---FGEA 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P      +D +  + A     AA HL +GG+L  ITRHM+GLF G P +R  R  L ++
Sbjct: 251 DP-----HEDAFAAVEAFEPHIAA-HLATGGRLHDITRHMLGLFTGRPGARAFRRRLAID 304

Query: 301 AGASTATHHIIETAFN 316
              + A   ++  A +
Sbjct: 305 GVKADAGLDVLRAAVD 320


>gi|284051988|ref|ZP_06382198.1| tRNA-dihydrouridine synthase A [Arthrospira platensis str. Paraca]
          Length = 331

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 139/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +L FS  EKPLALQ+GG D  
Sbjct: 22  MMDRTDRHFRYFMRQITRRPLLYTEMVTSAAIINGDRHKLLDFSPVEKPLALQVGGDDPE 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+EINLNVGCPSARV  G+FGACLM  P+ V + I+AM KA++IPVT
Sbjct: 82  QLATCAKIAEDWGYDEINLNVGCPSARVQNGNFGACLMAEPERVAEAISAMKKAVNIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     +   V+ +  SG     +HARKA L+GLSPKDNR IP L Y  V+
Sbjct: 142 VKHRIGIDNRDRYEDMTAFVRVVAASGCQRFTVHARKAWLQGLSPKDNRNIPPLRYGDVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K E P L I +NGG   + Q  + L  VD VM+GRAAY N  +    D E + + +  
Sbjct: 202 RLKAEFPHLTIEINGGFTTLEQVKQQLKKVDAVMMGRAAYDNPYLFAIADREIYGDNI-- 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P +         ++   M  Y    L  GG+L  + RH++ LF G P ++  +  L+ 
Sbjct: 260 NPPTR--------HQVVEQMLPYIENWLSQGGRLNSVVRHILQLFAGQPGTKAWKRHLSE 311

Query: 300 EAGASTATHHIIETAF 315
            A    A   +++ A 
Sbjct: 312 NAHLPGAGVEVVKAAL 327


>gi|229845624|ref|ZP_04465749.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 6P18H1]
 gi|229811424|gb|EEP47128.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 6P18H1]
          Length = 327

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 137/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APVVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|167919102|ref|ZP_02506193.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei BCC215]
          Length = 339

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EQVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|307545712|ref|YP_003898191.1| tRNA-dihydrouridine synthase A [Halomonas elongata DSM 2581]
 gi|307217736|emb|CBV43006.1| tRNA-dihydrouridine synthase A [Halomonas elongata DSM 2581]
          Length = 336

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 143/322 (44%), Positives = 194/322 (60%), Gaps = 12/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADI 59
           M+DWT R YR FAR LT +ALLYTEM+   AIL G  ++  LG+   E PLALQ+GG+D 
Sbjct: 18  MMDWTTRDYRAFARTLTRHALLYTEMVTTGAILYGSPRERFLGYDAIEHPLALQLGGSDA 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L E A I E +GY+E+NLNVGCPS RV     GACLM  PD V   + AM  A+SIPV
Sbjct: 78  GELAECAAIAEAWGYDEVNLNVGCPSDRVQNNLIGACLMAYPDKVAAAVKAMQAAVSIPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIG+DDQ     L + ++ +  +G +   +HARKA L+GLSPK NR +P L+Y  +
Sbjct: 138 TVKCRIGIDDQDEDADLAHFIQRVADAGCSTFIVHARKAWLEGLSPKQNRDVPPLNYPRI 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           + +K ++P+L IGLNGGL+ +      L  VD VM+GR AY+N  +L +VD   +  P  
Sbjct: 198 HRLKAQHPELHIGLNGGLKTLENCQAQLAHVDSVMVGREAYQNPWLLASVDSRLYGEP-- 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P + R         + ++  Y A+ L  G +L  +TRH++GLF G P  RR R  L+
Sbjct: 256 --DPAEDR------HSAARALRPYIAQRLEEGARLNHLTRHLLGLFQGCPGGRRFRRHLS 307

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   + + A  L+ E
Sbjct: 308 ENAHRDGAGLAVFDDALGLVAE 329


>gi|53719465|ref|YP_108451.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei K96243]
 gi|126438522|ref|YP_001058864.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 668]
 gi|126452196|ref|YP_001066108.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106a]
 gi|167719732|ref|ZP_02402968.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei DM98]
 gi|167738727|ref|ZP_02411501.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 14]
 gi|167815950|ref|ZP_02447630.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 91]
 gi|167911080|ref|ZP_02498171.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 112]
 gi|52209879|emb|CAH35851.1| conserved hypothetical protein [Burkholderia pseudomallei K96243]
 gi|126218015|gb|ABN81521.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 668]
 gi|126225838|gb|ABN89378.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106a]
          Length = 339

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|254524233|ref|ZP_05136288.1| tRNA-dihydrouridine synthase A [Stenotrophomonas sp. SKA14]
 gi|219721824|gb|EED40349.1| tRNA-dihydrouridine synthase A [Stenotrophomonas sp. SKA14]
          Length = 334

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 139/315 (44%), Positives = 192/315 (60%), Gaps = 11/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L   A LYTEM+ A+A++ GD++ +LGF   E+PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRVLAPGARLYTEMVHANAVIHGDRERLLGFDRSEQPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM  A+ IPVT
Sbjct: 79  LLAQAARIAAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPVLVAECVAAMVDAVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD+          V     +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDEDNDYDVFAAFVDRQVAAGAAMVVVHARNAWLKGLSPKENREVPPLKYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGGL  +         VDGVM+GRAAY +  +L  ++      L   
Sbjct: 199 RLKQERPALPVVLNGGLASLEAVQAQAAHVDGVMLGRAAYHDPYLLHQLET-----LHTG 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++ R D      +  ++  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 254 APLQARGD------LLRALRPYVEARLGEGLALKHITRHLLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAF 315
           A    A   ++E A 
Sbjct: 308 AHRPGADWSLVEQAL 322


>gi|237812120|ref|YP_002896571.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei MSHR346]
 gi|237505677|gb|ACQ97995.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei MSHR346]
          Length = 439

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 405


>gi|16272577|ref|NP_438794.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae Rd KW20]
 gi|260581551|ref|ZP_05849356.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae RdAW]
 gi|1176344|sp|P44794|DUSA_HAEIN RecName: Full=tRNA-dihydrouridine synthase A
 gi|1573630|gb|AAC22293.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260091796|gb|EEW75754.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae RdAW]
          Length = 327

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|294084658|ref|YP_003551416.1| tRNA-dihydrouridine synthase A [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292664231|gb|ADE39332.1| tRNA-dihydrouridine synthase A [Candidatus Puniceispirillum marinum
           IMCC1322]
          Length = 337

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 140/309 (45%), Positives = 192/309 (62%), Gaps = 14/309 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+  +ALL+TEM+ ADAI+ GD + +LG    E PLALQ+GG+D  
Sbjct: 18  MMDWTDRHCRFFLRLVAPDALLFTEMVTADAIIHGDCERLLGHDLAEHPLALQLGGSDPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSI 117
           KL +A++I  D+G+ EINLNVGCPS RV  G FGACLM  P +V +C +AM     A  +
Sbjct: 78  KLAKASRIAMDYGFAEINLNVGCPSDRVQSGRFGACLMAEPALVAECCSAMASVTTAFDV 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VKCRIG+DD      L     ++  +GV  +++HARKA LKGLSPK+NR IP LDY 
Sbjct: 138 PVSVKCRIGIDDMDSETGLDAFTHAVADAGVTLLYVHARKAWLKGLSPKENRDIPPLDYA 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            V  +    P + I +NGG+  +  A ++ P   G+M+GRAAYK   +L  +    +  L
Sbjct: 198 RVKRLVGAFPAIDIHINGGIVALDTARELAPDFAGMMLGRAAYKTPMILPQI----AYEL 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            G+ P  +R D      I+ASM DYA     +   L  ITRHM+GL++G   ++  R  L
Sbjct: 254 YGTKP-PSRAD------IAASMADYADIKTAADVPLHAITRHMLGLYNGQRGAKLWRRSL 306

Query: 298 TVEAGASTA 306
             +A + +A
Sbjct: 307 GEDARSRSA 315


>gi|242317073|ref|ZP_04816089.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106b]
 gi|242140312|gb|EES26714.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106b]
          Length = 439

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 405


>gi|53723486|ref|YP_102906.1| tRNA-dihydrouridine synthase A [Burkholderia mallei ATCC 23344]
 gi|124383650|ref|YP_001026373.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10229]
 gi|126449152|ref|YP_001080353.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10247]
 gi|167894436|ref|ZP_02481838.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 7894]
 gi|254199845|ref|ZP_04906211.1| tRNA-dihydrouridine synthase A [Burkholderia mallei FMH]
 gi|254206173|ref|ZP_04912525.1| tRNA-dihydrouridine synthase A [Burkholderia mallei JHU]
 gi|254358573|ref|ZP_04974846.1| tRNA-dihydrouridine synthase A [Burkholderia mallei 2002721280]
 gi|52426909|gb|AAU47502.1| dihydrouridine synthase [Burkholderia mallei ATCC 23344]
 gi|124291670|gb|ABN00939.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10229]
 gi|126242022|gb|ABO05115.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10247]
 gi|147749441|gb|EDK56515.1| tRNA-dihydrouridine synthase A [Burkholderia mallei FMH]
 gi|147753616|gb|EDK60681.1| tRNA-dihydrouridine synthase A [Burkholderia mallei JHU]
 gi|148027700|gb|EDK85721.1| tRNA-dihydrouridine synthase A [Burkholderia mallei 2002721280]
          Length = 339

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|254258242|ref|ZP_04949296.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1710a]
 gi|254216931|gb|EET06315.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1710a]
          Length = 339

 Score =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|167902837|ref|ZP_02490042.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei NCTC
           13177]
          Length = 339

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVATAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|121600739|ref|YP_993040.1| tRNA-dihydrouridine synthase A [Burkholderia mallei SAVP1]
 gi|251768090|ref|ZP_04820399.1| tRNA-dihydrouridine synthase A [Burkholderia mallei PRL-20]
 gi|121229549|gb|ABM52067.1| tRNA-dihydrouridine synthase A [Burkholderia mallei SAVP1]
 gi|243060848|gb|EES43034.1| tRNA-dihydrouridine synthase A [Burkholderia mallei PRL-20]
          Length = 436

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 114 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 173

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 174 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 233

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 234 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 293

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 294 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 350

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 351 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 402


>gi|76809017|ref|YP_333391.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1710b]
 gi|76578470|gb|ABA47945.1| dihydrouridine synthase [Burkholderia pseudomallei 1710b]
          Length = 442

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 120 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 179

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 180 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 239

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 240 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 299

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 300 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 356

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 357 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 408


>gi|134282264|ref|ZP_01768969.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 305]
 gi|134246302|gb|EBA46391.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 305]
          Length = 379

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 57  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 116

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 117 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 176

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 177 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 236

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 237 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 293

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 294 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 345


>gi|254415230|ref|ZP_05028992.1| TIM-barrel protein, yjbN family [Microcoleus chthonoplastes PCC
           7420]
 gi|196178036|gb|EDX73038.1| TIM-barrel protein, yjbN family [Microcoleus chthonoplastes PCC
           7420]
          Length = 338

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 136/299 (45%), Positives = 185/299 (61%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +LGFS +EKPL LQ+GG +  
Sbjct: 26  MMDRTDRHFRYFMRQITRRTLLYTEMVTSAAIIHGDRDRLLGFSAEEKPLVLQVGGDNPL 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A+I E  GY++INLNVGCPS RV  G+FGACLM  P+ V   + AM KA++IPVT
Sbjct: 86  ELAECARIAEGMGYDQINLNVGCPSDRVQNGNFGACLMAQPERVARGVEAMIKAVTIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      + N V+ + ++G     +HARKA L+GLSPK+NR +P L Y  V+
Sbjct: 146 VKHRIGIDECDRYEDMANFVRIVSEAGCQHFSVHARKAWLQGLSPKENRTVPPLRYSDVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+E P LFI +NGG   + Q  + L  VD VMIGRAAY N  +    D + F      
Sbjct: 206 RLKQEFPQLFIEINGGFTSLEQVQEQLKFVDAVMIGRAAYDNPYLFAQADCQIFEEECI- 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             P +         +++  M DY    +  G KL +ITRH++ LF G P SR  +  LT
Sbjct: 265 -PPTR--------HQVAEGMLDYIDHWVAKGLKLNKITRHILQLFSGQPGSRAWKRHLT 314


>gi|254179915|ref|ZP_04886514.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1655]
 gi|184210455|gb|EDU07498.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1655]
          Length = 339

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRYVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|90581341|ref|ZP_01237137.1| putative NifR3/Smm1 family protein [Vibrio angustum S14]
 gi|90437451|gb|EAS62646.1| putative NifR3/Smm1 family protein [Vibrio angustum S14]
          Length = 346

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 136/318 (42%), Positives = 198/318 (62%), Gaps = 13/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++  ALLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRLMSKEALLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPI 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   ++V  C+ AM   + IPVT
Sbjct: 91  DLARCAKLAQERGYDEINLNVGCPSDRVQNGMFGACLMGEAELVAQCVTAMRDVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L++ +  + +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDDQDSYEFLKDFIHVVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++   +  + L  +DGVM+GR AY++  ++  VD+     L G
Sbjct: 211 YQLKQDFAHLTMAINGGIKTFEEMEEHLKHMDGVMVGREAYQSPYLMAEVDQR----LFG 266

Query: 240 SS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  P+  R      R++  +M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++
Sbjct: 267 SERPVMKR------REVVEAMYPYIEKQLANGSYLGHITRHMLGLFQSMPGARQWRRHIS 320

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   +++ A +
Sbjct: 321 ENAHKPGAGIEVVQQALD 338


>gi|126640633|ref|YP_001083617.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 17978]
          Length = 318

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 138/317 (43%), Positives = 190/317 (59%), Gaps = 15/317 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG+   +
Sbjct: 1   MDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSTPQE 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVTV
Sbjct: 61  LATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY 
Sbjct: 121 KHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      +
Sbjct: 181 LKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LEA 236

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P   R D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+   
Sbjct: 237 P--DRFD------IMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS--- 285

Query: 302 GASTATHHIIETAFNLM 318
           G +  T   +E A + M
Sbjct: 286 GGNAKTLTDVENAIHNM 302


>gi|84499208|ref|ZP_00997496.1| tRNA-dihydrouridine synthase A [Oceanicola batsensis HTCC2597]
 gi|84392352|gb|EAQ04563.1| tRNA-dihydrouridine synthase A [Oceanicola batsensis HTCC2597]
          Length = 314

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 146/323 (45%), Positives = 201/323 (62%), Gaps = 12/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ +ALLYTEM+ A A++RG   ++L FS +E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSRHALLYTEMVTAPALVRGGAVHLLDFSPREHPVALQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++ +  GY+EINLN GCPS RV  G FGA LM +P  V DC+AAM +A+ + VT
Sbjct: 61  ELAAAARLGQAAGYDEINLNCGCPSDRVQSGVFGAVLMRDPGRVADCVAAMREAVEVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  +  +G     IHARKA L+GLSPK+NR IP LDYD+V 
Sbjct: 121 VKCRIGVDDQNPEEVLPEFLSRVGAAGCGRFIIHARKAWLQGLSPKENRDIPPLDYDLVQ 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            ++     L + +NGG+  + QA + L + +DGVM+GRAAY + A ML   D        
Sbjct: 181 RMRGMFSGLHLSVNGGIVSLDQAERFLEAGLDGVMVGRAAYHDPASMLAQADRR------ 234

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
               I    +      ++ +M  Y   HL +GGKL Q+TRHM+GLF G P +R  R IL+
Sbjct: 235 ----IFGAGEDADAVAVARAMLPYIEAHLAAGGKLGQVTRHMLGLFAGRPGARHWRRILS 290

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++E A   ++++
Sbjct: 291 EGAHRPGAGPELVEQALEPVLQA 313


>gi|197286568|ref|YP_002152440.1| tRNA-dihydrouridine synthase A [Proteus mirabilis HI4320]
 gi|194684055|emb|CAR45390.1| tRNA-dihydrouridine synthase A [Proteus mirabilis HI4320]
          Length = 344

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 137/322 (42%), Positives = 197/322 (61%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT N LLYTEM+   AI+ G K + L +S +E P++LQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFFRQLTKNTLLYTEMVTTGAIIHG-KGDYLKYSNEEHPISLQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   + IPVT
Sbjct: 92  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ + +  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDNQDSYQFLCDFIDTVSRDNNCDTFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLT 238
           Y++K++   L + +NGG++ + +A + L  +DGVM+GR AY+N ++L  VD   F N L 
Sbjct: 212 YQLKRDFSHLTMAINGGIKSLEEAQEHLKYMDGVMVGREAYQNPSILAHVDHVLFDNQLP 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++ +              +M  Y  + L  G  L  ITRHM+G+F G P +R+ R  L+
Sbjct: 272 VANAVAA----------VKAMYPYIEKELSQGTYLGHITRHMLGIFQGIPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A   + E
Sbjct: 322 ENAHKQGADLTVLENALKFVTE 343


>gi|238563470|ref|ZP_00438839.2| tRNA-dihydrouridine synthase A [Burkholderia mallei GB8 horse 4]
 gi|238520653|gb|EEP84111.1| tRNA-dihydrouridine synthase A [Burkholderia mallei GB8 horse 4]
          Length = 439

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 405


>gi|254197994|ref|ZP_04904416.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei S13]
 gi|169654735|gb|EDS87428.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei S13]
          Length = 377

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 55  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 114

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 115 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 174

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 175 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 234

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 235 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 291

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 292 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 343


>gi|170720872|ref|YP_001748560.1| tRNA-dihydrouridine synthase A [Pseudomonas putida W619]
 gi|169758875|gb|ACA72191.1| TIM-barrel protein, yjbN family [Pseudomonas putida W619]
          Length = 321

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 130/300 (43%), Positives = 185/300 (61%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ + LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 10  MMDWTDRHCRFFLRLLSRHTLLYTEMVTTGALLHNDAHRFLRHDVSEHPLALQLGGSVPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 70  DLAACARLAEQAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 130 VKHRIGINGRDSYAELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + ++   L + DGVM+GR AY N  +L  VD+        +
Sbjct: 190 QLKADFPDLEIVLNGGIKTLEESKAHLETFDGVMLGREAYHNPYVLAEVDQVL---FGSN 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 247 APVVSRSEA------MAKLRPYIVAHIESGGAMHHVTRHILGLGQGFKGARRFRQLLSAD 300


>gi|15806701|ref|NP_295421.1| tRNA-dihydrouridine synthase A [Deinococcus radiodurans R1]
 gi|6459466|gb|AAF11254.1|AE002011_5 conserved hypothetical protein [Deinococcus radiodurans R1]
          Length = 333

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 135/316 (42%), Positives = 186/316 (58%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT   LLYTEM+   AIL GD+   L FS  E PLALQ+GG+D +
Sbjct: 16  MMDWTDRHCRMFHRTLTRRTLLYTEMVTTGAILHGDQGRHLDFSAPEHPLALQLGGSDAA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A++ ED+GY+E+NLN GCPS RV  GSFGACLM  PD+V   + AM  A  +PVT
Sbjct: 76  ALAECARLAEDWGYDEVNLNCGCPSDRVSSGSFGACLMGTPDVVARAVEAMRAATRLPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+++  +G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 136 VKHRIGIDDLDSYEHLTGFVRTVAAAGCEQFIVHARKAWLSGLSPKENREIPPLRYEVVQ 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K + P L + LNGG++ +++A + L   DGVMIGRAAY+   +L   D + F      
Sbjct: 196 QLKADFPQLTVVLNGGVKSLTEAQQALAWADGVMIGRAAYQEPYLLAAADRDVFGEDAQA 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S           R+   +   Y A  + +G  L ++ +H +GLF G P +R  +  L+ 
Sbjct: 256 VSR----------REAIEAYLPYVAAQVEAGQPLNRMMKHTLGLFAGQPGARHWKRTLSE 305

Query: 300 EAGASTATHHIIETAF 315
           +     A   ++  A 
Sbjct: 306 QGHKPGAGLDVVRAAL 321


>gi|217423368|ref|ZP_03454869.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 576]
 gi|217393226|gb|EEC33247.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 576]
          Length = 439

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 405


>gi|226196332|ref|ZP_03791914.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei Pakistan
           9]
 gi|254297746|ref|ZP_04965199.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 406e]
 gi|157807557|gb|EDO84727.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 406e]
 gi|225931549|gb|EEH27554.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei Pakistan
           9]
          Length = 323

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 181 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 238 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 289


>gi|167582008|ref|ZP_02374882.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis TXDOH]
          Length = 339

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  +A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  ELAHSARLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAIEDYAFVRDFVGTVASAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPQLEIVINGGITTLDEVEQHLRHVDGVMLGREAYHNPYVLAGVDARFYG---AT 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 EPAPTR------EAVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVTGARGWRRVLS 305


>gi|291615814|ref|YP_003518556.1| DusA [Pantoea ananatis LMG 20103]
 gi|291150844|gb|ADD75428.1| DusA [Pantoea ananatis LMG 20103]
          Length = 331

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 142/324 (43%), Positives = 195/324 (60%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G K + L +S QE P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTADTLLYTEMVTTGAIIHG-KGDYLAYSEQEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+E+NLNVGCPS RV  G FGACLM    +V D I AM   + IPVT
Sbjct: 74  ALAQCAALAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEAGLVADGIKAMRDVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLTDFIGTVAERGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPQLTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGRDRP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AVDPV----------AVVRAMYPYIEAELSKGTYLGHVTRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 304 ENAHKPGADVRVLEAALALVADKI 327


>gi|73541705|ref|YP_296225.1| tRNA-dihydrouridine synthase A [Ralstonia eutropha JMP134]
 gi|72119118|gb|AAZ61381.1| Dihydrouridine synthase TIM-barrel protein yjbN [Ralstonia eutropha
           JMP134]
          Length = 341

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/317 (42%), Positives = 192/317 (60%), Gaps = 9/317 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++ +
Sbjct: 13  MMDWTDRHCRTFHRQLSRHTWLYTEMVTTGALLHGDVPRHLDFNAAEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++ + +GY E+NLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 73  DLAVAARLGQQWGYAEVNLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMRDAVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 133 VKHRIGIDKVEHYGFVRDFVGTVAQAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+    +    L +VDGVMIGR AY    +L  +D  F       
Sbjct: 193 QLKQDFPQLEILINGGIVSYDEMASHLENVDGVMIGREAYHQPYVLAEMDGRFYG--DAE 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+++R+D      +  +M  Y    +  GG +  +TRHM+GL+ G    R  R +L+  
Sbjct: 251 APVRSRLD------VELAMQRYIGELVERGGYMGAVTRHMLGLYRGVAGGRGWRRVLSDA 304

Query: 301 AGASTA-THHIIETAFN 316
              S A TH  ++  F 
Sbjct: 305 KRMSAARTHANVDALFE 321


>gi|327396079|dbj|BAK13501.1| tRNA-dihydrouridine synthase A DusA [Pantoea ananatis AJ13355]
          Length = 331

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 142/324 (43%), Positives = 195/324 (60%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G K + L +S QE P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTADTLLYTEMVTTGAIIHG-KGDYLAYSEQEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+E+NLNVGCPS RV  G FGACLM    +V D I AM   + IPVT
Sbjct: 74  ALAQCAALAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEAGLVADGIKAMRDVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLTDFIGTVAERGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPQLTIAINGGVKTLGEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGRDRP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AVDPV----------AVVRAMYPYIEAELSKGTYLGHVTRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 304 ENAHKPGADVRVLEAALALVADKI 327


>gi|83721523|ref|YP_443015.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis E264]
 gi|167620175|ref|ZP_02388806.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis Bt4]
 gi|257139245|ref|ZP_05587507.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis E264]
 gi|83655348|gb|ABC39411.1| dihydrouridine synthase [Burkholderia thailandensis E264]
          Length = 339

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  +A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  ELAHSARLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAIEDYAFVRDFVGTVASAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPQLEIVINGGITTLDEVEQHLRHVDGVMLGREAYHNPYVLAGVDARFYG---AT 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 254 EPAPTR------EAVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 305


>gi|239815113|ref|YP_002944023.1| tRNA-dihydrouridine synthase A [Variovorax paradoxus S110]
 gi|239801690|gb|ACS18757.1| TIM-barrel protein, yjbN family [Variovorax paradoxus S110]
          Length = 333

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/316 (42%), Positives = 191/316 (60%), Gaps = 12/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 20  MMDWTDRHCRYFHRLMSRHALLYTEMVTTGALVHGDVPRHLRFNEEEHPVALQLGGSEPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A  +PVT
Sbjct: 80  DLAHCARLGEEWGYDEINLNCGCPSERVQRGAFGACLMAEPALVADCVKAMVDATRLPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++ ++G  G  +HAR A L+GLSPK NR+IP L Y++V+
Sbjct: 140 VKHRIGIDKIESYEFVRDFVGAVSEAGCRGFIVHARNAWLQGLSPKQNREIPPLRYELVH 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L   +NGG+   +Q  + L  +DGVM+GR AY N   L   D  F     G+
Sbjct: 200 RLKHEFPELDFSINGGISASAQVHEHLRLLDGVMVGREAYHNPWWLAEWDAEF----YGA 255

Query: 241 SPIK-TRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P   TR D      + + M DY  R     G +   I RHM+GL +G P +RR R + +
Sbjct: 256 VPQPLTRED------VESLMCDYMVREAAEHGTQWSSIARHMLGLRNGLPGARRWRQVWS 309

Query: 299 VEAGASTATHHIIETA 314
                +   H ++  A
Sbjct: 310 DHRLKTRPPHEVMALA 325


>gi|229589108|ref|YP_002871227.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens SBW25]
 gi|229360974|emb|CAY47834.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens SBW25]
          Length = 336

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 136/300 (45%), Positives = 190/300 (63%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ +ALLYTEM+   AIL GD    L  +  E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKHALLYTEMVTTGAILHGDHDRFLRHNEAEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GA LM +P +V +C+ AM  A+SIPVT
Sbjct: 85  DLAACARMAEAAGYDEVNLNVGCPSDRVQNNMIGAILMAHPALVAECVKAMRDAVSIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++K +G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAQLCDFVGTVKDAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKQDFPELEIVLNGGIKTLEQCHEHLQTFDGVMLGREAYHNPYVLAEVDQQL---FGSE 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +          +  Y A HL SGG +  ITRH++GL  GFP +R+ R +L+V+
Sbjct: 262 APVISRAEA------LVQLRPYIAEHLASGGSMHHITRHILGLGTGFPGARKFRQLLSVD 315


>gi|317493445|ref|ZP_07951866.1| tRNA dihydrouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918388|gb|EFV39726.1| tRNA dihydrouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 337

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 141/323 (43%), Positives = 197/323 (60%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+   LLYTEM+   AI+ G K + L +S +E PLALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRKLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPLALQLGGSDPE 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV  G FGACLM    +V D I AM   +SIPVT
Sbjct: 83  ALAHCARLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + +  +   G  N   +HARKA L GLSPK+NR+IP LDY+ V
Sbjct: 143 VKTRIGIDDQDSYEFLCDFIDIVSGKGECNSFTVHARKAWLSGLSPKENREIPPLDYERV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY++ ++L  VD E F +   
Sbjct: 203 YQLKRDFPHLNIAINGGVKTLEEAKIHLQHLDGVMMGREAYQSPSILAHVDRELFDS--- 259

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++ +   +D      +  S+  Y  R L +G  L  ITRH++GLF   P +R+ R  L+
Sbjct: 260 -TADVPNSID------VVRSLYPYIERELSNGTYLGHITRHILGLFQSIPGARQWRRHLS 312

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++E A   + +S
Sbjct: 313 ENAHKPGAGVEVVEAALQFVSQS 335


>gi|167824321|ref|ZP_02455792.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 9]
          Length = 334

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 181 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 238 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 289


>gi|152978183|ref|YP_001343812.1| tRNA-dihydrouridine synthase A [Actinobacillus succinogenes 130Z]
 gi|150839906|gb|ABR73877.1| TIM-barrel protein, yjbN family [Actinobacillus succinogenes 130Z]
          Length = 326

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 135/318 (42%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+     + L F T E P+ALQ+GG+D  
Sbjct: 17  MLDWTTRHCRYFHRQFSRHALLYTEMVTTQAIVHAGYDH-LAFDTAENPVALQLGGSDPV 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY EINLNVGCPS RV  G FGACLM   D+V +C+  M  A+SIPVT
Sbjct: 76  QLAHCAKLAEERGYREINLNVGCPSDRVQNGMFGACLMAKADLVAECVTKMQAAVSIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + V  I  +G   + +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 136 VKTRIGIDELDSYEFLYDFVHKITNAGCQELIVHARKAWLSGLSPKENREIPPLDYERVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P + I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 196 QLKRDFPHILISINGGIKTIEEMTAHLQQVDGVMVGREAYQNPSLLGYIDQALFDP---T 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + I T       R+   +M  Y  + L+ G  L  I RH++G F G   +R+ R  L+  
Sbjct: 253 ARIVTA------REAVENMFPYIEQQLNRGVYLNHIVRHILGAFQGCKGARQWRRYLSEN 306

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ TA + +
Sbjct: 307 AYKPGADAEVVRTALSFV 324


>gi|325282314|ref|YP_004254855.1| TIM-barrel protein, yjbN family [Deinococcus proteolyticus MRP]
 gi|324314123|gb|ADY25238.1| TIM-barrel protein, yjbN family [Deinococcus proteolyticus MRP]
          Length = 346

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 138/299 (46%), Positives = 188/299 (62%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT+ ALLYTEM+   A+L GD+   L F   E PLALQ+GG+D +
Sbjct: 29  MLDWTDRHCRAFHRCLTSRALLYTEMVTTGAVLHGDRARHLDFGAAEHPLALQLGGSDPA 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A + E +GY+E+NLN GCPS RV  G+FGACLM  PD+V  C+AAM +A  +PVT
Sbjct: 89  ALAECAALAEHWGYDEVNLNCGCPSDRVQSGAFGACLMATPDVVAACVAAMQEATRLPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ   + LR  V+++  +G     +HARKA LKGLSPK+NR+IP L Y++V 
Sbjct: 149 VKHRIGIDDQEDYMDLRRFVETVAGAGCRTFIVHARKAWLKGLSPKENREIPPLRYELVE 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
           ++K E P+L I LNGG++ ++QA + L   DGVM+GRAAY+   +L  VD+  F      
Sbjct: 209 QLKAEFPELTISLNGGVQTLAQAQEHLTWADGVMVGRAAYQTPYLLARVDQDIFGE--DA 266

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S P +        R++ A    Y  + L  G     +T+  +GLF G   +R  +  L+
Sbjct: 267 SPPTR--------REVLARFRPYVVQGLAEGQSFHHLTKSTLGLFAGQHGARHYKRTLS 317


>gi|116329329|ref|YP_799049.1| tRNA-dihydrouridine synthase A [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116330067|ref|YP_799785.1| tRNA-dihydrouridine synthase A [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116122073|gb|ABJ80116.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116123756|gb|ABJ75027.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 339

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 137/300 (45%), Positives = 188/300 (62%), Gaps = 11/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F RL++ +  LYTEMI   AIL GD++  L +S +E PLA+Q+GG +  
Sbjct: 19  MMDRTDRHFRYFLRLISKHTFLYTEMIHTGAILHGDRRRFLSYSPEELPLAIQLGGDNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E++KI ED+GY+EINLNVGCPS RV EG+FGACLM  P+ V + + AM   +SIPVT
Sbjct: 79  ALAESSKIGEDYGYSEINLNVGCPSDRVREGNFGACLMETPERVAELVCAMDGNVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+  +     L   ++ ++++GV    +HAR AIL GLSP  NR+IP L Y  V 
Sbjct: 139 VKCRIGISGKETLEDLCRFIECVRQAGVRRFIVHARIAILGGLSPAQNRQIPPLRYAHVE 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PDL I +NGG+  +++    L + DGVMIGRAAY+   + + VD  F      +
Sbjct: 199 SLKKEFPDLLIEINGGIRTLAEMQDRLKTNDGVMIGRAAYETPYLFSEVDSLF---FHDN 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           SP  +R      R++   M DY    +     GK     RHM+GLFHG   +R  R ++T
Sbjct: 256 SPSLSR------REVLLRMRDYIEEVVLKEKNGKPHHALRHMLGLFHGEKGARSFRRVVT 309


>gi|297565479|ref|YP_003684451.1| TIM-barrel protein, yjbN family [Meiothermus silvanus DSM 9946]
 gi|296849928|gb|ADH62943.1| TIM-barrel protein, yjbN family [Meiothermus silvanus DSM 9946]
          Length = 345

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 136/321 (42%), Positives = 191/321 (59%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+  RL +    LYTEM+   AIL G++  +L F   E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHFRYLVRLCSRGVRLYTEMVTDRAILHGNRPRLLDFDPSEHPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I +D+GY+EINLN+GCPS RV  G FGACLM  PD+V +C AAM +A+ +PVT
Sbjct: 75  LLAEAARIGQDWGYDEINLNLGCPSERVQGGGFGACLMKEPDLVAECFAAMREAVQLPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+GVDD      L   V+ +   GV    +HARKA L+GLSPK+NR+IP L Y  VY
Sbjct: 135 AKHRLGVDDLEDYGYLARFVEKLASVGVEVFIVHARKAWLQGLSPKENREIPELRYGWVY 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L   LNGG++ + +A   L  VDGVM+GRA Y++  +L   D  F       
Sbjct: 195 RLKEDFPHLIFVLNGGVKTLDEAGAHLEHVDGVMLGRAVYEDPFVLEEADRRFFG----- 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             ++ R  +    +++ +M  YA   L  G  L  I RHM+ LF G    +R R  L+  
Sbjct: 250 --LEHRPQR---LQVAQAMIAYAEARLEEGVPLWSIARHMLNLFKGQRGGKRWRRYLSEH 304

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++  A   + ++
Sbjct: 305 AIRPQAKAQVLWEALEQVTKT 325


>gi|226356731|ref|YP_002786471.1| tRNA-dihydrouridine synthase A [Deinococcus deserti VCD115]
 gi|226318721|gb|ACO46717.1| putative tRNA-dihydrouridine synthase A [Deinococcus deserti
           VCD115]
          Length = 346

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 139/317 (43%), Positives = 189/317 (59%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT   LLYTEM+   AIL GD++  LGF+  E P+ALQ+GG+D +
Sbjct: 21  MMDWTDRHCRVFHRTLTRRTLLYTEMVTTGAILHGDRERHLGFNRVEHPVALQLGGSDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E  ++ ED+GY+EINLN GCPS RV  GSFGACLM  PD+V   + AM     +PVT
Sbjct: 81  ALAECTRMAEDYGYDEINLNCGCPSDRVSSGSFGACLMGTPDVVARAVEAMRGVTRLPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V++++ +G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 141 VKHRIGIDDLDSYEHLTRFVRTVEAAGCQTFIVHARKAWLSGLSPKENREIPPLRYEVVE 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K + P L + LNGG+ D+ QA   L   DGVMIGRAAY+   +L   D E F      
Sbjct: 201 QLKADFPHLTVVLNGGVLDLRQAQGALNWADGVMIGRAAYQTPYVLAAADHEIFGE---A 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P+ TR      R+   +   Y A  L +G  L ++ +H +GLF G P +R  +  L+ 
Sbjct: 258 AVPV-TR------REAIEAFLPYVAGQLAAGQPLNRMMKHTLGLFAGQPGARHWKRTLSE 310

Query: 300 EAGASTATHHIIETAFN 316
           +     A   ++  A  
Sbjct: 311 QGHRDGAGLEVVRAALE 327


>gi|152980796|ref|YP_001354180.1| tRNA-dihydrouridine synthase A [Janthinobacterium sp. Marseille]
 gi|151280873|gb|ABR89283.1| tRNA-dihydrouridine synthase [Janthinobacterium sp. Marseille]
          Length = 344

 Score =  263 bits (671), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 136/299 (45%), Positives = 189/299 (63%), Gaps = 3/299 (1%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T +  LYTEM+   A+L GD    L F+ +E P+ALQ+GG++ +
Sbjct: 23  MMDWTDRHCRMFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFNEEEHPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+ E +GY+E+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+SI VT
Sbjct: 83  DLAKSAKLGEQWGYDEVNLNCGCPSERVQKGAFGACLMNETGLVADCVKAMRDAVSIDVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      +R+ V +I  +G N   +HAR AILKGLSPK+NR+IP L Y+  Y
Sbjct: 143 VKHRIGIDDITSYDFVRDFVGTIADAGCNTFIVHARNAILKGLSPKENREIPPLRYEFAY 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++KK+ P L I +NGG + +++    L  VDGVM+GR AY N  +++T D  Y+ +  T 
Sbjct: 203 QLKKDFPALEIIINGGTKTVAEIDTHLQHVDGVMLGREAYHNPFLMSTFDARYYGDDAT- 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S  +  V +     I A +  +       G K+  ITRHM+GL  G PNSR  R  L+
Sbjct: 262 -SKTRAEVVQAMIPYIHAQLQLHGKSEKGGGLKVNSITRHMLGLMAGLPNSRAFRQTLS 319


>gi|89075955|ref|ZP_01162327.1| putative NifR3/Smm1 family protein [Photobacterium sp. SKA34]
 gi|89048304|gb|EAR53883.1| putative NifR3/Smm1 family protein [Photobacterium sp. SKA34]
          Length = 348

 Score =  263 bits (671), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 136/318 (42%), Positives = 197/318 (61%), Gaps = 13/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++  ALLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 34  MLDWTDRHCRYFHRLMSKEALLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNSI 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   ++V  C+ AM   + IPVT
Sbjct: 93  DLARCAKLAQERGYDEINLNVGCPSDRVQNGMFGACLMGEAELVAQCVTAMRDVVDIPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L++ +  + +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 153 VKTRIGIDDQDSYEFLKDFIHVVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 212

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++   +    L  +DGVM+GR AY++  ++  VD+     L G
Sbjct: 213 YQLKQDFAHLTMAINGGIKTFEEMEAHLKHMDGVMVGREAYQSPYLMAEVDQR----LFG 268

Query: 240 SS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  P+  R      R++  +M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++
Sbjct: 269 SERPVMKR------REVVEAMYPYIEKQLANGSYLGHITRHMLGLFQSMPGARQWRRHIS 322

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   +++ A +
Sbjct: 323 ENAHKPGAGIEVVQQALD 340


>gi|52426107|ref|YP_089244.1| tRNA-dihydrouridine synthase A [Mannheimia succiniciproducens
           MBEL55E]
 gi|52308159|gb|AAU38659.1| unknown [Mannheimia succiniciproducens MBEL55E]
          Length = 327

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 139/320 (43%), Positives = 190/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F   E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSRHALLYTEMVTAPAIIHA-KYDHLEFDPAENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY EINLNVGCPS RV  G FGACLM   D+V +C+  M   + IPVT
Sbjct: 77  QLQHCAKLAEQRGYTEINLNVGCPSDRVQNGMFGACLMAKADLVAECVEKMQAEVEIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ +   G N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDNLDSYQFLCDFIQKVHSKGCNEFIVHARKAWLSGLSPKENREIPPLDYNRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY+N A+L  +D         +
Sbjct: 197 QLKRDFPQLSISINGGIKTIEEMTAHLQYVDGVMVGREAYQNPALLGQIDRAL---FDLN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+    M  Y  R L  G  L  I RHM+G F     +R+ R +L+  
Sbjct: 254 APIVTP------REAVEKMFPYIERQLSRGVHLNHIVRHMLGAFQNCKGARQWRRLLSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
           A  + A   I+ETA + + E
Sbjct: 308 AHKTGAGIEILETALHFVEE 327


>gi|254514697|ref|ZP_05126758.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR5-3]
 gi|219676940|gb|EED33305.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR5-3]
          Length = 343

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 133/316 (42%), Positives = 192/316 (60%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW++RH R+F RLL+ +A LYTEM+   A++ GD++  L F+ +E P+ALQ+GG++  
Sbjct: 30  MMDWSNRHCRYFWRLLSQHARLYTEMVTTGALIHGDRQRFLQFNAEETPIALQLGGSNPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A   E +GY+E+NLN GCPS RV  G+FGACLM  P++V D ++AM  A  I VT
Sbjct: 90  DLARCAAWAEAWGYDEVNLNCGCPSDRVQNGAFGACLMAEPELVRDAVSAMRSACEIDVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L + V ++   G +   +HARKA LKGLSPK+NR++P L Y  VY
Sbjct: 150 VKHRIGIDHMESYEELCHFVGTVADGGCSVFIVHARKAWLKGLSPKENREVPPLTYPWVY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+E +      L  VDGVM+GR+AY N  +L  VD          
Sbjct: 210 RLKRDFPALTIVINGGIESIDDCEPHLARVDGVMLGRSAYHNPWVLAEVDRRLFG----- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R  +D    I  ++  Y  + L SG +L QITRH++GL+   P ++R R +L+ +
Sbjct: 265 EPQQPRCRED----IIDALMPYVEKELASGTRLNQITRHILGLYQEVPGAKRYRRLLSEQ 320

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++  A N
Sbjct: 321 AHRPDAGADVLRAAVN 336


>gi|167626460|ref|YP_001676960.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167596461|gb|ABZ86459.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 324

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 131/310 (42%), Positives = 186/310 (60%), Gaps = 13/310 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+HYR+  RL+T   +LYTEMI  +AI+ G+K  +L ++ +E P+ LQ+GG    
Sbjct: 13  MLDWTDKHYRYMMRLITKQTMLYTEMITLNAIIHGNKDFLLKYNPEENPVTLQLGGCVPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ ++ GYNEIN+NVGCPS RV +G+FG  LM  P++V +C+ AM   L IP++
Sbjct: 73  DFITCGKLAQNLGYNEININVGCPSERVKKGNFGLSLMAEPELVANCVKAMKDNLDIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D+      L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDNNDSYEELYNFVNKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  +    + L  VD VMIGR AY N  +    D  F N P+  
Sbjct: 193 NIKKDFPNLELGINGGVTTIEDTQEHLKYVDSVMIGREAYHNPMLFKNFDNLFYNQPIND 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHS--GGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            SP+          +++  M +Y    L+S    KL  IT+H + LF+G  N++  R  L
Sbjct: 253 ISPL----------EVAYEMAEYIKIQLNSDPNMKLNNITKHTLNLFNGLHNAKVFRRYL 302

Query: 298 TVEAGASTAT 307
           +  A    A 
Sbjct: 303 SENATKKDAN 312


>gi|325923106|ref|ZP_08184799.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas gardneri ATCC
           19865]
 gi|325546421|gb|EGD17582.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas gardneri ATCC
           19865]
          Length = 334

 Score =  262 bits (670), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 140/316 (44%), Positives = 198/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG++ +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRTRLIGFDPVEHPLALQLGGSEPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++GY+EINLN GCPS RV  G FGACLM  P +VG+C+AAMC A ++PVT
Sbjct: 79  LLAQAAAIAQEWGYDEINLNCGCPSDRVQAGRFGACLMREPALVGECVAAMCAATTLPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCR+GVDD    +   + V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 IKCRLGVDDDGDYLVFASFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGG+  +  AL+ L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPQLPVVINGGIAAVDTALEHLQHTDGVMLGRAAYHDPYVLHCLDAALNR----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P ++R        +  ++  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQSR------EALLRALQPYVESQLEQGLALKHITRHVLGLFHGKPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A  S A   ++E A  
Sbjct: 308 AHRSGAGWDLVEQALQ 323


>gi|284800241|ref|ZP_05985987.2| tRNA dihydrouridine synthase A [Neisseria subflava NJ9703]
 gi|284795603|gb|EFC50950.1| tRNA dihydrouridine synthase A [Neisseria subflava NJ9703]
          Length = 317

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 188/301 (62%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T NA LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHYRFMARQITRNAWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  A K  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM  A+ IPVT
Sbjct: 61  DLAIATKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDAVEIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR++P L Y+ V
Sbjct: 121 VKHRIGVDRQTEYQVVADFVGTLREKTACRTFIVHARNAWLDGLSPKENREVPPLKYEYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 181 YRLKQDFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDTMFYN--DA 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  ++A +  Y+     L  G  L+ I RH +GL HG  N+R  R +L
Sbjct: 239 HAPIQ-------YADLAAWLYAYSREQIALGRGTILRHIVRHALGLMHGLKNARTWRRML 291

Query: 298 T 298
           +
Sbjct: 292 S 292


>gi|308451158|ref|XP_003088566.1| hypothetical protein CRE_10759 [Caenorhabditis remanei]
 gi|308246538|gb|EFO90490.1| hypothetical protein CRE_10759 [Caenorhabditis remanei]
          Length = 338

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 134/315 (42%), Positives = 188/315 (59%), Gaps = 15/315 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRFFARL   N +LYTEM+   AI+ G     L ++ +E P+ LQ+GG++  
Sbjct: 20  MMDWTTRDYRFFARLFNPNIILYTEMVTTGAIIYGGANRHLDYNHEEHPIVLQLGGSNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +K+ +D+GY+EINLNVGCPS RV     GACLM  PD+V +CIA M  A+ IPVT
Sbjct: 80  DLATCSKMAQDWGYDEINLNVGCPSDRVQNNKIGACLMAEPDLVAECIAEMRNAVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G +   +HAR A+L+GLSPK+NR +P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAKTGCDNFIVHARIALLQGLSPKENRDVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++  L   
Sbjct: 200 RLKQERPELLIEINGGVKTFAETQAHLKHVDGVMIGREAYHNPYLLAELGQLWNLDL--- 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                R D      I   M  Y A+ +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 257 ---PDRFD------IIDQMLPYIAKRMQEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAF 315
            G +  T   +E A 
Sbjct: 306 -GGNAKTFADVENAI 319


>gi|309973873|gb|ADO97074.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R2846]
          Length = 327

 Score =  262 bits (669), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 138/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G+D+      L + ++ ++  G     IHARKA L GLS K+NR+IP LDY  VY
Sbjct: 137 VKTRTGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSAKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L+ G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVQSMLPYIEQQLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IETA + +
Sbjct: 308 AFKQGAGVEVIETALSFV 325


>gi|332304623|ref|YP_004432474.1| TIM-barrel protein, yjbN family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332171952|gb|AEE21206.1| TIM-barrel protein, yjbN family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 345

 Score =  262 bits (669), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/298 (45%), Positives = 183/298 (61%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F R ++ +ALLYTEM+   AI+ G K + L F+  E P+ALQ+GG+D +
Sbjct: 17  MLDWTDKHCRYFLRQISKHALLYTEMVTTGAIIFG-KGDYLAFNEAEHPVALQLGGSDPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A + ++ GY+E+N+NVGCPS RV  G FGACLM  P  V DCI AM K + IPVT
Sbjct: 76  DMARCAVLAQERGYDEVNINVGCPSDRVQNGRFGACLMAEPKTVADCINAMQKEVDIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ I  +G     +HARKA LKGLSPK+NR IP L YD VY
Sbjct: 136 VKSRIGIDDMDEYKDLTDFIQVIADAGCEIFTVHARKAWLKGLSPKENRDIPPLMYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGG++ +  A   L  +DGVMIGR  Y N  +L  VD+ F    T  
Sbjct: 196 ALKEEFPHLNLSINGGVKTLDDAALHLDKLDGVMIGREVYSNPYILADVDKRFYQDQT-- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P+ +R       +I  +M  Y  + + SG +   I RHM+GLF G P  R  R  L+
Sbjct: 254 -PVPSR------EEIVHAMLPYVEKQMASGARAWNIARHMLGLFQGQPGGRVWRRYLS 304


>gi|92113327|ref|YP_573255.1| tRNA-dihydrouridine synthase A [Chromohalobacter salexigens DSM
           3043]
 gi|91796417|gb|ABE58556.1| tRNA-U16,U17-dihydrouridine synthase [Chromohalobacter salexigens
           DSM 3043]
          Length = 346

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 144/318 (45%), Positives = 194/318 (61%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADI 59
           M+DWT R YR FAR LT  ALLYTEM+   AIL G  ++  LG+S  E PLALQ+GG+D 
Sbjct: 29  MMDWTTRDYRAFARTLTREALLYTEMVTTGAILHGSPRERFLGYSDVEHPLALQLGGSDP 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L E A I E +GY+E+NLNVGCPS RV     GACLM  PD V   + AM  A+SIPV
Sbjct: 89  AELAECAAIAEAWGYDEVNLNVGCPSDRVQNNLIGACLMAYPDKVAAAVRAMQAAVSIPV 148

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIG+DDQ     L   + ++  +G +   IHARKA L+GLSPK+NR +P L+Y  V
Sbjct: 149 TVKCRIGIDDQDEDADLARFIGTVADAGADTFIIHARKAWLEGLSPKENRDVPPLNYARV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           + +K + P L IG+NGG++ +      L  VD VMIGR AY+N  +L  VD   +  P  
Sbjct: 209 HRLKTQYPALHIGINGGIKSLEDCQAHLEHVDSVMIGREAYQNPWLLAGVDAALYGTP-- 266

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             SP+ +R      ++ + ++  Y A  L +G KL  +TRH++GLF G P  R+ R  L+
Sbjct: 267 --SPVTSR------QEAARALRPYIAERLAAGAKLNHVTRHLLGLFQGCPGGRQFRRHLS 318

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   + + A +
Sbjct: 319 ENAHRPGADLAVFDEALS 336


>gi|91783334|ref|YP_558540.1| tRNA-dihydrouridine synthase A [Burkholderia xenovorans LB400]
 gi|91687288|gb|ABE30488.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia xenovorans
           LB400]
          Length = 333

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 135/298 (45%), Positives = 186/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRVISRHTWLYTEMVTTGALLHGDVPRHLAFTPVEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I  +G N   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEEYGFVRDFVGTIADAGCNVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 197 QLKRDFPHLEIIINGGIKTLDEVETHLQHVDGVMLGREAYHNPYLLAGVDARFYG--SAD 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++ A + DY A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 255 TPL-TR------EQVEAKLIDYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 305


>gi|94310927|ref|YP_584137.1| tRNA-dihydrouridine synthase A [Cupriavidus metallidurans CH34]
 gi|93354779|gb|ABF08868.1| tRNA-dihydrouridine synthase A [Cupriavidus metallidurans CH34]
          Length = 351

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 136/298 (45%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L FS  E+P+ALQ+GG++  
Sbjct: 30  MMDWTDRHCRTFHRALSQHTWLYTEMVTTGALLHGDVARHLDFSAAEQPVALQLGGSEPV 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK+ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 90  DLAQAAKLGEQWGYKEINLNCGCPSERVQRGAFGACLMAEPQLVADCVRAMRDVVSVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G +   +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 150 VKHRIGIDTIEHYGFVRDFVGTIAEAGCDIFIVHARNAILKGLSPKENREIPPLRYEVAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+E P L I +NGG+    +  + L  VDGVMIGR AY +   L+ +D  F     G+
Sbjct: 210 ELKREFPHLEILINGGVVSYGEIDEHLRHVDGVMIGRQAYHDPYFLSEMDARFYG---GT 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +PI TR   +       +M  Y    +  GG +   TRHM+GL  G    R  R +L+
Sbjct: 267 APIVTREMAEL------TMQAYIGDLVEKGGYMGAATRHMLGLHRGIYGGRGWRRVLS 318


>gi|238918205|ref|YP_002931719.1| hypothetical protein NT01EI_0241 [Edwardsiella ictaluri 93-146]
 gi|238867773|gb|ACR67484.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 349

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 138/319 (43%), Positives = 190/319 (59%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +  +E PLALQ+GG++ +
Sbjct: 36  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYCEEEHPLALQLGGSNPA 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 95  DLARCARLAETRGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++   G  +   +HARKA L GLSP++NR++P LDY  V
Sbjct: 155 VKTRIGIDEQDSYPFLCDFIGTVAGQGECDTFIVHARKAWLSGLSPRENREVPPLDYPRV 214

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P L I LNGG++ + +A   L  VDGVM+GR AY N  +L  VD   S     
Sbjct: 215 YRLKQDFPHLTIALNGGVKRLDEARAHLQHVDGVMVGREAYHNPGILAQVD---SQLFDA 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + +   V       +  ++  Y  R L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 272 DAAVPDSV------AVVRALYPYIGRELAQGTYLGHITRHILGLFQGIPGARQWRRHLSE 325

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 326 NAHRPGAGIDVVEQALRFV 344


>gi|307244957|ref|ZP_07527054.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307253910|ref|ZP_07535762.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307258364|ref|ZP_07540105.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306854122|gb|EFM86330.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306863114|gb|EFM95056.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306867548|gb|EFM99395.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 325

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYECVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 QPLVTA------REAVEKMLPYIAAQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 304 ATKQGAGVEVVEQALSFVQES 324


>gi|296157694|ref|ZP_06840528.1| TIM-barrel protein, yjbN family [Burkholderia sp. Ch1-1]
 gi|295891940|gb|EFG71724.1| TIM-barrel protein, yjbN family [Burkholderia sp. Ch1-1]
          Length = 317

 Score =  262 bits (669), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 136/298 (45%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRSLHRVISRHTWLYTEMVTTGALLHGDVPRHLAFTPAEAPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I  +G N   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEEYGFVRDFVGTIADAGCNVFIVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N   L  VD  F    +  
Sbjct: 181 QLKRDFPHLEIIINGGIKTLDEVETHLQHVDGVMLGREAYHNPYRLADVDARFYG--STD 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           SP+ TR       ++ A + DY A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 239 SPL-TR------EQVEAKLIDYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 289


>gi|190149417|ref|YP_001967942.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|307262734|ref|ZP_07544361.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|189914548|gb|ACE60800.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|306871879|gb|EFN03596.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 329

 Score =  262 bits (669), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYECVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 197 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 QPLVTA------REAVEKMLPYIAAQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|114320734|ref|YP_742417.1| tRNA-dihydrouridine synthase A [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227128|gb|ABI56927.1| tRNA-U16,U17-dihydrouridine synthase [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 343

 Score =  261 bits (668), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 134/322 (41%), Positives = 186/322 (57%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RLL    LL+TEM+ A A+   D +  L +S  E+PLA+Q GG+D  
Sbjct: 26  MMEWTDRHARYFLRLLAPRTLLFTEMVPALAVWHNDPERFLAYSAAERPLAVQFGGSDPE 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E + Y+E+NLNVGCPS RV  G+FGACLM +P  V DC+AAM ++  +PVT
Sbjct: 86  QLAHCARLAEAWSYDEVNLNVGCPSDRVQAGAFGACLMADPGRVADCVAAMAESTRLPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       L   V  +  +G    ++HARKA L+GLSPK+NR++P LDY  VY
Sbjct: 146 VKHRIGVDHLDSYDHLTGFVDQVAAAGCRTFYVHARKAWLQGLSPKENREVPPLDYGRVY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K++ P L + LNGG+      L+ L   +DG M+GR AY N   L   D         
Sbjct: 206 RLKRDFPALEVILNGGITRTETLLETLDRGLDGAMVGREAYTNPWALAGWDRALFGAAGA 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +    + F          Y    L  G +LQ + RH++GLF+G P  RR R  ++ 
Sbjct: 266 GVPDRHAAVRAF--------LPYVETELAGGARLQHLARHILGLFNGCPGGRRWRRHISE 317

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A  S A   +IE A  L+ E+
Sbjct: 318 QAHRSGAGPEVIEQALALVPEA 339


>gi|330445027|ref|ZP_08308681.1| tRNA-dihydrouridine synthase A [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328493145|dbj|GAA03178.1| tRNA-dihydrouridine synthase A [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 346

 Score =  261 bits (668), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 199/318 (62%), Gaps = 13/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+++  ALLYTEM+   AI+ G K + L ++ +E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRIMSKEALLYTEMVTTGAIIHG-KGDFLAYNEEEHPVALQLGGSNPI 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   ++V  C+ AM   + IPVT
Sbjct: 91  DLARCAKLAQERGYDEINLNVGCPSDRVQNGMFGACLMGEAELVAQCVTAMRDVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L++ +  + +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDDQDSYEFLKDFIHVVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++   +  + L  +DGVM+GR AY++  +++ VD+     L G
Sbjct: 211 YQLKQDFAHLTMAINGGIKTFEEMEEHLKHMDGVMVGREAYQSPYLMSEVDQR----LFG 266

Query: 240 SS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  P+  R      R++  +M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++
Sbjct: 267 SDRPVMKR------REVVEAMYPYIEKQLANGSYLGHITRHMLGLFQNMPGARQWRRHIS 320

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   +++ A +
Sbjct: 321 ENAHKPGAGIEVVQQALD 338


>gi|145629754|ref|ZP_01785549.1| hypothetical protein CGSHi22121_00292 [Haemophilus influenzae
           22.1-21]
 gi|145632012|ref|ZP_01787761.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
 gi|144977993|gb|EDJ87777.1| hypothetical protein CGSHi22121_00292 [Haemophilus influenzae
           22.1-21]
 gi|144982331|gb|EDJ89920.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
          Length = 327

 Score =  261 bits (668), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 136/318 (42%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+   K + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M   + IPVT
Sbjct: 77  QLKYCARLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQGVVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVQSMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|91763046|ref|ZP_01265010.1| hypothetical protein PU1002_00270 [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91717459|gb|EAS84110.1| hypothetical protein PU1002_00270 [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 320

 Score =  261 bits (667), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 132/285 (46%), Positives = 176/285 (61%), Gaps = 10/285 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +D TDRH RFF RL++ N LLY+EM+V++AI RGDKK +L F+  EKP+ALQIGG+  + 
Sbjct: 1   MDCTDRHERFFLRLISKNTLLYSEMVVSEAIHRGDKKKLLEFNINEKPIALQIGGSSPTL 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EA K  EDFGY+EINLN+GCPS +V +  FGACLM  P++V DC++ M     +PVT+
Sbjct: 61  LAEATKAGEDFGYDEINLNLGCPSKKVEKNKFGACLMKEPNLVADCLSKMQSVTKLPVTI 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DD      L + + ++K +GV    IHARKAIL   +PK N  IP L YD VY 
Sbjct: 121 KTRIGYDDTEDYENLHHFISTLKSTGVKTFIIHARKAILGKFTPKQNLNIPPLKYDFVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +KK+ P+  I +NGG+    Q    L  VDGVMIGRAAY    +L  ++    N    + 
Sbjct: 181 LKKDFPNEEIIINGGITTTDQMKDHLDKVDGVMIGRAAYHTPYLLADIERDIFN----NE 236

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
            + +R D      +   +  Y    +  G +L QI RH +GLFHG
Sbjct: 237 NVPSRQD------VIEQLLPYVREEIKKGTRLNQIMRHTLGLFHG 275


>gi|325277336|ref|ZP_08142961.1| tRNA-dihydrouridine synthase A [Pseudomonas sp. TJI-51]
 gi|324097526|gb|EGB95747.1| tRNA-dihydrouridine synthase A [Pseudomonas sp. TJI-51]
          Length = 336

 Score =  261 bits (667), Expect = 9e-68,   Method: Compositional matrix adjust.
 Identities = 130/318 (40%), Positives = 188/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKQTLLYTEMVTTGALLHNDADRFLRHDVSEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A++ PVT
Sbjct: 85  DLAACARLAEQAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVATPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKADFPDLEIVLNGGIKTLGECQAHLQTFDGVMLGREAYHNPYLLAEVDQQL---FGSE 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 262 AAVISRSEA------LAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKAAQPLAVFDQAVELL 333


>gi|315633448|ref|ZP_07888738.1| tRNA-dihydrouridine synthase A [Aggregatibacter segnis ATCC 33393]
 gi|315477490|gb|EFU68232.1| tRNA-dihydrouridine synthase A [Aggregatibacter segnis ATCC 33393]
          Length = 327

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 136/320 (42%), Positives = 191/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+   K + L F T E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSRHALLYTEMVTTQAIIHA-KYDHLDFDTAENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ +  GY EINLNVGCPS RV  G FGACLM N ++V +C+  M  A+ IPVT
Sbjct: 77  QLQHCAQLAQQRGYQEINLNVGCPSDRVQNGMFGACLMANAELVAECVQQMQSAVHIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V+ + ++G     +HARKA L GLSPK NR+IP L+Y+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLCDFVQKVHQAGCQEFIVHARKAWLSGLSPKQNREIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++   +  + L  VDGVM+GR AY+N A+L  +D         +
Sbjct: 197 QLKQDFPHLLISINGGIKTTEEMQQHLKYVDGVMVGREAYQNPALLGHIDHTL---FDAN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+   +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIITP------RQAVENMFPYIEQQLSQGVYLNHIVRHMLGAFQHCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
           A  + A   ++ETA   + E
Sbjct: 308 AYKAGAGIDVVETALGFVEE 327


>gi|187923745|ref|YP_001895387.1| tRNA-dihydrouridine synthase A [Burkholderia phytofirmans PsJN]
 gi|187714939|gb|ACD16163.1| TIM-barrel protein, yjbN family [Burkholderia phytofirmans PsJN]
          Length = 333

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 187/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+ +E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRVISRHTWLYTEMVTTGALLHGDVPRHLAFTPEEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G N   +HAR AILKGLSPK+NR+IP L Y+  Y
Sbjct: 137 VKHRIGVDAVEEYGFVRDFVGTIAEAGCNVFIVHARNAILKGLSPKENREIPPLKYEYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F       
Sbjct: 197 QLKRDFPQLEIIINGGIKTLDEVEAHLEHVDGVMLGREAYHNPYVLADVDARFYG--AAQ 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 255 TPL-TR------EQVEAKLIEYCAAEMVRGTYLGAITRHALGLYRGEAGARGWRRVLS 305


>gi|269137592|ref|YP_003294292.1| tRNA-dihydrouridine synthase [Edwardsiella tarda EIB202]
 gi|267983252|gb|ACY83081.1| tRNA-dihydrouridine synthase [Edwardsiella tarda EIB202]
 gi|304557663|gb|ADM40327.1| tRNA dihydrouridine synthase A [Edwardsiella tarda FL6-60]
          Length = 352

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 139/319 (43%), Positives = 188/319 (58%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E PLALQ+GG++ +
Sbjct: 39  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPLALQLGGSNPA 97

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 98  DLARCAHLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 157

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D Q     L + + ++   G  +   +HARKA L GLSPK+NR++P LDY  V
Sbjct: 158 VKTRIGIDAQDSYPFLCDFIGTVAGQGECDTFIVHARKAWLSGLSPKENREVPPLDYPRV 217

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P   I LNGG++ + +AL  L  VDGVM+GR AY N  +L  VD         
Sbjct: 218 YRLKQDFPQFTIALNGGVKRLDEALTHLQHVDGVMMGREAYHNPGILAQVDRQL---FDA 274

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + +   V       +  ++  Y  R L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 275 DAAVPDSV------AVVRALYPYIERELAQGTYLGHITRHILGLFQGIPGARQWRRHLSE 328

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 329 NAHRPGAGIDVVEQALRFV 347


>gi|194364005|ref|YP_002026615.1| tRNA-dihydrouridine synthase A [Stenotrophomonas maltophilia
           R551-3]
 gi|194346809|gb|ACF49932.1| dihydrouridine synthase DuS [Stenotrophomonas maltophilia R551-3]
          Length = 343

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 139/315 (44%), Positives = 191/315 (60%), Gaps = 11/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L   A LYTEM+ A+A++ GD++ +LGF   E+PLALQ+GG+D +
Sbjct: 28  MMDWTDRHCRVFHRVLAPGARLYTEMVHANAVIHGDRERLLGFDRSEQPLALQLGGSDPA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM  A+ IPVT
Sbjct: 88  LLAQAARIAAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPALVAECVAAMVNAVDIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD+          V     +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 148 VKCRLGVDEDNDYDVFAAFVDRQVAAGAAMVVVHARNAWLKGLSPKENREVPPLKYDWAY 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGGL  +         VDGVM+GRAAY +  +L  ++      L   
Sbjct: 208 RLKQERPALPVVLNGGLASLEAVQAQAVHVDGVMLGRAAYHDPYLLHQLEA-----LHTG 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++ R D      +  ++  Y    L  G  L+ ITRH++GLFHG    R  R +L+  
Sbjct: 263 APLQARGD------LLRALRPYVEARLGEGLALKHITRHVLGLFHGQAGGRAFRQVLSEG 316

Query: 301 AGASTATHHIIETAF 315
           A    A   +IE A 
Sbjct: 317 AHRPGADWRLIEQAL 331


>gi|167845866|ref|ZP_02471374.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei B7210]
          Length = 333

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 132/297 (44%), Positives = 184/297 (61%), Gaps = 9/297 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ + 
Sbjct: 1   MDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVTV
Sbjct: 61  LAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y 
Sbjct: 121 KHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S+
Sbjct: 181 LKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---ASA 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 238 PAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLS 288


>gi|110834374|ref|YP_693233.1| tRNA-dihydrouridine synthase A [Alcanivorax borkumensis SK2]
 gi|110647485|emb|CAL16961.1| TIM-barrel protein, yjbN family [Alcanivorax borkumensis SK2]
          Length = 348

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 137/318 (43%), Positives = 185/318 (58%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRF ARL+T + LLYTEM+VA AIL GD+   L F+ +E P+ALQ+GG+D  
Sbjct: 39  MMDWTTRDYRFLARLITRHTLLYTEMVVAQAILHGDRDRFLDFNDEEHPVALQLGGSDPQ 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A +I  D+GY+EINLNVGCPS RV +G  GA LM  P++V  C+ AM   +++PVT
Sbjct: 99  QLAQATRIAGDYGYDEINLNVGCPSDRVQQGKIGAILMAEPELVARCVEAMQAEVTVPVT 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V  ++ SG   + IHARKAIL GLSPK+NR IP L Y   Y
Sbjct: 159 VKTRIGIDDQDDYDFLYRFVDRMEASGCTSLTIHARKAILSGLSPKENRDIPPLIYQRAY 218

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK   P + I LNGG++ +++  + +  VDGVMIGR AY+N   L   D          
Sbjct: 219 AIKHAFPHIEIILNGGVKTLNEVHEHMGEVDGVMIGREAYQNPYFLAEADRVV---FGDD 275

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R      + I+     Y  R    G   +   RH++ LF G P +RR R  L+  
Sbjct: 276 HAIPSR------QTIAEQFLPYVERRYALGHAPKHSLRHILNLFQGQPGARRFRRHLSEN 329

Query: 301 AGASTATHHIIETAFNLM 318
                 T  ++  A + +
Sbjct: 330 MHKPGTTPQVLMDALSQL 347


>gi|307256171|ref|ZP_07537958.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865352|gb|EFM97248.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 334

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 24  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 83  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 143 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 202 QLKRDFPHLNISINGGIKTIEEIKQHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 259 QPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 312

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 313 ATKQGAGVEVVEQALSFVQES 333


>gi|85060114|ref|YP_455816.1| tRNA-dihydrouridine synthase A [Sodalis glossinidius str.
           'morsitans']
 gi|84780634|dbj|BAE75411.1| conserced hypothetical protein [Sodalis glossinidius str.
           'morsitans']
          Length = 343

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 141/303 (46%), Positives = 186/303 (61%), Gaps = 13/303 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H RFF R L+  ALLYTEM+   A+L G K + L +   E PLALQ+GG++  
Sbjct: 33  MLDWTDSHCRFFLRQLSRRALLYTEMVTTGALLFG-KGDYLAYHDAEHPLALQLGGSEPD 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   D V  CIAAM +A+++P+T
Sbjct: 92  ALARCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEKDRVAACIAAMREAVTLPIT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L   + ++    G     IHARKA L GLSPK+NR+IP LDYD V
Sbjct: 152 VKTRIGIDEQDSYAFLCEFIDTVATHGGCETFIIHARKAWLNGLSPKENREIPPLDYDRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + LNGG++ +  A + L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPALRLMLNGGIKTLHDAREHLQKLDGVMMGREAYQNPGILARVDSELFGD--A 269

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P +  V           M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 270 DTLPNQAAVID--------VMLPYIERELSQGAALGHITRHMLGLFQGMPGARQWRRYLS 321

Query: 299 VEA 301
             A
Sbjct: 322 EHA 324


>gi|225075955|ref|ZP_03719154.1| hypothetical protein NEIFLAOT_00980 [Neisseria flavescens
           NRL30031/H210]
 gi|224952670|gb|EEG33879.1| hypothetical protein NEIFLAOT_00980 [Neisseria flavescens
           NRL30031/H210]
          Length = 319

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 187/301 (62%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T N  LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHYRFMARQITRNTWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM  A+ IPVT
Sbjct: 61  DLAIAAKAAETYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDAVEIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V  ++ K+      +HAR A L GLSPK+NR++P L Y+ V
Sbjct: 121 VKHRIGVDRQTEYQVVADFVGMLREKTACRTYIVHARNAWLDGLSPKENREVPPLKYEYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 181 YRLKQEFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDARFYN--DT 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  ++A +  Y+   + SG    L+ I RH +GL H   N+R  R +L
Sbjct: 239 HAPIQ-------YADLAAWLYAYSREQIASGRGTILRHIVRHALGLMHSLKNARTWRRML 291

Query: 298 T 298
           +
Sbjct: 292 S 292


>gi|300312882|ref|YP_003776974.1| hypothetical protein Hsero_3587 [Herbaspirillum seropedicae SmR1]
 gi|300075667|gb|ADJ65066.1| conserved hypothetical protein [Herbaspirillum seropedicae SmR1]
          Length = 357

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 136/304 (44%), Positives = 186/304 (61%), Gaps = 13/304 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T +  LYTEM+   A+L GD    L F  QE P+ALQ+GG++ +
Sbjct: 32  MMDWTDRHCRVFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFDEQEHPVALQLGGSEPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV +G+FGACLM  P +V DC+ AM  A+SI VT
Sbjct: 92  DLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAMRDAVSIDVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +R+ V  I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 152 VKHRIGIDEVESYDFVRDFVGQIAEAGCQTFIVHARNAILKGLSPKENREIPPLKYDYAY 211

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +  + L  VDGVM+GR AY N  ++   D  +   L G 
Sbjct: 212 QLKKDFPSLEILINGGIKTLPEIDEHLKHVDGVMLGREAYHNPYLMAGFDARYYAALEGG 271

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLH------SGGKLQQITRHMIGLFHGFPNSRRCR 294
              ++R +      +  +M  Y  R L        G +L  ITRHM+GL  G P +R  R
Sbjct: 272 LQ-RSRAE------VIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGLMAGMPGARAFR 324

Query: 295 HILT 298
             L+
Sbjct: 325 QTLS 328


>gi|91788026|ref|YP_548978.1| tRNA-dihydrouridine synthase A [Polaromonas sp. JS666]
 gi|91697251|gb|ABE44080.1| tRNA-U16,U17-dihydrouridine synthase [Polaromonas sp. JS666]
          Length = 344

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 135/299 (45%), Positives = 184/299 (61%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+ +ALLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 31  MMDWTDRHCRHFHRLLSGHALLYTEMVTTGALIHGDVARHLRFGVEEHPVALQLGGSEPA 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A + E +GY+EINLN GCPS RV  GSFGACLM  P +V DC+ AM   +S+PVT
Sbjct: 91  ELAQCATLGEQWGYDEINLNCGCPSERVQRGSFGACLMAEPQLVADCVKAMVDVVSVPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++ ++G +   +HAR A LKGLSPK+NR++P L Y++V+
Sbjct: 151 VKHRIGIDKGESYGFVRDFVGAVSEAGCSTFIVHARNAWLKGLSPKENREVPPLRYELVH 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG+   +Q  + L  +DGVMIGR AY N   L+  D  F       
Sbjct: 211 RLKAEFPQLTIAINGGITTSTQVAEQLQQLDGVMIGREAYHNPWWLSVWDAAFYGVADAG 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              +TR        + A M DY AR     G     I RHM+GL HG P +RR R + +
Sbjct: 271 ---RTR------ESVEAQMVDYMAREAAEHGTPWSSIARHMLGLRHGLPGARRWRQVWS 320


>gi|120611162|ref|YP_970840.1| tRNA-dihydrouridine synthase A [Acidovorax citrulli AAC00-1]
 gi|120589626|gb|ABM33066.1| tRNA-U16,U17-dihydrouridine synthase [Acidovorax citrulli AAC00-1]
          Length = 347

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 134/301 (44%), Positives = 184/301 (61%), Gaps = 13/301 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A++ GD +  L F+ +E P+ALQ+GG++  
Sbjct: 28  MMDWTDRHCRYFHRLLSRHALLYTEMVTTGALVHGDVERHLRFNAEEHPVALQLGGSEPG 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 88  DLAHSARLGERWGYGEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDAVSVPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+        +R+ V ++ ++G     +HAR A L+GLSPK+NR+IP L YD+V+
Sbjct: 148 VKHRIGIGRSEEYAFVRDFVGTVAEAGCRVFIVHARNAWLEGLSPKENREIPPLRYDVVH 207

Query: 181 EIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLT 238
            +K E PDL I +NGGL  D +    +   +DG MIGR AY N   L   D  YF +  +
Sbjct: 208 RLKAEFPDLVIAINGGLATDAAVQEALGGGLDGAMIGREAYHNPWWLARWDALYFGDAAS 267

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           G     TR           +M DY AR     G     + RHM+GL +G P +RR R + 
Sbjct: 268 G----LTR------EAAEEAMVDYMAREAAQHGTSWYSVARHMLGLRNGLPGARRWRQVW 317

Query: 298 T 298
           +
Sbjct: 318 S 318


>gi|295676394|ref|YP_003604918.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1002]
 gi|295436237|gb|ADG15407.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1002]
          Length = 333

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDTVEEYGFVRDFVGTIAEAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    T S
Sbjct: 197 QLKRDFPQLEIIINGGIKTLDEVDTHLQHVDGVMLGREAYHNPYVLADVDARFYGS-TQS 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P + +V+        A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 256 PPTRDQVE--------AKLIEYCATEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 305


>gi|126207634|ref|YP_001052859.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           L20]
 gi|165975602|ref|YP_001651195.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|307260603|ref|ZP_07542295.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|126096426|gb|ABN73254.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
 gi|165875703|gb|ABY68751.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|306869680|gb|EFN01465.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 325

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 304 ATKQGAGVEVVEQALSFVQES 324


>gi|167855851|ref|ZP_02478602.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis 29755]
 gi|167853001|gb|EDS24264.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis 29755]
          Length = 323

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 139/318 (43%), Positives = 193/318 (60%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  T ++LLY+EMI+A AIL   K ++L +   E P+ALQ+GG+D  
Sbjct: 15  MLDWTTRHCRYFHRQFTQHSLLYSEMIIAPAILHA-KYDLLAYDPTENPVALQLGGSDPE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V  C+ AM K +SIPVT
Sbjct: 74  QLAKCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMGKADLVARCVEAMKKEVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKIQPY-CNDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D+   +P    
Sbjct: 193 QLKRDFPHLKISINGGIKTIEEIKHHLQFVDGVMVGREAYQNPSLLGYIDQELFDPNADI 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  V+K         M  Y  + L  G  L  I RH++G F     +RR R  L+  
Sbjct: 253 VTPKQAVEK---------MLPYIEQQLSQGVYLNHIVRHILGAFQNCKGARRWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A + +
Sbjct: 304 ACKQGAGVEVVEQALSFL 321


>gi|224824837|ref|ZP_03697944.1| TIM-barrel protein, yjbN family [Lutiella nitroferrum 2002]
 gi|224603330|gb|EEG09506.1| TIM-barrel protein, yjbN family [Lutiella nitroferrum 2002]
          Length = 313

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 131/299 (43%), Positives = 186/299 (62%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR +T +  LYTEM+   A+L GD    L +   E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHYRFFARQITRHTWLYTEMVTTGALLYGDVARHLRYHECEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E++GY+E+NLNVGCPS RV +G+FGACLM  P +V DC+ AM  A+ I VT
Sbjct: 61  ELARCARLAEEWGYDEVNLNVGCPSERVQKGAFGACLMAEPQLVADCVKAMRDAVGIDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  I ++G     +HAR AILKGLSPK+NR+IP L YD VY
Sbjct: 121 VKHRIGIDAVEDYGYVRDFVGHIVEAGCATFIVHARNAILKGLSPKENREIPPLKYDYVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PD+ I LNGG++   +  + L  VDGVM+GR AY N  ++   D  F +     
Sbjct: 181 RLKRDFPDVEILLNGGVKSNDEIARHLQHVDGVMVGREAYHNPWLMADWDARFYD----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL-HSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
               T   +D    +  +M  Y  + L     +L+ + RH++GL+ G P +R  R +L+
Sbjct: 236 -DAHTEATRD---AVVEAMLPYIEQRLAEPATQLRHVARHILGLYQGLPGARAWRRMLS 290


>gi|303249850|ref|ZP_07336054.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|303251970|ref|ZP_07338141.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302649400|gb|EFL79585.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302651417|gb|EFL81569.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 325

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLANCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 304 ATKQGAGVEVVEQALSFVQES 324


>gi|32034537|ref|ZP_00134701.1| COG0042: tRNA-dihydrouridine synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
          Length = 329

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 197 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|254482016|ref|ZP_05095258.1| tRNA dihydrouridine synthase A subfamily protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037706|gb|EEB78371.1| tRNA dihydrouridine synthase A subfamily protein [marine gamma
           proteobacterium HTCC2148]
          Length = 315

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 134/316 (42%), Positives = 191/316 (60%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+D H R+F RLL+  ALLYTEM+   A++ GD++  L F+ +E P+ALQ+GG++ +
Sbjct: 1   MMDWSDHHCRYFWRLLSKQALLYTEMVTTGALIHGDRERFLRFNAEEHPVALQLGGSNPN 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+  +++ Y+E+NLN GCPS RV  G FGACLM  P++V D + AM  A  +PVT
Sbjct: 61  DLAQCARWAQEWHYDEVNLNCGCPSDRVQSGMFGACLMAQPELVADGVKAMRDATLLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V  +  +G     +HARKA LKGLSPK+NR+IP L YD VY
Sbjct: 121 VKHRIGIDDMDSYEQMLDFVGPVADAGCEVFIVHARKAWLKGLSPKENREIPPLVYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG++ +      L  VDGVMIGR AY+N  ML  VD    + L G 
Sbjct: 181 RLKRDLPDLEIVINGGIQTIEDCEDHLAHVDGVMIGREAYQNPWMLAEVD----SRLFGI 236

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +    D      +   +  Y  + L  G  L  ITRH++GL+ G P +R+ R  L+  
Sbjct: 237 DKVAESRD-----DVLLGLLPYVEQQLALGTHLNHITRHILGLYQGVPGARKFRRHLSEN 291

Query: 301 AGASTATHHIIETAFN 316
           A    A  +++  AF 
Sbjct: 292 AYKKDAGLNVLIDAFE 307


>gi|307247131|ref|ZP_07529183.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307251674|ref|ZP_07533579.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306856380|gb|EFM88531.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306860871|gb|EFM92879.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 329

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLANCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 197 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|194289932|ref|YP_002005839.1| tRNA-dihydrouridine synthase a [Cupriavidus taiwanensis LMG 19424]
 gi|193223767|emb|CAQ69774.1| tRNA-dihydrouridine synthase A [Cupriavidus taiwanensis LMG 19424]
          Length = 337

 Score =  259 bits (663), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 181/298 (60%), Gaps = 8/298 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 13  MMDWTDRHCRMFHRQLSRHTWLYTEMVTTGALLHGDVPRHLDFDAAEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ + +GY EINLN GCPS RV  G+FGACLM  P++V DC+ AM  A+ IPVT
Sbjct: 73  DLAMAAKLGQQWGYAEINLNCGCPSERVQRGAFGACLMAEPELVADCVKAMRDAVEIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 133 VKHRIGIDKIEHYDFVRDFVGKVAQAGCGTFIVHARNAILKGLSPKENREIPPLRYEVAY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E P+L I +NGG+    +  + L  VDGVMIGR AY    +L  +D  F      S
Sbjct: 193 QLKREFPELEILINGGILSHDEIARHLEHVDGVMIGREAYHQPYILAEMDARFYG--DAS 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ +R+       +  +M  Y    +  GG +   TRHM+GL  G    R  R +L+
Sbjct: 251 APVPSRL------AVELAMQRYIGDFVEQGGYMGAATRHMLGLHRGIAGGRGWRRVLS 302


>gi|332525913|ref|ZP_08402054.1| tRNA-dihydrouridine synthase A [Rubrivivax benzoatilyticus JA2]
 gi|332109464|gb|EGJ10387.1| tRNA-dihydrouridine synthase A [Rubrivivax benzoatilyticus JA2]
          Length = 320

 Score =  259 bits (663), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 131/299 (43%), Positives = 181/299 (60%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT +A LYTEM+   A+L GD+   L F  +E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHCRHFHRLLTQHARLYTEMVTTGALLHGDQPRHLDFGDEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E +GY+E+NLN GCPS RV  G+FGACLM  P +V D + AM  A+S+PVT
Sbjct: 61  DLAACAKLAERWGYDEVNLNCGCPSPRVQRGAFGACLMNEPALVADAVKAMRDAVSLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+        +R+ V S+ ++G     +HAR A L+GLSPK+NR IP L Y++ +
Sbjct: 121 VKHRIGLGKDESYAFVRDFVGSVAEAGCEVFIVHARNAWLEGLSPKENRDIPPLRYEVAH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K E P L I +NGG+         L  VDGVM+GRAAY     L+T DE +F  P   
Sbjct: 181 RLKTEFPQLTIVVNGGIAGDEAIAAQLAHVDGVMVGRAAYHEPWTLSTWDERFFGEP--- 237

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +P + R        +  +M  Y  R   +G     + RHM+GL++G P +RR R + +
Sbjct: 238 -APAQDRA------AVELAMVRYMERQAAAGVPWAHVARHMLGLWNGEPGARRWRQVWS 289


>gi|226952909|ref|ZP_03823373.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ATCC 27244]
 gi|226836354|gb|EEH68737.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ATCC 27244]
          Length = 343

 Score =  259 bits (663), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 133/314 (42%), Positives = 189/314 (60%), Gaps = 15/314 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AI+ G     L F+ +E P+ LQ+GG++  
Sbjct: 24  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAIIYGGANRHLDFNKEEHPIVLQLGGSNPQ 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  P++V +CI +M KA+SIPVT
Sbjct: 84  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPNLVAECIHSMQKAVSIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AIL+GLSPK+NR++P L YD VY
Sbjct: 144 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFIVHARIAILQGLSPKENREVPPLRYDDVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++   +  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 204 RLKQERPHLTIEINGGIKTFDETQQHLQHVDGVMIGREAYHNPYLLAEMGQLWN----LE 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +         +I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 260 APDRF--------EIMQQMMPYIHQRVAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 309

Query: 301 AGASTATHHIIETA 314
            G +  T + IE A
Sbjct: 310 -GGNAKTINDIENA 322


>gi|309378640|emb|CBX22711.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 336

 Score =  259 bits (662), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 138/301 (45%), Positives = 184/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK VE +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAVEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPDLEIIINGGITANEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YADLVQLLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|254362517|ref|ZP_04978621.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|153094117|gb|EDN75017.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
          Length = 325

 Score =  259 bits (662), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 142/318 (44%), Positives = 189/318 (59%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  +  ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRQALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V + GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 77  QLAHCAKLVAERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVEIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLTGLSPKENREIPPLDYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N +ML  +D    N     
Sbjct: 196 QLKRDFPHLKISINGGIKTIEEIKQHLQFVDGVMVGREAYQNPSMLGEIDSQIFNENRPL 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  V+K         M  Y  R L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 256 VTAKEAVEK---------MFPYIERELAKGIYLNHIVRHMLGAFQHCKGARQWRRHLSEN 306

Query: 301 AGASTATHHIIETAFNLM 318
           A  S A   ++E A   +
Sbjct: 307 ATKSGAGVEVVEQALAFI 324


>gi|262374231|ref|ZP_06067507.1| tRNA-dihydrouridine synthase A [Acinetobacter junii SH205]
 gi|262310789|gb|EEY91877.1| tRNA-dihydrouridine synthase A [Acinetobacter junii SH205]
          Length = 338

 Score =  259 bits (662), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 134/315 (42%), Positives = 185/315 (58%), Gaps = 15/315 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AI+ G     L F+ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAIIYGGANRHLDFNQQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GYNE+NLNVGCPS RV     GACLM  P++V +CI +M KA+SIPVT
Sbjct: 80  ELATCTKMAEDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPNLVAECIHSMQKAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AIL+GLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFIVHARIAILQGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG++   +  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKLERPHLTIEINGGIKTFEETKQHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LDAPDRFDIMQQMMPYIHQRVAEGAPLSIITRHILGLFQNLPGARKWRQSLS-- 305

Query: 301 AGASTATHHIIETAF 315
            G +  T   IE A 
Sbjct: 306 -GGNAKTITDIENAI 319


>gi|294649316|ref|ZP_06726749.1| tRNA-dihydrouridine synthase A [Acinetobacter haemolyticus ATCC
           19194]
 gi|292824795|gb|EFF83565.1| tRNA-dihydrouridine synthase A [Acinetobacter haemolyticus ATCC
           19194]
          Length = 339

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 131/316 (41%), Positives = 189/316 (59%), Gaps = 15/316 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AI+ G     L F+ +E P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAIIYGGANRHLDFNKEEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  P++V +CI +M KA+SIPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPNLVAECIHSMQKAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AIL+GLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFIVHARIAILQGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++ + +  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTLEETQQHLQHVDGVMIGREAYHNPYLLAEMGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++     +I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LEAPDRFEIMQQMMPYIHQRVAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFN 316
            G +  T + IE A  
Sbjct: 306 -GGNAKTINDIENAIQ 320


>gi|323526215|ref|YP_004228368.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1001]
 gi|323383217|gb|ADX55308.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1001]
          Length = 333

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 184/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPH 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYSFVRDFVGTIAQAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 197 RLKRDFPQLEIVINGGIKTLDEVETHLQHVDGVMLGREAYHNPYLLADVDARFYG--SSE 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 255 APL-TR------EQVEAKLVEYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 305


>gi|113868264|ref|YP_726753.1| tRNA-dihydrouridine synthase A [Ralstonia eutropha H16]
 gi|113527040|emb|CAJ93385.1| transfer RNA-dihydrouridine synthase [Ralstonia eutropha H16]
          Length = 345

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 180/298 (60%), Gaps = 8/298 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 21  MMDWTDRHCRMFHRQLSRHTWLYTEMVTTGALLHGDVPRHLDFDAAEHPVALQLGGSEPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ + +GY E+NLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 81  DLAMAAKLGQQWGYAEVNLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMRDAVDIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 141 VKHRIGIDKIEHYDFVRDFVGRVAEAGCGTFIVHARNAILKGLSPKENREIPPLRYEVAY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E P+L I +NGG+    +    L  VDGVMIGR AY    +L  +D  F      S
Sbjct: 201 QLKQEFPELEILINGGIVSYDEVAAHLEHVDGVMIGREAYHQPYVLAEMDARFYG--DAS 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P  +R+D      +  +M  Y    +  GG +  +TRHM+GL  G    R  R +L+
Sbjct: 259 APAPSRLD------VELAMQRYIGDLVERGGYMGAVTRHMLGLHRGIAGGRGWRRVLS 310


>gi|307249353|ref|ZP_07531347.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306858647|gb|EFM90709.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 329

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 193/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N I +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYSNNFI-VHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 197 QLKRDFPHLNISINGGIKTVEEIKRHLAFVDGVMVGREAYQNPSLLGEID---SQIFGEN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y       G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 RPLVTA------REAVEKMLPYIETQTKKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|327480282|gb|AEA83592.1| tRNA-dihydrouridine synthase A [Pseudomonas stutzeri DSM 4166]
          Length = 322

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 133/300 (44%), Positives = 188/300 (62%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L G+    L +   E PLALQ+GG+   
Sbjct: 11  MMDWTDRHCRFFLRQLSKHALLYTEMVTTGALLHGNTARFLRYDETEHPLALQLGGSVPG 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ + VT
Sbjct: 71  DLAACAKLAEAAGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCVKAMRDAVGVEVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AILKGLSPK NR +P L YD+  
Sbjct: 131 VKHRIGINGRDSYSQLCDFVGQVREAGCRSFTVHARIAILKGLSPKQNRDVPPLRYDVAA 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +  + L + DGVM+GR AY N  +L  VD   S+    +
Sbjct: 191 QLKRDFPDLEIILNGGIKTLEECREHLQTFDGVMLGREAYHNPYLLAQVD---SSLFGSN 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   +M  Y  RHL  GG +  +TRH++GL  GFP +RR R +L+V+
Sbjct: 248 APVISRA------QALRNMRPYIERHLAEGGAMHHVTRHVLGLGQGFPGARRFRQLLSVD 301


>gi|262369896|ref|ZP_06063223.1| tRNA-dihydrouridine synthase A [Acinetobacter johnsonii SH046]
 gi|262314935|gb|EEY95975.1| tRNA-dihydrouridine synthase A [Acinetobacter johnsonii SH046]
          Length = 340

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 132/314 (42%), Positives = 188/314 (59%), Gaps = 15/314 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL G     L ++ +E P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVILYTEMVTTGAILFGGANRHLDYNNEEHPIVLQLGGSNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ +D+GY+E+NLNVGCPS RV     GACLM  PD+V +CIA M  A+ IPVT
Sbjct: 80  DLATCTKMAQDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIAEMQNAVEIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G +   +HAR A+L+GLSPK+NR IP L Y+ VY
Sbjct: 140 VKHRIGIDDMHSYEEMLHFVDTVTKTGCDNFIVHARIALLQGLSPKENRDIPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++  ++  + L  VDGVMIGR AY N  +L  + + ++  L   
Sbjct: 200 RLKQERPNLLIEINGGIKTFAETQEHLKHVDGVMIGREAYHNPYLLAELGQLWNLDLPDR 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I   +D+         M  Y A+ +     L  ITRH++GLF   P +R+ R  L+  
Sbjct: 260 FEI---IDQ---------MLPYIAKRMAEDAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETA 314
            G +  T   +E A
Sbjct: 306 -GGNAKTFADVENA 318


>gi|89068926|ref|ZP_01156308.1| tRNA-dihydrouridine synthase A [Oceanicola granulosus HTCC2516]
 gi|89045507|gb|EAR51571.1| tRNA-dihydrouridine synthase A [Oceanicola granulosus HTCC2516]
          Length = 319

 Score =  259 bits (661), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  ALLYTEM+ A A++RG   ++L     E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYFHRLLSREALLYTEMVTAPALVRGGAVHLLEHDPAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLN GCPS RV  G+FGA LM  P+ V +C AAM  A    VT
Sbjct: 61  ELAEAARLGAAAGYDEINLNCGCPSDRVQSGTFGAVLMNAPERVAECCAAMIGAQPREVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q+P   L   ++++  +GV  + IHARKA L+GLSPK+NR +P LDYD+V 
Sbjct: 121 VKCRIGVDEQVPEEVLPRFLEAVAAAGVRRVAIHARKAWLQGLSPKENRDVPPLDYDLVV 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K   P L I +NGG+  +  A  +L   +DG M+GRAAY   A +          L  
Sbjct: 181 AMKAAFPGLHISINGGIATLDAARALLARGLDGAMVGRAAYHEPAAIL---------LPA 231

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLH-SGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + I  R  +      + +M  Y  RHL   GG+L Q+TRHM+GLF G P +R  R  L+
Sbjct: 232 DAAIFGRASEMTAEDAALAMLPYIERHLAGEGGRLIQVTRHMLGLFAGRPGARAWRRHLS 291

Query: 299 VEAGASTATHHIIETAFNLMIES 321
                  A   ++E A  L+ ++
Sbjct: 292 ENGTRPGAGPEVVEAALALVRQA 314


>gi|238899063|ref|YP_002924745.1| tRNA-dihydrouridine synthase A [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229466823|gb|ACQ68597.1| tRNA-dihydrouridine synthase A [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 343

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 200/321 (62%), Gaps = 17/321 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT NA LYTEM+   A++ G + + L +S +E+P+ALQ+GG +  
Sbjct: 33  MLDWTDRHCRYFHRLLTKNAFLYTEMVTTGALIYG-QADYLDYSEEEQPVALQLGGHNPF 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A++ E  GY EINLN+GCPS RV +G+FGA LM + + V  C+ AMC  +SIPVT
Sbjct: 92  ELAQCAQLGEQRGYQEINLNLGCPSPRVKKGAFGAALMQDIEQVCVCLKAMCDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIGVD+Q     L   ++ I +  ++ + IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 152 IKIRIGVDEQDSYEFLSQFIEKISRE-IDTVIIHARKAWLSGLSPKENREIPPLDYPRVY 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG+  + +A + L  V+GVMIGRAAY+N  +LT VD    N     
Sbjct: 211 QLKKDFPKLNIVINGGISTLEEAKQHLQYVEGVMIGRAAYQNPTLLTQVDSELFNA---- 266

Query: 241 SPIKTRVDKDFWRKISASMT---DYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                   +D    I+AS+     Y  + L  G  L+ + R M+GLF G   +R+ R  L
Sbjct: 267 --------QDPLIDITASIKAFYPYIEQELSRGTFLKHLIRPMLGLFQGCAGARQWRRYL 318

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +  A  S A   +I+ A + +
Sbjct: 319 SENAYQSGADVSVIDRALSFV 339


>gi|332289875|ref|YP_004420727.1| tRNA-dihydrouridine synthase A [Gallibacterium anatis UMN179]
 gi|330432771|gb|AEC17830.1| tRNA-dihydrouridine synthase A [Gallibacterium anatis UMN179]
          Length = 326

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 137/318 (43%), Positives = 188/318 (59%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH RFF R  + + LLYTEM+ A AI+     ++L +  QE PLALQ+GG+D  
Sbjct: 18  MLDWTTRHCRFFHRQFSRHTLLYTEMVTAPAIIYAKYDHLL-YHPQELPLALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A + E  GY+E+NLNVGCPS RV  G FGACLM   D+V  CI AM + ++IPVT
Sbjct: 77  QLADCAALAEQRGYSEVNLNVGCPSDRVQNGFFGACLMAKADLVAQCIDAMQQRINIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V+ +   G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDDLDSYEFLCDFVEKVAAVGCQDFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N  +L  +D+   +P    
Sbjct: 197 QLKRDFPQLKIAINGGIKTIEEIQQHLQYVDGVMVGREAYQNPQLLGYIDQALFDPNAAI 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 V+K         M  Y  R L  G  L  ITRHM+G F     +R+ R  L+  
Sbjct: 257 VTPLEAVEK---------MFPYIERELQQGVPLGAITRHMLGAFQNQRGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++E A + +
Sbjct: 308 AHKTGAGIEVVEKALSFV 325


>gi|207723253|ref|YP_002253652.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum MolK2]
 gi|206588451|emb|CAQ35414.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum MolK2]
          Length = 327

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++++  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRYFHRQISSHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 121 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 181 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-V 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 APTRAEVED--------AMIGYIGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 289


>gi|330962294|gb|EGH62554.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 300

 Score =  258 bits (660), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 129/287 (44%), Positives = 184/287 (64%), Gaps = 9/287 (3%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           RLL+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  + L   A++ E+ G
Sbjct: 2   RLLSKHALLYTEMVATGALLHGDRERFLRHDDTEHPLALQLGGSTAADLAACARLAEEAG 61

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           Y+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVTVK RIG++ +   
Sbjct: 62  YDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVTVKHRIGINGRDSY 121

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + P+L I L
Sbjct: 122 AELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKTDFPELEIVL 181

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           NGG++ + Q  + L + DGVM+GR AY N  +L  VD+        ++P+ +R D     
Sbjct: 182 NGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FGSTAPVISRYDA---- 234

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 235 --LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 279


>gi|240950331|ref|ZP_04754601.1| tRNA-dihydrouridine synthase A [Actinobacillus minor NM305]
 gi|240295142|gb|EER45961.1| tRNA-dihydrouridine synthase A [Actinobacillus minor NM305]
          Length = 329

 Score =  258 bits (660), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 139/321 (43%), Positives = 195/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQHALLYTEMITAPAIIHA-KYDLLEYDPAENPVALQLGGSDPT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V++ GY E+NLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVQERGYAEVNLNVGCPSDRVQNGMFGACLMGKADLVADCIKAMQDAVEIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDELDSYAFLCDFIEKIQPYS-NDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKHHLQFVDGVMVGREAYQNPSLLGEID---SQIFNEN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 KPLVTA------REAVEKMLPYIEKELAKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   ++E A + + ES
Sbjct: 304 ACKAGAGVEVVEQALSFVQES 324


>gi|209520920|ref|ZP_03269659.1| TIM-barrel protein, yjbN family [Burkholderia sp. H160]
 gi|209498644|gb|EDZ98760.1| TIM-barrel protein, yjbN family [Burkholderia sp. H160]
          Length = 317

 Score =  258 bits (660), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 186/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+ +E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPEEAPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 61  DLARSARLGEQWGYDEINLNCGCPSERVRRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDTVEEYGFVRDFVGTIAQAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 181 QLKRDFPQLEIIINGGIKTLDEVDTHLQHVDGVMLGREAYHNPYVLAEVDSRFYG--STQ 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 239 APL-TR------EQVEAKLIEYCATEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 289


>gi|109900349|ref|YP_663604.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas atlantica T6c]
 gi|109702630|gb|ABG42550.1| tRNA-U16,U17-dihydrouridine synthase [Pseudoalteromonas atlantica
           T6c]
          Length = 345

 Score =  258 bits (660), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 182/298 (61%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F R ++ ++LLYTEM+   AI+ G K + L F+  E P+ALQ+GG+D  
Sbjct: 17  MLDWTDKHCRYFLRQISKHSLLYTEMVTTGAIIFG-KGDYLAFNDTEHPVALQLGGSDPV 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A + ++ GY+E+N+NVGCPS RV  G FGACLM  P+ V  CI AM K + IPVT
Sbjct: 76  DMARCAVLAQEQGYDEVNINVGCPSDRVQNGRFGACLMAEPETVAACIQAMQKEVDIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ +  +G +   +HARKA LKGLSPK+NR IP L YD VY
Sbjct: 136 VKSRIGIDDMDEYKDLTDFIQIVADAGCDIFTVHARKAWLKGLSPKENRDIPPLMYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGG++ +  A   L  +DGVMIGR  Y N  +L  VD+ F       
Sbjct: 196 ALKEEFPQLNLSINGGVKTLDDATMHLEKLDGVMIGREVYSNPYILADVDKLF---YQDD 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           SP+ +R       +I  +M  Y    + SG +   I RHM+GLF G P  R  R  L+
Sbjct: 253 SPVPSR------EEIVHAMLPYVEAQMASGARAWNIARHMLGLFQGQPGGRIWRRYLS 304


>gi|83749666|ref|ZP_00946647.1| NIFR3-like protein [Ralstonia solanacearum UW551]
 gi|83723668|gb|EAP70865.1| NIFR3-like protein [Ralstonia solanacearum UW551]
          Length = 344

 Score =  258 bits (659), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 182/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 18  MMDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 78  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 138 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 198 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-V 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 257 APTRAEVED--------AMIGYIGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 306


>gi|207743351|ref|YP_002259743.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
 gi|206594748|emb|CAQ61675.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
          Length = 327

 Score =  258 bits (659), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 182/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 121 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 181 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-V 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 APTRAEVED--------AMIGYIGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 289


>gi|318042981|ref|ZP_07974937.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CB0101]
          Length = 364

 Score =  258 bits (659), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 137/321 (42%), Positives = 190/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D+TDRH+R   R +T  +LLYTEM+VA A+   +++  ++ F   E P+ALQ+GG D 
Sbjct: 49  MMDYTDRHFRVLMRQITRRSLLYTEMVVAQALHYSERRERLIDFDPIEHPIALQVGGDDP 108

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA+I  D GY+EINLNVGCPS +V +G FGACLM  PD V  CI+AM  A  +PV
Sbjct: 109 QLLAEAARIAADRGYDEINLNVGCPSEKVQKGRFGACLMAEPDHVARCISAMAAASPLPV 168

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+D++     L   V ++  +G     +HARKA L+GL PK NR IP L Y++V
Sbjct: 169 TVKHRIGIDERDSYAELLAFVDAVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLRYELV 228

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K++ P+L I LNGGL D++   + L  VDGVM+GRAAY +     TVD    N    
Sbjct: 229 HQLKQDRPELTIELNGGLLDLASCSEQLQQVDGVMVGRAAYDHPLRWATVDRDLFN--DS 286

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S P+ +         +   +  YA R  + GG+L  I RH++ +  G   +R  R  L  
Sbjct: 287 SQPMASA------STVVRGLIPYAERWCNGGGRLWAIARHLVQVVEGVSGARHWRRDLGQ 340

Query: 300 EAGASTATHHIIETAFNLMIE 320
            AGA  A   + E A   + E
Sbjct: 341 AAGARDAGPEVFERAAAQLEE 361


>gi|33151604|ref|NP_872957.1| tRNA-dihydrouridine synthase A [Haemophilus ducreyi 35000HP]
 gi|38604736|sp|Q7VNV2|DUSA_HAEDU RecName: Full=tRNA-dihydrouridine synthase A
 gi|33147824|gb|AAP95346.1| conserved hypothetical protein [Haemophilus ducreyi 35000HP]
          Length = 323

 Score =  258 bits (659), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 139/320 (43%), Positives = 191/320 (59%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  +  ALLYTEMI A AIL   K ++L +   E+P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQQALLYTEMITAPAILHA-KYDLLEYDPAEQPVALQLGGSDPT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V+  GY EINLNVGCPS RV  G FGACLM N D+V DCI AM   + IPVT
Sbjct: 74  QLANCAKLVQARGYTEINLNVGCPSDRVQNGMFGACLMANADLVADCIKAMQDVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+D       L + +  I+    + I +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 IKHRIGIDTLDSYAFLCDFIDKIQPYSQDFI-VHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N A+L  +D+        +
Sbjct: 193 QLKRDFPQLNISINGGIKTIDEIKQHLTKVDGVMVGREAYQNPALLGEIDQQL---FDQN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R    +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 QPLITA------RIAVENMLPYIEQQLSKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++E A   + E
Sbjct: 304 ACKQGAGIEVVEQALRFVTE 323


>gi|87301565|ref|ZP_01084405.1| hypothetical protein WH5701_02784 [Synechococcus sp. WH 5701]
 gi|87283782|gb|EAQ75736.1| hypothetical protein WH5701_02784 [Synechococcus sp. WH 5701]
          Length = 315

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 134/314 (42%), Positives = 186/314 (59%), Gaps = 8/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   R ++  ALLYTEM+VA A+  G +  +L F  QE PLALQ+GG D +
Sbjct: 1   MMDCTDRHFRVLMRQISRRALLYTEMVVAQALHHGRRDTLLDFDPQEHPLALQLGGDDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+A++   +GY+EINLNVGCPS +V +G FGACLM +PD V  C+ AM  A S+PVT
Sbjct: 61  LLAESAQLAAAWGYDEINLNVGCPSPKVQQGRFGACLMADPDRVARCVEAMANASSLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V  +  +G +   +HARKA L GL PK NR IP L +D+V+
Sbjct: 121 VKHRIGIDDQDSYELLLAFVDKVAGAGASRFSVHARKAWLHGLDPKQNRTIPPLRHDLVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P   I LNGGL  +    + L  VDGVM+GRAAY +     +VD+     L  +
Sbjct: 181 QLKRDRPQFTIELNGGLLSLENCQEHLGQVDGVMVGRAAYDHPLRWASVDQELFGCLERA 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               + V +         +  +A+R   +G +L  I RH++ L  G P +R  R  L   
Sbjct: 241 PASASTVVR--------GLIPHASRWCGAGRRLWPIARHLVHLVEGVPGARHWRRRLGER 292

Query: 301 AGASTATHHIIETA 314
           AG  +A   ++E A
Sbjct: 293 AGERSAGPEVLEAA 306


>gi|261494145|ref|ZP_05990648.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
 gi|261496014|ref|ZP_05992424.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261308264|gb|EEY09557.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261310311|gb|EEY11511.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
          Length = 325

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 141/318 (44%), Positives = 188/318 (59%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  +  ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRQALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V + GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 77  QLAHCAKLVAERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVEIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLTGLSPKENREIPPLDYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N +ML  +D    N     
Sbjct: 196 QLKRDFPHLKISINGGIKTIEEIKQHLQFVDGVMVGREAYQNPSMLGEIDSQIFNENRPL 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  V+K         M  Y  R L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 256 VTAKEAVEK---------MFPYIERELAKGVYLNHIVRHMLGAFQHCKGARQWRRHLSEN 306

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A   +
Sbjct: 307 ATKPGAGVEVVEQALAFI 324


>gi|261866807|ref|YP_003254729.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412139|gb|ACX81510.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 327

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 132/318 (41%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+   K + L F   E+P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRHALLYTEMVTTQAIIHA-KYDHLDFDPAEQPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E  GY EINLNVGCPS RV  G FGACLM   ++V +C+  M +A+ IPVT
Sbjct: 77  QLKHCAQLAEQRGYQEINLNVGCPSDRVQNGMFGACLMAKAELVAECVQQMQEAVRIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++++G     +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLCDFIEKVQQAGCREFIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   N    +
Sbjct: 197 QLKRDFPHLLISINGGIKTIDEMQQHLQRVDGVMVGREAYQNPSLLGYIDQALFN---AN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+    M  Y  + L  G  L  I RH++  F     +R+ R  L+  
Sbjct: 254 APIVTP------REAVEKMLPYIEQQLSRGVYLNHIVRHILSAFQHCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA   +
Sbjct: 308 AYKEGAGIEVVETALGFV 325


>gi|257464833|ref|ZP_05629204.1| tRNA-dihydrouridine synthase A [Actinobacillus minor 202]
 gi|257450493|gb|EEV24536.1| tRNA-dihydrouridine synthase A [Actinobacillus minor 202]
          Length = 324

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 139/321 (43%), Positives = 195/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQHALLYTEMITAPAIIHA-KYDLLEYDPAENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V++ GY E+NLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVQERGYAEVNLNVGCPSDRVQNGMFGACLMGKADLVADCIKAMQDAVEIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDELDSYAFLCDFIEKIQPYS-NDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVMIGR AY+N ++L  +D   S     +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKHHLQFVDGVMIGREAYQNPSLLGEID---SQIFNEN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 KPLVTA------REAVEKMLPYIEKELAKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   ++E A + + E+
Sbjct: 304 ACKAGAGVEVVEQALSFVQEN 324


>gi|326317525|ref|YP_004235197.1| TIM-barrel protein, yjbN family [Acidovorax avenae subsp. avenae
           ATCC 19860]
 gi|323374361|gb|ADX46630.1| TIM-barrel protein, yjbN family [Acidovorax avenae subsp. avenae
           ATCC 19860]
          Length = 320

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 133/301 (44%), Positives = 184/301 (61%), Gaps = 13/301 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A++ G+ +  L F+ +E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRYFHRLLSRHALLYTEMVTTGALVHGNVERHLRFNAEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLAHSARLGERWGYGEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+        +R+ V ++ ++G     +HAR A L+GLSPK+NR+IP L YD+V+
Sbjct: 121 VKHRIGIGRSEEYAFVRDFVGTVAEAGCRVFIVHARNAWLEGLSPKENREIPPLRYDVVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLT 238
            +K E PDL I +NGGL       + L   +DG MIGR AY N   L   D  YF +  +
Sbjct: 181 RLKAEFPDLVIAINGGLATDDAVQEALGGGLDGAMIGREAYHNPWWLARWDALYFGDAAS 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           G     TR           +M DY AR     G     + RHM+GL +G P +RR R + 
Sbjct: 241 G----LTR------EAAEEAMVDYMAREAAQHGTSWYSVARHMLGLRNGLPGARRWRQVW 290

Query: 298 T 298
           +
Sbjct: 291 S 291


>gi|170692264|ref|ZP_02883427.1| TIM-barrel protein, yjbN family [Burkholderia graminis C4D1M]
 gi|170142694|gb|EDT10859.1| TIM-barrel protein, yjbN family [Burkholderia graminis C4D1M]
          Length = 317

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 185/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 61  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G +   +HAR AILKGLSPK+NR+IP L Y+  Y
Sbjct: 121 VKHRIGVDAVEEYGFVRDFVGTIAEAGCDVFIVHARNAILKGLSPKENREIPPLKYEYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 181 QLKRDFPHLEIIINGGIRTLDEVETHLQHVDGVMLGREAYHNPYLLADVDARFYG--STQ 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 239 APL-TR------EQVEAQLIEYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 289


>gi|254462050|ref|ZP_05075466.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2083]
 gi|206678639|gb|EDZ43126.1| tRNA-dihydrouridine synthase A [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 305

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 139/305 (45%), Positives = 190/305 (62%), Gaps = 11/305 (3%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           +++ ALLYTEM+ + A++RG   ++L +ST E P+ALQ+GG+D ++L EAA+I  + GY 
Sbjct: 1   MSSRALLYTEMVTSPALVRGGALHLLKYSTVEHPVALQLGGSDPAELAEAARIGAEHGYA 60

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           EINLNVGCPS RV  G+FGA LM +P +V +C AAM KA ++ VTVKCRIGVDDQ P+  
Sbjct: 61  EINLNVGCPSDRVQNGAFGAILMRDPKLVAECCAAMIKASAVEVTVKCRIGVDDQTPSDV 120

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           L   +  +  +GV    IHARKA L+GLSPK+NR IP LDY +V ++K   P L + LNG
Sbjct: 121 LPEFLARVAGAGVGRFTIHARKAWLQGLSPKENRDIPPLDYGLVQQMKGLFPALHLSLNG 180

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           G+  ++QA   L   +DGVMIGRAAY   A +L   D          +P   R  +D   
Sbjct: 181 GITTLAQAQDALERGMDGVMIGRAAYHQPADILMEADHMIYG-----APKVERTRED--- 232

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            I   M  Y   H+  GGKL Q+TRHM+G+F G P +R  +  L+  A   ++  H +  
Sbjct: 233 -IVMEMLPYIDAHIAEGGKLGQVTRHMLGIFAGQPGARYWKRHLSENAHKHSSGSHTVVD 291

Query: 314 AFNLM 318
           A  +M
Sbjct: 292 AIEMM 296


>gi|284929214|ref|YP_003421736.1| tRNA-U16,U17-dihydrouridine synthase [cyanobacterium UCYN-A]
 gi|284809658|gb|ADB95355.1| tRNA-U16,U17-dihydrouridine synthase [cyanobacterium UCYN-A]
          Length = 324

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 134/302 (44%), Positives = 186/302 (61%), Gaps = 17/302 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T + LLYTEMI A A+  G+K  +L FS+ EKPL+LQ+GG D  
Sbjct: 14  MMDRTDRHFRYFIRQITKHTLLYTEMISATAVQNGNKSKLLDFSSDEKPLSLQLGGNDPY 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A I ED+GY+E+NLN+GCPS RV  G FGACLM  P++V   +  M +++ IP+T
Sbjct: 74  TLAECAIIAEDWGYDEVNLNIGCPSDRVQNGRFGACLMAEPELVAKSVEKMQESVDIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+     +L+  V+ + +SG     +HARKA L+GLSPK+NR IP L Y  VY
Sbjct: 134 VKHRIGIDECDDYESLKYFVRIVSESGCKKFIVHARKAWLQGLSPKENRNIPPLRYQDVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SNP 236
            +KK+ P L I +NGG+ ++ Q    L  +D VM+GR AY N  +L TVD+ F    + P
Sbjct: 194 SLKKDFPHLTIEINGGITNLEQISHHLQFIDSVMLGRIAYNNPYLLATVDKDFYKSSTTP 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           LT    I+  +             +Y A H   G KL  ITRH++ LF G   ++  +  
Sbjct: 254 LTRYQIIENIL----------PYVEYWASH---GLKLHSITRHLLSLFIGISGTKEWKRY 300

Query: 297 LT 298
           +T
Sbjct: 301 IT 302


>gi|307729510|ref|YP_003906734.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1003]
 gi|307584045|gb|ADN57443.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1003]
          Length = 333

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 183/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ +PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVGVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYSFVRDFVGTIAEAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 197 RLKRDFPQLEIVINGGIKTLDEVEAHLQHVDGVMLGREAYHNPYLLADVDARFYG--SAE 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++ A + +Y    +  G  L  ITRH +GL+ G   +R  R +L+
Sbjct: 255 APL-TR------EQVEAKLIEYCGVEMARGTYLGAITRHALGLYRGEAGARGWRRVLS 305


>gi|187928263|ref|YP_001898750.1| tRNA-dihydrouridine synthase A [Ralstonia pickettii 12J]
 gi|187725153|gb|ACD26318.1| TIM-barrel protein, yjbN family [Ralstonia pickettii 12J]
          Length = 327

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEFEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++ + +GY EINLN GCPS RV  G+FGACLM  P +V   + AM  A+SIPVT
Sbjct: 61  DLAQAARLGQQWGYKEINLNCGCPSERVQRGAFGACLMAEPKLVAQGVTAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 121 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 181 QLKRDFPHLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMAAFDARYYGAGT-E 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 APTRAEVED--------AMIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 289


>gi|299067351|emb|CBJ38550.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum CMR15]
          Length = 326

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 131/297 (44%), Positives = 183/297 (61%), Gaps = 9/297 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++   
Sbjct: 1   MDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPDD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V D + AM  A+SIPVTV
Sbjct: 61  LAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPRLVADGVKAMRDAVSIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY+
Sbjct: 121 KHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVYQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P L I LNGG++ + Q    L  +DGVMIGR AY +  ++   D  +    T  +
Sbjct: 181 LKRDFPRLEILLNGGVQTLEQIDTHLAHIDGVMIGREAYHHPHLMAGFDARYYGADT-VA 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           P +T V+         +M DY  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 PTRTEVED--------AMIDYIGRWVARGGYAGAAVRHMLGLYRGVAGARGWRRVLS 288


>gi|319639148|ref|ZP_07993902.1| hypothetical protein HMPREF0604_01526 [Neisseria mucosa C102]
 gi|317399587|gb|EFV80254.1| hypothetical protein HMPREF0604_01526 [Neisseria mucosa C102]
          Length = 334

 Score =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 190/301 (63%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T NA LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 16  MLDWTDRHYRFMARQITRNAWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM  A+ IPVT
Sbjct: 76  DLAIAAKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDAVEIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR++P L Y+ +
Sbjct: 136 VKHRIGVDRQTEYQVVADFVGALREKTACRTFIVHARNAWLDGLSPKENREVPPLKYEYI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 196 YRLKQDFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDALFYN--DA 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  ++A +  Y+   + SG    L+ I RH +GL HG  N+R  R +L
Sbjct: 254 HAPIQ-------YADLAAWLYAYSREQIASGRGTILRHIVRHALGLMHGLKNARTWRRML 306

Query: 298 T 298
           +
Sbjct: 307 S 307


>gi|300704326|ref|YP_003745929.1| tRNA-dihydrouridine synthase a [Ralstonia solanacearum CFBP2957]
 gi|299071990|emb|CBJ43320.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum CFBP2957]
          Length = 326

 Score =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 129/297 (43%), Positives = 181/297 (60%), Gaps = 9/297 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++   
Sbjct: 1   MDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPDD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVTV
Sbjct: 61  LAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y+
Sbjct: 121 KHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAYQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  +
Sbjct: 181 LKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-VA 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 PTRAEVED--------AMIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 288


>gi|166713916|ref|ZP_02245123.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 334

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +LGF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLLGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  WLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCTATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDAAMAHLQHTDGVMLGRAAYHDPYVLHCLDAVLNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  ++  Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRALQPYVEAQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALQ 323


>gi|113460197|ref|YP_718254.1| tRNA-dihydrouridine synthase A [Haemophilus somnus 129PT]
 gi|112822240|gb|ABI24329.1| tRNA-U16,U17-dihydrouridine synthase [Haemophilus somnus 129PT]
          Length = 328

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 136/320 (42%), Positives = 189/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH RFF R  +   LLYTEM+   AI+   K + L +   E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRFFHRQFSQYTLLYTEMVTTGAIIHA-KYDHLAYDVSENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL   AK  E+ GY EINLNVGCPS RV  G FGACLM   D+V +C+ AM  A++IPVT
Sbjct: 77  KLQYCAKKAEERGYQEINLNVGCPSDRVQNGMFGACLMARADLVAECVNAMQSAVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L + ++ +   G     IHARKA L GLSPK+NR+IP L+Y+ VY
Sbjct: 137 VKTRLGIDEFDSYEFLCDFIEKVHNIGCQEFIIHARKAWLSGLSPKENREIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   S
Sbjct: 197 QLKKDFPDLLISINGGIKTLEEIQRHLNYVDGVMVGREAYQNPSLLGYIDQALFDP---S 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I T       R+   +M  Y  + L  G  L  I RH++G F     +R+ R  ++  
Sbjct: 254 CAIITP------RQAIENMFPYIEQQLSQGVYLNHIARHLLGAFQQCKGARQWRRYMSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
              S A   +IE A   + E
Sbjct: 308 IHKSHAGVEVIEKALTFIEE 327


>gi|87122404|ref|ZP_01078285.1| hypothetical protein MED121_00605 [Marinomonas sp. MED121]
 gi|86162379|gb|EAQ63663.1| hypothetical protein MED121_00605 [Marinomonas sp. MED121]
          Length = 349

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 132/323 (40%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWT   YR FAR LT   LLYTEM+   A+L+GD  +  L F   E P+ALQ+GG+D 
Sbjct: 26  MLDWTTSDYRVFARALTTETLLYTEMVTTGALLKGDNPERFLRFEDIEHPIALQLGGSDA 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L + AK+ E FGY+E+NLN GCPS +V     GA LM +P+ V D + AM  A SIPV
Sbjct: 86  NALAQCAKLAEKFGYDEVNLNAGCPSYKVQHSLIGAILMAHPEKVKDAMKAMQDACSIPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+DDQ     +R+ +  +  +G     +HAR AIL GLSPK NR+IP L YD V
Sbjct: 146 TLKHRIGLDDQQDYSIVRDFIGDVATTGTQTFIVHARNAILAGLSPKQNREIPPLKYDFV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ PDL I +NGG++ + +    L  +DGVM+GR AY N  +L+ VD   S     
Sbjct: 206 YQLKKDFPDLEIIINGGIKTLDECEHHLKHLDGVMVGREAYNNPWILSQVD---SRLFDK 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              ++ R+      +   +   +    L++G +L  +TRH++G+F G P  ++ R  L+ 
Sbjct: 263 EDQVQDRI------QALRNFVPFVEHRLNNGERLSHLTRHIMGIFLGQPGGKQFRRYLSE 316

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           +     A+  +++ A +L+ E L
Sbjct: 317 QGHKKDASIDVLKQAIDLVTEQL 339


>gi|241662836|ref|YP_002981196.1| tRNA-dihydrouridine synthase A [Ralstonia pickettii 12D]
 gi|240864863|gb|ACS62524.1| TIM-barrel protein, yjbN family [Ralstonia pickettii 12D]
          Length = 346

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEFEHPVALQLGGSEPD 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++ + +GY EINLN GCPS RV  G+FGACLM  P +V   + AM  A+SIPVT
Sbjct: 80  DLAQAARLGQQWGYKEINLNCGCPSERVQRGAFGACLMAEPKLVAQGVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 140 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 200 QLKRDFPHLEILLNGGVQTLEQIDAHLAHVDGVMIGREAYHHPHLMAAFDARYYGAGT-E 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 259 APTRAEVED--------AMIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 308


>gi|296136585|ref|YP_003643827.1| TIM-barrel protein, yjbN family [Thiomonas intermedia K12]
 gi|295796707|gb|ADG31497.1| TIM-barrel protein, yjbN family [Thiomonas intermedia K12]
          Length = 349

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 185/298 (62%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T  ALLYTEM+   A+L GD    L +S+ E P+ALQ+GG++  
Sbjct: 10  MLDWTDRHCRYFHRLITQRALLYTEMVTTGALLYGDVARHLDYSSHEHPVALQLGGSEPV 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
            L   AK+  ++GY+EINLN GCPS RV  G+FGACLM  P  V D +AAM +A+S  IP
Sbjct: 70  DLARCAKLALEWGYDEINLNCGCPSPRVQRGAFGACLMAEPSRVRDSVAAMVEAVSGTIP 129

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIGVD +     +R+ V ++ + G     +HAR A L GLSPK+NR IP L  + 
Sbjct: 130 VTVKHRIGVDHEDSYGFVRDFVGTVSQGGCETFIVHARSAWLDGLSPKENRDIPPLRPEF 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           + +++++ P L   LNGG++   Q  + LP V GVM+GRAAY++   L+T D  F     
Sbjct: 190 ILQLRRDFPALAFVLNGGIKTEQQIREWLPQVSGVMVGRAAYQDPWSLSTWDREFLGSAD 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            ++P +  V++    ++ A +  +  + LH     Q ITRHM+ L+ G P  RR R +
Sbjct: 250 SAAPEREIVEE----QMGAYIAAWKVKGLHP----QAITRHMLNLWKGQPGGRRWRQV 299


>gi|332142739|ref|YP_004428477.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|332142839|ref|YP_004428577.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552761|gb|AEA99479.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552861|gb|AEA99579.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 348

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 124/298 (41%), Positives = 187/298 (62%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + LLYTEM+   AI+ G K + LG++ +E P+A+Q+GG+D S
Sbjct: 25  MLDWTDRHCRYFLRLMSKHTLLYTEMVTTGAIIYG-KGDYLGYNKEEHPIAVQLGGSDPS 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + + A++ ++ GY+E+N+NVGCPS RV  GSFGACLM  P++V +C+ AM  A+ IPVT
Sbjct: 84  DMAKCAELSQERGYDEVNINVGCPSDRVKNGSFGACLMAQPEVVANCVKAMQSAVDIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DD          + ++  +G +   +HARKA L+GLSPK+NR+IP L+Y  V+
Sbjct: 144 VKCRIGIDDMDEDEDFARFIDTVADAGCDTFIVHARKAWLQGLSPKENREIPPLNYPRVH 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG++ +++  + L SVDGVM+GR  Y N  ++++VD+         
Sbjct: 204 RLKQARPELSISINGGIKTLAETQQQLESVDGVMVGREVYANPYIMSSVDKDIFGDANAQ 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  +        R+I   M  Y  R      K     RH++GL+ G    R  R  L+
Sbjct: 264 SLSR--------REIVLQMQQYIERQEDPYFKPWHAARHILGLYQGQAGGRIWRRYLS 313


>gi|309782238|ref|ZP_07676967.1| tRNA-dihydrouridine synthase A [Ralstonia sp. 5_7_47FAA]
 gi|308919009|gb|EFP64677.1| tRNA-dihydrouridine synthase A [Ralstonia sp. 5_7_47FAA]
          Length = 346

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEFEHPVALQLGGSEPD 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++ + +GY EINLN GCPS RV  G+FGACLM  P +V   + AM  A+SIPVT
Sbjct: 80  DLAQAARLGQQWGYKEINLNCGCPSERVQRGAFGACLMAEPKLVAQGVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 140 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 200 QLKRDFPHLEILLNGGVQTLEQIDAHLAHVDGVMIGREAYHHPHLMAAFDARYYGAGT-E 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 259 APTRAEVED--------AMIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 308


>gi|313667754|ref|YP_004048038.1| dihydrouridine synthase [Neisseria lactamica ST-640]
 gi|313005216|emb|CBN86649.1| Putative dihydrouridine synthase [Neisseria lactamica 020-06]
          Length = 336

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 183/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK VE +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAVEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVHIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACRTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGITANEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|17546018|ref|NP_519420.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum GMI1000]
 gi|17428313|emb|CAD15001.1| putative trna-dihydrouridine synthase protein [Ralstonia
           solanacearum GMI1000]
          Length = 344

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 182/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 18  MMDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEAEHPVALQLGGSEPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V D + AM  A+SIPVT
Sbjct: 78  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADGVKAMRDAVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 138 VKHRIGIDAIETYDFVRDFVGAIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +       
Sbjct: 198 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMAGFDARYYG-ADAV 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+         +M DY  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 257 APTRAEVED--------AMIDYIGRWVARGGYAGAAVRHMLGLYRGVAGARGWRRVLS 306


>gi|330897594|gb|EGH29013.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 300

 Score =  255 bits (652), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 127/287 (44%), Positives = 183/287 (63%), Gaps = 9/287 (3%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  + L   +++ ++ G
Sbjct: 2   RKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAADLAACSRLAQEAG 61

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           Y+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVTVK RIG++ +   
Sbjct: 62  YDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVTVKHRIGINGRDSY 121

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + PDL I L
Sbjct: 122 AELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKSDFPDLEIVL 181

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           NGG++ + Q  + L + DGVM+GR AY N  +L  VD+        ++P+ +R D     
Sbjct: 182 NGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FGSTAPVISRYDA---- 234

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 235 --LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 279


>gi|293391683|ref|ZP_06636017.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952217|gb|EFE02336.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 327

 Score =  255 bits (652), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 131/318 (41%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WT RH R+F R  + +ALLYTEM+   AI+   K + L F   E+P+ALQ+GG+D +
Sbjct: 18  MLNWTTRHCRYFHRQFSRHALLYTEMVTTQAIIHA-KYDHLDFDPAEQPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E  GY EINLNVGCPS RV  G FGACLM   ++V +C+  M +A+ IPVT
Sbjct: 77  QLKHCAQLAEQRGYQEINLNVGCPSDRVQNGMFGACLMAKAELVAECVQQMQEAVRIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++++G     +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLCDFIEKVQQAGCREFIVHARKAWLSGLSPKQNREIPPLDYEQVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   N    +
Sbjct: 197 QLKRDFPHLLISINGGIKTIDEMQQHLQLVDGVMVGREAYQNPSLLGYIDQALFN---AN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+    M  Y  + L  G  L  I RH++  F     +R+ R  L+  
Sbjct: 254 APIVTP------REAVEKMLPYIEQQLSRGVYLNHIVRHILSAFQHCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++ETA   +
Sbjct: 308 AYKAGAGIEVVETALGFV 325


>gi|58580044|ref|YP_199060.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84622040|ref|YP_449412.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188578985|ref|YP_001915914.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|58424638|gb|AAW73675.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84365980|dbj|BAE67138.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188523437|gb|ACD61382.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 334

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +LGF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLLGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCTATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            + +E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLNQERPGLPVVLNGGIVAVDAAMAHLQHTDGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  ++  Y A  L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRALQPYVASQLAQGLALKHMTRHVLGLFHGQPGGRSFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALQ 323


>gi|219871369|ref|YP_002475744.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis SH0165]
 gi|219691573|gb|ACL32796.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis SH0165]
          Length = 323

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 137/318 (43%), Positives = 191/318 (60%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  T ++LLY+EMI A AIL   K ++L +   E P+ALQ+GG+D  
Sbjct: 15  MLDWTTRHCRYFHRQFTQHSLLYSEMITAPAILHA-KYDLLAYDPTENPVALQLGGSDPE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V  C+ AM K +SIPVT
Sbjct: 74  QLAKCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMGKADLVARCVEAMKKEVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKIQPY-CNDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG++ + +    L  VDGVM+GR AY+N ++L  +D    +P    
Sbjct: 193 QLKRDFPHLKMSINGGIKTIEEIKHHLQFVDGVMVGREAYQNPSLLGYIDRELFDPNAEI 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K  V+K         M  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 253 VTPKQAVEK---------MLPYIEQQLSQGVYLNHIVRHILGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A + +
Sbjct: 304 ACKQGAGVEVVEQALSFL 321


>gi|317403413|gb|EFV83926.1| hypothetical protein HMPREF0005_02052 [Achromobacter xylosoxidans
           C54]
          Length = 327

 Score =  255 bits (651), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 187/300 (62%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L G+    L F   E P+ALQ+GG++  
Sbjct: 1   MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLYGNVARHLDFDEAEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ + +GY+EINLN GCPS RV +G+FGACLM  PD+V DCI AM  A+ IPVT
Sbjct: 61  ALAQSARLGQQWGYDEINLNCGCPSERVQKGAFGACLMAEPDLVADCIKAMQDAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G      HAR A+LKGLSPKDNR+IP L YD+V 
Sbjct: 121 VKHRLGLDYDESYAFVRDFVGKIYDTGCRVFIAHARNAVLKGLSPKDNREIPPLRYDVVS 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV--DEYFSNPLT 238
           ++K++ PD    LNGGL D +Q+++     DGVM+GRAA+    +L+ V    + S  L 
Sbjct: 181 QLKRDFPDCVFVLNGGLADAAQSVRAAADFDGVMLGRAAWHTPRVLSEVSLQLWPSVRLP 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G +            ++  +M +YAAR +  G  L+ +TR M+GL +G   +RR R +L+
Sbjct: 241 GDA------------QVVDAMMEYAARQVAQGVPLRVMTRPMLGLVNGQSGARRWRRMLS 288


>gi|254786572|ref|YP_003074001.1| tRNA-dihydrouridine synthase A [Teredinibacter turnerae T7901]
 gi|237683391|gb|ACR10655.1| tRNA-dihydrouridine synthase A [Teredinibacter turnerae T7901]
          Length = 338

 Score =  255 bits (651), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 138/319 (43%), Positives = 193/319 (60%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M++W+DRH R+F RLLT NALLYTEM+   A+L   D +  L F+++E PLALQ+GG++ 
Sbjct: 19  MMEWSDRHCRYFWRLLTKNALLYTEMVTTGALLNNSDVERFLKFNSEEHPLALQLGGSNP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L   A + + +GY+E+NLN GCPS RV EG  GA LM  P++V  C++AM     IPV
Sbjct: 79  DELARCAAMAQQWGYDEVNLNCGCPSDRVQEGKIGAVLMTEPELVAQCVSAMQAECDIPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIGVDDQ     L+  VK + ++G     +HARKA LKGLSPK+NR IP L+Y+ V
Sbjct: 139 TVKHRIGVDDQDEYNDLQRFVKVVSEAGCKRFIVHARKAWLKGLSPKENRDIPPLNYERV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++K+E+  L I +NGG+  +SQ   +L  +DGVMIGR AY N  +L  VD      L G
Sbjct: 199 VQLKQEHTALDIVINGGITTLSQCSALLSQLDGVMIGREAYHNPYLLAGVDA----ELYG 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S  I   V +D           Y    + +G KL  ++RH++GL+ G   +R  R  +T 
Sbjct: 255 SDNIPP-VTRD---AALEQFVVYCREQIAAGQKLHHMSRHILGLYAGEYGARTFRRYITE 310

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A+  ++  A + M
Sbjct: 311 RANQPGASADVLLDARDAM 329


>gi|317968407|ref|ZP_07969797.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CB0205]
          Length = 332

 Score =  255 bits (651), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 136/325 (41%), Positives = 191/325 (58%), Gaps = 17/325 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D+TDRH+R   R ++  +LLYTEM+VA A+   ++++ ++ F   E P+ALQ+GG D 
Sbjct: 17  MMDYTDRHFRVLMRQISRRSLLYTEMVVAQALHHSERRDRLIDFDPIEHPIALQVGGDDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA+I  D GY+EINLNVGCPS +V +G FGACLM  P+ V  CI+AM +A  +PV
Sbjct: 77  VLLAEAARIAADRGYDEINLNVGCPSEKVQKGRFGACLMAEPEQVARCISAMAQASPLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+D++     L   V ++  +G     +HARKA L+GL PK NR IP L Y++V
Sbjct: 137 TVKHRIGIDERDSYGELLAFVDTVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLRYELV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
           +++K + P L I LNGGL ++S  L+ L +VDGVM+GRAAY +     TVD       S 
Sbjct: 197 HQLKADRPQLTIELNGGLLELSSCLEQLEAVDGVMVGRAAYDHPLRWATVDRDLFGDSSQ 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P+  +S             +   +  YA R   SGG+L  I RH++ +  G   +R  R 
Sbjct: 257 PVAKAS------------TVVRGLIPYAERWCGSGGRLWSIARHLVQVVEGVSGARHWRR 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L   AG   A   + E A   + E
Sbjct: 305 DLGQAAGQRDAGPEVFERAARQLEE 329


>gi|148241114|ref|YP_001226271.1| tRNA-dihydrouridine synthase A [Synechococcus sp. RCC307]
 gi|147849424|emb|CAK26918.1| tRNA-dihydrouridine synthase A [Synechococcus sp. RCC307]
          Length = 335

 Score =  255 bits (651), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 139/321 (43%), Positives = 198/321 (61%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R   R ++ +ALLYTEM+VA A+  G +  +LGF   EKP+ALQ+GG D +
Sbjct: 21  MMDYTDRHFRVVMRQVSRHALLYTEMVVAQALHHGRQDTLLGFDPLEKPIALQLGGDDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA++ E +GY+EINLNVGCPS +V +G FGACLM  P  V  C+ AM  A  +PVT
Sbjct: 81  LLAEAAELAERWGYDEINLNVGCPSPKVKKGRFGACLMAEPQQVARCVEAMGAACRLPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     L + V ++  +G     +HARKA L+GL PK NR +P L YD+V+
Sbjct: 141 VKHRIGIDERDSYDELLDFVDTVAAAGCQRFAVHARKAWLEGLDPKQNRTVPPLRYDLVH 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K++ P L + LNGGLE +S   + L +VDGVM+GRAAY +      VD E F +  + 
Sbjct: 201 ALKRDRPALIVELNGGLESLSACQEQLHAVDGVMVGRAAYAHPLQWNRVDQEIFGD--SN 258

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++PIK         ++   +  +A     SGG+L  I RH++ L  G   +R  R  L+V
Sbjct: 259 ATPIKA-------SEVLQGVLPHAEHWCSSGGRLWPIARHLVHLVEGVSGARYWRRQLSV 311

Query: 300 EAGASTATHHIIETAFNLMIE 320
           EA   +A   ++E A   + E
Sbjct: 312 EASDRSARPDVLERAMRQLQE 332


>gi|330942603|gb|EGH45179.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 299

 Score =  255 bits (651), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 125/281 (44%), Positives = 179/281 (63%), Gaps = 9/281 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+  R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDQPCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FGST 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHML 299


>gi|241766211|ref|ZP_04764111.1| TIM-barrel protein, yjbN family [Acidovorax delafieldii 2AN]
 gi|241363710|gb|EER59087.1| TIM-barrel protein, yjbN family [Acidovorax delafieldii 2AN]
          Length = 313

 Score =  255 bits (651), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 126/300 (42%), Positives = 185/300 (61%), Gaps = 12/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ + LLYTEM+   A++ GD +  L ++ +E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRYLHRLLSRHTLLYTEMVTTGALIHGDVERHLRYNAEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + IPVT
Sbjct: 61  DLAHCARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVQIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ + ++  +G     +HAR A LKGLSPK+NR++P L Y +V+
Sbjct: 121 VKHRIGIDKDESYGFVRDFIGTVAAAGCEVFIVHARNAWLKGLSPKENREVPPLRYAVVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
           ++K++ P L I +NGG++      + L  +DGVM+GR AY N   L   D  Y+  P   
Sbjct: 181 QLKRDFPHLTIAINGGIQTDDVVHEQLGHLDGVMVGREAYHNPWWLARWDALYYGAP--- 237

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILT 298
               ++ + +D    + A+M +Y AR   + G     I RHM+GL HG   SRR R + +
Sbjct: 238 ----ESSLTRD---DVEATMVEYMAREAAAHGTPWASIARHMLGLRHGLAGSRRWRQVWS 290


>gi|311695131|gb|ADP98004.1| tRNA-dihydrouridine synthase, TIM-barrel, YjbN [marine bacterium
           HP15]
          Length = 344

 Score =  254 bits (650), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 132/321 (41%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  HYR+ AR L+ + LLYTEM+   A++ GD    L     E PLALQ+GG+D  
Sbjct: 25  MMDWTTSHYRYLARQLSRHTLLYTEMVTTGALIHGDTARFLRHDEAEYPLALQLGGSDAG 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ + +G++E+NLNVGCPS RV     GACLM +PD V + + AM +A  +PVT
Sbjct: 85  ELAHCARLAQQYGFDEVNLNVGCPSDRVQNNMIGACLMGHPDKVAEGVRAMIEATDLPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     L   V+ + ++G     +HAR AIL+GLSPK+NR++P L YD VY
Sbjct: 145 VKHRIGIDGRESWDDLCEFVEKVSEAGCRTFIVHARIAILEGLSPKENREVPPLKYDWVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K + P L I +NGG++   +  + L   DGVM+GR AY N  +L  VD E+F      
Sbjct: 205 RLKAKYPHLEIIINGGIKTFGECHEHLRHTDGVMLGREAYHNPWLLAGVDPEFFGQ---- 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P++TR       +   +M  +    L  G  L  ++RH++GLFHG P  R+ R  ++ 
Sbjct: 261 AAPVETR------HQALRAMLPFIGSELERGVFLTHMSRHLLGLFHGQPGGRQFRRYISE 314

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A  S A   +IETA   + E
Sbjct: 315 NAHKSGAGLEVIETALEKVRE 335


>gi|78049674|ref|YP_365849.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78038104|emb|CAJ25849.1| putative dihydrouridine synthase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
          Length = 334

 Score =  254 bits (648), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDTAMAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P ++R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQSR------ESLLRAYQPYVESQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|134095593|ref|YP_001100668.1| tRNA-dihydrouridine synthase A [Herminiimonas arsenicoxydans]
 gi|133739496|emb|CAL62547.1| tRNA-dihydrouridine synthase A [Herminiimonas arsenicoxydans]
          Length = 338

 Score =  254 bits (648), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 185/298 (62%), Gaps = 1/298 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T +   YTEM+   A+L GD    L F+ +E P+ALQ+GG++ +
Sbjct: 16  MMDWTDRHCRMFHRQITRHTWFYTEMVTTGALLHGDVSRHLDFNHEEHPVALQLGGSEPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+ E +GY+EINLN GCPS RV +G+FGACLM    +V DC+ AM  A+ I VT
Sbjct: 76  DLAKSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMNEAALVADCVKAMRDAVQIDVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      +R+ V ++ ++G N   +HAR A+LKGLSPK+NR+IP L Y+  Y
Sbjct: 136 VKHRIGIDDIASYDFVRDFVGTVAEAGCNTFIVHARNAVLKGLSPKENREIPPLRYEFAY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +++    L  VDGVM+GR AY N  +++  D  +   +   
Sbjct: 196 QLKQDFPQLEIIINGGIKTLAEIDTHLVHVDGVMLGREAYHNPYLMSAFDARYYGDIAAP 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              + +V       I A +  +       G +L  ITRHM+GL  G PN+R  R  L+
Sbjct: 256 KS-RAQVLHAMLPYIRAQLELHGKSEKGGGLRLNSITRHMLGLMAGLPNARGFRQSLS 312


>gi|325928271|ref|ZP_08189474.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas perforans 91-118]
 gi|325541361|gb|EGD12900.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas perforans 91-118]
          Length = 334

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYTLFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDTAMAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P ++R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQSR------ESLLRAYQPYVESQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|294340713|emb|CAZ89105.1| tRNA-dihydrouridine synthase A [Thiomonas sp. 3As]
          Length = 352

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 185/298 (62%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T  ALLYTEM+   A+L GD    L +S+ E P+ALQ+GG++  
Sbjct: 10  MLDWTDRHCRYFHRLITRQALLYTEMVTTGALLYGDVARHLDYSSHEHPVALQLGGSEPV 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
            L   A++  ++GY+EINLN GCPS RV  G+FGACLM  P  V D +AAM +A+S  IP
Sbjct: 70  DLACCARLALEWGYDEINLNCGCPSPRVQRGAFGACLMAEPSRVRDSVAAMVEAVSGTIP 129

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIGVD +     +R+ V ++ + G     +HAR A L GLSPK+NR IP L  + 
Sbjct: 130 VTVKHRIGVDHEDSYGFVRDFVGTVSQGGCETFIVHARSAWLDGLSPKENRDIPPLRPEF 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           + +++++ P L   LNGG++   Q  + LP V GVM+GRAAY++   L T D  F     
Sbjct: 190 ILQLRRDFPALAFVLNGGIKTGQQIGEWLPQVSGVMVGRAAYQDPWSLATWDREFLGSAD 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            ++P +  V++    ++ A +  + A+ LH     Q ITRHM+ L+ G P  RR R +
Sbjct: 250 SAAPEREIVEE----QMGAYIAAWKAKGLHP----QAITRHMLNLWKGQPGGRRWRQV 299


>gi|319788129|ref|YP_004147604.1| TIM-barrel protein, yjbN family [Pseudoxanthomonas suwonensis 11-1]
 gi|317466641|gb|ADV28373.1| TIM-barrel protein, yjbN family [Pseudoxanthomonas suwonensis 11-1]
          Length = 337

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 134/328 (40%), Positives = 192/328 (58%), Gaps = 18/328 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +LGF   E P+ALQ+GG++  
Sbjct: 19  MMDWTDRHCRVFHRLLAPHARLYTEMVHANAVVLGDRGRLLGFDPVEHPVALQLGGSEPG 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---- 116
            L  A +I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM +  +    
Sbjct: 79  ALANATRIGAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPSLVAECVAAMIEGAAASGR 138

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVTVKCR+GVD+          + ++  +G     +HAR A L+GLSPK+NR++P L 
Sbjct: 139 NVPVTVKCRLGVDEDHEYERFAAFIDAVAAAGCRTFVVHARNAWLQGLSPKENREVPPLR 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFS 234
           YD  + +K+E P L I +NGG+   +Q  + L  VDGVM+GRAAY +  +L  +D   + 
Sbjct: 199 YDWAWRLKRERPGLEILVNGGIASEAQVHEQLAHVDGVMLGRAAYHDPYLLHRLDVALYG 258

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             L   + +  R            +  Y    L SG  L+ ITRH++GLFHG P  R  R
Sbjct: 259 GELADRASLLRR------------LRPYVEAQLASGLALKHITRHVLGLFHGQPGGRLFR 306

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
            +L+  A    A   ++E A +    +L
Sbjct: 307 QVLSEGAHRPGAGWDLVEQALDATAGAL 334


>gi|325134929|gb|EGC57561.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M13399]
          Length = 336

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEVYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|238027482|ref|YP_002911713.1| dihydrouridine synthase [Burkholderia glumae BGR1]
 gi|237876676|gb|ACR29009.1| Dihydrouridine synthase [Burkholderia glumae BGR1]
          Length = 336

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 126/298 (42%), Positives = 182/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R ++ +  LYTEM+   A++ GD    L F+  E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRSLHRTISRHTWLYTEMVTTGALMHGDVARHLAFTPDEAPVALQLGGSEPD 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 80  DLAKSARLGENWGYDEINLNCGCPSERVQRGAFGACLMNEPGLVADCVKAMRDAVSVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 140 VKHRIGVDAVEEYAFVRDFVGTVAQAGCDVFIVHARNAILKGLSPKENREIPPLKYDYAY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG+  + +    L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 200 RLKQDFPDLEIIINGGITTLDEVEAHLQHVDGVMLGREAYHNPFVLAEVDRRFYGA-AAA 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  +++         +  Y    +  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 259 APTREEIEE--------RLIAYCVAEIARGTYLGAIVRHALGLYRGVHGARGWRRVLS 308


>gi|330816761|ref|YP_004360466.1| Dihydrouridine synthase [Burkholderia gladioli BSR3]
 gi|327369154|gb|AEA60510.1| Dihydrouridine synthase [Burkholderia gladioli BSR3]
          Length = 345

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 180/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R ++ +  LYTEM+   A+L GD    L F  +E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRSLHRSISRHTWLYTEMVTTGALLHGDVARHLAFMPEEAPVALQLGGSEPE 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 80  DLAKSARLGENWGYDEINLNCGCPSERVQRGAFGACLMNEPALVADCVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 140 VKHRIGVDAVEDYAFVRDFVGTVAEAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG+  + +    L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 200 RLKQDFPDLEILINGGITTLDEVETHLQHVDGVMLGREAYHNPFVLAEVDARFYG---AA 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P  TR       +I   +  Y    +  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 257 RPAPTR------EEIEDRLIAYCIDEVARGNYLGAIVRHALGLYRGVHGARGWRRVLS 308


>gi|294666631|ref|ZP_06731869.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292603598|gb|EFF47011.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 334

 Score =  253 bits (646), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPGLVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYTLFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDPAIAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRAYQPYVESRLAQGVGLKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A  S A   ++E A  
Sbjct: 308 AHRSGAGWELVEQALE 323


>gi|33860574|ref|NP_892135.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|33633516|emb|CAE18473.1| conserved hypothetical protein [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
          Length = 334

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 131/302 (43%), Positives = 188/302 (62%), Gaps = 10/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  DKK   L F+++E PL++Q GG + 
Sbjct: 20  MMDCTDKHFRMIIRKISSKALLYTEMIVAQSLIYTDKKERFLDFNSEEHPLSIQFGGDNP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAAK+ +D+GY+EIN NVGCPS RV  G+FGA LM  P  V  CI ++    S+PV
Sbjct: 80  KMLEEAAKMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKEPIKVAKCIESLKNNCSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD++     L + VK I  +G +   +HARKAILKGL+PK NR IP L YD+V
Sbjct: 140 TIKHRIGVDEEDSFDKLDSFVKEIANAGADRFTVHARKAILKGLNPKQNRTIPPLKYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++KK NP L I +NGG  ++ Q ++ L  +DGVMIGR+AYK     + +D+      T 
Sbjct: 200 RKLKKNNPKLIIEINGGFTNIDQCIEALNDLDGVMIGRSAYKYPLRWSEIDQKIYGESTK 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S             +I  S+  Y  +HL + GK   I +H+I L  G PN++  R+ ++ 
Sbjct: 260 SKKAS---------EIIFSLVPYIEKHLKNEGKTWDICKHLINLVEGIPNAKVWRNEIST 310

Query: 300 EA 301
           ++
Sbjct: 311 KS 312


>gi|229512584|ref|ZP_04402054.1| tRNA dihydrouridine synthase A [Vibrio cholerae TMA 21]
 gi|229350366|gb|EEO15316.1| tRNA dihydrouridine synthase A [Vibrio cholerae TMA 21]
          Length = 315

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 133/305 (43%), Positives = 183/305 (60%), Gaps = 11/305 (3%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RLL+   LLYTEM+   AI+ G + + L ++ +E P+ALQ GG++   L   AK+ ++
Sbjct: 11  FHRLLSAQTLLYTEMVTTGAIIHG-RGDFLAYNQEEHPVALQFGGSNPKDLAHCAKLAQE 69

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVTVK RIG+DDQ 
Sbjct: 70  RGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVTVKTRIGIDDQD 129

Query: 132 PAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
               L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   Y+IK++ P L 
Sbjct: 130 SYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRAYQIKRDFPHLT 189

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+         +P+K R    
Sbjct: 190 IAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQI---FGLETPVKKR---- 242

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
              ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++  A    A   +
Sbjct: 243 --SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISENAHKPGAGLEV 300

Query: 311 IETAF 315
           +E A 
Sbjct: 301 VEQAL 305


>gi|320335164|ref|YP_004171875.1| TIM-barrel protein, yjbN family [Deinococcus maricopensis DSM
           21211]
 gi|319756453|gb|ADV68210.1| TIM-barrel protein, yjbN family [Deinococcus maricopensis DSM
           21211]
          Length = 340

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 179/301 (59%), Gaps = 9/301 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RL+T + LLYTEMI   AIL GD+   L FS QE P+ALQ+GG+D  
Sbjct: 17  MLDWTDRHCRAFHRLITRHTLLYTEMITTGAILHGDEARHLSFSPQEHPVALQLGGSDPV 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+  E +GY E+NLNVGCPS RV  G FGACLM  PD+V   + AM  A  +PVT
Sbjct: 77  ALAECARRAEGYGYAEVNLNVGCPSDRVQNGRFGACLMATPDVVARGVEAMRGATGLPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+++  +G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 137 VKHRIGIDDLDSYELLTAFVRTVADAGCETFIVHARKAWLSGLSPKENREIPPLRYEVVR 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L   LNGG++ + +A   L SVDGVMIGR AY N  +L   D         +
Sbjct: 197 QLKMDFPQLTFVLNGGVKSLDEAETHLRSVDGVMIGREAYGNPYLLALADARL---FGDA 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + TR      R++   +  YA   L     L ++T+H +GLF G   +R  +  ++  
Sbjct: 254 HVVPTR------REVVEGLIGYAEEMLARDVYLSRVTKHALGLFAGQAGARGWKRTISER 307

Query: 301 A 301
           A
Sbjct: 308 A 308


>gi|331006974|ref|ZP_08330216.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC1989]
 gi|330419221|gb|EGG93645.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC1989]
          Length = 310

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 125/307 (40%), Positives = 181/307 (58%), Gaps = 9/307 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+  RL++ ++ LYTEM+   A+L  +    L ++ +E PLALQ+GG+D  
Sbjct: 1   MMDWSDRHCRYLWRLISQHSRLYTEMVTTGALLHREPARFLDYNPEEHPLALQLGGSDAG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A + E +GY E+NLN GCPS RV  G  GACLM +P+ V D   AM   + I VT
Sbjct: 61  DLARCAILAEQWGYYEVNLNCGCPSDRVQNGMIGACLMAHPEKVADAYQAMQDKVDIEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD      + N ++ I   G     +HARKA LKGLSPK+NR++P L+Y  V+
Sbjct: 121 IKHRIGIDDMDDYEGMVNFIRPIAARGCQTFIVHARKAWLKGLSPKENREVPPLEYAFVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++ +   L  L  VDGVM+GR AY N  +L  VD++       S
Sbjct: 181 RLKQEFPELTIVINGGIKTLDDTLMHLTKVDGVMVGREAYSNPYLLAEVDQHV---FGDS 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            PI +R        I+    DY  + +  G +L  ++RH++GL+ G P +R  R  ++  
Sbjct: 238 HPIPSRT------AIAEQYIDYCVKQMDKGSRLNHLSRHILGLYQGEPGARAFRRHISEN 291

Query: 301 AGASTAT 307
           A    AT
Sbjct: 292 AHRDNAT 298


>gi|126695351|ref|YP_001090237.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9301]
 gi|126542394|gb|ABO16636.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9301]
          Length = 334

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 132/304 (43%), Positives = 193/304 (63%), Gaps = 14/304 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  DKK   L F+++E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKISSEALLYTEMIVAQSLVYTDKKEYFLDFNSEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS RV  G+FGA LM +P+ V  CI ++    ++PV
Sbjct: 80  KILKEAAQMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKDPEKVAKCIESLKNNCNLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L+YD+V
Sbjct: 140 TIKHRIGVDNDDSFVNLNNFVRIIANAGADRFTVHARKAILKGLNPKQNRTIPPLNYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPL 237
            ++KK NP+L I +NGGL ++ Q+LK L   DGVMIGR+ YK+    + +D+  Y  N  
Sbjct: 200 KKLKKSNPELLIEINGGLTNIDQSLKALNDFDGVMIGRSIYKHPLRWSEIDQKIYGINKK 259

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             S+             I  S+  Y   H+ +GGK   I +H+I L  G P ++  R+ +
Sbjct: 260 NKSA-----------SNIIFSLIPYIEAHISNGGKSWDICKHLINLVEGIPKAKIWRNQI 308

Query: 298 TVEA 301
           + ++
Sbjct: 309 SKKS 312


>gi|89900729|ref|YP_523200.1| tRNA-dihydrouridine synthase A [Rhodoferax ferrireducens T118]
 gi|89345466|gb|ABD69669.1| TIM-barrel protein, yjbN family [Rhodoferax ferrireducens T118]
          Length = 331

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 130/299 (43%), Positives = 184/299 (61%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT +ALLYTEM+   A++ GD    L ++ QE P+ALQ+GG++ +
Sbjct: 19  MLDWTDRHCRYFHRLLTQHALLYTEMVTTGALIYGDVSRHLRYNEQEHPVALQLGGSEPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E++GY+E+NLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 79  DLARCAKLGEEWGYDEVNLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMVDVVSVPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V S+ ++G     +HAR A LKGLSPK+NR +P L Y++ Y
Sbjct: 139 VKHRIGIDKTESYEFVRDFVGSVSEAGCRTFIVHARNAWLKGLSPKENRDVPPLRYELAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+   +Q    L  +DGVM+GR AY N   L + D  F     G+
Sbjct: 199 QLKRDFPSLVIVINGGITSSAQIAGHLLHLDGVMLGREAYHNPWWLASWDATF----FGA 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              +T  +     ++   M DY  R     G     + RHM+GL HG P +R  R + +
Sbjct: 255 DATETTRE-----QVEQQMCDYMTREAAEHGTPWPTMARHMLGLRHGLPGARHWRQVWS 308


>gi|289666419|ref|ZP_06488000.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           vasculorum NCPPB702]
 gi|289669253|ref|ZP_06490328.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 334

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 136/316 (43%), Positives = 189/316 (59%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDVVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSP++NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDHAVFAGFVDQVVAAGAAMVVVHARNAWLKGLSPRENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  AL  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGITAVDTALAHLQHTDGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 QPEQPR------ESLLRAFRPYVESQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A        ++E A  
Sbjct: 308 AHRPGVGWQLVEQALQ 323


>gi|330825043|ref|YP_004388346.1| TIM-barrel protein, yjbN family [Alicycliphilus denitrificans K601]
 gi|329310415|gb|AEB84830.1| TIM-barrel protein, yjbN family [Alicycliphilus denitrificans K601]
          Length = 316

 Score =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 8/298 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   RLL+ +ALLYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 6   MMDWTDRHCRHLHRLLSRHALLYTEMVTTGALLHGDVPRHLRFGEAEHPVALQLGGSEPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 66  DLAHSARLGAQWGYDEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDVVDMPVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++  
Sbjct: 126 VKHRIGIDQTEDYGFVRDFVGTVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYEVAA 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NG L+  +  L+ L  VDGVM+GR AY N   LT  DE F     G+
Sbjct: 186 RLKSDFPQLTIAINGSLQTDAAVLEQLALVDGVMVGREAYHNPWWLTRWDELFFGAKPGT 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              + +V+++    + A M   AA H   G     + RHM+GL +G P +RR R + +
Sbjct: 246 L-TREQVEEE----MVAYMEREAAAH---GTHWYAVARHMLGLRNGLPGARRWRQVWS 295


>gi|319762963|ref|YP_004126900.1| tim-barrel protein, yjbn family [Alicycliphilus denitrificans BC]
 gi|317117524|gb|ADV00013.1| TIM-barrel protein, yjbN family [Alicycliphilus denitrificans BC]
          Length = 316

 Score =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 8/298 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   RLL+ +ALLYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 6   MMDWTDRHCRHLHRLLSRHALLYTEMVTTGALLHGDVPRHLRFGEAEHPVALQLGGSEPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 66  DLAHSARLGAQWGYDEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDVVDMPVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++  
Sbjct: 126 VKHRIGIDQTEGYGFVRDFVGTVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYEVAA 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NG L+  +  L+ L  VDGVM+GR AY N   LT  DE F     G+
Sbjct: 186 RLKSDFPQLTIAINGSLQTDAAVLEQLALVDGVMVGREAYHNPWWLTRWDELFFGAKPGT 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              + +V+++    + A M   AA H   G     + RHM+GL +G P +RR R + +
Sbjct: 246 L-TREQVEEE----MVAYMEREAAAH---GTHWYAVARHMLGLRNGLPGARRWRQVWS 295


>gi|304319794|ref|YP_003853437.1| NifR3/Smm1 family protein [Parvularcula bermudensis HTCC2503]
 gi|303298697|gb|ADM08296.1| NifR3/Smm1 family protein [Parvularcula bermudensis HTCC2503]
          Length = 335

 Score =  252 bits (643), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 138/307 (44%), Positives = 186/307 (60%), Gaps = 14/307 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR+ R+  RLL+  A LYTEM+V +AIL GD+  +LGF + E P+ALQIGG+D  
Sbjct: 17  MIDWTDRYCRWVHRLLSAKARLYTEMVVDEAILHGDRDRLLGFDSAEHPVALQIGGSDPR 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL E A I    GY+EINLNVGCPS RV  G FGACLM  P+ V + + AM  A+   VT
Sbjct: 77  KLAEVAAIGAQAGYDEINLNVGCPSDRVQSGRFGACLMAEPETVAEGVRAMAAAVPCEVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL   + +++ +GV  + +HARKA L+GLSPK+NR IP LDYD+V 
Sbjct: 137 VKCRIGIDDQSPEEALPRFLDAVEAAGVRTVIVHARKAWLEGLSPKENRTIPPLDYDLVV 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
              +  P L   LNGGL   + A + L +  GVM+GRAAY+   +L+ VD+  F  P   
Sbjct: 197 REAQRRPALSFILNGGLAGGAAAERWLTTFPGVMLGRAAYEQPFLLSEVDQRLFGAPPAA 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            S ++              +   A R       + +  RHM+GL+HG P ++  R  L+ 
Sbjct: 257 RSRLEI-------------VEAVADRAAAEAVPIWRYARHMLGLYHGQPGAKTWRRQLSE 303

Query: 300 EAGASTA 306
           E  ++ A
Sbjct: 304 EGRSAKA 310


>gi|21244742|ref|NP_644324.1| tRNA-dihydrouridine synthase A [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|38604924|sp|Q8PFF8|DUSA_XANAC RecName: Full=tRNA-dihydrouridine synthase A
 gi|21110436|gb|AAM38860.1| conserved hypothetical protein [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 334

 Score =  252 bits (643), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 190/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDPVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVEPAIAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRAYQPYVESQLAQGLGLKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|285017064|ref|YP_003374775.1| tRNA-dihydrouridine synthase a protein [Xanthomonas albilineans GPE
           PC73]
 gi|283472282|emb|CBA14788.1| probable trna-dihydrouridine synthase a protein [Xanthomonas
           albilineans]
          Length = 328

 Score =  252 bits (643), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 142/317 (44%), Positives = 197/317 (62%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +L +   E PLALQ+GG+D +
Sbjct: 14  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVVLGDRARLLDYDAAEHPLALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I +D+GY+EINLN GCPS RV  G FGACLM  P +V +C+AAM  A+ +PVT
Sbjct: 74  LLAQAARIGQDWGYDEINLNCGCPSDRVQAGRFGACLMREPGLVAECVAAMAAAVDVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD      A    V  +  +G     +HAR A L+GLSPK+NR++P L YD VY
Sbjct: 134 VKCRLGVDQDNDEAAFLAFVDHVAAAGCRQFVVHARNAWLQGLSPKENREVPPLRYDWVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGGL ++  A      VDGVM+GRAAY +  +L  +D      LTG+
Sbjct: 194 RLKRERPQLQVVLNGGLANVETAQAQFVVVDGVMLGRAAYHDPYVLHRLDA----ALTGA 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + ++ R +      +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +L+  
Sbjct: 250 A-LRPRAE------LLRALRPYVEVRLAEGLALKHIARHLLGLFHGQPGGRAFRQVLSEG 302

Query: 301 AGASTATHHIIETAFNL 317
           A  S A   ++E A  +
Sbjct: 303 AHRSGADWALLEQALQV 319


>gi|322515077|ref|ZP_08068085.1| tRNA dihydrouridine synthase A [Actinobacillus ureae ATCC 25976]
 gi|322118957|gb|EFX91134.1| tRNA dihydrouridine synthase A [Actinobacillus ureae ATCC 25976]
          Length = 323

 Score =  252 bits (643), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 136/318 (42%), Positives = 189/318 (59%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+   K ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQHALLYTEMITAPAIIHA-KYDLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   ++V DCI AM   + IPVT
Sbjct: 74  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKANLVADCIKAMQDTVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D   S     +
Sbjct: 193 QLKRDFPHLNISINGGIKTVDEIKQHLVFVDGVMVGREAYQNPSLLGEID---SQIFGEN 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y       G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 RPLVTA------REAVEKMLPYIEAQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A + +
Sbjct: 304 ATKQGAGVEVVEQALSFV 321


>gi|152996532|ref|YP_001341367.1| tRNA-dihydrouridine synthase A [Marinomonas sp. MWYL1]
 gi|150837456|gb|ABR71432.1| TIM-barrel protein, yjbN family [Marinomonas sp. MWYL1]
          Length = 341

 Score =  251 bits (642), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 133/319 (41%), Positives = 192/319 (60%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWT   YR FAR L+ N LLYTEM+   A+L+G+  +  L +   E P+ALQ+GG+D 
Sbjct: 25  MMDWTTSDYRVFARTLSKNTLLYTEMVTTGALLQGNHPERFLRYDECEHPIALQLGGSDA 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L + AK+ E  G++E+NLNVGCPS RV     GACLM +PD V + + AM    SIPV
Sbjct: 85  VALGKCAKMAEQAGFDEVNLNVGCPSDRVQNSLIGACLMAHPDKVKEAMRAMQDNCSIPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+DDQ     +R+ V  +  +GV    +HAR AIL+GLSPK+NR++P L Y  V
Sbjct: 145 TIKHRIGLDDQEDYSVVRDFVGDVATTGVTTFIVHARNAILEGLSPKENREVPPLKYHYV 204

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++KK+ PDL I +NGG++ + +  + L  VDGVM+GR AY N  +L+ VDE     L G
Sbjct: 205 HQLKKDFPDLEIIINGGIKTLDECKEQLAHVDGVMVGREAYHNPWILSQVDEV----LFG 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+      D +  + A    Y  R L  G +L  +TRH++G+F G    ++ R  L+ 
Sbjct: 261 GQPLVN----DRYEALEA-FVPYVERKLQEGERLMHLTRHILGIFQGEAGGKQFRRYLSE 315

Query: 300 EAGASTATHHIIETAFNLM 318
               + A  +++  A  L+
Sbjct: 316 NGHKADAQVNVLLEAIELV 334


>gi|325130878|gb|EGC53608.1| tRNA dihydrouridine synthase A [Neisseria meningitidis OX99.30304]
          Length = 336

 Score =  251 bits (641), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 138/301 (45%), Positives = 185/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPDLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYG--DT 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YSDLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|294626706|ref|ZP_06705301.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292598954|gb|EFF43096.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 334

 Score =  251 bits (641), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 190/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPGLVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYTLFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDPAIAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRAYQPYVESRLAQGVGLKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|254526125|ref|ZP_05138177.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
 gi|221537549|gb|EEE40002.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
          Length = 334

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 135/325 (41%), Positives = 196/325 (60%), Gaps = 21/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +T+ ALLYTEMIVA +++   KK   L F+++E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKITSKALLYTEMIVAQSLVYTKKKEKFLDFNSEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS +V  G+FGA LM +P+ V  C+ ++    S+PV
Sbjct: 80  KILKEAARMAQDWGYDEINFNVGCPSPKVCSGNFGASLMKDPEKVAKCMESLKNNCSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+D+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L+YDIV
Sbjct: 140 TIKHRIGLDNNDSFVTLNNFVRVIANAGADRFTVHARKAILKGLNPKQNRTIPPLNYDIV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
            ++KK NP+L I +NGGL +++++LK L   DGVMIGR+ Y++    + +D+      + 
Sbjct: 200 KKLKKSNPELLIEINGGLANINESLKALNDFDGVMIGRSVYQHPLRWSEIDQKIYGINTK 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P + S              I  S+  Y   HL  GGK   I +H+I L  G P ++  R+
Sbjct: 260 PKSASD-------------IIFSLIPYIEAHLSKGGKSWDICKHLINLVEGIPKAKIWRN 306

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            ++     S      IE  F L  E
Sbjct: 307 QIS---NKSIKKELNIEYLFKLTTE 328


>gi|33239466|ref|NP_874408.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33236991|gb|AAP99060.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
          Length = 333

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 136/314 (43%), Positives = 188/314 (59%), Gaps = 9/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   R +T  AL+YTEMIVA A+   ++K++L F   E P+ALQ+GG D  
Sbjct: 20  MLDCTDRHFRVLMRQITGRALVYTEMIVAKALKYKNRKSLLDFDEIEHPIALQVGGDDPI 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E++GY+EINLN+GCPS +V  G+FGACLM  PD V  CI AM K  +IPVT
Sbjct: 80  VLSEAAQIAEEWGYDEINLNLGCPSPKVQSGNFGACLMGQPDQVFKCIEAMKKKTNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G+D+      L + V  +  +G +   IHARKA+L G + K+NR IP L+Y+ V 
Sbjct: 140 IKHRTGIDNLDSEQLLLDFVDKMASAGADRFSIHARKALLNGFNAKENRSIPPLEYEKVA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IKK  P+L I LNGGL++    +K L + DGVM+GRA Y N  M   +D+ F     G 
Sbjct: 200 KIKKCRPNLKIELNGGLQNQYDCIKALKTFDGVMVGRAIYSNPLMWKEIDDIF----FGE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +K          I   +  YA +HL   G+L  I +H + L  G   +R+ R+ L+ +
Sbjct: 256 KKVKINAS-----IILRGLIPYAEKHLSKNGRLWDICKHTLHLVQGVKGARKWRNELSQK 310

Query: 301 AGASTATHHIIETA 314
           A    A   I+E A
Sbjct: 311 AQNPKAELIILEKA 324


>gi|157412352|ref|YP_001483218.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9215]
 gi|157386927|gb|ABV49632.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9215]
          Length = 334

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 135/325 (41%), Positives = 197/325 (60%), Gaps = 21/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +T+ ALLYTEMIVA +++   KK   L F+++E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKITSKALLYTEMIVAQSLVYTKKKEKFLDFNSEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS +V  G+FGA LM +P+ V  C+ ++    S+PV
Sbjct: 80  KILKEAARMAQDWGYDEINFNVGCPSPKVCSGNFGASLMKDPEKVAKCMESLKNNSSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+D+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L+YDIV
Sbjct: 140 TIKHRIGLDNDDSFVTLNNFVRVIANAGADRFTVHARKAILKGLNPKQNRTIPPLNYDIV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
            ++KK NP+L I +NGGL +++++LK L   DGVMIGR+ Y++    + +D+      + 
Sbjct: 200 KKLKKSNPELLIEINGGLANINESLKALNDFDGVMIGRSVYQHPLRWSEIDQKIYGINTR 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P + S              I  S+  Y   HL  GGK   I +H+I L  G P ++  R+
Sbjct: 260 PKSASD-------------IIFSLIPYIEAHLSKGGKSWDICKHLINLVEGIPKAKIWRN 306

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            ++ +   S      IE  F L  E
Sbjct: 307 QISKK---SIKKELSIEYLFKLTTE 328


>gi|293604638|ref|ZP_06687040.1| tRNA dihydrouridine synthase A [Achromobacter piechaudii ATCC
           43553]
 gi|292816969|gb|EFF76048.1| tRNA dihydrouridine synthase A [Achromobacter piechaudii ATCC
           43553]
          Length = 326

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 136/315 (43%), Positives = 188/315 (59%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RLL   A LYTEMI   A+  G+    L F   E P+ALQ+GG++  
Sbjct: 1   MIDVTDRHCRFFHRLLAPRARLYTEMITTGALQHGNIPRHLDFDEAEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+   +GY+EINLN GCPS RV +G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 61  ALAQSAKLGRQWGYDEINLNCGCPSERVQKGAFGACLMAEPALVADCMKAMQDAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D +     +R+ V  I  +G      HAR A+LKGLSPKDNR+IP L YD+V 
Sbjct: 121 VKHRLGLDYENSYSFVRDFVGKIYDTGCRVFIAHARNAVLKGLSPKDNREIPPLRYDVVK 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD    LNGGL D  Q++      DGVM+GRAA+    +L+ V           
Sbjct: 181 QLKQDFPDCTFVLNGGLADADQSVSAADEFDGVMLGRAAWHTPRVLSEVSLRLWP----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                R+  D   ++  +MT+YAAR +  G  L+ +TR M+GL +G   +RR R +L+  
Sbjct: 236 ---SVRLPSDA--QVVDAMTEYAARQVAKGVPLRVMTRPMLGLVNGQSGARRWRRMLSDP 290

Query: 301 AGASTATHHIIETAF 315
           A  +     +I  A+
Sbjct: 291 ALLAANNPELIYDAW 305


>gi|116074290|ref|ZP_01471552.1| hypothetical protein RS9916_37607 [Synechococcus sp. RS9916]
 gi|116069595|gb|EAU75347.1| hypothetical protein RS9916_37607 [Synechococcus sp. RS9916]
          Length = 334

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 135/327 (41%), Positives = 188/327 (57%), Gaps = 20/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+   +++  +L F   E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISTRALLYSEMVVAQALHHTNRRERLLDFDPVEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++  D+GY+EINLNVGCPS RV  G+FGACLM  PD V  C+ AM +A  +PV
Sbjct: 80  VLLAEAAQMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPDRVARCVEAMGQASRLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D       L+  V  +  +G     +HARKA L+GL PK NR IP L YD V
Sbjct: 140 TVKHRVGIDHLDSDALLQAFVDRVAAAGATRFAVHARKAWLEGLDPKQNRTIPPLQYDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P+L I LNGGL+   Q L+ L S DG M+GRAAY +      +DE        
Sbjct: 200 IALKQRRPELTIELNGGLDTPDQCLEALESCDGAMVGRAAYAHPLRWGCIDE-------- 251

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 R+  +  R ++AS     +  YA  HL  GG+L  + RH++ L  G P +R  R
Sbjct: 252 ------RIYGEAARTVTASDVVLGLIPYAQAHLARGGRLWDLCRHLVQLVEGVPGARHWR 305

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             L + A    A   ++E A   ++++
Sbjct: 306 RNLGLNAQRQGADIPVLEDAARQLLDA 332


>gi|149376568|ref|ZP_01894328.1| tRNA-dihydrouridine synthase A [Marinobacter algicola DG893]
 gi|149359086|gb|EDM47550.1| tRNA-dihydrouridine synthase A [Marinobacter algicola DG893]
          Length = 320

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 130/316 (41%), Positives = 184/316 (58%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  HYR+ AR L+ + LLYTEM+   A++ GD    L     E PLALQ+GG++  
Sbjct: 1   MMDWTTSHYRYLARQLSRHTLLYTEMVTTGALIHGDTARFLRHDPTEYPLALQLGGSNPQ 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A + E +G++E+NLNVGCPS RV     GACLM +PD V + + AM  A S+PVT
Sbjct: 61  ELAHCANLAEQYGFDEVNLNVGCPSDRVQNNMIGACLMAHPDKVAEGVQAMIAATSLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     L   ++ + ++G     +HAR A+L+GLSPK+NR IP L YD VY
Sbjct: 121 VKHRIGIDGRESWDDLCEFIEKVSEAGCRTFIVHARIAVLEGLSPKENRDIPPLKYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K   P L I +NGG++  ++  + L   DGVM+GR AY N  +L  VD E+F  P+  
Sbjct: 181 RLKARYPHLEIIINGGIKTFAECREHLEHTDGVMLGREAYHNPWLLAGVDTEFFGRPM-- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PI +R D         ++  +    L  G  L  I+RH++GLFHG P  R+ R  ++ 
Sbjct: 239 --PISSRHDA------LRAVLPFIQSELDRGVYLSHISRHLMGLFHGQPGGRQFRRYISE 290

Query: 300 EAGASTATHHIIETAF 315
            A    +   +IE A 
Sbjct: 291 NAHKPGSGIEVIEQAM 306


>gi|213859447|ref|ZP_03385151.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 284

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 129/275 (46%), Positives = 175/275 (63%), Gaps = 13/275 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            + P+           +  +M  Y  R L  G  L
Sbjct: 259 DTDPV----------AVVRAMYPYIERELSQGAYL 283


>gi|123965248|ref|YP_001010329.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9515]
 gi|123199614|gb|ABM71222.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9515]
          Length = 334

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 184/300 (61%), Gaps = 12/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  DKK   L F+ +E PL++Q GG + 
Sbjct: 20  MMDCTDKHFRMIIRQISSKALLYTEMIVAQSLVYTDKKEKFLNFNKEEHPLSIQFGGDNP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAAK+ +D+GY+EIN NVGCPS RV  G+FGA LM  P  V  CI ++    ++P+
Sbjct: 80  QMLKEAAKMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKEPAKVAKCIESLKNNCNLPI 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD++     L   VK +  +G     +HARKAILKGL+PK NR IP L YD+V
Sbjct: 140 TIKHRIGVDEEDSFDQLNTFVKEVANAGAERFTVHARKAILKGLNPKQNRTIPPLRYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
            ++K+ NP L I +NGG  ++ Q +K L  +DGVMIGR+ YK     + +D + +   +T
Sbjct: 200 QKLKENNPQLLIEINGGFTNIDQCIKALERLDGVMIGRSVYKYPLRWSQIDNKIYGKNIT 259

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             S            +I  S+  Y   HL +GGK   I +H+I L  G PN++  R+ ++
Sbjct: 260 SKSA----------SEIIFSLIPYIENHLQNGGKTWDICKHLINLVEGIPNAKIWRNQIS 309


>gi|78778399|ref|YP_396511.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9312]
 gi|78711898|gb|ABB49075.1| tRNA-U16,U17-dihydrouridine synthase [Prochlorococcus marinus str.
           MIT 9312]
          Length = 334

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 128/306 (41%), Positives = 191/306 (62%), Gaps = 18/306 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA + I   +K+  L F+ +E P+++Q GG + 
Sbjct: 20  MMDCTDKHFRMIMRKISSKALLYTEMIVAQSLIYTNEKEKFLDFNNEEHPISIQFGGDNP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L E AK+ +D+GY+EIN NVGCPS RV  G+FGA LM +P+ V  CI ++  + S+PV
Sbjct: 80  KILKEGAKMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKDPEKVAKCIESLKNSCSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L YD+V
Sbjct: 140 TIKHRIGVDEDDSFVNLNNFVRYIANAGADRFTVHARKAILKGLNPKQNRTIPPLKYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
            ++KK NP+L I +NGG  +++++L+ L + DGVMIGR+ YK+    + +D+      + 
Sbjct: 200 KKLKKLNPELLIEINGGFTNINESLEALSNFDGVMIGRSVYKHPLRWSEIDQKVYGINTK 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P + S              I  S+  Y   HL +GGK   I +H+I L  G P ++  R+
Sbjct: 260 PKSASD-------------IIFSLIPYIEEHLSNGGKSWDICKHLINLVEGIPKAKVWRN 306

Query: 296 ILTVEA 301
            ++ ++
Sbjct: 307 QISTKS 312


>gi|119946739|ref|YP_944419.1| tRNA-dihydrouridine synthase A [Psychromonas ingrahamii 37]
 gi|119865343|gb|ABM04820.1| tRNA-dihydrouridine synthase [Psychromonas ingrahamii 37]
          Length = 330

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 131/320 (40%), Positives = 187/320 (58%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+++ N LLY+EM+   AIL G K + L     E P+ LQ+GG+   
Sbjct: 20  MLDWTDRHCRYFHRVMSKNTLLYSEMVTTGAILYG-KGDYLQKDAAEHPVCLQLGGSAPV 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A   ++ G++EINLNVGCPS RV  G FGACLM   ++VGD I AM  A  +PV+
Sbjct: 79  DLATSALAGKERGFDEINLNVGCPSDRVQNGRFGACLMSEGELVGDAIKAMKDATGLPVS 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V  + + G +   +HARKA L GLSPK NR +P LDY+ VY
Sbjct: 139 VKTRIGIDDLDSYAFLCDFVGKVAEKGCDTFVVHARKAWLSGLSPKQNRDVPPLDYERVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  +DGVM+GR  Y N  +L++VD+       G+
Sbjct: 199 QLKKDFPQLTIAINGGIKTLDECETHLQYLDGVMLGREIYTNPYLLSSVDQRL---FAGN 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I TR +      +   M  Y  + L +G   + + RHM+GLF G P +R  R  L+  
Sbjct: 256 EKILTRFE------VLEKMYPYIEQQLSNGAYFKHVARHMLGLFQGLPGARAWRRHLSEN 309

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++E A   ++E
Sbjct: 310 GHLPGAGIEVMEKAAAFVVE 329


>gi|124267105|ref|YP_001021109.1| tRNA-dihydrouridine synthase A [Methylibium petroleiphilum PM1]
 gi|124259880|gb|ABM94874.1| tRNA-dihydrouridine synthase A [Methylibium petroleiphilum PM1]
          Length = 352

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 128/299 (42%), Positives = 180/299 (60%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+ +  LYTEM+   A+L GD    L F  +E P+ALQ+GG++  
Sbjct: 35  MMDWTDRHCRHFHRLLSRHTRLYTEMVTTGALLHGDVPRHLDFGPEEHPVALQLGGSEPE 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E +GY+EINLN GCPS RV  G+FGACLM  PD+V D + AM  A+ IPVT
Sbjct: 95  DLAACAKLGERWGYDEINLNCGCPSERVQRGAFGACLMAEPDLVADGVKAMRDAVGIPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ + ++  +G     +HAR A LKGLSPK+NR++P L ++ VY
Sbjct: 155 VKHRIGIDRTESYGFVRDFIGTVAAAGCEVFIVHARNAWLKGLSPKENRELPPLRHEWVY 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I LNGG++   +    L  VDGVM+GR AY +  ++   D  F     G 
Sbjct: 215 RLKRDFPALTIVLNGGVKTHDEIATHLAQVDGVMLGREAYHHPWLMADWDVRF----FGD 270

Query: 241 SPI-KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ + R D      I A+M  Y       G    +++RHM+GL+ G   +RR R + +
Sbjct: 271 APLERDRAD------IEAAMVRYMELQRLQGEPWSRVSRHMLGLWSGMSGARRWRQVWS 323


>gi|257454432|ref|ZP_05619694.1| tRNA-dihydrouridine synthase A [Enhydrobacter aerosaccus SK60]
 gi|257448198|gb|EEV23179.1| tRNA-dihydrouridine synthase A [Enhydrobacter aerosaccus SK60]
          Length = 330

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 132/306 (43%), Positives = 178/306 (58%), Gaps = 12/306 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+ R Y +FARL      LYTEMI   AIL+GD    L F   E PL LQ+GG+D +
Sbjct: 22  MIDWSTRDYCYFARLFNPYTYLYTEMISTSAILQGDTDYQLRFYPNEHPLVLQLGGSDPN 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI +D+GY+EINLNVGCPS RV     GACLM  P +V D ++AM  A+ IPVT
Sbjct: 82  ELARCAKIGQDYGYDEINLNVGCPSDRVQHYKIGACLMAEPKLVADIVSAMRDAVDIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      + + V  + K+G   + +HAR A L+GLSPK NR+IP L Y+ VY
Sbjct: 142 VKHRIGIDNFDSYEFMADFVDHVVKAGCQHVIVHARTAWLQGLSPKQNREIPPLRYEDVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PD+F+ +NGG+  + +    L  VDGVMIGR AY N  +L    + +       
Sbjct: 202 RLKQDFPDVFVEINGGITTIDEIKTHLTKVDGVMIGREAYHNPYILAEAMQLWGE----- 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R D      I   + D+ A     G  L  I RH +GLF G   SR+ R  L+ +
Sbjct: 257 -PVPSRAD------IFYQLLDFLAASDARGTPLTVIMRHYLGLFQGLTGSRKWRQALSGQ 309

Query: 301 AGASTA 306
              S A
Sbjct: 310 KSLSVA 315


>gi|170718234|ref|YP_001785255.1| tRNA-dihydrouridine synthase A [Haemophilus somnus 2336]
 gi|168826363|gb|ACA31734.1| TIM-barrel protein, yjbN family [Haemophilus somnus 2336]
          Length = 328

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 134/320 (41%), Positives = 187/320 (58%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH RFF R  +   LLYTEM+   AI+   K + L +   E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRFFHRQFSRYTLLYTEMVTTGAIIHA-KYDHLAYDVSENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL   AK  E+ GY EINLNVGCPS RV  G FGACLM    +V +C+ AM  A++IPVT
Sbjct: 77  KLQYCAKKGEERGYQEINLNVGCPSDRVQNGMFGACLMARAALVAECVNAMQSAVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L + ++ +   G     IHARKA L GLSPK+NR+IP L+Y+ VY
Sbjct: 137 VKTRLGIDEFDSYEFLCDFIEKVHNIGCQEFIIHARKAWLSGLSPKENREIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   S
Sbjct: 197 QLKKDFPHLLISINGGIKTLEEIQQHLNYVDGVMVGREAYQNPSLLGYIDQALFDP---S 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I T       R+   +M  Y  + L  G  L  I RH++G F     +R+ R  ++  
Sbjct: 254 CAIITP------RQAIENMFPYIEQQLSQGVYLNHIARHLLGAFQQCKGARQWRRYMSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
              S A   +IE A   + E
Sbjct: 308 IHKSHAGVEVIEKALTFIEE 327


>gi|261365796|ref|ZP_05978679.1| tRNA dihydrouridine synthase A [Neisseria mucosa ATCC 25996]
 gi|288565649|gb|EFC87209.1| tRNA dihydrouridine synthase A [Neisseria mucosa ATCC 25996]
          Length = 334

 Score =  248 bits (634), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 185/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ + AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 16  MLDWTDRHYRYLARQITRNTWLYSEMVNSGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 76  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVMLVADCLNAMQDAVQIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD QI    + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 136 VKHRIGVDRQIEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 196 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYG--DT 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 254 RSPIE-------YADLVQRLYTYSQTQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 306

Query: 298 T 298
           +
Sbjct: 307 S 307


>gi|254671973|emb|CBA04409.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha275]
 gi|325202832|gb|ADY98286.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M01-240149]
 gi|325208825|gb|ADZ04277.1| tRNA dihydrouridine synthase A [Neisseria meningitidis NZ-05/33]
          Length = 336

 Score =  248 bits (634), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 185/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+    +  + L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEEIAQHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DT 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|269213818|ref|ZP_05982915.2| tRNA dihydrouridine synthase A [Neisseria cinerea ATCC 14685]
 gi|269145448|gb|EEZ71866.1| tRNA dihydrouridine synthase A [Neisseria cinerea ATCC 14685]
          Length = 319

 Score =  248 bits (633), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 183/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ + AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 1   MLDWTDRHYRYLARQITRNTWLYSEMVNSGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 61  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVMLVADCLNAMQDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 121 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 181 YRLKQEFPDLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 239 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 291

Query: 298 T 298
           +
Sbjct: 292 S 292


>gi|212212648|ref|YP_002303584.1| tRNA-dihydrouridine synthase A [Coxiella burnetii CbuG_Q212]
 gi|212011058|gb|ACJ18439.1| NIFR3-like protein [Coxiella burnetii CbuG_Q212]
          Length = 353

 Score =  248 bits (633), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 127/297 (42%), Positives = 181/297 (60%), Gaps = 1/297 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 36  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 96  SLALCARLAEEKGFDEINLNVGCPSGRVTAGRFGACLLKEAELVADCVAAMSAEVNIPVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 156 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N       D+  S P+   
Sbjct: 216 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANPLFCAAFDD-LSKPVFSL 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L
Sbjct: 275 GVTDKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFL 331


>gi|87123334|ref|ZP_01079185.1| uncharacterized protein family protein [Synechococcus sp. RS9917]
 gi|86169054|gb|EAQ70310.1| uncharacterized protein family protein [Synechococcus sp. RS9917]
          Length = 334

 Score =  248 bits (633), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 132/320 (41%), Positives = 179/320 (55%), Gaps = 20/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+V  A+   +++  +L F   E PLALQ+GG D 
Sbjct: 20  MLDCTDRHFRMLMRQISRRALLYSEMVVVQALHHSERRERLLDFDPMEHPLALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L EA ++  D+GY+EINLNVGCPS RV  G+FGACLM  PD V  C+ AM +A  +PV
Sbjct: 80  ALLAEATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPDTVARCVEAMVRASPLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L+  V  +  +G +   +HARKA L GL PK NR IP L YD V
Sbjct: 140 TVKHRVGIDDLDSDALLQAFVDRLADAGASRFAVHARKAWLDGLDPKQNRTIPPLQYDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P+L I LNGGL+     L+ L   DG M+GRA Y +    T +D         
Sbjct: 200 IALKRRRPELLIELNGGLDTPDDCLEALQHCDGAMVGRAVYAHPLRWTAIDALIYG---- 255

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                     D  R ISA+     +  +A RHL  GG+L  + RH++ L  G P +R  R
Sbjct: 256 ----------DPARSISAAGVVRGLLPHAERHLQRGGRLWDLGRHLVHLVEGVPGARHWR 305

Query: 295 HILTVEAGASTATHHIIETA 314
             L   A    A   +++ A
Sbjct: 306 RDLGQNAQRKGADLSVLDDA 325


>gi|332528538|ref|ZP_08404526.1| tRNA-dihydrouridine synthase A [Hylemonella gracilis ATCC 19624]
 gi|332042049|gb|EGI78387.1| tRNA-dihydrouridine synthase A [Hylemonella gracilis ATCC 19624]
          Length = 339

 Score =  248 bits (633), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 138/321 (42%), Positives = 183/321 (57%), Gaps = 33/321 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  A LYTEMI   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 1   MIDWTDRHCRYFHRLLSRRARLYTEMITTGALLHGDVARHLRFDDAEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---- 116
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  AL     
Sbjct: 61  DLAACARLGEQWGYDEINLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMRDALQNPER 120

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVTVK R+G+D       +R+ V ++ ++G     +HAR A L+GLSPK+NR+IP L Y
Sbjct: 121 VPVTVKHRVGIDRVERYDFVRDFVGTVAEAGCTTFIVHARNAWLQGLSPKENREIPPLRY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-----------------VDGVMIGRAA 219
           + V+ +K++ P L + +NGGL   +Q L+ L                   +DG MIGR A
Sbjct: 181 EFVHRLKRDFPSLKVVINGGLTSDAQVLEQLQGADSPQAAADQAGGGPVPLDGAMIGREA 240

Query: 220 YKNSAMLTTVDE-YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR-HLHSGGKLQQIT 277
           Y N   L + D  YF  P  GS+   TR D      I   M DY  R     G     I 
Sbjct: 241 YHNPWWLASWDRLYFGEP--GSA--ATRED------IEERMVDYMLRMQAEEGLGWYGIA 290

Query: 278 RHMIGLFHGFPNSRRCRHILT 298
           RHM+GL HG P +RR R + +
Sbjct: 291 RHMLGLRHGLPGARRWRQVWS 311


>gi|209363933|ref|YP_001424351.2| tRNA-dihydrouridine synthase A [Coxiella burnetii Dugway 5J108-111]
 gi|212218379|ref|YP_002305166.1| tRNA-dihydrouridine synthase A [Coxiella burnetii CbuK_Q154]
 gi|207081866|gb|ABS78105.2| NIFR3-like protein [Coxiella burnetii Dugway 5J108-111]
 gi|212012641|gb|ACJ20021.1| NIFR3-like protein [Coxiella burnetii CbuK_Q154]
          Length = 353

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 127/297 (42%), Positives = 181/297 (60%), Gaps = 1/297 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 36  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 96  SLALCARLAEEKGFDEINLNVGCPSGRVTAGRFGACLLKEAELVADCVAAMSAEVNIPVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 156 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N       D+  S P+   
Sbjct: 216 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANPLFCAAFDD-LSKPVFSL 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L
Sbjct: 275 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFL 331


>gi|164685730|ref|ZP_01945619.2| tRNA dihydrouridine synthase A [Coxiella burnetii 'MSU Goat Q177']
 gi|165918518|ref|ZP_02218604.1| tRNA dihydrouridine synthase A [Coxiella burnetii RSA 334]
 gi|164601240|gb|EAX33765.2| tRNA dihydrouridine synthase A [Coxiella burnetii 'MSU Goat Q177']
 gi|165917764|gb|EDR36368.1| tRNA dihydrouridine synthase A [Coxiella burnetii RSA 334]
          Length = 328

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 127/297 (42%), Positives = 181/297 (60%), Gaps = 1/297 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 11  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 71  SLALCARLAEEKGFDEINLNVGCPSGRVTAGRFGACLLKEAELVADCVAAMSAEVNIPVS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 131 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N       D+  S P+   
Sbjct: 191 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANPLFCAAFDD-LSKPVFSL 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L
Sbjct: 250 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFL 306


>gi|90408335|ref|ZP_01216499.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
 gi|90310566|gb|EAS38687.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
          Length = 333

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 133/322 (41%), Positives = 186/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+   LLYTEM+   AIL G K + L     E P+ALQ+GG    
Sbjct: 20  MLDWTDRHCRHFHRILSKETLLYTEMVTTGAILYG-KGDYLQKGDAEHPVALQLGGFAAV 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA   ++ GY+EINLN+GCPS RV  G FGACLM  P++V D +AAM  A  +P+T
Sbjct: 79  DLAKAALAGKERGYDEINLNIGCPSDRVQNGRFGACLMAEPELVADAVAAMRDATGLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + +  +   G +   IHARKA L GLSPK NR +P LD+D VY
Sbjct: 139 VKTRIGIDDLDSYEFLCDFISKVHAKGCDNFIIHARKAWLSGLSPKQNRDVPPLDHDRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  +DGVM+GR AY N  +L+ VD+         
Sbjct: 199 QLKKDFPQLMIAINGGIKTLDECKTHLQHLDGVMLGREAYANPYLLSQVDKALFG--CTK 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ TR +      +   M  Y  + L +G  L  + RHM+GLF G P +R  R  L+  
Sbjct: 257 KPL-TRFE------VLEQMYPYIEQQLSNGSYLNHMGRHMLGLFQGLPGARAWRRHLSEN 309

Query: 301 AGASTATHHIIETAFNLMIESL 322
                +   +++ A + + E +
Sbjct: 310 GHLPGSGIEVMQKAASFVTEEI 331


>gi|328675719|gb|AEB28394.1| tRNA-dihydrouridine synthase A [Francisella cf. novicida 3523]
          Length = 301

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 130/308 (42%), Positives = 181/308 (58%), Gaps = 13/308 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG      +   K+ E+ G
Sbjct: 3   RLITKHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPKDFISCGKLAEELG 62

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           YNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++VKCRIG D     
Sbjct: 63  YNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPISVKCRIGYDHNDSY 122

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             L N V    ++GV+ + IHARK  L GLSPK+NR IP L YDIVY IKK+ P+L +G+
Sbjct: 123 EELYNFVDKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDIVYSIKKDFPNLELGI 182

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFW 252
           NGG+  + +  + L  VD VMIGR AY N  +    D  F N P TG S +         
Sbjct: 183 NGGITTIEETQQHLKCVDSVMIGREAYHNPMLFKDFDNIFYNQPTTGISAL--------- 233

Query: 253 RKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
            +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+  A    A    
Sbjct: 234 -EIAYKMAEYIKVQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLSENATKKEANVDT 292

Query: 311 IETAFNLM 318
             TA  + 
Sbjct: 293 FLTALEVF 300


>gi|29654227|ref|NP_819919.1| tRNA-dihydrouridine synthase A [Coxiella burnetii RSA 493]
 gi|29541493|gb|AAO90433.1| NifR3-like protein [Coxiella burnetii RSA 493]
          Length = 353

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 127/297 (42%), Positives = 181/297 (60%), Gaps = 1/297 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 36  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 96  SLALCARLAEEKGFDEINLNVGCPSGRVIAGRFGACLLKEAELVADCVAAMSAEVNIPVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 156 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N       D+  S P+   
Sbjct: 216 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANPLFCAAFDD-LSKPVFSL 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L
Sbjct: 275 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFL 331


>gi|161831190|ref|YP_001596802.1| tRNA-dihydrouridine synthase A [Coxiella burnetii RSA 331]
 gi|161763057|gb|ABX78699.1| tRNA dihydrouridine synthase A [Coxiella burnetii RSA 331]
          Length = 328

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 127/297 (42%), Positives = 181/297 (60%), Gaps = 1/297 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 11  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 71  SLALCARLAEEKGFDEINLNVGCPSGRVIAGRFGACLLKEAELVADCVAAMSAEVNIPVS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 131 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N       D+  S P+   
Sbjct: 191 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANPLFCAAFDD-LSKPVFSL 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L
Sbjct: 250 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFL 306


>gi|332284552|ref|YP_004416463.1| tRNA-dihydrouridine synthase A [Pusillimonas sp. T7-7]
 gi|330428505|gb|AEC19839.1| tRNA-dihydrouridine synthase A [Pusillimonas sp. T7-7]
          Length = 334

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 131/315 (41%), Positives = 182/315 (57%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TD+H R+F RLL   A LYTEMI   A++ G     L F   E+P+ALQ+GG++  
Sbjct: 18  MIDVTDKHCRYFHRLLAPQARLYTEMITTGALMHGKVARHLDFDPAEEPVALQLGGSEPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+AK+ + +GY+EINLN GCPS RV  G+FGACLM  P +V DCI AM  A+++PVT
Sbjct: 78  ALAESAKLGQQWGYDEINLNCGCPSERVQRGAFGACLMAEPQLVADCIKAMQDAVTVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD   
Sbjct: 138 VKHRLGLDYDDSYGFVRDFVGVIHNTGCRVFIVHARNAVLKGLSPKDNREIPPLRYDAAA 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + PD    LNGG+   SQAL+++   DGVM+GRAA+    +L+ +    +  +   
Sbjct: 198 RLKADFPDSVFVLNGGIAQASQALELMRQFDGVMLGRAAWHQPGVLSEISRAMAPDVAPL 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P           +I  +M  YAA  +  G  L+ I R M+G   G   SR  R  L+  
Sbjct: 258 EPA----------QIIQAMQTYAAGQVEQGVPLRMIVRPMLGWMSGRAGSRHWRRTLSDA 307

Query: 301 AGASTATHHIIETAF 315
           A  +     ++E A+
Sbjct: 308 ALLNQNDAGLLEKAW 322


>gi|304386595|ref|ZP_07368883.1| tRNA dihydrouridine synthase A [Neisseria meningitidis ATCC 13091]
 gi|304339424|gb|EFM05496.1| tRNA dihydrouridine synthase A [Neisseria meningitidis ATCC 13091]
          Length = 348

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 184/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 30  MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 90  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 150 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 210 YRLKQEFPELEIIINGGITANEAIAGHLQHVDGVMVGREAYHNPIVMREWDRLFYGDT-- 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 268 RSPIE-------YTDLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 320

Query: 298 T 298
           +
Sbjct: 321 S 321


>gi|296840825|ref|ZP_06863533.2| tRNA dihydrouridine synthase A [Neisseria polysaccharea ATCC 43768]
 gi|296839826|gb|EFH23764.1| tRNA dihydrouridine synthase A [Neisseria polysaccharea ATCC 43768]
          Length = 319

 Score =  246 bits (629), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 183/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 1   MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDSS 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 61  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 121 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 181 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 239 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 291

Query: 298 T 298
           +
Sbjct: 292 S 292


>gi|261401825|ref|ZP_05987950.1| tRNA dihydrouridine synthase A [Neisseria lactamica ATCC 23970]
 gi|269208032|gb|EEZ74487.1| tRNA dihydrouridine synthase A [Neisseria lactamica ATCC 23970]
          Length = 336

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 183/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM +A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQEAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DT 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|123967550|ref|YP_001008408.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str.
           AS9601]
 gi|123197660|gb|ABM69301.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. AS9601]
          Length = 334

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 128/303 (42%), Positives = 189/303 (62%), Gaps = 18/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  +KK N L F+ +E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKISSEALLYTEMIVAQSLVHTNKKENFLDFNGEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS RV  G+FGA LM +P+ V  CI ++     +PV
Sbjct: 80  KILKEAARMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKDPEKVAKCIESLKLNCDLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD+    V L N V+ +  +G +   +HARKAIL GL+PK NR IP L+YD+V
Sbjct: 140 TIKHRIGVDNDDSFVKLNNFVRIVANAGADRFTVHARKAILTGLNPKQNRTIPPLNYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
            ++K  NP L I +NGGL ++ ++LK L   DGVMIGR+ YK+    + +D+      + 
Sbjct: 200 KKLKNLNPSLLIEINGGLTNIDESLKALNDFDGVMIGRSIYKHPLRWSEIDQKIYGINTK 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P + S+             I  S+  Y  +HL +GGK   I +H+I L  G P ++  R+
Sbjct: 260 PKSASN-------------IIFSLIPYIEKHLSNGGKSWDICKHLINLVEGIPKAKIWRN 306

Query: 296 ILT 298
            ++
Sbjct: 307 QIS 309


>gi|298369820|ref|ZP_06981136.1| tRNA dihydrouridine synthase A [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298281280|gb|EFI22769.1| tRNA dihydrouridine synthase A [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 345

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 186/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+ AR +T NA LY+EMI A AI+ GDK   L F+  E+P+ALQ+GG++ +
Sbjct: 27  MLDWTDRHFRYMARQITENAWLYSEMINAGAIIYGDKDRFLMFNEGEQPVALQLGGSEPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNEINLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 87  DLAKAAKAAEEYGYNEINLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVDIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q         V ++ +K+      +HAR A L GLSPK+NR++P L YD V
Sbjct: 147 VKHRIGVDRQTEYGVAAEFVGTLYEKTACRTFIVHARNAWLDGLSPKENREVPPLKYDYV 206

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P+L I +NGG+    Q  + L  VDGVM+GR AY N  ++   D  F      
Sbjct: 207 YRLKQDFPELEIIINGGITTNEQISEHLKHVDGVMVGREAYHNPMIMRDWDRLFYGE--- 263

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
           SSP     D      +   + +Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 264 SSPPVEYAD------LVLKLYEYSRAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 317

Query: 298 T 298
           +
Sbjct: 318 S 318


>gi|159902555|ref|YP_001549899.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9211]
 gi|159887731|gb|ABX07945.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9211]
          Length = 333

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 135/326 (41%), Positives = 192/326 (58%), Gaps = 21/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   R ++  +LLYTEMIVA A+     + +L F   E P++LQ+GG +  
Sbjct: 20  MLDCTDRHFRVIFRQVSRRSLLYTEMIVAKALQHQKGRRLLDFDEIEHPISLQVGGDNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AAK+ ED+GY+EINLN+GCPS RV  G+FGACLM  P+ V  CI AM  A  IPVT
Sbjct: 80  ELADAAKLAEDWGYDEINLNLGCPSPRVQSGNFGACLMATPNQVAKCIEAMKNATQIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G+D+      L + V  I K+G +   IHARKA L+GL+PK NR IP L+Y  V 
Sbjct: 140 IKHRTGIDNFDSEEFLFSFVDQIAKAGADRFAIHARKAWLEGLNPKQNRTIPPLEYLKVK 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD------EYFS 234
           ++K + P+L I  NGGL    + +K L   DG M+GR+AY N  +   +D      +YF 
Sbjct: 200 KLKLKRPELKIEFNGGLHTPEECVKTLKIFDGAMVGRSAYSNPMLWQEMDSLIYGEDYF- 258

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            P+  S  I+             ++  YA +HL + G+L  I++H++ L    P +R  R
Sbjct: 259 -PVKASQVIQ-------------NLIPYAQKHLDNEGRLWDISKHLLQLVQAVPGARAWR 304

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
           H L+ +A  S+A   I+E A   + E
Sbjct: 305 HNLSTKAQKSSAKLIILEKAAQQLEE 330


>gi|311105398|ref|YP_003978251.1| tRNA-dihydrouridine synthase A [Achromobacter xylosoxidans A8]
 gi|310760087|gb|ADP15536.1| tRNA-dihydrouridine synthase A [Achromobacter xylosoxidans A8]
          Length = 326

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 133/316 (42%), Positives = 190/316 (60%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RLL   A LYTEMI   A+L G+ +  L F   E P+ALQ+GG++  
Sbjct: 1   MIDVTDRHCRFFHRLLAPRARLYTEMITTGALLHGNVERHLDFDEAEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ + +GY+EINLN GCPS RV +G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 61  ALAHSARLGKKWGYDEINLNCGCPSERVQKGAFGACLMAEPALVADCMKAMQDAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  +  +G      HAR A+LKGL+PKDNR+IP L Y++V 
Sbjct: 121 VKHRLGLDYDESYEFVRDFVGKVYDTGCRVFIAHARNAVLKGLTPKDNREIPPLRYEVVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD    LNGGL D  Q+++     DGVM+GRAA+    +L+ V       L   
Sbjct: 181 QLKRDFPDCTFVLNGGLADAGQSVRAAGDFDGVMLGRAAWHTPRVLSEVSLQLWPSL--- 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                R+  D   ++  +M +YAAR +  G  L+ +TR M+GL +G   +RR R +L+  
Sbjct: 238 -----RLPSDA--QVVDAMMEYAARQVAVGVPLRVMTRPMLGLVNGQSGARRWRRMLSDP 290

Query: 301 AGASTATHHIIETAFN 316
           A  +     +I  A+ 
Sbjct: 291 ALLAANNPELIYDAWR 306


>gi|325128934|gb|EGC51788.1| tRNA dihydrouridine synthase A [Neisseria meningitidis N1568]
          Length = 336

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 134/301 (44%), Positives = 185/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  L++EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLHSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+    +  + L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEEIAQHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DT 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|328950080|ref|YP_004367415.1| TIM-barrel protein, yjbN family [Marinithermus hydrothermalis DSM
           14884]
 gi|328450404|gb|AEB11305.1| TIM-barrel protein, yjbN family [Marinithermus hydrothermalis DSM
           14884]
          Length = 339

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 133/322 (41%), Positives = 190/322 (59%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+  R ++    LYTEM+V  A++ GD+  +L F  +E PLALQIG +D  
Sbjct: 17  MMDWTDRHFRYLMRQVSRKVRLYTEMVVDRALIHGDRARLLAFHPEEHPLALQIGSSDPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              EAA+I   +GY+EINLNVGCPS RV EG FGACLM +P+ V +   AM +A  + VT
Sbjct: 77  LAFEAARIGVAWGYDEINLNVGCPSNRVQEGGFGACLMADPERVREITRAMREAAPV-VT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L   V+++ ++GV    +HARKA L+GLSPK+NR +P L Y  VY
Sbjct: 136 VKHRIGIDHLDEYRHLARFVETVAETGVTVFIVHARKAWLQGLSPKENRAVPPLRYGEVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I LNGG+  +  A+  L   DGVMIGRAAY+        D+     + G 
Sbjct: 196 RLKQDFPELTIVLNGGVRTLDAAMAHLEHTDGVMIGRAAYETPWAWAGADQQ----VFGL 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               +R      R++  +M  Y    L  G  L++I RH++ LF G P  RR R +L+  
Sbjct: 252 DRAPSR------REVVMAMLPYIEARLMEGVPLRRIARHLLNLFKGAPGGRRFRRVLSEG 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
               TA   +++ A   + +++
Sbjct: 306 LLDPTAGPELVQRALEAIPDAV 327


>gi|260436656|ref|ZP_05790626.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 8109]
 gi|260414530|gb|EEX07826.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 8109]
          Length = 331

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 135/327 (41%), Positives = 186/327 (56%), Gaps = 20/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+    ++N +L F   E P+ALQ+GG D 
Sbjct: 17  MLDCTDRHFRVLMRQISRRALLYSEMVVAQALHHNKRRNKLLDFDLVEHPIALQVGGDDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EINLNVGCPS +V  G+FGACLM  PD+V  C+ AM  A  +PV
Sbjct: 77  VLLAEAARLAQDWGYDEINLNVGCPSQKVQAGNFGACLMAEPDLVARCVEAMVDAGGLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L N V  +  +G +   +HARKA L+GL PK NR IP L ++ V
Sbjct: 137 TVKHRIGIDDLDSDALLTNFVDRVALAGASRFAVHARKAWLEGLDPKQNRTIPPLQHERV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L+ L   DG M+GRAAY +    T+VD       + 
Sbjct: 197 VALKQRRPDLVIELNGGLESPEDCLQALEGCDGAMVGRAAYSHPLRWTSVDALIFGEES- 255

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                        R+I AS     +  +AA HL  GG++  + RH++ L  G   +R  R
Sbjct: 256 -------------RQILASDVVNGLLPHAAAHLERGGRIWDLCRHLVQLVEGVRGARHWR 302

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             L  +A    A   ++  A   + E+
Sbjct: 303 RELGEKAQRPGADLDVLLNAGQQLKEA 329


>gi|126664937|ref|ZP_01735920.1| Dihydrouridine synthase TIM-barrel protein yjbN [Marinobacter sp.
           ELB17]
 gi|126630307|gb|EBA00922.1| Dihydrouridine synthase TIM-barrel protein yjbN [Marinobacter sp.
           ELB17]
          Length = 321

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 125/302 (41%), Positives = 183/302 (60%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  HYR+ AR L+ +ALLYTEM+   A++ GD +  L  +  E PLALQ+GG++  
Sbjct: 1   MMDWTTPHYRYMARQLSKHALLYTEMVTTGALIHGDTERFLHHNAAEYPLALQLGGSNAG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A + + FG++E+NLNVGCPS +V     GACLM +PDIV +   AM  A  IPVT
Sbjct: 61  ELAHCADLAQQFGFSEVNLNVGCPSDKVQNNMIGACLMGHPDIVAEGFKAMQAATDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G++ +     L   ++++  +G     +HAR A+L+GLSPK+NR +P L YD VY
Sbjct: 121 VKHRTGINGRESWDELCGFIETVAAAGCKTFIVHARIAVLEGLSPKENRDVPPLKYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K + P L I +NGG++ +++  + L   DGVM+GR AY N  +LT VD E+F  P   
Sbjct: 181 HLKAKYPQLEIIINGGIKTVNECHQHLAHTDGVMLGREAYHNPWILTQVDSEFFGEP--- 237

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
               +  V++    +   +M  +  + L  G  L  I+RHM+GLFHG P  R+ R  ++ 
Sbjct: 238 ----EKAVNR---HEALEAMYPFIEQELARGVYLGHISRHMLGLFHGVPGGRQFRRYISE 290

Query: 300 EA 301
            A
Sbjct: 291 NA 292


>gi|222111076|ref|YP_002553340.1| tRNA-dihydrouridine synthase a [Acidovorax ebreus TPSY]
 gi|221730520|gb|ACM33340.1| TIM-barrel protein, yjbN family [Acidovorax ebreus TPSY]
          Length = 351

 Score =  245 bits (626), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 129/298 (43%), Positives = 179/298 (60%), Gaps = 8/298 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ + LLYTEM+   A+  GD +  L F   E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRYLHRLLSRHTLLYTEMVTTGALAHGDVQRHLRFDAAEHPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 77  DLAHCARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVQVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  +  +G     +HAR A LKGLSPK+NR+IP L YD+  
Sbjct: 137 VKHRIGIDQNEDYGFVRDFVGVVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYDVAA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG +  +  L+ L  VDGVM+GR AY N   L   DE F      +
Sbjct: 197 RLKADFPQLTIAINGGFQTDAAVLEELARVDGVMVGREAYHNPWWLARWDEQFFG-AAPA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P + +V++D    + A M   A  H   G     + RHM+GL +G P +RR R + +
Sbjct: 256 APTREQVEED----MVAYMEREATAH---GTHWYAVARHMLGLRNGLPGARRWRQVWS 306


>gi|329896416|ref|ZP_08271515.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC3088]
 gi|328921836|gb|EGG29207.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC3088]
          Length = 319

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 130/322 (40%), Positives = 181/322 (56%), Gaps = 12/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++W+DRH R+F RL+   ALLYTEM+   A+L GDK   L F   E P+ALQ+GG +  
Sbjct: 1   MMEWSDRHCRYFWRLIAPQALLYTEMVTTGALLFGDKPYHLDFHDSEHPVALQLGGNEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ + +GY+E+NLN GCPS RV  G FGA LM  P  V  C+ AM  A  +PVT
Sbjct: 61  ALARCAELAQQWGYDEVNLNCGCPSDRVQSGGFGAYLMGEPKTVSACVQAMRNATDLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D Q     L   V+++ ++G     +HARKA LKGLSPK NR IP L+Y+ VY
Sbjct: 121 VKHRLGIDHQDSYEELLEFVQTVAEAGCRHFVVHARKAWLKGLSPKQNRDIPPLNYEWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K+  P+L I +NGG+    + ++ L  VDGVMIGR AY +   L  + E  F      
Sbjct: 181 RLKQTLPELTIVINGGITQPQECVEHLQHVDGVMIGREAYYHPWHLRAISEAVFGKQNLL 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S P           +I   M  Y+   L  G KL  +TRH+I  + G   +++ R  L+ 
Sbjct: 241 SQP-----------EIMTEMVRYSKEQLEKGVKLNHVTRHLINFYQGCRGAKQFRRYLSE 289

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   I+  A  L+ ++
Sbjct: 290 NAHRPGANEQILVDALALVEQA 311


>gi|88809349|ref|ZP_01124857.1| hypothetical protein WH7805_09364 [Synechococcus sp. WH 7805]
 gi|88786568|gb|EAR17727.1| hypothetical protein WH7805_09364 [Synechococcus sp. WH 7805]
          Length = 334

 Score =  245 bits (625), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 133/327 (40%), Positives = 186/327 (56%), Gaps = 20/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   RL++ ++LLY+EM+VA A+   +++  +LGF  +E P+ LQ+GG + 
Sbjct: 20  MLDCTDRHFRQLMRLISRHSLLYSEMVVAQALHHSNRRERLLGFDPEEHPIVLQVGGDEP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EA ++  D+GY+EINLNVGCPS RV  G+FGACLM  P+ V  C+ AM  A   P+
Sbjct: 80  RLLAEATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPERVAQCVEAMVSASDRPI 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L   V  +  +G +   +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRVGIDDLDSDDLLTAFVDRVADAGASRFSVHARKAWLEGLDPKQNRTIPPLQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +KK  P L I LNGGL+   Q L  L   DG M+GRAAY +     +VDE        
Sbjct: 200 IALKKRRPQLTIELNGGLDTPEQCLDALQHCDGAMVGRAAYAHPLRWASVDELIYG---- 255

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                     D  R + AS     +  +A RHL  GG+L  I RH++ L  G P +R  R
Sbjct: 256 ----------DVCRTVRASDVLIGLIPHAERHLQRGGRLWDIGRHLVQLVEGVPGARHWR 305

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             L   A  + A   ++E++   +I++
Sbjct: 306 RDLGQNAQRAGADLTVLESSARQLIDA 332


>gi|15676263|ref|NP_273397.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis MC58]
 gi|7225569|gb|AAF40791.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|316984353|gb|EFV63327.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis H44/76]
 gi|325140997|gb|EGC63503.1| tRNA dihydrouridine synthase A [Neisseria meningitidis CU385]
 gi|325199542|gb|ADY94997.1| tRNA dihydrouridine synthase A [Neisseria meningitidis H44/76]
          Length = 336

 Score =  244 bits (624), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DT 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|254494393|ref|ZP_05107564.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 1291]
 gi|268595490|ref|ZP_06129657.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|268599350|ref|ZP_06133517.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|268602043|ref|ZP_06136210.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|268604377|ref|ZP_06138544.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|268684995|ref|ZP_06151857.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|268687257|ref|ZP_06154119.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
 gi|226513433|gb|EEH62778.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 1291]
 gi|268548879|gb|EEZ44297.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|268583481|gb|EEZ48157.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|268586174|gb|EEZ50850.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|268588508|gb|EEZ53184.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|268625279|gb|EEZ57679.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|268627541|gb|EEZ59941.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
          Length = 338

 Score =  244 bits (624), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 134/301 (44%), Positives = 184/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 20  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 80  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 140 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 200 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DN 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 258 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 310

Query: 298 T 298
           +
Sbjct: 311 S 311


>gi|59801940|ref|YP_208652.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA 1090]
 gi|194099440|ref|YP_002002542.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae NCCP11945]
 gi|239999677|ref|ZP_04719601.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|240014854|ref|ZP_04721767.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI18]
 gi|240017300|ref|ZP_04723840.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA6140]
 gi|240113270|ref|ZP_04727760.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|240116376|ref|ZP_04730438.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|240118665|ref|ZP_04732727.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|240121373|ref|ZP_04734335.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID24-1]
 gi|240126411|ref|ZP_04739297.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|240128876|ref|ZP_04741537.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
 gi|260439804|ref|ZP_05793620.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|291043074|ref|ZP_06568797.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|293398413|ref|ZP_06642591.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae F62]
 gi|59718835|gb|AAW90240.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193934730|gb|ACF30554.1| Conserved hypothetical protein [Neisseria gonorrhoeae NCCP11945]
 gi|291012680|gb|EFE04663.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|291610884|gb|EFF39981.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae F62]
 gi|317164939|gb|ADV08480.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 348

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 134/301 (44%), Positives = 184/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 30  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 90  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 150 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 210 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DN 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 268 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 320

Query: 298 T 298
           +
Sbjct: 321 S 321


>gi|319411177|emb|CBY91582.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis WUE 2594]
          Length = 336

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQTQIQAGCGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|161870721|ref|YP_001599894.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis 053442]
 gi|161596274|gb|ABX73934.1| conserved hypothetical protein [Neisseria meningitidis 053442]
          Length = 336

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 134/301 (44%), Positives = 182/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGVTTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|121635516|ref|YP_975761.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis FAM18]
 gi|120867222|emb|CAM10991.1| conserved hypothetical protein [Neisseria meningitidis FAM18]
 gi|325132903|gb|EGC55580.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M6190]
 gi|325143034|gb|EGC65386.1| tRNA dihydrouridine synthase A [Neisseria meningitidis 961-5945]
 gi|325145143|gb|EGC67425.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M01-240013]
 gi|325198962|gb|ADY94418.1| tRNA dihydrouridine synthase A [Neisseria meningitidis G2136]
          Length = 336

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|254805616|ref|YP_003083837.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha14]
 gi|254669158|emb|CBA07852.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha14]
          Length = 336

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|148238351|ref|YP_001223738.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 7803]
 gi|147846890|emb|CAK22441.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 7803]
          Length = 334

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 132/322 (40%), Positives = 183/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  +LLY+EM+VA A+   +++  +LGF  +E P+ LQ+GG D 
Sbjct: 20  MLDCTDRHFRQLMRQISRRSLLYSEMVVAQALHHSNRRERLLGFDPEEHPIVLQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EA ++  D+GY+EINLNVGCPS RV  G+FGACLM  P+ V  C+ AM  A   PV
Sbjct: 80  QLLAEATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPERVAQCVEAMVSASDRPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L   V  +  +G +   +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRVGIDDLDSDDLLTAFVDRVADAGASRFSVHARKAWLEGLDPKQNRTIPPLQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K   P L I LNGGL+   Q L  L   DG M+GRAAY +     +VD      + G
Sbjct: 200 IALKARRPQLTIELNGGLDTPEQCLDALQHCDGAMVGRAAYAHPLRWASVDTL----IYG 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P   R        +   +  +A RHL  GG+L  I RH++ L  G P +R  R  L  
Sbjct: 256 DAPQTVRAS-----DVLIGLIPHAERHLQRGGRLWDIGRHLVQLVEGVPGARHWRRDLGQ 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A  S A   ++E +   +I++
Sbjct: 311 KAQRSGADLTVLEASARQLIDA 332


>gi|261391873|emb|CAX49332.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis 8013]
          Length = 336

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 135/301 (44%), Positives = 181/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|120554835|ref|YP_959186.1| tRNA-dihydrouridine synthase A [Marinobacter aquaeolei VT8]
 gi|120324684|gb|ABM18999.1| tRNA-U16,U17-dihydrouridine synthase [Marinobacter aquaeolei VT8]
          Length = 337

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 184/315 (58%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  H+R+ AR+L+  ALLYTEM+   A++ GD +  L     E PLALQ+GG+D +
Sbjct: 20  MMDWTTPHFRYLARILSKRALLYTEMVTTGALIHGDTERFLRHDVSEYPLALQLGGSDAN 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ + FG++E+NLNVGCPS RV     GACLM +PD V + ++AM +A  +PVT
Sbjct: 80  ELAHCARLAQQFGFSEVNLNVGCPSDRVQNNMIGACLMGHPDKVAEGVSAMIEATDLPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L   ++++  +G     +HAR A+L+GLSPK+NR IP L YD VY
Sbjct: 140 VKHRIGINGRESWEELCEFIETVAAAGCKTFIVHARIAVLEGLSPKENRDIPPLKYDWVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P L I +NGG++   +  + L   DGVM+GR AY N  +L  VD      L G 
Sbjct: 200 RLKQAYPHLEIIINGGIKTFGECHEHLTHTDGVMLGREAYHNPWLLAEVD----AALFGE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  T   +        +M  +  + L  G  L  ITRH++GLF G P  R+ R  L+  
Sbjct: 256 PPAVTSRHEAL-----RAMFPFIQQELDRGVYLTHITRHIMGLFLGQPGGRQFRRHLSEN 310

Query: 301 AGASTATHHIIETAF 315
           A    +   ++E A 
Sbjct: 311 ANKPGSGLEVVEQAL 325


>gi|188580153|ref|YP_001923598.1| tRNA-dihydrouridine synthase A [Methylobacterium populi BJ001]
 gi|179343651|gb|ACB79063.1| dihydrouridine synthase DuS [Methylobacterium populi BJ001]
          Length = 324

 Score =  244 bits (622), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 145/307 (47%), Positives = 191/307 (62%), Gaps = 11/307 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+P+A+Q+GG++  
Sbjct: 1   MMDWTDRQCRAFHRALSRRARLYTEMVTTGAVLHGDRERLLGFDAGEQPVAVQLGGSNPH 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  D+GY EINLNVGCPS RV EG FGACLM  P +VG+C+AAM  A+++PVT
Sbjct: 61  DLAAAARIAADYGYAEINLNVGCPSDRVQEGRFGACLMREPGLVGECVAAMKAAVAVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 121 VKCRLGVDDQDIEEALDAVAGAVVAAGVDGLIVHARKAWLKGLSPRENRDVPPLDYGRVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+  PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD E F      
Sbjct: 181 RLKQVRPDLPIAVNGGIADIAAAKARLTEVDGVMIGRAAYTEPALLLDVDPELFGEAAPA 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +                 +     A  L  G +L   TRHM+GLF+G P +R  R  L  
Sbjct: 241 ADAFAA----------VEAFEPVVAAGLERGLRLHAYTRHMLGLFNGRPGARAYRRHLAT 290

Query: 300 EAGASTA 306
              A+ A
Sbjct: 291 AGMAAEA 297


>gi|156972389|ref|YP_001443296.1| tRNA-dihydrouridine synthase A [Vibrio harveyi ATCC BAA-1116]
 gi|156523983|gb|ABU69069.1| hypothetical protein VIBHAR_00009 [Vibrio harveyi ATCC BAA-1116]
          Length = 300

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 129/301 (42%), Positives = 182/301 (60%), Gaps = 11/301 (3%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           +T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++ + L   AK+ ++ GY+
Sbjct: 1   MTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPADLATCAKLAQERGYD 59

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + +PVTVK RIG+DDQ     
Sbjct: 60  EINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDVPVTVKTRIGIDDQDSYEF 119

Query: 136 LRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   Y++KK+   L I +N
Sbjct: 120 LTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRAYQLKKDFSHLTIAIN 179

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           GG++ + +A + L  +DGVMIGR AY++  +L +VD+        ++P+K R +      
Sbjct: 180 GGVKLLEEAKEHLQYLDGVMIGREAYQSPYLLASVDQEL---FGSNTPVKKRSE------ 230

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
           I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++  A    +   +++ A
Sbjct: 231 IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISENAHKPGSGLEVLQDA 290

Query: 315 F 315
            
Sbjct: 291 L 291


>gi|332971008|gb|EGK09980.1| tRNA dihydrouridine synthase A [Psychrobacter sp. 1501(2011)]
          Length = 340

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 124/298 (41%), Positives = 173/298 (58%), Gaps = 12/298 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YRFFARL   +  LYTEMI   AI+ G+   +L F   E PL LQ+GGADI 
Sbjct: 20  MIDWTTTDYRFFARLFNPHTYLYTEMISTGAIINGNTDRLLRFDNTEHPLVLQLGGADIG 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++   A   +  G++E+N+NVGCPS RV     GACLM  P+ V   +  M   + IPVT
Sbjct: 80  EMTHGAVEAQKRGFDEVNINVGCPSDRVQHNKIGACLMAEPETVASLVRHMQAEVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +++ V++  ++G     +HAR A LKGLSPK+NR+IP L YD VY
Sbjct: 140 VKHRIGIDEHDSYQFMKDFVQASAEAGCQRFIVHARIAWLKGLSPKENREIPPLRYDDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++ + Q    L  VDGVMIGRAAY N  +L    + +       
Sbjct: 200 RLKQEFPELQIEINGGIDSLEQIKSHLQHVDGVMIGRAAYHNPYLLAEAMQLWGE----E 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +          I + +  Y  + +  G  L  I+RH++GLF G P +RR R  L+
Sbjct: 256 APSR--------EYILSQLYPYLEKQVAKGEPLTSISRHLLGLFQGLPGARRWRQSLS 305


>gi|218660217|ref|ZP_03516147.1| tRNA-dihydrouridine synthase A [Rhizobium etli IE4771]
          Length = 249

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 118/218 (54%), Positives = 148/218 (67%), Gaps = 1/218 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D  
Sbjct: 13  MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDVAEHPLALQLGGSDPG 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 73  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAACVAAMKAVATAPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEDALPALISRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKE-NPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +      L           ++       VDGVM+GR
Sbjct: 193 RDETALARRLHRASTAASARSTRPRATSAHVDGVMLGR 230


>gi|325205425|gb|ADZ00878.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M04-240196]
          Length = 336

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 137/303 (45%), Positives = 182/303 (60%), Gaps = 16/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F    +N
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 257

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P+ G + +  R+      +I A            G  L+ I RH +GL HG   +R  R 
Sbjct: 258 PI-GYADLVQRLYTYSQAQIQAG----------RGTILRHIVRHSLGLMHGLKGARTWRR 306

Query: 296 ILT 298
           +L+
Sbjct: 307 MLS 309


>gi|72383178|ref|YP_292533.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str.
           NATL2A]
 gi|72003028|gb|AAZ58830.1| tRNA-U16,U17-dihydrouridine synthase [Prochlorococcus marinus str.
           NATL2A]
          Length = 335

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 129/314 (41%), Positives = 189/314 (60%), Gaps = 12/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R +T  +LLYTEMIVA A+     +N +L F   E P+++Q+GG + 
Sbjct: 21  MMDCTDRHFRVLMRQITKKSLLYTEMIVAQALHYSKNRNKLLDFDEIEHPISIQLGGDNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ ED+GY+EINLN+GCPS +V  G+FGACLM  P+IV  CI  M K  +IP+
Sbjct: 81  KLLAEAAQMAEDWGYDEINLNIGCPSPKVKSGNFGACLMGKPNIVASCIEKMKKTCNIPI 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D+      L   V +   +G +   +HARKA L GL+PK+NR IP L Y+ V
Sbjct: 141 TVKHRLGIDNLDSDDYLLKFVDTCSLAGADRFIVHARKAWLNGLNPKENRSIPPLQYERV 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K   P+L I LNGG+  ++ +++ L   DG M+GRAAY +  + T +D         
Sbjct: 201 QNLKNNRPELIIELNGGINTINDSIEALKVFDGAMVGRAAYSHPFLWTKID--------- 251

Query: 240 SSPIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S I  + +K   R KI   +  +A +HL +GG+L QI+RH++ L    PN++  R  L+
Sbjct: 252 -SLIFGQKEKYLSRSKIIKKLIPFAQKHLENGGRLWQISRHILNLIENIPNAKILRQELS 310

Query: 299 VEAGASTATHHIIE 312
            +     A   I++
Sbjct: 311 EKCQTQKADISILK 324


>gi|254670181|emb|CBA05275.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha153]
 gi|325138888|gb|EGC61438.1| tRNA dihydrouridine synthase A [Neisseria meningitidis ES14902]
          Length = 336

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 134/301 (44%), Positives = 182/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|319794422|ref|YP_004156062.1| tim-barrel protein, yjbn family [Variovorax paradoxus EPS]
 gi|315596885|gb|ADU37951.1| TIM-barrel protein, yjbN family [Variovorax paradoxus EPS]
          Length = 324

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 133/317 (41%), Positives = 191/317 (60%), Gaps = 14/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 11  MMDWTDRHCRYFHRLMSRHALLYTEMVTTGALVHGDVPRHLRFNAEEHPVALQLGGSEPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 71  DLAHCAKLGEEWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVSVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  + ++G +   +HAR A L+GLSPK NR+IP L Y +V+
Sbjct: 131 VKHRIGIDKIERYEFVRDFVGQVSEAGCDTFIVHARNAWLQGLSPKQNREIPPLRYALVH 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K + P L   +NGG+    Q  + L  +DGVM+GR AY N   L   D E+F     G
Sbjct: 191 RLKHDFPGLKFSINGGISVNEQVHEHLRLLDGVMVGREAYHNPWWLAEWDAEFF-----G 245

Query: 240 SSPIK-TRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           ++P   TR       ++ + M DY  R     G +   I RHM+GL +G P +RR R + 
Sbjct: 246 AAPQPLTR------EEVESLMCDYMVREAAEHGTQWSSIARHMLGLRNGLPGARRWRQVW 299

Query: 298 TVEAGASTATHHIIETA 314
           +     +   H ++  A
Sbjct: 300 SDHRMKTRPPHEVMALA 316


>gi|240081060|ref|ZP_04725603.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|240124208|ref|ZP_04737164.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID332]
          Length = 348

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 133/301 (44%), Positives = 184/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 30  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 90  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 150 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 210 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DN 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   ++  R +L
Sbjct: 268 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGAQTWRRML 320

Query: 298 T 298
           +
Sbjct: 321 S 321


>gi|268597171|ref|ZP_06131338.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|268682834|ref|ZP_06149696.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID332]
 gi|268550959|gb|EEZ45978.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|268623118|gb|EEZ55518.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID332]
          Length = 338

 Score =  243 bits (619), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 133/301 (44%), Positives = 184/301 (61%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 20  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 80  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 140 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 200 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DN 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   ++  R +L
Sbjct: 258 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGAQTWRRML 310

Query: 298 T 298
           +
Sbjct: 311 S 311


>gi|88800086|ref|ZP_01115656.1| hypothetical protein MED297_16794 [Reinekea sp. MED297]
 gi|88777212|gb|EAR08417.1| hypothetical protein MED297_16794 [Reinekea sp. MED297]
          Length = 338

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 124/299 (41%), Positives = 186/299 (62%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT    R F RLLT  ALLYTEM+   A++ G+    L + T+E P+ALQ+GG D  
Sbjct: 14  MMDWTTSECRQFHRLLTRQALLYTEMVTTGALIHGNAGRFLRYDTEEHPIALQLGGHDAD 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ E+ GY+++NLN GCPS RV  G  GA LM + D V D + AM   ++IPVT
Sbjct: 74  ELAHCTKMAEEHGYDQVNLNAGCPSDRVQNGMIGAILMAHADKVTDALKAMQDRVNIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD      LR+ V  +  SG +   +HARKAIL GLSPK+NR+IP LDYD V 
Sbjct: 134 LKHRIGIDDYDSYEFLRDFVGQVSLSGCDTFIVHARKAILSGLSPKENREIPPLDYDRVI 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K++ P+L I +NGG++   +A  ++   +DGVM+GR AY+N  +L+ VD  +      
Sbjct: 194 RLKQDFPNLNIVINGGIKSHQEAQALINRGLDGVMLGREAYQNPLILSEVDHIYYGHENP 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           ++ I+T         ++A +TD+  + + +G  L+ + +H +GL+ G P S++ R +L+
Sbjct: 254 NADIET---------LNARITDWVEQKVETGVPLKFLAKHTLGLYAGHPGSKQFRRMLS 303


>gi|121594416|ref|YP_986312.1| tRNA-dihydrouridine synthase A [Acidovorax sp. JS42]
 gi|120606496|gb|ABM42236.1| tRNA-U16,U17-dihydrouridine synthase [Acidovorax sp. JS42]
          Length = 351

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 130/301 (43%), Positives = 180/301 (59%), Gaps = 14/301 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ + LLYTEM+   A+  GD +  L F   E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRYLHRLLSRHTLLYTEMVTTGALAHGDVQRHLRFDAAEHPVALQLGGSEPT 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 77  DLAHCARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVQVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  +  +G     +HAR A LKGLSPK+NR+IP L YD+  
Sbjct: 137 VKHRIGIDQNEDYGFVRDFVGVVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYDVAA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG +  +  L+ L  VDGVM+GR AY N   L   DE F     G+
Sbjct: 197 RLKADFPQLTIAINGGFQTDAAVLQELARVDGVMVGREAYHNPWWLARWDEQF----FGA 252

Query: 241 SP---IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           +P    + +V++D    + A M   A  H   G     + RHM+GL +G P +RR R + 
Sbjct: 253 APAALTREQVEED----MVAYMEREATAH---GTHWYAVARHMLGLRNGLPGARRWRQVW 305

Query: 298 T 298
           +
Sbjct: 306 S 306


>gi|299531032|ref|ZP_07044445.1| tRNA-dihydrouridine synthase A [Comamonas testosteroni S44]
 gi|298720989|gb|EFI61933.1| tRNA-dihydrouridine synthase A [Comamonas testosteroni S44]
          Length = 327

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 185/315 (58%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RLL+ + LLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 6   MMDWTDKHCRYFHRLLSQHTLLYTEMVTTGALVHGDVARHLRFEAEEHPVALQLGGSEPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   +S+PVT
Sbjct: 66  DLAHSARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEAALVADCVKAMADVVSVPVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++V 
Sbjct: 126 VKHRIGIDKIESYDFVRDFVGTVADAGCQVFVVHARNAWLKGLSPKENREIPPLRYEVVA 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  VDGVM+GR AY N   + + D  +       
Sbjct: 186 QLKRDFPGLTIAVNGGIKTDDVVQQQLQQVDGVMVGREAYHNPWWMASWDALYYQ---DE 242

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S  +TR       +I   M  Y  R     G     I RHM+GL +G   +RR R + + 
Sbjct: 243 SRERTR------EQIEEQMVLYMEREAREHGTHWYSIARHMLGLRNGLAGARRWRQVWSD 296

Query: 300 EAGASTATHHIIETA 314
               +   H +++ A
Sbjct: 297 HRLKTLPAHEVMKLA 311


>gi|264678472|ref|YP_003278379.1| TIM-barrel protein, yjbN family [Comamonas testosteroni CNB-2]
 gi|262208985|gb|ACY33083.1| TIM-barrel protein, yjbN family [Comamonas testosteroni CNB-2]
          Length = 344

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 185/315 (58%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RLL+ + LLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 23  MMDWTDKHCRYFHRLLSQHTLLYTEMVTTGALVHGDVARHLRFEAEEHPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   +S+PVT
Sbjct: 83  DLAHSARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEAALVADCVKAMADVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++V 
Sbjct: 143 VKHRIGIDKIESYDFVRDFVGTVADAGCQVFVVHARNAWLKGLSPKENREIPPLRYEVVA 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  VDGVM+GR AY N   + + D  +       
Sbjct: 203 QLKRDFPGLTIAVNGGIKTDDVVQQQLQQVDGVMVGREAYHNPWWMASWDVLYYQ---DE 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S  +TR       +I   M  Y  R     G     I RHM+GL +G   +RR R + + 
Sbjct: 260 SRERTR------EQIEEQMVLYMEREAREHGTHWYSIARHMLGLRNGLAGARRWRQVWSD 313

Query: 300 EAGASTATHHIIETA 314
               +   H +++ A
Sbjct: 314 HRLKTLPAHEVMKLA 328


>gi|218768876|ref|YP_002343388.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis Z2491]
 gi|121052884|emb|CAM09236.1| conserved hypothetical protein [Neisseria meningitidis Z2491]
          Length = 336

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 136/303 (44%), Positives = 183/303 (60%), Gaps = 16/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F    +N
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 257

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P+ G + +  R+      +I A            G  L+ I RH +GL HG   +R  R 
Sbjct: 258 PI-GYADLVQRLYTYSQAQIQAG----------RGTILRHIVRHSLGLMHGLKGARTWRR 306

Query: 296 ILT 298
           +L+
Sbjct: 307 MLS 309


>gi|319411116|emb|CBY91521.1| K05539 tRNA-dihydrouridine synthase A [Neisseria meningitidis WUE
           2594]
          Length = 338

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 136/303 (44%), Positives = 183/303 (60%), Gaps = 16/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 20  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 80  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 140 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F    +N
Sbjct: 200 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P+ G + +  R+      +I A            G  L+ I RH +GL HG   +R  R 
Sbjct: 260 PI-GYADLVQRLYTYSQAQIQAG----------RGTILRHIVRHSLGLMHGLKGARTWRR 308

Query: 296 ILT 298
           +L+
Sbjct: 309 MLS 311


>gi|148653531|ref|YP_001280624.1| tRNA-dihydrouridine synthase A [Psychrobacter sp. PRwf-1]
 gi|148572615|gb|ABQ94674.1| TIM-barrel protein, yjbN family [Psychrobacter sp. PRwf-1]
          Length = 348

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 123/298 (41%), Positives = 170/298 (57%), Gaps = 12/298 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YRFFARL   +  LYTEMI   AIL+G    +L + T E PL LQ+GGADIS
Sbjct: 28  MIDWTTTDYRFFARLFNPHTYLYTEMISTSAILQGKTDRLLRYDTLEHPLVLQLGGADIS 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ + A   +  G+NE+N+NVGCPS RV     GACLM  PD V   +  M   + IPVT
Sbjct: 88  EMTQCAVEAQKRGFNEVNINVGCPSDRVQHNKIGACLMAEPDTVAALVRNMQAHVDIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +++ V +  ++G     +HAR A L GLSPK+NR+IP L Y+ VY
Sbjct: 148 VKHRIGIDEHDSYEFMQDFVSASAEAGCQRFIVHARIAWLNGLSPKENREIPPLRYEDVY 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG++ + Q    L  VDGVMIGRAAY N  +L     ++       
Sbjct: 208 RLKQAFPELHIEINGGIDSIEQIKAHLQQVDGVMIGRAAYHNPYILAEAMSFWGEAAPSR 267

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           + I T+            +  Y  + +  G  L  + RH +GLF G P +R+ R  L+
Sbjct: 268 AQILTK------------LYPYLEQQVAKGEPLPSLARHFLGLFQGLPGARKWRQALS 313


>gi|113955552|ref|YP_729254.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9311]
 gi|113882903|gb|ABI47861.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9311]
          Length = 334

 Score =  242 bits (617), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 131/327 (40%), Positives = 189/327 (57%), Gaps = 20/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  +LLY+EM+VA A+    ++  +L F  +E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRMLMRQISKQSLLYSEMVVAQALHHSKRRERLLDFDAEEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +A ++  D+GY+EINLNVGCPS RV  G+FGACLM  P  V  C+ AM  A S+PV
Sbjct: 80  ALLADATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPQTVARCVEAMVAASSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      LR  V  + ++G     +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRVGIDDLDSDDLLRQFVDQVAEAGALRFSVHARKAWLEGLDPKQNRTIPALQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P L I LNGGL+     L  L   DG M+GRAAY +      +D      + G
Sbjct: 200 IALKESRPALTIELNGGLDTPEDCLNALKHCDGAMVGRAAYAHPLRWREIDSL----IYG 255

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           ++P          R++ AS     +  +A RHL  GG+L  + RH++ +    P +R  R
Sbjct: 256 AAP----------RQVLASDVVLGLIPHAERHLQRGGRLWDLCRHLVQVVEAVPGARYWR 305

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
           + L+ +A  + A   IIE A   ++++
Sbjct: 306 NNLSTKAQRAGAGIEIIEEAAQQLLDA 332


>gi|300980481|ref|ZP_07175028.1| tRNA dihydrouridine synthase A [Escherichia coli MS 200-1]
 gi|300992960|ref|ZP_07180115.1| tRNA dihydrouridine synthase A [Escherichia coli MS 45-1]
 gi|300307783|gb|EFJ62303.1| tRNA dihydrouridine synthase A [Escherichia coli MS 200-1]
 gi|300406734|gb|EFJ90272.1| tRNA dihydrouridine synthase A [Escherichia coli MS 45-1]
 gi|315287860|gb|EFU47262.1| tRNA dihydrouridine synthase A [Escherichia coli MS 110-3]
 gi|315291520|gb|EFU50880.1| tRNA dihydrouridine synthase A [Escherichia coli MS 153-1]
 gi|315297520|gb|EFU56799.1| tRNA dihydrouridine synthase A [Escherichia coli MS 16-3]
 gi|324007804|gb|EGB77023.1| tRNA dihydrouridine synthase A [Escherichia coli MS 57-2]
          Length = 288

 Score =  242 bits (617), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 130/297 (43%), Positives = 183/297 (61%), Gaps = 13/297 (4%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G K + L +S +E P+ALQ+GG+D + L + AK+ E  GY+EINLNVGCPS
Sbjct: 1   MVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPAALAQCAKLAEARGYDEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM N  +V DC+ AM   +SIPVTVK RIG+DDQ     L + + ++  
Sbjct: 60  DRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKTRIGIDDQDSYEFLCDFINTVSG 119

Query: 146 SGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            G   ++ IHARKA L GLSPK+NR+IP LDY  VY++K++ P L + +NGG++ + +A 
Sbjct: 120 KGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAK 179

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
             L  +DGVM+GR AY+N  +L  VD E F +  T + P+           +  +M  Y 
Sbjct: 180 AHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDTDADPV----------AVVRAMYPYI 229

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
            R L  G  L  ITRHM+GLF G P +R+ R  L+  A  + A  +++E A  L+ +
Sbjct: 230 ERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADINVLEHALKLVAD 286


>gi|325203461|gb|ADY98914.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M01-240355]
          Length = 336

 Score =  242 bits (617), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 133/301 (44%), Positives = 182/301 (60%), Gaps = 12/301 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ I VT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGITVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYG--DN 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 HAPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 T 298
           +
Sbjct: 309 S 309


>gi|121996919|ref|YP_001001706.1| tRNA-dihydrouridine synthase A [Halorhodospira halophila SL1]
 gi|121588324|gb|ABM60904.1| tRNA-U16,U17-dihydrouridine synthase [Halorhodospira halophila SL1]
          Length = 328

 Score =  242 bits (617), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 126/316 (39%), Positives = 175/316 (55%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WT    R+F RLL  +  LYTEM+ A A+  G  +  L F   E P+A+Q GG+D  
Sbjct: 16  MMEWTTPAARYFLRLLAPHVRLYTEMVPAVALWHGAAERFLPFHPAEHPVAVQFGGSDPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++ E +GY+E+NLNVGCPS RV  G FGACLML P  V DC+AAM    ++PVT
Sbjct: 76  ELAYAARLAEQWGYDEVNLNVGCPSDRVQSGRFGACLMLEPSRVADCVAAMRAETNLPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      L   V+++  +G     +HARKA L GLSPK+NR++P LDY  V+
Sbjct: 136 VKSRIGVDEHDSESFLDAFVETVAAAGCRTFIVHARKAWLAGLSPKENREVPPLDYQRVH 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+L + +NGG+ D     + L  VDGVM+GR A+ N   L   D        G 
Sbjct: 196 RLKARRPELEVAINGGIADTVTLQEQLQWVDGVMVGREAFSNPYALAHWDRLL---FGGE 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +        R +  +   Y       G  + Q+ + ++GLF+G P +R  R  LT  
Sbjct: 253 LPER--------RGVVVAYLPYVEARRREGVPMSQLVKVLMGLFNGLPGARAWRRTLTEG 304

Query: 301 AGASTATHHIIETAFN 316
           +    A   +IE A  
Sbjct: 305 SQQPGAGPEVIERALT 320


>gi|308388557|gb|ADO30877.1| yjbN; tRNA-dihydrouridine synthase A [Neisseria meningitidis
           alpha710]
 gi|325136923|gb|EGC59520.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M0579]
          Length = 336

 Score =  241 bits (616), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 137/303 (45%), Positives = 182/303 (60%), Gaps = 16/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ I VT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGITVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++ K+      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF----SN 235
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F    +N
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 257

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P+ G + +  R+      +I A            G  L+ I RH +GL HG   +R  R 
Sbjct: 258 PI-GYADLVQRLYTYSQAQIQAG----------RGTILRHIVRHSLGLMHGLKGARTWRR 306

Query: 296 ILT 298
           +L+
Sbjct: 307 MLS 309


>gi|33601086|ref|NP_888646.1| tRNA-dihydrouridine synthase A [Bordetella bronchiseptica RB50]
 gi|33575521|emb|CAE32599.1| conserved hypothetical protein [Bordetella bronchiseptica RB50]
          Length = 337

 Score =  241 bits (615), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 179/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGDVARHLDFDAAEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 73  ALAQAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPGLVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYDESYGFVRDFVGQIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAR 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD  I LNGGL D   A  +    DGVM+GRAA+    +L+ V       L   
Sbjct: 193 QLKRDFPDCVIVLNGGLADAQAARAVAGEFDGVMLGRAAWHTPRVLSEVS------LQWW 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             I+   D     ++  +M  YAA  +  G  L+ +TR ++GL +G   +RR R +L+
Sbjct: 247 PAIRLPSDA----QVVDAMMQYAATQIARGVPLRVMTRPLLGLVNGQAGARRWRRLLS 300


>gi|33596533|ref|NP_884176.1| tRNA-dihydrouridine synthase A [Bordetella parapertussis 12822]
 gi|33566302|emb|CAE37215.1| conserved hypothetical protein [Bordetella parapertussis]
          Length = 337

 Score =  241 bits (615), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 179/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGDVARHLDFDAAEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 73  ALAQAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPGLVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYDESYGFVRDFVGQIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAR 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD  I LNGGL D   A  +    DGVM+GRAA+    +L+ V       L   
Sbjct: 193 QLKRDFPDCVIVLNGGLADAQAARAVAGEFDGVMLGRAAWHTPRVLSEVS------LQWW 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             I+   D     ++  +M  YAA  +  G  L+ +TR ++GL +G   +RR R +L+
Sbjct: 247 PAIRLPSDA----QVVDAMMQYAATQIARGVPLRVMTRPLLGLVNGQAGARRWRRLLS 300


>gi|33592223|ref|NP_879867.1| tRNA-dihydrouridine synthase A [Bordetella pertussis Tohama I]
 gi|33571868|emb|CAE41383.1| conserved hypothetical protein [Bordetella pertussis Tohama I]
 gi|332381640|gb|AEE66487.1| tRNA-dihydrouridine synthase A [Bordetella pertussis CS]
          Length = 337

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 179/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGDVARHLDFDAAEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 73  ALAQAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPALVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYDESYGFVRDFVGQIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAR 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD  I LNGGL D   A  +    DGVM+GRAA+    +L+ V       L   
Sbjct: 193 QLKRDFPDCVIVLNGGLADAQAAQAVAGEFDGVMLGRAAWHTPRVLSEVS------LQWW 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             I+   D     ++  +M  YAA  +  G  L+ +TR ++GL +G   +RR R +L+
Sbjct: 247 PAIRLPSDA----QVVDAMMQYAATQIARGVPLRVMTRPLLGLVNGQAGARRWRRLLS 300


>gi|124024726|ref|YP_001013842.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str.
           NATL1A]
 gi|123959794|gb|ABM74577.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. NATL1A]
          Length = 335

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 129/314 (41%), Positives = 190/314 (60%), Gaps = 12/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R +T  +LLYTEMIVA A+     +N +L F   E P+++Q+GG + 
Sbjct: 21  MMDCTDRHFRVLMRQITKKSLLYTEMIVAQALHYSKNRNKLLDFDEIEHPISIQLGGDNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ ED+GY+EINLN+GCPS RV  G+FGACLM  P IV +CI  M ++ +IP+
Sbjct: 81  KLLAEAAQMAEDWGYDEINLNIGCPSPRVKSGNFGACLMGKPKIVANCIEKMKESCNIPI 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D+      L   V +   +G +   IHARKA L GL+PK+NR IP L Y+ V
Sbjct: 141 TVKHRLGIDNLDSDDYLLTFVDTCSLAGADRFIIHARKAWLNGLNPKENRTIPPLQYERV 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++K   P+L I LNGG+  ++ +++ L   DG M+GRAAY +  + T +D         
Sbjct: 201 QKLKNHRPELIIELNGGINTINDSIEALKVFDGAMVGRAAYSHPFLWTKID--------- 251

Query: 240 SSPIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S I  + +K   R KI   +  +A +HL + G+L QI+RH++ L    PN++  R  L+
Sbjct: 252 -SLIFGQKEKYLSRSKIIKRLIPFAEKHLENDGRLWQISRHILNLIENIPNAKILRQELS 310

Query: 299 VEAGASTATHHIIE 312
            +     A   I++
Sbjct: 311 EKCQTQKADISILK 324


>gi|93005625|ref|YP_580062.1| tRNA-dihydrouridine synthase A [Psychrobacter cryohalolentis K5]
 gi|92393303|gb|ABE74578.1| TIM-barrel protein, yjbN family [Psychrobacter cryohalolentis K5]
          Length = 321

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 170/298 (57%), Gaps = 12/298 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YR+FARL   +  LYTEMI   A++ G++   L F T E PL LQ+GGADI+
Sbjct: 14  MIDWTTTDYRYFARLFNPHVYLYTEMISTGALIHGNRARHLRFDTLEHPLVLQLGGADIT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ + A+  +  GY+E+N+NVGCPS RV     GACLM  P+ V D +  M  A+ IPVT
Sbjct: 74  EMTQCAEFAQQHGYDEVNINVGCPSDRVQHNKIGACLMAEPNTVADLVKHMQAAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V+ +   G     +HAR A L+GLSPK NR+IP L Y+ VY
Sbjct: 134 VKHRIGIDDFDSYEFMADFVQKVAAGGCTRFIVHARTAWLQGLSPKQNREIPPLRYEDVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+E ++     L  +DGVMIGRA Y N  +L   +  +  P+   
Sbjct: 194 RLKQDFPTLDIEINGGIETVADIEAHLEHIDGVMIGRAFYHNPYLLAEANSLWDTPVPKR 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S             I A +  Y    +  G  L  +TRH +GLF G   +R+ R  L+
Sbjct: 254 S------------VILAQLYPYLEEQIAKGEALPTMTRHYLGLFQGLVGARKWRQALS 299


>gi|332974563|gb|EGK11483.1| tRNA dihydrouridine synthase A [Kingella kingae ATCC 23330]
          Length = 357

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 132/302 (43%), Positives = 186/302 (61%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR  AR +T +  LYTEMI A AI+ GD    L  +  E P+ALQ+GG++ +
Sbjct: 34  MLDWTDRHYRHMARQITRHTWLYTEMINAGAIVYGDPDRFLQRNECENPVALQLGGSEPT 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA+    + Y+EINLN GCPS RV +G+FGACLML+ ++V DC+ AM  A+ +IP+
Sbjct: 94  LLAQAAQKAAQYSYDEINLNCGCPSPRVQKGAFGACLMLDVNLVADCLNAMQDAVPAIPI 153

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K RIG+D Q     L + V S+  K+      +HAR A L GLSPK+NR+IP L YD 
Sbjct: 154 TIKHRIGIDKQTEYQPLADFVGSLHDKTACRTFIVHARNAWLDGLSPKENREIPPLRYDF 213

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E PDL I +NGG++  +Q  + L  VDGVM+GR AY N  ++   D  F     
Sbjct: 214 VYRLKQEFPDLEIIINGGVQTNTQIAEHLQHVDGVMMGREAYHNPYIMHDWDTLFYGE-- 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            + P  TR       +I+  + +YA + L    G  L+ + RH +GL HG   ++  R +
Sbjct: 272 -TQPAPTR------EQITQQLYNYATQQLSRQQGTILRHMVRHYLGLTHGLNGAKIWRRM 324

Query: 297 LT 298
           L+
Sbjct: 325 LS 326


>gi|238021360|ref|ZP_04601786.1| hypothetical protein GCWU000324_01259 [Kingella oralis ATCC 51147]
 gi|237868340|gb|EEP69346.1| hypothetical protein GCWU000324_01259 [Kingella oralis ATCC 51147]
          Length = 367

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 128/302 (42%), Positives = 187/302 (61%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+ AR ++ +  LYTEMI A AI+ GD    L ++  E P+ALQ+GG+D +
Sbjct: 51  MLDWTDRHFRYLARQISRHTWLYTEMINAGAIIHGDPARFLAYNESEHPIALQLGGSDPA 110

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
           +L +AAK V  + Y+EINLN GCPS RV +G+FGACLM +  +V DC+ AM +A     +
Sbjct: 111 QLAQAAKKVAQYQYDEINLNCGCPSPRVQKGAFGACLMNDVGLVADCLNAMQQAAPDCEI 170

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIGVD Q     +R+ V +++ K+ V    +HAR A L GLSPK+NR IP L Y  
Sbjct: 171 TVKHRIGVDKQTEYRIVRDFVGTLREKTPVRTYIVHARNAWLDGLSPKENRDIPPLKYHY 230

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY++K++ PDL I +NGG++  ++  + L  VDGVMIGR AY N+ ++   D  F +   
Sbjct: 231 VYQLKQDFPDLEIIINGGIKTNAEIAEHLRHVDGVMIGREAYHNTMIMRDWDRLFYD--- 287

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHI 296
                 +R  +  + ++   +  YA   L +G    L+ + RH +GL HG   +R  R +
Sbjct: 288 ------SRQPEISYPELIQRLYAYAQTQLAAGRGTILRHMARHYLGLMHGLHGARAWRQM 341

Query: 297 LT 298
           L+
Sbjct: 342 LS 343


>gi|88811969|ref|ZP_01127222.1| Dihydrouridine synthase TIM-barrel protein yjbN [Nitrococcus
           mobilis Nb-231]
 gi|88790853|gb|EAR21967.1| Dihydrouridine synthase TIM-barrel protein yjbN [Nitrococcus
           mobilis Nb-231]
          Length = 295

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 121/297 (40%), Positives = 176/297 (59%), Gaps = 9/297 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A A+  G  + +L ++++E P+A+Q GG+D  +L   A++ E +GY+E+NLNVGCPS
Sbjct: 1   MVPAQAVWHGRGERLLAYNSEEHPVAVQFGGSDPRQLAYCARMAEAYGYDEVNLNVGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM  P++V + +AAM +A ++PVTVK RIG+D Q     L   V+ +  
Sbjct: 61  ERVQAGRFGACLMAEPNLVAELVAAMRQATTLPVTVKTRIGIDQQDDYAVLAEFVEYVAN 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G     +HARKA LKGLSPK+NR  P L YD V+ +K++ P+L I LNGG+  + QA  
Sbjct: 121 AGCRTFIVHARKAWLKGLSPKENRARPPLRYDRVWRLKRDFPELEIVLNGGMRTLEQAEG 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L SVDGVM GR AY+N  +L   D +       + P+ TR       ++  +   Y  R
Sbjct: 181 QLASVDGVMFGREAYRNPYLLAKADVWL---FGDTRPVPTR------HELVHAYLPYIER 231

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            L +G +L  +TRH++GL+ G P +R  R  L+     S A   +I  A  L+   L
Sbjct: 232 QLAAGARLSCMTRHLLGLYQGMPGARAWRSHLSARGPRSGAGVEVIMQALRLLPREL 288


>gi|254252479|ref|ZP_04945797.1| TIM-barrel protein, yjbN family [Burkholderia dolosa AUO158]
 gi|124895088|gb|EAY68968.1| TIM-barrel protein, yjbN family [Burkholderia dolosa AUO158]
          Length = 242

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 118/226 (52%), Positives = 151/226 (66%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  LGF+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVQRHLGFTPSESPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMKEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAIEDYAFVRDFVGTIADAGCRTFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            +K++ P L I +NGG++ + +    L  VDG M+GR AY N  +L
Sbjct: 197 RLKRDFPSLEIVINGGIKTLDEVALHLEHVDGAMLGREAYHNPYVL 242


>gi|323144476|ref|ZP_08079078.1| tRNA dihydrouridine synthase A [Succinatimonas hippei YIT 12066]
 gi|322415754|gb|EFY06486.1| tRNA dihydrouridine synthase A [Succinatimonas hippei YIT 12066]
          Length = 337

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 135/321 (42%), Positives = 185/321 (57%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TD  +R  ARL +  ++LYTEMI ADA++ G K  +L F  +E P  LQ+GG+D  
Sbjct: 18  MVDVTDSVFRRLARLFSKKSMLYTEMIAADAVIHG-KNYLLEFHDEELPCVLQLGGSDPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL  AAKI   FGY EINLN GCPS +V  G+FGA LM  PD++ DC+ AM  A+S+PVT
Sbjct: 77  KLAAAAKIGAGFGYTEINLNAGCPSDKVQSGNFGAVLMKTPDLIADCVKAMQDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+         LV++I  +G   + +HARKA L GLSPK+NR IP LDY+ VY
Sbjct: 137 VKTRIGVDEDDSVDFTLKLVETIAATGCRHVILHARKAWLNGLSPKENRTIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+L I +NGG+  +      L  VDGVM+GRA   N  +L+ VD   S      
Sbjct: 197 LVKSAFPNLRITINGGITTIDAVKDQLKRVDGVMLGRAIIDNPFILSKVD---SEIFGSI 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       ++     D AA+    G  +  + RH++GLF+  P +R  R  L+  
Sbjct: 254 EPMPSR------EELLYKAVDLAAKIKAEGIPVHHLMRHLLGLFNSCPGARLYRRYLSEH 307

Query: 301 AGASTATHHIIETAFNLMIES 321
                A   ++  A+  M ++
Sbjct: 308 MTQLGAGPDVLIKAYKSMTDA 328


>gi|71065349|ref|YP_264076.1| tRNA-dihydrouridine synthase A [Psychrobacter arcticus 273-4]
 gi|71038334|gb|AAZ18642.1| possible dihydrouridine synthase, TIM-barrel protein family
           [Psychrobacter arcticus 273-4]
          Length = 323

 Score =  239 bits (609), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 124/298 (41%), Positives = 173/298 (58%), Gaps = 12/298 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YR+FARL   +  LYTEMI   A++ G++   L F   E PL LQ+GGAD++
Sbjct: 14  MIDWTTTDYRYFARLFNPHVYLYTEMISTGALIHGNRARHLRFDALEHPLVLQLGGADMT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ + A+  +  GY+E+N+NVGCPS RV     GACLM  P+ V D +  M  A+ IPVT
Sbjct: 74  EMTQCAEFAQQHGYDEVNINVGCPSDRVQHNKIGACLMAEPNTVADLVKHMQAAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V+ +   G     +HAR A L+GLSPK NR+IP L Y+ VY
Sbjct: 134 VKHRIGIDDFDSYEFMADFVQKVAAGGCTRFIVHARTAWLQGLSPKQNREIPPLRYEDVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+E ++     L  +DGVMIGRA Y N  +L       +N L G 
Sbjct: 194 RLKQDFPALDIEINGGIETVADIEAHLEHIDGVMIGRAFYHNPYLLAE-----ANSLWG- 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+  R D      I A +  Y    +  G  L  +TRH +GLF G   +R+ R  L+
Sbjct: 248 TPVPKRSD------ILAQLYPYLEEQIAKGEALPTMTRHYLGLFQGLVGARKWRQALS 299


>gi|124021729|ref|YP_001016036.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9303]
 gi|123962015|gb|ABM76771.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9303]
          Length = 334

 Score =  239 bits (609), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 130/320 (40%), Positives = 184/320 (57%), Gaps = 20/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLYTEM+VA A+   ++  ++L F   E PL+LQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISRRALLYTEMLVAQALHHSNRLDHLLDFDIIEHPLSLQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ + +GY+EINLNVGCPS+R   G+FGACLM  PD V  C+ AM  A  +PV
Sbjct: 80  KMLAEAARLADAWGYDEINLNVGCPSSRAKAGNFGACLMAKPDQVARCVEAMAMASPLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L   V  +  +G     +HARKA L+GL PK NR IP L +  V
Sbjct: 140 TVKHRLGIDDFDSDALLMTFVDRVSLAGATRFTVHARKAWLEGLDPKQNRTIPPLQHQRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K++ P L I +NGGLE  +  L  L + DG M+GRAAY +     ++DE     + G
Sbjct: 200 THLKQQRPQLTIEINGGLEHPADCLTALQTCDGAMVGRAAYAHPLRWKSMDEL----VYG 255

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             P          R I+AS     +  +A  HL  GG+L  + RH++ L  G P ++  R
Sbjct: 256 EEP----------RSINASQVIGGLLPHAETHLSRGGRLWDLCRHLLQLVEGVPGAKSWR 305

Query: 295 HILTVEAGASTATHHIIETA 314
             L ++A  + A   +++ A
Sbjct: 306 RDLGIKAQKADADLTVLQKA 325


>gi|78183599|ref|YP_376033.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9902]
 gi|78167893|gb|ABB24990.1| uncharacterized protein family UPF0034 [Synechococcus sp. CC9902]
          Length = 334

 Score =  238 bits (608), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 133/315 (42%), Positives = 185/315 (58%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+   ++++ +L F   E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISRRALLYSEMVVAQALHYTNRRDRLLDFDPIEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +AA++  D+GY+EINLNVGCPS RV  G+FGACLM +PD+V  C+ AM +A ++PV
Sbjct: 80  NLLADAARLALDWGYDEINLNVGCPSQRVQAGNFGACLMADPDLVARCVEAMGQATALPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L   V  +  +G     +HARKA L+GL PK NR IP L ++ V
Sbjct: 140 TVKHRIGIDDLDNDELLTAFVDRVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLQHERV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L  L   DG M+GRAAY +      +D      L  
Sbjct: 200 VALKQRRPDLLIELNGGLETPEDCLAALHECDGAMVGRAAYAHPLRWADIDH-----LIY 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  +  D    +   +  +AA HLH GG+L  + RH++ L  G P +R  R  L  
Sbjct: 255 GEPPRQLLASD----VVEGLIPHAALHLHRGGRLWDLCRHLVQLVEGVPGARHWRRELGE 310

Query: 300 EAGASTATHHIIETA 314
            +    A  +I+E A
Sbjct: 311 RSQRKGADLNILEEA 325


>gi|291326742|ref|ZP_06125653.2| tRNA dihydrouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291313086|gb|EFE53539.1| tRNA dihydrouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 288

 Score =  238 bits (608), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 128/295 (43%), Positives = 182/295 (61%), Gaps = 13/295 (4%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G K + L FS +E P+ALQ+GG+D + L + AK+ ++ GY+EINLNVGCPS
Sbjct: 1   MVTTGAIIYG-KGDYLAFSEEEHPVALQLGGSDPAALAQCAKLAQERGYDEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK- 144
            RV  G FGACLM +  +V DC+ AM   +SIPVTVK RIG+D+Q     L + ++++  
Sbjct: 60  DRVQNGRFGACLMGDAQLVADCVKAMQDVVSIPVTVKTRIGIDEQDSYAFLCDFIETVSD 119

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L + +NGG++ + +A 
Sbjct: 120 KGGCEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMAINGGVKTLEEAK 179

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS-PIKTRVDKDFWRKISASMTDYA 263
           + L  +DGVM+GR AY+N ++LT VD    N L G   P+   VD         +M  Y 
Sbjct: 180 EHLQHLDGVMVGREAYQNPSILTVVD----NQLFGEHFPVTNGVDA------VRAMYPYI 229

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            + L  G  L  +TRHM+G+F G P +R+ R  L+  A    A   ++E A   +
Sbjct: 230 EKELSKGAYLGHMTRHMLGIFQGIPGARQWRRHLSENAHKKGADLAVVEQALEFV 284


>gi|71274660|ref|ZP_00650948.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Dixon]
 gi|71899628|ref|ZP_00681782.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
 gi|170730927|ref|YP_001776360.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa M12]
 gi|71164392|gb|EAO14106.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Dixon]
 gi|71730580|gb|EAO32657.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
 gi|167965720|gb|ACA12730.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa M12]
          Length = 340

 Score =  238 bits (608), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 138/319 (43%), Positives = 196/319 (61%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAARIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V  + + S    I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVSRASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN    
Sbjct: 203 YRLKRERPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSNAPLL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT 
Sbjct: 263 PR-----------TLLLRALRPYVEAWLEQGLALRHIVRHLLGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|171058412|ref|YP_001790761.1| tRNA-dihydrouridine synthase A [Leptothrix cholodnii SP-6]
 gi|170775857|gb|ACB33996.1| TIM-barrel protein, yjbN family [Leptothrix cholodnii SP-6]
          Length = 342

 Score =  238 bits (608), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 125/299 (41%), Positives = 175/299 (58%), Gaps = 11/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT    LYTEM+   A+L GD+   L F   E P+ALQ+GG+D +
Sbjct: 24  MLDWTDRHCRHFHRLLTRRTRLYTEMVTTGALLHGDQARHLDFDAIEHPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ + +GY+E+NLN GCPS RV +G+FGACLM  P +V D + AM  A+ +PVT
Sbjct: 84  DLAACARLAQRWGYDEVNLNCGCPSERVQKGAFGACLMAEPALVADGVKAMRDAVDVPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A L+GLSPK+NR IP L Y+ VY
Sbjct: 144 VKHRIGIDRGESYDFVRDFVGTLADAGCEVFIVHARNAWLQGLSPKENRDIPPLRYEQVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+    +    L  VDGVM+GR AY     +   D  F      +
Sbjct: 204 QLKRDFPQLTIVINGGIRTDDEIAAHLAHVDGVMVGRQAYHEPWQMAGWDLRF---FGEA 260

Query: 241 SPIKTRVDKDFWRKISASMTDY-AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P   R       ++ A+  DY  A+HL  G    Q  RH +GL++G   +R  R   +
Sbjct: 261 APAGERA------QVEAAWMDYLQAQHL-GGRPWPQAMRHALGLWNGVAGARSWRQFWS 312


>gi|119505356|ref|ZP_01627430.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2080]
 gi|119458811|gb|EAW39912.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2080]
          Length = 295

 Score =  238 bits (607), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 126/290 (43%), Positives = 172/290 (59%), Gaps = 9/290 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A+L GD    L + +QE PLALQ+GG++   L   AK+ E   Y+E+NLN GCPS
Sbjct: 1   MVTTGALLHGDIDRHLNYGSQEHPLALQLGGSNPQDLARCAKLAEARHYDEVNLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM  P++V DCI AM +A+ IPVTVK RIG+D Q     LR+ V  + +
Sbjct: 61  DRVQNGRFGACLMAEPELVRDCITAMREAVDIPVTVKQRIGIDHQESFDELRDFVGIVAE 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G N   +HARKA L+GLSPK NR+IP L+Y  VY +K++ P L I LNGG++ + +   
Sbjct: 121 GGCNVFIVHARKAWLEGLSPKQNREIPPLNYTWVYALKEQFPQLTIVLNGGIQSLEECEH 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GRAAY+   +L++VD   S       P  +R        +   ++DY   
Sbjct: 181 HLTKVDGVMLGRAAYQTPWLLSSVD---SRIFGAEDPAYSR------ESVIYKLSDYVET 231

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
           +L  GG+L  +TRH++GLFH  P  R  R  L+  A  S A   ++  A 
Sbjct: 232 YLAQGGRLNHVTRHILGLFHQQPGGRLFRRALSEGAHLSGADATVLLAAL 281


>gi|261415030|ref|YP_003248713.1| TIM-barrel protein, yjbN family [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371486|gb|ACX74231.1| TIM-barrel protein, yjbN family [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302326032|gb|ADL25233.1| tRNA-dihydrouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 345

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 123/313 (39%), Positives = 189/313 (60%), Gaps = 18/313 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M+D TDRH R+F RLL+ + LLY+EM+V+  +L  + K++ LG    E P  LQ+GG++ 
Sbjct: 14  MLDCTDRHERYFLRLLSKHILLYSEMVVSTGLLHCENKDLFLGHEPFEHPAVLQLGGSNP 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L  A+K+VE  G++E+NLN GCPS RV  G+FGACLM   ++V DC  AM  A+SIPV
Sbjct: 74  ADLASASKLVEAAGFSEVNLNCGCPSDRVQNGNFGACLMKEKNVVADCFKAMQDAVSIPV 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++KCRIGVDD        + +++++ +G     +HARKA LKGLSPK+NR++P L Y+ V
Sbjct: 134 SIKCRIGVDDLDSWEFFTDFIQTVRDAGCKIFIVHARKAWLKGLSPKENREVPPLHYEFV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF------ 233
           + +K E P+L + +NGG++ + Q  + L  +DGVM+GR AY+N   L   D         
Sbjct: 194 HRLKAEMPELNLSINGGIKTLDQIEEQLKDLDGVMVGREAYENPWFLHDADARIFGDVRP 253

Query: 234 --SNP---LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             ++P   + G++   TR      + +  +   Y  +    G     + +H+ GLF G P
Sbjct: 254 ESNDPAEIIAGNARPATR------KALLEAYLPYVEKQTAEGCPATILVKHLYGLFAGLP 307

Query: 289 NSRRCRHILTVEA 301
            +R+ R  L+ E+
Sbjct: 308 GARKFRATLSNES 320


>gi|303256981|ref|ZP_07342995.1| tRNA-dihydrouridine synthase A [Burkholderiales bacterium 1_1_47]
 gi|330999169|ref|ZP_08322888.1| tRNA dihydrouridine synthase A [Parasutterella excrementihominis
           YIT 11859]
 gi|302860472|gb|EFL83549.1| tRNA-dihydrouridine synthase A [Burkholderiales bacterium 1_1_47]
 gi|329575369|gb|EGG56913.1| tRNA dihydrouridine synthase A [Parasutterella excrementihominis
           YIT 11859]
          Length = 343

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 180/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL++ A LYTEM+   A++ GD  + L FS  E  +ALQ+GG+D  
Sbjct: 18  MLDLTDRHCRYFHRLLSHRARLYTEMVTTGALVHGDVPHHLDFSEAEHRVALQLGGSDPK 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ + +GY+E+NLN GCPS RV +GSFGACLM  P +V DC+ AM  A  +PVT
Sbjct: 78  DLAHGAKLAQQWGYDEVNLNCGCPSERVQKGSFGACLMAEPGLVADCVKAMQDATHLPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G+D       +R+ V ++  +GV    +HAR A LKGLSPK+NR+IP L  ++VY
Sbjct: 138 IKHRVGIDANNDYGFVRDFVGTLFNAGVRVFIVHARNAWLKGLSPKENREIPPLRREVVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P+  I +NG L+D+ +    L  VDGVM+GRAAY    +LT VD    N     
Sbjct: 198 QLKKDFPEAIIVINGALQDLGECEAELKHVDGVMLGRAAYYTPWLLTDVDARLYN--DEH 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P+ TR       ++  +M +Y          L+   RHM GL  G   ++  R  L+
Sbjct: 256 APV-TR------DRVIDAMEEYVRFIKPDDHSLRACCRHMHGLLTGLAGAKVWRRTLS 306


>gi|28199556|ref|NP_779870.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa Temecula1]
 gi|182682292|ref|YP_001830452.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa M23]
 gi|38604766|sp|Q87AY2|DUSA_XYLFT RecName: Full=tRNA-dihydrouridine synthase A
 gi|28057671|gb|AAO29519.1| conserved hypothetical protein [Xylella fastidiosa Temecula1]
 gi|182632402|gb|ACB93178.1| dihydrouridine synthase DuS [Xylella fastidiosa M23]
          Length = 332

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 141/319 (44%), Positives = 198/319 (62%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAASIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVK-SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V   I  S    I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVIGASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN    
Sbjct: 203 YRLKRECPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSN---- 258

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+  R        +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT 
Sbjct: 259 -APVLPRA------LLLRALRPYVEAWLEQGVTLRHIVRHLLGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|328676669|gb|AEB27539.1| tRNA-dihydrouridine synthase A [Francisella cf. novicida Fx1]
          Length = 295

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 125/305 (40%), Positives = 176/305 (57%), Gaps = 13/305 (4%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG      +   K+ E+ GYNEIN+N
Sbjct: 1   MLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPKDFISCGKLAEELGYNEININ 60

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           VGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++VKCRIG D       L + V
Sbjct: 61  VGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPISVKCRIGYDHNDSYEELYDFV 120

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
               ++GV+ + IHARK  L GLSPK+NR IP L YD+VY IKK+ P+L +G+NGG+  +
Sbjct: 121 DKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVYSIKKDFPNLELGINGGITTI 180

Query: 201 SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFWRKISASM 259
            +  + L  VD VMIGR AY N  +    D  F N P T  S +          +I+  M
Sbjct: 181 QETQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTDISAL----------EIAYKM 230

Query: 260 TDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +Y    + +    KL  IT+H + LF+G PN++  R  L+  A    A      TA  +
Sbjct: 231 AEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLSENATKKEANVDTFLTALEV 290

Query: 318 MIESL 322
               L
Sbjct: 291 FENKL 295


>gi|78211573|ref|YP_380352.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9605]
 gi|78196032|gb|ABB33797.1| uncharacterized protein family UPF0034 [Synechococcus sp. CC9605]
          Length = 331

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 135/307 (43%), Positives = 181/307 (58%), Gaps = 20/307 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+    ++N +L F   E P+ALQ+GG D 
Sbjct: 17  MLDCTDRHFRVLMRQISRRALLYSEMVVAQALHHSKRRNKLLDFDPVEHPIALQVGGDDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L EAA++ +D+GY+EINLNVGCPS +V  G+FGACLM  PD+V  C+ AM  A  +PV
Sbjct: 77  ALLAEAARLAQDWGYDEINLNVGCPSQKVQAGNFGACLMAEPDLVARCVEAMVGAGGLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD    V L N V  +  +G +   IHARKA L+GL PK NR IP L ++ V
Sbjct: 137 TVKHRIGIDDLDSDVLLMNFVDRVALAGASRFAIHARKAWLEGLDPKQNRTIPPLQHERV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L+ L   DG M+GRAAY +    T+VD       + 
Sbjct: 197 VALKQRRPDLVIELNGGLECPEDCLQALEGCDGAMVGRAAYSHPLRWTSVDALIFGEES- 255

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                        R+I AS     +  +AA HL  GG+L  + RH++ L  G   +R  R
Sbjct: 256 -------------RQILASDIVDGLLPHAAAHLEQGGRLWDLCRHLVQLVEGVRGARHWR 302

Query: 295 HILTVEA 301
             L  +A
Sbjct: 303 RELGEKA 309


>gi|325267704|ref|ZP_08134355.1| tRNA dihydrouridine synthase A [Kingella denitrificans ATCC 33394]
 gi|324980828|gb|EGC16489.1| tRNA dihydrouridine synthase A [Kingella denitrificans ATCC 33394]
          Length = 383

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 128/302 (42%), Positives = 179/302 (59%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T +  LYTEM+ A AI+ GD    L  +  E P+ALQ+GG++ +
Sbjct: 63  MLDWTDRHYRYMARQITRHTWLYTEMVNAGAIVFGDPDRFLARNECENPVALQLGGSEPN 122

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
            L +AA+   ++GY+EINLN GCPS RV +G+FGACLML+  +V DC+ AM  A     V
Sbjct: 123 LLAQAARKAAEYGYDEINLNCGCPSPRVQKGAFGACLMLDAPLVADCLNAMQDAAPDTAV 182

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D Q     L + V   ++ +      +HAR A L GLSPK+NR++P L Y++
Sbjct: 183 TVKHRIGIDRQTEYAPLADFVGHLVRHTPCRTFVVHARNAWLDGLSPKENREVPPLRYEL 242

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F     
Sbjct: 243 VYRLKQEFPDLEIIINGGIRTNEDIALHLQHVDGVMVGREAYHNPFVMHDWDRLF---YR 299

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              P   R +      I   + +YA + L  + G  L+ + RH +GL HG P +R  R +
Sbjct: 300 EKQPAPERDE------IVQRLYEYAQQQLSKNQGTILRHMARHYLGLLHGLPKARVWRRM 353

Query: 297 LT 298
           L+
Sbjct: 354 LS 355


>gi|221066936|ref|ZP_03543041.1| TIM-barrel protein, yjbN family [Comamonas testosteroni KF-1]
 gi|220711959|gb|EED67327.1| TIM-barrel protein, yjbN family [Comamonas testosteroni KF-1]
          Length = 322

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 126/315 (40%), Positives = 183/315 (58%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RLL+ + LLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 1   MMDWTDKHCRYFHRLLSQHTLLYTEMVTTGALVHGDVARHLRFEAEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++   +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   +S+PVT
Sbjct: 61  DLAHSARLGVQWGYDEINLNCGCPSERVQRGAFGACLMNEAALVADCVKAMADVVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G +   +HAR A LKGLSPK+NR+IP L Y++V 
Sbjct: 121 VKHRIGIDKIESYDFVRDFVGTVADAGCHVFVVHARNAWLKGLSPKENREIPPLRYEVVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  VDGVM+GR AY N   + + D  +       
Sbjct: 181 QLKRDFPGLTIAVNGGIKTDDVVQQQLQQVDGVMVGREAYHNPWWMASWDALY---YQDE 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S  +TR        I   M  Y  R     G     I RHM+GL +G   +RR R + + 
Sbjct: 238 SRERTR------EGIEEQMVLYMEREAREHGTHWYSIARHMLGLRNGLAGARRWRQVWSD 291

Query: 300 EAGASTATHHIIETA 314
                   H +++ A
Sbjct: 292 HRLKPLPPHEVMKLA 306


>gi|116071792|ref|ZP_01469060.1| hypothetical protein BL107_06569 [Synechococcus sp. BL107]
 gi|116065415|gb|EAU71173.1| hypothetical protein BL107_06569 [Synechococcus sp. BL107]
          Length = 334

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 134/315 (42%), Positives = 183/315 (58%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLYTEM+VA A+   ++++ +L F   E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISRRALLYTEMVVAQALHYTNRRDRLLDFDPIEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +AA++  D+GY+EINLNVGCPS RV  G+FGACLM +PD+V  C+ AM +A  +PV
Sbjct: 80  NLLADAARLALDWGYDEINLNVGCPSQRVQAGNFGACLMADPDLVARCVEAMGRASGLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L   V  +  +G     +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRIGIDDLDNDELLTAFVDRVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L  L   DG M+GRAAY +      +D      L  
Sbjct: 200 VALKQRRPDLLIELNGGLETPEDCLVALHECDGAMVGRAAYAHPLRWADIDH-----LIY 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  +  D    +   +  +AA HL  GG+L  + RH++ L  G P +R  R  L  
Sbjct: 255 GEPPRQLLASD----VVEGLMPHAALHLQRGGRLWDLCRHLVQLVEGVPGARHWRRELGE 310

Query: 300 EAGASTATHHIIETA 314
            +    A  +I+E A
Sbjct: 311 RSQRKGADLNILEEA 325


>gi|319779632|ref|YP_004130545.1| tRNA dihydrouridine synthase A [Taylorella equigenitalis MCE9]
 gi|317109656|gb|ADU92402.1| tRNA dihydrouridine synthase A [Taylorella equigenitalis MCE9]
          Length = 325

 Score =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 177/298 (59%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TD+H RFF RLL+  ALL+TEM+   A++ GD    L F+ +E P+ALQ+GGA+  
Sbjct: 17  MLDVTDKHCRFFHRLLSPEALLFTEMVTTGALIFGDVPRHLDFNVEEHPVALQLGGAEPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +K+ E++GY+EINLN GCPS RV +GSFGACLML PD+V DC  AM +  ++P++
Sbjct: 77  DLAYCSKLGEEWGYDEINLNCGCPSDRVQKGSFGACLMLEPDLVADCWVAMNECTTVPIS 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+GVDD      + + V  +   G      HAR A LKGLSPKDNR IP L YD V 
Sbjct: 137 IKHRLGVDDHNDYEFVYHFVSKLYDVGCRLFITHARNAFLKGLSPKDNRSIPPLKYDYVS 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + PD    +NGG+ +   A+++L   DG+M+GR A+        +    +     S
Sbjct: 197 RLKADFPDANFVINGGISNYELAMQLLEEFDGIMLGRLAWHEPRAFMNIA---TTEFERS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P      +D       ++  YA +++ +GG L+++   ++G  +G   +R+ R IL+
Sbjct: 254 EPPNFTFIRD-------ALIGYAKKNIENGGSLREVVNPVLGFMNGLKGARKFRQILS 304


>gi|71901816|ref|ZP_00683882.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
 gi|71728415|gb|EAO30580.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
          Length = 332

 Score =  236 bits (602), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 139/319 (43%), Positives = 195/319 (61%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAARIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V   I  S    I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVIGASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN    
Sbjct: 203 YRLKRECPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSNAPLL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT 
Sbjct: 263 PR-----------ALLLRALRPYVEAWLEQGLTLRHIVRHLLGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|160899058|ref|YP_001564640.1| tRNA-dihydrouridine synthase A [Delftia acidovorans SPH-1]
 gi|160364642|gb|ABX36255.1| TIM-barrel protein, yjbN family [Delftia acidovorans SPH-1]
          Length = 336

 Score =  236 bits (602), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 127/299 (42%), Positives = 178/299 (59%), Gaps = 10/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+  RLL+ + LLYTEM+   A+L GD    L F  +E P+ALQ+GG++ S
Sbjct: 20  MMDWTDKHCRYLHRLLSRHTLLYTEMVTTGALLHGDVPRHLRFEAEEHPVALQLGGSEPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   + +PVT
Sbjct: 80  DLAQAARLGAQWGYDEINLNCGCPSERVQRGAFGACLMNEAPLVADCVKAMVDVVDVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y+IV 
Sbjct: 140 VKHRIGIDKDESYEFVRDFVGTVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYEIVA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I +NGG++  +    +L  VDGVM+GR AY N   L + D  +      +
Sbjct: 200 RLKQDFPELTIAINGGIKADATVQDLLQQVDGVMVGREAYHNPWWLASWDALYYG---DA 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S   TR        I   M  Y  R   + G     I RHM+GL +G   +RR R + +
Sbjct: 257 SVEHTR------ESIEEQMVAYMEREARTHGTHWYSIARHMLGLRNGLAGARRWRQVWS 309


>gi|15836989|ref|NP_297677.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa 9a5c]
 gi|38605069|sp|Q9PGB5|DUSA_XYLFA RecName: Full=tRNA-dihydrouridine synthase A
 gi|9105221|gb|AAF83197.1|AE003890_6 conserved hypothetical protein [Xylella fastidiosa 9a5c]
          Length = 340

 Score =  236 bits (601), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 138/319 (43%), Positives = 195/319 (61%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D+GY+EINLN GCPS RV  GSFGA LM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAARIAVDWGYSEINLNCGCPSDRVQAGSFGARLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V  + + S    I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVSRASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L   D   SN    
Sbjct: 203 YRLKRERPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFDCALSNAPLL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y    L  G  L+ I RH+ GLFHG P  R  R +LT 
Sbjct: 263 PR-----------ALLLRALRPYVEVWLEQGLTLRHIVRHLFGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|33862288|ref|NP_893848.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9313]
 gi|33640401|emb|CAE20190.1| conserved hypothetical protein [Prochlorococcus marinus str. MIT
           9313]
          Length = 339

 Score =  236 bits (601), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 129/320 (40%), Positives = 183/320 (57%), Gaps = 20/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLYTEM+VA A+   ++  ++L F   E PL+LQ+GG D 
Sbjct: 25  MLDCTDRHFRVLMRQISRRALLYTEMLVAQALHHSNRLDHLLDFDIIEHPLSLQVGGDDP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ + +GY+EINLNVGCPS+R   G+FGACLM  PD V  C+ AM  A  +PV
Sbjct: 85  KILAEAARLADAWGYDEINLNVGCPSSRAKAGNFGACLMAKPDQVARCVEAMAMASPLPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D+      L   V  +  +G     +HARKA L+GL PK NR IP L +  V
Sbjct: 145 TVKHRLGIDNFDSDALLMTFVDRVSIAGATRFTVHARKAWLEGLDPKQNRTIPPLQHQRV 204

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K++ P L I +NGGLE  +  L  L + DG M+GRAAY +     ++DE     + G
Sbjct: 205 THLKQQRPQLTIEINGGLEHPADCLTALQTCDGAMVGRAAYAHPLRWQSMDEL----VYG 260

Query: 240 SSPIKTRVDKDFWRKISAS-----MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             P          R I+AS     +  +A  HL  GG+L  + RH++ L  G P ++  R
Sbjct: 261 EQP----------RSINASQVIGGLLPHAETHLSRGGRLWDLCRHLLQLVEGVPGAKAWR 310

Query: 295 HILTVEAGASTATHHIIETA 314
             L ++A    A   +++ A
Sbjct: 311 RDLGIKAQKVDADLRVLQKA 330


>gi|145548359|ref|XP_001459860.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124427687|emb|CAK92463.1| unnamed protein product [Paramecium tetraurelia]
          Length = 346

 Score =  235 bits (600), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 127/305 (41%), Positives = 184/305 (60%), Gaps = 16/305 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI----LRGDKKNILGFSTQEKPLALQIGG 56
           M+D T  H+R F RLLT N +LYTEMI  +AI    +      +L +S  E P+  Q+GG
Sbjct: 14  MIDITYEHFRVFFRLLTKNCVLYTEMIHENAINLSRVLKPFPLVLDYSQVEHPVVCQLGG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  KL +AA+I E  G++EINLNVGCPS RV +G+FGACLM  P +V  C+  M +A+ 
Sbjct: 74  NDPEKLAKAAQIAEQAGFDEINLNVGCPSERVQDGAFGACLMKEPHLVAQCMKKMKEAVK 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLD 175
           IP T+KCR+GVD+      +RN V+ + K G VN   +HARKA LKGL+P +NR +P L 
Sbjct: 134 IPCTLKCRLGVDNLDSYEFVRNFVEIVYKEGEVNHFIMHARKAFLKGLNPHENRTVPPLK 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           YD VY++KKE P++   LNGG++      ++LP+VDG+MIGR+A++N  M +  D  +  
Sbjct: 194 YDWVYQLKKEFPEIKFTLNGGIKCTEHIDQVLPNVDGIMIGRSAHENPWMFSDFDRLY-- 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL--QQITRHMIGLFHGFPNSRRC 293
              G +    R      ++I     ++      +G K+  Q   + +I LF+G  N++R 
Sbjct: 252 -YGGENQNYNR------KEILEQYAEFVEEKRATGCKVSTQMCVKPIINLFNGESNNKRY 304

Query: 294 RHILT 298
           R  L+
Sbjct: 305 RQFLS 309


>gi|307578569|gb|ADN62538.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 309

 Score =  235 bits (599), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 140/318 (44%), Positives = 197/318 (61%), Gaps = 12/318 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           ++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ + 
Sbjct: 1   MNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPAL 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L +AA I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVTV
Sbjct: 61  LAKAASIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           KCR+GV++          V   I  S    I +HAR A L+GLSPK+NR+IP L YD VY
Sbjct: 121 KCRLGVNEDDDYGRFAKFVDWVIGASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN     
Sbjct: 181 RLKRECPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSN----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+  R        +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT  
Sbjct: 236 APVLPRA------LLLRALRPYVEAWLEQGVTLRHIVRHLLGLFHGQPGGRVFRQVLTQG 289

Query: 301 AGASTATHHIIETAFNLM 318
              S A   ++E A +++
Sbjct: 290 GQRSDADWSLVEQALSII 307


>gi|121607273|ref|YP_995080.1| tRNA-dihydrouridine synthase A [Verminephrobacter eiseniae EF01-2]
 gi|121551913|gb|ABM56062.1| TIM-barrel protein, yjbN family [Verminephrobacter eiseniae EF01-2]
          Length = 360

 Score =  235 bits (599), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 127/302 (42%), Positives = 177/302 (58%), Gaps = 10/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT    LYTEM+ A A+L G  +  L  + +E P+ALQ+GG + +
Sbjct: 37  MMDWTDRHCRYFHRLLTRQTRLYTEMVNAGAVLHGGTERHLRLNAEEHPVALQLGGNEPA 96

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++   +GY+EINLN GCPS RV  G+FGA LM  P  V DC+ AM   +  PVT
Sbjct: 97  DLARAARLGAQWGYDEINLNCGCPSDRVQRGAFGARLMQTPQRVADCVKAMRDMVDRPVT 156

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  +  +G +   +HAR A L+GLSPK+NR+IP L Y +V+
Sbjct: 157 VKHRIGIDQGQSYGFVRDFVGVVADAGCSVFIVHARNAWLQGLSPKENREIPPLRYALVH 216

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSN---P 236
           ++K + P L + +NGG+   +   + L  +DGVM+GR AY     L   D  Y++N   P
Sbjct: 217 QLKADFPRLTVVINGGIATDAVVQQQLHLLDGVMVGRQAYHQPWWLARWDALYYANRSGP 276

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             G+SP+     +   R + A M   AA H   G     I RHM+GL H  P +R  R +
Sbjct: 277 CAGASPLTREAVE---RAMVAYMEREAALH---GTPWPHIARHMLGLRHSLPGARLWRQL 330

Query: 297 LT 298
            +
Sbjct: 331 WS 332


>gi|330813858|ref|YP_004358097.1| hypothetical protein SAR11G3_00883 [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486953|gb|AEA81358.1| hypothetical protein SAR11G3_00883 [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 294

 Score =  234 bits (598), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 126/296 (42%), Positives = 178/296 (60%), Gaps = 16/296 (5%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A L GD++ +LGF+  EKPLALQ+GG++ + L E AKI ED GY+EIN+N+GCPS
Sbjct: 1   MVSTGAALNGDREKVLGFNNFEKPLALQVGGSNKNDLAEVAKIAEDMGYDEININLGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            +V +  FGACL+  PD+V DCI +M  A  IPVT K RIG DD      L + V  +  
Sbjct: 61  KKVQKNQFGACLIKEPDLVADCIDSMVNACKIPVTAKTRIGYDDVEEFNYLNSFVNKMSN 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G   + +HAR+AILKGLSPK+N  IP L+Y +V +IK+ENP+L I +NGG+ + S+  +
Sbjct: 121 AGCKTVILHARRAILKGLSPKENLNIPKLNYPMVNQIKQENPNLEIIINGGITECSEIKE 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            L  VDGVMIGR  Y++   L  ++ E F+N     S I TR       +I   +  Y +
Sbjct: 181 HLLHVDGVMIGRKIYQSPYFLADIEREIFNN-----SEILTRA------QIVEEIVKYVS 229

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTA----THHIIETAFN 316
             +  G ++ QI RH +GL+HG   S   +  L+    A  +     +HI+E   N
Sbjct: 230 YEVQKGTRVNQIMRHTVGLYHGQKGSTEWKRYLSNNMMARDSDFQKVNHILEIVQN 285


>gi|160872814|ref|ZP_02062946.1| tRNA-dihydrouridine synthase A [Rickettsiella grylli]
 gi|159121613|gb|EDP46951.1| tRNA-dihydrouridine synthase A [Rickettsiella grylli]
          Length = 330

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 126/299 (42%), Positives = 176/299 (58%), Gaps = 9/299 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADI 59
           M+ WT RHY +F RL+   A LYTEM  A AIL+   ++ +L     EK LA+Q+GG   
Sbjct: 17  MLGWTTRHYHYFFRLICKKAQLYTEMFTAQAILKSPARERLLTVDANEKALAIQLGGGIA 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S L +AAKIVE +GY+EINLNVGCPS +V  G FG  L+  P+ V D IAAM   + +PV
Sbjct: 77  SDLSKAAKIVESYGYSEINLNVGCPSEKVQSGGFGVVLLKEPNRVADAIAAMKAVVRLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIGVD+      L + ++ +  +G +   IHARKA L G+SPK+NR+IP L+Y  V
Sbjct: 137 TVKTRIGVDNDESYDYLASFIRQVSLAGCDTFIIHARKAWLHGVSPKENREIPPLNYPWV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I LNGG+  + +A + L  VD VMIGRAA+ N  +   +D   S     
Sbjct: 197 YQIKRDFPHLTIVLNGGITCLKRAYQQLQHVDAVMIGRAAWYNPYLFAQLDALISPQDRF 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             P +  +   +          Y  + L SG  L  + + ++GLFHG   +++ R  L+
Sbjct: 257 IVPHRFSIILQY--------LPYLEKALKSGENLAHLIQPLLGLFHGVVGTKQWRQTLS 307


>gi|329905074|ref|ZP_08274002.1| tRNA-dihydrouridine synthase A [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327547746|gb|EGF32522.1| tRNA-dihydrouridine synthase A [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 295

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 118/274 (43%), Positives = 173/274 (63%), Gaps = 3/274 (1%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A++ GD    L F+ +E P+ALQ+GG+D + L  +A++ + +GY+EINLN GCPS
Sbjct: 1   MVTTGALVHGDVARHLDFNDEEHPVALQLGGSDPADLAHSARLGQQWGYDEINLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV +G+FGACLM  P +V DC+ AM  A+SI VTVK RIG+D       +R+ V ++ +
Sbjct: 61  ERVQKGAFGACLMAEPQLVADCVKAMRDAVSIDVTVKHRIGIDKNESYAFMRDFVGTVAE 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G     +HAR AILKGLSPK+NR++P L YD VY++K+E PDL I +NGG++  ++   
Sbjct: 121 AGCTTFIVHARNAILKGLSPKENREVPPLRYDAVYQLKREFPDLEIIINGGIKTEAEIDL 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            L  VDGVM+GR AY N  ++   D  Y+ +P T  +  +T V +     I + +    +
Sbjct: 181 HLQHVDGVMLGREAYHNPYLMAGFDARYYDDPATPRT--RTEVLEAMLPYIRSQLGPTPS 238

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             L +G +L  ITRHM+GL  G P +R  R  L+
Sbjct: 239 IPLKAGPRLNSITRHMLGLMAGLPGARHFRQTLS 272


>gi|218294737|ref|ZP_03495591.1| dihydrouridine synthase DuS [Thermus aquaticus Y51MC23]
 gi|218244645|gb|EED11169.1| dihydrouridine synthase DuS [Thermus aquaticus Y51MC23]
          Length = 342

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/299 (40%), Positives = 178/299 (59%), Gaps = 13/299 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+R+  R ++    LYTEM V  A+L+G+++ +LGF  +E+PLALQ+ G D  
Sbjct: 11  MVDRTDRHFRYLVRQVSRGVRLYTEMTVDQAVLKGNRERLLGFRPEERPLALQLAGHDPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E FGY+E+NLN+GCPS R  EG +GACL+ +P  V + + AM +A+ +PV+
Sbjct: 71  SLAEAARIGEAFGYDEVNLNLGCPSERAQEGGYGACLLRDPGRVAEILRAMVQAVRVPVS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D      AL  LV+   +SGV    +HAR A+L  LS + NR+IP L ++ VY
Sbjct: 131 VKMRLGLDGGESYPALARLVERFAQSGVEVFIVHARSALL-ALSTRANREIPPLRHEWVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE-YFSNPLTG 239
            +K++ P L    NGG+  + +AL  L  VDG M+GRA Y++  +L   D+  F  P   
Sbjct: 190 RLKEDFPHLTFVTNGGIRSLEEALAHLKRVDGAMLGRAVYEDPFVLEEADQKVFGLP--- 246

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             P + +V +        +M  Y    +  G     + RHM+ LF G P  R  R +L+
Sbjct: 247 HRPSRLQVAR--------AMRAYLEEEVALGTPPWAVLRHMLNLFRGRPKGRLWRRLLS 297


>gi|163857356|ref|YP_001631654.1| tRNA-dihydrouridine synthase A [Bordetella petrii DSM 12804]
 gi|163261084|emb|CAP43386.1| putative dihydrouridine synthase [Bordetella petrii]
          Length = 358

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 131/298 (43%), Positives = 180/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L G+    L F   E P+ALQ+GG++  
Sbjct: 34  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGNVGRHLDFDAAEHPVALQLGGSEPD 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ +PVT
Sbjct: 94  ALAHAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPALVADCMKAMQDAVDLPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G+D       +R+ V +I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 154 IKHRLGLDYDESYSFVRDFVGAIHATGCRVFIVHARNAVLKGLSPKDNREIPPLRYDVAR 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PD  I LNGGL D +QA+      DGVM+GRAA+    +L+ V    S  L  S
Sbjct: 214 QLKADFPDSVIVLNGGLADAAQAVGAAGEFDGVMLGRAAWHTPRVLSEV----SMQLWPS 269

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             + T        ++  +M  YAA  +  G  L+ I R ++GL +G   +RR R +L+
Sbjct: 270 VRLPTDA------QVVDAMVRYAAGQVAQGVPLRVIVRPLLGLVNGQSGARRWRRMLS 321


>gi|187478770|ref|YP_786794.1| tRNA-dihydrouridine synthase A [Bordetella avium 197N]
 gi|115423356|emb|CAJ49890.1| tRNA-dihydrouridine synthase A [Bordetella avium 197N]
          Length = 327

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 181/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL  +A LYTEMI   A++ G+ +  L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPHARLYTEMITTGALMHGNVERHLDFDETEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++   +GY+E+NLN GCPS RV  G+FGACLM  PD+V DC+ AM  A+ IPVT
Sbjct: 73  ALAAAARLGRQWGYDEVNLNCGCPSERVQRGAFGACLMAEPDLVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYNESYAFVRDFVGKIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAA 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+  I LNGGL D +QAL      DGVM+GRAA+    +L+ +    S  L  S
Sbjct: 193 QLKHDFPEATIVLNGGLADATQALDAASRFDGVMLGRAAWHTPRVLSEL----SLRLWPS 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           + + T        ++  +M +Y  R +  G  L+ + R ++GL +    +R  R +L+
Sbjct: 249 TRLPTDA------QVVDAMVEYTTRQVARGVPLRVMLRPLLGLVNNQSGARGWRRLLS 300


>gi|254430822|ref|ZP_05044525.1| tRNA-dihydrouridine synthase A [Cyanobium sp. PCC 7001]
 gi|197625275|gb|EDY37834.1| tRNA-dihydrouridine synthase A [Cyanobium sp. PCC 7001]
          Length = 345

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 135/325 (41%), Positives = 183/325 (56%), Gaps = 19/325 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------GDKKNILGFSTQEKP 49
           M+D TDRH+R   R +T ++LLYTEM+VA A+             G  + +LGF   EKP
Sbjct: 20  MMDCTDRHFRVLMRQITRHSLLYTEMVVALALHHARQAPGAEAPGGRLERLLGFDRIEKP 79

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +ALQ+GG D + L EA ++ E +GY+E+NLNVGCPS RV +G FGACLM +P+ V  C+A
Sbjct: 80  IALQLGGDDPALLAEACRLAEAWGYDEVNLNVGCPSDRVRKGRFGACLMAHPEQVAACVA 139

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           AM  A S+PVTVK RIG+D       L   V ++  +G     +HARKA L+GL PK NR
Sbjct: 140 AMAAACSLPVTVKHRIGIDHHDSYPELLGFVDTVAAAGACRFSVHARKAWLEGLDPKQNR 199

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
            IP L YD V+ +K++ P L + LNGGLE      + L  VDG M+GRAAY +      V
Sbjct: 200 TIPPLRYDWVHRLKRDRPQLIVELNGGLETPEACRQQLDHVDGAMVGRAAYAHPLRWAGV 259

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           D       +   P  + V +         +  +A R    GG+L  I RH++ +  G P 
Sbjct: 260 DRSLHGDPSRGEPQASDVVR--------GLVPHAERWCGRGGRLWPIARHLVHVVEGVPG 311

Query: 290 SRRCRHILTVEAGASTATHHIIETA 314
           +RR R  LT  A    A   ++E A
Sbjct: 312 ARRWRQALTEAASRPGAGPEVLELA 336


>gi|149201731|ref|ZP_01878705.1| tRNA-dihydrouridine synthase A [Roseovarius sp. TM1035]
 gi|149144779|gb|EDM32808.1| tRNA-dihydrouridine synthase A [Roseovarius sp. TM1035]
          Length = 296

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 131/292 (44%), Positives = 173/292 (59%), Gaps = 11/292 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A A++RG    +L  S +E P+ALQ+GG+D ++L +AA++    GY EINLN GCPS
Sbjct: 1   MVTAPALVRGGAVYLLEHSPEEYPVALQLGGSDPAELAQAARMGAQAGYAEINLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGA LM  P +V  C  AM +A  + VTVKCRIGVDDQ P   L   +  +  
Sbjct: 61  DRVQSGRFGAILMTEPALVAACCVAMREAQPVEVTVKCRIGVDDQNPEEVLPEFLAHVVA 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +GV  + IHARKA L GLSPK+NR IP LDYD+V  +K   P+L I +NGG+  + QA+ 
Sbjct: 121 AGVQRVQIHARKAWLDGLSPKENRDIPPLDYDLVQRMKMLFPNLHISINGGITSLDQAVS 180

Query: 206 IL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
           +L   +DGVM+GRAAY   A +L   D      + G+S   T  +         +M  Y 
Sbjct: 181 LLDQGLDGVMVGRAAYHQPADILCAADRR----IFGTSGPDTTPEGAVH-----AMLPYI 231

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
             HL SGG+L QITRHM+GLF G P +R  R  L+  A    A   ++E A 
Sbjct: 232 EAHLASGGRLNQITRHMLGLFAGKPGARAWRRHLSEGASRPGAGPELVERAL 283


>gi|301169351|emb|CBW28951.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 10810]
          Length = 285

 Score =  232 bits (591), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 124/293 (42%), Positives = 175/293 (59%), Gaps = 10/293 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+   K + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPEQLKYCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++ + +  +
Sbjct: 120 KGCQEFIIHARKAWLSGLSPKENREIPPLDYARVYQLKRDFPHLTIAINGGIKTIEEMKQ 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY+N ++L  +D+   +P   ++PI T        +   SM  Y  +
Sbjct: 180 HLQYVDGVMVGREAYQNPSLLGQIDQALFDP---NAPIVTA------HEAVQSMLPYIEQ 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            L  G  L  I RHM+G F     +R+ R  L+  A    A   ++ETA + +
Sbjct: 231 QLSQGVHLNHIVRHMLGAFQNCKGARQWRRYLSENAFKQGAGVEVVETALSFV 283


>gi|261855785|ref|YP_003263068.1| dihydrouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836254|gb|ACX96021.1| dihydrouridine synthase DuS [Halothiobacillus neapolitanus c2]
          Length = 357

 Score =  231 bits (590), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 132/322 (40%), Positives = 185/322 (57%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD HYR  ARL+T NA LYTEM+   A+L GD    L F+  E P+ALQ+GG+D S
Sbjct: 16  MLDWTDTHYRVLARLMTRNARLYTEMVTTGALLHGDVSRHLSFNAAEHPVALQLGGSDPS 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA +  ++GY+EINLNVGCPS RV  GSFGACLM  P++V   + AM  ++ +PVT
Sbjct: 76  DLAAAAVLGAEWGYDEINLNVGCPSDRVQNGSFGACLMATPEVVAKGVRAMQASVDVPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G+D      A    +  +   G   ++ IHARKA L GLSPK+NR+IP L  D V
Sbjct: 136 LKTRVGIDRSDSFEAFARFIDIVAGQGGCEVFIIHARKAWLDGLSPKENREIPPLRRDFV 195

Query: 180 YEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           Y I+   P+L   LNG LE   +M   L  +P   G+M+GRAAY++   L  VD+     
Sbjct: 196 YRIQDAYPELTFVLNGKLETIPEMQAELARVPG--GIMVGRAAYQHVDWLRFVDQML--- 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S+PI TR        +      Y  + L SG  +  + + ++ LF+G P +R  R  
Sbjct: 251 FDHSAPIPTR------SAVVQGYRAYMLQALESGTPMPPLLKPLLTLFNGLPGARAFRRH 304

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L+ +        H+++ A +L+
Sbjct: 305 LSEQGPRRKTDIHVLDEALDLI 326


>gi|319897830|ref|YP_004136027.1| tRNA-dihydrouridine synthase a [Haemophilus influenzae F3031]
 gi|317433336|emb|CBY81713.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae F3031]
          Length = 285

 Score =  231 bits (590), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 125/293 (42%), Positives = 175/293 (59%), Gaps = 10/293 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+   K + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPEQLKYCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++ + +  +
Sbjct: 120 KGCQEFIIHARKAWLSGLSPKENREIPPLDYARVYQLKRDFPHLTIAINGGIKTIEKMKQ 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY+N ++L  +D+   +P   ++PI T        +   SM  Y  +
Sbjct: 180 HLQYVDGVMVGREAYQNPSLLGQIDQALFDP---NAPIVTA------HEAVQSMLPYIEQ 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            L  G  L  I RHM+G F     +R+ R  L+  A    A   +IETA + +
Sbjct: 231 QLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSENAFKQGAGVEVIETALSFV 283


>gi|269103588|ref|ZP_06156285.1| putative NifR3/Smm1 family protein [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163486|gb|EEZ41982.1| putative NifR3/Smm1 family protein [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 290

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 117/291 (40%), Positives = 179/291 (61%), Gaps = 11/291 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G K + L ++ +E PL LQ+GG++ + L   AK+ ++ GY+EINLNVGCPS
Sbjct: 1   MVTTGAIIHG-KGDFLAYNEEEHPLVLQLGGSNPADLARCAKLAQERGYDEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI-K 144
            RV  G FGACLM   ++V  C+AAM + + IPVTVK RIG+D+Q     L + + ++ +
Sbjct: 60  DRVQNGMFGACLMGEAELVAHCVAAMREVVDIPVTVKTRIGIDEQDSYEFLTDFIGTVAE 119

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K G +   IHARKA LKGLSPK+NR+IP LDY  VY++K++ P+L +G+NGG++   +  
Sbjct: 120 KGGCDNFTIHARKAWLKGLSPKENREIPPLDYPRVYQLKRDFPELTMGINGGIKTFEEME 179

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           + L  +DGVM+GR AY++  ++  VD+        + P+  R      R++  +M  Y  
Sbjct: 180 EHLQHMDGVMVGREAYQSPYLMAEVDQRL---FGSTKPVMKR------REVVEAMYPYIE 230

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
           + L  G  L  ITRHM+GLF   P +R+ R  ++  A    +   +++ A 
Sbjct: 231 QQLAQGSYLGHITRHMLGLFQNMPGARQWRRHISENAHKPGSGIEVLQQAL 281


>gi|300691712|ref|YP_003752707.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum PSI07]
 gi|299078772|emb|CBJ51432.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum PSI07]
          Length = 302

 Score =  228 bits (581), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 117/273 (42%), Positives = 165/273 (60%), Gaps = 9/273 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A+L GD    L F   E P+ALQ+GG++   L ++A++ E +GY EINLN GCPS
Sbjct: 1   MVTTGALLHGDVPRHLDFDEMEHPVALQLGGSEPGDLAQSARLGERWGYREINLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G+FGACLM  P +V DC+ AM   +SIPVTVK RIG+D       +R+ V +I +
Sbjct: 61  ERVQRGAFGACLMAEPKLVADCVKAMRDTVSIPVTVKHRIGIDAIETYDFVRDFVGTIAE 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G     +HAR AILKGLSPK+NR+IP L Y++VY++K++ P L I LNGG++ + Q   
Sbjct: 121 AGCETFIVHARNAILKGLSPKENREIPPLRYEVVYQLKRDFPQLEILLNGGVQALEQIDA 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVMIGR AY +  ++ + D  +    T  +P +  V+         +M DY  R
Sbjct: 181 HLAHVDGVMIGREAYHHPHLMASFDARYYGADT-VAPTRAEVED--------AMVDYIGR 231

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 232 WVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 264


>gi|319775424|ref|YP_004137912.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae F3047]
 gi|329122550|ref|ZP_08251132.1| tRNA-dihydrouridine synthase A [Haemophilus aegyptius ATCC 11116]
 gi|317450015|emb|CBY86228.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae F3047]
 gi|327473133|gb|EGF18558.1| tRNA-dihydrouridine synthase A [Haemophilus aegyptius ATCC 11116]
          Length = 287

 Score =  228 bits (581), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 123/293 (41%), Positives = 174/293 (59%), Gaps = 10/293 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+   K + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPEQLKHCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++ + +  +
Sbjct: 120 KGCQEFIIHARKAWLSGLSPKENREIPPLDYARVYQLKRDFPHLTIAINGGIKTIEEMKQ 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY+N ++L  +D+    P   ++ I T        +   SM  Y  +
Sbjct: 180 HLQYVDGVMVGREAYQNPSLLGQIDQALFYP---NAAIVTA------HEAVQSMLPYIEQ 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            L+ G  L  I RHM+G F     +R+ R  L+  A    A   ++ETA + +
Sbjct: 231 QLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSENAFKQGAGVEVVETALSFV 283


>gi|33864554|ref|NP_896113.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 8102]
 gi|33632077|emb|CAE06530.1| Uncharacterized protein family UPF0034 [Synechococcus sp. WH 8102]
          Length = 330

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 130/322 (40%), Positives = 185/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++ +ALLY+EM+VA A+   ++++ +L F   E P+ALQ+GG D 
Sbjct: 16  MLDCTDRHFRVLMRQISRHALLYSEMVVAQALHHSNRRDKLLDFDAVEHPIALQVGGDDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +AA++  D+ Y+EINLN+GCPS +V  G+FGACLM  PD+V  C+ AM  A S+PV
Sbjct: 76  ALLADAARLASDWNYDEINLNIGCPSQKVQAGNFGACLMAEPDLVARCVEAMSNATSLPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L   V  +  +G +   +HARKA L GL PK NR IP L +D V
Sbjct: 136 TVKHRIGIDDLDSDDLLTAFVDRVASAGASRFSVHARKAWLDGLDPKQNRTIPPLQHDRV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P L I LNGGLE     ++ L + DG M+GRAAY +      +D      L  
Sbjct: 196 QALKQRRPHLTIELNGGLESPEDCIEALRTCDGAMVGRAAYSHPLRWAAMDH-----LVF 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  +  D    +   +  +AA HL SGG+L  + RH++ L  G   +R  R  L  
Sbjct: 251 GKPPRDLLASD----VVTGLLPHAAAHLSSGGRLWDLCRHLVQLVEGVRGARHWRRELGD 306

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   + E+
Sbjct: 307 RAQRPGADLTVLEEAGRQLREA 328


>gi|329119729|ref|ZP_08248409.1| tRNA dihydrouridine synthase A [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327464178|gb|EGF10483.1| tRNA dihydrouridine synthase A [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 346

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 130/302 (43%), Positives = 181/302 (59%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+RF AR ++ +ALLYTEM+ A A++ GD    L  +  E P+ALQ+GG++ +
Sbjct: 21  MLDWTDRHFRFLARQISRHALLYTEMVNAGAVVHGDAARFLLKNDCENPVALQLGGSEPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA     +GY+EINLN GCPS RV +G+FGACLM    +V DC+ AM  A     V
Sbjct: 81  LLAKAAAEAAAWGYDEINLNCGCPSPRVQKGAFGACLMNEVALVADCLNAMQDAAPDCAV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D Q     L + V ++ +K+      +HAR A L GLSPK+NR +P L YD 
Sbjct: 141 TVKHRIGIDRQTDYQPLADFVGTLSEKTACTVFIVHARNAWLDGLSPKENRDVPPLKYDY 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E P L I LNGG++  ++A   L   DGVM+GR  Y N  ++   D  F     
Sbjct: 201 VYRLKREFPALQIVLNGGIKTNAEAALHLQHTDGVMVGRECYHNPMLMRDWDRLFYG--- 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHS--GGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 TR +   + +++  + DYAA  L    G  L+ ITRH +GL HG   +R+ R +
Sbjct: 258 -----DTR-EPAVYAELAERLRDYAAERLADGRGSILRHITRHCLGLMHGLNGARQWRRM 311

Query: 297 LT 298
           L+
Sbjct: 312 LS 313


>gi|194476882|ref|YP_002049061.1| hypothetical protein PCC_0411 [Paulinella chromatophora]
 gi|171191889|gb|ACB42851.1| hypothetical protein PCC_0411 [Paulinella chromatophora]
          Length = 325

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 127/324 (39%), Positives = 179/324 (55%), Gaps = 18/324 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKN---------ILGFSTQEKPL 50
           M+ +TDRH+R   R ++ + L+YTEM+ A A+    D++N         ++GF   EKP+
Sbjct: 1   MMGYTDRHFRVMIRQISKHCLVYTEMVAAQALQECRDQENQTATQNIERLIGFDNCEKPI 60

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ALQ+GG     L EAAK+   + Y+EINLNVGCPS  V +G FGACLM  P  V  C+ A
Sbjct: 61  ALQVGGDSPKLLAEAAKLATHWNYDEINLNVGCPSENVQKGRFGACLMAEPAHVARCVNA 120

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           M K   IP+TVK RIG+D+Q     L N +  + ++G N   IHARKA L GL PK NR 
Sbjct: 121 MAKVSKIPITVKHRIGIDNQDSYEQLLNFIDQVAEAGANRFCIHARKAWLTGLDPKQNRT 180

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           IP L Y++V ++K + P +FI +NGG E++  + K L   DGVM+GR  Y +      +D
Sbjct: 181 IPLLKYELVKQLKIDRPFIFIDINGGFENLMDSKKQLNWADGVMVGRQVYDHPLRWGELD 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               +    S+   +R        I AS+  YA +    GG+L  I RH++    G   +
Sbjct: 241 RIIFDDYGISANKPSR--------IIASLFPYAEKWYAIGGRLWPIARHLVHTVEGIKGA 292

Query: 291 RRCRHILTVEAGASTATHHIIETA 314
           R  R   T  A   TA+  ++  A
Sbjct: 293 RHWRRWFTEAANELTASPSLLLNA 316


>gi|46200284|ref|YP_005951.1| tRNA-dihydrouridine synthase A [Thermus thermophilus HB27]
 gi|46197912|gb|AAS82324.1| nifR3-like protein [Thermus thermophilus HB27]
          Length = 342

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 121/299 (40%), Positives = 178/299 (59%), Gaps = 13/299 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+RF  R ++    LYTEM V  A+LRG+++ +L F  +E P+ALQ+ G+D  
Sbjct: 11  MVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E FGY+EINLN+GCPS +  EG +GACL+L+   V + + AM +A+ +PVT
Sbjct: 71  SLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVQEILKAMGEAVRVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G++ +     L   V+++ ++GV    +HAR A+L  LS K NR+IP L +D V+
Sbjct: 131 VKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALL-ALSTKANREIPPLRHDWVH 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K++ P L    NGG+  + +AL  L  VDGVM+GRA Y++  +L   D   F  P   
Sbjct: 190 RLKRDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRP 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S     R++      ++  M  Y    +  G     + RHM+ LF G P  R  R +L+
Sbjct: 250 S-----RLE------VARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLS 297


>gi|326559961|gb|EGE10359.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 46P47B1]
          Length = 322

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 124/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P IV D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQIVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|294669488|ref|ZP_06734555.1| hypothetical protein NEIELOOT_01386 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308401|gb|EFE49644.1| hypothetical protein NEIELOOT_01386 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 328

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 126/302 (41%), Positives = 177/302 (58%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR  AR +T +  LYTEMI A A++ GD    L  +  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHYRHMARQITRHTWLYTEMINAGAVIYGDPDRFLLKNDGENPVALQLGGSEPQ 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA     +GY+EINLN GCPS RV +G+FGACLM   D+V DC+ AM +A     V
Sbjct: 61  DLAKAAAKAAAYGYDEINLNCGCPSPRVQKGAFGACLMKEADLVADCLNAMQEAAPDCAV 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D +     L + V ++ +K+      +HAR A L+GLSPK+NR +P L YD 
Sbjct: 121 TVKHRIGLDCETDYQPLADFVGTLAEKTDCTTFIVHARNAWLEGLSPKENRDVPPLRYDY 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E P L I +NGG++   +    L  VDGVM+GR  Y N  ++   D  F     
Sbjct: 181 VYRLKREFPALEIIINGGIKTNDEIAAHLQHVDGVMVGRECYHNPMLMRDWDRLFYG--D 238

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHI 296
             +P+        + ++   + DYAA  L +G    L+ + RH +GL HG   +R  R +
Sbjct: 239 DHAPVS-------YAELVGRLKDYAAAQLAAGRGTILRHMARHYLGLMHGLNGARHWRRM 291

Query: 297 LT 298
           L+
Sbjct: 292 LS 293


>gi|326565214|gb|EGE15400.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 103P14B1]
 gi|326573992|gb|EGE23941.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis CO72]
          Length = 322

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 123/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIHTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|326566665|gb|EGE16806.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 12P80B1]
 gi|326569455|gb|EGE19515.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis BC8]
          Length = 322

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|326577039|gb|EGE26934.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 101P30B1]
          Length = 321

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 11  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 70

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 71  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 130

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 131 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 191 VYRLKQDFPDLTIEINGGISHLDDIHTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 246 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 298


>gi|296112920|ref|YP_003626858.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis RH4]
 gi|295920614|gb|ADG60965.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis RH4]
 gi|326567964|gb|EGE18061.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis BC1]
          Length = 322

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|326577440|gb|EGE27324.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis O35E]
          Length = 321

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 11  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 70

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 71  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 130

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 131 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 191 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 246 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 298


>gi|225025575|ref|ZP_03714767.1| hypothetical protein EIKCOROL_02477 [Eikenella corrodens ATCC
           23834]
 gi|224941613|gb|EEG22822.1| hypothetical protein EIKCOROL_02477 [Eikenella corrodens ATCC
           23834]
          Length = 317

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 126/302 (41%), Positives = 181/302 (59%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR ++ +A LYTEMI A AI+ G  +  LG    E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHYRYMARQISRHAWLYTEMIHAGAIIHGQAERFLGKDESENPVALQLGGSNPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA I   +GY+EINLN GCPS RV +G+FGACLM   D+V DC+ AM +A     V
Sbjct: 61  DLAKAAAIAAGWGYDEINLNCGCPSPRVQKGAFGACLMNEVDLVADCLNAMQEAAPDCAV 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D Q     + + V ++  K+      +HAR A L+GLSPK+NR +P L YD 
Sbjct: 121 TVKHRIGIDRQTEYQTVCDFVGTLSDKTACRTYIVHARNAWLEGLSPKENRDVPPLKYDY 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ P L I +NGG++  ++  + L  VDGVMIGR AY N  ++ + D  F     
Sbjct: 181 VYRLKQDFPHLEIIINGGIKTNTEIAEHLQHVDGVMIGREAYHNPMLMQSWDRLFYGERL 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHS--GGKLQQITRHMIGLFHGFPNSRRCRHI 296
             +   T +          ++  Y  R L +  G  ++ + RH +GL HG  ++R  R +
Sbjct: 241 PETDFNTLIH---------TLYRYMQRSLAADPGLTIRHMLRHYLGLLHGRNHARVWRQM 291

Query: 297 LT 298
           L+
Sbjct: 292 LS 293


>gi|198283800|ref|YP_002220121.1| dihydrouridine synthase DuS [Acidithiobacillus ferrooxidans ATCC
           53993]
 gi|198248321|gb|ACH83914.1| dihydrouridine synthase DuS [Acidithiobacillus ferrooxidans ATCC
           53993]
          Length = 325

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/308 (39%), Positives = 178/308 (57%), Gaps = 14/308 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R+F RL+  + +LYTEM+   A+L G D +  L FS  E PL LQ+GG D 
Sbjct: 19  MLDWTDRHCRYFLRLVCPSCVLYTEMVTTSALLLGRDPERFLEFSGAEHPLILQLGGDDP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  A ++   +GY+ +NLNVGCPS RV +GSFGACLM  PD+V + +AAM ++  +PV
Sbjct: 79  HAMHAAGRMARAYGYDGLNLNVGCPSPRVQKGSFGACLMTTPDLVAELVAAMGES-GLPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G+D +    ALR  V+++  +G     +HAR A LKGLSP +NR +P L +D V
Sbjct: 138 SVKHRLGLDREEDYAALRAFVETVATAGCRHFIVHARNAWLKGLSPAENRDVPPLRWDWV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K++ P L I +NGG  D++       +VDGVM+GRAAY +  +L  ++       T 
Sbjct: 198 HQLKRDLPHLTIEINGGFNDLAAVTAQFSAVDGVMLGRAAYHHPLLLAEIERALGRRETL 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL-T 298
             P            I + +  YA R         +++RH+ GL  G   +   R  L T
Sbjct: 258 PEP----------EVILSGLIAYAER-WGEWLPAPRLSRHLHGLRFGQRGAGAWRRFLGT 306

Query: 299 VEAGASTA 306
            E G S A
Sbjct: 307 AEPGESAA 314


>gi|326561145|gb|EGE11510.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 7169]
          Length = 322

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 124/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++     Y    L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC--YL---LW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|326572785|gb|EGE22771.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis BC7]
          Length = 322

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVE--DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRMTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++        + L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-----HLLW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPSH-------RQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|294789628|ref|ZP_06754862.1| tRNA dihydrouridine synthase A [Simonsiella muelleri ATCC 29453]
 gi|294482429|gb|EFG30122.1| tRNA dihydrouridine synthase A [Simonsiella muelleri ATCC 29453]
          Length = 352

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 126/302 (41%), Positives = 175/302 (57%), Gaps = 13/302 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LYTEMI A AI+ GD    L  +  E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHYRYMARQITKNTWLYTEMINAGAIIHGDPNRFLLKNECENPIALQLGGSDSA 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA     +GY+EINLN GCPS RV +G+FGACLM   ++V  C+ A+  A  +  +
Sbjct: 95  DLAKAAAKAAQYGYDEINLNCGCPSPRVQKGAFGACLMNEVNLVSGCLNAIQDAAPNCDI 154

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K RIG+D Q     L + V  + +S       +HAR A L GLSPK+NR +P L YD 
Sbjct: 155 TIKHRIGLDKQTEYQPLADFVGELARSTNCRTFIVHARNAWLDGLSPKENRDVPPLRYDY 214

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY++K+E  DL I +NGG+    Q  + L  VDGVM+GR AY N  ++ + D  F    T
Sbjct: 215 VYQLKQEFVDLEIIINGGITTNEQIHQHLQYVDGVMVGREAYHNPMLMKSWDAQFYGDTT 274

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +++         + DYA   L  + G  L+ + RH +GL HG   +R  R +
Sbjct: 275 PEITYDELINR---------LYDYAKIQLAANRGTILRHMARHYLGLMHGLHGARTWRRM 325

Query: 297 LT 298
           L+
Sbjct: 326 LS 327


>gi|218665650|ref|YP_002426431.1| tRNA-dihydrouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|218517863|gb|ACK78449.1| tRNA-dihydrouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 330

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 123/308 (39%), Positives = 178/308 (57%), Gaps = 14/308 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R+F RL+  + +LYTEM+   A+L G D +  L FS  E PL LQ+GG D 
Sbjct: 24  MLDWTDRHCRYFLRLVCPSCVLYTEMVTTSALLLGRDPERFLEFSGAEHPLILQLGGDDP 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  A ++   +GY+ +NLNVGCPS RV +GSFGACLM  PD+V + +AAM ++  +PV
Sbjct: 84  HAMHAAGRMARAYGYDGLNLNVGCPSPRVQKGSFGACLMTTPDLVAELVAAMGES-GLPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G+D +    ALR  V+++  +G     +HAR A LKGLSP +NR +P L +D V
Sbjct: 143 SVKHRLGLDREEDYAALRAFVETVATAGCRHFIVHARNAWLKGLSPAENRDVPPLRWDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K++ P L I +NGG  D++       +VDGVM+GRAAY +  +L  ++       T 
Sbjct: 203 HQLKRDLPHLTIEINGGFNDLAAVTAQFSAVDGVMLGRAAYHHPLLLAEIERALGRRETL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL-T 298
             P            I + +  YA R         +++RH+ GL  G   +   R  L T
Sbjct: 263 PEP----------EVILSGLIAYAER-WGEWLPAPRLSRHLHGLRFGQRGAGAWRRFLGT 311

Query: 299 VEAGASTA 306
            E G S A
Sbjct: 312 AEPGESAA 319


>gi|320449546|ref|YP_004201642.1| tRNA-dihydrouridine synthase A [Thermus scotoductus SA-01]
 gi|320149715|gb|ADW21093.1| tRNA-dihydrouridine synthase A [Thermus scotoductus SA-01]
          Length = 344

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 120/299 (40%), Positives = 178/299 (59%), Gaps = 14/299 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+R+  R ++    LYTEM V  A+LRG  + +L F  +E P+ALQ+ G+D  
Sbjct: 11  MVDRTDRHFRYLVRQISRKVRLYTEMTVDQAVLRGKAERLLAFHPEEHPIALQLAGSDPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I + +GY+E+NLN+GCPS +  EG FGACL+L+P  V + + AM +A+ IPVT
Sbjct: 71  SLAEAARIGQAWGYDEVNLNLGCPSEKAQEGGFGACLLLDPIRVREILKAMVEAVEIPVT 130

Query: 121 VKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK R+GV+ +  P +A    V++  ++GV    +HAR A+L  LS + NR++P L +D V
Sbjct: 131 VKLRLGVEGESYPLLA--RWVEAYGETGVRVFIVHARSALLN-LSTRKNREVPPLRHDWV 187

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + +K + P L   LNGG+  + +AL  L  VDGVM+GRA Y++  +L   D      + G
Sbjct: 188 HRLKADFPHLTFILNGGVRTLEEALPHLKKVDGVMMGRAVYEDPFVLEEADRR----VFG 243

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +   +R+D      ++  M  Y       G     + RHM+ LF G P  R  R +L+
Sbjct: 244 LAHRPSRLD------VARRMRLYLEAEAQKGTPPWAVLRHMLNLFRGQPGGRLWRRLLS 296


>gi|239994762|ref|ZP_04715286.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii ATCC 27126]
          Length = 309

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 114/284 (40%), Positives = 170/284 (59%), Gaps = 11/284 (3%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           ++ + LLYTEM+   AI+ G K + LG++ +E P+A+Q+GG++ S + + A++ +  GY+
Sbjct: 1   MSKHTLLYTEMVTTGAIIYG-KGDYLGYNQEEHPVAVQLGGSEPSDMAKCAELSQARGYD 59

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           E+N+NVGCPS RV  GSFGACLM  P++V  C+ AM  A+ IPVTVKCRIG+DD      
Sbjct: 60  EVNINVGCPSDRVKNGSFGACLMAQPEVVASCVKAMQAAVDIPVTVKCRIGIDDMDEDED 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
               + ++  +G +   +HARKA L+GLSPK+NR+IP L+Y  V+ +K+  P+L I +NG
Sbjct: 120 FARFIDTVADAGCDTFIVHARKAWLQGLSPKENREIPPLNYPRVHRLKQARPELSISING 179

Query: 196 GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRK 254
           G++ + +  + L  VDGVM+GR  Y N  ++ TVD E F +         T       R+
Sbjct: 180 GVKTLGETQQQLELVDGVMVGREVYANPYIMATVDKEIFGD---------TEAQSMSRRE 230

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           I   M  Y  R      K     RH++GL+ G    R  R  L+
Sbjct: 231 IVLKMQQYIERQDDPYFKPWHAARHILGLYQGQAGGRIWRRYLS 274


>gi|289165076|ref|YP_003455214.1| tRNA-dihydrouridine synthase A [Legionella longbeachae NSW150]
 gi|288858249|emb|CBJ12117.1| tRNA-dihydrouridine synthase A [Legionella longbeachae NSW150]
          Length = 329

 Score =  223 bits (567), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 121/297 (40%), Positives = 176/297 (59%), Gaps = 11/297 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  H+R F R+L  NALLYTEM    A+     ++ L F+ +E PLALQ+GG++ +
Sbjct: 14  MIDWTYSHFRVFMRILAPNALLYTEMQTTGAVCNNPIRS-LQFNRKEHPLALQLGGSEPN 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+  E  GY+EIN+N+GCPS +V  G+FGACLM  P+ VGDCI AM +A++IPVT
Sbjct: 73  LLAQCARRAEQEGYDEININLGCPSDKVQAGNFGACLMKEPEKVGDCIRAMREAVNIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIGVD Q       N V  + ++G   I +HARKA L+GL+PK NR IP + YD VY
Sbjct: 133 AKTRIGVDHQDSYEFFSNFVHQLVEAGAQKIIVHARKAWLQGLNPKQNRTIPPVHYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PD+ I +NG + ++++  + L  VDGVM+GR A  N   + TV       +T  
Sbjct: 193 RLKKEIPDIPIVINGNILNLNEINEHLNYVDGVMLGRLACDNPFQIATVHHGLYPEITKR 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           S  ++++  D+         +Y     + G  L  + + +  L  G P + + +  L
Sbjct: 253 S--RSQIFNDY--------LEYLLDEFYKGVSLSLLIKPIFNLGFGLPGASQWKRKL 299


>gi|270160148|ref|ZP_06188804.1| tRNA-dihydrouridine synthase A [Legionella longbeachae D-4968]
 gi|269988487|gb|EEZ94742.1| tRNA-dihydrouridine synthase A [Legionella longbeachae D-4968]
          Length = 316

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 121/297 (40%), Positives = 176/297 (59%), Gaps = 11/297 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  H+R F R+L  NALLYTEM    A+     ++ L F+ +E PLALQ+GG++ +
Sbjct: 1   MIDWTYSHFRVFMRILAPNALLYTEMQTTGAVCNNPIRS-LQFNRKEHPLALQLGGSEPN 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+  E  GY+EIN+N+GCPS +V  G+FGACLM  P+ VGDCI AM +A++IPVT
Sbjct: 60  LLAQCARRAEQEGYDEININLGCPSDKVQAGNFGACLMKEPEKVGDCIRAMREAVNIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIGVD Q       N V  + ++G   I +HARKA L+GL+PK NR IP + YD VY
Sbjct: 120 AKTRIGVDHQDSYEFFSNFVHQLVEAGAQKIIVHARKAWLQGLNPKQNRTIPPVHYDYVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PD+ I +NG + ++++  + L  VDGVM+GR A  N   + TV       +T  
Sbjct: 180 RLKKEIPDIPIVINGNILNLNEINEHLNYVDGVMLGRLACDNPFQIATVHHGLYPEITKR 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           S  ++++  D+         +Y     + G  L  + + +  L  G P + + +  L
Sbjct: 240 S--RSQIFNDY--------LEYLLDEFYKGVSLSLLIKPIFNLGFGLPGASQWKRKL 286


>gi|55979985|ref|YP_143282.1| tRNA-dihydrouridine synthase A [Thermus thermophilus HB8]
 gi|55771398|dbj|BAD69839.1| tRNA-dihydrouridine synthase [Thermus thermophilus HB8]
          Length = 342

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 121/299 (40%), Positives = 177/299 (59%), Gaps = 13/299 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+RF  R ++    LYTEM V  A+LRG+++ +L F  +E P+ALQ+ G+D  
Sbjct: 11  MVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E FGY+EINLN+GCPS +  EG +GACL+L+   V + + AM +A+ +PVT
Sbjct: 71  SLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G++ +     L   V+++ ++GV    +HAR A+L  LS K NR+IP L +D V+
Sbjct: 131 VKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALL-ALSTKANREIPPLRHDWVH 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K + P L    NGG+  + +AL  L  VDGVM+GRA Y++  +L   D   F  P   
Sbjct: 190 RLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRP 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S     R++      ++  M  Y    +  G     + RHM+ LF G P  R  R +L+
Sbjct: 250 S-----RLE------VARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLS 297


>gi|149923826|ref|ZP_01912217.1| hypothetical protein PPSIR1_20159 [Plesiocystis pacifica SIR-1]
 gi|149815338|gb|EDM74882.1| hypothetical protein PPSIR1_20159 [Plesiocystis pacifica SIR-1]
          Length = 362

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 120/303 (39%), Positives = 176/303 (58%), Gaps = 9/303 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   RL+T + LLYTEM+   A+L GD+++ILG+   E PLALQ+GG D  
Sbjct: 28  MMDRTDRHFRRLMRLITRHTLLYTEMVTCPAVLHGDREHILGYHPSEHPLALQLGGDDPE 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A+I  + GY+E+N+NVGCPS RV  G+FG CLM +P  V DC+ AM +A+ +PVT
Sbjct: 88  ALAACARIAAELGYDEVNINVGCPSDRVQSGNFGVCLMKDPARVRDCVVAMREAVELPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      + + V  +  +  +   +HARKA L+GLSPK NR +P L Y  V+
Sbjct: 148 VKHRIGVDELDRYEDMLHFVDVVAAAEPDLFTVHARKAWLQGLSPKQNRNVPPLRYAEVH 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            + +E P +F+ +NGG +      + L  VD VM+GRAA+ +  +   VD+ F       
Sbjct: 208 RLARERPGVFVEINGGFKTADAIAEQLERVDAVMLGRAAWDDPWLFAAVDQRF---FASE 264

Query: 241 SPIKTR--VDKDFWRKISASMTDYAAR----HLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +P  TR  V + +   +   +    AR      + G     + R ++ LF G P ++R +
Sbjct: 265 APAPTRPAVVEAYLEHVHEQLAMARARVEAGSRYKGPSATILLRPIMNLFTGRPGAKRWK 324

Query: 295 HIL 297
             L
Sbjct: 325 RTL 327


>gi|319941968|ref|ZP_08016289.1| TRNA-dihydrouridine synthase A [Sutterella wadsworthensis 3_1_45B]
 gi|319804621|gb|EFW01491.1| TRNA-dihydrouridine synthase A [Sutterella wadsworthensis 3_1_45B]
          Length = 347

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 125/303 (41%), Positives = 171/303 (56%), Gaps = 14/303 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  RFF RLLT    LYTEM+   AI  G +  +LG S    P ALQ+GG+D  
Sbjct: 27  MLDWTDRPCRFFERLLTRRGRLYTEMVTTGAIRFGSRDALLGNSRVAGPTALQLGGSDPK 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  A +    +GY+E NLN GCPS RV +GSFGACLML+  +V +C+ AM  A   PVT
Sbjct: 87  ELAFAVEAAAPYGYDEFNLNCGCPSPRVQKGSFGACLMLDAKLVAECVRAMRDATDKPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD++     +R+ V  +  +G     +HAR A L+GLSPK+NR++P L     +
Sbjct: 147 VKHRIGVDERSDYGFVRDFVGEVYDAGCRTFIVHARAAWLQGLSPKENREVPPLMRSRAW 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV------DGVMIGRAAYKNSAMLTTVDEYFS 234
           E+K++ PD  I LNG ++  ++   +L  V      DGVM+GRAAY+   ML+ VD    
Sbjct: 207 ELKRDFPDAVIVLNGAVKTTAECRALLDEVHDGVRIDGVMVGRAAYQTPWMLSEVDSV-- 264

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             L G S  +T   +     + A +  Y A   H    ++   RH+ GL  G   +R  R
Sbjct: 265 --LYGES-CRTLTREAVIAAVEAEVEQYYAADEHV---IRAFARHLNGLCQGLSGARVWR 318

Query: 295 HIL 297
             L
Sbjct: 319 RTL 321


>gi|319943752|ref|ZP_08018033.1| tRNA-dihydrouridine synthase A [Lautropia mirabilis ATCC 51599]
 gi|319742985|gb|EFV95391.1| tRNA-dihydrouridine synthase A [Lautropia mirabilis ATCC 51599]
          Length = 382

 Score =  221 bits (564), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 124/335 (37%), Positives = 181/335 (54%), Gaps = 43/335 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+    LYTEM+ A AI  GD  ++LG   +   + LQ+GG D  
Sbjct: 21  MMDWTDRHCRSFHRLLSRRTWLYTEMVTAQAIAHGDLDHLLGRGEEGDRVVLQLGGNDPQ 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+  + +GY+EINLN GCPS RV EG+FGACLM  P+ V DC+AAM   + +PVT
Sbjct: 81  LLARAAREGQAYGYDEINLNCGCPSDRVREGAFGACLMAEPERVADCVAAMQAVVQVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     + + V  +  +G     +HAR A L GL PK NR+IP L Y++V+
Sbjct: 141 VKHRIGIDRREDYEFVHHFVDVVAAAGCRRFVVHARNAWLDGLDPKQNREIPPLRYEVVH 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL-KILPS----------------VD------------ 211
            + ++ P     LNGGL+D++  L  + P+                VD            
Sbjct: 201 RLAQDFPHCAFELNGGLQDLAHGLAAVCPTEASGPDSETASEGPAVVDAMAGAEADSPAT 260

Query: 212 ---GVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRVDKDFWRKISASMTDYA 263
              G M GR AY +  +L  VD++ +      P+T ++   TR        + A++  Y 
Sbjct: 261 RLVGAMYGRRAYHDPWLLAGVDDWLARHAAEAPVTDAAQPLTRA------AVVAALVGYL 314

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            R    G +++ + RH++GL+ G P +R  R +L+
Sbjct: 315 ERGAAHGVEVRHLARHVLGLYLGHPAARLWRRMLS 349


>gi|221134737|ref|ZP_03561040.1| tRNA-dihydrouridine synthase A [Glaciecola sp. HTCC2999]
          Length = 305

 Score =  221 bits (564), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 173/298 (58%), Gaps = 8/298 (2%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G K + LGF+  E+P+ALQ+GG+    +   A   +++GY+E+N+NVGCPS
Sbjct: 1   MVTTGAIIFG-KGDYLGFNAAEQPVALQLGGSVPEDMTHCAIKAQEYGYDEVNINVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM  P  V DC++AM   + IPVTVK RIG+DD      L   ++ + +
Sbjct: 60  DRVQNGRFGACLMAEPQTVADCVSAMQAQVDIPVTVKSRIGIDDMDEYEDLSAFIEQVAE 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G +   +HARKA L+GLSPK NR++P L Y+ VY++K+E P L + +NGG++ +++A  
Sbjct: 120 AGCDTFIVHARKAWLQGLSPKQNREVPPLMYERVYQLKEEFPHLHVSINGGVKTLAEAQH 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDE--YFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            L  VDGVMIGR AY N  +L+ VD   Y  N    S   +  + K     I   +   A
Sbjct: 180 HLSYVDGVMIGREAYSNPYILSEVDHLIYGDNQAVLS---RIEIVKRMHSYIVEQLA--A 234

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
                 G K+  I RHM+GLF G P  R  R  L+  A     +  ++  A + ++E+
Sbjct: 235 PNQFGQGTKVWHIVRHMLGLFQGQPGGRVWRRYLSENAVGRNTSPDVLFAALDALLET 292


>gi|145589360|ref|YP_001155957.1| tRNA-dihydrouridine synthase A [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145047766|gb|ABP34393.1| tRNA-U16,U17-dihydrouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
          Length = 347

 Score =  221 bits (564), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 118/314 (37%), Positives = 180/314 (57%), Gaps = 19/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R LT  A+LYTEM+   A++ GD    L +S  + P+ LQ+GG++ +
Sbjct: 1   MMEWTDRHCRSFHRALTTEAVLYTEMVTTGALMHGDVPRHLDYSQDQHPVVLQLGGSEPN 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ + +GY+EI+LN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IP++
Sbjct: 61  DLARSAELAQQWGYDEIDLNCGCPSERVQRGAFGACLMAEPKLVADCVKAMQNAVDIPIS 120

Query: 121 VKCRIGVDDQIPAVALR------NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           VK R+G+D    A + +      + + ++  +G + + IHAR A+LKGLSPK+NR  P L
Sbjct: 121 VKHRLGLDSMDAANSEKDYQFALDFIMAVADAGASQVTIHARNAVLKGLSPKENRSKPPL 180

Query: 175 DYDIVYEIK----KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            Y++  +++    K+ P+L + LNGGLE   Q        DG M+GRAAY   AML   D
Sbjct: 181 RYEVAAKLRLDAQKQFPNLKVLLNGGLESNDQIAGHWHDFDGFMVGRAAYHFPAMLLGWD 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGK---LQQITRHMIGLF 284
           +  +     +  + +  +   W +I  ++            + GK   +   TRH++GL 
Sbjct: 241 DMINTNGDAAGYLFSETE---WHRIQIALVKQVQSWFDECQAKGKPFYIGAFTRHILGLA 297

Query: 285 HGFPNSRRCRHILT 298
           HG   SR  R  L+
Sbjct: 298 HGRAGSRYWRQRLS 311


>gi|297520781|ref|ZP_06939167.1| tRNA-dihydrouridine synthase A [Escherichia coli OP50]
          Length = 261

 Score =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 117/269 (43%), Positives = 164/269 (60%), Gaps = 12/269 (4%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG+D + L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM  
Sbjct: 1   LGGSDPAALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRD 60

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIP 172
            +SIPVTVK RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP
Sbjct: 61  VVSIPVTVKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIP 120

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-E 231
            LDY  VY++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E
Sbjct: 121 PLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDRE 180

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
            F +    + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R
Sbjct: 181 IFGSSDIDADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGAR 230

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMIE 320
           + R  L+  A  + A  +++E A  L+ +
Sbjct: 231 QWRRYLSENAHKAGADINVLEHALKLVAD 259


>gi|312796563|ref|YP_004029485.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
 gi|312168338|emb|CBW75341.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
          Length = 233

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 99/202 (49%), Positives = 138/202 (68%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +  LYTEM+   A+L GD    L F+ QE P+ALQ+GG++  
Sbjct: 30  MMDWTDRHCRYFHRQLSRHVYLYTEMVTTGALLFGDVARHLSFTPQEAPIALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E +GY+E+NLN GCPS RV  G+FGACLM    +V DC+ AMC A+++PVT
Sbjct: 90  ELARCAKLSEQWGYDEVNLNCGCPSERVQRGAFGACLMKEATLVADCVKAMCDAVAVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ + G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAIDDYGFVRDFVGTVAQGGCRVFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQ 202
            +K++ P+  I +NGG++ + +
Sbjct: 210 RLKRDFPEFEIVINGGIKTLDE 231


>gi|332991645|gb|AEF01700.1| tRNA-dihydrouridine synthase A [Alteromonas sp. SN2]
          Length = 308

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 117/291 (40%), Positives = 169/291 (58%), Gaps = 7/291 (2%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G K + LGF+ QE P+ALQ+GG++   + + A + ++ GY+E+N+NVGCPS
Sbjct: 1   MVTTGAIIYG-KGDYLGFNEQEHPVALQLGGSNPEHMAKCAALAQERGYDEVNINVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  GSFGACLM  P++V D + AM   + IPVTVKCRIG+DD          +  +  
Sbjct: 60  DRVKNGSFGACLMAQPEVVADNVKAMQAEVDIPVTVKCRIGIDDMDEYKDFARFIDIVAT 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G +   +HARKA L+GLSPK+NR IP L+Y  V+ +K+ +P+L I +NGG++ ++ A +
Sbjct: 120 AGCDTFIVHARKAWLQGLSPKENRDIPPLNYPRVHMLKESHPELSISINGGIKSLADAQE 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            L  VDGVMIGR  Y N  +L+TVD E F +      PI  R   D   K+   +    A
Sbjct: 180 QLKYVDGVMIGREVYANPYILSTVDAEIFGD--NSVQPISRR---DVVLKMQQYIEKCIA 234

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
           R      K   + RHM+GL+ G    R  R  L+      +   H++  A 
Sbjct: 235 RQDDPYFKPWHVARHMLGLYQGQAGGRIWRRYLSQNGTGKSPDPHLLMNAL 285


>gi|289807774|ref|ZP_06538403.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 258

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 115/261 (44%), Positives = 157/261 (60%), Gaps = 12/261 (4%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVTV
Sbjct: 6   LSHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTV 65

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K RIG+DDQ     L + + ++   G   ++ IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 66  KTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVY 125

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T 
Sbjct: 126 QLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTTD 185

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 186 TDPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLSE 235

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A  + A   ++E A  L+ +
Sbjct: 236 NAHKAGADAAVLEQALKLIAD 256


>gi|146329044|ref|YP_001209939.1| tRNA-dihydrouridine synthase A [Dichelobacter nodosus VCS1703A]
 gi|146232514|gb|ABQ13492.1| tRNA-dihydrouridine synthase A [Dichelobacter nodosus VCS1703A]
          Length = 335

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 123/319 (38%), Positives = 177/319 (55%), Gaps = 15/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT    R   R+L   A LY+EMI   AIL GD +  L     E P ALQ+GG++  
Sbjct: 14  MMDWTTPACRQIHRILLPKARLYSEMITTGAILFGDAQRYLTHQNDE-PCALQLGGSNPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  A  I + + Y E+NLNVGCPS RV     GACLM +P +V  C+ AM K   +PV+
Sbjct: 73  ELARATAIAQSYHYAEMNLNVGCPSDRVQNNQIGACLMKSPRLVAQCLTAMQKESDVPVS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G+D+Q   +   + V  I +     I+I HARKA L GLSPK+NR  P L Y+IV
Sbjct: 133 IKHRLGIDEQDEHLVF-DFVDQISQESPCRIFIVHARKAWLSGLSPKENRTAPPLHYEIV 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P+L I +NGG++ ++     L  VDGVM+GRAAY+   +L      F + +  
Sbjct: 192 YKIKEQFPELTIIINGGIDFIAACQNHLHYVDGVMLGRAAYQQPQLLLAARALFGDAVMS 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +            +I   +T      L  G +L   TRH++GLFHG   ++R R IL+ 
Sbjct: 252 ET------------EIVPQITQLLMNALDRGERLHDYTRHLLGLFHGKNGAKRFRQILSE 299

Query: 300 EAGASTATHHIIETAFNLM 318
            A  + +  ++ + A   M
Sbjct: 300 CAPRAGSDINVWQQALAAM 318


>gi|258545773|ref|ZP_05706007.1| tRNA dihydrouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258519018|gb|EEV87877.1| tRNA dihydrouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 309

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 125/316 (39%), Positives = 172/316 (54%), Gaps = 14/316 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT    R   RL T  ALLYTEM+   A++ GD +  L     + P ALQ+GG +  
Sbjct: 1   MLDWTTPECRALHRLFTRRALLYTEMVTTGALIYGDAERHLQHHG-DAPCALQLGGGEPE 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            L  A  I   +GY EINLNVGCPS RV     GACLM +  +V +C++AM   A ++PV
Sbjct: 60  ALAHACAIALPYGYQEINLNVGCPSDRVQNNRIGACLMDDAALVAECVSAMQAAAGAVPV 119

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+ +D+Q        +     +S      IHARKA L+GLSPK NR +P L+Y +V
Sbjct: 120 TVKHRLAIDEQDEREVFHFVETVASRSPCRVFIIHARKAWLQGLSPKANRDVPPLNYPLV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           YE+K+  P+L I +NGG+ D++Q    L  VDGVM+GRAAY+N  +L   D  +      
Sbjct: 180 YEVKRRFPELTIVINGGIGDLAQCQAHLQHVDGVMLGRAAYQNPELLLLADTLYGEAAQT 239

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              +  R        I A + +  AR    G  L   TRH++GLF G   ++  R IL+ 
Sbjct: 240 LDAVLPR--------IRALIAERLAR----GEVLSHYTRHLLGLFPGVRGAKIYRRILSE 287

Query: 300 EAGASTATHHIIETAF 315
           +A +  A   + E A 
Sbjct: 288 DARSPDAGIAVFERAL 303


>gi|52841692|ref|YP_095491.1| tRNA-dihydrouridine synthase A [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52628803|gb|AAU27544.1| zinc binding TIM barrel protein, YjbN family [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
          Length = 334

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 120/319 (37%), Positives = 178/319 (55%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A+ + +    L F++ E PLA+Q+GGAD S
Sbjct: 18  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGAV-QNNPDRALYFNSVEHPLAIQLGGADKS 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 77  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPEHVADCIRAIKQVVGIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 137 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +         
Sbjct: 197 ELKKEIPHIFITINGNILTVEEINNHLKHVDGVMLGRLACDNPYQIAEIHQ-------AL 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
            P   ++ +    ++  +  DY      +   L  + + +  L  G P ++  +  L   
Sbjct: 250 YPEFIKIKRS---QLLMNYLDYWFDQSRANLSLSILVKPLFNLAFGLPGAKHWKKKLMNI 306

Query: 299 VEAGASTATHHIIETAFNL 317
           ++   ++    +I+   NL
Sbjct: 307 IQEKNTSGFSELIQYLLNL 325


>gi|209364495|dbj|BAG74734.1| tRNA dihydrouridine synthase [Vibrio parahaemolyticus]
          Length = 211

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 102/201 (50%), Positives = 138/201 (68%), Gaps = 2/201 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G K + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHG-KGDFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM + + +PVT
Sbjct: 71  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVAECVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDM 200
           Y++K++   L I +NGG++ +
Sbjct: 191 YQLKQDFSHLTIAINGGVKSL 211


>gi|254518234|ref|ZP_05130290.1| tRNA-dihydrouridine synthase A [Clostridium sp. 7_2_43FAA]
 gi|226911983|gb|EEH97184.1| tRNA-dihydrouridine synthase A [Clostridium sp. 7_2_43FAA]
          Length = 348

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 119/330 (36%), Positives = 180/330 (54%), Gaps = 20/330 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD + RH+R+F+RLLT +ALLYTEM+ A AI+ GD+  IL F  +E P+ALQI  ++  
Sbjct: 18  MVDKSHRHFRYFSRLLTKDALLYTEMVTAQAIINGDRDKILYFREEEGPVALQIAASNPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              +A K+   + Y E+NLN GCPS RV     GA LM + ++V + + AM +A + P+T
Sbjct: 78  DAYKAVKLANYYNYTEVNLNCGCPSDRVSGNLMGAALMSSKELVYEILCAMKEATTKPIT 137

Query: 121 VKCRIGVD---------DQIPAVALRNLVKS---IKKSGVNGIWIHARKAILKGLSPKDN 168
           +K RIG+D          +I      +L++    + K+  +   IHAR AILKGLSPKDN
Sbjct: 138 IKHRIGIDGTDVIENEKSKIIMSGYEDLLEFLDIVSKAKPDRYTIHARSAILKGLSPKDN 197

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R+IP LDYD+VY +K++   L I +NGG + +      L  VDGVMIGRA+Y+N  +L  
Sbjct: 198 REIPPLDYDMVYRLKRDFNHLNIEINGGFKTLDSIRDALTKVDGVMIGRASYENCYLLAN 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             + + N     +  +  + K +        T Y    +  G  +  +   +  LF G  
Sbjct: 258 FHKLYENNQNTKAISRGEIIKSY--------TPYVIEEIKKGNSIHSLIAPLQSLFQGQR 309

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLM 318
            S++ + +L+           I+ T   +M
Sbjct: 310 GSKKYKQLLSSSNVKKENIIEILNTILEVM 339


>gi|269121360|ref|YP_003309537.1| dihydrouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615238|gb|ACZ09606.1| dihydrouridine synthase DuS [Sebaldella termitidis ATCC 33386]
          Length = 337

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 121/313 (38%), Positives = 175/313 (55%), Gaps = 28/313 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDR++R F R++  + LLYTEM+ A AI+ GD + ILGF   E P+ALQI      
Sbjct: 13  MVDKTDRYFRNFVRMINKDVLLYTEMVTAQAIIHGDLERILGFDEAEHPIALQIAATTPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              +A K  E++ Y+EINLNVGCPS RV     GACLM  P++V D + A+ +A    VT
Sbjct: 73  DAYKAVKTAENYAYDEINLNVGCPSDRVSGNMMGACLMAYPELVLDILKAIKEATGKAVT 132

Query: 121 VKCRIGVDDQ--IPAVA----------LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +K RIG+D +  +P  A          + N +  I+K+G +   +HAR A+L GL PK N
Sbjct: 133 IKHRIGIDGKGILPDNAEKTLFDKYEDMLNFINIIEKAGADRYTVHARIAVLAGLDPKQN 192

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAM 225
           R++P L YD VY +K E P + I +NGG+   ED+++ LK    VDGVMIGR  Y N  +
Sbjct: 193 REVPPLRYDEVYRLKAEKPYMQIEINGGIKTKEDITEHLKY---VDGVMIGREFYDNPML 249

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           L  V+ +++N   G   I          ++   M  Y  +   +  +     RH +GLFH
Sbjct: 250 LAEVNSFYNN---GEENISR-------YQVLEKMIPYLEKMEMNNERTHLFLRHTLGLFH 299

Query: 286 GFPNSRRCRHILT 298
               S+  ++ ++
Sbjct: 300 NVKGSKYWKNSIS 312


>gi|171463466|ref|YP_001797579.1| dihydrouridine synthase DuS [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|171193004|gb|ACB43965.1| dihydrouridine synthase DuS [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 362

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 116/315 (36%), Positives = 180/315 (57%), Gaps = 21/315 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R LT  A+LYTEM+   A++ GD    L +S  + P+ LQ+GG++ +
Sbjct: 16  MMEWTDRHCRSFHRALTKKAVLYTEMVTTGALMHGDVPRHLDYSQDQHPVILQLGGSEPN 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ + +GY+EI+LN GCPS R+  G+FGACLM  P++V +C+ +M  A+ +P++
Sbjct: 76  DLAKSAELAQQWGYDEIDLNCGCPSERMQRGAFGACLMAEPNLVAECVKSMKSAVDVPIS 135

Query: 121 VKCRIGVDDQIPA-------VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           VK R+G+D    A        AL N + ++  +G + + IHAR A+LKGLSPK+NR  P 
Sbjct: 136 VKHRLGLDSMDAAHSEADYQFAL-NFILAVADAGASQVTIHARNAVLKGLSPKENRSRPP 194

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           L Y++  +++ +     P L + LNGGLE   Q        DG M+GRAAY   A+L   
Sbjct: 195 LRYEVAAKLRLDAQIHFPKLKVLLNGGLETNEQIAGHWNGFDGFMVGRAAYHFPALLLGW 254

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGK---LQQITRHMIGL 283
           D+  +     +  + +  +   W +I  ++            S GK   +   TRH++GL
Sbjct: 255 DDMITTDGDAAGYLFSESE---WHRIQIALVKQVHAWFDECQSKGKPFYIGVFTRHILGL 311

Query: 284 FHGFPNSRRCRHILT 298
            HG   SR  R  L+
Sbjct: 312 AHGRAGSRYWRQRLS 326


>gi|229594322|ref|XP_001029812.3| TIM-barrel protein, yjbN family [Tetrahymena thermophila]
 gi|225566933|gb|EAR82149.3| TIM-barrel protein, yjbN family [Tetrahymena thermophila SB210]
          Length = 466

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 122/310 (39%), Positives = 174/310 (56%), Gaps = 17/310 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI---LRGDKKNILGFSTQEKPLALQIGGA 57
           M+D TD H+R F RLLT  ++LYTEMI   A+   +RG ++  L F   + P+ +Q+GG 
Sbjct: 95  MIDITDVHFRNFIRLLTRYSILYTEMIHEQAVHHNIRGPQE-FLRFDPVQHPVVIQLGGN 153

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   L +AAKI E+ GY+E+NLNVGCPS RV  G FGACLM  P++V + +  M +A SI
Sbjct: 154 DPDNLAKAAKICEEIGYDEVNLNVGCPSDRVQSGKFGACLMKEPELVAEIMRKMKEACSI 213

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCR+GVD+       R+ +K++ + G V    +HARKA LKGL+P  NR +P L Y
Sbjct: 214 PVTVKCRLGVDNFDSYEFARDFIKTVSEKGQVQHFVVHARKAFLKGLNPAQNRNVPPLKY 273

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVD-EY 232
           D V  +K+E P L   +NGG +   Q   IL   +G+   M+GRAAY+   + + +D  Y
Sbjct: 274 DYVLRLKQEFPHLHFSINGGFKTYDQISDILKQENGLHGCMLGRAAYETPWLFSDMDRRY 333

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F     G S    R     W +    +             +  + + +I LF G  +S +
Sbjct: 334 FGKQNPGFS---RREILQIWGQYGKLVI-----QQQPAISIPTLNKPIINLFAGEKHSAK 385

Query: 293 CRHILTVEAG 302
            RH ++  A 
Sbjct: 386 YRHFISDRAN 395


>gi|148358992|ref|YP_001250199.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|296107041|ref|YP_003618741.1| tRNA-dihydrouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
 gi|148280765|gb|ABQ54853.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|295648942|gb|ADG24789.1| tRNA-dihydrouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
          Length = 330

 Score =  212 bits (539), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 108/231 (46%), Positives = 148/231 (64%), Gaps = 1/231 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A+ + +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGAV-QNNPDRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPEHVADCIRAIKQVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +
Sbjct: 193 ELKKEIPHIFITINGNILTVEEINSHLKHVDGVMLGRLACDNPYQIAEIHQ 243


>gi|54294497|ref|YP_126912.1| tRNA-dihydrouridine synthase A [Legionella pneumophila str. Lens]
 gi|53754329|emb|CAH15806.1| hypothetical protein lpl1566 [Legionella pneumophila str. Lens]
          Length = 330

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 108/231 (46%), Positives = 148/231 (64%), Gaps = 1/231 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A+ + +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGAV-QNNPDRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPEHVADCIRAIKQVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +
Sbjct: 193 ELKKEIPHIFITINGNILTVEEINSHLKHVDGVMLGRLACDNPYQIAEIHQ 243


>gi|307610165|emb|CBW99713.1| hypothetical protein LPW_14811 [Legionella pneumophila 130b]
          Length = 330

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 108/231 (46%), Positives = 147/231 (63%), Gaps = 1/231 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A+ + +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGAV-QNNPDRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P  V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPGHVADCIRAIKQVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +
Sbjct: 193 ELKKEIPHIFITINGNILTVEEINSHLKHVDGVMLGRLACDNPYQIAEIHQ 243


>gi|54297373|ref|YP_123742.1| tRNA-dihydrouridine synthase A [Legionella pneumophila str. Paris]
 gi|53751158|emb|CAH12569.1| hypothetical protein lpp1418 [Legionella pneumophila str. Paris]
          Length = 330

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 107/231 (46%), Positives = 148/231 (64%), Gaps = 1/231 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A+ + +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGAV-QNNPGRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMREPEHVADCIRAIKEVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + +HARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIVHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +
Sbjct: 193 ELKKEIPHIFITINGNILTIEEINSHLMYVDGVMLGRLACDNPYQIAEIHQ 243


>gi|307106508|gb|EFN54753.1| hypothetical protein CHLNCDRAFT_23819 [Chlorella variabilis]
          Length = 374

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 126/320 (39%), Positives = 182/320 (56%), Gaps = 26/320 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---DKKNILGFSTQEKPLALQIGGAD 58
           +DWTD +YR  ARL++ +  LYTEM+V   I+     DK   L F  ++ P+  Q+GG+D
Sbjct: 1   MDWTDLYYRQLARLISRHTWLYTEMVVDQTIIHTPFIDK--FLWFPPEQHPIVCQLGGSD 58

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + L  AA IVE +GY+EINLN GCPS RV   G FGA +ML P +V DC  AM +A+ +
Sbjct: 59  PTLLARAAAIVERYGYDEINLNCGCPSDRVAGAGCFGAAMMLRPQLVADCCKAMREAVLM 118

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P+TVKCR+GVD       L N V+ + K SGV+   IHARK +LKGL+P  NR +P L Y
Sbjct: 119 PITVKCRLGVDSFDSYPQLVNFVEVVSKGSGVSHFVIHARKCLLKGLNPHQNRTVPPLRY 178

Query: 177 DIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSA-MLTTVDEY 232
           + V+ +K++ P L   LNGG   LE+++ AL +   + GVM+GRAAY      L   D  
Sbjct: 179 EWVWALKRDFPHLEFSLNGGVLTLEEVASALAL--GIMGVMVGRAAYNMPWDALGDADRA 236

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL------HSGGKLQQITRHMIGLFHG 286
                  ++  + +V  D+     A+  D    H       H    ++ + + ++G+FHG
Sbjct: 237 IFGAEANAATSRRQVLHDY-----AAWADSMIGHWRVEEDGHKSPNVRMLVKPLLGMFHG 291

Query: 287 FPNSRRCRHILTVEAGASTA 306
            P +++ R    V+A   TA
Sbjct: 292 EPRAKKWR--AAVDAALKTA 309


>gi|226493267|ref|NP_001141027.1| hypothetical protein LOC100273106 [Zea mays]
 gi|194702264|gb|ACF85216.1| unknown [Zea mays]
 gi|195645254|gb|ACG42095.1| tRNA-dihydrouridine synthase A [Zea mays]
          Length = 425

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 118/294 (40%), Positives = 174/294 (59%), Gaps = 11/294 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+  + +    L F  ++ P+ LQIGG++
Sbjct: 63  MMDWTDNHYRTLARLISRHAWLYTEMVVAETIVHQKDNLDRFLAFPEEQHPIVLQIGGSN 122

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++  D+ Y+EINLN GCPS +V   G FGA LM +P+ VGD ++ +     +
Sbjct: 123 LENLAKATELANDYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSTIAANCDV 182

Query: 118 PVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V K I KS      IHARKA+L GLSP +NRKIP L Y
Sbjct: 183 PVSVKCRIGVDDRDSYEELCEFVDKVISKSPTRHFIIHARKALLSGLSPAENRKIPPLKY 242

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNS-AMLTTVDEYFS 234
           +  + + ++ P++   LNGG+ ++SQ +  +     GVM+GRAAY N   ML  VD    
Sbjct: 243 EYYFALLRDFPEIKFTLNGGITNVSQVSASMRQGAHGVMVGRAAYNNPWNMLGHVDGEIY 302

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              T    I  R   + ++    S+ D   ++  S   ++Q+ + ++ LFH  P
Sbjct: 303 GKQTRY--ISRRQILENYQAYGDSIID---QYGPSRPNVRQLVKPLLNLFHSEP 351


>gi|168068461|ref|XP_001786082.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162662169|gb|EDQ49105.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 402

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 128/298 (42%), Positives = 174/298 (58%), Gaps = 22/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VAD I+  + +    L F+  + P+ LQ+GG+D
Sbjct: 31  MMDWTDNHYRTLARLMSKHAWLYTEMVVADTIIHQQDNLDKFLKFNEVQHPIVLQLGGSD 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCK-ALS 116
             KL++A+ +   + Y+EINLN GCPS +V   G FGA LML   +V +C+AA+ + +  
Sbjct: 91  PEKLLKASLLASVYEYDEINLNCGCPSEKVAGHGCFGASLMLESGLVAECMAAIAEGSPG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLD 175
            PVTVKCRIGVDD      L   V ++  S       +HARKAILKGLSP  NR IP L 
Sbjct: 151 TPVTVKCRIGVDDFDSYDLLHKFVTTVSSSSPTQHFVVHARKAILKGLSPAANRTIPPLK 210

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNS-AMLTTVDEYF 233
           Y+ VY + ++ P+L   LNGG+ +  Q  + L   V GVM+GRAAY    A L  VD   
Sbjct: 211 YEYVYALIRDFPNLKFTLNGGVVNTHQVNEALQEGVFGVMLGRAAYNYPWATLGNVD--- 267

Query: 234 SNPLTG-SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI----GLFHG 286
            N + G S+P  TR      R+I     +YA   LH  G  +   RH++    G+FH 
Sbjct: 268 -NSVYGDSTPRLTR------RQILEKYVEYADAELHKYGPKKPSVRHLVKPLLGIFHA 318


>gi|255021033|ref|ZP_05293086.1| tRNA-dihydrouridine synthase A [Acidithiobacillus caldus ATCC
           51756]
 gi|254969447|gb|EET26956.1| tRNA-dihydrouridine synthase A [Acidithiobacillus caldus ATCC
           51756]
          Length = 335

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 121/318 (38%), Positives = 167/318 (52%), Gaps = 13/318 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R+F RL+  + +LYTEMI   A++ G   +  L F+  E+PL LQ+GG D 
Sbjct: 22  MLDWTDRHCRYFLRLICPSCVLYTEMIHTSALVLGKSPERYLAFTAAEQPLVLQLGGDDP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  AA +  D+GY  +NLNVGCPS RV  G+FGACLML P +V + I A+  +  +PV
Sbjct: 82  EAMARAAILARDYGYTGVNLNVGCPSTRVQRGNFGACLMLTPALVREIIDALAGS-GLPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G+D Q     L + V  +         +HAR A L+GLSP  NR IP L +D V
Sbjct: 141 SVKHRLGLDRQEDYGQLADFVAQVAAGSCRHFVVHARNAWLRGLSPAANRTIPPLRWDWV 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K++ P L   LNGGL+ + +       VDGVMIGRAAY     LT ++        G
Sbjct: 201 ARLKEDFPGLRFELNGGLDTVPKVEAQWSRVDGVMIGRAAYHRPLFLTELELAL-----G 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 R  + F   + A   D+ A          ++TRH+ G F G P +   R  L  
Sbjct: 256 RRQAPARRAEVF-AALLAYTEDWGA-----ALPAPRLTRHLHGFFFGEPGANAWRQFLGC 309

Query: 300 EAGASTATHHIIETAFNL 317
                +A     E +  L
Sbjct: 310 ARPDQSAAQFFRENSARL 327


>gi|260889590|ref|ZP_05900853.1| tRNA dihydrouridine synthase A [Leptotrichia hofstadii F0254]
 gi|260861001|gb|EEX75501.1| tRNA dihydrouridine synthase A [Leptotrichia hofstadii F0254]
          Length = 332

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 122/319 (38%), Positives = 168/319 (52%), Gaps = 24/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDR++R F R++  + LLYTEMI A A+L GD   ILGF   E P+ LQI   +  
Sbjct: 15  MVDRTDRNFRNFVRMINKDVLLYTEMITAQAVLNGDLDYILGFDEVEHPIVLQIAATNPK 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +  +A KI E + Y+EINLNVGCPS RV     GA LM  P+ V + + +M  A   PV+
Sbjct: 75  EAYQAVKIAEKYNYDEINLNVGCPSDRVSGNMMGAYLMAFPEEVANIVKSMKDATGKPVS 134

Query: 121 VKCRIGVDDQ--IPAVALR----------NLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           VK RIG+D +  +P    R          N +   K++GV+   IHAR AIL GL PK N
Sbjct: 135 VKHRIGIDGKNVLPNSFKRTLLDKYEDMENFISITKQAGVSKYIIHARIAILAGLDPKQN 194

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R IP L YD VY +KK+NPDL I +NGG++ + +  + L  VD  M+GR  Y N  +LT 
Sbjct: 195 RSIPPLRYDEVYRVKKDNPDLHIEINGGIKTVEEIDEHLKYVDSAMLGREIYDNPMILTE 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             +Y+   +  +            ++I   M  Y         +      H  GLFH   
Sbjct: 255 FGKYYGKEINITR-----------KEIIEKMIYYVENMEKQQLRPHLFLMHAHGLFHNVR 303

Query: 289 NSRRCRHILTVEAGASTAT 307
            S+  +  +  E  A++ T
Sbjct: 304 GSKAWKRAIN-EPKANSGT 321


>gi|116309197|emb|CAH66291.1| OSIGBa0113C11.1 [Oryza sativa Indica Group]
          Length = 368

 Score =  206 bits (523), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 117/295 (39%), Positives = 173/295 (58%), Gaps = 13/295 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+  + +    L F  ++ P+ LQIGG++
Sbjct: 1   MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V   G FGA LM +P+ VGD ++A+    ++
Sbjct: 61  LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 120

Query: 118 PVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V K + KS      IHARKA+L GLSP +NRK+P L Y
Sbjct: 121 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRKVPPLKY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNS-AMLTTVD-EYF 233
           +  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD E +
Sbjct: 181 EYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVDSEVY 240

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P   SS  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P
Sbjct: 241 GMPTRRSS--RRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEP 289


>gi|125547565|gb|EAY93387.1| hypothetical protein OsI_15183 [Oryza sativa Indica Group]
          Length = 437

 Score =  205 bits (521), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 122/317 (38%), Positives = 181/317 (57%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+   K N+   L F  ++ P+ LQIGG+
Sbjct: 70  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVH-QKDNLDRFLAFPAEQHPIVLQIGGS 128

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           ++  L +A ++   + Y+EINLN GCPS +V   G FGA LM +P+ VGD ++A+    +
Sbjct: 129 NLDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCN 188

Query: 117 IPVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +PV++KCRIGVDD+     L   V K + KS      IHARKA+L GLSP +NRK+P L 
Sbjct: 189 VPVSIKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRKVPPLK 248

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNS-AMLTTVD-EY 232
           Y+  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD E 
Sbjct: 249 YEYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVDSEV 308

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-- 290
           +  P   SS  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P +  
Sbjct: 309 YGMPTRRSS--RRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEPGNGL 362

Query: 291 ------RRCRHILTVEA 301
                    RH  T+E+
Sbjct: 363 WKRKADSTLRHCKTLES 379


>gi|325182221|emb|CCA16675.1| tRNAdihydrouridine synthase putative [Albugo laibachii Nc14]
          Length = 563

 Score =  205 bits (521), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 108/229 (47%), Positives = 146/229 (63%), Gaps = 10/229 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGAD 58
           +DWTDRHYR+  RL+T++  LYTEM+V D  L   K N+   LG    E PLA+Q+GG  
Sbjct: 218 MDWTDRHYRYLMRLITHHTQLYTEMLV-DQTLLYQKDNLHYFLGHDDDESPLAVQLGGNS 276

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA--- 114
           I  L  AA++  ++G +NEINLN GCPS +V +  FGA LML P+ V D  A M  A   
Sbjct: 277 IDTLAAAAQLCREYGGFNEINLNCGCPSPKVSKQCFGAQLMLQPERVRDICAGMIGANSS 336

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +   +TVKCRIGVDD      L+  +  +  SGV    +HARK  L GL+P +NR IP L
Sbjct: 337 MDPEITVKCRIGVDDCDSYEELKRFISVVSASGVEHFIVHARKCWLSGLNPHENRTIPTL 396

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           +YD VY++K + P+L   LNGG+  + +A ++L +  +DG+MIGRAAYK
Sbjct: 397 NYDFVYQLKSDFPNLAFTLNGGVASIEEAHRLLQTSNMDGIMIGRAAYK 445


>gi|257126021|ref|YP_003164135.1| dihydrouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257049960|gb|ACV39144.1| dihydrouridine synthase DuS [Leptotrichia buccalis C-1013-b]
          Length = 331

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 119/304 (39%), Positives = 160/304 (52%), Gaps = 24/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           MVD TDR++R F R++  + LLYTEMI A AI+     N +LGF   E P+ LQI   + 
Sbjct: 13  MVDRTDRNFRNFVRMINKDVLLYTEMITAQAIINTKDLNYLLGFDKIENPIVLQIAATNP 72

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +  EA KI E + Y+EINLN+GCPS RV     GA LM  P++V D I AM  A + P+
Sbjct: 73  KEAYEAVKIAEKYDYDEINLNIGCPSDRVSGNMMGAYLMAFPEVVADIIKAMKDATNKPI 132

Query: 120 TVKCRIGVDDQ--IPAVALR----------NLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           ++K RIG+D +  +P    R          N +   KK+GVN   IHAR A+L GL PK 
Sbjct: 133 SIKHRIGIDGKNILPDYFERTLLDKYEDMMNFINITKKTGVNKYIIHARIAVLAGLDPKQ 192

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           NR IP L YD VY +KKENPDL I +NG ++ + +  + L   D VM+GR  Y N  +LT
Sbjct: 193 NRSIPPLRYDEVYRVKKENPDLHIEINGEIKSVDEIDEHLKYTDSVMMGREIYDNPMILT 252

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
              +Y+   +  +             +I   M  Y         +      H  GLFH  
Sbjct: 253 EFGKYYGKDINITR-----------EEIIEKMIYYVENMERQNIRPHLFLMHTHGLFHNV 301

Query: 288 PNSR 291
             S+
Sbjct: 302 RGSK 305


>gi|167998448|ref|XP_001751930.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162697028|gb|EDQ83365.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 373

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 127/332 (38%), Positives = 183/332 (55%), Gaps = 19/332 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWT+ H+R  ARL++ +A LYTEM+V D I   + +   IL F     P+ LQ+GG +
Sbjct: 20  MMDWTNNHFRTIARLMSKHAWLYTEMVVDDTINYQQDNLDMILKFPESHHPIVLQLGGCN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSI 117
             KL  A+++   +GY+EINLN GCPS  V   SFGA LML P++VG C+ A+ K +   
Sbjct: 80  PEKLFRASQLASLYGYDEINLNCGCPSDNVTGRSFGAALMLEPELVGQCVTAIAKGSPGT 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L N ++ +   S      IHARKA+LKGLSP +NR+IP L Y
Sbjct: 140 PVSVKCRIGVDDFDSYDFLHNFIRIVSSTSPTKHFIIHARKAVLKGLSPDENRRIPPLKY 199

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS-AMLTTVDEYFS 234
           D V+ + ++ P+L   LNGG+  + Q  + L   V GVM+GR AY +  ++L  VD    
Sbjct: 200 DYVFALMRDFPNLKFTLNGGVVGIHQVNEALNRGVFGVMLGRTAYNSPWSVLANVDRVVY 259

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFHGFPNS 290
             +T   P+ TR      R+I      Y    LH  G     ++QI + + GLF+     
Sbjct: 260 GDMT---PVLTR------RQILEKYVVYGDAELHRYGYKKPGIRQIAQPLSGLFYREKGV 310

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R  L     +S   H ++     ++ +S+
Sbjct: 311 GLWRRALDEYIRSSQTLHALLRDTLRVIPDSV 342


>gi|297602354|ref|NP_001052360.2| Os04g0278900 [Oryza sativa Japonica Group]
 gi|255675275|dbj|BAF14274.2| Os04g0278900 [Oryza sativa Japonica Group]
          Length = 368

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 116/295 (39%), Positives = 172/295 (58%), Gaps = 13/295 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+  + +    L F  ++ P+ LQIGG++
Sbjct: 1   MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V   G FGA LM +P+ VGD ++A+    ++
Sbjct: 61  LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 120

Query: 118 PVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V K + KS      IHARKA+L GLSP +NR +P L Y
Sbjct: 121 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRNVPPLKY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNS-AMLTTVD-EYF 233
           +  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD E +
Sbjct: 181 EYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVDSEVY 240

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P   SS  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P
Sbjct: 241 GMPTRRSS--RRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEP 289


>gi|242072588|ref|XP_002446230.1| hypothetical protein SORBIDRAFT_06g006720 [Sorghum bicolor]
 gi|241937413|gb|EES10558.1| hypothetical protein SORBIDRAFT_06g006720 [Sorghum bicolor]
          Length = 368

 Score =  203 bits (517), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 115/294 (39%), Positives = 171/294 (58%), Gaps = 11/294 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+  + +    L F  ++ P+ LQIGG++
Sbjct: 1   MMDWTDNHYRTLARLISRHAWLYTEMVVAETIVHQKDNLDRFLAFPEEQHPIVLQIGGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++  D+ Y+EINLN GCPS +V   G FGA LM  P+ VGD ++ +     +
Sbjct: 61  LENLAKATELANDYSYDEINLNCGCPSGKVAGHGCFGARLMFEPEFVGDAMSTIAANCDV 120

Query: 118 PVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V K + KS      IHARKA+L GLSP +NRK+P L Y
Sbjct: 121 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRKVPPLKY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNS-AMLTTVDEYFS 234
           +  + + ++ P +   +NGG+ ++ Q +  I     GVM+GRAAY N   ML  VD    
Sbjct: 181 EYYFALLRDFPGIKFTVNGGITNVGQVSASIRQGAHGVMVGRAAYNNPWNMLGHVDGEIY 240

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              T    I  R   + ++    S+ D   ++  S   ++Q+ + ++ LFH  P
Sbjct: 241 GKQTRC--ISRRQILESYQAYGDSIID---QYGPSRPNVRQLVKPLLNLFHSEP 289


>gi|313678961|ref|YP_004056700.1| tRNA-u16,u17-dihydrouridine synthase [Oceanithermus profundus DSM
           14977]
 gi|313151676|gb|ADR35527.1| tRNA-U16,U17-dihydrouridine synthase [Oceanithermus profundus DSM
           14977]
          Length = 321

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 109/297 (36%), Positives = 157/297 (52%), Gaps = 10/297 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+RF  RL++    LY+EM+V   ++ GD    L F   E P+ALQ+G AD  
Sbjct: 11  MMERTDRHFRFLMRLVSRRTRLYSEMVVDRTLIHGDPPRHLDFHPAEHPVALQLGSADPR 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
               A  +   +GY+E+NLNVGCPS RV  G FG  LM  P+ V + + A+ +   + +T
Sbjct: 71  LAARAVAVTRPWGYDEVNLNVGCPSPRVQAGGFGVVLMRRPERVAEIVRAVHQETGVRMT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L   V+ +  +GV    +HARKA  +GL PK NR +P L++  VY
Sbjct: 131 VKHRVGLDEDDDYAFLARFVEVVAAAGVQVFVVHARKAWTEGLDPKANRTVPPLEHAKVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I  NGG+ D  +A   L  VDGVM+GRA +       + D      L G 
Sbjct: 191 RLKRDFPELTIVTNGGVADPEEARAHLEHVDGVMVGRAMWDRPWRWASADRV----LWGD 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           + +  R      R +      Y    L  G  L+ + R +  LF G P  RR R  L
Sbjct: 247 ARVPDR------RTVLERYEAYLHERLAEGVPLRALVRPLFNLFKGEPGGRRWRRTL 297


>gi|297817686|ref|XP_002876726.1| hypothetical protein ARALYDRAFT_486864 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297322564|gb|EFH52985.1| hypothetical protein ARALYDRAFT_486864 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 405

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 105/236 (44%), Positives = 150/236 (63%), Gaps = 6/236 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD HYR  ARL+T +A LYTEMI A+ ++  + +    L FS Q+ P+ LQ+GG++
Sbjct: 44  MMEWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQANLDRFLAFSPQQHPIVLQLGGSN 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +AAK+ + +GY+EINLN GCPS +V   G FG  LML P +VG+ ++A+    ++
Sbjct: 104 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVRLMLKPKLVGEAMSAIAANTNV 163

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVDD      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y
Sbjct: 164 PVTVKCRIGVDDHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKY 223

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNS-AMLTTVD 230
           +  Y + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N   ML  VD
Sbjct: 224 EYFYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNNPWQMLGHVD 279


>gi|218515463|ref|ZP_03512303.1| tRNA-dihydrouridine synthase A [Rhizobium etli 8C-3]
          Length = 156

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 92/156 (58%), Positives = 114/156 (73%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D  
Sbjct: 1   MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPV 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  CIAAM    + PVT
Sbjct: 61  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAGCIAAMKAVSTAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHAR
Sbjct: 121 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHAR 156


>gi|224531739|ref|ZP_03672371.1| tRNA-dihydrouridine synthase A [Borrelia valaisiana VS116]
 gi|224511204|gb|EEF81610.1| tRNA-dihydrouridine synthase A [Borrelia valaisiana VS116]
          Length = 335

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 184/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   ++GACLM N + VG+ +  M ++ + PV
Sbjct: 72  DALKAIQILEKYFNFDEYNLNVGCPSLKIQNANYGACLMNNANQVGEILKTMKESTNKPV 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N V+ I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRLLTSDYKNESYSEVKNFVRIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L +VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSAVDSVMIGRSAFENPYFIAKASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEIPTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E++
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPENI 330


>gi|224028635|gb|ACN33393.1| unknown [Zea mays]
          Length = 296

 Score =  202 bits (513), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 102/231 (44%), Positives = 147/231 (63%), Gaps = 5/231 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+  + +    L F  ++ P+ LQIGG++
Sbjct: 63  MMDWTDNHYRTLARLISRHAWLYTEMVVAETIVHQKDNLDRFLAFPEEQHPIVLQIGGSN 122

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++  D+ Y+EINLN GCPS +V   G FGA LM +P+ VGD ++ +     +
Sbjct: 123 LENLAKATELANDYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSTIAANCDV 182

Query: 118 PVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V K I KS      IHARKA+L GLSP +NRKIP L Y
Sbjct: 183 PVSVKCRIGVDDRDSYEELCEFVDKVISKSPTRHFIIHARKALLSGLSPAENRKIPPLKY 242

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNSAML 226
           +  + + ++ P++   LNGG+ ++SQ +  +     GVM+GRAAY    + 
Sbjct: 243 EYYFALLRDFPEIKFTLNGGITNVSQVSASMRQGAHGVMVGRAAYNKYVLF 293


>gi|262037496|ref|ZP_06010955.1| tRNA-dihydrouridine synthase A [Leptotrichia goodfellowii F0264]
 gi|261748426|gb|EEY35806.1| tRNA-dihydrouridine synthase A [Leptotrichia goodfellowii F0264]
          Length = 329

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 119/318 (37%), Positives = 167/318 (52%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDR++R F R++  + LLYTEMI A A++ GD   IL F   E P+ LQ+   +  
Sbjct: 10  MVDRTDRNFRNFVRMINKDVLLYTEMITAQAVINGDSDYILEFDDTEHPIVLQLAVTNKK 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +  EA KI E + Y+EINLNVGCPS RV     GA LM  P+ V + +A + KA   PV+
Sbjct: 70  EAYEAIKIAEKYDYDEINLNVGCPSDRVSGNMMGAYLMAFPETVAEIVAGIKKATDKPVS 129

Query: 121 VKCRIGVDDQ--IPAVALR----------NLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +K RIG+D +  +P    R          N V   +K+GV    +HAR A+L+GL PK N
Sbjct: 130 IKHRIGIDGKNILPETFKRTLLDKYEDMLNFVNITQKAGVKKYVVHARIAVLEGLDPKQN 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R+IP L Y+ VY +KKE P+L I +NGG++   Q  + L   D VM+GR  Y N  +L+ 
Sbjct: 190 REIPPLRYEEVYRLKKERPELHIEINGGIKTTEQIDEHLKYADSVMLGREIYDNPMILSK 249

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             +Y+   +  +             +I   M  Y  +      +      H  GLFHG  
Sbjct: 250 FGKYYGKNIEIAR-----------EEIIEKMILYVEKMERENKRPHLFLMHTHGLFHGVK 298

Query: 289 NSRRC-RHILTVEAGAST 305
            S+   R I   +A + T
Sbjct: 299 GSKYWKREINAPQADSKT 316


>gi|21536881|gb|AAM61213.1| unknown [Arabidopsis thaliana]
          Length = 404

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 101/227 (44%), Positives = 146/227 (64%), Gaps = 5/227 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL+T +A LYTEMI A+ ++  + +    L FS Q+ P+ LQ+GG++
Sbjct: 44  MMDWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSN 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +AAK+ + +GY+EINLN GCPS +V   G FG  LML P +VG+ ++A+    ++
Sbjct: 104 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKLVGEAMSAIAANTNV 163

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVD+      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y
Sbjct: 164 PVTVKCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKY 223

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN 222
           +  Y + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N
Sbjct: 224 EYYYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNN 270


>gi|145339824|ref|NP_567149.2| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|24030197|gb|AAN41279.1| unknown protein [Arabidopsis thaliana]
 gi|332646975|gb|AEE80496.1| FMN-linked oxidoreductase-like protein protein [Arabidopsis
           thaliana]
          Length = 419

 Score =  201 bits (510), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/227 (44%), Positives = 146/227 (64%), Gaps = 5/227 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL+T +A LYTEMI A+ ++  + +    L FS Q+ P+ LQ+GG++
Sbjct: 59  MMDWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSN 118

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +AAK+ + +GY+EINLN GCPS +V   G FG  LML P +VG+ ++A+    ++
Sbjct: 119 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKLVGEAMSAIAANTNV 178

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVD+      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y
Sbjct: 179 PVTVKCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKY 238

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN 222
           +  Y + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N
Sbjct: 239 EYYYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNN 285


>gi|301092884|ref|XP_002997293.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262111428|gb|EEY69480.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 379

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 113/252 (44%), Positives = 151/252 (59%), Gaps = 18/252 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+DWTDRHYRF  R++T   LL+TEM+V D  L   +KN+   LG    E PLALQ+GG 
Sbjct: 15  MMDWTDRHYRFMMRMITKKTLLFTEMVV-DQTLLYQRKNLDYFLGHDPAEAPLALQLGGN 73

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +  L  AA + + +G + EINLN GCPSA V    FGA LML P+ V D   +M  +++
Sbjct: 74  SVEDLGAAAHLSQSYGGFCEINLNTGCPSALVSSRCFGARLMLEPERVRDICDSMRHSVA 133

Query: 117 I-----------PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +            VTVKCRIGVDD      L + V ++  +GV  I +HARK +LKGLS 
Sbjct: 134 LASEGNPDHPTAEVTVKCRIGVDDCDSYDELHHYVAAVASAGVRHIIVHARKCLLKGLST 193

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
           KDNR IP L Y++VY +K++ P+L   LNGG++ +  A ++L   +VDG+MIGRAAY   
Sbjct: 194 KDNRTIPPLRYEVVYRLKQDFPELSFTLNGGVKSIQHARELLNTTNVDGIMIGRAAYNTP 253

Query: 224 AMLTTVDEYFSN 235
                 D    N
Sbjct: 254 WNFRDADRLIFN 265


>gi|302789157|ref|XP_002976347.1| hypothetical protein SELMODRAFT_104800 [Selaginella moellendorffii]
 gi|300155977|gb|EFJ22607.1| hypothetical protein SELMODRAFT_104800 [Selaginella moellendorffii]
          Length = 358

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 117/327 (35%), Positives = 182/327 (55%), Gaps = 10/327 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD H+R  AR+L+  + LYTEM+VA+ I+    D +  L F   + P+ LQ+GG++
Sbjct: 9   MMEWTDNHFRALARILSRCSWLYTEMVVAETIVHHENDLERWLEFPAAQHPIVLQLGGSN 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L +AAK+V  FGY+EIN N GCPS++V   G FGA LML+P +VG+ + A+ +  S 
Sbjct: 69  LANLSKAAKLVSAFGYDEINFNCGCPSSKVAGHGCFGARLMLSPRLVGEAMQAIAEESSA 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVDD      L N V ++   S      IHARKA+L+GLSP  NR  P L Y
Sbjct: 129 PVTVKCRIGVDDSDSYDQLCNFVSTVSSLSPTRHFIIHARKALLEGLSPAQNRVAPPLKY 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + V  + ++ PDL   LNGG+  + Q   ++    V+GVM+GRAAY N+   T      +
Sbjct: 189 EYVLALMRDFPDLQFTLNGGITTVEQVNYLITDKGVNGVMLGRAAY-NTPWCTLAR---A 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +      P +    +   R+          ++ ++   ++ + + +  LFHG   S R R
Sbjct: 245 DSCIYGMPERRITRRQVLREYEEYAESVIGKYGNNKPGIRVLVKPVANLFHGEKGSSRWR 304

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             +      + A++ +   +   ++ S
Sbjct: 305 QAIDEHVRHAKASNTLSSFSLRFVLSS 331


>gi|111115049|ref|YP_709667.1| tRNA-dihydrouridine synthase A [Borrelia afzelii PKo]
 gi|110890323|gb|ABH01491.1| conserved hypothetical protein [Borrelia afzelii PKo]
          Length = 333

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 114/330 (34%), Positives = 181/330 (54%), Gaps = 19/330 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNSKN 69

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   ++GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAVQILEKHFNFDEYNLNVGCPSLKIQNANYGACLMSNANQVGEILKTMKETTNKPI 129

Query: 120 TVKCRIGVDDQIPA-------VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           ++K R+G+   +P+         +++ VK I   G+    +HAR AILKG SPK+NR IP
Sbjct: 130 SIKHRLGIR-LLPSDYKNESYSEVKSFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIP 188

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            L ++ VY++KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      
Sbjct: 189 KLRHEFVYKLKKENKNLFIETNGGISNSEQIKKHLSVVDSVMIGRSAFENPYFIANASRE 248

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F   L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++
Sbjct: 249 F---LNETDKILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKK 298

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIESL 322
            R  LT     +   H I+  A   + E +
Sbjct: 299 FRQNLTAPFPKNLRKHEILLKAMETLPEKI 328


>gi|216263891|ref|ZP_03435885.1| tRNA-dihydrouridine synthase A [Borrelia afzelii ACA-1]
 gi|215979935|gb|EEC20757.1| tRNA-dihydrouridine synthase A [Borrelia afzelii ACA-1]
          Length = 335

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 114/330 (34%), Positives = 181/330 (54%), Gaps = 19/330 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   ++GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAVQILEKHFNFDEYNLNVGCPSLKIQNANYGACLMSNANQVGEILKTMKETTNKPI 131

Query: 120 TVKCRIGVDDQIPA-------VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           ++K R+G+   +P+         +++ VK I   G+    +HAR AILKG SPK+NR IP
Sbjct: 132 SIKHRLGIR-LLPSDYKNESYSEVKSFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIP 190

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            L ++ VY++KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      
Sbjct: 191 KLRHEFVYKLKKENKNLFIETNGGISNSEQIKKHLSVVDSVMIGRSAFENPYFIANASRE 250

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F   L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++
Sbjct: 251 F---LNETDKILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKK 300

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIESL 322
            R  LT     +   H I+  A   + E +
Sbjct: 301 FRQNLTAPFPKNLRKHEILLKAMETLPEKI 330


>gi|225551987|ref|ZP_03772927.1| tRNA-dihydrouridine synthase A [Borrelia sp. SV1]
 gi|225370985|gb|EEH00415.1| tRNA-dihydrouridine synthase A [Borrelia sp. SV1]
          Length = 335

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MINITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    IHAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIIHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|302811002|ref|XP_002987191.1| hypothetical protein SELMODRAFT_125523 [Selaginella moellendorffii]
 gi|300145088|gb|EFJ11767.1| hypothetical protein SELMODRAFT_125523 [Selaginella moellendorffii]
          Length = 363

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 115/303 (37%), Positives = 173/303 (57%), Gaps = 10/303 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD H+R  AR+L+  + LYTEM+VA+ I+    D +  L F   + P+ LQ+GG++
Sbjct: 9   MMEWTDNHFRALARILSRCSWLYTEMVVAETIVHHENDLERWLEFPAAQHPIVLQLGGSN 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L +AAK+V  FGY+EIN N GCPS++V   G FGA LML+P +VG+ + A+ +  S 
Sbjct: 69  LANLSKAAKLVSAFGYDEINFNCGCPSSKVAGHGCFGARLMLSPRLVGEAMQAIGEESSA 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVDD      L N V ++   S      IHARKA+L+GLSP  NR  P L Y
Sbjct: 129 PVTVKCRIGVDDSDSYDQLCNFVSTVSSLSPTQHFIIHARKALLEGLSPAQNRVAPPLKY 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + V  + ++ PDL   LNGG+  + Q   ++    V+GVM+GRAAY N+   T      +
Sbjct: 189 EYVLALMRDFPDLQFTLNGGITTVEQVNYLISDKGVNGVMLGRAAY-NTPWCTLAR---A 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +      P +    +   R+          ++ ++   ++ + + +  LFHG   S R R
Sbjct: 245 DSCIYGMPERRITRRQVLREYEEYAESVIGKYGNNKPGIRVLVKPVANLFHGEKGSSRWR 304

Query: 295 HIL 297
             +
Sbjct: 305 QAI 307


>gi|221217675|ref|ZP_03589143.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 72a]
 gi|223888837|ref|ZP_03623428.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 64b]
 gi|224532647|ref|ZP_03673268.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi WI91-23]
 gi|221192352|gb|EEE18571.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 72a]
 gi|223885653|gb|EEF56752.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 64b]
 gi|224512427|gb|EEF82807.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi WI91-23]
          Length = 335

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|225550111|ref|ZP_03771071.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 118a]
 gi|225369223|gb|EEG98676.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 118a]
          Length = 333

 Score =  198 bits (504), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 69

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 129

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 250 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAIETLPEKI 328


>gi|203284144|ref|YP_002221884.1| tRNA-dihydrouridine synthase A [Borrelia duttonii Ly]
 gi|201083587|gb|ACH93178.1| tRNA-dihydrouridine synthase A [Borrelia duttonii Ly]
          Length = 335

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 115/327 (35%), Positives = 175/327 (53%), Gaps = 17/327 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ G+   I+  +  + P+A+QI     +
Sbjct: 12  MVEITDEHFRYIIRLLSKKITLYTPMISAKSIIMGELNTIVKQNPNDSPIAIQIATNCEN 71

Query: 61  KLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E +F ++E NLNVGCPS+R+ + ++GACLM NP  VG  + AM K  + P+
Sbjct: 72  DAAKAIEILEKNFNFDEYNLNVGCPSSRIQKANYGACLMQNPIQVGKILKAMQKNTNKPI 131

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+        +     L+  V  I + G+    +HAR AIL G SPKDN  IP 
Sbjct: 132 SIKHRIGIRHNKKEYQEETYTELKQFVDKIIEYGIKNFIVHARIAILNGYSPKDNHNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L YD VY++KKE  + FI +NGG+ + +     L  VD VMIGRAA +N   +  +   F
Sbjct: 192 LKYDFVYQLKKEYKNTFIEINGGIINSNHIETHLSYVDSVMIGRAAAQNPYFVAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR      ++I   M +Y   + +    +  I RH++ + +   N+R+ 
Sbjct: 252 ---LGEKEQIPTR------KEILFQMVEYIKEY-NEHPTINTILRHIMRVIYSQKNARKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R  LT     +   H I+  A   + E
Sbjct: 302 RQALTAPFNQNLKNHEILLNAIEHLKE 328


>gi|195941421|ref|ZP_03086803.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 80a]
          Length = 324

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 181/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 1   MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 60

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 61  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 120

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 121 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 181 LRHEFVYNLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 240

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 241 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 290

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 291 RQNLTAPFPKNLKKHEILLKAIETLPEKI 319


>gi|216264796|ref|ZP_03436788.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 156a]
 gi|225549125|ref|ZP_03770100.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 94a]
 gi|215981269|gb|EEC22076.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 156a]
 gi|225370351|gb|EEG99789.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 94a]
 gi|312148382|gb|ADQ31041.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi JD1]
          Length = 335

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|15594570|ref|NP_212359.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi B31]
 gi|218249426|ref|YP_002374748.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi ZS7]
 gi|226321543|ref|ZP_03797069.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi Bol26]
 gi|2688130|gb|AAC66623.1| conserved hypothetical protein [Borrelia burgdorferi B31]
 gi|218164614|gb|ACK74675.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi ZS7]
 gi|226232732|gb|EEH31485.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi Bol26]
 gi|312149107|gb|ADQ29178.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi N40]
          Length = 335

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|219684515|ref|ZP_03539458.1| tRNA-dihydrouridine synthase A [Borrelia garinii PBr]
 gi|219671877|gb|EED28931.1| tRNA-dihydrouridine synthase A [Borrelia garinii PBr]
          Length = 335

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 180/329 (54%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K ++  +  E P+A+QI      
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKVVKQTPLESPIAIQIATNCKF 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRLLNSDYKNESYSEVKNFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L+ +  I TR D      I   M +Y   +  +   +  + +H++G+      +R+ 
Sbjct: 252 ---LSETDKIPTRKD------ILMQMVEYVKEY-ENYLSINILFKHLMGIIFSKEGARKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAMETLPEKI 330


>gi|84999912|ref|XP_954677.1| hypothetical protein [Theileria annulata]
 gi|65305672|emb|CAI73997.1| hypothetical protein, conserved [Theileria annulata]
          Length = 408

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 116/309 (37%), Positives = 175/309 (56%), Gaps = 25/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D T   +R F RLLT    L+TEM VA +++   ++++   L F   E P+  Q+GG 
Sbjct: 91  MLDVTYLQFRQFMRLLTRKTQLWTEMFVASSLINASEESVSRWLKFEENEHPIVAQLGGN 150

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
               LVEA +I++ FGY+EINLNVGCPS RV  +G FGA LM   ++V D +  M K L 
Sbjct: 151 CPETLVEAGRILKKFGYDEINLNVGCPSPRVSGKGCFGASLMREKELVRDIVHNMIKELE 210

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R+GVD+      +++ V ++ +SG     IH+RKA LKG++PK NR +P L Y
Sbjct: 211 IPVTVKTRLGVDESDSYEFVKDFVSTVSQSGCEHFIIHSRKAWLKGINPKKNRTVPPLQY 270

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-----------VDGVMIGRAAYKNSAM 225
           + V+ ++++ P L   +NGG + M   L  L S           ++GVMIGR AY+N  +
Sbjct: 271 EKVFRLQRDFPHLKFTINGGFKTMESILDALNSENVDTDNNPHKLNGVMIGRLAYENPCI 330

Query: 226 LTTVDEYF---SNPLTGSSPIKTRVDKDFWRKISASMTDYAAR-----HLHSGGKLQQIT 277
           L+ VD+      NP T  +  +  + + F+ K  A+  +YA          +   +  I 
Sbjct: 331 LSNVDKIIYGVENPDTCYT--RRILLEVFYLKFIANFQNYANYIDENVEETANMNISLIV 388

Query: 278 RHMIGLFHG 286
           + ++G+FHG
Sbjct: 389 KPILGVFHG 397


>gi|226321200|ref|ZP_03796737.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 29805]
 gi|226233397|gb|EEH32141.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 29805]
          Length = 335

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANKVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|219685843|ref|ZP_03540651.1| tRNA-dihydrouridine synthase A [Borrelia garinii Far04]
 gi|219672617|gb|EED29648.1| tRNA-dihydrouridine synthase A [Borrelia garinii Far04]
          Length = 333

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 180/329 (54%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K ++  +  E P+A+QI      
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKVVKQTPLESPIAIQIATNCKF 69

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMRENTNKPI 129

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRLLNSDYKNESYSEVKNFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L+ +  I TR D      I   M +Y   +  +   +  + +H++G+      +R+ 
Sbjct: 250 ---LSETDKIPTRKD------ILMQMVEYVKEY-ENYLSINILFKHLMGIIFSKEGARKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAMETLPEKI 328


>gi|224533852|ref|ZP_03674440.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi CA-11.2a]
 gi|224513145|gb|EEF83508.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi CA-11.2a]
          Length = 333

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 115/329 (34%), Positives = 182/329 (55%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 69

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPI 129

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 250 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAIETLPEKI 328


>gi|224534214|ref|ZP_03674792.1| tRNA-dihydrouridine synthase A [Borrelia spielmanii A14S]
 gi|224514316|gb|EEF84632.1| tRNA-dihydrouridine synthase A [Borrelia spielmanii A14S]
          Length = 335

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 113/330 (34%), Positives = 181/330 (54%), Gaps = 19/330 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNCKN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   ++GACLM   D VG  +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANYGACLMSKADQVGKILKTMKENTNKPI 131

Query: 120 TVKCRIGVDDQIPA-------VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           ++K R+G+   +P+         +++ VK I   G+    +HAR AILKG SPK+NR IP
Sbjct: 132 SIKHRLGIR-LLPSDYKNESYSEVKSFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIP 190

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            L ++ VY++K EN +LFI +NGG+ ++ Q  K L  VD VMIGR+A++N   +      
Sbjct: 191 KLKHEFVYKLKNENKNLFIEINGGINNLEQIKKHLSVVDSVMIGRSAFENPYFIANASRE 250

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F   L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++
Sbjct: 251 F---LNETDKILTRKD------ILMKMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKK 300

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIESL 322
            R  LT     +   H I+  A   + E++
Sbjct: 301 FRQNLTAPFPKNLRKHEILLKAIETLPETI 330


>gi|203287682|ref|YP_002222697.1| tRNA-dihydrouridine synthase A [Borrelia recurrentis A1]
 gi|201084902|gb|ACH94476.1| tRNA-dihydrouridine synthase A [Borrelia recurrentis A1]
          Length = 335

 Score =  195 bits (495), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 115/327 (35%), Positives = 174/327 (53%), Gaps = 17/327 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ G+   I+  +  + P+A+QI     +
Sbjct: 12  MVEITDEHFRYIIRLLSKKITLYTPMISAKSIIIGELNTIVKQNPNDSPIAIQIATNCEN 71

Query: 61  KLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E +F ++E NLNVGCPS+R+ + ++GACLM NP  VG  + AM K  + P+
Sbjct: 72  DAAKAIEILEKNFNFDEYNLNVGCPSSRIQKANYGACLMQNPIQVGKILKAMQKNTNKPI 131

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+        +     L+  V  I + G+    +HAR AIL G SPKDN  IP 
Sbjct: 132 SIKHRIGIRHNKKEYQEETYTELKQFVDKIIEYGIKNFIVHARIAILNGYSPKDNHNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L YD VY++KKE  + FI +NGG+ + +     L  VD VMIGRAA +N   +  +   F
Sbjct: 192 LKYDFVYQLKKEYKNTFIEINGGIINSNHIETHLSYVDSVMIGRAAAQNPYFVAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR      ++I   M +Y  +  +    +  I RH++ + H   N+ + 
Sbjct: 252 ---LGEKEQIPTR------KEILFQMVEY-IKEYNEHPTINTILRHIMRVIHSQKNACKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R  LT     +   H I+  A   + E
Sbjct: 302 RQALTAPFNQNLKNHEILLNAIEHLKE 328


>gi|51598486|ref|YP_072674.1| tRNA-dihydrouridine synthase A [Borrelia garinii PBi]
 gi|51573057|gb|AAU07082.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 333

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 114/329 (34%), Positives = 179/329 (54%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K ++  +  E P+A+QI      
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKVVKQTPLESPIAIQIATNCKF 69

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E  F ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 129

Query: 120 TVKCRIGV-----DDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+     D +  + + ++N +K I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRLLNSDYKNESYSEVKNFIKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +R+ 
Sbjct: 250 ---LGETDKIPTRKD------ILMKMVEYIKEY-ENYLSINILCKHLMGITFSKEGARKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAMETLPEKI 328


>gi|255553550|ref|XP_002517816.1| tRNA-dihydrouridine synthase A, putative [Ricinus communis]
 gi|223543088|gb|EEF44623.1| tRNA-dihydrouridine synthase A, putative [Ricinus communis]
          Length = 375

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 107/295 (36%), Positives = 172/295 (58%), Gaps = 13/295 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ ++ LYTEM+ A+ I+  +G+    L FS Q+ P+ LQIGG++
Sbjct: 16  MMDWTDHHYRTLARLISKHSWLYTEMLAAETIVYQQGNLDRFLAFSPQQHPIVLQIGGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   +GY+EIN N GCPS RV   G FG  LML+P  VG+ ++ +     +
Sbjct: 76  LDNLAKATELATAYGYDEINFNCGCPSPRVAGHGCFGVRLMLDPKFVGEAMSVIAANTDV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVD+      L + +  +   S      IH+RKA+L G+SP +NRKIP L Y
Sbjct: 136 PVSVKCRIGVDNHDSYNELCDFIYKVSSLSPTKHFIIHSRKALLNGISPAENRKIPPLKY 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNS-AMLTTVDE-YF 233
           +  + + ++ PDL   +NGG+  + +  L +     GVM+GRAA+ N   +L  VD   +
Sbjct: 196 EYYFALLRDFPDLRFTINGGINCIDEVNLALREGAHGVMVGRAAFNNPWTVLGHVDSAIY 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P +G +  + +V + +     A +  Y     ++   ++ + + ++GLF+  P
Sbjct: 256 GAPESGLT--RRQVLEQYQAYADAILGTYG----NNRPNVRDVVKPLLGLFYSEP 304


>gi|224055152|ref|XP_002298425.1| predicted protein [Populus trichocarpa]
 gi|222845683|gb|EEE83230.1| predicted protein [Populus trichocarpa]
          Length = 378

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/227 (42%), Positives = 144/227 (63%), Gaps = 9/227 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  AR+++ +A LYTEM+ A+ I+  +GD    L FS ++ P+ LQIGG +
Sbjct: 16  MMDWTDNHYRTVARIISKHAWLYTEMLAAETIVHQQGDLDRFLAFSPEQHPIVLQIGGNN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   +GY+EINLN GCPS +V   G FG  LML+P  VG+ ++ +     +
Sbjct: 76  LDNIAKATRLANSYGYDEINLNCGCPSPKVAGHGCFGVRLMLDPKFVGEAMSVIAANTDV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIG+DD      L + +  +   S      IH+RKA+L G+SP DNR+IP L Y
Sbjct: 136 PVSVKCRIGLDDHDSYNELCDFIYKVSSLSPTKHFIIHSRKALLNGISPADNRRIPPLKY 195

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAY 220
           +  Y + ++ PDL   +NGG+   ++++ AL+      GVM+GRAAY
Sbjct: 196 EYYYALLRDFPDLRFTINGGINCVDEVNAALR--EGAHGVMVGRAAY 240


>gi|217075895|gb|ACJ86307.1| unknown [Medicago truncatula]
          Length = 432

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 110/295 (37%), Positives = 169/295 (57%), Gaps = 14/295 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+ A+ I+  + +    L +S ++ P+ LQIGG++
Sbjct: 74  MMDWTDNHYRTLARLISKHAWLYTEMLAAETIVHQKDNLDRFLAYSPEQHPIVLQIGGSN 133

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  L +A ++   + Y+EINLN GCPS RV   GSFG  LML+P  V + ++A+    ++
Sbjct: 134 IESLAKATELANAYCYDEINLNCGCPSPRVAGHGSFGVSLMLDPKFVAEAMSAIAANTNV 193

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V ++   S      IH+RKA+L G+SP +NR IP L Y
Sbjct: 194 PVSVKCRIGVDDRDSYDELCEFVSTVSSLSPTKHFIIHSRKALLNGISPAENRSIPPLKY 253

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNS-AMLTTVDE-YF 233
           +  Y + ++ PDL   +NGG+  + +      +   GVMIGRAA+ N   +L  VD   +
Sbjct: 254 EYFYGLLRDFPDLTFTINGGITSVDEVNAARDAGAHGVMIGRAAFYNPWHILGHVDTAIY 313

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P  G +  + +V + +     + +  Y  R       ++ I + ++ LFH  P
Sbjct: 314 GAPSCGLT--RRQVLEKYIVYGDSELGKYGHR-----PTVRDIVKPLLNLFHSAP 361


>gi|297795405|ref|XP_002865587.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297311422|gb|EFH41846.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 388

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 116/296 (39%), Positives = 164/296 (55%), Gaps = 21/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+ WTD HYR  ARL+T +A LYTEM+ A+ I+  +    + L +S  + P+ LQIGG +
Sbjct: 17  MMGWTDNHYRTLARLITKHAWLYTEMLAAETIVYQEDNLDSFLAYSPDQHPIVLQIGGRN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   +GY+EIN N GCPS +V   G FGA LML+P  VG+ ++ +    + 
Sbjct: 77  LENLAKATRLANAYGYDEINFNCGCPSPKVSGRGCFGALLMLDPKFVGEAMSVIASNTNA 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            VTVKCRIGVDD      L + +  +   S      IH+RKA+L GLSP DNR+IP L Y
Sbjct: 137 AVTVKCRIGVDDHDSYNELCDFIHIVSSLSPTKHFIIHSRKALLSGLSPSDNRRIPPLKY 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNS-AMLTTVDEY-F 233
           +  + + ++ PDL   +NGG+  + +A   L S   GVM+GRA Y N    L  VD   +
Sbjct: 197 EFFFALLRDFPDLKFTINGGINSVVEADAALRSGAHGVMLGRAVYYNPWHTLGHVDTVIY 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFH 285
            +P +G     TR      R++      Y    L   GK    L+ I R +I LFH
Sbjct: 257 GSPSSGI----TR------RQVLEKYQVYGESVLGKYGKGRPNLRDIVRPLINLFH 302


>gi|224106093|ref|XP_002314040.1| predicted protein [Populus trichocarpa]
 gi|222850448|gb|EEE87995.1| predicted protein [Populus trichocarpa]
          Length = 380

 Score =  189 bits (481), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 107/297 (36%), Positives = 175/297 (58%), Gaps = 17/297 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD+HYR  AR+++ +A LYTEM+ A+ I+  +G+    L F +++ P+ LQIGG +
Sbjct: 16  MMEWTDKHYRTVARIISKHAWLYTEMLAAETIVYQQGNLDRFLAFPSEQHPIVLQIGGNN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   +G++EINLN GCPSA+V   G FGA LML+P  V + ++ +     +
Sbjct: 76  LDNIAKATQLANAYGFDEINLNCGCPSAKVAGHGCFGARLMLDPKFVSEAMSVIAANTDV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L + +  +   S      IH+RKA+L G+SP DNR+IP L Y
Sbjct: 136 PVSVKCRIGVDDHDSYNELCDFIYKVSSLSPTKHFIIHSRKALLNGISPADNRRIPPLKY 195

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN-SAMLTTVDE- 231
           +  Y + ++ PDL   +NGG+   ++++ AL+      GVM+GRAAY N    L  VD  
Sbjct: 196 EYYYALLRDFPDLRFTINGGIDCVDEVNAALR--EGAHGVMVGRAAYNNLWNTLAHVDSA 253

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
            +  P +G +  + +V + +     A +  Y     ++   ++++ R + G F+  P
Sbjct: 254 VYGEPSSGLT--RRQVLEQYQVYGDAVLGTYG----NNRPNMRELIRPLSGFFYSEP 304


>gi|269123581|ref|YP_003306158.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
 gi|268314907|gb|ACZ01281.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
          Length = 317

 Score =  189 bits (481), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 110/303 (36%), Positives = 162/303 (53%), Gaps = 18/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TD H+R F  ++  +  LYTEMI   AIL GD+  IL  +  E P+ LQI  +++ 
Sbjct: 9   MVDRTDIHFRNFISMINKDIELYTEMITTQAILNGDRSKILKITNVENPVVLQIATSNLK 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           + +EAAK ++   YN +N+NVGCPS RV   + GA LM  P++V D   A+ +     VT
Sbjct: 69  ESIEAAKYIKYTNYNAVNINVGCPSDRVSGHNMGAYLMSEPELVRDIAQAVKEYSGKDVT 128

Query: 121 VKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +K RIG+D      +    V    L+  I  + V+   +HAR AILKGLSPK+NR IP L
Sbjct: 129 IKNRIGIDGKGILENDRKIVRYEELLNFIDITNVSKYIVHARIAILKGLSPKENRTIPEL 188

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DY++VY +K++ P+L I +NGG++ +         VD VMIGRA Y N  +   ++    
Sbjct: 189 DYEMVYRLKRDRPNLMIEINGGIKTIEDIKIHHNYVDSVMIGRAFYDNPMLANEIN---- 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             L     +K   +      I   M  Y      +  K     RH +GLF+    S+  +
Sbjct: 245 --LLNDKSVKKHTE------IVKEMFHYVKMLEENNEKPHHFLRHTLGLFYNTKYSKMWK 296

Query: 295 HIL 297
           +++
Sbjct: 297 NMI 299


>gi|15238854|ref|NP_199608.1| nitrogen regulation family protein [Arabidopsis thaliana]
 gi|145334771|ref|NP_001078731.1| nitrogen regulation family protein [Arabidopsis thaliana]
 gi|10177748|dbj|BAB11061.1| unnamed protein product [Arabidopsis thaliana]
 gi|18175722|gb|AAL59916.1| unknown protein [Arabidopsis thaliana]
 gi|20466015|gb|AAM20229.1| unknown protein [Arabidopsis thaliana]
 gi|332008217|gb|AED95600.1| tRNA-dihydrouridine synthase A [Arabidopsis thaliana]
 gi|332008218|gb|AED95601.1| tRNA-dihydrouridine synthase A [Arabidopsis thaliana]
          Length = 387

 Score =  189 bits (481), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 116/296 (39%), Positives = 164/296 (55%), Gaps = 21/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+ WTD HYR  ARL+T +A LYTEM+ A+ I+  +    + L FS  + P+ LQIGG +
Sbjct: 17  MMGWTDNHYRTLARLITKHAWLYTEMLAAETIVYQEDNLDSFLAFSPDQHPIVLQIGGRN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EIN N GCPS +V   G FGA LML+P  VG+ ++ +    + 
Sbjct: 77  LENLAKATRLANAYAYDEINFNCGCPSPKVSGRGCFGALLMLDPKFVGEAMSVIAANTNA 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            VTVKCRIGVDD      L + +  +   S      IH+RKA+L GLSP DNR+IP L Y
Sbjct: 137 AVTVKCRIGVDDHDSYNELCDFIHIVSSLSPTKHFIIHSRKALLSGLSPSDNRRIPPLKY 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNS-AMLTTVDE-YF 233
           +  + + ++ PDL   +NGG+  + +A   L S   GVM+GRA Y N   +L  VD   +
Sbjct: 197 EFFFALLRDFPDLKFTINGGINSVVEADAALRSGAHGVMLGRAVYYNPWHILGHVDTVVY 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFH 285
            +P +G     TR      R++      Y    L   GK    L+ I R +I LFH
Sbjct: 257 GSPSSGI----TR------RQVLEKYKLYGESVLGKYGKGRPNLRDIVRPLINLFH 302


>gi|145332939|ref|NP_001078335.1| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|332646976|gb|AEE80497.1| FMN-linked oxidoreductase-like protein protein [Arabidopsis
           thaliana]
          Length = 386

 Score =  189 bits (480), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 97/223 (43%), Positives = 142/223 (63%), Gaps = 5/223 (2%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKL 62
           +D HYR  ARL+T +A LYTEMI A+ ++  + +    L FS Q+ P+ LQ+GG+++  L
Sbjct: 30  SDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSNVENL 89

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +AAK+ + +GY+EINLN GCPS +V   G FG  LML P +VG+ ++A+    ++PVTV
Sbjct: 90  AKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKLVGEAMSAIAANTNVPVTV 149

Query: 122 KCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           KCRIGVD+      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y+  Y
Sbjct: 150 KCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKYEYYY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN 222
            + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N
Sbjct: 210 ALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNN 252


>gi|254496444|ref|ZP_05109322.1| tRNA-dihydrouridine synthase A [Legionella drancourtii LLAP12]
 gi|254354340|gb|EET12997.1| tRNA-dihydrouridine synthase A [Legionella drancourtii LLAP12]
          Length = 305

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 100/218 (45%), Positives = 133/218 (61%), Gaps = 1/218 (0%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           R+L  +ALLYTEM    AI    +++ L F+ QE PLALQ+GG+D   L   AK+ E  G
Sbjct: 2   RILAPHALLYTEMQTTGAIQNNPRRS-LPFNHQEHPLALQLGGSDPGALGRCAKLAEQEG 60

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           Y+E+N+N+GCPS +V  G FGACLM  P  V  CI AM +  SIPVT K RIG+D Q   
Sbjct: 61  YDEVNINLGCPSDKVKAGHFGACLMNEPAQVMACIKAMREETSIPVTAKVRIGIDHQDSY 120

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                 V+ +  +G   I +HARKA L GLSPK NR +P ++YD VY IKKE P + + +
Sbjct: 121 EFFSAFVQQLIAAGSQKIIVHARKAWLNGLSPKQNRTVPPVNYDYVYRIKKEIPHIPVVI 180

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           NG + +  +  + L  VDGVM+GR A  N   +  + E
Sbjct: 181 NGNILNSQEINEHLHYVDGVMLGRLACDNPYQIAEIHE 218


>gi|225450085|ref|XP_002277955.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 433

 Score =  185 bits (469), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 96/229 (41%), Positives = 142/229 (62%), Gaps = 9/229 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWT+ HYR  ARL++ +A LYTEMI A+ I+  +K     L FS  + P+ LQIGG +
Sbjct: 72  MMDWTNNHYRTLARLISKHAWLYTEMIAAETIVYQEKNLDRFLEFSPDQHPIVLQIGGNN 131

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   + Y+EINLN GCPS +V   G FG  LML+P  V + ++ +     +
Sbjct: 132 LDNIAKATELANSYCYDEINLNCGCPSPKVAGHGCFGVRLMLDPKFVAEAMSVIAANSDV 191

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L + +  +  +S      IH+RKA+L G+SP DNRKIP L Y
Sbjct: 192 PVSVKCRIGVDDHDSYNELCDFIYKVSSQSPTRHFIIHSRKALLNGISPADNRKIPPLKY 251

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
           +  + + ++ PDL   +NGG+   ++++ AL+      GVM+GRAAY N
Sbjct: 252 EYYFGLLRDFPDLRFTINGGINCVDEVNAALR--QGAHGVMVGRAAYHN 298


>gi|124506924|ref|XP_001352059.1| dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|23505088|emb|CAD51870.1| dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 577

 Score =  185 bits (469), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 116/339 (34%), Positives = 179/339 (52%), Gaps = 37/339 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R++T  A L+TEMIV         + +  LGF   E P+  Q+GG D
Sbjct: 205 MINVTNRHFRAMVRIITKRAQLWTEMIVDNTLLYNLNNLEEHLGFDNNEHPIVCQLGGCD 264

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ + EAA +VE  GY+EIN+NVGCPS +V ++G+FGA LM NP+ V + +  + K + I
Sbjct: 265 MNSMSEAAILVEQAGYDEININVGCPSTKVANKGAFGASLMKNPEQVRNIVYEIKKKVQI 324

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVD+      L+  ++++   G N   +HARKA LKGL PK NRKIP L+Y 
Sbjct: 325 PVTVKIRTGVDNYDSFDFLKTFIETVSSVGCNHFIVHARKAWLKGLDPKQNRKIPPLEYY 384

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS---------------------------- 209
            VY++ K  P L   LNGG++ + +A+ +L                              
Sbjct: 385 KVYDLCKLYPHLKFTLNGGIQTIQEAIALLNGYMPENYNNNNNNNNDTSNFIQIDNYNIN 444

Query: 210 -VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            ++G+MIGRA  +N  +L+  D+   N    S+    R   + ++K     + +   +L 
Sbjct: 445 PLNGIMIGRACMENITVLSQTDKLVYNQDIPSTAYSRRTILEAYKKYLEKNSLFY--NLS 502

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTAT 307
           S  +L    + ++G+  G P  R  R+ L       T+T
Sbjct: 503 SSFEL---LKPVLGILKGMPGHRIFRNKLDTYIRNYTST 538


>gi|119953021|ref|YP_945230.1| tRNA-dihydrouridine synthase A [Borrelia turicatae 91E135]
 gi|119861792|gb|AAX17560.1| NIFR3-like protein [Borrelia turicatae 91E135]
          Length = 335

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 112/327 (34%), Positives = 177/327 (54%), Gaps = 17/327 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV  TD H+R+  RLL+    LYT MI A +I+ G    I+  +  + P+A+QI     +
Sbjct: 12  MVAITDEHFRYIIRLLSKKVTLYTPMISAKSIIMGKLNTIVKQTPTDSPIAIQIATDCEN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E+ F ++E NLNVGCPS+RV + ++GACLM  P  VG  + AM K  + PV
Sbjct: 72  DAAKAIEILENKFNFDEYNLNVGCPSSRVQDANYGACLMQTPTQVGKILQAMKKNTNKPV 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+        +     L+  V+ I +  +    IHAR AIL G SPKDN+ IP 
Sbjct: 132 SIKHRIGIRHNKREYHETNYRELKQFVEKIIEYEIKNFTIHARVAILNGYSPKDNQNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L +++VY++K+++ ++FI +NGG+   +     L  VD VMIGRAA K+   +  +   F
Sbjct: 192 LRHELVYQLKQDHKNIFIEINGGIISSNHIKTHLSYVDSVMIGRAAAKDPYFIAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR  ++   K+   + +Y   HL     +  I +H++ +     N+R+ 
Sbjct: 252 ---LEEKEKIPTR--EEVLLKMVEYIKEY-NEHL----SINTILKHIMRIVFAKDNARKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R IL+     +   H I+ +A   + E
Sbjct: 302 RQILSAPFPKNLKNHEILLSAIEHLRE 328


>gi|297736275|emb|CBI24913.3| unnamed protein product [Vitis vinifera]
          Length = 423

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 96/229 (41%), Positives = 142/229 (62%), Gaps = 9/229 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWT+ HYR  ARL++ +A LYTEMI A+ I+  +K     L FS  + P+ LQIGG +
Sbjct: 62  MMDWTNNHYRTLARLISKHAWLYTEMIAAETIVYQEKNLDRFLEFSPDQHPIVLQIGGNN 121

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   + Y+EINLN GCPS +V   G FG  LML+P  V + ++ +     +
Sbjct: 122 LDNIAKATELANSYCYDEINLNCGCPSPKVAGHGCFGVRLMLDPKFVAEAMSVIAANSDV 181

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L + +  +  +S      IH+RKA+L G+SP DNRKIP L Y
Sbjct: 182 PVSVKCRIGVDDHDSYNELCDFIYKVSSQSPTRHFIIHSRKALLNGISPADNRKIPPLKY 241

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
           +  + + ++ PDL   +NGG+   ++++ AL+      GVM+GRAAY N
Sbjct: 242 EYYFGLLRDFPDLRFTINGGINCVDEVNAALR--QGAHGVMVGRAAYHN 288


>gi|187918097|ref|YP_001883660.1| tRNA-dihydrouridine synthase A [Borrelia hermsii DAH]
 gi|119860945|gb|AAX16740.1| NIFR3-like protein [Borrelia hermsii DAH]
          Length = 335

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 107/327 (32%), Positives = 172/327 (52%), Gaps = 17/327 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV  TD H+R+  RLL+    LYT MI A +I+ G+   ++  +  + P+A+QI  +  +
Sbjct: 12  MVAITDEHFRYMIRLLSKKVTLYTPMISAKSIIMGNLNKVVKQTPTDSPIAIQIATSCEN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E+ F ++E NLNVGCPS++V   ++GACLM  P  VG  + AM K  + PV
Sbjct: 72  DAAKAIEILENKFNFDEYNLNVGCPSSKVQNANYGACLMQTPTQVGKILKAMKKNTNKPV 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+ +      +     L+  V+ I +  +    +HAR AIL G SPKDN+ IP 
Sbjct: 132 SIKHRIGIRNNKREYHEENYTELQQFVEKIMEYEIKNFTVHARIAILNGYSPKDNQNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L +D VY +K+E+ ++FI +NGG++        L  VD VMIGRA  K+  ++  +   F
Sbjct: 192 LRHDFVYRLKQEHKNIFIEVNGGIKSSDHIKTHLSYVDSVMIGRAVAKDPYLIAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR       +I   M +Y  +       +  I +H++ +     N+ + 
Sbjct: 252 ---LEEKEKIPTR------EEILLKMVEY-IKEYDECLSISTILKHIMSIVFAKENACKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R  L+     +   H I+ +A   + E
Sbjct: 302 RQTLSAPFPKNLKNHEILLSAIEHLRE 328


>gi|82753060|ref|XP_727524.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23483411|gb|EAA19089.1| Uncharacterized protein family UPF0034, putative [Plasmodium yoelii
           yoelii]
          Length = 531

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 110/327 (33%), Positives = 177/327 (54%), Gaps = 37/327 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R+++    L+TEMIV + +L    + +  LGF+  E P+  Q+GG+D
Sbjct: 159 MINVTNRHFRALVRIISKKVQLWTEMIVDNTLLYNINNLEEHLGFNKNEHPIVCQLGGSD 218

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA +VE  GY+EIN+NVGCPS +V ++G+FGA LM NP +V + +  + K + I
Sbjct: 219 PTSLSEAAILVEQAGYDEININVGCPSTKVANKGAFGAYLMKNPQLVKNIVYEIKKKVQI 278

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVD+      LR+ ++++  +G +   IH+RKA LKGL PK NR IP L+Y+
Sbjct: 279 PVTVKIRTGVDNLDSFSFLRSFIETVSSAGCDHFIIHSRKAWLKGLDPKQNRSIPPLEYN 338

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--------------PSVD------------ 211
            V+++ K  P +   LNGG++ + Q + +L               S D            
Sbjct: 339 KVFDLCKLYPHIKFTLNGGIKSIEQGVALLNGYAPINNMSGKHNNSTDNNYIKIEDYDIN 398

Query: 212 ---GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
              GVMIGRA  +N  +L   D+   N  + S+    R   D ++      + +     +
Sbjct: 399 PLYGVMIGRACMENITVLAKTDKLVYNYDSPSTAHSRRTVLDAYKFYLEQNSSF-----Y 453

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRH 295
           +     ++ + ++G+  G P  R  R+
Sbjct: 454 TLVNAFELLKPILGILKGMPGHRLFRN 480


>gi|221054640|ref|XP_002258459.1| dihydrouridine synthase [Plasmodium knowlesi strain H]
 gi|193808528|emb|CAQ39231.1| dihydrouridine synthase, putative [Plasmodium knowlesi strain H]
          Length = 508

 Score =  180 bits (456), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 110/318 (34%), Positives = 167/318 (52%), Gaps = 32/318 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M++ T+RH+R F R +T  A L+TEMIV + +L          GF++ E P+  Q+GG+D
Sbjct: 141 MINVTNRHFRAFVRTITRRAQLWTEMIVDNTLLYNLNNLEEYLGFNSNEHPVVCQLGGSD 200

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA +VE  GY+EINLNVGCPS +V ++G+FGA LM  P+ V + +  + + + I
Sbjct: 201 PTSLAEAAVLVEQAGYDEINLNVGCPSTKVANKGAFGAYLMKKPEHVRNIVYEIKRKVQI 260

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R GVDD      LR+ ++ +   G     +HARKA LKGL PK NR +P L Y 
Sbjct: 261 PVSVKIRTGVDDCDSFPFLRSFIECVSSVGCTHFIVHARKAWLKGLDPKQNRSVPPLQYS 320

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI----LPSVD--------------------GV 213
            VY + +  P L   LNGG++ + +A+ +    LP  D                    GV
Sbjct: 321 KVYTLCQLYPHLKFTLNGGIKTIEEAVALLNGYLPREDKCDGEKTYVQVQNYHVNPLNGV 380

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GRA  +N+ +L+  D+   N     +    R   D ++      +      L S    
Sbjct: 381 MLGRACMENTTVLSQTDQLVYNEKPPHTAFSRRTVLDAYKSYLEENSS-----LCSLSSA 435

Query: 274 QQITRHMIGLFHGFPNSR 291
            ++ + ++G+  G P  R
Sbjct: 436 FELLKPILGILKGMPGHR 453


>gi|221481338|gb|EEE19732.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii GT1]
 gi|221502060|gb|EEE27806.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 394

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 118/328 (35%), Positives = 165/328 (50%), Gaps = 40/328 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DK-KNILGFSTQEKPLALQIGGAD 58
           M+  T+ H+R F R  T  A L+TEM+   AIL   D+ +  L     E P+  Q+GG+D
Sbjct: 20  MLAVTNTHFRNFMRCFTREAQLWTEMVTDGAILNNMDRLQQNLCLEDIEHPIVCQLGGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L EA K++E  G++EINLNVGCPS RV  +G FGA LM  P+ V D +  + + + I
Sbjct: 80  PKTLAEAGKLIEKLGFDEINLNVGCPSNRVVSQGCFGAALMKTPETVRDIVHEIRRHVQI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D       LRN V+++   G     IHARKA LKG+ PK NR +P L Y 
Sbjct: 140 PVTVKTRIGYDHCDSRDVLRNFVQTVSAGGCRHFIIHARKAWLKGVDPKKNRSVPPLLYG 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQAL------------------------KILPSVDGV 213
            VY++  + P L   LNGG+  + QA+                        K +  + GV
Sbjct: 200 RVYDLCDQFPHLDFSLNGGVRSIQQAIDLAAGKWTDGTAEMDALLRRITRDKTVKPLRGV 259

Query: 214 MIGRAAYKNSAMLTTVDEYF----SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
           M+GRAA  +  +L  VD  F    +NP T  S  +  V + +   I     D    H   
Sbjct: 260 MLGRAASADPCILANVDTDFYGADANPPTSHS--RRTVLEAYRNYIKPFAEDGEYSHF-- 315

Query: 270 GGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                 + + ++G+F+G P +R  R  L
Sbjct: 316 -----ALLKPVLGVFNGMPGNRLFRFTL 338


>gi|156097374|ref|XP_001614720.1| tRNA-dihydrouridine synthase A [Plasmodium vivax SaI-1]
 gi|148803594|gb|EDL44993.1| tRNA-dihydrouridine synthase A, putative [Plasmodium vivax]
          Length = 509

 Score =  179 bits (453), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 112/324 (34%), Positives = 172/324 (53%), Gaps = 32/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R +T  A ++TEMIV         + +  LGF++ E P+  Q+GG+D
Sbjct: 142 MINVTNRHFRALVRTITRRAQVWTEMIVDNTLLYNLNNLEEHLGFNSNEHPIVCQLGGSD 201

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA +VE  GY+EINLNVGCPS +V ++G+FGA LM  P+ V + +  + + + I
Sbjct: 202 ATSLAEAAVLVEQAGYDEINLNVGCPSTKVANKGAFGAYLMKKPEHVRNIVYEIKRKVHI 261

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R GVDD      LR+ V+ I   G +   +HARKA LKGL PK NR +P L+Y 
Sbjct: 262 PVSVKIRTGVDDCDSFPFLRSFVECISSVGCSHFIVHARKAWLKGLDPKQNRSVPPLEYP 321

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-------SVD-----------------GV 213
            VY + +  P L   LNGG++ + +A+ +L        +VD                 GV
Sbjct: 322 KVYSLCQLYPHLKFTLNGGVKTVEEAVALLNGYLPKKGNVDSEKTYVQVKNYQVNPLHGV 381

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GRA  +N+ +L+  D+   N     +    R   D ++      +      L S    
Sbjct: 382 MLGRACMENTTVLSQTDQLVYNEKPPHTAFSRRTVLDAYKSYLEENSS-----LCSLSSA 436

Query: 274 QQITRHMIGLFHGFPNSRRCRHIL 297
            ++ + ++G+  G P  R  R+ L
Sbjct: 437 FELLKPVLGILKGMPGHRIFRNKL 460


>gi|237838939|ref|XP_002368767.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211966431|gb|EEB01627.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
          Length = 394

 Score =  178 bits (452), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 117/328 (35%), Positives = 165/328 (50%), Gaps = 40/328 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DK-KNILGFSTQEKPLALQIGGAD 58
           M+  T+ H+R F R  T  A L+TEM+   AIL   D+ +  L     E P+  Q+GG+D
Sbjct: 20  MLAVTNTHFRNFMRCFTREAQLWTEMVTDGAILNNMDRLQQNLCLEDIEHPIVCQLGGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L EA K++E  G++EINLNVGCPS RV  +G FGA LM  P+ V D +  + + + I
Sbjct: 80  PKTLAEAGKLIEKLGFDEINLNVGCPSNRVVSQGCFGAALMKTPETVRDIVHEIRRHVQI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D       LRN V+++   G     +HARKA LKG+ PK NR +P L Y 
Sbjct: 140 PVTVKTRIGYDHCDSRDVLRNFVQTVSAGGCRHFIVHARKAWLKGVDPKKNRSVPPLLYG 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQAL------------------------KILPSVDGV 213
            VY++  + P L   LNGG+  + QA+                        K +  + GV
Sbjct: 200 RVYDLCDQFPHLDFSLNGGVRSIQQAIDLAAGKWTDGTAEMDALLRRITRDKTVKPLRGV 259

Query: 214 MIGRAAYKNSAMLTTVDEYF----SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
           M+GRAA  +  +L  VD  F    +NP T  S  +  V + +   I     D    H   
Sbjct: 260 MLGRAASADPCILANVDTDFYGADANPPTSHS--RRTVLEAYRNYIKPFAEDGEYSHF-- 315

Query: 270 GGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                 + + ++G+F+G P +R  R  L
Sbjct: 316 -----ALLKPVLGVFNGMPGNRLFRFTL 338


>gi|68071985|ref|XP_677906.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56498194|emb|CAH96102.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 441

 Score =  177 bits (450), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 106/327 (32%), Positives = 174/327 (53%), Gaps = 37/327 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R+++    L+TEMIV + +L    + +  LGF+  E P+  Q+GG+D
Sbjct: 69  MINVTNRHFRALVRIISKKVQLWTEMIVDNTLLYNINNLEEHLGFNKNEHPIVCQLGGSD 128

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L EAA +VE  GY+E+N+NVGCPS +V ++G+FGA LM  P +V + +  + K + I
Sbjct: 129 PISLSEAAILVEQAGYDELNINVGCPSTKVANKGAFGAYLMKKPQLVKNIVYEIKKKVQI 188

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVDD      LR+ ++++  +G +   IH+RKA LKGL PK NR IP L+Y+
Sbjct: 189 PVTVKIRTGVDDLDSFSFLRSFIETVSSAGCDHFIIHSRKAWLKGLDPKQNRSIPPLEYN 248

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS---------------------------- 209
            V+++ K  P++   LNGG++ + Q + +L                              
Sbjct: 249 KVFDLCKLYPNIKFTLNGGIKSIEQGVALLNGYAPINNMSGKHNNCTDNNYIKIKDYDIN 308

Query: 210 -VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            + GVMIGR+  +N  +L   D+   N    ++    R   D ++      + +     +
Sbjct: 309 PLYGVMIGRSCMENITVLAKTDKLVYNYDIPTTAYNRRTVLDAYKSYLEQNSSF-----Y 363

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRH 295
           S     ++ + ++G+  G P  R  R+
Sbjct: 364 SLVNAFELLKPILGILKGMPGHRLFRN 390


>gi|298708539|emb|CBJ49172.1| FAD binding / catalytic/ tRNA dihydrouridine synthase [Ectocarpus
           siliculosus]
          Length = 469

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 109/307 (35%), Positives = 163/307 (53%), Gaps = 22/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQ-EKPLALQIGGA 57
           M+++TDRH R+  RLLT   +L+TEM+ +  I+    D    L ++ + E P+ LQIGG+
Sbjct: 87  MMEYTDRHMRYLLRLLTTRTVLWTEMVPSSTIIHNPDDLGRFLDYNEEVEHPVVLQIGGS 146

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           D + + EA ++   + Y+ INLN GCPS +V  +G+FGA LM +P +V D   AM     
Sbjct: 147 DTTDVREACRLARPYKYDAINLNCGCPSEKVAGKGAFGAALMRSPSLVKDLCLAMKDGAG 206

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPN 173
              P+TVKCRIGVD+      L   V+ + + +GV    +HARKAIL GLSP  NR IP 
Sbjct: 207 EDTPITVKCRIGVDNDDSYEQLAAFVEEVSRGAGVPHFIVHARKAILGGLSPAQNRNIPP 266

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEY 232
           L YD VY + K+ PD+   LNGG+    +A+  L     GVM+GR+   N    +  D  
Sbjct: 267 LKYDFVYRLVKDFPDVDFTLNGGVNTYEEAVSCLEQGAHGVMVGRSWSSNPWYWSQADSM 326

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-----LQQITRHMIGLFHGF 287
                    P  TR      R++     +Y  R   + G+      +++ + +  +FHG 
Sbjct: 327 L---FGAKDPGLTR------REVLERYAEYGERQEKACGEKWLACRRRLAKPIWHMFHGE 377

Query: 288 PNSRRCR 294
              ++ R
Sbjct: 378 KGGKKFR 384


>gi|7573334|emb|CAB87804.1| putative protein [Arabidopsis thaliana]
          Length = 456

 Score =  177 bits (449), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 102/279 (36%), Positives = 146/279 (52%), Gaps = 57/279 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL+T +A LYTEMI A+ ++  + +    L FS Q+ P+ LQ+GG++
Sbjct: 44  MMDWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSN 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDI-------------- 103
           +  L +AAK+ + +GY+EINLN GCPS +V   G FG  LML P +              
Sbjct: 104 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKVRYFTPPHDFKRYLL 163

Query: 104 ----------VGDCIAAMCKALSIPVTVKCRIGVDDQ----------------------- 130
                     VG+ ++A+    ++PVTVKCRIGVD+                        
Sbjct: 164 FLNFTLSFKLVGEAMSAIAANTNVPVTVKCRIGVDNHDSYDELCELFLLSVFLKSRMDLP 223

Query: 131 ------IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
                  P +    + K    S      +H+RKA+L G+SP DNR+IP L Y+  Y + +
Sbjct: 224 LRSNTAFPLLLGDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKYEYYYALVR 283

Query: 185 ENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN 222
           + PDL   +NGG+  +S+    L     GVM+GRAAY N
Sbjct: 284 DFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNN 322


>gi|71031827|ref|XP_765555.1| tRNA-dihydrouridine synthase A [Theileria parva strain Muguga]
 gi|68352512|gb|EAN33272.1| tRNA-dihydrouridine synthase A, putative [Theileria parva]
          Length = 471

 Score =  177 bits (448), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 120/372 (32%), Positives = 186/372 (50%), Gaps = 58/372 (15%)

Query: 1   MVDWTDRHYRFFA----------RLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQE 47
           M+D T  H+R+F           RLLT    L+TEM VA +++    +++   L F   E
Sbjct: 91  MLDVTYLHFRYFMDFKFDFRQFMRLLTRKTQLWTEMFVASSLINASNESVSRWLKFEENE 150

Query: 48  KPLALQIG----------GADISKLVEAAKIVEDFGYNEINLNVGCPSARV--------- 88
            P+  Q+G          G     LVEA +I++ FGY+EINLN GCPS RV         
Sbjct: 151 HPIVAQLGIFYQHKIVPGGNCPETLVEAGRILKKFGYDEINLNAGCPSPRVSGKGIYKFM 210

Query: 89  ----HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
               + G FGA LM   ++V D    M + L +PVTVK R+GVD+      +R+ V ++ 
Sbjct: 211 LKLFNLGCFGASLMKEKELVRDIAHHMLRELEMPVTVKTRLGVDEFDSYEFVRDFVSTVS 270

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           +SG +   IH+RKA LKG++PK NR IP L Y+ VY ++++ P L   +NGG + M   L
Sbjct: 271 ESGCDHFIIHSRKAWLKGINPKQNRTIPPLQYEKVYRLQRDFPHLKFTINGGFKTMESIL 330

Query: 205 KILPS-----------VDGVMIGRAAYKNSAMLTTVDEYF---SNPLTGSSPIKTRVDKD 250
           + L S           ++GVMIGR AY+N  +L+ VD+      NP T  +  +  + ++
Sbjct: 331 EALNSENLDSNNNPHKLNGVMIGRLAYENPCLLSNVDKLIYGVENPDTCYT--RRILLEN 388

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           +   I  +  D A         +  I + ++G+FHG   ++  R  L+         +H 
Sbjct: 389 YANYIDENQVDTA------NLNISLIVKPILGVFHGEQGNKIFRQSLSNVYDYDDFIYHS 442

Query: 311 IETAFNLMIESL 322
            E+  ++ I  +
Sbjct: 443 GESRHSMFIHKV 454


>gi|156082854|ref|XP_001608911.1| dihydrouridine synthase (Dus) domain containing protein [Babesia
           bovis T2Bo]
 gi|154796161|gb|EDO05343.1| dihydrouridine synthase (Dus) domain containing protein [Babesia
           bovis]
          Length = 362

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 108/303 (35%), Positives = 161/303 (53%), Gaps = 9/303 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D T   +R F RL+T  A L+TEM+   +++ GD   +   L     E P+ LQ+GG 
Sbjct: 23  MLDITYYEFRQFMRLITKRAQLWTEMMADGSLIYGDSDKVGSMLHCDANEHPIVLQLGGN 82

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           ++  L +A  I   +GY E NLNVGCPS RV  +G FGA LM +  +VG  +  +   L 
Sbjct: 83  NLDSLSKAGNIALGYGYTEFNLNVGCPSTRVSGKGCFGAALMNDAPLVGRIVKHLRSELG 142

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R+GVD       +R+ + ++   G     +HARKA L G++P+ NR IP LD+
Sbjct: 143 TPVTVKHRLGVDHNDSYEFVRDFISTVADQGCTDFIVHARKAWLNGINPRKNRSIPPLDH 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + VY + +E P+L I +NGG++ + +    L   V GVM+GR AY+N   L  VD     
Sbjct: 203 ERVYRLCQEFPNLNISINGGIKSLEEIKYALSRGVYGVMVGRMAYENPCGLVRVDTDIYG 262

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T  +  KTR       +  A+  D  A    S   +  + + ++G FHG   ++  R 
Sbjct: 263 EATNPATCKTR---RILLETYANFIDSQASRT-SDMNVCMLVKPILGTFHGEVGTKIFRQ 318

Query: 296 ILT 298
            L+
Sbjct: 319 ALS 321


>gi|298707058|emb|CBJ29860.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 379

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 89/203 (43%), Positives = 132/203 (65%), Gaps = 3/203 (1%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+  TDR++R+  R L+  + LYTEM V   +L  + +  N L     E PLA+Q+GG D
Sbjct: 15  MMAVTDRYFRYLFRQLSRRSKLYTEMYVDKTLLHQQDNLHNFLSHRAAEGPLAVQLGGND 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              L EAA++ E + ++EINLN GCPS++V +  FGA LML+P+ V +    M + ++  
Sbjct: 75  PDTLAEAAEMCEQWAFSEINLNCGCPSSKVSDRCFGARLMLDPERVREITYGMIRKVTRT 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVKCRIGVDD+     L   V+++K +G++ + +HARK +LKGLS   NR IP L YD
Sbjct: 135 PVTVKCRIGVDDKDSYDELTTFVRAVKAAGIDHVVVHARKCLLKGLSTSANRTIPPLRYD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDM 200
           +V+ + +E P+L I LNGG++ +
Sbjct: 195 VVHRLAQEFPELEIVLNGGIDSL 217


>gi|300706178|ref|XP_002995385.1| hypothetical protein NCER_101742 [Nosema ceranae BRL01]
 gi|239604450|gb|EEQ81714.1| hypothetical protein NCER_101742 [Nosema ceranae BRL01]
          Length = 336

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 91/238 (38%), Positives = 146/238 (61%), Gaps = 6/238 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG-FSTQEKPLALQIGGADI 59
           M+D T  ++R F RL + + +L+TE+IVA+ ++  DK+ ++      ++   +QIGG+D+
Sbjct: 22  MLDVTTANFRRFVRLTSEHTILFTELIVANTVIHIDKEKLIERLGDIDERTVVQIGGSDV 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           +++V A  +++D G    NLNVGCPS RV +G FGA LM N +++ + I ++ K   I +
Sbjct: 82  NEIVNAICVLKDVGCKHFNLNVGCPSTRVQKGCFGAVLMKNKELISEIINSVYKKCDIVL 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++K R GVD+       R+ V   +K + V   ++HARK  L GLSPK NR IP L+Y  
Sbjct: 142 SLKIRTGVDNYDTYEFFRDFVHFLVKNTPVKKFYVHARKCWLLGLSPKQNRNIPPLNYSF 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP----SVDGVMIGRAAYKNSAMLTTVDEY 232
           VY+IK+E P +   LNGGL+ ++   K+      ++DG+MIGR A KN  +  + + Y
Sbjct: 202 VYKIKEEFPHVLFILNGGLKKIADFNKLFCNNNLTLDGIMIGREAIKNILVFRSFENY 259


>gi|255079776|ref|XP_002503468.1| predicted protein [Micromonas sp. RCC299]
 gi|226518735|gb|ACO64726.1| predicted protein [Micromonas sp. RCC299]
          Length = 499

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 106/278 (38%), Positives = 153/278 (55%), Gaps = 28/278 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ TD H+R   RL++  A L+TEM+  DA++     K  +L +  +E PL +Q+GGA 
Sbjct: 38  MLECTDTHFRRVCRLVSRRAHLWTEMVNQDAVVHSWRSKPEMLAYGDEEHPLTVQLGGAS 97

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGS-----FGACLMLNPDIVGDCIAAMC 112
             +L  AA + + ++ Y+EINLN GCPS RV         FGA LM +P  VG+C+  M 
Sbjct: 98  PERLALAATVCDAEYRYDEINLNCGCPSNRVVNKKDVATCFGAALMRDPTHVGECLRRMR 157

Query: 113 KALSIPVTVKCRIGV-------DDQIPAVALRNLVKSI--KKSGVNGIWIHARKAILKGL 163
           +A+ +PVTVK R+GV       DD + + A  +    +  + SGV    +HAR A+L GL
Sbjct: 158 EAVDVPVTVKHRLGVRPTEKSPDDSMDSYAFVSEFVDVVNQASGVKHFIVHARAAVLSGL 217

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           S   NR +P L +  V+ +  + P L   LNGG+E M QA + L S  + GVM+GRA Y+
Sbjct: 218 STTGNRTVPPLRHAEVHALADDFPSLGFTLNGGIETMDQAAEHLESGKLRGVMLGRAVYR 277

Query: 222 NSAMLTTVD---------EYFSNPLTGSSPIKTRVDKD 250
           N A+L  VD         E F     G + +  R D D
Sbjct: 278 NPAVLAEVDARFYGDEPREAFRERYAGEARVAGRWDSD 315


>gi|303272601|ref|XP_003055662.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463636|gb|EEH60914.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 252

 Score =  172 bits (436), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 97/241 (40%), Positives = 145/241 (60%), Gaps = 15/241 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+D TD H+R   R  +    L+TEMI  DA++     +  +LG    E PL +Q+GG+ 
Sbjct: 9   MLDCTDAHFRAVCRSFSRRTHLWTEMIHQDAVIHSHASRPEMLGHDASEHPLTVQLGGSS 68

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARV-----HEGSFGACLMLNPDIVGDCIAAMC 112
             +L  AA+I +  +GY+E+NLN GCPSA+V      E  FGA LM +P++VG+C+  M 
Sbjct: 69  PGRLARAAEICDAAYGYDEVNLNAGCPSAKVTSKSDAEKCFGAVLMRDPELVGECLRRMR 128

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKI 171
           +A+ +PVT+K R+G  D    V+  + V+ + + SGV    +HAR A+L GLSP  NR I
Sbjct: 129 EAVDVPVTLKHRLG--DNYAYVS--DFVQRVHELSGVTHFIVHARAAVLGGLSPAANRSI 184

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           P L +  V+ +  + P L   LNGG+E +  A++ L S  + GVM+GRA Y++  +L  V
Sbjct: 185 PPLRHREVHALASDFPKLGFSLNGGVETVDDAVRHLSSGKLKGVMLGRAVYRDPTILHDV 244

Query: 230 D 230
           D
Sbjct: 245 D 245


>gi|303390009|ref|XP_003073236.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
 gi|303302381|gb|ADM11876.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
          Length = 357

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 111/306 (36%), Positives = 171/306 (55%), Gaps = 22/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M+D T  H+R   RL +++ +L+TEMIV++ ++   R   +  LG    +    +QIGG+
Sbjct: 20  MMDVTTAHFRRLIRLTSSSTILFTEMIVSNTVIHISRDRLREKLG--EYDDKTVVQIGGS 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D  ++VEA KI++D GY   NLN GCPS+RV +GSFGA LMLN ++V + I  + K    
Sbjct: 78  DAGQIVEAVKILQDLGYRMFNLNCGCPSSRVKKGSFGAVLMLNKELVAEIINKVYKETGE 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-GIWIHARKAILKGLSPKDNRKIPNLDY 176
            +++K R+GVD+      L+  V  IK++  N   ++HARK  L+GLSP+ NRK+P LDY
Sbjct: 138 ILSLKIRVGVDNHEGIDFLKEFVGYIKENTPNRTFYVHARKCWLEGLSPEQNRKLPPLDY 197

Query: 177 DIVYEIKKENPDLFIGLNG--GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D VY IK+  P+L I LNG  G+ ++ +    +  +DGVM+GR A ++  +   +D   S
Sbjct: 198 DSVYMIKRLYPELKIVLNGCIGINNLDR----IKDLDGVMVGREAIRDILVFWDIDRKLS 253

Query: 235 NPLTGSSPIKTR----VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                            D D  +KI    +D  A+   +  K++ + R     F GFP S
Sbjct: 254 MKCDKGERRDCEELFPFDMDM-KKIECR-SDSEAKEWRA-QKIRSVVRE---YFEGFPPS 307

Query: 291 RRCRHI 296
            + + I
Sbjct: 308 DQLKSI 313


>gi|219127844|ref|XP_002184137.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404368|gb|EEC44315.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 330

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 101/248 (40%), Positives = 138/248 (55%), Gaps = 30/248 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M+++TDRH+R   RL++N  LLYTEM+ A+A+    K   L  G    E P  LQ+GG+D
Sbjct: 6   MMEYTDRHFRHLVRLVSNRTLLYTEMVAANALANERKNRYLAQGRVMPEGPSVLQLGGSD 65

Query: 59  ISKLVEAAKIVEDF------GYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAM 111
             ++ +AA+ V D        Y  INLN GCPS +V  +G FGA LM  P +V +   A+
Sbjct: 66  PEQMFQAAQTVLDMTARGHCDYTAINLNCGCPSPKVAGKGCFGAALMDEPQLVAELTKAL 125

Query: 112 CKALS--IPVTVKCRIG--------------VDDQIPAVALRNLVKSIKKSG-VNGIWIH 154
            +     +PVTVKCRIG              +D +     LR+ ++++   G V    +H
Sbjct: 126 HEGTEGRLPVTVKCRIGTDSDQAFTRQAYAAIDPEQEYSKLRSFIETVASDGIVTDFSVH 185

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSV 210
           AR A+L K  SP DNRKIP L YDIV  + +E PD    LNGG+E +SQA       P +
Sbjct: 186 ARIAVLQKSFSPSDNRKIPPLKYDIVRRLVQEYPDFTFSLNGGVESISQAQAEFATSPGL 245

Query: 211 DGVMIGRA 218
            GVMIGR+
Sbjct: 246 KGVMIGRS 253


>gi|222628527|gb|EEE60659.1| hypothetical protein OsJ_14110 [Oryza sativa Japonica Group]
          Length = 257

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 86/181 (47%), Positives = 119/181 (65%), Gaps = 6/181 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+   K N+   L F  ++ P+ LQIGG+
Sbjct: 70  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVH-QKDNLDRFLAFPAEQHPIVLQIGGS 128

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           ++  L +A ++   + Y+EINLN GCPS +V   G FGA LM +P+ VGD ++A+    +
Sbjct: 129 NLDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCN 188

Query: 117 IPVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +PV+VKCRIGVDD+     L   V K + KS      IHARKA+L GLSP +NR +P L 
Sbjct: 189 VPVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRNVPPLK 248

Query: 176 Y 176
           Y
Sbjct: 249 Y 249


>gi|218674123|ref|ZP_03523792.1| tRNA-dihydrouridine synthase A [Rhizobium etli GR56]
          Length = 182

 Score =  169 bits (427), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 81/171 (47%), Positives = 110/171 (64%), Gaps = 11/171 (6%)

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY +K+  P++FIG+NGG+  + +A  
Sbjct: 5   AGADAIWIHARKAWLKGLSPKENREIPPLDYEIVYRMKQRWPEVFIGINGGIRTLDEAAS 64

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            L  VDGVM+GRAAY+N+A+L  VD  +F  P            +  W  +   M  YA 
Sbjct: 65  HLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAA----------EPDWPALCERMMAYAE 114

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
           RH+  GG+LQ + RHM+GLF G P +RR R IL+ +A  S A   ++  AF
Sbjct: 115 RHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSTDAAKSGAGPEVLAAAF 165


>gi|39546256|emb|CAD39831.3| OSJNBa0079F16.4 [Oryza sativa Japonica Group]
          Length = 1708

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 85/179 (47%), Positives = 118/179 (65%), Gaps = 6/179 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+   K N+   L F  ++ P+ LQIGG+
Sbjct: 70  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVH-QKDNLDRFLAFPAEQHPIVLQIGGS 128

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           ++  L +A ++   + Y+EINLN GCPS +V   G FGA LM +P+ VGD ++A+    +
Sbjct: 129 NLDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCN 188

Query: 117 IPVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +PV+VKCRIGVDD+     L   V K + KS      IHARKA+L GLSP +NR +P L
Sbjct: 189 VPVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRNVPPL 247


>gi|255082067|ref|XP_002508252.1| predicted protein [Micromonas sp. RCC299]
 gi|226523528|gb|ACO69510.1| predicted protein [Micromonas sp. RCC299]
          Length = 401

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 112/323 (34%), Positives = 169/323 (52%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D+T  H+R   RLL+ +  LYTEM V   ++  D   +   L F T   P  LQ+GG+
Sbjct: 12  MMDYTTAHFRHLCRLLSRHTWLYTEMEVDQTLVHTDHPRLDRYLDFPTATHPSVLQLGGS 71

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCK-AL 115
           D   +  A  +   +GY+EINLN GCPS +V  +G+FGA LML P++V D +AAM + + 
Sbjct: 72  DPETMARATAVAAPYGYDEINLNCGCPSPKVAGKGAFGAALMLEPELVRDVVAAMRENSG 131

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSI-------KKSGVNGIWIHARKAILKGLSPKDN 168
             PVTVKCRIGVDD      L   V+++       +  G     IHARKA+L GLSP +N
Sbjct: 132 GAPVTVKCRIGVDDHDSYDDLCRFVETVACAMVPTRTDGRPLFAIHARKALLAGLSPAEN 191

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---------GVMIGRAA 219
           R +P L Y+  Y + ++ P++   +NGG++ + +A ++   V          G MIGRA 
Sbjct: 192 RTVPPLRYEWAYALARDFPEVAFVVNGGIDTLEEAAEVARGVGVPTGGGRLVGTMIGRAV 251

Query: 220 YKNS-AMLTTVD-EYFSNPLTGSSPIKTRVD--KDFWRKISASMTDYAARHLHSGGKLQQ 275
           + +   +L+  D   F      S+P  +R D   ++ +   A+   +        G    
Sbjct: 252 HADPWGVLSDADVRVFG---AESNPRTSRRDLLNEYVKYCDATRGRFGTT---KDGYSVP 305

Query: 276 ITRHMI----GLFHGFPNSRRCR 294
            TRH++     LF G PN++  R
Sbjct: 306 STRHLMHPLQNLFLGEPNAKVWR 328


>gi|116515275|ref|YP_802904.1| tRNA-dihydrouridine synthase A [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116257129|gb|ABJ90811.1| tRNA-dihydrouridine synthase A [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 348

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 104/317 (32%), Positives = 163/317 (51%), Gaps = 15/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M  +TD+H  +F R LT    LYTEMI    +L   K        +  P+A+Q+ G +  
Sbjct: 36  MFKYTDQHCLYFYRQLTKKTFLYTEMITIQKMLFSKKLFKKKQIKKNNPIAIQLAGNNPL 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK     G+ EINLN+GCPS +   G+FG  LM NP +V + I A+   + I ++
Sbjct: 96  FLSLCAKKAYFLGFKEINLNIGCPSKKAKSGNFGIYLMNNPILVYNLIKAIYLTVPIQIS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G ++      L+N ++ + K+     +I HAR A L+  SPK NR IP L+Y  V
Sbjct: 156 IKIRLGTNENKNYRFLKNFIQLVSKNNYCIKYIIHARIANLQINSPKKNRNIPLLNYSYV 215

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ +++  + L +VDGVM+GR  YKN   L  +D+        
Sbjct: 216 YKIKKDFPHLIIIINGGIKTINEINEHLKNVDGVMMGREIYKNPLFLRKIDKKIFFQKKQ 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
               K              M++Y  + +  G    +I +HM+ +F+  P +++ +H    
Sbjct: 276 IKIKKF----------IKKMSNYIKKKIIKGVPAIKIIKHMLNIFYKLPQAKKWKH---- 321

Query: 300 EAGASTATHHIIETAFN 316
           E    T   + I+  FN
Sbjct: 322 ELIQKTIYKNQIDDIFN 338


>gi|323454823|gb|EGB10692.1| hypothetical protein AURANDRAFT_22498 [Aureococcus anophagefferens]
          Length = 378

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 115/343 (33%), Positives = 168/343 (48%), Gaps = 26/343 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-------RGDKKNILGFSTQEKPLALQ 53
           M+D+TDRH+R+  RLL+  A+LYTEM+ A  ++        GD    LG+        LQ
Sbjct: 26  MMDYTDRHFRYLLRLLSREAVLYTEMVTAATLVDGAGAPRHGDGARWLGYDDDAGRTVLQ 85

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMC 112
           +GGAD ++L  AA++    GY  +NLN GCPS RV  +G FGA LM +  +V DC+ A+ 
Sbjct: 86  LGGADPAQLGAAARLAAPRGYAGVNLNCGCPSDRVAGQGCFGAALMRDAALVADCVDAL- 144

Query: 113 KALSIPVTVKCRIGV---------DDQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKG 162
            A   PV+VKCR+GV         DD+     L N V ++   G    + +HAR A+L G
Sbjct: 145 -AEHAPVSVKCRVGVCDTVSDMVDDDEALYAGLANFVSTVAARGTCAHFVVHARVAVLSG 203

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYK 221
           LSP  NRK+P L   +V  +  E P+L +  NG +     A  +   +V GVM GR   K
Sbjct: 204 LSPDKNRKVPPLKPRLVSRLADEFPELTVVSNGEISSYESARDRSEGNVAGVMAGRDVCK 263

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQITRHM 280
                  VD         + P  +R D       +A    + A H  +     + + +  
Sbjct: 264 RPWYYANVDSALFG--ADADPAASRRDV-LLGAYAAYAAAFEADHARADWSPRRALLKPA 320

Query: 281 IGLFHGFPNSRRC-RHILTVEAGASTATHHIIETAFNLMIESL 322
           +GLFHG P + R  R +  +  G       I+E A  L+ + +
Sbjct: 321 LGLFHGSPGAGRFKREVDALAKGGDAGVREILERAAALVPDDV 363


>gi|308807222|ref|XP_003080922.1| nitrogen regulation family protein (ISS) [Ostreococcus tauri]
 gi|116059383|emb|CAL55090.1| nitrogen regulation family protein (ISS) [Ostreococcus tauri]
          Length = 490

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 112/323 (34%), Positives = 168/323 (52%), Gaps = 28/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV----ADAILRGDK-KNILGFSTQEKPLALQIG 55
           M+++T  H+R   RL++    L+TEM V      A+L G +    L +  +     LQ+G
Sbjct: 107 MMEYTTAHFRVMCRLMSAKTWLWTEMEVDQTLTHAVLEGTRVDRFLDYPVETAATVLQLG 166

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCK- 113
           G+D   L  A  I   +GY EINLN GCPS +V  +G FGA LM  P +V +C+ AM + 
Sbjct: 167 GSDPEILGRATAIAAPYGYEEINLNSGCPSPKVAGKGCFGAALMTEPRLVAECLQAMNEN 226

Query: 114 -ALSIPVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKI 171
                PV++KCRIGVD+     AL   V +I + S     ++HARKA+L GLSP +NR +
Sbjct: 227 APSGTPVSIKCRIGVDECDSYDALCEYVDTIVRASATRRFYVHARKALLNGLSPAENRSV 286

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPS----VDGVMIGRAAYKNS- 223
           P L ++  Y + ++ P+    LNGG   L+D+  A+   P     + GVMIGR A+ +  
Sbjct: 287 PPLKHEWAYALARDFPECEFHLNGGLKTLKDVENAIHRGPEGGGPIAGVMIGRQAHADPW 346

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITRHMI 281
            +L+  D       T  +P  +R  +DF  K      D   R+     G ++  + RHM+
Sbjct: 347 GLLSAADTTIFGEST--NPCASR--RDFLEKYVEYADDTIGRYGTAKDGYRIPSV-RHMM 401

Query: 282 ----GLFHGFPNSRRCRHILTVE 300
                LFHG  N++  R ++  E
Sbjct: 402 HPIQNLFHGCANNKMWRRLVDEE 424


>gi|70929895|ref|XP_736939.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56511905|emb|CAH87272.1| hypothetical protein PC302401.00.0 [Plasmodium chabaudi chabaudi]
          Length = 265

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 83/197 (42%), Positives = 128/197 (64%), Gaps = 3/197 (1%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R+++    L+TEMIV + +L    + +  LGF+  E P+  Q+GG+D
Sbjct: 69  MINVTNRHFRALVRIISKKVQLWTEMIVDNTLLYNINNLEEHLGFNKNEHPIVCQLGGSD 128

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA ++E  GY+EIN+NVGCPS +V ++G+FGA LM  P++V + +  + K + I
Sbjct: 129 PTSLSEAAVLIEQAGYDEININVGCPSTKVANKGAFGAYLMKKPELVKNIVYEIKKKVQI 188

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVDD      L++ ++++   G     IH+RKA LKGL PK NR +P L+Y+
Sbjct: 189 PVTVKIRTGVDDLDSFSFLKSFIETVSSVGCEHFIIHSRKAWLKGLDPKQNRSVPPLEYN 248

Query: 178 IVYEIKKENPDLFIGLN 194
            V+++ K  P+L   LN
Sbjct: 249 KVFDLCKLYPNLKFTLN 265


>gi|145350035|ref|XP_001419429.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144579660|gb|ABO97722.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 355

 Score =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 111/320 (34%), Positives = 167/320 (52%), Gaps = 28/320 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDK-KNILGFSTQEKPLALQIG 55
           M+++T  H+R  ARL++   +L+TEM V   +      GD+    L +        LQ+G
Sbjct: 7   MMEYTTPHFRVMARLMSRRVMLWTEMEVDQTVTHSARDGDRVDKFLDYPAATFGTVLQLG 66

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCK- 113
           G+    L  A  I   +GY+EINLN GCPS +V  +G FGA LM  P +V +C+AAM + 
Sbjct: 67  GSTPEYLGRATAIAAPYGYDEINLNSGCPSPKVAGKGCFGAALMAEPGLVAECLAAMAEN 126

Query: 114 -ALSIPVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKI 171
                PV+VKCRIGVDD      L + V+ I   S     ++HARKA+L GLSP +NR +
Sbjct: 127 APEGTPVSVKCRIGVDDVDSYDDLCDYVERIVAGSSTRRFYVHARKALLAGLSPAENRTV 186

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPS----VDGVMIGRAAYKNS- 223
           P L ++  Y + ++ P+    LNGGL+   D+   LK  P     + G MIGR A+ +  
Sbjct: 187 PPLKHEWAYALARDFPECEFHLNGGLKTLNDVKNVLKRGPEDGGPIVGAMIGRQAHADPW 246

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITRHMI 281
            +L+  D         S+P  +R  +DF  K +    +   R+     G ++  + RHM+
Sbjct: 247 GLLSAADTTLFG--EASNPSASR--RDFLNKYAVYADETIGRYGTAKDGYRIPSV-RHMM 301

Query: 282 ----GLFHGFPNSRRCRHIL 297
                LFHG  N++  R ++
Sbjct: 302 HPIQNLFHGCANNKAWRRLV 321


>gi|19074540|ref|NP_586046.1| similarity to HYPOTHETICAL PROTEINS YJBN_ECOLI and Y926_YEAST
           [Encephalitozoon cuniculi GB-M1]
 gi|19069182|emb|CAD25650.1| similarity to HYPOTHETICAL PROTEINS YJBN_ECOLI and Y926_YEAST
           [Encephalitozoon cuniculi GB-M1]
          Length = 357

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 94/238 (39%), Positives = 140/238 (58%), Gaps = 8/238 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M+D T  H+R F RL +   +L+TEMIV++ ++   R   +  LG    +    +QIGG+
Sbjct: 20  MMDVTTAHFRRFIRLTSEKTVLFTEMIVSNTVIHVPRDKLRERLG--EYDDRTVVQIGGS 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D + +VEA +I++  GY   NLN GCPS+RV +GSFGA LMLN ++V + I  +      
Sbjct: 78  DATSMVEAVRILQGLGYRMFNLNCGCPSSRVKKGSFGAVLMLNRELVAEIINRVYGETGA 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +++K R GVD+      L   V  IKK +     ++HAR+  L+GLSP+ NRK P LDY
Sbjct: 138 VLSLKIRTGVDEHDGVDFLDGFVSHIKKNTPTRTFYVHARRCWLEGLSPQQNRKAPPLDY 197

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             VY IK  +P+L I LNG + + +  L  + ++DGVMIGR A +N  +   ++   S
Sbjct: 198 ASVYAIKSLHPELRIILNGSIGEGN--LDKIHNLDGVMIGRGAIRNVFVFWDIENRMS 253


>gi|213025593|ref|ZP_03340040.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 146

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 74/128 (57%), Positives = 93/128 (72%), Gaps = 1/128 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVD 128
           VK RIG+D
Sbjct: 139 VKTRIGID 146


>gi|294932843|ref|XP_002780469.1| tRNA-dihydrouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
 gi|239890403|gb|EER12264.1| tRNA-dihydrouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
          Length = 403

 Score =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 102/266 (38%), Positives = 147/266 (55%), Gaps = 27/266 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-----KNILGFSTQEKPLALQIG 55
           MVD +DR +R F RLL++   ++TEM+V  A++  +      + I+GF+  E P+  Q+G
Sbjct: 1   MVDVSDRDFRMFMRLLSSKCEVWTEMLVDQALVHNEDIPRQLEKIIGFTEAEHPIVCQLG 60

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKA 114
           G D SKL  AA+I    GY+E+NLNVGCPS+RV   G  G  LM  P++V DC+  +   
Sbjct: 61  GHDPSKLAAAARIAHRRGYDEVNLNVGCPSSRVAGHGLMGVALMKTPELVRDCLRTLDD- 119

Query: 115 LSIP-VTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIW---IHARKAILKGLSPK 166
             +P V++K R+GVDD    +     L  ++  +  S     +   +H RKA L+GLSP 
Sbjct: 120 -EVPHVSIKTRLGVDDLDTEEFTRSFLGTILPPLASSAAQQPYRVIMHCRKAWLQGLSPA 178

Query: 167 DNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS------VDGVMIGRAA 219
           +NR +P LDY     +       +   LNGG+E + QA  +L S      ++GVMIGRAA
Sbjct: 179 ENRTVPPLDYPRACRVLGAFGSRVRWTLNGGIETLWQAKDVLTSEIAPANLEGVMIGRAA 238

Query: 220 YKNSAMLTTVDEYF----SNPLTGSS 241
           Y N  ML   D Y      NP++  S
Sbjct: 239 YNNPCMLHDADVYLYGCDENPVSAES 264


>gi|269861290|ref|XP_002650357.1| NIFR3-like protein [Enterocytozoon bieneusi H348]
 gi|220066217|gb|EED43710.1| NIFR3-like protein [Enterocytozoon bieneusi H348]
          Length = 321

 Score =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 89/234 (38%), Positives = 134/234 (57%), Gaps = 6/234 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M+  T   +R   +L+    +LYTEMI A  I+   D+K  +     +    +QIGG++ 
Sbjct: 16  MMKVTTPCFRKLIQLIAPTTILYTEMITASTIINLNDEKLQITLGNPDNQTVVQIGGSNP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +V A K ++  G+   NLN GCPS RV +G FGA LM   ++V + I  +     I +
Sbjct: 76  KDIVNAIKRLKQCGWRLFNLNCGCPSTRVQKGMFGAILMKYKELVIEIINTVYIETQIIL 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++KCR G+D+      L+  ++SI K +  N  +IHARK  L+G++PK NR IP L+YD 
Sbjct: 136 SIKCRTGIDEFDSYEFLKEFIESISKNTPCNIFYIHARKCWLQGINPKQNRNIPPLNYDY 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTV 229
           ++ IKKE P LFIG+NGG+   +  LK    + + DG+MIGR A KN  +   +
Sbjct: 196 IFRIKKEFPHLFIGINGGI-TYNSYLKYKFQMDTCDGIMIGREAIKNPLIFAEI 248


>gi|300120278|emb|CBK19832.2| unnamed protein product [Blastocystis hominis]
          Length = 407

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 106/352 (30%), Positives = 164/352 (46%), Gaps = 71/352 (20%)

Query: 8   HYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADISKLVEAA 66
           + R+  RL++ +  LY+EM V + ++    + N++ F   E P+  Q+GG++  K++EAA
Sbjct: 14  YQRYIVRLMSKHTTLYSEMFVDEMLIHSQFRSNLIRFDKSEHPIIAQLGGSNKYKMLEAA 73

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K++E  GY+ IN+N GCPS +V EG FGA LML+P  V D +  + + LSIPVTVKCRIG
Sbjct: 74  KLLEAEGYDGININCGCPSPKVAEGCFGARLMLSPWRVYDIVQHLQRHLSIPVTVKCRIG 133

Query: 127 V----------------------------------------------DDQIPAVALRNLV 140
           V                                              DD+  +  L   V
Sbjct: 134 VDRIYFLKLCFAHNIVEYDSYEELCRFIRIVSGAGTEQDRKSFASASDDEAESDPLMPPV 193

Query: 141 KS----IKKSGVNGIW------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           +S    I++  +   +      IHARK +L GLS K NR +P L YD VY +  + P + 
Sbjct: 194 QSESDGIQRQEIQPCYGAKHFIIHARKCLLSGLSAKQNRSVPPLHYDWVYRLLDDFPCID 253

Query: 191 IGLNGGLEDMSQALKILP-------SVDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSP 242
             +NGG+  + QA  +L         + GVMIGR   K       +D++F   P    SP
Sbjct: 254 FSINGGVLSLGQAKDLLERKSQSGRQLRGVMIGRLLTKAPWNFHFIDQFFYGEPNPSLSP 313

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            +T +   +         +   +H  +     ++ + +  +F   P S RCR
Sbjct: 314 FETVM--KYVEYCEQMEKNGYTQHFSTN----ELLKPLFNIFVDIPGSLRCR 359


>gi|213420476|ref|ZP_03353542.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 181

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 70/122 (57%), Positives = 88/122 (72%), Gaps = 1/122 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VK 122
           VK
Sbjct: 139 VK 140


>gi|303279296|ref|XP_003058941.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460101|gb|EEH57396.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 376

 Score =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 111/337 (32%), Positives = 164/337 (48%), Gaps = 51/337 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D+T  H+R   R+L+    LYTEM V   +   D   +   L F  Q  P  LQ+GG+
Sbjct: 13  MMDYTTAHFRAMCRMLSRKTWLYTEMEVDQTLTHVDHPRLDRYLDFPLQTHPSVLQLGGS 72

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAM-CKAL 115
           D   L  AA I   + Y+E+NLN GCPS +V  +G+FGA LML P++V DC+AAM   + 
Sbjct: 73  DPESLGRAAAIAAPYAYDELNLNCGCPSPKVAGKGNFGAALMLEPELVADCVAAMAANSG 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSI-----KKSGVNG---IWIHARKAILK------ 161
             PVTVKCRIGVDD     AL   V+++      + G +      IHARKA+L+      
Sbjct: 133 GAPVTVKCRIGVDDVDSYDALCAFVETVAARMPPRRGEDARPLFAIHARKALLRRVLYTG 192

Query: 162 -----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS------- 209
                GLSP +NR +P L ++ V+ + ++ PD+   +NGG+  + +A+ I          
Sbjct: 193 SHTTAGLSPAENRTVPPLRHEWVHALARDFPDVAFAINGGINTLEEAVAIARGEGTPVGG 252

Query: 210 --VDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIKTR---------VDKDFWRKISA 257
             + G MIGR A+ +   +L   D         S P  +R              W +   
Sbjct: 253 GRLVGTMIGRRAHADPWGLLARADTAVFG--EASDPCVSRRALLETYAAYADATWARYGT 310

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +   YA         ++ +   +  LF G PN++R R
Sbjct: 311 TKDGYAV------PSIRHLMHPLQNLFLGEPNAKRWR 341


>gi|308808940|ref|XP_003081780.1| Dihydrouridine synthase TIM-barrel protein yjbN (ISS) [Ostreococcus
           tauri]
 gi|116060246|emb|CAL56305.1| Dihydrouridine synthase TIM-barrel protein yjbN (ISS) [Ostreococcus
           tauri]
          Length = 418

 Score =  148 bits (374), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 98/265 (36%), Positives = 144/265 (54%), Gaps = 25/265 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +D T  H+R  AR +T  A L+TEM   D + R     +   +  E  +  Q+GG+  S 
Sbjct: 15  LDVTTPHHRALARAMTTRARLWTEMAHHDCVTRMCSSTM---TRSETHVTAQVGGSRPSG 71

Query: 62  LVEAAKIVE-DFGYNEINLNVGCPSARV-----HEGSFGACLMLNPDIVGDCIAAMCKAL 115
           L  AA+I+E ++GY+E+NLN GCPS RV        SFGA +M++ +   +C+  M +A+
Sbjct: 72  LARAAEILESEYGYDEVNLNCGCPSERVCRKDDETSSFGAAMMIDVENTAECVRRMVEAV 131

Query: 116 -SIPVTVKCRIGVD-DQIPAV-----ALRNLVKSIKK----SGVNGIWIHARKAILKGLS 164
            +  +TVK R+GV  D+   V     +  ++VK I+     +GV+   +HAR A++ GLS
Sbjct: 132 DATKITVKHRLGVRFDKTMTVKEETDSYEHVVKFIEAIKDAAGVDHFIVHARSAVMGGLS 191

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAAY 220
           P  NRKIP L YD V+ +  E       LNGG+E + QA  +L   D    GVM+GRA Y
Sbjct: 192 PDANRKIPPLRYDEVFALCDEFSKCDFTLNGGVETLEQAKGLLEREDGKLAGVMMGRAFY 251

Query: 221 KNSAMLTTVDEY-FSNPLTGSSPIK 244
           K+  ML  +D   F  P     P +
Sbjct: 252 KHPCMLADIDRVIFGEPTADPPPTR 276


>gi|330893302|gb|EGH25963.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
          Length = 139

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 66/128 (51%), Positives = 89/128 (69%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 3   MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 63  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 122

Query: 121 VKCRIGVD 128
           VK RIG++
Sbjct: 123 VKHRIGIN 130


>gi|270700755|ref|ZP_06223017.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae HK1212]
 gi|270315907|gb|EFA27986.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae HK1212]
          Length = 145

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 73/146 (50%), Positives = 95/146 (65%), Gaps = 1/146 (0%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+   K + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHA-KYDHLDFDLQENPVALQLGGSDPEQLKHCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKI 171
            G     IHARK  L GLSPK+NR+I
Sbjct: 120 KGCQEFIIHARKVWLSGLSPKENREI 145


>gi|104294976|gb|ABF71992.1| hypothetical protein MA4_111B14.10 [Musa acuminata]
          Length = 220

 Score =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 65/133 (48%), Positives = 93/133 (69%), Gaps = 3/133 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+   +     L FS  + P+ LQIGG++
Sbjct: 11  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQSENLDRFLAFSPIQHPIVLQIGGSN 70

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L +AA++   + Y+EINLN GCPS +V   G FGA LM +P+ VGD ++A+     +
Sbjct: 71  LTNLAKAAELANSYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIASNCDV 130

Query: 118 PVTVKCRIGVDDQ 130
           PV+VKCRIGVDD+
Sbjct: 131 PVSVKCRIGVDDR 143


>gi|257484388|ref|ZP_05638429.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 148

 Score =  139 bits (350), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 62/121 (51%), Positives = 82/121 (67%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM  P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAYPQLVADCVKAMRDAVGIPVT 147

Query: 121 V 121
           V
Sbjct: 148 V 148


>gi|145351342|ref|XP_001420040.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580273|gb|ABO98333.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 425

 Score =  138 bits (348), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 97/251 (38%), Positives = 140/251 (55%), Gaps = 26/251 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADIS 60
           +D T  +YR  AR +T  A ++TEM   DA+ R  K N L   T+ + LA  Q+GGAD S
Sbjct: 23  LDVTTPYYRALARAMTKRARVWTEMAHHDAVERL-KSNTL---TRGETLATAQLGGADPS 78

Query: 61  KLVEAAKIVE-DFGYNEINLNVGCPSARV-----HEGSFGACLMLNPDIVGDCIAAMCKA 114
            L  A ++ E ++GY+E+NLN GCPS RV      E  FGA +ML+ +   +C   M +A
Sbjct: 79  GLARAVEVCEGEYGYDEVNLNCGCPSDRVCGKGETEKRFGASMMLDVERAAECARRMAEA 138

Query: 115 LS-IPVTVKCRIGV---------DDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGL 163
                +T+K R+GV         ++      + N V++I + +GV    +HAR A++ GL
Sbjct: 139 SDRAKITIKHRLGVRYDKTMMKHEETDCYDYVVNFVEAIHEAAGVEHFIVHARSAVMGGL 198

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAA 219
           +P  NRKIP L YD V+ +  E       LNGG+  ++QA ++L   D    GVM+GRA 
Sbjct: 199 NPDANRKIPPLRYDEVFALCDEFGRCDFTLNGGVNSLAQAKELLDREDGKLAGVMMGRAF 258

Query: 220 YKNSAMLTTVD 230
           YK+  ML  VD
Sbjct: 259 YKHPCMLADVD 269


>gi|209882914|ref|XP_002142892.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209558498|gb|EEA08543.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 469

 Score =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/240 (35%), Positives = 131/240 (54%), Gaps = 30/240 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD---------KKNILGFSTQEKPLA 51
           M+D T+ H+R F RLL+ N  L+TEM+V+D I+            ++  L  S  ++P+ 
Sbjct: 17  MLDVTNIHFRHFCRLLSTNVQLWTEMVVSDTIIYCHNDPDREILLREGSLQKSDVDEPIV 76

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAA 110
           LQIGG D +K+ +A +I   +G+   NLN+GCPS RV  +G+FGA L  +PD+V   +  
Sbjct: 77  LQIGGNDPTKVADAIEIAIKYGFRSFNLNIGCPSQRVACKGNFGAYLYKDPDLVAKIVGT 136

Query: 111 M---CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS-----------------GVNG 150
           +    K+L+  ++VK RIGVDD      L N +  +  +                 G   
Sbjct: 137 VNHRIKSLNTRISVKTRIGVDDCDSYDILHNFISVVSGTTPRIGKSQGVGSEEDFLGATC 196

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
             IH+RKA L GL P+ NR IP+L Y  VY++  + P L   +NGG++ + +A ++L  V
Sbjct: 197 YIIHSRKAWLDGLDPQKNRTIPSLKYTWVYKLVCDFPHLDFVINGGIDSLDKAEELLWGV 256


>gi|257484387|ref|ZP_05638428.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 187

 Score =  136 bits (343), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 71/175 (40%), Positives = 105/175 (60%), Gaps = 9/175 (5%)

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V ++K +
Sbjct: 1   GINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKSD 60

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
            PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        ++P+ +
Sbjct: 61  FPDLEIVLNGGIKTLDQCGEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDSTAPVIS 117

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 118 RYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 166


>gi|224007851|ref|XP_002292885.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971747|gb|EED90081.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 233

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 120/228 (52%), Gaps = 34/228 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-------PLALQ 53
           M+++TDRH+R   RL+++  LLYTEM+ A+AI       +LG    +           LQ
Sbjct: 6   MMEYTDRHFRHLVRLISDRTLLYTEMVAANAIAHERNDALLGIEISDTLNTHSLGASVLQ 65

Query: 54  IGGADISKLVEAAKIVEDFG--------YNEINLNVGCPSARVH-EGSFGACLMLNPDIV 104
           +GG+D  +L  AAK +            Y  +NLN GCPS +V  +G FGA LM  PD+V
Sbjct: 66  LGGSDPEQLFLAAKTLMQQSNYPAIYCDYTALNLNCGCPSPKVAGKGCFGAALMSEPDLV 125

Query: 105 GDCIAAMCKAL--SIPVTVKCRIGVDD--------------QIPAVALRNLVKSIKKSG- 147
                +M K    +IP+TVKCRIG D+              +    +L+N ++++   G 
Sbjct: 126 RQLTTSMHKGSEGTIPITVKCRIGTDEGYTFTHKDYLSRSQEEEYSSLKNFIETVASDGI 185

Query: 148 VNGIWIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           V    IHAR A+L K  SP DNRK+P L Y  V  + +E P+L I LN
Sbjct: 186 VTDFQIHARIAVLGKSYSPADNRKVPPLRYHHVQRLAQEFPELNISLN 233


>gi|323452300|gb|EGB08174.1| hypothetical protein AURANDRAFT_12844 [Aureococcus anophagefferens]
          Length = 329

 Score =  135 bits (341), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 113/323 (34%), Positives = 161/323 (49%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-----LGFSTQEKPLALQIG 55
           M+  TDRH+R+ AR ++   LLYTEM+V D  L  +  N+     LG    E P+A+Q+G
Sbjct: 16  MMGVTDRHWRWMARQMSRKTLLYTEMVV-DNALNHNAHNLGGTQFLGHDACEAPVAVQLG 74

Query: 56  GADISKLVEAAKIVED-FGYN--EINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAM 111
           G D   L +AA +  D FG +  EINLN GCPS  V     FGA LML+P+ V   +  +
Sbjct: 75  GNDAKALGDAAALCVDYFGDSCVEINLNCGCPSNVVAARNEFGARLMLDPEKVRGIVHEL 134

Query: 112 CKAL-SIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAIL-KGLSP 165
            +   S PVTVK R+G D    D    +A    V++ + +G     +HAR+A+L K  S 
Sbjct: 135 IRRCPSTPVTVKHRLGTDLSGSDYATTLA---FVRASRAAGCRHFVLHAREAVLDKKFST 191

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALK---ILPSVDGVMIGRAA 219
           + NR IP L  D+ + + ++ PD    +NG    LED +  L     LP V   M+GRAA
Sbjct: 192 QQNRTIPPLKPDVAHRLARDLPDCTFAMNGMLRSLEDCAAHLSGWNGLPPVHSTMVGRAA 251

Query: 220 -YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ-IT 277
            Y+   +L T D         S P  +R      R +  +  DYA     +    +  + 
Sbjct: 252 WYQPWDLLATADTALYG--AASDPAASR------RDVLEAYLDYADEQYAALDVAEDCLY 303

Query: 278 RHMIGLFHGFPNSRRCRHILTVE 300
           R +  LF G  NS++ R  L  E
Sbjct: 304 RPLFYLFGGEQNSKKFRVRLADE 326


>gi|302848098|ref|XP_002955582.1| hypothetical protein VOLCADRAFT_43118 [Volvox carteri f.
           nagariensis]
 gi|300259205|gb|EFJ43435.1| hypothetical protein VOLCADRAFT_43118 [Volvox carteri f.
           nagariensis]
          Length = 320

 Score =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 100/304 (32%), Positives = 148/304 (48%), Gaps = 15/304 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADIS 60
           +DWTD H+R  ARLL+    L+TEM+V   IL        L F  +++PL LQ+GG+D +
Sbjct: 10  MDWTDMHFRQLARLLSRRTWLWTEMVVDKTILHTQNLDKFLWFPPEQRPLVLQLGGSDPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSIP- 118
            L  AA    ++GY+EINLN GCPS RV   G FGA LM+ P +V  C AAM +A+    
Sbjct: 70  TLAAAAARAVEYGYDEINLNCGCPSDRVASAGCFGAALMMRPHLVARCTAAMAEAMKGDL 129

Query: 119 --VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V + C  G        ++R       +S            +++GLSP  NR +P L +
Sbjct: 130 RLVMMTCYPGGRYLGAIFSVRCCTILTARSPPPLPPGVRPPWVVQGLSPHQNRTVPPLRH 189

Query: 177 DIVYEIKKENPDLFIGLNGGL----EDMSQALKI---LPSVDGVMIGRAAYKNS-AMLTT 228
              + + ++ P L   LNGG+    E   Q L +      + GVMIGR AY +    L  
Sbjct: 190 QWAWALARDFPHLQFSLNGGVLNCHEARFQGLSVGGNGGGIVGVMIGRGAYNDPWGCLAD 249

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
            D          +P +  V + + R+ + SM        H+   ++ + R ++ LFHG P
Sbjct: 250 ADRAVYGEPYNPAPSRRWVIERY-REYAESMVGRYPDG-HADPSIRTLMRPLLNLFHGEP 307

Query: 289 NSRR 292
             +R
Sbjct: 308 GCKR 311


>gi|330891419|gb|EGH24080.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
          Length = 172

 Score =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 68/158 (43%), Positives = 98/158 (62%), Gaps = 9/158 (5%)

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           + ++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + PDL I LNGG++ + Q
Sbjct: 3   VHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKSDFPDLEIVLNGGIKTLDQ 62

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
             + L + DGVM+GR AY N  +L  VD+        ++P+ +R D         SM  Y
Sbjct: 63  CGEHLQTFDGVMLGREAYHNPYLLAHVDQQL---FDSTAPVISRYDA------LESMRPY 113

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 114 IAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 151


>gi|223995337|ref|XP_002287352.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220976468|gb|EED94795.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 353

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 134/323 (41%), Gaps = 79/323 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----------------LRGDKKNILGF 43
           M+D +   +R+F RLLT  A ++TEM+VA+ +                 L  D K   G+
Sbjct: 14  MLDVSTVEFRYFMRLLTKRAFIWTEMVVAETLWHQSNQKGVLSSGDDLELEPDLKRHCGW 73

Query: 44  STQE----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
              +     P+  QIG  D  +   A ++V   GY+ I+LN  CPS RV    FGA LM 
Sbjct: 74  YEDQYLNPHPVVCQIGTNDPKQAEFATRVVHKLGYDRIDLNAECPSDRVAGREFGAALMR 133

Query: 100 NPDIVGDCIAAMCKALS-------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           + D   + + AM            IPV+VK RIGVD+      L   V+ +  +G     
Sbjct: 134 DHDTAIEVVRAMVDTAQSTKSDNPIPVSVKTRIGVDEFDTFEHLEGWVQRLVDAGCTWFI 193

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI------ 206
           IHARK   +GLSP  NR +P L+Y  VY + +  P      NGG+  +  A ++      
Sbjct: 194 IHARKVYTQGLSPAQNRTVPPLNYPRVYRLLQRFPSCDFWFNGGIMSLEHAKQVAFGYTG 253

Query: 207 -------------------------------------------LPSVDGVMIGRAAYKNS 223
                                                      LP++ GVM+GR A  + 
Sbjct: 254 VGDSDLIRETSSEETDCIDDDHTVPCQRCGVPHGSCIAPPRMSLPNLKGVMVGRLARDHP 313

Query: 224 AMLTTVDEYFSNPLTGSSPIKTR 246
           + L T+D +F      S P K R
Sbjct: 314 SELATIDSHFYG--EASDPCKNR 334


>gi|219130828|ref|XP_002185557.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402965|gb|EEC42922.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 243

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 74/216 (34%), Positives = 111/216 (51%), Gaps = 23/216 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----------------RGDKKNILGF 43
           M+  +   +R F R+LT  A L+TEM+V + +                  R D  +    
Sbjct: 29  MIRVSTPEFRAFVRILTKKATLWTEMVVDETLWYHRNDPGALQTYLGSLKRTDSNDHEIS 88

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV-----HEGSFGACLM 98
           + Q  P+  Q+GG       +A +I+  FGY+EINLN+ CPSARV         FGA LM
Sbjct: 89  AQQRNPIVCQLGGITPKHTAKATQIITAFGYDEINLNMDCPSARVSPQPRRRRQFGAILM 148

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
              D   + +  + +   +PV+VKCR+GVD++     L  +V+S++       +IHARK 
Sbjct: 149 KETDRAVELVKTIWENTHLPVSVKCRVGVDNEDSWEFLEAIVRSLRPY-CQRFYIHARKC 207

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           +L+GLSP  NR +P L+Y  VY + +  PD    LN
Sbjct: 208 LLQGLSPAQNRIVPPLNYPCVYRLCESFPDCEFYLN 243


>gi|300176192|emb|CBK23503.2| unnamed protein product [Blastocystis hominis]
          Length = 311

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 88/263 (33%), Positives = 125/263 (47%), Gaps = 45/263 (17%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  AAKI++D GYNEINLN GCPS  V   +FGA LML+P +V   I +M   ++IP+TV
Sbjct: 2   LAYAAKILQDRGYNEINLNCGCPSKTVSSHNFGAKLMLDPPLVRRIIESMKAEVTIPITV 61

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSG------------------------VNGIWIHARK 157
           KCRIGVD+     +L + +  +                            V+   +HARK
Sbjct: 62  KCRIGVDNCDSYESLVHFISVVSGVSPSSDSSAEEATEPTDASAASAAPLVSHFIVHARK 121

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD------ 211
             L G++ ++NR+IP+L  D V+ +  + P L   LNGG++  ++A + L  +       
Sbjct: 122 CWLNGVNTRENRRIPDLRPDWVFRLLDDFPTLDFTLNGGIKSFAEAQRYLDELSPKRGRK 181

Query: 212 --GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR---- 265
             GVMIGR A +   M   VDE F        P  +R      R+I     DY  +    
Sbjct: 182 LRGVMIGRMAMQCPWMFRHVDEIFYG---CKGPGLSR------RQIVERYCDYVEKLQET 232

Query: 266 HLHSGGKLQQITRHMIGLFHGFP 288
           H     K   + R +  LF G P
Sbjct: 233 HQKWKPKNDVVFRPLCTLFSGAP 255


>gi|46206232|ref|ZP_00047549.2| COG0042: tRNA-dihydrouridine synthase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 182

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 73/166 (43%), Positives = 98/166 (59%), Gaps = 16/166 (9%)

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G +G+ +HARKA LKGLSP++NR +P LDY  V  +K  +P+L I +NGG+ D+S A  
Sbjct: 8   AGXDGLIVHARKAWLKGLSPRENRDVPPLDYGRVARLKAAHPNLPIAINGGIADLSAAKA 67

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            L  VDGVM+GRAAY + A+L  VD E F  P     P+      D +  I A +    A
Sbjct: 68  RLAEVDGVMMGRAAYTDPALLLAVDPELFGEP----PPV-----ADAFAAIEA-LEPTLA 117

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRC-RHILTV----EAGAST 305
             L  G +L   TRHM+GLF+G P +R   RH+ T     EAG +T
Sbjct: 118 EGLARGLRLHAYTRHMLGLFNGRPGARAYRRHLATAGMAPEAGLAT 163


>gi|213027525|ref|ZP_03341972.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 160

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 66/164 (40%), Positives = 95/164 (57%), Gaps = 12/164 (7%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           IG+ DQ     L + + ++   G   ++I HARKA L GLSPK+NR+IP LDY  VY++K
Sbjct: 7   IGIVDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLK 66

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSP 242
           ++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T + P
Sbjct: 67  RDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTTDTDP 126

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +           +  +M  Y  R L  G  L  ITRHM+GLF G
Sbjct: 127 V----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQG 160


>gi|219130876|ref|XP_002185580.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402988|gb|EEC42945.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 216

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 75/213 (35%), Positives = 114/213 (53%), Gaps = 11/213 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-------GDKKNILGFS-TQEKPLAL 52
           M+  + R +R   R+L+   +L+TEM+V + +         G  +  LG+  T E P+  
Sbjct: 4   MLHVSTREFRQLFRILSKRVVLWTEMVVDELVYHNHEDRSNGTLETHLGYDDTNEHPVIC 63

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAM 111
           Q+GG   S    A ++  + GY+EINLNVGCPS RV  +  FGA LM     +   + AM
Sbjct: 64  QLGGIVPSHTALATQLAVERGYDEINLNVGCPSDRVSGKREFGAVLMKQLSRLLLLVQAM 123

Query: 112 CK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            + A   P++VKCR+GVDD      L   V +++       ++HARK +L+ LSP  NR 
Sbjct: 124 RENAGDTPISVKCRLGVDDWDSWEVLEEFVDTLRPY-CRIFYVHARKCLLQVLSPAQNRL 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +P L+Y  VY + +  PD    +NGG+  +  A
Sbjct: 183 VPPLNYPRVYRLCERFPDCDFYINGGIPGLRAA 215


>gi|67594542|ref|XP_665807.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54656648|gb|EAL35578.1| uncharacterized protein family UPF0034 [Cryptosporidium hominis]
          Length = 531

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/260 (33%), Positives = 125/260 (48%), Gaps = 53/260 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILG---FSTQ--EKPLA 51
           M+D T+ H+R   R+++    L+TEM+V D I+      +++ IL    F     E PL 
Sbjct: 33  MLDVTNSHFRMLCRIISKKTELWTEMVVDDTIIHCYNDENRRKILQDVHFKKNDIENPLV 92

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAA 110
           LQ+GG +  K+ +A +I   +G+   NLNVGCPS +V  +GSFGA L  NP  V   +  
Sbjct: 93  LQLGGNNPQKMEKAIEIAYKYGFQNFNLNVGCPSCKVASKGSFGASLFKNPLRVAKIVDQ 152

Query: 111 MCKAL------SIPVTVKCRIGVDD--------------------------------QIP 132
             K L      +  ++VK RIGVD                                 Q  
Sbjct: 153 CNKKLIDLGLVNKRISVKTRIGVDQYDTYQHLYNFISLVSGCNINNQNKKDYSCIFPQSD 212

Query: 133 AVALRNLVKSI-----KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
             + +N+++SI     K  G N   IHARKA L G++P  NR IP L Y  VY +  + P
Sbjct: 213 DHSDQNILESIDYTENKFIGANVFIIHARKAWLNGINPSKNRTIPKLKYYWVYMLTLDFP 272

Query: 188 DLFIGLNGGLEDMSQALKIL 207
           +L   LNGG+  + + + IL
Sbjct: 273 NLTFILNGGVTSIQECISIL 292


>gi|66358732|ref|XP_626544.1| YjbN-like Dus1p tRNA dihydouriding synthase Tim barrel
           [Cryptosporidium parvum Iowa II]
 gi|46227752|gb|EAK88672.1| YjbN-like Dus1p tRNA dihydouriding synthase Tim barrel
           [Cryptosporidium parvum Iowa II]
          Length = 519

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/260 (32%), Positives = 121/260 (46%), Gaps = 53/260 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILG---FSTQ--EKPLA 51
           M+D T+ H+R   R+++    L+TEM+V D I+      +++ IL    F     E PL 
Sbjct: 33  MLDVTNSHFRMLCRIISKKTELWTEMVVDDTIIHCYNDENRRKILQDVHFKKNDIENPLV 92

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAA 110
           LQ+GG +  K+ +A +I   +G+   NLNVGCPS +V  +GSFGA L  NP  V   +  
Sbjct: 93  LQLGGNNPQKMEKAIEIAYKYGFQNFNLNVGCPSCKVASKGSFGASLFKNPLRVAKIVDT 152

Query: 111 MCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSI---------KKS--------- 146
             K L      +  ++VK RIGVD       L N +  +         KK          
Sbjct: 153 CNKKLIHLGLVNKRISVKTRIGVDQYDTYQHLYNFISLVSGCNINNQNKKDYSCIFPQSD 212

Query: 147 -------------------GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                              G N   IHARKA L G++P  NR IP L Y  VY +  + P
Sbjct: 213 DDSDSNILESIDYTENNFIGANVFIIHARKAWLNGINPSKNRTIPKLKYYWVYMLTLDFP 272

Query: 188 DLFIGLNGGLEDMSQALKIL 207
           +L   LNGG+  + + + IL
Sbjct: 273 NLTFILNGGVTSIQECISIL 292


>gi|218134816|ref|ZP_03463620.1| hypothetical protein BACPEC_02719 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990201|gb|EEC56212.1| hypothetical protein BACPEC_02719 [Bacteroides pectinophilus ATCC
           43243]
          Length = 319

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 91/303 (30%), Positives = 151/303 (49%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      +LY+EM+ A AI+  ++    +L    +E P+A+Q+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGCGMLYSEMVSAKAIMYNNRNTDELLKVRPEENPVAVQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ I++N+GCP  +V     G+ LM NP +VG  ++AM KA+  P
Sbjct: 76  PQIMADMAKRIEELPFDTIDVNMGCPVPKVVNNGEGSALMKNPLLVGQIVSAMAKAVKKP 135

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  DD I A  + ++   I++SG   + +H R         ++       D+D
Sbjct: 136 VTVKIRKGFNDDMINAPEIAHI---IEESGGACVAVHGRT--------REQYYTGKADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG + D   A  +L     D VMIGRAA  N  +   V EY  N
Sbjct: 185 IIRQVKQRVHIPVIG-NGDITDALSARAMLDETGCDAVMIGRAARGNPWIFREVSEYLQN 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
              G+ P +   D+D    +   +  +A   +   G+   ++++ +H      GFPNS  
Sbjct: 244 ---GTIPQRPS-DED----VRNMILRHARLLVECKGEFTGIREMRKHFAWYTAGFPNSSM 295

Query: 293 CRH 295
            R+
Sbjct: 296 LRN 298


>gi|110597836|ref|ZP_01386119.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           ferrooxidans DSM 13031]
 gi|110340561|gb|EAT59044.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           ferrooxidans DSM 13031]
          Length = 347

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 151/308 (49%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE I A+A+ RG +K +  L   T E+PLA+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKQHGAD-IVYTEFISAEALRRGAEKTVRKLRADTVERPLAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++EAA I E+F  + +++N GCP+ +V     GA L+  P+ +     A+ KA+SIP
Sbjct: 76  VESMIEAAVIAEEFRPDYLDINFGCPTKKVAGKGAGAALLREPEKMTLIAEAVVKAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VT K RIG D +  ++ + +++  ++ +G+  + +H   R  + KG +          D+
Sbjct: 136 VTAKTRIGWDRE--SINIIDVLHRLEGAGIQALAVHGRTRSEMYKGRA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+ KE   + I  NG +     A+++      DGVMIGR +  N  +     +   
Sbjct: 184 NWIREV-KEQASIPIIANGDIWSAEDAVRMFAETGADGVMIGRGSIGNPFIFAAAKQLLH 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRR 292
             +    P       DF ++I A++          G K  + ++ RH      G P   +
Sbjct: 243 TGIPLPPP-------DFRQRIDAAVEHLKLSVEFKGDKYGVLEMRRHYSTYLKGLPMVSQ 295

Query: 293 CRHILTVE 300
            R+ L  E
Sbjct: 296 VRNKLVRE 303


>gi|317478240|ref|ZP_07937405.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
 gi|316905547|gb|EFV27336.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
          Length = 326

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 93/323 (28%), Positives = 151/323 (46%), Gaps = 32/323 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R  G  +  L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKHFGAD-MVYTEFVSADALIRSVGKTQQKLNISDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TATMVEAARIVEQAHPDTLDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++        V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWFFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
              TG    P+ +      WR  +     + +   L     +  + RH+    LF G PN
Sbjct: 246 ---TGEELPPLSSE-----WRLNVLRQEVEDSVNLLDERRGILHVRRHLAASPLFKGIPN 297

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
            R  R I  + A      + I E
Sbjct: 298 FRDTR-IAMLRAETKEELYRIFE 319


>gi|251794118|ref|YP_003008849.1| hypothetical protein Pjdr2_0082 [Paenibacillus sp. JDR-2]
 gi|247541744|gb|ACS98762.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. JDR-2]
          Length = 338

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 91/303 (30%), Positives = 152/303 (50%), Gaps = 30/303 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL G+K+   +L    +EKPL+LQI G D   LVEAA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAILHGNKRTMEMLFVDEREKPLSLQIFGGDRESLVEAA 84

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V +    + I++N+GCP  +V +   GA  +L+P+ + + ++A+  A+S PVTVK RI
Sbjct: 85  KVVDQQTNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVTAAVSKPVTVKMRI 144

Query: 126 GVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G DD+ I AV   +  K+++ +G   + +H R         ++ +     ++DI+ ++K+
Sbjct: 145 GWDDEHIYAV---DNAKAVESAGGKAVSVHGRT--------REQQYTGKANWDIIRDVKQ 193

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                 IG NG +     A ++L     DGVMIGR A  N  ML    +Y  +      P
Sbjct: 194 AVSIPVIG-NGDVFSPEDARRMLDHTGCDGVMIGRGALGNPWMLYRTIQYLESGELLPDP 252

Query: 243 I---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +   K  V      ++ A   + AA        ++++ +HM     G P + R + ++  
Sbjct: 253 LPREKLEVAILHMDRLVALRGEAAA--------VREMRKHMAWYLKGLPGAARVKDVIME 304

Query: 300 EAG 302
           E G
Sbjct: 305 ETG 307


>gi|281422351|ref|ZP_06253350.1| tRNA-dihydrouridine synthase B [Prevotella copri DSM 18205]
 gi|281403582|gb|EFB34262.1| tRNA-dihydrouridine synthase B [Prevotella copri DSM 18205]
          Length = 328

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 146/305 (47%), Gaps = 32/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G  
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRSIKSTVSKLTISDEERPVGIQIYGRT 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + I++N GCP  +V     GA ++ N  ++ D    + KA+++P
Sbjct: 77  TEDMVEAAKIVEQAKPDVIDINFGCPVKKVAGKGAGAGMLRNIPLMLDITREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDCE--NLIITDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A        VD VMIGRA +    +   + +Y  
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDITTPEEAKLAFERYGVDAVMIGRATFGRPWIFKEIRDYLD 245

Query: 235 NPLTGSSPIKTRVDKDFWR---KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
           N  TG++P+      D      +I+    D     LH+        RH+    +F G P+
Sbjct: 246 N--TGAAPLTVDEKIDLLEEQLRINVERIDEYRGILHT-------RRHLAASPIFKGIPD 296

Query: 290 SRRCR 294
            R+ R
Sbjct: 297 FRQTR 301


>gi|154484004|ref|ZP_02026452.1| hypothetical protein EUBVEN_01712 [Eubacterium ventriosum ATCC
           27560]
 gi|149735046|gb|EDM50932.1| hypothetical protein EUBVEN_01712 [Eubacterium ventriosum ATCC
           27560]
          Length = 317

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 89/309 (28%), Positives = 147/309 (47%), Gaps = 33/309 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      +LYTEM+ A AIL  +K    +L     E P+A+Q+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGCGMLYTEMVSAKAILYKNKNTNILLNIDKAEHPIAVQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV---HEGSFGACLMLNPDIVGDCIAAMCKAL 115
              + E    V +   + I++N+GCP  ++   HEGS+   L+  P +V   +  M KA+
Sbjct: 76  PDIMAEIGAKVAEGPCDFIDINMGCPVPKIVNNHEGSY---LLTQPKLVEQILTKMVKAI 132

Query: 116 SIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             PVT+K R G  D +I A  +  + +S    GV+ I +H R         ++       
Sbjct: 133 KKPVTIKVRKGFKDGEIQAPEIARIAES---CGVSAIAVHGRT--------REQYYSGKA 181

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D++ E+K+      IG NG +     ++A+K     DG+M+GRAA  N  +   + EY
Sbjct: 182 DWDVIKEVKEAVKIPVIG-NGDIFSAKDAKAMKEYTGCDGLMVGRAARGNPWIFKQIKEY 240

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-- 290
             N +    P  T V +D   K +  + DY   +      ++++ +H+     G P+S  
Sbjct: 241 LENGIIVDEPSSTEV-RDMVLKHARMLIDYKGEYT----AVREMRKHIAWYTQGLPHSAE 295

Query: 291 --RRCRHIL 297
             RRC  I+
Sbjct: 296 LRRRCNEIV 304


>gi|160891700|ref|ZP_02072703.1| hypothetical protein BACUNI_04155 [Bacteroides uniformis ATCC 8492]
 gi|270295204|ref|ZP_06201405.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|156859107|gb|EDO52538.1| hypothetical protein BACUNI_04155 [Bacteroides uniformis ATCC 8492]
 gi|270274451|gb|EFA20312.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 326

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 91/321 (28%), Positives = 147/321 (45%), Gaps = 28/321 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R  G  +  L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKHFGAD-MVYTEFVSADALIRSVGKTQQKLNISDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TATMVEAARIVEQAHPDTLDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++        V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWFFKEVKHYLE 245

Query: 235 NPLTGSSPIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
                  P         WR  +     + +   L     +  + RH+    LF G PN R
Sbjct: 246 TGEELPPPSSE------WRLNVLRQEVEDSVNLLDERRGILHVRRHLAASPLFKGIPNFR 299

Query: 292 RCRHILTVEAGASTATHHIIE 312
             R I  + A      + I E
Sbjct: 300 DTR-IAMLRAETKEELYRIFE 319


>gi|85858573|ref|YP_460775.1| tRNA-dihydrouridine synthase [Syntrophus aciditrophicus SB]
 gi|85721664|gb|ABC76607.1| tRNA-dihydrouridine synthase [Syntrophus aciditrophicus SB]
          Length = 326

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 131/240 (54%), Gaps = 18/240 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  AR     AL +TEMI A+ ++RG +K+   +     +KPL +QI G D + + +A 
Sbjct: 26  FRMMARE-AGCALAFTEMISANGLVRGIEKSQQYMKSCIDDKPLGVQIFGNDPTTMADAV 84

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +IV+D+G + I+LN+GCP  +V +   GA L+ +P +V   + ++ KA   P+TVK R G
Sbjct: 85  RIVDDYGADLIDLNMGCPVKKVVKNGAGAALLKDPGLVSQILESVRKATRKPLTVKIRSG 144

Query: 127 VDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            + Q I AV +  +    ++ G++ +++HAR A+ +G +        + D+ I+ EIK  
Sbjct: 145 WNLQSINAVQIARIA---EQQGIDAVFVHARTAV-QGFA-------GSADWRIIEEIKNS 193

Query: 186 NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
                IG NG ++  + A ++  +   DGVMIGR A  N  +      Y S   T S P+
Sbjct: 194 VGIKVIG-NGDVKSGADAWRMIKMTGCDGVMIGRGALGNPWIFNEALNYQSTVQTHSEPV 252


>gi|219116258|ref|XP_002178924.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409691|gb|EEC49622.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 497

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 92/300 (30%), Positives = 131/300 (43%), Gaps = 67/300 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM-IVADAILRGDK------------KNILGFSTQE 47
           M  +T    R   R L+ NA L+TEM  V D +  G K            +N    S+Q 
Sbjct: 42  MQCYTHAPLRQLYRTLSANATLWTEMEKVEDLLATGSKGLERRFGRYWTNRNTHASSSQP 101

Query: 48  KPLALQIGGADISKLVEA-------AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLML 99
           + L LQIGG    KL E        ++  + F + ++NLN GCP        ++GA LM 
Sbjct: 102 ENLVLQIGGNQPDKLRECLLRLSAQSQDQDAFPFTQVNLNCGCPGIEAGGATTYGASLMK 161

Query: 100 NPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRN------------------- 138
            PD  G  +  M   L  +  V++KCRIGV D    ++LR                    
Sbjct: 162 QPDYTGTLLQTMRDVLPSTTKVSLKCRIGVVDTPADLSLRTEATRSGGDAVHDTTTVASY 221

Query: 139 -----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                 V   + +GV+ + +HAR A+L GLSP  NR +P+LDY +V  I  + PDL + L
Sbjct: 222 QALHRYVSIARDAGVSHVILHARVAVLTGLSPSKNRIVPSLDYRMVERIATDFPDLRVTL 281

Query: 194 NGGLEDMS--QALK---------------ILPS---VDGVMIGRAAYKNSAMLTTVDEYF 233
           NGG+ ++   Q L+               +LP    V   M GR   +    L  V +YF
Sbjct: 282 NGGIRNLGDLQRLRRFTSSPTTKTTCTPPVLPENSLVASHMAGRWMLRRPLDLAAVQDYF 341


>gi|302390915|ref|YP_003826735.1| tRNA-U20-dihydrouridine synthase [Acetohalobium arabaticum DSM
           5501]
 gi|302202992|gb|ADL11670.1| tRNA-U20-dihydrouridine synthase [Acetohalobium arabaticum DSM
           5501]
          Length = 322

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 84/303 (27%), Positives = 150/303 (49%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A  ++ G  +   +L  S QE+P++LQI G++
Sbjct: 17  MAGVTDLPFRRIVKEF-GCGLVCTEMVSAKGLVYGSSRTEELLTISDQERPVSLQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA + +E++  + I++N+GCP+ ++ +G  G+ LM  PD+VG  + A+ +A  IP
Sbjct: 76  PEIMAEAVEKIEEYRPDIIDVNLGCPTPKIVKGGAGSVLMKEPDLVGRIVDALVRATEIP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           +TVK R G D D + AV    + ++ ++SGV  + +H   R+   KG            D
Sbjct: 136 ITVKMRKGWDEDHVNAV---EIAQTAEESGVQAVAVHGRTREQFYKG----------EAD 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           ++I+ E+K+      IG NG +     A +++ +   DGVMI R A  N  +      Y 
Sbjct: 183 WNIIKEVKEAVEVPVIG-NGDIFSPQDAEEMIDTTGCDGVMIARGAQGNPWIFKRTLHYL 241

Query: 234 -SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +  L     I+ R++    R + A + DY   ++     ++++ RH +    G  N   
Sbjct: 242 ETGELLPPPTIQERIEM-VVRHLEA-LVDYKGEYI----AVREMRRHTVQYIKGLYNCTE 295

Query: 293 CRH 295
            + 
Sbjct: 296 VKQ 298


>gi|332884058|gb|EGK04338.1| hypothetical protein HMPREF9456_01366 [Dysgonomonas mossii DSM
           22836]
          Length = 331

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/302 (27%), Positives = 145/302 (48%), Gaps = 25/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G +
Sbjct: 18  MEDVTDMGFRLMCKQFGAD-MVYTEFVSSDALIRHVNKTQAKLTISEEERPVAIQIYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKI E+   N +++N GCP  +V     G+ +M  P+++ +  AA+ KA+ IP
Sbjct: 77  VDAMVEAAKICEEANPNILDINFGCPVKKVAGKGAGSGMMKTPELMVEITAAVVKAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +      + D+++
Sbjct: 137 VTVKTRLGWDHESKIIV--ELAEQLQDVGIQALTIHGRT--------RSQMYTGDADWEL 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL----PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++K  NP + I + G  +  S  +         VD VMIGR +  +  +   V  Y  
Sbjct: 187 IGDVKN-NPRIHIPIVGNGDVTSPEICKRRFDETGVDAVMIGRGSIGSPWIFEEVKHYLR 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              TG +  K     +++  +   M      H    G +    RH+    LF G P+ ++
Sbjct: 246 ---TGETLPKKEF--EWYLDVLKEMIRKNVVHSGERGGIIHSRRHLAASSLFKGLPDFKK 300

Query: 293 CR 294
            R
Sbjct: 301 VR 302


>gi|304405776|ref|ZP_07387434.1| TIM-barrel protein, nifR3 family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345019|gb|EFM10855.1| TIM-barrel protein, nifR3 family [Paenibacillus curdlanolyticus
           YK9]
          Length = 342

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 128/232 (55%), Gaps = 17/232 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL G+K+ +  L    +EKPL+LQI G D   LVEAA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAILHGNKRTLEMLYVDEREKPLSLQIFGGDRESLVEAA 84

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           KIV+     + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +A+  PVTVK RI
Sbjct: 85  KIVDKQTNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVTEAVDKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G DD+    A+ N  ++++++G + + +H R         ++       ++DI+ E+K+ 
Sbjct: 145 GWDDE-HIFAVEN-ARAVERAGGSAVSVHGRT--------REQLYTGKANWDIIKEVKEA 194

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                IG NG +     A ++L    VDGVMIGR A  N  ML    +Y +N
Sbjct: 195 VSIPVIG-NGDVFTPEDAKRMLDHTGVDGVMIGRGALGNPWMLYRTIQYLTN 245


>gi|329962719|ref|ZP_08300642.1| putative tRNA-dihydrouridine synthase B [Bacteroides fluxus YIT
           12057]
 gi|328529553|gb|EGF56456.1| putative tRNA-dihydrouridine synthase B [Bacteroides fluxus YIT
           12057]
          Length = 325

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 93/329 (28%), Positives = 153/329 (46%), Gaps = 32/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R  G  +  L  S  E+P+ +QI G D
Sbjct: 18  MEDVTDPAFRLMCKQFGAD-MVYTEFVSADALIRSVGKTRQKLNISDAERPVTIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNVPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMRIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
              TG    P+ +      WR ++     + +   L     +  + RH+    LF G PN
Sbjct: 246 ---TGEELPPLSSE-----WRMEVLRREVEDSVNLLDERRGILHVRRHLAASPLFKGIPN 297

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLM 318
            R  R I  + A      + I +T   L+
Sbjct: 298 FRDTR-IAMLRAETKEELYRIFDTIAPLL 325


>gi|288800405|ref|ZP_06405863.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 299 str. F0039]
 gi|288332618|gb|EFC71098.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 299 str. F0039]
          Length = 333

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 91/324 (28%), Positives = 154/324 (47%), Gaps = 33/324 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  I  L  +  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRNIKSTINKLSIADSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I+LN GCP  +V     G+ ++ N  ++ D    + KA+  P
Sbjct: 77  VESMVEAAKIVEQVSPDVIDLNFGCPVKKVASKGAGSGMLRNIPLMLDITREVVKAVKTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + +  L + ++  G+  + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDSE--NLVITTLAEQLQDCGIEALTIHGRT--------RAQMYTGNADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+ K+NP + I +  NG +    +A        VD VM+GRA +    +   ++E   
Sbjct: 187 IKEV-KDNPRIHIPIIGNGDITTAEEAKMAFEQYGVDAVMVGRATFGRPWVFKEMNELIQ 245

Query: 235 NPLTGSSPIKTRVDK-DFWR---KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFP 288
             + G++   T  DK D  +   +I+    D     LH+        RH+    +F G P
Sbjct: 246 G-IDGTNTALTIDDKIDILKEQLEINVEKIDEYRGILHT-------RRHLASSPIFKGIP 297

Query: 289 NSRRCRHILTVEAGASTATHHIIE 312
           + ++ R I  + A      + I+E
Sbjct: 298 DFKQTR-IAMLRANTVNELNSILE 320


>gi|319900676|ref|YP_004160404.1| tRNA-U20-dihydrouridine synthase [Bacteroides helcogenes P 36-108]
 gi|319415707|gb|ADV42818.1| tRNA-U20-dihydrouridine synthase [Bacteroides helcogenes P 36-108]
          Length = 332

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 92/307 (29%), Positives = 145/307 (47%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K    L  ST+E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKQFGAD-MVYTEFVSADALIRSVSKTEQKLNISTEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADHKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++        V  Y  
Sbjct: 187 IGEVKK-NPRMHIPVIGNGDITTPERAKECFDLYGVDAIMIGRASFGRPWFFKEVRHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSPEWKLNVLRREVEDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRDTR 302


>gi|323141551|ref|ZP_08076436.1| TIM-barrel protein, nifR3 family [Phascolarctobacterium sp. YIT
           12067]
 gi|322413963|gb|EFY04797.1| TIM-barrel protein, nifR3 family [Phascolarctobacterium sp. YIT
           12067]
          Length = 360

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 87/304 (28%), Positives = 146/304 (48%), Gaps = 33/304 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    +  +EM+ A  +L  + K   +L     E+P A+Q+ G+ 
Sbjct: 42  MAGITDLPFRLICRRL-GCGMTVSEMVSAKGLLYKNVKTTEMLRIDDGERPTAIQLFGSV 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++L EAA++VE  G + I+ N+GCP  ++     G+ LM NP +  D +AAM KA+ IP
Sbjct: 101 PAELAEAARMVEASGADMIDFNMGCPVPKIVNNGEGSALMKNPQLAHDILAAMVKAVKIP 160

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VTVK R G DD     A RN V   ++++ +GV+ + +H R         +        D
Sbjct: 161 VTVKFRAGWDD-----ANRNAVEVARAVEAAGVSAVAVHGRT--------RQQFYEGKAD 207

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           + I+ ++K+       G NG +  ++  L++L     DG+MIGR A  N  + T +    
Sbjct: 208 WSIIADVKQAVKVPVFG-NGDIFTVADGLRMLEQTGCDGLMIGRGADGNPWLFTALAAAL 266

Query: 234 -SNPLTGSSPIKTRVDK--DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              PL     +K R+ +  +    +SA   +  A        ++++ RH+     G P++
Sbjct: 267 RGEPLPQPPSLKERLAQAAEHLEMLSAYKNEVVA--------VKEMRRHISAYLKGMPHA 318

Query: 291 RRCR 294
              R
Sbjct: 319 AEFR 322


>gi|282879049|ref|ZP_06287809.1| TIM-barrel protein, nifR3 family [Prevotella buccalis ATCC 35310]
 gi|281298783|gb|EFA91192.1| TIM-barrel protein, nifR3 family [Prevotella buccalis ATCC 35310]
          Length = 329

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 92/333 (27%), Positives = 158/333 (47%), Gaps = 32/333 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     +++YTE + A+A++R  +   N L  S  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRQLCKRF-GVSMVYTEFVSAEALVRSIQASLNKLTISDAERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I++N GCP  +V     GA ++ N  ++ +    + KA+  P
Sbjct: 77  VESMVEAAKIVEQAHPDVIDINFGCPVKKVAGKGAGAGMLRNIPLLLEITREVVKAVHTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + +  L + ++  G+  + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDEN--NLIITELAEQLQDCGIQALTIHGRT--------RSQMYTGNADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF- 233
           + E+K  NP + I +  NG +    +A +      VD +M+GRAA+    +   + +Y  
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDITSPQEAKQAFERFGVDAIMVGRAAFGQPWIFKEMRDYLD 245

Query: 234 SNPLTGSSPIKTRVD--KDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
             P   S  I  ++D  K+    I+ S  D     LH+        RH+    +F G P+
Sbjct: 246 GKPYDASLGINKKIDILKEQLH-INVSRIDEYRGILHT-------RRHLAASPIFKGIPD 297

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            R+ R I  + A       +I+E     +++ L
Sbjct: 298 FRQTR-IAMLRASTVVELENILEACRKRLVDEL 329


>gi|303237786|ref|ZP_07324344.1| TIM-barrel protein, nifR3 family [Prevotella disiens FB035-09AN]
 gi|302482011|gb|EFL45048.1| TIM-barrel protein, nifR3 family [Prevotella disiens FB035-09AN]
          Length = 321

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 126/237 (53%), Gaps = 18/237 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADA++R  K   N +    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAVIRSIKSTLNKIVIDDEERPVGIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE+   + I++N GCP  +V     G+ ++ N  ++ +    + KA+  P
Sbjct: 77  VASMVEAAKIVEEVHPDVIDINFGCPVKKVANKGAGSGMLRNIPLLLEITREVVKAVKTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    + + +L + ++  G+  + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDDN--NLIITDLAEQLQNCGIQALTIHGRT--------RAQMYTGNADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           + E+K  NP + I +  NG +E+++ A K      VD VMIGRA +    + +  D+
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDIENIADAHKHFDKYGVDAVMIGRATFGCPWLFSETDD 242


>gi|313906481|ref|ZP_07839815.1| TIM-barrel protein, nifR3 family [Eubacterium cellulosolvens 6]
 gi|313468671|gb|EFR64039.1| TIM-barrel protein, nifR3 family [Eubacterium cellulosolvens 6]
          Length = 322

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 141/298 (47%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+YTEM+ A AIL  ++    ++     E+P++LQ+ G++
Sbjct: 20  MAGVTDLPFRLLCRE-QGAGLVYTEMVSAKAILYKNRNTEALMQIDPGERPVSLQLFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA  +E+  ++  + N+GCP  +V     G+ LM +P + G+ IAA+ K +  P
Sbjct: 79  PEIVAEAAAQIEERPFDIFDFNMGCPVPKVVNNHEGSALMKDPKLAGEIIAAVVKRVHKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D Q  +V    + K ++ +G   I +H R         +        D+D+
Sbjct: 139 VTVKIRKGWDCQ--SVNAVEVAKVLEDAGAAAIAVHGRT--------RSQYYAGEADWDV 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ KE   + +  NG ++   +A  ++    VDG+MI R A  N  +   V  Y    
Sbjct: 189 IRQV-KEAVSIPVFGNGDVDSPEKAAALVEQTGVDGIMIARGARGNPWLFGRVRRYLEEG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +    P    V +   R +   +T+Y   +      L+++ +H+     GFPNS   R
Sbjct: 248 VIPEKPSPKEVYEMIMRHMKM-LTEYKGDYTG----LREMRKHVAWYTTGFPNSAMLR 300


>gi|325299590|ref|YP_004259507.1| TIM-barrel protein, nifR3 family [Bacteroides salanitronis DSM
           18170]
 gi|324319143|gb|ADY37034.1| TIM-barrel protein, nifR3 family [Bacteroides salanitronis DSM
           18170]
          Length = 338

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 92/307 (29%), Positives = 143/307 (46%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K +  L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLLCKEFGAD-MVYTEFVSSDALIRSVDKTMMKLNISAAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQARPDILDLNFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVNAVQIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDENHKVIV--ELAEQLQDCGIEALTIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMRIPIIGNGDITTPQRAKECFDRYGVDSIMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRK-ISASMTDYAARH--LHSGGKLQQITRHMIG--LFHGF 287
              TG    P+  R   D  R+ I  S+     R   LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFRWKLDVLRREIQDSINLLNERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRDTR 302


>gi|78188223|ref|YP_378561.1| dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           chlorochromatii CaD3]
 gi|78170422|gb|ABB27518.1| tRNA-U20-dihydrouridine synthase [Chlorobium chlorochromatii CaD3]
          Length = 348

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 82/308 (26%), Positives = 149/308 (48%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE I A+A+ RG +K++  L     E+P A+QI G+ 
Sbjct: 17  MEDVTDRSFRQLCKRHGAD-IVYTEFISAEALRRGAEKSLRKLKVDDMERPYAIQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I   +  + +++N GCP  +V     GA L+  P+ +    AA+ KA++IP
Sbjct: 76  VESMVEAAIIAASYQPDYLDINFGCPVKKVAGKGAGAALLREPEKMAAISAAVVKAVAIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VT K RIG D    ++ + +++  ++ +G+  + +H   R  + KG +          D+
Sbjct: 136 VTAKTRIGWD--FDSINILDIIPRLEDAGIQALALHGRTRSQMYKGTA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    KE   + +  NG + +   A ++  + + DGVMIGR +  N  +      + +
Sbjct: 184 QWI-RAAKEKAHIPLIANGDIWNAEDAARMFDVTAADGVMIGRGSIGNPFIFQQAKHFLA 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRR 292
           +      P       DF ++I+ ++  +     + G K  + ++ RH      G P   R
Sbjct: 243 HGTLLPPP-------DFRQRIAVAIEHFQLSLAYKGEKYGVLEMRRHYSTYLKGLPMVSR 295

Query: 293 CRHILTVE 300
            R+ L  E
Sbjct: 296 VRNKLVRE 303


>gi|241888813|ref|ZP_04776119.1| tRNA-dihydrouridine synthase B [Gemella haemolysans ATCC 10379]
 gi|241864489|gb|EER68865.1| tRNA-dihydrouridine synthase B [Gemella haemolysans ATCC 10379]
          Length = 335

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 83/234 (35%), Positives = 132/234 (56%), Gaps = 17/234 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+   AIL  +KK  N+L    +E+PL+LQI G +I  LVEAAK V+ +   + I
Sbjct: 37  LVCAEMVSDKAILFNNKKTMNMLYIDPRERPLSLQIFGGEIETLVEAAKYVDKNTEADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP  ++ +   G+ L+L+PD V + IA +  ++S PVTVK R+G DD+   + + 
Sbjct: 97  DLNMGCPVPKITKVDAGSKLLLDPDKVYEVIARLVDSVSKPVTVKMRMGWDDE--HIYIM 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  ++ +++G + I IH R  + +  S K N       +D++ ++KKE     IG NG +
Sbjct: 155 DNARNAERAGASAIAIHGRTKV-QMYSGKAN-------WDVIRDVKKELKIPVIG-NGDV 205

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
                A K+L   + D VMIGRAA  N  ML    +Y  +  LT     + ++D
Sbjct: 206 TSPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLETGELTEEPSPREKID 259


>gi|329767828|ref|ZP_08259344.1| tRNA-dihydrouridine synthase 1 [Gemella haemolysans M341]
 gi|328838929|gb|EGF88523.1| tRNA-dihydrouridine synthase 1 [Gemella haemolysans M341]
          Length = 335

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/234 (35%), Positives = 132/234 (56%), Gaps = 17/234 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+   AIL  +KK  N+L    +E+PL+LQI G +I  LVEAAK V+ +   + I
Sbjct: 37  LVCAEMVSDKAILFNNKKTMNMLYIDPRERPLSLQIFGGEIDTLVEAAKYVDKNTEADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP  ++ +   G+ L+L+PD V + IA +  ++S PVTVK R+G DD+   + + 
Sbjct: 97  DLNMGCPVPKITKVDAGSKLLLDPDKVYEVIARLVDSVSKPVTVKMRMGWDDE--HIYIM 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  ++ +++G + I IH R  + +  S K N       +D++ ++KKE     IG NG +
Sbjct: 155 DNARNAERAGASAIAIHGRTKV-QMYSGKAN-------WDVIRDVKKELKIPVIG-NGDV 205

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
                A K+L   + D VMIGRAA  N  ML    +Y  +  LT     + ++D
Sbjct: 206 TTPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLETGELTEEPTPREKID 259


>gi|194337545|ref|YP_002019339.1| TIM-barrel protein, nifR3 family [Pelodictyon phaeoclathratiforme
           BU-1]
 gi|194310022|gb|ACF44722.1| TIM-barrel protein, nifR3 family [Pelodictyon phaeoclathratiforme
           BU-1]
          Length = 352

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 88/310 (28%), Positives = 146/310 (47%), Gaps = 29/310 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M D TDR +R   +    + ++YTE I A+A+ RG +K++    T E  +P A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKRHGAD-IVYTEFISAEALRRGVEKSLRKLKTDEVERPFAIQIFGSS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +V+AA I E +  + +++N GCP+ +V     GA L+  P+ +     A+ KA+SIP
Sbjct: 76  IESMVDAAVIAEGYCPDYLDINFGCPTKKVAGKGAGAALLREPEKMTAISEAVVKAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK RIG D  + ++ + +++  ++  G+  + +H   R  + KG   + NR       
Sbjct: 136 VTVKTRIGWD--LESINILDILPRLEDVGIQALALHGRTRSEMFKG---RANR------- 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           + + ++ KE   + +  NG +     AL +      DGVMIGR +  N  +     E   
Sbjct: 184 EWIRQV-KEQARIPVIANGDIWSAEDALAMFAETGADGVMIGRGSIGNPFIFEAAKELLK 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRR 292
                  P       DF  +I  ++          G K  + ++ RH      G P   R
Sbjct: 243 TGKPMPPP-------DFRARIDVAIEHLKLSVQFKGEKYGVLEMRRHYSTYLKGLPMVSR 295

Query: 293 CRHILTVEAG 302
            R+ L  E G
Sbjct: 296 VRNKLVREDG 305


>gi|238922487|ref|YP_002936000.1| tRNA-dihydrouridine synthase [Eubacterium rectale ATCC 33656]
 gi|238874159|gb|ACR73866.1| tRNA-dihydrouridine synthase [Eubacterium rectale ATCC 33656]
          Length = 323

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/299 (27%), Positives = 143/299 (47%), Gaps = 23/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L    +EKP++LQ+ G+D
Sbjct: 25  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTESLLSIDEREKPVSLQMFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ +++N+GCP  ++     G+ LM NP + G  I ++ KA+  P
Sbjct: 84  PQIMAQIAKQIEERPFDILDINMGCPVPKIVNNGEGSALMKNPLLAGQIIESIVKAIDKP 143

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD+ + AV L ++    ++SG + + +H R         ++       D+D
Sbjct: 144 VTVKIRKGFDDEHVNAVELAHVA---EESGASAVAVHGRT--------REQYYSGKADWD 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG L      +K+      DG MI R A  N  + + +  YF  
Sbjct: 193 IIRQVKEAVSIPVIG-NGDLLSAEDVIKMQEQTGCDGFMIARGAQGNPWIFSQILHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P    V +   R  +  M ++   +      + ++ +H      G+P+S R R
Sbjct: 252 GEHQEKPSFEEVRRMILRH-ARMMIEFKGEYT----GIHEMRKHTAWYTAGYPHSSRLR 305


>gi|323343751|ref|ZP_08083978.1| tRNA-dihydrouridine synthase B [Prevotella oralis ATCC 33269]
 gi|323095570|gb|EFZ38144.1| tRNA-dihydrouridine synthase B [Prevotella oralis ATCC 33269]
          Length = 346

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/304 (28%), Positives = 150/304 (49%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE I A+A++R  K  +  L  S +E+P+ +QI G D
Sbjct: 38  MEDVTDIGFRLLCKRF-GAAMVYTEFISAEALVRSIKATMSKLTISDEERPVGIQIYGRD 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE+   + I+LN GCP  +V     GA ++ N  ++ +    + KA+  P
Sbjct: 97  VVSMVEAAKIVEEAHPDVIDLNFGCPVKKVASKGAGAGMLRNIPLLLEITREVVKAVHTP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +A  +L + ++  G++ + IH R         +        D+ +
Sbjct: 157 VTVKTRLGWDANNLIIA--DLAEQLQDCGIHALTIHGRT--------RSQMYTGKADWTL 206

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K+ NP + I +  NG +   S+A +       D VMIGRA +    +   + ++  
Sbjct: 207 IGEVKR-NPRIHIPIIGNGDIASPSEAKEAFDRYGTDAVMIGRATFGRPWIFREIIDFLE 265

Query: 235 NPLTGSS-PIKTRVD-KDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
           N  T ++  +  ++D  +   +I+    D     LH+        RH+    +F G P+ 
Sbjct: 266 NSDTPAALTLNDKIDILEEQLRINVERIDEYRGILHT-------RRHLAASPVFKGIPDF 318

Query: 291 RRCR 294
           R+ R
Sbjct: 319 RQTR 322


>gi|317495837|ref|ZP_07954200.1| dihydrouridine synthase [Gemella moribillum M424]
 gi|316914014|gb|EFV35497.1| dihydrouridine synthase [Gemella moribillum M424]
          Length = 335

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 126/227 (55%), Gaps = 16/227 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+   AIL  ++K  N+L    +E+PL+LQI G +I  LVEAAK V+ +   + I
Sbjct: 37  LVCAEMVSDKAILFNNQKTMNMLYIDPRERPLSLQIFGGEIDTLVEAAKYVDKNTEADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP  ++ +   G+ L+L+PD V + IA +  A+S PVTVK R+G DD+   + + 
Sbjct: 97  DLNMGCPVPKITKVDAGSKLLLDPDKVYEVIARLVDAVSKPVTVKMRMGWDDE--HIYIM 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  ++ +++G + I IH R  + +  S K N       +D++ ++KKE     IG NG +
Sbjct: 155 DNARNAERAGASAIAIHGRTKV-QMYSGKAN-------WDVIRDVKKELKIPVIG-NGDV 205

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                A K+L   + D VMIGRAA  N  ML    +Y         P
Sbjct: 206 TTPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLETGELSDEP 252


>gi|281424760|ref|ZP_06255673.1| tRNA-dihydrouridine synthase [Prevotella oris F0302]
 gi|281401130|gb|EFB31961.1| tRNA-dihydrouridine synthase [Prevotella oris F0302]
          Length = 334

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 143/305 (46%), Gaps = 32/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +  +  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRMLCKRY-GAAMVYTEFVSADAIIRSIKSTLDKMAINDAERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I+LN GCP  +V     G+ ++ N  ++ D    + KA+S P
Sbjct: 77  VESMVEAAKIVEQVKPDLIDLNFGCPVKKVAGKGAGSGMLRNIPLLLDITRNVVKAVSTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ + +L + ++  G+  + IH R          D   I N+    
Sbjct: 137 VTVKTRLGWDND--SLIITDLAEQLQDCGIQALTIHGRTRAQMYTGEADWTLIGNV---- 190

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
                K NP + I +  NG +    +A        VD VM+GRA +    +   + ++  
Sbjct: 191 -----KSNPRIHIPIIGNGDITTPEEAKHAFDDYGVDAVMVGRATFGRPWVFKEMRDFID 245

Query: 235 NPLTGSSPIKTRVDKDFWR---KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
           N  T SSP+      D      +I+    D     +H+        RH+    +F G P+
Sbjct: 246 N--TTSSPLTIDDKIDILEEQLRINVERIDEYRGIIHT-------RRHLASSPIFKGIPD 296

Query: 290 SRRCR 294
            ++ R
Sbjct: 297 FKQTR 301


>gi|189464643|ref|ZP_03013428.1| hypothetical protein BACINT_00986 [Bacteroides intestinalis DSM
           17393]
 gi|189436917|gb|EDV05902.1| hypothetical protein BACINT_00986 [Bacteroides intestinalis DSM
           17393]
          Length = 329

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 92/307 (29%), Positives = 144/307 (46%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    N ++YTE + ADA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAN-MVYTEFVSADALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE+   + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEEARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDVTTPQRAKECFELYGVDAIMIGRASFGRPWIFKEVRHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+         R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSAEWKLGVLRQEVIDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRDTR 302


>gi|212692328|ref|ZP_03300456.1| hypothetical protein BACDOR_01824 [Bacteroides dorei DSM 17855]
 gi|237711412|ref|ZP_04541893.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|237726127|ref|ZP_04556608.1| dehydrogenase [Bacteroides sp. D4]
 gi|265752818|ref|ZP_06088387.1| dehydrogenase [Bacteroides sp. 3_1_33FAA]
 gi|212665205|gb|EEB25777.1| hypothetical protein BACDOR_01824 [Bacteroides dorei DSM 17855]
 gi|229435935|gb|EEO46012.1| dehydrogenase [Bacteroides dorei 5_1_36/D4]
 gi|229454107|gb|EEO59828.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|263236004|gb|EEZ21499.1| dehydrogenase [Bacteroides sp. 3_1_33FAA]
          Length = 329

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/304 (28%), Positives = 147/304 (48%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K +  L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSADALIRSVGKTMQKLNINDEERPVAVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEEAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNEHKIIV--DLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++    +   +  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWIFKEIKHYIE 245

Query: 235 NPLTGSSPIKTRVDKDFWR--KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG        +   WR   +   + D +   L     +  + RH+    LF G PN 
Sbjct: 246 ---TGKELPALSFE---WRLNVLRQEVLD-SVNLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           +  R
Sbjct: 299 KETR 302


>gi|291526763|emb|CBK92349.1| tRNA-U20-dihydrouridine synthase [Eubacterium rectale M104/1]
          Length = 323

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/299 (27%), Positives = 143/299 (47%), Gaps = 23/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L    +EKP++LQ+ G+D
Sbjct: 25  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTESLLSIDEREKPVSLQMFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ +++N+GCP  ++     G+ LM NP + G  I ++ KA+  P
Sbjct: 84  PQIMAQIAKQIEERPFDILDINMGCPVPKIVNNGEGSALMKNPILAGQIIESIVKAIDKP 143

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD+ + AV L ++    ++SG + + +H R         ++       D+D
Sbjct: 144 VTVKIRKGFDDEHVNAVELAHVA---EESGASAVAVHGRT--------REQYYSGKADWD 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG L      +K+      DG MI R A  N  + + +  YF  
Sbjct: 193 IIRQVKEAVSIPVIG-NGDLLCAEDVIKMQEQTGCDGFMIARGAQGNPWIFSQILHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P    V +   R  +  M ++   +      + ++ +H      G+P+S R R
Sbjct: 252 GEHQEKPSFEEVRRMILRH-ARMMIEFKGEYT----GIHEMRKHTAWYTAGYPHSSRLR 305


>gi|210610329|ref|ZP_03288358.1| hypothetical protein CLONEX_00548 [Clostridium nexile DSM 1787]
 gi|210152559|gb|EEA83565.1| hypothetical protein CLONEX_00548 [Clostridium nexile DSM 1787]
          Length = 324

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/302 (28%), Positives = 145/302 (48%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K  K +L    +E P++LQ+ G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYNNKNTKALLEIHPEELPVSLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  ++ +   G+ LM NP +V + +    +A+  P
Sbjct: 79  PDVISEIAKRIEELPFSILDINMGCPVPKIVKNGEGSALMKNPKLVYEIVRKTARAIQKP 138

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I AV    + K I+ +G   + +H R         ++       D+D
Sbjct: 139 VTVKIRKGFDDTCINAV---EIAKIIEDAGGKAVAVHGRT--------REQYYSGKADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +     A+ I      DGVMIGR A  N  + + + EY   
Sbjct: 188 IIRQVKEAVSIPVIG-NGDVVSGESAIAIQKETGCDGVMIGRGAQGNPWIFSELLEYER- 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG  P++  V+      I   M  +A   +   G+   ++++ +H+     G PNS +
Sbjct: 246 --TGKMPLRPSVE-----AIKKMMIRHAQLQMQYKGEYLGIREMRKHVSWYTSGLPNSAK 298

Query: 293 CR 294
            R
Sbjct: 299 LR 300


>gi|198274476|ref|ZP_03207008.1| hypothetical protein BACPLE_00624 [Bacteroides plebeius DSM 17135]
 gi|198272678|gb|EDY96947.1| hypothetical protein BACPLE_00624 [Bacteroides plebeius DSM 17135]
          Length = 328

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 145/307 (47%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K +L    S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKQFGAD-MVYTEFVSSDALIRSVGKTMLKLNISEKERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     G+ ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQAKPDILDLNFGCPVKRVAGKGAGSGMLQNVPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAEHKIIV--ELAEQLQDCGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMRIPIIGNGDITTPQRAKECFEQYGVDAIMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+  +   D  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFKWRMDVLRQEVLDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN +  R
Sbjct: 296 PNFKDTR 302


>gi|168830124|gb|ACA34352.1| tRNA-dihydrouridine synthase [Paenibacillus polymyxa]
          Length = 342

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/300 (29%), Positives = 153/300 (51%), Gaps = 28/300 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D   LVEAA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAIIHGNKRTREMLFVDEREKPLSLQIFGGDRKSLVEAA 84

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V ++   + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +++S PVTVK RI
Sbjct: 85  KVVNQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVVESVSKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D +    A+ N  ++++++G   + +H R         ++     + ++DI+ E+K+ 
Sbjct: 145 GWDSE-HIYAVEN-ARAVERAGGQAVSVHGRT--------REQLYTGHANWDIIKEVKEA 194

Query: 186 NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSS 241
                IG NG +     A ++  L + DGVMIGR A  N  ML    EY      L   S
Sbjct: 195 VSIPVIG-NGDVASPEDARRMLDLTNCDGVMIGRGALGNPWMLYRTIEYLQTGELLPDPS 253

Query: 242 P-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           P  K R+      ++ A   +  A        ++++ +H+     GF  S R + ++  E
Sbjct: 254 PEEKIRIAILHMDRLVALKGEAVA--------VREMRKHLAWYLKGFKGSARIKDVIMEE 305


>gi|283795849|ref|ZP_06345002.1| tRNA-dihydrouridine synthase [Clostridium sp. M62/1]
 gi|291076480|gb|EFE13844.1| tRNA-dihydrouridine synthase [Clostridium sp. M62/1]
 gi|295091061|emb|CBK77168.1| tRNA-U20-dihydrouridine synthase [Clostridium cf. saccharolyticum
           K10]
          Length = 319

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 83/320 (25%), Positives = 152/320 (47%), Gaps = 29/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+ TEM+ A A+L  ++  K +L    +E+P+A+Q+ G+D
Sbjct: 19  MAGVTDLPFRILCRE-QGCGLMCTEMVSAKALLYKNRNTKPLLETKPEERPVAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A ++E+  Y+ I++N+GCP  ++     G+ LM NP + G+ ++AM + L  P
Sbjct: 78  PEIMSEMALMLEEGPYDIIDVNMGCPVPKIVNNGEGSALMKNPKLAGEILSAMTRKLKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D+  +V      K  ++SG   + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFNDE--SVNAVEFAKMAEQSGAAAVAVHGRT--------REQFYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN- 235
           + ++K+      IG NG +     A +++     DGVM+ R A  N  + + +D Y    
Sbjct: 188 IRQVKEAVSIPVIG-NGDIFTPQDAGRMMEETGCDGVMVARGAKGNPWIFSRIDHYLKTG 246

Query: 236 ---PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P  G   +K  + +     + A   +Y A        ++++ +H+     G+P+S  
Sbjct: 247 EVLPKQGPEEVKQMILRHA-ELLVAFKGEYTA--------MREMRKHVSWYTAGYPHSAA 297

Query: 293 CRHILTVEAGASTATHHIIE 312
            R+ + +       T  ++E
Sbjct: 298 LRNEINLVETMEELTELVLE 317


>gi|78186164|ref|YP_374207.1| dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           luteolum DSM 273]
 gi|78166066|gb|ABB23164.1| tRNA-U20-dihydrouridine synthase [Chlorobium luteolum DSM 273]
          Length = 354

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/308 (27%), Positives = 146/308 (47%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE + A+A+ RG +K +  L     E+PLA+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKRHGAD-IVYTEFVSAEALRRGIEKTVRKLKADPVERPLAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I E+F  + +++N GCP+ +V     GA L+  P+ +     A+ KA+ +P
Sbjct: 76  VESMVEAAVIAEEFQPDYLDINFGCPTKKVAGKGAGAALLKEPEKMAAIAEAVVKAVRLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VT K RIG D +  ++ + ++++ ++ +G+  + +H R    + KG +          D+
Sbjct: 136 VTAKTRIGWDHE--SINILDVLRRLEDAGIQALALHGRTRSDMYKGKA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E K+      I  NG +     AL++      DGVMIGR +  N  + +       
Sbjct: 184 GWIAEAKRHARIPLIA-NGDVWSPEDALRMFLETGADGVMIGRGSIGNPFIFSGTKHLLK 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRR 292
              TG+ P       DF  +I A++          G K    ++ RH      G P    
Sbjct: 243 ---TGTPPPPP----DFRLRIKAAIEHLQLSVEFKGEKYGTLEMRRHYATYLKGLPKVSV 295

Query: 293 CRHILTVE 300
            R+ L  E
Sbjct: 296 VRNKLVRE 303


>gi|224537320|ref|ZP_03677859.1| hypothetical protein BACCELL_02198 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521051|gb|EEF90156.1| hypothetical protein BACCELL_02198 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 329

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 91/307 (29%), Positives = 143/307 (46%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSADALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE+   + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEEARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +   L  VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDITSPQRAKECFDLYGVDAIMIGRASFGRPWIFKEVRHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+         R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSAEWKLSVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRETR 302


>gi|289422453|ref|ZP_06424296.1| tRNA-dihydrouridine synthase B [Peptostreptococcus anaerobius
           653-L]
 gi|289157025|gb|EFD05647.1| tRNA-dihydrouridine synthase B [Peptostreptococcus anaerobius
           653-L]
          Length = 319

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/303 (29%), Positives = 144/303 (47%), Gaps = 23/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L    LLYTEMI A A+   D+  K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKEL-GCGLLYTEMINAKALCYDDQNTKKMLNILDEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI+ D+    +++N+GCP+ +V +   G+ LM NP +  D +  + K  + P
Sbjct: 76  PEYMGRAAKILNDYPNEILDINMGCPAPKVIKNGDGSALMKNPKLAADVLTNVVKNSNKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G++ I +H R         ++       D+DI
Sbjct: 136 VTLKIRKGWDDD--SVNAVEIAKIAEDCGIDAIAVHGRT--------REQFYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K       IG NG +  +   +KI  + + D VMIGR A  N  +   +D Y    
Sbjct: 186 IGQVKNAVSIPVIG-NGDIVSVEDVVKIREMTNCDAVMIGRGAQGNPWIFKRIDHYLK-- 242

Query: 237 LTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            TG   P  T+ DK     I+      A +       ++++ +H+     G  NS R R 
Sbjct: 243 -TGEILPGPTKEDK---INIAIKHMGLAVKEHGEYVAVREMRKHIGWYLKGMKNSARFRD 298

Query: 296 ILT 298
           ++ 
Sbjct: 299 MIN 301


>gi|291526252|emb|CBK91839.1| tRNA-U20-dihydrouridine synthase [Eubacterium rectale DSM 17629]
          Length = 328

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/299 (27%), Positives = 143/299 (47%), Gaps = 23/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L    +EKP++LQ+ G+D
Sbjct: 25  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTESLLSIDEREKPVSLQMFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ +++N+GCP  ++     G+ LM NP + G  I ++ KA+  P
Sbjct: 84  PQIMAQIAKQIEERPFDILDINMGCPVPKIVNNGEGSALMKNPILAGRIIESIVKAIDKP 143

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD+ + AV L ++    ++SG + + +H R         ++       D+D
Sbjct: 144 VTVKIRKGFDDEHVNAVELAHVA---EESGASAVAVHGRT--------REQYYSGKADWD 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG L      +K+      DG MI R A  N  + + +  YF  
Sbjct: 193 IIRQVKEAVSIPVIG-NGDLLCAEDVIKMQEQTGCDGFMIARGAQGNPWIFSQILHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P    V +   R  +  M ++   +      + ++ +H      G+P+S R R
Sbjct: 252 GEHQEKPSFEEVRRMILRH-ARMMIEFKGEYT----GIHEMRKHTAWYTAGYPHSSRLR 305


>gi|224025557|ref|ZP_03643923.1| hypothetical protein BACCOPRO_02297 [Bacteroides coprophilus DSM
           18228]
 gi|224018793|gb|EEF76791.1| hypothetical protein BACCOPRO_02297 [Bacteroides coprophilus DSM
           18228]
          Length = 327

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 144/307 (46%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K +L    S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSADALIRSVSKTLLKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     G+ L+ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQAKPDILDLNFGCPVKRVAGKGAGSGLLQNIPKMLEITRAVVNAVRIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAEHKIIV--PLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD +M+GRA++    +   +  +  
Sbjct: 187 IGEVKN-NPRMRIPIIGNGDVTTPQRAQECFDRYGVDAIMVGRASFGRPWIFKEIKHFLQ 245

Query: 235 NPLTGSS--PIKTRVDKDFWR---KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+  +   D  R   K S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFQWRMDVLRQEVKDSVALLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRDTR 302


>gi|317504340|ref|ZP_07962326.1| tRNA-dihydrouridine synthase [Prevotella salivae DSM 15606]
 gi|315664531|gb|EFV04212.1| tRNA-dihydrouridine synthase [Prevotella salivae DSM 15606]
          Length = 335

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 147/303 (48%), Gaps = 28/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +  +  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRMLCKRY-GAAMVYTEFVSADAIIRSIKSTLDKMSINDAERPVGVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I+LN GCP  +V     G+ ++ N  ++ D    + +A+S P
Sbjct: 77  VESMVEAARIVERVNPDLIDLNFGCPVKKVAGKGAGSGMLRNIPLLLDITRNVVQAVSTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--SLVITELAEQLQDCGIKALTIHGRT--------RAQMYTGEADWRL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K+ NP + I +  NG +    +A +      VD VM+GRA +    +   + +Y  
Sbjct: 187 IGEVKR-NPRIHIPIIGNGDITTPEEAKRAFDDYGVDAVMVGRATFGRPWVFKEMRDYID 245

Query: 235 NPLTGSSPIKTRVD-KDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
           N  + +  +  ++D  +   +I+    D     +H+        RH+    +F G P+ +
Sbjct: 246 NTPSTALTLDDKIDILEEQLRINVERIDEYRGIIHT-------RRHLASSPIFKGIPDFK 298

Query: 292 RCR 294
             R
Sbjct: 299 STR 301


>gi|307243172|ref|ZP_07525345.1| TIM-barrel protein, nifR3 family [Peptostreptococcus stomatis DSM
           17678]
 gi|306493433|gb|EFM65413.1| TIM-barrel protein, nifR3 family [Peptostreptococcus stomatis DSM
           17678]
          Length = 319

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 145/317 (45%), Gaps = 25/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L    LLYTEMI A A+   DK  K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKEL-GCGLLYTEMINAKALCYDDKNTKKMLNILDEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+I+ D+    +++N+GCP+ +V +   G+ LM NP + G  +  + K    P
Sbjct: 76  PEFMGKAAQILNDYPNEILDINMGCPAPKVVKNGDGSALMRNPKLAGQVLDQVVKNSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G+  I IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDDN--SVNALEIAKIAEDCGICAITIHGRT--------REQYYSGQADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K +     IG NG +  +  A++I      D +MIGR A  N  +   +D Y    
Sbjct: 186 IGEVKSQISIPVIG-NGDVTSVEDAIRIKDHTGCDAIMIGRGAQGNPWIFKRIDHYMKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
                P      KD    I+    D A +       ++++ +H+     G  +S R R  
Sbjct: 245 QLLDPP-----SKDEKIDIAIKHMDLAIKEHGEYVAVREMRKHIGWYLKGMKHSARLRDQ 299

Query: 295 --HILTVEAGASTATHH 309
             H++T +    T   +
Sbjct: 300 INHMVTAKEVIDTLNQY 316


>gi|254881117|ref|ZP_05253827.1| dehydrogenase [Bacteroides sp. 4_3_47FAA]
 gi|294777525|ref|ZP_06742976.1| TIM-barrel protein, nifR3 family [Bacteroides vulgatus PC510]
 gi|319640124|ref|ZP_07994851.1| hypothetical protein HMPREF9011_00448 [Bacteroides sp. 3_1_40A]
 gi|254833910|gb|EET14219.1| dehydrogenase [Bacteroides sp. 4_3_47FAA]
 gi|294448593|gb|EFG17142.1| TIM-barrel protein, nifR3 family [Bacteroides vulgatus PC510]
 gi|317388402|gb|EFV69254.1| hypothetical protein HMPREF9011_00448 [Bacteroides sp. 3_1_40A]
          Length = 329

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 145/304 (47%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K +  L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSADALIRSVGKTMQKLNINDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  RV     GA ++ N  ++ +   A+   + IP
Sbjct: 77  TETMVEAAKIVEEAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDTVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNEHKIIV--DLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDITTPQRAKECFDQYGVDAIMIGRASFGRPWIFKEVKHYIE 245

Query: 235 NPLTGSSPIKTRVDKDFWR--KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG        +   WR   +   + D +   L     +  + RH+    LF G PN 
Sbjct: 246 ---TGKELPALSFE---WRLNVLRQEVLD-SVNLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           +  R
Sbjct: 299 KETR 302


>gi|300727518|ref|ZP_07060909.1| TIM-barrel protein, NifR3 family [Prevotella bryantii B14]
 gi|299775221|gb|EFI71822.1| TIM-barrel protein, NifR3 family [Prevotella bryantii B14]
          Length = 333

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 93/330 (28%), Positives = 155/330 (46%), Gaps = 35/330 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K   N +     E+P+ +QI G +
Sbjct: 18  MEDVTDIGFRKLCKRY-GAAMMYTEFVSADAIIRSIKSTLNKMIIDDDERPVGIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE F  + I++N GCP  +V     GA L+ N  ++ D    + +A+++P
Sbjct: 77  VESMVEAAKIVEQFHPDVIDINFGCPVKKVAGKGAGAGLLRNIPLMLDIAKHVVEAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D     + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTAKTRLGWDQD--NLVITDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + E+KK NP + I +  NG +   E+  +A      VD VM+GRA +    +   + +Y 
Sbjct: 187 IGEVKK-NPRIHIPIIGNGDITTPEECKRAFDDF-GVDAVMVGRATFGRPWIFKEIRDYL 244

Query: 234 S-NPLTGSSPIKTRVD-KDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
              P      I  ++D  +   KI+    D     LH+        RH+    +F G P+
Sbjct: 245 DGKPDDKLLDINKKIDILEEQLKINVERIDEYRGILHT-------RRHLAASPIFKGIPD 297

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMI 319
            ++ R    +    +T T  +IE   N  I
Sbjct: 298 FKQTR----IAMLRATKTDDLIEILENCRI 323


>gi|78044326|ref|YP_361166.1| nifR3 family TIM-barrel protein [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996441|gb|ABB15340.1| putative TIM-barrel protein, NifR3 family [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 321

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 85/304 (27%), Positives = 146/304 (48%), Gaps = 27/304 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   +      L  TEMI   A+L G+ K   ++    +  P+A+QI G+ 
Sbjct: 19  MAGVTDKAFRLICQSF-GAGLTVTEMINDLALLHGNSKTRQMIDLQGEAMPVAVQIFGSS 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             K+ EAA+IVE+ G + I++N+GCP+ ++ +   GA LML P++    + A+  A+S+P
Sbjct: 78  PEKMAEAARIVEEAGASMIDINMGCPAPKIVKNGEGAALMLKPELAEKIVMAVKNAVSVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R G DD    V      + ++ +G + I +H R         ++       D++I
Sbjct: 138 VSVKIRKGFDDN--TVNAIEFAQRMEAAGADLITVHGRT--------REQFYSGKADWEI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + K+   + +  NG ++   +A ++L    VD VMIGRA   N  ++  +  Y    
Sbjct: 188 IRRV-KQAVKVKVAGNGDVDSPQKAKEMLELTGVDFVMIGRAVMGNPWLIQQIVFYLERG 246

Query: 237 --LTGSSPI-KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
             L   SP  K  V    +  +     +Y A        ++++ +H    F G P + R 
Sbjct: 247 EILPKPSPQEKAEVALRHFEYLLKFKGEYIA--------VREMRKHGGWYFKGLPGASRL 298

Query: 294 RHIL 297
           R IL
Sbjct: 299 REIL 302


>gi|329770278|ref|ZP_08261666.1| tRNA-dihydrouridine synthase 1 [Gemella sanguinis M325]
 gi|328836836|gb|EGF86484.1| tRNA-dihydrouridine synthase 1 [Gemella sanguinis M325]
          Length = 335

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 132/234 (56%), Gaps = 17/234 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+   AIL  +KK  N+L    +E+PL+LQI G +I  LVEAAK V+ +   + I
Sbjct: 37  LVCAEMVSDKAILFNNKKTMNMLYIDPRERPLSLQIFGGEIDTLVEAAKYVDKNTEADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP  ++ +   G+ L+L+PD V + I+ +  ++S PVTVK R+G DD+   + + 
Sbjct: 97  DLNMGCPVPKITKVDAGSKLLLDPDKVYEVISRIVDSVSKPVTVKMRMGWDDE--HIFVM 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  ++ +++G + + IH R  + +  S K N       +D++ ++KKE     IG NG +
Sbjct: 155 DNARNAERAGASAVAIHGRTKV-QMYSGKAN-------WDVIRDVKKELKIPVIG-NGDV 205

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
                A K+L   + D VMIGRAA  N  ML    +Y  +  LT     + ++D
Sbjct: 206 TTPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLETGELTPEPTPREKID 259


>gi|219121503|ref|XP_002185974.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582823|gb|ACI65444.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 321

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 85/267 (31%), Positives = 124/267 (46%), Gaps = 46/267 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  T+RHYR+F RL +    LYTEM+ A  I++  ++          P+ LQIGG D  
Sbjct: 62  MMGHTNRHYRYFVRLFSERTHLYTEMVPASQIVQAFRR---------APVVLQIGGGDPE 112

Query: 61  KLVEAAKIVEDFGYN-EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA----- 114
            L +AA I   +G   +INLN GCPS  V   S GA LM +P  V  C+ AM +      
Sbjct: 113 VLRQAAAIGAAYGGYVDINLNCGCPSNAVRGRSAGAALMRDPSHVAHCVEAMQEGIFEMG 172

Query: 115 -----LSIPVTVKCRIGV--------------DDQIPAVALRNLVKSIKKSG-VNGIWIH 154
                L   VTVK R+GV              DD     + R  V +I  +G V    +H
Sbjct: 173 QGTNKLKPNVTVKHRLGVRDAATFDASADRSKDDAEAYRSCRQFVNAIALTGAVAKCHVH 232

Query: 155 ARKAILKGLSPK--DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP---- 208
           AR  +L   +P    NR +P L   IV ++ ++ P +    NGG++ + +  +++     
Sbjct: 233 ARYGLLGDFTPTTIQNRNVPPLRPSIVNQLAEDFPSVEFVTNGGVKSLDEVSQVVRGGRH 292

Query: 209 -----SVDGVMIGRAAYKNSAMLTTVD 230
                +V G M+GRAA  +       D
Sbjct: 293 GSGVNNVVGAMVGRAAINHPCSFAAAD 319


>gi|189347606|ref|YP_001944135.1| TIM-barrel protein, nifR3 family [Chlorobium limicola DSM 245]
 gi|189341753|gb|ACD91156.1| TIM-barrel protein, nifR3 family [Chlorobium limicola DSM 245]
          Length = 347

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 87/328 (26%), Positives = 147/328 (44%), Gaps = 33/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE I A+A+ RG +K +  L     E+P+A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKRCGAD-IVYTEFISAEALRRGVEKTMRKLAVDEIERPVAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++EAA + E +  + +++N GCP+ +V     GA L+  P+ +     A+ K++ IP
Sbjct: 76  VESMIEAAAVAETYNPDFLDINFGCPTKKVAGKGAGAALLREPEKMQAIAEAVVKSVGIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VT K RIG D    ++ +  ++  ++ +G+  + IH R    + KG +          D 
Sbjct: 136 VTAKTRIGWDHD--SINIIEVLHRLEDAGIRALAIHGRTRSDMYKGRA----------DR 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E K+E     I  NG +     AL +      DGVMIGR +  N  + +       
Sbjct: 184 ERIAEAKREASIPVIA-NGDIWSAEDALAMFDQTGADGVMIGRGSIGNPFIFSQAKHLIR 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRR 292
                  P        F  +I A++        + G K    ++ RH      G P   +
Sbjct: 243 TGTPAPPP-------GFRERIHAAIEHLKLSVQYKGEKYGNLEMRRHYATYLKGLPKVSQ 295

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIE 320
            R+ L  E G      HI+E      +E
Sbjct: 296 VRNKLVREDG----WEHIVEILLAYEVE 319


>gi|299142013|ref|ZP_07035147.1| dehydrogenase [Prevotella oris C735]
 gi|298576475|gb|EFI48347.1| dehydrogenase [Prevotella oris C735]
          Length = 336

 Score =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 84/305 (27%), Positives = 147/305 (48%), Gaps = 32/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +  +  E+P+ +QI G +
Sbjct: 18  MEDVTDIGFRMLCKRY-GAAMVYTEFVSADAIIRSIKSTLDKMTINDAERPVGIQIYGRN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I+LN GCP  +V     G+ ++ N  ++ D    + KA+S P
Sbjct: 77  VESMVEAAKIVEQVKPDLIDLNFGCPVKKVAGKGAGSGMLRNIPLLLDITRNVVKAVSTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--SLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++ K NP + I +  NG +    +A +      VD VM+GRA +    +   + ++  
Sbjct: 187 IGKV-KSNPRIHIPIIGNGDITTPEEAKRAFDDYGVDAVMVGRATFGRPWVFKEMRDFID 245

Query: 235 NPLTGSSPIKTRVDKDFWR---KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPN 289
           N  T SSP+      D      +I+    D     +H+        RH+    +F G P+
Sbjct: 246 N--TTSSPLTIDDKIDILEEQLRINVERIDEYRGIIHT-------RRHLASSPIFKGIPD 296

Query: 290 SRRCR 294
            ++ R
Sbjct: 297 FKQTR 301


>gi|153853506|ref|ZP_01994886.1| hypothetical protein DORLON_00875 [Dorea longicatena DSM 13814]
 gi|149753661|gb|EDM63592.1| hypothetical protein DORLON_00875 [Dorea longicatena DSM 13814]
          Length = 318

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 88/302 (29%), Positives = 145/302 (48%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K  K +L    +E P++LQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGAGLLCMEMISAKALQYKNKNTKALLAIHPEEYPVSLQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK++E+  +  +++N+GCP  +V     G+ LM NP +V + ++A+ KA+  P
Sbjct: 76  PKIMSEMAKMIEELPFQILDINMGCPVPKVVRNGEGSALMKNPKLVHEIVSAVSKAIEKP 135

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  DD I AV    + K I+ +G   + +H R         ++       D+D
Sbjct: 136 VTVKIRKGFDDDHINAV---EIAKIIEDAGGAAVAVHGRT--------REQYYSGKADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +AL++      DGVMIGR A  N  +   + EY   
Sbjct: 185 IIRQVKEAVSIPVIG-NGDVISGEKALQMRRETGCDGVMIGRGAQGNPWIFHELQEYER- 242

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG  P +   +     KI  +M  +A   +   G    ++++ +H+     G   S +
Sbjct: 243 --TGVVPPRPTPE-----KIKETMLRHARLQIEFKGDFIGIREMRKHVAWYTKGMKGSAK 295

Query: 293 CR 294
            R
Sbjct: 296 LR 297


>gi|160893102|ref|ZP_02073890.1| hypothetical protein CLOL250_00648 [Clostridium sp. L2-50]
 gi|156865185|gb|EDO58616.1| hypothetical protein CLOL250_00648 [Clostridium sp. L2-50]
          Length = 317

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 83/300 (27%), Positives = 149/300 (49%), Gaps = 29/300 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           D+ +R  A+    + +LYTEMI A  +   +K  +  L  S +E P+ +Q+ G+D   L 
Sbjct: 17  DQPFRLLAKEQGCD-ILYTEMISAKGLYYDNKNTVPLLAVSPEEDPIGVQLFGSDPELLA 75

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E AK +ED G+  +++N+GCP  ++     G+ LM NP ++G  ++AM KA  +PVT+K 
Sbjct: 76  EMAKKIEDRGFAFVDVNMGCPVPKIVNNGEGSALMKNPLLIGKIVSAMTKACKLPVTIKI 135

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G D +   +    +    ++SGV  + +H R         ++     + D+ ++ ++K
Sbjct: 136 RSGFDSE--HINAPEVAHIAEESGVAAVAVHGRT--------REQYYHGHADWGVIADVK 185

Query: 184 KENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                  IG NG +   ED+ + +K   + D  MIGR A  N  +   +  YF    TG 
Sbjct: 186 AAVNIPVIG-NGDILTPEDVIR-MKEQTNCDAFMIGRGARGNPWIFHELKTYFE---TGE 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRRCRHIL 297
            P   R DK   +++  +M  +A   +   G+   + ++ +H+     G  +S R R+++
Sbjct: 241 IP--PRPDK---QQVKETMLRHARLMIDFKGEFTGIHEMRKHVAWYSAGMYDSSRLRNLI 295


>gi|332826846|gb|EGJ99646.1| hypothetical protein HMPREF9455_03909 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 330

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 85/305 (27%), Positives = 151/305 (49%), Gaps = 31/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G +
Sbjct: 18  MEDVTDMGFRLMCKRFGAD-MVYTEFVSSDALIRHVNKTQAKLTISEEERPVAIQIYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKI E+   + +++N GCP  +V     G+ +M  P+++ +  AA+ KA++IP
Sbjct: 77  VDAMVEAAKICEEASPDILDINFGCPVKKVAGKGAGSGMMRTPELMVEITAAVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    L + ++ +G+  + +H R         +        D+ +
Sbjct: 137 VTVKTRLGWDNDSKIIV--ELAEQLQDTGIQALTLHGRT--------RAQMYSGEADWSL 186

Query: 179 VYEIKKENPDLFIGLNGG----LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP + I + G       ++ +       VD VMIGR +     +   V  Y +
Sbjct: 187 IGAVKN-NPRMHIPIIGNGDVTTPEICKRRFDETGVDAVMIGRGSIGGPWIFEEVKHYLA 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHL-HSG--GKLQQITRHMIG--LFHGFPN 289
              TG    K    K+F   +   + D  +R++ HSG  G +    RH+ G  +F G P+
Sbjct: 246 ---TGELMPK----KEFTWYLDV-LKDLVSRNIAHSGERGGIIHSRRHLAGSPVFKGIPD 297

Query: 290 SRRCR 294
            ++ R
Sbjct: 298 FKKVR 302


>gi|323485860|ref|ZP_08091195.1| hypothetical protein HMPREF9474_02946 [Clostridium symbiosum
           WAL-14163]
 gi|323400848|gb|EGA93211.1| hypothetical protein HMPREF9474_02946 [Clostridium symbiosum
           WAL-14163]
          Length = 319

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 82/300 (27%), Positives = 141/300 (47%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+ TEM+ A A+L  ++  K IL    QE+P+A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGCGLMCTEMVSAKALLYNNRNTKPILAVREQERPVAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E+  Y+ I++N+GCP  ++     G+ LM NP++    + +M K L  P
Sbjct: 78  PDIMSDMALRLEEGPYDIIDVNMGCPVPKIVNNGEGSALMKNPELAEAILTSMVKKLHKP 137

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  + AV    + +S    GV+ + +H R         ++       D+D
Sbjct: 138 VTVKFRKGFDDSCVNAVEFARMAES---CGVSAVAVHGRT--------REQYYSGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +     A ++  L   DGVM+ R A  N  +   ++ Y   
Sbjct: 187 IIRQVKEAVKIPVIG-NGDIFTPQDAKRMIDLTGCDGVMVARGAKGNPWLFGRINHYLDT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P +  +     R      T++   H+     ++++  H+     G+PNS   R+
Sbjct: 246 GILLPPPDREELKATIIRH-GRLQTEFKGEHI----AMREMRGHVAWYTAGYPNSSSLRN 300


>gi|332970947|gb|EGK09921.1| tRNA-dihydrouridine synthase [Desmospora sp. 8437]
          Length = 335

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 123/232 (53%), Gaps = 17/232 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  AR      L+  EM+   AIL G+   K +L    +EKPL+LQI G D   LVEAA
Sbjct: 30  FRLIAREF-GTGLVCAEMVSDKAILHGNARTKKMLLVDEREKPLSLQIFGGDKETLVEAA 88

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           ++V+     + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +A+  PVTVK R 
Sbjct: 89  RVVDKQTNADIIDINMGCPVPKVIKCDAGARWLLDPNKIEEMVSAVVEAVDKPVTVKMRT 148

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D+     A+ N  K+++++G   + +H R         +        D+DI+ ++K+ 
Sbjct: 149 GWDEN-HIYAVEN-AKALERAGAQAVSLHGRT--------RQQMYTGKADWDIIRQVKEA 198

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
                IG NG ++    A ++L +   DGVMIGRAA  N  ML     Y S 
Sbjct: 199 VKIPVIG-NGDVQTPQDAKRMLDTTGCDGVMIGRAALGNPWMLYRTIHYLST 249


>gi|189501100|ref|YP_001960570.1| TIM-barrel protein, nifR3 family [Chlorobium phaeobacteroides BS1]
 gi|189496541|gb|ACE05089.1| TIM-barrel protein, nifR3 family [Chlorobium phaeobacteroides BS1]
          Length = 346

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 90/308 (29%), Positives = 143/308 (46%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE + A+A+ RG  K+I  + F   E+P  +QI G  
Sbjct: 17  MEDVTDRSFRKICKRFGAD-IVYTEFVSAEALRRGVGKSIQKMLFEESERPAVIQIFGNS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA I      + +++N GCP+ +V     GA L+  P+ +    AA+ KA+SIP
Sbjct: 76  GEAMAEAAVIAASAKPDYLDINFGCPAKKVAGKGAGAALLREPEKMAAITAAVVKAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK RIG D    +V + +++  ++ +G+  I +H   R  + KG +          D+
Sbjct: 136 VTVKTRIGWDRD--SVNILDIIPRLEDAGIAAIAVHGRTRSEMYKGRA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  + KE+  + +  NG +     AL +      DG+MIGR A  N  +   V E   
Sbjct: 184 DWIARV-KEHAKIPVIANGDIWSPQDALAMFSHTGADGIMIGRGAIGNPFIFRQVKELLQ 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRR 292
                + P       DF  +IS ++   +    H G K    ++ RH      G P   R
Sbjct: 243 GGAVTTLP-------DFRDRISVAIEHLSLSVEHKGEKYGTLEMRRHYSTYLKGLPRVSR 295

Query: 293 CRHILTVE 300
            R  L  E
Sbjct: 296 VRDKLVRE 303


>gi|145632062|ref|ZP_01787801.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
 gi|144982266|gb|EDJ89879.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
          Length = 152

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 83/141 (58%), Gaps = 9/141 (6%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L+K  K+ G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++
Sbjct: 7   LLKRFKEKGSKEFIIHARKAWLSGLSPKENREIPPLDYIRVYQLKRDFPHLTIAINGGIK 66

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            + +  + L  VDGVM+GR AY+N ++L  +D+   +P   ++PI T        +   S
Sbjct: 67  TIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---NAPIVTA------HEAVES 117

Query: 259 MTDYAARHLHSGGKLQQITRH 279
           M  Y  + L  G  L  I RH
Sbjct: 118 MLPYIEQQLSQGIHLNHIVRH 138


>gi|189459730|ref|ZP_03008515.1| hypothetical protein BACCOP_00358 [Bacteroides coprocola DSM 17136]
 gi|189433577|gb|EDV02562.1| hypothetical protein BACCOP_00358 [Bacteroides coprocola DSM 17136]
          Length = 328

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 143/307 (46%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K +L    S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLLCKEFGAD-MVYTEFVSSDALIRSVGKTMLKLNISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     G+ ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQANPDILDLNFGCPVKRVAGKGAGSGMLQNVPKMLEITKAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAEHKIIV--ELAEQLQDCGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPQRAQECFDRYGVDAIMIGRASFGRPWIFKEVKHYLK 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+  +   D  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFKWKMDVLRREVQDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN +  R
Sbjct: 296 PNFKDTR 302


>gi|253576834|ref|ZP_04854159.1| tRNA-dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251843701|gb|EES71724.1| tRNA-dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 333

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/297 (28%), Positives = 146/297 (49%), Gaps = 22/297 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL G+K+   +L    +EKPL+LQI G D + LVEAA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAILHGNKRTREMLFVDEREKPLSLQIFGGDRASLVEAA 84

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V ++   + I++N+GCP  +V +   GA  +L+P+ + + +AA+  A+S PVTVK RI
Sbjct: 85  KVVDQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVAAVVDAVSKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D +   + + +  K+++++G   + +H R         ++       D+  + ++K+ 
Sbjct: 145 GWDAE--HIYVVDNAKAVERAGGKAVSVHGRT--------REQLYTGKADWSYIRQVKEA 194

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
                IG NG +     A ++L     DGVMIGR A  N  ML    EY    +    P 
Sbjct: 195 VSIPVIG-NGDVATPEDAKRMLDETGCDGVMIGRGALGNPWMLYRTVEYLKTGVLLPEP- 252

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               D +   +I+    D  A        ++++ +H+     G   + R + ++  E
Sbjct: 253 ----DAEEKIRIAILHMDRLAALKGELVAVREMRKHLAWYLKGLKGAARIKDLIMEE 305


>gi|315606822|ref|ZP_07881831.1| tRNA-dihydrouridine synthase B [Prevotella buccae ATCC 33574]
 gi|315251487|gb|EFU31467.1| tRNA-dihydrouridine synthase B [Prevotella buccae ATCC 33574]
          Length = 321

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/302 (28%), Positives = 144/302 (47%), Gaps = 36/302 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G  
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRSIKSTVSKLTISDEERPVGIQIYGRT 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  +V     GA ++ N  ++ D    + KA+ +P
Sbjct: 77  VEDMVEAARIVEQARPDVIDINFGCPVKKVAGKGAGAGMLKNVPLMLDITREVVKAVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDSN--NLIISELAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +  +++A +      VD VMIGRA +    + +       
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDIGSIAEAHEAFDRYGVDAVMIGRATFGQPWLFS------E 239

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
            PLT     K  V ++  R     + +Y    LH+        RH+    +F G PN R+
Sbjct: 240 QPLTYEE--KIGVLEEQLRINVERIGEYRG-ILHT-------RRHLAASPIFKGIPNFRQ 289

Query: 293 CR 294
            R
Sbjct: 290 TR 291


>gi|288925390|ref|ZP_06419324.1| TIM-barrel protein, putative, NifR3 family [Prevotella buccae D17]
 gi|288337861|gb|EFC76213.1| TIM-barrel protein, putative, NifR3 family [Prevotella buccae D17]
          Length = 321

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/302 (28%), Positives = 144/302 (47%), Gaps = 36/302 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G  
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRSIKSTVSKLTISDEERPVGIQIYGRT 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  +V     GA ++ N  ++ D    + KA+ +P
Sbjct: 77  VEDMVEAARIVEQARPDVIDINFGCPVKKVAGKGAGAGMLKNVPLMLDITREVVKAVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDSN--NLIISELAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +  +++A +      VD VMIGRA +    + +       
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDIGSIAEAHEAFDRYGVDAVMIGRATFGQPWLFS------E 239

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
            PLT    I   V ++  R     + +Y    LH+        RH+    +F G PN R+
Sbjct: 240 QPLTYEEKIG--VLEEQLRINVERIGEYRG-ILHT-------RRHLAASPIFKGIPNFRQ 289

Query: 293 CR 294
            R
Sbjct: 290 TR 291


>gi|282880523|ref|ZP_06289230.1| TIM-barrel protein, nifR3 family [Prevotella timonensis CRIS 5C-B1]
 gi|281305626|gb|EFA97679.1| TIM-barrel protein, nifR3 family [Prevotella timonensis CRIS 5C-B1]
          Length = 327

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 89/330 (26%), Positives = 156/330 (47%), Gaps = 30/330 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     +++YTE + A+A++R  K   N L    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GVSMVYTEFVSAEALVRSIKSTVNKLTICEEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IV     + I+LN GCP  +V     GA ++ N  ++ +    + KA+ IP
Sbjct: 77  VASMVEAAQIVAQSKPDVIDLNFGCPVKKVAGKGAGAGMLQNIPLMLEITREVVKAVHIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAS--HLIITELAEQLQDCGIQALTIHGRT--------RSQMYTGKADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF- 233
           + E+KK NP + I +  NG +    +A     +  VDGVM+GRA++    +   +  Y  
Sbjct: 187 IGEVKK-NPRIHIPIIGNGDITSAEEAKHAFETYGVDGVMVGRASFGCPWIFKEMRNYLD 245

Query: 234 SNPLTGSSPIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
             P   S  +  ++D    +  I+ +  D     LH+        RH+    +F G P+ 
Sbjct: 246 GKPSDESFDLNKKLDILLEQLHINVARIDEYRGILHT-------RRHLAASPIFKGIPDF 298

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
           R+ R I  + A        I+E    ++++
Sbjct: 299 RQTR-IAMLRATTVKELEDILEKCREIIVK 327


>gi|169825710|ref|YP_001695868.1| tRNA-dihydrouridine synthase 1 [Lysinibacillus sphaericus C3-41]
 gi|168990198|gb|ACA37738.1| Probable tRNA-dihydrouridine synthase 1 [Lysinibacillus sphaericus
           C3-41]
          Length = 346

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 131/234 (55%), Gaps = 17/234 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+Y EMI    I++ ++K +  L    +E PL+LQI G D   LVEAAK V ++   + I
Sbjct: 44  LVYAEMISDKGIVQKNEKTLGMLYIDERENPLSLQIFGGDKETLVEAAKYVDQNTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA L+L+P+ V + +AA+  A+  P++VK RIG DD+    A+ 
Sbjct: 104 DINMGCPVNKIIKCEAGARLLLDPNKVYEMVAAVVDAVKKPISVKMRIGWDDE-HIFAIE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N  ++++++G + + +H R  + +    K N       +DI+ ++ KEN  + +  NG +
Sbjct: 163 N-AQAVERAGASAVAVHGRTRV-QMYEGKAN-------WDIIRQV-KENVKIPVLGNGDV 212

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP-IKTRVD 248
           E    A ++L +  VD VMIGRAA  N  M+    +Y         P ++ ++D
Sbjct: 213 ETPQDAKRMLETTGVDAVMIGRAALGNPWMIYRTVQYLETGELKEEPSVREKMD 266


>gi|89100493|ref|ZP_01173354.1| YacF [Bacillus sp. NRRL B-14911]
 gi|89084759|gb|EAR63899.1| YacF [Bacillus sp. NRRL B-14911]
          Length = 338

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 131/237 (55%), Gaps = 21/237 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EMI    I+  ++K  N+L    +EKPL+LQI G +   LVEAAK V E+   + 
Sbjct: 44  GLVCAEMISDKGIVMKNEKTMNMLYIDEREKPLSLQIFGGEKDTLVEAAKFVDENTNADI 103

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP  ++ +   GA  +L+PD + + ++A+  A+S PVTVK R+G DD     A+
Sbjct: 104 IDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVTAAVSKPVTVKMRMGWDDD-HIYAV 162

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           RN  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG N
Sbjct: 163 RN-AQAVERAGGKAVALHGRTRVQMYEGQA----------NWDIIKEVKQNISIPLIG-N 210

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G ++    A ++L    VDGVMIGRAA  N  M+    +Y  +  L     ++ ++D
Sbjct: 211 GDVQTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVKYLETGQLMDEPSVREKID 267


>gi|261403946|ref|YP_003240187.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. Y412MC10]
 gi|261280409|gb|ACX62380.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. Y412MC10]
          Length = 343

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 126/240 (52%), Gaps = 19/240 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D   LVEAA
Sbjct: 28  FRLIAKEF-GTGLVCAEMVSGKAIVHGNKRTQEMLFVDEREKPLSLQIFGGDRVSLVEAA 86

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V +    + I++N+GCP+ +V +   GA  +L+ + + + +AA+  A++ PVTVK R 
Sbjct: 87  KVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLDSNKIYEMVAAVVDAVNKPVTVKMRT 146

Query: 126 GVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G D D I AV      ++++++G   + +H R         +D     + D+DI+ ++K+
Sbjct: 147 GWDSDHIYAV---ENAQAVERAGGQAVSVHGRT--------RDQLYTGHADWDIIRQVKE 195

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                 IG NG +     A ++L +   DGVMIGR A  N  ML    EY       S P
Sbjct: 196 AVSIPVIG-NGDVVTPEDARRMLDTTGCDGVMIGRGALGNPWMLYRTVEYLKTGQLLSDP 254


>gi|306821056|ref|ZP_07454674.1| tRNA-dihydrouridine synthase [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550892|gb|EFM38865.1| tRNA-dihydrouridine synthase [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 329

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 126/243 (51%), Gaps = 23/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD  +R        N   +TEMI A A+   D+K   +L  S Q+K + +QI G++
Sbjct: 25  MAGFTDLPFRLICEEYGCN-FTFTEMINAKALCYHDEKTTQMLDVSGQKKYVGVQIFGSE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  + +A KI+ D   ++ I++N+GCP+ ++ +   G+ LM NP +    +    K  SI
Sbjct: 84  IEYIGKAVKIINDLERFSHIDINMGCPAPKIVKNGDGSALMKNPSLASKIVEEAKKNSSI 143

Query: 118 PVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNL 174
           PVTVK R G D+  I AV      K +++SG + I +H R  +    G++          
Sbjct: 144 PVTVKIRKGFDEHNINAV---EFAKMLEQSGADAITVHGRTTRQYYSGVA---------- 190

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           D+DI+ E+K+      IG NG ++    A +++   S D V+I RAA  N  +   +++Y
Sbjct: 191 DWDIIAEVKQAVKVPVIG-NGDVKSPEDAKRMMEYTSCDSVLIARAAQGNPFLFAQINDY 249

Query: 233 FSN 235
           F N
Sbjct: 250 FEN 252


>gi|294675099|ref|YP_003575715.1| hypothetical protein PRU_2465 [Prevotella ruminicola 23]
 gi|294473955|gb|ADE83344.1| putative TIM-barrel protein, NifR3 family [Prevotella ruminicola
           23]
          Length = 315

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/304 (27%), Positives = 143/304 (47%), Gaps = 40/304 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  I  L  S  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYTEFVSAEALIRDVKSTISKLTISDTERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE  G + I++N GCP  +V     GA ++ N   + +  + +  A+ +P
Sbjct: 77  VEAMVEAAKIVEQAGPDLIDINFGCPVKKVAGKGAGAGMLQNIPKMLEITSKVVDAVKLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G + +   + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWNHE--QLIITELAEQLQDCGIKALTIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K+ NP + I +  NG +  + +A +   +  VD +MIGRA +              
Sbjct: 187 IGEVKR-NPRIHIPIIGNGDIHSLDEADEAFKTYGVDAIMIGRATF-------------- 231

Query: 235 NPLTGSSPIKTRVDKDFWRK--ISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
               G   I +R + DF +K  I   +       +     +    RH+    +F G P+ 
Sbjct: 232 ----GCPWIFSREELDFNQKLDILEELLRINVERIDEKRGILHTRRHLAATPIFKGIPDF 287

Query: 291 RRCR 294
           R+ R
Sbjct: 288 RQTR 291


>gi|126653300|ref|ZP_01725411.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) protein [Bacillus sp. B14905]
 gi|126589974|gb|EAZ84103.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) protein [Bacillus sp. B14905]
          Length = 346

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 126/227 (55%), Gaps = 16/227 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+Y EMI    I++ ++K +  L    +E PL+LQI G D   LVEAAK V ++   + I
Sbjct: 44  LVYAEMISDKGIVQKNEKTLGMLYIDERENPLSLQIFGGDKETLVEAAKYVDQNTSADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA L+L+P+ V + +AA+  A+  P++VK RIG DD+    A+ 
Sbjct: 104 DINMGCPVNKIIKCEAGARLLLDPNKVYEMVAAVVDAVKKPISVKMRIGWDDE-HIFAIE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N  ++++++G + + +H R  + +    K N       +DI+ ++ KEN  + +  NG +
Sbjct: 163 N-AQAVERAGASAVAVHGRTRV-QMYEGKAN-------WDIIRQV-KENVKIPVLGNGDV 212

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           E    A ++L +  VD VMIGRAA  N  M+    +Y         P
Sbjct: 213 ETPQDAKRMLETTGVDAVMIGRAALGNPWMIYRTVQYLETGELKEEP 259


>gi|150392209|ref|YP_001322258.1| nifR3 family TIM-barrel protein [Alkaliphilus metalliredigens QYMF]
 gi|149952071|gb|ABR50599.1| putative TIM-barrel protein, nifR3 family [Alkaliphilus
           metalliredigens QYMF]
          Length = 321

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 84/304 (27%), Positives = 145/304 (47%), Gaps = 25/304 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +  + ++Y EM+ A  +  GDKK   +L    +EKP ALQI G++
Sbjct: 17  MAGVTDLPFRLICKKM-GSGMVYMEMVSAKGLYYGDKKTERLLQIHPEEKPAALQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++ D     +++N+GCP+ ++ +   G+ LML+P      + A+ +    P
Sbjct: 76  PDIMAKAAYMLNDRENIILDINMGCPTPKIVKNGDGSALMLDPPRAARVVKAVVRESIKP 135

Query: 119 VTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD QI AV    + K ++ SG   I +H R         ++       D+D
Sbjct: 136 VTVKIRKGWDDKQINAV---EMAKILEDSGAQAIAVHGRT--------REQFYSGKADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +  +  A  +L     DG+MIGR A  N  +   VD Y  N
Sbjct: 185 IIKQVKEAVTIPVIG-NGDVFSVEDARDMLEQTQCDGIMIGRGAQGNPWIFKRVDAYMKN 243

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               + P ++ RV+      +     D   ++      ++++ +H+     G  NS   R
Sbjct: 244 GEVLAEPGLEERVE------MILEHMDLVIKYKGEYIGIREMRKHVGWYLKGLKNSASIR 297

Query: 295 HILT 298
           +++ 
Sbjct: 298 NLIN 301


>gi|315644402|ref|ZP_07897542.1| TIM-barrel protein, nifR3 family [Paenibacillus vortex V453]
 gi|315280279|gb|EFU43571.1| TIM-barrel protein, nifR3 family [Paenibacillus vortex V453]
          Length = 343

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 125/234 (53%), Gaps = 21/234 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D   LVEAA
Sbjct: 28  FRLIAKEF-GTGLVCAEMVSGKAIVHGNKRTQEMLFVDEREKPLSLQIFGGDRDSLVEAA 86

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V +    + I++N+GCP+ +V +   GA  +LN + + + +AA+  A++ PVTVK R 
Sbjct: 87  KVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLNSNKIYEMVAAVVDAVNKPVTVKMRT 146

Query: 126 GVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G D D I AV      ++++++G   + +H R         ++     + D+DI+ ++K+
Sbjct: 147 GWDSDHIYAV---ENAQAVERAGGQAVSVHGRT--------REQLYTGHADWDIIRQVKE 195

Query: 185 ENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                 IG NG +   ED  + L I    DGVMIGR A  N  ML    EY  +
Sbjct: 196 AVSIPVIG-NGDVVTPEDARRMLDIT-GCDGVMIGRGALGNPWMLYRTIEYLKS 247


>gi|150003654|ref|YP_001298398.1| dehydrogenase [Bacteroides vulgatus ATCC 8482]
 gi|149932078|gb|ABR38776.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Bacteroides vulgatus ATCC 8482]
          Length = 329

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 85/304 (27%), Positives = 144/304 (47%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K +  L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSADALIRSVGKTMQKLNINDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AAKIVE+   + +++N GCP  RV     GA ++ N  ++ +   A+   + IP
Sbjct: 77  TETMVAAAKIVEEAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDTVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNEHKIIV--DLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDITTPQRAKECFDQYGVDAIMIGRASFGRPWIFKEVKHYIE 245

Query: 235 NPLTGSSPIKTRVDKDFWR--KISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG        +   WR   +   + D +   L     +  + RH+    LF G PN 
Sbjct: 246 ---TGKELPALSFE---WRLNVLRQEVLD-SVNLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           +  R
Sbjct: 299 KETR 302


>gi|325268625|ref|ZP_08135255.1| tRNA-dihydrouridine synthase B [Prevotella multiformis DSM 16608]
 gi|324989153|gb|EGC21106.1| tRNA-dihydrouridine synthase B [Prevotella multiformis DSM 16608]
          Length = 319

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 122/226 (53%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  +  +  +    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAIIRSIRSTLSKMVIDDRERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IVE  G + I++N GCP  +V     G+ ++ N  ++ +    + KA+ +P
Sbjct: 77  VASMVEAARIVEQAGPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLEITREVVKAVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G+  + IH R         +      + D+ +
Sbjct: 137 VTVKTRLGWDHD--HLIITDLAEQLQDCGIQTLTIHGRT--------RAQMYTGSADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAY 220
           + E+KK NP + I +  NG ++D+  A +      VD VMIGRA +
Sbjct: 187 IGEVKK-NPRIHIPVIGNGDVKDVGDAREKFDRYGVDAVMIGRATF 231


>gi|167763922|ref|ZP_02436049.1| hypothetical protein BACSTE_02304 [Bacteroides stercoris ATCC
           43183]
 gi|167698038|gb|EDS14617.1| hypothetical protein BACSTE_02304 [Bacteroides stercoris ATCC
           43183]
          Length = 325

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 142/304 (46%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKGFGAD-MVYTEFVSSDALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVADAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAGSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPQRAKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG    P+ +    +  R+      + + + L     +  + RH+    LF G PN 
Sbjct: 246 ---TGEEIPPLSSEWKLNVLRQ----EVEDSVKLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           R  R
Sbjct: 299 RETR 302


>gi|166030713|ref|ZP_02233542.1| hypothetical protein DORFOR_00387 [Dorea formicigenerans ATCC
           27755]
 gi|166029505|gb|EDR48262.1| hypothetical protein DORFOR_00387 [Dorea formicigenerans ATCC
           27755]
          Length = 318

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 85/302 (28%), Positives = 145/302 (48%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K  K +L    QE P++LQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGAGLLCMEMISAKALQYKNKNTKVLLAIHPQEYPVSLQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  +  +++N+GCP  +V +   G+ LM NP +V + ++ + KA+  P
Sbjct: 76  PKIISEQAKRIEDLPFQILDINMGCPVPKVVKNGEGSALMKNPKLVFEIVSQLVKAIEKP 135

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  DD I AV    + K  +++G + + +H R         ++       D+D
Sbjct: 136 VTVKIRKGFDDDHINAV---EIAKIAEEAGASAVAVHGRT--------REQYYSGEADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A  ++ +   DGVMIGR    N  +   + EY   
Sbjct: 185 IIRQVKEAVHIPVIG-NGDVTSAEKAAEMRKITGCDGVMIGRGVQGNPWIFRELAEYDR- 242

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG+ P +   +     +I   M  +A   L   G+   ++++ +H+     G   + +
Sbjct: 243 --TGTIPPRPTQE-----EIRNMMLRHARMQLEFKGEYLGIREMRKHVAWYVKGMKGAAK 295

Query: 293 CR 294
            R
Sbjct: 296 FR 297


>gi|323693199|ref|ZP_08107417.1| TIM-barrel protein [Clostridium symbiosum WAL-14673]
 gi|323502682|gb|EGB18526.1| TIM-barrel protein [Clostridium symbiosum WAL-14673]
          Length = 319

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 140/300 (46%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+ TEM+ A A+L  ++  K IL    +E+P+A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGCGLMCTEMVSAKALLYNNRNTKPILAVREEERPVAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E+  Y+ I++N+GCP  ++     G+ LM NP +    + +M K L  P
Sbjct: 78  PDIMSDMALRLEEGPYDIIDVNMGCPVPKIVNNGEGSALMKNPKLAEAILTSMVKKLHKP 137

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  + AV    + +S    GV+ + +H R         ++       D+D
Sbjct: 138 VTVKFRKGFDDSCVNAVEFARMAES---CGVSAVAVHGRT--------REQYYSGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +     A ++  L   DGVM+ R A  N  +   ++ Y   
Sbjct: 187 IIRQVKEAVKIPVIG-NGDIFTPQDAKRMIDLTGCDGVMVARGAKGNPWLFGRINHYLDT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P +  +     R      T++   H+     ++++  H+     G+PNS   R+
Sbjct: 246 GILLPPPDREELKATIIRH-GRLQTEFKGEHI----AMREMRGHVAWYTAGYPNSSSLRN 300


>gi|310639544|ref|YP_003944302.1| tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa SC2]
 gi|309244494|gb|ADO54061.1| tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa SC2]
          Length = 342

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 127/233 (54%), Gaps = 19/233 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D   LV+AA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAIIHGNKRTREMLFVDEREKPLSLQIFGGDRESLVKAA 84

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V ++   + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +++S PVTVK RI
Sbjct: 85  KVVDQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVVESVSKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D +    A+ N  ++++++G   + +H R         ++     + ++DI+ E+K+ 
Sbjct: 145 GWDSE-HIYAVEN-ARAVERAGGQAVSVHGRT--------REQLYTGHANWDIIKEVKEA 194

Query: 186 NPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                IG NG +   ED  + L  L   DGVMIGR A  N  ML    EY   
Sbjct: 195 VSIPVIG-NGDVVTPEDARRMLD-LTHCDGVMIGRGALGNPWMLYRTIEYLQT 245


>gi|21674741|ref|NP_662806.1| NifR3 family TIM-barrel protein [Chlorobium tepidum TLS]
 gi|21647952|gb|AAM73148.1| TIM-barrel protein, nifR3 family [Chlorobium tepidum TLS]
          Length = 352

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 82/308 (26%), Positives = 148/308 (48%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE I A+A+ RG +K+I  +  +  E+P+A+QI G  
Sbjct: 22  MEDVTDRAFRQLCKQHGAD-IVYTEFISAEALRRGVEKSIRKITVADHERPVAVQIFGNT 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I E +  + +++N GCP  +V     GA L+  P+ + +  +A+  A+S+P
Sbjct: 81  VESMVEAAAIAETYEPDYLDINFGCPVKKVAGRGAGAALLKEPEKLSEIASAVVNAVSLP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VT K RIG D    ++ + + V+ ++ +G+  + +H R    + KG +          D+
Sbjct: 141 VTAKTRIGWDHD--SINITDTVRRLEDAGIRAVAVHGRTRSDMYKGRA----------DW 188

Query: 177 DIVYEIKKENPDLFIGLNGG--LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E K+      I  NG   L + + A+      DG+MIGR +  N  +         
Sbjct: 189 GRIAEAKQACSIPVIA-NGDVWLPEDAVAMFERTGADGIMIGRGSIGNPFIFEQAKSLVK 247

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRR 292
             +  S+P        + ++I A++        + G K  + ++ RH      G P   +
Sbjct: 248 EGVRLSAP-------SYRQRIQAAVDHLRLSLEYKGEKYGVLEMRRHYSTYLKGLPGVSK 300

Query: 293 CRHILTVE 300
            R++L  E
Sbjct: 301 VRNLLVRE 308


>gi|260893702|ref|YP_003239799.1| TIM-barrel protein, nifR3 family [Ammonifex degensii KC4]
 gi|260865843|gb|ACX52949.1| TIM-barrel protein, nifR3 family [Ammonifex degensii KC4]
          Length = 326

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/248 (31%), Positives = 126/248 (50%), Gaps = 24/248 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R  AR      L +TEM+ A A+ R    +K++L F  +E  +A Q+ G+D
Sbjct: 22  MAGITDRAFRLVARE-GGARLCWTEMLPAPALARSSEARKHLLDFLGEEGVVA-QLFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA +VE+ G   ++LN+GCP  +V +   GA L+ +P      + A+C+ + +P
Sbjct: 80  PEEMAEAALVVEEAGAVAVDLNMGCPVEKVVKIGAGAALLRDPRQAAAIVEAVCRRVKVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R G D++ P      + + ++++G   + +H   R     G +          D+
Sbjct: 140 VTVKLRKGWDEKSPPAW--EMARLLEEAGAKALIVHGRYRHEFFGGRA----------DW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K+      IG NG +     AL++L S   DGVM+GRAA  N  + T    Y  
Sbjct: 188 EAIRRVKEAVKIPVIG-NGDVRTPEDALRMLASTGCDGVMVGRAARGNPWIFTRCQLY-- 244

Query: 235 NPLTGSSP 242
             L+G  P
Sbjct: 245 -SLSGEIP 251


>gi|329925512|ref|ZP_08280386.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. HGF5]
 gi|328939795|gb|EGG36135.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. HGF5]
          Length = 343

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 126/240 (52%), Gaps = 19/240 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D   LVEAA
Sbjct: 28  FRLIAKEF-GTGLVCAEMVSGKAIVHGNKRTQEMLFVDEREKPLSLQIFGGDRVSLVEAA 86

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V +    + I++N+GCP+ +V +   GA  +L+ + + + +AA+  A++ PVTVK R 
Sbjct: 87  KVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLDSNKIYEMVAAVVDAVNKPVTVKMRT 146

Query: 126 GVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G D D I AV      ++++++G   + +H R         ++     + D+DI+ ++K+
Sbjct: 147 GWDSDHIYAV---ENAQAVERAGGQAVSVHGRT--------REQLYTGHADWDIIRQVKE 195

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                 IG NG +     A ++L +   DGVMIGR A  N  ML    EY       S P
Sbjct: 196 AVSIPVIG-NGDVVTPEDARRMLDTTGCDGVMIGRGALGNPWMLYRTVEYLKTGQLLSDP 254


>gi|310658259|ref|YP_003935980.1| tim-barrel protein [Clostridium sticklandii DSM 519]
 gi|308825037|emb|CBH21075.1| putative TIM-barrel protein, , NifR3 family [Clostridium
           sticklandii]
          Length = 322

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 84/304 (27%), Positives = 150/304 (49%), Gaps = 27/304 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +     +LLYTEMI A A+   DK   ++L    QEKP+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKQF-EASLLYTEMINAKAVCYEDKNTFDMLLVEDQEKPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA+ + +    EI ++N+GCP+ +V +   G+ LM NP +  D +  +  A ++
Sbjct: 76  PGFMAEAARTLTELNRFEIIDINMGCPAPKVVKAGDGSALMKNPKLAYDIVNKVKAATNL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D++  ++      K ++++G + + +H R         ++       D++
Sbjct: 136 PVTVKFRKGWDEK--SINALEFGKLMQEAGADAVTLHGRT--------REQYYSGTADWE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+ KE   + +  NG +     A +IL     D +MIGR A  N  +   V++Y  +
Sbjct: 186 IIKEL-KEKLTIPVIANGDITSFDAAERILDITKADALMIGRGAQGNPFIFKEVNDYMES 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            +     I  ++      KI  +++ Y  A ++      + ++ +H+     G  NS R 
Sbjct: 245 AILPKE-ICPKL------KIDTAISHYKLALKYKTQHKAVTEMRKHLGWYLKGLKNSARI 297

Query: 294 R-HI 296
           + HI
Sbjct: 298 KDHI 301


>gi|313885908|ref|ZP_07819648.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312924663|gb|EFR35432.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 329

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 89/311 (28%), Positives = 145/311 (46%), Gaps = 43/311 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +     +L+YTE I ADA++R     +  +     E+P+A+QI G D
Sbjct: 18  MEDVSDAPFRLLCKQF-GASLVYTEFISADALVRYVPSTMRKMRIDPAERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I      + ++LN GCP  RV     G+ ++ +P+++ +  AA+  A S P
Sbjct: 77  VETMCEAARIACQLEPDLLDLNFGCPVKRVAGKGAGSGMLRDPELLLEITAAVVAAASCP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  L   ++  G+  + IH R    + KG          + D+
Sbjct: 137 VTVKTRLGWDHD--SLIITELAPRLQACGIAALTIHGRTRSDMYKG----------SADW 184

Query: 177 DIVYEIKKENPDLFIGL--NGGL---EDMSQALKILPSVDGVMIGRAAYKNS----AMLT 227
            ++ E++  NP++ I +  NG +   E++  A      VDGVM+GRAA         M  
Sbjct: 185 TLIGEVRS-NPEIQIPIIGNGDITTGEEVRHAFDTY-GVDGVMVGRAAIGQPWIFGEMRA 242

Query: 228 TVDEYFSNPLTGSSP----IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            VD  F+ P   S      +K  V K+  +        ++ RHL +             L
Sbjct: 243 AVDPTFTAPQLTSQQQLEILKEIVHKNIEKLDERRGILHSRRHLAA-----------TPL 291

Query: 284 FHGFPNSRRCR 294
           F G PN R  R
Sbjct: 292 FKGIPNFRALR 302


>gi|288929784|ref|ZP_06423627.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 317 str. F0108]
 gi|288328885|gb|EFC67473.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 317 str. F0108]
          Length = 329

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 82/304 (26%), Positives = 145/304 (47%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYTEFVSAEALVRSVKSTVSKLTISDEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  +V     GA ++ N  ++ +    + +A+  P
Sbjct: 77  VESMVEAARIVEQSRPDVIDINFGCPVKKVAGKGAGAGMLRNVPLMLEITREVVRAVRTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + +  L + ++  G+  + IH R         +        D+  
Sbjct: 137 VTVKTRLGWDCE--EIIIPTLAEQLQDCGIAALTIHGRT--------RSQMYTGEADWRY 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    QA ++     VD VM+GRA +    +   + ++  
Sbjct: 187 IGEVKA-NPRIHIPIIGNGDICTPQQAKEVFSRYGVDAVMVGRATFGRPWVFKEMKDHLE 245

Query: 235 N-PLTGSSPIKTRVD-KDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
             P   S  I  ++D  +   +I+    D     LH+        RH+    +F G P+ 
Sbjct: 246 GLPQDPSLTIDRKIDLLEEQLRINIERIDEYRGILHT-------RRHLAASPIFKGIPDF 298

Query: 291 RRCR 294
           ++ R
Sbjct: 299 KQTR 302


>gi|282858670|ref|ZP_06267828.1| TIM-barrel protein, nifR3 family [Prevotella bivia JCVIHMP010]
 gi|282588588|gb|EFB93735.1| TIM-barrel protein, nifR3 family [Prevotella bivia JCVIHMP010]
          Length = 325

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 118/226 (52%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +    +E+P  +QI G +
Sbjct: 18  MEDVTDIGFRKMCKRY-GAAMVYTEFVSADAIIRSIKSTLSKMVIDDEERPTGIQIYGNN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE+   + I++N GCP  +V     G+ ++ N  ++ D    + KA+++P
Sbjct: 77  VESMVEAAKIVEEAKPDVIDINFGCPVKKVAGKGAGSGMLKNIPLLLDITREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + +  L + I+  G   + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDEN--NLVITELAEQIQDCGAKALTIHGRT--------RAQMYTGNADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + E+KK NP + I +  NG +  +  A +      VD VMIGRA +
Sbjct: 187 IGEVKK-NPRIHIPIIGNGDITSVKDAYEHFDKYGVDAVMIGRATF 231


>gi|325860196|ref|ZP_08173321.1| TIM-barrel protein, nifR3 family [Prevotella denticola CRIS 18C-A]
 gi|325482283|gb|EGC85291.1| TIM-barrel protein, nifR3 family [Prevotella denticola CRIS 18C-A]
          Length = 319

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 84/303 (27%), Positives = 146/303 (48%), Gaps = 36/303 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  +  +  +     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAIIRSIRSTLSKMVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IVE    + I++N GCP  +V     G+ ++ N  ++ +    + KA+SIP
Sbjct: 77  VASMVEAARIVEQAKPDVIDINFGCPVKKVAGKGAGSGMLKNIPLLLEITREVVKAVSIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +A  +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDKDNLVIA--DLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +  + +A +      VD VMIGRA +    +    +    
Sbjct: 187 IGEVKK-NPRIHIPIIGNGDVTSVREAGEKFDRYGVDAVMIGRATFGCPWIFRQGE---- 241

Query: 235 NPLTGSSPIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
               G  P+  ++D  +   +I+    D     +H+        RH+    +F G P+ R
Sbjct: 242 ----GELPLDEKIDVLEEMLRINVERIDEYRGIIHT-------RRHLAASPIFKGIPDFR 290

Query: 292 RCR 294
           + R
Sbjct: 291 QTR 293


>gi|325281330|ref|YP_004253872.1| TIM-barrel protein, nifR3 family [Odoribacter splanchnicus DSM
           20712]
 gi|324313139|gb|ADY33692.1| TIM-barrel protein, nifR3 family [Odoribacter splanchnicus DSM
           20712]
          Length = 333

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 80/301 (26%), Positives = 143/301 (47%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D T+  +R F +    +  LY+E + ADA++R   K++  L     E+P+ +QI G  
Sbjct: 18  MEDVTNPPFRKFCKKYGAD-WLYSEFVSADALVRSVNKSLKKLTIDETERPVTIQIYGRF 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAAKIVE+   + I++N GCP  RV +   GA ++ +  ++ +    + +A+ IP
Sbjct: 77  IDSMVEAAKIVEEVRPDFIDINFGCPVKRVAQKGAGAGMLKDIPLMVEMTRQIVQAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D +   + + ++ + ++  G+  + IH R         +        D++ 
Sbjct: 137 VTAKTRLGWDCE--HIIIEDIAERLQDVGIQALAIHGRT--------RSQMYSGEADWEP 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF- 233
           +  +K  NP + I +  NG +    +A +      VDGVMIGRA   +  +   +  YF 
Sbjct: 187 IARVKN-NPRIKIPILGNGDITSPEKAKEAFERYGVDGVMIGRATIGHPWIFKQIRHYFE 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +  L     +K +++      +       +   +     L  + RHM  +F G P+ R  
Sbjct: 246 TGELLPDLSVKEQIE------VIKEQILLSVEWIDEVRGLLHMRRHMASMFKGLPHFRDL 299

Query: 294 R 294
           R
Sbjct: 300 R 300


>gi|238917594|ref|YP_002931111.1| hypothetical protein EUBELI_01673 [Eubacterium eligens ATCC 27750]
 gi|238872954|gb|ACR72664.1| Hypothetical protein EUBELI_01673 [Eubacterium eligens ATCC 27750]
          Length = 321

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 123/239 (51%), Gaps = 16/239 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A A+L  +K  ++++     E+PLALQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGCGLMCTEMVSAKAVLYNNKNTEDLMKTVPGERPLALQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK + +  ++ I++N+GCP  +V     G+ LM +P +VG  +  M  AL  P
Sbjct: 76  PDIMADIAKRLSEREFDIIDVNMGCPVPKVVNNGEGSALMKDPVLVGRIVEKMADALDKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G D+   ++    +   I++SG   + +HAR         +      + D+DI
Sbjct: 136 LTIKIRAGFDEN--SINAPEIAHVIEESGGAAVAVHART--------RQQYYSGHADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K+      IG NG ++    A+ ++     DG+MIGRAA  N  +   V EY +N
Sbjct: 186 IRQVKEAVSIPVIG-NGDIKSGEDAVNMMKQTGCDGIMIGRAARGNPWIFRQVSEYMNN 243


>gi|40063277|gb|AAR38095.1| NifR3/Smm1 family protein [uncultured marine bacterium 578]
          Length = 322

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 133/256 (51%), Gaps = 25/256 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   +D+ +R   R     AL  +EM+V    +L  +K K+ L F +++ P+++QI G++
Sbjct: 17  MAGTSDKPFRMICRE-QGAALTTSEMVVMQKHLLNTNKSKHRLDFRSEQSPISIQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L E+AK   +FG + I++N+GCP+ +V   + G+ LM N  +V D I A+  A++IP
Sbjct: 76  SQELAESAKQALEFGADIIDINMGCPAKKVCNKAAGSALMKNEKLVEDIIKAVVNAVNIP 135

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G +++    P +A     K  + +G+  + IH R         +  +   + +
Sbjct: 136 VTLKMRTGWNEENKNAPTIA-----KIAEDNGIKMLAIHGR--------TRAQKYNGDAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD V +IK     + +  NG +    +A K+L     D VM+GRA   N  ++  ++ Y 
Sbjct: 183 YDTVKKIKGI-VSIPVVANGDITSAQKAKKVLDYTGADAVMLGRATQGNPWLVGQINNYL 241

Query: 234 SNPLTGSSPIKTRVDK 249
               TG SP    +DK
Sbjct: 242 K---TGKSPKAPLLDK 254


>gi|333029581|ref|ZP_08457642.1| TIM-barrel protein, nifR3 family [Bacteroides coprosuis DSM 18011]
 gi|332740178|gb|EGJ70660.1| TIM-barrel protein, nifR3 family [Bacteroides coprosuis DSM 18011]
          Length = 329

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/302 (28%), Positives = 139/302 (46%), Gaps = 25/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L    +E+P+A+QI G +
Sbjct: 18  MEDVTDPAFRLMCKRFGAD-MVYTEFVSSDALIRYVNKTTEKLKIYDEERPVAIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  +V     G+ +M  P+ +     A+  A+ IP
Sbjct: 77  TDAMVEAAKIVEEAKPDILDINFGCPVRKVAGKGAGSGMMKTPEKMIAITKAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDDDNKIIV--ELAEQLQDFGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +     A        VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDITSAESAKDHFEKYGVDAIMIGRASFGRPWIFEEVKHYLE 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              TG   ++ R  K +   +   + +   R     G L    RH+    LF G PN + 
Sbjct: 246 ---TGEK-LEPRPFKWYLSILKEQVANSIERLDERRGILHT-RRHLASTPLFKGIPNFKE 300

Query: 293 CR 294
            R
Sbjct: 301 TR 302


>gi|228470160|ref|ZP_04055069.1| NifR3 family protein [Porphyromonas uenonis 60-3]
 gi|228308298|gb|EEK17153.1| NifR3 family protein [Porphyromonas uenonis 60-3]
          Length = 330

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 91/309 (29%), Positives = 146/309 (47%), Gaps = 39/309 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +     +L+YTE I ADA++R     +  +     E+P+A+QI G D
Sbjct: 18  MEDVSDAPFRLLCKQF-GASLVYTEFISADALVRYVPSTMRKMRIDPAERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I      + ++LN GCP  RV     G+ ++  P+++ +  AA+  A + P
Sbjct: 77  VETMCEAARIACQLEPDLLDLNFGCPVKRVAGKGAGSGMLREPELLLEITAAVVAAANCP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  L   ++  G+  + IH R    + KG          + D+
Sbjct: 137 VTVKTRLGWDHN--SLIITELAPRLQACGIAALTIHGRTRSDMYKG----------SADW 184

Query: 177 DIVYEIKKENPDLFIGL--NGGL---EDMSQALKILPSVDGVMIGRAAYKNS----AMLT 227
            ++ E++  NP++ I +  NG +   E++  A      VDGVM+GRAA         M  
Sbjct: 185 TLIGEVRS-NPEIQIPIIGNGDITTGEEVRHAFDTY-GVDGVMVGRAAIGQPWIFGEMRA 242

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFH 285
            VD  F+ P   SS  +  + K+   K +    D     LHS        RH+    LF 
Sbjct: 243 AVDPTFTAPKL-SSQQQLEILKEIVHK-NIEKLDERRGILHS-------RRHLAATPLFK 293

Query: 286 GFPNSRRCR 294
           G PN R  R
Sbjct: 294 GIPNFRALR 302


>gi|291561472|emb|CBL40271.1| tRNA-U20-dihydrouridine synthase [butyrate-producing bacterium
           SS3/4]
          Length = 319

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 145/303 (47%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R      L+  EM+ A AIL  +K  + +L    +E+P++LQ+ G+D
Sbjct: 19  MAGVTDMPYRILCRE-QGAGLVCMEMVSAKAILYKNKNTQELLKVDERERPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +ED  Y+  ++N+GCP  ++ +   G+ LM NP +V + +  + KA+  P
Sbjct: 78  PDIVADIAASLEDGPYDIFDINMGCPVPKIVKNGEGSALMRNPKLVEEILTKLVKAVKKP 137

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I AV +  + +S   +GV  + +H R         ++       D++
Sbjct: 138 VTVKFRKGFDDTCINAVEIAKIAES---AGVAAVAVHGRT--------REQYYSGKADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK      IG NG +     A +++     DG+M+ R A  N  +   +  Y   
Sbjct: 187 IIREVKKAVKIPVIG-NGDVFTPQDAKRLVEETGCDGIMVARGAKGNPWIFKQITHYLE- 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFHGFPNSRR 292
             TG    +  V+     ++ A +  +    +   G+L   +++ +H+     G+PNS  
Sbjct: 245 --TGELLPRPSVE-----ELKAMILRHGQMMMEFKGELAGMREMRKHVAWYTAGYPNSAA 297

Query: 293 CRH 295
            R+
Sbjct: 298 LRN 300


>gi|261878855|ref|ZP_06005282.1| tRNA-dihydrouridine synthase [Prevotella bergensis DSM 17361]
 gi|270334534|gb|EFA45320.1| tRNA-dihydrouridine synthase [Prevotella bergensis DSM 17361]
          Length = 336

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 83/309 (26%), Positives = 146/309 (47%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + A+AI+R  K  +  +     E+P+ +QI G D
Sbjct: 19  MEDVTDIGFRKLCKRYGAD-MMYTEFVSAEAIIRNIKSTLDKMQIDDDERPVGIQIYGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAK+VE    + I++N GCP  +V     GA ++ N  ++ D   A+  A+ +P
Sbjct: 78  VESMVEAAKMVETVEPDVIDINFGCPVKKVAGKGAGAGMLKNIPLMLDITRAVVDAVRVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D  +  + + +L + ++  G+  + IH R         +      + D+ +
Sbjct: 138 VTAKTRLGWD--LDNLIITDLAEQLQDCGIRALTIHGRT--------RSQMYTGDADWSL 187

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K+ NP + I +  NG +    QA +      VD VMIGRA +    +   + +Y +
Sbjct: 188 IGEVKR-NPRIHIPIIGNGDITTPEQAKQAFERYGVDAVMIGRATFGCPWIFKEMRDYLN 246

Query: 235 NPLTG----SSPIKTRVDKDFWR---KISASMTDYAARHLHSGGKLQQITRHMIG--LFH 285
           +   G    ++P+      D      +I+    D     LH+        RH+    +F 
Sbjct: 247 STSGGGLEPAAPLTVDDKIDILEEQLRINVERIDEYRGILHT-------RRHLASSPIFK 299

Query: 286 GFPNSRRCR 294
             PN R+ R
Sbjct: 300 NIPNFRQTR 308


>gi|332300620|ref|YP_004442541.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica DSM
           20707]
 gi|332177683|gb|AEE13373.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica DSM
           20707]
          Length = 331

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/311 (28%), Positives = 145/311 (46%), Gaps = 43/311 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +     +L+YTE I ADA++R     +  +     E+P+A+QI G +
Sbjct: 18  MEDVSDAPFRLLCKQF-GASLVYTEFISADALVRYVPSTMRKMRIDPAERPVAIQIYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I      + ++LN GCP  RV     G+ ++ +P+++ +  AA+  A S P
Sbjct: 77  VETMCEAARIACQLEPDLLDLNFGCPVKRVAGKGAGSGMLRDPELLLEITAAVVAAASCP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  L   ++  G+  + IH R    + KG          + D+
Sbjct: 137 VTVKTRLGWDHN--SLIITELAPRLQACGIAALTIHGRTRSDMYKG----------SADW 184

Query: 177 DIVYEIKKENPDLFIGL--NGGL---EDMSQALKILPSVDGVMIGRAAYKNS----AMLT 227
            ++ E++  NP++ I +  NG +   E++  A      VDGVM+GRAA         M  
Sbjct: 185 TLIGEVRS-NPEIQIPIIGNGDITTGEEVRHAFDTY-GVDGVMVGRAAIGQPWIFGEMRA 242

Query: 228 TVDEYFSNPLTGSSP----IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            VD  F+ P   S      +K  V K+  +        ++ RHL +             L
Sbjct: 243 AVDPTFTAPQLTSQQQLEILKEIVHKNIEKLDERRGILHSRRHLAA-----------TPL 291

Query: 284 FHGFPNSRRCR 294
           F G PN R  R
Sbjct: 292 FKGIPNFRALR 302


>gi|295085714|emb|CBK67237.1| tRNA-U20-dihydrouridine synthase [Bacteroides xylanisolvens XB1A]
          Length = 331

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLICKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|255693550|ref|ZP_05417225.1| zinc-binding TIM-barrel protein, nifR3 family [Bacteroides
           finegoldii DSM 17565]
 gi|260620615|gb|EEX43486.1| zinc-binding TIM-barrel protein, nifR3 family [Bacteroides
           finegoldii DSM 17565]
          Length = 325

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 90/307 (29%), Positives = 142/307 (46%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKAAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEEAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKK-NPRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      D  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFGWCMDVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
            N R  R
Sbjct: 296 SNFRNTR 302


>gi|291515732|emb|CBK64942.1| tRNA-U20-dihydrouridine synthase [Alistipes shahii WAL 8301]
          Length = 340

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/312 (27%), Positives = 147/312 (47%), Gaps = 47/312 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R+  +    + ++YTE I +D ++R   K++  L     E+P+ +QI G  
Sbjct: 18  MEDVTDPSFRYMCKRFGAD-MVYTEFISSDGLIRDAAKSLKKLEIDDAERPVGIQIYGHL 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAA++ E  G + I++N GCP  ++     G+ +M +  ++ +    +  A+  P
Sbjct: 77  IDPMVEAARMAEAAGPDVIDINFGCPVKKIAGRGAGSGMMRDVPLMVEMTRRIVAAVKKP 136

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VTVK R+G D++   I  +ALR     ++  G+  + IH R    + +G           
Sbjct: 137 VTVKTRLGWDEESKNIEEIALR-----LQDVGIAALTIHGRTRAQMYRG----------E 181

Query: 174 LDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
            D+ ++ ++K  NP + I +  NG ++   +A ++     VDGVMIGRA Y    +   V
Sbjct: 182 ADWTLIGKVKN-NPQIRIPIIGNGDVDSGPKAREMFDRYGVDGVMIGRATYGRPWIFREV 240

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-------QITRHMIG 282
             Y S   TG +  +  V         A     A  HL    +++       ++ RHM  
Sbjct: 241 KHYLS---TGEALPQPSV---------AERVAIAKEHLQKSLEIKGDHVGILEMRRHMTN 288

Query: 283 LFHGFPNSRRCR 294
            F G P+ +  R
Sbjct: 289 YFKGLPDFKSTR 300


>gi|189485309|ref|YP_001956250.1| putative tRNA-dihydrouridine synthase [uncultured Termite group 1
           bacterium phylotype Rs-D17]
 gi|170287268|dbj|BAG13789.1| putative tRNA-dihydrouridine synthase [uncultured Termite group 1
           bacterium phylotype Rs-D17]
          Length = 320

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 131/258 (50%), Gaps = 18/258 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD   R  A+      L+YT M+ A A++R D+K   +L  +  E+P+A QI G+ 
Sbjct: 20  MAGITDLPLRRLAKS-GGAGLVYTGMLSARALVRSDEKTEKLLKTTEDERPVAAQIFGSA 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAKIV + G + I++N+GCP  +V +   GA L+ +  +V + + ++ K++ +P
Sbjct: 79  AHIMAEAAKIVRNSGADIIDVNLGCPVKKVAKAGAGAKLLADEKLVSEILESVVKSVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G+  +  A     ++K     G+  + +HAR A       + +   P+L    
Sbjct: 139 VTVKIRTGLLPEHNAAT--EIIKVAYNCGIKMVAVHARPA------SQGHSGFPDLK--- 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++        + +  NGG+ D   A   L  P+  G+MIGR A  N ++   ++ +FS+ 
Sbjct: 188 LFAASCAGAKIPVIANGGVVDEKTAADFLRVPNCAGIMIGRGALGNYSIFKRLEAFFSS- 246

Query: 237 LTGSSPIKTRVDKDFWRK 254
                P+ ++ +K  W K
Sbjct: 247 -GKKLPLPSKTEKVEWLK 263


>gi|218674773|ref|ZP_03524442.1| tRNA-dihydrouridine synthase A [Rhizobium etli GR56]
          Length = 88

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 43/76 (56%), Positives = 58/76 (76%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
          M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 13 MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDVAEHPLALQLGGSDPA 72

Query: 61 KLVEAAKIVEDFGYNE 76
          KL EA +I E +GY+E
Sbjct: 73 KLAEAVRIAEPYGYDE 88


>gi|327312701|ref|YP_004328138.1| TIM-barrel protein, nifR3 family [Prevotella denticola F0289]
 gi|326945572|gb|AEA21457.1| TIM-barrel protein, nifR3 family [Prevotella denticola F0289]
          Length = 355

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 119/226 (52%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  +  +  +     E+P+ +QI G D
Sbjct: 47  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAIIRSIRSTLSKMVIDDSERPVGIQIYGRD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IVE    + I++N GCP  +V     G+ ++ N  ++ +    + KA+SIP
Sbjct: 106 VASMVEAARIVEQAKPDVIDINFGCPVKKVAGKGAGSGMLKNIPLLLEITREVVKAVSIP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 166 VTVKTRLGWDKD--NLVITDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWTL 215

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAY 220
           + E+KK NP + I +  NG +  + +A +      VD VMIGRA +
Sbjct: 216 IGEVKK-NPRIHIPIIGNGDVTSVREAGEKFDRYGVDAVMIGRATF 260


>gi|237717083|ref|ZP_04547564.1| dehydrogenase [Bacteroides sp. D1]
 gi|262405851|ref|ZP_06082401.1| dehydrogenase [Bacteroides sp. 2_1_22]
 gi|294647812|ref|ZP_06725364.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CC 2a]
 gi|294806206|ref|ZP_06765053.1| TIM-barrel protein, nifR3 family [Bacteroides xylanisolvens SD CC
           1b]
 gi|229443066|gb|EEO48857.1| dehydrogenase [Bacteroides sp. D1]
 gi|262356726|gb|EEZ05816.1| dehydrogenase [Bacteroides sp. 2_1_22]
 gi|292636720|gb|EFF55186.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CC 2a]
 gi|294446462|gb|EFG15082.1| TIM-barrel protein, nifR3 family [Bacteroides xylanisolvens SD CC
           1b]
          Length = 331

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|160934849|ref|ZP_02082235.1| hypothetical protein CLOLEP_03724 [Clostridium leptum DSM 753]
 gi|156866302|gb|EDO59674.1| hypothetical protein CLOLEP_03724 [Clostridium leptum DSM 753]
          Length = 330

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 121/246 (49%), Gaps = 16/246 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR +R         A + +EM+ A A+  GDKK+  ++  S+QE+P A+Q+ G D
Sbjct: 18  MAGTADRAFREICASF-GAAYVISEMVSAKALTYGDKKSRELMELSSQERPAAIQLFGDD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA +  ++    I+LN+GCP+ ++     G+ LM  P + G  + A+ KA+ +P
Sbjct: 77  PQTMAEAAVLALEYQPEIIDLNMGCPAPKITSNGCGSALMKKPALCGRIVEAVKKAVPVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D +   V    + K  + +G + I +H R         ++    P+ D++ 
Sbjct: 137 VTVKIRKGWDTRT--VNAVEVAKICENAGADAIAVHGRT--------REQMYAPSADWES 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+      IG NG +     A  +L     D VMIGR A  N  +   V+ +  + 
Sbjct: 187 IRQVKEAVSIPVIG-NGDVFTAEDAAAMLEQTGCDLVMIGRGALGNPWIFQQVNAWLGSQ 245

Query: 237 LTGSSP 242
           +   +P
Sbjct: 246 VQLPAP 251


>gi|146295635|ref|YP_001179406.1| nifR3 family TIM-barrel protein [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409211|gb|ABP66215.1| tRNA-U20-dihydrouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 328

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 140/302 (46%), Gaps = 28/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        +  + TEM+ A AI  G +K   ++ FS  EK   +QI G+D
Sbjct: 13  MAGFTDKVFRSLCSRFGADVTV-TEMVSAKAITMGSQKTKELISFSEDEKIKGVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EA KI++D F Y+ I++N+GCP  +V +   G+ LM NP +    +  + K    
Sbjct: 72  PHVMAEAVKIIQDEFEYDFIDINMGCPVPKVVKSGEGSALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++   +        +++SG + I +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEE--NINAPEFACIMQESGASFITVHGR--------TRTQMYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  + KE   + +  NG + D   A K   +   D +MIGRAA  N  +   + E F N
Sbjct: 182 IIKMV-KEKVKIPVVANGDIVDFESAKKAYEITEADSIMIGRAALGNPWVFLQIKEGFEN 240

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
               +  +   K +V  +F+R++    ++  A        + +  +H+     G  N+ +
Sbjct: 241 GQVTTRVLPHEKVKVAIEFFRQLCTEKSEKMA--------VLEARKHLSFFIKGIENAAK 292

Query: 293 CR 294
            R
Sbjct: 293 IR 294


>gi|110834874|ref|YP_693733.1| NifR3 family TIM-barrel protein [Alcanivorax borkumensis SK2]
 gi|110647985|emb|CAL17461.1| TIM-barrel protein, putative, NifR3 family, putative [Alcanivorax
           borkumensis SK2]
          Length = 346

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 130/255 (50%), Gaps = 24/255 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    LL +EM+ +D  L   +K+   L  S +  P+++QI G +
Sbjct: 17  MAGVTDRPFRRLCRDL-GAGLLVSEMVTSDTRLWNSRKSRQRLDHSGEPGPISVQIAGGE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V + + G+ L+ +PD+V   + A+ +A+++P
Sbjct: 76  PAMLAEAARANVEHGAQIIDINMGCPAKKVCKRAAGSALLADPDLVARILDAVTQAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D DQ  A+   ++ +  + +G+  + IH R             +    + D
Sbjct: 136 VTLKIRTGPDRDQRNAI---DIARIAETAGIQALAIHGRT------------RADKFNGD 180

Query: 178 IVYEIKKENPD---LFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
             Y   K+  D   + I  NG ++   +A ++L S   DG+MIGRAA  N  +      Y
Sbjct: 181 AEYATIKQVVDAVNIPIMANGDVDSPEKAKRVLESTGADGIMIGRAAQGNPWIFRDTLYY 240

Query: 233 FSNPLTGSSPIKTRV 247
             +    ++P+ T V
Sbjct: 241 LEHGSLPAAPLVTEV 255


>gi|116749246|ref|YP_845933.1| nifR3 family TIM-barrel protein [Syntrophobacter fumaroxidans MPOB]
 gi|116698310|gb|ABK17498.1| putative TIM-barrel protein, nifR3 family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 352

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 87/304 (28%), Positives = 142/304 (46%), Gaps = 31/304 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP----LALQIGG 56
           M   TD  YR         A++ TEM+    ++R +++  L    Q+ P    LA+Q+ G
Sbjct: 29  MAGVTDSAYRALMADF-GAAMVTTEMVSIQGLVR-NQRATLDLCRQQHPVGVPLAVQVFG 86

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D + + EAA++VE  G   I++N GCP  +V     GA L+ +PD +   + A+ +A+S
Sbjct: 87  RDPAVMAEAARLVEQGGAALIDINAGCPVRKVVRQGAGAILLKDPDRLAAMVEAVKRAVS 146

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNL 174
           +PVTVK R+G D+    VA   L + +  +GV+ I +H R A  +  G +          
Sbjct: 147 VPVTVKIRVGWDNAANGVA--GLARQLVSAGVDAITVHGRTAAQMYSGRA---------- 194

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K       IG NG +     A +++     DGVMIGRA+  N  +   +   
Sbjct: 195 DWSRIAEVKAAVAVPVIG-NGDVTSPELAERMIHETGCDGVMIGRASLGNPWLFAVISRR 253

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR- 291
           +     G+         DF R   A +  +      + G L+++   +I    G P+S  
Sbjct: 254 WGR---GARQGDCPGWNDFLRTAEAHLESFRTMRPRADGHLKKL---LIWYSKGCPDSAG 307

Query: 292 -RCR 294
            RCR
Sbjct: 308 LRCR 311


>gi|329956495|ref|ZP_08297092.1| TIM-barrel protein, nifR3 family [Bacteroides clarus YIT 12056]
 gi|328524392|gb|EGF51462.1| TIM-barrel protein, nifR3 family [Bacteroides clarus YIT 12056]
          Length = 325

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 85/304 (27%), Positives = 141/304 (46%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKGFGAD-MVYTEFVSSDALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVADAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAGNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPVIGNGDVTTPQRAKECFDRYGVDAIMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG    P+      +  R+      + + + L     +  + RH+    LF G PN 
Sbjct: 246 ---TGEEMPPLSAEWKLNVLRR----EVEDSVKLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           R  R
Sbjct: 299 RDTR 302


>gi|302345940|ref|YP_003814293.1| TIM-barrel protein, nifR3 family [Prevotella melaninogenica ATCC
           25845]
 gi|302150111|gb|ADK96373.1| TIM-barrel protein, nifR3 family [Prevotella melaninogenica ATCC
           25845]
          Length = 318

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 118/226 (52%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADA++R  K  +  L     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAVIRSIKSTLSKLVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE    + I++N GCP  +V     G+ ++ N  ++ D    + KA++ P
Sbjct: 77  VASMVEAAKIVEQVKPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLDITREVVKAVNTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--NLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAY 220
           + E+K  NP + I +  NG +  + +A +      VD VMIGRA +
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDVTSIEEAHEKFDRYGVDAVMIGRATF 231


>gi|258648271|ref|ZP_05735740.1| tRNA-dihydrouridine synthase B [Prevotella tannerae ATCC 51259]
 gi|260852187|gb|EEX72056.1| tRNA-dihydrouridine synthase B [Prevotella tannerae ATCC 51259]
          Length = 343

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 86/310 (27%), Positives = 147/310 (47%), Gaps = 31/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   R +   A+ Y+E + +DA++R  ++++  L  S  E+P+A+QI G  
Sbjct: 18  MEDVTDIGFRRLCRQM-GAAMAYSEFVASDALVRNVRRSLDKLAVSDAERPVAIQIYGRF 76

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAAKIVE+  + +I +LN GCP  RV     GA L+ N  ++ +    + +A+ I
Sbjct: 77  PDAMAEAAKIVEETSHPDILDLNFGCPVKRVAGKGAGAGLLQNVPLMLEITRRVVEAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           PVTVK R+G D +   +    L + ++  G++ + IH R    + KG            D
Sbjct: 137 PVTVKTRLGWDSEHEIIT--ELAEQLQDCGISALTIHGRTRAQMYKG----------EAD 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGL---EDMSQALKILPSVDGVMIGRAAYKN----SAML 226
           + ++ E+K+ NP + I +  NG L   ED+ +A +    VD  M+GRA +        M 
Sbjct: 185 WRLIGEVKR-NPRIHIPIIGNGDLTTGEDVRRAFEHY-GVDACMVGRATFGRPWIFKEMY 242

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LF 284
             V +    P+         +  D+   +  +    +   +     +  + RH+    LF
Sbjct: 243 DAVHDQHHTPVNAIESSYEPLSADWKLDVLKAQVVQSVNRIDEYRGILHVRRHIAATPLF 302

Query: 285 HGFPNSRRCR 294
            G P+ R  R
Sbjct: 303 KGIPDFREKR 312


>gi|288803773|ref|ZP_06409201.1| TIM-barrel protein, putative, NifR3 family [Prevotella
           melaninogenica D18]
 gi|288333760|gb|EFC72207.1| TIM-barrel protein, putative, NifR3 family [Prevotella
           melaninogenica D18]
          Length = 319

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 118/226 (52%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADA++R  K  +  L     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAVIRSIKSTLSKLVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE    + I++N GCP  +V     G+ ++ N  ++ D    + KA++ P
Sbjct: 77  VASMVEAAKIVEQVKPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLDITREVVKAVNTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--NLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAY 220
           + E+K  NP + I +  NG +  + +A +      VD VMIGRA +
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDVTSIEEAHEKFDHYGVDAVMIGRATF 231


>gi|229829710|ref|ZP_04455779.1| hypothetical protein GCWU000342_01807 [Shuttleworthia satelles DSM
           14600]
 gi|229791699|gb|EEP27813.1| hypothetical protein GCWU000342_01807 [Shuttleworthia satelles DSM
           14600]
          Length = 341

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/294 (27%), Positives = 144/294 (48%), Gaps = 29/294 (9%)

Query: 14  RLLTNN---ALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           RLL +     L+ TEM+ A AI   ++  K +L  S +E+P++LQI G+D   + E A+ 
Sbjct: 47  RLLCHEQGAGLVCTEMVSAKAIAYKNRNTKELLKVSDEERPVSLQIFGSDPVIMAEQARQ 106

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +ED  ++ +++N+GCP  +V     G+ L+ NP + G  I A+  A+  P+TVK R+GV 
Sbjct: 107 IEDLHWDILDINMGCPVPKVFNNGDGSALLRNPLLAGQIIEAVAGAIHKPLTVKIRLGVS 166

Query: 129 -DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            D I AV + ++    ++SG   + +H R         +D   +   D++ +  +K+   
Sbjct: 167 PDTINAVEMAHIA---QESGAAAVAVHGRT--------RDQFYMGAADWEQIARVKQAVS 215

Query: 188 DLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
              IG NG ++  +  QA+     VD  MI RAA  N  +   +  ++     G  P+K 
Sbjct: 216 IPVIG-NGDIKSPADVQAMYEQTGVDAYMIARAAQGNPWIFRQILHFYQE---GEEPVKP 271

Query: 246 RVDK--DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +  D   + +  M D    +L     ++++ +       G+P S R R ++
Sbjct: 272 GPQEMCDTMLRQARMMCDLKGEYL----GIREMRKQAAWYTAGYPRSARLRGMV 321


>gi|295136512|ref|YP_003587188.1| tRNA-dihydrouridine synthase [Zunongwangia profunda SM-A87]
 gi|294984527|gb|ADF54992.1| tRNA-dihydrouridine synthase [Zunongwangia profunda SM-A87]
          Length = 330

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 148/303 (48%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++E+ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLESVEIVEKSGPDIIDINFGCPVKKVVSKGAGAGILKDVDLMVSLTKAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G D    ++ +  + + ++  G   I IH R    + KG++          D+
Sbjct: 138 ITVKTRLGWDHD--SIKIMEVAERLQDVGCKAISIHGRTRAQMYKGVA----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG ++   +A+++     +DG MIGRA+  N      V  Y
Sbjct: 186 KPIADVKN-NPRMHIPVFGNGDVDTPEKAVEMRDQYGLDGAMIGRASIGNPWFFREVKHY 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           F      S P ++ RV+    RK      D+    L     + +  RH    F G P+ +
Sbjct: 245 FKTGEHLSPPTLQERVEAA--RKHLQMSIDWKGEKL----GVFETRRHYTNYFKGIPHFK 298

Query: 292 RCR 294
             R
Sbjct: 299 EYR 301


>gi|225375159|ref|ZP_03752380.1| hypothetical protein ROSEINA2194_00783 [Roseburia inulinivorans DSM
           16841]
 gi|225213033|gb|EEG95387.1| hypothetical protein ROSEINA2194_00783 [Roseburia inulinivorans DSM
           16841]
          Length = 327

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 146/302 (48%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  + +L    +EKP++LQ+ G+D
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTEELLTIDPREKPVSLQLFGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ LM NP + G  I    KA+  P
Sbjct: 82  PDIMSEIAKQIEERPFDILDINMGCPVPKVVNNGDGSALMKNPLLAGKIIEKTAKAIKKP 141

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  DD I AV + ++    ++SG   I +H R         ++       D+D
Sbjct: 142 VTVKIRKGFDDDHINAVEMAHIA---EESGAAAIAVHGRT--------REQFYSGKADWD 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +      +++    + DG MI R A  N  +   +  YF+ 
Sbjct: 191 IIRQVKEAVSIPVIG-NGDILTADDVIRMQDETNCDGFMIARGAEGNPWIFKQILHYFA- 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG      +++K  + +++  +  +A   +   G+   ++++ +H      G+ NS R
Sbjct: 249 --TGE-----KLEKPSFAEVTDMILRHAQMQIGFKGEYTGIREMRKHAAWYTAGYKNSSR 301

Query: 293 CR 294
            R
Sbjct: 302 LR 303


>gi|209963474|ref|YP_002296389.1| tRNA-dihydrouridine synthase B, putative [Rhodospirillum centenum
           SW]
 gi|209956940|gb|ACI97576.1| tRNA-dihydrouridine synthase B, putative [Rhodospirillum centenum
           SW]
          Length = 338

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 145/303 (47%), Gaps = 31/303 (10%)

Query: 12  FARLL--TNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAK 67
           F RL+  T   L+ +EMI + A++R  ++++L   +S +E P+++Q+ G D   + EAA+
Sbjct: 32  FRRLVKRTGAGLVVSEMIASQAMIRASRESMLKTEWSPEEAPISMQLAGCDPEAMAEAAR 91

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           + ED G + I++N GCP  +V  G  G+ LM +  + G  +    KA+S+PVT+K R G 
Sbjct: 92  LNEDRGAHIIDINFGCPVKKVVNGYAGSALMKDEPLAGRIMEQTVKAVSVPVTMKMRKGW 151

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           D     +    L +  ++ G+  + +H R    +  G +          D+  +  + KE
Sbjct: 152 DAG--NLNAPRLARIAEECGIRMVTVHGRTRCQMYNGTA----------DWKFIRTV-KE 198

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              + +  NG +  ++  ++ L     DGVMIGR  Y     L  V  Y     TG +  
Sbjct: 199 AVSIPVIANGDINTLADVVRCLEESGADGVMIGRGTYGRPWFLAQVMHYLR---TGEA-- 253

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRH-ILTVE 300
             R D     +++  +  Y A   H G +  L+   +H+     G P S   R+ I+T++
Sbjct: 254 --RPDPSLAEQLTIVLEHYEAILEHYGAEAGLRIARKHVAWYSKGLPGSADYRNAIMTMD 311

Query: 301 AGA 303
             A
Sbjct: 312 QPA 314


>gi|213962326|ref|ZP_03390589.1| tRNA-dihydrouridine synthase B [Capnocytophaga sputigena Capno]
 gi|213954992|gb|EEB66311.1| tRNA-dihydrouridine synthase B [Capnocytophaga sputigena Capno]
          Length = 326

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 82/314 (26%), Positives = 155/314 (49%), Gaps = 36/314 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   ++   + +LY+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKMHGAD-MLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+  + ++P
Sbjct: 78  EEAMALSAKIVATVNPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVNSTTLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+Q  ++ +  + + ++  G++ + IHA  R  + KG S          D+
Sbjct: 138 VTVKTRLGWDEQ--SINIEEVAERLQDVGISALTIHARTRSQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG ++   +AL+   +  +DG+MIGRAA     +   +  Y
Sbjct: 186 SYIAKVKN-NPRMHIPIFGNGDIDSPEKALEYRNTYGIDGIMIGRAAIGYPWIFNEIKHY 244

Query: 233 F-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ---QITRHMIGLFHGFP 288
           F +  L  S  I  RV+         +  ++    +   G+ Q   ++ RH    F G P
Sbjct: 245 FATGELLPSPTIADRVE---------AAKNHLLWSVEWKGERQGVVEMRRHYANYFKGIP 295

Query: 289 NSRRCRH-ILTVEA 301
           N +  RH ++T++A
Sbjct: 296 NFKEHRHKLVTLDA 309


>gi|160884735|ref|ZP_02065738.1| hypothetical protein BACOVA_02724 [Bacteroides ovatus ATCC 8483]
 gi|156109770|gb|EDO11515.1| hypothetical protein BACOVA_02724 [Bacteroides ovatus ATCC 8483]
          Length = 331

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   +  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEIKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|319654916|ref|ZP_08008990.1| YacF protein [Bacillus sp. 2_A_57_CT2]
 gi|317393341|gb|EFV74105.1| YacF protein [Bacillus sp. 2_A_57_CT2]
          Length = 333

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 129/236 (54%), Gaps = 19/236 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
            L+  EM+    I+  ++K  N+L    +EKPL+LQI G +   LVEAAK V+ +   + 
Sbjct: 36  GLVCAEMVSDKGIVTKNEKTMNMLYIDEREKPLSLQIFGGEKETLVEAAKFVDKNTNADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  ++ +   GA  +L+PD + + ++ +  A+  PVTVK R+G D D I AV 
Sbjct: 96  IDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSVVTDAVEKPVTVKMRMGWDEDHIYAV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            RN  ++++++G   + +H R  + +    K N       +DI+ E+K+      IG NG
Sbjct: 155 -RN-AQAVERAGGKAVALHGRTRV-QMYEGKAN-------WDIIREVKQSINIPLIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            ++    A ++L     DGVMIGRAA  N  M+    +Y  +  L G   I+ ++D
Sbjct: 204 DVQTPEDAKRMLDETGCDGVMIGRAALGNPWMIYRTVKYLETGELMGEPSIREKID 259


>gi|153807028|ref|ZP_01959696.1| hypothetical protein BACCAC_01305 [Bacteroides caccae ATCC 43185]
 gi|149130148|gb|EDM21358.1| hypothetical protein BACCAC_01305 [Bacteroides caccae ATCC 43185]
          Length = 331

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 140/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPQMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   +  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEMKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVIDSVNLLDERKGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRDTR 302


>gi|149278184|ref|ZP_01884322.1| probable TIM-barrel protein, NifR3 family [Pedobacter sp. BAL39]
 gi|149230950|gb|EDM36331.1| probable TIM-barrel protein, NifR3 family [Pedobacter sp. BAL39]
          Length = 335

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 90/331 (27%), Positives = 154/331 (46%), Gaps = 41/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +RF  +  +   ++YTE I ++ ++R   K+   L     E+P+ +QI G++
Sbjct: 20  MEDVSDPPFRFVCKQ-SGVDMMYTEFISSEGLIRDAAKSRAKLDIFEYERPIGIQIFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I    G + +++N GCP  +V     G+ L+ + D + +   A+  A  +P
Sbjct: 79  IDHMREATEIASMAGPDLMDINYGCPVKQVACRGAGSALLQDIDKMVEMTKAVVNATHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    V    + + ++  G+ G+ IH R    + KG            D+
Sbjct: 139 VTVKTRLGWDDNTKNV--EEVAERLQDIGIQGLTIHGRTRAQMYKG----------EADW 186

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ EIK+ NP + I +  NG ++ + +A   ++   VDG+MIGRAA     +   +  +
Sbjct: 187 TLIREIKR-NPRIKIPIFGNGDVDSIQKAADWRLEYEVDGIMIGRAAIGYPWIFREIKHF 245

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPN 289
           F    T   P I+ RV        +   T         G K+   ++ RH    F G P+
Sbjct: 246 FKTGQTLPGPTIEERV--------AVCRTHLEKSIAWKGPKVGVFEMRRHYSNYFKGLPD 297

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIE 320
            +  R  L  E          IET +N++ E
Sbjct: 298 FKSYRMSLVKEDN--------IETIYNILDE 320


>gi|299144973|ref|ZP_07038041.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 3_1_23]
 gi|298515464|gb|EFI39345.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 3_1_23]
          Length = 331

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPQRCKECFDHYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFDWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|91206014|ref|YP_538369.1| putative dihydrouridine synthase Dus [Rickettsia bellii RML369-C]
 gi|122425270|sp|Q1RH84|DUS_RICBR RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|91069558|gb|ABE05280.1| Putative dihydrouridine synthase Dus [Rickettsia bellii RML369-C]
          Length = 326

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 141/296 (47%), Gaps = 24/296 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGADISK 61
           TD  +R   +      L+ +EMI + A++   ++++   S  +       +Q+ G + + 
Sbjct: 22  TDLEFRRLVKRF-GAGLVVSEMIASRAMIVESRQSLQKCSIMQDDATSACVQLAGCEPNV 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ IPVTV
Sbjct: 81  IAEAAKMNEDMGAKIIDLNFGCPAKKVVNGYSGSALMRDEGLAAKIFEAAVKAVKIPVTV 140

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DDQ        L K  ++SG+  + +H R         +      N D++ +  
Sbjct: 141 KMRMGWDDQTKNAP--TLAKIAERSGIQMVTVHGRT--------RCQFYSGNADWEFIKN 190

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE   + +  NG + + ++A + L   S DGVM+GR AY    +++ +D Y       
Sbjct: 191 V-KEAVKIPVIANGDITNFAKAKEALEKSSADGVMVGRGAYGKPWLISQIDHYLKTGEEK 249

Query: 240 SSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            +P I++++  D   +   ++ DY   +  S G +    +HM     G PNS   R
Sbjct: 250 PAPSIESQL--DIVLEHYQAIVDY---YGESAG-VPIARKHMGWYSSGLPNSAEFR 299


>gi|295093088|emb|CBK82179.1| tRNA-U20-dihydrouridine synthase [Coprococcus sp. ART55/1]
          Length = 322

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/278 (27%), Positives = 131/278 (47%), Gaps = 20/278 (7%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +LY+EM+ A AI   +K  K +L    +EKP  LQ+ G+D   + E AK +E  GY+ I+
Sbjct: 31  ILYSEMVSAKAIYYKNKNTKPLLAMDEREKPFGLQLFGSDPEIMAEMAKRIESNGYSFID 90

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP  +V     G+ LM +P +VG  + AM KA+SIP+T+K R G D +   +    
Sbjct: 91  VNMGCPVPKVVNNGEGSALMKDPVLVGRIVEAMAKAISIPLTIKIRSGFDSE--HINAPE 148

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +    ++SG   + +H R         +      + D+ ++  +K+      IG NG + 
Sbjct: 149 IAHIAQESGAAAVAVHGRT--------RQQYYQGHADWSVIARVKEACIIPIIG-NGDIN 199

Query: 199 DMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
                  ++   + DG MIGR A  N  +   +  Y+ +      P    V KD   + +
Sbjct: 200 TPQDIIDMRAQTNCDGFMIGRGARGNPWIFRDMKYYYEHGELPDKPDIYEV-KDMMLRHA 258

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             M ++   +      + ++ +H+     G  +S R R
Sbjct: 259 RLMVEFKGEYT----GIHEMRKHVAWYSVGMYDSARLR 292


>gi|225026968|ref|ZP_03716160.1| hypothetical protein EUBHAL_01224 [Eubacterium hallii DSM 3353]
 gi|224955704|gb|EEG36913.1| hypothetical protein EUBHAL_01224 [Eubacterium hallii DSM 3353]
          Length = 316

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 121/252 (48%), Gaps = 18/252 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD  +R   +    + ++ TEMI A A+  G+K  +    T+E  KP+ +QI G++
Sbjct: 18  MAGITDLPFRILCKEQGADVMV-TEMISAKALFYGNKNTLPLMQTEEEEKPIGVQIFGSE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +ED G++ I++N+GCP  ++     G+ LMLNP++ G  +  + KA+S+P
Sbjct: 77  PELMGEMAHKIEDKGFSYIDINMGCPVPKIVNNKEGSALMLNPELAGRIVKEVSKAVSLP 136

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D D I A     +   ++++G   + +H R  +               D+D
Sbjct: 137 VTVKFRKGFDADHINAPEFAQI---MEENGAAAVAVHGRTRV--------QYYTGQADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K       IG NG +     A+K+      DG+M+ R A  N  +   V    S 
Sbjct: 186 IIRDVKNAVSIPVIG-NGDIFKGEDAVKMRDYTGCDGIMVARGAKGNPWIFREVKAALSG 244

Query: 236 PLTGSSPIKTRV 247
                 P +  V
Sbjct: 245 KPIPERPTEEEV 256


>gi|145219156|ref|YP_001129865.1| nifR3 family TIM-barrel protein [Prosthecochloris vibrioformis DSM
           265]
 gi|145205320|gb|ABP36363.1| tRNA-U20-dihydrouridine synthase [Chlorobium phaeovibrioides DSM
           265]
          Length = 354

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 144/308 (46%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE + A+A+ RG +K    L     E+P+A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKRHGAD-IVYTEFVSAEALRRGVEKTTRKLIADPVERPIAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I E F  + +++N GCP+ +V     GA L+  P+ +     A+ +A++IP
Sbjct: 76  VESMTEAARIAESFEPDYLDINFGCPTKKVAGKGAGAALLREPEKMAAITEAVVRAVNIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VT K R+G D    ++ + ++++ ++ +G+  + +H   R  + KG +          D+
Sbjct: 136 VTAKTRLGWDRD--SINIIDVLRRLEDAGIQALALHGRTRSEMYKGRA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + E  + +  + +  NG +     AL++      +G+MIGR A  N  + +       
Sbjct: 184 DWIAETVR-HASIPVIANGDVWSPEDALQMFNHTGAEGIMIGRGAIGNPFIFSGTRHLLK 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRR 292
                S P       DF  +I A++          G +    ++ RH      G P    
Sbjct: 243 TGNLPSPP-------DFRDRIEAALEHLELSVQFKGERYGTLEMRRHYSTYLKGLPKVSV 295

Query: 293 CRHILTVE 300
            R+ L  E
Sbjct: 296 VRNKLVRE 303


>gi|218131619|ref|ZP_03460423.1| hypothetical protein BACEGG_03239 [Bacteroides eggerthii DSM 20697]
 gi|217985922|gb|EEC52261.1| hypothetical protein BACEGG_03239 [Bacteroides eggerthii DSM 20697]
          Length = 327

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 83/304 (27%), Positives = 142/304 (46%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKNFGAD-MVYTEFVSSDALIRSVSKTEQKLKISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   ++  A+ IP
Sbjct: 77  TDTMVEAARIVEQAHPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRSVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDASNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E++  NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVRN-NPRMHIPIIGNGDITTPQRAKECFDRYGVDAIMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG    P+ +    +  R+      + + + L     +  + RH+    LF G PN 
Sbjct: 246 ---TGEEMPPLSSEWKLNVLRQ----EVEDSVKLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           R  R
Sbjct: 299 RDTR 302


>gi|258513601|ref|YP_003189823.1| TIM-barrel protein, nifR3 family [Desulfotomaculum acetoxidans DSM
           771]
 gi|257777306|gb|ACV61200.1| TIM-barrel protein, nifR3 family [Desulfotomaculum acetoxidans DSM
           771]
          Length = 322

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 119/237 (50%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKP-LALQIGGAD 58
           M   TDR YR  A+      L+ TEMI   A+L G+ K NIL   T E P +++QI G+ 
Sbjct: 18  MAGITDRAYRILAKE-AGCGLVCTEMISDQALLYGNPKTNILLDCTGETPPISMQIFGSS 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA I E  G + I++N+GCP+ ++ +   GA LM  P++    I+ + +++ +P
Sbjct: 77  PEYMARAASITEARGASIIDINMGCPTPKIVKNGEGAALMRKPELAQKIISDVVQSVRVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+  P      L+   +++G   + +H R         +        D+DI
Sbjct: 137 VTVKIRKGWDESFPNAVEMALLA--EEAGAKAVTVHGRT--------RSQFYSGKADWDI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +KK      IG NG + +   A+++L     D VMIGRA+  N  + ++   + 
Sbjct: 187 IKSVKKAVTIPVIG-NGDIREPRDAVRMLMHTGCDAVMIGRASLGNPWIFSSTVHFL 242


>gi|88799449|ref|ZP_01115026.1| tRNA-dihydrouridine synthase B [Reinekea sp. MED297]
 gi|88777759|gb|EAR08957.1| tRNA-dihydrouridine synthase B [Reinekea sp. MED297]
          Length = 329

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/262 (28%), Positives = 129/262 (49%), Gaps = 18/262 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L    K+   L  S + +P+++QI G D
Sbjct: 18  MAGVTDQPFRKLCRSL-GAGLVVSEMVTSDKRLWKTNKSRWRLDHSGEAEPISVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAAK   +FG   I++N+GCP+ +V   + G+ LM +  +V + + A+  A+S+P
Sbjct: 77  AQMLAEAAKTNAEFGAQVIDINMGCPAKKVCNKAAGSALMKDERLVHEILTAVTAAVSVP 136

Query: 119 VTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D Q   A+A+  + +    +G+  + +H R         + +    + +YD
Sbjct: 137 VTLKIRTGWDRQSKNAIAIARMAED---AGIALLSVHGRT--------RADAYRGDAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KE   + +  NG ++   +A ++L     DGVMIGRAA  N  +   ++ Y   
Sbjct: 186 TIARV-KEAVSIPVLANGDIDHPEKAAQVLRDTGADGVMIGRAAQGNPWIFREINHYLKT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISA 257
               + P    V       +SA
Sbjct: 245 GECLAPPAFEEVQTTLLNHLSA 266


>gi|317474747|ref|ZP_07934021.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|316909428|gb|EFV31108.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 327

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 83/304 (27%), Positives = 142/304 (46%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKNFGAD-MVYTEFVSSDALIRSVSKTEQKLKISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   ++  A+ IP
Sbjct: 77  TDTMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRSVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDASNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E++  NP + I +  NG +    +A +      VD +MIGRA++    +   V  Y  
Sbjct: 187 IGEVRN-NPRMHIPIIGNGDITTPQRAKECFDRYGVDAIMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
              TG    P+ +    +  R+      + + + L     +  + RH+    LF G PN 
Sbjct: 246 ---TGEEMPPLSSEWKLNVLRQ----EVEDSVKLLDERRGILHVRRHLAASPLFKGIPNF 298

Query: 291 RRCR 294
           R  R
Sbjct: 299 RDTR 302


>gi|298482601|ref|ZP_07000786.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. D22]
 gi|298271308|gb|EFI12884.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. D22]
          Length = 331

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   +  Y  
Sbjct: 187 IGEVKN-NPRIHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEIKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|167745535|ref|ZP_02417662.1| hypothetical protein ANACAC_00226 [Anaerostipes caccae DSM 14662]
 gi|167655256|gb|EDR99385.1| hypothetical protein ANACAC_00226 [Anaerostipes caccae DSM 14662]
          Length = 332

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 79/298 (26%), Positives = 134/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    LLYTEM+ A  +         +L     E+P+A QI G++
Sbjct: 26  MAGVTDLPYRLLCKEM-GAGLLYTEMVSAKGMYYNSPNTGPLLAKEEWERPIAAQIFGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  V++ G++ I++N+GCP  ++     G+ LM +P + G  I AM   LS+P
Sbjct: 85  PELMADMAVRVQEMGFDLIDINMGCPVPKIVNNGDGSALMKDPVLAGKIIKAMADRLSVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    + K  ++SG   + +H R         ++       D+DI
Sbjct: 145 VTVKIRKGFDDE--HVNAVEMAKIAEQSGAAAVAVHGRT--------REQYYSGKADWDI 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+      IG NG +     A  +L     DG MI R A  N  +   +  YF   
Sbjct: 195 IRQVKEAVSIPVIG-NGDINSPLDAEAMLRETGCDGFMIARGAKGNPWIFKELCHYFDTG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    + +   R  +  M +Y   ++     ++++ +H+    HG   + + R
Sbjct: 254 ELMPRPEIEEIIQMILRH-ARMMIEYKGEYI----GIREMRKHVSWYTHGLAGAAKLR 306


>gi|157826622|ref|YP_001495686.1| putative dihydrouridine synthase Dus [Rickettsia bellii OSU 85-389]
 gi|157801926|gb|ABV78649.1| Putative dihydrouridine synthase Dus [Rickettsia bellii OSU 85-389]
          Length = 406

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 83/298 (27%), Positives = 141/298 (47%), Gaps = 28/298 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGADISK 61
           TD  +R   +      L+ +EMI + A++   ++++   S  +       +Q+ G + + 
Sbjct: 102 TDLEFRRLVKRF-GAGLVVSEMIASRAMIVESRQSLQKCSIMQDDATSACVQLAGCEPNV 160

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ IPVTV
Sbjct: 161 IAEAAKMNEDMGAKIIDLNFGCPAKKVVNGYSGSALMRDEGLAAKIFEAAVKAVKIPVTV 220

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIV 179
           K R+G DDQ        L K  ++SG+  + +H R       G          N D++ +
Sbjct: 221 KMRMGWDDQTKNAP--TLAKIAERSGIQMVTVHGRTRCQFYSG----------NADWEFI 268

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + KE   + +  NG + + ++A + L   S DGVM+GR AY    +++ +D Y     
Sbjct: 269 KNV-KEAVKIPVIANGDITNFAKAKEALEKSSADGVMVGRGAYGKPWLISQIDHYLKTGE 327

Query: 238 TGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              +P I++++  D   +   ++ DY   +  S G +    +HM     G PNS   R
Sbjct: 328 EKPAPSIESQL--DIVLEHYQAIVDY---YGESAG-VPIARKHMGWYSSGLPNSAEFR 379


>gi|229074137|ref|ZP_04207184.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-18]
 gi|229100873|ref|ZP_04231680.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-28]
 gi|228682551|gb|EEL36621.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-28]
 gi|228709031|gb|EEL61157.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-18]
          Length = 339

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 104 DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 163 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 210

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 211 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|253569151|ref|ZP_04846561.1| dehydrogenase [Bacteroides sp. 1_1_6]
 gi|251841170|gb|EES69251.1| dehydrogenase [Bacteroides sp. 1_1_6]
          Length = 330

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 146/326 (44%), Gaps = 36/326 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAIVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  N  + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IEEVKN-NQRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVIDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCRHILTVEAGASTATHHIIET 313
           PN +  R I  + A        I ET
Sbjct: 296 PNFKETR-IAMLRAETKEELFRIFET 320


>gi|94967061|ref|YP_589109.1| dihydrouridine synthase TIM-barrel protein nifR3 [Candidatus
           Koribacter versatilis Ellin345]
 gi|94549111|gb|ABF39035.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Candidatus
           Koribacter versatilis Ellin345]
          Length = 370

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 75/254 (29%), Positives = 128/254 (50%), Gaps = 19/254 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R F R L    L+ TE   AD + R      +  L F   E+P++ Q+ G+
Sbjct: 39  MAGVTDTVFRRFIRNLGGCGLMMTEFTSADGLARMREAKARRYLTFYGNERPISAQLFGS 98

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   L +AAK+V+D G++ ++LN+GCPS RV + + G+ L+ +   +     ++ KA++I
Sbjct: 99  DAETLADAAKVVQDLGFDLVDLNLGCPSKRVVKCNGGSGLLRDLPQIKVIFESVRKAVTI 158

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R G +++   +    L K  +  G+N + +HAR    +G S + N       + 
Sbjct: 159 PFTVKFRAGWNEK--ELVFLELAKLAENCGLNAVAMHARTR-EQGYSGQAN-------WG 208

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K+      IG NG +     A  ++     D VMIGR+A  N  +   +++Y + 
Sbjct: 209 WIADLKQVVKIPVIG-NGDIRTPEDAAAMVAKTGCDAVMIGRSAASNPWIFRQIEQYTA- 266

Query: 236 PLTGSSPIKTRVDK 249
             TG   + T  D+
Sbjct: 267 --TGRYDLPTNEDR 278


>gi|260172925|ref|ZP_05759337.1| dehydrogenase [Bacteroides sp. D2]
 gi|315921208|ref|ZP_07917448.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313695083|gb|EFS31918.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 331

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 139/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVRIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPKRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFDWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|218895212|ref|YP_002443623.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus G9842]
 gi|218540937|gb|ACK93331.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus G9842]
          Length = 332

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++I+++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAIERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|56961898|ref|YP_173620.1| tRNA-dihydrouridine synthase [Bacillus clausii KSM-K16]
 gi|56908132|dbj|BAD62659.1| tRNA-dihydrouridine synthase [Bacillus clausii KSM-K16]
          Length = 333

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 78/242 (32%), Positives = 129/242 (53%), Gaps = 23/242 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL  ++K++  L    +EKPL+LQI G +   LVEAA
Sbjct: 26  FRLIAKEF-GAGLVCAEMVSDKAILHKNEKSLQMLYVDEREKPLSLQIFGGEKDTLVEAA 84

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           + V ++   + I++N+GCP  ++ +   GA  +L+P  + + +AA+  A+  PVTVK RI
Sbjct: 85  RFVDQNTNADIIDINMGCPVPKITKCDAGARWLLDPKKIYEMVAAVVDAVKKPVTVKMRI 144

Query: 126 GVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEI 182
           G D D I A+      ++++++G + + +H R  +   +G++          D++I+ ++
Sbjct: 145 GWDEDHIYAI---ENARAVERAGGSAVAVHGRTRVQMYEGVA----------DWNIIGDV 191

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           KK      IG NG +     A ++L    VDGVMIGRAA  N  ML    +Y  N     
Sbjct: 192 KKAVNIPVIG-NGDVATPQDAKRMLDEYGVDGVMIGRAALGNPWMLYRTIQYLENGTLPP 250

Query: 241 SP 242
            P
Sbjct: 251 EP 252


>gi|254427671|ref|ZP_05041378.1| putative TIM-barrel protein, nifR3 family [Alcanivorax sp. DG881]
 gi|196193840|gb|EDX88799.1| putative TIM-barrel protein, nifR3 family [Alcanivorax sp. DG881]
          Length = 346

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 128/255 (50%), Gaps = 24/255 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    LL +EM+ +D  L   +K+   L  S +  P+++QI G +
Sbjct: 17  MAGVTDRPFRRLCRDL-GAGLLVSEMVTSDTRLWNSRKSRQRLDHSGEPGPISVQIAGGE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   D G   I++N+GCP+ +V + + G+ L+ +PD+V   + A+  A+ +P
Sbjct: 76  PTMLAEAARANVDHGAQIIDINMGCPAKKVCKRAAGSALLADPDLVSRILDAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D DQ  A+A+  + ++   +G+  + IH R             +    + D
Sbjct: 136 VTLKIRTGPDRDQRNALAIARIAEA---AGIQALAIHGRT------------RADKFNGD 180

Query: 178 IVYEIKKENPD---LFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
             Y   K+  D   + +  NG ++   +A ++L S    G+MIGRAA  N  +      Y
Sbjct: 181 AEYTTIKQVVDAVNIPVMANGDVDSPEKAKRVLESTGAGGIMIGRAAQGNPWIFRDTLYY 240

Query: 233 FSNPLTGSSPIKTRV 247
             +    ++P+ T V
Sbjct: 241 LEHGSLPAAPLVTEV 255


>gi|291534721|emb|CBL07833.1| tRNA-U20-dihydrouridine synthase [Roseburia intestinalis M50/1]
          Length = 330

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 143/302 (47%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  ++  + +L    +E P++LQ+ G+D
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNRNTEELLTIDKRENPVSLQLFGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  ++ +++N+GCP  +V     G+ LM NP + G+ I    +A+  P
Sbjct: 82  PDIMSEIAKQIEDRPFDILDINMGCPVPKVVNNGDGSALMKNPKLAGEIIEKTARAIKKP 141

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D++ + AV + ++    ++SG   + +H R         +        D+D
Sbjct: 142 VTVKIRKGFDEEHVNAVEMAHIA---QESGAAAVAVHGRT--------RSQFYSGKADWD 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +   +   A++     DG MI R A  N  +   +  YF  
Sbjct: 191 IIRQVKEAVSIPVIG-NGDILTAADVIAMQKQTGCDGFMIARGAEGNPWIFAQILHYFK- 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG       + K  + +++  +  +A   L   G+   +++I +H      G+ NS +
Sbjct: 249 --TGEE-----LPKPTFEEVTQMLLRHARMQLEFKGEYTGIREIRKHAAWYTSGYRNSSK 301

Query: 293 CR 294
            R
Sbjct: 302 LR 303


>gi|240143461|ref|ZP_04742062.1| tRNA-dihydrouridine synthase [Roseburia intestinalis L1-82]
 gi|257204494|gb|EEV02779.1| tRNA-dihydrouridine synthase [Roseburia intestinalis L1-82]
          Length = 330

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 143/302 (47%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  ++  + +L    +E P++LQ+ G+D
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNRNTEELLTIDKRENPVSLQLFGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  ++ +++N+GCP  +V     G+ LM NP + G+ I    +A+  P
Sbjct: 82  PDIMSEIAKQIEDRPFDILDINMGCPVPKVVNNGDGSALMKNPKLAGEIIEKTARAIKKP 141

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D++ + AV + ++    ++SG   + +H R         +        D+D
Sbjct: 142 VTVKIRKGFDEEHVNAVEMAHIA---QESGAAAVAVHGRT--------RSQFYSGKADWD 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +   +   A++     DG MI R A  N  +   +  YF  
Sbjct: 191 IIRQVKEAVSIPVIG-NGDILTAADVIAMQKQTGCDGFMIARGAEGNPWIFAQILHYFK- 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG       + K  + +++  +  +A   L   G+   +++I +H      G+ NS +
Sbjct: 249 --TGEE-----LPKPTFEEVTQMLLRHARMQLEFKGEYTGIREIRKHAAWYTSGYRNSSK 301

Query: 293 CR 294
            R
Sbjct: 302 LR 303


>gi|71065857|ref|YP_264584.1| NifR3 family TIM-barrel protein [Psychrobacter arcticus 273-4]
 gi|71038842|gb|AAZ19150.1| probable TIM-barrel protein, nifR3 family [Psychrobacter arcticus
           273-4]
          Length = 343

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 77/281 (27%), Positives = 137/281 (48%), Gaps = 20/281 (7%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL EAA+   D G   I++N+
Sbjct: 61  SEMIIADTALYARKKSLYRANFDNEIAPISAQIAGAEPDKLAEAARYQIDNGAQIIDINM 120

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + A   A+  PVT+K R+G ++    + LR + K
Sbjct: 121 GCPAKKVCRKLAGSALLQDEDLVARLLDAAVNAVDAPVTLKTRLGYENGRENI-LR-VAK 178

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             +++G+  I IH R         +++       YD++ E+ KE+  + +  NG ++   
Sbjct: 179 RAEQAGIAAIAIHGRT--------REDMYTGEARYDLIREV-KESISIPVIANGDIDSAQ 229

Query: 202 QALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
           +A ++  L   D VMIGRAA     +   ++ +  +  T + P  + + K     +    
Sbjct: 230 KAQRVYELTGCDAVMIGRAAQGQPWIFRDIEHFLRSGETLAPPSVSEIKKIVLTHLEELY 289

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             Y     +SG ++ +  +H+     G PNS   R  +  E
Sbjct: 290 GFYGE---YSGCRIAR--KHIAWYTTGIPNSNAFRQAMYGE 325


>gi|228905872|ref|ZP_04069770.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 200]
 gi|228853812|gb|EEM98571.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 200]
          Length = 332

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++I+++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAIERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|260591922|ref|ZP_05857380.1| tRNA-dihydrouridine synthase [Prevotella veroralis F0319]
 gi|260536206|gb|EEX18823.1| tRNA-dihydrouridine synthase [Prevotella veroralis F0319]
          Length = 318

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 120/226 (53%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRY-GAAMVYTEFVSADAIIRSIKSTLSKMVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE    + I++N GCP  +V     G+ ++ N  ++ +    + KA+++P
Sbjct: 77  VASMVEAAKIVEQVKPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLEITREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDTE--HLIITDLAEQLQDCGIQALTIHGRT--------RSQMYTGQADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + E+ K NP + I +  NG + +  +A +   +  VD VMIGRA +
Sbjct: 187 IGEVTK-NPRIKIPIIGNGDVTNRLEASEKFDTYGVDAVMIGRATF 231


>gi|228963176|ref|ZP_04124346.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228796561|gb|EEM43999.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 332

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++I+++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAIERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|228898829|ref|ZP_04063112.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 4222]
 gi|228860854|gb|EEN05231.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 4222]
          Length = 332

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++I+++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAIERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|229113752|ref|ZP_04243188.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-3]
 gi|228669749|gb|EEL25155.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-3]
          Length = 339

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 104 DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 163 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 210

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 211 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|326792443|ref|YP_004310264.1| hypothetical protein Clole_3376 [Clostridium lentocellum DSM 5427]
 gi|326543207|gb|ADZ85066.1| TIM-barrel protein, nifR3 family [Clostridium lentocellum DSM 5427]
          Length = 324

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 120/239 (50%), Gaps = 16/239 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      ++ TEM+ A  +L   G   ++L    +E P+  Q+ G+D
Sbjct: 17  MAGITDLPFRLICKEF-GVGMMTTEMVSAKGLLYENGKTNDLLYIDPKEHPIGAQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK VE    + I++N+GCP+ ++ +   G+ L+ NP+++G+ + A+ KAL+ P
Sbjct: 76  PKILSEMAKQVEQSDVDFIDINMGCPAPKITKNGEGSALLKNPELIGEIVYAVAKALTKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G +D++  V    + K I+++G + I +H R         ++     + D+DI
Sbjct: 136 LTVKIRKGFNDEM--VNAVEVAKIIEEAGASAIALHGRT--------REQFYSGSADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K+      IG NG +     A ++L     D V+I RAA  N  +      Y   
Sbjct: 186 IKEVKQHIHIPLIG-NGDIRTPQDAKRMLDYTGCDAVLIARAAQGNPWIFKRTVHYLET 243


>gi|152973924|ref|YP_001373441.1| nifR3 family TIM-barrel protein [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152022676|gb|ABS20446.1| putative TIM-barrel protein, nifR3 family [Bacillus cytotoxicus NVH
           391-98]
          Length = 332

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 79/237 (33%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LVEAAK V ++   + I
Sbjct: 37  LVCAEMVSDKAILFNNKRTLDMLYIDEREKPLSLQIFGGEKETLVEAAKYVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +E    A ++L    VDGVMIGRAA  N  M+    +Y  +  L      + +VD
Sbjct: 203 GDVETPQDAKRMLDEIGVDGVMIGRAALGNPWMIYRTVKYLETGELMPEPTAREKVD 259


>gi|237721929|ref|ZP_04552410.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|229448798|gb|EEO54589.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
          Length = 331

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 138/307 (44%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + + YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRFGAD-MAYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPERCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFDWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|229053922|ref|ZP_04195357.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH603]
 gi|228721463|gb|EEL72983.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH603]
          Length = 332

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I AV  
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHIFAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 -ENARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVETPQDAKRMLDEVGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|227202714|dbj|BAH56830.1| AT3G63510 [Arabidopsis thaliana]
          Length = 261

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 52/127 (40%), Positives = 77/127 (60%), Gaps = 2/127 (1%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHAR 156
           ML P +VG+ ++A+    ++PVTVKCRIGVD+      L + +  +   S      +H+R
Sbjct: 1   MLKPKLVGEAMSAIAANTNVPVTVKCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSR 60

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMI 215
           KA+L G+SP DNR+IP L Y+  Y + ++ PDL   +NGG+  +S+    L     GVM+
Sbjct: 61  KALLGGISPADNRRIPPLKYEYYYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMV 120

Query: 216 GRAAYKN 222
           GRAAY N
Sbjct: 121 GRAAYNN 127


>gi|311029014|ref|ZP_07707104.1| YacF [Bacillus sp. m3-13]
 gi|311032310|ref|ZP_07710400.1| YacF [Bacillus sp. m3-13]
          Length = 333

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 127/235 (54%), Gaps = 17/235 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
            L+  EM+   AIL  + K +  L    +EKPL+LQI G +   LVEAAK V+ +   + 
Sbjct: 36  GLVCAEMVSDKAILYKNAKTMGMLYIDEREKPLSLQIFGGEKDTLVEAAKFVDKNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK R G D+     A+
Sbjct: 96  IDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVDKPVTVKMRTGWDED-HIFAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            N  ++++++G   + +H R  +             + D+DI+ ++K+      IG NG 
Sbjct: 155 EN-ARAVERAGGQAVAVHGRTRV--------QMYEGHADWDIIKQVKESVNIPVIG-NGD 204

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           ++    A ++L    VDGVMIGRAA  N  M+ +  +Y  +  L G   ++ ++D
Sbjct: 205 VQTPQDAKRMLEETGVDGVMIGRAALGNPWMIYSTVQYLETGKLVGEPSVREKMD 259


>gi|317472901|ref|ZP_07932207.1| dihydrouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316899621|gb|EFV21629.1| dihydrouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 332

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 78/298 (26%), Positives = 134/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    LLYTEM+ A  +         +L     E+P+A QI G++
Sbjct: 26  MAGVTDLPYRLLCKEM-GAGLLYTEMVSAKGMYYNSPNTGPLLAKEEWERPIAAQIFGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  V++ G++ I++N+GCP  ++     G+ LM +P + G  I AM   LS+P
Sbjct: 85  PELMADMAVRVQEMGFDLIDINMGCPVPKIVNNGDGSALMKDPVLAGKIIKAMADRLSVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    + +  ++SG   + +H R         ++       D+DI
Sbjct: 145 VTVKIRKGFDDE--HVNAVEMARIAEQSGAAAVAVHGRT--------REQYYSGKADWDI 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+      IG NG +     A  +L     DG MI R A  N  +   +  YF   
Sbjct: 195 IRQVKEAVSIPVIG-NGDINSPLDAEAMLRETGCDGFMIARGAKGNPWIFKELCHYFDTG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    + +   R  +  M +Y   ++     ++++ +H+    HG   + + R
Sbjct: 254 ELMPRPEIEEIIQMILRH-ARMMIEYKGEYI----GIREMRKHVSWYTHGLAGAAKLR 306


>gi|228937378|ref|ZP_04100025.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970264|ref|ZP_04130924.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228976834|ref|ZP_04137247.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis Bt407]
 gi|228782930|gb|EEM31095.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis Bt407]
 gi|228789499|gb|EEM37418.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228822336|gb|EEM68317.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|326937868|gb|AEA13764.1| Nif3 family protein [Bacillus thuringiensis serovar chinensis
           CT-43]
          Length = 332

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|225389821|ref|ZP_03759545.1| hypothetical protein CLOSTASPAR_03569 [Clostridium asparagiforme
           DSM 15981]
 gi|225044131|gb|EEG54377.1| hypothetical protein CLOSTASPAR_03569 [Clostridium asparagiforme
           DSM 15981]
          Length = 319

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 82/309 (26%), Positives = 139/309 (44%), Gaps = 25/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      ++ TEM+ A AIL  +K  K +L   ++E+P A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGCGMVVTEMVSAKAILYKNKNTKELLTVRSEERPAAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +ED  Y+ I++N+GCP  ++     G+ LM +P      ++AM +A+  P
Sbjct: 78  PEIMAEIAAQIEDGPYDVIDVNMGCPVPKIVNNGEGSALMKDPKRAEAVLSAMVRAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D+  +V      K  +  GV  + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFNDE--SVNAVEFAKMAESCGVAAVAVHGRT--------REQYYSGTADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+      IG NG +     A ++L     DG+M+ R A  N  +   ++ Y    
Sbjct: 188 IRRVKEAVKIPVIG-NGDVFTPEDAGRLLEQTGCDGIMVARGAKGNPWIFHRINHYLETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI----GLFHGFPNSRR 292
            +   P    + +   R  S  + DY    +     ++++  HM     GL H     R 
Sbjct: 247 ESLPGPSVQEIREMILRH-SRMLADYKGERV----AMREMRSHMAWYTSGLAHSASIRRE 301

Query: 293 CRHILTVEA 301
              + T+E 
Sbjct: 302 INGVETMEG 310


>gi|298385818|ref|ZP_06995375.1| hypothetical protein HMPREF9007_02527 [Bacteroides sp. 1_1_14]
 gi|298261046|gb|EFI03913.1| hypothetical protein HMPREF9007_02527 [Bacteroides sp. 1_1_14]
          Length = 330

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 146/326 (44%), Gaps = 36/326 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  N  + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NQRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVIDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCRHILTVEAGASTATHHIIET 313
           PN +  R I  + A        I ET
Sbjct: 296 PNFKETR-IAMLRAETKEELFRIFET 320


>gi|29348482|ref|NP_811985.1| dehydrogenase [Bacteroides thetaiotaomicron VPI-5482]
 gi|29340386|gb|AAO78179.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Bacteroides thetaiotaomicron VPI-5482]
          Length = 330

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 92/326 (28%), Positives = 146/326 (44%), Gaps = 36/326 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRAVSKTAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  N  + I +  NG +    +  +      VD VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NQRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFEWCMEVLRQEVIDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCRHILTVEAGASTATHHIIET 313
           PN +  R I  + A        I ET
Sbjct: 296 PNFKETR-IAMLRAETKEELFRIFET 320


>gi|293373770|ref|ZP_06620116.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CMC 3f]
 gi|292631260|gb|EFF49892.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CMC 3f]
          Length = 331

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 138/307 (44%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + + YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRFGAD-MAYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +  +      +D VMIGRA++    +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTPQRCKECFDHYGIDAVMIGRASFGRPWIFKEVKHYLE 245

Query: 235 NPLTGSS--PIKTRVDKDFWRKI---SASMTDYAARHLHSGGKLQQITRHMIG--LFHGF 287
              TG    P+      +  R+    S ++ D     LH       + RH+    LF G 
Sbjct: 246 ---TGEELPPLSFDWCMEVLRQEVVDSVNLLDERRGILH-------VRRHLAASPLFKGI 295

Query: 288 PNSRRCR 294
           PN R  R
Sbjct: 296 PNFRNTR 302


>gi|239626632|ref|ZP_04669663.1| TIM-barrel protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516778|gb|EEQ56644.1| TIM-barrel protein [Clostridiales bacterium 1_7_47FAA]
          Length = 328

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 114/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R       + TEM+ A AIL  ++  K ++    QE+P A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGAGCVVTEMVSAKAILYNNRNTKELMQIHPQERPAAIQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +ED  Y+ I++N+GCP  ++     G+ LM NP++    ++AM KA+  P
Sbjct: 78  PDIMAQIAARIEDGPYDFIDVNMGCPVPKIVNNGEGSALMKNPELAEKILSAMVKAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D    V      K  + SGV  + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFNDT--CVNAVEFAKMAEASGVAAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           + ++K+      IG NG +     A +++     DG+M+ R A  N  +   +  Y 
Sbjct: 188 IRQVKEAVKIPVIG-NGDIFTPQDAGRMMEETGCDGIMVARGAKGNPWIFRRISHYL 243


>gi|229083394|ref|ZP_04215744.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-44]
 gi|228699930|gb|EEL52565.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-44]
          Length = 332

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 79/237 (33%), Positives = 129/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +++  ++L    +EKPL+LQI G +   LV AAK V+     +I 
Sbjct: 37  LVCAEMVSDKAILLNNQRTLDMLYIDEREKPLSLQIFGGEKETLVGAAKYVDKSTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+PD V + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPDKVYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  ++I+++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-ARAIERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +E    A ++L    VDGVMIGRAA  N  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVETPQDAKRMLDEIGVDGVMIGRAALGNPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|229027922|ref|ZP_04184077.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1271]
 gi|229170926|ref|ZP_04298529.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus MM3]
 gi|228612592|gb|EEK69811.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus MM3]
 gi|228733436|gb|EEL84263.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1271]
          Length = 339

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 131/237 (55%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIIKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDADHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|239946645|ref|ZP_04698398.1| tRNA-dihydrouridine synthase [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239920921|gb|EER20945.1| tRNA-dihydrouridine synthase [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 325

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 85/323 (26%), Positives = 145/323 (44%), Gaps = 26/323 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   ++++   +          +Q+ G + + 
Sbjct: 22  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLQKSAIMRDDATSACIQLAGCEPNV 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ +PVTV
Sbjct: 81  IAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVKAVKLPVTV 140

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD         L K  + SGV  + +H R         +      N D+D +  
Sbjct: 141 KMRMGWDDNTKNAP--TLAKIAESSGVQMVTVHGRT--------RCQFYSGNADWDFIRS 190

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE   + +  NG + + ++A + L    VDG+M+GR AY    +++ +D Y       
Sbjct: 191 V-KEAVKIPVIANGDITNFAKAKEALQKSGVDGIMVGRGAYGKPWLISQIDHYLKTGKEK 249

Query: 240 SSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCRHIL 297
           S+P I  ++  D   +   ++ DY    +        I R  IG +  G PNS   R  +
Sbjct: 250 SAPSIAEQL--DIVTEHYDAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFRGAV 302

Query: 298 TVEAGASTATHHIIETAFNLMIE 320
            +    +     I E   N+M E
Sbjct: 303 NLMNDPAAVKEKIAEFYNNVMKE 325


>gi|260910934|ref|ZP_05917575.1| dihydrouridine synthase [Prevotella sp. oral taxon 472 str. F0295]
 gi|260634925|gb|EEX52974.1| dihydrouridine synthase [Prevotella sp. oral taxon 472 str. F0295]
          Length = 333

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 81/304 (26%), Positives = 144/304 (47%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYTEFVSAEALVRSVKSTVSKLTISDEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  RV     GA ++ N  ++ +    + +A+  P
Sbjct: 77  VESMVEAARIVEQSHPDVIDINFGCPVKRVAGKGAGAGMLRNVPLMLEITREVVRAVRTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G + +   + +  L + ++  G+  + IH R         +        D+  
Sbjct: 137 VTVKTRLGWNCE--EIIIPTLAEQLQDCGIAALTIHGRT--------RSQMYTGEADWRY 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    QA +      VD VM+GRA +    +   + ++  
Sbjct: 187 IGEVKA-NPRIHIPIIGNGDICTPQQAKEAFDRYGVDAVMVGRATFGRPWVFKEMKDHLE 245

Query: 235 N-PLTGSSPIKTRVD-KDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNS 290
             P   S  +  ++D  +   +I+    D     LH+        RH+    +F G P+ 
Sbjct: 246 GLPQDPSLTLDRKIDLLEEQLRINIERIDEYRGILHT-------RRHLAASPIFKGIPDF 298

Query: 291 RRCR 294
           ++ R
Sbjct: 299 KQTR 302


>gi|83311464|ref|YP_421728.1| NifR3-like protein [Magnetospirillum magneticum AMB-1]
 gi|82946305|dbj|BAE51169.1| NifR3-like protein [Magnetospirillum magneticum AMB-1]
          Length = 305

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 79/291 (27%), Positives = 139/291 (47%), Gaps = 25/291 (8%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK 67
           R   RL     L+ +EMI + A++R +++   +   + +E P+++Q+ G +   + EAAK
Sbjct: 5   RLVKRL--GAGLVVSEMIASQAMIRQNRQTMQMAQHTAEEFPMSVQLAGCEPKVMAEAAK 62

Query: 68  IVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + +D G   I++N+GCP  +V  +G  G+ LM N ++    + A+ KA+ IPVT+K R G
Sbjct: 63  LNQDLGAAIIDINMGCPVKKVALKGEAGSALMRNENLAARILTAVVKAVDIPVTLKMRTG 122

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            D  + +    +L +  ++ G+  + +H R         ++       D+  + E+K+  
Sbjct: 123 WD--MNSRNAPSLARVAEECGIRMVTVHGRT--------RNQMYTGQADWAFIGEVKRAV 172

Query: 187 PDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS-PI 243
               IG NG +E +  A+++  L   DGVMIGR  Y    +   V  Y +   TG   P 
Sbjct: 173 SIPVIG-NGDVESIDDAVRMLELSGADGVMIGRGTYGRPWLPGQVAHYLA---TGERLPD 228

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            +R ++    +I     D    H  S   ++   +HM     G P S   R
Sbjct: 229 PSRAEQ---LQIMLEHLDAMLSHYGSEPGVRIARKHMAWYSKGLPGSAEFR 276


>gi|311745604|ref|ZP_07719389.1| TIM-barrel protein, putative, NifR3 family [Algoriphagus sp. PR1]
 gi|126578167|gb|EAZ82387.1| TIM-barrel protein, putative, NifR3 family [Algoriphagus sp. PR1]
          Length = 329

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 89/305 (29%), Positives = 148/305 (48%), Gaps = 33/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A L+YTE I ++ ++R   K++  L     EKP+ +QI G 
Sbjct: 19  MEDVSDPPFRAVCK--QNGADLMYTEFISSEGLIRDAAKSVQKLDIYDYEKPIGIQIFGN 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           DI  + EAA I  + G + +++N GCP  +V     GA ++L+ D +    A + KA+ I
Sbjct: 77  DIESMREAAAIAAEAGPDILDINYGCPVNKVACKGAGAGILLDIDKMVSMTAEIVKAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G D+    + +  + + ++  G+  I IHA  RK + KG            +
Sbjct: 137 PVTVKTRLGWDND--TIRIVEVAERLQDVGIQAISIHARTRKQMYKG------------E 182

Query: 176 YDIVY-EIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVD 230
            D  Y  + KENP L I +  NG ++   +AL  K   +VDG+MIGRA+     +   + 
Sbjct: 183 ADWSYLNLVKENPRLHIPVFGNGDIDSPEKALEYKTKYNVDGMMIGRASIGYPWIFNEIK 242

Query: 231 EYFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            + +      +P I+ R+       ++    D++         + ++ RH    F G PN
Sbjct: 243 HFLATGEKLEAPSIEERI------AVAKQHLDFSVEWKGEKQGILEMRRHYTNYFRGMPN 296

Query: 290 SRRCR 294
            +  R
Sbjct: 297 FKPIR 301


>gi|291542003|emb|CBL15113.1| tRNA-U20-dihydrouridine synthase [Ruminococcus bromii L2-63]
          Length = 328

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 83/312 (26%), Positives = 144/312 (46%), Gaps = 36/312 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +DR YR    +    A   +EM+ + A+    KK+  ++  S  E+P  +QI G D
Sbjct: 24  MAGVSDRAYRELC-VRFGAAYCVSEMVSSKALSFNSKKSEELMEISDLERPCGIQIFGDD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAK   +   + I++N+GCP+ ++     G+ LM NP + G+ + A+     IP
Sbjct: 83  PKCMADAAKHALENKPDIIDINMGCPAPKISSNGSGSALMKNPRLCGEIVKAVTAVTDIP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD   +V    + K  + +G   I +H R         +     P +DYDI
Sbjct: 143 VTVKIRKGWDDD--SVNAVEVAKICESAGAAAITVHGRT--------RQQYYKPPVDYDI 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +E+  + +  NG ++   +A +++     D VMIGRA   N  + + ++ Y  NP
Sbjct: 193 IRAV-RESVSVPVIANGDIDSAERAKEVMDITGCDLVMIGRATLGNPWIFSQINAYLENP 251

Query: 237 LTGSSPIKTRVDKDFWRKIS------ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              +  I T    D   ++       + M +Y   H+     + Q  + ++G F G   +
Sbjct: 252 ---NVKIHT---PDLEERLGVMIEHISKMVEYKGEHM----AMLQARKLVVGYFKGMKGA 301

Query: 291 RRCRHILTVEAG 302
              R+    EAG
Sbjct: 302 AALRN----EAG 309


>gi|255529934|ref|YP_003090306.1| TIM-barrel protein, nifR3 family [Pedobacter heparinus DSM 2366]
 gi|255342918|gb|ACU02244.1| TIM-barrel protein, nifR3 family [Pedobacter heparinus DSM 2366]
          Length = 335

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 88/323 (27%), Positives = 152/323 (47%), Gaps = 34/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +RF  +  +   ++YTE I ++ ++R   K+   L     E+P+ +QI G++
Sbjct: 20  MEDVSDPPFRFVCKQ-SGVDMMYTEFISSEGLIRDAAKSRAKLDIFEYERPIGIQIFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I    G + +++N GCP   V     GA L+ + D +     A+ KA  +P
Sbjct: 79  IDHMREATEIATLAGPDLMDINYGCPVKNVACRGAGASLLQDIDKMVRMTEAVVKATHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    V    + + ++  G+  + IH R    + KG            D+
Sbjct: 139 VTVKTRLGWDDNTKNV--EEVAERLQDIGIQALTIHGRTRAQLYKG----------EADW 186

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ +IK+ NP + I +  NG ++ + +A   ++   VDG+MIGRAA     +   +  +
Sbjct: 187 TLIRQIKR-NPRIKIPIFGNGDVDSIRKAADWRLEYEVDGIMIGRAAIGYPWIFREIRHF 245

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPN 289
           F+   T + P I+ RV        S   T +       G ++   ++ RH    F G P+
Sbjct: 246 FNTGKTLAGPSIEERV--------SVCRTHFEKSIAWKGPRVGIFEMRRHYANYFKGIPD 297

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
            +  R  L  E    T  H I++
Sbjct: 298 FKSYRMQLVKEENIDT-IHSILD 319


>gi|168335421|ref|ZP_02693512.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Epulopiscium sp. 'N.t. morphotype B']
          Length = 315

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 85/303 (28%), Positives = 146/303 (48%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  YR   +      L+YTEM+ A A+L  + K   +L  +  E P+A Q+ G+D
Sbjct: 17  MAGFTDLPYRNICKEF-GAGLVYTEMVSAKALLYENDKTCVLLQVADTEHPVAAQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S L   A+ V +   + I+LN+GCP+ ++ +   G+ L+ NP +V   ++A+ KA   P
Sbjct: 76  PSILSAMAQQVSESSVDFIDLNMGCPAPKITKNGEGSALLANPKLVYTIVSAVAKASPKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  +    V    + ++I+ +G + I +H R         +D       D+DI
Sbjct: 136 VTVKIRKGYTE----VNAIEVAQAIEAAGASAITLHGRT--------RDQFYSGVADWDI 183

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K +     IG NG ++    A  +L   + D +MIGRAA  N  +      Y +  
Sbjct: 184 IKKVKSKIAIPLIG-NGDIKSPEDAKAMLDYTNCDAIMIGRAALGNPWIFQRTLHYLN-- 240

Query: 237 LTGS-SPIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            TG   P  T  +K +   K + S+  +   ++     ++++  H+     GFP + + R
Sbjct: 241 -TGELLPDPTLPEKIEIILKHTQSLIAFKGEYIG----IREMRAHLSCYIKGFPQAAKLR 295

Query: 295 HIL 297
             L
Sbjct: 296 SDL 298


>gi|34539899|ref|NP_904378.1| NifR3 family TIM-barrel protein [Porphyromonas gingivalis W83]
 gi|34396210|gb|AAQ65277.1| TIM-barrel protein, putative, NifR3 family [Porphyromonas
           gingivalis W83]
          Length = 333

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + L+Y+E + ADA++R        +     E+P+A+QI G D
Sbjct: 18  MEDVTDVAFRIMCKQFGAD-LVYSEFLSADALIRQVAGTFRKMAIDESERPMAVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA++ E  G N I+LN GCP  RV     G+ ++ N  ++ +    + KA+ +P
Sbjct: 77  VASMVEAARLCESAGPNLIDLNFGCPVKRVAGKGAGSGMLRNIPLMIEITREVVKAVKLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNDSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGTADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD VM+GRA+     +   +  +  
Sbjct: 187 IGEVKN-NPRMQIPIIGNGDVTTPQEARRAFDVYGVDAVMVGRASIGQPWIFEDMKHFLR 245

Query: 235 NPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              T  S P        ++  I    T    R L     +    RH+    +F G PN +
Sbjct: 246 TGETLPSRPFS------YYMDILRRQTLNNIRKLDERRGILHTRRHIAASPIFKGIPNFK 299

Query: 292 RCR 294
             R
Sbjct: 300 PMR 302


>gi|114565683|ref|YP_752837.1| nifR3 family TIM-barrel protein [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114336618|gb|ABI67466.1| putative TIM-barrel protein, NifR3 family [Syntrophomonas wolfei
           subsp. wolfei str. Goettingen]
          Length = 318

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 81/308 (26%), Positives = 143/308 (46%), Gaps = 39/308 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D+ YR  AR      L+ +EM+    ++ G  +   I   S +++P+A+QI G++
Sbjct: 18  MAGVSDKAYRVLARDF-GCGLVCSEMVSDKGLVYGQGRTSKIADSSGEKRPVAVQIFGSE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+IVE+ G + I++N+GCP+ ++ +   GA LML+       +  + + + +P
Sbjct: 77  AESMATAARIVEEMGADIIDINMGCPTPKIVKNGEGAALMLDITKSRGIVREVLRVVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDY 176
           VTVK R G D+   ++    L + +++ GV  I +H  +R+    G          + D+
Sbjct: 137 VTVKMRKGWDEN--SINCLELAQKLEEEGVAAICLHPRSRQQFFSG----------SADW 184

Query: 177 DIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +++ E+KKE     IG NG +   D +Q +      D VMIGRAA  N  +     E   
Sbjct: 185 NLIKEMKKELKIPVIG-NGDIWSADDAQRMIDFTGCDAVMIGRAALGNPFIFRETFELLE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-------SGGKLQQITRHMIGLFHGF 287
           N      P  +R ++             A RHL+           ++++ +H      G 
Sbjct: 244 N--NRRIPPPSREER----------LQTATRHLNLVCQFKSEAVAVREMRKHFAWYIKGL 291

Query: 288 PNSRRCRH 295
           P + R R 
Sbjct: 292 PGATRVRQ 299


>gi|293571080|ref|ZP_06682121.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E980]
 gi|291608863|gb|EFF38144.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E980]
          Length = 334

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/222 (34%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ VE+    + I
Sbjct: 40  LVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGNKDSLVEAAQFVEENTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + + A+  A+ IPVTVK RIG D++    A+ 
Sbjct: 100 DINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDIPVTVKMRIGWDEE-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + + +G + I +H R  +   +G +          D++I+ E+KK     F+G NG
Sbjct: 159 NALAA-QSAGASAIAMHGRTRVQMYEGKA----------DWEILKEVKKHLTIPFMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A ++L  V  DGVMIGRAA  N  M+     Y   
Sbjct: 207 DVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248


>gi|144899194|emb|CAM76058.1| Dihydrouridine synthase, DuS [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 335

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 120/236 (50%), Gaps = 19/236 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+ +EMI + A++R +++ +   S   +E P+++Q+ G +   + EAA++  D G   I+
Sbjct: 44  LVVSEMIASQAMIRANRQTMKMASNCAEEHPMSVQLAGCEPEVMAEAARMNADRGAAIID 103

Query: 79  LNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +N+GCP  +V  +G  G+ LM +  + G  + A  +A+ +PVT+KCR+G D     +   
Sbjct: 104 INMGCPVKKVAVKGEAGSALMKDEILAGQLMEATVRAVDVPVTLKCRMGWDHN--RLNAP 161

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L +  ++SG+  + IH R         +        D+  V ++ K+  D+ + +NG +
Sbjct: 162 RLARIAQESGIKMVTIHGRT--------RQQFYTGTADWKFVRQV-KDAVDIPVIVNGDI 212

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           E +  A++ L     DGVMIGR +Y        V  Y +   TG  P    +D+  
Sbjct: 213 ETIDDAIRALAESGADGVMIGRGSYGRPWFPGQVAHYLA---TGERPADPALDQQL 265


>gi|227552661|ref|ZP_03982710.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257888629|ref|ZP_05668282.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897416|ref|ZP_05677069.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|293378826|ref|ZP_06624981.1| TIM-barrel protein, nifR3 family [Enterococcus faecium PC4.1]
 gi|227178190|gb|EEI59162.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257824683|gb|EEV51615.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257833981|gb|EEV60402.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|292642367|gb|EFF60522.1| TIM-barrel protein, nifR3 family [Enterococcus faecium PC4.1]
          Length = 334

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/222 (34%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ VE+    + I
Sbjct: 40  LVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGNKDSLVEAAQFVEENTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + + A+  A+ IPVTVK RIG D++    A+ 
Sbjct: 100 DINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDIPVTVKMRIGWDEE-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + + +G + I +H R  +   +G +          D++I+ E+KK     F+G NG
Sbjct: 159 NALAA-QSAGASAIAMHGRTRVQMYEGKA----------DWEILKEVKKHLTIPFMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A ++L  V  DGVMIGRAA  N  M+     Y   
Sbjct: 207 DVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248


>gi|157803198|ref|YP_001491747.1| nifR3-like protein [Rickettsia canadensis str. McKiel]
 gi|157784461|gb|ABV72962.1| nifR3-like protein [Rickettsia canadensis str. McKiel]
          Length = 326

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 137/297 (46%), Gaps = 26/297 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   ++++   +          +Q+ G + + 
Sbjct: 22  TDLEFRRLVKRF-GVGLVVSEMVASRAMIVESRQSLQKSAIMRDDATSACVQLAGCEPNV 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ ED G   I+LN GCP+ +V EG  G+ LM +  +      A  KA+ IPVTV
Sbjct: 81  IAEAAKMNEDMGAKIIDLNFGCPAKKVVEGYSGSALMRDEQLAAKIFEATVKAVKIPVTV 140

Query: 122 KCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R+G DDQ   A  L N+ ++   SG+  + +H R         +      N D+D + 
Sbjct: 141 KMRMGWDDQTKNAPTLANIAEN---SGIQMVTVHGRT--------RCQFYSGNADWDFIR 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + KE  ++ +  NG + + ++A + L     DG+MIGR AY    +++ +D Y      
Sbjct: 190 SV-KEVVNIPVIANGDITNFTKAKEALQKSGADGIMIGRGAYGKPWLISQIDHYLKTGEA 248

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
             +P       D   +   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 249 KPAP-SIAEQLDIVTEHYEAIIDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 299


>gi|163938084|ref|YP_001642968.1| nifR3 family TIM-barrel protein [Bacillus weihenstephanensis KBAB4]
 gi|229009585|ref|ZP_04166812.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides DSM 2048]
 gi|229131083|ref|ZP_04259996.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST196]
 gi|229165064|ref|ZP_04292860.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH621]
 gi|163860281|gb|ABY41340.1| putative TIM-barrel protein, nifR3 family [Bacillus
           weihenstephanensis KBAB4]
 gi|228618449|gb|EEK75478.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH621]
 gi|228652420|gb|EEL08344.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST196]
 gi|228751729|gb|EEM01528.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides DSM 2048]
          Length = 332

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 131/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   I +H R  +   +G +          D++I+ ++K+      IG NG
Sbjct: 156 N-ARAVERAGGQAIAVHGRTRVQMYEGKA----------DWNIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|260439202|ref|ZP_05793018.1| tRNA-dihydrouridine synthase B [Butyrivibrio crossotus DSM 2876]
 gi|292808217|gb|EFF67422.1| tRNA-dihydrouridine synthase B [Butyrivibrio crossotus DSM 2876]
          Length = 320

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/288 (26%), Positives = 135/288 (46%), Gaps = 19/288 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TD  YR   + +  + ++ TEM+ A A+L  +K   +   T  +E P ALQ+ G+D
Sbjct: 17  MAGVTDLPYRLICKEMGCDYMV-TEMVSAKAVLYNNKNTDILLQTLPEEAPSALQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E  G+   ++N+GCP  ++     G+ LM NP + G  +  M K ++ P
Sbjct: 76  PEIMADIALRLEPLGFAAFDINMGCPVPKIVNNGEGSSLMKNPSLAGKIVDTMVKKITKP 135

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D++ + AV   ++   +++SG   + +H R         ++       D+D
Sbjct: 136 VTVKFRKGFDEEHVNAVEFAHI---MEESGAAAVTVHGRT--------REQFYSGKADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K +      G NG +     ALK+      DG+ +GR A  N  +   +      
Sbjct: 185 IIAAVKDKVKIPVFG-NGDIFSSEDALKMFHYTGCDGIAVGRGAKGNPWLFREIKAAIHG 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +  + P  T + KD  +K +  MT+Y   ++      + ++ +  GL
Sbjct: 244 DVIPARPSLTEI-KDMIKKHATLMTEYKPEYMVVREMRKHVSWYTTGL 290


>gi|123430787|ref|XP_001307959.1| TIM-barrel protein, nifR3 family protein [Trichomonas vaginalis G3]
 gi|121889614|gb|EAX95029.1| TIM-barrel protein, nifR3 family protein [Trichomonas vaginalis G3]
          Length = 301

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 127/235 (54%), Gaps = 18/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R  A     + +  TEM+ A A++  +KK I  L  S +EK +A+QI G+D
Sbjct: 1   MAGYTDIAFREVATEKGAD-ITVTEMVSAMALVYENKKTIDLLDISPKEKKVAVQIFGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I+ D+ ++ +++N+GCP+ ++ + + G+ L+ NP +V D + ++ K  + P
Sbjct: 60  PDVMGEAARILNDYDFSYVDINMGCPAPKIVKNNSGSHLLSNPSLVYDIVKSVVKNSNKP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G    I  V+    +K+I+ +G + + +H R         ++       D+D 
Sbjct: 120 VTAKVRKG----IGGVSSMKAIKNIEAAGASFVTVHGR--------TREEYYTGKADWDF 167

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           + E+ KEN  + +  NG ++    A++ +    VDG+ IGR A  N  +   ++E
Sbjct: 168 IKEV-KENVKIPVIGNGDVDSPEDAIEKINYSKVDGLAIGRGAIGNPYIFNQIEE 221


>gi|257899975|ref|ZP_05679628.1| dihydrouridine synthase [Enterococcus faecium Com15]
 gi|257837887|gb|EEV62961.1| dihydrouridine synthase [Enterococcus faecium Com15]
          Length = 334

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/222 (34%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ VE+    + I
Sbjct: 40  LVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGNKDSLVEAAQFVEENTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + + A+  A+ IPVTVK RIG D++    A+ 
Sbjct: 100 DINMGCPVNKVIKAEAGAKWLLDPEKVYEMVKAVSSAVDIPVTVKMRIGWDEE-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + + +G + I +H R  +   +G +          D++I+ E+KK     F+G NG
Sbjct: 159 NALAA-QSAGASAIAMHGRTRVQMYEGKA----------DWEILKEVKKHLTIPFMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A ++L  V  DGVMIGRAA  N  M+     Y   
Sbjct: 207 DVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248


>gi|312136045|ref|YP_004003383.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor owensensis
           OL]
 gi|311776096|gb|ADQ05583.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor owensensis
           OL]
          Length = 328

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/302 (24%), Positives = 143/302 (47%), Gaps = 28/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        N  + TEM+ + A++ G  K   ++ FS +EK   +QI G+D
Sbjct: 13  MAGFTDKVFRRLCSRFGANVTV-TEMVSSKALVLGSTKTKELISFSQEEKIRGVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++ +   G  LM NP +    + ++ K    
Sbjct: 72  PKVMAQSVKILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLASRIVESIAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++  ++        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEE--SINAPEFAYILQESGASFVTVHGR--------TRTQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++ KE   + +  NG + D   A ++  +   D +MIGRAA  N  +   + E F  
Sbjct: 182 IIRKV-KEKVKIPVVANGDITDFESAKRVYEVTGADSIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
               +  +   K RV  +F+R++ +   +  A        + +  +H+     G  N+ +
Sbjct: 241 GYVETKVLPHMKIRVAIEFFRQLCSEKGEKMA--------VLEARKHLSFFVKGIENAAK 292

Query: 293 CR 294
            R
Sbjct: 293 IR 294


>gi|167768161|ref|ZP_02440214.1| hypothetical protein CLOSS21_02717 [Clostridium sp. SS2/1]
 gi|317499618|ref|ZP_07957880.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167709685|gb|EDS20264.1| hypothetical protein CLOSS21_02717 [Clostridium sp. SS2/1]
 gi|291560187|emb|CBL38987.1| tRNA-U20-dihydrouridine synthase [butyrate-producing bacterium
           SSC/2]
 gi|316893093|gb|EFV15313.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 332

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/299 (25%), Positives = 137/299 (45%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   +      ++ TEM+ A  +  G++K+  ++    +E P+A+QI G+D
Sbjct: 25  MAGVTDLPYRLLCKE-QGAGMMCTEMVSAKGLYYGNRKSEPLMATDPKEIPIAIQIFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  V D  +  I++N+GCP  ++     G+ LM NP++ G  I A+  A+ IP
Sbjct: 84  PEIMGQMAAKVNDGRFQMIDINMGCPVPKIVNNGDGSALMKNPELAGKVIKAVVDAVDIP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D++  +    + +  +++G   I +H R         ++       D+ I
Sbjct: 144 VTVKIRKGFNDEL--INAPEMAQVAQENGAAAIAVHGRT--------REQYYSGTADWSI 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ KE  D+ +  NG +      L++      DG MIGR A  N  +   +  +F   
Sbjct: 194 IRKV-KEAVDIPVIGNGDITCAKDVLRMQEETGCDGFMIGRRAKGNPWIFKEILHFFETG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P    V     R     M D+   ++     ++++ +H+     GFP + + R 
Sbjct: 253 EEMPRPSLEEVVAMMLRH-GQMMIDFKGEYIG----VREMRKHVAWYTFGFPGAAKLRE 306


>gi|288554691|ref|YP_003426626.1| nitrogen regulation transcriptional regulator [Bacillus
           pseudofirmus OF4]
 gi|288545851|gb|ADC49734.1| nitrogen regulation transcriptional regulator [Bacillus
           pseudofirmus OF4]
          Length = 333

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/235 (32%), Positives = 127/235 (54%), Gaps = 23/235 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL  +++++  L    +EKPL+LQI G +   LVEAA
Sbjct: 26  FRLIAKEF-GAGLVCAEMVSDKAILHKNERSLSMLYVDDREKPLSLQIFGGEKETLVEAA 84

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA   A+  PVTVK RI
Sbjct: 85  KFVDKNTNADIIDINMGCPVPKITKCDAGARWLLDPNKIYEMVAATVDAVDKPVTVKMRI 144

Query: 126 GVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEI 182
           G D D I AV      ++++++G + + +H R  +   +G          + D++I+ E+
Sbjct: 145 GWDEDHIFAV---ENARAVERAGGSAVAVHGRTRVQMYEG----------HADWNIIKEV 191

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           K       IG NG ++    A +++    VDGVMIGRAA  N  ML    +Y  N
Sbjct: 192 KDAVNIPVIG-NGDVQSPQDARRMIDEIGVDGVMIGRAALGNPWMLYRTVKYLEN 245


>gi|332879824|ref|ZP_08447513.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332682201|gb|EGJ55109.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 324

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/320 (25%), Positives = 154/320 (48%), Gaps = 36/320 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L   + +LY+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKLHGAD-MLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+ ++  +P
Sbjct: 78  EEAMALSAKIVATVRPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVRSTDLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+   ++ +  + + ++  G++ + IHA  R  + KG S          D+
Sbjct: 138 VTVKTRLGWDES--SINIEEVAERLQDVGISALTIHARTRSQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG +++  +AL+      VDG+MIGRAA     +   +  Y
Sbjct: 186 SYIAKVKN-NPRIHIPIFGNGDIDNPEKALEYRNKYGVDGIMIGRAAIGYPWIFREIKHY 244

Query: 233 FSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ---QITRHMIGLFHGFP 288
           F+   L     I  RV         A+  ++    +   G+ Q   ++ RH    F G P
Sbjct: 245 FATGELLAPPTIADRV---------AAARNHLIWSVEWKGERQGVLEMRRHYANYFKGLP 295

Query: 289 NSRRCRH-ILTVEAGASTAT 307
           N +  R  ++T+++ A   T
Sbjct: 296 NFKEHRQRLVTLDSAAEIVT 315


>gi|257886013|ref|ZP_05665666.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
 gi|293553701|ref|ZP_06674325.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1039]
 gi|257821869|gb|EEV48999.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
 gi|291602276|gb|EFF32504.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1039]
          Length = 334

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/222 (33%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ VE+    + I
Sbjct: 40  LVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGNKDSLVEAAQFVEENTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + + A+  A+ IPVTVK RIG D++    A+ 
Sbjct: 100 DINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDIPVTVKMRIGWDEE-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + + +G + I +H R  +   +G +          D++++ E+KK     F+G NG
Sbjct: 159 NALAA-QSAGASAIAMHGRTRVQMYEGKA----------DWEVLKEVKKHLTIPFMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A ++L  V  DGVMIGRAA  N  M+     Y   
Sbjct: 207 DVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248


>gi|238019651|ref|ZP_04600077.1| hypothetical protein VEIDISOL_01525 [Veillonella dispar ATCC 17748]
 gi|237863692|gb|EEP64982.1| hypothetical protein VEIDISOL_01525 [Veillonella dispar ATCC 17748]
          Length = 328

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 119/242 (49%), Gaps = 16/242 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++   +
Sbjct: 26  SDIAYRLLAKE-HGAALVCTEMVSAMGIKYKNERTHELLRIEEVERPVSMQIFGSNPEAI 84

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  KA+ +PVTVK
Sbjct: 85  ALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVKAVDVPVTVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  +  +
Sbjct: 145 MRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSYIKAV 194

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K+      IG NG + +   A ++L     D VM+GR A  N  +   +  Y +     +
Sbjct: 195 KEAVSVPVIG-NGDIVEPEDAKQMLDETGCDAVMVGRGAQGNPWIFNRIHHYLATGEVLA 253

Query: 241 SP 242
           +P
Sbjct: 254 AP 255


>gi|66818553|ref|XP_642936.1| hypothetical protein DDB_G0277081 [Dictyostelium discoideum AX4]
 gi|60471072|gb|EAL69042.1| hypothetical protein DDB_G0277081 [Dictyostelium discoideum AX4]
          Length = 392

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 118/236 (50%), Gaps = 17/236 (7%)

Query: 1   MVDWTDRHYRFF-ARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D TD  +RF  A  +    +++ E + AD + R  +  I  LG+STQEKP+  Q  G 
Sbjct: 18  MADVTDISFRFLLANCMGKPNVIFNEFVSADGLARNREALIDKLGYSTQEKPIVAQFFGN 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARV--HEGSFGACLMLNPDIVGDCIAAMCKAL 115
                 E+AKI  + GY+ +++N+GCPS +V   + + GA L+ NP +  + +    +AL
Sbjct: 78  KPEYFYESAKIANELGYDGVDINMGCPSRKVLSPKQASGAALITNPSLAKEIVKITKEAL 137

Query: 116 SI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +   PV+VK RIG D     + +   +  I +S    + +H R      L P       +
Sbjct: 138 NFEKPVSVKTRIGFD----KIEIDEWIPLILESEPACLTLHLRTKKELSLVPA---HWEH 190

Query: 174 LDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
              D V E++ + +P+  +  NG +E   Q +  +    +DGVMIGRA Y N  + 
Sbjct: 191 QVLDRVVELRNQISPNTLLVGNGDVETYEQGIDYINQFGIDGVMIGRAVYGNPWLF 246


>gi|261206686|ref|ZP_05921384.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium TC 6]
 gi|289565048|ref|ZP_06445502.1| tRNA-dihydrouridine synthase 1 [Enterococcus faecium D344SRF]
 gi|294614891|ref|ZP_06694782.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1636]
 gi|260079179|gb|EEW66872.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium TC 6]
 gi|289163255|gb|EFD11101.1| tRNA-dihydrouridine synthase 1 [Enterococcus faecium D344SRF]
 gi|291592177|gb|EFF23795.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1636]
          Length = 331

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/222 (33%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ VE+    + I
Sbjct: 40  LVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGNKDSLVEAAQFVEENTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + + A+  A+ IPVTVK RIG D++    A+ 
Sbjct: 100 DINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDIPVTVKMRIGWDEE-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + + +G + I +H R  +   +G +          D++++ E+KK     F+G NG
Sbjct: 159 NALAA-QSAGASAIAMHGRTRVQMYEGKA----------DWEVLKEVKKHLTIPFMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A ++L  V  DGVMIGRAA  N  M+     Y   
Sbjct: 207 DVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248


>gi|193214513|ref|YP_001995712.1| TIM-barrel protein, nifR3 family [Chloroherpeton thalassium ATCC
           35110]
 gi|193087990|gb|ACF13265.1| TIM-barrel protein, nifR3 family [Chloroherpeton thalassium ATCC
           35110]
          Length = 402

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 88/314 (28%), Positives = 142/314 (45%), Gaps = 41/314 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + +++TE I +D ++R     K  L     E+P+A+QI G  
Sbjct: 61  MEDVTDPSFRRLCKHYGAD-IVFTEFISSDGLIRHAVKSKRKLDVFDDERPVAIQIFGNQ 119

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAA++ E  G + I++N GCP+ +V     G+ L+  PD++     A+ KA+ +P
Sbjct: 120 IEPMVEAAQMAEAAGPDFIDINYGCPAKKVAGKGAGSGLLCQPDLMEKITDAVVKAVRLP 179

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT K RIG D++  ++++ + V+ ++  G+  + IH R    + KG +          D+
Sbjct: 180 VTAKTRIGWDER--SISILDTVRRLEGCGIQALSIHGRTRAQMYKGRA----------DW 227

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
             +   K+      IG NG +     A ++     VDGVMIGR A  N  +         
Sbjct: 228 SWIARAKEVATIPIIG-NGDIWTAEDAKRMFDETGVDGVMIGRGAIGNPFLFREAKHLIQ 286

Query: 235 NPLTGSS-PIKTRVDKDFWRKISASMTDYAARHLH-----SGGK--LQQITRHMIGLFHG 286
              TG   P  T  ++             A RHL       G K  + ++ RH      G
Sbjct: 287 ---TGEHLPQATHRER----------VAVAIRHLEMSLERKGEKYGVLEMRRHYSTYLKG 333

Query: 287 FPNSRRCRHILTVE 300
            PN  + R  L  E
Sbjct: 334 LPNVSKVRDYLVRE 347


>gi|317126821|ref|YP_004093103.1| hypothetical protein Bcell_0081 [Bacillus cellulosilyticus DSM
           2522]
 gi|315471769|gb|ADU28372.1| TIM-barrel protein, nifR3 family [Bacillus cellulosilyticus DSM
           2522]
          Length = 331

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/241 (31%), Positives = 126/241 (52%), Gaps = 21/241 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL  +++++  L    +EKPL+LQI G D   LVEAA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAILHKNQRSLKMLYVDDREKPLSLQIFGGDKDTLVEAA 84

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V+     + I++N+GCP  ++     GA  +LNPD + + ++ +  A+  PVTVK RI
Sbjct: 85  KVVDKQTNADIIDINMGCPVPKITSCDAGARWLLNPDKIYEMVSYVVDAVDKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIK 183
           G D++    A+ N  ++++++G   + +H R  +   +G +          ++DI+ ++K
Sbjct: 145 GWDEE-HIFAIEN-AEAVERAGGKAVAVHGRTRVQMYEGEA----------NWDIIRDVK 192

Query: 184 KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                  IG NG ++    A +++ +  VDGVMIGRAA  N  ML     Y         
Sbjct: 193 NAVNIPVIG-NGDIKTPEDAKRMIDTTGVDGVMIGRAALGNPWMLYRTIHYLQTGENKPE 251

Query: 242 P 242
           P
Sbjct: 252 P 252


>gi|302872718|ref|YP_003841354.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor obsidiansis
           OB47]
 gi|302575577|gb|ADL43368.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor obsidiansis
           OB47]
          Length = 328

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/306 (25%), Positives = 145/306 (47%), Gaps = 36/306 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        +  + TEM+ + A++ G  K   ++ FS +EK   +QI G+D
Sbjct: 13  MAGFTDKVFRRLCSRFGADVTV-TEMVSSKALVLGSTKTKELISFSQEEKIRGVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+I++D F Y+ I++N+GCP  ++ +   G  LM NP +    +  + K    
Sbjct: 72  PEVMAQAAEILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLASRIVERVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PV+VK R G D++  ++        +++SG + + +H   RK +  G            D
Sbjct: 132 PVSVKIRKGFDEE--SINAPEFAYILQESGASFVTVHGRTRKQLYSG----------KAD 179

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++I+ ++ KE   + +  NG + D   A ++  +   D +MIGRAA  N  +   + E F
Sbjct: 180 WEIIRKV-KERLKIPVVANGDITDFESAKRVYEITGADSIMIGRAALGNPWVFLQIKEGF 238

Query: 234 SNPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFP 288
                 +  +   K RV  +F+R++           +  G K+   +  +H+     G  
Sbjct: 239 EKGYVETEVLPHMKIRVAIEFFRQLC----------IEKGEKMAVLEARKHLSFFVKGIE 288

Query: 289 NSRRCR 294
           N+ + R
Sbjct: 289 NAAKIR 294


>gi|315224769|ref|ZP_07866591.1| tRNA-dihydrouridine synthase B [Capnocytophaga ochracea F0287]
 gi|314945262|gb|EFS97289.1| tRNA-dihydrouridine synthase B [Capnocytophaga ochracea F0287]
          Length = 327

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 148/310 (47%), Gaps = 35/310 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   ++   + +LY+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKMHGAD-MLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMALSAKIVATVNPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVNSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+Q  ++ +  + + ++  G++ + IHA  R  + KG S          D+
Sbjct: 138 VTVKTRLGWDEQ--SINIEEVAERLQDVGISALTIHARTRSQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG ++   +AL+   +  VDG+MIGRAA     +   +  Y
Sbjct: 186 SYIAKVKN-NPRIHIPIFGNGDIDSPEKALEYRNTYGVDGIMIGRAAIGYPWIFNEIKHY 244

Query: 233 F-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ---QITRHMIGLFHGFP 288
           F +  L  S  I  RV+         +  ++    +   G+ Q   ++ RH    F G P
Sbjct: 245 FATGELLPSPTISDRVE---------AAKNHLLWSVEWKGERQGVLEMRRHYANYFKGIP 295

Query: 289 NSRRCRHILT 298
           N +  R  L 
Sbjct: 296 NFKEHRQRLV 305


>gi|293374618|ref|ZP_06620934.1| TIM-barrel protein, nifR3 family [Turicibacter sanguinis PC909]
 gi|325841874|ref|ZP_08167505.1| TIM-barrel protein, nifR3 family [Turicibacter sp. HGF1]
 gi|292646768|gb|EFF64762.1| TIM-barrel protein, nifR3 family [Turicibacter sanguinis PC909]
 gi|325489829|gb|EGC92182.1| TIM-barrel protein, nifR3 family [Turicibacter sp. HGF1]
          Length = 336

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 119/222 (53%), Gaps = 19/222 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+Y EM+   A++  +KK  ++L     E+PL++QI G+D    VEAAK V+ +   + I
Sbjct: 38  LIYAEMVSDKAVVYQNKKTLDMLYVDPAERPLSMQIFGSDKETFVEAAKYVDANCDCDII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA L+L PD + D +A +   +  PVTVK R G D +    A+ 
Sbjct: 98  DINMGCPVPKVTKNEAGARLLLEPDKIYDIVANVVDVVKKPVTVKMRTGWDKE-HIYAIE 156

Query: 138 NLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N +K I+++G + I +H   R  + +G +          D+ I+ ++K     + +  NG
Sbjct: 157 NALK-IEQAGASAIAVHGRTRSQMYEGKA----------DWGIIKDVKDAIKTIPVIGNG 205

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A ++L    VDG+MIGRAA  N  ++  +  Y + 
Sbjct: 206 DINSPEMAKRVLEESGVDGIMIGRAALGNPWLMKKIVHYLAT 247


>gi|126701180|ref|YP_001090077.1| tRNA-dihydrouridine synthase [Clostridium difficile 630]
 gi|254977180|ref|ZP_05273652.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-66c26]
 gi|255094510|ref|ZP_05323988.1| tRNA-dihydrouridine synthase [Clostridium difficile CIP 107932]
 gi|255102766|ref|ZP_05331743.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-63q42]
 gi|255308587|ref|ZP_05352758.1| tRNA-dihydrouridine synthase [Clostridium difficile ATCC 43255]
 gi|255316261|ref|ZP_05357844.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-76w55]
 gi|255518922|ref|ZP_05386598.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-97b34]
 gi|255652101|ref|ZP_05399003.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-37x79]
 gi|260685074|ref|YP_003216359.1| tRNA-dihydrouridine synthase [Clostridium difficile CD196]
 gi|260688732|ref|YP_003219866.1| tRNA-dihydrouridine synthase [Clostridium difficile R20291]
 gi|306521835|ref|ZP_07408182.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-32g58]
 gi|115252617|emb|CAJ70460.1| transfer RNA-dihydrouridine synthase [Clostridium difficile]
 gi|260211237|emb|CBA66759.1| tRNA-dihydrouridine synthase [Clostridium difficile CD196]
 gi|260214749|emb|CBE07441.1| tRNA-dihydrouridine synthase [Clostridium difficile R20291]
          Length = 322

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 137/300 (45%), Gaps = 25/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LLYTEMI   A+   D+  K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKE-QGCGLLYTEMINGKALCYDDENTKKMLKIEEEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I+ D+    +++N+GCP+ +V +   G+ LM NP +  + + A+ K    P
Sbjct: 76  PEFMGRAAEIMNDYSNEILDINMGCPAPKVVKNGDGSALMKNPKLAEEVLRAVVKNSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G++ + IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDDN--SVNAVEIAKIAEDCGISALAIHGR--------TREQFYTGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK      IG NG +  +  ++ +L     D +MIGR A  N  +   ++ Y +  
Sbjct: 186 IAEIKKNLSIPVIG-NGDVFTIEDSINMLDKTGCDAIMIGRGAQGNPWIFKRINHYMNTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMT--DYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P           KIS ++     A         ++++ +H+     G  NS + R
Sbjct: 245 EILPEPT-------LNEKISTAIKHLKLAVEEHGEYVAVREMRKHIAWYLKGLRNSAKLR 297


>gi|256819324|ref|YP_003140603.1| TIM-barrel protein, nifR3 family [Capnocytophaga ochracea DSM 7271]
 gi|256580907|gb|ACU92042.1| TIM-barrel protein, nifR3 family [Capnocytophaga ochracea DSM 7271]
          Length = 327

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 148/310 (47%), Gaps = 35/310 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   ++   + +LY+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKMHGAD-MLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMALSAKIVATVNPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVNSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+Q  ++ +  + + ++  G++ + IHA  R  + KG S          D+
Sbjct: 138 VTVKTRLGWDEQ--SINIEEVAERLQDVGISALTIHARTRSQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG ++   +AL+   +  VDG+MIGRAA     +   +  Y
Sbjct: 186 SYIAKVKN-NPRIHIPIFGNGDIDSPEKALEYRNTYGVDGIMIGRAAIGYPWIFNEIKHY 244

Query: 233 F-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ---QITRHMIGLFHGFP 288
           F +  L  S  I  RV+         +  ++    +   G+ Q   ++ RH    F G P
Sbjct: 245 FATGKLLPSPTISDRVE---------AAKNHLLWSVEWKGERQGVLEMRRHYANYFKGIP 295

Query: 289 NSRRCRHILT 298
           N +  R  L 
Sbjct: 296 NFKEHRQRLV 305


>gi|313158033|gb|EFR57439.1| TIM-barrel protein, nifR3 family [Alistipes sp. HGB5]
          Length = 340

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/308 (25%), Positives = 146/308 (47%), Gaps = 39/308 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R+  +    + ++YTE I +D ++R   K++  L     E+P+ +Q+ G  
Sbjct: 18  MEDVTDPSFRYMCKRFGAD-VVYTEFISSDGLIRDAAKSLKKLEIDAAERPVGIQLYGHL 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAA++ E  G + I++N GCP  ++     G+ +M +  ++ +    + +A+  P
Sbjct: 77  IEPMVEAARMAEAAGPDIIDINFGCPVKKIAGRGAGSGMMRDVPLMVEMTRRIVQAVRKP 136

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VTVK R+G D++   I  +ALR     ++  G+  + +H R    + +G           
Sbjct: 137 VTVKTRLGWDEESKNIEEIALR-----LQDVGIAALTVHGRTRAQMYRG----------E 181

Query: 174 LDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
            D+ ++ ++K  NP + I +  NG ++   +A ++     VDGVMIGRA Y    +   V
Sbjct: 182 ADWTLIGKVKN-NPQIHIPIIGNGDVDSGPKAAEMFDRYGVDGVMIGRATYGRPWIFREV 240

Query: 230 DEYFSNPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             Y +       P    +  + K+  RK      ++          + ++ RH+   F G
Sbjct: 241 KHYLATGEVLPQPSVCERVEIAKEHLRKSLEVKGEFVG--------ILEMRRHLSNYFKG 292

Query: 287 FPNSRRCR 294
            P+ +  R
Sbjct: 293 LPDFKPTR 300


>gi|119358060|ref|YP_912704.1| nifR3 family TIM-barrel protein [Chlorobium phaeobacteroides DSM
           266]
 gi|119355409|gb|ABL66280.1| tRNA-U20-dihydrouridine synthase [Chlorobium phaeobacteroides DSM
           266]
          Length = 347

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 118/228 (51%), Gaps = 20/228 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE + A+A+ RG +K +  L     E+P+A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKRFGAD-IVYTEFVSAEALRRGAEKTLRKLVLEAGERPVAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEA  + E++  + I++N GCP+ +V     GA L+  P  +     A+ +  S+P
Sbjct: 76  VESMVEATAVAEEYAPDFIDINFGCPTKKVAGKGAGAALLREPGKMAAIAEAVVRRSSLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VT K RIG D    ++ + ++++ ++ +G+  + IH R    + KG +          D+
Sbjct: 136 VTAKTRIGWDHD--SINIIDVLRRLEDAGIQALAIHGRTRSDMYKGRA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           + + E  K +  + +  NG +     AL +      DG+MIGR A  N
Sbjct: 184 NWIAE-AKNHARIPVIANGDIWSAEDALAMFRHTGADGIMIGRGAIGN 230


>gi|319936962|ref|ZP_08011372.1| transcriptional regulator [Coprobacillus sp. 29_1]
 gi|319807898|gb|EFW04477.1| transcriptional regulator [Coprobacillus sp. 29_1]
          Length = 335

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 124/237 (52%), Gaps = 19/237 (8%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+ +EM+   A+  G++K I  L     E P+++Q+ G D+  +V AAK V E+   + 
Sbjct: 35  GLVVSEMVSDKALCYGNQKTIEMLKVDENEHPMSIQVFGGDVESMVTAAKFVDENSNCDI 94

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  +V +   G+ L+  PD+V D + ++ +A+S PVTVK RIG D D I  V 
Sbjct: 95  IDINMGCPVNKVLKAHAGSYLLQFPDLVYDIVKSVVEAVSKPVTVKIRIGYDFDSINCVE 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L   I+++G + I +H R         +      + D+  + ++K+      IG NG
Sbjct: 155 IAQL---IERAGASAIAVHGR--------TRSQMYEGHADWSWIKKVKEAVSIPVIG-NG 202

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP-LTGSSPIKTRVDK 249
            ++    A ++L     D VM+GRAA  N  ++  + EY  +  L G      R+D+
Sbjct: 203 DVKTAKDAKRMLEETGCDAVMVGRAALGNPWVIKQMVEYVEHDILLGDPTADERIDQ 259


>gi|297582412|ref|YP_003698192.1| TIM-barrel protein, nifR3 family [Bacillus selenitireducens MLS10]
 gi|297140869|gb|ADH97626.1| TIM-barrel protein, nifR3 family [Bacillus selenitireducens MLS10]
          Length = 332

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/225 (34%), Positives = 118/225 (52%), Gaps = 21/225 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL  +K+  N+L  + +EKPL+LQI G     LVEAA
Sbjct: 27  FRLIAKEF-GTGLVCAEMVSDKAILHQNKRSINMLYVAEREKPLSLQIFGGTKETLVEAA 85

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           KIV+     + I++N+GCP  +V     GA  +LNPD + + + A+ +A+  PVTVK R 
Sbjct: 86  KIVDTQTNADIIDINMGCPVPKVTSCDAGARWLLNPDRIYEMVDAVVQAVDKPVTVKMRK 145

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIK 183
           G DD     A+ N  K+++ +G   I +H R  +   +G            D+ I+  +K
Sbjct: 146 GWDDDT-VYAVDN-AKAVEAAGGKAIALHGRTRVQMYEG----------EADWSIIKTVK 193

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           +      IG NG ++    A +++     DGVMIGRAA  N  ML
Sbjct: 194 EAVGIPIIG-NGDVQTPEDAKRMMTETGADGVMIGRAALGNPWML 237


>gi|153815945|ref|ZP_01968613.1| hypothetical protein RUMTOR_02190 [Ruminococcus torques ATCC 27756]
 gi|317500709|ref|ZP_07958927.1| tRNA-dihydrouridine synthase B [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331089816|ref|ZP_08338709.1| hypothetical protein HMPREF1025_02292 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145846764|gb|EDK23682.1| hypothetical protein RUMTOR_02190 [Ruminococcus torques ATCC 27756]
 gi|316897903|gb|EFV19956.1| tRNA-dihydrouridine synthase B [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330403513|gb|EGG83071.1| hypothetical protein HMPREF1025_02292 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 319

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/300 (25%), Positives = 145/300 (48%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  + ++    +E+P++LQ+ G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLGMEMVSAKAILYQNKNTEKLMEIHPEEQPVSLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V +   G+ LM NP +V + + A+ KA+  P
Sbjct: 79  PKIMSEMAKRIEERPFAILDINMGCPVPKVVKNGEGSALMKNPSLVYEIVNAIVKAIEKP 138

Query: 119 VTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  + AV    + ++ +++G + + +H R         ++       D+D
Sbjct: 139 VTVKIRKGFDDAHVNAV---EVARAAEEAGASAVAVHGRT--------REQYYSGEADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A +++ +   DG+MI R A  N  + +   E    
Sbjct: 188 IIRQVKEAVSIPVIG-NGDVTTPEKAEELVQTTGCDGIMIARGAQGNPWIFS---EMIGK 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              G +P   R DK+  R +    +    ++      ++++ +H+     G   +   R 
Sbjct: 244 EKNGVTP--PRPDKEAIRNMILRHSKLQIQYRGEFAGMREMRKHVAWYTKGLTGAADLRR 301


>gi|255657504|ref|ZP_05402913.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-23m63]
 gi|296452824|ref|ZP_06894511.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP08]
 gi|296879924|ref|ZP_06903896.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP07]
 gi|296258372|gb|EFH05280.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP08]
 gi|296429038|gb|EFH14913.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP07]
          Length = 322

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 137/300 (45%), Gaps = 25/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LLYTEMI   A+   D+  K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKE-QGCGLLYTEMINGKALCYDDENTKKMLKIEDEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I+ D+    +++N+GCP+ +V +   G+ LM NP +  + + A+ K    P
Sbjct: 76  PEFMGRAAEIMNDYSNEILDINMGCPAPKVVKNGDGSALMKNPKLAEEVLRAVVKNSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G++ + IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDDN--SVNAVEIAKIAEDCGISALAIHGR--------TREQFYTGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK      IG NG +  +  ++ +L     D +MIGR A  N  +   ++ Y +  
Sbjct: 186 IAEIKKNLSIPVIG-NGDVFTIEDSINMLDKTGCDAIMIGRGAQGNPWIFKRINHYMNTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMT--DYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P           KIS ++     A         ++++ +H+     G  NS + R
Sbjct: 245 EILPEPT-------LNEKISTAIKHLKLAVEEHGEYVAVREMRKHIAWYLKGLRNSAKLR 297


>gi|93005906|ref|YP_580343.1| dihydrouridine synthase TIM-barrel protein nifR3 [Psychrobacter
           cryohalolentis K5]
 gi|92393584|gb|ABE74859.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Psychrobacter
           cryohalolentis K5]
          Length = 343

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/297 (26%), Positives = 142/297 (47%), Gaps = 21/297 (7%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL EAA+   D G   I++N+
Sbjct: 61  SEMIIADTALYARKKSLYRANFDNEIAPISAQIAGAEPDKLAEAARYQIDNGAQIIDINM 120

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + A   A+  PVT+K R+G ++    + LR + K
Sbjct: 121 GCPAKKVCRKLAGSALLQDEDLVARLLDAAVNAVDAPVTLKTRLGYENGRENI-LR-VAK 178

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             +++G+  I IH R         +++       Y+++ E+ KE+  + +  NG ++   
Sbjct: 179 RAEQAGIAAIAIHGRT--------REDMYTGEARYELIREV-KESISIPVIANGDIDSAQ 229

Query: 202 QALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
           +A ++  L   D VMIGRAA     +   ++ +     T +SP  + +       +    
Sbjct: 230 KAQRVYELTGCDAVMIGRAAQGQPWIFRDIEHFLRTGETLASPSVSEIKGIVLTHLEELY 289

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
             Y     +SG ++ +  +H+     G PNS   R  +  E  ++     ++E   N
Sbjct: 290 GFYGE---YSGCRIAR--KHIAWYTTGIPNSNAFRQAMYGEE-STAGQFRVVEDFLN 340


>gi|206972564|ref|ZP_03233507.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH1134]
 gi|206732466|gb|EDZ49645.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH1134]
          Length = 332

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 130/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G           +D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAVERAGGQAVAVHGRTRVQMYEG----------KVDWDIIKQVKQSVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|256855221|ref|ZP_05560582.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecalis
           T8]
 gi|256709734|gb|EEU24781.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecalis
           T8]
 gi|315028814|gb|EFT40746.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4000]
          Length = 332

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G           +++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEG----------TVNWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|257084202|ref|ZP_05578563.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Fly1]
 gi|256992232|gb|EEU79534.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Fly1]
          Length = 332

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLSIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|229094797|ref|ZP_04225803.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-29]
 gi|228688665|gb|EEL42537.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-29]
          Length = 339

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 130/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 104 DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++ +G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 163 N-ARAVECAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 210

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 211 DVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|256956805|ref|ZP_05560976.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis DS5]
 gi|257078474|ref|ZP_05572835.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis JH1]
 gi|294779307|ref|ZP_06744710.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis PC1.1]
 gi|307268520|ref|ZP_07549895.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4248]
 gi|256947301|gb|EEU63933.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis DS5]
 gi|256986504|gb|EEU73806.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis JH1]
 gi|294453593|gb|EFG21992.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis PC1.1]
 gi|306515181|gb|EFM83721.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4248]
 gi|315032987|gb|EFT44919.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0017]
 gi|315036600|gb|EFT48532.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0027]
          Length = 332

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|315172633|gb|EFU16650.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1346]
          Length = 332

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLSIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|228989283|ref|ZP_04149276.1| tRNA-dihydrouridine synthase 1 [Bacillus pseudomycoides DSM 12442]
 gi|228995466|ref|ZP_04155136.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock3-17]
 gi|229003089|ref|ZP_04160941.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock1-4]
 gi|228758172|gb|EEM07365.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock1-4]
 gi|228764327|gb|EEM13204.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock3-17]
 gi|228770493|gb|EEM19064.1| tRNA-dihydrouridine synthase 1 [Bacillus pseudomycoides DSM 12442]
          Length = 332

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+   AIL  ++K  ++L    +EKPL+LQI G +   LV AAK V+ +   + I
Sbjct: 37  LVCAEMVSDKAILFNNQKTLDMLYIDEREKPLSLQIFGGEKETLVGAAKYVDKNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+PD V + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPDKVYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDIETPQDAKRMLDEVGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKMD 259


>gi|29374908|ref|NP_814061.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecalis
           V583]
 gi|227520052|ref|ZP_03950101.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
 gi|227555913|ref|ZP_03985960.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|229546903|ref|ZP_04435628.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|255971767|ref|ZP_05422353.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255974767|ref|ZP_05425353.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256618323|ref|ZP_05475169.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis ATCC 4200]
 gi|256960610|ref|ZP_05564781.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Merz96]
 gi|257081554|ref|ZP_05575915.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis E1Sol]
 gi|257417632|ref|ZP_05594626.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis AR01/DG]
 gi|257418643|ref|ZP_05595637.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257421556|ref|ZP_05598546.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|293382697|ref|ZP_06628622.1| tRNA-dihydrouridine synthase [Enterococcus faecalis R712]
 gi|293388121|ref|ZP_06632648.1| tRNA-dihydrouridine synthase [Enterococcus faecalis S613]
 gi|300862204|ref|ZP_07108284.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TUSoD Ef11]
 gi|307276456|ref|ZP_07557579.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2134]
 gi|307278666|ref|ZP_07559736.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0860]
 gi|307286954|ref|ZP_07567029.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0109]
 gi|307290187|ref|ZP_07570105.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0411]
 gi|312901061|ref|ZP_07760350.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0470]
 gi|312904624|ref|ZP_07763779.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0635]
 gi|312908593|ref|ZP_07767535.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 512]
 gi|312909259|ref|ZP_07768116.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 516]
 gi|312952667|ref|ZP_07771531.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0102]
 gi|29342366|gb|AAO80132.1| zinc-binding TIM-barrel protein, nifR3 family, putative
           [Enterococcus faecalis V583]
 gi|227072600|gb|EEI10563.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
 gi|227174970|gb|EEI55942.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|229307831|gb|EEN73818.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|255962785|gb|EET95261.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255967639|gb|EET98261.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256597850|gb|EEU17026.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis ATCC 4200]
 gi|256951106|gb|EEU67738.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Merz96]
 gi|256989584|gb|EEU76886.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis E1Sol]
 gi|257159460|gb|EEU89420.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis ARO1/DG]
 gi|257160471|gb|EEU90431.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257163380|gb|EEU93340.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|291079857|gb|EFE17221.1| tRNA-dihydrouridine synthase [Enterococcus faecalis R712]
 gi|291082497|gb|EFE19460.1| tRNA-dihydrouridine synthase [Enterococcus faecalis S613]
 gi|300848729|gb|EFK76486.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TUSoD Ef11]
 gi|306498743|gb|EFM68242.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0411]
 gi|306501900|gb|EFM71189.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0109]
 gi|306504726|gb|EFM73926.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0860]
 gi|306506936|gb|EFM76083.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2134]
 gi|310625380|gb|EFQ08663.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 512]
 gi|310629455|gb|EFQ12738.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0102]
 gi|310631976|gb|EFQ15259.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0635]
 gi|311290501|gb|EFQ69057.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 516]
 gi|311291807|gb|EFQ70363.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0470]
 gi|315145397|gb|EFT89413.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2141]
 gi|315147111|gb|EFT91127.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4244]
 gi|315151136|gb|EFT95152.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0012]
 gi|315153549|gb|EFT97565.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0031]
 gi|315156271|gb|EFU00288.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0043]
 gi|315158584|gb|EFU02601.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0312]
 gi|315160787|gb|EFU04804.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0645]
 gi|315165841|gb|EFU09858.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1302]
 gi|315168160|gb|EFU12177.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1341]
 gi|315573575|gb|EFU85766.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0309B]
 gi|315579386|gb|EFU91577.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0630]
 gi|315582077|gb|EFU94268.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0309A]
 gi|323479480|gb|ADX78919.1| TIM-barrel protein, nifR3 family protein [Enterococcus faecalis 62]
          Length = 332

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|325261220|ref|ZP_08127958.1| TIM-barrel protein, NifR3 family [Clostridium sp. D5]
 gi|324032674|gb|EGB93951.1| TIM-barrel protein, NifR3 family [Clostridium sp. D5]
          Length = 319

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 146/302 (48%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+  EM+ A  IL  +K  +++L     E P +LQ+ G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLVCMEMVSAKGILYNNKNTESLLEIHPDEMPASLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V     G+ LM NP +V + ++A+ KA+  P
Sbjct: 79  PKIVSEMAKKIEERPFAILDINMGCPVPKVVRNGEGSALMKNPKLVYELVSAVVKAIKKP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D D + AV    + K I+++G   + +H R         ++       D++
Sbjct: 139 VTVKIRKGFDEDHVNAV---EIAKIIEEAGAAAVGVHGRT--------REQYYSGKADWE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A+ +      DGVMI R A  N  + + +  Y   
Sbjct: 188 IIRKVKEAVSIPVIG-NGDVTSGEKAIAMREQTGCDGVMIARGAQGNPWIFSELTVYEQ- 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             +G+ P +  ++     ++  +M  +AA  L   G+   ++++ +H+     G   + R
Sbjct: 246 --SGTLPPRPSLE-----EVKKTMLRHAALQLEYKGEYLGIREMRKHVAWYVKGLHGAAR 298

Query: 293 CR 294
            R
Sbjct: 299 LR 300


>gi|229550492|ref|ZP_04439217.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
 gi|229304349|gb|EEN70345.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|229015478|ref|ZP_04172477.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1273]
 gi|229021687|ref|ZP_04178270.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1272]
 gi|228739623|gb|EEL90036.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1272]
 gi|228745821|gb|EEL95824.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1273]
          Length = 339

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 131/237 (55%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  ++++++G   + +H R  +   +G +          D++I+ ++K+      IG N
Sbjct: 162 EN-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWNIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +E    A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|229107762|ref|ZP_04237399.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-15]
 gi|228675735|gb|EEL30942.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-15]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 129/234 (55%), Gaps = 17/234 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N  ++++++G   + +H R  +       + R     D+DI+ ++K+      IG NG +
Sbjct: 156 N-ARAVERAGGQAVAVHGRTRV----QMYEGRA----DWDIIKQVKQSVNIPVIG-NGDV 205

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
                A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 206 ATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|206977953|ref|ZP_03238840.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           H3081.97]
 gi|206743859|gb|EDZ55279.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           H3081.97]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 129/236 (54%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D+     A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDED-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNISVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|324324066|gb|ADY19326.1| putative TIM-barrel protein, NifR3 family [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|313894573|ref|ZP_07828136.1| TIM-barrel protein, nifR3 family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313440763|gb|EFR59192.1| TIM-barrel protein, nifR3 family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 328

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 139/297 (46%), Gaps = 25/297 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++   +
Sbjct: 26  SDIAYRLLAKE-HGAALVCTEMVSAMGIKYKNERTHELLRLEEVERPVSMQIFGSNPEAI 84

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              A++V D G + +++N+GCP  +V     G+ LM NPD+      A  KA+++PVTVK
Sbjct: 85  ALGAQVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVKAVNVPVTVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG D    ++ + +  K ++ +GV  I +H R         K+     + D+  +  +
Sbjct: 145 MRIGWDSD--SINVVDFAKRVESTGVAAIAVHGRT--------KEQMYSGHADWSYIKAV 194

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K+      IG NG + +   A ++L     D VM+GR A  N  +   +  Y +   TG 
Sbjct: 195 KEAVSVPVIG-NGDIVEPEDAKRMLDETGCDAVMVGRGAQGNPWIFGRIHHYLA---TGE 250

Query: 241 S-PIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             P  T +++ D   K    +  Y    +     +++I  H      G P S   R+
Sbjct: 251 ILPAPTDIERLDMLLKHFDLLCQYKGESM----AVKEIRTHAGWYMKGLPESSYWRN 303


>gi|120437655|ref|YP_863341.1| tRNA-dihydrouridine synthase [Gramella forsetii KT0803]
 gi|117579805|emb|CAL68274.1| tRNA-dihydrouridine synthase [Gramella forsetii KT0803]
          Length = 330

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 83/310 (26%), Positives = 146/310 (47%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K+   L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIREAAKSTMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K  S+P
Sbjct: 78  LESMLQSVEIVEKSGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKNTSLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G D    ++ +  + + ++  G   I IH R    + KG            D+
Sbjct: 138 ITVKTRLGWDHD--SIKIVEVAERLQDVGCKAISIHGRTRAQMYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  NP + I +  NG ++   +A+++  +  +DG MIGRA+         V  Y
Sbjct: 186 APIAEVKN-NPRMHIPVFGNGDVDSPEKAMEMRDNFGLDGAMIGRASIGYPWFFREVKHY 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
           F      + P ++ RVD              A RHL       G +L   +  RH    F
Sbjct: 245 FETGKHLAPPTLEERVDA-------------ARRHLQMAIDWKGERLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G P+ +  R
Sbjct: 292 KGIPHFKEYR 301


>gi|257088029|ref|ZP_05582390.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis D6]
 gi|256996059|gb|EEU83361.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis D6]
 gi|315026775|gb|EFT38707.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2137]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|197301311|ref|ZP_03166396.1| hypothetical protein RUMLAC_00042 [Ruminococcus lactaris ATCC
           29176]
 gi|197299629|gb|EDY34144.1| hypothetical protein RUMLAC_00042 [Ruminococcus lactaris ATCC
           29176]
          Length = 320

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 85/300 (28%), Positives = 140/300 (46%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  + +L     E+P++LQ  G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYNNKNTETLLEIHPDEQPVSLQFFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK VE+  ++ +++N+GCP  +V +   G+ LM NP +  + I+AM KA+  P
Sbjct: 79  PQIMSEMAKRVEERPFDIMDINMGCPVPKVVKNGEGSALMKNPKLAHEIISAMVKAIRKP 138

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I AV    + K  + +G   I +H R         ++       D++
Sbjct: 139 VTVKIRKGFDDNCINAV---EMAKIAEDAGAAAIAVHGRT--------REQYYSGKADWE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A  ++     DGVMI R A  N  + + + E+   
Sbjct: 188 IIRQVKEAVSIPVIG-NGDVTSPERADAMVKETGCDGVMIARGAQGNPWIFSEMIEHERT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S P    + K   R     +  Y   +L     ++++ +H+     G P S + R 
Sbjct: 247 GKIPSRPTNEEIRKMMLRHAKLQL-QYKGEYLG----IREMRKHVAWYTKGLPGSAKLRE 301


>gi|193211956|ref|YP_001997909.1| TIM-barrel protein, nifR3 family [Chlorobaculum parvum NCIB 8327]
 gi|193085433|gb|ACF10709.1| TIM-barrel protein, nifR3 family [Chlorobaculum parvum NCIB 8327]
          Length = 347

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 88/314 (28%), Positives = 145/314 (46%), Gaps = 41/314 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +    + ++YTE + A+AI RG +K+I  L     E+P+A+QI G  
Sbjct: 17  MEDVTDRAFRQLCKRHGAD-IVYTEFVSAEAIRRGAEKSIRKLRMDAHERPVAVQIFGNT 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I E F  + +++N GCP  +V     GA L+  P+ +    AA+  A+S+P
Sbjct: 76  VESMVEAASIAESFEPDCLDINFGCPVKKVAGRGAGAALLKEPEKLSAIAAAVVGAVSLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           VT K RIG D    ++ + + V+ ++ +G+  + +H R    + KG +          D+
Sbjct: 136 VTAKTRIGWDHD--SINITDTVRRLEDAGIQAVAVHGRTRSDMYKGRA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
             + E K+      I  NG +     A+ +      DG+MIGR +  N  +         
Sbjct: 184 GRIAEAKRACSIPVIA-NGDVWSADDAVAMFAETGADGIMIGRGSIGNPFIFAQAKSLVK 242

Query: 235 NPLTGSS-PIKTRVDKDFWRKISASMTDYAARHL-----HSGGK--LQQITRHMIGLFHG 286
              TG   P+ +  D+           D A  HL     + G K  + ++ RH      G
Sbjct: 243 ---TGERLPLPSYRDR----------IDAAREHLRLSLEYKGEKHGVLEMRRHYSTYLKG 289

Query: 287 FPNSRRCRHILTVE 300
            P   + R++L  E
Sbjct: 290 LPGVSKVRNLLVRE 303


>gi|284053044|ref|ZP_06383254.1| dihydrouridine synthase TIM-barrel protein nifR3 [Arthrospira
           platensis str. Paraca]
 gi|291568799|dbj|BAI91071.1| hypothetical protein [Arthrospira platensis NIES-39]
          Length = 338

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 79/306 (25%), Positives = 147/306 (48%), Gaps = 26/306 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+++YTEM+ A  I+   K  IL      E+P+++Q+       LV
Sbjct: 39  TDLVFRRLVRRYAPNSMMYTEMVHASQIIHVRKLPILMEIDPGERPISIQLFDCRPDFLV 98

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+   + G + I++N+GCP  ++ +   G+ L+  P+I    + ++ +A+S+P+TVK 
Sbjct: 99  EAARKAVEEGADTIDVNMGCPVNKITKNGGGSSLLRQPEIAEKIVRSLNEAVSVPITVKT 158

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G DD    + + +  K ++ +G   + IH R    +G + K N       ++ +  + 
Sbjct: 159 RLGWDDD--EINILDFSKRMEDAGAQMLTIHGRTRA-QGYTGKAN-------WEWIARV- 207

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K++  + +  NG +  +S A++ L     DGVM  R       ++  +D +       ++
Sbjct: 208 KQSLSIPVIANGDIVSVSSAVQCLQETGADGVMCSRGTLGYPFLVGEIDYFLKTGQMKTA 267

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL--- 297
           P  T V+     ++  +     A  ++ G + + Q  +HM     GFP +   R  L   
Sbjct: 268 P--TVVE-----RLECAKEHLQALWVYKGQRGIYQSRKHMTWYAKGFPGANELREQLAKV 320

Query: 298 -TVEAG 302
            TVE G
Sbjct: 321 ETVEQG 326


>gi|315171400|gb|EFU15417.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1342]
          Length = 337

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|301051814|ref|YP_003790025.1| putative TIM-barrel protein [Bacillus anthracis CI]
 gi|300373983|gb|ADK02887.1| possible TIM-barrel protein, NifR3 family [Bacillus cereus biovar
           anthracis str. CI]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 129/236 (54%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D+     A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDED-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|42779155|ref|NP_976402.1| NifR3 family TIM-barrel protein [Bacillus cereus ATCC 10987]
 gi|217957652|ref|YP_002336194.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH187]
 gi|42735070|gb|AAS39010.1| TIM-barrel protein, putative, NifR3 family [Bacillus cereus ATCC
           10987]
 gi|217063780|gb|ACJ78030.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH187]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|256762062|ref|ZP_05502642.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis T3]
 gi|256964190|ref|ZP_05568361.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis HIP11704]
 gi|307274231|ref|ZP_07555439.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0855]
 gi|256683313|gb|EEU23008.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis T3]
 gi|256954686|gb|EEU71318.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis HIP11704]
 gi|306509193|gb|EFM78255.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0855]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTQAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGAA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|218901278|ref|YP_002449112.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH820]
 gi|218538152|gb|ACK90550.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH820]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|327534064|gb|AEA92898.1| tRNA-dihydrouridine synthase [Enterococcus faecalis OG1RF]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTKAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLSIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|254724217|ref|ZP_05186002.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. A1055]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|222093846|ref|YP_002527895.1| tim-barrel protein, putative, nifr3 family [Bacillus cereus Q1]
 gi|221237893|gb|ACM10603.1| TIM-barrel protein, putative, NifR3 family [Bacillus cereus Q1]
          Length = 324

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 29  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 88

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 89  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 146

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 147 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 194

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 195 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 251


>gi|229136922|ref|ZP_04265550.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST26]
 gi|229153854|ref|ZP_04281985.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 4342]
 gi|228629658|gb|EEK86354.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 4342]
 gi|228646587|gb|EEL02793.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST26]
          Length = 339

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|294668302|ref|ZP_06733406.1| hypothetical protein NEIELOOT_00215 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291309756|gb|EFE50999.1| hypothetical protein NEIELOOT_00215 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 340

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 152/326 (46%), Gaps = 38/326 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R  AR         +EM+ +D +LR  KK++    F  ++   A+QI G+D
Sbjct: 18  MAGITDKPFRRLARRF-GAGYAVSEMLASDPLLRHTKKSLSRGDFDGEDGLRAVQIAGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+   + G   I++N+GCP  +V     G+ L+ N  +V D + A+  A+ +P
Sbjct: 77  PKQMAEAARYNVENGAQIIDINMGCPVKKVCNVLAGSALLQNEKLVDDILRAVVSAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VT+K R+G  +    +  R + K  +++G+  + +H   R+ + KG +           Y
Sbjct: 137 VTLKTRLGFAENNKNI--RTVAKMAEQAGIAALAVHGRTREQMYKGQA----------SY 184

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D++ E+K    D+ I L  NG +    +A ++L     DGVMIGR A     +   +  +
Sbjct: 185 DLIAEVKH---DISIPLWVNGDITTPQKAAEVLRQTGADGVMIGRGAQGRPWLFADIAHF 241

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHG-FPN 289
             +   GS P         ++  SA+M ++        G+    +I R  IG +   FP+
Sbjct: 242 LQH---GSLPAPVT-----FQTASAAMLEHLREMYDFYGETAGLRIARKHIGWYLAPFPD 293

Query: 290 SRRCR---HILTVEAGASTATHHIIE 312
              CR   +IL   A    A    +E
Sbjct: 294 GEACRKHINILDFAAAQYDAVSAFLE 319


>gi|52145141|ref|YP_081688.1| NifR3 family TIM-barrel protein [Bacillus cereus E33L]
 gi|196041789|ref|ZP_03109079.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           NVH0597-99]
 gi|196047389|ref|ZP_03114602.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB108]
 gi|225862129|ref|YP_002747507.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB102]
 gi|51978610|gb|AAU20160.1| possible TIM-barrel protein, NifR3 family [Bacillus cereus E33L]
 gi|196021791|gb|EDX60485.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB108]
 gi|196027409|gb|EDX66026.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           NVH0597-99]
 gi|225787877|gb|ACO28094.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB102]
          Length = 332

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|47570200|ref|ZP_00240854.1| NifR3/smm1 family protein [Bacillus cereus G9241]
 gi|47553144|gb|EAL11541.1| NifR3/smm1 family protein [Bacillus cereus G9241]
          Length = 324

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 29  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 88

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 89  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 146

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 147 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 194

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 195 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 251


>gi|295110733|emb|CBL24686.1| tRNA-U20-dihydrouridine synthase [Ruminococcus obeum A2-162]
          Length = 321

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 116/239 (48%), Gaps = 16/239 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL TEM+ A AI   +K  I  +     E P+++QI G++
Sbjct: 21  MAGVTDLPFRMLCKE-QGAGLLCTEMVSAKAISFHNKNTISLMQIDPSEHPVSMQIFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ L+ NP+++ + +  +  A+  P
Sbjct: 80  PDLMAEVAKSIEEQPFDILDINMGCPVPKVVNNGEGSALLKNPELIREIVTQVSHAVKKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG +D    V    + K I+ SG   + +H R         +        D+D 
Sbjct: 140 VTAKIRIGFEDY--PVDPVEIAKIIEDSGAAAVAVHGRT--------RQQYYAGEADWDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+      IG NG ++   +A K++     DGVMIGRA   N  +   ++ YF+ 
Sbjct: 190 IRRIKEAVSIPVIG-NGDVDSPKKAEKLVRETGCDGVMIGRAVRGNPWIFREMNHYFTT 247


>gi|30018347|ref|NP_829978.1| Nif3 family protein [Bacillus cereus ATCC 14579]
 gi|218231778|ref|YP_002364926.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus B4264]
 gi|228950624|ref|ZP_04112759.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228956517|ref|ZP_04118314.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229067840|ref|ZP_04201158.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus F65185]
 gi|229125593|ref|ZP_04254626.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-Cer4]
 gi|229142882|ref|ZP_04271324.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST24]
 gi|229148485|ref|ZP_04276742.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1550]
 gi|229176676|ref|ZP_04304081.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 172560W]
 gi|29893887|gb|AAP07179.1| Nif3 family protein [Bacillus cereus ATCC 14579]
 gi|218159735|gb|ACK59727.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus B4264]
 gi|228606843|gb|EEK64259.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 172560W]
 gi|228635027|gb|EEK91599.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1550]
 gi|228640594|gb|EEK96982.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST24]
 gi|228657910|gb|EEL13715.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-Cer4]
 gi|228715324|gb|EEL67182.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus F65185]
 gi|228803207|gb|EEM50028.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228809099|gb|EEM55583.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 332

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 130/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|228983331|ref|ZP_04143545.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228776445|gb|EEM24797.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 339

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLGTGELMPEPTVREKID 266


>gi|118475847|ref|YP_892998.1| NifR3 family TIM-barrel protein [Bacillus thuringiensis str. Al
           Hakam]
 gi|229089207|ref|ZP_04220489.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-42]
 gi|229182470|ref|ZP_04309722.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BGSC 6E1]
 gi|118415072|gb|ABK83491.1| tRNA-U20-dihydrouridine synthase [Bacillus thuringiensis str. Al
           Hakam]
 gi|228601050|gb|EEK58618.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BGSC 6E1]
 gi|228694170|gb|EEL47851.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-42]
          Length = 339

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|49481554|ref|YP_034429.1| NifR3 family TIM-barrel protein [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|167635018|ref|ZP_02393335.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0442]
 gi|170688920|ref|ZP_02880122.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0465]
 gi|196036383|ref|ZP_03103780.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus W]
 gi|254682297|ref|ZP_05146158.1| NifR3 family TIM-barrel protein [Bacillus anthracis str.
           CNEVA-9066]
 gi|254744620|ref|ZP_05202299.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. Kruger B]
 gi|300119171|ref|ZP_07056872.1| NifR3 family TIM-barrel protein [Bacillus cereus SJ1]
 gi|49333110|gb|AAT63756.1| possible TIM-barrel protein, NifR3 family [Bacillus thuringiensis
           serovar konkukian str. 97-27]
 gi|167529492|gb|EDR92242.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0442]
 gi|170667144|gb|EDT17905.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0465]
 gi|195991013|gb|EDX54984.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus W]
 gi|298723493|gb|EFI64234.1| NifR3 family TIM-barrel protein [Bacillus cereus SJ1]
          Length = 332

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 155 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 203 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|228919026|ref|ZP_04082406.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840675|gb|EEM85936.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 324

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 130/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 29  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 88

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 89  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 147

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 148 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-NG 195

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 196 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 251


>gi|229194466|ref|ZP_04321270.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1293]
 gi|228589056|gb|EEK47070.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1293]
          Length = 339

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVKKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|257088706|ref|ZP_05583067.1| dihydrouridine synthase [Enterococcus faecalis CH188]
 gi|256997518|gb|EEU84038.1| dihydrouridine synthase [Enterococcus faecalis CH188]
          Length = 332

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I   +KK +  L    +E PL++QI G D   LVEAAK VE+     I 
Sbjct: 37  LVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGDKETLVEAAKFVEENTKAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK R G D D + AV  
Sbjct: 97  DINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVKMRTGWDEDHLYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +   + +++G + I +H R  +   +G +          ++D++ E+KK     F+G N
Sbjct: 155 -DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDVLKEVKKHLTIPFMG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 203 GDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245


>gi|228912815|ref|ZP_04076463.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228925329|ref|ZP_04088426.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228931578|ref|ZP_04094485.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228943882|ref|ZP_04106268.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229119738|ref|ZP_04249000.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 95/8201]
 gi|228663763|gb|EEL19341.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 95/8201]
 gi|228815839|gb|EEM62074.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228828130|gb|EEM73857.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228834376|gb|EEM79916.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228846875|gb|EEM91879.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 339

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|15612660|ref|NP_240963.1| nitrogen regulation transcriptional regulator [Bacillus halodurans
           C-125]
 gi|10172709|dbj|BAB03816.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) [Bacillus halodurans C-125]
          Length = 334

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 126/234 (53%), Gaps = 21/234 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AIL  ++K++  L    +EKPL+LQI G +   LVEAA
Sbjct: 26  FRLIAKEF-GAGLVCAEMVSDKAILHKNEKSLSMLYVDEREKPLSLQIFGGEKETLVEAA 84

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K V+ +   + I++N+GCP  ++ +   GA  +L+P+ + D ++A+   +  PVTVK RI
Sbjct: 85  KFVDKNTNADIIDINMGCPVPKITKCDAGARWLLDPNKIYDMVSAVVDEVDKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIK 183
           G D++    A+ N  ++++++G   + +H R  +   +G +          D++I+ E+K
Sbjct: 145 GWDEE-HIYAVEN-AQAVERAGGAAVAVHGRTRVQMYEGTA----------DWNIIREVK 192

Query: 184 KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +      IG NG ++    A ++L    VDGVMIGRAA  N  ML     Y   
Sbjct: 193 QAVGIPVIG-NGDVKTPQDAKRMLDEIGVDGVMIGRAALGNPWMLYRTIHYLET 245


>gi|322381161|ref|ZP_08055164.1| tRNA-dihydrouridine synthase B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154737|gb|EFX47008.1| tRNA-dihydrouridine synthase B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 326

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 74/233 (31%), Positives = 121/233 (51%), Gaps = 19/233 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+ +   +L    +EKPL+LQI G D   LV AA
Sbjct: 14  FRLIAKEF-GCGLVCAEMVSDKAIVHGNSRTMEMLYVDEREKPLSLQIFGGDKETLVAAA 72

Query: 67  KIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           K V D   N   I++N+GCP  +V +   GA  +L+P  + + ++A+ + +S PVTVK R
Sbjct: 73  KYV-DLNTNADIIDINMGCPVPKVTKCDAGARWLLDPQKIEEMVSAVVEVVSKPVTVKMR 131

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G D +    A+RN  ++++++G + + +H R         ++       ++DI+ E+K+
Sbjct: 132 MGWDSE-HIYAVRN-AQAVERAGGSAVSLHGRT--------REQLYTGTANWDIIREVKQ 181

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
                 IG NG +     A ++L     DGVMIGR A  N  ML     Y + 
Sbjct: 182 SISIPLIG-NGDVVTPEDAKRMLEETGCDGVMIGRGALGNPWMLYRTVHYLTE 233


>gi|307564816|ref|ZP_07627344.1| TIM-barrel protein, nifR3 family [Prevotella amnii CRIS 21A-A]
 gi|307346538|gb|EFN91847.1| TIM-barrel protein, nifR3 family [Prevotella amnii CRIS 21A-A]
          Length = 325

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 117/226 (51%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +     E+P  +QI G +
Sbjct: 18  MEDVTDIGFRSMCKRY-GAAMVYTEFVSADAIIRNIKSTLSKMVIDDNERPTGIQIYGNN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE+   + I++N GCP  +V     GA L+ N  ++ + +  + KA+++P
Sbjct: 77  VESMVEAAKIVEEAKPDVIDINFGCPVKKVAGKGAGAGLLRNIPLLLNIVREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + + +L + I+  G   + IH R         ++       D+ +
Sbjct: 137 VTVKTRLGWDEH--NLIITDLAEQIQDCGAKALTIHGRT--------REQMYTGKADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + ++ K NP + I +  NG +  +  A        VD VMIGRA +
Sbjct: 187 IGKVAK-NPHITIPIIGNGDIVSVKDAYDHFDKYGVDAVMIGRATF 231


>gi|229188361|ref|ZP_04315410.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 10876]
 gi|228595160|gb|EEK52930.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 10876]
          Length = 324

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 130/236 (55%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 29  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 88

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 89  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 147

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 148 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 195

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 196 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 251


>gi|229039981|ref|ZP_04189745.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH676]
 gi|228727389|gb|EEL78582.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH676]
          Length = 332

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 129/236 (54%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+     Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVRYLETGELMPEPTVREKID 259


>gi|118442953|ref|YP_877134.1| NifR3 family protein [Clostridium novyi NT]
 gi|118133409|gb|ABK60453.1| nifR3 family enzyme [Clostridium novyi NT]
          Length = 321

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 152/317 (47%), Gaps = 47/317 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    L+YTEMI A  +   ++  K +L  S +EKP+A QI G+D
Sbjct: 17  MAGVTDIAYRGLCKEM-GCGLVYTEMISAKGMYYDNENTKKLLKLSEEEKPVAAQIFGSD 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I+ ED G   +++N+GCP+ ++ +   G+ LM NP + G+ +  M K  + 
Sbjct: 76  PKVMARACEILNEDDGVGIVDINMGCPAPKIVKNGEGSALMKNPKLAGEIVREMKKVSNK 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNL 174
           PVTVK R G D D I AV   +   +++++G + + IH R    + +G +          
Sbjct: 136 PVTVKFRKGFDNDNINAV---DFAMAMEQAGADAVAIHGRTRAQMYEGKA---------- 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D+DI+ ++K+      IG NG +   ED + ALK   + DG+M+ R A  N  +   + +
Sbjct: 183 DWDIIRKVKESVSIPVIG-NGDVFSAED-AFALKNSTNCDGIMVARGAMGNPWIFKQIQQ 240

Query: 232 YFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHL----HSGGKLQ---QITRHMIGL 283
             +   +   +PI+                D   RHL    H  G+L+   ++ +H+   
Sbjct: 241 AINEEEVIYPTPIEK--------------IDLCIRHLNLAVHYHGELKGVREMRKHIAWY 286

Query: 284 FHGFPNSRRCRHILTVE 300
             G       ++ + VE
Sbjct: 287 IKGIKKCTEIKNKINVE 303


>gi|312109228|ref|YP_003987544.1| hypothetical protein GY4MC1_0077 [Geobacillus sp. Y4.1MC1]
 gi|311214329|gb|ADP72933.1| TIM-barrel protein, nifR3 family [Geobacillus sp. Y4.1MC1]
          Length = 333

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/221 (33%), Positives = 120/221 (54%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+    I+  ++K  N+L    +EKPL+LQI G +   LVEAAK V+     +I 
Sbjct: 37  LVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGEKETLVEAAKFVDKHTNADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ + D +AA+  A+  PVTVK RIG D+     A+ 
Sbjct: 97  DINMGCPVPKVTKCDAGAKWLLDPNKIYDVVAAIVDAVEKPVTVKMRIGWDEN-HIYAVE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D++I+ ++K+      IG NG
Sbjct: 156 N-AQAVERAGGKAVAVHGRTRVQMYEGKA----------DWNIIKQVKEAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++    A ++L    VDGVMIGRAA  N  M+     Y  
Sbjct: 204 DVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVRYLE 244


>gi|89897831|ref|YP_514941.1| dehydrogenases [Chlamydophila felis Fe/C-56]
 gi|89331203|dbj|BAE80796.1| dehydrogenases [Chlamydophila felis Fe/C-56]
          Length = 339

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 77/318 (24%), Positives = 147/318 (46%), Gaps = 23/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  YR  + L    AL++ EM+  + +     + +  L +S   +P+  Q+ G+ 
Sbjct: 21  LAGFSDYPYRRMSSLYGLPALMFCEMVKIEGLHYSPSRTLKLLEYSESMRPIGGQLCGSK 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAAK++E  G++ I+LN GCP+ R+ +   G+ L+  P+++G  +  +  ++SIP
Sbjct: 81  PEMAGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGLLKTPELIGKVLEKIIGSVSIP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     + +   V+ IK++G + +++H R      + P       NL+Y I
Sbjct: 141 VTVKIRSGWDGN--NINVEETVRIIKEAGASAVFVHGRTRAQGYVGPS------NLEY-I 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
                    D  +  NG +     A  +L S   DGV++ R       +   +++Y +  
Sbjct: 192 ARAKAAAGKDFPVFGNGDVFSPEAAKLMLDSTGCDGVLVARGTMGAPWIARQIEDYLTTG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  TR  + F + +      +   +  S  K    TR + G  H   ++ + R +
Sbjct: 252 TYQKMPFSTR-KQAFLQHL-----HWVEEYYQSEAKFLCETRKLCG--HYLISAAKVRFL 303

Query: 297 LTVEAGAST--ATHHIIE 312
            +  + A++  A + +IE
Sbjct: 304 RSALSKATSVQAVYQLIE 321


>gi|148655022|ref|YP_001275227.1| nifR3 family TIM-barrel protein [Roseiflexus sp. RS-1]
 gi|148567132|gb|ABQ89277.1| putative TIM-barrel protein, nifR3 family [Roseiflexus sp. RS-1]
          Length = 349

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 94/329 (28%), Positives = 154/329 (46%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MV  TD  +R     L    L+ +EM  A A+      +   L +  +E+P+A+Q+ G D
Sbjct: 39  MVGVTDSIFRRMILSLGGCGLVCSEMTSASAVSPRARSRHRQLDYLPEERPIAMQLSGND 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++VE+ G + +++N GCPS +V  G  G+ L+ +   +   + A+C A+ IP
Sbjct: 99  PDLVAAAARVVEELGADILDINCGCPSPKVTGGGHGSALLRDLPTMERLLKAVCAAVQIP 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+   ++   +  K  +++GV  + +H R    +G S          D+  
Sbjct: 159 VTLKFRAGWDEA--SLNYLDTAKMAEQAGVAALALHPRTRA-QGYSGV-------ADWTR 208

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+K+      IG +G + D + AL+ L     DGVMIGR A  N  +   + +     
Sbjct: 209 VAEVKRAVSIPVIG-SGDVRDAADALRRLHESGADGVMIGRGAMHNPWIFRQIAQLR--- 264

Query: 237 LTGSSPIK-TRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRC 293
            TG  P+  T  DK DF  +      D     L +  KL+Q    +IG F    P +   
Sbjct: 265 -TGMQPMTVTPADKYDFLTRYLEMCCDEMPERL-ALNKLKQ----LIGQFGIELPGAAAL 318

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  +   +  + A  H +E  F   IE++
Sbjct: 319 RSAVHHSSSVAEARDH-LERFFAWHIEAM 346


>gi|325105644|ref|YP_004275298.1| tRNA-U20-dihydrouridine synthase [Pedobacter saltans DSM 12145]
 gi|324974492|gb|ADY53476.1| tRNA-U20-dihydrouridine synthase [Pedobacter saltans DSM 12145]
          Length = 330

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 84/305 (27%), Positives = 139/305 (45%), Gaps = 33/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      L+YTE I ++ ++R     +  L     E+P+ +QI G+D
Sbjct: 20  MEDVSDPPFRYVCKQ-NGVDLMYTEFISSEGLIRDAAKSRQKLDVFEYERPIGIQIFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I      + I++N GCP   V     G+ L+ + D +    AA+ KA  +P
Sbjct: 79  IDHMFEATEIATQANPDLIDINYGCPVKNVACRGAGSALLQDIDKMVAMTAAVVKATHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    +    + + ++  G+  + IH R    + KG +          D+
Sbjct: 139 VTVKTRLGWDDNTKNIY--EVAERLQDVGIQALSIHGRTRAQMYKGEA----------DW 186

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ E+KK NP + I +  NG ++   +A   ++   +DG+MIGRAA     +   V  +
Sbjct: 187 TLIKEVKK-NPRIKIPIFGNGDVDSAIKAANWRLEYEIDGIMIGRAAIGYPWIFREVKHF 245

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPN 289
           F        P I  RVD          +T         G K  + ++ RH    F G PN
Sbjct: 246 FKTGQHLEGPTIDERVD--------VCLTHLRKSVEWKGPKTGIFEMRRHYANYFKGVPN 297

Query: 290 SRRCR 294
            +  R
Sbjct: 298 FKEYR 302


>gi|29840744|ref|NP_829850.1| nifR3 family TIM-barrel protein [Chlamydophila caviae GPIC]
 gi|29835094|gb|AAP05728.1| putative TIM-barrel protein, nifR3 family [Chlamydophila caviae
           GPIC]
          Length = 339

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 120/250 (48%), Gaps = 13/250 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  YR  + L    AL++ EM+  + +     + +  L +S   +P+  Q+ G+ 
Sbjct: 21  LAGFSDYPYRRMSSLYGPPALMFCEMVKIEGLHYSPSRTLKLLEYSESMRPIGGQLCGSK 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAAK++E  G++ I+LN GCP+ R+ +   G+ ++ +P+++G  +  +  A+SIP
Sbjct: 81  PDMAGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGMLKSPELIGKVLEKIIGAVSIP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     + +   V+ IK +G + I++H R      + P       NL+Y I
Sbjct: 141 VTVKIRSGWDGN--NINVEETVRIIKDAGASAIFVHGRTRAQGYVGPS------NLEY-I 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
                    D  +  NG +     A  +L +   DGV++ R       ++  +++Y +  
Sbjct: 192 TRAKAAAGKDFPVFGNGDVFSPEAAKVMLDTTGCDGVLVARGTMGTPWIVRQIEDYLNTG 251

Query: 237 LTGSSPIKTR 246
                P  TR
Sbjct: 252 TYEKMPFSTR 261


>gi|295401955|ref|ZP_06811917.1| TIM-barrel protein, nifR3 family [Geobacillus thermoglucosidasius
           C56-YS93]
 gi|294975957|gb|EFG51573.1| TIM-barrel protein, nifR3 family [Geobacillus thermoglucosidasius
           C56-YS93]
          Length = 333

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/221 (33%), Positives = 120/221 (54%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+    I+  ++K  N+L    +EKPL+LQI G +   LVEAAK V+     +I 
Sbjct: 37  LVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGEKETLVEAAKFVDKHTNADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ + D +AA+  A+  PVTVK RIG D+     A+ 
Sbjct: 97  DINMGCPVPKVTKCDAGAKWLLDPNKIYDVVAAIVDAVEKPVTVKMRIGWDEN-HIYAVE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D++I+ ++K+      IG NG
Sbjct: 156 N-AQAVERAGGKAVAVHGRTRVQMYEGKA----------DWNIIKQVKEAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++    A ++L    VDGVMIGRAA  N  M+     Y  
Sbjct: 204 DVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVRYLE 244


>gi|332970433|gb|EGK09425.1| tRNA-dihydrouridine synthase B [Kingella kingae ATCC 23330]
          Length = 340

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 123/241 (51%), Gaps = 20/241 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR  R  AR    N  + +EM+ +D  L+  +K  N      ++  + +QI G+D
Sbjct: 25  MAGITDRPTRQLARQFGANWTV-SEMLSSDPTLQNTQKSRNRRNHDGEQGVIVVQIAGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++L +AA++  + G   I++N+GCP+ +V     G+ L+ N  +V   + A+ +A S+P
Sbjct: 84  PTQLADAARLNAEHGAQVIDINMGCPAKKVCNVLAGSALLQNEKLVEQILHAVVQAASVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VT+K R+G DD+   +    + K  +++G+  + IH   R  + KG +           Y
Sbjct: 144 VTLKTRLGWDDEHKNIL--TIAKMAEQAGIVALAIHGRTRTQMYKGQA----------QY 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           D++ E+ K+   L +  NG ++   +A ++L     DG++IGRAA     +   V  +  
Sbjct: 192 DLIAEV-KQTISLPVWANGDIDSPQKARQVLQQTGADGILIGRAAQGQPWLFADVAHFLQ 250

Query: 235 N 235
           +
Sbjct: 251 H 251


>gi|255527649|ref|ZP_05394509.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
 gi|296186914|ref|ZP_06855315.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
 gi|255508662|gb|EET85042.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
 gi|296048628|gb|EFG88061.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
          Length = 326

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 85/298 (28%), Positives = 140/298 (46%), Gaps = 40/298 (13%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-- 76
           L+YTEMI A A+  G K  K++L  S QE P A+QI G D   LV  AK  + F  NE  
Sbjct: 36  LVYTEMISAKALFYGSKNTKDMLVISKQEAPAAVQIFGND--PLV-MAKACDFFNDNEDI 92

Query: 77  --INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPA 133
             +++N+GCP+ ++ +   G+ LM +P +    +  + KA S PVT K R G D D I A
Sbjct: 93  CLVDINMGCPAPKIVKNGEGSALMKDPKLAAQIVKEVKKASSKPVTAKFRKGFDSDNINA 152

Query: 134 VALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           V      K ++++GV+ + +H   R+ + +G +          D++++ ++K+      I
Sbjct: 153 V---EFAKELEQAGVDAVTVHGRTREQMYEGKA----------DWNMIEKVKQAVSIPVI 199

Query: 192 GLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD- 248
           G NG +     A+ I  +   D +MIGR A  N  +   +DE   N        + R+D 
Sbjct: 200 G-NGDVVTPEDAVSIFKTTNCDAIMIGRGAMGNPWIFNQIDEKIKNINVTYPSEEDRIDM 258

Query: 249 --KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAS 304
             + + R IS      A R +          +H+     G  N++  +  +  E  + 
Sbjct: 259 CMEHYRRAISYEGEAKAVREMR---------KHVGWYLKGLSNNKEIKDAVNYEKSSE 307


>gi|315650052|ref|ZP_07903131.1| tRNA-dihydrouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315487681|gb|EFU77985.1| tRNA-dihydrouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 334

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/279 (25%), Positives = 135/279 (48%), Gaps = 21/279 (7%)

Query: 20  ALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           +LL TEM+ A AI   +K  ++++     E P++LQ+ G+D   + + A  +ED  ++  
Sbjct: 53  SLLVTEMVSAKAIYFKNKNTRSLMKTDKYEHPISLQLFGSDPDIIADMAASIEDGDFDIF 112

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           + N+GCP  ++     G  LM NP +V + ++ + K++  PVT+K R G D +  ++   
Sbjct: 113 DFNMGCPVPKIVNNGEGCALMKNPKLVEEILSKLVKSVKKPVTLKIRRGFDSE--SINAV 170

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++ K  + +GV+ + +H R         ++   +   D+DI+ ++K       IG NG +
Sbjct: 171 DIAKIAENAGVSAVTVHGR--------TREQYYLGKADWDIIKDVKSAVNIPVIG-NGDV 221

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
            D   A ++      DG+M+ RAA  N  +   + EY +   T   P K  + +   R  
Sbjct: 222 ADGESAKRMYEYTGCDGIMVARAARGNPWIFREIREYLTG-YTVKKPSKEEIIEMILRHC 280

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              M +Y    +     ++++ +H+    HG  NS   R
Sbjct: 281 RLQM-EYDDEVM----AVRKMRKHVAWYTHGMKNSSVLR 314


>gi|303230948|ref|ZP_07317691.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514330|gb|EFL56329.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 330

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 140/307 (45%), Gaps = 29/307 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     +++ TEM+ A  I   +++   +L     E P+++QI G+D   +
Sbjct: 25  SDIAYRLLAKE-HGASMVCTEMVSAMGIKYKNERTHELLRMEAVEHPVSMQIFGSDPEAI 83

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V D G + +++N+GCP  +V     G+ LM  PD+      A  KA+ +PVTVK
Sbjct: 84  ALGAKVVADAGADIVDINMGCPVKKVVSSGDGSALMKTPDLAARVAEAAVKAVDVPVTVK 143

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG DD    + + +  K I+ +GV  + +H R         ++   +   ++  +  +
Sbjct: 144 MRIGWDDD--HINVVDFAKRIESTGVAAVAVHGRT--------REQMYMGRANWSYIKAV 193

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K       IG NG +     AL+++     D VMIGR A  N  +    + Y +   TG 
Sbjct: 194 KDSLSIPVIG-NGDVWTPEDALRMMQETGCDAVMIGRGAQGNPWIFERTNHYLT---TGE 249

Query: 241 -SPIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS----RRCR 294
            SP  T +++ D   K    +  Y    L     +++I  H      G P +     R  
Sbjct: 250 LSPEPTYLERLDMLLKHFELLCQYKGDSL----GVREIRTHAGWYMKGMPEAAYWRNRVN 305

Query: 295 HILTVEA 301
            I TVE+
Sbjct: 306 TIHTVES 312


>gi|167752089|ref|ZP_02424216.1| hypothetical protein ALIPUT_00331 [Alistipes putredinis DSM 17216]
 gi|167660330|gb|EDS04460.1| hypothetical protein ALIPUT_00331 [Alistipes putredinis DSM 17216]
          Length = 340

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 147/309 (47%), Gaps = 41/309 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R+  +    + ++YTE I +D ++R   K++  L  +  E+P+ +Q+ G  
Sbjct: 18  MEDVTDPSFRYMCKRFGAD-VVYTEFISSDGLIRDAGKSLAKLRIAESERPVGIQLYGHL 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+I E    + I++N GCP  ++     G+ +M +  ++ +    + +A+  P
Sbjct: 77  VEPMVEAARIAEAADPDIIDINFGCPVKKIAGRGAGSGMMRDVPLMVEMTRRIVEAVKKP 136

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VTVK R+G D++   I  +ALR     ++  G+  + IH R    + +G           
Sbjct: 137 VTVKTRLGWDEESKNIEEIALR-----LQDVGIAALTIHGRTRAQMYRG----------E 181

Query: 174 LDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
            D+ ++ ++K  NP + I +  NG ++   +A ++     VDGVMIGRA Y    +   V
Sbjct: 182 ADWTLIGKVKN-NPAIRIPIIGNGDIDSGPKAREMFDRYGVDGVMIGRATYGRPWIFREV 240

Query: 230 DEYFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFH 285
             +         P +  RV+            ++ A+ L   G    + ++ RH+   F 
Sbjct: 241 KHFLETGEVMPQPSVAERVE---------IAKEHLAKSLEIKGDRVGILEMRRHLSNYFK 291

Query: 286 GFPNSRRCR 294
           G PN +  R
Sbjct: 292 GLPNFKETR 300


>gi|69250952|ref|ZP_00605186.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium DO]
 gi|257879863|ref|ZP_05659516.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257882589|ref|ZP_05662242.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|257891704|ref|ZP_05671357.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257894179|ref|ZP_05673832.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|258614292|ref|ZP_05712062.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecium
           DO]
 gi|260559535|ref|ZP_05831716.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium C68]
 gi|293563202|ref|ZP_06677658.1| NifR3 family protein [Enterococcus faecium E1162]
 gi|293570124|ref|ZP_06681204.1| NifR3 family protein [Enterococcus faecium E1071]
 gi|294618637|ref|ZP_06698176.1| NifR3 family protein [Enterococcus faecium E1679]
 gi|294623713|ref|ZP_06702546.1| NifR3 family protein [Enterococcus faecium U0317]
 gi|314938206|ref|ZP_07845506.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a04]
 gi|314943101|ref|ZP_07849900.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133C]
 gi|314949298|ref|ZP_07852641.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0082]
 gi|314952231|ref|ZP_07855246.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133A]
 gi|314992089|ref|ZP_07857539.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133B]
 gi|314996272|ref|ZP_07861328.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a01]
 gi|68193901|gb|EAN08482.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium DO]
 gi|257814091|gb|EEV42849.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818247|gb|EEV45575.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|257828064|gb|EEV54690.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257830558|gb|EEV57165.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|260074634|gb|EEW62955.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium C68]
 gi|291587496|gb|EFF19380.1| NifR3 family protein [Enterococcus faecium E1071]
 gi|291595156|gb|EFF26494.1| NifR3 family protein [Enterococcus faecium E1679]
 gi|291596928|gb|EFF28146.1| NifR3 family protein [Enterococcus faecium U0317]
 gi|291604852|gb|EFF34330.1| NifR3 family protein [Enterococcus faecium E1162]
 gi|313589516|gb|EFR68361.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a01]
 gi|313593303|gb|EFR72148.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133B]
 gi|313595626|gb|EFR74471.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133A]
 gi|313598160|gb|EFR77005.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133C]
 gi|313642402|gb|EFS06982.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a04]
 gi|313644304|gb|EFS08884.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0082]
          Length = 334

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 74/222 (33%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ VE+    + I
Sbjct: 40  LVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGNKDSLVEAAQFVEENTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + + A+  A++IPVT+K RIG D++    A+ 
Sbjct: 100 DINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVNIPVTIKMRIGWDEE-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + + +G + I +H R  +   +G +          D++++ E+KK     F+G NG
Sbjct: 159 NALAA-QSAGASAIAMHGRTRVQMYEGKA----------DWEVLKEVKKHLTIPFMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A  +L  V  DGVMIGRAA  N  M+     Y   
Sbjct: 207 DVKTPEDAKWMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248


>gi|226309767|ref|YP_002769661.1| tRNA-dihydrouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226092715|dbj|BAH41157.1| probable tRNA-dihydrouridine synthase [Brevibacillus brevis NBRC
           100599]
          Length = 342

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 124/241 (51%), Gaps = 21/241 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+    I+ G+KK I  L    +EKPL+LQI G D   LV AA
Sbjct: 25  FRLIAKEF-GTGLVCAEMVSDKGIVHGNKKTIDMLFVDEREKPLSLQIFGGDKETLVSAA 83

Query: 67  KIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K V+     +I ++N+GCP  ++     GA L+L+PD + + ++++  A+  PVTVK R+
Sbjct: 84  KYVDQHTNADIIDINMGCPVPKITSCDAGARLLLDPDKIYEVVSSVVDAVDKPVTVKMRL 143

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIK 183
           G D+    + + +  K+++++G   I +H R  +   KG +          D+D +  +K
Sbjct: 144 GWDED--HLYVLDNAKAVERAGGKAIAVHGRTRVQMYKGKA----------DWDWIRRVK 191

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +      IG NG +     A ++L +   DGVMIGRAA  N  ML    +Y +    G  
Sbjct: 192 ETVSIPVIG-NGDVATPEDARRMLDTTGCDGVMIGRAALGNPWMLYRTIQYLTTGELGPE 250

Query: 242 P 242
           P
Sbjct: 251 P 251


>gi|164686644|ref|ZP_02210672.1| hypothetical protein CLOBAR_00237 [Clostridium bartlettii DSM
           16795]
 gi|164604373|gb|EDQ97838.1| hypothetical protein CLOBAR_00237 [Clostridium bartlettii DSM
           16795]
          Length = 322

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 79/301 (26%), Positives = 139/301 (46%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      +LYTEMI A A+   D+  K +     +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKQ-KGCGMLYTEMINAKALCYNDENTKKMTKIEDEEHPIAIQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I+       +++N+GCP+ +V +   G+ LM NP +    + A+ +  + P
Sbjct: 76  PEYMGRAAEILNSHSNEILDINMGCPAPKVIKNGDGSALMKNPKLAEQVMRAVVEHSTKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +++G++ + IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDDN--SVNAVEIAKIAEQAGISALAIHGR--------TREQYYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK       IG NG + ++  A+ +L   + D +MIGR A  N  +   ++ Y    
Sbjct: 186 IKEIKDSISIPVIG-NGDVFEIEDAINMLEKTNCDAIMIGRGAQGNPWIFNRINHYMQTG 244

Query: 237 LTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              + P    K     +  +   A   +Y A        ++++ +H+     G  NS R 
Sbjct: 245 EILAKPTAEEKISTAIEHMKLAVAEHGEYVA--------VREMRKHIGWYIKGLKNSARY 296

Query: 294 R 294
           R
Sbjct: 297 R 297


>gi|229077366|ref|ZP_04210033.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-2]
 gi|228705945|gb|EEL58264.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-2]
          Length = 332

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 129/236 (54%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDKYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEE-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D+DI+  +K+      IG NG
Sbjct: 156 N-ARAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKRVKQSVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|229159249|ref|ZP_04287274.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus R309803]
 gi|228624264|gb|EEK81065.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus R309803]
          Length = 339

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVKKPVTVKMRIGWDEDHI--FAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 162 EN-AKAVERAGGQAVAVHGRTRVQMYEGKA----------DWDIIKQVKQSVNIPVIG-N 209

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A +++    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 210 GDVATPQDAKRMIDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|89889708|ref|ZP_01201219.1| tRNA-dihydrouridine synthase [Flavobacteria bacterium BBFL7]
 gi|89517981|gb|EAS20637.1| tRNA-dihydrouridine synthase [Flavobacteria bacterium BBFL7]
          Length = 330

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 85/311 (27%), Positives = 145/311 (46%), Gaps = 45/311 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A ++YTE I ++ ++R   K+   L     E+P+ +QI GA
Sbjct: 19  MEDVSDPPFRALCK--ENGADVVYTEFISSEGLIRDAAKSTMKLDIYEAERPVGIQIFGA 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++  ++++ +IVE    + I++N GCP  +V     GA ++ + D++    AAM K   +
Sbjct: 77  NLDSMLQSVEIVERTKPDIIDINFGCPVKKVVSRGAGAGILKDIDLMVSLTAAMVKHTDL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           P+TVK R+G DD   ++ +  + + ++  G+  I IH R    + KG          N D
Sbjct: 137 PITVKTRLGWDDD--SIKIVEVAERLQDVGIKAISIHGRTRAQMYKG----------NAD 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +  + ++K  NP + I +  NG +    +A+++     +DG MIGRA+         V  
Sbjct: 185 WKPIADVKN-NPRMHIPVFGNGDVNTPERAVEMRDEYGLDGAMIGRASIGYPWFFREVKH 243

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQQIT--RHMIGL 283
           +F      + P ++ RV             + A RHL       G  L  I   RH    
Sbjct: 244 FFETGTHMAKPTMQERV-------------EVARRHLEMSIAWKGETLGVIETRRHYTNY 290

Query: 284 FHGFPNSRRCR 294
           F G PN +  R
Sbjct: 291 FKGIPNFKEYR 301


>gi|311070728|ref|YP_003975651.1| tRNA-dihydrouridine synthase B [Bacillus atrophaeus 1942]
 gi|310871245|gb|ADP34720.1| tRNA-dihydrouridine synthase B [Bacillus atrophaeus 1942]
          Length = 333

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 124/230 (53%), Gaps = 22/230 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  + K +  L    +EKPL+LQI G     LVEAAK V ++   + I
Sbjct: 37  LVCAEMVSDKAILYNNAKTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+PD + + ++A+ +++  PVTVK R+G D D I AV  
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVESVDKPVTVKMRMGWDEDHIFAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           +N  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG N
Sbjct: 155 KN-AQAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           G ++    A ++L    VDGVMIGRAA  N  M+    +Y         P
Sbjct: 203 GDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLETGELKDEP 252


>gi|188993880|ref|YP_001928132.1| putative TIM-barrel protein [Porphyromonas gingivalis ATCC 33277]
 gi|188593560|dbj|BAG32535.1| putative TIM-barrel protein [Porphyromonas gingivalis ATCC 33277]
          Length = 333

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + L+Y+E + ADA++R        +     E+P+A+QI G D
Sbjct: 18  MEDVTDVAFRIMCKQFGAD-LVYSEFLSADALIRQVAGTFRKMAIDESERPMAVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA++ E  G + I+LN GCP  RV     G+ ++ N  ++ +    + KA+ +P
Sbjct: 77  VASMVEAARLCESAGPDLIDLNFGCPVKRVAGKGAGSGMLRNIPLMIEITREVVKAVKLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNDSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGTADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +    +A +      VD VM+GRA+     +   +  +  
Sbjct: 187 IGEVKN-NPRMQIPIIGNGDVTTPQEARRAFDVYGVDAVMVGRASIGQPWIFEDMKHFLR 245

Query: 235 NPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              T  S P        ++  I    T    R L     +    RH+    +F G PN +
Sbjct: 246 TGETLPSRPFC------YYMDILRRQTLNNIRKLDERRGILHTRRHIAASPIFKGIPNFK 299

Query: 292 RCR 294
             R
Sbjct: 300 PMR 302


>gi|321313751|ref|YP_004206038.1| tRNA-dihydrouridine synthase B [Bacillus subtilis BSn5]
 gi|320020025|gb|ADV95011.1| tRNA-dihydrouridine synthase B [Bacillus subtilis BSn5]
          Length = 333

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 124/231 (53%), Gaps = 22/231 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EM+   AIL  + + +  L    +EKPL+LQI G     LVEAAK V ++   + 
Sbjct: 36  GLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  ++ +   GA  +L+PD + + ++A+  A++ PVTVK R+G D D I AV 
Sbjct: 96  IDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            +N  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG 
Sbjct: 155 -KN-AQAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG- 201

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG ++    A ++L    VDGVMIGRAA  N  M+    +Y         P
Sbjct: 202 NGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLETGELKEEP 252


>gi|260061331|ref|YP_003194411.1| hypothetical protein RB2501_07020 [Robiginitalea biformata
           HTCC2501]
 gi|88785463|gb|EAR16632.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Robiginitalea biformata HTCC2501]
          Length = 330

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 140/307 (45%), Gaps = 37/307 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRTLCKEQGAD-VMYTEFISSEGLIRDAAKSVVKLDIYEKERPIGIQIFGAE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++A  IV + G + I++N GCP  +V   + GA ++ +  ++     AM K   +P
Sbjct: 78  LDSMLQAVDIVTETGPDIIDINFGCPVKKVVCKNAGAGILRDIPLMVKLTEAMVKRTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G+  I IH R  +       D R I  +    
Sbjct: 138 VTVKTRLGWDHN--SIKIVEVAERLQDVGIQSIAIHGRTRVQMYKGEADWRPIAEV---- 191

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
                K NP + I +  NG ++    A+++     +DG MIGRA+         V  YF 
Sbjct: 192 -----KNNPRMHIPVFGNGDVDTPEAAVRMRDEYGLDGAMIGRASIGYPWFFREVKHYFE 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLFHGF 287
                  P       D   +++A     A RHL       G KL   +  RH    F G 
Sbjct: 247 TGEHLPPP-------DMEARVAA-----ARRHLQMAIDWKGEKLGVFETRRHYTNYFKGI 294

Query: 288 PNSRRCR 294
           PN +  R
Sbjct: 295 PNFKPYR 301


>gi|16077149|ref|NP_387962.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221307891|ref|ZP_03589738.1| hypothetical protein Bsubs1_00410 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312213|ref|ZP_03594018.1| hypothetical protein BsubsN3_00410 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317146|ref|ZP_03598440.1| hypothetical protein BsubsJ_00410 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221321409|ref|ZP_03602703.1| hypothetical protein BsubsS_00410 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|586896|sp|P37567|DUS1_BACSU RecName: Full=Probable tRNA-dihydrouridine synthase 1
 gi|467469|dbj|BAA05315.1| unknown [Bacillus subtilis]
 gi|2632348|emb|CAB11857.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|291482453|dbj|BAI83528.1| hypothetical protein BSNT_00139 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 333

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 124/231 (53%), Gaps = 22/231 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EM+   AIL  + + +  L    +EKPL+LQI G     LVEAAK V ++   + 
Sbjct: 36  GLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  ++ +   GA  +L+PD + + ++A+  A++ PVTVK R+G D D I AV 
Sbjct: 96  IDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNKPVTVKMRMGWDEDHIFAV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            +N  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG 
Sbjct: 155 -KN-AQAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG- 201

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG ++    A ++L    VDGVMIGRAA  N  M+    +Y         P
Sbjct: 202 NGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLETGKLKEEP 252


>gi|296131768|ref|YP_003639015.1| TIM-barrel protein, nifR3 family [Thermincola sp. JR]
 gi|296030346|gb|ADG81114.1| TIM-barrel protein, nifR3 family [Thermincola potens JR]
          Length = 340

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 81/306 (26%), Positives = 140/306 (45%), Gaps = 35/306 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD+ YR  A L   + L+ TEM+ A A+    +  K +L  S ++ P+++QI G  
Sbjct: 30  MAGVTDKAYRLIAEL-AGSGLVCTEMVSATALRYNSERTKTMLDLSGEKGPISVQIFGNQ 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK  E  G   I++N+GCP+ +V +   G  LM +  +  + ++A+ KA+ IP
Sbjct: 89  PELMSRAAKFAETQGAAIIDINMGCPAPKVVKNFEGCALMRDLPLAREIMSAVVKAVQIP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++  +V    L K  +++G+  + +H R         +        D+DI
Sbjct: 149 VTVKMRKGWDEE--SVNAVELAKMAQETGIAAVTVHGRT--------RGQFYSGKADWDI 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+      IG NG + +   AL ++     D VMIGR A  N  + +   +     
Sbjct: 199 IARVKEAVQIPVIG-NGDIFEPVHALAMMKQTGCDAVMIGRGALGNPWLFSRTVKLLE-- 255

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG-------GKLQQITRHMIGLFHGFPN 289
            TG  P +  +D+           + A +HL            ++++ +H+     G   
Sbjct: 256 -TGEIPPEPSIDERL---------EMAKKHLQLAVAFKGEYRAVREMRKHIAWYIKGLRE 305

Query: 290 SRRCRH 295
           + R R 
Sbjct: 306 AARVRE 311


>gi|162448213|ref|YP_001621345.1| tRNA-dihydrouridine synthase [Acholeplasma laidlawii PG-8A]
 gi|161986320|gb|ABX81969.1| tRNA-dihydrouridine synthase [Acholeplasma laidlawii PG-8A]
          Length = 336

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 90/311 (28%), Positives = 147/311 (47%), Gaps = 46/311 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   ++  +R  AR L    +++ EM+   AI   + K +  L  + +EKP A QI G+D
Sbjct: 19  MAGVSNHPFRLMARQL-GAGVVFAEMVSDKAIFFQNPKTLQMLYMTVEEKPAAQQIFGSD 77

Query: 59  ISKLVEAAKIVE-----DFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMC 112
           +  +VEAA  ++     DF    I++N+GCP  +V  G+  GA LM +P  + D + A+ 
Sbjct: 78  LETMVEAAMFIDKNSNCDF----IDINMGCPVPKVAIGAQAGASLMKDPQKIYDIVKAIK 133

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           + +S PVTVK R G D +  +V    + K I+K+G + I +HAR    +G S +      
Sbjct: 134 EKVSKPVTVKIRSGWDSE--SVNAVEVAKMIEKAGASLITVHARTR-AQGYSGEP----- 185

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
             D D++  +K+      IG NG + D   A  +L     D VMIGRA+  N  +   ++
Sbjct: 186 --DLDVIKAVKEAVSIPVIG-NGNIVDGKSAKHMLEYTGCDAVMIGRASLGNPWIFREIN 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-------QITRHMIGL 283
            Y +   T   P++T      + ++   M     RH     KL+       ++  H    
Sbjct: 243 AYLNGEET---PVRT------YEEVKTLMI----RHFDDLAKLKGEHTACLEMRSHGPWY 289

Query: 284 FHGFPNSRRCR 294
             G P + + R
Sbjct: 290 LKGLPKASQVR 300


>gi|308171971|ref|YP_003918676.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens DSM 7]
 gi|307604835|emb|CBI41206.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens DSM 7]
 gi|328551782|gb|AEB22274.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens TA208]
 gi|328910042|gb|AEB61638.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens LL3]
          Length = 333

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 124/230 (53%), Gaps = 22/230 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  + K +  L    +EKPL+LQI G +   LVEAAK V ++   + I
Sbjct: 37  LVCAEMVSDKAILYNNAKTMGMLFIEEREKPLSLQIFGGEKETLVEAAKFVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  PVTVK R+G D D I AV  
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVDAVDKPVTVKMRMGWDEDHIYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           +N  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG N
Sbjct: 155 KN-AQAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKEVKQSLSIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           G ++    A ++L    VDGVMIGRAA  N  M+    +Y         P
Sbjct: 203 GDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVQYLETGELKDEP 252


>gi|325662824|ref|ZP_08151393.1| hypothetical protein HMPREF0490_02133 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325470876|gb|EGC74105.1| hypothetical protein HMPREF0490_02133 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 325

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 121/237 (51%), Gaps = 18/237 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K  +++L    +E+P++LQ+ G++
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYKNKNTQDLLRIHEEERPVSLQLFGSE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  ++ +   G+ LM  P +V + ++   KA+  P
Sbjct: 82  PDTISEIAKQIEELPFAILDINMGCPVPKIVKNGEGSALMKQPKLVYEIVSKTVKAIQKP 141

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I AV    + K I+++G   + +H R         ++       D++
Sbjct: 142 VTVKIRKGFDDSCINAV---EIAKVIEEAGGAAVAVHGRT--------REQYYSGKADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           I+ ++K+      IG NG +     A+++  L   DGVM+GR A  N  +   + EY
Sbjct: 191 IIRKVKEAVSIPVIG-NGDVTSAEDAVRMQKLTGCDGVMVGRGAQGNPWIFRELVEY 246


>gi|331086547|ref|ZP_08335625.1| hypothetical protein HMPREF0987_01928 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330410380|gb|EGG89812.1| hypothetical protein HMPREF0987_01928 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 325

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 121/237 (51%), Gaps = 18/237 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K  +++L    +E+P++LQ+ G++
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYKNKNTQDLLRIHEEERPVSLQLFGSE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  ++ +   G+ LM  P +V + ++   KA+  P
Sbjct: 82  PDTISEIAKQIEELPFAILDINMGCPVPKIVKNGEGSALMKQPKLVYEIVSKTVKAIQKP 141

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I AV    + K I+++G   + +H R         ++       D++
Sbjct: 142 VTVKIRKGFDDSCINAV---EIAKVIEEAGGAAVAVHGRT--------REQYYSGKADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           I+ ++K+      IG NG +     A+++  L   DGVM+GR A  N  +   + EY
Sbjct: 191 IIRKVKEAVSIPVIG-NGDVTSAEDAVRMQKLTGCDGVMVGRGAQGNPWIFRELVEY 246


>gi|326798717|ref|YP_004316536.1| hypothetical protein Sph21_1303 [Sphingobacterium sp. 21]
 gi|326549481|gb|ADZ77866.1| TIM-barrel protein, nifR3 family [Sphingobacterium sp. 21]
          Length = 333

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 86/328 (26%), Positives = 144/328 (43%), Gaps = 33/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R     K  L     E+P+ +QI G+D
Sbjct: 21  MEDVSDPPFRYVCKQ-NGVDMMYTEFISSEGLIRHAAKSKQKLDIFEYERPIGIQIFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I      + I++N GCP   V     GA L+ + D +     A+  A  +P
Sbjct: 80  IKSMEEATEIATLAKPDLIDINYGCPVKNVACRGAGASLLQDIDKMVAMTKAVVNATHLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    +    + + ++  G+  + IH   R  + KG          + D+
Sbjct: 140 VTVKTRLGWDDHTKNIY--EVAERLQDIGIQALSIHGRTRSQMYKG----------SADW 187

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ ++KK NP + I +  NG ++ + +  A ++   VDG+MIGRA+     +   +  +
Sbjct: 188 SLIKKVKK-NPRIHIPIFGNGDVDSVEKAAAWRLEYEVDGIMIGRASIGYPWIFREIKHF 246

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPN 289
           F        P IK RVD           T +       G K  + ++ RH    F G PN
Sbjct: 247 FETGTYLDGPTIKERVD--------VCKTHFVKSIEWKGEKTGIFEMRRHYANYFKGIPN 298

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNL 317
            +  R  L            + E AF  
Sbjct: 299 FKEYRMKLVSLDKVPEINEVLDEIAFQF 326


>gi|266624024|ref|ZP_06116959.1| tRNA-dihydrouridine synthase B [Clostridium hathewayi DSM 13479]
 gi|288864155|gb|EFC96453.1| tRNA-dihydrouridine synthase B [Clostridium hathewayi DSM 13479]
          Length = 328

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 80/301 (26%), Positives = 140/301 (46%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      ++ TEM+ A AIL  ++  K +L    +E+P+++Q+ G+D
Sbjct: 19  MAGVTDLPFRVLCKE-QGCGMVVTEMVSAKAILYKNRNTKALLEVEERERPVSVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK++E   ++ I++N+GCP  ++     G+ +M NP +    + AM KA+  P
Sbjct: 78  PEIMADIAKLIEPGPFDIIDVNMGCPVPKIVNNGEGSAMMKNPRLAEAVLGAMVKAVKKP 137

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  D  + AV    + +S    GV  + +H R         ++       D+D
Sbjct: 138 VTVKFRKGFTDSDVNAVEFAKMAES---CGVAAVAVHGRT--------REQYYSGTADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           I+  +K+      IG NG +   ED ++AL      DG+MI R A  N  + +    Y  
Sbjct: 187 IIRRVKEAVKIPVIG-NGDVFAPED-AKALLDETGCDGIMIARGAKGNPWIFSRTIHYLE 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P    +     R    S+ +Y   +L     ++++ +HM     G P+S + R
Sbjct: 245 TGELLPPPSMEELQNMVLRHAEMSV-EYKGEYLG----IREMRKHMAWYTAGLPHSAKLR 299

Query: 295 H 295
           +
Sbjct: 300 N 300


>gi|225572777|ref|ZP_03781532.1| hypothetical protein RUMHYD_00968 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039834|gb|EEG50080.1| hypothetical protein RUMHYD_00968 [Blautia hydrogenotrophica DSM
           10507]
          Length = 320

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/298 (24%), Positives = 142/298 (47%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    LL  EM+ A AI   +K  ++++     E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRLLCKEM-GAGLLCMEMVSAKAIYYKNKNTESLMEIHPAEHPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E+  +  +++N+GCP  +V     G+ L+ NP ++ + +  +  A+  P
Sbjct: 78  ADLMAQIATQIEERPFEILDINMGCPVPKVVNNGEGSALLKNPKLIREIVTKVSGAIRKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG +     V +  + K I+ SG   I +H R         ++     + D+D 
Sbjct: 138 LTVKVRIGFEGY--PVDVVEIAKIIEDSGAAAIAVHGRT--------REQYYSGHADWDA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+      IG NG ++   +A+++L     DG+MIGRAA  N  +   ++ +    
Sbjct: 188 IRRVKEAVQIPVIG-NGDVDSPQKAVQLLEETGCDGIMIGRAAQGNPWIFREINHWMKTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P ++++ +   R     + +Y   +      ++++ +H+     G P+S R R
Sbjct: 247 EFLPRPGRSQIVEMILRHARLQI-EYKGEYT----GIREMRKHVAWYTQGLPHSARLR 299


>gi|163815371|ref|ZP_02206746.1| hypothetical protein COPEUT_01536 [Coprococcus eutactus ATCC 27759]
 gi|158449345|gb|EDP26340.1| hypothetical protein COPEUT_01536 [Coprococcus eutactus ATCC 27759]
          Length = 324

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 76/283 (26%), Positives = 134/283 (47%), Gaps = 22/283 (7%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +LY+EM+ A AI   +K  K +L    +EKP  LQ+ G+D   + E AK +E  GY+ I+
Sbjct: 35  ILYSEMVSAKAIYYNNKNTKPLLAMDEREKPFGLQLFGSDPVIMAEMAKKIEGNGYSFID 94

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALR 137
           +N+GCP  +V     G+ LM +P +VG  +  +  A+SIP+T+K R G D + I A  + 
Sbjct: 95  INMGCPVPKVVNNGEGSALMKDPLLVGRIVETVANAISIPLTIKIRSGFDPEHINAPEIA 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++    ++SG   + +H R         +      + D+D++  +K+      IG NG +
Sbjct: 155 HIA---QESGAAAVAVHGRT--------RQQYYQGHADWDVIARVKQVCNIPVIG-NGDI 202

Query: 198 EDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                 + +      DG MIGR A  N  +   +  Y+ +      P    V     R  
Sbjct: 203 NTPKDIIDMRNQTDCDGFMIGRGARGNPWIFRDMKYYYEHGDLPPRPDAHEVRGMILRH- 261

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +  MT++   ++     + ++ +H+     G  +S R R ++ 
Sbjct: 262 ARLMTEFKGEYI----GIHEMRKHVAWYSAGMYDSARLRGLVN 300


>gi|65317537|ref|ZP_00390496.1| COG0042: tRNA-dihydrouridine synthase [Bacillus anthracis str.
           A2012]
 gi|270000590|ref|NP_842644.2| NifR3 family TIM-barrel protein [Bacillus anthracis str. Ames]
 gi|269850221|gb|AAP24130.2| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Ames]
          Length = 339

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 129/236 (54%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 44  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D+     A+ 
Sbjct: 104 DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDED-HIFAIE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 163 N-AKAVERAGGQVVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 210

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 211 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 266


>gi|300857284|ref|YP_003782268.1| putative tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
 gi|300437399|gb|ADK17166.1| predicted tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
          Length = 320

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 88/315 (27%), Positives = 154/315 (48%), Gaps = 43/315 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    +       YTEMI A A+       K +L  S+ EKPL +QI G+D
Sbjct: 17  MAGVTDRAFRELC-IEMKCGFTYTEMISAKALFYDSDRTKQMLKVSSIEKPLGVQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              L+  AK+ + F  NE    I++N+GCP+ ++ +   G+ LM N  +    +  + KA
Sbjct: 76  --PLI-MAKVCDFFNCNEDIAIIDINMGCPAPKIVKNGEGSALMKNSSLASQIVKEVKKA 132

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKI 171
            + PVTVK RIG D D I  V   +  + +++SG + + +H R +  +  G         
Sbjct: 133 SAKPVTVKMRIGFDFDNINVV---DFAQIMEQSGADAVTVHGRTSTQMYNG--------- 180

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTV 229
            + ++DI+ ++KK+     IG NG +     A+++  +   DGVM+GR +  N  +   +
Sbjct: 181 -SANWDIISQVKKKVNIPVIG-NGDVFTAEDAIRLFNNTGCDGVMVGRGSMGNPWIFKQI 238

Query: 230 DEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFH 285
            E  ++ P+   SP++         KI+  M  Y  R ++  G+   ++++ +H+     
Sbjct: 239 CEIRNHQPVIFPSPLE---------KINLCMEHY-RRAIYYNGEDRAVREMRKHIAWYIK 288

Query: 286 GFPNSRRCRHILTVE 300
           G  NS+  +  +  E
Sbjct: 289 GLKNSKEIKDKINCE 303


>gi|47525329|ref|YP_016678.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49183110|ref|YP_026362.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. Sterne]
 gi|47500477|gb|AAT29153.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           'Ames Ancestor']
 gi|49177037|gb|AAT52413.1| TIM-barrel protein, putative, NifR3 family [Bacillus anthracis str.
           Sterne]
          Length = 324

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 23/237 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 29  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 88

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D D I   A+
Sbjct: 89  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDEDHI--FAI 146

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG N
Sbjct: 147 EN-AKAVERAGGQVVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-N 194

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           G +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 195 GDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 251


>gi|227824807|ref|ZP_03989639.1| conserved hypothetical protein [Acidaminococcus sp. D21]
 gi|226905306|gb|EEH91224.1| conserved hypothetical protein [Acidaminococcus sp. D21]
          Length = 321

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 117/235 (49%), Gaps = 20/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKN--ILGFSTQEKPLALQIGG 56
           M   TD  +R   R    N   YT  EM+ A A+L  ++K   +L    +E P A+Q+ G
Sbjct: 16  MAGVTDLPFRVICR---ENGADYTVSEMVSAKALLYKNQKTFAMLTIDPKEHPTAIQLFG 72

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +  S+L  A KIVE  G + I++N+GCP  ++     G+ LM +PD V   +AA+  A+S
Sbjct: 73  SVPSELAAAGKIVESRGADMIDVNMGCPVHKIVSNGEGSALMKDPDKVYAILAALVDAVS 132

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R G D+     A+  + +  +K+GV+ + +H R         +        D+
Sbjct: 133 IPVTVKFRAGWDEAHKNAAV--IAQMAEKAGVSAVCVHGRT--------RAQFYQGKADW 182

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTV 229
           DI+  +K+      +G NG +     AL++      DGVMI R A  N  +   V
Sbjct: 183 DIIRAVKESVGIPVLG-NGDIFHAEDALRMKEETGCDGVMIARGAEGNPWIFRDV 236


>gi|165872591|ref|ZP_02217223.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0488]
 gi|167641547|ref|ZP_02399795.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0193]
 gi|170707493|ref|ZP_02897946.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0389]
 gi|177655621|ref|ZP_02936984.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0174]
 gi|190569012|ref|ZP_03021913.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis
           Tsiankovskii-I]
 gi|227812750|ref|YP_002812759.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           CDC 684]
 gi|229600702|ref|YP_002864728.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0248]
 gi|254735478|ref|ZP_05193186.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Western North America USA6153]
 gi|254756325|ref|ZP_05208354.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Vollum]
 gi|254762381|ref|ZP_05214223.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Australia 94]
 gi|164711719|gb|EDR17264.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0488]
 gi|167510532|gb|EDR85930.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0193]
 gi|170127489|gb|EDS96363.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0389]
 gi|172080032|gb|EDT65131.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0174]
 gi|190559936|gb|EDV13920.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis
           Tsiankovskii-I]
 gi|227005785|gb|ACP15528.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           CDC 684]
 gi|229265110|gb|ACQ46747.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0248]
          Length = 332

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 129/236 (54%), Gaps = 21/236 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EM+   AIL  +K+  ++L    +EKPL+LQI G +   LV+AAK V+ +   +I 
Sbjct: 37  LVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGEKETLVDAAKYVDQYTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK RIG D+     A+ 
Sbjct: 97  DINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEKPVTVKMRIGWDED-HIFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  K+++++G   + +H R  +   +G +          D+DI+ ++K+      IG NG
Sbjct: 156 N-AKAVERAGGQVVAVHGRTRVQMYEGKA----------DWDIIKQVKQAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
            +     A ++L    VDGVMIGRAA  +  M+    +Y  +  L     ++ ++D
Sbjct: 204 DVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLETGELMPEPTVREKID 259


>gi|312130655|ref|YP_003997995.1| tRNA-u20-dihydrouridine synthase [Leadbetterella byssophila DSM
           17132]
 gi|311907201|gb|ADQ17642.1| tRNA-U20-dihydrouridine synthase [Leadbetterella byssophila DSM
           17132]
          Length = 348

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 85/326 (26%), Positives = 151/326 (46%), Gaps = 41/326 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A ++YTE + ++ ++R   K++  L     E+P+ +Q+ G+
Sbjct: 25  MEDVSDPPFRQVCK--ENGADMMYTEFVSSEGLIRNAVKSVRKLDIFPYERPIGIQLFGS 82

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D+  + E  KI  +   + I++N GCP  +V     GA L+ +  ++     A+ KA  +
Sbjct: 83  DVETMAECTKISTEVNPDLIDINYGCPVKKVACRGAGAALLQDIPLMARMTEAVVKATHL 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           PVTVK R+G DD    +    + + ++  G+  + IH R    + KG +          D
Sbjct: 143 PVTVKTRLGWDDSTKNI--EEVAERLQDVGIQALTIHGRTRAQLYKGEA----------D 190

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + ++ ++K  NP + I +  NG ++   +AL  K    VDG+MIGRAA     +   +  
Sbjct: 191 WSLIAKVKN-NPRIKIPIFGNGDIDSPEKALEYKNRFGVDGIMIGRAAIGYPWIFNEIKH 249

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGF 287
           YF       +P ++ RV+         + T +    +   G+   + ++ RH    F G 
Sbjct: 250 YFQTGEYLPAPNMEQRVN---------AATQHLKFSVEWKGETLGILEMRRHYSNYFKGL 300

Query: 288 PNSRRCRHILTVEAGASTATHHIIET 313
           PN +  R  L      S     I+ET
Sbjct: 301 PNFKEHRMKLV----QSMNLEEILET 322


>gi|167758614|ref|ZP_02430741.1| hypothetical protein CLOSCI_00954 [Clostridium scindens ATCC 35704]
 gi|167663810|gb|EDS07940.1| hypothetical protein CLOSCI_00954 [Clostridium scindens ATCC 35704]
          Length = 318

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/299 (27%), Positives = 139/299 (46%), Gaps = 23/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K  K +L    +E P++LQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCQE-QGAGLLCMEMISAKALQYKNKNTKTLLSIHPKEHPVSLQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V +   G+ LM NP ++ D ++   KA+  P
Sbjct: 76  PYIISEMAKRIEELPFQILDINMGCPVPKVVKNGEGSALMKNPRLIYDIVSRTAKAIRKP 135

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT K R G DD  I AV    + + I+++G   + +H R         ++       D+ 
Sbjct: 136 VTAKIRKGFDDACINAV---EIARVIEEAGGAAVAVHGRT--------REEYYSGKADWK 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +AL +      DGVMIGR A  N  +   + EY   
Sbjct: 185 IIRQVKEAVSIPVIG-NGDVTSGEKALAMREQTGCDGVMIGRGAQGNPWIFRELVEYERT 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P K  + KD   + +    ++   +L     ++++ +H+     G   S + R
Sbjct: 244 GALPPRPSKQEI-KDTMLRHARLQIEFKGDYLG----IREMRKHVAWYTKGMEGSAKLR 297


>gi|167629403|ref|YP_001679902.1| dihydrouridine synthase tim-barrel nifr3 family protein
           [Heliobacterium modesticaldum Ice1]
 gi|167592143|gb|ABZ83891.1| dihydrouridine synthase tim-barrel nifr3 family protein
           [Heliobacterium modesticaldum Ice1]
          Length = 331

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 108/211 (51%), Gaps = 15/211 (7%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+YTEMI   A+   ++    IL  + + +P+A+QI G++ + + EAA+IVE  G + I+
Sbjct: 44  LVYTEMISDKALTYANRNTMEILDITGEARPIAVQIFGSEPAVMAEAARIVEAAGASIID 103

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ ++     GACL+  PD+  D   A+ +A+ +PVTVK RIG       +    
Sbjct: 104 INMGCPAPKIVRNGEGACLLKTPDLAVDIAEAVVRAVQVPVTVKMRIGWSSG--RIVAPE 161

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L   ++  GV  + +H R         ++       D+ ++ E  ++     IG NG + 
Sbjct: 162 LAPRLEAVGVQALTVHGRT--------REMFYSGQADWSVIAETVRQVSIPVIG-NGDVW 212

Query: 199 DMSQALKILPSVD--GVMIGRAAYKNSAMLT 227
           +   AL++L       VMIGR    N  + +
Sbjct: 213 EPDDALRMLVETGCAAVMIGRGCMGNPWIFS 243


>gi|154684599|ref|YP_001419760.1| YacF [Bacillus amyloliquefaciens FZB42]
 gi|154350450|gb|ABS72529.1| YacF [Bacillus amyloliquefaciens FZB42]
          Length = 333

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 122/229 (53%), Gaps = 20/229 (8%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  + + +  L    +EKPL+LQI G     LVEAAK V ++   + I
Sbjct: 37  LVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+PD + + ++A+  A+  PVTVK R+G D++    A++
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVDKPVTVKMRMGWDEE-HIYAVK 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG NG
Sbjct: 156 N-AQAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            ++    A ++L    VDGVMIGRAA  N  M+     Y         P
Sbjct: 204 DVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVHYLETGELKDEP 252


>gi|304383997|ref|ZP_07366453.1| tRNA-dihydrouridine synthase B [Prevotella marshii DSM 16973]
 gi|304334889|gb|EFM01163.1| tRNA-dihydrouridine synthase B [Prevotella marshii DSM 16973]
          Length = 326

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 119/240 (49%), Gaps = 18/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     +++YTE + A+A++R  +  +  L    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRY-GASMVYTEFVSAEALVRSIRSTMSKLTICDEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + I+LN GCP  +V     GA ++ N  ++ +    + KA++ P
Sbjct: 77  KDAMVEAARIVERAKPDVIDLNFGCPVKKVAGKGAGAGMLRNVPLMLEITREVVKAVNTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + + +L + ++  G+  + IH R         +        D+  
Sbjct: 137 VTVKTRLGWDAE--NIIIEDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSW 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++K  NP L I +  NG +    QA +      VD VMIGRA +    +   +++   
Sbjct: 187 IGKVKA-NPRLHIPVIGNGDIASPEQAKEAFEQYGVDAVMIGRATFGRPWIFKEINDSLQ 245


>gi|332662824|ref|YP_004445612.1| TIM-barrel protein, nifR3 family [Haliscomenobacter hydrossis DSM
           1100]
 gi|332331638|gb|AEE48739.1| TIM-barrel protein, nifR3 family [Haliscomenobacter hydrossis DSM
           1100]
          Length = 352

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 141/296 (47%), Gaps = 42/296 (14%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           ++YTE I  + ++R   K++  L    +E+P+ +QI GA++  ++ AA+IVE      ++
Sbjct: 57  MMYTEFISVEGLIRDATKSLQKLDIYDEERPIGVQIFGAELDSMMRAAEIVEAANPEVLD 116

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N GCP  +V     GA ++ +   + +   A+ K+ ++PVTVK R+G D     + +  
Sbjct: 117 INYGCPVQKVVCKMAGAGILRDVKKMVELTQAVVKSTNLPVTVKTRLGWDHN--TIFIEE 174

Query: 139 LVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--N 194
           + + ++  G+  + IHAR  +   KG S          D+  + ++K  NP + I +  N
Sbjct: 175 VAERLQDIGIKALSIHARTRVQMYKGES----------DWSWISKVKN-NPRIHIPIFGN 223

Query: 195 GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDF 251
           G ++   +A++     +VDG+MIGRA+     +   +  Y +   L     I  RVD   
Sbjct: 224 GDIDTPQKAVEYRERYAVDGIMIGRASIGYPWIFREIKHYMATGELLPPPDIHERVDA-- 281

Query: 252 WRKISASMTDYAARHL-HS----GGKLQ--QITRHMIGLFHGFPNSRRCRHILTVE 300
                        +HL HS    G KL   ++ RH    F GFP  +  R  L  E
Sbjct: 282 -----------VRQHLQHSIDWKGAKLGVVEMRRHYTNYFRGFPGIKEFRSQLVTE 326


>gi|73668536|ref|YP_304551.1| hypothetical protein Mbar_A1003 [Methanosarcina barkeri str.
           Fusaro]
 gi|72395698|gb|AAZ69971.1| tRNA-U20-dihydrouridine synthase [Methanosarcina barkeri str.
           Fusaro]
          Length = 323

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 90/303 (29%), Positives = 143/303 (47%), Gaps = 32/303 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNIL-GFSTQE-KPLALQIGGA 57
           M D T+  +R   R   N A L YTEMI ADA+L  ++K++L G S+ E +P  +Q+ G+
Sbjct: 22  MADVTNLAFRLLCR--QNGADLTYTEMISADALLNENRKSLLKGLSSPEDRPFGVQLVGS 79

Query: 58  DISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              KL EAA  +ED    E I++N+GCP+ R+     G+ L+ +  ++ + I+ +   L 
Sbjct: 80  SPEKLREAALFIEDEYRPELIDVNMGCPAKRITGTGCGSALLNSKKLIYEIISDLTDVLK 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNL 174
            PVT K RI   D+        + + I+++G + + IH R+A  +  G S          
Sbjct: 140 TPVTAKIRILKRDE----KTLEIARLIEEAGASALTIHGRRAEQMYSGSS---------- 185

Query: 175 DYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D  ++  +K+E     I  NG +  E+ ++A       DG+MIGRAA  N  +   +  Y
Sbjct: 186 DLTVIRAVKQELSIPVIA-NGDIRNEESAEAALDFTECDGLMIGRAAMGNPFIFKRIRHY 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      + R  +DF   I A + +Y    LH+      I  H      G   SR+
Sbjct: 245 LETGERLEFDRQVRQLEDFENYI-ALLEEY---DLHAS---TNIRMHAHWFTKGLRGSRQ 297

Query: 293 CRH 295
            R 
Sbjct: 298 IRE 300


>gi|294895585|ref|XP_002775215.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239881269|gb|EER07031.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 125

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 50/117 (42%), Positives = 74/117 (63%), Gaps = 6/117 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-----KNILGFSTQEKPLALQIG 55
           MVD +DR +R F RLL++   ++TEM+V  A++  +      + ++GF+  E P+  Q+G
Sbjct: 1   MVDVSDRDFRMFMRLLSSKCEVWTEMLVDQALVHNEDIPRQLEKVIGFTEAEHPIVCQLG 60

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAM 111
           G D SKL  AA+I    GY+E+NLNVGCPS+RV   G  G  LM  P++V DC+  +
Sbjct: 61  GHDPSKLAAAARIAHRRGYDEVNLNVGCPSSRVAGHGLMGVALMKTPELVRDCLRTL 117


>gi|209526027|ref|ZP_03274560.1| TIM-barrel protein, nifR3 family [Arthrospira maxima CS-328]
 gi|209493553|gb|EDZ93875.1| TIM-barrel protein, nifR3 family [Arthrospira maxima CS-328]
          Length = 335

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/306 (25%), Positives = 147/306 (48%), Gaps = 26/306 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+++YTEM+ A  I+   +  IL      E+P+++Q+       LV
Sbjct: 36  TDLVFRRLVRRYAPNSMMYTEMVHASQIIHVRELPILMEIDPGERPISIQLFDCRPDFLV 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+   + G + I++N+GCP  ++ +   G+ L+  P+I    + ++ +A+S+P+TVK 
Sbjct: 96  EAARKAVEEGADTIDVNMGCPVNKITKNGGGSSLLRQPEIAEKIVRSLNEAVSVPITVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D+    + + +  K ++ +G   + IH R    +G + K N       ++ +  + 
Sbjct: 156 RLGWDED--EINILDFSKRMENAGAQMLTIHGRTRA-QGYTGKAN-------WEWIARV- 204

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K+N  + +  NG +  +S A++ L     DGVM  R       ++  +D +       ++
Sbjct: 205 KQNVSIPVIANGDIVSVSSAVQCLQETGADGVMCSRGTLGYPFLVGEIDYFLKTGQMKTA 264

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL--- 297
           P  T V+     ++  +     A  ++ G + + Q  +HM     GFP +   R  L   
Sbjct: 265 P--TVVE-----RLECAKEHLQALWVYKGQRGIYQSRKHMTWYAKGFPGANELREQLAKV 317

Query: 298 -TVEAG 302
            TV+ G
Sbjct: 318 ETVQQG 323


>gi|46202328|ref|ZP_00053405.2| COG0042: tRNA-dihydrouridine synthase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 335

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 79/300 (26%), Positives = 143/300 (47%), Gaps = 24/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD   R   + L    L+ +EMI + A++R +++   +   + +E P+++Q+ G +
Sbjct: 25  MAGVTDMPNRRLVKRL-GAGLVVSEMIASQAMIRQNRQTMQMAQHTAEEFPMSVQLAGCE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAAK+ +D G   I++N+GCP  +V  +G  G+ LM N ++    ++A+ KA+ I
Sbjct: 84  PKVMAEAAKLNQDLGVAIIDINMGCPVKKVALKGEAGSALMRNENLAARIMSAVVKAVDI 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D  + +    +L +  ++ G+  + +H R         ++       D+ 
Sbjct: 144 PVTLKMRTGWD--MNSRNAPSLARVAEECGIRMVTVHGRT--------RNQMYTGQADWA 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K+      IG NG +E +  A+++  L   DGVMIGR  Y    +   V  + + 
Sbjct: 194 FIGEVKRAVSIPVIG-NGDVESIDDAVRMLELSDADGVMIGRGTYGRPWLPGQVAHFLA- 251

Query: 236 PLTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             TG   P  +R ++    +I     D    H  S   ++   +H+     G P S   R
Sbjct: 252 --TGERLPDPSRAEQ---LEIMLGHLDAMLSHYGSEPGVRIARKHVAWYSKGLPGSAEFR 306


>gi|149173427|ref|ZP_01852057.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
 gi|148847609|gb|EDL61942.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
          Length = 355

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 56/159 (35%), Positives = 90/159 (56%), Gaps = 6/159 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +T   +R   R L    L  T++++A  +L G +K+  +L  S  ++PL +QI G  
Sbjct: 30  LAGYTQHAFRVAIRELGGVGLCTTDLVLASHLLSGSRKSKALLTTSPADRPLTIQIFGGI 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++LV AA+ +E  GY  ++LN+GCP A+++    GA +M  PD     +A +  A+SIP
Sbjct: 90  TAELVAAARWLEQHGYAAVDLNMGCPMAKINGNGGGARIMCAPDAACQLVAEVVDAVSIP 149

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VTVK R+G D D I A     L +  +++GV  I +H R
Sbjct: 150 VTVKMRLGWDRDSITAPL---LAREFEQAGVAAITVHGR 185


>gi|52078576|ref|YP_077367.1| putative dihydrouridine synthase TIM-barrel protein [Bacillus
           licheniformis ATCC 14580]
 gi|52783937|ref|YP_089766.1| YacF [Bacillus licheniformis ATCC 14580]
 gi|319648605|ref|ZP_08002819.1| tRNA-dihydrouridine synthase 1 [Bacillus sp. BT1B_CT2]
 gi|52001787|gb|AAU21729.1| putative Dihydrouridine synthase TIM-barrel protein [Bacillus
           licheniformis ATCC 14580]
 gi|52346439|gb|AAU39073.1| YacF [Bacillus licheniformis ATCC 14580]
 gi|317389372|gb|EFV70185.1| tRNA-dihydrouridine synthase 1 [Bacillus sp. BT1B_CT2]
          Length = 333

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 122/231 (52%), Gaps = 22/231 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EM+   AIL  + K +  L    +EKPL+LQI G +   LVEAAK V ++   + 
Sbjct: 36  GLVCAEMVSDKAILYNNAKTMGMLYIDEREKPLSLQIFGGEKETLVEAAKFVDQNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  ++ +   GA  +L+P+ + + ++A+ +A+  PVTVK R+G D D I AV 
Sbjct: 96  IDINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVEAVDKPVTVKMRMGWDEDHIFAV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG 
Sbjct: 155 --ENARAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG- 201

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG ++    A ++L    VDGVMIGRAA  N  M+     Y         P
Sbjct: 202 NGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVHYLETGELKDEP 252


>gi|308066907|ref|YP_003868512.1| tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa E681]
 gi|305856186|gb|ADM67974.1| Probable tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa
           E681]
          Length = 342

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 127/232 (54%), Gaps = 17/232 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D   LV+AA
Sbjct: 26  FRLIAKEF-GTGLVCAEMVSDKAIIHGNKRTREMLFVDEREKPLSLQIFGGDRESLVKAA 84

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K+V ++   + I++N+GCP  +V +   GA  +L+P+ + + ++++ +++S PVTVK RI
Sbjct: 85  KVVDQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSSVVESVSKPVTVKMRI 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D +    A+ N  ++++++G   + +H R         ++     + ++DI+ E+K+ 
Sbjct: 145 GWDSE-HIYAVEN-ARAVERAGGQAVSVHGRT--------REQLYTGHANWDIIKEVKEA 194

Query: 186 NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                IG NG +     A ++  L   DGVMIGR A  N  ML    EY  +
Sbjct: 195 VSIPVIG-NGDVASPEDARRMLDLTHCDGVMIGRGALGNPWMLYRTIEYLQS 245


>gi|225012555|ref|ZP_03702991.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-2A]
 gi|225003532|gb|EEG41506.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-2A]
          Length = 312

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 88/331 (26%), Positives = 154/331 (46%), Gaps = 46/331 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + L  + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 1   MEDVSDPPFRALCKELGAD-VVYTEFISSEGLIRDAAKSVQKLDIYEKERPVGIQIFGAN 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ +  ++     AM K   +P
Sbjct: 60  LDSMLRSVEIVEASNPDIIDINFGCPVKKVVSKGAGAGILKDIPLMVKLTEAMAKHTHLP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G DD   ++ +  + + ++ +G   I IH R    + KG          + ++
Sbjct: 120 ITVKTRLGWDDA--SIKIVEVAERLQDAGAKAISIHGRTRAQMYKG----------DANW 167

Query: 177 DIVYEIKKENPDLFIGLNG-GLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  N  + I + G G  D  +  K++     +DG MIGRA+  N      V  +
Sbjct: 168 HPIAEVKN-NQRMQIPIFGNGDVDSPEKAKLMRDEFGLDGAMIGRASIGNPWFFNEVKHF 226

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSG----GKLQ---QITRHMIGLF 284
           F      ++P I+ RV               A RHL       G++Q   +  RH    F
Sbjct: 227 FETGTYAAAPSIEDRV-------------AVARRHLEMAIDWKGEIQGVLETRRHYTNYF 273

Query: 285 HGFPNSR--RCRHILTVE-AGASTATHHIIE 312
            G PN +  R R + + + AG       IIE
Sbjct: 274 KGIPNFKPLRTRMVTSNDSAGVFEVFDEIIE 304


>gi|312126436|ref|YP_003991310.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311776455|gb|ADQ05941.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 328

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/303 (25%), Positives = 143/303 (47%), Gaps = 30/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        +  + TEM+ + A++ G    K ++ FS +EK  ++QI G+D
Sbjct: 13  MAGFTDKVFRRLCSRFGADVTV-TEMVSSKALVLGSAKTKELISFSEEEKIRSVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + E+ KI++D F Y+ I++N+GCP  +V +   G+ LM NP +    +  + K    
Sbjct: 72  AKIMAESVKILQDEFEYDFIDINMGCPVPKVVKSGEGSALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           PV+VK R G DD+   +        +++SG + + +H R +A L              D+
Sbjct: 132 PVSVKIRKGFDDE--NINAPEFAYILQESGASFVTVHGRTRAQLYS---------GKADW 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+ ++ KE   + +  NG + D   A +   +   D +MIGRAA  N  +   + E F 
Sbjct: 181 EIIRKV-KEKVKIPVIANGDIVDFESAKRAYEVTRADSIMIGRAALGNPWVFLQIKEGFE 239

Query: 235 NPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                +  +   K RV  +F+ ++ +   +  A        + +  +H+     G  N+ 
Sbjct: 240 KGYVETKVLPHMKIRVAIEFFTQLCSEKGEKMA--------VLEARKHLSFFVKGIENAA 291

Query: 292 RCR 294
           + R
Sbjct: 292 KIR 294


>gi|296329583|ref|ZP_06872069.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305672780|ref|YP_003864451.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|296153326|gb|EFG94189.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305411023|gb|ADM36141.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           str. W23]
          Length = 333

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 121/231 (52%), Gaps = 22/231 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EM+   AIL  + + +  L    +EKPL+LQI G     LVEAAK V ++   + 
Sbjct: 36  GLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGKKETLVEAAKFVDQNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  ++ +   GA  +L+PD + + ++A+  A+  PVTVK R+G D D I AV 
Sbjct: 96  IDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVDKPVTVKMRMGWDEDHIFAV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                K+++++G   + +H R  +   +G +          ++DI+ ++K+      IG 
Sbjct: 155 --ENAKAVERAGGKAVALHGRTRVQMYEGTA----------NWDIIKDVKQSVSIPVIG- 201

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG ++    A ++L    VDGVMIGRAA  N  M+    +Y         P
Sbjct: 202 NGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLETGELKEEP 252


>gi|222152139|ref|YP_002561299.1| hypothetical protein MCCL_1896 [Macrococcus caseolyticus JCSC5402]
 gi|222121268|dbj|BAH18603.1| conserved hypothetical protein [Macrococcus caseolyticus JCSC5402]
          Length = 334

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 120/228 (52%), Gaps = 16/228 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  ++K +  L     E+PL+LQI G +   LVEAAK V ++   + I
Sbjct: 37  LVCAEMVSDKAILFNNEKTMKMLYIDENERPLSLQIFGGEKETLVEAAKYVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP +++ +   GA  +L+P  + + ++A+ +A++ PVTVK RIG DD+    A+ 
Sbjct: 97  DINMGCPVSKIIKCEAGARWLLDPPKIYEMVSAVVEAVNKPVTVKMRIGWDDE-HIYAVE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N  K I+K+G + I +H R  +             + D+D++ ++K+      IG NG +
Sbjct: 156 N-AKMIEKAGASAIAVHGRTRV--------QMYEGHADWDVIRQVKEAVSIPVIG-NGDV 205

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
                A K+L    VD VMIGR A  N  M+     Y         P+
Sbjct: 206 TSPELAKKMLDETGVDAVMIGREALGNPWMIYRTVHYLETGELMPEPL 253


>gi|330892748|gb|EGH25409.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
          Length = 109

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/82 (48%), Positives = 57/82 (69%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVG 82
            L   +++ E+ GY+E+NLNVG
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVG 109


>gi|210623235|ref|ZP_03293674.1| hypothetical protein CLOHIR_01624 [Clostridium hiranonis DSM 13275]
 gi|210153772|gb|EEA84778.1| hypothetical protein CLOHIR_01624 [Clostridium hiranonis DSM 13275]
          Length = 322

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 87/304 (28%), Positives = 134/304 (44%), Gaps = 33/304 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +    + LLYTEMI A A+   D+K   +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLAFRLICKEY-GSGLLYTEMINAKALCYDDEKTKGMLKIEEEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  A +I+ +     +++N+GCP+ +V +   G+ LM  P++    I A  K    P
Sbjct: 76  PEFIAGATEILNEHSNEILDINMGCPAPKVVKNGDGSALMKTPELAAKVIEAAAKKSKKP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D D I AV    + ++   SG   I IH R         +        D+D
Sbjct: 136 VTVKFRKGWDEDSINAVEFAKMAEA---SGAQAITIHGR--------TRAQYYSGTADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ EIK       IG NG +  +  A+ I      D +MIGR A  N  +   ++ Y   
Sbjct: 185 IIEEIKNAVKIPVIG-NGDIVTIEDAINIRKKTGCDAIMIGRGAQGNPWIFNRINHYMKT 243

Query: 236 -----PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                  T    I+T + K F   I     +Y A        ++++ +H+     G   S
Sbjct: 244 GEILPEPTAEEKIRTAI-KHFNLAIKED-GEYVA--------VREMRKHLGWYLKGMKKS 293

Query: 291 RRCR 294
            R R
Sbjct: 294 ARLR 297


>gi|331091971|ref|ZP_08340803.1| hypothetical protein HMPREF9477_01446 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330402870|gb|EGG82437.1| hypothetical protein HMPREF9477_01446 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 321

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 79/298 (26%), Positives = 137/298 (45%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K  + +L    +E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYKNKNTQALLKIHPEECPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  ++ +   G+ LM NP +V   +  +  A+  P
Sbjct: 78  PDVMSEVAKSIEELPFAILDINMGCPVPKIVKNGEGSALMQNPKLVEQIVKKVSGAIQKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D+  +V    + K I+ SG   + +H R         ++       D+DI
Sbjct: 138 VTVKIRKGFNDE--SVNAVEIAKIIEASGGAAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ KE   + +  NG +     A++I      DG+MIGR A  N  + + +  Y  + 
Sbjct: 188 IRQV-KEAVSIPVIANGDVTCGQDAIEIQKQTNCDGIMIGRGAQGNPWIFSELLYYEKHG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    V K   R     M  Y   +L     ++++ +H+     G  NS + R
Sbjct: 247 EMPERPDVHEVKKTMLRHAKLQM-QYKGDYLG----IREMRKHIAWYTTGMKNSAKLR 299


>gi|237735422|ref|ZP_04565903.1| transcriptional regulator [Mollicutes bacterium D7]
 gi|229381167|gb|EEO31258.1| transcriptional regulator [Coprobacillus sp. D7]
          Length = 331

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 120/228 (52%), Gaps = 18/228 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+Y+EM+   A+  G+ K I  L     E P+++Q+ G ++  +V+AAK ++     +I 
Sbjct: 42  LVYSEMVSDKALCYGNAKTIEMLQVDDGEHPVSIQLFGGEVETMVQAAKYIDKHSNCDII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   G+ L+L PD + + +  +   ++ PVTVK R G D + I A+ +
Sbjct: 102 DINMGCPVNKVLKADAGSKLLLYPDKIYEIVKGVVDNVTKPVTVKIRSGFDKEHINAIEV 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L   I+K+G + I IH R         +      + D++I+ ++K+      IG NG 
Sbjct: 162 AQL---IEKAGASAIAIHGR--------TRSQMYEGHADWEIIRQVKEAVKIPVIG-NGD 209

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           ++ +  A ++L    VD VMIGRAA  N  ++  V E      T S P
Sbjct: 210 IKSVEDAKRMLEETKVDAVMIGRAALGNPWLIKQVVESLKTGETISEP 257


>gi|150009773|ref|YP_001304516.1| putative TIM-barrel enzyme [Parabacteroides distasonis ATCC 8503]
 gi|149938197|gb|ABR44894.1| putative TIM-barrel enzyme [Parabacteroides distasonis ATCC 8503]
          Length = 329

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRFGAD-MVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP + I +  NG +       +      VD VMIGRA+     +   V  Y +
Sbjct: 187 IRAVKN-NPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLT 245

Query: 235 N-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              L    P    +D      I     + +   L     +  I RH+    LF G  + +
Sbjct: 246 TGELLPQEPFSWYLD------ILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFK 299

Query: 292 RCR 294
           + R
Sbjct: 300 QTR 302


>gi|284048925|ref|YP_003399264.1| TIM-barrel protein, nifR3 family [Acidaminococcus fermentans DSM
           20731]
 gi|283953146|gb|ADB47949.1| TIM-barrel protein, nifR3 family [Acidaminococcus fermentans DSM
           20731]
          Length = 331

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 84/304 (27%), Positives = 141/304 (46%), Gaps = 28/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L  +  + +EM+ A A+L  + K   +L    +E P+A+Q+ G+ 
Sbjct: 24  MAGVTDLPFRVICRELGADYTV-SEMVSAKALLFKNPKTFAMLEVDPREHPVAIQLFGSV 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +LV+ AKIV + G + I+ N+GCP  ++     G+ LM +P+    C+AA+  A+  P
Sbjct: 83  PEELVKGAKIVAEHGADIIDFNMGCPVHKIVANGEGSALMKDPERAYACLAALVDAVDRP 142

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D D   AV +  L    +K+GV  + +H R         +        D+D
Sbjct: 143 VTVKFRAGWDEDHRNAVEIARLA---EKAGVAAVAVHGRT--------RGQFYSGKADWD 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      +G NG +     AL +L +   DGVMI R A  N  +   V    + 
Sbjct: 192 IIRQVKEAVSIPVLG-NGDVFTAQDALDLLAATHCDGVMIARGAQGNPWIFREVQAVLAG 250

Query: 236 PLTGSSPIKTRVD--KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  ++ R    +   R ++A   +  A        ++++  H    F G P+S   
Sbjct: 251 KTIPPVTLEERFAMVRRHLRDLTAFKGEKVA--------IREMRHHGACYFTGLPHSAHY 302

Query: 294 RHIL 297
           R+ +
Sbjct: 303 RNAI 306


>gi|167754846|ref|ZP_02426973.1| hypothetical protein CLORAM_00350 [Clostridium ramosum DSM 1402]
 gi|167704896|gb|EDS19475.1| hypothetical protein CLORAM_00350 [Clostridium ramosum DSM 1402]
          Length = 326

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 120/228 (52%), Gaps = 18/228 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+Y+EM+   A+  G+ K I  L     E P+++Q+ G ++  +V+AAK ++     +I 
Sbjct: 37  LVYSEMVSDKALCYGNAKTIEMLQVDDGEHPVSIQLFGGEVETMVQAAKYIDKHSNCDII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   G+ L+L PD + + +  +   ++ PVTVK R G D + I A+ +
Sbjct: 97  DINMGCPVNKVLKADAGSKLLLYPDKIYEIVKGVVDNVTKPVTVKIRSGFDKEHINAIEV 156

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L   I+K+G + I IH R         +      + D++I+ ++K+      IG NG 
Sbjct: 157 AQL---IEKAGASAIAIHGR--------TRSQMYEGHADWEIIRQVKEAVKIPVIG-NGD 204

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           ++ +  A ++L    VD VMIGRAA  N  ++  V E      T S P
Sbjct: 205 IKSVEDAKRMLEETKVDAVMIGRAALGNPWLIKQVVESLKTGETISEP 252


>gi|291520200|emb|CBK75421.1| tRNA-U20-dihydrouridine synthase [Butyrivibrio fibrisolvens 16/4]
          Length = 327

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 124/253 (49%), Gaps = 19/253 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +     AL   EM+ A  I+  +K  +++L    +E+P++LQ+ G+D
Sbjct: 21  MAGVTDLPFRLLCKE-QGAALCCMEMVSAKGIMYNNKNTESLLTVDERERPVSLQLFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  +E   ++ +++N+GCP  +V     G+ LM NP + G  I +M KA+  P
Sbjct: 80  PEIMGAMAAKIEHRNFDILDINMGCPVPKVVNNGDGSALMKNPVLAGKIIESMVKAIEKP 139

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D++ + AV + ++    ++SG   + +H R         ++       D+ 
Sbjct: 140 VTVKIRKGFDEEHVNAVEMAHVA---QESGAAAVAVHGRT--------REQFYSGKADWS 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYF-S 234
           I+ ++K       IG NG + D     ALK   + DG MIGR A  N  +   +  YF +
Sbjct: 189 IIADVKNAVSIPVIG-NGDILDAKDVIALKEQTNCDGFMIGRGAQGNPWIFHQILHYFET 247

Query: 235 NPLTGSSPIKTRV 247
             L G  P++  V
Sbjct: 248 GELIGKPPMEEMV 260


>gi|147676594|ref|YP_001210809.1| tRNA-dihydrouridine synthase [Pelotomaculum thermopropionicum SI]
 gi|146272691|dbj|BAF58440.1| tRNA-dihydrouridine synthase [Pelotomaculum thermopropionicum SI]
          Length = 324

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 119/249 (47%), Gaps = 20/249 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD+ +R  AR      L+ TEM+   A+L G+ K  ++L  + +  P+++QI G++
Sbjct: 17  MAGITDKAFRILAREF-GCGLVCTEMVSDQALLHGNPKTCSLLDVAGEAGPVSVQIFGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA I E  G   I++N+GCP+ ++ +   GA LM  P+     + A+ + + +P
Sbjct: 76  AACMAEAAGIAESRGAGIIDINMGCPTPKIVKNGEGAALMREPEKAARIVRAVVERVKVP 135

Query: 119 VTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  P AV L  L      + V    +H R         +        D++
Sbjct: 136 VTVKMRKGWDDNSPNAVELARLAAEAGAAAVT---VHGRT--------RSQLYAGKADWE 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+      IG NG +     AL +L     DGVMIGRAA  N  +      +   
Sbjct: 185 IIAAVKRAVDVPVIG-NGDVWTPQDALAMLEQTGCDGVMIGRAALGNPWIFRRTVHFLKT 243

Query: 236 P--LTGSSP 242
              L G +P
Sbjct: 244 GELLPGPTP 252


>gi|56707655|ref|YP_169551.1| Nif3 family protein [Francisella tularensis subsp. tularensis SCHU
           S4]
 gi|110670126|ref|YP_666683.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC198]
 gi|134302001|ref|YP_001121970.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|224456726|ref|ZP_03665199.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370168|ref|ZP_04986174.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254874472|ref|ZP_05247182.1| nif3 family protein [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|56604147|emb|CAG45152.1| Nif3 family protein [Francisella tularensis subsp. tularensis SCHU
           S4]
 gi|110320459|emb|CAL08535.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC198]
 gi|134049778|gb|ABO46849.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151568412|gb|EDN34066.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254840471|gb|EET18907.1| nif3 family protein [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|282158815|gb|ADA78206.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 327

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 143/285 (50%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI+  V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVEHNWETMEMLYMENSEKPLGIQIFGTDINSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|54114569|gb|AAV29918.1| NT02FT1147 [synthetic construct]
          Length = 327

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 143/285 (50%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI+  V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVEHNWETMEMLYMENSEKPLGIQIFGTDINSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|291520867|emb|CBK79160.1| tRNA-U20-dihydrouridine synthase [Coprococcus catus GD/7]
          Length = 338

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/303 (24%), Positives = 138/303 (45%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TD  +R   R      ++ TEM+ A AI   +K       T  QE+P++LQ+ G+D
Sbjct: 22  MAGVTDLPFRVLCRE-QGCGMVCTEMVSAKAITYKNKNTFFLMETVPQERPVSLQLFGSD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+++ D  ++ +++N+GCP  +V     G+ LM  P++ G  + ++ + +  P
Sbjct: 81  PDIMAEAARMIADRDFDVLDVNMGCPVPKVVNNGEGSALMKQPELAGRIVRSLVETIDKP 140

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  DD I AV +  +V++   +G   + +H R         ++       D+ 
Sbjct: 141 VTVKIRKGFDDDHINAVEMAKIVEA---NGAAAVAVHGRT--------REQYYSGKADWQ 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+      IG NG +     A +++     D +M  R A  N  +   + +Y   
Sbjct: 190 IIRRVKEAVKIPVIG-NGDVFTPQDAKRMIEETGCDAIMAARGARGNPWLFRDIIDYLEK 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ---QITRHMIGLFHGFPNSRR 292
            +    P          ++++  M  +A  H+   G+ Q   ++ +H+     G+  S R
Sbjct: 249 GILHEKP--------SLKEMTDMMLRHAEMHIRYKGEYQGIREMRKHVAWYTAGYHGSAR 300

Query: 293 CRH 295
            R 
Sbjct: 301 MRQ 303


>gi|255012934|ref|ZP_05285060.1| putative TIM-barrel enzyme [Bacteroides sp. 2_1_7]
          Length = 329

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRFGAD-MVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITKEVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP + I +  NG +       +      VD VMIGRA+     +   V  Y +
Sbjct: 187 IGAVKN-NPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLT 245

Query: 235 N-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              L    P    +D      I     + +   L     +  I RH+    LF G  + +
Sbjct: 246 TGELLPQEPFSWYLD------ILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFK 299

Query: 292 RCR 294
           + R
Sbjct: 300 QTR 302


>gi|187931839|ref|YP_001891824.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712748|gb|ACD31045.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 327

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 143/285 (50%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI+  V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDINSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|124002638|ref|ZP_01687490.1| NifR [Microscilla marina ATCC 23134]
 gi|123991866|gb|EAY31253.1| NifR [Microscilla marina ATCC 23134]
          Length = 330

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 89/316 (28%), Positives = 150/316 (47%), Gaps = 38/316 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R  A    N A ++YTE I A+ ++R   K++  L     E+P+ +QI GA
Sbjct: 19  MEDVSDPPFR--AACKQNGADVMYTEFIAAEGLIRDAHKSVQKLDIYDYERPIGIQIFGA 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +I  +  AA IVE      +++N GCP  +V     GA ++ +   +      + K + +
Sbjct: 77  NIESMRLAADIVERTQPEILDINYGCPVKKVACKGAGAGILQDLPKMQKMTEEIVKRVKL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G DD   ++ +  + K ++  G+  + IH   RK + KG +          +
Sbjct: 137 PVTVKTRLGWDDS--SIKIMEVAKRLQDVGIKALSIHGRTRKQMYKGEA----------N 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ + E+K  NPD+ I +  NG ++   +AL  K    +DG+MIGRAA     +   +  
Sbjct: 185 WEPIAEVKN-NPDIHIPIFGNGDIDTPEKALEYKNRYGIDGIMIGRAAIGYPWIFNEIKH 243

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQ---QITRHMIGLFHGF 287
           Y +     + P ++ RV         A    +    +   G+ Q   ++ RH    F GF
Sbjct: 244 YMATGKKLAPPTLEQRV---------AVCHQHLVHSVEWKGEKQGVFEMRRHYTNYFRGF 294

Query: 288 PNSRRCRHILTVEAGA 303
              +  R  L VEAG+
Sbjct: 295 HGFKPFRTRL-VEAGS 309


>gi|329943329|ref|ZP_08292103.1| TIM-barrel , nifR3 family protein [Chlamydophila psittaci Cal10]
 gi|313848477|emb|CBY17481.1| putative dihydrouridine synthase [Chlamydophila psittaci RD1]
 gi|328814876|gb|EGF84866.1| TIM-barrel , nifR3 family protein [Chlamydophila psittaci Cal10]
 gi|328915169|gb|AEB56002.1| NifR3/Smm1 family protein [Chlamydophila psittaci 6BC]
          Length = 332

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/288 (23%), Positives = 131/288 (45%), Gaps = 19/288 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  YR  +      AL++ EM+  + +     + +  L +S   +P+  Q+ G+ 
Sbjct: 21  LAGFSDYPYRKMSSFYGPPALMFCEMVKVEGLHYSPSRTLKLLEYSESMRPIGGQLCGSK 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAAK++E  G++ I+LN GCP+ R+ +   G+ L+ +P+++G  +  + +A+SIP
Sbjct: 81  PEMAGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGLLKSPELIGKILEKIIEAVSIP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     + +   V+ I+ +G + +++H R      + P       NL+Y I
Sbjct: 141 VTVKIRSGWDCN--NINVEETVRIIRDAGASAVFVHGRTRAQGYVGPS------NLEY-I 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
                    DL +  NG +     A  ++ S   DGV++ R       ++  ++ Y ++ 
Sbjct: 192 ARAKAAAGKDLPVFGNGDIFSPEAAKLMMDSTQCDGVLVARGTMGAPWIVRQIESYLASG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                P   R      ++       +   +  S  K    TR + G +
Sbjct: 252 TYQKVPFSKR------KQAFIQHLQWVEEYYQSEAKFLSETRKLCGHY 293


>gi|218258330|ref|ZP_03474732.1| hypothetical protein PRABACTJOHN_00387 [Parabacteroides johnsonii
           DSM 18315]
 gi|218225570|gb|EEC98220.1| hypothetical protein PRABACTJOHN_00387 [Parabacteroides johnsonii
           DSM 18315]
          Length = 343

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 118/241 (48%), Gaps = 18/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K    L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDVSFRLMCKRFGAD-MVYTEFVSADALIRSVNKTQQKLNVANEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+I E    + +++N GCP  RV     GA ++ N  ++ D    + KA++IP
Sbjct: 77  VPTMVEAAQICEAAHPDILDINFGCPVKRVAGKGAGAGMLRNISLMLDITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRIIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+KK NP + I +  NG +       +      VD VMIGR +     +   V  + +
Sbjct: 187 IGEVKK-NPRMQIPIIGNGDVTSAEICKQRFEQYGVDAVMIGRGSIGRPWIFREVKHFLN 245

Query: 235 N 235
            
Sbjct: 246 T 246


>gi|225874633|ref|YP_002756092.1| putative tRNA-dihydrouridine synthase [Acidobacterium capsulatum
           ATCC 51196]
 gi|225791394|gb|ACO31484.1| putative tRNA-dihydrouridine synthase [Acidobacterium capsulatum
           ATCC 51196]
          Length = 398

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 22/229 (9%)

Query: 14  RLLTNN----ALLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           R +TN      L+ TE   AD + +     +K  L F   E P+A Q+ G++   L E A
Sbjct: 69  REVTNQQSGCGLIMTEFTSADGLSKMRESKRKRYLTFYEDEHPIAAQLFGSNPETLAEGA 128

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +IVED G++ ++LN+GCP+ RV   + G+ L+ +  ++     A+  A+ IP TVK R+G
Sbjct: 129 RIVEDTGFDMVDLNLGCPAKRVVACNGGSGLLRDLPLIAKIFEAVRGAVKIPFTVKFRLG 188

Query: 127 VDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            +DQ I  V L  L    ++SG+N + +HAR         ++        ++ + E+K  
Sbjct: 189 WNDQHIICVPLARLA---EESGLNAVSLHART--------REQGYSGQARWEHIAEVKDA 237

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
                IG NG +     A  ++     DGVMIGRAA  N  +   + +Y
Sbjct: 238 VRIPVIG-NGDVRTPEDACALVAKTGCDGVMIGRAAPANPWIFRQIAQY 285


>gi|284928866|ref|YP_003421388.1| hypothetical protein UCYN_02850 [cyanobacterium UCYN-A]
 gi|284809325|gb|ADB95030.1| putative TIM-barrel protein, nifR3 family [cyanobacterium UCYN-A]
          Length = 322

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 140/307 (45%), Gaps = 35/307 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TDR +R   R  + N+++YTEMI A  +    K   L    ++KP+ +QI  +    +VE
Sbjct: 25  TDRIFRKLVRRYSPNSMIYTEMINATELCHLKKVQQL-VDIEQKPIGVQIFDSRYDFIVE 83

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK +E  G   I++N+GCP  ++ +   G+ L+  P +    I  + + + IP+TVK R
Sbjct: 84  AAKKIESQGAQIIDINMGCPVNKITKKGGGSSLLKQPKVAQKIIYEITRIVKIPITVKTR 143

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           IG +D    + + +  K ++ +G   + IHAR         +D        +  V +I K
Sbjct: 144 IGWNDS--GIDILDFAKMMEDAGAAMLTIHAR--------TRDQGYNGTSHWKWVKKI-K 192

Query: 185 ENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF-----SNPL 237
           EN  + I  NG +  +  A+K L   + DGVM  R       ++  +D +F     S  +
Sbjct: 193 ENLLIPIIANGNIFSIEDAVKCLEITNADGVMCSRGTLGYPFLVGEIDYFFQTGYCSQII 252

Query: 238 TGSSPIKTRVD--KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR- 294
           T    +K   +  K+ W K   +   Y  R            +H+     GFP +   R 
Sbjct: 253 TPYQRLKCAKEHLKELW-KYKGNQGIYQGR------------KHLRWYCQGFPGASELRK 299

Query: 295 HILTVEA 301
            I+ +E+
Sbjct: 300 KIICIES 306


>gi|153952822|ref|YP_001393587.1| Dus [Clostridium kluyveri DSM 555]
 gi|146345703|gb|EDK32239.1| Dus [Clostridium kluyveri DSM 555]
          Length = 320

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 89/317 (28%), Positives = 151/317 (47%), Gaps = 47/317 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    +     L+YTEMI A A+  G K  +++L  S  E P+A+QI G D
Sbjct: 17  MAGITDRAFRELC-IEFKCGLVYTEMISAKALFYGSKATESMLIVSPVEAPIAVQIFGND 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
               V  AK  + F  N+    +++N+GCP+ ++     G+ LM NP +  + +  + KA
Sbjct: 76  ---PVIMAKACDYFNENKDICMVDINMGCPAPKIVRNGEGSALMKNPKLASEIVKEVKKA 132

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
              PVTVK RIG D +  ++   N  + +++SG + + IH R +  +  + K N      
Sbjct: 133 SLKPVTVKMRIGFDSE--SINAVNFARIMEQSGADAVTIHGRTS-TQMYNGKAN------ 183

Query: 175 DYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            +DI+ ++K+        N D+F      +ED S+  +     DG+MIGR +  N  + +
Sbjct: 184 -WDIISDVKQSIKIPVIGNGDVFT-----VEDASRLFE-FTKCDGIMIGRGSLGNPWIFS 236

Query: 228 TVDE-YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF 284
            + E   S  +T  +P          +KI   +  Y  R ++  G+ + +   R  IG +
Sbjct: 237 QIYENKNSRSITYPTP---------QQKIDMCIEHY-NRAIYYNGEYKAVREMRKQIGWY 286

Query: 285 -HGFPNSRRCRHILTVE 300
             G  NS+  +  +  E
Sbjct: 287 IKGLKNSKEIKEKINCE 303


>gi|225010313|ref|ZP_03700785.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-3C]
 gi|225005792|gb|EEG43742.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-3C]
          Length = 330

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 145/310 (46%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K+   L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSTMKLDIYEKERPVGIQIFGAE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++A +IVE    + I++N GCP  +V   + GA ++ +  ++     AM K   +P
Sbjct: 78  MDSMLQAIEIVEASKPDIIDINFGCPVKKVVCKNAGAGILRDIPLMVKLTEAMVKHTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDY 176
           VTVK R+G D  + ++ +  + + ++  G+  I IH R  +   KG          N D+
Sbjct: 138 VTVKTRLGWD--LDSIKIVEVAERLQDVGIAAISIHGRTRVQMYKG----------NADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  NP + I +  NG ++    A+K+     +DG MIGRA+         V  +
Sbjct: 186 GPIAEVKN-NPRMHIPVFGNGDVDTPEMAVKMRDEYGLDGAMIGRASIGYPWFFNEVKHF 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
           F      + P ++ RV+              A RHL       G KL   +  RH    F
Sbjct: 245 FKTGTHKAPPTLEERVEA-------------ARRHLQMSIDWKGEKLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G PN +  R
Sbjct: 292 KGIPNFKEYR 301


>gi|219853487|ref|YP_002470609.1| hypothetical protein CKR_0144 [Clostridium kluyveri NBRC 12016]
 gi|219567211|dbj|BAH05195.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 322

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/313 (28%), Positives = 151/313 (48%), Gaps = 39/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    +     L+YTEMI A A+  G K  +++L  S  E P+A+QI G D
Sbjct: 19  MAGITDRAFRELC-IEFKCGLVYTEMISAKALFYGSKATESMLIVSPVEAPIAVQIFGND 77

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
               V  AK  + F  N+    +++N+GCP+ ++     G+ LM NP +  + +  + KA
Sbjct: 78  ---PVIMAKACDYFNENKDICMVDINMGCPAPKIVRNGEGSALMKNPKLASEIVKEVKKA 134

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
              PVTVK RIG D +  ++   N  + +++SG + + IH R +  +  + K N      
Sbjct: 135 SLKPVTVKMRIGFDSE--SINAVNFARIMEQSGADAVTIHGRTS-TQMYNGKAN------ 185

Query: 175 DYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +DI+ ++K+      IG NG    +ED S+  +     DG+MIGR +  N  + + + E
Sbjct: 186 -WDIISDVKQSIKIPVIG-NGDVFTVEDASRLFE-FTKCDGIMIGRGSLGNPWIFSQIYE 242

Query: 232 -YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGF 287
              S  +T  +P          +KI   +  Y  R ++  G+ + +   R  IG +  G 
Sbjct: 243 NKNSRSITYPTP---------QQKIDMCIEHY-NRAIYYNGEYKAVREMRKQIGWYIKGL 292

Query: 288 PNSRRCRHILTVE 300
            NS+  +  +  E
Sbjct: 293 KNSKEIKEKINCE 305


>gi|53715845|ref|YP_101837.1| putative TIM-barrel enzyme [Bacteroides fragilis YCH46]
 gi|60683764|ref|YP_213908.1| putative TIM-barrel protein, dihydrouridine synthase [Bacteroides
           fragilis NCTC 9343]
 gi|253564624|ref|ZP_04842081.1| conserved hypothetical protein [Bacteroides sp. 3_2_5]
 gi|265764712|ref|ZP_06092987.1| conserved hypothetical protein [Bacteroides sp. 2_1_16]
 gi|52218710|dbj|BAD51303.1| putative TIM-barrel enzyme [Bacteroides fragilis YCH46]
 gi|60495198|emb|CAH10019.1| putative TIM-barrel protein, possible dihydrouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|251948400|gb|EES88682.1| conserved hypothetical protein [Bacteroides sp. 3_2_5]
 gi|263254096|gb|EEZ25530.1| conserved hypothetical protein [Bacteroides sp. 2_1_16]
 gi|301165349|emb|CBW24921.1| putative TIM-barrel protein, possible dihydrouridine synthase
           [Bacteroides fragilis 638R]
          Length = 324

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 136/302 (45%), Gaps = 25/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L    +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAD-MVYTEFVSSDALIRSVNKTTQKLTICDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AA+IVE+   + +++N GCP  +V     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TEAMVGAARIVEEAQPDILDINFGCPVKKVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADHKIIV--DLAEQLQDCGIAALAIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +   + A +      VD +MIGR +     +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTTAAGAKECFERYGVDAIMIGRGSIGRPWIFREVKHYLE 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              TG      R   +++  +       +   L     +  I RH+    LF G PN R 
Sbjct: 246 ---TGEE--LPRESFEWYLDVLREEVLNSVARLDERRGIIHIRRHLAATPLFKGIPNFRE 300

Query: 293 CR 294
            R
Sbjct: 301 TR 302


>gi|301312349|ref|ZP_07218266.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 20_3]
 gi|300829771|gb|EFK60424.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 20_3]
          Length = 329

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKSFGAD-MVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITKEVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP + I +  NG +       +      VD VMIGRA+     +   V  Y +
Sbjct: 187 IGAVKN-NPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLT 245

Query: 235 N-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              L    P    +D      I     + +   L     +  I RH+    LF G  + +
Sbjct: 246 TGELLPQEPFSWYLD------ILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFK 299

Query: 292 RCR 294
           + R
Sbjct: 300 QTR 302


>gi|325115288|emb|CBZ50843.1| hypothetical protein NCLIV_039180 [Neospora caninum Liverpool]
          Length = 491

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 87/322 (27%), Positives = 130/322 (40%), Gaps = 85/322 (26%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  T+ H+R F R LT  A L+TEM+   AIL                        ++ 
Sbjct: 20  MLAVTNTHFRNFMRCLTREAQLWTEMVTDGAILN-----------------------NMD 56

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +  ++ ED  +  I   +GC         FGA LM  P++V D +  + + + IPVT
Sbjct: 57  RLQQNLRL-EDIEH-PIVCQLGC---------FGAALMKTPELVRDIVHEIGRQVQIPVT 105

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG D       LRN V                    +G+ PK NR +P L Y  VY
Sbjct: 106 VKTRIGYDYYDSFDVLRNFV--------------------QGVDPKRNRSVPPLLYGRVY 145

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL------------------------KILPSVDGVMIG 216
            +  + PDL   LNGG+  + +A+                        K +  + GVM+G
Sbjct: 146 NLCDQFPDLDFTLNGGVTSIQEAIDLAAGKWTDGTTEMDALLRRITRDKTVQPLRGVMLG 205

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQ 275
           RAA  +  +L +VD  F           +R      R +  +  DY       GG  L  
Sbjct: 206 RAASNDPCILGSVDTDFYGASANPPSSHSR------RTVLEAYGDYLKPFAEDGGYSLFA 259

Query: 276 ITRHMIGLFHGFPNSRRCRHIL 297
           + + ++G+ +G P  R  R  L
Sbjct: 260 LLKPVLGVLNGMPGHRLFRFTL 281


>gi|124025154|ref|YP_001014270.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. NATL1A]
 gi|123960222|gb|ABM75005.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. NATL1A]
          Length = 330

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 139/297 (46%), Gaps = 22/297 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           +D+ +R F R  +  ALL+TEM+ A ++  G  ++ ++  S +  P+ +Q+       +V
Sbjct: 31  SDQIFRNFVRRWSPKALLFTEMVNAKSLELGHGEEKVIELSEESGPIGVQLFDHRPDSMV 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA   E  G   I++N+GCP  ++     G+ L+  P++    +  + KA+SIPVTVK 
Sbjct: 91  DAAIKAESSGAFLIDINMGCPVKKIARKGGGSALLKEPELAQLIVKKVSKAISIPVTVKI 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G  +        +    ++++G   I +H R    +G S   N       +  + +IK
Sbjct: 151 RLGWCETTSDPV--SFALGLQEAGAQLITVHGRTR-RQGFSGHSN-------WKAIAQIK 200

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K + D+ +  NG +++   A++ L   + DGVMIGRA+     ++  +DE   N  T   
Sbjct: 201 K-SLDIPVIANGDIKNSRDAIECLKITNADGVMIGRASMGAPWLVGQIDEEIKNQTTFKP 259

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR-HMIGLFHGFPNSRRCRHIL 297
           P       D   K+S S+          G     I R HM     GF  +   RH L
Sbjct: 260 P-------DAKMKVSLSLEHLKLLVSKKGSHGLLIARKHMNWTCRGFEGASTLRHKL 309


>gi|154489885|ref|ZP_02030146.1| hypothetical protein PARMER_00114 [Parabacteroides merdae ATCC
           43184]
 gi|154089327|gb|EDN88371.1| hypothetical protein PARMER_00114 [Parabacteroides merdae ATCC
           43184]
          Length = 343

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 86/314 (27%), Positives = 145/314 (46%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + ADA++R   K    L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRFGAD-MVYTEFVSADALIRSVNKTQQKLNVADEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+I E    + +++N GCP  RV     GA ++ N  ++ D    + KA++IP
Sbjct: 77  VPTMVEAAQICEAAHPDILDINFGCPVKRVAGKGAGAGMLRNIPLMLDITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRIIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +       +      VD VMIGR +     +   V  Y  
Sbjct: 187 IGEVKN-NPRIQIPIIGNGDVTSAEICKQRFEQYGVDAVMIGRGSIGRPWIFREVRHYLD 245

Query: 235 NPLTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              TG + P ++     ++  I     + +   L     +  I RH+    LF G  + +
Sbjct: 246 ---TGETLPAES---FSWYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGIADFK 299

Query: 292 RCRHIL----TVEA 301
           + R  +    TVEA
Sbjct: 300 QTRVAMLRAETVEA 313


>gi|90415235|ref|ZP_01223169.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2207]
 gi|90332558|gb|EAS47728.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2207]
          Length = 348

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 141/308 (45%), Gaps = 28/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R   R +    ++ +EM+ AD      +K+ L   F+ +  P ++QI G D
Sbjct: 37  MAGVTDLPFRQLCREM-GAGMVVSEMVAADPSTWSSRKSKLRIQFADEPAPRSVQIAGYD 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+     G   I++N+GCP+ +V + + G+ L+ +PD+V D + A+  ++ +P
Sbjct: 96  PLMMAEAARFNVQQGAEIIDINMGCPAKKVLKKAAGSALLQHPDLVQDILRAVVDSVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D Q      RN V   K  + +G+  + IH R         +  R +  ++
Sbjct: 156 VTLKIRTGWDRQ-----NRNAVSIAKIAEDAGIAALAIHGRT--------RACRFVKEVE 202

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +  E   + +  NG +    +AL +L       VMIGR A  N  +   ++ + 
Sbjct: 203 YDTIANV-VEALSIPVIANGDITTPEKALAVLEQTGAAAVMIGRGAQGNPWIFNQINHFL 261

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR- 292
            +      P    ++    R + A    Y     H+G K+ +  +H+   F   P  ++ 
Sbjct: 262 EHGEAAEKPSIEDIELVVCRHLQALHAFYGP---HAGVKIAR--KHIGWYFSALPGGKQF 316

Query: 293 CRHILTVE 300
            RH   +E
Sbjct: 317 ARHFNRIE 324


>gi|212637921|ref|YP_002314441.1| tRNA-dihydrouridine synthase [Anoxybacillus flavithermus WK1]
 gi|212559401|gb|ACJ32456.1| tRNA-dihydrouridine synthase [Anoxybacillus flavithermus WK1]
          Length = 351

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 119/222 (53%), Gaps = 20/222 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L+  EM+   AIL  + K +  L    +EKPL+LQI G +   LV+AAK V+     +I
Sbjct: 54  GLVCAEMVSDKAILFNNPKTMGMLYIDEREKPLSLQIFGGEKETLVQAAKYVDQHTNADI 113

Query: 78  -NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
            ++N+GCP  ++ +   GA  +L+P+ + D +AA+  A+  PVTVK RIG D+     A+
Sbjct: 114 IDINMGCPVPKITKCDAGAKWLLDPNKIYDMVAAVVDAVEKPVTVKMRIGWDEN-HIYAV 172

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N  ++++++G   + +H R  +   +G +          D++++ ++K+      IG N
Sbjct: 173 EN-AQAVERAGGQAVAVHGRTRVQMYEGKA----------DWNVIKQVKEAVRIPVIG-N 220

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           G ++    A ++L    VDGVMIGRAA  N  M+     Y  
Sbjct: 221 GDVQTPQDAKRMLEQTGVDGVMIGRAALGNPWMIYRTVRYLE 262


>gi|62259886|gb|AAX77872.1| unknown protein [synthetic construct]
          Length = 362

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 144/285 (50%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++  + +   +L     EKPL +QI G DI+  V A K I E+   + +
Sbjct: 64  LIYTEMVSNKAVVEHNWETMEMLYMENSEKPLGIQIFGTDINSFVGATKYIAENTECDFL 123

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 124 DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 182

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 183 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 231

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 232 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 290

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 291 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 327


>gi|294056396|ref|YP_003550054.1| TIM-barrel protein, nifR3 family [Coraliomargarita akajimensis DSM
           45221]
 gi|293615729|gb|ADE55884.1| TIM-barrel protein, nifR3 family [Coraliomargarita akajimensis DSM
           45221]
          Length = 333

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 84/306 (27%), Positives = 144/306 (47%), Gaps = 26/306 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD  +R F +    + ++ TE + ADAI RGD +    + F+  ++P+ +QI G++
Sbjct: 17  MARFTDIVFRQFCKEQGADVMV-TEFVQADAITRGDDRLWETVDFTESQRPMGVQIFGSN 75

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
              + +AA+ IV+    + I++N GCP+ RV     G+ ++ NP  +G  +AA+ KA+  
Sbjct: 76  PVTMGQAARMIVDRMQPDFIDINFGCPAERVICMDAGSSMLRNPRKLGTVVAAVIKAVPD 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R G DD    +  + +   ++  G   + IH R   ++G   + N       +
Sbjct: 136 TPVTAKIRTGWDDD--TIVAKEVGHIVESEGGQALAIHGRTK-MQGYRGEAN-------W 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFS 234
            I+ E+ +E     IG NG +      ++I  +    G+MIGRAA     +   +  Y +
Sbjct: 186 PIIAEVAEELTIPVIG-NGNIRSAEDVIRIRETTRCAGLMIGRAALGYPWIFRDIKHYLA 244

Query: 235 NPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +      P    + +   D+ R I   M+       HS   L+ +    I L  G P SR
Sbjct: 245 HGTIPEPPTIGERWQTIIDYTRGI---MSRPFREQKHS--DLRWMRPKFIALTKGMPGSR 299

Query: 292 RCRHIL 297
           + R  L
Sbjct: 300 KIRTAL 305


>gi|255012000|ref|ZP_05284126.1| putative TIM-barrel protein, dihydrouridine synthase [Bacteroides
           fragilis 3_1_12]
 gi|313149838|ref|ZP_07812031.1| dehydrogenase [Bacteroides fragilis 3_1_12]
 gi|313138605|gb|EFR55965.1| dehydrogenase [Bacteroides fragilis 3_1_12]
          Length = 325

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/302 (27%), Positives = 138/302 (45%), Gaps = 25/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L    +E+P+A+QI G D
Sbjct: 18  MEDVTDLAFRLMCKKFGAD-MVYTEFVSSDALIRSVNKTTQKLTICDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AA+IVE+   + +++N GCP  +V     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TEAMVGAARIVEEAQPDILDINFGCPVKKVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADHKIIV--DLAEQLQDCGIAALAIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NP + I +  NG +   + A +      VD +MIGR +     +   V  Y  
Sbjct: 187 IGEVKN-NPRMHIPIIGNGDVTSATGAKECFERYGVDAIMIGRGSIGRPWIFREVKYYLE 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              TG    +   +  +   +   + +  AR L     +  I RH+    LF G PN R 
Sbjct: 246 ---TGEELPQESFEW-YLNVLREEVLNSVAR-LDERRGIIHIRRHLAATPLFKGIPNFRE 300

Query: 293 CR 294
            R
Sbjct: 301 TR 302


>gi|298207228|ref|YP_003715407.1| putative TIM-barrel enzyme, possible dehydrogenase [Croceibacter
           atlanticus HTCC2559]
 gi|83849864|gb|EAP87732.1| putative TIM-barrel enzyme, possible dehydrogenase [Croceibacter
           atlanticus HTCC2559]
          Length = 330

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 148/310 (47%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LESMLKSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D++  ++ +  + + ++  G   I IH   RK + KG          +  +
Sbjct: 138 VTVKTRLGWDEE--SIKIVEVAERLQDVGCAAIAIHGRTRKQMYKG----------DAKW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
           + + ++K  NP + I +  NG +    +A+++     +DG MIGRA+         V  +
Sbjct: 186 EQIADVKN-NPRMHIPVFGNGDVNTPERAVEMRDKYGLDGAMIGRASIGYPWFFREVKHF 244

Query: 233 FSNPLTGSS-PIKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
           F    TG   P    +++           D A RHL       G KL   +  RH    F
Sbjct: 245 FE---TGKHLPPPNMIER----------LDAARRHLQMSIDWKGEKLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G P+ +  R
Sbjct: 292 KGIPHFKEYR 301


>gi|188992985|ref|YP_001904995.1| Putative TIM-barrel protein; NifR3 family [Xanthomonas campestris
           pv. campestris str. B100]
 gi|167734745|emb|CAP52955.1| Putative TIM-barrel protein; NifR3 family [Xanthomonas campestris
           pv. campestris]
          Length = 468

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 153 MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 211

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   ++A+ +A+ +P
Sbjct: 212 PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILSAVVRAVDVP 271

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D       +
Sbjct: 272 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGTAE 318

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L    VD VMIGRAA     +   V  Y 
Sbjct: 319 YATIAQIKAAL-QIPVIANGDIDSPQKAAQVLRDTGVDAVMIGRAAQGRPWIFGEVAHYL 377

Query: 234 SN 235
           + 
Sbjct: 378 AT 379


>gi|114331206|ref|YP_747428.1| putative TIM-barrel protein, nifR3 family protein [Nitrosomonas
           eutropha C91]
 gi|114308220|gb|ABI59463.1| tRNA-U20-dihydrouridine synthase [Nitrosomonas eutropha C91]
          Length = 337

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 125/242 (51%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +   A+  +EMI ++++L G +K +       + KP+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAAMAVSEMISSNSLLYGSEKTLRRARHEGEVKPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + +AA+   D G   I++N+GCP+ ++     G+ L+ + D+V   + A+ +A+ IP
Sbjct: 76  PAMMAQAARHNADHGAEIIDINMGCPAKKICNVMAGSALLKDEDLVSKILGAVVQAVDIP 135

Query: 119 VTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D Q   AVA+  + +S   +G+  + IH R      +G +          +
Sbjct: 136 VTLKIRTGWDTQHKNAVAVARIAES---AGIQALAIHGRTRACAYRGQA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K    ++ +  NG +    +A ++L    VD VMIGRAA     +   ++ Y 
Sbjct: 183 YDTIATVKAA-INIPVIANGDINTPEKAREVLEYTGVDAVMIGRAAQGRPWIFREINHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|256838548|ref|ZP_05544058.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|298374169|ref|ZP_06984127.1| hypothetical protein HMPREF0104_00320 [Bacteroides sp. 3_1_19]
 gi|256739467|gb|EEU52791.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|298268537|gb|EFI10192.1| hypothetical protein HMPREF0104_00320 [Bacteroides sp. 3_1_19]
          Length = 329

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRFGAD-MVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEAHPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP + I +  NG +       +      VD VMIGRA+     +   +  Y +
Sbjct: 187 IGAVKN-NPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREIKHYLT 245

Query: 235 N-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              L    P    +D      I     + +   L     +  I RH+    LF G  + +
Sbjct: 246 TGKLLPQEPFSWYLD------ILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFK 299

Query: 292 RCR 294
           + R
Sbjct: 300 QTR 302


>gi|332678280|gb|AEE87409.1| tRNA dihydrouridine synthase B [Francisella cf. novicida Fx1]
          Length = 325

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 142/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|62185558|ref|YP_220343.1| putative dihydrouridine synthase [Chlamydophila abortus S26/3]
 gi|62148625|emb|CAH64397.1| putative dihydrouridine synthase [Chlamydophila abortus S26/3]
          Length = 339

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 60/239 (25%), Positives = 118/239 (49%), Gaps = 13/239 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  YR  +      AL++ EM+  + +     + +  L +S   +P+  Q+ G+ 
Sbjct: 21  LAGFSDYPYRKMSSFYGPPALMFCEMVKVEGVHYSPARTLKLLEYSESMRPIGGQLCGSK 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK++E  G++ I+LN GCP+ R+ +   G+ L+ +P+++G  +  + +A+S+P
Sbjct: 81  PEMVGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGLLKSPELIGKVLEKIVEAVSVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     + +   V+ I+ +G + +++H R      + P       NL+Y I
Sbjct: 141 VTVKIRSGWDGS--NINVEETVRIIRDAGASAVFVHGRTRAQGYVDPS------NLEY-I 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
                    D  +  NG +     A  +L S   DGV++ R       ++  ++ Y ++
Sbjct: 192 ARAKAAAGKDFPVFGNGDVFSPEAAKLMLDSTQCDGVLVARGTMGAPWIVRQIESYLTS 250


>gi|15673943|ref|NP_268118.1| oxidoreductase [Lactococcus lactis subsp. lactis Il1403]
 gi|12725003|gb|AAK06059.1|AE006426_5 oxidoreductase [Lactococcus lactis subsp. lactis Il1403]
 gi|326407498|gb|ADZ64569.1| oxidoreductase [Lactococcus lactis subsp. lactis CV56]
          Length = 334

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 76/221 (34%), Positives = 119/221 (53%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+ TEMI    I   +KK +  + F     PL++QI G ++  LVEAAK VE     +I 
Sbjct: 46  LVVTEMISDKGIEHRNKKTLEMMDFEGVPHPLSMQIFGGEVDTLVEAAKFVEANTVADII 105

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+ L+L+PD V D ++A+ KA+S P+TVK RIG DD     A+ 
Sbjct: 106 DINMGCPVPKVTKNEAGSRLLLDPDKVYDVVSAVSKAISRPLTVKIRIGWDDD-HLFAVE 164

Query: 138 NLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLN 194
           N  K+I+  G   + +HAR KA     + ++N           + +KK  EN ++ +  N
Sbjct: 165 N-AKAIEAGGGAAVSMHARTKAQAYTGNAQENW----------HWLKKLTENVNIPVIGN 213

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           G ++    A +++    V  VM+GRAA  N  +L   + Y 
Sbjct: 214 GDVKTPEDAKRMIDETGVTAVMMGRAALGNPWILHRTEHYL 254


>gi|281492559|ref|YP_003354539.1| tRNA-dihydrouridine synthase [Lactococcus lactis subsp. lactis
           KF147]
 gi|281376223|gb|ADA65714.1| tRNA-dihydrouridine synthase [Lactococcus lactis subsp. lactis
           KF147]
          Length = 334

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 76/221 (34%), Positives = 119/221 (53%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+ TEMI    I   +KK +  + F     PL++QI G ++  LVEAAK VE     +I 
Sbjct: 46  LVVTEMISDKGIEHRNKKTLEMMDFEGVPHPLSMQIFGGEVDTLVEAAKFVEANTVADII 105

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+ L+L+PD V D ++A+ KA+S P+TVK RIG DD     A+ 
Sbjct: 106 DINMGCPVPKVTKNEAGSRLLLDPDKVYDVVSAVSKAISRPLTVKIRIGWDDD-HLFAVE 164

Query: 138 NLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLN 194
           N  K+I+  G   + +HAR KA     + ++N           + +KK  EN ++ +  N
Sbjct: 165 N-AKAIEAGGGAAVSMHARTKAQAYTGNAQENW----------HWLKKLTENVNIPVIGN 213

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           G ++    A +++    V  VM+GRAA  N  +L   + Y 
Sbjct: 214 GDVKTPEDAKRMIDETGVTAVMMGRAALGNPWILHRTEHYL 254


>gi|262382918|ref|ZP_06076055.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
 gi|262295796|gb|EEY83727.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
          Length = 329

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRFGAD-MVYTEFVSSDALIRNVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRIIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP + I +  NG +       +      VD VMIGRA+     +   V  Y +
Sbjct: 187 IGAVKN-NPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLT 245

Query: 235 N-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
              L    P    +D      I     + +   L     +  I RH+    LF G  + +
Sbjct: 246 TGELLPQEPFSWYLD------ILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFK 299

Query: 292 RCR 294
           + R
Sbjct: 300 QTR 302


>gi|254468654|ref|ZP_05082060.1| tRNA-dihydrouridine synthase B [beta proteobacterium KB13]
 gi|207087464|gb|EDZ64747.1| tRNA-dihydrouridine synthase B [beta proteobacterium KB13]
          Length = 336

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 114/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   +      +  +EM+ ++++L G  K I       + +P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKY-GAGMAVSEMVTSNSLLYGSSKTIRRANHDGEVEPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G   I++N+GCP+ ++     G+ L+ + D+V   + A+ KA  IP
Sbjct: 76  PQMMAEAAQYNADKGAQIIDINMGCPAKKICNVMAGSALLQHEDLVKRILEAVVKASPIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + K  + SG+  + IH R         +      + +Y+ 
Sbjct: 136 VTLKIRTGWDKQNKNAI--TIAKIAENSGIQALAIHGRT--------RACHYTGDAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +K +     I  NG +    +AL +L   S DGVMIGRAA     +   +D Y 
Sbjct: 186 IAAVKDQIKIPVIA-NGDITSPEKALHVLKKTSADGVMIGRAAQGRPWIFREIDHYI 241


>gi|160939910|ref|ZP_02087257.1| hypothetical protein CLOBOL_04801 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437344|gb|EDP15109.1| hypothetical protein CLOBOL_04801 [Clostridium bolteae ATCC
           BAA-613]
          Length = 321

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 79/301 (26%), Positives = 134/301 (44%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R       + TEM+ A A+L  +K  + +L     E+P A+Q+ G++
Sbjct: 19  MAGVTDLPFRVLCRE-QGAGCVVTEMVSAKAVLYNNKNTRELLQIDPAERPAAVQLFGSE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +E+  Y+ I++N+GCP  ++     G+ LM NP+   + + AM KA+  P
Sbjct: 78  PDIMAEIAARLEEGPYDYIDVNMGCPVPKIVNNGEGSALMKNPERAKEVLTAMVKAVKKP 137

Query: 119 VTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G +D  + AV    + +S    GV  + +H R         ++       D+D
Sbjct: 138 VTVKFRKGFNDLSVNAVEFAKMAES---CGVAAVAVHGRT--------REQYYSGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           I+ ++K+      IG NG +   ED  + LK     DG+M+ R A  N  +   ++ Y  
Sbjct: 187 IIRQVKEAVRIPVIG-NGDIFTPEDAGRMLKET-GCDGIMVARGAKGNPWLFGRINHYLD 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P    +     R     +  +       G  ++++  HM     G P+S   R
Sbjct: 245 TGEVLPGPSMAEIKAMILRH-GRMLVQFKG----EGVAMREMRGHMAWYTKGMPHSATLR 299

Query: 295 H 295
           +
Sbjct: 300 N 300


>gi|307544768|ref|YP_003897247.1| hypothetical protein HELO_2178 [Halomonas elongata DSM 2581]
 gi|307216792|emb|CBV42062.1| putative TIM-barrel protein, nifR3 family [Halomonas elongata DSM
           2581]
          Length = 363

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 79/289 (27%), Positives = 134/289 (46%), Gaps = 24/289 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R  AR L    L+  EM+ +D  L   +K+ L    + +P   A+QI G D
Sbjct: 35  MAGVTDRPFRALARRL-GAGLVVGEMVTSDPNLWHTRKSRLRMDHRGEPGPRAVQIAGGD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA++  + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ IP
Sbjct: 94  AAMLAEAARLNAEMGAEVIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVAAVDIP 153

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G   +    V +  L +S   +G+  + +H R         +  R     +YD
Sbjct: 154 VTLKIRTGWCAESNNGVRVARLAES---AGIQALAVHGRH--------RQQRYGGEAEYD 202

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  IK     + +  NG ++   +A ++L     D VMIGR A  N  +   +D Y  +
Sbjct: 203 TIAAIKAAV-GIPVFANGDIDSPEKARRVLDYTGADAVMIGRGAQGNPWIFREIDHYLRH 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               + P  T         +SA + D+   H+       +I R  IG +
Sbjct: 262 GRRMAPPDDTERAAVLRDHLSA-LHDFYGEHMGV-----RIARKHIGWY 304


>gi|312876693|ref|ZP_07736673.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796533|gb|EFR12882.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 328

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 77/305 (25%), Positives = 144/305 (47%), Gaps = 34/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA--LLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGG 56
           M  +TD+ +R   RL +     +  TEM+ + A++ G    K ++ FS +EK   +QI G
Sbjct: 13  MAGFTDKVFR---RLCSKFGADVTVTEMVSSKALVLGSAKTKELISFSEEEKIRGIQIFG 69

Query: 57  ADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           +D   + ++ KI++D F Y+ I++N+GCP  ++ +   G  LM NP +    +  + K  
Sbjct: 70  SDPEVMAQSVKILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLAAKIVEEVAKVS 129

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNL 174
             PV+VK R G D++   +        +++SG + + +H R +A L              
Sbjct: 130 RKPVSVKIRKGFDEE--DINAPEFAYILQESGASFVTVHGRTRAQLYS---------GKA 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D++I+ ++ KE   + +  NG + D   A +   +   DG+MIGRAA  N  +   + E 
Sbjct: 179 DWEIIRKV-KEKVKIPVVANGDITDFESAKRAYEVTRADGIMIGRAALGNPWVFLQIKEG 237

Query: 233 FSNPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           F      +  +   K RV  +F+ ++ +   +  A        + +  +H+     G  N
Sbjct: 238 FEKGYVETKVLPHMKIRVAIEFFSQLCSEKGEKMA--------VLEARKHLSFFVKGIEN 289

Query: 290 SRRCR 294
           + + R
Sbjct: 290 AAKIR 294


>gi|312794505|ref|YP_004027428.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181645|gb|ADQ41815.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 328

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 77/305 (25%), Positives = 144/305 (47%), Gaps = 34/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA--LLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGG 56
           M  +TD+ +R   RL +     +  TEM+ + A++ G    K ++ FS +EK   +QI G
Sbjct: 13  MAGFTDKVFR---RLCSKFGADVTVTEMVSSKALVLGSAKTKELISFSEEEKIRGIQIFG 69

Query: 57  ADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           +D   + ++ KI++D F Y+ I++N+GCP  ++ +   G  LM NP +    +  + K  
Sbjct: 70  SDPEVMAQSVKILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLAAKIVEEVAKVS 129

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNL 174
             PV+VK R G D++   +        +++SG + + +H R +A L              
Sbjct: 130 RKPVSVKIRKGFDEE--DINAPEFAYILQESGASFVTVHGRTRAQLYS---------GKA 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D++I+ ++ KE   + +  NG + D   A +   +   DG+MIGRAA  N  +   + E 
Sbjct: 179 DWEIIRKV-KEKVKIPVVANGDITDFESAKRAYEVTRADGIMIGRAALGNPWVFLQIKEG 237

Query: 233 FSNPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           F      +  +   K RV  +F+ ++ +   +  A        + +  +H+     G  N
Sbjct: 238 FEKGYVETKVLPHMKIRVAIEFFSQLCSEKGEKMA--------VLEARKHLSFFVKGIEN 289

Query: 290 SRRCR 294
           + + R
Sbjct: 290 AAKIR 294


>gi|224541983|ref|ZP_03682522.1| hypothetical protein CATMIT_01156 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525040|gb|EEF94145.1| hypothetical protein CATMIT_01156 [Catenibacterium mitsuokai DSM
           15897]
          Length = 325

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 79/288 (27%), Positives = 140/288 (48%), Gaps = 28/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  YR   +      L+ +EM+   A+  G++K I  L     E P+++QI G +
Sbjct: 18  MAGITNVAYRRLVKEF-GAGLVVSEMVSDKALCYGNQKTIDMLAVGEDEHPMSMQIFGGE 76

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V+AAK VE+    +I ++N+GCP  +V +   G+ LM  P++  D + A+ +A+++
Sbjct: 77  VETMVKAAKFVEEHSDCDIIDINMGCPVNKVLKAHAGSYLMQYPELAYDIVKAVVEAVNV 136

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVK RIG D   I  V +  L   ++K+G + + IH R         +      + D+
Sbjct: 137 PVTVKMRIGYDMKHINCVEMAQL---MEKAGASAVAIHGR--------TRSQMYEGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K+      IG NG +     A +++     D VM+GR A  N  ++  + +Y  
Sbjct: 186 SWIKKVKEAVSIPVIG-NGDVRTPEDAKRMMEETGCDAVMVGRGALGNPFVIRRMVKYLE 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             +    P       D+  +I   + D+A R + + G+   I R M G
Sbjct: 245 EGILEEEP-------DYHARIQLCI-DHAHRLVKTEGEKNAI-RQMRG 283


>gi|138893752|ref|YP_001124205.1| nitrogen regulation transcriptional regulator [Geobacillus
           thermodenitrificans NG80-2]
 gi|134265265|gb|ABO65460.1| Transcriptional regulator involved in nitrogen regulation,
           NifR3/Smm1 family [Geobacillus thermodenitrificans
           NG80-2]
          Length = 333

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 122/233 (52%), Gaps = 20/233 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+    I+  ++K  N+L    +EKPL+LQI G +   LV+AAK V+ +   + I
Sbjct: 37  LVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGEKETLVKAAKFVDKNTNADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V     GA  +L+P+ + D +A++  A+  PVTVK RIG D+     A+ 
Sbjct: 97  DINMGCPVPKVTNCDAGAKWLLDPNKIYDVVASIVDAVEKPVTVKMRIGWDEH-HIYAVE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D++I+ ++K+      IG NG
Sbjct: 156 N-AQAVERAGGKAVAVHGRTRVQMYEGKA----------DWNIIKQVKEAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
            ++    A ++L    VDGVMIGRAA  N  M+     Y         P  T 
Sbjct: 204 DVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVHYLETGELIPEPTPTE 256


>gi|56418608|ref|YP_145926.1| nitrogen regulation transcriptional regulator [Geobacillus
           kaustophilus HTA426]
 gi|261417574|ref|YP_003251256.1| hypothetical protein GYMC61_0074 [Geobacillus sp. Y412MC61]
 gi|297528448|ref|YP_003669723.1| hypothetical protein GC56T3_0072 [Geobacillus sp. C56-T3]
 gi|319765232|ref|YP_004130733.1| hypothetical protein GYMC52_0075 [Geobacillus sp. Y412MC52]
 gi|56378450|dbj|BAD74358.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) [Geobacillus kaustophilus HTA426]
 gi|261374031|gb|ACX76774.1| TIM-barrel protein, nifR3 family [Geobacillus sp. Y412MC61]
 gi|297251700|gb|ADI25146.1| TIM-barrel protein, nifR3 family [Geobacillus sp. C56-T3]
 gi|317110098|gb|ADU92590.1| TIM-barrel protein, nifR3 family [Geobacillus sp. Y412MC52]
          Length = 333

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 121/221 (54%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EM+    I+  ++K  N+L    +EKP++LQI G +   LV+AAK V+ +   + I
Sbjct: 37  LVCAEMVSDKGIVYNNEKTLNMLYIDEREKPISLQIFGGEKETLVKAAKFVDKNTNADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++     GA  +L+P+ + D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVPKITNCDAGAKWLLDPNKIYDVVAAIVDAVEKPVTVKMRIGWDEK-HIYAVE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N  ++++++G   + +H R  +   +G +          D++I+ ++K+      IG NG
Sbjct: 156 N-AQAVERAGGKAVAVHGRTRVQMYEGKA----------DWNIIKQVKEAVNIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++    A ++L    VDGVMIGRAA  N  M+     Y  
Sbjct: 204 DVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVRYLE 244


>gi|157827878|ref|YP_001494120.1| nifR3-like protein [Rickettsia rickettsii str. 'Sheila Smith']
 gi|157800359|gb|ABV75612.1| nifR3-like protein [Rickettsia rickettsii str. 'Sheila Smith']
          Length = 331

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 129/296 (43%), Gaps = 24/296 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G + + 
Sbjct: 22  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGCEPNV 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +PVTV
Sbjct: 81  IAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVEAVKLPVTV 140

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD         L K  + SGV  I +H R         +      N D+D +  
Sbjct: 141 KMRMGWDDNTKNAP--TLAKIAESSGVQMITVHGR--------TRCQFYSGNADWDFIRS 190

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y       
Sbjct: 191 V-KESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKTGEEK 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
           S+P       D   K   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 250 SAP-SIAEQLDIVTKHYEAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 299


>gi|21230237|ref|NP_636154.1| hypothetical protein XCC0763 [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66769771|ref|YP_244533.1| hypothetical protein XC_3469 [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|38604923|sp|Q8PCH1|DUSB_XANCP RecName: Full=tRNA-dihydrouridine synthase B
 gi|21111780|gb|AAM40078.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575103|gb|AAY50513.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. 8004]
          Length = 332

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   ++A+ +A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILSAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D       +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGTAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L    VD VMIGRAA     +   V  Y 
Sbjct: 183 YATIAQIKAAL-QIPVIANGDIDSPQKAAQVLRDTGVDAVMIGRAAQGRPWIFGEVAHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|296120472|ref|YP_003628250.1| dihydrouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296012812|gb|ADG66051.1| dihydrouridine synthase DuS [Planctomyces limnophilus DSM 3776]
          Length = 362

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 57/172 (33%), Positives = 95/172 (55%), Gaps = 5/172 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           +  +T R +R   R L    L  T+++ A  +L  +   + ++  S  ++PL++Q+ GAD
Sbjct: 37  LAGYTQRPFRVALRELGGMGLATTDLVHAVKLLSNNAFSQQLIATSLLDQPLSVQLFGAD 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +  AA+ +ED GY  ++LN+GCP A+V+    GA LM +P      +A +  ++SIP
Sbjct: 97  PTHVATAARWLEDLGYEGVDLNMGCPMAKVNSQGGGARLMCDPTGATRLVALVVASVSIP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           VTVK R+G D Q  +  L  L +  ++ G   I IH R    +G S K +R+
Sbjct: 157 VTVKMRLGWDAQSLSAPL--LARQFEEVGAAAITIHGRTRA-QGFSGKVSRE 205


>gi|72383560|ref|YP_292915.1| dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. NATL2A]
 gi|72003410|gb|AAZ59212.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. NATL2A]
          Length = 330

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 139/297 (46%), Gaps = 22/297 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           +D+ +R F R  +  ALL+TEM+ A ++  G  ++ ++  S +  P+ +Q+       +V
Sbjct: 31  SDQIFRNFVRRWSPKALLFTEMVNAKSLELGHGEEKVIELSEESGPIGVQLFDHRPDSMV 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA   E  G   I++N+GCP  ++     G+ L+  P++    +  + KA+SIPVTVK 
Sbjct: 91  DAAIKAESSGAFLIDINMGCPVKKIARKGGGSALLKEPELAQLIVKKVSKAISIPVTVKI 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G  +        +    ++++G   I +H R    +G S   N       +  + +IK
Sbjct: 151 RLGWCETTSDPV--SFALGLQEAGAQLITVHGRTR-RQGFSGHAN-------WKAIAKIK 200

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K + D+ +  NG +++   A++ L   + DGVMIGRA+     ++  +DE   N  T   
Sbjct: 201 K-SLDIPVIANGDIKNSRDAIECLKITNADGVMIGRASMGAPWLVGQIDEEIKNQTTFKP 259

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR-HMIGLFHGFPNSRRCRHIL 297
           P       D   K+S S+          G     I R HM     GF  +   RH L
Sbjct: 260 P-------DAKMKVSLSLEHLKLLVSKKGNHGLLIARKHMNWTCRGFEGASNLRHKL 309


>gi|311696116|gb|ADP98989.1| tRNA-dihydrouridine synthase B [marine bacterium HP15]
          Length = 332

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 126/254 (49%), Gaps = 21/254 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM++AD+ L   +K+   L    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRL-GAGLAVSEMVIADSKLWHTRKSQTRLNHEGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   +FG   I++N+GCP+ +V   + G+ LM +  +V D + ++ +A+ +P
Sbjct: 80  PQMLADAARQNAEFGAQIIDINMGCPAKKVCNKAAGSALMKDEALVRDILESVVQAVDVP 139

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D   A+ +  + +    +G+  + IH R         + ++   N +YD
Sbjct: 140 VTLKMRTGWDRDNRNALVIARMAED---AGIQAVAIHGRT--------RADKYEGNAEYD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K     + +  NG +    +A  +L     DG++IGRAA  +  +   +  +   
Sbjct: 189 TIADVKSRI-SIPVFANGDVTSPEKARDVLRHTGADGLLIGRAAQGSPWIFREIRHFLE- 246

Query: 236 PLTGSSPIKTRVDK 249
             TGS      +D+
Sbjct: 247 --TGSHMAAPELDE 258


>gi|165932567|ref|YP_001649356.1| tRNA-dihydrouridine synthase [Rickettsia rickettsii str. Iowa]
 gi|165907654|gb|ABY71950.1| tRNA-dihydrouridine synthase [Rickettsia rickettsii str. Iowa]
          Length = 339

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 129/296 (43%), Gaps = 24/296 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G + + 
Sbjct: 30  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGCEPNV 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +PVTV
Sbjct: 89  IAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVEAVKLPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD         L K  + SGV  I +H R         +      N D+D +  
Sbjct: 149 KMRMGWDDNTKNAP--TLAKIAESSGVQMITVHGR--------TRCQFYSGNADWDFIRS 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y       
Sbjct: 199 V-KESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKTGEEK 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
           S+P       D   K   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 258 SAP-SIAEQLDIVTKHYEAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 307


>gi|331268356|ref|YP_004394848.1| putative TIM-barrel protein, nifR3 family [Clostridium botulinum
           BKT015925]
 gi|329124906|gb|AEB74851.1| putative TIM-barrel protein, nifR3 family [Clostridium botulinum
           BKT015925]
          Length = 320

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 90/336 (26%), Positives = 155/336 (46%), Gaps = 49/336 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    L+YTEMI A  +   ++  K +L  S +EKP+A QI G+D
Sbjct: 17  MAGVTDIAYRGLCKEM-GCGLVYTEMISAKGMYYNNENTKKLLMLSKEEKPVAAQIFGSD 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I+ ED G   I++N+GCP+ ++ +   G+ LM  P++  + +  M K    
Sbjct: 76  PLVMARACEILNEDNGVCIIDINMGCPAPKIVKNGEGSALMKTPELAAEIVLEMKKISKK 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNL 174
           PVTVK R G D D I A+      K ++++G + I IH R    + +G +          
Sbjct: 136 PVTVKFRKGFDNDNINAI---EFAKRMEQAGADAIAIHGRTRAQMYEGKA---------- 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           D+DI+  +K+      IG NG +    +A ++    + DG+MI R A  N  +   +   
Sbjct: 183 DWDIIRRVKESVNIPVIG-NGDVFSAEKAFQLREETNCDGIMIARGAMGNPWIFKQIQLA 241

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG----GKLQ---QITRHMIGLFH 285
            +N             ++     S    D   RHL+      G+L+   ++ +H+     
Sbjct: 242 LNN-------------EEVIYPTSEEKIDMCIRHLNLAIQYHGELKAVREMRKHIAWYIK 288

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIE--TAFNLMI 319
           G  N    ++ + VE      +H++I+  T +  M+
Sbjct: 289 GIKNCTDIKNKINVE----KESHNVIKILTEYKAML 320


>gi|67458404|ref|YP_246028.1| nifR3 family TIM-barrel protein [Rickettsia felis URRWXCal2]
 gi|75537122|sp|Q4UNJ4|DUS_RICFE RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|67003937|gb|AAY60863.1| Putative TIM-barrel protein, nifR3 family [Rickettsia felis
           URRWXCal2]
          Length = 325

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/326 (25%), Positives = 145/326 (44%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLA--LQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++   +   + P +  +Q+ G 
Sbjct: 18  MSDITDLEFRKLVKRF-GAGLVVSEMIASRAMVVKSRQSMQKCAIVHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDEQLAAKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G DD        +L K  + SGV  + +H R         +      N D+D
Sbjct: 137 PITVKMRMGWDDNTKNAP--DLAKIAESSGVQMVTVHGRT--------RCQFYSGNADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KE   + +  NG + + ++A + L     DG+M+GR AY    +++ +  Y   
Sbjct: 187 FIRSV-KEAVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLVSQIAHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
                +P       D   +   ++ DY    +        I R  IG +  G P+S   R
Sbjct: 246 GEEKPAP-SIAEQLDIVTEHYNAILDYYGESVGV-----PIARKHIGWYSSGLPSSAEFR 299

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
             + +    +     I E   ++M E
Sbjct: 300 GAVNLMNDPAEVKEKIAEFYTSVMKE 325


>gi|291551191|emb|CBL27453.1| tRNA-U20-dihydrouridine synthase [Ruminococcus torques L2-14]
          Length = 321

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 85/303 (28%), Positives = 145/303 (47%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L     E+P++LQ  G+D
Sbjct: 21  MAGVTDLPFRVLCKE-QGAGLLCMEMVSAKAILYNNKNTESLLEIHPDEQPVSLQFFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK VE+  ++ +++N+GCP  +V     G+ LM NP +V + ++AM KA+  P
Sbjct: 80  PKIMSEMAKRVEERPFDIMDINMGCPVPKVVRNGEGSALMKNPKLVYEIVSAMVKAIDKP 139

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  + AV +  +++    + V       R+    G +          D+D
Sbjct: 140 VTVKIRKGFDDSCVNAVEIAKIIEEAGAAAVAVH-GRTREQYYSGQA----------DWD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A +++     DG+MI R A  N  + + +  Y   
Sbjct: 189 IIRQVKEAVSIPVIG-NGDVTSPQKAEELVKQTGCDGIMIARGAQGNPWIFSEMITYEE- 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG+ P   R  K+  R +   M  +A   L   G+   ++++ +H+     G   S +
Sbjct: 247 --TGTLP--ERPGKEEVRDM---MLRHARLQLKYKGEFIGIREMRKHVAWYTKGLKGSAK 299

Query: 293 CRH 295
            R 
Sbjct: 300 LRE 302


>gi|328675866|gb|AEB28541.1| tRNA dihydrouridine synthase B [Francisella cf. novicida 3523]
          Length = 325

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 117/221 (52%), Gaps = 19/221 (8%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG DDQ I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDDQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGR--------TREQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +     ++A+     VD VM+GRA+  N  +   + EY +
Sbjct: 206 DVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246


>gi|157825185|ref|YP_001492905.1| nifR3 family TIM-barrel protein [Rickettsia akari str. Hartford]
 gi|157799143|gb|ABV74397.1| Putative TIM-barrel protein, nifR3 family [Rickettsia akari str.
           Hartford]
          Length = 327

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 117/238 (49%), Gaps = 17/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLA--LQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++   +   + P +  +Q+ G 
Sbjct: 18  MSDITDLEFRKLVKRF-GAGLVVSEMIASRAMVVKSRQSMQKCAIMHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  GA LM +  +      A  KA+ I
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGAALMSDEQLASKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G DD         L K  + SG+  + +H R         +      N D++
Sbjct: 137 PITVKMRMGWDDNTKNAP--TLSKIAENSGIQMVTVHGRT--------RCQFYSGNADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            +  + KE   + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y 
Sbjct: 187 FIRSV-KEAVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWIISQIDHYL 243


>gi|222530304|ref|YP_002574186.1| NifR3 family protein [Caldicellulosiruptor bescii DSM 6725]
 gi|222457151|gb|ACM61413.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor bescii DSM
           6725]
          Length = 328

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 78/303 (25%), Positives = 140/303 (46%), Gaps = 30/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        +  + TEMI + A++ G    K+++ FS +EK   +QI G D
Sbjct: 13  MAGFTDKVFRRLCSRFGADVTV-TEMISSKALVLGSAKTKDLISFSEEEKIRGVQIFGND 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++     G  LM NP +    +  + K    
Sbjct: 72  PEVMAQSVKILQDEFEYHFIDINMGCPVPKLVRSGEGCALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           PV+VK R G DD+   +        +++SG + + +H R +A L              D+
Sbjct: 132 PVSVKIRKGFDDE--NINAPEFAYILQESGASFVTVHGRTRAQLYS---------GKADW 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+ ++ KE   + +  NG + D   A K   +   D +MIGRAA  N  +   + E F 
Sbjct: 181 EIIRKV-KEKLKIPVIANGDIVDFESAKKAYEVTRADSIMIGRAALGNPWVFLQIKEGFE 239

Query: 235 NPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                +  +   K RV  +F+ ++ +   D  A        + +  +H+     G  N+ 
Sbjct: 240 KGYVETKVLPHMKIRVAIEFFTQLCSEKGDKMA--------VLEARKHLSFFVKGIENAA 291

Query: 292 RCR 294
           + R
Sbjct: 292 KIR 294


>gi|312890783|ref|ZP_07750313.1| tRNA-U20-dihydrouridine synthase [Mucilaginibacter paludis DSM
           18603]
 gi|311296746|gb|EFQ73885.1| tRNA-U20-dihydrouridine synthase [Mucilaginibacter paludis DSM
           18603]
          Length = 330

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 130/261 (49%), Gaps = 31/261 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQI 54
           M D +D  +R+  +   N A ++YTE I ++ ++R   K     +I G+   E+P+ +QI
Sbjct: 20  MEDVSDPPFRYVCK--QNGADMMYTEFISSEGLIRDAAKSRKKLDIFGY---ERPIGIQI 74

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G+DI  + EA +I      + +++N GCP  +V     GA L+ + D +     A+ ++
Sbjct: 75  FGSDIESMREATRIATKAEPDLMDINYGCPVKQVACRGAGASLLQDIDKMVAMTRAVVES 134

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIP 172
             +PVTVK R+G DD    V    + + +++ G+  + IH R    + KG          
Sbjct: 135 THLPVTVKTRLGWDDNTKNVY--EVAERLQEVGIKALTIHGRTRAQMYKG---------- 182

Query: 173 NLDYDIVYEIKKENPDLFIGL--NGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
             D+ ++ EIKK NP++ I +  NG ++   +A   ++   VDG+MIGRAA     +   
Sbjct: 183 EADWRLIAEIKK-NPNIEIPIFGNGDIDSPEKAANWRLEYGVDGMMIGRAAIGYPWIFRE 241

Query: 229 VDEYFSNPLTGSSP-IKTRVD 248
           +  +F        P I  RVD
Sbjct: 242 IKHFFETGEHRDKPTIAERVD 262


>gi|313889105|ref|ZP_07822761.1| TIM-barrel protein, nifR3 family [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844845|gb|EFR32250.1| TIM-barrel protein, nifR3 family [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 308

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 80/308 (25%), Positives = 149/308 (48%), Gaps = 38/308 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R  A     + +  TEM+ A A++  +KK I  L  S +EK +A+QI G+D
Sbjct: 8   MAGYTDIAFREVATEKGAD-ITVTEMVSAMALVYENKKTIDLLDISPKEKKVAVQIFGSD 66

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+I+ D+ ++ +++N+GCP+ ++ + + G+ L+ +P +V D + ++ K  + P
Sbjct: 67  PDVMGQAARILNDYDFSYVDINMGCPAPKIVKNNSGSHLLSDPSLVYDIVKSVVKNSNKP 126

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G    I  ++    +K+I+ +G   + +H R         ++       D+D 
Sbjct: 127 VTAKVRKG----IGGLSSMKAIKNIEAAGATFVTVHGR--------TREEYYTGKADWDF 174

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K       IG NG ++    A++ +    VDG+ IGR A  N  +   ++E     
Sbjct: 175 IKEVKANVKIPVIG-NGDVDSPEDAIEKINYSKVDGLAIGRGAIGNPYIFNQIEELIE-- 231

Query: 237 LTGSSPIKTRVDKDFWRKISAS----MTDYAARHL-HSGGKLQ--QITRHMIGLFHGFPN 289
            TG          D+++         M D   R + + G KL   ++ +     F G  +
Sbjct: 232 -TG----------DYYKPSDKEKLLLMIDELERKISYKGEKLGILEMRKVYAEYFKGMKD 280

Query: 290 SRRCRHIL 297
           S+  R+ L
Sbjct: 281 SKEVRNKL 288


>gi|253681232|ref|ZP_04862030.1| tRNA-dihydrouridine synthase B [Clostridium botulinum D str. 1873]
 gi|253562470|gb|EES91921.1| tRNA-dihydrouridine synthase B [Clostridium botulinum D str. 1873]
          Length = 320

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 77/243 (31%), Positives = 122/243 (50%), Gaps = 23/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    L+YTEMI A  +   ++  K +L  S +EKP+A QI G+D
Sbjct: 17  MAGVTDIAYRGLCKEM-GCGLVYTEMISAKGMYYNNENTKKLLMLSKEEKPVAAQIFGSD 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I+ ED G   I++N+GCP+ ++ +   G+ LM  P++    +  M K    
Sbjct: 76  PLVMARACEILNEDNGVCIIDINMGCPAPKIVKNGEGSALMKTPELAAKIVMEMKKISKK 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNL 174
           PVTVK R G D D I AV      K ++++GV+ + IH R    + +G +          
Sbjct: 136 PVTVKFRKGFDNDNINAV---EFAKRMEQAGVDAVAIHGRTRAQMYEGKA---------- 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+DI+  + KE  D+ +  NG +    +A  LK   + DG+MI R A  N  +   +   
Sbjct: 183 DWDIIRRV-KEAVDIPVIGNGDVFSAEKAFQLKEETNCDGIMIARGAMGNPWIFKQIQLA 241

Query: 233 FSN 235
            +N
Sbjct: 242 LNN 244


>gi|116871611|ref|YP_848392.1| dihydrouridine synthase family protein [Listeria welshimeri serovar
           6b str. SLCC5334]
 gi|116740489|emb|CAK19609.1| dihydrouridine synthase family protein [Listeria welshimeri serovar
           6b str. SLCC5334]
          Length = 331

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/211 (33%), Positives = 117/211 (55%), Gaps = 16/211 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D ++A+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVSAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R  +             + ++D++ ++K+E    F+  NG +
Sbjct: 156 NALAA-ERAGASAVAMHGRTRV--------QMYEGSANWDVLRDVKRELKIPFMA-NGDV 205

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           +    A +IL     DGVMIGRAA  N  M+
Sbjct: 206 KTPEDAKRILEHTGADGVMIGRAALGNPWMI 236


>gi|322807847|emb|CBZ05422.1| tRNA dihydrouridine synthase B [Clostridium botulinum H04402 065]
          Length = 323

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 148/323 (45%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +  A   VE F  N     +++N+GCP+ ++ +   G+ LM +P +  + I AM K 
Sbjct: 76  PEIMANA---VEFFNDNNDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKV 132

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              P+TVK R G D + I AV      K +++SG + I IH   R+ + +G +       
Sbjct: 133 AKKPITVKFRKGFDKNNINAV---EFAKVMEQSGADAITIHGRTREQMYEGKA------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+ I+ ++K       IG NG +     A++++   + DGVM+GR A  N  +   +
Sbjct: 183 ---DWTIISKVKNAVSIPVIG-NGDVFSAEDAIEMINKTNCDGVMVGRGAQGNPWIFKQI 238

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           +E            + R+D      I  +    A  +      ++++ +H+     G  N
Sbjct: 239 NEKIKGEHVYYPTSQERID------ICINHYKRALEYFEEHKAVREMRKHVAVYVKGLKN 292

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
               +  + +E G+      +I+
Sbjct: 293 CTDIKDKVNMEKGSDKVLEELIK 315


>gi|241668651|ref|ZP_04756229.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877184|ref|ZP_05249894.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843205|gb|EET21619.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 324

 Score = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 117/222 (52%), Gaps = 19/222 (8%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENIEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + D + + + A+ KA+  PVTVK RIG DD+ I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVDKIHEILTAVVKAVHKPVTVKMRIGWDDENINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACEDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     ++A+     VD VM+GRA+  N  +   + EY + 
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNT 247


>gi|302390600|ref|YP_003826421.1| tRNA-U20-dihydrouridine synthase [Thermosediminibacter oceani DSM
           16646]
 gi|302201228|gb|ADL08798.1| tRNA-U20-dihydrouridine synthase [Thermosediminibacter oceani DSM
           16646]
          Length = 340

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 77/300 (25%), Positives = 129/300 (43%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L  + ++ TEM+    I   D K   +L     E P+ +Q+ G D
Sbjct: 28  MAGITDLPFRTICKELGADVVI-TEMVSTRGIYYNDSKTAALLTIDPCEHPIGVQLFGND 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                 A K +ED  ++ IN+N+GCP+ ++ +   G  LM +P++ G  I A  KA   P
Sbjct: 87  PEFFAHAVKKIEDIPFDFININMGCPTPKIVKNGDGCALMKDPELAGKIIEATAKASDRP 146

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D D   AV    +    ++SG   + IH R         ++       D+D
Sbjct: 147 VTVKIRKGWDEDSANAVEFSRMA---QESGAAMVIIHGRT--------REQFYSGKADWD 195

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+      IG NG +     A K+L     DGVM+GR A  N  +   +  +   
Sbjct: 196 IIRRVKEAVSIPVIG-NGDVFSAQDAAKMLEYTGCDGVMVGRGALGNPFIFREIKHFLKT 254

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +  ++ +  ++  +  R       + ++ +H+     G P+S   + 
Sbjct: 255 GEKLPPPALEEKKEVIFKHLDMALEFHGERV-----GILEMRKHIAWYLKGLPHSSAVKQ 309


>gi|254372943|ref|ZP_04988432.1| hypothetical protein FTCG_00514 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151570670|gb|EDN36324.1| hypothetical protein FTCG_00514 [Francisella novicida GA99-3549]
          Length = 327

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 141/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG DD+ I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDDKNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+  ++K    + IG NG
Sbjct: 157 --EVAKACEDAGVSAIAIHGRT--------REQMYTGKANWDIIRNVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|229825760|ref|ZP_04451829.1| hypothetical protein GCWU000182_01123 [Abiotrophia defectiva ATCC
           49176]
 gi|229790323|gb|EEP26437.1| hypothetical protein GCWU000182_01123 [Abiotrophia defectiva ATCC
           49176]
          Length = 331

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 77/287 (26%), Positives = 134/287 (46%), Gaps = 36/287 (12%)

Query: 20  ALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL YTEM+ A      +K  + ++    +E+P +LQI G+D   + E A  V D  ++ +
Sbjct: 38  ALTYTEMVSAKGFKYKNKNTEELITVDERERPTSLQIFGSDADIMGEMAAAVNDRNFDIL 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V     G+ LM  P+ + + + ++ K    PVT+K R G       VA +
Sbjct: 98  DVNMGCPVPKVVNNGEGSALMEQPEKIAEIVKSLKKNSKKPVTIKIRAGF-----TVANK 152

Query: 138 NLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           N V+  K    +GV+ I +H R         +        D++I+  +K+      IG N
Sbjct: 153 NAVEVAKIAEAAGVDAIAVHGRT--------RSQYYSGQADWNIIKAVKEAVSIPIIG-N 203

Query: 195 GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRV 247
           G +     A K+L   S DG+MI R A  N  +   ++ Y        P T    +   +
Sbjct: 204 GDVVTELDAKKMLEETSCDGIMIARGARGNPWIFNRINTYLEKGEILPPPTADEFLNMIL 263

Query: 248 DKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            +  W      M +Y  + L++G  ++++ +H+     G+PNS + R
Sbjct: 264 RQATW------MIEY--KGLYTG--VREMRKHIAWFTAGYPNSTKLR 300


>gi|15834638|ref|NP_296397.1| NifR3/Smm1 family protein [Chlamydia muridarum Nigg]
 gi|270284804|ref|ZP_06194198.1| NifR3/Smm1 family protein [Chlamydia muridarum Nigg]
 gi|270288833|ref|ZP_06195135.1| NifR3/Smm1 family protein [Chlamydia muridarum Weiss]
 gi|301336184|ref|ZP_07224386.1| NifR3/Smm1 family protein [Chlamydia muridarum MopnTet14]
 gi|7190054|gb|AAF38906.1| NifR3/Smm1 family protein [Chlamydia muridarum Nigg]
          Length = 334

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/311 (26%), Positives = 149/311 (47%), Gaps = 24/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  YR  + L  + AL++ EMI  + +    K+ +  L FS   +P+  Q+ G+ 
Sbjct: 21  LAGFSDYPYRRMSALY-HPALMFCEMIKMEGLHYCPKRTLRLLDFSESMRPIGGQLCGSR 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                E+AKI+E  G++ I+LN GCP+ R+ +   G+ ++  P ++G  + ++ +A+S+P
Sbjct: 80  PDLAGESAKILEGLGFDLIDLNCGCPTDRITKDGSGSGMLKTPQLIGKVVESIVEAVSVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D +   + +   V  IK+SG + +++H R        P       NL++  
Sbjct: 140 VTVKIRSGWDFE--HINVEETVHIIKESGASAVFVHGRTRSQGYQGPS------NLEF-- 189

Query: 179 VYEIKKENPDLF-IGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +   K+   + F +  NG +     A  +L +   DGV++ R       +   +++Y + 
Sbjct: 190 IARAKRAAGEHFPVFGNGDVFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T SSP  +   + F + +      +   +  S  KL   TR + G  H    S R R 
Sbjct: 250 G-TYSSPSFSMRKQAFVQHL-----QWIEEYYQSEEKLLTDTRKLCG--HYLILSPRVRS 301

Query: 296 ILTVEAGASTA 306
           +    A AS++
Sbjct: 302 LRASLAKASSS 312


>gi|153813030|ref|ZP_01965698.1| hypothetical protein RUMOBE_03438 [Ruminococcus obeum ATCC 29174]
 gi|149830832|gb|EDM85922.1| hypothetical protein RUMOBE_03438 [Ruminococcus obeum ATCC 29174]
          Length = 327

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/302 (25%), Positives = 139/302 (46%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL TEM+ A AI   +K  I  +     E P+++QI G++
Sbjct: 25  MAGVTDLPFRILCKE-QGAGLLCTEMVSAKAISFHNKNTISLMQIDPVEHPVSMQIFGSE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ L+ NP+++ + +  + +A+  P
Sbjct: 84  PDLMAEVAKSIEEQPFDILDINMGCPVPKVVNNGEGSALLKNPELIREIVTKVSRAVKKP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG +     V    + K I+ SG   + +H R         +        D+D 
Sbjct: 144 VTAKIRIGFEGY--PVDPVEIAKIIEDSGAAAVAVHGRT--------RQQYYAGEADWDT 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+      IG NG ++   +A  ++     DG+MIGRA   N  +   ++ YF+  
Sbjct: 194 IRRIKEAVSIPVIG-NGDVDSPKKAEALVRETGCDGIMIGRAVRGNPWIFREMNHYFT-- 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRRC 293
            TG       + +  W +I   +  +A   +   G+   ++++ +H+     G  +S   
Sbjct: 251 -TGEL-----LPRPSWEEIREMILRHARMQIELKGEFTGIREMRKHIAWYTSGMRHSAGL 304

Query: 294 RH 295
           R 
Sbjct: 305 RR 306


>gi|170760677|ref|YP_001788862.1| dihydrouridine synthase [Clostridium botulinum A3 str. Loch Maree]
 gi|169407666|gb|ACA56077.1| dihydrouridine synthase [Clostridium botulinum A3 str. Loch Maree]
          Length = 323

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 147/323 (45%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +  A   VE F  N+    +++N+GCP+ ++ +   G+ LM +P +  + I AM K 
Sbjct: 76  PEIMANA---VEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKV 132

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              P+TVK R G D + I AV      K +++SGV+ I IH   R+ + +G +       
Sbjct: 133 AKKPITVKFRKGFDKNNINAV---EFAKIMEQSGVDAITIHGRTREQMYEGKA------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+ I+ ++K       IG NG +     AL+++     DG+MIGR A  N  +   +
Sbjct: 183 ---DWAIISKVKNSVSIPVIG-NGDVFSSEDALEMINKTDCDGIMIGRGAQGNPWIFKQI 238

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           +E            + R+D      I  +    +  +      ++++ +H+     G  N
Sbjct: 239 NEKIKGKHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAAYVKGLKN 292

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
               +  + +E         +I+
Sbjct: 293 CTDIKDKVNMEKDPDKVLEELIK 315


>gi|294664625|ref|ZP_06729963.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292605605|gb|EFF48918.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 332

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     N +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGNAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|116512883|ref|YP_811790.1| tRNA-dihydrouridine synthase [Lactococcus lactis subsp. cremoris
           SK11]
 gi|125624976|ref|YP_001033459.1| tRNA-dihydrouridine synthase B [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|116108537|gb|ABJ73677.1| tRNA-U20-dihydrouridine synthase [Lactococcus lactis subsp.
           cremoris SK11]
 gi|124493784|emb|CAL98776.1| tRNA-dihydrouridine synthase B (EC 1.-.-.-) [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300071776|gb|ADJ61176.1| tRNA-dihydrouridine synthase B [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 334

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/221 (33%), Positives = 119/221 (53%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+ TEMI    I   +KK +  + F     PL++QI G ++  LVEAAK VE     +I 
Sbjct: 46  LVVTEMISDKGIEHRNKKTLEMMDFEGVPHPLSMQIFGGEVDTLVEAAKFVEANTVADII 105

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+ L+L+PD V D ++A+ KA+S P+TVK RIG DD     A+ 
Sbjct: 106 DINMGCPVPKVTKNEAGSRLLLDPDKVYDVVSAVSKAISRPLTVKIRIGWDDD-HLFAVE 164

Query: 138 NLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLN 194
           N  K+I+  G   + +HAR KA     + ++N           + +KK  +N ++ +  N
Sbjct: 165 N-AKAIEAGGGAAVSMHARTKAQAYTGNAQENW----------HWLKKLTDNVNIPVIGN 213

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           G ++    A +++    V  VM+GRAA  N  +L   + Y 
Sbjct: 214 GDVKTPEDAKRMIDETGVTAVMMGRAALGNPWILHRTEHYL 254


>gi|158319498|ref|YP_001512005.1| nifR3 family TIM-barrel protein [Alkaliphilus oremlandii OhILAs]
 gi|158139697|gb|ABW18009.1| putative TIM-barrel protein, nifR3 family [Alkaliphilus oremlandii
           OhILAs]
          Length = 324

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 116/238 (48%), Gaps = 16/238 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + + +  ++Y EM+ A  +   DKK   +L     EKP+ALQI G++
Sbjct: 17  MAGVTDLSFRLICKAM-DCGMVYMEMVSAKGLYYKDKKTEELLKIHDHEKPVALQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA ++ D     +++N+GCP+ ++ +   G+ LM +  + G+ I A+ K    P
Sbjct: 76  PDIMARAAYMLNDRANAILDINMGCPTPKIVKNGDGSALMKDIKLAGEVIKAVVKESIKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   +V    L K I+ SG   + +H R         ++       D+ I
Sbjct: 136 VTVKIRKGWDEH--SVNAVELAKVIEDSGAKAVAVHGR--------TREQFYAGKADWSI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K+      IG NG +  +   +++L   + DG+MIGR +  N  +   +  Y  
Sbjct: 186 IKEVKEAVTIPVIG-NGDVFTIEDGIRLLEYTNCDGIMIGRGSQGNPWLFKRLVHYMK 242


>gi|225016372|ref|ZP_03705564.1| hypothetical protein CLOSTMETH_00275 [Clostridium methylpentosum
           DSM 5476]
 gi|224950868|gb|EEG32077.1| hypothetical protein CLOSTMETH_00275 [Clostridium methylpentosum
           DSM 5476]
          Length = 328

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 115/241 (47%), Gaps = 20/241 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +DR YR   +     A +  EM+ A  +   D+K+  +L  S QE+P+A+Q+ G D
Sbjct: 20  MASVSDRAYRETCKQF-EAAYVVGEMVSAKGLHYSDRKSEELLSVSAQERPMAVQLFGDD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA      +  + I++N+GCP  +V     G+ LM NP + G+ + A   A  +P
Sbjct: 79  PGYMAEAVHKALRYEPDLIDINMGCPVPKVAGNGCGSALMKNPVLAGEIVRAAADASRVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R G DD   +V      K +++SG   + +H   R+ + +G            D+
Sbjct: 139 VTVKFRKGWDDS--SVNAVEFAKRMEQSGAAAVTVHGRTRRQMYQG----------EADW 186

Query: 177 DIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            I+ ++K+      IG NG +   + ++A+     VD VM+ R +Y    +   + +Y  
Sbjct: 187 QIIRQVKEAVSIPVIG-NGDVVSPESAKAMYDQTGVDLVMVARGSYGRPWLFGQIRDYLE 245

Query: 235 N 235
            
Sbjct: 246 T 246


>gi|326335679|ref|ZP_08201865.1| tRNA-dihydrouridine synthase B [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325692108|gb|EGD34061.1| tRNA-dihydrouridine synthase B [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 326

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 82/331 (24%), Positives = 151/331 (45%), Gaps = 41/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L   + +LY+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKLHGAD-MLYSEFISSEGLIRDAIKSRKKLDIFEDERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +A+IVE    + +++N GCP  +V     GA ++ + D++     A+ ++ ++P
Sbjct: 78  EEAMSLSARIVETVSPDVVDINFGCPVKKVVAKGAGAAVLKDIDLMVRLAKAVVRSTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++  G+  + IHAR  +   KG S          D+
Sbjct: 138 VTVKTRLGWDTD--SINIEEVAERLQDVGIQALSIHARTRVQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG ++   +AL  K    VDG+MIGRAA     +   + +Y
Sbjct: 186 SYIAKVKN-NPRIHIPIFGNGDIDSPEKALVYKNKYGVDGIMIGRAAIGYPWIFHEIKQY 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL-----HSGGKLQ--QITRHMIGLFH 285
            +     + P  ++              D A +HL       G +L   +  RH    F 
Sbjct: 245 LATGEKVAPPTLSQ------------RADVALQHLLWAVEWKGERLGILETRRHYANYFK 292

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           G P+ +  +  L      S   + ++E   N
Sbjct: 293 GIPHFKEYKQQLVTLDDLSALKNLLLEVKNN 323


>gi|220933549|ref|YP_002512448.1| nifR3 family TIM-barrel protein [Thioalkalivibrio sp. HL-EbGR7]
 gi|219994859|gb|ACL71461.1| nifR3 family TIM-barrel protein [Thioalkalivibrio sp. HL-EbGR7]
          Length = 327

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 124/249 (49%), Gaps = 28/249 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L  + +  +EM++AD  L    K+   L  + +  P+++QI GA+
Sbjct: 17  MAGVTDRPFRLLCRRLGAD-MAVSEMVIADTRLWHTPKSRQRLDHAGEPDPISVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   D G   I++N+GCP+ +V   + G+ L+ +  +V + +  + KA+ +P
Sbjct: 76  PAMLAEAARRNADNGAQIIDINMGCPAKKVCNRAAGSALLGDERLVSEILETVVKAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R+G+D D + A+    + +  + SG+  + +H   R    KG           +D
Sbjct: 136 VTLKIRLGLDRDHLNAL---TIARIAEHSGIQALAVHGRTRACAYKG----------TVD 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA------YKNSAMLT 227
           YD +  + K++  + +  NG +    QA  +L     D +MIGRAA      ++  A   
Sbjct: 183 YDAIAAV-KQSVRIPVIANGDINTPEQARAVLARTGADALMIGRAAQGRPWIFREMAHFL 241

Query: 228 TVDEYFSNP 236
              ++   P
Sbjct: 242 ATGQHLPAP 250


>gi|239630367|ref|ZP_04673398.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|301067518|ref|YP_003789541.1| tRNA-dihydrouridine synthase [Lactobacillus casei str. Zhang]
 gi|239526650|gb|EEQ65651.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|300439925|gb|ADK19691.1| tRNA-dihydrouridine synthase [Lactobacillus casei str. Zhang]
          Length = 333

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 119/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  ++K  N+L    +E P+++QI G     LV AAK V ++   + I
Sbjct: 37  LVVCEMISDRGIMYKNEKTLNMLFVDPREHPISIQIFGGTKETLVNAAKFVDQNTAADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S PVTVK R G D++    A++
Sbjct: 97  DINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSKPVTVKMRTGWDEK-HVYAVQ 155

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + ++ G   + +H   RK +  G          + D++I+ E+K+     F+G NG
Sbjct: 156 NALAA-ERGGAAALAMHGRTRKQLYSG----------HADWNILKEVKQHLTIPFMG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A ++L  V  D VM+GRAA  N  +L  +  Y  +
Sbjct: 204 DVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMSAYLED 245


>gi|134047750|sp|Q92JQ6|DUS_RICCN RecName: Full=Probable tRNA-dihydrouridine synthase
          Length = 331

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 129/296 (43%), Gaps = 24/296 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G + + 
Sbjct: 22  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGCEPNV 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +PVTV
Sbjct: 81  IAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMKDEQLAAKIFEATVEAVKLPVTV 140

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD         L K  + SGV  I +H R         +      N D+D +  
Sbjct: 141 KMRMGWDDNTKNAP--TLAKIAESSGVQMITVHGR--------TRCQFYSGNADWDFIRS 190

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y       
Sbjct: 191 V-KESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKTGEEK 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
           S+P       D   +   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 250 SAP-SIAEQLDIVTEHYEAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 299


>gi|254490327|ref|ZP_05103516.1| putative TIM-barrel protein, nifR3 family [Methylophaga thiooxidans
           DMS010]
 gi|224464460|gb|EEF80720.1| putative TIM-barrel protein, nifR3 family [Methylophaga thiooxydans
           DMS010]
          Length = 334

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 123/247 (49%), Gaps = 18/247 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EMI A+  L   KK++L      + +P ++QI GAD
Sbjct: 22  MAGVTDRPFRQLCRRL-GAGMAVSEMITANKALWASKKSLLRANHEGEPEPRSVQIAGAD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G + I++N+GCP+ +V     G+ L+ +  +V D + ++ KA+ +P
Sbjct: 81  PVMMAEAARHNVDQGAHIIDINMGCPAKKVCNVMAGSALLQHETLVADILESVVKAVDVP 140

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    V +  +    +++G+  + +H R         + +    + +YD
Sbjct: 141 VTLKIRTGWDRDNRNGVTIARIA---EEAGIQLLSVHGRT--------RADAYKGDAEYD 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            + EIK       I  NG ++   +A  +L     DG+MIGRAA  N  +   +  Y ++
Sbjct: 190 TIAEIKSRISIPLIA-NGDIDSPQKAQLVLEKTGADGLMIGRAAQGNPWIFKQILHYLNH 248

Query: 236 PLTGSSP 242
               ++P
Sbjct: 249 GQLLATP 255


>gi|89256322|ref|YP_513684.1| Nif3 family protein [Francisella tularensis subsp. holarctica LVS]
 gi|156502395|ref|YP_001428460.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica FTNF002-00]
 gi|167010847|ref|ZP_02275778.1| NifR3/Smm1 family protein [Francisella tularensis subsp. holarctica
           FSC200]
 gi|254367656|ref|ZP_04983677.1| nif3 family protein [Francisella tularensis subsp. holarctica 257]
 gi|290952884|ref|ZP_06557505.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica URFT1]
 gi|295313929|ref|ZP_06804494.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica URFT1]
 gi|89144153|emb|CAJ79414.1| Nif3 family protein [Francisella tularensis subsp. holarctica LVS]
 gi|134253467|gb|EBA52561.1| nif3 family protein [Francisella tularensis subsp. holarctica 257]
 gi|156252998|gb|ABU61504.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica FTNF002-00]
          Length = 327

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 141/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           ++Y EM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  MIYMEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 98  DINIGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|282891207|ref|ZP_06299710.1| hypothetical protein pah_c048o037 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498900|gb|EFB41216.1| hypothetical protein pah_c048o037 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 342

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 49/139 (35%), Positives = 79/139 (56%), Gaps = 4/139 (2%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L+Y EM+  DA++R D     +L F     P+  Q+ G+      +AAKI+ED G++ +
Sbjct: 41  GLMYCEMVKMDALVRHDPNTFRMLDFDKDMHPIGGQLCGSKPQLAAKAAKIIEDLGFDVV 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP  +V +   G+ L+ NP ++G+ ++ M  A+ IPVTVK R G DD+   +   
Sbjct: 101 DLNCGCPVDKVTKDGSGSGLLKNPLLIGEILSEMVAAVKIPVTVKIRAGWDDE--NLCAE 158

Query: 138 NLVKSIKKSGVNGIWIHAR 156
            + +  +K+G   I IH R
Sbjct: 159 EITQIAEKAGAKAITIHGR 177


>gi|118589891|ref|ZP_01547295.1| tRNA-dihydrouridine synthase, putative [Stappia aggregata IAM
           12614]
 gi|118437388|gb|EAV44025.1| tRNA-dihydrouridine synthase, putative [Stappia aggregata IAM
           12614]
          Length = 334

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/267 (26%), Positives = 124/267 (46%), Gaps = 19/267 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLV 63
           TD  +R  A       ++ +EM+ +++ ++GD +  +    Q+K L  +Q+ G +   + 
Sbjct: 24  TDLPFRRLAARY-GAGMVVSEMVASESFVKGDAETQMRAEAQDKGLHVVQLAGREARWMG 82

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK+V   G + I++N+GCP+ +V  G  G+ LM + D     I A   A+ IPVT+K 
Sbjct: 83  EAAKVVAGLGADVIDINMGCPAKKVTSGYSGSALMRDLDHALTLIEATVAAVDIPVTLKM 142

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYE 181
           R+G DD+  ++    L +  + +G+  I +H R      KG          N D+  +  
Sbjct: 143 RLGWDDK--SLNAPELARRAEAAGIKLITVHGRTRCQFYKG----------NADWRAIAA 190

Query: 182 IKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+      I  NG  +    AL++  L   DGVMIGR AY    +   +  + +     
Sbjct: 191 VKEAISVPLIA-NGDCKGFENALRMLELSGADGVMIGRGAYGRPWLPGHIGHFLATGEKL 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARH 266
            +P    + +       A ++ Y  R 
Sbjct: 250 EAPRGAELAELVAEHYEAVLSHYGERQ 276


>gi|15891934|ref|NP_359648.1| nifR3-like protein [Rickettsia conorii str. Malish 7]
 gi|15619043|gb|AAL02549.1| nifR3-like protein [Rickettsia conorii str. Malish 7]
          Length = 339

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 129/296 (43%), Gaps = 24/296 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G + + 
Sbjct: 30  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGCEPNV 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +PVTV
Sbjct: 89  IAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMKDEQLAAKIFEATVEAVKLPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD         L K  + SGV  I +H R         +      N D+D +  
Sbjct: 149 KMRMGWDDNTKNAP--TLAKIAESSGVQMITVHGR--------TRCQFYSGNADWDFIRS 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y       
Sbjct: 199 V-KESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKTGEEK 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
           S+P       D   +   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 258 SAP-SIAEQLDIVTEHYEAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 307


>gi|194017978|ref|ZP_03056585.1| tRNA-dihydrouridine synthase B [Bacillus pumilus ATCC 7061]
 gi|194010315|gb|EDW19890.1| tRNA-dihydrouridine synthase B [Bacillus pumilus ATCC 7061]
          Length = 333

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 121/230 (52%), Gaps = 22/230 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI   AIL  + + +  L    +EKPL+LQI G +   LVEAAK V ++   + I
Sbjct: 37  LVCAEMISDKAILINNARTMGMLYIDEREKPLSLQIFGGEKDTLVEAAKFVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  PVTVK R+G D D I A+  
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVDAVDKPVTVKMRMGWDEDHIFAI-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG N
Sbjct: 155 -DNARAVERAGGQAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG-N 202

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           G ++    A ++L    VD VMIGRAA  N  M+     Y         P
Sbjct: 203 GDVKTPQDAKRMLDETGVDAVMIGRAALGNPWMIYRTVHYLETGELKEEP 252


>gi|87199943|ref|YP_497200.1| dihydrouridine synthase TIM-barrel protein nifR3 [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87135624|gb|ABD26366.1| tRNA-U20-dihydrouridine synthase [Novosphingobium aromaticivorans
           DSM 12444]
          Length = 351

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/241 (29%), Positives = 121/241 (50%), Gaps = 24/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G +
Sbjct: 29  MTGVSDLPFRTIVRRF-GSGLNVTEMIASPAAIRETRQSIQKAAWHPTEEPVSMQLVGCE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ ED G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+ +P
Sbjct: 88  PEQMAEAAKLSEDKGAAIIDINMGCPVRKVVNGDAGSALMRDIPLATRLIEATVKAVKVP 147

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VTVK R+G   D + A  L  + + +   G   I +H   R  + KG          + D
Sbjct: 148 VTVKMRMGWCHDSLNAPELARIAEDL---GAKMITVHGRTRNQMYKG----------SAD 194

Query: 176 YDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           +  V  + KE   + + +NG   G+ED++ A++     DGVMIGR +Y    +L  +  +
Sbjct: 195 WAFVRSV-KEAVSIPVIVNGDICGIEDVATAIE-QSGADGVMIGRGSYGRPWLLGQIMHW 252

Query: 233 F 233
            
Sbjct: 253 L 253


>gi|208779377|ref|ZP_03246723.1| putative TIM-barrel protein, nifR3 family [Francisella novicida
           FTG]
 gi|208745177|gb|EDZ91475.1| putative TIM-barrel protein, nifR3 family [Francisella novicida
           FTG]
          Length = 328

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 142/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG ++Q I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWNEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACEDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|148553172|ref|YP_001260754.1| nifR3 family TIM-barrel protein [Sphingomonas wittichii RW1]
 gi|148498362|gb|ABQ66616.1| putative TIM-barrel protein, nifR3 family [Sphingomonas wittichii
           RW1]
          Length = 333

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 115/226 (50%), Gaps = 23/226 (10%)

Query: 18  NNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
            + L  TEMI + A +R  ++++    +   E+P+++Q+ G    ++ EAAK+ +D G  
Sbjct: 40  GSGLNVTEMIASQAAIRETRQSVQKALWDPAEEPVSMQLVGCTPKEMGEAAKLSQDRGAA 99

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAV 134
            I++N+GCP  +V  G  G+ LM  P++  + + A   A+ +PVT+K R+G D D + A 
Sbjct: 100 IIDINMGCPVRKVVNGDAGSALMRTPELAVEIVKATVAAVEVPVTLKMRMGWDHDSLNAP 159

Query: 135 ALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            L  + + +   GV  I +H R    + KG          + D+  +  + KE   + + 
Sbjct: 160 ELARIAEDV---GVKMITVHGRTRCQMYKG----------SADWAFIRRV-KEAVSIPVI 205

Query: 193 LNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +NG    +ED   AL      DG+MIGR AY    +L+ V  Y + 
Sbjct: 206 VNGDICSIEDAETALD-QSGADGLMIGRGAYGRPWLLSQVMHYLAT 250


>gi|110636783|ref|YP_676990.1| NifR3 family TIM-barrel protein [Cytophaga hutchinsonii ATCC 33406]
 gi|110279464|gb|ABG57650.1| tRNA-U20-dihydrouridine synthase [Cytophaga hutchinsonii ATCC
           33406]
          Length = 329

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 83/329 (25%), Positives = 150/329 (45%), Gaps = 30/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I A+ ++R   K++  L     E+P+ +QI G  
Sbjct: 19  MEDVSDPPFRALCKQQGAD-MMYTEFIAAEGLIRDAAKSVHKLDIFDYERPMGIQIFGDK 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + +AA I E+ G   +++N GCP  +V     G+  +L+   +      + K  ++P
Sbjct: 78  IDVMCDAAAIAEEAGPELVDINFGCPVKKVACKGAGSGALLDIPKMVKMTEEIVKRCTLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ + ++ + ++  G+  + IH   R+ + KG            D+
Sbjct: 138 VTVKTRLGWDHD--SIHIVDIARRLQDVGIKALTIHGRTRQQMYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             + ++ KE  D+ I +  NG ++   +AL  K    VDG+MIGRAA     +   V  +
Sbjct: 186 SWIAKV-KEQQDIHIPIFGNGDIDSPEKALEYKNRYGVDGIMIGRAAIGYPWIFKEVKHF 244

Query: 233 F-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           F +    G   I+ RV+      +      ++         + ++  H    F G  N +
Sbjct: 245 FATGEKLGPPTIRERVE------VCKKHLAFSVEWKGPKEGIFEMRMHYTNYFRGIQNFK 298

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMIE 320
             R  L VEAG+   T  I++     + E
Sbjct: 299 PYRQRL-VEAGSYEDTFAILDEVAEQLSE 326


>gi|220930307|ref|YP_002507216.1| hypothetical protein Ccel_2942 [Clostridium cellulolyticum H10]
 gi|220000635|gb|ACL77236.1| TIM-barrel protein, nifR3 family [Clostridium cellulolyticum H10]
          Length = 320

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 119/247 (48%), Gaps = 18/247 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGF-STQEKPLALQIGGAD 58
           M   TD  +R   +      L+YTEM+ A  +    DK N L     +E+P A+QI G+D
Sbjct: 17  MAGVTDMPFRILCKE-QECGLVYTEMVSAKGMHYDDDKSNKLTLMHEKERPGAVQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ +       I++N+GCP+ ++ +   G+ LM NP++V + I ++  A   P
Sbjct: 76  PKIMAEVAEKLNKSDAAIIDINMGCPAPKITKNGEGSALMKNPELVAEIIKSVVSASQKP 135

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I A+ +  +    +K+G   I +H R         ++       D+D
Sbjct: 136 VTVKIRKGWDDSTINAIEIARIA---EKNGARAIAVHGR--------TREQYYSGKADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A K+L     D +M+GR A  N  +   + ++  +
Sbjct: 185 IIRQVKEAVSIPVIG-NGDVTGPKEAQKLLEETRCDAIMVGRGAQGNPWIFKKIVKFLED 243

Query: 236 PLTGSSP 242
               S P
Sbjct: 244 GTIISDP 250


>gi|167628121|ref|YP_001678621.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167598122|gb|ABZ88120.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 324

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 117/221 (52%), Gaps = 19/221 (8%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENIEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG DD+ I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDDENINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ ++KK    + IG NG
Sbjct: 157 --EVAKACEDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVKKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +     ++A+     VD VM+GRA+  N  +   + EY +
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246


>gi|312621326|ref|YP_004022939.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312201793|gb|ADQ45120.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 328

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/303 (25%), Positives = 139/303 (45%), Gaps = 30/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        +  + TEM+ + A++ G    K ++ FS +EK   +QI G D
Sbjct: 13  MAGFTDKVFRRLCSRFGADVTV-TEMVSSKALVLGSAKTKELISFSDEEKIRGVQIFGND 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++     G  LM NP +    +  + K    
Sbjct: 72  PEVMAQSVKILQDEFEYHFIDINMGCPVPKLVRSGEGCALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           PV+VK R G DD+   +        +++SG + + +H R +A L              D+
Sbjct: 132 PVSVKIRKGFDDE--NINAPEFAYILQESGASFVTVHGRTRAQLYS---------GKADW 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+ ++ KE   + +  NG + D   A K   +   D +MIGRAA  N  +   + E F 
Sbjct: 181 EIIRKV-KEKLKIPVIANGDIVDFESAKKAYEVTRADSIMIGRAALGNPWVFLQIKEGFE 239

Query: 235 NPLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                +  +   K RV  +F+ ++ +   D  A        + +  +H+     G  N+ 
Sbjct: 240 KGYVETKVLPHMKIRVAIEFFTQLCSEKGDKMA--------VLEARKHLSFFVKGIENAA 291

Query: 292 RCR 294
           + R
Sbjct: 292 KIR 294


>gi|299536698|ref|ZP_07050008.1| tRNA-dihydrouridine synthase 1 [Lysinibacillus fusiformis ZC1]
 gi|298727812|gb|EFI68377.1| tRNA-dihydrouridine synthase 1 [Lysinibacillus fusiformis ZC1]
          Length = 346

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 130/235 (55%), Gaps = 17/235 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+Y EMI    I++ ++K +  L    +E PL+LQI G D   LVEAAK V E+   + 
Sbjct: 43  GLVYAEMISDKGIVQKNEKTLGMLYIDERENPLSLQIFGGDKETLVEAAKYVDENTTADI 102

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP  ++ +   GA L+L+P+ V + +AA+  A+  PV+VK RIG D++    A+
Sbjct: 103 IDINMGCPVNKIIKCEAGARLLLDPNKVYEMVAAVVDAVKKPVSVKMRIGWDEE-HIFAI 161

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            N  ++++++G   + +H R  + +    K N       +D + ++ KEN  + +  NG 
Sbjct: 162 EN-AQAVERAGAAAVAVHGRTRV-QMYEGKAN-------WDYIRQV-KENVSIPVLGNGD 211

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP-IKTRVD 248
           +E    A ++L +  VD VMIGRAA  N  M+    +Y +       P ++ ++D
Sbjct: 212 VETPQDAKRMLETTGVDAVMIGRAALGNPWMIYRTVQYLATGELKEEPSVREKMD 266


>gi|77919588|ref|YP_357403.1| dihydrouridine synthase [Pelobacter carbinolicus DSM 2380]
 gi|77545671|gb|ABA89233.1| tRNA-U20-dihydrouridine synthase [Pelobacter carbinolicus DSM 2380]
          Length = 342

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/206 (33%), Positives = 107/206 (51%), Gaps = 16/206 (7%)

Query: 21  LLYTEMIVADA-ILRGD-KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L +TEMI A+  +L GD  +++L  +  ++PL +Q+ G +   L +A K VE  G + I+
Sbjct: 55  LAFTEMISANGLVLGGDATRDLLASTPSDRPLGIQLFGENPKYLSQACKQVESHG-DLID 113

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCP  +V     G+ LM  P  V   IAAM +A  +P+TVK R G D     +    
Sbjct: 114 LNIGCPVKKVVRSGAGSALMQTPARVAQIIAAMRRATHLPLTVKIRAGWDAS--HINFLE 171

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +    ++ GV+ I +H R    +G S   N       +D++ E+K+ +    IG +G + 
Sbjct: 172 IAHIAEQEGVDAITLHPRTRS-QGFSGSAN-------WDLIAELKRRSTIPVIG-SGDIF 222

Query: 199 DMSQALKILPSV--DGVMIGRAAYKN 222
           +   A ++L     D VMIGR  Y N
Sbjct: 223 EAQYAQRMLQQTGCDAVMIGRGCYGN 248


>gi|160878583|ref|YP_001557551.1| NifR3 family TIM-barrel protein [Clostridium phytofermentans ISDg]
 gi|160427249|gb|ABX40812.1| TIM-barrel protein, nifR3 family [Clostridium phytofermentans ISDg]
          Length = 324

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD  +R   +    + L+YTEM+ A  I   +K   +    +E  +P+ALQ+ G D
Sbjct: 19  MAGVTDLPFRLLCKEQGAD-LIYTEMVSAKGIYYNNKNTEVLLEVEEKERPVALQLFGED 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E   ++ +++N+GCP  +V     G+ LML P+ +G+ ++A+ KA+  P
Sbjct: 78  PYIMSEMAKRIEHRNFDFLDINMGCPVPKVVNNGEGSALMLKPERIGEIVSAISKAIKKP 137

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G   D I AV    + K I++SG   I +H R         ++       D+D
Sbjct: 138 VTVKIRKGFTKDNINAV---EVAKVIEQSGGAAIAVHGRT--------REQYYSGEADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+      IG NG ++      +++     D VMI R    N    +    Y + 
Sbjct: 187 IIKAVKEAVSIPVIG-NGDVQTPEDVKRMMSYTGCDAVMIARGVRGNPWFFSQAKHYLNT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMT---DYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
               + P    V +   R    ++    ++ A H        ++ +H+     G+P S +
Sbjct: 246 GEILAKPSVPEVIEMILRHGRLAIEVKGEFTAMH--------EMRKHVAWYTMGYPKSAK 297

Query: 293 CRH 295
            R+
Sbjct: 298 LRN 300


>gi|134047751|sp|Q9ZED2|DUS_RICPR RecName: Full=Probable tRNA-dihydrouridine synthase
          Length = 327

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 83/326 (25%), Positives = 143/326 (43%), Gaps = 28/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLA--LQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++   +   + P +  +Q+ G 
Sbjct: 18  MSDVTDLEFRKLVKRF-GAGLVVSEMIASRAMIMKSRQSMQKCAIMHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPDVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDEQLAAKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVTVK RIG DD       RN   L K    SGV  + +H R         +      N 
Sbjct: 137 PVTVKMRIGWDDNT-----RNAPTLAKIAANSGVQMVTVHGRT--------RCQFYSGNA 183

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++D +  + KE   + +  NG + + ++A + L     DG+M+GR  Y    +++ +  Y
Sbjct: 184 NWDFIRTV-KEAVKIPVIANGDITNFAKAKEALQRSGADGIMVGRGVYGKPWLISQIAYY 242

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                   +P       D   K   ++ DY  + +     +    +H+I   +G P+S  
Sbjct: 243 LKTGKEKPAP-SIAEQLDIITKHYDAIIDYYGKSVG----VPIARKHIIWYSNGLPSSAE 297

Query: 293 CRHILTVEAGASTATHHIIETAFNLM 318
            R  + +          I E   ++M
Sbjct: 298 FRCTVNLMKDPIAVKEKIAEFYMSVM 323


>gi|134298050|ref|YP_001111546.1| nifR3 family TIM-barrel protein [Desulfotomaculum reducens MI-1]
 gi|134050750|gb|ABO48721.1| tRNA-U20-dihydrouridine synthase [Desulfotomaculum reducens MI-1]
          Length = 319

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 122/248 (49%), Gaps = 19/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR      L  TEMI   A+L  + +   +L F  +  PL++QI G++
Sbjct: 17  MAGVTDRAYRILARE-QGCGLAVTEMISDLALLYANPRTYRMLDFRGETVPLSVQIFGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
              + +AA IV + G   +++N+GCP+ ++ + + G+ LM  P +    + A+ K++ ++
Sbjct: 76  PESMGKAAAIVVERGATIVDINMGCPTPKIVKNNEGSALMKTPQLAAKIVEAVVKSVPAV 135

Query: 118 PVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVK R G D+Q + AV    LV++   +G + + +H R         +        D+
Sbjct: 136 PVTVKIRKGWDEQSVNAVEFARLVEA---AGASAVAVHGRT--------RSQFYSGKADW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + ++K+      IG NG +     A K+L     DGVM+GR A  N  +   +  Y  
Sbjct: 185 ESIRKVKEALKIPVIG-NGDIWCARDAAKMLELTGCDGVMVGRGAMGNPWIFREIVYYLK 243

Query: 235 NPLTGSSP 242
             +    P
Sbjct: 244 TGMELPCP 251


>gi|325926552|ref|ZP_08187868.1| tRNA-U20-dihydrouridine synthase [Xanthomonas perforans 91-118]
 gi|325543060|gb|EGD14507.1| tRNA-U20-dihydrouridine synthase [Xanthomonas perforans 91-118]
          Length = 332

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           S 
Sbjct: 242 ST 243


>gi|163786900|ref|ZP_02181348.1| probable TIM-barrel protein, NifR3 family [Flavobacteriales
           bacterium ALC-1]
 gi|159878760|gb|EDP72816.1| probable TIM-barrel protein, NifR3 family [Flavobacteriales
           bacterium ALC-1]
          Length = 331

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/311 (26%), Positives = 141/311 (45%), Gaps = 45/311 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE + ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFVSSEGLIRNAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++   IVE    + I++N GCP  +V     GA ++ +  ++    A M K  ++P
Sbjct: 78  MESMLQTIDIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDICLMEKLTAEMVKRTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++  G   I IH R    + KG          + D+
Sbjct: 138 VTVKTRLGWDHD--SIKIVEVAERLQDVGCKSIAIHGRTRAQMYKG----------DADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  NP + I +  NG +    +A ++  S  +DG MIGRA   N      V  Y
Sbjct: 186 KPIAEVKN-NPRMHIPVFGNGDINTPERAAEMRDSYGLDGAMIGRATIGNPWFFKQVKHY 244

Query: 233 FSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-------QITRHMIGL 283
           F    TG   +PI             A   + A RHL      +       ++ RH    
Sbjct: 245 FE---TGEHLAPISL-----------AERVEAARRHLQMSIDWKGEVLGVFEMRRHYTNY 290

Query: 284 FHGFPNSRRCR 294
           F G P+ +  R
Sbjct: 291 FKGIPHFKEYR 301


>gi|313672939|ref|YP_004051050.1| dihydrouridine synthase dus [Calditerrivibrio nitroreducens DSM
           19672]
 gi|312939695|gb|ADR18887.1| dihydrouridine synthase DuS [Calditerrivibrio nitroreducens DSM
           19672]
          Length = 315

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/294 (26%), Positives = 136/294 (46%), Gaps = 24/294 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           T+  +R   RL  +N L++TEM+  + + RG+K+ +  +   ++E P+ +Q+ G +    
Sbjct: 21  TNHPFRKLVRLF-HNGLIFTEMVSVEGVKRGNKQTLKLIDVRSEENPVGIQLFGGNPESF 79

Query: 63  VEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            EA K++ED F +   ++N+GCP  +V +   GA L+ +       I+A+ KA   P+ V
Sbjct: 80  SEAVKVIEDNFDFFCFDINMGCPVKKVLKSKAGAYLLTDLKTAVGIISAVRKATRKPLFV 139

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D++   +  R ++K  +  GV+ + IH R         K       ++YD + E
Sbjct: 140 KTRLGWDEK--NLIYREILKICEGEGVDVLTIHGR--------TKSQLYSGKVNYDAIAE 189

Query: 182 IKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +K  +    IG NG + D+   AL     VD +MIGR   K+  +   + +    P+   
Sbjct: 190 VKSLSKIPIIG-NGDVVDLKMFALMKNTGVDAIMIGRGMMKSPWIFKALMDN-KEPINYL 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            P + R    F       + +   R       L    ++ +    GF NS   R
Sbjct: 248 KPEEIRYTLLF-------LLEEEKRFREGKYFLAPFKKYAVWFSKGFKNSSDFR 294


>gi|199598783|ref|ZP_03212195.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus HN001]
 gi|229551627|ref|ZP_04440352.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258509504|ref|YP_003172255.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus GG]
 gi|258540706|ref|YP_003175205.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus Lc 705]
 gi|199590288|gb|EDY98382.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus HN001]
 gi|229315031|gb|EEN81004.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257149431|emb|CAR88404.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus GG]
 gi|257152382|emb|CAR91354.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus Lc 705]
 gi|259650775|dbj|BAI42937.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus GG]
          Length = 333

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 119/223 (53%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  +KK  ++L    +E P+++QI G     LV AAK V ++   + I
Sbjct: 37  LVVCEMISDRGIMYKNKKTLSMLFVDPREHPISIQIFGGTKETLVNAAKFVDQNTAADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S PVTVK R G D D I AV  
Sbjct: 97  DINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSKPVTVKMRTGWDEDHIYAV-- 154

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           +N + + ++ G   + +H   RK +  G          + D++I+ E+K+     FIG N
Sbjct: 155 QNALAA-ERGGAAALAMHGRTRKQLYSG----------HADWNILKEVKQHLSIPFIG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G +     A ++L  V  D VM+GRAA  N  +L  +  Y  +
Sbjct: 203 GDVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMAAYLDH 245


>gi|15603891|ref|NP_220406.1| NIFR3-like protein (nifR3) [Rickettsia prowazekii str. Madrid E]
 gi|3860582|emb|CAA14483.1| NIFR3-LIKE PROTEIN (nifR3) [Rickettsia prowazekii]
 gi|292571607|gb|ADE29522.1| Putative dihydrouridine synthase Dus [Rickettsia prowazekii Rp22]
          Length = 341

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 84/326 (25%), Positives = 145/326 (44%), Gaps = 28/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLA--LQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++   +   + P +  +Q+ G 
Sbjct: 32  MSDVTDLEFRKLVKRF-GAGLVVSEMIASRAMIMKSRQSMQKCAIMHDDPTSACVQLAGC 90

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 91  EPDVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDEQLAAKIFEATVKAVKI 150

Query: 118 PVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVTVK RIG DD       RN   L K    SGV  + +H R         +      N 
Sbjct: 151 PVTVKMRIGWDDNT-----RNAPTLAKIAANSGVQMVTVHGRT--------RCQFYSGNA 197

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++D +  + KE   + +  NG + + ++A + L     DG+M+GR  Y    +++ +  Y
Sbjct: 198 NWDFIRTV-KEAVKIPVIANGDITNFAKAKEALQRSGADGIMVGRGVYGKPWLISQIAYY 256

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                   +P       D   K   ++ DY  + +  G  + +  +H+I   +G P+S  
Sbjct: 257 LKTGKEKPAP-SIAEQLDIITKHYDAIIDYYGKSV--GVPIAR--KHIIWYSNGLPSSAE 311

Query: 293 CRHILTVEAGASTATHHIIETAFNLM 318
            R  + +          I E   ++M
Sbjct: 312 FRCTVNLMKDPIAVKEKIAEFYMSVM 337


>gi|254475986|ref|ZP_05089372.1| tRNA-dihydrouridine synthase B [Ruegeria sp. R11]
 gi|214030229|gb|EEB71064.1| tRNA-dihydrouridine synthase B [Ruegeria sp. R11]
          Length = 331

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 114/235 (48%), Gaps = 20/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G D
Sbjct: 19  MAGITDRPFRDLVRGF-GVGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ VED G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+S+P
Sbjct: 78  AYWMAEAARQVEDRGAKVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVGAVSVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R+G DD   ++   ++ +  + +GV  + IH R      KG          + D+
Sbjct: 138 VTLKTRLGWDDN--SLNAADVARRAQNAGVQMVTIHGRTRCQFYKG----------SADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
             + E+K    D+ +  NG + D + A + L     DGVMIGR A     +L  V
Sbjct: 186 GAISEVKAAL-DVPLLANGDIIDTATAREALKRSGADGVMIGRGAQGKPWLLAQV 239


>gi|78046424|ref|YP_362599.1| nifR3 family TIM-barrel protein [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78034854|emb|CAJ22499.1| putative TIM-barrel protein; NifR3 family [Xanthomonas campestris
           pv. vesicatoria str. 85-10]
          Length = 332

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           S 
Sbjct: 242 ST 243


>gi|226942843|ref|YP_002797916.1| Dihydrouridine synthase [Azotobacter vinelandii DJ]
 gi|226717770|gb|ACO76941.1| Dihydrouridine synthase [Azotobacter vinelandii DJ]
          Length = 322

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 122/241 (50%), Gaps = 24/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EM+ +D  L   +K+ L      + +P ++QI G D
Sbjct: 10  MAGVTDRPFRALCRRL-GAGMTVSEMLTSDVRLWNSRKSRLRLPHGDEPEPRSVQIAGGD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   + G   I++N+GCP+ +V   + G+ LM +  +V + + A+  A+ +P
Sbjct: 69  PQRLAEAARRNVELGAQIIDINMGCPAKKVCNKAAGSALMRDEALVAEILRAVVTAVEVP 128

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNL 174
           VT+K R G D      A RN   + +  +++G+  + +H R +A L G +          
Sbjct: 129 VTLKIRTGWDR-----ANRNGVGIARLAEQAGIAALAVHGRTRADLYGGAA--------- 174

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  IK+    + +  NG ++   +A ++L +   DG++IGRAA     +   ++ Y
Sbjct: 175 EYDTIAAIKRAV-SIPVFANGDIDSPEKARQVLDATGADGLLIGRAAQGRPWIFREIEHY 233

Query: 233 F 233
            
Sbjct: 234 L 234


>gi|329766573|ref|ZP_08258116.1| nifR3 family TIM-barrel protein [Candidatus Nitrosoarchaeum limnia
           SFB1]
 gi|329136828|gb|EGG41121.1| nifR3 family TIM-barrel protein [Candidatus Nitrosoarchaeum limnia
           SFB1]
          Length = 321

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/266 (28%), Positives = 132/266 (49%), Gaps = 26/266 (9%)

Query: 26  MIVADAILRGDKKNI---LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           +I  +  L+ +KK I   L +S +E+PL++Q+ G+D+  L +AAKIVE F ++ I+ N+G
Sbjct: 44  IIAKEHQLKENKKTIQEFLEYSEKERPLSVQLFGSDLLALEKAAKIVEPF-FDIIDYNMG 102

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP+  + +   G  L+   ++     + +  A+  PVT+K R GV D     A R L K 
Sbjct: 103 CPAPHITQQMAGGALLQEINLTQQIFSTLVNAVKKPVTLKIRSGVTD-----ASRYLFKD 157

Query: 143 I----KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           I    +  G+  I +H R  + +G S        N D+ ++ E+K+ +    +G NG + 
Sbjct: 158 IATIAEDEGIQMITLHPR-TVSQGYS-------GNADWKMIKELKEISNIPIVG-NGDIT 208

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               A  ++     D VMIGR A  N  +   +++Y          +K ++D  F+  +S
Sbjct: 209 TPEDAKNMIDQTGCDYVMIGRGAMGNPFLFEQINDYLKTGTYKQYSLKDKID-SFFEYLS 267

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIG 282
            S T Y  +  +  G+  + T+ + G
Sbjct: 268 LS-TQYKIKFSNIKGQAMRFTKGIKG 292


>gi|86144145|ref|ZP_01062482.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Leeuwenhoekiella blandensis MED217]
 gi|85829407|gb|EAQ47872.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Leeuwenhoekiella blandensis MED217]
          Length = 334

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 145/310 (46%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLQSVEIVEASKPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G D    ++ +  + + ++  G   I IH R    + KG          N D+
Sbjct: 138 ITVKTRLGWDHD--SIKIVEVAERLQDVGCKAIAIHGRTRAQMYKG----------NADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  N  + I +  NG ++   +A+++     +DG MIGRA+         V  +
Sbjct: 186 KPIAEVKN-NQRMHIPVFGNGDVDTPERAVEMRDQYGLDGAMIGRASIGYPWFFREVKHF 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
           F+     + P ++ RVD              A RHL       G KL   +  RH    F
Sbjct: 245 FNTGEHMAPPTMQERVDA-------------ARRHLQMSIDWKGEKLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G P  +  R
Sbjct: 292 KGIPGFKPYR 301


>gi|294795205|ref|ZP_06760339.1| tRNA-dihydrouridine synthase [Veillonella sp. 3_1_44]
 gi|294453997|gb|EFG22372.1| tRNA-dihydrouridine synthase [Veillonella sp. 3_1_44]
          Length = 328

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 138/297 (46%), Gaps = 25/297 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++   +
Sbjct: 26  SDIAYRLLAKK-HGAALVCTEMVSAMGIKYKNERTHELLRIEEAERPVSMQIFGSNPEAI 84

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +PVTVK
Sbjct: 85  ALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAIDVPVTVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  +  +
Sbjct: 145 MRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSYIKAV 194

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K+      +G NG + +   A ++L     D VM+GR A  N  +   +  Y +   TG 
Sbjct: 195 KEAVSVPVLG-NGDIVNPEDAKQMLDETGCDAVMVGRGAQGNPWIFGRIHHYLA---TGE 250

Query: 241 S-PIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             P  T +++ D   K    +  Y    +     +++I  H      G P S   R+
Sbjct: 251 VLPAPTDIERLDMLLKHFDLLCQYKGESM----AVKEIRTHAGWYMKGLPESAYWRN 303


>gi|116495964|ref|YP_807698.1| tRNA-dihydrouridine synthase [Lactobacillus casei ATCC 334]
 gi|116106114|gb|ABJ71256.1| tRNA-U20-dihydrouridine synthase [Lactobacillus casei ATCC 334]
          Length = 333

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  ++K  N+L    +E P+++QI G     LV AAK V ++   + I
Sbjct: 37  LVVCEMISDRGIMYKNEKTLNMLFVDPREHPISIQIFGGTKETLVNAAKFVDQNTAADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S PVTVK R G D+     A++
Sbjct: 97  DINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSKPVTVKMRTGWDEN-HVYAVQ 155

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + ++ G   + +H   RK +  G          + D++I+ E+K+     F+G NG
Sbjct: 156 NALAA-ERGGAAALAMHGRTRKQLYAG----------HADWNILKEVKQHLTIPFMG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A ++L  V  D VM+GRAA  N  +L  +  Y  +
Sbjct: 204 DVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMSAYLED 245


>gi|238650328|ref|YP_002916180.1| nifR3-like protein [Rickettsia peacockii str. Rustic]
 gi|238624426|gb|ACR47132.1| nifR3-like protein [Rickettsia peacockii str. Rustic]
          Length = 339

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 128/296 (43%), Gaps = 24/296 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G + + 
Sbjct: 30  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGCEPNV 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +PVTV
Sbjct: 89  IAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVEAVKLPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD         L K  + SGV  I +H R         +      N D+D +  
Sbjct: 149 KMRMGWDDNTKNAP--TLAKIAESSGVQMITVHGRT--------RCQFYSGNADWDFIRS 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE+  + +  NG + + ++A   L     DG+M+GR AY    +++ +D Y       
Sbjct: 199 V-KESVKIPVIANGDITNFAKAKAALQKSGADGIMVGRGAYGKPWLISQIDHYLKTGEEK 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
           S+P       D   +   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 258 SAP-SIAEQLDIVTEHYEAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 307


>gi|191639443|ref|YP_001988609.1| tRNA-dihydrouridine synthase [Lactobacillus casei BL23]
 gi|227533060|ref|ZP_03963109.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|190713745|emb|CAQ67751.1| tRNA-dihydrouridine synthase [Lactobacillus casei BL23]
 gi|227189311|gb|EEI69378.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|327383535|gb|AEA55011.1| tRNA-dihydrouridine synthase [Lactobacillus casei LC2W]
 gi|327386728|gb|AEA58202.1| tRNA-dihydrouridine synthase [Lactobacillus casei BD-II]
          Length = 333

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 118/222 (53%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  ++K  N+L    +E P+++QI G     LV AAK V ++   + I
Sbjct: 37  LVVCEMISDRGIMYKNEKTLNMLFVDPREHPISIQIFGGTKETLVNAAKFVDQNTAADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S PVTVK R G D+     A++
Sbjct: 97  DINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSKPVTVKMRTGWDEN-HVYAVQ 155

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + ++ G   + +H   RK +  G          + D++I+ E+K+     F+G NG
Sbjct: 156 NALAA-ERGGAAALAMHGRTRKQLYAG----------HADWNILKEVKQHLTIPFMG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A ++L  V  D VM+GRAA  N  +L  +  Y  +
Sbjct: 204 DVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMSAYLED 245


>gi|327438060|dbj|BAK14425.1| tRNA-dihydrouridine synthase [Solibacillus silvestris StLB046]
          Length = 336

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 121/234 (51%), Gaps = 17/234 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+Y EMI   A+   +KK  ++L    +E P+ LQI G D   LVEAAK V+     +I 
Sbjct: 44  LVYAEMISDKALNTRNKKTLDMLYIDERENPMTLQIFGGDKENLVEAAKFVDKHTTADII 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  PV+VK RIG D++    A+ 
Sbjct: 104 DINMGCPVNKIIKCEAGAKWLLDPNKIYEMVSAVVDAVDKPVSVKMRIGWDEE-RVFAVE 162

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N   + +        +H R  + +    K N       +D++ E+KK     FI  NG +
Sbjct: 163 NAQAAERAGAAAIA-MHGRTRV-QMYEGKAN-------WDVLAEVKKNISIPFIA-NGDV 212

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP-IKTRVD 248
           E    A +IL     DGVMIGRAA  N  M+    +Y  + +    P ++ ++D
Sbjct: 213 ETPEDAKRILEHTKADGVMIGRAALGNPWMIYQTVKYLESGVQIPEPSVREKMD 266


>gi|254495051|ref|ZP_01053788.2| dihydrouridine synthase (Dus) [Polaribacter sp. MED152]
 gi|213690633|gb|EAQ43216.2| dihydrouridine synthase (Dus) [Polaribacter sp. MED152]
          Length = 315

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 83/310 (26%), Positives = 143/310 (46%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A ++YTE I ++ ++R   K++  L    +E+P+ +QI GA
Sbjct: 1   MEDVSDPPFRALCK--ENGADVVYTEFISSEGLIRDAAKSVIKLDIYEKERPVGIQIFGA 58

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++  +++  +IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++
Sbjct: 59  NLDSMLKTIEIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNL 118

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           P+TVK R+G D    ++ +  + + ++  G   I IH R    + KG          N D
Sbjct: 119 PITVKTRLGWDHD--SIRIVEVAERLQDVGCKAISIHGRTRAQMYKG----------NAD 166

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +  +  +K  NP + I +  NG +    +A+++     +DG MIGRA+         V  
Sbjct: 167 WVPIAAVKN-NPRMHIPVFGNGDVTTPERAMEMRDKYGLDGAMIGRASIGYPWFFNEVKH 225

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
           +F    TG    K  +         A  T  A RHL       G +L   +  RH    F
Sbjct: 226 FFK---TGEHLAKPSI---------AERTKVARRHLQMAIDWKGERLGVVETRRHYTNYF 273

Query: 285 HGFPNSRRCR 294
            G P+ +  R
Sbjct: 274 KGIPHFKDYR 283


>gi|120556355|ref|YP_960706.1| nifR3 family TIM-barrel protein [Marinobacter aquaeolei VT8]
 gi|120326204|gb|ABM20519.1| tRNA-U20-dihydrouridine synthase [Marinobacter aquaeolei VT8]
          Length = 332

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 119/242 (49%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    L  +EM++AD+ L   +K+   L    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRM-GAGLAVSEMVIADSKLWHTRKSRTRLNHEGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   +FG   I++N+GCP+ +V   + G+ LM +  +V + + A+ KA+ +P
Sbjct: 80  PEMLADAARQNAEFGAQIIDINMGCPAKKVCNKAAGSALMKDEKLVREILEAVVKAVDVP 139

Query: 119 VTVKCRIGVD---DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D      P +A     +  + +G+  + +H R         + ++   + +
Sbjct: 140 VTLKMRTGWDRDNRNAPVIA-----RMAEDAGIQALAVHGRT--------RADKYNGDAE 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + E+K  +  + +  NG +    +A ++L     DG++IGR A     +   +  Y 
Sbjct: 187 YDTIAEVKA-SVGIPVFANGDITTPEKARQVLSHTGADGLLIGRGAQGRPWIFREILHYL 245

Query: 234 SN 235
             
Sbjct: 246 ET 247


>gi|319952943|ref|YP_004164210.1| tRNA-u20-dihydrouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319421603|gb|ADV48712.1| tRNA-U20-dihydrouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 332

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 83/310 (26%), Positives = 140/310 (45%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++  IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLQSVAIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G DD   ++ +  + + ++  G   I IH R    + KG    D    P  D 
Sbjct: 138 ITVKTRLGWDDD--SIRIVEVAERLQDVGCKAIAIHGRTRAQMYKG----DANWAPIADV 191

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
                  K N  + I +  NG +     A+K+     +DG MIGRA+         V  +
Sbjct: 192 -------KNNQRMHIPVFGNGDVNTPEAAMKMRDEYGLDGAMIGRASIGYPWFFNEVKHF 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
           F      + P I+ RV+              A RHL       G +L   +  RH    F
Sbjct: 245 FKTGEHLAPPTIQERVEA-------------AQRHLQMAIDWKGEQLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G PN +  R
Sbjct: 292 KGIPNFKEHR 301


>gi|168180991|ref|ZP_02615655.1| dihydrouridine synthase [Clostridium botulinum NCTC 2916]
 gi|168183602|ref|ZP_02618266.1| dihydrouridine synthase [Clostridium botulinum Bf]
 gi|226950978|ref|YP_002806069.1| dihydrouridine synthase [Clostridium botulinum A2 str. Kyoto]
 gi|237796983|ref|YP_002864535.1| dihydrouridine synthase [Clostridium botulinum Ba4 str. 657]
 gi|182668088|gb|EDT80067.1| dihydrouridine synthase [Clostridium botulinum NCTC 2916]
 gi|182673187|gb|EDT85148.1| dihydrouridine synthase [Clostridium botulinum Bf]
 gi|226844028|gb|ACO86694.1| dihydrouridine synthase [Clostridium botulinum A2 str. Kyoto]
 gi|229261947|gb|ACQ52980.1| dihydrouridine synthase [Clostridium botulinum Ba4 str. 657]
          Length = 323

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 147/323 (45%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +  A   VE F  N+    +++N+GCP+ ++ +   G+ LM +P +  + I AM K 
Sbjct: 76  PEIMANA---VEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKV 132

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              P+TVK R G D + I AV      K +++SGV+ I IH   R+ + +G +       
Sbjct: 133 AKKPITVKFRKGFDKNNINAVE---FAKIMEQSGVDAITIHGRTREQMYEGKA------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+ I+ ++K       IG NG +     AL+++     DG+MIGR A  N  +   +
Sbjct: 183 ---DWAIISKVKNSVSIPVIG-NGDVFSSEDALEMINKTDCDGIMIGRGAQGNPWIFKQI 238

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           +E            + R+D      I  +    +  +      ++++ +H+     G  N
Sbjct: 239 NEKIKGEHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAVYVKGLKN 292

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
               +  + +E         +I+
Sbjct: 293 CTDIKDKVNMEKDPDKVLEELIK 315


>gi|153941130|ref|YP_001392876.1| dihydrouridine synthase [Clostridium botulinum F str. Langeland]
 gi|170756229|ref|YP_001783162.1| dihydrouridine synthase [Clostridium botulinum B1 str. Okra]
 gi|152937026|gb|ABS42524.1| dihydrouridine synthase [Clostridium botulinum F str. Langeland]
 gi|169121441|gb|ACA45277.1| dihydrouridine synthase [Clostridium botulinum B1 str. Okra]
 gi|295320853|gb|ADG01231.1| dihydrouridine synthase [Clostridium botulinum F str. 230613]
          Length = 323

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 147/323 (45%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +  A   VE F  N+    +++N+GCP+ ++ +   G+ LM +P +  + I AM K 
Sbjct: 76  PEIMANA---VEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKV 132

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              P+TVK R G D + I AV      K +++SGV+ I IH   R+ + +G +       
Sbjct: 133 AKKPITVKFRKGFDKNNINAV---EFAKIMEQSGVDAITIHGRTREQMYEGKA------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+ I+ ++K       IG NG +     AL+++     DG+MIGR A  N  +   +
Sbjct: 183 ---DWAIISKVKSSVSIPVIG-NGDVFSSEDALEMINKTDCDGIMIGRGAQGNPWIFKQI 238

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           +E            + R+D      I  +    +  +      ++++ +H+     G  N
Sbjct: 239 NEKIKGEHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAVYVKGLKN 292

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
               +  + +E         +I+
Sbjct: 293 CTDIKDKVNMEKDPDKVLEELIK 315


>gi|172056107|ref|YP_001812567.1| NifR3 family TIM-barrel protein [Exiguobacterium sibiricum 255-15]
 gi|171988628|gb|ACB59550.1| TIM-barrel protein, nifR3 family [Exiguobacterium sibiricum 255-15]
          Length = 332

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+    IL  +++   +L    +EKPL+LQI G     LV+AA
Sbjct: 29  FRLIAKEF-GAGLVCAEMVSDKGILYENERTMQMLYVDDREKPLSLQIYGGSKETLVQAA 87

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           + V+ +   + I++N+GCP  +V +   GA  +L+PD V + + A+ +A+  PVTVK R 
Sbjct: 88  QYVDANTNADIIDINMGCPVPKVTKCDAGAKWLLDPDKVYEMVHAVSQAVDKPVTVKMRT 147

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D     +   + V++ +  G   + IH R         +  +     D++I+ E K+ 
Sbjct: 148 GWDSH--HIYCVDNVRAAEAGGAKAVAIHGRT--------RSQKYEGVADWNIIGEAKRA 197

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                IG NG ++    A +++    VDGVMIGRAA  N  ML    +Y  +      P
Sbjct: 198 VTIPIIG-NGDVQTPQDAKRMIDEIGVDGVMIGRAALGNPWMLYQTIQYLESGTLSVEP 255


>gi|254374394|ref|ZP_04989876.1| hypothetical protein FTDG_00561 [Francisella novicida GA99-3548]
 gi|151572114|gb|EDN37768.1| hypothetical protein FTDG_00561 [Francisella novicida GA99-3548]
          Length = 324

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 142/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG DD+ I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDDKNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACEDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDIVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + +Y +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAKYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|307292784|ref|ZP_07572630.1| TIM-barrel protein, nifR3 family [Sphingobium chlorophenolicum L-1]
 gi|306880850|gb|EFN12066.1| TIM-barrel protein, nifR3 family [Sphingobium chlorophenolicum L-1]
          Length = 339

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI   A++R  ++++    +   E+P+++Q+ G  
Sbjct: 23  MTGVTDMPFRTLVRRY-GSGLNVTEMIATAAMIRETRQSLQKAAWHPLEEPVSMQLAGCS 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAK+  D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+ +P
Sbjct: 82  PTEMAEAAKLNADRGAAIIDINMGCPVKKVVNGDAGSALMRDLPLAASLIEATVKAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++    L +  +  G   I +H R    + KG          + D+
Sbjct: 142 VTVKMRMGWDHA--SLNAPELARIAEDLGAKLITVHGRTRCQMYKG----------SADW 189

Query: 177 DIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V  + KE   L + +NG    ++D   AL+     DGVMIGR AY    ++  V  +F
Sbjct: 190 AFVRSV-KEAVSLPVIVNGDICSIDDAETALE-QSGADGVMIGRGAYGRPWLIGQVMHWF 247


>gi|332685806|ref|YP_004455580.1| tRNA dihydrouridine synthase B [Melissococcus plutonius ATCC 35311]
 gi|332369815|dbj|BAK20771.1| tRNA dihydrouridine synthase B [Melissococcus plutonius ATCC 35311]
          Length = 336

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 79/233 (33%), Positives = 116/233 (49%), Gaps = 20/233 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK  ++L     E PL++QI G D   LVEAA+ V E+   + I
Sbjct: 37  LVVCEMISDKGIHFRNKKTLDMLYIDENEHPLSIQIFGGDKDTLVEAAQFVQENTKADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+PD V + I A+  A+ IPVTVK R G DDQ   +A+ 
Sbjct: 97  DINMGCPVNKVIKAEAGAKWLLDPDKVYEMIHAVSSAVDIPVTVKMRTGWDDQ-HILAIE 155

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + K        +H   R  + +G +          +++I+ E+K+     FIG NG
Sbjct: 156 NAIAAEKAGAAAIA-MHGRTRTQMYEGKA----------NWEILKEVKQHVAIPFIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
            ++    A K+L  V  DGVMIGRA   N  M+     Y         P  T 
Sbjct: 204 DVKTPEDAKKMLEYVKADGVMIGRAILGNPWMIHRTTNYLETGTLMVEPTPTE 256


>gi|163845808|ref|YP_001633852.1| NifR3 family TIM-barrel protein [Chloroflexus aurantiacus J-10-fl]
 gi|222523518|ref|YP_002567988.1| TIM-barrel protein, nifR3 family [Chloroflexus sp. Y-400-fl]
 gi|163667097|gb|ABY33463.1| TIM-barrel protein, nifR3 family [Chloroflexus aurantiacus J-10-fl]
 gi|222447397|gb|ACM51663.1| TIM-barrel protein, nifR3 family [Chloroflexus sp. Y-400-fl]
          Length = 350

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 97/332 (29%), Positives = 148/332 (44%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI----LRGDKKNILGFSTQEKPLALQIGG 56
           M   TD  +R     L    L+ TEM  A ++    LR  +  +L +  +E+PL +QI G
Sbjct: 33  MAGVTDSIFRRMILRLGGCGLVSTEMTNAASVSPKALR--RHRLLDYLPEERPLTMQISG 90

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   +  AA++VE  G + I++N GCPS +V  G  G+ L+ +   +   + A+ +A+ 
Sbjct: 91  NDPDLVANAARVVEQLGADIIDINCGCPSPKVTGGGHGSALLRDLPKMERLLRAVREAVQ 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT+K R G D+Q  ++      K  + +GV+ + +H R         ++       D+
Sbjct: 151 IPVTLKFRAGWDEQ--SLNFIEAGKRAEAAGVSALALHPRT--------REQGYKGQADW 200

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             V  +K+      IG +G +     AL  L     DGVMIGR A  N  +   + +   
Sbjct: 201 SRVAALKQAVSIPVIG-SGDVTSAHDALIRLRDSGADGVMIGRGAMANPWIFRQIADLRR 259

Query: 235 NPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
               G +P + T  DK   R +        A  L     L +I + +IG FH G P S  
Sbjct: 260 ----GVTPYVPTPADK---RNLLIEYMTICAEELPERLALNKI-KQLIGQFHVGLPGSNH 311

Query: 293 CR---HILTVEAGASTATHHIIETAFNLMIES 321
            R   H  T  A A  A    IE  F   +ES
Sbjct: 312 LRVAVHTSTSLAEARDA----IERFFAPFLES 339


>gi|313206097|ref|YP_004045274.1| tRNA-u20-dihydrouridine synthase [Riemerella anatipestifer DSM
           15868]
 gi|312445413|gb|ADQ81768.1| tRNA-U20-dihydrouridine synthase [Riemerella anatipestifer DSM
           15868]
 gi|315023721|gb|EFT36724.1| tRNA dihydrouridine synthase B [Riemerella anatipestifer RA-YM]
 gi|325336459|gb|ADZ12733.1| tRNA-dihydrouridine synthase [Riemerella anatipestifer RA-GD]
          Length = 325

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 86/325 (26%), Positives = 157/325 (48%), Gaps = 34/325 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   ++   + L+Y+E I ++ ++R     K  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKMHGAD-LMYSEFISSEGLIRDAIKSKKKLDIFDYERPIGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIVE    + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMAMSAKIVETVQPDLVDINFGCPVKKVVCKGAGAGVLKDIDLMVRLTKAVVNSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++++G+  + IHAR    + KG +          D+
Sbjct: 138 VTVKTRLGWDTN--SINIDEVAERLQEAGIKALTIHARTRAQMYKGEA----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           + +  I K+NP++ I +  NG ++   +AL  K   + DGVMIGRAA     +   V  +
Sbjct: 186 EHISRI-KQNPNIEIPIFGNGDIDSPQKALDYKNKYACDGVMIGRAAIGYPWIFNEVKHF 244

Query: 233 F-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           F +  L     ++ R+     R+ +    ++    L     L ++ +H    F G P+ +
Sbjct: 245 FQTGKLLPEPTLQDRLTA--VRQHAEWSAEWKGERL----GLIEMRQHYSNYFRGVPHFK 298

Query: 292 RCR----HILTVEAGASTATHHIIE 312
             R     ILT+E   S  +  IIE
Sbjct: 299 EYRKRFLEILTLEEMDSLIS-QIIE 322


>gi|149376839|ref|ZP_01894595.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Marinobacter
           algicola DG893]
 gi|149358846|gb|EDM47314.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Marinobacter
           algicola DG893]
          Length = 332

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 111/223 (49%), Gaps = 16/223 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    L  +EM++AD+ L   +K+   +    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRM-GAGLAVSEMVIADSKLWHTRKSKTRMNHEGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA++  +FG   I++N+GCP+ +V   + G+ LM +  +V D + A+  A+ IP
Sbjct: 80  PEMLANAARLNAEFGAQIIDINMGCPAKKVCNKAAGSALMKDEALVRDILKAVVAAVDIP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +     L  + +  + +G+  + IH R         + +      +YD 
Sbjct: 140 VTLKMRTGWDREHRNAPL--IARMAEDAGIQALAIHGRT--------RADAYKGEAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           + ++K     + +  NG +    QA  +L     DG++IGR A
Sbjct: 190 IADVKSRV-SIPVFANGDINSPEQAQHVLKFTGADGLLIGRGA 231


>gi|148381462|ref|YP_001256003.1| dihydrouridine synthase [Clostridium botulinum A str. ATCC 3502]
 gi|153932994|ref|YP_001385837.1| dihydrouridine synthase [Clostridium botulinum A str. ATCC 19397]
 gi|153935504|ref|YP_001389244.1| dihydrouridine synthase [Clostridium botulinum A str. Hall]
 gi|148290946|emb|CAL85082.1| putative dihydrouridine synthase [Clostridium botulinum A str. ATCC
           3502]
 gi|152929038|gb|ABS34538.1| dihydrouridine synthase [Clostridium botulinum A str. ATCC 19397]
 gi|152931418|gb|ABS36917.1| dihydrouridine synthase [Clostridium botulinum A str. Hall]
          Length = 323

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 147/323 (45%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +  A   VE F  N+    +++N+GCP+ ++ +   G+ LM +P +  + I AM K 
Sbjct: 76  PEIMANA---VEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKV 132

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              P+TVK R G D + I AV      K +++SGV+ I IH   R+ + +G +       
Sbjct: 133 AKKPITVKFRKGFDKNNINAV---EFAKIMEQSGVDAITIHGRTREQMYEGKA------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTV 229
              D+ I+ ++K       IG NG +     AL+++     DG+MIGR A  N  +   +
Sbjct: 183 ---DWAIISKVKNSVSIPVIG-NGDVFSSEDALEMINKTYCDGIMIGRGAQGNPWIFKQI 238

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           +E            + R+D      I  +    +  +      ++++ +H+     G  N
Sbjct: 239 NEKIKGEHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAVYVKGLKN 292

Query: 290 SRRCRHILTVEAGASTATHHIIE 312
               +  + +E         +I+
Sbjct: 293 CTDIKDKVNMEKDPDKVLEELIK 315


>gi|319639135|ref|ZP_07993891.1| tRNA-dihydrouridine synthase B [Neisseria mucosa C102]
 gi|317399612|gb|EFV80277.1| tRNA-dihydrouridine synthase B [Neisseria mucosa C102]
          Length = 334

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 116/241 (48%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPTLRNTKKTLRRSDFEGEGGVVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +V + +AA+  A+ +P
Sbjct: 76  PQQMAEAAQYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAEILAAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D+   +P +A     K  ++SG+  + IH   R  + KG           
Sbjct: 136 VTLKTRLGWHDEHQNLPTIA-----KIAEESGIAALAIHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A     +   +  
Sbjct: 181 ARYELIAETKG-RLNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWLFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|154505277|ref|ZP_02042015.1| hypothetical protein RUMGNA_02791 [Ruminococcus gnavus ATCC 29149]
 gi|153794475|gb|EDN76895.1| hypothetical protein RUMGNA_02791 [Ruminococcus gnavus ATCC 29149]
          Length = 319

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 86/313 (27%), Positives = 147/313 (46%), Gaps = 30/313 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A  I   +K  +++L    +E P++LQ  G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKGIFYNNKNTESLLQIHPEEVPVSLQFFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK VE+  ++ +++N+GCP  +V     G+ LM NP +V + ++A  KA+  P
Sbjct: 79  PKIVSEMAKRVEERPFSILDINMGCPVPKVVRNGEGSALMKNPKLVYELVSATVKAIKKP 138

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD+ I AV +  +++    + V       R+    G +          D++
Sbjct: 139 VTVKIRKGFDDEHINAVEIAKIIEEAGAAAVAVH-GRTREQYYSGKA----------DWE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A+ +      DGVMI R A  N  + + + EY   
Sbjct: 188 IIRQVKEAVSIPVIG-NGDVTSGEKAIAMREQTGCDGVMIARGAQGNPWIFSELLEYER- 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG  P +  V+     +I  +M  +A   +   G    ++++ +H+     G   + R
Sbjct: 246 --TGRLPDRPDVE-----EIKQTMLRHARLQIEYKGDFTGIREMRKHVAWYTKGLHGAAR 298

Query: 293 CR-HILTVEAGAS 304
            R  I  VE+ A 
Sbjct: 299 LRDQINQVESYAE 311


>gi|118497579|ref|YP_898629.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           novicida U112]
 gi|195536275|ref|ZP_03079282.1| putative TIM-barrel protein, nifR3 family [Francisella tularensis
           subsp. novicida FTE]
 gi|118423485|gb|ABK89875.1| tRNA-dihydrouridine synthase [Francisella novicida U112]
 gi|194372752|gb|EDX27463.1| putative TIM-barrel protein, nifR3 family [Francisella tularensis
           subsp. novicida FTE]
          Length = 328

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 142/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+YTEM+   A++    +   +L     EKPL +QI G DI   V A K I E+   + +
Sbjct: 38  LIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG DD+ I A+ 
Sbjct: 98  DINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDDKNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACEDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDIVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + +Y +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAKYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|331003606|ref|ZP_08327102.1| hypothetical protein HMPREF0491_01964 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412326|gb|EGG91718.1| hypothetical protein HMPREF0491_01964 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 320

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 116/233 (49%), Gaps = 18/233 (7%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           +LL TEM+ A AI   +K    ++     E P+ALQ+ G+D   +   A  +E+  ++  
Sbjct: 40  SLLVTEMVSAKAIYFKNKNTEPLMKIDKDEHPVALQLFGSDPDIIALMAAQIENRDFDIF 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVAL 136
           + N+GCP  ++     G+ LM NP +V + ++ + K++  PVT+K R G  +D I AV +
Sbjct: 100 DFNMGCPVPKIVNNGEGSALMKNPKLVEEILSKLVKSVKKPVTLKIRKGFNEDNINAVEI 159

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + ++   SGV+ I +HAR         ++       D+ I+  +K       IG NG 
Sbjct: 160 AKIAEA---SGVSAIAVHAR--------TREQYYSGKADWSIIKAVKSAVNIPVIG-NGD 207

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           ++D   A ++      DG+MI RAA  N  +   + +YF +  T   P K  V
Sbjct: 208 VKDGKSAEEMYEYTGCDGIMIARAARGNPWIFREIRDYFCSK-TVEKPAKDEV 259


>gi|91774082|ref|YP_566774.1| dihydrouridine synthase, DuS [Methanococcoides burtonii DSM 6242]
 gi|91713097|gb|ABE53024.1| tRNA-dihydrouridine synthase [Methanococcoides burtonii DSM 6242]
          Length = 318

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 62/221 (28%), Positives = 110/221 (49%), Gaps = 18/221 (8%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAKIVEDFGYNE- 76
           +L +TEMI +DA++ G+  + +   T  +E+P  LQ+ G     + EAA ++ED  Y + 
Sbjct: 35  SLCFTEMISSDAVVYGNASSAMRGITCDEERPFGLQLFGNSPEVITEAALVLEDMFYPDM 94

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+  +     G+ L+ +P++V D  + +C+ +  PVT K R+         A 
Sbjct: 95  IDINLGCPAPVITNAGCGSALLESPELVSDIFSTLCEGVDTPVTAKIRV----LESRAAT 150

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++   ++ +GV  I +H R    +G S   +     L         KE   + + +NG 
Sbjct: 151 LDMAHRLEDAGVCAITVHGRTC-EQGYSGTADHSYAKL--------IKEELSIPVIVNGD 201

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + D   A K+L     DG+MIGRAA  +  +   +  Y  +
Sbjct: 202 IRDGVSAEKVLEYTGCDGLMIGRAAMGDPHVFHRISRYLDD 242


>gi|326387744|ref|ZP_08209350.1| dihydrouridine synthase TIM-barrel protein nifR3 [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326207790|gb|EGD58601.1| dihydrouridine synthase TIM-barrel protein nifR3 [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 342

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 142/303 (46%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G +
Sbjct: 29  MTGVSDLPFRRMVRRF-GSGLNVTEMIASPAAIRETRQSIQKAAWDPAEEPVSMQLVGCE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ ED G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 88  PEQMGEAAKLSEDRGAAIIDINMGCPVRKVVNGDAGSALMRDIPLAARLIEATVKAVSVP 147

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VTVK R+G   D + A  L  + + +   G   I +H   R  + KG          + D
Sbjct: 148 VTVKMRMGWCHDSLNAPELARIAQDL---GAKMITVHGRTRNQMYKG----------SAD 194

Query: 176 YDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           +  V ++ K+   + + +NG    + D++ AL+     DGVMIGR AY    +L  +  +
Sbjct: 195 WGFVRKV-KDAVSIPVIVNGDICSIADVATALE-QSGADGVMIGRGAYGRPWLLGQIMHW 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                TG       +D+ +   I       +     +GG + +  +H+     G P S  
Sbjct: 253 LR---TGEELADPALDQQYEVIIEHYQDMLSHYGAMTGGNMAR--KHLGWYTKGLPGSAE 307

Query: 293 CRH 295
            R+
Sbjct: 308 FRN 310


>gi|298372677|ref|ZP_06982667.1| hypothetical protein HMPREF0156_00722 [Bacteroidetes oral taxon 274
           str. F0058]
 gi|298275581|gb|EFI17132.1| hypothetical protein HMPREF0156_00722 [Bacteroidetes oral taxon 274
           str. F0058]
          Length = 325

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 18/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + L+YTE + ADA++R   + +  L    +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLVCKEFGAD-LVYTEFVSADALVRFVNRTMQKLTIVDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V+AAKIV +   + I++N GCP  ++     GA L+ +   + D   ++ KA+++P
Sbjct: 77  PQTMVDAAKIVAESNPDIIDINFGCPVKKIASKGAGAGLLRDIPRLLDITQSVVKAVNLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDDNSKIIC--TLARQLQDCGIAALAIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
           + E+K + P + I +  NG +     A        VD +M+GR A  N+ +   +
Sbjct: 187 IGEVKND-PKIKIPIIGNGDITTPEVAEDKFHRYGVDAIMVGRGAIGNAWIFAEI 240


>gi|294011661|ref|YP_003545121.1| tRNA-dihydrouridine synthase [Sphingobium japonicum UT26S]
 gi|292674991|dbj|BAI96509.1| tRNA-dihydrouridine synthase [Sphingobium japonicum UT26S]
          Length = 339

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 141/307 (45%), Gaps = 35/307 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI   A++R  ++++    +   E+P+++Q+ G   S++
Sbjct: 27  TDMPFRTLVRRY-GSGLNVTEMIATAAMIRETRQSLQKAAWHPLEEPVSMQLAGCSPSEM 85

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAK+  D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+ +PVTVK
Sbjct: 86  AEAAKLNADRGAAIIDINMGCPVKKVVNGDAGSALMRDLPLAASLIEATVKAVDVPVTVK 145

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
            R+G D    ++    L +  +  G   I +H R    + KG          + D+  V 
Sbjct: 146 MRMGWDHA--SLNAPELARIAEDLGAKLITVHGRTRCQMYKG----------SADWAFVR 193

Query: 181 EIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            + K+   L + +NG    ++D   AL+     DGVMIGR AY    ++  V  +F    
Sbjct: 194 SV-KDAVSLPVIVNGDICSIDDAETALE-QSGADGVMIGRGAYGRPWLIGQVMHWFRTGQ 251

Query: 238 TGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRC 293
             + P    + RV  + +R +     +      H+G     + R  IG +  G P S   
Sbjct: 252 RLADPSLEEQYRVITEHYRAMLEHYDN------HTG---VNMARKHIGWYTKGLPGSAEF 302

Query: 294 RHILTVE 300
           R+ +  E
Sbjct: 303 RNAVNQE 309


>gi|323456305|gb|EGB12172.1| hypothetical protein AURANDRAFT_36241 [Aureococcus anophagefferens]
          Length = 367

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 108/238 (45%), Gaps = 19/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M  +T+ H  F  R L  +  L+TEM  A  +L  D       ++     + P  LQ+GG
Sbjct: 25  MQTYTNAHLNFLLRRLAPDVTLWTEMEKAADVLACDDAALASRLVAGGADDAPPVLQLGG 84

Query: 57  AD----ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            D     +    A ++  D    E+N+N GCP+       +GA LM +       + A+ 
Sbjct: 85  DDPRALAAATTRACRLRTDL--REVNINAGCPAIASGGADYGATLMRDAAATRRLVEAVR 142

Query: 113 KAL--SIPVTVKCRIGV----DDQIPAV--ALRNLVKSIKKSG-VNGIWIHARKAILKGL 163
            A   S  V++KCR+GV     D+ PA    L   V     SG ++ + +H R AIL GL
Sbjct: 143 DAAPPSCAVSLKCRVGVRETWSDEAPARYDELHAFVAETSSSGCLDHVVVHCRLAILAGL 202

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
           +P  NR  P L  D    + ++ P L +  NGG+     +      +DGVM GRA  +
Sbjct: 203 APGANRCRPPLHPDFARRLARDFPALRVTRNGGIGSFGDSDARDDGLDGVMAGRAVLR 260


>gi|303242623|ref|ZP_07329098.1| TIM-barrel protein, nifR3 family [Acetivibrio cellulolyticus CD2]
 gi|302589831|gb|EFL59604.1| TIM-barrel protein, nifR3 family [Acetivibrio cellulolyticus CD2]
          Length = 325

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 83/300 (27%), Positives = 133/300 (44%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LLYTEMI A  I   D K+  +      E+P A+QI G++
Sbjct: 17  MAGVTDMPFRILCKE-QGCGLLYTEMISAKGIYYNDVKSFKLTEIDPLEEPTAIQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A+ +       I++N+GCP+ ++ +   G+ LM NP +V   I+ + +A S P
Sbjct: 76  PDIMAKVAERLSQLNTAIIDINMGCPTPKITKNGEGSALMRNPLLVRKIISEVSRASSKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   +V    + K  + SG   I +H R         ++       D+DI
Sbjct: 136 VTVKIRKGWDEN--SVNAVEIAKIAEDSGAAAIAVHGR--------TREQFYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS-N 235
           + ++K+      IG NG +     A K+L     D +M+GR A  N  +   + EY   N
Sbjct: 186 IKKVKEAVSIPVIG-NGDIFTEEDARKMLEETGCDAIMVGRGAQGNPWIFKNILEYLKFN 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P      +    D+D    I   M         S G ++++ +H+     G  NS   R 
Sbjct: 245 P-----KLSDIYDEDKIDMIKRHMEMLVKLKGESSG-IKEMRKHIAWYVKGMKNSAILRE 298


>gi|297616351|ref|YP_003701510.1| hypothetical protein Slip_0145 [Syntrophothermus lipocalidus DSM
           12680]
 gi|297144188|gb|ADI00945.1| TIM-barrel protein, nifR3 family [Syntrophothermus lipocalidus DSM
           12680]
          Length = 329

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 147/302 (48%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNA--LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGG 56
           M  +TD+ +R    +L N+   L+ TEMI A A++ G +K +  L  S +E P+A+Q+ G
Sbjct: 18  MAGFTDKAFRI---ILKNHGAGLVATEMISAQALVYGQEKTMFMLDLSGEEPPVAVQLFG 74

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D   + +AA+I  D G + I++N+GCP+ R+ +   GA LM +P+     + A+ KA+S
Sbjct: 75  SDPRIIAQAARIAADRGAHIIDINMGCPTPRIVKNGEGAALMRDPNRAVRIVEAVVKAVS 134

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNL 174
           +PVTVK R G D+   ++    +    +++G + + +H   R+ +  G +          
Sbjct: 135 VPVTVKMRSGWDEN--SINCCQIAVLAEEAGAHAVTVHPRTREQLFSGKA---------- 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+ ++  +K+      IG NG +    +A ++L     D VMIGR    N  +     +Y
Sbjct: 183 DWSLIRAVKQVVKIPVIG-NGDVTSPQKARQMLEETGCDAVMIGRGCLGNPFIFRRTLQY 241

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                TG  P +   ++     ++      A R       + ++ +H+     G P++  
Sbjct: 242 LE---TGEIPPEPTAEERI--NVARQHLVLACRFKGETKAVLEMRKHLGWYIKGLPHATA 296

Query: 293 CR 294
            R
Sbjct: 297 VR 298


>gi|301060119|ref|ZP_07200986.1| putative tRNA-dihydrouridine synthase B [delta proteobacterium
           NaphS2]
 gi|300445631|gb|EFK09529.1| putative tRNA-dihydrouridine synthase B [delta proteobacterium
           NaphS2]
          Length = 331

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 84/306 (27%), Positives = 139/306 (45%), Gaps = 30/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R L    L  TEM+ A  + RG +K    L    +EKP+A+QI GAD
Sbjct: 18  MAGITNPPFRQIVREL-GAGLTVTEMVSAVGLSRGHQKTFHYLESVAREKPVAVQIFGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+     G + +++N+GCP+ +V +   G  L+ +P  +   + A+ KA +IP
Sbjct: 77  PVIMAAAAEKAVSKGADLVDINMGCPARKVIKNGSGGALLRSPSAIERMVTAVRKACTIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G   +        +   ++  GV+ + +H R  + +G S +        D+ I
Sbjct: 137 LTVKIRAGWSPE--EANFLEITDILEDCGVDAVTVHPR-FVKQGFSGRA-------DWRI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK      IG NG +     AL++      DGVMIGR A  N  +   + +     
Sbjct: 187 IREIKKRLTIPVIG-NGDVSRPEMALEMRKETGCDGVMIGRGALGNPWIFRQILDLEKG- 244

Query: 237 LTGSSPI----KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
             G+ P     + R+ +  +  +S  M +Y A  +        +   ++    G P+S R
Sbjct: 245 -IGAQPPDLFERKRIIRLHFSLLSRMMGEYVAAKM--------MRAQLLWYTKGLPHSSR 295

Query: 293 CRHILT 298
            R   T
Sbjct: 296 FRGAFT 301


>gi|282850019|ref|ZP_06259401.1| TIM-barrel protein, nifR3 family [Veillonella parvula ATCC 17745]
 gi|282580208|gb|EFB85609.1| TIM-barrel protein, nifR3 family [Veillonella parvula ATCC 17745]
          Length = 328

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 150/326 (46%), Gaps = 34/326 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++   +
Sbjct: 26  SDIAYRLLAKK-HGAALVCTEMVSAMGIKYKNERTHELLRIEEAERPVSMQIFGSNPEAI 84

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +PVTVK
Sbjct: 85  ALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAVDVPVTVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  +  +
Sbjct: 145 MRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSYIKAV 194

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K+      +G NG + +   A ++L     D VMIGR A  N  +   +  Y +   TG 
Sbjct: 195 KEAVSVPVLG-NGDIVEPEDAKQMLDETGCDAVMIGRGAQGNPWIFDRIHHYLA---TGE 250

Query: 241 S-PIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS----RRCR 294
             P  T +++ D   K    +  Y    +     +++I  H      G P S     R  
Sbjct: 251 VLPAPTDIERLDMLLKHFDLLCQYKGESM----AVKEIRTHAGWYMKGLPESAYWRNRVN 306

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
            I TV     T+ H+ +E+   ++ E
Sbjct: 307 TIHTV-----TSFHNELESYRKILFE 327


>gi|241761902|ref|ZP_04759987.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ATCC 10988]
 gi|260752443|ref|YP_003225336.1| hypothetical protein Za10_0199 [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|241373582|gb|EER63154.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ATCC 10988]
 gi|258551806|gb|ACV74752.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
          Length = 341

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 147/310 (47%), Gaps = 33/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 32  MTGVTDLPFRRIVRRY-GSGLNVTEMIASQAMIRETRQSLQKSTWDPSEEPISVQLVGCT 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E+AK+ +D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 91  PDDMAESAKLNQDRGAAIIDINMGCPVRKVVSGDAGSALMRDLKLAASIIEATVKAVSLP 150

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R+G D + + A  L  + + I   GV  + +H   R  + KG          + D
Sbjct: 151 VTLKMRMGWDLNSLNAPELARIAQDI---GVQMVTVHGRTRNQLYKG----------HAD 197

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V ++K     P +  G    L+D   AL+     DG+M+GR +Y    +L+ + +  
Sbjct: 198 WAFVRQVKDAVSIPVIVNGDINSLDDAKTALQ-QSGADGIMVGRGSYGKPWLLSQLMQGL 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLF-HGFPNS 290
           ++     +P    +D+ +      ++T++    L   G +    I R  IG +  G P S
Sbjct: 257 TDGEMEKAP---SIDEQY-----RTITEHYDHMLSYYGTITGVNIARKHIGWYTKGLPAS 308

Query: 291 RRCRHILTVE 300
              R+ +  E
Sbjct: 309 AEFRNKINRE 318


>gi|228473706|ref|ZP_04058454.1| tRNA-dihydrouridine synthase B [Capnocytophaga gingivalis ATCC
           33624]
 gi|228274853|gb|EEK13670.1| tRNA-dihydrouridine synthase B [Capnocytophaga gingivalis ATCC
           33624]
          Length = 324

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 77/311 (24%), Positives = 140/311 (45%), Gaps = 37/311 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + +LY+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKKYGAD-MLYSEFISSEGLIRDAIKSRKKLDIFDDERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +A+IVE    + +++N GCP  +V     GA ++ + D++     A+ K+  +P
Sbjct: 78  EEAMALSARIVETVSPDVVDINFGCPVKKVVAKGAGAAVLKDIDLMVRLTQAVVKSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDY 176
           VTVK R+G D +   + +  + + ++  G+  + IHAR  +   KG S          D+
Sbjct: 138 VTVKTRLGWDSE--TINIEEVAERLQDVGIQALSIHARTRVQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG ++   +AL  K    VDG+MIGRAA     +   +  Y
Sbjct: 186 SYIAKVKN-NPRIHIPIFGNGDIDSPEKALEYKERYGVDGIMIGRAAIGYPWIFQEIKHY 244

Query: 233 FSN-----PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +      P T S   +  +    W        ++    L     + +  RH    F G 
Sbjct: 245 MATRELLPPPTLSERAEAALQHLLW------AVEWKGERL----GILETRRHYSNYFKGI 294

Query: 288 PNSRRCRHILT 298
           P+ +  +  L 
Sbjct: 295 PHFKEYKQQLV 305


>gi|182420030|ref|ZP_02951264.1| tRNA-dihydrouridine synthase B [Clostridium butyricum 5521]
 gi|237669513|ref|ZP_04529493.1| tRNA-dihydrouridine synthase B [Clostridium butyricum E4 str. BoNT
           E BL5262]
 gi|182376067|gb|EDT73654.1| tRNA-dihydrouridine synthase B [Clostridium butyricum 5521]
 gi|237654957|gb|EEP52517.1| tRNA-dihydrouridine synthase B [Clostridium butyricum E4 str. BoNT
           E BL5262]
          Length = 321

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 149/313 (47%), Gaps = 40/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G +  K +L  + +EKP+A+QI G +
Sbjct: 17  MAGVTDISFRGLCKEM-GCGLVYTEMVSAKALYYGSENTKELLRIAEEEKPVAVQIFGRE 75

Query: 59  ---ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              ++K+VE     E F + +    I++N+GCP+ ++ +   G+ LM  P++    +  +
Sbjct: 76  PEIMAKMVE-----EHFNHRDDICIIDINMGCPATKIVKNGEGSALMKEPELAYKIVRKI 130

Query: 112 CKALSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDN 168
            +  + PVTVK R G D++ I AV      K ++++G + + IH   RK + +G +    
Sbjct: 131 KEVSTKPVTVKFRKGFDEENINAV---EFAKGMEQAGADAVAIHGRTRKQMYQGKA---- 183

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
                 D+DI+  + KEN  + +  NG +     AL++  L + DG+MI R +  N  + 
Sbjct: 184 ------DWDIIKSV-KENVSIPVIGNGDVFSPEDALRMKELTNCDGIMIARGSQGNPWLF 236

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             + +     +      K RV+      +     + A ++      ++++ +H      G
Sbjct: 237 RQIKDVLEGKIPQEVTNKERVE------MCLRHYELAIKYDGEYKAIREMRKHASWYIKG 290

Query: 287 FPNSRRCRHILTV 299
            P     R+ + V
Sbjct: 291 LPKCTDIRNEINV 303


>gi|269468440|gb|EEZ80105.1| tRNA-dihydrouridine synthase [uncultured SUP05 cluster bacterium]
          Length = 306

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   +D+ +R   R     AL  +EM+V    L G    K+ L FS +  P+++QI G+ 
Sbjct: 1   MAGTSDKPFRAICRA-QGAALTTSEMVVIQKHLLGTNKSKHRLDFSGEPAPISIQIAGSQ 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  +A+    FG + I++N+GCP+ +V   + G+ LM +  +V   + A+  A+ IP
Sbjct: 60  ADELAYSAQQALKFGADIIDINMGCPAKKVCNKAAGSALMQDEALVKSILNAVVSAVDIP 119

Query: 119 VTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G    +   P +A     K  +++G+  + +H R         ++++     +
Sbjct: 120 VTLKMRTGWNVSNKNAPTIA-----KIAEEAGIQMLSVHGR--------TREDKYTGMAE 166

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K +     I  NG +    +A  +L     DGVM+GRA   N  ++  +D Y 
Sbjct: 167 YDTIKAVKSQVGIPVIA-NGDITSAKKAQSVLQYTGADGVMVGRATQGNPWIIHEIDHYL 225


>gi|294626097|ref|ZP_06704705.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292599633|gb|EFF43762.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 332

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLYRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|260072681|gb|ACX30578.1| tRNA-dihydrouridine synthase [uncultured SUP05 cluster bacterium]
          Length = 324

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   +D+ +R   R     AL  +EM+V    L G    K+ L FS +  P+++QI G+ 
Sbjct: 19  MAGTSDKPFRAICRA-QGAALTTSEMVVIQKHLLGTNKSKHRLDFSGEPAPISIQIAGSQ 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  +A+    FG + I++N+GCP+ +V   + G+ LM +  +V   + A+  A+ IP
Sbjct: 78  ADELAYSAQQALKFGADIIDINMGCPAKKVCNKAAGSALMQDEALVKSILNAVVSAVDIP 137

Query: 119 VTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G    +   P +A     K  +++G+  + +H R         ++++     +
Sbjct: 138 VTLKMRTGWNVSNKNAPTIA-----KIAEEAGIQMLSVHGR--------TREDKYTGMAE 184

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K +     I  NG +    +A  +L     DGVM+GRA   N  ++  +D Y 
Sbjct: 185 YDTIKAVKSQVGIPVIA-NGDITSAKKAQSVLQYTGADGVMVGRATQGNPWIIHEIDHYL 243


>gi|169351459|ref|ZP_02868397.1| hypothetical protein CLOSPI_02239 [Clostridium spiroforme DSM 1552]
 gi|169291681|gb|EDS73814.1| hypothetical protein CLOSPI_02239 [Clostridium spiroforme DSM 1552]
          Length = 326

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 81/295 (27%), Positives = 136/295 (46%), Gaps = 43/295 (14%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L+Y+EM+   A+  G+ K I  L     E P+++Q+ G ++  +V+AAK ++     +I
Sbjct: 36  GLVYSEMVSDKALCYGNTKTIDMLQVDDGEHPVSIQLFGGEVGTMVKAAKFIDQHSNCDI 95

Query: 78  -NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
            ++N+GCP  +V +   G+ L+L PD + + +  +   +S PVTVK R G D + I AV 
Sbjct: 96  IDINMGCPVNKVLKADAGSKLLLYPDKIYEIVKGIVDNVSKPVTVKIRSGFDSKHINAVE 155

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L   I+K+G + I IH R         +        D+ I+ ++K       IG NG
Sbjct: 156 VAKL---IEKAGASAIAIHGR--------TRSQMYEGKADWKIIADVKAAVKIPVIG-NG 203

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            +  +  A ++L    VD VMIGRAA  N  ++  V +     +    P        +  
Sbjct: 204 DVRSVEDARRMLEETGVDAVMIGRAALGNPWLIKQVVQSLETGVIIEEPT-------YQE 256

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFH----------GFPNSRRCRHILT 298
           KI        A+ L    KL +I    + +F           G  +S R ++ L+
Sbjct: 257 KI--------AQCLSHAKKLMEIEPEKVAMFQMRGHAPWYIKGLKSSARVKNELS 303


>gi|225075968|ref|ZP_03719167.1| hypothetical protein NEIFLAOT_00993 [Neisseria flavescens
           NRL30031/H210]
 gi|224952683|gb|EEG33892.1| hypothetical protein NEIFLAOT_00993 [Neisseria flavescens
           NRL30031/H210]
          Length = 334

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 116/241 (48%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPSLRHTKKTLRRSDFEGEGGVVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +VG+ + A+  A+ +P
Sbjct: 76  PQQMAEAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVGEILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D+   +P +A     K  ++SG+  + IH   R  + KG           
Sbjct: 136 VTLKTRLGWHDEHQNLPTIA-----KIAEESGIAALAIHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A     +   +  
Sbjct: 181 ARYELIAETKG-RLNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWLFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|289663593|ref|ZP_06485174.1| hypothetical protein XcampvN_11094 [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 332

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDRRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVRAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPVIARIAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|229824537|ref|ZP_04450606.1| hypothetical protein GCWU000282_01881 [Catonella morbi ATCC 51271]
 gi|229785908|gb|EEP22022.1| hypothetical protein GCWU000282_01881 [Catonella morbi ATCC 51271]
          Length = 357

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 125/239 (52%), Gaps = 22/239 (9%)

Query: 21  LLYTEMIVADAI-LRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I  R DK  ++L     E PL++QI G +   LVEAAK V E+     I
Sbjct: 51  LVVCEMISDKGIQFRNDKTLSMLHIEPNEYPLSIQIMGGNKETLVEAAKYVAENTECAII 110

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+  PVTVK R G DD+    A+ 
Sbjct: 111 DINMGCPVNKVIKAEAGARWLLDPNKVYEMVAAVVDAVQKPVTVKMRTGWDDE-HLYAIE 169

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL-FIGLNGG 196
           N + + +++G + + +H R  + +    K N       +DI+ ++KKE   + F+G NG 
Sbjct: 170 NALAA-ERAGASMVAMHGRTRV-QMYEGKAN-------WDILAQVKKELKTIPFVG-NGD 219

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRVD 248
           +    +   +L +  VDGVM+GRAA  N  ++  +  Y         +T    I T +D
Sbjct: 220 VRTPEELKYLLDTTGVDGVMVGRAALGNPWVIQQMVHYVETGELLPAMTARQKIDTAID 278


>gi|310829340|ref|YP_003961697.1| tRNA-dihydrouridine synthase [Eubacterium limosum KIST612]
 gi|308741074|gb|ADO38734.1| tRNA-dihydrouridine synthase [Eubacterium limosum KIST612]
          Length = 324

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 124/249 (49%), Gaps = 21/249 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +T+  +R  A+     A+ ++EMI    +   DKK   ++    +E P  +Q+ G++
Sbjct: 18  MAGYTNLPFRLIAKRYGAGAV-FSEMISGKGLYYKDKKTAELMLTCDEEAPAGIQLFGSE 76

Query: 59  ---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +S++VE  K +    +  ++ N GCP+ ++ +   G+ LM NP+ +G  I A+ K  
Sbjct: 77  PEILSEVVE--KYINATAFAFLDFNAGCPAPKIVKNGEGSALMRNPERLGAVIRAIKKVS 134

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PV +K RIG D Q  +V +R + + ++++G +   IH R         +D       D
Sbjct: 135 EKPVIIKTRIGWDAQ--SVNVREVAEILEEAGADAHTIHGRT--------RDAFYSGKAD 184

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           + I+ E+KK N  + I LNG ++   +A++   +   D VMIGRA+  N  +   ++   
Sbjct: 185 WKIIEEVKK-NSRIPIILNGDIDSGEKAVQAFETTGCDAVMIGRASVGNPFIFREINHRL 243

Query: 234 SNPLTGSSP 242
           S   T   P
Sbjct: 244 STGETLPVP 252


>gi|81429207|ref|YP_396208.1| putative dihydrouridine synthetase [Lactobacillus sakei subsp.
           sakei 23K]
 gi|78610850|emb|CAI55902.1| Putative dihydrouridine synthetase [Lactobacillus sakei subsp.
           sakei 23K]
          Length = 328

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 124/239 (51%), Gaps = 23/239 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           T+  +R  A+      L+  EMI    I+  +KK +  +     E P+++QI G     L
Sbjct: 23  TNAAFRVTAKEF-GAGLVVCEMISDRGIMHNNKKTMGMMFVDPNEHPVSIQIFGGSKDTL 81

Query: 63  VEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           VEAAK V+     +I ++N+GCP  +V +   GA  +L+P+ V + ++ +  A+  PVTV
Sbjct: 82  VEAAKFVDQHTQADIIDINMGCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKKPVTV 141

Query: 122 KCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDI 178
           K R G D D I   A++N + + +++G + + +H   RK +  G +          D+DI
Sbjct: 142 KMRTGWDEDHI--FAVQNALAA-ERAGASALAMHGRTRKQMYTGKA----------DWDI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K E    F+G NG +     A ++L  V  D VMIGRAA  N  +L  V+ Y  +
Sbjct: 189 LKQVKAELKIPFMG-NGDVRTPQDAKRMLDEVGADAVMIGRAALGNPWILRQVETYLRS 246


>gi|217976714|ref|YP_002360861.1| TIM-barrel protein, nifR3 family [Methylocella silvestris BL2]
 gi|217502090|gb|ACK49499.1| TIM-barrel protein, nifR3 family [Methylocella silvestris BL2]
          Length = 327

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 112/227 (49%), Gaps = 16/227 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +L++TEM+ A+A  +GD +N L    +   P  +QI G D   +  AA+I  D G   ++
Sbjct: 35  SLVFTEMVAAEAYAKGDAENRLKAEGRGVDPHVVQIAGCDAQSMARAARIAADSGAAILD 94

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALR 137
           +N+GCP+ +V  G  G+ LM +  +  D I A  +A+ IPVT+K R+G D+  I A  L 
Sbjct: 95  INMGCPAKKVINGYSGSHLMRDLPLALDLIRATVRAVDIPVTLKMRLGWDEASINAAELG 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L ++    G+  + +H R         +        D+  +  + KE   + +  NG  
Sbjct: 155 RLAEA---EGIAMLTVHGRT--------RSQFYNGKADWRAIRAV-KEAVSIPVVANGDC 202

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             ++ A +++     D VMIGRAA     ++  + E  +  + G+ P
Sbjct: 203 ASLADAARMMDVSGADAVMIGRAAIGQPWLVGMIAERLATGVVGAEP 249


>gi|332982222|ref|YP_004463663.1| tRNA-U20-dihydrouridine synthase [Mahella australiensis 50-1 BON]
 gi|332699900|gb|AEE96841.1| tRNA-U20-dihydrouridine synthase [Mahella australiensis 50-1 BON]
          Length = 326

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 117/238 (49%), Gaps = 19/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R          L+ TEM+ A  +L   K +I   S++E+P+A+Q+ G +  
Sbjct: 20  MAGVTDMAFRILCHR-EGCGLVATEMVSAKGVLYNSKDDIWHVSSEERPVAIQLFGHEPD 78

Query: 61  KLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            + EAAKI+  +   + I++N+GCP A+V   S G  LM +  +    + A+  A+  PV
Sbjct: 79  VMAEAAKIICHNVFPDIIDINMGCPVAKVVNKSEGCALMRDIPLAFSIMKAVVNAVRQPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYD 177
           TVK R G D+Q   V    L  + + +G++ + +H   R+    G++          D+D
Sbjct: 139 TVKIRKGWDEQ--HVNAAELAVAAEHAGISAVTVHGRTREQFYTGIA----------DWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           I+  +K+      IG NG ++    A ++L     DGVMIGRAA  N  +      Y 
Sbjct: 187 IIGAVKQSVSIPVIG-NGDVKSPHDAKQMLEYTGCDGVMIGRAACGNPWVFKRTIHYL 243


>gi|157690863|ref|YP_001485325.1| dihydrouridine synthase [Bacillus pumilus SAFR-032]
 gi|157679621|gb|ABV60765.1| dihydrouridine synthase [Bacillus pumilus SAFR-032]
          Length = 333

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 120/230 (52%), Gaps = 22/230 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  + + +  L    +EKPL+LQI G +   LVEAAK V ++   + I
Sbjct: 37  LVCAEMVSDKAILINNARTMGMLYIDEREKPLSLQIFGGEKDTLVEAAKFVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  PVTVK R+G D D I A+  
Sbjct: 97  DINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVDAVDKPVTVKMRMGWDEDHIFAI-- 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +  ++++++G   + +H R  +   +G +          ++DI+ E+K+      IG N
Sbjct: 155 -DNARAVERAGGQAVALHGRTRVQMYEGTA----------NWDIIKEVKQSVSIPVIG-N 202

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           G ++    A ++L     D VMIGRAA  N  M+     Y         P
Sbjct: 203 GDVKTPQDAKRMLDETGADAVMIGRAALGNPWMIYRTVHYLETGELKEEP 252


>gi|288958350|ref|YP_003448691.1| tRNA-dihydrouridine synthase B [Azospirillum sp. B510]
 gi|288910658|dbj|BAI72147.1| tRNA-dihydrouridine synthase B [Azospirillum sp. B510]
          Length = 340

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 113/228 (49%), Gaps = 17/228 (7%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAK 67
           F RL+  +   L+ +EMI + A++R +++ +    T+  E P+A+Q+ G +   + EAAK
Sbjct: 39  FRRLVKRSGCGLVVSEMIASQAMIRENRQTLRMVETEPEEFPMAVQLAGCEPEVMAEAAK 98

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           + +D G   +++N GCP  +V  G  G+ LM +  + G  + A+ KA+SIPVT+K R+G 
Sbjct: 99  LNQDRGAAVVDINFGCPVKKVVNGHAGSSLMRDEALAGRILEAVVKAVSIPVTLKMRLGW 158

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D     +   +L +  ++ G+  + +H R  +               D+  V  + KE  
Sbjct: 159 DGT--RLNAPSLARIAEQCGIRMVTVHGRTRM--------QFYTGTADWTAVRAV-KEAV 207

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            + + +NG +       + L     DGVMIGR +Y      + V  Y 
Sbjct: 208 SIPVVVNGDVTSFDAVDRALSESGADGVMIGRGSYGRPWFPSQVMRYL 255


>gi|294793386|ref|ZP_06758531.1| tRNA-dihydrouridine synthase [Veillonella sp. 6_1_27]
 gi|294455817|gb|EFG24182.1| tRNA-dihydrouridine synthase [Veillonella sp. 6_1_27]
          Length = 328

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 138/297 (46%), Gaps = 25/297 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++   +
Sbjct: 26  SDIAYRLLAKK-HGAALVCTEMVSAMGIKYKNERTHELLRIEEAERPVSMQIFGSNPEAI 84

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +PVTVK
Sbjct: 85  ALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAVDVPVTVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  +  +
Sbjct: 145 MRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSYIKAV 194

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K+      +G NG + +   A ++L     D VMIGR A  N  +   +  Y +   TG 
Sbjct: 195 KEAVSVPVLG-NGDIVEPEDAKQMLDETGCDAVMIGRGAQGNPWIFDRIHHYLA---TGE 250

Query: 241 S-PIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             P  T +++ D   K    +  Y    +     +++I  H      G P S   R+
Sbjct: 251 VLPAPTDIERLDMLLKHFDLLCQYKGESM----AVKEIRTHAGWYMKGLPESAYWRN 303


>gi|205371966|ref|ZP_03224784.1| YacF [Bacillus coahuilensis m4-4]
          Length = 332

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/221 (32%), Positives = 113/221 (51%), Gaps = 18/221 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L+  EM+    I+  + K  N+L    +E PL+LQI G +   LVEAAK V+      I
Sbjct: 36  GLVCAEMVSDKGIVLQNAKTMNMLYIDEREYPLSLQIFGGEKETLVEAAKFVDKHSNAAI 95

Query: 78  -NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
            ++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  PVTVK R+G D D I AV 
Sbjct: 96  IDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVDKPVTVKMRMGWDEDHIYAV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
                + I+++G   + +H R  +               ++DI+ E+K+      IG NG
Sbjct: 155 --ENARMIERAGGQAVSLHGRTRV--------QMYEGEANWDIIREVKQSVGIPVIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++    A ++L     DGVMIGRAA  N  M+    +Y  
Sbjct: 204 DVQTPQDAKRMLDETGADGVMIGRAALGNPWMIYRTVKYLE 244


>gi|325915592|ref|ZP_08177900.1| tRNA-U20-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
 gi|325538152|gb|EGD09840.1| tRNA-U20-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
          Length = 354

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 115/242 (47%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 39  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+ +A+ +P
Sbjct: 98  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEALVARILRAVVQAVDVP 157

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D       +
Sbjct: 158 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGTAE 204

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + EIK     + +  NG ++   +A ++L    VD VMIGRAA     +   V  Y 
Sbjct: 205 YATIGEIKAAL-QIPVIANGDIDSPQKAAQVLRDTGVDAVMIGRAAQGRPWIFGEVAHYL 263

Query: 234 SN 235
           + 
Sbjct: 264 AT 265


>gi|330997166|ref|ZP_08321019.1| TIM-barrel protein, nifR3 family [Paraprevotella xylaniphila YIT
           11841]
 gi|329570961|gb|EGG52668.1| TIM-barrel protein, nifR3 family [Paraprevotella xylaniphila YIT
           11841]
          Length = 346

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 79/312 (25%), Positives = 142/312 (45%), Gaps = 34/312 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++Y+E + ADA++R   +++  L     E+P+A+QI G +
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYSEFVAADALVRMVNRSLEKLAVCDDERPVAIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+IV +    ++ +LN GCP  RV     GA ++ N   + +   A+  A+ I
Sbjct: 77  PGPVADAARIVVERARPDVLDLNFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ 
Sbjct: 137 PVTVKTRLGWDESSKVIV--DLAERLQDCGIRALTIHGRT--------RAQMYTGEADWT 186

Query: 178 IVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ E+K  NP + I +  NG +    +A +      VD VM+GRA +    +   + +  
Sbjct: 187 LIGEVKN-NPRMTIPIIGNGDITSPERARECFDRYGVDAVMVGRATFGRPWIFKEITDVL 245

Query: 234 SNPLTGSS---------PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-- 282
            NP + S+         P+ +    D+   +       + R +     +    RH+    
Sbjct: 246 -NPGSASAAHEAVKSGYPVMS---ADWKIDVLKEQVLTSVRRIDEYRGILHSRRHLAASP 301

Query: 283 LFHGFPNSRRCR 294
           +F G PN R  R
Sbjct: 302 VFKGIPNFRETR 313


>gi|5834292|gb|AAD53896.1|AF176314_6 NifR3-like protein [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 344

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 147/310 (47%), Gaps = 33/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 32  MTGVTDLPFRRIVRRY-GSGLNVTEMIASQAMIRETRQSLQKSTWDPYEEPISVQLVGCT 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E+AK+ +D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 91  PDDMAESAKLNQDRGAAIIDINMGCPVRKVVSGDAGSALMRDLKLAASIIEATVKAVSLP 150

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R+G D + + A  L  + + I   GV  + +H   R  + KG          + D
Sbjct: 151 VTLKMRMGWDLNSLNAPELARIAQDI---GVQMVTVHGRTRNQLYKG----------HAD 197

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V ++K     P +  G    L+D   AL+     DG+M+GR +Y    +L+ + +  
Sbjct: 198 WAFVRQVKDAVSIPVIVNGDINSLDDAKTALQ-QSGADGIMVGRGSYGKPWLLSQLMQGL 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLF-HGFPNS 290
           ++     +P    +D+ +      ++T++    L   G +    I R  IG +  G P S
Sbjct: 257 TDGEMEKAP---SIDEQY-----RTITEHYDHMLSYYGTITGVNIARKHIGWYTKGLPAS 308

Query: 291 RRCRHILTVE 300
              R+ +  E
Sbjct: 309 AEFRNKINRE 318


>gi|56552023|ref|YP_162862.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|56543597|gb|AAV89751.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ZM4]
          Length = 341

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 147/310 (47%), Gaps = 33/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 32  MTGVTDLPFRRIVRRY-GSGLNVTEMIASQAMIRETRQSLQKSTWDPYEEPISVQLVGCT 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E+AK+ +D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 91  PDDMAESAKLNQDRGAAIIDINMGCPVRKVVSGDAGSALMRDLKLAASIIEATVKAVSLP 150

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R+G D + + A  L  + + I   GV  + +H   R  + KG          + D
Sbjct: 151 VTLKMRMGWDLNSLNAPELARIAQDI---GVQMVTVHGRTRNQLYKG----------HAD 197

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V ++K     P +  G    L+D   AL+     DG+M+GR +Y    +L+ + +  
Sbjct: 198 WAFVRQVKDAVSIPVIVNGDINSLDDAKTALQ-QSGADGIMVGRGSYGKPWLLSQLMQGL 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLF-HGFPNS 290
           ++     +P    +D+ +      ++T++    L   G +    I R  IG +  G P S
Sbjct: 257 TDGEMEKAP---SIDEQY-----RTITEHYDHMLSYYGTITGVNIARKHIGWYTKGLPAS 308

Query: 291 RRCRHILTVE 300
              R+ +  E
Sbjct: 309 AEFRNKINRE 318


>gi|229586241|ref|YP_002844742.1| Putative dihydrouridine synthase Dus [Rickettsia africae ESF-5]
 gi|228021291|gb|ACP52999.1| Putative dihydrouridine synthase Dus [Rickettsia africae ESF-5]
          Length = 339

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 77/297 (25%), Positives = 134/297 (45%), Gaps = 26/297 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGADISK 61
           TD  +R   +      L+ +EM+ + A++   ++++   +          +Q+ G + + 
Sbjct: 30  TDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGCEPNV 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK+ E  G   I+LN GCP+ +V  G  G  LM +  +      A  +A+ +PVTV
Sbjct: 89  IAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGLVLMRDEQLAAKIFEATVEAVKLPVTV 148

Query: 122 KCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R+G DD    A  L  + +S+   GV  I +H R         +      N+D+D + 
Sbjct: 149 KMRMGWDDNTKNAPTLAKIAESL---GVQMITVHGR--------TRCQFYSGNVDWDFIR 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + KE+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y      
Sbjct: 198 SV-KESVKIQVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKTGEE 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCR 294
            S+P       D   +   ++ DY    +        I R  IG +  G PNS   R
Sbjct: 257 KSAP-SIAEQLDIVTEHYEAILDYYGESVGV-----PIARKHIGWYSSGLPNSAEFR 307


>gi|116053000|ref|YP_793318.1| hypothetical protein PA14_64180 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|296391685|ref|ZP_06881160.1| hypothetical protein PaerPAb_26189 [Pseudomonas aeruginosa PAb1]
 gi|115588221|gb|ABJ14236.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 332

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 121/238 (50%), Gaps = 18/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    V++  L    +++G+  + +H R         + +      +Y+
Sbjct: 139 VTLKIRTGWDRDNRNGVSVARLA---EQAGIQALAVHGRT--------RADLYTGEAEYE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            +  I K+   + +  NG ++   +A K++    VD ++IGRAA     +   +D Y 
Sbjct: 188 TIAAI-KQAVSIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYL 244


>gi|167771298|ref|ZP_02443351.1| hypothetical protein ANACOL_02656 [Anaerotruncus colihominis DSM
           17241]
 gi|167666549|gb|EDS10679.1| hypothetical protein ANACOL_02656 [Anaerotruncus colihominis DSM
           17241]
          Length = 324

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 115/235 (48%), Gaps = 18/235 (7%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           A +  EM  A  +   D+K   +LG +  E+P+A+Q+ G +   + EAAK    F  + I
Sbjct: 35  AYMVGEMASAKGMHYSDRKTARLLGVNDVERPVAVQLFGDEPEIVAEAAKKALAFCPDVI 94

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVAL 136
           ++N+GCP+ +V     GA LM N  +      A  KA+ +PVTVK R G DD  + AV  
Sbjct: 95  DINMGCPAPKVAGNGGGAALMKNVALAARITEATVKAVDLPVTVKFRKGWDDAHVNAV-- 152

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
               +++++SG   + +H R  +            P +D DI+  +K       IG NG 
Sbjct: 153 -EFARAMEQSGAAALTVHGRTRM--------QYYAPPVDLDIIAAVKAAVSIPVIG-NGD 202

Query: 197 LEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP-IKTRVD 248
             D+   + +      D VMIGR A  +  + + V  Y  + +T  +P ++TR+D
Sbjct: 203 CIDIQSVVNMYDYTKCDLVMIGRGALGSPWIFSQVARYLKDGVTLPTPNLQTRMD 257


>gi|115314770|ref|YP_763493.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|115129669|gb|ABI82856.1| probable tRNA-dihydrouridine synthase [Francisella tularensis
           subsp. holarctica OSU18]
          Length = 327

 Score = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 79/285 (27%), Positives = 140/285 (49%), Gaps = 32/285 (11%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           ++Y EM+   A++    +   +L     EKPL +QI   DI   V A K I E+   + +
Sbjct: 38  MIYMEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFSTDIDSFVGATKYIAENTECDFL 97

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
           ++N+GCP  +V +    GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I A+ 
Sbjct: 98  DINIGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNINAI- 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+ + +GV+ I IH R         ++       ++DI+ +++K    + IG NG
Sbjct: 157 --EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVIG-NG 205

Query: 196 GL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVD--K 249
            +     ++A+     VD VM+GRA+  N  +   + EY +    +   +P++ RVD  +
Sbjct: 206 DVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVE-RVDVLE 264

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  R++    T   A        +++I  H        PNS+  R
Sbjct: 265 EHLRRLIKLKTAKVA--------VKEIRTHASFYLQDLPNSKEFR 301


>gi|116071136|ref|ZP_01468405.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           BL107]
 gi|116066541|gb|EAU72298.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           BL107]
          Length = 338

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 76/320 (23%), Positives = 146/320 (45%), Gaps = 31/320 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG-FSTQEKPLALQIGGADISKLV 63
           TD+ +R   R  + ++LL+TEM+ A ++  G     +    +++ P+A+Q+       + 
Sbjct: 37  TDKIFRGLVRRWSRDSLLFTEMVNATSLELGHGYGKMDDLLSEDGPIAVQLFDHRPQAMA 96

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   +++N+GCP  ++ +   G+ L+ +PD+    + A+ +A+SIPVTVK 
Sbjct: 97  DAARRAEQAGAFLVDINMGCPVRKIAKKGGGSGLIRDPDLATQILEAVVEAVSIPVTVKT 156

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    +  P    R L    + +G   + +H R         ++       D++ +  
Sbjct: 157 RLGWCGSNSDPITWCRQL----QNAGAQMLTLHGRT--------REQGFKGQADWNAIAA 204

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN---P 236
           +K+      I  NG +   + AL+ L     DGVM+GR    +  ++  ++  F N   P
Sbjct: 205 VKQALTIPVIA-NGDINSPTDALQCLDVTGADGVMVGRGTMGSPWLVGQIEAAFMNRPIP 263

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  S  +  + K+    + +S   +          L    +HM     GFP + + RH 
Sbjct: 264 ATPDSGARLHLAKEQLHDLVSSRGSHG---------LLIARKHMSWTCTGFPGASQLRHA 314

Query: 297 LTVEAGASTATHHIIETAFN 316
           L + A      + +++ A N
Sbjct: 315 L-MRAPTPNDAYQLLDKAIN 333


>gi|86606306|ref|YP_475069.1| dihydrouridine synthase family protein [Synechococcus sp. JA-3-3Ab]
 gi|86554848|gb|ABC99806.1| dihydrouridine synthase family protein [Synechococcus sp. JA-3-3Ab]
          Length = 346

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 73/298 (24%), Positives = 134/298 (44%), Gaps = 24/298 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD+ +R   R     +L+YTEM+ A  +    +   I+     E+P+ +Q+       L 
Sbjct: 25  TDKVFRGLVRRFGPQSLVYTEMVNATGLHYARELPRIMEVGEGEQPIGIQLFDCRPHFLA 84

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA++  D G   +++N+GCP  ++     G+ L+  PD     + A+ KA+ +PVTVK 
Sbjct: 85  EAARMAVDEGATLVDINMGCPVNKITRNGGGSALLREPDTAARIVEAVAKAVPVPVTVKT 144

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G  DQ   + + +    ++++G   + +H R    +G S K         +D +  + 
Sbjct: 145 RLGWSDQ--EINILDFAHRLQEAGAQLLTLHGRTRA-QGFSGKAR-------WDWIRRV- 193

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           KE+  + +  NG +     A+K L     DGVM  R       ++  +D +     TG  
Sbjct: 194 KEHLRIPVIANGDIFSTDAAVKCLEETGADGVMCSRGTMGYPFLVGQIDHFLK---TGQE 250

Query: 242 -PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL 297
            P  T +D     +I  ++        + G + ++Q  +HM      F  + + R +L
Sbjct: 251 RPAPTPLD-----RIQMALEHLRGLWEYKGERGIRQARKHMTWYIKDFAGASQFRALL 303


>gi|256383848|gb|ACU78418.1| tRNA-dihydrouridine synthase B [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384679|gb|ACU79248.1| tRNA-dihydrouridine synthase B [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455465|gb|ADH21700.1| tRNA-dihydrouridine synthase B [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 324

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 115/220 (52%), Gaps = 17/220 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
           +L+Y EM+    ++  +KK  N+L  +  E P+++QI G D+ + ++A + +E +   + 
Sbjct: 35  SLVYAEMVSVAGMVHDNKKTLNMLNVNEIEHPMSMQIFGNDVDEFIKATQWIEKNVDCDI 94

Query: 77  INLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           I+LN+GCP+ +V      G+ L+  PD++ + +  + K  + PVT K R+G D    +V 
Sbjct: 95  IDLNLGCPAPKVAIRSQSGSALLKTPDLIYEIVKNVVKNTTKPVTAKIRLGWDKN--SVN 152

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K I+K+G + I +HAR         +++    + D++ + E+K+      IG NG
Sbjct: 153 AVEVAKLIEKAGASAIAVHAR--------TRNDFYTGHADWEKIKEVKQAVSIPVIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + D   A K+L     D VM+ RA   N  +   ++ Y 
Sbjct: 204 DVIDAKSAKKMLDETGCDAVMVSRACQGNPWIFDQINHYL 243


>gi|187777496|ref|ZP_02993969.1| hypothetical protein CLOSPO_01071 [Clostridium sporogenes ATCC
           15579]
 gi|187774424|gb|EDU38226.1| hypothetical protein CLOSPO_01071 [Clostridium sporogenes ATCC
           15579]
          Length = 323

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 80/320 (25%), Positives = 144/320 (45%), Gaps = 29/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+  G  +   +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYGSNNTTELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  A +I  D   N++   ++N+GCP+ ++ +   G+ LM +P +    I AM K  
Sbjct: 76  PDIMANAVEIFND--NNDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASQIIKAMKKVA 133

Query: 116 SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             P+TVK R G D + I AV      K +++SG + I IH R         ++       
Sbjct: 134 KKPITVKFRKGFDKNNINAV---EFAKIMEQSGADAITIHGR--------TREQMYEGKA 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+ I+ ++K       IG NG +     A++++   + DGVM+GR A  N  +   ++E 
Sbjct: 183 DWTIISKVKNAVSIPVIG-NGDVFSAEDAIEMINKTNCDGVMVGRGAQGNPWIFKQINEK 241

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      + R+D      I  +    A  +      ++++ +H+     G  N   
Sbjct: 242 IKGEHVYYPTSQERID------ICINHYKRALEYFEEHKAVREMRKHVAVYVKGLKNCTD 295

Query: 293 CRHILTVEAGASTATHHIIE 312
            +  + +E  +      +I+
Sbjct: 296 IKDKVNMEKDSHKVLEELIK 315


>gi|91217813|ref|ZP_01254768.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Psychroflexus torquis ATCC 700755]
 gi|91184014|gb|EAS70402.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Psychroflexus torquis ATCC 700755]
          Length = 330

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 78/309 (25%), Positives = 140/309 (45%), Gaps = 41/309 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE + ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEYGAD-MVYTEFVSSEGLIRDAAKSMQKLDIYERERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ + D++      M K   +P
Sbjct: 78  LDSMLRSVEIVEKTKPDVIDINFGCPVKKVVSKGAGAGILKDIDLMVKLTGEMVKHTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G D    ++ +  + + ++  G   I IH R    + KG            D+
Sbjct: 138 ITVKTRLGWDHD--SIKIYEVAERLQDVGCKAISIHGRTRAQMYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  NP + I +  NG +    +A  ++    +DG MIGR++  +      V  Y
Sbjct: 186 KPIAEVKN-NPRMHIPVFGNGDVNSPEKAALMRDEYGLDGAMIGRSSIGSPWFFKAVKHY 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLFH 285
           F        P  + V++           D A RHL       G KL   +  RH    F 
Sbjct: 245 FETGTHCEPP--SLVER----------VDIARRHLQMAIDWKGEKLGVFETRRHYTNYFK 292

Query: 286 GFPNSRRCR 294
           G P+ +  R
Sbjct: 293 GIPHFKDYR 301


>gi|291547778|emb|CBL20886.1| tRNA-U20-dihydrouridine synthase [Ruminococcus sp. SR1/5]
          Length = 324

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 113/228 (49%), Gaps = 16/228 (7%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       L+  EM+ A AI   +K    ++     E P+++Q+ G++   + E AK
Sbjct: 29  FRRLCKEQGAGLICMEMVSAKAISFHNKNTEALMEIDPGEHPVSMQLFGSEPDLMAEVAK 88

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            +E+  ++ +++N+GCP  +V     G+ L+ +P ++ + + ++  A+S PVTVK RIG 
Sbjct: 89  SIEERPFDILDINMGCPVPKVVNNGEGSALLKDPQLIEEIVRSVSGAVSKPVTVKVRIGF 148

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D+  P V +  + K ++ +G   I +H R         +        D+D +  +K+   
Sbjct: 149 DENTP-VDVVEIAKRVEDAGAAAIAVHGRT--------RQQYYSGQADWDAIRRVKEAVT 199

Query: 188 DLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              IG NG +   + ++A+      D VMIGRA   N  +   ++ YF
Sbjct: 200 IPVIG-NGDIVSPETAEAMFKETGCDAVMIGRAVRGNPWIFRELNHYF 246


>gi|305665851|ref|YP_003862138.1| putative TIM-barrel enzyme, putative dehydrogenase [Maribacter sp.
           HTCC2170]
 gi|88710622|gb|EAR02854.1| putative TIM-barrel enzyme, possible dehydrogenase [Maribacter sp.
           HTCC2170]
          Length = 332

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 142/308 (46%), Gaps = 39/308 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ + D++     AM +   +P
Sbjct: 78  LDSMLRSVEIVEASNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTKAMVEHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +  ++ +  + + ++  G   I IH R  +   +   +   +P      
Sbjct: 138 VTVKTRLGWDQE--SIKIVEVAERLQDVGCKAISIHGRTRV--QMYKGEANWVP------ 187

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  N  + I +  NG ++    A+++     +DG MIGRA+         V  YF 
Sbjct: 188 IAEVKN-NQRMHIPVFGNGDVDSPEAAMRMRDEFGLDGAMIGRASIGYPWFFNEVKHYFK 246

Query: 235 NPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLFHG 286
                + P ++ RV+              A RHL       G KL   +  RH    F G
Sbjct: 247 TGRHLAPPTMQERVEA-------------ARRHLQMAIDWKGEKLGVFETRRHYTNYFKG 293

Query: 287 FPNSRRCR 294
            PN +  R
Sbjct: 294 IPNFKEYR 301


>gi|253580949|ref|ZP_04858211.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847791|gb|EES75759.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 321

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 116/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+  EMI A AI   +K  I  +     E P+++Q+ G++
Sbjct: 21  MAGVTDLPFRTLCKE-QGAGLICMEMISAKAISFHNKNTIALMEIDPCEHPVSMQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  ++ +++N+GCP  +V     G+ L+ NP+++ + +  +  A+S P
Sbjct: 80  PDLMAEVAKSIEDRDFDILDINMGCPVPKVVNNGEGSALLKNPNLIEEIVRKVSSAISKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG +++   V +  + K I+ +G   + +H R         +        D+D 
Sbjct: 140 LTVKVRIGFENE--PVDIVEIAKRIEDAGAAALAVHGRT--------RQQYYSGTADWDT 189

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +K+      IG NG ++    ++AL      D VM+GRA   N  +   ++ YF
Sbjct: 190 IRRVKEAITIPVIG-NGDVDSPLKAEALVKQTGCDAVMVGRAVRGNPWLFRELNHYF 245


>gi|152986975|ref|YP_001350893.1| hypothetical protein PSPA7_5572 [Pseudomonas aeruginosa PA7]
 gi|150962133|gb|ABR84158.1| conserved hypothetical protein [Pseudomonas aeruginosa PA7]
          Length = 332

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 120/238 (50%), Gaps = 18/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    V +  L    +++G+  + +H R         + +      +Y+
Sbjct: 139 VTLKIRTGWDRDNRNGVTVARLA---EQAGIQALAVHGRT--------RADLYTGEAEYE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            +  I K+   + +  NG ++   +A K++    VD ++IGRAA     +   +D Y 
Sbjct: 188 TIAAI-KQAVSIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYL 244


>gi|20088934|ref|NP_615009.1| hypothetical protein MA0035 [Methanosarcina acetivorans C2A]
 gi|19913780|gb|AAM03489.1| conserved hypothetical protein [Methanosarcina acetivorans C2A]
          Length = 323

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/264 (29%), Positives = 128/264 (48%), Gaps = 25/264 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGF-STQEKPLALQIGGAD 58
           M D T+  +R   R      L YTEMI ADA+L   +K+ I G  S +++P  +Q+ G+ 
Sbjct: 22  MADVTNLAFRLLCRQ-DGADLAYTEMINADALLNESRKSFIKGLNSPEDRPFGVQLVGSC 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             KL EAA  VE+ +    I++N+GCP+  +     G+ L+ +P++V   I+ +  AL+ 
Sbjct: 81  PKKLREAALFVEEEYEPEVIDINMGCPAKCITGAGCGSALLNSPELVRKIISELADALNT 140

Query: 118 PVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNL 174
           PV+ K R +G +++   +A       I+K+G + + +H R A  +  G          N 
Sbjct: 141 PVSAKIRLLGKEEKTLEIACL-----IEKAGASALTVHGRTAAQMYSG----------NA 185

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +   +  +K E     I  NG ++D   A K L     DG+MIGRAA  N  +   +  Y
Sbjct: 186 NLMGIKAVKNELSIPVIA-NGDIKDEESAKKTLELTGCDGLMIGRAAMGNPFIFRRIRHY 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKIS 256
                      + R  +DF + IS
Sbjct: 245 LETGEKLEVERQARQLEDFEKYIS 268


>gi|15600045|ref|NP_253539.1| hypothetical protein PA4852 [Pseudomonas aeruginosa PAO1]
 gi|107103951|ref|ZP_01367869.1| hypothetical protein PaerPA_01005022 [Pseudomonas aeruginosa PACS2]
 gi|218893946|ref|YP_002442815.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
 gi|254238426|ref|ZP_04931749.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|254244250|ref|ZP_04937572.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|313109844|ref|ZP_07795778.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
 gi|38605049|sp|Q9HUW1|DUSB_PSEAE RecName: Full=tRNA-dihydrouridine synthase B
 gi|9951123|gb|AAG08237.1|AE004898_8 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|126170357|gb|EAZ55868.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|126197628|gb|EAZ61691.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|218774174|emb|CAW29991.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
 gi|310882280|gb|EFQ40874.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
          Length = 332

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 120/238 (50%), Gaps = 18/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    V +  L    +++G+  + +H R         + +      +Y+
Sbjct: 139 VTLKIRTGWDRDNRNGVTVAKLA---EQAGIQALAVHGRT--------RADLYTGEAEYE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            +  I K+   + +  NG ++   +A K++    VD ++IGRAA     +   +D Y 
Sbjct: 188 TIAAI-KQAVSIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYL 244


>gi|241759199|ref|ZP_04757306.1| NifR3 family protein [Neisseria flavescens SK114]
 gi|241320520|gb|EER56809.1| NifR3 family protein [Neisseria flavescens SK114]
          Length = 334

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 116/241 (48%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   + +QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPSLRHTKKTLRRSDFEGEGGVVVVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +VG+ + A+  A+ +P
Sbjct: 76  PQQMAEAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVGEILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D+   +P +A     K  ++SG+  + IH   R  + KG           
Sbjct: 136 VTLKTRLGWHDEHQNLPTIA-----KIAEESGIAALAIHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A+ +L   + DG+MIGR A     +   +  
Sbjct: 181 ARYELIAETKG-RLNIPVWVNGDITSPQKAVAVLKQTAADGIMIGRGAQGRPWLFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|163754515|ref|ZP_02161637.1| probable TIM-barrel protein, NifR3 family [Kordia algicida OT-1]
 gi|161325456|gb|EDP96783.1| probable TIM-barrel protein, NifR3 family [Kordia algicida OT-1]
          Length = 330

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 84/331 (25%), Positives = 151/331 (45%), Gaps = 42/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K+   L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSTMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LDSMLKSVEIVEKSGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+    + +  + + ++  G   I IH R    + KG            ++
Sbjct: 138 VTVKTRLGWDEN--TIKIVEVAERLQDVGCASIAIHGRTRAQMYKG----------EANW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             +  +K  NP + I +  NG ++   +A+ +     +DG MIGRA+         V  +
Sbjct: 186 HPIAAVKN-NPRMHIPVFGNGDVDSPEKAMLMRDKFGLDGAMIGRASIGYPWFFREVKHF 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLFH 285
           F    TG    K  +++    +I A     A RHL       G +L   +  RH    F 
Sbjct: 245 FE---TGEHMAKPTMEE----RIEA-----ARRHLQMSIDWKGERLGVFETRRHYTNYFK 292

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           G P+ +  R  L V    S     +++  + 
Sbjct: 293 GIPHFKEYRQRL-VTTDDSAGVFQVLDEVYE 322


>gi|49088166|gb|AAT51539.1| PA4852 [synthetic construct]
          Length = 333

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 120/238 (50%), Gaps = 18/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIHINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    V +  L    +++G+  + +H R         + +      +Y+
Sbjct: 139 VTLKIRTGWDRDNRNGVTVAKLA---EQAGIQALAVHGRT--------RADLYTGEAEYE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            +  IK+    + +  NG ++   +A K++    VD ++IGRAA     +   +D Y 
Sbjct: 188 TIAAIKQAV-SIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYL 244


>gi|116625730|ref|YP_827886.1| nifR3 family TIM-barrel protein [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116228892|gb|ABJ87601.1| putative TIM-barrel protein, nifR3 family [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 337

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/298 (27%), Positives = 140/298 (46%), Gaps = 28/298 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA---DAILRGDKKN-----ILGFSTQEKPLAL 52
           M   TD  +R F R L    L+ TE   +    A L+  K N      L F   E P++ 
Sbjct: 24  MAGVTDTVFRRFIRNLDGCGLIMTEFTSSHGVSAALKAKKPNKTMKRYLNFEPDEHPISA 83

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ GAD + + +AA++ +D G++ ++LN GCP  +V + + G+ L+ +  +V   + ++ 
Sbjct: 84  QLFGADPAVMADAARVCQDLGFDILDLNFGCPVNKVVKCNGGSGLLRDLPLVEKLLRSVR 143

Query: 113 KALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            A++IP T+K R G +D ++ AVA+  L +     G+  I +H R         ++    
Sbjct: 144 AAITIPFTMKFRAGWNDRELVAVAMAKLAED---CGLQAIALHPRT--------REQGYA 192

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+  + E+K       IG NG +     A++++   + D VMIGR A  N  +   +
Sbjct: 193 GKADWTRIAEVKAAVKIPVIG-NGDIVTPEDAVRMVRETNCDAVMIGRGASSNPWIFRQI 251

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-GLFHG 286
            +Y +   TG     T  D+    +    M   A R   + GK++Q   +   G+ HG
Sbjct: 252 QQYLA---TGRYDEPTHGDRYQMMRQYYDML-IARREDDAVGKMKQFATYFTHGVRHG 305


>gi|172037594|ref|YP_001804095.1| putative dihydrouridine synthase TIM-barrel protein nifR3
           [Cyanothece sp. ATCC 51142]
 gi|171699048|gb|ACB52029.1| putative dihydrouridine synthase TIM-barrel protein nifR3
           [Cyanothece sp. ATCC 51142]
          Length = 335

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 77/323 (23%), Positives = 146/323 (45%), Gaps = 31/323 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R  + N+++YTEM+ A  I    +   ++     E+P+++Q+       + 
Sbjct: 36  TDLVFRRLVRRYSPNSMMYTEMVSATEIHHLKQLPRLMEIDPHEQPISIQLFDCRPDFMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  + KA+ +PVTVK 
Sbjct: 96  EAAQKAVGEGAKTIDINMGCPVNKITKKGGGSSLLRQPEIAEKLVKEVVKAVDVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG DD    + +    + ++ SG + + +H R    +G + K         ++ + ++ 
Sbjct: 156 RIGWDDN--EINILEFAQKMQDSGASMLTLHGRTRA-QGYTGKAR-------WEWIKKV- 204

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           KE   + I  NG +  +  A+  L     DGVM  R       ++  +D +F      + 
Sbjct: 205 KEILTIPIIANGDIFSVEAAINCLEITGADGVMCSRGTLGYPFLVGEIDHFFQTGKLQNQ 264

Query: 242 PIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR----HI 296
           P  T +D+ +  ++    + DY  +       + Q  +H+     GFP +   R     I
Sbjct: 265 P--TPIDRLECAKEHLKGLWDYKGKR-----GIYQARKHLSWYCKGFPGASELRDKVSRI 317

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
            TVE G     + +++    L+I
Sbjct: 318 ETVEEG-----YQLLDQGIELII 335


>gi|288559354|ref|YP_003422840.1| tRNA-dihydrouridine synthase DusA1 [Methanobrevibacter ruminantium
           M1]
 gi|288542064|gb|ADC45948.1| tRNA-dihydrouridine synthase DusA1 [Methanobrevibacter ruminantium
           M1]
          Length = 329

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 120/237 (50%), Gaps = 22/237 (9%)

Query: 20  ALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNE 76
            L+ TEM+   A++ G+   K +L  +  E+P++ QI G+DI  L  A+K ++D    + 
Sbjct: 37  GLIETEMVSDKAVMYGNWKTKEMLYMTDYERPISQQIVGSDIESLTFASKYIQDNTNVDI 96

Query: 77  INLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAV 134
           I++N+GCP  +V + G  G+ L+ +PD +   + ++  ++ IPVT K R G D   I AV
Sbjct: 97  IDINMGCPVTKVTNRGKAGSALLKSPDKIKSIVESIVDSVDIPVTAKIRSGWDKSCINAV 156

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               + K I+ +G + I +H R         KD       D+ I+ ++K+      IG N
Sbjct: 157 ---EIAKIIEDAGASAITVHPR--------TKDQAYSGKADWSIIKKVKQSVNIPVIG-N 204

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
           G +     A ++L     D VMIGRAA  N  ++     Y  N   G  P++  +++
Sbjct: 205 GDVRTCFDAKRMLDETDCDAVMIGRAALGNPWLIRDCVNYLDN---GDLPMEVTIEE 258


>gi|299820638|ref|ZP_07052527.1| tRNA-dihydrouridine synthase [Listeria grayi DSM 20601]
 gi|299817659|gb|EFI84894.1| tRNA-dihydrouridine synthase [Listeria grayi DSM 20601]
          Length = 335

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/221 (33%), Positives = 115/221 (52%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 43  LVCCEMISDKGIAYRNTKTLDMLYIDEKEKPLSLQIFGGEKDTLVEAAKFVAENTTADII 102

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V + ++A+  A+  PVTVK RIG DD     A+ 
Sbjct: 103 DINMGCPVNKIIKCEAGAKWLLDPNKVYEMVSAVVDAVDKPVTVKMRIGWDDD-HIFAIE 161

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N   + +        +H R  +   +G          N D+D++ ++KKE    F+  NG
Sbjct: 162 NAQAAERAGAAAVA-MHGRTRVQMYEG----------NADWDVLRDVKKEIKIPFMA-NG 209

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++    A +IL   + DGVMIGRAA  N  M+    +Y  
Sbjct: 210 DVKTPEDAKRILEHTNADGVMIGRAALGNPWMIYRTVKYLE 250


>gi|20806861|ref|NP_622032.1| hypothetical protein TTE0344 [Thermoanaerobacter tengcongensis MB4]
 gi|20515331|gb|AAM23636.1| predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Thermoanaerobacter tengcongensis MB4]
          Length = 322

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/301 (26%), Positives = 136/301 (45%), Gaps = 26/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + +    L YTEM+ A  +  G +  K +L     EK +A+QI G+D
Sbjct: 17  MAGVTDKPFRLICQEM-GAGLTYTEMVSAKGLYYGSENTKALLDIDDGEK-VAIQIFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ + +     I++N+GCP+ ++ +   GA LML PD+    + A+ KA   P
Sbjct: 75  PEIMGEIARRLNESKALIIDINMGCPTPKIVKNGDGAALMLKPDLAEKVMEAVVKASYKP 134

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  D+ + AV +  + + +   G+  + +H R         ++       D++
Sbjct: 135 VTVKIRKGWNDNNVNAVEIAQIAERV---GIKAVAVHGRT--------REQFYSGKADWE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-S 234
           I+ ++K+      IG NG +     A ++L     D VMIGR A  N  +      Y  +
Sbjct: 184 IIKKVKESVKIPVIG-NGDIFTPEDAKRMLDETGCDAVMIGRGAQGNPWIFKRTVHYLKT 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             L     IK +V  D   +    M +Y          + ++ +H+     G P S R R
Sbjct: 243 GELLPEPTIKEKV--DLMIRHLTMMVEYKGERTG----VVEMRKHIAWYLKGLPGSARMR 296

Query: 295 H 295
            
Sbjct: 297 E 297


>gi|229917391|ref|YP_002886037.1| TIM-barrel protein, nifR3 family [Exiguobacterium sp. AT1b]
 gi|229468820|gb|ACQ70592.1| TIM-barrel protein, nifR3 family [Exiguobacterium sp. AT1b]
          Length = 331

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 117/243 (48%), Gaps = 20/243 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           T+  +R  A+      L+  EM+    IL  + + +  L    +EKPL+LQI G     L
Sbjct: 24  TNPAFRLIAKEF-GAGLVCAEMVSDKGILLENARTMRMLYVDEREKPLSLQIFGGSKDTL 82

Query: 63  VEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           V AA+ V ++   + I++N+GCP  +V +   GA  +L+PD V + + A+   +  PVTV
Sbjct: 83  VRAAQYVDQNTNADIIDINMGCPVPKVTKCDAGAKWLLDPDKVYEMVNAVTNVVEKPVTV 142

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD    + + + VK+ +  G   I IH R         +  +     ++D + E
Sbjct: 143 KMRLGWDDD--HIFILDNVKAAQTGGAAAIAIHGRT--------RAQQYEGTANWDWIGE 192

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            KK      IG NG +     A +++    VD VMIGRAA  N  ML    +Y     TG
Sbjct: 193 AKKVATVPIIG-NGDIATPQDAKRVIDQYGVDAVMIGRAALGNPWMLYQTVQYLE---TG 248

Query: 240 SSP 242
             P
Sbjct: 249 ELP 251


>gi|332184999|ref|ZP_08386748.1| TIM-barrel , nifR3 family protein [Sphingomonas sp. S17]
 gi|332014723|gb|EGI56779.1| TIM-barrel , nifR3 family protein [Sphingomonas sp. S17]
          Length = 333

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 117/239 (48%), Gaps = 24/239 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G    ++
Sbjct: 27  TDMPFRTLVRRY-GSGLNVTEMIASQAAIRATRQSIQKAAWHPLEEPVSMQLVGCTPYEM 85

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAK+  D G   I++N+GCP  +V  G  G+ LM +  +  + I A  KA+ +PVT+K
Sbjct: 86  GEAAKLNADRGAAIIDINMGCPVRKVVNGDAGSALMRDLKLASEIIRATVKAVDVPVTLK 145

Query: 123 CRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
            R+G   D + A  L  + + I   GV  I +H   R  + KG          + D+  +
Sbjct: 146 MRMGWCHDSLNAPELSRIAEDI---GVKMITVHGRTRNQMYKG----------SADWGFI 192

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             + KE   + +  NG    ++D   AL      DGVMIGR AY    +L  V  +F+ 
Sbjct: 193 RNV-KEAVSIPVIANGDICSIDDADTALD-QSGADGVMIGRGAYGRPWLLGQVMHWFAT 249


>gi|320105775|ref|YP_004181365.1| TIM-barrel protein, nifR3 family [Terriglobus saanensis SP1PR4]
 gi|319924296|gb|ADV81371.1| TIM-barrel protein, nifR3 family [Terriglobus saanensis SP1PR4]
          Length = 413

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 119/234 (50%), Gaps = 19/234 (8%)

Query: 21  LLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           L+ TE   AD + R     +K  L +   E P++ Q+ G++   L E+A+IV+D G++ +
Sbjct: 81  LIVTEFTSADGLARMRETKRKRYLTYYEDEHPISAQLFGSNPETLAESARIVQDAGFDMV 140

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP+ RV   + G+ L+ +  ++ +    +  +++IP TVK R+G +D+   +   
Sbjct: 141 DLNLGCPAKRVVSSNGGSGLLRDLPLIQNIFEKVRASVTIPFTVKFRMGWNDK--QIVCV 198

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K  ++SG+N + +HAR         +++       ++ +  +K       IG NG +
Sbjct: 199 ELAKMAQESGLNAVALHART--------REDGYSGEARWEWIAAVKDAVSIPVIG-NGDV 249

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
                A  ++     D VMIGRAA  N  +   + ++ +   TG+    T +D+
Sbjct: 250 RTPEDAAAMVEKTGCDAVMIGRAAPANPWIFRQIAQFTA---TGNYDRPTEMDR 300


>gi|148284888|ref|YP_001248978.1| putative tRNA-dihydrouridine synthase [Orientia tsutsugamushi str.
           Boryong]
 gi|146740327|emb|CAM80734.1| putative tRNA-dihydrouridine synthase [Orientia tsutsugamushi str.
           Boryong]
          Length = 322

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 80/321 (24%), Positives = 144/321 (44%), Gaps = 29/321 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA---LQIGGADISK 61
           TD  +R   +      L+ +EM+ + A+++  +++++  +  E  +    +Q+ G +   
Sbjct: 23  TDLPFRKLVKQF-GAGLVVSEMVASRAMIQETRRSMMKSAIIENDITGSCVQLAGCEPDV 81

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + +AAK+ +D G   I++N GCP+ +V  G  G+ LM +  +    +A   K++SIPVT+
Sbjct: 82  VADAAKMNQDMGAQIIDINFGCPAKKVVGGYAGSALMKDESLAAKILAETVKSVSIPVTL 141

Query: 122 KCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K R G D+     + RN   + K  +  G+  I +H R    +  S K        D+  
Sbjct: 142 KMRTGWDE-----SCRNAHIIAKIAEDCGIQMITVHGRTR-CQFYSGKS-------DWAF 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ KE+  + +  NG +  +  A+  L     DGVM+GR AY    +L+ +  Y +  
Sbjct: 189 IRKV-KESIKIPVVANGDITSVDDAIDCLRISGADGVMVGRGAYGKPWLLSQISHYLAFQ 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP      K       + ++ Y   H   G K+ +  +H+     G PNS   R  
Sbjct: 248 DYLPSPSLIEQKKIILNHYESMLSYYGTEH---GIKIAR--KHLGWYSKGLPNSTEFRSK 302

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +T           II   F L
Sbjct: 303 VTTITSVEQ-VQEIINQFFQL 322


>gi|85708679|ref|ZP_01039745.1| tRNA-dihydrouridine synthase [Erythrobacter sp. NAP1]
 gi|85690213|gb|EAQ30216.1| tRNA-dihydrouridine synthase [Erythrobacter sp. NAP1]
          Length = 340

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 125/254 (49%), Gaps = 25/254 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI ++A +R  ++++    +   E+P+++Q+ G D S +
Sbjct: 33  TDMPFRTLVRRY-GSGLNVTEMIASEAAIRETRQSVQKAEWDKTEEPVSMQLVGCDPSSM 91

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAK+ E  G   I++N GCP  +V     G+ LM    +    + A  KA+ +PVTVK
Sbjct: 92  GEAAKLQEGNGAAIIDINFGCPVRKVVGQFAGSALMREVPLATKLMEATVKAVDVPVTVK 151

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVY 180
            R+G D Q  ++    + +  +  GV  I +H   R  + KG          + D+  + 
Sbjct: 152 MRMGWDHQ--SLNAPEMARIAEDLGVKMITVHGRTRNQMYKG----------SADWSFIR 199

Query: 181 EIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           ++ KE  ++ + +NG    ++D + AL+     DG+MIGR AY    +L  V  ++    
Sbjct: 200 KV-KEAVNIPVIVNGDICTIQDAATALE-QSGADGLMIGRGAYGKPWLLGQVMHWWR--- 254

Query: 238 TGSSPIKTRVDKDF 251
           TG S      D+ +
Sbjct: 255 TGESIPTPSFDEQY 268


>gi|21241586|ref|NP_641168.1| hypothetical protein XAC0816 [Xanthomonas axonopodis pv. citri str.
           306]
 gi|38604925|sp|Q8PP72|DUSB_XANAC RecName: Full=tRNA-dihydrouridine synthase B
 gi|21106942|gb|AAM35704.1| conserved hypothetical protein [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 332

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 117/242 (48%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + ++V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEELVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARIAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|46447621|ref|YP_008986.1| hypothetical protein pc1987 [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46401262|emb|CAF24711.1| conserved hypothetical protein [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 297

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 45/133 (33%), Positives = 81/133 (60%), Gaps = 4/133 (3%)

Query: 26  MIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+  DA++R D    +IL ++    P+  Q+ G+  S   +AAKI+E+ G++ ++LN GC
Sbjct: 1   MVKMDALIRHDPHTYHILDYAANMHPIGGQLCGSKPSIAGQAAKIIEELGFDIVDLNCGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P  ++ +   G+ L+  P+++G+ +  M  A+ IPVTVK R G D+Q   + + N+V+ +
Sbjct: 61  PVDKITKDGSGSGLLKTPELIGEIVCNMVSAVKIPVTVKIRAGWDEQ--QIQVENIVQIV 118

Query: 144 KKSGVNGIWIHAR 156
           +++G   I IH R
Sbjct: 119 EQAGAQAICIHGR 131


>gi|331083389|ref|ZP_08332501.1| hypothetical protein HMPREF0992_01425 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330404082|gb|EGG83630.1| hypothetical protein HMPREF0992_01425 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 318

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/302 (24%), Positives = 145/302 (48%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A AI   +K  ++++    +E+P++LQ+ G++
Sbjct: 19  MAGVTDLPFRLLCKE-QGAGLICTEMVSAKAIHFKNKNTESLMEIDERERPVSLQLFGSE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E   ++ +++N+GCP  +V     G+ LM NP +V + +  + +A+  P
Sbjct: 78  PDLMAEIAKQIEHRNFDILDINMGCPVPKVVNNGEGSALMKNPKLVHEIVYKVSRAIKKP 137

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +TVK R G  +D + AV +  +++    + V       R+    G +          D+D
Sbjct: 138 LTVKIRKGFTEDSVNAVEIAKILEDAGAAAVAVH-GRTREQYYSGQA----------DWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A K++     DG+M+GRA   N  + + +  Y   
Sbjct: 187 IIRQVKEAVSIPIIG-NGDVTSPEKAEKLVKETGCDGIMLGRAVQGNPWLFSEILYYQET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    + K   R     + +Y  + +++G  ++++ +H+     G P+S   R 
Sbjct: 246 GKMKPKPSMEEIKKMMLRHAKLQL-EY--KGVYTG--MREMRKHVAWYTSGMPHSASVRR 300

Query: 296 IL 297
           ++
Sbjct: 301 MV 302


>gi|257439182|ref|ZP_05614937.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii A2-165]
 gi|257198315|gb|EEU96599.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii A2-165]
          Length = 340

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 114/236 (48%), Gaps = 20/236 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNI--LGFSTQEKPLALQIGG 56
           M  +TD   R   RL+  +   +T  EM+ + A++ GD K +  L       P  +QI G
Sbjct: 56  MAGFTDAPAR---RLMAQHGAGFTVSEMVSSRALVYGDHKTVSLLKAEPNGAPYGVQIFG 112

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + +AA  VE + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  + K  S
Sbjct: 113 EVPEIMGQAAAAVEQYAFDFLDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEEVVKNTS 172

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R G D +   V      K+ +++G   I +HAR         ++    P +D 
Sbjct: 173 RPVTVKMRKGWDAE--HVTAVECAKACEQAGAVLIAVHART--------REQMYTPGIDP 222

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
            I+  +K       +G NG +     A++++     DGVMI RAA  +  +   V+
Sbjct: 223 SIIAAVKDAVHVPVLG-NGDIRTAEDAVRMVEETGCDGVMIARAALGDPWLFERVN 277


>gi|83814729|ref|YP_446617.1| NifR3 family protein [Salinibacter ruber DSM 13855]
 gi|83756123|gb|ABC44236.1| NifR3 family enzyme [Salinibacter ruber DSM 13855]
          Length = 443

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/302 (24%), Positives = 142/302 (47%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE + +  +LR  +     L    +E+P+ +Q+ G  
Sbjct: 82  MEDVSDPPFRILCKRYGAD-MMYTEFVSSAGLLREQEHEHQKLEIFDEERPIGIQVWGGG 140

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I ++  A  +V+  G + I++N GCP  ++ +   GA ++ N D + +  AA+ +  + P
Sbjct: 141 IDEVRNATPMVDAAGPDVIDINFGCPVRKIVQKDGGAGVLRNLDKMRNITAAVMEEATRP 200

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD   ++ + ++ + ++  GV  + +HAR         ++ +   +  ++ 
Sbjct: 201 VTVKTRLGWDDD--SIHIVDVARMLEDMGVAALTVHART--------REQKYKGDARWEW 250

Query: 179 VYEIKKENP-DL-FIGLNGGLEDMS-QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+E   D+ FIG    L+  + +A+     VDGVM+GR A  N  +      Y   
Sbjct: 251 LRTIKEEGTRDMPFIGNGDALDPEAIEAMFEETGVDGVMLGRGALGNPWIFERAKTYME- 309

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG  P     ++    ++ A         L     + ++ ++    F GF N+   RH
Sbjct: 310 --TGELPPPPDWEERV--QVVAEHLSLKCEWLGERTGVMEMRKNYSSYFKGFRNASTLRH 365

Query: 296 IL 297
            L
Sbjct: 366 EL 367


>gi|284037281|ref|YP_003387211.1| hypothetical protein Slin_2392 [Spirosoma linguale DSM 74]
 gi|283816574|gb|ADB38412.1| TIM-barrel protein, nifR3 family [Spirosoma linguale DSM 74]
          Length = 329

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 86/330 (26%), Positives = 149/330 (45%), Gaps = 31/330 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A L+YTE I ++ ++R   K++  L     E+P+ +Q+ G+
Sbjct: 19  MEDVSDPPFRAVCK--ANGADLMYTEFISSEGLIRDAAKSVQKLDIFEYERPIGIQLFGS 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D+  + E A+I      + I++N GCP   V     GA L+ +   +     A+ KA  +
Sbjct: 77  DVETMGECARIASRANPDLIDINYGCPVKNVACRGAGAALLQDIPKMVRMTDAVVKATHL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLD 175
           PVTVK R+G D+    V    + + ++  G+  + +H R  +   KG +          D
Sbjct: 137 PVTVKTRLGWDESTKNVG--EVAERLQDIGIKALTVHGRTRVQMYKGEA----------D 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + ++  I K+NP + I +  NG ++   +A+  K    VDGVMIGRA+  +  +   +  
Sbjct: 185 WTLIGRI-KDNPRIQIPIFGNGDIDSPEKAVEYKNRFGVDGVMIGRASIGHPWVFNEIKH 243

Query: 232 YFSNPLTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +     TG   P  T  D+     +     D++ R       L ++ RH    F G P+ 
Sbjct: 244 FVQ---TGQHLPPPTVADR---VAVCRQHLDFSIRWKGEIVGLFEMRRHYANYFKGLPDF 297

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
           +  R  L      S  +  + E   N + E
Sbjct: 298 KPYRMRLVTTDSYSGVSDILAEIQENYITE 327


>gi|260584305|ref|ZP_05852052.1| zinc-binding TIM-barrel protein, nifR3 family [Granulicatella
           elegans ATCC 700633]
 gi|260157823|gb|EEW92892.1| zinc-binding TIM-barrel protein, nifR3 family [Granulicatella
           elegans ATCC 700633]
          Length = 339

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/219 (33%), Positives = 115/219 (52%), Gaps = 15/219 (6%)

Query: 21  LLYTEMIVADAI-LRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I  R +K  ++L     E PL++QI G +   LVEAAK V E+     I
Sbjct: 38  LVVCEMISDKGIQFRNEKTLSMLHIEPNEYPLSVQIMGGNKDTLVEAAKYVAENTEAAII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+  PVTVK R G DD+    A+ 
Sbjct: 98  DINMGCPVNKVIKAEAGAKWLLDPNKVYEMVAAVVDAVDKPVTVKMRTGWDDE-HLYAVE 156

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R  + +    K N       ++I+ E+KK    + +  NG +
Sbjct: 157 NALAA-ERAGASAVAMHGRTRV-QMYDGKAN-------WEILGEVKKNLTRIPLIGNGDV 207

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
                A K++    VDGVMIGRAA  N  M+     Y  
Sbjct: 208 RSPQDAKKMIEIAGVDGVMIGRAALANPWMIKQTVHYLE 246


>gi|257868307|ref|ZP_05647960.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257874420|ref|ZP_05654073.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|257877912|ref|ZP_05657565.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
 gi|257802421|gb|EEV31293.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257808584|gb|EEV37406.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|257812078|gb|EEV40898.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
          Length = 337

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 109/220 (49%), Gaps = 16/220 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK +  L     E PL++QI G + + LVEAA+ V E+   + I
Sbjct: 42  LVVCEMISDRGIQLRNKKTLEMLFIDETEHPLSIQIFGGNKASLVEAAQFVAENTTADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+PD V + + A+  A+  PVTVK RIG D+Q       
Sbjct: 102 DINMGCPVNKIIKAEAGAKWLLDPDKVYEMVHAVSSAIDKPVTVKMRIGWDEQHVFAVEN 161

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                   +   G+    R  + +G          + D+D++ ++K+     F+G NG +
Sbjct: 162 AQAAEAAGAAAIGMHGRTRVQMYEG----------SADWDVLKQVKQSITIPFMG-NGDV 210

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +    A ++L  V  D VMIGRAA  N  M+    +Y   
Sbjct: 211 KTPEDAKRMLEEVGADAVMIGRAALGNPWMIHRTKQYLET 250


>gi|256848391|ref|ZP_05553834.1| nifR3 family TIM-barrel protein [Lactobacillus coleohominis
           101-4-CHN]
 gi|256714989|gb|EEU29967.1| nifR3 family TIM-barrel protein [Lactobacillus coleohominis
           101-4-CHN]
          Length = 334

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 120/243 (49%), Gaps = 23/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST---QEKPLALQIGGA 57
           M   T++ +R   +       +  EMI    I+  +KK  L  +T    E P+ +QI G 
Sbjct: 19  MAGVTNKAFRVICKKF-GAGYVVCEMISDRGIMYHNKKT-LSMTTVDPHEHPMGIQIFGG 76

Query: 58  DISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               LVE AK ++     + I++N+GCP  +V     GA  +L+P+ V + ++ +  A+ 
Sbjct: 77  TKETLVEGAKFIDQHTAADVIDINMGCPVNKVVNTDAGARWLLDPNKVYEMVSYVVDAVQ 136

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNL 174
            PVTVK R G DD+    A+ N + + +++G + I +H   RK +  G          + 
Sbjct: 137 KPVTVKMRTGWDDK-HIFAVENALAA-ERAGASAIAMHGRTRKQMYTG----------HA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+DI+ E+  +    F+G NG ++    A ++L  V  D VMIGRAA  N  MLT  + Y
Sbjct: 185 DWDILKEVAGQLTIPFMG-NGDVKTPEDAKRMLDEVGADAVMIGRAAMGNPWMLTRTEHY 243

Query: 233 FSN 235
              
Sbjct: 244 LET 246


>gi|255281436|ref|ZP_05345991.1| tRNA-dihydrouridine synthase B [Bryantella formatexigens DSM 14469]
 gi|255267924|gb|EET61129.1| tRNA-dihydrouridine synthase B [Bryantella formatexigens DSM 14469]
          Length = 333

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 135/302 (44%), Gaps = 29/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    LL TEM+ A AI   +K  + ++     E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRLLCKEM-GAGLLCTEMVSAKAISFHNKNTERLMETGDGEHPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ +E+  ++ ++ N+GCP  +V     G+ LM NP +  + +     A+  P
Sbjct: 78  ADLICEVARQIEERPFDILDFNMGCPVPKVVNNGEGSALMKNPALAEEIVRKTAAAIKKP 137

Query: 119 VTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  DD + AV      K ++ +G   I +H R         +        D+D
Sbjct: 138 VTVKFRKGFDDDHVNAV---EFAKRMEAAGAAAIAVHGRT--------RAQYYAGRADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG ++    A K+      DG+MIGRAA  N  +   +  Y   
Sbjct: 187 IIRQVKEAVKIPVIG-NGDVDGPESARKMFAETGCDGIMIGRAARGNPWIFQELAAYDKG 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
                 P    V     R        +AA  +   G+   ++++ +H+     G+P+S  
Sbjct: 246 GSIPERPQPAEVKNMILR--------HAALQIQYKGEYTGIREMRKHVAWYTAGYPHSAA 297

Query: 293 CR 294
            R
Sbjct: 298 LR 299


>gi|325286202|ref|YP_004261992.1| TIM-barrel protein, nifR3 family [Cellulophaga lytica DSM 7489]
 gi|324321656|gb|ADY29121.1| TIM-barrel protein, nifR3 family [Cellulophaga lytica DSM 7489]
          Length = 330

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 80/310 (25%), Positives = 142/310 (45%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LDSMLRSVEIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVKLTDAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++  G   I IH R  +   KG          N D+
Sbjct: 138 VTVKTRLGWDTD--SIKIVEVAERLQDVGCAAIAIHGRTRVQMYKG----------NADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  N  + I +  NG ++    A+K+     +DG MIGRA+         V  +
Sbjct: 186 KPIAQVKN-NQRMHIPVFGNGDVDSPEAAVKMRDEYGLDGAMIGRASIGYPWFFNEVKHF 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGLF 284
                  + P ++ RV+              A RHL       G KL   +  RH    F
Sbjct: 245 IKTGEHKAPPTMQERVEA-------------ARRHLQMAIDWKGEKLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G P+ ++ R
Sbjct: 292 KGIPDFKQYR 301


>gi|294508555|ref|YP_003572614.1| tRNA-dihydrouridine synthase B [Salinibacter ruber M8]
 gi|294344884|emb|CBH25662.1| tRNA-dihydrouridine synthase B [Salinibacter ruber M8]
          Length = 492

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/302 (24%), Positives = 143/302 (47%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE + +  +LR  +     L    +E+P+ +Q+ G  
Sbjct: 131 MEDVSDPPFRILCKRYGAD-MMYTEFVSSAGLLREQEHEHQKLEIFDEERPIGIQVWGGG 189

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I ++  A  +V+  G + I++N GCP  ++ +   GA ++ N D + +  AA+ +  + P
Sbjct: 190 IDEVRNATPMVDAAGPDVIDINFGCPVRKIVQKDGGAGVLRNLDKMRNITAAVMEEATRP 249

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD   ++ + ++ + ++  GV  + +HAR         ++ +   +  ++ 
Sbjct: 250 VTVKTRLGWDDD--SIHIVDVARMLEDMGVAALTVHART--------REQKYKGDARWEW 299

Query: 179 VYEIKKENP-DL-FIGLNGGLEDMS-QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+E   D+ FIG    L+  + +A+     VDGVM+GR A  N  +     +Y   
Sbjct: 300 LRTIKEEGTRDMPFIGNGDALDPEAIEAMFEETGVDGVMLGRGALGNPWIFERAKKYME- 358

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG  P     ++    ++ A         L     + ++ ++    F GF N+   RH
Sbjct: 359 --TGELPPPPDWEERV--QVVAEHLSLKCEWLGERTGVMEMRKNYSSYFKGFRNASTLRH 414

Query: 296 IL 297
            L
Sbjct: 415 EL 416


>gi|298715097|emb|CBJ27785.1| dihydrouridine synthase [Ectocarpus siliculosus]
          Length = 450

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 115/235 (48%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIG 55
           MV+ ++  +R+  R     L    +L+ E    D   +  ++   G   +E +PL +Q  
Sbjct: 101 MVEQSEAAFRYLVRRHGCGLAYTQMLHAEKFAPDNAEKFRRRRFDGVDDEEDRPLIVQFC 160

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +   +V AA+ VE    + ++LN+GCP     +G++GA L+ NP +  D +AAM + L
Sbjct: 161 GNNPDTVVRAARHVE-HRCDAVDLNLGCPQKIAKKGNYGAYLLPNPQLCEDIVAAMSREL 219

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S+PVTVK R   D +   +   +L + ++ +G   + +H R             K    D
Sbjct: 220 SVPVTVKIR-AQDRESDTL---DLARRLEGAGAQLLTVHGRTV------SSQKTKQGAAD 269

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
           +DI+ ++ KE  D+ +  NGG+E  + A ++L     D VM      +N A+  +
Sbjct: 270 WDIIRKV-KEVVDIPVVANGGIETGADAERLLEETGADAVMSSEGLLENPALFDS 323


>gi|325568181|ref|ZP_08144622.1| tRNA-dihydrouridine synthase [Enterococcus casseliflavus ATCC
           12755]
 gi|325158382|gb|EGC70533.1| tRNA-dihydrouridine synthase [Enterococcus casseliflavus ATCC
           12755]
          Length = 337

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 108/220 (49%), Gaps = 16/220 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK +  L     E PL++QI G + + LVEAA+ V E+   + I
Sbjct: 42  LVVCEMISDRGIQLRNKKTLEMLFIDETEHPLSIQIFGGNKASLVEAAQFVAENTTADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+PD V + + A+  A+  PVTVK RIG D+Q       
Sbjct: 102 DINMGCPVNKIIKAEAGAKWLLDPDKVYEMVHAVSSAIDKPVTVKMRIGWDEQHVFAVEN 161

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                   +   G+    R  + +G          + D+D++ ++K+     F+G NG +
Sbjct: 162 AQAAEAAGAAAIGMHGRTRVQMYEG----------SADWDVLKQVKQSITIPFMG-NGDV 210

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
                A ++L  V  D VMIGRAA  N  M+    +Y   
Sbjct: 211 RTPEDAKRMLEEVGADAVMIGRAALGNPWMIHRTKQYLET 250


>gi|291166185|gb|EFE28231.1| TIM-barrel protein, NifR3 family [Filifactor alocis ATCC 35896]
          Length = 319

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 137/302 (45%), Gaps = 34/302 (11%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEI 77
           L YTEMI A A+  GD+    ++     E  +A+QI G +   + EA + +E    +  I
Sbjct: 36  LTYTEMINAKALCYGDENTWKMMQVHPDEGDVAIQIFGNEPEFIAEAVRKIEQLSRFVLI 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVAL 136
           ++N+GCP+ +V +   G+ LM  P++    +    +   +PVTVK R G D  Q+ A+  
Sbjct: 96  DINMGCPAPKVVKNGDGSALMKKPELAQKIVETAKQNTILPVTVKFRKGWDSTQVNAL-- 153

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL- 193
               K ++++G + + +H   R+    G++          D++IV EIKK    L+I + 
Sbjct: 154 -EFAKQMQEAGADAVTVHGRTREEFYSGVA----------DWNIVKEIKKA---LYIPVI 199

Query: 194 -NGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG ++D    +    L SVD VMIGR A  N         +  N L  + P K  V   
Sbjct: 200 GNGDIKDQETFEERVKLSSVDAVMIGRGAQGNP--------FLFNSLVRNGPKKENVPFQ 251

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
               I     +  A +      ++++ +H+     G P + + R+ +       TA   +
Sbjct: 252 EIYDIVKEHYELEAEYKGIDKAVREMRKHIGWYIKGLPMAAKVRNEINQTTDIQTAQKLL 311

Query: 311 IE 312
            E
Sbjct: 312 TE 313


>gi|330444003|ref|YP_004376989.1| putative TIM-barrel protein, nifR3 family [Chlamydophila pecorum
           E58]
 gi|328807113|gb|AEB41286.1| putative TIM-barrel protein, nifR3 family [Chlamydophila pecorum
           E58]
          Length = 327

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/287 (21%), Positives = 131/287 (45%), Gaps = 19/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  ++D  YR  + L    AL++ EM+  + +L   ++   +L +S + +P+  Q+  ++
Sbjct: 21  LAGFSDYPYRRMSALYAP-ALMFCEMVKVEGLLYSPQRTMKLLEYSEEMRPIGGQLCCSN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AKI+ED G++ I+LN GCP+ ++ +   G+ L+  P ++G  +  +   +S+P
Sbjct: 80  PEIVGEGAKILEDLGFDLIDLNCGCPTDKITKDGSGSGLLKTPSLIGVLVEKIVNTVSVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D +   + +  +VK ++++G + +++H R        P +   I       
Sbjct: 140 VTVKIRSGWDSE--HINVEEIVKILREAGASAVFVHGRTRAQGYHGPSNREYIARAKV-- 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              +  E   +F   NG +     A ++  +  DG+++ R       +   ++EY +   
Sbjct: 196 ---VAGEAFPVF--GNGDIFSPEAAKEMFATGCDGLLVARGTMGAPWIGKQIEEYLTTGS 250

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               P   R      ++       +   +  S  K    TR + G +
Sbjct: 251 YQPVPFTMR------KQAFVQHLQWVEEYYQSEAKFLSETRKLCGHY 291


>gi|269797571|ref|YP_003311471.1| hypothetical protein Vpar_0508 [Veillonella parvula DSM 2008]
 gi|269094200|gb|ACZ24191.1| TIM-barrel protein, nifR3 family [Veillonella parvula DSM 2008]
          Length = 328

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 86/326 (26%), Positives = 154/326 (47%), Gaps = 34/326 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++   +
Sbjct: 26  SDIAYRLLAKE-HGAALVCTEMVSAMGIKYKNERTHELLRIEDVERPVSMQIFGSNPEAI 84

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V + G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +PVTVK
Sbjct: 85  ALGAKVVANAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAVDVPVTVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  +  +
Sbjct: 145 MRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSYIKAV 194

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LT 238
           K+      +G NG + +   A ++L     D VM+GR A  N  +   +  Y +    L 
Sbjct: 195 KEAVSVPVLG-NGDIVEPEDAKQMLDETGCDAVMVGRGAQGNPWIFGRIHHYLATGEVLP 253

Query: 239 GSSPIKTRVD---KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           G + I+ R+D   K F         D   ++   G  +++I  H      G P S   R+
Sbjct: 254 GPTDIE-RLDMLLKHF---------DLLCQYKGEGMAVKEIRTHAGWYMKGLPESAYWRN 303

Query: 296 -ILTVEAGASTATHHIIETAFNLMIE 320
            + T++    T+ H+ +E+   ++ E
Sbjct: 304 RVNTIQ--TVTSFHNELESYRKILSE 327


>gi|307942245|ref|ZP_07657596.1| tRNA-dihydrouridine synthase B [Roseibium sp. TrichSKD4]
 gi|307774531|gb|EFO33741.1| tRNA-dihydrouridine synthase B [Roseibium sp. TrichSKD4]
          Length = 354

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 115/244 (47%), Gaps = 21/244 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLV 63
           TD  +R FA       ++ +EM+ +++ ++GD +  +    Q   L  +Q+ G +   + 
Sbjct: 41  TDLPFRRFAARY-GAGMVVSEMVASESFVKGDAETQMRAEAQNNGLHVVQLAGREARWMG 99

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK + D G + I++N+GCP+ +V  G  G+ LM + D     I A  +A+ +PVT+K 
Sbjct: 100 EAAKTIADLGADIIDINMGCPAKKVTSGYSGSALMRDLDHALTLIEATVEAVDVPVTLKM 159

Query: 124 RIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVY 180
           R+G D D I A     L +  + +G+  I +H   R    KG +          D+  + 
Sbjct: 160 RLGWDHDSINAP---ELARRAENAGIQLITVHGRTRNQFYKGTA----------DWSAIA 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+E     I  NG  +    A ++L     D VMIGR AY    +   +  Y  + + 
Sbjct: 207 AVKQEISVPLIA-NGDCQSYDDASEMLARSGADAVMIGRGAYGRPWLPGHIGTYLKSGIR 265

Query: 239 GSSP 242
              P
Sbjct: 266 TPQP 269


>gi|78484786|ref|YP_390711.1| dihydrouridine synthase TIM-barrel protein nifR3 [Thiomicrospira
           crunogena XCL-2]
 gi|78363072|gb|ABB41037.1| Dihydrouridine synthase [Thiomicrospira crunogena XCL-2]
          Length = 320

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 113/224 (50%), Gaps = 18/224 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M   TDR YR   R  +  +   +EM+ +   LR   K+    +  T+  P  +Q+ G  
Sbjct: 17  MAGITDRVYRDICRE-SGASYAVSEMVASKKQLRESAKSSTRHADKTETSPRIVQLLGTH 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +LV+AA   +  G + I+LN+GCP+ +V + + G+ LM  P+ V D   ++ +A+ +P
Sbjct: 76  PEELVDAALWQQSQGADIIDLNMGCPAKKVCDVAAGSALMGQPERVADIFKSLTEAIDLP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D D I AV +  L + +   G+  I IH R         + ++     +YD
Sbjct: 136 VTVKIRTGTDVDNINAVEIAKLAQEL---GLKAITIHGRT--------RADKFNGQAEYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
            +  + K+  D+ +  NG +    +A  +L     DG+MIGRAA
Sbjct: 185 TIKAV-KQAVDIPVIANGDICSPKEAQFVLKYTGSDGIMIGRAA 227


>gi|166710692|ref|ZP_02241899.1| hypothetical protein Xoryp_04310 [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 328

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 116/242 (47%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + ++V   + A+ +A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEELVARILTAVVQAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARLAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-RIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|163746230|ref|ZP_02153588.1| tRNA-dihydrouridine synthase [Oceanibulbus indolifex HEL-45]
 gi|161380115|gb|EDQ04526.1| tRNA-dihydrouridine synthase [Oceanibulbus indolifex HEL-45]
          Length = 330

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 115/237 (48%), Gaps = 24/237 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  YR   AR      L+ +EM+ +  +L  R   +            ++Q+ G 
Sbjct: 17  MAGITDLPYRSLVARF--GAGLVVSEMVASQELLSRRPGTREKAELGLDVIGTSVQLAGR 74

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAA++VE  G   I++N+GCP+ +V +G+ G+ LM  PD     I A+  A+++
Sbjct: 75  EAEPMAEAARMVEAMGARIIDINMGCPAKKVTQGASGSALMKTPDHALRLIEAVVGAVNV 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           PVT+K R+G DD +   A   + K  + +GV  I IH R      KG +          D
Sbjct: 135 PVTLKTRLGWDDNMLNAA--PIAKRAEDAGVQMITIHGRTRCQFYKGRA----------D 182

Query: 176 YDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           +  +  + KE  ++ +  NG   G ++  QALK L   DGVM+GR A     +L  +
Sbjct: 183 WAAIRAV-KETVNVPVIANGDIIGSDEARQALK-LSGADGVMVGRGAQGRPWLLAQI 237


>gi|192361714|ref|YP_001983204.1| tRNA-dihydrouridine synthase [Cellvibrio japonicus Ueda107]
 gi|190687879|gb|ACE85557.1| tRNA-dihydrouridine synthase [Cellvibrio japonicus Ueda107]
          Length = 329

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/251 (26%), Positives = 122/251 (48%), Gaps = 16/251 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ AD+ L   +K+ L    + + +P+A+QI G D
Sbjct: 18  MAGVTDRPFRQLCREL-GAGMVVSEMLTADSTLWSSRKSSLRMDHTGEAEPIAVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++    G   I++N+GCP+ +V + + G+ L+ +  +V   + A+ KA+ +P
Sbjct: 77  PEMLAEAARLNAANGAQIIDINMGCPAKKVCKKAAGSALLQDEPLVASILEAVVKAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   ++   ALR + +  + SG+  + +H R         + +    + +YD 
Sbjct: 137 VTLKFRTGWSSEVRN-ALR-IARIAEDSGIQALALHGRT--------RADGFAGSAEYDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +    + +  NG +    +A  +L       VMIGRAA     +   ++ Y    
Sbjct: 187 IASVVQAV-KIPVFANGDIASPEKAKAVLQHTGAAAVMIGRAAQGRPWIFREIEHYLRTG 245

Query: 237 LTGSSPIKTRV 247
                P  T+V
Sbjct: 246 EQLPEPPLTQV 256


>gi|58583410|ref|YP_202426.1| hypothetical protein XOO3787 [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84625224|ref|YP_452596.1| hypothetical protein XOO_3567 [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188575339|ref|YP_001912268.1| tRNA-dihydrouridine synthase B [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|58428004|gb|AAW77041.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84369164|dbj|BAE70322.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188519791|gb|ACD57736.1| tRNA-dihydrouridine synthase B [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 332

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 116/242 (47%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + ++V   + A+ +A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEELVARILTAVVQAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D     + +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPTIARLAQDCGIAALAVHGRT--------RDQHYTGSAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + 
Sbjct: 183 YATIAQIKAAL-RIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|114327892|ref|YP_745049.1| tRNA-dihydrouridine synthase [Granulibacter bethesdensis CGDNIH1]
 gi|114316066|gb|ABI62126.1| tRNA-dihydrouridine synthase [Granulibacter bethesdensis CGDNIH1]
          Length = 370

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 113/239 (47%), Gaps = 20/239 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-----LGFSTQEKPLALQIGGADI 59
           TD  +R  AR +    ++ +EMI + A++R +K  +      G  +   P ALQ+ G D 
Sbjct: 52  TDLPFRMLAREM-GTGMVVSEMIASWAMVRENKTTLRMAEPAGPPSPGSPNALQLAGCDP 110

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EAA+I  D G   I++N GCP  +V  G S G+ LM +       + A  KA+S+P
Sbjct: 111 EAMAEAARIAIDKGAELIDINFGCPVKKVAVGQSAGSALMRDEVTAAKILEATVKAVSVP 170

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D Q  ++    L K  + SG+  I +H R         +        D+  
Sbjct: 171 VTLKMRMGWDHQ--SLNAPALAKIAEASGIRMITVHGRT--------RQQFYEGKADWAF 220

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V  +K+    L + +NG ++ + QA   + +   DGVM+GR  Y        V  Y  +
Sbjct: 221 VARVKQAT-SLPVIVNGDIQTVEQAAEARAISGADGVMVGRGCYGRPWFPRQVAAYLRD 278


>gi|225569858|ref|ZP_03778883.1| hypothetical protein CLOHYLEM_05952 [Clostridium hylemonae DSM
           15053]
 gi|225161328|gb|EEG73947.1| hypothetical protein CLOHYLEM_05952 [Clostridium hylemonae DSM
           15053]
          Length = 320

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/306 (26%), Positives = 141/306 (46%), Gaps = 22/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A A+   +K  K +L    +E P++LQ+ G+D
Sbjct: 18  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKALQYNNKNTKLLLAIHPEEYPVSLQLFGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK +E+  +  +++N+GCP  +V     G+ LM +P ++ D +    KA+  P
Sbjct: 77  PRIMSEAAKRIEELPFQILDINMGCPVPKVVRNGEGSALMKDPGLIYDIVHETVKAIDKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+         V +++ + V  I      A+      ++       D+DI
Sbjct: 137 VTVKIRKGFDDE--------HVNAVEAARV--IEEAGAAAVAVHGRTREQYYAGKADWDI 186

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+      IG NG +     S A++     D VMIGRAA  N  +   +  Y ++ 
Sbjct: 187 IRKVKEAVSIPVIG-NGDVVSGPSSAAMQEQTGCDMVMIGRAAQGNPWIFRELRAYAADG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-H 295
                P +  V +   +     M +Y   +L     ++++ +H+     G   + + R  
Sbjct: 246 TVLPRPAEAEVRQTMLKHAKMQM-EYKGEYLG----IREMRKHVAWYTKGLKGASKLRAQ 300

Query: 296 ILTVEA 301
           I +VE+
Sbjct: 301 INSVES 306


>gi|1171716|sp|P45672|DUS_AZOBR RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|599600|emb|CAA86063.1| nifR3-like protein [Azospirillum brasilense]
          Length = 328

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 111/228 (48%), Gaps = 17/228 (7%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL+  +   L+ +EM+ + A++R +++ +  +    ++ P+A+Q+ G +   + EAAK
Sbjct: 27  FRRLVKQSGCGLVVSEMVASQAMIRENRQTLRMVECEPEQFPMAVQLAGCEPDVMAEAAK 86

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           + ED G   I++N GCP  +V  G  G+ LM +  +    + A  KA++IPVT+K R G 
Sbjct: 87  LNEDRGAAIIDINFGCPVKKVVNGHAGSSLMRDEALAARILEATAKAVTIPVTLKMRKGW 146

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD   ++    L +  ++ G+  + +H R         ++       D+  +  + KE  
Sbjct: 147 DDS--SLNAPRLARIAEECGIKLVTVHGRT--------REQFYNGTADWSFIRSV-KEAV 195

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            + + +NG +       + L     DGVMIGR AY        V  Y 
Sbjct: 196 SIPVVVNGDITSFDAVDRALAESGADGVMIGRGAYGRPWFPAQVMHYI 243


>gi|94500040|ref|ZP_01306575.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Oceanobacter sp.
           RED65]
 gi|94427898|gb|EAT12873.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Oceanobacter sp.
           RED65]
          Length = 328

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 122/250 (48%), Gaps = 24/250 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+   L  + + +P+++QI G D
Sbjct: 18  MAGVTDRPFRQLCRQL-GAGLVVSEMVTSDVKLWNSRKSRQRLDHAGEAEPISVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +    G   I++N+GCP+ +V   + G+ LM +  +V D + A+  ++ IP
Sbjct: 77  PEMMAQAAIMSAAHGAQIIDINMGCPAKKVCNKAAGSALMKDEVLVRDILQAVVDSVDIP 136

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G   +   A  L  + + I   G+  + IH   R    KG           ++
Sbjct: 137 VTLKMRTGWAPEHKNAPVLAGMAEEI---GIAALAIHGRTRSCGYKG----------EVE 183

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+N ++ +  NG + +  QA  +L     DGVM+GRAA     +   ++ + 
Sbjct: 184 YDTIKTI-KQNVNIPVLANGDITNAEQAKFVLDYTGADGVMLGRAAQGRPWIFREINHFL 242

Query: 234 S--NPLTGSS 241
           +   PL   S
Sbjct: 243 TTGEPLAAPS 252


>gi|291287718|ref|YP_003504534.1| dihydrouridine synthase DuS [Denitrovibrio acetiphilus DSM 12809]
 gi|290884878|gb|ADD68578.1| dihydrouridine synthase DuS [Denitrovibrio acetiphilus DSM 12809]
          Length = 340

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/297 (25%), Positives = 140/297 (47%), Gaps = 34/297 (11%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK 67
           F +LL    + L+YTEM+  + + R   + +  L  +  ++P+ +Q+ G+      EA +
Sbjct: 33  FRKLLRKYFDGLIYTEMVSVEGVRRKADRTLSYLSITESDQPIGVQLFGSKPEAYTEAIE 92

Query: 68  IVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRI 125
           +V+D+   E +++N+GCP  +V +   G  +M +P   G  +AA  KAL  +P+TVK R+
Sbjct: 93  VVQDYIKAEFVDINMGCPVKKVLKSGSGCAMMKDPVNSGKIVAAAKKALGDVPLTVKIRL 152

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIK 183
           G D +   +    ++K   + G   + +H R    +  G+          ++YD++ +  
Sbjct: 153 GWDKK--NLNYNEMIKIAYEEGAEAVTVHGRTKTEMFSGV----------VNYDLIAD-A 199

Query: 184 KENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           K N  L I  NG + D++   K+L + VDGVMIGR   K   +       F + L G  P
Sbjct: 200 KANAKLPIIGNGDVVDVATYEKMLATGVDGVMIGRGMMKQPWL-------FESILNGRDP 252

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                    +  I   + +     ++ G    L+ + ++++    G P +   R+ L
Sbjct: 253 SGYMTYDKLYELIKELVRN---EKIYKGEMFFLETVKKYIVWFLKGMPGAAALRNKL 306


>gi|331703079|ref|YP_004399766.1| hypothetical protein MLC_0590 [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328801634|emb|CBW53787.1| Conserved hypothetical protein, probable tRNA dihydrouridine
           synthase (NifR3 family) [Mycoplasma mycoides subsp.
           capri LC str. 95010]
          Length = 324

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 115/220 (52%), Gaps = 17/220 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
           +L+Y EM+    ++  +KK  N+L  +  E P+++QI G D+ + ++A + +E +   + 
Sbjct: 35  SLVYAEMVSVAGMVHDNKKTLNMLNVNEIEHPMSMQIFGNDVDEFIKATQWIEKNVDCDI 94

Query: 77  INLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           I+LN+GCP+ +V      G+ L+  PD++ + +  + K  + PVT K R+G D    +V 
Sbjct: 95  IDLNLGCPAPKVAIRSQSGSALLKTPDLIYEIVKNVVKNTTKPVTAKIRLGWDKN--SVN 152

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K I+K+G + I +HAR         +++    + +++ + E+K+      IG NG
Sbjct: 153 AVEVAKLIEKAGASAIAVHAR--------TRNDFYTGHANWEKIKEVKQAVSIPVIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + D   A K+L     D VM+ RA   N  +   ++ Y 
Sbjct: 204 DVIDAKSAKKMLDETGCDAVMVSRACQGNPWIFDQINHYL 243


>gi|325288416|ref|YP_004264597.1| tRNA-U20-dihydrouridine synthase [Syntrophobotulus glycolicus DSM
           8271]
 gi|324963817|gb|ADY54596.1| tRNA-U20-dihydrouridine synthase [Syntrophobotulus glycolicus DSM
           8271]
          Length = 321

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/295 (25%), Positives = 142/295 (48%), Gaps = 23/295 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD+ +R   R L     +YTEMI   A++  + K I  L    +E+P  +Q+ G++   +
Sbjct: 21  TDKAFRQIVRQL-GGKYMYTEMISDKALIFHNPKTIKMLDLKEEEEPRIVQLFGSEPRIM 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAKI ++ G   I++N+GCP+ ++ +   GA L+ N     +  + + KA+ +PV+VK
Sbjct: 80  GEAAKIAQNCGATVIDINMGCPTPKIVKNGEGAALLKNIQSAVEIASNVVKAVDVPVSVK 139

Query: 123 CRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R+G D   I AV    L + ++++GV  + +HAR         ++       D++ + +
Sbjct: 140 MRLGWDRGNIVAV---ELGRRLEEAGVVMLTLHAR--------TREQYYAGEADWEWIAK 188

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K++     IG NG +     A K++ +   DGVMIGR    N  ++     +  +  + 
Sbjct: 189 LKEKVKIPVIG-NGDICSPQDAAKMISNTGCDGVMIGRGVMGNPWIIERTAIFLKDHFSK 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             P   +   +  R+  A +  Y    +     + ++ +H +    G  +S R R
Sbjct: 248 QEP-GNQERLEVLRRHFALLLKYKGERIG----VNEMRKHAVWYTKGIRHSARFR 297


>gi|268315976|ref|YP_003289695.1| TIM-barrel protein, nifR3 family [Rhodothermus marinus DSM 4252]
 gi|262333510|gb|ACY47307.1| TIM-barrel protein, nifR3 family [Rhodothermus marinus DSM 4252]
          Length = 358

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/303 (24%), Positives = 141/303 (46%), Gaps = 24/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + +++TE I +  ++   +  +  L    +E+P+ +QI G +
Sbjct: 18  MEDVSDPPFRLLCKRYGAD-MVFTEFISSGGLVHESEDAVKKLDIYDEERPVGIQIFGGE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + ++ EAA+IV+  G + I++N GCP  +V     GA ++ + + +     A+ +  + P
Sbjct: 77  LEQVREAARIVDQIGPDVIDINFGCPVRKVVCKDAGAGVLRDLNKMRALTEAVIEVATRP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD+  ++ +  + + ++  GV  + +HAR    + KG          +  +
Sbjct: 137 VTVKTRLGWDDR--SIRILEVARMLEDCGVQALTVHARTRAQMYKG----------SARW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K+    + I  NG      +  ++     VDGVMIGR A  N  +      Y  
Sbjct: 185 EWLRRLKELGLSIPIIGNGDALTPEKVKQMFDETGVDGVMIGRGAIGNPWIFRDAKIYME 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              TG  P     ++    ++ A   +   + L     + ++ R   G F GFP + R R
Sbjct: 245 ---TGELPPPPSWEERV--RVVAEHLELKCQWLGERKGVLEMRRMYGGYFKGFPGASRLR 299

Query: 295 HIL 297
            +L
Sbjct: 300 QLL 302


>gi|254503074|ref|ZP_05115225.1| putative TIM-barrel protein, nifR3 family [Labrenzia alexandrii
           DFL-11]
 gi|222439145|gb|EEE45824.1| putative TIM-barrel protein, nifR3 family [Labrenzia alexandrii
           DFL-11]
          Length = 315

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 114/238 (47%), Gaps = 20/238 (8%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKI 68
           R  AR      ++ +EM+ +++ ++GD +  +    Q+  L  +Q+ G +   + EAAK+
Sbjct: 11  RLAARF--GAGMVVSEMVASESFVKGDAETQMRAEAQDGGLHVVQLAGREARWMGEAAKV 68

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +   G + I++N+GCP+ +V  G  G+ LM + D     I A  +A+ +PVT+K R+G D
Sbjct: 69  IAGLGADIIDINMGCPAKKVTSGYSGSALMRDLDHALTLIEATVEAVDVPVTLKMRLGWD 128

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKE- 185
           D    +    L +  + +GV  I +H R      KG +          D++ +  +K E 
Sbjct: 129 DTT--INAPELARRAEAAGVQLITVHGRTRCQFYKGTA----------DWNAISAVKSEI 176

Query: 186 -NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             P +  G   G+E  + A+ +    D VMIGR AY    +   V  Y       S+P
Sbjct: 177 SVPLIANGDCTGIES-ADAMLVASGADAVMIGRGAYGRPWLPGLVGHYLETGEILSAP 233


>gi|86609094|ref|YP_477856.1| dihydrouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557636|gb|ABD02593.1| dihydrouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 361

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/309 (23%), Positives = 143/309 (46%), Gaps = 28/309 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD+ +R   R    ++L+YTEM+ A  +    +   I+     E+P+ +Q+       L 
Sbjct: 37  TDQVFRGLVRRFAPHSLVYTEMVSATGLHYARQLPRIMEVGEGEQPIGIQLFDCRPDFLA 96

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA++  D G   +++N+GCP  ++ +   G+ L+ +PD     + A+  A+ +PVTVK 
Sbjct: 97  EAARMAVDEGATLVDINMGCPVNKITKNGGGSSLLRDPDTAARIVEAVANAVEVPVTVKT 156

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G  DQ   + + +    ++++G   + +HAR    +G + K         +D +  + 
Sbjct: 157 RLGWSDQ--EINILDFAHRLQEAGAQLLTLHARTRA-QGFNGKAR-------WDWIRRV- 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K++  + +  NG +   + A+K L     DGVM  R       ++  +D +     TG  
Sbjct: 206 KQHLRIPVIANGDIFSTAAAVKCLEETGADGVMCSRGTMGYPFLVGEIDHFLK---TGQE 262

Query: 242 -PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL-- 297
            P  T ++     +I  ++        + G + ++Q  +HM      F  + + R +L  
Sbjct: 263 RPAPTPLE-----RIQMALEHLRGLWEYKGERGIRQARKHMTWYIKDFAGASQFRALLCR 317

Query: 298 --TVEAGAS 304
             TV+ G +
Sbjct: 318 IETVQEGEA 326


>gi|126651951|ref|ZP_01724143.1| hypothetical protein BB14905_03460 [Bacillus sp. B14905]
 gi|126591220|gb|EAZ85329.1| hypothetical protein BB14905_03460 [Bacillus sp. B14905]
          Length = 325

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    D     +N L F+  E+P+   I G
Sbjct: 20  MEDVTDVVFRHVISEAGRPDVFFTEFTNTTSYCHPDGMDSVRNRLAFTEDEQPIVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  +++ G+  I++N+GCP   V E   GA L+L+P++  + I A  KA  
Sbjct: 80  DNPEHFRQMSIGMKELGFKGIDINMGCPVDNVAERGKGAGLILHPELASEIIQA-AKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R       + ++  K+P   +
Sbjct: 139 LPVSVKTRLGFTD---VAEWREWLTHILKQNIANLSIHLR-------TREEMSKVP-AHW 187

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +IKK      PD  + +NG + D    LK+     +DGVMIGR  + N
Sbjct: 188 ELIADIKKLRDEIAPDTLLTINGDIPDRVTGLKLAEQYGIDGVMIGRGVFSN 239


>gi|293609802|ref|ZP_06692104.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828254|gb|EFF86617.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 341

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVTAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGRT--------REDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD++  + KE  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDLIKHV-KELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V       ++     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKDVLLGHLTELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE+ A  A   ++E  FN ++
Sbjct: 297 RQNMYKVESTAEQAI--VVENYFNQLL 321


>gi|255036755|ref|YP_003087376.1| TIM-barrel protein, nifR3 family [Dyadobacter fermentans DSM 18053]
 gi|254949511|gb|ACT94211.1| TIM-barrel protein, nifR3 family [Dyadobacter fermentans DSM 18053]
          Length = 329

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 144/311 (46%), Gaps = 32/311 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A L+YTE + ++ ++R   K++  L     E+P+ +Q+ G+
Sbjct: 19  MEDVSDPPFRAVCK--ENGADLMYTEFVSSEGLIRDAAKSVQKLDIFEYERPVGIQLFGS 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D+  +   A+I      + I++N GCP   V     GA L+ +   +     ++ K+  +
Sbjct: 77  DVETMGSCAEIASRVNPDLIDINYGCPVKNVACRGAGAALLQDVPKMVKMTESVIKSTHL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLD 175
           PVTVK R+G DD    +  + + + ++  G+  + IH R  +   KG +          D
Sbjct: 137 PVTVKTRLGWDDNTKNI--QEVAERLQDIGIKALSIHGRTRVQMYKGAA----------D 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + ++ ++ KENP + I +  NG ++   +AL  K    VDG+MIGRA   N  +   +  
Sbjct: 185 WSLIAKV-KENPRITIPIFGNGDVDTPEKALEYKNTYGVDGIMIGRATIGNPWIFNEIKH 243

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           Y         P ++ RVD      +     +++ R       + ++ RH    F G  + 
Sbjct: 244 YLKTGEKLPPPTMEQRVD------VCRRHLEFSIRWKGPVAGVFEMRRHYTNYFKGLEHF 297

Query: 291 RRCRHILTVEA 301
           +  R  L VEA
Sbjct: 298 KPYRMRL-VEA 307


>gi|92117380|ref|YP_577109.1| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrobacter
           hamburgensis X14]
 gi|91800274|gb|ABE62649.1| tRNA-U20-dihydrouridine synthase [Nitrobacter hamburgensis X14]
          Length = 349

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 111/229 (48%), Gaps = 25/229 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLV 63
           TDR +R  A  L    L+ +EM  +D ++RG   ++L   +T   P  +Q+ G +   + 
Sbjct: 37  TDRPFRGLAEAL-GAGLVVSEMTASDDLVRGRPMSVLRCEATGGGPHVVQLAGCETHWMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K 
Sbjct: 96  EGARIAEGAGADIIDINMGCPARHVTGGQSGSALMRDLDHALRLIEATVGAVKVPVTLKM 155

Query: 124 RIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDI 178
           R+G DD+    PA+A R      + +GV  + +H R      KG          + D+  
Sbjct: 156 RLGWDDRSLNAPALAQRA-----ESAGVQMMTVHGRTRCQFYKG----------SADWQA 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
           V  + K+  D+ + +NG +     A+  L +   D VM+GR A     M
Sbjct: 201 VRAV-KDAVDIPVVVNGDITSFDAAVAALEASGADAVMVGRGAQGQPWM 248


>gi|126207677|ref|YP_001052902.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           L20]
 gi|126096469|gb|ABN73297.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 320

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 126/246 (51%), Gaps = 30/246 (12%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   RL T    +L ++EM+  +  +   +K+ L  +  E+    A+QI G
Sbjct: 17  MAGITDQPFR---RLCTKLGASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D +++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ 
Sbjct: 74  SDPAEMAMAAKVNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
           +PVT+K R G D +      RN   + K  +K+G++ + IH R    + +G         
Sbjct: 134 VPVTLKIRTGWDQEN-----RNCLEIAKIAEKAGISALTIHGRTRHCLFEG--------- 179

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            N +YD +  + K+   + I  NG +    +A  +L     D VMIGR ++    +   V
Sbjct: 180 -NAEYDSIKAV-KQAVSIPIIANGDITSAEKAKYVLDYTQADAVMIGRGSFGRPWLFKEV 237

Query: 230 DEYFSN 235
           +++  N
Sbjct: 238 EQFLEN 243


>gi|253583466|ref|ZP_04860664.1| dihydrouridine-tRNA ligase [Fusobacterium varium ATCC 27725]
 gi|251834038|gb|EES62601.1| dihydrouridine-tRNA ligase [Fusobacterium varium ATCC 27725]
          Length = 320

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 116/235 (49%), Gaps = 19/235 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  YR   +    + LL+TEM+  +A+    +K +       +  ++Q+ G DI K+VE
Sbjct: 13  TDYTYRGILKEFKPD-LLFTEMVSINALEVACEKTLKVILRLREGDSVQLFGKDIKKMVE 71

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           +AK VE  G   I++N GCP  ++    +GA LM  P++V   ++ +  AL+    +++K
Sbjct: 72  SAKFVESLGVKHIDINSGCPMKKIVNNGYGAALMEQPELVKAMLSEVRSALNDKTDLSIK 131

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G  +    V    + K  +++G   I IH R         ++       D+ I+ E+
Sbjct: 132 IRVGYKESKNPV---EIAKIAQETGCKHITIHGR--------TREQMYTGKADWSIIKEV 180

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            KE+ D+ +  NG +   ED  + +     VDG+M+ R  + N  ++  + EYF 
Sbjct: 181 -KESVDIPVIGNGDIFTAEDAKERVD-YSGVDGIMLARGIFGNPWLIRDIREYFE 233


>gi|307256215|ref|ZP_07538002.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865396|gb|EFM97292.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 320

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 125/246 (50%), Gaps = 30/246 (12%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   RL T    +L ++EM+  +  +   +K+ L  +  E+    A+QI G
Sbjct: 17  MAGITDQPFR---RLCTKLGASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D +++  AAK   ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ 
Sbjct: 74  SDPAEMAMAAKFNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPKDNRKI 171
           +PVT+K R G D +      RN +K  K   K+G++ + IH R    + +G         
Sbjct: 134 VPVTLKIRTGWDQEN-----RNCLKIAKIAEKAGISALTIHGRTRHCLFEG--------- 179

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            N +YD +  + K+   + I  NG +    +A  +L     D VMIGR ++    +   V
Sbjct: 180 -NAEYDSIKAV-KQAVSIPIIANGDITSAEKAKYVLDYTQADAVMIGRGSFGRPWLFKEV 237

Query: 230 DEYFSN 235
           +++  N
Sbjct: 238 EQFLEN 243


>gi|53728909|ref|ZP_00134632.2| COG0042: tRNA-dihydrouridine synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|165975645|ref|YP_001651238.1| putative dehydrogenase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|190149460|ref|YP_001967985.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|303250745|ref|ZP_07336941.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307245001|ref|ZP_07527098.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307249401|ref|ZP_07531393.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307251720|ref|ZP_07533624.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253954|ref|ZP_07535806.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307258409|ref|ZP_07540150.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|307260647|ref|ZP_07542339.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307262779|ref|ZP_07544406.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|165875746|gb|ABY68794.1| putative dehydrogenase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|189914591|gb|ACE60843.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|302650415|gb|EFL80575.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306854166|gb|EFM86374.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306858587|gb|EFM90651.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306860806|gb|EFM92815.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306863158|gb|EFM95100.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306867593|gb|EFM99440.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306869724|gb|EFN01509.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306871924|gb|EFN03641.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 320

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 126/246 (51%), Gaps = 30/246 (12%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   RL T    +L ++EM+  +  +   +K+ L  +  E+    A+QI G
Sbjct: 17  MAGITDQPFR---RLCTKLGASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D +++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ 
Sbjct: 74  SDPAEMAMAAKVNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
           +PVT+K R G D +      RN   + K  +K+G++ + IH R    + +G         
Sbjct: 134 VPVTLKIRTGWDQEN-----RNCLEIAKIAEKAGISALTIHGRTRHCLFEG--------- 179

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            N +YD +  + K+   + I  NG +    +A  +L     D VMIGR ++    +   V
Sbjct: 180 -NAEYDSIKAV-KQAVSIPIIANGDITSAEKAKYVLDYTQADAVMIGRGSFGRPWLFKEV 237

Query: 230 DEYFSN 235
           +++  N
Sbjct: 238 EQFLEN 243


>gi|325118139|emb|CBZ53690.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 654

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 79/315 (25%), Positives = 126/315 (40%), Gaps = 98/315 (31%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI---------------VADAILRGDKKNILGFST 45
           M+D+T+RH+R    L++    LYTEM+               +  +I R   + I   ST
Sbjct: 104 MMDYTNRHWRHLISLMSRRVTLYTEMVSVPPAPCESSECSQDLPPSIKRKLWEEISSLST 163

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNE------------------INLNVGCPSAR 87
               + LQ+G   ++  +  A+      ++E                  +NLN GCPS R
Sbjct: 164 VPNHVVLQVGVGSVASAIAVARAFNSHEFSENRGQCEQGTGTGRQRTFSVNLNCGCPSPR 223

Query: 88  VHEGSFGACLMLNPDIV--------------------------------GDCIAAMCKAL 115
           V +GSFG  LM +P  V                                GD +  M K  
Sbjct: 224 VAKGSFGLILMEDPKRVAEICQVLLDGANSRESQQGRNVADEATGMCAGGDTMNRMAKTD 283

Query: 116 SI------PVTVKCRIGVDDQIPAV---------------------ALRNLVKSIKK-SG 147
            +       V+VKCR+G+++    +                      L + + ++ + S 
Sbjct: 284 EVLRMDNSAVSVKCRVGIEEDRRFLRSGSNLFSATTFSSSSTCTYEKLASFIATVTEASP 343

Query: 148 VNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--- 203
           V    IHAR  IL G LSPK+N +IP    + VY + ++ P++    NGG++   +A   
Sbjct: 344 VRHFIIHARPGILVGKLSPKENLQIPQRRPEWVYRLCQDFPNVSFTFNGGVKSFHEAEGH 403

Query: 204 -LKILPSVDGVMIGR 217
            L     + GVM+GR
Sbjct: 404 LLNTNDKLGGVMVGR 418


>gi|325954824|ref|YP_004238484.1| hypothetical protein Weevi_1197 [Weeksella virosa DSM 16922]
 gi|323437442|gb|ADX67906.1| TIM-barrel protein, nifR3 family [Weeksella virosa DSM 16922]
          Length = 332

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 145/310 (46%), Gaps = 31/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGA 57
           M D +D  +R   ++  N A L+YTE I ++ ++R     +  L    +E+P+ +QI G 
Sbjct: 19  MEDVSDPPFRRLCKM--NGADLMYTEFISSEGLIRDAIKSRKKLDIFDEERPIGIQIFGG 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  +AKIVE    + +++N GCP  +V     GA ++ + D++     ++ ++  +
Sbjct: 77  DEEAMAMSAKIVETVEPDLVDINFGCPVKKVVCKGAGAGVLKDVDLMVRLTKSVVESTHL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           PVTVK R+G D    ++ +  + + ++++G+  + IH R    + KG S          D
Sbjct: 137 PVTVKTRLGWDHD--SINIDEVAERLQETGIKALAIHGRTRAQMYKGHS----------D 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +  +  +K  NP++ I +  NG ++   +A++      VDG+MIGRAA  +  +   +  
Sbjct: 185 WSHIARVKA-NPNIEIPIFGNGDIDSPQKAIEFKEKYGVDGIMIGRAAIGHPWIFNKIKH 243

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           Y         P I+ RV+       + +   +A         + +   H    F G PN 
Sbjct: 244 YRETGEFLPEPTIQERVEA------ARNHLLWAMEWKGERTGILETRMHYTNYFKGIPNF 297

Query: 291 RRCRHILTVE 300
           +  R  L  +
Sbjct: 298 KPYRTKLVTQ 307


>gi|299769181|ref|YP_003731207.1| TIM-barrel protein, nifR3 family protein [Acinetobacter sp. DR1]
 gi|298699269|gb|ADI89834.1| TIM-barrel protein, nifR3 family protein [Acinetobacter sp. DR1]
          Length = 341

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/327 (24%), Positives = 149/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVTAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  ++ G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEVGIAALALHGRT--------REDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD++  + KE  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDLIKHV-KELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V       +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKHVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE+ A  A   ++E  FN ++
Sbjct: 297 RQNMYKVESTAEQAL--VVENYFNQLL 321


>gi|303252012|ref|ZP_07338183.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307247175|ref|ZP_07529226.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|302649442|gb|EFL79627.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306856313|gb|EFM88465.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
          Length = 320

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 126/246 (51%), Gaps = 30/246 (12%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   RL T    +L ++EM+  +  +   +K+ L  +  E+    A+QI G
Sbjct: 17  MAGITDQPFR---RLCTKLGASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D +++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ 
Sbjct: 74  SDPAEMAMAAKVNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
           +PVT+K R G D +      RN   + K  +K+G++ + IH R    + +G         
Sbjct: 134 VPVTLKIRTGWDQEN-----RNCLEIAKIAEKAGISALTIHGRTRHCLFEG--------- 179

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            N +YD +  + K+   + I  NG +    +A  +L     D VMIGR ++    +   V
Sbjct: 180 -NAEYDSIKAV-KQAVSIPIIANGDITSAGKAKYVLDYTQADAVMIGRGSFGRPWLFKEV 237

Query: 230 DEYFSN 235
           +++  N
Sbjct: 238 EQFLEN 243


>gi|116326862|ref|YP_796582.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116329809|ref|YP_799527.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116119606|gb|ABJ77649.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116123498|gb|ABJ74769.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 318

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 109/217 (50%), Gaps = 21/217 (9%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           A  YTE +  D ++    K   +  F  +E+P+  QI G  +  + EA +I+++   + I
Sbjct: 36  AFSYTEFVNTDELVHKAPKAFKMFRFHPEERPITFQIFGNRLEIISEATEIIQELEPDII 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GC + +V     GA L+  P + G  I AM K ++IPVT K RIG D        R
Sbjct: 96  DLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAMKKRVNIPVTAKIRIGWD-----ATSR 150

Query: 138 NLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           N +   K +++SG++ + +H R         K+       D+D + E+K  N  + I  N
Sbjct: 151 NYLEVSKILEESGIDALTVHGRT--------KEMAYTGFADWDAIGEVKV-NRKIPIFGN 201

Query: 195 GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
           G ++   +A   +   S+DGV+IGR A  N  + + V
Sbjct: 202 GDIKSFQEANSKINKYSLDGVLIGRNAIGNPWIFSEV 238


>gi|254360638|ref|ZP_04976787.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|261493347|ref|ZP_05989873.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. BOVINE]
 gi|261496613|ref|ZP_05992993.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|110735319|gb|ABG89230.1| putative nitrogen fixation protein [Mannheimia haemolytica]
 gi|153091178|gb|EDN73183.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|261307816|gb|EEY09139.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|261310991|gb|EEY12168.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. BOVINE]
          Length = 329

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/260 (26%), Positives = 134/260 (51%), Gaps = 30/260 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L  +  ++    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSRLRLAHHDEIGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AAKI  ++G + I++N+GCP+ +V++   G+ L+ NP +V   + ++  A+ +P
Sbjct: 76  PVEMAKAAKINVEYGADIIDINMGCPAKKVNKNMAGSALLRNPKLVAQILDSVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G D +      RN   + K  +++G+  + IH   R  +  G +         
Sbjct: 136 VTLKIRTGWDQEN-----RNCLQIAKIAEQAGIKALTIHGRTRSCLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  + KE   + +  NG ++   +A  +L     D +MIGRA++ N  +   +++
Sbjct: 182 -EYESIKAV-KEAISIPVIANGDIDSAEKAKFVLDYTKADAIMIGRASFGNPWIFKEIND 239

Query: 232 YFSNPLTGSSPIKTRVDKDF 251
           +F   L  SSP+   +DK +
Sbjct: 240 FFETGL--SSPLS--IDKKY 255


>gi|313115110|ref|ZP_07800598.1| TIM-barrel protein, nifR3 family [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622587|gb|EFQ06054.1| TIM-barrel protein, nifR3 family [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 371

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 81/306 (26%), Positives = 137/306 (44%), Gaps = 26/306 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNI--LGFSTQEKPLALQIGG 56
           M  +TD   R   RL+  +   +T  EM+ + A++ GD K +  L       P  +QI G
Sbjct: 52  MAGFTDAPCR---RLMAQHGAGFTVSEMVSSRALVYGDHKTVSLLKAEPNGAPYGVQIFG 108

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + EA   +E + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  +     
Sbjct: 109 EVPEIMGEATAAIEQYEFDFVDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEQVVANTK 168

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            PVTVK R G D D I AV      K+ +++G   I +HAR         ++    P +D
Sbjct: 169 RPVTVKMRKGWDADHITAV---ECAKACEQAGAALIAVHART--------REQMYTPGID 217

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            +I+  +K       +G NG +     A++++ +   DGVMI R A  +  +   V+   
Sbjct: 218 PEIIARVKDAVRVPVLG-NGDIHSAEDAVEMMQATGCDGVMIARGALGDPWLFERVNAAI 276

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P   +  ++ R++    R+    M +     +       Q   +M GL  G  N RR
Sbjct: 277 EGLPAPKAPNLQARMNA--LRRQVEEMVEQKGEFVAMPQARSQTMHYMKGL-KGAANLRR 333

Query: 293 CRHILT 298
               LT
Sbjct: 334 YCCTLT 339


>gi|225024157|ref|ZP_03713349.1| hypothetical protein EIKCOROL_01025 [Eikenella corrodens ATCC
           23834]
 gi|224943182|gb|EEG24391.1| hypothetical protein EIKCOROL_01025 [Eikenella corrodens ATCC
           23834]
          Length = 334

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 121/246 (49%), Gaps = 19/246 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD+ +R  AR          EMI ++  L+  +K  N +  S +   +A+QI G++
Sbjct: 17  MAGITDKPFRMLARQF-GAGWTVGEMISSNPDLQNTRKTLNRIDRSGESGVIAVQIAGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAA+     G   I++N+GCP+ +V +   G+ L+ N  +V + + A+ +A+ +P
Sbjct: 76  PAQMAEAARYNVAQGAQLIDINMGCPAKKVCQVQAGSALLQNEPLVAEILHAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D+   +    + +  + +G+  I IH R         +        +Y +
Sbjct: 136 VTLKTRLGWHDEHKNIL--TIARMAEDAGIAAIAIHGRT--------RTQMYRGQAEYGL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K+    + + +NG ++   +A ++L     DGVMIGR A     +   V  Y ++ 
Sbjct: 186 IAEAKRRL-SIPVWVNGDIDSPQKAARVLAETGADGVMIGRTAQGRPWLFRDVAHYLAH- 243

Query: 237 LTGSSP 242
             GS P
Sbjct: 244 --GSLP 247


>gi|332800061|ref|YP_004461560.1| TIM-barrel protein, nifR3 family [Tepidanaerobacter sp. Re1]
 gi|332697796|gb|AEE92253.1| TIM-barrel protein, nifR3 family [Tepidanaerobacter sp. Re1]
          Length = 323

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 80/328 (24%), Positives = 148/328 (45%), Gaps = 32/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +  + L+ TEMI    ++  D K   +L  +  E P+ +Q+ G  
Sbjct: 15  MAGITDMPFRTICKQMGADVLM-TEMISTRGLVYNDNKTAKLLQVNPDENPIGVQLFGNA 73

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                E+ K ++D  ++ IN+N+GCP+ ++ +   G  LM +  +    I    +A   P
Sbjct: 74  PKDFEESVKKIDDLPFDFININMGCPTPKIVKNGDGCALMKDVKLASSIIKVTARASRKP 133

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           V+VK R G D D I AV   +   + + SG + I IH R         ++       D+D
Sbjct: 134 VSVKIRKGWDKDSINAVEFSS---AAEDSGASMIIIHGRT--------REMFYSGKADWD 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  + K+  D+ +  NG +     A+++L     DG+MIGR A  N  +   V  +   
Sbjct: 183 IIKSV-KDAVDIAVVGNGDVFTSEDAVEMLKKTGCDGIMIGRGALGNPWIFREVKYFLKT 241

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS---- 290
               ++P +K R++       +A    Y   HL     + ++ +H+     G P+S    
Sbjct: 242 GKKTAAPTLKERLEIMLLHLNNA--ISYHGEHLG----VLEMRKHLAWYIKGLPHSAPVK 295

Query: 291 ---RRCRHILTVEAGASTATHHIIETAF 315
              ++CR + ++E   +   + + +T +
Sbjct: 296 NALQQCRDVGSIEEILNNYFYRLKQTGY 323


>gi|325108020|ref|YP_004269088.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
 gi|324968288|gb|ADY59066.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
          Length = 362

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 59/159 (37%), Positives = 86/159 (54%), Gaps = 6/159 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           +  +T    R   R L    L  T++I+A  +L   KK+ +  ST E  +PL++QI G  
Sbjct: 37  LAGYTHLPLRTALRELGGIGLATTDLILAPQLLADSKKSRILLSTSEADRPLSVQIFGGR 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV AA+ +E+ GY  I++N+GCP  +V+    GA LM + D      AA+ +A+ IP
Sbjct: 97  TEDLVRAAQRLEERGYEGIDINMGCPMGKVNSSGGGARLMCDCDNATQMTAAVVEAVDIP 156

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VTVK R+G D D I A     L ++ +  GV  I IH R
Sbjct: 157 VTVKMRLGWDADNITAPI---LARAFEDVGVAAITIHGR 192


>gi|332881487|ref|ZP_08449136.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332680485|gb|EGJ53433.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 341

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 142/309 (45%), Gaps = 28/309 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++Y+E + ADA++R   +++  L     E+P+A+QI G +
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYSEFVAADALVRMVNRSLEKLAVCDDERPVAIQIYGKE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+IV E    + ++LN GCP  RV     GA ++ N   + +   A+  A+ I
Sbjct: 77  PGPVADAARIVVERARPDMLDLNFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ 
Sbjct: 137 PVTVKTRLGWDESSKVIV--DLAERLQDCGIRALTIHGRT--------RAQMYTGEADWT 186

Query: 178 IVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ E+K  NP + I +  NG +    +A +      VD VM+GRA +    +   + +  
Sbjct: 187 LIGEVKN-NPRMTIPIIGNGDITSPERARECFDCYGVDAVMVGRATFGRPWIFKEIMDVL 245

Query: 234 SNPLTGS---SPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFH 285
            NP + S     +K+    +  D+   +       + R +     +    RH+    +F 
Sbjct: 246 -NPESVSVAHEAVKSGYPVMSADWKIDVLKEQVLTSVRRIDEYRGILHSRRHLAASPVFK 304

Query: 286 GFPNSRRCR 294
           G PN R  R
Sbjct: 305 GIPNFRETR 313


>gi|121535055|ref|ZP_01666872.1| putative TIM-barrel protein, nifR3 family [Thermosinus
           carboxydivorans Nor1]
 gi|121306305|gb|EAX47230.1| putative TIM-barrel protein, nifR3 family [Thermosinus
           carboxydivorans Nor1]
          Length = 317

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 122/240 (50%), Gaps = 18/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A+ +    L+Y+EM+    +L  +    +++    +E+P+A+QI G++
Sbjct: 17  MAGVTDLPFRLLAKEM-GCGLVYSEMVSDKGLLYNNANTLSLIRIDERERPVAIQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+IV   G + I++N+GCP+ ++ +   GA LM  P++    IA++ +A  +P
Sbjct: 76  PESMAAAARIVARAGADIIDINMGCPTPKIVKNGEGAALMRRPELAYRIIASVVEAAEVP 135

Query: 119 VTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D+  I AV +  L    +++G + + +H R         ++       D+ 
Sbjct: 136 VTVKMRKGWDESSINAVEIARLA---ERAGASAVSVHGRT--------REQFYAGQADWS 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  + KE   + +  NG +     A ++L     DG+MIGR A  N  +L  V  Y + 
Sbjct: 185 IIRAV-KEAVTIPVNGNGDVRTPQDAARMLTETGCDGIMIGRGAQGNPWLLRQVAHYLAT 243


>gi|303256192|ref|ZP_07342208.1| tRNA-dihydrouridine synthase B [Burkholderiales bacterium 1_1_47]
 gi|331001248|ref|ZP_08324874.1| tRNA-dihydrouridine synthase B [Parasutterella excrementihominis
           YIT 11859]
 gi|302860921|gb|EFL83996.1| tRNA-dihydrouridine synthase B [Burkholderiales bacterium 1_1_47]
 gi|329568975|gb|EGG50771.1| tRNA-dihydrouridine synthase B [Parasutterella excrementihominis
           YIT 11859]
          Length = 326

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 71/289 (24%), Positives = 139/289 (48%), Gaps = 24/289 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           +  +TD  +R   R L   A    EM+ +   LR  +K+   FS  ++  P A+Q+ G+D
Sbjct: 22  LAGFTDLPFRQICRKL-GAAYAVAEMVASQKHLRESRKSQERFSLGSESYPRAIQLLGSD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L + A+     G   ++ N GCP+ +V     G+ L+ +  +V   + A+ +A+ +P
Sbjct: 81  PVDLADTARYAVQCGAQIVDFNCGCPAKKVCSVECGSALLKDEALVEKLLKALTEAVDVP 140

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R+G D + I A+   N+    +++G+  + +H R         ++      +DY 
Sbjct: 141 VTLKYRLGWDAEHINAL---NIAAIAQEAGIKMLVLHGRT--------REQGFKGEVDYQ 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K  + D+ +  NG ++ + +A  +L     DG+MIGRAA  N  + + +++  S 
Sbjct: 190 RIAEVKA-SVDIPVIANGDIDSVEKAEAVLAQTGADGIMIGRAAIGNPWIFSQINDKLSG 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            +   +P K+++ +     +    + Y          L+ I +H+ G F
Sbjct: 249 RIP-QAPSKSQLIETIGEHLQLHFSFYEKEK-----GLKTIRKHLSGYF 291


>gi|163731736|ref|ZP_02139183.1| tRNA-dihydrouridine synthase [Roseobacter litoralis Och 149]
 gi|161395190|gb|EDQ19512.1| tRNA-dihydrouridine synthase [Roseobacter litoralis Och 149]
          Length = 327

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 116/245 (47%), Gaps = 40/245 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           M   TDR +R          L+ +EM+ +  IL       +K  LG S +    A+Q+ G
Sbjct: 19  MAGITDRPFRDLVASF-GAGLVVSEMVASADILNARPGSQEKAELGLSAEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+ KA+ 
Sbjct: 76  REPGLMAEAARMVEGQGARIIDINMGCPAKKVTQGYSGSALMRTPDHAMTLIEAVVKAVK 135

Query: 117 IPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
           IPVT+K R+G DD +   P +A R      +++G+  + IH R      KG         
Sbjct: 136 IPVTLKTRLGWDDAMLNAPQIARRA-----EEAGIRMLTIHGRTRCQFYKG--------- 181

Query: 172 PNLDYDIVYEIKK-------ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
            + D+  +  +K         N D+   ++       QAL+ L   DGVMIGR A     
Sbjct: 182 -HADWAAIAGVKSVVSIPVIANGDILCSVSA-----KQALR-LSGADGVMIGRGARGKPW 234

Query: 225 MLTTV 229
           +L+ +
Sbjct: 235 LLSQI 239


>gi|15618677|ref|NP_224963.1| oxidoreductase [Chlamydophila pneumoniae CWL029]
 gi|15836301|ref|NP_300825.1| oxidoreductase [Chlamydophila pneumoniae J138]
 gi|16752273|ref|NP_445641.1| hypothetical protein CP1104 [Chlamydophila pneumoniae AR39]
 gi|33242127|ref|NP_877068.1| nitrogen regulating protein [Chlamydophila pneumoniae TW-183]
 gi|4377076|gb|AAD18906.1| predicted oxidoreductase [Chlamydophila pneumoniae CWL029]
 gi|7190016|gb|AAF38872.1| conserved hypothetical protein [Chlamydophila pneumoniae AR39]
 gi|8979141|dbj|BAA98976.1| oxidoreductase [Chlamydophila pneumoniae J138]
 gi|33236637|gb|AAP98725.1| nitrogen regulating protein [Chlamydophila pneumoniae TW-183]
          Length = 335

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 45/158 (28%), Positives = 91/158 (57%), Gaps = 5/158 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  ++D  YR  + L     L++ EM+  + IL   ++   +L ++   +P+  Q+ G++
Sbjct: 21  LAGFSDYPYRCMSALY-QPGLMFCEMVKVEGILYAPERTSKLLDYNENMRPIGAQLCGSN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAAKI+E  G++ I+LN GCP+ ++ +   G+ L+  P+++G  +  +  ++SIP
Sbjct: 80  PETSGEAAKILEGLGFDLIDLNCGCPTDKITKDGSGSGLLKTPELIGRILDKIINSVSIP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VTVK R G D  +  + + + V+ I+ +G + +++H R
Sbjct: 140 VTVKIRSGWD--MEHINVEDTVRIIRDAGASAVFVHGR 175


>gi|85374084|ref|YP_458146.1| tRNA-dihydrouridine synthase [Erythrobacter litoralis HTCC2594]
 gi|84787167|gb|ABC63349.1| tRNA-dihydrouridine synthase [Erythrobacter litoralis HTCC2594]
          Length = 338

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 116/238 (48%), Gaps = 22/238 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI ++A +R  ++++    +   E P+++Q+ G D   +
Sbjct: 33  TDLPFRTLVRRF-GSGLNVTEMIASEAAIRETRQSVQKAAWDKTEDPVSMQLVGCDPVSM 91

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAK+ ED G   I++N GCP  +V     G+ LM    +    + A   A+ +PVTVK
Sbjct: 92  GEAAKLQEDNGAAIIDINFGCPVRKVVGQLAGSALMREVPLATRLMEATVNAVDVPVTVK 151

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVY 180
            R+G D    ++    L +  +  GV  I +H   R  + KG          + D+  + 
Sbjct: 152 MRMGWDHA--SLNAPELARIAEDLGVQMITVHGRTRNQMYKG----------SADWSFIR 199

Query: 181 EIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ K+   + + +NG   G+ED + AL+     DG+MIGR AY    +L  V  ++  
Sbjct: 200 KV-KDAVSIPVIVNGDICGIEDAANALE-QSGADGLMIGRGAYGKPWLLAQVMHWWKT 255


>gi|88802043|ref|ZP_01117571.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Polaribacter irgensii 23-P]
 gi|88782701|gb|EAR13878.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Polaribacter irgensii 23-P]
          Length = 333

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 82/309 (26%), Positives = 137/309 (44%), Gaps = 41/309 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A ++YTE I ++ ++R   K++  L    +E+P+ +QI GA
Sbjct: 19  MEDVSDPPFRALCK--ENGADVVYTEFISSEGLIRDAAKSLMKLDIYEKERPVGIQIFGA 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++  ++   +IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++
Sbjct: 77  NLESMLRTIEIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G D    ++ +  + + ++  G   I IH R          D + I  +   
Sbjct: 137 PITVKTRLGWDHD--SIRIVEVAERLQDVGCAAISIHGRTRAQMYKGEADWKPIAAV--- 191

Query: 178 IVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
                 K N  + I +  NG +    +A+++  S  +DG MIGRAA         V  YF
Sbjct: 192 ------KNNQRMHIPVFGNGDVTTPEKAMEMRDSYGLDGAMIGRAAIGYPWFFNEVKHYF 245

Query: 234 -SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG----GKLQ---QITRHMIGLFH 285
            +    G   I  RV             + A RHL       G L    +  RH    F 
Sbjct: 246 KTGEHLGQPTIAQRV-------------EMARRHLQMAIDWKGPLLGVFETRRHYTNYFK 292

Query: 286 GFPNSRRCR 294
           G P+ +  R
Sbjct: 293 GIPHFKEHR 301


>gi|326570396|gb|EGE20436.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis BC8]
          Length = 341

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 131/278 (47%), Gaps = 26/278 (9%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL +AA+     G   +++N+
Sbjct: 59  SEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAEPDKLAQAAQFQVANGAQIVDINM 118

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + +   A+ +PVT+K R+G      A    N++K
Sbjct: 119 GCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVPVTLKTRLGF-----ANGQENILK 173

Query: 142 SIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +   ++GV  I IH R         +++       Y+++ ++KK    + I +NG ++
Sbjct: 174 IAQIAEQAGVAAITIHGRT--------REDFYTGQARYELITQVKKA-AKIPIIVNGDID 224

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +AL I      D VMIGRAA     +   +  + +     +SP    + +   R + 
Sbjct: 225 SPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTGELLASPTAGEIHEVVLRHLD 284

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                Y     +SG ++ +  +H+     G PNS   R
Sbjct: 285 ELYRFYGE---YSGCRIAR--KHIAWYTGGLPNSNAFR 317


>gi|332287905|ref|YP_004422806.1| dihydrouridine synthase family protein [Chlamydophila psittaci 6BC]
 gi|325507219|gb|ADZ18857.1| dihydrouridine synthase family protein [Chlamydophila psittaci 6BC]
          Length = 291

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 63/267 (23%), Positives = 122/267 (45%), Gaps = 19/267 (7%)

Query: 22  LYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ EM+  + +     + +  L +S   +P+  Q+ G+      EAAK++E  G++ I+L
Sbjct: 1   MFCEMVKVEGLHYSPSRTLKLLEYSESMRPIGGQLCGSKPEMAGEAAKVLEGLGFDLIDL 60

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N GCP+ R+ +   G+ L+ +P+++G  +  + +A+SIPVTVK R G D     + +   
Sbjct: 61  NCGCPTDRITKDGSGSGLLKSPELIGKILEKIIEAVSIPVTVKIRSGWD--CNNINVEET 118

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           V+ I+ +G + +++H R      + P       NL+Y I         DL +  NG +  
Sbjct: 119 VRIIRDAGASAVFVHGRTRAQGYVGPS------NLEY-IARAKAAAGKDLPVFGNGDIFS 171

Query: 200 MSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              A  ++ S   DGV++ R       ++  ++ Y ++      P   R      ++   
Sbjct: 172 PEAAKLMMDSTQCDGVLVARGTMGAPWIVRQIESYLASGTYQKVPFSKR------KQAFI 225

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLF 284
               +   +  S  K    TR + G +
Sbjct: 226 QHLQWVEEYYQSEAKFLSETRKLCGHY 252


>gi|260556608|ref|ZP_05828826.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii ATCC 19606]
 gi|260409867|gb|EEX03167.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii ATCC 19606]
          Length = 341

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVIAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGRT--------REDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YELIKHV-KELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKEVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 297 RQNMYKVETTAEQAL--VVESYFNQLL 321


>gi|256424776|ref|YP_003125429.1| hypothetical protein Cpin_5809 [Chitinophaga pinensis DSM 2588]
 gi|256039684|gb|ACU63228.1| TIM-barrel protein, nifR3 family [Chitinophaga pinensis DSM 2588]
          Length = 345

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 81/315 (25%), Positives = 145/315 (46%), Gaps = 32/315 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M D +D  +R   R   N A LLYTE I ++ +++  +K    L    +E+P  +QI G 
Sbjct: 19  MEDVSDPPFRVVCR--ENGADLLYTEFISSEGLVKDTEKCRRKLAIFDEERPAGVQIFGG 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D  KL  AA+IV+    + +++N GCP   +     G+ ++ + D++    AA  K+  +
Sbjct: 77  DEGKLSMAARIVDMTQPDLLDINFGCPIKGIVSKGAGSGVLKDIDLMVRLTAACVKSTKL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G D+    +    + + ++  G+  + IH   R  + KG             
Sbjct: 137 PVTVKTRLGWDEDTQNI--EEVAERLQDVGIKALAIHGRTRTQMYKG----------EAS 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++++ ++K  NP + I +  NG ++   +AL  K    VDG+MIGRAA     +   V  
Sbjct: 185 WELIAKVKN-NPRIHIPIFGNGDIDSPQKALEYKNRYGVDGIMIGRAAIGYPWIFREVKH 243

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           Y        +P ++ R+       +     + + +    G  +  + +H      G P+ 
Sbjct: 244 YLQTGEMLPAPTLEDRI------AVCKRQLEKSVQWRGEGHGIFAMRKHYFNYLKGLPDF 297

Query: 291 RRCR-HILTVEAGAS 304
           +  R  ++T EA A 
Sbjct: 298 KAFRSRLVTPEASAE 312


>gi|260549656|ref|ZP_05823873.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. RUH2624]
 gi|260407173|gb|EEX00649.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. RUH2624]
          Length = 341

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVIAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGRT--------REDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YELIKHV-KELINIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V       +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKDVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 297 RQNMYKVETTAEQAL--VVESYFNQLL 321


>gi|330796961|ref|XP_003286532.1| hypothetical protein DICPUDRAFT_87182 [Dictyostelium purpureum]
 gi|325083513|gb|EGC36964.1| hypothetical protein DICPUDRAFT_87182 [Dictyostelium purpureum]
          Length = 399

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 123/261 (47%), Gaps = 29/261 (11%)

Query: 1   MVDWTDRHYRFFAR-------LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQ 53
           M D T+  +RF          +  NN +L+ E +  + + R      L +S  EKP+  Q
Sbjct: 17  MADVTEVSFRFLIANVINKYWIKPNNVVLFNEFLATEGVCRDHIAQQLEYSEIEKPIVAQ 76

Query: 54  IGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV--HEGSFGACLMLNPDIVGDCIAA 110
             G        +A+I    + Y+ I++N+GCPS +V   + + GA L+ NP +  + I A
Sbjct: 77  FFGCRPEAFKISAEIACNKYNYDGIDINMGCPSRKVVSPKQAAGAALITNPKLAQEIIYA 136

Query: 111 MCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             + A S PV+VK RIG D    ++ + + +  I ++  + + +H R      L P    
Sbjct: 137 TKEGAGSKPVSVKTRIGFD----SIDIESWIPKILEAKPSCLTLHLRTKKELSLVPA--- 189

Query: 170 KIPNLDYDI---VYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              + +++I   V E++   +P+  I  NG +E M QA +      +DGVMIGRA Y N 
Sbjct: 190 ---HWEHEILDRVLEMRNSISPETLIMGNGDVETMEQAYQYSKEFGIDGVMIGRANYGNP 246

Query: 224 AMLTT--VDEYFSNPLTGSSP 242
            +L    V EY     T   P
Sbjct: 247 WLLNPNLVFEYIEPRTTDCGP 267


>gi|85715510|ref|ZP_01046491.1| dihydrouridine synthase TIM-barrel protein [Nitrobacter sp.
           Nb-311A]
 gi|85697705|gb|EAQ35581.1| dihydrouridine synthase TIM-barrel protein [Nitrobacter sp.
           Nb-311A]
          Length = 331

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 111/227 (48%), Gaps = 21/227 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLV 63
           TDR +R  A  L    L+ +EM  +D ++RG   ++L   +T   P  +Q+ G +   + 
Sbjct: 19  TDRPFRRLAESL-GAGLVVSEMTASDDLVRGRPMSVLRCEATGYGPHVVQLAGCEARWMA 77

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K 
Sbjct: 78  EGARIAEAAGADIIDINMGCPARHVTGGQSGSALMRDLDHALPLIEATVGAVKVPVTLKM 137

Query: 124 RIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
           R+G DD+ + A AL    +S+   GV  I +HAR      KG +          D+  V 
Sbjct: 138 RLGWDDRSLNAPALAQRAESV---GVQMITVHARTRCQFYKGCA----------DWQAVR 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
            + KE   + + +NG +     A+  L +   D VM+GR A     M
Sbjct: 185 AV-KEAVRIPVVVNGDITSFEAAVAALKASGADAVMVGRGAQGRPWM 230


>gi|221488352|gb|EEE26566.1| conserved hypothetical protein [Toxoplasma gondii GT1]
 gi|221508854|gb|EEE34423.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 668

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 84/316 (26%), Positives = 124/316 (39%), Gaps = 103/316 (32%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRG-DKKNILGFSTQEKPL-------- 50
           M+D+T+RH+R    L++    LYTEM+ V  A     D    L FS + K L        
Sbjct: 106 MMDYTNRHWRCLISLMSRRLTLYTEMVPVPPAPCESPDSSQDLPFSVKRKLLEEAGSLAS 165

Query: 51  -----ALQIGGADISKLVEAAKIVEDFGYNE----------------INLNVGCPSARVH 89
                 LQ+G          A+++ +F  +                 +NLN GCPS RV 
Sbjct: 166 IPNDVVLQVGVGSAQSATAVARVLNEFSVDRDHAEPVTRMRGKRTFLVNLNCGCPSPRVA 225

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL---------------------------------- 115
           +GSFG  LM +P  V    A MC+ L                                  
Sbjct: 226 KGSFGLILMEDPKRV----AEMCQILVDGANNREGQKRCSLDVMGKSARGDTKDRTVHTN 281

Query: 116 ------SIPVTVKCRIGVDDQ---------------IPAVA-------LRNLVKS-IKKS 146
                 S+ V+VKCR+G+++                 P  +       L   V + ++ S
Sbjct: 282 DSPETDSVAVSVKCRVGIEEDKQFLRSGSSPISRATTPYSSSSCTYDKLAEFVGTVVETS 341

Query: 147 GVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            V    IHAR  IL G LSPK N +IP    + VY +  + P +    NGG++    A +
Sbjct: 342 PVRHFIIHARPGILVGKLSPKQNLQIPQRRPEWVYRLCSDFPTVSFTFNGGVKSFQNAEE 401

Query: 206 ILPSVD----GVMIGR 217
            L + +    G+M+GR
Sbjct: 402 HLLNTNDKLAGIMVGR 417


>gi|237833185|ref|XP_002365890.1| hypothetical protein TGME49_072570 [Toxoplasma gondii ME49]
 gi|211963554|gb|EEA98749.1| hypothetical protein TGME49_072570 [Toxoplasma gondii ME49]
          Length = 668

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 83/316 (26%), Positives = 122/316 (38%), Gaps = 103/316 (32%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRG-DKKNILGFSTQEKPL-------- 50
           M+D+T+RH+R    L++    LYTEM+ V  A     D    L FS + K L        
Sbjct: 106 MMDYTNRHWRRLISLMSRRLTLYTEMVPVPPAPCESPDSSQDLPFSVKRKLLEEAGSLAS 165

Query: 51  -----ALQIGGADISKLVEAAKIVEDFGYNE----------------INLNVGCPSARVH 89
                 LQ+G          A+++ +F  +                 +NLN GCPS RV 
Sbjct: 166 VPNDVVLQVGVGSAQSATAVARVLNEFSVDRDHAEPVTRMRGKRTFLVNLNCGCPSPRVA 225

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL---------------------------------- 115
           +GSFG  LM +P  V    A MC+ L                                  
Sbjct: 226 KGSFGLILMEDPKRV----AEMCQILVDGANNREGQKRCSLDVMGKSARGDTKDRTVHTN 281

Query: 116 ------SIPVTVKCRIGVDD--------QIPAVALRNLVKS---------------IKKS 146
                 S+ V+VKCR+G+++          P  +      S               ++ S
Sbjct: 282 DSPETDSVAVSVKCRVGIEEDKQFLRSGSSPISSATTPYSSSSCTYDKLAEFVGTVVETS 341

Query: 147 GVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            V    IHAR  IL G LSPK N +IP    + VY +  + P +    NGG++    A +
Sbjct: 342 PVRHFIIHARPGILVGKLSPKQNLQIPQRRPEWVYRLCSDFPTVSFTFNGGVKSFQNAEE 401

Query: 206 ILPSVD----GVMIGR 217
            L + +    G+M+GR
Sbjct: 402 HLLNTNDKLAGIMVGR 417


>gi|184154699|ref|YP_001843039.1| hypothetical protein LAF_0223 [Lactobacillus fermentum IFO 3956]
 gi|227514339|ref|ZP_03944388.1| tRNA-dihydrouridine synthase [Lactobacillus fermentum ATCC 14931]
 gi|183226043|dbj|BAG26559.1| conserved hypothetical protein [Lactobacillus fermentum IFO 3956]
 gi|227087311|gb|EEI22623.1| tRNA-dihydrouridine synthase [Lactobacillus fermentum ATCC 14931]
          Length = 333

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 104/217 (47%), Gaps = 16/217 (7%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EMI    I+  +KK +  +G    E P+ LQI G     LVEAAK V E+   + I++N
Sbjct: 41  SEMISDRGIMYHNKKTLQMMGVDPVEHPMGLQIFGGTKETLVEAAKFVDENTDADVIDIN 100

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP  ++     G+  +L+P+ V + ++ +  A+  PVTVK R G DDQ        L 
Sbjct: 101 MGCPVNKIVNTEAGSRWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDDQHIFAVENALA 160

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
                +    +    RK + +G          + D+DI+ E+  +    F+  NG ++  
Sbjct: 161 AQRAGAAAVAMHGRTRKQMYRG----------HADWDILKEVASQLTIPFMA-NGDIKTA 209

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +A  +L     D +MIGRAA  N  MLT    Y  N
Sbjct: 210 EEAKYVLEYTGADAIMIGRAAMGNPWMLTQTVHYLEN 246


>gi|28209975|ref|NP_780919.1| nitrogen regulation protein nifR3 [Clostridium tetani E88]
 gi|28202410|gb|AAO34856.1| nitrogen regulation protein nifR3 [Clostridium tetani E88]
          Length = 322

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 124/239 (51%), Gaps = 30/239 (12%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILR-GDK-KNILGFSTQEKPLALQIGGADISKL 62
           TD  +R   + +    L+YTEM+ A A+    DK K++L FS +E P+A+QI G +   +
Sbjct: 21  TDLAFRGLCKRM-GCTLVYTEMVSAKALFYDSDKTKDMLRFSKEELPIAVQIFGKEPDIM 79

Query: 63  VEAAKIVED-FGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              A +VE  F  N+    I++N+GCP+ ++ +   G+ LM NP +  D + ++ K  + 
Sbjct: 80  ---ANVVEKYFNSNDNVCLIDINMGCPAPKIVKNGEGSALMKNPKLASDIVESIKKVSTK 136

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNL 174
           PVTVK R G D D I A+      K ++ SG + + IH   R+ + +G +          
Sbjct: 137 PVTVKFRKGFDNDNINAL---EFAKIMENSGADALTIHGRTREQMYQGKA---------- 183

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
           D++I+ ++K+      IG NG +     A+ ++ S   DGVM+ R A  N  +   + E
Sbjct: 184 DWEIIKKVKESVKIPVIG-NGDVFTGEDAINMIESTNCDGVMVARGALGNPWIFNQISE 241


>gi|109067839|ref|XP_001093588.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Macaca mulatta]
          Length = 317

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   ++  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVETP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  + +GV+ I +H R A        + R  P + 
Sbjct: 152 GFSVSIKIRIH-DDLKRTV---DLCRKAEATGVSWITVHGRTA--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSI-KIIKENMSIPVIANGDIRSLKEAENVWQITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|149177590|ref|ZP_01856192.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
 gi|148843570|gb|EDL57931.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
          Length = 365

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 121/238 (50%), Gaps = 18/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           +  +T+  +R   R L    L  T+++ A  +L G +K +    T  ++ P A+QI G++
Sbjct: 35  LAGYTNLPFRRIVRELGGVGLATTDLVNARGLLEGSEKTLQLTQTCPEDSPFAVQIFGSE 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+++E  G + I++N+GCP  R+ +G  GA +M  P      +  + +A+ IP
Sbjct: 95  PQQMKDAAQLLESRGVHSIDINMGCPVNRIVKGGAGASMMCRPSDTVSLVQTVVEAVKIP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           V+VK R+G DD    ++     +  +K GV  + IH   R+   +G+          +++
Sbjct: 155 VSVKMRLGWDDS--ELSAPFFSREFEKVGVVAVAIHGRTREQGFRGV----------VNH 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
           D +  + +    + +  NG + ++++A  +L +    GV IGR A  N  +   + ++
Sbjct: 203 DGIRRVVEAVDSIPVIGNGDVTNVAEADFMLKTTGCAGVSIGRGALANPWIFRQLVQW 260


>gi|257467996|ref|ZP_05632092.1| nitrogen regulation protein NIFR3 [Fusobacterium ulcerans ATCC
           49185]
 gi|317062282|ref|ZP_07926767.1| nitrogen regulation protein NIFR3 [Fusobacterium ulcerans ATCC
           49185]
 gi|313687958|gb|EFS24793.1| nitrogen regulation protein NIFR3 [Fusobacterium ulcerans ATCC
           49185]
          Length = 320

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 116/236 (49%), Gaps = 19/236 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  YR   +    + LL+TEM+  +A+    +K +       +  ++Q+ G DI K+VE
Sbjct: 13  TDYTYRGILKEFKPD-LLFTEMVSINALEVACEKTLKVILRLREGDSVQLFGKDIKKMVE 71

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK 122
           +AK VE  G   I++N GCP  ++    +GA LM  P++V   ++ M  AL     +++K
Sbjct: 72  SAKFVESLGVKHIDINSGCPMKKIVNNGYGAALMEQPELVRAMLSEMRSALDDKTDLSIK 131

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G  +    V    + K  +++G   I +H R         ++       D+ ++ ++
Sbjct: 132 IRVGYKESKNPV---EIAKIAQETGCKHITVHGR--------TREQMYTGKADWSLIKQV 180

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            KE+ D+ +  NG +   ED  + +     VDG+M+ R  + N  ++  + EYF +
Sbjct: 181 -KESVDIPVIGNGDIFTAEDAKERVD-YSGVDGIMLARGIFGNPWLIRDIREYFEH 234


>gi|31742496|ref|NP_853559.1| tRNA-dihydrouridine synthase 4-like [Homo sapiens]
 gi|114615410|ref|XP_001164272.1| PREDICTED: tRNA-dihydrouridine synthase 4-like isoform 5 [Pan
           troglodytes]
 gi|332868275|ref|XP_519306.3| PREDICTED: tRNA-dihydrouridine synthase 4-like isoform 6 [Pan
           troglodytes]
 gi|110808215|sp|O95620|DUS4L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 4-like; AltName:
           Full=pp35
 gi|51095148|gb|EAL24391.1| protein similar to E.coli yhdg and R. capsulatus nifR3 [Homo
           sapiens]
 gi|119603807|gb|EAW83401.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
 gi|119603808|gb|EAW83402.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
 gi|119603810|gb|EAW83404.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
          Length = 317

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   ++  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVQDMVKQVRNQVETP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  + +GV+ I +H R A        + R  P + 
Sbjct: 152 GFSVSIKIRIH-DDLKRTV---DLCQKAEATGVSWITVHGRTA--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSI-KIIKENMSIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|226951473|ref|ZP_03821937.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. ATCC 27244]
 gi|226837766|gb|EEH70149.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. ATCC 27244]
          Length = 341

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 79/332 (23%), Positives = 153/332 (46%), Gaps = 38/332 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDTVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  + +  
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGR--------TREDMYLNHAR 182

Query: 176 YDIVYEIKKENPDLFIGL----NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
           Y+++ ++K+      IG+    NG ++   +A  +L     D +MIGRAA     +   +
Sbjct: 183 YELIKQVKQ-----LIGIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREI 237

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
             Y       ++P  + V       +S     Y     +SG ++ +  +H+     G  +
Sbjct: 238 AHYLKTGEHLATPDISEVKAVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRS 292

Query: 290 SRRCRH-ILTVEAGASTATHHIIETAFNLMIE 320
           S   R  +  VE+ A  A   ++E  F+ +++
Sbjct: 293 SNEFRQNMYKVESTADQAK--VVEAYFDQLLD 322


>gi|58584719|ref|YP_198292.1| tRNA-dihydrouridine synthase [Wolbachia endosymbiont strain TRS of
           Brugia malayi]
 gi|58419035|gb|AAW71050.1| tRNA-dihydrouridine synthase [Wolbachia endosymbiont strain TRS of
           Brugia malayi]
          Length = 310

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 88/298 (29%), Positives = 133/298 (44%), Gaps = 33/298 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++   ++++      E   A+Q+ G +   + E
Sbjct: 15  TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSMQKAKVDE-LTAVQLAGCEPDIMAE 72

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V  G  G+ LM N     + I A+ KA+++PVTVK R
Sbjct: 73  AAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRNEKKAAEIIEAVVKAVNVPVTVKIR 132

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            G +++      RN   L K  +  G   I +H R          D + I N+       
Sbjct: 133 TGWNNE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQADWKFIRNV------- 180

Query: 182 IKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             KE   + + +NG    L D+  ALK     DGVMIGR AY    ++     + S    
Sbjct: 181 --KEQVKIPVIVNGDIKSLNDIQNALK-ESRADGVMIGRGAYGRPWLINQAINFLSGSEV 237

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLF-HGFPNSRRCR 294
            S P  +        K+S  +  Y     + G     +I R  IG +  GF NS   R
Sbjct: 238 -SEPTAS-------EKLSIILEHYDNILEYYGNDAGIKIARKHIGWYSSGFKNSSEFR 287


>gi|113475058|ref|YP_721119.1| nifR3 family TIM-barrel protein [Trichodesmium erythraeum IMS101]
 gi|110166106|gb|ABG50646.1| putative TIM-barrel protein, nifR3 family [Trichodesmium erythraeum
           IMS101]
          Length = 334

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/297 (22%), Positives = 130/297 (43%), Gaps = 22/297 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  +    +   I+     E+P+++Q+       L 
Sbjct: 36  TDLVFRRLVRRHAPESMMYTEMVNATGLHYVKELPQIMEVDNNERPISIQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA++    G + +++N+GCP  ++ +   G+ L+  P++ G+ ++ + KA+ IPVTVK 
Sbjct: 96  EAAEMAVKEGADTVDINMGCPVNKITKNGGGSSLLRQPELAGEIVSKVVKAVPIPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  +Q   + +    + ++ +G   + +H R        P     I  +         
Sbjct: 156 RIGWSNQ--EINILEFAQRMEDAGAQMLTLHGRTRAQGYNGPARWEWITKV--------- 204

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           KE   + +  NG +  +  A++ L     DGVM  R       ++  +D +  N +   S
Sbjct: 205 KEILSIPVIANGDIFSVDAAIRCLEETRADGVMCSRGTLGYPFLVGEIDYFLKNGVKKVS 264

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL 297
           P           K+  +     A   + G + ++Q  +H+     GFP +   R  L
Sbjct: 265 PTAA-------EKLECAKEHLRALWEYKGDRGIRQARKHLTWYSKGFPGAGELRGQL 314


>gi|149184568|ref|ZP_01862886.1| tRNA-dihydrouridine synthase [Erythrobacter sp. SD-21]
 gi|148831888|gb|EDL50321.1| tRNA-dihydrouridine synthase [Erythrobacter sp. SD-21]
          Length = 339

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 120/244 (49%), Gaps = 20/244 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI ++A +R  ++++    +   E+P+++Q+ G D S +
Sbjct: 34  TDLPFRKLVRKY-GSGLNVTEMIASEAAIRETRQSVQKAAWDPIEEPVSMQLVGCDPSSM 92

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAK+ +  G + I++N GCP  +V     G+ LM    +    + A  +A+ +PVTVK
Sbjct: 93  AEAAKLQQGNGADIIDINFGCPVRKVVGQLAGSALMREVPLATRLMEATVRAVDVPVTVK 152

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVY 180
            R+G D     +    L +  +  GV  + +H   R  + KG          + D++ V 
Sbjct: 153 MRMGWDHA--DLNAPELARIAEDLGVKMVTVHGRTRNQMYKG----------SADWEFVR 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           ++ K+  ++ + +NG +  +  A K L     DG+MIGR AY N  +L  V  ++     
Sbjct: 201 KV-KDAVNIPVIVNGDICTIDDAAKALDQSGADGLMIGRGAYGNPWLLAQVMHWWHTGER 259

Query: 239 GSSP 242
             SP
Sbjct: 260 LESP 263


>gi|4097493|gb|AAD00100.1| PP35 [Homo sapiens]
          Length = 307

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 78/283 (27%), Positives = 131/283 (46%), Gaps = 32/283 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   ++  K     F+T +   PL +Q    D
Sbjct: 24  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 83  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVQDMVKQVRNQVETP 141

Query: 119 -VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             +V  +I ++D +      +L +  + +GV+ I +H R A        + R  P + YD
Sbjct: 142 GFSVSIKIRINDDLKRTV--DLCQKAEATGVSWITVHGRTA--------EERHQP-VHYD 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E    
Sbjct: 191 SI-KIIKENMCIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE---- 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 246 -----TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 280


>gi|213420477|ref|ZP_03353543.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 79

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 39/76 (51%), Positives = 56/76 (73%)

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
           IHARKA L GLSPK+NR+IP LDY  VY++K++ P L + +NGG++ + +A + L  +DG
Sbjct: 4   IHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDG 63

Query: 213 VMIGRAAYKNSAMLTT 228
           VM+GR AY+N  +L  
Sbjct: 64  VMVGREAYQNPGILAA 79


>gi|326560525|gb|EGE10907.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 7169]
          Length = 341

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 131/278 (47%), Gaps = 26/278 (9%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL +AA+     G   +++N+
Sbjct: 59  SEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAEPDKLAQAAQFQVANGAQIVDINM 118

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + +   A+ +PVT+K R+G      A    N++K
Sbjct: 119 GCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVPVTLKTRLGF-----ANGQENILK 173

Query: 142 SIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +   ++GV  I IH R         +++       Y+++ ++KK    + I +NG ++
Sbjct: 174 IAQIAEQAGVAAITIHGRT--------REDFYTGQARYELITQVKKA-AKIPIIVNGDID 224

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +AL I      D VMIGRAA     +   +  + +     +SP    + +   R + 
Sbjct: 225 SPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTGELLASPTVGEIHEVVLRHLD 284

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                Y     +SG ++ +  +H+     G PNS   R
Sbjct: 285 ELYRFYGE---YSGCRIAR--KHIAWYTGGLPNSNAFR 317


>gi|261379246|ref|ZP_05983819.1| tRNA-dihydrouridine synthase B [Neisseria subflava NJ9703]
 gi|284797670|gb|EFC53017.1| tRNA-dihydrouridine synthase B [Neisseria subflava NJ9703]
          Length = 334

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 116/241 (48%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPSLRHTKKTLRRSDFEGEGGVVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +V + + A+  A+ +P
Sbjct: 76  PQQMAEAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAEILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  ++   +P +A     K  ++SG+  + IH   R  + KG           
Sbjct: 136 VTLKTRLGWHNEHQNLPTIA-----KIAEESGIAALAIHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A  +  +   +  
Sbjct: 181 ARYELIAETKG-RLNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGSPWLFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|326565385|gb|EGE15562.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 103P14B1]
 gi|326573374|gb|EGE23342.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 101P30B1]
          Length = 341

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 131/278 (47%), Gaps = 26/278 (9%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL +AA+     G   +++N+
Sbjct: 59  SEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAEPDKLAQAAQFQVANGAQIVDINM 118

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + +   A+ +PVT+K R+G      A    N++K
Sbjct: 119 GCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVPVTLKTRLGF-----ANGQENILK 173

Query: 142 SIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +   ++GV  I IH R         +++       Y+++ ++KK    + I +NG ++
Sbjct: 174 IAQIAEQAGVAAITIHGRT--------REDFYTGQARYELITQVKKA-AKIPIIVNGDID 224

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +AL I      D VMIGRAA     +   +  + +     +SP    + +   R + 
Sbjct: 225 SPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTGELLASPTVGEIHEVVLRHLD 284

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                Y     +SG ++ +  +H+     G PNS   R
Sbjct: 285 ELYRFYGE---YSGCRIAR--KHIAWYTGGLPNSNAFR 317


>gi|326575731|gb|EGE25654.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis CO72]
          Length = 341

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 131/278 (47%), Gaps = 26/278 (9%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL +AA+     G   +++N+
Sbjct: 59  SEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAEPDKLAQAAQFQVANGAQIVDINM 118

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + +   A+ +PVT+K R+G      A    N++K
Sbjct: 119 GCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVPVTLKTRLGF-----ANGQENILK 173

Query: 142 SIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +   ++GV  I IH R         +++       Y+++ ++KK    + I +NG ++
Sbjct: 174 IAQIAEQAGVAAITIHGRT--------REDFYTGQARYELITQVKKA-AKIPIIVNGDID 224

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +AL I      D VMIGRAA     +   +  + +     +SP    + +   R + 
Sbjct: 225 SPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTGELLASPTVGEIHEVVLRHLD 284

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                Y     +SG ++ +  +H+     G PNS   R
Sbjct: 285 ELYRFYGE---YSGCRIAR--KHIAWYTGGLPNSNAFR 317


>gi|260588921|ref|ZP_05854834.1| tRNA-dihydrouridine synthase B [Blautia hansenii DSM 20583]
 gi|260540700|gb|EEX21269.1| tRNA-dihydrouridine synthase B [Blautia hansenii DSM 20583]
          Length = 318

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 76/305 (24%), Positives = 145/305 (47%), Gaps = 29/305 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A AI   +K  ++++    +E+P++LQ+ G++
Sbjct: 19  MAGVTDLPFRLLCKE-QGAGLICTEMVSAKAIHFKNKNTESLMEIDERERPVSLQLFGSE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E   ++ +++N+GCP  +V     G+ LM NP +V + +  + +A+  P
Sbjct: 78  PDLMADIAKQIEYRNFDILDINMGCPVPKVVNNGEGSALMKNPKLVHEIVYKVSRAIKKP 137

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +TVK R G  +D + AV +  +++    + V       R+    G +          D+D
Sbjct: 138 LTVKIRKGFTEDSVNAVEIAKILEDAGAAAVAVH-GRTREQYYSGQA----------DWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +    +A K++     DG+MIGRA   N  + + +  Y   
Sbjct: 187 IIRQVKEAVSIPVIG-NGDVTSPEKAEKLVKETGCDGIMIGRAVQGNPWLFSEILYYQE- 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRR 292
             TG    K  ++     +I   M  +A   L   G    ++++ +H+     G P+S  
Sbjct: 245 --TGKIKPKPSME-----EIKEMMLRHARLQLEYKGTYTGMREMRKHVAWYTSGMPHSAS 297

Query: 293 CRHIL 297
            R ++
Sbjct: 298 VRRMV 302


>gi|296113151|ref|YP_003627089.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis RH4]
 gi|295920845|gb|ADG61196.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis RH4]
 gi|326560349|gb|EGE10736.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 46P47B1]
 gi|326565746|gb|EGE15908.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis BC1]
 gi|326577196|gb|EGE27090.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis O35E]
          Length = 341

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 131/278 (47%), Gaps = 26/278 (9%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL +AA+     G   +++N+
Sbjct: 59  SEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAEPDKLAQAAQFQVANGAQIVDINM 118

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + +   A+ +PVT+K R+G      A    N++K
Sbjct: 119 GCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVPVTLKTRLGF-----ANGQENILK 173

Query: 142 SIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +   ++GV  I IH R         +++       Y+++ ++KK    + I +NG ++
Sbjct: 174 IAQIAEQAGVAAITIHGRT--------REDFYTGQARYELITQVKKA-AKIPIIVNGDID 224

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +AL I      D VMIGRAA     +   +  + +     +SP    + +   R + 
Sbjct: 225 SPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTGELLASPTVGEIHEVVLRHLD 284

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                Y     +SG ++ +  +H+     G PNS   R
Sbjct: 285 ELYRFYGE---YSGCRIAR--KHIAWYTGGLPNSNAFR 317


>gi|291391307|ref|XP_002712160.1| PREDICTED: dihydrouridine synthase 4-like [Oryctolagus cuniculus]
          Length = 317

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 84/288 (29%), Positives = 130/288 (45%), Gaps = 42/288 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R   N  L YT MIVA   ++  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKY-NCDLCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSEAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
              V++K RI  D       LR   +L +  + +GV+ I IH R          + R  P
Sbjct: 152 RFSVSIKIRIHED-------LRRTVDLCQKAEATGVSWITIHGRTV--------EERHQP 196

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
            + YD + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +
Sbjct: 197 -VHYDAI-KIIKENISIPVIANGDIRSLKEAENVWQVTGTDGVMVARGLLANPAMFAGYE 254

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
           E         +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 255 E---------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|326564876|gb|EGE15080.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 12P80B1]
          Length = 340

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 131/278 (47%), Gaps = 26/278 (9%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EMI+AD  L   KK++    F  +  P++ QI GA+  KL +AA+     G   +++N+
Sbjct: 58  SEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAEPDKLAQAAQFQVANGAQIVDINM 117

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + +   A+ +PVT+K R+G      A    N++K
Sbjct: 118 GCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVPVTLKTRLGF-----ANGQENILK 172

Query: 142 SIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +   ++GV  I IH R         +++       Y+++ ++KK    + I +NG ++
Sbjct: 173 IAQIAEQAGVAAITIHGRT--------REDFYTGQARYELITQVKKA-AKIPIIVNGDID 223

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +AL I      D VMIGRAA     +   +  + +     +SP    + +   R + 
Sbjct: 224 SPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTGELLASPTVGEIHEVVLRHLD 283

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                Y     +SG ++ +  +H+     G PNS   R
Sbjct: 284 ELYRFYGE---YSGCRIAR--KHIAWYTGGLPNSNAFR 316


>gi|296284138|ref|ZP_06862136.1| tRNA-dihydrouridine synthase [Citromicrobium bathyomarinum JL354]
          Length = 339

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 121/239 (50%), Gaps = 24/239 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI ++A +R  ++++    +   E+P+++Q+ G D + +
Sbjct: 34  TDMPFRTLVRRY-GSGLNVTEMIASEAAIRETRQSVQKAAWDRIEEPVSMQLVGCDPASM 92

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAK+ E  G   I++N GCP  +V     G+ LM    +    + A  KA+ +PVTVK
Sbjct: 93  AEAAKLQEGNGAAIIDINFGCPVRKVVGQLAGSALMREVPLATKLMEATVKAVDVPVTVK 152

Query: 123 CRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
            R+G D D + A  L  + + +   GV  I +H   R  + KG          + D+  +
Sbjct: 153 MRMGWDHDSLNAPELARIAEDL---GVKMITVHGRTRNQMYKG----------SADWSFI 199

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++ K+  ++ + +NG    ++D ++AL+     DG+MIGR AY    +L  V  ++  
Sbjct: 200 AKV-KDAVNIPVIVNGDICSIDDAARALE-QSGADGLMIGRGAYGRPWLLGQVMHWWQT 256


>gi|167749581|ref|ZP_02421708.1| hypothetical protein EUBSIR_00539 [Eubacterium siraeum DSM 15702]
 gi|167657435|gb|EDS01565.1| hypothetical protein EUBSIR_00539 [Eubacterium siraeum DSM 15702]
          Length = 327

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/284 (25%), Positives = 129/284 (45%), Gaps = 26/284 (9%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           ALL  EM  A  +   D+K   +L  +  E+P+A+Q+ G++   + +AA I   +  + I
Sbjct: 38  ALLTGEMASAKGLCYSDRKTAALLTVTDYERPMAIQLFGSEPEFMAKAAVIAAQYKPDFI 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N GCP  +V     G+ LM +P ++G  + A+ KA  IPVTVK R G D++   V   
Sbjct: 98  DINCGCPVPKVAGNGAGSALMNDPVLLGHIVEAVVKATDIPVTVKIRKGWDEK--NVNAV 155

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + +  ++SG + + +H R         K+       D +I+ E+K+      IG NG +
Sbjct: 156 EVARVAQESGASAVAVHGRT--------KNQMYSGKADLEIIAEVKQALSIAVIG-NGDV 206

Query: 198 EDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI---KTRVDKDFW 252
           +      ++      D VM+GRAA     + + +  Y     T   P    +  +  +  
Sbjct: 207 DSGESCKRMYDYTGCDLVMVGRAACGRPWIFSEIKHYLETGETLPPPSPDEQLEIMNEHI 266

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           R + A   +Y          +++  +H      G P + + R++
Sbjct: 267 RLLCADKGEYIG--------MKEARKHTAWYLKGRPGAAKLRNM 302


>gi|295104372|emb|CBL01916.1| tRNA-U20-dihydrouridine synthase [Faecalibacterium prausnitzii
           SL3/3]
          Length = 339

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 77/301 (25%), Positives = 134/301 (44%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNI--LGFSTQEKPLALQIGG 56
           M  +TD   R   RL+  +   +T  EM+ + A++ GD K +  L  +    P  +QI G
Sbjct: 20  MAGFTDAPCR---RLMAQHGAGFTVSEMVSSRALVYGDHKTVSLLKAAPNGAPYGVQIFG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + EA   +E + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  +     
Sbjct: 77  EVPEIMGEATAAIEQYEFDFVDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEQVVAHTK 136

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            PVTVK R G D D I AV      K+ +++G   + +HAR         ++    P +D
Sbjct: 137 RPVTVKMRKGWDADHITAV---ECAKACEQAGAALVAVHART--------REQMYTPGID 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            +I+  +K       +G NG +     AL+++   + DGVMI R+A  +  +   V+   
Sbjct: 186 PEIIARVKDAVKVPVLG-NGDIHCAEDALRMVRETNCDGVMIARSALGDPWLFERVNAAL 244

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P      ++ R++    R+    M +     +       Q   +M GL       R 
Sbjct: 245 EGLPAPKEPNLQARMNA--LRRQVEEMVEQKGEFVAMPQARAQTMHYMKGLKGAAALRRY 302

Query: 293 C 293
           C
Sbjct: 303 C 303


>gi|325201880|gb|ADY97334.1| dihydrouridine synthase [Neisseria meningitidis M01-240149]
 gi|325208367|gb|ADZ03819.1| dihydrouridine synthase [Neisseria meningitidis NZ-05/33]
          Length = 336

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 114/241 (47%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNAQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PAVA     +  +  G+  + +H   R  + KG +         
Sbjct: 136 VTLKTRLGWHDDHKNLPAVA-----RIAEDCGIAALAVHGRTRTQMYKGEAA-------- 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 183 --YDLIAETKCR-LNIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|126664725|ref|ZP_01735709.1| hypothetical protein MELB17_02765 [Marinobacter sp. ELB17]
 gi|126631051|gb|EBA01665.1| hypothetical protein MELB17_02765 [Marinobacter sp. ELB17]
          Length = 332

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 113/223 (50%), Gaps = 16/223 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    L  +EM++AD+ +   +K+   L    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRM-GAGLAVSEMVIADSKMWHTRKSRSRLNHQGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +    G   I++N+GCP+ +V   + G+ LM +  +V   + A+  A+ IP
Sbjct: 80  PEMLAQAACMNAASGAQIIDINMGCPAKKVCNKAAGSALMKDEALVLQILKAVVAAVDIP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+      +  + +  +++G+  + IH R         + ++   N +YD 
Sbjct: 140 VTLKMRTGWDENHRNAPI--IARMAEEAGIQALAIHGRT--------RTDKYTGNAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           +  +K +   + +  NG +    +A ++L     DG++IGRAA
Sbjct: 190 IARVKSDV-GIPVFANGDITSPEKAREVLQYTGADGLLIGRAA 231


>gi|332237993|ref|XP_003268188.1| PREDICTED: tRNA-dihydrouridine synthase 4 isoform 1 [Nomascus
           leucogenys]
 gi|332237995|ref|XP_003268189.1| PREDICTED: tRNA-dihydrouridine synthase 4 isoform 2 [Nomascus
           leucogenys]
          Length = 317

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MI+A   ++  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIIAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVETP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  + +GV+ I +H R A        + R  P + 
Sbjct: 152 GFSVSIKIRIH-DDLKRTV---DLCRKAEATGVSWITVHGRTA--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSI-KIIKENMSIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|304317751|ref|YP_003852896.1| hypothetical protein Tthe_2344 [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302779253|gb|ADL69812.1| TIM-barrel protein, nifR3 family [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 333

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 135/303 (44%), Gaps = 26/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ YR   + +      YTEM+ A  +  G +    L     E+ +ALQI G+D 
Sbjct: 31  MAGVTDKPYRLICKDM-GCGFAYTEMVSAKGLYYGSENTEFLTDIDDEENVALQIFGSDP 89

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK +       I++N+GCP+ ++ +   G+ LML PD+    I A+ K    PV
Sbjct: 90  YIMGEIAKRLNTSNAKTIDINMGCPTPKIVKNGDGSALMLKPDLAESIIKAVVKNSIKPV 149

Query: 120 TVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K R G  DD I AV +  + +S    GV  + IH R         ++       D+DI
Sbjct: 150 TIKIRKGWDDDHINAVEIAKMAES---CGVKAVAIHGR--------TREQFYSGRADWDI 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K       IG NG +     A +++     D VM+GR A  N  +   +  Y +  
Sbjct: 199 IKKVKDNLKIPVIG-NGDIFTPEDAKRMIDETGCDAVMVGRGAEGNPWIFKRILHYLN-- 255

Query: 237 LTGSS-PIKTRVDK-DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            TG   P  T  +K D   K    M DY   H+     + ++ +H+     G   + + +
Sbjct: 256 -TGEILPEPTVSEKIDMILKHLDMMIDYKGEHVG----ILEMRKHIAWYLKGIRGASKIK 310

Query: 295 HIL 297
            ++
Sbjct: 311 QMV 313


>gi|126662469|ref|ZP_01733468.1| probable TIM-barrel protein, NifR3 family [Flavobacteria bacterium
           BAL38]
 gi|126625848|gb|EAZ96537.1| probable TIM-barrel protein, NifR3 family [Flavobacteria bacterium
           BAL38]
          Length = 316

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 123/242 (50%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L   + L+Y+E I ++ ++R     K  L     E+P+ +QI G D
Sbjct: 1   MEDVSDPPFRRLCKLHGAD-LMYSEFISSEGLIRDAMKSKQKLDIFDYERPVGIQIFGGD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +++IV+    + +++N GCP  +V     GA ++ + D++     A+ K  S+P
Sbjct: 60  EEAMEMSSRIVDAVQPDLVDINFGCPVKKVVCKGAGAGVLKDVDLMVRLTKAVIKGTSLP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+   ++ +  + + ++  GV  + +HAR    + KG S          D+
Sbjct: 120 VTVKTRLGWDES--SINIDEVAERLQDIGVQALTVHARTRAQMYKGHS----------DW 167

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             +  I KENP + + +  NG ++   +AL+      +DG+MIGRAA     +   +  Y
Sbjct: 168 SHIQRI-KENPRITMPIFGNGDIDSPEKALEYKNKFGLDGMMIGRAAIGYPWIFNEIKHY 226

Query: 233 FS 234
           F+
Sbjct: 227 FA 228


>gi|103486763|ref|YP_616324.1| dihydrouridine synthase TIM-barrel protein nifR3 [Sphingopyxis
           alaskensis RB2256]
 gi|98976840|gb|ABF52991.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sphingopyxis
           alaskensis RB2256]
          Length = 332

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 114/234 (48%), Gaps = 18/234 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G  
Sbjct: 23  MTGVTDLPFRKLVRYY-GSGLNVTEMIASQAAIRETRQSIQKAAWDPVEEPVSMQLVGCT 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ ED G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 82  PYEMGEAAKLNEDRGAAIIDINMGCPVRKVTNGDAGSALMRDLRLAAALIDACVKAVSVP 141

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R+G   D + A  L ++ + +   G   + +H R         ++       D+ 
Sbjct: 142 VTVKMRMGWCHDSLNAPELAHIAEDL---GAKLVTVHGRT--------RNQMYRGEADWG 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            V ++ KE   + + +NG +     A   L     DGVMIGR AY    +L  V
Sbjct: 191 FVRKV-KEAVSIPVIVNGDICSADDARTALAQSGADGVMIGRGAYGRPWLLGQV 243


>gi|205374743|ref|ZP_03227537.1| tRNA-dihydrouridine synthase [Bacillus coahuilensis m4-4]
          Length = 334

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+PL   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNTESYCHPDGIQSVRGRLTFTEDEQPLVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V +   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGMAEMGFKGIDLNMGCPVPNVTQNGKGSGLILRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGFSD---LEEWRGWLTHILKQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK++    VDGVMIGR  + N
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRETGLKLVEQYGVDGVMIGRGIFHN 238


>gi|313676850|ref|YP_004054846.1| tRNA-u20-dihydrouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312943548|gb|ADR22738.1| tRNA-U20-dihydrouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 332

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 81/311 (26%), Positives = 142/311 (45%), Gaps = 45/311 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGA 57
           M D +D  +R   +   N A L+YTE I ++ ++R     +  L     EKP+ +QI G 
Sbjct: 19  MEDVSDPPFRAVCK--ENGADLMYTEFISSEGLIRDAIKSRQKLDIFDYEKPIGIQIFGG 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  A  IV     + +++N GCP  +V     GA ++ + D++     A+ K+  +
Sbjct: 77  DEEAMSMATSIVNVTQPDLVDINFGCPVKKVVTKGAGAGVLKDVDLMVRLTEAVVKSTDL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G D+   +  +  + + ++  G+  + IH   R+ + KG +          D
Sbjct: 137 PVTVKTRLGWDES--SKNIEEVAERLQDVGIKALSIHGRTRQQMYKGEA----------D 184

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           + ++ ++K  NP + I +  NG ++   +AL+      VDG+MIGRAA     +   +  
Sbjct: 185 WSLIAKVKN-NPRINIPIFGNGDIDSPQKALEYRNRYGVDGLMIGRAAIGYPWIFNEIKH 243

Query: 232 YFSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQ--QITRHMIGL 283
           YF        P ++ R++              A +HL       G KL   ++ RH    
Sbjct: 244 YFETGEVLPPPNLEDRIET-------------AKKHLKFSVEWKGEKLGIFEMRRHYTNY 290

Query: 284 FHGFPNSRRCR 294
           F G P+ +  R
Sbjct: 291 FKGIPHFKPYR 301


>gi|149369324|ref|ZP_01889176.1| probable TIM-barrel protein, NifR3 family [unidentified eubacterium
           SCB49]
 gi|149356751|gb|EDM45306.1| probable TIM-barrel protein, NifR3 family [unidentified eubacterium
           SCB49]
          Length = 332

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 140/302 (46%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA 
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE  G + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LESMLRSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++  G   I IH R    + KG          + D+
Sbjct: 138 VTVKTRLGWDHD--SIKIVEVAERLQDVGCKAISIHGRTRAQMYKG----------DADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  N  + I +  NG ++   +A+ +     +DG MIGRA+         V  +
Sbjct: 186 APIAEVKN-NQRMHIPVFGNGDVDTPEKAILMRDKYGLDGAMIGRASIGYPWFFKEVKHF 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +     + P  T   +   R +  ++ D+    L     + +  RH    F G P+ + 
Sbjct: 245 MATGTHAAPPTMTERVEAARRHLQMAI-DWKGETL----GVFETRRHYTNYFKGIPHFKE 299

Query: 293 CR 294
            R
Sbjct: 300 YR 301


>gi|269302558|gb|ACZ32658.1| dihydrouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 335

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 44/158 (27%), Positives = 91/158 (57%), Gaps = 5/158 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  ++D  YR  + L     L++ EM+  + +L   ++   +L ++   +P+  Q+ G++
Sbjct: 21  LAGFSDYPYRCMSALY-QPGLMFCEMVKVEGMLYAPERTSKLLDYNENMRPIGAQLCGSN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAAKI+E  G++ I+LN GCP+ ++ +   G+ L+  P+++G  +  +  ++SIP
Sbjct: 80  PETSGEAAKILEGLGFDLIDLNCGCPTDKITKDGSGSGLLKTPELIGRILDKIINSVSIP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VTVK R G D  +  + + + V+ I+ +G + +++H R
Sbjct: 140 VTVKIRSGWD--MEHINIEDTVRIIRDAGASAVFVHGR 175


>gi|118595290|ref|ZP_01552637.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Methylophilales
           bacterium HTCC2181]
 gi|118441068|gb|EAV47695.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Methylophilales
           bacterium HTCC2181]
          Length = 341

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 125/255 (49%), Gaps = 30/255 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   +      +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKSF-GAGVAVSEMVTSNSLLYGSEKTKRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAK   D G   I++N+GCP+ ++     G+ L+ +  +V D + A+  ++ IP
Sbjct: 76  PKMMADAAKYNRDRGAQIIDINMGCPAKKICNVMAGSALLKHEQLVDDILQAVVGSVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D +      RN +K  +   ++G+  + IH R    + +G          +
Sbjct: 136 VTLKIRTGWDRE-----NRNAIKIAQIAEEAGIKALAIHGRTRACLYRG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD + E+ K+N ++ +  NG +    +A  +L     D VMIGRAA     +   ++ 
Sbjct: 181 AEYDTIAEV-KQNINIPVIANGDIVSPEKAQYVLNYTKADAVMIGRAAQGRPWIFREIEH 239

Query: 232 YFSNPLTGS-SPIKT 245
           +     TGS  P+ T
Sbjct: 240 FLE---TGSHHPLPT 251


>gi|289433582|ref|YP_003463454.1| dihydrouridine synthase family protein [Listeria seeligeri serovar
           1/2b str. SLCC3954]
 gi|289169826|emb|CBH26364.1| dihydrouridine synthase family protein [Listeria seeligeri serovar
           1/2b str. SLCC3954]
          Length = 331

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 72/221 (32%), Positives = 115/221 (52%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +        +H R  +   +G          + ++D++ ++K+E    F+  NG
Sbjct: 156 NALAAERAGAAAVA-MHGRTRVQMYEG----------SANWDVLRDVKRELKIPFMA-NG 203

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A +IL     DGVMIGRAA  N  M+    +Y  
Sbjct: 204 DVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKYLE 244


>gi|226942119|ref|YP_002797193.1| NifR3 [Laribacter hongkongensis HLHK9]
 gi|226717046|gb|ACO76184.1| NifR3 [Laribacter hongkongensis HLHK9]
          Length = 341

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 118/240 (49%), Gaps = 18/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L  +EMI ++  L   +K +     + +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCRRF-GAGLAVSEMIASNTALATSRKTLKRADHTGEPGPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+   D+G   I++N+GCP+ +V   + G+ L+ +  +V   + A+ +A+ +P
Sbjct: 76  PQEMADAARRNVDYGAQIIDINMGCPAKKVCNVAAGSALLKDEPLVARILEAVVRAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G   +   A+A+  L    ++SG+  + +H R         ++++ +   +YD
Sbjct: 136 VTLKTRTGWSREHRNALAVARLA---EESGIAALALHGRT--------REDKYLGEAEYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       I  NG ++   +A  +L     D +MIGRAA     +   +  + + 
Sbjct: 185 TIRAVKAAVRIPVIA-NGDIDSPEKARHVLDYTGADAIMIGRAAQGRPWLFRDIQHFLAT 243


>gi|254523878|ref|ZP_05135933.1| tRNA-dihydrouridine synthase B [Stenotrophomonas sp. SKA14]
 gi|219721469|gb|EED39994.1| tRNA-dihydrouridine synthase B [Stenotrophomonas sp. SKA14]
          Length = 357

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 112/242 (46%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K+I  +    +  P+++QI G +
Sbjct: 43  MAGVTDKPFRLLCKRL-GAGLAASEMTISDPRFWNTRKSIHRMDHDGEPAPISVQIAGTE 101

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 102 PQQLAEAARYNVDHGAQIIDINMGCPAKKVCNAWAGSALMRDEQLVARILEAVVNAVDVP 161

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  + SG+  + +H R         +D       +
Sbjct: 162 VTLKIRTGWD-----CDHRNGPLIARIAEDSGIAALAVHGRT--------RDQHYTGQAE 208

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + EIK     + +  NG ++   +A  +L    VD VMIGR+A     +   V  Y 
Sbjct: 209 YGTIGEIKAAL-RIPVIANGDIDSPQKAALVLKQTGVDAVMIGRSAQGRPWIFREVAHYL 267

Query: 234 SN 235
           + 
Sbjct: 268 AT 269


>gi|254478500|ref|ZP_05091876.1| putative TIM-barrel protein, nifR3 family [Carboxydibrachium
           pacificum DSM 12653]
 gi|214035589|gb|EEB76287.1| putative TIM-barrel protein, nifR3 family [Carboxydibrachium
           pacificum DSM 12653]
          Length = 291

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/282 (27%), Positives = 128/282 (45%), Gaps = 25/282 (8%)

Query: 20  ALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L YTEM+ A  +  G +  K +L     EK +A+QI G+D   + E A+ + +     I
Sbjct: 4   GLTYTEMVSAKGLYYGSENTKALLDIDNGEK-VAIQIFGSDSEIMGEIARRLNESKALII 62

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVAL 136
           ++N+GCP+ ++ +   GA LML PD+    + A+ KA   PVTVK R G  D+ + AV +
Sbjct: 63  DINMGCPTPKIVKNGDGAALMLKPDLAEKVMEAVVKASYKPVTVKIRKGWNDNNVNAVEI 122

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + + +   G+  + +H R         ++       D++I+ ++K+      IG NG 
Sbjct: 123 AQIAERV---GIKAVAVHGR--------TREQFYSGKADWEIIKKVKESVKIPVIG-NGD 170

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVDKDFWR 253
           +     A ++L     D VMIGR A  N  +      Y  +  L     IK +V  D   
Sbjct: 171 IFTPEDAKRMLDETGCDAVMIGRGAQGNPWIFKRTVHYLKTGELLPEPTIKEKV--DLMI 228

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           +    M +Y          + ++ +H+     G P S R R 
Sbjct: 229 RHLTMMVEYKGEKTG----VVEMRKHIAWYLKGLPGSARMRE 266


>gi|190572832|ref|YP_001970677.1| putative tRNA-dihydrouridine synthase B [Stenotrophomonas
           maltophilia K279a]
 gi|190010754|emb|CAQ44363.1| putative tRNA-dihydrouridine synthase B [Stenotrophomonas
           maltophilia K279a]
          Length = 331

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 111/242 (45%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K+I  +    +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAASEMTISDPRFWNTRKSIHRMDHDGEPAPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQIIDINMGCPAKKVCNAWAGSALMRDEQLVARILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  + SG+  + +H R         +D       +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPLIARIAEDSGIAALAVHGRT--------RDQHYTGQAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + EIK       I  NG ++   +A  +L    VD VMIGR+A     +   V  Y 
Sbjct: 183 YATIGEIKAALRIPVIA-NGDIDSPQKAAYVLKETGVDAVMIGRSAQGRPWIFREVAHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|66802582|ref|XP_635163.1| tRNA-dihydrouridine synthase 4-like protein [Dictyostelium
           discoideum AX4]
 gi|60463479|gb|EAL61664.1| tRNA-dihydrouridine synthase 4-like protein [Dictyostelium
           discoideum AX4]
          Length = 344

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 110/217 (50%), Gaps = 22/217 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           + YT MI+A    R +      F+    ++PL +Q G  +  +LV AA+ V+D+    I+
Sbjct: 81  ITYTPMIMAAEFNRSEAARDSDFTINKLDEPLIVQFGVNNAEELVSAAEKVKDYCQG-ID 139

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVAL 136
           +N GCP   V +  FGA L+L+P+ + D +  +   + IP+++K R+  D  D I     
Sbjct: 140 INCGCPQRWVMKEGFGANLLLHPERIYDMVKQINNRVPIPISIKIRVQSDLKDTI----- 194

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L K  ++ GV+ I +H R + +K   P        +DYD + ++ K+N  L +  NG 
Sbjct: 195 -ELAKRAERIGVSWITVHGRTSAMKSSHP--------VDYDAI-KLVKDNVTLPVFANGD 244

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +  +SQ+ +I     V+GVM  R    N A+    D+
Sbjct: 245 VFTLSQSNEIREKTGVNGVMSARGLLTNPALFQGYDK 281


>gi|296166415|ref|ZP_06848847.1| dihydrouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295898176|gb|EFG77750.1| dihydrouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 377

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/313 (25%), Positives = 134/313 (42%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERSKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIVDEGLADHIDMNFGCPVPKVTKRGGGAALPYKRRLFGQIVAAA 136

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK R+G+DD+       +  +  +  G   + +HAR A          
Sbjct: 137 VRATEGARIPVTVKFRVGIDDE--HHTHLDAGRIAESEGAAAVALHARTAA--------Q 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D S AL ++ +   DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQHVRTIPVLGNGDIYDASDALTMMATTGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F++    + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTDSPAPTPPTLGEV-ADIVRRHGKLL----AAHFGEDKGMRDIRKHIGWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAM 314


>gi|331701913|ref|YP_004398872.1| TIM-barrel protein, nifR3 family [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129256|gb|AEB73809.1| TIM-barrel protein, nifR3 family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 335

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 84/297 (28%), Positives = 139/297 (46%), Gaps = 35/297 (11%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EMI    I+  +KK  +++    +E P+++QI G     LV+AAK V ++   + 
Sbjct: 37  GLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGTKETLVQAAKFVDQNTAADI 96

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  PVTVK R G D D I AV 
Sbjct: 97  IDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKKPVTVKMRTGWDEDHIYAV- 155

Query: 136 LRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             N + + +++G + + +H   RK + +G          + D+ I+ ++ +E    F+G 
Sbjct: 156 -ENALAA-ERAGASALAMHGRTRKQMYEG----------HADWGILKQVAQEIHIPFMG- 202

Query: 194 NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI---KTRVD 248
           NG +     A K+L  V  D VM+GRA   N  +L     Y       + P    K    
Sbjct: 203 NGDVRTPQDAKKMLTEVGTDAVMMGRAVEGNPWILKQTQHYLETGELLAEPTPEEKVVTA 262

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCRHILTVEAGAS 304
           K+   ++     DY   H   G           G +  G P+S R +  LT  +G S
Sbjct: 263 KEHLHRLVELKGDYIGSHEFRG---------QAGYYLKGIPHSARTKVALTNASGES 310


>gi|255536036|ref|YP_003096407.1| tRNA dihydrouridine synthase B [Flavobacteriaceae bacterium
           3519-10]
 gi|255342232|gb|ACU08345.1| tRNA dihydrouridine synthase B [Flavobacteriaceae bacterium
           3519-10]
          Length = 332

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/306 (25%), Positives = 145/306 (47%), Gaps = 35/306 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +R   ++   + L+Y+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKMHGAD-LMYSEFISSEGLIRDAMKSRKKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIVE    + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMALSAKIVEAVEPDIVDINFGCPVKKVVCKGAGAGVLKDIDLMIRLTKAVVSSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D +   + +  + + +++ GV  + IHAR    + KG            D+
Sbjct: 138 VTVKTRLGWDTE--GINIMEVAERLQEVGVKALTIHARTRAQMYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           + ++ +K  NP++ I +  NG ++   +AL  K     DG+MIGR A     +   V  +
Sbjct: 186 NYIHAVKN-NPNIEIPIFGNGDVDSPEKALEYKQKYDCDGIMIGRGAIGYPWIFNEVKHF 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFP 288
           F+       P I  R++         ++  +A   +   G+   L ++ +H    F G P
Sbjct: 245 FATGEKLPEPTISQRLE---------AVRQHAEWSMEWKGERLGLIEMRQHYSNYFRGIP 295

Query: 289 NSRRCR 294
           + +  R
Sbjct: 296 HFKDFR 301


>gi|78779403|ref|YP_397515.1| dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9312]
 gi|78712902|gb|ABB50079.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9312]
          Length = 335

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 117/231 (50%), Gaps = 18/231 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+LL+TEMI A ++ +G   + I   + +E P+ +QI       + 
Sbjct: 29  TDNIFRRLVRKWAPNSLLFTEMINATSLKKGFGTQKINQINLEEGPVGVQIFDNRPYAVS 88

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVTVK 
Sbjct: 89  EAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVKIPVTVKT 148

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D +   +   + +  ++ +G   I +H R    +G S K        D++++  +K
Sbjct: 149 RLGWDSKEENI--EDFLFKLQDAGATMITLHGRTR-KQGFSGKS-------DWEMIGRLK 198

Query: 184 K--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           K  E P   +  NG +++   AL  L   + DGVMIGR    +   L  +D
Sbjct: 199 KLLEIP---VIANGDIKNPDDALNCLNKTNADGVMIGRGILGSPWKLGEID 246


>gi|294495034|ref|YP_003541527.1| hypothetical protein Mmah_0350 [Methanohalophilus mahii DSM 5219]
 gi|292666033|gb|ADE35882.1| TIM-barrel protein, nifR3 family [Methanohalophilus mahii DSM 5219]
          Length = 317

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 123/243 (50%), Gaps = 25/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M + T+  YR   R     +  +TEM+ ++AIL G++K+    S+   E    +QI G  
Sbjct: 17  MAEVTNLAYRVVCRR-RGASFAFTEMVNSEAILHGNRKSYQMASSCADEGIFGIQIFGNS 75

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA I+E+  +  I ++N GCPS R+ +   G+ LM  PD++ + +  + +++++
Sbjct: 76  PVSMAKAAGILENTKFPSIIDINAGCPSPRIRKTGAGSMLMEKPDVLENIVRCVVESVTV 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILK--GLSPKDNRKIPNL 174
           PVTVK R+  D  Q   +A R     ++ +G + I +H R A  +  GL+          
Sbjct: 136 PVTVKIRVFRDVSQTVELASR-----LENAGASAITVHGRTATQQYSGLA---------- 180

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           D+     IK+E     I  NG + + + A ++L     DG+MIGRAA  +  +   ++ +
Sbjct: 181 DHLYARRIKEELSIPVIA-NGDIRNGAFAAQLLEYTGCDGLMIGRAAMGDPDVFLRIETF 239

Query: 233 FSN 235
             N
Sbjct: 240 LEN 242


>gi|189183831|ref|YP_001937616.1| NifR3 protein [Orientia tsutsugamushi str. Ikeda]
 gi|189180602|dbj|BAG40382.1| NifR3 protein [Orientia tsutsugamushi str. Ikeda]
          Length = 320

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 76/302 (25%), Positives = 142/302 (47%), Gaps = 28/302 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA---LQIGGADISK 61
           TD  +R   +      L+ +EM+ + A+++  +K+++  +  E  +    +Q+ G +   
Sbjct: 23  TDLPFRKLVKQF-GAGLVVSEMVASRAMIQETRKSMMKSAIIENDITGSCVQLAGCEPDV 81

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + +AAK+ +D G   I++N GCP+ +V  G  G+ LM +  +    +A   K++SIPVT+
Sbjct: 82  IADAAKMNQDMGAQIIDINFGCPAKKVVGGYAGSALMRDEILAAKILAETVKSVSIPVTL 141

Query: 122 KCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K R G D     V+ RN   + K  ++ G+  I +H R    +  S K        D+  
Sbjct: 142 KMRTGWD-----VSCRNANIIAKIAEECGIQMITVHGRTR-CQFYSGKS-------DWAF 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ KE+  + +  NG +  +  A+  L +   DGVMIGR AY    +L+ +  Y +  
Sbjct: 189 IRKV-KESIKIPVVANGDITSVDDAIDCLKASGADGVMIGRGAYGKPWLLSQISHYLAFQ 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP      +       + ++ Y      +G K+ +  +H+     G PN+   R  
Sbjct: 248 DYLPSPSLIEQKQIILNHYESILSYYGT---EAGMKIAR--KHLGWYSKGLPNATEFRSK 302

Query: 297 LT 298
           +T
Sbjct: 303 VT 304


>gi|301755675|ref|XP_002913683.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Ailuropoda
           melanoleuca]
 gi|281349138|gb|EFB24722.1| hypothetical protein PANDA_001508 [Ailuropoda melanoleuca]
          Length = 317

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLTRTV---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ + +I KEN  + +  NG + ++ +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YEAI-KIIKENLSIPVIANGDIRNLKEAENVWHITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|50364844|ref|YP_053269.1| tRNA dihydrouridine synthetase [Mesoplasma florum L1]
 gi|50363400|gb|AAT75385.1| tRNA dihydrouridine synthetase [Mesoplasma florum L1]
          Length = 325

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 133/281 (47%), Gaps = 29/281 (10%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+  EM+  + +   +KK  ++L    +E P+++QI G D+   + A K I E+   + I
Sbjct: 36  LVCAEMVSVEGMTHNNKKTFSMLAVEKKEHPMSMQIFGNDVESFIVATKWIDENVDCDII 95

Query: 78  NLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +LN+GCP+ +V    + G+ L+  P+++ D + A+ +  S PVT K R+G D +  +V  
Sbjct: 96  DLNIGCPAPKVAVRSASGSSLLKTPELIYDIVKAVVENTSKPVTAKIRLGWDKE--SVNA 153

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + K I+K+G +GI +H R         +      + D++ + E+K+      IG NG 
Sbjct: 154 VEVSKLIEKAGASGITVHGRT--------RSEFYSGHADWEKIKEVKEAVNIPVIG-NGD 204

Query: 197 LED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR- 253
           + D   ++A+  L   DGVMI R    N  +   +  +     TG    K    +  W+ 
Sbjct: 205 VIDGPSAKAMLELTGCDGVMISRGCQGNPWIFREIAHFLE---TGEELDKPSFAE--WKE 259

Query: 254 ---KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
              K +  + DY       G  +++  +H+   F   P + 
Sbjct: 260 TVLKHAKMLIDYKQ---DEGSAIREFRKHLTWYFAALPKTE 297


>gi|226324186|ref|ZP_03799704.1| hypothetical protein COPCOM_01965 [Coprococcus comes ATCC 27758]
 gi|225207735|gb|EEG90089.1| hypothetical protein COPCOM_01965 [Coprococcus comes ATCC 27758]
          Length = 322

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 81/304 (26%), Positives = 132/304 (43%), Gaps = 33/304 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K  K +L    +E P++LQ+ G D
Sbjct: 21  MAGVTDLPFRLLCKE-QGAGLLCMEMISAKALRYKNKNTKALLAIDPREYPVSLQLFGED 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V     G+ LM +P  + D +    +A+  P
Sbjct: 80  PDIISEQAKRIEELPFQILDINMGCPVPKVVRNGEGSALMKDPKRIYDIVYKTARAIKKP 139

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G DD     P +A            V+G     R+    G          N D
Sbjct: 140 VTIKIRKGFDDTCINAPEIAKVAEEAGAAAIAVHG---RTREQYYSG----------NAD 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           ++I+ ++K+      IG NG +    +AL +      DGVMIGR    N  +     E  
Sbjct: 187 WEIIRKVKEAVKIPVIG-NGDVTSGQKALDMFEQTGCDGVMIGRGCQGNPWIFR---ELL 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNS 290
           +   TGS P +   D     +I  +M  +A   +   G    ++++ +H+     G   S
Sbjct: 243 AYEETGSIPERPGTD-----QIRETMLRHARLQIEFKGDYIGIREMRKHVAWYTKGMQGS 297

Query: 291 RRCR 294
            + R
Sbjct: 298 AKLR 301


>gi|160944625|ref|ZP_02091852.1| hypothetical protein FAEPRAM212_02138 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443809|gb|EDP20813.1| hypothetical protein FAEPRAM212_02138 [Faecalibacterium prausnitzii
           M21/2]
          Length = 354

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/301 (25%), Positives = 133/301 (44%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNI--LGFSTQEKPLALQIGG 56
           M  +TD   R   RL+  +   +T  EM+ + A++ GD K +  L  +    P  +QI G
Sbjct: 35  MAGFTDAPCR---RLMAQHGAGFTVSEMVSSRALVYGDHKTVSLLKAAPNGAPYGVQIFG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + EA   +E + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  +     
Sbjct: 92  EVPEIMGEATAAIEQYEFDFVDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEQVVAHTK 151

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            PVTVK R G D D I AV      K+ +++G   + +HAR         ++    P +D
Sbjct: 152 RPVTVKMRKGWDADHITAV---ECAKACEQAGAALVAVHART--------REQMYTPGID 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            +I+  +K       +G NG +     AL+++   + DGVMI R A  +  +   V+   
Sbjct: 201 PEIIARVKDAVKVPVLG-NGDIHCAEDALRMVRETNCDGVMIARGALGDPWLFERVNAAL 259

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P      ++ R++    R+    M +     +       Q   +M GL       R 
Sbjct: 260 EGLPAPKEPNLQARMNA--LRRQVEEMVEQKGEFVAMPQARAQTMHYMKGLKGAAALRRY 317

Query: 293 C 293
           C
Sbjct: 318 C 318


>gi|56207834|emb|CAI20920.1| novel protein similar to human and mouse protein similar to E. coli
           yhdg and R. capsulatus nifR3 (PP35) [Danio rerio]
          Length = 307

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 79/285 (27%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+A   +R  K     F+T   ++PL +Q    D
Sbjct: 23  MVRYSKLAFRTLVRKYDCD-VCFTPMIIAADFMRSAKARDSEFTTNKNDRPLIVQFAAKD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 82  AQTLADAACVVSPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQIDNP 140

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L + ++ +GV+ I +H R AI         R  P + 
Sbjct: 141 NYAVSIKIRIHKDVRQTV----DLCQKVEAAGVSYITVHGRTAI--------ERHQP-VH 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K++  + +  NG ++ M   +A+  L  VDGVM  R    N AM +  +E  
Sbjct: 188 YDTIKTI-KDSLSIPVIANGDIKSMQDVEAVCELTGVDGVMSARGLLSNPAMFSGFEE-- 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P++   D   W  I+A   T +   H H    L++IT
Sbjct: 245 -------TPLQCVWD---WVDIAAEHGTPFTCFHHHLIHMLERIT 279


>gi|82701266|ref|YP_410832.1| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrosospira
           multiformis ATCC 25196]
 gi|82409331|gb|ABB73440.1| tRNA-U20-dihydrouridine synthase [Nitrosospira multiformis ATCC
           25196]
          Length = 337

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 118/244 (48%), Gaps = 19/244 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKSM-GAGMAVSEMVSSNSLLWGSEKTRRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+     G   I++N+GCP+ ++     G+ L+ +P +VG  + A+  A+ +P
Sbjct: 76  PAMMAEAARYNVAQGAQIIDINMGCPAKKICNVMAGSALLQDPPLVGRILDAVIGAVRVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q       ++ +  + +G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWDTQHKNAL--SIARIAENAGIQALAIHGRT--------RACAYTGHAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +    +A  +L     D VMIGRAA     +   +D Y +  
Sbjct: 186 IAAVKAE-VRIPVVANGDITTPEKAKHVLDYTGADAVMIGRAAQGRPWIFREIDHYLA-- 242

Query: 237 LTGS 240
            TGS
Sbjct: 243 -TGS 245


>gi|194364415|ref|YP_002027025.1| TIM-barrel protein, nifR3 family [Stenotrophomonas maltophilia
           R551-3]
 gi|194347219|gb|ACF50342.1| TIM-barrel protein, nifR3 family [Stenotrophomonas maltophilia
           R551-3]
          Length = 331

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 111/242 (45%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K+I  +    +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAASEMTISDPRFWNTRKSIHRMDHDGEPAPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQIIDINMGCPAKKVCNAWAGSALMRDEQLVARILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  + SG+  + +H R         +D       +
Sbjct: 136 VTLKIRTGWD-----CDHRNGPLIARIAEDSGIAALAVHGRT--------RDQHYTGQAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + EIK       I  NG ++   +A  +L    VD VMIGR+A     +   V  Y 
Sbjct: 183 YATIGEIKAALRIPVIA-NGDIDSPQKAAFVLKQTGVDAVMIGRSAQGRPWIFREVAHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 AT 243


>gi|150026283|ref|YP_001297109.1| tRNA-dihydrouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772824|emb|CAL44308.1| Probable tRNA-dihydrouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
          Length = 330

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 130/258 (50%), Gaps = 26/258 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L   + L+Y+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKLHGAD-LMYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV+    + +++N GCP  +V     GA ++ + D++     A+ ++ ++P
Sbjct: 78  EEAMAMSAKIVDAVHPDLVDINYGCPVKKVVCKGAGAGVLKDVDLMVRLTKAVIRSTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD   ++ +  + + ++  GV  + +HAR    + KG S          D+
Sbjct: 138 VTVKTRLGWDDN--SINIDEVAERLQDIGVQALTVHARTRAQMYKGHS----------DW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             +  +K  NP + + +  NG ++   +AL+      +DG+MIGRAA     +   +  Y
Sbjct: 186 THIERVKN-NPRITMPIFGNGDIDSPEKALEYKNKFGLDGMMIGRAAIGYPWIFNEIKHY 244

Query: 233 FSNPLTGSS-PIKTRVDK 249
           F+   TG   P  T +D+
Sbjct: 245 FA---TGEHLPAPTVIDR 259


>gi|51011069|ref|NP_001003490.1| tRNA-dihydrouridine synthase 4-like [Danio rerio]
 gi|50417946|gb|AAH78413.1| Zgc:92033 [Danio rerio]
          Length = 285

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 79/285 (27%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+A   +R  K     F+T   ++PL +Q    D
Sbjct: 1   MVRYSKLAFRSLVRKYDCD-VCFTPMIIAADFMRSAKARDSEFTTNKNDRPLIVQFAAKD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 60  AQTLADAACVVSPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQIDNP 118

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L + ++ +GV+ I +H R AI         R  P + 
Sbjct: 119 NYAVSIKIRIHKDVRQTV----DLCQKVEAAGVSYITVHGRTAI--------ERHQP-VH 165

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K++  + +  NG ++ M   +A+  L  VDGVM  R    N AM +  +E  
Sbjct: 166 YDTIKTI-KDSLSIPVIANGDIKSMQDVEAVCELTGVDGVMSARGLLSNPAMFSGFEE-- 222

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P++   D   W  I+A   T +   H H    L++IT
Sbjct: 223 -------TPLQCVWD---WVDIAAEHGTPFTCFHHHLIHMLERIT 257


>gi|83320047|ref|YP_424779.1| tRNA-dihydrouridine synthase [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|83283933|gb|ABC01865.1| tRNA-dihydrouridine synthase [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 308

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 113/220 (51%), Gaps = 17/220 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
           +L+Y EM+    ++  +KK  ++L  +  E P+++QI G ++ + + A K +E +   + 
Sbjct: 19  SLVYAEMVSVAGMVHDNKKTLDMLNVNKVEHPISMQIFGNNVEEFITATKWIESNVDCDI 78

Query: 77  INLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           I+LN+GCP+ +V      G+ L+  P+++ + +  + K  + PVT K R+G D    +V 
Sbjct: 79  IDLNLGCPAPKVAIRSQSGSALLKTPELIYEIVKNVVKNTTKPVTAKIRLGWDKN--SVN 136

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K I+K+G + I +HAR         + +    + D++ + E+K+      IG NG
Sbjct: 137 AVEVAKLIQKAGASAIAVHAR--------TRSDFYTGHADWEKIKEVKQAVSIPVIG-NG 187

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + D   A K+L     D VMI RA   N  +   ++ Y 
Sbjct: 188 DVIDAKSAKKMLDETGCDAVMISRACQGNPWIFEQINHYL 227


>gi|261856280|ref|YP_003263563.1| hypothetical protein Hneap_1691 [Halothiobacillus neapolitanus c2]
 gi|261836749|gb|ACX96516.1| TIM-barrel protein, nifR3 family [Halothiobacillus neapolitanus c2]
          Length = 333

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/292 (26%), Positives = 131/292 (44%), Gaps = 30/292 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   +DR +R   R      L+ TEM+ A   L+   K+ L    S   +P A+Q+ G D
Sbjct: 31  MAGVSDRPFRQLCREY-GAGLVVTEMMSAKPELQSSAKSRLRQIDSNDIEPRAVQLLGND 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   I+LN+GCP+ +V + + G+ LM  PD V   + A+  A+  P
Sbjct: 90  PFELAEAARFAVSQGAQLIDLNLGCPAKKVCKRAAGSALMAEPDTVARLLEALVAAVDCP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           V++K R G D +      RN V   K  + +G++ + IH R         + +R     +
Sbjct: 150 VSLKMRTGPDRE-----WRNAVAIAKIAENAGISMLSIHGRT--------RADRYEGEAE 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + E+     DL +  NG +    +A +++      G+M+GR A+    + + +    
Sbjct: 197 YDTIAEVVAAV-DLPVFANGDITTPQKARQVIAHTGAAGIMVGRGAFGQPWIFSALKAEL 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLF 284
           +     S P       D   ++ A    +   + H G  L  +I R  +G +
Sbjct: 256 TGQPLPSPP-------DRAERVVAIKKQFEKIYHHYGDSLGIRIARKHLGWY 300


>gi|99081204|ref|YP_613358.1| dihydrouridine synthase TIM-barrel protein nifR3 [Ruegeria sp.
           TM1040]
 gi|99037484|gb|ABF64096.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ruegeria sp.
           TM1040]
          Length = 328

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 108/235 (45%), Gaps = 20/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  ++QI G D
Sbjct: 19  MAGITDRPFRDLVRSF-GAGLVVSEMVASQEMVQAKPGVREKAELSADVENTSVQIAGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+ +A+ +P
Sbjct: 78  AYWMAEAARQVADRGARMIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVQAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R+G DD     A  ++ +  + +GV  + IH R      KG          + D+
Sbjct: 138 VTLKTRLGWDDNCLNAA--DVARRAEAAGVQMVTIHGRTRCQFYKG----------HADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
             + EIK       +  NG + D   A K L     DGVMIGR       +L  +
Sbjct: 186 AAISEIKNAISVPLLA-NGDIVDAKSAGKALSDSGADGVMIGRGVQGRPWLLAQI 239


>gi|332519407|ref|ZP_08395874.1| TIM-barrel protein, nifR3 family [Lacinutrix algicola 5H-3-7-4]
 gi|332045255|gb|EGI81448.1| TIM-barrel protein, nifR3 family [Lacinutrix algicola 5H-3-7-4]
          Length = 331

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 139/310 (44%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE + ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFVSSEGLIRNAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++E   IV     + I++N GCP  +V     GA ++ +  ++    A M K  +IP
Sbjct: 78  MDSMLETIDIVSASNPDIIDINFGCPVKKVVSKGAGAGILKDICLMEQLTAEMVKRTNIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           +TVK R+G D    ++ +  + + ++  G   I IH R    + KG            D+
Sbjct: 138 ITVKTRLGWDHD--SIKIVEVAERLQDVGCKAIAIHGRTRAQMYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + ++K  NP + I +  NG +    +A+++     +DG MIGRA   N      V  +
Sbjct: 186 KPIAQVKN-NPRMHIPVFGNGDVTSPERAMEMRDDYGLDGCMIGRATIGNPWFFKQVKHF 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQ-------QITRHMIGLF 284
           F    TG          + +R I+     + A RHL      +       +  RH    F
Sbjct: 245 FE---TG----------EHYRPITMQERVEAARRHLQMSIDWKGEVLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G P+ +  R
Sbjct: 292 KGIPHFKEYR 301


>gi|297622174|ref|YP_003710311.1| putative tRNA-dihydrouridine synthase B [Waddlia chondrophila WSU
           86-1044]
 gi|297377475|gb|ADI39305.1| putative tRNA-dihydrouridine synthase B [Waddlia chondrophila WSU
           86-1044]
          Length = 326

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 125/258 (48%), Gaps = 25/258 (9%)

Query: 18  NNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           N  L+Y EM+  DA++R D    +IL +     P+  Q+ G+      +AAKI+ED G++
Sbjct: 40  NPGLIYCEMVKMDALIRHDPATFHILDYEEGMHPIGAQLCGSKPELAGKAAKILEDLGFD 99

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I+LN GCP  +V +   G+ L+  P+ + + ++ M  A+S+PVTVK R G DD+  ++ 
Sbjct: 100 VIDLNCGCPVDKVTKDGSGSGLLKQPEKIAEILSEMVAAVSVPVTVKIRAGWDDE--SII 157

Query: 136 LRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
              + +  +K+G   I IH   RK   +G          + ++D +   K+    + +  
Sbjct: 158 AEEITRLAEKAGAAAIAIHGRTRKQAYRG----------DANWDYIKACKETAGKIKVIG 207

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + D   A ++      D V++ R       +   +  +    L G  P++  ++ D 
Sbjct: 208 NGDVFDAEAAEQMFRYTGCDAVLVSRGTMGKPWIAEDIQRH----LCGLKPVERTLEDD- 262

Query: 252 WRKISASMTDYAARHLHS 269
            RK       +A+R+ HS
Sbjct: 263 -RKALLEHYRFASRY-HS 278


>gi|262278220|ref|ZP_06056005.1| tRNA-dihydrouridine synthase B [Acinetobacter calcoaceticus
           RUH2202]
 gi|262258571|gb|EEY77304.1| tRNA-dihydrouridine synthase B [Acinetobacter calcoaceticus
           RUH2202]
          Length = 341

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 78/324 (24%), Positives = 151/324 (46%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  L+  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLQMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PEQLAEAARHQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDTVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + LR + K  +++G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQENI-LR-VAKRAEEAGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + KE  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHV-KELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKQVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYKVESTAEQAI--VVENYFNQLL 321


>gi|149704573|ref|XP_001491222.1| PREDICTED: dihydrouridine synthase 4-like (S. cerevisiae) [Equus
           caballus]
          Length = 317

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVQDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLTRTV---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ + +I K+N  + +  NG +  + +A  ++ +   DGVM+ R    N AM    +E  
Sbjct: 199 YEAI-KIIKDNASIPVIANGDIRSLKEAENVRHITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCVSD---WVDIALELGTPYICFHQHLMYMMEKIT 290


>gi|58038941|ref|YP_190905.1| nitrogen assimilation regulatory protein NifR3 [Gluconobacter
           oxydans 621H]
 gi|58001355|gb|AAW60249.1| Nitrogen assimilation regulatory protein NifR3 [Gluconobacter
           oxydans 621H]
          Length = 371

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 110/220 (50%), Gaps = 16/220 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADISKLV 63
           TD  +R  AR L    L+ +EMI + A++R ++  + +    +  P A+Q+ G D   + 
Sbjct: 46  TDLPFRQLARDL-GAGLVVSEMIASWAMIRENENTMRMARMAERGPNAVQLAGCDPKAMA 104

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +AAKI  D G N I++N GCP  +V  G   G+ LM +  + G  + A  +A+++PVT+K
Sbjct: 105 QAAKISVDGGANLIDINFGCPVKKVAIGQMAGSALMRDEVLAGKLLEATARAVNVPVTLK 164

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G D    ++    L K  ++SG+  + +H R   +      D R +  +        
Sbjct: 165 MRMGWDHN--SLNAPRLAKIAEESGIRLVTVHGRTRQMFYNGTADWRFVKTV-------- 214

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
            K+   L + +NG +  +  A + L     DGVMIGR  Y
Sbjct: 215 -KDAVSLPVIVNGDINTIRDAREALHQSQADGVMIGRGCY 253


>gi|257871359|ref|ZP_05651012.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
 gi|257805523|gb|EEV34345.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
          Length = 336

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/220 (30%), Positives = 105/220 (47%), Gaps = 16/220 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G +   LVEAA+ V E+   + I
Sbjct: 41  LVVCEMISDRGIQLRNKKTLEMLYIDETEHPLSLQIFGGNKESLVEAAQFVSENTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+PD V + + A+  A+  PVTVK RIG DD+       
Sbjct: 101 DINMGCPVNKIIKAEAGAKWLLDPDKVYEMVHAVATAIDKPVTVKMRIGWDDEHIFAVQN 160

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                   +   G+    R  + +G +          ++ ++ E+K+     F+G NG +
Sbjct: 161 AQAAEAAGAAAIGMHGRTRVQMYEGAA----------NWSVLREVKQAISIPFMG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
                A ++L  V  D VMIGRAA  N  M+     Y   
Sbjct: 210 RTPEDAKRMLEEVGADAVMIGRAALGNPWMIHRTKHYLET 249


>gi|313665725|ref|YP_004047596.1| TIM-barrel protein, nifR3 family [Mycoplasma leachii PG50]
 gi|312949868|gb|ADR24464.1| TIM-barrel protein, nifR3 family [Mycoplasma leachii PG50]
          Length = 324

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 120/240 (50%), Gaps = 22/240 (9%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNE 76
           +L+Y EM+    ++  +KK  ++L  +  E P+++QI G ++ + + A K +E+    + 
Sbjct: 35  SLVYAEMVSVAGMVHDNKKTLDMLNVNKIEHPISMQIFGNNVEEFITATKWIENNVNCDI 94

Query: 77  INLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           I+LN+GCP+ +V      G+ L+  P+++ + +  + K  + PVT K R+G D    +V 
Sbjct: 95  IDLNLGCPAPKVAIRSQSGSALLKTPELIYEIVKNVVKNTTKPVTAKIRLGWDKN--SVN 152

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K I+K+G + I +HAR         + +    + D++ + E+K+      IG NG
Sbjct: 153 AVEVAKLIQKAGASAIAVHAR--------TRSDFYTGHADWEKIKEVKQAVSIPVIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D   A K+L     D VMI RA   N  +   ++ Y     TG    K   D+  W+
Sbjct: 204 DVIDAKSAKKMLDETGCDAVMISRACQGNPWIFEQINHYLK---TGKELEKPNFDE--WK 258


>gi|42519943|ref|NP_965858.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|42409680|gb|AAS13792.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 320

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 118/251 (47%), Gaps = 27/251 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++   +++ L  +  +   A+Q+ G +   + E
Sbjct: 23  TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQS-LQKAKVDALTAVQLAGCEPDVMAE 80

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVTVK R
Sbjct: 81  AAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNMPVTVKMR 140

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIV 179
            G +D+      RN   L K  +  G   I +H R    +  G +          D+  V
Sbjct: 141 TGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQA----------DWKFV 185

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + KE   + + +NG    L D+  ALK     DGVMIGR AY    ++     + S  
Sbjct: 186 RNV-KEQVKIPVIVNGDIKNLNDIQNALK-ESGADGVMIGRGAYGKPWLINQAMNFLSGS 243

Query: 237 LTGSSPIKTRV 247
            T       R+
Sbjct: 244 ETSEPTASERL 254


>gi|187607636|ref|NP_001120313.1| hypothetical protein LOC100145375 [Xenopus (Silurana) tropicalis]
 gi|156914833|gb|AAI52625.1| Zgc:92033 protein [Danio rerio]
 gi|170285083|gb|AAI60936.1| LOC100145375 protein [Xenopus (Silurana) tropicalis]
          Length = 306

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 79/285 (27%), Positives = 132/285 (46%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+A   +R  K     F+T   ++PL +Q    D
Sbjct: 22  MVCYSKLAFRSLVRKYDCD-VCFTPMIIAADFMRSAKARDSEFTTHKNDRPLIVQFAAKD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 81  AQTLADAACVVSPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQIDNP 139

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L + ++ +GV+ I +H R AI         R  P + 
Sbjct: 140 NYAVSIKIRIHKDVRQTV----DLCQKVEAAGVSYITVHGRTAI--------ERHQP-VH 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K++  + +  NG ++ M   +A+  L  VDGVM  R    N AM +  +E  
Sbjct: 187 YDTIKTI-KDSLSIPVIANGDIKSMQDVEAVCELTGVDGVMSARGLLSNPAMFSGFEE-- 243

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P++   D   W  I+A   T +   H H    L++IT
Sbjct: 244 -------TPLQCVWD---WVDIAAEHGTPFTCFHHHLIHMLERIT 278


>gi|325138386|gb|EGC60954.1| dihydrouridine synthase [Neisseria meningitidis ES14902]
 gi|325142617|gb|EGC65009.1| dihydrouridine synthase [Neisseria meningitidis 961-5945]
          Length = 374

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 114 PQQMADAARYNVSLGAQVIDINMGCPAKKVCNAQAGSALMQNEPLVAAILEAVVRAVDVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PAVA     +  +  G+  + +H   R  + KG +         
Sbjct: 174 VTLKTRLGWHDDHKNLPAVA-----RIAEDCGIAALAVHGRTRTQMYKGEAA-------- 220

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +    + DG+MIGR A         +  
Sbjct: 221 --YDLIAETKCR-LNIPVWVNGDITSPQKAAAVFKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|187932418|ref|YP_001884422.1| NifR3 family protein [Clostridium botulinum B str. Eklund 17B]
 gi|187720571|gb|ACD21792.1| NifR3 family protein [Clostridium botulinum B str. Eklund 17B]
          Length = 321

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/310 (24%), Positives = 147/310 (47%), Gaps = 34/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G +  + +L  S +E P+A+QI G +
Sbjct: 17  MAGVTDLSFRGLCKEM-GCGLVYTEMVSAKALYYGSENTQTLLRVSNEEAPVAVQIFGRE 75

Query: 59  ISKLVEAAKIV----EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              + E  +      ED     I++N+GCP+ ++     G+ LML P++  D + A+ K 
Sbjct: 76  PEIMAEICEKYLNPREDVCI--IDINMGCPAPKIVRNKEGSALMLEPNLAHDIVKAIKKV 133

Query: 115 LSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              PVTVK R G DD+ I AV      K+++++G + I +H   RK + +G S       
Sbjct: 134 SKKPVTVKFRKGYDDEHINAVEFG---KALEEAGADAIAVHGRTRKQMYEGHS------- 183

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
              D++I+ ++K+      +G NG +     A+K+  L + DG++I R +  N  +   +
Sbjct: 184 ---DWEIIKKVKEAVSIPVLG-NGDVFSPEDAIKMKELTNCDGILIARGSMGNPWIFKQI 239

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            +  +  +      + +++      +     + A ++      ++++ +H      G P 
Sbjct: 240 QDALNGKIVEEISYQDKIN------MCIRHYELAIKNDGEYKAIREMRKHASWYIKGLPR 293

Query: 290 SRRCRHILTV 299
           S   ++ + +
Sbjct: 294 STDIKNQINI 303


>gi|260663747|ref|ZP_05864635.1| transcription regulator [Lactobacillus fermentum 28-3-CHN]
 gi|260551798|gb|EEX24914.1| transcription regulator [Lactobacillus fermentum 28-3-CHN]
          Length = 333

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 104/217 (47%), Gaps = 16/217 (7%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EMI    I+  +KK +  +G    E P+ LQI G     LVEAAK V E+   + I++N
Sbjct: 41  SEMISDRGIMYHNKKTLQMMGVDPVEHPMGLQIFGGTKETLVEAAKFVDENTDADVIDIN 100

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP  ++     G+  +L+P+ V + ++ +  A+  PVTVK R G DDQ        L 
Sbjct: 101 MGCPVNKIVNTEAGSRWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDDQHIFAVENALA 160

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
                +    +    RK + +G          + D+DI+ E+  +    F+  NG ++  
Sbjct: 161 AQRAGAAAVAMHGRTRKQMYRG----------HADWDILKEVASQLTIPFMA-NGDIKTA 209

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +A  +L     + +MIGRAA  N  MLT    Y  N
Sbjct: 210 EEAKYVLEYTGAEAIMIGRAAMGNPWMLTQTVHYLEN 246


>gi|255994138|ref|ZP_05427273.1| tRNA-dihydrouridine synthase [Eubacterium saphenum ATCC 49989]
 gi|255993806|gb|EEU03895.1| tRNA-dihydrouridine synthase [Eubacterium saphenum ATCC 49989]
          Length = 336

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 118/246 (47%), Gaps = 18/246 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  +TD   R  A L     L+Y+EM+ A  ++   K  + +L F   +  +A+QI G+D
Sbjct: 22  LAGFTDNAVRTIA-LEFGAGLVYSEMVSAKGLIYEQKNTEELLDFRGADGFIAIQIFGSD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +    + +E+ G   +++N+GCP  ++ +   GA LM  PDI+ D +    K    P
Sbjct: 81  PDAVAHGIQCIENKGNAIVDINMGCPMQKIVKSGSGAALMKRPDIIYDMVKDAVKITQKP 140

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT K RIG D + I AV   +  K+I+ +G + + +H R A          +   +++ D
Sbjct: 141 VTAKIRIGWDNNNINAV---DCAKAIESAGASAVAVHGRTA--------KQKYEGSVNRD 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++  +K+      IG NG ++   +AL+ +     D VMIGR A     +  + +   S 
Sbjct: 190 VIASVKQSVSIPVIG-NGDIKSAKEALEFMDETGCDMVMIGRGAIGKPWIFKSCNMALSE 248

Query: 236 PLTGSS 241
              G S
Sbjct: 249 IRKGKS 254


>gi|225629894|ref|YP_002726685.1| NifR3 family protein [Wolbachia sp. wRi]
 gi|225591875|gb|ACN94894.1| NifR3 family protein [Wolbachia sp. wRi]
          Length = 320

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 118/251 (47%), Gaps = 27/251 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++   +++ L  +  +   A+Q+ G +   + E
Sbjct: 23  TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQS-LQKAKVDALTAVQLAGCEPDVMAE 80

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVTVK R
Sbjct: 81  AAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNMPVTVKMR 140

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIV 179
            G +D+      RN   L K  +  G   I +H R    +  G +          D+  V
Sbjct: 141 TGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQA----------DWKFV 185

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + KE   + + +NG    L D+  ALK     DGVMIGR AY    ++     + S  
Sbjct: 186 RNV-KEQVKIPVIVNGDIKNLNDIQNALK-ESGADGVMIGRGAYGKPWLINQAMNFLSGS 243

Query: 237 LTGSSPIKTRV 247
            T       R+
Sbjct: 244 ETSEPTASERL 254


>gi|167948845|ref|ZP_02535919.1| tRNA-dihydrouridine synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 109

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/83 (45%), Positives = 56/83 (67%), Gaps = 1/83 (1%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGA 95
           ++  L F   E P+A+Q+GG++ +      + + E  GY+E+NLNVGCPS RV  G  GA
Sbjct: 17  QERFLEFDVSEHPVAIQLGGSNPAGACRGRRGLAETAGYDEVNLNVGCPSDRVQNGMIGA 76

Query: 96  CLMLNPDIVGDCIAAMCKALSIP 118
           CLM +P++V DC+ AM +A+SIP
Sbjct: 77  CLMAHPELVADCVRAMKEAVSIP 99


>gi|302385513|ref|YP_003821335.1| TIM-barrel protein, nifR3 family [Clostridium saccharolyticum WM1]
 gi|302196141|gb|ADL03712.1| TIM-barrel protein, nifR3 family [Clostridium saccharolyticum WM1]
          Length = 326

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 80/301 (26%), Positives = 132/301 (43%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +RF  R      +  TEM+ A AIL  ++    +L  +  E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRFLCRE-QGCGMAVTEMVSAKAILYKNRNTNELLKVAPGEGPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  VE+  Y  I++N+GCP  ++     G+ LM +  +    + +M KA+  P
Sbjct: 78  PEIMADIAAQVEEGPYAFIDVNMGCPMPKIVNNGEGSALMKDIGLAERILTSMVKAVKKP 137

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G  ++   AV    + +S    GV  + +H R         ++       D+ 
Sbjct: 138 VTVKFRKGFTEEDCNAVEFAKMAES---CGVAAVAVHGRT--------REQYYSGTADWT 186

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           I+ ++K+      IG NG +   ED ++AL      DGVMI R A  N  +      Y  
Sbjct: 187 IIRKVKEAVAIPVIG-NGDVFKPED-AKALMEETGCDGVMIARGAKGNPWIFKRTLHYLE 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                S P +  + K   R  +         H      ++++  HM     G P+S + R
Sbjct: 245 TGELLSGPDREEISKMIIRHGA-----LETEHKGEAVAMREMRGHMAWYTAGLPHSAKLR 299

Query: 295 H 295
           +
Sbjct: 300 N 300


>gi|317131177|ref|YP_004090491.1| TIM-barrel protein, nifR3 family [Ethanoligenens harbinense YUAN-3]
 gi|315469156|gb|ADU25760.1| TIM-barrel protein, nifR3 family [Ethanoligenens harbinense YUAN-3]
          Length = 319

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 56/198 (28%), Positives = 100/198 (50%), Gaps = 15/198 (7%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
            +LG +  E+P+A+Q+ G++   + EAA+    F  + I++N+GCP+ +V     G+ L+
Sbjct: 56  ELLGVTDAERPMAIQLFGSEPDVMAEAARRALAFSPDIIDINMGCPAPKVAGNGGGSALL 115

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
            +P + G  + A+  A+ +PVTVK R G D   + AV    + +  +++G   + +H R 
Sbjct: 116 KDPALAGRIVRAVANAVPVPVTVKIRKGWDAAHVNAV---EIARIAEENGAAAVAVHGRT 172

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMI 215
                   +  +  P  D+DI+  +++      IG NG ++    A  +L     D VMI
Sbjct: 173 --------RAQQYAPPADWDIIAAVRRAVRIPVIG-NGDVDSPQAAAHMLAQTGCDLVMI 223

Query: 216 GRAAYKNSAMLTTVDEYF 233
           GRAA     +   V+ Y 
Sbjct: 224 GRAALGRPWLFGQVETYL 241


>gi|148241561|ref|YP_001226718.1| tRNA-dihydrouridine synthase [Synechococcus sp. RCC307]
 gi|147849871|emb|CAK27365.1| Probable tRNA-dihydrouridine synthase [Synechococcus sp. RCC307]
          Length = 335

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/301 (23%), Positives = 134/301 (44%), Gaps = 30/301 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           +D+ +R   R    +ALL+TEM+ A ++  G  +  +   +T+E P+ +Q+       + 
Sbjct: 30  SDKVFRRLVRRWCPDALLFTEMVNATSLELGHGRGKVEELATEEGPIGVQLFDYRPQAMA 89

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK  E  G   I++N+GCP  ++ +   G+ L+  PD+    + A+ +A+ +PVTVK 
Sbjct: 90  EAAKRAEGAGAFLIDINMGCPVKKIAKKGGGSGLIREPDLAARIVEAVSQAVQVPVTVKT 149

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D  P        + ++ +G   + +H R         ++     + D+  + +
Sbjct: 150 RLGWCGSDADPV----TWCQQLQNAGAQLLTLHGRT--------REQGFKGHADWQAIAQ 197

Query: 182 IKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN---P 236
           +K       I  NG +   D +Q    +   DGVM+GR +     ++  +D        P
Sbjct: 198 VKAALTIPVIA-NGDINTPDDAQRCLAITGADGVMVGRGSMGAPWLVGQIDAALRGLPMP 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           L   +  + ++ K+    + +   D+          L    +HM     GFP + + RH 
Sbjct: 257 LAPDASGRLQLAKEQLLALVSERGDHG---------LLIARKHMGWTCTGFPGAPQLRHQ 307

Query: 297 L 297
           L
Sbjct: 308 L 308


>gi|220930917|ref|YP_002507825.1| putative TIM-barrel protein, nifR3 family [Halothermothrix orenii H
           168]
 gi|219992227|gb|ACL68830.1| putative TIM-barrel protein, nifR3 family [Halothermothrix orenii H
           168]
          Length = 333

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 120/233 (51%), Gaps = 20/233 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPL-ALQIGGA 57
           M   TD  +R  +R + N  L+YTEM+ +  ++ G++K  +++ F   +K L  +QI G 
Sbjct: 17  MAGVTDYPFRQISREM-NCQLIYTEMVSSKGLIYGNRKTRDLMDFDRGKKGLIGIQIFGG 75

Query: 58  DISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D   +  AA +I   +  + I++N+GCP+ ++ +   GA LM  P+     + A+  A+ 
Sbjct: 76  DPETMARAAVQIKNHYRPDLIDINMGCPTPKIVKNGSGAALMKVPERAKRVMEAVASAVD 135

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           IPVTVK R+G D   + AV   ++ K  ++ G+  + IH R         +++      +
Sbjct: 136 IPVTVKIRMGWDHSHVNAV---DIAKIAEEVGLKAVAIHGRT--------REDFYRGEAN 184

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           +DI+ E+K+E     IG NG +     A K++     DGVM+ R    N  +L
Sbjct: 185 WDIIREVKREVTIPVIG-NGDVFTPEDAKKMMEETGCDGVMVARGVRGNPWLL 236


>gi|58698977|ref|ZP_00373831.1| dihydrouridine synthase [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534506|gb|EAL58651.1| dihydrouridine synthase [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 302

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 118/251 (47%), Gaps = 27/251 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++   +++ L  +  +   A+Q+ G +   + E
Sbjct: 5   TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQS-LQKAKVDALTAVQLAGCEPDVMAE 62

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVTVK R
Sbjct: 63  AAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNMPVTVKMR 122

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIV 179
            G +D+      RN   L K  +  G   I +H R    +  G +          D+  V
Sbjct: 123 TGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQA----------DWKFV 167

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + KE   + + +NG    L D+  ALK     DGVMIGR AY    ++     + S  
Sbjct: 168 RNV-KEQVKIPVIVNGDIKNLNDIQNALK-ESGADGVMIGRGAYGKPWLINQAMNFLSGS 225

Query: 237 LTGSSPIKTRV 247
            T       R+
Sbjct: 226 ETSEPTASERL 236


>gi|254805203|ref|YP_003083424.1| putative tRNA-dihydrouridine synthase [Neisseria meningitidis
           alpha14]
 gi|254668745|emb|CBA06597.1| putative tRNA-dihydrouridine synthase [Neisseria meningitidis
           alpha14]
          Length = 374

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 113/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 114 PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PAVA     +  +  G+  + +H   R  + KG +         
Sbjct: 174 VTLKTRLGWHDDHKNLPAVA-----RIAEDCGIAALAVHGRTRTQMYKGEAA-------- 220

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 221 --YDLIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|123966327|ref|YP_001011408.1| nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9515]
 gi|123200693|gb|ABM72301.1| putative nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9515]
          Length = 335

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 116/231 (50%), Gaps = 18/231 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD+ +R   R    ++LL+TEMI A ++  G   + I     ++ P+ +QI       + 
Sbjct: 29  TDKVFRKLVRKWAPDSLLFTEMINATSLKEGHGTQKIKQLELEQGPIGVQIFDNRPFAVS 88

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK+ ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVTVK 
Sbjct: 89  EAAKLAEDSGAFLIDINMGCPVKKISKKGGGSALIKDRLLAVELVKRVSKAVKIPVTVKT 148

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D++   +     + S++ SG   I +H   RK    G +          D+D++  
Sbjct: 149 RLGWDNKEENI--EEFLLSLQDSGATMITLHGRTRKEGFSGAA----------DWDMIGR 196

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           I KE+ ++ +  NG ++    A   L   + DG+MIGR    +   +  +D
Sbjct: 197 I-KEHLEIPVIANGDIKTPEDAFNCLKKTNADGLMIGRGILGSPWKIGEID 246


>gi|47093172|ref|ZP_00230947.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           4b H7858]
 gi|47097267|ref|ZP_00234827.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           1/2a F6854]
 gi|85700164|ref|YP_012849.2| dihydrouridine synthase family protein [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|226222856|ref|YP_002756963.1| hypothetical protein Lm4b_00225 [Listeria monocytogenes Clip81459]
 gi|254826415|ref|ZP_05231416.1| dihydrouridine synthase [Listeria monocytogenes FSL J1-194]
 gi|254829644|ref|ZP_05234331.1| dihydrouridine synthase [Listeria monocytogenes FSL N3-165]
 gi|254832544|ref|ZP_05237199.1| lysyl-tRNA synthetase [Listeria monocytogenes 10403S]
 gi|254854615|ref|ZP_05243963.1| dihydrouridine synthase [Listeria monocytogenes FSL R2-503]
 gi|254901221|ref|ZP_05261145.1| lysyl-tRNA synthetase [Listeria monocytogenes J0161]
 gi|254914104|ref|ZP_05264116.1| dihydrouridine synthase family protein [Listeria monocytogenes
           J2818]
 gi|254933691|ref|ZP_05267050.1| dihydrouridine synthase [Listeria monocytogenes HPB2262]
 gi|254938416|ref|ZP_05270113.1| dihydrouridine synthase [Listeria monocytogenes F6900]
 gi|254992592|ref|ZP_05274782.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           J2-064]
 gi|255026879|ref|ZP_05298865.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           J2-003]
 gi|284803033|ref|YP_003414898.1| hypothetical protein LM5578_2790 [Listeria monocytogenes 08-5578]
 gi|284996174|ref|YP_003417942.1| hypothetical protein LM5923_2739 [Listeria monocytogenes 08-5923]
 gi|300766504|ref|ZP_07076452.1| dihydrouridine synthase [Listeria monocytogenes FSL N1-017]
 gi|47014367|gb|EAL05340.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           1/2a F6854]
 gi|47018479|gb|EAL09237.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           4b H7858]
 gi|83316100|gb|AAT03026.2| dihydrouridine synthase family protein [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|225875318|emb|CAS04015.1| unnamed protein product [Listeria monocytogenes serotype 4b str.
           CLIP 80459]
 gi|258602062|gb|EEW15387.1| dihydrouridine synthase [Listeria monocytogenes FSL N3-165]
 gi|258608010|gb|EEW20618.1| dihydrouridine synthase [Listeria monocytogenes FSL R2-503]
 gi|258611030|gb|EEW23638.1| dihydrouridine synthase [Listeria monocytogenes F6900]
 gi|284058595|gb|ADB69536.1| hypothetical protein LM5578_2790 [Listeria monocytogenes 08-5578]
 gi|284061641|gb|ADB72580.1| hypothetical protein LM5923_2739 [Listeria monocytogenes 08-5923]
 gi|293585255|gb|EFF97287.1| dihydrouridine synthase [Listeria monocytogenes HPB2262]
 gi|293592702|gb|EFG00463.1| dihydrouridine synthase family protein [Listeria monocytogenes
           J2818]
 gi|293595656|gb|EFG03417.1| dihydrouridine synthase [Listeria monocytogenes FSL J1-194]
 gi|300512786|gb|EFK39885.1| dihydrouridine synthase [Listeria monocytogenes FSL N1-017]
 gi|328467945|gb|EGF38975.1| dihydrouridine synthase family protein [Listeria monocytogenes
           1816]
 gi|332310638|gb|EGJ23733.1| Putative tRNA-dihydrouridine synthase 1 [Listeria monocytogenes
           str. Scott A]
          Length = 331

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/213 (33%), Positives = 113/213 (53%), Gaps = 20/213 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +        +H R  +   +G          + ++D++ ++K+E    F+  NG
Sbjct: 156 NALAAERAGAAAVA-MHGRTRVQMYEG----------SANWDVLRDVKRELKIPFMA-NG 203

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +     A +IL     DGVMIGRAA  N  M+
Sbjct: 204 DVRTPEDAKRILEHTGADGVMIGRAALGNPWMI 236


>gi|217965686|ref|YP_002351364.1| transcriptional regulator [Listeria monocytogenes HCC23]
 gi|290894521|ref|ZP_06557473.1| dihydrouridine synthase [Listeria monocytogenes FSL J2-071]
 gi|217334956|gb|ACK40750.1| transcriptional regulator involved in nitrogen regulation [Listeria
           monocytogenes HCC23]
 gi|290555922|gb|EFD89484.1| dihydrouridine synthase [Listeria monocytogenes FSL J2-071]
 gi|307569766|emb|CAR82945.1| dihydrouridine synthase [Listeria monocytogenes L99]
          Length = 331

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/213 (33%), Positives = 113/213 (53%), Gaps = 20/213 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +        +H R  +   +G          + ++D++ ++K+E    F+  NG
Sbjct: 156 NALAAERAGAAAVA-MHGRTRVQMYEG----------SANWDVLRDVKRELKIPFMA-NG 203

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +     A +IL     DGVMIGRAA  N  M+
Sbjct: 204 DVRTPEDAKRILEHTGADGVMIGRAALGNPWMI 236


>gi|312144282|ref|YP_003995728.1| TIM-barrel protein, nifR3 family [Halanaerobium sp. 'sapolanicus']
 gi|311904933|gb|ADQ15374.1| TIM-barrel protein, nifR3 family [Halanaerobium sp. 'sapolanicus']
          Length = 327

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 122/244 (50%), Gaps = 24/244 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEK-PLALQIGGA 57
           M   +D  YR   R +    LLYTEM+ A     G+   K ++ F  +E   +A+QI G 
Sbjct: 19  MAGVSDYPYRQIVREMGVK-LLYTEMVSAKGYEYGNNRTKELVEFEKKEDGKIAVQIFGE 77

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   +  AAK I  D+  + I++N+GCP+ ++     G+ LM N ++  + I  + +A+S
Sbjct: 78  EADFMAAAAKNIANDYDIDIIDINMGCPARKIVSNGAGSALMKNLELAENIIGRVVEAVS 137

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           IPVTVK R G D D I AV    L K+ +K G  G+ +H   RK   KG +         
Sbjct: 138 IPVTVKMRSGWDEDNINAV---ELAKTAEKMGAAGLAVHGRTRKQFYKGKA--------- 185

Query: 174 LDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            D+ I+ ++    E P +  G     ED ++A   + +  G+MIGRAA  N  +   V E
Sbjct: 186 -DWQIIKDVVDAVEIPVIANGDIFSAEDAAKAFDFI-NCSGIMIGRAAQGNPWIFKEVIE 243

Query: 232 YFSN 235
           Y  N
Sbjct: 244 YLKN 247


>gi|259047582|ref|ZP_05737983.1| tRNA-dihydrouridine synthase [Granulicatella adiacens ATCC 49175]
 gi|259035773|gb|EEW37028.1| tRNA-dihydrouridine synthase [Granulicatella adiacens ATCC 49175]
          Length = 348

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 113/219 (51%), Gaps = 15/219 (6%)

Query: 21  LLYTEMIVADAI-LRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I  R +K  ++L     E PL++QI G +   LVEAAK V E+     I
Sbjct: 48  LVVCEMISDKGIQFRNEKTLSMLHIEPNEYPLSVQIMGGNKDTLVEAAKYVAENTEAAII 107

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+P+ V + +AA+  A+  PVTVK R G D +    A+ 
Sbjct: 108 DINMGCPVNKVIKAEAGAKWLLDPNKVYEMVAAVVDAVDKPVTVKMRTGWDHE-HLYAVE 166

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + + +G + + +H R  +       D +     D++I+ E+KK    + +  NG +
Sbjct: 167 NALAA-EHAGASAVAMHGRTRV----QMYDGKA----DWEILGEVKKNLTRIPLIGNGDV 217

Query: 198 EDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                A ++  +  VDGVMIGRAA  N  M+     Y  
Sbjct: 218 RSPEDAKRMIDIAGVDGVMIGRAALANPWMIRQTVHYLE 256


>gi|326204271|ref|ZP_08194130.1| TIM-barrel protein, nifR3 family [Clostridium papyrosolvens DSM
           2782]
 gi|325985546|gb|EGD46383.1| TIM-barrel protein, nifR3 family [Clostridium papyrosolvens DSM
           2782]
          Length = 320

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 114/239 (47%), Gaps = 16/239 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQ-EKPLALQIGGAD 58
           M   TD  +R   +      L+YTEM+ A  +    DK N L    + EKP A+QI G+D
Sbjct: 17  MAGVTDMPFRILCKE-QECGLVYTEMVSAKGMHYDDDKSNKLTLMHEIEKPGAVQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + E  + +       I++N+GCP+ ++ +   G+ LM NP ++ + I A+  A   P
Sbjct: 76  PTIMAEVTEKLNASDAAIIDINMGCPAPKITKNGEGSALMKNPQLIAEIIRAVAAASQKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+ +  +    + +  +++G + + +H R         ++       D+DI
Sbjct: 136 VTVKIRKGWDESL--INAVEIARIAEENGASAVAVHGRT--------REQYYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K+      IG NG +    +A K+L     D +M+GR A  N  +   +  +  +
Sbjct: 186 IRRVKEAVSIPVIG-NGDVTGPKEARKLLEETKCDAIMVGRGAQGNPWIFKKIVRFLED 243


>gi|121635111|ref|YP_975356.1| hypothetical protein NMC1354 [Neisseria meningitidis FAM18]
 gi|120866817|emb|CAM10575.1| conserved hypothetical protein [Neisseria meningitidis FAM18]
 gi|325132397|gb|EGC55090.1| dihydrouridine synthase [Neisseria meningitidis M6190]
 gi|325198556|gb|ADY94012.1| dihydrouridine synthase [Neisseria meningitidis G2136]
          Length = 336

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNAQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PAVA     +  +  G+  + +H   R  + KG +         
Sbjct: 136 VTLKTRLGWHDDHKNLPAVA-----RIAEDCGIAALAVHGRTRTQMYKGEAA-------- 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +    + DG+MIGR A         +  
Sbjct: 183 --YDLIAETKCR-LNIPVWVNGDITSPQKAAAVFKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|224500852|ref|ZP_03669201.1| dihydrouridine synthase family protein [Listeria monocytogenes
           Finland 1988]
          Length = 331

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/213 (33%), Positives = 113/213 (53%), Gaps = 20/213 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +        +H R  +   +G          + ++D++ ++K+E    F+  NG
Sbjct: 156 NALAAERAGAAAVA-MHGRTRVQMYEG----------SANWDVLRDVKRELKIPFMA-NG 203

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +     A +IL     DGVMIGRAA  N  M+
Sbjct: 204 DVRTPEDAKRILEHTGADGVMIGRAALGNPWMI 236


>gi|16799336|ref|NP_469604.1| hypothetical protein lin0259 [Listeria innocua Clip11262]
 gi|16412688|emb|CAC95492.1| lin0259 [Listeria innocua Clip11262]
          Length = 331

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/213 (33%), Positives = 113/213 (53%), Gaps = 20/213 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +        +H R  +   +G          + ++D++ ++K+E    F+  NG
Sbjct: 156 NALAAERAGAAAVA-MHGRTRVQMYEG----------SANWDVLRDVKRELKIPFMA-NG 203

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +     A +IL     DGVMIGRAA  N  M+
Sbjct: 204 DVRTPEDAKRILEHTGADGVMIGRAALGNPWMI 236


>gi|296123913|ref|YP_003631691.1| dihydrouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296016253|gb|ADG69492.1| dihydrouridine synthase DuS [Planctomyces limnophilus DSM 3776]
          Length = 322

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 109/227 (48%), Gaps = 24/227 (10%)

Query: 6   DRHYRFFARLLTNN---ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADIS 60
           + H     RL+      +L+ +E I A  +   DK+ I  L  ++ E+P   QI G D +
Sbjct: 18  EEHTSLPFRLICKQQGASLVCSERIDAKDVAERDKRAIKLLSTTSAERPAVGQISGNDAA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ EAA+++E+ G++ ++LN  CP  R+     G  LM  P  + + +AA  +A+SIPVT
Sbjct: 78  QIGEAARVIEELGFSMVDLNFECPIRRLVGRGEGGALMGQPQRIAELVAAAKQAVSIPVT 137

Query: 121 VKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VK R G    +D     A R     ++++G   I +HAR          +   +   D+ 
Sbjct: 138 VKLRTGPKAGEDTAVETAQR-----VEQAGGAAIILHARSV--------EQAYLGGPDWQ 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            V  +K+      +G +GG+     A+  L S   DGV IGR    N
Sbjct: 185 HVTRVKEAVSIPVLG-SGGVRTPQDAISFLESSGADGVAIGRGCLGN 230


>gi|16802273|ref|NP_463758.1| hypothetical protein lmo0227 [Listeria monocytogenes EGD-e]
 gi|224503816|ref|ZP_03672123.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           R2-561]
 gi|255029456|ref|ZP_05301407.1| dihydrouridine synthase family protein [Listeria monocytogenes
           LO28]
 gi|16409592|emb|CAD00754.1| lmo0227 [Listeria monocytogenes EGD-e]
          Length = 331

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/211 (33%), Positives = 111/211 (52%), Gaps = 16/211 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ 
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +        +H R  +             + ++D++ ++K+E    F+  NG +
Sbjct: 156 NALAAERAGAAAVA-MHGRTRV--------QMYEGSANWDVLRDVKRELKIPFMA-NGDV 205

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAML 226
                A +IL     DGVMIGRAA  N  M+
Sbjct: 206 RTPEDAKRILEHTGADGVMIGRAALGNPWMI 236


>gi|212550478|ref|YP_002308795.1| tRNA-dihydrouridine synthase [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|212548716|dbj|BAG83384.1| tRNA-dihydrouridine synthase [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
          Length = 340

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 110/219 (50%), Gaps = 17/219 (7%)

Query: 21  LLYTEMIVADAILRG-DK-KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           ++YTE I ADA++R  DK +  L     E P+A+QI G D   +VEAA+I E+   + ++
Sbjct: 44  MVYTEFISADALIRHVDKIQGKLKIINSEHPIAVQIYGQDKDTMVEAARICEEMQPDFLD 103

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN GCP  ++   + GA ++  P  + +    +  +++IP+TVK R+G D+    +   +
Sbjct: 104 LNFGCPVKKIVRRNAGAGMLRVPKKMIEITQQVVHSVNIPITVKTRLGWDENSKIIV--D 161

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGG 196
           L + ++ +G+  + IH R                  D++++  + K NP ++I +  NG 
Sbjct: 162 LAERLQDTGIALLTIHGRTG--------SQMYSGKADWNLIGAV-KNNPRMYIPICGNGD 212

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           +    Q  +      VD VMIGRA+     +   V  Y 
Sbjct: 213 IVSPQQCEQAFNRYGVDAVMIGRASIGAPWIFQEVKYYL 251


>gi|150014995|ref|YP_001307249.1| nifR3 family TIM-barrel protein [Clostridium beijerinckii NCIMB
           8052]
 gi|149901460|gb|ABR32293.1| putative TIM-barrel protein, nifR3 family [Clostridium beijerinckii
           NCIMB 8052]
          Length = 321

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 144/310 (46%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G +  + +L  + +EKP+A QI G +
Sbjct: 17  MAGVTDISFRGLCKEM-GCGLVYTEMVSAKALYYGSENTQTLLRIADEEKPVAAQIFGRE 75

Query: 59  ISKLVEAAKIVEDFGYNE-----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              +   A+I E++  N      I++N+GCP+ ++ +   G+ LM  P++  D +  + K
Sbjct: 76  PDVM---ARICEEYLNNRKDICIIDINMGCPAPKIVKNGEGSALMKEPELAYDIVRTIKK 132

Query: 114 ALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRK 170
             + PVTVK R G D D I AV      K ++++G + I +H   RK + +G +      
Sbjct: 133 VSTKPVTVKFRKGFDEDNINAV---EFAKGMEQAGADAIAVHGRTRKQMYQGKA------ 183

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
               D+DI+  +K       IG NG +     A+++    + DG+MI R +  N  +   
Sbjct: 184 ----DWDIIKRVKDSVSIPVIG-NGDVFSPEDAIRMKRTTNCDGIMIARGSQGNPWIFRQ 238

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGKLQQITRHMIGLFHG 286
           +     N L     I+   D +   KI   +  Y  A ++      ++++ +H      G
Sbjct: 239 I-----NNLLNGEVIQEVSDNE---KIEMCIRHYELAIKYDGEFKAIREMRKHASWYIKG 290

Query: 287 FPNSRRCRHI 296
            P   RC  +
Sbjct: 291 LP---RCTEL 297


>gi|254526611|ref|ZP_05138663.1| NifR3 family enzyme [Prochlorococcus marinus str. MIT 9202]
 gi|221538035|gb|EEE40488.1| NifR3 family enzyme [Prochlorococcus marinus str. MIT 9202]
          Length = 345

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 118/243 (48%), Gaps = 18/243 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+LL+TEMI A ++ +G  K+ I     +E P+ +QI       + 
Sbjct: 33  TDDIFRRLVRKWAPNSLLFTEMINATSLKKGFGKQKINQIDLEEGPVGVQIFDYRPHAVS 92

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVTVK 
Sbjct: 93  EAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVKIPVTVKT 152

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D +   +   + +  ++ +G   I +H R    +G S K        D++++  +K
Sbjct: 153 RLGWDSKEENI--EDFLFKLQDAGATMITLHGRTR-KQGFSGKS-------DWEMIGRLK 202

Query: 184 K--ENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
              E P   +  NG +++   AL  L   + DGVMIGR    +   +  +D   S     
Sbjct: 203 SLLEIP---VIANGDIKNPDDALNCLKKTNADGVMIGRGILGSPWKIGEIDYAISENKNF 259

Query: 240 SSP 242
             P
Sbjct: 260 KKP 262


>gi|289670979|ref|ZP_06492054.1| nifR3 family TIM-barrel protein [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 299

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 109/222 (49%), Gaps = 21/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L  +EM ++D    G +K++  +  + +  P+++QI G +  +L EAA+   D G   I+
Sbjct: 3   LAVSEMTISDRRFWGTRKSLHRMDHAGEPDPISVQIAGTEPQQLAEAARYNVDHGAQLID 62

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V     G+ LM + D+V   + A+ +A+++PVT+K R G D        RN
Sbjct: 63  INMGCPAKKVCNAWAGSALMRDEDLVARILIAVVRAVNVPVTLKIRTGWD-----CDHRN 117

Query: 139 ---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  +  G+  + +H R         +D     + +Y  + +IK     + +  NG
Sbjct: 118 GPVIARIAQDCGIAALAVHGRT--------RDQHYTGSAEYATIAQIKAAL-QIPVVANG 168

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++   +A ++L     D VMIGRAA     +   V  + + 
Sbjct: 169 DIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLAT 210


>gi|114771140|ref|ZP_01448580.1| tRNA-dihydrouridine synthase, putative [alpha proteobacterium
           HTCC2255]
 gi|114548422|gb|EAU51308.1| tRNA-dihydrouridine synthase, putative [alpha proteobacterium
           HTCC2255]
          Length = 324

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 110/237 (46%), Gaps = 20/237 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGGADIS 60
           TD  YR          L+ +EM+ +  I++  K    +  LGF+ +    ++QI G D  
Sbjct: 20  TDLPYRNLVSSF-GAGLVVSEMVASHEIMQKGKDARARAELGFNVEGT--SVQIAGRDAF 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + E AK++E  G   I++N+GCP+  V  G+ G+ LM  PD+    I A+  A+ IPVT
Sbjct: 77  WMSECAKLIEGNGAKIIDINMGCPAKSVVNGASGSALMRTPDLALKLIEAVVNAVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G D      A  +L  S +K G+  I IH R          D RKI  +      
Sbjct: 137 LKTRLGWDHNDLNAA--DLSSSAEKIGIQMITIHGRTRCQFYKGDADWRKIREV------ 188

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
              KE  ++ +  NG + D   A   +     DGVMIGR A     +L+ +     N
Sbjct: 189 ---KEAVNIPVIANGDIIDTPTAKLAMKQSKADGVMIGRGAQGKPWLLSQIASEIFN 242


>gi|94496405|ref|ZP_01302982.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sphingomonas sp.
           SKA58]
 gi|94424151|gb|EAT09175.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sphingomonas sp.
           SKA58]
          Length = 343

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 120/239 (50%), Gaps = 24/239 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G    ++
Sbjct: 30  TDMPFRTLVRRY-GSGLNVTEMIASAAMIRETRQSLQKAAWHPLEEPVSMQLAGCSPREM 88

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            +AA++  D G   I++N+GCP  +V  G  G+ LM +  +    I A  +A+ +PVTVK
Sbjct: 89  ADAARLNADRGAAIIDINMGCPVKKVVNGDAGSALMRDLPLAASLIKATVEAVDVPVTVK 148

Query: 123 CRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
            R+G D   + A  L ++ + +   G   I +H   R  + KG          + D+  V
Sbjct: 149 MRMGWDHASLNAPELAHIAEDL---GAKLITVHGRTRNQMYKG----------SADWAFV 195

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++ K+   L + +NG    +ED   AL+     DGVMIGR AY    ++  V  + ++
Sbjct: 196 RKV-KDAVKLPVVVNGDICSIEDADTALE-QSGADGVMIGRGAYGRPWLIGQVMAWLTD 252


>gi|119899182|ref|YP_934395.1| putative tRNA-dihydrouridine synthase [Azoarcus sp. BH72]
 gi|119671595|emb|CAL95508.1| conserved hypothetical tRNA-dihydrouridine synthase [Azoarcus sp.
           BH72]
          Length = 357

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 117/240 (48%), Gaps = 17/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L  +EM+ ++++L G  K         +  P+++QI GAD
Sbjct: 27  MAGVTDRPFRQLCKKL-GAGLAVSEMVTSNSLLYGSAKTQRRANHDGEVDPISVQIAGAD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA+   
Sbjct: 86  PAMMAEAARHNADRGAQIIDINMGCPAKKVCNVMAGSALMQDEPLVARILEAVVKAVPDT 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G + Q     +  + +  ++SG+ GI IH R         + ++ + + +YD
Sbjct: 146 PVTLKFRTGWNRQNKNAPI--IARIAEESGIQGIAIHGRT--------RADQYMGDAEYD 195

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       I  NG +    +A  +L     DGVMIGRAA     +   ++ + + 
Sbjct: 196 TIALVKTLVKIPVIA-NGDITTPQKARHVLDYTGADGVMIGRAAQGRPWIFREIEHFLAT 254


>gi|299135626|ref|ZP_07028810.1| dihydrouridine synthase DuS [Acidobacterium sp. MP5ACTX8]
 gi|298601750|gb|EFI57904.1| dihydrouridine synthase DuS [Acidobacterium sp. MP5ACTX8]
          Length = 425

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/262 (27%), Positives = 121/262 (46%), Gaps = 21/262 (8%)

Query: 21  LLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           L+ TE   AD + R     +K  L +   E P++ Q+ G++ + L E+A I +D G++ +
Sbjct: 87  LIMTEFTSADGLSRMRETKRKRYLTYYEDEHPISAQLFGSNPATLAESAIICQDAGFDLV 146

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP+ RV   + G+ L+ +   +      +  A++IP TVK R+G +D    +   
Sbjct: 147 DLNLGCPAKRVVACNGGSGLLRDLPAIRTIFERVRAAVTIPFTVKFRMGWNDS--NIVCV 204

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K  +  G+N + +HAR         ++        ++ +  +K       IG NG +
Sbjct: 205 ELAKMAEDCGLNAVALHART--------REQGYTGVARWEWIAAVKDAVTIPVIG-NGDI 255

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVDKDFWRK 254
                A  ++ +   D VMIGRAA  N  +   + +Y  S   TG        D D +R 
Sbjct: 256 RTPEDAAAMVEATHCDAVMIGRAAPANPWIFRQIAQYTASKQATGVGTYDKPTDMDRYRM 315

Query: 255 ISASMTDYAARHLHSGGKLQQI 276
           I     DY  R +H   +  +I
Sbjct: 316 IR----DYFERLMHEVAEHPEI 333


>gi|259416525|ref|ZP_05740445.1| probable tRNA-dihydrouridine synthase [Silicibacter sp. TrichCH4B]
 gi|259347964|gb|EEW59741.1| probable tRNA-dihydrouridine synthase [Silicibacter sp. TrichCH4B]
          Length = 328

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 84/318 (26%), Positives = 140/318 (44%), Gaps = 42/318 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  ++QI G +
Sbjct: 19  MAGITDRPFRDLVRSF-GAGLVVSEMVASQEMVQAKPGVREKAELSADVENTSVQIAGRE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V   G   I++N+GCP+ +V  G  G+ L+  PD     I A+ KA+ +P
Sbjct: 78  AYWMAEAARRVAGSGARMIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVKAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R+G DD     A  ++ +  + +GV  + IH R      KG +          D+
Sbjct: 138 VTLKTRLGWDDNCLNAA--DVARRAQDAGVQMVTIHGRTRCQFYKGQA----------DW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E++       +  NG + D + A + L +   DGVMIGR       +L  V    +
Sbjct: 186 AAIAEVRNAISVPLLA-NGDIVDAATAQQALGASGADGVMIGRGVQGKPWLLAQV----A 240

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS-----GGKLQ-QITRHMIGLF---H 285
           + L GS+        DF         D  +RH  +     G  L  ++ R  +G +    
Sbjct: 241 HELWGSAAPDIPTQGDF--------VDMVSRHYEAMLAFYGNDLGLRVARKHLGWYMDEA 292

Query: 286 GFPNSRRCRHILTVEAGA 303
           G P + R R +LT +  A
Sbjct: 293 GTPTALR-REVLTAKTPA 309


>gi|254442182|ref|ZP_05055658.1| putative TIM-barrel protein, nifR3 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198256490|gb|EDY80798.1| putative TIM-barrel protein, nifR3 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 367

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 120/239 (50%), Gaps = 18/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  +T+  +R  A+ L    L+ T+++ A ++L G      ++    +E+P+A+Q+ G  
Sbjct: 17  LAGYTNLPFRLTAKSLGGLGLVTTDLVNARSLLEGRAVAYKMIATDVREQPMAVQLFGGV 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I ++ G   +++N+GCP  +V +   G+ +M N +   + +  M  A+ IP
Sbjct: 77  AEEMRDAAVICQERGAQSVDINMGCPVKKVVKTGSGSSMMKNHEKTQELVKGMIDAVDIP 136

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT K R+G D D I A     L ++++  GV+ I+IH R    +G S         +D +
Sbjct: 137 VTAKMRLGWDSDNITAP---ELARALEDVGVSAIFIHGRTRA-QGFS-------GGVDLE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + ++K+    + +  NG +    +A +I+      DGV IGR A+ N  +      Y 
Sbjct: 186 GIRKVKEAVSSVPVIGNGDVTS-PEAARIMFERTGCDGVSIGRGAFYNPWIFRQTVHYL 243


>gi|294650996|ref|ZP_06728336.1| tRNA-dihydrouridine synthase B [Acinetobacter haemolyticus ATCC
           19194]
 gi|292823097|gb|EFF81960.1| tRNA-dihydrouridine synthase B [Acinetobacter haemolyticus ATCC
           19194]
          Length = 341

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 78/328 (23%), Positives = 150/328 (45%), Gaps = 30/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDTVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  + +  
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGR--------TREDMYLNHAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++ ++K+      I  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YELIKQVKQLISIPVIA-NGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIGHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V       +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLATPDIAEVKTVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMIE 320
           R  +  VE+ A  A   ++E  F+ +++
Sbjct: 297 RQNMYKVESTADQAK--VVEAYFDQLLD 322


>gi|330718778|ref|ZP_08313378.1| probable tRNA-dihydrouridine synthase [Leuconostoc fallax KCTC
           3537]
          Length = 314

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/320 (25%), Positives = 146/320 (45%), Gaps = 34/320 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGGADIS 60
           TD  +R       +  + YTE   A +++    K      L +   E+    QI G+   
Sbjct: 5   TDTIFRRVVEKAASPDVYYTEFTNASSMVHPKAKFSVQGRLAYMPDEQIPVAQIWGSRPD 64

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +  A K++ + GY  ++LN+GCP   V +   G+ L+ + D+  D I+A  K+  +PV+
Sbjct: 65  DIAGAVKLLPEMGYQAVDLNMGCPDGTVIKNGGGSDLIRHQDLACDIISA-AKSTPLPVS 123

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDY-DI 178
           VK R+G +  +     R  +  I K  V  + +H R       S K+  K+P + +Y D 
Sbjct: 124 VKTRLGFNSPL---EFREWLPLILKQDVAVLTVHLR-------SRKEMSKVPAHYEYIDE 173

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  ++ E  P   I  NG ++D  + L I    P +DG+MIGR  ++N      V +  S
Sbjct: 174 ILAMRDELAPKTLIQFNGDIKDRQEGLAIAKAHPGIDGIMIGRGIFENPFAFEKVQQ--S 231

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           + L  S  +  +     + +++A++T    +H  +  +  +I         GFP++   R
Sbjct: 232 HTLRESIEL-LKCQLTLFDEVNATVT---PKHFEALKRFFKI------YLRGFPHASGLR 281

Query: 295 HILTVEAGASTATHHIIETA 314
             L +E  A+     I++ A
Sbjct: 282 QAL-METHATDEVRTILDEA 300


>gi|300776181|ref|ZP_07086040.1| tRNA-dihydrouridine synthase B [Chryseobacterium gleum ATCC 35910]
 gi|300505314|gb|EFK36453.1| tRNA-dihydrouridine synthase B [Chryseobacterium gleum ATCC 35910]
          Length = 331

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/303 (25%), Positives = 145/303 (47%), Gaps = 29/303 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   ++   + L+Y+E I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKMHGAD-LMYSEFISSEGLIRDAIKSRKKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +A+IVE    + +++N GCP  +V     GA ++ + D++     A+  +  + 
Sbjct: 78  EEAMAMSARIVETVNPDLVDINFGCPVKKVVCKGAGAGVLKDIDLMVRLTKAVVSSTHLS 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++++G+  + IHAR    + KG            D+
Sbjct: 138 VTVKTRLGWDST--SINIDEVAERLQETGIKALTIHARTRAQMYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           + +  I K+NP++ I +  NG ++   +AL  K   + DG+MIGRAA     +   +  +
Sbjct: 186 EHISRI-KQNPNIEIPIFGNGDIDSAEKALEYKQKYACDGIMIGRAAIGYPWIFNEIKHF 244

Query: 233 FSNPLTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           F    TG   P  T  D+    +  A   +++A        L ++ +H    F G P+ +
Sbjct: 245 FK---TGEHLPEPTISDRLLAVRQHA---EWSAEWKGERLGLVEMRQHYSNYFRGIPHFK 298

Query: 292 RCR 294
             R
Sbjct: 299 EFR 301


>gi|189502204|ref|YP_001957921.1| hypothetical protein Aasi_0818 [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189497645|gb|ACE06192.1| hypothetical protein Aasi_0818 [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 327

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 143/310 (46%), Gaps = 33/310 (10%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+YTE I A+ ++R   K+I  L     E+P+ +QI G  I  + EAA I E      ++
Sbjct: 38  LMYTEFISAEGLIREADKSIKKLDIYDYERPIGIQIFGEKIESMREAAAIAEAASPALLD 97

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N GCP   V     GA ++L+   +    A + K +S+PVTVK R+G D  + ++ +  
Sbjct: 98  INYGCPVNNVACRGAGAGILLDLPKMQTMTAEIVKRVSLPVTVKTRLGWD--VNSIKIVE 155

Query: 139 LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--N 194
           + + ++ +G+  + IH   R+ + KG            D+  + ++K  +P + I +  N
Sbjct: 156 VAQRLQDAGIQALTIHGRTRQQMYKG----------EADWSYIADVKN-HPAIRIPIFGN 204

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G ++   +AL       +DG+MIGRA+     +   +  +F      + P       D  
Sbjct: 205 GDIDTPQKALAYRNEYGIDGIMIGRASIGYPWIFQEIKHFFKTGEQLAPP-------DLQ 257

Query: 253 RKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHH 309
            +I A++  +    +   G+   + ++ RH      G P  +  R +L VEAG       
Sbjct: 258 ERI-ATLQKHLQHAIQWKGERTGILEMRRHYTNYLKGLPEVKTYRQML-VEAGDLLTVES 315

Query: 310 IIETAFNLMI 319
           I+    N ++
Sbjct: 316 ILAELVNKLM 325


>gi|258645918|ref|ZP_05733387.1| tRNA-dihydrouridine synthase [Dialister invisus DSM 15470]
 gi|260403288|gb|EEW96835.1| tRNA-dihydrouridine synthase [Dialister invisus DSM 15470]
          Length = 330

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 86/311 (27%), Positives = 144/311 (46%), Gaps = 45/311 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR +   AL   EM+ A  +   ++K  ++L  + +E P++LQ+ G+D
Sbjct: 20  MAGVSDLAYRVIARKM-GAALTTAEMVSAKGLYYHNEKTKDMLKIAEEEHPVSLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +   AK++E  G + +++N+GCP  +V +   G+ LM N  +  + I+A+  A+ IP
Sbjct: 79  PAVMALGAKVMEKAGADIVDINMGCPMQKVVKNGDGSALMKNVTLAAEIISAVTAAVKIP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R+G   D I AV L    +S   + +    +H R         +++  +   D+ 
Sbjct: 139 VTIKMRLGWSRDTINAVELAMAAESAGAAAIT---VHGRT--------REDFYMGTADW- 186

Query: 178 IVYEIKKENPDLFIGL--NGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              EIKK    + I +  NG + D   ++AL        V IGRAA+ N  +   V+ Y 
Sbjct: 187 --REIKKVVDAVRIPVIGNGDVGDGPAAKALMEETGCAAVAIGRAAWGNPWVFGAVNTYL 244

Query: 234 SNP--LTGSSPIKTRVDKDFWRKISASMTDYAARHLHS-----GGKL--QQITRHMIGLF 284
                L G S          W +  A     A +HLH      G ++  +++  H    F
Sbjct: 245 ETGEILPGPS----------WEERLA----MARKHLHGLCVEKGERIAVREMRAHASRYF 290

Query: 285 HGFPNSRRCRH 295
           HG P +   R 
Sbjct: 291 HGLPKATVLRR 301


>gi|308270351|emb|CBX26963.1| Probable tRNA-dihydrouridine synthase [uncultured Desulfobacterium
           sp.]
          Length = 351

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 118/250 (47%), Gaps = 20/250 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           T+  +R  A+      L+ +EM+ A+ I+ G KK +  L   ++E+P++ QI G+D   +
Sbjct: 46  TNLPFRLIAKR-AGCGLVCSEMVSANGIVYGSKKTLGMLDSLSEERPVSFQIFGSDPLIM 104

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA IVE  G + I++N GC   +V +   G  LM  P      + A+ K + IPVT+K
Sbjct: 105 AEAAVIVESSGADIIDINFGCSVKKVVKTGAGVALMKEPGRTEAILMAIKKCVKIPVTIK 164

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVY 180
            R G  ++    AL+   K  +  G++ I +H R A    +GL+          D+ ++ 
Sbjct: 165 IRTGW-EKTGEQALKT-AKIAEHCGIDAIAVHPRTASQGFRGLA----------DWSVIS 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+      IG NG +     A+ +      D VMIGRAA  N  +   +    S    
Sbjct: 213 RVKQNVSIPVIG-NGDILTAYDAVSMQSQTGCDAVMIGRAAIGNPWIFEQIRALMSKEPI 271

Query: 239 GSSPIKTRVD 248
             + +  R D
Sbjct: 272 APASLAQRFD 281


>gi|255320752|ref|ZP_05361927.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SK82]
 gi|262379471|ref|ZP_06072627.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SH164]
 gi|255302129|gb|EET81371.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SK82]
 gi|262298928|gb|EEY86841.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SH164]
          Length = 347

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/249 (27%), Positives = 119/249 (47%), Gaps = 28/249 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 24  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   I++N+GCP+ +V     G+ L+ + ++V   +  +  A+ +P
Sbjct: 83  PEQLAEAARYQIANGAQIIDINMGCPAKKVCNKLAGSALLQDEELVARILDTVVAAVDVP 142

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  + +  
Sbjct: 143 VTLKTRLGYLNGQENILRVA-----KRAEEAGIAALALHGRT--------REDMYLNHAR 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA------YKNSAMLT 227
           YD++ E+KK      I  NG ++   +A  +L     D +MIGRAA      ++  A   
Sbjct: 190 YDLIREVKKIIHIPVIA-NGDIDSPEKAKFVLEHTGADAIMIGRAAQGRPWIFREIAHYL 248

Query: 228 TVDEYFSNP 236
              EY   P
Sbjct: 249 NTGEYLKAP 257


>gi|21227445|ref|NP_633367.1| NifR3-like protein [Methanosarcina mazei Go1]
 gi|20905814|gb|AAM31039.1| NifR3-like protein [Methanosarcina mazei Go1]
          Length = 323

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 75/262 (28%), Positives = 125/262 (47%), Gaps = 21/262 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQE-KPLALQIGGAD 58
           M D T+  +R   R    + L YTEMI  DA+L   +K+ I G S++E +P  +Q+ G  
Sbjct: 22  MADVTNLAFRLLCRRYGAD-LTYTEMINVDALLNESRKSFIKGLSSEEDRPFGVQLVGGC 80

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             KL  AA  +E+    EI ++N+GCP+  +     G+ L+ +P++V   I  + ++L  
Sbjct: 81  PDKLKRAALFIEEEYRPEIIDVNMGCPARCITGAGCGSALLNSPELVYSIILELTESLDT 140

Query: 118 PVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+ K R +G +++   +A     + I+K+G + + +H R A              N + 
Sbjct: 141 PVSAKIRLLGREEKTLEIA-----RLIEKAGASAVTVHGRTAA--------QMYSGNSNL 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K E     I  NG ++D   A + L     DG+MIGRAA  N  +   +  Y  
Sbjct: 188 EGIRAVKNELSIPVIA-NGDVKDEESAERTLELTGCDGLMIGRAAMGNPFIFKKIRHYLE 246

Query: 235 NPLTGSSPIKTRVDKDFWRKIS 256
                 +    R  +DF   IS
Sbjct: 247 TGEKLGADKPFRQLEDFNSYIS 268


>gi|309804685|ref|ZP_07698750.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           09V1-c]
 gi|309807001|ref|ZP_07700983.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           03V1-b]
 gi|309809597|ref|ZP_07703454.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN
           2503V10-D]
 gi|308166077|gb|EFO68295.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           09V1-c]
 gi|308166621|gb|EFO68818.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           03V1-b]
 gi|308170078|gb|EFO72114.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN
           2503V10-D]
          Length = 331

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 131/285 (45%), Gaps = 33/285 (11%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++     E P++LQI G     LVEAA+ V+D  + +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLDMMKIDPNEHPMSLQIFGGSEETLVEAARYVDDNTHADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           N+N+GCP  +V +   GA  +L+PD +   + A+   +  PVTVK R G D D I AV  
Sbjct: 100 NINMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQKPVTVKMRTGWDEDHIYAV-- 157

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + +++G   + +H   RK +  G          + D+ I+ E+       F+G N
Sbjct: 158 ENALAA-QEAGACAVAMHGRTRKQLYTG----------HADWGILKEVSDALTIPFVG-N 205

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD--K 249
           G +     A K+L  V    VM+GRA   N  +L  +  Y  +  L     ++ RV   K
Sbjct: 206 GDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDTGELLAPQTVEERVTTCK 265

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  RK+     +  A        + +  R       G P S R R
Sbjct: 266 EQLRKLVELKGEKIA--------VPEFRRQAAYYLKGIPRSARTR 302


>gi|157413462|ref|YP_001484328.1| dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9215]
 gi|157388037|gb|ABV50742.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9215]
          Length = 341

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 116/235 (49%), Gaps = 18/235 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+LL+TEMI A ++ +G   + I     +E P+ +QI       + 
Sbjct: 29  TDDIFRRLVRKWAPNSLLFTEMINATSLKKGFGTQKINQIDLEEGPVGIQIFDYRPHAVS 88

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVTVK 
Sbjct: 89  EAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAMELVKNVVKAVKIPVTVKT 148

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D +   +   + +  ++ +G   I IH R    +G S K        D++++  +K
Sbjct: 149 RLGWDSKEENI--EDFLFKLQDAGATMITIHGRTR-KQGFSGKS-------DWEMIGRLK 198

Query: 184 K--ENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
              E P   +  NG +++   AL  L   + DGVMIGR    +   +  +D   S
Sbjct: 199 SLLEIP---VIANGDIKNPDDALNCLKKTNADGVMIGRGILGSPWKIGEIDYAIS 250


>gi|260886975|ref|ZP_05898238.1| tRNA-dihydrouridine synthase [Selenomonas sputigena ATCC 35185]
 gi|330839239|ref|YP_004413819.1| TIM-barrel protein, nifR3 family [Selenomonas sputigena ATCC 35185]
 gi|260863037|gb|EEX77537.1| tRNA-dihydrouridine synthase [Selenomonas sputigena ATCC 35185]
 gi|329747003|gb|AEC00360.1| TIM-barrel protein, nifR3 family [Selenomonas sputigena ATCC 35185]
          Length = 318

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 120/251 (47%), Gaps = 19/251 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TD  YR     +    L+YTEM+  + I   +++ +    T  +E+PLA+Q+ G +
Sbjct: 17  MAGVTDMAYRILVHEM-GCPLVYTEMVSTNGINYRNERTLKMLQTDPRERPLAMQLFGNE 75

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  AA  VE  G  + I+ N+GCP+ ++ +   G+ L+L+P      + A+ +A+ +
Sbjct: 76  PEAVARAAAYVESLGVADVIDFNMGCPAPKIVKNGEGSALLLDPVRAERILKALKRAVKL 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVK R G D   + AV    +    + +GV+ I +H R         ++       D+
Sbjct: 136 PVTVKIRKGWDAAHVNAV---EIAVRAEAAGVDAIAVHGRT--------REQFYSGEADW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            I++ + KE   + +  NG +  +   ++I  +   DGVM+GRAA  N  +   +  +  
Sbjct: 185 AIIHAV-KERVAIPVIANGDVRSVVDLVRIFEVTDADGVMVGRAAQGNPWIFREMAGFLR 243

Query: 235 NPLTGSSPIKT 245
                + P  +
Sbjct: 244 TGEVAAPPTAS 254


>gi|15904035|ref|NP_359585.1| hypothetical protein spr1994 [Streptococcus pneumoniae R6]
 gi|182685127|ref|YP_001836874.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae CGSP14]
 gi|15459698|gb|AAL00796.1| Conserved hypothetical protein [Streptococcus pneumoniae R6]
 gi|182630461|gb|ACB91409.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae CGSP14]
          Length = 336

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 202 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 260


>gi|116493271|ref|YP_805006.1| tRNA-dihydrouridine synthase [Pediococcus pentosaceus ATCC 25745]
 gi|116103421|gb|ABJ68564.1| tRNA-U20-dihydrouridine synthase [Pediococcus pentosaceus ATCC
           25745]
          Length = 332

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 88/317 (27%), Positives = 148/317 (46%), Gaps = 44/317 (13%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EMI    I+ G+KK  +++     E P+++QI G     LVEAAK V ++   + 
Sbjct: 37  GLVVCEMISDRGIIYGNKKTLSMMTVDPNEHPMSIQIFGGTKETLVEAAKFVDQNTDADI 96

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP  +V     GA  +L+P+ V + ++ +  A+  PVTVK R G D     +A+
Sbjct: 97  IDINMGCPVNKVVNTDAGARWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDAN-HILAV 155

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + +++G + + +H   RK +  G +          D++I+ E+  +    F+G N
Sbjct: 156 ENALAA-ERAGASALAMHGRTRKQMYTGQA----------DWNILKEVGSQLHIPFMG-N 203

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G +     A ++L  V  D VMIGRA   N   L  +  Y ++         T +D+   
Sbjct: 204 GDVRTPEDAKRMLDEVGADAVMIGRAVLGNPWELQRISAYLND--------GTVIDEPTP 255

Query: 253 RKISASMTDYAARHLHSGGKLQ-------QITRHMIGLFHGFPNSRRCRHILTVEAGAST 305
           R+      + A  HLH+  +L+       +          G P+S R +  +T   GA T
Sbjct: 256 RE----KIEIAKEHLHALVELKGENVGPREFRGQAAYYLKGIPHSARTKVAVT---GADT 308

Query: 306 ATHHIIETAFNLMIESL 322
               I    F+  IE L
Sbjct: 309 EQQMI--NIFDSFIEKL 323


>gi|217969866|ref|YP_002355100.1| hypothetical protein Tmz1t_1445 [Thauera sp. MZ1T]
 gi|217507193|gb|ACK54204.1| TIM-barrel protein, nifR3 family [Thauera sp. MZ1T]
          Length = 346

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 23/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EM+ ++++L G +K       + +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGVAVSEMVTSNSLLYGSEKTRRRADHTGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + EAAK   D G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA+   
Sbjct: 76  PAMMAEAAKFNADNGAQIIDINMGCPAKKVCNVMAGSALMQDEPLVARILEAVVKAVPDT 135

Query: 118 PVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVT+K R G    +   P +A     +  ++SG+  I IH R         + ++ +   
Sbjct: 136 PVTLKFRTGWNRANKNAPTIA-----RIAEESGIRAIAIHGRT--------RADQYMGEA 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K    ++ +  NG +    +A  +L     DGVMIGRAA     +   ++ +
Sbjct: 183 EYDTIAHVKTLV-NIPVIANGDIGSPQKAKHVLDYTGADGVMIGRAAQGRPWIFREIEHF 241

Query: 233 FSN 235
            + 
Sbjct: 242 LAT 244


>gi|302672113|ref|YP_003832073.1| tRNA dihydrouridine synthase A DusA2 [Butyrivibrio proteoclasticus
           B316]
 gi|302396586|gb|ADL35491.1| tRNA dihydrouridine synthase A DusA2 [Butyrivibrio proteoclasticus
           B316]
          Length = 325

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/302 (23%), Positives = 139/302 (46%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R +    L+  EM+ A AI   +K    ++     E P++LQ+ G++
Sbjct: 23  MAGVSDLPFRLLCREM-GAGLVCMEMVSAKAITYKNKNTNMLMEIHEDEHPVSLQLFGSE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +A ++++D  Y+ +++N+GCP  +V     G+ LM NP+++   + A+ +    P
Sbjct: 82  PEIMQQAVEMIKDRPYDILDVNMGCPVPKVVGNGEGSALMKNPELIEKIVKALTEVSDRP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  +   +V       + ++ G   + +H R         ++       D+ I
Sbjct: 142 VTVKIRRGFTEA--SVNAVECALAAQEGGAAAVAVHGRT--------REQYYSGRADWTI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+      IG NG + D     ++      DGVM+ RAA  N  +   +  YF   
Sbjct: 192 IRQVKEALKIPVIG-NGDVVDGPSTKRMFEETGCDGVMVARAAQGNPFLFREIKSYFE-- 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSRRC 293
            TG +      ++   ++I  ++  +A   L   G+   ++++ +H+     G P S R 
Sbjct: 249 -TGEA-----CERPTAQEIYDTVIRHADLQLKYKGEFIGIREMRKHVSWYTVGMPGSARF 302

Query: 294 RH 295
           R+
Sbjct: 303 RN 304


>gi|304312297|ref|YP_003811895.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HdN1]
 gi|301798030|emb|CBL46252.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HdN1]
          Length = 332

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 118/244 (48%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD  +R   R L       +EM+  +  L   +K+ L       E   A+QI G D
Sbjct: 21  MAGITDLPFRTLCRKL-GAGYTVSEMVAGNPKLINTRKSSLRLRHDGDESLRAVQIVGWD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I  D G   I++N+GCP+ +V   + G+ L+ +  +V   + A+ KA+ +P
Sbjct: 80  PQSMAEAARINADQGAGVIDINMGCPAKKVCSKAAGSALLKDEALVERILNAVVKAVDVP 139

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D +Q   V +  +    +++G+  + +H R      KGL+          +
Sbjct: 140 VTLKIRTGWDANQRNGVTIARIA---EQAGIQALAVHGRTRACAFKGLA----------E 186

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           YD + +IK     ++I +  NG +    +A ++L   +VDG+M+GR+A  N  +   +  
Sbjct: 187 YDTIAQIKAA---IYIPVMANGDISSPEKAKEVLEHTAVDGIMVGRSALGNPWVFRAITH 243

Query: 232 YFSN 235
           Y   
Sbjct: 244 YLKT 247


>gi|219847108|ref|YP_002461541.1| TIM-barrel protein, nifR3 family [Chloroflexus aggregans DSM 9485]
 gi|219541367|gb|ACL23105.1| TIM-barrel protein, nifR3 family [Chloroflexus aggregans DSM 9485]
          Length = 351

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 95/334 (28%), Positives = 148/334 (44%), Gaps = 40/334 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI----LRGDKKNILGFSTQEKPLALQIGG 56
           M   TD  +R     L    L+ TEM  A ++    LR  +  +L +  +E+PL +QI G
Sbjct: 33  MAGVTDSIFRRMILRLGGCGLVSTEMTNAASVSPKALR--RHRLLDYLPEERPLTMQISG 90

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   +  AA++VE  G + I++N GCPS +V  G  G+ L+ +   +   + A+  A+ 
Sbjct: 91  NDPDLVANAARVVEQLGADIIDINCGCPSPKVTGGGHGSALLRDLPKMERLLRAVRAAVQ 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKK---SGVNGIWIHARKAILKGLSPKDNRKIPN 173
           IPVT+K R G D+     A  N +++ ++   +GV  + +H R         ++      
Sbjct: 151 IPVTLKLRAGWDE-----ASLNFIEAGQRAEAAGVAALTLHPRT--------REQGYKGQ 197

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            D+  V  +K+      IG +G +     AL  L     DGVMIGR A  N  +   V +
Sbjct: 198 ADWSRVAALKRAVSIPVIG-SGDVVTAQDALIRLRDSGADGVMIGRGAIANPWIFRQVAD 256

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNS 290
                  G +P +     D +  +   M  Y A  L     L +I + +IG F+ G P S
Sbjct: 257 LRQ----GRTPFEP-TPADKYHLLLEYMAIY-AEELPERLALNKI-KQLIGQFYIGLPGS 309

Query: 291 RRCR---HILTVEAGASTATHHIIETAFNLMIES 321
              R   H  T  A A  A    IE  F   +E+
Sbjct: 310 NHLRVAVHTSTSLAAAQEA----IERFFAPYLET 339


>gi|332978428|gb|EGK15144.1| tRNA-dihydrouridine synthase B [Psychrobacter sp. 1501(2011)]
          Length = 346

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/223 (28%), Positives = 116/223 (52%), Gaps = 15/223 (6%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ ADA L   KK++    F  +  P++ QI GAD+ KL EAA+   + G   I++N+
Sbjct: 58  SEMMTADATLYAHKKSLFRANFDGEIAPISAQIAGADVDKLAEAAQYQVNNGAQIIDINM 117

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + A   A+  PVT+K R+G ++    + LR + K
Sbjct: 118 GCPAKKVCRKLAGSALLKDEDLVARLLDATVAAVDAPVTLKTRLGYENGQENI-LR-VAK 175

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             +++G+  I IH R         ++++   N  YD++ E+ K+  ++ +  NG ++   
Sbjct: 176 RAEEAGIAAIAIHGRT--------REDKYGGNARYDLIREV-KQLVNIPVIANGDIDSPQ 226

Query: 202 QALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           +++++      D +MIGRAA     +   +  Y        SP
Sbjct: 227 KSIEVYNQTGCDAIMIGRAAQGQPWLFRDIAHYLQTGEVLPSP 269


>gi|255068432|ref|ZP_05320287.1| tRNA-dihydrouridine synthase B [Neisseria sicca ATCC 29256]
 gi|255047318|gb|EET42782.1| tRNA-dihydrouridine synthase B [Neisseria sicca ATCC 29256]
          Length = 334

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLRRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     +  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHDDHKNLPAIA-----RIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +L   + DG+MIGR A     +   +  
Sbjct: 181 ATYDLIAETKGR-LNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWLFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|148988833|ref|ZP_01820248.1| hypothetical protein CGSSp6BS73_07143 [Streptococcus pneumoniae
           SP6-BS73]
 gi|148991954|ref|ZP_01821728.1| replicative DNA helicase [Streptococcus pneumoniae SP9-BS68]
 gi|149003048|ref|ZP_01827957.1| hypothetical protein CGSSp14BS69_11215 [Streptococcus pneumoniae
           SP14-BS69]
 gi|149020105|ref|ZP_01835079.1| hypothetical protein CGSSp23BS72_08719 [Streptococcus pneumoniae
           SP23-BS72]
 gi|168486294|ref|ZP_02710802.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1087-00]
 gi|168489262|ref|ZP_02713461.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae SP195]
 gi|168491720|ref|ZP_02715863.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC0288-04]
 gi|194397168|ref|YP_002038780.1| dihydrouridine synthase [Streptococcus pneumoniae G54]
 gi|221232891|ref|YP_002512045.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225855683|ref|YP_002737195.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae JJA]
 gi|237650706|ref|ZP_04524958.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae CCRI
           1974]
 gi|237821964|ref|ZP_04597809.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae CCRI
           1974M2]
 gi|303253994|ref|ZP_07340113.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae BS455]
 gi|303262142|ref|ZP_07348087.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP14-BS292]
 gi|303266234|ref|ZP_07352126.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS457]
 gi|303268867|ref|ZP_07354653.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS458]
 gi|307128454|ref|YP_003880485.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 670-6B]
 gi|147758789|gb|EDK65785.1| hypothetical protein CGSSp14BS69_11215 [Streptococcus pneumoniae
           SP14-BS69]
 gi|147925644|gb|EDK76720.1| hypothetical protein CGSSp6BS73_07143 [Streptococcus pneumoniae
           SP6-BS73]
 gi|147929003|gb|EDK80014.1| replicative DNA helicase [Streptococcus pneumoniae SP9-BS68]
 gi|147930783|gb|EDK81764.1| hypothetical protein CGSSp23BS72_08719 [Streptococcus pneumoniae
           SP23-BS72]
 gi|183570643|gb|EDT91171.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1087-00]
 gi|183572275|gb|EDT92803.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae SP195]
 gi|183574050|gb|EDT94578.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC0288-04]
 gi|194356835|gb|ACF55283.1| Dihydrouridine synthase (Dus) [Streptococcus pneumoniae G54]
 gi|220675353|emb|CAR69952.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722760|gb|ACO18613.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae JJA]
 gi|301802853|emb|CBW35631.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           INV200]
 gi|302599025|gb|EFL66052.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae BS455]
 gi|302636782|gb|EFL67272.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP14-BS292]
 gi|302641566|gb|EFL71927.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS458]
 gi|302644282|gb|EFL74537.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS457]
 gi|306485516|gb|ADM92385.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 670-6B]
 gi|332071458|gb|EGI81952.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA41301]
 gi|332071628|gb|EGI82121.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA17570]
          Length = 326

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|15901996|ref|NP_346600.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae TIGR4]
 gi|111657242|ref|ZP_01408011.1| hypothetical protein SpneT_02001540 [Streptococcus pneumoniae
           TIGR4]
 gi|14973700|gb|AAK76240.1| putative TIM-barrel protein, NifR3 family [Streptococcus pneumoniae
           TIGR4]
          Length = 318

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 184 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 242


>gi|309803746|ref|ZP_07697832.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           11V1-d]
 gi|309808758|ref|ZP_07702644.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           01V1-a]
 gi|312872541|ref|ZP_07732609.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF
           2062A-h1]
 gi|312874764|ref|ZP_07734783.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2053A-b]
 gi|325912444|ref|ZP_08174839.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 143-D]
 gi|325913104|ref|ZP_08175474.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 60-B]
 gi|329920464|ref|ZP_08277196.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN 1401G]
 gi|308164155|gb|EFO66416.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           11V1-d]
 gi|308167994|gb|EFO70126.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           01V1-a]
 gi|311089509|gb|EFQ47934.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2053A-b]
 gi|311091903|gb|EFQ50279.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF
           2062A-h1]
 gi|325475786|gb|EGC78957.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 143-D]
 gi|325477525|gb|EGC80667.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 60-B]
 gi|328936140|gb|EGG32593.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN 1401G]
          Length = 331

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 130/285 (45%), Gaps = 33/285 (11%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  +     E P++LQI G     LVEAA+ V+D  + +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLEMMKIDPNEHPMSLQIFGGSEETLVEAARYVDDNTHADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           N+N+GCP  +V +   GA  +L+PD +   + A+   +  PVTVK R G D D I AV  
Sbjct: 100 NINMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQKPVTVKMRTGWDEDHIYAV-- 157

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + +++G   + +H   RK +  G          + D+ I+ E+       F+G N
Sbjct: 158 ENALAA-QEAGACAVAMHGRTRKQLYTG----------HADWGILKEVSDALTIPFVG-N 205

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD--K 249
           G +     A K+L  V    VM+GRA   N  +L  +  Y  +  L     ++ RV   K
Sbjct: 206 GDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDTGELLAPQTVEERVTTCK 265

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  RK+     +  A        + +  R       G P S R R
Sbjct: 266 EQLRKLVELKGEKIA--------VPEFRRQAAYYLKGIPRSARTR 302


>gi|256380793|ref|YP_003104453.1| TIM-barrel protein, nifR3 family [Actinosynnema mirum DSM 43827]
 gi|255925096|gb|ACU40607.1| TIM-barrel protein, nifR3 family [Actinosynnema mirum DSM 43827]
          Length = 393

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 78/309 (25%), Positives = 128/309 (41%), Gaps = 26/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT-EMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R   +   LY  EMI A A++  D K   +L F   E P ++Q+   
Sbjct: 39  MAGITNIAFRQLCREFGSPGSLYVCEMITARAVVERDSKTMEMLAFGPDEHPRSMQLYSV 98

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           D   + EA K++  ED   + I++N GCP  +V     GA L     +  + + A  +A 
Sbjct: 99  DPVSMSEAVKLITGEDRA-DHIDMNFGCPVPKVTRKGGGAALPYKRKLFREIVRAAVRAA 157

Query: 116 S---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               +PVTVK RIG+DD+   +   +  +  +  G   + +HAR A          R   
Sbjct: 158 EPAGVPVTVKFRIGIDDE--HLTYLDAGRIAEDEGAQAVALHARTAA--------QRYSG 207

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
             D+  +  +K+    + +  NG +     AL ++     DGV++GR       +   + 
Sbjct: 208 TADWSAITRLKEAVTSIPVLGNGDIFSARDALDMVARTGCDGVVVGRGCLGRPWLFGELQ 267

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F      + P   +V    WR   A + D    HL     ++ + +HM     GFP  
Sbjct: 268 AAFRGEPLPAPPTLGKVADILWRH-GALLAD----HLGEEKGVRDLRKHMAWYLKGFPVG 322

Query: 291 RRCRHILTV 299
              R  L +
Sbjct: 323 GDLRRSLAM 331


>gi|123968631|ref|YP_001009489.1| nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. AS9601]
 gi|123198741|gb|ABM70382.1| putative nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. AS9601]
          Length = 335

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 111/219 (50%), Gaps = 18/219 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+LL+TEMI A ++ +G   + I     +E P+ +QI       + 
Sbjct: 29  TDNIFRRLVRKWAPNSLLFTEMINATSLKKGYGTQKINQIDLEEGPIGVQIFDNRPYAVS 88

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ +PVTVK 
Sbjct: 89  EAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVRVPVTVKT 148

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D +   +   + +  ++ +G   I +H R    +G S K        D++++  +K
Sbjct: 149 RLGWDSKEENI--EDFLFKLQDAGATMITLHGRTR-KQGFSGKS-------DWEMIGRLK 198

Query: 184 K--ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
           K  E P   +  NG +++   AL  L     DGVMIGR 
Sbjct: 199 KLLEIP---VIANGDIKNPDDALNCLKKTKADGVMIGRG 234


>gi|116516462|ref|YP_817401.1| TIM-barrel protein, nifR3 family protein, putative [Streptococcus
           pneumoniae D39]
 gi|116077038|gb|ABJ54758.1| TIM-barrel protein, nifR3 family protein, putative [Streptococcus
           pneumoniae D39]
          Length = 318

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 184 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 242


>gi|309778095|ref|ZP_07673033.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 3_1_53]
 gi|308914154|gb|EFP59956.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 3_1_53]
          Length = 338

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 110/225 (48%), Gaps = 24/225 (10%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGADISKLVEAAKIV-EDFGYN 75
            L+YTEM V+D  L  D +  +G +    QE PL +QI G DI  +V AAK + E    +
Sbjct: 40  GLIYTEM-VSDKALYYDNEKTVGMTDVEEQEHPLTMQIFGHDIETMVYAAKFLDEKTACD 98

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAV 134
            I++N+GCP  ++ +   G+ LM + D   +   A+ +++  PVTVK RIG D DQI  V
Sbjct: 99  IIDINMGCPVTKIVKSFAGSALMKDVDHAVEMSRAVVQSVKKPVTVKMRIGWDMDQITCV 158

Query: 135 ALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
               L K ++  GV  + +H R  K + +G          + D+  +  +K+      +G
Sbjct: 159 ---ELAKGLEAVGVQALAVHGRTKKQMYEG----------SADWSYIRRVKEAVSIPVMG 205

Query: 193 LNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            NG +     A ++L     D VMIGR    +  ++  +  Y   
Sbjct: 206 -NGDVRSGEDAQRMLEETGCDAVMIGRGVLGDPWLIKDIVHYLDT 249


>gi|148984490|ref|ZP_01817778.1| hypothetical protein CGSSp3BS71_10563 [Streptococcus pneumoniae
           SP3-BS71]
 gi|168494054|ref|ZP_02718197.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC3059-06]
 gi|147923267|gb|EDK74381.1| hypothetical protein CGSSp3BS71_10563 [Streptococcus pneumoniae
           SP3-BS71]
 gi|183575963|gb|EDT96491.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC3059-06]
 gi|301800925|emb|CBW33584.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           OXC141]
          Length = 326

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|149006830|ref|ZP_01830511.1| hypothetical protein CGSSp18BS74_11461 [Streptococcus pneumoniae
           SP18-BS74]
 gi|149013437|ref|ZP_01834118.1| hypothetical protein CGSSp19BS75_00095 [Streptococcus pneumoniae
           SP19-BS75]
 gi|169833585|ref|YP_001695544.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Hungary19A-6]
 gi|147761431|gb|EDK68396.1| hypothetical protein CGSSp18BS74_11461 [Streptococcus pneumoniae
           SP18-BS74]
 gi|147762863|gb|EDK69813.1| hypothetical protein CGSSp19BS75_00095 [Streptococcus pneumoniae
           SP19-BS75]
 gi|168996087|gb|ACA36699.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Hungary19A-6]
 gi|332071268|gb|EGI81763.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA17545]
          Length = 326

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|312113493|ref|YP_004011089.1| hypothetical protein Rvan_0714 [Rhodomicrobium vannielii ATCC
           17100]
 gi|311218622|gb|ADP69990.1| TIM-barrel protein, nifR3 family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 338

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 82/314 (26%), Positives = 139/314 (44%), Gaps = 29/314 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP---LALQIGGADISK 61
           TDR +R   R    + L+ TEM+ + +++R  +K  L  S +E     LA+Q+ G D + 
Sbjct: 38  TDRPFRRIVRKFGAD-LVVTEMLASKSVIRQQRKT-LRMSERETDGGLLAVQLAGRDPTI 95

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + +AA++ ED G + I+LN GCP  +V +   G+ LM +         A+  A+++PVT+
Sbjct: 96  MADAARLAEDRGADIIDLNFGCPVKKVVKDMVGSALMRDEVHAAKIFEAVVNAVTVPVTL 155

Query: 122 KCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIV 179
           K R+G   D++ A  L  + +     G+  + +H R +    G          + D+  V
Sbjct: 156 KMRMGWSPDELNAPRLARIAEG---CGIAMVTVHGRTRCQFYG---------GDADWGFV 203

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + KE   + + +NG +   + A++ L +   DGVMIGR AY    ++  V        
Sbjct: 204 RRV-KEAVSIPVIVNGDIVTPADAVRALAASGADGVMIGRGAYGRPWIIAQVAAALRGET 262

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCRHI 296
               P   RV  D   +   +M DY             I R   G +  G P +   R  
Sbjct: 263 VSDEP-SLRVRLDTMAEHFEAMLDYYGERAGV-----PIARKHFGWYSAGLPGATAFRDA 316

Query: 297 LTVEAGASTATHHI 310
           + V   A+     +
Sbjct: 317 VNVAEAAADVRRQM 330


>gi|168483984|ref|ZP_02708936.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1873-00]
 gi|225857757|ref|YP_002739268.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae P1031]
 gi|225859959|ref|YP_002741469.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 70585]
 gi|172042699|gb|EDT50745.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1873-00]
 gi|225720185|gb|ACO16039.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 70585]
 gi|225726197|gb|ACO22049.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae P1031]
 gi|301795102|emb|CBW37572.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           INV104]
 gi|332198809|gb|EGJ12891.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA47368]
 gi|332199009|gb|EGJ13090.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA47901]
          Length = 326

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|52424587|ref|YP_087724.1| hypothetical protein MS0532 [Mannheimia succiniciproducens MBEL55E]
 gi|52306639|gb|AAU37139.1| unknown [Mannheimia succiniciproducens MBEL55E]
          Length = 341

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 125/258 (48%), Gaps = 29/258 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  +     A+QI G+D
Sbjct: 35  MAGITDQPFRKLCAAY-GAGLTFSEMMSTNPQVWHTEKSRLRLAHHQAAGINAVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  D+G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+S+P
Sbjct: 94  PKEIAKAAQINVDYGAEIIDINMGCPAKKVNRKMAGSALLQYPDLVRQILEHVVNAVSVP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN V   K  ++SG+  + IH   R+ + +G          N
Sbjct: 154 VTLKIRTGWNKE-----HRNCVEIAKIAEQSGIQALTIHGRTRECLFEG----------N 198

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG +    +A  +L     D VMIGR A  N  +  +V+ 
Sbjct: 199 AEYDNIKAVKRQVSIPVIA-NGDITSAEKAKSVLEYTGADAVMIGRGALGNPWLFKSVES 257

Query: 232 YFSNPLTGSSPIKTRVDK 249
                 TGS   +  +D+
Sbjct: 258 LVE---TGSIVFEPSLDE 272


>gi|325266282|ref|ZP_08132961.1| tRNA-dihydrouridine synthase B [Kingella denitrificans ATCC 33394]
 gi|324982244|gb|EGC17877.1| tRNA-dihydrouridine synthase B [Kingella denitrificans ATCC 33394]
          Length = 336

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 115/229 (50%), Gaps = 25/229 (10%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ +D  L+  +K  N      ++  + +QI G+D  ++  AA+   + G   I++N+
Sbjct: 42  SEMLSSDPGLQHTQKSRNRRNHEGEDGVIVVQIAGSDPEQMAHAARHNAEHGAQIIDINM 101

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV- 140
           GCP  +V     G+ L+ N  +V   + A+ +   +PVT+K R+G DD+      RN++ 
Sbjct: 102 GCPVKKVCNVLAGSALLQNEPLVERILHAVVRNAGVPVTLKTRLGWDDE-----HRNILT 156

Query: 141 --KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             K  +++G+  + IH   R  + +G          N +YD++ ++ K    L + +NG 
Sbjct: 157 IAKMAEQAGIAALAIHGRTRTQMYQG----------NAEYDLIAQV-KHTVSLPVWVNGD 205

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           ++   +A ++L     DGVM+GRAA     +   + ++  +     +P+
Sbjct: 206 IDSPQKAARVLQQTQADGVMVGRAAQGQPWIFRDIAQFLQHGRIPEAPV 254


>gi|291619129|ref|YP_003521871.1| DusB [Pantoea ananatis LMG 20103]
 gi|291154159|gb|ADD78743.1| DusB [Pantoea ananatis LMG 20103]
          Length = 349

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 116/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 45  MAGITDRPFRTLCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+ +P
Sbjct: 104 PSEMAQAARINVDAGAQVIDINMGCPAKKVNRKMAGSALLQYPSVVESILSAVVNAVDVP 163

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D +    VA+  L    ++ G+  + IH R    +  G          + +
Sbjct: 164 VTLKIRTGWDPENRNCVAIAQLA---ERCGIQALTIHGRTRACLFNG----------DAE 210

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 211 YDSIRTV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 269


>gi|254520540|ref|ZP_05132596.1| nifR3 family TIM-barrel protein [Clostridium sp. 7_2_43FAA]
 gi|226914289|gb|EEH99490.1| nifR3 family TIM-barrel protein [Clostridium sp. 7_2_43FAA]
          Length = 328

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 80/316 (25%), Positives = 150/316 (47%), Gaps = 48/316 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G++  K++L  + +E P+A QI G D
Sbjct: 17  MAGVTDISFRGLCKEM-GCGLVYTEMVSAKALYYGNENTKSLLRIADEETPVAAQIFGND 75

Query: 59  ISKLVEAAKIVEDFGYNE------INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +   A++V+ + +NE      +++N+GCP  ++ +   G+ L+ +P++  + +  + 
Sbjct: 76  PRIM---AEVVQRY-FNEREDICLVDINMGCPVNKITKNGEGSALLKHPELAANIVREIK 131

Query: 113 KALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           K  + PVTVK R G D+  I AV      K ++++GV+ + +H R         K+    
Sbjct: 132 KVSTKPVTVKFRKGWDEGNINAV---EFAKRLEEAGVDAVTVHGR--------TKEQMYE 180

Query: 172 PNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
              D+DI+ ++K         N D+F       ED  + LK   + DG+MI R +  N  
Sbjct: 181 GKADWDIIGKVKDSVSIPVLGNGDVFTS-----EDAIE-LKNKTNCDGIMIARGSMGNPW 234

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIG 282
           +   + EY    L G  P++      +  +I+  +  Y     + G +  ++++ +H   
Sbjct: 235 IFKQI-EY---ALKGKVPLEIT----YLDRINMCLRHYELALKYDGERKAVREMRKHASW 286

Query: 283 LFHGFPNSRRCRHILT 298
              G P S   R ++ 
Sbjct: 287 YIKGLPKSADIRGVMN 302


>gi|261363918|ref|ZP_05976801.1| tRNA-dihydrouridine synthase B [Neisseria mucosa ATCC 25996]
 gi|288567925|gb|EFC89485.1| tRNA-dihydrouridine synthase B [Neisseria mucosa ATCC 25996]
          Length = 334

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 114/241 (47%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLRRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     +  +  G+  + +H   R  + KG +         
Sbjct: 136 VTLKTRLGWHDDHKNLPAIA-----RIAEDCGIAALAVHGRTRTQMYKGEAA-------- 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K     + + +NG +    +A  +L   + DG+MIGR A     +   +  
Sbjct: 183 --YDLIAETKGRL-KIPVWVNGDITSPQKAATVLKQTAADGIMIGRGAQGRPWLFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|296209951|ref|XP_002751783.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Callithrix jacchus]
          Length = 317

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 130/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   ++  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVKSIKARDSEFTTNRGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARVLSDAARIVSPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVRDMVTQVRNQVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  +  GV+ I +H R          + R  P + 
Sbjct: 152 GFSVSIKIRIH-DDLKRTV---DLCRKAEAIGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSI-KIIKENMSIPVIANGDIRSLKEAENVWQITGTDGVMVARGLLTNPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|322514995|ref|ZP_08068006.1| tRNA-dihydrouridine synthase B [Actinobacillus ureae ATCC 25976]
 gi|322119011|gb|EFX91182.1| tRNA-dihydrouridine synthase B [Actinobacillus ureae ATCC 25976]
          Length = 339

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/255 (25%), Positives = 125/255 (49%), Gaps = 22/255 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L  +  E+    A+QI GAD
Sbjct: 36  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSRLRLAHHEEIGVNAVQIAGAD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 95  PQEMAAAAKVNVEYGAEIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVDVP 154

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D +      RN   + K  +K+G++ + IH R         +D       +
Sbjct: 155 VTLKIRTGWDQEN-----RNCLEIAKIAEKAGISALTIHGR--------TRDCLFNGEAE 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  + K+   + I  NG +    +A  +L     D VMIGR ++    +   V ++ 
Sbjct: 202 YESIKAV-KQAVSIPIIANGDVTSAEKAKYVLDYTKADAVMIGRGSFGRPWLFKEVKDFL 260

Query: 234 SNPLTGSSPIKTRVD 248
            N  + +S +  + +
Sbjct: 261 ENGRSSNSSLDEKCE 275


>gi|303228846|ref|ZP_07315659.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516466|gb|EFL58395.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 330

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 79/307 (25%), Positives = 139/307 (45%), Gaps = 29/307 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKL 62
           +D  YR  A+     +++ TEM+ A  I   +++   +L     E P+++QI G++   +
Sbjct: 25  SDIAYRLLAKE-HGASMVCTEMVSAMGIKYKNERTHELLRMEEVEHPVSMQIFGSNPEAI 83

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              AK+V   G + +++N+GCP  +V     G+ LM  PD+      A  KA+ +PVTVK
Sbjct: 84  ALGAKVVAAAGADIVDINMGCPVKKVVSSGDGSALMKTPDLAARVAEAAVKAVDVPVTVK 143

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG DD+   + + +  K I+ +GV  + +H R         ++   +   D+  +  +
Sbjct: 144 MRIGWDDE--HINVVDFAKRIESTGVAAVAVHGRT--------REQMYMGRADWSYIKAV 193

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K       IG NG +     AL+++     D VMIGR A  N  +    + Y +   TG 
Sbjct: 194 KDSLSIPVIG-NGDVWTPEDALRMMQETGCDAVMIGRGAQGNPWIFERTNHYLT---TG- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKL--QQITRHMIGLFHGFPNS----RRCR 294
              + R +  +  ++   +  +     + G  L  ++I  H      G P +     R  
Sbjct: 249 ---ELRPEPTYLERLDMLLKHFELLCRYKGAALGVREIRTHAGWYMRGMPEAAYWRNRVN 305

Query: 295 HILTVEA 301
            I TVE+
Sbjct: 306 TIHTVES 312


>gi|332291315|ref|YP_004429924.1| TIM-barrel protein, nifR3 family [Krokinobacter diaphorus 4H-3-7-5]
 gi|332169401|gb|AEE18656.1| TIM-barrel protein, nifR3 family [Krokinobacter diaphorus 4H-3-7-5]
          Length = 330

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 138/310 (44%), Gaps = 43/310 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA 
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ + +IVE  G + I++N GCP  +V     GA ++ + D++     AM     +P
Sbjct: 78  EESMLRSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTKAMVNHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ +  + + ++  G   I IH R    + KG          + D+
Sbjct: 138 VTVKTRLGWDHD--SIKIVEVAERLQDVGCAAISIHGRTRAQMYKG----------DADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + E+K  NP + I +  NG +    +A+++     +DG MIGRA+         V  +
Sbjct: 186 GPIAEVKN-NPRMQIPVFGNGDVNTPERAVEMRDKYGLDGAMIGRASIGYPWFFNEVKHF 244

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-------QITRHMIGLF 284
                  + P +K R++              A RHL      +       +  RH    F
Sbjct: 245 METGTHKAPPTMKERIEA-------------ARRHLQMSIDWKGEVLGVFETRRHYTNYF 291

Query: 285 HGFPNSRRCR 294
            G P+ +  R
Sbjct: 292 RGIPHFKEYR 301


>gi|292900840|ref|YP_003540209.1| tRNA-dihydrouridine synthase B [Erwinia amylovora ATCC 49946]
 gi|291200688|emb|CBJ47820.1| tRNA-dihydrouridine synthase B [Erwinia amylovora ATCC 49946]
 gi|312170828|emb|CBX79088.1| putative dehydrogenase [Erwinia amylovora ATCC BAA-2158]
          Length = 321

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 114/240 (47%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMMSSNPEVWASDKSRLRMVHSDEPGVRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   + A+  A+ +P
Sbjct: 76  PQEMAEAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILTAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L    ++ G+  + IH R    +  G +          +
Sbjct: 136 VTLKIRTGWDSDNRNCVEIAQLA---ERCGIQALTIHGRTRACLFNGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + +  NG + D  +A  +L     DG+MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQNVSIPVIANGDITDPHKARAVLDYTGADGLMIGRAAQGRPWIFREIQHYL 241


>gi|254423948|ref|ZP_05037666.1| putative TIM-barrel protein, nifR3 family [Synechococcus sp. PCC
           7335]
 gi|196191437|gb|EDX86401.1| putative TIM-barrel protein, nifR3 family [Synechococcus sp. PCC
           7335]
          Length = 362

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/317 (24%), Positives = 141/317 (44%), Gaps = 28/317 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADISKLV 63
           TD+ +R   R     +++YTEM+ A  +    +  IL      E+P+++Q+       L 
Sbjct: 63  TDKVFRRLVRRYAPQSMMYTEMVSAAELHHLQRLPILMDIDPDERPISIQLFDRRPDFLA 122

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA    D G + I++N+GCP  ++ +   G+ L+ +PD     + A+CKA+ +PVTVK 
Sbjct: 123 TAACKAVDQGADTIDINMGCPVNKITKNGGGSSLLRDPDTAVRIVDAVCKAVDVPVTVKT 182

Query: 124 RIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           RIG  D++I AV   +  + ++ +G   + +H R         +         ++ +  +
Sbjct: 183 RIGWSDEEINAV---DFARRMESAGAQMLTLHGRT--------RAQGYTGTARWEWIARV 231

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K       I  NG +  +  AL+ L     DG+M  R       ++  +D +      G 
Sbjct: 232 KAALTIPVIA-NGDIFSIESALRCLVETKADGIMCSRGTLGYPFLVGEIDHFIKT--GGI 288

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-----RRCRH 295
            P  + V++    K   +M  +  + +     ++Q  +HM      FP +     R CR 
Sbjct: 289 RPAPSVVERLTCAKEHLTML-WEYKGIRG---IRQARKHMAWYAKDFPGAAELRDRLCR- 343

Query: 296 ILTVEAGASTATHHIIE 312
           I +VEAG       I++
Sbjct: 344 IDSVEAGCDLLDQTILQ 360


>gi|148998011|ref|ZP_01825524.1| replicative DNA helicase [Streptococcus pneumoniae SP11-BS70]
 gi|168576061|ref|ZP_02721966.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae MLV-016]
 gi|307068800|ref|YP_003877766.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae AP200]
 gi|147756021|gb|EDK63064.1| replicative DNA helicase [Streptococcus pneumoniae SP11-BS70]
 gi|183578142|gb|EDT98670.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae MLV-016]
 gi|306410337|gb|ADM85764.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae AP200]
 gi|332198603|gb|EGJ12686.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA41317]
          Length = 326

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|304391548|ref|ZP_07373490.1| tRNA-dihydrouridine synthase B [Ahrensia sp. R2A130]
 gi|303295777|gb|EFL90135.1| tRNA-dihydrouridine synthase B [Ahrensia sp. R2A130]
          Length = 342

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 109/221 (49%), Gaps = 19/221 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGADISKLV 63
           TD  +R  A       ++ +EM+ ++A+  G  + +L  +    P   +Q+ G +   + 
Sbjct: 32  TDVPFRRLA-WRYGAGMVVSEMVASEALTTGMDEMVLKAAGAGLPDHMVQLAGREPQWMD 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            A ++ ED G   I++N+GCPS RV  G  G+ LM + D     I A+  A  +PVT+K 
Sbjct: 91  RATRMAEDAGATIIDINMGCPSKRVTNGYSGSALMRDLDNAEGLINAVVAATDLPVTLKM 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D+Q  ++    L +  + +GV  + +H   R    KG +          D+D +  
Sbjct: 151 RLGWDEQ--SINAPELARRAENAGVQMLTVHGRTRNQFYKGTA----------DWDAIRA 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           + +E   L + +NG + D + A   L     DGVMIGRA+Y
Sbjct: 199 V-REASRLPLVVNGDICDEATACAALIASGADGVMIGRASY 238


>gi|75906868|ref|YP_321164.1| dihydrouridine synthase TIM-barrel protein nifR3 [Anabaena
           variabilis ATCC 29413]
 gi|75700593|gb|ABA20269.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Anabaena
           variabilis ATCC 29413]
          Length = 350

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 72/301 (23%), Positives = 137/301 (45%), Gaps = 26/301 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    ++++YTEM+ A  +    +   I+     E+P+++Q+       L 
Sbjct: 36  TDMVFRRLVRRYAPDSMMYTEMVNATGLHYVQQLPKIMEVDPNERPISIQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + I++N+GCP  ++ +   G+ L+  P++    +  + KA+++PVTVK 
Sbjct: 96  EAAIKAVAEGADTIDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVNVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG +D+   + + +  K ++ +G   I +H R    +G +        N  ++ +  +K
Sbjct: 156 RIGWNDR--EITILDFAKRMEDAGAQMITVHGRTRA-QGYN-------GNARWEWIARVK 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTG 239
           +      IG NG +  +  A+K L     DGVM  R       ++  +D +      LT 
Sbjct: 206 EILSIPVIG-NGDIFSVESAVKCLEETGADGVMCSRGTLGYPFLVGEIDHFLKTGELLTA 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILT 298
            +PI+         ++  +     A   + G + ++Q  +HM     GF  +   R  L+
Sbjct: 265 PTPIQ---------RLECARDHLQALWEYKGDRGVRQARKHMTWYAKGFVGAAELRGQLS 315

Query: 299 V 299
           V
Sbjct: 316 V 316


>gi|289577559|ref|YP_003476186.1| hypothetical protein Thit_0307 [Thermoanaerobacter italicus Ab9]
 gi|289527272|gb|ADD01624.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter italicus Ab9]
          Length = 321

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQI G+D 
Sbjct: 17  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKMLTDIGEEEKVALQIFGSDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + A+ KA + PV
Sbjct: 76  DIMGEIARKLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMEAVVKASNKPV 135

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K+GV  + +H R         ++       D+ I
Sbjct: 136 TVKIRKGWDDNHVNAVEIAQIA---EKAGVKAVAVHGR--------TREQFYSGKADWSI 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++ KE+  + +  NG +     A ++      D ++IGR A  N  +      Y  N
Sbjct: 185 IKKV-KESVKIPVMGNGDIFTPQDAKRMFEETGCDAILIGRGAQGNPWIFKRTLHYLEN 242


>gi|225631215|ref|ZP_03787910.1| NifR3 family protein [Wolbachia endosymbiont of Muscidifurax
           uniraptor]
 gi|225591088|gb|EEH12275.1| NifR3 family protein [Wolbachia endosymbiont of Muscidifurax
           uniraptor]
          Length = 310

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 117/251 (46%), Gaps = 27/251 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++    ++ L  +  +   A+Q+ G +   + E
Sbjct: 13  TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTHQS-LQKAKVDALTAVQLAGCEPYVMAE 70

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVTVK R
Sbjct: 71  AAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNVPVTVKMR 130

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIV 179
            G +D+      RN   L K  +  G   I +H R    +  G +          D+  V
Sbjct: 131 TGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQA----------DWKFV 175

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + KE   + + +NG    L D+  ALK     DGVMIGR AY    ++     + S  
Sbjct: 176 RNV-KEQVKIPVIVNGDIKNLNDIQNALK-ESGADGVMIGRGAYGKPWLINQAMNFLSGS 233

Query: 237 LTGSSPIKTRV 247
            T       R+
Sbjct: 234 ETSEPTASERL 244


>gi|261378953|ref|ZP_05983526.1| tRNA-dihydrouridine synthase B [Neisseria cinerea ATCC 14685]
 gi|269144654|gb|EEZ71072.1| tRNA-dihydrouridine synthase B [Neisseria cinerea ATCC 14685]
          Length = 336

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 113/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +    A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGVAAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PAVA     +  +  G+  + +H   R  + KG +         
Sbjct: 136 VTLKTRLGWHDDYKNLPAVA-----RIAEDCGIASLAVHGRTRTQMYKGEAA-------- 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 183 --YDLIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|229495227|ref|ZP_04388962.1| TIM-barrel protein, NifR3 family [Porphyromonas endodontalis ATCC
           35406]
 gi|229317670|gb|EEN83568.1| TIM-barrel protein, NifR3 family [Porphyromonas endodontalis ATCC
           35406]
          Length = 334

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/255 (27%), Positives = 122/255 (47%), Gaps = 19/255 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D +D  +R   R     +++Y+E I ADA++R  +   N L     E P  +QI G D
Sbjct: 18  MEDVSDSAFRLLCRGF-GASMVYSEFISADALIRSVRGACNKLFIHPDEHPAVIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ + EAA I    G   +++N GCP  RV     G+ ++ N  ++ +   A+ KA  +P
Sbjct: 77  VASMAEAAAIASTTGAEILDINFGCPVKRVAGKGAGSGMLRNIPLLLEITRAVVKASRVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D Q   + + +L ++++  G+  + IH R         + +    N D+ +
Sbjct: 137 VTVKTRLGWDHQ--NIIIEDLAEALQDCGIAALTIHGRT--------RSDMYNGNADWSL 186

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF- 233
           +  +K  NP + I +  NG +    +A +      VD VM+GRA+     +   +  Y  
Sbjct: 187 IGAVKN-NPRITIPIIGNGDITTPQEAKEAFDRYGVDAVMVGRASIGRPWVFEEMRHYLD 245

Query: 234 SNPLTGSSPIKTRVD 248
           +  L    P   R+D
Sbjct: 246 TGELLQDRPASERLD 260


>gi|225181735|ref|ZP_03735174.1| TIM-barrel protein, nifR3 family [Dethiobacter alkaliphilus AHT 1]
 gi|225167606|gb|EEG76418.1| TIM-barrel protein, nifR3 family [Dethiobacter alkaliphilus AHT 1]
          Length = 319

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 113/236 (47%), Gaps = 18/236 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKL 62
           TD  +R  AR +   AL++TEMI A   +   ++   I  F+ QE+P+ +Q+ G+D    
Sbjct: 21  TDSSFRILAREM-GCALVFTEMISAKGAVCAPEQTLKIARFTAQERPIGIQLFGSDPEIF 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A ++      + +++N+GCP  +V     G  LM +PD       A+C A ++PVTVK
Sbjct: 80  ARATELCNGQAPDLLDINMGCPVKKVAGKGEGCALMRDPDKAYAITKAVCDAATMPVTVK 139

Query: 123 CRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R G DD ++ AV    +  +++++G   + +H R    +G S +        D+ ++  
Sbjct: 140 MRKGWDDSEVNAV---EVALAVQEAGAAAVTVHGRTRA-QGYSGR-------ADWSVIAR 188

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +K+      +G NG + +   A ++L     D VM+ R    N  ++     Y   
Sbjct: 189 VKEALRVPVVG-NGDIWEPQDAQRMLQQTGCDAVMLARGVLGNLWLIRRTVHYLET 243


>gi|15606718|ref|NP_214098.1| hypothetical protein aq_1598 [Aquifex aeolicus VF5]
 gi|39930814|sp|O67533|DUS_AQUAE RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|2983958|gb|AAC07506.1| hypothetical protein aq_1598 [Aquifex aeolicus VF5]
          Length = 316

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 77/301 (25%), Positives = 141/301 (46%), Gaps = 31/301 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M  +T   +R   R L  +   YTE+I A  +LR G    +  F+ +E+P+ +Q+ G++ 
Sbjct: 13  MASYTHSAFRRLCRRLGADRT-YTELISAVGVLRNGIPMKLAYFTEEERPIHIQVFGSNP 71

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            ++ +A+ ++ ++   + I++N GC   +V        ++  P ++G+ +    +AL   
Sbjct: 72  EEIAQASVVIAKELKPDFIDINFGCSVPKVLRNKAAGYMLQCPPLMGEVVKETVEALKPY 131

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPV+ K R+G +       +  +V+ ++K+GV+ I IHAR A  +G S K         
Sbjct: 132 GIPVSAKIRLGFEKD----EVERIVEELQKAGVSLIAIHARTA-KQGFSGKAL------- 179

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           +  + E KK      IG +G ++      ++      DGVM+GRAA  N  +       F
Sbjct: 180 WHRIKEAKKVASVPIIG-SGDVKSWRDIERMFEETECDGVMVGRAALSNPWIFKE----F 234

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                    +K R+  DF  +  + MT+Y +R         +I   ++ +  G PNSR  
Sbjct: 235 KEKRDIEVGLKERM--DFILEELSMMTEYMSREKACA----EIKSQIVQILKGVPNSREL 288

Query: 294 R 294
           +
Sbjct: 289 K 289


>gi|30248878|ref|NP_840948.1| hypothetical protein NE0874 [Nitrosomonas europaea ATCC 19718]
 gi|30138495|emb|CAD84785.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Nitrosomonas europaea ATCC 19718]
          Length = 337

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 121/247 (48%), Gaps = 25/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +   A+  +EM+ ++++L G +K         + KP+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAAMAVSEMVSSNSLLYGSEKTRRRACHDGEVKPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   I++N+GCP+ ++     G+ L+ + ++V   + A+ +A+ IP
Sbjct: 76  PVMMAQAARHNADQGAEIIDINMGCPAKKICNVMAGSALLKDENLVSRILDAVVQAVDIP 135

Query: 119 VTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D Q   A+ +  + +S   +G+  + IH R      +G            +
Sbjct: 136 VTLKIRTGWDTQHKNAITVARIAES---AGIQALAIHGRTRACAYRG----------QAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K  +  + I  NG +    +A  +L     D VMIGRAA     +    D Y 
Sbjct: 183 YDTIAAVKT-SIRIPIIANGDITTPEKAWAVLEYTGADAVMIGRAAQGKPWIFRETDHYL 241

Query: 234 SNPLTGS 240
           +   TGS
Sbjct: 242 T---TGS 245


>gi|218781043|ref|YP_002432361.1| TIM-barrel protein, nifR3 family [Desulfatibacillum alkenivorans
           AK-01]
 gi|218762427|gb|ACL04893.1| TIM-barrel protein, nifR3 family [Desulfatibacillum alkenivorans
           AK-01]
          Length = 332

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 141/302 (46%), Gaps = 24/302 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL+ +EMI ++ ++R  KK   ++    +E+PL++QI G+D   L ++A+IV + G + +
Sbjct: 36  ALVCSEMISSNGLIRYQKKTMELMASKEEERPLSIQIFGSDPGVLADSARIVAEHGADIV 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVAL 136
           ++N GC   +V +G  G+ LM +       +  + KA+S+P T+K R G D     A+AL
Sbjct: 96  DINFGCSVKKVLKGGAGSALMADLPRAEKILKEVRKAISLPFTIKMRSGWDASGDEAMAL 155

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + +    +GV+ + +H R A  +G S        + D+  +  +K+E     IG NG 
Sbjct: 156 GRIAQD---AGVDAVALHPRTA-KQGFS-------GHSDWSQIKRLKQELTIPVIG-NGD 203

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           +      L+++     DGVMIGRA      +         N      P++  +D D  +K
Sbjct: 204 VTKPEHVLEMMEQTGCDGVMIGRAVLYAPWIFRQALCLLEN-----RPME-EIDLDDRKK 257

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
           +     D    +L      + +   +     G PN+ + R  +T  A    A   +IE  
Sbjct: 258 VLFDYLDDTMDYLGEEHGCRVMRSRLAWFVKGLPNAAKFRGEITRIASKEQA-RDLIEEF 316

Query: 315 FN 316
           F 
Sbjct: 317 FR 318


>gi|42560628|ref|NP_975079.1| NifR transcriptional regulator [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492124|emb|CAE76721.1| Transcriptional regulator (involved in nitrogen regulation; NifR3
           family [Mycoplasma mycoides subsp. mycoides SC str. PG1]
 gi|301321309|gb|ADK69952.1| TIM-barrel protein, nifR3 family [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 324

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 114/220 (51%), Gaps = 17/220 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
           +L+Y EM+    ++  +KK  N+L  +  E P+++QI G D+ + ++A + +E +   + 
Sbjct: 35  SLVYAEMVSVAGMVHDNKKTLNMLNVNKIEYPMSMQIFGNDVDEFIKATQWIEKNVDCDI 94

Query: 77  INLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           I+LN+GCP+ +V      G+ L+  P+++ + +  +    + PVT K R+G D    +V 
Sbjct: 95  IDLNLGCPAPKVAIRSQSGSALLKTPELIYEIVKNVVNNTNKPVTAKIRLGWDKN--SVN 152

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K I+K+G + I +HAR         +++    + D++ + E+K+      IG NG
Sbjct: 153 AVEVAKLIEKAGASAIAVHAR--------TRNDFYTGHADWEKIKEVKQAVSIPVIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + D   A K+L     D VM+ RA   N  +   ++ Y 
Sbjct: 204 DVIDAKSAKKMLDETGCDAVMVSRACQGNPWIFDQINYYL 243


>gi|253995778|ref|YP_003047842.1| TIM-barrel protein, nifR3 family [Methylotenera mobilis JLW8]
 gi|253982457|gb|ACT47315.1| TIM-barrel protein, nifR3 family [Methylotenera mobilis JLW8]
          Length = 347

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 81/313 (25%), Positives = 141/313 (45%), Gaps = 45/313 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSEKTKRRANHEGEVNPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVAQILRAVVGAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D Q      RN ++  K +   GV  + +H R      +         + +
Sbjct: 136 VTLKIRTGWDKQN-----RNAIQIAKMAEDLGVQALAMHGRTRACAYMG--------DAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K+      I  NG +    +A  +L     D VMIGRAA     +   ++ Y 
Sbjct: 183 YDTIAAVKQAIKIPLIA-NGDITTPEKAKFVLDYTGADAVMIGRAAQGRPWIFREIEHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---------SGGKLQQITRHMIGLF 284
           +   TG+  +   VD     +I A M +    HLH         +G ++ +  +H+    
Sbjct: 242 T---TGTHLLPPTVD-----EIHAVMLE----HLHDLYEFYGDLTGMRMAR--KHISWYT 287

Query: 285 HGFPNSRRCRHIL 297
            G   S + RH +
Sbjct: 288 KGLAGSAQFRHTM 300


>gi|302879858|ref|YP_003848422.1| TIM-barrel protein, nifR3 family [Gallionella capsiferriformans
           ES-2]
 gi|302582647|gb|ADL56658.1| TIM-barrel protein, nifR3 family [Gallionella capsiferriformans
           ES-2]
          Length = 340

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 131/302 (43%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKRM-GAGMAVSEMVASNSLLYGSEKTKRRANHEGEVDPISVQIVGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAAK   D G   I++N+GCP+ ++     G+ L+ N  +V   + A+  A++ P
Sbjct: 76  PKMLAEAAKYNVDHGAQIIDINMGCPAKKICNVMAGSALLQNEPLVAKLLEAVVGAVNAP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN V+  +    SG+  + IH R         +      + +
Sbjct: 136 VTLKIRTGWDTHN-----RNAVRIAQIAEASGIQALAIHGRT--------RACAYTGDAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K  +  + I  NG +    +A  +L     D VMIGRAA     +   ++ + 
Sbjct: 183 YDTIRAVKA-SVTIPIIANGDITTPEKARYVLQYSGADAVMIGRAAQGRPWLFREIEHFL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  SP  + + +     +   + D+   H      L+   +H+     G   S   
Sbjct: 242 QTGEHMPSPEVSEIHRVLLAHV-VELYDFYGEHT----GLRIARKHISWYTKGLAGSAHF 296

Query: 294 RH 295
           RH
Sbjct: 297 RH 298


>gi|38604693|sp|O52533|DUSB_PROVU RecName: Full=tRNA-dihydrouridine synthase B
 gi|3885442|gb|AAC77884.1| yhdG homolog [Proteus vulgaris]
          Length = 323

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 119/240 (49%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + + DK  +    + E  + ++QI G+D
Sbjct: 17  MAGVTDRPFRSLCYDM-GAGMTVSEMLSSNPQVWQTDKSRLRMVHSDELGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  D G   I++N+GCP+ +V++   G+ L+ +PD+V + ++A+  A+ +P
Sbjct: 76  PVDMAAAAKINADSGAQIIDINMGCPAKKVNKKLAGSALLRHPDLVAEILSAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G   D+   V +  L    ++ G+  + IH   R+ + KG            +
Sbjct: 136 VTLKIRTGWSPDERNCVEIAKLA---ERCGIQALTIHGRTRECLFKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQNVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|226329369|ref|ZP_03804887.1| hypothetical protein PROPEN_03274 [Proteus penneri ATCC 35198]
 gi|225202555|gb|EEG84909.1| hypothetical protein PROPEN_03274 [Proteus penneri ATCC 35198]
          Length = 307

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 119/240 (49%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + + DK  +    + E  + ++QI G+D
Sbjct: 1   MAGVTDRPFRSLCYDM-GAGMTVSEMLSSNPQVWQTDKSRLRMVHSDELGIRSVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  D G   I++N+GCP+ +V++   G+ L+ +PD+V + ++A+  A+ +P
Sbjct: 60  PVDMAAAAKINADSGAQIIDINMGCPAKKVNKKLAGSALLRHPDLVAEILSAVVNAVDVP 119

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G   D+   V +  L    ++ G+  + IH   R+ + KG            +
Sbjct: 120 VTLKIRTGWSPDERNCVEIAKLA---ERCGIQALTIHGRTRECLFKG----------EAE 166

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 167 YDSIRTV-KQNVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 225


>gi|268610842|ref|ZP_06144569.1| tRNA-dihydrouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 330

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 110/235 (46%), Gaps = 17/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M    DR YR   +     A + +EM+ A  I   D+K  ++   + +E+P+A+Q+ G++
Sbjct: 21  MAGVADRAYRLMCKKY-GAAYVVSEMVSAKGICYSDRKTASLCTVTAEERPMAVQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              + EA KIV ++  + I++N+GCP  +V     G+ LM +  +      A  KA   +
Sbjct: 80  PEFMAEAVKIVLEYEPDIIDINMGCPVPKVVNTGAGSALMKDVPLAAKITEAAVKAAGDV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G     P      + K+++ SG   + +H R         +D         D
Sbjct: 140 PVTVKHRAGWHYGEPNAV--EMAKALEASGAAAVAVHGRS--------RDQYYSGQSHND 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
           I+ ++K+      IG NG + D    +++      D VMIGR +Y N  +   ++
Sbjct: 190 IIRDVKQAVSIPVIG-NGDITDADSCMRMYEETGCDLVMIGRGSYGNPFIFREIE 243


>gi|92114408|ref|YP_574336.1| dihydrouridine synthase TIM-barrel protein nifR3 [Chromohalobacter
           salexigens DSM 3043]
 gi|91797498|gb|ABE59637.1| tRNA-U20-dihydrouridine synthase [Chromohalobacter salexigens DSM
           3043]
          Length = 343

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+   L  + +  P A+QI G D
Sbjct: 29  MAGVTDRPFRQLCREL-GAGLVVSEMVTSDTRLWHTRKSRQRLDHTGEPGPRAVQIAGGD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA++    G   +++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 88  AAMLAEAARLNVAQGAEIVDINMGCPAKKVCNKAAGSALLRDERLVAEILEAVVAAVDVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G   Q      RN V+  K    +G+  + +H R         ++ R     +
Sbjct: 148 VTLKIRTGWCPQT-----RNGVRVAKLAESAGIQALAVHGRT--------REQRYRGEAE 194

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    L +  NG ++   +A ++L     D VMIGR A  N  +   +D Y 
Sbjct: 195 YDTIAAIKQAV-SLPVFANGDIDGAEKAARVLDYTKADAVMIGRGAQGNPWIFREIDHYL 253


>gi|296122547|ref|YP_003630325.1| hypothetical protein Plim_2300 [Planctomyces limnophilus DSM 3776]
 gi|296014887|gb|ADG68126.1| TIM-barrel protein, nifR3 family [Planctomyces limnophilus DSM
           3776]
          Length = 351

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 116/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           +  +T+  +R     L    L  T+++ A  +L G +K +   +T   ++P A+QI G +
Sbjct: 21  LAGFTNLPFRRVVHELGGLGLGTTDLVNARGLLAGSEKTLRLIATHPIDRPFAVQIFGGE 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S + +AA+++E  G + I++N+GCP  +V +   GA LM + D   + + A+ +A+ +P
Sbjct: 81  ASIMRDAAQLLEARGVDSIDINMGCPVLKVVKTGAGASLMCHADAATELVKAVVEAVHVP 140

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R+G D  Q+ A       +  ++ GV  + IH R    +G S   NR       D
Sbjct: 141 VTVKMRLGWDASQLTA---PRFAREFEQVGVAAVAIHGRTRA-QGFSGTVNR-------D 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
            + ++ +    + +  NG +  +  A+ +        + IGR A  N  +   + E+
Sbjct: 190 GIRQVVEAVDSIPVIANGDIRSVDDAIAMYDETGCQAISIGRGALANPWIFRQLTEW 246


>gi|300770292|ref|ZP_07080171.1| tRNA-dihydrouridine synthase B [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300762768|gb|EFK59585.1| tRNA-dihydrouridine synthase B [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 331

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/326 (23%), Positives = 145/326 (44%), Gaps = 36/326 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R     +  L     E+P+ +QI G++
Sbjct: 21  MEDVSDPPFRYVCKQ-NGVDMMYTEFISSEGLIRDAAKSRQKLDIFEYERPIGIQIFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + ++++I      + I++N GCP   V     G+ L+ + D +     A+ +A  +P
Sbjct: 80  IEHMRQSSEICSLANPDLIDINYGCPVKNVVCKGAGSSLLQDVDKMVAMTKAVVEATHLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    V    + + ++  G+  + IH R    + KG +          D+
Sbjct: 140 VTVKTRLGWDDNTKNVY--EVAERLQDVGIKALSIHGRTRAQMYKGQA----------DW 187

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ ++K+ NP + I +  NG ++ + +  A +    VDG+MIGRA+     +   +  +
Sbjct: 188 SMIRDVKR-NPRIKIPIFGNGDIDSVEKAAAWRQEFEVDGIMIGRASIGYPWIFREIKHF 246

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNS 290
           F        P  T V+     ++    T         G K  + ++ RH    F G PN 
Sbjct: 247 FETGQRLEGP--TIVE-----RVEVCRTHLTKSIEWKGEKTGIFEMRRHYANYFKGIPNF 299

Query: 291 RRCRHILTVEAGASTATHHIIETAFN 316
           +  R  L         +HH I    +
Sbjct: 300 KEYRMKLV-----GLQSHHEIHEVLD 320


>gi|241204538|ref|YP_002975634.1| TIM-barrel protein, nifR3 family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240858428|gb|ACS56095.1| TIM-barrel protein, nifR3 family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 338

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 107/211 (50%), Gaps = 18/211 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +RF A L+    ++ +  +V D      + +  GF    +P  +Q+ G +   + EAAKI
Sbjct: 46  WRFGAGLVVTE-MVASRELVNDTAESWSRLSAAGF----RPHMVQLAGREAHWMAEAAKI 100

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
             D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+K R+G D
Sbjct: 101 AADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPVTLKMRLGWD 160

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   ++   ++ +  + +G+  + IH R      +   + R     D+D +  + +E   
Sbjct: 161 EN--SINAPDIARRAEAAGIQLVTIHGRTR----MQFYEGRA----DWDAIRAV-REVIS 209

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           + +  NG +E  S A +IL     D VMIGR
Sbjct: 210 IPLIANGDVETASDAQEILRRSGADAVMIGR 240


>gi|327388929|gb|EGE87277.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA04375]
          Length = 326

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 117/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  +  PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKGPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|259501002|ref|ZP_05743904.1| tRNA-dihydrouridine synthase [Lactobacillus iners DSM 13335]
 gi|302190549|ref|ZP_07266803.1| tRNA-dihydrouridine synthase [Lactobacillus iners AB-1]
 gi|259167696|gb|EEW52191.1| tRNA-dihydrouridine synthase [Lactobacillus iners DSM 13335]
          Length = 331

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 131/285 (45%), Gaps = 33/285 (11%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++     E P++LQI G     LVEAA+ V+D  + +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLDMMKIDPNEHPMSLQIFGGSEETLVEAARYVDDNTHADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           N+N+GCP  +V +   GA  +L+PD +   + A+   +  PVTVK R G D D I AV  
Sbjct: 100 NINMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQKPVTVKMRTGWDEDHIYAV-- 157

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + +++G   + +H   RK +  G          + D+ I+ E+       F+G N
Sbjct: 158 ENALAA-QEAGACAVAMHGRTRKQLYTG----------HADWGILKEVSDALTIPFVG-N 205

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRV--DK 249
           G +     A K+L  V    VM+GRA   N  +L  +  Y  +  L     ++ RV   K
Sbjct: 206 GDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDTGELLAPQTVEERVITCK 265

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  RK+     +  A        + +  R       G P S R R
Sbjct: 266 EQLRKLVELKGEKIA--------VPEFRRQAAYYLKGIPRSARTR 302


>gi|225862005|ref|YP_002743514.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298229280|ref|ZP_06962961.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298254679|ref|ZP_06978265.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|225727928|gb|ACO23779.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Taiwan19F-14]
          Length = 326

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 117/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  +  PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKGPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|298501698|ref|YP_003723638.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|298237293|gb|ADI68424.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 311

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  +  PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKGPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +Y++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|291612763|ref|YP_003522920.1| TIM-barrel protein, nifR3 family [Sideroxydans lithotrophicus ES-1]
 gi|291582875|gb|ADE10533.1| TIM-barrel protein, nifR3 family [Sideroxydans lithotrophicus ES-1]
          Length = 335

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 115/239 (48%), Gaps = 18/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKRM-GAGMAVSEMVASNSLLYGSEKTKRRANHEGEVDPISVQIVGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   D G   I++N+GCP+ ++     G+ LM N  +V + +  +  A+ +P
Sbjct: 76  PKMLAQAARYNVDNGAQIIDINMGCPAKKICNVMAGSALMQNEKLVAEILEEVVGAVEVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D +   AV   N+ +  + SG+  + IH R         +      + +YD
Sbjct: 136 VTLKIRTGWDKNNRNAV---NIARIAEASGIQALAIHGRT--------RACAYTGDAEYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  +K E  ++ +  NG +    +A  +L     D VMIGRAA     +   ++ +  
Sbjct: 185 TIRAVKAE-VNIPVIANGDITTPEKARFVLQHTGADAVMIGRAAQGRPWLFREIEHFLQ 242


>gi|169830145|ref|YP_001700303.1| tRNA-dihydrouridine synthase 2 [Lysinibacillus sphaericus C3-41]
 gi|168994633|gb|ACA42173.1| Probable tRNA-dihydrouridine synthase 2 [Lysinibacillus sphaericus
           C3-41]
          Length = 325

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    D     +N L F+  E+P+   I G
Sbjct: 20  MEDVTDVVFRHVISEAGRPDVFFTEFTNTTSYCHPDGMDSVRNRLAFTEDEQPMVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +++ G+  I++N+GCP   V E   GA L+L+P +  + I A  KA  
Sbjct: 80  DTPEHFRQMSIGMKELGFKGIDINMGCPVDNVAERGKGAGLILHPALASEIIQA-AKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R       + ++  K+P   +
Sbjct: 139 LPVSVKTRLGFTD---VAEWREWLTHILKQNIANLSIHLR-------TREEMSKVP-AHW 187

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +IKK      P+  + +NG + D    LK+     +DG+MIGR  + N
Sbjct: 188 ELIADIKKLRDDIAPETLLTINGDIPDRVTGLKLAEQYGIDGIMIGRGVFSN 239


>gi|294083784|ref|YP_003550541.1| NifR3-like protein [Candidatus Puniceispirillum marinum IMCC1322]
 gi|292663356|gb|ADE38457.1| NifR3-like protein [Candidatus Puniceispirillum marinum IMCC1322]
          Length = 328

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 128/296 (43%), Gaps = 21/296 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGADISK 61
           TD  +R   R      L+ TEMI + A+L   K  +    T+   E PL++Q+ G + S 
Sbjct: 23  TDWPFRRAVRR-AGGGLVVTEMIASAAMLAEVKTEMRKLKTEVATEAPLSIQLAGWEPSV 81

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + +AAK+  D G + I++N+GCP+ +V     G+ LM +       + A+ KA+ IPVT+
Sbjct: 82  MADAAKVSADLGASIIDINMGCPAKKVTGKQSGSALMRDEHHAAAILDAVVKAVDIPVTL 141

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD   ++    L K  +  G+  + +H R          D +KI  +   +   
Sbjct: 142 KMRLGWDDA--SLNAPQLAKIAQDVGIRMVAVHGRTRCQMYTGSADWQKIGEVVAAVSIP 199

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +   N D+       L+D+  AL       GVMIGR A      +    +  +       
Sbjct: 200 VIA-NGDIRT-----LDDVRMALH-HSHAAGVMIGRGAQGRPWFVAQAGDLLNGQQVRPE 252

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCRHI 296
           P    +   F   + A + D      H G    ++ R  I  + HG P S   R +
Sbjct: 253 P-SIAIRHQF---MLAHLEDMLT---HYGSAAMRLARKHIAWYAHGLPGSAELRDV 301


>gi|149199028|ref|ZP_01876068.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Lentisphaera araneosa HTCC2155]
 gi|149137817|gb|EDM26230.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Lentisphaera araneosa HTCC2155]
          Length = 330

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 116/222 (52%), Gaps = 23/222 (10%)

Query: 21  LLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           LL TE I   +    +R  KK I+   + + PL++QI G +   + E+AK+V D G + +
Sbjct: 34  LLCTEFIRISSHKPSMRSLKKQIV--KSGDIPLSVQIMGNNAELMAESAKLVVDCGADAV 91

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP+ R  +G  G+ ++ +P +    +A+M + +   ++ K R G D++     + 
Sbjct: 92  DVNMGCPTKRAVKGGVGSAMLKDPKLCYQVLASMREQVPCALSAKIRAGFDNK---EGVF 148

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            ++++I  SG + + +H R+ +   +G S          D+ I+  +K+++P   IG NG
Sbjct: 149 EILQAIVDSGADYLAVHPRRRVDHYEGHS----------DWRIISALKEKSPIPVIG-NG 197

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +   + A+++      DGVMIGR A  N  +     +  S+
Sbjct: 198 DVRTAADAVRMFKETQCDGVMIGRGALSNPWIFLQTSQVLSD 239


>gi|309791641|ref|ZP_07686133.1| NifR3 family TIM-barrel protein [Oscillochloris trichoides DG6]
 gi|308226263|gb|EFO79999.1| NifR3 family TIM-barrel protein [Oscillochloris trichoides DG6]
          Length = 336

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 113/238 (47%), Gaps = 21/238 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R     L    L+ TEM  A ++      + ++L F  QE+PL +Q+ G D
Sbjct: 31  MAGVTDSVFRRVILGLGGCGLVCTEMTNAASVTPKALKRHHLLDFLPQERPLTMQLSGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA  VE  G + I++N GCPS +V  G  G+ L+ +   +   + A+  A+ +P
Sbjct: 91  PDLVAAAALSVERLGADMIDINCGCPSPKVTGGGHGSALLKDLPKLERVLRAVTAAVQVP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G DD     A  N +++ +    +G+  + +H R         ++       D
Sbjct: 151 VTLKFRAGWDD-----ARLNYLETARIAEDAGIAALTLHPRT--------REQEYHGRAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +  V E+K+      +G +G ++    AL  L    VDGVMIGR A +N  +   + +
Sbjct: 198 WSRVAEVKRAVTIPVVG-SGDVKTAEDALLRLHETGVDGVMIGRGAMENPWIFLQIQQ 254


>gi|227509314|ref|ZP_03939363.1| tRNA-dihydrouridine synthase [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227191244|gb|EEI71311.1| tRNA-dihydrouridine synthase [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 335

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 116/222 (52%), Gaps = 18/222 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EMI    I+  +KK  +++    +E P+++QI G     LV+AAK V ++   + 
Sbjct: 37  GLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGTKETLVQAAKFVDQNTAADI 96

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  PVTVK R G D D I AV 
Sbjct: 97  IDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKKPVTVKMRTGWDEDHIYAV- 155

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
             N + + +++G + + +H R         +    + + ++DI+ E+  +    F+G NG
Sbjct: 156 -ENALAA-ERAGASALAMHGRT--------RKQMYMGHANWDILKEVAGQLHIPFMG-NG 204

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K+L  V  D VM+GRA   N  +L+ V+ Y   
Sbjct: 205 DVRTPQDAKKMLEDVGADAVMMGRAVEGNPWVLSQVEHYLET 246


>gi|188588843|ref|YP_001919615.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188499124|gb|ACD52260.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E3 str.
           Alaska E43]
          Length = 321

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 75/310 (24%), Positives = 147/310 (47%), Gaps = 34/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+ TEM+ A A+  G +  + +L  S +E P+A+QI G +
Sbjct: 17  MAGVTDLSFRGLCKEM-GCGLVCTEMVSAKALYYGSENTQTLLRVSDKEAPVAVQIFGRE 75

Query: 59  ISKLVEAAKIV----EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              + E  +      ED     I++N+GCP+ ++ +   G+ LML PD+  D + A+ K 
Sbjct: 76  PEIMAEICEKYLNPREDVCI--IDINMGCPAPKIVKNKEGSALMLEPDLAHDIVKAIKKV 133

Query: 115 LSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              PVTVK R G DD+ I AV      K+++++G + I +H   RK + +G S       
Sbjct: 134 SKKPVTVKFRKGYDDEHINAVEFG---KALEEAGADAIAVHGRTRKQMYEGHS------- 183

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
              D++I+ ++K+      +G NG +     A+K+  L + DG++I R +  N  +   +
Sbjct: 184 ---DWEIIKKVKEAVSIPVLG-NGDVFSPEDAIKMKELTNCDGILIARGSMGNPWIFKQI 239

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            +  +  +      + +++      +     + A ++      ++++ +H      G P 
Sbjct: 240 QDALNGKIVEEISYQDKIN------MCIRHYELAIKNDGEYKAIREMRKHASWYIKGIPR 293

Query: 290 SRRCRHILTV 299
           S   ++ + +
Sbjct: 294 STEIKNQINI 303


>gi|227538764|ref|ZP_03968813.1| tRNA-dihydrouridine synthase [Sphingobacterium spiritivorum ATCC
           33300]
 gi|227241273|gb|EEI91288.1| tRNA-dihydrouridine synthase [Sphingobacterium spiritivorum ATCC
           33300]
          Length = 331

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/325 (23%), Positives = 144/325 (44%), Gaps = 34/325 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R     +  L     E+P+ +QI G++
Sbjct: 21  MEDVSDPPFRYVCKQ-NGVDMMYTEFISSEGLIRDAAKSRQKLDIFEYERPIGIQIFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + ++++I      + I++N GCP   V     G+ L+ + D +     A+ +A  +P
Sbjct: 80  IEHMRQSSEICSLANPDLIDINYGCPVKNVVCKGAGSSLLQDIDKMVAMTKAVVEATHLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    V    + + ++  G+  + IH R    + KG +          D+
Sbjct: 140 VTVKTRLGWDDNTKNVY--EVAERLQDVGIKALSIHGRTRAQMYKGQA----------DW 187

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ ++K+ NP + I +  NG ++ + +  A +    VDG+MIGRA+     +   +  +
Sbjct: 188 SMIRDVKR-NPRIKIPIFGNGDIDSVEKAAAWRQEFEVDGIMIGRASIGYPWIFREIKHF 246

Query: 233 FSNPLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           F        P I  RV+      +  +    +         + ++ RH    F G PN +
Sbjct: 247 FETGQRLEGPTIAERVE------VCRTHLTKSIEWKGEKTGIFEMRRHYANYFKGIPNFK 300

Query: 292 RCRHILTVEAGASTATHHIIETAFN 316
             R  L         +HH I    +
Sbjct: 301 EYRMKLV-----GLQSHHEIHEVLD 320


>gi|148543507|ref|YP_001270877.1| nifR3 family TIM-barrel protein [Lactobacillus reuteri DSM 20016]
 gi|184152914|ref|YP_001841255.1| transcription regulator [Lactobacillus reuteri JCM 1112]
 gi|194467682|ref|ZP_03073669.1| TIM-barrel protein, nifR3 family [Lactobacillus reuteri 100-23]
 gi|227363656|ref|ZP_03847770.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325681851|ref|ZP_08161370.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM4-1A]
 gi|148530541|gb|ABQ82540.1| tRNA-U20-dihydrouridine synthase [Lactobacillus reuteri DSM 20016]
 gi|183224258|dbj|BAG24775.1| transcription regulator [Lactobacillus reuteri JCM 1112]
 gi|194454718|gb|EDX43615.1| TIM-barrel protein, nifR3 family [Lactobacillus reuteri 100-23]
 gi|227071325|gb|EEI09634.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324978942|gb|EGC15890.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM4-1A]
          Length = 333

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 112/218 (51%), Gaps = 20/218 (9%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNV 81
           EMI    I+  +++  N++    +E P+ +QI G     LVEAAK V+     + I++N+
Sbjct: 42  EMISDRGIMYHNQRTLNMMDVDPEEHPMGIQIFGGTKETLVEAAKYVDQHTAADVIDINM 101

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   GA  +L+P+ V + ++ +  A+  PVTVK R G DD+   +A+ N + 
Sbjct: 102 GCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDDK-HILAVENALA 160

Query: 142 SIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           + +++G + I +H   RK +  G +          D++I+ E+  +    F+  NG ++ 
Sbjct: 161 A-ERAGASAIAMHGRTRKQMYTGQA----------DWNILKEVASQLKIPFMA-NGDVKT 208

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
              A KIL        MIGRAA  N  ML   + Y + 
Sbjct: 209 PEDAKKILDMTGATAAMIGRAAMGNPWMLKRTEHYLAT 246


>gi|170717873|ref|YP_001784929.1| nifR3 family TIM-barrel protein [Haemophilus somnus 2336]
 gi|168826002|gb|ACA31373.1| putative TIM-barrel protein, nifR3 family [Haemophilus somnus 2336]
          Length = 327

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 123/251 (49%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L  +EM+ A+  +   +K+ L  +  +     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSFY-GAGLTCSEMMSANPQVWHTEKSRLRLAHHQDAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + ++ KA+++P
Sbjct: 76  PVEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKKILYSVVKAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN +   K  +++G+  + IH   R+ +  G          N
Sbjct: 136 VTLKIRTGWNQE-----HRNCIDIAKIAEQAGIQALSIHGRTRECLFNG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD + ++ KE   + +  NG +    QA ++L     DG+MIGR A     +  ++  
Sbjct: 181 AEYDSIKKV-KEQISIPVIANGDITTAKQAQEVLSYTGTDGIMIGRGALGKPWLFQSIVS 239

Query: 232 YFSNPLTGSSP 242
                +T   P
Sbjct: 240 LIETGITIPEP 250


>gi|296314359|ref|ZP_06864300.1| tRNA-dihydrouridine synthase B [Neisseria polysaccharea ATCC 43768]
 gi|296838915|gb|EFH22853.1| tRNA-dihydrouridine synthase B [Neisseria polysaccharea ATCC 43768]
          Length = 336

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R F R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRFCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PAVA     +  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHDDHKNLPAVA-----RIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|115375744|ref|ZP_01462997.1| tRNA-dihydrouridine synthase B [Stigmatella aurantiaca DW4/3-1]
 gi|115367218|gb|EAU66200.1| tRNA-dihydrouridine synthase B [Stigmatella aurantiaca DW4/3-1]
          Length = 369

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 111/230 (48%), Gaps = 22/230 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQ-EKPLALQIGGA 57
           M   ++R +R  A      AL  TE++ A  ++R +++ +  L FS + E+P +LQI G 
Sbjct: 50  MAGVSERPFRVIA-FKWGAALCPTELVSAQGLMRANQRTLKYLRFSPEVERPYSLQIFGG 108

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AA + +  G   I++N+GCP  +V +   G+ LM  P      + A+ +A  +
Sbjct: 109 EPEAMAQAALVGKAHGAQIIDINMGCPVKKVTKNGAGSALMCEPLRAARIVQAIAEATGL 168

Query: 118 PVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVT K R G D        RN ++    +  +G   + IH R         +D       
Sbjct: 169 PVTCKIRSGWDAH-----HRNYLQMAGELFSAGCAALAIHPRT--------RDQGYSGFA 215

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           D+ ++ ++K+  PD  +  NG ++  + A ++  +   D VMIGR A  N
Sbjct: 216 DWSVIADLKRHFPDRTLIGNGDVKTPADARRMRETTGCDFVMIGRGALGN 265


>gi|222148571|ref|YP_002549528.1| nitrogen regulation protein [Agrobacterium vitis S4]
 gi|221735557|gb|ACM36520.1| nitrogen regulation protein [Agrobacterium vitis S4]
          Length = 332

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 58/174 (33%), Positives = 92/174 (52%), Gaps = 17/174 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G D   + EAAKI E  G + I++N+GCP+ +V  G  G+ LM  P+I    I
Sbjct: 74  PHMVQLAGRDPHWMAEAAKIAEANGADIIDINMGCPAKKVIGGYAGSALMREPEIALAMI 133

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A  KA+SIPVTVK R+G D    ++   +L +  + +GV  I +H R      +   + 
Sbjct: 134 EATVKAVSIPVTVKMRLGWDSD--SINAPDLSRRAQDAGVQAITVHGRTR----MQFYEG 187

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKIL--PSVDGVMIGRA 218
           R     D+D +  ++     ++I L  NG ++ +  A +IL     D +M+GRA
Sbjct: 188 RA----DWDAIAAVRDA---IYIPLIANGDIDTLGDAQEILRRSGADAIMLGRA 234


>gi|312874301|ref|ZP_07734333.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2052A-d]
 gi|315653938|ref|ZP_07906854.1| tRNA-dihydrouridine synthase [Lactobacillus iners ATCC 55195]
 gi|311090174|gb|EFQ48586.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2052A-d]
 gi|315488634|gb|EFU78280.1| tRNA-dihydrouridine synthase [Lactobacillus iners ATCC 55195]
          Length = 331

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 130/285 (45%), Gaps = 33/285 (11%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  +     E P++LQI G     LVEAA+ V+D  + +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLEMMKIDPNEHPMSLQIFGGSEETLVEAARYVDDNTHADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           N+N+GCP  +V +   GA  +L+PD +   + A+   +  PVTVK R G D D I AV  
Sbjct: 100 NINMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQKPVTVKMRTGWDEDHIYAV-- 157

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + +++G   + +H   RK +  G          + D+ I+ E+       F+G N
Sbjct: 158 ENALAA-QEAGACAVAMHGRTRKQLYTG----------HADWGILKEVSDALTIPFVG-N 205

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRV--DK 249
           G +     A K+L  V    VM+GRA   N  +L  +  Y  +  L     ++ RV   K
Sbjct: 206 GDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDTGELLAPQTVEERVITCK 265

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  RK+     +  A        + +  R       G P S R R
Sbjct: 266 EQLRKLVELKGEKIA--------VPEFRRQAAYYLKGIPRSARTR 302


>gi|251780604|ref|ZP_04823524.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243084919|gb|EES50809.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 321

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 75/310 (24%), Positives = 147/310 (47%), Gaps = 34/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+ TEM+ A A+  G +  + +L  S +E P+A+QI G +
Sbjct: 17  MAGVTDLSFRGLCKEM-GCGLVCTEMVSAKALYYGSENTQTLLRVSDKEAPVAVQIFGRE 75

Query: 59  ISKLVEAAKIV----EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              + E  +      ED     I++N+GCP+ ++ +   G+ LML PD+  D + A+ K 
Sbjct: 76  PEIMAEICEKYLNPREDVCI--IDINMGCPAPKIVKNKEGSALMLEPDLAYDIVKAIKKV 133

Query: 115 LSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              PVTVK R G DD+ I AV      K+++++G + I +H   RK + +G S       
Sbjct: 134 SKKPVTVKFRKGYDDEHINAVEFG---KALEEAGADAIAVHGRTRKQMYEGHS------- 183

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
              D++I+ ++K+      +G NG +     A+K+  L + DG++I R +  N  +   +
Sbjct: 184 ---DWEIIKKVKEAVSIPVLG-NGDVFSPEDAIKMKELTNCDGILIARGSMGNPWIFKQI 239

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            +  +  +      + +++      +     + A ++      ++++ +H      G P 
Sbjct: 240 QDALNGKIVKEISYQDKIN------MCIRHYELAIKNDGEYKAIREMRKHASWYIKGIPR 293

Query: 290 SRRCRHILTV 299
           S   ++ + +
Sbjct: 294 STEIKNQINI 303


>gi|110679975|ref|YP_682982.1| tRNA-dihydrouridine synthase [Roseobacter denitrificans OCh 114]
 gi|109456091|gb|ABG32296.1| tRNA-dihydrouridine synthase [Roseobacter denitrificans OCh 114]
          Length = 327

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 115/240 (47%), Gaps = 30/240 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           M   TDR +R          L+ +EM+ +  IL       +K  LG S +    A+Q+ G
Sbjct: 19  MAGITDRPFRDLVASF-GAGLVVSEMVASADILNARPGTQEKAELGLSAEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     + A+ KA++
Sbjct: 76  REPGLMAEAARMVEGQGARIIDINMGCPAKKVTQGYSGSALMRTPDHAMTLVEAVVKAVN 135

Query: 117 IPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
           IPVT+K R+G DD +   P +A R      +++G+  + IH R      KG         
Sbjct: 136 IPVTLKTRLGWDDAMLNAPQIARRA-----EEAGIRMLTIHGRTRCQFYKG--------- 181

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
            + D+  +  +K       I  NG +   + A++   L   DGVMIGR A     +L  +
Sbjct: 182 -HADWAAIAGVKSVVSIPVIA-NGDILCSATAMEALRLSGADGVMIGRGARGKPWLLAQI 239


>gi|91201593|emb|CAJ74653.1| strongly similar to tRNA-dihydrouridine synthase [Candidatus
           Kuenenia stuttgartiensis]
          Length = 341

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 113/226 (50%), Gaps = 22/226 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  YR   R     ++ YTE++    I+  +KK   +L F  +E+P+  Q+ G D
Sbjct: 40  MAGFSDMPYRLICRRF-GMSMSYTEVVSVSGIVWNNKKTFKLLDFKEEERPVTFQVVGND 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EA K +E  G + I++N+GC  + +     GA ++ +P  +      +  +LS+P
Sbjct: 99  ECQITEACKKIEQLGPDIIDINMGCSVSDIAGKGAGAGMLKHPSKISKMFNNLTGSLSVP 158

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT K R+G D +      RN +   + ++++G + I +H R         +        D
Sbjct: 159 VTGKIRLGWDHK-----TRNYIEVARILEENGASLIAVHGRT--------RSQYFSGAAD 205

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAA 219
           +D + E+ K++  + +  NG +  ++    +K   + DGVMIGRAA
Sbjct: 206 WDAIAEV-KQSVKIPVIANGDVRSVADIAEIKKRTACDGVMIGRAA 250


>gi|327402492|ref|YP_004343330.1| tRNA-U20-dihydrouridine synthase [Fluviicola taffensis DSM 16823]
 gi|327318000|gb|AEA42492.1| tRNA-U20-dihydrouridine synthase [Fluviicola taffensis DSM 16823]
          Length = 333

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 117/237 (49%), Gaps = 22/237 (9%)

Query: 21  LLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+YTE I ++ ++R     +  L     EKP+ +QI G D   +  +AKIV+    + ++
Sbjct: 38  LMYTEFISSEGLIRDAIKSRQKLDIFDYEKPIGIQIFGGDEEAMAMSAKIVDATAPDLLD 97

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N GCP  +V     GA ++ + D++     A  K+ S+PVTVK R+G DD +  + +  
Sbjct: 98  INFGCPVKKVVSKGAGAGVLKDVDLMVRLTQACIKSTSLPVTVKTRLGWDDSM--INIME 155

Query: 139 LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--N 194
           + + ++  GV  + IH   R  + KG            D+  +  +K  NP + I +  N
Sbjct: 156 VAERLQDIGVEALSIHGRTRSQMYKG----------EADWSYIAAVKN-NPRIKIPIFGN 204

Query: 195 GGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP-IKTRVD 248
           G ++   +A+  K    VDG+M+GRA+     +   +  + +     + P +K RV+
Sbjct: 205 GDIDSPEKAVEYKNRYGVDGIMVGRASIGYPWIFNEIKHFMATGEHLAVPGVKERVE 261


>gi|325982360|ref|YP_004294762.1| TIM-barrel protein, nifR3 family [Nitrosomonas sp. AL212]
 gi|325531879|gb|ADZ26600.1| TIM-barrel protein, nifR3 family [Nitrosomonas sp. AL212]
          Length = 335

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 18/247 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G KK         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKSM-GAGMAVSEMVSSNSLLWGSKKTQRRANHEGEVSPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+   + G   I++N+GCP+ ++     G+ L+ +  +V   + A+ +A+ IP
Sbjct: 76  PQMLAAAAQYNAENGAQIIDINMGCPAKKICNVMAGSALLQDEKLVEKILIAVVRAVDIP 135

Query: 119 VTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D Q   A+A+ ++ ++   SG+  + IH R         +        +YD
Sbjct: 136 VTLKIRTGWDKQHKNALAIAHIAEN---SGIQALAIHGRT--------RACAYTGTAEYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       I  NG +    +A +IL     D +MIGRAA     +   +D + + 
Sbjct: 185 TIAAVKAAVRIPVIA-NGDITTPEKAKQILVYTKADAIMIGRAAQGRPWIFREIDHFLTT 243

Query: 236 PLTGSSP 242
                SP
Sbjct: 244 GQHLQSP 250


>gi|237748976|ref|ZP_04579456.1| tRNA-dihydrouridine synthase [Oxalobacter formigenes OXCC13]
 gi|229380338|gb|EEO30429.1| tRNA-dihydrouridine synthase [Oxalobacter formigenes OXCC13]
          Length = 324

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 20/241 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  A+ +LR   K+   +    + +P A+QI G+D
Sbjct: 17  MAGITDRPFRQLCKKL-GAGYAVSEMAAANPLLRNTPKSRRRIIHEGEVEPRAVQIVGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + ++A+   D G   I++N+GCP+ +V     G+ L+ N  +VG  + A+  A+S+P
Sbjct: 76  PATMADSARYNVDQGAQIIDINMGCPAKKVCNNWCGSALLQNEPLVGQILEAVTDAVSVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VT+K R G D     +    + K  + +G+  + +H   R+   +G++          +Y
Sbjct: 136 VTLKFRTGWDRS--HINAPEIAKIAESAGIAALTLHGRTREDAYRGMA----------EY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           D + E+K     + +  NG ++   +A  +L     D +MIGR A     +   +D +  
Sbjct: 184 DTIAEVKSLV-SIPVVANGDIDSPEKAKAVLEKTGADAIMIGRGAQGKPWIFREIDYFLK 242

Query: 235 N 235
           N
Sbjct: 243 N 243


>gi|17228722|ref|NP_485270.1| hypothetical protein all1227 [Nostoc sp. PCC 7120]
 gi|17130574|dbj|BAB73184.1| all1227 [Nostoc sp. PCC 7120]
          Length = 350

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 71/301 (23%), Positives = 138/301 (45%), Gaps = 26/301 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    ++++YTEM+ A  +    +   I+    +E+P+++Q+       L 
Sbjct: 36  TDMVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPKERPISIQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + I++N+GCP  ++ +   G+ L+  P++    +  + KA+++PVTVK 
Sbjct: 96  EAAIKAVAEGADTIDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVNVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG +D+   + + +  K ++ +G   I +H R    +G +        N  ++ +  +K
Sbjct: 156 RIGWNDR--EITILDFAKRMEDAGAQMITVHGRTRA-QGYN-------GNARWEWIARVK 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTG 239
           +      IG NG +  +  A+K L     DGVM  R       ++  +D +F     L  
Sbjct: 206 EILSIPVIG-NGDIFSVESAVKCLEETGADGVMCSRGTLGYPFLVGEIDHFFKTGELLPA 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILT 298
            +PI+         ++  +     A   + G + ++Q  +HM     GF  +   R  L+
Sbjct: 265 PTPIQ---------RLECARDHLQALWEYKGDRGVRQARKHMTWYAKGFVGAAELRGQLS 315

Query: 299 V 299
           +
Sbjct: 316 L 316


>gi|170743988|ref|YP_001772643.1| NifR3 family TIM-barrel protein [Methylobacterium sp. 4-46]
 gi|168198262|gb|ACA20209.1| TIM-barrel protein, nifR3 family [Methylobacterium sp. 4-46]
          Length = 358

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 113/231 (48%), Gaps = 21/231 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLV 63
           TD H R  AR    +A++ +EM+ A+ + RG  +  L    +  +P  +Q+ G D   + 
Sbjct: 39  TDLHLRRIARRCGASAVV-SEMVAAEDLARGSAEARLRAEGEGVRPHVVQLAGCDPRWMA 97

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A++ E  G + I++N+GCP+ +V  G  G+ LM + D     +AA+ +A+++PVTVK 
Sbjct: 98  EGARLAEANGADVIDVNMGCPAKKVTGGEAGSALMRDLDHAARLLAAVREAVAVPVTVKM 157

Query: 124 RIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           R+G DD     A RN   L +  +  G++ + +H R         +        D+  + 
Sbjct: 158 RLGWDD-----ASRNAPDLARRAEALGLSAVTVHGRT--------RQQFYAGRADWAAIR 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
            +  E   + +  NG +  +++A   L       VMIGRAA     ++  V
Sbjct: 205 AV-VEAVSIPVVANGDVGSLAEARACLAESGAAAVMIGRAAVGRPWLVGAV 254


>gi|148704961|gb|EDL36908.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_a [Mus
           musculus]
          Length = 327

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 129/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MI+A   +R  K     F+T +   PL +Q    D
Sbjct: 37  MVRYSKLAFRTLVRKYSCD-LCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 96  ARLLSDAALLVCPYA-NGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 154

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 155 RFSVSIKIRIH-DDLARTI---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 202 YDAIKMI-KENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLTNPAMFAGYEE-- 258

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 259 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 293


>gi|126737682|ref|ZP_01753412.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. SK209-2-6]
 gi|126721075|gb|EBA17779.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. SK209-2-6]
          Length = 313

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 140/310 (45%), Gaps = 36/310 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G +
Sbjct: 1   MAGITDRPFRDLVRSF-GAGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRE 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+ +A+ IP
Sbjct: 60  AEWMAEAARQVADRGARIIDINMGCPAKKVTNGYSGSALLKTPDHALRLIEAVVEAVDIP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R+G DD+    A  ++    + +GV  + IH R      KG +          D+
Sbjct: 120 VTLKTRLGWDDKCLNAA--SVAARAEDAGVQMVTIHGRTRCQFYKGQA----------DW 167

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  KE   + +  NG +     A + L     DGVM+GR       +L  +    S
Sbjct: 168 SAIRQT-KEAITVPLLANGDITSTETAKRALEQSGADGVMVGRGTQGKPWLLAQI----S 222

Query: 235 NPLTGSSPIKTRVDKDFWRKIS---ASMTDYAARHLHSGGKLQQITRHMIGLF---HGFP 288
           + L G++  +     D  R +S    +M ++  + L       ++ R  +G +    G P
Sbjct: 223 HDLWGATKPEIPRGNDLIRMVSEHYEAMLEFYGQDLG-----LRVARKHLGWYMDEAGTP 277

Query: 289 NSRRCRHILT 298
           ++ R R ILT
Sbjct: 278 SALR-RQILT 286


>gi|312871514|ref|ZP_07731607.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 3008A-a]
 gi|311092909|gb|EFQ51260.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 3008A-a]
          Length = 331

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 130/285 (45%), Gaps = 33/285 (11%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  +     E P++LQI G     LVEAA+ V+D  + +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLEMMKIDPNEHPMSLQIFGGSEETLVEAARYVDDNTHADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           N+N+GCP  +V +   GA  +L+PD +   + A+   +  PVTVK R G D D I AV  
Sbjct: 100 NINMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQKPVTVKMRTGWDEDHIYAV-- 157

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + +++G   + +H   RK +  G          + D+ I+ E+       F+G N
Sbjct: 158 ENALAA-QEAGACAVAMHGRTRKQLYTG----------HADWGILKEVSDALTIPFVG-N 205

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRV--DK 249
           G +     A K+L  V    VM+GRA   N  +L  +  Y  +  L     ++ RV   K
Sbjct: 206 GDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDTGELLSPQTVEERVITCK 265

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  RK+     +  A        + +  R       G P S R R
Sbjct: 266 EQLRKLVELKGEKIA--------VPEFRRQAAYYLKGIPRSARTR 302


>gi|310824089|ref|YP_003956447.1| tRNA-dihydrouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309397161|gb|ADO74620.1| tRNA-dihydrouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 354

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 111/230 (48%), Gaps = 22/230 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQ-EKPLALQIGGA 57
           M   ++R +R  A      AL  TE++ A  ++R +++ +  L FS + E+P +LQI G 
Sbjct: 35  MAGVSERPFRVIA-FKWGAALCPTELVSAQGLMRANQRTLKYLRFSPEVERPYSLQIFGG 93

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AA + +  G   I++N+GCP  +V +   G+ LM  P      + A+ +A  +
Sbjct: 94  EPEAMAQAALVGKAHGAQIIDINMGCPVKKVTKNGAGSALMCEPLRAARIVQAIAEATGL 153

Query: 118 PVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVT K R G D        RN ++    +  +G   + IH R         +D       
Sbjct: 154 PVTCKIRSGWDAH-----HRNYLQMAGELFSAGCAALAIHPRT--------RDQGYSGFA 200

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           D+ ++ ++K+  PD  +  NG ++  + A ++  +   D VMIGR A  N
Sbjct: 201 DWSVIADLKRHFPDRTLIGNGDVKTPADARRMRETTGCDFVMIGRGALGN 250


>gi|331267284|ref|YP_004326914.1| tRNA-dihydrouridine synthase, putative [Streptococcus oralis Uo5]
 gi|326683956|emb|CBZ01574.1| tRNA-dihydrouridine synthase, putative [Streptococcus oralis Uo5]
          Length = 326

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHTDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|322375163|ref|ZP_08049677.1| TIM-barrel protein, NifR3 family [Streptococcus sp. C300]
 gi|321280663|gb|EFX57702.1| TIM-barrel protein, NifR3 family [Streptococcus sp. C300]
          Length = 336

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 119/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 202 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 260


>gi|68171250|ref|ZP_00544653.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ehrlichia
           chaffeensis str. Sapulpa]
 gi|88657985|ref|YP_507556.1| putative tRNA-dihydrouridine synthase [Ehrlichia chaffeensis str.
           Arkansas]
 gi|67999332|gb|EAM85978.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ehrlichia
           chaffeensis str. Sapulpa]
 gi|88599442|gb|ABD44911.1| putative tRNA-dihydrouridine synthase [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 317

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 107/218 (49%), Gaps = 15/218 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R+  + L    LL +EMI + A++   K++ L  S  +   A+Q+ G D + + +
Sbjct: 21  TDFPFRYLVKSL-GAGLLVSEMIASRAMIIQTKQS-LQKSQIQINTAVQLAGCDPTIMAD 78

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V     G+ LM +       + ++ KA+ IPVT+K R
Sbjct: 79  AAKLNEDMGAQIIDINFGCPVKKVVNSYAGSALMKDETTAAKILESVVKAVKIPVTLKMR 138

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G D+    +    L K  +++G+  I IH R         +        D+  +  IKK
Sbjct: 139 TGWDNN--NLNSPKLAKIAEETGIKMITIHGRT--------RTQMFTGKADWKFIRNIKK 188

Query: 185 --ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
             + P +  G    L D+  +L+     DG+MIGR AY
Sbjct: 189 CVKIPVIVNGDIKNLNDIKTSLE-ESQADGIMIGRGAY 225


>gi|306828659|ref|ZP_07461852.1| tRNA-dihydrouridine synthase [Streptococcus mitis ATCC 6249]
 gi|304429165|gb|EFM32252.1| tRNA-dihydrouridine synthase [Streptococcus mitis ATCC 6249]
          Length = 326

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|240080043|ref|ZP_04724586.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA19]
          Length = 364

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDESLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 166 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|167038326|ref|YP_001665904.1| nifR3 family TIM-barrel protein [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320116727|ref|YP_004186886.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166857160|gb|ABY95568.1| putative TIM-barrel protein, nifR3 family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319929818|gb|ADV80503.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 336

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 113/226 (50%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQI G+D 
Sbjct: 32  MAGVTDKSFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEKVALQIFGSDP 90

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 91  DIMGEIARRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 150

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K+G+  + +H R         ++       D+ I
Sbjct: 151 TVKIRKGWDDNHVNAVEIAQIA---EKAGIKAVAVHGR--------TREQFYSGKADWSI 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + ++K+      IG NG +     A ++L     D ++IGR A  N
Sbjct: 200 IKKVKESVKIPVIG-NGDIFTPEDAKRMLEETGCDAILIGRGAQGN 244


>gi|313204550|ref|YP_004043207.1| tRNA-u20-dihydrouridine synthase [Paludibacter propionicigenes WB4]
 gi|312443866|gb|ADQ80222.1| tRNA-U20-dihydrouridine synthase [Paludibacter propionicigenes WB4]
          Length = 341

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 89/315 (28%), Positives = 148/315 (46%), Gaps = 38/315 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    + ++YTE I ADA++R  K+    L    +E+P+A+Q+ G +
Sbjct: 18  MEDVTDPAFRLLCKRFGVD-MVYTEFISADALIRSVKRTEQKLTIYDEERPVAIQLYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I  +     I+LN GCP  +V     GA L+ +   +    + + KA+++P
Sbjct: 77  ADAMAEAARIAAEACPEFIDLNFGCPVKKVAGKGAGAGLLRDIPKMLQITSEVVKAVNLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D+    +    L + ++  G+  + IH   R  + KG          + D+
Sbjct: 137 VTVKTRLGWDEDSKVIV--ELAERLQDCGIAALAIHGRTRSQMYKG----------DADW 184

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
            ++ E+K  NP + I +  NG +    +A +      VD VM+GRAA     +   + +Y
Sbjct: 185 TLIGEVKN-NPRMHIPIIGNGDVTTAERAAECFDRYGVDAVMVGRAAIGRPWVFAEMKQY 243

Query: 233 FSNPLTGS-SPIKTRVDKD--FWRKISAS-----MTDYAARHLHSGGKLQQIT---RHMI 281
           F    TG   P+ T  ++       I AS     + D  A    S  +L+ I    RH+ 
Sbjct: 244 FQ---TGEIHPVLTFEEQKNILKEHIIASVRWLDIDDNTAIESVSNQRLKGIIHSRRHLA 300

Query: 282 G--LFHGFPNSRRCR 294
              +F G PN +  R
Sbjct: 301 ATPVFKGIPNFKETR 315


>gi|292486759|ref|YP_003529629.1| putative dehydrogenase [Erwinia amylovora CFBP1430]
 gi|291552176|emb|CBA19213.1| putative dehydrogenase [Erwinia amylovora CFBP1430]
          Length = 321

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 113/240 (47%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMMSSNPEVWASDKSRLRMVHSDEPGVRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   + A   A+ +P
Sbjct: 76  PQEMAEAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILTAEVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L    ++ G+  + IH R    +  G +          +
Sbjct: 136 VTLKIRTGWDSDNRNCVEIAQLA---ERCGIQALTIHGRTRACLFNGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + +  NG + D  +A  +L     DG+MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQNVSIPVIANGDITDPHKARAVLDYTGADGLMIGRAAQGRPWIFREIQHYL 241


>gi|78184219|ref|YP_376654.1| dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9902]
 gi|78168513|gb|ABB25610.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9902]
          Length = 356

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 80/320 (25%), Positives = 144/320 (45%), Gaps = 31/320 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG-FSTQEKPLALQIGGADISKLV 63
           TD+ +R   R  + ++LL+TEM+ A ++  G     +     +E P+A+Q+       + 
Sbjct: 48  TDKIFRGLVRRWSRDSLLFTEMVNATSLELGHGYGKMDDLKAEEGPIAVQLFDHRPHAMA 107

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA+  E  G   I++N+GCP  ++ +   G+ L+ +P++    + A+  A+SIPVTVK 
Sbjct: 108 HAARRAEQAGAFLIDINMGCPVRKIAKKGGGSGLIRDPNLATQILEAVVDAVSIPVTVKT 167

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G       P    R L    + +G   + +H R    +G   + N       ++ + E
Sbjct: 168 RLGWCGSSSDPITWCRQL----QNAGAQMLTLHGRTR-EQGFKGQAN-------WNAIAE 215

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN---P 236
           +K+      I  NG +   + AL+ L     DGVM+GR    +  ++  ++  F N   P
Sbjct: 216 VKQALTIPVIA-NGDINSPTDALRCLEITGADGVMVGRGTMGSPWLVGQIEAAFMNRPIP 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  S  +  + K+    + +S   +          L    +HM     GFP + + RH 
Sbjct: 275 ATPDSGARLHLAKEQLHDLVSSRGSHG---------LLIARKHMSWTCTGFPGAPQLRHS 325

Query: 297 LTVEAGASTATHHIIETAFN 316
           L + A      + +I+ A N
Sbjct: 326 L-MRATTPDDAYQLIDNAIN 344


>gi|313667869|ref|YP_004048153.1| tRNA-dihydrouridine synthase [Neisseria lactamica ST-640]
 gi|313005331|emb|CBN86764.1| putative tRNA-dihydrouridine synthase [Neisseria lactamica 020-06]
          Length = 336

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHDDHKNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCR-LNIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|299541815|ref|ZP_07052138.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
 gi|298725553|gb|EFI66194.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
          Length = 325

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE     +    D     +N L F+  E+P+   I G
Sbjct: 20  MEDVTDVVFRHVIQEAGRPDVYFTEFTNTTSYCHPDGLDNVRNRLAFTEDEQPIVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  +++ G+  I++N+GCP   V E   GA L+L+P++  D I A  KA  
Sbjct: 80  DNPEHFRQMSIGMKELGFKGIDINMGCPVDNVAERGKGAGLILHPELAADIIQA-AKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         ++        +
Sbjct: 139 LPVSVKTRLGFTD---VTEWREWLTHILKQDIANLSIHLRT--------REEMSKVAAHW 187

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +IKK      P   + +NG + D    LK++    +DG+MIGR  + N
Sbjct: 188 ELIGDIKKLRDEVAPHTLLTINGDIPDRLTGLKLVEQYGIDGIMIGRGVFSN 239


>gi|148704962|gb|EDL36909.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_b [Mus
           musculus]
          Length = 324

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 129/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MI+A   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALLVCPYA-NGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLARTI---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMI-KENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLTNPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 290


>gi|310766173|gb|ADP11123.1| tRNA-dihydrouridine synthase B [Erwinia sp. Ejp617]
          Length = 305

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 114/240 (47%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 1   MAGITDRPFRTLCYAM-GAGMTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRTVQIAGCD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 60  PQEMAEAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILSAVVNAVDVP 119

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L    ++ G+  + IH R    +  G          + +
Sbjct: 120 VTLKIRTGWDSDNRNCVEIAQLA---ERCGIQALTIHGRTRACLFNG----------DAE 166

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 167 YDSIRTV-KQNVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 225


>gi|88607437|ref|YP_505166.1| putative tRNA-dihydrouridine synthase [Anaplasma phagocytophilum
           HZ]
 gi|88598500|gb|ABD43970.1| putative tRNA-dihydrouridine synthase [Anaplasma phagocytophilum
           HZ]
          Length = 315

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 115/247 (46%), Gaps = 21/247 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGADISKLV 63
           TD  +R   R L    LL +EM+ + A++   ++++    ++  P  ++Q+ G     + 
Sbjct: 19  TDLPFRTTVRKL-GAGLLISEMVASRAMILKTRQSMQ--KSEVCPNTSVQLAGCTPEIMA 75

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAKI ED G   I+LN GCP+ +V +G  G+ LM +  I    + ++ KA+ +PVTVK 
Sbjct: 76  EAAKINEDLGAKSIDLNFGCPAKKVVDGYAGSALMKDEVIATKIMESVVKAVKVPVTVKM 135

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D     +    L K  +  G+  I IH   R  +  G          + D+  V  
Sbjct: 136 RMGWDTT--NLNAPTLAKVAEDVGIQMITIHGRTRSQMFSG----------SADWKFVKR 183

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE   + + +NG +  +   +  L     DGVMIGR AY    ++     +  N    
Sbjct: 184 V-KECVKIPVIVNGDIRTLDDIVVALNESGADGVMIGRGAYGKPWLIKQALSFMKNSEIL 242

Query: 240 SSPIKTR 246
             P K+ 
Sbjct: 243 PEPTKSE 249


>gi|325295522|ref|YP_004282036.1| dihydrouridine synthase DuS [Desulfurobacterium thermolithotrophum
           DSM 11699]
 gi|325065970|gb|ADY73977.1| dihydrouridine synthase DuS [Desulfurobacterium thermolithotrophum
           DSM 11699]
          Length = 310

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 109/216 (50%), Gaps = 19/216 (8%)

Query: 23  YTEMIVADAIL-RGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLN 80
           Y+E++ A  I+ +G++K +  F+ +E+P+ LQ+ G +  ++ EAA KI E +    I++N
Sbjct: 35  YSELMNATGIIYKGEEKELAYFTDEERPIHLQVYGRNPEEIAEAARKIAEKYKPEAIDIN 94

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKCRIGVDDQIPAVALR 137
            GC   +V +      L+  P  +G  +AA  KA   L++PVT K R+G  +      L 
Sbjct: 95  FGCSVKKVLKAKAAGYLLQFPKEMGKIVAATAKALKPLNVPVTAKIRLGFYED----TLE 150

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + + + K+ V+ I +H R A  +G S        N +++ V ++KK   D  I  +G +
Sbjct: 151 EIAEELLKANVSAIALHPRTA-KQGFS-------GNANWERVKDLKKIAGDTPIIGSGDI 202

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
               +  +       DGVMIGRAA  N  +     E
Sbjct: 203 RSWKEIDQKFEETGCDGVMIGRAALANPWIFKEFKE 238


>gi|285019545|ref|YP_003377256.1| tRNA-dihydrouridine synthase b protein [Xanthomonas albilineans GPE
           PC73]
 gi|283474763|emb|CBA17262.1| probable trna-dihydrouridine synthase b protein [Xanthomonas
           albilineans]
          Length = 332

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 22/249 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K++  +  + +  P+++QI G  
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTLSDPRFWQTRKSLQRMDHAGEPDPISVQIAGTQ 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L +AA+   D G   I++N+GCP+ +V     G+ LM +  +V   ++A+ KA  +P
Sbjct: 76  PQQLADAARYNADHGAQLIDINMGCPAKKVCNAWAGSALMRDEALVARILSAVVKASPVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + +  +  G+  + +H R         +D       +
Sbjct: 136 VTLKIRTGWDSD-----HRNGPTIARIAEDCGIAALAVHGRT--------RDQHYSGQAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK       I  NG ++   +A ++L +   D VMIGRAA     +   +  Y 
Sbjct: 183 YATIAQIKAMLRIPVIA-NGDIDSPHKAAQVLAATGADAVMIGRAAQGRPWIFGEIAHYL 241

Query: 234 SNPLTGSSP 242
           ++     +P
Sbjct: 242 AHGEVSPAP 250


>gi|126696436|ref|YP_001091322.1| nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9301]
 gi|126543479|gb|ABO17721.1| putative nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9301]
          Length = 335

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 112/219 (51%), Gaps = 18/219 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    N+LL+TEMI A ++ +G   + I     +E P+ +QI       + 
Sbjct: 29  TDIIFRRLVRKWAPNSLLFTEMINATSLKKGYGTQKINQIDLEEGPIGVQIFDNRPYAVS 88

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ +PVTVK 
Sbjct: 89  EAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVRVPVTVKT 148

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D +   +   + +  ++ +G   I +H R    +G S K        D++++  +K
Sbjct: 149 RLGWDSKEENI--EDFLFKLQDAGATMITLHGRTR-KQGFSGKS-------DWEMIGRLK 198

Query: 184 K--ENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           K  E P   +  NG +++   AL  L   + DGVMIGR 
Sbjct: 199 KLLEIP---VIANGDIKNPDDALNCLKKTNADGVMIGRG 234


>gi|322387011|ref|ZP_08060624.1| tRNA-dihydrouridine synthase [Streptococcus infantis ATCC 700779]
 gi|321142155|gb|EFX37647.1| tRNA-dihydrouridine synthase [Streptococcus infantis ATCC 700779]
          Length = 326

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|306834510|ref|ZP_07467623.1| tRNA-dihydrouridine synthase [Streptococcus bovis ATCC 700338]
 gi|304423312|gb|EFM26465.1| tRNA-dihydrouridine synthase [Streptococcus bovis ATCC 700338]
          Length = 325

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 118/240 (49%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ + E+   + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEFIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIINEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDS--ELAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG + ++  A  ++    VD VM+GRAA  N  + T ++ YF 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRNVHDAKYMIEEIGVDAVMVGRAAMNNPYIFTQINHYFE 250


>gi|21312100|ref|NP_082278.1| tRNA-dihydrouridine synthase 4-like [Mus musculus]
 gi|12845370|dbj|BAB26724.1| unnamed protein product [Mus musculus]
          Length = 324

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 129/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MI+A   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALLVCPYA-NGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLARTI---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMI-KENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLTNPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 290


>gi|160916172|ref|ZP_02078379.1| hypothetical protein EUBDOL_02199 [Eubacterium dolichum DSM 3991]
 gi|158431896|gb|EDP10185.1| hypothetical protein EUBDOL_02199 [Eubacterium dolichum DSM 3991]
          Length = 335

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 78/288 (27%), Positives = 131/288 (45%), Gaps = 31/288 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGFST---QEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
           L+YTEM V+D  L  D +  +G +     E PLALQ+ G DI  +V AAK++ E    + 
Sbjct: 41  LIYTEM-VSDKALYYDNEKTIGMTAVEENEHPLALQLFGHDIETMVYAAKLMDEKTNCDI 99

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP  ++ + + G+ LM +P+     + A+ + +  PVTVK RIG D  +  +  
Sbjct: 100 IDINMGCPVTKIVKSNAGSALMKDPEHAIAMVKAVVENVKKPVTVKMRIGWD--LEHINC 157

Query: 137 RNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L K ++  GV  I +H R  K + +G          + D+  +  +K       IG N
Sbjct: 158 VELAKGLEAVGVAAIAVHGRTKKQMYEG----------HADWSYIKMVKDAVSIPVIG-N 206

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF- 251
           G +     A ++L     D VM+GR    +  ++  +  Y      G       + + F 
Sbjct: 207 GDIHCGEDAKRMLEETGCDAVMVGRGVLGDPWLIKDIVAYLE---CGEHLEAVSLQEKFA 263

Query: 252 -WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             R  +  + D    H+     ++++  H      G P S R +  LT
Sbjct: 264 MARLHAKRLMDLKGEHI----GIREMRGHAAWYVKGLPKSHRLKDALT 307


>gi|209542669|ref|YP_002274898.1| TIM-barrel protein, nifR3 family [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209530346|gb|ACI50283.1| TIM-barrel protein, nifR3 family [Gluconacetobacter diazotrophicus
           PAl 5]
          Length = 353

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 25/240 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R  AR L    L+ +EMI + A++R ++  +     +  + P A+Q+ G +   +
Sbjct: 30  TDLPFRRLARRL-GAGLVISEMIASWAMVRENQATLRMAEVADDDGPNAVQLAGCEPEAM 88

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +AA+I  D G + +++N GCP  +V  G   G+ LM +  +    + A+ +A+ +PVT+
Sbjct: 89  AQAARIAVDRGADMVDINFGCPVKKVAVGQQAGSALMRDEALAARLLDAVVRAVDVPVTL 148

Query: 122 KCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K R+G D      PA+A     +  +++G+  + +H R         +        D+  
Sbjct: 149 KMRMGWDHASLNAPALA-----RIAEQTGIRMVTVHGRT--------RQQFYNGTADWSF 195

Query: 179 VYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V ++ K+   L + +NG ++   D  QAL  L   DGVMIGR  Y     L  V +  + 
Sbjct: 196 VRQV-KDAVSLPVIVNGDIQTVDDARQALA-LSGADGVMIGRGCYGRPWFLAQVAQALTT 253


>gi|315612212|ref|ZP_07887126.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis ATCC 49296]
 gi|315315605|gb|EFU63643.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis ATCC 49296]
          Length = 326

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|313899890|ref|ZP_07833393.1| TIM-barrel protein, nifR3 family [Clostridium sp. HGF2]
 gi|312955505|gb|EFR37170.1| TIM-barrel protein, nifR3 family [Clostridium sp. HGF2]
          Length = 338

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 113/224 (50%), Gaps = 24/224 (10%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGADISKLVEAAKIV-EDFGYN 75
            L+YTEM V+D  L  D +  +G +    QE PLA+QI G DI  +V AAK + E    +
Sbjct: 40  GLIYTEM-VSDKALYYDNEKTVGMTDVEEQEHPLAMQIFGHDIEIMVYAAKFLDEKTDCD 98

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAV 134
            I++N+GCP  ++ +   G+ LM + D   +   A+ +++  PVTVK RIG D DQI  +
Sbjct: 99  IIDINMGCPVTKIVKSFAGSALMKDVDHAVEMSRAVVQSVKKPVTVKMRIGWDMDQITCL 158

Query: 135 ALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            L   ++S+   GV  + +H   RK + +G +          D+  + ++K+      +G
Sbjct: 159 ELARGLESV---GVQALAVHGRTRKQMYEGCA----------DWSYIKKVKEAVSIPVMG 205

Query: 193 LNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            NG +     A ++L     D VMIGR    +  ++  +  Y  
Sbjct: 206 -NGDVRSGEDAERMLKETGCDAVMIGRGVLGDPWLIKDIAHYLE 248


>gi|288906346|ref|YP_003431568.1| tRNA-dihydrouridine synthase [Streptococcus gallolyticus UCN34]
 gi|306832388|ref|ZP_07465541.1| tRNA-dihydrouridine synthase [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325979357|ref|YP_004289073.1| putative tRNA-dihydrouridine synthase [Streptococcus gallolyticus
           subsp. gallolyticus ATCC BAA-2069]
 gi|288733072|emb|CBI14653.1| putative tRNA-dihydrouridine synthase [Streptococcus gallolyticus
           UCN34]
 gi|304425428|gb|EFM28547.1| tRNA-dihydrouridine synthase [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325179285|emb|CBZ49329.1| putative tRNA-dihydrouridine synthase [Streptococcus gallolyticus
           subsp. gallolyticus ATCC BAA-2069]
          Length = 325

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 118/240 (49%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ + E+   + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEFIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIINEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDS--ELAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG + ++  A  ++    VD VM+GRAA  N  + T ++ YF 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRNVHDAKYMIEEIGVDAVMVGRAAMNNPYIFTQINHYFE 250


>gi|73666942|ref|YP_302958.1| dihydrouridine synthase TIM-barrel protein nifR3 [Ehrlichia canis
           str. Jake]
 gi|72394083|gb|AAZ68360.1| tRNA-U20-dihydrouridine synthase [Ehrlichia canis str. Jake]
          Length = 317

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 69/217 (31%), Positives = 106/217 (48%), Gaps = 21/217 (9%)

Query: 11  FFARLLTNN---ALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F  R L  N    LL +EMI + A++   K+++     Q    A+Q+ G D + + EAAK
Sbjct: 23  FPFRCLVKNIGAGLLVSEMIASRAMIIQTKQSLQKSQIQAN-TAVQLAGCDPAIMAEAAK 81

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           + ED G   I++N GCP  +V     G+ LM +       + ++ KA+ IPVT+K R G 
Sbjct: 82  LNEDMGAKIIDINFGCPVKKVVNSYAGSALMKDEITAAKILESVVKAVKIPVTLKMRTGW 141

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKK- 184
           D+    +    L K  ++SG+  I IH   R  +  G +          D+  +  IKK 
Sbjct: 142 DNN--NLNSPKLAKIAEESGIKMITIHGRTRTQMFNGKA----------DWKFISNIKKC 189

Query: 185 -ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
            + P +  G    L+D+  +L+     DGVMIGR AY
Sbjct: 190 VKIPVIANGDIKNLDDIKTSLE-ESQADGVMIGRGAY 225


>gi|239998283|ref|ZP_04718207.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 35/02]
 gi|240114998|ref|ZP_04729060.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID18]
          Length = 364

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 166 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|327395459|dbj|BAK12881.1| tRNA-dihydrouridine synthase B DusB [Pantoea ananatis AJ13355]
          Length = 337

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 116/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +   DK  +    + E  + A+QI G D
Sbjct: 33  MAGITDRPFRTLCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDESGIRAVQIAGCD 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+ +P
Sbjct: 92  PSEMAQAARINVDAGAQVIDINMGCPAKKVNRKMAGSALLQYPSVVESILSAVVNAVDVP 151

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D +    VA+  L    ++ G+  + IH R    +  G          + +
Sbjct: 152 VTLKIRTGWDPENRNCVAIAQLA---ERCGIQALTIHGRTRACLFNG----------DAE 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 199 YDSIRTV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 257


>gi|110808216|sp|Q32M08|DUS4L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 4-like
 gi|80478497|gb|AAI09352.1| Dihydrouridine synthase 4-like (S. cerevisiae) [Mus musculus]
          Length = 324

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 129/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MI+A   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALLVCPYA-NGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLARTI---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMI-KENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 290


>gi|326796326|ref|YP_004314146.1| hypothetical protein Marme_3091 [Marinomonas mediterranea MMB-1]
 gi|326547090|gb|ADZ92310.1| TIM-barrel protein, nifR3 family [Marinomonas mediterranea MMB-1]
          Length = 329

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 113/240 (47%), Gaps = 23/240 (9%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       L+ +EM+ +D  L      K+ L    + +P ++QI GA+   +VEAA+
Sbjct: 27  FRRLCYQQGAGLVVSEMVTSDVRLWNSTKSKHRLVHDKEIQPRSVQIAGANAEMMVEAAQ 86

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
              + G   I++N+GCP+ +V   + G+ L+ +  +V D + ++  ++ +PVT+K R G 
Sbjct: 87  KNVELGAQIIDINMGCPAKKVLNKAAGSALLKDESLVQDILKSVVDSVEVPVTLKIRTGW 146

Query: 128 DDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
             +      RN   + K  +  G+  + +H R    K             +YD + EI K
Sbjct: 147 SSE-----QRNGLTIAKIAEDCGIQALAVHGRTRACKFQG--------EAEYDTIAEI-K 192

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           ++  + +  NG + D   A +++     D VMIGRAA     +   ++ Y  +     SP
Sbjct: 193 QSVGIPVFANGDITDAQTAQRVMTYTKADAVMIGRAAQGRPWIFNEINHYLRHGELPPSP 252


>gi|160902971|ref|YP_001568552.1| dihydrouridine synthase DuS [Petrotoga mobilis SJ95]
 gi|160360615|gb|ABX32229.1| dihydrouridine synthase DuS [Petrotoga mobilis SJ95]
          Length = 301

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/157 (29%), Positives = 87/157 (55%), Gaps = 7/157 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M D+TD  +R   R        +TEMI  D+I+R ++K   +     E  + +Q+ G + 
Sbjct: 11  MADYTDYPFREICRRF-GAKFTFTEMISVDSIIRENEKVEKMLPQKGEDNIGVQLFGNET 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           +K +EAAK ++    + I++N  CP  +V +   GA L+ NP ++GD +  + K++ +PV
Sbjct: 70  TKFIEAAKSIQHLA-SWIDINAACPVNKVVKKGSGAALLKNPKLLGDIVFNLKKSIDLPV 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            VK R+G D     + +  + ++++K+G + I +H R
Sbjct: 129 GVKVRLGYDQ----INIEEVAETVEKAGADYIIVHGR 161


>gi|34495999|ref|NP_900214.1| regulatory gene required to sense and relay the nitrogen status
           [Chromobacterium violaceum ATCC 12472]
 gi|34101852|gb|AAQ58220.1| Regulatory gene required to sense and relay the nitrogen status
           [Chromobacterium violaceum ATCC 12472]
          Length = 352

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/247 (24%), Positives = 116/247 (46%), Gaps = 16/247 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EMI A+  L    K +       + +P+ +QI G +
Sbjct: 17  MAGVTDRPFRMLCKRL-GAGMAVSEMITANKALWTTPKTLRRANHEGEVEPIVVQIAGGE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA++  + G   I++N+GCP+ +V   + G+ L+ + D VG  + A+ KA+ +P
Sbjct: 76  PQMLADAARLNVEHGAQIIDINMGCPAKKVCNVAAGSALLRDLDNVGRILEAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   ++       + K  + +G+  + +H R         +++    + +YD 
Sbjct: 136 VTLKTRTGWSREVKTALA--VAKMAEDAGIAALALHGRT--------REDMYRGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + K+   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAV-KQAVSIPVVANGDIDSPQKARHVLDYTGADAIMIGRAAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPI 243
           +    P+
Sbjct: 245 IELPPPM 251


>gi|86357567|ref|YP_469459.1| tRNA-dihydrouridine synthase protein [Rhizobium etli CFN 42]
 gi|1171717|sp|P41504|DUS_RHILP RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|581522|emb|CAA50567.1| unnamed protein product [Rhizobium phaseoli]
 gi|86281669|gb|ABC90732.1| probable tRNA-dihydrouridine synthase protein [Rhizobium etli CFN
           42]
          Length = 317

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 104/211 (49%), Gaps = 18/211 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +RF A L+    ++ +  +V D      +    GF    +P  +Q+ G +   + EAAKI
Sbjct: 25  WRFGAGLVVTE-MVASRELVNDTAESWSRLKAAGF----RPHMVQLAGREAHWMAEAAKI 79

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
             D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+K R+G D
Sbjct: 80  AADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPVTLKMRLGWD 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   ++   ++ +  + SG+  + IH R      +   + R     D+D +  +++    
Sbjct: 140 EN--SINAPDIARRAEASGIQLVTIHGRTR----MQFYEGRA----DWDAIRAVREVISV 189

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             I  NG +E    A +IL     D VMIGR
Sbjct: 190 PLIA-NGDVETAHDAQEILRRSGADAVMIGR 219


>gi|319943013|ref|ZP_08017296.1| tRNA-dihydrouridine synthase B [Lautropia mirabilis ATCC 51599]
 gi|319743555|gb|EFV95959.1| tRNA-dihydrouridine synthase B [Lautropia mirabilis ATCC 51599]
          Length = 358

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 79/293 (26%), Positives = 128/293 (43%), Gaps = 32/293 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR YR   + L       +EM  ++  L    K    +  + + +P A+QI GAD
Sbjct: 32  MAGVTDRPYRQLCKRL-GAGYAVSEMAASNPRLWNSVKTSRRIDHAGEIEPKAVQIAGAD 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+   + G   I++N+GCP  +V     G+ LM N  +  + I  + KA+ +P
Sbjct: 91  PAMMAEAARFNVERGAQIIDINMGCPVKKVCNVYAGSALMGNEPLAIEIIERVVKAVPVP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG---IWIHARKAILKGLSPKDNRKIPNLD 175
           VTVK R G+D        RN V   + +   G   I +H R    +   P        +D
Sbjct: 151 VTVKMRTGIDPD-----HRNAVALARAAEAAGAVMITVHGRSRACRYHGP--------VD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + E+K     + +  NG ++   +A  +L     D VMIGRAA     +   VD Y 
Sbjct: 198 YTTIAEVKAAV-GIPVVANGNIDSPEKARDVLAQTGADAVMIGRAAQGRPWIFREVDHYL 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF 284
           ++         TR+    WR++   + ++   H    G+   +   R  IG +
Sbjct: 257 AH--------GTRLPAPTWREVRDLLLEHLNDHYRFYGEFTGVRTARKHIGWY 301


>gi|20257536|gb|AAM15930.1|AF494454_1 NifR3-like protein [Gluconacetobacter diazotrophicus]
          Length = 325

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 25/240 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R  AR L    L+ +EMI + A++R ++  +     +  + P A+Q+ G +   +
Sbjct: 2   TDLPFRRLARRL-GAGLVISEMIASWAMVRENQATLRMAEVADDDGPNAVQLAGCEPEAM 60

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +AA+I  D G + +++N GCP  +V  G   G+ LM +  +    + A+ +A+ +PVT+
Sbjct: 61  AQAARIAVDRGADMVDINFGCPVKKVAVGQQAGSALMRDEALAARLLDAVVRAVDVPVTL 120

Query: 122 KCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K R+G D      PA+A     +  +++G+  + +H R         +        D+  
Sbjct: 121 KMRMGWDHASLNAPALA-----RIAEQTGIRMVTVHGRT--------RQQFYNGTADWSF 167

Query: 179 VYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V ++ K+   L + +NG ++   D  QAL  L   DGVMIGR  Y     L  V +  + 
Sbjct: 168 VRQV-KDAVSLPVIVNGDIQTVDDARQALA-LSGADGVMIGRGCYGRPWFLAQVAQALTT 225


>gi|218768425|ref|YP_002342937.1| hypothetical protein NMA1633 [Neisseria meningitidis Z2491]
 gi|121052433|emb|CAM08769.1| conserved hypothetical protein [Neisseria meningitidis Z2491]
          Length = 336

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG +         
Sbjct: 136 VTLKTRLGWHDDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKGEAA-------- 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 183 --YDLIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|46204191|ref|ZP_00050361.2| COG0042: tRNA-dihydrouridine synthase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 324

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/220 (29%), Positives = 110/220 (50%), Gaps = 19/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLV 63
           TD H R  A+ L  +A++ +EM+ A  + +GD ++ +        P  +Q+ G     + 
Sbjct: 14  TDLHMRRLAQGLGASAVV-SEMVAAAELAKGDAESRVRAEGAGVSPHIVQLAGCAPEPMA 72

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+ +A+ +PVTVK 
Sbjct: 73  EAARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVREAVEVPVTVKM 132

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D    ++   +L +  +  G++G+ +H   R+   KG            D+  +  
Sbjct: 133 RLGWDHA--SLNAPDLARRAESLGLDGVTVHGRTRQQFYKG----------RADWSAIRS 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +  E   L +  NG +  + +A   L +    GVMIGRAA
Sbjct: 181 V-VEAVSLPVIANGDIASLEEARACLAASGATGVMIGRAA 219


>gi|117926944|ref|YP_867561.1| nifR3 family TIM-barrel protein [Magnetococcus sp. MC-1]
 gi|117610700|gb|ABK46155.1| tRNA-U20-dihydrouridine synthase [Magnetococcus sp. MC-1]
          Length = 336

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 143/304 (47%), Gaps = 33/304 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R  AR    + L  +EMI + A++R   K++L      +E PL++QI G+D
Sbjct: 27  MAGVTDAPFRLIARRYGAD-LTVSEMIASQAMIRNTSKSLLIGTAHEEEHPLSVQIAGSD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++  D G   I++N+GCP  +V +G  GA LM +  +V   +AA+  A+ +P
Sbjct: 86  PQVMAEAARMNVDRGAEIIDINMGCPVKKVVKGQAGAALMRDEALVARILAAVVAAVPVP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R+G D     +    + +  ++ GV  + +H R    + +G          + D+
Sbjct: 146 VTLKIRLGWDKS--NLNGARIGQIAEQQGVRMLTVHGRTRMQMYRG----------HADW 193

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  IK+      +G NG L    +A +  +L  VDG+MIGRAA     +   +  Y  
Sbjct: 194 QCIASIKQAVTIPVVG-NGDLHTPQEAKEKWLLSGVDGLMIGRAAMGCPWLFGQIAHYLR 252

Query: 235 NPLTGSSP----IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +      P        V + F R I     D+   H+  G ++ +  +H+     G PNS
Sbjct: 253 SGQEKPPPDLAEQHALVLEHFDRLI-----DFYGPHI--GNRMAR--KHLAWYAKGLPNS 303

Query: 291 RRCR 294
              R
Sbjct: 304 AHYR 307


>gi|268596189|ref|ZP_06130356.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA19]
 gi|268549977|gb|EEZ44996.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA19]
          Length = 340

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 23  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 82  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDESLVAAILEAVVKAAGVP 141

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 142 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 187 ARYELIAETKSR-LNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 245

Query: 232 Y 232
           Y
Sbjct: 246 Y 246


>gi|240122834|ref|ZP_04735790.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID332]
          Length = 364

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 166 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|323340116|ref|ZP_08080381.1| tRNA-dihydrouridine synthase [Lactobacillus ruminis ATCC 25644]
 gi|323092493|gb|EFZ35100.1| tRNA-dihydrouridine synthase [Lactobacillus ruminis ATCC 25644]
          Length = 329

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/223 (32%), Positives = 112/223 (50%), Gaps = 22/223 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK +  L     E P+++QI G     LVEAA+ V E+   + I
Sbjct: 38  LVVCEMISDKGIHFRNKKTLGMLFVDPTEHPVSVQIFGGSKESLVEAAQFVAENTSADII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   G+  +L+PD V + + A+  ++  PVTVK R G D D I AV  
Sbjct: 98  DINMGCPVPKVTKTDAGSRWLLDPDKVYEMVDAVTHSIDKPVTVKMRTGWDEDHIYAV-- 155

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + ++ G   + +H   RK +  G          + D++I++E+  +    F+G N
Sbjct: 156 ENALAA-QEGGAKALAMHGRTRKQLYSG----------HADWNILHEVAGKLTIPFMG-N 203

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G +     A K+L  V  D VMIGRAA  N  +L     Y   
Sbjct: 204 GDVRTPQDAKKMLDEVGCDAVMIGRAALGNPWILKQTVHYLET 246


>gi|301155534|emb|CBW15002.1| tRNA-dihydrouridine synthase B [Haemophilus parainfluenzae T3T1]
          Length = 326

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/253 (27%), Positives = 124/253 (49%), Gaps = 30/253 (11%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   RL  +    L ++EM+  +  +   +K+ L  +  E+    A+QI G
Sbjct: 17  MAGITDQPFR---RLCAHYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEELGLNAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D  ++ +AA I   +G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ 
Sbjct: 74  SDPLEMAQAAAINVAYGAEIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILKEVVNAVD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHAR--KAILKGLSPKDNRKI 171
           +PVT+K R G D      A RN V   K  ++SG+  + IH R  + + +G +  DN + 
Sbjct: 134 VPVTLKIRTGWDK-----ANRNCVQIGKIAEQSGIQALTIHGRTKECLFEGEAEYDNIRA 188

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
                       K++  + +  NG ++  S+A K+L     D +MIGRAA  N  +   V
Sbjct: 189 V-----------KQSISIPVIANGDIDSASKAKKVLEYTGADAIMIGRAALGNPWLFQAV 237

Query: 230 DEYFSNPLTGSSP 242
           +    +     +P
Sbjct: 238 EALVEHDTIIQTP 250


>gi|162148051|ref|YP_001602512.1| tRNA-dihydrouridine synthase [Gluconacetobacter diazotrophicus PAl
           5]
 gi|161786628|emb|CAP56210.1| tRNA-dihydrouridine synthase [Gluconacetobacter diazotrophicus PAl
           5]
          Length = 356

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 25/240 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R  AR L    L+ +EMI + A++R ++  +     +  + P A+Q+ G +   +
Sbjct: 33  TDLPFRRLARRL-GAGLVISEMIASWAMVRENQATLRMAEVADDDGPNAVQLAGCEPEAM 91

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +AA+I  D G + +++N GCP  +V  G   G+ LM +  +    + A+ +A+ +PVT+
Sbjct: 92  AQAARIAVDRGADMVDINFGCPVKKVAVGQQAGSALMRDEALAARLLDAVVRAVDVPVTL 151

Query: 122 KCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K R+G D      PA+A     +  +++G+  + +H R         +        D+  
Sbjct: 152 KMRMGWDHASLNAPALA-----RIAEQTGIRMVTVHGRT--------RQQFYNGTADWSF 198

Query: 179 VYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V ++ K+   L + +NG ++   D  QAL  L   DGVMIGR  Y     L  V +  + 
Sbjct: 199 VRQV-KDAVSLPVIVNGDIQTVDDARQALA-LSGADGVMIGRGCYGRPWFLAQVAQALTT 256


>gi|315640560|ref|ZP_07895668.1| tRNA-dihydrouridine synthase [Enterococcus italicus DSM 15952]
 gi|315483764|gb|EFU74252.1| tRNA-dihydrouridine synthase [Enterococcus italicus DSM 15952]
          Length = 329

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 110/222 (49%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EMI    I   +KK +  L     E PL+LQI G+    LVEAA+ VE +   + I
Sbjct: 40  LVVCEMISDKGIQLRNKKTLEMLYIDETEHPLSLQIFGSTKESLVEAAQFVEKNTTADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+SIPVTVK R G D++    A+ 
Sbjct: 100 DINMGCPVNKIIKAEAGAKWLLDPNKVYEMVQAVASAVSIPVTVKMRTGWDEE-HLFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + +          +H R  +   +G +          D+ ++ E+KK+     +G NG
Sbjct: 159 NALAAQAAGAAAVA-MHGRTRVQMYEGKA----------DWSVLREVKKKLSIPLMG-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A ++   V  D VMIGRAA  N  M+   + Y   
Sbjct: 207 DVRTPEDARRMFEEVGCDAVMIGRAALGNPWMIGRTNHYLQT 248


>gi|227873295|ref|ZP_03991560.1| dihydrouridine synthase [Oribacterium sinus F0268]
 gi|227840862|gb|EEJ51227.1| dihydrouridine synthase [Oribacterium sinus F0268]
          Length = 344

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 81/305 (26%), Positives = 133/305 (43%), Gaps = 24/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +   +L +TEM+ A AI  G++   ++L    +   ++ Q+ G+D
Sbjct: 46  MAGVTDLPYRILCKEM-GLSLSFTEMVSAKAIYYGNQNTDSLLVHKGEPGLVSAQLFGSD 104

Query: 59  ISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + + E A +I EDF  + I++N+GCP  +V     G+ LM N  +    ++ M KAL  
Sbjct: 105 PALMAEMACRIEEDF--DGIDVNMGCPVPKVVRNQEGSALMTNLPLAEQVLSTMAKALKK 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK RIG  D   A+ +    K  + SGV  + IH R         ++       ++ 
Sbjct: 163 PLTVKFRIGFTDD--AINVVEFAKMAEASGVASVTIHGRT--------REQYYRGKANWQ 212

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E K+       G NG +     AL +L S  VDGV + R    N  ++       S 
Sbjct: 213 YIKEAKEAVKIPVFG-NGDIFQEEDALAMLLSTGVDGVALARGIQGNPFLIRACVSLLSE 271

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+     K+   +    M +    HL     L ++ +H+     G  N+ R R 
Sbjct: 272 G-KKLPPVSLSERKEMMLRHLKLMVEIKGEHL----ALLEMRKHLSWYMEGLENAARWRQ 326

Query: 296 ILTVE 300
            +  E
Sbjct: 327 RVNTE 331


>gi|148255455|ref|YP_001240040.1| putative tRNA-dihydrouridine synthase [Bradyrhizobium sp. BTAi1]
 gi|146407628|gb|ABQ36134.1| tRNA-U20-dihydrouridine synthase [Bradyrhizobium sp. BTAi1]
          Length = 317

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 110/221 (49%), Gaps = 21/221 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLV 63
           TD  +R  A  L    L+ +EM  +D ++RG   + L   ++   P  +Q+ G +   + 
Sbjct: 5   TDAPFRRLAADL-GAGLVVSEMTASDDLVRGRWISRLRCEASGVGPHVVQLAGCEAHWMA 63

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E AK+ ED G + I++N+GCP+  V  G  G+ LM + D     I A  +A+ +PVT+K 
Sbjct: 64  EGAKVAEDGGADVIDINMGCPARHVTGGQSGSALMRDLDHALALIEATVEAVDVPVTLKM 123

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D++  ++    L +  + +GV  I +H   R+   KG            D+  V  
Sbjct: 124 RLGWDER--SLNAPELARRAEAAGVQLITVHGRTRQQFYKG----------EADWSAVRA 171

Query: 182 IKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           + K+  DL + +NG +   ED  +AL      D VMIGR A
Sbjct: 172 V-KQAVDLPVVVNGDITSYEDAREALDA-SGADAVMIGRGA 210


>gi|227544677|ref|ZP_03974726.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|300909081|ref|ZP_07126544.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri SD2112]
 gi|227185323|gb|EEI65394.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|300894488|gb|EFK87846.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri SD2112]
          Length = 333

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 111/218 (50%), Gaps = 20/218 (9%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNV 81
           EMI    I+  +++  N++    +E P+ +QI G     LVEAAK V+     + I++N+
Sbjct: 42  EMISDRGIVYHNQRTLNMMDVDPEEHPMGIQIFGGTKETLVEAAKYVDQHTAADVIDINM 101

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   GA  +L+P+ V + ++ +  A+  PVTVK R G DD+   +A+ N + 
Sbjct: 102 GCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDDK-HILAVENALA 160

Query: 142 SIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           + +++G + I +H   RK +  G +          D++I+ E+  +    F+  NG ++ 
Sbjct: 161 A-ERAGASAIAMHGRTRKQMYTGQA----------DWNILKEVASQLKIPFMA-NGDVKT 208

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
              A KIL        MIGRAA  N  ML   + Y   
Sbjct: 209 PEDAKKILDMTGATAAMIGRAAMGNPWMLKRTEHYLET 246


>gi|313891460|ref|ZP_07825076.1| TIM-barrel protein, nifR3 family [Dialister microaerophilus UPII
           345-E]
 gi|313120235|gb|EFR43411.1| TIM-barrel protein, nifR3 family [Dialister microaerophilus UPII
           345-E]
          Length = 327

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 78/301 (25%), Positives = 135/301 (44%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR     A+   EM+ +  +   ++K   +L  +  E P+ALQ+ G  
Sbjct: 20  MAGVSDLAYRVIARK-HGAAMTTAEMVSSRGLYYKNEKTEEMLKIAPDEHPVALQLFGNQ 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK VE+ G + I++N+GCP  +V +   G  +M + D     + AM KA+ +P
Sbjct: 79  AEIMALAAKEVEEAGADVIDINMGCPMQKVVKNGDGCSMMKDIDNSAKVVEAMVKAVKVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D +   +    L K+++ +G   I +H R         ++       D D 
Sbjct: 139 VTVKMRIGWDRE--NLNSPELAKAVEAAGAAAITVHGRT--------REEMYSGKADLDA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  E   + +  NG + D   A +++      GV IGRAA+ N  +   V+ Y  + 
Sbjct: 189 IRKV-VEAVKIPVFGNGDIVDGPSAKRMMEETGCVGVAIGRAAWGNPWIFNAVNTYLESG 247

Query: 237 LTGSSP---IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            T   P   ++  + +     +     +Y A        ++++  H    FHG P +   
Sbjct: 248 ETVEEPSWEMRLSMARTHLGNLVKEKGEYTA--------IREMRAHASHYFHGLPKATAL 299

Query: 294 R 294
           R
Sbjct: 300 R 300


>gi|213019483|ref|ZP_03335289.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212994905|gb|EEB55547.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 298

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 112/237 (47%), Gaps = 25/237 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++   ++++      E   A+Q+ G +   + E
Sbjct: 5   TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSMQKAKVDE-LTAVQLAGCEPDVMAE 62

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ E  G   I++N GCP  +V  G  G+ LM +     + I A+ KA+S+PVTVK R
Sbjct: 63  AAKLNEGMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVSVPVTVKMR 122

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVY 180
            G +D+      RN   L K  +  G   I +H R +A L              D+  V 
Sbjct: 123 TGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYN---------GQADWKFVR 168

Query: 181 EIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + KE   + + +NG    L D+  ALK     DGVMIGR  Y    ++     + S
Sbjct: 169 NV-KEQVKIPVIVNGDIKSLNDVQSALK-ESGADGVMIGRGTYGKPWLINQAINFLS 223


>gi|257453865|ref|ZP_05619143.1| tRNA-dihydrouridine synthase B [Enhydrobacter aerosaccus SK60]
 gi|257448792|gb|EEV23757.1| tRNA-dihydrouridine synthase B [Enhydrobacter aerosaccus SK60]
          Length = 332

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 77/321 (23%), Positives = 147/321 (45%), Gaps = 24/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD+ +R  A+       + +EM+ +DA L    K +    F  +  P++ QI G++
Sbjct: 26  MAGVTDKPFRMLAKSFGAGHAV-SEMMTSDATLFAHHKTLYRANFEGEIAPISAQIAGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             K+ EAA+     G   +++N+GCP+ +V +   G+ L+ + D+V   + A   A+ +P
Sbjct: 85  PEKIAEAARYQVANGAQIVDINMGCPAKKVCKKLAGSALLKDEDLVKRLLDATVNAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + LR + +  +++G+  I IH R         ++++ + +  Y++
Sbjct: 145 VTLKTRLGYANGEENI-LR-VAQMAEEAGIAMIVIHGRT--------REDKYLGSARYEL 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K       I +NG ++   +A ++      DG+MIGRA      +   +  Y    
Sbjct: 195 IKEVKNLLTIPVI-VNGDIDSPQKAKQVYEQTGADGIMIGRAGQGQPWIFRDIAHYLETG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP    + +     +S     YA    +SG ++ +  +H+     G  NS   R  
Sbjct: 254 EILPSPTMDELKEIV---LSHLQEIYAFYGEYSGCRIAR--KHIAWYTSGIANSNAFRQA 308

Query: 297 LTVE---AGASTATHHIIETA 314
           +  E   AG        ++TA
Sbjct: 309 MYEEDTTAGQFNVVARFLKTA 329


>gi|329118447|ref|ZP_08247153.1| tRNA-dihydrouridine synthase B [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327465493|gb|EGF11772.1| tRNA-dihydrouridine synthase B [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 332

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/258 (28%), Positives = 127/258 (49%), Gaps = 27/258 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R  AR         +EM+ +D  LR  KK++    F+ +    A+QI G+D
Sbjct: 18  MAGITDKPFRALARQF-GAGYAVSEMLNSDPALRQTKKSLHRSDFAGEAGIRAVQIAGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             K+ EAA+   + G   I++N+GCP  +V     G+ L+ N  +VGD + A+  A  +P
Sbjct: 77  PQKMAEAARYNVEQGAQIIDINMGCPVKKVCNVLAGSALLQNEKLVGDILRAVVAAAGVP 136

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G       I A+A     K+ +++G+  I +H   R+ + KG          +
Sbjct: 137 VTLKTRLGYCEGSKNILAIA-----KTAEQAGIAAIAVHGRTREQMYKG----------S 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             YD++ E+ K++  + +  NG +    +A ++L     DGVM+GRAA     +   +  
Sbjct: 182 ASYDLIAEV-KQSVAIPVWANGDITSPQKAAEVLRQTGADGVMVGRAAQGRPWLFAQIRH 240

Query: 232 YFSNPLTGSS-PIKTRVD 248
           +  +    +  P +T  D
Sbjct: 241 FLRHGTPPAPLPFQTAAD 258


>gi|312866800|ref|ZP_07727013.1| TIM-barrel protein, nifR3 family [Streptococcus parasanguinis
           F0405]
 gi|311097583|gb|EFQ55814.1| TIM-barrel protein, nifR3 family [Streptococcus parasanguinis
           F0405]
          Length = 335

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 202 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 260


>gi|194097785|ref|YP_002000828.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae NCCP11945]
 gi|254493061|ref|ZP_05106232.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 1291]
 gi|268600667|ref|ZP_06134834.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID18]
 gi|268681451|ref|ZP_06148313.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID332]
 gi|268685922|ref|ZP_06152784.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-93-1035]
 gi|193933075|gb|ACF28899.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae NCCP11945]
 gi|226512101|gb|EEH61446.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 1291]
 gi|268584798|gb|EEZ49474.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID18]
 gi|268621735|gb|EEZ54135.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID332]
 gi|268626206|gb|EEZ58606.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-93-1035]
 gi|317163563|gb|ADV07104.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 334

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|190570967|ref|YP_001975325.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357239|emb|CAQ54661.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 316

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 112/238 (47%), Gaps = 27/238 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L   +LL +EMI + A++   ++++      E   A+Q+ G +   + E
Sbjct: 23  TDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSMQKAKVDELT-AVQLAGCEPDVMAE 80

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ E  G   I++N GCP  +V  G  G+ LM +     + I A+ KA+S+PVTVK R
Sbjct: 81  AAKLNEGMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVSVPVTVKMR 140

Query: 125 IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIV 179
            G +D+      RN   L K  +  G   I +H R    +  G +          D+  V
Sbjct: 141 TGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQA----------DWKFV 185

Query: 180 YEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + KE   + + +NG    L D+  ALK     DGVMIGR  Y    ++     + S
Sbjct: 186 RNV-KEQVKIPVIVNGDIKSLNDVQSALK-ESGADGVMIGRGTYGKPWLINQAINFLS 241


>gi|84516240|ref|ZP_01003600.1| tRNA-dihydrouridine synthase, putative [Loktanella vestfoldensis
           SKA53]
 gi|84509936|gb|EAQ06393.1| tRNA-dihydrouridine synthase, putative [Loktanella vestfoldensis
           SKA53]
          Length = 333

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 108/223 (48%), Gaps = 21/223 (9%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           F A  + +  +   EM+ A   +R  ++  LG+  Q    A+QI G +   L EAA+++E
Sbjct: 42  FGAGWVVSEMVASQEMVQAKPGVR--ERAELGYDQQGT--AVQIAGREAYWLAEAARMIE 97

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
             G   I++N+GCP+ +V  G  G+ L+ +PD     I A+  A+ +PVT+K R+G D  
Sbjct: 98  ANGAAMIDINMGCPAKKVTNGYSGSALLRDPDHALRLIEAVVNAVKLPVTLKTRLGWDHD 157

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKK--EN 186
               A  ++ +  + +G+  + IH R      KG +          D+  + EIK+    
Sbjct: 158 CLNAA--DVARRAQDAGIRLVTIHGRTRCQFYKGAA----------DWRAIREIKQAVSI 205

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           P +  G   G E   QAL  L   DGVMIGR A     +L  V
Sbjct: 206 PVIANGDITGPEAAKQALA-LSGADGVMIGRGAQGRPWVLAQV 247


>gi|322377962|ref|ZP_08052450.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M334]
 gi|321281138|gb|EFX58150.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M334]
          Length = 336

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 202 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 260


>gi|240127544|ref|ZP_04740205.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-93-1035]
          Length = 372

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 114 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 174 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 218

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 219 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|300743944|ref|ZP_07072964.1| putative tRNA-dihydrouridine synthase [Rothia dentocariosa M567]
 gi|300380305|gb|EFJ76868.1| putative tRNA-dihydrouridine synthase [Rothia dentocariosa M567]
          Length = 402

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/296 (24%), Positives = 129/296 (43%), Gaps = 23/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T++ +R   R      L  TEM+ A A++  + +   I+     E+  ++QI G D
Sbjct: 43  MAGVTNKAFRRLCREY-GGGLYVTEMVTARALVERKPESMRIIEHDADEQIRSIQIYGVD 101

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A + +VE+   + I+LN GCP+ +V +   GA L    D+    +    K  S 
Sbjct: 102 AVNVGKAIRLVVEEDRADHIDLNFGCPAPKVTKRGGGAALPWKTDLFTAIVHTAVKEASR 161

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + +GV  I +H R A                
Sbjct: 162 NDIPLTIKMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTAA--------QHYSGTA 211

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + ++++  PD+ I  NG +     A++++    VDGV+IGR       +   +   
Sbjct: 212 DWDSIAQLREAIPDVPILGNGDIFAAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNA 271

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           F        P  + V    +R     +  +A  +      L++I +H+   F G+P
Sbjct: 272 FEGSTERIRPTLSEVAAMIYRHAELLVETFADEY----KGLREIRKHVAWYFKGYP 323


>gi|323705755|ref|ZP_08117328.1| TIM-barrel protein, nifR3 family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323534973|gb|EGB24751.1| TIM-barrel protein, nifR3 family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 323

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/301 (24%), Positives = 134/301 (44%), Gaps = 22/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGDKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ YR     +      YTEM+ A  +    +    L     ++ +ALQI G+D 
Sbjct: 21  MAGVTDKPYRCICSEM-GCGFTYTEMVSAKGLYYESENTEFLTDIDDDENVALQIFGSDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK +       I++N+GCP+ ++ +   G+ LML P++    I A+ K  S PV
Sbjct: 80  YIMGEIAKRLNTSNAKVIDINMGCPTPKIVKNGDGSALMLKPELAESVIKAVVKNSSKPV 139

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K R G DD  + AV +  + ++    GV  + +H R         ++     N D+DI
Sbjct: 140 TIKIRKGWDDAHVNAVEIAKMAEN---CGVKAVAVHGR--------TREQFYSGNADWDI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ K+N  + +  NG +     A +++     D VM+GR A  N  +   +  Y +  
Sbjct: 189 IKKV-KDNLKIPVIGNGDVFSPEDAKRMIDETGCDAVMVGRGAEGNPWIFKRILHYLNTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                PI +       R +   M +Y   H+     + ++ +H+     G   + + + +
Sbjct: 248 ELLPEPIVSEKIDMILRHLDV-MIEYKGEHIG----ILEMRKHIAWYLKGIRGASKIKQM 302

Query: 297 L 297
           +
Sbjct: 303 V 303


>gi|169825841|ref|YP_001695999.1| hypothetical protein Bsph_0238 [Lysinibacillus sphaericus C3-41]
 gi|168990329|gb|ACA37869.1| conserved hypothetical protein [Lysinibacillus sphaericus C3-41]
          Length = 322

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    + +K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRQVVSEAGRPDVFFTEFTNSDSYCHPEGQKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + ++ + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSRGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D          +  I K  +  + IH R    K +S  D        +
Sbjct: 138 LPVSVKTRLGYKD---VEEWEEWLTHIFKQDIANLSIHLRTR--KEMSQVDAH------W 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDCIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFKN 238


>gi|268594138|ref|ZP_06128305.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 35/02]
 gi|268547527|gb|EEZ42945.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 35/02]
          Length = 340

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 23  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 82  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 141

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 142 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 187 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 245

Query: 232 Y 232
           Y
Sbjct: 246 Y 246


>gi|167856275|ref|ZP_02479007.1| DNA-binding protein Fis [Haemophilus parasuis 29755]
 gi|219871522|ref|YP_002475897.1| tRNA-dihydrouridine synthase B [Haemophilus parasuis SH0165]
 gi|167852599|gb|EDS23881.1| DNA-binding protein Fis [Haemophilus parasuis 29755]
 gi|219691726|gb|ACL32949.1| tRNA-dihydrouridine synthase B [Haemophilus parasuis SH0165]
          Length = 325

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 122/241 (50%), Gaps = 22/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L  S   +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSKLRLSHHHEIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAKI   +G   I++N+GCP+ +V++   G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PTEMAEAAKINVAYGAEIIDINMGCPAKKVNKKMAGSALLREPDLVARILDAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G D +    + + N+    +++G++ + IH   R  + +G +          +
Sbjct: 136 VTLKIRTGWDPENRNCLEIANIA---EQAGISALTIHGRTRSCLFEGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+   + I  NG +    +A ++L     D VMIGR +     + + + ++F
Sbjct: 183 YDSIKAV-KQAVSIPIIANGDITSAEKAKQVLDYTQADAVMIGRGSLGRPWLFSEIGKFF 241

Query: 234 S 234
            
Sbjct: 242 E 242


>gi|116252011|ref|YP_767849.1| tRNA-dihydrouridine synthase (nitrogen regulation protein)
           [Rhizobium leguminosarum bv. viciae 3841]
 gi|115256659|emb|CAK07747.1| putative tRNA-dihydrouridine synthase (nitrogen regulation protein)
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 338

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 106/211 (50%), Gaps = 18/211 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +RF A L+    ++ +  +V D      + +  GF    +P  +Q+ G +   + EAAKI
Sbjct: 46  WRFGAGLVVTE-MVASRELVNDTAESWSRLSAAGF----RPHMVQLAGREAHWMAEAAKI 100

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
             D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+K R+G D
Sbjct: 101 AADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHAIGLIEATVKAVDIPVTLKMRLGWD 160

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   ++   ++ +  + +GV  + IH R      +   + R     D+D +  + +E   
Sbjct: 161 EN--SINAPDIARRAEAAGVQLVTIHGRTR----MQFYEGRA----DWDAIRAV-REVIS 209

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           + +  NG +E    A +IL     D VMIGR
Sbjct: 210 IPLIANGDVETAGDAQEILRRSGADAVMIGR 240


>gi|322390392|ref|ZP_08063914.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC 903]
 gi|321142903|gb|EFX38359.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC 903]
          Length = 325

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLRDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|223041958|ref|ZP_03612142.1| tRNA-dihydrouridine synthase B [Actinobacillus minor 202]
 gi|240950369|ref|ZP_04754638.1| tRNA-dihydrouridine synthase B [Actinobacillus minor NM305]
 gi|223017215|gb|EEF15643.1| tRNA-dihydrouridine synthase B [Actinobacillus minor 202]
 gi|240295126|gb|EER45948.1| tRNA-dihydrouridine synthase B [Actinobacillus minor NM305]
          Length = 322

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 123/244 (50%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L  +        A+QI GAD
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSKLRLAHHRDIGVNAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAK+   +G   I++N+GCP+ +V++   G+ L+  P +V + + A+  A+ +P
Sbjct: 76  PTEMAEAAKVNVAYGAEIIDINMGCPAKKVNKKMAGSALLREPKLVENILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G D     +  RN ++     ++SGV+ + IH   R  + +G++         
Sbjct: 136 VTLKIRTGWD-----LENRNCLEIAHIAEQSGVSALTIHGRTRSCLFEGVA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  + K+   + I  NG +    +A ++L     D VMIGR AY    +   V++
Sbjct: 182 -EYESIKAV-KQAVSIPIIANGDITSAEKAKEVLDYTGADAVMIGRGAYGRPWLFKEVND 239

Query: 232 YFSN 235
           +  +
Sbjct: 240 FLEH 243


>gi|161529033|ref|YP_001582859.1| nifR3 family TIM-barrel protein [Nitrosopumilus maritimus SCM1]
 gi|160340334|gb|ABX13421.1| putative TIM-barrel protein, nifR3 family [Nitrosopumilus maritimus
           SCM1]
          Length = 320

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 104/216 (48%), Gaps = 13/216 (6%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +  + FS QE+P+++Q+ G+D+  L +AA IVE + ++ I+ N+GCP+  + +   G  L
Sbjct: 59  QEFIEFSEQERPISVQLFGSDLYALEKAATIVEPY-FDIIDYNMGCPAPHITQQMAGGAL 117

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   ++       +  A+  PVT+K R GV D       R++ +  +  G+  I  H R 
Sbjct: 118 LQEVNLTQQIFETLVNAVKKPVTLKIRSGVTDA-SKFLFRDIAEIAEDQGIQMITFHPR- 175

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMI 215
            + +G S        + D+ ++ E+K+ +    +G NG +     A  +L     D VMI
Sbjct: 176 TVSQGYS-------GSADWKLIKELKEISNIPVVG-NGDITTPEDAKMMLDETGCDYVMI 227

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           GR A  N  +   +++Y           K R+D  F
Sbjct: 228 GRGAMGNPFLFEQINDYLKTGSYKEYSFKDRLDSFF 263


>gi|51473224|ref|YP_066981.1| NifR3-like protein [Rickettsia typhi str. Wilmington]
 gi|81826343|sp|Q68XZ3|DUS_RICTY RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|51459536|gb|AAU03499.1| NifR3-like protein [Rickettsia typhi str. Wilmington]
          Length = 327

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/299 (24%), Positives = 134/299 (44%), Gaps = 22/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLA--LQIGGA 57
           M + TD  +R   +      L+ +EMI + A++   ++++   +   + P +  +Q+ G 
Sbjct: 18  MSNITDLEFRKLVKRF-GAGLVVSEMIASRAMIMKSRQSMQKCAIMHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPDVIADAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDERLATKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         ++ +   SGV  + +H R         +      N ++D
Sbjct: 137 PVTVKMRMGWDDNTKNAPTLAVIAA--SSGVQMVTVHGRT--------RCQFYSGNANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KE   + +  NG + + ++A + L     DG+M+GR  Y    +++ +  Y   
Sbjct: 187 FI-RVVKEAVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGVYGKPWLISQIAYYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                +P       D   K   ++ DY  + +     +    +H+I    G P+S   R
Sbjct: 246 GKEKPAP-SIAEQLDIIIKHYDAIIDYYGKSVG----VPIARKHIIWYSSGLPSSAEFR 299


>gi|303259674|ref|ZP_07345650.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP-BS293]
 gi|303264577|ref|ZP_07350496.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS397]
 gi|307707852|ref|ZP_07644329.1| transcriptional regulator [Streptococcus mitis NCTC 12261]
 gi|307710303|ref|ZP_07646744.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK564]
 gi|307711175|ref|ZP_07647597.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK321]
 gi|302639226|gb|EFL69685.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP-BS293]
 gi|302645947|gb|EFL76175.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS397]
 gi|307616112|gb|EFN95308.1| transcriptional regulator [Streptococcus mitis NCTC 12261]
 gi|307617137|gb|EFN96315.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK321]
 gi|307618895|gb|EFN98030.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK564]
          Length = 326

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|302876583|ref|YP_003845216.1| TIM-barrel protein, nifR3 family [Clostridium cellulovorans 743B]
 gi|307687258|ref|ZP_07629704.1| TIM-barrel protein, nifR3 family [Clostridium cellulovorans 743B]
 gi|302579440|gb|ADL53452.1| TIM-barrel protein, nifR3 family [Clostridium cellulovorans 743B]
          Length = 321

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 121/246 (49%), Gaps = 29/246 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R    L     L+YTEM+ A  +  G +    +L    +E+P+A+QI G D
Sbjct: 17  MAGVTDSPFRTLC-LEQGCGLVYTEMVSAKGLFYGSENTEALLKVIDEERPVAVQIFGRD 75

Query: 59  ---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              ++K  E     ++F    I++N+GCP+ ++ +   G+ LM  P++  + +  +    
Sbjct: 76  PYIMAKACEYFDKKDEFCI--IDVNMGCPAPKIVKNGEGSALMKEPELAYEIVKTLKNTT 133

Query: 116 SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIP 172
           S PVTVK R G D D I AV      K I+++G + I +H R    + +G +        
Sbjct: 134 SKPVTVKFRKGFDEDNINAV---EFAKVIEEAGADAIAVHGRTRAQMYQGKA-------- 182

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             D++I+ ++KK      IG NG +   ED +Q L  + + DG+M+ R +  N  +   +
Sbjct: 183 --DWNIIAQVKKAVTIPVIG-NGDVFSHED-AQNLIHISNCDGIMVARGSQGNPWLFNQI 238

Query: 230 DEYFSN 235
            +  SN
Sbjct: 239 KQKLSN 244


>gi|227114010|ref|ZP_03827666.1| tRNA-dihydrouridine synthase B [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 321

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 114/242 (47%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++++ KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSSVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   K  +  G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTIHGRTRACLFNGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|209447024|ref|NP_001129275.1| tRNA-dihydrouridine synthase 4-like [Rattus norvegicus]
 gi|149051085|gb|EDM03258.1| dihydrouridine synthase 4-like (S. cerevisiae) (predicted) [Rattus
           norvegicus]
          Length = 321

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 130/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA IV  +  + I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALIVCPYA-SGIDINCGCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L + ++ +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLARTI---DLCRKVEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMI-KENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T +   H H    +++IT
Sbjct: 256 -------TPLKCVWD---WVDIALELGTPFMCFHQHLMYMMEKIT 290


>gi|148652760|ref|YP_001279853.1| nifR3 family TIM-barrel protein [Psychrobacter sp. PRwf-1]
 gi|148571844|gb|ABQ93903.1| putative TIM-barrel protein, nifR3 family [Psychrobacter sp.
           PRwf-1]
          Length = 344

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 113/216 (52%), Gaps = 15/216 (6%)

Query: 24  TEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ ADA L   KK++    F  +  P++ QI GAD+ K+ EAA+   + G   I++N+
Sbjct: 58  SEMMTADATLYAHKKSLFRANFEGEIAPISAQIAGADVDKIAEAAQYQVNNGAQIIDINM 117

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP+ +V     G+ L+ + D+V   + A   A+  PVT+K R+G ++    + LR + K
Sbjct: 118 GCPAKKVCRKLAGSALLKDEDLVARLLDATVAAVDAPVTLKTRLGYENGQENI-LR-VAK 175

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             +++G+  I IH R         ++++      YD++ E+ K+  ++ +  NG ++   
Sbjct: 176 RAEEAGIAAIAIHGRT--------REDKYGGQARYDLIREV-KQLVNIPVIANGDIDSPQ 226

Query: 202 QALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +A+++      D +MIGRAA     +   +  Y   
Sbjct: 227 KAIEVYEQTGCDAIMIGRAAQGQPWLFRDIAHYLQT 262


>gi|56118841|ref|NP_001007929.1| dihydrouridine synthase 4-like [Xenopus (Silurana) tropicalis]
 gi|51513200|gb|AAH80375.1| MGC79829 protein [Xenopus (Silurana) tropicalis]
          Length = 308

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 110/238 (46%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + L YT MI+A   ++  K     F+T +  +PL +Q    +
Sbjct: 24  MVRYSKLAFRTLVRKYDCD-LCYTPMIIAADFVKSVKARDSEFTTNQGDRPLIVQFAAKE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + I+LN GCP        +GACL+ NP++V D +  +   +  P
Sbjct: 83  AQVLADAASLVSPFA-SGIDLNCGCPQRWAMAEGYGACLINNPELVSDMVKQVRNQVGDP 141

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RI  D         +L +  + +GV+ I +H R          D R  P + 
Sbjct: 142 GFTISIKIRIHADISRTV----DLCRKAEAAGVSWITVHGRT--------HDERHQP-VH 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           YD +  I KE+  + +  NG ++ + +A  I  +   DGVM  R    N AM    +E
Sbjct: 189 YDAIKSI-KESLSIPVVANGDVKSLKEAENIREITGADGVMAARGLLANPAMFAGYEE 245


>gi|159897989|ref|YP_001544236.1| nifR3 family TIM-barrel protein [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159891028|gb|ABX04108.1| putative TIM-barrel protein, nifR3 family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 362

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 140/310 (45%), Gaps = 25/310 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R     L    L+ +EM  A ++     K   +L +  +E+P+++Q+ G D
Sbjct: 32  MAGVTDSVFRRLVLSLGGCGLVVSEMTNAASVSPKAMKRHRLLDYLPEERPISIQLSGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+ VE+ G + I++N GCPS +V  G  G+ L+ +   +   + A+  A++IP
Sbjct: 92  PDLVATAARFVEELGPDVIDINCGCPSPKVTGGGHGSALLKDLPKMQQMLKAVYAAINIP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            T+K R G D+Q  ++   +  K  + +G   I +H R  + +G S        + D+  
Sbjct: 152 FTLKFRAGWDEQ--SLNYIDTAKIAEDAGCAAITLHPRTKV-QGYS-------GDADWSR 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+ +      IG +G +   + AL  L    V  VMIGRAA  N  +   + +     
Sbjct: 202 VAEVVQAVSIPVIG-SGDVRTPADALARLEQTGVAAVMIGRAAMANPWIFRQIAQ----- 255

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGKLQQ-ITRHMIGLFHGFPNSRR 292
           L    PI      D  R +     D  A  +    + GKL+Q I +  IGL+      R 
Sbjct: 256 LRAGEPIFVPTPSD-KRDLLVRYVDMCAETMVERQALGKLKQLIGQFSIGLYASNQLRRD 314

Query: 293 CRHILTVEAG 302
            +    +EA 
Sbjct: 315 VQRANEIEAA 324


>gi|296875651|ref|ZP_06899720.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC
           15912]
 gi|296433335|gb|EFH19113.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC
           15912]
          Length = 325

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|319946107|ref|ZP_08020355.1| tRNA-dihydrouridine synthase [Streptococcus australis ATCC 700641]
 gi|319747753|gb|EFV99998.1| tRNA-dihydrouridine synthase [Streptococcus australis ATCC 700641]
          Length = 326

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|227512326|ref|ZP_03942375.1| tRNA-dihydrouridine synthase [Lactobacillus buchneri ATCC 11577]
 gi|227084501|gb|EEI19813.1| tRNA-dihydrouridine synthase [Lactobacillus buchneri ATCC 11577]
          Length = 335

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 116/221 (52%), Gaps = 18/221 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     LV+AAK V ++   + I
Sbjct: 38  LVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGTKETLVQAAKFVDQNTAADII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   GA  +L+P  V + ++ +  A+  PVTVK R G D D I AV  
Sbjct: 98  DINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKKPVTVKMRTGWDEDHIYAV-- 155

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            N + + +++G + + +H R         +    + + ++DI+ ++  +    F+G NG 
Sbjct: 156 ENALAA-ERAGASALAMHGRT--------RKQMYMGHANWDILKQVAGQLHIPFMG-NGD 205

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     A K+L  V  D VM+GRA   N  +L+ V+ Y   
Sbjct: 206 VRTPQDAKKMLEDVGADAVMMGRAVEGNPWVLSQVEHYLET 246


>gi|113460710|ref|YP_718776.1| tRNA-dihydrouridine synthase B [Haemophilus somnus 129PT]
 gi|112822753|gb|ABI24842.1| tRNA-U20-dihydrouridine synthase [Haemophilus somnus 129PT]
          Length = 327

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 123/251 (49%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L  +EM+ A+  +   +K+ L  +  +     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSFY-GAGLTCSEMMSANPQVWHTEKSRLRLAHHQDAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + ++ +A+++P
Sbjct: 76  PIEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKKILYSVVRAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN +   K  +++G+  + IH   R+ +  G          N
Sbjct: 136 VTLKIRTGWNQE-----HRNCIDIAKIAEQAGIQALSIHGRTRECLFNG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD + ++ KE   + +  NG +    QA ++L     DG+MIGR A     +  ++  
Sbjct: 181 AEYDSIKKV-KEQISIPVIANGDITTAKQAQEVLNYTGTDGIMIGRGALGKPWLFQSIVS 239

Query: 232 YFSNPLTGSSP 242
                +T   P
Sbjct: 240 LIETGITIPEP 250


>gi|322410957|gb|EFY01865.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 325

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 117/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  TEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++ K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLAQVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|322386176|ref|ZP_08059809.1| tRNA-dihydrouridine synthase [Streptococcus cristatus ATCC 51100]
 gi|321269756|gb|EFX52683.1| tRNA-dihydrouridine synthase [Streptococcus cristatus ATCC 51100]
          Length = 325

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/239 (25%), Positives = 119/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|322391264|ref|ZP_08064735.1| tRNA-dihydrouridine synthase [Streptococcus peroris ATCC 700780]
 gi|321145868|gb|EFX41258.1| tRNA-dihydrouridine synthase [Streptococcus peroris ATCC 700780]
          Length = 326

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 117/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENALAA-ESAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|119509215|ref|ZP_01628365.1| Dihydrouridine synthase TIM-barrel protein [Nodularia spumigena
           CCY9414]
 gi|119466057|gb|EAW46944.1| Dihydrouridine synthase TIM-barrel protein [Nodularia spumigena
           CCY9414]
          Length = 363

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/301 (23%), Positives = 136/301 (45%), Gaps = 26/301 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    +++LYTEM+ A  +    +   I+    +E+P+++Q+       L 
Sbjct: 49  TDMVFRRLVRRYAPDSMLYTEMVNATGLHYVKELPKIMEVDPRERPISIQLFDCRPDFLA 108

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + I++N+GCP  ++ +   G+ L+  P++    +  + KA+ +PVTVK 
Sbjct: 109 EAAIKAVAEGADTIDINMGCPVNKITKNGGGSSLLRQPEVAEAIVQEVVKAVKVPVTVKT 168

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG +D+   + + +  K ++ +G   I +H R    +G +        N  ++ +  +K
Sbjct: 169 RIGWNDK--EITILDFAKRMEDAGAQMITVHGRTRA-QGYN-------GNARWEWITRVK 218

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTG 239
           +      IG NG +  +  A++ L     DGVM  R       ++  +D +      L  
Sbjct: 219 EVLSIPVIG-NGDIFSVEAAVRCLEQTGADGVMCSRGTLGYPFLVGEIDHFLKTGEMLAP 277

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILT 298
            SPI+         ++  +     A   + G + ++Q  +HM     GF  +   R  L+
Sbjct: 278 PSPIQ---------RLECARDHLQALWEYKGDRGVRQARKHMTWYAKGFVGAAELRGKLS 328

Query: 299 V 299
           +
Sbjct: 329 L 329


>gi|301092882|ref|XP_002997292.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262111427|gb|EEY69479.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 199

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 44/133 (33%), Positives = 75/133 (56%), Gaps = 8/133 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----RGDKKNILGFSTQEKPLALQIG 55
           M + TD  +R     +   ++++TE +  +A+      R      L ++ QE+P+  Q+ 
Sbjct: 1   MANVTDTAFRRLISEIAKPSVMWTEFVSCEALTHDPDSRRRMMTTLKYAEQERPVVAQLF 60

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-- 113
           G+   +  E+A IV D G++ I++N+GCP   V+    GA L+L PD+  D +AA CK  
Sbjct: 61  GSKPEQFYESAMIVRDLGFDGIDINMGCPETNVNSQGSGAALILQPDLAVDIVAA-CKRG 119

Query: 114 ALSIPVTVKCRIG 126
           A ++PV++K RIG
Sbjct: 120 AGNLPVSIKTRIG 132


>gi|322437060|ref|YP_004219272.1| TIM-barrel protein, nifR3 family [Acidobacterium sp. MP5ACTX9]
 gi|321164787|gb|ADW70492.1| TIM-barrel protein, nifR3 family [Acidobacterium sp. MP5ACTX9]
          Length = 409

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 117/243 (48%), Gaps = 21/243 (8%)

Query: 20  ALLYTEMIVADAILRG---DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
            L+ TE   AD + R     +K  L +   E P++ QI G++   L ++A+I +D G++ 
Sbjct: 78  GLIMTEFTSADGLSRMREVKRKRYLTYYDDEHPISAQIFGSNPETLADSARICQDAGFDI 137

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           ++LN+GCP+ RV   + G+ L+ +  ++      +  A+SIP TVK R+G +D+   +  
Sbjct: 138 VDLNLGCPAKRVVACNGGSGLLRDLPLIETIFKRVRGAISIPFTVKFRMGWNDK--NIVC 195

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L K  +  G+N + +HAR         +++       ++ +  +K       IG NG 
Sbjct: 196 VELAKIAEDCGLNAVALHART--------REDGYSGQARWEYIAAVKDAVGIPVIG-NGD 246

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           +     A+ +      D VMIGRAA  N  +   + +Y     TG   + T  D D +R 
Sbjct: 247 ILTPEDAVAMTHQTRCDAVMIGRAAPANPWIFRQIAQYTE---TGRYDLAT--DDDRYRM 301

Query: 255 ISA 257
           I A
Sbjct: 302 IKA 304


>gi|194015963|ref|ZP_03054578.1| probable tRNA-dihydrouridine synthase [Bacillus pumilus ATCC 7061]
 gi|194012318|gb|EDW21885.1| probable tRNA-dihydrouridine synthase [Bacillus pumilus ATCC 7061]
          Length = 324

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++    D     K  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGIQSVKGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFQGLDINMGCPVPNVTQNGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  ++ I +  +  + IH R    K +S  D        +
Sbjct: 138 LPVSVKTRLGFTE---VDEWRGWLRHILEQDIVNLSIHLRTR--KEMSQVDAH------W 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDGVMIGR  + N
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGVMIGRGIFHN 238


>gi|254449283|ref|ZP_05062729.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HTCC5015]
 gi|198261092|gb|EDY85391.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HTCC5015]
          Length = 270

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 100/189 (52%), Gaps = 13/189 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +QI GAD ++L EAA+   + G + I++N+GCP+ +V   + G+ L+ +  +V   +
Sbjct: 9   PIIVQIAGADPAQLAEAAQFNAEHGADIIDINMGCPAKKVCNVAAGSALLSDEPLVSRIL 68

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +  A+ IPVT+K R G     P+   RN V+  + +  +GI + A    L G + +D 
Sbjct: 69  TTVVNAVDIPVTLKTRTG-----PSADTRNAVRIAQLAEDSGIQMFA----LHGRT-RDQ 118

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
               + +YD +  +++   D+ +  NG ++   +A ++L     DG+MIGRAA  N  + 
Sbjct: 119 LYKGHAEYDTIASVRRAI-DIPLVANGDIDSPERARQVLDHTGADGLMIGRAAQGNPWIF 177

Query: 227 TTVDEYFSN 235
             V  +   
Sbjct: 178 REVAHFLET 186


>gi|73981937|ref|XP_540383.2| PREDICTED: similar to dihydrouridine synthase 4-like [Canis
           familiaris]
          Length = 317

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 79/285 (27%), Positives = 130/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R    + L YT MIVA   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYGCD-LCYTPMIVAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLTRTI---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ + +I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YEAI-KIIKENMSIPVIANGDIRSLKEAENVWHITGTDGVMVARGLLANPAMFAGYNE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P++   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLQCIWD---WIDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|146298835|ref|YP_001193426.1| nifR3 family TIM-barrel protein [Flavobacterium johnsoniae UW101]
 gi|146153253|gb|ABQ04107.1| tRNA-dihydrouridine synthase B-like protein [Flavobacterium
           johnsoniae UW101]
          Length = 332

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/300 (25%), Positives = 138/300 (46%), Gaps = 34/300 (11%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAK 67
           F RL   +   ++Y+E I ++ ++R   K+ +       E+P+ +QI G D   +  ++K
Sbjct: 29  FRRLCKTHGADMMYSEFISSEGLIRDAIKSRMKLDIFDYERPVGIQIFGGDEEAMEMSSK 88

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           IV     + +++N GCP  +V     GA ++ + D++     A+ K   +PVTVK R+G 
Sbjct: 89  IVSTVKPDLVDINFGCPVKKVVCRGAGAGVLKDVDLMVRLTKAVIKGTDLPVTVKTRLGW 148

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           D+   ++ +  + + ++  GV  + IHAR    + KG S          D+  +  +K  
Sbjct: 149 DES--SINIDEVAERLQDIGVQALTIHARTRAQMYKGHS----------DWSHIARVKN- 195

Query: 186 NPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           NP + + +  NG ++   +AL+      +DG+MIGRAA     +   +  YF    TG  
Sbjct: 196 NPRITMPIFGNGDIDSPEKALQYKNEYGIDGIMIGRAAIGYPWIFNEIKHYFK---TGEH 252

Query: 242 -PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRRCRHILT 298
            P  T +D     ++ A+           G +L   ++ RH    F G  + +  +  L 
Sbjct: 253 LPAPTVID-----RVEAARNHLKWSMEWKGERLGIVEMRRHYTNYFKGIHSFKEFKQKLV 307


>gi|261819596|ref|YP_003257702.1| tRNA-dihydrouridine synthase B [Pectobacterium wasabiae WPP163]
 gi|261603609|gb|ACX86095.1| TIM-barrel protein, nifR3 family [Pectobacterium wasabiae WPP163]
          Length = 321

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   K  +  G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTIHGRTRACLFNGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQAVSIPIIA-NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|253686643|ref|YP_003015833.1| TIM-barrel protein, nifR3 family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251753221|gb|ACT11297.1| TIM-barrel protein, nifR3 family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 321

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 115/241 (47%), Gaps = 24/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++++ KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSSVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNL 174
           VT+K R G      A   RN V   K  +  G+  + IH R +A L   S          
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTIHGRTRACLFNGS---------A 181

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y
Sbjct: 182 EYDSIRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHY 240

Query: 233 F 233
            
Sbjct: 241 L 241


>gi|227327926|ref|ZP_03831950.1| tRNA-dihydrouridine synthase B [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 321

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   K  +  G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTIHGRTRACLFNGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|258593836|emb|CBE70177.1| putative tRNA-dihydrouridine synthase (Nitrogen regulation protein
           nifR3) [NC10 bacterium 'Dutch sediment']
          Length = 336

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 133/302 (44%), Gaps = 28/302 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    +  +EM+ ++++L G +K         +  P+++Q+ GAD
Sbjct: 17  MAGVTDRPFRMLCRSM-GAGMAVSEMVASNSLLYGSEKTKRRANHEGETDPISVQLLGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   D G   I++N+GCP+ ++     G+ L+ N  +V   +  +  A+S+P
Sbjct: 76  PKMLAQAARYNVDAGAQIIDINMGCPAKKICNVMAGSALLQNEALVAQILETVVAAVSVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D Q      RN V+  +    SG+  + IH R         +        +
Sbjct: 136 VTLKIRTGWDTQN-----RNAVRIAQIAEISGIQALAIHGRT--------RACAYTGEAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K  +  + I  NG +    +A  ++     D VMIGRAA     +   +  + 
Sbjct: 183 YDTIAAVKA-SVKIPIIANGDITTPEKAHYVVQHTGADAVMIGRAAQGRPWLFREIAHFL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL--QQITRHMIGLFHGFPNSR 291
              L   +P    + +     +      Y     H+G ++  + I+ +  GL  G    R
Sbjct: 242 DTGLHLPAPQVVEIQRVLLNHLHGLYDLYGE---HTGLRVARKHISWYTKGLA-GSAQFR 297

Query: 292 RC 293
           RC
Sbjct: 298 RC 299


>gi|89266831|emb|CAJ83965.1| dihydrouridine synthase 4-like (S. cerevisiae) [Xenopus (Silurana)
           tropicalis]
          Length = 324

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 110/238 (46%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + L YT MI+A   ++  K     F+T +  +PL +Q    +
Sbjct: 40  MVRYSKLAFRTLVRKYDCD-LCYTPMIIAADFVKSVKARDSEFTTNQGDRPLIVQFAAKE 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + I+LN GCP        +GACL+ NP++V D +  +   +  P
Sbjct: 99  AQVLADAASLVSPFA-SGIDLNCGCPQRWAMAEGYGACLINNPELVSDMVKQVRNQVGDP 157

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RI  D         +L +  + +GV+ I +H R          D R  P + 
Sbjct: 158 GFTISIKIRIHADISRTV----DLCRKAEAAGVSWITVHGRT--------HDERHQP-VH 204

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           YD +  I KE+  + +  NG ++ + +A  I  +   DGVM  R    N AM    +E
Sbjct: 205 YDAIKSI-KESLSIPVVANGDVKSLKEAENIREITGADGVMAARGLLANPAMFAGYEE 261


>gi|332524006|ref|ZP_08400258.1| putative tRNA-dihydrouridine synthase B [Streptococcus porcinus
           str. Jelinkova 176]
 gi|332315270|gb|EGJ28255.1| putative tRNA-dihydrouridine synthase B [Streptococcus porcinus
           str. Jelinkova 176]
          Length = 317

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 117/241 (48%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 16  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   ++ +   L I
Sbjct: 75  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVSEVTSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV  + +H R         ++     + D+D
Sbjct: 135 PLTVKMRTGWADS--SLAVENALAA-ESAGVAALAMHGRT--------REQMYTGSCDHD 183

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 184 TLARVSKALTKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 242

Query: 235 N 235
            
Sbjct: 243 T 243


>gi|50119216|ref|YP_048383.1| tRNA-dihydrouridine synthase B [Pectobacterium atrosepticum
           SCRI1043]
 gi|49609742|emb|CAG73176.1| putative dihydrourdine synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 321

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   K  +  G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTIHGRTRACLFNGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQAVSIPIIA-NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|87120520|ref|ZP_01076414.1| Dihydrouridine synthase TIM-barrel protein [Marinomonas sp. MED121]
 gi|86164163|gb|EAQ65434.1| Dihydrouridine synthase TIM-barrel protein [Marinomonas sp. MED121]
          Length = 322

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/270 (25%), Positives = 125/270 (46%), Gaps = 25/270 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+ +EM+ +D  L    K  N L    +  P ++QI G D   + +AA+   + G   I+
Sbjct: 38  LVVSEMVTSDVRLWNTNKSRNRLVHDAEVSPRSVQIAGGDADMMAQAARQNIELGAQIID 97

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALR 137
           +N+GCP+ +V   + G+ L+ +  +V + + A+ +++  PVT+K R G  +DQ   + + 
Sbjct: 98  INMGCPAKKVCNKAAGSALLKDEALVREILEAVVESVDAPVTLKIRTGWSEDQKNGLRIA 157

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + + I   G+  + +H R    K           N +YD + EIK+    + +  NG +
Sbjct: 158 RMAEDI---GIQALAVHGRTRACKFQG--------NAEYDTIAEIKQA-LSIPVFANGDI 205

Query: 198 EDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
            D  +A  +K     DG+MIGRAA     +   V  +  +    S+P    V +      
Sbjct: 206 NDAHKAKFVKDYTGADGIMIGRAAQGRPWIFREVAHFLEHNEELSAPTLDEVKQ------ 259

Query: 256 SASMTDYAARHLHSGGKLQ-QITRHMIGLF 284
              ++  AA H   G  L  +I R  +G +
Sbjct: 260 -LVLSHVAALHQFYGDYLGVRIARKHVGWY 288


>gi|153873343|ref|ZP_02001955.1| Dihydrouridine synthase, DuS [Beggiatoa sp. PS]
 gi|152070190|gb|EDN68044.1| Dihydrouridine synthase, DuS [Beggiatoa sp. PS]
          Length = 259

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 115/242 (47%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR YR   +      +  +EMI ++++L G +K         + +P  +QI GAD
Sbjct: 17  MAGVTDRPYRQLCKQW-GAGMAVSEMISSNSLLWGSEKTKRRANHEGETEPRCIQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   I++N+GCP+ +V     G+ L+ +  +VG  + A+ KA+ +P
Sbjct: 76  PELMAKAAQYNVDNGAQIIDINMGCPAKKVCHVMAGSALLKDEGLVGKILEAVVKAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D +      RN V+  +   +SG+  + +H R    +             +
Sbjct: 136 VTLKIRTGWDKE-----HRNGVRIAQIAEQSGIQALAVHGRTRACQFSG--------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  IK     + +  NG +++  +A  +L     D VM+GRAA     +   ++ Y 
Sbjct: 183 YETIAAIKA-TIKIPVIANGDIDNPEKAKSVLDYTGADAVMVGRAALGQPWLFREMEHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 NT 243


>gi|227522412|ref|ZP_03952461.1| tRNA-dihydrouridine synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227090470|gb|EEI25782.1| tRNA-dihydrouridine synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 335

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 116/222 (52%), Gaps = 18/222 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EMI    I+  +KK  +++    +E P+++QI G     LV+AAK V ++   + 
Sbjct: 37  GLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGTKETLVQAAKFVDQNTAADI 96

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  PVTVK R G D D I AV 
Sbjct: 97  IDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKKPVTVKMRTGWDEDHIYAV- 155

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
             N + + +++G + + +H R         +    + + ++DI+ ++  +    F+G NG
Sbjct: 156 -ENALAA-ERAGASDLAMHGRT--------RKQMYMGHANWDILKQVAGQLHIPFMG-NG 204

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K+L  V  D VM+GRA   N  +L+ V+ Y   
Sbjct: 205 DVRTPQDAKKMLEDVGADAVMMGRAVEGNPWVLSQVEHYLET 246


>gi|296535536|ref|ZP_06897718.1| tRNA-dihydrouridine synthase B [Roseomonas cervicalis ATCC 49957]
 gi|296264122|gb|EFH10565.1| tRNA-dihydrouridine synthase B [Roseomonas cervicalis ATCC 49957]
          Length = 374

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 78/298 (26%), Positives = 132/298 (44%), Gaps = 28/298 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADI 59
           TD  +R   R L    ++ +EMI + A++R +++ +      GF     P ++Q+ G D 
Sbjct: 42  TDLPFRRLCREL-QAPMVVSEMIASQAMVRENRQTLKMAEVDGFG---GPTSVQLAGCDP 97

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIP 118
           + + EAAK+  D G   +++N GCP  +V  G   G+ LM +       + A+ KA+S P
Sbjct: 98  AVMAEAAKLAVDHGAAIVDINFGCPVKKVALGQQAGSALMRDEIGAARILEAVVKAVSTP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D    ++    L K  ++SG+  + +H R   +      D   + N+    
Sbjct: 158 VTLKMRMGWDHN--SLNAPRLAKIAEESGIKLVTVHGRTRQMFYTGTADWAFVANV---- 211

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                K+   L + +NG +     A + L     DGVMIGR  Y    +L  +  Y +  
Sbjct: 212 -----KQAVGLPVIVNGDILTPQHAAEALRQSGADGVMIGRGCYGRPWLLARIATYLTTG 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P       D  R+   +M ++     H G +L +  +H+     G P S   R
Sbjct: 267 EDLPEP-DLATQYDILRRHYHAMLEHHGP--HPGVRLAR--KHLAWYSKGLPGSAEFR 319


>gi|257466741|ref|ZP_05631052.1| nitrogen regulation protein NIFR3 [Fusobacterium gonidiaformans
           ATCC 25563]
 gi|315917890|ref|ZP_07914130.1| nitrogen regulation protein NIFR3 [Fusobacterium gonidiaformans
           ATCC 25563]
 gi|313691765|gb|EFS28600.1| nitrogen regulation protein NIFR3 [Fusobacterium gonidiaformans
           ATCC 25563]
          Length = 314

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 74/305 (24%), Positives = 133/305 (43%), Gaps = 42/305 (13%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  YR        + LL+TEM+ +DA+   + K I           +Q+ G D+ K++ 
Sbjct: 13  TDYTYRGILEEFHPD-LLFTEMVSSDALAALNDKTISQILRLRPGNGVQLFGKDVEKMLY 71

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           +AK VE  G   I++N GCP  RV     GA L+ +PD + + ++ + + L     +++K
Sbjct: 72  SAKYVEKLGVKHIDINSGCPMKRVVHSGHGAALLKSPDKIKEILSTLREGLQEDTDLSIK 131

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
            RIG +     + +  + + +   G + I +H R    +  G +          D+ ++ 
Sbjct: 132 IRIGYEKPENYIQIAKIAEEV---GCSHITVHGRTRAQLYTGFA----------DWSLIK 178

Query: 181 EIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           EI KEN  + +  NG +   ED  + ++    VDGVM+ R  + N  ++  + E      
Sbjct: 179 EI-KENVSIPVIGNGDIFTAEDAKEKIE-YSGVDGVMLARGIFGNPWLIREIREILQ--- 233

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-------LQQITRHMIGLFHGFPNS 290
                +KT+V        +    D A  H+    K       +  + +H+     G  NS
Sbjct: 234 --YGQVKTKV-------TAEDKIDMAIHHIEEIAKDNPQREFVFDVRKHICWYLKGISNS 284

Query: 291 RRCRH 295
             C++
Sbjct: 285 AECKN 289


>gi|82617391|emb|CAI64302.1| dihydrouridine synthase like protein [uncultured archaeon]
          Length = 318

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 121/242 (50%), Gaps = 23/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQ-EKPLALQIGGAD 58
           M + T+  +R   +     AL Y+EMI A+A++R G+K    G + + E+P  +Q+ G  
Sbjct: 17  MANVTNLAFRMLCKKY-GAALTYSEMISANAVVRQGEKTMQRGLTCEDEQPFCIQMFGNS 75

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA I+E+ +    I++N+GCP+  +     G+ L+ +P +V D ++++   +S 
Sbjct: 76  TDTMTEAALILEETYRPAIIDVNMGCPAPLIVRQECGSALLNSPSLVHDIVSSLADNIST 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLD 175
           PV+ K R+  D+    +    + ++I+ +G   I +H   R+ +  G S        +L+
Sbjct: 136 PVSTKIRV-FDNMEKTL---EIARTIESAGACAITVHGRTREQMYSGTS--------SLE 183

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y     IKKE     I  NG ++D   A   L     DG+MIGRAA  +  +   V  Y 
Sbjct: 184 Y--AKRIKKELSIPVIA-NGDIKDGESAKHALEYTECDGLMIGRAAIGHPFIFRQVSHYL 240

Query: 234 SN 235
            +
Sbjct: 241 EH 242


>gi|91774707|ref|YP_544463.1| dihydrouridine synthase TIM-barrel protein nifR3 [Methylobacillus
           flagellatus KT]
 gi|91708694|gb|ABE48622.1| tRNA-U20-dihydrouridine synthase [Methylobacillus flagellatus KT]
          Length = 343

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 110/225 (48%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G  K +       +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRVLCKKM-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVAQILKAVVNAVEVP 135

Query: 119 VTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           VT+K R G D     AVA+  + + I   GV  + IH R +A L            + +Y
Sbjct: 136 VTLKIRTGWDKHNRNAVAVARMAEDI---GVQALAIHGRTRACL---------YTGDAEY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           D +  +K+      I  NG +    +A  +L     D VMIGRAA
Sbjct: 184 DTIAAVKQAIRIPLIA-NGDITTPEKAKFVLDYTKADAVMIGRAA 227


>gi|163793260|ref|ZP_02187236.1| tRNA-dihydrouridine synthase [alpha proteobacterium BAL199]
 gi|159181906|gb|EDP66418.1| tRNA-dihydrouridine synthase [alpha proteobacterium BAL199]
          Length = 328

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 84/305 (27%), Positives = 139/305 (45%), Gaps = 29/305 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKL 62
           TDR YR   R      L+ +EMI +DA+LR  ++ +L     T + P  +Q+ G D + +
Sbjct: 23  TDRPYRRIVRSF-GVGLVISEMIASDAMLREVREELLKAEIDTDDAPAVVQLAGWDPATM 81

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA++    G   I++N+GCP+ +V     G+ LM +  + G  IAA+  A+ +PVT+K
Sbjct: 82  AEAARLAVAGGAAVIDINMGCPAKKVVNRLAGSALMRDEALAGQIIAAVVNAVPVPVTLK 141

Query: 123 CRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            R G D+       RN   L +  + +GV  I +H R         +        D++ +
Sbjct: 142 MRTGWDEND-----RNAPRLARIAEDAGVRMITVHGRT--------RCQMYTGQADWEFI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+      +  NG +     A+  L     DGVMIGR AY    +L  +    +   
Sbjct: 189 RRVKEVVSVPVVA-NGDITSPEDAMACLQQSDADGVMIGRGAYGRPWILKQIAARIAGQA 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +P    +     + + A ++ Y    +HSG  L+   +H+     G P+S   R  +
Sbjct: 248 VVPAPSVGEIKAIIVQHLEAMLSHYG---IHSG--LRNARKHIGWYSQGLPDSAEFRQAV 302

Query: 298 --TVE 300
             TVE
Sbjct: 303 NNTVE 307


>gi|307705860|ref|ZP_07642699.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK597]
 gi|307620588|gb|EFN99685.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK597]
          Length = 326

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEYIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|126340537|ref|XP_001363271.1| PREDICTED: similar to dihydrouridine synthase 4-like [Monodelphis
           domestica]
          Length = 317

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 129/285 (45%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKY-NCDLCYTPMIVAADFVRSTKARDSEFTTNKGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  AQLLSDAARIVCPYA-NGIDINCGCPQRWAITEGYGACLINKPELVQDMVKQVRSQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    +   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 NFSVSIKIRIH-DDLTRTI---DLCRKAEATGVSWITVHGRNI--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I KEN  + I  NG ++ + +A  +  +   +G+M+ R    N AM     E  
Sbjct: 199 YDAI-KIIKENLSIPIIANGDIKSLKEAENVQEMTGTNGIMVARGLLANPAMFAGYKE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+    T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALEHGTPFMCFHHHLMYMMERIT 290


>gi|293399909|ref|ZP_06644055.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291306309|gb|EFE47552.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 338

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/288 (26%), Positives = 134/288 (46%), Gaps = 31/288 (10%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+YTEM+   A+   ++K  ++     +E PL +QI G DI  +V AAK++ E    + I
Sbjct: 41  LIYTEMVSDKALYYENEKTLHMTAVEKEEHPLTMQIFGHDIETMVYAAKLLDEKSDCDII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++ + + G+ LM + D       A+  ++  PVTVK RIG D D I  V  
Sbjct: 101 DINMGCPVNKIIKSNAGSALMKDIDHAVTMTKAVVDSVKKPVTVKMRIGWDMDSINCV-- 158

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L K +   GV+ + +H   RK + +G +          D+  +  +K+      +G N
Sbjct: 159 -ELAKGLASVGVSALAVHGRTRKQMYEGKA----------DWQYIKAVKQAVSIPVMG-N 206

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G +     A ++L +   D +M+GR    +  ++  +  Y +   TG       V++ F 
Sbjct: 207 GDIRSSEDAKRMLDTTGCDAIMVGRGVLGDPWLIKEIATYLA---TGEKLPPVSVNEKFT 263

Query: 253 --RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             R  +  + D    H+     ++++  H      G P S + +  LT
Sbjct: 264 MARLHAKRLCDLKGEHV----GMREMRGHAAWYVKGLPKSHQLKDSLT 307


>gi|269215243|ref|ZP_05987998.2| tRNA-dihydrouridine synthase B [Neisseria lactamica ATCC 23970]
 gi|269207980|gb|EEZ74435.1| tRNA-dihydrouridine synthase B [Neisseria lactamica ATCC 23970]
          Length = 366

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRDF-GAGWAVCEMLASDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 106 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 166 VTLKTRLGWHDDHKNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKCRL-NIPVWVNGDITSPQKAQTVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|169627854|ref|YP_001701503.1| tRNA-dihydrouridine synthase [Mycobacterium abscessus ATCC 19977]
 gi|169239821|emb|CAM60849.1| Probable tRNA-dihydrouridine synthase [Mycobacterium abscessus]
          Length = 391

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 81/317 (25%), Positives = 131/317 (41%), Gaps = 37/317 (11%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A+        ++  FS +E P +L
Sbjct: 31  MAGVTNVAFRTLCRELELATTGTVSGLYVCEMVTARALAERHPVTLHMTTFSPEESPRSL 90

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK+V D G  + I++N GCP  +V     GA L     + G  +AA 
Sbjct: 91  QLYSVDPETTYRAAKMVVDEGLADHIDMNFGCPVPKVTRNGGGAALPYKRRLFGQIVAAA 150

Query: 112 CKALS---IPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            +A +   IPVTVK R+G+DD     + A A+       +  G   + +HAR A      
Sbjct: 151 VRATAGTDIPVTVKFRVGIDDDHHTHLDAGAI------AESEGAAAVALHARTA------ 198

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
               R     D+  +  +K     + +  NG + D + A+ ++     DGV+IGR     
Sbjct: 199 --SQRYSGTADWSQIAALKNHVTTIPVLGNGDIFDAADAVAMMEQTGCDGVVIGRGCLGR 256

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             +   +   F+     + P   +V     R+ +  + D    H      L+ + +H+  
Sbjct: 257 PWLFAELSAVFNGQTIPAPPNLGQVTV-IMRRHAELLVD----HFGEDKALRDMRKHIAW 311

Query: 283 LFHGFPNSRRCRHILTV 299
             HGFP     R  L +
Sbjct: 312 YLHGFPAGGDIRRALAL 328


>gi|270291880|ref|ZP_06198095.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M143]
 gi|270279408|gb|EFA25250.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M143]
          Length = 336

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++     +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQKNTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 202 TLHDVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 260


>gi|126731334|ref|ZP_01747141.1| tRNA-dihydrouridine synthase, putative [Sagittula stellata E-37]
 gi|126708245|gb|EBA07304.1| tRNA-dihydrouridine synthase, putative [Sagittula stellata E-37]
          Length = 314

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 101/215 (46%), Gaps = 19/215 (8%)

Query: 21  LLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+ +EMI +   L  R   +       Q +  ++QI G +   + EAA++V D G   I+
Sbjct: 25  LVVSEMIASGEFLTARPGTREKAELGAQVENTSVQIAGREPEPMAEAARMVADMGARVID 84

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V  G  G+ LM  PD     I A+  A+ +PVT+K R+G DD    +    
Sbjct: 85  INMGCPAKKVTGGWSGSALMRVPDHALRLIEAVVAAVDLPVTLKTRLGWDDT--DLNAPE 142

Query: 139 LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           L +  + +GV  I IH R      KG +          D+  +  + K+   + +  NG 
Sbjct: 143 LARRAEGAGVRMIVIHGRTRCQFYKGRA----------DWAAIRPV-KDAVSIPVVANGD 191

Query: 197 LEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
           + D   A +   L   DGVM+GR A     ML  +
Sbjct: 192 ITDADTARRALDLSGADGVMVGRGAQGAPWMLAEI 226


>gi|242241086|ref|YP_002989267.1| tRNA-dihydrouridine synthase B [Dickeya dadantii Ech703]
 gi|242133143|gb|ACS87445.1| TIM-barrel protein, nifR3 family [Dickeya dadantii Ech703]
          Length = 321

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 114/242 (47%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R    L     +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGVSDRPFRVLC-LTMGAGMAVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AA I  D G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ K++S+P
Sbjct: 76  PAEMAAAASINMDSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKRILTAVVKSVSVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V+  + +   G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIARLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRTVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|308067621|ref|YP_003869226.1| tRNA-dihydrouridine synthase 2 [Paenibacillus polymyxa E681]
 gi|305856900|gb|ADM68688.1| Probable tRNA-dihydrouridine synthase 2 [Paenibacillus polymyxa
           E681]
          Length = 329

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 108/235 (45%), Gaps = 28/235 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDK--KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++     G+K  +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNKSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  I++N+GCP A V E   G+ L+  P+I  D I A  KA  
Sbjct: 79  DKPEYFREMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPEIAADIIQA-AKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   VD+       R+ +  I K  +  + IH R         ++     +
Sbjct: 138 LPVSVKTRLGFTTVDE------WRDWLTHILKQDIVNLSIHLRT--------REEMSKVD 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  ++N
Sbjct: 184 AHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFQN 238


>gi|322420178|ref|YP_004199401.1| TIM-barrel protein, nifR3 family [Geobacter sp. M18]
 gi|320126565|gb|ADW14125.1| TIM-barrel protein, nifR3 family [Geobacter sp. M18]
          Length = 321

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 80/310 (25%), Positives = 138/310 (44%), Gaps = 47/310 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+   R  AR     +L +TEM+  + + R  +K  ++L  ++ ++P+ +Q+ G +
Sbjct: 21  MAGITNLPMRLIARE-GGASLTFTEMVSVNGLTREGRKSFDLLKTTSGDRPIGMQLFGDE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++VE++G   +++N+GCP  +V     G+ LM +P  VG  + ++ KA  +P
Sbjct: 80  PEMLAEAARLVEEYG-ELLDINMGCPVKKVVGTGAGSALMKDPLKVGRIVRSVRKATRLP 138

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
            TVK R G    DD  P V      +  ++ G + I +H  +R  + +G           
Sbjct: 139 FTVKIRTGWVCGDDTFPEVG-----RIAQEEGCDAITLHPRSRAQMFEG----------K 183

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            D+  + E+K       IG +G L      +++L     D VM+ R A  N  +      
Sbjct: 184 ADWAKIGELKSTLKIPVIG-SGDLFSADDVVRMLSETGCDAVMVARGAMGNPWLFREALA 242

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-----SGGK--LQQITRHMIGLF 284
                L G +P+   V         A     A RHL       GG+  L ++ +H+    
Sbjct: 243 L----LAGETPVPPTV---------AERLAVARRHLELFTEFEGGRVALMEMRKHLSWYS 289

Query: 285 HGFPNSRRCR 294
            G P + + R
Sbjct: 290 KGLPGAAQFR 299


>gi|330799310|ref|XP_003287689.1| hypothetical protein DICPUDRAFT_151810 [Dictyostelium purpureum]
 gi|325082309|gb|EGC35795.1| hypothetical protein DICPUDRAFT_151810 [Dictyostelium purpureum]
          Length = 324

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 112/235 (47%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + YT MI+A    R +      ++T   E  + +Q G  +
Sbjct: 42  MVRFSRLPFRMLCRKWGCD-ITYTPMIMAAEFNRSESARDSDYTTNQFEDQMIVQFGVNN 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA+ V +   + I++N GCP   V +  +GA L+LNPD + D +  +   + +P
Sbjct: 101 AEELCAAAEKVAN-TCSGIDINCGCPQRWVMKEGYGANLLLNPDKIYDMVKQLNNRVPVP 159

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            ++K RI  D          LVK  +K GV+ I +H R + ++   P        +DYD 
Sbjct: 160 CSIKIRIQPDLN----KTIELVKRAEKIGVSWITVHGRTSAMRSSHP--------VDYDA 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + ++ KEN  L +  NG +  + QA  +K    V+GVM  R    N A+    D+
Sbjct: 208 I-KLVKENTSLPVFANGDVFTLEQANTIKEKTGVNGVMAARGLLSNPALFMGYDK 261


>gi|310640378|ref|YP_003945136.1| dihydrouridine synthase dus [Paenibacillus polymyxa SC2]
 gi|309245328|gb|ADO54895.1| Dihydrouridine synthase DuS [Paenibacillus polymyxa SC2]
          Length = 329

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 108/235 (45%), Gaps = 28/235 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDK--KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++     G+K  +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNKSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  I++N+GCP A V E   G+ L+  P+I  D I A  KA  
Sbjct: 79  DKPEYFREMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPEIAADIIQA-AKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   VD+       R+ +  I K  +  + IH R         ++     +
Sbjct: 138 LPVSVKTRLGFTAVDE------WRDWLTHILKQDIVNLSIHLRT--------REEMSKVD 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  ++N
Sbjct: 184 AHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFQN 238


>gi|297543866|ref|YP_003676168.1| NifR3 family TIM-barrel domain-containing protein
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296841641|gb|ADH60157.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
          Length = 321

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 113/226 (50%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQ+ G+D 
Sbjct: 17  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKMLTDIDEEEKVALQVFGSDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 76  DIMGEIARKLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 135

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K+G+  + +H R         ++       D+ I
Sbjct: 136 TVKIRKGWDDNHVNAVEIAQIA---EKAGIKAVAVHGR--------TREQFYSGKADWSI 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + ++K+      IG NG +     A ++L     D ++IGR A  N
Sbjct: 185 IKKVKESVKIPVIG-NGDIFTPQDAKRMLEETGCDAILIGRGAQGN 229


>gi|295694791|ref|YP_003588029.1| TIM-barrel protein, nifR3 family [Bacillus tusciae DSM 2912]
 gi|295410393|gb|ADG04885.1| TIM-barrel protein, nifR3 family [Bacillus tusciae DSM 2912]
          Length = 331

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 113/233 (48%), Gaps = 23/233 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+ +    ++  EM+    I+  + K +  L     E P++LQ+ G+D+  +V AA
Sbjct: 30  FRILAKEM-GAGMVCAEMVATKGIVNANAKTLRMLHILPDEHPVSLQLVGSDLDSMVRAA 88

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           + V      + I++N+GCP  ++++   GA L  +PD     + A+ + +  PVTVK R 
Sbjct: 89  ETVGTATNADVIDINMGCPVLKIYKNGSGAALARDPDYAARIVRAVVQTVDKPVTVKFRK 148

Query: 126 GV-DDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEI 182
           G  DD + AV    +  +++++G   + +H R  K +  G          + D+ I+ ++
Sbjct: 149 GWDDDHVNAV---EVALAVEEAGAKAVTVHGRTAKQMYSG----------HADWSIIRQV 195

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           K+      IG NG +     A+++L     DGVMIGR A  N  +      Y 
Sbjct: 196 KEAVRIPVIG-NGDVSTPEAAVQMLQETGCDGVMIGRGALGNPWIFRETVHYL 247


>gi|326390246|ref|ZP_08211806.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus JW
           200]
 gi|325993691|gb|EGD52123.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus JW
           200]
          Length = 336

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 112/226 (49%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQI G+D 
Sbjct: 32  MAGVTDKPFRVICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEKVALQIFGSDP 90

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 91  DIMGEIARRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 150

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K GV  + +H R         ++       D+ I
Sbjct: 151 TVKIRKGWDDNHVNAVEIAQIA---EKVGVKAVAVHGR--------TREQFYSGKADWSI 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + ++K+      IG NG +     A ++L     D ++IGR A  N
Sbjct: 200 IKKVKESVKIPVIG-NGDIFTPEDAKRMLEETGCDAILIGRGAQGN 244


>gi|240117283|ref|ZP_04731345.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID1]
 gi|240125030|ref|ZP_04737916.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-92-679]
          Length = 364

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 166 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++   +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|196228193|ref|ZP_03127060.1| TIM-barrel protein, nifR3 family [Chthoniobacter flavus Ellin428]
 gi|196227596|gb|EDY22099.1| TIM-barrel protein, nifR3 family [Chthoniobacter flavus Ellin428]
          Length = 328

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 131/280 (46%), Gaps = 22/280 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-I 77
           ++ TE + A+ I R +++ +  L F   E+PL +Q+ G D   L EAA++V ++   + I
Sbjct: 35  VMVTEFVSAEGIFRRNERTLEYLEFIEAERPLGVQLFGGDPEHLGEAARMVGEWKQPDFI 94

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVAL 136
           +LN GCP  +V   + G+ L+ +  ++     A+ K A  +PVT K RIG  +Q   +  
Sbjct: 95  DLNFGCPVNKVVSKNGGSSLLRDCPLLERVARAVVKGAAPLPVTAKIRIGWCEQ--TINA 152

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
               + ++  GV  I +H R    +G S + N       +D++ E+        IG NG 
Sbjct: 153 TTTARILEDCGVQAIAVHGRTK-EQGYSGRAN-------WDVIAEVAAATSLPVIG-NGD 203

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFWRK 254
           +   + A+  +   V G+MIGRAA     +   +  Y S   +    P++T+    F  +
Sbjct: 204 IASAADAVGAMKCGVRGLMIGRAAMSTPWIFREIKHYVSTGEILAPPPLETQW--AFIIR 261

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +     LH+   +Q +   ++    G P +++ R
Sbjct: 262 HCRWKVEVEGSELHA---MQSMRTRLMAYSRGMPEAKQLR 298


>gi|254294026|ref|YP_003060049.1| dihydrouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042557|gb|ACT59352.1| dihydrouridine synthase DuS [Hirschia baltica ATCC 49814]
          Length = 337

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 107/222 (48%), Gaps = 21/222 (9%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           ++ TEMI    +  G +  +   +  E   P  +Q+ G D   + EAA+I    G + I+
Sbjct: 37  VVITEMIAGSELATGRQDMVWRITKPENTFPFVVQLAGRDPKWMYEAARISASAGADIID 96

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI---PAVA 135
           +N+GCPS +V  G  GA LM + D+  + I A  +   +PV+VK R+G DD     PA+A
Sbjct: 97  INMGCPSRQVTGGQSGAALMRDLDLARELIIAAREGGGLPVSVKMRLGWDDDTLNAPALA 156

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
                K  ++  V  I +H R         +        D++ V E+K  + +L + +NG
Sbjct: 157 -----KICEEEHVKLITVHGRT--------RCQFYTGKADWNKVKEVKLAS-NLPLIVNG 202

Query: 196 GLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++    A +  +L   DGVMIGRAA     +L  +    +N
Sbjct: 203 DIDSSKTAKQAILLSQADGVMIGRAALGRPWLLGKIASDLAN 244


>gi|190891640|ref|YP_001978182.1| tRNA-dihydrouridine synthase [Rhizobium etli CIAT 652]
 gi|190696919|gb|ACE91004.1| tRNA-dihydrouridine synthase protein [Rhizobium etli CIAT 652]
          Length = 339

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 103/211 (48%), Gaps = 18/211 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +RF A L+    ++ +  +V D      +    GF    +P  +Q+ G +   + EAA+I
Sbjct: 47  WRFGAGLVVTE-MVASRELVNDTAESWSRLKAAGF----RPHMVQLAGREAHWMAEAARI 101

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
             D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+K R+G D
Sbjct: 102 AADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPVTLKMRLGWD 161

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   ++   ++ +  + +G+  + IH R      +   D R     D+D +  ++     
Sbjct: 162 EN--SINAPDIARRAEAAGIQLVTIHGRTR----MQFYDGRA----DWDAIRAVRDVISI 211

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             I  NG +E    A +IL     D VMIGR
Sbjct: 212 PLIA-NGDVETAEDAQEILRRSGADAVMIGR 241


>gi|320354884|ref|YP_004196223.1| dihydrouridine synthase DuS [Desulfobulbus propionicus DSM 2032]
 gi|320123386|gb|ADW18932.1| dihydrouridine synthase DuS [Desulfobulbus propionicus DSM 2032]
          Length = 347

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 107/206 (51%), Gaps = 15/206 (7%)

Query: 21  LLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           LL TEM+ A  +     D    L  +T+E PL+ Q+   D   +  A   +   G + I+
Sbjct: 37  LLSTEMLSAARLPAESVDHSPYLFRTTKESPLSHQLMLTDEKHIAPAFAALHRLGADVID 96

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCP+ ++     G+ LM +P  V   +A+  +  S+P+T K R+G  + + A  LR+
Sbjct: 97  LNLGCPAPQIRRSGGGSRLMEDPARVRRLVASARQHTSLPLTAKIRLG--ETLDAAKLRD 154

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             + ++  GV+ I +HAR   L+G S     +     ++ V  +K+   D+ +  NGG++
Sbjct: 155 FCRMLEGEGVDMITVHAR---LRGESFARRPR-----WEWVANVKRWI-DIPVVANGGID 205

Query: 199 DMSQALKILPS--VDGVMIGRAAYKN 222
            ++ A   L     DG+MIGRAA ++
Sbjct: 206 SIASARTCLEQSGADGLMIGRAAARS 231


>gi|313891107|ref|ZP_07824726.1| TIM-barrel protein, nifR3 family [Streptococcus pseudoporcinus SPIN
           20026]
 gi|313120470|gb|EFR43590.1| TIM-barrel protein, nifR3 family [Streptococcus pseudoporcinus SPIN
           20026]
          Length = 325

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 116/241 (48%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   ++ +   L I
Sbjct: 83  AEGLKRAADFIQTKTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVSQVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV  + +H R         ++       D+D
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVAALAMHGRT--------REQMYTGRCDHD 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKALTKIPFIG-NGDVRTVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250

Query: 235 N 235
            
Sbjct: 251 T 251


>gi|255327241|ref|ZP_05368315.1| putative tRNA-dihydrouridine synthase [Rothia mucilaginosa ATCC
           25296]
 gi|255295521|gb|EET74864.1| putative tRNA-dihydrouridine synthase [Rothia mucilaginosa ATCC
           25296]
          Length = 430

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/289 (25%), Positives = 124/289 (42%), Gaps = 24/289 (8%)

Query: 10  RFFARLLTN--NALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEA 65
           + F RL +     L  TEM+ A A++  + +   I+     EK  ++QI G D   + +A
Sbjct: 77  KAFRRLCSEYGGGLYVTEMVTARALVERKPESMRIIEHDPDEKIRSIQIYGVDAVNVGKA 136

Query: 66  AK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTV 121
            + +VE+   + I+LN GCP+ +V     GA L    D+    +    K  S   IP+T+
Sbjct: 137 VRMVVEEDRADHIDLNFGCPAPKVTRRGGGAALPWKTDLFTAIVQTAVKEASRNDIPLTI 196

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+DD    +      K  + +GV  I +H R A                D+D + +
Sbjct: 197 KMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTAA--------QHYSGKADWDSIAQ 246

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++  PD+ I  NG +     A++++    VDGV+IGR       +   +   F      
Sbjct: 247 LRELIPDVPILGNGDIFSAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNAFEGSSER 306

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P  T V    +R     +  +          L++I +H+   F G+P
Sbjct: 307 IRPTLTEVSDMIYRHAELLVETFGDETR----GLREIRKHVAWYFKGYP 351


>gi|254419994|ref|ZP_05033718.1| putative TIM-barrel protein, nifR3 family [Brevundimonas sp. BAL3]
 gi|196186171|gb|EDX81147.1| putative TIM-barrel protein, nifR3 family [Brevundimonas sp. BAL3]
          Length = 357

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 107/227 (47%), Gaps = 22/227 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL---QIGGA 57
           M   TD  +R  A  L   A + TEM+ A  + R ++ +++  +     L L   Q+ G 
Sbjct: 27  MTGVTDLPFRVLASRL-GAAYVATEMVAAKELAR-ERPDVVRRAAVGAGLPLTVIQLVGR 84

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D  ++ E A++ E  G + ++LN GCP+  V   + G+ LM  PD+    + A  +A S 
Sbjct: 85  DPGQMAEGARMAEKAGADIVDLNFGCPAKEVTGSAAGSALMRTPDLACRIMEAAVQATSR 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G DD     A   L K  ++ GV  + +H   RK    G++          D
Sbjct: 145 PVTVKMRLGWDDDSRNAA--ELAKRAEEIGVRAVTVHGRTRKQFYTGVA----------D 192

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           +  V E+K     + + +NG +     A + L     DG+M+GR  Y
Sbjct: 193 WAAVGEVKAAV-GIPVIVNGDITTAEAARQALAQSGADGLMLGRGVY 238


>gi|50913499|ref|YP_059471.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10394]
 gi|50902573|gb|AAT86288.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10394]
          Length = 325

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSVFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D+D
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHD 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|254469483|ref|ZP_05082888.1| tRNA-dihydrouridine synthase B [Pseudovibrio sp. JE062]
 gi|211961318|gb|EEA96513.1| tRNA-dihydrouridine synthase B [Pseudovibrio sp. JE062]
          Length = 308

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 58/220 (26%), Positives = 105/220 (47%), Gaps = 17/220 (7%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM+ ++A+  G  ++++    +   P  +Q+ G D   + E A++ E  G + I++
Sbjct: 14  LVVSEMVASEALCTGHPESLMRAEGEGIDPHIVQLAGKDPHWMGEGARMAEKAGADVIDI 73

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM + D     + A  +A+S+PVT+K R+G D+   ++    L
Sbjct: 74  NMGCPAKKVTSGYSGSALMKDLDHAMTLVEATLEAVSVPVTLKMRLGWDEA--SINAPEL 131

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K    +GV  I +H   R    KG            D+  + +++   PD+ +  NG  
Sbjct: 132 AKRAVDAGVKMITVHGRTRSQFYKG----------QADWRAIRQVRDVIPDVPLVANGDC 181

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
                A ++L     D VM+GR AY    +   +  Y   
Sbjct: 182 CSFDDADEMLAQSGADLVMVGRGAYGRPWVPGRIAHYLET 221


>gi|50554003|ref|XP_504410.1| YALI0E26059p [Yarrowia lipolytica]
 gi|49650279|emb|CAG80011.1| YALI0E26059p [Yarrowia lipolytica]
          Length = 359

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 80/289 (27%), Positives = 135/289 (46%), Gaps = 39/289 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R    + ++Y+ M++A    R     +  F+T +   PL +Q+GG +
Sbjct: 51  MVRYSKLPFRALVRHFDCD-VVYSPMMLAREFCRNQTARLCDFTTNKDDFPLIVQLGGNN 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              +V+A K+++ +  + + +N GCP   ++ EG  GA LM  PD+V + +AA+ K    
Sbjct: 110 AEDMVKAVKMLQPY-VDGVGINCGCPIKEQIREG-VGAALMTAPDLVAEMVAAIRKECGA 167

Query: 116 SIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            I V VK RI  D  D +      +  K ++ +G + I +H R      L P+ +R  PN
Sbjct: 168 EIYVEVKMRIHKDLNDTV------HFAKLVEAAGADSISVHGR------LVPQRSRTAPN 215

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
             YD + +I K++ D+ +  NG     +   +I  L   DGVM  R    N AM      
Sbjct: 216 --YDGI-KIVKDSVDVPVIANGDAFTTTNIEEIVELTGCDGVMAARGILSNPAM------ 266

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRH 279
                  G +    R  + FW  ++A    YA    H    L+ ++TR+
Sbjct: 267 -----FAGYTKTPWRAVELFWDYVTAYGLPYALTIHHFSEMLEAELTRY 310


>gi|270290207|ref|ZP_06196433.1| tRNA-dihydrouridine synthase B [Pediococcus acidilactici 7_4]
 gi|304385524|ref|ZP_07367868.1| tRNA-dihydrouridine synthase [Pediococcus acidilactici DSM 20284]
 gi|270281744|gb|EFA27576.1| tRNA-dihydrouridine synthase B [Pediococcus acidilactici 7_4]
 gi|304328028|gb|EFL95250.1| tRNA-dihydrouridine synthase [Pediococcus acidilactici DSM 20284]
          Length = 332

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 87/318 (27%), Positives = 134/318 (42%), Gaps = 46/318 (14%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L+  EMI    I+ G+KK  +++     E P+++QI G     LVEAAK V ++   + 
Sbjct: 37  GLVVCEMISDRGIIYGNKKTLSMMQVDPNEHPMSIQIFGGTKETLVEAAKFVDQNTEADI 96

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP  +V     GA  +L+P+ V + ++ +  A+  PVTVK R G DD+      
Sbjct: 97  IDINMGCPVNKVVNTDAGARWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDDKHIYAVE 156

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L      +    +    RK +  G          + D+DI+ E+  +    F+G NG 
Sbjct: 157 NALAAQRAGAAALAMHGRTRKQMYTG----------HADWDILKEVASQLHIPFMG-NGD 205

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           +     A ++L  V  D VMIGRA   N   L  V  Y ++      P            
Sbjct: 206 VRTPQDAKRMLDEVGADAVMIGRAVLGNPWELQKVAAYLNDGTLIDEP------------ 253

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIG----------LFHGFPNSRRCRHILTVEAGAS 304
             A     A  HLH    L ++    IG             G P+S R +    V   A+
Sbjct: 254 TPAEKIKIAKEHLHG---LVELKGENIGPREFRGQAAYYLKGVPHSARTK----VALNAA 306

Query: 305 TATHHIIETAFNLMIESL 322
                +I+  F+  IE L
Sbjct: 307 ETEQEMIDI-FDRFIEKL 323


>gi|108761670|ref|YP_634429.1| putative tRNA-dihydrouridine synthase [Myxococcus xanthus DK 1622]
 gi|108465550|gb|ABF90735.1| putative tRNA-dihydrouridine synthase [Myxococcus xanthus DK 1622]
          Length = 337

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 116/227 (51%), Gaps = 16/227 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQ-EKPLALQIGGA 57
           M   ++  +R  A  L   AL  TE++ +  ++R +++ +  L +  + E+P +LQI G 
Sbjct: 18  MAGVSEMPFRVLAFRL-GAALCPTELVSSQGLMRANQRTLKYLRYDAEVERPYSLQIYGG 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   +  AA +  + G   I++N+GCP  +V +   G+ L+ +     D +  + +A  +
Sbjct: 77  EPEAMARAAVVGREAGAQIIDINMGCPVKKVVKNGAGSGLLCDVPRAADIVRRIREATGL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R G D +  ++    +  +++++G  G+ IH R         ++       D+ 
Sbjct: 137 PVTCKIRSGWDAR--SLNYLQVAGALQEAGCAGLAIHPRT--------REQGYSGQADWS 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           ++ ++K+  P+L I  NG ++  + A ++L +   D VMIGRAA  N
Sbjct: 187 VIADLKRHFPELPIIGNGDVKTPADAARMLETTGCDFVMIGRAALGN 233


>gi|293364460|ref|ZP_06611186.1| tRNA-dihydrouridine synthase [Streptococcus oralis ATCC 35037]
 gi|291317306|gb|EFE57733.1| tRNA-dihydrouridine synthase [Streptococcus oralis ATCC 35037]
          Length = 318

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 184 TLHKVAQALTKIPFIANGDIRTVQDAKQRVEEVGADAVMIGRAAMGNPYLFNQINHYFE 242


>gi|320547612|ref|ZP_08041897.1| tRNA-dihydrouridine synthase [Streptococcus equinus ATCC 9812]
 gi|320447687|gb|EFW88445.1| tRNA-dihydrouridine synthase [Streptococcus equinus ATCC 9812]
          Length = 325

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ I E+   + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEYIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIIDEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D +
Sbjct: 143 PLTVKMRTGWSDN--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGKCDLE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VM+GRAA  N  + T ++ YF 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVHDAKYMIEEVGVDAVMVGRAAMNNPYIFTQINHYFE 250


>gi|88608299|ref|YP_506262.1| putative tRNA-dihydrouridine synthase [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600468|gb|ABD45936.1| putative tRNA-dihydrouridine synthase [Neorickettsia sennetsu str.
           Miyayama]
          Length = 331

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/225 (32%), Positives = 105/225 (46%), Gaps = 26/225 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  YR   +      L+ +EMI + A++   K  +  +  S +E   A+Q+ G +   +
Sbjct: 23  TDMPYRDLVKSF-GAGLVVSEMIASRAMILKTKDTMKKVSLSPREDITAIQLAGFEPDVM 81

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAKI ED G   I++N GCP  +V  G  G+ LM +       + A  KA+ IPVT+K
Sbjct: 82  AEAAKINEDMGAKIIDINFGCPVKKVVNGYAGSYLMKDECHAAKILEATVKAVKIPVTLK 141

Query: 123 CRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
            R G D+       RN   L K  +  G+  I IH R    + KG S          D+ 
Sbjct: 142 MRTGWDEN-----HRNAPKLAKIAEDLGIKMITIHGRTRAQMYKGKS----------DWQ 186

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
            +  +K   + P +  G     ED  +AL +    DG+MIGR AY
Sbjct: 187 FIRTVKNTVKIPVIANGDIKTYEDAERAL-VESGADGIMIGRGAY 230


>gi|329115748|ref|ZP_08244465.1| TIM-barrel protein, nifR3 family [Streptococcus parauberis NCFD
           2020]
 gi|326906153|gb|EGE53067.1| TIM-barrel protein, nifR3 family [Streptococcus parauberis NCFD
           2020]
          Length = 325

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 116/241 (48%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K +  L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  L  AA  ++     +I ++N+GCP  +V +   GA  + +P+ +   I  +   L I
Sbjct: 83  IEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYQIIKEVTAVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G +D   ++A+ N + + + +GV  + +H R         +        D++
Sbjct: 143 PLTVKMRTGWNDS--SLAVENALAA-ESAGVAALAMHGRT--------RKQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG + ++  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITTIPFIG-NGDVRNVQDAKFMIEEIGVDAVMIGRAAMSNPYLFTQINHFFE 250

Query: 235 N 235
            
Sbjct: 251 T 251


>gi|299535227|ref|ZP_07048551.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
 gi|298729348|gb|EFI69899.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
          Length = 322

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    + KK++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGKKSVRGRLLFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     E +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  K   
Sbjct: 79  DNPVYFREMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKVGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D        + +  I K  +  + IH R         +    + +  +
Sbjct: 138 LPVSVKTRLGYKD---VNEWEDWLTHILKQDIANLSIHLRT--------RKEMSLVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEQYGIDGVMIGRGIFKN 238


>gi|67924974|ref|ZP_00518361.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Crocosphaera
           watsonii WH 8501]
 gi|67853187|gb|EAM48559.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Crocosphaera
           watsonii WH 8501]
          Length = 341

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/307 (22%), Positives = 135/307 (43%), Gaps = 28/307 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R  + N+++YTEM+ A  I    +   ++     E+P+++Q+       + 
Sbjct: 36  TDLVFRRLVRRYSPNSMMYTEMVSATEIHHLKQLPRLMEIDENEQPISIQLFDCRPDFMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+     G   I++N+GCP  ++ +   G+ L+  P +    +A + K++ +PVTVK 
Sbjct: 96  EAAQKAVAEGAKTIDINMGCPVNKITKKGGGSSLLRQPHLAQTLVAEVVKSVEVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYE 181
           RIG DD+   + +    + ++ +G   + +H R      KG          N  ++ + +
Sbjct: 156 RIGWDDK--EINILEFAQKMEDAGAAMLTLHGRTRAQGYKG----------NARWEWIKK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE   + +  NG +  +  A+  L     DGVM  R       ++  +D +F   +  
Sbjct: 204 V-KEILTIPVIANGDIFSVEAAINCLEITGADGVMCSRGTLGYPFLVGEIDHFFCTGIKQ 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR----H 295
           + P   R   +  ++    + +Y  +       + Q  +H+      FP +   R     
Sbjct: 263 NKPT-PREKLECAKEHLQGLWEYKGKR-----GIYQARKHLSWYCKEFPGASELRDKVSR 316

Query: 296 ILTVEAG 302
           I TVE G
Sbjct: 317 IETVEEG 323


>gi|146283597|ref|YP_001173750.1| NifR3 family TIM-barrel protein [Pseudomonas stutzeri A1501]
 gi|145571802|gb|ABP80908.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas stutzeri
           A1501]
          Length = 337

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 124/261 (47%), Gaps = 16/261 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R     AL  +EM+ +D  L   +K+ L    + + +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRF-GAALEVSEMLTSDVRLWNSRKSRLRMPHADEPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ LM +  +V D + A+  A+ +P
Sbjct: 79  PQMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALMRDERLVADILEAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q    A   + +  ++SG+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRQNKNGA--TIARIAEQSGIAALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG ++   +A ++L     DG++IGRAA     +   V+ Y    
Sbjct: 189 IAAI-KQAVSIPVFANGDIDSPHKAARVLQVTGADGLLIGRAAQGRPWIFREVEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISA 257
              ++P    V+      + A
Sbjct: 248 ELLAAPTLGEVESTLLEHVQA 268


>gi|306826116|ref|ZP_07459452.1| tRNA-dihydrouridine synthase [Streptococcus sp. oral taxon 071 str.
           73H25AP]
 gi|304431832|gb|EFM34812.1| tRNA-dihydrouridine synthase [Streptococcus sp. oral taxon 071 str.
           73H25AP]
          Length = 326

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRVEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|328543927|ref|YP_004304036.1| TRNA-dihydrouridine synthase [polymorphum gilvum SL003B-26A1]
 gi|326413671|gb|ADZ70734.1| TRNA-dihydrouridine synthase, putative [Polymorphum gilvum
           SL003B-26A1]
          Length = 310

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 115/241 (47%), Gaps = 26/241 (10%)

Query: 12  FARLLT--NNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL---QIGGADISKLVEAA 66
           F RL +     ++ +EM+ ++++++GD +  +    + K + L   Q+ G +   + EAA
Sbjct: 9   FRRLASRFGAGVVVSEMVASESLVQGDVE--MRTRAEGKGIGLHVVQLAGREARWMAEAA 66

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +I E  G + I++N+GCP+ RV  G  G+ LM + D     I A   A+S+PVTVK R+G
Sbjct: 67  RIAEGAGASIIDINMGCPAKRVTTGYSGSALMRDLDHALGLIEATVGAVSVPVTVKMRLG 126

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            D Q  ++    L +  + +GV  + +H   R    KG +          D+  +  +  
Sbjct: 127 WDAQ--SINAPELARRAQAAGVQLVTVHGRTRNQFYKGAA----------DWAAIRAV-V 173

Query: 185 ENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           E  D+ +  NG     +D  + L  L    GVMIGR AY    ++  V  Y       + 
Sbjct: 174 EAVDIPVIANGDCLSFDDADRMLA-LSGAAGVMIGRGAYGRPWLVGHVGAYLQTGERQAE 232

Query: 242 P 242
           P
Sbjct: 233 P 233


>gi|268602979|ref|ZP_06137146.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID1]
 gi|268683619|ref|ZP_06150481.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-92-679]
 gi|268587110|gb|EEZ51786.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID1]
 gi|268623903|gb|EEZ56303.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-92-679]
          Length = 334

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++   +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|126658167|ref|ZP_01729318.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Cyanothece sp.
           CCY0110]
 gi|126620538|gb|EAZ91256.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Cyanothece sp.
           CCY0110]
          Length = 337

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 75/311 (24%), Positives = 135/311 (43%), Gaps = 36/311 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R  + N+++YTEM+ A  I    +   ++     E+P+++Q+       + 
Sbjct: 36  TDLVFRRLVRRYSPNSMMYTEMVSATEIHHLKQLPRLMEIDPNEQPISIQLFDCRPDFMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+     G   I++N+GCP  ++ +   G+ L+  P+I  + +  + K + IPVTVK 
Sbjct: 96  EAAQKAVGEGAKTIDINMGCPVNKITKKGGGSSLLRQPEIAENLVKEVVKTVDIPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG DD    + +    + ++ +G + + +H R         +      N  ++ + ++K
Sbjct: 156 RIGWDDN--EINILEFAQKMEDAGASMLTLHGRT--------RAQGYTGNARWEWIKKVK 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K      I  NG +  +  A+  L     DGVM  R       ++  +D +F    TG  
Sbjct: 206 KILTIPVIA-NGDIFSVEAAINCLEITGADGVMCSRGTLGYPFLVGEIDYFFQ---TG-- 259

Query: 242 PIKTRVDKDFWRKISASMTDYAARHL-----HSGGK-LQQITRHMIGLFHGFPNSRRCR- 294
                  K+  +  S    + A  HL     + G + + Q  +H+     GF  +   R 
Sbjct: 260 -------KELIKPTSIERLECAKEHLKGLWEYKGKRGIYQARKHLSWYCKGFIGASELRD 312

Query: 295 ---HILTVEAG 302
               I TVE G
Sbjct: 313 KVSRIETVEEG 323


>gi|308048175|ref|YP_003911741.1| tRNA-U20-dihydrouridine synthase [Ferrimonas balearica DSM 9799]
 gi|307630365|gb|ADN74667.1| tRNA-U20-dihydrouridine synthase [Ferrimonas balearica DSM 9799]
          Length = 321

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 121/242 (50%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    L  +EM+ ++ ++   +K++  +  S++    ++QI G +
Sbjct: 19  MAGVTDLPFRQLCRRL-GAGLAVSEMLSSNPLVWATEKSMARMDHSSESGIRSVQIAGCE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+ +PD+V   + A+  A+ +P
Sbjct: 78  PELMAQAAQFNVERGAQIIDINMGCPAKKVNKKLAGSALLRHPDLVRQILHAVVNAVEVP 137

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  +    ++SG+  + +H   R+ + KG            +
Sbjct: 138 VTLKIRTGWDPDNRNGVEIAQIA---EQSGIAALAVHGRTRQCMYKG----------EAE 184

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+ +  + +  NG ++   +A  +L    VDG+MIGR A     +   +  Y 
Sbjct: 185 YDTIAAIKR-SVSIPVIANGDIDSPEKAKFVLDHTGVDGLMIGRPAQGRPWIFREIQHYL 243

Query: 234 SN 235
           + 
Sbjct: 244 AT 245


>gi|114320555|ref|YP_742238.1| nifR3 family TIM-barrel protein [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226949|gb|ABI56748.1| tRNA-U20-dihydrouridine synthase [Alkalilimnicola ehrlichii MLHE-1]
          Length = 356

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 109/245 (44%), Gaps = 22/245 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKL 62
           TD  +R   R     AL  +EM+ AD  LR  +K+      +  E P   QI GAD   L
Sbjct: 48  TDLPFRQLCRQW-GAALAVSEMLSADPTLRKTRKSQWRATLADDECPRVAQIAGADPVAL 106

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+     G   I++N+GCP+ +V     G+ L+ +  +V   + A+  A+ +PVT+K
Sbjct: 107 AEAARYNVQRGAQVIDINMGCPAKKVCNRMAGSALLADEPLVRRILTAVVSAVEVPVTLK 166

Query: 123 CRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            R G     P+   RN V   +  + +GV  + +H R  +       + R +  +   + 
Sbjct: 167 YRTG-----PSPERRNAVAIARMAEDAGVAALTLHGRTRVQAYQGQAEYRSVEAVCRAV- 220

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                   D+ +  NG ++   +A ++L     D VM+GRAA     +   +  Y     
Sbjct: 221 --------DIPVVANGDIDSPDKARQVLDETGADAVMVGRAAQGRPWLFQAIHTYLETGT 272

Query: 238 TGSSP 242
             ++P
Sbjct: 273 RVATP 277


>gi|212696521|ref|ZP_03304649.1| hypothetical protein ANHYDRO_01059 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676457|gb|EEB36064.1| hypothetical protein ANHYDRO_01059 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 321

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 134/288 (46%), Gaps = 35/288 (12%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGY----N 75
           +TEM+  +A+   +KK  ++L  S  EK   +Q+ G   SK     K+++D   Y     
Sbjct: 36  FTEMVSVNALYYDNKKTNDLLFISENEKNCNIQLFG---SKPEVIEKVIKDKINYIEKSK 92

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           EI+ N+GCP A++ +   G+ LM NP +V +    + K+    + +K R+G+DD+   + 
Sbjct: 93  EISFNMGCPVAKITKNGEGSQLMANPKLVEEICKTLRKSTDKKLNIKFRLGIDDK--HIN 150

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
             ++ K  + +G++ + +HAR         KD     N ++D + ++ KEN  + +  NG
Sbjct: 151 YLDIGKIAQDTGIDYVILHAR--------TKDQMYSGNANWDHIRKL-KENLQIPVIANG 201

Query: 196 GLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVDKDFW 252
            +  +   + +  L   DGVM+ R A  N  +   + +Y  +   +  SPI+        
Sbjct: 202 DIFSVEDFINVIDLTKADGVMLARGAMGNPFLFKEIKDYIKTGKYSKPSPIEI------- 254

Query: 253 RKISASMTDYAARHLHSGGKL--QQITRHMIGLFHGFPNSRRCRHILT 298
             I   +  Y     +   KL   Q+ +H+     G  NS + R ++ 
Sbjct: 255 --IDQLIDQYKLELKYKEEKLVVTQMRKHLSWYIKGLENSSKIRDLVN 300


>gi|307702576|ref|ZP_07639528.1| TIM-barrel protein, nifR3 family protein [Streptococcus oralis ATCC
           35037]
 gi|307623692|gb|EFO02677.1| TIM-barrel protein, nifR3 family protein [Streptococcus oralis ATCC
           35037]
          Length = 326

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 117/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRVEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|297568450|ref|YP_003689794.1| hypothetical protein [Desulfurivibrio alkaliphilus AHT2]
 gi|296924365|gb|ADH85175.1| TIM-barrel protein, nifR3 family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 313

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 106/223 (47%), Gaps = 16/223 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R      L Y+EMI    ++R     +  L     E+P+ +Q+ GA+
Sbjct: 22  LAGFSDLAFRLLCREY-GAGLCYSEMISCHGLVRQQPSTLELLATVPAERPVIMQLFGAE 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA I+     + I++N+GCP  +V +   GA LM  P++    + A+ KA  +P
Sbjct: 81  PEVMGQAAAILSRLPIDGIDINMGCPVKKVVKKGAGAALMRQPELAAAIVTAVVKATELP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G + Q   +      +  +  G   I +H R     G S + +++       +
Sbjct: 141 VTVKIRTGWNHQ--RITAPEFARRCEDCGAAAITVHGRT-WSDGFSGRADQR-------L 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           +  +K+      IG NG +    +A+ ++ +   DGVMIGR A
Sbjct: 191 IAAVKQAVKVPVIG-NGDVTCHQEAVAMMANTGCDGVMIGRGA 232


>gi|283458530|ref|YP_003363158.1| tRNA -dihydrouridine synthase [Rothia mucilaginosa DY-18]
 gi|283134573|dbj|BAI65338.1| tRNA-dihydrouridine synthase [Rothia mucilaginosa DY-18]
          Length = 442

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 73/289 (25%), Positives = 124/289 (42%), Gaps = 24/289 (8%)

Query: 10  RFFARLLTN--NALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEA 65
           + F RL +     L  TEM+ A A++  + +   I+     EK  ++QI G D   + +A
Sbjct: 89  KAFRRLCSEYGGGLYVTEMVTARALVERKPESMRIIEHDPDEKIRSIQIYGVDAVNVGKA 148

Query: 66  AK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTV 121
            + +VE+   + I+LN GCP+ +V     GA L    D+    +    K  S   IP+T+
Sbjct: 149 VRMVVEEDRADHIDLNFGCPAPKVTRRGGGAALPWKTDLFTAIVQTAVKEASRNDIPLTI 208

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+DD    +      K  + +GV  I +H R A                D+D + +
Sbjct: 209 KMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTAA--------QHYSGKADWDSIAQ 258

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++  PD+ I  NG +     A++++    VDGV+IGR       +   +   F      
Sbjct: 259 LRELIPDVPILGNGDIFSAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNAFEGSSER 318

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P  T V    +R     +  +          L++I +H+   F G+P
Sbjct: 319 IRPTLTEVSDMIYRHAELLVETFGDETR----GLREIRKHVAWYFKGYP 363


>gi|240015904|ref|ZP_04722444.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA6140]
 gi|240112253|ref|ZP_04726743.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae MS11]
          Length = 364

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 166 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|329121393|ref|ZP_08250018.1| tRNA-dihydrouridine synthase [Dialister micraerophilus DSM 19965]
 gi|327469683|gb|EGF15150.1| tRNA-dihydrouridine synthase [Dialister micraerophilus DSM 19965]
          Length = 327

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 77/302 (25%), Positives = 135/302 (44%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR     A+   EM+ +  +   ++K   +L  +  E P+ALQ+ G  
Sbjct: 20  MAGVSDLAYRVIARK-HGAAMTTAEMVSSRGLYYKNEKTEEMLKIAPDEHPVALQLFGNQ 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK VE+ G + I++N+GCP  +V +   G  +M + D     + AM KA+ +P
Sbjct: 79  AEIMALAAKEVEEAGADVIDINMGCPMQKVVKNGDGCSMMKDIDNSAKVVEAMVKAVKVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D +   +    L K+++ +G   I +H R         ++       D D 
Sbjct: 139 VTVKMRIGWDRE--NLNSPELAKAVEAAGAAAITVHGRT--------REEMYSGKADLDA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  E   + +  NG + D   A +++      GV IGRAA+ N  +   V+ Y  + 
Sbjct: 189 IRKV-VETVKIPVFGNGDIVDGPSAKRMMEETGCVGVAIGRAAWGNPWIFNAVNTYLESG 247

Query: 237 LTGSSP---IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            T   P   ++  + +     +     +Y A        ++++  H    F+G P +   
Sbjct: 248 ETVEEPSWEMRLSMARTHLGNLVKEKGEYTA--------IREMRAHASHYFYGLPKATAL 299

Query: 294 RH 295
           R 
Sbjct: 300 RR 301


>gi|320530154|ref|ZP_08031224.1| TIM-barrel protein, nifR3 family [Selenomonas artemidis F0399]
 gi|320137587|gb|EFW29499.1| TIM-barrel protein, nifR3 family [Selenomonas artemidis F0399]
          Length = 323

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 113/230 (49%), Gaps = 23/230 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   TD  YR  AR +    L + EM+ +  I   ++  +L   ++  E+PLA+QI    
Sbjct: 20  MAGVTDTAYRIIAREM-GCPLAFAEMVSSQGIHYRNEYTLLMLRSEPAERPLAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  +I + N+GCP+ +V +   G+ LM +P    + + A+ +A ++
Sbjct: 79  AAMAAEAAAYIEELGTADILDFNMGCPAPKVVKNGEGSALMRDPKKAEEILKAIRRATTL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           P TVK R+G DD       RN V   +  + +GV+ + +H R         +      + 
Sbjct: 139 PFTVKMRLGWDDDS-----RNAVEIARIAEGAGVDAVAVHGRT--------RAQFYSGSA 185

Query: 175 DYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           DY+ + E+K+    P +  G      D+ +AL I    DGVMIGR A  N
Sbjct: 186 DYEAIAEVKRAVGIPVIVSGDIRRPADLKRALDIT-GADGVMIGRGAQGN 234


>gi|260433535|ref|ZP_05787506.1| NifR3 family protein [Silicibacter lacuscaerulensis ITI-1157]
 gi|260417363|gb|EEX10622.1| NifR3 family protein [Silicibacter lacuscaerulensis ITI-1157]
          Length = 352

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 113/249 (45%), Gaps = 33/249 (13%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TDR +R     F A ++ +  +   EM+ A   +R   +     S   +  A+Q+ 
Sbjct: 44  MAGITDRPFRDLVMRFGAGMVVSEMVASQEMVQAKPGVRERAE----LSADVENTAVQLA 99

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+
Sbjct: 100 GRDAYWMAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALTLIEAVVGAV 159

Query: 116 SIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRK 170
            +PVT+K R+G DD +   P VA R      +++GV  + IH R      KG        
Sbjct: 160 DVPVTLKTRLGWDDTLLNAPDVARRA-----QEAGVQMVTIHGRTRCQFYKG-------- 206

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
               D+  +  + K+   + +  NG +    +A   L     DGVM+GR A     +L  
Sbjct: 207 --EADWAAIRAV-KDAVSIPVVANGDITSPGRAQAALEQSGADGVMVGRGAQGKPWLLAQ 263

Query: 229 V-DEYFSNP 236
           +  E +  P
Sbjct: 264 IAHELWGTP 272


>gi|148262987|ref|YP_001229693.1| nifR3 family TIM-barrel protein [Geobacter uraniireducens Rf4]
 gi|146396487|gb|ABQ25120.1| tRNA-U20-dihydrouridine synthase [Geobacter uraniireducens Rf4]
          Length = 347

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 80/307 (26%), Positives = 140/307 (45%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+   R  AR     AL +TEM+  + ++R  KK  ++L    +++PL +QI G D
Sbjct: 42  MAGLTNLPMRVLARE-CGAALTFTEMVSVNGLVREGKKTFDLLRRDQEDRPLGIQIFGDD 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E A++VE +G   I++N+GCP  +V     G+ L+  P  V   + A+ KA S+P
Sbjct: 101 PDLLAEGARLVEPYG-ELIDINMGCPVRKVVGSGAGSALLREPAKVALILKAVRKATSLP 159

Query: 119 VTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNL 174
           +T+K R G  V++Q    +   + +  +  GV+ + +H  +R  + +G          + 
Sbjct: 160 LTIKIRTGWVVEEQ----SFLEIGRIAEAEGVDAVTLHPRSRAQMFEG----------HA 205

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K       IG +G +   +    +L     DGVMI R    N  +       
Sbjct: 206 DWSRITELKGALSIPVIG-SGDIFSAADVTAMLAQTGCDGVMIARGGLGNPWIFREALAL 264

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMT--DYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               L G  PI   V +    K++A+M   D           L+++ +H+     G P  
Sbjct: 265 ----LRGEEPIPPAVGE----KLAAAMRHLDLFIETFGEHTALREMRKHLSWYAKGVPGV 316

Query: 291 RRCRHIL 297
            + R+++
Sbjct: 317 AQFRNMI 323


>gi|313894860|ref|ZP_07828420.1| TIM-barrel protein, nifR3 family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312976541|gb|EFR41996.1| TIM-barrel protein, nifR3 family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 323

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 113/230 (49%), Gaps = 23/230 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++  +L   ++  E+PLA+QI    
Sbjct: 20  MAGVTDTAYRIIASEM-GCPLAFAEMVSSQGIHYRNEHTLLMLRSEPAERPLAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  +I + N+GCP+ +V +   G+ LM +P    + + A+ +A+ +
Sbjct: 79  AAMAAEAAAYIEELGTADILDFNMGCPAPKVVKNGEGSALMRDPKKAEEILKAIRRAVKL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           P TVK R+G DD       RN V   +  + +GV+ + +H R         ++     + 
Sbjct: 139 PFTVKMRLGWDD-----TSRNAVEIARIAEAAGVDAVAVHGRT--------REQFYSGSA 185

Query: 175 DYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           DY+ + E+K+    P +  G      D+ +AL I    DGVMIGR A  N
Sbjct: 186 DYEAIAEVKRAVGIPVIVSGDIRRPADLRRALAIT-GADGVMIGRGAQGN 234


>gi|257452894|ref|ZP_05618193.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_5R]
 gi|317059436|ref|ZP_07923921.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_5R]
 gi|313685112|gb|EFS21947.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_5R]
          Length = 314

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/298 (23%), Positives = 133/298 (44%), Gaps = 28/298 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  YR        + LL+TEM+ +DA+   + K I           +Q+ G DI K++ 
Sbjct: 13  TDYTYRGILEEFHPD-LLFTEMVSSDALAALNDKTISQILRLRPGNGVQLFGKDIEKMLY 71

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           +AK VE  G   I++N GCP  RV     GA L+ +PD + + ++ + + L     +++K
Sbjct: 72  SAKYVEKLGVKHIDINSGCPMKRVVHSGHGAALLKSPDKIKEILSTLREGLQEDTDLSIK 131

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
            R+G +     + +  + + +   G + I +H R    +  G +          D+ ++ 
Sbjct: 132 IRVGYEKPENYIQIAKIAEEV---GCSHITVHGRTRAQLYTGFA----------DWSLIK 178

Query: 181 EIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           EI KEN  + +  NG +   ED  + ++    VDGVM+ R  + N  ++  + E      
Sbjct: 179 EI-KENVSIPVIGNGDIFTAEDAKEKIE-YSGVDGVMLARGIFGNPWLIREIREILQ--- 233

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +KT+V  +    ++    +  A+       +  + +H+     G  NS  C++
Sbjct: 234 --YGQVKTKVTAEDKINMAIHHIEEIAKDNPQREFVFDVRKHICWYLKGISNSAECKN 289


>gi|227821859|ref|YP_002825829.1| tRNA-dihydrouridine synthase [Sinorhizobium fredii NGR234]
 gi|227340858|gb|ACP25076.1| tRNA-dihydrouridine synthase [Sinorhizobium fredii NGR234]
          Length = 342

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 55/174 (31%), Positives = 91/174 (52%), Gaps = 17/174 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G +   + EAAKIVE  G + +++N+GCP+ +V  G  G+ LM +PD     I
Sbjct: 81  PHIVQLAGREAHWMAEAAKIVEANGADIVDINMGCPAKKVTGGYSGSALMRDPDHALSLI 140

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPK 166
            A  KA+ +PVT+K R+G D+      L  + +  +++GV  I IH R  +    G    
Sbjct: 141 EATVKAVRVPVTLKMRLGWDENSINAPL--IARRAEEAGVQAITIHGRTRMQFYNG---- 194

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
                 N D+D +  ++       I  NG ++ ++ A++IL     D VM+GR+
Sbjct: 195 ------NADWDAIRAVRDVISIPLIA-NGDVDTIADAMEILRRSGADAVMLGRS 241


>gi|268598315|ref|ZP_06132482.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae MS11]
 gi|268582446|gb|EEZ47122.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae MS11]
          Length = 334

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|307267135|ref|ZP_07548645.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|306917855|gb|EFN48119.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter wiegelii
           Rt8.B1]
          Length = 321

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 113/226 (50%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQI G+D 
Sbjct: 17  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEKVALQIFGSDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 76  DIMGEIARRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 135

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K GV  + +H R         ++       D+ I
Sbjct: 136 TVKIRKGWDDNHVNAVEIAQIA---EKVGVKAVAVHGR--------TREQFYSGKADWSI 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + ++ KE+  + +  NG +     A ++L     D ++IGR A  N
Sbjct: 185 IKKV-KESVKIPVMGNGDVFTPEDAKRMLEETGCDAILIGRGAQGN 229


>gi|222152337|ref|YP_002561512.1| tRNA-dihydrouridine synthase [Streptococcus uberis 0140J]
 gi|222113148|emb|CAR40571.1| putative tRNA-dihydrouridine synthase [Streptococcus uberis 0140J]
          Length = 325

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 117/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   ++ +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVSEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRTVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|294677333|ref|YP_003577948.1| tRNA-dihydrouridine synthase B [Rhodobacter capsulatus SB 1003]
 gi|1171718|sp|Q08111|DUS_RHOCA RecName: Full=Probable tRNA-dihydrouridine synthase; AltName:
           Full=Nitrogen regulation protein nifR3
 gi|581498|emb|CAA51073.1| nifR3 [Rhodobacter capsulatus SB 1003]
 gi|294476153|gb|ADE85541.1| tRNA-dihydrouridine synthase B [Rhodobacter capsulatus SB 1003]
          Length = 324

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 47/123 (38%), Positives = 70/123 (56%), Gaps = 4/123 (3%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           RF A L+ +  +   EM+ A   +R   +  L   T   P ++Q+ G + + + EAAKIV
Sbjct: 33  RFGAGLVVSEMVASGEMLTAKPSVRAKAQAEL---TAGLPTSVQLAGREAAPMAEAAKIV 89

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD- 128
            D G   I++N+GCP+ +V  G  GA LM NPD     I A+  A+ +PVT+K R+G D 
Sbjct: 90  ADMGAEIIDINMGCPAKKVTGGLSGAALMRNPDHALRLIEAVVGAVDLPVTLKMRLGWDE 149

Query: 129 DQI 131
           DQ+
Sbjct: 150 DQL 152


>gi|255262537|ref|ZP_05341879.1| probable tRNA-dihydrouridine synthase [Thalassiobium sp. R2A62]
 gi|255104872|gb|EET47546.1| probable tRNA-dihydrouridine synthase [Thalassiobium sp. R2A62]
          Length = 325

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 109/234 (46%), Gaps = 26/234 (11%)

Query: 5   TDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           TD  +R     F A L+ +  +   EM+ +    R  +K  LG    +   ++Q+ G D 
Sbjct: 21  TDLPFRQLVGGFGAGLVVSEMVASQEMVQSKPGAR--EKAELGLGLADT--SVQLAGRDA 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  AA+IVED G   I++N+GCP+ +V  G  G+ LM + D     I A+   + IPV
Sbjct: 77  EWMARAARIVEDSGARLIDINMGCPAKKVTNGYSGSALMRDLDHALTLIDAVVNEVDIPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
           T+K R+G DD +  +    L K  + +GV+ I IH R      KG          + D+ 
Sbjct: 137 TLKTRLGWDDAM--LNAPTLAKRAENAGVSMITIHGRTRCQFYKG----------HADWT 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            +  +K       I  NG + D   A + L S   DGVMIGR A     +L  V
Sbjct: 185 AISAVKDAVTIPVIA-NGDIVDSESARRALTSSGADGVMIGRGAQGLPWLLAQV 237


>gi|225871383|ref|YP_002747330.1| tRNA-dihydrouridine synthase [Streptococcus equi subsp. equi 4047]
 gi|225700787|emb|CAW95466.1| putative tRNA-dihydrouridine synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 325

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 116/241 (48%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQSHTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIQEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + +    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSRAITRIPFIG-NGDVRTVQDARFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250

Query: 235 N 235
            
Sbjct: 251 T 251


>gi|224475660|ref|YP_002633266.1| putative tRNA-dihydrouridine synthase 1 [Staphylococcus carnosus
           subsp. carnosus TM300]
 gi|222420267|emb|CAL27081.1| putative tRNA-dihydrouridine synthase 1 [Staphylococcus carnosus
           subsp. carnosus TM300]
          Length = 331

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 116/235 (49%), Gaps = 19/235 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EM+   AIL  + K  N+L     E+PL+LQI G +   LVEAA  V ++   + I
Sbjct: 37  LVCAEMVSDKAILFNNPKTMNMLYIDENERPLSLQIFGGEKESLVEAAVYVDQNTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  ++     GA  +L+P+ + + ++A+ + +S PVT K RIG D D I AV  
Sbjct: 97  DINMGCPVNKIIRCEAGARWLLDPNKIYEMVSAVTEKVSKPVTCKMRIGWDEDHIYAVEN 156

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
               +    + ++   +H R  +             + D+DI+ ++K+      IG NG 
Sbjct: 157 AKAAERAGAAAIS---LHGRTRV--------QMYEGHADWDIIRQVKEAVNIPVIG-NGD 204

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVD 248
           +     A K+L    VD VMIGR A  N  M+     Y  +  L     +K +V+
Sbjct: 205 VTSPELAQKMLDETGVDAVMIGREALGNPWMIYRTVHYLETGELMDEPTVKEKVE 259


>gi|90407140|ref|ZP_01215328.1| tRNA-dihydrouridine synthase [Psychromonas sp. CNPT3]
 gi|90311716|gb|EAS39813.1| tRNA-dihydrouridine synthase [Psychromonas sp. CNPT3]
          Length = 319

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/257 (26%), Positives = 127/257 (49%), Gaps = 31/257 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD  +R   R L    L  +EM+ ++  +   KK+ L    + +    ++QI GAD
Sbjct: 17  MAGVTDLPFRELCRKL-GAGLAVSEMLSSNPRVWDSKKSRLRMDQRNESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++    G   I++N+GCP+ +V++   G+ L+ +P +V   + ++  A+ +P
Sbjct: 76  PGEMAKAAQVCVQNGAQIIDINMGCPAKKVNKKKAGSALLPHPKLVQAILESVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G D +      RN   + +  ++SG+  + +H   R+ + KG          +
Sbjct: 136 VTLKIRTGWDPEN-----RNGLQIAQIAQQSGIQALAVHGRTRQCLYKG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD + +I KEN  + +  NG +  + +A  +L     D +MIGR A     +   ++ 
Sbjct: 181 AEYDTI-KIIKENVTIPVIANGDITSVEKAKYVLDYTGADAIMIGRGAQGAPWIFNEINH 239

Query: 232 YFSNPLTGS--SPIKTR 246
           Y     TG   SP++ +
Sbjct: 240 YLK---TGEKKSPLEKK 253


>gi|317494239|ref|ZP_07952655.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316918012|gb|EFV39355.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 334

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGMAVSEMLSSNPEVWQTDKSRLRMVHLDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  D G   I++N+GCP+ +V+    G+ L+  PD+VG  ++A+  A+ +P
Sbjct: 76  PDDMAAAAKINADSGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVGKILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN V   +  ++ G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGWSPE-----HRNCVEIAQLAERCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRTV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|95930445|ref|ZP_01313181.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Desulfuromonas
           acetoxidans DSM 684]
 gi|95133485|gb|EAT15148.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Desulfuromonas
           acetoxidans DSM 684]
          Length = 325

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 108/233 (46%), Gaps = 17/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  YR    + +  AL Y+EMI  + ++R   + +  L  +  E P A+Q+ G D
Sbjct: 22  MAGITNSPYRQIV-MESGAALTYSEMISGNGLIRDGLRTLELLKRTLVETPFAVQLFGDD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA I   +G   I+LN+GCP  +V     G+ LM  P  V   I AM +A S+P
Sbjct: 81  PEVLAEAAHIASRYG-ELIDLNMGCPVKKVVRSGAGSALMQEPQKVAKIICAMRQATSLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G    +  +  + + +  +  G + + +H R    +G     N       +  
Sbjct: 140 LTVKIRSGWT--VADINFQLIGQICQDEGADAVILHPRTRC-QGFGGHSN-------WQH 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTV 229
           + ++K+      IG +G +     A  +L     DG+MIGR +Y N  +   +
Sbjct: 190 IRQLKQHLTIPVIG-SGDIITADDAFAMLEQTGCDGIMIGRGSYGNPWLFNAI 241


>gi|90962324|ref|YP_536240.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius UCC118]
 gi|90821518|gb|ABE00157.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius UCC118]
          Length = 330

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 110/223 (49%), Gaps = 21/223 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK  ++L     E P+++QI G     LVEAA+ V E+   + I
Sbjct: 38  LVVCEMISDKGIHFRNKKTLDMLFVDPTEHPVSVQIFGGSKETLVEAAQFVAENTATDII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   GA  +L+PD + + + A+  ++  PVTVK R G D D I  +A+
Sbjct: 98  DINMGCPVPKVTKTDAGARWLLDPDKIYEMVHAVTSSIDKPVTVKMRTGWDEDHI--LAV 155

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + ++ G   + +H   RK +  G          + D+ I+ E+      +    N
Sbjct: 156 ENALAA-EEGGAKALAMHGRTRKQLYTG----------HADWGILKEVADHLTKIPFMGN 204

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G +    +A K+L  V  D VMIGRAA  N  ++     Y   
Sbjct: 205 GDVRTPEEAKKMLDEVGADAVMIGRAALGNPWIVKQTTHYLET 247


>gi|323126378|gb|ADX23675.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 325

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADS--SLAIENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|15828169|ref|NP_302432.1| NifR3/Smm1 family transcriptional regulator [Mycobacterium leprae
           TN]
 gi|221230646|ref|YP_002504062.1| transcriptional regulator (NifR3/Smm1 family) [Mycobacterium leprae
           Br4923]
 gi|2833435|sp|Q50049|DUS_MYCLE RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|699230|gb|AAA62994.1| ntrB [Mycobacterium leprae]
 gi|13093723|emb|CAC31141.1| transcriptional regulator (NifR3/Smm1 family) [Mycobacterium
           leprae]
 gi|219933753|emb|CAR72283.1| transcriptional regulator (NifR3/Smm1 family) [Mycobacterium leprae
           Br4923]
          Length = 384

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 76/291 (26%), Positives = 123/291 (42%), Gaps = 23/291 (7%)

Query: 17  TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
           T + L   EM+ A A++  +   I    F+  E P +LQ+   D +    AAK+V D G 
Sbjct: 46  TISGLYVCEMVTARALVERNAVTIHMTTFAPDESPRSLQLYTVDPATTYTAAKMVADEGL 105

Query: 75  -NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQ 130
            + I++N GCP  +V     GA L     + G  +AA  +A     IPVTVK RIG+DD+
Sbjct: 106 ADHIDMNFGCPMPKVTRRGGGAALPYKRRLFGQIVAAAVRATEGTKIPVTVKFRIGIDDE 165

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                  +  +  +  G   + +HAR A          R     D+  + ++K++   + 
Sbjct: 166 --HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWAQIAQLKQQVRTIP 215

Query: 191 IGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG + D S AL ++     DGV+IGR       +   +   F+     + P    V 
Sbjct: 216 VLGNGDIYDASDALAMMAVTGCDGVVIGRGCLGRPWLFAELSAAFTGRPAPAPPTLGEV- 274

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                +I          H      ++ I +H+    HGFP     R+ L +
Sbjct: 275 ----AEIVRRHGKLLVAHFGEDKGMRDIRKHIAWYLHGFPAGSELRNALAL 321


>gi|227891607|ref|ZP_04009412.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius ATCC 11741]
 gi|227866754|gb|EEJ74175.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius ATCC 11741]
 gi|300214974|gb|ADJ79390.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 330

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 110/223 (49%), Gaps = 21/223 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK  ++L     E P+++QI G     LVEAA+ V E+   + I
Sbjct: 38  LVVCEMISDKGIHFRNKKTLDMLFVDPTEHPVSVQIFGGSKETLVEAAQFVAENTATDII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   GA  +L+PD + + + A+  ++  PVTVK R G D D I  +A+
Sbjct: 98  DINMGCPVPKVTKTDAGARWLLDPDKIYEMVHAVTSSIDKPVTVKMRTGWDEDHI--LAV 155

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + ++ G   + +H   RK +  G          + D+ I+ E+      +    N
Sbjct: 156 ENALAA-EEGGAKALAMHGRTRKQLYTG----------HADWGILKEVADHLTKIPFMGN 204

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G +    +A K+L  V  D VMIGRAA  N  ++     Y   
Sbjct: 205 GDVRTPEEAKKMLDEVGADAVMIGRAALGNPWIVKQTTHYLET 247


>gi|83593011|ref|YP_426763.1| dihydrouridine synthase TIM-barrel protein nifR3 [Rhodospirillum
           rubrum ATCC 11170]
 gi|83575925|gb|ABC22476.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodospirillum
           rubrum ATCC 11170]
          Length = 362

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 116/231 (50%), Gaps = 28/231 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI------LGFSTQEKPLALQI 54
           M   TD  +R  A       L +TEM+ +  +LR   + +         + +  P A+Q+
Sbjct: 19  MAGVTDSPFRRLAHDY-GCPLSWTEMVASRELLRERARGVDPRLGGGAEAGRAGPFAVQL 77

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G D   + EAA+ VE  G   I++N+GCP  +V  G  G+ LM +  +    + A+  A
Sbjct: 78  AGCDPLIMAEAARRVEGAGAELIDINMGCPVRKVVGGLGGSALMRDLPLAARILEAVVGA 137

Query: 115 LSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRK 170
           +++PV++K R+G DD     A RN   L +  + +G++ + +H R +A +      D R 
Sbjct: 138 VTLPVSLKMRLGWDD-----ASRNAVELARLAESAGISRLTVHGRTRAQM-----YDGRA 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
               D+  +  +K+    L +  NG + ++S+A +IL     DGVMIGRAA
Sbjct: 188 ----DWPAIGLVKRAV-SLPVIANGDVTNLSEAREILAVTGADGVMIGRAA 233


>gi|330501709|ref|YP_004378578.1| nifR3 family TIM-barrel protein [Pseudomonas mendocina NK-01]
 gi|328915995|gb|AEB56826.1| nifR3 family TIM-barrel protein [Pseudomonas mendocina NK-01]
          Length = 313

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 71/301 (23%), Positives = 138/301 (45%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 1   MAGVTDRPFRQLCRRL-GAGLVVSEMVTSDVRLWNSRKSSLRLLHAGDPEPRSVQIAGGD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 60  PQMMADAARKNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEPLVREILDAVVGAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q     +  + K  + +G++ + +H R         + +      +Y+ 
Sbjct: 120 VTLKIRTGWDRQNKNGII--VAKIAEDAGISALAVHGRT--------RADLYTGEAEYET 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG ++   +A  +L +   D ++IGRAA     +   ++ Y    
Sbjct: 170 IAAI-KQAVSIPVFANGDIDSPEKAKAVLDATGADALLIGRAAQGRPWIFREIEHYLRTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHG-FPNSRRC 293
               +P    V++     ++A    Y        G+L   +I R  +G +    P +R  
Sbjct: 229 EILPAPSLLEVERILLEHLAALHAFY--------GELMGVRIARKHVGWYLATLPGAREF 280

Query: 294 R 294
           R
Sbjct: 281 R 281


>gi|188532430|ref|YP_001906227.1| tRNA-dihydrouridine synthase B [Erwinia tasmaniensis Et1/99]
 gi|188027472|emb|CAO95319.1| tRNA-dihydrouridine synthase B [Erwinia tasmaniensis Et1/99]
          Length = 321

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 113/240 (47%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 76  PTEMAGAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILSAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L    ++ G+  + IH R    +  G            +
Sbjct: 136 VTLKIRTGWDSDNRNCVEIAQLA---ERCGIQALTIHGRTRACLFNG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQNVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|125975167|ref|YP_001039077.1| nifR3 family TIM-barrel protein [Clostridium thermocellum ATCC
           27405]
 gi|256003170|ref|ZP_05428162.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum DSM
           2360]
 gi|281418412|ref|ZP_06249431.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum JW20]
 gi|125715392|gb|ABN53884.1| tRNA-U20-dihydrouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|255992861|gb|EEU02951.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum DSM
           2360]
 gi|281407496|gb|EFB37755.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum JW20]
 gi|316939332|gb|ADU73366.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum DSM
           1313]
          Length = 322

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 80/308 (25%), Positives = 135/308 (43%), Gaps = 38/308 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L YTEM+ A  I   D+K   +      E  +ALQI G+D
Sbjct: 17  MAGITDIPFRLLCKE-QGCGLTYTEMVSAKGIYYNDEKTKKLTAVDAAEGKVALQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +  + + D     I++N+GCP+ ++ +   G  LM  P++VG  +  + KA   P
Sbjct: 76  PVIMAKVTEQLNDSDACIIDINMGCPTPKITKNGDGCALMRQPELVGKIVREVSKASVKP 135

Query: 119 VTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G D+ +I AV +  +    +++G   I +H R         ++       D+ 
Sbjct: 136 VTVKIRKGWDENRINAVEIARIA---EENGAAAITVHGR--------TREQFYSGKADWS 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+      IG NG +     A ++      D +MIGR A  N  +   + +Y   
Sbjct: 185 IIREVKQSVSIPVIG-NGDVFTPEDARRMFEETNCDAIMIGRGAQGNPWIFRKIIKY--- 240

Query: 236 PLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQ-------QITRHMIGLFHGF 287
            L GS        +DF   IS  +  +   RH+    +L+       ++ +H+     G 
Sbjct: 241 -LEGS--------EDFDLDISLETKINIIKRHMQMLVELKGEQCGVREMRKHIAWYIKGM 291

Query: 288 PNSRRCRH 295
            N+ R + 
Sbjct: 292 RNASRIKE 299


>gi|110633972|ref|YP_674180.1| nifR3 family TIM-barrel protein [Mesorhizobium sp. BNC1]
 gi|110284956|gb|ABG63015.1| tRNA-U20-dihydrouridine synthase [Chelativorans sp. BNC1]
          Length = 354

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 80/306 (26%), Positives = 129/306 (42%), Gaps = 35/306 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADISKLV 63
           TD  +R  A       L+ +EM+ +  + +G  ++       +  + + QI G +   + 
Sbjct: 46  TDLPFRMRA-YAHGAGLVVSEMVASGELAKGRAESARRIRRPDIDVHMVQIAGREARWMA 104

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+I  D G + +++N+GCP+ +V  G  G+ LM  PD     I A+ KA+ +PVTVK 
Sbjct: 105 EAARIAVDEGADIVDINMGCPAKKVTGGYSGSALMREPDHALSLIEAVVKAVDVPVTVKM 164

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G DD    +    L +  + +GV  + +H R         +        ++  + E+K
Sbjct: 165 RLGWDDAC--LNAPELARRAEAAGVAMVTVHGRT--------RCQFYTGQANWKAIAEVK 214

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +    + +  NG  E   +A  +L     D VMIGRA Y        +            
Sbjct: 215 QAV-SIPVVANGDGEGPLEAATMLTQSGADAVMIGRAHYGAPWKAGALAHAADGSAAPGV 273

Query: 242 PIKTRVDKDFWRKISASMTDYAARHL-----HSG-GKLQQITRHMIGLF---HGFPNSRR 292
           P  T           A M DY A H      H G G+  +  R  IG +   H  P+   
Sbjct: 274 PAGT-----------AEMADYVAAHYVDMLSHYGTGQGTRHARKHIGWYLDRHSAPDPAL 322

Query: 293 CRHILT 298
            R I+T
Sbjct: 323 RRSIMT 328


>gi|223982705|ref|ZP_03632935.1| hypothetical protein HOLDEFILI_00209 [Holdemania filiformis DSM
           12042]
 gi|223965301|gb|EEF69583.1| hypothetical protein HOLDEFILI_00209 [Holdemania filiformis DSM
           12042]
          Length = 333

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 55/218 (25%), Positives = 107/218 (49%), Gaps = 15/218 (6%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+YTEMI   AI   +KK   +   +  E P+A+Q+ G + + +++AA++++    + I+
Sbjct: 37  LIYTEMISDKAICYSNKKTMEMTQLAPDEHPIAMQLFGHEEASMIQAAQVLDKTDCDVID 96

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP  +V     G+ +M +P+     +  +   +  PVT K R+G D    ++ +  
Sbjct: 97  INMGCPVPKVVNSGSGSAMMKDPEATYQLVRKIVAVVEKPVTAKIRLGWDSS--SINVLE 154

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + + ++ +GV+ + +H R         +        D+  + ++K+      IG NG L 
Sbjct: 155 MARGLEAAGVSALAVHGRT--------RSQLYEGKADWSWIKKVKEAVSIPVIG-NGDLR 205

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A+  +    VD VMIGR    N  ++  +   FS
Sbjct: 206 SVEDAMARIQETQVDAVMIGRGVLGNPWLIRDLVCAFS 243


>gi|310778159|ref|YP_003966492.1| TIM-barrel protein, nifR3 family [Ilyobacter polytropus DSM 2926]
 gi|309747482|gb|ADO82144.1| TIM-barrel protein, nifR3 family [Ilyobacter polytropus DSM 2926]
          Length = 311

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 75/322 (23%), Positives = 143/322 (44%), Gaps = 28/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  YR   +    + L++TEM+  +A+   ++K I          A+QI G DI 
Sbjct: 8   MAGVTDYTYRRIMKEFHPD-LMFTEMVSVNAVEMANEKTINKMLRLLPDDAVQIFGKDIE 66

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP 118
            +  +AK VE+ G   I++N+GCP  ++ +  +G+ ++ +P+     +  + K+L     
Sbjct: 67  IMKNSAKYVENLGVKHIDVNMGCPVPKIVKNGYGSAMLEDPEHARKMMLELRKSLKPETC 126

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K RIG  +    +      K  +++G   I IH R         K+       D+D+
Sbjct: 127 LSMKIRIGYKNHKDPL---KFAKIAEEAGCEHITIHGRT--------KEQMYSGTADWDV 175

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K +     IG NG +     A +  +   VDGVM+ R  Y N  ++  V E F   
Sbjct: 176 IKDVKSQVNIPVIG-NGDIFTPEDAYEKAMYSKVDGVMLARGIYGNPWLIKQVREIFQEG 234

Query: 237 LTGSSPI-KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              + P  + ++D    + +  +  D+  R  +      +I +H+     G  N+   ++
Sbjct: 235 TVKTIPTAEDKIDMAI-KHVKYAREDHPDRDFYF-----EIRKHLCWYIKGLKNATHGKN 288

Query: 296 ILTVEAGASTATHHIIETAFNL 317
           ++      S +   I+E   NL
Sbjct: 289 LIN----RSESYEEILEILENL 306


>gi|171777588|ref|ZP_02919276.1| hypothetical protein STRINF_00111 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171283197|gb|EDT48621.1| hypothetical protein STRINF_00111 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 325

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ I E+   + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEYIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIIDKVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++       D +
Sbjct: 143 PLTVKMRTGWSDN--ELAVENALAA-ESAGVSALAMHGRT--------REQMYTGKCDLE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VM+GRAA  N  + T ++ YF 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVHDAKYMIEEIGVDAVMVGRAAMNNPYIFTQINHYFE 250


>gi|94993507|ref|YP_601605.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10750]
 gi|94547015|gb|ABF37061.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10750]
          Length = 349

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 216 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 274


>gi|146329061|ref|YP_001209337.1| dihydrouridine synthase [Dichelobacter nodosus VCS1703A]
 gi|146232531|gb|ABQ13509.1| dihydrouridine synthase [Dichelobacter nodosus VCS1703A]
          Length = 318

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 95/180 (52%), Gaps = 13/180 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G D   + E A++++  G + I++N+GCP+ +V + + G+ L+ +   V   +
Sbjct: 69  PKIVQLVGGDPYLMAETAQVMQALGCDVIDINMGCPAKKVGKQNAGSALLSDLPQVEKIL 128

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           A + + +SIPVT+K R+G ++Q   + +  + K  + +GV  + +H R         +  
Sbjct: 129 AQVTRVVSIPVTLKTRLGFNEQ--TMTIETVAKIAENTGVAALTVHGRT--------RAQ 178

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           R      YD +  +K +   L I +NG +   +QA  ++     DGVMIGRAA  N  +L
Sbjct: 179 RFNGTAHYDEIGRVKAQT-SLPIIVNGDITTTAQAQDLIQQFGFDGVMIGRAACGNPWLL 237


>gi|126649588|ref|ZP_01721829.1| hypothetical protein BB14905_06608 [Bacillus sp. B14905]
 gi|126593913|gb|EAZ87836.1| hypothetical protein BB14905_06608 [Bacillus sp. B14905]
          Length = 324

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    + +K++ G   F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRQVVSEAGRPDVFFTEFTNSDSYCHPEGQKSVRGRLIFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 81  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D          +  I K  +  + IH R    K +S  D        +
Sbjct: 140 LPVSVKTRLGYKD---VEEWEEWLTHIFKQDIANLSIHLRTR--KEMSQVDAH------W 188

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 189 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFKN 240


>gi|94989615|ref|YP_597715.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10270]
 gi|94543123|gb|ABF33171.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10270]
          Length = 349

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 115/240 (47%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K +  L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 216 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 274


>gi|94263194|ref|ZP_01287011.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
 gi|93456412|gb|EAT06532.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
          Length = 313

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 112/241 (46%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R      L Y+EM+    ++R     I  L  +  E+PL +Q+ GA+
Sbjct: 20  LAGYSDLPFRLLCREY-GAGLCYSEMLSCHGLVRRQPATIEMLATTAAERPLLMQLFGAE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              + EAA I+     + I++N+GCP  +V +   GA LM +P++      A+  A   +
Sbjct: 79  PEVMGEAAAILSRLPIDGIDINMGCPVRKVVKKGAGAALMRDPELAAAITGAVTAAAGDL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G + +   +   +  + +   G   + IHAR     G + +        D+ 
Sbjct: 139 PVTVKIRSGWNHK--QINAPDFARLLVAHGAAAVTIHART-WSDGFTGRA-------DWA 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++  +K+      IG NG +    QAL ++ +   DGVMIGR A     + T   E   N
Sbjct: 189 VIAAVKRAVSVPVIG-NGDIGSYEQALAMMAATGCDGVMIGRGALGAPWVFTPGAE--QN 245

Query: 236 P 236
           P
Sbjct: 246 P 246


>gi|262368472|ref|ZP_06061801.1| tRNA-dihydrouridine synthase B [Acinetobacter johnsonii SH046]
 gi|262316150|gb|EEY97188.1| tRNA-dihydrouridine synthase B [Acinetobacter johnsonii SH046]
          Length = 341

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 116/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ +D  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRSLCKYFGAGHAV-SEMMTSDQTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PKELAEAARYQVSNGAQIVDINMGCPAKKVCNKLAGSALLKDEDLVARILDEVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + LR + K  + +G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGHENI-LR-VAKRAEDAGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + ++ K+   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 186 IKDV-KQLIRIPVVANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241


>gi|300814628|ref|ZP_07094879.1| TIM-barrel protein, nifR3 family [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300511247|gb|EFK38496.1| TIM-barrel protein, nifR3 family [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 310

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 121/237 (51%), Gaps = 26/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY--TEMIVADAILRGDKK--NILGFSTQEKPLALQIGG 56
           M  +TDR +R   +L+  N L +  TEM+ A A+   D+K   +L     EK   +QI  
Sbjct: 9   MAGYTDRAFR---QLIYENGLDHAVTEMVSAKALCFNDRKTLELLKKFPGEKNTGVQIFA 65

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D+  + +A+ ++ DF ++ I++N+GCP+ ++ +   G+ L+ NP++V + +    K  +
Sbjct: 66  SDVESISKASYLLNDFDFSYIDINMGCPAPKIVKNGCGSALIKNPNLVYELVKGAVKNSN 125

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNL 174
             +++K R   D+ +      +++++ + +G   + +H  +R+   K  S          
Sbjct: 126 KKISIKTRKSFDNTLSL----DIIRAAQDAGAFAVTVHPRSREEYYKNKS---------- 171

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           D+  + +IKK      IG NG +  +  AL  +    VDG+ IGR A +N  + + +
Sbjct: 172 DWQYLIKIKKFLTIPLIG-NGDILTVEDALYKIKKYDVDGIAIGRGAIENPLIFSQI 227


>gi|296114943|ref|ZP_06833589.1| TIM-barrel protein, nifR3 family [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978501|gb|EFG85233.1| TIM-barrel protein, nifR3 family [Gluconacetobacter hansenii ATCC
           23769]
          Length = 385

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 108/221 (48%), Gaps = 18/221 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLV 63
           TD  +R  AR L    L+ +EMI + A++R +   +         L A+Q+ G D   + 
Sbjct: 59  TDLPFRRLARRL-GAGLVVSEMIASWAMVRENSNTLRMAEVAGDGLNAVQLAGCDPDAMA 117

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +AA+I  D G N I++N GCP  +V  G   G+ LM +  +    +A + +A+ +PVT+K
Sbjct: 118 QAARIAVDRGANLIDINFGCPVKKVAVGQQAGSALMRDEALAARLLATVVRAVDVPVTLK 177

Query: 123 CRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R+G D D + A     L +  +++G+  + +H R         +        D+  V  
Sbjct: 178 MRMGWDHDSLNAP---TLARIAQEAGIRMVTVHGRT--------RQQFYNGTADWRFVRR 226

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + KE  DL + +NG +  +  A + L     DGVMIGR  Y
Sbjct: 227 V-KEAIDLPVIVNGDILTVGDAREALAQSGADGVMIGRGCY 266


>gi|15896446|ref|NP_349795.1| NifR3 family protein [Clostridium acetobutylicum ATCC 824]
 gi|15026269|gb|AAK81135.1|AE007815_5 NifR3 family enzyme [Clostridium acetobutylicum ATCC 824]
 gi|325510604|gb|ADZ22240.1| NifR3 family enzyme [Clostridium acetobutylicum EA 2018]
          Length = 321

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 111/210 (52%), Gaps = 22/210 (10%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEI 77
           L YTEM+ A A+  G +  + ++  S +E+  A+Q+ G++   + +A  K  ED     I
Sbjct: 36  LTYTEMVSAKALYYGSENTEELMKISDEEEYAAVQMFGSEPDIMAKACEKFNEDDKICII 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP+ ++ +   G+ LM +P +  + + A+ KA + PVTVK R G D D I AV  
Sbjct: 96  DINMGCPAHKIVKNGEGSALMKSPKLAYEIVKAVKKASNKPVTVKFRKGFDEDNINAV-- 153

Query: 137 RNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               K I+ +G + I +H R    + +G +          D+DI+  +KK      IG N
Sbjct: 154 -EFAKVIEDAGADMITVHGRTRAQMYEGKA----------DWDIIKAVKKSVSIPVIG-N 201

Query: 195 GGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           G +     A+++L   + DGVM+ RAA  N
Sbjct: 202 GDIVSGEDAVRMLEYTNCDGVMVARAAMGN 231


>gi|209549216|ref|YP_002281133.1| hypothetical protein Rleg2_1617 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209534972|gb|ACI54907.1| TIM-barrel protein, nifR3 family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 315

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 102/211 (48%), Gaps = 18/211 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +RF A L+    ++ +  +V D      +    GF    +P  +Q+ G +   + EAAKI
Sbjct: 23  WRFGAGLVVTE-MVASRELVNDTAESWSRLRAAGF----RPHMVQLAGREAHWMAEAAKI 77

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
             D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+K R+G D
Sbjct: 78  AADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPVTLKMRLGWD 137

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   ++    + +  + +G+  + IH R      +   + R     D+D +  ++     
Sbjct: 138 EN--SINAPEIARRAEAAGIQLVTIHGRTR----MQFYEGRA----DWDAIRPVRDVISI 187

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             I  NG +E    A +IL     D VMIGR
Sbjct: 188 PLIA-NGDVETAEDAQEILRRSGADAVMIGR 217


>gi|71902768|ref|YP_279571.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS6180]
 gi|71801863|gb|AAX71216.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS6180]
          Length = 349

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 216 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 274


>gi|19745298|ref|NP_606434.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS8232]
 gi|306828200|ref|ZP_07461461.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes ATCC 10782]
 gi|19747397|gb|AAL96933.1| hypothetical protein spyM18_0122 [Streptococcus pyogenes MGAS8232]
 gi|304429578|gb|EFM32626.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes ATCC 10782]
          Length = 325

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|15674339|ref|NP_268513.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes M1 GAS]
 gi|21909631|ref|NP_663899.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS315]
 gi|28895009|ref|NP_801359.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes SSI-1]
 gi|71909918|ref|YP_281468.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS5005]
 gi|209558683|ref|YP_002285155.1| putative transcriptional regulator [Streptococcus pyogenes NZ131]
 gi|4033718|gb|AAC97155.1| unknown [Streptococcus pyogenes]
 gi|13621424|gb|AAK33234.1| possible transcriptional regulator [Streptococcus pyogenes M1 GAS]
 gi|21903813|gb|AAM78702.1| putative transcriptional regulator [Streptococcus pyogenes MGAS315]
 gi|28810254|dbj|BAC63192.1| putative transcriptional regulator [Streptococcus pyogenes SSI-1]
 gi|71852700|gb|AAZ50723.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS5005]
 gi|209539884|gb|ACI60460.1| putative transcriptional regulator [Streptococcus pyogenes NZ131]
          Length = 325

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|298491317|ref|YP_003721494.1| TIM-barrel protein ['Nostoc azollae' 0708]
 gi|298233235|gb|ADI64371.1| TIM-barrel protein, nifR3 family ['Nostoc azollae' 0708]
          Length = 351

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 74/300 (24%), Positives = 131/300 (43%), Gaps = 24/300 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  +        I+     E+P+++Q+       L 
Sbjct: 36  TDMVFRRLVRRYAPESMMYTEMVNATGLHYVKHLPKIMEVDPNERPISIQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + +++N+GCP  ++ +   G+ L+  PD+    +  + KA+ +PVTVK 
Sbjct: 96  EAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPDVAEAIVREVVKAVDVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG +DQ   + + +  K ++ +G   I +H R    +G +        N  ++ + ++K
Sbjct: 156 RIGWNDQ--EITILDFAKRMEDAGAQMITVHGRTRA-QGYN-------GNARWEWIGQVK 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTG 239
           +      IG NG +  +  A+K L     DGVM  R       ++  VD +      L  
Sbjct: 206 EVLSIPVIG-NGDIFSVEAAVKCLEETGADGVMCSRGTLGYPFLVGEVDHFLKTGELLPP 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PI+        R   A    YA         ++Q  +HM     GF  +   R  L++
Sbjct: 265 PNPIQ--------RMECAREHLYALWEYKGDRGVRQARKHMTWYAKGFVGAAELRGYLSL 316


>gi|156740075|ref|YP_001430204.1| nifR3 family TIM-barrel protein [Roseiflexus castenholzii DSM
           13941]
 gi|156231403|gb|ABU56186.1| putative TIM-barrel protein, nifR3 family [Roseiflexus castenholzii
           DSM 13941]
          Length = 335

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 91/327 (27%), Positives = 153/327 (46%), Gaps = 26/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MV  TD  +R     L    L+ +EM  A A+      +   L +  +E+P+A+Q+ G++
Sbjct: 25  MVGVTDSIFRRMILSLGGCGLVCSEMTNASAVSPRARSRHRQLDYLPEERPIAMQLSGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++VE  G + +++N GCPS +V  G  G+ L+ +   +   + A+C A+ IP
Sbjct: 85  PDLVAAAARVVEALGADILDINCGCPSPKVTGGGHGSALLRDLPKMERLLKAVCAAVQIP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD+   +   +  K  ++ GV  + +H R    +G S          D+  
Sbjct: 145 VTLKFRAGWDDE--NLNYLDTAKMAEQVGVAALALHPRTRA-QGYSGV-------ADWRR 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K+      IG +G + D + AL+ L     DGVMIGRAA  N  +   + +  +  
Sbjct: 195 VADVKRAVRIPVIG-SGDVRDAADALRRLRESGADGVMIGRAAMHNPWIFRQIAQLRA-- 251

Query: 237 LTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCR 294
             G+ P + T  DK  +      M   A     +  KL+Q    +IG F    P +   R
Sbjct: 252 --GTQPMVVTPSDKYEFLMHYLDMCHEALPERLALNKLKQ----LIGQFGIELPGAAALR 305

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             +   +G + A  H +E  F   +E+
Sbjct: 306 SAIHHSSGVAEARDH-LERFFAQYVET 331


>gi|259906958|ref|YP_002647314.1| tRNA-dihydrouridine synthase B [Erwinia pyrifoliae Ep1/96]
 gi|224962580|emb|CAX54035.1| tRNA-dihydrouridine synthase B [Erwinia pyrifoliae Ep1/96]
 gi|283476752|emb|CAY72590.1| putative dehydrogenase [Erwinia pyrifoliae DSM 12163]
          Length = 286

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 58/220 (26%), Positives = 107/220 (48%), Gaps = 21/220 (9%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  +    K+ L     ++P    +QI G D  ++ EAA+I    G   I+
Sbjct: 1   MTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRTVQIAGCDPQEMAEAARINAASGAQVID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALR 137
           +N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +PVT+K R G D D    V + 
Sbjct: 61  INMGCPAKKVNRKMAGSALLQHPELVKSILSAVVNAVDVPVTLKIRTGWDSDNRNCVEIA 120

Query: 138 NLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            L    ++ G+  + IH R    +  G          + +YD +  + K+N  + +  NG
Sbjct: 121 QLA---ERCGIQALTIHGRTRACLFNG----------DAEYDSIRTV-KQNVSIPVIANG 166

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 167 DITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 206


>gi|94987736|ref|YP_595837.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS9429]
 gi|94991604|ref|YP_599703.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS2096]
 gi|94541244|gb|ABF31293.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS9429]
 gi|94545112|gb|ABF35159.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS2096]
          Length = 349

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 216 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 274


>gi|261392320|emb|CAX49847.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis 8013]
          Length = 336

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|150396307|ref|YP_001326774.1| nifR3 family TIM-barrel protein [Sinorhizobium medicae WSM419]
 gi|150027822|gb|ABR59939.1| putative TIM-barrel protein, nifR3 family [Sinorhizobium medicae
           WSM419]
          Length = 337

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 54/172 (31%), Positives = 92/172 (53%), Gaps = 13/172 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G +   + EAA+IVE  G + I++N+GCP+ +V  G  G+ LM +PD     I
Sbjct: 76  PHIVQLAGREAHWMAEAARIVEANGADIIDINMGCPAKKVTGGYSGSALMRDPDHALSLI 135

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A  KA ++PVT+K R+G D+      L  + +  +++GV  I IH R   ++  + K  
Sbjct: 136 EATVKAATVPVTLKMRLGWDENSINAPL--IARRAEEAGVKAITIHGRTR-MQFYNGK-- 190

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
                 D+D +  +++      I  NG ++ ++ A +IL     D VM+GR+
Sbjct: 191 -----ADWDAIRSVREVTSVPLIA-NGDVDSVADAHEILRRSGADAVMVGRS 236


>gi|229916707|ref|YP_002885353.1| dihydrouridine synthase DuS [Exiguobacterium sp. AT1b]
 gi|229468136|gb|ACQ69908.1| dihydrouridine synthase DuS [Exiguobacterium sp. AT1b]
          Length = 330

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 103/228 (45%), Gaps = 14/228 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+      +G  +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVAHAGRPDVFFTEFANSDSYCHPEGKGSLRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + GY  +++N+GCP   V +   G+ L+L P++  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAEMGYKGLDINMGCPVPNVAKRGKGSGLILRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPV+VK R+G          R+ +  + K  +  + IH R              IP    
Sbjct: 138 IPVSVKTRLGF---AKLDEWRDWLTHLLKQDIANLSIHLRTRNEMSKVDAHWEMIP---- 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           DIV    +  PD  I +NG + D    L+++    VDGVMIGR  +KN
Sbjct: 191 DIVKLRDEIAPDTLITINGDILDRQMGLELVEKYGVDGVMIGRGIFKN 238


>gi|86138358|ref|ZP_01056932.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. MED193]
 gi|85824883|gb|EAQ45084.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. MED193]
          Length = 310

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 108/231 (46%), Gaps = 20/231 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKL 62
           TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G + S +
Sbjct: 5   TDRPFRDLVRSF-GVGLMVSEMVASQEMVQSKPGVRERAELSADVENTAVQLAGREASWM 63

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+ +A+ IPVT+K
Sbjct: 64  AEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVEAVDIPVTLK 123

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
            R+G DD    +   ++    + +G+  + IH R      KG +          D+  + 
Sbjct: 124 TRLGWDDN--CLNAASVAARAEAAGIQMVTIHGRTRCQFYKGRA----------DWSAIR 171

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            + KE   L +  NG + D + A   L     DGVMIGR       +L  V
Sbjct: 172 AV-KEAVGLPVLANGDIVDSATATSALERSGADGVMIGRGIQGKPWLLAQV 221


>gi|146340809|ref|YP_001205857.1| putative tRNA-dihydrouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146193615|emb|CAL77632.1| putative tRNA-dihydrouridine synthase (Nitrogen regulation protein
           nifR3) [Bradyrhizobium sp. ORS278]
          Length = 317

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 107/221 (48%), Gaps = 21/221 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLV 63
           TD  +R  A  L    L+ +EM  +D ++RG   + L        P  +Q+ G +   + 
Sbjct: 5   TDAPFRRLAAEL-GAGLVVSEMTASDDLVRGRWISRLRCEAGGIGPHVVQLAGCEAHWMA 63

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E AK+  D G + I++N+GCP+  V  G  G+ LM + D     I A  +A+ +PVT+K 
Sbjct: 64  EGAKVAADGGADIIDINMGCPARHVTGGQSGSALMRDLDHALTLIEATVEAVDVPVTLKM 123

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D++  ++    L +  + +GV  I +H   R+   KG            D+  V  
Sbjct: 124 RLGWDER--SLNAPELARRAEAAGVQLITVHGRTRQQFYKG----------EADWSAVRA 171

Query: 182 IKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           + K+  DL + +NG +   ED  +AL      D VMIGR A
Sbjct: 172 V-KQAVDLPVVVNGDITSYEDAREALDA-SGADAVMIGRGA 210


>gi|325128475|gb|EGC51355.1| dihydrouridine synthase [Neisseria meningitidis N1568]
          Length = 374

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 174 VTLKTRLGWHDDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 218

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 219 ARYELIAETKCR-LNIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|167038941|ref|YP_001661926.1| nifR3 family TIM-barrel protein [Thermoanaerobacter sp. X514]
 gi|300913469|ref|ZP_07130786.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter sp. X561]
 gi|307723516|ref|YP_003903267.1| NifR3 family TIM-barrel domain-containing protein
           [Thermoanaerobacter sp. X513]
 gi|166853181|gb|ABY91590.1| putative TIM-barrel protein, nifR3 family [Thermoanaerobacter sp.
           X514]
 gi|300890154|gb|EFK85299.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter sp. X561]
 gi|307580577|gb|ADN53976.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter sp. X513]
          Length = 347

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 110/226 (48%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   L     E + +ALQI G+D 
Sbjct: 40  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKLLTDIDEGESVALQIFGSDP 98

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 99  DIMGEIAKRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 158

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K GV  + +H R         ++       D+ I
Sbjct: 159 TVKIRKGWDDNHVNAVEIAQIA---EKVGVKAVAVHGR--------TREQFYSGKADWSI 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + ++K+      IG NG +     A ++L     D ++IGR A  N
Sbjct: 208 IKKVKESVKIPVIG-NGDIFTPEDAKRMLEETGCDAILIGRGAQGN 252


>gi|183219434|ref|YP_001837430.1| putative tRNA-dihydrouridine synthase [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
 gi|189909580|ref|YP_001961135.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167774256|gb|ABZ92557.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167777856|gb|ABZ96154.1| Putative tRNA-dihydrouridine synthase [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 337

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 112/228 (49%), Gaps = 20/228 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  YR   +    +A  YTE +  + +  G+ K  ++  F   E+P+  QI G+D
Sbjct: 18  MAGISDSPYRQITKRF-GSAFSYTEFVSTEQLKLGNAKSLDMFRFVEMERPIVFQIFGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +V A++I  +   + I+LN+GC  ++V     GA L+ N  + G  I  +    ++P
Sbjct: 77  LDTVVNASEIAAEQKPDIIDLNMGCSVSKVSHNGSGAGLLKNIRLAGKMIEGIRNRTNLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL--KGLSPKDNRKIPNLDY 176
           VT K R+G D    ++     +K ++ SGV+ I +H R   +   G++          D+
Sbjct: 137 VTAKIRLGWDAN--SLNYLETLKVLEDSGVSAISVHGRTKAMAYTGIA----------DW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKN 222
           + + EIK    ++ I  NG ++   +AL  K    VD V+IGR A  N
Sbjct: 185 NAIGEIKSR-ANVPIYGNGDVQSYKEALEKKKTYGVDLVLIGRKAIGN 231


>gi|282882553|ref|ZP_06291174.1| probable tRNA-dihydrouridine synthase [Peptoniphilus lacrimalis
           315-B]
 gi|281297695|gb|EFA90170.1| probable tRNA-dihydrouridine synthase [Peptoniphilus lacrimalis
           315-B]
          Length = 310

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 121/237 (51%), Gaps = 26/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY--TEMIVADAILRGDKK--NILGFSTQEKPLALQIGG 56
           M  +TDR +R   +L+  N L +  TEM+ A A+   D+K   +L     EK   +QI  
Sbjct: 9   MAGYTDRAFR---QLIYENGLDHAVTEMVSARALCFNDRKTLELLKKFPGEKNTGVQIFA 65

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D+  + +A+ ++ DF ++ I++N+GCP+ ++ +   G+ L+ NP++V + +    K  +
Sbjct: 66  SDVESISKASYLLNDFDFSYIDINMGCPAPKIVKNGCGSALIKNPNLVYELVKGAVKNSN 125

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNL 174
             +++K R   D+ +      +++++ + +G   + +H  +R+   K  S          
Sbjct: 126 KKISIKTRKSFDNTLSL----DIIRAAQDAGAFAVTVHPRSREEYYKNKS---------- 171

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           D+  + +IKK      IG NG +  +  AL  +    VDG+ IGR A +N  + + +
Sbjct: 172 DWQYLIKIKKFLTIPLIG-NGDILTVEDALYKIKKYDVDGIAIGRGAIENPLIFSQI 227


>gi|218288833|ref|ZP_03493084.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           LAA1]
 gi|218240922|gb|EED08099.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           LAA1]
          Length = 328

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 117/232 (50%), Gaps = 22/232 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+ L    ++  EM+    ++ G++K+  +      E P++LQ+ G D++ + +AA
Sbjct: 27  FRRLAKEL-GAGMVCAEMVSDKGLVSGNEKSKKMTTILPDEHPVSLQLVGYDLASMEQAA 85

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           ++V +   + I++N+GCP  ++ +   GA L  +P+     + A+   ++ PVTVK R G
Sbjct: 86  EMVGETNADLIDINMGCPVLKICKTGSGAALARDPNYAAKIVRAVVSRVNKPVTVKFRKG 145

Query: 127 V-DDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIK 183
             DD + AV    +  +++++G   + +H R  K +  G +          D+DI+  +K
Sbjct: 146 WDDDHVNAV---EVALAVQEAGAQAVAVHGRTAKQMYSGKA----------DWDIIRRVK 192

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           +      IG NG + D   A +++     D VM+GRAA  N  +   +  Y 
Sbjct: 193 EAVRIPVIG-NGDVVDPISAKRLMEETGCDAVMVGRAALGNPWIFREIAHYL 243


>gi|38604694|sp|O52539|DUSB_ERWCA RecName: Full=tRNA-dihydrouridine synthase B
 gi|3885444|gb|AAC77892.1| yhdG homolog [Pectobacterium carotovorum]
          Length = 321

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  A +I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAARRINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   K  +  G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTIHGRTRACLFNGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQAVSIPIIA-NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|258512048|ref|YP_003185482.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257478774|gb|ACV59093.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
          Length = 328

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 117/232 (50%), Gaps = 22/232 (9%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+ L    ++  EM+    ++ G++K+  +      E P++LQ+ G D++ + +AA
Sbjct: 27  FRRLAKEL-GAGMVCAEMVSDKGLVSGNEKSKKMTTILPDEHPVSLQLVGYDLASMEQAA 85

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           ++V +   + I++N+GCP  ++ +   GA L  +P+     + A+   ++ PVTVK R G
Sbjct: 86  EMVGETNADLIDINMGCPVLKICKTGSGAALARDPNYAAKIVRAVVSRVNKPVTVKFRKG 145

Query: 127 V-DDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIK 183
             DD + AV    +  +++++G   + +H R  K +  G +          D+DI+  +K
Sbjct: 146 WDDDHVNAV---EVALAVQEAGAQAVAVHGRTAKQMYSGKA----------DWDIIRRVK 192

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           +      IG NG + D   A +++     D VM+GRAA  N  +   +  Y 
Sbjct: 193 EAVRIPVIG-NGDVVDPISAKRLMEETGCDAVMVGRAALGNPWIFREIAHYL 243


>gi|251781585|ref|YP_002995886.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390213|dbj|BAH80672.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 354

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 53  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 111

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 112 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 171

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 172 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 220

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 221 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 279


>gi|169830345|ref|YP_001716327.1| nifR3 family TIM-barrel protein [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637189|gb|ACA58695.1| putative TIM-barrel protein, nifR3 family [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 334

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 82/300 (27%), Positives = 141/300 (47%), Gaps = 20/300 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M   TDR +R  AR +    L +TEMI A A+++G+++   L   + E P+A+Q+ G+D 
Sbjct: 19  MAGITDRAFRDLAREM-GCGLTWTEMISAQALIQGNRRTAELLEVSGEHPIAVQVFGSDP 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + +V AA++  + G + ++LN+GCP+ ++ +   GA LM +P+  G+ +AA+  A+ +PV
Sbjct: 78  NTMVRAARLAAEAGADIVDLNMGCPTPKIVKSCEGAALMRDPERAGEIVAAVAAAVPVPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D+  P+        +   +    +    R     G +          D+ ++
Sbjct: 138 TVKMRKGWDEGYPSAVELARAVAQAGAAAVTVHGRLRSEFFGGRA----------DWSVI 187

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+      IG NG +     A ++L     D VMIGRAA  N  +   V +      
Sbjct: 188 GAVKQAVSIPVIG-NGDVRIGPDAARMLAETRCDAVMIGRAALGNPWVFRQVRDCLE--- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           TG  P    +D+     ++    D   R+      +Q++ +H      G   S R R  L
Sbjct: 244 TGQEPPPPTMDERV--AMALRHFDLLIRYKGEARAVQEMRKHAAWYTRGLRGSARLRERL 301


>gi|54022573|ref|YP_116815.1| putative dihydrouridine synthase [Nocardia farcinica IFM 10152]
 gi|54014081|dbj|BAD55451.1| putative dihydrouridine synthase [Nocardia farcinica IFM 10152]
          Length = 382

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 71/297 (23%), Positives = 125/297 (42%), Gaps = 24/297 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT-EMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R   +   +Y  EMI A A++  ++K  +++ F   E P ++Q+ G 
Sbjct: 27  MAGITNLAFRKLCREFGSATSIYVCEMITARAVVERNEKTLHMMSFDADEHPRSMQLYGV 86

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D   L EA +I+   G+ + I++N+GCP  +V     GA L     +    + AM  A  
Sbjct: 87  DPQTLGEAVRIIVGEGWADHIDMNLGCPVPKVTRLGGGAALPYKRALFARIVRAMVAAAE 146

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVTVK RIG+DD        +  +  +  G   + +HAR A          R    
Sbjct: 147 PAGVPVTVKFRIGIDDD--HHTYLDTGRIAEAEGARAVSLHARTAA--------QRYSGQ 196

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            D+  +  +K+    + +  NG +     A++++     DGV++GR       +   +  
Sbjct: 197 ADWSAIARLKEAVTTIPVLGNGDIFAAEDAVRMMAETGCDGVVVGRGCLGRPWLFAELQA 256

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                     P   RV +  +R  +       + HL     ++ + +HM     GFP
Sbjct: 257 ALRGQPLPEPPNLGRVGEVLYRHGA-----LLSEHLGEDKAMRDLRKHMAWYLMGFP 308


>gi|55820279|ref|YP_138721.1| putative transcriptional regulator [Streptococcus thermophilus LMG
           18311]
 gi|55736264|gb|AAV59906.1| possible transcriptional regulator [Streptococcus thermophilus LMG
           18311]
          Length = 350

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 118/240 (49%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+  +   L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 49  MAGVTNSAFRTIAKEFSA-GLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 107

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 108 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++     + D++
Sbjct: 168 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGR--------TREQMYTGHCDHE 216

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG + ++  A  ++    VD VM+GRAA  N  + T ++ +F 
Sbjct: 217 TLARVAKAITKIPFIG-NGDVRNVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFE 275


>gi|261404875|ref|YP_003241116.1| dihydrouridine synthase DuS [Paenibacillus sp. Y412MC10]
 gi|261281338|gb|ACX63309.1| dihydrouridine synthase DuS [Paenibacillus sp. Y412MC10]
          Length = 329

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 105/235 (44%), Gaps = 28/235 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPDGNHSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V E   G+ L+  PDI  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPDIAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   VD+       R+ +  I K  +  + IH R         ++     +
Sbjct: 138 LPVSVKTRLGFSAVDE------WRDWLTHILKQDIVNLSIHLRT--------REEMSKVD 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 184 AHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFHN 238


>gi|15677280|ref|NP_274433.1| nifR3 protein [Neisseria meningitidis MC58]
 gi|7226660|gb|AAF41782.1| nifR3 protein [Neisseria meningitidis MC58]
 gi|316985807|gb|EFV64750.1| TIM-barrel , nifR3 family protein [Neisseria meningitidis H44/76]
 gi|325140374|gb|EGC62895.1| dihydrouridine synthase [Neisseria meningitidis CU385]
 gi|325199962|gb|ADY95417.1| dihydrouridine synthase [Neisseria meningitidis H44/76]
          Length = 336

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|327481992|gb|AEA85302.1| NifR3 family TIM-barrel protein [Pseudomonas stutzeri DSM 4166]
          Length = 337

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 67/261 (25%), Positives = 125/261 (47%), Gaps = 16/261 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R     A++ +EM+ +D  L   +K+ L    + + +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRF-GAAMVVSEMLTSDVRLWNSRKSRLRMPHADEPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ LM +  +V D + A+  A+ +P
Sbjct: 79  PQMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALMRDERLVADILEAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q    A   + +  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRQNKNGAA--IARIAEQAGIAALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG ++   +A ++L     DG++IGRAA     +   V+ Y    
Sbjct: 189 IAAI-KQAVSIPVFANGDIDSPHKAARVLQVTGADGLLIGRAAQGRPWIFREVEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISA 257
              ++P    V+      + A
Sbjct: 248 ELLAAPTLGEVESTLLEHVQA 268


>gi|282852631|ref|ZP_06261973.1| TIM-barrel protein, nifR3 family [Lactobacillus gasseri 224-1]
 gi|282556373|gb|EFB61993.1| TIM-barrel protein, nifR3 family [Lactobacillus gasseri 224-1]
          Length = 335

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 109/218 (50%), Gaps = 16/218 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  L    +E P+++QI G     LVEAA  V+     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGSEETLVEAAHYVDTHTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  +V +   GA  +L+P+ +   + A+ + +S PVTVK R G  DQ    A+ 
Sbjct: 101 NINMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSKPVTVKMRTGW-DQKHIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R         +    +   D++ + E+       F+G NG +
Sbjct: 160 NALAA-QEAGASAVAMHGRT--------RKQMYMGEADWETLKEVADALTIPFVG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
               +A  +L  V  D VM+GRAA  N  ++  +  Y 
Sbjct: 210 TTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYL 247


>gi|237736815|ref|ZP_04567296.1| nitrogen regulation protein NIFR3 [Fusobacterium mortiferum ATCC
           9817]
 gi|229420677|gb|EEO35724.1| nitrogen regulation protein NIFR3 [Fusobacterium mortiferum ATCC
           9817]
          Length = 318

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/296 (23%), Positives = 130/296 (43%), Gaps = 34/296 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  YR   +   N  +L+TEM+  +A+    +K +       +  ++Q+ G DI K+VE
Sbjct: 13  TDYTYRGILKEF-NPDMLFTEMVSINAMECASEKTLKVILRLREGDSVQLFGKDIPKMVE 71

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           +AK VE  G   I++N GCP  ++    +G+ LM NP+ +   ++ +  AL+    +++K
Sbjct: 72  SAKFVERLGVKHIDINSGCPMKKITSNGYGSALMANPEHIKAMLSELRSALNDDTGLSIK 131

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +    V +  + + +   G   I +H R         ++       D+ I+  +
Sbjct: 132 IRAGYKEFKNPVEIAKIAEEV---GCKHITVHGRT--------REQMYTGKADWSIIKAV 180

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS----- 234
           K+      IG NG +   ED  + +     VDG+M+ R  + N  ++  + EY       
Sbjct: 181 KESVGIPVIG-NGDIFTAEDAKERID-YSGVDGIMLARGIFGNPWLIRDIREYLEYGKIL 238

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           NP+T    I   ++     +I     D+          + ++ +H+     G  NS
Sbjct: 239 NPVTPLDRINMAIEHTRRTQIEHPERDF----------IFELRKHICWYLKGIRNS 284


>gi|325579238|ref|ZP_08149194.1| tRNA-dihydrouridine synthase B [Haemophilus parainfluenzae ATCC
           33392]
 gi|325159473|gb|EGC71607.1| tRNA-dihydrouridine synthase B [Haemophilus parainfluenzae ATCC
           33392]
          Length = 326

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 68/253 (26%), Positives = 123/253 (48%), Gaps = 30/253 (11%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   RL  +    L ++EM+  +  +   +K+ L  +  E+    A+QI G
Sbjct: 17  MAGITDQPFR---RLCAHYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEELGLNAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D  ++ +AA I   +G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ 
Sbjct: 74  SDPLEMAQAAAINVAYGAEIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILKEVVNAVD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHAR--KAILKGLSPKDNRKI 171
           +PVT+K R G D        RN V   K  ++SG+  + IH R  + + +G +  DN + 
Sbjct: 134 VPVTLKIRTGWDK-----VNRNCVQIGKIAEQSGIQALTIHGRTKECLFEGEAEYDNIRA 188

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
                       K++  + +  NG ++  S+A K+L     D +MIGRA+  N  +   V
Sbjct: 189 V-----------KQSISIPVIANGDIDSASKAKKVLEYTGADAIMIGRASLGNPWLFQAV 237

Query: 230 DEYFSNPLTGSSP 242
           +    +     +P
Sbjct: 238 EALVEHDTIIQTP 250


>gi|309389966|gb|ADO77846.1| tRNA-U20-dihydrouridine synthase [Halanaerobium praevalens DSM
           2228]
          Length = 324

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 78/275 (28%), Positives = 123/275 (44%), Gaps = 24/275 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP---LALQIGGA 57
           M   +D  YR   R +    LLYTEM+ A     G+++     +  EKP   +A+QI G 
Sbjct: 17  MAGVSDYPYRQLIREM-GVELLYTEMVSAKGYEYGNRRTSELITFSEKPQAKIAVQIFGE 75

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D   + +AA  IVE++G + I++N+GCP+ ++ +   G+ LM N ++  + I A+  +  
Sbjct: 76  DPKFMAQAAAGIVEEYGADLIDINMGCPARKIVKNGAGSALMKNLNLAAEVIEAVVDSAK 135

Query: 117 IPVTVKCRIGVDDQ-IPAVAL--RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVTVK R G D + I AV L             V+G     R    KG +         
Sbjct: 136 VPVTVKMRSGWDQKNINAVELAKVAAEAGAAAVAVHG---RTRNQFYKGEA--------- 183

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            D++I+  +        IG NG +   + A  I       G+MIGRAA     +   V +
Sbjct: 184 -DWEIIKAVVAAVEIPVIG-NGDIFSAAAAKAIFEQTKCQGIMIGRAAQGYPWIFKEVIQ 241

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
           Y        SP   +  +   R +  ++  Y  RH
Sbjct: 242 YLKTGKIIDSPAAYQKIEMAIRHLKLAVNYYGERH 276


>gi|301100330|ref|XP_002899255.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262104172|gb|EEY62224.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 377

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 109/232 (46%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R   R L  +     +L++ +    A  R   + +     Q++PL +Q  G
Sbjct: 31  MVDQSELAFRMLCRKLGADCCYTPMLHSRLFAESAEYR---EKMFEHHIQDRPLVVQFCG 87

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   ++ AAK+VE    + ++LN+GCP     +G +G+ LM + + V   +  +   L+
Sbjct: 88  NDPKTVLAAAKMVEGHC-DAVDLNLGCPQGIARKGHYGSFLMHDKETVKATVKTLSAGLN 146

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R+  DD             ++++G + + +H R   +   +      +  +++
Sbjct: 147 IPVTVKIRVFPDDN----ETLEFADMLQEAGCDLLTVHGRTKEMNKTA------VREVNW 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           DI+  I KE   + +  NGG+E      + L +   DGVM      +N A+ 
Sbjct: 197 DIIRRI-KERLTIPVIANGGIETHEDIARCLEATGCDGVMSSEGLLENPALF 247


>gi|116628953|ref|YP_814125.1| tRNA-dihydrouridine synthase [Lactobacillus gasseri ATCC 33323]
 gi|238853552|ref|ZP_04643924.1| tRNA-dihydrouridine synthase B [Lactobacillus gasseri 202-4]
 gi|311111242|ref|ZP_07712639.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           gasseri MV-22]
 gi|116094535|gb|ABJ59687.1| tRNA-U20-dihydrouridine synthase [Lactobacillus gasseri ATCC 33323]
 gi|238833848|gb|EEQ26113.1| tRNA-dihydrouridine synthase B [Lactobacillus gasseri 202-4]
 gi|311066396|gb|EFQ46736.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           gasseri MV-22]
          Length = 335

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 109/218 (50%), Gaps = 16/218 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  L    +E P+++QI G     LVEAA  V+     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGSEETLVEAAHYVDTHTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  +V +   GA  +L+P+ +   + A+ + +S PVTVK R G  DQ    A+ 
Sbjct: 101 NINMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSKPVTVKMRTGW-DQKHIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R         +    +   D++ + E+       F+G NG +
Sbjct: 160 NALAA-QEAGASAVAMHGRT--------RKQMYMGEADWETLKEVADALTIPFVG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
               +A  +L  V  D VM+GRAA  N  ++  +  Y 
Sbjct: 210 TTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYL 247


>gi|83589019|ref|YP_429028.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moorella
           thermoacetica ATCC 39073]
 gi|83571933|gb|ABC18485.1| tRNA-U20-dihydrouridine synthase [Moorella thermoacetica ATCC
           39073]
          Length = 334

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 82/307 (26%), Positives = 128/307 (41%), Gaps = 36/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TDR +R  AR     AL YTEMI A  ++  +K    +L    +  P+A+Q+ G +
Sbjct: 21  MAGYTDRVFRLLARE-AGAALTYTEMISAQGLIYNNKNTHALLDLKGEPGPVAVQLFGRE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              +  A +I    G   I+LN+GCP+ ++ +   G+ LM +       +AAM +A   +
Sbjct: 80  PEIMAAATRIAVAAGAAIIDLNMGCPTPKIVKNGEGSALMRDLPRAAAIVAAMVRAAGPV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    V           +    I    R     G +          D+ 
Sbjct: 140 PVTVKMRLGWDEDSINVVEAARAVVYAGAAAVAIHGRTRSQFYSGRA----------DWS 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
               + KE  D+ +  NG +     A+ +L     DGVM+GR A  N  +LT +      
Sbjct: 190 YFRRV-KEAVDVPVIGNGDVRTARDAVTMLAETGCDGVMVGRGAVGNPWLLTAIRAVLEG 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-------SGGKLQQITRHMIGLFHGFP 288
                 P    VD      +   MT  A RHL            ++++ +H+   F G P
Sbjct: 249 -----RPEPPPVD------VRTRMT-MACRHLKLLVELKGETTAVKEMRKHLACYFRGLP 296

Query: 289 NSRRCRH 295
            + R R 
Sbjct: 297 GAARLRQ 303


>gi|256419707|ref|YP_003120360.1| hypothetical protein Cpin_0661 [Chitinophaga pinensis DSM 2588]
 gi|256034615|gb|ACU58159.1| TIM-barrel protein, nifR3 family [Chitinophaga pinensis DSM 2588]
          Length = 354

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 86/349 (24%), Positives = 150/349 (42%), Gaps = 54/349 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + L+YTE I ++ ++R     +  L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRAVCKEKGAD-LMYTEFISSEGLIRDAIKSRRKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+IVE    + +++N GCP  +V     G+ ++ +   +    AA+ KA  +P
Sbjct: 78  EEPMAMAAQIVEATNPDLLDINYGCPVKKVVCKGAGSGILKDIPKMVKLTAAVVKATKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G DD    +    + + ++  G+  + IH   R  + KG          + D+
Sbjct: 138 VTVKTRLGWDDDTKNI--EEVAERLQDVGIQALTIHGRTRTQMYKG----------HADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
            ++ ++K  NP + I +  NG +    QA+       VDGVMIGRAA     +   +  +
Sbjct: 186 TLIGKVKN-NPRIHIPIFGNGDICTPEQAIAAREKYGVDGVMIGRAAIGYPWIFNEIKHF 244

Query: 233 FSNPLTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-------QITRHMIGLF 284
                TG   P  + +++           +   +HL    + +       ++ RH     
Sbjct: 245 MQ---TGEHLPPPSVLER----------VEVCKKHLQHSVQWKGDVVGILEMRRHYTNYL 291

Query: 285 HGFPNSRRCRHIL-----------TVEAGASTATHHIIETAFNLMIESL 322
            G P+ +  R  L            ++A A     HIIE    L  +SL
Sbjct: 292 KGLPHIKEFRQQLVTCSTLAAVEDVLDAIALHYKDHIIERTSPLTDQSL 340


>gi|291543545|emb|CBL16654.1| tRNA-U20-dihydrouridine synthase [Ruminococcus sp. 18P13]
          Length = 336

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 105/234 (44%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR YR   R      ++ +E+I A  +   D K   +   + +E+P+ALQ+ G++
Sbjct: 20  MASVADRAYRQLCRSF-GACMVTSELISAKGMCYNDSKTAELCTITPEERPMALQLFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +A K++  F  + I+LN+GCP  +V     G+ LM + +   D +AA   A  +P
Sbjct: 79  PKFIQQAVKLLLPFQPDVIDLNMGCPVPKVVNTGAGSALMQDLNTAADLVAAARMASDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  +    V        + ++G   I IH R         +        D+  
Sbjct: 139 VTVKIRRGWSEDT--VNCVEFACRMAEAGAQAIAIHGRT--------RSQMYSGKADWSC 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           +  +K+      IG NG +   +  L +      D VM+GRA+Y N  +   +D
Sbjct: 189 IRAVKQAVSVPVIG-NGDVCSGADCLNMYRETGCDLVMVGRASYGNPWIFQEID 241


>gi|119486469|ref|ZP_01620527.1| Dihydrouridine synthase TIM-barrel protein [Lyngbya sp. PCC 8106]
 gi|119456371|gb|EAW37502.1| Dihydrouridine synthase TIM-barrel protein [Lyngbya sp. PCC 8106]
          Length = 344

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 73/306 (23%), Positives = 138/306 (45%), Gaps = 26/306 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  +   ++   ++     E+P+++Q+       L 
Sbjct: 36  TDLVFRRLVRRYAPESMMYTEMVHASQVRHLEELPQMMEVDPNERPISIQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+     G N +++N+GCP  ++ +   G+ L+  P +    + ++ +A+++PVTVK 
Sbjct: 96  EAAQRAVTEGANTVDINMGCPVNKITKKGGGSSLLRQPKVAEAIVQSVVEAVNVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG DD    + + +  K ++ SG   I IHAR     G + K N       ++ + ++K
Sbjct: 156 RIGWDDN--EINILDFAKRMEDSGAAMITIHARTR-AAGYNGKAN-------WEWIAKVK 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +      I  NG +  +  A+  L     DGVM  R       ++  +D +     TG  
Sbjct: 206 QILSIPVIA-NGDIISVESAIDCLQLTGADGVMCSRGTLGYPFLVGEIDAFLK---TG-- 259

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL--- 297
             + +   +   ++  +     A   + G + + Q  +HM     GF  +   R+ L   
Sbjct: 260 --EVKPGANIMERLLCAKEHLKALGEYKGERGIYQSRKHMTWYAKGFAGANELRNQLAKI 317

Query: 298 -TVEAG 302
            +VE G
Sbjct: 318 ESVEQG 323


>gi|315633700|ref|ZP_07888990.1| tRNA-dihydrouridine synthase B [Aggregatibacter segnis ATCC 33393]
 gi|315477742|gb|EFU68484.1| tRNA-dihydrouridine synthase B [Aggregatibacter segnis ATCC 33393]
          Length = 342

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 111/218 (50%), Gaps = 25/218 (11%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L ++EM+  +  +   +K+ L  +  +     A+QI G+D  ++ +AA++  ++G   I+
Sbjct: 58  LTFSEMMSTNPQVWHTEKSKLRLAHHQDAGINAVQIAGSDPDEMAQAAQVNVEYGAQIID 117

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+  PD+V   + A+ K++++PVT+K R G D +      RN
Sbjct: 118 INMGCPAKKVNRKMAGSALLQYPDLVQQILEAVVKSVNVPVTLKIRTGWDTE-----NRN 172

Query: 139 LV---KSIKKSGVNGIWIHARKAILK--GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            V   K  ++SG+  + +H R    K  G++          +YD +  +K+      I  
Sbjct: 173 CVEIAKIAEQSGIQALTVHGRTRACKFEGVA----------EYDSIKAVKQAVSIPVIA- 221

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
           NG +    QA  +L     DGVMIGR A     +  T+
Sbjct: 222 NGDMISPQQAKFVLDYTGADGVMIGRGALGRPWVFQTM 259


>gi|302382892|ref|YP_003818715.1| hypothetical protein Bresu_1781 [Brevundimonas subvibrioides ATCC
           15264]
 gi|302193520|gb|ADL01092.1| TIM-barrel protein, nifR3 family [Brevundimonas subvibrioides ATCC
           15264]
          Length = 352

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 107/228 (46%), Gaps = 24/228 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL---QIGGA 57
           M   TD  +R  A  L   A + TEM+ +  + RG + +++  +     L L   Q+ G 
Sbjct: 21  MTGITDLPFRQLACRL-GAAYVATEMVASAELARG-RPDVMRRAAVGDGLPLTVIQLVGR 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D + + + A++ E  G + ++LN GCP+  V   + G+ LM  PD+ G  +AA+  A S 
Sbjct: 79  DPAAMAQGARMAEAAGADIVDLNFGCPAKEVTGSASGSALMRTPDLAGRIMAAVVAATSR 138

Query: 118 PVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVTVK R+G DD     A RN   L    +  GV  + +H R         +      + 
Sbjct: 139 PVTVKMRLGWDD-----ASRNAAELAARAEDLGVKAVTVHGRT--------RQQFYTGHA 185

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           D+D +  +K     + + +NG +    QA + L     D +M+GR  Y
Sbjct: 186 DWDAIAAVKTAV-GIPVIVNGDIITADQAREALQKSGADALMLGRGVY 232


>gi|255505161|ref|ZP_05344831.3| dihydrouridine synthase family protein [Bryantella formatexigens
           DSM 14469]
 gi|255269367|gb|EET62572.1| dihydrouridine synthase family protein [Bryantella formatexigens
           DSM 14469]
          Length = 285

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI        V  AK ++++GY+E+N+N+GCPS  V     GA  + +P+ V D +A + 
Sbjct: 70  QILTNKWEDFVWTAKHLQEYGYDEVNINLGCPSKTVVSKKRGAGFLADPEGVDDFLAHIF 129

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKI 171
            AL + ++VK R+G +D    V  R L++   K  +  + IH R +    G +P      
Sbjct: 130 DALDMKISVKTRLGRED---PVEFRWLLEIYNKYPLAELIIHPRTQKEFYGFTPH----- 181

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
               Y++  E  +E   L +  NG +   ED  +  K  P + GVM+GR   +N  ++  
Sbjct: 182 ----YEMFAEALEET-SLPVCYNGDVNTKEDCREIEKRFPQITGVMMGRGILRNPGLIGE 236

Query: 229 V 229
           +
Sbjct: 237 I 237


>gi|324324412|gb|ADY19672.1| putative tRNA-dihydrouridine synthase [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 329

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        N +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWENWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|304405948|ref|ZP_07387606.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
 gi|304345191|gb|EFM11027.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
          Length = 326

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFTNTESYCHPDGHQSVRGRLAFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V +   G+ L+  P+     I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAQQGFKGIDINMGCPVANVAQNGQGSGLICRPETAAAIIQA-TKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G D        R+ +  I K G+  + IH R       +  +  K+ +  +
Sbjct: 138 LPVSVKTRLGFD---AIEEWRDWLTHILKQGIANLSIHLR-------TRAEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFNN 238


>gi|329927628|ref|ZP_08281775.1| dihydrouridine synthase (Dus) [Paenibacillus sp. HGF5]
 gi|328938326|gb|EGG34717.1| dihydrouridine synthase (Dus) [Paenibacillus sp. HGF5]
          Length = 329

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 105/235 (44%), Gaps = 28/235 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V E   G+ L+  PDI  D I A  KA  
Sbjct: 79  DKPEFFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPDIAADIIQA-AKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   VD+       R+ +  I K  +  + IH R         ++     +
Sbjct: 138 LPVSVKTRLGFTAVDE------WRDWLTHILKQDIVNLSIHLRT--------REEMSKVD 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 184 AHWELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFHN 238


>gi|326433345|gb|EGD78915.1| hypothetical protein PTSG_01890 [Salpingoeca sp. ATCC 50818]
          Length = 459

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 115/246 (46%), Gaps = 27/246 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R  AR    + L YT M+ +   +R      L F+T  +++PL +Q  G D
Sbjct: 25  MVDQSELSWRLLARAYGAH-LCYTPMLHSGVFVRDANYRKLNFTTCAEDRPLIVQFCGND 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++EAAK VED   + ++LN+GCP      G +GA L    D +   +  +   LS+P
Sbjct: 84  PDTVLEAAKYVED-KCDAVDLNLGCPQNIARRGRYGAFLQDEWDTISAIVKRLHAELSVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  DD    +A     + +++SG   + +H R  + KG  P+    + N DY  
Sbjct: 143 VTCKIRI-FDDLDKTLA---YARMLEESGCQLLTVHGRTRVQKG--PRSG--LANWDY-- 192

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT-------- 227
             +  K    + +  NG +    D+ + ++    VDGVM       N A+ +        
Sbjct: 193 -IKAIKNAVSIPVVANGNILYTSDIDKCIEYT-GVDGVMSSETHLVNPAVFSGQYPLLWE 250

Query: 228 TVDEYF 233
            VDEY 
Sbjct: 251 MVDEYM 256


>gi|118399013|ref|XP_001031833.1| dihydrouridine synthase [Tetrahymena thermophila]
 gi|89286167|gb|EAR84170.1| dihydrouridine synthase [Tetrahymena thermophila SB210]
          Length = 444

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 112/234 (47%), Gaps = 22/234 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           MVD ++  +R   R      L YT MI +  +     G   ++     +++PL  Q  G 
Sbjct: 79  MVDQSELAFRMLCRKY-GTTLAYTPMIHSKVLQDQGYGYLNSVFSTCQEDRPLFAQFCGN 137

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   L+  A+ VED   + I++N GCP      G +G+ L+  PD +   +  + + LSI
Sbjct: 138 NPDALLAGARYVED-KCDAIDINFGCPQGIAKRGRYGSYLLSEPDTIVALVKKLHENLSI 196

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-DY 176
           PVT K RI  + Q        L K I+ +G + + +H R       + + N+    L D+
Sbjct: 197 PVTCKIRILPNRQ----QTIELAKKIEAAGCSILTVHGR-------TKEQNKDTVGLCDW 245

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           DI+ +I KE   + +  NGG+   ED+ + L+    VDGVM   +  +N A+ +
Sbjct: 246 DII-KIIKEELSIPVFANGGIYTYEDVQKCLEYT-GVDGVMSAESLLENPALFS 297


>gi|94266587|ref|ZP_01290270.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
 gi|93452782|gb|EAT03317.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
          Length = 313

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 112/241 (46%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R      L Y+EM+    ++R     I  L  +  E+PL +Q+ GA+
Sbjct: 20  LAGYSDLPFRLLCREY-GAGLCYSEMLSCHGLVRRQPATIEMLATTAAERPLLMQLFGAE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              + EAA I+     + I++N+GCP  +V +   GA LM +P++      A+  A   +
Sbjct: 79  PEVMGEAAAILSRLPIDGIDINMGCPVKKVVKKGAGAALMRDPELAAAITGAVTAAAGDL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G + +   +   +  + +   G   + IHAR     G + +        D+ 
Sbjct: 139 PVTVKIRSGWNHK--QLNAPDFARLLVAHGAAAVTIHART-WSDGFAGRA-------DWA 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++  +K+      IG NG +    QAL ++ +   DGVMIGR A     + T   E   N
Sbjct: 189 VIAAVKRAVSVPVIG-NGDIGSYEQALAMMAATGCDGVMIGRGALGAPWVFTPGAE--QN 245

Query: 236 P 236
           P
Sbjct: 246 P 246


>gi|89094591|ref|ZP_01167529.1| hypothetical protein MED92_01129 [Oceanospirillum sp. MED92]
 gi|89081190|gb|EAR60424.1| hypothetical protein MED92_01129 [Oceanospirillum sp. MED92]
          Length = 328

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 114/240 (47%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ +D  L   +K+   L  + + +P ++QI G D
Sbjct: 18  MAGVTDRPFRQLCKRM-GAGLVVSEMVTSDTRLWKSRKSTYRLNHTGEAEPRSVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA +  + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 77  PIMMAEAAAMNVERGAQIIDINMGCPAKKVCNKAAGSALLKDEALVSDILHAVVNAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D Q      RN   + +  + +G+  + +H R    +    K   +  N  
Sbjct: 137 VTLKIRTGWDQQ-----NRNGITIAQIAEDAGIQALAVHGRT---RSCGYKGEAEY-NTI 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYF 233
            DIV  +        +  NG +    +A ++L       VMIGRAA  +  +   +D Y 
Sbjct: 188 ADIVNAV-----SFPVFANGDISSPEKAKQVLEHTGCAAVMIGRAAQGSPWLFREIDHYL 242


>gi|163760105|ref|ZP_02167188.1| probable tRNA-dihydrouridine synthase protein [Hoeflea
           phototrophica DFL-43]
 gi|162282504|gb|EDQ32792.1| probable tRNA-dihydrouridine synthase protein [Hoeflea
           phototrophica DFL-43]
          Length = 304

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 78/268 (29%), Positives = 117/268 (43%), Gaps = 35/268 (13%)

Query: 9   YRFFARLLTNNAL----LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           +R+ A L+    +    L TE   +   LRGD  N         P  +Q+ G +   + +
Sbjct: 3   WRYGAGLVVTEMVASRELVTERRESQVRLRGDGIN---------PHVVQLAGREADWMAK 53

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AA+I E  G   I++N+GCP+ +V  G  G+ LM +PD   + I A  KA+S+PVT+K R
Sbjct: 54  AARIAEGEGAAMIDINMGCPAKKVTGGYSGSALMRDPDHALELIEATVKAVSVPVTLKMR 113

Query: 125 IGVD-DQI--PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           +G D D I  P +A R      + +G+  I IH R  +       D   I  +       
Sbjct: 114 LGWDHDNINAPLIAAR-----AEAAGIQMITIHGRTRMQFYEGSADWVAIAKV------- 161

Query: 182 IKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             +E   + +  NG +    D+   LK     D VMIGRA+     +   + E    P  
Sbjct: 162 --REAVSVPLVANGDVASRADIEACLK-HSGADAVMIGRASRGRPWICGDLAESDKAPAP 218

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARH 266
           GS      V+  +W  I     D   RH
Sbjct: 219 GSQQRAIAVEH-YWMMIEHYGEDVGVRH 245


>gi|256821476|ref|YP_003145439.1| TIM-barrel protein, nifR3 family [Kangiella koreensis DSM 16069]
 gi|256795015|gb|ACV25671.1| TIM-barrel protein, nifR3 family [Kangiella koreensis DSM 16069]
          Length = 329

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 122/239 (51%), Gaps = 18/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R   + L    L  +EMI A+  LR  +K++   + Q +P   ++QI GA+
Sbjct: 20  MAGVTDRPFRQLCKEL-GAGLTVSEMIAANPQLRNTRKSMQRSNHQGEPGIRSVQIAGAE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+     G   I++N+GCP+ +V + + G+ L+ +P +V D + A+  A+ +P
Sbjct: 79  PEMLAQAAQYNVQNGAEIIDINMGCPAKKVCKKAAGSALLQDPQLVEDILNAVVAAVEVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G + D    V    + +  +++G+  + +H R         + ++ + N +YD
Sbjct: 139 VTLKIRTGWNHDNRNGV---QIARIAEQAGIQSLAVHGRT--------RADKYLGNAEYD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  I K++  + +  NG +    +A  +L    VDG+MIGR A  N  +   V  Y  
Sbjct: 188 TIATI-KQSVSIPVVANGDITSPEKAKFVLDYTGVDGLMIGRGAQGNPWIFREVWHYLQ 245


>gi|294937192|ref|XP_002782004.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
 gi|239893217|gb|EER13799.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
          Length = 438

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 102/225 (45%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A +     K     F T   + PLA Q  G D
Sbjct: 35  MVDQSELAFRMMTRKY-GAQFCYTPMMHAKSFATSKKYREKNFETAPGDSPLAAQFCGDD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAK +ED   + I+LN+GCP      G +G+ L+  P++V   +  M K +  P
Sbjct: 94  GDVIVEAAKHIED-QVSCIDLNLGCPQGIARRGHYGSFLLEEPELVLGIVEKMVKGIKCP 152

Query: 119 VTVKCRI--GVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           V+VK R+    DD    +    A +  VK +   GV+ I +H R    KG      +   
Sbjct: 153 VSVKIRLMTAKDDDGSGRPDVAATKEFVKRLDALGVDLIALHPRTKEWKG------QLTQ 206

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVM 214
              +    E++   PD+   +NGG+   ED+ +  K+    D VM
Sbjct: 207 ACWWQAAAEVRACVPDIPFIVNGGISCFEDVEKCFKVT-KCDAVM 250


>gi|167465717|ref|ZP_02330806.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) protein [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 201

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 58/188 (30%), Positives = 101/188 (53%), Gaps = 16/188 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA 66
           +R  A+      L+  EM+   AI+ G+ + +  L    +EKPL+LQI G D   LV AA
Sbjct: 26  FRLIAKEF-GCGLVCAEMVSDKAIVHGNSRTMEMLYVDEREKPLSLQIFGGDKETLVAAA 84

Query: 67  KIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           K V D   N   I++N+GCP  +V +   GA  +L+P  + + ++A+ + +S PVTVK R
Sbjct: 85  KYV-DLNTNADIIDINMGCPVPKVTKCDAGARWLLDPQKIEEMVSAVVEVVSKPVTVKMR 143

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G D +    A+RN  ++++++G + + +H R         ++       ++DI+ E+K+
Sbjct: 144 MGWDSE-HIYAVRN-AQAVERAGGSAVSLHGRT--------REQLYTGTANWDIIREVKQ 193

Query: 185 ENPDLFIG 192
                 IG
Sbjct: 194 SISIPLIG 201


>gi|225869383|ref|YP_002745331.1| tRNA-dihydrouridine synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225702659|emb|CAX00744.1| putative tRNA-dihydrouridine synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 325

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 111/241 (46%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQSHTRADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIQEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   +        + + +GV+ + +H R         ++       DY+
Sbjct: 143 PLTVKMRTGWSD---SSLALENALAAEAAGVSALAMHGRT--------REQMYTGTCDYE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITRIPFIG-NGDVRTVQDAAFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250

Query: 235 N 235
            
Sbjct: 251 T 251


>gi|329577257|gb|EGG58721.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1467]
          Length = 252

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/179 (32%), Positives = 97/179 (54%), Gaps = 20/179 (11%)

Query: 63  VEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +EAAK VE+     I ++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTV
Sbjct: 1   MEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTV 60

Query: 122 KCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDI 178
           K R G D D + AV   +   + +++G + I +H R  +   +G +          ++D+
Sbjct: 61  KMRTGWDEDHLYAV---DNALAAEQAGASAIAMHGRTRVQMYEGTA----------NWDV 107

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     F+G NG ++    A ++L  V  DGVMIGRAA  N  M+    EY   
Sbjct: 108 LKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 165


>gi|254486875|ref|ZP_05100080.1| tRNA-dihydrouridine synthase B [Roseobacter sp. GAI101]
 gi|214043744|gb|EEB84382.1| tRNA-dihydrouridine synthase B [Roseobacter sp. GAI101]
          Length = 328

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 113/238 (47%), Gaps = 26/238 (10%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  YR     F A L+ +  +   +MI A    R  +K  LG   +    A+Q+ 
Sbjct: 19  MAGITDLPYRNLVASFGAGLVVSEMVASEDMINARPGTR--EKAELGLGIEGT--AVQLA 74

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G + + L EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+  A+
Sbjct: 75  GREAAPLAEAARMVEAQGARIIDINMGCPAKKVTQGYSGSALMRTPDYALTLIEAVVNAV 134

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
            +PVT+K R+G DD +  +    +  + + +G+  I IH R      KG +         
Sbjct: 135 KVPVTLKTRLGWDDAM--LNAPQIAAAAEAAGITMITIHGRTRCQFYKGAA--------- 183

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            D+  + ++ K+   + +  NG + D   A   L     DGVM+GR +     +L  +
Sbjct: 184 -DWAAISKV-KDAVSIPVIANGDIIDTDSASTALNQSRADGVMVGRGSQGQPWILAEI 239


>gi|327273572|ref|XP_003221554.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Anolis
           carolinensis]
          Length = 325

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 75/283 (26%), Positives = 127/283 (44%), Gaps = 32/283 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R   N  L YT MIVA   +R +K     F+T +  +PL +Q    +
Sbjct: 41  MVRYSKLSFRTLVRKY-NCDLCYTPMIVAADFVRSEKARHSEFTTNQGDRPLIVQFAAKE 99

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA IV  F  + I+LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 100 AQVLADAACIVSPFA-DGIDLNCGCPQRWAMAEGYGACLINKPELVQDMVKLVKNQVENP 158

Query: 119 V-TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           + +V  +I + D +      +L +  + +GV+ I +H R          + R  P +  D
Sbjct: 159 LFSVSIKIRIHDDLKRTI--DLCQKAEAAGVSWITVHGRNV--------EERHQP-VHCD 207

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +I KE+  + +  NG ++ +     +  +   DGVM+ R    N AM    +E    
Sbjct: 208 AI-KIIKESVSIPVVANGDMKSLKDVEDVHQITGTDGVMVARGLLANPAMFAGYEE---- 262

Query: 236 PLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                +P++   D   W  I+    T +   H H    L++IT
Sbjct: 263 -----TPLECVQD---WVHIALEHGTPFMCFHHHLMYMLERIT 297


>gi|328873275|gb|EGG21642.1| tRNA-dihydrouridine synthase 1-like protein [Dictyostelium
           fasciculatum]
          Length = 426

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/272 (25%), Positives = 123/272 (45%), Gaps = 31/272 (11%)

Query: 7   RHYRFFARLLTNN---ALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISK 61
            H     RLLT      ++YT M  +  I   D      FST  Q++P+ +Q  G ++  
Sbjct: 63  EHSLLAFRLLTRKFGADVVYTPMYNS-KIFSHDATYRCNFSTNPQDRPMVVQFCGNEVDH 121

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +V++AK+VED   + +++N+GCP     +G +GA L+  PDIV   + A+ K L +P+  
Sbjct: 122 IVKSAKMVEDHC-DAVDINLGCPQGIARKGFYGAFLLERPDIVLPMVRALHKELKVPIFC 180

Query: 122 KCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           K R+   +DD I       L   ++++G   + +H R    KG        + + D+  +
Sbjct: 181 KIRLLPDIDDTI------KLALQLQEAGCQLLTVHGRTKEQKG------EFLCHADWKAI 228

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + KE   + +  NG +++    +  L     DGVM       N AM + +D   ++  
Sbjct: 229 RRV-KEAVSIPVFANGSVDEYKDIVPCLEESGADGVMSADGILANPAMFSGLDMTLTDVC 287

Query: 238 TGSSPIKTRVDKDF-------WRKISASMTDY 262
                I  ++  DF       ++ +   M DY
Sbjct: 288 REYLDICDQIPTDFFLIRSHCYKMLKRHMDDY 319


>gi|226227146|ref|YP_002761252.1| putative tRNA-dihydrouridine synthase [Gemmatimonas aurantiaca
           T-27]
 gi|226090337|dbj|BAH38782.1| putative tRNA-dihydrouridine synthase [Gemmatimonas aurantiaca
           T-27]
          Length = 349

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 135/288 (46%), Gaps = 32/288 (11%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEI 77
           ++ TE + A+ I R ++  I  L F+ +E+P+ +QI G++ S + +AA +V D F  + +
Sbjct: 40  VVVTEFLSAEGIRRENEATISKLRFAPEERPIGVQIFGSEPSAMADAAALVTDMFSPDFV 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP---AV 134
           ++N GCP  +V   + G+  + + D+V + I A+ KA  +PVTVK R G ++++     +
Sbjct: 100 DINFGCPVKKVVRRNGGSGCLKDLDLVEEIIRAVSKATPLPVTVKTRSGWNEEMRDPVGI 159

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           ALR     ++ +G     +HAR         +      + ++D +  +  E  D+ +  N
Sbjct: 160 ALR-----MQDAGAKVFALHART--------RTQMYSGSANWDEIARV-AEALDIPVLGN 205

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTR--VDK 249
           G ++    A ++L     DG+MIGR +Y    +           P+  +  ++ R  +  
Sbjct: 206 GDIKTALDAKRMLDHTKADGIMIGRGSYGQPWVFKQTRALIDGTPVPETPGVQERFAIAL 265

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           D  R +     D       + G   +  +H+     G PNS   R  L
Sbjct: 266 DHARMVQGYEVD-------AIGAALEFRKHLGWYVKGLPNSAELRAKL 306


>gi|325134359|gb|EGC57004.1| dihydrouridine synthase [Neisseria meningitidis M13399]
 gi|325205824|gb|ADZ01277.1| dihydrouridine synthase [Neisseria meningitidis M04-240196]
          Length = 374

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 174 VTLKTRLGWHDDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 218

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 219 ARYELIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|262373055|ref|ZP_06066334.1| tRNA-dihydrouridine synthase B [Acinetobacter junii SH205]
 gi|262313080|gb|EEY94165.1| tRNA-dihydrouridine synthase B [Acinetobacter junii SH205]
          Length = 341

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 81/329 (24%), Positives = 153/329 (46%), Gaps = 30/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G    ++ I  VA     K  + +G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGEENILRVA-----KRAEDAGIAALALHGR--------TREDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++ E+KK N  + +  NG ++   +A  +L     D VMIGRAA     +   +  Y 
Sbjct: 183 YELIREVKK-NIHIPLIANGDIDSPEKAKYVLDYTGADAVMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     ++     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 ETGEHLAAPEIVEVKQVLMGHLAELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMIES 321
           R  +  VE  A  A   ++E+ F+ +++ 
Sbjct: 297 RQNMYKVENTADQAK--VVESYFDQLLDQ 323


>gi|257871421|ref|ZP_05651074.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
 gi|257805585|gb|EEV34407.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
          Length = 319

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D     +  L F+  E+P+   I G
Sbjct: 1   MEDVTDVVFRHVVQTAGAPDVFFTEFTNSDSYCHPDGIESVRGRLTFTEDEQPIVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 61  DKPEFFRQMSIGMAEMGFKGIDINMGCPVPNVAGRGKGSGLILRPDVAAELIEA-AKAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + +H R       + K+  K+P   +
Sbjct: 120 LPVSVKTRIGYTEM---AEMEAWITHLLQQDIANLSVHLR-------TRKEMSKVP-AHW 168

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           D++ E+     +  P   I +NG + D    L +     VDG+MIGR  +KN
Sbjct: 169 DLIPEVLAIRDRVAPQTLITINGDIPDRQAGLALAQQYGVDGIMIGRGIFKN 220


>gi|222054815|ref|YP_002537177.1| TIM-barrel protein, nifR3 family [Geobacter sp. FRC-32]
 gi|221564104|gb|ACM20076.1| TIM-barrel protein, nifR3 family [Geobacter sp. FRC-32]
          Length = 326

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 80/312 (25%), Positives = 140/312 (44%), Gaps = 45/312 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+   R  AR     AL +TEMI  + ++R  KK  ++L     ++P+ +QI G D
Sbjct: 21  MAGLTNLPMRILARE-CGAALTFTEMISVNGLVREGKKTFDLLRRDPMDRPMGIQIFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E A++VE +G   I++N+GCP  +V     G+ L+  P  VG  I A+ KA S+P
Sbjct: 80  PQLLAEGARLVEQYG-ELIDINMGCPVRKVVGSGAGSALLREPAKVGMIIKAVRKATSLP 138

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNL 174
           +T+K R   G  D         + +  +  GV+G+ +H  +R  + +G          + 
Sbjct: 139 LTIKIRTGWGAADH----TFLEIGRIAEAEGVDGVTLHPRSRAQMFEG----------HA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K+      IG +G +   +  + ++     DGVM+ R    N  +       
Sbjct: 185 DWSRIRELKEALSIPVIG-SGDIFTAADVVAMIDQTGCDGVMVARGGLGNPWLFREALAL 243

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH----LHSGGK---LQQITRHMIGLFH 285
               L+G+ PI            +A     A RH    L + G+   ++++ +H+     
Sbjct: 244 ----LSGNEPIP---------PTAAEKRSLALRHLDLFLEATGEHVAVREMRKHLSWYAK 290

Query: 286 GFPNSRRCRHIL 297
           G P +   R ++
Sbjct: 291 GMPGAAHFRAMI 302


>gi|256751234|ref|ZP_05492115.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|256749959|gb|EEU62982.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus
           CCSD1]
          Length = 344

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 111/226 (49%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   L     E + +ALQI G+D 
Sbjct: 40  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKLLTDIDEGESVALQIFGSDP 98

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 99  DIMGEIAKRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 158

Query: 120 TVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G DD  + AV +  +    +K GV  + +H R         ++       D+ I
Sbjct: 159 TVKIRKGWDDNHVNAVEIAQIA---EKVGVKAVAVHGR--------TREQFYSGKADWSI 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + ++ KE+  + +  NG +     A ++L     D ++IGR A  N
Sbjct: 208 IKKV-KESVKIPVMGNGDVFTPEDAKRMLEETGCDAILIGRGAQGN 252


>gi|238022274|ref|ZP_04602700.1| hypothetical protein GCWU000324_02181 [Kingella oralis ATCC 51147]
 gi|237866888|gb|EEP67930.1| hypothetical protein GCWU000324_02181 [Kingella oralis ATCC 51147]
          Length = 333

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/258 (25%), Positives = 121/258 (46%), Gaps = 34/258 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +A+QI G+D ++L  AA+     G   I++N+GCP  +V     G+ L+ N  +V   + 
Sbjct: 66  IAVQIAGSDPAQLAAAAQHNVALGAQVIDINMGCPVKKVCNVLAGSALLQNEKLVAQILN 125

Query: 110 AMCKALSIPVTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLS 164
            + +A+++PVT+K R+G DD+   IP +A     +  + +G+  + IH   R  + +G +
Sbjct: 126 TVVRAVNVPVTLKTRLGWDDEHQNIPTIA-----QIAEDAGIAALAIHGRTRSQMYRGQA 180

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
                      Y+++  +K+++  L I  NG +    +A  +L     D +MIGR A   
Sbjct: 181 ----------QYELIAAVKQQS-RLPIWANGDITSPQKAAAVLAQTGADAIMIGRGAQGQ 229

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGKLQQITRHM 280
             +   +  Y  +   G+ P         ++  SA++  +  A  H +      +I R  
Sbjct: 230 PWLFADIQHYLQH---GTLPPPMP-----FQAASATILRHLAAMHHFYGDNAGTRIARKH 281

Query: 281 IGLFHG-FPNSRRCRHIL 297
           IG +    PNS+  R  L
Sbjct: 282 IGWYLARIPNSQTARQHL 299


>gi|42518373|ref|NP_964303.1| hypothetical protein LJ0286 [Lactobacillus johnsonii NCC 533]
 gi|41582658|gb|AAS08269.1| hypothetical protein LJ_0286 [Lactobacillus johnsonii NCC 533]
          Length = 335

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 116/239 (48%), Gaps = 21/239 (8%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  L    +E P+++QI G     LVEAA  V+     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGSEETLVEAAHYVDTHTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  +V +   GA  +L+P+ +   + A+ + +S PVTVK R G  DQ    A+ 
Sbjct: 101 NINMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSKPVTVKMRTGW-DQKHIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R         +    +   D++ + ++       F+G NG +
Sbjct: 160 NALAA-QEAGASAVAMHGRT--------RKQMYMGEADWETLKDVADALTIPFVG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRVDK 249
               +A  +L  V  D VM+GRAA  N  ++  +  Y        P T    ++T  D+
Sbjct: 210 TTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYLDTGEKLRPQTVEEKVETAKDQ 268


>gi|152978326|ref|YP_001343955.1| nifR3 family TIM-barrel protein [Actinobacillus succinogenes 130Z]
 gi|150840049|gb|ABR74020.1| putative TIM-barrel protein, nifR3 family [Actinobacillus
           succinogenes 130Z]
          Length = 331

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 112/231 (48%), Gaps = 25/231 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L ++EM+ A+  +   +K+ L  +  E     A+QI G+D  ++ +AA++  ++G   I+
Sbjct: 36  LTFSEMMSANPQVWHTEKSKLRLAHHEDAGINAVQIAGSDPQEMAQAARVNVEYGAQIID 95

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+  P+++ D + A+  A+ +PVT+K R G D +      RN
Sbjct: 96  INMGCPAKKVNRKLAGSALLQFPELIRDILTAVVNAVDVPVTLKIRTGWDRK-----HRN 150

Query: 139 ---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
              + K  ++ G+  + +H   R+ +  G +  DN K             KE   + +  
Sbjct: 151 CLDIAKIAEQCGIRALTVHGRTRECLFDGEAEYDNIKAV-----------KEQVSIPVIA 199

Query: 194 NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG +    +A  +L     D VMIGRAA     +  +V     N    S P
Sbjct: 200 NGDIISAEKARLVLEYTGADAVMIGRAALGRPWIFRSVAGLIENGSIISEP 250


>gi|114569990|ref|YP_756670.1| nifR3 family TIM-barrel protein [Maricaulis maris MCS10]
 gi|114340452|gb|ABI65732.1| tRNA-U20-dihydrouridine synthase [Maricaulis maris MCS10]
          Length = 356

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 111/250 (44%), Gaps = 20/250 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R  A+      ++ +EM+ +DA+  G +  I         KP  +Q+ G     +
Sbjct: 47  TDLPFRRQAQRF-GAGMVVSEMVASDALAAGRRDMIRKAALDASLKPCVIQLAGRQAHWM 105

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I ED G   I++N+GCP+ +V +G  G+ LM + D     I A   A S PVT+K
Sbjct: 106 SEGARIAEDAGAEVIDINMGCPARQVTKGLSGSALMRDLDHALTLIEATVGATSKPVTLK 165

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVY 180
            R+G D    ++    L +  + +GV  + +H   R+   KG            D+  V 
Sbjct: 166 MRLGWDH--ASLNAPELARRARDAGVKLLTVHGRTRQQFYKG----------QADWAAVR 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           ++  E  DL + +NG +   + A   L       VM+GRAA     +L  +         
Sbjct: 214 KV-VEAVDLPVIVNGDIHTTADARAALDQSGAAAVMVGRAAQGRPWLLGEIGRELLGEPA 272

Query: 239 GSSPIKTRVD 248
             +P   ++D
Sbjct: 273 ARTPWNDKID 282


>gi|296331895|ref|ZP_06874360.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii ATCC 6633]
 gi|296150973|gb|EFG91857.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii ATCC 6633]
          Length = 327

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 106/233 (45%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       RN +  + K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGYTD---VDEWRNWLTHVLKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTN 238


>gi|229083615|ref|ZP_04215942.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-44]
 gi|228699693|gb|EEL52351.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-44]
          Length = 332

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        N +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWENWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|325144658|gb|EGC66956.1| dihydrouridine synthase [Neisseria meningitidis M01-240013]
          Length = 336

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|23098238|ref|NP_691704.1| hypothetical protein OB0783 [Oceanobacillus iheyensis HTE831]
 gi|22776463|dbj|BAC12739.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 326

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 111/235 (47%), Gaps = 28/235 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D +      L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVTEAARPDVFFTEFTNSESYCHPDGRQSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP A V     G+ L+  P+I  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAEMGFKGLDINMGCPVANVAGNGKGSGLINRPEIAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   +D+       +  +K + +  +  + IH R       + K+  K+ +
Sbjct: 138 LPVSVKTRLGYTYIDE------WKEWLKHVLEQDIVNLSIHLR-------TRKEMSKV-D 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++++ EIKK      PD  + +NG + D    LK++    VDGVMIGR  +KN
Sbjct: 184 AHWELIPEIKKLRDEIAPDTLLTINGDIPDRQTGLKLVEEYGVDGVMIGRGVFKN 238


>gi|195978929|ref|YP_002124173.1| probable tRNA-dihydrouridine synthase Dus [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
 gi|195975634|gb|ACG63160.1| probable tRNA-dihydrouridine synthase Dus [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
          Length = 313

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 116/241 (48%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G +
Sbjct: 12  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEHPISIQLFGGN 70

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 71  AEGLKRAADFIQSHAKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIREVTSVLDI 130

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 131 PLTVKMRTGWADS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGTCDHE 179

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + +    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 180 TLARVSRAITRIPFIG-NGDVRTVQDAAFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 238

Query: 235 N 235
            
Sbjct: 239 T 239


>gi|332531770|ref|ZP_08407655.1| tRNA dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038746|gb|EGI75188.1| tRNA dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 326

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K  N +  S +    A+QI GAD
Sbjct: 20  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPKVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  +    ++ G+  + +H R    + KG          + +
Sbjct: 139 VTLKIRTGWDPDNRNGVEIARIA---ERYGIASLAVHGRTRACMYKG----------DAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y 
Sbjct: 186 YATIRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYL 244


>gi|315127804|ref|YP_004069807.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas sp. SM9913]
 gi|315016318|gb|ADT69656.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas sp. SM9913]
          Length = 326

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K  N +  S +    A+QI GAD
Sbjct: 20  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPKVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  +    ++ G+  + +H R    + KG          + +
Sbjct: 139 VTLKIRTGWDQDNRNGVEIARIA---ERYGIASLAVHGRTRACMYKG----------DAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y 
Sbjct: 186 YATIRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYL 244


>gi|251791404|ref|YP_003006125.1| tRNA-dihydrouridine synthase B [Dickeya zeae Ech1591]
 gi|247540025|gb|ACT08646.1| TIM-barrel protein, nifR3 family [Dickeya zeae Ech1591]
          Length = 321

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 114/242 (47%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGVSDRPFRALCYAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  + G   I++N+GCP+ +V+    G+ L+  P++V   + A+ KA+ +P
Sbjct: 76  PDEMAEAARINAENGAQVIDINMGCPAKKVNRKMAGSALLQYPELVKQILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + +H R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTVHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRTV-KQSVSIPVIANGDITDPRKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|225619221|ref|YP_002720447.1| dihydrouridine synthase-like FMN-binding domain-containing protein
           [Brachyspira hyodysenteriae WA1]
 gi|225214040|gb|ACN82774.1| Dihydrouridine synthase-like (DUS-like) FMN-binding domain protein
           [Brachyspira hyodysenteriae WA1]
          Length = 325

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 122/242 (50%), Gaps = 20/242 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R  +R      LL TE++ A A+ R  KK    +     E P++LQ+ GA+
Sbjct: 21  MAGYTDYVFRRLSRKF-GAGLLVTELVSAAALARQVKKTYRYMEHKEDEYPISLQLFGAN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                 A +I +  G++ I++N+GCP+ +V + + GA L+ + D +   + A+     +P
Sbjct: 80  EDDYKRAIEITDLSGFSFIDINMGCPTKKVVKNNGGAGLLEDTDKMISVLNAVKSVSPLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           V+VK R+G+         R L  ++K++G   + +H R A  + +G +          D+
Sbjct: 140 VSVKIRLGLKRGEGGEIERAL--AMKENGACFLTLHGRYASDMYRGTA----------DW 187

Query: 177 DIVYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + + +IK+    D  +  NG ++    A+K   +  VDG+M+GR A  N  + T ++  F
Sbjct: 188 EAIAKIKEALGEDYILIGNGDIKSKEDAVKAFDISKVDGIMVGRGAIGNPWIFTELNTIF 247

Query: 234 SN 235
            +
Sbjct: 248 ED 249


>gi|295100970|emb|CBK98515.1| tRNA-U20-dihydrouridine synthase [Faecalibacterium prausnitzii
           L2-6]
          Length = 339

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 81/301 (26%), Positives = 138/301 (45%), Gaps = 26/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNI--LGFSTQEKPLALQIGG 56
           M  +TD   R   RL+  +   +T  EM+ + A++  D K +  L       P  +QI G
Sbjct: 20  MAGFTDAPCR---RLMAQHGAGFTVSEMVSSRALVYHDHKTVSLLKAEPNGAPYGVQIFG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + EAA  +E++ ++ +++N+GCP+ ++  G  G+ LML+PD+ G  +  +    +
Sbjct: 77  EVPQIMGEAAAAIEEYEFDFLDINMGCPAPKIVSGGAGSKLMLDPDLCGRIVEQVKAHTT 136

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            PVTVK R G D D I AV      K+ +++G   I +HAR         ++    P +D
Sbjct: 137 RPVTVKMRKGWDADHITAV---ECAKACEQAGAELIAVHART--------REQMYAPGID 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
            DI+ ++K       +G NG +     A++++     DGVMI RAA  +  +   V+   
Sbjct: 186 PDIIAKVKAAVKVPVLG-NGDIHTAEDAVEMMQRTGCDGVMIARAALGDPWLFERVNAAI 244

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P      ++ R++    R+    M +    +        Q   +M GL  G    RR
Sbjct: 245 EGLPAPKEPNLQARMNA--LRRQVEEMVEQKGEYTAMPQARAQTMHYMKGL-KGAAALRR 301

Query: 293 C 293
           C
Sbjct: 302 C 302


>gi|240120537|ref|ZP_04733499.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID24-1]
          Length = 364

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 166 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++   +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 211 ARYELIAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 269

Query: 232 Y 232
           Y
Sbjct: 270 Y 270


>gi|227888863|ref|ZP_04006668.1| tRNA-dihydrouridine synthase [Lactobacillus johnsonii ATCC 33200]
 gi|268318841|ref|YP_003292497.1| tRNA-dihydrouridine synthase B [Lactobacillus johnsonii FI9785]
 gi|227850700|gb|EEJ60786.1| tRNA-dihydrouridine synthase [Lactobacillus johnsonii ATCC 33200]
 gi|262397216|emb|CAX66230.1| tRNA-dihydrouridine synthase B [Lactobacillus johnsonii FI9785]
          Length = 335

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 116/239 (48%), Gaps = 21/239 (8%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  L    +E P+++QI G     LVEAA  V+     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGSEETLVEAAHYVDTHTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  +V +   GA  +L+P+ +   + A+ + +S PVTVK R G  DQ    A+ 
Sbjct: 101 NINMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSKPVTVKMRTGW-DQKHIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R         +    +   D++ + ++       F+G NG +
Sbjct: 160 NALAA-QEAGASAVAMHGRT--------RKQMYMGEADWETLKDVADALTIPFVG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRVDK 249
               +A  +L  V  D VM+GRAA  N  ++  +  Y        P T    ++T  D+
Sbjct: 210 TTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYLDTGEKLRPQTVEEKVETAKDQ 268


>gi|148726263|emb|CAL07960.2| putative dihydrouridine synthase [Ruminococcus flavefaciens]
          Length = 332

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 107/228 (46%), Gaps = 19/228 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR YR   +     A + +EM+ A  I   D+K   +   + +E+P+A+Q+ G++
Sbjct: 21  MAGVADRAYRLMCKRY-GAAYVVSEMVSAKGICYSDRKTAELCTVTEEERPMAVQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              + EA KIV D+  + I++N+GCP  +V     G+ LM +P +      A  KA    
Sbjct: 80  PDFMAEAVKIVLDYRPDIIDINMGCPVPKVVGTGAGSALMKDPALAAAITEAAVKAAGDT 139

Query: 118 PVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVK R G   D I A     + ++++ SG   I +H R         +D       D 
Sbjct: 140 PVTVKIRSGWSSDSINAP---EMARALEASGTAAIAVHGRT--------RDMFYSGQSDM 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           +++  +K+      IG NG + D     ++      D VMIGR +Y N
Sbjct: 189 NVIKAVKEAVSVPVIG-NGDITDAESCAEMYGRTGCDLVMIGRGSYGN 235


>gi|58697366|ref|ZP_00372700.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           simulans]
 gi|58536243|gb|EAL59783.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           simulans]
          Length = 262

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 95/205 (46%), Gaps = 25/205 (12%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           A+Q+ G +   + EAAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A
Sbjct: 9   AVQLAGCEPDVMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEA 68

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSP 165
           + KA+++PVTVK R G +D+      RN   L K  +  G   I +H R    +  G + 
Sbjct: 69  VVKAVNMPVTVKMRTGWNDE-----NRNAPRLAKIAEDLGAKMITVHGRTRAQLYNGQA- 122

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKN 222
                    D+  V  + KE   + + +NG    L D+  ALK     DGVMIGR AY  
Sbjct: 123 ---------DWKFVRNV-KEQVKIPVIVNGDIKNLNDIQNALK-ESGADGVMIGRGAYGK 171

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRV 247
             ++     + S   T       R+
Sbjct: 172 PWLINQAMNFLSGSETSEPTASERL 196


>gi|254409857|ref|ZP_05023638.1| putative TIM-barrel protein, nifR3 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196183854|gb|EDX78837.1| putative TIM-barrel protein, nifR3 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 334

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 76/310 (24%), Positives = 138/310 (44%), Gaps = 30/310 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R   R     +++YTEM+ A  +  ++G  K I+     EKP+++Q+       L
Sbjct: 36  TDLVFRRLVRRYAPESMMYTEMVHAAGLHHVQGLSK-IMDVDPNEKPISIQLFDCRPDFL 94

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+     G + +++N+GCP  ++ +   G+ L+  P+     + A+ +A+S+PVTVK
Sbjct: 95  GEAAQKAVAEGADTVDINMGCPVNKITKKGGGSSLLREPETAVAIVRAVVEAVSVPVTVK 154

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG  D    + + N  + ++++G   + +HAR    +    K   K     ++ + ++
Sbjct: 155 TRIGWSDD--EINILNFAQRMEEAGAQMLTLHART---RAQGYKGEAK-----WEWIGKV 204

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN--PLT 238
           K+      I  NG +  +  A++ L     DGVM  R       ++  +D +      L 
Sbjct: 205 KQILSIPVIA-NGDIFSVESAVRCLEQTGADGVMCSRGTLGYPFLVGEIDHFLKTGKQLA 263

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR---- 294
             +P++        R I A     A         +QQ  +H+     GF  +   R    
Sbjct: 264 PPTPVE--------RLICAKEHLQALWEYKGDRGVQQARKHLAWYTKGFVGASDLRDQLS 315

Query: 295 HILTVEAGAS 304
            I TVE G +
Sbjct: 316 RIETVEQGVT 325


>gi|325204406|gb|ADY99859.1| dihydrouridine synthase [Neisseria meningitidis M01-240355]
          Length = 336

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 111/241 (46%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  +    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHEDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCR-LNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|59800609|ref|YP_207321.1| hypothetical protein NGO0151 [Neisseria gonorrhoeae FA 1090]
 gi|240013465|ref|ZP_04720378.1| hypothetical protein NgonD_02246 [Neisseria gonorrhoeae DGI18]
 gi|260441186|ref|ZP_05795002.1| hypothetical protein NgonDG_08906 [Neisseria gonorrhoeae DGI2]
 gi|59717504|gb|AAW88909.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
          Length = 334

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 136 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++   +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|206974138|ref|ZP_03235055.1| conserved hypothetical protein [Bacillus cereus H3081.97]
 gi|217957892|ref|YP_002336436.1| hypothetical protein BCAH187_A0408 [Bacillus cereus AH187]
 gi|222094091|ref|YP_002528148.1| dihydrouridine synthase family protein [Bacillus cereus Q1]
 gi|206747378|gb|EDZ58768.1| conserved hypothetical protein [Bacillus cereus H3081.97]
 gi|217065496|gb|ACJ79746.1| conserved hypothetical protein [Bacillus cereus AH187]
 gi|221238146|gb|ACM10856.1| dihydrouridine synthase family protein [Bacillus cereus Q1]
          Length = 329

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     E +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFREMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|88858409|ref|ZP_01133051.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas tunicata D2]
 gi|88820026|gb|EAR29839.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas tunicata D2]
          Length = 323

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/249 (27%), Positives = 120/249 (48%), Gaps = 28/249 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K  N +  S +    A+QI GAD
Sbjct: 17  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPDVWKTEKSMNRMDHSGESGIRAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   +++N+GCP+ +V++   G+ L+  PD+V + I A+  A+ +P
Sbjct: 76  PELMAQAAQFNVANGAQIVDINMGCPAKKVNKKLAGSALLQYPDLVEEIIKAVVSAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V    + K  +++G+  + +H R    + KG +          +
Sbjct: 136 VTLKIRTGWDTDNRNGV---EIAKIAERNGIASLAVHGRTKACMYKGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA------YKNSAMLT 227
           Y  + +IK+ +  + I  NG +    +A ++L     D +MIGRAA      ++ +A   
Sbjct: 183 YQTIRDIKR-SVSIPIVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFRETAHYL 241

Query: 228 TVDEYFSNP 236
              E    P
Sbjct: 242 QTGELLPTP 250


>gi|229142705|ref|ZP_04271179.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST26]
 gi|228640768|gb|EEK97125.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 336

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     E +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFREMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 245


>gi|291044520|ref|ZP_06570229.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae DGI2]
 gi|293397656|ref|ZP_06641862.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae F62]
 gi|291011414|gb|EFE03410.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae DGI2]
 gi|291611602|gb|EFF40671.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae F62]
          Length = 340

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 23  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 82  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 141

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
           VT+K R+G  D    +PA+A     K  +  G+  + +H  AR  + KG           
Sbjct: 142 VTLKTRLGWHDDHQNLPAIA-----KIAEDCGIAALAVHGRARTQMYKG----------E 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++   +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 187 ARYELIAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 245

Query: 232 Y 232
           Y
Sbjct: 246 Y 246


>gi|188582181|ref|YP_001925626.1| hypothetical protein Mpop_2936 [Methylobacterium populi BJ001]
 gi|179345679|gb|ACB81091.1| TIM-barrel protein, nifR3 family [Methylobacterium populi BJ001]
          Length = 342

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/220 (29%), Positives = 110/220 (50%), Gaps = 19/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLV 63
           TD H R  A+ L  +A++ +EM+ A  + +GD ++ +        P  +Q+ G   + + 
Sbjct: 32  TDLHMRRLAQRLGASAVV-SEMVAAAELAKGDAESQVRAEGAGISPHVVQLAGCAPAPMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+++PVTVK 
Sbjct: 91  EAARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVAVPVTVKM 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D    ++   +L    +  G+NG+ +H   R+   KG +          D+  +  
Sbjct: 151 RLGWDHA--SLNAPDLACRAEALGLNGVTVHGRTRQQFYKGRA----------DWSAIRA 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           +  E   + +  NG +  + +A   L      GVMIGRAA
Sbjct: 199 V-VEAVGIPVIANGDITSLDEARVCLRESGAAGVMIGRAA 237


>gi|55822169|ref|YP_140610.1| putative transcriptional regulator [Streptococcus thermophilus
           CNRZ1066]
 gi|55738154|gb|AAV61795.1| possible transcriptional regulator [Streptococcus thermophilus
           CNRZ1066]
          Length = 350

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 117/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 49  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 107

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 108 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++     + D++
Sbjct: 168 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGR--------TREQMYTGHCDHE 216

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG + ++  A  ++    VD VM+GRAA  N  + T ++ +F 
Sbjct: 217 TLARVAKAITKIPFIG-NGDVRNVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFE 275


>gi|307720977|ref|YP_003892117.1| TIM-barrel protein, nifR3 family [Sulfurimonas autotrophica DSM
           16294]
 gi|306979070|gb|ADN09105.1| TIM-barrel protein, nifR3 family [Sulfurimonas autotrophica DSM
           16294]
          Length = 317

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 116/222 (52%), Gaps = 20/222 (9%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISK 61
           +TD  +R   +    + L  +EM+ ++A+  G +K  ++L  S+ E P ++QI GAD+  
Sbjct: 20  FTDLPFRSVVKKFGAD-LTVSEMLSSNALAHGSQKTLHMLEKSSLEDPYSVQIAGADVDI 78

Query: 62  LVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +  A +I+ E  G + I+LN GCP  +V     G+ L+L+  ++G+ I  +    +  +T
Sbjct: 79  VRSAVEILNEQEGIDIIDLNCGCPVPKVVGHGSGSSLLLDLPLMGEIIKTIKDTSNKSMT 138

Query: 121 -VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            VK R+G +++       ++ K ++ SG + I +H R         +  +    +DYD +
Sbjct: 139 SVKIRLGFEEKKHV----DIAKVVQDSGADFIAVHGR--------TRAGKFKAAVDYDAI 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            EI KE  D+ +  NG ++   +A  +L     DGVMIGR A
Sbjct: 187 REI-KEAVDIPVIANGDIDSYEKAKWVLEHTGADGVMIGRGA 227


>gi|321314532|ref|YP_004206819.1| putative tRNA-dihydrouridine synthase [Bacillus subtilis BSn5]
 gi|320020806|gb|ADV95792.1| putative tRNA-dihydrouridine synthase [Bacillus subtilis BSn5]
          Length = 325

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 106/233 (45%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRKMSIGMAELGFKGLDINMGCPVPNVTQNGKGSGLIRRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       R  +  I K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGFTD---VDEWREWLTHILKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTN 238


>gi|303390091|ref|XP_003073277.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
 gi|303302422|gb|ADM11917.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
          Length = 341

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 114/236 (48%), Gaps = 25/236 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQE--KPLALQIGG 56
           MV  ++  +R  ++    N L YTEM+  ++ LRG +  +    ++T E  +PL +QI G
Sbjct: 18  MVGNSEEAWRRLSKRHGAN-LFYTEMVHCESFLRGSRNPVKNRWYTTSESDRPLVIQICG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                ++EAA I+++   + I++N GCP     +G +GA L  N D+    +  +   L+
Sbjct: 77  NSPKTMLEAALIMQNHC-DAIDINFGCPQKVARKGGYGAYLQENWDLTERIVKVLSTGLN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+  C+I V + I         K I+K+G + + +H R    KG         P +  
Sbjct: 136 VPVS--CKIRVFESIEKTV--EYAKMIEKAGCSLLAVHGRTRDQKG---------PAMGL 182

Query: 177 DIVYEIK--KENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
                IK  KEN  + +  NG +   ED+ + L+     DGVM+G A   N  + T
Sbjct: 183 ASWDHIKAVKENLKIPVLSNGNIMTHEDVWKCLE-YTKCDGVMVGEAHLYNPLIFT 237


>gi|50085634|ref|YP_047144.1| hypothetical protein ACIAD2557 [Acinetobacter sp. ADP1]
 gi|49531610|emb|CAG69322.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. ADP1]
          Length = 341

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 82/327 (25%), Positives = 149/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  ++SG+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KQAEQSGIAALALHGR--------TREDMYLSTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD++ ++K       I  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDLIKQVKSILTIPVIA-NGDIDSPQKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPDIAEVKEVLLGHLSELYRFYGE---YSGCRIAR--KHIAWYTKGLHSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE+ A  A   ++E  FN ++
Sbjct: 297 RQNMYQVESTAEQA--RLVEAYFNHLL 321


>gi|119946821|ref|YP_944501.1| tRNA-dihydrouridine synthase [Psychromonas ingrahamii 37]
 gi|119865425|gb|ABM04902.1| tRNA-dihydrouridine synthase [Psychromonas ingrahamii 37]
          Length = 319

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/256 (24%), Positives = 121/256 (47%), Gaps = 26/256 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L  +EM+ ++  +   +K+ L   +  +    ++QI G++
Sbjct: 17  MAGVTDRPFRELCRK-QGAGLAVSEMLSSNPRVWNSRKSKLRMDYHNESGIRSVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++    G   I++N+GCP+ +V++   G+ L+ +P++V   +  +  A+ +P
Sbjct: 76  PLAMATAAQLSVQQGAQIIDINMGCPAKKVNKKKAGSALLPHPELVRAILETVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G D        RN   + +  ++SG+  + +H   R+    G +         
Sbjct: 136 VTLKIRTGWDPD-----SRNGLEIARIAEQSGIQALAVHGRTRQCFYNGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD + +I K+N  + +  NG +  + +A  +L     D +MIGR A     +   ++ 
Sbjct: 182 -EYDTIKKI-KQNVTIPVIANGDITSVEKAKFVLDYTGADAIMIGRGAQGAPWIFNEINH 239

Query: 232 YFSNPLTGSSPIKTRV 247
           Y +     SSP K  +
Sbjct: 240 YLTTGEQLSSPAKAEI 255


>gi|116627125|ref|YP_819744.1| putative transcriptional regulator [Streptococcus thermophilus
           LMD-9]
 gi|116100402|gb|ABJ65548.1| tRNA-dihydrouridine synthase [Streptococcus thermophilus LMD-9]
 gi|312277599|gb|ADQ62256.1| tRNA-dihydrouridine synthase B [Streptococcus thermophilus ND03]
          Length = 325

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 117/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG + ++  A  ++    VD VM+GRAA  N  + T ++ +F 
Sbjct: 192 TLARVAKAITKIPFIG-NGDVRNVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFE 250


>gi|300023200|ref|YP_003755811.1| hypothetical protein Hden_1683 [Hyphomicrobium denitrificans ATCC
           51888]
 gi|299525021|gb|ADJ23490.1| TIM-barrel protein, nifR3 family [Hyphomicrobium denitrificans ATCC
           51888]
          Length = 328

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 112/243 (46%), Gaps = 22/243 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLV 63
           +D  +R  A  L     + +EMI ++ +++     +     +E  P  +Q+ G +   + 
Sbjct: 21  SDLPFRRLAHRL-GATFVVSEMIASEELVKSRADVLRRAEGRELTPFVMQLAGREERWMA 79

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           + A+I E  G + I++N+GCP+  V     G+ LM N D     I A+ +A+++PVT+K 
Sbjct: 80  DGARIAEAKGADVIDINMGCPAKEVTGKLSGSALMRNLDHAQSLIRAVVQAVNVPVTLKM 139

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D+     A  +L +  +  GV  I +H R       G +          D+  V  
Sbjct: 140 RLGWDETSRNAA--DLARRAEAEGVKLITVHGRTRCQFFTGTA----------DWQGVRP 187

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   L + +NG +   S A K L +   DGVM+GR AY    M   +   FS   TG
Sbjct: 188 V-VEATSLPVLVNGDINGPSDARKALDASGADGVMVGRGAYGAPWMPGRIAATFS---TG 243

Query: 240 SSP 242
             P
Sbjct: 244 RDP 246


>gi|304405943|ref|ZP_07387601.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
 gi|304345186|gb|EFM11022.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
          Length = 312

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+P+   I G
Sbjct: 5   MEDVTDVVFRHVVSEAGRPDVFFTEFTNTESYCHPDGNQSVRGRLAFTEDEQPIVAHIWG 64

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V +   G+ L+  P+     I A  KA  
Sbjct: 65  DKPEYFRQMSIGMAQQGFKGIDINMGCPVANVAQNGQGSGLICRPETAAAIIQA-TKAGG 123

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G D        R+ +  I K G+  + IH R       +  +  K+ +  +
Sbjct: 124 LPVSVKTRLGFD---AIEEWRDWLTHILKQGIANLSIHLR-------TRAEMSKV-DAHW 172

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 173 ELIPEIKKLRDEVAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFNN 224


>gi|262283589|ref|ZP_06061354.1| tRNA-dihydrouridine synthase B [Streptococcus sp. 2_1_36FAA]
 gi|262260646|gb|EEY79347.1| tRNA-dihydrouridine synthase B [Streptococcus sp. 2_1_36FAA]
          Length = 325

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFE 250


>gi|254820536|ref|ZP_05225537.1| dihydrouridine synthase [Mycobacterium intracellulare ATCC 13950]
          Length = 377

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 76/295 (25%), Positives = 129/295 (43%), Gaps = 23/295 (7%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           +++ T + L   EM+ A A++       ++  F+  E P +LQ+   D +    AAK++ 
Sbjct: 35  SKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSLQLYTVDPATTYAAAKMIA 94

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIG 126
           D G  + I++N GCP  +V +   G+ L     + G  +AA  +A     IPVTVK RIG
Sbjct: 95  DEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAAVRATEGTQIPVTVKFRIG 154

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD+       +  +  +  G   + +HAR A          R     D+D +  +K+  
Sbjct: 155 IDDE--HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWDEIARLKQHV 204

Query: 187 PDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             + +  NG + D S AL ++ +   DGV+IGR       +   +   F+     + P  
Sbjct: 205 RTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLFAELSAAFTGSPPPTPPTL 264

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             V  D  R+    +    A H      ++ I +H+    HGFP     R  L +
Sbjct: 265 GEV-ADIVRRHGQLL----AAHFGEDKGMRDIRKHIAWYLHGFPAGSELRRALAM 314


>gi|322834713|ref|YP_004214740.1| TIM-barrel protein, nifR3 family [Rahnella sp. Y9602]
 gi|321169914|gb|ADW75613.1| TIM-barrel protein, nifR3 family [Rahnella sp. Y9602]
          Length = 321

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  + A+QI G D
Sbjct: 17  MAGITDRPFRALCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHNDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ KA+ +P
Sbjct: 76  PEDMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V+  +     G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVQIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRTV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|311113192|ref|YP_003984414.1| tRNA-dihydrouridine synthase B [Rothia dentocariosa ATCC 17931]
 gi|310944686|gb|ADP40980.1| tRNA-dihydrouridine synthase B [Rothia dentocariosa ATCC 17931]
          Length = 388

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/296 (24%), Positives = 128/296 (43%), Gaps = 23/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T++ +R   R      L  TEM+ A A++  + +   I+     E+  ++QI G D
Sbjct: 29  MAGVTNKAFRRLCREY-GGGLYVTEMVTARALVERKPESMRIIEHDADEQIRSIQIYGVD 87

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A + +VE+   + I+LN GCP+ +V +   GA L    D+    +    K  S 
Sbjct: 88  AVNVGKAIRLVVEEDRADHIDLNFGCPAPKVTKRGGGAALPWKTDLFTAIVHTAVKEASR 147

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + +GV  I +H R A                
Sbjct: 148 NDIPLTIKMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTAA--------QHYSGTA 197

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + ++++   D+ I  NG +     A++++    VDGV+IGR       +   +   
Sbjct: 198 DWDSIAQLREAISDVPILGNGDIFAAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNA 257

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           F        P  + V    +R     +  +A  +      L++I +H+   F G+P
Sbjct: 258 FEGSTERIRPTLSEVAAMIYRHAELLVETFADEY----KGLREIRKHVAWYFKGYP 309


>gi|325188155|emb|CCA22696.1| tRNAdihydrouridine synthase putative [Albugo laibachii Nc14]
          Length = 367

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 114/248 (45%), Gaps = 23/248 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M  +       +     F    +++PL +Q  G D
Sbjct: 26  MVDQSELAFRMLCRH-HGAQLCYTPMFHSRLFAESQEYRTRMFEQHVRDRPLIVQFCGND 84

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +V AAK VE  G+ + +++N+GCP     +G++GA LM     V + +  +   +++
Sbjct: 85  GDTMVAAAKYVE--GHCDAVDINLGCPQGIARKGNYGAFLMKEKTRVCEIVEKLVAEVAV 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R+  D+           + ++K+G + + IH R   +  ++      +  +D++
Sbjct: 143 PVTCKIRVFPDE----AETIEFSRMLEKAGCDLLVIHGRTKEMNKVT------VGQVDWE 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  IK     + +  NGG+E     +K L   S DGVM   A   N A+    DE F N
Sbjct: 193 IIKRIKS-TLSIPVIANGGIETADDIVKCLEATSADGVMSSEAILGNPALF---DEPFRN 248

Query: 236 -PLTGSSP 242
            PL    P
Sbjct: 249 DPLDPKGP 256


>gi|71909277|ref|YP_286864.1| dihydrouridine synthase TIM-barrel protein nifR3 [Dechloromonas
           aromatica RCB]
 gi|71848898|gb|AAZ48394.1| tRNA-U20-dihydrouridine synthase [Dechloromonas aromatica RCB]
          Length = 337

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 111/241 (46%), Gaps = 23/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G  K +       +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
              + EAAK   D G   I++N+GCP+ +V     G+ LM +   VG  + A+  A+ + 
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKVCNVMAGSALMQDEQQVGRILDAVVAAIPNT 135

Query: 118 PVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVT+K R G    +   P +A     +  + +G+  + IH R         +  +     
Sbjct: 136 PVTLKFRTGWNLANKNAPTIA-----RIAESAGIRAVAIHGRT--------RCQQYTGEA 182

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K       I  NG +    +A  +L     DGVMIGRAA     +   ++ Y
Sbjct: 183 EYDTIAMVKTLISIPVIA-NGDITTPEKAKHVLDVTGADGVMIGRAAQGRPWLFREIEHY 241

Query: 233 F 233
            
Sbjct: 242 L 242


>gi|317497926|ref|ZP_07956235.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894805|gb|EFV16978.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 312

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 101/231 (43%), Gaps = 34/231 (14%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI        +  AK +++ GY+E+NLN+GCPS  V     G+  +  P+++ D +  + 
Sbjct: 64  QILTKSSEDFIRTAKELKELGYDEVNLNLGCPSRTVVAKQKGSGFLREPEVLDDFLTEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +AL + +++K RIG+ D         ++    +  V  + IH R      L  +  +  P
Sbjct: 124 EALDMKISIKTRIGLRD---TEEFEEILSIYNRHPVYELTIHPR------LQQEFYKGKP 174

Query: 173 NLDYDIVYEI---KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT-- 227
           +LD   V+E      ENP  + G     ED        P VD VMIGR   +N A++   
Sbjct: 175 HLD---VFEYAVNHSENPLCYNGDIVTKEDYDNITTRFPDVDAVMIGRGLLRNPALVREI 231

Query: 228 ----------------TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                           T+ E +   L+G   +  ++ K+FW   +   T++
Sbjct: 232 KYGQKLTKRELLKMHDTLYEAYQGYLSGDKNVLYKM-KEFWNNAAVMFTNH 281


>gi|114762893|ref|ZP_01442325.1| tRNA-dihydrouridine synthase, putative [Pelagibaca bermudensis
           HTCC2601]
 gi|114544503|gb|EAU47510.1| tRNA-dihydrouridine synthase, putative [Roseovarius sp. HTCC2601]
          Length = 327

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 105/214 (49%), Gaps = 21/214 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           R+ A L+ +  +   E + A    R  +K  LG + +    ++QI G     + EAA++V
Sbjct: 33  RWGAGLVVSEMIASGEFLTARPGTR--EKAELGAAIENT--SVQIAGRAPEPMAEAARMV 88

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            D G   I++N+GCP+ +V  G  G+ LM +PD     I A+  A+ +PVT+K R+G DD
Sbjct: 89  ADMGARVIDINMGCPAKKVTGGYSGSALMRDPDHALRLIEAVVAAVDLPVTLKTRLGWDD 148

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
              ++    L    + +G+  I IH R      KG +          D+  + ++ KE  
Sbjct: 149 G--SLNAPELAARAEAAGIRMIVIHGRTRCQFYKGRA----------DWAAIRKV-KEAV 195

Query: 188 DLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
            + +  NG + D + A +   L   DGVM+GR A
Sbjct: 196 SVPLVANGDITDAASAREALRLSGADGVMVGRGA 229


>gi|322373801|ref|ZP_08048336.1| tRNA-dihydrouridine synthase family protein [Streptococcus sp.
           C150]
 gi|321277173|gb|EFX54243.1| tRNA-dihydrouridine synthase family protein [Streptococcus sp.
           C150]
          Length = 349

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++     + D++
Sbjct: 167 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGR--------TREQMYTGHCDHE 215

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VM+GRAA  N  + T ++ +F 
Sbjct: 216 TLARVAKAITKIPFIG-NGDVRSVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFE 274


>gi|229159471|ref|ZP_04287488.1| tRNA-dihydrouridine synthase [Bacillus cereus R309803]
 gi|228623979|gb|EEK80788.1| tRNA-dihydrouridine synthase [Bacillus cereus R309803]
          Length = 336

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 245


>gi|254303688|ref|ZP_04971046.1| dihydrouridine--tRNA ligase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323880|gb|EDK89130.1| dihydrouridine--tRNA ligase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 307

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/254 (28%), Positives = 114/254 (44%), Gaps = 43/254 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       +  A+QI G DI K+ E+AK +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIKKIKESAKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    ++VK RIG  +    + +  
Sbjct: 88  CGCPMKKIVNCGYGAALVREPEKIKKILSEIKSILNDDTKLSVKIRIGYKEPENYIQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + I   G + I IH R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEI---GCDHITIHGRTREQLYSGKADWKYIKEVKDNVSIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS-----NPLTGSSPI- 243
           F G    LE +S +     +VDGVM+ R  + N  ++  + E         P T    I 
Sbjct: 195 FTG-EDALEKISYS-----NVDGVMLARGIFGNPWLIRDIREILEYGEIKTPTTKEDKIN 248

Query: 244 -------KTRVDKD 250
                  + RVD D
Sbjct: 249 MAIEHLKRIRVDND 262


>gi|332289637|ref|YP_004420489.1| tRNA-dihydrouridine synthase B [Gallibacterium anatis UMN179]
 gi|330432533|gb|AEC17592.1| tRNA-dihydrouridine synthase B [Gallibacterium anatis UMN179]
          Length = 324

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/218 (27%), Positives = 106/218 (48%), Gaps = 19/218 (8%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL ++EM+  +  +   +K+ L  +   Q    A+QI G+D  ++ +AA++   +G   I
Sbjct: 35  ALTFSEMMSTNPDVWHTEKSKLRLAHHPQIGINAVQIAGSDPDEMAQAAQVNVGYGAEII 94

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +PVT+K R G D Q     L 
Sbjct: 95  DINMGCPAKKVNRKLAGSALLQYPDLVAKILNAVVSAVDVPVTLKIRTGWDQQHKNCVL- 153

Query: 138 NLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            + K  + +G+  + IH R    +  G            +YD +  +KK      I  NG
Sbjct: 154 -IAKIAQDAGIQALSIHGRTRACLFNG----------EAEYDSIKAVKKAVSIPVIA-NG 201

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            ++   +A  +L     D +M+GR A  N  +   + E
Sbjct: 202 DIDSAEKAKYVLDYTEADAIMLGRGALGNPWIFREITE 239


>gi|156935780|ref|YP_001439696.1| tRNA-dihydrouridine synthase B [Cronobacter sakazakii ATCC BAA-894]
 gi|156534034|gb|ABU78860.1| hypothetical protein ESA_03650 [Cronobacter sakazakii ATCC BAA-894]
          Length = 327

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 23  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPEVWASDKSRLRMVHVDEPGIRTVQIAGSV 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 82  PEEMAEAARINVDNGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTAVVNAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      A RN V   +  ++ G+  + IH R    + +G          N
Sbjct: 142 VTLKIRTGWDP-----ANRNCVEIAQLAEECGIQALTIHGRTRACLFQG----------N 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG +    +A  +L     D +MIGRAA     +   +  
Sbjct: 187 AEYDSIRTVKQKVSIPVIA-NGDITSPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 245

Query: 232 YF 233
           Y 
Sbjct: 246 YL 247


>gi|298369297|ref|ZP_06980615.1| tRNA-dihydrouridine synthase B [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298283300|gb|EFI24787.1| tRNA-dihydrouridine synthase B [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 332

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 104/236 (44%), Gaps = 16/236 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D   R   K +    F  +E   A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVGEMLHSDPAFRNTAKTLHRSDFGGEEGVAAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA      G   I++N+GCP+ +V     G+ LM N  +V   + A+  A  +P
Sbjct: 76  PRQMAEAAVYNVALGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVGAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    +    + +  ++SG+  I IH R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHKNIL--TVARIAEESGIAAIAIHGRT--------RTQMYRGEASYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           + E K    ++ + +NG +    +A  +L     DGVMIGR A     +   +  Y
Sbjct: 186 IAEAKGRL-NIPVWVNGDITSPQKAAAVLRQTGADGVMIGRGAQGRPWLFRDLAHY 240


>gi|261206596|ref|ZP_05921294.1| dihydrouridine synthase [Enterococcus faecium TC 6]
 gi|289564958|ref|ZP_06445412.1| tRNA dihydrouridine synthase B [Enterococcus faecium D344SRF]
 gi|294617006|ref|ZP_06696726.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1636]
 gi|260079089|gb|EEW66782.1| dihydrouridine synthase [Enterococcus faecium TC 6]
 gi|289163165|gb|EFD11011.1| tRNA dihydrouridine synthase B [Enterococcus faecium D344SRF]
 gi|291590160|gb|EFF21949.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1636]
          Length = 327

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSSAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D     ++     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKN 238


>gi|301300310|ref|ZP_07206517.1| TIM-barrel protein, nifR3 family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852083|gb|EFK79760.1| TIM-barrel protein, nifR3 family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 330

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 110/223 (49%), Gaps = 21/223 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +KK  ++L     E P+++QI G     LVEAA+ V ++   + I
Sbjct: 38  LVVCEMISDKGIHFRNKKTLDMLFVDPTEHPVSVQIFGGSKETLVEAAQFVAKNTATDII 97

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVAL 136
           ++N+GCP  +V +   GA  +L+PD + + + A+  ++  PVTVK R G D D I  +A+
Sbjct: 98  DINMGCPVPKVTKTDAGARWLLDPDKIYEMVHAVTSSIDKPVTVKMRTGWDEDHI--LAV 155

Query: 137 RNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            N + + ++ G   + +H   RK +  G          + D+ I+ E+      +    N
Sbjct: 156 ENALAA-EEGGAKALAMHGRTRKQLYTG----------HADWGILKEVADHLTKIPFMGN 204

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           G +    +A K+L  V  D VMIGRAA  N  ++     Y   
Sbjct: 205 GDVRTPEEAKKMLDEVGADAVMIGRAALGNPWIVKQTTHYLET 247


>gi|329666682|gb|AEB92630.1| tRNA-dihydrouridine synthase [Lactobacillus johnsonii DPC 6026]
          Length = 335

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 116/239 (48%), Gaps = 21/239 (8%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  L    +E P+++QI G     LVEAA  V+     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGSEETLVEAAHYVDTHTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  +V +   GA  +L+P+ +   + A+ + +S PVTVK R G  DQ    A+ 
Sbjct: 101 NINMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSKPVTVKMRTGW-DQKHIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R         +    +   D++ + ++       F+G NG +
Sbjct: 160 NALAA-QEAGASAVAMHGRT--------RKQMYMGEADWETLKDVADALTIPFVG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRVDK 249
               +A  +L  V  D VM+GRAA  N  ++  +  Y        P T    ++T  D+
Sbjct: 210 TTPEKAKVMLEDVGADAVMVGRAALGNPWIIKDMVHYLDTGEKLRPQTVEEKVETAKDQ 268


>gi|228476444|ref|ZP_04061134.1| tRNA-dihydrouridine synthase B [Streptococcus salivarius SK126]
 gi|228251865|gb|EEK10911.1| tRNA-dihydrouridine synthase B [Streptococcus salivarius SK126]
          Length = 325

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VM+GRAA  N  + T ++ +F 
Sbjct: 192 TLARVAKAITKIPFIG-NGDVRSVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFE 250


>gi|83648649|ref|YP_437084.1| tRNA-dihydrouridine synthase [Hahella chejuensis KCTC 2396]
 gi|83636692|gb|ABC32659.1| tRNA-dihydrouridine synthase [Hahella chejuensis KCTC 2396]
          Length = 336

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 120/242 (49%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ A+  LR  +K+ L      + +P+A+QI GA+
Sbjct: 24  MAGVTDRPFRLLCRSL-GAGLAVSEMMAANPDLRDTRKSRLRMDHDGEGEPIAVQIAGAE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+S+P
Sbjct: 83  PEMLAEAARYNVEHGAQIIDINMGCPAKKVCNKAAGSALLRDEALVKDILTAVVSAVSVP 142

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G   Q      RN   + +  +  G+  + +H R         ++ +     +
Sbjct: 143 VTLKIRTGWSRQ-----SRNGVTVARIAEDCGIQSLAVHGRT--------RECKYEGTAE 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + EI K++  + +  NG +  + QA  +L    VD +MIGR A     +   ++ + 
Sbjct: 190 YDTIAEI-KQSVSIPVVANGDITCVEQARHVLDYTGVDALMIGRGAQGRPWIFREIEHFI 248

Query: 234 SN 235
           + 
Sbjct: 249 AT 250


>gi|229095037|ref|ZP_04226033.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-29]
 gi|229113990|ref|ZP_04243416.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-3]
 gi|228669449|gb|EEL24865.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-3]
 gi|228688367|gb|EEL42249.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-29]
          Length = 336

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|255659250|ref|ZP_05404659.1| tRNA-dihydrouridine synthase [Mitsuokella multacida DSM 20544]
 gi|260848704|gb|EEX68711.1| tRNA-dihydrouridine synthase [Mitsuokella multacida DSM 20544]
          Length = 322

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 118/240 (49%), Gaps = 17/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   +++ +  L    +E+PLA+QI    
Sbjct: 17  MAGVTDTAYRIIAHDM-GCPLCFAEMVSSQGIHFRNERTLAMLQSEKEERPLAMQIFANT 75

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                EAA  VE  G  +I + N+GCP+ ++ +   G+ LM +P+     ++A+ KA+ +
Sbjct: 76  PEMAAEAAAFVEALGTADILDFNMGCPAPKIVKNGEGSALMRDPERAFAILSAIRKAVKM 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D    +V +  + K  +++GV+ I +H R         ++       D++
Sbjct: 136 PVTVKMRKGWD--AASVNVVEMAKLAEEAGVDAIAVHGRT--------REQFYTGRADWE 185

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+  + P +  G     +D+ + ++ +   DGVMIGRAA  N  +      Y   
Sbjct: 186 IIGEVKRAVKIPVIANGDVRTFDDLDK-IRAVTGCDGVMIGRAAQGNPWIFRQFTHYLET 244


>gi|77359313|ref|YP_338888.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874224|emb|CAI85445.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 326

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K  N +  S +    A+QI GAD
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGLAVSEMLSSNPDVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  +    ++ G+  + +H R    + KG +          +
Sbjct: 139 VTLKIRTGWDLDNRNGVEIARIA---ERYGIASLAVHGRTRACMYKGEA----------E 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y 
Sbjct: 186 YATIRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYL 244


>gi|315645321|ref|ZP_07898446.1| histidine phosphokinase/phophatase, putative [Paenibacillus vortex
           V453]
 gi|315279363|gb|EFU42669.1| histidine phosphokinase/phophatase, putative [Paenibacillus vortex
           V453]
          Length = 329

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 102/232 (43%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V E   G+ L+  PDI  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPDIAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R  +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFSS---VDEWRGWLTHILKQDIVNLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  ++N
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFQN 238


>gi|330685277|gb|EGG96938.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU121]
          Length = 326

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/221 (27%), Positives = 107/221 (48%), Gaps = 31/221 (14%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E+P+   I G    +  E +  + 
Sbjct: 40  FFTEFTNTASFCHPEGIHS---VRGR----LTFSEDEQPMVAHIWGDQPEQFREMSIGLA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---V 127
           + G+  I+LN+GCP A V +   G+ L+L P++  + I A  KA  +PV+VK R+G   +
Sbjct: 93  EMGFKGIDLNMGCPVANVAQKGKGSGLILRPEVAAEIIQA-TKAGGLPVSVKTRLGFYEI 151

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN- 186
           D+       R+ +K + +  +  + IH R       + K+  K+ +  ++++  IK+   
Sbjct: 152 DE------WRDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHWELIEAIKQLRD 197

Query: 187 ---PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 198 EIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFHN 238


>gi|254464462|ref|ZP_05077873.1| tRNA-dihydrouridine synthase B [Rhodobacterales bacterium Y4I]
 gi|206685370|gb|EDZ45852.1| tRNA-dihydrouridine synthase B [Rhodobacterales bacterium Y4I]
          Length = 319

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G +
Sbjct: 10  MAGITDRPFRDLVRSF-GVGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRE 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK V   G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+ +P
Sbjct: 69  EYWIAEAAKQVAGQGARIIDINMGCPAKKVTNGYSGSALLKTPDHALRLIEAVVGAVDVP 128

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R+G DD     P VA R       ++GV  + IH R      KG          +
Sbjct: 129 VTLKTRLGWDDNCLNAPDVARR-----AAEAGVQMVTIHGRTRCQFYKG----------S 173

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
            D+  +  + K+  ++ +  NG + D + A +   L   DGVMIGR A     +L  V  
Sbjct: 174 ADWAAIRSV-KDAVNVPVLANGDIVDTASARQALELSGADGVMIGRGAEGKPWLLAEVAH 232

Query: 232 YF 233
           + 
Sbjct: 233 HL 234


>gi|157363261|ref|YP_001470028.1| dihydrouridine synthase DuS [Thermotoga lettingae TMO]
 gi|157313865|gb|ABV32964.1| dihydrouridine synthase DuS [Thermotoga lettingae TMO]
          Length = 305

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 125/273 (45%), Gaps = 28/273 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           +TEMI A++++R  K         E  +A+Q+ G D   L +AAKIVE +    I++N  
Sbjct: 22  FTEMISAESVVRNFKTVQRMLPKDEPNVAVQLFGNDPKTLAQAAKIVEPYAA-WIDINAA 80

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP  +V + + G  L+ + + +   I ++  ++  PVTVK RIG +  I    L  +V S
Sbjct: 81  CPVKKVIKKNSGGALLNDLERLEKIIGSVKSSVQKPVTVKIRIGFEKNI----LDQIVHS 136

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
             K+G +GI +H R  + K  S K    +    Y I   +   + D+F       ED  +
Sbjct: 137 CIKAGADGIEVHGRTVVQK-YSGKAFWDLKLSQYGISTAV---SGDIFEA-----EDFHK 187

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           AL+ +   +  +I R A +   +   + +         +P  T + + F + +   + D 
Sbjct: 188 ALE-MSGANSALIARGALRKPWIFAQITQ-------KRTPKITEIKETFTKHLKMQIEDE 239

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             R ++   K++Q    + G  HG   +R  R 
Sbjct: 240 GERSIY---KMRQF---VAGYTHGMRGAREFRE 266


>gi|239635868|ref|ZP_04676891.1| dihydrouridine synthase DuS [Staphylococcus warneri L37603]
 gi|239598492|gb|EEQ80966.1| dihydrouridine synthase DuS [Staphylococcus warneri L37603]
          Length = 326

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/221 (27%), Positives = 107/221 (48%), Gaps = 31/221 (14%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E+P+   I G    +  E +  + 
Sbjct: 40  FFTEFTNTASFCHPEGIHS---VRGR----LTFSEDEQPMVAHIWGDQPEQFREMSIGLA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---V 127
           + G+  I+LN+GCP A V +   G+ L+L P++  + I A  KA  +PV+VK R+G   +
Sbjct: 93  EMGFKGIDLNMGCPVANVAQKGKGSGLILRPEVAAEIIQA-TKAGGLPVSVKTRLGFYEI 151

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN- 186
           D+       R+ +K + +  +  + IH R       + K+  K+ +  ++++  IK+   
Sbjct: 152 DE------WRDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHWELIEAIKQLRD 197

Query: 187 ---PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 198 EIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFHN 238


>gi|307321967|ref|ZP_07601348.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti AK83]
 gi|306892391|gb|EFN23196.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti AK83]
          Length = 342

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/172 (31%), Positives = 93/172 (54%), Gaps = 13/172 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G +   + EAA+IVE  G + I++N+GCP+ +V  G  G+ LM +PD     I
Sbjct: 81  PHIVQLAGREAHWMAEAARIVEANGADIIDINMGCPAKKVTGGYSGSALMRDPDHALSLI 140

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A  KA +IPVT+K R+G D+      L  + +  +++GV  I IH R   ++  + K  
Sbjct: 141 EATVKAATIPVTLKMRLGWDENSINAPL--IARRAEEAGVKAITIHGRTR-MQFYNGK-- 195

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
                 D+D +  + +E   + +  NG ++ ++ A +IL     D VM+GR+
Sbjct: 196 -----ADWDAIRAV-REVVSIPLIANGDVDSVADAHEILRRSGADAVMVGRS 241


>gi|28377433|ref|NP_784325.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|254555616|ref|YP_003062033.1| transcription regulator [Lactobacillus plantarum JDM1]
 gi|300768966|ref|ZP_07078857.1| tRNA-dihydrouridine synthase [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308179646|ref|YP_003923774.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28270265|emb|CAD63166.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|254044543|gb|ACT61336.1| transcription regulator [Lactobacillus plantarum JDM1]
 gi|300493487|gb|EFK28664.1| tRNA-dihydrouridine synthase [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308045137|gb|ADN97680.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 335

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 110/230 (47%), Gaps = 18/230 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  ++K +  +    +E P+++QI G   + LV+AA+ V +    + I
Sbjct: 40  LVVCEMISDRGIMYHNRKTLEMMFVDPKEHPMSIQIFGGSKATLVQAAQFVDQQTNADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   GA  +L+PD V + +AA+  A++ PVTVK R G D +       
Sbjct: 100 DINMGCPVNKVVKTDAGAKWLLSPDKVYEMVAAVTAAVNKPVTVKMRTGWDAEHVYAVEN 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                   +    +    RK + +G          + D+D++  +        +G NG +
Sbjct: 160 ARAAERAGAAAVAMHGRTRKQMYQG----------HADWDVLKRVADALTIPLMG-NGDV 208

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPI 243
           +    A ++L  V  D VMIGRA   N  MLT    Y +    LT  +P+
Sbjct: 209 QTPQDAARMLDEVGADAVMIGRAVEGNPWMLTQTVHYLATGELLTPPTPM 258


>gi|327398323|ref|YP_004339192.1| dihydrouridine synthase DuS [Hippea maritima DSM 10411]
 gi|327180952|gb|AEA33133.1| dihydrouridine synthase DuS [Hippea maritima DSM 10411]
          Length = 320

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/306 (24%), Positives = 136/306 (44%), Gaps = 38/306 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD+ +R   R      L ++E+I  +AI   +KK +  +     +KP  +Q+ G+D
Sbjct: 17  MAGYTDKPFRKLCREF-GCGLTFSELISVNAIYYKNKKTLKLIERDITDKPYCIQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               + AA+ VE F  + I++N GCP+ +V     G+ L+  P  +      + K L  P
Sbjct: 76  ERLFLYAAQFVEPFC-DCIDINAGCPAPKVIRAKAGSYLLKEPKKLISITQTLRKHLKKP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDY 176
           +++K RIG +   P      L K +++SG++ I IH R      KG           +DY
Sbjct: 135 LSIKMRIGYEKINPV----ELYKELERSGIDFITIHGRLKSQYFKG----------EVDY 180

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           + + +I   N  L I +  NGG++    +Q +K +   + +MIG+AA     +   +++ 
Sbjct: 181 NHIGQI---NSVLSIPVVANGGIDSFKKAQQVKRITGCEYLMIGQAAIGKPFIFEDLNK- 236

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                     + T  D  F + +      Y          ++Q  +       G+PN +R
Sbjct: 237 ---------KVDTNRDLGFVKAVMKRHLQYMI-DFWGDTAIRQFRKFFHAYLKGYPNIKR 286

Query: 293 CRHILT 298
             +++ 
Sbjct: 287 FNNMIN 292


>gi|294779128|ref|ZP_06744538.1| dihydrouridine synthase (Dus) [Enterococcus faecalis PC1.1]
 gi|294453761|gb|EFG22153.1| dihydrouridine synthase (Dus) [Enterococcus faecalis PC1.1]
          Length = 324

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 187 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 238


>gi|322517559|ref|ZP_08070428.1| tRNA-dihydrouridine synthase [Streptococcus vestibularis ATCC
           49124]
 gi|322123819|gb|EFX95393.1| tRNA-dihydrouridine synthase [Streptococcus vestibularis ATCC
           49124]
          Length = 325

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VM+GRAA  N  + T ++ +F 
Sbjct: 192 TLARVAKAITKIPFIG-NGDVRSVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFE 250


>gi|325677940|ref|ZP_08157582.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 8]
 gi|324110494|gb|EGC04668.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 8]
          Length = 325

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 78/324 (24%), Positives = 134/324 (41%), Gaps = 37/324 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M    D+ YR   R     A + +EMI +  +  GD+K   +     QE+P ALQI G D
Sbjct: 20  MASVADKSYRLLCREF-GAAYMVSEMISSKGLCYGDRKTGELCEIEPQERPYALQIFGED 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++ ++  + I++N+GCP  ++     G+ LM +     +      K    P
Sbjct: 79  PYYMGKAAYLLGEYKPDIIDINMGCPVPKIVGNGSGSALMKDIPRAVEIARETVKNAGCP 138

Query: 119 VTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVK R G DD  I AV      K+++++GV  + +H R         +        D +
Sbjct: 139 VTVKFRAGWDDTSINAV---EFAKALEQTGVAAMAVHGRT--------RAQFYSGEADRE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+       G NG + D     ++      D VM+ R +Y    +   +  Y   
Sbjct: 188 IIRQVKQAVSVPVFG-NGDVTDGESCKQMYEQTGCDLVMLARGSYGRPWVFREIRHYLET 246

Query: 236 -----PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                PLT    +K R++      I      Y  ++      +++  +++     G PNS
Sbjct: 247 GEVLPPLT----VKERME------IMLKHCGYLCKYKGEERGMKEARKNVAWYVKGLPNS 296

Query: 291 RR----CRHILTVEAGASTATHHI 310
            +    C  + T E     A   I
Sbjct: 297 AKLRAECGELSTYEQAEEMAARVI 320


>gi|42779507|ref|NP_976754.1| hypothetical protein BCE_0426 [Bacillus cereus ATCC 10987]
 gi|42735423|gb|AAS39362.1| hypothetical conserved protein [Bacillus cereus ATCC 10987]
          Length = 329

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|119473198|ref|ZP_01614895.1| tRNA-dihydrouridine synthase B [Alteromonadales bacterium TW-7]
 gi|119444562|gb|EAW25877.1| tRNA-dihydrouridine synthase B [Alteromonadales bacterium TW-7]
          Length = 259

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K  N +  S +    A+QI GAD
Sbjct: 20  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPKVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  +    ++ G+  + +H R    + KG +          +
Sbjct: 139 VTLKIRTGWDPDNRNGVEIARIA---ERYGIASLAVHGRTRACMYKGEA----------E 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y 
Sbjct: 186 YATIRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYL 244


>gi|222085889|ref|YP_002544420.1| tRNA-dihydrouridine synthase protein [Agrobacterium radiobacter
           K84]
 gi|221723337|gb|ACM26493.1| tRNA-dihydrouridine synthase protein [Agrobacterium radiobacter
           K84]
          Length = 342

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 110/216 (50%), Gaps = 15/216 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLV 63
           TD  +R  A L     L+ TEM+ +  +++   ++     S   KP  +Q+ G +   + 
Sbjct: 38  TDLPFRQLA-LRYGAGLVVTEMVASRELVQDTAESWARLKSAGLKPHMVQLAGREAYWMA 96

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ +PVT+K 
Sbjct: 97  EAAKIAADNGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDVPVTLKM 156

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D+   ++   ++ +  +++G+  + IH R      +   + R     D+D +  + 
Sbjct: 157 RLGWDEN--SINAPHIARRAEEAGIQLVTIHGRTR----MQFYEGRA----DWDAIRAV- 205

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           ++   + +  NG ++    A +IL     D VM+GR
Sbjct: 206 RDVISIPLVANGDVDTPEDASEILRRSGADAVMVGR 241


>gi|29377655|ref|NP_816809.1| dihydrouridine synthase family protein [Enterococcus faecalis V583]
 gi|29345123|gb|AAO82879.1| dihydrouridine synthase family protein [Enterococcus faecalis V583]
          Length = 324

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 187 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 238


>gi|42521773|ref|NP_967153.1| transcription regulator homolog yacF [Bdellovibrio bacteriovorus
           HD100]
 gi|39574303|emb|CAE77807.1| transcription regulator homolog yacF [Bdellovibrio bacteriovorus
           HD100]
          Length = 337

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 115/229 (50%), Gaps = 22/229 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKK-NILGFSTQEKPLALQIGGAD 58
           M   TD  +R F + L + +++ TE++ A  I  + D+   ++ F   ++P+ +Q+ G +
Sbjct: 17  MAGITDHAFRTFIKKL-DASVVVTELVSASGIEYKSDRTLKLMSFDESQRPIGIQLFGEE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++ E  G + ++LN GCP  +V +   G+ ++ +P  V   ++ +  A+ IP
Sbjct: 76  PEIVARAAQVAEADGCDFVDLNFGCPVPKVVKKGAGSAILKDPAAVQKMVSTVKAAIKIP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLD 175
           +T+K R G D +   A  + N+  +    GV+ + IH R       GL+          D
Sbjct: 136 LTIKIRTGWDANSRNATEICNIAYN---EGVSWVAIHGRTRAQSYTGLA----------D 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPS-VDGVMIGRAAYKN 222
           +D + ++K       +G NG +    QA L++  S  DGVMIGR   KN
Sbjct: 183 WDFIADVKANTKIPILG-NGDILTPRQANLRLQQSGCDGVMIGRGCLKN 230


>gi|323465360|gb|ADX77513.1| dihydrouridine synthase TIM-barrel protein, putative
           [Staphylococcus pseudintermedius ED99]
          Length = 330

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 113/223 (50%), Gaps = 22/223 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
            L+  EM+   AIL  + K +  L     E+PL+LQI G +   LVEAA+ V+ +   + 
Sbjct: 36  GLVCAEMVSDKAILFNNPKTMKMLYIDENERPLSLQIFGGEKETLVEAAEYVDKNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP +++ +   GA  +L+P+ + + ++A+ + +S PVT K RIG D D I AV 
Sbjct: 96  IDINMGCPVSKIIKCEAGARWLLDPNKIYEMVSAVTERVSKPVTCKMRIGWDEDHIFAVE 155

Query: 136 LRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                +    + ++   +H R  +   +G +          D+DI+ ++K+      IG 
Sbjct: 156 NAKAAERAGAAAIS---LHGRTRVQMYEGKA----------DWDIIRQVKEAVNIPVIG- 201

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           NG +     A K+L    VD VMIGR A  N  M+     Y  
Sbjct: 202 NGDVTSPELAEKMLKETGVDAVMIGREALGNPWMIYRTVHYLE 244


>gi|295114506|emb|CBL33143.1| tRNA-dihydrouridine synthase [Enterococcus sp. 7L76]
 gi|323479133|gb|ADX78572.1| dihydrouridine synthase (Dus) family protein [Enterococcus faecalis
           62]
          Length = 324

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 187 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 238


>gi|240171884|ref|ZP_04750543.1| transcriptional regulator [Mycobacterium kansasii ATCC 12478]
          Length = 396

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 77/301 (25%), Positives = 126/301 (41%), Gaps = 23/301 (7%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVE 64
           R  R  A++ T   L   EM+ A A++       ++  F+  E P +LQ+   D      
Sbjct: 48  RSPREQAKVGTVGGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSLQLYTVDPDTTYA 107

Query: 65  AAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKALSIPVT 120
           AA+++ D G  + I++N GCP  +V +   GA L     + G          +   IPVT
Sbjct: 108 AARMIADEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGRIVAAAVRAAEGTGIPVT 167

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD        +  +  +  G   + +HAR A          R     D+D + 
Sbjct: 168 VKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWDQIS 217

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + +  NG + D S AL ++ +   DGV+IGR       +   +   F+    
Sbjct: 218 RLKQQVTTIPVLGNGDIYDASDALAMMATTGCDGVVIGRGCLGRPWLFAELSAAFTGRPA 277

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P    V  D  R+  A +    A H      ++ I +H+    HGFP     R  L 
Sbjct: 278 PTPPTLGEV-ADVIRRHGALL----AAHFGEDKGMRDIRKHIAWYLHGFPAGSDVRRALA 332

Query: 299 V 299
           +
Sbjct: 333 L 333


>gi|229194708|ref|ZP_04321501.1| tRNA-dihydrouridine synthase [Bacillus cereus m1293]
 gi|228588811|gb|EEK46836.1| tRNA-dihydrouridine synthase [Bacillus cereus m1293]
          Length = 336

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 245


>gi|290579684|ref|YP_003484076.1| hypothetical protein SmuNN2025_0158 [Streptococcus mutans NN2025]
 gi|254996583|dbj|BAH87184.1| hypothetical protein [Streptococcus mutans NN2025]
          Length = 325

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 119/238 (50%), Gaps = 17/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++ +   + +++N+GCP  ++ +   GA  + +P+ +   I+++   L+I
Sbjct: 83  GDSLARAAEFIQANTKTDLVDINMGCPVNKIVKNEAGAMWLKDPEKIYSVISSVKSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV  + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSD--ASLAVENALAA-ESAGVAALAMHGRT--------REQMYTGSCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + ++ K    +    NG +  +  A  ++  V  D VMIGRAA  N  + T ++ YF
Sbjct: 192 TLAKVAKAITKVPFIANGDIRSVEDAQFMIDQVGADAVMIGRAARSNPYIFTQINHYF 249


>gi|52144914|ref|YP_081915.1| dihydrouridine synthase [Bacillus cereus E33L]
 gi|51978383|gb|AAU19933.1| conserved hypothetical protein; probable dihydrouridine synthase
           [Bacillus cereus E33L]
          Length = 329

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|41406755|ref|NP_959591.1| hypothetical protein MAP0657c [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395105|gb|AAS02974.1| hypothetical protein MAP_0657c [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 377

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 75/291 (25%), Positives = 129/291 (44%), Gaps = 23/291 (7%)

Query: 17  TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
           T + L   EM+ A A++       +++ F+  E P +LQ+   D +    AAK++ D G 
Sbjct: 39  TVSGLYVYEMVTARALVERHPATMHMITFAPDESPRSLQLYTVDPATTYAAAKMIADEGL 98

Query: 75  -NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQ 130
            + I++N GCP  +V +   G+ L     + G  +AA  +A     IPVTVK RIG+DD+
Sbjct: 99  ADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAAVRATQGTEIPVTVKFRIGIDDE 158

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                  +  +  +  G   + +HAR A          R     D++ +  +K++   + 
Sbjct: 159 --HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWEQIALLKQQVRTIP 208

Query: 191 IGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG + D S AL ++ +   DGV+IGR       +   +   F+     + P   +V 
Sbjct: 209 VLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLFAELSAAFTGSPPPTPPTLGQV- 267

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            D  R+    +    A H      ++ I +H+    HGFP     R  L +
Sbjct: 268 ADIVRRHGRLL----AAHFGEDKGMRDIRKHIAWYLHGFPAGSELRRALAM 314


>gi|70726229|ref|YP_253143.1| hypothetical protein SH1228 [Staphylococcus haemolyticus JCSC1435]
 gi|68446953|dbj|BAE04537.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 325

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSFGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + K  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYD---IEEWRDWLKHVFKQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKN 222
           +++  IK+      P+  + +NG + D      L +   VDGVMIGR  + N
Sbjct: 187 ELIAAIKQLRDDIAPNTLLTINGDIPDRKTGHELAMKYGVDGVMIGRGIFNN 238


>gi|157151554|ref|YP_001451243.1| transcriptional regulator [Streptococcus gordonii str. Challis
           substr. CH1]
 gi|157076348|gb|ABV11031.1| possible transcriptional regulator [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 317

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 184 TLHDVAQALTKIPFIANGDIRSVQEAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 242


>gi|319891470|ref|YP_004148345.1| tRNA dihydrouridine synthase B [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317161166|gb|ADV04709.1| tRNA dihydrouridine synthase B [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 330

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 113/223 (50%), Gaps = 22/223 (9%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
            L+  EM+   AIL  + K +  L     E+PL+LQI G +   LVEAA+ V+ +   + 
Sbjct: 36  GLVCAEMVSDKAILFNNPKTMKMLYIDENERPLSLQIFGGEKETLVEAAEYVDKNTTADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP +++ +   GA  +L+P+ + + ++A+ + +S PVT K RIG D D I AV 
Sbjct: 96  IDINMGCPVSKIIKCEAGARWLLDPNKIYEMVSAVTERVSKPVTCKMRIGWDEDHIFAVE 155

Query: 136 LRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                +    + ++   +H R  +   +G +          D+DI+ ++K+      IG 
Sbjct: 156 NAKAAERAGAAAIS---LHGRTRVQMYEGKA----------DWDIIRQVKEAVNIPVIG- 201

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           NG +     A K+L    VD VMIGR A  N  M+     Y  
Sbjct: 202 NGDVTSPELAEKMLKETGVDAVMIGREALGNPWMIYRTVHYLE 244


>gi|311033028|ref|ZP_07711118.1| histidine phosphokinase/phophatase, putative [Bacillus sp. m3-13]
          Length = 322

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 111/232 (47%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R   R      + +TE   +D+    + K+++ G   F+ +E+P+   I G
Sbjct: 19  MEDVTDVVFRTVVRKAGRPDVFFTEFTNSDSYCHPEGKESVRGRLLFTEEEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+  PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVATRGKGSGLIQRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +K I +  +  + IH R    K +S  D        +
Sbjct: 138 LPVSVKTRLGFTE---VDEWKEWLKHILEQDIANLSIHLRTR--KEMSEVDAH------W 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKN 222
           +++ EIK+      P+  I +NG + +  + Q L     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKELRDRIAPETLITINGDIPNRQVGQELAEKYDIDGVMIGRGIFKN 238


>gi|256854872|ref|ZP_05560236.1| dihydrouridine synthase [Enterococcus faecalis T8]
 gi|256710432|gb|EEU25476.1| dihydrouridine synthase [Enterococcus faecalis T8]
          Length = 326

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 189 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 240


>gi|24378701|ref|NP_720656.1| hypothetical protein SMU.187c [Streptococcus mutans UA159]
 gi|24376565|gb|AAN57962.1|AE014869_7 conserved hypothetical protein [Streptococcus mutans UA159]
          Length = 325

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 119/238 (50%), Gaps = 17/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++ +   + +++N+GCP  ++ +   GA  + +P+ +   I+++   L+I
Sbjct: 83  GDSLARAAEFIQANTKTDLVDINMGCPVNKIVKNEAGAMWLKDPEKIYSVISSVKSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV  + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSD--ASLAVENALAA-ESAGVAALAMHGRT--------REQMYTGSCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + ++ K    +    NG +  +  A  ++  V  D VMIGRAA  N  + T ++ YF
Sbjct: 192 TLAKVAKAITKVPFIANGDIRSVEDAQFMIDQVGADAVMIGRAARSNPYIFTQINHYF 249


>gi|257083126|ref|ZP_05577487.1| dihydrouridine synthase [Enterococcus faecalis Fly1]
 gi|256991156|gb|EEU78458.1| dihydrouridine synthase [Enterococcus faecalis Fly1]
          Length = 326

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 189 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 240


>gi|229015715|ref|ZP_04172697.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1273]
 gi|229021912|ref|ZP_04178476.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1272]
 gi|228739384|gb|EEL89816.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1272]
 gi|228745572|gb|EEL95592.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1273]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|256958478|ref|ZP_05562649.1| dihydrouridine synthase [Enterococcus faecalis DS5]
 gi|257078210|ref|ZP_05572571.1| dihydrouridine synthase [Enterococcus faecalis JH1]
 gi|256948974|gb|EEU65606.1| dihydrouridine synthase [Enterococcus faecalis DS5]
 gi|256986240|gb|EEU73542.1| dihydrouridine synthase [Enterococcus faecalis JH1]
          Length = 326

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 189 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 240


>gi|220908982|ref|YP_002484293.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7425]
 gi|219865593|gb|ACL45932.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7425]
          Length = 357

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/299 (23%), Positives = 133/299 (44%), Gaps = 26/299 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R   R    ++++YTEM+ A  +  +R   K I+     E+P+++Q+       L
Sbjct: 36  TDLVFRRLVRRYAPDSMMYTEMVNATGLHYVRQLPK-IMEVDPNERPISIQLFDCRPDFL 94

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA++    G + +++N+GCP  ++ +   G+ L+ +P+     + ++ +A+++PVTVK
Sbjct: 95  AEAAQMAVAEGADTVDINMGCPVNKITKNGGGSSLLRDPETAEAIVRSVVQAVNVPVTVK 154

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG  ++   + +    + ++ +G   I +H R        P     I  +        
Sbjct: 155 TRIGWTEK--EINIIEFAQRMQDAGAQMITVHGRTRAQGYNGPAKWEWIRRV-------- 204

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            KE   + +  NG +  +  A+  L     DGVM  R       ++  VD +     TG 
Sbjct: 205 -KEALTIPVIANGDIFSVEAAVNCLEQTGADGVMCSRGTMGYPFLVGEVDHFLK---TGE 260

Query: 241 -SPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHIL 297
             P  T ++     ++  +     A   + G + ++Q  +HM     GFP +   R  L
Sbjct: 261 HKPAPTVIE-----RLQCAREHLQALWEYKGDRGVRQARKHMTWYAKGFPGAAELRGAL 314


>gi|312864362|ref|ZP_07724595.1| TIM-barrel protein, nifR3 family [Streptococcus downei F0415]
 gi|311100083|gb|EFQ58294.1| TIM-barrel protein, nifR3 family [Streptococcus downei F0415]
          Length = 326

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 122/241 (50%), Gaps = 19/241 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L   EM+    IL  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLAVMEMVSDKGILYNNEKTLHMLHIDEGEHPVSIQLFGND 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++ +   + +++N+GCP  ++ +   GA  + +PD +   I  +   L+I
Sbjct: 83  GDSLARAAEFIQANTKTDLVDINMGCPVNKIVKNEAGAMWLKDPDKIYQVIKTVKSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + +++GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-EEAGVSALTMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++ +    + FIG NG ++ +  A  ++  V  D VMIGR A  N  + T ++ +F 
Sbjct: 192 TLAQVAQAIKTIPFIG-NGDIKTVEDARFMIEEVGCDAVMIGRGALNNPYLFTQINHFFE 250

Query: 235 N 235
           +
Sbjct: 251 S 251


>gi|291279750|ref|YP_003496585.1| tRNA-dihydrouridine synthase [Deferribacter desulfuricans SSM1]
 gi|290754452|dbj|BAI80829.1| tRNA-dihydrouridine synthase [Deferribacter desulfuricans SSM1]
          Length = 320

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 107/207 (51%), Gaps = 14/207 (6%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           + L+YTEM+ A+ + R  K  +     Q  ++P+ +Q+ G++   + EA KI ED    E
Sbjct: 37  DGLIYTEMVSAEGLKRKVKATLDYIKIQPIDRPIFIQVFGSNPDTIYEAIKICEDLASPE 96

Query: 77  -INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
             +LN GCP  +V + + G+ L+ + + + + I  M KA   P++VK R+G D    ++ 
Sbjct: 97  GYDLNAGCPVKKVIKANAGSYLLKDLNNLTNIIKNMRKATDKPISVKTRLGWDYN--SLV 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            + ++   +  GV+ + IHAR         K      ++ +D + E+     ++ +  NG
Sbjct: 155 YKEILNMCENEGVDILTIHAR--------TKTEMFSGDIHFDALSELATLKKNVTLIGNG 206

Query: 196 GLEDMSQALKILPS-VDGVMIGRAAYK 221
            + D +   K++ + VD +MIGRA  K
Sbjct: 207 NVVDKTSFDKMIETGVDAIMIGRAYMK 233


>gi|161870286|ref|YP_001599456.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis 053442]
 gi|161595839|gb|ABX73499.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis 053442]
          Length = 374

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  +    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 174 VTLKTRLGWHEDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 218

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 219 ARYELIAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|229547942|ref|ZP_04436667.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
 gi|293385258|ref|ZP_06631074.1| dihydrouridine synthase family protein [Enterococcus faecalis R712]
 gi|293389729|ref|ZP_06634173.1| dihydrouridine synthase family protein [Enterococcus faecalis S613]
 gi|307284767|ref|ZP_07564923.1| dihydrouridine synthase [Enterococcus faecalis TX0860]
 gi|312906609|ref|ZP_07765609.1| dihydrouridine synthase [Enterococcus faecalis DAPTO 512]
 gi|312910930|ref|ZP_07769765.1| dihydrouridine synthase (Dus) [Enterococcus faecalis DAPTO 516]
 gi|312953310|ref|ZP_07772153.1| dihydrouridine synthase [Enterococcus faecalis TX0102]
 gi|229306963|gb|EEN72959.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
 gi|291077458|gb|EFE14822.1| dihydrouridine synthase family protein [Enterococcus faecalis R712]
 gi|291080976|gb|EFE17939.1| dihydrouridine synthase family protein [Enterococcus faecalis S613]
 gi|306503026|gb|EFM72283.1| dihydrouridine synthase [Enterococcus faecalis TX0860]
 gi|310627257|gb|EFQ10540.1| dihydrouridine synthase [Enterococcus faecalis DAPTO 512]
 gi|310628768|gb|EFQ12051.1| dihydrouridine synthase [Enterococcus faecalis TX0102]
 gi|311288798|gb|EFQ67354.1| dihydrouridine synthase (Dus) [Enterococcus faecalis DAPTO 516]
 gi|315144170|gb|EFT88186.1| dihydrouridine synthase [Enterococcus faecalis TX2141]
 gi|315152877|gb|EFT96893.1| dihydrouridine synthase [Enterococcus faecalis TX0031]
 gi|315154625|gb|EFT98641.1| dihydrouridine synthase [Enterococcus faecalis TX0043]
 gi|315159573|gb|EFU03590.1| dihydrouridine synthase [Enterococcus faecalis TX0312]
 gi|315161258|gb|EFU05275.1| dihydrouridine synthase [Enterococcus faecalis TX0645]
 gi|315167078|gb|EFU11095.1| dihydrouridine synthase [Enterococcus faecalis TX1341]
 gi|315579569|gb|EFU91760.1| dihydrouridine synthase [Enterococcus faecalis TX0630]
 gi|327536326|gb|AEA95160.1| dihydrouridine synthase [Enterococcus faecalis OG1RF]
          Length = 337

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 199

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 200 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 251


>gi|256963036|ref|ZP_05567207.1| dihydrouridine synthase [Enterococcus faecalis HIP11704]
 gi|256953532|gb|EEU70164.1| dihydrouridine synthase [Enterococcus faecalis HIP11704]
          Length = 326

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 189 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 240


>gi|255970603|ref|ZP_05421189.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255974183|ref|ZP_05424769.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256618039|ref|ZP_05474885.1| dihydrouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256760977|ref|ZP_05501557.1| dihydrouridine synthase [Enterococcus faecalis T3]
 gi|256960544|ref|ZP_05564715.1| dihydrouridine synthase [Enterococcus faecalis Merz96]
 gi|257080404|ref|ZP_05574765.1| dihydrouridine synthase [Enterococcus faecalis E1Sol]
 gi|257088308|ref|ZP_05582669.1| dihydrouridine synthase [Enterococcus faecalis D6]
 gi|257091440|ref|ZP_05585801.1| dihydrouridine synthase [Enterococcus faecalis CH188]
 gi|257417325|ref|ZP_05594319.1| dihydrouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257418042|ref|ZP_05595036.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257420355|ref|ZP_05597345.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|307276567|ref|ZP_07557685.1| dihydrouridine synthase [Enterococcus faecalis TX2134]
 gi|255961621|gb|EET94097.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255967055|gb|EET97677.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256597566|gb|EEU16742.1| dihydrouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256682228|gb|EEU21923.1| dihydrouridine synthase [Enterococcus faecalis T3]
 gi|256951040|gb|EEU67672.1| dihydrouridine synthase [Enterococcus faecalis Merz96]
 gi|256988434|gb|EEU75736.1| dihydrouridine synthase [Enterococcus faecalis E1Sol]
 gi|256996338|gb|EEU83640.1| dihydrouridine synthase [Enterococcus faecalis D6]
 gi|257000252|gb|EEU86772.1| dihydrouridine synthase [Enterococcus faecalis CH188]
 gi|257159153|gb|EEU89113.1| dihydrouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|257159870|gb|EEU89830.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257162179|gb|EEU92139.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|306506677|gb|EFM75829.1| dihydrouridine synthase [Enterococcus faecalis TX2134]
          Length = 326

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 189 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 240


>gi|315031899|gb|EFT43831.1| dihydrouridine synthase [Enterococcus faecalis TX0017]
          Length = 337

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 199

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 200 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 251


>gi|87303078|ref|ZP_01085876.1| Dihydrouridine synthase TIM-barrel protein [Synechococcus sp. WH
           5701]
 gi|87282245|gb|EAQ74205.1| Dihydrouridine synthase TIM-barrel protein [Synechococcus sp. WH
           5701]
          Length = 339

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 118/248 (47%), Gaps = 26/248 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLV 63
           +DR +R F R    +ALL+TEM+ A ++  G   + + G   +  P+A+Q+       + 
Sbjct: 35  SDRIFRGFVRRWAPDALLFTEMVNATSLELGHGSDKMAGLEAETGPIAVQLFDHRPGAMA 94

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+  E  G   +++N+GCP  ++     G+ L+ +P +    + A+  A+++PVTVK 
Sbjct: 95  EAARRAEGAGAFLVDINMGCPVRKIARKGGGSGLLRDPALACRIVEAVSAAVTVPVTVKT 154

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G   D   P         +++++G   + +H R         ++     + D+D +  
Sbjct: 155 RLGWCGDSSDPV----GFALALQEAGAQALTLHGRT--------REQGFSGSADWDAIAR 202

Query: 182 IKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN-- 235
           +K+    LFI L  NG +    QAL  L     DGVM+GR       ++  +D   S   
Sbjct: 203 VKQA---LFIPLIANGDITGPEQALACLERTGADGVMVGRGTLGAPWLVGRIDAALSGRA 259

Query: 236 --PLTGSS 241
             PL G +
Sbjct: 260 LPPLPGPA 267


>gi|229009817|ref|ZP_04167037.1| tRNA-dihydrouridine synthase [Bacillus mycoides DSM 2048]
 gi|228751435|gb|EEM01241.1| tRNA-dihydrouridine synthase [Bacillus mycoides DSM 2048]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R       +  + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGSPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|126736292|ref|ZP_01752034.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. CCS2]
 gi|126714113|gb|EBA10982.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. CCS2]
          Length = 333

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 111/234 (47%), Gaps = 26/234 (11%)

Query: 5   TDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           TD  +R     F A  + +  +   EM+ A   +R  ++  LG+   +   A+QI G + 
Sbjct: 31  TDLPFRQLVASFGAGWVVSEMVASQEMVQAKPGVR--ERAELGYD--QAGTAVQIAGRET 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++    G   I++N+GCP+ +V  G  G+ L+  PD     + A+  A+ +PV
Sbjct: 87  YWMAEAARMAAGNGAAIIDINMGCPAKKVTNGYSGSALLRTPDHALRLMEAVVNAVDVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
           T+K R+G DD   ++   N+ K  + +G+  + IH R      KG +          D+ 
Sbjct: 147 TLKTRLGWDDD--SLNAANVAKRAEDAGIRLVTIHGRTRCQFYKGAA----------DWA 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
            +++I KE   + +  NG + D   A     L   DGVMIGR A     +L  V
Sbjct: 195 AIHKI-KEAVSIPVIANGDIVDAGTARNALRLSGADGVMIGRGAQGRPWVLAQV 247


>gi|315172916|gb|EFU16933.1| dihydrouridine synthase [Enterococcus faecalis TX1346]
          Length = 337

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 199

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 200 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 251


>gi|292669421|ref|ZP_06602847.1| tRNA-dihydrouridine synthase B [Selenomonas noxia ATCC 43541]
 gi|292648942|gb|EFF66914.1| tRNA-dihydrouridine synthase B [Selenomonas noxia ATCC 43541]
          Length = 323

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 108/227 (47%), Gaps = 17/227 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++  +    T+  E+P+A+QI    
Sbjct: 20  MAGVTDTAYRVIAHDM-GCPLAFAEMVSSQGIHYRNEHTMKMLRTEPDERPIAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  +I + N+GCP+ +V +   G+ LM +P    + + A+ +A  +
Sbjct: 79  AAMAAEAAAYIEEIGTADILDFNMGCPAPKVVKNGEGSALMRDPKRAEEILTAIRRATKL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R+G DD     A   + K  +  GV+ + +H R         ++     N DY 
Sbjct: 139 PFTVKMRLGWDDSSRNAA--EIAKMAEAVGVDAVAVHGRT--------REQFYSGNADYA 188

Query: 178 IVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
            + E+K+    P +  G      D+S+AL +    D VMIGR A  N
Sbjct: 189 AIAEVKRAVGIPVIVSGDIRRSADLSRALAVT-EADAVMIGRGAQGN 234


>gi|170017367|ref|YP_001728286.1| tRNA-dihydrouridine synthase [Leuconostoc citreum KM20]
 gi|169804224|gb|ACA82842.1| tRNA-dihydrouridine synthase [Leuconostoc citreum KM20]
          Length = 378

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 103/212 (48%), Gaps = 21/212 (9%)

Query: 21  LLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           + YTE   A +++    K      L  +  E     QI G+    +  AAKI+   GY  
Sbjct: 56  VYYTEFTNASSMVHPKAKFSVQGRLAVAENEAQPVAQIWGSRPEDIAGAAKILPTMGYRA 115

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N+GCP A V +   G+ L+ + D+    I+A  K   +PV+VK R+G      A   
Sbjct: 116 VDINMGCPDATVIKNGAGSDLIRHDDLAEKIISA-AKTSGLPVSVKTRLGF---YHAEEF 171

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDY--DIVYEIKKENPDLFIGL 193
           R+ +  I +  V  + +H R       S K+  K P +++Y  +I+    K  P   I +
Sbjct: 172 RDWLPIILRQNVAVLTVHLR-------SRKEMSKAPAHVEYIDEILAMRDKLAPKTLIQI 224

Query: 194 NGGLEDMSQAL---KILPSVDGVMIGRAAYKN 222
           NG ++  ++ L   KI P +DG+MIGR  ++N
Sbjct: 225 NGDIKTRAEGLALAKIHPGIDGIMIGRGIFEN 256


>gi|229176913|ref|ZP_04304309.1| tRNA-dihydrouridine synthase [Bacillus cereus 172560W]
 gi|228606586|gb|EEK64011.1| tRNA-dihydrouridine synthase [Bacillus cereus 172560W]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|254672934|emb|CBA07315.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis alpha275]
          Length = 374

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  +    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 174 VTLKTRLGWHEDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 218

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 219 ARYELIAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|296501149|ref|YP_003662849.1| nitrogen regulation protein NIFR3 [Bacillus thuringiensis BMB171]
 gi|296322201|gb|ADH05129.1| nitrogen regulation protein NIFR3 [Bacillus thuringiensis BMB171]
          Length = 329

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|229366234|gb|ACQ58097.1| tRNA-dihydrouridine synthase 4-like PP35 [Anoplopoma fimbria]
          Length = 318

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 114/247 (46%), Gaps = 32/247 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + + ++ MIVA   +R  K     F+T E  +PL +Q    D
Sbjct: 29  MVRYSKLAFRSLVRKYDCD-ICFSPMIVASDFMRSVKARDSEFTTNESDRPLIVQFAAPD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        FGACL+  P++V D +  +   +  P
Sbjct: 88  AQTLADAACVVAPFS-DGVDLNCGCPQRWAMSAGFGACLINKPELVKDMVRHVRNQVDNP 146

Query: 119 ---VTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               ++K RI  D       LR   +L +  + +GV+ I +H R A        + R  P
Sbjct: 147 NYTASIKIRIHKD-------LRQTVDLCQKAESAGVSWITVHGRTA--------EERHQP 191

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            ++YD +  I K++  + +  NG ++ +   ++   L  VDGVM  R    N AM +   
Sbjct: 192 -VNYDAIKTI-KDSVSIPVIANGDIKHLRDVESTYQLTGVDGVMAARGLLTNPAMFSG-- 247

Query: 231 EYFSNPL 237
            Y   PL
Sbjct: 248 -YEDTPL 253


>gi|228906094|ref|ZP_04069983.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228853503|gb|EEM98271.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 200]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|218895442|ref|YP_002443853.1| probable tRNA-dihydrouridine synthase 2 [Bacillus cereus G9842]
 gi|218543849|gb|ACK96243.1| probable tRNA-dihydrouridine synthase 2 [Bacillus cereus G9842]
          Length = 329

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|206968108|ref|ZP_03229064.1| conserved hypothetical protein [Bacillus cereus AH1134]
 gi|206737028|gb|EDZ54175.1| conserved hypothetical protein [Bacillus cereus AH1134]
          Length = 329

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|229125817|ref|ZP_04254843.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228657674|gb|EEL13486.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-Cer4]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|227554623|ref|ZP_03984670.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|227176236|gb|EEI57208.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|315573226|gb|EFU85417.1| dihydrouridine synthase [Enterococcus faecalis TX0309B]
 gi|315581272|gb|EFU93463.1| dihydrouridine synthase [Enterococcus faecalis TX0309A]
          Length = 362

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 225 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 276


>gi|308389527|gb|ADO31847.1| nifR3 protein [Neisseria meningitidis alpha710]
 gi|325130494|gb|EGC53251.1| dihydrouridine synthase [Neisseria meningitidis OX99.30304]
          Length = 374

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  +    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 174 VTLKTRLGWHEDHQNLPVIA-----KIAEDCGITALAVHGRTRTQMYKG----------E 218

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 219 ARYELIAETKCR-LNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 277

Query: 232 Y 232
           Y
Sbjct: 278 Y 278


>gi|307129031|ref|YP_003881047.1| tRNA-dihydrouridine synthase B [Dickeya dadantii 3937]
 gi|306526560|gb|ADM96490.1| tRNA-dihydrouridine synthase B [Dickeya dadantii 3937]
          Length = 321

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 112/239 (46%), Gaps = 20/239 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGVSDRPFRALCYAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P++V   + A+ KA+ +P
Sbjct: 76  PDEMAAAARINAENGAQVIDINMGCPAKKVNRKMAGSALLQYPELVKQILIAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G   +    A   + K  +  G+  + +H R    +  G            +Y
Sbjct: 136 VTLKIRTGWAPEHRNCA--EIAKLAEDCGIQALTVHGRTRACLFNG----------EAEY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 184 DSIRTV-KQSVSIPIIANGDITDPRKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|228950876|ref|ZP_04112999.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228808805|gb|EEM55301.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|229068075|ref|ZP_04201383.1| tRNA-dihydrouridine synthase [Bacillus cereus F65185]
 gi|229077679|ref|ZP_04210309.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock4-2]
 gi|228705620|gb|EEL57976.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock4-2]
 gi|228715083|gb|EEL66950.1| tRNA-dihydrouridine synthase [Bacillus cereus F65185]
          Length = 336

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|30018573|ref|NP_830204.1| nitrogen regulation protein NIFR3 [Bacillus cereus ATCC 14579]
 gi|29894114|gb|AAP07405.1| Nitrogen regulation protein NIFR3 [Bacillus cereus ATCC 14579]
          Length = 329

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|305673507|ref|YP_003865179.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|305411751|gb|ADM36870.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii str. W23]
          Length = 327

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  ++P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDDQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       RN +  + K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGYTD---VDEWRNWLTHVLKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTN 238


>gi|228899051|ref|ZP_04063324.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228970175|ref|ZP_04130851.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228789541|gb|EEM37446.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228860626|gb|EEN05013.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|228919255|ref|ZP_04082625.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228956783|ref|ZP_04118568.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229188590|ref|ZP_04315629.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 10876]
 gi|228594779|gb|EEK52559.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 10876]
 gi|228802824|gb|EEM49657.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228840362|gb|EEM85633.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|65317756|ref|ZP_00390715.1| COG0042: tRNA-dihydrouridine synthase [Bacillus anthracis str.
           A2012]
 gi|167634108|ref|ZP_02392430.1| conserved hypothetical protein [Bacillus anthracis str. A0442]
 gi|177653669|ref|ZP_02935808.1| conserved hypothetical protein [Bacillus anthracis str. A0174]
 gi|167530422|gb|EDR93137.1| conserved hypothetical protein [Bacillus anthracis str. A0442]
 gi|172081249|gb|EDT66324.1| conserved hypothetical protein [Bacillus anthracis str. A0174]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 245


>gi|304387247|ref|ZP_07369443.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis ATCC 13091]
 gi|304338714|gb|EFM04828.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis ATCC 13091]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  +    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHEDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCR-LNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|229107992|ref|ZP_04237619.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-15]
 gi|228675495|gb|EEL30712.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-15]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|307273704|ref|ZP_07554932.1| dihydrouridine synthase [Enterococcus faecalis TX0855]
 gi|306509717|gb|EFM78759.1| dihydrouridine synthase [Enterococcus faecalis TX0855]
          Length = 362

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 225 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 276


>gi|228913068|ref|ZP_04076707.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228846473|gb|EEM91486.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 245


>gi|229148723|ref|ZP_04276973.1| tRNA-dihydrouridine synthase [Bacillus cereus m1550]
 gi|228634731|gb|EEK91310.1| tRNA-dihydrouridine synthase [Bacillus cereus m1550]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|47569585|ref|ZP_00240263.1| dihydrouridine synthase family protein [Bacillus cereus G9241]
 gi|47553768|gb|EAL12141.1| dihydrouridine synthase family protein [Bacillus cereus G9241]
          Length = 329

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|260204013|ref|ZP_05771504.1| putative transcriptional regulatory protein [Mycobacterium
           tuberculosis K85]
 gi|289573441|ref|ZP_06453668.1| transcriptional regulator [Mycobacterium tuberculosis K85]
 gi|289537872|gb|EFD42450.1| transcriptional regulator [Mycobacterium tuberculosis K85]
          Length = 389

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGCGAALPFKRRLFGQIVAAA 148

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|229547370|ref|ZP_04436095.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|307270477|ref|ZP_07551776.1| dihydrouridine synthase [Enterococcus faecalis TX4248]
 gi|307292224|ref|ZP_07572088.1| dihydrouridine synthase [Enterococcus faecalis TX0411]
 gi|229307519|gb|EEN73506.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|306496730|gb|EFM66283.1| dihydrouridine synthase [Enterococcus faecalis TX0411]
 gi|306513178|gb|EFM81811.1| dihydrouridine synthase [Enterococcus faecalis TX4248]
 gi|315028673|gb|EFT40605.1| dihydrouridine synthase [Enterococcus faecalis TX4000]
 gi|315034772|gb|EFT46704.1| dihydrouridine synthase [Enterococcus faecalis TX0027]
          Length = 362

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 225 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 276


>gi|196040201|ref|ZP_03107503.1| conserved hypothetical protein [Bacillus cereus NVH0597-99]
 gi|196029056|gb|EDX67661.1| conserved hypothetical protein [Bacillus cereus NVH0597-99]
          Length = 329

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|307288357|ref|ZP_07568349.1| dihydrouridine synthase [Enterococcus faecalis TX0109]
 gi|306500657|gb|EFM69982.1| dihydrouridine synthase [Enterococcus faecalis TX0109]
 gi|315026494|gb|EFT38426.1| dihydrouridine synthase [Enterococcus faecalis TX2137]
 gi|315146498|gb|EFT90514.1| dihydrouridine synthase [Enterococcus faecalis TX4244]
 gi|315164353|gb|EFU08370.1| dihydrouridine synthase [Enterococcus faecalis TX1302]
 gi|315171103|gb|EFU15120.1| dihydrouridine synthase [Enterococcus faecalis TX1342]
          Length = 362

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 225 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 276


>gi|228925577|ref|ZP_04088666.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228983574|ref|ZP_04143779.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229154086|ref|ZP_04282211.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 4342]
 gi|228629366|gb|EEK86068.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 4342]
 gi|228776170|gb|EEM24531.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228834055|gb|EEM79603.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 245


>gi|261366358|ref|ZP_05979241.1| tRNA-dihydrouridine synthase B [Subdoligranulum variabile DSM
           15176]
 gi|282571961|gb|EFB77496.1| tRNA-dihydrouridine synthase B [Subdoligranulum variabile DSM
           15176]
          Length = 325

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 120/243 (49%), Gaps = 32/243 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNILGFSTQEKP-----LALQ 53
           M   TD   R   R++ ++   +T  EM  A A+  GD+K+   F+  + P      A+Q
Sbjct: 17  MAGLTDAACR---RMMADHGAAWTVSEMASAKALNFGDRKS---FALLKDPDPHGIYAIQ 70

Query: 54  IGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + GA+   L +A  +V + G  ++ +++N+GCP+ ++     G+ L+L+P + G  +AA 
Sbjct: 71  LFGAEPETLAKAILLVREKGIRFDILDINMGCPAPKITSSGAGSHLLLDPPLCGAMVAAA 130

Query: 112 CKALS--IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KAL    P+TVK RIG D D +  V    + +  + +G + + +H R         ++ 
Sbjct: 131 RKALGDDTPLTVKMRIGWDADHMTGV---EVARQCEANGADLLAVHGRT--------REQ 179

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
             IP +D D +  +K+    + +  NG +     AL +L     DGVMIGR A  +  + 
Sbjct: 180 MYIPPIDTDAIAAVKQAV-QIPVLANGDVTTAEGALDLLAKTGCDGVMIGRGALGDPWLF 238

Query: 227 TTV 229
             V
Sbjct: 239 ERV 241


>gi|182412757|ref|YP_001817823.1| NifR3 family TIM-barrel protein [Opitutus terrae PB90-1]
 gi|177839971|gb|ACB74223.1| TIM-barrel protein, nifR3 family [Opitutus terrae PB90-1]
          Length = 370

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 40/158 (25%), Positives = 88/158 (55%), Gaps = 4/158 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           +  +T+  +R   R L     + T+++ A ++L  +     ++  S +++P+++Q+ G+ 
Sbjct: 17  LAGYTNLPFRLTLRELGGLGWVTTDLVNARSLLERNPAALKLVASSAEDRPMSIQLFGSV 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ +AA+I ED G   +++N+GCP  +V     G+ +M   +     +  M +A+ IP
Sbjct: 77  PTEMRDAARICEDLGAQAVDINMGCPVRKVVRVGGGSAMMTELNQTAALVRGMIEAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VT K R+G DD+   +   +L + ++ +GV  +++H R
Sbjct: 137 VTAKMRLGWDDE--NLTAPDLARVLEDAGVAAVFVHGR 172


>gi|30260504|ref|NP_842881.1| hypothetical protein BA_0334 [Bacillus anthracis str. Ames]
 gi|47525601|ref|YP_016950.1| hypothetical protein GBAA_0334 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49183347|ref|YP_026599.1| hypothetical protein BAS0319 [Bacillus anthracis str. Sterne]
 gi|165871396|ref|ZP_02216044.1| conserved hypothetical protein [Bacillus anthracis str. A0488]
 gi|167640100|ref|ZP_02398367.1| conserved hypothetical protein [Bacillus anthracis str. A0193]
 gi|170688341|ref|ZP_02879550.1| conserved hypothetical protein [Bacillus anthracis str. A0465]
 gi|170708765|ref|ZP_02899202.1| conserved hypothetical protein [Bacillus anthracis str. A0389]
 gi|190567484|ref|ZP_03020397.1| conserved hypothetical protein [Bacillus anthracis Tsiankovskii-I]
 gi|227812999|ref|YP_002813008.1| hypothetical protein BAMEG_0394 [Bacillus anthracis str. CDC 684]
 gi|229602511|ref|YP_002864949.1| hypothetical protein BAA_0391 [Bacillus anthracis str. A0248]
 gi|254686718|ref|ZP_05150576.1| hypothetical protein BantC_23150 [Bacillus anthracis str.
           CNEVA-9066]
 gi|254724794|ref|ZP_05186577.1| hypothetical protein BantA1_20374 [Bacillus anthracis str. A1055]
 gi|254739057|ref|ZP_05196759.1| hypothetical protein BantWNA_28205 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254742322|ref|ZP_05200008.1| hypothetical protein BantKB_15138 [Bacillus anthracis str. Kruger
           B]
 gi|254756097|ref|ZP_05208126.1| hypothetical protein BantV_26846 [Bacillus anthracis str. Vollum]
 gi|254761915|ref|ZP_05213764.1| hypothetical protein BantA9_25851 [Bacillus anthracis str.
           Australia 94]
 gi|30253872|gb|AAP24367.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
 gi|47500749|gb|AAT29425.1| conserved hypothetical protein [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49177274|gb|AAT52650.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
 gi|164712880|gb|EDR18409.1| conserved hypothetical protein [Bacillus anthracis str. A0488]
 gi|167511911|gb|EDR87290.1| conserved hypothetical protein [Bacillus anthracis str. A0193]
 gi|170126344|gb|EDS95234.1| conserved hypothetical protein [Bacillus anthracis str. A0389]
 gi|170667673|gb|EDT18427.1| conserved hypothetical protein [Bacillus anthracis str. A0465]
 gi|190561271|gb|EDV15243.1| conserved hypothetical protein [Bacillus anthracis Tsiankovskii-I]
 gi|227003040|gb|ACP12783.1| conserved hypothetical protein [Bacillus anthracis str. CDC 684]
 gi|229266919|gb|ACQ48556.1| conserved hypothetical protein [Bacillus anthracis str. A0248]
          Length = 329

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKN 238


>gi|158334547|ref|YP_001515719.1| dihydrouridine synthase [Acaryochloris marina MBIC11017]
 gi|158304788|gb|ABW26405.1| dihydrouridine synthase (Dus) [Acaryochloris marina MBIC11017]
          Length = 342

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/307 (22%), Positives = 126/307 (41%), Gaps = 28/307 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     ++LYTEM+ A  +    +   ++     E+P+++Q+       L 
Sbjct: 39  TDLVFRRLVRRYAPESMLYTEMVHASQVCHARELSKVMDVDLDEQPISVQLFDCRPHFLA 98

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA++    G + I+LN+GCP  ++ +   G+ L+ +P+     + A+  A+ +PVTVK 
Sbjct: 99  EAAQMAVQEGADTIDLNMGCPVNKITKKGGGSSLLRDPETAEAIVRAVVSAVKVPVTVKT 158

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  +    + +    + ++ +G   I +H R        P     I  +         
Sbjct: 159 RIGWKED--EINILEFAQRMQDAGAKMITVHGRTRAQGYNGPAQWHWIKQV--------- 207

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           KE   + +  NG +  +  A+  L     DGVM  R       ++  +D +       + 
Sbjct: 208 KEKLSIPVIANGDIVSVESAMACLEMTGADGVMCSRGTLGYPYLVGEIDYFLKTGQQKAP 267

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNS-----RRCRH 295
           P           ++  +         + G K + Q  +HM     GF  +     R CR 
Sbjct: 268 PT-------IIERLQCAREHLQGLWEYKGIKGIHQARKHMTWYVKGFVGAAELRDRLCR- 319

Query: 296 ILTVEAG 302
           I +VE G
Sbjct: 320 INSVEEG 326


>gi|228937614|ref|ZP_04100252.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970501|ref|ZP_04131152.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977070|ref|ZP_04137473.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis Bt407]
 gi|228782687|gb|EEM30862.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis Bt407]
 gi|228789233|gb|EEM37161.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228822095|gb|EEM68085.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|229143117|ref|ZP_04271550.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228640390|gb|EEK96787.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST24]
          Length = 336

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|203284633|ref|YP_002222373.1| histidine phosphokinase/phophatase, putative [Borrelia duttonii Ly]
 gi|201084076|gb|ACH93667.1| histidine phosphokinase/phophatase, putative [Borrelia duttonii Ly]
          Length = 339

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 112/235 (47%), Gaps = 21/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNILGFSTQE----KPLAL 52
           M D TD  +R    L+ N      + +TE I    +L   K ++    T+     +PL  
Sbjct: 25  MEDVTDTVFRNLVNLIGNGKDGPDIYFTEFISVKGLLNKSKNSMQHILTKNDELSRPLIA 84

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G D  K V+A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 85  QIWGDDPDKFVKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAHEIIIASK 144

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C    +P++VK R G         + + +  + K G++ + +H R  I +   P D  
Sbjct: 145 EACLKYGLPLSVKTRHG----FFCSEVEDWLGFLLKLGIDMLTVHPRLVINQSEGPID-- 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
              N+  ++V    K NP + I  NG +  ++QA +++   S+DG+M GR   KN
Sbjct: 199 --VNVFDELVKLRNKINPYVVIIGNGDVLSLNQAYQMINKYSIDGIMFGRGILKN 251


>gi|254512463|ref|ZP_05124530.1| NifR3 family protein [Rhodobacteraceae bacterium KLH11]
 gi|221536174|gb|EEE39162.1| NifR3 family protein [Rhodobacteraceae bacterium KLH11]
          Length = 364

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 109/241 (45%), Gaps = 32/241 (13%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TDR +R     F A ++ +  +   EM+ A   +R   +     S   +  A+Q+ 
Sbjct: 56  MAGITDRPFRDLVMRFGAGMVVSEMVASQEMVQAKPGVRERAE----LSADVENTAVQLA 111

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +   + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+
Sbjct: 112 GREAHWMAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALTLIEAVVAAV 171

Query: 116 SIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRK 170
            IPVT+K R+G DD +   P VA R      + +G+  + IH R      KG +      
Sbjct: 172 DIPVTLKTRLGWDDSLLNAPDVARRA-----QDAGIQMVTIHGRTRCQFYKGRA------ 220

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
               D+  +  + KE   + +  NG +     A   L     DGVM+GR A     +L  
Sbjct: 221 ----DWQAIGAV-KEAVSVPVIANGDITGPGAARTALDQSGADGVMVGRGAQGRPWLLAQ 275

Query: 229 V 229
           +
Sbjct: 276 I 276


>gi|269215618|ref|ZP_06159472.1| tRNA-dihydrouridine synthase B [Slackia exigua ATCC 700122]
 gi|269131105|gb|EEZ62180.1| tRNA-dihydrouridine synthase B [Slackia exigua ATCC 700122]
          Length = 318

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 76/300 (25%), Positives = 129/300 (43%), Gaps = 37/300 (12%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       L YTEMI + A+   ++K  ++L  +  E+ +A+Q+ G +   +   A 
Sbjct: 9   FRRLCLEQGCDLTYTEMISSKALSFANEKTRHLLDLAEGERRVAIQLFGHEPKVMAREAA 68

Query: 68  IVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
            VED        I++N+GCP+ ++ +   G+ LM + D+    +  + +A+S PVTVK R
Sbjct: 69  WVEDELGDALALIDINMGCPAHKIVKKGDGSALMRDQDLAASIVRDVARAVSCPVTVKFR 128

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G   +        L   ++ +G   + +H R A      P         +++ V  +K 
Sbjct: 129 RGFGAEEETAVDFGL--RMEDAGAAAVTVHGRTAAQMYRGPS--------EWECVARVKA 178

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                 IG NG +   + A  ++ +   DGVMI R A  N  +   V           +P
Sbjct: 179 ALSVPVIG-NGDIVSGASAADMVRATGCDGVMIARGAQGNPWIFADVRRVLDG--MPPAP 235

Query: 243 IKTRVDKDFWRKISASMTDYAARHLH-----SGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             TR D+           + A RH+H      G  +  + +H++   HG P + R R  L
Sbjct: 236 DPTRQDR----------VEMARRHIHLLSSRLGNTVVYMRKHVMWYLHGVPGASRARAAL 285


>gi|254796745|ref|YP_003081581.1| NifR3 family protein [Neorickettsia risticii str. Illinois]
 gi|254589992|gb|ACT69354.1| NifR3 family protein [Neorickettsia risticii str. Illinois]
          Length = 313

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 103/225 (45%), Gaps = 26/225 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  YR   +      L+ +EMI + A++   K  +  +  S +E   A+Q+ G +   +
Sbjct: 5   TDMPYRDLVKSF-GAGLVVSEMIASRAMILKTKDTMKKVSLSPREDITAIQLAGFEPDVM 63

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAKI ED G   I++N GCP  +V  G  G+ LM +       +    KA+ IPVT+K
Sbjct: 64  AEAAKINEDMGAKIIDINFGCPVKKVVNGYAGSYLMKDECHAAKILETTVKAVKIPVTLK 123

Query: 123 CRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
            R G D+       RN   L K  +  G+  I IH R    + KG S          D+ 
Sbjct: 124 MRTGWDEN-----HRNAPKLAKIAEDLGIKMITIHGRTRAQMYKGKS----------DWQ 168

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
            +  + K    + +  NG ++    A + L     DG+M+GR AY
Sbjct: 169 FIRMV-KNTVKIPVIANGDIKTYEDAERALAESGADGIMVGRGAY 212


>gi|31792011|ref|NP_854504.1| transcriptional regulatory protein [Mycobacterium bovis AF2122/97]
 gi|121636747|ref|YP_976970.1| putative transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|224989218|ref|YP_002643905.1| putative transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Tokyo 172]
 gi|31617598|emb|CAD93708.1| POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [Mycobacterium bovis
           AF2122/97]
 gi|121492394|emb|CAL70862.1| Possible transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|224772331|dbj|BAH25137.1| putative transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Tokyo 172]
          Length = 389

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGCGAALPFKRRLFGQIVAAA 148

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|225862371|ref|YP_002747749.1| hypothetical protein BCA_0408 [Bacillus cereus 03BB102]
 gi|225786832|gb|ACO27049.1| conserved hypothetical protein [Bacillus cereus 03BB102]
          Length = 329

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSMGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|74318474|ref|YP_316214.1| dihydrouridine synthase [Thiobacillus denitrificans ATCC 25259]
 gi|74057969|gb|AAZ98409.1| dihydrouridine synthase [Thiobacillus denitrificans ATCC 25259]
          Length = 350

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 114/239 (47%), Gaps = 19/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EM+ ++++L G  K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGMAVSEMVTSNSLLYGSAKTARRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
              + EAA+   D G   I++N+GCP+ +V     G+ L+ +  +VG  + A+  A+  +
Sbjct: 76  PRMMAEAARHNADRGAQIIDINMGCPAKKVCNVMAGSALLQDEALVGRILDAVVAAVPEL 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVT+K R G D +   A+A+  + ++   +GV  + IH R     G S +        +Y
Sbjct: 136 PVTLKIRTGWDREHRNALAILGIAEN---AGVKALAIHGRTRAC-GYSGE-------AEY 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +  +K       I  NG +    +A  +L     D VMIGRAA     +   ++ Y 
Sbjct: 185 DTIRAVKAAARIPVIA-NGDITTPEKARHVLEHTGADAVMIGRAAQGRPWIFREIEHYL 242


>gi|329577778|gb|EGG59203.1| dihydrouridine synthase [Enterococcus faecalis TX1467]
          Length = 342

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 37  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 96

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 97  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 155

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 156 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 204

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 205 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 256


>gi|229028175|ref|ZP_04184316.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1271]
 gi|228733123|gb|EEL83964.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1271]
          Length = 336

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRKVGLELAEKYGIDGVMIGRGIFKN 245


>gi|152992909|ref|YP_001358630.1| tRNA-dihydrouridine synthase [Sulfurovum sp. NBC37-1]
 gi|151424770|dbj|BAF72273.1| tRNA-dihydrouridine synthase [Sulfurovum sp. NBC37-1]
          Length = 318

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 112/224 (50%), Gaps = 19/224 (8%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L  +EMI ++A++   KK   +L  S +E P ++QI G+D+  +  A +I+ E  G + I
Sbjct: 35  LTVSEMISSNALVHNSKKTHKMLEKSPREDPYSIQIAGSDLEVIRRAVEIINEQEGVSVI 94

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVAL 136
           +LN GCP+ +V     G+ L+ +   +G  I  +    + P T +K R+G +++      
Sbjct: 95  DLNCGCPAPKVVNNLQGSSLLTDLPQMGKVIETIKTHSNKPYTSMKMRLGFNEKNHV--- 151

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + +  + SG + I +H R    +  +P        +DYD + EI KE  ++ +  NG 
Sbjct: 152 -EIARIAEASGADYIAVHGRTRAGRYKAP--------VDYDAIREI-KEAVNIPVIANGD 201

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           ++   +A  +L     DGVMIGRAA     +   + E  + P +
Sbjct: 202 IDSPEKAQWVLEHTGADGVMIGRAAVGKPWIFKQIKEGMAQPTS 245


>gi|294886251|ref|XP_002771632.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
 gi|239875338|gb|EER03448.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
          Length = 720

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 102/225 (45%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A +     K     F T   + PLA Q  G D
Sbjct: 317 MVDQSELAFRMMTRKY-GAQFCYTPMMHAKSFATSKKYREKNFETAPGDSPLAAQFCGDD 375

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAK +ED   + I+LN+GCP      G +G+ L+  P++V   +  M K +  P
Sbjct: 376 GDVIVEAAKHIED-QVSCIDLNLGCPQGIARRGHYGSFLLEEPELVLRIVEKMVKGIKCP 434

Query: 119 VTVKCRI--GVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           V+VK R+    DD    +    A +  VK +   GV+ I +H R    KG      +   
Sbjct: 435 VSVKIRLMTAKDDDGSGRPDVAATKEFVKRLDSLGVDLIALHPRTKEWKG------QLTQ 488

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVM 214
              +    E++   PD+   +NGG+   ED+ +  ++    D VM
Sbjct: 489 ACWWQAAAEVRACVPDIPFIVNGGISCFEDVEKCFEVT-KCDAVM 532


>gi|86131460|ref|ZP_01050058.1| dihydrouridine synthase (Dus) [Dokdonia donghaensis MED134]
 gi|85817905|gb|EAQ39073.1| dihydrouridine synthase (Dus) [Dokdonia donghaensis MED134]
          Length = 330

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 79/332 (23%), Positives = 145/332 (43%), Gaps = 43/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +    + ++YTE I ++ ++R   K++  L    +E+P+ +QI GA 
Sbjct: 19  MEDVSDPPFRALCKEQGAD-VVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ + +IVE  G + I++N GCP  +V     GA ++ + D++     +M +   +P
Sbjct: 78  EESMLRSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVKLTKSMVEHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VTVK R+G D +  ++ +  + + ++  G   I IH R    + KG          + D+
Sbjct: 138 VTVKTRLGWDHE--SIKIVEVAERLQDVGCAAISIHGRTRAQMYKG----------DADW 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             +  +K  N  + I +  NG +    +A+++     +DG MIGRA+         V  +
Sbjct: 186 KPIAAVKN-NQRMHIPVFGNGDVNSPERAVEMRDEYGLDGAMIGRASIGYPWFFNEVKHF 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-------QITRHMIGLFH 285
                    P  T V++           + A RHL      +       +  RH    F 
Sbjct: 245 MKTGEHKKPP--TLVER----------VEAARRHLEMSIAWKGEILGVFETRRHYTNYFR 292

Query: 286 GFPNSRRCRHILTVEAGAST--ATHHIIETAF 315
           G P+ +  R  L     +    A  ++IE  F
Sbjct: 293 GIPHFKEYRMKLVTSDKSEDVFAALNLIEEKF 324


>gi|75675635|ref|YP_318056.1| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrobacter
           winogradskyi Nb-255]
 gi|74420505|gb|ABA04704.1| tRNA-U20-dihydrouridine synthase [Nitrobacter winogradskyi Nb-255]
          Length = 349

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 116/246 (47%), Gaps = 19/246 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLV 63
           TDR +R     L   AL+ +EM  +D ++RG   ++L   +T   P  +Q+ G +   + 
Sbjct: 37  TDRPFRRLTESL-GAALVVSEMTASDDLVRGRPMSVLRCEATGHGPHVVQLAGCETRWMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+I E  G + I++N+GCP+  V  G  G+ LM +PD   D I A   A+++PVT+K 
Sbjct: 96  EAARIAEAAGADIIDINMGCPARHVTGGQSGSALMRDPDHALDLIEATVGAVNVPVTLKM 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D    +    +L +  + +GV  I +H R      KG +          D+  V  
Sbjct: 156 RLGWDGH--SFNAPSLARRAESAGVRMITVHGRTRCQFYKGRA----------DWRAVRA 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + KE   + + +NG +     A+  L +   D VM+GR A     +   +       +  
Sbjct: 204 V-KEAVRVPVVVNGDITSFDAAVAALEASGADAVMVGRGAQGRPWLPGQIGRRLETGIEE 262

Query: 240 SSPIKT 245
           S P  T
Sbjct: 263 SHPSLT 268


>gi|167967511|ref|ZP_02549788.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis H37Ra]
 gi|215426084|ref|ZP_03424003.1| transcriptional regulator [Mycobacterium tuberculosis T92]
 gi|306806659|ref|ZP_07443327.1| transcriptional regulator [Mycobacterium tuberculosis SUMu007]
 gi|308397233|ref|ZP_07492455.2| transcriptional regulator [Mycobacterium tuberculosis SUMu012]
 gi|308346868|gb|EFP35719.1| transcriptional regulator [Mycobacterium tuberculosis SUMu007]
 gi|308366954|gb|EFP55805.1| transcriptional regulator [Mycobacterium tuberculosis SUMu012]
 gi|323720747|gb|EGB29819.1| transcriptional regulator [Mycobacterium tuberculosis CDC1551A]
          Length = 377

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 17  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 77  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 136

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 137 VRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSALRRALAM 314


>gi|332304569|ref|YP_004432420.1| TIM-barrel protein, nifR3 family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332171898|gb|AEE21152.1| TIM-barrel protein, nifR3 family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 333

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/257 (25%), Positives = 120/257 (46%), Gaps = 28/257 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  + R +K         EK + A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAGLVVSEMLSSNPDVWRSNKSKQRMDHVGEKGIRAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   +++N+GCP+ +V++   G+ L+ +P +V   + ++ +A+ +P
Sbjct: 76  PLLMAQAAQFNVDNGAQIVDINMGCPAKKVNKKLAGSALLQDPQLVEQIVQSVVEAVQVP 135

Query: 119 VTVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           VT+K R G +       QI  +A +N ++S+   G        R  + KG          
Sbjct: 136 VTLKIRTGWNTDNRNGVQIAKIAEQNGIQSLAVHG------RTRACMYKG---------- 179

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           N +YD +  IK+    + +  NG +  +  A  +L     D +MIGR A  N  +   + 
Sbjct: 180 NAEYDTIKAIKQA-VSIPVVANGDITCVHSAKHVLEYTKADALMIGRGAQGNPWIFRQIQ 238

Query: 231 EYFSNPLTGSSPIKTRV 247
            +        SP  + V
Sbjct: 239 HFLQTGEILPSPPLSEV 255


>gi|312905510|ref|ZP_07764624.1| dihydrouridine synthase [Enterococcus faecalis TX0635]
 gi|310631239|gb|EFQ14522.1| dihydrouridine synthase [Enterococcus faecalis TX0635]
          Length = 337

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV++K RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 151 LPVSIKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 199

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 200 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 251


>gi|27379597|ref|NP_771126.1| nitrogen regulation protein [Bradyrhizobium japonicum USDA 110]
 gi|27352749|dbj|BAC49751.1| nitrogen regulation protein [Bradyrhizobium japonicum USDA 110]
          Length = 371

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 101/216 (46%), Gaps = 22/216 (10%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKI 68
           R  A L     L+ +EM  +D +  G + + L   +T   P  +Q+ G +   + E A+I
Sbjct: 65  RLVAEL--GAGLVVSEMTASDELANGHRMSRLRCEATGIGPHVVQLAGCEAHWMAEGARI 122

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G D
Sbjct: 123 AEAEGADIIDINMGCPARHVTGGQSGSALMRDLDHAVGLIDATIAAVKVPVTLKMRLGWD 182

Query: 129 DQ---IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           D+    P +A R     IK   V+G     R    KG            D+D +  + +E
Sbjct: 183 DRSRNAPELARRAEAAGIKLVTVHG---RTRCQFYKG----------EADWDAIRTV-RE 228

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
              + + +NG +    +AL  L S   D VMIGR A
Sbjct: 229 AISIPLIVNGDITSYEKALAALESSGADAVMIGRGA 264


>gi|229101138|ref|ZP_04231904.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-28]
 gi|228682266|gb|EEL36377.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-28]
          Length = 336

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R       +  + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGSPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEEWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|254363760|ref|ZP_04979806.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis str. Haarlem]
 gi|134149274|gb|EBA41319.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis str. Haarlem]
          Length = 339

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 148

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|183984825|ref|YP_001853116.1| transcriptional regulator [Mycobacterium marinum M]
 gi|183178151|gb|ACC43261.1| transcriptional regulator [Mycobacterium marinum M]
          Length = 377

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 76/296 (25%), Positives = 129/296 (43%), Gaps = 25/296 (8%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           A++ T + L   EM+ A A++       ++  F+  E P +LQ+   D      AA+++ 
Sbjct: 35  AKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSLQLYTVDPDTTYAAARMIA 94

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIG 126
           + G  + I++N GCP  +V +   GA L     + G  +AA  + +    IPVTVK RIG
Sbjct: 95  EEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAAVRGVEGTDIPVTVKFRIG 154

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD        +  +  +  G   + +HAR A          R     D++ +  +K+  
Sbjct: 155 IDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWEQIALLKQHV 204

Query: 187 PDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS-NPLTGSSPI 243
             + +  NG + D S AL ++ +   DGV+IGR       +   +   F+ NP  G +P 
Sbjct: 205 RTVPVLGNGDIYDASDALAMMAATGCDGVVIGRGCLGRPWLFAELSAAFTGNP--GPTPP 262

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 D  R+      +  A H      ++ I +H+    HGFP     R  L +
Sbjct: 263 TLGEVTDIIRRHG----ELLAAHFGEDKGMRDIRKHVAWYLHGFPAGSDLRRALAL 314


>gi|116617846|ref|YP_818217.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
 gi|116096693|gb|ABJ61844.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
          Length = 365

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 111/227 (48%), Gaps = 30/227 (13%)

Query: 12  FARLLTNNA---LLYTEMIVADAILRGDKKNILGFSTQ---------EKPLALQIGGADI 59
           F R++   A   + YTE   A +++    K    FS Q         ++P+A QI G+  
Sbjct: 41  FRRVVAKAAAPDVYYTEFTNASSMVHPKAK----FSVQGRLAVAEGEQQPVA-QIWGSRP 95

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++  + +++ D GY  +++N+GCP   V + S G+ L+ +PD+  + I A  ++ S+PV
Sbjct: 96  KEIAGSIEVLADMGYQAVDINMGCPDGTVIKNSSGSDLIRHPDLAEEIIVA-AQSGSLPV 154

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G          R  +  I +  V  + +H R       +P     I     D +
Sbjct: 155 SVKTRLGF---YKPEEFREWLPIILRHQVAVLTVHLRSRKEMSKAPAHYEHI-----DEI 206

Query: 180 YEIKKE-NPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
             ++ E  P+  I +NG ++  +Q + ++   P +DG+MIGR  ++N
Sbjct: 207 LAMRDEIAPNTLIQINGDIKTRAQGIALVQEHPGIDGIMIGRGIFEN 253


>gi|325123027|gb|ADY82550.1| tRNA-dihydrouridine synthase B [Acinetobacter calcoaceticus PHEA-2]
          Length = 341

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 151/324 (46%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + LR + K  + +G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQENI-LR-VAKRAEDAGIAALALHGR--------TREDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + KE  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHV-KELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKQVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYKVESTAEQAI--VVENYFNQLL 321


>gi|229171166|ref|ZP_04298760.1| tRNA-dihydrouridine synthase [Bacillus cereus MM3]
 gi|228612344|gb|EEK69572.1| tRNA-dihydrouridine synthase [Bacillus cereus MM3]
          Length = 336

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R       +  + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGSPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEEWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|297582892|ref|YP_003698672.1| dihydrouridine synthase DuS [Bacillus selenitireducens MLS10]
 gi|297141349|gb|ADH98106.1| dihydrouridine synthase DuS [Bacillus selenitireducens MLS10]
          Length = 343

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 108/237 (45%), Gaps = 28/237 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGADIS 60
           TD  +R          + +TE   +D+      R   K  L F+  E+P+   I G    
Sbjct: 23  TDVVFRHVVSEAAAPDVFFTEFANSDSFCHPKGRESLKGRLMFTEDEQPIVAHIWGDKPE 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
                +  + + GY  I++N+GCP   V     GA L+  PD+  + I A  KA  +PV+
Sbjct: 83  HFRTMSVAMAEMGYKGIDINMGCPVHNVAGDGKGAGLIKRPDVAAELIEA-AKAGGLPVS 141

Query: 121 VKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VK RIG   +D+       +N ++ I +  +  + IH R       + K+   +P   ++
Sbjct: 142 VKTRIGFSKIDE------WQNWLRHILEQDIVNLSIHLR-------TKKEMSDVP-AHWE 187

Query: 178 IVYEIK----KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           ++ +IK    +  P+  + +NG ++D    L++     VDG+MIGR  +KN     T
Sbjct: 188 LIPDIKALRDEVAPNTLLTINGDIDDRQTGLELAEKYGVDGIMIGRGIFKNPFAFET 244


>gi|218235838|ref|YP_002365163.1| hypothetical protein BCB4264_A0382 [Bacillus cereus B4264]
 gi|218163795|gb|ACK63787.1| conserved hypothetical protein [Bacillus cereus B4264]
 gi|326938108|gb|AEA14004.1| nitrogen regulation protein NIFR3 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 329

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|84501088|ref|ZP_00999323.1| tRNA-dihydrouridine synthase, putative [Oceanicola batsensis
           HTCC2597]
 gi|84391155|gb|EAQ03573.1| tRNA-dihydrouridine synthase, putative [Oceanicola batsensis
           HTCC2597]
          Length = 326

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 75/141 (53%), Gaps = 10/141 (7%)

Query: 21  LLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+ +EM+ +  +L  R   +            ++Q+ G D + + EAA+ V D G   I+
Sbjct: 38  LVVSEMVASGELLTDRPGTRERAELGLGRAATSVQLAGRDPAVMAEAARQVADLGARVID 97

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V  G  G+ LM +PD+    IAA+  A+ +PVTVK R+G DD       RN
Sbjct: 98  INMGCPAKKVTGGLSGSALMRDPDLALSLIAAVAGAVDLPVTVKMRLGWDDDT-----RN 152

Query: 139 ---LVKSIKKSGVNGIWIHAR 156
              L +  + +GV  + +H R
Sbjct: 153 APDLARRAEAAGVRMVVVHGR 173


>gi|297537586|ref|YP_003673355.1| TIM-barrel protein, nifR3 family [Methylotenera sp. 301]
 gi|297256933|gb|ADI28778.1| TIM-barrel protein, nifR3 family [Methylotenera sp. 301]
          Length = 346

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 115/239 (48%), Gaps = 20/239 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G +K +       +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSEKTLRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PQMMAEAARHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVAQILRAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           VT+K R G D +   AV +  + + +   GV  + +H R +A L            + +Y
Sbjct: 136 VTLKIRTGWDKNNRNAVQIARIAEDL---GVQALAMHGRTRACL---------YTGDAEY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +  +K+      I  NG +    +A  +L     D VMIGRAA     +   ++ + 
Sbjct: 184 DTIAAVKQAIKIPLIA-NGDITTPEKAKFVLDYTGADAVMIGRAAQGRPWIFREIEHFI 241


>gi|70944501|ref|XP_742175.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56521005|emb|CAH88154.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 251

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 92/205 (44%), Gaps = 34/205 (16%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R GVDD      L++ ++++   G     IH+RKA LKGL PK NR +P L+Y+ V
Sbjct: 1   SVKIRTGVDDLDSFSFLKSFIETVSSVGCEHFIIHSRKAWLKGLDPKQNRSVPPLEYNKV 60

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS-----------------------------V 210
           +++ K  P+L   LNGG++ + Q + +L                               +
Sbjct: 61  FDLCKLYPNLKFTLNGGIKSIEQGVALLNGYVPINKTTGNHNKYTDNNYIKVEDYDINPL 120

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
            GVMIGRA   N  +L   D+   N  T ++    R   + ++      + +     +S 
Sbjct: 121 YGVMIGRACMDNITVLAKTDKLVYNHDTLATAYSRRTVLEAYKSYLEQNSSF-----YSL 175

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ + ++G+  G P  R  R+
Sbjct: 176 VNAFELLKPILGVLKGMPGHRLFRN 200


>gi|289752872|ref|ZP_06512250.1| LOW QUALITY PROTEIN: transcriptional regulatory protein
           [Mycobacterium tuberculosis EAS054]
 gi|289693459|gb|EFD60888.1| LOW QUALITY PROTEIN: transcriptional regulatory protein
           [Mycobacterium tuberculosis EAS054]
          Length = 362

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 74/295 (25%), Positives = 125/295 (42%), Gaps = 23/295 (7%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           +++ T + L   EM+ A A++       ++  FS  E P +LQ+   D      AA+++ 
Sbjct: 20  SKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSLQLYTVDPDTTYAAARMIA 79

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIG 126
             G  + I++N GCP  +V +   GA L     + G  +AA  +A     IPVTVK RIG
Sbjct: 80  GEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAAVRATEGTDIPVTVKFRIG 139

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD        +  +  +  G   + +HAR A          R     D++ +  +K+  
Sbjct: 140 IDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWEQIARLKQHV 189

Query: 187 PDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             + +  NG + D   AL ++ +   DGV+IGR       +   +   F+     + P  
Sbjct: 190 RTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLFAELSAAFTGSPAPTPPTL 249

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             V  D  R+    +    A H      ++ I +H+    HGFP     R  L +
Sbjct: 250 GEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHGFPAGSALRRALAM 299


>gi|89098483|ref|ZP_01171366.1| hypothetical protein B14911_09737 [Bacillus sp. NRRL B-14911]
 gi|89086728|gb|EAR65846.1| hypothetical protein B14911_09737 [Bacillus sp. NRRL B-14911]
          Length = 304

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDK--KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++     G++  +  L F+  E+P+   I G
Sbjct: 1   MEDVTDVVFRHVVSEAARPDVFFTEFTNTESYCHPEGNQSVRGRLTFTEDEQPMVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  V + G+  I++N+GCP   V +   G+ L+L PD+  D + A  KA  
Sbjct: 61  DKPEFFRQTSIGVAEQGFRGIDINMGCPVPNVAQRGKGSGLILRPDVAADIVQA-AKAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +  I +  +  + IH R    K +S  D        +
Sbjct: 120 LPVSVKTRLGYTE---VDEWQDWLTHILEQDIANLSIHLRTR--KEMSEVDAH------W 168

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D     +++    VDGVMIGR  +KN
Sbjct: 169 ELIPEIKKLRDRVAPDTLLTINGDILDRQAGQQLVDQYGVDGVMIGRGIFKN 220


>gi|203288167|ref|YP_002223182.1| histidine phosphokinase/phophatase, putative [Borrelia recurrentis
           A1]
 gi|201085387|gb|ACH94961.1| histidine phosphokinase/phophatase, putative [Borrelia recurrentis
           A1]
          Length = 339

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 112/235 (47%), Gaps = 21/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNILGFSTQE----KPLAL 52
           M D TD  +R    L+ N      + +TE I    +L   K ++    T+     +PL  
Sbjct: 25  MEDVTDTVFRNLINLIGNGKDGPDIYFTEFISVKGLLNKSKNSMQHILTKNDELSRPLIA 84

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G D  K V+A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 85  QIWGDDPDKFVKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAHEIIIASK 144

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C    +P++VK R G         + + +  + K G++ + +H R  I +   P D  
Sbjct: 145 EACLKYGLPLSVKTRHG----FFCSEVEDWLGFLLKLGIDMLTVHPRLVINQSEGPID-- 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
              N+  ++V    K NP + I  NG +  ++QA +++   S+DG+M GR   KN
Sbjct: 199 --VNVFDELVKLRNKINPYVVIIGNGDVLSLNQAYQMINKYSIDGIMFGRGILKN 251


>gi|89054727|ref|YP_510178.1| dihydrouridine synthase TIM-barrel protein nifR3 [Jannaschia sp.
           CCS1]
 gi|88864276|gb|ABD55153.1| tRNA-U20-dihydrouridine synthase [Jannaschia sp. CCS1]
          Length = 347

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 88/320 (27%), Positives = 143/320 (44%), Gaps = 45/320 (14%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     F A L+ +  +   EM+ A A +R   +  LGF   E   A+Q+ 
Sbjct: 38  MAGITDLPFRRLVASFGAGLVVSEMVASQEMVEAKASVRARAE--LGFG--ENATAVQLA 93

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +   + EAA+I E  G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+
Sbjct: 94  GREAHWMAEAARIAEGQGARIIDINMGCPAKKVVGGLSGSALMRDLDHALRLIDAVVGAV 153

Query: 116 SIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRK 170
           ++PVT+K R+G DD+    PA+A R      + +G+  I IH R      KG +      
Sbjct: 154 NVPVTLKTRLGWDDKTLNAPALAQRA-----ETAGIRMITIHGRTRCQFYKGTA------ 202

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
                +  +  + K+   + +  NG + D   A + L     DGVM+GR       ++  
Sbjct: 203 ----KWGAIRAV-KDAVSIPVIANGDITDAPAAAQALRCSGADGVMVGRGIQGQPWLVAE 257

Query: 229 VD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLF-- 284
           +    F  P    +P+  + D      ++A   D  A +    GGK   + R  +G +  
Sbjct: 258 IGAALFGTP----TPVAPQGDA-LVAMVAAHYEDMLAFYGRDLGGK---VARKHLGWYMD 309

Query: 285 -HGFPNSRRCRHILTVEAGA 303
             G P + R   + T + GA
Sbjct: 310 GAGTPPALRKEVLTTKDPGA 329


>gi|15607963|ref|NP_215338.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           H37Rv]
 gi|15840236|ref|NP_335273.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis CDC1551]
 gi|148660601|ref|YP_001282124.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis H37Ra]
 gi|148822029|ref|YP_001286783.1| transcriptional regulator [Mycobacterium tuberculosis F11]
 gi|215410393|ref|ZP_03419201.1| transcriptional regulator [Mycobacterium tuberculosis 94_M4241A]
 gi|218752486|ref|ZP_03531282.1| transcriptional regulator [Mycobacterium tuberculosis GM 1503]
 gi|219556682|ref|ZP_03535758.1| transcriptional regulator [Mycobacterium tuberculosis T17]
 gi|253797770|ref|YP_003030771.1| transcriptional regulator [Mycobacterium tuberculosis KZN 1435]
 gi|254231135|ref|ZP_04924462.1| hypothetical protein TBCG_00813 [Mycobacterium tuberculosis C]
 gi|254549795|ref|ZP_05140242.1| transcriptional regulator [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260185716|ref|ZP_05763190.1| transcriptional regulator [Mycobacterium tuberculosis CPHL_A]
 gi|260199838|ref|ZP_05767329.1| transcriptional regulator [Mycobacterium tuberculosis T46]
 gi|289442226|ref|ZP_06431970.1| transcriptional regulator [Mycobacterium tuberculosis T46]
 gi|289446387|ref|ZP_06436131.1| transcriptional regulator [Mycobacterium tuberculosis CPHL_A]
 gi|289553080|ref|ZP_06442290.1| transcriptional regulator [Mycobacterium tuberculosis KZN 605]
 gi|289568776|ref|ZP_06449003.1| transcriptional regulator [Mycobacterium tuberculosis T17]
 gi|289749339|ref|ZP_06508717.1| transcriptional regulator [Mycobacterium tuberculosis T92]
 gi|289760952|ref|ZP_06520330.1| transcriptional regulatory protein [Mycobacterium tuberculosis GM
           1503]
 gi|297633335|ref|ZP_06951115.1| transcriptional regulator [Mycobacterium tuberculosis KZN 4207]
 gi|297730319|ref|ZP_06959437.1| transcriptional regulator [Mycobacterium tuberculosis KZN R506]
 gi|298524313|ref|ZP_07011722.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|306774946|ref|ZP_07413283.1| transcriptional regulator [Mycobacterium tuberculosis SUMu001]
 gi|306783489|ref|ZP_07421811.1| transcriptional regulator [Mycobacterium tuberculosis SUMu003]
 gi|306787853|ref|ZP_07426175.1| transcriptional regulator [Mycobacterium tuberculosis SUMu004]
 gi|306796592|ref|ZP_07434894.1| transcriptional regulator [Mycobacterium tuberculosis SUMu006]
 gi|306802450|ref|ZP_07439118.1| transcriptional regulator [Mycobacterium tuberculosis SUMu008]
 gi|306966858|ref|ZP_07479519.1| transcriptional regulator [Mycobacterium tuberculosis SUMu009]
 gi|307078781|ref|ZP_07487951.1| transcriptional regulator [Mycobacterium tuberculosis SUMu011]
 gi|308370149|ref|ZP_07420479.2| transcriptional regulator [Mycobacterium tuberculosis SUMu002]
 gi|308378726|ref|ZP_07483710.2| transcriptional regulator [Mycobacterium tuberculosis SUMu010]
 gi|313657644|ref|ZP_07814524.1| transcriptional regulator [Mycobacterium tuberculosis KZN V2475]
 gi|6647988|sp|O53835|DUS_MYCTU RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|2916881|emb|CAA17629.1| POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [Mycobacterium
           tuberculosis H37Rv]
 gi|13880393|gb|AAK45087.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis CDC1551]
 gi|124600194|gb|EAY59204.1| hypothetical protein TBCG_00813 [Mycobacterium tuberculosis C]
 gi|148504753|gb|ABQ72562.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis H37Ra]
 gi|148720556|gb|ABR05181.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis F11]
 gi|253319273|gb|ACT23876.1| transcriptional regulator [Mycobacterium tuberculosis KZN 1435]
 gi|289415145|gb|EFD12385.1| transcriptional regulator [Mycobacterium tuberculosis T46]
 gi|289419345|gb|EFD16546.1| transcriptional regulator [Mycobacterium tuberculosis CPHL_A]
 gi|289437712|gb|EFD20205.1| transcriptional regulator [Mycobacterium tuberculosis KZN 605]
 gi|289542530|gb|EFD46178.1| transcriptional regulator [Mycobacterium tuberculosis T17]
 gi|289689926|gb|EFD57355.1| transcriptional regulator [Mycobacterium tuberculosis T92]
 gi|289708458|gb|EFD72474.1| transcriptional regulatory protein [Mycobacterium tuberculosis GM
           1503]
 gi|298494107|gb|EFI29401.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|308216500|gb|EFO75899.1| transcriptional regulator [Mycobacterium tuberculosis SUMu001]
 gi|308325163|gb|EFP14014.1| transcriptional regulator [Mycobacterium tuberculosis SUMu002]
 gi|308331710|gb|EFP20561.1| transcriptional regulator [Mycobacterium tuberculosis SUMu003]
 gi|308335508|gb|EFP24359.1| transcriptional regulator [Mycobacterium tuberculosis SUMu004]
 gi|308342985|gb|EFP31836.1| transcriptional regulator [Mycobacterium tuberculosis SUMu006]
 gi|308350809|gb|EFP39660.1| transcriptional regulator [Mycobacterium tuberculosis SUMu008]
 gi|308355442|gb|EFP44293.1| transcriptional regulator [Mycobacterium tuberculosis SUMu009]
 gi|308359398|gb|EFP48249.1| transcriptional regulator [Mycobacterium tuberculosis SUMu010]
 gi|308363303|gb|EFP52154.1| transcriptional regulator [Mycobacterium tuberculosis SUMu011]
 gi|328457549|gb|AEB02972.1| transcriptional regulator [Mycobacterium tuberculosis KZN 4207]
          Length = 389

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 148

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|293553600|ref|ZP_06674224.1| probable tRNA-dihydrouridine synthase [Enterococcus faecium E1039]
 gi|291602175|gb|EFF32403.1| probable tRNA-dihydrouridine synthase [Enterococcus faecium E1039]
          Length = 327

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D     ++     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKN 238


>gi|282874789|ref|ZP_06283668.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis SK135]
 gi|281296505|gb|EFA89020.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis SK135]
          Length = 326

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 103/218 (47%), Gaps = 25/218 (11%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E+P+   I G    +  E +  + 
Sbjct: 40  FFTEFTNTESYCHPEGIHS---VRGR----LTFSDDEQPMVAHIWGDKPEQFREMSIGLA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  +PV+VK R+G  D 
Sbjct: 93  DMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGGLPVSVKTRLGYYD- 150

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---- 186
                 R+ +K + +  +  + IH R       + K+  K+ +  ++++  IK       
Sbjct: 151 --IDEWRDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHWELIEAIKTLRDEIA 200

Query: 187 PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           P+  + +NG + D    L++     +DG+MIGR  + N
Sbjct: 201 PNTLLTINGDIPDRQTGLELASKYGIDGIMIGRGIFHN 238


>gi|257882496|ref|ZP_05662149.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|294620960|ref|ZP_06700160.1| tRNA-dihydrouridine synthase [Enterococcus faecium U0317]
 gi|257818154|gb|EEV45482.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|291599490|gb|EFF30507.1| tRNA-dihydrouridine synthase [Enterococcus faecium U0317]
          Length = 327

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D     ++     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKN 238


>gi|69245524|ref|ZP_00603488.1| Dihydrouridine synthase, DuS [Enterococcus faecium DO]
 gi|257879771|ref|ZP_05659424.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257891612|ref|ZP_05671265.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257894880|ref|ZP_05674533.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|260559446|ref|ZP_05831627.1| dihydrouridine synthase [Enterococcus faecium C68]
 gi|293564087|ref|ZP_06678493.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1162]
 gi|293570023|ref|ZP_06681103.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1071]
 gi|294618242|ref|ZP_06697824.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1679]
 gi|314940100|ref|ZP_07847283.1| dihydrouridine synthase [Enterococcus faecium TX0133a04]
 gi|314942492|ref|ZP_07849331.1| dihydrouridine synthase [Enterococcus faecium TX0133C]
 gi|314949401|ref|ZP_07852742.1| dihydrouridine synthase [Enterococcus faecium TX0082]
 gi|314952861|ref|ZP_07855833.1| dihydrouridine synthase [Enterococcus faecium TX0133A]
 gi|314993706|ref|ZP_07859051.1| dihydrouridine synthase [Enterococcus faecium TX0133B]
 gi|314994770|ref|ZP_07859902.1| dihydrouridine synthase [Enterococcus faecium TX0133a01]
 gi|68195775|gb|EAN10212.1| Dihydrouridine synthase, DuS [Enterococcus faecium DO]
 gi|257813999|gb|EEV42757.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257827972|gb|EEV54598.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257831259|gb|EEV57866.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|260074545|gb|EEW62866.1| dihydrouridine synthase [Enterococcus faecium C68]
 gi|291587395|gb|EFF19279.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1071]
 gi|291595458|gb|EFF26769.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1679]
 gi|291604005|gb|EFF33533.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1162]
 gi|313590954|gb|EFR69799.1| dihydrouridine synthase [Enterococcus faecium TX0133a01]
 gi|313591806|gb|EFR70651.1| dihydrouridine synthase [Enterococcus faecium TX0133B]
 gi|313595095|gb|EFR73940.1| dihydrouridine synthase [Enterococcus faecium TX0133A]
 gi|313598713|gb|EFR77558.1| dihydrouridine synthase [Enterococcus faecium TX0133C]
 gi|313640700|gb|EFS05280.1| dihydrouridine synthase [Enterococcus faecium TX0133a04]
 gi|313644232|gb|EFS08812.1| dihydrouridine synthase [Enterococcus faecium TX0082]
          Length = 327

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D     ++     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKN 238


>gi|329889586|ref|ZP_08267929.1| putative tRNA-dihydrouridine synthase [Brevundimonas diminuta ATCC
           11568]
 gi|328844887|gb|EGF94451.1| putative tRNA-dihydrouridine synthase [Brevundimonas diminuta ATCC
           11568]
          Length = 349

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 106/227 (46%), Gaps = 22/227 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL---QIGGA 57
           M   TD  +R  A  L   A + TEM+ A  + R  + +++  +     L L   Q+ G 
Sbjct: 21  MTGITDLPFRVLASKL-GAAYVATEMVAAAELARA-RPDVVRRAAVGGGLPLTVIQLVGG 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   + E A++ E  G + I+LN GCP+  V   + G+ LM  PD     + A+  A+S 
Sbjct: 79  DPVAMAEGARMAEAAGADLIDLNFGCPAKEVTGAACGSALMRTPDQAARIMEAVVGAVSR 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PV+VK R+G D+     A  +L +  +  GV  + +H   RK    G++          D
Sbjct: 139 PVSVKMRLGWDENSHNAA--DLARRAETLGVAAVTVHGRTRKQFYTGVA----------D 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           +D V E+K+      I +NG +    QA + L     D +M+GR  Y
Sbjct: 187 WDAVAEVKQVVTIPVI-VNGDIITAEQAREALDRSGADALMLGRGVY 232


>gi|224093091|ref|XP_002192992.1| PREDICTED: similar to dihydrouridine synthase 4-like [Taeniopygia
           guttata]
          Length = 316

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 112/238 (47%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  + + L YT MIVA   +R  K     F+T   + PL +Q    +
Sbjct: 32  MVRYSKLAFRTLVRKYSCD-LCYTPMIVAADFVRSAKARDSEFTTNKGDHPLIVQFAAKE 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA I+  F  + I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 91  AQVLCDAACIICPFA-DGIDVNCGCPQRWAISEGYGACLINKPELVKDMVRHVRNQIDNP 149

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R          + R  P + 
Sbjct: 150 KFSVSIKIRIHEDLKRTV----DLCQKAEAAGVSWITVHGRTI--------EERHQP-VH 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           YD + +I K++  + I  NG ++ + +A  +  L   DGVM+ R    N AM    +E
Sbjct: 197 YDAI-KIIKQSMSIPIVANGDIKSLKEAENVHHLTEADGVMVARGLLANPAMFAGYEE 253


>gi|49480076|ref|YP_034652.1| dihydrouridine synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|49331632|gb|AAT62278.1| conserved hypothetical protein, probable dihydrouridine synthase
           [Bacillus thuringiensis serovar konkukian str. 97-27]
          Length = 329

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|300861503|ref|ZP_07107587.1| dihydrouridine synthase (Dus) [Enterococcus faecalis TUSoD Ef11]
 gi|300848964|gb|EFK76717.1| dihydrouridine synthase (Dus) [Enterococcus faecalis TUSoD Ef11]
          Length = 324

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGFTEM---AEMDAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 187 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 238


>gi|311067292|ref|YP_003972215.1| histidine phosphokinase/phophatase [Bacillus atrophaeus 1942]
 gi|310867809|gb|ADP31284.1| histidine phosphokinase/phophatase, putative [Bacillus atrophaeus
           1942]
          Length = 327

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       R+ +  + K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGYTD---VDEWRDWLTHVLKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAQQYGVDGIMIGRGIFTN 238


>gi|220926307|ref|YP_002501609.1| TIM-barrel protein, nifR3 family [Methylobacterium nodulans ORS
           2060]
 gi|219950914|gb|ACL61306.1| TIM-barrel protein, nifR3 family [Methylobacterium nodulans ORS
           2060]
          Length = 357

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 106/228 (46%), Gaps = 15/228 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLV 63
           TD H R  AR L   A++ +EM+ A+   RG  +  L    +   P  +Q+ G D   + 
Sbjct: 42  TDLHLRRIARRLGATAVV-SEMVAAEDFARGTAEARLRAEGEGVLPHVVQLAGCDPHWMA 100

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A++ E  G + I++N+GCP+ +V  G  G+ LM + D     +AA+  A+++PVTVK 
Sbjct: 101 EGARLAEANGADVIDVNMGCPAKKVTGGEAGSALMRDLDHAARLLAAVRGAVAVPVTVKM 160

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D    A+    L +  +  G+  + +H R         +        D+  +  + 
Sbjct: 161 RLGWDHA--ALNAPELARRAEDLGLAAVTVHGRT--------RQQFYTGRADWAAIRAV- 209

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            E   + +  NG ++ +  A   L       VMIGRAA     ++  V
Sbjct: 210 VETVSIPVVANGDVDGLEAARACLNASGAAAVMIGRAAVGRPWLVGAV 257


>gi|281207360|gb|EFA81543.1| tRNA-dihydrouridine synthase 1-like protein [Polysphondylium
           pallidum PN500]
          Length = 430

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 112/243 (46%), Gaps = 21/243 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M+D T   +R   R    + L+YT M  +          +  F  + +++PL +Q  G +
Sbjct: 81  MIDHTFLAFRMLCRKYGAD-LVYTPMFHSKNYATNATYRLENFEIAKEDRPLVVQFCGNE 139

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +V+AAK+VE    + ++LN+GCP      G++GA L+  PD++   + A+ K LS+P
Sbjct: 140 VDYIVQAAKMVES-QCDAVDLNLGCPQGIARRGNYGAFLLEKPDVILPMVRALHKELSVP 198

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  K R+   +DD I       L   ++++G   + +H R    KG +       P+ ++
Sbjct: 199 IFCKIRLLPNLDDTI------KLALQLQEAGCQLLTVHGRTKEQKGHTQ------PHANW 246

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  IK+    P +  G  G   D+ + LK     DGVM       N AM    +   S
Sbjct: 247 KAIRAIKEALVIPVIANGSVGEWGDIEECLKET-GADGVMSADGILNNPAMFNGAERIGS 305

Query: 235 NPL 237
             L
Sbjct: 306 TTL 308


>gi|229003320|ref|ZP_04161150.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock1-4]
 gi|228757938|gb|EEM07153.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock1-4]
          Length = 336

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LNEWEEWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKN 245


>gi|157691447|ref|YP_001485909.1| tRNA-dihydrouridine synthase [Bacillus pumilus SAFR-032]
 gi|157680205|gb|ABV61349.1| tRNA-dihydrouridine synthase [Bacillus pumilus SAFR-032]
          Length = 324

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++    D     K  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGIQSVKGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFQGLDINMGCPVPNVTQNGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + ++ I +  +  + IH R    K +S  D        +
Sbjct: 138 LPVSVKTRLGFTE---VDEWHDWLRHILEQDIVNLSIHLRTR--KEMSQVDAH------W 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EI K      PD  + +NG + D    LK+     VDGVMIGR  + N
Sbjct: 187 ELIPEIIKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGVMIGRGIFHN 238


>gi|228995691|ref|ZP_04155354.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock3-17]
 gi|228764068|gb|EEM12952.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock3-17]
          Length = 336

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LNEWEEWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKN 245


>gi|328713887|ref|XP_001951826.2| PREDICTED: tRNA-dihydrouridine synthase 4-like [Acyrthosiphon
           pisum]
          Length = 350

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 118/245 (48%), Gaps = 25/245 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R+   + L +T MI+AD  ++  K     F T   ++PL +Q G  +
Sbjct: 24  MVRYSRLQFRKLIRMYECD-LCFTPMIMADCYVKSAKARAHEFQTDTDDRPLIVQFGANN 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI- 117
            S  V A+ ++  +  + ++LN GCP        +GA L+ NP+I+ DC+  +   L   
Sbjct: 83  SSDFVNASNLIIPYC-DGVDLNCGCPQRWALNEGYGAQLLKNPEIIKDCVRQLRNHLPTN 141

Query: 118 -PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             ++VK R+ +DD   +V   +L + I+ +GV+ I +H R A+ K   P D   +     
Sbjct: 142 KTISVKLRL-LDDHRKSV---DLCQQIEATGVSFITVHGRTALQKN-EPIDQECL----- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
               ++  E+  + + LNG ++++S A+ +       G+M  R    N  +      Y +
Sbjct: 192 ----KLINESVSVPVILNGDIKNLSDAITMQEYTGCRGMMSARGILHNPGLFAG---YQT 244

Query: 235 NPLTG 239
            PL+ 
Sbjct: 245 TPLSA 249


>gi|156085996|ref|XP_001610407.1| dihydrouridine synthase [Babesia bovis T2Bo]
 gi|154797660|gb|EDO06839.1| dihydrouridine synthase, putative [Babesia bovis]
          Length = 355

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 106/218 (48%), Gaps = 15/218 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV+ ++  +R   R   N  L YT M+     +  +K   + F T +  +PL  Q+ G D
Sbjct: 19  MVNQSELPFRLLCRRY-NVDLTYTPMLHGRIFVENEKYRAVHFQTSDDDRPLIAQVCGDD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA++++    + ++LN+GCP A   +G +G+ L+  PD+V   ++ + + + I 
Sbjct: 78  AGTITQAARLLKGH-VSAVDLNLGCPQAIAKDGHYGSFLLDEPDLVTGIVSRVTREVGIA 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT  C+I   D+    +  NL  S+++SG   + +H R    KG +      +   D+D 
Sbjct: 137 VT--CKIRKVDKDSLQSTLNLCYSLEQSGCKALTVHGRHRSEKGTN------VGAADWDA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVM 214
           +  I K    + +  NGG+E  +   + L     D VM
Sbjct: 189 I-RIIKSRLRIPVIANGGIETFADVERCLSYTGADAVM 225


>gi|300864213|ref|ZP_07109097.1| nifR3 family TIM-barrel protein [Oscillatoria sp. PCC 6506]
 gi|300337787|emb|CBN54243.1| nifR3 family TIM-barrel protein [Oscillatoria sp. PCC 6506]
          Length = 334

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 76/311 (24%), Positives = 133/311 (42%), Gaps = 36/311 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  +    +   I+     E+P+++Q+       L 
Sbjct: 36  TDLVFRRLVRRYAPESMMYTEMVNATGLHYVKQLPRIMEVDPNERPISIQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA + E  G + I++N+GCP  ++ +   G+ L+ +P+     + ++ KA+++PVTVK 
Sbjct: 96  AAAVMAEKEGADTIDINMGCPVNKITKNGGGSSLLRDPENAEAIVRSVVKAVNVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  D+   + +    K ++ +G   I +H R        P     I  +         
Sbjct: 156 RIGWSDK--EITILEFAKRMQDAGAQMITVHGRTRAQGYNGPAKWEWIRRV--------- 204

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           KE   + +  NG +  +  A+  L     DGVM  R       ++  +D YF        
Sbjct: 205 KEILSIPVIANGDIFSVEAAVNCLAETGADGVMCSRGTLGYPFLVGEID-YF-------- 255

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHS------GGKLQQITRHMIGLFHGFPNSRRCRH 295
            +KT ++K     I     + A  HL +         ++Q  +H+     GF N+   R 
Sbjct: 256 -LKTGMEKILPTPI--ERLECAKEHLRALWEYKGESGIRQARKHLTWYAKGFANAGELRG 312

Query: 296 IL----TVEAG 302
            L    TVE G
Sbjct: 313 QLAIVETVEEG 323


>gi|229002247|dbj|BAH57713.1| conserved hypothetical protein orfY [Staphylococcus aureus]
          Length = 312

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 3   MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 62

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 63  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 121

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 122 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLR--TRKEMSKVDAHWELI 173

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 174 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 222


>gi|139472982|ref|YP_001127697.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes str. Manfredo]
 gi|134271228|emb|CAM29444.1| putative tRNA-dihydrouridine synthase [Streptococcus pyogenes str.
           Manfredo]
          Length = 325

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 115/240 (47%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPNKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D+ 
Sbjct: 143 PLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGR--------TREQMYTGTCDHK 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F 
Sbjct: 192 TLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFE 250


>gi|228989497|ref|ZP_04149482.1| tRNA-dihydrouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228770222|gb|EEM18801.1| tRNA-dihydrouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 336

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LNEWEEWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKN 245


>gi|37520616|ref|NP_923993.1| hypothetical protein gll1047 [Gloeobacter violaceus PCC 7421]
 gi|35211610|dbj|BAC88988.1| gll1047 [Gloeobacter violaceus PCC 7421]
          Length = 342

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 110/232 (47%), Gaps = 14/232 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD+ +R   R    ++LLYTEM+ A  +        I+  +  E P+ +Q+       L 
Sbjct: 35  TDKAFRQLVRRYAPHSLLYTEMVSASGLHYSRSLPQIMDIAPGETPIGIQLFDCRPDFLA 94

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA++ E  G + I++N+GCP  ++ +   G+ L+ +P      +A +  A+S+PVTVK 
Sbjct: 95  EAARVAEAQGADVIDINMGCPVNKITKNGGGSSLLRDPATAAKIVAVVAAAVSLPVTVKT 154

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G  D    + +    + +++SG   + +HAR    +  S +   +     ++ +  +K
Sbjct: 155 RLGWSDG--EINILEFARLMQESGAQMLTVHART---RAQSFEGTAR-----WEWIARVK 204

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
            +     I  NG +  +  A++ L     DGVM  R       ++  +D Y 
Sbjct: 205 AQLAIPVIA-NGDIFSIDAAIRCLELTGADGVMCARGTMGAPHLVGQIDHYL 255


>gi|315442689|ref|YP_004075568.1| hypothetical protein Mspyr1_10440 [Mycobacterium sp. Spyr1]
 gi|315260992|gb|ADT97733.1| putative TIM-barrel protein, nifR3 family [Mycobacterium sp. Spyr1]
          Length = 361

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 123/286 (43%), Gaps = 25/286 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            +R  T + L   EM+ A A++       ++  F+ +E P +LQ+   D      AAK++
Sbjct: 18  LSRAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSLQLYTVDPVNTYAAAKMI 77

Query: 70  --EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCR 124
             ED   + I++N GCP  +V     GA L     + G  ++A  +A     IPVTVK R
Sbjct: 78  VDEDLA-DHIDMNFGCPVPKVTRRGGGAALPYKRRLFGQIVSAAVRATEGTDIPVTVKFR 136

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           IG+DD+       +  +   + G   + +HAR A          R   + D+D +  +K 
Sbjct: 137 IGIDDE--HHTHLDAGRIAAEEGAAAVALHARTAA--------QRYSGSADWDQIAALKA 186

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
              ++ +  NG + D   AL ++ +   DGV+IGR       +   +   F+     + P
Sbjct: 187 HVTNVPVLGNGDIFDARDALAMMAATGCDGVVIGRGCLGRPWLFAELSAAFTGATPATPP 246

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
               V +   R       +  A H      ++ I +H+    HGFP
Sbjct: 247 TLGEVAQIIRRH-----GELLAAHFGEDKGMRDIRKHVAWYMHGFP 287


>gi|300362399|ref|ZP_07058575.1| tRNA-dihydrouridine synthase [Lactobacillus gasseri JV-V03]
 gi|300353390|gb|EFJ69262.1| tRNA-dihydrouridine synthase [Lactobacillus gasseri JV-V03]
          Length = 335

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/218 (28%), Positives = 109/218 (50%), Gaps = 16/218 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK +  L    +E P+++QI G     LVEAA  V+     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGSEETLVEAAHYVDTHTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  +V +   GA  +L+P+ +   + A+ + ++ PVTVK R G  DQ    A+ 
Sbjct: 101 NINMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVNKPVTVKMRTGW-DQKHIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G + + +H R         +    +   D++ + ++       F+G NG +
Sbjct: 160 NALAA-QEAGASAVAMHGRT--------RKQMYMGEADWETLKDVADALTIPFVG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
               +A  +L  V  D VM+GRAA  N  ++  +  Y 
Sbjct: 210 TTPEKAKSMLEDVGADAVMVGRAALGNPWIIKDMVHYL 247


>gi|148228148|ref|NP_001089272.1| dihydrouridine synthase 4-like [Xenopus laevis]
 gi|58702004|gb|AAH90192.1| MGC85035 protein [Xenopus laevis]
          Length = 308

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 108/238 (45%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R    + L YT MI+A   ++  K     F+T +   PL +Q    +
Sbjct: 24  MVRYSKLAFRTLVRKYDCD-LCYTPMIIAADFVKSVKARDSEFTTNQGDCPLIVQFAAKE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              L +AA +V  F  + I+LN GCP        +GACL+ NP++V D +  +   +   
Sbjct: 83  AQVLADAASLVSPFA-SGIDLNCGCPQRWAMAEGYGACLINNPELVSDMVRQVRNQVGSS 141

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RI  D         +L +  + +GV+ I +H R          D R  P + 
Sbjct: 142 EFTISIKIRIHADISRTV----DLCRKAEAAGVSWITVHGRT--------HDERHQP-VH 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           Y+ +  I KE+  + I  NG ++ + +A  I  +   DGVM  R    N AM    +E
Sbjct: 189 YNAIKNI-KESLSIPIVANGDIKSLKEAENIHQITGADGVMAARGLLANPAMFAGYEE 245


>gi|332638352|ref|ZP_08417215.1| probable tRNA-dihydrouridine synthase [Weissella cibaria KACC
           11862]
          Length = 353

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 106/225 (47%), Gaps = 26/225 (11%)

Query: 12  FARLLTNNA---LLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVE 64
           F R++   A   + YTE   A +I     K      L     EK   +QI G       +
Sbjct: 44  FRRVVDKAAAPDVYYTEFTNARSITHPKAKFTVQGRLHVDKSEKVPVVQIWGNRGEDFEK 103

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           ++  + D GYN I+LN+GCP + V +   G+ L+ + +   + I A  K   +PV+VK R
Sbjct: 104 SSLELRDRGYNAIDLNMGCPDSTVIKNGGGSDLIRHYESAQEVIQA-AKTAGLPVSVKTR 162

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G +D       R  +  + K  +  + +H R       + K+  K+P   Y+ + EI K
Sbjct: 163 LGFND---LETFREWIPFLLKQDIQVLTVHLR-------TRKEMSKVP-AHYEYIDEIVK 211

Query: 185 EN----PDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
                 PD  + +NG ++   + L+++   P VDGVMIGR  ++N
Sbjct: 212 MRDEIAPDTLLQINGDVKTRQEGLELVRQHPGVDGVMIGRGVFEN 256


>gi|317402229|gb|EFV82818.1| hypothetical protein HMPREF0005_00223 [Achromobacter xylosoxidans
           C54]
          Length = 341

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 111/245 (45%), Gaps = 19/245 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD + +
Sbjct: 21  TDRPFRQLCKKL-GAGYAVSEMAASNPKLWDSVKTSRRLNHDGEIAPISVQIAGADPAMM 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKALSIPV 119
            EAA    + G   I++N+GCP  +V   + G+ L+ + D++    D +   C  L +PV
Sbjct: 80  AEAAVFNANKGARIIDINMGCPVKKVCNVASGSALLRHEDLIARILDAVVEACAPLGVPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G D     V LR + +  + +G+  + +H R         + +      +YD +
Sbjct: 140 TLKTRTGWDRDSRNV-LR-VARLAENAGIAALTLHGRT--------RADLYTGEAEYDTI 189

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             ++ E     I  NG ++   +A ++L     D VMIGRAA     +   VD Y     
Sbjct: 190 RAVRAELKIPLIA-NGDIDSPEKAKRVLDYTGADAVMIGRAAQGRPWIFREVDHYLRTGE 248

Query: 238 TGSSP 242
           T + P
Sbjct: 249 TLAPP 253


>gi|323341866|ref|ZP_08082099.1| dihydrouridine synthase [Erysipelothrix rhusiopathiae ATCC 19414]
 gi|322464291|gb|EFY09484.1| dihydrouridine synthase [Erysipelothrix rhusiopathiae ATCC 19414]
          Length = 327

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++      R   +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVAKAAQPDVYFTEFTNSESYFHAKGRESLRGRLLFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP+  V +   G+ L+L P++  + I +  KA  
Sbjct: 79  DNPDYFRDMSIGLAEMGFQGIDINMGCPAPNVFKHGRGSGLILRPEVAAEIIQS-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       ++ +  + +  ++ + IH R         K      +  +
Sbjct: 138 LPVSVKTRLGHRD---VQEYKSWIAHVLRQDISNLSIHLRT--------KTEMSKVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKN 222
           +++ EI K      PD  I +NG + D  M + L  L  VDGVMIGR  + N
Sbjct: 187 ELIPEILKLRDEIAPDTLITINGDIMDYKMGKELADLYGVDGVMIGRGIFHN 238


>gi|315150824|gb|EFT94840.1| dihydrouridine synthase [Enterococcus faecalis TX0012]
          Length = 337

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 151 LPVSVKTRIGFTEM---AEMDAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 199

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 200 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 251


>gi|282915420|ref|ZP_06323192.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           D139]
 gi|282320523|gb|EFB50861.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           D139]
          Length = 330

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 102/222 (45%), Gaps = 33/222 (14%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E+P+   I G    +  E +  + 
Sbjct: 40  FFTEFTNTESFCHPEGIHS---VRGR----LTFSEDEQPMVAHIWGDKPEQFRETSIQLA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---V 127
             G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  +PV+VK R+G   +
Sbjct: 93  KMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGGLPVSVKTRLGYYEI 151

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN-----RKIPNLDYDIVYEI 182
           D+       ++ +K + +  +  + IH R    K +S  D        I NL  +I    
Sbjct: 152 DE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELIEAIKNLRDEIA--- 200

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 201 ----PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|260596118|ref|YP_003208689.1| tRNA-dihydrouridine synthase B [Cronobacter turicensis z3032]
 gi|260215295|emb|CBA27235.1| tRNA-dihydrouridine synthase B [Cronobacter turicensis z3032]
          Length = 327

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 23  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPEVWASDKSRLRMVHVDEPGIRTVQIAGSV 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  D G   I++N+GCP+ +V+    G+ L+  P++V   + A+  A+ +P
Sbjct: 82  PEEMAEAARINVDNGAQIIDINMGCPAKKVNRKLAGSALLQYPELVKSILTAVVNAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      A RN V   +  ++ G+  + IH R    + +G          N
Sbjct: 142 VTLKIRTGWDP-----ANRNCVEIAQLAEECGIQALTIHGRTRACLFQG----------N 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG +    +A  +L     D +MIGRAA     +   +  
Sbjct: 187 AEYDSIRTVKQKVSIPVIA-NGDITSPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 245

Query: 232 YF 233
           Y 
Sbjct: 246 YL 247


>gi|73661474|ref|YP_300255.1| hypothetical protein SSP0165 [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72493989|dbj|BAE17310.1| conserved hypothetical protein [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 324

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 105/234 (44%), Gaps = 26/234 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNTESYCHPEGVHSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V     G+ L+  P+I  + I A  KA  
Sbjct: 79  DKPDHFREMSIGMAEMGFKGIDLNMGCPVPNVATKGKGSGLIQRPEIAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD- 175
           IPV+VK R+G  +       R+ ++ + +  +  + IH R            R++  +D 
Sbjct: 138 IPVSVKTRLGYSE---IDEWRDWLRHVFEQDIANLSIHLRT----------RREMSKVDA 184

Query: 176 -YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            ++++ EIKK      PD  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 185 HWELIGEIKKLRDEIAPDTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|302185202|ref|ZP_07261875.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae 642]
          Length = 337

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 127/264 (48%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I K+   + +  NG ++   +A  +L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAQI-KQAVSIPVFANGDIDSPEKARHVLKATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
               T  +P  + V++     ++A
Sbjct: 245 RTGETLPAPQSSEVERILLEHLAA 268


>gi|300118953|ref|ZP_07056664.1| histidine phosphokinase/phophatase, putative [Bacillus cereus SJ1]
 gi|298723569|gb|EFI64300.1| histidine phosphokinase/phophatase, putative [Bacillus cereus SJ1]
          Length = 329

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|330953066|gb|EGH53326.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae Cit 7]
          Length = 337

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 127/264 (48%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I K+   + +  NG ++   +A  +L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAQI-KQAVSIPVFANGDIDSPEKARHVLKATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
               T  +P  + V++     ++A
Sbjct: 245 RTGETLPAPQSSEVERILLEHLAA 268


>gi|283469330|emb|CAQ48541.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           ST398]
          Length = 328

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|57652431|ref|YP_184972.1| hypothetical protein SACOL0067 [Staphylococcus aureus subsp. aureus
           COL]
 gi|87161344|ref|YP_492806.1| hypothetical protein SAUSA300_0089 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88193860|ref|YP_498645.1| hypothetical protein SAOUHSC_00039 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|57286617|gb|AAW38711.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           COL]
 gi|87127318|gb|ABD21832.1| Probable tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87201418|gb|ABD29228.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
          Length = 310

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 102/222 (45%), Gaps = 33/222 (14%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E+P+   I G    +  E +  + 
Sbjct: 22  FFTEFTNTESFCHPEGIHS---VRGR----LTFSEDEQPMVAHIWGDKPEQFRETSIQLA 74

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---V 127
             G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  +PV+VK R+G   +
Sbjct: 75  KMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGGLPVSVKTRLGYYEI 133

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN-----RKIPNLDYDIVYEI 182
           D+       ++ +K + +  +  + IH R    K +S  D        I NL  +I    
Sbjct: 134 DE------WKDWLKHVFEQDIANLSIHLR--TRKEMSKVDAHWELIEAIKNLRDEIA--- 182

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 183 ----PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 220


>gi|293572798|ref|ZP_06683752.1| tRNA-dihydrouridine synthase [Enterococcus faecium E980]
 gi|291607148|gb|EFF36516.1| tRNA-dihydrouridine synthase [Enterococcus faecium E980]
          Length = 327

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D    + L     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRRTGEELAEKYGVDGIMIGRGIFKN 238


>gi|325136535|gb|EGC59139.1| dihydrouridine synthase [Neisseria meningitidis M0579]
          Length = 336

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R+G  +    +P +A     K  +  G+  + +H   R  + KG           
Sbjct: 136 VTLKTRLGWHEDHQNLPVIA-----KIAEDCGIAALAVHGRTRTQMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  
Sbjct: 181 ARYELIAETKCR-LNIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKH 239

Query: 232 Y 232
           Y
Sbjct: 240 Y 240


>gi|330895634|gb|EGH27940.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330976782|gb|EGH76819.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 337

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 127/264 (48%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I K+   + +  NG ++   +A  +L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAQI-KQAVSIPVFANGDIDSPQKARHVLKATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
               T  +P  + V++     ++A
Sbjct: 245 RTGETLPAPQSSEVERILLEHLAA 268


>gi|218440381|ref|YP_002378710.1| hypothetical protein PCC7424_3447 [Cyanothece sp. PCC 7424]
 gi|218173109|gb|ACK71842.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7424]
          Length = 337

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 77/327 (23%), Positives = 144/327 (44%), Gaps = 35/327 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  I    +   I+   +QE P+++Q+       + 
Sbjct: 36  TDLVFRRLVRRYAPISMMYTEMVSATEIHHLKQLPKIMEIDSQEHPISIQLFDCRPDFMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G   +++N+GCP  ++ +   G+ L+  P+I  + +  + KA+ +PVTVK 
Sbjct: 96  EAAMKAVAQGAKTVDINMGCPVNKITKKGGGSSLLRQPEIAQNIVKTVVKAVDVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-I 182
           RIG +D    + + +  K ++ +G   + +HAR             +    +    +E I
Sbjct: 156 RIGWNDD--EINILDFAKKMEDAGAAMLTLHART------------RAQGYNGTARWEWI 201

Query: 183 KKENPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           KK    L I +  NG +  +  A++ L     DGVM  R       ++  +D YF    T
Sbjct: 202 KKVKEVLSIPVIANGDIFSVDAAIRCLEETGADGVMCSRGTLGYPFLVGEID-YFLKTGT 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR---- 294
             +P  +    +  ++    + DY  +       + Q  +H+     GF  +   R    
Sbjct: 261 LLTPPTSLQRLECAKEHLQGLWDYKGQR-----GIYQSRKHLTWYCKGFAGASVLRDQVS 315

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
           +I ++E G     +H+I+ A   ++ S
Sbjct: 316 NINSLEEG-----YHLIDQAIASLVNS 337


>gi|21281788|ref|NP_644874.1| hypothetical protein MW0059 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49484964|ref|YP_042185.1| hypothetical protein SAS0059 [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|82749810|ref|YP_415551.1| hypothetical protein SAB0033c [Staphylococcus aureus RF122]
 gi|151220242|ref|YP_001331065.1| hypothetical protein NWMN_0030 [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|161508354|ref|YP_001574013.1| hypothetical protein USA300HOU_0096 [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|258424849|ref|ZP_05687722.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|258452233|ref|ZP_05700247.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282923748|ref|ZP_06331425.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9765]
 gi|284023097|ref|ZP_06377495.1| hypothetical protein Saura13_00779 [Staphylococcus aureus subsp.
           aureus 132]
 gi|294850441|ref|ZP_06791172.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9754]
 gi|297209414|ref|ZP_06925812.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|300911413|ref|ZP_07128862.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus TCH70]
 gi|39930905|sp|Q8NYV4|DUS_STAAW RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|81650227|sp|Q6GD38|DUS_STAAS RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|84028932|sp|Q5HJT5|DUS_STAAC RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|21203223|dbj|BAB93924.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49243407|emb|CAG41827.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|82655341|emb|CAI79721.1| probable nitrogen regulation protein [Staphylococcus aureus RF122]
 gi|150373042|dbj|BAF66302.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160367163|gb|ABX28134.1| possible tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|257844941|gb|EEV68982.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|257860070|gb|EEV82904.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282592990|gb|EFB97991.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9765]
 gi|294822711|gb|EFG39149.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9754]
 gi|296885875|gb|EFH24810.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|298693361|gb|ADI96583.1| hypothetical protein SAOV_0041 [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300887592|gb|EFK82788.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus TCH70]
 gi|315196066|gb|EFU26425.1| possible tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320139505|gb|EFW31376.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320142108|gb|EFW33928.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329731636|gb|EGG67996.1| dihydrouridine synthase (Dus) [Staphylococcus aureus subsp. aureus
           21189]
 gi|329732272|gb|EGG68622.1| dihydrouridine synthase (Dus) [Staphylococcus aureus subsp. aureus
           21193]
          Length = 328

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|282902679|ref|ZP_06310572.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus C160]
 gi|282921360|ref|ZP_06329078.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|283767833|ref|ZP_06340748.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           H19]
 gi|282315775|gb|EFB46159.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282597138|gb|EFC02097.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus C160]
 gi|283461712|gb|EFC08796.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           H19]
 gi|302331835|gb|ADL22028.1| tRNA dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           JKD6159]
          Length = 328

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|293603643|ref|ZP_06686064.1| tRNA-dihydrouridine synthase B [Achromobacter piechaudii ATCC
           43553]
 gi|292818079|gb|EFF77139.1| tRNA-dihydrouridine synthase B [Achromobacter piechaudii ATCC
           43553]
          Length = 341

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 112/244 (45%), Gaps = 22/244 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD + +
Sbjct: 21  TDRPFRQLCKKL-GAGYAVSEMAASNPKLWDSVKTSRRLNHDGEIAPISVQIAGADPAMM 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKALSIPV 119
            EAA    + G   I++N+GCP  +V   + G+ L+ + D++    D + + C  L +PV
Sbjct: 80  AEAAVFNANKGARIIDINMGCPVKKVCNVASGSALLRHEDLIVRILDAVVSACAPLGVPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G D +    ALR + K  + +G+  + +H R         + +      +YD +
Sbjct: 140 TLKTRTGWDRE-SRNALR-VAKLAENAGIAALTLHGRT--------RADLYTGEAEYDTI 189

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E     I  NG ++   +A  +L     D VMIGRAA     +   +D Y     
Sbjct: 190 RAVKAELTIPVIA-NGDIDSPEKAKHVLDYTGADAVMIGRAAQGRPWIFREIDHYLR--- 245

Query: 238 TGSS 241
           TG S
Sbjct: 246 TGES 249


>gi|253730438|ref|ZP_04864603.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253725822|gb|EES94551.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 328

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKIGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|154685282|ref|YP_001420443.1| YfjN [Bacillus amyloliquefaciens FZB42]
 gi|154351133|gb|ABS73212.1| YfjN [Bacillus amyloliquefaciens FZB42]
          Length = 327

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 105/233 (45%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       R  +  I K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGYTD---IDEWRGWLTHILKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKKLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTN 238


>gi|53803919|ref|YP_114184.1| YjbN family TIM-barrel protein [Methylococcus capsulatus str. Bath]
 gi|53757680|gb|AAU91971.1| TIM-barrel protein, yjbN family [Methylococcus capsulatus str.
           Bath]
          Length = 327

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 125/262 (47%), Gaps = 37/262 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L  +EMI A   L+  +K+ L      +  P+++QI GAD
Sbjct: 17  MAGVTDLPFRRLCRQF-GAGLAVSEMISASPALQATRKSRLRQDHRGEPGPISVQIVGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+   D G + I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 76  PREMAEAARRTVDLGADIIDINMGCPAKKVCNVAAGSALLRDEKLVANILEAVVQAVPVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPN 173
           VT+K R G D      A RN V   K  + +G+  + +H R       G +         
Sbjct: 136 VTLKIRTGWDS-----ASRNAVSIGKIAESAGIRALTVHGRTRACGFAGAA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGL----NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
            +Y  + E+KK      IG+    NG ++   +A  +L S   D VMIGR A+    +L 
Sbjct: 182 -EYSTITEVKKA-----IGIPVIANGDIDSPGKAEAVLRSTGADAVMIGRGAWGRPWLLR 235

Query: 228 TVDEYFSNPLTGSSPIKTRVDK 249
            +D    +   G  P+   +D+
Sbjct: 236 EIDARLKD---GRQPLPPTLDE 254


>gi|329117282|ref|ZP_08245999.1| dihydrouridine synthase (Dus) [Streptococcus parauberis NCFD 2020]
 gi|326907687|gb|EGE54601.1| dihydrouridine synthase (Dus) [Streptococcus parauberis NCFD 2020]
          Length = 319

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 106/239 (44%), Gaps = 22/239 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   + +    D     K  L ++  E+PL   I G
Sbjct: 20  MEDVTDVAFRHVVAKAGRPDVFFTEFTNSASYCHPDGIESVKGRLTYTHDEQPLVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E AK +++ G+  +++N+GCP+  V +   G+ L+L P++    I A  K   
Sbjct: 80  DVPDNFAEMAKGMKEMGFAGVDINMGCPAPNVFKHGRGSGLILRPEVAAQLIHA-TKEGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          +  +K + + G+  + IH R         K      +  +
Sbjct: 139 LPVSVKTRLG---HAKPEEYKVWLKHVLEQGIANLSIHLRT--------KTEMSKVDAHW 187

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           +++ EIK+      PD  + +NG + +    L+++    VDGVMIGR  + N      V
Sbjct: 188 EMIGEIKELRDRIAPDTLLTINGDIPNRQVGLELVEKYGVDGVMIGRGIFHNPYAFEKV 246


>gi|57865821|ref|YP_189958.1| hypothetical protein SERP2413 [Staphylococcus epidermidis RP62A]
 gi|293367518|ref|ZP_06614173.1| dihydrouridine synthase [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|81672956|sp|Q5HKD5|DUS_STAEQ RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|57636479|gb|AAW53267.1| conserved hypothetical protein [Staphylococcus epidermidis RP62A]
 gi|291318346|gb|EFE58737.1| dihydrouridine synthase [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329732120|gb|EGG68474.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU144]
 gi|329733723|gb|EGG70050.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU028]
 gi|329737784|gb|EGG74023.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU045]
          Length = 326

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSDDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSIGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYD---IDEWRDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++  IK       P+  + +NG + D    L++     +DG+MIGR  + N
Sbjct: 187 ELIEAIKTLRDEIAPNTLLTINGDIPDRQTGLELANKYGIDGIMIGRGIFHN 238


>gi|49482339|ref|YP_039563.1| hypothetical protein SAR0099 [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257424237|ref|ZP_05600666.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257426913|ref|ZP_05603315.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257429551|ref|ZP_05605938.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257432197|ref|ZP_05608560.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257435157|ref|ZP_05611208.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282907090|ref|ZP_06314938.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282910084|ref|ZP_06317892.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282912336|ref|ZP_06320132.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282912954|ref|ZP_06320746.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M899]
 gi|282922580|ref|ZP_06330270.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C101]
 gi|283959546|ref|ZP_06376987.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|293498009|ref|ZP_06665863.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293511598|ref|ZP_06670292.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|293550207|ref|ZP_06672879.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M1015]
 gi|295426642|ref|ZP_06819281.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589157|ref|ZP_06947798.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|81652014|sp|Q6GKK9|DUS_STAAR RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|49240468|emb|CAG39125.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257273255|gb|EEV05357.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257276544|gb|EEV07995.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257280032|gb|EEV10619.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257283076|gb|EEV13208.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257285753|gb|EEV15869.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282314801|gb|EFB45187.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C101]
 gi|282323054|gb|EFB53373.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M899]
 gi|282324032|gb|EFB54348.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326150|gb|EFB56455.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282329989|gb|EFB59510.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|283789138|gb|EFC27965.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|290919254|gb|EFD96330.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M1015]
 gi|291096940|gb|EFE27198.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291465556|gb|EFF08088.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|295129094|gb|EFG58721.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297577668|gb|EFH96381.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|312436792|gb|ADQ75863.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus TCH60]
 gi|315194550|gb|EFU24939.1| hypothetical protein CGSSa00_00231 [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 328

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|196045371|ref|ZP_03112603.1| conserved hypothetical protein [Bacillus cereus 03BB108]
 gi|301052047|ref|YP_003790258.1| putative dihydrouridine synthase [Bacillus anthracis CI]
 gi|196023955|gb|EDX62630.1| conserved hypothetical protein [Bacillus cereus 03BB108]
 gi|300374216|gb|ADK03120.1| probable dihydrouridine synthase [Bacillus cereus biovar anthracis
           str. CI]
          Length = 329

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|163852236|ref|YP_001640279.1| NifR3 family TIM-barrel protein [Methylobacterium extorquens PA1]
 gi|163663841|gb|ABY31208.1| TIM-barrel protein, nifR3 family [Methylobacterium extorquens PA1]
          Length = 342

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 107/220 (48%), Gaps = 19/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLV 63
           TD H R  A+ L  +A++ +EM+ A  + +GD ++ +        P  +Q+ G     + 
Sbjct: 32  TDLHMRRLAQRLGASAVV-SEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPEPMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTVK 
Sbjct: 91  EGARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTVKM 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D    ++    L +  +  G++G+ +H   R+   KG +          D+  +  
Sbjct: 151 RLGWDHA--SLNAAELAQRAEALGLDGVTVHGRTRQQFYKGRA----------DWSAIRP 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +  E   + +  NG +  + +A   L      GVMIGRAA
Sbjct: 199 V-VEAVRIPVIANGDITGLEEARACLSQSGAAGVMIGRAA 237


>gi|78777367|ref|YP_393682.1| dihydrouridine synthase TIM-barrel protein nifR3 [Sulfurimonas
           denitrificans DSM 1251]
 gi|78497907|gb|ABB44447.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sulfurimonas
           denitrificans DSM 1251]
          Length = 318

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 116/225 (51%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + L  +EM+ ++A++ G  K +  +  S  E P ++QI GA+
Sbjct: 18  LAGYTDLPFRSVVKKFGAD-LTVSEMLSSNALVHGSSKTLGMIEKSPNEDPYSVQIAGAE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ +  A +I+ E  G + I+LN GCP  ++     G+ L+LN  ++G+ I  +    + 
Sbjct: 77  VNVIRRAVEILNEQDGIDIIDLNCGCPVPKIVGHGSGSSLLLNLPLMGEIIRTIKNTSNK 136

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G + +       ++ K ++ SG + I +H R    K  +P        +DY
Sbjct: 137 NLTSVKIRLGFEKKNHV----DIAKMVEDSGADFIAVHGRTRAGKFKAP--------VDY 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D + EI KE  ++ +  NG ++   +A  +L     DGVMIGR A
Sbjct: 185 DAIREI-KEAINIPVIANGDIDSYEKAEWVLEHTGADGVMIGRGA 228


>gi|15965210|ref|NP_385563.1| putative NIFR3-like protein [Sinorhizobium meliloti 1021]
 gi|307309224|ref|ZP_07588895.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti BL225C]
 gi|15074390|emb|CAC46036.1| tRNA-dihydrouridine synthase B [Sinorhizobium meliloti 1021]
 gi|306900370|gb|EFN30986.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti BL225C]
          Length = 342

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 108/217 (49%), Gaps = 15/217 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLV 63
           TD  +R  A        + TEM+ +  ++    ++          P  +Q+ G +   + 
Sbjct: 37  TDLPFRMLAWRF-GAGFVVTEMVASRELVGNAAESWARLKNSGIDPHIVQLAGREAHWMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+IVE  G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA ++PVT+K 
Sbjct: 96  EAARIVEANGADIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVKAATVPVTLKM 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D+      L  + +  +++GV  I IH R   ++  + K        D+D +  + 
Sbjct: 156 RLGWDENSINAPL--IARRAEEAGVKAITIHGRTR-MQFYNGK-------ADWDAIGAV- 204

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +E   + +  NG ++ ++ A +IL     D VM+GR+
Sbjct: 205 REVVSIPLIANGDVDSVADAHEILRRSGADAVMVGRS 241


>gi|312898246|ref|ZP_07757637.1| TIM-barrel protein, nifR3 family [Megasphaera micronuciformis
           F0359]
 gi|310620743|gb|EFQ04312.1| TIM-barrel protein, nifR3 family [Megasphaera micronuciformis
           F0359]
          Length = 327

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 112/241 (46%), Gaps = 22/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M    D  YR  AR     AL+  EM+ A  ++ G+K  + +L     E PL++Q+ GA+
Sbjct: 24  MAGVCDLPYRMIARK-HGAALVCAEMVSAKGLVYGNKHTREMLTVHKNEHPLSMQLFGAE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK+ +++G + I++N+GCP  +V +   G+ LM N  +    ++A+ KA+S+P
Sbjct: 83  PEIMARAAKVAQEYGADIIDINMGCPVRKVVQNGEGSALMKNLPLAEKVVSAVVKAVSVP 142

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VTVK R G DD     P +A R          V+G     R+    G +          D
Sbjct: 143 VTVKMRTGWDDIEFVAPELARRCEAAGAAALAVHG---RTREQFYSGRA----------D 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            + +  + K      IG NG + D     ++        VMIGR A  N  +   V +Y 
Sbjct: 190 LEKIAAVVKAVSIPVIG-NGDITDGPSCARMFEETGCTAVMIGRGAQGNPWIFEEVRDYL 248

Query: 234 S 234
           S
Sbjct: 249 S 249


>gi|196034769|ref|ZP_03102177.1| conserved hypothetical protein [Bacillus cereus W]
 gi|218901524|ref|YP_002449358.1| hypothetical protein BCAH820_0366 [Bacillus cereus AH820]
 gi|195992812|gb|EDX56772.1| conserved hypothetical protein [Bacillus cereus W]
 gi|218535642|gb|ACK88040.1| conserved hypothetical protein [Bacillus cereus AH820]
          Length = 329

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 238


>gi|118082094|ref|XP_001231915.1| PREDICTED: similar to Dihydrouridine synthase 4-like (S.
           cerevisiae) isoform 1 [Gallus gallus]
          Length = 317

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 76/285 (26%), Positives = 127/285 (44%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + L YT M+VA   +R  K     F+T   + PL +Q    +
Sbjct: 32  MVRYSKLAFRTLVRRYGCD-LCYTPMVVAADFVRSAKARDSEFTTNRGDNPLIVQFAAKE 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 91  AQVLCDAALLVCPFA-DGVDLNCGCPQRWAMAEGYGACLINKPELVRDMVRHVRNQIDNP 149

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L K  + +GV+ I +H R          + R  P + 
Sbjct: 150 RFSVSIKIRIHEDLKKTV----DLCKKAEATGVSWITVHGRNI--------EERHQP-VH 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + ++ KE+  + +  NG ++ +  A  +  L   DGVM+ R    N AM    +E  
Sbjct: 197 YDAI-KVIKESIHIPVVANGDIKTLKDAENVHHLTGADGVMVARGLLANPAMFAGYEE-- 253

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+    T +   H H    +++IT
Sbjct: 254 -------TPLKCIQD---WVDIALEHGTPFTCFHHHLMYMMERIT 288


>gi|312869850|ref|ZP_07729991.1| TIM-barrel protein, nifR3 family [Lactobacillus oris PB013-T2-3]
 gi|311094629|gb|EFQ52932.1| TIM-barrel protein, nifR3 family [Lactobacillus oris PB013-T2-3]
          Length = 332

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 99/216 (45%), Gaps = 16/216 (7%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNV 81
           EMI    I+  ++K  N++     E P+ +QI G     LVEAAK V++    + I++N+
Sbjct: 42  EMISDRGIMYHNQKTLNMMDVDPTEHPMGIQIFGGTKETLVEAAKYVDEHTAADVIDINM 101

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   GA  +L+P  V + ++ +  A+  PVTVK R G DD+        L  
Sbjct: 102 GCPVNKVVKTDAGARWLLDPQKVYEMVSYVTDAVKKPVTVKMRTGWDDKHIYAVENALAA 161

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
               +    +    RK +  G          + D++I+ E+  +    F+  NG +    
Sbjct: 162 ERAGAAAIAMHGRTRKQMYTG----------HADWNILKEVASQLTIPFMA-NGDIRTPE 210

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            A K+L        MIGRAA  N  MLT  + Y   
Sbjct: 211 DAKKVLDMTGATAAMIGRAAMGNPWMLTRTEHYLET 246


>gi|228944129|ref|ZP_04106508.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229119980|ref|ZP_04249235.1| tRNA-dihydrouridine synthase [Bacillus cereus 95/8201]
 gi|228663446|gb|EEL19031.1| tRNA-dihydrouridine synthase [Bacillus cereus 95/8201]
 gi|228815518|gb|EEM61760.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 336

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|15888769|ref|NP_354450.1| nitrogen regulation protein [Agrobacterium tumefaciens str. C58]
 gi|15156519|gb|AAK87235.1| nitrogen regulation protein [Agrobacterium tumefaciens str. C58]
          Length = 338

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 106/221 (47%), Gaps = 21/221 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R  A       L+ TEM+ +  ++  RG+    L  +    P  +Q+ G +   +
Sbjct: 35  TDLPFRQLA-WRYGAGLVVTEMVASRELVANRGESWARLKNAGM-VPHMVQLAGREAHFM 92

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAKI  D G   I++N+GCP+ +V  G  G+ LM +PD     I A   A+ +PVT+K
Sbjct: 93  AEAAKIAADNGAGIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVGAVDVPVTLK 152

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIVY 180
            R+G D+   ++    + +  + +GV  I IH R  +   +G +          D+D + 
Sbjct: 153 MRLGWDEN--SINAPEIARRAEAAGVQLITIHGRTRMQFYEGRA----------DWDAIR 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
            +++      I  NG +E    A +IL     D VM+GR A
Sbjct: 201 AVREVISVPLIA-NGDVETAEDAREILRRSGADAVMVGRGA 240


>gi|118476082|ref|YP_893233.1| dihydrouridine synthase family protein [Bacillus thuringiensis str.
           Al Hakam]
 gi|228931824|ref|ZP_04094720.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|229089448|ref|ZP_04220719.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-42]
 gi|229182715|ref|ZP_04309956.1| tRNA-dihydrouridine synthase [Bacillus cereus BGSC 6E1]
 gi|118415307|gb|ABK83726.1| conserved hypothetical protein [Bacillus thuringiensis str. Al
           Hakam]
 gi|228600800|gb|EEK58379.1| tRNA-dihydrouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228693925|gb|EEL47617.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-42]
 gi|228827804|gb|EEM73542.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 336

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|227486471|ref|ZP_03916787.1| dihydrouridine--tRNA ligase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235652|gb|EEI85667.1| dihydrouridine--tRNA ligase [Anaerococcus lactolyticus ATCC 51172]
          Length = 332

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 110/221 (49%), Gaps = 23/221 (10%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL--VEAAKIVEDFGYNEIN 78
           +TEM+  +A+   +K   +I+  S  EK   +QI G+D+ K+  V   KI       EI+
Sbjct: 36  FTEMVSVNALSFDNKATADIMFISDMEKNANIQIFGSDVDKIKRVVEEKINPLTNIKEIS 95

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
            N+GCP+ ++     G+ L+ NP  V     A+ +A    + +K R+GVDD   A+    
Sbjct: 96  FNMGCPAPKIFNNGEGSALLKNPHQVYKITKALREATDKVINIKFRLGVDDD--AINYLE 153

Query: 139 LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             K+++++G + + +HA  RKA+  G +  D + I NL         KE  ++ +  NG 
Sbjct: 154 NGKAMEEAGADYLILHARTRKAMYSGHA--DWQAIKNL---------KEAVNIPVIANGD 202

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +   ED  +A++I    DG MI R A  N  +   + EY  
Sbjct: 203 IFTPEDFIRAMEI-TGADGAMIARGAMGNPFIFRYIKEYLE 242


>gi|27467074|ref|NP_763711.1| hypothetical protein SE0156 [Staphylococcus epidermidis ATCC 12228]
 gi|251811498|ref|ZP_04825971.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|39930886|sp|Q8CU07|DUS_STAES RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|27314616|gb|AAO03753.1|AE016744_156 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251805002|gb|EES57659.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis
           BCM-HMP0060]
          Length = 326

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 103/218 (47%), Gaps = 25/218 (11%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E+P+   I G    +  E +  + 
Sbjct: 40  FFTEFTNTESYCHPEGIHS---VRGR----LTFSDDEQPMVAHIWGDKPEQFREMSIGLA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  +PV+VK R+G  D 
Sbjct: 93  DMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGGLPVSVKTRLGYYD- 150

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---- 186
                 R+ +K + +  +  + IH R       + K+  K+ +  ++++  IK       
Sbjct: 151 --IDEWRDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHWELIEAIKTLRDEIA 200

Query: 187 PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           P+  + +NG + D    L++     +DG+MIGR  + N
Sbjct: 201 PNTLLTINGDIPDRQTGLELANKYGIDGIMIGRGIFHN 238


>gi|327472537|gb|EGF17968.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK408]
 gi|328944686|gb|EGG38847.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1087]
          Length = 325

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG + ++  A + +  V  D +MIGRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRNVQDAKQRIEEVGADAIMIGRAAMGNPYLFNQINHYFE 250


>gi|33861565|ref|NP_893126.1| nitrogen regulation protein NifR3 family protein [Prochlorococcus
           marinus subsp. pastoris str. CCMP1986]
 gi|33634142|emb|CAE19468.1| putative nitrogen regulation protein NifR3 family homolog
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 340

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 115/229 (50%), Gaps = 14/229 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           TD+ +R   R     +LL+TEMI A ++  G   + I     ++ P+ +QI       + 
Sbjct: 34  TDKIFRKLVRKWAPESLLFTEMINATSLKHGYGTQKIKQLELEKGPIGVQIFDNRPFAVS 93

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK+ ED G   I++N+GCP  ++     G+ L+ +  +  + +  +  A+ +PVTVK 
Sbjct: 94  EAAKLAEDSGAFLIDINMGCPVKKISRKGGGSALINDRLLAIELVKRVSNAVKVPVTVKT 153

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G +++   +     + S++ +G   I +H R    +G S K        D++++ +I 
Sbjct: 154 RLGWENKEENI--EEFLLSLQDAGAEMITLHGRTR-KEGFSGK-------ADWEMIGKI- 202

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           KE  ++ +  NG +++   A   L   + DG+MIGR    +   +  +D
Sbjct: 203 KELLEIPVIANGDIKNPKDAYNCLKKTNADGLMIGRGILGSPWKIGEID 251


>gi|229055160|ref|ZP_04195587.1| tRNA-dihydrouridine synthase [Bacillus cereus AH603]
 gi|228721152|gb|EEL72682.1| tRNA-dihydrouridine synthase [Bacillus cereus AH603]
          Length = 336

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|307150162|ref|YP_003885546.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7822]
 gi|306980390|gb|ADN12271.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7822]
          Length = 337

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 42/153 (27%), Positives = 79/153 (51%), Gaps = 3/153 (1%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  I    +   I+    QE P+++Q+       + 
Sbjct: 36  TDLIFRRLVRRYAPTSMMYTEMVSATEIHHLQQLPKIMEIDPQEHPISIQLFDCRPDFMA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G   +++N+GCP  ++ +   G+ L+  P+I  + +  +  A+ +PVTVK 
Sbjct: 96  EAATKAVAEGAKTVDINMGCPVNKITKKGGGSSLLRQPEIAQEIVKTVVSAVEVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           RIG +D+   + + +  K ++ +G   + +HAR
Sbjct: 156 RIGWNDE--EITILDFAKRMEDAGAAMLTLHAR 186


>gi|323703650|ref|ZP_08115292.1| TIM-barrel protein, nifR3 family [Desulfotomaculum nigrificans DSM
           574]
 gi|323531365|gb|EGB21262.1| TIM-barrel protein, nifR3 family [Desulfotomaculum nigrificans DSM
           574]
          Length = 323

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 120/240 (50%), Gaps = 17/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR      L+ TEM+   A++  + +   +L F  +  PL++QI G++
Sbjct: 17  MAGVTDRAYRILARE-QGCGLVVTEMVSDLALIYANPRTYRMLDFRGEAPPLSVQIFGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI-VGDCIAAMCKALSI 117
              + +AA IV + G N +++N+GCP+ ++ +   G+ LM NP +      A +     +
Sbjct: 76  PETMGQAAAIVVERGANIVDINMGCPTPKIVKNGEGSALMKNPGLAARIVAAVVAAVPGV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+   +V    L +++ ++G   + +H R         ++       D+D
Sbjct: 136 PVTVKMRKGWDET--SVNAVELAQAVVEAGAAAVAVHGRT--------RNQFYSGKADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+      IG NG +     A +++     DGVMIGRAA  N  +   +  Y +N
Sbjct: 186 IIRQVKEAVKVPVIG-NGDIWHARDAARMMAETGCDGVMIGRAAMGNPWIFRDIIHYLAN 244


>gi|19074582|ref|NP_586088.1| similarity to HYPOTHETICAL PROTEIN YM10_yeast [Encephalitozoon
           cuniculi GB-M1]
 gi|19069224|emb|CAD25692.1| similarity to HYPOTHETICAL PROTEIN YM10_yeast [Encephalitozoon
           cuniculi GB-M1]
          Length = 341

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 29/241 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQE--KPLALQIGG 56
           MV  ++  +R  ++    N + YTEM+  D+ LRG +  +    ++T E  +PL +QI G
Sbjct: 18  MVGNSEEAWRRLSKRHGAN-IFYTEMVHCDSFLRGSRNPVKNRWYTTSEGDRPLVVQICG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                ++EAA I++D   + I++N GCP     +G +GA L  N  + G+ +  +   L+
Sbjct: 77  NSPEVMLEAALIIQDHC-DAIDVNFGCPQKVARKGGYGAYLQENWKLTGEIVKVLSSGLN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG-----LSPKDNRKI 171
           +PV   C+I V   I         K I+++G + + +H R    +G      S K  R I
Sbjct: 136 VPVF--CKIRVFGSIEKTV--EYAKMIEEAGCSLLAVHGRTRDQRGAAMGFASWKHIRAI 191

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
                       KEN  + +  NG +       + L     DGVM+G A   N  + T  
Sbjct: 192 ------------KENLRIPVLSNGNIMTHHDVWRCLEYTGCDGVMVGEAHLHNPLIFTGE 239

Query: 230 D 230
           D
Sbjct: 240 D 240


>gi|255004171|ref|ZP_05278972.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Virginia]
          Length = 304

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 102/212 (48%), Gaps = 34/212 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           LL +EMI + A++   +++ L  S      A+Q+ G     + EAAKI +D G   I++N
Sbjct: 20  LLVSEMIASRAMIIKTRQS-LQKSDVGANTAVQLAGCVPEIMAEAAKINQDMGARSIDIN 78

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPAVALR 137
            GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G    D   P     
Sbjct: 79  FGCPVKKIVDGHAGSALMKDEEKAAKIMESVVKAVTIPVTVKMRMGWSATDLNAP----- 133

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSP-------KDNRKIPNLDYDIVYEIKKENPD 188
            L K  +  G+  + +H   R  +  G +        KD  KIP +           N D
Sbjct: 134 RLAKIAEDVGIQMVTVHGRTRTQMFSGTADWKFIKCVKDCVKIPVI----------ANGD 183

Query: 189 LFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           +       L+D++ AL  L   DGVMIGR AY
Sbjct: 184 IRT-----LQDITSALS-LSGADGVMIGRGAY 209


>gi|213401397|ref|XP_002171471.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|211999518|gb|EEB05178.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 403

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 77/297 (25%), Positives = 132/297 (44%), Gaps = 35/297 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST----QEKPLALQIGG 56
           MVD ++  +R  AR  +   + +T M  +             FST    +EKPL +Q  G
Sbjct: 26  MVDQSELPWRILARR-SGADMCFTPMFHSRLFSESKDYRDKVFSTKDIPEEKPLIVQFCG 84

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            ++  +++AAK+ E +    ++LN+GCP     +G +G+ +  N +++   I+ +   LS
Sbjct: 85  NEVETMLQAAKLAEPYCVA-VDLNLGCPQGIARKGKYGSFMQDNWELIEAIISKLHAELS 143

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K RI  D   P+  L    K I ++G + + +H R    +G+    N  I   D+
Sbjct: 144 VPVTAKIRIFPD---PSRTL-EYAKMILRAGASILTVHGRTREQRGI----NTGI--ADW 193

Query: 177 DIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D +  ++++ P D  +  NG +    D+ + L+    VDGVM    +  N  +  +    
Sbjct: 194 DQIKMLREKLPADTVLFANGNILHSSDIERCLEYT-GVDGVMSAEGSLYNPKVFLSP--- 249

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITRHMIGLFHGF 287
            S P T   P   RVD     K+     D    H        L  +  H+  + H F
Sbjct: 250 -SRPYTELYP---RVD-----KMCEEYFDIVREHGLTKDYSSLSAMKGHLFKILHSF 297


>gi|196230050|ref|ZP_03128913.1| dihydrouridine synthase DuS [Chthoniobacter flavus Ellin428]
 gi|196225647|gb|EDY20154.1| dihydrouridine synthase DuS [Chthoniobacter flavus Ellin428]
          Length = 330

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/268 (24%), Positives = 119/268 (44%), Gaps = 28/268 (10%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           IL    KN  G     +P+  Q+ G DI  LV AAK +E      I+LN+GCP   V+  
Sbjct: 39  ILASITKNPTG-----RPVVAQMMGNDIPSLVRAAKELEQHPVAAIDLNLGCPVPVVYRK 93

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             G  L+ +P+ V   + A+ +A++IP TVK RIG DD  P+V    ++    +  ++ +
Sbjct: 94  CAGGGLLRDPERVDSILGALREAVTIPFTVKTRIGFDD--PSV-FEQMLPIYARHSLDLL 150

Query: 152 WIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--L 207
            +H R  K + +            + Y+ +       P   +  NG +  +  A ++  L
Sbjct: 151 TVHGRTVKEMYRS----------EVHYEYIARAVAAMPCPVVA-NGNVSSVHSAEEVLNL 199

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
               G+MIGRAA +N  +   + ++       S PI     ++    I A         +
Sbjct: 200 TGARGLMIGRAAIRNPWIFQQIRQHRR-----SEPIYQPTGREVLEYIQALYEAVCDPQV 254

Query: 268 HSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++Q++ +++  +  G   + + +H
Sbjct: 255 RETSQVQKMKKYLTYISDGVEPTGQFQH 282


>gi|323440393|gb|EGA98106.1| hypothetical protein SAO11_0837 [Staphylococcus aureus O11]
 gi|323443127|gb|EGB00746.1| hypothetical protein SAO46_0916 [Staphylococcus aureus O46]
          Length = 328

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DG+MIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGIMIGRGIFHN 238


>gi|297180133|gb|ADI16356.1| hypothetical protein [uncultured bacterium HF130_01F24]
          Length = 329

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/250 (26%), Positives = 125/250 (50%), Gaps = 24/250 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT-EMIVADAILRGDKKNILGFSTQ--EKPLALQIGGA 57
           MV  +D+ +R       N A L T EM+ +++ L  +++N L  +      P  +QI G+
Sbjct: 17  MVGVSDKPFREVCE--QNGAGLTTAEMLTSNSDLWKNERNRLKRTQPILSGPNVVQIAGS 74

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   + +AA++  ++G + I++N+GCP+ +V + + G+ L+ +P +V   + ++  ++ I
Sbjct: 75  DPKMMSQAAQLNAEWGADVIDINMGCPAKKVLKKAAGSALLKDPKLVRSILESVINSVDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVT+K R G        A +N V+  K     GV  + +H R         ++ R    +
Sbjct: 135 PVTLKIRTGW-----CPATKNGVEVAKIAEDCGVALLTVHGRT--------RECRFKGKV 181

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +Y+ + +I K++  + I  NG +     A ++L     DG+MIGR+A     +   V +Y
Sbjct: 182 EYETIAKI-KQSVRIPIIANGDINSPQTAKRVLEYTKADGLMIGRSAIGKPWIFDQVHQY 240

Query: 233 FSNPLTGSSP 242
             +    S P
Sbjct: 241 LVSGTEKSEP 250


>gi|255003049|ref|ZP_05278013.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Puerto Rico]
          Length = 298

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 102/212 (48%), Gaps = 34/212 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           LL +EMI + A++   +++ L  S      A+Q+ G     + EAAKI +D G   I++N
Sbjct: 14  LLVSEMIASRAMIIKTRQS-LQKSDVGANTAVQLAGCVPEIMAEAAKINQDMGARSIDIN 72

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPAVALR 137
            GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G    D   P     
Sbjct: 73  FGCPVKKIVDGHAGSALMKDEEKAAKIMESVVKAVTIPVTVKMRMGWSATDLNAP----- 127

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSP-------KDNRKIPNLDYDIVYEIKKENPD 188
            L K  +  G+  + +H   R  +  G +        KD  KIP +           N D
Sbjct: 128 RLAKIAEDVGIQMVTVHGRTRTQMFSGTADWKFIKCVKDCVKIPVI----------ANGD 177

Query: 189 LFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           +       L+D++ AL  L   DGVMIGR AY
Sbjct: 178 IRT-----LQDITSALS-LSGADGVMIGRGAY 203


>gi|169632777|ref|YP_001706513.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii SDF]
 gi|169151569|emb|CAP00342.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii]
          Length = 341

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQAANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGRT--------REDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YELIKHV-KELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKEVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 297 RQNMYKVETTAEQAL--VVESYFNQLL 321


>gi|118616290|ref|YP_904622.1| transcriptional regulator [Mycobacterium ulcerans Agy99]
 gi|118568400|gb|ABL03151.1| transcriptional regulator [Mycobacterium ulcerans Agy99]
          Length = 377

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 76/296 (25%), Positives = 129/296 (43%), Gaps = 25/296 (8%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           A++ T + L   EM+ A A++       ++  F+  E P +LQ+   D      AA+++ 
Sbjct: 35  AKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSLQLYTVDPDTTYAAARMIA 94

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIG 126
           + G  + I++N GCP  +V +   GA L     + G  +AA  + +    IPVTVK RIG
Sbjct: 95  EEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAAVRGVEGTDIPVTVKFRIG 154

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD        +  +  +  G   + +HAR A          R     D++ +  +K+  
Sbjct: 155 IDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------QRYSGTADWEQIALLKQHV 204

Query: 187 PDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS-NPLTGSSPI 243
             + +  NG + D S AL ++ +   DGV+IGR       +   +   F+ NP  G +P 
Sbjct: 205 RTVPVLGNGDIYDASDALAMIAATGCDGVVIGRGCLGRPWLFAELSAAFTGNP--GPTPP 262

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 D  R+      +  A H      ++ I +H+    HGFP     R  L +
Sbjct: 263 TLGEVTDIIRR----HGELLAAHFGEDKGVRDIRKHVAWYLHGFPAGSDLRRALAL 314


>gi|45655921|ref|YP_000007.1| nifR3-like protein [Leptospira interrogans serovar Copenhageni str.
           Fiocruz L1-130]
 gi|45599154|gb|AAS68644.1| nifR3-like protein [Leptospira interrogans serovar Copenhageni str.
           Fiocruz L1-130]
          Length = 329

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 110/214 (51%), Gaps = 15/214 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           A  YTE +  D ++    K   +  + ++E+P+  QI G  +  + EAA+I+++   + I
Sbjct: 36  AFSYTEFVNTDELVHRAPKALKMFRYKSEERPITFQIFGNRLEIIAEAAEIIQELKPDII 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GC + +V     GA L+  P + G  I A+ K ++IPVT K RIG D    +    
Sbjct: 96  DLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAIKKRVNIPVTAKIRIGWDST--SRNYL 153

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K +++SGV+ + +H R         K+       D+D + EIK  N  + I  NG +
Sbjct: 154 EVSKILEESGVDALTVHGR--------TKEMAYTGFADWDAIGEIKV-NRKIPIFGNGDI 204

Query: 198 EDMSQA-LKILPS-VDGVMIGRAAYKNSAMLTTV 229
           +   +A  KI    +DGV+IGR A  N  + + V
Sbjct: 205 KSFQEANFKIDKYLLDGVLIGRNAIGNPWIFSGV 238


>gi|109896601|ref|YP_659856.1| nifR3 family TIM-barrel protein [Pseudoalteromonas atlantica T6c]
 gi|109698882|gb|ABG38802.1| tRNA-U20-dihydrouridine synthase [Pseudoalteromonas atlantica T6c]
          Length = 333

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 65/252 (25%), Positives = 118/252 (46%), Gaps = 28/252 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  + R  K         EK + A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAGLVVSEMLSSNPDVWRSSKSKQRMDHVGEKGIRAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   +++N+GCP+ +V++   G+ L+ +P +V   + ++ +A+ +P
Sbjct: 76  PLLMAQAAQFNVDNGAQIVDINMGCPAKKVNKKLAGSALLQDPQLVERIVQSVVEAVQVP 135

Query: 119 VTVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           VT+K R G +       QI  +A +N ++S+   G        R  + KG          
Sbjct: 136 VTLKIRTGWNTDNRNGVQIAKIAEQNGIQSLAVHG------RTRACMYKG---------- 179

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           N +YD +  IK+    + +  NG +  +  A  +L   + D +MIGR A  N  +   + 
Sbjct: 180 NAEYDTIKAIKQA-VSIPVVANGDITCVHSAKHVLEYTNADALMIGRGAQGNPWIFRQIQ 238

Query: 231 EYFSNPLTGSSP 242
            +        SP
Sbjct: 239 HFLQTGEILPSP 250


>gi|145222259|ref|YP_001132937.1| nifR3 family TIM-barrel protein [Mycobacterium gilvum PYR-GCK]
 gi|145214745|gb|ABP44149.1| putative TIM-barrel protein, nifR3 family [Mycobacterium gilvum
           PYR-GCK]
          Length = 455

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 73/285 (25%), Positives = 123/285 (43%), Gaps = 23/285 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK-I 68
            +R  T + L   EM+ A A++       ++  F+ +E P +LQ+   D      AAK I
Sbjct: 112 LSRAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSLQLYTVDPVNTYAAAKMI 171

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
           V++   + I++N GCP  +V     GA L     + G  ++A  +A     IPVTVK RI
Sbjct: 172 VDENLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGQIVSAAVRATEGTDIPVTVKFRI 231

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD+       +  +   + G   + +HAR A          R   + D+D +  +K  
Sbjct: 232 GIDDE--HHTHLDAGRIAAEEGAAAVALHARTAA--------QRYSGSADWDQIAALKAH 281

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
             ++ +  NG + D   AL ++ +   DGV+IGR       +   +   F+     + P 
Sbjct: 282 VTNVPVLGNGDIFDARDALAMMAATGCDGVVIGRGCLGRPWLFAELSAAFTGATPATPPT 341

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              V +   R       +  A H      ++ I +H+    HGFP
Sbjct: 342 LGEVAQIIRRH-----GELLAAHFGEDKGMRDIRKHVAWYMHGFP 381


>gi|289675674|ref|ZP_06496564.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae FF5]
          Length = 320

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 127/264 (48%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 3   MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 61

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 62  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 121

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 122 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGITALAVHGRT--------RADLYTGEAE 168

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD + +I K+   + +  NG ++   +A  +L +   DG++IGRAA     +   ++ + 
Sbjct: 169 YDTIAQI-KQAVSIPVFANGDIDSPQKARHVLKATGADGLLIGRAAQGRPWIFREIEHFL 227

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
               T  +P  + V++     ++A
Sbjct: 228 RTGETLPAPQSSEVERILLEHLAA 251


>gi|24212707|ref|NP_710188.1| tRNA-dihydrouridine synthase [Leptospira interrogans serovar Lai
           str. 56601]
 gi|24193338|gb|AAN47206.1| tRNA-dihydrouridine synthase [Leptospira interrogans serovar Lai
           str. 56601]
          Length = 329

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 110/214 (51%), Gaps = 15/214 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           A  YTE +  D ++    K   +  + ++E+P+  QI G  +  + EAA+I+++   + I
Sbjct: 36  AFSYTEFVNTDELVHRAPKALKMFRYKSEERPITFQIFGNRLEIIAEAAEIIQELKPDII 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GC + +V     GA L+  P + G  I A+ K ++IPVT K RIG D    +    
Sbjct: 96  DLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAIKKRVNIPVTAKIRIGWDST--SRNYL 153

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K +++SGV+ + +H R         K+       D+D + EIK  N  + I  NG +
Sbjct: 154 EVSKILEESGVDALTVHGR--------TKEMAYTGFADWDAIGEIKV-NRKIPIFGNGDI 204

Query: 198 EDMSQA-LKILPS-VDGVMIGRAAYKNSAMLTTV 229
           +   +A  KI    +DGV+IGR A  N  + + V
Sbjct: 205 KSFQEANFKIDKYLLDGVLIGRNAIGNPWIFSGV 238


>gi|260494139|ref|ZP_05814270.1| dihydrouridine-tRNA ligase [Fusobacterium sp. 3_1_33]
 gi|260198285|gb|EEW95801.1| dihydrouridine-tRNA ligase [Fusobacterium sp. 3_1_33]
          Length = 299

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 115/254 (45%), Gaps = 43/254 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       +  A+QI G DI+K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIAKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    +++K RIG  +    + +  
Sbjct: 88  CGCPMKKIVNCGYGAALLREPEKIKRILSEIKSILNDDTKLSIKIRIGYKEPENYIQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           L + I   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 LAEEI---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF-----SNPLTGSSPI- 243
           F G +  LE +S +     +VDGVM+ R  + N  ++  + E         P T    I 
Sbjct: 195 FTGKD-ALEKISYS-----NVDGVMLARGIFGNPWLIRDIREILKYGEIKTPTTKEDKIN 248

Query: 244 -------KTRVDKD 250
                  +TRVD D
Sbjct: 249 MAIEHLKRTRVDND 262


>gi|229042218|ref|ZP_04189972.1| tRNA-dihydrouridine synthase [Bacillus cereus AH676]
 gi|228727153|gb|EEL78356.1| tRNA-dihydrouridine synthase [Bacillus cereus AH676]
          Length = 336

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFK---ALSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKN 245


>gi|227517187|ref|ZP_03947236.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
 gi|227075410|gb|EEI13373.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
          Length = 337

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+      K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPAGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 199

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN
Sbjct: 200 EVIPQIMAIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKN 251


>gi|241952224|ref|XP_002418834.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223642173|emb|CAX44140.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 463

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 78/297 (26%), Positives = 126/297 (42%), Gaps = 34/297 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-------KNILGFSTQEKPLALQ 53
           MVD ++  +R  +R      L YT M  A      +K        N+ G  T ++PL +Q
Sbjct: 63  MVDQSELAWRILSRRY-GAQLCYTPMFHAKLFATQEKYRNSMWTTNLDGNQTLDRPLVVQ 121

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
               D   L++AAK++ED   + I+LN+GCP     +G +GA LM + D+V   I  +  
Sbjct: 122 FCANDPDYLLQAAKLIED-ECDAIDLNLGCPQGIARKGKYGAFLMDDWDLVYKLIKNLHD 180

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            LSIPVT K RI  DD   ++      K +  +G   I +H R   +KG      +    
Sbjct: 181 NLSIPVTAKIRI-YDDYEKSL---KYAKMVLDAGAQFITVHGRTREMKG------QATGL 230

Query: 174 LDYDIVYEIKKENP-DLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            ++ I+  ++   P D     NG +   S  Q  +   S D VM       N  +  T+D
Sbjct: 231 ANWKILKYLRDNLPQDQVFFSNGNVLYPSDLQRCQSETSCDAVMSAEGNLYNPGVFWTLD 290

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +          P   ++ ++++  +  +    A+RH         +  H   L H F
Sbjct: 291 DNKDKQF----PRVDKILREYFEIVKENYDSLASRH--------AMKSHFFKLLHAF 335


>gi|260818049|ref|XP_002603897.1| hypothetical protein BRAFLDRAFT_129997 [Branchiostoma floridae]
 gi|229289221|gb|EEN59908.1| hypothetical protein BRAFLDRAFT_129997 [Branchiostoma floridae]
          Length = 347

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 129/288 (44%), Gaps = 42/288 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L ++ MI+A++ ++  K     F+T   ++PL +Q    D
Sbjct: 33  MVRYSKLPFRALVRRY-NCDLAFSPMIIAESFVKSLKARDSEFTTNSADRPLVVQFAARD 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              L +AA+IV  +  + ++LN GCP        +G+CL+ NP++V D +      +S  
Sbjct: 92  GVTLADAAEIVAPYS-DGVDLNCGCPQRWAMAEGYGSCLLKNPELVSDMVRQAKARVSDK 150

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKK---SGVNGIWIHARKAILKGLSPKDNRKIP 172
              V++K R+  D       LR  V   +K   +GV+ I +H R    +G  P +   I 
Sbjct: 151 DFSVSIKIRLHKD-------LRETVDMCQKAEHAGVSWIAVHGRTPSQRG-EPVNTEAI- 201

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
                    + K++  + +  NG ++++    ++  L  VDGVM  R   +N  M    D
Sbjct: 202 --------SLIKQSLSIPVIANGDIKNLEDVKRVQSLTGVDGVMAARGILQNPGMYAGYD 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
           +         +P++   D   W  IS  + T +   H H     +++T
Sbjct: 254 Q---------TPLQCVQD---WVDISLKLGTHFTCFHHHLMYMFERVT 289


>gi|197287426|ref|YP_002153298.1| tRNA-dihydrouridine synthase B [Proteus mirabilis HI4320]
 gi|227358312|ref|ZP_03842653.1| tRNA-dihydrouridine synthase B [Proteus mirabilis ATCC 29906]
 gi|194684913|emb|CAR47079.1| tRNA-dihydrouridine synthase B [Proteus mirabilis HI4320]
 gi|227161648|gb|EEI46685.1| tRNA-dihydrouridine synthase B [Proteus mirabilis ATCC 29906]
          Length = 323

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + + DK  +    + E  + ++QI G+D
Sbjct: 17  MAGVTDRPFRSLCYDM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHSDELGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  + G   I++N+GCP+ +V++   G+ L+  PD+V + ++A+  A+ +P
Sbjct: 76  PVDMATAAKINVEGGAQIIDINMGCPAKKVNKKLAGSALLRYPDLVAEILSAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G   D+   V +  L +     G+  + IH   R+ + KG            +
Sbjct: 136 VTLKIRTGWSPDERNCVEIAKLAED---CGIAALTIHGRTRECLFKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQSVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|152974153|ref|YP_001373670.1| dihydrouridine synthase DuS [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152022905|gb|ABS20675.1| dihydrouridine synthase DuS [Bacillus cytotoxicus NVH 391-98]
          Length = 319

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++        +
Sbjct: 138 LPVSVKTRLGFKE---VNEWEEWLTHIFKQDIANLSIHLRT--------REEMSQVAAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKN 238


>gi|300869979|ref|YP_003784850.1| dihydrouridine synthase like protein [Brachyspira pilosicoli
           95/1000]
 gi|300687678|gb|ADK30349.1| dihydrouridine synthase like, DUS like/ FMN binding domain protein
           [Brachyspira pilosicoli 95/1000]
          Length = 323

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 119/243 (48%), Gaps = 22/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R  +R      LL TE++ A A+ R  KK    +     E P++LQI G  
Sbjct: 21  MAGYTDYVFRRLSRRF-GAGLLVTELVSAAALARMIKKTYRYMEHKEDEYPISLQIFGNK 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                +A ++ +  G++ I++N+GCP+ +V   + GA L+ + D +   +  +     +P
Sbjct: 80  EDDFKKAIELTDLSGFSFIDINMGCPTKKVVRNNGGAGLLSDTDKMVSILNTVKSVSPLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           V+VK R+G          R L  ++K++G   + +H R A  + +G++          D+
Sbjct: 140 VSVKIRLGFQRGEGGEIERAL--ALKENGAVFLTLHGRYASDLYRGVA----------DW 187

Query: 177 DIVYEIKKENPDLFIGLNGG----LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           + +  +K+   D +I +  G     ED  +A +I   VDG+M+GRAA  N  +   ++  
Sbjct: 188 EAIANVKEALGDDYILIGNGDIKTKEDAKRAFEI-SKVDGIMVGRAAIGNPWVFRELNTI 246

Query: 233 FSN 235
           F +
Sbjct: 247 FDD 249


>gi|134103510|ref|YP_001109171.1| dihydrouridine synthase TIM-barrel protein nifR3 [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291005944|ref|ZP_06563917.1| dihydrouridine synthase TIM-barrel protein nifR3 [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133916133|emb|CAM06246.1| dihydrouridine synthase TIM-barrel protein nifR3 [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 387

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 70/310 (22%), Positives = 128/310 (41%), Gaps = 24/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R+  R      L   EMI + A++        ++ F   E P ++Q+ G D
Sbjct: 34  MAGITNVAFRWLCREY-GAGLYVCEMITSRALVERHPTTMQMVTFDPDEHPRSMQLYGVD 92

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A + IVE+   + +++N GCP  +V     G+ L     + G+ + A  +A   
Sbjct: 93  PETMGQAVRMIVEEGLADHVDMNFGCPVPKVTRKGGGSALPYKRRLFGEIVRAAVRAAEP 152

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+DD+   +   +  +  + +G   + +H R A          R     
Sbjct: 153 AGVPVTVKFRIGIDDE--HITYLDAGRIAEDNGAAAVALHGRTAA--------QRYSGQA 202

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K+    + +  NG +     AL+++     DGV++GR       +   +   
Sbjct: 203 DWSAIARLKETVRTIPVLGNGDIFSADDALRMVAETGCDGVVVGRGCLGRPWLFRDLQAA 262

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +   R       +  A H+     L+ + +HM     GFP    
Sbjct: 263 FAGEPVPEGPNLGEVCRVLRRH-----GELLADHMGEEKGLRDLRKHMAQYLRGFPVGSD 317

Query: 293 CRHILTVEAG 302
            RH   + +G
Sbjct: 318 LRHRFGLVSG 327


>gi|325688860|gb|EGD30868.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK115]
          Length = 325

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 117/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|171319643|ref|ZP_02908737.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria MEX-5]
 gi|171095134|gb|EDT40140.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria MEX-5]
          Length = 355

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PNAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKSA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQHVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANGFRH 304


>gi|157372656|ref|YP_001480645.1| tRNA-dihydrouridine synthase B [Serratia proteamaculans 568]
 gi|157324420|gb|ABV43517.1| putative TIM-barrel protein, nifR3 family [Serratia proteamaculans
           568]
          Length = 321

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  + ++QI G D
Sbjct: 17  MAGITDRPFRALCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAARINVAGGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILHAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G + +      RN V   +  +  G+  + IH R    +  G          N
Sbjct: 136 VTLKIRTGWEPE-----HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|319783399|ref|YP_004142875.1| hypothetical protein Mesci_3706 [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169287|gb|ADV12825.1| TIM-barrel protein, nifR3 family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 342

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 103/219 (47%), Gaps = 15/219 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADISKLV 63
           TD  +R  A       L+ +EM+ +  + +G     L       P+ + Q+ G +   + 
Sbjct: 31  TDEPFRQRAHA-HGAGLVVSEMVASGELAKGRAGFNLRIRHSGLPVHMVQLAGREAVHMA 89

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I    G + I++N+GCP+ +V  G  G+ LML+ D     I A+  A+ +PVTVK 
Sbjct: 90  EGARIAAGEGADIIDINMGCPAKKVTGGYAGSALMLDLDHALSLIDAVVGAVEVPVTVKM 149

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D+   A+    L +  +++GV+ + +H R          D R I  +         
Sbjct: 150 RLGWDEG--ALNAPMLARRAEQAGVSMVTVHGRTRCQFYQGKADWRAIARV--------- 198

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           KE   + +  NG +   ++A  IL     D VMIGRA Y
Sbjct: 199 KETVSIPVVANGDVSSPAEAADILDQSGADAVMIGRAHY 237


>gi|325529035|gb|EGD06045.1| tRNA-dihydrouridine synthase B [Burkholderia sp. TJI49]
          Length = 355

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 142/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKKL-GAGYAVSEMVASNAQLWKSAKTMRRANHTGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G +      
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITIARLAEA---AGISMLTVHGRTRADLYRGEA------ 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 188 ----EYDTIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQHVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANGFRH 304


>gi|251793182|ref|YP_003007910.1| tRNA-dihydrouridine synthase B [Aggregatibacter aphrophilus NJ8700]
 gi|247534577|gb|ACS97823.1| tRNA-dihydrouridine synthase B [Aggregatibacter aphrophilus NJ8700]
          Length = 320

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 111/236 (47%), Gaps = 22/236 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  ++    A+QI G+D
Sbjct: 17  MAGITDQPFRRICATY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHHQEAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  P +V   +  + K++ +P
Sbjct: 76  PDEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPQLVRQILETVVKSVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D     +  RN V   K  ++SG+  + IH R    K     +   I    
Sbjct: 136 VTLKIRTGWD-----LENRNCVEIAKIAEQSGIQALTIHGRTRACKFEGEAEYEHI---- 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
                 + K+   + +  NG +    +A  +L     DG+MIGR A     +  +V
Sbjct: 187 -----RLVKQQVSIPVIANGDITSAQKAKAVLDYTGADGIMIGRGALGRPWLFQSV 237


>gi|332365222|gb|EGJ42985.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1059]
          Length = 325

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 117/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|221142266|ref|ZP_03566759.1| hypothetical protein SauraJ_11637 [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|304380055|ref|ZP_07362778.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|269939624|emb|CBI47992.1| probable tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|302749979|gb|ADL64156.1| tRNA dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           str. JKD6008]
 gi|304341375|gb|EFM07291.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|329312793|gb|AEB87206.1| tRNA dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           T0131]
          Length = 328

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 106/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPVVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|320353935|ref|YP_004195274.1| tRNA-U20-dihydrouridine synthase [Desulfobulbus propionicus DSM
           2032]
 gi|320122437|gb|ADW17983.1| tRNA-U20-dihydrouridine synthase [Desulfobulbus propionicus DSM
           2032]
          Length = 329

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 109/231 (47%), Gaps = 16/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           +  +TD  +R   R     AL ++EMI    ++   K  +    T  +E+P A+Q+ G++
Sbjct: 28  LAGYTDLPFRLLCRE-NGAALCFSEMISCHGLVYEQKNTLELLRTVPEERPFAVQLFGSE 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  A  +V     + I++N+GCP  +V +   GA LM +P      I A+C   S+P
Sbjct: 87  PELMARATAMVSSGPVDLIDINMGCPVRKVIKKGCGAALMKDPQRAEAIIRAVCAQTSLP 146

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G   +  +V         + +G + + IH R  + +G   + +R+       +
Sbjct: 147 VTVKFRSGWTGE--SVNAPQFAAMAEAAGASAVTIHGRTWV-QGFGGRADRR-------V 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +  +K       IG NG +   + AL+++     DGVM+GR A  N  + +
Sbjct: 197 IRAVKDAVSIPVIG-NGDILTRADALEMMAETGCDGVMVGRGALGNPWLFS 246


>gi|170748588|ref|YP_001754848.1| NifR3 family TIM-barrel protein [Methylobacterium radiotolerans JCM
           2831]
 gi|170655110|gb|ACB24165.1| TIM-barrel protein, nifR3 family [Methylobacterium radiotolerans
           JCM 2831]
          Length = 341

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 105/220 (47%), Gaps = 19/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLV 63
           TD H R  AR    +A++ +EM+ A    RG  +  L        L  +Q+ G +   + 
Sbjct: 35  TDLHMRRIARRCGADAVI-SEMVAAREFTRGSGEATLRAEGSGVDLHVVQLAGCEAGPMA 93

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA++ E  G + I++N+GCP+  V   + G+ LM + D     +A++  A+SIPVTVK 
Sbjct: 94  EAARLAEAGGADVIDVNMGCPAKIVTGIASGSALMRDLDHAERLLASVRGAVSIPVTVKM 153

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G DD     A  +L    ++ G+N + +H   R+   KG            D+  +  
Sbjct: 154 RLGWDDASRNAA--DLAARAERLGLNAVTVHGRTRQQFYKG----------RADWAAIRA 201

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +        I  NG + D + A   L +    GVMIGRAA
Sbjct: 202 VVAAVSIPVIA-NGDVTDFASARACLDASGAAGVMIGRAA 240


>gi|124808213|ref|XP_001348259.1| tRNA-dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|23497150|gb|AAN36698.1| tRNA-dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 340

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 71/256 (27%), Positives = 112/256 (43%), Gaps = 24/256 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ +   +  +K  K        +KP+  Q  G D
Sbjct: 33  MVDLSELPFRLLCRKY-NCDLTFTPMLHSKNFVEHEKYRKGYFKSCDMDKPVIAQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EA   ++D   N +++N+GCP     +G++GA L+   D V + I+ +     IP
Sbjct: 92  SKILLEAINFIKD-DVNAVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLISDITNNCVIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R  +D+        NL   ++  G+  I +H R    KG++      I   DY+I
Sbjct: 151 ITCKIR-KIDNDYQKTL--NLCYDLQSRGIKMITVHGRTKEEKGIN------IKQCDYEI 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA--------AYKNSAMLTT 228
           +  I KE  ++ I  NG +E      K L     D VM            + KN   +  
Sbjct: 202 I-RIIKERLNIPIIANGSIEHFEDIKKCLNYTKADAVMCAEILLEKPYFFSNKNIDAVNI 260

Query: 229 VDEYFSNPLTGSSPIK 244
           V+EYF   L   S  K
Sbjct: 261 VNEYFELYLKYESNTK 276


>gi|269201723|ref|YP_003280992.1| hypothetical protein SAAV_0037 [Staphylococcus aureus subsp. aureus
           ED98]
 gi|262074013|gb|ACY09986.1| hypothetical protein SAAV_0037 [Staphylococcus aureus subsp. aureus
           ED98]
          Length = 310

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 101/222 (45%), Gaps = 33/222 (14%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E P+   I G    +  E +  + 
Sbjct: 22  FFTEFTNTESFCHPEGIHS---VRGR----LTFSEDEHPMVAHIWGDKPEQFRETSIQLA 74

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---V 127
             G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  +PV+VK R+G   +
Sbjct: 75  KMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGGLPVSVKTRLGYYEI 133

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN-----RKIPNLDYDIVYEI 182
           D+       ++ +K + +  +  + IH R    K +S  D        I NL  +I    
Sbjct: 134 DE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELIEAIKNLRDEIA--- 182

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 183 ----PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 220


>gi|288940563|ref|YP_003442803.1| TIM-barrel protein, nifR3 family [Allochromatium vinosum DSM 180]
 gi|288895935|gb|ADC61771.1| TIM-barrel protein, nifR3 family [Allochromatium vinosum DSM 180]
          Length = 338

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 114/226 (50%), Gaps = 22/226 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L   EM+ A+  L G +K++  L +  +  P++ QI G+D
Sbjct: 24  MAGITDRPFRTLCRRL-GAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAA++  + G + +++N+GCP+ +V + + G+ L+ +   V   + A+  A+  P
Sbjct: 83  PAEMAEAARLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEAP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G   +      RN V   +  ++SG+  + +H R       +P         +
Sbjct: 143 VTLKIRTGWSPE-----ERNAVRIARIARESGIAALTVHGRTRACTYGAPA--------E 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           YD +  I+  + D+ +  NG +     A ++L     D +MIGRAA
Sbjct: 190 YDTIRAIRA-SVDIPLIANGDIASAQDARRVLDYTGADAIMIGRAA 234


>gi|215402614|ref|ZP_03414795.1| transcriptional regulator [Mycobacterium tuberculosis 02_1987]
 gi|215444960|ref|ZP_03431712.1| transcriptional regulator [Mycobacterium tuberculosis T85]
 gi|289744547|ref|ZP_06503925.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           02_1987]
 gi|289756910|ref|ZP_06516288.1| transcriptional regulatory protein [Mycobacterium tuberculosis T85]
 gi|294996303|ref|ZP_06801994.1| transcriptional regulator [Mycobacterium tuberculosis 210]
 gi|289685075|gb|EFD52563.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           02_1987]
 gi|289712474|gb|EFD76486.1| transcriptional regulatory protein [Mycobacterium tuberculosis T85]
 gi|326904957|gb|EGE51890.1| transcriptional regulator [Mycobacterium tuberculosis W-148]
          Length = 388

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 79/314 (25%), Positives = 130/314 (41%), Gaps = 29/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 148

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTVE 300
           FP     R +  V+
Sbjct: 314 FPAGSARRALAMVK 327


>gi|172059673|ref|YP_001807325.1| NifR3 family TIM-barrel protein [Burkholderia ambifaria MC40-6]
 gi|171992190|gb|ACB63109.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria MC40-6]
          Length = 355

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQHVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANGFRH 304


>gi|38605042|sp|Q9CLW3|DUSB_PASMU RecName: Full=tRNA-dihydrouridine synthase B
          Length = 332

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 118/241 (48%), Gaps = 30/241 (12%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   R+ T+    L ++EM+  +  +   +K+ L  +  ++    A+QI G
Sbjct: 17  MAGITDQPFR---RICTHYGAGLTFSEMMSTNPQVWHTEKSKLRLAHHQEAGINAVQIAG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  ++ +AA+I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  + K+++
Sbjct: 74  CDPDEMAKAAQINVEYGAEIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILNKVVKSVT 133

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
           +PVT+K R G D        RN   + K  ++ G+  + IH   R  + +G +  DN K 
Sbjct: 134 VPVTLKIRTGWDKD-----NRNCLEIAKIAEQCGIQALTIHGRTRSCMFEGEAEYDNIKA 188

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
                       KE   + I  NG +    +A  +L   + D +MIGR +  N  +   +
Sbjct: 189 V-----------KEQLSIPIIANGDITSAEKAKYVLDYTNADAIMIGRGSLGNPWLFRVM 237

Query: 230 D 230
           +
Sbjct: 238 E 238


>gi|107021769|ref|YP_620096.1| dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           cenocepacia AU 1054]
 gi|116688716|ref|YP_834339.1| nifR3 family TIM-barrel protein [Burkholderia cenocepacia HI2424]
 gi|170732013|ref|YP_001763960.1| NifR3 family TIM-barrel protein [Burkholderia cenocepacia MC0-3]
 gi|254246304|ref|ZP_04939625.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           cenocepacia PC184]
 gi|105891958|gb|ABF75123.1| tRNA-U20-dihydrouridine synthase [Burkholderia cenocepacia AU 1054]
 gi|116646805|gb|ABK07446.1| tRNA-U20-dihydrouridine synthase [Burkholderia cenocepacia HI2424]
 gi|124871080|gb|EAY62796.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           cenocepacia PC184]
 gi|169815255|gb|ACA89838.1| TIM-barrel protein, nifR3 family [Burkholderia cenocepacia MC0-3]
          Length = 355

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQHVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANGFRH 304


>gi|222475071|ref|YP_002563486.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Florida]
 gi|222419207|gb|ACM49230.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Florida]
          Length = 320

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 105/216 (48%), Gaps = 42/216 (19%)

Query: 21  LLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           LL +EMI + A++    +  +K+ +G +T     A+Q+ G     + EAAKI +D G   
Sbjct: 36  LLVSEMIASRAMIIKTRQSLQKSDVGANT-----AVQLAGCVPEIMAEAAKINQDMGARS 90

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPA 133
           I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G    D   P 
Sbjct: 91  IDINFGCPVKKIVDGHAGSALMKDEEKAAKIMESVVKAVTIPVTVKMRMGWSATDLNAP- 149

Query: 134 VALRNLVKSIKKSGVNGIWIHA--RKAILKGLSP-------KDNRKIPNLDYDIVYEIKK 184
                L K  +  G+  + +H   R  +  G +        KD  KIP +          
Sbjct: 150 ----RLAKIAEDVGIQMVTVHGRTRTQMFSGTADWKFIKCVKDCVKIPVI---------- 195

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
            N D+       L+D++ AL  L   DGVMIGR AY
Sbjct: 196 ANGDIRT-----LQDITSALS-LSGADGVMIGRGAY 225


>gi|15923079|ref|NP_370613.1| hypothetical protein SAV0089 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15925793|ref|NP_373326.1| hypothetical protein SA0085 [Staphylococcus aureus subsp. aureus
           N315]
 gi|148266519|ref|YP_001245462.1| hypothetical protein SaurJH9_0077 [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150392555|ref|YP_001315230.1| hypothetical protein SaurJH1_0079 [Staphylococcus aureus subsp.
           aureus JH1]
 gi|156978419|ref|YP_001440678.1| hypothetical protein SAHV_0088 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253733809|ref|ZP_04867974.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|254664018|ref|ZP_05143490.1| hypothetical protein SauraM_00430 [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257794441|ref|ZP_05643420.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9781]
 gi|258407597|ref|ZP_05680733.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9763]
 gi|258419873|ref|ZP_05682835.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9719]
 gi|258438612|ref|ZP_05689835.1| dihydrouridine synthase DuS [Staphylococcus aureus A9299]
 gi|258443931|ref|ZP_05692269.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|258445131|ref|ZP_05693368.1| dihydrouridine synthase DuS [Staphylococcus aureus A6300]
 gi|258447736|ref|ZP_05695875.1| dihydrouridine synthase [Staphylococcus aureus A6224]
 gi|258455641|ref|ZP_05703596.1| dihydrouridine synthase DuS [Staphylococcus aureus A5937]
 gi|282894311|ref|ZP_06302541.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8117]
 gi|282928341|ref|ZP_06335944.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A10102]
 gi|295405362|ref|ZP_06815172.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8819]
 gi|297244698|ref|ZP_06928578.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8796]
 gi|54037013|sp|P67717|DUS_STAAN RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|54040779|sp|P67716|DUS_STAAM RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|13700005|dbj|BAB41304.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14245856|dbj|BAB56251.1| probable dehydrogenases, nifR3 family [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|147739588|gb|ABQ47886.1| dihydrouridine synthase, DuS [Staphylococcus aureus subsp. aureus
           JH9]
 gi|149945007|gb|ABR50943.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           JH1]
 gi|156720554|dbj|BAF76971.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253728112|gb|EES96841.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257788413|gb|EEV26753.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9781]
 gi|257840822|gb|EEV65279.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9763]
 gi|257844155|gb|EEV68542.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9719]
 gi|257848171|gb|EEV72163.1| dihydrouridine synthase DuS [Staphylococcus aureus A9299]
 gi|257850815|gb|EEV74759.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|257856039|gb|EEV78958.1| dihydrouridine synthase DuS [Staphylococcus aureus A6300]
 gi|257859018|gb|EEV81882.1| dihydrouridine synthase [Staphylococcus aureus A6224]
 gi|257861853|gb|EEV84626.1| dihydrouridine synthase DuS [Staphylococcus aureus A5937]
 gi|282589925|gb|EFB95008.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A10102]
 gi|282763356|gb|EFC03486.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8117]
 gi|285815814|gb|ADC36301.1| tRNA dihydrouridine synthase B [Staphylococcus aureus 04-02981]
 gi|294969437|gb|EFG45456.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8819]
 gi|297178215|gb|EFH37462.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8796]
 gi|312828608|emb|CBX33450.1| dihydrouridine synthase (Dus) family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315129069|gb|EFT85065.1| hypothetical protein CGSSa03_13652 [Staphylococcus aureus subsp.
           aureus CGS03]
          Length = 328

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 105/236 (44%), Gaps = 30/236 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEHPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN----- 168
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R    K +S  D      
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRTR--KEMSKVDAHWELI 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             I NL  +I        P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 190 EAIKNLRDEIA-------PNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|317049793|ref|YP_004117441.1| TIM-barrel protein, nifR3 family [Pantoea sp. At-9b]
 gi|316951410|gb|ADU70885.1| TIM-barrel protein, nifR3 family [Pantoea sp. At-9b]
          Length = 321

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGA 57
           M   TD+ +R       N A +  +EM+ ++  +    K+ L     ++P   A+QI G 
Sbjct: 17  MAGVTDKPFRTLC--YENGAGMTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGC 74

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D  ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P +V   + A+  A+ +
Sbjct: 75  DPDEMAAAARINVASGAQVIDINMGCPAKKVNRKMAGSALLQHPQLVESILTAVVNAVDV 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIP 172
           PVT+K R G D +      RN V   +  ++ G+  + IH R    + +G +        
Sbjct: 135 PVTLKIRTGWDKEN-----RNCVEIAQLAERCGIQALTIHGRTRACLFEGQA-------- 181

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             +YD +  + K++  + +  NG + D  +A  +L     D +MIGRAA     +   + 
Sbjct: 182 --EYDSIRTV-KQSVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQ 238

Query: 231 EYF 233
            Y 
Sbjct: 239 HYL 241


>gi|15602952|ref|NP_246024.1| hypothetical protein PM1087 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|12721426|gb|AAK03171.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 334

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 118/241 (48%), Gaps = 30/241 (12%)

Query: 1   MVDWTDRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGG 56
           M   TD+ +R   R+ T+    L ++EM+  +  +   +K+ L  +  ++    A+QI G
Sbjct: 19  MAGITDQPFR---RICTHYGAGLTFSEMMSTNPQVWHTEKSKLRLAHHQEAGINAVQIAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  ++ +AA+I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  + K+++
Sbjct: 76  CDPDEMAKAAQINVEYGAEIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILNKVVKSVT 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
           +PVT+K R G D        RN   + K  ++ G+  + IH   R  + +G +  DN K 
Sbjct: 136 VPVTLKIRTGWDKD-----NRNCLEIAKIAEQCGIQALTIHGRTRSCMFEGEAEYDNIKA 190

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
                       KE   + I  NG +    +A  +L   + D +MIGR +  N  +   +
Sbjct: 191 V-----------KEQLSIPIIANGDITSAEKAKYVLDYTNADAIMIGRGSLGNPWLFRVM 239

Query: 230 D 230
           +
Sbjct: 240 E 240


>gi|256027949|ref|ZP_05441783.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D11]
 gi|289765894|ref|ZP_06525272.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D11]
 gi|289717449|gb|EFD81461.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D11]
          Length = 308

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 115/254 (45%), Gaps = 43/254 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       +  A+QI G DI+K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIAKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    +++K RIG  +    + +  
Sbjct: 88  CGCPMKKIVNCGYGAALLREPEKIKRILSEIKSVLNDDTKLSIKIRIGYKEPENYIQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + I   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEI---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF-----SNPLTGSSPI- 243
           F G +  LE +S +     +VDGVM+ R  + N  ++  + E         P T    I 
Sbjct: 195 FTGKD-ALEKISYS-----NVDGVMLARGIFGNPWLIRDIREILKYGEIKTPTTKEDKIN 248

Query: 244 -------KTRVDKD 250
                  +TRVD D
Sbjct: 249 MAIEHLKRTRVDND 262


>gi|257462573|ref|ZP_05626984.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D12]
 gi|317060226|ref|ZP_07924711.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D12]
 gi|313685902|gb|EFS22737.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D12]
          Length = 322

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 111/233 (47%), Gaps = 21/233 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  YR        + LL+TEM+ +DA+   + K I           +Q+ G D  K++ 
Sbjct: 13  TDYTYRGILEEFQPD-LLFTEMVSSDALAALNDKTISQILRLRSGNGVQLFGKDTEKMIY 71

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK 122
           +AK +E  G   I++N GCP  RV     G+ L+ +P+ + + +  + + L  S  +++K
Sbjct: 72  SAKYIEKLGVKNIDINAGCPMKRVVHSGHGSALLKSPEKIKEILFTLREQLEESTKLSIK 131

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
            R+G D   P   L+ + K  +++G + I +H R    +  GL+          D+ ++ 
Sbjct: 132 IRVGYDR--PENYLQ-IAKIAEEAGCSHITVHGRTRAQLYTGLA----------DWSLIK 178

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           EIK+      IG NG +     A + +    VDGVM+ R  + N  ++  + E
Sbjct: 179 EIKEHVTIPVIG-NGDIFTAEAAKEKIEDSGVDGVMLARGIFGNPWLIRDIRE 230


>gi|33594297|ref|NP_881941.1| hypothetical protein BP3414 [Bordetella pertussis Tohama I]
 gi|33598080|ref|NP_885723.1| hypothetical protein BPP3564 [Bordetella parapertussis 12822]
 gi|33602973|ref|NP_890533.1| hypothetical protein BB3999 [Bordetella bronchiseptica RB50]
 gi|33564372|emb|CAE43677.1| conserved hypothetical protein [Bordetella pertussis Tohama I]
 gi|33566638|emb|CAE38848.1| conserved hypothetical protein [Bordetella parapertussis]
 gi|33568604|emb|CAE34362.1| conserved hypothetical protein [Bordetella bronchiseptica RB50]
 gi|332383708|gb|AEE68555.1| hypothetical protein BPTD_3366 [Bordetella pertussis CS]
          Length = 343

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 110/236 (46%), Gaps = 19/236 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TDR YR   + L       +EM  ++  L    K    L    +  P+++QI GAD + +
Sbjct: 23  TDRPYRQLCKRL-GAGYAVSEMAASNPRLWDSVKTSRRLNHEGEIDPISVQIAGADPTMM 81

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKALSIPV 119
            EAA      G   I++N+GCP  +V   + G+ L+ + D++    + + A C  L +PV
Sbjct: 82  AEAAAFNVAKGARIIDINMGCPVKKVCNVASGSALLRHEDLIVRILEAVVAACAPLGVPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G D +    ALR + +  +++G+  + +H R         + +      +YD +
Sbjct: 142 TLKTRTGWDRE-HRNALR-VGRLAEQAGIAALTLHGRT--------RADLYTGQAEYDTI 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +K E     I  NG ++   +A ++L     D VMIGRAA     +   +D Y 
Sbjct: 192 RAVKAELKIPVIA-NGDIDSPEKARQVLDYTGADAVMIGRAAQGRPWIFREIDHYL 246


>gi|149180942|ref|ZP_01859444.1| hypothetical protein BSG1_00885 [Bacillus sp. SG-1]
 gi|148851461|gb|EDL65609.1| hypothetical protein BSG1_00885 [Bacillus sp. SG-1]
          Length = 332

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++      R   +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPNGRQSVRGRLTFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  I++N+GCP A V     G+ L+  P++  + I A  KA  
Sbjct: 86  DKPEFFREMSIGMAKEGFRGIDINMGCPVANVAGNGKGSGLIRRPEVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R+ +  + K  +  + IH R       + K+  K+ +  +
Sbjct: 145 LPVSVKTRLGYSE---VDEWRDWLTHLLKQDIVNLSIHLR-------TKKEMSKV-DAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    L+++    VDGVMIGR  + N
Sbjct: 194 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLELVEKYGVDGVMIGRGIFHN 245


>gi|187479247|ref|YP_787272.1| tRNA-dihydrouridine synthase B [Bordetella avium 197N]
 gi|115423834|emb|CAJ50385.1| tRNA-dihydrouridine synthase B [Bordetella avium 197N]
          Length = 341

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/253 (26%), Positives = 115/253 (45%), Gaps = 27/253 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMAASNPRLWDSVKTSRRLNHDGEIAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKAL 115
            + + EAA    + G   I++N+GCP  +V   + G+ L+ + D++    D +   C  L
Sbjct: 76  PAMMAEAAVFNVNKGARIIDINMGCPVKKVCNMASGSALLRHEDLIARILDAVVGACAPL 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +    ALR + +  ++SG+  + +H R         + +      +
Sbjct: 136 GVPVTLKTRTGWDRE-SRNALR-VARMAEQSGIALLTLHGRT--------RCDLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGL----NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
           YD +  +K E     IG+    NG ++   +A  +L     D VMIGRAA     +   +
Sbjct: 186 YDTLRAVKAE-----IGIPVVANGDIDSPEKARDVLRYTGADAVMIGRAAQGRPWIFREI 240

Query: 230 DEYFSNPLTGSSP 242
           D +     T + P
Sbjct: 241 DHFLRTGETLAPP 253


>gi|254994912|ref|ZP_05277102.1| hypothetical protein AmarM_02227 [Anaplasma marginale str.
           Mississippi]
          Length = 298

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/212 (31%), Positives = 102/212 (48%), Gaps = 34/212 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           LL +EMI + A++   +++ L  S      A+Q+ G     + EAAKI +D G   I++N
Sbjct: 14  LLVSEMIASRAMIIKTRQS-LQKSDVGANTAVQLAGCVPEIMAEAAKINQDMGARSIDIN 72

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPAVALR 137
            GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G    D   P     
Sbjct: 73  FGCPVKKIVDGHAGSALMKDEEKATKIMESVVKAVTIPVTVKMRMGWSATDLNAP----- 127

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSP-------KDNRKIPNLDYDIVYEIKKENPD 188
            L K  +  G+  + +H   R  +  G +        KD  KIP +           N D
Sbjct: 128 RLAKIAEDVGIQMVTVHGRTRTQMFSGTADWKFIKCVKDCVKIPVI----------ANGD 177

Query: 189 LFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           +       L+D++ AL  L   DGVMIGR AY
Sbjct: 178 IRT-----LQDITSALS-LSGADGVMIGRGAY 203


>gi|242208769|ref|XP_002470234.1| predicted protein [Postia placenta Mad-698-R]
 gi|220730684|gb|EED84537.1| predicted protein [Postia placenta Mad-698-R]
          Length = 260

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 119/240 (49%), Gaps = 27/240 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF------STQEKPLALQI 54
           MV+ +D  +R   R   N  L+YT+M+++D +L  +  + L F         ++P+ +Q+
Sbjct: 6   MVNQSDLPFRRLVRRY-NATLVYTQMLLSDRLL--NDHDYLQFHLRGLGEPNDRPVVVQL 62

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCIAAMC 112
            G D   +V A K V+    + I+ N+GCP     +  +GA L+   D  +V +  A+M 
Sbjct: 63  CGNDPELVVRAGKQVQSHC-DAIDFNLGCPQEAARDAHYGAYLLGQNDWPLVENIAASMS 121

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            +L++PV+ K R+      PA A  +L + ++ +G + + +HAR   ++       R+  
Sbjct: 122 NSLTVPVSAKLRLCQ----PASATLDLARRLEHAGASWVTLHARTVSVR------RRRQG 171

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             D + +  + K+N  + +  NG +   ED+ + L  L   DG+M+G +   N  +   +
Sbjct: 172 AADLEQIKTL-KDNLSIPVISNGNVRVWEDVERNLA-LTGADGIMVGESLLANPCLFADI 229


>gi|229131322|ref|ZP_04260223.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228652143|gb|EEL08079.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 336

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DTPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|115350640|ref|YP_772479.1| nifR3 family TIM-barrel protein [Burkholderia ambifaria AMMD]
 gi|170699610|ref|ZP_02890649.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria IOP40-10]
 gi|115280628|gb|ABI86145.1| tRNA-U20-dihydrouridine synthase [Burkholderia ambifaria AMMD]
 gi|170135492|gb|EDT03781.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria IOP40-10]
          Length = 355

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQHVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANGFRH 304


>gi|116075024|ref|ZP_01472284.1| hypothetical protein RS9916_25729 [Synechococcus sp. RS9916]
 gi|116067221|gb|EAU72975.1| hypothetical protein RS9916_25729 [Synechococcus sp. RS9916]
          Length = 339

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 71/301 (23%), Positives = 136/301 (45%), Gaps = 27/301 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G  ++ +   + +  P+ +Q+       + 
Sbjct: 37  SDRIFRHLVRRWAPDALLFTEMVNATSLELGHGRRKVEELAQEAGPIGVQLFDHRPQAMA 96

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+  E  G   I++N+GCP  ++ +   G+ L+  PD+    +  +  A++IPVTVK 
Sbjct: 97  EAARRAEASGAFLIDINMGCPVKKIAKKGGGSGLIREPDLAARIVDTVAAAVAIPVTVKT 156

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D   A A+    + ++++G   + +H R         ++ +     D+  +  
Sbjct: 157 RLGWCGSDGSAADAV-QWCQQLEEAGARLLTLHGRT--------REQKFSGRADWQAIAA 207

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN---P 236
           + K+   + +  NG +     AL+ L     DGVM+GR    +  ++  +D   S    P
Sbjct: 208 V-KDALSIPVIANGDVNTPDDALRCLAETGADGVMVGRGTMGSPWLVGQIDSALSGRPIP 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +  +  + ++    + A   D+          L    +HM     GFP + + RH 
Sbjct: 267 TTPGAAERLTIAREQLVALVADRGDHG---------LLIARKHMSWTCTGFPGAPQLRHA 317

Query: 297 L 297
           L
Sbjct: 318 L 318


>gi|67479621|ref|XP_655192.1| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
 gi|56472312|gb|EAL49806.1| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
          Length = 339

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 117/238 (49%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD +D  +R   R     L    ++ ++M V   + R +  N L    +E+P+ +QI G
Sbjct: 29  MVDGSDLTFRILVRRHGVNLCYTPMVLSKMFVESKVYRNEVVNSL--DPKEQPIIIQIVG 86

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D +++   AK ++ +  + I++N+GCP     +G++GA L L+ D   + + A+ +A++
Sbjct: 87  SDANEMARTAKFLQSYC-DAIDINLGCPQKIAQKGNYGAYLALDFDHTKEIVNAVIEAVN 145

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPV  K R+  D++         V+ +++ G+ GI +H R    K       R      +
Sbjct: 146 IPVYCKVRVFEDEE----KTMRFVEMLQECGIWGIAVHGRTITEKQSMNYHAR------W 195

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT-TVD 230
           + + +I KE   + +  NG +   E + +  K+  S DG MIG     N  M   T+D
Sbjct: 196 NYIAKI-KERLKIPVIANGEMRSREKIEECKKVTHS-DGYMIGFGLLMNPGMCEGTID 251


>gi|169795120|ref|YP_001712913.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AYE]
 gi|213158218|ref|YP_002320269.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AB0057]
 gi|215482668|ref|YP_002324864.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB307-0294]
 gi|301345210|ref|ZP_07225951.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB056]
 gi|301594626|ref|ZP_07239634.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB059]
 gi|332854000|ref|ZP_08435116.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013150]
 gi|332869720|ref|ZP_08438908.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013113]
 gi|169148047|emb|CAM85910.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AYE]
 gi|213057378|gb|ACJ42280.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AB0057]
 gi|213987896|gb|ACJ58195.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB307-0294]
 gi|332728282|gb|EGJ59664.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013150]
 gi|332732622|gb|EGJ63855.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013113]
          Length = 341

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGR--------TREDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YELIKHV-KELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKEVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 297 RQNMYKVETTAEQAL--VVESYFNQLL 321


>gi|271498831|ref|YP_003331856.1| nifR3 family TIM-barrel protein [Dickeya dadantii Ech586]
 gi|270342386|gb|ACZ75151.1| TIM-barrel protein, nifR3 family [Dickeya dadantii Ech586]
          Length = 321

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGVSDRPFRALCYAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PDEMAQAARINAESGAQIIDINMGCPAKKVNRKMAGSALLQYPALVKQILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V+  K +   G+  + +H R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEDCGIQALTVHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRTV-KQSVSIPVIANGDITDPRKARAVLDYSGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|329894590|ref|ZP_08270396.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC3088]
 gi|328922944|gb|EGG30272.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC3088]
          Length = 325

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 106/225 (47%), Gaps = 20/225 (8%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKI 68
           F RL   +   Y   EMI A+   R  +K+         +   +QI G D  +L EAA++
Sbjct: 26  FRRLCLEHGASYAVAEMISANPDTRQTQKSQWRSVIDSNQAHIVQIVGHDPEQLAEAARL 85

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            ++ G + I++N+GCP+ +V + + G+ L+ N  +V D + A+  A+ IPVT+K R G  
Sbjct: 86  NQEAGADIIDINMGCPAKKVCKKAAGSALLANEALVQDILVAVKSAVDIPVTLKIRTGTS 145

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
                     L+   + +G+  + IH R      KG           ++YD + E+    
Sbjct: 146 PNERNATTIALIA--QDAGIAALTIHGRTKACAFKGA----------VEYDTIAEVVS-R 192

Query: 187 PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            D+ +  NG +    QALK+L      G+M+GR A     +L  +
Sbjct: 193 VDIPVIANGDITHPDQALKVLNYTGAAGIMVGRGAQGQPWLLGQI 237


>gi|125718973|ref|YP_001036106.1| hypothetical protein SSA_2191 [Streptococcus sanguinis SK36]
 gi|125498890|gb|ABN45556.1| Conserved uncharacterized protein [Streptococcus sanguinis SK36]
          Length = 317

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 184 TLHDVAHSLTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 242


>gi|229165352|ref|ZP_04293139.1| tRNA-dihydrouridine synthase [Bacillus cereus AH621]
 gi|228618177|gb|EEK75215.1| tRNA-dihydrouridine synthase [Bacillus cereus AH621]
          Length = 336

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DTPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 245


>gi|289209406|ref|YP_003461472.1| hypothetical protein TK90_2246 [Thioalkalivibrio sp. K90mix]
 gi|288945037|gb|ADC72736.1| TIM-barrel protein, nifR3 family [Thioalkalivibrio sp. K90mix]
          Length = 330

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 109/223 (48%), Gaps = 16/223 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +DR  R  AR L  +A + +EM+ +D  L G  K+   L    + +P  +Q+ G +
Sbjct: 18  MAGVSDRPLRLIARRLGASAAV-SEMVTSDTRLWGSDKSRHRLDHRQEPRPRIVQLLGNE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+     G + I+LN+GCP+ +V   + G+ L+  P+ V + + A+ +++ +P
Sbjct: 77  PEPLAEAARENVRRGADVIDLNLGCPAKKVCSKAAGSALLGEPERVRELLTALVESVEVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G+D +   V    +    +  G+  + +H R         + +      DY+ 
Sbjct: 137 VTLKMRLGLDRE--RVNAETIAGIAQDCGIAMLTVHGRT--------RADAYRGTADYEA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           +  + +    + +  NG + D+  A + L      G+MIGR A
Sbjct: 187 IARVVRAV-SIPVLANGDVVDIGSARRALAISGATGLMIGRGA 228


>gi|314936531|ref|ZP_07843878.1| dihydrouridine synthase family protein [Staphylococcus hominis
           subsp. hominis C80]
 gi|313655150|gb|EFS18895.1| dihydrouridine synthase family protein [Staphylococcus hominis
           subsp. hominis C80]
          Length = 324

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFKEMSFGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  ++ + K  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYN---IEEWKEWLRHVFKQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++  IK+      P   + +NG + D  + +++     +DGVMIGR  + N
Sbjct: 187 ELIEAIKEMRDEVAPQTLLTINGDIPDRQKGMELATKYGIDGVMIGRGIFHN 238


>gi|312901978|ref|ZP_07761240.1| dihydrouridine synthase [Enterococcus faecalis TX0470]
 gi|311290914|gb|EFQ69470.1| dihydrouridine synthase [Enterococcus faecalis TX0470]
          Length = 362

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 109/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLR-------TRKEMSKV-DAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + +  + L++     VDG+MIGR  +KN
Sbjct: 225 EVIPQIMSIRDRVAPQTTITINGDIPNRQKGLELAEQYGVDGIMIGRGIFKN 276


>gi|46447213|ref|YP_008578.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Candidatus Protochlamydia amoebophila UWE25]
 gi|46400854|emb|CAF24303.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Candidatus Protochlamydia amoebophila UWE25]
          Length = 326

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 112/238 (47%), Gaps = 22/238 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P A Q+ G+D   + E A+ VE  G   I+LN GCPS  V     G+ L+  PD +    
Sbjct: 69  PQAAQLMGSDPELMAEMARAVERRGAQRIDLNCGCPSNTVTGRGAGSSLLKEPDHLYKVA 128

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +M +A+++PVT K R G  D   ++   NL+ + + SG+  + +H R  +  G  P   
Sbjct: 129 KSMVEAVNVPVTAKLRSGFTDT--SLFHDNLL-AAQASGIKYLTLHPRTKV-DGYGPPAK 184

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
                  ++++ + K+      +G NG +  +  AL +L     DG+MIGR +  N  + 
Sbjct: 185 -------WELIAQAKQLLKIPVVG-NGDILTVQDALNMLKQTKCDGLMIGRGSVINPFIF 236

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             +  +FS     + P + + D  F R I     D   + +   G+L ++ + M  LF
Sbjct: 237 HEIKSHFS-----AQPFEKKWDV-FSRYIDVFTEDL--KEMSVKGQLNKLKQLMSFLF 286


>gi|293394168|ref|ZP_06638468.1| tRNA-dihydrouridine synthase B [Serratia odorifera DSM 4582]
 gi|291423146|gb|EFE96375.1| tRNA-dihydrouridine synthase B [Serratia odorifera DSM 4582]
          Length = 321

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  + ++QI G D
Sbjct: 17  MAGITDRPFRTLCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAAQINVASGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILLAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+N  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQNVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|317127197|ref|YP_004093479.1| dihydrouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315472145|gb|ADU28748.1| dihydrouridine synthase DuS [Bacillus cellulosilyticus DSM 2522]
          Length = 323

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDK--KNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++     G+K  K  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSAAARPDVFFTEFANSESYCHPEGNKSVKGRLTFTDDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPENFRKMSIGMAEQGFKGLDINMGCPVPNVARHGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFTE---LDEWREWLTHILKQDIANLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDGVMIGR  + N
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDILDRQTGLKLANQYGVDGVMIGRGIFHN 238


>gi|228474963|ref|ZP_04059691.1| conserved hypothetical protein [Staphylococcus hominis SK119]
 gi|228270948|gb|EEK12336.1| conserved hypothetical protein [Staphylococcus hominis SK119]
          Length = 324

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFKEMSFGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  ++ + K  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYN---IEEWKEWLRHVFKQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++  IK+      P   + +NG + D  + +++     +DGVMIGR  + N
Sbjct: 187 ELIEAIKEMRDEVAPQTLLTINGDIPDRQKGMELATKYGIDGVMIGRGIFHN 238


>gi|163938324|ref|YP_001643208.1| dihydrouridine synthase DuS [Bacillus weihenstephanensis KBAB4]
 gi|163860521|gb|ABY41580.1| dihydrouridine synthase DuS [Bacillus weihenstephanensis KBAB4]
          Length = 329

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILG---FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    +  K++ G   F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DTPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKE---LSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKN 238


>gi|94309374|ref|YP_582584.1| dihydrouridine synthase TIM-barrel protein nifR3 [Cupriavidus
           metallidurans CH34]
 gi|93353226|gb|ABF07315.1| tRNA-dihydrouridine synthase B [Cupriavidus metallidurans CH34]
          Length = 381

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 120/248 (48%), Gaps = 18/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+++QI GA+
Sbjct: 44  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPISVQIAGAE 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            S + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 103 PSMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVEAVVAAVGDR 162

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +    ALR + + ++ +G++ + IH R         + +      +Y
Sbjct: 163 VPVTLKIRTGWDREHKN-ALR-VARMVEDAGISMLTIHGRT--------RADLYHGEAEY 212

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG +    +A  +L     D +MIGRAA     +   ++ Y  
Sbjct: 213 ETIAAVKS-SIRIPVVANGDITTPQKARHVLAVTGADAIMIGRAAQGRPWLFREIEHYLK 271

Query: 235 NPLTGSSP 242
                 SP
Sbjct: 272 TGELLPSP 279


>gi|239501090|ref|ZP_04660400.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB900]
 gi|193077993|gb|ABO12912.2| putative protein NifR3 family [Acinetobacter baumannii ATCC 17978]
 gi|322509004|gb|ADX04458.1| dusB [Acinetobacter baumannii 1656-2]
 gi|323518988|gb|ADX93369.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 341

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGR--------TREDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YELIKHV-KELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGEHLAAPNIEEVKEVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 297 RQNMYKVETTAEQAL--VVESYFNQLL 321


>gi|184159024|ref|YP_001847363.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|183210618|gb|ACC58016.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
          Length = 325

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 1   MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 60  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 119

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 120 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGR--------TREDMYLNTAR 166

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 167 YELIKHV-KELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 225

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 226 KTGEHLAAPNIEEVKEVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 280

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 281 RQNMYKVETTAEQAL--VVESYFNQLL 305


>gi|114773260|ref|ZP_01450495.1| tRNA-dihydrouridine synthase B [alpha proteobacterium HTCC2255]
 gi|114546379|gb|EAU49288.1| tRNA-dihydrouridine synthase B [alpha proteobacterium HTCC2255]
          Length = 333

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 120/242 (49%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  +   +K  +    T E  + ++QI G+D
Sbjct: 21  MAGVTDRPFRQMCKQM-GAGLVVSEMLSSNPKVWHTEKSKMRMDHTGEHGVRSVQIAGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+   + G   I++N+GCP+ +V++   G+ L+  P+IV + + A+  ++ +P
Sbjct: 80  PNLMAEAAQFNVNNGAQIIDINMGCPAKKVNKKMAGSALLQYPEIVEEILDAVVNSVDVP 139

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L    ++  +  + +H R    + KG          N +
Sbjct: 140 VTLKIRTGWDTDNRNGVQIAKLA---QQYNIQSLAVHGRTKACMYKG----------NAE 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+   ++ +  NG +    +A  +L   + DG+MIGR A  N  +   +  Y 
Sbjct: 187 YDTIRAIKRA-VEIPVIANGDITTPEKAKYVLQHTNADGLMIGRGAQGNPWIFREILHYL 245

Query: 234 SN 235
            +
Sbjct: 246 EH 247


>gi|18311449|ref|NP_563383.1| putative dihydrouridine synthase [Clostridium perfringens str. 13]
 gi|110799132|ref|YP_697155.1| putative dihydrouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|110803269|ref|YP_699723.1| putative dihydrouridine synthase [Clostridium perfringens SM101]
 gi|168206862|ref|ZP_02632867.1| putative dihydrouridine synthase [Clostridium perfringens E str.
           JGS1987]
 gi|168211211|ref|ZP_02636836.1| putative dihydrouridine synthase [Clostridium perfringens B str.
           ATCC 3626]
 gi|168215145|ref|ZP_02640770.1| putative dihydrouridine synthase [Clostridium perfringens CPE str.
           F4969]
 gi|168218227|ref|ZP_02643852.1| putative dihydrouridine synthase [Clostridium perfringens NCTC
           8239]
 gi|182626021|ref|ZP_02953784.1| putative dihydrouridine synthase [Clostridium perfringens D str.
           JGS1721]
 gi|18146133|dbj|BAB82173.1| probable transcriptional regulator [Clostridium perfringens str.
           13]
 gi|110673779|gb|ABG82766.1| putative dihydrouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|110683770|gb|ABG87140.1| putative dihydrouridine synthase [Clostridium perfringens SM101]
 gi|170661755|gb|EDT14438.1| putative dihydrouridine synthase [Clostridium perfringens E str.
           JGS1987]
 gi|170710780|gb|EDT22962.1| putative dihydrouridine synthase [Clostridium perfringens B str.
           ATCC 3626]
 gi|170713442|gb|EDT25624.1| putative dihydrouridine synthase [Clostridium perfringens CPE str.
           F4969]
 gi|177908728|gb|EDT71239.1| putative dihydrouridine synthase [Clostridium perfringens D str.
           JGS1721]
 gi|182379765|gb|EDT77244.1| putative dihydrouridine synthase [Clostridium perfringens NCTC
           8239]
          Length = 326

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 75/320 (23%), Positives = 148/320 (46%), Gaps = 50/320 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    ++ TEM+ A A+  G +  K ++  + +EKP++ Q+ G D
Sbjct: 17  MAGVTDISFRGLCKEM-GAGIVCTEMVSAKALYYGSENTKELMRIADEEKPVSCQMFGND 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +    +  + F  N+    I++N+GCP+ ++ +   G+ LM NP +  + ++++ K 
Sbjct: 76  PEIMAYVTE--KHFNTNDDICIIDVNMGCPAPKIVKNGEGSALMKNPKLAYEIMSSIKKV 133

Query: 115 LSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
            + PVTVK R+G D++ I AV      K ++++GV+ I +H R    + +G +       
Sbjct: 134 ATKPVTVKFRMGFDEENINAV---EFAKIMEEAGVDAIAVHGRTRAQMYEGKA------- 183

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
              ++DI+ ++K+      IG NG +   ED + +LK   + DG+M+ R +         
Sbjct: 184 ---NWDIIRQVKEAVNIPVIG-NGDVFTAED-ALSLKNQTNCDGIMVARGS--------- 229

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-------LQQITRHMI 281
                 NP      ++    ++ +        D   RH +   K       ++++ +H  
Sbjct: 230 ----MGNPWIFKQIVQKLNGEEVYMPTPEEKIDMCIRHYNLSLKYDGEYKAVREMRKHAA 285

Query: 282 GLFHGFPNSRRCRHILTVEA 301
               G  N    ++ L +EA
Sbjct: 286 WYIKGLNNCTEVKNRLNLEA 305


>gi|311104203|ref|YP_003977056.1| tRNA-dihydrouridine synthase B [Achromobacter xylosoxidans A8]
 gi|310758892|gb|ADP14341.1| tRNA-dihydrouridine synthase B [Achromobacter xylosoxidans A8]
          Length = 341

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 109/245 (44%), Gaps = 19/245 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD + +
Sbjct: 21  TDRPFRQLCKKL-GAGYAVSEMAASNPKLWDSVKTSRRLNHDGEIAPISVQIAGADPAMM 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKALSIPV 119
            EAA      G   I++N+GCP  +V   + G+ L+ + D +    D +   C  L +PV
Sbjct: 80  AEAAVFNASKGARIIDINMGCPVKKVCNVASGSALLRHEDQIARILDAVVGACAPLDVPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G D +    ALR + K  + +G+  + +H R         + +      +YD +
Sbjct: 140 TLKTRTGWDRE-SRNALR-VAKMAENAGIAALTLHGRT--------RADLYTGEAEYDTI 189

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG +    +A  +L     D VMIGRAA     +   +D Y     
Sbjct: 190 RAVKAEL-KIPVVANGDITTPEKAKHVLDYTGADAVMIGRAAQGRPWIFREIDHYLRTGE 248

Query: 238 TGSSP 242
           T + P
Sbjct: 249 TLAPP 253


>gi|206561672|ref|YP_002232437.1| putative nitrogen regulation-related protein [Burkholderia
           cenocepacia J2315]
 gi|198037714|emb|CAR53657.1| putative nitrogen regulation-related protein [Burkholderia
           cenocepacia J2315]
          Length = 355

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 140/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PEMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQHVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANGFRH 304


>gi|327463514|gb|EGF09833.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1057]
          Length = 325

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +     A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSAQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|161525860|ref|YP_001580872.1| NifR3 family TIM-barrel protein [Burkholderia multivorans ATCC
           17616]
 gi|189349419|ref|YP_001945047.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans ATCC
           17616]
 gi|221202292|ref|ZP_03575326.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2M]
 gi|221209106|ref|ZP_03582100.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2]
 gi|221214496|ref|ZP_03587467.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD1]
 gi|160343289|gb|ABX16375.1| TIM-barrel protein, nifR3 family [Burkholderia multivorans ATCC
           17616]
 gi|189333441|dbj|BAG42511.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans ATCC
           17616]
 gi|221165753|gb|EED98228.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD1]
 gi|221171010|gb|EEE03463.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2]
 gi|221177866|gb|EEE10279.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2M]
          Length = 354

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 76/310 (24%), Positives = 142/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKKL-GAGYAVSEMVASNAQLWKSAKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G +      
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITIARLAEA---AGISMLTVHGRTRADLYRGEA------ 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               +Y+ +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 188 ----EYETIAAVKAA-VRIPVVANGDITSPAKAKAVLEATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANAFRH 304


>gi|332874803|ref|ZP_08442673.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6014059]
 gi|332737064|gb|EGJ68021.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6014059]
          Length = 348

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 80/327 (24%), Positives = 150/327 (45%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 24  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 83  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 142

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 143 VTLKTRLGFLNGQENILRVA-----KRAEEAGIAALALHGR--------TREDMYLNTAR 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  + KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 190 YELIKHV-KELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 248

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V +     +S     Y     +SG ++ +  +H+     G  +S   
Sbjct: 249 KTGEHLAAPNIEEVKEVLLGHLSELYQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEF 303

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMI 319
           R  +  VE  A  A   ++E+ FN ++
Sbjct: 304 RQNMYKVETTAEQAL--VVESYFNQLL 328


>gi|17987147|ref|NP_539781.1| nitrogen regulation protein NIFR3 [Brucella melitensis bv. 1 str.
           16M]
 gi|225852620|ref|YP_002732853.1| TIM-barrel protein nifR3 family protein [Brucella melitensis ATCC
           23457]
 gi|256044776|ref|ZP_05447680.1| TIM-barrel protein nifR3 family protein [Brucella melitensis bv. 1
           str. Rev.1]
 gi|256113675|ref|ZP_05454486.1| TIM-barrel protein nifR3 family protein [Brucella melitensis bv. 3
           str. Ether]
 gi|256263888|ref|ZP_05466420.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 2 str.
           63/9]
 gi|265991200|ref|ZP_06103757.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995036|ref|ZP_06107593.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 3 str.
           Ether]
 gi|17982812|gb|AAL52045.1| nitrogen regulation protein nifr3 [Brucella melitensis bv. 1 str.
           16M]
 gi|225640985|gb|ACO00899.1| TIM-barrel protein nifR3 family protein [Brucella melitensis ATCC
           23457]
 gi|262766149|gb|EEZ11938.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 3 str.
           Ether]
 gi|263001984|gb|EEZ14559.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263094019|gb|EEZ17953.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 2 str.
           63/9]
 gi|326538846|gb|ADZ87061.1| TIM-barrel protein nifR3 family protein [Brucella melitensis M5-90]
          Length = 333

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGTDIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 254 ANGILDYIIRHYEDMLDHYGSKI 276


>gi|260565621|ref|ZP_05836105.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 1 str.
           16M]
 gi|260151689|gb|EEW86783.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 1 str.
           16M]
          Length = 332

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGTDIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 253 ANGILDYIIRHYEDMLDHYGSKI 275


>gi|237744277|ref|ZP_04574758.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 7_1]
 gi|229431506|gb|EEO41718.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 7_1]
          Length = 308

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 115/254 (45%), Gaps = 43/254 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       +  A+QI G DI+K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIAKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    +++K RIG  +    + +  
Sbjct: 88  CGCPMKKIVNCGYGAALLREPEKIKRILSEIKSILNDDTKLSIKIRIGYKEPENYIQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + I   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEI---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF-----SNPLTGSSPI- 243
           F G +  LE +S +     +VDGVM+ R  + N  ++  + E         P T    I 
Sbjct: 195 FTGKD-ALEKISYS-----NVDGVMLARGIFGNPWLIRDIREILKYGEIKTPTTKEDKIN 248

Query: 244 -------KTRVDKD 250
                  +TRVD D
Sbjct: 249 MAIEHLKRTRVDND 262


>gi|325697325|gb|EGD39211.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK160]
          Length = 325

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|332365647|gb|EGJ43406.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK355]
          Length = 325

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A   +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKHRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|270263300|ref|ZP_06191570.1| tRNA-dihydrouridine synthase B [Serratia odorifera 4Rx13]
 gi|270042988|gb|EFA16082.1| tRNA-dihydrouridine synthase B [Serratia odorifera 4Rx13]
          Length = 321

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  + ++QI G D
Sbjct: 17  MAGITDRPFRTLCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAARINVAGGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILHAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          N
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|197119180|ref|YP_002139607.1| TIM barrel oxidoreductase NifR3 [Geobacter bemidjiensis Bem]
 gi|197088540|gb|ACH39811.1| TIM barrel oxidoreductase NifR3 [Geobacter bemidjiensis Bem]
          Length = 321

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 132/288 (45%), Gaps = 46/288 (15%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +TEM+  + + R  +K  ++L  S +++P+ +Q+ G D   L EAA++VE++G   I++N
Sbjct: 42  FTEMVSVNGLTREGQKSFDLLKSSPEDRPIGMQLFGDDPEMLAEAARLVEEYG-ELIDIN 100

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV---DDQIPAVALR 137
           +GCP  +V     G+ LM +P  VG  + ++  A  +P+T+K R G    DD    V   
Sbjct: 101 MGCPVRKVVGTGAGSALMKDPQKVGRIVRSVRAATKLPLTIKIRTGWVCGDDTFLEVG-- 158

Query: 138 NLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              +  ++ G + + +H  +R  + +G            D+  + E+K       IG +G
Sbjct: 159 ---RIAQEEGCDAVTLHPRSRAQMFEG----------KADWSRIGELKSALSIPVIG-SG 204

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            L   + A+ +L     D VM+ R A  N  +           L G  P    V +    
Sbjct: 205 DLFSAADAVGMLAETGCDSVMVARGAMGNPWIFREALSL----LAGEEPAPPTVQE---- 256

Query: 254 KISASMTDYAARHLH-----SGGK--LQQITRHMIGLFHGFPNSRRCR 294
           +++ S      RHL      +GG+  L ++ +H+     G P + + R
Sbjct: 257 RLAVSR-----RHLELFAEFAGGRVALMEMRKHLSWYSKGLPGAAQFR 299


>gi|119475082|ref|ZP_01615435.1| Dihydrouridine synthase TIM-barrel protein nifR3 [marine gamma
           proteobacterium HTCC2143]
 gi|119451285|gb|EAW32518.1| Dihydrouridine synthase TIM-barrel protein nifR3 [marine gamma
           proteobacterium HTCC2143]
          Length = 351

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 119/254 (46%), Gaps = 22/254 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    L+ +EM+ +D  L   +K+   L  S +  P ++QI G D
Sbjct: 10  MAGVTDLPFRQLCRRL-GAGLVVSEMVTSDTRLWHTRKSQQRLNHSGETGPRSVQIAGGD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA +    G   I++N+GCP+ +V + + G+ L+ +P +V D + A+  A+ +P
Sbjct: 69  AAMMAEAASMNVARGAQIIDINMGCPAKKVCKKAAGSALLKDPGLVTDILTAVIAAVDVP 128

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G      +   RN   + +  + +G+  + +H R    K           + +
Sbjct: 129 VTLKIRTGW-----STDYRNGVEIARIAEDAGIAALAVHGRTRACKFNG--------DAE 175

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK     + I  NG +    +AL ++     D VM+GRAA     +   +D + 
Sbjct: 176 YDTIAAIKSA-VSIPIIANGDITSPQKALAVMQYTGADAVMVGRAAQGQPWICGEIDHFL 234

Query: 234 SNPLTGSSPIKTRV 247
               T + P +  +
Sbjct: 235 RTGNTLAPPSRESI 248


>gi|24753769|gb|AAN64017.1|AF434658_14 NifR [Leptospira interrogans]
          Length = 329

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 109/214 (50%), Gaps = 15/214 (7%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           A  YTE +  D ++    K   +  +  +E+P+  QI G  +  + EAA+I+++   + I
Sbjct: 36  AFSYTEFVNTDELVHRAPKALKMFRYKLEERPITFQIFGNRLEIIAEAAEIIQELKPDII 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GC + +V     GA L+  P + G  I A+ K ++IPVT K RIG D    +    
Sbjct: 96  DLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAIKKRVNIPVTAKIRIGWDST--SRNYL 153

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K +++SGV+ + +H R         K+       D+D + EIK  N  + I  NG +
Sbjct: 154 EVSKILEESGVDALTVHGR--------TKEMAYTGFADWDAIGEIKV-NRKIPIFGNGDI 204

Query: 198 EDMSQA-LKILPS-VDGVMIGRAAYKNSAMLTTV 229
           +   +A  KI    +DGV+IGR A  N  + + V
Sbjct: 205 KSFQEANFKIDKYLLDGVLIGRNAIGNPWIFSGV 238


>gi|332143328|ref|YP_004429066.1| tRNA-dihydrouridine synthase B [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327553350|gb|AEB00069.1| tRNA-dihydrouridine synthase B [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 332

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 113/243 (46%), Gaps = 26/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L+ +EM+ ++  +    K+   +    +E   ++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGLVVSEMLSSNPKVWNTAKSQARMNHEGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   I++N+GCP+ +V++   G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PELMAQAAQFNVDNGAQIIDINMGCPAKKVNKKLAGSALLQYPDTVEAIVKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G + +      RN   + +  +++G+  + +H R    + KG +         
Sbjct: 136 VTLKIRTGWNPE-----NRNGVEIARIAEQNGIQSLAVHGRTRACMYKGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y  +  IK       I  NG +    +A ++L     DGVMIGR A     +   +  
Sbjct: 182 -EYSTIRRIKAAISIPVIA-NGDITSPQKAQEVLNYTGADGVMIGRGAQGKPWIFNQIQH 239

Query: 232 YFS 234
           Y  
Sbjct: 240 YLE 242


>gi|261314157|ref|ZP_05953354.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M163/99/10]
 gi|261317754|ref|ZP_05956951.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis B2/94]
 gi|261296977|gb|EEY00474.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis B2/94]
 gi|261303183|gb|EEY06680.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M163/99/10]
          Length = 332

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 253 ANGILDYIIRHYEDMLDHYGSKI 275


>gi|332360096|gb|EGJ37910.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1056]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|332358130|gb|EGJ35962.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK49]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|327467879|gb|EGF13369.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK330]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAADFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|158522876|ref|YP_001530746.1| nifR3 family TIM-barrel protein [Desulfococcus oleovorans Hxd3]
 gi|158511702|gb|ABW68669.1| putative TIM-barrel protein, nifR3 family [Desulfococcus oleovorans
           Hxd3]
          Length = 326

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/220 (29%), Positives = 109/220 (49%), Gaps = 18/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKL 62
           TD  +R  A+     AL+Y+EM+ +  +    +K   +L  + +E P A+QI G   + +
Sbjct: 21  TDAPFRRLAKA-AGCALVYSEMVSSHGLFYQSEKTGAMLRTTPEEAPFAVQIFGGKPAVM 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             AA +V+  G + I++N GC   ++ +   GA LM +  +  + I A+  A+SIP+T+K
Sbjct: 80  GRAAAMVQASGAHMIDINFGCSVKKILKSGAGAALMKDLPLAAEVIQAVRDAVSIPLTIK 139

Query: 123 CRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R G + D   A  L  + ++    GVN + +H R A  +G            D+ ++  
Sbjct: 140 MRSGWNPDGSDAFHLAEIAEA---RGVNAVALHPRTAT-QGFG-------GTADWSLIAA 188

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           +K+      IG NG +     A ++L     D VM+GRAA
Sbjct: 189 LKQRTGLPVIG-NGDIVLPEDARRMLDQTGCDAVMVGRAA 227


>gi|324989868|gb|EGC21811.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK353]
          Length = 317

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 184 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 242


>gi|148560180|ref|YP_001259040.1| nitrogen regulation protein Nifr3 [Brucella ovis ATCC 25840]
 gi|254706696|ref|ZP_05168524.1| TIM-barrel protein nifR3 family protein [Brucella pinnipedialis
           M163/99/10]
 gi|254710196|ref|ZP_05172007.1| TIM-barrel protein nifR3 family protein [Brucella pinnipedialis
           B2/94]
 gi|256031690|ref|ZP_05445304.1| TIM-barrel protein nifR3 family protein [Brucella pinnipedialis
           M292/94/1]
 gi|256061202|ref|ZP_05451354.1| TIM-barrel protein nifR3 family protein [Brucella neotomae 5K33]
 gi|256369546|ref|YP_003107056.1| nitrogen regulation protein Nifr3 [Brucella microti CCM 4915]
 gi|261325210|ref|ZP_05964407.1| nifR3 family TIM-barrel protein [Brucella neotomae 5K33]
 gi|265988785|ref|ZP_06101342.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M292/94/1]
 gi|148371437|gb|ABQ61416.1| nitrogen regulation protein Nifr3 [Brucella ovis ATCC 25840]
 gi|255999708|gb|ACU48107.1| nitrogen regulation protein Nifr3 [Brucella microti CCM 4915]
 gi|261301190|gb|EEY04687.1| nifR3 family TIM-barrel protein [Brucella neotomae 5K33]
 gi|264660982|gb|EEZ31243.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M292/94/1]
          Length = 333

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 254 ANGILDYIIRHYEDMLDHYGSKI 276


>gi|319956594|ref|YP_004167857.1| tim-barrel protein, nifr3 family [Nitratifractor salsuginis DSM
           16511]
 gi|319418998|gb|ADV46108.1| TIM-barrel protein, nifR3 family [Nitratifractor salsuginis DSM
           16511]
          Length = 320

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/282 (25%), Positives = 132/282 (46%), Gaps = 27/282 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + L  +EMI ++A+   + K +  L  S  E P ++QI G+D
Sbjct: 15  LAGFTDLPFRSMVKKFDVD-LTVSEMISSNALAHENAKTLKMLEKSPLEDPYSVQIAGSD 73

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A  ++    G + ++LN GCP+ +V     G+ L+ +P+ +G  +  +    + 
Sbjct: 74  PETIKRALDVINAREGIDIVDLNCGCPAPKVFNNLQGSALLGDPEKLGRAVETIKAYSNK 133

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P T VK R+GV ++        L K I+++G + I +H R    +  +P        +DY
Sbjct: 134 PYTSVKMRLGVREKNHV----ELAKVIEEAGADFIAVHGRTRAGRYKAP--------VDY 181

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + E+ KE   + +  NG ++   +A  ++     DG+MIGRAA     +   + E   
Sbjct: 182 DAIREV-KEAVRIPVIANGDIDSPQKARWVREYTGCDGIMIGRAAVGRPWIFAQIKEGLD 240

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAA----RHLHSGGK 272
            P   S  +   V  + + ++ A   DY      +HLH+  K
Sbjct: 241 EP---SVDLIREVVLEHFDQMIAHYGDYGVFLFRKHLHTYSK 279


>gi|326409138|gb|ADZ66203.1| TIM-barrel protein nifR3 family protein [Brucella melitensis M28]
          Length = 319

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 30  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGTDIIDI 89

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 90  NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 147

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 148 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 196

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 197 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 239

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 240 ANGILDYIIRHYEDMLDHYGSKI 262


>gi|312863979|ref|ZP_07724215.1| TIM-barrel protein, nifR3 family [Streptococcus vestibularis F0396]
 gi|311100392|gb|EFQ58599.1| TIM-barrel protein, nifR3 family [Streptococcus vestibularis F0396]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 114/240 (47%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D    +A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDS--DLAVENALAA-ESAGVSALAMHGRT--------REQMYTGYCDHE 191

Query: 178 IVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  + K    + FIG NG +  +  A  ++    VD VM+GRA   N  + T ++ +F 
Sbjct: 192 TLARVAKAITKIPFIG-NGDVRSVQDAKLMIEELGVDAVMVGRAVMNNPYIFTQINHFFE 250


>gi|291534002|emb|CBL07115.1| tRNA-U20-dihydrouridine synthase [Megamonas hypermegale ART12/1]
          Length = 318

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/255 (25%), Positives = 120/255 (47%), Gaps = 21/255 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TD  Y   A+ +    L+Y+EM+    I   +++ +    T  +++PLA+Q+   +
Sbjct: 17  MAGVTDTAYCILAQRM-GCGLVYSEMVSDQGINFHNERTLEMLKTVPEQRPLAIQLFSGN 75

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
             ++ +AA  V      + I++N+GCP+ ++   + G+ LM +P +  + + A  +A+  
Sbjct: 76  PERMYKAASFVASLNCCDMIDINMGCPAPKIVRNNEGSALMKDPVLAYEIMCATREAVKD 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVTVK R G D +   V    +    +K+G++ I +H R         ++     + D+
Sbjct: 136 MPVTVKMRKGWDSEHCNVV--EMAGLAQKAGLDAIAVHGRT--------REEFYRGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ E+K+      IG NG +        I      D VMIGR A  N  +     E+  
Sbjct: 186 DIIREVKQAVDIPVIG-NGDVRTCQDLKNIFERTGCDAVMIGRGAQGNPWIFRRFKEFL- 243

Query: 235 NPLTGSSPIKTRVDK 249
              TG  P +  +D+
Sbjct: 244 --FTGVDPGEPSIDE 256


>gi|56416705|ref|YP_153779.1| hypothetical protein AM492 [Anaplasma marginale str. St. Maries]
 gi|56387937|gb|AAV86524.1| hypothetical protein AM492 [Anaplasma marginale str. St. Maries]
          Length = 320

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 105/216 (48%), Gaps = 42/216 (19%)

Query: 21  LLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           LL +EMI + A++    +  +K+ +G +T     A+Q+ G     + EAAKI +D G   
Sbjct: 36  LLVSEMIASRAMIIKTRQSLQKSDVGANT-----AVQLAGCVPEIMAEAAKINQDMGARS 90

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPA 133
           I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G    D   P 
Sbjct: 91  IDINFGCPVKKIVDGHAGSALMKDEEKATKIMESVVKAVTIPVTVKMRMGWSATDLNAP- 149

Query: 134 VALRNLVKSIKKSGVNGIWIHA--RKAILKGLSP-------KDNRKIPNLDYDIVYEIKK 184
                L K  +  G+  + +H   R  +  G +        KD  KIP +          
Sbjct: 150 ----RLAKIAEDVGIQMVTVHGRTRTQMFSGTADWKFIKCVKDCVKIPVI---------- 195

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
            N D+       L+D++ AL  L   DGVMIGR AY
Sbjct: 196 ANGDIRT-----LQDITSALS-LSGADGVMIGRGAY 225


>gi|324992591|gb|EGC24512.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK405]
          Length = 317

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 184 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 242


>gi|227552753|ref|ZP_03982802.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257888745|ref|ZP_05668398.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897323|ref|ZP_05676976.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|257899874|ref|ZP_05679527.1| dihydrouridine synthase [Enterococcus faecium Com15]
 gi|293378937|ref|ZP_06625092.1| dihydrouridine synthase (Dus) [Enterococcus faecium PC4.1]
 gi|227178153|gb|EEI59125.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257824799|gb|EEV51731.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257833888|gb|EEV60309.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|257837786|gb|EEV62860.1| dihydrouridine synthase [Enterococcus faecium Com15]
 gi|292642478|gb|EFF60633.1| dihydrouridine synthase (Dus) [Enterococcus faecium PC4.1]
          Length = 327

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  K   
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKTGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D    + L     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRRTGEELAEKYGVDGIMIGRGIFKN 238


>gi|309799512|ref|ZP_07693742.1| tRNA-dihydrouridine synthase [Streptococcus infantis SK1302]
 gi|308116868|gb|EFO54314.1| tRNA-dihydrouridine synthase [Streptococcus infantis SK1302]
          Length = 234

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 113/226 (50%), Gaps = 17/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K +  L     E P+++Q+ G+D
Sbjct: 1   MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 60  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 120 PLTVKMRTGWSD--PSLAVENALAA-EAAGVSALAMHGR--------TREQMYTGHADLE 168

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYK 221
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA +
Sbjct: 169 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAME 214


>gi|259501966|ref|ZP_05744868.1| tRNA-dihydrouridine synthase [Lactobacillus antri DSM 16041]
 gi|259170143|gb|EEW54638.1| tRNA-dihydrouridine synthase [Lactobacillus antri DSM 16041]
          Length = 332

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 98/215 (45%), Gaps = 16/215 (7%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNV 81
           EMI    I+  ++K  N++     E P+ +QI G     LVEAAK V++    + I++N+
Sbjct: 42  EMISDRGIMYHNQKTLNMMDVDPTEHPMGIQIFGGTKETLVEAAKYVDEHTAADVIDINM 101

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   GA  +L+P  V + ++ +  A+  PVTVK R G DD+        L  
Sbjct: 102 GCPVNKVVKTDAGARWLLDPQKVYEMVSYVTDAVKKPVTVKMRTGWDDKHIYAVENALAA 161

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
               +    +    RK +  G          + D++I+ E+  +    F+  NG +    
Sbjct: 162 ERAGAAAIAMHGRTRKQMYTG----------HADWNILKEVANQLTIPFMA-NGDIRTPE 210

Query: 202 QALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            A K+L        MIGRAA  N  MLT    Y  
Sbjct: 211 DAKKVLEMTGATAAMIGRAAMGNPWMLTRTAHYLE 245


>gi|325695385|gb|EGD37285.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK150]
          Length = 326

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|289549381|ref|YP_003470285.1| tRNA dihydrouridine synthase B [Staphylococcus lugdunensis
           HKU09-01]
 gi|315659951|ref|ZP_07912809.1| dihydrouridine synthase [Staphylococcus lugdunensis M23590]
 gi|289178913|gb|ADC86158.1| tRNA dihydrouridine synthase B [Staphylococcus lugdunensis
           HKU09-01]
 gi|315494852|gb|EFU83189.1| dihydrouridine synthase [Staphylococcus lugdunensis M23590]
          Length = 326

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSFGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       ++ +K + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYD---IDEWKDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++  IK       P+  + +NG + D    +++     +DGVMIGR  + N
Sbjct: 187 ELIEAIKHMRDEIAPNTLLTINGDIPDRKTGMELATKYGIDGVMIGRGIFHN 238


>gi|306841846|ref|ZP_07474528.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO2]
 gi|306288073|gb|EFM59470.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO2]
          Length = 320

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 105/205 (51%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 31  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 90

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 91  NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 148

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G++          D+D ++ + ++   + +  NG +
Sbjct: 149 ARRAEDAGIAMVTVHGRTRCQFYEGMA----------DWDAIHAV-RDAVRIPLVANGDV 197

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
              + A +IL     D VM+GRA+Y
Sbjct: 198 SSRADAEEILRRSGADAVMVGRASY 222


>gi|296112003|ref|YP_003622385.1| transcription regulator [Leuconostoc kimchii IMSNU 11154]
 gi|295833535|gb|ADG41416.1| transcription regulator [Leuconostoc kimchii IMSNU 11154]
          Length = 374

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 101/212 (47%), Gaps = 21/212 (9%)

Query: 21  LLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           + YTE   A +++    K      L  +  E+    QI G+   ++  AAK +   GY  
Sbjct: 56  VYYTEFTNASSMVHPQAKFSVQGRLAVAEHEQQPVAQIWGSHPEEIAGAAKKLPSMGYQA 115

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N+GCP + V + + G+ L+  PD+  + +AA  K   +PV+VK R+G          
Sbjct: 116 VDINMGCPDSSVIKNNAGSALIRTPDLASEIVAA-AKLSGLPVSVKTRLGF---YKPEEF 171

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDY--DIVYEIKKENPDLFIGL 193
           R  +  I K  V  + +H R       S K+  K P + +Y  +I+       P   I +
Sbjct: 172 REWLPIILKQNVAVLTVHLR-------SRKEMSKAPAHEEYIDEILAMRDAIAPQTLIQI 224

Query: 194 NGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
           NG ++  S  L+++     +DG+MIGR  ++N
Sbjct: 225 NGDIKTRSAGLQLVKRHSGIDGIMIGRGIFEN 256


>gi|291483244|dbj|BAI84319.1| hypothetical protein BSNT_01340 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 332

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P +  + I A  KA  
Sbjct: 86  DKPENFRKMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPAVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R       +  +  K+ +  +
Sbjct: 145 LPVSVKTRLGYTD---VDEWREWLTHILKQDIANLSIHLR-------TRAEMSKV-DAHW 193

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 194 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTN 245


>gi|242243139|ref|ZP_04797584.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis W23144]
 gi|242233391|gb|EES35703.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis W23144]
 gi|319399949|gb|EFV88191.1| dihydrouridine synthase (Dus) family protein [Staphylococcus
           epidermidis FRI909]
          Length = 326

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSDDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSIGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYD---IDEWRDWLKHVFEQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++  IK       P+  + +NG + D    L++     +DG+MIGR  + N
Sbjct: 187 ELIEAIKTLRDEIAPNTLLTINGDIPDRQTGLELANKYGIDGIMIGRGIFHN 238


>gi|325686690|gb|EGD28716.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK72]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|261752425|ref|ZP_05996134.1| nifR3 family TIM-barrel protein [Brucella suis bv. 5 str. 513]
 gi|261742178|gb|EEY30104.1| nifR3 family TIM-barrel protein [Brucella suis bv. 5 str. 513]
          Length = 332

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 118/251 (47%), Gaps = 35/251 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELYNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARH 266
           +  + DY  RH
Sbjct: 253 ANGILDYIIRH 263


>gi|260459491|ref|ZP_05807746.1| TIM-barrel protein, nifR3 family [Mesorhizobium opportunistum
           WSM2075]
 gi|259035045|gb|EEW36301.1| TIM-barrel protein, nifR3 family [Mesorhizobium opportunistum
           WSM2075]
          Length = 340

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 104/219 (47%), Gaps = 15/219 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADISKLV 63
           TD+ +R  A       L+ +EM+ +  + +G     L       P+ + Q+ G +   + 
Sbjct: 31  TDQPFRQRAHA-HGAGLVVSEMVASGELAKGRAGFDLRIRHSGLPVHMVQLAGREAIHMA 89

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I    G + I++N+GCP+ +V  G  G+ LML+ D     I A+  A+ +PVTVK 
Sbjct: 90  EGARIAAGEGADIIDINMGCPAKKVTGGYAGSALMLDLDHALSLIEAVVGAVKVPVTVKM 149

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D+   A+    L +  +++GV+ + +H R          D R I  +         
Sbjct: 150 RLGWDEG--ALNAPTLARRAEQAGVSMVTVHGRTRCQFYQGKADWRAIARV--------- 198

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           KE   + +  NG +   ++A  IL     D VM+GRA Y
Sbjct: 199 KEAVSIPVVANGDVCSPAEAAAILDQSGADAVMVGRAHY 237


>gi|182678493|ref|YP_001832639.1| NifR3 family TIM-barrel protein [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182634376|gb|ACB95150.1| TIM-barrel protein, nifR3 family [Beijerinckia indica subsp. indica
           ATCC 9039]
          Length = 350

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 120/275 (43%), Gaps = 23/275 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A+      L+ +EM+ +D   +GD  N L    Q  +   +QI G D 
Sbjct: 42  MAGITDLGMRRLAQQF-GAGLVVSEMVSSDEYAKGDAANRLKAGGQGIEQSVVQIAGCDP 100

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+  E  G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+ +PV
Sbjct: 101 VAMGEAARQAEGSGAAMIDINMGCPARKVIGGYAGSHLMRDLDRAVALIRAVIGAVRVPV 160

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
           +VK R+G DDQ    A  +L +  +  GV  + +H R      +G            D+ 
Sbjct: 161 SVKMRLGWDDQQRNAA--DLGRLAEAEGVAMLSVHGRTRCQFYRG----------KADWA 208

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  + KE   + + +NG     + A  +L     D VMIGRAA     ++  +  Y   
Sbjct: 209 AVRAV-KEAVTIPVVVNGDCTGPAVASAMLAQSGADAVMIGRAAVGKPWLVGDIAYYLET 267

Query: 236 PLTGSSP---IKTRVDKDFWRK-ISASMTDYAARH 266
                 P   I+     D +   +S   T++  RH
Sbjct: 268 GEVRPEPSAQIQAEATLDHYETLLSLYGTEHGVRH 302


>gi|254453092|ref|ZP_05066529.1| tRNA-dihydrouridine synthase B [Octadecabacter antarcticus 238]
 gi|198267498|gb|EDY91768.1| tRNA-dihydrouridine synthase B [Octadecabacter antarcticus 238]
          Length = 333

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 112/239 (46%), Gaps = 27/239 (11%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           F A  + +  +   EM+ A   +R  +K  LGF+      A+Q+ G +   + EAA+ VE
Sbjct: 34  FGAGWVVSEMIASQEMVQAKPGVR--EKAELGFNQANT--AVQLAGREAHWMAEAARHVE 89

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
             G   I++N+GCP+ +V  G  G+ L+ + D     I A+  A+ IPVT+K R+G DD 
Sbjct: 90  ANGAAMIDINMGCPAKKVTSGYSGSALLRDLDHALTLIDAVVGAVDIPVTLKTRLGWDDA 149

Query: 131 I---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           +   P +A+R      + +G+  I IH R      KG +          ++D +  +K  
Sbjct: 150 LLNAPDLAVR-----AENAGIARIVIHGRTRCQFYKGRA----------NWDAIALVKNA 194

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                I  NG + D S A   L +   DG+MIGR A     ML  V    S  +  + P
Sbjct: 195 VSIPVIA-NGDIIDASTAKTALDASGADGLMIGRGAQGCPWMLRDVAAQLSGNVAPAPP 252


>gi|299144544|ref|ZP_07037623.1| tRNA-dihydrouridine synthase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
 gi|298517632|gb|EFI41372.1| tRNA-dihydrouridine synthase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
          Length = 313

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 75/303 (24%), Positives = 140/303 (46%), Gaps = 33/303 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           +  +TD  +R       N  +  TEMI A A+  GDKK   +L  S  EK +A+QI G D
Sbjct: 13  LAGYTDIAFREICSQ-KNAYMTVTEMISAKALYYGDKKTNELLKVSPFEKNVAVQIFGDD 71

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +    K  +    ++ I++N+GCP+ ++ + + G+ L+  P++    I ++ +  ++
Sbjct: 72  PDIMGYVVKNSLNSLNFSCIDINMGCPAPKIVKNNNGSALLDQPNLAYSIIRSVVENSNV 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PV+VK R G+ +         + +  +K+G + I +H   R+    GLS          D
Sbjct: 132 PVSVKIRKGIRN----TNSMEVARLAQKAGASFITVHGRTREEYYSGLS----------D 177

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +  E     IG NG ++    A++ +    V GV IGR A  N  +    DE +
Sbjct: 178 WNYIKSVVDELTIPVIG-NGDVQSYEDAMEKIKFSGVSGVSIGRGAIGNPFIF---DEIY 233

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSR 291
              +  +    T ++     KI  +++   +   + G K+   ++ +H +G F G   S+
Sbjct: 234 KKSIGCNYEKPTDLE-----KIEMALSHLKSNCAYKGEKIGILEMRKHFVGYFKGMKGSK 288

Query: 292 RCR 294
             R
Sbjct: 289 ELR 291


>gi|294852457|ref|ZP_06793130.1| tRNA-dihydrouridine synthase B [Brucella sp. NVSL 07-0026]
 gi|294821046|gb|EFG38045.1| tRNA-dihydrouridine synthase B [Brucella sp. NVSL 07-0026]
          Length = 304

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRHSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 253 ANGILDYIIRHYEDMLDHYGSKI 275


>gi|327459994|gb|EGF06333.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1]
 gi|327488584|gb|EGF20384.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1058]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVHDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|16077870|ref|NP_388684.1| tRNA-dihydrouridine synthase 2 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221308639|ref|ZP_03590486.1| hypothetical protein Bsubs1_04473 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312963|ref|ZP_03594768.1| hypothetical protein BsubsN3_04424 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317889|ref|ZP_03599183.1| hypothetical protein BsubsJ_04368 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322162|ref|ZP_03603456.1| hypothetical protein BsubsS_04464 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|39930914|sp|O31546|DUS2_BACSU RecName: Full=Probable tRNA-dihydrouridine synthase 2
 gi|2633127|emb|CAB12632.1| tRNA-dihydrouridine synthase 2 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|2780398|dbj|BAA24299.1| YfjN [Bacillus subtilis]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 104/233 (44%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P +  + I A  KA  
Sbjct: 79  DKPENFRKMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPAVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       R  +  I K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGYTD---VDEWREWLTHILKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTN 238


>gi|254701862|ref|ZP_05163690.1| nitrogen regulation protein NifR3 [Brucella suis bv. 5 str. 513]
          Length = 333

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 118/251 (47%), Gaps = 35/251 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELYNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARH 266
           +  + DY  RH
Sbjct: 254 ANGILDYIIRH 264


>gi|269122887|ref|YP_003305464.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
 gi|268314213|gb|ACZ00587.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
          Length = 305

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 104/216 (48%), Gaps = 19/216 (8%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           +TEM+  D +L  +   IL          +QI G DI  + +AAK +E  G  EINLN G
Sbjct: 31  FTEMVSVDKLLYKEVPKILKLRENN---IVQIFGKDIYLMQKAAKYIESMGVKEINLNCG 87

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLV 140
           CP  ++     G+ L+ +P  + + + A+ + L     +++K R+G D     + +  + 
Sbjct: 88  CPMKKIVNSGHGSALIKDPRKIEEILTALREVLDPKTALSLKIRVGYDKPENYLEIAKIA 147

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           + +K S    I IH R         ++ +     D+  + E+ K+N ++ +  NG + D 
Sbjct: 148 EKLKCS---NIIIHGR--------TREQKYSGEADWKYIKEV-KDNVNIKVIGNGDIFDA 195

Query: 201 SQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             A++ +   +VDG+M+ R    N  +++ + E F 
Sbjct: 196 KNAIEKIRETNVDGIMLARGILGNPWLISQIKELFE 231


>gi|326692782|ref|ZP_08229787.1| probable tRNA-dihydrouridine synthase [Leuconostoc argentinum KCTC
           3773]
          Length = 374

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 95/184 (51%), Gaps = 20/184 (10%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + +P+A QI G+    +  AAK++ D GY  ++LN+GCP   V +   G+ L+ + D+  
Sbjct: 86  ETQPVA-QIWGSRPEDIAGAAKLLPDMGYRAVDLNMGCPDPTVVKNGAGSDLIRHQDLAA 144

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             ++A  K   +PV+VK R+G  D +     R+ +  I +  V  + +H R       S 
Sbjct: 145 QLVSA-AKESGLPVSVKTRLGFYDPM---EFRDWLPVILQQDVAVLTVHLR-------SR 193

Query: 166 KDNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRA 218
           K+  K P   ++++ EI        P++ + +NG ++  ++     K  P VDG+MIGR 
Sbjct: 194 KEMSKAP-AHFELIDEIVAMRDAIAPNILLQINGDIKSRAEGEALAKAHPGVDGIMIGRG 252

Query: 219 AYKN 222
            ++N
Sbjct: 253 IFEN 256


>gi|332995671|gb|AEF05726.1| tRNA-dihydrouridine synthase B [Alteromonas sp. SN2]
          Length = 332

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 115/241 (47%), Gaps = 22/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  +    K+   +    +E   ++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAGLVVSEMLSSNPKVWNTAKSQARMNHEGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P  V   I A+  A+ +P
Sbjct: 76  PELMAQAAQFNVENGAQIIDINMGCPAKKVNKKLAGSALLQYPSTVESIIKAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G + D    V +  +    +++G+  + +H R    + KG +          +
Sbjct: 136 VTLKIRTGWNTDNRNGVEIARIA---EQNGIQSLAVHGRTRACMYKGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  I KE   + +  NG +    +A ++L     DGVMIGR A  N  +   +  Y 
Sbjct: 183 FDTIRRI-KEAISIPVIANGDITSPEKAQQVLNCTGADGVMIGRGAQGNPWIFKEILHYL 241

Query: 234 S 234
            
Sbjct: 242 E 242


>gi|323350640|ref|ZP_08086302.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis VMC66]
 gi|322123322|gb|EFX95007.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis VMC66]
          Length = 325

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVHDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|72008833|ref|XP_786210.1| PREDICTED: similar to MGC79829 protein [Strongylocentrotus
           purpuratus]
 gi|115930963|ref|XP_001189238.1| PREDICTED: similar to MGC79829 protein [Strongylocentrotus
           purpuratus]
          Length = 351

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 109/238 (45%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + L +T MIV D+ ++  K     F++ E  +PL +Q   ++
Sbjct: 25  MVRYSKLAFRTLVRSYDCD-LTFTPMIVCDSFVKSAKARDSEFTSNEGDRPLIVQFAASN 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              L +AA++V  +  + ++LN GCP        +GACL+ +PD++ D +      +   
Sbjct: 84  AKDLADAAELVARYT-DGVDLNCGCPQRWAVAEGYGACLIKHPDLIKDMVQQTWNRVDRS 142

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K R+  D +        L +  + +GV+ I +H R    +G  P D+  I    
Sbjct: 143 DFTTSIKIRLHKDIRETV----ELCRRAEHAGVSWITVHGRTKEQRG-EPADHDAI---- 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
                 I KE   + +  NG ++ M    +I+    VDGVM  R   +N AM    D+
Sbjct: 194 -----RIIKEGVGVPVVANGDVKLMEDVRRIVEQTGVDGVMSARGILRNPAMYAGYDD 246


>gi|242372562|ref|ZP_04818136.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis M23864:W1]
 gi|242349779|gb|EES41380.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis M23864:W1]
          Length = 326

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 106/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  K   
Sbjct: 79  DKPEQFREMSIGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQA-TKEGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       ++ +K + +  +  + IH R       S K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYYD---IDEWKDWLKHVFEQDIANLSIHLR-------SRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++  IK       PD  + +NG + D    +++     +DGVMIGR  + N
Sbjct: 187 ELIEAIKNLRDEIAPDTLLTINGDIPDRQTGMELATKYGIDGVMIGRGIFNN 238


>gi|209885217|ref|YP_002289074.1| probable tRNA-dihydrouridine synthase [Oligotropha carboxidovorans
           OM5]
 gi|209873413|gb|ACI93209.1| probable tRNA-dihydrouridine synthase [Oligotropha carboxidovorans
           OM5]
          Length = 343

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 108/239 (45%), Gaps = 22/239 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKI 68
           R  ARL     L+ +EM  +D + RG   ++L   ++   P  +Q+ G +   + E A+I
Sbjct: 37  RVAARL--GAGLVVSEMTASDDLARGRPMSVLRCEASGVGPHVVQLAGCETKWMAEGARI 94

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G D
Sbjct: 95  AEGGGADIIDINMGCPARHVTGGQSGSALMRDLDHAMALIEATIAAVKVPVTLKMRLGWD 154

Query: 129 D---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
                 P +A R+ V  I+   V+G     R    KG            D+  V  + +E
Sbjct: 155 HASLNAPELARRSEVAGIRMVTVHG---RTRCQFYKG----------EADWQAVRAV-RE 200

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
              + + +NG +     A++ L +   D VMIGR A     +   +    +   + + P
Sbjct: 201 AIRIPLVVNGDIATYDDAVEALAASGADAVMIGRGAQGRPWLPGQIGRRLAGGASETDP 259


>gi|170099590|ref|XP_001881013.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164643692|gb|EDR07943.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 234

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 115/238 (48%), Gaps = 33/238 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----------EKPL 50
           MV   D  +R   R     +L YT+M++ D IL  + ++ L +  +          E+P+
Sbjct: 13  MVKQADGPFRLLVRKY-GASLTYTQMLLPDRIL--NDQDYLEYHLRDLSIASDDGLERPV 69

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCI 108
            +Q+ G D   +V+A + ++    + I+LN+GCP     +G FGA L+   N  +V + +
Sbjct: 70  VIQLCGHDPQTIVKAGRKLQGH-CDAIDLNLGCPQESARDGHFGAYLLGQKNWPLVEEIV 128

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +AM  + S+PVT K R+      P+ A  +L + ++  GV+ + +HAR    +    +  
Sbjct: 129 SAMSSSFSVPVTAKLRLCQ----PSHATLDLSQRLEACGVSWVTLHARNVSAR----RRR 180

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQAL--KILPSVDGVMIGRAAYKN 222
           +   NLD     E+K+   +L + +  NG + + S  L        DGVM+G     N
Sbjct: 181 QGSANLD-----EVKRLKGNLQVPVVSNGNVREFSDLLANTEYTGADGVMVGETLLGN 233


>gi|260546585|ref|ZP_05822324.1| nitrogen regulation protein NifR3 [Brucella abortus NCTC 8038]
 gi|260754862|ref|ZP_05867210.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 6 str. 870]
 gi|260758079|ref|ZP_05870427.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 4 str. 292]
 gi|260761903|ref|ZP_05874246.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 2 str.
           86/8/59]
 gi|261214113|ref|ZP_05928394.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 3 str. Tulya]
 gi|297248433|ref|ZP_06932151.1| tRNA-dihydrouridine synthase B [Brucella abortus bv. 5 str. B3196]
 gi|260095635|gb|EEW79512.1| nitrogen regulation protein NifR3 [Brucella abortus NCTC 8038]
 gi|260668397|gb|EEX55337.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 4 str. 292]
 gi|260672335|gb|EEX59156.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260674970|gb|EEX61791.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 6 str. 870]
 gi|260915720|gb|EEX82581.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 3 str. Tulya]
 gi|297175602|gb|EFH34949.1| tRNA-dihydrouridine synthase B [Brucella abortus bv. 5 str. B3196]
          Length = 332

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 118/251 (47%), Gaps = 35/251 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARH 266
           +  + DY  RH
Sbjct: 253 ANGILDYIIRH 263


>gi|62290033|ref|YP_221826.1| NifR3, nitrogen regulation protein Nifr3 [Brucella abortus bv. 1
           str. 9-941]
 gi|82699960|ref|YP_414534.1| hypothetical protein BAB1_1142 [Brucella melitensis biovar Abortus
           2308]
 gi|189024273|ref|YP_001935041.1| nitrogen regulation protein NifR3 [Brucella abortus S19]
 gi|237815542|ref|ZP_04594539.1| TIM-barrel protein, nifR3 family [Brucella abortus str. 2308 A]
 gi|254689345|ref|ZP_05152599.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 6 str. 870]
 gi|254693829|ref|ZP_05155657.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697478|ref|ZP_05159306.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254730375|ref|ZP_05188953.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 4 str. 292]
 gi|256257591|ref|ZP_05463127.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 9 str. C68]
 gi|260883874|ref|ZP_05895488.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 9 str. C68]
 gi|62196165|gb|AAX74465.1| NifR3, nitrogen regulation protein Nifr3 [Brucella abortus bv. 1
           str. 9-941]
 gi|82616061|emb|CAJ11098.1| Protein of unknown function UPF0034:FMN/related compound-binding
           core:Putative TIM-barrel protein nifR3 family [Brucella
           melitensis biovar Abortus 2308]
 gi|189019845|gb|ACD72567.1| nitrogen regulation protein NifR3 [Brucella abortus S19]
 gi|237788840|gb|EEP63051.1| TIM-barrel protein, nifR3 family [Brucella abortus str. 2308 A]
 gi|260873402|gb|EEX80471.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 9 str. C68]
          Length = 333

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 118/251 (47%), Gaps = 35/251 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARH 266
           +  + DY  RH
Sbjct: 254 ANGILDYIIRH 264


>gi|169343168|ref|ZP_02864189.1| putative dihydrouridine synthase [Clostridium perfringens C str.
           JGS1495]
 gi|169298720|gb|EDS80796.1| putative dihydrouridine synthase [Clostridium perfringens C str.
           JGS1495]
          Length = 326

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 74/324 (22%), Positives = 147/324 (45%), Gaps = 58/324 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    ++ TEM+ A A+  G +  K ++  + +EKP++ Q+ G D
Sbjct: 17  MAGVTDISFRGLCKEM-GVGIVCTEMVSAKALYYGSENTKELMRIADEEKPVSCQMFGND 75

Query: 59  ISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +    +  + F  N+    I++N+GCP+ ++ +   G+ LM NP +  + ++++ K 
Sbjct: 76  PEIMAYVTE--KHFNTNDDICIIDVNMGCPAPKIVKNGEGSALMKNPKLAYEIMSSIKKV 133

Query: 115 LSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKI 171
            + PVTVK R+G D++ I AV      K ++++GV+ I +H R    + +G +       
Sbjct: 134 ATKPVTVKFRMGFDEENINAV---EFAKIMEEAGVDAIAVHGRTRAQMYEGKA------- 183

Query: 172 PNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
              ++DI+ ++K+        N D+F       ED + +LK   + DG+M+ R +     
Sbjct: 184 ---NWDIIRQVKEAVNIPVIGNGDVFTA-----ED-ALSLKNQTNCDGIMVARGS----- 229

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-------LQQIT 277
                     NP      ++    ++ +        D   RH +   K       ++++ 
Sbjct: 230 --------MGNPWIFKQIVQKLNGEEVYMPTPEEKIDMCIRHYNLSLKYDGEYKAVREMR 281

Query: 278 RHMIGLFHGFPNSRRCRHILTVEA 301
           +H      G  N    ++ L +EA
Sbjct: 282 KHAAWYIKGLNNCTEVKNRLNLEA 305


>gi|163741114|ref|ZP_02148506.1| tRNA-dihydrouridine synthase, putative [Phaeobacter gallaeciensis
           2.10]
 gi|161385467|gb|EDQ09844.1| tRNA-dihydrouridine synthase, putative [Phaeobacter gallaeciensis
           2.10]
          Length = 319

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 140/307 (45%), Gaps = 32/307 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKL 62
           TDR +R   R      L+ +EM+ +  +++     +     S   +  A+QI G D   +
Sbjct: 5   TDRPFRDLVRSF-GAGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQIAGRDAYWM 63

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+ VE  G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+S+PVT+K
Sbjct: 64  AEAARQVESRGAKVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVAAVSVPVTLK 123

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
            R+G DD   ++   ++ +  + +GV  + IH R      KG +          D+  + 
Sbjct: 124 TRLGWDDN--SLNAADVARRAQDAGVQMVTIHGRTRCQFYKGTA----------DWKAIA 171

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K    D+ +  NG + D + A   L     DGVMIGR       +L  V    ++ + 
Sbjct: 172 AVKAAL-DVPLLANGDIVDTATARTALAQSGADGVMIGRGVQGKPWLLAQV----AHDIW 226

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLF---HGFPNSRRCR 294
           GS+  +  +  D  + +SA    Y A     G  L  ++ R  +G +      P   R R
Sbjct: 227 GSAAPEVPIGSDLVQMVSAH---YEAMIAFYGADLGLRVARKHLGWYMDEAATPAPLR-R 282

Query: 295 HILTVEA 301
            +LT +A
Sbjct: 283 EVLTAKA 289


>gi|116333187|ref|YP_794714.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
 gi|116098534|gb|ABJ63683.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
          Length = 340

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 104/219 (47%), Gaps = 16/219 (7%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   +++ +  +  + QE P+++QI G     LV+AA+ V +    + I
Sbjct: 41  LVECEMISGQGIHYHNQRTLRMMAVNAQEHPMSIQIFGGTQETLVQAAQFVDQQTAADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V     GA  +L+P  V D +AA+  A+  PVTVK R G DD        
Sbjct: 101 DINMGCPVNKVVNTDAGAKWLLDPQKVHDMVAAVVAAVKKPVTVKMRTGWDDHHIFAVDN 160

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L      +    +    RK + +G +          D+ I+ E+ +     F+G NG +
Sbjct: 161 ALAAQRAGAAAVAMHGRTRKQMYQGQA----------DWQILAEVAQHLTIPFMG-NGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
                A ++L  V  D VMIGRA   N  +L  ++ Y +
Sbjct: 210 RTPQDAQRMLNEVGADAVMIGRAVMGNPWLLQRINHYLA 248


>gi|315186658|gb|EFU20417.1| TIM-barrel protein, nifR3 family [Spirochaeta thermophila DSM 6578]
          Length = 333

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/297 (22%), Positives = 127/297 (42%), Gaps = 21/297 (7%)

Query: 20  ALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           ++ YTEM+ A+ I+   G   +++  S +E+   +Q+  +    L  A +++        
Sbjct: 44  SMTYTEMVSAEGIVYNTGKTFSLVRRSPKERFWGIQLFSSRPDMLARAVEMLSPLAPTLF 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP  +V +   GA LM +P+ V   + AM +A S+PVTVK R G DD   ++  R
Sbjct: 104 DLNCGCPIPKVVKTGAGAALMRDPERVYAMVKAMREASSVPVTVKIRSGWDDL--SLTYR 161

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + ++  ++G   + +H R         +         ++ + ++K  +P   +  +G +
Sbjct: 162 EVAQAAFEAGAGAVCLHPRT--------RAQGYAGAARWEHIADLKARHPSHPVIASGDI 213

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                A  +L     D V++ R A     +   + +       G +PI  R   +  R+ 
Sbjct: 214 LSPEAARAVLEETGCDAVLVARGALGAPWIFRQIRDLLET--GGYAPISLRERVETMREH 271

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312
                 Y    +      +++ +HM     G P + R R  L V A    A   I+E
Sbjct: 272 LERAIAYKGEEI----ACREMRKHMGWYVKGLPGAARVRERL-VRASTREAYLTILE 323


>gi|16579860|gb|AAL26675.1| unknown [Staphylococcus aureus]
          Length = 289

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 108/235 (45%), Gaps = 28/235 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESCCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+    I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAKIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R       + K+  K+ +
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLR-------TRKEMSKV-D 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++++  IK       P+  + +NG + D    L++     +DGVMIGR  + N
Sbjct: 184 AHWELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHN 238


>gi|296125339|ref|YP_003632591.1| dihydrouridine synthase DuS [Brachyspira murdochii DSM 12563]
 gi|296017155|gb|ADG70392.1| dihydrouridine synthase DuS [Brachyspira murdochii DSM 12563]
          Length = 324

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 120/242 (49%), Gaps = 20/242 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R  +R      LL TE++ A A+ R  KK    +     E P++LQ+ GA+
Sbjct: 21  MAGYTDYIFRRLSRRF-GAGLLITELVSAAALARQVKKTYRYMEHKEDEYPISLQLFGAN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                +A +I    G++ I++N+GCP+ +V + + GA L+ +   +   + A+     +P
Sbjct: 80  EDDYKKAIEITNLSGFSFIDINMGCPTKKVVKNNGGAGLLEDTGKMVSILNAVKSVSPLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDY 176
           V+VK R+G+         R L  ++K++G   + +H R A  + +G +          D+
Sbjct: 140 VSVKIRLGLKRGEGGEIERAL--ALKENGACFLTLHGRYASDLYRGTA----------DW 187

Query: 177 DIVYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  +K+    D  +  NG ++    ALK   + +VDG+M+GR A  N  +   ++  F
Sbjct: 188 EAIARVKEALGKDYILIGNGDIKTKEDALKAFNISNVDGIMVGRGAVGNPWIFRELNTIF 247

Query: 234 SN 235
            +
Sbjct: 248 ED 249


>gi|134294770|ref|YP_001118505.1| nifR3 family TIM-barrel protein [Burkholderia vietnamiensis G4]
 gi|134137927|gb|ABO53670.1| tRNA-U20-dihydrouridine synthase [Burkholderia vietnamiensis G4]
          Length = 355

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 76/308 (24%), Positives = 140/308 (45%), Gaps = 34/308 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             ++PVT+K R G D +   AV +  L ++   +G++ + +H R         + +    
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAVTVARLAEA---AGISMLTVHGRT--------RADLYHG 185

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
           + +Y+ +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   +D
Sbjct: 186 DAEYETIAAVKAA-VGIPVVANGDIASPAKAKAVLDATGADALMIGRAAQGRPWLFREID 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGF 287
            +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G 
Sbjct: 245 HFLQ---TGELLPPPRID-----EIRQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGL 296

Query: 288 PNSRRCRH 295
             +   RH
Sbjct: 297 SGANGFRH 304


>gi|113866532|ref|YP_725021.1| transfer RNA-dihydrouridine synthase [Ralstonia eutropha H16]
 gi|113525308|emb|CAJ91653.1| transfer RNA-dihydrouridine synthase [Ralstonia eutropha H16]
          Length = 353

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 120/248 (48%), Gaps = 18/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            S + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PSMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVQAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G + +    ALR +   ++ +G++ + IH R         + +    N +Y
Sbjct: 136 VPVTLKIRTGWNRE-NRNALR-IAHMVEDAGISMLTIHGRT--------RADLYHGNAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K     + +  NG +    +A ++L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVKAA-VSIPVVANGDITTPQKAKQVLALTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSP 242
                 SP
Sbjct: 245 TGEMLPSP 252


>gi|329295746|ref|ZP_08253082.1| TIM-barrel protein, nifR3 family [Plautia stali symbiont]
          Length = 321

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 112/233 (48%), Gaps = 27/233 (11%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAK 67
           F  L  +N   +  +EM+ +++ +    K+ L     ++P   A+QI G D  ++  AA+
Sbjct: 25  FRTLCYDNGAGMTVSEMLSSNSEVWASDKSRLRMVHSDEPGIRAVQIAGCDPDEMAAAAR 84

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           I    G   I++N+GCP+ +V+    G+ L+ +P +V   + A+  A+ +PVT+K R G 
Sbjct: 85  INVASGAQVIDINMGCPAKKVNRKMAGSALLQHPQLVESILRAVVNAVDVPVTLKIRTGW 144

Query: 128 DDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEI 182
           D +      RN V   +  ++ G+  + IH R    + +G +          +YD +  +
Sbjct: 145 DKEN-----RNCVEIAQLAERCGIQALTIHGRTRACLFEGQA----------EYDSIRTV 189

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            K++  + I  NG + D  +A  +L     D +M+GRAA     +   +  Y 
Sbjct: 190 -KQSVAIPIIANGDITDPHKARAVLDYTGADALMVGRAAQGRPWIFREIQHYL 241


>gi|295398418|ref|ZP_06808458.1| tRNA-dihydrouridine synthase [Aerococcus viridans ATCC 11563]
 gi|294973371|gb|EFG49158.1| tRNA-dihydrouridine synthase [Aerococcus viridans ATCC 11563]
          Length = 339

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 105/232 (45%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG----FSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +++ +    ++ L     F+  EKP+   I G
Sbjct: 34  MEDVTDTVFRHVVQKAAKPDVYFTEFTNSESYVHPKGRDSLNSRLLFTEDEKPIVAHIWG 93

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +       AK + + GY  +++N+GCP+  V +   G+ L+L PD+  + I A  K   
Sbjct: 94  DNPDHFAAMAKGMNEMGYAGLDINMGCPAPNVFKHGRGSGLILRPDVAVELIQA-AKEGG 152

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +  + K  +  + IH R         K      +  +
Sbjct: 153 LPVSVKTRLGHQN---TEEYKEWLSLLLKQDIANLSIHLRT--------KTEMSKVDAHW 201

Query: 177 DIVYEIKKEN----PDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKN 222
           +++ EIKK      P   + +NG + +  + Q L     VDGVMIGR  + N
Sbjct: 202 ELIPEIKKLRDEIAPQTLLTINGDIPNRQVGQELVDKYGVDGVMIGRGIFHN 253


>gi|239995215|ref|ZP_04715739.1| tRNA-dihydrouridine synthase B [Alteromonas macleodii ATCC 27126]
          Length = 320

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 114/243 (46%), Gaps = 26/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L+ +EM+ ++  +    K+   +    +E   ++QI GAD
Sbjct: 5   MAGVTDRPFRQLCKRL-GAGLVVSEMLSSNPKVWNTAKSQARMNHEGEEGIRSVQIAGAD 63

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PD V   I A+  A+ +P
Sbjct: 64  PELMAQAAQFNVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDTVEAIIKAVVNAVDVP 123

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G + +      RN   + +  +++G+  + +H R    + KG +         
Sbjct: 124 VTLKIRTGWNPE-----NRNGVEIARIAEQNGIQSLAVHGRTRACMYKGEA--------- 169

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y  + +IK       I  NG +    +A ++L     DGVMIGR A     +   +  
Sbjct: 170 -EYSTIRQIKAAISIPVIA-NGDITSPEKAQEVLNYTGADGVMIGRGAQGKPWIFKQIQH 227

Query: 232 YFS 234
           Y  
Sbjct: 228 YLE 230


>gi|78065255|ref|YP_368024.1| dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia sp.
           383]
 gi|77966000|gb|ABB07380.1| tRNA-U20-dihydrouridine synthase [Burkholderia sp. 383]
          Length = 355

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 119/246 (48%), Gaps = 27/246 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFS 234
           +D +  
Sbjct: 243 IDHFLQ 248


>gi|302339678|ref|YP_003804884.1| hypothetical protein Spirs_3192 [Spirochaeta smaragdinae DSM 11293]
 gi|301636863|gb|ADK82290.1| TIM-barrel protein, nifR3 family [Spirochaeta smaragdinae DSM
           11293]
          Length = 327

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 74/301 (24%), Positives = 126/301 (41%), Gaps = 22/301 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TDR +R    +       YTEM+  +A+ RG+ K I  L  +  EK L +QI  +   + 
Sbjct: 16  TDRGFRRIC-IEHGAPFTYTEMVSGEALARGNAKTIALLRRAKGEKLLGVQIFLSSPEQA 74

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A  ++E      I+LN GCP  +V +   GA LM +P+ +   ++ + K+ S P+TVK
Sbjct: 75  ERALPVIEKADPTLIDLNCGCPVPKVVKTGAGAALMRSPETIYRIVSLLSKSSSRPITVK 134

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G D +   +      ++ + +G + I +H R         +      + D+D + E+
Sbjct: 135 IRTGWDSK--TINYLEAAQASESAGASMITLHGRS--------RSQGYSGSADWDTIAEL 184

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +      IG NG       A ++L      GVM  R A  N  +         +  TG 
Sbjct: 185 VQTVRVPVIG-NGDAFSPEAAKRLLMETGCSGVMFARGAMGNPFIFEQTRRLLEHDSTGK 243

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH-ILTV 299
            P    + K    ++  ++ +   R        +++ + M G   G   S   R  I+T 
Sbjct: 244 IPSVAEIMKAALTQLHYTIEEKGERV-----ACREMRKQMTGYTKGLDGSAALRQSIVTC 298

Query: 300 E 300
           E
Sbjct: 299 E 299


>gi|186684114|ref|YP_001867310.1| nifR3 family TIM-barrel protein [Nostoc punctiforme PCC 73102]
 gi|186466566|gb|ACC82367.1| putative TIM-barrel protein, nifR3 family [Nostoc punctiforme PCC
           73102]
          Length = 351

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 69/301 (22%), Positives = 134/301 (44%), Gaps = 26/301 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    ++++YTEM+ A  +    +   I+     E+P+++Q+       L 
Sbjct: 36  TDMVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPNERPISVQLFDCRPDFLA 95

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + +++N+GCP  ++ +   G+ L+  P++    +  + KA+ +PVTVK 
Sbjct: 96  EAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVDVPVTVKT 155

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG +D    + + +  K ++ +G   I +H R    +G +        N  ++ +  +K
Sbjct: 156 RIGWNDN--EITILDFAKRMEDAGAQMITVHGRTRA-QGYN-------GNARWEWITRVK 205

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTG 239
           +      IG NG +  +  A+K L     DGVM  R       ++  +D +      L  
Sbjct: 206 EVLSIPVIG-NGDIFSVEAAVKCLEQTGADGVMCSRGTLGYPFLVGEIDHFLKTGEILPT 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILT 298
            +PI+         ++  +     A   + G + ++Q  +HM     GF  +   R  L+
Sbjct: 265 PTPIQ---------RLECARDHLQALWEYKGDRGVRQARKHMTWYAKGFVGAAELRGQLS 315

Query: 299 V 299
           +
Sbjct: 316 L 316


>gi|187736076|ref|YP_001878188.1| TIM-barrel protein, nifR3 family [Akkermansia muciniphila ATCC
           BAA-835]
 gi|187426128|gb|ACD05407.1| TIM-barrel protein, nifR3 family [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 334

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 82/309 (26%), Positives = 139/309 (44%), Gaps = 31/309 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L  + ++ TE + A+ IL+  ++N          +P+ +Q+ GAD
Sbjct: 24  MAGVTDPIFRTICKELGVDVMV-TEFVSAEGILQAWERNRRYTKIENAHRPIGIQLFGAD 82

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
            + + EAA+I+ D    + I++N GCP  +V   + G+ L+ +  ++      + KA+  
Sbjct: 83  GNHMGEAARIILDHEKPDFIDINFGCPVPKVVGKNGGSSLLKDLPLLASVAGGVVKAVGE 142

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT K RIG D Q  ++   +  + ++  G++ I IH R         +  +     +
Sbjct: 143 RIPVTAKIRIGWDFQ--SLCAMDACRLLENEGISMITIHGRT--------RSQQYSGTAN 192

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEY 232
           +DI+ E  +      IG NG +    QA+  +    +V GVMIGRAA +N  +      Y
Sbjct: 193 WDIIDECARAMSVPVIG-NGDI-STPQAVAYVKENTAVSGVMIGRAAMENPWIFGDAKYY 250

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM----IGLFHGFP 288
               L G+ P     D      +       A    H G +L  + RHM    +    GFP
Sbjct: 251 L---LHGTMPPAR--DPQEKAALILRHARMALESRHYGDELHTM-RHMRSRILAYTKGFP 304

Query: 289 NSRRCRHIL 297
            ++  R  L
Sbjct: 305 GAKEMRSRL 313


>gi|299473005|emb|CBN77406.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 461

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 111/234 (47%), Gaps = 23/234 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R   +N L YT M  +   A+    +K+      +++PL +Q  G D
Sbjct: 93  MVDQSELAFRRLCRRYGSN-LCYTPMYNSKCFAVSSAYRKSNFDPHPEDRPLIVQFCGHD 151

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L+ +AK VE    + I+LN+GCP     +G +GA L+    ++ D ++ + K LSIP
Sbjct: 152 PALLLASAKFVEK-ECDAIDLNLGCPQGIARKGRYGAFLLEEWALLRDIVSTLAKNLSIP 210

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           VT K R+   V+D I       + K +  +G   I +H R    K      ++     ++
Sbjct: 211 VTCKVRLLDSVEDTI------TMCKMLVAAGARIITVHGRTKEQK------SKATAGCNW 258

Query: 177 DIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           D +  IK+  P + +  NG    LED+ + L+     DGVM      +   + +
Sbjct: 259 DAIRRIKEALP-VPVFSNGAISSLEDVERCLRET-GCDGVMSSEGVLERPGLFS 310


>gi|312797262|ref|YP_004030184.1| tRNA-dihydrouridine synthase [Burkholderia rhizoxinica HKI 454]
 gi|312169037|emb|CBW76040.1| tRNA-dihydrouridine synthase [Burkholderia rhizoxinica HKI 454]
          Length = 392

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 74/310 (23%), Positives = 141/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +   +   +EM+ ++A L   +K +       + +P+A+QI GAD
Sbjct: 56  MAGVTDRPFRQLCKRM-GASYAVSEMVASNAQLWKSEKTMRRANHDGEVEPIAVQIAGAD 114

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + L +AA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+ +A+S  
Sbjct: 115 PAMLAQAAQYNVAHGAQIIDINMGCPAKKVCNVAAGSALLQNEALVARILEAVVRAVSTG 174

Query: 117 ---IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
              +PVT+K R G D +      RN   + +  +++G++ + +H R         + +  
Sbjct: 175 PDAVPVTLKIRTGWDRE-----HRNALTIARLAEQAGISMLTVHGRT--------RADLY 221

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
               +YD +  +K  +  + +  NG +    +A ++L     D +MIGRAA     +   
Sbjct: 222 HGQAEYDTIAAVKA-SVHIPVVANGDITTPHKAREVLSITGADAIMIGRAAQGRPWLFRE 280

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +  + +   TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 281 IGHFLA---TGEVLPPPRID-----EIQQWMNEHLQDHYAFYGEFTGVRTARKHIGWYTR 332

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 333 GLSGANAFRH 342


>gi|296272247|ref|YP_003654878.1| dihydrouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296096422|gb|ADG92372.1| dihydrouridine synthase DuS [Arcobacter nitrofigilis DSM 7299]
          Length = 316

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 115/225 (51%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + L  +EMI ++A++   +K   ++  S  E P  +QI G  
Sbjct: 16  LAGYTDLPFRAVVKKFGAD-LTISEMISSNALVYNSQKTFKMIEKSPSEDPYFVQIAGNK 74

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LS 116
              + +A +I+ D  G + I+LN GCP+ +V     G+ L+ +   + + +  + K    
Sbjct: 75  AELVRDAVEILNDMEGIDGIDLNCGCPAPKVFNHGSGSNLLGDLKKLEEILGTVKKYNKK 134

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  + K RIGV+++IP     ++ K+++  GV+ I +H R    K  +P        +DY
Sbjct: 135 LYTSAKVRIGVNEKIPV----DIAKAVESCGVDFISVHGRTRAGKYKAP--------VDY 182

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D +  I KE   + +  NG ++D ++A ++L     DG+MIGR A
Sbjct: 183 DAIKAI-KEAVSIPVIANGDIKDYAKAKEVLAHTKADGLMIGRGA 226


>gi|260427626|ref|ZP_05781605.1| probable tRNA-dihydrouridine synthase [Citreicella sp. SE45]
 gi|260422118|gb|EEX15369.1| probable tRNA-dihydrouridine synthase [Citreicella sp. SE45]
          Length = 327

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/214 (29%), Positives = 102/214 (47%), Gaps = 21/214 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           R+ A L+ +  +   E + A    R  +K  LG        ++Q+ G     + EAA++V
Sbjct: 33  RWGAGLVVSEMIASGEFLTARPGTR--EKAELGAGIANT--SVQLAGRAPGPMAEAARMV 88

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            D G   I++N+GCP+ +V  G  G+ LM  PD     I A+  A+ +PVT+K R+G DD
Sbjct: 89  ADMGARVIDINMGCPAKKVTGGYSGSALMREPDHALRLIEAVVGAVDVPVTLKTRLGWDD 148

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
              ++    L +  + +GV  I IH R      KG +          D+  +  + K+  
Sbjct: 149 G--SLNAPELARRAEAAGVCMIVIHGRTRCQFYKGRA----------DWAAIRAV-KDAV 195

Query: 188 DLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
            + +  NG + D + A +   L   DGVM+GR A
Sbjct: 196 SVPVVANGDITDAATAREALDLSGADGVMVGRGA 229


>gi|66047631|ref|YP_237472.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae B728a]
 gi|63258338|gb|AAY39434.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae B728a]
 gi|330969391|gb|EGH69457.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 337

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 66/264 (25%), Positives = 126/264 (47%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGITALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG ++   +A  +L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIALI-KQAVSIPVFANGDIDSPEKARHVLKATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
               T  +P  + V++     ++A
Sbjct: 245 RTGETLPAPQSSEVERILLEHLAA 268


>gi|324995879|gb|EGC27790.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK678]
          Length = 325

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 116/239 (48%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + + + +G++ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDS--SLAVENALAA-EAAGISALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++      +    NG +  +  A + +  V  D VM+GRAA  N  +   ++ YF 
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVHDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFE 250


>gi|227528915|ref|ZP_03958964.1| tRNA-dihydrouridine synthase [Lactobacillus vaginalis ATCC 49540]
 gi|227351189|gb|EEJ41480.1| tRNA-dihydrouridine synthase [Lactobacillus vaginalis ATCC 49540]
          Length = 336

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 98/215 (45%), Gaps = 16/215 (7%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNV 81
           EMI    I+  +KK  N++     E P+ +QI G     LV+AAK V++    + I++N+
Sbjct: 42  EMISDRGIMYHNKKTLNMMDVDPSEHPMGIQIFGGTKETLVQAAKYVDEHTAADVIDINM 101

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   GA  +L+P+ V + ++ +  A+  PVTVK R G DD+        L  
Sbjct: 102 GCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKKPVTVKMRTGWDDKHIYAVENALAA 161

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
               +    +    RK +  G          + D++I+ E+       F+  NG +    
Sbjct: 162 ERAGAAALAMHGRTRKQMYTG----------HADWNILKEVADHLSIPFMA-NGDVRTPE 210

Query: 202 QALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            A +IL        MIGRAA  N  ML   + Y  
Sbjct: 211 DAKRILDETGATAAMIGRAALGNPWMLKRTEHYLE 245


>gi|209696242|ref|YP_002264172.1| tRNA-dihydrouridine synthase B [Aliivibrio salmonicida LFI1238]
 gi|208010195|emb|CAQ80522.1| tRNA-dihydrouridine synthase B [Aliivibrio salmonicida LFI1238]
          Length = 322

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/192 (27%), Positives = 94/192 (48%), Gaps = 23/192 (11%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ + + A
Sbjct: 68  SVQIAGADPKLMAEAARYCVETGAQIIDINMGCPAKKVNKKLAGSALLQRPDLIEEILLA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSP 165
           + KA+ +PVT+K R G D        RN V+  K   + G+  + +H R    + KG   
Sbjct: 128 VVKAVDVPVTLKTRTGWDPDN-----RNCVQVAKMAEQCGIQALALHGRTRACMYKG--- 179

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                  + +YD +  + KE   + +  NG ++   +A  +L     D +MIGR A    
Sbjct: 180 -------DAEYDNIKAV-KEAISIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRP 231

Query: 224 AMLTTVDEYFSN 235
            +   +  Y   
Sbjct: 232 WIFQEIQHYLET 243


>gi|303235002|ref|ZP_07321626.1| TIM-barrel protein, nifR3 family [Finegoldia magna BVS033A4]
 gi|302493857|gb|EFL53639.1| TIM-barrel protein, nifR3 family [Finegoldia magna BVS033A4]
          Length = 310

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 130/283 (45%), Gaps = 35/283 (12%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
            L +TEMI A A+   DKK   +L    +EK  ++QI G +   +  A + + E++ +  
Sbjct: 35  GLCFTEMISAKALYYDDKKTKKLLDTDPREKSTSVQIFGHEPEIIAYATRFLTENYNFKS 94

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ ++ +   G+ LM + ++  D I A      +PV+VK R+G+D+   ++  
Sbjct: 95  IDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLPVSVKFRLGIDEN--SMNY 152

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKD----NRKIPNLDYDIVYEIKKENPDLFIG 192
             L +  ++  V+ I +HAR   +      D     R + N+D  +       N D F  
Sbjct: 153 MQLAQICERLKVDYITLHARTRKMFYSGEADWSHIKRVVENVDIPVF-----GNGDCFTK 207

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
                ED+ + ++   + DGV++ R A +N  +       FS+    S   K  V     
Sbjct: 208 -----EDIRKNME-YSNCDGVLLARGAMQNPFI-------FSDDENKS---KEEVIDTIK 251

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           + +   +  Y  R       + ++ +H+     GF NS + ++
Sbjct: 252 KHMQLKLEFYEERR-----AILEMRKHIQWYLKGFRNSNKVKN 289


>gi|229543049|ref|ZP_04432109.1| dihydrouridine synthase DuS [Bacillus coagulans 36D1]
 gi|229327469|gb|EEN93144.1| dihydrouridine synthase DuS [Bacillus coagulans 36D1]
          Length = 327

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSKAGRPDVFFTEFTNTESYCHPEGNQSVRGRLAFTADEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G++ +++N+GCP   V     G+ L+  PD+  + I A  KA  
Sbjct: 79  DKPEYFRQMSMGMAKLGFSGVDINMGCPVPNVATKGKGSGLIRRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + +  I K  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGY---TYVEEWWDWLTHILKQDIVNLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D    LK+     VDGVMIGR  +KN
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDVPDRQTGLKLARQYGVDGVMIGRGIFKN 238


>gi|227432272|ref|ZP_03914267.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
 gi|227351971|gb|EEJ42202.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
          Length = 365

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 113/230 (49%), Gaps = 36/230 (15%)

Query: 12  FARLLTNNA---LLYTEMIVADAILRGDKKNILGFSTQ---------EKPLALQIGGADI 59
           F R++   A   + YTE   A +++    K    FS Q         ++P+A QI G+  
Sbjct: 41  FRRVVAKAAAPDVYYTEFTNASSMVHHKAK----FSVQGRLAVAEGEQQPVA-QIWGSRP 95

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++  + +++   GY  +++N+GCP   V + S G+ L+ +PD+  + I A  ++ S+PV
Sbjct: 96  KEIAGSIEVLAGMGYQAVDINMGCPDGTVIKNSSGSDLIRHPDLAEEIIVA-AQSGSLPV 154

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G          R  +  I +  V  + +H R       S K+  K P   Y+ +
Sbjct: 155 SVKTRLGF---YKPEEFREWLPIILRHQVAVLTVHLR-------SRKEMSKAP-AHYEHI 203

Query: 180 YEI----KKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
            EI     +  P+  I +NG ++  +Q + ++   P +DG+MIGR  ++N
Sbjct: 204 DEILAMRDEIAPNTLIQINGDIKTRAQGIALVQEHPGIDGIMIGRGIFEN 253


>gi|167381962|ref|XP_001735922.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165901877|gb|EDR27854.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 340

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 86/160 (53%), Gaps = 11/160 (6%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD +D  +R   R     L    ++ ++M V   + R +  N L    +E+P+ +Q+ G
Sbjct: 30  MVDGSDLTFRILVRRHGVNLCYTPMVLSKMFVESKVYRNEVVNSL--DPKERPIIIQVVG 87

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D +++   AK ++ +  + I++N+GCP     +G++GA L L+ D   + + A+ +A++
Sbjct: 88  SDANEMARTAKFLQSYC-DAIDINLGCPQKIAQKGNYGAYLALDFDHTKEIVNAVIEAVN 146

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           IPV  K R+  D+          V+ +++ G+ GI +H R
Sbjct: 147 IPVYCKVRVFEDED----KTMKFVEMLQECGIWGIAVHGR 182


>gi|319654161|ref|ZP_08008250.1| tRNA-dihydrouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317394095|gb|EFV74844.1| tRNA-dihydrouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 325

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 107/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +D+    +  N     L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSDSYCHPEGINSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+  P++  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAELGFKGLDINMGCPVPNVAQHGKGSGLIRRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +K I +  +  + IH R       +  +  K+P   +
Sbjct: 138 LPVSVKTRLGFTE---VDEWKVWLKHILEQDIANLSIHLR-------TRDEMSKVP-AHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      PD  + +NG + D  + L++     +DGVMIGR  + N
Sbjct: 187 ELIPEIKKLRDQVAPDTLLTINGDIPDRQKGLELAEKYGIDGVMIGRGIFHN 238


>gi|291458632|ref|ZP_06598022.1| tRNA-dihydrouridine synthase B [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291419165|gb|EFE92884.1| tRNA-dihydrouridine synthase B [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 316

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 70/278 (25%), Positives = 125/278 (44%), Gaps = 27/278 (9%)

Query: 20  ALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL  TEM+ A A+L   +  + IL     E PLA+Q+ G+D   + E A  +E+  ++ +
Sbjct: 35  ALSCTEMVSAKAVLYESRNTEAILERGKGESPLAVQLFGSDPEIMGEIAVRLEER-FDVL 93

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV---DDQIPAV 134
           ++N+GCP  ++     G+ LM  P++ G  I AM   +  PVTVK R G    +   P  
Sbjct: 94  DVNMGCPVPKIVRNGEGSALMRKPELAGRIIKAMVSRVHKPVTVKFRKGFSAGESTAPEF 153

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           A     K ++ +G   + +H R         ++       D++++  +K+      IG N
Sbjct: 154 A-----KRMEDAGAAAVTVHGRT--------REQYYSGKADWEVLRSVKEAVSIPVIG-N 199

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G +     A ++L S  VDG+ + RA   N  ++     +  + +    P      +   
Sbjct: 200 GDVFSPEDAKRMLKSTGVDGIALARAVRGNPWLIRRTVLFLESGVLPEEPGLEERLRLME 259

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           R I A M +Y    +     ++++ +H+     G P S
Sbjct: 260 RHI-ALMVEYKGERV----AVREMRKHLSWYTAGLPRS 292


>gi|215429674|ref|ZP_03427593.1| transcriptional regulator [Mycobacterium tuberculosis EAS054]
          Length = 330

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 68/263 (25%), Positives = 110/263 (41%), Gaps = 21/263 (7%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNP 101
           FS  E P +LQ+   D      AA+++   G  + I++N GCP  +V +   GA L    
Sbjct: 20  FSADESPRSLQLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKR 79

Query: 102 DIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            + G  +AA  +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A
Sbjct: 80  RLFGQIVAAAVRATEGTDIPVTVKFRIGIDDA--HHTHLDAGRIAEAEGAAAVALHARTA 137

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIG 216
                     R     D++ +  +K+    + +  NG + D   AL ++ +   DGV+IG
Sbjct: 138 A--------QRYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIG 189

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           R       +   +   F+     + P    V  D  R+    +    A H      ++ I
Sbjct: 190 RGCLGRPWLFAELSAAFTGSPAPTPPTLGEV-ADIIRRHGTLL----AAHFGEDKGMRDI 244

Query: 277 TRHMIGLFHGFPNSRRCRHILTV 299
            +H+    HGFP     R  L +
Sbjct: 245 RKHIAWYLHGFPAGSALRRALAM 267


>gi|118466583|ref|YP_880044.1| dihydrouridine synthase [Mycobacterium avium 104]
 gi|118167870|gb|ABK68767.1| dihydrouridine synthase [Mycobacterium avium 104]
          Length = 377

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 78/313 (24%), Positives = 135/313 (43%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERELVGTVSGLYVCEMVTARALVERHPATMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ + G  + I++N GCP  +V +   G+ L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIANEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAA 136

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+D++       +  +  +  G   + +HAR A          
Sbjct: 137 VRATQGTEIPVTVKFRIGIDEE--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K++   + +  NG + D S AL ++ +   DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQQVRTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P   +V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPPPTPPTLGQV-ADIVRRHGRLL----AAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAI 314


>gi|34556610|ref|NP_906425.1| putative transcriptional regulator [Wolinella succinogenes DSM
           1740]
 gi|34482324|emb|CAE09325.1| PUTATIVE TRANSCRIPTIONAL REGULATOR [Wolinella succinogenes]
          Length = 346

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 117/237 (49%), Gaps = 19/237 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +TD  +R  A+    + +  +EMI   A+   +++   ++  +  E P ++QI G  
Sbjct: 42  LAGYTDLPFRSVAKSFGAD-ITVSEMISVHALAYKNRRTAKMVEKAPNENPYSVQIAGNH 100

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +  A +++  F G + ++LN GCP+ +V     G+ L+ + D + + +  + K  +I
Sbjct: 101 LDIIQRAVEVLNAFEGIDILDLNGGCPAPKVSGHGSGSSLLKDLDKMVEILRLIKKTTTI 160

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P T VK RIG + +IPA     +  ++  + ++ + +H R       +  D  K   +DY
Sbjct: 161 PYTSVKVRIGFETKIPA----EIAHALNDAPIDFVVVHGR-------TKSDGYKKERIDY 209

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           D +  +KK      I  NG ++  S+A ++L     DG+MIGRAA     +   + E
Sbjct: 210 DSIALMKKILKVPLIA-NGEIDSFSKAQEVLAHTGADGLMIGRAAVAKPWIFRQIKE 265


>gi|304437091|ref|ZP_07397054.1| tRNA-dihydrouridine synthase B [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304370042|gb|EFM23704.1| tRNA-dihydrouridine synthase B [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 323

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 109/230 (47%), Gaps = 23/230 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++   N+L     E+P+A+QI    
Sbjct: 20  MAGVTDTAYRVIAHGM-GCPLAFAEMVSSQGIHYRNEHTMNMLRTEPDERPIAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  +I + N+GCP+ +V     G+ LM +P    + + A+ +A  +
Sbjct: 79  AAMAAEAAAYIEELGTADILDFNMGCPAPKVVRNGEGSALMRDPKRAEEILTAIRRATRL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLSPKDNRKIPNL 174
           P TVK R+G DD     A RN V+  + +   GV+ + +H R         ++     + 
Sbjct: 139 PFTVKMRLGWDD-----ASRNAVEIARMAEAVGVDAVAVHGRT--------REQFYSGSA 185

Query: 175 DYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           DY  +  +K+    P +  G      D+ +AL+I    D VMIGR A  N
Sbjct: 186 DYAAIAAVKRAVGIPVIVSGDVRRPADLKRALEIT-GADAVMIGRGAQGN 234


>gi|265984180|ref|ZP_06096915.1| nifR3 family TIM-barrel protein [Brucella sp. 83/13]
 gi|264662772|gb|EEZ33033.1| nifR3 family TIM-barrel protein [Brucella sp. 83/13]
          Length = 332

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 104/205 (50%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVKIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
              + A +IL     D VM+GRA+Y
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASY 234


>gi|326404424|ref|YP_004284506.1| putative tRNA-dihydrouridine synthase [Acidiphilium multivorum
           AIU301]
 gi|325051286|dbj|BAJ81624.1| putative tRNA-dihydrouridine synthase [Acidiphilium multivorum
           AIU301]
          Length = 353

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 80/299 (26%), Positives = 135/299 (45%), Gaps = 30/299 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGADISKL 62
           TD  +R   + +    L+ +EMI + A++R +   +   S  E   P ++Q+ G D + +
Sbjct: 41  TDLPFRRLVKSM-GAGLVVSEMIASWAMIRENAATLRMASVDEGTGPNSVQLAGCDPAAM 99

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIPVTV 121
            EAA+I    G + +++N GCP  +V  G   G+ LM +    G  + A  KA+ +PVT+
Sbjct: 100 AEAARIAVAGGADLVDINFGCPVKKVAVGQMAGSALMRDEVQAGRILEATAKAVDVPVTL 159

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
           K R+G D Q  ++    L +  ++SG+  + +H   R+   +G +          D+D +
Sbjct: 160 KMRMGWDRQ--SLNAPTLARIAQESGIAMVTVHGRTRQQFYEGTA----------DWDFI 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K       I  NG +    +A + L     DGVMIGR AY     L  V  Y +   
Sbjct: 208 ASVKAAVAIPVIA-NGDITTEDEAEEALRRSQADGVMIGRGAYGRPWFLAQVARYLATGQ 266

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLF-HGFPNSRRCR 294
              +P     D +  R +   +  Y A   H G +   ++ R  IG +  G P +   R
Sbjct: 267 KLPAP-----DMEMRRDV--LIGHYRAMRAHYGEQPGLRVARKHIGWYVRGLPGAAEFR 318


>gi|257886417|ref|ZP_05666070.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822273|gb|EEV49403.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
          Length = 327

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L  +  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTITEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRIGYTEM---SEMEEWISHLLHQDIANLSVHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ +I     +  P   I +NG + D     ++     VDG+MIGR  +KN
Sbjct: 187 EVIPKIIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKN 238


>gi|311277777|ref|YP_003940008.1| TIM-barrel protein, nifR3 family [Enterobacter cloacae SCF1]
 gi|308746972|gb|ADO46724.1| TIM-barrel protein, nifR3 family [Enterobacter cloacae SCF1]
          Length = 321

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  + G   I++N+GCP+ +V+    G+ L+ +P +V   + A+ KA+ +P
Sbjct: 76  PEEMAEAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQHPSLVESILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V+  K +   G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAKLAEGCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQTVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|238754658|ref|ZP_04616011.1| tRNA-dihydrouridine synthase B [Yersinia ruckeri ATCC 29473]
 gi|238707117|gb|EEP99481.1| tRNA-dihydrouridine synthase B [Yersinia ruckeri ATCC 29473]
          Length = 321

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 110/240 (45%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  +  +QI G D
Sbjct: 17  MAGITDRPFRALCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   ++A+  A+ +P
Sbjct: 76  PDDMAAAARINVAGGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G   +    + +  L +S    G+  + IH R    +  G            +
Sbjct: 136 VTLKIRTGWAPEHRNCIEIAQLAES---CGIQALTIHGRTRACLFNG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRAV-KQHVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|254719183|ref|ZP_05180994.1| nitrogen regulation protein Nifr3 [Brucella sp. 83/13]
 gi|306838176|ref|ZP_07471032.1| putative TIM-barrel protein, nifR3 family [Brucella sp. NF 2653]
 gi|306406766|gb|EFM62989.1| putative TIM-barrel protein, nifR3 family [Brucella sp. NF 2653]
          Length = 333

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 104/205 (50%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVKIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
              + A +IL     D VM+GRA+Y
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASY 235


>gi|51894293|ref|YP_076984.1| putative transcriptional regulator [Symbiobacterium thermophilum
           IAM 14863]
 gi|51857982|dbj|BAD42140.1| putative transcriptional regulator [Symbiobacterium thermophilum
           IAM 14863]
          Length = 345

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/247 (26%), Positives = 120/247 (48%), Gaps = 22/247 (8%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA- 66
           F RL   +   L+ TE +   A+L   K+   ++     E+P  +Q+ GAD   +  AA 
Sbjct: 36  FRRLCKEHGCGLVVTEFVSDKALLYDSKRTREMIRLLPDERPAGVQLFGADPDTMARAAA 95

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRI 125
           ++VE    + I++N+GCP+ +V +G  G+ L+  P++  + +  + +A++  PVTVK RI
Sbjct: 96  RVVELEQPDLIDINMGCPAPKVTKGRGGSSLLKEPELAQEIVRRVVQAVAPTPVTVKMRI 155

Query: 126 GVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G D + I AV    + K ++++G   I +H R         K+       D+ ++  + +
Sbjct: 156 GWDSRSINAV---EVAKRVEEAGARMITVHGRT--------KEQHYSGRADWGVIAAVAR 204

Query: 185 ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF-SNPLTGSS 241
                 +G NG + D  +A   L +  V G+ +GR A  N  + +    Y  +  L    
Sbjct: 205 AVSIPVLG-NGDIADPREAEARLRTSGVAGLAVGRGALGNPWIFSRTLHYLETGELLPEP 263

Query: 242 PIKTRVD 248
            ++ RV+
Sbjct: 264 GVRERVE 270


>gi|330989163|gb|EGH87266.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 337

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 127/264 (48%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANIELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +    + +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGDAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAMI-KQAVSIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
                  +P  + V++     ++A
Sbjct: 245 RTGEKLPAPQSSEVERILLEHLAA 268


>gi|254253220|ref|ZP_04946538.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           dolosa AUO158]
 gi|124895829|gb|EAY69709.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           dolosa AUO158]
          Length = 355

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 76/310 (24%), Positives = 140/310 (45%), Gaps = 38/310 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               +Y+ +  +K     + +  NG +   ++A  +L +   D +MIGRAA     +   
Sbjct: 186 --EAEYETIAAVKAA-VRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-H 285
           +D +     TG      R+D     +I   M ++   H    G+   +   R  IG +  
Sbjct: 243 IDHFLQ---TGELLPPPRID-----EIQLVMNEHLEDHYAFYGEFTGVRTARKHIGWYTR 294

Query: 286 GFPNSRRCRH 295
           G   +   RH
Sbjct: 295 GLSGANAFRH 304


>gi|238782959|ref|ZP_04626987.1| tRNA-dihydrouridine synthase B [Yersinia bercovieri ATCC 43970]
 gi|238716162|gb|EEQ08146.1| tRNA-dihydrouridine synthase B [Yersinia bercovieri ATCC 43970]
          Length = 321

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  +  +QI G+D
Sbjct: 17  MAGITDRPFRALCHSM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDDMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G           
Sbjct: 136 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQTVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|85713368|ref|ZP_01044378.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
 gi|85692806|gb|EAQ30794.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
          Length = 60

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/60 (53%), Positives = 46/60 (76%), Gaps = 1/60 (1%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
          M+DWTDRH R+F RLL+ N LLYT+M+   AI+ G +++ L ++ +E P+ALQ+GGAD S
Sbjct: 1  MLDWTDRHCRYFHRLLSPNTLLYTDMVTTGAIIYG-QQDFLAYNDEEHPVALQLGGADPS 59


>gi|238797912|ref|ZP_04641403.1| tRNA-dihydrouridine synthase B [Yersinia mollaretii ATCC 43969]
 gi|238718217|gb|EEQ10042.1| tRNA-dihydrouridine synthase B [Yersinia mollaretii ATCC 43969]
          Length = 321

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  +  +QI G+D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDDMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G           
Sbjct: 136 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQTVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|223937326|ref|ZP_03629232.1| TIM-barrel protein, nifR3 family [bacterium Ellin514]
 gi|223894111|gb|EEF60566.1| TIM-barrel protein, nifR3 family [bacterium Ellin514]
          Length = 369

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 42/158 (26%), Positives = 85/158 (53%), Gaps = 4/158 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           +  +T+  +R   R +    L  T+++ A ++L  + K   ++  +  ++PLA+Q+ G+ 
Sbjct: 18  LAGYTNLPFRLALREVGGLDLATTDLVNARSLLEKNPKAFKLIETNAADRPLAVQLFGSV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA  +E  G + I++N+GCP  +V +   G+ +M   D     +  M  A+ IP
Sbjct: 78  PEEMRDAAVFLESIGISSIDINMGCPVRKVCKVGGGSAMMTELDKTSALVKGMVDAVKIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VT K R+G DD    +   +L ++++  G+  I++H R
Sbjct: 138 VTAKMRLGWDDD--NLTAPDLARALEDVGITAIFVHGR 173


>gi|33151668|ref|NP_873021.1| putative dehydrogenase [Haemophilus ducreyi 35000HP]
 gi|38604734|sp|Q7VNP2|DUSB_HAEDU RecName: Full=tRNA-dihydrouridine synthase B
 gi|33147889|gb|AAP95410.1| putative dehydrogenase [Haemophilus ducreyi 35000HP]
          Length = 320

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 59/241 (24%), Positives = 116/241 (48%), Gaps = 20/241 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L  +   +    A+QI G++
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSRLRLAHHAEIGINAVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAKI   +G   I++N+GCP+ +V++   G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PTEIAEAAKINVAYGAQIIDINMGCPAKKVNKKMAGSALLREPQLVARILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +K+G++ + IH R         +D       +Y+ 
Sbjct: 136 VTLKIRTGWDK--THKNFLQIAKIAEKAGISALTIHGRT--------RDCLFNGQAEYES 185

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K+    +F+ +  NG +    +A  +L     D VMIGR ++    +   + ++  
Sbjct: 186 IKAVKQA---VFMPIIANGDITSPQKAKDVLDYTGADAVMIGRGSFGRPWLFQELKQFLE 242

Query: 235 N 235
            
Sbjct: 243 T 243


>gi|71735544|ref|YP_276563.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71556097|gb|AAZ35308.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|320322743|gb|EFW78836.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320330472|gb|EFW86451.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 337

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 126/264 (47%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAMI-KQAVSIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
                  +P  + V++     ++A
Sbjct: 245 RTGEKLPAPQSSEVERILLEHLAA 268


>gi|306843984|ref|ZP_07476579.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO1]
 gi|306275739|gb|EFM57463.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO1]
          Length = 333

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 104/205 (50%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVKIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
              + A +IL     D VM+GRA+Y
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASY 235


>gi|119776357|ref|YP_929097.1| tRNA-dihydrouridine synthase B [Shewanella amazonensis SB2B]
 gi|119768857|gb|ABM01428.1| tRNA-dihydrouridine synthase B [Shewanella amazonensis SB2B]
          Length = 323

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 115/242 (47%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    A+  +EM+ A+  L    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLC-LRYGAAMAVSEMLSANPELWDTDKSRQRMAHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+   + G   I++N+GCP+ +V++   G+ LM  PD+V   + A+  A+ +P
Sbjct: 76  PEQMAWAARFNVEQGAQIIDINMGCPAKKVNKKQAGSALMQYPDLVEQILRAVVGAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN   + +  +  G+  + +H   R+ + KG          N
Sbjct: 136 VTLKIRTGWEPE-----HRNGVQIARIAEDCGIASLAVHGRTRQCMYKG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K++  + +  NG +    +A  +L     D +MIGR A     +   +  
Sbjct: 181 AEYDTIRAI-KQSVSIPVVANGDIVSPEKARFVLDYTGADALMIGRGAQGRPWIFREIQH 239

Query: 232 YF 233
           + 
Sbjct: 240 FL 241


>gi|257483333|ref|ZP_05637374.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289647824|ref|ZP_06479167.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298488946|ref|ZP_07006969.1| tRNA dihydrouridine synthase B [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298156444|gb|EFH97541.1| tRNA dihydrouridine synthase B [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|331012552|gb|EGH92608.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 337

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 126/264 (47%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAMI-KQAVSIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
                  +P  + V++     ++A
Sbjct: 245 RTGEKLPAPQSSEVERILLEHLAA 268


>gi|196250795|ref|ZP_03149482.1| dihydrouridine synthase DuS [Geobacillus sp. G11MC16]
 gi|196209745|gb|EDY04517.1| dihydrouridine synthase DuS [Geobacillus sp. G11MC16]
          Length = 188

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 43/114 (37%), Positives = 69/114 (60%), Gaps = 3/114 (2%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
            L+  EM+    I+  ++K  N+L    +EKPL+LQI G +   LV+AAK V+ +   + 
Sbjct: 36  GLVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGEKETLVKAAKFVDKNTNADI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           I++N+GCP  +V     GA  +L+P+ + D +A++  A+  PVTVK RIG D+ 
Sbjct: 96  IDINMGCPVPKVTNCDAGAKWLLDPNKIYDVVASIVDAVEKPVTVKMRIGWDEH 149


>gi|325292774|ref|YP_004278638.1| nitrogen regulation protein [Agrobacterium sp. H13-3]
 gi|325060627|gb|ADY64318.1| nitrogen regulation protein [Agrobacterium sp. H13-3]
          Length = 333

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 104/219 (47%), Gaps = 17/219 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R  A       L+ TEM+ +  ++  RG+    L  +    P  +Q+ G +   +
Sbjct: 30  TDLPFRQLA-WRYGAGLVVTEMVASRELVANRGESWARLKNAGM-VPHMVQLAGREAHFM 87

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAAKI  D G   I++N+GCP+ +V  G  G+ LM +PD     I A   A+ +PVT+K
Sbjct: 88  AEAAKIAADNGAGIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVGAVDVPVTLK 147

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G D+    +    + +  + +GV  I IH R      +   + R     ++D +  +
Sbjct: 148 MRLGWDENT--INAPEIARRAQAAGVQLITIHGRTR----MQFYEGRA----NWDAIRAV 197

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           ++      I  NG +E    A +IL     D VM+GR A
Sbjct: 198 REVISVPLIA-NGDVETAEDAREILSRSGADAVMVGRGA 235


>gi|188591247|ref|YP_001795847.1| tRNA-dihydrouridine synthase b [Cupriavidus taiwanensis LMG 19424]
 gi|170938141|emb|CAP63127.1| tRNA-dihydrouridine synthase B [Cupriavidus taiwanensis LMG 19424]
          Length = 353

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 121/248 (48%), Gaps = 18/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            S + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PSMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVEAVVAAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G + +    ALR + + ++ +G++ + IH R         + +    + +Y
Sbjct: 136 VPVTLKIRTGWNRE-NRNALR-VAQMVQDAGISMLTIHGRT--------RADLYHGDAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K     + +  NG +    +A ++L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVKAA-VSIPVVANGDITTPQKAKQVLALTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSP 242
                 SP
Sbjct: 245 TGEMLPSP 252


>gi|120406034|ref|YP_955863.1| nifR3 family TIM-barrel protein [Mycobacterium vanbaalenii PYR-1]
 gi|119958852|gb|ABM15857.1| putative TIM-barrel protein, nifR3 family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 377

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 123/296 (41%), Gaps = 23/296 (7%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK-I 68
            +R  T + L   EM+ A A++       ++  F+ +E P +LQ+   D +    AAK I
Sbjct: 34  LSRAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSLQLYTVDPANTYAAAKMI 93

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
           V++   + I++N GCP  +V     GA L     + G  I A   A     IPVTVK RI
Sbjct: 94  VDENLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGQIIRAAVAATEGTDIPVTVKFRI 153

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD        +  +     G   + +HAR A          R   + D++ +  +K  
Sbjct: 154 GIDDA--HHTHLDAGRIAADEGAAAVALHARTAA--------QRYSGSADWEQIAALKAH 203

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
             ++ +  NG + D   AL ++ +   DGV+IGR       +   +   F+     + P 
Sbjct: 204 VTNIPVLGNGDIFDARDALAMMAATGCDGVVIGRGCLGRPWLFAELSAAFNGTAPATPPT 263

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              V +   R       +  A H      ++ I +H+    HGFP     R  L +
Sbjct: 264 LGEVAQIIRRH-----GELLAAHFGEDKGMRDIRKHVAWYMHGFPAGADLRRSLAL 314


>gi|268553095|ref|XP_002634530.1| Hypothetical protein CBG08326 [Caenorhabditis briggsae]
 gi|187032698|emb|CAP28172.1| hypothetical protein CBG_08326 [Caenorhabditis briggsae AF16]
          Length = 551

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 79/279 (28%), Positives = 124/279 (44%), Gaps = 28/279 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A +IL G   + ++L     EK   +Q+ G     + +AA+IV E+F  + +++N+
Sbjct: 231 EMALATSILSGAASEYSLLKRHPSEKIFGVQLAGGFADTMAKAAQIVVENFDVDFVDINM 290

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV 140
           GCP   V++   G  L   P+ + + + A    L   P+TVK R G  + I  +     V
Sbjct: 291 GCPIDVVNQKGGGCALPSRPNKLYEVLTATKSVLGDTPMTVKIRTGQKEGI--LKAPETV 348

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNR--KIPNLDYDI-VYEIKKENPDLFIGLNGGL 197
           + +KK+     W H    I      K+ R  K+ N DY I V E     P    G     
Sbjct: 349 EFMKKNP----W-HCPDLITFHPRSKEQRYTKLANWDYTIPVAEAAAPVPLWVCGDVLSW 403

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           ED  + L+  P+V+G+MIGR A     + T +DE  +  +T +     R D      +  
Sbjct: 404 EDYYERLEKYPNVNGIMIGRGALIKPWIFTEIDERRTWDITATE----RFD------LLK 453

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             T Y   H  S     + TR  +  F  F    +CR+I
Sbjct: 454 KFTSYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 488


>gi|83858330|ref|ZP_00951852.1| putative nitrogen regulation protein [Oceanicaulis alexandrii
           HTCC2633]
 gi|83853153|gb|EAP91005.1| putative nitrogen regulation protein [Oceanicaulis alexandrii
           HTCC2633]
          Length = 339

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 108/226 (47%), Gaps = 25/226 (11%)

Query: 1   MVDWTDRH--YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGG 56
           + DW  R   +RF A       L+ +EM+  + + +G +  I          P  +Q+ G
Sbjct: 30  VTDWPIRKQAHRFGA------GLVVSEMVACETLAQGREDVIRRMRADGDCGPHVIQLAG 83

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   +   A++ E+ G + I++N+GCP+ +V  G  G+ LM + D     + A  KA+S
Sbjct: 84  REAHWMDVGARLAEEVGADIIDINMGCPARQVTRGLSGSALMRDLDHALTLVEATVKAVS 143

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +PVT+K R+G D D + A     L +  + +GV  + +H R         +        D
Sbjct: 144 VPVTLKMRLGWDHDSLNAP---ELARRAEAAGVQMVTVHGRT--------RQQFYKDKAD 192

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
           +  V  + K+   + + +NG ++   QA +   L   DGVM+GRA+
Sbjct: 193 WSAVARV-KDAVSIPLVVNGDIQTPQQAREALRLSGADGVMVGRAS 237


>gi|319778453|ref|YP_004129366.1| tRNA dihydrouridine synthase B [Taylorella equigenitalis MCE9]
 gi|317108477|gb|ADU91223.1| tRNA dihydrouridine synthase B [Taylorella equigenitalis MCE9]
          Length = 326

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 78/331 (23%), Positives = 145/331 (43%), Gaps = 35/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM  ++  L    K    L    + +P+A+Q+ GAD
Sbjct: 17  MAGVTDRPFRKLCRKL-GAGYAVSEMAASNPQLWDSIKTARRLDHKGEVEPIAVQLLGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA---MCKAL 115
              + +AA      G   I++N+GCP+ +V   + G+ LM +   V   + +   +C   
Sbjct: 76  PDMMAQAALFNISKGARIIDINLGCPAKKVCNVACGSALMRDLGKVESILKSVIKICNPY 135

Query: 116 SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +PVT+K R G D +   A+ +  L +S+   GV+ I IH R         + +      
Sbjct: 136 DVPVTLKTRTGWDREHKNALEIAMLAESL---GVSAITIHGRT--------RADLYTGEA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +Y+ +  + KEN  + +  NG ++   +A  +L     DG+MIGRAA  N  +   ++ Y
Sbjct: 185 EYETIKTV-KENIAIPVIANGDIDSPQKAKYVLDYTGADGLMIGRAAQGNPWIFKEINHY 243

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT---RHMIGLFHGFPN 289
             N      P         + ++   + ++   H    G++  +    +H+      FP 
Sbjct: 244 LKNNKIFPQPT--------FSEMQTVILEHLEEHYEFYGEVSGVKTARKHLSWYLAPFPQ 295

Query: 290 SRR-CRHILTVEAGASTATHHIIETAFNLMI 319
           ++   + +L +E   + + +  ++  FN  I
Sbjct: 296 AQDFVKSLLLIE--TTKSQYRAVDQWFNQQI 324


>gi|237798366|ref|ZP_04586827.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331021218|gb|EGI01275.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 337

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 120/248 (48%), Gaps = 25/248 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLANAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    + +  NG ++   +A ++L +   DG++IGRAA     +   ++ Y 
Sbjct: 186 YDTIAAIKQA-VSIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHYL 244

Query: 234 SNPLTGSS 241
              LTG +
Sbjct: 245 ---LTGET 249


>gi|326803024|ref|YP_004320842.1| TIM-barrel protein, nifR3 family [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326650489|gb|AEA00672.1| TIM-barrel protein, nifR3 family [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 349

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 107/207 (51%), Gaps = 16/207 (7%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           L+  EMI    I   +KK  ++L    +E PL++QI G     L EAA+ +E +     I
Sbjct: 37  LVVCEMISDQGIHFRNKKTLSMLHIEDEEWPLSVQIFGGQADSLAEAAQFIEANTKAAII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+P+ V + +  +  A+SIPVTVK R G DD    +A+ 
Sbjct: 97  DINMGCPVNKVVKTDAGSKALLDPNEVYNRVKMVADAVSIPVTVKMRTGWDDD-HILAVE 155

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N + + +++G   I +H R         ++       +++I+ ++ ++    F G NG +
Sbjct: 156 NALAA-QEAGAKMIAMHGR--------TREQMYTGKANWNIIKQVSQKLSVPFYG-NGDI 205

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKN 222
               +A   L +  VDGVM+GR    N
Sbjct: 206 RTPEEAKYALDNYGVDGVMVGRGCLGN 232


>gi|262376252|ref|ZP_06069482.1| tRNA-dihydrouridine synthase B [Acinetobacter lwoffii SH145]
 gi|262308853|gb|EEY89986.1| tRNA-dihydrouridine synthase B [Acinetobacter lwoffii SH145]
          Length = 341

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 79/328 (24%), Positives = 148/328 (45%), Gaps = 30/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ +D  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTSDKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PHDLAEAARYQVANGAQIVDINMGCPAKKVCNRLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R+G     + I  VA     K  +++G+  + +H R         +++  +    
Sbjct: 136 VTLKTRLGYLNGQENIIRVA-----KRAEQAGIAALALHGR--------TREDMYLNTAR 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y ++ ++ KE   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YSLIKDV-KEMLKIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYL 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P  T V       ++     Y     +SG ++ +  +H+     G  +S   
Sbjct: 242 KTGQHLDAPSITEVKDVLLGHLTELYEFYGE---YSGCRISR--KHIAWYTKGLRSSNEF 296

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMIE 320
           R  +  VE  A    + ++E  FN ++E
Sbjct: 297 RQNMYQVENTAD--QYRVVEDYFNALLE 322


>gi|148261024|ref|YP_001235151.1| nifR3 family TIM-barrel protein [Acidiphilium cryptum JF-5]
 gi|146402705|gb|ABQ31232.1| tRNA-U20-dihydrouridine synthase [Acidiphilium cryptum JF-5]
          Length = 353

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 79/299 (26%), Positives = 133/299 (44%), Gaps = 30/299 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGADISKL 62
           TD  +R   + +    L+ +EMI + A++R +   +   S  E   P ++Q+ G D + +
Sbjct: 41  TDLPFRRLVKSM-GAGLVVSEMIASWAMIRENAATLRMASVDEGTGPNSVQLAGCDPAAM 99

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIPVTV 121
            EAA+I    G + +++N GCP  +V  G   G+ LM +    G  + A  KA+ +PVT+
Sbjct: 100 AEAARIAVAGGADLVDINFGCPVKKVAVGQMAGSALMRDEVQAGRILEATAKAVDVPVTL 159

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
           K R+G D Q  ++    L +  ++SG+  + +H   R+   +G +          D+D +
Sbjct: 160 KMRMGWDRQ--SLNAPTLARIAQESGIAMVTVHGRTRQQFYEGTA----------DWDFI 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K       I  NG +    +A + L     DGVMIGR AY     L  V  Y +   
Sbjct: 208 ASVKAAVAIPVIA-NGDITTEDEAEEALRRSQADGVMIGRGAYGRPWFLAQVARYLATGQ 266

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLF-HGFPNSRRCR 294
              +P       D   +    +  Y A   H G +   ++ R  IG +  G P +   R
Sbjct: 267 KLPAP-------DLEMRRDVLIGHYRAMRAHYGEQPGLRVARKHIGWYVRGLPGAAEFR 318


>gi|187918594|ref|YP_001884157.1| histidine phosphokinase/phophatase, putative [Borrelia hermsii DAH]
 gi|119861442|gb|AAX17237.1| histidine phosphokinase/phophatase, putative [Borrelia hermsii DAH]
          Length = 331

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/256 (25%), Positives = 118/256 (46%), Gaps = 30/256 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNILGFSTQE----KPLAL 52
           M D TD  +R    L+ N      + +TE I    +L   K+++    T+     +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGNGKDVPDIYFTEFISVKGLLNKSKQSMQHILTKNDELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G +  +  +A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGKEPDEFFKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAREIIMASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C    +P++VK R G         + + +  + + G++ + +H R A+ +   P    
Sbjct: 137 EACLKFGLPLSVKTRHG----FFYSEVEDWLGFLLELGIDMLIVHPRLAVNQSEGP---- 188

Query: 170 KIPNLDYDIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +D  + +E+ K     NP   I  NGG+  + QA +I+   S+DGVM G   ++N 
Sbjct: 189 ----IDVAVFHELVKLRDQINPSALIIGNGGILSLEQAHQIVREYSIDGVMFGCGIFRNL 244

Query: 224 AMLTT-VDEYFSNPLT 238
            +    +  + SN L 
Sbjct: 245 NLFRKGLSNFLSNNLN 260


>gi|330815564|ref|YP_004359269.1| Putative TIM-barrel protein, nifR3 family protein [Burkholderia
           gladioli BSR3]
 gi|327367957|gb|AEA59313.1| Putative TIM-barrel protein, nifR3 family protein [Burkholderia
           gladioli BSR3]
          Length = 347

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 123/254 (48%), Gaps = 27/254 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   ++A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVSAVVAAVGSG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D D   A+ +  L    +++G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDRDHKNALTIARLA---EEAGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               +Y+ +  +K  +  + +  NG +    +A  +L +   D +MIGRAA     +   
Sbjct: 186 --EAEYETIAAVKA-SVKIPVVANGDITSPRKARAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSNPLTGSSP 242
           +D +     T  +P
Sbjct: 243 IDHFLQTGETLPAP 256


>gi|331006292|ref|ZP_08329609.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC1989]
 gi|330419913|gb|EGG94262.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC1989]
          Length = 334

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 115/251 (45%), Gaps = 33/251 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST---------QEKPLA 51
           M   TD  +R     L    +  +EM+ +D  L   +K+    S+         ++   +
Sbjct: 1   MAGVTDEPFRRLCSEL-GAGMTVSEMVTSDERLWSSRKSQQRLSSLTSIKDRANRKDIRS 59

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G D   +  AAK     G + I++N+GCP+ +V + + G+ L+ +  +V + + A+
Sbjct: 60  VQLAGNDPEMMAAAAKTNAKMGADVIDINMGCPAKKVCKKAAGSALLKDEKLVSEILNAV 119

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ IPVT+K R G   +     LRN   + +  + SG+  + +H R      KG    
Sbjct: 120 VGAVDIPVTLKIRTGWSPE-----LRNGVTIAQIAEDSGIQALAVHGRTRACAFKG---- 170

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSA 224
                 + +YD + EI ++   + +  NG +    +A  +L   D   VMIGRAA  N  
Sbjct: 171 ------HAEYDTIAEIVQQ-ISIPVFANGDIYSAEKAKMVLQHTDAAAVMIGRAAQGNPW 223

Query: 225 MLTTVDEYFSN 235
           +   ++ Y + 
Sbjct: 224 IFREINHYLAT 234


>gi|308172670|ref|YP_003919375.1| tRNA-dihydrouridine synthase 2 [Bacillus amyloliquefaciens DSM 7]
 gi|307605534|emb|CBI41905.1| tRNA-dihydrouridine synthase 2 [Bacillus amyloliquefaciens DSM 7]
 gi|328552438|gb|AEB22930.1| probable tRNA-dihydrouridine synthase [Bacillus amyloliquefaciens
           TA208]
          Length = 327

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 104/233 (44%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D ++     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGRDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       R  +  + K  +  + IH R +A +  +         +  
Sbjct: 138 LPVSVKTRLGYTD---VDEWRGWLTHVLKQDIANLSIHLRTRAEMSKV---------DAH 185

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIK       PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 186 WELIPEIKNLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTN 238


>gi|257877859|ref|ZP_05657512.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
 gi|257812025|gb|EEV40845.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
          Length = 328

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+      R   +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVQAAGAPDVFFTEFTNSDSYCHPEGRDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEYFREMSIGLAEMGFKGIDLNMGCPVPNVAGRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYTE---LGEMEAWLTHVLQQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ E+     +  P   + +NG + D ++ L++     VDG+MIGR  +KN
Sbjct: 187 ELIPEVVALRDRIAPQTKLTINGDIPDRTKGLELAEKYGVDGIMIGRGIFKN 238


>gi|149914887|ref|ZP_01903416.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseobacter sp.
           AzwK-3b]
 gi|149811075|gb|EDM70912.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseobacter sp.
           AzwK-3b]
          Length = 323

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 113/241 (46%), Gaps = 25/241 (10%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           RF A L+ +  +   EM+ A   +R  ++  LGF  +    A+Q+ G +   + EAA+ V
Sbjct: 25  RFGAGLVVSEMVASQEMVQAKPGVR--ERAELGFGIENT--AVQLAGREAHWMAEAARKV 80

Query: 70  EDFGYNEINLNVGCPSARVHE----GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
              G   I++N+GCP+ +V      G+ G+ LM + D     I A+  A+ IPVT+K R+
Sbjct: 81  AANGARIIDINMGCPAKKVTSASGTGASGSALMKDLDHALSLIEAVVGAVDIPVTLKTRL 140

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIK 183
           G DD++  +    L +  + +G+  I IH R      KG +          D+  +  + 
Sbjct: 141 GWDDRL--MNAPELARRAEGAGIAMITIHGRTRCQFYKGRA----------DWAAIRAV- 187

Query: 184 KENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K+  ++ +  NG + D   A     L   DGVMIGR A     +L+ V    +      +
Sbjct: 188 KDAVEIPVIANGDIVDAGSARDALRLSGGDGVMIGRGAQGRPWLLSQVAAELAGQPVPKA 247

Query: 242 P 242
           P
Sbjct: 248 P 248


>gi|330993258|ref|ZP_08317194.1| putative tRNA-dihydrouridine synthase [Gluconacetobacter sp.
           SXCC-1]
 gi|329759660|gb|EGG76168.1| putative tRNA-dihydrouridine synthase [Gluconacetobacter sp.
           SXCC-1]
          Length = 353

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 117/249 (46%), Gaps = 22/249 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M   TD  +R  AR L    L+ +EMI + A++R ++  + +     + P ++Q+ G D 
Sbjct: 26  MAGVTDLPFRRLARRL-GAGLVVSEMIASWAMVRENQTTLRMAEVADDGPNSVQLAGCDP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIP 118
             + +AA+I  D G + I++N GCP  +V  G   G+ LM +       +  + +A+ +P
Sbjct: 85  DAMGQAARIAVDRGADIIDINFGCPVKKVAVGQLAGSALMRDEVQAARLLEGVVRAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D +   +    L +  ++SG+  + +H R            ++  N   D 
Sbjct: 145 VTLKMRMGWDHE--HLNAPRLARIAQESGIRMVTVHGRT----------RQQFYNGTADW 192

Query: 179 VYEIKK--ENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            Y ++K  +  DL + +NG +   ED   AL+      GVMIGR  Y     L  V    
Sbjct: 193 -YFVRKVVDAVDLPVIVNGDILTVEDARVALE-RSGARGVMIGRGCYGRPWFLAQVARAL 250

Query: 234 SNPLTGSSP 242
            + +  + P
Sbjct: 251 MDGVAVAEP 259


>gi|328910783|gb|AEB62379.1| tRNA-dihydrouridine synthase 2 [Bacillus amyloliquefaciens LL3]
          Length = 309

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 104/233 (44%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D ++     L F+  E+P+   I G
Sbjct: 1   MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGRDSVRGRLTFTEDEQPMVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 61  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           +PV+VK R+G  D       R  +  + K  +  + IH R +A +  +         +  
Sbjct: 120 LPVSVKTRLGYTD---VDEWRGWLTHVLKQDIANLSIHLRTRAEMSKV---------DAH 167

Query: 176 YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           ++++ EIK       PD  + +NG + D    LK+     VDG+MIGR  + N
Sbjct: 168 WELIPEIKNLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTN 220


>gi|289625299|ref|ZP_06458253.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|330867132|gb|EGH01841.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330871020|gb|EGH05729.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 337

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 126/264 (47%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAMI-KQAVSIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
                  +P  + V++     ++A
Sbjct: 245 RTGEKLPAPQSSEVERILLEHLAA 268


>gi|262066716|ref|ZP_06026328.1| NifR3 family protein [Fusobacterium periodonticum ATCC 33693]
 gi|291379515|gb|EFE87033.1| NifR3 family protein [Fusobacterium periodonticum ATCC 33693]
          Length = 307

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/247 (24%), Positives = 116/247 (46%), Gaps = 29/247 (11%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I          A+QI G DI K+  +A+ +++ G  +INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLRDGNAVQIFGEDIEKIKSSAQYIQNLGVKDINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+ +P+ +   ++ +   L+  + ++VK RIG  +    V +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKDPEKIKRILSEIKSILNDDVKLSVKIRIGYKEPENYVQIAK 147

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + + +   G + I +H R         ++       D+  + E+ K+N  + +  NG + 
Sbjct: 148 IAEEV---GCDHITVHGR--------TREQLYSGKADWTYIKEV-KDNVSIPVIGNGDIF 195

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS-----NPLTGSSPI-------- 243
               AL+ +   +VDGVM+ R  + N  ++  + E        NP+T    I        
Sbjct: 196 TAEDALERISYSNVDGVMLARGIFGNPWLIRDIREILEYGEVKNPVTKEEKINMAIEHLK 255

Query: 244 KTRVDKD 250
           + R+D D
Sbjct: 256 RIRIDND 262


>gi|260914496|ref|ZP_05920965.1| tRNA-dihydrouridine synthase B [Pasteurella dagmatis ATCC 43325]
 gi|260631597|gb|EEX49779.1| tRNA-dihydrouridine synthase B [Pasteurella dagmatis ATCC 43325]
          Length = 316

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 56/220 (25%), Positives = 112/220 (50%), Gaps = 25/220 (11%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL ++EM+  +  +   +K+ L  +  +     A+QI G+D  ++  AA++  ++G   I
Sbjct: 19  ALTFSEMMSTNPRVWHTEKSKLRLAHHQDAGINAVQIAGSDPIEMAAAAQVNVEYGAQII 78

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +PVT+K R G D +      R
Sbjct: 79  DINMGCPAKKVNRKMAGSALLQYPDLVKQILEAVVNAVDVPVTLKIRTGWDKE-----NR 133

Query: 138 N---LVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           N   + +  +++G+  + IH R    + +G          + +YD +  + K++  + + 
Sbjct: 134 NCLEIAQIAEQAGIQALTIHGRTKTCMFEG----------DAEYDSIRAV-KQHISIPVI 182

Query: 193 LNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
            NG +    +A  +L   + D VMIGR A  +  +   V+
Sbjct: 183 ANGDITSAEKAKFVLDYTNADAVMIGRGALGSPWIFNQVN 222


>gi|87125619|ref|ZP_01081464.1| putative nitrogen regulation protein NifR3 family-like protein
           [Synechococcus sp. RS9917]
 gi|86166919|gb|EAQ68181.1| putative nitrogen regulation protein NifR3 family-like protein
           [Synechococcus sp. RS9917]
          Length = 343

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 76/320 (23%), Positives = 146/320 (45%), Gaps = 32/320 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G  ++ +   + +  P+ +Q+     + + 
Sbjct: 37  SDRVFRSLVRRWAPDALLFTEMVNATSLELGHGRRKVEELAEESGPIGVQLFDHRPAAMA 96

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA+  E  G   I++N+GCP  ++     G+ L+  P++    +  +  A+SIPVTVK 
Sbjct: 97  EAARRAEAAGAFLIDINMGCPVRKIARKGGGSGLIQTPELACSIVETVAAAVSIPVTVKT 156

Query: 124 RIGVDD-QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVY 180
           R+G  + +  + A  +  + ++++G   + +H  +R    KG +          D+  + 
Sbjct: 157 RLGWSERETGSAAAVHWCRQLERAGAQLLTLHGRSRSQGFKGAA----------DWQAIA 206

Query: 181 EIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-- 235
            + +E   + +  NG +   ED  + L I     GVM+GR +     ++  +D       
Sbjct: 207 AV-QEALTIPVIANGDVNSPEDARRCLTIT-GAAGVMVGRGSMGAPWLVGQIDAALCGRP 264

Query: 236 -PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            P T   P +  + +D    + AS  D+          L    +HM     GFP + + R
Sbjct: 265 IPATPGGPERLELARDQLLALVASRGDHG---------LLIARKHMSWTCTGFPGAPQLR 315

Query: 295 HILTVEAGASTATHHIIETA 314
           H L + A    A   ++++A
Sbjct: 316 HAL-MRAPTPAAALELLDSA 334


>gi|237739609|ref|ZP_04570090.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 2_1_31]
 gi|229423217|gb|EEO38264.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 2_1_31]
          Length = 307

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 115/247 (46%), Gaps = 29/247 (11%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I          A+QI G DI K+  +AK +++ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLRDGNAVQIFGEDIEKIKLSAKYIQNLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+ +P+ +   ++ +   L+  + ++VK RIG  +    V +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKDPEKIKRILSEIKSVLNDDVKLSVKIRIGYKEPENYVQIGK 147

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + + +   G + I +H R         ++       D+  + E+ K+N  + +  NG + 
Sbjct: 148 IAEEV---GCDHITVHGR--------TREQLYSGKADWSYIKEV-KDNISIPVIGNGDIF 195

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS-----NPLTGSSPI-------- 243
               AL+ +   +VDGVM+ R  + N  ++  + E        NP+T    I        
Sbjct: 196 TAEDALEKISYSNVDGVMLARGIFGNPWLIRDIREILEYGEVKNPVTKDEKINMAIEHLK 255

Query: 244 KTRVDKD 250
           + RVD D
Sbjct: 256 RIRVDND 262


>gi|312884763|ref|ZP_07744464.1| NifR3/Smm1 family protein [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367676|gb|EFP95227.1| NifR3/Smm1 family protein [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 322

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 111/244 (45%), Gaps = 20/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L      K  +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDIIEDILRAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G D +       ++ K  +  G+    +H R    + KGL+          +Y
Sbjct: 136 VTLKTRTGWDTENKNCV--HIAKLAEDCGIQAFALHGRTKACMYKGLA----------EY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  +  
Sbjct: 184 DSIKAVKQAISIPVIA-NGDIDSPERAKHVLDYTGADALMIGRPAQGRPWIFQEIQHFLE 242

Query: 235 NPLT 238
           N  T
Sbjct: 243 NGTT 246


>gi|171912320|ref|ZP_02927790.1| putative transcriptional regulator [Verrucomicrobium spinosum DSM
           4136]
          Length = 331

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 73/303 (24%), Positives = 134/303 (44%), Gaps = 27/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L  + ++ TE + A+ IL+ D++      F   ++ + +Q+ GAD
Sbjct: 17  MAGVTDMVFRSLCKELGADVMV-TEFVSAEGILQADERTRKYTEFDDAQRTVGVQLFGAD 75

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             ++ EAA+ + D+   + I++N GCP  +V   + G+ L+ +  ++    A + KA+ +
Sbjct: 76  GQRMGEAARKIVDWKSPDFIDINFGCPVNKVVAKNGGSSLLKDCPLLSSVAAGIVKAVPV 135

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVT K RIG D   I AV +  L   ++ +G+  I IH R         +        D+
Sbjct: 136 PVTAKIRIGWDATSINAVEVCRL---LEDTGIQAIAIHGRT--------RAQGYTGQADW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKNSAMLTTVDE 231
            ++ E         IG NG   D++  + +        V GVMIGRAA  N  +      
Sbjct: 185 GVIAECAAAVKIPIIG-NG---DIATGMDVARRQRETGVHGVMIGRAAMGNPWVFREAKH 240

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +  +      P   +  +   R    ++  ++ R+      L+ +   ++    G P S+
Sbjct: 241 FLQHGTHLQPPTTEQRFELMLRHTRLAV--HSKRYGSEIQALRSMRNRLMTYTQGLPGSK 298

Query: 292 RCR 294
             R
Sbjct: 299 HLR 301


>gi|313837246|gb|EFS74960.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL037PA2]
 gi|314927734|gb|EFS91565.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL044PA1]
 gi|314972018|gb|EFT16116.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL037PA3]
          Length = 355

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 119/286 (41%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K  ++L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 19  GLYVCEMITSRGLVYGDHKTHDMLAFAEGEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D     I+A  +   A  +PVTVK RIG+D     
Sbjct: 79  VDLNFGCPVPKVTRKGGGGVLPWKLDRFTAVISAAVQAGDAHGVPVTVKIRIGIDPD--H 136

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + ++ K      IG 
Sbjct: 137 ITYMDSTRAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGDLVKAVDVPVIG- 187

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 188 NGDIWEASDAMAMVERTGCAGVEVGRGCLGRPWLFRDLADAFAGRGTTTLPSLGEVCA-M 246

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH L
Sbjct: 247 IRRHTELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGEIRHAL 287


>gi|295677642|ref|YP_003606166.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1002]
 gi|295437485|gb|ADG16655.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1002]
          Length = 358

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 72/307 (23%), Positives = 138/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PDMMAEAARYNVGNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVNAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWNRENKNAL--NVARLAQAAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K    D+ +  NG +    +A ++L +   D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVKAA-VDIPVVANGDITSPQKAREVLAATGADAIMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 246 FLQ---TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 297

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 298 GANLFRH 304


>gi|328907204|gb|EGG26970.1| TIM-barrel protein, nifR3 family [Propionibacterium sp. P08]
          Length = 418

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 119/286 (41%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K  ++L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 82  GLYVCEMITSRGLVYGDHKTHDMLAFAEGEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 141

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D     I+A  +   A  +PVTVK RIG+D     
Sbjct: 142 VDLNFGCPVPKVTRKGGGGVLPWKLDRFTAVISAAVQAGDAHGVPVTVKIRIGIDPD--H 199

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + ++ K      IG 
Sbjct: 200 ITYMDSTRAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGDLVKAVDVPVIG- 250

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 251 NGDIWEASDAMAMVERTGCAGVEVGRGCLGRPWLFRDLADAFAGRGTTTLPSLGEVCA-M 309

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH L
Sbjct: 310 IRRHTELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGEIRHAL 350


>gi|288555000|ref|YP_003426935.1| tRNA-dihydrouridine synthase [Bacillus pseudofirmus OF4]
 gi|288546160|gb|ADC50043.1| tRNA-dihydrouridine synthase [Bacillus pseudofirmus OF4]
          Length = 327

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++    D     +  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGMKSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+  P++  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAELGFKGLDINMGCPVPNVVQNGKGSGLIRRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +       R+ +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRIGFAE---VDEWRDWLTHILKQDIVNLSIHLRT--------RNEMSKVDAHW 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P   + +NG + D    LK++    VDGVMIGR  + N
Sbjct: 187 ELIPEIKKLRDEVAPHTLLTINGDIPDRQTGLKLVEQYGVDGVMIGRGIFHN 238


>gi|172059012|ref|YP_001815472.1| dihydrouridine synthase DuS [Exiguobacterium sibiricum 255-15]
 gi|171991533|gb|ACB62455.1| dihydrouridine synthase DuS [Exiguobacterium sibiricum 255-15]
          Length = 331

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 102/232 (43%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++      K      L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVAKAARPDVFFTEFTNTESYCHPKGKQSVRGRLEFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V     G+ L+  PD+  + I A  KA  
Sbjct: 79  DKPEYFREMSIGMAEMGFKGIDINMGCPVQNVAVNGKGSGLINRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + ++ I +  +  + IH R       + K+   +P   +
Sbjct: 138 LPVSVKTRLGYSK---VEEWHDWLRHILEQDIANLSIHLR-------TRKEMSAVP-AHF 186

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P   + +NG + D    L+++    VDGVMIGR  + N
Sbjct: 187 ELIPEIKKLRDEVAPQTLLTINGDINDRQHGLELVEQYGVDGVMIGRGIFHN 238


>gi|254773708|ref|ZP_05215224.1| dihydrouridine synthase [Mycobacterium avium subsp. avium ATCC
           25291]
          Length = 377

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 78/313 (24%), Positives = 135/313 (43%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERELVGTVSGLYVCEMVTARALVERHPATMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ + G  + I++N GCP  +V +   G+ L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIANEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAA 136

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+D++       +  +  +  G   + +HAR A          
Sbjct: 137 VRATQGTEIPVTVKFRIGIDEE--HHTHLDAGRIAEAEGAAAVALHARTAA--------Q 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K++   + +  NG + D S AL ++ +   DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQQVRTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P   +V  D  R+    +    A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPPPTPPTLGQV-ADIVRRHGRLL----AAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAM 314


>gi|159027862|emb|CAO87075.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 350

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 60/248 (24%), Positives = 113/248 (45%), Gaps = 18/248 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    +++LY  M+ A  I +  +   ++    +E+P+++Q+       + 
Sbjct: 43  TDLVFRRLVRRFAPDSMLYRSMVNATEISQLQELPQLMVIGDKEQPISMQLFDCRPDFMA 102

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  + +A+S+PVTVK 
Sbjct: 103 VAAEKAVKEGAMTIDINMGCPVNKITKKGGGSSLLRQPEIAEQIVREVVRAVSVPVTVKT 162

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G + Q   + + +  + ++ +GV  + +HAR        P D + I  +         
Sbjct: 163 RLGWNAQ--EINIIDFARRLEDAGVQMLTLHARTREQGYHGPADWQWIKRV--------- 211

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           KE   + +  NG +  +  A+  L     DGVM  R       ++  +D Y     TG  
Sbjct: 212 KEVLSIPVIANGDIVSVETAINCLEFTEADGVMCSRGTLGYPYLVGEIDYYLK---TGKK 268

Query: 242 -PIKTRVD 248
            P  T +D
Sbjct: 269 LPKPTSID 276


>gi|255018963|ref|ZP_05291089.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           F2-515]
          Length = 200

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 46/113 (40%), Positives = 69/113 (61%), Gaps = 3/113 (2%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 22  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 81

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           ++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVTVK RIG D++
Sbjct: 82  DINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE 134


>gi|167516252|ref|XP_001742467.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163779091|gb|EDQ92705.1| predicted protein [Monosiga brevicollis MX1]
          Length = 291

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 105/232 (45%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M  +   +R    +K +      ++PL +Q  G D
Sbjct: 17  MVDQSELAWRMLCRR-KGAVLCYTPMFNSKVFVRDASYRKRMFKAIEGDRPLVVQFCGDD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L+EAAK VE +  + I+LN GCP      G +GA L    +++ + ++ + K LSI 
Sbjct: 76  AATLLEAAKHVEPYC-DAISLNCGCPQGIARRGHYGAFLQDEWELLAEIVSTLSKNLSIA 134

Query: 119 VTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V  K RI  D      A R L   K  + +G + + +H R    KG       +    D+
Sbjct: 135 VECKIRIHDD------AERTLAYAKMFEAAGCDLLTVHGRTREQKGT------RTGLADW 182

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
            +V  IK+E   + +  NG +   +  L  L    VDG+M   +   N AM 
Sbjct: 183 SLVKRIKEEL-KIPVVSNGNILYRADCLACLEETGVDGIMSSESNLSNPAMF 233


>gi|118473981|ref|YP_890003.1| tRNA-dihydrouridine synthase [Mycobacterium smegmatis str. MC2 155]
 gi|118175268|gb|ABK76164.1| tRNA-dihydrouridine synthase, putative [Mycobacterium smegmatis
           str. MC2 155]
          Length = 389

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 78/295 (26%), Positives = 125/295 (42%), Gaps = 21/295 (7%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            AR  T + L   EM+ A A++       ++  F+ +E P +LQ+   D     +AAK++
Sbjct: 46  IARAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSLQLYTVDPENTYKAAKMI 105

Query: 70  --EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCR 124
             ED   + I++N GCP  +V +   GA L     + G  +AA  +A     IPVTVK R
Sbjct: 106 VDEDLA-DHIDMNFGCPVPKVTKRGGGAALPYKRRLFGQIVAAAVRATEGTDIPVTVKFR 164

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           IG+DD+       +  +   + G   + +HAR A  +     D  +I  L   +      
Sbjct: 165 IGIDDE--HHTHLDAGRIAAEEGAAAVALHARTAAQRYSGTADWEQIAALKAHVTGIPVL 222

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
            N D+F        D + A+      DGV+IGR       +   +   F+N    + P  
Sbjct: 223 GNGDIF------EADDALAMMAATGCDGVVIGRGCLGRPWLFAELSAAFNNRPIPTPPTL 276

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             V  D  R+      +  +RH      ++ I +H+    HGFP     R  L +
Sbjct: 277 GEV-ADIVRR----HGELLSRHFGEDKGMRDIRKHVAWYLHGFPAGADLRRALAL 326


>gi|148549897|ref|YP_001269999.1| nifR3 family TIM-barrel protein [Pseudomonas putida F1]
 gi|148513955|gb|ABQ80815.1| putative TIM-barrel protein, nifR3 family [Pseudomonas putida F1]
 gi|313500799|gb|ADR62165.1| TRNA-dihydrouridine synthase B [Pseudomonas putida BIRD-1]
          Length = 337

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 116/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAAKANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVSAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+     L N+ K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGW-DRANKNGL-NVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           +  I K+   + +  NG +    +A  +L +  VDG++IGRAA     +   ++ Y 
Sbjct: 189 IAAI-KQAVSIPVFANGDITSPEKARAVLETTGVDGLLIGRAAQGRPWIFREIEHYL 244


>gi|77408418|ref|ZP_00785157.1| NifR3/Smm1 family protein [Streptococcus agalactiae COH1]
 gi|77172941|gb|EAO76071.1| NifR3/Smm1 family protein [Streptococcus agalactiae COH1]
          Length = 325

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 112/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  +++    +I ++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQNNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV   N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAV--ENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++ K    +    NG +  +  A  ++  +  D +M+GR A  N  + T ++ +F 
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFE 250


>gi|319745777|gb|EFV98072.1| tRNA-dihydrouridine synthase [Streptococcus agalactiae ATCC 13813]
          Length = 325

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 112/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +P+ +   +  +   L+I
Sbjct: 83  AEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV   N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAV--ENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++ K    +    NG +  +  A  ++  +  D +M+GR A  N  + T ++ +F 
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFE 250


>gi|302380164|ref|ZP_07268636.1| TIM-barrel protein, nifR3 family [Finegoldia magna ACS-171-V-Col3]
 gi|302311947|gb|EFK93956.1| TIM-barrel protein, nifR3 family [Finegoldia magna ACS-171-V-Col3]
          Length = 310

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 68/283 (24%), Positives = 130/283 (45%), Gaps = 35/283 (12%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
            L +TEMI A A+   DKK   +L   ++E   ++QI G +   +  A + + E++ +  
Sbjct: 35  GLCFTEMISAKALYYDDKKTKKLLDTDSRENDTSVQIFGHEPEIIAYATRFLTENYNFKS 94

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ ++ +   G+ LM + ++  D I A      +PV+VK R+G+D+   ++  
Sbjct: 95  IDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLPVSVKFRLGIDEN--SMNY 152

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKD----NRKIPNLDYDIVYEIKKENPDLFIG 192
             L +  ++  V+ I +HAR   +      D     R + N+D  +       N D F  
Sbjct: 153 MQLAQICERLKVDYITLHARTRKMFYSGEADWSHIKRVVENVDIPVF-----GNGDCFTK 207

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
                ED+ + ++   + DGV++ R A +N  +       FS+    S   K  V     
Sbjct: 208 -----EDIRKNME-YSNCDGVLLARGAMQNPFI-------FSDDENKS---KEEVIDTIK 251

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           + +   +  Y  R       + ++ +H+     GF NS + ++
Sbjct: 252 KHMQLKLEFYEERR-----AILEMRKHIQWYLKGFRNSNKVKN 289


>gi|83032642|ref|XP_729128.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23486029|gb|EAA20693.1| Drosophila melanogaster CG3645 gene product [Plasmodium yoelii
           yoelii]
          Length = 338

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 117/245 (47%), Gaps = 24/245 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ +   +   K  I  F    Q+KPL  Q  G D
Sbjct: 32  MVDLSELPFRLLCRNY-NCDLAFTPMLHSKNFVEHSKYRIGYFKKCDQDKPLIAQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S +++A   ++D   N +++N+GCP     +G++GA L+   D V + I+ +    ++P
Sbjct: 91  PSTILKAIDYIKD-DVNGVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLISDITNNCNVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R  +D+        NL   ++   V  I +H R    KG++ K+       DY+I
Sbjct: 150 ISCKIR-KIDNDYQKTL--NLCYDLQSRNVKMITVHGRTKEEKGVNIKE------CDYEI 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM-----IGRAAYKNSAMLTTVD- 230
           + +I KE  ++ I  NG +E      K L     D VM     + + ++ ++  + TVD 
Sbjct: 201 I-KIIKERLNIPIIANGSIEHFEDIEKCLNYTKTDAVMCAEILLEKPSFFSNKNINTVDL 259

Query: 231 --EYF 233
             EY+
Sbjct: 260 VNEYY 264


>gi|323347278|gb|EGA81552.1| Dus1p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 301

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 83/166 (50%), Gaps = 9/166 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L+ ++       R D  + L  S+ ++PL +Q   
Sbjct: 36  MVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L 
Sbjct: 96  NDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNLK 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PVT K RI  DD   ++   N  K +  +G   + +H R    KG
Sbjct: 155 VPVTAKIRI-FDDCEKSL---NYAKMVLDAGAQFLTVHGRVREQKG 196


>gi|261377469|ref|ZP_05982042.1| tRNA-dihydrouridine synthase C [Neisseria cinerea ATCC 14685]
 gi|269146198|gb|EEZ72616.1| tRNA-dihydrouridine synthase C [Neisseria cinerea ATCC 14685]
          Length = 333

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 54/197 (27%), Positives = 99/197 (50%), Gaps = 17/197 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   + E A     FG ++I+LN GCP+  V++   GA L+  P ++   +
Sbjct: 76  PCTVQLLGSDADNMAENALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             M + L   IP+T K R+G +D+IPA+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTMRERLPAHIPLTGKMRLGYEDKIPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
            +       ++ + +I ++N D+ +  NG +  +     +K +   + VM+GR A     
Sbjct: 192 AH-------WEWIRKI-RDNVDIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPD 243

Query: 225 MLTTVDEYFSN-PLTGS 240
           +   + +Y S  P+T +
Sbjct: 244 LARQIKQYESGLPVTDT 260


>gi|198476736|ref|XP_002132430.1| GA25459 [Drosophila pseudoobscura pseudoobscura]
 gi|198137829|gb|EDY69832.1| GA25459 [Drosophila pseudoobscura pseudoobscura]
          Length = 507

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 110/234 (47%), Gaps = 25/234 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 34  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFAHDPKYRKDALQTCPEDRPLIIQFCGND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ D +  + + LS+P
Sbjct: 93  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTDIVRTLHEKLSVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +     LR   K ++ +G   + +H R    K  L G++          
Sbjct: 152 VTCKIRIFEDRE---KTLR-YAKMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 197

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D+  + E++K  + P    G   GLED+ + L     VDGVM       N A+ 
Sbjct: 198 DWSYIQEVRKHLKIPMFANGNILGLEDVHRCLDET-GVDGVMTAEGNLHNPAIF 250


>gi|104783798|ref|YP_610296.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           entomophila L48]
 gi|95112785|emb|CAK17513.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           entomophila L48]
          Length = 337

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 124/261 (47%), Gaps = 16/261 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCKRL-GAGMVVSEMVTSDMSLWNSRKSSLRRIHEGDAEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAARANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVGAVEVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+     L N+ K  +++G+  + +H R         + +    + +YD 
Sbjct: 139 VTLKIRTGW-DRANKNGL-NVAKIAEQAGIQALAVHGRT--------RADLYTGDAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG +    +A  +L +   DG++IGRAA     +   V+ Y    
Sbjct: 189 IAAI-KQAVSIPVFANGDITSPQKARAVLDATGADGLLIGRAAQGRPWIFREVEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISA 257
               +P    V++     ++A
Sbjct: 248 EHLPAPALDEVERILLEHLAA 268


>gi|261191538|ref|XP_002622177.1| dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239589943|gb|EEQ72586.1| dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239612649|gb|EEQ89636.1| dihydrouridine synthase [Ajellomyces dermatitidis ER-3]
 gi|327351718|gb|EGE80575.1| dihydrouridine synthase [Ajellomyces dermatitidis ATCC 18188]
          Length = 564

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 60/203 (29%), Positives = 94/203 (46%), Gaps = 14/203 (6%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
            ++ L GD + + G    ++PL +Q    D   L++AA+ VE F  + ++LN+GCP    
Sbjct: 94  GESPLPGDIRYLDGNPALDRPLIVQFCANDPDDLLQAARTVEPF-CDAVDLNLGCPQGIA 152

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            +G +GA L  +PD++   I  + + LSIPVT K RI    Q          + I  +G 
Sbjct: 153 RKGHYGAFLQEHPDLIYKLINTLHRELSIPVTAKFRI----QETKEKTLEYARMILSAGA 208

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALK 205
           + I +H R+   KG     N  + +  Y I Y      PD  I  NG +    D+ + L+
Sbjct: 209 SIIAVHGRRREQKG----HNTGLADWSY-IRYLRDNLPPDTVIFANGNILNHGDIERCLE 263

Query: 206 ILPSVDGVMIGRAAYKNSAMLTT 228
                DGVM       +  + TT
Sbjct: 264 AT-GADGVMSAEGNLCDPTIFTT 285


>gi|330960008|gb|EGH60268.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 337

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 75/306 (24%), Positives = 140/306 (45%), Gaps = 31/306 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    + +  NG +    +A ++L +   DG++IGRAA     +   ++ Y 
Sbjct: 186 YDTIATIKQA-VSIPVFANGDINSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLFHG-FPNSR 291
               T  +   + V++         +   AA H+  G  +  +I R  +G +    P +R
Sbjct: 245 RTGETLPALQLSEVERIL-------LEHLAALHVFYGDVMGVRIARKHVGWYLATLPGAR 297

Query: 292 RCRHIL 297
             R + 
Sbjct: 298 EFRALF 303


>gi|260779561|ref|ZP_05888451.1| tRNA-dihydrouridine synthase B [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260604370|gb|EEX30674.1| tRNA-dihydrouridine synthase B [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 285

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 53/193 (27%), Positives = 93/193 (48%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A
Sbjct: 33  SVQIAGADPQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRFPDIIEDILKA 92

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+ +PVT+K R G D D    V +  L +     G+  + +H R    + KG     
Sbjct: 93  VVNAVDVPVTLKTRTGWDPDNKNCVQIAKLAED---CGIQALALHGRTKACMYKG----- 144

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K+      I  NG ++   +A ++L     D +MIGR A     +
Sbjct: 145 -----EAEYDSIRAVKQAISIPVIA-NGDIDSPEKAKRVLEYTGADALMIGRPAQGRPWI 198

Query: 226 LTTVDEYFSNPLT 238
              +  +  N  T
Sbjct: 199 FQEIQHFLENGTT 211


>gi|289168865|ref|YP_003447134.1| tRNA-dihydrouridine synthase [Streptococcus mitis B6]
 gi|288908432|emb|CBJ23274.1| tRNA-dihydrouridine synthase [Streptococcus mitis B6]
          Length = 348

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 113/239 (47%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 49  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 107

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 108 EESLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + +          +H R         ++     + D +
Sbjct: 168 PLTVKMRTGWAD--PSLAVENALAAEAAGVAALA-MHGRT--------REQMYTGHADLE 216

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++++ +    +    NG +  + +A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 217 TLHDVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFHQINHYFE 275


>gi|163843386|ref|YP_001627790.1| NifR3 family TIM-barrel protein [Brucella suis ATCC 23445]
 gi|163674109|gb|ABY38220.1| TIM-barrel protein, nifR3 family [Brucella suis ATCC 23445]
          Length = 333

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 122/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GC + +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H GGK+
Sbjct: 254 ANGILDYIIRHYEDMLDHYGGKI 276


>gi|16272917|ref|NP_439142.1| hypothetical protein HI0979 [Haemophilus influenzae Rd KW20]
 gi|1176212|sp|P44965|DUSB_HAEIN RecName: Full=tRNA-dihydrouridine synthase B
 gi|1574007|gb|AAC22639.1| nitrogen fixation protein (nifR3) [Haemophilus influenzae Rd KW20]
          Length = 330

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLNYTGADAIMIGRAALGNPWLFQAVE 238


>gi|314968036|gb|EFT12135.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL037PA1]
          Length = 355

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 74/286 (25%), Positives = 117/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  +L GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 19  GLYVCEMITSRGLLYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 79  VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 136

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 137 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 187

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 188 NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCAMI 247

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 248 -RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 287


>gi|50303583|ref|XP_451733.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640865|emb|CAH02126.1| KLLA0B04499p [Kluyveromyces lactis]
          Length = 425

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 108/238 (45%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K        + G    ++PL +Q 
Sbjct: 25  MVDQSELAWRILSRKY-GATLAYTPMFHAKLFATSEKYRKDMWCELDGDEKIDRPLVVQF 83

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK+V++   + ++LN+GCP     +G +GA LM + D++   I+ + + 
Sbjct: 84  CANDPEYLLQAAKLVQN-KCDAVDLNIGCPQGIARKGKYGAFLMEDWDLISRLISTLHEH 142

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K R+  + +          K I KSG   + +H R      L  +  ++    
Sbjct: 143 LDVPVTAKIRVFPERE----KTLEYAKMILKSGAQFLTVHGR------LREQKGQQTGLA 192

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           D++I+  ++   P D     NG +   ED+S+ +  +   DGVM       N  +  T
Sbjct: 193 DWEIIKYLRDNLPQDTVFFANGNILYPEDISRCMNKI-HCDGVMSAEGNLYNPGIFNT 249


>gi|115524762|ref|YP_781673.1| nifR3 family TIM-barrel protein [Rhodopseudomonas palustris BisA53]
 gi|115518709|gb|ABJ06693.1| putative TIM-barrel protein, nifR3 family [Rhodopseudomonas
           palustris BisA53]
          Length = 344

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 107/246 (43%), Gaps = 25/246 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLV 63
           TD  +R  A  L    ++ +EM  +D ++ G   ++         P  +Q+ G +   + 
Sbjct: 32  TDAPFRRLAASL-GAGVVVSEMTASDDLVNGRPMSVRRCDAGGIGPHVVQLAGCEPHWMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I E  G + I++N+GCP+  V  G  G+ LM +       I A   A+++PVT+K 
Sbjct: 91  EGARIAEAGGADIIDINMGCPARHVTGGQSGSALMRDLAHALTLIEATVNAVNVPVTLKM 150

Query: 124 RIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDI 178
           R+G DD+      RN   L +  + +GV  I +H R      KG            D+  
Sbjct: 151 RLGWDDRC-----RNAPELARRAEAAGVQLITVHGRTRHQFYKG----------EADWRA 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+K       + +NG +     A K L     D VMIGR AY    +   +  +    
Sbjct: 196 VREVKNAVTIPTV-VNGDIVSRETAAKALEQSGADAVMIGRGAYGQPWLPGQIGRWLDTG 254

Query: 237 LTGSSP 242
           +   +P
Sbjct: 255 VVEPTP 260


>gi|218530995|ref|YP_002421811.1| hypothetical protein Mchl_3045 [Methylobacterium chloromethanicum
           CM4]
 gi|218523298|gb|ACK83883.1| TIM-barrel protein, nifR3 family [Methylobacterium chloromethanicum
           CM4]
          Length = 342

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 106/220 (48%), Gaps = 19/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLV 63
           TD H R  A+ L  +A++ +EM+ A  + +GD ++ +        P  +Q+ G     + 
Sbjct: 32  TDLHMRRLAQRLGASAVV-SEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPEPMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTVK 
Sbjct: 91  EGARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTVKM 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D    ++    L +  +  G++G+ +H   R+   KG            D+  +  
Sbjct: 151 RLGWDHA--SLNAAELARRAEALGLDGVTVHGRTRQQFYKG----------QADWSAIRP 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +  E   + +  NG +  + +A   L      GVM+GRAA
Sbjct: 199 V-VEAVRIPVIANGDITGLEEARACLSQSGAAGVMVGRAA 237


>gi|151946084|gb|EDN64315.1| tRNA dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|259148496|emb|CAY81741.1| Dus1p [Saccharomyces cerevisiae EC1118]
          Length = 423

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 83/166 (50%), Gaps = 9/166 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L+ ++       R D  + L  S+ ++PL +Q   
Sbjct: 36  MVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L 
Sbjct: 96  NDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNLK 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PVT K RI  DD   ++   N  K +  +G   + +H R    KG
Sbjct: 155 VPVTAKIRI-FDDCEKSL---NYAKMVLDAGAQFLTVHGRVREQKG 196


>gi|145637283|ref|ZP_01792944.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittHH]
 gi|145269535|gb|EDK09477.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittHH]
          Length = 326

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 116/251 (46%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+ 
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVEN 239

Query: 232 YFSNPLTGSSP 242
              +      P
Sbjct: 240 LIEHDSISQMP 250


>gi|225715276|gb|ACO13484.1| tRNA-dihydrouridine synthase 4-like PP35 [Esox lucius]
          Length = 320

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 110/241 (45%), Gaps = 29/241 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + +T MIVA   LR  K     F+T   ++PL +Q   +D
Sbjct: 28  MVRYSKLAFRSLVRKYDCD-ICFTPMIVAPDFLRSVKARDSEFTTNKADRPLIVQFAASD 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 87  AQTLADAACVVAPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQVDNP 145

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKK---SGVNGIWIHARKAILKGLSPKDNRKIP 172
               ++K RI  +       LR  V   +K   +GV+ I +H R A        + R  P
Sbjct: 146 NYTTSIKIRIHKE-------LRRTVDMCQKAEAAGVSWITVHGRTA--------EERHQP 190

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            + +D +  I K++  + +  NG ++ +   +    L  VDGVM  R    N AM    +
Sbjct: 191 -VHFDAIKTI-KDSLSVPVIANGDIKSLQDVETTHQLTGVDGVMAARGLLANPAMFAGYN 248

Query: 231 E 231
           E
Sbjct: 249 E 249


>gi|309751355|gb|ADO81339.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae R2866]
          Length = 326

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKLVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|256269754|gb|EEU05021.1| Dus1p [Saccharomyces cerevisiae JAY291]
          Length = 423

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 83/166 (50%), Gaps = 9/166 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L+ ++       R D  + L  S+ ++PL +Q   
Sbjct: 36  MVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L 
Sbjct: 96  NDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNLK 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PVT K RI  DD   ++   N  K +  +G   + +H R    KG
Sbjct: 155 VPVTAKIRI-FDDCEKSL---NYAKMVLDAGAQFLTVHGRVREQKG 196


>gi|213968003|ref|ZP_03396149.1| TIM-barrel protein, NifR3 family [Pseudomonas syringae pv. tomato
           T1]
 gi|301383681|ref|ZP_07232099.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato Max13]
 gi|302059950|ref|ZP_07251491.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato K40]
 gi|302131616|ref|ZP_07257606.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato NCPPB 1108]
 gi|213927346|gb|EEB60895.1| TIM-barrel protein, NifR3 family [Pseudomonas syringae pv. tomato
           T1]
 gi|330873654|gb|EGH07803.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 337

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 121/248 (48%), Gaps = 25/248 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  AQMMADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    + +  NG ++   +A  +L +   DG++IGRAA     +   ++ Y 
Sbjct: 186 YDTIAMIKQA-VSIPVFANGDIDSPEKARHVLQATGADGLLIGRAAQGRPWIFREIEHYL 244

Query: 234 SNPLTGSS 241
              LTG +
Sbjct: 245 ---LTGET 249


>gi|76788535|ref|YP_330442.1| tRNA-dihydrouridine synthase family protein [Streptococcus
           agalactiae A909]
 gi|77405658|ref|ZP_00782746.1| NifR3/Smm1 family protein [Streptococcus agalactiae H36B]
 gi|77411533|ref|ZP_00787876.1| NifR3/Smm1 family protein [Streptococcus agalactiae CJB111]
 gi|76563592|gb|ABA46176.1| tRNA-dihydrouridine synthase family protein [Streptococcus
           agalactiae A909]
 gi|77162387|gb|EAO73355.1| NifR3/Smm1 family protein [Streptococcus agalactiae CJB111]
 gi|77175731|gb|EAO78512.1| NifR3/Smm1 family protein [Streptococcus agalactiae H36B]
          Length = 325

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 111/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV   N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAV--ENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++ K    +    NG +  +  A  ++  +  D +M+GR A  N  + T ++ +F 
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFE 250


>gi|219870355|ref|YP_002474730.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis SH0165]
 gi|219690559|gb|ACL31782.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis SH0165]
          Length = 306

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 123/281 (43%), Gaps = 38/281 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G     L E A +  + G + ++LN GCPS  V+  + G  L+  P
Sbjct: 50  GFTLSGTPVRVQLLGQHPQWLAENAALAVELGSHGVDLNCGCPSKTVNGSNGGVSLLKQP 109

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            ++     AM +A+   +PV+VK R+G D    A  + +   ++ + G   I +H R  +
Sbjct: 110 KLIYRATKAMREAVPSHLPVSVKVRLGWDSSEQAFEIAD---AVVQGGATEITVHGRTKM 166

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                  D  +   +++  + EIKK  P   I  NG + D   A K   + + D +MIGR
Sbjct: 167 -------DGYRAERINWQAIGEIKKRLPIPVIA-NGEIWDYLSAKKCREVTACDALMIGR 218

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA--ARHLHSG----G 271
            A  N   L+ V +Y + P            K  W ++   +  Y      L +G     
Sbjct: 219 GAL-NVPNLSKVVKY-NQP------------KMAWNEVLQLLFQYVHMENELDTGFYHVA 264

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312
           +++Q  R+   L   +P + +   IL  E G      HII+
Sbjct: 265 RIKQWLRY---LDKEYPEAVQLFDILKTEHGYEGLKQHIIQ 302


>gi|319775087|ref|YP_004137575.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae F3047]
 gi|329123002|ref|ZP_08251573.1| tRNA-dihydrouridine synthase B [Haemophilus aegyptius ATCC 11116]
 gi|317449678|emb|CBY85884.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae F3047]
 gi|327471933|gb|EGF17373.1| tRNA-dihydrouridine synthase B [Haemophilus aegyptius ATCC 11116]
          Length = 326

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|73540195|ref|YP_294715.1| dihydrouridine synthase TIM-barrel protein nifR3 [Ralstonia
           eutropha JMP134]
 gi|72117608|gb|AAZ59871.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ralstonia
           eutropha JMP134]
          Length = 356

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 62/248 (25%), Positives = 121/248 (48%), Gaps = 18/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+++QI GA+
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPISVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PGMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVEAVVAAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G + +    ALR + + ++ +G++ + IH R         + +    + +Y
Sbjct: 136 VPVTLKIRTGWNRE-NRNALR-IARMVEDAGISMLTIHGRT--------RADLYHGDAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K E   + +  NG +    +A ++L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVKAE-LRIPVVANGDITTPQKAKQVLALTGADAIMIGRAAQGRPWLFREIEHFMK 244

Query: 235 NPLTGSSP 242
                 SP
Sbjct: 245 TGELLPSP 252


>gi|13470630|ref|NP_102199.1| nitrogen reguration protein nifR3 protein [Mesorhizobium loti
           MAFF303099]
 gi|14021372|dbj|BAB47985.1| nitrogen reguration protein; NifR3 [Mesorhizobium loti MAFF303099]
          Length = 357

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 102/219 (46%), Gaps = 15/219 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADISKLV 63
           TD  +R  A       L+ +EM+ +  + +G     L       P+ + Q+ G +   + 
Sbjct: 46  TDEPFRRRAHA-HGAGLVVSEMVASGELAKGRAGFDLRIRHSGLPVHMVQLAGREAIHMA 104

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I    G + I++N+GCP+ +V  G  G+ LML+ D     I A+  A+ +PVTVK 
Sbjct: 105 EGARIAAGEGADIIDINMGCPAKKVTGGYAGSALMLDLDHALSLIEAVVGAVKVPVTVKM 164

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G D+   A+    L +  +++GV  + +H R          D R I  +         
Sbjct: 165 RLGWDEG--ALNAPILARRAEQAGVKMVTVHGRTRCQFYQGKADWRAIARV--------- 213

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           KE   + +  NG +   ++A  IL     D VM+GRA Y
Sbjct: 214 KEAVSIPVVANGDVCSPAEAAAILDQSGADAVMVGRAHY 252


>gi|6323560|ref|NP_013631.1| Dus1p [Saccharomyces cerevisiae S288c]
 gi|1730621|sp|P53759|DUS1_YEAST RecName: Full=tRNA-dihydrouridine synthase 1
 gi|587531|emb|CAA86498.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285813922|tpg|DAA09817.1| TPA: Dus1p [Saccharomyces cerevisiae S288c]
          Length = 423

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 50/166 (30%), Positives = 83/166 (50%), Gaps = 9/166 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L+ ++       R D  + L  S+ ++PL +Q   
Sbjct: 36  MVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L 
Sbjct: 96  NDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNLK 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PVT K RI  DD   ++   N  K +  +G   + +H R    KG
Sbjct: 155 VPVTAKIRI-FDDCEKSL---NYAKMVLDAGAQFLTVHGRVREQKG 196


>gi|26991500|ref|NP_746925.1| NifR3 family TIM-barrel protein [Pseudomonas putida KT2440]
 gi|38604777|sp|Q88DK5|DUSB_PSEPK RecName: Full=tRNA-dihydrouridine synthase B
 gi|24986580|gb|AAN70389.1|AE016680_9 TIM-barrel protein, putative, NifR3 family [Pseudomonas putida
           KT2440]
          Length = 337

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 116/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAAKANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVSAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+     L N+ K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGW-DRANKNGL-NVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           +  I K+   + +  NG +    +A  +L +  VDG++IGRAA     +   ++ Y 
Sbjct: 189 IGAI-KQAVSIPVFANGDITSPEKARAVLETTGVDGLLIGRAAQGRPWIFREIEHYL 244


>gi|320539409|ref|ZP_08039078.1| putative tRNA-dihydrouridine synthase B [Serratia symbiotica str.
           Tucson]
 gi|320030534|gb|EFW12544.1| putative tRNA-dihydrouridine synthase B [Serratia symbiotica str.
           Tucson]
          Length = 335

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 105/238 (44%), Gaps = 17/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  L ++QI G D
Sbjct: 17  MAGITDRPFRALCHTM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGLRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ + 
Sbjct: 76  PDDMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILHAVVNAVDVT 135

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G   +    V +  L +      +  I    R  +  G          N +YD
Sbjct: 136 VTLKIRTGWAPEHRNCVEIAQLAEDCGIQALTTIHGRTRACLFNG----------NAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            +    K+N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 186 SI-RAAKQNVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGKPWIFREIQHYL 242


>gi|28871979|ref|NP_794598.1| TIM-barrel protein , NifR3 family [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|38604772|sp|Q87VS1|DUSB_PSESM RecName: Full=tRNA-dihydrouridine synthase B
 gi|28855232|gb|AAO58293.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato str. DC3000]
 gi|331014695|gb|EGH94751.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 337

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 121/248 (48%), Gaps = 25/248 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  AQMMADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    + +  NG ++   +A  +L +   DG++IGRAA     +   ++ Y 
Sbjct: 186 YDTIAMIKQA-VSIPVFANGDIDSPEKARHVLQATGADGLLIGRAAQGRPWIFREIEHYL 244

Query: 234 SNPLTGSS 241
              LTG +
Sbjct: 245 ---LTGKT 249


>gi|154248321|ref|YP_001419279.1| nifR3 family TIM-barrel protein [Xanthobacter autotrophicus Py2]
 gi|154162406|gb|ABS69622.1| putative TIM-barrel protein, nifR3 family [Xanthobacter
           autotrophicus Py2]
          Length = 345

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 65/202 (32%), Positives = 105/202 (51%), Gaps = 14/202 (6%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM+ ++A+L G  + +L    +  PL A+QI G D   + EAA++ E  G   I++
Sbjct: 47  LVISEMVASEALLEGHPEMVLRAEGEGVPLHAVQIAGNDPYLMGEAARVAEAAGAGIIDI 106

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ RV  G+ GA L+ +  +    + A+  A+SIPVTVK R+G DD   A    +L
Sbjct: 107 NMGCPAKRVTTGAAGAALLRDLPLAQAILEAVRGAVSIPVTVKTRLGWDDT--ASTAVDL 164

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +  ++SG+  + IH R         +        D+  +  + K+   + +  NG +  
Sbjct: 165 ARMAQESGLAMVTIHGRT--------RCQFYTGRADWTAIRAV-KDAVSIPVIANGDVTA 215

Query: 200 MSQALKILPS--VDGVMIGRAA 219
            S    IL +   DGVMIGR A
Sbjct: 216 PSDGPAILDASGADGVMIGRGA 237


>gi|22537964|ref|NP_688815.1| NifR3/Smm1 family protein [Streptococcus agalactiae 2603V/R]
 gi|25011905|ref|NP_736300.1| hypothetical protein gbs1866 [Streptococcus agalactiae NEM316]
 gi|76797858|ref|ZP_00780121.1| possible transcriptional regulator [Streptococcus agalactiae
           18RS21]
 gi|77414267|ref|ZP_00790427.1| NifR3/Smm1 family protein [Streptococcus agalactiae 515]
 gi|22534864|gb|AAN00688.1|AE014274_18 NifR3/Smm1 family protein [Streptococcus agalactiae 2603V/R]
 gi|24413447|emb|CAD47525.1| Unknown [Streptococcus agalactiae NEM316]
 gi|76586761|gb|EAO63256.1| possible transcriptional regulator [Streptococcus agalactiae
           18RS21]
 gi|77159683|gb|EAO70834.1| NifR3/Smm1 family protein [Streptococcus agalactiae 515]
          Length = 325

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 56/239 (23%), Positives = 112/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K  ++L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     +I ++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   + A+ N + + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDS--SNAIENALAA-ESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++ K    +    NG +  +  A  ++  +  D +M+GR A  N  + T ++ +F 
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFE 250


>gi|309973521|gb|ADO96722.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae R2846]
          Length = 326

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|254561982|ref|YP_003069077.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens DM4]
 gi|254269260|emb|CAX25226.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens DM4]
          Length = 342

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 107/220 (48%), Gaps = 19/220 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLV 63
           TD H R  A+ L  +A++ +EM+ A  + +GD ++ +        P  +Q+ G     + 
Sbjct: 32  TDLHMRRLAQRLGASAVV-SEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPEPMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTVK 
Sbjct: 91  EGARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTVKM 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G D    ++    L +  +  G++G+ +H   R+   KG +          D+  +  
Sbjct: 151 RLGWDHA--SLNAAELARRAEALGLDGVTVHGRTRQQFYKGRA----------DWSAIRP 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           +  E   + +  NG +  + +A   L      GVM+GRAA
Sbjct: 199 V-VEAVRIPVIANGDITGLEEARACLSQSGAAGVMVGRAA 237


>gi|154498409|ref|ZP_02036787.1| hypothetical protein BACCAP_02398 [Bacteroides capillosus ATCC
           29799]
 gi|150272477|gb|EDM99662.1| hypothetical protein BACCAP_02398 [Bacteroides capillosus ATCC
           29799]
          Length = 307

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 112/258 (43%), Gaps = 25/258 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L     + TEM+ A A+   DKK+I  L     E P A QI G+D
Sbjct: 1   MAGVTDMAFRTICRELGAGYTI-TEMVSAKALCYQDKKSIPLLKLGEGEHPCAAQIFGSD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
              + EAA I  E  G + I++N+GCP  +V     G+ LM + D       A+ + A  
Sbjct: 60  EKCMEEAAAIAGEVSGADIIDINMGCPVPKVANSGDGSGLMRDVDKAVRVAEAVVRGAGE 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R+G D    ++      K+++ +GV+ + +H R         +        ++
Sbjct: 120 RPVTVKFRLGWDKG--SINCVEFAKAMEAAGVSAVAVHGRT--------RTQMYAGTANW 169

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + E+K+      I  NG + D   A  IL     D  MIGR  + N  +         
Sbjct: 170 DYIREVKQAVSIPVIA-NGDVFDGPAAAHILRYTGADMAMIGRGCFGNPWVFQQARAALE 228

Query: 235 N----PLTGSSPIKTRVD 248
                PL    P+  RVD
Sbjct: 229 GEEIPPL---PPLAERVD 243


>gi|167035862|ref|YP_001671093.1| NifR3 family TIM-barrel protein [Pseudomonas putida GB-1]
 gi|166862350|gb|ABZ00758.1| TIM-barrel protein, nifR3 family [Pseudomonas putida GB-1]
          Length = 337

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 117/237 (49%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAAKANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVGAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+     L N+ K  +++G+  + +H R         + +    + +YD 
Sbjct: 139 VTLKIRTGW-DRANKNGL-NVAKIAEQAGIQALAVHGRT--------RADLYTGDAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           +  IK+    + +  NG +    +A  +L +  VDG++IGRAA     +   ++ Y 
Sbjct: 189 IAAIKQA-VSIPVFANGDITSPEKARAVLDATGVDGLLIGRAAQGRPWIFREIEHYL 244


>gi|90020455|ref|YP_526282.1| cell division protein, FtsL -like protein [Saccharophagus degradans
           2-40]
 gi|89950055|gb|ABD80070.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Saccharophagus
           degradans 2-40]
          Length = 336

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 59/234 (25%), Positives = 114/234 (48%), Gaps = 18/234 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGDKKNI-LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L  +EM+ +D  L + DK  + L +S +  P+++QI G++
Sbjct: 18  MAGVTDLPFRQICRHY-GVGLATSEMVTSDTRLWQSDKSRLRLTYSAELAPVSVQIAGSE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA      G   +++N+GCP+ +V +   G+ L+ +   V + + A+  A+ +P
Sbjct: 77  PDMMAQAAIECVKLGAQIVDINMGCPAKKVCKKLAGSALLQDEKRVAEILTAVVNAVDVP 136

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G   +    V +  + ++I   G+  + +H R         ++ R     +YD
Sbjct: 137 VTLKTRTGWSPENRNGVTIARMAENI---GIAALTVHGRT--------RECRFKGQAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            + +I  +N  + +  NG ++   +A  +L       VM+GRAA  N  +L ++
Sbjct: 186 TLADI-VQNVSIPVIANGDIDSTDKAKHVLDYTGAQAVMVGRAALGNPWLLQSI 238


>gi|327438626|dbj|BAK14991.1| tRNA-dihydrouridine synthase [Solibacillus silvestris StLB046]
          Length = 322

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 107/239 (44%), Gaps = 22/239 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDLVFRHVVAEAGRPDVFFTEFTNSESYCHPDGIKSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPDNFRKMSIGMAELGFKGIDINMGCPVPNVAGRGKGSGLILRPDVAAELIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +  I K  +  + IH R    K +S  D        +
Sbjct: 138 LPVSVKTRLGYKE---IDEWKEWLTHILKQDIANLSIHLRTR--KEMSAVDAH------W 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           +++ EIK    +  P+  + +NG + D    L++     +DG+MIGR  +KN      V
Sbjct: 187 ELIPEIKALRDEIAPNTLLTINGDIPDRQVGLELAEKYGIDGIMIGRGIFKNPFAFEKV 245


>gi|91228890|ref|ZP_01262792.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
 gi|91187555|gb|EAS73885.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
          Length = 322

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 115/245 (46%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P+I+ + + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L ++    G+  + +H R    + KG +          +
Sbjct: 136 VTLKTRTGWDTDNKNCVQIAKLAEN---CGIQALALHGRTKACMYKGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 183 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYL 241

Query: 234 SNPLT 238
            N  T
Sbjct: 242 ENGTT 246


>gi|320103323|ref|YP_004178914.1| tRNA-U20-dihydrouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319750605|gb|ADV62365.1| tRNA-U20-dihydrouridine synthase [Isosphaera pallida ATCC 43644]
          Length = 393

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 121/264 (45%), Gaps = 17/264 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M  +T   +R   R      L+ T+++   ++L   ++ +    T   ++P+A+Q+ G+ 
Sbjct: 65  MAGFTSLAFRLSVRERGGLGLVTTDLVNCRSLLENRQRALELTETDPADRPVAMQLYGSK 124

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I ++  AA  + + G   +++N+GCP  +V +   G+ LM   D     +  M KA+ +P
Sbjct: 125 IEEMTAAAARLVERGATLVDINMGCPVRKVVKTGGGSALMCEVDNAARLVEEMVKAVEVP 184

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D+    ++  +L ++ +++G   + +H R    +G     NR+        
Sbjct: 185 VTIKTRLGWDEHT--LSAPDLARAFEQAGAAALVVHGRTRA-QGFKGPVNRE----GIRA 237

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E  K  P   +G NG +  +  A  +        V +GR A  N  +   +D +    
Sbjct: 238 VVEAVKTMP--VVG-NGDIRTIHDAETMFRETGCAAVSLGRGALANPFIFRHLDHWARTG 294

Query: 237 LTGSSP-IKTRVD--KDFWRKISA 257
             G  P    RVD  +  +R++ A
Sbjct: 295 EAGPEPEFAERVDLVRRHFRRLVA 318


>gi|312079658|ref|XP_003142269.1| tRNA-dihydrouridine synthase 4 [Loa loa]
 gi|307762565|gb|EFO21799.1| tRNA-dihydrouridine synthase 4 [Loa loa]
          Length = 333

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 110/233 (47%), Gaps = 23/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL   + + +T MI A   +  ++     FST   + P  +Q    +
Sbjct: 37  MVRYSKLPFRMLVRLYAVD-VAFTPMIYAKHFIASEQCRSAEFSTCPGDNPTIVQFATNN 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +   AA  +  +    I+LN GCP   V +  +G+ L+++P+ + D +A   + +S P
Sbjct: 96  PEEFFTAAMFISRYSRG-IDLNCGCPQRDVMKEGYGSSLLVDPERIADIVATARRRISKP 154

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K R+  + Q+     R      +K+GV+ I +H R          + R  P  D
Sbjct: 155 DFTVSIKIRLKTNRQLTLETCRQ----AEKAGVSFITVHGRTP--------EQRSEP-AD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           Y+++ ++ K +  + +  NG ++   QAL+++    VDGVM      +N AM 
Sbjct: 202 YEMI-KLIKSSLSIPVIANGNIKSYEQALQVVKYTGVDGVMSANGLLENPAMF 253


>gi|319789225|ref|YP_004150858.1| dihydrouridine synthase DuS [Thermovibrio ammonificans HB-1]
 gi|317113727|gb|ADU96217.1| dihydrouridine synthase DuS [Thermovibrio ammonificans HB-1]
          Length = 316

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 113/238 (47%), Gaps = 20/238 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M  +T   +R   R L  +   Y+E++ A  I R G++K +  F+  E+P+ LQ+ G + 
Sbjct: 14  MAGYTHSAFRLLCRELGADRT-YSELMNATGIARRGEEKELSFFTDSERPIHLQVYGQNP 72

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            ++ + A ++   +    I++N GC   +V +      L+  P+ +G  +    KAL   
Sbjct: 73  EEIAQGAYVLASKYRPEAIDINFGCSVKKVLKAKAAGYLLQYPEEMGRIVEETVKALKPL 132

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVTVK R+G  +      L  + +++ K+GV+ I +H R A+ +G S        + D
Sbjct: 133 GIPVTVKIRLGFYED----TLEEIAENLLKAGVSAIALHPRLAV-QGFS-------GSAD 180

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
           +  V  +K+    + +  +G +    Q  +       +GVM+GRAA  N  +     E
Sbjct: 181 WSRVKALKEIAGSVPVIGSGDVRSWRQIDEKFEQTGCNGVMVGRAAVSNPWIFKEYKE 238


>gi|156400870|ref|XP_001639015.1| predicted protein [Nematostella vectensis]
 gi|156226140|gb|EDO46952.1| predicted protein [Nematostella vectensis]
          Length = 317

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 71/283 (25%), Positives = 125/283 (44%), Gaps = 34/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + L +T MI++++ ++  K     F+T   ++P+ +Q     
Sbjct: 35  MVRYSKLSFRELVRRYDCD-LCFTPMIISESFVKSQKARDSEFTTNSGDRPIVVQFAANC 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSI 117
              L +A +I+  F  + ++LN GCP     +  +GA L+  P++V D +     +   I
Sbjct: 94  AKDLADATEIISPF-VDGVDLNCGCPQRWAIQERYGAHLINQPELVKDMVRQTKSRVTGI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV++K RI  D +       +L K  + +G + I IH R +       K   + P+++  
Sbjct: 153 PVSIKIRIHQDKRKTV----DLCKRAEHAGASWITIHGRTS-------KQRTEPPSME-- 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
              ++ KEN  + +  NG +      LK+  +   +GVM  R    N AM          
Sbjct: 200 -TIKLVKENLSIPVVANGDIRCTDDFLKVCEATGANGVMAARGILSNPAM---------- 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
              G S       KD W  IS S+ T +   H H    +++IT
Sbjct: 249 -YAGYSVTPVECIKD-WIDISLSLGTSFTIFHHHLLYMMEKIT 289


>gi|294790522|ref|ZP_06755680.1| putative tRNA-dihydrouridine synthase [Scardovia inopinata F0304]
 gi|294458419|gb|EFG26772.1| putative tRNA-dihydrouridine synthase [Scardovia inopinata F0304]
          Length = 398

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 74/298 (24%), Positives = 123/298 (41%), Gaps = 26/298 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++ G+ K   +  F+  EK  +LQ+ G +
Sbjct: 38  MAGVTNWPFRVLCEDYGPDGLYVAEMITARALVAGNPKAFRLTRFAPSEKFRSLQLYGVN 97

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            + + +AA ++ D    + ++LN GCP  +V     G+ L    D++ D I    A+C+ 
Sbjct: 98  PAIVQQAAAMIVDGNLADHLDLNFGCPVPKVTRRGGGSALPWKTDLLQDIIHRVVAVCQP 157

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             IPVT K R G+DD      +R     I+  G   + +HAR       G S        
Sbjct: 158 AGIPVTAKIRTGIDDD--HSTMREAATIIEGEGCACVTLHARTTAQYYGGHS-------- 207

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
             D+  + E+K+      IG NG +     AL ++     DGV +GR       +   + 
Sbjct: 208 --DWSKIAELKQLVSIPVIG-NGDIWSAEDALAMVEQTGCDGVAVGRGCQGRPWLFADLK 264

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             F+      SP   +V +   R     +  Y      +   +  + +H+     GFP
Sbjct: 265 NAFAGSCQRVSPSLGQVCQVIMRHARLLVDFYDGDETMA---VHDLRKHIAWYLKGFP 319


>gi|260580070|ref|ZP_05847900.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           RdAW]
 gi|260093354|gb|EEW77287.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           RdAW]
          Length = 357

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLNYTGADAIMIGRAALGNPWLFQAVE 265


>gi|237752877|ref|ZP_04583357.1| conserved hypothetical protein [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375144|gb|EEO25235.1| conserved hypothetical protein [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 319

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 71/261 (27%), Positives = 129/261 (49%), Gaps = 28/261 (10%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEIN 78
           +EMI   A+   +KK +  +  S  E P ALQI G D   I++ VE     +D G   ++
Sbjct: 39  SEMISVHALAFKNKKTLKMVEKSPLENPFALQIAGNDFGIIARAVEYLNTQKD-GIQILD 97

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALR 137
           LN GCP+ +V     G+ L+ + + + + +  + K   IP ++VK R+G D +IP     
Sbjct: 98  LNCGCPAPKVSSHGSGSSLLKDLNKLVEILKLIRKVSEIPYLSVKVRLGFDQKIPL---- 153

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + +++K + ++ + +H R  +       D  K   +DYD +  I K+N  + +  NG +
Sbjct: 154 EIAQALKDTPIDYVVVHGRTKV-------DGYKKEKIDYDSIALI-KQNLKVPLIANGEI 205

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             + ++ ++L     DGVMIGRAA +   +   + E  +     S  ++ RV  + + + 
Sbjct: 206 NSVKKSQEVLEKTGADGVMIGRAAVEKPWIFAQIKEGLTE---DSVKLRERVVLEHFDRT 262

Query: 256 SASMTDYAA----RHLHSGGK 272
            +   DY A    ++LH+  K
Sbjct: 263 ISFRGDYGAIMFRKNLHAYSK 283


>gi|169824686|ref|YP_001692297.1| nitrogen regulation protein [Finegoldia magna ATCC 29328]
 gi|167831491|dbj|BAG08407.1| nitrogen regulation protein [Finegoldia magna ATCC 29328]
          Length = 305

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 68/283 (24%), Positives = 129/283 (45%), Gaps = 35/283 (12%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
            L +TEMI A  +   DKK   +L    +EK  ++QI G +   +  A + + E++ +  
Sbjct: 30  GLCFTEMISAKGLYYDDKKTKKLLDTDPREKSTSVQIFGHEPEIIAYATRFLTENYNFKS 89

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ ++ +   G+ LM + ++  D I A      +PV+VK R+G+D+   ++  
Sbjct: 90  IDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLPVSVKFRLGIDEN--SMNY 147

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKD----NRKIPNLDYDIVYEIKKENPDLFIG 192
             L +  ++  V+ I +HAR   +      D     R + N+D  +       N D F  
Sbjct: 148 MQLAQICERLKVDYITLHARTRKMFYSGEADWLHIKRVVENVDIPVF-----GNGDCFTK 202

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
                ED+ + ++   + DGV++ R A +N  +       FS+    S   K  V     
Sbjct: 203 -----EDIRKNME-YSNCDGVLLARGAMQNPFI-------FSDDENKS---KEEVIDTIK 246

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           + +   +  Y  R       + ++ +H+     GF NS + ++
Sbjct: 247 KHMQLKLEFYEERR-----AILEMRKHIQWYLKGFRNSNKVKN 284


>gi|332285254|ref|YP_004417165.1| hypothetical protein PT7_2001 [Pusillimonas sp. T7-7]
 gi|330429207|gb|AEC20541.1| hypothetical protein PT7_2001 [Pusillimonas sp. T7-7]
          Length = 353

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 111/243 (45%), Gaps = 25/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR YR   + L       +EM  ++  L  + K    L    +  P+A+QI G+D
Sbjct: 17  MAGVTDRPYRKLCKTL-GAGYAVSEMAASNPRLWNNVKTSRRLNHEGEIDPVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CKAL 115
              + EAA    D G   I++N+GCP  +V   + G+ L+ N  +V   + ++   C+  
Sbjct: 76  PDMMAEAAIFNIDKGARIIDINMGCPVKKVCNVASGSALLRNEQLVARILRSVVDACQPR 135

Query: 116 SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
            +PVT+K R G D +   AV +  L + I   GV  I +H R    + +G          
Sbjct: 136 DVPVTLKTRTGWDRESRNAVHIAQLAQDI---GVAAITLHGRTRCDLYQG---------- 182

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
             +YD + ++K+    + +  NG ++   +A  +L   + D VM+GRAA     +   + 
Sbjct: 183 EAEYDTIRDVKRAL-QIPVIANGDIDSPEKAKYVLEYTNADAVMVGRAAQGRPWIFREIS 241

Query: 231 EYF 233
            Y 
Sbjct: 242 HYL 244


>gi|302676381|ref|XP_003027874.1| hypothetical protein SCHCODRAFT_60830 [Schizophyllum commune H4-8]
 gi|300101561|gb|EFI92971.1| hypothetical protein SCHCODRAFT_60830 [Schizophyllum commune H4-8]
          Length = 282

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 67/260 (25%), Positives = 118/260 (45%), Gaps = 29/260 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE----------KPL 50
           MV+ +D  +R   R     A  YT+M+  D IL  + ++ L F  ++           P 
Sbjct: 13  MVNQSDLPFRMLVRKYGATAT-YTQMLNPDKIL--NDRDYLEFHQRDLELASNAPDGSPT 69

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCI 108
            +Q+ G D   +V+AAK V+      I+LN+GCP     EG +GA L+   D  +V D +
Sbjct: 70  IVQVCGNDTELVVQAAKRVQTLCQG-IDLNLGCPQDAAREGHYGAYLLGQKDWPLVNDIV 128

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +++  +L+IPV+ K R+      P++       +++ SG + + +H R    +       
Sbjct: 129 SSLSYSLTIPVSAKLRLCQ----PSIKTLAFATALEASGASWVTLHPRTVSAR------R 178

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           R+    D ++V  +K     P +  G     +D+ + L  L   DGVM+G     N   +
Sbjct: 179 RRQGAADLEVVRALKSALTVPVVSNGNVRHWDDVPKNLA-LTGADGVMVGETLLGNPWSV 237

Query: 227 TTVDEYFSNPLTGSSPIKTR 246
             +  +    LT +S   +R
Sbjct: 238 LQIRAFSKRALTHASKASSR 257


>gi|167855021|ref|ZP_02477795.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis 29755]
 gi|167853869|gb|EDS25109.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis 29755]
          Length = 317

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 120/281 (42%), Gaps = 38/281 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +QI G     L E A +  + G + ++LN GCPS  V+  + G  L+  P
Sbjct: 61  GFTPSGTPVRVQILGQHPQWLAENAALAVELGSHGVDLNCGCPSKTVNGSNGGVSLLKQP 120

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            ++     AM +A+   +PV+VK R+G D    A  + +   ++ + G   I +H R  +
Sbjct: 121 KLIYRATKAMREAVPSHLPVSVKVRLGWDSSEQAFEIAD---AVVQGGATEITVHGRTKM 177

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                  D  +   +++  + EIKK  P   I  NG + D   A K   + + D +MIGR
Sbjct: 178 -------DGYRAERINWQAIGEIKKRLPIPVIA-NGEIWDYLSAKKCREVTARDALMIGR 229

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA--ARHLHSG----G 271
            A  N   L+ V             +K    K  W  +   +  Y      L +G     
Sbjct: 230 GAL-NVPNLSKV-------------VKYNQPKMAWNDVLQLLFQYVHMENELDTGFYHVA 275

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312
           +++Q  R+   L   +P + +   IL  E G      HII+
Sbjct: 276 RIKQWLRY---LDKEYPEAVQLFDILKTEHGYEGLKQHIIQ 313


>gi|95931069|ref|ZP_01313796.1| dihydrouridine synthase, DuS [Desulfuromonas acetoxidans DSM 684]
 gi|95132878|gb|EAT14550.1| dihydrouridine synthase, DuS [Desulfuromonas acetoxidans DSM 684]
          Length = 320

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 81/166 (48%), Gaps = 9/166 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----GDKKNILGFSTQEKPLALQIG 55
           M   T+R  R     +    +++TE +    + R      D++ IL     + PL +Q+ 
Sbjct: 18  MQGLTNRAMRAVQCDIGQPDVVFTEFVRVSHVARQRITPNDRREILA-GVDDVPLVVQLI 76

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G     L EAA+IV D G   +NLN+GCP  R   G  G  ++  P+ +GDC+ A+  A 
Sbjct: 77  GHRSESLAEAAQIVADLGGAHVNLNMGCPFGRTTTGKTGGAMLQEPEKIGDCLRAIRAAF 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
              V+VK R G DD      + +L+   +K GV+ I +H R  + K
Sbjct: 137 HGSVSVKVRAGYDD---PEQIFDLLPVFEKYGVDFIVLHPRTVVQK 179


>gi|253316294|ref|ZP_04839507.1| hypothetical protein SauraC_09171 [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
          Length = 234

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 106/231 (45%), Gaps = 28/231 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEHPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R       + K+  K+ +
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLR-------TRKEMSKV-D 183

Query: 174 LDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
             ++++  IK       P+  + +NG + D    L++     +DGVMIGR 
Sbjct: 184 AHWELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRG 234


>gi|222112079|ref|YP_002554343.1| tim-barrel protein, nifr3 family [Acidovorax ebreus TPSY]
 gi|221731523|gb|ACM34343.1| TIM-barrel protein, nifR3 family [Acidovorax ebreus TPSY]
          Length = 353

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 75/312 (24%), Positives = 129/312 (41%), Gaps = 33/312 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+A+QI
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 71

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G D + + EAA    D G   I++N+GCP+ +V     G+ LM N  +   + + + A 
Sbjct: 72  AGTDAAMMAEAALYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAEAVVAA 131

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           C    +PVT+K R G   Q     +  L +  +  G+  + +H R         ++    
Sbjct: 132 CAPRGVPVTLKMRTGWCQQHKNAVV--LARRFEDVGIQMLTVHGRT--------REQGYK 181

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTV 229
              +YD +  +K     + +  NG +    +A  +L +   D VMIGRAA     +   +
Sbjct: 182 GQAEYDTIAAVKAAV-RVPVVANGDITSPEKARAVLAATGADAVMIGRAAQGRPWIFREI 240

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
             Y +     + P+   V     R +   + D+   +  + G ++   +H+       P 
Sbjct: 241 GHYLATGEHLAPPLVAEVR----RLLLEHLQDHYGLYGEASG-VRSARKHIAWYVRALPG 295

Query: 290 SRRCR-HILTVE 300
               R HI T+E
Sbjct: 296 GEALRQHINTIE 307


>gi|253575078|ref|ZP_04852417.1| dihydrouridine synthase DuS [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251845534|gb|EES73543.1| dihydrouridine synthase DuS [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 324

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 87/188 (46%), Gaps = 18/188 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L F+  E+P+   I G       + +  +   G+  I++N+GCP   V     G+ L+L 
Sbjct: 63  LLFTEDEQPIVAHIWGDKPEYFAKMSIGMAKQGFQGIDINMGCPVPNVATNGMGSGLILR 122

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           P +  + I A  KA  +PV+VK R+G ++       R+ +  I K  +  + IH R    
Sbjct: 123 PTVAAEVIQA-AKAGGLPVSVKTRLGFNE---VEEWRDWLTHILKQDIVNLSIHLRT--- 175

Query: 161 KGLSPKDNRKIPNLDYDIVYEIK----KENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
                ++        ++++ EIK    +  P   + +NG + D    LK+     VDG+M
Sbjct: 176 -----REEMSQVAAHWELIPEIKALRDQVAPQTLLTINGDIPDRQTGLKLAEQYGVDGIM 230

Query: 215 IGRAAYKN 222
           IGR  +KN
Sbjct: 231 IGRGIFKN 238


>gi|145640649|ref|ZP_01796232.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           R3021]
 gi|145274575|gb|EDK14438.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           22.4-21]
          Length = 353

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 116/251 (46%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+ 
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVEN 266

Query: 232 YFSNPLTGSSP 242
              +      P
Sbjct: 267 LIEHDSISQMP 277


>gi|113954689|ref|YP_729811.1| dihydrouridine synthase family protein [Synechococcus sp. CC9311]
 gi|113882040|gb|ABI46998.1| dihydrouridine synthase family protein [Synechococcus sp. CC9311]
          Length = 331

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 116/244 (47%), Gaps = 15/244 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G  +  + G   +  P+ +Q+       + 
Sbjct: 27  SDRIFRQLVRRWAPDALLFTEMVNATSLELGHGRLKMDGLQEETGPIGVQLFDHHPDAMA 86

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+   D G   I++N+GCP  ++     G+ L+ +PD+    +  +  A+ +PVTVK 
Sbjct: 87  DAARRAADAGAFLIDINMGCPVRKIARKGGGSGLIRDPDLACRIVDTVVAAVGLPVTVKT 146

Query: 124 RIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           R+G     + + A A  N  + ++++G   + +H R         ++ R     D++ + 
Sbjct: 147 RLGWCGEHNAVKAQAAVNWCRRLEEAGARMLTLHGRT--------REQRFSGTADWNAIA 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K       I  NG +    +AL+ L     DGVM+GR +     ++  +D   S+   
Sbjct: 199 AVKAALSIPVIA-NGDVNSPEEALRCLRITGADGVMVGRGSMGAPWLVGQIDAALSDRPI 257

Query: 239 GSSP 242
            ++P
Sbjct: 258 PATP 261


>gi|188584754|ref|YP_001916299.1| TIM-barrel protein, nifR3 family [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|179349441|gb|ACB83711.1| TIM-barrel protein, nifR3 family [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 327

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 65/252 (25%), Positives = 122/252 (48%), Gaps = 34/252 (13%)

Query: 1   MVDWTDRHYRFFARLLT--NNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGG 56
           M   TD  YR   R+L   +  L+  EM+ A  ++ G+KK   ++    Q    + QI G
Sbjct: 20  MAGVTDYPYR---RILAKFSPGLICGEMVSAKGMVYGNKKTEEMVIHHNQGVHYSQQIFG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D   + +AA  +E+ G + I++N+GCP+ ++ +   G+ L+  P +  + +  +  +++
Sbjct: 77  SDPKVMADAAVKLENLGVDSIDVNMGCPAPKIVKNGEGSALLKKPHLAQEIVREIVNSVN 136

Query: 117 IPVTVKCRIGVDDQIP---AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVTVK R G D +      +ALR     +++ G+  + +H R          + +    
Sbjct: 137 LPVTVKIRKGFDRKSSDPLELALR-----LQEVGIKALAVHGRTC--------EQQYSGK 183

Query: 174 LDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV- 229
            D+++V ++K       IG NG +   ED   AL+ + + DG+M+GR    N  ++    
Sbjct: 184 ADWEVVAKLKNYLDIPVIG-NGDIFSSEDAVSALE-MTACDGIMLGRGLMGNPWLIEQTK 241

Query: 230 -----DEYFSNP 236
                DE   +P
Sbjct: 242 GMLIKDEKIESP 253


>gi|310815776|ref|YP_003963740.1| tRNA-dihydrouridine synthase, putative [Ketogulonicigenium vulgare
           Y25]
 gi|308754511|gb|ADO42440.1| tRNA-dihydrouridine synthase, putative [Ketogulonicigenium vulgare
           Y25]
          Length = 337

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 104/232 (44%), Gaps = 22/232 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADIS 60
           TD  YR           + +EMI +  IL      I    LG    +   A+Q+ G +  
Sbjct: 33  TDLPYRQMVGAF-GAGWVVSEMIASQEILTNRPGTIEKAELGLD--QANTAVQLAGREAE 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK++E  G   I++N+GCP+ +V  G  G+ LM + D     I A   A+ +PVT
Sbjct: 90  WMAEAAKMIEGNGAQLIDINMGCPAKKVTSGLSGSALMRDLDHALRLIEATVGAVKVPVT 149

Query: 121 VKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G  DDQI A     L K  + +G+  + IH R         +        D+  +
Sbjct: 150 LKMRLGWDDDQINA---PELAKRAEGAGIKLVTIHGRT--------RCQFYTGRADWAAI 198

Query: 180 YEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             +K+    P +  G    ++D   AL+     DGVMIGR A     +L  V
Sbjct: 199 RAVKQAVSIPVIANGDICSVQDARDALE-QSGADGVMIGRGAQGRPWLLAEV 249


>gi|317968889|ref|ZP_07970279.1| nitrogen regulation protein NifR3 family protein [Synechococcus sp.
           CB0205]
          Length = 347

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 76/321 (23%), Positives = 142/321 (44%), Gaps = 30/321 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G   + +   + ++ P+ +Q+       + 
Sbjct: 47  SDRIFRGLVRRWAPDALLFTEMVNATSLELGHGLQKVEELALEQGPIGVQLFDHRPQSMA 106

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++ +   G+ L+  PD+    +  +  A+SIP+TVK 
Sbjct: 107 DAARRAEAAGAFLIDINMGCPVKKIAKKGGGSGLIREPDLASRIVETVSAAVSIPITVKT 166

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D  P    R L    + +G   + +H R         ++     + D+  +  
Sbjct: 167 RLGWCGSDLDPVAWCRQL----ESAGAQLLTLHGRT--------REQGFKGSADWQAIAA 214

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN---P 236
            K+      I  NG +   + AL+ L     DGVM+GR +     ++  +D   S    P
Sbjct: 215 FKRALAIPVIA-NGDINSAADALRCLEQTGADGVMVGRGSMGAPWLVGQIDAALSGRPIP 273

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            + S+  +  + K+  + + A+  D+          L    +HM    +GF  + + RH 
Sbjct: 274 ESPSALERVLLAKEQLQALVAAKGDHG---------LLIARKHMGWTCNGFTGAPQLRHA 324

Query: 297 LTVEAGASTATHHIIETAFNL 317
           L      + A   + +TA  L
Sbjct: 325 LMRAPTPAEAIALLDQTAAAL 345


>gi|224003889|ref|XP_002291616.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220973392|gb|EED91723.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 333

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 75/298 (25%), Positives = 128/298 (42%), Gaps = 30/298 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           MVD +D  YR   R   N +L +T MI A   +   K       I G  +Q++PL  Q  
Sbjct: 3   MVDASDLPYRLLTRRY-NTSLCFTPMIHAKMFIDKPKYREKFWKIEGMPSQDRPLIAQFC 61

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMCK 113
           G D + L++A K++E    + +++N GCP      G +GA LM   N D + + +  +  
Sbjct: 62  GHDKNVLLQAMKVLEPH-VDGVDINCGCPQNIAKRGRYGAFLMEEDNGDKIVEIVQHLTA 120

Query: 114 ALSIPVTVKCRI---GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            L++PV+VK RI   G++D +       L K +  +G   + IH R         K +  
Sbjct: 121 NLNVPVSVKLRILPTGIEDSLA------LYKRLVDAGAAMLTIHGRTR----FQNKVDTG 170

Query: 171 IPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
             N DY   +V  +    P +  G    L+++ +  ++   VDGVM      +   + T 
Sbjct: 171 TANWDYIRQVVDLVGDRVPVIANGNICNLDEVRKCFEVT-GVDGVMSSEGILEYPPLFTE 229

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
            +   S     + P + ++ +D+         +Y +     G  L+ I  H+    H 
Sbjct: 230 TN-VESTGFKRTGPGRLQMAEDYLELCK----EYPSEEGGQGSGLKCIRAHLHRFLHA 282


>gi|157148839|ref|YP_001456158.1| tRNA-dihydrouridine synthase B [Citrobacter koseri ATCC BAA-895]
 gi|157086044|gb|ABV15722.1| hypothetical protein CKO_04672 [Citrobacter koseri ATCC BAA-895]
          Length = 321

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGVRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKV-SIPIIANGDITDPHKARAVLNYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|219685551|ref|ZP_03540368.1| putative histidine phosphokinase/phophatase [Borrelia garinii
           Far04]
 gi|219672950|gb|EED29972.1| putative histidine phosphokinase/phophatase [Borrelia garinii
           Far04]
          Length = 329

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 115/250 (46%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISVKGILNGSKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G D  +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNDPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +   G++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEV--NDWLGFLLGFGIDMLTVYPRLAVNQSEGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKFSSKHF 254


>gi|145632364|ref|ZP_01788099.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           3655]
 gi|144987271|gb|EDJ93801.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           3655]
          Length = 353

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLNYTGADAIMIGRAALGNPWLFQAVE 265


>gi|145628084|ref|ZP_01783885.1| DNA-binding protein Fis [Haemophilus influenzae 22.1-21]
 gi|145630072|ref|ZP_01785854.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           R3021]
 gi|145638199|ref|ZP_01793809.1| DNA-binding protein Fis [Haemophilus influenzae PittII]
 gi|144979859|gb|EDJ89518.1| DNA-binding protein Fis [Haemophilus influenzae 22.1-21]
 gi|144984353|gb|EDJ91776.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           R3021]
 gi|145272528|gb|EDK12435.1| DNA-binding protein Fis [Haemophilus influenzae PittII]
          Length = 353

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 116/251 (46%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+ 
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKLVLDYTGADAIMIGRAALGNPWLFQAVEN 266

Query: 232 YFSNPLTGSSP 242
              +      P
Sbjct: 267 LIEHNSISQMP 277


>gi|300692483|ref|YP_003753478.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum PSI07]
 gi|299079543|emb|CBJ52221.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum PSI07]
          Length = 356

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 117/242 (48%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  +++G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRE-----HRNALTVARIAQEAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYDTIAAVKG-SVRIPVVANGDITTPAKARHVLDVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YF 233
           + 
Sbjct: 242 FL 243


>gi|328875032|gb|EGG23397.1| nuclear receptor coactivator NC0A-62 [Dictyostelium fasciculatum]
          Length = 1243

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 97/204 (47%), Gaps = 14/204 (6%)

Query: 38   KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
            K  L F   ++P+  Q+ G D     +AA +V+D G++ +++N+GCP  +V + S G+ L
Sbjct: 851  KQDLAFHEIQRPIVAQLFGCDPEAFKKAASLVKDLGFDAVDINMGCPVRKVLKQSAGSAL 910

Query: 98   MLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++ PD+  D I A  + +  SIPV VK RIG ++      +   +  +  +  + I +H 
Sbjct: 911  IVQPDLARDIIIATREGVDNSIPVFVKTRIGFEEN----EMDRWIPQLVDAQPDAISLHL 966

Query: 156  RKAILKGLSPKD----NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            R        P      ++ I  ++  +          L I  NG ++   +A + L S  
Sbjct: 967  RTKKELSDCPAHWELVDKFISTVEDRVGGSASTLRRPLLIA-NGDIDSRHEAKEKLESYK 1025

Query: 210  -VDGVMIGRAAYKNSAMLTTVDEY 232
             ++GVM+GR  Y N       D+Y
Sbjct: 1026 RLNGVMVGRGLYGNPWFFCEDDKY 1049


>gi|237730178|ref|ZP_04560659.1| tRNA-dihydrouridine synthase B [Citrobacter sp. 30_2]
 gi|226908784|gb|EEH94702.1| tRNA-dihydrouridine synthase B [Citrobacter sp. 30_2]
          Length = 321

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|330963424|gb|EGH63684.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 337

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/247 (26%), Positives = 120/247 (48%), Gaps = 25/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  AQMMADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    + +  NG ++   +A  +L +   DG++IGRAA     +   ++ Y 
Sbjct: 186 YDTIAMIKQA-VSIPVFANGDIDSPEKARHVLQATGADGLLIGRAAQGRPWIFREIEHYL 244

Query: 234 SNPLTGS 240
              LTG 
Sbjct: 245 ---LTGE 248


>gi|315640501|ref|ZP_07895609.1| dihydrouridine synthase [Enterococcus italicus DSM 15952]
 gi|315483705|gb|EFU74193.1| dihydrouridine synthase [Enterococcus italicus DSM 15952]
          Length = 331

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVQQAGAPDVFFTEFTNSDSYCHPDGIESVRGRLVFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFRQMSLGMAEMGFKGIDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G ++       ++ ++ + +  +  + IH R              IP    
Sbjct: 138 LPVSVKTRLGFEE---LAEHQDWIEHLLRQDIANLSIHLRTRKEMSKVAAHWEMIP---- 190

Query: 177 DIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            +V  I+ +  P   I +NG + D +  L +     VDG+MIGR  +KN
Sbjct: 191 -LVTAIRDRVAPQTTITINGDIPDRATGLALAEKYGVDGIMIGRGIFKN 238


>gi|301169704|emb|CBW29305.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae 10810]
          Length = 326

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNSVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|229846037|ref|ZP_04466149.1| DNA-binding protein Fis [Haemophilus influenzae 7P49H1]
 gi|229811041|gb|EEP46758.1| DNA-binding protein Fis [Haemophilus influenzae 7P49H1]
          Length = 353

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 116/251 (46%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+ 
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVEN 266

Query: 232 YFSNPLTGSSP 242
              +      P
Sbjct: 267 LIEHNSISQMP 277


>gi|197302990|ref|ZP_03168039.1| hypothetical protein RUMLAC_01717 [Ruminococcus lactaris ATCC
           29176]
 gi|197297939|gb|EDY32490.1| hypothetical protein RUMLAC_01717 [Ruminococcus lactaris ATCC
           29176]
          Length = 352

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 53/194 (27%), Positives = 84/194 (43%), Gaps = 20/194 (10%)

Query: 43  FSTQEKPLAL-----------QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           FST+EK   L           QI        +E AK + ++GY E+NLN+GCPS  V   
Sbjct: 82  FSTREKKDVLPENNRGVLAVPQILTNQAEDFIETAKKLAEYGYEEVNLNLGCPSRTVVTK 141

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             GA  +  PD +   +  + K     ++VK RIG+ +         L+K   +  +  +
Sbjct: 142 GRGAGFLEEPDRLDRFLDEIFKKREWKISVKTRIGMSE---PEEFEELLKIYNRYPLEEL 198

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
            +H R      L     +  PNLD   +   +  NP  + G     ED+ +  +  P +D
Sbjct: 199 IVHPR------LQKDFYKNTPNLDVFAMAAEESRNPLCYNGDICNAEDLKRLRERFPKLD 252

Query: 212 GVMIGRAAYKNSAM 225
            VM+GR    + A+
Sbjct: 253 CVMVGRGVLADPAL 266


>gi|146313333|ref|YP_001178407.1| tRNA-dihydrouridine synthase B [Enterobacter sp. 638]
 gi|145320209|gb|ABP62356.1| tRNA-U20-dihydrouridine synthase [Enterobacter sp. 638]
          Length = 321

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   +  +  A+ +P
Sbjct: 76  PEEMAQAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILLGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          N
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPIIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|302342599|ref|YP_003807128.1| dihydrouridine synthase DuS [Desulfarculus baarsii DSM 2075]
 gi|301639212|gb|ADK84534.1| dihydrouridine synthase DuS [Desulfarculus baarsii DSM 2075]
          Length = 326

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 100/208 (48%), Gaps = 21/208 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L+YTEMI A  ++RG KK +    T  +E+P+ALQ+ GAD   +  AA +      + I+
Sbjct: 36  LVYTEMISAVGLVRGHKKTLELCLTLPEERPVALQLFGADPEIMGRAAALASRMPVDLID 95

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V     G+ L+ +       +AA+ +A S+P TVK R+G  D      L  
Sbjct: 96  INMGCPARKVRRQGAGSALLEDIPRAAAVMAAVAQAASLPATVKLRLGPSDD----DLER 151

Query: 139 LVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +V  +  +G   + +HAR  +    G            D+  +  +    P   IG NG 
Sbjct: 152 IVPPLLAAGAKAVCLHARTTRQAFAG----------QADWAAIARLSAWCPVPVIG-NGD 200

Query: 197 LEDMSQALKILPSVD--GVMIGRAAYKN 222
           +     AL +L   +   VMIGR A  +
Sbjct: 201 VRGEQDALGMLRQTNCQAVMIGRGAMGD 228


>gi|167586152|ref|ZP_02378540.1| putative TIM-barrel protein, nifR3 family [Burkholderia ubonensis
           Bu]
          Length = 354

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 118/246 (47%), Gaps = 27/246 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVKQIVEAVVGAVGTG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G +      
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAITVARLAEA---AGISMLTVHGRTRADLYRGEA------ 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               +Y+ +  +K     + +  NG +    +A  +L +   D +MIGRAA     +   
Sbjct: 188 ----EYETIAAVKAA-VGIPVVANGDITSPQKAKAVLDATGADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFS 234
           +D +  
Sbjct: 243 IDHFLQ 248


>gi|254230100|ref|ZP_04923497.1| tRNA-dihydrouridine synthase B [Vibrio sp. Ex25]
 gi|151937389|gb|EDN56250.1| tRNA-dihydrouridine synthase B [Vibrio sp. Ex25]
          Length = 340

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 115/245 (46%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 35  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P+I+ + + A+  A+ +P
Sbjct: 94  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVP 153

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L ++    G+  + +H R    + KG +          +
Sbjct: 154 VTLKTRTGWDTDNKNCVQIAKLAEN---CGIQALALHGRTKACMYKGEA----------E 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 201 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYL 259

Query: 234 SNPLT 238
            N  T
Sbjct: 260 ENGTT 264


>gi|68249564|ref|YP_248676.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae 86-028NP]
 gi|68057763|gb|AAX88016.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae 86-028NP]
          Length = 326

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 114/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNI-LGFSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K  + L +S      A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAYSDDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVEKILREVVAAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN  I  
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGKAEYDN--IKA 188

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           +   IV  +           NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 189 VKQAIVIPVIA---------NGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|70734170|ref|YP_257810.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens Pf-5]
 gi|68348469|gb|AAY96075.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens Pf-5]
          Length = 337

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 126/261 (48%), Gaps = 16/261 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVNEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRENKNGL--TVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ + S  
Sbjct: 189 IAAI-KQAVSIPVFANGDIDSPEKARRVLHATGADGLLIGRAAQGRPWIFREIEHFLSTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISA 257
            T  +P    V++     ++A
Sbjct: 248 ETLPAPELFEVERILLEHLAA 268


>gi|54295685|ref|YP_128100.1| hypothetical protein lpl2773 [Legionella pneumophila str. Lens]
 gi|53755517|emb|CAH17016.1| hypothetical protein lpl2773 [Legionella pneumophila str. Lens]
          Length = 328

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 113/239 (47%), Gaps = 24/239 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G +   L EAA
Sbjct: 33  FRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKLLAYQISGNEPHVLAEAA 92

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
             ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+T+K RI 
Sbjct: 93  AKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISKVRAAISIPLTIKIRIQ 152

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            +++   +A     K I+ +G + + +H R+       P + ++I N+         K  
Sbjct: 153 NNEKDLTLA-----KQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI---------KNA 198

Query: 187 PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA------YKNSAMLTTVDEYFSNPL 237
            ++ + +NG + ++S   K L   + DG MI RA       Y++   L T D  F   L
Sbjct: 199 VNIPVIVNGDISNISSLRKALEISACDGFMISRAGTGKPWLYRDLLNLETNDVAFDEKL 257


>gi|148826373|ref|YP_001291126.1| DNA-binding protein Fis [Haemophilus influenzae PittEE]
 gi|148716533|gb|ABQ98743.1| DNA-binding protein Fis [Haemophilus influenzae PittEE]
          Length = 353

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 116/251 (46%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+ 
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVEN 266

Query: 232 YFSNPLTGSSP 242
              +      P
Sbjct: 267 LIEHNSISQMP 277


>gi|188025691|ref|ZP_02959486.2| hypothetical protein PROSTU_01344 [Providencia stuartii ATCC 25827]
 gi|188022767|gb|EDU60807.1| hypothetical protein PROSTU_01344 [Providencia stuartii ATCC 25827]
          Length = 337

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    +++P   ++QI G D
Sbjct: 33  MAGITDRPFRSLCYDM-GAGMTVSEMLSSNPQVWKTDKSRLRMIHRDEPGVRSVQIAGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   ++A+ KA+ +P
Sbjct: 92  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPDLVKSILSAVVKAVDVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   K  +  G+  + IH R    +  G           
Sbjct: 152 VTLKIRTGWSPE-----ERNCIEIAKLAEDCGIQALTIHGRTRACLFNG----------E 196

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +M+GRAA     +   +  
Sbjct: 197 AEYDNIRAVKQTVAIPVIA-NGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQH 255

Query: 232 YF 233
           Y 
Sbjct: 256 YL 257


>gi|326927225|ref|XP_003209793.1| PREDICTED: tRNA-dihydrouridine synthase 2-like, partial [Meleagris
           gallopavo]
          Length = 497

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 87/185 (47%), Gaps = 24/185 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G AD  + +  AK+VE      I++N+GCP     +G  GA L+ +PD +   + 
Sbjct: 83  VVFQMGSADAERALAVAKLVES-DVAGIDINMGCPKEYSTKGGMGAALLSDPDKIESILT 141

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K +  PVT K RI   V+D +      NLVK I+K+G+  I +H RK        K+
Sbjct: 142 TLVKGICKPVTCKIRILPSVEDTV------NLVKRIEKTGIAAIAVHGRK--------KE 187

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM------SQALKILPSVDGVMIGRAAYK 221
            R    +  D++  I  E   + +  NGG  D        +  +   +   VMI RAA  
Sbjct: 188 ERPQHPVHCDVIKAI-SEAVSIPVIANGGSHDFIKEYTDIETFQKATAASSVMIARAAMW 246

Query: 222 NSAML 226
           N ++ 
Sbjct: 247 NPSIF 251


>gi|300705135|ref|YP_003746738.1| tRNA-dihydrouridine synthase b [Ralstonia solanacearum CFBP2957]
 gi|299072799|emb|CBJ44154.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum CFBP2957]
          Length = 357

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 118/243 (48%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  +++G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRE-----HRNALTVARIAQEAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  +  + +  NG +   ++A ++L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYETIAAVKA-SVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YFS 234
           +  
Sbjct: 242 FLQ 244


>gi|224823445|ref|ZP_03696554.1| TIM-barrel protein, nifR3 family [Lutiella nitroferrum 2002]
 gi|224603900|gb|EEG10074.1| TIM-barrel protein, nifR3 family [Lutiella nitroferrum 2002]
          Length = 342

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 119/246 (48%), Gaps = 16/246 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EMI ++  L    K +       + +P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKRL-GAGMAVSEMITSNKALWTTAKTLRRANHDGEVEPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AA++  + G   I++N+GCP+ +V   + G+ L+ +  +VG  + A+ +A+ +P
Sbjct: 76  PAQMAAAARLNVEQGAQIIDINMGCPAKKVCNVAAGSALLRDEALVGRILEAVVQAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +    ALR + +  +  G+  + +H R         +++      +YD 
Sbjct: 136 VTLKTRTGWSRE-HKTALR-VARLAEDCGIAALALHGRT--------REDMYHGAAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+      I  NG ++   +A ++L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAISIPLIA-NGDIDSPQRARQVLDYTGADAIMIGRAAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSP 242
            T  +P
Sbjct: 245 ETLPAP 250


>gi|302694715|ref|XP_003037036.1| hypothetical protein SCHCODRAFT_37482 [Schizophyllum commune H4-8]
 gi|300110733|gb|EFJ02134.1| hypothetical protein SCHCODRAFT_37482 [Schizophyllum commune H4-8]
          Length = 284

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 107/221 (48%), Gaps = 18/221 (8%)

Query: 16  LTNNALLYTEMIVADAI----LRGDKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVE 70
           + + A+L+ E +V          G  ++I   S  EKP L  QIG AD    V+AAK+V 
Sbjct: 36  IVDKAILHAERVVDPDTGIISYNGKSRSIYQCSPVEKPYLIYQIGSADPELAVQAAKVVM 95

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDD 129
               + I+LN GCP         GA L+  PD++   + A+ +A+   + V C+I  +  
Sbjct: 96  -HDVSGIDLNCGCPKPFSTHAGMGAALLSTPDLLCSILRALREAMPPEIAVSCKIRLLST 154

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           Q   +A   LV  I ++G++ + +H R    + +  +D   I  L  +IV  +K    D+
Sbjct: 155 QEETLA---LVGKIIETGISALTVHCRT---RSMRDRDAAMIERLK-EIVDFVKASGKDI 207

Query: 190 FIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            +  NG   G ED ++ ++ +   D VMI RAA  N +  +
Sbjct: 208 AVVENGDCKGYED-AKRIREMTGCDSVMIARAAESNPSCFS 247


>gi|302530992|ref|ZP_07283334.1| dihydrouridine synthase TIM-barrel protein nifR3 [Streptomyces sp.
           AA4]
 gi|302439887|gb|EFL11703.1| dihydrouridine synthase TIM-barrel protein nifR3 [Streptomyces sp.
           AA4]
          Length = 381

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/278 (23%), Positives = 112/278 (40%), Gaps = 23/278 (8%)

Query: 25  EMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNV 81
           EMI A A++       +++ F   EKP ++Q+ G D   + EA +I+   G  + ++ N 
Sbjct: 52  EMITARAVVERHPGTMHMMTFGENEKPRSMQLYGVDPKTMAEAVRIIVGEGLADHVDSNF 111

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRN 138
           GCP A+V     GA L     +  D +    KA +   +P TVK R+G+DD        +
Sbjct: 112 GCPVAKVTRKGGGAALPFKRRLFADIVRESAKAAAEGGVPFTVKFRVGIDDD--HHTFLD 169

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +  +  G   + +HAR A          R     D+  +  +K+    + +  NG + 
Sbjct: 170 AGRIAEAEGAAAVSLHARTAA--------QRYSGQADWSKIAALKEAVTSIPVLGNGDIF 221

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               AL+++     DGV++GR       +   ++  F        P    V +   R   
Sbjct: 222 SADDALRMVAETGCDGVVVGRGCLGRPWLFGELEAAFQGREIPEGPNLGEVARVLRRH-- 279

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T+    H      ++ I +HM     GFP     R
Sbjct: 280 ---TELLIEHDGPDKAMRDIRKHMAWYLMGFPVGSELR 314


>gi|322795085|gb|EFZ17930.1| hypothetical protein SINV_15746 [Solenopsis invicta]
          Length = 357

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/281 (23%), Positives = 129/281 (45%), Gaps = 31/281 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+AD+ ++  K     F+T   ++PL +Q     
Sbjct: 28  MVRYSKLQFRTLVRQYGCD-ICFTPMILADSFVQSSKARDNEFTTHKNDQPLIVQFAANT 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  V+A+ +V  +  N ++LN GCP     +  +GA L+  P++V D +  +   +  P
Sbjct: 87  VNDFVDASVMVAPYC-NGVDLNCGCPQRWAMQEGYGADLLKKPELVKDLVYQVRNRIPRP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I    L  L ++++K+G + + +HAR       +PK   +  +LD   
Sbjct: 146 FTVSAKIRLLKDIRQTIL--LCQTLEKAGASFLTVHAR-------TPKMRNEPIDLD--- 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             +  +++  L +  NG  + +  A  +      +GVM  R    N A+ +    Y   P
Sbjct: 194 SLKFLRDHVQLPLVANGDAKSLETAKSLFKESRCEGVMSARGILTNPALFSG---YSVTP 250

Query: 237 LTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQI 276
           LT             W  I++++ T++   H H    L++I
Sbjct: 251 LTCIQD---------WLNITSTIPTEFQCFHHHLIFMLEKI 282


>gi|257868259|ref|ZP_05647912.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257874468|ref|ZP_05654121.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|325568131|ref|ZP_08144572.1| dihydrouridine synthase [Enterococcus casseliflavus ATCC 12755]
 gi|257802373|gb|EEV31245.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257808632|gb|EEV37454.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|325158332|gb|EGC70483.1| dihydrouridine synthase [Enterococcus casseliflavus ATCC 12755]
          Length = 328

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 108/232 (46%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+      R   +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVQAAGAPDVFFTEFTNSDSYCHPEGRDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V     G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEYFREMSIGLAEMGFKGIDLNMGCPVPNVAGRGKGSGLILRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +      +   +  + +  +  + IH R       + K+  K+ +  +
Sbjct: 138 LPVSVKTRLGYTE---LGEMEAWLTHVLQQDIANLSIHLR-------TRKEMSKV-DAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ E+     +  P   + +NG + D ++ L++     VDG+MIGR  +KN
Sbjct: 187 ELIPEVVALRDRIAPQTKLTINGDIPDRTKGLELAEKYGVDGIMIGRGIFKN 238


>gi|195155541|ref|XP_002018662.1| GL25830 [Drosophila persimilis]
 gi|194114815|gb|EDW36858.1| GL25830 [Drosophila persimilis]
          Length = 507

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 110/234 (47%), Gaps = 25/234 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 34  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFAHDPKYRKDALQTCPEDRPLIIQFCGND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ D +  + + LS+P
Sbjct: 93  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTDIVRTLHEKLSVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +     LR   K ++ +G   + +H R    K  L G++          
Sbjct: 152 VTCKIRIFEDRE---KTLR-YAKMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 197

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D+  + E+++  + P    G   GLED+ + L     VDGVM       N A+ 
Sbjct: 198 DWSYIQEVRQHLKIPMFANGNILGLEDVHRCLDET-GVDGVMTAEGNLHNPAIF 250


>gi|323492069|ref|ZP_08097231.1| NifR3/Smm1 family protein [Vibrio brasiliensis LMG 20546]
 gi|323313630|gb|EGA66732.1| NifR3/Smm1 family protein [Vibrio brasiliensis LMG 20546]
          Length = 280

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 53/193 (27%), Positives = 92/193 (47%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A
Sbjct: 28  SVQIAGADPQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIEDILKA 87

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+ +PVT+K R G D D    V +  L +     G+  + +H R    + KG     
Sbjct: 88  VVNAVDVPVTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKG----- 139

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K+      I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 140 -----EAEYDSIKAVKQAISIPVIA-NGDIDSPEKAKYVLEYTGADALMIGRPAQGRPWI 193

Query: 226 LTTVDEYFSNPLT 238
              +  +  N  T
Sbjct: 194 FQEIQHFLENGTT 206


>gi|194334749|ref|YP_002016609.1| TIM-barrel protein, nifR3 family [Prosthecochloris aestuarii DSM
           271]
 gi|194312567|gb|ACF46962.1| TIM-barrel protein, nifR3 family [Prosthecochloris aestuarii DSM
           271]
          Length = 347

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 135/308 (43%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M + TDR +R   +    + ++YTE I A+AI R    ++  + F   E P+ +QI G  
Sbjct: 17  MEEVTDRSFRKICKRFGAD-VVYTEFISAEAIRRQVDTSLRKMRFDDDEAPVVVQIFGNS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA I        I++N GCP+ +V     GA L+  PD +    AA+ +A+++P
Sbjct: 76  QEAMAEAAVIAASCSPAWIDINFGCPAKKVAGKGAGAALLKEPDKMVAIAAAVVRAVNLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G D    ++ + ++V  ++  GV  + IH   R  + +G++          D+
Sbjct: 136 VTVKTRLGWDRD--SINIVDIVPRLEDVGVQALAIHGRTRSEMYRGVA----------DW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           + + ++  E   + +  NG +   + A  +      D VMIGR A  N  +     E   
Sbjct: 184 EWIRKV-TEKARIPVIANGDIWSAADARAMFAETGADAVMIGRGAIGNPFIFAQARELLD 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRR 292
                + P       D+  +I+ ++          G K    ++ RH      G P   R
Sbjct: 243 TGRVVTHP-------DYRDRIAVAVEHLKLSVEFKGEKYGSLEMRRHYSTYLKGLPRVSR 295

Query: 293 CRHILTVE 300
            R  L  E
Sbjct: 296 VRDKLVRE 303


>gi|51597867|ref|YP_072058.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis IP
           32953]
 gi|108809658|ref|YP_653574.1| tRNA-dihydrouridine synthase B [Yersinia pestis Antiqua]
 gi|108813677|ref|YP_649444.1| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516]
 gi|145597577|ref|YP_001161653.1| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides F]
 gi|153948925|ref|YP_001399379.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis IP
           31758]
 gi|153997407|ref|ZP_02022507.1| tRNA-dihydrouridine synthase B [Yersinia pestis CA88-4125]
 gi|165937393|ref|ZP_02225956.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|166011363|ref|ZP_02232261.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166214187|ref|ZP_02240222.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167420730|ref|ZP_02312483.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167425544|ref|ZP_02317297.1| dihydrouridine synthase [Yersinia pestis biovar Mediaevalis str.
           K1973002]
 gi|170022704|ref|YP_001719209.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis YPIII]
 gi|186897062|ref|YP_001874174.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis PB1/+]
 gi|218930665|ref|YP_002348540.1| tRNA-dihydrouridine synthase B [Yersinia pestis CO92]
 gi|229836798|ref|ZP_04456963.1| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides A]
 gi|229839302|ref|ZP_04459461.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229899866|ref|ZP_04515007.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229904177|ref|ZP_04519288.1| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516]
 gi|270488618|ref|ZP_06205692.1| TIM-barrel protein, nifR3 family [Yersinia pestis KIM D27]
 gi|294505248|ref|YP_003569310.1| hypothetical protein YPZ3_3139 [Yersinia pestis Z176003]
 gi|38604949|sp|Q8ZAX7|DUSB_YERPE RecName: Full=tRNA-dihydrouridine synthase B
 gi|51591149|emb|CAH22814.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108777325|gb|ABG19844.1| hypothetical protein YPN_3517 [Yersinia pestis Nepal516]
 gi|108781571|gb|ABG15629.1| hypothetical protein YPA_3667 [Yersinia pestis Antiqua]
 gi|115349276|emb|CAL22243.1| conserved hypothetical protein [Yersinia pestis CO92]
 gi|145209273|gb|ABP38680.1| hypothetical protein YPDSF_0261 [Yersinia pestis Pestoides F]
 gi|149289044|gb|EDM39124.1| tRNA-dihydrouridine synthase B [Yersinia pestis CA88-4125]
 gi|152960420|gb|ABS47881.1| dihydrouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|165914498|gb|EDR33112.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|165989747|gb|EDR42048.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166204674|gb|EDR49154.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166961536|gb|EDR57557.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167055558|gb|EDR65351.1| dihydrouridine synthase [Yersinia pestis biovar Mediaevalis str.
           K1973002]
 gi|169749238|gb|ACA66756.1| TIM-barrel protein, nifR3 family [Yersinia pseudotuberculosis
           YPIII]
 gi|186700088|gb|ACC90717.1| TIM-barrel protein, nifR3 family [Yersinia pseudotuberculosis
           PB1/+]
 gi|229678295|gb|EEO74400.1| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516]
 gi|229687358|gb|EEO79433.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229695668|gb|EEO85715.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229705741|gb|EEO91750.1| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides A]
 gi|262363311|gb|ACY60032.1| hypothetical protein YPD4_3128 [Yersinia pestis D106004]
 gi|270337122|gb|EFA47899.1| TIM-barrel protein, nifR3 family [Yersinia pestis KIM D27]
 gi|294355707|gb|ADE66048.1| hypothetical protein YPZ3_3139 [Yersinia pestis Z176003]
 gi|320017182|gb|ADW00754.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 321

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPLA-LQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  +  +QI G D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G +         
Sbjct: 136 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAV-KQTVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|262367311|gb|ACY63868.1| hypothetical protein YPD8_3198 [Yersinia pestis D182038]
          Length = 305

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPLA-LQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  +  +QI G D
Sbjct: 1   MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 60  PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G +         
Sbjct: 120 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNGEA--------- 165

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 166 -EYDSIRAV-KQTVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 223

Query: 232 YF 233
           Y 
Sbjct: 224 YL 225


>gi|291457508|ref|ZP_06596898.1| putative tRNA-dihydrouridine synthase [Bifidobacterium breve DSM
           20213]
 gi|291381343|gb|EFE88861.1| putative tRNA-dihydrouridine synthase [Bifidobacterium breve DSM
           20213]
          Length = 453

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/243 (26%), Positives = 104/243 (42%), Gaps = 19/243 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F++ EK  +LQ+ G +
Sbjct: 93  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVARNPKALRLCHFASSEKIRSLQLYGVN 152

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  + I    A+C+ 
Sbjct: 153 PSITEQAAKIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELIQRVVAVCEP 212

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 213 AGIPVTAKIRVGIDHDHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 270

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ D+ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 271 ---------KEHLDIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 321

Query: 233 FSN 235
           F +
Sbjct: 322 FED 324


>gi|50289099|ref|XP_446979.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49526288|emb|CAG59912.1| unnamed protein product [Candida glabrata]
          Length = 412

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 109/239 (45%), Gaps = 25/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K       ++ G S  ++PL +Q 
Sbjct: 29  MVDQSELAWRVLSRRY-GATLCYTPMFHAKLFATSEKYRREMWCDLDGDSKLDRPLVVQF 87

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK+VED   + ++LN+GCP     +G +G+ LM   D++   I  + + 
Sbjct: 88  CANDPEYLLQAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHKLIKTLHEN 146

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L+IPVT K R+  D Q       +  K +  +G   + +H R    KG      ++    
Sbjct: 147 LNIPVTAKIRVFPDRQ----KTLDYAKMVLDAGAQFLTVHGRLREQKG------QQTGLA 196

Query: 175 DYDIVYEIKKENPD--LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           D+DI+  +++  PD  +F   NG +   ED+ + +  +   D VM       N  +   
Sbjct: 197 DWDIIKYLRENLPDNTVFFA-NGNILYPEDIDRCISQI-KCDAVMSAEGNLYNPGVFNV 253


>gi|170723771|ref|YP_001751459.1| NifR3 family TIM-barrel protein [Pseudomonas putida W619]
 gi|169761774|gb|ACA75090.1| TIM-barrel protein, nifR3 family [Pseudomonas putida W619]
          Length = 337

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 124/261 (47%), Gaps = 16/261 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCKRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAARANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVGAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+     L N+ +  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGW-DRANKNGL-NVARIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG +    +A  +L +  VDG++IGRAA     +   ++ Y    
Sbjct: 189 IAAI-KQAVSIPVFANGDITSPEKARAVLDATGVDGLLIGRAAQGRPWIFREIEHYLGTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISA 257
               +P    V++     ++A
Sbjct: 248 QHLPAPQLDEVERILLEHLAA 268


>gi|116332915|ref|YP_794442.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
 gi|116098262|gb|ABJ63411.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
          Length = 331

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 92/183 (50%), Gaps = 24/183 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+A Q+ G D      AA+ V+D GY  I++N+GCP + V +   G+ L+ N D     I
Sbjct: 81  PVA-QLWGNDGEAFARAAEAVKDLGYEAIDINMGCPDSTVIKNHGGSDLICNFDSAAAVI 139

Query: 109 AAMCKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           A   K   +PV+VK R+G    D+      R+ +  + +  +  + IH R       + K
Sbjct: 140 AG-AKTAGLPVSVKTRLGYSRLDE-----WRDWLTFLFQQDIPLLTIHLR-------TKK 186

Query: 167 DNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAA 219
           +  ++P   Y+++ +I K      PD  + LNG +E+ +  + +    P VDG+MIGR  
Sbjct: 187 EMSRVP-AHYEMIDDIVKLRDEIAPDTLLQLNGDIENYTDGVTLAQAHPGVDGIMIGRGI 245

Query: 220 YKN 222
           + +
Sbjct: 246 FTS 248


>gi|326436672|gb|EGD82242.1| dihydrouridine synthase [Salpingoeca sp. ATCC 50818]
          Length = 434

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/208 (28%), Positives = 98/208 (47%), Gaps = 26/208 (12%)

Query: 12  FARLLTNNA---LLYTEMIVADAILRGD---KKNILGFST-----QEKPLALQIGGADIS 60
           F RL+T      L YT M+ AD +L  +   + ++          +  PL  Q+   +  
Sbjct: 42  FRRLVTAEGGCDLAYTPMMHADQLLENNLAAQSHLTDLRQDMERGRPYPLLGQLCATNAD 101

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             V+AA++VE +  + ++LN+GCP      G FGA LM +PD V   +      L +PV 
Sbjct: 102 DFVQAAQLVEPY-VDAVDLNLGCPQRTAQAGGFGAFLMEHPDTVAAIVQRASTTLQVPVC 160

Query: 121 VKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            K R+  D D+  A A     + +++SG + + +H R       + + +   P+  YD V
Sbjct: 161 CKIRVFTDVDKTVAFA-----RMLQESGCSMLAVHGRTR-----AQRHHEGTPH--YDTV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL 207
             I  E  D+ + +NGG+    QA  IL
Sbjct: 209 RAI-VEALDIPVVVNGGIATRQQADAIL 235


>gi|313772422|gb|EFS38388.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL074PA1]
 gi|313807433|gb|EFS45920.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL087PA2]
 gi|313809940|gb|EFS47661.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL083PA1]
 gi|313813022|gb|EFS50736.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL025PA1]
 gi|313818478|gb|EFS56192.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL046PA2]
 gi|313820241|gb|EFS57955.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL036PA1]
 gi|313822949|gb|EFS60663.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL036PA2]
 gi|313825122|gb|EFS62836.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL063PA1]
 gi|313830271|gb|EFS67985.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL007PA1]
 gi|313834072|gb|EFS71786.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL056PA1]
 gi|314925128|gb|EFS88959.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL036PA3]
 gi|314960085|gb|EFT04187.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL002PA2]
 gi|314973277|gb|EFT17373.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL053PA1]
 gi|314975952|gb|EFT20047.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL045PA1]
 gi|314978290|gb|EFT22384.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL072PA2]
 gi|314984029|gb|EFT28121.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA1]
 gi|314987792|gb|EFT31883.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA2]
 gi|314990014|gb|EFT34105.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA3]
 gi|315084401|gb|EFT56377.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL027PA2]
 gi|315088841|gb|EFT60817.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL072PA1]
 gi|315096190|gb|EFT68166.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL038PA1]
 gi|315105467|gb|EFT77443.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL030PA1]
 gi|327326106|gb|EGE67896.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL096PA2]
 gi|327330171|gb|EGE71920.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL097PA1]
 gi|327332023|gb|EGE73760.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL096PA3]
 gi|327443226|gb|EGE89880.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL013PA2]
 gi|327446010|gb|EGE92664.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL043PA2]
 gi|327448010|gb|EGE94664.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL043PA1]
 gi|328753553|gb|EGF67169.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL020PA1]
 gi|328760675|gb|EGF74242.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL099PA1]
          Length = 355

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 117/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 19  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 79  VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 136

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 137 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 187

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 188 NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCAMI 247

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 248 -RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 287


>gi|152996996|ref|YP_001341831.1| nifR3 family TIM-barrel protein [Marinomonas sp. MWYL1]
 gi|150837920|gb|ABR71896.1| putative TIM-barrel protein, nifR3 family [Marinomonas sp. MWYL1]
          Length = 322

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 114/231 (49%), Gaps = 19/231 (8%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL  +    L+ +EM+ +D  L    K  + L    +  P ++QI G D   + EAA+
Sbjct: 27  FRRLCHDQGAGLVVSEMVTSDVRLWNSTKSRHRLIHDAEVSPRSVQIAGGDPQMMAEAAQ 86

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
              + G   I++N+GCP+ +V   + G+ L+ +  +V + + ++  ++S+PVT+K R G 
Sbjct: 87  QNVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVREILESVVNSVSVPVTLKIRTGW 146

Query: 128 D-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
             DQ   +A+  + + I   G+  + IH R         ++ +    ++YD + EI K +
Sbjct: 147 SLDQKNGLAIAKMAEDI---GIQALAIHGRT--------RECKFQGQVEYDTIAEI-KHH 194

Query: 187 PDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             + I  NG ++D   A  +K     DG+MIGRAA     +   ++ Y   
Sbjct: 195 LSIPIFANGDIKDAQSAKFVKDYTQADGIMIGRAAQGRPWIFREINHYLET 245


>gi|213966461|ref|ZP_03394635.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           amycolatum SK46]
 gi|213950887|gb|EEB62295.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           amycolatum SK46]
          Length = 385

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 102/215 (47%), Gaps = 13/215 (6%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-I 68
             R  T + L   EM+ A A++  ++K  ++  F+  E P +LQ+   D     EAAK I
Sbjct: 34  LQRTGTVSGLYVCEMVTARALVERNEKTMHMTTFAPDENPRSLQLYTTDPKWTYEAAKMI 93

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
           V++   + I++N GCP  +V     G+ L     + G+ +AA  KA     IPVTVK R+
Sbjct: 94  VDENLADHIDMNFGCPVPKVTRKGGGSALPYKRRLFGNIVAAAVKATEGTDIPVTVKFRV 153

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD+       +  +   + G   + +HAR A  +     D  +I  L   +V     +
Sbjct: 154 GIDDE--HHTHLDAGRIAAEMGAQAVALHARTAAQRYSGHADWSQIARLKEHMVDSSFSD 211

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
            P L    NG +   + A K+L     DGV++GR 
Sbjct: 212 IPVLG---NGDIFASTDARKMLDETGCDGVVVGRG 243


>gi|289427130|ref|ZP_06428846.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J165]
 gi|295130515|ref|YP_003581178.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK137]
 gi|289159599|gb|EFD07787.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J165]
 gi|291376434|gb|ADE00289.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK137]
 gi|315080730|gb|EFT52706.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL078PA1]
 gi|315085740|gb|EFT57716.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL002PA3]
          Length = 409

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 117/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 73  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 132

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 133 VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 190

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 191 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 241

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 242 NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCA-M 300

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 301 IRRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 341


>gi|172087771|ref|YP_205772.2| tRNA-dihydrouridine synthase B [Vibrio fischeri ES114]
 gi|171902358|gb|AAW86884.2| tRNA-dihydrouridine synthase B [Vibrio fischeri ES114]
          Length = 349

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 110/244 (45%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R    +     +  +EM+ ++  L    K  N +    +    ++QI GAD
Sbjct: 44  MAGVTDRPFRELC-MRYGAGMAVSEMMSSNPKLWKTSKSQNRMVHEGESGIRSVQIAGAD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ + + A+  A+ +P
Sbjct: 103 PKLMAEAAQHCVETGAQIIDINMGCPAKKVNKKLAGSALLQRPDLIEEILLAVVNAVDVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D        RN V+  K   + G+  + +H R    + KG +  DN K   
Sbjct: 163 VTLKTRTGWDPDN-----RNCVQVAKMAEQCGIQALALHGRTRACMYKGEAEYDNIK--- 214

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     KE   + +  NG ++   +A  +L     D +MIGR A     +   +  
Sbjct: 215 --------AVKEAISIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFKEIQH 266

Query: 232 YFSN 235
           Y   
Sbjct: 267 YLET 270


>gi|297588656|ref|ZP_06947299.1| NifR3 family TIM-barrel protein [Finegoldia magna ATCC 53516]
 gi|297574029|gb|EFH92750.1| NifR3 family TIM-barrel protein [Finegoldia magna ATCC 53516]
          Length = 310

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/214 (26%), Positives = 107/214 (50%), Gaps = 18/214 (8%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
            L +TEMI A A+   DKK   +L   ++E   ++QI G +   +  A + + E++ +  
Sbjct: 35  GLCFTEMISAKALYYDDKKTKKLLDTDSRENNTSVQIFGHEPEIIAYATRFLTENYNFKS 94

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ ++ +   G+ LM + ++  D I A      +PV+VK R+G+D+   ++  
Sbjct: 95  IDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLPVSVKFRLGIDEN--SMNY 152

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L +  ++  V+ I +HAR   +      D   I  L          EN D+ +  NG 
Sbjct: 153 MQLGQICERLKVDYITLHARTRKMFYSGEADWAHIKRL---------VENVDIPVFGNGD 203

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
               ED+ + ++   + DGV++ R A +N  + +
Sbjct: 204 CFTKEDIRKNME-YSNCDGVLLARGAMQNPFIFS 236


>gi|301167381|emb|CBW26963.1| tRNA-dihydrouridine synthase [Bacteriovorax marinus SJ]
          Length = 363

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/281 (23%), Positives = 126/281 (44%), Gaps = 28/281 (9%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +E+I    I  G++K I  L     EK + +Q+ G D   + +AAK+  +     I++N+
Sbjct: 65  SELISCHGINYGNEKTIRMLSIHPDEKNIGIQLFGEDAESMAKAAKVALESRPKFIDINM 124

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V     G+ LM +   +G+    + KA+ +P+T+K R G DD   ++    ++ 
Sbjct: 125 GCPVRKVVSKGSGSALMKDTSKLGNFFGTIKKAIDVPLTIKIRTGWDDD--SINANEIIH 182

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             K+ GV  + IH R         +  +     +++++ E+   +P   IG NG L   S
Sbjct: 183 IAKEEGVEFVAIHGRT--------RTQQYKGKANWELLEELASTSPLPIIG-NGDLHSAS 233

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAML--TTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              K +     D  M+ R   ++  +   + ++E  +   T S         D+W +I+ 
Sbjct: 234 LVKKRMRNSKCDAFMLARGPLRDPFIFLESYIEEGENINFTPS---------DYW-EITN 283

Query: 258 SMTDYAARHLHSGGKLQQITR-HMIGLFHGFPNSRRCRHIL 297
            + +Y   +      L  + R HM+    G  N+   R+++
Sbjct: 284 RLFEYNQMYTDRERTLLVMMRKHMVWFAAGLSNAANFRNMI 324


>gi|262273282|ref|ZP_06051097.1| tRNA dihydrouridine synthase B [Grimontia hollisae CIP 101886]
 gi|262222655|gb|EEY73965.1| tRNA dihydrouridine synthase B [Grimontia hollisae CIP 101886]
          Length = 335

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 111/242 (45%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  +      KN +    ++   ++QI GA+
Sbjct: 31  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPAMWHTAKSKNRMVHLDEKGIRSVQIAGAE 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+   D G   +++N+GCP  +V++   G+ L+  PDI+   + A+  A+ +P
Sbjct: 90  PALMAEAARFCVDNGAQIVDINMGCPVKKVNKKLAGSALLTRPDIIEQILKAVVSAVDVP 149

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +    + K  +  G+  + +H R    + KG            +
Sbjct: 150 VTLKTRTGWDPDNKNCI---QIAKMAEDCGIQALALHGRTRACMYKG----------EAE 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 197 YDSIKAV-KEAVSIPVIANGDIDSPQKAKFVLDYTGADALMIGRPAQGRPWIFREIQHYL 255

Query: 234 SN 235
           + 
Sbjct: 256 TT 257


>gi|224064274|ref|XP_002192167.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog (S.
           cerevisiae) [Taeniopygia guttata]
          Length = 490

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 87/185 (47%), Gaps = 24/185 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G AD  + +  AK+VE      I++N+GCP     +G  GA L+ +PD +   + 
Sbjct: 83  VVFQMGSADAERALAVAKLVES-DVAGIDINMGCPKEYSTKGGMGAALLSDPDKIESILT 141

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K +  PVT K RI   V+D +      NLVK I+K+G+  I +H RK        K+
Sbjct: 142 TLVKGICKPVTCKIRILPSVEDTV------NLVKRIEKTGIAAIAVHGRK--------KE 187

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM------SQALKILPSVDGVMIGRAAYK 221
            R    +  D++  I  E   + +  NGG  D        +  +   +   VMI RAA  
Sbjct: 188 ERPQHPVHCDVIKAI-SEAVSIPVIANGGSHDFIKEYADIETFQKATAASSVMIARAAMW 246

Query: 222 NSAML 226
           N ++ 
Sbjct: 247 NPSVF 251


>gi|213403071|ref|XP_002172308.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|212000355|gb|EEB06015.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 347

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 111/242 (45%), Gaps = 25/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   L  + +    FST EK   L +Q G  D
Sbjct: 27  MVRYSKLPFRQLVRDY-NADIVYTPMILAKEFLHPEGR-YFDFSTNEKDRSLVVQFGVED 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +A++IV  +  + I +N GCP     +   G+ L+  P  V + + ++  AL   
Sbjct: 85  PVILAQASEIVAPYT-DAIGINCGCPQPWAIQEGIGSALLKQPQKVHELVRSVKSALGET 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
             V+ +I +D+ +     R L+++ +++G + I +H R+   +   P D           
Sbjct: 144 FCVEVKIRLDNDLEKT--RQLMQTAERAGADFITVHGRRRADRSSFPVD----------- 190

Query: 179 VYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  I+   P + I +  NG + D+   LKI    + DGVM  R   +N A+      Y S
Sbjct: 191 LEAIRSVRPCVSIPVVANGDVNDLDTGLKIAEYTNTDGVMSARGLMENPALFAG---YTS 247

Query: 235 NP 236
            P
Sbjct: 248 TP 249


>gi|219684394|ref|ZP_03539338.1| putative histidine phosphokinase/phophatase [Borrelia garinii PBr]
 gi|219672383|gb|EED29436.1| putative histidine phosphokinase/phophatase [Borrelia garinii PBr]
          Length = 329

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/250 (24%), Positives = 115/250 (46%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISVKGILNGSKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G D  +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNDPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P+++K R G     P V   + +  +   G++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSIKTRHGF--SYPEV--NDWLGFLLGFGIDMLTVYPRLAVNQSEGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKFSSKHF 254


>gi|320527911|ref|ZP_08029078.1| TIM-barrel protein, nifR3 family [Solobacterium moorei F0204]
 gi|320131707|gb|EFW24270.1| TIM-barrel protein, nifR3 family [Solobacterium moorei F0204]
          Length = 328

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 75/288 (26%), Positives = 131/288 (45%), Gaps = 30/288 (10%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
            L+ +EMI   A+   + K  ++   S  E P+ALQ+ G+D   + EAA+ + ++   + 
Sbjct: 36  GLVVSEMISDKALHYQNAKTQDMCRISEGEHPVALQLFGSDPITMAEAAEYLTKNTNCDM 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I++N+GCP  +V +   G+ LM  P++  + + A+      PVTVK R G D D I  V 
Sbjct: 96  IDINMGCPVQKVVKAHSGSYLMQKPELAYEVMHAVVTHTDRPVTVKMRAGWDSDHINCVE 155

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L    +K+GV+ + +H R    +     +N  I  +         K+  ++ +  NG
Sbjct: 156 IAKLA---EKAGVSAVTVHGRTRGQQYTGHSNNAYIKAV---------KDAVNIPVIGNG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            +     A ++L     D +MIGR        L  VD Y +          T V+ D+  
Sbjct: 204 DIRIPEDAKRMLEETGCDAIMIGRGLLGRPFFLQEVDAYLNG--------GTYVEPDYNE 255

Query: 254 KISASMTDYAARHLHSGGKLQQIT--RHMIGLF-HGFPNSRRCRHILT 298
           K+  +   YA +     G+   I   R M G +  G P++   ++ L+
Sbjct: 256 KLDLAY-HYAEKLCEYEGERNGICMMRGMAGWYITGLPHASEYKNRLS 302


>gi|126304888|ref|XP_001373897.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 495

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/195 (30%), Positives = 94/195 (48%), Gaps = 27/195 (13%)

Query: 43  FSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F T E+    +  Q+G AD  + +  AK+VE+     I++N+GCP     +G  G  L+ 
Sbjct: 74  FRTCERERNKVVFQMGSADAERALAVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGVALLS 132

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +PD +   ++ + K +  PVT K RI   ++D +      NLVK I+++GV  I +H RK
Sbjct: 133 DPDKIEKILSTLVKGICKPVTCKIRILPSLEDTL------NLVKRIERTGVAAIAVHGRK 186

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ------ALKILPSVD 211
                   K+ R    +  DI+  I  E   + I  NGG  D  +      A + + S  
Sbjct: 187 --------KEERPQHPVHCDIIKAI-AEAVSIPIIANGGSHDHIKVYSDLDAFRQVTSAS 237

Query: 212 GVMIGRAAYKNSAML 226
            VM+ RAA  N ++ 
Sbjct: 238 SVMVARAAMWNPSIF 252


>gi|83749328|ref|ZP_00946325.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
 gi|83724006|gb|EAP71187.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
          Length = 382

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 118/243 (48%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 43  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 101

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 102 PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 161

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  +++G++ + +H R         + +     
Sbjct: 162 VPVTLKIRTGWDRK-----HRNALTVARIAQEAGISMLTVHGRT--------RADLYHGE 208

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  +  + +  NG +   ++A ++L     D +MIGRAA     +   ++ 
Sbjct: 209 AEYETIAAVKA-SVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAAQGRPWLFREIEH 267

Query: 232 YFS 234
           +  
Sbjct: 268 FLQ 270


>gi|111115566|ref|YP_710184.1| histidine phosphokinase/phophatase, putative [Borrelia afzelii PKo]
 gi|216263364|ref|ZP_03435359.1| putative histidine phosphokinase/phophatase [Borrelia afzelii
           ACA-1]
 gi|110890840|gb|ABH02008.1| histidine phosphokinase/phophatase, putative [Borrelia afzelii PKo]
 gi|215980208|gb|EEC21029.1| putative histidine phosphokinase/phophatase [Borrelia afzelii
           ACA-1]
          Length = 334

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/250 (25%), Positives = 114/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDSVFRNLIHLIGSKEGEPHIYFTEFISVKGILNGSKQSIQHILLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +  +A +I+   G+  I++N+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYKAIEILGSMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P +   N +  +   G++ + ++ R A+ +   P    
Sbjct: 137 EACAKFNLPLSVKTRHGF--SYPEID--NWLGFLLGFGIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKKE----NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +D+DI YE+ K     +P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 189 ----VDFDIFYELVKLRNNISPSTLIIGNGDVWSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKFSSKHF 254


>gi|218460042|ref|ZP_03500133.1| tRNA-dihydrouridine synthase protein [Rhizobium etli Kim 5]
          Length = 174

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 83/158 (52%), Gaps = 13/158 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+
Sbjct: 1   MAEAAKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPVTL 60

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D+   ++   ++ +  + +G+  + IH R      +   + R     D+D ++ 
Sbjct: 61  KMRLGWDEN--SINAPDIARRAEAAGIQLVTIHGRTR----MQFYEGRA----DWDAIHA 110

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           ++       I  NG +E  + A +IL     D VMIGR
Sbjct: 111 VRDVISIPLIA-NGDVETAADAQEILRRSGADAVMIGR 147


>gi|50842438|ref|YP_055665.1| NifR3 family TIM-barrel protein [Propionibacterium acnes KPA171202]
 gi|50840040|gb|AAT82707.1| TIM-barrel enzyme, NifR3 family [Propionibacterium acnes KPA171202]
 gi|332675350|gb|AEE72166.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes 266]
          Length = 411

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 117/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 75  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 134

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 135 VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 192

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 193 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 243

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 244 NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCA-M 302

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 303 IRRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 343


>gi|256844991|ref|ZP_05550449.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_36A2]
 gi|256718550|gb|EEU32105.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_36A2]
          Length = 307

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 103/222 (46%), Gaps = 30/222 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       K  A+QI G ++ K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLRKGNAVQIFGENVEKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    +++K RIG       V +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKLSIKIRIGYKKPENYVQIAK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + I   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEI---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           F G    LE +S +     +VDGVM+ R  + N  ++  + E
Sbjct: 195 FTG-EDALEKISYS-----NVDGVMLARGIFGNPWLIRDIRE 230


>gi|123443997|ref|YP_001007967.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090958|emb|CAL13840.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 321

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  +  +QI G D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDEMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G      +   RN +   +  +  G+  + IH   R  +  G +         
Sbjct: 136 VTLKIRTGW-----SAEHRNCIEIAQLAENCGIQALTIHGRTRSCLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRSVKQIVSIPVIA-NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|119502731|ref|ZP_01624816.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2080]
 gi|119461077|gb|EAW42167.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2080]
          Length = 352

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 104/206 (50%), Gaps = 21/206 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +   EM+ +D  L   +K+ L    S +    ++QI G++  +L  AA++  D G + I+
Sbjct: 50  MAVAEMLTSDPKLLASRKSSLRRRHSAKGGLRSVQIVGSEPQQLANAARLNADDGADVID 109

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V + + G+ L+ + D V + + A+  A+ +PVT+K R GV  Q      RN
Sbjct: 110 INMGCPAKKVCKKAAGSALLADEDRVAEILKAVVSAVDVPVTLKIRTGVSPQ-----QRN 164

Query: 139 ---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K  + +G+  + +H R         + +R     +Y  +  I  +   + +  NG
Sbjct: 165 GVAIAKIAEDAGIQLLTVHGRT--------RADRFKGEAEYHTIERI-VDAVSIPVLANG 215

Query: 196 GLEDMSQALKILPSVD--GVMIGRAA 219
            +   +QAL +L      G+MIGRAA
Sbjct: 216 DITTPAQALAVLQKTGAAGIMIGRAA 241


>gi|165927556|ref|ZP_02223388.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165920450|gb|EDR37727.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
          Length = 323

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPLA-LQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  +  +QI G D
Sbjct: 19  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 78  PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G +         
Sbjct: 138 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNGEA--------- 183

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 184 -EYDSIRAV-KQTVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 241

Query: 232 YF 233
           Y 
Sbjct: 242 YL 243


>gi|68076617|ref|XP_680228.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56501126|emb|CAH94784.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 338

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 112/245 (45%), Gaps = 24/245 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ +   +   K     F    Q+KPL  Q  G D
Sbjct: 32  MVDLSELPFRLLCRNY-NCDLAFTPMLHSKNFVEHSKYRTGYFKKCDQDKPLIAQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S ++ A   ++D   N +++N+GCP     +G++GA L+   D V + I+ +    ++P
Sbjct: 91  PSTILRAIDYIKD-EVNGVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLISDITNNCNVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R  +D+        NL   ++   V  I +H R    KG++ K+       DY+I
Sbjct: 150 ISCKIR-KIDNDYQKTL--NLCYDLQSRNVKMITVHGRTKEEKGVNIKE------CDYEI 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA--------AYKNSAMLTT 228
           + +I KE  ++ I  NG +E+     K L     D VM            + KN   +  
Sbjct: 201 I-KIIKERLNIPIIANGSIENFEDIEKCLNYTKTDAVMCAEILLEKPSFFSNKNINTIDL 259

Query: 229 VDEYF 233
           V+EY+
Sbjct: 260 VNEYY 264


>gi|51246454|ref|YP_066338.1| tRNA-dihydrouridine synthase [Desulfotalea psychrophila LSv54]
 gi|50877491|emb|CAG37331.1| tRNA-dihydrouridine synthase [Desulfotalea psychrophila LSv54]
          Length = 328

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 99/226 (43%), Gaps = 16/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  +TD  +R        +  + +EMI    +    ++ +  L    +E+P++ Q+ GA+
Sbjct: 18  LAGYTDLSFRLLCHQFGADYTV-SEMISCHGLFYNQQRTLEMLASLPEERPVSFQLFGAE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +A  I+ DF  + I++N+GCP  +V +   GA LM  P++  D I ++     IP
Sbjct: 77  PDIMAKATLILNDFQPDMIDINMGCPVRKVTKKGAGAALMSTPELAYDVIRSVVDNTDIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R GV           L+     +    +    R     G++          D  I
Sbjct: 137 VTVKFRAGVSSTELNGVEFGLMTERAGAAAVAVHGRTRAQAFSGVA----------DRGI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
           + E+K+      IG NG +      L ++     DGVM+GR A  N
Sbjct: 187 IKEVKEALSIPVIG-NGDILSYQDGLDMMAETGCDGVMVGRGALGN 231


>gi|207742357|ref|YP_002258749.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
 gi|206593747|emb|CAQ60674.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
          Length = 356

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 118/243 (48%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  +++G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRK-----HRNALTVARIAQEAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  +  + +  NG +   ++A ++L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYETIAAVKA-SVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YFS 234
           +  
Sbjct: 242 FLQ 244


>gi|167519967|ref|XP_001744323.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163777409|gb|EDQ91026.1| predicted protein [Monosiga brevicollis MX1]
          Length = 353

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/213 (25%), Positives = 95/213 (44%), Gaps = 15/213 (7%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EM +A ++L+G   +  ++     E    +QI G     L   A+++ E+   + I+LN
Sbjct: 36  SEMAMASSLLQGSSSDWALVRRHESEDLFGIQICGNQPDMLARCAELLSEETDASFIDLN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
            GCP  ++ +   G+ L+     + D +  M     IP+TVK R GV    P      +V
Sbjct: 96  CGCPIDQIFQKGCGSALLARRQRLKDIVQGMRVCSKIPITVKVRTGVHGDRPTT--HKMV 153

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
             ++  GV+ + IH R         +  R     ++D + +  +  PDL I  NG +   
Sbjct: 154 HEMRSWGVSALTIHGRS--------RQQRYTKYANWDYIKDCVEAAPDLPIFGNGDILSW 205

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
             A++   S  V GVM+ R A     + T + E
Sbjct: 206 EHAVQHQASTGVSGVMLARGALIKPWLFTEIKE 238


>gi|225717662|gb|ACO14677.1| tRNA-dihydrouridine synthase 4-like [Caligus clemensi]
          Length = 308

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/251 (24%), Positives = 116/251 (46%), Gaps = 31/251 (12%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFST---QEKPLALQIGGADISKLVEAA 66
           F RL+ +    + ++ MI+AD+ +   +     F+T   +++PL +Q     +   V AA
Sbjct: 28  FRRLILSYGADVAFSPMILADSFVSSPEARFNEFTTDPLRDRPLIVQFASKSVDDFVSAA 87

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR 124
           ++V       ++LN GCP         GA L+  P+ + D + +       S+ V+VK R
Sbjct: 88  QLVAPHAEG-VDLNCGCPQGWAIREGIGAALLQRPEFISDVVRSTKNRTQHSLSVSVKIR 146

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +  D +       +LVK+++ +G + I +H R         KD +    +D + V  + K
Sbjct: 147 LQKDHR----RTWDLVKAVENAGADFITVHGRT--------KDQQSGDPVDLEGVKYV-K 193

Query: 185 ENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLT--------TVDEYFS 234
           E+  + +  NG ++ + +A  ++ L  VDGVM  R   +N AM           V+++  
Sbjct: 194 ESLSIPVVANGDIKSLHEAHCVRELTGVDGVMAARGLLENPAMYAGYGITPKECVEDWLR 253

Query: 235 NPLTGSSPIKT 245
             L   +P +T
Sbjct: 254 ISLETGTPFQT 264


>gi|313792228|gb|EFS40329.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA1]
 gi|313801823|gb|EFS43057.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA2]
 gi|313827691|gb|EFS65405.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL063PA2]
 gi|313838649|gb|EFS76363.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL086PA1]
 gi|314962886|gb|EFT06986.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL082PA1]
 gi|315078100|gb|EFT50151.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL053PA2]
 gi|315108413|gb|EFT80389.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL030PA2]
 gi|327453057|gb|EGE99711.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL092PA1]
          Length = 355

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 117/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 19  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 79  VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 136

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 137 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 187

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 188 NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCAMI 247

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 248 -RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 287


>gi|291276558|ref|YP_003516330.1| putative Dihydrouridine synthase [Helicobacter mustelae 12198]
 gi|290963752|emb|CBG39587.1| putative Dihydrouridine synthase [Helicobacter mustelae 12198]
          Length = 327

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 112/225 (49%), Gaps = 19/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + +  +EMI + A++    K +  L  S QE P A+QI G+ 
Sbjct: 12  LAGYTDLPFRSVVKQFGVD-ITVSEMISSHALVYQSAKTLKMLCKSPQESPYAVQISGSK 70

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  + +A + + +  G + I+ N GCP+ +V     G+ L+ N  ++   +  + +  + 
Sbjct: 71  IEIIKQAVERINEIDGIDIIDFNCGCPAPKVANHGNGSGLLKNLSLLVKLLNTIKETSNK 130

Query: 118 PV-TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P  +VK R+G D +IP      +  ++K + V+ + +H R       +  D  K   +DY
Sbjct: 131 PYSSVKVRLGFDQKIP----EEIANALKDANVDYVVVHGR-------TRSDGYKKERIDY 179

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           + + +IK+      I  NG + D + A ++L     +G+MIGRAA
Sbjct: 180 ESIAKIKQILSAPVIA-NGEITDYASARRVLEITGANGLMIGRAA 223


>gi|22124133|ref|NP_667556.1| tRNA-dihydrouridine synthase B [Yersinia pestis KIM 10]
 gi|45443621|ref|NP_995160.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Microtus
           str. 91001]
 gi|162420960|ref|YP_001605752.1| tRNA-dihydrouridine synthase B [Yersinia pestis Angola]
 gi|167401994|ref|ZP_02307477.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|21956887|gb|AAM83807.1|AE013621_7 putative dehydrogenase [Yersinia pestis KIM 10]
 gi|45438491|gb|AAS64037.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Yersinia pestis biovar Microtus str. 91001]
 gi|162353775|gb|ABX87723.1| dihydrouridine synthase [Yersinia pestis Angola]
 gi|167048580|gb|EDR59988.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
          Length = 355

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPLA-LQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  +  +QI G D
Sbjct: 51  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 110 PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 169

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G           
Sbjct: 170 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNG----------E 214

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 215 AEYDSIRAV-KQTVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 273

Query: 232 YF 233
           Y 
Sbjct: 274 YL 275


>gi|269966802|ref|ZP_06180875.1| tRNA-dihydrouridine synthase B [Vibrio alginolyticus 40B]
 gi|269828469|gb|EEZ82730.1| tRNA-dihydrouridine synthase B [Vibrio alginolyticus 40B]
          Length = 340

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 114/245 (46%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 35  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP  +V++   G+ L+  P+I+ + + A+  A+ +P
Sbjct: 94  PQLMADAAQFSVENGAQIIDINMGCPDKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVP 153

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L ++    G+  + +H R    + KG +          +
Sbjct: 154 VTLKTRTGWDTDNKNCVQIAKLAEN---CGIQALALHGRTKACMYKGEA----------E 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 201 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYL 259

Query: 234 SNPLT 238
            N  T
Sbjct: 260 ENGTT 264


>gi|163736351|ref|ZP_02143770.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Phaeobacter
           gallaeciensis BS107]
 gi|161390221|gb|EDQ14571.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Phaeobacter
           gallaeciensis BS107]
          Length = 319

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 74/264 (28%), Positives = 121/264 (45%), Gaps = 26/264 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+QI G D
Sbjct: 1   MAGITDRPFRDLVRSF-GAGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQIAGRD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ VE  G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+S+P
Sbjct: 60  AYWMAEAARQVESRGAKVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVAAVSVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R+G DD   ++   ++ +  + +GV  + IH R      KG +          D+
Sbjct: 120 VTLKTRLGWDDN--SLNAADVARRAQDAGVQMVTIHGRTRCQFYKGTA----------DW 167

Query: 177 DIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
             +  +K   N  L    NG + D + A   L     DGVMIGR       +L  V    
Sbjct: 168 KAIAAVKTALNVPLLA--NGDIVDTATARTALAQSGADGVMIGRGVQGKPWLLAEV---- 221

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
           ++ + GS+  +     D  + +SA
Sbjct: 222 AHDIWGSAAPEVPTGSDLVQMVSA 245


>gi|149927720|ref|ZP_01915972.1| dihydrouridine synthase [Limnobacter sp. MED105]
 gi|149823546|gb|EDM82776.1| dihydrouridine synthase [Limnobacter sp. MED105]
          Length = 333

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 113/241 (46%), Gaps = 21/241 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNI-LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L     + +EM  ++ A+ + DK    L    + KP+A+QI GAD
Sbjct: 1   MAGVTDRPFRQLCKKLGAGHAV-SEMAASNPALWKTDKSTRRLNHYGETKPIAVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CKAL 115
              +  AA    + G   I++N+GCP+ +V   + G+ L+ N  +V   + A+   C+  
Sbjct: 60  PEMMAHAAAYNIERGAQIIDINMGCPAKKVCAVAAGSALLQNESLVEQILKAVHAECEQR 119

Query: 116 SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +P+T+K R G   +   A+ +  + +SI   GV+ + +H R         +      + 
Sbjct: 120 GVPLTLKYRTGWSPEHKNAIHIAQMAESI---GVSLLTLHGRT--------RACGYTGDA 168

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K+      I  NG +    +A  +L     DG+MIGRAA  N  +   V  Y
Sbjct: 169 EYDTIKAVKQAVSIPVIA-NGDITSPEKAKHVLDYTGADGLMIGRAAQGNPWIFREVLHY 227

Query: 233 F 233
            
Sbjct: 228 L 228


>gi|19704027|ref|NP_603589.1| nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714217|gb|AAL94888.1| Nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 307

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 112/254 (44%), Gaps = 43/254 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       +  A+QI G DI K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIEKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    ++VK RIG  +    + +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKLSVKIRIGYKEPENYIQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + +   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEL---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS-----NPLTGSSPI- 243
           F G     ED  + +    +VDGVM+ R  + N  ++  + E         P T +  I 
Sbjct: 195 FTG-----EDALEKI-FYSNVDGVMLARGIFGNPWLIRDIREILEYGEIKTPTTKTDKIN 248

Query: 244 -------KTRVDKD 250
                  + RVD D
Sbjct: 249 MAIEHLKRIRVDND 262


>gi|149202616|ref|ZP_01879588.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseovarius sp.
           TM1035]
 gi|149143898|gb|EDM31932.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseovarius sp.
           TM1035]
          Length = 333

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 88/327 (26%), Positives = 140/327 (42%), Gaps = 46/327 (14%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     F A L+ +  +   EM+ A    RG  K  LG   +    A+Q+ 
Sbjct: 18  MAGITDLPFRNVVASFGAGLVVSEMVASQEMVQAKPSARG--KAELGLGAEST--AVQLA 73

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARV----HEGSFGACLMLNPDIVGDCIAAM 111
           G D   + EAA++V D G   I++N+GCP+ +V      G+ G+ LM +PD     I A+
Sbjct: 74  GCDAQWMAEAARVVADHGARIIDINMGCPAKKVVSGSGSGASGSALMRDPDHALRLIEAV 133

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A+ +PVT+K R+G D     +    L +  + +GV  + +H R          D   I
Sbjct: 134 VGAVDVPVTLKMRLGWDHDC--LNAPELARRAESAGVAMVTVHGRTRCQFYTGAADWAAI 191

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
                DIV  +     ++ + +NG + D + A K +      GVMIGR A     +L  V
Sbjct: 192 ----SDIVAAV-----NIPVIVNGDIVDSATARKAVAQSGAAGVMIGRGARGRPWVLAEV 242

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS-----GGKLQ-QITRHMIGL 283
                    G++P+  +          A++ D  A H  +     GG L  ++ R  +G 
Sbjct: 243 AAAMGQ---GAAPLVPQ---------GAALADLVAGHYEAMLGFYGGDLGLRVARKHLGW 290

Query: 284 FHGFPNS--RRCRHILTVEAGASTATH 308
           +     +  R  R +LT    A    H
Sbjct: 291 YMDAAGTGDRLRRAVLTARTPAVVLEH 317


>gi|237741667|ref|ZP_04572148.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 4_1_13]
 gi|294785722|ref|ZP_06751010.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_27]
 gi|229429315|gb|EEO39527.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 4_1_13]
 gi|294487436|gb|EFG34798.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_27]
          Length = 307

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 103/222 (46%), Gaps = 30/222 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       K  A+QI G ++ K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLRKGNAVQIFGENVEKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    +++K RIG       V +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKLSIKIRIGYKKPENYVQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + I   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEI---GCDHITVHGRTREQLYSGKADWKYIKEVKDNVSIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           F G    LE +S +     +VDGVM+ R  + N  ++  + E
Sbjct: 195 FTG-EDALEKISYS-----NVDGVMLARGIFGNPWLIRDIRE 230


>gi|307206649|gb|EFN84621.1| tRNA-dihydrouridine synthase 1-like [Harpegnathos saltator]
          Length = 304

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 46/165 (27%), Positives = 85/165 (51%), Gaps = 10/165 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K  +  L  +++++PL +Q  G+D
Sbjct: 36  MVDASELPWRLLSRR-HGAELCYTPMLHSSVFCRDPKYRREALTSTSEDRPLIVQFCGSD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA++ E +  + +++N+GCP A    G +GA L  + D++   ++ + + L IP
Sbjct: 95  PEVLLEAARLAEPYC-DAVDINIGCPQAIAKRGHYGAFLQDDWDLLQKIVSTLKRGLRIP 153

Query: 119 VTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKG 162
           VT K R+      P V       + ++ +G + + +H R    KG
Sbjct: 154 VTCKLRV-----FPEVGRTVEYARMLENAGASLLTVHGRTREQKG 193


>gi|282897396|ref|ZP_06305398.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Raphidiopsis
           brookii D9]
 gi|281198048|gb|EFA72942.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Raphidiopsis
           brookii D9]
          Length = 339

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 114/245 (46%), Gaps = 14/245 (5%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    ++++YTEM+ A  +    +   I+     E+P+++Q+       L 
Sbjct: 34  TDLVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPNERPISIQLFDCRPDFLA 93

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + +++N+GCP  ++ +   G+ L+  P++    +  +  A+++PVTVK 
Sbjct: 94  EAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVNAINVPVTVKT 153

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  D+   + + +  K ++ +G   I +H R    +G +        N  ++ + ++K
Sbjct: 154 RIGWSDK--EITILDFAKRMEDAGAKMITVHGRTRA-QGYN-------GNARWEWIAKVK 203

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +      I  NG +  ++ A+K L     DGVM  R       ++  VD +        S
Sbjct: 204 QILSIPVIA-NGDIFSVAAAVKCLEETGADGVMCSRGTLGYPFLVGEVDHFLKTGELLPS 262

Query: 242 PIKTR 246
           P  T+
Sbjct: 263 PTPTQ 267


>gi|37527935|ref|NP_931280.1| tRNA-dihydrouridine synthase B [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787371|emb|CAE16460.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 321

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 111/244 (45%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G+D
Sbjct: 17  MAGITDRPFRSLCYKM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHSDEPGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAKI    G   I++N+GCP+ +V+    G+ L+  P++V   ++A+  A+ +P
Sbjct: 76  PDEMAAAAKINVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELVEKILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN VK  +     G+  + IH   R  +  G           
Sbjct: 136 VTLKIRTGWSPE-----ERNCVKIAQLAEHCGIQALAIHGRTRSCLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDNIRTVKQTVAIPVIA-NGDITDPLKARAVLEYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YFSN 235
           Y + 
Sbjct: 240 YLAT 243


>gi|282901225|ref|ZP_06309154.1| Dihydrouridine synthase TIM-barrel protein nifR3
           [Cylindrospermopsis raciborskii CS-505]
 gi|281193925|gb|EFA68893.1| Dihydrouridine synthase TIM-barrel protein nifR3
           [Cylindrospermopsis raciborskii CS-505]
          Length = 340

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 111/234 (47%), Gaps = 14/234 (5%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    ++++YTEM+ A  +    +   I+     E+P+++Q+       L 
Sbjct: 34  TDLVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPNERPISIQLFDCRPDFLA 93

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + +++N+GCP  ++ +   G+ L+  P++    +  + KA+++PVTVK 
Sbjct: 94  EAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVNVPVTVKT 153

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  D+   + + +  K ++ +G   I +H R    +G +        N  ++ + ++K
Sbjct: 154 RIGWSDK--EITILDFAKRMEDAGAKMITVHGRTRA-QGYN-------GNARWEWIAKVK 203

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           +      I  NG +  ++ A+K L     DGVM  R       ++  VD +   
Sbjct: 204 QILSIPVIA-NGDIFSVAAAVKCLAETGADGVMCSRGTLGYPFLVGEVDHFLKT 256


>gi|261250467|ref|ZP_05943042.1| tRNA-dihydrouridine synthase B [Vibrio orientalis CIP 102891]
 gi|260939036|gb|EEX95023.1| tRNA-dihydrouridine synthase B [Vibrio orientalis CIP 102891]
          Length = 285

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/193 (27%), Positives = 92/193 (47%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A
Sbjct: 33  SVQIAGADPQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKDILQA 92

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+ +PVT+K R G D D    V +  L +     G+  + +H R    + KG     
Sbjct: 93  VVNAVDVPVTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKG----- 144

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K+      I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 145 -----EAEYDSIKAVKQAISIPVIA-NGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWI 198

Query: 226 LTTVDEYFSNPLT 238
              +  +  N  T
Sbjct: 199 FQEIQHFLENGTT 211


>gi|53720502|ref|YP_109488.1| putative nitrogen regulation-related protein [Burkholderia
           pseudomallei K96243]
 gi|53726195|ref|YP_103916.1| dihydrouridine synthase [Burkholderia mallei ATCC 23344]
 gi|76810759|ref|YP_334772.1| dihydrouridine synthase [Burkholderia pseudomallei 1710b]
 gi|121599461|ref|YP_991623.1| tRNA-dihydrouridine synthase B [Burkholderia mallei SAVP1]
 gi|124384557|ref|YP_001027118.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10229]
 gi|126442123|ref|YP_001060371.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 668]
 gi|126451189|ref|YP_001082064.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10247]
 gi|134280126|ref|ZP_01766837.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 305]
 gi|167000510|ref|ZP_02266322.1| tRNA-dihydrouridine synthase B [Burkholderia mallei PRL-20]
 gi|167721169|ref|ZP_02404405.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei DM98]
 gi|167740145|ref|ZP_02412919.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 14]
 gi|167817358|ref|ZP_02449038.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 91]
 gi|167825766|ref|ZP_02457237.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 9]
 gi|167895835|ref|ZP_02483237.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 7894]
 gi|167904226|ref|ZP_02491431.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei NCTC
           13177]
 gi|167920438|ref|ZP_02507529.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei BCC215]
 gi|217420460|ref|ZP_03451965.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 576]
 gi|226198391|ref|ZP_03793960.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pakistan
           9]
 gi|237813759|ref|YP_002898210.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei MSHR346]
 gi|238561989|ref|ZP_00441078.2| tRNA-dihydrouridine synthase B [Burkholderia mallei GB8 horse 4]
 gi|254178920|ref|ZP_04885574.1| tRNA-dihydrouridine synthase B [Burkholderia mallei ATCC 10399]
 gi|254180692|ref|ZP_04887290.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1655]
 gi|254191521|ref|ZP_04898024.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pasteur
           52237]
 gi|254194903|ref|ZP_04901333.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei S13]
 gi|254202628|ref|ZP_04908991.1| tRNA-dihydrouridine synthase B [Burkholderia mallei FMH]
 gi|254207967|ref|ZP_04914317.1| tRNA-dihydrouridine synthase B [Burkholderia mallei JHU]
 gi|254261098|ref|ZP_04952152.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1710a]
 gi|254299222|ref|ZP_04966672.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 406e]
 gi|254355893|ref|ZP_04972171.1| tRNA-dihydrouridine synthase B [Burkholderia mallei 2002721280]
 gi|52210916|emb|CAH36904.1| putative nitrogen regulation-related protein [Burkholderia
           pseudomallei K96243]
 gi|52429618|gb|AAU50211.1| dihydrouridine synthase [Burkholderia mallei ATCC 23344]
 gi|76580212|gb|ABA49687.1| dihydrouridine synthase [Burkholderia pseudomallei 1710b]
 gi|121228271|gb|ABM50789.1| tRNA-dihydrouridine synthase B [Burkholderia mallei SAVP1]
 gi|124292577|gb|ABN01846.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10229]
 gi|126221616|gb|ABN85122.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 668]
 gi|126244059|gb|ABO07152.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10247]
 gi|134248133|gb|EBA48216.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 305]
 gi|147746875|gb|EDK53952.1| tRNA-dihydrouridine synthase B [Burkholderia mallei FMH]
 gi|147751861|gb|EDK58928.1| tRNA-dihydrouridine synthase B [Burkholderia mallei JHU]
 gi|148024868|gb|EDK83046.1| tRNA-dihydrouridine synthase B [Burkholderia mallei 2002721280]
 gi|157809277|gb|EDO86447.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 406e]
 gi|157939192|gb|EDO94862.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pasteur
           52237]
 gi|160694834|gb|EDP84842.1| tRNA-dihydrouridine synthase B [Burkholderia mallei ATCC 10399]
 gi|169651652|gb|EDS84345.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei S13]
 gi|184211231|gb|EDU08274.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1655]
 gi|217395872|gb|EEC35889.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 576]
 gi|225929574|gb|EEH25592.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pakistan
           9]
 gi|237502697|gb|ACQ95015.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei MSHR346]
 gi|238523449|gb|EEP86887.1| tRNA-dihydrouridine synthase B [Burkholderia mallei GB8 horse 4]
 gi|243063564|gb|EES45750.1| tRNA-dihydrouridine synthase B [Burkholderia mallei PRL-20]
 gi|254219787|gb|EET09171.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1710a]
          Length = 354

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 120/247 (48%), Gaps = 27/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGAG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D D   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 PDAVPVTLKIRTGWDRDHKNALRIATLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +    +A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPRKAKAVLDATRADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSN 235
           +D +  +
Sbjct: 243 IDHFLQS 249


>gi|253576271|ref|ZP_04853602.1| dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844398|gb|EES72415.1| dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 326

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 85/188 (45%), Gaps = 18/188 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L F+  E+P+   I G       + +  +   G+  I++N+GCP   V     G+ L+L 
Sbjct: 65  LLFTEDEQPMVAHIWGDKPEYFEKMSIDMAKLGFQGIDINMGCPVPNVATNGKGSGLILR 124

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           P +  + I A  KA  +PV+VK R+G  +       R  +  I K  +  + IH R    
Sbjct: 125 PSVAAEVIQA-AKAGGLPVSVKTRLGFTE---VEEWREWLTHILKQDIVNLSIHLRT--- 177

Query: 161 KGLSPKDNRKIPNLDYDIVYEIK----KENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
                ++        ++++ EIK    +  P   + +NG + D    LK+     VDG+M
Sbjct: 178 -----REEMSQVAAHWELIPEIKALRDQVAPQTLLTINGDIPDRQTGLKLAEQYGVDGIM 232

Query: 215 IGRAAYKN 222
           IGR  +KN
Sbjct: 233 IGRGIFKN 240


>gi|83720266|ref|YP_441799.1| dihydrouridine synthase [Burkholderia thailandensis E264]
 gi|167580621|ref|ZP_02373495.1| dihydrouridine synthase [Burkholderia thailandensis TXDOH]
 gi|167618727|ref|ZP_02387358.1| dihydrouridine synthase [Burkholderia thailandensis Bt4]
 gi|257137966|ref|ZP_05586228.1| dihydrouridine synthase [Burkholderia thailandensis E264]
 gi|83654091|gb|ABC38154.1| dihydrouridine synthase [Burkholderia thailandensis E264]
          Length = 355

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 118/248 (47%), Gaps = 31/248 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVDAVGTG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKA--ILKGLSPKDN 168
             ++PVT+K R G D +      +N VK  K    +G++ + +H R    + +G      
Sbjct: 137 PDAVPVTLKIRTGWDRE-----HKNAVKIAKLAEAAGISMLTVHGRTRADLYRG------ 185

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
               + +YD +  +K     + +  NG +    +A  +L +   D +MIGRAA     + 
Sbjct: 186 ----DAEYDTIAAVKAA-VRIPVVANGDITSPQKAKAVLDATGADALMIGRAAQGRPWLF 240

Query: 227 TTVDEYFS 234
             +D +  
Sbjct: 241 REIDHFLQ 248


>gi|293391553|ref|ZP_06635887.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952087|gb|EFE02206.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 349

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 116/229 (50%), Gaps = 27/229 (11%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAK 67
           F R+  N    L ++EM+  +  +   +K+ L  +  ++    A+QI G+D   + +AA+
Sbjct: 47  FRRICANYGAGLTFSEMMSTNPQVWYTEKSKLRLAHHQEAGINAVQIAGSDPDGMAQAAQ 106

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ KA+ +PVT+K R G 
Sbjct: 107 VNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVRRILEAVVKAVKVPVTLKIRTGW 166

Query: 128 DDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILK--GLSPKDNRKIPNLDYDIVYEI 182
           D     +  RN V   K  ++SG+  + +H R    K  G++          +YD +  +
Sbjct: 167 D-----MENRNCVEIAKIAEQSGIQALTVHGRTRACKFEGVA----------EYDSIKAV 211

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            K+N  L +  NG +    QA  +L     DG+MIGR A     +  TV
Sbjct: 212 -KQNVSLPVIANGDITSAEQAKFVLDYTGADGIMIGRGALGRPWLFQTV 259


>gi|283788098|ref|YP_003367963.1| tRNA-dihydrouridine synthase B [Citrobacter rodentium ICC168]
 gi|282951552|emb|CBG91251.1| tRNA-dihydrouridine synthase B [Citrobacter rodentium ICC168]
          Length = 321

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGVRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|197336031|ref|YP_002157182.1| tRNA-dihydrouridine synthase B [Vibrio fischeri MJ11]
 gi|197317521|gb|ACH66968.1| tRNA-dihydrouridine synthase B [Vibrio fischeri MJ11]
          Length = 293

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/192 (27%), Positives = 91/192 (47%), Gaps = 23/192 (11%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ + + A
Sbjct: 39  SVQIAGADPKLMAEAAQHCVETGAQIIDINMGCPAKKVNKKLAGSALLQRPDLIEEILLA 98

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSP 165
           +  A+ +PVT+K R G D        RN V+  K   + G+  + +H R    + KG + 
Sbjct: 99  VVNAVDVPVTLKTRTGWDPDN-----RNCVQVAKMAEQCGIQALALHGRTRACMYKGEAE 153

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            DN K             KE   + +  NG ++   +A  +L     D +MIGR A    
Sbjct: 154 YDNIK-----------AVKEAISIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRP 202

Query: 224 AMLTTVDEYFSN 235
            +   +  Y   
Sbjct: 203 WIFKEIQHYLET 214


>gi|241662015|ref|YP_002980375.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12D]
 gi|240864042|gb|ACS61703.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12D]
          Length = 355

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 116/243 (47%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  + +G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRE-----HRNALSVARIAQDAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYDTIAAVKA-SVRIPVVANGDITTPAKAKHVLAVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YFS 234
           +  
Sbjct: 242 FLQ 244


>gi|330444963|ref|ZP_08308617.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328493081|dbj|GAA03114.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 321

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 111/244 (45%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L    K  N +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPDLWKTSKSLNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD+V D +  +  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQYPDLVEDILRTVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D     +  RN V   K  ++ G+  + +H R    + KG           
Sbjct: 136 VTLKTRTGWD-----LENRNCVDIAKLAEQCGIQALALHGRTKACMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  
Sbjct: 181 AEYDYIRAVKQAISIPVIA-NGDIDSPEKARFVLDYTGADALMIGRPAQGKPWIFREIHH 239

Query: 232 YFSN 235
           Y + 
Sbjct: 240 YLTT 243


>gi|195434933|ref|XP_002065456.1| GK14658 [Drosophila willistoni]
 gi|194161541|gb|EDW76442.1| GK14658 [Drosophila willistoni]
          Length = 404

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 111/232 (47%), Gaps = 19/232 (8%)

Query: 7   RHYRF-FARLLTNNA--LLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGADISK 61
           R+ +F F +LL  N   L +T M+++++I   +K     FST +  +PL  Q    D S+
Sbjct: 36  RYSKFEFRKLLRQNGVQLCFTPMMISESINNSEKARQNEFSTDQDDQPLVAQFAAKDASE 95

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
            V +A+++  +  + I+LN GCP +      +G  L+  P+ V D +  + + L     V
Sbjct: 96  FVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGLLRQPEQVKDIVREVRRVLPTDFSV 154

Query: 120 TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +VK R +G   +       +L + ++ +GV  + +H R    K    KD   IP ++   
Sbjct: 155 SVKMRLLGGSQETSLERTIDLARQLEHTGVTFLTLHGRTPAQK--HSKDTLNIPAMN--- 209

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTT 228
             E++K +  + + +NG +E    A+++       GVM  R    N A+  +
Sbjct: 210 --EVQK-SLQIPLIVNGNVESWEDAIELQSQTGAAGVMAARGLLANPALFNS 258


>gi|289808099|ref|ZP_06538728.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. AG3]
          Length = 62

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/57 (54%), Positives = 42/57 (73%), Gaps = 1/57 (1%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGA 57
          M+DWTDRH R+F RLL+   LLYTEM+   AI+ G K + L +S +E P+ALQ+GG+
Sbjct: 7  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVALQLGGS 62


>gi|319764305|ref|YP_004128242.1| tim-barrel protein, nifr3 family [Alicycliphilus denitrificans BC]
 gi|317118866|gb|ADV01355.1| TIM-barrel protein, nifR3 family [Alicycliphilus denitrificans BC]
          Length = 352

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 74/309 (23%), Positives = 126/309 (40%), Gaps = 27/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKDLWASLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +   + + + A C   
Sbjct: 76  AAMMAEAAVYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVQIAEAVVAACAPR 135

Query: 116 SIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +PVT+K R G       AV    L ++ +  GV  + +H R         ++       
Sbjct: 136 GVPVTLKMRTGWCQRHRNAV---QLARAFEGVGVQMLTVHGRT--------REQGYKGQA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K +     +  NG +    +A  +L     D VMIGRAA     +   +  Y
Sbjct: 185 EYDTIAAVKAQVAVPVVA-NGDITSPEKACAVLAHTGADAVMIGRAAQGRPWIFREIGHY 243

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +     + P+   V     R +   + D+   +  + G ++   +H+       P    
Sbjct: 244 LATGEHLAPPLVAEVR----RLLLEHLQDHYGLYGQASG-VRSARKHIAWYVRDLPGGEA 298

Query: 293 CR-HILTVE 300
            R HI T+E
Sbjct: 299 FRQHINTIE 307


>gi|238026250|ref|YP_002910481.1| putative TIM-barrel protein, nifR3 family protein [Burkholderia
           glumae BGR1]
 gi|237875444|gb|ACR27777.1| Putative TIM-barrel protein, nifR3 family protein [Burkholderia
           glumae BGR1]
          Length = 347

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/256 (24%), Positives = 121/256 (47%), Gaps = 31/256 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   ++A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVSAVVAAVGTG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA--ILKGLSPKDN 168
             ++PVT+K R G D +      RN   + +  + +G+  + +H R    + +G      
Sbjct: 137 PDAVPVTLKIRTGWDRE-----HRNALTIARLAEDAGIAMLTVHGRTRADLYRG------ 185

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
               + +Y+ +  +K     + +  NG +   ++A  +L     D +MIGRAA     + 
Sbjct: 186 ----DAEYETIAAVKAA-VKIPVVANGDITSPAKAKAVLDFTGADALMIGRAAQGRPWLF 240

Query: 227 TTVDEYFSNPLTGSSP 242
             +D +     T  +P
Sbjct: 241 REIDHFLQTGTTLPAP 256


>gi|34763049|ref|ZP_00144023.1| Nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|27887275|gb|EAA24372.1| Nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
          Length = 307

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 103/222 (46%), Gaps = 30/222 (13%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I       K  A+QI G ++ K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLRKGNAVQIFGENVEKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    +++K RIG       V +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKLSIKIRIGYKKPENYVQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + I   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEI---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           F G    LE +S +     +VDGVM+ R  + N  ++  + E
Sbjct: 195 FTG-EDALEKISYS-----NVDGVMLARGIFGNPWLIRDIRE 230


>gi|289425437|ref|ZP_06427214.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK187]
 gi|289154415|gb|EFD03103.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK187]
          Length = 409

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 74/286 (25%), Positives = 116/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 73  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 132

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 133 VDLNFGCPVPKVTRKGGGGVLPWKLDQFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 190

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 191 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 241

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A+ ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 242 NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCAMI 301

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R    S+  Y   H      L  + +HM     GFP     RH+L
Sbjct: 302 RRHAELSV-KYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 341


>gi|261868732|ref|YP_003256654.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261414064|gb|ACX83435.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 349

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 116/229 (50%), Gaps = 27/229 (11%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAK 67
           F R+  N    L ++EM+  +  +   +K+ L  +  ++    A+QI G+D   + +AA+
Sbjct: 47  FRRICANYGAGLTFSEMMSTNPQVWYTEKSKLRLAHHQEAGINAVQIAGSDPDGMAQAAQ 106

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ KA+ +PVT+K R G 
Sbjct: 107 VNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVRRILEAVVKAVKVPVTLKIRTGW 166

Query: 128 DDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILK--GLSPKDNRKIPNLDYDIVYEI 182
           D     +  RN V   K  ++SG+  + +H R    K  G++          +YD +  +
Sbjct: 167 D-----MENRNCVEIAKIAEQSGIQALTVHGRTRACKFEGVA----------EYDSIKAV 211

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            K+N  L +  NG +    QA  +L     DG+MIGR A     +  TV
Sbjct: 212 -KQNVSLPVIANGDITSAEQAKFVLDYTGADGIMIGRGALGRPWLFQTV 259


>gi|238758368|ref|ZP_04619546.1| tRNA-dihydrouridine synthase B [Yersinia aldovae ATCC 35236]
 gi|238703491|gb|EEP96030.1| tRNA-dihydrouridine synthase B [Yersinia aldovae ATCC 35236]
          Length = 321

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  +  +QI G D
Sbjct: 17  MAGITDRPFRTLCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 76  PHEMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPELVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G +         
Sbjct: 136 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQTVTIPVIA-NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|190408164|gb|EDV11429.1| tRNA dihydrouridine synthase [Saccharomyces cerevisiae RM11-1a]
          Length = 423

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 82/166 (49%), Gaps = 9/166 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L+ ++       R D  + L  S+ ++PL +Q   
Sbjct: 36  MVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ +    + K L 
Sbjct: 96  NDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLTNTLHKNLK 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PVT K RI  DD   ++   N  K +  +G   + +H R    KG
Sbjct: 155 VPVTAKIRI-FDDCEKSL---NYAKMVLDAGAQFLTVHGRVREQKG 196


>gi|198436587|ref|XP_002123151.1| PREDICTED: similar to PP3111 protein [Ciona intestinalis]
          Length = 474

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/164 (29%), Positives = 83/164 (50%), Gaps = 8/164 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ A   LR  +  I G ++  +++PL +Q    D
Sbjct: 26  MVDQSELAWRMLSRKY-GAELCYTPMLHASVFLRDPQYRIDGLASCPEDRPLIVQFCAND 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L ++A + +D   + +++N+GCP      G++GA L  N ++V   I A  + LS+P
Sbjct: 85  PDILTKSALLAQDHC-DAVDINLGCPQTIAKRGNYGAFLGENWELVTKLIKACHEKLSVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           VT K RI  D +          K I+++G   + +H R   +KG
Sbjct: 144 VTCKIRIFTDVE----KTVQYAKMIERAGCQLLTVHGRTKEMKG 183


>gi|187927485|ref|YP_001897972.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12J]
 gi|309779813|ref|ZP_07674568.1| tRNA-dihydrouridine synthase B [Ralstonia sp. 5_7_47FAA]
 gi|187724375|gb|ACD25540.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12J]
 gi|308921390|gb|EFP67032.1| tRNA-dihydrouridine synthase B [Ralstonia sp. 5_7_47FAA]
          Length = 355

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 116/243 (47%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  + +G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRE-----HRNALSVARIAQDAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYDTIAAVKA-SVRIPVVANGDITTPAKAKHVLAVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YFS 234
           +  
Sbjct: 242 FLQ 244


>gi|3915489|sp|O52536|DUSB_KLEPN RecName: Full=tRNA-dihydrouridine synthase B
 gi|2773320|gb|AAC77888.1| yhdG homolog [Klebsiella pneumoniae]
          Length = 321

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+ KA+ +P
Sbjct: 76  PKEMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G + +      RN V   +  ++ G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGWEPE-----HRNCVEIAQLAEECGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|146305745|ref|YP_001186210.1| nifR3 family TIM-barrel protein [Pseudomonas mendocina ymp]
 gi|145573946|gb|ABP83478.1| tRNA-U20-dihydrouridine synthase [Pseudomonas mendocina ymp]
          Length = 332

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 114/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGLVVSEMVTSDVRLWNSRKSSLRLLHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  PQMLAEAARKNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEPLVREILEAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + K  + +G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRQNKNGI--TVAKIAEDAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           +  IK+    + +  NG ++   +A  +L +   D ++IGRAA     +   ++ Y 
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPQKAKAVLDATGADALLIGRAAQGRPWIFREIEHYL 244


>gi|315499857|ref|YP_004088660.1| tim-barrel protein, nifr3 family [Asticcacaulis excentricus CB 48]
 gi|315417869|gb|ADU14509.1| TIM-barrel protein, nifR3 family [Asticcacaulis excentricus CB 48]
          Length = 327

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 104/242 (42%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +D  +R  A  L   A   TEM+    + RG    +  F+  E      +Q+ G D
Sbjct: 21  MTGVSDLPFRRMASKL-GAAYAATEMVACAELERGRPDVVRKFALGEHAGLKIVQLIGKD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +   A + E  G + ++LN GCP+  V     G+ LM + D     + A   A S P
Sbjct: 80  PAFIARGAALAEASGAHIVDLNFGCPAKEVTGVLCGSALMRDLDAASRLMEAAVSATSRP 139

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VTVK R+G D+Q    P +A R     I+   V+G     R+   KG            D
Sbjct: 140 VTVKMRMGWDNQSRNAPELARRAEAIGIQAVTVHG---RTRQQFYKG----------EAD 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V ++ KE   + + +NG + D  +A + L     DG+MIGR  Y    +   +D   
Sbjct: 187 WAFVQQV-KEAVSIPVIVNGDITDGEKAREALAQSGADGLMIGRGVYGRPWLAAQLDAAL 245

Query: 234 SN 235
           S 
Sbjct: 246 SG 247


>gi|312958742|ref|ZP_07773262.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens WH6]
 gi|311287285|gb|EFQ65846.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens WH6]
          Length = 337

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/267 (23%), Positives = 127/267 (47%), Gaps = 18/267 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ +        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRMRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+     G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVALGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVAEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    +    + K  +++G+  + +H R         + +      +YD
Sbjct: 139 VTLKIRTGWDRDNKNGL---TVAKIAEQAGITALAVHGRT--------RADLYTGEAEYD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ +   
Sbjct: 188 TIAAI-KQAVSMPVFANGDIDSAEKARRVLHATDADGLLIGRAAQGRPWIFREIEHFLRT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDY 262
             T  +P    V++     ++A  T Y
Sbjct: 247 GETLPAPELFEVERILLEHLAALHTFY 273


>gi|238764617|ref|ZP_04625563.1| tRNA-dihydrouridine synthase B [Yersinia kristensenii ATCC 33638]
 gi|238697207|gb|EEP89978.1| tRNA-dihydrouridine synthase B [Yersinia kristensenii ATCC 33638]
          Length = 321

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  + A+QI G D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 76  PDEMAAAAQINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPELVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH   R  +  G +         
Sbjct: 136 VTLKIRTGWSPE-----HRNCIEIAQLAENCGIQALTIHGRTRSCLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQIVSIPVIA-NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|78221481|ref|YP_383228.1| dihydrouridine synthase, DuS [Geobacter metallireducens GS-15]
 gi|78192736|gb|ABB30503.1| tRNA-U20a,U20b-dihydrouridine synthase [Geobacter metallireducens
           GS-15]
          Length = 331

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 89/180 (49%), Gaps = 14/180 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G D   LV AA+  ++ G   INLN+GCP  R+  G  G  ++  P+ + + I
Sbjct: 83  PLVVQLIGHDHKALVAAARTAQEAGAVHINLNLGCPYGRMTSGLTGGGMLHRPEALEELI 142

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+ +A++   +VK R G DD   +  +  L+   +++GV+ + +H R  +         
Sbjct: 143 PALRRAIAGTFSVKVRAGYDD---SGQIMTLLPLFEEAGVDFLVLHPRTVV--------Q 191

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
               + D+ +  E+ ++   L +  NG +   +  L++L      G+M+GR A  +  + 
Sbjct: 192 EYTGHADHAVTAEVVRQT-RLPVIANGDVRSAADGLRVLRKTGATGLMLGRGAIADPLLF 250


>gi|71003213|ref|XP_756287.1| hypothetical protein UM00140.1 [Ustilago maydis 521]
 gi|46096292|gb|EAK81525.1| hypothetical protein UM00140.1 [Ustilago maydis 521]
          Length = 364

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/199 (26%), Positives = 94/199 (47%), Gaps = 30/199 (15%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDI 103
           Q  P  +Q+ G ++ +LVEAA+ V  +  + I+LN+GCP     +G +GACL+   N  +
Sbjct: 84  QSAPQVVQLAGNNVQQLVEAARRVAPYA-DAIDLNLGCPQRHAEQGHYGACLLPKQNWPL 142

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V + ++ M +A+ +P+T K R+ V    P      L   +  +G + + +H R       
Sbjct: 143 VAEIVSGMVQAVDVPITTKIRLPV----PKEQTAQLAVMLAHAGSSLVTVHPR------F 192

Query: 164 SPKDNRKIPNLDYDIVYEIKK-----------ENP--DLFIGLNGGL---EDMSQALKIL 207
           +    R+    D D V ++++           E P  D  +  NG +   +D+   L+ L
Sbjct: 193 ASSARRRKGLADLDQVVKVREALQAQGLLRSAEQPHKDTAVVSNGNVQCWQDVVNNLE-L 251

Query: 208 PSVDGVMIGRAAYKNSAML 226
               GVM+G    +N A+ 
Sbjct: 252 TGASGVMVGETLLQNPALF 270


>gi|15803794|ref|NP_289828.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 EDL933]
 gi|15833386|ref|NP_312159.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           Sakai]
 gi|16131148|ref|NP_417726.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           MG1655]
 gi|26249852|ref|NP_755892.1| tRNA-dihydrouridine synthase B [Escherichia coli CFT073]
 gi|74313789|ref|YP_312208.1| tRNA-dihydrouridine synthase B [Shigella sonnei Ss046]
 gi|82545631|ref|YP_409578.1| tRNA-dihydrouridine synthase B [Shigella boydii Sb227]
 gi|82778569|ref|YP_404918.1| tRNA-dihydrouridine synthase B [Shigella dysenteriae Sd197]
 gi|89110020|ref|AP_003800.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           W3110]
 gi|91212691|ref|YP_542677.1| tRNA-dihydrouridine synthase B [Escherichia coli UTI89]
 gi|110643504|ref|YP_671234.1| tRNA-dihydrouridine synthase B [Escherichia coli 536]
 gi|117625551|ref|YP_858874.1| tRNA-dihydrouridine synthase B [Escherichia coli APEC O1]
 gi|157156175|ref|YP_001464734.1| tRNA-dihydrouridine synthase B [Escherichia coli E24377A]
 gi|157162741|ref|YP_001460059.1| tRNA-dihydrouridine synthase B [Escherichia coli HS]
 gi|168752560|ref|ZP_02777582.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4113]
 gi|168758937|ref|ZP_02783944.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764879|ref|ZP_02789886.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4501]
 gi|168769123|ref|ZP_02794130.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4486]
 gi|168777676|ref|ZP_02802683.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4196]
 gi|168783829|ref|ZP_02808836.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4076]
 gi|168786153|ref|ZP_02811160.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC869]
 gi|168802602|ref|ZP_02827609.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC508]
 gi|170018497|ref|YP_001723451.1| tRNA-dihydrouridine synthase B [Escherichia coli ATCC 8739]
 gi|170082788|ref|YP_001732108.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170680881|ref|YP_001745531.1| tRNA-dihydrouridine synthase B [Escherichia coli SMS-3-5]
 gi|170765665|ref|ZP_02900476.1| tRNA-dihydrouridine synthase B [Escherichia albertii TW07627]
 gi|187734046|ref|YP_001881952.1| tRNA-dihydrouridine synthase B [Shigella boydii CDC 3083-94]
 gi|188491759|ref|ZP_02999029.1| tRNA-dihydrouridine synthase B [Escherichia coli 53638]
 gi|191169157|ref|ZP_03030915.1| tRNA-dihydrouridine synthase B [Escherichia coli B7A]
 gi|191173814|ref|ZP_03035335.1| tRNA-dihydrouridine synthase B [Escherichia coli F11]
 gi|193066463|ref|ZP_03047508.1| tRNA-dihydrouridine synthase B [Escherichia coli E22]
 gi|193071520|ref|ZP_03052430.1| tRNA-dihydrouridine synthase B [Escherichia coli E110019]
 gi|194435099|ref|ZP_03067336.1| tRNA-dihydrouridine synthase B [Shigella dysenteriae 1012]
 gi|194440027|ref|ZP_03072084.1| tRNA-dihydrouridine synthase B [Escherichia coli 101-1]
 gi|195940004|ref|ZP_03085386.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4024]
 gi|208806407|ref|ZP_03248744.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814013|ref|ZP_03255342.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821905|ref|ZP_03262225.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4042]
 gi|209396246|ref|YP_002272722.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920732|ref|YP_002294816.1| tRNA-dihydrouridine synthase B [Escherichia coli SE11]
 gi|215488567|ref|YP_002330998.1| tRNA-dihydrouridine synthase B [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217327776|ref|ZP_03443859.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14588]
 gi|218550544|ref|YP_002384335.1| tRNA-dihydrouridine synthase B [Escherichia fergusonii ATCC 35469]
 gi|218555824|ref|YP_002388737.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI1]
 gi|218560329|ref|YP_002393242.1| tRNA-dihydrouridine synthase B [Escherichia coli S88]
 gi|218691551|ref|YP_002399763.1| tRNA-dihydrouridine synthase B [Escherichia coli ED1a]
 gi|218696959|ref|YP_002404626.1| tRNA-dihydrouridine synthase B [Escherichia coli 55989]
 gi|218702033|ref|YP_002409662.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI39]
 gi|218706874|ref|YP_002414393.1| tRNA -dihydrouridine synthase B [Escherichia coli UMN026]
 gi|227887986|ref|ZP_04005791.1| tRNA-dihydrouridine synthase B [Escherichia coli 83972]
 gi|237705982|ref|ZP_04536463.1| tRNA-dihydrouridine synthase B [Escherichia sp. 3_2_53FAA]
 gi|238902359|ref|YP_002928155.1| tRNA-dihydrouridine synthase B [Escherichia coli BW2952]
 gi|253771910|ref|YP_003034741.1| tRNA-dihydrouridine synthase B [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038424|ref|ZP_04872482.1| tRNA-dihydrouridine synthase B [Escherichia sp. 1_1_43]
 gi|254163195|ref|YP_003046303.1| tRNA-dihydrouridine synthase B [Escherichia coli B str. REL606]
 gi|254795203|ref|YP_003080040.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14359]
 gi|256018826|ref|ZP_05432691.1| tRNA-dihydrouridine synthase B [Shigella sp. D9]
 gi|256024166|ref|ZP_05438031.1| tRNA-dihydrouridine synthase B [Escherichia sp. 4_1_40B]
 gi|260846065|ref|YP_003223843.1| tRNA-dihydrouridine synthase B [Escherichia coli O103:H2 str.
           12009]
 gi|260857387|ref|YP_003231278.1| tRNA-dihydrouridine synthase B [Escherichia coli O26:H11 str.
           11368]
 gi|260870011|ref|YP_003236413.1| tRNA-dihydrouridine synthase B [Escherichia coli O111:H- str.
           11128]
 gi|261255121|ref|ZP_05947654.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284627|ref|YP_003501445.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str.
           CB9615]
 gi|293406862|ref|ZP_06650788.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1412]
 gi|293412628|ref|ZP_06655351.1| tRNA-dihydrouridine synthase B [Escherichia coli B354]
 gi|293416685|ref|ZP_06659324.1| tRNA-dihydrouridine synthase B [Escherichia coli B185]
 gi|293449583|ref|ZP_06664004.1| tRNA-dihydrouridine synthase B [Escherichia coli B088]
 gi|297519369|ref|ZP_06937755.1| tRNA-dihydrouridine synthase B [Escherichia coli OP50]
 gi|298382603|ref|ZP_06992200.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1302]
 gi|300824972|ref|ZP_07105071.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 119-7]
 gi|300898032|ref|ZP_07116403.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 198-1]
 gi|300904454|ref|ZP_07122300.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 84-1]
 gi|300917419|ref|ZP_07134084.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 115-1]
 gi|300925995|ref|ZP_07141818.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 182-1]
 gi|300928705|ref|ZP_07144223.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 187-1]
 gi|300937387|ref|ZP_07152222.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 21-1]
 gi|300948346|ref|ZP_07162454.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 116-1]
 gi|300958258|ref|ZP_07170405.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 175-1]
 gi|300979714|ref|ZP_07174664.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 200-1]
 gi|300991058|ref|ZP_07179479.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 45-1]
 gi|301022203|ref|ZP_07186118.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 69-1]
 gi|301047884|ref|ZP_07194931.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 185-1]
 gi|301304273|ref|ZP_07210387.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 124-1]
 gi|301647036|ref|ZP_07246868.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 146-1]
 gi|306816397|ref|ZP_07450529.1| tRNA-dihydrouridine synthase B [Escherichia coli NC101]
 gi|307314983|ref|ZP_07594571.1| TIM-barrel protein, nifR3 family [Escherichia coli W]
 gi|309785585|ref|ZP_07680216.1| TIM-barrel , nifR3 family protein [Shigella dysenteriae 1617]
 gi|309793839|ref|ZP_07688265.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 145-7]
 gi|331643960|ref|ZP_08345091.1| tRNA-dihydrouridine synthase B [Escherichia coli H736]
 gi|331649061|ref|ZP_08350149.1| tRNA-dihydrouridine synthase B [Escherichia coli M605]
 gi|331654858|ref|ZP_08355858.1| tRNA-dihydrouridine synthase B [Escherichia coli M718]
 gi|331659549|ref|ZP_08360491.1| tRNA-dihydrouridine synthase B [Escherichia coli TA206]
 gi|331664869|ref|ZP_08365774.1| tRNA-dihydrouridine synthase B [Escherichia coli TA143]
 gi|331670084|ref|ZP_08370929.1| tRNA-dihydrouridine synthase B [Escherichia coli TA271]
 gi|331679333|ref|ZP_08380005.1| tRNA-dihydrouridine synthase B [Escherichia coli H591]
 gi|331684900|ref|ZP_08385492.1| tRNA-dihydrouridine synthase B [Escherichia coli H299]
 gi|332279908|ref|ZP_08392321.1| tRNA-dihydrouridine synthase B [Shigella sp. D9]
 gi|78100049|sp|P0ABT7|DUSB_ECO57 RecName: Full=tRNA-dihydrouridine synthase B
 gi|78100050|sp|P0ABT6|DUSB_ECOL6 RecName: Full=tRNA-dihydrouridine synthase B
 gi|78100051|sp|P0ABT5|DUSB_ECOLI RecName: Full=tRNA-dihydrouridine synthase B
 gi|12517887|gb|AAG58388.1|AE005553_10 putative dehydrogenase [Escherichia coli O157:H7 str. EDL933]
 gi|26110280|gb|AAN82466.1|AE016767_226 Hypothetical protein yhdG [Escherichia coli CFT073]
 gi|145976|gb|AAA23782.1| 'ORF1' [Escherichia coli]
 gi|606201|gb|AAA58064.1| ORF_o321 [Escherichia coli str. K-12 substr. MG1655]
 gi|1789660|gb|AAC76292.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           MG1655]
 gi|13363605|dbj|BAB37555.1| putative dehydrogenase [Escherichia coli O157:H7 str. Sakai]
 gi|73857266|gb|AAZ89973.1| putative dehydrogenase [Shigella sonnei Ss046]
 gi|81242717|gb|ABB63427.1| putative dehydrogenase [Shigella dysenteriae Sd197]
 gi|81247042|gb|ABB67750.1| putative dehydrogenase [Shigella boydii Sb227]
 gi|85676051|dbj|BAE77301.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K12 substr.
           W3110]
 gi|91074265|gb|ABE09146.1| putative dehydrogenase [Escherichia coli UTI89]
 gi|110345096|gb|ABG71333.1| tRNA-dihydrouridine synthase B [Escherichia coli 536]
 gi|115514675|gb|ABJ02750.1| tRNA-dihydrouridine synthase B [Escherichia coli APEC O1]
 gi|157068421|gb|ABV07676.1| tRNA-dihydrouridine synthase B [Escherichia coli HS]
 gi|157078205|gb|ABV17913.1| tRNA-dihydrouridine synthase B [Escherichia coli E24377A]
 gi|169753425|gb|ACA76124.1| TIM-barrel protein, nifR3 family [Escherichia coli ATCC 8739]
 gi|169890623|gb|ACB04330.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170124811|gb|EDS93742.1| tRNA-dihydrouridine synthase B [Escherichia albertii TW07627]
 gi|170518599|gb|ACB16777.1| tRNA-dihydrouridine synthase B [Escherichia coli SMS-3-5]
 gi|187431038|gb|ACD10312.1| tRNA-dihydrouridine synthase B [Shigella boydii CDC 3083-94]
 gi|187767124|gb|EDU30968.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4196]
 gi|188013631|gb|EDU51753.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4113]
 gi|188486958|gb|EDU62061.1| tRNA-dihydrouridine synthase B [Escherichia coli 53638]
 gi|188998885|gb|EDU67871.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4076]
 gi|189354344|gb|EDU72763.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4401]
 gi|189361809|gb|EDU80228.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365202|gb|EDU83618.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4501]
 gi|189373964|gb|EDU92380.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC869]
 gi|189375438|gb|EDU93854.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC508]
 gi|190900799|gb|EDV60590.1| tRNA-dihydrouridine synthase B [Escherichia coli B7A]
 gi|190905864|gb|EDV65482.1| tRNA-dihydrouridine synthase B [Escherichia coli F11]
 gi|192925892|gb|EDV80541.1| tRNA-dihydrouridine synthase B [Escherichia coli E22]
 gi|192955157|gb|EDV85650.1| tRNA-dihydrouridine synthase B [Escherichia coli E110019]
 gi|194416661|gb|EDX32793.1| tRNA-dihydrouridine synthase B [Shigella dysenteriae 1012]
 gi|194421031|gb|EDX37061.1| tRNA-dihydrouridine synthase B [Escherichia coli 101-1]
 gi|208726208|gb|EDZ75809.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735290|gb|EDZ83977.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4045]
 gi|208742028|gb|EDZ89710.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4042]
 gi|209157646|gb|ACI35079.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4115]
 gi|209757538|gb|ACI77081.1| putative dehydrogenase [Escherichia coli]
 gi|209757540|gb|ACI77082.1| putative dehydrogenase [Escherichia coli]
 gi|209757542|gb|ACI77083.1| putative dehydrogenase [Escherichia coli]
 gi|209757544|gb|ACI77084.1| putative dehydrogenase [Escherichia coli]
 gi|209757546|gb|ACI77085.1| putative dehydrogenase [Escherichia coli]
 gi|209913991|dbj|BAG79065.1| putative tRNA-dihydrouridine synthase B [Escherichia coli SE11]
 gi|215266639|emb|CAS11078.1| tRNA-dihydrouridine synthase B [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217320143|gb|EEC28568.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353691|emb|CAU99946.1| tRNA-dihydrouridine synthase B [Escherichia coli 55989]
 gi|218358085|emb|CAQ90731.1| tRNA-dihydrouridine synthase B [Escherichia fergusonii ATCC 35469]
 gi|218362592|emb|CAR00217.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI1]
 gi|218367098|emb|CAR04871.1| tRNA-dihydrouridine synthase B [Escherichia coli S88]
 gi|218372019|emb|CAR19875.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI39]
 gi|218429115|emb|CAR09922.1| tRNA-dihydrouridine synthase B [Escherichia coli ED1a]
 gi|218433971|emb|CAR14888.1| tRNA-dihydrouridine synthase B [Escherichia coli UMN026]
 gi|222034976|emb|CAP77719.1| tRNA-dihydrouridine synthase B [Escherichia coli LF82]
 gi|226840048|gb|EEH72069.1| tRNA-dihydrouridine synthase B [Escherichia sp. 1_1_43]
 gi|226899022|gb|EEH85281.1| tRNA-dihydrouridine synthase B [Escherichia sp. 3_2_53FAA]
 gi|227835382|gb|EEJ45848.1| tRNA-dihydrouridine synthase B [Escherichia coli 83972]
 gi|238863714|gb|ACR65712.1| tRNA-dihydrouridine synthase B [Escherichia coli BW2952]
 gi|242378794|emb|CAQ33586.1| tRNA dihydrouridine synthase [Escherichia coli BL21(DE3)]
 gi|253322954|gb|ACT27556.1| TIM-barrel protein, nifR3 family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975096|gb|ACT40767.1| tRNA-dihydrouridine synthase B [Escherichia coli B str. REL606]
 gi|253979252|gb|ACT44922.1| tRNA-dihydrouridine synthase B [Escherichia coli BL21(DE3)]
 gi|254594603|gb|ACT73964.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14359]
 gi|257756036|dbj|BAI27538.1| tRNA-dihydrouridine synthase B [Escherichia coli O26:H11 str.
           11368]
 gi|257761212|dbj|BAI32709.1| tRNA-dihydrouridine synthase B [Escherichia coli O103:H2 str.
           12009]
 gi|257766367|dbj|BAI37862.1| tRNA-dihydrouridine synthase B [Escherichia coli O111:H- str.
           11128]
 gi|260447713|gb|ACX38135.1| TIM-barrel protein, nifR3 family [Escherichia coli DH1]
 gi|281180302|dbj|BAI56632.1| putative tRNA-dihydrouridine synthase B [Escherichia coli SE15]
 gi|284923274|emb|CBG36368.1| tRNA-dihydrouridine synthase B [Escherichia coli 042]
 gi|290764500|gb|ADD58461.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str.
           CB9615]
 gi|291322673|gb|EFE62102.1| tRNA-dihydrouridine synthase B [Escherichia coli B088]
 gi|291426868|gb|EFE99900.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1412]
 gi|291432041|gb|EFF05024.1| tRNA-dihydrouridine synthase B [Escherichia coli B185]
 gi|291469399|gb|EFF11890.1| tRNA-dihydrouridine synthase B [Escherichia coli B354]
 gi|294493598|gb|ADE92354.1| tRNA-dihydrouridine synthase B [Escherichia coli IHE3034]
 gi|298277743|gb|EFI19259.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1302]
 gi|300300227|gb|EFJ56612.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 185-1]
 gi|300307932|gb|EFJ62452.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 200-1]
 gi|300315076|gb|EFJ64860.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 175-1]
 gi|300358251|gb|EFJ74121.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 198-1]
 gi|300397616|gb|EFJ81154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 69-1]
 gi|300403616|gb|EFJ87154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 84-1]
 gi|300406979|gb|EFJ90517.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 45-1]
 gi|300415329|gb|EFJ98639.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 115-1]
 gi|300417939|gb|EFK01250.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 182-1]
 gi|300452135|gb|EFK15755.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 116-1]
 gi|300457561|gb|EFK21054.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 21-1]
 gi|300463294|gb|EFK26787.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 187-1]
 gi|300522538|gb|EFK43607.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 119-7]
 gi|300840399|gb|EFK68159.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 124-1]
 gi|301074786|gb|EFK89592.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 146-1]
 gi|305849962|gb|EFM50421.1| tRNA-dihydrouridine synthase B [Escherichia coli NC101]
 gi|306905566|gb|EFN36098.1| TIM-barrel protein, nifR3 family [Escherichia coli W]
 gi|307555354|gb|ADN48129.1| tRNA-dihydrouridine synthase B [Escherichia coli ABU 83972]
 gi|308122796|gb|EFO60058.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 145-7]
 gi|308926705|gb|EFP72181.1| TIM-barrel , nifR3 family protein [Shigella dysenteriae 1617]
 gi|309703679|emb|CBJ03020.1| tRNA-dihydrouridine synthase B [Escherichia coli ETEC H10407]
 gi|312947817|gb|ADR28644.1| tRNA-dihydrouridine synthase B [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315137843|dbj|BAJ45002.1| tRNA-dihydrouridine synthase B [Escherichia coli DH1]
 gi|315257186|gb|EFU37154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 85-1]
 gi|315289033|gb|EFU48431.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 110-3]
 gi|315294811|gb|EFU54154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 153-1]
 gi|315300924|gb|EFU60144.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 16-3]
 gi|320177099|gb|EFW52115.1| tRNA dihydrouridine synthase B [Shigella dysenteriae CDC 74-1112]
 gi|320640052|gb|EFX09633.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           G5101]
 gi|320645622|gb|EFX14631.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H- str.
           493-89]
 gi|320662003|gb|EFX29411.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str. USDA
           5905]
 gi|323376854|gb|ADX49122.1| TIM-barrel protein, nifR3 family [Escherichia coli KO11]
 gi|323936257|gb|EGB32549.1| dihydrouridine synthase [Escherichia coli E1520]
 gi|323941647|gb|EGB37826.1| dihydrouridine synthase [Escherichia coli E482]
 gi|323946893|gb|EGB42909.1| dihydrouridine synthase [Escherichia coli H120]
 gi|323951220|gb|EGB47095.1| dihydrouridine synthase [Escherichia coli H252]
 gi|323957592|gb|EGB53306.1| dihydrouridine synthase [Escherichia coli H263]
 gi|323961092|gb|EGB56706.1| dihydrouridine synthase [Escherichia coli H489]
 gi|323966438|gb|EGB61872.1| dihydrouridine synthase [Escherichia coli M863]
 gi|323970325|gb|EGB65595.1| dihydrouridine synthase [Escherichia coli TA007]
 gi|323979021|gb|EGB74099.1| dihydrouridine synthase [Escherichia coli TW10509]
 gi|324009089|gb|EGB78308.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 57-2]
 gi|324015869|gb|EGB85088.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 60-1]
 gi|324020742|gb|EGB89961.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 117-3]
 gi|324115136|gb|EGC09100.1| dihydrouridine synthase [Escherichia fergusonii B253]
 gi|324119440|gb|EGC13323.1| dihydrouridine synthase [Escherichia coli E1167]
 gi|331037431|gb|EGI09655.1| tRNA-dihydrouridine synthase B [Escherichia coli H736]
 gi|331042808|gb|EGI14950.1| tRNA-dihydrouridine synthase B [Escherichia coli M605]
 gi|331048240|gb|EGI20317.1| tRNA-dihydrouridine synthase B [Escherichia coli M718]
 gi|331054131|gb|EGI26160.1| tRNA-dihydrouridine synthase B [Escherichia coli TA206]
 gi|331058117|gb|EGI30099.1| tRNA-dihydrouridine synthase B [Escherichia coli TA143]
 gi|331062997|gb|EGI34911.1| tRNA-dihydrouridine synthase B [Escherichia coli TA271]
 gi|331073398|gb|EGI44721.1| tRNA-dihydrouridine synthase B [Escherichia coli H591]
 gi|331078515|gb|EGI49721.1| tRNA-dihydrouridine synthase B [Escherichia coli H299]
 gi|332102260|gb|EGJ05606.1| tRNA-dihydrouridine synthase B [Shigella sp. D9]
          Length = 321

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|330887987|gb|EGH20648.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. mori str.
           301020]
          Length = 337

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 125/264 (47%), Gaps = 22/264 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  +  H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAGHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ + 
Sbjct: 186 YDTIAMI-KQAVSIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISA 257
                  +P  + V++     ++A
Sbjct: 245 RTGEKLPAPQSSEVERILLEHLAA 268


>gi|306836817|ref|ZP_07469775.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49726]
 gi|304567278|gb|EFM42885.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49726]
          Length = 381

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/293 (24%), Positives = 123/293 (41%), Gaps = 25/293 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            AR  T + L   EM+ A A++  ++K  ++  F+  E P +LQI   D     +AAKI+
Sbjct: 36  LARTGTVSGLYVCEMVTARALVERNEKTMHMTTFAPDEDPRSLQIYTVDPEYTYKAAKII 95

Query: 70  EDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKCRI 125
            D    + I++N GCP  +V     G+ L     + G+ ++A  KA    +IPVTVK R+
Sbjct: 96  VDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAAVKATEGTNIPVTVKMRV 155

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD+       +  +    SG   + +H R A          R   +  +D +  +K+ 
Sbjct: 156 GIDDE--HHTHLDAGRIAVDSGAAAVTLHGRTAA--------QRYSGDARWDEIARLKEH 205

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             D  + +  NG +     A +++ +   DGV +GR       +   +          + 
Sbjct: 206 LADTGVPVLGNGDIFRADDARRMMEATGCDGVQVGRGCLGRPWLFAELSAALRGESIPAE 265

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           P    V +   R       +  A+H       + I +H+     GFP   + R
Sbjct: 266 PTLGEVTQVIHRH-----AELLAQHEGEDHASRDIRKHIGWYLRGFPVGGQVR 313


>gi|325273604|ref|ZP_08139822.1| tRNA-dihydrouridine synthase B [Pseudomonas sp. TJI-51]
 gi|324101258|gb|EGB98886.1| tRNA-dihydrouridine synthase B [Pseudomonas sp. TJI-51]
          Length = 337

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 116/237 (48%), Gaps = 16/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMNLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAARANVEAGAQIIDINMGCPAKKVCNKAAGSALLKDEALVHEILHAVVGAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+     L N+ K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGW-DRANKNGL-NVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           +  IK+    + +  NG +    +A  +L +  VDG++IGRAA     +   ++ Y 
Sbjct: 189 IAAIKQA-VSIPVFANGDITSPEKARAVLDATGVDGLLIGRAAQGRPWIFREIEHYL 244


>gi|298505124|gb|ADI83847.1| TIM barrel oxidoreductase NifR3 [Geobacter sulfurreducens KN400]
          Length = 325

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 134/300 (44%), Gaps = 27/300 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  AR      L +TEM+  + ++R  KK+  +L     ++PL +Q+ G D
Sbjct: 21  MAGITNLPFRLLARE-QGAGLCFTEMVSVNGLVREGKKSFELLRSVPGDRPLGIQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  V+ +G + I++N+GCP  +V     G+ LM  PD V   + A+ +A  +P
Sbjct: 80  PDVMGRVAATVDGYG-DLIDINMGCPVKKVVGTGAGSALMREPDKVRAIVRAVRRATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDY 176
           +TVK R G   +        + +  ++ G N + +H  +R  + +G +          D+
Sbjct: 139 LTVKIRSGWSCE--DANFIQIARIAEEEGCNAVTLHPRSRAQMFEGTA----------DW 186

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E+K+      IG +G L   +    +L     DGVMI R A  N  +     +  +
Sbjct: 187 TKLAELKRAVAIPVIG-SGDLFSAADVAAMLDRTGCDGVMIARGALGNPWIFRQALDLMA 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                ++    R+     R+  A  T+ A   + +    +++ +H+    HG P + + R
Sbjct: 246 GREPAAASPAERL--AVARRHLALFTEMAGERVAA----REMRKHLGWYSHGLPGAAQFR 299


>gi|194430249|ref|ZP_03062746.1| tRNA-dihydrouridine synthase B [Escherichia coli B171]
 gi|194411720|gb|EDX28045.1| tRNA-dihydrouridine synthase B [Escherichia coli B171]
          Length = 321

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|300817485|ref|ZP_07097701.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 107-1]
 gi|300529783|gb|EFK50845.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 107-1]
          Length = 321

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|227502147|ref|ZP_03932196.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49725]
 gi|227077131|gb|EEI15094.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49725]
          Length = 381

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/293 (24%), Positives = 123/293 (41%), Gaps = 25/293 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            AR  T + L   EM+ A A++  ++K  ++  F+  E P +LQI   D     +AAKI+
Sbjct: 36  LARTGTVSGLYVCEMVTARALVERNEKTMHMTTFAPNEDPRSLQIYTVDPEYTYKAAKII 95

Query: 70  EDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKCRI 125
            D    + I++N GCP  +V     G+ L     + G+ ++A  KA    +IPVTVK R+
Sbjct: 96  VDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAAVKATEGTNIPVTVKMRV 155

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD+       +  +    SG   + +H R A          R   +  +D +  +K+ 
Sbjct: 156 GIDDE--HHTHLDAGRIAVDSGAAAVTLHGRTAA--------QRYSGDARWDEIARLKEH 205

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             D  + +  NG +     A +++ +   DGV +GR       +   +          + 
Sbjct: 206 LADTGVPVLGNGDIFRADDARRMMEATGCDGVQVGRGCLGRPWLFAELGAALRGESIPAE 265

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           P    V +   R       +  A+H       + I +H+     GFP   + R
Sbjct: 266 PTLGEVTQVILRH-----AELLAQHEGEDHASRDIRKHIGWYLRGFPVGGQVR 313


>gi|54298852|ref|YP_125221.1| hypothetical protein lpp2919 [Legionella pneumophila str. Paris]
 gi|53752637|emb|CAH14072.1| hypothetical protein lpp2919 [Legionella pneumophila str. Paris]
          Length = 328

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 112/239 (46%), Gaps = 24/239 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G +   L EAA
Sbjct: 33  FRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKLLAYQISGNEPHVLAEAA 92

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
             ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+T+K RI 
Sbjct: 93  AKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISRVRAAISIPLTIKIRIQ 152

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            +++   +A     K I+ +G + + +H R+       P + ++I N+         K  
Sbjct: 153 NNEKDLTLA-----KQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI---------KNA 198

Query: 187 PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA------YKNSAMLTTVDEYFSNPL 237
            ++ + +NG + ++S   K L     DG MI RA       Y++   L T D  F   L
Sbjct: 199 VNIPVIVNGDISNISSLRKALEISMCDGFMISRAGTGKPWLYRDLLNLETNDVAFDEKL 257


>gi|320583070|gb|EFW97286.1| tRNA-dihydrouridine synthase 1 [Pichia angusta DL-1]
          Length = 402

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 109/239 (45%), Gaps = 20/239 (8%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L  + +L++ +   D   R      +  S  ++PL +Q   
Sbjct: 25  MVDGSELAWRMISRKYGADLCYSPMLHSRLFATDDKYREKMFGPMDGSEVDRPLIVQFCA 84

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L++AAK VED   + ++LN+GCP     +G +G+ LM + D++   I  + + L 
Sbjct: 85  NDPDYLLQAAKHVED-RCDAVDLNLGCPQGIARKGHYGSFLMEDWDLISKLINTLHRNLK 143

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT K R+  DD   ++A     K    +G   + +H R   +KG      +K    ++
Sbjct: 144 IPVTAKIRV-YDDWEKSLA---YAKMCLDAGAQFLTVHGRTREMKG------QKTGFANW 193

Query: 177 DIVYEIKKENPDLFIGLNGG----LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +V  IK   P   + L+ G     ED+ + +K +   D VM       N  +  T  E
Sbjct: 194 KLVKYIKDNLPPETVFLSNGNILYPEDIDRCIKEV-GCDAVMSAEGNLYNPGIFWTETE 251


>gi|254787030|ref|YP_003074459.1| tRNA-dihydrouridine synthase B [Teredinibacter turnerae T7901]
 gi|237684325|gb|ACR11589.1| tRNA-dihydrouridine synthase B [Teredinibacter turnerae T7901]
          Length = 330

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/262 (24%), Positives = 120/262 (45%), Gaps = 19/262 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK---PLALQIGGA 57
           M   TD  +R   R +    L  +EM+ +D  L   +K     S  E+   P+++QI G+
Sbjct: 18  MAGVTDAPFRRICREM-GAGLATSEMVTSDVNLWQSRKTRARLSALEQELAPVSVQIAGS 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AA      G   +++N+GCP+ +V + + G+ L+ +  +V      + +A+ +
Sbjct: 77  EPQMMAQAAVAAVVQGAQIVDINMGCPAKKVCKKAAGSALLRDEALVDAITRTVVEAVDV 136

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVT+K R G D  Q  A+   N+ +  + +G+  + +H R         +  R     +Y
Sbjct: 137 PVTLKIRTGWDTSQRNAI---NIARIAENNGIQALAVHGRT--------RACRFNGTAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + ++        I  NG ++  ++A K+L       VMIGRAA  N  +   ++++  
Sbjct: 186 DTIAQVVNSVAIPVIA-NGDIDSPAKARKVLQHTGAQAVMIGRAALGNPWLFGQIEQFLE 244

Query: 235 NPLTGSSPIKTRVDKDFWRKIS 256
                  P  + V K   R ++
Sbjct: 245 QGEIRELPATSEVCKTIERHLT 266


>gi|307824225|ref|ZP_07654451.1| TIM-barrel protein, nifR3 family [Methylobacter tundripaludum SV96]
 gi|307734605|gb|EFO05456.1| TIM-barrel protein, nifR3 family [Methylobacter tundripaludum SV96]
          Length = 327

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 112/242 (46%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   +DR +R   +      L  +EM+ ++  LR  K+ +L      +    ++QI G +
Sbjct: 17  MAGISDRPFRELCKQF-GAGLAVSEMVASNPALRQHKRTLLKADHDGETGIRSVQILGTN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAK+    G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+ IP
Sbjct: 76  PQLMADAAKLNAQRGAQIIDINMGCPAKKVCSVAAGSALLRDEALVKRILDAVVNAVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D     +  RN V   +  + +G+  + IH R    K     ++  +  + 
Sbjct: 136 VTLKIRTGWD-----LHSRNAVEIARIAENAGIAALTIHGRTRACKFEGRAEHETLKKVK 190

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
             I          + +  NG ++   QA  +L S   D +MIGRAA  N  + + +  + 
Sbjct: 191 RAI---------SIPVIANGDIDSPEQARFVLESTGADAIMIGRAAQGNPWLFSQISHFI 241

Query: 234 SN 235
           ++
Sbjct: 242 NH 243


>gi|329898406|ref|ZP_08272396.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC3088]
 gi|328920835|gb|EGG28282.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC3088]
          Length = 313

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 85/182 (46%), Gaps = 16/182 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G ++   P+ LQ+ G++   L + A    D G   I+LN GCP+  V++   GA L+  P
Sbjct: 50  GVTSNNTPVYLQLLGSNPQILAKNALRAVDLGAKGIDLNFGCPAKTVNKSKGGASLLQTP 109

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D+VGD +A +   +   IPVT K R+G  D         L++ + K+    I +HAR  +
Sbjct: 110 DLVGDIVACVRDQVPSHIPVTAKVRLGFSDD---TLFETLIRRLDKAAPTEITVHARTKV 166

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                P    +I ++         K   D+ I  NG +   + AL+   +   D +M+ R
Sbjct: 167 QGYKPPAHWHRINDV---------KSLTDIPIVANGEVWSTADALQCANVSGCDRLMLAR 217

Query: 218 AA 219
            A
Sbjct: 218 GA 219


>gi|160897010|ref|YP_001562592.1| NifR3 family TIM-barrel protein [Delftia acidovorans SPH-1]
 gi|160362594|gb|ABX34207.1| TIM-barrel protein, nifR3 family [Delftia acidovorans SPH-1]
          Length = 356

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/259 (27%), Positives = 111/259 (42%), Gaps = 43/259 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+A+QI
Sbjct: 22  MAGVTDRPFRQLCKAL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 76

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G D   + EAA+   D G   I++N+GCP+ +V     G+ LM N  +   +   +   
Sbjct: 77  AGTDAEMMAEAARYNLDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAQAVVEA 136

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPK 166
           C    +PVT+K R G  D     A RN   L +  ++ G+  + +H   R+   KG +  
Sbjct: 137 CAPHGVPVTLKMRTGWCD-----AHRNAVVLARRFEEVGIQMLTVHGRTREQGYKGFA-- 189

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA----- 219
                   +YD +  +K     + +  NG +    +A  +L     D VMIGRAA     
Sbjct: 190 --------EYDTIAAVKAAV-RVPVVANGDITSPEKARDVLAYTGADAVMIGRAAQGRPW 240

Query: 220 -YKNSAMLTTVDEYFSNPL 237
            ++  A      E+ + PL
Sbjct: 241 IFREIAHFMATGEHMAPPL 259


>gi|254440340|ref|ZP_05053834.1| putative TIM-barrel protein, nifR3 family [Octadecabacter
           antarcticus 307]
 gi|198255786|gb|EDY80100.1| putative TIM-barrel protein, nifR3 family [Octadecabacter
           antarcticus 307]
          Length = 329

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 112/247 (45%), Gaps = 26/247 (10%)

Query: 5   TDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           TD  +R     F A  + +  +   EM+ A   +R  +K  LG S  +   A+Q+ G + 
Sbjct: 23  TDLPFRQLVASFGAGWVVSEMIASQEMVQAKPGVR--EKAELGLS--QASTAVQLAGREA 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+ V   G   I++N+GCP+ +V  G  G+ L+ + D     I A+  A+ IPV
Sbjct: 79  HWMAEAARHVAANGAAMIDINMGCPAKKVTSGYSGSALLRDLDHALTLIDAVVGAVDIPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
           T+K R+G DD++   A   L    + +G+  I IH R      KG          + +++
Sbjct: 139 TLKTRLGWDDRLLNAA--ELAIRAENAGIARIVIHGRTRCQFYKG----------HANWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K       I  NG + D   A   L     DGVMIGR A     +L  V    S 
Sbjct: 187 AIAQVKNAVSIPVIA-NGDIIDAVTAKTALNASGADGVMIGRGAQGRPWILRDVAAQLSG 245

Query: 236 PLTGSSP 242
            +  + P
Sbjct: 246 HVVPAPP 252


>gi|218247166|ref|YP_002372537.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 8801]
 gi|257060238|ref|YP_003138126.1| hypothetical protein Cyan8802_2418 [Cyanothece sp. PCC 8802]
 gi|218167644|gb|ACK66381.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 8801]
 gi|256590404|gb|ACV01291.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 8802]
          Length = 336

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 112/233 (48%), Gaps = 17/233 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R   R     +++YTEM+ A  I  L+   + ++  +  E P+++Q+       +
Sbjct: 32  TDLVFRRLVRRYAPQSMMYTEMVSATEIHHLKAIPR-LMEIAPDEDPISIQLFDCRPDFM 90

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  + K + IPVTVK
Sbjct: 91  AEAAEKAVAEGAKTIDINMGCPVNKITKKGGGSSLLRQPEIAQAIVKEVVKTVDIPVTVK 150

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG DDQ   + + +  K ++ +G   + IH R    +G + K         ++ + ++
Sbjct: 151 TRIGWDDQ--EITILDFAKKMEDAGAQMLTIHGRTR-AQGYNGKAR-------WEWIAKV 200

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
            KE   + +  NG +  +  A+K L     DGVM  R       ++  +D YF
Sbjct: 201 -KEIVSIPVIANGDIFSVDAAIKCLEETNADGVMCSRGTLGYPFLVGEID-YF 251


>gi|332098832|gb|EGJ03789.1| TIM-barrel protein, nifR3 family protein [Shigella boydii 3594-74]
          Length = 305

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 1   MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 60  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 120 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 164

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 165 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 223

Query: 232 YF 233
           Y 
Sbjct: 224 YL 225


>gi|39996108|ref|NP_952059.1| dihydrouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39982873|gb|AAR34332.1| dihydrouridine synthase family protein [Geobacter sulfurreducens
           PCA]
          Length = 325

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 134/300 (44%), Gaps = 27/300 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  AR      L +TEM+  + ++R  KK+  +L     ++PL +Q+ G D
Sbjct: 21  MAGITNLPFRLLARE-QGAGLCFTEMVSVNGLVREGKKSFELLRSVPGDRPLGIQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  V+ +G + I++N+GCP  +V     G+ LM  PD V   + A+ +A  +P
Sbjct: 80  PDVMGRVAATVDGYG-DLIDINMGCPVKKVVGTGAGSALMREPDKVRAIVRAVRRATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDY 176
           +TVK R G   +        + +  ++ G N + +H  +R  + +G +          D+
Sbjct: 139 LTVKIRSGWSCE--DANFIQIARIAEEEGCNAVTLHPRSRAQMFEGTA----------DW 186

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E+K+      IG +G L   +    +L     DGVMI R A  N  +     +  +
Sbjct: 187 TKLAELKQAVAIPVIG-SGDLFSAADVAAMLDRTGCDGVMIARGALGNPWIFRQALDLMA 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                ++    R+     R+  A  T+ A   + +    +++ +H+    HG P + + R
Sbjct: 246 GREPAAASPAERL--AVARRHLALFTEMAGERVAA----REMRKHLGWYSHGLPGAAQFR 299


>gi|39935657|ref|NP_947933.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris CGA009]
 gi|39649510|emb|CAE28032.1| putative nitrogen regulation protein nifR3 [Rhodopseudomonas
           palustris CGA009]
          Length = 333

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 112/243 (46%), Gaps = 25/243 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM  ++ ++ G + ++       + P  +Q+ G +   + E A+I E  G + I++
Sbjct: 36  LVVSEMTASEDLVAGRRMSVRRCDKVGQGPHVVQLAGCEARWMAEGARIAEAGGADIIDI 95

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN- 138
           N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G DD+      RN 
Sbjct: 96  NMGCPARHVTGGLSGSALMRDLDHALTLIEATIGAVRVPVTLKMRLGWDDRS-----RNA 150

Query: 139 --LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L +  + +GV  + +H   R+   KG            D+D V  + ++   + + +N
Sbjct: 151 PELARRAQDAGVQLVTVHGRTRQQFYKG----------EADWDAVRAV-RDAISIPLVVN 199

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G +   + A++ L     D VMIGR A     +   V    +       P  T + +D+ 
Sbjct: 200 GDITCHASAVEALKRSGADAVMIGRGAQGRPWLPGQVGRQLTTGKAEGEPSLT-MQRDYL 258

Query: 253 RKI 255
           R +
Sbjct: 259 RTL 261


>gi|316934214|ref|YP_004109196.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris DX-1]
 gi|315601928|gb|ADU44463.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris DX-1]
          Length = 344

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 110/243 (45%), Gaps = 25/243 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM  ++ ++ G + ++       + P  +Q+ G +   + E A+I E  G + I++
Sbjct: 47  LVVSEMTASEDLVAGRRMSVRRCDKVGQGPHVVQLAGCEARWMAEGARIAEAGGADIIDI 106

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN- 138
           N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G DD+      RN 
Sbjct: 107 NMGCPARHVTGGLSGSALMRDLDHALTLIEATIGAVRVPVTLKMRLGWDDRS-----RNA 161

Query: 139 --LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L +  + +GV  + +H   R+   KG            D+  V  + ++   + + +N
Sbjct: 162 PELARRAQDAGVQLVTVHGRTRQQFYKG----------EADWGAVRAV-RDAISIPLVVN 210

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G +     AL+ L     D VMIGR A     +   V    +    G+ P      +D+ 
Sbjct: 211 GDITCHDTALEALQRSGADAVMIGRGAQGRPWLPGQVGRQLTTGQAGAEP-PLAAQRDYL 269

Query: 253 RKI 255
           R +
Sbjct: 270 RTL 272


>gi|194765691|ref|XP_001964960.1| GF22874 [Drosophila ananassae]
 gi|190617570|gb|EDV33094.1| GF22874 [Drosophila ananassae]
          Length = 509

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 111/234 (47%), Gaps = 25/234 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R    + L YT M  A+      K  K+ L     ++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRYGAH-LCYTPMYHANLFATDPKYRKDALQTCAGDRPLVIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA   +D   + +++N+GCP A    G +G+ L    +++ + ++ + K LSIP
Sbjct: 94  AQQILDAALAAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHKKLSIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D    A  +R   + ++ +G   + +H R    K  L G++          
Sbjct: 153 VTCKIRIFEDR---AKTIR-YAQMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 198

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D+  + E+++  + P    G   GLED+ + L+    VDGVM       N A+ 
Sbjct: 199 DWSYIKEVRQHIKIPMFANGNILGLEDVHRCLEET-GVDGVMSAEGNLHNPAIF 251


>gi|163789796|ref|ZP_02184233.1| hypothetical protein CAT7_06176 [Carnobacterium sp. AT7]
 gi|159875018|gb|EDP69085.1| hypothetical protein CAT7_06176 [Carnobacterium sp. AT7]
          Length = 326

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 105/234 (44%), Gaps = 26/234 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    D ++     L F+  E+PL   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFTNTVSYCHPDGRDSVRGRLTFTEDEQPLVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+   ++  + I A  KA  
Sbjct: 79  DEPKYFRQMSIGMAEEGFKGIDINMGCPVPNVAGKGKGSGLIRRSEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNL 174
           +PV+VK R+G  +       R+ +  I +  +  + IH   RK + KG +          
Sbjct: 138 LPVSVKTRLGYTN---IEEWRDWLTHIFEQDIANLSIHLRTRKEMSKGAA---------- 184

Query: 175 DYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            ++++ E+KK      P   + +NG + D    LK++    VDGVMIGR  ++N
Sbjct: 185 HWEMISEVKKLRDEIAPQTLLTINGDIPDRETGLKLVEEYGVDGVMIGRGIFQN 238


>gi|299067934|emb|CBJ39148.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum CMR15]
          Length = 356

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 117/242 (48%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  +++G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRE-----HRNALTVARIAQEAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYETIAAVKA-SVRIPVVANGDIGTPAKARHVLEVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YF 233
           + 
Sbjct: 242 FL 243


>gi|56476040|ref|YP_157629.1| tRNA-dihydrouridine synthase [Aromatoleum aromaticum EbN1]
 gi|56312083|emb|CAI06728.1| tRNA-dihydrouridine synthase [Aromatoleum aromaticum EbN1]
          Length = 350

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 115/243 (47%), Gaps = 23/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EM+ ++++L G  K       + +  P+++QI GAD
Sbjct: 28  MAGVTDRPFRQLCKKL-GAGVAVSEMVTSNSLLYGSAKTRRRAEHAGEADPISVQIAGAD 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + +AA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+   
Sbjct: 87  PAMMADAARYNADNGAQIIDINMGCPAKKVCNVMAGSALMQDEPLVARILEAVVAAVPGT 146

Query: 118 PVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           PVT+K R G    +   P +A     +  + SG+  + IH R         + ++   N 
Sbjct: 147 PVTLKFRTGWNRDNRNAPTIA-----RIAEASGIRAVAIHGRT--------RADQYTGNA 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD + E+K       I  NG +    +A  +L     DGVMIGRAA     +   ++ Y
Sbjct: 194 EYDTIAEVKSLVKIPVIA-NGDITTPEKARYVLDYTGADGVMIGRAAQGRPWIFREIEHY 252

Query: 233 FSN 235
            + 
Sbjct: 253 LAT 255


>gi|330826412|ref|YP_004389715.1| TIM-barrel protein, nifR3 family [Alicycliphilus denitrificans
           K601]
 gi|329311784|gb|AEB86199.1| TIM-barrel protein, nifR3 family [Alicycliphilus denitrificans
           K601]
          Length = 352

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 74/309 (23%), Positives = 126/309 (40%), Gaps = 27/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKDLWASLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +   + + + A C   
Sbjct: 76  AAMMAEAAVYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVQIAEAVVAACAPR 135

Query: 116 SIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +PVT+K R G       AV    L ++ +  GV  + +H R         ++       
Sbjct: 136 GVPVTLKMRTGWCQRHKNAV---QLARAFEGVGVQMLTVHGRT--------REQGYKGQA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K +     +  NG +    +A  +L     D VMIGRAA     +   +  Y
Sbjct: 185 EYDTIAAVKAQVAVPVVA-NGDITSPEKARAVLAHTGADAVMIGRAAQGRPWIFREIGHY 243

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +     + P+   V     R +   + D+   +  + G ++   +H+       P    
Sbjct: 244 LATGEHLAPPLVAEVR----RLLLEHLQDHYGLYGQASG-VRSARKHIAWYVRDLPGGEA 298

Query: 293 CR-HILTVE 300
            R HI T+E
Sbjct: 299 FRQHINTIE 307


>gi|291239208|ref|XP_002739522.1| PREDICTED: dihydrouridine synthase 4-like [Saccoglossus
           kowalevskii]
          Length = 367

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 55/214 (25%), Positives = 102/214 (47%), Gaps = 26/214 (12%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           + +T MIV+D+ ++  K     FST   ++PL +Q    +    V A +++  F  + ++
Sbjct: 58  VTFTPMIVSDSFIKSIKARDNEFSTHKGDQPLIVQFAANNTKDFVTATELIAPFA-DGVD 116

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-----MCKALSIPVTVKCRIGVDDQIPA 133
           LN GCP        FGA L+ +P++V D +         +  S+ + ++ R  + D +  
Sbjct: 117 LNCGCPQRWAMANGFGANLIKHPELVKDMVQQTRNKIQDEKFSVSIKIRLRHNLRDTL-- 174

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
               +L +  + +GV+ I +H R          + R  P ++Y+ + +I KEN  + +  
Sbjct: 175 ----DLCQKAEHAGVSWITVHGRTT--------EQRTEP-VNYEDI-KIIKENLSIPVIA 220

Query: 194 NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAM 225
           NG ++ +    ++  L  VDGVM  R    N AM
Sbjct: 221 NGDVKSLKDVNRVHELTKVDGVMAARGMLHNPAM 254


>gi|196000454|ref|XP_002110095.1| hypothetical protein TRIADDRAFT_21776 [Trichoplax adhaerens]
 gi|190588219|gb|EDV28261.1| hypothetical protein TRIADDRAFT_21776 [Trichoplax adhaerens]
          Length = 427

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 111/236 (47%), Gaps = 27/236 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ +   +R        F T  +++PL +Q  G D
Sbjct: 18  MVDQSELAWRLLCRRY-GAQLCYTPMLHSAVFIRDATYRRENFKTCPEDRPLIVQFCGND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE    + ++LN+GCP A    G +GA L  +  ++   ++ + + L IP
Sbjct: 77  PDTLLKAAKIVEPHC-DAVDLNLGCPQAIAKRGHYGAFLQDDWKLLEKIVSHLHQNLKIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  +D    V    L   ++K+G   + +H R    K  L GL+          
Sbjct: 136 VTCKIRI-FNDLDKTVKYAQL---LEKAGCQLLTVHGRTREQKKELTGLA---------- 181

Query: 175 DYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           D++ + ++ K++  + +  NG +   ED+ +       VDG+M       N A+ +
Sbjct: 182 DWNFI-KVIKDSLSIPVFANGNIQYFEDLERCF-TATGVDGIMSAEGILTNPALFS 235


>gi|152981141|ref|YP_001351996.1| tRNA-dihydrouridine synthase [Janthinobacterium sp. Marseille]
 gi|151281218|gb|ABR89628.1| tRNA-dihydrouridine synthase [Janthinobacterium sp. Marseille]
          Length = 338

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 114/251 (45%), Gaps = 16/251 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K+        + +P A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMAASNPRLWASDKSTRRTNHDGEVEPKAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK   D G   I++N+GCP  +V     G+ L+ +  +V + + A+  ++++P
Sbjct: 76  PVLLAECAKFNVDRGAQIIDINMGCPVKKVCNSWCGSALLQHESLVAEILEAVVASVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+    AL N+ +  ++SG+  + +H R         + +    + +Y+ 
Sbjct: 136 VTLKFRTGW-DRAHKNAL-NIARIAEQSGIAMLTLHGRT--------RADGYSGDAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ Y    
Sbjct: 186 ITAVKAA-VSIPVVANGDITTPEKARYVLDVTGADAIMIGRAAQGRPWIFREIEHYLRTG 244

Query: 237 LTGSSPIKTRV 247
               +P+   V
Sbjct: 245 TYLPAPMIAEV 255


>gi|68482886|ref|XP_714669.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68483082|ref|XP_714575.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436155|gb|EAK95523.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436256|gb|EAK95622.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|238883810|gb|EEQ47448.1| tRNA-dihydrouridine synthase 1 [Candida albicans WO-1]
          Length = 467

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 75/297 (25%), Positives = 125/297 (42%), Gaps = 34/297 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-------KNILGFSTQEKPLALQ 53
           MVD ++  +R  +R      L YT M  A      +K        N+ G    ++PL +Q
Sbjct: 65  MVDQSELAWRILSRRY-GAQLCYTPMFHAKLFATQEKYRNSMWTTNLDGNKDLDRPLVVQ 123

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
               D   L++AAK++E+   + I+LN+GCP     +G +GA LM + D+V   I  +  
Sbjct: 124 FCANDPDYLLQAAKLIEN-ECDAIDLNLGCPQGIARKGKYGAFLMDDWDLVYKLIKNLHD 182

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            LSIPVT K RI  DD   ++      K +  +G   I +H R   +KG      +    
Sbjct: 183 NLSIPVTAKIRI-YDDYEKSLK---YAKMVLDAGAQFITVHGRTREMKG------QATGL 232

Query: 174 LDYDIVYEIKKENP-DLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            ++ I+  ++   P D     NG +   S  Q  +   + D VM       N  +  T+D
Sbjct: 233 ANWKILKYLRDNLPQDQVFFSNGNILYPSDIQRCQSETACDAVMSAEGNLYNPGVFWTLD 292

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +          P   ++ ++++  +  +    A+RH         +  H   L H F
Sbjct: 293 DNKDKQF----PRVDKILREYFEIVKENYDSLASRH--------AMKSHFFKLLHAF 337


>gi|326334004|ref|ZP_08200233.1| putative tRNA-dihydrouridine synthase [Nocardioidaceae bacterium
           Broad-1]
 gi|325948153|gb|EGD40264.1| putative tRNA-dihydrouridine synthase [Nocardioidaceae bacterium
           Broad-1]
          Length = 378

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/296 (23%), Positives = 130/296 (43%), Gaps = 26/296 (8%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       L   EMI +  ++ GD+  K++L F   E   ++Q+ G D   + +A +
Sbjct: 31  FRRLCAEQGAGLYVCEMITSRGLVEGDQHTKDMLVFDEAETVRSVQLYGTDPVYVGKATE 90

Query: 68  IV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKC 123
           I+  D+G   ++LN GCP  +V     G  L     ++G+ +    +A     +PVT+K 
Sbjct: 91  ILCADYGVAHVDLNFGCPVPKVTRKGGGGALPYKRGLLGEILEHAVRAAEPYDVPVTMKT 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G+DD    +   +  +  ++SG   I +H R  + +  S          D+D + E+K
Sbjct: 151 RKGIDDD--HLTYMDAGRIAQESGAAAIALHGR-TVAQAYS-------GTADWDAIAELK 200

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             + D+ +  NG + + + A++++    VDGV+IGR       +   +   F+       
Sbjct: 201 A-SVDIPVLGNGDIWEAADAIRMVEETGVDGVVIGRGCLGRPWLFRDLVAAFAGETVNVL 259

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P    V  D  R+ +  + +    H+      ++I +H+     GF      R  L
Sbjct: 260 PNLGEV-TDIMRRHAELLCE----HMGEERGCKEIRKHIAWYLKGFGAGGELRRTL 310


>gi|302024537|ref|ZP_07249748.1| tRNA-dihydrouridine synthase [Streptococcus suis 05HAS68]
 gi|330833584|ref|YP_004402409.1| TIM-barrel protein, nifR3 family [Streptococcus suis ST3]
 gi|329307807|gb|AEB82223.1| TIM-barrel protein, nifR3 family [Streptococcus suis ST3]
          Length = 334

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 112/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K +  L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKANIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++    +A+ N + + + +GV+ + +H R         ++      +D +
Sbjct: 143 PLTVKMRTGWNNT--DLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTVDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++      +    NG + ++  A + +  V  D VM+GR A  N  +   ++ Y  
Sbjct: 192 TLTKVAGSLTKIPFIANGDIRNVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLE 250


>gi|308453103|ref|XP_003089301.1| hypothetical protein CRE_11589 [Caenorhabditis remanei]
 gi|308241223|gb|EFO85175.1| hypothetical protein CRE_11589 [Caenorhabditis remanei]
          Length = 548

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 79/279 (28%), Positives = 126/279 (45%), Gaps = 29/279 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A +IL G   + ++L     EK   +Q+ G     + +AA+IV E+F  + +++N+
Sbjct: 229 EMALATSILSGAASEYSLLKRHPSEKIFGVQLAGGFADTMAKAAQIVVENFDVDFVDINM 288

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV 140
           GCP   V++   G  L   P+ + + +AA    L   P+TVK R G  + +  +     V
Sbjct: 289 GCPIDVVNQKGGGCALPSRPNKLYEVLAATKSVLGDCPMTVKIRTGQKEGV--LKAPETV 346

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNR--KIPNLDYD-IVYEIKKENPDLFIGLNGGL 197
           + +KKS     W H    I      K+ R  K+ N DY   V E  K+ P    G     
Sbjct: 347 EFMKKSP----W-HCPDLITFHPRSKEQRYTKLANWDYTHAVAEASKQVPLWVCGDVLSW 401

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           ED  + L+  P V+G+MIGR A     + T +DE  +  ++ +     R D      +  
Sbjct: 402 EDYYERLENHP-VNGIMIGRGALIKPWIFTEIDERRTWDISATE----RFD------LLK 450

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             T+Y   H  S     + TR  +  F  F    +CR+I
Sbjct: 451 KFTNYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 485


>gi|56461388|ref|YP_156669.1| tRNA-dihydrouridine synthase [Idiomarina loihiensis L2TR]
 gi|56180398|gb|AAV83120.1| Predicted tRNA-dihydrouridine synthase [Idiomarina loihiensis L2TR]
          Length = 323

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 76/301 (25%), Positives = 138/301 (45%), Gaps = 45/301 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R      T   L  +EM+ ++  + + DK +  +  S +    A+QI G++
Sbjct: 17  MAGVTDQPFRQLC-YSTGAGLTVSEMLSSNPKVWQTDKSRQRMDHSGELGIRAVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA++    G   I++N+GCP+ +V++   G+ LM +P +V + + A+  A+ +P
Sbjct: 76  PALMAEAARVNVSMGAQIIDINMGCPAKKVNKKMAGSALMQHPGLVEEILTAVVAAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D +      RN   + +  ++ G+  + IH R    + KG++         
Sbjct: 136 VTLKTRTGWDPE-----HRNGIDIAQLAERCGIQSLAIHGRTRACMYKGIA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  IKK    + +  NG +    QA ++L     D +MIGR A  N  +   +  
Sbjct: 182 -EYDTIKAIKKA-VSIPVVANGDIRTPLQAQQVLEYTGADAIMIGRGAQGNPWLFREIAH 239

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +       S P               S+T+ A   +H  GKL +      G + G   +R
Sbjct: 240 FLETGQELSPP---------------SLTEVAETVIHHVGKLHEF----YGSYQGVRIAR 280

Query: 292 R 292
           +
Sbjct: 281 K 281


>gi|260774378|ref|ZP_05883292.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
 gi|260610505|gb|EEX35710.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
          Length = 265

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/193 (26%), Positives = 93/193 (48%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D  ++ EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++   + A
Sbjct: 11  SVQIAGSDPQQMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEHILKA 70

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKD 167
           +  A+ +PVT+K R G D D    V +  L ++    G+    +H   R  + KG     
Sbjct: 71  VVDAVKVPVTLKTRTGWDTDNKNCVYIAQLAEN---CGIQAFALHGRTRTCMYKG----- 122

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
                  +YD +  +K+      I  NG ++   +A ++L     D +MIGR A     +
Sbjct: 123 -----EAEYDSIKAVKQAISIPVIA-NGDIDSPQKAKQVLDYTGADALMIGRPAQGRPWI 176

Query: 226 LTTVDEYFSNPLT 238
              +  Y  +  T
Sbjct: 177 FQEIQHYLESGTT 189


>gi|15807427|ref|NP_296160.1| nifR3 protein [Deinococcus radiodurans R1]
 gi|6460259|gb|AAF11984.1|AE002074_2 nifR3 protein [Deinococcus radiodurans R1]
          Length = 406

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 104/236 (44%), Gaps = 23/236 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNILGFSTQ---EKPLALQIG 55
           M  ++D   R   +L      L+T  EMI A  ++ G ++  L        E+  A+Q+ 
Sbjct: 99  MAGYSDAPMR---QLAAEQGALWTVSEMISARGLVLGSEQESLSLGRPYPGEQGRAVQLF 155

Query: 56  GADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           GAD   L +A    E  F    I+LN+GCP  +V  G  GACL+  P++  + + AM +A
Sbjct: 156 GADPDVLADAVGKAEAWFAPAAIDLNLGCPVPKVR-GKGGACLLQTPEVAYELVRAMRQA 214

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             + V+ K R+G D+         + + ++ +G   + +H R +          R   N 
Sbjct: 215 TGLDVSAKIRLGWDENRSV----EIAQGLEAAGAAVVTVHGRTSA--------QRYTGNA 262

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTV 229
           D+D +  + +      IG    L  +    ++  S V  VMIGR A  N  M   +
Sbjct: 263 DWDAIGRVAQAVRIPVIGSGDVLSPVQARERMQQSGVAAVMIGRGAVGNPWMFRAI 318


>gi|260581942|ref|ZP_05849738.1| tRNA-dihydrouridine synthase [Haemophilus influenzae NT127]
 gi|260095135|gb|EEW79027.1| tRNA-dihydrouridine synthase [Haemophilus influenzae NT127]
          Length = 353

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 115/251 (45%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                     K+   + +  NG ++   +A  +L     D +MIGRA   N  +   V+ 
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRATLGNPWLFQAVEN 266

Query: 232 YFSNPLTGSSP 242
              +      P
Sbjct: 267 LIEHNSISQMP 277


>gi|22298534|ref|NP_681781.1| nitrogen regulation protein NifR3-like protein [Thermosynechococcus
           elongatus BP-1]
 gi|22294714|dbj|BAC08543.1| tll0991 [Thermosynechococcus elongatus BP-1]
          Length = 347

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/307 (23%), Positives = 130/307 (42%), Gaps = 28/307 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R     +++YTEM+ A  +        I+     E P+++Q+       L 
Sbjct: 38  TDLVFRRLVRRYAPESMMYTEMVSASGLHYLKTLPRIMEVDANEHPISIQLFDCRPDFLA 97

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAA      G + +++N+GCP  ++ +   G+ L+ +       +  + KA+ +PVTVK 
Sbjct: 98  EAAIKAVAEGADTVDINMGCPVNKITKNGGGSSLLRDVQTAVAIVRTVSKAVPVPVTVKT 157

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  D+   + + +  K+++ +G   I +H R        P     I  +         
Sbjct: 158 RIGWSDE--EINILDFAKAMEDAGAAMITVHGRTRAQGFNGPARWEWIARV--------- 206

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGS- 240
           KE   + +  NG +  +  A++ L     DGVM  R       ++  +D +     TG  
Sbjct: 207 KERVSIPVIANGDIFSVEAAVRCLEQTGADGVMCSRGTMGYPFLVGEIDHFLK---TGEL 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCR----H 295
            P  T V+     ++  +     A   + G + ++Q  +H+     GF ++   R     
Sbjct: 264 RPAPTVVE-----RLQCARDHLIALWEYKGERGIRQARKHLTWYAKGFADAAELRSELCR 318

Query: 296 ILTVEAG 302
           I T+EAG
Sbjct: 319 IETLEAG 325


>gi|319897509|ref|YP_004135706.1| tRNA-dihydrouridine synthase b [Haemophilus influenzae F3031]
 gi|317433015|emb|CBY81386.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae F3031]
          Length = 326

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 113/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAINVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++  +  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCSIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|313764539|gb|EFS35903.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL013PA1]
 gi|313816081|gb|EFS53795.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL059PA1]
 gi|314915535|gb|EFS79366.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA4]
 gi|314918342|gb|EFS82173.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL050PA1]
 gi|314919997|gb|EFS83828.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL050PA3]
 gi|314955880|gb|EFT00280.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL027PA1]
 gi|314958193|gb|EFT02296.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL002PA1]
 gi|315098451|gb|EFT70427.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL059PA2]
 gi|315101191|gb|EFT73167.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL046PA1]
 gi|327450866|gb|EGE97520.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL087PA3]
 gi|327453786|gb|EGF00441.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL083PA2]
 gi|328754285|gb|EGF67901.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL087PA1]
 gi|328754462|gb|EGF68078.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL025PA2]
          Length = 355

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 116/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 19  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 79  VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 136

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D + E+ K      IG 
Sbjct: 137 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG- 187

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A  ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 188 NGDIWEASDATAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCAMI 247

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 248 -RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 287


>gi|300721814|ref|YP_003711092.1| tRNA -dihydrouridine synthase B [Xenorhabdus nematophila ATCC
           19061]
 gi|297628309|emb|CBJ88870.1| tRNA-dihydrouridine synthase B [Xenorhabdus nematophila ATCC 19061]
          Length = 296

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 105/219 (47%), Gaps = 25/219 (11%)

Query: 24  TEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ ++  +    K+ L     ++P   ++QI G+D  ++  AAKI  D G   I++N+
Sbjct: 8   SEMLSSNPQVWKTDKSRLRMVHSDEPGVRSVQIAGSDPDEMAAAAKINVDNGAQIIDINM 67

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV- 140
           GCP+ +V+    G+ L+  P++V   ++A+  A+ +PVT+K R G   +      RN V 
Sbjct: 68  GCPAKKVNRKLAGSALLRYPELVEKILSAVVNAVDVPVTLKIRTGWSPE-----ERNCVE 122

Query: 141 --KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             +  ++ G+  + IH R    +  G            +YD +  + K+   + I  NG 
Sbjct: 123 IAQLAERCGIQALTIHGRTRACLFNG----------EAEYDNIRTV-KQTVAIPIIANGD 171

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 172 ITDPLKARAVLEYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|23501997|ref|NP_698124.1| nitrogen regulation protein Nifr3 [Brucella suis 1330]
 gi|23347948|gb|AAN30039.1| nitrogen regulation protein Nifr3 [Brucella suis 1330]
          Length = 333

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/263 (23%), Positives = 121/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GC + +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 254 ANGILDYIIRHYEDMLDHYGSKI 276


>gi|323498782|ref|ZP_08103768.1| NifR3/Smm1 family protein [Vibrio sinaloensis DSM 21326]
 gi|323316144|gb|EGA69169.1| NifR3/Smm1 family protein [Vibrio sinaloensis DSM 21326]
          Length = 320

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 113/242 (46%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L    K++  +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPKLWNTSKSMQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P+I+ D + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQFPEIIEDILKAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L +     G+  + +H R    + KG +          +
Sbjct: 136 VTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKGEA----------E 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 183 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIQHFL 241

Query: 234 SN 235
            N
Sbjct: 242 EN 243


>gi|260566345|ref|ZP_05836815.1| nitrogen regulation protein NifR3 [Brucella suis bv. 4 str. 40]
 gi|260155863|gb|EEW90943.1| nitrogen regulation protein NifR3 [Brucella suis bv. 4 str. 40]
          Length = 332

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/263 (23%), Positives = 121/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GC + +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 253 ANGILDYIIRHYEDMLDHYGSKI 275


>gi|296327905|ref|ZP_06870441.1| NifR3 family protein [Fusobacterium nucleatum subsp. nucleatum ATCC
           23726]
 gi|296155039|gb|EFG95820.1| NifR3 family protein [Fusobacterium nucleatum subsp. nucleatum ATCC
           23726]
          Length = 307

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 111/254 (43%), Gaps = 43/254 (16%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           L++TEM+  +A+   + K I          A+QI G DI K+  + K +E+ G   INLN
Sbjct: 28  LIFTEMVSVNALSVLNDKTISKILKLRAGNAVQIFGEDIEKIKASVKYIENLGVKHINLN 87

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP  ++    +GA L+  P+ +   ++ +   L+    ++VK RIG  +    + +  
Sbjct: 88  CGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKLSVKIRIGYKEPENYIQIGK 147

Query: 139 LVKSIKKSGVNGIWIHAR--------KAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDL 189
           + + +   G + I +H R        KA  K +   KDN  IP +           N D+
Sbjct: 148 IAEEL---GCDHITVHGRTREQLYSGKADWKYIKEVKDNISIPVIG----------NGDI 194

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS-----NPLTGSSPI- 243
           F G     ED  + +    +VDGVM+ R  + N  ++  + E         P T +  I 
Sbjct: 195 FTG-----EDALEKI-FYSNVDGVMLARGIFGNPWLIRDIREILEYGEIKTPTTKADKIN 248

Query: 244 -------KTRVDKD 250
                  + RVD D
Sbjct: 249 MAIEHLKRIRVDND 262


>gi|85711853|ref|ZP_01042908.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
 gi|85694250|gb|EAQ32193.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
          Length = 320

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 95/188 (50%), Gaps = 20/188 (10%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G++   + +AAKI    G   I++N+GCP+ +V++   G+ LM +P +V   + A
Sbjct: 68  SVQIAGSEPELMAQAAKINVSQGAQIIDINMGCPAKKVNKKLAGSALMQHPALVESILTA 127

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           + +A+ +PVT+K R G + D    + +  +    ++ G+  + +H R    + KG +   
Sbjct: 128 VVEAVDVPVTLKTRTGWNLDHKNGIEIAQIA---ERCGIQALAVHGRTRACMYKGEA--- 181

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
                  +Y+ +  I KE   + +  NG +    QA  +L     D +MIGR A  N  +
Sbjct: 182 -------EYNTIRAI-KETISIPVIANGDITSPEQAAHVLRYTGADAIMIGRGAQGNPWI 233

Query: 226 LTTVDEYF 233
              + +YF
Sbjct: 234 FKQI-QYF 240


>gi|291299569|ref|YP_003510847.1| TIM-barrel protein, nifR3 family [Stackebrandtia nassauensis DSM
           44728]
 gi|290568789|gb|ADD41754.1| TIM-barrel protein, nifR3 family [Stackebrandtia nassauensis DSM
           44728]
          Length = 394

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/216 (27%), Positives = 110/216 (50%), Gaps = 21/216 (9%)

Query: 12  FARLLTNN-ALLYT-EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL     A +YT EM++  A+L  + K   ++ F   E+P +LQ+ G D   + +A +
Sbjct: 29  FRRLCAEQGAGIYTCEMVMTRALLERNPKTTRMIAFGPGERPRSLQLYGVDPVTVRKAVE 88

Query: 68  IV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCR 124
           ++  ED   + I++N GC   +V     G+ +    ++ G  + +A+  A  IPVTVK R
Sbjct: 89  MIVDEDLA-DHIDMNFGCSVPKVTRKGGGSAIPYKRNLFGQIVRSAVEAAGDIPVTVKMR 147

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G+DD++  +   +  +  + +G   + +HAR A          R     D+D + E+K+
Sbjct: 148 KGIDDEL--LTFVDAGRVAQDAGAAWVALHARTAA--------QRYSGTADWDAITELKR 197

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
              D+ +  NG + + + AL+++     DGV++GR 
Sbjct: 198 AL-DIPVLGNGDIWEATDALRMVEETGCDGVVVGRG 232


>gi|50547431|ref|XP_501185.1| YALI0B21516p [Yarrowia lipolytica]
 gi|49647051|emb|CAG83438.1| YALI0B21516p [Yarrowia lipolytica]
          Length = 423

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 111/236 (47%), Gaps = 23/236 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------ILGFSTQEKPLALQI 54
           MVD ++  +R  +R    + L YT M  A      ++        + G  T ++PL +Q 
Sbjct: 35  MVDQSELAWRILSRRHGAD-LCYTPMFHAKLFGTSERYREEMFGPMDGDQTTDRPLVVQF 93

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D  +L+ AAK+VED   + ++LN+GCP     +G +G+ LM + D++   I  +   
Sbjct: 94  CANDPDELLAAAKLVED-RCDAVDLNLGCPQGIARKGHYGSFLMEDWDLIHKLINKLHLE 152

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K R+  DD+   +      K I  +G   + IH R   +KG      ++    
Sbjct: 153 LKVPVTAKMRV-FDDRDKTL---EYAKMIINAGAQFLTIHGRTREMKG------QQTGLA 202

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D++I+  +++  P D  +  NG +   ED+ + ++   + D VM       N A+ 
Sbjct: 203 DWEIIKYVRENLPKDTVVFANGNVLYSEDIEKCMEET-TTDAVMSAEGNLYNPAIF 257


>gi|283836191|ref|ZP_06355932.1| tRNA-dihydrouridine synthase B [Citrobacter youngae ATCC 29220]
 gi|291067542|gb|EFE05651.1| tRNA-dihydrouridine synthase B [Citrobacter youngae ATCC 29220]
          Length = 321

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGVRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVKSGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPIIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|261755085|ref|ZP_05998794.1| nifR3 family TIM-barrel protein [Brucella suis bv. 3 str. 686]
 gi|261744838|gb|EEY32764.1| nifR3 family TIM-barrel protein [Brucella suis bv. 3 str. 686]
          Length = 332

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/263 (23%), Positives = 121/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GC + +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 103 NMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 160

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 161 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 209

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 210 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 252

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 253 ANGILDYIIRHYEDMLDHYGSKI 275


>gi|284008660|emb|CBA75295.1| tRNA-dihydrouridine synthase B [Arsenophonus nasoniae]
          Length = 458

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 113/243 (46%), Gaps = 26/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + + DK  +    + E  + ++QI G+D
Sbjct: 46  MAGITDRPFRSLCYSM-GAGMTVSEMLSSNPQVWKTDKSRLRMIHSDELGIRSVQIAGSD 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+  P+++   + A+  A+ +P
Sbjct: 105 PDEMATAARINVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELIEKILLAVVNAVDVP 164

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +K  +   + G+  + IH R    +  G +         
Sbjct: 165 VTLKVRTGWSPE-----ERNCIKIAQLAERCGIQAVTIHGRTRACLFNGAA--------- 210

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +    K+N  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 211 -EYDSI-RAAKQNVTIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 268

Query: 232 YFS 234
           Y  
Sbjct: 269 YLE 271


>gi|301166477|emb|CBW26053.1| putative dihydrouridine synthase (tRNA modification protein)
           [Bacteriovorax marinus SJ]
          Length = 322

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 94/196 (47%), Gaps = 19/196 (9%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           F+    P   QI   ++ + + AAK  +D G  ++NLN+GCP   V   + G+ L+L+P 
Sbjct: 58  FTKNLIPTTAQILTKEVDQFIHAAKHFKDLGVQKVNLNMGCPYPMVANRTKGSGLLLHPG 117

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAIL 160
            V   +  + +   + ++VK R+G + +     ++ ++  I    +    IHAR  K + 
Sbjct: 118 RVEKLLTEIKERCPLELSVKIRLGRESK---DEIKEIIPIINALDIKDFTIHARLGKQLY 174

Query: 161 KGLSPKDNRK--IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
           KG+   D  +  +P L Y   Y    + P  F       E++S   K  P +   MIGRA
Sbjct: 175 KGVVDLDGFEECLPLLKYTPCYNGDIKTPSDF-------ENIS---KRFPQIKRWMIGRA 224

Query: 219 AYKNSAMLTTV--DEY 232
           A  N A+L+ +  +EY
Sbjct: 225 ALSNPALLSQIRGEEY 240


>gi|294637763|ref|ZP_06716038.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda ATCC 23685]
 gi|291089111|gb|EFE21672.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda ATCC 23685]
          Length = 334

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 115/242 (47%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  + A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHMDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAKI  DFG   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+++P
Sbjct: 76  PDEMAAAAKINADFGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVEQILRAVVGAVAVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      A RN V   +  ++ G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGWDP-----AHRNCVEIAQLAERCGIQALTIHGRTRACLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRTV-KQHVSIPIIANGDITDPHKAKAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|150866685|ref|XP_001386359.2| dihydrouridine synthase [Scheffersomyces stipitis CBS 6054]
 gi|149387941|gb|ABN68330.2| dihydrouridine synthase [Scheffersomyces stipitis CBS 6054]
          Length = 369

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D      F+T +K   + +Q+G  +
Sbjct: 60  MVRYSKLPFRELVRNY-NTDIVYTPMILAREFVRNDIARSSDFTTNDKDRCVIVQVGSNN 118

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L++  +++  +  + I LN GCP   +V EG  GA LM  PD+V   + A+ +    
Sbjct: 119 VEDLLKFVEMIHPY-VDGIGLNCGCPIKEQVREG-IGAALMSEPDLVASMVKAVKEKYGN 176

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++ +I +   +        VK ++ SGV+ I +H R         K+ R     ++D
Sbjct: 177 TVCIETKIRIHPNLDETIA--FVKKVEASGVDFITVHGRT--------KNTRSSQPANWD 226

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            + ++ KE   + +  NG    +  A  I     VDGVM  R    N A+ 
Sbjct: 227 AI-KLIKETVSVPVVANGDCFSLEDAYSIAEHTGVDGVMSARGILSNPALF 276


>gi|269958877|ref|YP_003328666.1| dihydrouridine synthase [Anaplasma centrale str. Israel]
 gi|269848708|gb|ACZ49352.1| dihydrouridine synthase [Anaplasma centrale str. Israel]
          Length = 304

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 105/228 (46%), Gaps = 35/228 (15%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R     L    LL +EMI + A++   +++ L  S      ++Q+ G     + E
Sbjct: 5   TDMPFRSIVGEL-GAGLLVSEMIASRAMIIKTRQS-LQKSDVGANTSVQLAGCVPEIMAE 62

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAKI +D G   I++N GCP  ++ +G  G+ LM +       + ++  A++IPVTVK R
Sbjct: 63  AAKINQDMGAMSIDINFGCPVKKIVDGHAGSALMKDEAKAAKIMESVVNAVTIPVTVKMR 122

Query: 125 IG---VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSP-------KDNRKIP 172
           +G    D   P      L K  + +G+  + +H   R  +  G +        KD  KIP
Sbjct: 123 MGWSPTDLNAP-----RLAKIAEDAGIRMVTVHGRTRSQMFSGTADWKFIKCVKDCVKIP 177

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
            +           N D+        +D++ AL  L   DGVMIGR AY
Sbjct: 178 VI----------ANGDIRT-----FQDITDALN-LSGADGVMIGRGAY 209


>gi|126642530|ref|YP_001085514.1| NifR3 family protein [Acinetobacter baumannii ATCC 17978]
          Length = 301

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 74/302 (24%), Positives = 140/302 (46%), Gaps = 29/302 (9%)

Query: 26  MIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ AD  LR  KK++    F  +  P++ QI G+D  +L EAA+     G   +++N+GC
Sbjct: 1   MMTADKTLRMTKKSLYRANFDGELAPISAQIAGSDPEQLAEAARYQVANGAQIVDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV---DDQIPAVALRNLV 140
           P+ +V     G+ L+ + D+V   + A+  A+ +PVT+K R+G     + I  VA     
Sbjct: 61  PAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVPVTLKTRLGFLNGQENILRVA----- 115

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           K  +++G+  + +H R         +++  +    Y+++  + KE   + +  NG ++  
Sbjct: 116 KRAEEAGIAALALHGR--------TREDMYLNTARYELIKHV-KELIHIPVIANGDIDSP 166

Query: 201 SQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            +A  +L     D +MIGRAA     +   +  Y       ++P    V +     +S  
Sbjct: 167 EKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTGEHLAAPNIEEVKEVLLGHLSEL 226

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH-ILTVEAGASTATHHIIETAFNL 317
              Y     +SG ++ +  +H+     G  +S   R  +  VE  A  A   ++E+ FN 
Sbjct: 227 YQFYGE---YSGCRIAR--KHIAWYTKGLRSSNEFRQNMYKVETTAEQAL--VVESYFNQ 279

Query: 318 MI 319
           ++
Sbjct: 280 LL 281


>gi|161619071|ref|YP_001592958.1| NifR3 family TIM-barrel protein [Brucella canis ATCC 23365]
 gi|161335882|gb|ABX62187.1| TIM-barrel protein, nifR3 family [Brucella canis ATCC 23365]
          Length = 333

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/263 (23%), Positives = 121/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GC + +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 254 ANGILDYIIRHYEDMLDHYGSKI 276


>gi|89069985|ref|ZP_01157317.1| tRNA-dihydrouridine synthase, putative [Oceanicola granulosus
           HTCC2516]
 gi|89044433|gb|EAR50564.1| tRNA-dihydrouridine synthase, putative [Oceanicola granulosus
           HTCC2516]
          Length = 331

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 42/119 (35%), Positives = 65/119 (54%), Gaps = 4/119 (3%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           RF A  + +  +   EM+ A    R  +K  LGF   +   A+QI G +   + EAA+I 
Sbjct: 39  RFGAGWVVSEMVASQEMVQARPGTR--EKAELGFGEHDT--AVQIAGREAHWMAEAARIA 94

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           E  G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+++PVT+K R+G D
Sbjct: 95  EANGARLIDINMGCPAKKVTNGWSGSALLRTPDHALRLIEAVVGAVTVPVTLKTRLGWD 153


>gi|253998095|ref|YP_003050158.1| TIM-barrel protein, nifR3 family [Methylovorus sp. SIP3-4]
 gi|253984774|gb|ACT49631.1| TIM-barrel protein, nifR3 family [Methylovorus sp. SIP3-4]
          Length = 350

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 112/225 (49%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L  +EM+ ++++L G  K +       + +P+++QI GAD
Sbjct: 24  MAGVTDRPFRMLCKKL-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVEPISVQIAGAD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 83  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVSQILKAVVAAVDVP 142

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           VT+K R G D +   AVA+  + + I   GV  + +H R +A L            + +Y
Sbjct: 143 VTLKIRTGWDKNNRNAVAVARMAEDI---GVQALAMHGRTRACLYN---------GDAEY 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D +  +K+      I  NG +    +A  +L     D VMIGRAA
Sbjct: 191 DTIAAVKQAIKIPLIA-NGDITTPEKAKFVLEYTQADAVMIGRAA 234


>gi|218662153|ref|ZP_03518083.1| tRNA-dihydrouridine synthase protein [Rhizobium etli IE4771]
          Length = 241

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 49/154 (31%), Positives = 81/154 (52%), Gaps = 13/154 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI  D G + I++N+GCP+ +V  G  G+ LM +PD+    I A  KA+ IPVT+K R+
Sbjct: 1   AKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDLALGLIEATVKAVDIPVTLKMRL 60

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D+   ++   ++ +  + +G+  + IH R      +   + R     D+D ++ ++  
Sbjct: 61  GWDEN--SINAPDIARRAEAAGIQLVTIHGRTR----MQFYEGRA----DWDAIHAVRDV 110

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
                I  NG +E  + A +IL     D VMIGR
Sbjct: 111 ISIPLIA-NGDVETAADAQEILRRSGADAVMIGR 143


>gi|166153985|ref|YP_001654103.1| putative oxidoreductase [Chlamydia trachomatis 434/Bu]
 gi|166154860|ref|YP_001653115.1| putative oxidoreductase [Chlamydia trachomatis L2b/UCH-1/proctitis]
 gi|301335182|ref|ZP_07223426.1| putative oxidoreductase [Chlamydia trachomatis L2tet1]
 gi|165929973|emb|CAP03456.1| putative oxidoreductase [Chlamydia trachomatis 434/Bu]
 gi|165930848|emb|CAP06410.1| putative oxidoreductase [Chlamydia trachomatis L2b/UCH-1/proctitis]
          Length = 334

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 72/298 (24%), Positives = 136/298 (45%), Gaps = 21/298 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL++ EM+  + +    ++ +  L F+   +P+  Q+ G+      E+AKI+E  G++ I
Sbjct: 39  ALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSRPDLAGESAKILEGLGFDLI 98

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP+ R+ +   G+ ++  P+++G  +  M + +S+PVTVK R G D     + + 
Sbjct: 99  DLNCGCPTDRITKDGSGSGMLKTPELIGKVVEKMVEVVSVPVTVKIRSGWD--FDHINVE 156

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
             V+ IK+SG + +++H R        P       NL++ I    +    D  +  NG +
Sbjct: 157 ETVRIIKESGASAVFVHGRTRSQGYQGPS------NLEF-ISRAKQAAGDDFPVFGNGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                A  +L +   DGV++ R       +   +++Y +     S    TR      ++ 
Sbjct: 210 FSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTGTYSSPSFSTR------KQA 263

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRHILTVEAGASTATHHIIE 312
                 +   +  S  KL   TR + G +    P  R  R  L  +A +S   + +I+
Sbjct: 264 FVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRANL-AKASSSQEVYQLID 320


>gi|323488887|ref|ZP_08094126.1| probable tRNA-dihydrouridine synthase [Planococcus donghaensis
           MPA1U2]
 gi|323397450|gb|EGA90257.1| probable tRNA-dihydrouridine synthase [Planococcus donghaensis
           MPA1U2]
          Length = 331

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 97/218 (44%), Gaps = 25/218 (11%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L F+  E+P+   I G       E +  + 
Sbjct: 40  FFTEFTNTESYCHPEGIFS---VRGR----LTFTEDEQPMVAHIWGNKPEHFREMSIGMA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
             G+  +++N+GCP   V     G+ L+  PD   + I A  KA  +PV+VK R+G  D 
Sbjct: 93  KQGFKGVDINMGCPVPNVAAKGKGSGLIRYPDNAAEIIQA-AKAGGLPVSVKTRLGYTD- 150

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---- 186
                 +  +  + +  +  + IH R       + K+   +P   ++++ EIKK      
Sbjct: 151 --VEEWKGWLTHVFEQDIANLSIHLR-------TKKEMSAVP-AHWELIPEIKKLRDKIA 200

Query: 187 PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           PD  I +NG + D    L++     +DGVMIGR  + N
Sbjct: 201 PDTLITINGDIPDRQVGLELAEKYGIDGVMIGRGIFHN 238


>gi|325107227|ref|YP_004268295.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
 gi|324967495|gb|ADY58273.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
          Length = 376

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 80/159 (50%), Gaps = 5/159 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           +  +T+  +R   R      L   +++ A A++ G  K++    T+  + P A+QI G+D
Sbjct: 45  LAKYTNLPFRLVVRACGGLGLGTCDLVNARALMAGSSKSLALIRTEPEDTPFAVQIFGSD 104

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + + +AA+ +E  G  + I++N+GCP   V +   GA +M   D     +  + +A  +
Sbjct: 105 PAYMRDAAQYLEGLGTVDAIDINMGCPVDHVTKNGAGAGMMCERDKTCQLVQTVVEATRL 164

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           PVTVK R+G DD    +      +  ++ G+  + IH R
Sbjct: 165 PVTVKMRLGWDDT--QLTAPRFAREFEQIGIKAVAIHGR 201


>gi|262038887|ref|ZP_06012232.1| nitrogen regulation protein nifr3 [Leptotrichia goodfellowii F0264]
 gi|261747090|gb|EEY34584.1| nitrogen regulation protein nifr3 [Leptotrichia goodfellowii F0264]
          Length = 311

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 116/241 (48%), Gaps = 26/241 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK---KNILGFSTQEKPLALQIGGA 57
           M  +TD  YR   +   N  LL+TEM+ A  +   D+   K +L    +E    +Q+ G+
Sbjct: 8   MAGYTDYSYRKILKKF-NPDLLFTEMVSAHLLNENDEATEKELLKCDDKENE-GVQVFGS 65

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
           D ++L++A   +E+ G+  +NLN+GCP  ++ +   G+ L+   D V   ++ +   LS 
Sbjct: 66  DKNELIKAFLKLENKGFKNLNLNMGCPQTKIIKNGAGSALLPQTDFVDSLLSELKSKLSD 125

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPN 173
              +++K RIG  D        +L     K  ++ I IH   R+ +  G +         
Sbjct: 126 KTKLSIKIRIGYRDFSSPELYIDLA---NKYNLDFICIHGRTREQLYNGKA--------- 173

Query: 174 LDYDIVYEIKKENPDL-FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
            D+DIV E+      + FIG NG L +    + ++   ++DG+M+ R    N  +++ + 
Sbjct: 174 -DWDIVSELSNRPRKIDFIG-NGDLFEAKDIVSLIKKSNLDGIMLSRGIIGNPWLISQIR 231

Query: 231 E 231
           E
Sbjct: 232 E 232


>gi|328779117|ref|XP_623545.2| PREDICTED: tRNA-dihydrouridine synthase 4-like [Apis mellifera]
          Length = 349

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 68/281 (24%), Positives = 128/281 (45%), Gaps = 31/281 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+AD+ ++ +K     FST   +KPL +Q    +
Sbjct: 21  MVRYSKLQFRTLVRQYDCD-ICFTPMILADSFIQSEKARNNEFSTNNSDKPLIVQFAAKN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   + AA++V  +  + ++LN GCP     +  +GA L+  PD V D I  +   +  P
Sbjct: 80  VYDFLNAAELVAPYC-SGVDLNCGCPQRWALKEGYGADLLKKPDFVKDLIYQVRNRIPHP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I      N  + ++K+G + + IHAR       +P+   +  NLD   
Sbjct: 139 FTVSVKIRLLKDIHKTI--NFCRILEKAGASFLTIHAR-------TPEMRCEPINLDN-- 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             ++ +++  L +  NG ++ +  A  +    + D VM  R    N A+ +         
Sbjct: 188 -LKLIRDSVKLPLIANGDVKSLENAENLYRESNCDAVMSARGILTNPALFSGY------- 239

Query: 237 LTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQI 276
               +P+    D   W  I++++ T +   H H    L++I
Sbjct: 240 --SVTPLNCVQD---WLDITSTIPTPFTCFHHHLVFMLEKI 275


>gi|209517509|ref|ZP_03266349.1| TIM-barrel protein, nifR3 family [Burkholderia sp. H160]
 gi|209502042|gb|EEA02058.1| TIM-barrel protein, nifR3 family [Burkholderia sp. H160]
          Length = 353

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 71/307 (23%), Positives = 137/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PDMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVNAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWNRENKNAL--NVARLAQAAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A ++L +   D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVKAA-VRIPVVANGDITSPQKAREVLAATGADAIMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 246 FLQ---TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 297

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 298 GANLFRH 304


>gi|321469164|gb|EFX80145.1| hypothetical protein DAPPUDRAFT_304174 [Daphnia pulex]
          Length = 303

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 68/274 (24%), Positives = 126/274 (45%), Gaps = 34/274 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + L +T MI++D+ ++  K   + F+T   ++PL +Q    +
Sbjct: 18  MVRYSKLPFRLLVRKYGCD-LAFTPMIISDSFIQAPKARDIEFTTCDADQPLIVQFAAHN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            +    AA++V     N ++LN GCP     +  +GACL+  P+++ D +      + S 
Sbjct: 77  STDFATAAELVAS-TCNGVDLNCGCPQKWAMQQGYGACLINKPELLRDVVLQTRNRIPSN 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDY 176
             TV  +I +  +I       L + ++ +G++ + +H R         KD R  P NL+ 
Sbjct: 136 DFTVSIKIRIHPEIRKTV--ELCQQVEAAGLSFLTVHGRT--------KDQRSDPVNLEG 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
               ++ KE+  + +  NG +  +  A  ++ + +V+GVM  R   +N AM     E   
Sbjct: 186 ---VKLIKESVRVPVIANGDICSLQDAEHVQQITNVNGVMSARGILENPAMFAGFSE--- 239

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
                 +PI+   D   W K+S   T  +  H H
Sbjct: 240 ------TPIECIKD---WMKLSLE-TGISFTHFH 263


>gi|242277846|ref|YP_002989975.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
 gi|242120740|gb|ACS78436.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
          Length = 348

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 64/205 (31%), Positives = 100/205 (48%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           L +TEM  A A+   + +    FS  E     L  QI GA+  ++V AA+ VE  G+  +
Sbjct: 56  LAFTEMCSARAVPTENPRISPVFSWHEWELPSLVCQIVGAEPEEMVIAAERVEREGFFGV 115

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-PAVAL 136
           ++N+GC +  + +   GA L+  P+     + A+ KA+SIPV VK R G   +I PAVA 
Sbjct: 116 DINMGCSARGMIKREAGAALLKTPEKAVAIVEAVRKAVSIPVFVKFRTGWSKEIGPAVA- 174

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L K ++ +G + +  H R      ++P    + P +D+  +  IKK       G NG 
Sbjct: 175 --LAKDLEAAGADCLVFHPR------VAPDKRTRPPYIDH--IRYIKKAVSIPVFG-NGD 223

Query: 197 LEDMSQALKILPSV--DGVMIGRAA 219
           +        +L     DG+ IGR A
Sbjct: 224 VTTPQHCQNMLERTGCDGISIGRMA 248


>gi|253700031|ref|YP_003021220.1| hypothetical protein GM21_1403 [Geobacter sp. M21]
 gi|251774881|gb|ACT17462.1| TIM-barrel protein, nifR3 family [Geobacter sp. M21]
          Length = 321

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 126/288 (43%), Gaps = 46/288 (15%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +TEM+  + + R  +K  ++L    +++P+ +Q+ G D   L EAA++VED G   I++N
Sbjct: 42  FTEMVSVNGLTREGRKSFDLLKSCAEDRPIGMQLFGDDPEMLAEAARLVEDHG-ELIDIN 100

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV---DDQIPAVALR 137
           +GCP  +V     G+ LM +P  VG  + ++  A  +P+T+K R G    DD    V   
Sbjct: 101 MGCPVRKVVGTGAGSALMKDPRKVGRIVRSVRAATRLPLTIKIRTGWVCGDDTFLEVG-- 158

Query: 138 NLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              +  ++ G + + +H  +R  + +G            D+  + E+K       IG +G
Sbjct: 159 ---RIAQEEGCDAVTLHPRSRAQMFEG----------KADWSRIAELKSTLSIPVIG-SG 204

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            L   +    +L     D VM+ R A  N  +     E  S  L G  P    V +    
Sbjct: 205 DLFSAADVAGMLAETGCDAVMVARGAMGNPWIFR---EALSL-LAGEEPAPPSVQERL-- 258

Query: 254 KISASMTDYAARHLH-----SGGK--LQQITRHMIGLFHGFPNSRRCR 294
                    + RHL      +GG+  L ++ +H+     G P +   R
Sbjct: 259 -------ALSRRHLELFTEFAGGRVALMEMRKHLSWYSKGLPGAAHFR 299


>gi|282854101|ref|ZP_06263438.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J139]
 gi|282583554|gb|EFB88934.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J139]
          Length = 364

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 75/287 (26%), Positives = 117/287 (40%), Gaps = 27/287 (9%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 28  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 87

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVD-DQIP 132
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D D I 
Sbjct: 88  VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPDHIT 147

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            +   +  ++   SG   + +HAR                +  +D + E+ K      IG
Sbjct: 148 YI---DSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG 196

Query: 193 LNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG + + S A+ ++      GV +GR       +   + + F+   T + P    V   
Sbjct: 197 -NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCA- 254

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             R+ +  +  Y   H      L  + +HM     GFP     RH L
Sbjct: 255 MIRRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHAL 296


>gi|154253571|ref|YP_001414395.1| nifR3 family TIM-barrel protein [Parvibaculum lavamentivorans DS-1]
 gi|154157521|gb|ABS64738.1| putative TIM-barrel protein, nifR3 family [Parvibaculum
           lavamentivorans DS-1]
          Length = 341

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 108/236 (45%), Gaps = 22/236 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R  A  L    L+ +EM+ +D ++R   D       + +  PLA+Q+ G +   +
Sbjct: 23  TDLPFRRVAHRL-GAGLVVSEMVASDELVRARPDVVRRAAGAGEFAPLAIQLAGREAHWM 81

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A++    G + I++N+GCP+ +V  G  G+ LM + D     I A   A+S+PVT+K
Sbjct: 82  AEGARVAAAAGADIIDINMGCPAKQVTTGLSGSALMRDLDHAESLIEATVGAVSLPVTLK 141

Query: 123 CRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            R G DD     P +A R     +K   V+G     R    K  +          D++ +
Sbjct: 142 MRTGWDDTKRNAPELAQRAEALGVKMVTVHG---RTRCQFYKSRA----------DWNFI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            E+KK      I  NG +     A  IL +   DGVMIGR A      L  V ++ 
Sbjct: 189 SEVKKAVSIPVIA-NGDVTSEEDARAILDASGADGVMIGRGAQGRPWFLAQVAQFL 243


>gi|254704408|ref|ZP_05166236.1| NifR3 family TIM-barrel protein [Brucella suis bv. 3 str. 686]
          Length = 333

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/263 (23%), Positives = 121/263 (46%), Gaps = 40/263 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GC + +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++    L
Sbjct: 104 NMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G +          D+D ++ + ++   + +  NG +
Sbjct: 162 ARRAEDAGIAMVTVHGRTRCQFYEGTA----------DWDAIHAV-RDAVRIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              + A +IL     D VM+GRA+Y           + +  + GS         DF  + 
Sbjct: 211 SSRADAEEILRRSGADAVMVGRASYGQP--------WLAGAIAGS---------DFAPRD 253

Query: 256 SASMTDYAARHL-----HSGGKL 273
           +  + DY  RH      H G K+
Sbjct: 254 ANGILDYIIRHYEDMLDHYGSKI 276


>gi|253827463|ref|ZP_04870348.1| putative transcriptional regulator [Helicobacter canadensis MIT
           98-5491]
 gi|313141671|ref|ZP_07803864.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
 gi|253510869|gb|EES89528.1| putative transcriptional regulator [Helicobacter canadensis MIT
           98-5491]
 gi|313130702|gb|EFR48319.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
          Length = 328

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 119/260 (45%), Gaps = 27/260 (10%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDF--GYNEINL 79
           +EMI   A+   +KK I  +  S  E P ALQI G D   +  A + +  F      ++L
Sbjct: 49  SEMISVHALAFQNKKTIKMIEKSPLENPFALQIAGNDFEIIQRAVEFLNQFRDSIQILDL 108

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALRN 138
           N GCP+ +V     G+ L+ + + +   +  + K    P ++VK R+G D +IP      
Sbjct: 109 NCGCPAPKVSSHGSGSSLLKDLNKLVKILNLLRKISLFPYLSVKVRLGFDKKIPL----E 164

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K++  S ++ + +H R       +  D  K   +DYD +  IK+  P   I  NG + 
Sbjct: 165 IAKALSDSPIDYVVVHGR-------TKSDGYKKDKIDYDSIKIIKENIPHPLIA-NGEIN 216

Query: 199 DMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               A K+      DG+MIGR+A +   + T +     N L  S  ++ +V  + + +  
Sbjct: 217 SPETAKKVQEFTGADGIMIGRSAIEKPWIFTQI----KNNLEESVELRKQVALEHFDRTI 272

Query: 257 ASMTDYAA----RHLHSGGK 272
               DY A    ++LH+  K
Sbjct: 273 EFRGDYGAIMFRKNLHAYSK 292


>gi|192291239|ref|YP_001991844.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris TIE-1]
 gi|192284988|gb|ACF01369.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris TIE-1]
          Length = 333

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 113/243 (46%), Gaps = 25/243 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM  ++ ++ G + ++       + P  +Q+ G +   + E A+I E  G + I++
Sbjct: 36  LVVSEMTASEDLVAGRRMSVRRCDKVGQGPHVVQLAGCEPRWMAEGARIAEAGGADIIDI 95

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN- 138
           N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G DD+      RN 
Sbjct: 96  NMGCPARHVTGGLSGSALMRDLDHALTLIEATIGAVRVPVTLKMRLGWDDRS-----RNA 150

Query: 139 --LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L +  + +G+  + +H   R+   KG            D+D V  + ++   + + +N
Sbjct: 151 PELARRAQDAGIQLVTVHGRTRQQFYKG----------EADWDAVRAV-RDAISIPLVVN 199

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G +   + A++ L     D VMIGR A     +   V    +     + P  T + +D+ 
Sbjct: 200 GDITCHASAVEALKRSGADAVMIGRGAQGRPWLPGQVGRQLTTGKAEAEPSLT-MQRDYL 258

Query: 253 RKI 255
           R +
Sbjct: 259 RAL 261


>gi|88809287|ref|ZP_01124796.1| hypothetical protein WH7805_06326 [Synechococcus sp. WH 7805]
 gi|88787229|gb|EAR18387.1| hypothetical protein WH7805_06326 [Synechococcus sp. WH 7805]
          Length = 338

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 66/276 (23%), Positives = 124/276 (44%), Gaps = 35/276 (12%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLV 63
           +D+ +R   R  + +ALL+TEM+ A ++  G  +  +    QE  P+ +Q+       + 
Sbjct: 33  SDKIFRALVRRWSRDALLFTEMVNATSLELGHGRGKVEELRQEAGPIGVQLFDHRPESMA 92

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  ED G   I++N+GCP  ++     G+ L+ +PD+    + A+  A+ IPVTVK 
Sbjct: 93  DAARRAEDAGAFLIDINMGCPVRKIARKGGGSGLIRDPDLACTIVEAVVAAVGIPVTVKT 152

Query: 124 RIGV-------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           R+G        D    A+A     + ++ +G   + +H R         ++ R     D+
Sbjct: 153 RLGWCSVPQGGDSHAAAMA---WCRRLEAAGAQLLTLHGRT--------REQRFSGRADW 201

Query: 177 DIVYEIKK-------ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           + +  +K+        N D+F       ED  + L +    DGVM+GR       ++  +
Sbjct: 202 EAIAAVKRALRIPVIANGDVF-----SPEDARECLGVT-GADGVMVGRGTMGAPWLVGQI 255

Query: 230 DEYFSN---PLTGSSPIKTRVDKDFWRKISASMTDY 262
           D        P T  +  +  +  D  + + A+  D+
Sbjct: 256 DAALKGLPVPPTPGASERLMIAADQLQALVAARGDH 291


>gi|239620834|ref|ZP_04663865.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|322691517|ref|YP_004221087.1| dihydrouridine synthase [Bifidobacterium longum subsp. longum JCM
           1217]
 gi|239516410|gb|EEQ56277.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|320456373|dbj|BAJ66995.1| putative dihydrouridine synthase [Bifidobacterium longum subsp.
           longum JCM 1217]
          Length = 414

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 105/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR A        D  +I  L
Sbjct: 174 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTAAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|149190656|ref|ZP_01868924.1| tRNA-dihydrouridine synthase [Vibrio shilonii AK1]
 gi|148835539|gb|EDL52508.1| tRNA-dihydrouridine synthase [Vibrio shilonii AK1]
          Length = 309

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 53/190 (27%), Positives = 89/190 (46%), Gaps = 19/190 (10%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D +  
Sbjct: 55  SVQIAGADPKLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLKYPDIIEDILRT 114

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKD 167
           +  A+ +PVT+K R G D D    V +  L +     G+  + +H   R  + KG     
Sbjct: 115 VVDAVDVPVTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTRTCMYKG----- 166

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
                  +YD +  +K       I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 167 -----EAEYDSIKAVKNAISIPVIA-NGDIDSPEKAKFVLDYTGADALMIGRPAQGRPWI 220

Query: 226 LTTVDEYFSN 235
              +  Y  N
Sbjct: 221 FEEIQHYLEN 230


>gi|328773713|gb|EGF83750.1| hypothetical protein BATDEDRAFT_21188 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 327

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 109/247 (44%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---KPLALQIGGA 57
           MV ++   +R   R   N  L YT MI++D            F T +    P+ +Q   +
Sbjct: 32  MVRYSKLAFRELVRGY-NVDLAYTPMILSDVFKHSQISRETEFRTHQITDDPVIVQFAAS 90

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI--------- 108
           + + L +AA++V  +  N ++LN GCP         G+ LM +P++V D +         
Sbjct: 91  NPTDLADAAELVARYT-NGVDLNCGCPQKWAISEGIGSYLMEHPELVRDMVKQVKSRTSS 149

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLSP 165
             M    S P ++K RI  D       L+  V+ ++++   GV+ I +H R    K   P
Sbjct: 150 VKMANGTSFPCSIKIRIHSD-------LKKTVEFVRRAESIGVDWITVHGRTRKQKNTEP 202

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   L+ D +  I KE+  + +  NG +  +  A +++    VDGVM  R   +N 
Sbjct: 203 --------LNMDGI-RIAKESVGVPVFANGNVLTLGDADRLVEETRVDGVMAARGLLENP 253

Query: 224 AMLTTVD 230
           A+ +  D
Sbjct: 254 ALFSGYD 260


>gi|254461960|ref|ZP_05075376.1| tRNA-dihydrouridine synthase B [Rhodobacterales bacterium HTCC2083]
 gi|206678549|gb|EDZ43036.1| tRNA-dihydrouridine synthase B [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 331

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 106/234 (45%), Gaps = 26/234 (11%)

Query: 5   TDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           TD  +R     F A L+ +  +   EM+ A   +R  +K  LGF       ++QI G + 
Sbjct: 25  TDLPFRNLVCSFGAGLVVSEMVASQEMVKAKPGVR--EKAELGFGAART--SVQIAGREA 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++    G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+ +PV
Sbjct: 81  YWMAEAARLAAGNGAQIIDINMGCPAKKVTSGYSGSALMKDLDHALTLIEAVVGAVDVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYD 177
           T+K R+G D+ +   A   L    + +G+  I IH R      KG            ++ 
Sbjct: 141 TLKTRLGWDNHLLNAA--ELAVRAESAGIQMITIHGRTRCQFYKG----------QANWS 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            +  IK       I  NG + D++ A   L     DG+M+GR A     +L  +
Sbjct: 189 AIKGIKAAVRIPVIA-NGDIVDVATARAALSQSGADGIMVGRGAQGRPWILAQI 241


>gi|295425664|ref|ZP_06818351.1| tRNA-dihydrouridine synthase [Lactobacillus amylolyticus DSM 11664]
 gi|295064680|gb|EFG55601.1| tRNA-dihydrouridine synthase [Lactobacillus amylolyticus DSM 11664]
          Length = 341

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 116/222 (52%), Gaps = 22/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L+EAA+ V+     +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLSMMQVDPREHPMSIQIFGGTEETLLEAAQYVDKHTAADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +S PVTVK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDANKIYQMVHAVVQNVSKPVTVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G          + D+++++++       F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQG----------HADWEVLHDVANALDIPFVA-NG 206

Query: 196 GL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +   ED  +AL  + S   VM+GRAA  N  ++  +  Y  
Sbjct: 207 DIRTPEDAKKALDEIGST-AVMVGRAALGNPWIIKDMVHYLE 247


>gi|238927136|ref|ZP_04658896.1| dihydrouridine synthase [Selenomonas flueggei ATCC 43531]
 gi|238884918|gb|EEQ48556.1| dihydrouridine synthase [Selenomonas flueggei ATCC 43531]
          Length = 320

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 108/230 (46%), Gaps = 23/230 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++   N+L     E+P+A+QI    
Sbjct: 17  MAGVTDTSYRVIAHGM-GCPLAFAEMVSSQGIHYRNEHTMNMLRTEPDERPIAMQIFAKS 75

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                EAA  +E+ G  +I + N+GCP+ +V     G+ LM +P    + + A+ +A  +
Sbjct: 76  ARMAAEAAAYIEELGTADILDFNMGCPAPKVVRNGEGSALMRDPKRAEEILTAIRRATRL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLSPKDNRKIPNL 174
           P TVK R+G DD     A RN V+  + +   GV+ + +H R         ++     + 
Sbjct: 136 PFTVKMRLGWDD-----ASRNAVEIARMAEAVGVDAVAVHGRT--------REQFYSGSA 182

Query: 175 DYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           DY  +  +K+    P +  G      D+ +AL+I    D VMIGR A  N
Sbjct: 183 DYAAIAAVKRAVGIPVIVSGDVRRPADLKRALEIT-GADAVMIGRGAQGN 231


>gi|221639223|ref|YP_002525485.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides KD131]
 gi|221160004|gb|ACM00984.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides KD131]
          Length = 317

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 82/161 (50%), Gaps = 11/161 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A +     L+ +EM+ +  ++    + +        E   A+Q+ G D
Sbjct: 10  MAGITDLPFRRLA-VRFGAGLVVSEMVASREVVCAGAEARARAEIGAAEGRTAVQLAGCD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     I A+  A+++P
Sbjct: 69  PHWMAEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALIEAVVGAVAMP 128

Query: 119 VTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHAR 156
           VT+K R+G D+ +   P +A R      + +GV  I IH R
Sbjct: 129 VTLKMRLGWDEGMLNAPEIARRA-----EAAGVAMITIHGR 164


>gi|193636409|ref|XP_001949454.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Acyrthosiphon
           pisum]
          Length = 578

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 55/203 (27%), Positives = 102/203 (50%), Gaps = 18/203 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EM+++ ++L+G  +   +      E    +Q+ G +   L ++A+++ E+   + ++LN
Sbjct: 260 SEMVLSSSLLQGHNQEWALTKRHETEDIFGIQVCGNNPYMLAKSAQVLQENVDMDFLDLN 319

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNL 139
           +GCP  ++++   G+ L+L    +  C+ +M   L +P+TVK R GV+ DQ  A    +L
Sbjct: 320 LGCPLDQIYKQGAGSGLLLRSKKLEVCLKSMRTVLDVPLTVKTRSGVNKDQNVA---HDL 376

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
           +   K SGV+ I +H R         +D R     D++ V E  K    + +  +G +  
Sbjct: 377 IPMFKDSGVSLITVHGRS--------RDQRYTKMADWNYVNECAKLASPVQVFSSGDIMS 428

Query: 198 -EDMSQALKILPSVDGVMIGRAA 219
            ED   +    P + G MIGR A
Sbjct: 429 YEDYVDSKLQFPDITGAMIGRGA 451


>gi|314934906|ref|ZP_07842265.1| dihydrouridine synthase family protein [Staphylococcus caprae C87]
 gi|313652836|gb|EFS16599.1| dihydrouridine synthase family protein [Staphylococcus caprae C87]
          Length = 325

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 94/193 (48%), Gaps = 28/193 (14%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L FS  E+P+   I G    +  + +  +++ G+  I+LN+GCP A V +   G+ L+L 
Sbjct: 63  LTFSEDEQPMVAHIWGDKPEQFRKMSIGLKEMGFKGIDLNMGCPVANVAKKGKGSGLILR 122

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           P+   + I A  K   +PV+VK R+G   +D+       ++ +K + +  +  + IH R 
Sbjct: 123 PERAAEIIQA-TKEGGLPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRT 175

Query: 158 AILKGLSPKDNRKIPNLD--YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS-- 209
                      R++  +D  ++++  IK       P   + +NG + D  + L++     
Sbjct: 176 ----------RREMSKVDAHWELIEAIKTMRDEIAPHTLLTINGDIPDRQKGLELANKYG 225

Query: 210 VDGVMIGRAAYKN 222
           VDGVMIGR  + N
Sbjct: 226 VDGVMIGRGLFHN 238


>gi|223043632|ref|ZP_03613676.1| tRNA-dihydrouridine synthase [Staphylococcus capitis SK14]
 gi|222442910|gb|EEE49011.1| tRNA-dihydrouridine synthase [Staphylococcus capitis SK14]
          Length = 325

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 108/237 (45%), Gaps = 32/237 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  + +  +++ G+  I+LN+GCP A V +   G+ L+L P+   + I A  K   
Sbjct: 79  DKPEQFRKMSIGLKEMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQA-TKEGG 137

Query: 117 IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PV+VK R+G   +D+       ++ +K + +  +  + IH R            R++  
Sbjct: 138 LPVSVKTRLGYYEIDE------WKDWLKHVFEQDIANLSIHLRT----------RREMSK 181

Query: 174 LD--YDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +D  ++++  IK       P   + +NG + D  + L++     VDGVMIGR  + N
Sbjct: 182 VDAHWELIEAIKTMRDEIAPHTLLTINGDIPDRQKGLELANKYGVDGVMIGRGIFHN 238


>gi|213420756|ref|ZP_03353822.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 311

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 7   MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 65

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ IP
Sbjct: 66  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDIP 125

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G           
Sbjct: 126 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 170

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++   + I  NG + +  +A  +L     D +MIGRAA     +   +  
Sbjct: 171 AEYDSIRAVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 229

Query: 232 YF 233
           Y 
Sbjct: 230 YL 231


>gi|113970596|ref|YP_734389.1| dihydrouridine synthase, DuS [Shewanella sp. MR-4]
 gi|113885280|gb|ABI39332.1| dihydrouridine synthase, DuS [Shewanella sp. MR-4]
          Length = 315

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 111/236 (47%), Gaps = 33/236 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + D + AM +A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 NTIHDIVRAMRQAVPAEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
                  D  K P   ++ + E+++  P   I  NG +   ED  + + +    D +MIG
Sbjct: 174 -------DGYKPPAY-WEYITEVRERLPIPVIA-NGEIWNREDAERCMAVT-GCDSIMIG 223

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           R A     +  T+        TG++P +       W      M  Y  R L SG K
Sbjct: 224 RGAISLPNLADTIK-------TGAAPYR-------WADTLGLMLSYTQREL-SGRK 264


>gi|317057657|ref|YP_004106124.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 7]
 gi|315449926|gb|ADU23490.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 7]
          Length = 326

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 70/319 (21%), Positives = 128/319 (40%), Gaps = 27/319 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M    D+ YR   R     A L +EMI +  +   D+K   +     +E+P ALQ+ G D
Sbjct: 20  MASVADKSYRLLCREF-GAAYLVSEMISSKGLCYNDRKTGELCEIEDEERPYALQLFGED 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++     + I++N+GCP  ++     G+ LM +     +      K    P
Sbjct: 79  PYFMGKAAYLLGKHKPDIIDINMGCPVPKIVGNGSGSALMKDIPRAVEIAKETVKNACCP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD           K+++++G+  + +H R         +        D++I
Sbjct: 139 VTVKFRAGWDDTSKNAV--EFAKALEQTGIAAMAVHGRT--------RQQFYSGEADWEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+       G NG ++D     ++      D VM+ R +Y    +   +  +    
Sbjct: 189 IRQVKQAVSIPVFG-NGDVKDGESCKRMYEETGCDLVMLARGSYGRPWVFREIKHFLETG 247

Query: 237 LTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR--- 292
                P IK R++      I      Y  ++      +++  +++     G PNS +   
Sbjct: 248 EKLPEPDIKERME------IMLRHCRYLCKYKGEVRGMKEARKNVAWYVKGLPNSAKLRA 301

Query: 293 -CRHILTVEAGASTATHHI 310
            C  + T E     A   I
Sbjct: 302 ECGELSTYEQAEEIAARII 320


>gi|118096265|ref|XP_414079.2| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 518

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 86/183 (46%), Gaps = 24/183 (13%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+G AD  + +  AK+VE      I++N+GCP     +G  GA L+ +PD +   +  +
Sbjct: 113 FQMGSADAGRALAVAKLVES-DVAGIDINMGCPKEYSTKGGMGAALLSDPDKIESILTTL 171

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            K +  PVT K RI   V+D +      +LVK I+K+G+  I +H RK        K+ R
Sbjct: 172 VKGICKPVTCKIRILPSVEDTV------DLVKRIEKTGIAAIAVHGRK--------KEER 217

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM------SQALKILPSVDGVMIGRAAYKNS 223
               +  D++  I  E   + +  NGG  D        +  +   +   VMI RAA  N 
Sbjct: 218 PQHPVHCDVIKAI-SEAVSIPVIANGGSHDFIKEYGDIETFQKATAASSVMIARAAMWNP 276

Query: 224 AML 226
           ++ 
Sbjct: 277 SIF 279


>gi|255714418|ref|XP_002553491.1| KLTH0D18084p [Lachancea thermotolerans]
 gi|238934871|emb|CAR23053.1| KLTH0D18084p [Lachancea thermotolerans]
          Length = 430

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 106/238 (44%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNIL----GFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K  +++     G    ++PL +Q 
Sbjct: 37  MVDQSELAWRILSRRY-GATLAYTPMFHAKMFATSEKYRRDMWCKDDGSQELDRPLVVQF 95

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L+ AAK++ED   + ++LN+GCP     +G +G+ LM + D++   I  +   
Sbjct: 96  CANDSDYLLAAAKLIED-KCDAVDLNLGCPQGIAKKGHYGSFLMEDWDLIHKLIRTLHDN 154

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L IPVT K R+  +            K +  +G   + +H R      L  +  +K    
Sbjct: 155 LKIPVTAKIRVFSE----RAKTLEYAKMVLDAGAQFLTVHGR------LREQKGQKTGLA 204

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           D+DI+  +++E P D     NG +   ED+S+ +  +   D VM       N  +  T
Sbjct: 205 DWDIIQYLRQELPKDTVFFANGNILYPEDISRCMNEI-HCDAVMSAEGNLYNPGVFNT 261


>gi|313200160|ref|YP_004038818.1| tim-barrel protein, nifr3 family [Methylovorus sp. MP688]
 gi|312439476|gb|ADQ83582.1| TIM-barrel protein, nifR3 family [Methylovorus sp. MP688]
          Length = 343

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 112/225 (49%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L  +EM+ ++++L G  K +       + +P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKKL-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVEPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVSQILKAVVAAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDY 176
           VT+K R G D +   AVA+  + + I   GV  + +H R +A L            + +Y
Sbjct: 136 VTLKIRTGWDKNNRNAVAVARMAEDI---GVQALAMHGRTRACLYN---------GDAEY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D +  +K+      I  NG +    +A  +L     D VMIGRAA
Sbjct: 184 DTIAAVKQAIKIPLIA-NGDITTPEKAKFVLEYTQADAVMIGRAA 227


>gi|314923074|gb|EFS86905.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL001PA1]
 gi|314966844|gb|EFT10943.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL082PA2]
 gi|314981186|gb|EFT25280.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA3]
 gi|315092006|gb|EFT63982.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA4]
 gi|315093235|gb|EFT65211.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL060PA1]
 gi|315103509|gb|EFT75485.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL050PA2]
 gi|327327670|gb|EGE69446.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL103PA1]
          Length = 409

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 75/287 (26%), Positives = 117/287 (40%), Gaps = 27/287 (9%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 73  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 132

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVD-DQIP 132
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D D I 
Sbjct: 133 VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPDHIT 192

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            +   +  ++   SG   + +HAR                +  +D + E+ K      IG
Sbjct: 193 YI---DSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDAIGELVKTVDVPVIG 241

Query: 193 LNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG + + S A+ ++      GV +GR       +   + + F+   T + P    V   
Sbjct: 242 -NGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCA- 299

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             R+ +  +  Y   H      L  + +HM     GFP     RH L
Sbjct: 300 MIRRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHAL 341


>gi|311740227|ref|ZP_07714059.1| dihydrouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|311304782|gb|EFQ80853.1| dihydrouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 379

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 71/293 (24%), Positives = 122/293 (41%), Gaps = 25/293 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-I 68
             R  T + L   EM+ A A++  ++K  ++  F+ QE P +LQI   D     +AAK I
Sbjct: 34  LQRTGTVSGLYVCEMVTARALVERNEKTLHMTTFAPQEDPRSLQIYTVDPEYTYKAAKMI 93

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKCRI 125
           V++   + I++N GCP  +V     G+ L     + G+ ++A  KA    +IPVTVK R+
Sbjct: 94  VDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAAVKATEGTNIPVTVKMRV 153

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD+       +  +   +SG   + +H R A          R      +D +  +K+ 
Sbjct: 154 GIDDE--HHTHLDAGRIAVESGAAAVTLHGRTAA--------QRYSGEARWDEIARLKEH 203

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             D  + +  NG +     A +++     DGV +GR       +   +          + 
Sbjct: 204 LADTGVPVLGNGDIFRAEDARRMMEQTGCDGVQVGRGCLGRPWLFAELGAALRGESIPAE 263

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           P    V +   R       +  A H       + I +H+     GFP   + R
Sbjct: 264 PTLGEVTQVILRH-----AELLAEHDGEDNASRDIRKHIGWYLRGFPVGGQVR 311


>gi|424091|gb|AAA69019.1| ORF1 protein [Salmonella enterica subsp. enterica serovar
           Typhimurium]
          Length = 321

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 115/257 (44%), Gaps = 30/257 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + +  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPIIA-NGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YFSN----PLTGSSPIK 244
           Y       P   S+ +K
Sbjct: 240 YLDTGELLPRRASAEVK 256


>gi|300790789|ref|YP_003771080.1| dihydrouridine synthase [Amycolatopsis mediterranei U32]
 gi|299800303|gb|ADJ50678.1| putative dihydrouridine synthase [Amycolatopsis mediterranei U32]
          Length = 379

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 66/276 (23%), Positives = 112/276 (40%), Gaps = 21/276 (7%)

Query: 25  EMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNV 81
           EMI A A++       +++ F   EKP ++Q+ G D   + EA +I+   G  + ++ N 
Sbjct: 52  EMITARAVVERHPGTMHMMTFGADEKPRSMQLYGVDPKTIAEAVRIIVGEGLADHVDSNF 111

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLV 140
           GCP A+V     GA L     +    +    KA    P TVK RIG+DD        +  
Sbjct: 112 GCPVAKVTRKGGGAALPFKRKLFEAIVRESVKAAGDTPFTVKFRIGIDDD--HRTFLDAG 169

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +  +  G   + +HAR A          R     D+  + E+K+    + +  NG +   
Sbjct: 170 RIAEAEGAAAVSLHARTAA--------QRYSGQADWTKIAELKEAVTSIPVLGNGDIFSA 221

Query: 201 SQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
             AL+++     DGV++GR       +   ++  F+       P+ T  +      +   
Sbjct: 222 EDALRMVDETGCDGVVVGRGCLGRPWLFGELEAAFAG-----RPLPTPPNLGEVAAVLRR 276

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T+    H      ++ I +HM     GFP     R
Sbjct: 277 HTELLIEHDGHDKAMRDIRKHMAWYLMGFPVGSELR 312


>gi|119953515|ref|YP_945724.1| histidine phosphokinase/phophatase, putative [Borrelia turicatae
           91E135]
 gi|119862286|gb|AAX18054.1| histidine phosphokinase/phophatase, putative [Borrelia turicatae
           91E135]
          Length = 331

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 64/256 (25%), Positives = 119/256 (46%), Gaps = 30/256 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNILGFSTQE----KPLAL 52
           M D TD  +R    L+ N      + +TE I    +L   K+++    T+     +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGNGKDGPDIYFTEFISVKGLLNKSKQSMQHILTKNDELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G +  +  +A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNEPDEFFKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAREIIMASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C    + ++VK R G         + + +  + K G++ + +H R AI        N+
Sbjct: 137 EACLKFGLSLSVKTRHG----FFYSEVEDWLGFLLKLGIDMLTVHPRLAI--------NQ 184

Query: 170 KIPNLD---YDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              ++D   +D +  ++ + NP   I  NG +  + QA +I+   S+DGVM GR  ++N 
Sbjct: 185 SEGSIDISVFDKLVNLRDQINPSALIIGNGDILSLEQAHQIVEKHSIDGVMFGRGIFRNL 244

Query: 224 AMLTT-VDEYFSNPLT 238
            +    +  + SN L 
Sbjct: 245 NLFRKGLPNFLSNNLN 260


>gi|299133856|ref|ZP_07027050.1| TIM-barrel protein, nifR3 family [Afipia sp. 1NLS2]
 gi|298591692|gb|EFI51893.1| TIM-barrel protein, nifR3 family [Afipia sp. 1NLS2]
          Length = 344

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 46/148 (31%), Positives = 74/148 (50%), Gaps = 5/148 (3%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKI 68
           R  ARL     L+ +EM  +D + RG   ++L        P  +Q+ G +   + E A+I
Sbjct: 38  RVAARL--GAGLVVSEMTASDDLARGRAMSVLRCEAAGIGPHVVQLAGCEAKWMAEGARI 95

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ IPVT+K R+G D
Sbjct: 96  AESGGADIIDINMGCPARHVTGGQSGSALMRDLDHAMTLIEATIAAVKIPVTLKMRLGWD 155

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHAR 156
               ++    L +  + SG+  + +H R
Sbjct: 156 HA--SLNAPELARRAEASGIQMVTVHGR 181


>gi|168704071|ref|ZP_02736348.1| hypothetical protein GobsU_31344 [Gemmata obscuriglobus UQM 2246]
          Length = 346

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 59/241 (24%), Positives = 114/241 (47%), Gaps = 21/241 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +T+  +R   R L    L  T++I A AI+ G +K   +L     E+PL +QI G+ 
Sbjct: 12  LAGYTNLPFRLSVRELGGVGLCTTDLINARAIVDGIQKTMLLLAHDHAERPLFVQIFGSK 71

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
             ++  AAK +VE+   + I++N+GCP  +V +   G+ LM   D  G  +  + + +  
Sbjct: 72  PHEMAGAAKWLVENRIADGIDINMGCPVRKVVKTGGGSSLMC--DTTGATVGLVSQVVEA 129

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PV+VK R+G DD    ++     +  +K+GV  + IH R         ++      
Sbjct: 130 VRPVPVSVKMRLGWDDD--NLSAPYFAREFEKAGVAALTIHGRT--------REQGFAGG 179

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDE 231
           ++++ +  + +    + +  NG +  +  A +++      G+ IGR A  N  +    D 
Sbjct: 180 VNHEGIRRVVEAVEKIPVFGNGDVRSVQDAARMITETGCHGIAIGRGALANPWVFRQFDA 239

Query: 232 Y 232
           +
Sbjct: 240 W 240


>gi|224418136|ref|ZP_03656142.1| putative transcriptional regulator [Helicobacter canadensis MIT
           98-5491]
          Length = 317

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 119/260 (45%), Gaps = 27/260 (10%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDF--GYNEINL 79
           +EMI   A+   +KK I  +  S  E P ALQI G D   +  A + +  F      ++L
Sbjct: 38  SEMISVHALAFQNKKTIKMIEKSPLENPFALQIAGNDFEIIQRAVEFLNQFRDSIQILDL 97

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALRN 138
           N GCP+ +V     G+ L+ + + +   +  + K    P ++VK R+G D +IP      
Sbjct: 98  NCGCPAPKVSSHGSGSSLLKDLNKLVKILNLLRKISLFPYLSVKVRLGFDKKIPL----E 153

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K++  S ++ + +H R       +  D  K   +DYD +  IK+  P   I  NG + 
Sbjct: 154 IAKALSDSPIDYVVVHGR-------TKSDGYKKDKIDYDSIKIIKENIPHPLIA-NGEIN 205

Query: 199 DMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               A K+      DG+MIGR+A +   + T +     N L  S  ++ +V  + + +  
Sbjct: 206 SPETAKKVQEFTGADGIMIGRSAIEKPWIFTQI----KNNLEESVELRKQVALEHFDRTI 261

Query: 257 ASMTDYAA----RHLHSGGK 272
               DY A    ++LH+  K
Sbjct: 262 EFRGDYGAIMFRKNLHAYSK 281


>gi|145551887|ref|XP_001461620.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124429455|emb|CAK94247.1| unnamed protein product [Paramecium tetraurelia]
          Length = 360

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 114/234 (48%), Gaps = 23/234 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ +  +          F+T  +++PL  Q+ G D
Sbjct: 25  MVDQSELAFRMLTRKY-GTTLAYTPMLHSRIMTESKSYKDEFFTTCPEDRPLFAQLCGHD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AA +++D   + I++N+GCP     +G +GA L+   + V   +  + + +++P
Sbjct: 84  PQVLIKAALMIQD-QCDAIDINLGCPQGIARKGLYGAYLLEKREQVLTIVKELKQNINVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK-IPNLDYD 177
           VT K R+  D +       +L K I+++G + + +H R       + + N+  +   D+ 
Sbjct: 143 VTCKIRMFKDRK----RTLDLTKDIQEAGCSILTVHGR-------TKEQNKDFVGQCDWT 191

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           I+ EIK+  + P   +  NGG+   S   + L    VD VM   A  +N A+ +
Sbjct: 192 IIAEIKQILQIP---VFANGGIYTWSDVERCLQETKVDAVMSSEALLENPALFS 242


>gi|253580729|ref|ZP_04857993.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848100|gb|EES76066.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 326

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 48/191 (25%), Positives = 92/191 (48%), Gaps = 11/191 (5%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+I+  + +      QI   +    ++ A+ ++++GYNE+NLN+GCPS  V     GA
Sbjct: 47  EKKDIMPENNEGMYAVPQILTKNAEDFIQTAETLQEYGYNEVNLNLGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  PD +   +  + +   + +++K R+G+DD        +L+    K  +  + +HA
Sbjct: 107 GFLDRPDELDKFLDEIFRKCDMKISIKTRLGMDD---PEEFEDLLTIYNKYPLEELIVHA 163

Query: 156 RKAILKGLSPKDNRK-IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           R         KD  K  P L+       + ++P  + G     +D ++   + P++D +M
Sbjct: 164 RVQ-------KDYYKNTPRLETFGEAVERAKSPVCYNGDIVTAKDCTRLQDMFPTLDCIM 216

Query: 215 IGRAAYKNSAM 225
            GR   KN A+
Sbjct: 217 TGRGTLKNPAL 227


>gi|262163830|ref|ZP_06031570.1| tRNA dihydrouridine synthase B [Vibrio mimicus VM223]
 gi|262027810|gb|EEY46475.1| tRNA dihydrouridine synthase B [Vibrio mimicus VM223]
          Length = 331

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 113/245 (46%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++ + +  +  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIENILKTVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V++  L ++    G+  + +H R    + KG +          +
Sbjct: 145 VTLKTRTGWDTDNKNCVSIAQLAEN---CGIQALALHGRTRACMYKGEA----------E 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEHTGADALMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|328956746|ref|YP_004374132.1| tRNA-dihydrouridine synthase [Carnobacterium sp. 17-4]
 gi|328673070|gb|AEB29116.1| tRNA-dihydrouridine synthase [Carnobacterium sp. 17-4]
          Length = 326

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 52/190 (27%), Positives = 88/190 (46%), Gaps = 22/190 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L F+  E+P+   I G +     + +  + + G+  I++N+GCP   V     G+ L+  
Sbjct: 63  LTFTEDEQPMVAHIWGDEPEHFRQMSIGMAEQGFKGIDINMGCPVPNVAGKGKGSGLIRR 122

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKA 158
             +  D I A  K   +PV+VK R+G  +       R+ +  + +  +  + IH   RK 
Sbjct: 123 ATVAADLIQA-AKTGGLPVSVKTRLGYTN---IDEWRDWLTHVFEQDIANLSIHLRTRKE 178

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDG 212
           + KG          N  ++++ EIKK      P   + +NG + D    LK++    VDG
Sbjct: 179 MSKG----------NAHWEMISEIKKLRDEIAPQTLLTINGDIPDRETGLKLVEEYGVDG 228

Query: 213 VMIGRAAYKN 222
           VMIGR  + N
Sbjct: 229 VMIGRGVFHN 238


>gi|255325926|ref|ZP_05367018.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           tuberculostearicum SK141]
 gi|255297138|gb|EET76463.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           tuberculostearicum SK141]
          Length = 379

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 71/293 (24%), Positives = 122/293 (41%), Gaps = 25/293 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-I 68
             R  T + L   EM+ A A++  ++K  ++  F+ QE P +LQI   D     +AAK I
Sbjct: 34  LQRTGTVSGLYVCEMVTARALVERNEKTLHMTTFAPQEDPRSLQIYTVDPEYTYKAAKMI 93

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKCRI 125
           V++   + I++N GCP  +V     G+ L     + G+ ++A  KA    +IPVTVK R+
Sbjct: 94  VDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAAVKATEGTNIPVTVKMRV 153

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD+       +  +   +SG   + +H R A          R      +D +  +K+ 
Sbjct: 154 GIDDE--HHTHLDAGRIAVESGAAAVTLHGRTAA--------QRYSGEARWDEIARLKEH 203

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             D  + +  NG +     A +++     DGV +GR       +   +          + 
Sbjct: 204 LADTGVPVLGNGDIFRAEDARRMMEQTGCDGVQVGRGCLGRPWLFAELGAALRGESIPAE 263

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           P    V +   R       +  A H       + I +H+     GFP   + R
Sbjct: 264 PTLGEVTQVILRH-----AELLAEHDGEDNASRDIRKHIGWYLRGFPVGGQVR 311


>gi|314932010|gb|EFS95841.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL067PA1]
          Length = 355

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 73/286 (25%), Positives = 115/286 (40%), Gaps = 25/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
            L   EMI +  ++ GD K   +L F+  E   ++Q+ G D   + EA  I+ E +G N 
Sbjct: 19  GLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVDPGMVGEATSILCEKYGVNH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD---IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D    V         A  +PVTVK RIG+D +   
Sbjct: 79  VDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDAHGVPVTVKTRIGIDPE--H 136

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  ++   SG   + +HAR                +  +D   E+ K      IG 
Sbjct: 137 ITYIDSARAAVDSGAAAVCLHARTVA--------EAYAGHSHWDATGELVKTVDVPVIG- 187

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S A  ++      GV +GR       +   + + F+   T + P    V    
Sbjct: 188 NGDIWEASDATAMVGQTGCAGVEVGRGCLGRPWLFRDLADAFAGRDTTTLPTLGEVCAMI 247

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+ +  +  Y   H      L  + +HM     GFP     RH+L
Sbjct: 248 -RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGETRHVL 287


>gi|315226975|ref|ZP_07868763.1| tRNA-dihydrouridine synthase B [Parascardovia denticolens DSM
           10105]
 gi|315121107|gb|EFT84239.1| tRNA-dihydrouridine synthase B [Parascardovia denticolens DSM
           10105]
          Length = 386

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 102/243 (41%), Gaps = 19/243 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A+   + K   +  F+  EK  +LQ+ G +
Sbjct: 24  MAGVTNWPFRLLCEGYGPDGLYVAEMITARALTARNPKAFRLCRFAPSEKFRSLQLYGVN 83

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
              + EAAK+V D    + ++LN GCP  +V     G+ L    D++ D I    A+C+ 
Sbjct: 84  PLVVEEAAKMVVDGDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQDLIHRVVAVCQP 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + IPVT K R+GVDD+     +    K I+  G   + +HAR          D  +I  L
Sbjct: 144 VGIPVTAKIRVGVDDE--HETMIEAAKIIEGEGCAFVTLHARTTAQYYGGHSDWSRIAQL 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE   + +  NG +     A+ +      DGV IGR       +   +   
Sbjct: 202 ---------KEAVSIPVIGNGDIWTAEDAMAMARQTGCDGVAIGRGCQGRPWLFGDIRNA 252

Query: 233 FSN 235
           F  
Sbjct: 253 FEG 255


>gi|146417549|ref|XP_001484743.1| hypothetical protein PGUG_02472 [Meyerozyma guilliermondii ATCC
           6260]
 gi|146390216|gb|EDK38374.1| hypothetical protein PGUG_02472 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 416

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 82/168 (48%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE------KPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K     +S Q+      +PL +Q 
Sbjct: 25  MVDQSELAWRIISRRY-GAELCYTPMFHARLFATEEKYRQNMWSEQDGDRELDRPLIVQF 83

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D + L+EAAK+VED   + ++LN+GCP     +G +GA LM + D+V   I  +   
Sbjct: 84  CANDPNYLLEAAKLVED-KCDAVDLNLGCPQGIAKKGKYGAFLMDDWDLVHKLIRTLHDN 142

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           L  PVT K R+  DD   ++A     K +  +G   I +H R   +KG
Sbjct: 143 LKCPVTAKIRV-YDDWEKSLA---YAKMVLDAGAQFITVHGRTRDMKG 186


>gi|223933531|ref|ZP_03625513.1| TIM-barrel protein, nifR3 family [Streptococcus suis 89/1591]
 gi|223897791|gb|EEF64170.1| TIM-barrel protein, nifR3 family [Streptococcus suis 89/1591]
          Length = 334

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 111/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K +  L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQKNTKANIVDINMGCPVNKVIKNEAGAKWLKDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++    +A+ N + + + +GV+ + +H R         ++      +D +
Sbjct: 143 PLTVKMRTGWNNT--DLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTVDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++      +    NG +  +  A + +  V  D VM+GR A  N  +   ++ Y  
Sbjct: 192 TLTKVAGSLTKIPFIANGDIRTVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLE 250


>gi|217076849|ref|YP_002334565.1| NifR3 family protein [Thermosipho africanus TCF52B]
 gi|217036702|gb|ACJ75224.1| NifR3 family protein [Thermosipho africanus TCF52B]
          Length = 296

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 58/201 (28%), Positives = 100/201 (49%), Gaps = 22/201 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           YTEMI A++++R  K N   F   E+   +A+QI G+D   + +AA ++E+ G   I++N
Sbjct: 31  YTEMISAESVIRNLKINEYYFPKPEEKDKVAIQIFGSDPFVMAKAASMLENMG-AWIDIN 89

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
            GCP  +V +   G+ L+ + + + + I  +  A+S  V+VK RIG +          + 
Sbjct: 90  AGCPVKKVVKKGAGSALLKDLNRLKNIIMQVKSAVSCKVSVKVRIGFEKD----EFEKIY 145

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            ++  +G + I +H R A  +  S K    I N  Y  +Y            +NG +  +
Sbjct: 146 DTVVDAGADMIAVHGRTA-KQMYSGKATWNIKNKGYIPLY------------INGDIHSL 192

Query: 201 SQALKIL--PSVDGVMIGRAA 219
           S A + +     DGV+I RA+
Sbjct: 193 SDAKRAMEISKADGVLIARAS 213


>gi|255349030|ref|ZP_05381037.1| putative oxidoreductase [Chlamydia trachomatis 70]
 gi|255503568|ref|ZP_05381958.1| putative oxidoreductase [Chlamydia trachomatis 70s]
 gi|255507248|ref|ZP_05382887.1| putative oxidoreductase [Chlamydia trachomatis D(s)2923]
 gi|289525687|emb|CBJ15168.1| putative oxidoreductase [Chlamydia trachomatis Sweden2]
 gi|296435255|gb|ADH17433.1| putative oxidoreductase [Chlamydia trachomatis E/150]
 gi|296438974|gb|ADH21127.1| putative oxidoreductase [Chlamydia trachomatis E/11023]
          Length = 334

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 74/299 (24%), Positives = 141/299 (47%), Gaps = 21/299 (7%)

Query: 19  NALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           +AL++ EM+  + +    ++ +  L F+   +P+  Q+ G+      E+AKI+E  G++ 
Sbjct: 38  SALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSRPDLAGESAKILEGLGFDL 97

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I+LN GCP+ R+ +   G+ ++  P+++G  +  M + +S+PVTVK R G D     + +
Sbjct: 98  IDLNCGCPTDRITKDGSGSGMLKTPELIGKVVEKMVEVVSVPVTVKIRSGWD--FDHINV 155

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
              V+ IK+SG + +++H R        P       NL++ I    +    D  +  NG 
Sbjct: 156 EETVRIIKESGASAVFVHGRTRSQGYQGPS------NLEF-ISRAKQAAGNDFPVFGNGD 208

Query: 197 LEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           +     A  +L +   DGV++ R       +   +++Y +   T SSP  +   + F + 
Sbjct: 209 VFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTG-TYSSPSFSTKKQAFVQH 267

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRHILTVEAGASTATHHIIE 312
           +      +   +  S  KL   TR + G +    P  R  R  L  +A +S   + +I+
Sbjct: 268 L-----QWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRANL-AKASSSQEVYQLID 320


>gi|257092432|ref|YP_003166073.1| TIM-barrel protein, nifR3 family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257044956|gb|ACV34144.1| TIM-barrel protein, nifR3 family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 350

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 117/246 (47%), Gaps = 29/246 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--------PLAL 52
           M   TDR +R   + +    L  +EM+ ++++L G  K      TQ +        P+++
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSAK------TQRRARHDGEVAPVSV 69

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI GA  + + +AA+   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+ 
Sbjct: 70  QIAGASPAMMADAARYNVDRGAQIIDINMGCPAKKICNVMAGSALLRDESLVARILEAVV 129

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            A+   PVT+K R G  D+    ALR +++  ++SG+  + +H R     G S       
Sbjct: 130 TAVPDTPVTLKIRTGW-DKTNRNALR-ILQIAEQSGIRALAMHGRTRAC-GYSGA----- 181

Query: 172 PNLDYDIVYEIKKENPDLFIGLNG--GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              +Y+ + E+K       I  NG  G  + +Q +  L   D VMIGRAA     +   +
Sbjct: 182 --AEYETIREVKAVARIPVIA-NGDIGSPEKAQFVLDLTGADAVMIGRAAQGRPWLFREI 238

Query: 230 DEYFSN 235
           + +  +
Sbjct: 239 EHFLES 244


>gi|262405017|ref|ZP_06081569.1| tRNA dihydrouridine synthase B [Vibrio sp. RC586]
 gi|262348856|gb|EEY97997.1| tRNA dihydrouridine synthase B [Vibrio sp. RC586]
          Length = 287

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 94/193 (48%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D  ++ EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++ + +  
Sbjct: 33  SVQIAGSDPQQMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIENILKT 92

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+++PVT+K R G D D    V++  L +     G+  + +H R    + KG     
Sbjct: 93  VVNAVNVPVTLKTRTGWDTDNKNCVSIAQLAED---CGIQALALHGRTRACMYKG----- 144

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K       I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 145 -----EAEYDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWI 198

Query: 226 LTTVDEYFSNPLT 238
              +  +  +  T
Sbjct: 199 FQEIQHFLEHGTT 211


>gi|329934687|ref|ZP_08284728.1| tRNA dihydrouridine synthase B [Streptomyces griseoaurantiacus
           M045]
 gi|329305509|gb|EGG49365.1| tRNA dihydrouridine synthase B [Streptomyces griseoaurantiacus
           M045]
          Length = 380

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 108/225 (48%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY-TEMIVADAIL-RGDKK-NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    LY +EMI   A++ R DK   ++ F   EKP ++Q+ G 
Sbjct: 24  MAGITNAPFRTLCREFSAGKGLYVSEMITTRALVERNDKTMQLIRFDASEKPRSIQLYGV 83

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ + G  + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 84  DPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRSILREAVSGAG 143

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+D+    +   +  +   + GV  I +H R A                D
Sbjct: 144 DLPVTMKMRKGIDED--HLTYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTAD 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 194 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRG 238


>gi|186477299|ref|YP_001858769.1| NifR3 family TIM-barrel protein [Burkholderia phymatum STM815]
 gi|184193758|gb|ACC71723.1| TIM-barrel protein, nifR3 family [Burkholderia phymatum STM815]
          Length = 357

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 70/307 (22%), Positives = 137/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 21  MAGVTDRPFRQLCKRM-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 80  PQMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVNAVGVG 139

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +     
Sbjct: 140 PDAVPVTLKIRTGWNRENKNAL--NVARLAESAGISMLTVHGRT--------RADLYHGE 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K    ++ +  NG +    +A  +L +   D +MIGRAA     +   ++ 
Sbjct: 190 AEYETIAAVKAA-VNIPVVANGDITSPHKARAVLAATDADAIMIGRAAQGRPWLFREIEH 248

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 249 FLQ---TGELMEAPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 300

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 301 GANVFRH 307


>gi|300780503|ref|ZP_07090359.1| tRNA-dihydrouridine synthase B [Corynebacterium genitalium ATCC
           33030]
 gi|300534613|gb|EFK55672.1| tRNA-dihydrouridine synthase B [Corynebacterium genitalium ATCC
           33030]
          Length = 388

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 70/303 (23%), Positives = 132/303 (43%), Gaps = 30/303 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   TD  +R   R +      T + L   EMI A A++ G++K  ++  F+ QE P ++
Sbjct: 27  MAGVTDMPFRVLCREIEEDLTGTVSGLYVCEMITARALVEGNEKTLHMTTFAPQETPRSM 86

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +A + IVE    + +++N GCP  +V     G+ +     +  + ++A 
Sbjct: 87  QLYTVDPEYTYKAVRMIVEGDMADHVDMNFGCPVPKVTRRGGGSAIPYKRGLYRNIVSAA 146

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            KA    +PVTVK R+G+DD+         + +  + G + + +HAR A  +     D  
Sbjct: 147 VKAADGRVPVTVKFRVGIDDEHKTHLDAGRIAA--EEGASAVTLHARTAAQRYSGTADWD 204

Query: 168 --NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             +R + ++D   +  +   N D+F   +   E+M +      + DGV++GR       +
Sbjct: 205 EISRLVEHMDGTGIPVLG--NGDIFASTDA--EEMMERT----ACDGVVVGRGCLGRPWL 256

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +       +  + P   +V      +I A   +  A H       +++ +H+     
Sbjct: 257 FAQLSAQLRGEVVPAEPTLGQV-----ARIMARHGELLAAHNGEERGCRELRKHVGWYLR 311

Query: 286 GFP 288
           GFP
Sbjct: 312 GFP 314


>gi|307719541|ref|YP_003875073.1| hypothetical protein STHERM_c18650 [Spirochaeta thermophila DSM
           6192]
 gi|306533266|gb|ADN02800.1| hypothetical protein STHERM_c18650 [Spirochaeta thermophila DSM
           6192]
          Length = 333

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 61/282 (21%), Positives = 121/282 (42%), Gaps = 20/282 (7%)

Query: 20  ALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           ++ YTEM+ A+ I+   G   +++    +E+   +Q+  +    L  A +++        
Sbjct: 44  SMTYTEMVSAEGIVYHTGKTFSLVQRGPEERFWGIQLFSSRPDMLARAVEVLSPLAPTLF 103

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP  +V +   GA LM +P+ V   + AM +A  +PVTVK R G D+   ++  R
Sbjct: 104 DLNCGCPVPKVVKTGAGAALMRDPERVYAMVKAMRQASPVPVTVKIRSGWDEH--SLTYR 161

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + ++  ++G   + +H R         +         ++ + ++K  +P   I  +G +
Sbjct: 162 EVAQAAFEAGAGAVCLHPRT--------RAQGYAGAARWEHIADLKARHPSHPIIASGDI 213

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                A  ++     D V++ R A     +   + +       G +PI  R   +  R  
Sbjct: 214 LSPEAARAVVEETGCDAVLVARGALGAPWIFRQIRDLQEK--GGYAPISLRERVETMR-- 269

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +  + A  +   G   +++ +HM     G P + R R  L
Sbjct: 270 --AHLERAIAYKGEGIACREMRKHMGWYVKGLPGAARVRERL 309


>gi|167837831|ref|ZP_02464714.1| dihydrouridine synthase [Burkholderia thailandensis MSMB43]
          Length = 354

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 118/249 (47%), Gaps = 31/249 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVDAVGTG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKA--ILKGLSPKDN 168
             ++PVT+K R G D +      RN V   K  + +G++ + +H R    + +G      
Sbjct: 137 PGAVPVTLKIRTGWDRE-----HRNAVEIAKLAEAAGISMLTVHGRTRADLYRG------ 185

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
               + +YD +  +K     + +  NG +    +A  +L +   D +MIGRAA     + 
Sbjct: 186 ----DAEYDTITAVKAA-VRIPVVANGDITSPQKAKAVLDATGADALMIGRAAQGRPWLF 240

Query: 227 TTVDEYFSN 235
             +  +  +
Sbjct: 241 REIGHFLQS 249


>gi|156102342|ref|XP_001616864.1| tRNA-dihydrouridine synthase [Plasmodium vivax SaI-1]
 gi|148805738|gb|EDL47137.1| tRNA-dihydrouridine synthase, putative [Plasmodium vivax]
          Length = 340

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 69/256 (26%), Positives = 114/256 (44%), Gaps = 24/256 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ A   +  +K     F + EK  P+  Q  G +
Sbjct: 33  MVDLSELAFRLLCRNY-NCHLTFTPMLHAKNFVEHEKYRKSYFQSCEKDEPVIAQFCGNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ A + +++   N ++LN+GCP     +G++GA L+   D V + ++ +    +IP
Sbjct: 92  SKIILNAIEYIKN-EVNAVDLNLGCPQQIAKKGNYGAFLLQKHDEVVNLVSDITNNCNIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T  C+I   DQ     L NL   ++   V  I +H R    KG +      I   DY+I
Sbjct: 151 IT--CKIRKIDQDYQKTL-NLCYDLQSRNVKMITVHGRTKEEKGTN------IKQCDYEI 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA--------AYKNSAMLTT 228
           + +I KE  ++ I  NG +E      K L     D VM            + +N   +  
Sbjct: 202 I-KIIKERLNIPIIANGSIEHFEDIQKCLNYTKADAVMCAEILLEKPYFFSNQNVHTVDV 260

Query: 229 VDEYFSNPLTGSSPIK 244
           V+EY+   L   S  K
Sbjct: 261 VNEYYDLFLQYESNTK 276


>gi|301326298|ref|ZP_07219671.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 78-1]
 gi|300846999|gb|EFK74759.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 78-1]
          Length = 321

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +   + +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNTVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|237751061|ref|ZP_04581541.1| transcriptional regulator [Helicobacter bilis ATCC 43879]
 gi|229373506|gb|EEO23897.1| transcriptional regulator [Helicobacter bilis ATCC 43879]
          Length = 320

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/206 (30%), Positives = 105/206 (50%), Gaps = 20/206 (9%)

Query: 24  TEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLN 80
           +EMI + A++  ++K +     S  E P +LQI G+    L  A + + +  + +I + N
Sbjct: 29  SEMISSHALVYENEKTLKMALKSPNETPFSLQISGSKEEILKRAVEKINELSWVDIIDFN 88

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV-TVKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + D     +  + K  +  V +VK R+G D +IP     +L
Sbjct: 89  CGCPAPKVANHGNGSALLKDLDKFVSLLQIIRKYGNKQVYSVKVRLGFDKKIPL----DL 144

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---G 196
            ++I +S V+   +HAR  +       D  K   +DYD +  + KEN  + +  NG   G
Sbjct: 145 AEAINESSVDYCVVHARTKM-------DAYKKDKIDYDSL-ALMKENLKIPMIANGEIDG 196

Query: 197 LEDMSQALKILPSVDGVMIGRAAYKN 222
           LE   + ++I  + DG MIGRAA K+
Sbjct: 197 LESFQKVMQI-TNADGAMIGRAALKS 221


>gi|156364501|ref|XP_001626386.1| predicted protein [Nematostella vectensis]
 gi|156213260|gb|EDO34286.1| predicted protein [Nematostella vectensis]
          Length = 288

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 110/239 (46%), Gaps = 23/239 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    + +  M + D I R +   ++     ++PL +Q   
Sbjct: 33  MVDQSELAWRMLSRRYGAELCYTPMFHAGMFIRDPIYRSE---MMQTCVGDRPLIVQFCA 89

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA +VE    + ++LN+GCP      G +GA L    +++   +    + LS
Sbjct: 90  NDPEVFVQAALLVES-ECDGVDLNLGCPQHIAKRGHYGAFLQDEWELLEKMVKLAHEKLS 148

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-D 175
           +P+T K R+  DD    +A   +++S   +G   + +H R       + +  R++  L D
Sbjct: 149 VPITCKIRV-FDDVQKTIAYAKMLES---AGCQLLTVHGR-------TREQKRELTGLAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +D +  + +EN ++ +  NG ++ +S   + L     +GVM       N A+ T    Y
Sbjct: 198 WDQIKAV-RENLNIPVFANGNIQYLSDVTRCLEYTGCNGVMTAEGNLSNPALFTGSQPY 255


>gi|219666230|ref|YP_002456665.1| hypothetical protein Dhaf_0161 [Desulfitobacterium hafniense DCB-2]
 gi|219536490|gb|ACL18229.1| TIM-barrel protein, nifR3 family [Desulfitobacterium hafniense
           DCB-2]
          Length = 321

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 68/305 (22%), Positives = 138/305 (45%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R +     ++TEMI   A+   + + +  L  S +  P  +Q+ G++
Sbjct: 17  MAGVTDKAFRETVRSV-GGLHVWTEMISDKALTYMNSRTLEMLDLSGEASPRIVQLFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +  +     I++N+GCP+ ++ +   G+ L+ +  +      A+ KA+ +P
Sbjct: 76  PEVMAKAAALAVERDAEIIDINMGCPTPKIVKNGEGSALLQDLPLAQRIAEAVVKAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G   +   +    L K ++  GV  + +H   R+    G + +D         
Sbjct: 136 VTVKMRLGWTAE--RIVAPELAKRVEAVGVQMVSVHGRTREQFYAGTANRDG-------- 185

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
                IKK    + I +  NG +    +A  +L +   DGVM+GR +  N  ++  ++ +
Sbjct: 186 -----IKKVKGGVSIPVIANGDIFSPQEAKTVLEATGCDGVMVGRGSLGNPWLIPQINVF 240

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPN 289
            +  +    P          +K+  + T++  R L+  G+   L ++ +H +    G  N
Sbjct: 241 LNKGVLLEEP-------SLEQKLKVA-TEHFERVLNYKGERIGLNEMRKHAVWYIKGIRN 292

Query: 290 SRRCR 294
           + + R
Sbjct: 293 AAQMR 297


>gi|83952210|ref|ZP_00960942.1| tRNA-dihydrouridine synthase, putative [Roseovarius nubinhibens
           ISM]
 gi|83837216|gb|EAP76513.1| tRNA-dihydrouridine synthase, putative [Roseovarius nubinhibens
           ISM]
          Length = 331

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 91/312 (29%), Positives = 140/312 (44%), Gaps = 53/312 (16%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           RF A L+ +  +   EM+ A   +R  ++  LGF  +    A+Q+ G D   L EAA++V
Sbjct: 33  RFGAGLVVSEMVASQEMVQAKPGVR--ERAELGFGVENT--AVQLAGCDAEWLAEAARMV 88

Query: 70  EDFGYNEINLNVGCPSARVHE----GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           E  G   I++N+GCP+ +V      G+ G+ LM  PD     I A+ +A+ +PVT+K R+
Sbjct: 89  EANGAKIIDINMGCPAKKVTSASGNGASGSALMKTPDHALRLIEAVVEAVEVPVTLKTRL 148

Query: 126 GVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVY 180
           G D+ +   P +A R      + +GV  I IH R      KG +          D+  + 
Sbjct: 149 GWDEDLLNAPEIAAR-----AEAAGVQMITIHGRTRCQFYKGRA----------DWAAIA 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + KE   + +  NG +    +A   L     DGVMIGR A     +L  V    +  L 
Sbjct: 194 RV-KEAVAVPVIANGDITGPDEARTALAQSGGDGVMIGRGAQGRPWVLAQV----AAELW 248

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHS-----GGKLQ-QITRHMIGLFH---GFPN 289
           G++P              A + D  + H        GG L  ++ R  +G +    G P 
Sbjct: 249 GAAPPDV--------PQGAELVDLVSDHYDEMLRFYGGDLGLRVARKHLGWYMDGVGTPA 300

Query: 290 SRRCRHILTVEA 301
           + R R ILT  A
Sbjct: 301 NLR-RPILTARA 311


>gi|294787455|ref|ZP_06752708.1| putative tRNA-dihydrouridine synthase [Parascardovia denticolens
           F0305]
 gi|294484811|gb|EFG32446.1| putative tRNA-dihydrouridine synthase [Parascardovia denticolens
           F0305]
          Length = 417

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 103/241 (42%), Gaps = 15/241 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A+   + K   +  F+  EK  +LQ+ G +
Sbjct: 55  MAGVTNWPFRLLCEGYGPDGLYVAEMITARALTARNPKAFRLCRFAPSEKFRSLQLYGVN 114

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
              + EAAK+V D    + ++LN GCP  +V     G+ L    D++ D I    A+C+ 
Sbjct: 115 PLVVEEAAKMVVDGDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQDLIHRVVAVCQP 174

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + IPVT K R+GVDD+     +    K I+  G   + +HAR          D  +I  L
Sbjct: 175 VGIPVTAKIRVGVDDE--HETMIEAAKIIEGEGCAFVTLHARTTAQYYGGHSDWSRIAQL 232

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
              +   +   N D++       ED + A+      DGV IGR       +   +   F 
Sbjct: 233 KEAVSIPVIG-NGDIWTA-----ED-AMAMARQTGCDGVAIGRGCQGRPWLFGDIRNAFE 285

Query: 235 N 235
            
Sbjct: 286 G 286


>gi|297199529|ref|ZP_06916926.1| dihydrouridine synthase [Streptomyces sviceus ATCC 29083]
 gi|297147421|gb|EDY56956.2| dihydrouridine synthase [Streptomyces sviceus ATCC 29083]
          Length = 395

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 109/242 (45%), Gaps = 17/242 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   EKP ++Q+ G 
Sbjct: 40  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLVHFDESEKPRSIQLYGV 99

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKAL 115
           D + + +A +++ + G  + I+LN GCP  +V     G+ L    P +      A+  A 
Sbjct: 100 DPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSGAG 159

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 160 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVTAIALHGRTA--------SQHYGGTAD 209

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       + + +   F
Sbjct: 210 WDAIARLKEHVPEIPVLGNGDIWSARDALRMVRETGCDGVVVGRGCLGRPWLFSDLVAAF 269

Query: 234 SN 235
             
Sbjct: 270 EG 271


>gi|16766679|ref|NP_462294.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|62181892|ref|YP_218309.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|167552906|ref|ZP_02346657.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167993972|ref|ZP_02575065.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168233971|ref|ZP_02659029.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168239413|ref|ZP_02664471.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168245212|ref|ZP_02670144.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168463378|ref|ZP_02697295.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168822715|ref|ZP_02834715.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443531|ref|YP_002042640.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194450924|ref|YP_002047412.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194468944|ref|ZP_03074928.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194737360|ref|YP_002116332.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197247823|ref|YP_002148308.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197262350|ref|ZP_03162424.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198242306|ref|YP_002217354.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387464|ref|ZP_03214076.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204931223|ref|ZP_03222017.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205354285|ref|YP_002228086.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858632|ref|YP_002245283.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213051972|ref|ZP_03344850.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213428299|ref|ZP_03361049.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213580280|ref|ZP_03362106.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
 gi|213619017|ref|ZP_03372843.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213853023|ref|ZP_03382555.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|238913536|ref|ZP_04657373.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|60392220|sp|P0A2R6|DUSB_SALTY RecName: Full=tRNA-dihydrouridine synthase B
 gi|60392221|sp|P0A2R7|DUSB_SALTI RecName: Full=tRNA-dihydrouridine synthase B
 gi|16421945|gb|AAL22253.1| putative TIM-barrel enzyme [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|62129525|gb|AAX67228.1| putative TIM-barrel enzyme, possibly dehydrogenase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|194402194|gb|ACF62416.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194409228|gb|ACF69447.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194455308|gb|EDX44147.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194712862|gb|ACF92083.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|195633240|gb|EDX51654.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197211526|gb|ACH48923.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197240605|gb|EDY23225.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197287911|gb|EDY27299.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|197936822|gb|ACH74155.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199604562|gb|EDZ03107.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204319990|gb|EDZ05196.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205274066|emb|CAR39072.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205322522|gb|EDZ10361.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205328090|gb|EDZ14854.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205332030|gb|EDZ18794.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205336039|gb|EDZ22803.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205340899|gb|EDZ27663.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|206710435|emb|CAR34793.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|261248547|emb|CBG26385.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995593|gb|ACY90478.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159933|emb|CBW19452.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|320087832|emb|CBY97596.1| putative dehydrogenase [Salmonella enterica subsp. enterica serovar
           Weltevreden str. 2007-60-3289-1]
 gi|322643429|gb|EFY39993.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322684757|gb|EFY80758.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716382|gb|EFZ07953.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131746|gb|ADX19176.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323209994|gb|EFZ94899.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323219032|gb|EGA03538.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323247308|gb|EGA31273.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323263870|gb|EGA47389.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|326625133|gb|EGE31478.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629408|gb|EGE35751.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990242|gb|AEF09225.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 321

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + +  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPIIA-NGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|168262591|ref|ZP_02684564.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205348570|gb|EDZ35201.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 321

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + +  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRTVKQKVSIPIIA-NGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|16331567|ref|NP_442295.1| hypothetical protein slr0644 [Synechocystis sp. PCC 6803]
 gi|2833467|sp|Q55724|DUS1_SYNY3 RecName: Full=Probable tRNA-dihydrouridine synthase 1
 gi|1001634|dbj|BAA10365.1| slr0644 [Synechocystis sp. PCC 6803]
          Length = 355

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 106/235 (45%), Gaps = 16/235 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKL 62
           TD  +R   R     A+LYTEM+ A  I  LR     ++    +E P+++Q+       +
Sbjct: 53  TDLVFRRLVRRYAPQAMLYTEMVSATEIHHLR-TLPQVMEIDPRENPISIQLFDCRPDFM 111

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+     G   +++N+GCP  ++ +   G+ L+  P +    +  +  A+ +PVTVK
Sbjct: 112 AEAAQKAVAQGAQSVDINMGCPVNKITKKGGGSSLLRQPAVAEAIVKTVVAAVDVPVTVK 171

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G DD    + +    + ++ +G   + +H R    +G + +         +  + ++
Sbjct: 172 TRLGWDDG--EINIVEFAQRLQDAGAQMLTLHGRTRA-QGYNGRAR-------WQWIAKV 221

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           K+      I  NG +  +  A+  L     DGVM  R +     ++  ++ +F  
Sbjct: 222 KQALTIPVIA-NGDIFSVEAAIACLEETGADGVMCSRGSLGYPFLVGEIEHFFKT 275


>gi|304396993|ref|ZP_07378873.1| TIM-barrel protein, nifR3 family [Pantoea sp. aB]
 gi|304355789|gb|EFM20156.1| TIM-barrel protein, nifR3 family [Pantoea sp. aB]
          Length = 321

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRALCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+++P
Sbjct: 76  PSEMAQAARINVEAGAQVIDINMGCPAKKVNRKMAGSALLQYPTVVESILSAVVNAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D +    VA+  L    ++ G+  + IH R    +  G            +
Sbjct: 136 VTLKIRTGWDPENRNCVAIAQLA---ERCGIQALTIHGRTRACLFNG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|161616409|ref|YP_001590374.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|161365773|gb|ABX69541.1| hypothetical protein SPAB_04218 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 305

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 1   MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 60  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G           
Sbjct: 120 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 164

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + +  +A  +L     D +MIGRAA     +   +  
Sbjct: 165 AEYDSIRAVKQKVSIPIIA-NGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 223

Query: 232 YF 233
           Y 
Sbjct: 224 YL 225


>gi|283851081|ref|ZP_06368365.1| dihydrouridine synthase DuS [Desulfovibrio sp. FW1012B]
 gi|283573477|gb|EFC21453.1| dihydrouridine synthase DuS [Desulfovibrio sp. FW1012B]
          Length = 329

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 46/160 (28%), Positives = 81/160 (50%), Gaps = 4/160 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R L   A + TEM+ A  +    K  + +L  +  + PLA+Q+ GA+
Sbjct: 17  LAGFSDLPFRLLCRELGACAAV-TEMVSAKGLFYDSKNTRRLLATTPADAPLAVQLFGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  A   +   GY   +LN GC   +V +   GA L+ +PD + DC  AM +A ++P
Sbjct: 76  PEYLFRAVASLAGDGYALFDLNCGCSVRKVVKTGAGAALLGDPDRLVDCARAMARA-ALP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             V  ++ +  + P+ A  +L + +  +GV  + +H R A
Sbjct: 135 GRVGVKLRLGPKPPSFAALDLARRLADAGVAWLTLHPRHA 174


>gi|195386396|ref|XP_002051890.1| GJ17247 [Drosophila virilis]
 gi|194148347|gb|EDW64045.1| GJ17247 [Drosophila virilis]
          Length = 504

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 108/237 (45%), Gaps = 25/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+  A     +K+ L     ++PL +Q  G D
Sbjct: 32  MVDQSELAWRMLCRRYGAQ-LCYSPMYHANLFATDLKYRKDALQTCPADRPLIIQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA   +D   + +++N+GCP A    G +GA L     ++   +  + + LS+P
Sbjct: 91  PQQMLEAALAAQDHC-DAVDINLGCPQAIAKRGHYGAFLQDEWQLLTQIVRTLHEQLSVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +       N  K ++ +G   + +H R    K  L G++          
Sbjct: 150 VTCKIRIFEDRE----KTINYAKMLEAAGCQLLTVHGRTREQKGPLTGIA---------- 195

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D+  + ++++  + P    G   GLED+ + L+    VDGVM       N A+   +
Sbjct: 196 DWSYIKDVRQHIKIPMFANGNILGLEDVHRCLEAT-GVDGVMTAEGNLHNPAIFQGI 251


>gi|238896768|ref|YP_002921513.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae NTUH-K2044]
 gi|262042817|ref|ZP_06015970.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|329997541|ref|ZP_08302819.1| tRNA-dihydrouridine synthase B [Klebsiella sp. MS 92-3]
 gi|238549095|dbj|BAH65446.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259039884|gb|EEW41002.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328539024|gb|EGF65068.1| tRNA-dihydrouridine synthase B [Klebsiella sp. MS 92-3]
          Length = 321

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G + +      RN V   +  ++ G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGWEPE-----HRNCVEIAQLAEECGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|260943748|ref|XP_002616172.1| hypothetical protein CLUG_03413 [Clavispora lusitaniae ATCC 42720]
 gi|238849821|gb|EEQ39285.1| hypothetical protein CLUG_03413 [Clavispora lusitaniae ATCC 42720]
          Length = 367

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 107/232 (46%), Gaps = 19/232 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL  N  L+Y+ MI+A   +R        FST  ++ PL +Q+G ++
Sbjct: 50  MVRYSKLPFRELVRLY-NTDLVYSPMILAREFVRNGTARATDFSTNSRDSPLVVQVGASN 108

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV    ++ +   + I LN GCP   +V EG  GA LM  P+ V   + A+ +    
Sbjct: 109 AQDLVRFVDLIHEH-VDAIGLNCGCPIRDQVREG-IGAALMSQPENVASMVRAVKEKYGA 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V V+ +I +   +    LR  VK ++++GV+ I +H R    +   P         ++ 
Sbjct: 167 RVLVETKIRIHPDLQET-LR-WVKLVEEAGVDWITVHGRTRTTRSSQPA--------NWA 216

Query: 178 IVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            + E+KK    P +  G    LED  +  +     DGVM  R    N A+ +
Sbjct: 217 AIAEVKKAASVPVVANGDCFSLEDARRMARET-GCDGVMAVRGILANPALFS 267


>gi|86750001|ref|YP_486497.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris HaA2]
 gi|86573029|gb|ABD07586.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodopseudomonas
           palustris HaA2]
          Length = 354

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 98/205 (47%), Gaps = 20/205 (9%)

Query: 21  LLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM  ++ +++G   ++    +  + P  +Q+ G +   + EAA+I E  G + I++
Sbjct: 57  LVVSEMTASEDLVQGRAMSVRRCDAIDDGPHVVQLAGCEPHWMAEAARIAEAGGADIIDI 116

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ---IPAVAL 136
           N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G DD+    P +A 
Sbjct: 117 NMGCPARHVTGGQSGSALMRDLDHALTLIEATIGAVRVPVTLKMRLGWDDRSRNAPELAR 176

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           R     ++   V+G     R    KG            D+  V  + ++   + + +NG 
Sbjct: 177 RAEAAGVQLVTVHG---RTRSQFYKG----------EADWRAVRAV-RDAVGIPLVVNGD 222

Query: 197 LEDMSQALKIL--PSVDGVMIGRAA 219
           +     A++ L     D VMIGR A
Sbjct: 223 ITSYQMAVEALDQSGADAVMIGRGA 247


>gi|89892963|ref|YP_516450.1| hypothetical protein DSY0217 [Desulfitobacterium hafniense Y51]
 gi|89332411|dbj|BAE82006.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 326

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 68/305 (22%), Positives = 138/305 (45%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R +     ++TEMI   A+   + + +  L  S +  P  +Q+ G++
Sbjct: 22  MAGVTDKAFRETVRSV-GGLHVWTEMISDKALTYMNSRTLEMLDLSGEASPRIVQLFGSE 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +  +     I++N+GCP+ ++ +   G+ L+ +  +      A+ KA+ +P
Sbjct: 81  PEVMAKAAALAVERDAEIIDINMGCPTPKIVKNGEGSALLQDLPLAQRIAEAVVKAVEVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
           VTVK R+G   +   +    L K ++  GV  + +H   R+    G + +D         
Sbjct: 141 VTVKMRLGWTAE--RIVAPELAKRVEAVGVQMVSVHGRTREQFYAGTANRDG-------- 190

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
                IKK    + I +  NG +    +A  +L +   DGVM+GR +  N  ++  ++ +
Sbjct: 191 -----IKKVKGGVSIPVIANGDIFSPQEAKTVLEATGCDGVMVGRGSLGNPWLIPQINVF 245

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPN 289
            +  +    P          +K+  + T++  R L+  G+   L ++ +H +    G  N
Sbjct: 246 LNKGVLLEEP-------SLEQKLKVA-TEHFERVLNYKGERIGLNEMRKHAVWYIKGIRN 297

Query: 290 SRRCR 294
           + + R
Sbjct: 298 AAQMR 302


>gi|242013989|ref|XP_002427681.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212512111|gb|EEB14943.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 557

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 105/214 (49%), Gaps = 16/214 (7%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLN 80
           +EM +A ++L+G K    ++     E    +Q+ G +   + + A+++E+    + I++N
Sbjct: 238 SEMAMATSLLQGLKYEWALIKRHESEDLFGIQLCGNNPFVMTKCAQLLEESTNVDYIDIN 297

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP   V++   G+ L+    ++   I +M K +S+P+TVK R GV      VA R L+
Sbjct: 298 LGCPIDLVYQKGGGSGLLRREKVLESVIKSMSKVMSLPLTVKTRTGVYAD-KNVAHR-LI 355

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GL 197
                SGV+ I +H R         ++ R     D++ + E  K    + +  NG     
Sbjct: 356 PMFVDSGVSLITVHGRS--------REQRYTRTADWNYINECGKAASPIPVFGNGDVLSF 407

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ED ++ALK   +V GVM+GR A     +   + E
Sbjct: 408 EDYNRALKENNNVSGVMVGRGALYKPWIFKEIKE 441


>gi|91793740|ref|YP_563391.1| dihydrouridine synthase, DuS [Shewanella denitrificans OS217]
 gi|91715742|gb|ABE55668.1| dihydrouridine synthase, DuS [Shewanella denitrificans OS217]
          Length = 319

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 101/206 (49%), Gaps = 25/206 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G N ++ N GCP+  V+    GA L+  P
Sbjct: 59  GMTANGTPVRVQLLGQEPQCMAENAVRAIELGSNGVDANFGCPAKMVNRSKGGAVLLQCP 118

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D V D + AM +A+S   PVT K R+G +D+  ++ + N + ++ ++G   + IHAR   
Sbjct: 119 DKVHDIVKAMRQAVSSEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHAR--- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
               S  D  K P   ++ + E+++  P   I  NG +   ED  + +++    D VMIG
Sbjct: 173 ----SKTDGYKPPAY-WEYITEVRQRLPIPVIA-NGEIWSAEDARRCIEVT-GCDSVMIG 225

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSP 242
           R A     +  T+        TG++P
Sbjct: 226 RGAISLPNLADTIK-------TGAAP 244


>gi|121595878|ref|YP_987774.1| nifR3 family TIM-barrel protein [Acidovorax sp. JS42]
 gi|120607958|gb|ABM43698.1| tRNA-U20-dihydrouridine synthase [Acidovorax sp. JS42]
          Length = 353

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 74/312 (23%), Positives = 128/312 (41%), Gaps = 33/312 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+A+QI
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 71

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G D + +  AA    D G   I++N+GCP+ +V     G+ LM N  +   + + + A 
Sbjct: 72  AGTDAAMMAVAALYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAEAVVAA 131

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           C    +PVT+K R G   Q     +  L +  +  G+  + +H R         ++    
Sbjct: 132 CAPRGVPVTLKMRTGWCQQHKNAVV--LARRFEDVGIQMLTVHGRT--------REQGYK 181

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTV 229
              +YD +  +K     + +  NG +    +A  +L +   D VMIGRAA     +   +
Sbjct: 182 GQAEYDTIAAVKAAV-RVPVVANGDITSPEKARAVLAATGADAVMIGRAAQGRPWIFREI 240

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
             Y +     + P+   V     R +   + D+   +  + G ++   +H+       P 
Sbjct: 241 GHYLATGEHLAPPLVAEVR----RLLLEHLQDHYGLYGEASG-VRSARKHIAWYVRALPG 295

Query: 290 SRRCR-HILTVE 300
               R HI T+E
Sbjct: 296 GEALRQHINTIE 307


>gi|148361172|ref|YP_001252379.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|296108507|ref|YP_003620208.1| tRNA-dihydrouridine synthase B [Legionella pneumophila 2300/99
           Alcoy]
 gi|148282945|gb|ABQ57033.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|295650409|gb|ADG26256.1| tRNA-dihydrouridine synthase B [Legionella pneumophila 2300/99
           Alcoy]
          Length = 328

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 115/240 (47%), Gaps = 26/240 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G +   L EAA
Sbjct: 33  FRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKLLAYQISGNEPYLLAEAA 92

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
             ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+T+K RI 
Sbjct: 93  AKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISRVRAAISIPLTIKIRIQ 152

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            +++   +A     K I+ +G + + +H R+       P + ++I N+         K  
Sbjct: 153 NNEKDLTLA-----KQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI---------KNA 198

Query: 187 PDLFIGLNGGLED---MSQALKILPSVDGVMIGRAA------YKNSAMLTTVDEYFSNPL 237
            ++ + +NG + +   + +AL+I  + DG MI RA       Y++   L T D  F   L
Sbjct: 199 VNIPVIVNGDINNIFSLRKALEI-SACDGFMISRAGTGKPWLYRDLLNLETNDVAFDEKL 257


>gi|328789228|ref|XP_623799.3| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 2 [Apis
           mellifera]
          Length = 478

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 84/166 (50%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R    + L YT M+ +    R  K  +  L  + +++PL +Q  G D
Sbjct: 37  MVDASELAWRLLSRRHGAH-LCYTPMLHSSVFCRDPKYRREALASTAEDRPLVVQFCGND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S L+EAA + E +  + +++N+GCP A    G +GA L  + +++   ++ + K L +P
Sbjct: 96  PSTLLEAALLAEPYC-DAVDINIGCPQAIAKRGHYGAFLQDDWNLLQQIVSTLSKKLHVP 154

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           VT K R+   +D  +         + ++ +G   + +H R    KG
Sbjct: 155 VTCKLRVFAEIDKTV------KYAQMLEAAGAQLLTVHGRTREQKG 194


>gi|89075353|ref|ZP_01161775.1| putative Dihydrouridine synthase [Photobacterium sp. SKA34]
 gi|90581290|ref|ZP_01237087.1| putative Dihydrouridine synthase [Vibrio angustum S14]
 gi|89048902|gb|EAR54471.1| putative Dihydrouridine synthase [Photobacterium sp. SKA34]
 gi|90437529|gb|EAS62723.1| putative Dihydrouridine synthase [Vibrio angustum S14]
          Length = 321

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/244 (25%), Positives = 112/244 (45%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L    K  N +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPDLWKTSKSLNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  P+++ D + ++  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQYPNLIEDILRSVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D     +  RN V   K  ++ G+  + +H R    + KG           
Sbjct: 136 VTLKTRTGWD-----LENRNCVDIAKLAEQCGIQALALHGRTKACMYKG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  
Sbjct: 181 AEYDYIRAVKQAISIPVIA-NGDIDSPEKARFVLDYTGADALMIGRPAQGKPWIFREIHH 239

Query: 232 YFSN 235
           Y + 
Sbjct: 240 YLTT 243


>gi|148828154|ref|YP_001292907.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittGG]
 gi|148719396|gb|ABR00524.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittGG]
          Length = 326

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 113/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  P +V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPYLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 136 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 190 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 238


>gi|146319624|ref|YP_001199336.1| tRNA-dihydrouridine synthase [Streptococcus suis 05ZYH33]
 gi|146321822|ref|YP_001201533.1| tRNA-dihydrouridine synthase [Streptococcus suis 98HAH33]
 gi|145690430|gb|ABP90936.1| tRNA-dihydrouridine synthase [Streptococcus suis 05ZYH33]
 gi|145692628|gb|ABP93133.1| tRNA-dihydrouridine synthase [Streptococcus suis 98HAH33]
 gi|292559241|gb|ADE32242.1| Dihydrouridine synthase [Streptococcus suis GZ1]
          Length = 344

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 110/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K +  L     E P+++Q+ G D
Sbjct: 34  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 92

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 93  AEGLKRAADFIQKNTKANIVDINMGCPVNKVIKNEAGAKWLKDPDKIYHIIKEVTSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++    +A+ N + + +  GV  + +H R         ++      +D +
Sbjct: 153 PLTVKMRTGWNNT--DLAVENALAA-ESGGVAALAMHGRT--------REQMYTGTVDLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++      +    NG + ++  A + +  V  D VM+GR A  N  +   ++ Y  
Sbjct: 202 TLTKVAGSLTKIPFIANGDIRNVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLE 260


>gi|224438190|ref|ZP_03659125.1| hypothetical protein HcinC1_09430 [Helicobacter cinaedi CCUG 18818]
 gi|313144635|ref|ZP_07806828.1| transcriptional regulator [Helicobacter cinaedi CCUG 18818]
 gi|313129666|gb|EFR47283.1| transcriptional regulator [Helicobacter cinaedi CCUG 18818]
          Length = 328

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 56/202 (27%), Positives = 103/202 (50%), Gaps = 18/202 (8%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLN 80
           +EMI + A++  +K+ +     S QE+P ++QI G+    + +A +I+      + I+LN
Sbjct: 35  SEMISSHALVYSNKRTLKMTEKSPQEQPYSVQISGSKEEVIKQAVEILNTQKDIDIIDLN 94

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + +++      + +    P T +K R+G D +IP      +
Sbjct: 95  CGCPAPKVANHGNGSGLLKDLNLLVKIANLIKENAKTPYTSLKVRLGFDKKIP----HEI 150

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +++K    + + +H R       +  D  K   +DYD +  IK+  P   I  NG ++ 
Sbjct: 151 AQALKDVKSDFVVVHGR-------TRADGYKKEKIDYDAIAYIKQNIPMPLIA-NGEIDS 202

Query: 200 MSQALKILPSV--DGVMIGRAA 219
           + +A K+L     +GVMIGRAA
Sbjct: 203 VEKAQKVLEHTGANGVMIGRAA 224


>gi|326428503|gb|EGD74073.1| tRNA-dihydrouridine synthase [Salpingoeca sp. ATCC 50818]
          Length = 521

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 91/179 (50%), Gaps = 25/179 (13%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+G AD  + VE AK+VE+     I++N+GCP     +G  GA L+  PD+  D +AA+
Sbjct: 101 FQMGTADPQRAVEVAKLVEN-DVAGIDVNMGCPKNFSIKGGMGAALLREPDLAYDIMAAL 159

Query: 112 CKALSIPVTVKCRIGVDDQIPA-VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            KA+ +PVT K R+     +P   A  + +K ++ +G+  I +H R   L+   P++  +
Sbjct: 160 TKAVKVPVTCKIRL-----LPTREATMSFMKRMQSTGIAAIGLHGR---LREQRPREPVQ 211

Query: 171 IPNLDYDIVYEIKKENPDLFIGL--NGG---LEDMSQALKILPSV--DGVMIGRAAYKN 222
           +  +   I         D+ I +  NGG    ++ S+A   +     D +MI RAA  N
Sbjct: 212 LDAMTAAI--------GDMHIPVIANGGSLDFKNYSEAHAWMEKTGCDSLMIARAAQNN 262


>gi|161506059|ref|YP_001573171.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867406|gb|ABX24029.1| hypothetical protein SARI_04246 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 321

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G  
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGGS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILVGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+E     I  NG + +  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQEVSIPIIA-NGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|307611733|emb|CBX01438.1| hypothetical protein LPW_31271 [Legionella pneumophila 130b]
          Length = 328

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 111/239 (46%), Gaps = 24/239 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G +   L EAA
Sbjct: 33  FRDLFNIYTPPAYCVSEMCSAIDILHKHSPQSRYIYRAPTEKLLAYQISGNEPHVLAEAA 92

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
             ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+T+K RI 
Sbjct: 93  AKLQSLGADLIDINCGCPKSKICKKGAGSALLEDPQKLIAIISKVRAAISIPLTIKIRIQ 152

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            +++        L K I+ +G + + +H R+       P + ++I N+         K  
Sbjct: 153 NNEKD-----LTLAKQIEGAGAHALIVHGRRWTEDYDIPCNWQQIANI---------KNA 198

Query: 187 PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA------YKNSAMLTTVDEYFSNPL 237
            ++ + +NG + ++S   K L     DG MI RA       Y++   L T D  F   L
Sbjct: 199 VNIPVIVNGDISNISSLRKALEISVCDGFMISRAGTGKPWLYRDLLNLETNDVAFDEKL 257


>gi|38604767|sp|Q87KU1|DUSB_VIBPA RecName: Full=tRNA-dihydrouridine synthase B
 gi|328472220|gb|EGF43090.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus 10329]
          Length = 322

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 110/245 (44%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L      K  +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P I+ + + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPTIIEEILKAVVNAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L +     G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 183 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYL 241

Query: 234 SNPLT 238
            N  T
Sbjct: 242 ENGTT 246


>gi|308188309|ref|YP_003932440.1| dehydrogenase [Pantoea vagans C9-1]
 gi|308058819|gb|ADO10991.1| putative dehydrogenase [Pantoea vagans C9-1]
          Length = 321

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+++P
Sbjct: 76  PSEMAQAARINVEAGAQVIDINMGCPAKKVNRKMAGSALLQYPAVVESILSAVVNAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D +    VA+  L    ++ G+  + IH R    +  G            +
Sbjct: 136 VTLKIRTGWDPENRNCVAIAQLA---ERCGIQALTIHGRTRACLFNG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|291516129|emb|CBK69745.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. longum F8]
          Length = 414

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  + I    A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELIQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 174 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|218778247|ref|YP_002429565.1| dihydrouridine synthase DuS [Desulfatibacillum alkenivorans AK-01]
 gi|218759631|gb|ACL02097.1| dihydrouridine synthase DuS [Desulfatibacillum alkenivorans AK-01]
          Length = 328

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 103/224 (45%), Gaps = 16/224 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
           M   T   +R    L     LLYT M  A ++   + K    FS +EK L     QI G+
Sbjct: 17  MAGLTHIAFREVMALYGGYGLLYTGMAGAKSVPHENPKVSTVFSWREKELDHTVCQIFGS 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
               + +AA+ +E  G+  +++N GC +  +     GA L+  PD+    + A+ KA++I
Sbjct: 77  VPETMAKAAERIEAEGFFGVDINCGCSARAICRFDSGAALLAKPDLAAQVVRAVRKAVNI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G  D  PA A+ ++ +     G + +  H R      ++P    + P  +Y 
Sbjct: 137 PVIVKFRTGWKDD-PAHAV-SMARLFCDEGADALIFHPR------VAPDLRTRPPKWEY- 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
               + K+   + +  NG +  +  A K+L     DGV +GR A
Sbjct: 188 --IGLVKDAVKVPVFGNGNVISLDDAAKMLSMSGCDGVALGRIA 229


>gi|303242447|ref|ZP_07328929.1| dihydrouridine synthase DuS [Acetivibrio cellulolyticus CD2]
 gi|302590032|gb|EFL59798.1| dihydrouridine synthase DuS [Acetivibrio cellulolyticus CD2]
          Length = 313

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 98/222 (44%), Gaps = 13/222 (5%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK---KNIL-GFSTQEKPLALQIGGADISKLVEAAK 67
           FAR   N    YT  I +  + + +    K+IL  ++     L  Q+ G D ++    A 
Sbjct: 20  FARHFGNIDAYYTPFISSSEVDKVNNLLLKDILPEYNDPAVKLVPQLLGNDGAQFKAFAC 79

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            + D GY+EIN N+GCP   V +   G+ ++ +PD++   +   C   S  VTVK R+G 
Sbjct: 80  AISDIGYHEINWNIGCPYPTVTKKKKGSGILQHPDMIKKVLDTACSDSSYTVTVKMRLGW 139

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D     + + +++       + G+ IHAR  I       D  +   L     +E+   N 
Sbjct: 140 DKLEEGMRVMDVLNDYP---LGGVIIHARTGIQMYEGHVDLEEFETLAASCKHEVTY-NG 195

Query: 188 DLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D+F       +D  +    LP +   M+GR A  +  + T +
Sbjct: 196 DIFTH-----DDFLRISSRLPFIKNFMLGRGALSDPFLPTVI 232


>gi|52843056|ref|YP_096855.1| nitrogen regulation protein [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52630167|gb|AAU28908.1| nitrogen regulation protein [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 329

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 114/240 (47%), Gaps = 26/240 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G +   L EAA
Sbjct: 34  FRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKFLAYQISGNEPHVLAEAA 93

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
             ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+T+K RI 
Sbjct: 94  AKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISRVRAAISIPLTIKIRIQ 153

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            +++        L K I+ +G + + +H R+       P + ++I N+         K  
Sbjct: 154 NNEKD-----LTLAKQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI---------KNA 199

Query: 187 PDLFIGLNGGLED---MSQALKILPSVDGVMIGRAA------YKNSAMLTTVDEYFSNPL 237
            ++ + +NG + +   + +AL+I  + DG MI RA       Y++   L T D  F   L
Sbjct: 200 VNIPVIVNGDINNIFSLRKALEI-SACDGFMISRAGTGKPWLYRDLLNLETNDVAFDEKL 258


>gi|254506424|ref|ZP_05118566.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus 16]
 gi|219550598|gb|EED27581.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus 16]
          Length = 335

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 110/245 (44%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L      K  +    +    ++QI GAD
Sbjct: 32  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGAD 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A+  A+ +P
Sbjct: 91  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIEDILKAVVNAVDVP 150

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L +     G+  + +H R    + KG            +
Sbjct: 151 VTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKG----------EAE 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 198 YNSIKAVKQAISIPVIA-NGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIQHFL 256

Query: 234 SNPLT 238
            N  T
Sbjct: 257 ENGTT 261


>gi|152997627|ref|YP_001342462.1| dihydrouridine synthase DuS [Marinomonas sp. MWYL1]
 gi|150838551|gb|ABR72527.1| dihydrouridine synthase DuS [Marinomonas sp. MWYL1]
          Length = 335

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 67/263 (25%), Positives = 119/263 (45%), Gaps = 28/263 (10%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +T   P+  Q+ G++   + E+A      G   I++N GCP+ RV+    G+ L+  PD 
Sbjct: 77  TTHNHPVHTQLLGSNAELMAESALNATKAGAKHIDVNFGCPAKRVNGHGGGSVLLQTPDA 136

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + D ++A+   L   IPV+ K R+G +D+     L + V +I+ +GV  + IH R     
Sbjct: 137 LYDIMSAIRDTLPSDIPVSAKIRLGFEDE---ALLFDNVAAIEAAGVGTLTIHGR----- 188

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG---VMIGRA 218
             + KD  K P   ++ + EI+ +   + +  NG + D    L+   S+ G    MIGR 
Sbjct: 189 --TKKDGYK-PPARWEKIGEIQAKT-KMTVVANGDITDTKSLLRC-QSITGCQHFMIGRG 243

Query: 219 AYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
           +  N  +   +  E      T  +    R+   + R++     + AA      G+L+Q  
Sbjct: 244 SLNNPFVFQQIRKELNGQESTADTTNLNRLFISYSRELQEHYDEVAAL-----GRLKQWC 298

Query: 278 RHMIGLFHGFPNS----RRCRHI 296
            H+   F     +    RRC+ +
Sbjct: 299 GHLRFEFKEIKENLQTLRRCKSV 321


>gi|332654653|ref|ZP_08420396.1| TIM-barrel protein, NifR3 family [Ruminococcaceae bacterium D16]
 gi|332516617|gb|EGJ46223.1| TIM-barrel protein, NifR3 family [Ruminococcaceae bacterium D16]
          Length = 306

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 105/237 (44%), Gaps = 27/237 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L  TEM+ A A+   DKK +  L     E P A QI G+D
Sbjct: 1   MAGVTDVAFRTICRE-QGAGLTCTEMVSAKALCYQDKKTVPLLQLGEGEHPAAAQIFGSD 59

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + E A I  +  G + I++N+GCP  +V     G+ LM +PD     + A+ +    
Sbjct: 60  PVCMQEGAAIAHEVSGADLIDINMGCPVPKVANSGDGSGLMRDPDKAVKVLEAVIRGAGC 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D    ++      K+++++G   + +H R         ++       ++D
Sbjct: 120 PVTVKFRLGWDKG--SINCVEFAKAMEQAGAAAVAVHGRT--------RNQMYSGTANWD 169

Query: 178 IVYEIKK-------ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            + E+KK        N D+F G     ED  + LK     D  MIGR  + N  +  
Sbjct: 170 WIREVKKAVKIPVIANGDVFKG-----EDAPRILKYT-GADMAMIGRGVFGNPWLFA 220


>gi|46190134|ref|ZP_00206339.1| COG0042: tRNA-dihydrouridine synthase [Bifidobacterium longum
           DJO10A]
          Length = 361

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 71/296 (23%), Positives = 118/296 (39%), Gaps = 22/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 1   MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 60

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 61  PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 120

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 121 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 179 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 229

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           F       +P    V +   R        Y    + +   +  + +H+     GFP
Sbjct: 230 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFP 282


>gi|307208699|gb|EFN85989.1| tRNA-dihydrouridine synthase 4-like [Harpegnathos saltator]
          Length = 351

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 111/231 (48%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+A++ ++  K     F+T  ++KPL +Q     
Sbjct: 21  MVRYSKLQFRTLVRRYACD-ICFTPMIMANSFVQSSKARENEFTTYKEDKPLIVQFAANT 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  + A +++  +  N ++LN GCP     +  +GA L+  P++V D I  +   +  P
Sbjct: 80  VNDFISATEMIAPYS-NGVDLNCGCPQRWAIKDGYGADLLRKPELVSDLIYQVRNRIPKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I    +  L ++++K+G + + IHAR   ++     +  ++ NL    
Sbjct: 139 FTVSVKIRLLKDICKTIM--LCQTLEKAGASFLTIHARTPEMRN----EPIELDNL---- 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
             ++ ++   L    NG ++D+  A  +      +GVM  R    N A+ +
Sbjct: 189 --KLLRDCVQLPFIANGDVKDLESAEVLFRESRCEGVMSARGILTNPALFS 237


>gi|42528231|ref|NP_973329.1| NifR3 family TIM-barrel protein [Treponema denticola ATCC 35405]
 gi|41819501|gb|AAS13248.1| TIM-barrel protein, putative, NifR3 family [Treponema denticola
           ATCC 35405]
          Length = 333

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 71/307 (23%), Positives = 132/307 (42%), Gaps = 27/307 (8%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
             YTEM+ ++A++R   K  +++G +  EK  A+QI G++   + + A I+ E +    I
Sbjct: 41  FTYTEMVSSEALVRDSDKTESLIGRAPNEKAYAVQIFGSNPEYMAKTAVIIAEKYSPECI 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAV 134
           ++N GCP A++ +   G+ LM +  ++   + A+  A++   IPVT+K R G       +
Sbjct: 101 DINSGCPMAKITKNGAGSALMTDIPLLYRIVKAVNDAMAPYKIPVTLKIRSGFTAD--KL 158

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL- 193
             +    +   +GV  + +H R         +        D++I+ E+ +      I + 
Sbjct: 159 NWKEAASAAIDAGVKMLTLHPRT--------RSQVYSGKADWNILAELVQFAKPYQIPIF 210

Query: 194 -NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            +G L     A K+L      G+M  R A  N  + T   E  +N   G    + ++   
Sbjct: 211 GSGDLFSPEDAKKMLEETGCAGIMFARGAMGNPFIFTQTRELLTNGTYGEISTEQKIRTG 270

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           F   I      +           +++ +       G P+  R R  L V+A        I
Sbjct: 271 FKELI------FLCDEKGEEKGCREMRKRFAAYTKGIPDGSRLRQEL-VQASTIAEYKAI 323

Query: 311 IETAFNL 317
           I++AFN+
Sbjct: 324 IQSAFNI 330


>gi|258544513|ref|ZP_05704747.1| tRNA-dihydrouridine synthase B [Cardiobacterium hominis ATCC 15826]
 gi|258520248|gb|EEV89107.1| tRNA-dihydrouridine synthase B [Cardiobacterium hominis ATCC 15826]
          Length = 314

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 73/268 (27%), Positives = 123/268 (45%), Gaps = 21/268 (7%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKNI--LGFSTQEK-PLALQIGGADISKLVEAA 66
           F RL   N   Y+  EMI A   L     +   L F    + P  +Q+ G D + L EAA
Sbjct: 28  FRRLCQQNGADYSTAEMISAKPELLHTAYSAARLQFDLDPRYPKIVQLVGGDAALLAEAA 87

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
            +++  G + I+LN+GCP+  V +   G+ L+ +   V   +AA+ +A++IPVT+K R+G
Sbjct: 88  LLMQAKGADIIDLNMGCPAKTVAKQQAGSALLADLRQVEKILAAVVRAVNIPVTLKTRLG 147

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
             D  P +A   + +  +  G+  + +H R         +  R     DY  +   K + 
Sbjct: 148 YHDGEPVIA--EVARIAEACGIAALAVHGRS--------RAQRYQGEADYATIAAAKAKT 197

Query: 187 PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             L +  NG ++   QA  +L     DG+MIGRAA  +  +        +     ++   
Sbjct: 198 -RLPVIANGDIKSAEQAKTLLDRYGFDGIMIGRAALGDPWLFARCQALINGRDIPAAAKN 256

Query: 245 TRVD---KDFWRKISASMTDYAARHLHS 269
           T++    +D  +   A  T  A +HLH+
Sbjct: 257 TQIRAHLRDLHQHYGAQATAIARKHLHA 284


>gi|167768596|ref|ZP_02440649.1| hypothetical protein CLOSS21_03155 [Clostridium sp. SS2/1]
 gi|167710120|gb|EDS20699.1| hypothetical protein CLOSS21_03155 [Clostridium sp. SS2/1]
 gi|291560550|emb|CBL39350.1| tRNA-U20a,U20b-dihydrouridine synthase [butyrate-producing
           bacterium SSC/2]
          Length = 314

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 44/180 (24%), Positives = 85/180 (47%), Gaps = 15/180 (8%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    +  AK +++ GYNE+NLN+GCPS  V     G+  +  P+++ D +  + 
Sbjct: 64  QILTKNAQDFIRTAKELKELGYNEVNLNLGCPSRTVVAKQKGSGFLREPEVLDDFLTEIY 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +AL + +++K RIG+ +         ++    +  V  + IH R      L  +  +  P
Sbjct: 124 EALDMKISIKTRIGLRE---PEEFEEILSIYNRHPVYELTIHPR------LQQEFYKGKP 174

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           +LD   ++E   ++    +  NG +   +D          ++ VMIGR   +N A++  +
Sbjct: 175 HLD---IFEYATKHSGNPLCYNGDIVTKQDYDHITDRFKDINAVMIGRGLLRNPALVREI 231


>gi|302869263|ref|YP_003837900.1| TIM-barrel protein, nifR3 family [Micromonospora aurantiaca ATCC
           27029]
 gi|302572122|gb|ADL48324.1| TIM-barrel protein, nifR3 family [Micromonospora aurantiaca ATCC
           27029]
          Length = 387

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 76/304 (25%), Positives = 121/304 (39%), Gaps = 29/304 (9%)

Query: 12  FARLL--TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       +   EMI   A++  + K +  + F  +EKP +LQ+ G D      A +
Sbjct: 33  FRRLCREQGGGIYVCEMITTRALVERNPKTLRMIAFGAEEKPRSLQLYGTDPEITAAAVR 92

Query: 68  I-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKC 123
           I VE    + I+LN GCP  +V     G+ L     +    + A   A S   +PVTVK 
Sbjct: 93  IVVERDLADHIDLNFGCPVPKVTRRGGGSALPWRRRLFARLVRAAVDAASPAGVPVTVKM 152

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G+DD         L  + + +GV  + +H R A          R     D+D +  +K
Sbjct: 153 RKGIDDDHLTYVEAGL--AAQDAGVAAVALHGRTAA--------QRYSGTADWDAIATLK 202

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN------ 235
               D+ +  NG + +   AL+++    VDGV+IGR       +   ++  F+       
Sbjct: 203 SAL-DVPVLGNGDIWEADDALRMVAHTGVDGVVIGRGCLGRPWLFADLEAAFNGSAERRL 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P  G   +  R   +   +   +     AR    G       +H+     GFP     R 
Sbjct: 262 PSLGEVAVTMRRHAELLVEQFVAGARNPARGERDG--CTDFRKHVAWYLKGFPIGSELRR 319

Query: 296 ILTV 299
            L +
Sbjct: 320 SLAM 323


>gi|318603958|emb|CBY25456.1| tRNA dihydrouridine synthase B [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|330862841|emb|CBX72982.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica W22703]
          Length = 286

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 25/222 (11%)

Query: 21  LLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  + R DK  +    + E  +  +QI G D  ++  AA+I    G   I+
Sbjct: 1   MTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMATAARINVANGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G      +   RN
Sbjct: 61  INMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGW-----SAEHRN 115

Query: 139 LV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            +   +  +  G+  + IH   R  +  G +          +YD +  +K+      I  
Sbjct: 116 CIEIAQLAENCGIQALTIHGRTRSCLFNGEA----------EYDSIRSVKQIVSIPVIA- 164

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 165 NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 206


>gi|297624504|ref|YP_003705938.1| dihydrouridine synthase DuS [Truepera radiovictrix DSM 17093]
 gi|297165684|gb|ADI15395.1| dihydrouridine synthase DuS [Truepera radiovictrix DSM 17093]
          Length = 362

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 100/222 (45%), Gaps = 17/222 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   R    +A   TEM+ A A+  GD++   I      E+ L +Q+ G +
Sbjct: 69  MAGFSDAPFRRLCRRF-GSAWAVTEMVSAKALTVGDERGLEISAPYEGERDLVIQVFGGE 127

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +    +++ E F    ++LN+GCP  +V   S GA LM +P      I  + +A+ +
Sbjct: 128 PEVVAAGGRLLYERFSPAALDLNMGCPVKKVTGRSCGAKLMNDPGRAAAIIGQLARAVPV 187

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+G D     V    +  +++++G   I IH R A  K             D++
Sbjct: 188 PVSAKLRLGYDR----VNALEVALALQEAGAALITIHGRTAAQK--------YTGEADWE 235

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
            V EI        +G +G +    Q  +      GVM+GR A
Sbjct: 236 AVAEIAARLAIPVVG-SGDVTTQEQFRRYRAWGLGVMVGRGA 276


>gi|262392968|ref|YP_003284822.1| tRNA dihydrouridine synthase B [Vibrio sp. Ex25]
 gi|262336562|gb|ACY50357.1| tRNA dihydrouridine synthase B [Vibrio sp. Ex25]
          Length = 287

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 106/222 (47%), Gaps = 21/222 (9%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ A+  L G  K+   +    +    ++QI G+D   + +AA+   + G   I++N+
Sbjct: 4   SEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSDPQLMADAAQFSVENGAQIIDINM 63

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLV 140
           GCP+ +V++   G+ L+  P+I+ + + A+  A+ +PVT+K R G D D    V +  L 
Sbjct: 64  GCPAKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVPVTLKTRTGWDTDNKNCVQIAKLA 123

Query: 141 KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           ++    G+  + +H R    + KG            +YD +  + KE   + +  NG ++
Sbjct: 124 EN---CGIQALALHGRTKACMYKG----------EAEYDSIKAV-KEAISIPVIANGDID 169

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +A  +L     D +MIGR A     +   +  Y  N  T
Sbjct: 170 SPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENGTT 211


>gi|253752622|ref|YP_003025763.1| tRNA-dihydrouridine synthase [Streptococcus suis SC84]
 gi|253754448|ref|YP_003027589.1| tRNA-dihydrouridine synthase [Streptococcus suis P1/7]
 gi|253756381|ref|YP_003029521.1| tRNA-dihydrouridine synthase [Streptococcus suis BM407]
 gi|251816911|emb|CAZ52560.1| putative tRNA-dihydrouridine synthase [Streptococcus suis SC84]
 gi|251818845|emb|CAZ56688.1| putative tRNA-dihydrouridine synthase [Streptococcus suis BM407]
 gi|251820694|emb|CAR47456.1| putative tRNA-dihydrouridine synthase [Streptococcus suis P1/7]
 gi|319759039|gb|ADV70981.1| tRNA-dihydrouridine synthase [Streptococcus suis JS14]
          Length = 334

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 110/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K +  L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQKNTKANIVDINMGCPVNKVIKNEAGAKWLKDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++    +A+ N + + +  GV  + +H R         ++      +D +
Sbjct: 143 PLTVKMRTGWNNT--DLAVENALAA-ESGGVAALAMHGRT--------REQMYTGTVDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            + ++      +    NG + ++  A + +  V  D VM+GR A  N  +   ++ Y  
Sbjct: 192 TLTKVAGSLTKIPFIANGDIRNVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLE 250


>gi|126437460|ref|YP_001073151.1| nifR3 family TIM-barrel protein [Mycobacterium sp. JLS]
 gi|126237260|gb|ABO00661.1| putative TIM-barrel protein, nifR3 family [Mycobacterium sp. JLS]
          Length = 370

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 76/293 (25%), Positives = 119/293 (40%), Gaps = 19/293 (6%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           AR  T + L   EM+ A A++       ++  F++ E P +LQ+   D +    AAK++ 
Sbjct: 28  ARAGTVSGLYVCEMVTARALVERHPVTMHMTAFASDESPRSLQLYTVDPATTYAAAKMIA 87

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIG 126
           D    + I++N GCP  +V +   GA L     + G  + A   A     IPVTVK RIG
Sbjct: 88  DENMADHIDMNFGCPVPKVTKRGGGAALPYKRKLFGQIVRAAVTATEGTDIPVTVKFRIG 147

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD        +  +   + G   + +HAR A  +     D  +I  L   +       N
Sbjct: 148 IDDA--HHTHLDAGRIAAEEGAAAVALHARTAAQRYSGTADWDQIAALKAHVTAVPVLGN 205

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
            D+F        D + A+      DGV+IGR       +   +   F+       P    
Sbjct: 206 GDIFD------ADDALAMMAATGCDGVVIGRGCLGRPWLFAELSAKFTGRPLPVPPTLGE 259

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           V  D  R+    +TD    H      ++ I +H+    HGFP     R  L +
Sbjct: 260 V-ADIIRRHGELLTD----HFGEDKAMRDIRKHIAWYLHGFPAGSDLRRALAL 307


>gi|238923624|ref|YP_002937140.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Eubacterium rectale ATCC 33656]
 gi|238875299|gb|ACR75006.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Eubacterium rectale ATCC 33656]
          Length = 312

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 43/162 (26%), Positives = 78/162 (48%), Gaps = 14/162 (8%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
           +GY+EIN+N+GCPS  V     G+ ++  PD++   +  +      PV++K R+G +D  
Sbjct: 81  YGYDEINVNLGCPSGTVVSKKRGSGILAYPDMLDSFLDELYTKADFPVSIKTRVGFNDD- 139

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LF 190
                  L++   K  ++ + +H R  + K       +  P +D D    ++K NPD   
Sbjct: 140 --ELWHRLIEIYSKYPISELTVHPR--VQKDFY----KNTPRMD-DFALAMQKINPDKTT 190

Query: 191 IGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           +  NG + D    +      P +D +MIGR  + N A++  +
Sbjct: 191 LCYNGDITDTNSFNALTDCFPDIDEIMIGRGLFANPALIAEL 232


>gi|28899658|ref|NP_799263.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|308125328|ref|ZP_05774543.2| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus K5030]
 gi|28807910|dbj|BAC61147.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|308112839|gb|EFO50379.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus K5030]
          Length = 331

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L      K  +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P I+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPTIIEEILKAVVNAVDVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L +     G+  + +H R    + KG +          +
Sbjct: 145 VTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKGEA----------E 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 192 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYL 250

Query: 234 SNPLT 238
            N  T
Sbjct: 251 ENGTT 255


>gi|332163158|ref|YP_004299735.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325667388|gb|ADZ44032.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 290

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 25/222 (11%)

Query: 21  LLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  + R DK  +    + E  +  +QI G D  ++  AA+I    G   I+
Sbjct: 5   MTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMATAARINVANGAQIID 64

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G      +   RN
Sbjct: 65  INMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGW-----SAEHRN 119

Query: 139 LV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            +   +  +  G+  + IH   R  +  G +          +YD +  +K+      I  
Sbjct: 120 CIEIAQLAENCGIQALTIHGRTRSCLFNGEA----------EYDSIRSVKQIVSIPVIA- 168

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 169 NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|226308278|ref|YP_002768238.1| tRNA-dihydrouridine synthase [Rhodococcus erythropolis PR4]
 gi|229488396|ref|ZP_04382262.1| putative tRNA-dihydrouridine synthase [Rhodococcus erythropolis
           SK121]
 gi|226187395|dbj|BAH35499.1| putative tRNA-dihydrouridine synthase [Rhodococcus erythropolis
           PR4]
 gi|229323900|gb|EEN89655.1| putative tRNA-dihydrouridine synthase [Rhodococcus erythropolis
           SK121]
          Length = 380

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 71/285 (24%), Positives = 118/285 (41%), Gaps = 23/285 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-I 68
             R  + + L   EM+ A A++       ++  F   E P +LQ+   D      AAK I
Sbjct: 37  LERAGSTSGLYVCEMVTARALVERQPATMHMTTFGPTETPRSLQLYTVDPDTTYAAAKMI 96

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
           V++   + I++N GCP  +V     G+ L     + G  +AA  +A     IPVTVK R+
Sbjct: 97  VDENMADHIDMNFGCPVPKVTRKGGGSALPYKRRLFGQIVAAAVRATEGTDIPVTVKMRV 156

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+D +       +  +     G   + +HAR A          R     D++ +  +K+ 
Sbjct: 157 GIDPE--HHTHLDAGRIAAAEGAAAVALHARTA--------SQRYSGTADWNEITRLKEH 206

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
             D+ I  NG + D S A +++     DGV++GR       +   +    +     + P 
Sbjct: 207 VTDVPILGNGDIFDASDAARMMNETGCDGVVVGRGCLGRPWLFAELSAALNGQQIATPPT 266

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              V K   R         AA H    G L+++ +H+     GFP
Sbjct: 267 LGEVTKIIARHAQL----LAAHHGEMKG-LRELRKHVSWYMRGFP 306


>gi|108801475|ref|YP_641672.1| dihydrouridine synthase TIM-barrel protein nifR3 [Mycobacterium sp.
           MCS]
 gi|119870628|ref|YP_940580.1| nifR3 family TIM-barrel protein [Mycobacterium sp. KMS]
 gi|108771894|gb|ABG10616.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Mycobacterium sp.
           MCS]
 gi|119696717|gb|ABL93790.1| putative TIM-barrel protein, nifR3 family [Mycobacterium sp. KMS]
          Length = 370

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 76/293 (25%), Positives = 119/293 (40%), Gaps = 19/293 (6%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           AR  T + L   EM+ A A++       ++  F++ E P +LQ+   D +    AAK++ 
Sbjct: 28  ARAGTVSGLYVCEMVTARALVERHPVTMHMTAFASDESPRSLQLYTVDPATTYAAAKMIA 87

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIG 126
           D    + I++N GCP  +V +   GA L     + G  + A   A     IPVTVK RIG
Sbjct: 88  DENMADHIDMNFGCPVPKVTKRGGGAALPYKRKLFGQIVRAAVTATEGTDIPVTVKFRIG 147

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD        +  +   + G   + +HAR A  +     D  +I  L   +       N
Sbjct: 148 IDDA--HHTHLDAGRIAAEEGAAAVALHARTAAQRYSGTADWDQIAALKAHVTAVPVLGN 205

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
            D+F        D + A+      DGV+IGR       +   +   F+       P    
Sbjct: 206 GDIFD------ADDALAMMAATGCDGVVIGRGCLGRPWLFAELSAKFTGRPLPVPPTLGE 259

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           V  D  R+    +TD    H      ++ I +H+    HGFP     R  L +
Sbjct: 260 V-ADIIRRHGELLTD----HFGEDKAMRDIRKHIAWYLHGFPAGSDLRRALAL 307


>gi|320168879|gb|EFW45778.1| tRNA-dihydrouridine synthase 4-like protein [Capsaspora owczarzaki
           ATCC 30864]
          Length = 432

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 102/238 (42%), Gaps = 36/238 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + L YT M VA+  +   +     FST E   P+ +Q     
Sbjct: 90  MVRYSKLGFRELVRAFGCD-LAYTPMTVAENFILSKRGRDNDFSTNEYDHPVIVQFAAKH 148

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA++V  +  + I++N GCP        +G+ L+  P ++ D + A    ++IP
Sbjct: 149 TEMLCTAAEMVAPY-VDGIDINCGCPQRWAMSEGYGSALLRKPQLIYDMVRAAKSRITIP 207

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAILKGLSP-KDNRK 170
           V+VK RI +D +        L ++ +++G + I +H R         IL+G+   KDN  
Sbjct: 208 VSVKIRINLDFK----KTIELAQTAERAGADWIAVHGRTPSMRHEPVILEGIKAVKDNVS 263

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAML 226
           IP                  +  NG +  M    A+     VDGVM  R    N A+ 
Sbjct: 264 IP------------------VVANGDINSMLDVNAVAAATGVDGVMSARGLLANPALF 303


>gi|261415070|ref|YP_003248753.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371526|gb|ACX74271.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302327170|gb|ADL26371.1| dihydrouridine synthase family protein [Fibrobacter succinogenes
           subsp. succinogenes S85]
          Length = 392

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 111/237 (46%), Gaps = 23/237 (9%)

Query: 5   TDRHYRFFARLLTNN--ALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           TD  +R   R+L+ +   LL +E +    DA+   D    L F  +E+P  +QI G    
Sbjct: 33  TDAPFRRLCRVLSGDRMGLLVSEFVPTDGDAVFNPDGHKQLKFFPEERPFGVQIFGRFPD 92

Query: 61  KLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN----PDIVGDCIAAM-CKA 114
           ++  AA KI E +    I +N GCP+ +V     G+ L+ +     +I+ D  A +  K 
Sbjct: 93  RMAAAAGKIAERYHPEFIEVNAGCPAPKVAGKGSGSGLLRDLPRLQEILHDVKAVLDAKT 152

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+KCRIG DD   ++ +   +K  +  GV  + +H R   L+G +   N      
Sbjct: 153 PEIPLTLKCRIGWDDD--SINVMETLKIAEGEGVEMLTVHGRTR-LQGYNGLAN------ 203

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            +D + ++        IG NG +  +  A + + +  V GV IGR A  N  +   +
Sbjct: 204 -WDWIGKVAAAAKIPVIG-NGDVNSVECARERINTYGVSGVSIGRGAMHNPWIFGQI 258


>gi|163855213|ref|YP_001629511.1| dihydrouridine synthase [Bordetella petrii DSM 12804]
 gi|163258941|emb|CAP41240.1| dihydrouridine synthase [Bordetella petrii]
          Length = 349

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 116/246 (47%), Gaps = 21/246 (8%)

Query: 5   TDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISK 61
           TDR +R    RL   +A+  +EM  ++  L    K    L    +  P+A+QI GAD + 
Sbjct: 29  TDRPFRQLCKRLGAGHAV--SEMAASNPRLWDSVKTSRRLNHDGEIAPVAVQIAGADPAM 86

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKALSIP 118
           + EAA      G   I++N+GCP  +V   + G+ L+ + D+V    D + A C  L +P
Sbjct: 87  MAEAAAFNAARGARIIDINMGCPVKKVCNLASGSALLRDEDLVARILDAVVAACAPLGVP 146

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +    ALR + +  +++G+  + +H R         + +      +YD 
Sbjct: 147 VTLKTRTGWDRE-HRNALR-VARRAQEAGIAALALHGRT--------RADLYTGTAEYDT 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E     I  NG ++   +A ++L     D VMIGRAA     +   +D Y    
Sbjct: 197 IRAVKAELSIPVIA-NGDIDSPQKARRVLDYTGADAVMIGRAAQGRPWIFREIDHYLRTG 255

Query: 237 LTGSSP 242
            T + P
Sbjct: 256 DTLAPP 261


>gi|218961108|ref|YP_001740883.1| dihydrouridine synthase family protein [Candidatus Cloacamonas
           acidaminovorans]
 gi|167729765|emb|CAO80677.1| dihydrouridine synthase family protein [Candidatus Cloacamonas
           acidaminovorans]
          Length = 321

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 110/239 (46%), Gaps = 29/239 (12%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +LY+EM+ AD + R   K +  + F   E P  +QI G++   +  A +++     + ++
Sbjct: 35  VLYSEMVSADGLTRNSAKTLQYVQFDESEHPFGIQIFGSNPLIMARAVEVLLPLKPDFMD 94

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVAL 136
           +N+GCP  +V     G+ LM  P + G  +  +  AL   IP++VK R G + Q      
Sbjct: 95  INMGCPVKKVIRKGAGSALMQTPSLAGKIVKEVKNALLGRIPLSVKFRSGWNFQNQNYLQ 154

Query: 137 RNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L+  +++ G + + +H R +  +  G S  +  K           I K+N  + +  N
Sbjct: 155 FGLM--LQECGADFLCLHPRTSSQMFSGTSNWEQIK-----------ILKQNVQIPVVGN 201

Query: 195 GGLEDMSQALKILPSV--DGVMIGRAA------YKNSAMLTTVDEYFSNPLTGSSPIKT 245
           G ++    A +++     DG+MIGR A      +  S  L +   Y  NP+     +KT
Sbjct: 202 GDIKTPEDAQRMITETNCDGIMIGRGALGKPWLFAQSRQLISTGTY--NPVIQKEIVKT 258


>gi|90424075|ref|YP_532445.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris BisB18]
 gi|90106089|gb|ABD88126.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodopseudomonas
           palustris BisB18]
          Length = 356

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 105/245 (42%), Gaps = 21/245 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLV 63
           TD  +R     L    L+ +EM  +D + RG   ++    T    P  +Q+ G     + 
Sbjct: 42  TDAPFRRLTAAL-GAGLVVSEMTASDDLARGRPMSVRRCDTAGIGPHVVQLAGCQARWMA 100

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGS--FGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           E A+I E  G + I++N+GCP+  V  GS   G+ LM + D     I A   A+ +PVT+
Sbjct: 101 EGARIAEAGGADLIDINMGCPARHVTGGSGQSGSALMRDLDHALTLIEATVGAVRVPVTL 160

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
           K R+G D     +    L +  + +GV  I +H   R    KG +          D+  V
Sbjct: 161 KMRLGWDRDC--LNAPELARRAEAAGVQLITVHGRTRNQFYKGTA----------DWAAV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   L + +NG +  +  A + L     D VMIGR A     +   +       +
Sbjct: 209 RAV-REATSLPLVVNGDITSVEAAREALRQSGADAVMIGRGAQGQPWLPGQIGRQLQTGI 267

Query: 238 TGSSP 242
             + P
Sbjct: 268 AEAPP 272


>gi|315504262|ref|YP_004083149.1| tim-barrel protein, nifr3 family [Micromonospora sp. L5]
 gi|315410881|gb|ADU08998.1| TIM-barrel protein, nifR3 family [Micromonospora sp. L5]
          Length = 387

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 76/304 (25%), Positives = 121/304 (39%), Gaps = 29/304 (9%)

Query: 12  FARLL--TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       +   EMI   A++  + K +  + F  +EKP +LQ+ G D      A +
Sbjct: 33  FRRLCREQGGGIYVCEMITTRALVERNPKTLRMIAFGAEEKPRSLQLYGTDPEITAAAVR 92

Query: 68  I-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKC 123
           I VE    + I+LN GCP  +V     G+ L     +    + A   A S   +PVTVK 
Sbjct: 93  IVVERDLADHIDLNFGCPVPKVTRRGGGSALPWRRRLFARLVRAAVDAASPAGVPVTVKM 152

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G+DD         L  + + +GV  + +H R A          R     D+D +  +K
Sbjct: 153 RKGIDDDHLTYVEAGL--AAQDAGVAAVALHGRTAA--------QRYSGTADWDAIATLK 202

Query: 184 KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN------ 235
               D+ +  NG + +   AL+++    VDGV+IGR       +   ++  F+       
Sbjct: 203 AAL-DVPVLGNGDIWEADDALRMVAHTGVDGVVIGRGCLGRPWLFADLEAAFNGSAERRL 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P  G   +  R   +   +   +     AR    G       +H+     GFP     R 
Sbjct: 262 PSLGEVAVTMRRHAELLVEQFVAGARNPARGERDG--CTDFRKHVAWYLKGFPIGSELRR 319

Query: 296 ILTV 299
            L +
Sbjct: 320 SLAM 323


>gi|114047827|ref|YP_738377.1| dihydrouridine synthase, DuS [Shewanella sp. MR-7]
 gi|113889269|gb|ABI43320.1| dihydrouridine synthase, DuS [Shewanella sp. MR-7]
          Length = 315

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 110/236 (46%), Gaps = 33/236 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + D + AM +A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 NTIHDIVRAMRQAVPAEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
                  D  K P   ++ + E+++  P   I  NG +   ED  + + +    D +MIG
Sbjct: 174 -------DGYKPPAY-WEYITEVRERLPIPVIA-NGEIWNREDAERCMAVT-GCDSIMIG 223

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           R A     +  T+        TG++P         W      M  Y  R L SG K
Sbjct: 224 RGAISLPNLADTIK-------TGAAPYS-------WADTLGLMLSYTQREL-SGRK 264


>gi|296447367|ref|ZP_06889294.1| TIM-barrel protein, nifR3 family [Methylosinus trichosporium OB3b]
 gi|296255146|gb|EFH02246.1| TIM-barrel protein, nifR3 family [Methylosinus trichosporium OB3b]
          Length = 331

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 105/240 (43%), Gaps = 19/240 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD---KKNILGFSTQEKPLALQIGGA 57
           M   TD   R  A L    A    EM+ A A+ RGD   ++ + G         +QI   
Sbjct: 17  MAGVTDSAMRRIA-LRFGAAAAVGEMVGASALARGDLEARQRLDGAGLDAH--IVQIAAR 73

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D + + E A+  E  G   I++N+GCP  RV  G  GA LM +P +    + A   A+++
Sbjct: 74  DPASIAETARRAEAAGAKLIDINMGCPCKRVTGGLAGAALMRDPALAASLVRAAVGAVTV 133

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R+G DD     A   L + ++  G   + +H R         +        D+ 
Sbjct: 134 PVSVKMRLGWDDASRNAA--ELARLVESEGAAMVTVHGRT--------RAQFYEGRADWS 183

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+++    P +  G     ED +  L+     D VMIGRAA     ++  V  + ++
Sbjct: 184 AIAEVRRALRIPLVANGDCASPEDAAVMLE-RSGADAVMIGRAALGRPWLVGEVAHFLAS 242


>gi|284030422|ref|YP_003380353.1| TIM-barrel protein, nifR3 family [Kribbella flavida DSM 17836]
 gi|283809715|gb|ADB31554.1| TIM-barrel protein, nifR3 family [Kribbella flavida DSM 17836]
          Length = 381

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 71/286 (24%), Positives = 121/286 (42%), Gaps = 24/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNE 76
            L   EMI +  I+ GD+K  ++L F  +E   ++Q+ G D   +  A +++ D +G   
Sbjct: 44  GLYVCEMITSRGIVEGDQKSLDMLTFDERETVRSVQLYGVDPVYIGRAVELLCDAYGVAH 103

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPA 133
           I+LN GCP  +V     GA L    +++G  + +  KA +   +PVT+K RIG+D +   
Sbjct: 104 IDLNFGCPVPKVTRKGGGAALPWKRNLLGAILQSAVKAATPYDVPVTMKTRIGIDSE--H 161

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
               +  +  ++SG   I +H R A        D  KI  L          E+ D+ +  
Sbjct: 162 QTYLDAGRIAEESGAAAIGLHGRTAAQAYSGQADWTKIAEL---------VEHVDIPVLG 212

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S AL+++      GV++GR       +   +   F+     + P    V    
Sbjct: 213 NGDIWEASDALRMVEQTGCAGVIVGRGCLGRPWLFRDLAVAFAGGEALNLPTLGEV-ATV 271

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R+    + D           L+   +H+     GFP     R  L
Sbjct: 272 MRRHGELLADLMGEQR----GLRDFRKHVPWYLKGFPAGGELRAAL 313


>gi|19112778|ref|NP_595986.1| tRNA dihydrouridine synthase Dus1 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74638589|sp|Q9HGN6|DUS1_SCHPO RecName: Full=tRNA-dihydrouridine synthase 1
 gi|9967699|emb|CAC05725.1| tRNA dihydrouridine synthase Dus1 (predicted) [Schizosaccharomyces
           pombe]
          Length = 399

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 69/263 (26%), Positives = 119/263 (45%), Gaps = 42/263 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST----QEKPLALQIGG 56
           MVD ++  +R  AR  +   L Y+ M  +      +      FST    +E+PL +Q  G
Sbjct: 25  MVDQSELPWRILARR-SGADLCYSPMFHSRLFGESEDYRNKVFSTRTIPEERPLIIQFCG 83

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   +++AAKI   +  + +++N+GCP     +G +G+ L  N +++   I  +   LS
Sbjct: 84  NDPEIMLKAAKIAAPYC-DAVDVNLGCPQGIAKKGKYGSFLQENWNLIESIITKLHTELS 142

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIP 172
           IPVT K RI  D Q       +  K I K+G + + +H R    K    G++        
Sbjct: 143 IPVTAKIRIFPDPQ----KTLDYAKMILKAGASILAVHGRLREQKGHFTGIA-------- 190

Query: 173 NLDYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
             D++ +  ++K  P +  +  NG +   +D+ + +K    VDGV+    +  N  +   
Sbjct: 191 --DWEQIQMLRKNLPSETVLFANGNILHAQDIDRCIKYT-GVDGVLSAEGSLYNPRIF-- 245

Query: 229 VDEYFSNPLTGSSPIKT---RVD 248
                   L  SSP+ T   R+D
Sbjct: 246 --------LPPSSPLMTLYPRID 260


>gi|195156341|ref|XP_002019059.1| GL26162 [Drosophila persimilis]
 gi|194115212|gb|EDW37255.1| GL26162 [Drosophila persimilis]
          Length = 398

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/246 (23%), Positives = 117/246 (47%), Gaps = 20/246 (8%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAK 67
           F RL+  N   L +T M+++D+I   +K     FST   ++PL  Q    D ++ V +A+
Sbjct: 38  FRRLVRMNGVQLAFTPMMISDSINNSEKARQNEFSTDPDDQPLIAQFAAKDATEFVTSAQ 97

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR- 124
           ++  +  + I+LN GCP +      +G  L+  P+ V + +  + + L     V+VK R 
Sbjct: 98  LIYPY-VDGIDLNCGCPQSWAMSKGYGCGLLRQPEQVREVVQQVRRTLPSDFSVSVKMRL 156

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G  ++       +L + ++++GV  + +H R       +P        L+   + E++K
Sbjct: 157 LGGSEEDSVERTIDLARQLERAGVTFLTLHGR-------TPAQKHSKDTLNVSAMEEVRK 209

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            +  + + +NG +E  S A ++       GVM  R    N A+  +  +Y +   T S+ 
Sbjct: 210 -SLQIPLIVNGNVESWSDACELHAQTGAAGVMAARGLLANPALFNS--DYPTATTTPSAC 266

Query: 243 IKTRVD 248
           ++  +D
Sbjct: 267 VEQWLD 272


>gi|194765697|ref|XP_001964963.1| GF22885 [Drosophila ananassae]
 gi|190617573|gb|EDV33097.1| GF22885 [Drosophila ananassae]
          Length = 513

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 111/234 (47%), Gaps = 25/234 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R    + L YT M  A+      K  K+ L     ++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRYGAH-LCYTPMYHANLFATDPKYRKDALQTCAGDRPLVIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA   +D   + +++N+GCP A    G +G+ L    +++ +  + + K LSIP
Sbjct: 94  AQQILDAALAAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIESTLHKKLSIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  +D+   +    ++++   +G   + +H R    K  L G++          
Sbjct: 153 VTCKIRI-FEDRAKTIRYAQMLEA---AGCQLLTVHGRTREQKGPLTGVA---------- 198

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D+  + E+++  + P    G   GLED+ + L+    VDGVM       N A+ 
Sbjct: 199 DWSYIKEVRQHIKIPMFANGNILGLEDVHRCLEET-GVDGVMSAEGNLHNPAIF 251


>gi|328767911|gb|EGF77959.1| hypothetical protein BATDEDRAFT_13578 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 296

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 110/239 (46%), Gaps = 33/239 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  A       K     FST E  +PL +Q    D
Sbjct: 28  MVDQSEYAWRILSRRY-GAQLCYTPMFHAKLFSEHHKYRKQVFSTGEFDRPLIVQFCAND 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE    + I+LN+GCP     +G +G+ L    D++   + A+ + +S+P
Sbjct: 87  PETLLSAAKLVEA-QCDAIDLNLGCPQGIAKKGHYGSFLQDEWDLIASMVKAVHEHISVP 145

Query: 119 VTVKCRIGVDDQIP---AVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKI 171
           +T K RI  D +     A+ L+N       +G   + +H R    K  L GL+       
Sbjct: 146 ITCKIRIFPDVKKTIEYALMLQN-------AGCQLLTVHGRLREQKGQLTGLA------- 191

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              D+D + ++ KE   + +  NG +   +D+ + +K    VDGVM       N A+ +
Sbjct: 192 ---DWDQIRQV-KEALSIPVFANGNILYHDDVERCIK-ETGVDGVMTAEGNLYNPAIFS 245


>gi|145545963|ref|XP_001458665.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124426486|emb|CAK91268.1| unnamed protein product [Paramecium tetraurelia]
          Length = 358

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 23/234 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ +  +          F+T  +++PL  Q+ G D
Sbjct: 25  MVDQSELAFRMQTRKY-GTTLAYTPMLHSRIMTESKSYKDEFFTTCPEDRPLFAQLCGHD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +++AA +++D   + I+LN GCP     +G +GA L+   + V   +  + + + +P
Sbjct: 84  PQVIIKAALMIQD-QCDAIDLNFGCPQGIARKGLYGAFLLEKREQVLTIVKELKQNIKVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK-IPNLDYD 177
           VT K R+  D +       +L K I+ +G + + +H R       + + N+  +   D++
Sbjct: 143 VTCKIRVFKDRK----RTLDLTKDIQSAGCSILTVHGR-------TKEQNKDFVGQCDWN 191

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           I+ EIK+  + P   +  NGG+   S   + L    VD VM   A  +N A+ +
Sbjct: 192 IIAEIKQLLQIP---VFANGGIYTWSDVERCLQETKVDAVMSSEALLENPALFS 242


>gi|94501272|ref|ZP_01307793.1| hypothetical protein RED65_02629 [Oceanobacter sp. RED65]
 gi|94426543|gb|EAT11530.1| hypothetical protein RED65_02629 [Oceanobacter sp. RED65]
          Length = 321

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G+D   + E A    + G   +N+N GCPS  V+    GA L+  PD +   +
Sbjct: 64  PVHLQLLGSDPVAMAENACRAAELGAPVVNINFGCPSRFVNGRCGGAYLLQFPDQIHTIL 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            ++ KAL   +P+T K R+G  D   A+AL N  ++++ +GV  I IHAR  +     P 
Sbjct: 124 ESVRKALPEHVPLTAKMRLGFKDD--ALALAN-AQAMESAGVRDICIHARTKVQGYRPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSA 224
              +I N+         K+   + I  NG + +    +A K     + VM+GR A  +  
Sbjct: 181 HWHQIKNI---------KQQVKVPIIANGEIWNRRDYEACKAASHCEHVMLGRGAVADPE 231

Query: 225 MLTTV 229
           +  T+
Sbjct: 232 LAATI 236


>gi|227546857|ref|ZP_03976906.1| dihydrouridine synthase [Bifidobacterium longum subsp. infantis
           ATCC 55813]
 gi|227212819|gb|EEI80700.1| dihydrouridine synthase [Bifidobacterium longum subsp. infantis
           ATCC 55813]
          Length = 414

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKNRSLQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 174 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNVPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|41472|emb|CAA44270.1| ORF1 [Escherichia coli]
          Length = 321

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +   + +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNRVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|145634155|ref|ZP_01789866.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittAA]
 gi|229843962|ref|ZP_04464103.1| DNA-binding protein Fis [Haemophilus influenzae 6P18H1]
 gi|145268599|gb|EDK08592.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittAA]
 gi|229812956|gb|EEP48644.1| DNA-binding protein Fis [Haemophilus influenzae 6P18H1]
          Length = 353

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 113/239 (47%), Gaps = 26/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLCAYY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  P +V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPYLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K   
Sbjct: 163 VTLKIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIKAV- 216

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                     K+   + +  NG ++   +A  +L     D +MIGRAA  N  +   V+
Sbjct: 217 ----------KQAIAIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVE 265


>gi|238794627|ref|ZP_04638233.1| tRNA-dihydrouridine synthase B [Yersinia intermedia ATCC 29909]
 gi|238726016|gb|EEQ17564.1| tRNA-dihydrouridine synthase B [Yersinia intermedia ATCC 29909]
          Length = 290

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 25/222 (11%)

Query: 21  LLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  + R DK  +    + E  +  +QI G D  ++  AA+I    G   I+
Sbjct: 5   MTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMAAAARINVANGAQIID 64

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +      RN
Sbjct: 65  INMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSTE-----HRN 119

Query: 139 LV---KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            +   +  +  G+  + IH   R  +  G +          +YD +  +K+      I  
Sbjct: 120 CIEIAQLAENCGIQALTIHGRTRSCLFNGEA----------EYDSIRAVKQIVSIPVIA- 168

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 169 NGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|153839624|ref|ZP_01992291.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus AQ3810]
 gi|308094610|ref|ZP_05890528.2| NifR3 family protein [Vibrio parahaemolyticus AN-5034]
 gi|308095202|ref|ZP_05903963.2| NifR3 family protein [Vibrio parahaemolyticus Peru-466]
 gi|308126676|ref|ZP_05911720.2| NifR3 family protein [Vibrio parahaemolyticus AQ4037]
 gi|149746863|gb|EDM57851.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus AQ3810]
 gi|308088061|gb|EFO37756.1| NifR3 family protein [Vibrio parahaemolyticus Peru-466]
 gi|308094109|gb|EFO43804.1| NifR3 family protein [Vibrio parahaemolyticus AN-5034]
 gi|308109548|gb|EFO47088.1| NifR3 family protein [Vibrio parahaemolyticus AQ4037]
          Length = 340

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L      K  +    +    ++QI G+D
Sbjct: 35  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P I+ + + A+  A+ +P
Sbjct: 94  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPTIIEEILKAVVNAVDVP 153

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L +     G+  + +H R    + KG +          +
Sbjct: 154 VTLKTRTGWDTDNKNCVQIAKLAED---CGIQALALHGRTKACMYKGEA----------E 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 201 YDSIKAV-KEAISIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYL 259

Query: 234 SNPLT 238
            N  T
Sbjct: 260 ENGTT 264


>gi|313203243|ref|YP_004041900.1| dihydrouridine synthase dus [Paludibacter propionicigenes WB4]
 gi|312442559|gb|ADQ78915.1| dihydrouridine synthase DuS [Paludibacter propionicigenes WB4]
          Length = 326

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 117/257 (45%), Gaps = 30/257 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN---ALLYTEMIVADAILRGDKKNI----LGFSTQEKPL--- 50
           M D TD  +R   R ++ +    +++TE   AD +     +      L  S  E+ L   
Sbjct: 18  MEDVTDTVFREVIRSVSESDALHVMFTEFTSADGLCNEKGREFVATRLHVSETERELLKA 77

Query: 51  -----ALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                  QI G+D  K  E+AK++   G ++ I++N+GCP  +V +    + L+ +P++ 
Sbjct: 78  TNTKLVAQIWGSDPVKFHESAKLISAMGLFDGIDINMGCPVKKVVKNHSCSDLINHPEMA 137

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL--KG 162
              + A  +  ++PV+VK RIG      ++     +  + +     I IH R   +   G
Sbjct: 138 KQIVVATREGTNLPVSVKTRIG----FSSIVTEEWIGQLLEVHPAAITIHGRTRSMMSNG 193

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           L+  D      +   +    + ++  L +G NG ++  + AL  +    VDGVM+GR  +
Sbjct: 194 LALWD-----EIGKAVQLRNQSKSSTLILG-NGDVDSHATALAKVRDFGVDGVMVGRGVF 247

Query: 221 KNSAMLTTVDEYFSNPL 237
           KN  M   VD+  S  +
Sbjct: 248 KNPWMFNAVDKEISRQM 264


>gi|291525684|emb|CBK91271.1| tRNA-dihydrouridine synthase [Eubacterium rectale DSM 17629]
          Length = 312

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/163 (27%), Positives = 81/163 (49%), Gaps = 16/163 (9%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
           +GY+EIN+N+GCPS  V     G+ ++  PD++   +  +      PV++K R+G +D  
Sbjct: 81  YGYDEINVNLGCPSGTVVSKKRGSGILAYPDMLDSFLDELYTKADFPVSIKTRVGFNDD- 139

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LF 190
                  L++   K  ++ + +H R  + K       +  P +D D    ++K NPD   
Sbjct: 140 --ELWPRLIEIYSKYPISELIVHPR--VQKDFY----KNTPRMD-DFALAMQKINPDKTT 190

Query: 191 IGLNGGLEDMSQALKIL----PSVDGVMIGRAAYKNSAMLTTV 229
           +  NG + D + + K L    P +D +MIGR  + N A++  +
Sbjct: 191 LCYNGDITD-TNSFKALTDCFPDIDEIMIGRGLFANPALIAEL 232


>gi|117920895|ref|YP_870087.1| dihydrouridine synthase, DuS [Shewanella sp. ANA-3]
 gi|117613227|gb|ABK48681.1| dihydrouridine synthase, DuS [Shewanella sp. ANA-3]
          Length = 315

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 110/236 (46%), Gaps = 33/236 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + D + AM +A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 NTIHDIVRAMRQAVPAEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
                  D  K P   ++ + E+++  P   I  NG +   ED  + + +    D +MIG
Sbjct: 174 -------DGYKPPAY-WEYITEVRERLPIPVIA-NGEIWNREDAKRCMAVT-GCDSIMIG 223

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           R A     +  T+        TG++P         W      M  Y  R L SG K
Sbjct: 224 RGAISLPNLADTIK-------TGAAPYS-------WADTLGLMLSYTQREL-SGRK 264


>gi|238751413|ref|ZP_04612906.1| tRNA-dihydrouridine synthase B [Yersinia rohdei ATCC 43380]
 gi|238710471|gb|EEQ02696.1| tRNA-dihydrouridine synthase B [Yersinia rohdei ATCC 43380]
          Length = 290

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 103/217 (47%), Gaps = 21/217 (9%)

Query: 24  TEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ ++  + R DK  +    + E  +  +QI G D  ++  AA+I    G   I++N+
Sbjct: 8   SEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMAAAARINVANGAQIIDINM 67

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLV 140
           GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +    + +  L 
Sbjct: 68  GCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSAEHRNCIEIAQLA 127

Query: 141 KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +S    G+  + IH   R  +  G +          +YD +  +K+      I  NG + 
Sbjct: 128 ES---CGIQALTIHGRTRSCLFNGEA----------EYDSIRAVKQIVSIPVIA-NGDIT 173

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 174 DPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|330807319|ref|YP_004351781.1| tRNA-dihydrouridine synthase B [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327375427|gb|AEA66777.1| tRNA-dihydrouridine synthase B [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 335

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 71/300 (23%), Positives = 138/300 (46%), Gaps = 25/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLAEAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVTEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +     +  + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRENKNGLV--VAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K+   + +  NG ++   +A  +L +   DG++IGRAA     +   ++ +    
Sbjct: 189 IAAI-KQAVSIPVFANGDVDSPEKARYVLDATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLFHG-FPNSRRCR 294
              + P  + V++         +   AA H   G  +  +I R  +G +    P +R  R
Sbjct: 248 EKLAPPQLSEVERIL-------LEHLAALHAFYGEVMGVRIARKHVGWYLATLPGAREFR 300


>gi|290960587|ref|YP_003491769.1| dihydrouridine synthase [Streptomyces scabiei 87.22]
 gi|260650113|emb|CBG73229.1| putative dihydrouridine synthase [Streptomyces scabiei 87.22]
          Length = 384

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 106/225 (47%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 28  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDATETPRSIQLYGV 87

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ + G  + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 88  DPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGAG 147

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 148 DLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 198 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRG 242


>gi|257068855|ref|YP_003155110.1| putative TIM-barrel protein, nifR3 family [Brachybacterium faecium
           DSM 4810]
 gi|256559673|gb|ACU85520.1| putative TIM-barrel protein, nifR3 family [Brachybacterium faecium
           DSM 4810]
          Length = 415

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/287 (21%), Positives = 121/287 (42%), Gaps = 21/287 (7%)

Query: 18  NNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY- 74
           +  L  +EM+   A++   +++  ++    QE P ++Q+ G D + +  A +++ +    
Sbjct: 73  DGGLYVSEMVTTRALVEDHRESWRLVTMGAQETPRSVQLYGVDPATVRRAVEMIRERDLA 132

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIP 132
           + I+LN GCP  +V     G  L    ++    ++A  +A    +PVTVK RIG+DD+  
Sbjct: 133 DHIDLNFGCPVPKVTRRGGGGVLPWKSELFTRIVSAAVEAAGPEVPVTVKTRIGIDDE-- 190

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
               R+     ++ G   I +H R  +                +D + E+K+   D+ + 
Sbjct: 191 HQTFRDAGLIAQEVGAAAIALHGRTVV--------QHYSGTARWDAISELKELVTDIPVL 242

Query: 193 LNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG +     A+ ++     DGV++GR       +   +   F+       P    V + 
Sbjct: 243 GNGDIWCAEDAIDMMDRTGCDGVVVGRGCQGRPWLFADLAAGFAGRPERVRPSLGEVAQI 302

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             R     +  +       G  L+ + +H+   F G+P   + RH L
Sbjct: 303 LRRHAELLIEFFE----DEGRALRDLRKHVAWYFKGYPVGGQMRHRL 345


>gi|258624522|ref|ZP_05719466.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM603]
 gi|258583219|gb|EEW08024.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM603]
          Length = 331

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 110/245 (44%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++   +  +  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIESILKTVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V++  L +     G+  + +H R    + KG            +
Sbjct: 145 VTLKTRTGWDTDNKNCVSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|256544716|ref|ZP_05472088.1| tRNA-dihydrouridine synthase [Anaerococcus vaginalis ATCC 51170]
 gi|256399605|gb|EEU13210.1| tRNA-dihydrouridine synthase [Anaerococcus vaginalis ATCC 51170]
          Length = 321

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/285 (22%), Positives = 132/285 (46%), Gaps = 29/285 (10%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVED-----FGYN 75
           +TEM+  +A+   +KK  ++L  S  EK   +QI G+   +L+E  K+V+D         
Sbjct: 36  FTEMVSVNALYYDNKKTDDLLFISENEKNCNIQIFGSK-PELIE--KVVKDKINPIEKSK 92

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           EI+ N+GCP A++ +   G+ LM  P +V +    + K+    + +K R+G+DD+   + 
Sbjct: 93  EISFNMGCPVAKITKNGEGSALMAKPKLVEEICKILRKSTDKKINIKFRLGIDDK--NLN 150

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K  + +G++ + +HAR         K+       +++ + +I KEN  + +  NG
Sbjct: 151 YLEIGKIAQDAGIDYVILHAR--------TKEQMYSGKANWNHI-KILKENLSIPVIANG 201

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            +  +   +K++     DGVM+ R A  N  +   + +Y +       P  T++      
Sbjct: 202 DIFCVEDFVKVIDKTKADGVMLARGAMGNPFLFKEIKDYINKGFY-EKPSSTQIIDQLIE 260

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +    +     + +     + Q+ +H+     G  NS + R ++ 
Sbjct: 261 QYKLELKYKKEKLV-----VTQMRKHLSWYIKGLENSSKIRDLVN 300


>gi|292628574|ref|XP_001342694.3| PREDICTED: tRNA-dihydrouridine synthase 2-like [Danio rerio]
          Length = 504

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 111/240 (46%), Gaps = 44/240 (18%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G AD  + +  AK+VE+     +++N+GCP     +G  G+ L+ +P+ +   + 
Sbjct: 89  VVFQMGTADPERALAVAKLVEN-DVAAVDVNMGCPKEYSTKGGMGSALLSDPEKIEAILT 147

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K +S PVT K RI   ++D +      NLVK I+K+GV  I +H R         KD
Sbjct: 148 TLVKGISKPVTCKIRILSTIEDTV------NLVKRIEKTGVAAIAVHGRM--------KD 193

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS------VDGVMIGRAAYK 221
            R    +  D +  +  ++  + +  NGG  D+ +  + + +         VM+ RAA  
Sbjct: 194 ERPRHPVHCDYIQAV-AQSVSVPVIANGGSSDIVKEFEDIETFRESTGASSVMLARAAMW 252

Query: 222 NSAMLT-----TVDE-----------YFSNPLTGS----SPIKTRVDKDFWRKISASMTD 261
           N ++       +VD+           Y +NP          ++ RV+  F +++ A+ T+
Sbjct: 253 NPSVFRQQGALSVDQVMQEYITYAVRYDNNPFNTKYCLCQMLRDRVESPFGKRLHAAQTN 312


>gi|262199164|ref|YP_003270373.1| hypothetical protein Hoch_6005 [Haliangium ochraceum DSM 14365]
 gi|262082511|gb|ACY18480.1| TIM-barrel protein, nifR3 family [Haliangium ochraceum DSM 14365]
          Length = 348

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 107/219 (48%), Gaps = 23/219 (10%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L  TE + A A+  GD + +  L  S       +QI G ++  LV+AA++  D G + I+
Sbjct: 42  LTITEFLKATALCDGDAEVVDKLTASLDGVRFGVQIYGREVEPLVQAAQLALDIGASLID 101

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPA 133
           +N+GCP+ RV  G  GA LM  P++  + + A+  ++  S+PVTVK R G   ++   P 
Sbjct: 102 INMGCPAKRVVAGECGAALMQWPELSAELVRAVVASVPDSVPVTVKHRAGWNPLNRNAPE 161

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIG 192
            A      ++ ++G   + +H R         +      ++D +++  +++  P  + + 
Sbjct: 162 FAC-----AMVEAGAQMVTVHGRT--------RTQGFAGSVDLEVIRRVREAVPARVPVV 208

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
            NG +  +   L++      D VMIGR A  N  +  ++
Sbjct: 209 GNGDVVCVDDYLRMREHTGCDAVMIGRGALGNPWLFRSL 247


>gi|23464743|ref|NP_695346.1| NifR3-like protein [Bifidobacterium longum NCC2705]
 gi|189438998|ref|YP_001954079.1| tRNA-dihydrouridine synthase [Bifidobacterium longum DJO10A]
 gi|213691694|ref|YP_002322280.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|317481587|ref|ZP_07940623.1| dihydrouridine synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|23325312|gb|AAN23982.1| possible NifR3-like protein [Bifidobacterium longum NCC2705]
 gi|189427433|gb|ACD97581.1| tRNA-dihydrouridine synthase [Bifidobacterium longum DJO10A]
 gi|213523155|gb|ACJ51902.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|316916947|gb|EFV38333.1| dihydrouridine synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|320457785|dbj|BAJ68406.1| putative dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 414

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 174 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|18310257|ref|NP_562191.1| dihydrouridine synthase family protein [Clostridium perfringens
           str. 13]
 gi|168213028|ref|ZP_02638653.1| dihydrouridine synthase family protein [Clostridium perfringens CPE
           str. F4969]
 gi|18144936|dbj|BAB80981.1| probable transcriptional regulator [Clostridium perfringens str.
           13]
 gi|170715388|gb|EDT27570.1| dihydrouridine synthase family protein [Clostridium perfringens CPE
           str. F4969]
          Length = 321

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 110/237 (46%), Gaps = 21/237 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHKEELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   I +++K R+G+D          L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKIDDIKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  PNL+ +     + K NP  + G    LED ++ ++    VD +M+GR    N A++ 
Sbjct: 173 K--PNLEVFKDAISLSK-NPVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGVLANPALM- 228

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  N +  +  +  +V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 229 -------NEILNNEFMDKKVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|258620655|ref|ZP_05715692.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM573]
 gi|258587170|gb|EEW11882.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM573]
          Length = 331

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 110/245 (44%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++   +  +  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIESILKTVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V++  L +     G+  + +H R    + KG            +
Sbjct: 145 VTLKTRTGWDTDNRNCVSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|312132439|ref|YP_003999778.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp. longum
           BBMN68]
 gi|311773058|gb|ADQ02546.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp. longum
           BBMN68]
          Length = 414

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 174 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|195443038|ref|XP_002069246.1| GK21069 [Drosophila willistoni]
 gi|194165331|gb|EDW80232.1| GK21069 [Drosophila willistoni]
          Length = 519

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 109/237 (45%), Gaps = 25/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 37  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFANDVKYRKDALQTCAEDRPLIIQFCGND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA + +    + I++N+GCP A    G +G+ L    +++   ++ + + LSIP
Sbjct: 96  SQQILEAALLAQGHC-DAIDINLGCPQAIAKRGHYGSFLQDEWELLEKIVSTLHEKLSIP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +     +R   K ++ +G   + +H R    K  L G++          
Sbjct: 155 VTCKIRIFEDRE---KTIR-YAKMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 200

Query: 175 DYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D+  +  ++KE   P    G   GLED+ + L     VDGVM       N A+   +
Sbjct: 201 DWSYIRSVRKEIKIPMFANGNILGLEDVHRCLDTT-GVDGVMSAEGNLHNPAIFRGI 256


>gi|17545225|ref|NP_518627.1| NIFR3-like protein [Ralstonia solanacearum GMI1000]
 gi|17427516|emb|CAD14034.1| putative trna-dihydrouridine synthase protein [Ralstonia
           solanacearum GMI1000]
          Length = 356

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 117/242 (48%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   ++ +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSERTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   + G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVERGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +PVT+K R G D +      RN   + +  +++G++ + +H R         + +     
Sbjct: 136 VPVTLKIRTGWDRE-----HRNALTVARIAQEAGISMLTVHGRT--------RADLYHGE 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ 
Sbjct: 183 AEYETIAAVKA-SVRIPVVANGDIGTPAKARHVLEVTGADAIMIGRAAQGRPWLFREIEH 241

Query: 232 YF 233
           + 
Sbjct: 242 FL 243


>gi|229588163|ref|YP_002870282.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens SBW25]
 gi|229360029|emb|CAY46883.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens SBW25]
          Length = 337

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 125/262 (47%), Gaps = 18/262 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ +        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRMRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVAEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    +    + K  +++G+  + +H R         + +      +YD
Sbjct: 139 VTLKIRTGWDRDNKNGL---TVAKIAEQAGITALAVHGRT--------RADLYTGEAEYD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I K+   + +  NG ++   +A ++L +   DG++IGRAA     +   ++ +   
Sbjct: 188 TIAAI-KQAVSIPVFANGDIDSAEKARRVLHATGADGLLIGRAAQGRPWIFREIEHFLRT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISA 257
                +P    V++     ++A
Sbjct: 247 GDVLPAPELIEVERILLEHLAA 268


>gi|24371990|ref|NP_716032.1| hypothetical protein SO_0394 [Shewanella oneidensis MR-1]
 gi|38604872|sp|Q8EJR8|DUSB_SHEON RecName: Full=tRNA-dihydrouridine synthase B
 gi|24345845|gb|AAN53477.1|AE015487_11 conserved hypothetical protein [Shewanella oneidensis MR-1]
          Length = 322

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 81/332 (24%), Positives = 155/332 (46%), Gaps = 37/332 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK +  +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLC-LRYGAALAVSEMLSSNPEVWDTDKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G + I++N+GCP+ +V++   G+ LM NP +V D + A+  A+ +P
Sbjct: 76  PELMAQAAQFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKDILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN   + +  +  G+  + +H   R+ + KG          N
Sbjct: 136 VTLKIRTGWEPE-----HRNGVQIAQIAEDCGIASLAVHGRTRQCMYKG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K+N  + +  NG ++   +A  +L    VD +MIGR A     +   +  
Sbjct: 181 AEYDTIKAI-KQNVSIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQH 239

Query: 232 YFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           Y     TG+  +PI+    +    +    + D     L+   K  +  R  IG +    +
Sbjct: 240 YLE---TGNKLAPIEVAEQRQVMLEHLTKLYD-----LYGEYKGIRFARKHIGWYLDQED 291

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            R+ R     +   +   + ++E  F+ ++++
Sbjct: 292 QRQFRADFN-QLETAAEQYSLVEYYFDELVQN 322


>gi|294341441|emb|CAZ89858.1| tRNA-dihydrouridine synthase B [Thiomonas sp. 3As]
          Length = 331

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/258 (26%), Positives = 114/258 (44%), Gaps = 27/258 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR L       +EM+ + A LR   K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPYRRLARQL-GAGYCVSEMVTSRADLRDTLKTSRRANHDGEAAPIAVQIVGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKAL 115
             ++ EA +   + G + I++N+GCP+ +V     G+ LM + D+     +   A  +  
Sbjct: 76  PEQIAEATRYNLERGADIIDINMGCPAKKVCNRWAGSALMQDEDLAARLVEAAVAAARPF 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG---IWIHARKAILKGLSPKDNRKIP 172
             PVT+K R G  +     A RN  +  +++   G   + +H R         ++     
Sbjct: 136 GAPVTLKMRAGWCE-----AARNAPRIARRAEAAGAAMLVVHGRT--------REQGYGG 182

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             +Y  + E+K+ +  + +  NG ++   +A  +L     D VMIGRAA     +   V 
Sbjct: 183 EAEYATLAEVKR-SVGIPVVANGDIDSPQKAAAVLRQSGADAVMIGRAAMGRPWLFGQVA 241

Query: 231 EYFSNP--LTGSSPIKTR 246
            Y      L G +P++ R
Sbjct: 242 AYLERGVLLPGPAPVQWR 259


>gi|159469612|ref|XP_001692957.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158277759|gb|EDP03526.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 283

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/155 (29%), Positives = 78/155 (50%), Gaps = 8/155 (5%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKP-LALQIGGADISKLVEAAKIVE 70
           R++ +  ++  E+   D + RG +   + F T  +E+P L  Q+G AD    ++AA++V 
Sbjct: 41  RVIASTRVVNEELQSIDFLDRGGEHGRVMFRTTAEERPRLVFQLGAADAVLALQAAQVVA 100

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
                E+ LN+GCP A   +G  GA L+  P+I  D +  + + L+IPV+ K R+   DQ
Sbjct: 101 G-DVAEVGLNMGCPKAFSLQGGMGAALLRKPEIAEDIMKTLHRNLNIPVSCKIRLLDTDQ 159

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
                   L + +   G+N + +H R    +   P
Sbjct: 160 DTV----ELARRLAACGINALAVHGRTTQQRPRDP 190


>gi|117619221|ref|YP_857984.1| tRNA-dihydrouridine synthase B [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560628|gb|ABK37576.1| tRNA-dihydrouridine synthase B [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 321

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/256 (24%), Positives = 114/256 (44%), Gaps = 26/256 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM++A+  +   +K  +    S +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRLGAGMAVSEMLLANPDVWDTQKTRMRMDHSAEGGLRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   +++N+GCP+ +V++   G+ L+  PD+V     A+  A+ +P
Sbjct: 76  PEMMAFAARYNVEQGAQIVDINMGCPAKKVNKKLAGSALLRQPDLVRTICRAVVDAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPN 173
           VT+K R G D        RN   + +  +  G+  + +H R    + +G           
Sbjct: 136 VTLKIRTGWDPDN-----RNGEEIARIAEDCGIAALAVHGRTRTDLYRG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  IK+    + +  NG ++   +A  +L    VD VMIGRAA     +   +  
Sbjct: 181 AEYDTIRAIKQAV-SIPVVANGDIDSPEKARYVLDYTGVDAVMIGRAAQGRPWIFREIRH 239

Query: 232 YFSNPLTGSSPIKTRV 247
           +         P +  V
Sbjct: 240 FLETGTKLPPPEREEV 255


>gi|296104976|ref|YP_003615122.1| tRNA-dihydrouridine synthase B [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059435|gb|ADF64173.1| tRNA-dihydrouridine synthase B [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 321

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN V   +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGWSPE-----HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPIIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|195031103|ref|XP_001988289.1| GH11083 [Drosophila grimshawi]
 gi|193904289|gb|EDW03156.1| GH11083 [Drosophila grimshawi]
          Length = 398

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 67/257 (26%), Positives = 118/257 (45%), Gaps = 27/257 (10%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAK 67
           F RLL  N   L +T M+++D+I   +K     F+T   ++PL  Q    D ++ V +A+
Sbjct: 37  FRRLLRQNGVQLAFTPMMISDSINNSEKARQNEFTTGPDDQPLIAQFAAKDATEFVTSAQ 96

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI 125
           ++  +  + I+LN GCP +      +G  L+  PD + D I  + + L     V+VK R+
Sbjct: 97  LIYPY-VDGIDLNCGCPQSWAIAKGYGCGLLRQPDQMRDMIQCLRRTLPTGFSVSVKMRL 155

Query: 126 --GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
             G D  I       L + ++  GV  + +H R    K    KD   +  +  D+   ++
Sbjct: 156 LQGSDSDISLQKTIQLAQQLEHCGVTFLTLHGRTPAQK--HSKDTLNVAAM-ADVAQSLQ 212

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                + + +NG +E    A ++  +    GVM  R    N A+  +  +Y   PL  ++
Sbjct: 213 -----IPLIVNGNVESYRDACELHANTQAAGVMAARGLLANPALFNS--DY---PLAETT 262

Query: 242 PIKTRVDKDFWRKISAS 258
           P K+ V +  W  I+ S
Sbjct: 263 P-KSCVQQ--WLDIAQS 276


>gi|291528191|emb|CBK93777.1| tRNA-dihydrouridine synthase [Eubacterium rectale M104/1]
          Length = 312

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 43/162 (26%), Positives = 78/162 (48%), Gaps = 14/162 (8%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
           +GY+EIN+N+GCPS  V     G+ ++  PD++   +  +      PV++K R+G +D  
Sbjct: 81  YGYDEINVNLGCPSGTVVSKKRGSGILAYPDMLDSFLDELYTKADFPVSIKTRVGFNDD- 139

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LF 190
                  L++   K  ++ + +H R  + K       +  P +D D    ++K NPD   
Sbjct: 140 --ELWPKLIEIYSKYPISELTVHPR--VQKDFY----KNTPRMD-DFALAMQKINPDKTT 190

Query: 191 IGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           +  NG + D    +      P +D +MIGR  + N A++  +
Sbjct: 191 LCYNGDITDTNSFNALTDCFPDIDEIMIGRGLFANPALIAEL 232


>gi|257057698|ref|YP_003135530.1| putative TIM-barrel protein, nifR3 family [Saccharomonospora
           viridis DSM 43017]
 gi|256587570|gb|ACU98703.1| putative TIM-barrel protein, nifR3 family [Saccharomonospora
           viridis DSM 43017]
          Length = 379

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 73/293 (24%), Positives = 122/293 (41%), Gaps = 25/293 (8%)

Query: 12  FARLLTN-NALLYT-EMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL     A LY  EMI A A++       +++ F   E P ++Q+ G D + + EA K
Sbjct: 34  FRRLCREYGAGLYVCEMITARAVVERHPGTMHMMTFDASEYPRSMQLYGVDPATMKEAVK 93

Query: 68  IVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKC 123
           I+   G  + I+ N GCP A+V     GA L     + G+ + A  +A     +P TVK 
Sbjct: 94  IIVGEGLADHIDANFGCPVAKVTRKGGGAALPFKRKLFGNIVRASVEAAEPAGVPFTVKF 153

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G+DD        +  +  +  G   + +HAR A          R     D+  +  +K
Sbjct: 154 RVGIDDD--HHTYLDAGRIAEAEGAAAVALHARTAA--------QRYSGKADWSHIARLK 203

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +    + +  NG +     AL+++     DGV+IGR       +   ++  F+     + 
Sbjct: 204 EAVTSIPVLGNGDIFTAHDALRMVAETGCDGVVIGRGCLGRPWLFGELEAAFAGKPIPAG 263

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           P    V +   R       +    H      ++ + +HM   F GFP   + R
Sbjct: 264 PNLGEVARVLRRH-----AELLVEHDGPDKAMRDLRKHMAWYFMGFPVGSQLR 311


>gi|261342713|ref|ZP_05970571.1| tRNA-dihydrouridine synthase B [Enterobacter cancerogenus ATCC
           35316]
 gi|288315366|gb|EFC54304.1| tRNA-dihydrouridine synthase B [Enterobacter cancerogenus ATCC
           35316]
          Length = 321

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKAILTAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN V   +  +  G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGWSPE-----HRNCVEIAQLAEDCGIQALTIHGRTRACLFNGYA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRAVKQKVSIPIIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|145296565|ref|YP_001139386.1| hypothetical protein cgR_2473 [Corynebacterium glutamicum R]
 gi|140846485|dbj|BAF55484.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 363

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 74/287 (25%), Positives = 122/287 (42%), Gaps = 29/287 (10%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R  T + L   EM+ A A++  ++K  ++  F+  E P +LQ+   D     EAAK IV+
Sbjct: 20  RTGTISGLYVCEMVTARALVERNEKTMHMTTFAPDENPRSLQLYTVDPKYTYEAAKMIVD 79

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V     G+ +     +  + ++A  KA     IPVTVK R+G+
Sbjct: 80  ENLADHIDMNFGCPVPKVTRRGGGSAIPYKRRLFENIVSAAVKATEGTDIPVTVKFRVGI 139

Query: 128 DDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           DD+      A R  V +  KS    + +HAR A          R     D++ +  +K+ 
Sbjct: 140 DDEHHTHLDAGRIAVDAGAKS----VALHARTAA--------QRYSGEADWNEIARLKEH 187

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             D  I +  NG +   S A +++     DGV++GR       +   +            
Sbjct: 188 LADTGIPVLGNGDIFAASDATRMMEQTGCDGVVVGRGCLGRPWLFAELSAAVRGEEIPEE 247

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           P    V +   R     M     +H      L+ + +HM     GFP
Sbjct: 248 PTFGEVTQIILRHAELLM-----QHDGETKGLRDLRKHMGWYLRGFP 289


>gi|168057686|ref|XP_001780844.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667700|gb|EDQ54323.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 401

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 119/257 (46%), Gaps = 24/257 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  Y+ M+ +    +  K  +  FST  +++PL +Q    +
Sbjct: 51  MVDQSELPFRMLCRKYGATAA-YSPMLHSRLFAQDAKYRLKEFSTCPEDRPLFIQFCANN 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAAK+V+D   + +++N GCP      G++GA LM +  +V   +  +   L+ P
Sbjct: 110 PDTLLEAAKLVQD-DCDYVDINFGCPQRIAKRGNYGAFLMDDLPLVRSLVEKLSSGLTTP 168

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   ++D +         + I+++G + + +H R         KD + I   D+
Sbjct: 169 VSCKIRMFPKLEDTL------AYARMIEEAGCSLLAVHGRTR-----DQKDGKSI-RADW 216

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++  +K     P +  G    LED+ + ++    VDGVM   +  +N A+      Y  
Sbjct: 217 GVIKAVKSALRIPVVANGNIRWLEDVDECIRAT-GVDGVMSAESLLENPALFAG---YRM 272

Query: 235 NPLTGSSPIKTRVDKDF 251
            PL  S+      DK +
Sbjct: 273 KPLDSSAAEPDDHDKKY 289


>gi|193690494|ref|XP_001952087.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Acyrthosiphon
           pisum]
          Length = 456

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 95/206 (46%), Gaps = 26/206 (12%)

Query: 30  DAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           D I + D   +    ++EK  + LQIG +D  +  +AA++VE      I++N+GCP    
Sbjct: 66  DFIDKSDATVVFRTCSREKHNVVLQIGTSDPERAAKAAQVVEQ-DVAGIDINMGCPKDFS 124

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKS 146
            +G  GA L+ +PD     ++A+  A+ IPVT K R+   +DD +       L K +  +
Sbjct: 125 LKGGMGAALLFHPDKACAILSAVVSAVKIPVTCKIRVLQDIDDTVA------LCKKLAAT 178

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG------LEDM 200
           GV  I +H R    + +    N  I  +          E  D+ +  NGG       ED+
Sbjct: 179 GVAAICVHGRTINERPMHSNRNHFIKAIS---------EALDIPVIANGGSKEIKVFEDI 229

Query: 201 SQALKILPSVDGVMIGRAAYKNSAML 226
            +  K +     VMI R A KN ++ 
Sbjct: 230 IK-FKNITGCSSVMIARTAEKNCSIF 254


>gi|78223758|ref|YP_385505.1| dihydrouridine synthase TIM-barrel protein nifR3 [Geobacter
           metallireducens GS-15]
 gi|78195013|gb|ABB32780.1| tRNA-U20-dihydrouridine synthase [Geobacter metallireducens GS-15]
          Length = 324

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 107/228 (46%), Gaps = 21/228 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  AR     +L +TEM+  + ++R  +K   +L    +++PL +Q+ G D
Sbjct: 21  MAGITNLPFRLLARE-EGASLCFTEMVSVNGLVREGRKTFELLRSVPEDRPLGIQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E A++VE  G + I++N+GCP  +V     G+ L+  P  V   I    +A  +P
Sbjct: 80  PQLLAEGARMVEGHG-DLIDINMGCPVKKVVGTGAGSALLREPAKVRAIIRETRRATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDY 176
           +TVK R G           ++ +  ++ G + I +H  +R  + +G          + D+
Sbjct: 139 LTVKIRSGW--ACGEANFLDIAQIAEEEGCDAITLHPRSRSQMFEG----------HADW 186

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
             + E+K+      IG +G L   +    +L     DGVM+ R A  N
Sbjct: 187 QQIAEMKQSVKIPVIG-SGDLFTAADVTAMLAETGCDGVMVARGALGN 233


>gi|303278204|ref|XP_003058395.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459555|gb|EEH56850.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 440

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE----KPLALQIGG 56
           MVD ++  +R   R      L YT MI A   +   K     F+T E    +PL +Q   
Sbjct: 54  MVDQSELAFRTLCRRY-GATLAYTPMIHARLFVEDLKYRAEIFTTVEGIADRPLLVQFCA 112

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D + L+ AAK+V     + +++N GCP     +G +GA LM +   V D I+ + K LS
Sbjct: 113 NDPATLLAAAKLVAPHC-DGVDINFGCPQRIAKKGRYGAFLMDDWKTVHDLISILDKELS 171

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  DD   ++    +V++   +G   + IH R    K  S  D R     ++
Sbjct: 172 VPVTAKIRV-YDDLETSIQYAEMVQN---AGAQLVAIHGRTREQKRAS--DVRA----NW 221

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
             +  I KE   + +  NG +  +++A K L +   DGVM      +N ++       FS
Sbjct: 222 AFIKAI-KERLTVPVIANGDVRTLAEARKCLEATGADGVMSADPLLENPSL-------FS 273

Query: 235 NP 236
           +P
Sbjct: 274 DP 275


>gi|169335415|ref|ZP_02862608.1| hypothetical protein ANASTE_01827 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258153|gb|EDS72119.1| hypothetical protein ANASTE_01827 [Anaerofustis stercorihominis DSM
           17244]
          Length = 329

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/297 (21%), Positives = 130/297 (43%), Gaps = 32/297 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-----KPLALQIGGADISKLV 63
           YR F R +    +  +EM+ A  +    K       T E         +QI G++   + 
Sbjct: 31  YRLFMREM-GCKIFISEMVSAKGLYYKSKNTFPLMETNELEHKDSVTGIQIFGSEPEIMG 89

Query: 64  E-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           E   + + D  ++ I++N+GCP  ++     G+ L+ + D     +  +  A S PV+VK
Sbjct: 90  EITERYINDTAFDFIDINMGCPMKKIVNNGDGSALLKDLDKANKVVREVKSASSKPVSVK 149

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVY 180
            R+G ++ I    + +++K+I+  G + I +H   R+ +  G           +DYD + 
Sbjct: 150 VRLGFNENI----IEDIIKAIEDGGADMITVHGRTREQVFTG----------EVDYDGIK 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           +  KE   + +  NG L++  +A + +     DGVMIGR A  +  + +  +E  S    
Sbjct: 196 K-AKETASVPLIANGDLDNYLKAKEKMDYTGADGVMIGRGANYDPFIFSQFNECISGKKV 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ ++D       +    +   ++     K+ +  +++     G  NS + R+
Sbjct: 255 SEYSLRDKIDA------ARKHFEIHLKYSKDKKKVIEFRKYLYWYIKGIKNSAKIRN 305


>gi|156536943|ref|XP_001608232.1| PREDICTED: similar to MGC79829 protein [Nasonia vitripennis]
          Length = 346

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/281 (23%), Positives = 125/281 (44%), Gaps = 31/281 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+AD+ ++  K     FST E   PL +Q    +
Sbjct: 21  MVRYSKLPFRTLVRKYDCD-ICFTPMILADSFVQSSKARDSEFSTNEGDSPLIVQFAAKE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   VEA ++V  +  N ++LN GCP     +  +GA L+  P +V + ++ +   +  P
Sbjct: 80  VDDFVEATEMVAPYS-NGVDLNCGCPQRWALKDGYGADLLTKPQLVKELVSNVRNRIPKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I         ++I+ +GV+ + +HAR          D R  P +D D 
Sbjct: 139 FTVSVKIRILKDIKKTI--EFSRAIEHAGVSFLTVHARTP--------DMRNEP-IDLDS 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ +    L +  NG +     A  +      +GVM+      N A+ +         
Sbjct: 188 L-KLVRSCVHLPMIANGNVRSFEDAKTLYEESKCNGVMVAGGILTNPAIFSGY------- 239

Query: 237 LTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQI 276
              ++P++   D   W  I+++M T +   H H    L+++
Sbjct: 240 --KNTPVECIQD---WLDITSTMSTQFMCMHHHLVFMLEKV 275


>gi|195484353|ref|XP_002090658.1| GE13230 [Drosophila yakuba]
 gi|194176759|gb|EDW90370.1| GE13230 [Drosophila yakuba]
          Length = 395

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 110/235 (46%), Gaps = 17/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + +AL   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVRQVVQEVRRALPAD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+   +Q     + +L + ++++GV  + +H R       +P        LD 
Sbjct: 148 FSVSVKMRLLGGEQSLERTI-DLARQLEQAGVTFLTLHGR-------TPAQKHSKDTLDI 199

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTV 229
             + E++K +  + + +NG +E    A  +       GVM  R    N A+  ++
Sbjct: 200 PAMAEVRK-SLQIPLIVNGNVESYRDACDMHDQTGAAGVMAARGLLANPALFNSI 253


>gi|84393068|ref|ZP_00991834.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
 gi|84376320|gb|EAP93202.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
          Length = 322

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/193 (26%), Positives = 90/193 (46%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+   D G   I++N+GCP+ +V++   G+ L+ +P+++ D + A
Sbjct: 68  SVQIAGADPQLMAEAAQFNVDNGAQIIDINMGCPAKKVNKKLAGSALLQHPELIEDILKA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKD 167
           +  A+ +PVT+K R G D        RN V+  K     G+  + +H R          +
Sbjct: 128 VVNAVDVPVTLKTRTGWDTDN-----RNCVQIAKIAEDCGIQALALHGRTRACMYKGEAE 182

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
            + I         +  K+   + +  NG ++   +A  +L     D +MIGR A     +
Sbjct: 183 YKHI---------KAAKQAVSIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWI 233

Query: 226 LTTVDEYFSNPLT 238
              +  Y  N  T
Sbjct: 234 FNEILHYLENGTT 246


>gi|295707311|ref|YP_003600386.1| dihydrouridine synthase [Bacillus megaterium DSM 319]
 gi|294804970|gb|ADF42036.1| dihydrouridine synthase (Dus) [Bacillus megaterium DSM 319]
          Length = 332

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/194 (28%), Positives = 91/194 (46%), Gaps = 24/194 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K  L F+  E+P+   I G       + +  + + G+  I++N+GCP   V     G+ L
Sbjct: 60  KGRLTFTDDEQPIVAHIWGDKAEYFRQMSIGMAEMGFRGIDINMGCPVQNVAGNGKGSGL 119

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           +  PD   + I A  KA  +PV+VK R+G   VD+        + +K I +  +  + IH
Sbjct: 120 IRRPDTAAEIIQA-AKAGGLPVSVKTRLGYTQVDEWY------DWLKHILEQDIVNLSIH 172

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS- 209
            R    K +S  D        ++++ EIKK      P   + +NG + D  + L++    
Sbjct: 173 LRTK--KEMSDVDAH------WELIPEIKKLRDEIAPHTLLTINGDIPDRQKGLELAEKY 224

Query: 210 -VDGVMIGRAAYKN 222
            VDG+MIGR  + N
Sbjct: 225 GVDGIMIGRGIFHN 238


>gi|302499246|ref|XP_003011619.1| hypothetical protein ARB_02173 [Arthroderma benhamiae CBS 112371]
 gi|302667563|ref|XP_003025363.1| hypothetical protein TRV_00424 [Trichophyton verrucosum HKI 0517]
 gi|291175171|gb|EFE30979.1| hypothetical protein ARB_02173 [Arthroderma benhamiae CBS 112371]
 gi|291189471|gb|EFE44752.1| hypothetical protein TRV_00424 [Trichophyton verrucosum HKI 0517]
          Length = 567

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 101/208 (48%), Gaps = 21/208 (10%)

Query: 24  TEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           T+   A+  L G+ K+       ++PL +Q    D  +L++AA+ VE    + ++LN+GC
Sbjct: 115 TDETTAEPYLDGNPKH-------DRPLIVQFCANDPDELLKAARHVEAH-CDAVDLNLGC 166

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P     +G +GA L  +PD++   I  +   LSIPVT K RI ++ +   +    ++ S 
Sbjct: 167 PQGIAKKGHYGAFLQEDPDLIYKLINKLHNELSIPVTAKFRI-LETKEKTLEYARMILS- 224

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDM 200
             +G + + +H R+   KG     N  + N +Y I Y      P+  I  NG +    D+
Sbjct: 225 --AGASILSVHGRRREQKG----HNTGVANWEY-IRYLRDNLPPETVIFANGNILNHSDI 277

Query: 201 SQALKILPSVDGVMIGRAAYKNSAMLTT 228
           S+ L++    DGVM       +  + +T
Sbjct: 278 SRCLEVT-GADGVMSAEGNLSDPTIFST 304


>gi|296454480|ref|YP_003661623.1| putative TIM-barrel protein [Bifidobacterium longum subsp. longum
           JDM301]
 gi|296183911|gb|ADH00793.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. longum JDM301]
          Length = 414

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVARNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  + I    A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELIQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 174 AGIPVTSKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|23308951|ref|NP_601768.2| TIM-barrel containing enzyme [Corynebacterium glutamicum ATCC
           13032]
 gi|62391408|ref|YP_226810.1| hypothetical protein cg2841 [Corynebacterium glutamicum ATCC 13032]
 gi|21325342|dbj|BAB99963.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Corynebacterium glutamicum ATCC 13032]
 gi|41326749|emb|CAF21231.1| Predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           [Corynebacterium glutamicum ATCC 13032]
          Length = 381

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 70/285 (24%), Positives = 120/285 (42%), Gaps = 25/285 (8%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R  T + L   EM+ A A++  ++K  ++  F+  E P +LQ+   D     EAAK IV+
Sbjct: 38  RTGTISGLYVCEMVTARALVERNEKTMHMTTFAPDENPRSLQLYTVDPKYTYEAAKMIVD 97

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V     G+ +     +  + ++A  KA     IPVTVK R+G+
Sbjct: 98  ENLADHIDMNFGCPVPKVTRRGGGSAIPYKRRLFENIVSAAVKATEGTDIPVTVKFRVGI 157

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD+       +  +    +G   + +HAR A          R     D++ +  +K+   
Sbjct: 158 DDE--HHTHLDAGRIAVDAGAKSVALHARTAA--------QRYSGEADWNEIARLKEHLA 207

Query: 188 DLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           D  I +  NG +   S A +++     DGV++GR       +   +            P 
Sbjct: 208 DTGIPVLGNGDIFAASDATRMMEQTGCDGVVVGRGCLGRPWLFAELSAAVRGEEIPEEPT 267

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              V +   R     M     +H      L+ + +HM     GFP
Sbjct: 268 FGEVTQIILRHAELLM-----QHDGETKGLRDLRKHMGWYLRGFP 307


>gi|210630846|ref|ZP_03296620.1| hypothetical protein COLSTE_00505 [Collinsella stercoris DSM 13279]
 gi|210160280|gb|EEA91251.1| hypothetical protein COLSTE_00505 [Collinsella stercoris DSM 13279]
          Length = 317

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 94/214 (43%), Gaps = 27/214 (12%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   +  + V A K++ D GY E+NLN+GCPS  V     G+  + N D +   +  +C
Sbjct: 65  QLLTKNAEEFVWATKLLADMGYREVNLNLGCPSGTVVSKGKGSGFLRNLDELEVFLRDVC 124

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNR- 169
           +   IPV+VK R+G++D      + +L +S+    +  + +H R  K    G SP+  R 
Sbjct: 125 ERSPIPVSVKTRLGLEDDAEYERILDLYRSLP---LAELIVHPRVQKDRYTG-SPRQGRY 180

Query: 170 --KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              +    + + Y     N D+F+      ED S      P+   VM+GR    N A++ 
Sbjct: 181 GDTLARAPFPVAY-----NGDIFVP-----EDASALCAAYPATRHVMLGRGLLANPALVR 230

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
                    L G  P      K F  K+  +  D
Sbjct: 231 M--------LAGGVPATASELKQFHDKLFHAYVD 256


>gi|167564059|ref|ZP_02356975.1| dihydrouridine synthase [Burkholderia oklahomensis EO147]
 gi|167571203|ref|ZP_02364077.1| dihydrouridine synthase [Burkholderia oklahomensis C6786]
          Length = 334

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/247 (24%), Positives = 119/247 (48%), Gaps = 27/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 1   MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 60  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 119

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
             ++PVT+K R G D +   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 120 PDAVPVTLKIRTGWDREHKNAITVAKLAEA---AGISMLTVHGRTRADLYRG-------- 168

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +    +A  +L +   D +MIGRAA     +   
Sbjct: 169 --DAEYDTIAAVKAA-VRIPVVANGDITSPHKAKAVLDATGADALMIGRAAQGRPWLFRE 225

Query: 229 VDEYFSN 235
           +  +  +
Sbjct: 226 IGHFLQS 232


>gi|29832192|ref|NP_826826.1| dihydrouridine synthase [Streptomyces avermitilis MA-4680]
 gi|29609310|dbj|BAC73361.1| putative dihydrouridine synthase [Streptomyces avermitilis MA-4680]
          Length = 401

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 105/224 (46%), Gaps = 16/224 (7%)

Query: 18  NNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY- 74
              L  +EMI   A++  ++K   ++ F   EKP ++Q+ G D + + +A +++ + G  
Sbjct: 63  GKGLFVSEMITTRALVERNEKTMQLIHFDATEKPRSIQLYGVDPATVGKAVRMIAEEGLA 122

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCRIGVDDQIPA 133
           + I+LN GCP  +V     G+ L    +++   +  A+  A ++PVT+K R G+DD    
Sbjct: 123 DHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGAGNLPVTMKMRKGIDDD--H 180

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  +   + GV  I +H R A                D+D +  +K+  P++ +  
Sbjct: 181 ITYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTADWDAIARLKEHVPEIPVLG 232

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           NG +     A++++     DGV++GR       + + +   F  
Sbjct: 233 NGDIWSAEDAVRMVRETGCDGVVVGRGCLGRPWLFSDLVAAFEG 276


>gi|242309035|ref|ZP_04808190.1| conserved hypothetical protein [Helicobacter pullorum MIT 98-5489]
 gi|239524459|gb|EEQ64325.1| conserved hypothetical protein [Helicobacter pullorum MIT 98-5489]
          Length = 317

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 123/261 (47%), Gaps = 29/261 (11%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI---N 78
           +EMI   A+   +KK I  +  S  E P ALQI G D   + +A + + +F  NEI   +
Sbjct: 38  SEMISVHALAFKNKKTIKMIEKSPLENPFALQIAGNDFGIIQKAVEFLNEFK-NEIQILD 96

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALR 137
           LN GCP+ +V     G+ L+ + + +   +  + +    P ++VK R+G D +IP     
Sbjct: 97  LNCGCPAPKVSSHGSGSSLLKDLNKLVKILQLLRETSVFPYLSVKVRLGFDKKIPL---- 152

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  ++  S ++ + +H R       +  D  K   +DYD +  IK+      I  NG +
Sbjct: 153 EIANALNDSPIDYVVVHGR-------TKSDGYKKDKIDYDSIRLIKQNIQHPLIA-NGEI 204

Query: 198 EDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                A K+  L   +GVMIGRAA +   + T +     N L  S  ++ +V  + + + 
Sbjct: 205 TSPQIAKKVQELTGAEGVMIGRAAIEKPWIFTQI----KNNLEESIELRKQVALEHFDRT 260

Query: 256 SASMTDYAA----RHLHSGGK 272
            +   DY A    ++LH+  K
Sbjct: 261 ISFRGDYGAIMFRKNLHAYSK 281


>gi|323189128|gb|EFZ74412.1| TIM-barrel protein, nifR3 family protein [Escherichia coli RN587/1]
          Length = 290

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 103/222 (46%), Gaps = 25/222 (11%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L  +EM+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I+
Sbjct: 5   LTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIID 64

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G      A   RN
Sbjct: 65  INMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGW-----APEHRN 119

Query: 139 ---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
              + +  +  G+  + IH R    +  G            +YD +  +K++     I  
Sbjct: 120 CEEIAQLAEDCGIQALTIHGRTRACLFNG----------EAEYDSIRAVKQKVSIPVIA- 168

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 169 NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|295097749|emb|CBK86839.1| tRNA-U20-dihydrouridine synthase [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 321

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN V   +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGWSPE-----HRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|51598988|ref|YP_073176.1| histidine phosphokinase/phophatase, putative [Borrelia garinii PBi]
 gi|51573559|gb|AAU07584.1| histidine phosphokinase/phophatase, putative [Borrelia garinii PBi]
          Length = 329

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/250 (24%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL   K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISVKGILNESKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G D  +   A +I+   G+  I++N+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNDPEQFYRAIEILGGMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +   G++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEV--NDWLGFLLGFGIDMLTVYPRLAVNQSEGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKLSSKHF 254


>gi|302551272|ref|ZP_07303614.1| dihydrouridine synthase [Streptomyces viridochromogenes DSM 40736]
 gi|302468890|gb|EFL31983.1| dihydrouridine synthase [Streptomyces viridochromogenes DSM 40736]
          Length = 412

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/243 (23%), Positives = 110/243 (45%), Gaps = 19/243 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E+P ++Q+ G 
Sbjct: 56  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDASERPRSVQLYGV 115

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKA 114
           D + + +A +++  ED   + I+LN GCP  +V     G+ L     ++   +  A+  A
Sbjct: 116 DPATVGKAVRMIAEEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVSGA 174

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +   +  +   + GV  I +H R A                
Sbjct: 175 GDLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTA 224

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K+  P++ +  NG +     AL+++     DGV++GR       + + +   
Sbjct: 225 DWDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFSDLVAA 284

Query: 233 FSN 235
           F  
Sbjct: 285 FEG 287


>gi|312968409|ref|ZP_07782618.1| TIM-barrel , nifR3 family protein [Escherichia coli 2362-75]
 gi|312286627|gb|EFR14538.1| TIM-barrel , nifR3 family protein [Escherichia coli 2362-75]
          Length = 280

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 28  VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 87

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 88  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 138

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 139 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 191

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 192 IFREIQHYL 200


>gi|320194746|gb|EFW69376.1| tRNA dihydrouridine synthase B [Escherichia coli WV_060327]
          Length = 281

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|149919781|ref|ZP_01908258.1| hypothetical protein PPSIR1_32512 [Plesiocystis pacifica SIR-1]
 gi|149819388|gb|EDM78819.1| hypothetical protein PPSIR1_32512 [Plesiocystis pacifica SIR-1]
          Length = 406

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/223 (24%), Positives = 100/223 (44%), Gaps = 20/223 (8%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAA--KIVEDFGYNE 76
           L  +EMI A  ++ G++K   +  F   E P +LQ+ G D    V AA  ++V +     
Sbjct: 61  LFVSEMITARPLVEGNQKTARLASFGPDEAPRSLQLYGVD-PFFVRAAVERLVGEGRVEH 119

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAV 134
           I++N GCP  ++     G+ +   P ++   +AA  +     +PVT+K R G+DD++  +
Sbjct: 120 IDMNFGCPVPKITRRGGGSAIPAKPRLLARIVAAAVEGARGQVPVTIKFRKGIDDRL--I 177

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             R+  +  ++ G   + +HAR AI               D+  + E+  +      G N
Sbjct: 178 TFRDAGRVAQEEGCAAVGLHARTAI--------EFYEDGADWSCIAELVDQLSIPVFG-N 228

Query: 195 GGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSN 235
           G + +   A +++      GV+IGR       +   +   FS 
Sbjct: 229 GDIWEAEDAARMMAQTGCAGVIIGRGCLGRPWLFAELARLFSG 271


>gi|120609588|ref|YP_969266.1| nifR3 family TIM-barrel protein [Acidovorax citrulli AAC00-1]
 gi|120588052|gb|ABM31492.1| tRNA-U20-dihydrouridine synthase [Acidovorax citrulli AAC00-1]
          Length = 353

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 75/315 (23%), Positives = 133/315 (42%), Gaps = 39/315 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+A+QI
Sbjct: 17  MAGVTDRPFRQLCKAL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 71

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G D + + EAA    D G   I++N+GCP+ +V     G+ LM N  +   +   +   
Sbjct: 72  AGTDAAMMSEAALYNIDRGAEIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAQAVVDA 131

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           C   ++PVT+K R G   Q      RN   L ++ +  G+  + +H R         ++ 
Sbjct: 132 CAPRNVPVTLKMRTGWCQQ-----HRNAVQLARAFEGVGIQMLTVHGRT--------REQ 178

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
               + +YD +  +K     + +  NG ++   +A  +L +   D +MIGRAA     + 
Sbjct: 179 GYKGHAEYDTIAAVKAAV-RVPVVANGDIDSPEKAKAVLAATGADAIMIGRAAQGRPWIF 237

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +  Y +     + P+   V     R +   + D+ A +  + G ++   +H+      
Sbjct: 238 REIGHYLATGEHLAPPLVAEVR----RLLLDHLQDHYALYGEATG-VRSARKHIAWYVRA 292

Query: 287 FPNSRRCR-HILTVE 300
            P     R HI T++
Sbjct: 293 LPGGEAFRQHINTID 307


>gi|238789816|ref|ZP_04633598.1| tRNA-dihydrouridine synthase B [Yersinia frederiksenii ATCC 33641]
 gi|238722175|gb|EEQ13833.1| tRNA-dihydrouridine synthase B [Yersinia frederiksenii ATCC 33641]
          Length = 290

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 102/217 (47%), Gaps = 21/217 (9%)

Query: 24  TEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ ++  + R DK  +    + E  +  +QI G D   +  AA+I    G   I++N+
Sbjct: 8   SEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDDMAAAARINVANGAQIIDINM 67

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLV 140
           GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +    + +  L 
Sbjct: 68  GCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSPEHRNCIEIAQLA 127

Query: 141 KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +S    G+  + IH   R  +  G +          +YD +  +K+      I  NG + 
Sbjct: 128 ES---CGIQALTIHGRTRSCLFNGEA----------EYDSIRAVKQIVSIPVIA-NGDIT 173

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 174 DPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|261228265|ref|ZP_05942546.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|301028291|ref|ZP_07191551.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 196-1]
 gi|307139948|ref|ZP_07499304.1| tRNA-dihydrouridine synthase B [Escherichia coli H736]
 gi|312972471|ref|ZP_07786645.1| TIM-barrel , nifR3 family protein [Escherichia coli 1827-70]
 gi|299878634|gb|EFI86845.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 196-1]
 gi|307625140|gb|ADN69444.1| tRNA-dihydrouridine synthase B [Escherichia coli UM146]
 gi|310334848|gb|EFQ01053.1| TIM-barrel , nifR3 family protein [Escherichia coli 1827-70]
 gi|315617069|gb|EFU97679.1| TIM-barrel , nifR3 family protein [Escherichia coli 3431]
 gi|320189607|gb|EFW64266.1| tRNA dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC1212]
 gi|320202169|gb|EFW76744.1| tRNA dihydrouridine synthase B [Escherichia coli EC4100B]
 gi|320650932|gb|EFX19389.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H- str. H
           2687]
 gi|320656313|gb|EFX24225.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320666837|gb|EFX33816.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154479|gb|EFZ40680.1| TIM-barrel , nifR3 family protein [Escherichia coli EPECa14]
 gi|323162945|gb|EFZ48780.1| TIM-barrel protein, nifR3 family protein [Escherichia coli E128010]
 gi|323165221|gb|EFZ51011.1| TIM-barrel , nifR3 family protein [Shigella sonnei 53G]
 gi|323173481|gb|EFZ59110.1| TIM-barrel protein, nifR3 family protein [Escherichia coli LT-68]
 gi|323178560|gb|EFZ64136.1| TIM-barrel protein, nifR3 family protein [Escherichia coli 1180]
 gi|325498839|gb|EGC96698.1| tRNA-dihydrouridine synthase B [Escherichia fergusonii ECD227]
 gi|326337955|gb|EGD61789.1| tRNA dihydrouridine synthase B [Escherichia coli O157:H7 str. 1125]
 gi|326347524|gb|EGD71249.1| tRNA dihydrouridine synthase B [Escherichia coli O157:H7 str. 1044]
 gi|327251354|gb|EGE63043.1| TIM-barrel protein, nifR3 family protein [Escherichia coli STEC_7v]
 gi|330909311|gb|EGH37825.1| tRNA dihydrouridine synthase B [Escherichia coli AA86]
 gi|332086518|gb|EGI91665.1| TIM-barrel protein, nifR3 family protein [Shigella dysenteriae
           155-74]
 gi|332087251|gb|EGI92384.1| TIM-barrel protein, nifR3 family protein [Shigella boydii 5216-82]
 gi|332345215|gb|AEE58549.1| TIM-barrel protein, nifR3 family protein [Escherichia coli UMNK88]
          Length = 281

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|125986951|ref|XP_001357238.1| GA10353 [Drosophila pseudoobscura pseudoobscura]
 gi|54645569|gb|EAL34307.1| GA10353 [Drosophila pseudoobscura pseudoobscura]
          Length = 398

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 110/235 (46%), Gaps = 17/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R+     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRM-NGVQLAFTPMMISDSINNSEKARQNEFSTDPDDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  L+  P+ V + +  + + L   
Sbjct: 89  ATEFVTSAQLIYPY-VDGIDLNCGCPQSWAMSKGYGCGLLRQPEQVREVVQQVRRTLPSD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G  ++       +L + ++++GV  + +H R       +P        L+
Sbjct: 148 FSVSVKMRLLGGSEEDSVERTIDLARQLERAGVTFLTLHGR-------TPAQKHSKDTLN 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTT 228
              + E++K +  + + +NG +E  S A ++       GVM  R    N A+  +
Sbjct: 201 VSAMEEVRK-SLQIPLIVNGNVESWSDACELHAQTGAAGVMAARGLLANPALFNS 254


>gi|302795500|ref|XP_002979513.1| hypothetical protein SELMODRAFT_444257 [Selaginella moellendorffii]
 gi|300152761|gb|EFJ19402.1| hypothetical protein SELMODRAFT_444257 [Selaginella moellendorffii]
          Length = 378

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A       K     F+T  +++PL +Q    +
Sbjct: 59  MVDQSELPFRMLCRKYGATGA-YTPMLHARLFSEDRKYRNYEFTTCPEDRPLLIQFCANN 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE F  + I++N+GCP      G++GA LM +  +V   +  +   L +P
Sbjct: 118 PDTLLAAAKLVEPFC-DYIDINLGCPQRIAKRGNYGAFLMDDLPLVQALVTKLVSNLDVP 176

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   +DD I      +  K ++ SG + + +H R         K +R +   D+
Sbjct: 177 VSCKIRMFPSLDDTI------SYAKMLESSGCSLLAVHGRTR-----EQKCSRTV-RADW 224

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +++  +K+    P L  G    LED  + ++    VDGV+   +  +N A+  
Sbjct: 225 EVIRAVKQALRIPVLANGNIRSLEDAERCIQET-GVDGVLSAESLLENPALFA 276


>gi|315062559|gb|ADT76886.1| tRNA-dihydrouridine synthase B [Escherichia coli W]
 gi|323183019|gb|EFZ68418.1| TIM-barrel protein, nifR3 family protein [Escherichia coli 1357]
          Length = 286

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 34  VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 93

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 94  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 144

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 145 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 197

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 198 IFREIQHYL 206


>gi|260947234|ref|XP_002617914.1| conserved hypothetical protein [Clavispora lusitaniae ATCC 42720]
 gi|238847786|gb|EEQ37250.1| conserved hypothetical protein [Clavispora lusitaniae ATCC 42720]
          Length = 415

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 83/168 (49%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNIL-----GFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K +N +     G   +++PL +Q 
Sbjct: 25  MVDQSELAWRILSRRY-GAELCYTPMFHARLFATEEKYRNKMWSEWDGDREKDRPLVVQF 83

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK VED   + ++LN+GCP     +G++GA LM + D+V   I  +   
Sbjct: 84  CANDPEYLLQAAKFVED-KCDAVDLNLGCPQGIARKGNYGAFLMDDWDLVYKLIRKLHDN 142

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           L  PVT K R+  DD   ++    +V S   +G   I IH R   +KG
Sbjct: 143 LKCPVTAKIRV-YDDWEKSLEYAKMVLS---AGAQFITIHGRTRDMKG 186


>gi|117558547|gb|AAI27296.1| LOC548984 protein [Xenopus (Silurana) tropicalis]
          Length = 451

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/193 (27%), Positives = 93/193 (48%), Gaps = 23/193 (11%)

Query: 43  FSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F T E+    +  Q+G AD  + +  AK++++     I++N+GCP     +G  GA L+L
Sbjct: 26  FQTCERERHSVVFQMGTADAERALTVAKLIQN-DIAAIDINMGCPKEYSTKGGMGAALLL 84

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKA 158
            P+ +   ++ + K +S P+T K RI     +P++    +LVK I+K+GV  I +H R  
Sbjct: 85  CPEKIEMILSTLVKGISKPITCKIRI-----LPSLTETISLVKLIEKTGVAAIAVHGRS- 138

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-----ALKILPSVDGV 213
                  K+ R    +  D++  I +      I   G  E + Q     A + + S   V
Sbjct: 139 -------KNERPQHPVHCDVIKAISQAVSIPVIANGGSQEFIRQFQDISAFRSVTSASSV 191

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 192 MLARAAMWNPSVF 204


>gi|320184072|gb|EFW58892.1| tRNA dihydrouridine synthase B [Shigella flexneri CDC 796-83]
          Length = 281

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|195116601|ref|XP_002002842.1| GI17600 [Drosophila mojavensis]
 gi|193913417|gb|EDW12284.1| GI17600 [Drosophila mojavensis]
          Length = 397

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 102/227 (44%), Gaps = 19/227 (8%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAK 67
           F RLL  N   L +T M++AD+I   +K     F+T   ++PL  Q    D  + V A++
Sbjct: 37  FRRLLRQNGVQLAFTPMMIADSINNSEKARQNEFTTGLDDQPLIAQFAAKDALEFVTASQ 96

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI 125
           ++  +  + ++LN GCP        +G  L+  P+ V D I ++ + L     V+VK R+
Sbjct: 97  LIYPY-VDGVDLNCGCPQGWAIAKGYGCGLLRQPEQVRDIIQSLRRTLPTDFSVSVKMRL 155

Query: 126 --GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
               D+Q        L + ++  GV  + +H R       +P        L+ + + E+ 
Sbjct: 156 LNSSDNQTSVNKTIQLAQQLEYCGVTFLTLHGR-------TPAQKHSKDTLNVEAMAEVA 208

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTT 228
           K +  + + +NG +E    A ++       GVM  R    N A+  +
Sbjct: 209 K-SLQIPLIVNGNVESYQDACELHKQTQAAGVMAARGLLANPALFNS 254


>gi|62859019|ref|NP_001016230.1| dihydrouridine synthase 2-like, SMM1 homolog [Xenopus (Silurana)
           tropicalis]
 gi|89268176|emb|CAJ82133.1| similar to dus2l (dihydrouridine synthase 2-like) [Xenopus
           (Silurana) tropicalis]
          Length = 495

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/193 (27%), Positives = 93/193 (48%), Gaps = 23/193 (11%)

Query: 43  FSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F T E+    +  Q+G AD  + +  AK++++     I++N+GCP     +G  GA L+L
Sbjct: 70  FQTCERERHSVVFQMGTADAERALTVAKLIQN-DIAAIDINMGCPKEYSTKGGMGAALLL 128

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKA 158
            P+ +   ++ + K +S P+T K RI     +P++    +LVK I+K+GV  I +H R  
Sbjct: 129 CPEKIEMILSTLVKGISKPITCKIRI-----LPSLTETISLVKLIEKTGVAAIAVHGRS- 182

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-----ALKILPSVDGV 213
                  K+ R    +  D++  I +      I   G  E + Q     A + + S   V
Sbjct: 183 -------KNERPQHPVHCDVIKAISQAVSIPVIANGGSQEFIRQFQDISAFRSVTSASSV 235

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 236 MLARAAMWNPSVF 248


>gi|325282430|ref|YP_004254971.1| dihydrouridine synthase DuS [Deinococcus proteolyticus MRP]
 gi|324314239|gb|ADY25354.1| dihydrouridine synthase DuS [Deinococcus proteolyticus MRP]
          Length = 314

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 110/244 (45%), Gaps = 27/244 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNI-LGFS-TQEKPLALQIGG 56
           M  ++D   R   +L      L+T  EMI A  ++  D  ++ LG     E    +Q+ G
Sbjct: 19  MAGYSDAPMR---QLAAEQGALWTVSEMISARGLMEHDGPDLTLGRPYPGESARVVQLFG 75

Query: 57  ADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           A    L  A +  E+ F    I+LN+GCP  +VH G  GACL+  P++    I AM  A 
Sbjct: 76  AIPEYLAAAVQRTEEWFAPAAIDLNMGCPVPKVH-GKGGACLLQTPEVAYSLIRAMKSAT 134

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++ V+ K R+G D+         + + ++ +G   I +H R +          R     D
Sbjct: 135 TLDVSAKIRLGWDENRAV----EVAQGLEAAGAAMITVHGRTS--------KQRYTGEAD 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN----SAMLTTVD 230
           +D + ++        IG +G +  +  A +   S V  VMIGR A  N    +A+ +  D
Sbjct: 183 WDAIAQVAAAVNIPVIG-SGDITTLDAARQRQSSGVAAVMIGRGAVGNPWLFAALASGSD 241

Query: 231 EYFS 234
           EY S
Sbjct: 242 EYPS 245


>gi|221060526|ref|XP_002260908.1| tRNA-dihydrouridine synthase [Plasmodium knowlesi strain H]
 gi|193810982|emb|CAQ42880.1| tRNA-dihydrouridine synthase, putative [Plasmodium knowlesi strain
           H]
          Length = 340

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/255 (26%), Positives = 116/255 (45%), Gaps = 31/255 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ A   +  +K  K       +++P+  Q  G +
Sbjct: 33  MVDLSELAFRLLCRNY-NCHLAFTPMLHAKNFVEHEKYRKGYFQSCKKDEPVIAQFCGNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ A + +++   N ++LN+GCP     +G++GA L+   D V + ++ +    +IP
Sbjct: 92  SKIILSAIEYIKN-DVNAVDLNLGCPQQIAKKGNYGAFLLHKHDEVVNLVSDITNNCNIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T  C+I   DQ     L NL   ++   V  I +H R    KG++ K+       DY+I
Sbjct: 151 IT--CKIRKIDQDYQKTL-NLCYDLQSRNVKMITVHGRTKEEKGVNIKE------CDYEI 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA--------AYKNSAMLTT 228
           + +I KE  ++ I  NG +E      K L     D VM            + +N   +  
Sbjct: 202 I-KIIKERLNIPIIANGSIEHFEDVQKCLNYTKADAVMCAEILLEKPYFFSNQNVHAVDI 260

Query: 229 VDEYF-------SNP 236
           V+EY+       SNP
Sbjct: 261 VNEYYDLFLQYESNP 275


>gi|255714144|ref|XP_002553354.1| KLTH0D14806p [Lachancea thermotolerans]
 gi|238934734|emb|CAR22916.1| KLTH0D14806p [Lachancea thermotolerans]
          Length = 348

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 103/225 (45%), Gaps = 23/225 (10%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGADISKLVE 64
           RHY        N  ++YT MI+A   +R     +  FS+ E   PL +Q+G  +++ L+ 
Sbjct: 51  RHY--------NVDIVYTPMILAREYVRNCHARMADFSSNESDSPLIVQVGVNNVTDLLR 102

Query: 65  AAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
             ++V  +  + I +N GCP   +V EG  G+ L+ NP+++   ++A+       V ++ 
Sbjct: 103 FVEMVSPYC-DGIGINCGCPIKEQVREG-IGSALIYNPELLSSMVSAVKTKYGDKVRLET 160

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           +I + D        +L   +  +GV+ I IH R    +   P       NLD       K
Sbjct: 161 KIRIHDNWDQTV--DLCNQLCDAGVDWITIHGRTRTTRSSEPV------NLDAIKFITQK 212

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++ ++ +  NG   DMS   KIL     DGVM  R    N A+ 
Sbjct: 213 IKSRNVPVIANGDCFDMSDFQKILDYTGADGVMAVRGLLDNPALF 257


>gi|91787028|ref|YP_547980.1| dihydrouridine synthase TIM-barrel protein nifR3 [Polaromonas sp.
           JS666]
 gi|91696253|gb|ABE43082.1| tRNA-U20-dihydrouridine synthase [Polaromonas sp. JS666]
          Length = 356

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/262 (25%), Positives = 115/262 (43%), Gaps = 31/262 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-----DAILRGDKKNILGFSTQEKPLALQIG 55
           M   TDR +R   + L       +EM+ +     D++    + N  G   +  P+A+QI 
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVTSRRDLWDSLKTSRRANHAG---EAAPIAVQIA 72

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMC 112
           G D   + EAA    D G   I++N+GCP+ +V     G+ LM +  +   + + + A C
Sbjct: 73  GTDAQMMAEAAAYNVDRGAQIIDINMGCPAKKVCNKWAGSALMQDETLALQIVEAVVAAC 132

Query: 113 KALSIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNR 169
               +PVT+K R G       A+A   + ++ + +GV  + +H   R+   KGL+     
Sbjct: 133 APHGVPVTLKMRTGWCQAHKNALA---IARAAESAGVQMVTVHGRTREQGYKGLA----- 184

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
                +YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +  
Sbjct: 185 -----EYDTIAAVKSAL-RIPVVANGDISSPEKARDVLAYTGADAVMIGRAAQGRPWIFR 238

Query: 228 TVDEYFSNPLTGSSPIKTRVDK 249
            V  + +     + P+   V +
Sbjct: 239 EVAHFLATGTHLAPPLVAEVRR 260


>gi|300173156|ref|YP_003772322.1| tRNA-dihydrouridine synthase [Leuconostoc gasicomitatum LMG 18811]
 gi|299887535|emb|CBL91503.1| tRNA-dihydrouridine synthase [Leuconostoc gasicomitatum LMG 18811]
          Length = 376

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 102/212 (48%), Gaps = 21/212 (9%)

Query: 21  LLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           + YTE   A +++    K      L  +  EK    QI G+   ++  AAK++   GY  
Sbjct: 56  VYYTEFTNASSMVHPQAKFSVQGRLAVAENEKQPVAQIWGSRPEEIAGAAKVLATMGYQA 115

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N+GCP   V +   G+ L+ + ++  + I+A  K+  + V+VK R+G      A   
Sbjct: 116 VDINMGCPDTTVIKNGAGSDLIRHQELAKEIISAAKKS-GLAVSVKTRLGF---YQAEEF 171

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDY-DIVYEIKKE-NPDLFIGL 193
           R  +  I +  V  + IH R       S K+  K P + +Y D +  ++    P   I +
Sbjct: 172 REWLPIILRQQVAVLTIHLR-------SRKEMSKAPAHEEYIDEILAMRDAIAPQTLIQI 224

Query: 194 NGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
           NG ++     ++++   P +DG+MIGR  ++N
Sbjct: 225 NGDIKTRQSGMQLVKNHPGIDGIMIGRGIFEN 256


>gi|322689556|ref|YP_004209290.1| dihydrouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
 gi|320460892|dbj|BAJ71512.1| putative dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 414

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  ++Q+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSMQLYGVN 113

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D           +   ++ G   + +HAR          D  +I  L
Sbjct: 174 AGIPVTAKIRVGIDHNHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
                    KE+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 232 ---------KEHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FS-NP 236
           F  NP
Sbjct: 283 FEGNP 287


>gi|294501960|ref|YP_003565660.1| dihydrouridine synthase (Dus) [Bacillus megaterium QM B1551]
 gi|294351897|gb|ADE72226.1| dihydrouridine synthase (Dus) [Bacillus megaterium QM B1551]
          Length = 332

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/194 (28%), Positives = 91/194 (46%), Gaps = 24/194 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K  L F+  E+P+   I G       + +  + + G+  I++N+GCP   V     G+ L
Sbjct: 60  KGRLTFTEDEQPIVAHIWGDKPEYFRQMSIGMAEMGFRGIDINMGCPVQNVAGNGKGSGL 119

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           +  PD   + I A  KA  +PV+VK R+G   VD+        + +K I +  +  + IH
Sbjct: 120 IRRPDTAAEIIQA-AKAGGLPVSVKTRLGYTQVDEWY------DWLKHILEQDIVNLSIH 172

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS- 209
            R    K +S  D        ++++ EIKK      P   + +NG + D  + L++    
Sbjct: 173 LRTK--KEMSDVDAH------WELIPEIKKLRDEIAPHTLLTINGDIPDRQKGLELAEKY 224

Query: 210 -VDGVMIGRAAYKN 222
            VDG+MIGR  + N
Sbjct: 225 GVDGIMIGRGIFHN 238


>gi|157736711|ref|YP_001489394.1| tRNA-dihydrouridine synthase [Arcobacter butzleri RM4018]
 gi|315635883|ref|ZP_07891145.1| tRNA-dihydrouridine synthase B [Arcobacter butzleri JV22]
 gi|157698565|gb|ABV66725.1| probable tRNA-dihydrouridine synthase [Arcobacter butzleri RM4018]
 gi|315479862|gb|EFU70533.1| tRNA-dihydrouridine synthase B [Arcobacter butzleri JV22]
          Length = 309

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/222 (26%), Positives = 113/222 (50%), Gaps = 20/222 (9%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISK 61
           +TD  +R   +    + L  +EMI ++A++    + +  +  S  E P  +QI G  +  
Sbjct: 19  YTDLPFRSVVKKFGAD-LTISEMISSNALVYKSARTLKMVEKSPTEDPYFVQIAGNSVDL 77

Query: 62  LVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +  A +I+ D  G + I+LN GCP+ +V     G+ L+ +   + + ++ + K      T
Sbjct: 78  VKAAVEILNDVEGIDGIDLNCGCPAPKVFNHGSGSNLLGDLKKLEEILSTVKKYSKKQYT 137

Query: 121 -VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
             K R+GV+++IP      + K+++  GV+ + +H R    K  +P        +DYD +
Sbjct: 138 SAKVRLGVNEKIPV----EIGKAVEACGVDFVSVHGRTRAGKYKAP--------VDYDAI 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            ++ KE   + +  NG ++D ++A ++L     +GVMIGR A
Sbjct: 186 KQM-KEAISIPVIANGDIKDYAKAKEVLEYTKANGVMIGRGA 226


>gi|126135962|ref|XP_001384505.1| hypothetical protein PICST_58121 [Scheffersomyces stipitis CBS
           6054]
 gi|126091703|gb|ABN66476.1| tRNA dihydrouridine synthase [Scheffersomyces stipitis CBS 6054]
          Length = 415

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/168 (31%), Positives = 80/168 (47%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFSTQEKPLALQI 54
           MVD ++  +R  +R    + L YT M  A       K        + G   +++PL +Q 
Sbjct: 26  MVDQSELAWRILSRRYGAD-LCYTPMFHAKLFATEQKYRDNMWSELDGDFEKDRPLIVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK VED   + ++LN+GCP     +G +GA LM + D+V   I  +   
Sbjct: 85  CANDPDYLLQAAKFVED-KCDAVDLNLGCPQGIAKKGKYGAFLMDDWDLVHTLIKNLHDN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           L +PVT K RI  DD   ++      K I  +G   I +H R   +KG
Sbjct: 144 LKVPVTAKIRI-YDDWEKSL---QYAKMILDAGAQFITVHGRTRDMKG 187


>gi|110807120|ref|YP_690640.1| tRNA-dihydrouridine synthase B [Shigella flexneri 5 str. 8401]
 gi|38604763|sp|Q83PZ5|DUSB_SHIFL RecName: Full=tRNA-dihydrouridine synthase B
 gi|110616668|gb|ABF05335.1| putative dehydrogenase [Shigella flexneri 5 str. 8401]
 gi|281602637|gb|ADA75621.1| tRNA-dihydrouridine synthase B [Shigella flexneri 2002017]
 gi|313648498|gb|EFS12940.1| TIM-barrel , nifR3 family protein [Shigella flexneri 2a str. 2457T]
 gi|332752422|gb|EGJ82812.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri
           4343-70]
 gi|332752463|gb|EGJ82852.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-671]
 gi|332754236|gb|EGJ84602.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri
           2747-71]
 gi|332765259|gb|EGJ95486.1| tRNA dihydrouridine synthase [Shigella flexneri 2930-71]
 gi|333000253|gb|EGK19836.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-218]
 gi|333014546|gb|EGK33893.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-304]
          Length = 321

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSA 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|206580487|ref|YP_002236325.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae 342]
 gi|288933313|ref|YP_003437372.1| hypothetical protein Kvar_0430 [Klebsiella variicola At-22]
 gi|290511636|ref|ZP_06551005.1| tRNA-dihydrouridine synthase B [Klebsiella sp. 1_1_55]
 gi|206569545|gb|ACI11321.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae 342]
 gi|288888042|gb|ADC56360.1| TIM-barrel protein, nifR3 family [Klebsiella variicola At-22]
 gi|289776629|gb|EFD84628.1| tRNA-dihydrouridine synthase B [Klebsiella sp. 1_1_55]
          Length = 321

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 112/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P+ V   + A+  A+ +P
Sbjct: 76  PEEMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPEQVKSILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G + +      RN V   +  ++ G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGWEPE-----HRNCVEIAQLAEECGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|320010920|gb|ADW05770.1| TIM-barrel protein, nifR3 family [Streptomyces flavogriseus ATCC
           33331]
          Length = 382

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/255 (23%), Positives = 111/255 (43%), Gaps = 19/255 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDASETPRSIQLYGV 86

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKA 114
           D   + +A +++  ED   + I+LN GCP  +V     G+ L    P +      A+ +A
Sbjct: 87  DPVTVGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVAQA 145

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD        +  +   + GV  + +H R                  
Sbjct: 146 GDLPVTIKMRKGIDDD--HTTYLDAGRIAVEEGVTAVALHGRTTA--------QHYGGTA 195

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   
Sbjct: 196 DWDAIARLKEHVPEIPVLGNGDIWSADDALRMMRETGCDGVVVGRGCLGRPWLFGDLVSA 255

Query: 233 FSNPLTGSSPIKTRV 247
           F    T  +P+  +V
Sbjct: 256 FEGTGTRQAPVLRQV 270


>gi|332709280|ref|ZP_08429243.1| putative TIM-barrel protein, nifR3 family [Lyngbya majuscula 3L]
 gi|332351954|gb|EGJ31531.1| putative TIM-barrel protein, nifR3 family [Lyngbya majuscula 3L]
          Length = 297

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/291 (22%), Positives = 131/291 (45%), Gaps = 40/291 (13%)

Query: 21  LLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           ++YTEM+ A  +  LR +   ++     EKP+++Q+       L +AA+     G + ++
Sbjct: 1   MMYTEMVHASQLKYLR-ELPKVMEVDPLEKPISIQLFDCRPEFLAQAAQRAVAEGADTVD 59

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVALR 137
           +N+GCP  ++ +   G+ L+ +P+     + ++ KA+ +PVTVK RIG  +Q I AV   
Sbjct: 60  INMGCPVNKITKNGGGSALLRDPETAEAIVRSVVKAVEVPVTVKTRIGWTNQEINAV--- 116

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              + ++ +G   + +H R         +D     +  ++ +  + K+   + +  NG +
Sbjct: 117 EFAQRMEDAGAQMLTLHGRT--------RDQGYNGSARWEWIKRV-KDVLSIPVIANGDI 167

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVDKDFWR 253
             +  A++ L     DGVM  R       ++  +D +      L  ++P++         
Sbjct: 168 LSVDAAVRCLEETGADGVMCSRGTLGYPFLVGEIDYFLKTGQLLPPTTPVQ--------- 218

Query: 254 KISASMTDYAARHL----HSGGK--LQQITRHMIGLFHGFPNSRRCRHILT 298
                + + A  HL    H  G+  + Q  +HM     GFP +   R  L+
Sbjct: 219 -----LLECAKEHLQGLWHYKGERGIYQSRKHMAWYAKGFPGAGELRKKLS 264


>gi|239832008|ref|ZP_04680337.1| TIM-barrel protein, nifR3 family [Ochrobactrum intermedium LMG
           3301]
 gi|239824275|gb|EEQ95843.1| TIM-barrel protein, nifR3 family [Ochrobactrum intermedium LMG
           3301]
          Length = 335

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/205 (24%), Positives = 103/205 (50%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAA+I E  G + I++
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREAHWMGEAARIAEGEGADIIDI 103

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM + D     + A   A+++PVT+K R+G D++  ++    L
Sbjct: 104 NMGCPAKKVTGGYSGSALMRDLDHAMTLVEATVNAVNVPVTLKMRLGWDEK--SINAPEL 161

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G            D+D +  + ++   + +  NG +
Sbjct: 162 ARRAESAGIAMVTVHGRTRCQFYEG----------KADWDAIRAV-RDAVKIPLVANGDV 210

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
                A +IL     D VM+GRA+Y
Sbjct: 211 ACREDAEEILRRSGADAVMVGRASY 235


>gi|219117564|ref|XP_002179575.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408628|gb|EEC48561.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 233

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 108/238 (45%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI---LRGDKKNILGFST-QEKPLALQIGG 56
           MVD +D  +R   R    N L +T MI A      +   +K  L +   Q++PL  QI G
Sbjct: 6   MVDQSDLPFRLLCRSYGTN-LCFTPMIHARLFTTNVEYRRKFTLQYGPPQDRPLIAQICG 64

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D+  +V  A  ++ +  + I++N GCP      G++GA L+   D++   +  + + LS
Sbjct: 65  GDVQAVVACALAMQPYC-DGIDINCGCPQNIAKRGNYGAFLLEQEDVLLPLVHTLLQHLS 123

Query: 117 IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRK 170
           +P++VK R+      Q    A   L   +  +GV+ + IH R    K  L G +  D  +
Sbjct: 124 VPLSVKVRLLPAETRQASLEASLRLYTKLVDAGVHLLTIHGRTRHHKGPLTGAADWDAIR 183

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           +      +V  + +  P   I  NGG+  +  A   L +   DGVM   A  +  A+ 
Sbjct: 184 V------VVDRLGQRIP---IFANGGVASLRDAQACLATTHADGVMSSEALLEYPALF 232


>gi|242207487|ref|XP_002469597.1| predicted protein [Postia placenta Mad-698-R]
 gi|220731401|gb|EED85246.1| predicted protein [Postia placenta Mad-698-R]
          Length = 313

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 106/233 (45%), Gaps = 27/233 (11%)

Query: 18  NNALLYTEMIVADAI----LRGDKKNILGFSTQEKP-LALQIGGADISKLVEAAK-IVED 71
           + A+L+TE +V          G  K +      EKP L  QIG AD    V+AA+ +V+D
Sbjct: 38  DKAILHTERVVDPTTGVISYVGKTKALFTTHPIEKPYLIYQIGSADPELAVQAARTVVQD 97

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
                 +LN GCP         GA L+ NPD++   + A+ +A+   +++  +I +   +
Sbjct: 98  VA--GFDLNCGCPKPFSTHSGMGAALLSNPDLLCSILTALREAMPPEISISAKIRL---L 152

Query: 132 PAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           P+      LV+ I  +GVN + +H R    + +  ++   I  L  +IV  ++    D+ 
Sbjct: 153 PSQEDTLKLVERIVNTGVNALTVHCRT---RNMRKREKAHIDRL-REIVDFVRGLGRDVA 208

Query: 191 IGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           +  NG  ED   A++I         D VMI  AA  N    +       NPLT
Sbjct: 209 LIENGDCEDYQDAIRIREITGYVGADSVMIATAAEANPTCFS------PNPLT 255


>gi|187251875|ref|YP_001876357.1| dihydrouridine synthase DuS [Elusimicrobium minutum Pei191]
 gi|186972035|gb|ACC99020.1| Dihydrouridine synthase DuS [Elusimicrobium minutum Pei191]
          Length = 318

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 115/239 (48%), Gaps = 29/239 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   TD  +R     L N A ++  EM+ A A+   +KK++  L    +E P+++QI G 
Sbjct: 24  MAGITDTPFRI--HCLNNGAGIVCAEMVSAKAVEYDNKKSVKMLAVDKKEHPVSMQIFGG 81

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  AAK  E  G + I++N GCP  +++    G  L+ +  ++   + A   ++SI
Sbjct: 82  DAESISIAAKAAEAAGADIIDINAGCPVKKINRAGAGCVLIKDEKLLASIVNAAVNSVSI 141

Query: 118 PVTVKCRIGV------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           PVT+K RIG+       D+I  +A        +  G   + +HAR A      P D   +
Sbjct: 142 PVTLKTRIGLTAGDFKGDKIAKLA--------ENEGAAAVIMHARYAGNVHGGPADLEAL 193

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTV 229
                 +V  +K       IG NGG+ D++ A K+  + V G+M+GR A  N  +  ++
Sbjct: 194 A----KVVSAVKIP----VIG-NGGIVDVNTADKMFETGVRGIMVGRGAIGNINIFKSI 243


>gi|307166837|gb|EFN60767.1| tRNA-dihydrouridine synthase 4-like [Camponotus floridanus]
          Length = 748

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/273 (24%), Positives = 127/273 (46%), Gaps = 31/273 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+AD+ +R  K     F+T  ++ PL +Q     
Sbjct: 21  MVRYSKLQFRTLVRRYGCD-ICFTPMILADSFVRSLKARENEFTTHKEDNPLIVQFAAKT 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  V AA++V  +  N ++LN GCP     +  +GA L+  P++V D I  +   +  P
Sbjct: 80  VNDFVGAAEMVAPYC-NGVDLNCGCPQRWAIKEGYGADLLKKPELVKDLIYEIRNHIPRP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I    +  L + ++K+G + + +HAR   ++   P D   + NL    
Sbjct: 139 FTVSVKIRLLKDIRQTIM--LCQVLEKAGASFLTVHARTPEMRN-EPID---LDNL---- 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             ++ +++  L +  NG ++++  A  +      +GVM  R    N A+           
Sbjct: 189 --KLLRDHIQLPLVANGDVKNLEDAEFLFKESRCEGVMSARGILNNPAL----------- 235

Query: 237 LTGSSPIKTRVDKDFWRKISASM-TDYAARHLH 268
            +G S       +D W  I++++ T++   H H
Sbjct: 236 FSGHSTTPLVCIQD-WLNITSTIPTEFQCFHHH 267


>gi|120598516|ref|YP_963090.1| dihydrouridine synthase, DuS [Shewanella sp. W3-18-1]
 gi|146293405|ref|YP_001183829.1| dihydrouridine synthase, DuS [Shewanella putrefaciens CN-32]
 gi|120558609|gb|ABM24536.1| dihydrouridine synthase, DuS [Shewanella sp. W3-18-1]
 gi|145565095|gb|ABP76030.1| dihydrouridine synthase, DuS [Shewanella putrefaciens CN-32]
 gi|319426708|gb|ADV54782.1| dihydrouridine synthase DuS [Shewanella putrefaciens 200]
          Length = 317

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G + ++ N GCP+  V+  + GA L+  P
Sbjct: 57  GNTPSGTPVRVQLLGQEPQCMGENALRAVELGSHGVDANFGCPAKMVNRSNGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D + D + AM +A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 DSIHDIVRAMRQAVPSEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  K P   ++ + E++K  P   I  NG + +   A + +     D +MIGR
Sbjct: 174 -------DGYKPPAY-WEYITEVRKRLPIPVIA-NGEIWNSDDAKRCMAVTGCDSIMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W +  A M  Y  R L+
Sbjct: 225 GAISLPNLADTIK-------TGAAPYT-------WAQTLALMLSYTQRELN 261


>gi|294629227|ref|ZP_06707787.1| tRNA-dihydrouridine synthase [Streptomyces sp. e14]
 gi|292832560|gb|EFF90909.1| tRNA-dihydrouridine synthase [Streptomyces sp. e14]
          Length = 416

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/274 (23%), Positives = 119/274 (43%), Gaps = 30/274 (10%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E+P ++Q+ G 
Sbjct: 60  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDATEQPRSIQLYGV 119

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKA 114
           D + + +A +++  ED   + I+LN GCP  +V     G+ L    +++   +  A+  A
Sbjct: 120 DPATVGKAVRMIAEEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAIVREAVSGA 178

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +   +  +   + GV+ I +H R                  
Sbjct: 179 GDLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVSAIALHGRTTA--------QHYGGTA 228

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   
Sbjct: 229 DWDAIARLKEHVPEIPVLGNGDIWSAGDALRMVRETGCDGVVVGRGCLGRPWLFADLVAA 288

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
           F            R D DF R     + D   RH
Sbjct: 289 FEG----------RTD-DFVRPTLREVADVMVRH 311


>gi|302545533|ref|ZP_07297875.1| putative tRNA-dihydrouridine synthase [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463151|gb|EFL26244.1| putative tRNA-dihydrouridine synthase [Streptomyces himastatinicus
           ATCC 53653]
          Length = 383

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 105/226 (46%), Gaps = 19/226 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  D K   ++ F   EKP ++Q+ G 
Sbjct: 22  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERDAKTMRLIHFDGTEKPRSIQLYGV 81

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKA 114
           D   + +A +++  ED   + I+LN GCP  +V     G+ L    +++   +  A+  A
Sbjct: 82  DPVTVGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVTGA 140

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +   +  +   + GV  I +H R A                
Sbjct: 141 GPLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTA 190

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           D+D +  +K+  P++ +  NG +     A++++     DGV++GR 
Sbjct: 191 DWDAIARLKETVPEIPVLGNGDIWSAEDAVRMMDRTGCDGVVVGRG 236


>gi|239931403|ref|ZP_04688356.1| dihydrouridine synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 392

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/271 (23%), Positives = 121/271 (44%), Gaps = 18/271 (6%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAIL-RGDKK-NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++ R DK   ++ F   E+P +LQ+ G 
Sbjct: 28  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNDKTMQLITFDASERPRSLQLYGV 87

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A + IVE+   + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 88  DPATVGKAVRMIVEEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 147

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 148 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVRAIALHGRTTA--------QHYGGTAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT-VDEY 232
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +    V  +
Sbjct: 198 WEAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 257

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
                 G+  +  R  +   R+++  M  +A
Sbjct: 258 EGGTRAGAGDLGGRGTRPTLREVADIMVRHA 288


>gi|148977178|ref|ZP_01813805.1| NifR3/Smm1 family protein [Vibrionales bacterium SWAT-3]
 gi|145963460|gb|EDK28723.1| NifR3/Smm1 family protein [Vibrionales bacterium SWAT-3]
          Length = 322

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 51/193 (26%), Positives = 89/193 (46%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+   D G   I++N+GCP+ +V++   G+ L+  PD++ + + A
Sbjct: 68  SVQIAGADPQLMAEAAQFNVDNGAQIIDINMGCPAKKVNKKLAGSALLQYPDLIEEILKA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKD 167
           +  A+ +PVT+K R G D        RN V+  K     G+  + +H R          +
Sbjct: 128 VVNAVDVPVTLKTRTGWDTDN-----RNCVQIAKIAEDCGIQALALHGRTRACMYKGEAE 182

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
            + I         +  K+   + +  NG ++   +A  +L     D +MIGR A     +
Sbjct: 183 YKHI---------KAAKQAVSIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWI 233

Query: 226 LTTVDEYFSNPLT 238
              +  Y  N  T
Sbjct: 234 FNEILHYLENGTT 246


>gi|291439776|ref|ZP_06579166.1| dihydrouridine synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291342671|gb|EFE69627.1| dihydrouridine synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 398

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/271 (23%), Positives = 121/271 (44%), Gaps = 18/271 (6%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAIL-RGDKK-NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++ R DK   ++ F   E+P +LQ+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNDKTMQLITFDASERPRSLQLYGV 93

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A + IVE+   + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 94  DPATVGKAVRMIVEEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 154 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVRAIALHGRTTA--------QHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT-VDEY 232
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +    V  +
Sbjct: 204 WEAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 263

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
                 G+  +  R  +   R+++  M  +A
Sbjct: 264 EGGTRAGAGDLGGRGTRPTLREVADIMVRHA 294


>gi|158290529|ref|XP_312125.3| AGAP002791-PA [Anopheles gambiae str. PEST]
 gi|157017939|gb|EAA07861.3| AGAP002791-PA [Anopheles gambiae str. PEST]
          Length = 396

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/235 (22%), Positives = 106/235 (45%), Gaps = 25/235 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R    + L +T MI+AD+  + +K  +  F+T E+  PL  Q    +
Sbjct: 30  MVRYSKLEFRHLVRSYGTD-LAFTSMIMADSFCKSEKARLNEFTTNEEDTPLIAQFAANN 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               + A+++V  +  + ++LN GCP        +G+ L+  P+++ D +  + + +   
Sbjct: 89  TIDFLSASEMVYPY-VDGVDLNCGCPQRWAMAEGYGSALLKTPELIADMLGTVRRNMPST 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +V  ++ +          ++ + ++ +G+  + +H R A        +  K+P +  D 
Sbjct: 148 FSVSVKVRLLSSTDHKRTIDMCRQLEATGITFLTVHGRTA-------PEMTKVP-VHKDA 199

Query: 179 VYEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           + EIK+        N D+F      L+D  Q + +    DGVM  R    N A+ 
Sbjct: 200 LQEIKQSIGIPMVANGDIFT-----LDDAEQ-MYLQTKCDGVMTARGILSNPALF 248


>gi|332022244|gb|EGI62559.1| tRNA-dihydrouridine synthase 4-like protein [Acromyrmex echinatior]
          Length = 745

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/264 (23%), Positives = 119/264 (45%), Gaps = 30/264 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + + +T MI+AD+ ++  K     F+T E  +PL +Q     
Sbjct: 21  MVRYSKLQFRTLVRRYGCD-ICFTPMILADSFVQSSKARDNEFTTHEGDEPLIVQFAAKT 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  V A+ +V  +  N ++LN GCP     +  +GA L+  P++V D +  +   +  P
Sbjct: 80  VNDFVSASVMVAPYC-NGVDLNCGCPQRWAMQEGYGADLLKKPELVKDLVYQVRNRIPKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I       L ++++K+G + + IHAR   ++   P D   + NL    
Sbjct: 139 FTVSAKIRLLKDIRKTI--TLCQTLEKAGASFLTIHARTPEMRN-EPID---LNNL---- 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             ++ ++   L +  NG ++ +  A  +      +GVM  R    N A+ +         
Sbjct: 189 --KLLRDYVQLPLIANGDVKSLENAEFLFKESRCEGVMSARGILTNPALFS--------- 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMT 260
                P+   V    W  I+++M+
Sbjct: 238 ---GYPVTPLVCVQDWLDITSTMS 258


>gi|307110528|gb|EFN58764.1| hypothetical protein CHLNCDRAFT_140504 [Chlorella variabilis]
          Length = 451

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/213 (24%), Positives = 98/213 (46%), Gaps = 15/213 (7%)

Query: 23  YTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y+EM  A  +L+G++K   IL  +  E+   +QI    I + V A  +V + G + ++LN
Sbjct: 96  YSEMAFARQLLKGNRKELAILRRAGNEQCYGVQIATNVIDEGVRAGVLVAEAGADFLDLN 155

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
            GCP         GA L+  P  +   +  +   L +P+TVK R+G  +    + +  +V
Sbjct: 156 CGCPIYEATRRGLGAALLRKPHKLARLVNGIAARLPLPLTVKIRLG--ESADKINVHEMV 213

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
             ++++G   + +H R          + R     D+++V ++  ++    +G NG +   
Sbjct: 214 GLLEQAGAAAVTVHGRT--------MEQRYKKAADWELVQQVAAQHSVPLVG-NGDVLTH 264

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
            +  + L S  +  VM+GR A     +   V E
Sbjct: 265 YEVRRRLDSHGLLTVMVGRGALIKPWLFQEVKE 297


>gi|58617063|ref|YP_196262.1| putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Gardel]
 gi|58416675|emb|CAI27788.1| Putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Gardel]
          Length = 317

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 110/240 (45%), Gaps = 15/240 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L    LL +EMI +  +++  K ++     Q    A+Q+ G D   + E
Sbjct: 21  TDFPFRALVKNL-GAGLLVSEMIASRGMIKQTKDSLQKSHIQSNT-AVQLAGCDPLIMAE 78

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V     G+ LM +       + A+ KA+ +PVT+K R
Sbjct: 79  AAKLNEDMGAQIIDINFGCPVKKVVNSYAGSALMKDEITAAKILEAVVKAVKVPVTLKMR 138

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           IG D Q   +    L K  + +G+  I IH R         +        D+  +  IKK
Sbjct: 139 IGWDSQ--NLNSPRLAKIAENTGIKMITIHGRT--------RAQMFTGKADWKFISNIKK 188

Query: 185 --ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
               P +  G    L+D+  AL+     DG+MIGR AY    ++    ++  + +    P
Sbjct: 189 CVRIPIIVNGDIKTLDDIKIALE-ESQADGIMIGRGAYGKPWIINKALQFIKSGIILPDP 247


>gi|317050642|ref|YP_004111758.1| dihydrouridine synthase DuS [Desulfurispirillum indicum S5]
 gi|316945726|gb|ADU65202.1| dihydrouridine synthase DuS [Desulfurispirillum indicum S5]
          Length = 324

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 83/144 (57%), Gaps = 15/144 (10%)

Query: 22  LYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           ++TEM+ ++A+ R   K +    +G   + +P  +Q+ GA+ + + ++A+I  + G+  I
Sbjct: 41  IFTEMVSSEALSRHIPKTVEFLRVGAEERLRPF-VQLFGANPATMAQSARICTEEGFTLI 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV---DDQIP 132
           ++N+GCP  +V     G  LM +P + G+ ++ M  A      +TVK R+G+   D+ +P
Sbjct: 100 DINMGCPVKKVVRSGSGVELMQHPQLAGEIVSQMVAAAGACADITVKTRLGLIHGDELLP 159

Query: 133 AVALRNLVKSIKKSGVNGIWIHAR 156
            +AL+     ++++G + + +HAR
Sbjct: 160 ELALQ-----VQQAGASMLTVHAR 178


>gi|110801933|ref|YP_698595.1| dihydrouridine synthase family protein [Clostridium perfringens
           SM101]
 gi|110682434|gb|ABG85804.1| dihydrouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 321

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 110/237 (46%), Gaps = 21/237 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  AK ++D GYNEINLN+GCPS  V     GA  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGAGFLAHREELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   + +++K R+G+D          L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKINHMKISIKTRLGMDK---PEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  PNL+ +     + K NP  + G    LED ++ ++    VD +M+GR    N A++ 
Sbjct: 173 K--PNLEVFKDAISLSK-NPVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALM- 228

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  N +  +  +  +V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 229 -------NEILNNEFMDKKVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|33865189|ref|NP_896748.1| nitrogen regulation protein NifR3 family protein [Synechococcus sp.
           WH 8102]
 gi|33638873|emb|CAE07170.1| putative nitrogen regulation protein NifR3 family homolog
           [Synechococcus sp. WH 8102]
          Length = 333

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 71/299 (23%), Positives = 128/299 (42%), Gaps = 26/299 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G  +  +     ++ P+ +Q+       + 
Sbjct: 34  SDRVFRHLVRRWAPDALLFTEMVNATSLELGFGRGKVKELGDEQGPIGVQLFDHRPDAMA 93

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  ED G   I++N+GCP  ++     G+ L+ +P +    I A+  A+ +PVTVK 
Sbjct: 94  DAARRAEDAGAFLIDINMGCPVRKIARKGGGSGLIRDPHLASRIIEAVANAVRLPVTVKT 153

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D  P    R L    +++G   + +H R         ++       D+  +  
Sbjct: 154 RLGWCGSDAAPQTWCRQL----QEAGAQLLTLHGRT--------REQGFKGKADWAAIAA 201

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN-PLT 238
           +K+      I  NG +     A + L     DGVM+GR       ++  +D      P+ 
Sbjct: 202 VKQALTIPVIA-NGDINTPEDAQRCLAQTGADGVMVGRGTMGAPWLVGQIDAALKGLPIP 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            +     R+     R+   ++ +    H      L    +HM     GFP + + RH L
Sbjct: 261 ATPGPAARL--TLAREQLLALVEARGEH-----GLLIARKHMGWTCTGFPGAPQLRHAL 312


>gi|242097028|ref|XP_002439004.1| hypothetical protein SORBIDRAFT_10g029830 [Sorghum bicolor]
 gi|241917227|gb|EER90371.1| hypothetical protein SORBIDRAFT_10g029830 [Sorghum bicolor]
          Length = 421

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 109/233 (46%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 94  MVDNSELPFRMLCRRYGADAA-YTPMLHSRIFSENEKYRSMEFTTCKEDRPLFVQFCAND 152

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAK+VE    + +++N GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 153 PDILLQAAKMVEPHC-DYVDINFGCPQRIARRGNYGAFLMDNLPLVKSLVQNLAANLHVP 211

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+VK R+   ++D +         K ++++G + + +H R         KD +K    D+
Sbjct: 212 VSVKIRVFPRLEDTL------AYAKMLEEAGASLVAVHGRTR-----DEKDGKKF-RADW 259

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           D +  +K     P L  G    +ED+   L+     DGV+      +N A+  
Sbjct: 260 DAIKAVKDALRVPVLANGNIRHMEDVKNCLEHT-GADGVLSAETLLENPALFA 311


>gi|32476561|ref|NP_869555.1| hypothetical protein RB10683 [Rhodopirellula baltica SH 1]
 gi|32447107|emb|CAD76923.1| conserved hypothetical protein-putative protein belonging to the
           NifR3 family [Rhodopirellula baltica SH 1]
          Length = 364

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 108/231 (46%), Gaps = 25/231 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------ILGFSTQEKPLALQI 54
           M  +T+  +R   R      LL TEM+ A   +  D+        + G + + +PLA+QI
Sbjct: 35  MAGFTNAAFRHIVRQFGGAGLLATEMVNARGFVWLDENEAEHPDRLWGVADEPRPLAVQI 94

Query: 55  GGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMC 112
              D   + +  + + E++  + +++N GCP  +V E +  G+ L+  P+ +   I+ + 
Sbjct: 95  WDNDPETMAKVGRRLAEEYRVSVVDINFGCPVRQVTEKAHSGSYLLREPNRMHAIISRLV 154

Query: 113 KALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNR 169
           +  +  PVT K R+G   +   +    + + ++++G   + +H R A  + +G       
Sbjct: 155 QVCAPTPVTAKIRLGCSRE--NINCNEIARVVEEAGAAALTVHGRTAADMFRG------- 205

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              N D++ + EIK    ++ +  NG L+   + +       VD VMI RA
Sbjct: 206 ---NADWERISEIKSHLRNIPLIGNGDLDSAEKVVAAFDQYDVDAVMIARA 253


>gi|254517397|ref|ZP_05129454.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR5-3]
 gi|219674235|gb|EED30604.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR5-3]
          Length = 327

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 104/219 (47%), Gaps = 27/219 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGADISKLVEAAK 67
           R  AR  T   LL  EM+ +D  LR  +K+    S   +  P ++QI G D   + EAA+
Sbjct: 28  RLCARFGTG--LLVGEMVHSDPRLRESRKSQQRRSHDLEIDPRSVQIVGNDPLLMAEAAR 85

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
              + G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+S+PVT+K R G 
Sbjct: 86  YNVNCGAQVIDINMGCPAKKVCRKAAGSALLADEPLVASILHAVVNAVSVPVTLKIRTGA 145

Query: 128 DDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEI 182
           D        RN   + +  + +G+  + +H   R     G          ++++D    I
Sbjct: 146 DPH-----HRNGVSIARIAEDAGIALLAVHGRTRACAFSG----------DVEHDTTARI 190

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             E+ D+ +  NG +     A  +L      GVMIGRAA
Sbjct: 191 -VESIDIPVLANGDIRSADDARAVLAHTGAAGVMIGRAA 228


>gi|57239061|ref|YP_180197.1| putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Welgevonden]
 gi|58579004|ref|YP_197216.1| putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Welgevonden]
 gi|57161140|emb|CAH58053.1| conserved hypothetical protein [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417630|emb|CAI26834.1| Putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Welgevonden]
          Length = 317

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 110/240 (45%), Gaps = 15/240 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           TD  +R   + L    LL +EMI +  +++  K ++     Q    A+Q+ G D   + E
Sbjct: 21  TDFPFRSLVKNL-GAGLLVSEMIASRGMIKQTKDSLQKSHIQSNT-AVQLAGCDPLIMAE 78

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AAK+ ED G   I++N GCP  +V     G+ LM +       + A+ KA+ +PVT+K R
Sbjct: 79  AAKLNEDMGAQIIDINFGCPVKKVVNSYAGSALMKDEITAAKILEAVVKAVKVPVTLKMR 138

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           IG D Q   +    L K  + +G+  I IH R         +        D+  +  IKK
Sbjct: 139 IGWDSQ--NLNSPRLAKIAENTGIKMITIHGRT--------RAQMFTGKADWKFISNIKK 188

Query: 185 --ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
               P +  G    L+D+  AL+     DG+MIGR AY    ++    ++  + +    P
Sbjct: 189 CVRIPIIVNGDIKTLDDIKIALE-ESQADGIMIGRGAYGKPWIINKALQFIKSGIILPDP 247


>gi|251797245|ref|YP_003011976.1| dihydrouridine synthase [Paenibacillus sp. JDR-2]
 gi|247544871|gb|ACT01890.1| dihydrouridine synthase DuS [Paenibacillus sp. JDR-2]
          Length = 341

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 102/232 (43%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    D+          +  L F+  E+P+   + G
Sbjct: 20  MEDVTDVVFRHVVSTAAKPDVFFTEFTSTDSYCNPAGIESTRGRLTFTEDEQPIVAHLWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  ++  G+  I++N+GCP   V     GA L+ +P+     I A      
Sbjct: 80  NKPELFEQMSIDMKKLGFRGIDINMGCPVQNVASNGKGAGLIRHPEAAAAIIQAAKAG-G 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  +  I K  +  + IH R       + K+  K+ +  +
Sbjct: 139 LPVSVKTRLGYSE---VDEWRGWLTHILKQDIANLSIHLR-------TKKEMSKV-DAHW 187

Query: 177 DIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +++ EIKK      P+  + +NG + D +  LK++    VDGVMIGR  + N
Sbjct: 188 ELIPEIKKLRDEIAPNTLLTINGDIPDRATGLKLVEQYGVDGVMIGRGIFTN 239


>gi|302792084|ref|XP_002977808.1| hypothetical protein SELMODRAFT_443602 [Selaginella moellendorffii]
 gi|300154511|gb|EFJ21146.1| hypothetical protein SELMODRAFT_443602 [Selaginella moellendorffii]
          Length = 378

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A       K     F+T  +++PL +Q    +
Sbjct: 59  MVDQSELPFRMLCRKYGATGA-YTPMLHARLFSEDRKYRNYEFTTCPEDRPLLIQFCANN 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE F  + I++N+GCP      G++GA LM +  +V   +  +   L +P
Sbjct: 118 PDTLLAAAKLVEPFC-DYIDINLGCPQRIAKRGNYGAFLMDDLPLVQALVTKLVSNLDVP 176

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   +DD I      +  K ++ SG + + +H R         K +R +   D+
Sbjct: 177 VSCKIRMFPSLDDTI------SYAKMLESSGCSLLAVHGRTR-----EQKCSRTV-RADW 224

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +++  +K+    P L  G    LED  + ++    VDGV+   +  +N A+  
Sbjct: 225 EVIRAVKQALRIPVLANGNIRWLEDAERCIQET-GVDGVLSAESLLENPALFA 276


>gi|56696957|ref|YP_167319.1| tRNA-dihydrouridine synthase, putative [Ruegeria pomeroyi DSS-3]
 gi|56678694|gb|AAV95360.1| tRNA-dihydrouridine synthase, putative [Ruegeria pomeroyi DSS-3]
          Length = 327

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 111/241 (46%), Gaps = 32/241 (13%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TDR +R     F A ++ +  +   EM+ A   +R   +     S   +  A+Q+ 
Sbjct: 19  MAGITDRPFRDLVMEFGAGMVVSEMVASQEMVQAKPGVRERAE----LSADVENTAVQLA 74

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+
Sbjct: 75  GRDTHWIAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALRLIEAVVAAV 134

Query: 116 SIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRK 170
            +PVT+K R+G DD +   P VA R       ++GV  + IH R      KG +      
Sbjct: 135 DVPVTLKTRLGWDDTLMNAPDVARR-----AAEAGVRMVTIHGRTRCQFYKGRA------ 183

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
               D+  +  + +E  D+ +  NG +     A + L     DGVM+GR A     +L  
Sbjct: 184 ----DWAAIAAV-REAVDVPLIANGDITCAHTARQALDRSGADGVMVGRGAQGRPWLLAQ 238

Query: 229 V 229
           +
Sbjct: 239 I 239


>gi|319795861|ref|YP_004157501.1| tim-barrel protein, nifr3 family [Variovorax paradoxus EPS]
 gi|315598324|gb|ADU39390.1| TIM-barrel protein, nifR3 family [Variovorax paradoxus EPS]
          Length = 352

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 111/257 (43%), Gaps = 21/257 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM+ +   L G  K         +  P+A+QI G D
Sbjct: 19  MAGVTDRPFRMLCREL-GAGYAVSEMVTSRKELWGTLKTSRRANHDGEPGPIAVQIAGTD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EA     + G   I++N+GCP+ +V     G+ LM +  +  + + A+  A    
Sbjct: 78  AAMMAEATVYNIERGAQIIDINMGCPAKKVCNKWAGSALMRDEPLALEIVQAVVDAAQPF 137

Query: 116 SIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           ++PVT+K R G  +D   AV    L +  + +GV  + +H R         ++     + 
Sbjct: 138 NVPVTLKMRTGWSEDNRNAV---KLARDFESAGVQMLTVHGRT--------REQGYKGHA 186

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           +YD +  +K     + +  NG +    +A  +L +   D VMIGRAA     +   +  +
Sbjct: 187 EYDTIAAVKAA-VRVPVVANGDINSPEKARDVLAATGADAVMIGRAAQGRPWIFREIAHF 245

Query: 233 FSNPLTGSSPIKTRVDK 249
                  + P+   V +
Sbjct: 246 LETGTHRAPPLVAEVRR 262


>gi|327276491|ref|XP_003223003.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Anolis
           carolinensis]
          Length = 488

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/194 (28%), Positives = 91/194 (46%), Gaps = 25/194 (12%)

Query: 43  FSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F T E+    +  Q+G AD  + +  AK+VE+     I++N+GCP     +G  GA L+ 
Sbjct: 74  FRTCEREKDSVVFQMGTADAERALAVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLS 132

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKA 158
           +PD +   +  + K +  PVT K RI     +P      +LVK I+++GV  I +H RK 
Sbjct: 133 HPDKIESILTTLVKGVCKPVTCKIRI-----LPTKEETISLVKRIERTGVAAIAVHGRK- 186

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM------SQALKILPSVDG 212
                  K+ R   ++  D++  I  E   + +  NGG  D        +A +       
Sbjct: 187 -------KEERPQHSVHCDVIKAI-SETVSIPVIANGGSHDFIKEHSDIEAFREATGASS 238

Query: 213 VMIGRAAYKNSAML 226
           VM+ RAA  N ++ 
Sbjct: 239 VMVARAAMWNPSVF 252


>gi|321476981|gb|EFX87940.1| hypothetical protein DAPPUDRAFT_305459 [Daphnia pulex]
          Length = 484

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 109/239 (45%), Gaps = 27/239 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ A   +R  +  +  L   T+++PL  Q    D
Sbjct: 25  MVDASELPWRLLSRKY-GTQLAYTPMMNAGIFIREPRYRREHLESCTEDRPLIAQFCAND 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               ++AAK+ E    + I+LN+GCP +   +G +GA L    D++   +  + + LSIP
Sbjct: 84  TDIFLKAAKMAEQHC-DAIDLNLGCPQSIAKKGHYGAFLQDEWDLISKMVKLIHRELSIP 142

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPN 173
           +T K R+  D ++  A A     K +++SG   + +H R    K  L GL+         
Sbjct: 143 ITCKVRVFPDINKSIAYA-----KMLEESGCYALTVHGRTREQKGPLTGLA--------- 188

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
             +  +  +K    ++ +  NG ++  S   + L S   D VM+      N A+   + 
Sbjct: 189 -SWKHIQAVKAAV-NIPVIANGNIQYWSDVERCLESTGADAVMVAEGNLTNPALFANLQ 245


>gi|83953578|ref|ZP_00962299.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. NAS-14.1]
 gi|83841523|gb|EAP80692.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. NAS-14.1]
          Length = 328

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 79/269 (29%), Positives = 125/269 (46%), Gaps = 38/269 (14%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     F A L+ +  +   +MI  +A     +K  LG   +    A+Q+ 
Sbjct: 19  MAGITDLPFRTLVASFGAGLVVSEMVASVDMI--NARPGTLEKAELGLGVEGT--AVQLA 74

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G + + + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+  A+
Sbjct: 75  GREAAPMAEAARMVEGQGARVIDINMGCPAKKVTQGYSGSALMKTPDHALRLIEAVVNAV 134

Query: 116 SIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRK 170
           ++PVT+K R+G DD +   P +A R      + +G+  I IH R      KG        
Sbjct: 135 NVPVTLKTRLGWDDNMLNAPQIAARA-----EAAGITMITIHGRTRCQFYKG-------- 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
             + D+  +  +K+      I  NG +     A + L     DGVMIGR A     +L  
Sbjct: 182 --SADWAAIAGVKQAVSVPVIA-NGDIISTDAARQALAQSGADGVMIGRGAQGKPWLLAQ 238

Query: 229 V-DEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           V  + F  P    +P+  +   DF R +S
Sbjct: 239 VAHDLFGAP----APVIPQ-GADFARMVS 262


>gi|195470200|ref|XP_002087396.1| GE16327 [Drosophila yakuba]
 gi|194173497|gb|EDW87108.1| GE16327 [Drosophila yakuba]
          Length = 505

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 112/237 (47%), Gaps = 25/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L+IP
Sbjct: 94  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAQLAIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +     +R   K ++ +G   + +H R    K  L G++          
Sbjct: 153 VTCKIRIFEDLE---KTIR-YAKMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 198

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D++ +  +++  + P L  G   GLED+ + L     VDGVM       N A+   V
Sbjct: 199 DWNYIKSVRQHVKIPMLANGNILGLEDVHRCLAET-GVDGVMSAEGNLHNPAIFQGV 254


>gi|226479846|emb|CAX73219.1| dihydrouridine synthase 2-like, SMM1 homolog [Schistosoma
           japonicum]
          Length = 511

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 105/226 (46%), Gaps = 22/226 (9%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           R++ ++ +   E+   D IL          + ++  + +Q+G ++    ++AAK++E+  
Sbjct: 51  RVIRSSRIANDELNTVDFILPDGSVTFRTSAEEKNRVIVQLGTSNPETALKAAKVLEN-D 109

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
              I++N+GCP A   +G  GA L+  PD V + +  +   L IPVT K RI + +    
Sbjct: 110 VMAIDVNMGCPKAYSVKGGMGAALLTKPDTVKEILTTLTTNLRIPVTCKMRI-LPELDKT 168

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VAL  L++S   +GV  I IH R    + +    N  I  +   +          + I  
Sbjct: 169 VALAKLIES---TGVVAITIHGRTIHERSMHRNRNEVIQAIAQSV---------SIPILA 216

Query: 194 NGGLEDM------SQALKILPSVDGVMIGRAAYKNSAMLTT--VDE 231
           NGG  D+       +  + L    GV+I RAA  N A+  +  VDE
Sbjct: 217 NGGSRDIIRNHEDIEYFRQLTGAAGVVIARAAMWNPAIFKSLQVDE 262


>gi|224368016|ref|YP_002602179.1| Dhs2 [Desulfobacterium autotrophicum HRM2]
 gi|223690732|gb|ACN14015.1| Dhs2 [Desulfobacterium autotrophicum HRM2]
          Length = 330

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 101/207 (48%), Gaps = 16/207 (7%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           L+ +EM+ A  +    +K +    T   E+P+++QI GA+   +  AA+ I E    + I
Sbjct: 36  LVCSEMVSAKGLEFNSEKTVQLLRTDACERPVSVQIFGAEALSMANAARWIAERNVADII 95

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N GC   +V     G  LM + D     I A+ +A+S+P T+K R G D    A    
Sbjct: 96  DINFGCSVKKVARTGAGVALMKDMDNARAIIRAVRRAVSMPFTIKIRSGWDSS--ASQAF 153

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++ +  + +GV+ I IH R A  +G   +        D+ ++  +K+      IG NG +
Sbjct: 154 DIARMAEDNGVDAIAIHPRTA-AQGFRGR-------ADWSMIARLKEMLTIPVIG-NGDI 204

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKN 222
               Q + ++     DGVM+GRAA  N
Sbjct: 205 TTPEQGVAMIQETGCDGVMVGRAAMGN 231


>gi|330831061|ref|YP_004394013.1| tRNA-dihydrouridine synthase B [Aeromonas veronii B565]
 gi|328806197|gb|AEB51396.1| tRNA-dihydrouridine synthase B [Aeromonas veronii B565]
          Length = 305

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 112/254 (44%), Gaps = 22/254 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM++A+  +   +K  +    S +    ++QI GAD
Sbjct: 1   MAGVTDRPFRELC-LRLGAGMAVSEMLLANPDVWDTQKTRMRMDHSAEGGLRSVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   +++N+GCP+ +V++   G+ L+  PD V     A+  A+ +P
Sbjct: 60  PEMMAFAARYNVEQGAQIVDINMGCPAKKVNKKLAGSALLRAPDQVKAICRAVVDAVEVP 119

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  + +     G+  + +H R    + KG            +
Sbjct: 120 VTLKIRTGWDPDNRNGVEIARIAED---CGIAALAVHGRTRACLYKG----------EAE 166

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I K+   + +  NG +    +A  +L    VD VMIGRAA     +   +  + 
Sbjct: 167 YDTIRAI-KQAVSIPVVANGDINSPEKARYVLDYTGVDAVMIGRAAQGRPWIFREIRHFL 225

Query: 234 SNPLTGSSPIKTRV 247
                   P +  V
Sbjct: 226 ETGTKLPPPEREEV 239


>gi|308499933|ref|XP_003112152.1| hypothetical protein CRE_29758 [Caenorhabditis remanei]
 gi|308268633|gb|EFP12586.1| hypothetical protein CRE_29758 [Caenorhabditis remanei]
          Length = 529

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 78/166 (46%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R F R     LT   +++  + V D   R   +N L     ++PL +Q   
Sbjct: 80  MVDQSELAFRLFTRKYGAQLTFTPMIHAHLFVNDGTYR---RNSLALVKADRPLVVQFCA 136

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
             +   + A ++VED   + ++LN+GCP      G +G+ L    D++ + ++A+     
Sbjct: 137 NKVETFLAACRLVEDVC-DGVDLNLGCPQMVAKRGRYGSWLQDEVDLICEMVSAVRDYCK 195

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PV+ K R+  D Q      + LV     +G   + +H R   +KG
Sbjct: 196 LPVSCKIRVRDDRQQTVEYAKRLV----DAGATMLTVHGRTRDMKG 237


>gi|268590774|ref|ZP_06124995.1| tRNA-dihydrouridine synthase B [Providencia rettgeri DSM 1131]
 gi|291313551|gb|EFE54004.1| tRNA-dihydrouridine synthase B [Providencia rettgeri DSM 1131]
          Length = 327

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 51/190 (26%), Positives = 89/190 (46%), Gaps = 23/190 (12%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G D  ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PDIV   +  
Sbjct: 68  SVQIAGNDPDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPDIVKSILEG 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSP 165
           + KA+ +PVT+K R G   +      RN +   K  +  G+  + IH R    +  G   
Sbjct: 128 VVKAVDVPVTLKIRTGWSPE-----ERNCIEIAKLAEDCGIQALTIHGRTRACLFNG--- 179

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                    +YD +  + K+   + +  NG + D  +A  +L     D +M+GRAA    
Sbjct: 180 -------EAEYDNIRAV-KQTVTIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRP 231

Query: 224 AMLTTVDEYF 233
            +   +  Y 
Sbjct: 232 WIFREIQHYL 241


>gi|256088793|ref|XP_002580509.1| tRNA-dihydrouridine synthase [Schistosoma mansoni]
 gi|238666091|emb|CAZ36748.1| tRNA-dihydrouridine synthase, putative [Schistosoma mansoni]
          Length = 441

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/230 (26%), Positives = 106/230 (46%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L +T MI + A L   K  ++ L F+++++PL +Q     
Sbjct: 17  MVDGSELAWRMLGRKY-GVQLTFTPMINSTAFLINMKYRRSCLQFASEDRPLIVQFCANS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               V  AK+V+ F  + ++LN+GCP      G +GA L    + + + I+     L++P
Sbjct: 76  PDTFVRCAKLVQPFC-DAVDLNLGCPQGIAKRGHYGAFLQDEWNSLKEIISRASLELNVP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G + + +H R   +KG      +K    D++ 
Sbjct: 135 VTCKIRIFSDVERTV----QYAKLLEAAGASMLTVHGRTREMKG------QKTGLADWNQ 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           +  + KE   + +  NG ++ +S   + L S   D VM       N A+ 
Sbjct: 185 IRAV-KEAVKIPVIANGNIQYLSDVHQCLDSTKADAVMSAEGHLHNPALF 233


>gi|24373569|ref|NP_717612.1| NifR3/Smm1 family protein [Shewanella oneidensis MR-1]
 gi|38604869|sp|Q8EFG7|DUSC_SHEON RecName: Full=tRNA-dihydrouridine synthase C
 gi|24347891|gb|AAN55056.1|AE015643_3 NifR3/Smm1 family protein [Shewanella oneidensis MR-1]
          Length = 315

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 109/235 (46%), Gaps = 31/235 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P
Sbjct: 57  GYTPSGTPVRVQLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + D + AM +A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 NTIHDIVRAMRQAVPAEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  K P   ++ + E+++  P   I  NG + +   A + +     D +MIGR
Sbjct: 174 -------DGYKPPAY-WEYITEVRERLPIPVIA-NGEIWNRDDAKRCMQVTGCDSIMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
            A     +  T+        TG++P         W      M  Y  R L SG K
Sbjct: 225 GAISLPNLADTIK-------TGATPYS-------WADTLQLMLSYTQREL-SGRK 264


>gi|261210422|ref|ZP_05924716.1| tRNA dihydrouridine synthase B [Vibrio sp. RC341]
 gi|260840480|gb|EEX67046.1| tRNA dihydrouridine synthase B [Vibrio sp. RC341]
          Length = 287

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 92/193 (47%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D   + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++   +  
Sbjct: 33  SVQIAGSDPQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIESILKT 92

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+++PVT+K R G D D    V++  L +     G+  + +H R    + KG     
Sbjct: 93  VVNAVNVPVTLKTRTGWDTDNKNCVSIAQLAED---CGIQALALHGRTRACMYKG----- 144

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K       I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 145 -----EAEYDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWI 198

Query: 226 LTTVDEYFSNPLT 238
              +  +  +  T
Sbjct: 199 FQEIQHFLEHGTT 211


>gi|221090632|ref|XP_002157580.1| PREDICTED: similar to MGC79829 protein [Hydra magnipapillata]
          Length = 311

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 115/257 (44%), Gaps = 26/257 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++ + +R   R   N  L YT MI+AD+ ++  +     F+T   ++PL +Q    +
Sbjct: 16  MVRYSKQPFRHLVRRY-NCDLAYTPMIMADSFIKSIEARDSDFTTNKDDRPLVVQFAANN 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+I+  +  + + LN GCP        +GA L+  P+++ D I    + L  P
Sbjct: 75  AEDLALAAEIIYPYA-DGVGLNCGCPQRWAMAEGYGAQLISKPELINDMIKQTRQRL--P 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
               C I +          +L +  + +GV+ I +H R      L  + N  +   +YD 
Sbjct: 132 QDFSCEIKIRIHSDIRKTVDLCQKAEHAGVSWITVHGR------LPSQRNEPV---NYDA 182

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM--------LTT 228
           +  I K++  + +  NG +++   A  ++    V+GVM  +    N AM        L  
Sbjct: 183 IKTI-KDSLQIPVVANGDIKNKEDAWDVVKKTGVNGVMAAQGMLNNPAMYAGYEVTPLQC 241

Query: 229 VDEYFSNPLTGSSPIKT 245
           V ++ +  L+  +P  T
Sbjct: 242 VKDWVNIALSLGTPFVT 258


>gi|297194493|ref|ZP_06911891.1| dihydrouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
 gi|197718697|gb|EDY62605.1| dihydrouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
          Length = 389

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 105/226 (46%), Gaps = 19/226 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDETETPRSIQLYGV 93

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKA 114
           D   + +A +++  ED   + I+LN GCP  +V     G+ L    P +      A+  A
Sbjct: 94  DPVTVGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPFKRPLLRAILHEAVTNA 152

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT+K R G+DD    +   +  +   + GV  I +H R A                
Sbjct: 153 GALPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTA 202

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           D+D +  +K+  P++ +  NG +   + AL+++     DGV++GR 
Sbjct: 203 DWDAIARLKEHVPEIPVLGNGDIWSAADALRMMRETGCDGVVVGRG 248


>gi|170572143|ref|XP_001891998.1| tRNA-dihydrouridine synthase 4 [Brugia malayi]
 gi|158603133|gb|EDP39179.1| tRNA-dihydrouridine synthase 4, putative [Brugia malayi]
          Length = 321

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 55/233 (23%), Positives = 108/233 (46%), Gaps = 23/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL + + + +T MI A   +  ++     F+T   + P  +Q    +
Sbjct: 37  MVRYSKLPFRMLVRLYSVD-VAFTPMIYAKHFIASEQCRSAEFTTCPGDNPTVVQFASNE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +   AA  +  +    I+LN GCP   V    +G+ L+ +P  + D ++   + +S P
Sbjct: 96  PEEFSTAAMFISRYCRG-IDLNCGCPQRDVMREGYGSSLLTDPVRIADIVSTTRRRISRP 154

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K R+  + Q+     R      +++GV+ + +H R          + R  P  D
Sbjct: 155 DFTISIKIRLKPNRQLTLETCRQ----AERAGVSFVTVHGRTP--------EQRSEP-AD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           YD++ ++ K +  + +  NG ++   QAL+++    VDGVM      +N AM 
Sbjct: 202 YDMI-KLIKSSLSIPVIANGNIKSYEQALQVVKYTGVDGVMSANGLLENPAMF 253


>gi|239817593|ref|YP_002946503.1| hypothetical protein Vapar_4632 [Variovorax paradoxus S110]
 gi|239804170|gb|ACS21237.1| TIM-barrel protein, nifR3 family [Variovorax paradoxus S110]
          Length = 352

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/263 (24%), Positives = 116/263 (44%), Gaps = 33/263 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK------PLALQI 54
           M   TDR +R   R L       +EM+ +    R +  N L  S +        P+A+QI
Sbjct: 19  MAGVTDRPFRMLCREL-GAGYAVSEMVTS----RKELWNTLKTSRRANHDGEPGPIAVQI 73

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G D + + EAA    + G   I++N+GCP+ +V     G+ LM +  +  + + A+  A
Sbjct: 74  AGTDAAMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMRDEPLALEIVQAVVDA 133

Query: 115 L---SIPVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGLSPKDN 168
               ++PVT+K R G  ++      RN VK     + +GV  + +H R         ++ 
Sbjct: 134 AQPHNVPVTLKMRTGWSEE-----HRNAVKLARDFESAGVQMLTVHGRT--------REQ 180

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
               + +YD +  +K     + +  NG +    +A ++L +   D VMIGRAA     + 
Sbjct: 181 GYKGSAEYDTIAAVKAAV-RVPVVANGDIRSPEKAREVLAATGADAVMIGRAAQGRPWIF 239

Query: 227 TTVDEYFSNPLTGSSPIKTRVDK 249
             +  + +     + P+   V +
Sbjct: 240 REIAHFLATGTHLAPPLVAEVRR 262


>gi|229817348|ref|ZP_04447630.1| hypothetical protein BIFANG_02610 [Bifidobacterium angulatum DSM
           20098]
 gi|229785137|gb|EEP21251.1| hypothetical protein BIFANG_02610 [Bifidobacterium angulatum DSM
           20098]
          Length = 377

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 66/256 (25%), Positives = 110/256 (42%), Gaps = 29/256 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F   E+  +LQ+ G +
Sbjct: 17  MAGVTNWPFRVLCEQYGPSGLYVAEMITARALVARNPKALRLCRFDPSERVRSLQLYGVN 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D++ + I+    +C A
Sbjct: 77  PAIVEQAAKIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEIISRVVKVCSA 136

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
            +IPVT K R+G+D +         +   ++ G   + +HAR       G S        
Sbjct: 137 ANIPVTAKFRVGIDHEHETFLQAGHIA--QEEGCAAVTLHARTTAEYYGGHS-------- 186

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
             D+  + E+K+E  D+ +  NG +     AL ++     DGV IGR       +   + 
Sbjct: 187 --DWTRIAELKQEL-DIPVFGNGDIWGADDALAMIDQTGCDGVAIGRGCQGRPWLFADIK 243

Query: 231 EYFS------NPLTGS 240
             F       NP  G 
Sbjct: 244 HAFEGSTQRINPTLGE 259


>gi|71032309|ref|XP_765796.1| hypothetical protein [Theileria parva strain Muguga]
 gi|68352753|gb|EAN33513.1| hypothetical protein, conserved [Theileria parva]
          Length = 327

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 53/231 (22%), Positives = 106/231 (45%), Gaps = 16/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R  + + L YT M+ A      +    + F  S+ +KPL  Q  G D
Sbjct: 33  MVDQSELPFRLLCRRYSAD-LAYTPMLHAKIFSENENYRNIHFHTSSDDKPLIAQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +  + A+  +++   + I++N+GCP     +G +G+ L+  P ++ + + ++ +     
Sbjct: 92  PNAFILASSYIKN-DVSAIDINLGCPQGIARKGRYGSFLLEYPQLINEIVRSLTQT---G 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + V C+I   ++    +  NL  S++ SG   + +H R         +   +I   D+D 
Sbjct: 148 INVTCKIRKVEKDCLQSTLNLCYSLEASGCKALTVHGRH------RSETKTRISECDWDS 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           + +I K   ++ +  NGG+E      + L     D VM   A  +N  + +
Sbjct: 202 I-KIIKSKVNIPVIANGGIETFEDVKRCLEYTGADAVMSSEAILENPYLFS 251


>gi|85703153|ref|ZP_01034257.1| tRNA-dihydrouridine synthase, putative [Roseovarius sp. 217]
 gi|85672081|gb|EAQ26938.1| tRNA-dihydrouridine synthase, putative [Roseovarius sp. 217]
          Length = 339

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 115/251 (45%), Gaps = 25/251 (9%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     F A L+ +  +   EM+ A    RG  K  LGF  +    ++Q+ 
Sbjct: 18  MAGITDLPFRTVVAGFGAGLVVSEMVASQEMVQAKPSARG--KAELGFGIENT--SVQLA 73

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARV----HEGSFGACLMLNPDIVGDCIAAM 111
           G D   + EAA++V D G   I++N+GCP+ +V      G+ G+ LM + D     I A+
Sbjct: 74  GCDPHWMAEAARVVADHGARIIDINMGCPAKKVVSAAGAGASGSALMRDLDHALRLIEAV 133

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A+ +PVT+K R+G D+     A   L K  + +GV  I +H R          D   I
Sbjct: 134 VGAVDVPVTLKTRLGWDEGCSNAA--ELAKRAEAAGVAMITVHGRTRCQFYRGAADWAMI 191

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            ++   +   +   N D+ +G+      M+Q+     +  GVMIGR A     +L  V  
Sbjct: 192 SDIAQAVNIPVIA-NGDI-VGVASACRAMAQS-----NAAGVMIGRGARGRPWLLAEVAA 244

Query: 232 YFSNPLTGSSP 242
              +   G++P
Sbjct: 245 AMGH---GTAP 252


>gi|308493062|ref|XP_003108721.1| hypothetical protein CRE_11115 [Caenorhabditis remanei]
 gi|308248461|gb|EFO92413.1| hypothetical protein CRE_11115 [Caenorhabditis remanei]
          Length = 548

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 78/279 (27%), Positives = 124/279 (44%), Gaps = 29/279 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A +IL G   + ++L     EK   +Q+ G     + +AA+IV E+F  + +++N+
Sbjct: 229 EMALATSILSGAASEYSLLKRHPSEKIFGVQLAGGFADTMAKAAQIVVENFDVDFVDINM 288

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV 140
           GCP   V++   G  L   P+ + + +AA    L   P+TVK R G  + +  +     V
Sbjct: 289 GCPIDVVNQKGGGCALPSRPNKLYEVLAATKSVLGDCPMTVKIRTGQKEGV--LKAPETV 346

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNR--KIPNLDYD-IVYEIKKENPDLFIGLNGGL 197
           + +KKS     W H    I      K+ R  K+ N DY   V E  K  P    G     
Sbjct: 347 EFMKKSP----W-HCPDLITFHPRSKEQRYTKLANWDYTHAVAEASKPVPLWVCGDVLSW 401

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           ED  + L+  P V+G+MIGR A     + T +DE  +  ++ +     R D      +  
Sbjct: 402 EDYYERLENHP-VNGIMIGRGALIKPWIFTEIDERRTWDISATE----RFD------LLK 450

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +Y   H  S     + TR  +  F  F    +CR+I
Sbjct: 451 KFINYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 485


>gi|333027267|ref|ZP_08455331.1| putative dihydrouridine synthase [Streptomyces sp. Tu6071]
 gi|332747119|gb|EGJ77560.1| putative dihydrouridine synthase [Streptomyces sp. Tu6071]
          Length = 401

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 64/271 (23%), Positives = 117/271 (43%), Gaps = 25/271 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 46  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMRLVQFGPAETPRSIQLYGV 105

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +AA+++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 106 DPVTVGKAARMIRDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVAGAD 165

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +     G+  I +H R                  D
Sbjct: 166 GLPVTMKMRKGIDDD--HLTALDAGRIAVDEGITAIALHGRTTA--------QHYGGTAD 215

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P+L +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 216 WDAIARLKEHVPELPVLGNGDIWTAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 275

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
              L  + P          R+++A M  +AA
Sbjct: 276 EGALRPTPP--------GLREVAAVMLRHAA 298


>gi|328882334|emb|CCA55573.1| tRNA dihydrouridine synthase B [Streptomyces venezuelae ATCC 10712]
          Length = 389

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 104/226 (46%), Gaps = 19/226 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E+P ++Q+ G 
Sbjct: 33  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDATEQPRSIQLYGV 92

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKA 114
           D   + +A +++  ED   + I+LN GCP  +V     G+ L    P +      A+  A
Sbjct: 93  DPVTVGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILHEAVTNA 151

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +   +  +   + GV  I +H R A                
Sbjct: 152 GDLPVTMKMRKGIDDD--HITFLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTA 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           D+D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 202 DWDAIARLKEHVPEIPVLGNGDIWSADDALRMMRETGCDGVVVGRG 247


>gi|157127436|ref|XP_001654979.1| t-diRNAhydrouridine synthase [Aedes aegypti]
 gi|108882414|gb|EAT46639.1| t-diRNAhydrouridine synthase [Aedes aegypti]
          Length = 581

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 112/238 (47%), Gaps = 25/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +  K  K+ L    +++PL +Q  G D
Sbjct: 100 MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFSKDPKYRKDSLQTCPEDRPLIIQFCGND 158

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA + +D   + I++N+GCP A    G +GA L    D++ + ++ +   LS+P
Sbjct: 159 PKVLLEAALLAQDH-CDAIDINLGCPQAIAKRGHYGAFLQDEWDLLKEIVSTLHSKLSVP 217

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  +D    +      K ++ +G   + +H R    K  L G++          
Sbjct: 218 VTCKIRI-FEDMNKTI---RYAKMLEAAGCQMLTVHGRTRDQKGPLTGIA---------- 263

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           D+  V ++K+  + P L  G   G+ED+ + ++    V+G+M       N  +   V+
Sbjct: 264 DWKYVKKLKEILKIPVLSNGNIMGVEDVHRCMEET-GVNGIMTAEGNLFNPFLFEGVN 320


>gi|224534532|ref|ZP_03675108.1| putative histidine phosphokinase/phophatase [Borrelia spielmanii
           A14S]
 gi|224514209|gb|EEF84527.1| putative histidine phosphokinase/phophatase [Borrelia spielmanii
           A14S]
          Length = 334

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/250 (24%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL   K++I    L  +   +PL  
Sbjct: 17  MEDVTDSVFRNLIHLIGSGEGEPHIYFTEFISVKGILNRSKQSIQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP  ++ +    + L+ N  + G+ I A  
Sbjct: 77  QIWGNIPEQFYRAIEILGGMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAGEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +   G++ + ++ R A+ +   P    
Sbjct: 137 EACSKFNLPLSVKTRHGF--SYPEVD--DWLGFLLGFGIDMLTVYPRLAVNQSEGP---- 188

Query: 170 KIPNLDYDIVYEIKKE----NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 189 ----VNFDIFYELVKLRNNISPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKFSSKHF 254


>gi|297160659|gb|ADI10371.1| putative dihydrouridine synthase [Streptomyces bingchenggensis
           BCW-1]
          Length = 377

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 104/226 (46%), Gaps = 19/226 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  D K   ++ F   EKP ++Q+ G 
Sbjct: 22  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERDAKTMRLIHFDGTEKPRSIQLYGV 81

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKA 114
           D   + +A +++  ED   + I+LN GCP  +V     G+ L     ++   +  A+  A
Sbjct: 82  DPVTVGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRHLLRSILREAVTGA 140

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +   +  +   + GV  I +H R A                
Sbjct: 141 GPLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTA 190

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           D+D +  +K+  P++ +  NG +     A++++     DGV++GR 
Sbjct: 191 DWDAIARLKEAVPEIPVLGNGDIWSADDAVRMMRRTGCDGVVVGRG 236


>gi|83942358|ref|ZP_00954819.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. EE-36]
 gi|83846451|gb|EAP84327.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. EE-36]
          Length = 328

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 104/214 (48%), Gaps = 29/214 (13%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           A+Q+ G + + + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A
Sbjct: 70  AVQLAGREAAPMAEAARMVEGQGARVIDINMGCPAKKVTQGYSGSALMKTPDHALRLIEA 129

Query: 111 MCKALSIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSP 165
           +  A+++PVT+K R+G DD +   P +A R      + +G+  I IH R      KG   
Sbjct: 130 VVNAVNVPVTLKTRLGWDDNMLNAPQIAARA-----EAAGITMITIHGRTRCQFYKG--- 181

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                  + D+  +  +K+      I  NG +     A + L     DGVMIGR A    
Sbjct: 182 -------SADWAAIAGVKQAVSVPVIA-NGDIISTDAARQALAQSGADGVMIGRGAQGKP 233

Query: 224 AMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKIS 256
            +L  V  + F  P    +P+  +   DF R +S
Sbjct: 234 WLLAQVAYDLFGAP----APVIPQ-GTDFARMVS 262


>gi|50420411|ref|XP_458741.1| DEHA2D06512p [Debaryomyces hansenii CBS767]
 gi|49654408|emb|CAG86885.1| DEHA2D06512p [Debaryomyces hansenii]
          Length = 423

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 53/168 (31%), Positives = 82/168 (48%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFSTQEKPLALQI 54
           MVD ++  +R  +R    + L YT M  A      +K        + G   +++PL +Q 
Sbjct: 26  MVDQSELAWRILSRRYGAD-LCYTPMFHARLFATEEKYRNNMWSELDGDKEKDRPLIVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK VED   + ++LN+GCP     +G++GA LM + D+V   I  +   
Sbjct: 85  CANDSDYLLKAAKFVED-KCDAVDLNLGCPQGIAKKGNYGAFLMDDWDLVYKLIKNLHDN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           L  PVT K R+  DD   ++    LV +   +G   I IH R   +KG
Sbjct: 144 LKCPVTAKIRV-YDDWEKSLEYAKLVLN---AGAQFITIHGRTRDMKG 187


>gi|226498556|ref|NP_001142214.1| hypothetical protein LOC100274382 [Zea mays]
 gi|194707636|gb|ACF87902.1| unknown [Zea mays]
          Length = 420

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 109/233 (46%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 96  MVDNSELPFRMLCRRYGADAA-YTPMLHSRIFSENEKYRSMEFTTCKEDRPLFVQFCAND 154

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAK VE +  + +++N GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 155 PDILLQAAKKVEPYC-DYVDINFGCPQRIARRGNYGAFLMDNLPLVKSLVQNLAANLHVP 213

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+VK R+   ++D +         K ++++G + + +H R         KD +K    D+
Sbjct: 214 VSVKIRVFPRLEDTLA------YAKMLEEAGASLVAVHGRTR-----DEKDGKKF-RADW 261

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           D +  +K     P L  G    +ED+   L+     DGV+      +N A+  
Sbjct: 262 DAIKAVKDALRVPVLANGNIRHMEDVKNCLEHT-GADGVLSAETLLENPAVFA 313


>gi|270283991|ref|ZP_05965366.2| putative tRNA-dihydrouridine synthase [Bifidobacterium gallicum DSM
           20093]
 gi|270277877|gb|EFA23731.1| putative tRNA-dihydrouridine synthase [Bifidobacterium gallicum DSM
           20093]
          Length = 422

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 68/292 (23%), Positives = 116/292 (39%), Gaps = 22/292 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G + S +
Sbjct: 66  TNWPFRVLCEQYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVNPSIM 125

Query: 63  VEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CKALSIP 118
            +AAKIV D    + ++LN GCP  +V     G+ L    D+  D ++ +   C A  IP
Sbjct: 126 EQAAKIVVDEQMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFTDVVSRVVRVCDAAGIP 185

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G+D +             ++ G   + +HAR          D  +I  L    
Sbjct: 186 VTAKIRVGIDHE--HETFHEAGHIAQEEGCKAVTLHARTTAEYYGGHSDWSRIGEL---- 239

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNP 236
                 E  D+ +  NG +   + AL ++      GV IGR       +   +   F+  
Sbjct: 240 -----VEQLDVPVFGNGDIWGAADALAMVEQTGCAGVAIGRGCQGRPWLFADIKHAFAGS 294

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              + P   +V +   R  +     Y      +      + +H+     GFP
Sbjct: 295 DERTDPTLGQVCQVIMRHATYLTEFYDGDERMAA---HDMRKHVAWYLKGFP 343


>gi|322780739|gb|EFZ09996.1| hypothetical protein SINV_07882 [Solenopsis invicta]
          Length = 1167

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 68/127 (53%), Gaps = 4/127 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K  +  L  +++++PL +Q  G D
Sbjct: 732 MVDASELAWRLLSRR-HGAQLCYTPMLHSSVFCRDPKYRREALASTSEDRPLIVQFCGND 790

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA + E +  + I++N+GCP A    G +GA L  + D++   ++ +   L IP
Sbjct: 791 PDILLEAAHLAEPYC-DAIDINIGCPQAIAKRGHYGAFLQDDWDLLKKIVSTLKNGLRIP 849

Query: 119 VTVKCRI 125
           VT K R+
Sbjct: 850 VTCKLRV 856


>gi|156120523|ref|NP_001095407.1| dihydrouridine synthase 4-like [Bos taurus]
 gi|151555764|gb|AAI49230.1| DUS4L protein [Bos taurus]
 gi|296488502|gb|DAA30615.1| dihydrouridine synthase 4-like [Bos taurus]
          Length = 238

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 61/208 (29%), Positives = 99/208 (47%), Gaps = 21/208 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R    + L YT MIVA   +R  K     F+T +   PL +Q    D
Sbjct: 34  MVRYSKLSFRTLVRKYDCD-LCYTPMIVAADFVRSAKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPYA-NGIDINCGCPQRWALAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  DD    V   +L +  + +GV+ I +H R          + R  P + 
Sbjct: 152 RFSVSIKIRIH-DDLTRTV---DLCRKAEATGVSWITVHGRTV--------EERHQP-VH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           Y+ + +I KE+  + I  NG +  + +A
Sbjct: 199 YEAI-KIIKESMSIPIVANGDIRSLKEA 225


>gi|38234473|ref|NP_940240.1| hypothetical protein DIP1903 [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200736|emb|CAE50438.1| Putative exported protein [Corynebacterium diphtheriae]
          Length = 383

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 72/294 (24%), Positives = 121/294 (41%), Gaps = 25/294 (8%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R  T + L   EMI A A++  ++K  ++  F  QE   +LQ+   D     +AAK I E
Sbjct: 40  RTGTVSGLYICEMITARALVERNEKTLHMTTFGPQEDIRSLQLYTVDPEYTYKAAKMIAE 99

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V +   G+ L     + G+ +AA  K +    IP+TVK R+G+
Sbjct: 100 NNMADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGNIVAAAVKGVEGTDIPITVKFRMGI 159

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD    +   +  +   + G   + +HAR A          R   +  +D +  +K+   
Sbjct: 160 DDD--HLTYLDAGRIAAEEGAAAVTLHARTAA--------ERYSGDAHWDAIGTLKEHMR 209

Query: 188 DLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           D  I +  NG +     A  +L +   DGV++GR       +   +            P 
Sbjct: 210 DSGIPVLGNGDIFKAEDAKAMLDASGCDGVVVGRGCLGRPWLFAGISAALRGEELPPEPT 269

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              V +  +R       +  A H       + + +HM     GFP     R  L
Sbjct: 270 LGEVTRIIYRH-----AELLAEHDGEKKASRDMRKHMGWYMRGFPVGGEFRGAL 318


>gi|260890147|ref|ZP_05901410.1| putative dihydrouridine synthase [Leptotrichia hofstadii F0254]
 gi|260860170|gb|EEX74670.1| putative dihydrouridine synthase [Leptotrichia hofstadii F0254]
          Length = 325

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 53/220 (24%), Positives = 105/220 (47%), Gaps = 20/220 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
            L+TEM+ A+ + R D   I  L     ++    QI G D  +L+     +++FG+ +IN
Sbjct: 27  FLFTEMVNANLLNREDDTTINELLKCDDKQRTGTQIFGGDKDELISGILKLKNFGFKKIN 86

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP  ++ +   G+ L+ NPD+V D +    + +   +++K R+G  D        N
Sbjct: 87  VNMGCPQPKIIKNGAGSALLENPDLV-DQVLLETQNIGAEISIKIRVGYKDFNNPEIFLN 145

Query: 139 LVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           L     K  ++ I +H R  K +  G +          +++IV ++ K   ++    NG 
Sbjct: 146 LA---NKHNLDFICVHGRTQKQMYSGTA----------NWEIVEKLSKMPRNINFFGNGD 192

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           L + ++  +   S  +DG+++ R    N  +++   E+  
Sbjct: 193 LFEPTEIKRKTSSCNLDGIILSRGIIGNPWLISQTREFLQ 232


>gi|300718658|ref|YP_003743461.1| tRNA-dihydrouridine synthase B [Erwinia billingiae Eb661]
 gi|299064494|emb|CAX61614.1| tRNA-dihydrouridine synthase B [Erwinia billingiae Eb661]
          Length = 321

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 112/240 (46%), Gaps = 22/240 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMMSSNPEVWATDKSRLRMVHSDEPGIRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   + A+  A+ +P
Sbjct: 76  PHEMAEAARINALSGAQVIDINMGCPAKKVNRKLAGSALLQHPELVKSILLAVVDAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V +  L    ++ G+  + IH R    +  G            +
Sbjct: 136 VTLKIRTGWDPDNRNCVEIAQLA---ERCGIQALTIHGRTRACLFNG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 183 YDSIRTV-KQNVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 241


>gi|91977059|ref|YP_569718.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris BisB5]
 gi|91683515|gb|ABE39817.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodopseudomonas
           palustris BisB5]
          Length = 353

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 54/204 (26%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           L+ +EM  ++ +++G   ++      +  P  +Q+ G +   + E A+I E  G + I++
Sbjct: 56  LVVSEMTASEDLVQGRAMSVRRCDAIDGAPHVVQLAGCEPHWMAEGARIAEAGGADIIDI 115

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+  V  G  G+ LM + D     I A   A+ +PVT+K R+G D++  ++    L
Sbjct: 116 NMGCPARHVTGGQSGSALMRDLDHALTLIEATIDAVRVPVTLKMRLGWDER--SLNAPEL 173

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +GV  + +H   R    KG            D+  V  + +E   + + +NG +
Sbjct: 174 ARRAEAAGVQLVTVHGRTRSQFYKG----------EADWRAVRAV-REAISIPLVVNGDI 222

Query: 198 EDMSQALKIL--PSVDGVMIGRAA 219
                A++ L     D VMIGR A
Sbjct: 223 TTYHMAVEALDQSGADAVMIGRGA 246


>gi|291550701|emb|CBL26963.1| tRNA-U20a,U20b-dihydrouridine synthase [Ruminococcus torques L2-14]
          Length = 313

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 86/190 (45%), Gaps = 9/190 (4%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+++  + +      QI   ++   +  AK + D+GY E+NLN+GCPS  V     GA
Sbjct: 47  EKKDVMPENNEGMYAVPQILTNNVEDFLCTAKKLGDYGYKEVNLNLGCPSRTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  P  +   + A+ +  ++ +++K RIG++D         ++    K  +  + IH 
Sbjct: 107 GFLDEPQKLDRFLDAVFEKCNLEISIKTRIGMED---PEEFETILPIYNKYPLKELIIHP 163

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
           R      +  +  +  P LD         E+P  + G    +EDM Q     P  D VM+
Sbjct: 164 R------VQKEFYKNTPKLDTYAWAVEHSEHPLCYNGDICSVEDMEQLKIRFPQTDTVMM 217

Query: 216 GRAAYKNSAM 225
           GR    + A+
Sbjct: 218 GRGVLADPAL 227


>gi|75908388|ref|YP_322684.1| dihydrouridine synthase, DuS [Anabaena variabilis ATCC 29413]
 gi|75702113|gb|ABA21789.1| tRNA-U20a,U20b-dihydrouridine synthase [Anabaena variabilis ATCC
           29413]
          Length = 378

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 107/222 (48%), Gaps = 22/222 (9%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +P+  Q+ G  I  LV  AK +  +    ++LN+GCP+ R++  + G  L+L+P  V   
Sbjct: 73  RPVFAQMIGESIPDLVRTAKELCHYDIAGVDLNMGCPAPRIYRKNVGGGLLLSPGKVEQI 132

Query: 108 IAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLS 164
           +A + +A+S  P+TVK R+G ++         ++  + +  ++ + +H R  K +  G  
Sbjct: 133 LAELRQAVSDRPLTVKMRVGFEN---TDTFYEILDIVNRHNIDLLSLHGRTVKDMYHGA- 188

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKN 222
                    + YD++ E  K   D  +  NG +   + AL++L      GVM+GR A  N
Sbjct: 189 ---------VKYDLIAEAVKRV-DCPVLANGNIHSATTALEVLERTGAAGVMVGRWAIGN 238

Query: 223 SAMLTTVDEYF-SNPLTGSSPIKTR--VDKDFWRKISASMTD 261
             +   + +     P+T    ++ R  +D+ +    +A+M +
Sbjct: 239 PWLFNQIRQALRGEPITPVPLVEVRNYIDRLWQTPTAATMPE 280


>gi|227878374|ref|ZP_03996329.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus JV-V01]
 gi|293380365|ref|ZP_06626436.1| TIM-barrel protein, nifR3 family [Lactobacillus crispatus 214-1]
 gi|312978416|ref|ZP_07790158.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           crispatus CTV-05]
 gi|227862053|gb|EEJ69617.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus JV-V01]
 gi|290923048|gb|EFD99979.1| TIM-barrel protein, nifR3 family [Lactobacillus crispatus 214-1]
 gi|310894759|gb|EFQ43831.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           crispatus CTV-05]
          Length = 341

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 113/221 (51%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+ G+KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 40  LVVCEMISDHGIIYGNKKTLSMMDVDPREHPMSIQIFGGSEETLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK R G D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVKKPVSVKMRTGWDKK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+++++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEVLHDVAQVLDVPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A K L  +    VM+GRAA  N  +L  +  Y  
Sbjct: 207 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLE 247


>gi|149240295|ref|XP_001526023.1| tRNA-dihydrouridine synthase 1 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146450146|gb|EDK44402.1| tRNA-dihydrouridine synthase 1 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 516

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 49/167 (29%), Positives = 80/167 (47%), Gaps = 10/167 (5%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    + ++ +   D   R    N   G    ++PL +Q  
Sbjct: 97  MVDHSELAWRILSRRYGADLCYTPMFHSRLFATDPKYRQSMWNEKDGSRDNDRPLIVQFC 156

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L++AAK+VE+   + ++LN+GCP      G +GA LM + ++V   I  +   L
Sbjct: 157 ANDPDYLLQAAKLVEN-QCDAVDLNLGCPQGIARRGKYGAFLMDDWELVHKLIRTLHDNL 215

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+  DD   ++      K +  +G   I IH R   +KG
Sbjct: 216 SVPVTAKIRV-YDDWEKSL---EYAKMVLDAGAQFITIHGRTREMKG 258


>gi|195035293|ref|XP_001989112.1| GH10224 [Drosophila grimshawi]
 gi|193905112|gb|EDW03979.1| GH10224 [Drosophila grimshawi]
          Length = 503

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 110/237 (46%), Gaps = 25/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 33  MVDQSELAWRMLCRRY-GAQLCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA   +++  + +++N+GCP A    G +GA L    +++   +  + + LSIP
Sbjct: 92  PQQILEAALAAQNYC-DAVDINLGCPQAIAKRGHYGAFLQDEWELLTQIVRTLHEKLSIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K R   +D+   +      K ++ +G   + +H R    K  L G++          
Sbjct: 151 VTCKIR-RFEDRAKTI---EYAKMLEAAGCQLLTVHGRTREQKGPLTGIA---------- 196

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D+  + ++++  + P L  G   G+ED+ + L     VDGVM       N A+   +
Sbjct: 197 DWSYIKDVREHIKIPMLANGNILGVEDVHRCLTET-GVDGVMTAEGNLHNPALFEGI 252


>gi|256844417|ref|ZP_05549903.1| transcriptional regulator [Lactobacillus crispatus 125-2-CHN]
 gi|256849195|ref|ZP_05554628.1| transcriptional regulator [Lactobacillus crispatus MV-1A-US]
 gi|262047211|ref|ZP_06020169.1| transcriptional regulator [Lactobacillus crispatus MV-3A-US]
 gi|256613495|gb|EEU18698.1| transcriptional regulator [Lactobacillus crispatus 125-2-CHN]
 gi|256713971|gb|EEU28959.1| transcriptional regulator [Lactobacillus crispatus MV-1A-US]
 gi|260572456|gb|EEX29018.1| transcriptional regulator [Lactobacillus crispatus MV-3A-US]
          Length = 342

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 113/221 (51%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+ G+KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 41  LVVCEMISDHGIIYGNKKTLSMMDVDPREHPMSIQIFGGSEETLLQAAQYIDQHTDADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK R G D +    A+ 
Sbjct: 101 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVKKPVSVKMRTGWDKK-HIFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+++++++ +     F+  NG
Sbjct: 160 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEVLHDVAQVLDVPFVA-NG 207

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A K L  +    VM+GRAA  N  +L  +  Y  
Sbjct: 208 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLE 248


>gi|256080282|ref|XP_002576411.1| tRNA-dihydrouridine synthase [Schistosoma mansoni]
 gi|238661678|emb|CAZ32648.1| tRNA-dihydrouridine synthase, putative [Schistosoma mansoni]
          Length = 492

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 109/227 (48%), Gaps = 24/227 (10%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDF 72
           R++ ++ ++  E+   D +L  D       S +EK  + +Q+G  +    ++AAK++E+ 
Sbjct: 30  RIIRSSRVVNAELNTIDFVL-PDGSVTFRTSMEEKNRVIVQLGTPEPGTALQAAKMLEN- 87

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I++N+GCP A   +G  GA L+  P+IV + +  +   L IPVT K RI + +   
Sbjct: 88  DVMGIDVNMGCPKAYSIKGGMGAALLTKPEIVKEILTTLTTNLRIPVTCKIRI-LPELEK 146

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            +AL  L++S   +GV  I +H R    + +    N  I  +   +          + + 
Sbjct: 147 TIALAKLIES---TGVAAITVHGRTINERPVHRNRNEVIQTIANSV---------GIPVL 194

Query: 193 LNGGLEDM------SQALKILPSVDGVMIGRAAYKNSAMLTT--VDE 231
            NGG  D+       +  + L S  GV+I RAA  N A+  +  VDE
Sbjct: 195 ANGGSHDIIRNHEDIEYFRQLTSAAGVVIARAAMSNPAIFKSFQVDE 241


>gi|90413381|ref|ZP_01221374.1| putative Dihydrouridine synthase [Photobacterium profundum 3TCK]
 gi|90325623|gb|EAS42092.1| putative Dihydrouridine synthase [Photobacterium profundum 3TCK]
          Length = 321

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 58/242 (23%), Positives = 112/242 (46%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L      +N +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPDLWKTAKSQNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +P ++ + + ++  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQHPALIEEILRSVVGAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V   ++ K  ++ G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDLDNRNCV---DIAKIAEQCGIQALALHGRTKSCMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +    K+   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 183 YDYI-RAAKQAVSIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFREIQHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 TT 243


>gi|320583735|gb|EFW97948.1| dihydrouridine synthase [Pichia angusta DL-1]
          Length = 338

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 104/232 (44%), Gaps = 19/232 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + ++Y+ MI+A   +R        FST  +++PL +QIG  +
Sbjct: 29  MVRYSKLPFRELVRDYKVD-IVYSPMILAREFVRNHNARASDFSTNHRDRPLIVQIGANN 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L+    ++  +  + + LN GCP   +V EG  GA LM   ++V + + A+ +    
Sbjct: 88  VTDLLRMIDMIHPY-VDGVGLNCGCPIKDQVREG-IGAALMSKKELVAEMVHAVKEKYGS 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I V   I        VK ++ +GV+ I +H R    +   P +  KI  +   
Sbjct: 146 KLVIETKIRVHHDIQETI--EFVKMVEAAGVDFITVHGRTKNTRSSEPCNFEKIKAI--- 200

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
                 KE   + +  NG    +  A +I      DGVM  R    N AM  
Sbjct: 201 ------KEAVSVPVIANGDCRSLEDAFRIAKDTGCDGVMAARGILNNPAMFA 246


>gi|302560757|ref|ZP_07313099.1| tRNA-dihydrouridine synthase [Streptomyces griseoflavus Tu4000]
 gi|302478375|gb|EFL41468.1| tRNA-dihydrouridine synthase [Streptomyces griseoflavus Tu4000]
          Length = 390

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 54/225 (24%), Positives = 105/225 (46%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E+P ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDESERPRSIQLYGV 93

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ + G  + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 94  DPVTVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRSILREAVGGAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 154 DLPVTIKMRKGIDDD--HLTYLDAGRIAVEEGVTAVALHGRTTA--------QHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 204 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRG 248


>gi|119774440|ref|YP_927180.1| NifR3/Smm1 family protein [Shewanella amazonensis SB2B]
 gi|119766940|gb|ABL99510.1| NifR3/Smm1 family protein [Shewanella amazonensis SB2B]
          Length = 322

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 90/182 (49%), Gaps = 16/182 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +QI G +   + E A      G   ++ N GCP+  V+    GA L+  P
Sbjct: 62  GLTKSGTPVRVQILGQEPGWMAENALRAVTLGSRGVDANFGCPAKMVNRSKGGAVLLQYP 121

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++ D + AM +A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 122 ELIHDIVKAMRQAVPSEQPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHARSKV 178

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  K P   ++ + E+++  P   I  NG + +   AL+ +     D +MIGR
Sbjct: 179 -------DGYKPPAY-WEYITEVRERLPIPVIA-NGEIWNRDDALRCMEVTGCDSIMIGR 229

Query: 218 AA 219
            A
Sbjct: 230 GA 231


>gi|54310476|ref|YP_131496.1| putative dihydrouridine synthase [Photobacterium profundum SS9]
 gi|46914919|emb|CAG21694.1| putative Dihydrouridine synthase [Photobacterium profundum SS9]
          Length = 321

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 58/242 (23%), Positives = 112/242 (46%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L      +N +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPDLWKTAKSQNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +P ++ + + ++  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQHPALIEEILRSVVGAVDVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLD 175
           VT+K R G D D    V   ++ K  ++ G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDLDNRNCV---DIAKIAEQCGIQALALHGRTKSCMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +    K+   + +  NG ++   +A  +L     D +MIGR A     +   +  Y 
Sbjct: 183 YDYI-RAAKQAVSIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFREIQHYL 241

Query: 234 SN 235
           + 
Sbjct: 242 TT 243


>gi|224368204|ref|YP_002602367.1| dihydrouridine synthase family protein [Desulfobacterium
           autotrophicum HRM2]
 gi|223690920|gb|ACN14203.1| dihydrouridine synthase family protein [Desulfobacterium
           autotrophicum HRM2]
          Length = 350

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 68/253 (26%), Positives = 113/253 (44%), Gaps = 32/253 (12%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLA---LQIGGADISKLVEAAKIVEDFGYNEI 77
           LL+T M  A A+   +      F  +++ LA    QI G D   +  AA+ +E  G+  +
Sbjct: 59  LLFTGMCSAKALPHENPATSPVFKWRKQELATLVCQIFGPDPQSMAAAAQRIEAEGFFGV 118

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVAL 136
           +LN GC  A + +   GA ++  PD+  + +A +  ++SIPV VK R G ++D  PA+  
Sbjct: 119 DLNFGCSVAAICKRGCGAEILKTPDLAVEILARVRASVSIPVFVKFRTGWINDPRPAI-- 176

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            +L K  + +G + +  H R A        D R  P     I   + KE   + +  NG 
Sbjct: 177 -DLAKRFEDNGADALVFHPRVA-------PDRRSRPPRWEQI--SLIKEAVTIPVFGNGN 226

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +    D+S  +K     DG+ IGR A     +     + F+ P  G+           + 
Sbjct: 227 VFDANDLSTVVKQT-GCDGIAIGRMAVSRPWIFAQWTKGFT-PTIGT-----------YH 273

Query: 254 KISASMTDYAARH 266
             +  MT+  A+H
Sbjct: 274 HTAIRMTELLAKH 286


>gi|262172604|ref|ZP_06040282.1| tRNA dihydrouridine synthase B [Vibrio mimicus MB-451]
 gi|261893680|gb|EEY39666.1| tRNA dihydrouridine synthase B [Vibrio mimicus MB-451]
          Length = 287

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 92/193 (47%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D   + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++   +  
Sbjct: 33  SVQIAGSDPQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIESILKT 92

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+++PVT+K R G D D    +++  L +     G+  + +H R    + KG     
Sbjct: 93  VVNAVNVPVTLKTRTGWDTDNKNCISIAQLAED---CGIQALALHGRTRACMYKG----- 144

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K       I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 145 -----EAEYDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWI 198

Query: 226 LTTVDEYFSNPLT 238
              +  +  +  T
Sbjct: 199 FQEIQHFLEHGTT 211


>gi|153009400|ref|YP_001370615.1| nifR3 family TIM-barrel protein [Ochrobactrum anthropi ATCC 49188]
 gi|151561288|gb|ABS14786.1| putative TIM-barrel protein, nifR3 family [Ochrobactrum anthropi
           ATCC 49188]
          Length = 349

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 52/205 (25%), Positives = 101/205 (49%), Gaps = 18/205 (8%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    K+++L  S +      +Q+ G +   + EAA+I E  G + I++
Sbjct: 58  MVVSEMVASAELCNRHKESLLRLSGEGLGTHVVQLAGREAHWMGEAARIAEGEGADIIDI 117

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP+ +V  G  G+ LM + D     + A   A+ +PVT+K R+G D++  ++    L
Sbjct: 118 NMGCPAKKVTGGYSGSALMRDLDHAMTLVEATVNAVRVPVTLKMRLGWDEK--SINAPEL 175

Query: 140 VKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +  + +G+  + +H R      +G            D++ ++ ++       I  NG +
Sbjct: 176 ARRAEGAGIAMVTVHGRTRCQFYEG----------KADWNAIHAVRDAVRIPLIA-NGDV 224

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
                A +IL     D VM+GRA+Y
Sbjct: 225 ACRPDAEEILRRSGADAVMVGRASY 249


>gi|296436182|gb|ADH18356.1| putative oxidoreductase [Chlamydia trachomatis G/9768]
 gi|297140544|gb|ADH97302.1| putative oxidoreductase [Chlamydia trachomatis G/9301]
          Length = 334

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 71/298 (23%), Positives = 135/298 (45%), Gaps = 21/298 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL++ EM+  + +    ++ +  L F+   +P+  Q+ G+      E+AKI+E  G++ I
Sbjct: 39  ALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSHPDLAGESAKILEGLGFDLI 98

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP+ R+ +   G+ ++   +++G  +  M + +S+PVTVK R G D     + + 
Sbjct: 99  DLNCGCPTDRITKDGSGSGMLKTSELIGKVVEKMVEVVSVPVTVKIRSGWD--FDHINVE 156

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
             V+ IK+SG + +++H R        P       NL++ I    +    D  +  NG +
Sbjct: 157 ETVRIIKESGASAVFVHGRTRSQGYQGPS------NLEF-ISRAKQAAGNDFPVFGNGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                A  +L +   DGV++ R       +   +++Y +     S    TR      ++ 
Sbjct: 210 FSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTGTYSSPSFSTR------KQA 263

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRHILTVEAGASTATHHIIE 312
                 +   +  S  KL   TR + G +    P  R  R  L  +A +S   + +I+
Sbjct: 264 FVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRANL-AKASSSQEVYQLID 320


>gi|237785022|ref|YP_002905727.1| hypothetical protein ckrop_0405 [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237757934|gb|ACR17184.1| hypothetical protein ckrop_0405 [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 361

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 70/306 (22%), Positives = 122/306 (39%), Gaps = 31/306 (10%)

Query: 9   YRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADIS 60
           +R   R L      T + L   EM+ A A++  ++K +    F+ +E P ++Q+   D  
Sbjct: 3   FRLLCRELEIEKTGTTSGLYVCEMVTARALVERNEKTLHMTEFAPEETPRSMQLYTTDPK 62

Query: 61  KLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---S 116
              EAA+++ D    + I++N GCP  +V     GA L     + G+ +AA  + +   +
Sbjct: 63  WTYEAARMIADDNLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGEIVAAAVRGVEGTT 122

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R G+DD    +   +        G   + +HAR A          R     D+
Sbjct: 123 IPVTVKMRTGIDDD--HLTFLDAGAIAAAEGAQAVALHARTAA--------QRYSGTADW 172

Query: 177 DIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           + + E+K+      + +  NG +   + A  ++     DGV++GR       +   +   
Sbjct: 173 NRIGELKEHLSGTGVPVLGNGDIFKATDAADMMDQTGCDGVVVGRGCLGRPWLFAELSAA 232

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                  + P    V     R      T   A H       + + +HM     G+P    
Sbjct: 233 LRGEPLPAQPTFAEVCDVILRH-----TRLLAAHSGESTACRDMRKHMGWYLRGYPAGSD 287

Query: 293 CRHILT 298
            R  +T
Sbjct: 288 LRQKVT 293


>gi|15605376|ref|NP_220162.1| oxidoreductase [Chlamydia trachomatis D/UW-3/CX]
 gi|76789383|ref|YP_328469.1| oxidoreductase [Chlamydia trachomatis A/HAR-13]
 gi|237803073|ref|YP_002888267.1| putative oxidoreductase [Chlamydia trachomatis B/Jali20/OT]
 gi|237804994|ref|YP_002889148.1| putative oxidoreductase [Chlamydia trachomatis B/TZ1A828/OT]
 gi|255311468|ref|ZP_05354038.1| putative oxidoreductase [Chlamydia trachomatis 6276]
 gi|255317769|ref|ZP_05359015.1| putative oxidoreductase [Chlamydia trachomatis 6276s]
 gi|3329093|gb|AAC68821.1| predicted oxidoreductase [Chlamydia trachomatis D/UW-3/CX]
 gi|76167913|gb|AAX50921.1| predicted oxidoreductase [Chlamydia trachomatis A/HAR-13]
 gi|231273294|emb|CAX10209.1| putative oxidoreductase [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231274307|emb|CAX11102.1| putative oxidoreductase [Chlamydia trachomatis B/Jali20/OT]
 gi|296437111|gb|ADH19281.1| putative oxidoreductase [Chlamydia trachomatis G/11222]
 gi|296438042|gb|ADH20203.1| putative oxidoreductase [Chlamydia trachomatis G/11074]
 gi|297748774|gb|ADI51320.1| tRNA-dihydrouridine synthase [Chlamydia trachomatis D-EC]
 gi|297749654|gb|ADI52332.1| tRNA-dihydrouridine synthase [Chlamydia trachomatis D-LC]
          Length = 334

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 71/298 (23%), Positives = 135/298 (45%), Gaps = 21/298 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           AL++ EM+  + +    ++ +  L F+   +P+  Q+ G+      E+AKI+E  G++ I
Sbjct: 39  ALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSRPDLAGESAKILEGLGFDLI 98

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP+ R+ +   G+ ++   +++G  +  M + +S+PVTVK R G D     + + 
Sbjct: 99  DLNCGCPTDRITKDGSGSGMLKTSELIGKVVEKMVEVVSVPVTVKIRSGWD--FDHINVE 156

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
             V+ IK+SG + +++H R        P       NL++ I    +    D  +  NG +
Sbjct: 157 ETVRIIKESGASAVFVHGRTRSQGYQGPS------NLEF-ISRAKQAAGNDFPVFGNGDV 209

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                A  +L +   DGV++ R       +   +++Y +     S    TR      ++ 
Sbjct: 210 FSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTGTYSSPSFSTR------KQA 263

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRHILTVEAGASTATHHIIE 312
                 +   +  S  KL   TR + G +    P  R  R  L  +A +S   + +I+
Sbjct: 264 FVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRANL-AKASSSQEVYQLID 320


>gi|295692146|ref|YP_003600756.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus ST1]
 gi|295030252|emb|CBL49731.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus ST1]
          Length = 341

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 113/221 (51%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+ G+KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 40  LVVCEMISDHGIIYGNKKTLSMMDVDPREHPMSIQIFGGSEETLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK R G D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVKKPVSVKMRTGWDKK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+++++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEVLHDVAQVLDVPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A K L  +    VM+GRAA  N  +L  +  Y  
Sbjct: 207 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLE 247


>gi|326315661|ref|YP_004233333.1| TIM-barrel protein, nifR3 family [Acidovorax avenae subsp. avenae
           ATCC 19860]
 gi|323372497|gb|ADX44766.1| TIM-barrel protein, nifR3 family [Acidovorax avenae subsp. avenae
           ATCC 19860]
          Length = 353

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 113/263 (42%), Gaps = 33/263 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+A+QI
Sbjct: 17  MAGVTDRPFRQLCKAL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 71

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G D + + EAA    D G   I++N+GCP+ +V     G+ LM N  +   +   +   
Sbjct: 72  AGTDAAMMSEAALYNIDRGAEIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAQAVVEA 131

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           C   ++PVT+K R G   Q      RN   L ++ +  G+  + +H R         ++ 
Sbjct: 132 CAPRNVPVTLKMRTGWCQQ-----HRNAVQLARAFEDVGIRMLTVHGRT--------REQ 178

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
               + +Y+ +  +K     + +  NG ++   +A  +L +   D +MIGRAA     + 
Sbjct: 179 GYKGHAEYETIAAVKAAV-RVPVVANGDIDSPEKAKAVLAATGADAIMIGRAAQGRPWIF 237

Query: 227 TTVDEYFSNPLTGSSPIKTRVDK 249
             +  Y +     + P+   V +
Sbjct: 238 REIGHYLATGEHLAPPLVAEVRR 260


>gi|225677726|gb|EEH16010.1| tRNA-dihydrouridine synthase C [Paracoccidioides brasiliensis Pb03]
          Length = 526

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 85/189 (44%), Gaps = 12/189 (6%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  T ++PL +Q    D  +L+ AA+ VE F  + ++LN+GCP     +G +G+ L   P
Sbjct: 107 GNPTIDRPLIVQFCANDPDELLHAARTVEPF-CDAVDLNLGCPQGIARKGHYGSFLQEEP 165

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +++   I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 166 ELIYKLINTLHTQLSIPVTAKFRI----QETKEKTLEYARMILSAGASFISVHGRRRDQK 221

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           G     N  + +  Y I Y       D  I  NG + D    ++ L +   DGVM     
Sbjct: 222 G----HNTGLADWSY-IRYLRDNLPADTVIFANGNILDHGDIIRCLEATGADGVMSAEGN 276

Query: 220 YKNSAMLTT 228
             +  + TT
Sbjct: 277 LCDPTIFTT 285


>gi|315043678|ref|XP_003171215.1| hypothetical protein MGYG_07214 [Arthroderma gypseum CBS 118893]
 gi|311345004|gb|EFR04207.1| hypothetical protein MGYG_07214 [Arthroderma gypseum CBS 118893]
          Length = 568

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 101/208 (48%), Gaps = 21/208 (10%)

Query: 24  TEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           T+   A+A L G+ K        ++P  +Q    +  +L++AA+ VE+   + ++LN+GC
Sbjct: 114 TDEATAEAYLDGNPK-------YDRPFIVQFCANNPDELLKAARHVEEHC-DAVDLNLGC 165

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P     +G +GA L  +PD++   I  +   LSIPVT K RI ++ +   +    ++ S 
Sbjct: 166 PQGIAKKGHYGAFLQEDPDLIYKLINKLHTELSIPVTAKFRI-LETKEKTLEYARMIIS- 223

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDM 200
             +G + + +H R+   KG     N  + N +Y I Y      P+  I  NG +   +D+
Sbjct: 224 --AGASILSVHGRRREQKG----HNTGVANWEY-IRYLRDNLPPETVIFANGNILNHDDL 276

Query: 201 SQALKILPSVDGVMIGRAAYKNSAMLTT 228
           S+ L+     DGVM       +  + +T
Sbjct: 277 SRCLEAT-GADGVMSAEGNLSDPTIFST 303


>gi|126726844|ref|ZP_01742683.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodobacterales
           bacterium HTCC2150]
 gi|126703802|gb|EBA02896.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodobacterales
           bacterium HTCC2150]
          Length = 329

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 65/218 (29%), Positives = 107/218 (49%), Gaps = 25/218 (11%)

Query: 21  LLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           L+ +EM+ +  +++     +    LGF +     A+QI G +   + EAAK+    G   
Sbjct: 40  LVVSEMVASHEMMQAKPSTLAKAELGFDSANT--AVQIAGREAYWMSEAAKLCAANGAKI 97

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ +V  G  G+ L+ + D+    IAA+  A+ +PVT+K R+G DD     A 
Sbjct: 98  IDINMGCPAKKVTSGYSGSALLRDLDLAVSLIAAVVAAVDVPVTLKTRLGWDDDSHNAA- 156

Query: 137 RNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             L K  +  G+  I IH R      KG          + D++ + +I K+   + +  N
Sbjct: 157 -ELAKRAEAEGIAWITIHGRTRCQFYKG----------SADWEAISKI-KQAVKIPVFAN 204

Query: 195 GGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           G + D     QALK+    DG+M+GR A      L T+
Sbjct: 205 GDIVDDFSAKQALKV-SGADGIMVGRGAQGRPWQLATI 241


>gi|325125157|gb|ADY84487.1| Transcriptional regulator [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 344

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 111/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEI 77
           ++  EMI    I+ G+KK  ++L     E P+++QI GGA+ S L  A  I +    + I
Sbjct: 42  MVVCEMISDHGIIYGNKKTLSMLDVDPGEHPMSIQIFGGAEDSLLQAAQYIDQHTDADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   I  + + +  PV+VK RIG D +    A+ 
Sbjct: 102 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEKPVSVKMRIGWDRK-HIFAVE 160

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+ +     F+  NG
Sbjct: 161 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVAQVMDIPFVA-NG 208

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y + 
Sbjct: 209 DITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 250


>gi|116513521|ref|YP_812427.1| tRNA-dihydrouridine synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116092836|gb|ABJ57989.1| tRNA-U20-dihydrouridine synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
          Length = 342

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 111/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEI 77
           ++  EMI    I+ G+KK  ++L     E P+++QI GGA+ S L  A  I +    + I
Sbjct: 40  MVVCEMISDHGIIYGNKKTLSMLDVDPGEHPMSIQIFGGAEDSLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   I  + + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEKPVSVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+ +     F+  NG
Sbjct: 159 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVAQVMDIPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y + 
Sbjct: 207 DITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 248


>gi|168205517|ref|ZP_02631522.1| dihydrouridine synthase family protein [Clostridium perfringens E
           str. JGS1987]
 gi|170662991|gb|EDT15674.1| dihydrouridine synthase family protein [Clostridium perfringens E
           str. JGS1987]
          Length = 321

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 109/237 (45%), Gaps = 21/237 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHKEELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   I +++K R+G+D          L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKIDDIKISIKTRLGMDK---PEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  PNL+ +     + K NP  + G    LED ++ ++    VD +M+GR    N A++ 
Sbjct: 173 K--PNLEVFKDAISLSK-NPVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALM- 228

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  N +  +  +  +V K+F  ++     +      ++  +++++  +MI +F
Sbjct: 229 -------NEILNNEFMDKKVLKEFHDEVFNKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|158424712|ref|YP_001526004.1| nitrogen regulation protein [Azorhizobium caulinodans ORS 571]
 gi|158331601|dbj|BAF89086.1| nitrogen regulation protein [Azorhizobium caulinodans ORS 571]
          Length = 365

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 110/245 (44%), Gaps = 18/245 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD   R  A L     L  +EM+ ++A+L G  +  L        + A+Q+ G + 
Sbjct: 49  MAGITDAPVRRMA-LRYGAGLTVSEMVASEALLTGHAEMTLRAEGAGVDIHAVQLAGNEP 107

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++ E  G   I++N+GCP+ RV  G+ GA L+ +  +    + A+  A+S+PV
Sbjct: 108 HWMAEAARLAEASGAAIIDINMGCPAKRVTTGAAGAALLRDLPLATRILEAVRAAISVPV 167

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D     +    + +  +  G+  + IH R         +        D+  +
Sbjct: 168 TLKTRLGWDGA--EMTAPEIARRAEAIGIAMVTIHGRT--------RCQFYTGTADWAAI 217

Query: 180 YEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + K+   + +  NG L     + A+      DGVMIGR A         V +++    
Sbjct: 218 RAV-KDAVSIPVIANGDLTQTHDAAAMLAASGADGVMIGRGAQGRPWFPGAVAQHWR--- 273

Query: 238 TGSSP 242
           TG +P
Sbjct: 274 TGRAP 278


>gi|114776793|ref|ZP_01451836.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Mariprofundus
           ferrooxydans PV-1]
 gi|114552879|gb|EAU55310.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Mariprofundus
           ferrooxydans PV-1]
          Length = 341

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 132/288 (45%), Gaps = 28/288 (9%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L+ TEMI + A+  G ++   +      E P+++QI G+D   + EAA+     G + +
Sbjct: 43  GLMVTEMIASRAVDMGRERTERMAELGDDEHPVSIQIAGSDPEFVTEAARWAVGHGADFV 102

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  ++ +   G+ ++ +  +V   +AA+  A+ +PVT+K R G DDQ   V  +
Sbjct: 103 DINMGCPVKKICKQVAGSAMLRDEALVARVLAAVVAAVDVPVTLKIRTGWDDQSKNV--Q 160

Query: 138 NLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N+ +  + SG+  + +H R    +  G +  ++  +      I            IG NG
Sbjct: 161 NIARIAEDSGIQLLTVHGRTRAQMFHGHACWEDIGLAKAAVSIP----------VIG-NG 209

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFW 252
            + D   A +++   + DGVM+GRA   N  +L  V    +  P+    P  T  ++  W
Sbjct: 210 DIVDAESAREMIRVSNCDGVMVGRAVQGNPWVLGEVHAAIAGLPI---PPKPTAAER--W 264

Query: 253 RKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             +   M      H + +  KL +  +H+I    G   S   R    V
Sbjct: 265 LIVDEHMRHLVEHHGIRTASKLAR--KHVIWYSKGLHGSAEFRQSFQV 310


>gi|168217080|ref|ZP_02642705.1| dihydrouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
 gi|182380794|gb|EDT78273.1| dihydrouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
          Length = 321

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 109/237 (45%), Gaps = 21/237 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  A+ ++  GYNEINLN+GCPS  V     G+  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFISTARKLKQLGYNEINLNLGCPSGTVVGKKRGSGFLAHREELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   + +++K R+G+D          L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKIDDMKISIKTRLGMDK---PEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           R  PNL+ +     + K NP  + G    LED ++ ++    VD +M+GR    N A++ 
Sbjct: 173 R--PNLEVFKDAISLSK-NPVCYNGDIFTLEDHNKLVETFKEVDKIMLGRGVLANPALM- 228

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  N +  +  +  +V K+F  ++ +   +      ++  +++++  +MI +F
Sbjct: 229 -------NEILNNEFMDKKVLKEFHDEVFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|281211889|gb|EFA86051.1| hypothetical protein PPL_01287 [Polysphondylium pallidum PN500]
          Length = 334

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 46/171 (26%), Positives = 88/171 (51%), Gaps = 19/171 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA---------LLYTEMIVADAILRGDK--KNILGFSTQEKP 49
           MVD TD  +R    L + +          + +TE +  D +L      K++L +S  ++P
Sbjct: 19  MVDVTDHPFRQLVSLYSKSKDQSSSKSSFITWTEFVSVDGLLANPNRFKSLLDYSEIQRP 78

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE-GSFGACLMLNPDIVGDCI 108
           +  Q+ G+D  K   A KIV D G++ +++N+GCP  +V E  S G+ L+++       I
Sbjct: 79  IVCQLFGSDPDKFNRATKIVADLGFDGVDINMGCPVRKVVERQSSGSALIVDKPTAVSII 138

Query: 109 AAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A  +A++   + V+VK RIG D+    + +   + ++ ++  + + +H R
Sbjct: 139 NATKQAVAGTDMSVSVKTRIGFDE----IEIEQWIPTLLQTNPDLLTLHLR 185


>gi|224531764|ref|ZP_03672396.1| putative histidine phosphokinase/phophatase [Borrelia valaisiana
           VS116]
 gi|224511229|gb|EEF81635.1| putative histidine phosphokinase/phophatase [Borrelia valaisiana
           VS116]
          Length = 329

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 115/251 (45%), Gaps = 31/251 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I A  IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISAKGILNGSKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             C   ++P++VK R G     P V A    + S K   ++ + ++ R A+       D 
Sbjct: 137 EACAKFNLPLSVKTRHGF--SYPEVDAWLGFLLSFK---IDMLTVYPRLAV-------DQ 184

Query: 169 RKIPNLDYDIVYEIKKE----NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            K P +++DI +E+ K     +P   I  NG +  +  A   +    +DG+M GR  +KN
Sbjct: 185 SKGP-VNFDIFHELVKLRNNISPSTLIIGNGDVLSLKDAKYYVDKYLIDGIMFGRGIFKN 243

Query: 223 SAMLTTVDEYF 233
             +     ++F
Sbjct: 244 LNLFKLSSKHF 254


>gi|290476760|ref|YP_003469671.1| tRNA-dihydrouridine synthase B [Xenorhabdus bovienii SS-2004]
 gi|289176104|emb|CBJ82909.1| tRNA-dihydrouridine synthase B [Xenorhabdus bovienii SS-2004]
          Length = 287

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 90/191 (47%), Gaps = 23/191 (12%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D  ++  AA+I    G   I++N+GCP+ +V+    G+ L+  P++V   ++A
Sbjct: 28  SVQIAGSDPDEMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELVQAILSA 87

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHA--RKAILKGLSP 165
           +  A+ +PVT+K R G   +      RN V   +  ++ G+  + IH   R  +  G + 
Sbjct: 88  VVNAVDVPVTLKIRTGWSPE-----ERNCVEIAQLAERCGIQALTIHGRTRSCLFNGEAE 142

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            DN +             K+   + I  NG + D  +A  +L     D +MIGRAA    
Sbjct: 143 YDNIR-----------TVKQTVAIPIIANGDITDPLKARAVLEYTGADALMIGRAAQGRP 191

Query: 224 AMLTTVDEYFS 234
            +   +  Y  
Sbjct: 192 WIFREIQHYLE 202


>gi|157818491|ref|NP_001099651.1| tRNA-dihydrouridine synthase 2-like [Rattus norvegicus]
 gi|149038072|gb|EDL92432.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           (predicted), isoform CRA_a [Rattus norvegicus]
 gi|165971659|gb|AAI58729.1| Dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           [Rattus norvegicus]
          Length = 493

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 101/226 (44%), Gaps = 37/226 (16%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
            R + N  L   + +  D     D+        ++  +  Q+G +D  + +  A++VE+ 
Sbjct: 52  CRRVVNEVLSTVDFVAPD-----DRVVFRTCEREQSRVVFQMGTSDAERALAVARLVEN- 105

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQ 130
               I++N+GCP     +G  GA L+ +PD +   ++ + K    PVT K RI   ++D 
Sbjct: 106 DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDT 165

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           +      NLVK I+++G++ I +H R         +D R    +  +++  I  E   + 
Sbjct: 166 L------NLVKRIERTGISAIAVHGRN--------RDERPQHPVSCEVIRAI-AETLSIP 210

Query: 191 IGLNGG----------LEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           +  NGG          +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 211 VIANGGSHDHIQQHLDIEDFRQAT----AASSVMVARAAMWNPSIF 252


>gi|300706707|ref|XP_002995598.1| hypothetical protein NCER_101453 [Nosema ceranae BRL01]
 gi|239604766|gb|EEQ81927.1| hypothetical protein NCER_101453 [Nosema ceranae BRL01]
          Length = 327

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 92/169 (54%), Gaps = 12/169 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQ--EKPLALQIG 55
           MV  ++  +R  AR    + + YTEM+  D  +R  K N L    ++T   ++PL +QI 
Sbjct: 17  MVGNSELAWRILARRYGAD-ICYTEMVNCDTFIRS-KINPLSNRWYTTNKIDRPLIIQIC 74

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D++K+++ + I++++  + I++N+GCP     +G++G+ LM +   V + +  +   L
Sbjct: 75  GNDVNKMLKVSLILQEYC-DAIDINLGCPQEIARKGNYGSFLMDDLLKVKEIVTVLSNNL 133

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            +PVT  C+I + + I         K I+++G   + +H R    +GL+
Sbjct: 134 KVPVT--CKIRIFESIEKSV--EYAKMIEQAGCKMLTVHGRTRDQRGLN 178


>gi|225712694|gb|ACO12193.1| tRNA-dihydrouridine synthase 4-like [Lepeophtheirus salmonis]
          Length = 301

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 131/288 (45%), Gaps = 40/288 (13%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFSTQEK---PLALQIGGADISKLVEAA 66
           F RL+ ++   + ++ MI+AD+ +   +     F++  K   PL +Q     +   V+A+
Sbjct: 24  FRRLILSHGADVAFSPMILADSFVSSSEARDNEFTSDPKEDHPLVVQFAANKVQDFVDAS 83

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP---VTVKC 123
            +V  +    ++LN GCP +   +   GA L+  P+ + D + +    +  P   V+VK 
Sbjct: 84  VLVAPYAEG-VDLNCGCPQSWALKEGIGASLLQKPEFICDVVKSTKSVIPYPDFSVSVKI 142

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+  D +       +L K ++ SGV+ I +H R         KD    P +D + V  I 
Sbjct: 143 RLHRDKR----RTIDLCK-VENSGVDFITVHGRT--------KDQHSDP-VDLEGVKMI- 187

Query: 184 KENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           K+   + +  NG ++ +  A ++  +  VDGVM  R   +N AM    D          +
Sbjct: 188 KDALSIPVVANGDIKSLDDAYRVREVTGVDGVMAARGLLENPAMYAGFD---------IT 238

Query: 242 PIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQ-ITRHMIGLFHGF 287
           P K  +D   W KIS  + T +   H H    L++ ++R+   +F+  
Sbjct: 239 PAKCILD---WLKISLEVGTPFQTFHHHLSYMLERSLSRNERKIFNAL 283


>gi|123975618|ref|XP_001330358.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121896476|gb|EAY01626.1| hypothetical protein TVAG_292590 [Trichomonas vaginalis G3]
          Length = 333

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 59/185 (31%), Positives = 94/185 (50%), Gaps = 26/185 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D SK V+AA +V  F  + I+LN GCP +       G+ LM  P+IV D ++
Sbjct: 84  LIFQILTNDASKAVQAASVVVKFA-DAIDLNCGCPESFATSRGTGSSLMSEPEIVADVVS 142

Query: 110 AMCKALSIPVTVKCRI--GVDDQIP-AVALRNLVKSIKKSGVNGIWIHAR--KAILKGLS 164
           A+ +  ++P++VK RI   +++ I  AVA  N       +G + I +H R  +   KG  
Sbjct: 143 ALRRNYNVPISVKHRIHHNIEESIQFAVACEN-------AGASAIAVHGRLKEQKNKGSV 195

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
             DN K   L +D ++  K       IG NGG+++   A +++     + V+I  AA KN
Sbjct: 196 AYDNMK---LVFDHLHVAK-------IG-NGGVKNREMAKEMMEKTGCESVIISSAALKN 244

Query: 223 SAMLT 227
             + +
Sbjct: 245 PTIFS 249


>gi|165975764|ref|YP_001651357.1| putative nitrogen regulator protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|165875865|gb|ABY68913.1| putative nitrogen regulator protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 320

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 70/282 (24%), Positives = 121/282 (42%), Gaps = 33/282 (11%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +P
Sbjct: 62  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDP 121

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D++     AM +A+     V+VK R+G D    A     +  ++ + G N I +H R   
Sbjct: 122 DLIYRATKAMREAVPSDQTVSVKVRLGWDS---AAQCFEIADAVAQGGANEITVHGR--- 175

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGR 217
               + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MIGR
Sbjct: 176 ----TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMIGR 230

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--KLQ 274
            A  N+  L+ V             +K    K  W ++   +  Y    + H  G   + 
Sbjct: 231 GAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVA 276

Query: 275 QITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 277 RIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 317


>gi|326484320|gb|EGE08330.1| tRNA-dihydrouridine synthase [Trichophyton equinum CBS 127.97]
          Length = 566

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 53/190 (27%), Positives = 94/190 (49%), Gaps = 14/190 (7%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G    ++PL +Q    D  +L++AA+ VE+   + ++LN+GCP     +G +GA L  +P
Sbjct: 126 GNPKHDRPLIVQFCANDPDELLKAARHVEEH-CDAVDLNLGCPQGIAKKGHYGAFLQEDP 184

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++   I  +   LSIPVT K RI ++ +   +    ++ S   +G + + +H R+   K
Sbjct: 185 DLIYKLINKLHNELSIPVTAKFRI-LETKEKTLEYARMILS---AGASILSVHGRRREQK 240

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRA 218
           G S      + N +Y I Y      P+  I  NG +    D+++ L++    DGVM    
Sbjct: 241 GHS----TGVANWEY-IRYLRDNLPPETVIFANGNILNHSDINRCLEVT-GADGVMSAEG 294

Query: 219 AYKNSAMLTT 228
              +  + +T
Sbjct: 295 NLSDPTIFST 304


>gi|325281268|ref|YP_004253810.1| dihydrouridine synthase DuS [Odoribacter splanchnicus DSM 20712]
 gi|324313077|gb|ADY33630.1| dihydrouridine synthase DuS [Odoribacter splanchnicus DSM 20712]
          Length = 313

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 107/221 (48%), Gaps = 18/221 (8%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQI--GGAD 58
           +TDR YR  FA       + YT  I  +  A+ + D ++I   +     L  QI  G AD
Sbjct: 16  YTDRIYRNAFAHYFGGVEVYYTPFIRVEKGALRKRDLRDIEPETNTVADLIPQILPGSAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L+  A  V + GY +I++N+GCP   +     GA ++L P  V + +A + +   I 
Sbjct: 76  EFRLLTDA--VGEKGYRQIDINLGCPFPMIAGKHKGAGMLLYPAQVAEVLAPIAEYPEIQ 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-YD 177
            ++K R+G ++    + L  L+ +++   ++ I +HAR         +  +  P+L+ + 
Sbjct: 134 FSLKMRLGWENASECMVLVELLNTLR---LSRIALHARTG------KQQYKGHPDLEAFQ 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
             YE+  ++P  + G    L D+ Q L   P + GV IGR 
Sbjct: 185 GFYEL-CQHPLYYNGDIESLSDIRQILTRFPLLKGVFIGRG 224


>gi|16762143|ref|NP_457760.1| hypothetical protein STY3564 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29143632|ref|NP_806974.1| hypothetical protein t3299 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|56415311|ref|YP_152386.1| hypothetical protein SPA3251 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364241|ref|YP_002143878.1| hypothetical protein SSPA3037 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|224585182|ref|YP_002638981.1| hypothetical protein SPC_3455 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|25528230|pir||AE0913 conserved hypothetical protein STY3564 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504446|emb|CAD07899.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139267|gb|AAO70834.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|56129568|gb|AAV79074.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095718|emb|CAR61287.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|224469710|gb|ACN47540.1| hypothetical protein SPC_3455 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|312914412|dbj|BAJ38386.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321225194|gb|EFX50253.1| tRNA dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. TN061786]
 gi|322614525|gb|EFY11455.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322618253|gb|EFY15144.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625966|gb|EFY22780.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322626736|gb|EFY23533.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322631304|gb|EFY28064.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322635429|gb|EFY32143.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322647267|gb|EFY43765.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322649731|gb|EFY46158.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322655595|gb|EFY51901.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322658375|gb|EFY54640.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322664401|gb|EFY60597.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667379|gb|EFY63541.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322674627|gb|EFY70719.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675742|gb|EFY71815.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322682378|gb|EFY78401.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|323196165|gb|EFZ81325.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196731|gb|EFZ81876.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323204368|gb|EFZ89377.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323207716|gb|EFZ92663.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323214291|gb|EFZ99044.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323225046|gb|EGA09299.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323230398|gb|EGA14517.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233374|gb|EGA17468.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323239411|gb|EGA23461.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323242338|gb|EGA26364.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323250398|gb|EGA34282.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323256846|gb|EGA40561.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323264109|gb|EGA47617.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323271632|gb|EGA55051.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
          Length = 281

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 90/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN V   +  +  G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++   + I  NG + +  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|15240243|ref|NP_201523.1| nitrogen regulation family protein [Arabidopsis thaliana]
 gi|10177609|dbj|BAB10956.1| unnamed protein product [Arabidopsis thaliana]
 gi|15146316|gb|AAK83641.1| AT5g67220/K21H1_18 [Arabidopsis thaliana]
 gi|20908082|gb|AAM26724.1| AT5g67220/K21H1_18 [Arabidopsis thaliana]
 gi|332010932|gb|AED98315.1| tRNA-dihydrouridine synthase 4 [Arabidopsis thaliana]
          Length = 423

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 21/230 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   +     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 95  MVDNSELPFRLLCQKYGAQAA-YTPMLHSRIFTETEKYRNQEFTTCKEDRPLFVQFCAND 153

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAAK VE +  + +++N+GCP      G++GA LM N  +V   +  + + L++P
Sbjct: 154 PDTLLEAAKRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLAQNLNVP 212

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K RI   ++D +         K ++ +G + + +H R         KD +K    D+
Sbjct: 213 VSCKIRIFPNLEDTL------KYAKMLEDAGCSLLAVHGRTR-----DEKDGKKF-RADW 260

Query: 177 DIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
             + E+K     P L  G    +ED+   +K    V+GV+      +N A
Sbjct: 261 SAIKEVKNAMRIPVLANGNVRCIEDVDNCIKET-GVEGVLSAETLLENPA 309


>gi|327543426|gb|EGF29850.1| TIM-barrel protein, nifR3 family [Rhodopirellula baltica WH47]
          Length = 358

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 107/231 (46%), Gaps = 25/231 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------ILGFSTQEKPLALQI 54
           M  +T+  +R   R      LL TEM+ A   +  D+        + G + + +PLA+QI
Sbjct: 29  MAGFTNAAFRHIVRQFGGAGLLATEMVNARGFVWLDENEAEHPDRLWGVADEPRPLAVQI 88

Query: 55  GGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMC 112
              D   + +  + + E++  + +++N GCP  +V E +  G+ L+  P+ +   I+ + 
Sbjct: 89  WDNDPETMAKVGRRLAEEYRVSVVDINFGCPVRQVTEKAHSGSYLLREPNRMHAIISRLV 148

Query: 113 KALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNR 169
           +  +  PVT K R+G       +    + + ++++G   + +H R A  + +G       
Sbjct: 149 QVCAPTPVTAKIRLGCSRD--NINCNEIARVVEEAGAAALTVHGRTAADMFRG------- 199

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              N D++ + EIK    ++ +  NG L+   + +       VD VMI RA
Sbjct: 200 ---NADWERISEIKSHLRNIPLIGNGDLDSAEKVVAAFDQYDVDAVMIARA 247


>gi|268566179|ref|XP_002639655.1| Hypothetical protein CBG12371 [Caenorhabditis briggsae]
 gi|187029504|emb|CAP31359.1| hypothetical protein CBG_12371 [Caenorhabditis briggsae AF16]
          Length = 527

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 77/166 (46%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R F R     LT   +++  + V D   R   +N L     ++PL +Q   
Sbjct: 80  MVDQSELAFRLFTRKYGAQLTFTPMIHAHLFVNDGTYR---RNALALVKADRPLVVQFCA 136

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
             +   + A ++VED   + ++LN+GCP      G +G+ L    D++ + ++A+     
Sbjct: 137 NKVDTFLAACRLVEDVC-DGVDLNLGCPQMVAKRGRYGSWLQDEVDLICEMVSAVRDYCK 195

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           IPV+ K R+  D Q        LV     +G   + +H R   +KG
Sbjct: 196 IPVSCKIRVRDDRQETISYATRLV----DAGATMLTVHGRTRDMKG 237


>gi|294655199|ref|XP_002770100.1| DEHA2B07942p [Debaryomyces hansenii CBS767]
 gi|199429763|emb|CAR65470.1| DEHA2B07942p [Debaryomyces hansenii]
          Length = 364

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D   +  F+T   ++ + +Q+G  +
Sbjct: 55  MVRYSKLPFRELVRNF-NTDIVYTPMILAREFVRNDIARLSDFTTNAGDRSVIVQVGCNN 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L++   ++  +  + I LN GCP   +V EG  GA LM  P++V   + A+      
Sbjct: 114 VKDLLKFVDMIHPY-VDGIGLNCGCPIKEQVREG-IGAALMSEPELVSSMVKAVKDKYKD 171

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++ +I +   I        VK ++K+GV+ I +H R         K+ R     ++D
Sbjct: 172 SVVIETKIRIHPDINETI--KFVKLVEKNGVDFITVHGRT--------KNTRSSQPANFD 221

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
            +  I KE+  + +  NG    +  A +I     VDG+M  R    N  + 
Sbjct: 222 AIKAI-KESVAVPVVANGDCFSLKDAYEIAEYTGVDGIMAVRGILSNPGLF 271


>gi|194879780|ref|XP_001974300.1| GG21157 [Drosophila erecta]
 gi|190657487|gb|EDV54700.1| GG21157 [Drosophila erecta]
          Length = 396

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 109/235 (46%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVRQVVQEVRRTLPAD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G +  + +    +L + ++++GV  + +H R       +P        LD
Sbjct: 148 FSVSVKMRLLGGEKSLESTI--DLARQLEQAGVTFLTLHGR-------TPAQKHSKDTLD 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              + E++K +  + + +NG +E    A  I       GVM  R    N A+  +
Sbjct: 199 IAAMAEVRK-SLQIPLIVNGNVESYRDACDIHDQTGAAGVMAARGLLANPALFNS 252


>gi|307256335|ref|ZP_07538118.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307260774|ref|ZP_07542461.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306865161|gb|EFM97061.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306869500|gb|EFN01290.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 313

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 71/284 (25%), Positives = 123/284 (43%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +P
Sbjct: 55  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDP 114

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D++     AM +A+     V+VK R+G D    A     +  ++ + G N I +H R   
Sbjct: 115 DLIYRATKAMREAVPSDQTVSVKVRLGWDS---AAQCFEIADAVAQGGANEITVHGR--- 168

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQA--LKILPSVDGVMI 215
               + +D  +   +++  + EI+K    L I +  NG + D   A   +   +   +MI
Sbjct: 169 ----TKQDGYRAERINWQAIGEIQKR---LLIPVIANGEIWDFESAKNCQNTTACSSLMI 221

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 222 GRGAL-NTPNLSRV-------------VKFNQPKMPWNEVLQLLFQYVNMENEHDSGFYH 267

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 268 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 310


>gi|260575061|ref|ZP_05843062.1| TIM-barrel protein, nifR3 family [Rhodobacter sp. SW2]
 gi|259022683|gb|EEW25978.1| TIM-barrel protein, nifR3 family [Rhodobacter sp. SW2]
          Length = 332

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 48/157 (30%), Positives = 80/157 (50%), Gaps = 11/157 (7%)

Query: 5   TDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           TD  +R     F A L+ +  +   E++ A  + R   +  LGF   +   A+Q+ G + 
Sbjct: 30  TDLPFRRLVAGFGAGLVVSEMVASQEVVQARPLARARAE--LGFD--QASTAVQLAGREA 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+ V   G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+ +PV
Sbjct: 86  HWMAEAARFVAGQGARVIDINMGCPARKVTNGYSGSALMRDLDHALRLIEAVVGAVEVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           T+K R+G D+ +  +    L +  + +GV  I IH R
Sbjct: 146 TLKTRLGWDEAL--LNAPELAQRAESAGVAMITIHGR 180


>gi|157111456|ref|XP_001651572.1| tRNA-dihydrouridine synthase [Aedes aegypti]
 gi|108878341|gb|EAT42566.1| tRNA-dihydrouridine synthase [Aedes aegypti]
          Length = 391

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 109/237 (45%), Gaps = 32/237 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + L +T MI+AD+  + +K  +  F+T   + P+  Q    +
Sbjct: 30  MVRYSKLEFRNLVRSYGTD-LTFTSMIMADSFCQSEKARLNEFTTNRDDTPVIAQFAAKN 88

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
               + A ++   F Y + ++LN GCP     +  +G+ L+  P+++ D ++ + + L  
Sbjct: 89  AVDFLSATEMT--FPYVDGVDLNCGCPQRWAMQDGYGSALLRTPELIADMLSTVRRNLPS 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +  V+VK R+    Q    A  ++ + ++  G+  I +H R       +P     IP ++
Sbjct: 147 TFSVSVKVRLL---QKSLSATIDMCRQLEACGITFITVHGR-------TPAQKTNIP-VN 195

Query: 176 YDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
            + + EIK         N D+F      L+D + A+    + DGVM  R    N AM
Sbjct: 196 QEALKEIKSSLGIPVVANGDIF-----SLQD-ADAMHCKTNCDGVMSARGILSNPAM 246


>gi|307329095|ref|ZP_07608262.1| TIM-barrel protein, nifR3 family [Streptomyces violaceusniger Tu
           4113]
 gi|306885290|gb|EFN16309.1| TIM-barrel protein, nifR3 family [Streptomyces violaceusniger Tu
           4113]
          Length = 406

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 104/225 (46%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  D K   ++ F   EKP ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERDAKTMRLIHFDGSEKPRSIQLYGV 93

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A + IV++   + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 94  DPMTVGKAVQMIVDENLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRSILREAVTAAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 154 PLPVTMKMRKGIDDD--HITFLDAGRIAVEEGVTAIALHGRTAA--------QHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           ++ +  +K+  P++ +  NG +     A++++     DGV++GR 
Sbjct: 204 WEAIARLKEAVPEIPVLGNGDIWSADDAVRMMRETGCDGVVVGRG 248


>gi|168209608|ref|ZP_02635233.1| dihydrouridine synthase family protein [Clostridium perfringens B
           str. ATCC 3626]
 gi|170712244|gb|EDT24426.1| dihydrouridine synthase family protein [Clostridium perfringens B
           str. ATCC 3626]
          Length = 321

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 109/242 (45%), Gaps = 31/242 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHREELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   + +++K R+G+D          L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKIDDMKISIKTRLGMDK---PEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLDYDIVYEIKKE------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           +  PNL      E+ KE      NP  + G    LED ++ ++    VD +M+GR    N
Sbjct: 173 K--PNL------EVFKEAISLSKNPICYNGDIFTLEDHNKLVEEFKEVDKIMLGRGVLAN 224

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
            A++        N +  +  +  +V K+F  ++     +      ++  +++++  +MI 
Sbjct: 225 PALM--------NEILNNEFMDKKVLKEFHDEVFNKYREVFNEDRNAMFRMKELWGYMIY 276

Query: 283 LF 284
           +F
Sbjct: 277 MF 278


>gi|255732059|ref|XP_002550953.1| tRNA-dihydrouridine synthase 4 [Candida tropicalis MYA-3404]
 gi|240131239|gb|EER30799.1| tRNA-dihydrouridine synthase 4 [Candida tropicalis MYA-3404]
          Length = 342

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 103/234 (44%), Gaps = 14/234 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R +      F+T +  K + +Q+G  +
Sbjct: 33  MVRYSKLPFRELCRFY-NVDIVYTPMILAREFVRNETARYTDFTTNDIDKSVIVQVGVNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   ++   ++  F  + I +N GCP   +V EG  GA LM  PD+V D I A       
Sbjct: 92  VEDFMKFVDMIHPF-VDAIGINCGCPIKEQVREG-IGAALMSEPDLVADLIKAAKAKYGE 149

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + +  +I +   I         K +  +G + I +H R    +   P +   I      
Sbjct: 150 SICIDTKIRIHSDINQTV--EFAKKVVAAGTDMITVHGRTKSTRSTVPVNLEAI-----K 202

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           I+ +  K  P +  G    L+D ++  +    VDGVM  R    N A+ T +D+
Sbjct: 203 IIRDNVKTIPVIANGDCFTLDDCNRIAE-FTGVDGVMSARGILANPALFTGLDK 255


>gi|190346080|gb|EDK38084.2| hypothetical protein PGUG_02182 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 347

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D      F+T   ++ + +Q+G  +
Sbjct: 38  MVRYSKLPFRELVRHY-NTDIVYTPMILAREFVRNDVARASDFTTNPADRSVIVQVGCNN 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L++  +++  +  + I LN GCP   +V EG  GA LM  P++V   + A+ +    
Sbjct: 97  VEDLLKFVEMIHPY-VDGIGLNCGCPIKEQVREG-IGAALMSEPELVSSMVKAVKQKYGD 154

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I +   I        VK +++SGV+ I +H R         K+ R    ++ D
Sbjct: 155 KICIETKIRIHPDIKETL--KFVKMVEESGVDFITVHGRT--------KNTRSSVPVNLD 204

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
            +  + KE   + +  NG    +  A  I     VDGVM  R    N A+ 
Sbjct: 205 AIKAV-KEAVSVPVVANGDCFSLQDAYDIAEYTGVDGVMAVRGILANPALF 254


>gi|303318106|ref|XP_003069055.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
 gi|240108736|gb|EER26910.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
          Length = 538

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 80/170 (47%), Gaps = 12/170 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D  +L+EAA+ V+ +  + ++LN+GCP     +G +GA L   PD++  
Sbjct: 114 DRPLIVQFCANDPDELLEAARHVQQY-CDAVDLNLGCPQGIAKKGRYGAFLQEEPDLIYR 172

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  +   LSIPVT K RI    +          K I  +G + I +H R+   KG    
Sbjct: 173 LINKLHTGLSIPVTAKFRILETKE----KTLEYAKMILSAGASFITVHGRRREQKG---- 224

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
            N  + +  Y I Y      PD  I  NG + +     K L +   DGVM
Sbjct: 225 HNTGVADWSY-IRYLRDNLPPDTVIFANGNILNHDDIQKCLDATGADGVM 273


>gi|281412156|ref|YP_003346235.1| TIM-barrel protein, nifR3 family [Thermotoga naphthophila RKU-10]
 gi|281373259|gb|ADA66821.1| TIM-barrel protein, nifR3 family [Thermotoga naphthophila RKU-10]
          Length = 306

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 71/302 (23%), Positives = 133/302 (44%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M  +TD  +R  A         ++EM+ A   L   +K   L     E+ +A+QI G++ 
Sbjct: 10  MAGYTDSAFRTLA-FEWGADFAFSEMVSAKGFLMNSQKTEELLPQPHERNVAVQIFGSEP 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S+L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   
Sbjct: 69  SELSEAARILSE-KYKWIDLNAGCPVRKVVKKGAGGALLKDLRHFRYIVRELRKSVSGKF 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +        R LV    + GV+ ++IH R  +++G + K   K  ++     
Sbjct: 128 SVKTRLGWEKNEVEEIYRILV----EEGVDEVFIHTR-TVVQGFTGKAEWKALSV----- 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             ++K  P    G     ED  +AL+     DG+++ R A     +   + ++  +    
Sbjct: 178 --LEKRVPTFVSGDVFTPEDAKRALE-ESGCDGLLVARGAIGRPWIFKQIKDFLRSG-KY 233

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH-ILT 298
           S P +  + + F R +   +     R       + ++ + + G       +RR R  I+ 
Sbjct: 234 SEPSREEILRTFERHLELLIKTKGERKA-----VVEMRKFLAGYTKDLKGARRFREKIMK 288

Query: 299 VE 300
           +E
Sbjct: 289 IE 290


>gi|152972182|ref|YP_001337328.1| FMN-linked protein [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|150957031|gb|ABR79061.1| conserved protein, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 290

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 25/222 (11%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L  +EM+ ++  +    K+ L     ++P    +QI G+   ++  AA+I  + G   I+
Sbjct: 5   LTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSVPEEMAAAARINVESGAQIID 64

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+  PD V   + A+  A+ +PVT+K R G + +      RN
Sbjct: 65  INMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVNAVDVPVTLKIRTGWEPE-----HRN 119

Query: 139 LV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            V   +  ++ G+  + IH R    +  G          + +YD +  +K++     I  
Sbjct: 120 CVEIAQLAEECGIQALTIHGRTRACLFNG----------DAEYDSIRAVKQKVSIPIIA- 168

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           NG + D  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 169 NGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYL 210


>gi|195997917|ref|XP_002108827.1| hypothetical protein TRIADDRAFT_52208 [Trichoplax adhaerens]
 gi|190589603|gb|EDV29625.1| hypothetical protein TRIADDRAFT_52208 [Trichoplax adhaerens]
          Length = 309

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 123/264 (46%), Gaps = 37/264 (14%)

Query: 23  YTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +T MI++++ ++ +K     F+T   ++PL +Q   ++   L +A +++  +  + ++LN
Sbjct: 44  FTPMIISESFIKSEKARASEFTTVASDRPLIVQFAASNAFDLADATELIVPYA-DGVDLN 102

Query: 81  VGCPSA-RVHEGSFGACLMLNPDIVGDCI----AAMCKALSIPVTVKCRIGVDDQIPAVA 135
            GCP    +HEG +GA L+ +P++V + +    + +C   +  +++K RI  D       
Sbjct: 103 CGCPQRWAMHEG-YGAHLINHPELVKEMVRHTRSKICNE-NFSISIKIRIHNDINTTV-- 158

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
             +L +  + +GV+ I +H R           + K   + YD +  I K++  + +  NG
Sbjct: 159 --DLCRKAEAAGVSWITVHGRTT---------SEKHTPVHYDAIKTI-KDSVSIPVIANG 206

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            +  +  A +I    +VDGVM  R   +N A+             G S       +DF R
Sbjct: 207 NVFTVDDAQEIYDKTNVDGVMSARGILRNPAL-----------YAGYSKTPICCVEDFVR 255

Query: 254 KISASMTDYAARHLHSGGKLQQIT 277
             S   T +   H H    L++IT
Sbjct: 256 ITSELETHFTPFHRHLIFMLEKIT 279


>gi|34497784|ref|NP_901999.1| hypothetical protein CV_2329 [Chromobacterium violaceum ATCC 12472]
 gi|34103640|gb|AAQ60001.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 315

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 90/173 (52%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D+S L E        G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PVRVQLLGSDVSCLAENGAKAASLGAPGVDLNFGCPAPTVNRHRGGAVLLNEPELLNQIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+   +PVT K R+G +D+  A+      ++I  +G + + +H R  + +G  P 
Sbjct: 124 AAVRRAVPPEVPVTAKMRLGFEDKSRAL---ECAQAIASAGADELTVHGRTKV-EGYKPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
            +       +D +  I +E+  + +  NG +  ++  +A++     D VMIGR
Sbjct: 180 AH-------WDWIARI-RESVTIPVTANGEVWTLADYRAIREESGCDTVMIGR 224


>gi|313884075|ref|ZP_07817841.1| dihydrouridine synthase (Dus) [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620522|gb|EFR31945.1| dihydrouridine synthase (Dus) [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 320

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 100/232 (43%), Gaps = 22/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   + +    D     K  L F+  E+PL   I G
Sbjct: 20  MEDVTDVAFRHVIARAGRPDVFFTEFTNSASYCHPDGIESVKGRLTFTEDEQPLVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + AK +++ G+  +++N+GCP+  V +   G+ L+L   +  + I A  K   
Sbjct: 80  DVPEYFSQMAKGMQEMGFAGVDINMGCPAPNVFKHGRGSGLILRSQVAAELIQA-TKEGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          +  +K +    +  + IH R         K      +  +
Sbjct: 139 LPVSVKTRLG---HAKPEEYKEWLKHLFDQDIVNLSIHLRT--------KTEMSKVDAHW 187

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           D++ +IK    +  P   + +NG + +    L ++    VDGVMIGR  + N
Sbjct: 188 DMIGDIKALRDQIAPQTLLTINGDIPNRQVGLDLVDQYGVDGVMIGRGVFTN 239


>gi|28379386|ref|NP_786278.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|300768771|ref|ZP_07078667.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|28272225|emb|CAD65133.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|300493728|gb|EFK28900.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 334

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 82/187 (43%), Gaps = 11/187 (5%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G       +AA  V++ GY  I+LN+GCP   V +   G+ L+ + D   + I   
Sbjct: 83  VQLWGNSGEDFTKAAHEVKNQGYQAIDLNMGCPDMAVIKNHSGSDLIRHFDRAKEVIEGA 142

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +A  +PV+VK R+G DD          +  + +  V  + +H R  +     P     I
Sbjct: 143 RQA-ELPVSVKTRLGFDD---VHEYETWIPFLLQQQVPVLTVHVRTKMEMSKVPAHYELI 198

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTT 228
            NL    V       P   + +NG + D    LK+    P VDG+MIGR  ++N      
Sbjct: 199 DNL----VQMRDTLAPATLLQINGDILDYQAGLKLAKAHPGVDGIMIGRGIFQNPYAFEP 254

Query: 229 VDEYFSN 235
           + +  S 
Sbjct: 255 IPQPHST 261


>gi|262203780|ref|YP_003274988.1| hypothetical protein Gbro_3919 [Gordonia bronchialis DSM 43247]
 gi|262087127|gb|ACY23095.1| TIM-barrel protein, nifR3 family [Gordonia bronchialis DSM 43247]
          Length = 394

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 70/292 (23%), Positives = 119/292 (40%), Gaps = 25/292 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            AR  T + L   EM+ A A++       ++  F+ +E P ++Q+   D      AAK++
Sbjct: 51  IARTGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSMQLYTVDPEYTYAAAKMI 110

Query: 70  --EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCR 124
             ED   + I++N GCP  +V     G+ +     +    +AA  +A     IPVTVK R
Sbjct: 111 VDEDLA-DHIDMNFGCPVPKVTRKGGGSAIPYKRTLFRKIVAAAVRATEGTDIPVTVKFR 169

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           IG+DD+       +  +   + G   + +HAR A          R     D+D +  +K 
Sbjct: 170 IGIDDE--HRTHLDAGRIAAEEGAKAVALHARTA--------SQRYSGQADWDEIARLKD 219

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
              D+ +  NG + +   A++++     DGV+IGR       +   +    +     + P
Sbjct: 220 HVTDVPVLGNGDIFEPVDAVEMMRRTGCDGVVIGRGCLGRPWLFAELAAEMNGVEAPTPP 279

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               V     R          A H    G  ++I +H+     GFP     R
Sbjct: 280 TLGEVADIIVRHCEL----LVAHHGEMKG-CREIRKHVAWYLRGFPAGSELR 326


>gi|156379115|ref|XP_001631304.1| predicted protein [Nematostella vectensis]
 gi|156218342|gb|EDO39241.1| predicted protein [Nematostella vectensis]
          Length = 440

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 49/163 (30%), Positives = 78/163 (47%), Gaps = 24/163 (14%)

Query: 21  LLYTEMIVADAILRGDKK-----NILGF----------STQEKP--LALQIGGADISKLV 63
           L+YTE I+   +LR  +      N + F          + QE+   +  Q+G AD  + +
Sbjct: 30  LVYTEEIIDFKMLRTTRVKNELLNTVDFVMSDGTVVFRTCQEETTHVVFQVGTADADRAL 89

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           + AK+VE       ++N+GCP     +G  GA L+  P+ V   +  + K LSIPVT K 
Sbjct: 90  QVAKMVEK-DIAAFDVNMGCPKDYSVKGGMGAALLTEPEKVKKILTTLVKGLSIPVTCKI 148

Query: 124 RIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           RI     +P +A    L K I+ +GV  + +H R+   +   P
Sbjct: 149 RI-----LPTIAETVQLCKLIESTGVTALAVHGREKHERSRQP 186


>gi|254557522|ref|YP_003063939.1| transcription regulator [Lactobacillus plantarum JDM1]
 gi|254046449|gb|ACT63242.1| transcription regulator [Lactobacillus plantarum JDM1]
          Length = 334

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 82/187 (43%), Gaps = 11/187 (5%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G       +AA  V++ GY  I+LN+GCP   V +   G+ L+ + D   + I   
Sbjct: 83  VQLWGNSGEDFTKAAHEVKNQGYQAIDLNMGCPDMAVIKNHSGSDLIRHFDRAKEVIEGA 142

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +A  +PV+VK R+G DD          +  + +  V  + +H R  +     P     I
Sbjct: 143 RQA-ELPVSVKTRLGFDD---VHEYETWIPFLLQQQVPVLTVHVRTKMEMSKVPAHYELI 198

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTT 228
            NL    V       P   + +NG + D    LK+    P VDG+MIGR  ++N      
Sbjct: 199 DNL----VQMRDTLAPATLLQINGDILDYQAGLKLAKAHPGVDGIMIGRGIFQNPYAFEP 254

Query: 229 VDEYFSN 235
           + +  S 
Sbjct: 255 IPQPHST 261


>gi|326911232|ref|XP_003201965.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Meleagris
           gallopavo]
          Length = 262

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 109/246 (44%), Gaps = 33/246 (13%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           + ++     + PL +Q    +   L +AA +V  F  + ++LN GCP        +GACL
Sbjct: 15  QQLVTLHDSDNPLIVQFAAKEAQVLCDAALLVCPFA-DGVDLNCGCPQRWAMAEGYGACL 73

Query: 98  MLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           +  P++V D +  +   +  P   V++K RI  D +       +L K  + +GV+ I +H
Sbjct: 74  INKPELVQDMVRHVRNRIDNPRFSVSIKIRIHEDLKKTV----DLCKKAEATGVSWITVH 129

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDG 212
            R          + R  P + YD + ++ KE+  + +  NG ++ +  A  +  L   DG
Sbjct: 130 GRNT--------EERHQP-VHYDAI-KVIKESMHIPVVANGDIKSLKDAENVHRLTGADG 179

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGG 271
           VM+ R    N AM    +E         +P+K   D   W  I+    T +   H H   
Sbjct: 180 VMVARGLLANPAMFAGYEE---------TPLKCIQD---WVDIALEHGTPFTCFHHHLMY 227

Query: 272 KLQQIT 277
            +++IT
Sbjct: 228 MMERIT 233


>gi|33862473|ref|NP_894033.1| nitrogen regulation protein NifR3 family protein [Prochlorococcus
           marinus str. MIT 9313]
 gi|33640586|emb|CAE20375.1| putative nitrogen regulation protein NifR3 family homolog
           [Prochlorococcus marinus str. MIT 9313]
          Length = 336

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 71/300 (23%), Positives = 132/300 (44%), Gaps = 28/300 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           +D+ +R   R    +ALL+TEM+ A ++  G   + I   + +  P+ +Q+       + 
Sbjct: 28  SDQIFRSLVRRWAPDALLFTEMVNATSLELGHGLQKINELANEAGPIGVQLFDHRPEAMA 87

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    ++ +  A+ IPVTVK 
Sbjct: 88  DAAQRAEAAGAFLIDINMGCPVRKIARKGGGSGLIRDPQLAAKIVSTVAAAVKIPVTVKT 147

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D  P        +S++++G   + +HAR         ++     + D+  +  
Sbjct: 148 RLGWCGSDAKPI----EWCQSLEQAGAQMLTLHART--------REQGFKGSADWHAIAA 195

Query: 182 IKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PL 237
           +K       I  NG ++   D  + L I    DGVM+GR +     ++  +D   S  P+
Sbjct: 196 VKSALQIPVIA-NGDVKSDIDAKRCLAIT-GADGVMVGRGSLGAPWLVGQIDAALSGRPV 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +     R+     R+   ++      H      L    +HM     GFP + + RH L
Sbjct: 254 PATPGAAERL--TIAREQLEALVQAKGEH-----GLLIARKHMGWTCSGFPGASKLRHAL 306


>gi|169845315|ref|XP_001829377.1| tRNA-dihydrouridine synthase 2 [Coprinopsis cinerea okayama7#130]
 gi|116509442|gb|EAU92337.1| tRNA-dihydrouridine synthase 2 [Coprinopsis cinerea okayama7#130]
          Length = 454

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 59/191 (30%), Positives = 93/191 (48%), Gaps = 14/191 (7%)

Query: 43  FSTQ--EKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F+T   EKP L  QIG AD    V+AAK V+    + I+LN GCP         GA L+ 
Sbjct: 112 FTTHPIEKPYLIYQIGSADPELAVQAAKTVQQ-DVSGIDLNCGCPKPFSTHAGMGAALLT 170

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKA 158
           NPD++   + A+ KA+   +TV  +I +   +P+      LV+ I  +GV+ + +H R  
Sbjct: 171 NPDLLISILEALRKAMPPEITVTAKIRL---LPSQEDTLKLVERIVNTGVSALTVHCR-- 225

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIG 216
             + +  KD   I  L+ +IV  ++K    + +  NG   D   A ++  +     VMI 
Sbjct: 226 -TRNMREKDRAVIERLN-EIVEFVEKMGKGIAVIENGDCLDWEDAKRVRRVTGAHSVMIA 283

Query: 217 RAAYKNSAMLT 227
           R A  N +  +
Sbjct: 284 RGAEANPSCFS 294


>gi|304387694|ref|ZP_07369877.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis ATCC 13091]
 gi|304338263|gb|EFM04390.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis ATCC 13091]
          Length = 341

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 53/195 (27%), Positives = 93/195 (47%), Gaps = 13/195 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 84  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 143

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 144 KTLRERLPAHIPLTAKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 199

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 200 AHWEWIRKIRDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 253

Query: 227 TTVDEYFSN-PLTGS 240
             + +Y S  P+T +
Sbjct: 254 RQIKQYESGLPVTDT 268


>gi|17543114|ref|NP_500379.1| hypothetical protein Y37E11B.5 [Caenorhabditis elegans]
 gi|4226107|gb|AAD12825.1| Hypothetical protein Y37E11B.5 [Caenorhabditis elegans]
          Length = 554

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 76/280 (27%), Positives = 123/280 (43%), Gaps = 30/280 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A +IL G   + ++L     EK   +Q+ G     + +A++IV E+F  + I++N+
Sbjct: 234 EMALATSILSGTASEYSLLKRHPCEKIFGVQLAGGFADTMAKASQIVVENFDVDFIDINM 293

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNL 139
           GCP   V++   G  L   P  + + +AA    L    P+TVK R G+ + +  +     
Sbjct: 294 GCPIDVVNQKGGGCALPSRPQKLFEVLAATKSVLGGCCPLTVKIRTGMKEGV--LKAPEY 351

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNR--KIPNLDYDI-VYEIKKENPDLFIGLNGG 196
           V+ +KK      W H    I      K+ R  ++ N D+   V E  K  P    G    
Sbjct: 352 VEHMKKHS----W-HTPDLITFHPRSKEQRYTRLANWDFTFPVQEATKPVPLWVCGDILS 406

Query: 197 LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
            ED  + L+  P V+G+MIGR A     + T +DE  +  ++ +     R D      + 
Sbjct: 407 WEDYYERLEQYP-VNGIMIGRGALIKPWIFTEIDERRTWDISSTE----RFD------LL 455

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               DY   H  S     + TR  +  F  F    +CR+I
Sbjct: 456 KKFVDYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 491


>gi|195045040|ref|XP_001991926.1| GH12926 [Drosophila grimshawi]
 gi|193901684|gb|EDW00551.1| GH12926 [Drosophila grimshawi]
          Length = 460

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 85/182 (46%), Gaps = 19/182 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + LQ+G +D ++ +   K+V+      +++N+GCP     +G  GA L+  PD     + 
Sbjct: 84  VVLQMGTSDAARALAVGKLVQ-CDIAGLDINMGCPKEFSIKGGMGAALLAEPDKAAHILR 142

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +C  L IP+T K RI + D +  +   NLV+ +  +G+  I IHAR         +D R
Sbjct: 143 TLCSQLDIPITCKIRI-LPDPMDTI---NLVQKLAATGIAAIGIHART--------RDER 190

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNSA 224
                  D++  +     D+ I  NGG  +M         + L   D VM+ RAA  N +
Sbjct: 191 PQHRPHPDVLRAVASA-VDIPIIANGGSREMHTFEDLHKFQELCGADSVMVARAAQLNVS 249

Query: 225 ML 226
           + 
Sbjct: 250 IF 251


>gi|119185991|ref|XP_001243602.1| hypothetical protein CIMG_03043 [Coccidioides immitis RS]
          Length = 538

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 80/170 (47%), Gaps = 12/170 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D  +L+EAA+ V+ +  + ++LN+GCP     +G +GA L   PD++  
Sbjct: 114 DRPLIVQFCANDPDELLEAARHVQQY-CDAVDLNLGCPQGIAKKGRYGAFLQEEPDLIYR 172

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  +   LSIPVT K RI    +          K I  +G + I +H R+   KG    
Sbjct: 173 LINKLHTGLSIPVTAKFRILETKE----KTLEYAKMILSAGASFITVHGRRREQKG---- 224

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
            N  + +  Y I Y      PD  I  NG + +     K L +   DGVM
Sbjct: 225 HNTGVADWSY-IRYLRDNLPPDTVIFANGNILNHDDIQKCLDATGADGVM 273


>gi|170057436|ref|XP_001864482.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
 gi|167876880|gb|EDS40263.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
          Length = 378

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 57/233 (24%), Positives = 107/233 (45%), Gaps = 32/233 (13%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKL 62
           T   +R   R    + L ++ MI+AD+    +K  +  F+T   + P+ +Q    +    
Sbjct: 12  TKLEFRNLVRTFDTD-LTFSSMIMADSFCHSEKARLNEFTTNKDDTPMIVQFAANNTIDF 70

Query: 63  VEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           + AA++V  + Y++ ++LN GCP     +  +G+ L+  P+++ D +A + + L  S  V
Sbjct: 71  LSAAEMV--YPYSDGVDLNCGCPQRWAMQDGYGSALLKTPELIADMLATVRRNLPCSFSV 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+    Q    A  ++ + ++  G+  + +H R A        D   +P ++ D +
Sbjct: 129 SVKVRLL---QKSLAATVDMCRQLEACGITFLTVHGRTA-------ADKTNVP-VNKDAL 177

Query: 180 YEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
            EIK         N D+F      L+D  +  +I    DGVM  R    N  +
Sbjct: 178 KEIKASLSIPMVANGDIF-----SLQDADEMHRIT-GCDGVMSARGILSNPGL 224


>gi|171057225|ref|YP_001789574.1| NifR3 family TIM-barrel protein [Leptothrix cholodnii SP-6]
 gi|170774670|gb|ACB32809.1| TIM-barrel protein, nifR3 family [Leptothrix cholodnii SP-6]
          Length = 346

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 111/250 (44%), Gaps = 21/250 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   LR   K    L  + +  P+A+QI G +
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRPELRDSLKTSRRLDHTGEVAPIAVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
              + EAA+   + G   I++N+GCP+ +V     G+ LM N  +   + D + A     
Sbjct: 76  PEMMAEAARYNIERGAQIIDINMGCPAKKVCNVWAGSALMQNESLALRIIDAVVAASAPH 135

Query: 116 SIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +PVT+K R G   +Q  A+    + ++ + +G+  + +H R         ++       
Sbjct: 136 GVPVTLKMRTGWCQEQKNAL---QIARAAQDAGIAMVTVHGRT--------REQGYKGEA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           +Y  +  +K     + +  NG ++   +A ++L +   D VMIGRAA     +   +  +
Sbjct: 185 EYRTIAAVKAAL-QIPVVANGDIDSPEKAARVLRATGADAVMIGRAAQGRPWIFREIAHH 243

Query: 233 FSNPLTGSSP 242
            +      +P
Sbjct: 244 LATGQAMDAP 253


>gi|115469926|ref|NP_001058562.1| Os06g0712900 [Oryza sativa Japonica Group]
 gi|113596602|dbj|BAF20476.1| Os06g0712900 [Oryza sativa Japonica Group]
          Length = 421

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 106/232 (45%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 94  MVDNSELPFRMLCRRYGATGA-YTPMLHSRIFSENEKHRAMEFTTCKEDRPLFVQFCAND 152

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE +  + +++N GCP      G +GA LM N  +V   +  +   L +P
Sbjct: 153 PDILLQAAKIVEPYC-DYVDINFGCPQRIARRGYYGAFLMNNLPLVKSLVQNLSANLHVP 211

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K RI   ++D +         K ++++G + + +H R         KD +K    D+
Sbjct: 212 VSCKIRIFPRLEDTL------AYAKMLEEAGASLVAVHGRTR-----DEKDGKKF-RADW 259

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D +  +K     P L  G    L+D+   L+     DGV+      +N A+ 
Sbjct: 260 DAIKAVKDALRIPVLANGNIRHLDDVKDCLEHT-GADGVLSAETLLENPALF 310


>gi|307299179|ref|ZP_07578980.1| dihydrouridine synthase DuS [Thermotogales bacterium mesG1.Ag.4.2]
 gi|306914975|gb|EFN45361.1| dihydrouridine synthase DuS [Thermotogales bacterium mesG1.Ag.4.2]
          Length = 312

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 80/150 (53%), Gaps = 12/150 (8%)

Query: 21  LLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
            +++EMI  + +LR  G  + I+  +    P  +Q+ G+  S++ +AA  + +     I+
Sbjct: 29  FVFSEMISVEGVLRASGRTEEIVPVT----PTRIQLFGSSASRMAKAAMRLSEVA-TWID 83

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N GCP  +V     G+ L+  P+ + + I A+  ++ +PV+VK R+G D    A     
Sbjct: 84  INAGCPVKKVTRKGAGSALLRTPEKIAEMITALKNSIDVPVSVKIRLGND----ATDTEK 139

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           ++  I ++  + +++H R  +L+G S K N
Sbjct: 140 IIYQIIEAKPDAVFVHGR-TVLQGYSGKAN 168


>gi|218768088|ref|YP_002342600.1| hypothetical protein NMA1207 [Neisseria meningitidis Z2491]
 gi|38605054|sp|Q9JUP6|DUSC_NEIMA RecName: Full=tRNA-dihydrouridine synthase C
 gi|121052096|emb|CAM08407.1| hypothetical protein NMA1207 [Neisseria meningitidis Z2491]
 gi|319410331|emb|CBY90676.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis WUE 2594]
          Length = 333

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 52/207 (25%), Positives = 98/207 (47%), Gaps = 24/207 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V+    GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNRHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRERLPAHIPLTAKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
            +       ++ + +I +++ D+ +  NG +  +     +K +   + VM+GR A     
Sbjct: 192 AH-------WEWIRKI-RDSVDIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPD 243

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           +   + +Y         P+K   D DF
Sbjct: 244 LARQIKQY-----ENGGPVK---DTDF 262


>gi|308181599|ref|YP_003925727.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308047090|gb|ADN99633.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 334

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 82/187 (43%), Gaps = 11/187 (5%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G       +AA  V++ GY  I+LN+GCP   V +   G+ L+ + D   + I   
Sbjct: 83  VQLWGNSGEDFTKAAHEVKNQGYQAIDLNMGCPDMAVIKNHSGSDLIRHFDRAKEVIEGA 142

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +A  +PV+VK R+G DD          +  + +  V  + +H R  +     P     I
Sbjct: 143 RQA-ELPVSVKTRLGFDD---VHEYETWIPFLLQQQVPVLTVHVRTKMEMSKVPAHYELI 198

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTT 228
            NL    V       P   + +NG + D    LK+    P VDG+MIGR  ++N      
Sbjct: 199 DNL----VQMRDTLAPATLLQINGDILDYQAGLKLAKAHPGVDGIMIGRGIFQNPYAFEP 254

Query: 229 VDEYFSN 235
           + +  S 
Sbjct: 255 IPQPHST 261


>gi|71281750|ref|YP_267308.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
 gi|71147490|gb|AAZ27963.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
          Length = 338

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 50/195 (25%), Positives = 95/195 (48%), Gaps = 15/195 (7%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+   +L  AAK+  D G   I++N+GCP+ +V++   G+ L+  P  V   + +
Sbjct: 68  SVQIAGSCPDELAFAAKVNADNGAQIIDINMGCPAKKVNKKLAGSALLREPAQVERIVQS 127

Query: 111 MCKALSIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +  A+ IPVT+K R G  +D    +    + K  + SG+  + +H R         +++ 
Sbjct: 128 VVNAVDIPVTLKIRTGWCEDTRNGI---EIAKIAENSGIASLAVHGRT--------RNDF 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              N +YD +  IK     + +  NG +    +AL++L     D +M+GR A     +  
Sbjct: 177 YKGNAEYDTIKAIKLA-ISIPVVANGDITSPEKALQVLDHTGADAIMVGRGAQGRPWIFR 235

Query: 228 TVDEYFSNPLTGSSP 242
            ++ + +     S+P
Sbjct: 236 EINYFLATGNKMSAP 250


>gi|17507177|ref|NP_492379.1| hypothetical protein F36A2.2 [Caenorhabditis elegans]
 gi|3876775|emb|CAB03067.1| C. elegans protein F36A2.2, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 527

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 42/166 (25%), Positives = 78/166 (46%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R F R     LT   +++  + V D   R   +N L     ++PL +Q   
Sbjct: 80  MVDQSELAFRMFTRKYGAQLTFTPMIHAHLFVNDGTYR---RNSLALVKADRPLVVQFCA 136

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
             +   + A ++VED   + ++LN+GCP      G +G+ L    D++ + ++A+     
Sbjct: 137 NKVDTFLAACRLVEDVC-DGVDLNLGCPQMVAKRGRYGSWLQDEVDLICEMVSAVRDYCR 195

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +P++ K R+  D Q      + LV     +G   + +H R   +KG
Sbjct: 196 LPISCKIRVRDDRQQTVEYAKRLV----DAGATMLTVHGRTRDMKG 237


>gi|330837194|ref|YP_004411835.1| TIM-barrel protein, nifR3 family [Spirochaeta coccoides DSM 17374]
 gi|329749097|gb|AEC02453.1| TIM-barrel protein, nifR3 family [Spirochaeta coccoides DSM 17374]
          Length = 343

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 67/279 (24%), Positives = 119/279 (42%), Gaps = 15/279 (5%)

Query: 24  TEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ A+ + RG    + +L     E+   +QI G++ +++  A   +  +    I+ N 
Sbjct: 50  SEMVSAEGLARGSAGTEELLERYEGEEQFIIQIFGSETNQVERALPRLLCYKPTVIDFNC 109

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   G+ LM +P  +   + A+     +PV+VK R+G D    A++ R   +
Sbjct: 110 GCPVPKVVKTGAGSALMKHPQTIYAMVRAVRNQCDVPVSVKFRLGWDKD--AISWREFAQ 167

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           +  + G   + +HAR          D  +I  L    V  +K+ +P++ +  +G +    
Sbjct: 168 AALEGGAQMLTMHARTRSQGYSGVADWSRIAAL----VDMVKQMSPNVPVFGSGDVFTPH 223

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            A  +L    VDGVM  R A  N  +           L+G  P    ++      I   +
Sbjct: 224 DAQHMLEETGVDGVMFARGAIGNPFIFERTKALL---LSGQEPEAVPLET-IIGTIMRHL 279

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           T  A R        +Q+  H      G P S R R ++T
Sbjct: 280 TLLAERKGEEAA-CRQMRGHAGSYLKGLPGSSRIRGLIT 317


>gi|308176716|ref|YP_003916122.1| tRNA-dihydrouridine synthase [Arthrobacter arilaitensis Re117]
 gi|307744179|emb|CBT75151.1| putative tRNA-dihydrouridine synthase [Arthrobacter arilaitensis
           Re117]
          Length = 394

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 70/305 (22%), Positives = 124/305 (40%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+R +R   R      L  TEM+ A A++  + ++  I+     E+  ++QI G D
Sbjct: 35  MAGVTNRAFRRLCREY-GGGLYVTEMVTARALVERNPESLRIISHDPDEEIRSIQIYGVD 93

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              +  A ++V D    + ++LN GCP  +V     G+ L    D+    I A     + 
Sbjct: 94  PGTVRAAVRMVVDENLADHVDLNFGCPVPKVTRKGGGSALPWKSDLYTSIIEAATSEAAK 153

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+TVK RIG+D     +      K  +  G   + +HAR A              + 
Sbjct: 154 GDIPLTVKMRIGIDKD--HLTYLESAKIARDHGAAAVTLHARTA--------GQYYAGHS 203

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +++   D+ +  NG +     A++++      GVM+GR       +   +   
Sbjct: 204 DWDAITTLREAMDDMPVLGNGDIFSAEDAIEMVEQTGAAGVMVGRGCQGRPWIFGDLQAA 263

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P   +V    +R     +T++       G  ++ I +H+   F G+P    
Sbjct: 264 FEGREDRFRPGVRKVADTVYRH-GELLTEFFE---DEGKGMRDIRKHIAWYFKGYPVGGE 319

Query: 293 CRHIL 297
            R  L
Sbjct: 320 IRSQL 324


>gi|282892092|ref|ZP_06300567.1| hypothetical protein pah_c207o016 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281497987|gb|EFB40331.1| hypothetical protein pah_c207o016 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 304

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 95/188 (50%), Gaps = 14/188 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P A+QI G++   +   A+ +   G + I+LN GCPS  V     G+ L+ +P  +    
Sbjct: 51  PQAVQIMGSNPELMAAMAQELAQRGAHRIDLNCGCPSNTVTGRGAGSSLLKDPSQLYRIA 110

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            AM +A+S+PVT K R G +D   ++   NL+ + ++SG+  + +H R  +  G +P   
Sbjct: 111 KAMVEAVSVPVTAKLRSGYEDI--SLFKENLLAA-QESGIKFMTLHPRTKV-DGYTPPAR 166

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
                  +D++ E K       +G NG + ++  A+++L     D +M+GR +  N  + 
Sbjct: 167 -------WDLIAEAKALLKIPVVG-NGDILNVDDAVRMLKETGCDALMVGRGSVINPLIF 218

Query: 227 TTVDEYFS 234
             +  +F+
Sbjct: 219 HQIRAFFA 226


>gi|225438801|ref|XP_002283225.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 424

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 99  MVDNSELPFRMLCRKYGAQAA-YTPMLHSRIFSENEKYRSQEFTTCKEDRPLFVQFCAND 157

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA+ VE +  + +++N+GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 158 PDTLLEAAQRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLHVP 216

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   + D I      N  + ++ +G + + +H R         KD +K    D+
Sbjct: 217 VSCKIRVFPNLQDTI------NYARMLEDAGCSLLAVHGRTR-----DEKDGKKF-RADW 264

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           + +  +K     + +  NG +  M    + L     DGV+   +  +N A+ 
Sbjct: 265 NAIKAVKNAV-SIPVLANGDIRHMDDVQRCLEETGADGVLSAESLLENPALF 315


>gi|145590054|ref|YP_001156651.1| nifR3 family TIM-barrel protein [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048460|gb|ABP35087.1| tRNA-U20-dihydrouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
          Length = 338

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 122/248 (49%), Gaps = 31/248 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   TDR +R   + L       +EM+ ++A+L   +K     N +G   + KP+A+QI 
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVASNALLWKSEKTQRRANHIG---EFKPIAVQIA 72

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           GAD + +  AAKI  D G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+
Sbjct: 73  GADPAMMAAAAKINVDHGAQIIDINMGCPAKKVCNVAAGSALLRDEPLVQQILEAVVNAV 132

Query: 116 -----SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                ++PVT+K R G D +   A+ +  L    +KSG++ + +H R         + + 
Sbjct: 133 GVGPDAVPVTLKIRTGWDREHKNAIEIARLA---EKSGISMLTVHGRT--------RADL 181

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
                +Y+ +  +K  + ++ +  NG +   E   Q LKI    D +MIGRAA     + 
Sbjct: 182 YHGEAEYETITAVKN-SVNIPVVANGDIHSPEKAEQVLKIT-GADAIMIGRAAQGRPWIF 239

Query: 227 TTVDEYFS 234
             ++ Y  
Sbjct: 240 REINHYLE 247


>gi|320036772|gb|EFW18710.1| dihydrouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 538

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 80/170 (47%), Gaps = 12/170 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D  +L+EAA+ V+ +  + ++LN+GCP     +G +GA L   PD++  
Sbjct: 114 DRPLIVQFCANDPDELLEAARHVQQYC-DAVDLNLGCPQGIAKKGRYGAFLQEEPDLIYR 172

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  +   LSIPVT K RI    +          K I  +G + I +H R+   KG    
Sbjct: 173 LINKLHTGLSIPVTAKFRILETKE----KTLEYAKMILSAGASFITVHGRRREQKG---- 224

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
            N  + +  Y I Y      PD  I  NG + +     K L +   DGVM
Sbjct: 225 HNTGVADWSY-IRYLRDNLPPDTVIFANGNILNHDDIQKCLDATGADGVM 273


>gi|53792892|dbj|BAD54069.1| putative PP35 [Oryza sativa Japonica Group]
 gi|53793348|dbj|BAD54568.1| putative PP35 [Oryza sativa Japonica Group]
 gi|125598482|gb|EAZ38262.1| hypothetical protein OsJ_22639 [Oryza sativa Japonica Group]
          Length = 396

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 106/232 (45%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 69  MVDNSELPFRMLCRRYGATGA-YTPMLHSRIFSENEKHRAMEFTTCKEDRPLFVQFCAND 127

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE +  + +++N GCP      G +GA LM N  +V   +  +   L +P
Sbjct: 128 PDILLQAAKIVEPYC-DYVDINFGCPQRIARRGYYGAFLMNNLPLVKSLVQNLSANLHVP 186

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K RI   ++D +         K ++++G + + +H R         KD +K    D+
Sbjct: 187 VSCKIRIFPRLEDTLA------YAKMLEEAGASLVAVHGRTR-----DEKDGKKF-RADW 234

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D +  +K     P L  G    L+D+   L+     DGV+      +N A+ 
Sbjct: 235 DAIKAVKDALRIPVLANGNIRHLDDVKDCLEHT-GADGVLSAETLLENPALF 285


>gi|194853320|ref|XP_001968141.1| GG24669 [Drosophila erecta]
 gi|190660008|gb|EDV57200.1| GG24669 [Drosophila erecta]
          Length = 505

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 13/231 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L+IP
Sbjct: 94  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +     +R   K ++ +G   + +H R    KG        + N +Y  
Sbjct: 153 VTCKIRIFEDLE---KTIR-YAKMLEAAGCQLLTVHGRTREQKGPL----TGVANWNYIK 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
                 + P L  G   GLED+ + L     VDGVM       N A+   +
Sbjct: 205 SVRQHIKIPMLANGNILGLEDVHRCLAET-GVDGVMSAEGNLHNPAIFRGI 254


>gi|110625595|ref|NP_079794.1| tRNA-dihydrouridine synthase 2-like [Mus musculus]
 gi|73620836|sp|Q9D7B1|DUS2L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 2-like
 gi|12844161|dbj|BAB26260.1| unnamed protein product [Mus musculus]
 gi|109733553|gb|AAI16937.1| Dihydrouridine synthase 2-like (SMM1, S. cerevisiae) [Mus musculus]
 gi|109733887|gb|AAI16935.1| Dihydrouridine synthase 2-like (SMM1, S. cerevisiae) [Mus musculus]
 gi|148679394|gb|EDL11341.1| mCG20459, isoform CRA_b [Mus musculus]
          Length = 493

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 51/193 (26%), Positives = 92/193 (47%), Gaps = 32/193 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           ++  +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD + 
Sbjct: 80  EQSRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIE 138

Query: 106 DCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             ++ + K    PVT K RI   ++D +      NLVK I+++G++ I +H R       
Sbjct: 139 KILSTLVKGTHRPVTCKIRILPSLEDTL------NLVKRIERTGISAIAVHGRN------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGV 213
             +D R    +  +++  I  E   + +  NGG          +ED  QA     +   V
Sbjct: 187 --RDERPQHPVSCEVIRAI-AETLSIPVIANGGSHDHIQQHVDIEDFRQAT----AASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|302206819|gb|ADL11161.1| Dihydrouridine synthase-like (DUS-like) FMN-binding domain protein
           [Corynebacterium pseudotuberculosis C231]
 gi|308277071|gb|ADO26970.1| Dihydrouridine synthase-like (DUS-like) FMN-binding domain protein
           [Corynebacterium pseudotuberculosis I19]
          Length = 384

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 69/286 (24%), Positives = 123/286 (43%), Gaps = 27/286 (9%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           R  T + L   EMI A A++  ++K  ++  F  QE   +LQ+   D     +AAK++ D
Sbjct: 41  RTGTVSGLYICEMITARALVHRNEKTLHMTTFGPQEDVRSLQLYTVDPEYTFKAAKMIAD 100

Query: 72  FGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGV 127
            G  + I++N GCP  +V +   G+ L     + G+ IAA  K +   +IPVTVK R+G+
Sbjct: 101 EGIADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGNIIAAAVKGVEGTNIPVTVKFRMGI 160

Query: 128 D-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           D D +  +   +  +   + G   + +HAR A          R   +  +D + ++K+  
Sbjct: 161 DHDHLTHL---DAGRIAAEEGAAAVTLHARTAA--------ERYSGDAHWDEIGKLKEHL 209

Query: 187 PDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
               I +  NG +   + A+ ++ +   DGV++GR       +   +            P
Sbjct: 210 AHTGIPVLGNGDIFKPTDAIDMIKASGCDGVVVGRGCLGRPWLFAGLSAAMRGKEIPPEP 269

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
               V +  +R       +    H       + + +HM     GFP
Sbjct: 270 TLGEVTRIIYRH-----AELLVEHEGETKGCRDMRKHMGWYLRGFP 310


>gi|170034571|ref|XP_001845147.1| t-diRNAhydrouridine synthase [Culex quinquefasciatus]
 gi|167875928|gb|EDS39311.1| t-diRNAhydrouridine synthase [Culex quinquefasciatus]
          Length = 609

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 48/164 (29%), Positives = 81/164 (49%), Gaps = 8/164 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +  K  K+ L    +++PL +Q  G D
Sbjct: 112 MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFTKDPKYRKDSLQTCPEDRPLIIQFCGND 170

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EA  + +D   + I++N+GCP A    G +GA L    D++   ++ + + LS+P
Sbjct: 171 PKVLLEAGLLAQDH-CDAIDINLGCPQAIAKRGHYGAFLQDEWDLLKKIVSTLHQNLSVP 229

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           VT K RI  D    A  +R   K ++ +G   + +H R    KG
Sbjct: 230 VTCKVRIFEDM---AKTIR-YAKMLESAGCQMLVVHGRTRDQKG 269


>gi|172041286|ref|YP_001801000.1| hypothetical protein cur_1606 [Corynebacterium urealyticum DSM
           7109]
 gi|171852590|emb|CAQ05566.1| hypothetical protein cu1606 [Corynebacterium urealyticum DSM 7109]
          Length = 442

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 44/123 (35%), Positives = 66/123 (53%), Gaps = 6/123 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R+ +   L   EM+ A A++  + K  ++  F+  E P +LQ+   D     EAAK IV+
Sbjct: 100 RMGSVAGLYVCEMVTARALVERNPKTLHMTTFAPDEDPRSLQLYTTDPKYTYEAAKMIVD 159

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V     GA L     + G+ +AA  KA     IPVTVK RIG+
Sbjct: 160 ENMADHIDMNFGCPMPKVTRRGGGAALPYKRRLFGNIVAAAVKATEGTDIPVTVKMRIGI 219

Query: 128 DDQ 130
           DD+
Sbjct: 220 DDE 222


>gi|148269963|ref|YP_001244423.1| nifR3 family TIM-barrel protein [Thermotoga petrophila RKU-1]
 gi|170288648|ref|YP_001738886.1| NifR3 family TIM-barrel protein [Thermotoga sp. RQ2]
 gi|147735507|gb|ABQ46847.1| putative TIM-barrel protein, nifR3 family [Thermotoga petrophila
           RKU-1]
 gi|170176151|gb|ACB09203.1| TIM-barrel protein, nifR3 family [Thermotoga sp. RQ2]
          Length = 306

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 70/302 (23%), Positives = 133/302 (44%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M  +TD  +R  A         ++EM+ A   L   +K   L     E+ +A+QI G++ 
Sbjct: 10  MAGYTDSAFRTLA-FEWGADFAFSEMVSAKGFLMNSQKTEELLPQPHERNVAVQIFGSEP 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S+L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   
Sbjct: 69  SELSEAARILSE-KYKWIDLNAGCPVRKVVKKGAGGALLKDLRHFRYIVRELRKSVSGKF 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +        R LV    + GV+ ++IH R  +++G + K   K  ++     
Sbjct: 128 SVKTRLGWEKNEVEEIYRILV----EEGVDEVFIHTR-TVVQGFTGKAEWKALSV----- 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             ++K  P    G     ED  +AL+     DG+++ R A     +   + ++  +    
Sbjct: 178 --LEKRVPTFVSGDVFTPEDAKRALE-ESGCDGLLVARGAIGRPWIFKQIKDFLRSGRY- 233

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH-ILT 298
           S P +  + + F R +   +     R       + ++ + + G       +RR R  ++ 
Sbjct: 234 SEPSREEILRTFERHLELLIKTKGERKA-----VVEMRKFLAGYTKDLKGARRFREKVMK 288

Query: 299 VE 300
           +E
Sbjct: 289 IE 290


>gi|260102343|ref|ZP_05752580.1| tRNA-dihydrouridine synthase [Lactobacillus helveticus DSM 20075]
 gi|260083852|gb|EEW67972.1| tRNA-dihydrouridine synthase [Lactobacillus helveticus DSM 20075]
          Length = 341

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 112/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK R G D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRTGWDKK-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D++I++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEILHDVAQVLDVPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y   
Sbjct: 207 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMTHYLET 248


>gi|87309552|ref|ZP_01091687.1| hypothetical protein DSM3645_24660 [Blastopirellula marina DSM
           3645]
 gi|87287860|gb|EAQ79759.1| hypothetical protein DSM3645_24660 [Blastopirellula marina DSM
           3645]
          Length = 361

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 112/231 (48%), Gaps = 26/231 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M  +T+  +R   R      L  TEM+ A + +  D++      + G   + +PLA+Q+ 
Sbjct: 33  MAGYTNYAFRQIVRDYGGVGLQATEMVSARSFVWLDQQAEFPDRLWGIEDEPRPLAVQMW 92

Query: 56  GADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCK 113
             +   +     ++VE+F  + +++N GCP  +V + +  G+ L+  P+ +   I  + +
Sbjct: 93  DNEPDTMARVGERLVEEFQVSVVDINFGCPVKQVTQSAHSGSYLLRWPEKMFSIIRRVVE 152

Query: 114 ALS-IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNR 169
           A +  PVT K R+G   D+I A     + + ++++G   + +H R A    KG       
Sbjct: 153 ACAPTPVTAKIRLGCSRDKINA---NEIAQVVEEAGAAALTVHGRTAADFFKG------- 202

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              + D++ + EIK     + +  NG L+  ++ ++   S  VDGVMI RA
Sbjct: 203 ---SADWEKISEIKPYLKKIPLIGNGDLDSAAKVVEAFRSYQVDGVMIARA 250


>gi|319786120|ref|YP_004145595.1| hypothetical protein Psesu_0506 [Pseudoxanthomonas suwonensis 11-1]
 gi|317464632|gb|ADV26364.1| TIM-barrel protein, nifR3 family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 332

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 113/242 (46%), Gaps = 22/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKQL-GAGLAVSEMTISDPRFWNTRKSLQRMDHAGEPDPVSVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 76  PEQLAGAARYNVANGAQIIDINMGCPAKKVCNAWAGSALMRDEALVARILEAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G   ++     RN   + +  ++SG+  + IH R         ++       +
Sbjct: 136 VTLKIRTGWCAEV-----RNAPTIARIAEESGIAALAIHGRT--------RNQHYTGQAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + E+K     + +  NG ++  ++A  +L     D VM+GRAA     +   +  Y 
Sbjct: 183 YDTIAEVKSRL-RIPVLANGDIDSPAKAAFVLRHTGADAVMVGRAAQGRPWIFRQIAHYL 241

Query: 234 SN 235
             
Sbjct: 242 GT 243


>gi|307182359|gb|EFN69626.1| tRNA-dihydrouridine synthase 1-like [Camponotus floridanus]
          Length = 468

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 83/164 (50%), Gaps = 8/164 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K  +  L  +++++PL +Q  G D
Sbjct: 30  MVDASELAWRLLSRR-HGAQLCYTPMLHSTVFCRDPKYRREALASTSEDRPLIVQFCGND 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA++ E +  + I++N+GCP A    G +GA L  +  ++   ++ +   L IP
Sbjct: 89  PDVLLEAARLAEPYC-DAIDINIGCPQAIAKRGHYGAFLQDDWILLNRIVSTLKNGLHIP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           VT  C++ V  +I         + ++ +G + + IH R    KG
Sbjct: 148 VT--CKLRVFSEINRTV--EYARMLQDAGASLLTIHGRTREQKG 187


>gi|269103648|ref|ZP_06156345.1| tRNA dihydrouridine synthase B [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163546|gb|EEZ42042.1| tRNA dihydrouridine synthase B [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 348

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 111/243 (45%), Gaps = 26/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L    K  N +    +    ++QI G+D
Sbjct: 44  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPDLWKTSKSMNRMVHEGESGIRSVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  P ++ + +  +  A+ +P
Sbjct: 103 PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQYPHLIEEILKEVVGAVDVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D +      RN V   K  ++ G+  + +H R    + KG +         
Sbjct: 163 VTLKTRTGWDTEN-----RNCVDIAKLAEQCGIQALALHGRTKACMYKGEA--------- 208

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  
Sbjct: 209 -EYDYIRAVKQAVTIPVIA-NGDIDSPEKARFVLDYTGADALMIGRPAQGKPWIFREIHH 266

Query: 232 YFS 234
           Y +
Sbjct: 267 YLT 269


>gi|261344930|ref|ZP_05972574.1| tRNA-dihydrouridine synthase B [Providencia rustigianii DSM 4541]
 gi|282567071|gb|EFB72606.1| tRNA-dihydrouridine synthase B [Providencia rustigianii DSM 4541]
          Length = 331

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 58/242 (23%), Positives = 110/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TD+ +R     +    +  +EM+ ++  + + DK  +      E  + ++QI G D
Sbjct: 23  MAGITDKPFRTLCYAM-GAGMTVSEMLSSNPQVWKTDKSKLRMVHRDELGVRSVQIAGND 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P+IV   +  + K++ +P
Sbjct: 82  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPEIVKSILETVVKSVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   K  +  G+  + IH R    +  G           
Sbjct: 142 VTLKIRTGWSPE-----ERNCIEIAKLAEDCGIQALTIHGRTRACLFNG----------E 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +M+GRAA     +   +  
Sbjct: 187 AEYDNIRAV-KQTVSIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQH 245

Query: 232 YF 233
           Y 
Sbjct: 246 YL 247


>gi|254389020|ref|ZP_05004250.1| dihydrouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|197702737|gb|EDY48549.1| dihydrouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 391

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 16/231 (6%)

Query: 18  NNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY- 74
              L  +EMI   A++  ++K   ++ F   E P ++Q+ G D   + +A +++ D G  
Sbjct: 54  GKGLFVSEMITTRALVERNEKTMQLIHFDASETPRSIQLYGVDPVTVGKAVRMIVDEGLA 113

Query: 75  NEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           + I+LN GCP  +V     G+ L    P +      A+  A  +PVT+K R G+DD    
Sbjct: 114 DHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSNAGQLPVTMKMRKGIDDD--H 171

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  +     GV  I +H R A                D++ +  +K+  P++ +  
Sbjct: 172 LTFLDAGRIAVDEGVTAIALHGRTAA--------QHYGGTADWEAIARLKEHVPEIPVLG 223

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG +     AL+++     DGV++GR       +   +   F    + ++P
Sbjct: 224 NGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFGDLVSAFEGDGSAAAP 274


>gi|297794265|ref|XP_002865017.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297310852|gb|EFH41276.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 423

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 21/230 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   +     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 95  MVDNSELPFRLLCQKYGAQAA-YTPMLHSRIFTETEKYRNQEFTTCKEDRPLFVQFCAND 153

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAAK VE +  + +++N+GCP      G++GA LM N  +V   +  + + L++P
Sbjct: 154 PDTLLEAAKRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLAQNLNVP 212

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K RI   + D +         K ++ +G + + +H R         KD +K+   D+
Sbjct: 213 VSCKIRIFPNLQDTL------KYAKMLEDAGCSLLAVHGRTR-----DEKDGKKL-RADW 260

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
             + E+K     P L  G    +ED+   +K    V+GV+      +N A
Sbjct: 261 SAIKEVKNALRIPVLGNGNVRCIEDVDNCIKET-GVEGVLSAETLLENPA 309


>gi|297517944|ref|ZP_06936330.1| tRNA-dihydrouridine synthase A [Escherichia coli OP50]
          Length = 77

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/52 (55%), Positives = 38/52 (73%), Gaps = 1/52 (1%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL 52
          M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G K + L +S +E P+AL
Sbjct: 27 MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHG-KGDYLAYSEEEHPVAL 77


>gi|195166832|ref|XP_002024238.1| GL14922 [Drosophila persimilis]
 gi|198468810|ref|XP_002134128.1| GA26573 [Drosophila pseudoobscura pseudoobscura]
 gi|194107611|gb|EDW29654.1| GL14922 [Drosophila persimilis]
 gi|198146581|gb|EDY72755.1| GA26573 [Drosophila pseudoobscura pseudoobscura]
          Length = 463

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 87/184 (47%), Gaps = 23/184 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D ++ +   K+++    + +++N+GCP     +G  GA L+ +PD     + 
Sbjct: 87  LVLQMGTSDATRALAVGKLLQQ-DISGLDINMGCPKEFSIKGGMGAALLADPDKAALILR 145

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +C  L IPVT K RI   +DD I      +LV+ +  +G+  I IHAR         +D
Sbjct: 146 TLCSNLDIPVTCKIRILPDLDDTI------SLVQKLADTGIAAIGIHART--------RD 191

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKN 222
            R       D++  + K      I  NGG  ++ +   IL        D VM+ RAA  N
Sbjct: 192 ERPQHPPHPDVLRAVAKAVSIPIIA-NGGSRNVQKYEDILKFQLECGADSVMVARAAQIN 250

Query: 223 SAML 226
            ++ 
Sbjct: 251 VSIF 254


>gi|161506862|ref|YP_001576816.1| putative tRNA-dihydrouridine synthase [Lactobacillus helveticus DPC
           4571]
 gi|160347851|gb|ABX26525.1| putative tRNA-dihydrouridine synthase [Lactobacillus helveticus DPC
           4571]
          Length = 342

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 112/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYIDQHTDADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK R G D +    A+ 
Sbjct: 101 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRTGWDKK-HVFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D++I++++ +     F+  NG
Sbjct: 160 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEILHDVAQVLDVPFVA-NG 207

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y   
Sbjct: 208 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMTHYLET 249


>gi|300859124|ref|YP_003784107.1| hypothetical protein cpfrc_01707 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686578|gb|ADK29500.1| hypothetical protein cpfrc_01707 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302331381|gb|ADL21575.1| TIM-barrel containing enzyme [Corynebacterium pseudotuberculosis
           1002]
          Length = 384

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 69/286 (24%), Positives = 123/286 (43%), Gaps = 27/286 (9%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           R  T + L   EMI A A++  ++K  ++  F  QE   +LQ+   D     +AAK++ D
Sbjct: 41  RTGTVSGLYICEMITARALVHRNEKTLHMTTFGPQEDVRSLQLYTVDPEYTFKAAKMIAD 100

Query: 72  FGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGV 127
            G  + I++N GCP  +V +   G+ L     + G+ IAA  K +   +IPVTVK R+G+
Sbjct: 101 EGIADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGNIIAAAVKGVEGTNIPVTVKFRMGI 160

Query: 128 D-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           D D +  +   +  +   + G   + +HAR A          R   +  +D + ++K+  
Sbjct: 161 DHDHLTHL---DAGRIAAEEGAAAVTLHARTAA--------ERYSGDAHWDEIGKLKEHL 209

Query: 187 PDLFIGL--NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
               I +  NG +   + A+ ++ +   DGV++GR       +   +            P
Sbjct: 210 AHTGIPVLGNGDIFKPTDAIDMIKASGCDGVVVGRGCLGRPWLFAGLSAAMRGKEIPPEP 269

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
               V +  +R       +    H       + + +HM     GFP
Sbjct: 270 TLGEVTRIIYRH-----AELLVEHEGETKGCRDMRKHMGWYLRGFP 310


>gi|195114456|ref|XP_002001783.1| GI15082 [Drosophila mojavensis]
 gi|193912358|gb|EDW11225.1| GI15082 [Drosophila mojavensis]
          Length = 510

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 111/240 (46%), Gaps = 31/240 (12%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R   R     L  + + +  +   D   R   K+ L    +++PL +Q  G
Sbjct: 30  MVDQSELAWRMLCRRYGAQLCYSPMYHANLFATDLKYR---KDALQTCPEDRPLIIQFCG 86

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  +++EAA   +D   + +++N+GCP A    G +G+ L    +++ D +  + + LS
Sbjct: 87  NDPQQILEAALAAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTDIVRTLHEKLS 145

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIP 172
           +PVT K R   +D+   +      K ++ +G   + IH R    K  L G++        
Sbjct: 146 VPVTCKIR-RFEDREKTI---QYAKMLEAAGCQLLTIHGRTREQKGPLTGIA-------- 193

Query: 173 NLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             D+  + ++ +E+  + +  NG   GL+D+ + L     VDGVM       N A+   +
Sbjct: 194 --DWSYIKDV-REHIKIPMFANGNILGLDDVHRCLDET-GVDGVMSAEGNLHNPAIFQGI 249


>gi|323465811|gb|ADX69498.1| tRNA-dihydrouridine synthase B [Lactobacillus helveticus H10]
          Length = 342

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 112/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 41  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYIDQHTDADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK R G D +    A+ 
Sbjct: 101 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRTGWDKK-HVFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D++I++++ +     F+  NG
Sbjct: 160 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEILHDVAQVLDVPFVA-NG 207

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y   
Sbjct: 208 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMTHYLET 249


>gi|255079532|ref|XP_002503346.1| tRNA-dihydrouridine synthase [Micromonas sp. RCC299]
 gi|226518612|gb|ACO64604.1| tRNA-dihydrouridine synthase [Micromonas sp. RCC299]
          Length = 353

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 115/252 (45%), Gaps = 19/252 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R        YT MI A   +   K  K I      ++PL +Q    D
Sbjct: 42  MVDQSELAFRELCRR-HGATCAYTPMIHARLFVEDLKYRKEIFTTHINDRPLLVQFCAND 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AA IV     + +++N GCP      G +GA LM + + V + I  + K LS+P
Sbjct: 101 PDMLLKAASIVAPHC-DGVDINFGCPQRIAKRGRYGAFLMDDWETVHNLINKLDKHLSVP 159

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +    +L+   K ++ +G   I +H R    K  +  D R     ++  
Sbjct: 160 VTAKIRVYDDLE---TSLK-YAKMVEAAGAQLIAVHGRTREQKRAA--DVRA----NWAF 209

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK+   + +  NG +  +++A K L +   DGV+      +N ++ +  D    +P
Sbjct: 210 IREIKKQL-KVPVLANGDIRTLAEAEKCLEATGADGVLSAEPLLENPSLFS--DPPLYSP 266

Query: 237 LTGSSPIKTRVD 248
              + P+    D
Sbjct: 267 SDPAHPLPVEGD 278


>gi|104773526|ref|YP_618506.1| putative tRNA-dihydrouridine synthase [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|103422607|emb|CAI97210.1| Putative tRNA-dihydrouridine synthase [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
          Length = 344

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 110/222 (49%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEI 77
           ++  EMI    I+ G+KK  ++L     E P+++QI GGA+ S L  A  I +    + I
Sbjct: 42  MVVCEMISDHGIIYGNKKTLSMLDVDPGEHPMSIQIFGGAEDSLLQAAQYIDQHTDADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   I  +   +  PV+VK RIG D +    A+ 
Sbjct: 102 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVHNVEKPVSVKMRIGWDRK-HIFAVE 160

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+ +     F+  NG
Sbjct: 161 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVAQVMDIPFVA-NG 208

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y + 
Sbjct: 209 DITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 250


>gi|323699589|ref|ZP_08111501.1| dihydrouridine synthase DuS [Desulfovibrio sp. ND132]
 gi|323459521|gb|EGB15386.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans ND132]
          Length = 348

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 113/253 (44%), Gaps = 30/253 (11%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEI 77
           L +TEM  A ++         +  +   E P L  Q+ GA   +++ AA+ V++ G+   
Sbjct: 56  LTFTEMCGAKSLPTESPLVSPVFRWRAAELPRLVCQVAGATPEQMIPAARRVQECGFFGF 115

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-PAVAL 136
           ++N+GC  + + + + GA L+ +PD     +  + +A+SIP+ VK R G    I PAVA 
Sbjct: 116 DINMGCSVSGIIKKNAGAALLRDPDAALRVVEGVRRAISIPLFVKFRTGWTPDIGPAVA- 174

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L +  + +GV+ +  H R A        D R  P +   I   +   +  +F   NG 
Sbjct: 175 --LARRFEDAGVDCLVFHPRVA-------PDKRTRPPVREHIRAVVDAVSIPVFG--NGD 223

Query: 197 LEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           +      L +L +    GV +GR A     +       F+   TG +P  T      +R 
Sbjct: 224 VVSPEDCLDMLRTTGCAGVSVGRTAIARPWL-------FAQWTTGQTPPAT-----CFRD 271

Query: 255 ISASMTDYAARHL 267
            + ++ D  +RH 
Sbjct: 272 YALNLADALSRHF 284


>gi|326502988|dbj|BAJ95927.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 430

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 106/233 (45%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 101 MVDNSELPFRMLCRRYGADAA-YTPMLHSRIFSENEKHRDMEFTTCKEDRPLFVQFCAND 159

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAK+VE    + ++LN GCP      G +GA LM N  +V   +  +   L +P
Sbjct: 160 PDILLQAAKMVE-ANCDYVDLNFGCPQRIAKRGYYGAFLMDNLPLVKSLVQNLAGNLRVP 218

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K RI   ++D +         K ++++G   + +H R         KD +K    D+
Sbjct: 219 VSCKIRIFPRLEDTL------AYAKMLEEAGAALVAVHGRTR-----DEKDGKKF-RADW 266

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           D +  +K     P L  G    +ED+   L+     DGV+      +N A+  
Sbjct: 267 DAIKAVKDALRIPVLANGNIRHMEDVKSCLQHT-GADGVLSAEPLLENPALFA 318


>gi|325002690|ref|ZP_08123802.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudonocardia
           sp. P1]
          Length = 394

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 74/301 (24%), Positives = 124/301 (41%), Gaps = 36/301 (11%)

Query: 12  FARLLTNNALLY--TEMIVADAILRGDKKN-----ILGFSTQEKPLALQIGGADISKLVE 64
           F RL       Y   EMI A  ++   +KN     ++ F   E P ++Q+ G D   +  
Sbjct: 50  FRRLCREQGAGYYVCEMITARGLV---EKNPLTFRMIAFDADEHPRSMQLYGVDPDSMRR 106

Query: 65  AAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVK 122
           AA+ IVE    + I++N GCP  +V     GA L     +    ++A  + A   PVTVK
Sbjct: 107 AAQMIVERDLADHIDMNFGCPVPKVTRRGGGAALPFKRKLFERIVSAAVEGAGDRPVTVK 166

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG+DD        +  +    SG   + +HAR A          R     D+D +  +
Sbjct: 167 MRIGIDDD--HHTYLDAARIAVDSGAVAVALHARTA--------SQRYSGQADWDAISRL 216

Query: 183 KKENPDLFIGL-NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           ++  P     L NG +     AL ++     DGV++GR       +   ++  F+     
Sbjct: 217 REHVPAHVPVLGNGDIFSAQDALDMVARTGCDGVVVGRGCLGRPWLFGDLEAAFAGRELP 276

Query: 240 SSPIKTRVDKDFWRKISASMTDYA---ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           + P       D   +++A++  +A     H+     ++ + +H+     GFP     R  
Sbjct: 277 APP-------DLG-QVAATLRRHAVLLCEHMGDHKGIRDVRKHIAWYLKGFPVGPELRRS 328

Query: 297 L 297
           L
Sbjct: 329 L 329


>gi|182624205|ref|ZP_02951991.1| dihydrouridine synthase family protein [Clostridium perfringens D
           str. JGS1721]
 gi|177910619|gb|EDT72987.1| dihydrouridine synthase family protein [Clostridium perfringens D
           str. JGS1721]
          Length = 321

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 109/237 (45%), Gaps = 21/237 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHREELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   + +++K R+G+D          L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKIDDMKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  PNL+ +     + K NP  + G    LED ++ ++    VD +M+GR    N A++ 
Sbjct: 173 K--PNLEVFKDAISLSK-NPVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALM- 228

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  N +  +  +   V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 229 -------NEILNNEFMDKNVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|227894508|ref|ZP_04012313.1| tRNA-dihydrouridine synthase [Lactobacillus ultunensis DSM 16047]
 gi|227863667|gb|EEJ71088.1| tRNA-dihydrouridine synthase [Lactobacillus ultunensis DSM 16047]
          Length = 341

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 113/221 (51%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ ++     +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEDTLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVEKPVSVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+++++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGKA----------DWEVLHDVAQALNIPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A K L  +    VM+GRAA  N  +L  +  Y  
Sbjct: 207 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLE 247


>gi|218710863|ref|YP_002418484.1| tRNA-dihydrouridine synthase B [Vibrio splendidus LGP32]
 gi|218323882|emb|CAV20243.1| tRNA-dihydrouridine synthase B [Vibrio splendidus LGP32]
          Length = 325

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/195 (26%), Positives = 91/195 (46%), Gaps = 23/195 (11%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+     G   I++N+GCP+ +V++   G+ L+ +P+++ D + A
Sbjct: 71  SVQIAGADPQLMAEAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQHPELIEDILKA 130

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSP 165
           +  A+ +PVT+K R G D        RN V+  K     G+  + +H R    + KG + 
Sbjct: 131 VVNAVDVPVTLKTRTGWDTDN-----RNCVQIAKIAEDCGIQALALHGRTRACMYKGEAE 185

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             + K             K+   + +  NG ++   +A  +L     D +MIGR A    
Sbjct: 186 YKHIK-----------AAKQAVSIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRP 234

Query: 224 AMLTTVDEYFSNPLT 238
            +   +  Y  N  T
Sbjct: 235 WIFNEILHYLENGTT 249


>gi|160947348|ref|ZP_02094515.1| hypothetical protein PEPMIC_01282 [Parvimonas micra ATCC 33270]
 gi|158446482|gb|EDP23477.1| hypothetical protein PEPMIC_01282 [Parvimonas micra ATCC 33270]
          Length = 316

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 109/223 (48%), Gaps = 25/223 (11%)

Query: 20  ALLYTEMIVADAILR-GDKKNILGF-STQEKPLALQIGGAD---ISKLVEAAKIVEDFGY 74
            L +TEM+    +    DK +I+ +   +E P+ LQ+ G+D   ++++++      D  Y
Sbjct: 29  GLTFTEMVSIKGLYYDNDKTSIITYIDKREGPVGLQVFGSDENIMAEIIQNRFNKRDDIY 88

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
            +++LN+GCP+ ++ +   G+ LM +P  V   ++AM K   +PV+VK R+G D+     
Sbjct: 89  -QLDLNLGCPAPKIVKNHEGSYLMKDPKKVKTIVSAMVKNSKVPVSVKIRLGFDEN--NK 145

Query: 135 ALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
               +  +I ++G   I +HA  R+    G +          D++ +  +K   P   +G
Sbjct: 146 NFLEVADAIVEAGAYMITLHARTREMFYSGKA----------DWNAIKTLKNHVPIKVVG 195

Query: 193 LNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            NG    +ED  + +K     D V IGR A  N  +   + +Y
Sbjct: 196 -NGDVCSVEDYVR-MKEETGADAVAIGRHALGNPFIFKQIKDY 236


>gi|270158229|ref|ZP_06186886.1| putative tRNA-dihydrouridine synthase [Legionella longbeachae
           D-4968]
 gi|289163514|ref|YP_003453652.1| tRNA-dihydrouridine synthase B [Legionella longbeachae NSW150]
 gi|269990254|gb|EEZ96508.1| putative tRNA-dihydrouridine synthase [Legionella longbeachae
           D-4968]
 gi|288856687|emb|CBJ10498.1| putative tRNA-dihydrouridine synthase B [Legionella longbeachae
           NSW150]
          Length = 319

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 49/179 (27%), Positives = 90/179 (50%), Gaps = 20/179 (11%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +E+ LA Q+ G +   L +AA+ ++ +G + I++N GCP  ++ +   G+ L+  PD 
Sbjct: 70  APEEQILAYQLAGTEPHLLAQAAQNLQRYGADIIDINCGCPKPKIRKKGAGSALLEAPDQ 129

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +  +  A++IP+TVK RI  ++Q   +A     K I+++G + + +H R+ +    
Sbjct: 130 LVKIVKEVRAAITIPLTVKIRIQGNEQDFILA-----KKIQEAGADALIVHGRRWM---- 180

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRA 218
              D    P+L     ++I      L I +  NG + D+    K   L   D  MI RA
Sbjct: 181 --DDYEVTPDL-----HQIACIKQRLVIPVIANGDIHDLDSLKKTIALSGCDAYMISRA 232


>gi|323507663|emb|CBQ67534.1| related to tRNA dihydrouridine synthase [Sporisorium reilianum]
          Length = 362

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/302 (22%), Positives = 128/302 (42%), Gaps = 63/302 (20%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDI 103
           Q  P  +Q+ G D+ +LVEA++ V  F  + I+LN+GCP     +G +GA L+   N  +
Sbjct: 84  QAAPQIVQLAGNDVQQLVEASRKVAPFA-DAIDLNLGCPQRHAEQGHYGAYLLPKQNWPL 142

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI---- 159
           + + ++ + +A+ +P+T K R+ V    P    + L  ++ ++G + + +H R A     
Sbjct: 143 LAEIVSGLAQAVDVPITTKIRLTV----PKEQTQQLAVTLARAGSSLVTLHPRFASSVRR 198

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK-----------ENP--DLFIGLNGGLEDMSQALKI 206
            KGL+          D D V  +++           + P  D  +  NG +      +  
Sbjct: 199 RKGLA----------DLDQVVHVREALQAEGLLRSADQPCGDTAVVSNGNVRCWCDIVDN 248

Query: 207 LPSV--DGVMIGRAAYKNSAM----LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMT 260
           L S    GVM+G    +N A+    ++ +D        G+SP          + ++    
Sbjct: 249 LASTGASGVMVGETLLENPALFHPSISEIDR------VGTSP----------KDMALEYL 292

Query: 261 DYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           D   R+ H    L+   +H+  +    P +       T     + A HH    +   +I+
Sbjct: 293 DLRDRYDHFESPLKVAKQHLQSILGSIPYT-------TSTGPDNIAEHHRFAASMTHIIK 345

Query: 321 SL 322
           S+
Sbjct: 346 SM 347


>gi|89093255|ref|ZP_01166205.1| NifR3/Smm1 family protein [Oceanospirillum sp. MED92]
 gi|89082551|gb|EAR61773.1| NifR3/Smm1 family protein [Oceanospirillum sp. MED92]
          Length = 298

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 118/243 (48%), Gaps = 19/243 (7%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ LQ+ G+D S L   A+     G   I+LN GCP+  V+    GA L+  P
Sbjct: 42  GRTPSGTPVILQLLGSDPSVLAGNARKGAKLGAPGIDLNFGCPAKTVNRSKGGAVLLDTP 101

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++ + + A+ +A+   +PV+ K R+G  D+  ++A+ N   +IK +G + + +HAR   
Sbjct: 102 ELIYEIVKAVREAVPEGVPVSAKMRLGNKDK--SLAMEN-AHAIKDAGADSLAVHARTK- 157

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGR 217
           L+G  P  +       ++ +  I +E  D+ +  NG +   D  Q  + +   D VMIGR
Sbjct: 158 LEGYKPPAH-------WEWISRI-REAIDIPVVANGEVWSWDDYQRCREVSGCDDVMIGR 209

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  +   +  +  N  + +S     V K     ++    D AA+++H  G+++Q  
Sbjct: 210 GLIAKPDLAKVIKHHQVNE-SFTSFNWDHVLKLVELYLNRIEQDIAAKYVH--GRIKQWL 266

Query: 278 RHM 280
            H+
Sbjct: 267 HHL 269


>gi|86147886|ref|ZP_01066191.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
 gi|85834313|gb|EAQ52466.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
          Length = 322

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 89/193 (46%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   + EAA+     G   I++N+GCP+ +V++   G+ L+ +P+++ D + A
Sbjct: 68  SVQIAGADPQLMAEAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQHPELIEDILKA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKD 167
           +  A+ +PVT+K R G D        RN V+  K     G+  + +H R          +
Sbjct: 128 VVNAVDVPVTLKTRTGWDTDN-----RNCVQIAKIAEDCGIQALALHGRTRACMYKGEAE 182

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
            + I         +  K+   + +  NG ++   +A  +L     D +MIGR A     +
Sbjct: 183 YKHI---------KAAKQAVSIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWI 233

Query: 226 LTTVDEYFSNPLT 238
              +  Y  N  T
Sbjct: 234 FNEILHYLENGTT 246


>gi|281355584|ref|ZP_06242078.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
 gi|281318464|gb|EFB02484.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
          Length = 334

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 111/247 (44%), Gaps = 30/247 (12%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISK 61
           +TD  YR  AR        +TEM+   ++    +++  +L    +E+ L +Q+ GAD   
Sbjct: 17  FTDLPYRRAARA-GGCRFAFTEMVDVASLTYARERSAGMLRRGPEEEFLGVQLVGADHEF 75

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +  AA +V ++ ++ ++ N+GCP  +V +   GA L  + D    C A + +    PVT 
Sbjct: 76  IRRAADVVNEYEFSVVDFNLGCPVPKVAKKGAGAELGRHLDAALACFAIIAERSRHPVTA 135

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIV 179
           K RI VD + PA  L  L K + + G   I +H R  +A   G           +++ ++
Sbjct: 136 KIRI-VDAEDPAPTL-ALAKGLAELGAQAITVHGRIKEAFYSG----------PVNFGMI 183

Query: 180 YEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTT--------- 228
             +++  P + +  NGG+      Q ++       VM+ R A  N  +            
Sbjct: 184 RAVREALPGVQVIANGGVTGRVKYQEIRRETGCSLVMLARGAMGNPWLFNELSLGDAYVP 243

Query: 229 --VDEYF 233
             +DE+F
Sbjct: 244 PDIDEWF 250


>gi|295657937|ref|XP_002789532.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb01]
 gi|226283236|gb|EEH38802.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb01]
          Length = 563

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/175 (30%), Positives = 81/175 (46%), Gaps = 12/175 (6%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  T ++PL +Q    D  +L+ AA+ VE F  + ++LN+GCP     +G +GA L   P
Sbjct: 108 GNPTIDRPLIVQFCANDPDELLHAARTVEPF-CDAVDLNLGCPQGIARKGHYGAFLQEEP 166

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +++   I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 167 ELIYKLINTLHTELSIPVTAKFRI----QETKEKTLEYARMILSAGASFISVHGRRRDQK 222

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
           G     N  + +  Y I Y       D  I  NG + D    ++ L +   DGVM
Sbjct: 223 G----HNTGLADWSY-IRYLRDNLPADTVIFANGNILDNRDIMRCLEATGADGVM 272


>gi|294812524|ref|ZP_06771167.1| Putative dihydrouridine synthase [Streptomyces clavuligerus ATCC
           27064]
 gi|326441023|ref|ZP_08215757.1| dihydrouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|294325123|gb|EFG06766.1| Putative dihydrouridine synthase [Streptomyces clavuligerus ATCC
           27064]
          Length = 417

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 16/231 (6%)

Query: 18  NNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY- 74
              L  +EMI   A++  ++K   ++ F   E P ++Q+ G D   + +A +++ D G  
Sbjct: 80  GKGLFVSEMITTRALVERNEKTMQLIHFDASETPRSIQLYGVDPVTVGKAVRMIVDEGLA 139

Query: 75  NEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           + I+LN GCP  +V     G+ L    P +      A+  A  +PVT+K R G+DD    
Sbjct: 140 DHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSNAGQLPVTMKMRKGIDDD--H 197

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   +  +     GV  I +H R A                D++ +  +K+  P++ +  
Sbjct: 198 LTFLDAGRIAVDEGVTAIALHGRTAA--------QHYGGTADWEAIARLKEHVPEIPVLG 249

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           NG +     AL+++     DGV++GR       +   +   F    + ++P
Sbjct: 250 NGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFGDLVSAFEGDGSAAAP 300


>gi|78358129|ref|YP_389578.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
 gi|78220534|gb|ABB39883.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 376

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/217 (27%), Positives = 102/217 (47%), Gaps = 18/217 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKP-LALQIGGADISKLVEA 65
           YR          L++T M  A A+   +  +  +  +  +E P L  Q+ GAD   +  A
Sbjct: 72  YRQVLESFGGCGLVFTGMCSARAVPTENPARSPVFSWRPEELPALVCQLFGADPQDMAAA 131

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ VE  G+  +++N+GC  A + +   GA L+ +P+     + A+ +A+S+PV VK R 
Sbjct: 132 ARRVESEGFFGVDINMGCSVAPIVKKGCGADLLRDPERAVRMVDAVRRAVSVPVFVKMRT 191

Query: 126 G-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G   D  PAV   NL + ++ +G + +  H R      ++P      P   +     + K
Sbjct: 192 GWSPDPEPAV---NLARRLQDAGADALVFHPR------VAPDRRTHRPRTAH---IGLVK 239

Query: 185 ENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           +  D+ +  NG + D +    +L     DGV +GR A
Sbjct: 240 DAVDIPVIGNGDVFDAADCAAMLERTGCDGVSLGRLA 276


>gi|226295110|gb|EEH50530.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 556

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 85/189 (44%), Gaps = 12/189 (6%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  T ++PL +Q    D  +L+ AA+ VE F  + ++LN+GCP     +G +G+ L   P
Sbjct: 107 GNPTIDRPLIVQFCANDPDELLHAARTVEPF-CDAVDLNLGCPQGIARKGHYGSFLQEEP 165

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +++   I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 166 ELIYKLINILHTHLSIPVTAKFRI----QETKEKTLEYARMILSAGASFISVHGRRRDQK 221

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           G     N  + +  Y I Y       D  I  NG + D    ++ L +   DGVM     
Sbjct: 222 G----HNTGLADWSY-IRYLRDNLPADTVIFANGNILDHGDIIRCLEATGADGVMSAEGN 276

Query: 220 YKNSAMLTT 228
             +  + TT
Sbjct: 277 LCDPTIFTT 285


>gi|110801357|ref|YP_695925.1| dihydrouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|110676004|gb|ABG84991.1| dihydrouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
          Length = 321

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/239 (23%), Positives = 110/239 (46%), Gaps = 25/239 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  A+ ++  GYNEINLN+GCPS  V     G+  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFISTARKLKQLGYNEINLNLGCPSGTVVGKKRGSGFLAHKEELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            + K   + +++K R+G+D          L+K   K  +  + IH R       + +D  
Sbjct: 121 EIFKIDDMKLSIKTRLGMDK---PEEFYELIKIYNKYPMEELIIHPR-------TRQDFY 170

Query: 168 -NRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
            N+  PNL+ +     + K NP  + G    +ED ++ ++  P VD +M+GR    N A+
Sbjct: 171 ANK--PNLEVFKDAISLSK-NPICYNGDIFTVEDHNKLIETFPEVDKIMLGRGILANPAL 227

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +        N +  +  +  +V K+F  ++     +      ++  +++++  +MI +F
Sbjct: 228 M--------NEILNNEFMDKKVLKEFHDEVFNKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|328949131|ref|YP_004366468.1| TIM-barrel protein, nifR3 family [Treponema succinifaciens DSM
           2489]
 gi|328449455|gb|AEB15171.1| TIM-barrel protein, nifR3 family [Treponema succinifaciens DSM
           2489]
          Length = 336

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 113/243 (46%), Gaps = 21/243 (8%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNE 76
           +L  TEM+ A+A++RG+KK   ++  +  EK   +QI G +   + EAAKIV E    + 
Sbjct: 41  SLCTTEMVSAEALVRGNKKTELLMRRAPNEKVYCVQIFGGNAQTMAEAAKIVLEKTDCDC 100

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-----------SIPVTVKCRI 125
           I++N GCP  ++ +   G+ L   P+ +   + A+ ++            ++PVT+K R 
Sbjct: 101 IDINGGCPVPKITKTGAGSVLTKEPERLFSIVKAVKESSIKYTSLHPERGNVPVTIKIRS 160

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D     +  +    +  K+G + I IHAR    +G S K + +I      +V  + K 
Sbjct: 161 GWDSS--NITWKECADAALKAGADAITIHARTKA-QGYSGKADWEIQK---RLVEFVAKR 214

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
            P +F   +    + ++ +     VD VM  R A  +  +     ++ +     +   K 
Sbjct: 215 IP-VFGSGDAFNPETAKLMLEQTGVDAVMFARGAMGDPFLFRRTKQFLTEGKYETETPKE 273

Query: 246 RVD 248
           R++
Sbjct: 274 RLE 276


>gi|326384894|ref|ZP_08206569.1| TIM-barrel protein, nifR3 family [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326196413|gb|EGD53612.1| TIM-barrel protein, nifR3 family [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 390

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 70/296 (23%), Positives = 122/296 (41%), Gaps = 23/296 (7%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK-I 68
            AR  T + L   EM+ A A++       ++  F   E P ++Q+   D     +AAK I
Sbjct: 47  LARTGTVSGLYVCEMVTARALVERHPVTMHMTAFDPSETPRSMQLYTVDPEYTYQAAKMI 106

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
           V++   + I++N GCP  +V     G+ +     +  + +AA  +A     IPVTVK RI
Sbjct: 107 VDENLADHIDMNFGCPVPKVTRKGGGSAIPYKRRLFRNIVAAAVRATEGTDIPVTVKFRI 166

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD        +  +     G   + +HAR A          R      +D +  +K+ 
Sbjct: 167 GIDDD--HHTHLDAGRIAAAEGAQAVALHARTA--------SQRYSGTAAWDEIARLKEH 216

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
             D+ +  NG + +   A++++     DGV+IGR       +   +          + P 
Sbjct: 217 VTDVPVLGNGDIFEAEDAVRMMAQTGCDGVVIGRGCLGRPWLFAELSARLRGVEAPTPPN 276

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              V +   R       +  A H   G  +++I +H+     GFP     R  L++
Sbjct: 277 LGEVAEIMIRH-----GELLAAHHGEGKGMREIRKHVAWYLRGFPAGSDLRSSLSL 327


>gi|255725686|ref|XP_002547772.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
 gi|240135663|gb|EER35217.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
          Length = 252

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 80/169 (47%), Gaps = 13/169 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-------KNILGFSTQEKPLALQ 53
           MVD ++  +R  +R     AL YT M  A      +K       K + G    ++PL +Q
Sbjct: 37  MVDHSELAWRILSRRY-GAALCYTPMFNAKLFATQEKYRDSMWTKGLDGNEKLDRPLVVQ 95

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
               D   L+ AA+ +ED   + +++N+GCP     +G +GA LM + +++   I  +  
Sbjct: 96  FCANDPDYLLTAARFIED-QCDAVDINLGCPQGIARKGRYGAFLMDDWELIHKLIRNLHD 154

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            L IPVT K RI  DD   ++      K +  +G   I IH R   +KG
Sbjct: 155 NLKIPVTAKIRI-YDDYEKSL---EYAKMVLDAGAQFITIHGRTREMKG 199


>gi|125556734|gb|EAZ02340.1| hypothetical protein OsI_24443 [Oryza sativa Indica Group]
          Length = 396

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/233 (25%), Positives = 106/233 (45%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 69  MVDNSELPFRMLCRRYGATGA-YTPMLHSRIFSENEKHRAMEFTTCKEDRPLFVQFCAND 127

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE +  + +++N GCP      G +GA LM N  ++   +  +   L +P
Sbjct: 128 PDILLQAAKIVEPYC-DYVDINFGCPQRIARRGYYGAFLMDNLPLIKSLVQNLSANLHVP 186

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K RI   ++D +         K ++++G + + +H R         KD +K    D+
Sbjct: 187 VSCKIRIFPRLEDTLA------YAKMLEEAGASLVAVHGRTR-----DEKDGKKF-RADW 234

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           D +  +K     P L  G    L+D+   L+     DGV+      +N A+  
Sbjct: 235 DAIKAVKDALRIPVLANGNIRHLDDVKDCLEHT-GADGVLSAETLLENPALFA 286


>gi|158296576|ref|XP_316960.4| AGAP008484-PA [Anopheles gambiae str. PEST]
 gi|157014776|gb|EAA12777.4| AGAP008484-PA [Anopheles gambiae str. PEST]
          Length = 560

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 110/238 (46%), Gaps = 25/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +  K  K+ L    +++PL +Q  G D
Sbjct: 48  MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFTKDPKYRKDSLQTCPEDRPLIIQFCGND 106

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++EAA + +D   + I++N+GCP A    G +GA L    +++ + ++ + + L+IP
Sbjct: 107 PKIMLEAALLAQDHC-DAIDINLGCPQAIAKRGHYGAFLQDEWELLREIVSTLHRHLAIP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D    A  +R   + ++ +G   + +H R    K  L GL+          
Sbjct: 166 VTCKIRIFEDM---AKTIR-YARMLQDAGAQMLTVHGRTRDQKGPLTGLA---------- 211

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVD 230
           D+  V  + ++   + I  NG +  +    + +    V+GVM       N A+   V+
Sbjct: 212 DWKYV-RVLRQQLSIPIFSNGNIMSVHDVERCIAETGVNGVMTAEGNLHNPALFEGVN 268


>gi|254284133|ref|ZP_04959101.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR51-B]
 gi|219680336|gb|EED36685.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR51-B]
          Length = 320

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 46/130 (35%), Positives = 67/130 (51%), Gaps = 18/130 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           L GD K   G      P+ +Q+ G+D + + + A +    G   I+LN GCP+  V++ S
Sbjct: 53  LLGDGKTAAGI-----PVYVQLLGSDPALMADNAAVAARLGAPGIDLNFGCPAKTVNKSS 107

Query: 93  FGACLMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
            GA L+  P      IAA+C A+      SIPVT K R+G  D        ++V ++  S
Sbjct: 108 GGAILLRQPQR----IAAICTAVRATVPASIPVTAKIRLGYADDD---GFEDVVDAVADS 160

Query: 147 GVNGIWIHAR 156
           GV+ I IHAR
Sbjct: 161 GVSEITIHAR 170


>gi|315222400|ref|ZP_07864305.1| TIM-barrel protein, nifR3 family [Streptococcus anginosus F0211]
 gi|315188561|gb|EFU22271.1| TIM-barrel protein, nifR3 family [Streptococcus anginosus F0211]
          Length = 323

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 110/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTQTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYSIINKVRSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   ++A+ N + +          +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--ASLAVENALAAEAAGVAALA-MHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++ + +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHNVAQALTKIPFIANGDIRTVQDAQQRIEEVGADAVMIGRAAMGNPYLFHQINHYFE 250


>gi|302386025|ref|YP_003821847.1| dihydrouridine synthase DuS [Clostridium saccharolyticum WM1]
 gi|302196653|gb|ADL04224.1| dihydrouridine synthase DuS [Clostridium saccharolyticum WM1]
          Length = 320

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 79/176 (44%), Gaps = 25/176 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            + AAK ++ +GY E+NLN+GCPS  V     GA  +  PD++      +  AL + V+V
Sbjct: 73  FIWAAKELKRYGYEEVNLNLGCPSPTVVSKGRGAGFLGEPDLLEAFFDQIFSALDMKVSV 132

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL--------SPKDNRKIPN 173
           K RIG D    +     L++   K  +  + +H R  I K          S KD   I N
Sbjct: 133 KTRIGKDS---SEEFGRLMEIYNKYPIEELIVHPR--IQKDFYRNEPDWKSVKDAVSISN 187

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             + + Y     N +LF       ED  +     PS+D VM+GR    N  ++  +
Sbjct: 188 --FPLCY-----NGNLF-----SAEDFERFTADFPSIDRVMLGRGLVANPGLVRKI 231


>gi|224074477|ref|XP_002197358.1| PREDICTED: dihydrouridine synthase 1-like (S. cerevisiae)
           [Taeniopygia guttata]
          Length = 486

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---DKKNILGFSTQE-KPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   LR     ++N+ G +  E +PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRRENLYGEACPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLANEKLS 141

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +P+T K RI  D D+    A     + ++K+G   + +H R    KG
Sbjct: 142 VPITCKIRIFPDIDKTVKYA-----QMLEKAGCQLLTVHGRTKEQKG 183


>gi|169344007|ref|ZP_02864998.1| dihydrouridine synthase family protein [Clostridium perfringens C
           str. JGS1495]
 gi|169297915|gb|EDS80010.1| dihydrouridine synthase family protein [Clostridium perfringens C
           str. JGS1495]
          Length = 321

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 110/241 (45%), Gaps = 29/241 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    +  AK ++D GYNEINLN+GCPS  V     GA  + + + +   + 
Sbjct: 61  LVPQILTNDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGAGFLAHREELDKFLE 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDN 168
            + K   + +++K R+G+D    +     L+K   K  +  + IH R +    G     N
Sbjct: 121 EIFKIDHMKISIKTRLGMD---KSEEFYELIKIYNKYPMEELIIHPRTRQDFYG-----N 172

Query: 169 RKIPNLD-YDIVYEIKKE----NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS 223
           +  PNL+ +     + K     N D+F      LED ++ ++    VD +M+GR    N 
Sbjct: 173 K--PNLEVFKDAISLSKNTVCYNGDIFT-----LEDHNKLVEEFKEVDKIMLGRGILANP 225

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           A++        N +  +  +   V K+F  +I +   +      ++  +++++  +MI +
Sbjct: 226 ALM--------NEILNNEFMDKNVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYM 277

Query: 284 F 284
           F
Sbjct: 278 F 278


>gi|291390365|ref|XP_002711677.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog
           [Oryctolagus cuniculus]
          Length = 493

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 101/225 (44%), Gaps = 37/225 (16%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           R + N  L   + +  D     D+        ++  +  Q+G +D  + +  A++VE+  
Sbjct: 53  RRVVNEVLSTVDFVAPD-----DRVVFRTCEREQSRVVFQMGTSDAERALAVARLVEN-D 106

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQI 131
              I++N+GCP     +G  GA L+ +PD +   ++ + K    PVT K RI   ++D +
Sbjct: 107 VAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLEDTL 166

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                 +LVK I+K+G+  I +H RK        ++ R    +  +++  I  E   + +
Sbjct: 167 ------SLVKRIEKTGIAAIAVHGRK--------REERPQHPVSCEVIKAI-AETLSIPV 211

Query: 192 GLNGG----------LEDMSQALKILPSVDGVMIGRAAYKNSAML 226
             NGG          +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 212 IANGGSHDHIQQHLDIEDFRQAT----AASSVMVARAAMWNPSIF 252


>gi|296314205|ref|ZP_06864146.1| tRNA-dihydrouridine synthase [Neisseria polysaccharea ATCC 43768]
 gi|296839101|gb|EFH23039.1| tRNA-dihydrouridine synthase [Neisseria polysaccharea ATCC 43768]
          Length = 314

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 93/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P ++   +
Sbjct: 57  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             M + L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 117 KTMRERLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 173 AHWEWIRKIRDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 226

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 227 RQIKQY-----ENGGPVK---DTDF 243


>gi|291080756|ref|ZP_06534880.2| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 205

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 90/189 (47%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN V+  +     G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++   + I  NG + +  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQK-VSIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|319940025|ref|ZP_08014379.1| tRNA-dihydrouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319810739|gb|EFW07066.1| tRNA-dihydrouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 323

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 110/239 (46%), Gaps = 17/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K  ++L    +E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEEEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    +I ++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTQTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYSIINKVRSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   A        + + +G   + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD---ASLAVENALAAEAAGAAALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            ++ + +    +    NG +  +  A + +  V  D VMIGRAA  N  +   ++ YF 
Sbjct: 192 TLHNVAQALTKIPFIANGDIRTVQDAQQRIEEVGADAVMIGRAAMGNPYLFHQINHYFE 250


>gi|320333337|ref|YP_004170048.1| dihydrouridine synthase DuS [Deinococcus maricopensis DSM 21211]
 gi|319754626|gb|ADV66383.1| dihydrouridine synthase DuS [Deinococcus maricopensis DSM 21211]
          Length = 312

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 95/214 (44%), Gaps = 20/214 (9%)

Query: 15  LLTNNALLYT--EMIVADAILRGDKKNILGFS-TQEKPLALQIGGADISKLVEAAK-IVE 70
           L +    L+T  EM+ A  +L GD    LG     E+   LQ+ GAD   L   A+  V 
Sbjct: 31  LCSEQGALWTVSEMLSARGLLEGDLAVDLGQPYPGEQGRVLQLFGADPDILAAGAQEAVR 90

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
            F    ++LN+GCP  ++ +G  GACL+  PD+    + AM  A++I V+ K R+G D  
Sbjct: 91  LFQPAALDLNMGCPVPKI-KGKGGACLLQTPDVAYTLVKAMRDAVNIDVSAKIRLGWDTN 149

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                   + + ++ +G   I +H R +          R     D+D +  +        
Sbjct: 150 RSV----EIAQGLEAAGAALITVHGRTSA--------QRYTGYADWDAIAHVAASVRAPV 197

Query: 191 IGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKN 222
           IG +G +    Q  A +    V  VMIGR A  N
Sbjct: 198 IG-SGDVTSAEQAHARRAHSGVAAVMIGRGAVGN 230


>gi|283781134|ref|YP_003371889.1| dihydrouridine synthase DuS [Pirellula staleyi DSM 6068]
 gi|283439587|gb|ADB18029.1| dihydrouridine synthase DuS [Pirellula staleyi DSM 6068]
          Length = 354

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/203 (25%), Positives = 94/203 (46%), Gaps = 16/203 (7%)

Query: 33  LRGDKK---NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           L+GD+K   + L  + ++ P+A Q+ GA+ ++  + A  + + G++ I++N GCP  +V 
Sbjct: 54  LKGDRKKNRHFLYLTDEDHPVAGQLMGAEPAEFAQGALRLAEAGFDVIDINFGCPVKKVL 113

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDD-QIPAVALRNLVKSIKKS 146
               G   +  PD+  + +      +   IPVTVK R G+DD Q+       ++     +
Sbjct: 114 GRCRGGFHLSQPDVALEIVRRTRDIVPAHIPVTVKMRRGLDDTQLSRDRFFEILDGAFAA 173

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV  I +H R  + + + P          +  + E+K+      I  +G L      L +
Sbjct: 174 GVAAITVHGRTVVQRYVGPS--------RWSFLTEVKRHVGSRVILGSGDLFSAQDCLAM 225

Query: 207 L--PSVDGVMIGRAAYKNSAMLT 227
           +    VDGV + R A  N  + +
Sbjct: 226 MRETGVDGVTVARGAIGNPWIFS 248


>gi|149188159|ref|ZP_01866454.1| putative regulator protein [Vibrio shilonii AK1]
 gi|148838147|gb|EDL55089.1| putative regulator protein [Vibrio shilonii AK1]
          Length = 320

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 89/176 (50%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A      G   I+LN GCP+  V++   GA L+ +P+++ + +
Sbjct: 64  PVHIQLLGQDPRWMAENAVRAASLGAKGIDLNFGCPAKLVNKSKGGAALLQHPELIHNVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+  +IPVT K R+G ++         +V +I+++G N + +HAR       +  
Sbjct: 124 KACREAVDRNIPVTAKIRLGWENPDDCF---EIVDAIEQAGANELTVHAR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + ++ + EI+K+     I  NG + +     + + +  VD +M+ R A+
Sbjct: 174 GGYKASEIKWEYINEIRKKTSVPLIA-NGEIWNFEDGQRCIETTGVDSLMVCRGAF 228


>gi|269794702|ref|YP_003314157.1| TIM-barrel protein, nifR3 family [Sanguibacter keddieii DSM 10542]
 gi|269096887|gb|ACZ21323.1| putative TIM-barrel protein, nifR3 family [Sanguibacter keddieii
           DSM 10542]
          Length = 406

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 103/225 (45%), Gaps = 18/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EM+ + AI+  +++   I+ F   E P + Q+ G D
Sbjct: 46  MAGVTNTAFRKLCREHGPGGLYVAEMVTSRAIVERNEQALRIVTFEDGESPRSAQVYGVD 105

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
            + +  A +I+   G  + ++LN GCP  +V     GA L    ++    + A  +A + 
Sbjct: 106 PATVGAAVEIIAGEGRADHVDLNFGCPVPKVTRKGGGAVLPWKRELFTRIVDAAVEAGAR 165

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD         L+   +++GV  + +HAR A         +      
Sbjct: 166 HDVPVTIKMRKGIDDDHLTYLEAGLIA--EQAGVAAVALHARTAA--------DYYSGTA 215

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
           D+  + ++K+    + +  NG +     AL+++     DGV++GR
Sbjct: 216 DWSAIRQLKETVTSIPVLGNGDIWSAEDALEMVRQTGCDGVVVGR 260


>gi|66362388|ref|XP_628158.1| Dus1p, tRNA dihydrouridine synthase [Cryptosporidium parvum Iowa
           II]
 gi|46227613|gb|EAK88548.1| Dus1p, tRNA dihydrouridine synthase [Cryptosporidium parvum Iowa
           II]
          Length = 409

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 71/133 (53%), Gaps = 6/133 (4%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           L+G ++       ++ P+ +Q  G D   LV+A+K ++D     I++N GCP      G+
Sbjct: 59  LQGYRETNFQTCEEDDPMIVQFCGNDPETLVKASKFIDD-KVKGIDINFGCPQNIAKRGN 117

Query: 93  FGACLMLNPDIVGDCIAAMCKA-LSIPVTVKCRI-GVDDQIPAVALRNLVKSIKKSGVNG 150
           +GA L+ NPD++   I+ + ++ L  PV+ K RI    D  P +   NL+K ++ +G   
Sbjct: 118 YGAFLLSNPDLMERIISTLSESDLKCPVSCKIRILDHHDLQPTI---NLIKRLESAGACM 174

Query: 151 IWIHARKAILKGL 163
           I +H R    +G+
Sbjct: 175 IAVHGRTMTSRGV 187


>gi|301615796|ref|XP_002937362.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Xenopus (Silurana)
           tropicalis]
          Length = 486

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 83/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+     ++++PL +Q  
Sbjct: 37  MVDQSELAWRLLSRRHGVQLCYTPMLHAQVFVRDANYR--KENLYCEVCSEDRPLIVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   +    + L
Sbjct: 95  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQDEWDLLEKMVQLAHQKL 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         K ++K+G   + +H R    KG
Sbjct: 154 SVPVT--CKIRVFPEIEKTV--EYAKMLEKAGCQLLTVHGRTKEQKG 196


>gi|254572950|ref|XP_002493584.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|238033383|emb|CAY71405.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|328354588|emb|CCA40985.1| potential tRNA dihydrouridine synthase similar to S. cerevisiae
           DUS4 (YLR405W) [Pichia pastoris CBS 7435]
          Length = 352

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 106/247 (42%), Gaps = 27/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  L+YT MI+A   +R        F+T  ++ P  +QIG  +
Sbjct: 44  MVRYSKLPFRELVRFY-NVDLVYTPMILAREFVRNKVARYSDFTTNIRDTPTIVQIGCNN 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+    ++  +  + I+LN GCP   +V EG  GA LM  P+ V   +  + +    
Sbjct: 103 SVDLLRMVDMIHSY-VDGISLNCGCPIKEQVREG-IGAALMTEPEKVSQMVRVVKEKYGD 160

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++ +I + + I        VK ++ +GV+ I +H R    +   P D   I      
Sbjct: 161 SVCIETKIRIHNDIQETI--RFVKQVQDAGVDYITVHGRTKTTRSSKPVDLESI------ 212

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT-------- 227
               I KE   + +  NG   D+     IL     DGVM  R   +N ++ +        
Sbjct: 213 ---RIIKEVARVPVIANGDCVDVKSFEHILDVTKCDGVMSVRGLLENPSLFSGYNKTTWG 269

Query: 228 TVDEYFS 234
            V+ +FS
Sbjct: 270 CVERFFS 276


>gi|307262900|ref|ZP_07544524.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|306871805|gb|EFN03525.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 313

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 55  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 114

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 115 DLIYRATKAMREAVPQDQIVSVKVRLGWDSADQCFEIA-----DAVAQGGANEITVHGR- 168

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 169 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNATACSSLMI 221

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 222 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYH 267

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 268 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 310


>gi|332998380|gb|EGK17979.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri VA-6]
          Length = 281

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+   ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSAPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|240139568|ref|YP_002964044.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens AM1]
 gi|240009541|gb|ACS40767.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens AM1]
          Length = 307

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 104/215 (48%), Gaps = 19/215 (8%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLVEAAKI 68
           R  A+ L  +A++ +EM+ A  + +GD ++ +        P  +Q+ G     + E A+I
Sbjct: 2   RRLAQRLGASAVV-SEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPELMAEGARI 60

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
               G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTVK R+G D
Sbjct: 61  AVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTVKMRLGWD 120

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
               ++    L +  +  G++G+ +H   R+   KG +          D+  +  +  E 
Sbjct: 121 HA--SLNAAELARRAEALGLDGVTVHGRTRQQFYKGRA----------DWSAIRPV-VEA 167

Query: 187 PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
             + +  NG +  + +A   L      GVM+GRAA
Sbjct: 168 VRIPVIANGDITGVEEARACLSQSGAAGVMVGRAA 202


>gi|242011621|ref|XP_002426546.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212510683|gb|EEB13808.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 332

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/158 (27%), Positives = 80/158 (50%), Gaps = 6/158 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + L +T MI+AD+ ++ +K  I  F+T   + P+ +Q    +
Sbjct: 19  MVRYSKLEFRSLVRQYDCD-LCFTPMIMADSFIKSEKARINEFTTSSNDSPVIVQFAANN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAAK+V  F  + ++LN GCP     +   GA L+  P+ + D +  +   +S  
Sbjct: 78  TFDFSEAAKLVFPFS-DGVDLNCGCPQRWAMKIGIGAQLLSEPETIKDIVLNVKNQISCN 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            +V  ++ + + I +    +L K ++K+GV  + IH R
Sbjct: 137 YSVSVKLRLLNDIKSTV--DLCKKLEKTGVTFLTIHGR 172


>gi|323508721|dbj|BAJ77254.1| cgd1_3440 [Cryptosporidium parvum]
          Length = 407

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 71/133 (53%), Gaps = 6/133 (4%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           L+G ++       ++ P+ +Q  G D   LV+A+K ++D     I++N GCP      G+
Sbjct: 57  LQGYRETNFQTCEEDDPMIVQFCGNDPETLVKASKFIDD-KVKGIDINFGCPQNIAKRGN 115

Query: 93  FGACLMLNPDIVGDCIAAMCKA-LSIPVTVKCRI-GVDDQIPAVALRNLVKSIKKSGVNG 150
           +GA L+ NPD++   I+ + ++ L  PV+ K RI    D  P +   NL+K ++ +G   
Sbjct: 116 YGAFLLSNPDLMERIISTLSESDLKCPVSCKIRILDHHDLQPTI---NLIKRLESAGACM 172

Query: 151 IWIHARKAILKGL 163
           I +H R    +G+
Sbjct: 173 IAVHGRTMTSRGV 185


>gi|227495137|ref|ZP_03925453.1| dihydrouridine synthase [Actinomyces coleocanis DSM 15436]
 gi|226831589|gb|EEH63972.1| dihydrouridine synthase [Actinomyces coleocanis DSM 15436]
          Length = 410

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 103/211 (48%), Gaps = 23/211 (10%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYN 75
            L   EMI A A++  ++K  ++     Q++  +LQ+ G D   L +A  I+  EDF  +
Sbjct: 68  GLYVCEMITARALVEKNEKTMHMAKPDPQDRVRSLQLYGTDPVNLYKATHILLEEDF-VD 126

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----IPVTVKCRIGVDDQ 130
            I+LN GCP  +V +   GA L    D+  D + ++ +A++     +PVT+K R+G+DD 
Sbjct: 127 HIDLNFGCPVPKVTKKGGGAALPWKLDLFDDIVNSVVRAVTETGKDVPVTIKMRVGIDDA 186

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                 R+  +  + +G+  + +H R         +      + D+D + ++K++     
Sbjct: 187 --HHTFRDAGRIAEDAGIAAVALHGRT--------QAQYYSGHADWDTIAQLKQDLTVPV 236

Query: 191 IGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           +G NG +     A  ++     D V++GR A
Sbjct: 237 LG-NGDIFSAQDAKDVMAHTGCDAVVVGRGA 266


>gi|238855045|ref|ZP_04645373.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 269-3]
 gi|260664829|ref|ZP_05865680.1| transcriptional regulator [Lactobacillus jensenii SJ-7A-US]
 gi|282934831|ref|ZP_06340065.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
 gi|313472617|ref|ZP_07813106.1| zinc-binding TIM-barrel protein [Lactobacillus jensenii 1153]
 gi|238832289|gb|EEQ24598.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 269-3]
 gi|239529432|gb|EEQ68433.1| zinc-binding TIM-barrel protein [Lactobacillus jensenii 1153]
 gi|260561312|gb|EEX27285.1| transcriptional regulator [Lactobacillus jensenii SJ-7A-US]
 gi|281301103|gb|EFA93413.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
          Length = 342

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 117/237 (49%), Gaps = 25/237 (10%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  +KK  ++L  +  E P+++QI G     L+EAA+ + ++   + I
Sbjct: 42  LVVCEMISDHGIIYRNKKTLDMLQVAPNEHPMSIQIFGGTEDTLLEAAQYIDQNTAADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   +  + + +  PV+VK R+G D +    A+ 
Sbjct: 102 DINMGCPVPKVTKTDAGSKWLLDANKIYQMVHKVVQNVEKPVSVKMRLGWDRK-HIFAVE 160

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G +          D++ ++E+       F+G NG
Sbjct: 161 NALAA-QEAGASMLAMHGRTRKQMYQGEA----------DWETLHEVANALTIPFVG-NG 208

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKT 245
            +     A K++  V    VMIGRAA  N   +  +  Y        P T    I+T
Sbjct: 209 DITSPELAKKMIDEVGATAVMIGRAALGNPWEIKDMVHYLETGEKLRPQTVREKIET 265


>gi|225026778|ref|ZP_03715970.1| hypothetical protein EUBHAL_01030 [Eubacterium hallii DSM 3353]
 gi|224955897|gb|EEG37106.1| hypothetical protein EUBHAL_01030 [Eubacterium hallii DSM 3353]
          Length = 329

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 113/261 (43%), Gaps = 29/261 (11%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +I     +  P+  QI     +  ++ A ++E+ GY E+NLN+GCPS  V     G+
Sbjct: 53  EKNDIAPEHNKNIPVVPQILTNKAADFIKVAGMMEELGYKEVNLNLGCPSGTVVSKKKGS 112

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             + + + +      +   ++I V+VK R+GV++    + L N+  +     ++ + +HA
Sbjct: 113 GFLADLEGMKYFFDEVFSQVNIEVSVKTRLGVENPDEVIDLMNIYNAFP---ISEVIVHA 169

Query: 156 RKAILKGLSPKDNRKIPNL----DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
           R        P +            + + Y     N DLF      ++D+       P + 
Sbjct: 170 RVREDYYKRPVNQEAFAQCLAISKHPVCY-----NGDLFT-----VQDIENLTAKFPDIK 219

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTG-SSPIKTRVDKDF--WRKISASMTDYAARHLH 268
            VM+GR    N   LT V  +      G S+ ++ R   D+  W+     +  Y   H+ 
Sbjct: 220 AVMLGRGMIAN-PQLTEV--FCGREAHGDSTSVENRQGLDYVRWKAFLDELC-YGYEHIM 275

Query: 269 SGG-----KLQQITRHMIGLF 284
           SGG     KL+++  +MI  F
Sbjct: 276 SGGRNVLFKLKEVWSYMITFF 296


>gi|91791809|ref|YP_561460.1| dihydrouridine synthase TIM-barrel protein nifR3 [Shewanella
           denitrificans OS217]
 gi|91713811|gb|ABE53737.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Shewanella
           denitrificans OS217]
          Length = 322

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 118/246 (47%), Gaps = 32/246 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   +K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLC-LRYGAALAVSEMLSSNPEVWDTEKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G + I++N+GCP+ +V++   G+ LM +P +V D + A+  A+ +P
Sbjct: 76  PDLMANAAQFNVEQGAHIIDINMGCPAKKVNKKFAGSALMQDPALVKDILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRK 170
           VT+K R G D       QI  +A        +  G+  + +H   R+ + KG +      
Sbjct: 136 VTLKIRTGWDPEHKNGVQIAQIA--------QDCGIASLAVHGRTRQCMYKGFA------ 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
               +YD +  I K+N  + +  NG ++   +A  +L    VD +MIGR A     +   
Sbjct: 182 ----EYDTIKAI-KQNISIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFKE 236

Query: 229 VDEYFS 234
           +  Y  
Sbjct: 237 IQHYLE 242


>gi|67588468|ref|XP_665355.1| ENSANGP00000019228 [Cryptosporidium hominis TU502]
 gi|54656003|gb|EAL35125.1| ENSANGP00000019228 [Cryptosporidium hominis]
          Length = 384

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/133 (30%), Positives = 71/133 (53%), Gaps = 6/133 (4%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           L+G ++       ++ P+ +Q  G D   LV+A+K ++D     I++N GCP      G+
Sbjct: 34  LQGYRETNFQTCEEDDPMIVQFCGNDPETLVKASKFIDD-KVKGIDINFGCPQNIAKRGN 92

Query: 93  FGACLMLNPDIVGDCIAAMCKA-LSIPVTVKCRI-GVDDQIPAVALRNLVKSIKKSGVNG 150
           +GA L+ NPD++   I+ + ++ L  PV+ K RI    D  P +   NL+K ++ +G   
Sbjct: 93  YGAFLLSNPDLMERIISTLSESDLKCPVSCKIRILDHHDLQPTI---NLIKRLESAGACM 149

Query: 151 IWIHARKAILKGL 163
           I +H R    +G+
Sbjct: 150 IAVHGRTMTSRGV 162


>gi|240115548|ref|ZP_04729610.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID18]
 gi|260440642|ref|ZP_05794458.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI2]
 gi|268601220|ref|ZP_06135387.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID18]
 gi|268585351|gb|EEZ50027.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID18]
          Length = 333

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 94/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +     +D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIHDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|187928992|ref|YP_001899479.1| dihydrouridine synthase DuS [Ralstonia pickettii 12J]
 gi|187725882|gb|ACD27047.1| dihydrouridine synthase DuS [Ralstonia pickettii 12J]
          Length = 318

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 105/237 (44%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 50  GYTASGTPMTIQLLGSDPEWLARNAAYAATLTPHGIDLNFGCPAKVVNRHGGGAMLLATP 109

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++ D + A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 110 EVLHDIVRAVRAAVPANISVTAKMRLGVSDTSRAI---DCATALAEGGAESLVVHART-- 164

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                 +D+   P   +D +  I  +   + +  NG +  ++  +  + +     VMIGR
Sbjct: 165 ------RDHGYRPPAHWDWIARI-ADAVSIPVTANGEVWTVADWERCRAVSGCSDVMIGR 217

Query: 218 AAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +       P     PI      D+ +K+ A ++   A+H H   KL
Sbjct: 218 GAVSDPFLAQRIRAQMDQAPSAAEWPIVLGYLADYLKKLHARIS---AKHEHGRVKL 271


>gi|330873874|gb|EGH08023.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 228

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 110/223 (49%), Gaps = 22/223 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIG 216
           YD +  IK+    + +  NG ++   +A ++L +   DG++IG
Sbjct: 186 YDTIAMIKQA-VSIPVFANGDIDSPEKARRVLQATGADGILIG 227


>gi|190149581|ref|YP_001968106.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|189914712|gb|ACE60964.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
          Length = 320

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 62  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 121

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 122 DLIYRATKAMREAVPQDQIVSVKVRLGWDSADQCFEIA-----DAVAQGGANEITVHGR- 175

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 176 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNATACSSLMI 228

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 229 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYH 274

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 275 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 317


>gi|30064591|ref|NP_838762.1| putative dehydrogenase [Shigella flexneri 2a str. 2457T]
 gi|56480301|ref|NP_709055.2| putative dehydrogenase [Shigella flexneri 2a str. 301]
 gi|30042850|gb|AAP18573.1| putative dehydrogenase [Shigella flexneri 2a str. 2457T]
 gi|56383852|gb|AAN44762.2| putative dehydrogenase [Shigella flexneri 2a str. 301]
          Length = 280

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/189 (26%), Positives = 88/189 (46%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+   ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 28  VQIAGSAPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 87

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PVT+K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 88  VNAVDVPVTLKIRTGW-----APEHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 138

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 139 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 191

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 192 IFREIQHYL 200


>gi|325684701|gb|EGD26855.1| tRNA-dihydrouridine synthase [Lactobacillus delbrueckii subsp.
           lactis DSM 20072]
          Length = 344

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 111/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           ++  EMI    I+ G++K  ++L     E P+++QI G     L++AA+ ++     +I 
Sbjct: 42  MVVCEMISDHGIIYGNEKTLSMLDVDPGEHPMSIQIFGGTEDSLLQAAQYIDQHTDADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   I  + + +  PV+VK RIG D +    A+ 
Sbjct: 102 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEKPVSVKMRIGWDRK-HIFAVE 160

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+ +     F+  NG
Sbjct: 161 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVAQVMDIPFVA-NG 208

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y + 
Sbjct: 209 DITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 250


>gi|255585121|ref|XP_002533266.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
 gi|223526922|gb|EEF29128.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
          Length = 426

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 107/232 (46%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 98  MVDNSELPFRMLCRKYGADAA-YTPMLHSRIFTENEKYRTQEFTTCNEDRPLFVQFCAND 156

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA+ VE +  + +++N+GCP      G++GA LM N  +V   +  +   L++P
Sbjct: 157 PDILLEAARKVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLNVP 215

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   +DD I      +  + ++++G + + +H R         KD +K    D+
Sbjct: 216 VSCKIRLFPKLDDTI------SYARMLEEAGCSLLAVHGRTR-----DEKDGKKF-RADW 263

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
             +  ++       +  NG +  M      L     DGV+   +  +N A+ 
Sbjct: 264 KAIKAVRNAVKIPLLA-NGNVRHMDDVRNCLEETGADGVLSAESLLENPALF 314


>gi|313123089|ref|YP_004033348.1| tRNA-dihydrouridine synthase b [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312279652|gb|ADQ60371.1| tRNA-dihydrouridine synthase B [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 342

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 111/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           ++  EMI    I+ G++K  ++L     E P+++QI G     L++AA+ ++     +I 
Sbjct: 40  MVVCEMISDHGIIYGNEKTLSMLDVDPGEHPMSIQIFGGTEDSLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   I  + + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEKPVSVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+ +     F+  NG
Sbjct: 159 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVAQVMDIPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y + 
Sbjct: 207 DITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 248


>gi|168185494|ref|ZP_02620129.1| dihydrouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
 gi|169296460|gb|EDS78593.1| dihydrouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
          Length = 319

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 90/201 (44%), Gaps = 23/201 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +++L  + + K +  Q+   D  + +  A+ +++ GYNEINLN+GCPS  V     G+  
Sbjct: 49  RDVLPENNEVKNIVPQVLTNDSERFINIARKLQELGYNEINLNLGCPSGTVVSKYRGSGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   + +   +  + K   + +++K R+G D          L+K   K  +  + IH R 
Sbjct: 109 LAKREELDRFLEEIFKIDHMKISIKTRLGKDS---PEEFYELIKIFNKYSLEELIIHPR- 164

Query: 158 AILKGLSPKDNRK-IPNLDYDIVYEIKKE------NPDLFIGLNGGLEDMSQALKILPSV 210
                 + +D  K  PNL      E+ K+      NP  + G      D  Q  +  P V
Sbjct: 165 ------TREDFYKNKPNL------EVFKDALSLSVNPICYNGDIFTSTDYKQLTEAFPQV 212

Query: 211 DGVMIGRAAYKNSAMLTTVDE 231
           + VMIGR    N+ ++  + E
Sbjct: 213 ETVMIGRGILANTGLINEIKE 233


>gi|148238900|ref|YP_001224287.1| tRNA-dihydrouridine synthase [Synechococcus sp. WH 7803]
 gi|147847439|emb|CAK22990.1| Probable tRNA-dihydrouridine synthase [Synechococcus sp. WH 7803]
          Length = 338

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/273 (24%), Positives = 124/273 (45%), Gaps = 29/273 (10%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLV 63
           +D+ +R   R  + +ALL+TEM+ A ++  G  +  +    QE  P+ +Q+       + 
Sbjct: 33  SDKIFRALVRRWSLDALLFTEMVNATSLELGHGRGKVEELQQEAGPIGVQLFDHRPEAMA 92

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++     G+ L+ +PD+    + A+  A+ IPVTVK 
Sbjct: 93  DAARRAEAAGAFLIDINMGCPVRKIARKGGGSGLIRDPDLACSIVEAVVAAVGIPVTVKT 152

Query: 124 RIG--VDDQIP--AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           R+G   D Q      A  +  + ++ +G   + +H R         ++ R     +++ +
Sbjct: 153 RLGWCSDPQTADNHAAAMDWCRRLEAAGAQLLTLHGRT--------REQRFSGRANWEAI 204

Query: 180 YEIKK-------ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             +K+        N D+F       ED    L+I    DGVM+GR       ++  +D  
Sbjct: 205 AAVKRTLRIPVIANGDVF-----SPEDARACLEIT-GADGVMVGRGTMGAPWLVGQIDAA 258

Query: 233 FSN---PLTGSSPIKTRVDKDFWRKISASMTDY 262
                 P T S+  +  +  D  + + A+  D+
Sbjct: 259 LKGRPVPPTPSARERLTIAADQLQALVAARGDH 291


>gi|224372117|ref|YP_002606489.1| tRNA-dihydrouridine synthase B [Nautilia profundicola AmH]
 gi|223588677|gb|ACM92413.1| tRNA-dihydrouridine synthase B [Nautilia profundicola AmH]
          Length = 313

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 107/230 (46%), Gaps = 29/230 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + + ++EM   +AI   ++K   ++  S  E P  +QI   +
Sbjct: 18  LAGYTDLPFRSVVKKFGCD-MTFSEMTNVNAIAYQNEKTQKMMEKSPLENPYFVQIAANN 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMCKAL 115
           +   V+A +I+ +  + + I++N+GCP  +     FG  L+   N D + + +  + K  
Sbjct: 77  VENAVKAVEIINELNWIDGIDINLGCPVNKARRSGFGGVLLKDENRDFLKEVVGTIVKTS 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPN 173
             PV+ K RIG D  +    + +  K ++  G+  + IH R  K + KG +         
Sbjct: 137 KKPVSAKMRIGFDKSV----VEDRAKLLEDLGIVFLTIHGRTVKQMYKGEA--------- 183

Query: 174 LDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILP--SVDGVMIGRAA 219
            DYD   EIKK    + I +  NG + D  +A  +L      GV IGR A
Sbjct: 184 -DYD---EIKKGVNAVKIPVIANGDITDYEKAKYVLEYTGASGVSIGRGA 229


>gi|194289473|ref|YP_002005380.1| tRNA-dihydrouridine synthase c [Cupriavidus taiwanensis LMG 19424]
 gi|193223308|emb|CAQ69313.1| tRNA-dihydrouridine synthase C [Cupriavidus taiwanensis LMG 19424]
          Length = 318

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 90/193 (46%), Gaps = 18/193 (9%)

Query: 36  DKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           D   IL  G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    
Sbjct: 50  DTPEILSGGHTRSGTPMVIQLLGSDPEWLARNAAYAATLSPHGIDLNFGCPAKVVNRHGG 109

Query: 94  GACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           GA L+ NP ++   +A++  A+  +IPVT K R+GV D   A+   +   ++ + G   +
Sbjct: 110 GAMLLTNPALLNRIVASVRAAVPATIPVTAKMRLGVSDTALAI---DCATALAEGGAASL 166

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPS 209
            +HAR         +D+   P   +D +  I     D+ +  NG +  ++  ++   +  
Sbjct: 167 VVHART--------RDHGYRPPAHWDWIARIAAAV-DIPVIANGDVWTVADWVRCREVSG 217

Query: 210 VDGVMIGRAAYKN 222
            D VMIGR A  +
Sbjct: 218 CDDVMIGRGAVSD 230


>gi|291043950|ref|ZP_06569666.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI2]
 gi|291012413|gb|EFE04402.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI2]
          Length = 341

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 94/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 84  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 143

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 144 KTLRGRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTK-AEGYEPP 199

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +     +D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 200 AHWEWIRKIHDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 253

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 254 RQIKQY-----ENGGPVK---DTDF 270


>gi|226292672|gb|EEH48092.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 475

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 87/185 (47%), Gaps = 17/185 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     VEAAKI+       I++N GCP      G  GA L+  PD++   + 
Sbjct: 125 LIFQIGTASPILAVEAAKIIAP-DVAGIDVNAGCPKPFSTSGGMGAALLQKPDLLVSILT 183

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+   +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H R   ++    
Sbjct: 184 ALVTEVGAPHQISISVKIRLLSDPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRER 239

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I + N  + I +NG +E    ALK++    VDG MI  +A  NS
Sbjct: 240 AIRDQLP-----MIASICR-NAGVAILMNGDVESRDHALKLMKEYGVDGAMIATSAEANS 293

Query: 224 AMLTT 228
           +   T
Sbjct: 294 SCFRT 298


>gi|296141212|ref|YP_003648455.1| hypothetical protein Tpau_3537 [Tsukamurella paurometabola DSM
           20162]
 gi|296029346|gb|ADG80116.1| TIM-barrel protein, nifR3 family [Tsukamurella paurometabola DSM
           20162]
          Length = 396

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 67/294 (22%), Positives = 120/294 (40%), Gaps = 22/294 (7%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           AR  T   L   EM+ A A++       ++  F+  E P +LQ+   D     EAA+++ 
Sbjct: 43  ARTGTVAGLYVCEMVTARALVERHPVTMHMTTFAPDEDPRSLQLYTVDAHYTYEAARMIA 102

Query: 71  DFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-------IPVTVK 122
           + G  + +++N GCP  ++     G+ L    ++    + A  + +        IPVTVK
Sbjct: 103 EEGLADHLDMNFGCPVPKITRRGGGSALPYKRNLFASIVDAAVRGIEDGGQGGRIPVTVK 162

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG+DD+       +  +   + G   + +HAR A  +     D  +I  L   + +  
Sbjct: 163 FRIGIDDE--HHTHLDAGRIAAEQGAVAVALHARTAAQRYSGQADWDEIARLKEHVHHHF 220

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
               P L    NG +     A+ ++     DGV++GR       + + +    +     +
Sbjct: 221 GDAVPVLG---NGDIFAAEDAVTMMDRTGCDGVVVGRGCLGRPWLFSELSAALNGTPMPT 277

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            P    V +  +R         AA H    G +++I +H+     GFP     R
Sbjct: 278 PPNLGEVTEIMYRHGEL----LAAHHGEDKG-MREIRKHVAWYLRGFPAGGELR 326


>gi|256787882|ref|ZP_05526313.1| hypothetical protein SlivT_25631 [Streptomyces lividans TK24]
 gi|289771765|ref|ZP_06531143.1| dihydrouridine synthase [Streptomyces lividans TK24]
 gi|289701964|gb|EFD69393.1| dihydrouridine synthase [Streptomyces lividans TK24]
          Length = 406

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 103/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 32  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 91

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ + G  + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 92  DPVTVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAIVREAVTGAG 151

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 152 DLPVTMKMRKGLDDD--HLTYLDAGRIAVEEGVTAIALHGRTTA--------QHYGGTAD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 202 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRG 246


>gi|21220959|ref|NP_626738.1| hypothetical protein SCO2497 [Streptomyces coelicolor A3(2)]
 gi|6580664|emb|CAB63312.1| conserved hypothetical protein SCC82.03c [Streptomyces coelicolor
           A3(2)]
          Length = 406

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 103/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 32  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 91

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ + G  + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 92  DPVTVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAIVREAVTGAG 151

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 152 DLPVTMKMRKGLDDD--HLTYLDAGRIAVEEGVTAIALHGRTTA--------QHYGGTAD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 202 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRG 246


>gi|330800078|ref|XP_003288066.1| hypothetical protein DICPUDRAFT_152274 [Dictyostelium purpureum]
 gi|325081890|gb|EGC35390.1| hypothetical protein DICPUDRAFT_152274 [Dictyostelium purpureum]
          Length = 402

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 83/167 (49%), Gaps = 14/167 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD T   +R   R    + L+YT M  +   +         F+T  +++PL +Q  G D
Sbjct: 57  MVDHTYLAFRMLTRKYGAD-LVYTPMFHSKNFVTCKTYRKDNFTTCPEDRPLVVQFCGND 115

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V+AAK+VED   + I+LN+GCP      G++G+ L+  P I+   +  + K + +P
Sbjct: 116 PEWVVKAAKLVED-RCDAIDLNLGCPQQIARRGNYGSFLLDKPHIILPIVRELHKNIKVP 174

Query: 119 VTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKG 162
           +  K R+  D       L++ +K    ++++G   + +H R    KG
Sbjct: 175 IFCKIRLLPD-------LKDTIKLALDLQEAGCQLLTVHGRTKEQKG 214


>gi|227903176|ref|ZP_04020981.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus ATCC 4796]
 gi|227868981|gb|EEJ76402.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus ATCC 4796]
          Length = 341

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 114/221 (51%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ + ++   + I
Sbjct: 40  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYIDQNTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRIGWDRK-HVFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+++++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEVLHDVAQVLDVPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A K L  +    VM+GRAA  N  +L  +  Y  
Sbjct: 207 DIATPELAKKALDDIGCTAVMVGRAALGNPWILKDMVHYLE 247


>gi|59801293|ref|YP_208005.1| hypothetical protein NGO0894 [Neisseria gonorrhoeae FA 1090]
 gi|194098476|ref|YP_002001536.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae NCCP11945]
 gi|239998870|ref|ZP_04718794.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 35/02]
 gi|240014216|ref|ZP_04721129.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI18]
 gi|240016652|ref|ZP_04723192.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA6140]
 gi|240080841|ref|ZP_04725384.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA19]
 gi|240117840|ref|ZP_04731902.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID1]
 gi|240121779|ref|ZP_04734741.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID24-1]
 gi|240123398|ref|ZP_04736354.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID332]
 gi|240125646|ref|ZP_04738532.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-92-679]
 gi|254493655|ref|ZP_05106826.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 1291]
 gi|268594711|ref|ZP_06128878.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 35/02]
 gi|268596959|ref|ZP_06131126.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA19]
 gi|268603542|ref|ZP_06137709.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID1]
 gi|268682020|ref|ZP_06148882.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID332]
 gi|268684231|ref|ZP_06151093.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-92-679]
 gi|59718188|gb|AAW89593.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933766|gb|ACF29590.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae NCCP11945]
 gi|226512695|gb|EEH62040.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 1291]
 gi|268548100|gb|EEZ43518.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 35/02]
 gi|268550747|gb|EEZ45766.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA19]
 gi|268587673|gb|EEZ52349.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID1]
 gi|268622304|gb|EEZ54704.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID332]
 gi|268624515|gb|EEZ56915.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-92-679]
 gi|317164158|gb|ADV07699.1| hypothetical protein NGTW08_0728 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 333

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 94/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +     +D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIHDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|303249533|ref|ZP_07335740.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|303252549|ref|ZP_07338712.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302648517|gb|EFL78710.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302651607|gb|EFL81756.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 320

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 62  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 121

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 122 DLIYRATKAMREAVPSDQIVSVKVRLGWDSADQSFEIA-----DAVAQGGANEITVHGR- 175

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 176 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMI 228

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 229 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYH 274

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 275 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 317


>gi|293399153|ref|ZP_06643318.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae F62]
 gi|291610567|gb|EFF39677.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae F62]
          Length = 341

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 94/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 84  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 143

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 144 KTLRGRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTK-AEGYEPP 199

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +     +D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 200 AHWEWIRKIHDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 253

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 254 RQIKQY-----ENGGPVK---DTDF 270


>gi|237666036|ref|ZP_04526024.1| dihydrouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237658983|gb|EEP56535.1| dihydrouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 320

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/318 (22%), Positives = 133/318 (41%), Gaps = 38/318 (11%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGADISKLVEAAKI 68
           + +   N    +T  I+ +   R + K   ++L  + +   +  QI   D    +  +K 
Sbjct: 20  YEKFFHNIDKYFTPFIIPNESKRLNTKELIDVLPENNKGISIVSQILTNDSEGFILTSKK 79

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +++ GY+EINLN+GCPS  V     G+  +   + +   +  + +  +I +++K RIG D
Sbjct: 80  LQELGYSEINLNLGCPSGTVVGKGRGSGFLAKREELDKFLYEIFEKNNIKISIKTRIGKD 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSP-----KDNRKIPNLDYDIVYEI 182
            +       +L+K   K  +  + IH R +    G  P     KD   + N         
Sbjct: 140 SR---DEFYDLIKIYNKYPLEELIIHPRTQKDFYGNKPDWEVFKDALSLSN--------- 187

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
              NP  + G     ++ ++   + P VD +MIGR    N  ++        N + G+  
Sbjct: 188 ---NPVCYNGDIFTNDNYTKFTNLFPEVDRIMIGRGILANPGLI--------NEIIGNDM 236

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG----FPNSRRCRHILT 298
           I     K F  +I  +  D     + +  K++++  +MI +F        N RR ++I  
Sbjct: 237 ISKEKMKAFHDEILNAYIDLYPEDIGALFKMKELWSYMIYIFSNGKEYLKNIRRGKNIEE 296

Query: 299 VEAGAST--ATHHIIETA 314
            + G  +  +   II+ A
Sbjct: 297 YKEGVYSLFSEQEIIKGA 314


>gi|254458047|ref|ZP_05071474.1| tRNA-dihydrouridine synthase B [Campylobacterales bacterium GD 1]
 gi|207085440|gb|EDZ62725.1| tRNA-dihydrouridine synthase B [Campylobacterales bacterium GD 1]
          Length = 317

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 111/225 (49%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + L  +EM+ ++A+  G  K  ++L  ++ E P ++QI G+ 
Sbjct: 17  LAGFTDLPFRSVVKKFGAD-LTVSEMLSSNALAHGSVKTLHMLQKASIEDPYSVQISGSQ 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +++ E  G + I+LN GCP  +V     G+ L+LN  ++G+ I  +    + 
Sbjct: 76  SDMIRRAVEVLNEHDGIDIIDLNCGCPVPKVVGHGSGSSLLLNLPLMGEIIRTIKDTSNK 135

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G + +        + K ++ SG + + +H R         +  +    +DY
Sbjct: 136 SLTSVKIRLGFEKKNHI----EIAKMVEDSGADFLAVHGR--------TRAGKFKAAVDY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D + EI KE   + +  NG ++   +A  +L     DGVMIGR A
Sbjct: 184 DAIKEI-KEAVSIPVIANGDIDSYEKAKWVLEHTGADGVMIGRGA 227


>gi|126207791|ref|YP_001053016.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           L20]
 gi|126096583|gb|ABN73411.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 320

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 62  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 121

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 122 DLIYRATKAMREAVPQDQIVSVKVRLGWDSADQSFEIA-----DAVAQGGANEITVHGR- 175

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 176 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMI 228

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 229 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYH 274

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 275 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 317


>gi|46143827|ref|ZP_00133954.2| COG0042: tRNA-dihydrouridine synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307249523|ref|ZP_07531510.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306858378|gb|EFM90447.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 313

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 55  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 114

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 115 DLIYRATKAMREAVPQDQIVSVKVRLGWDSADQSFEIA-----DAVAQGGANEITVHGR- 168

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 169 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMI 221

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 222 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYH 267

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 268 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 310


>gi|332530304|ref|ZP_08406250.1| NifR3 family TIM-barrel protein [Hylemonella gracilis ATCC 19624]
 gi|332040290|gb|EGI76670.1| NifR3 family TIM-barrel protein [Hylemonella gracilis ATCC 19624]
          Length = 375

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/259 (24%), Positives = 110/259 (42%), Gaps = 25/259 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K       S +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRKLCKAL-GAGYAVSEMVTSRKELWNSLKTSRRADHSGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
            + + EAA    + G   I++N+GCP+ +V     G+ LM +  +   + + + A C+  
Sbjct: 76  AAMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMQDEALALEIAEAVVAACEPH 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            +PVT+K R G        A +N V    + + +G+  + +H R         ++     
Sbjct: 136 GVPVTLKMRTGW-----CQANKNAVTLACAFEGAGIRMLTVHGRT--------REQGYGG 182

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
             +YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   V 
Sbjct: 183 QAEYDTIAAVKAAV-RVPVVANGDITSPEKARAVLAHTGADAVMIGRAAQGRPWIFREVA 241

Query: 231 EYFSNPLTGSSPIKTRVDK 249
            Y +     + P+   V +
Sbjct: 242 HYLATGEHLAPPLVAEVKR 260


>gi|307247299|ref|ZP_07529347.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307251840|ref|ZP_07533741.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306856143|gb|EFM88298.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306860532|gb|EFM92544.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 313

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 55  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 114

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 115 DLIYRATKAMREAVPSDQIVSVKVRLGWDSADQSFEIA-----DAVAQGGANEITVHGR- 168

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 169 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMI 221

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 222 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYH 267

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 268 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 310


>gi|152967309|ref|YP_001363093.1| TIM-barrel protein, nifR3 family [Kineococcus radiotolerans
           SRS30216]
 gi|151361826|gb|ABS04829.1| putative TIM-barrel protein, nifR3 family [Kineococcus
           radiotolerans SRS30216]
          Length = 388

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/244 (22%), Positives = 106/244 (43%), Gaps = 21/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  YR   R         +EM+ + A++    +   ++ F+  E+P +LQ+ G D
Sbjct: 28  MAGITNTAYRQLCRE-HGEGFYVSEMVTSRALVERHAETMRLVTFTASERPRSLQLYGVD 86

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVGDCIAAMCK 113
            + +  A + +VED   + ++LN GCP  +V     G+ L    +    IV   +A   +
Sbjct: 87  PTTVAAAVRMVVEDDLADHVDLNFGCPVPKVTRKGGGSALPWKAELFRSIVRGAVAEASR 146

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              IP+TVK R G+DD    +      K+ ++ G   + +H R A               
Sbjct: 147 G-GIPLTVKMRKGIDDD--HLTYLQAGKAAEQEGAAAVALHGRTA--------SQHYSGQ 195

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            D++ +  +K+    + +  NG +     AL+++     DGV++GR       +   ++ 
Sbjct: 196 ADWEAIARLKETVTTIPVLGNGDVWSAEDALEMVRRTGCDGVVVGRGCLGRPWLFADLEA 255

Query: 232 YFSN 235
            F+ 
Sbjct: 256 GFAG 259


>gi|295672502|ref|XP_002796797.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
 gi|226282169|gb|EEH37735.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
          Length = 475

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 87/185 (47%), Gaps = 17/185 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     VEAAKI+       I++N GCP      G  GA L+  PD++   + 
Sbjct: 116 LIFQIGTASPILAVEAAKIIAP-DVAGIDVNAGCPKPFSTSGGMGAALLQKPDLLVSILT 174

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+   +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H R   ++    
Sbjct: 175 ALVTEVGAPHQISISVKIRLLSDPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRER 230

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I + N  + I +NG +E    ALK++    VDG MI  +A  NS
Sbjct: 231 AIRDQLP-----MIASICR-NAGVAILMNGDVESRDHALKLMKEYGVDGAMIATSAEANS 284

Query: 224 AMLTT 228
           +   T
Sbjct: 285 SCFRT 289


>gi|118443329|ref|YP_877508.1| transcriptional regulator [Clostridium novyi NT]
 gi|118133785|gb|ABK60829.1| probable transcriptional regulator [Clostridium novyi NT]
          Length = 321

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/254 (22%), Positives = 112/254 (44%), Gaps = 31/254 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +++L  + + K +  QI   D  + +  A+ +++ GYNEINLN+GCPS  V     G+  
Sbjct: 49  RDVLPENNEVKNIVPQILTNDSERFINIARKLQELGYNEINLNLGCPSGTVVSKYRGSGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   + +   +  + K   + +++K R+G D          L+K   K  +  + IH R 
Sbjct: 109 LAKREELDRFLEEIFKIDDMKISIKTRLGKDS---PEEFYELIKIFNKYPLEELIIHPR- 164

Query: 158 AILKGLSPKDNRK-IPNLDYDIVYEIKKE------NPDLFIGLNGGLEDMSQALKILPSV 210
                 + +D  K  PNL      E+ K+      NP  + G      D  Q  +  P V
Sbjct: 165 ------TREDFYKNKPNL------EVFKDALSLSVNPICYNGDIFTSTDYKQLTEAFPQV 212

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
           + VMIGR    N  ++  + E        +  +  +V ++F  ++  +  +      ++ 
Sbjct: 213 ETVMIGRGILANPGLINEIKE--------NKTLDKKVLREFHDEVLNNYRELFNEDRNAM 264

Query: 271 GKLQQITRHMIGLF 284
            +++++  +MI +F
Sbjct: 265 FRMKELWGYMIYIF 278


>gi|58336619|ref|YP_193204.1| transcriptional regulator [Lactobacillus acidophilus NCFM]
 gi|58253936|gb|AAV42173.1| transcriptional regulator [Lactobacillus acidophilus NCFM]
          Length = 342

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/221 (25%), Positives = 114/221 (51%), Gaps = 20/221 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ + ++   + I
Sbjct: 41  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYIDQNTDADII 100

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK RIG D +    A+ 
Sbjct: 101 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRIGWDRK-HVFAVE 159

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+++++++ +     F+  NG
Sbjct: 160 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWEVLHDVAQVLDVPFVA-NG 207

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
            +     A K L  +    VM+GRAA  N  +L  +  Y  
Sbjct: 208 DIATPELAKKALDDIGCTAVMVGRAALGNPWILKDMVHYLE 248


>gi|254382913|ref|ZP_04998269.1| dihydrouridine synthase [Streptomyces sp. Mg1]
 gi|194341814|gb|EDX22780.1| dihydrouridine synthase [Streptomyces sp. Mg1]
          Length = 398

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 106/225 (47%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   EKP ++Q+ G 
Sbjct: 42  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATEKPRSIQLYGV 101

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A + IVE+   + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 102 DPATVGKAVRMIVEEDRADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 161

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G++D    +   +  +   + GV  I +H R                  D
Sbjct: 162 DLPVTMKMRKGINDD--HLTYLDAGRIAVEEGVTAIALHGRTTA--------QHYGGTAD 211

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 212 WEAIARLKEHVPEIPVLGNGDIWCAEDALRMVRETGCDGVVVGRG 256


>gi|253991187|ref|YP_003042543.1| tRNA -dihydrouridine synthase B [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782637|emb|CAQ85801.1| tRNA-dihydrouridine synthase B [Photorhabdus asymbiotica]
          Length = 328

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 109/244 (44%), Gaps = 26/244 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 24  MAGITDRPFRSLCYAM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHSDEPGIRSVQIAGND 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA++    G   I++N+GCP+ +V+    G+ L+  P++V   ++A+  A+ +P
Sbjct: 83  PDEMAAAARVNVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELVEKILSAVVNAVDVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN VK  +     G+  + IH R    +  G           
Sbjct: 143 VTLKIRTGWSPE-----ERNCVKIAQLAEHCGIQALTIHGRTRACLFNG----------E 187

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K+      I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 188 AEYDNIRTVKQTVAIPVIA-NGDITDPLKARAVLEYTGADALMIGRAAQGRPWIFREIQH 246

Query: 232 YFSN 235
           Y   
Sbjct: 247 YLET 250


>gi|159044125|ref|YP_001532919.1| tRNA-dihydrouidine synthase [Dinoroseobacter shibae DFL 12]
 gi|157911885|gb|ABV93318.1| tRNA-dihydrouidine synthase [Dinoroseobacter shibae DFL 12]
          Length = 333

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/214 (29%), Positives = 104/214 (48%), Gaps = 21/214 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           RF A L+ +  +   EM+ A A +R   +  LGF  Q    A+Q+ G +   + EAA+ V
Sbjct: 33  RFGAGLVVSEMVASQEMVQAKASVRARAE--LGFGAQAT--AVQLAGREAYWMGEAARYV 88

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            D G   I++N+GCP+ +V  G+ G+ LM + D     I A+  A+ +PVT+K R+G DD
Sbjct: 89  ADQGARVIDINMGCPAKKVVNGASGSALMRDLDHALTLIDAVVAAVDVPVTLKTRLGWDD 148

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
               +   +L +  + +G+  + IH R      KG +          D+  +  +K+   
Sbjct: 149 DC--LNAPDLARRAEAAGIAMVTIHGRTRCQFYKGAA----------DWTAIGRVKRAVS 196

Query: 188 DLFIGLNGGLEDM--SQALKILPSVDGVMIGRAA 219
              I  NG + D   +   +     DG+M+GR A
Sbjct: 197 IPVIA-NGDIVDTAAAAQARAASGADGLMVGRGA 229


>gi|302308179|ref|NP_985016.2| AER158Cp [Ashbya gossypii ATCC 10895]
 gi|299789331|gb|AAS52840.2| AER158Cp [Ashbya gossypii ATCC 10895]
          Length = 434

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/168 (27%), Positives = 81/168 (48%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M+ A      +K       ++ G  + ++PL +Q 
Sbjct: 34  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSEKYRRDMWSDLDGDESIDRPLVVQF 92

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AA++VE+   + ++LN+GCP     +G +G+ LM   D+V + I  +   
Sbjct: 93  CANDPEYLLKAAQLVEN-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLVANLINTLHTK 151

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           L++PVT K RI  D +          K +  +G   + +H R    KG
Sbjct: 152 LAVPVTAKIRIFPDRE----KTLAYAKMVLDAGAQFLTVHGRLREQKG 195


>gi|167526513|ref|XP_001747590.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774036|gb|EDQ87670.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1116

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 55/176 (31%), Positives = 90/176 (51%), Gaps = 17/176 (9%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q++PL  Q+    +   V AA+I+E F  + I+LN+GCP        FGA LM +   V 
Sbjct: 99  QDRPLIAQLCATKVEDFVAAAQILEPF-VDAIDLNLGCPQNTAKREGFGAYLMDDLPRVE 157

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             + A    L  P+T K R+      P + A R  ++ ++ +G + I IHAR   L+G  
Sbjct: 158 AMLRAARAVLHKPITAKVRL-----FPTLTATRAYLQMLEAAGCSLIAIHAR---LRG-- 207

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
            + ++  P  D+ +V E  ++  D+ + +NGG+  + QA  +L    V GVM+  A
Sbjct: 208 QRHHQGQP--DFAMVRE-ARDAVDIPLLVNGGVRSLRQAESVLEYTGVAGVMVAGA 260


>gi|295839031|ref|ZP_06825964.1| tRNA-dihydrouridine synthase [Streptomyces sp. SPB74]
 gi|295827295|gb|EDY44581.2| tRNA-dihydrouridine synthase [Streptomyces sp. SPB74]
          Length = 402

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 104/222 (46%), Gaps = 19/222 (8%)

Query: 5   TDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISK 61
           T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G D + 
Sbjct: 51  TNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMRLVQFGPTETPRSIQLYGVDPAT 110

Query: 62  LVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPV 119
           + +AA++V E+   + I+LN GCP  +V     G+ L     ++   +  A+  A  +PV
Sbjct: 111 VGKAARMVREENLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVAGADGLPV 170

Query: 120 TVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K R G+D D + A    +  +     G+  I +H R                  D+D 
Sbjct: 171 TMKMRKGIDEDHLTAF---DAGRIAVDEGITAIALHGRTTA--------QHYGGTADWDA 219

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +  +K+  P+L +  NG +     AL+++     DGV++GR 
Sbjct: 220 IARLKEHVPELPVLGNGDIWTAEDALRMVRETGCDGVVVGRG 261


>gi|225680962|gb|EEH19246.1| tRNA dihydrouridine synthase [Paracoccidioides brasiliensis Pb03]
          Length = 484

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 87/185 (47%), Gaps = 17/185 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     VEAAKI+       I++N GCP      G  GA L+  PD++   + 
Sbjct: 125 LIFQIGTASPILAVEAAKIIAP-DVAGIDVNAGCPKPFSTSGGMGAALLQKPDLLVSILT 183

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+   +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H R   ++    
Sbjct: 184 ALVTEVGAPHQISISVKIRLLSDPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRER 239

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I + N  + I +NG +E    ALK++    VDG MI  +A  NS
Sbjct: 240 AIRDQLP-----MIASICR-NAGVAILMNGDVESRDHALKLMKEYGVDGAMIATSAEANS 293

Query: 224 AMLTT 228
           +   T
Sbjct: 294 SCFRT 298


>gi|319638462|ref|ZP_07993224.1| tRNA-dihydrouridine synthase C [Neisseria mucosa C102]
 gi|317400211|gb|EFV80870.1| tRNA-dihydrouridine synthase C [Neisseria mucosa C102]
          Length = 321

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 87/186 (46%), Gaps = 12/186 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +
Sbjct: 64  PCTVQLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  + +G  P 
Sbjct: 124 RTLRQRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKV-EGYEPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   D VM+GR A     + 
Sbjct: 180 AHWEWVRKIRDAVSIPVTANGDVF-----SLQDYLD-IKTVSGCDSVMLGRGAVIRPDLA 233

Query: 227 TTVDEY 232
             + +Y
Sbjct: 234 RQIKQY 239


>gi|307245120|ref|ZP_07527213.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307254076|ref|ZP_07535923.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307258531|ref|ZP_07540268.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306854009|gb|EFM86221.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306863001|gb|EFM94948.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306867435|gb|EFM99286.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 313

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/284 (25%), Positives = 122/284 (42%), Gaps = 37/284 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +P
Sbjct: 55  GLTDSGTPVRVQLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDP 114

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 115 DLIYRATKAMREAVPQDQIVSVKVRLGWDSADQSFEIA-----DAVAQGGANEITVHGR- 168

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 169 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMI 221

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--K 272
           GR A  N+  L+ V             +K    K  W ++   +  Y    + H  G   
Sbjct: 222 GRGAL-NTPNLSRV-------------VKFNQPKIAWNEVLQLLFQYVNMENEHDSGFYH 267

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           + +I + +  L   +P ++    IL  E G      H IE A N
Sbjct: 268 VARIKQWLHYLDKEYPQAKDLFQILKTEHGYDGLKTH-IERAVN 310


>gi|261380252|ref|ZP_05984825.1| tRNA-dihydrouridine synthase [Neisseria subflava NJ9703]
 gi|284797111|gb|EFC52458.1| tRNA-dihydrouridine synthase [Neisseria subflava NJ9703]
          Length = 321

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 87/186 (46%), Gaps = 12/186 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +
Sbjct: 64  PCTVQLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  + +G  P 
Sbjct: 124 HTLRQRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKV-EGYEPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   D VM+GR A     + 
Sbjct: 180 AHWEWVRKIRDAVSIPVTANGDVF-----SLQDYLD-IKTVSGCDSVMLGRGAVIRPDLA 233

Query: 227 TTVDEY 232
             + +Y
Sbjct: 234 RQIKQY 239


>gi|325128142|gb|EGC51035.1| dihydrouridine synthase, Dus family [Neisseria meningitidis N1568]
          Length = 333

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 93/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   + E A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAENALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|254567437|ref|XP_002490829.1| tRNA-dihydrouridine synthase 1 [Pichia pastoris GS115]
 gi|238030625|emb|CAY68549.1| tRNA-dihydrouridine synthase 1 [Pichia pastoris GS115]
 gi|328351211|emb|CCA37611.1| tRNA-dihydrouridine synthase 1 [Pichia pastoris CBS 7435]
          Length = 407

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 86/168 (51%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNIL----GFSTQEKPLALQI 54
           MVD ++  +R  +R    + L YT M  A      +K  K+++    G    ++PL +Q 
Sbjct: 26  MVDQSELAWRILSRRYGAD-LCYTPMFHAKLFATQEKYRKDMMSELDGDEKVDRPLIVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AA++V D   + ++LN+GCP     +G++G+ LM +  +V   I  + + 
Sbjct: 85  CANDPEYLLQAARLVAD-KCDAVDLNLGCPQGIAKKGNYGSFLMDDWKLVHRLIKHLHEN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           LSIPVT K R+  DD+  ++      K +  +G   + IH R   +KG
Sbjct: 144 LSIPVTAKIRV-YDDKEKSL---EYAKMVLDAGAQFLTIHGRTREMKG 187


>gi|300812108|ref|ZP_07092556.1| TIM-barrel protein, nifR3 family [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496947|gb|EFK32021.1| TIM-barrel protein, nifR3 family [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 342

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 111/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           ++  EMI    I+ G++K  ++L     E P+++QI G     L++AA+ ++     +I 
Sbjct: 40  MVVCEMISDHGIIYGNEKTLSMLDVDPGEHPMSIQIFGGTEDSLLQAAQYIDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   +  + + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHKVVQNVEKPVSVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+ +     F+  NG
Sbjct: 159 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVAQVMDIPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y + 
Sbjct: 207 DITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 248


>gi|76156585|gb|AAX27767.2| SJCHGC04037 protein [Schistosoma japonicum]
          Length = 181

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 82/165 (49%), Gaps = 10/165 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L +T MI + + L   K   + L F+++++P+ +Q     
Sbjct: 17  MVDGSELAWRMLGRKY-GVQLTFTPMINSTSFLVNKKYRHSCLQFASEDRPIIVQFCANS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               ++ AK+V+ F  + ++LN+GCP     +G +GA L    D +   I+     LS+P
Sbjct: 76  PDTFIKCAKLVQPFC-DAVDLNLGCPQGIAKKGHYGAFLQDEWDCLKHIISRASSELSVP 134

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           VT K RI  D D+    A     K ++ +G + + +H R   +KG
Sbjct: 135 VTCKIRIFSDVDRTVQYA-----KLLEAAGASMLTVHGRTREMKG 174


>gi|91082415|ref|XP_970120.1| PREDICTED: similar to tRNA-dihydrouridine synthase [Tribolium
           castaneum]
 gi|270007514|gb|EFA03962.1| hypothetical protein TcasGA2_TC014107 [Tribolium castaneum]
          Length = 455

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 103/232 (44%), Gaps = 29/232 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           ++DW     +F   +   N +L T     D + + D   +     +EK  + +Q+G  D 
Sbjct: 44  LIDW-----KFLKSIRRENDVLGT----VDYLDKSDGTVVFRTCPREKNRVVVQLGTCDP 94

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            + ++ AK++E+     I++N+GCP     +G  GA L+  P+     ++ + + + IP+
Sbjct: 95  QRALKVAKMIEN-DVAGIDINMGCPKEFSLKGGMGAALLKQPEKAKSILSTLTQNVKIPI 153

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T K R+       A    +LVK +  +G++ I IH R    +   P  N  I  +     
Sbjct: 154 TCKIRVFES----AEETLDLVKELVSTGISAIAIHGRTKAERPQHPNRNATIKFI----- 204

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAML 226
                EN  + +  NGG +++ +   I+          VMI RAA  N ++ 
Sbjct: 205 ----AENVSIPVVANGGSKEIEKYQDIIKFKEECGCSSVMIARAAEANCSIF 252


>gi|282861786|ref|ZP_06270850.1| TIM-barrel protein, nifR3 family [Streptomyces sp. ACTE]
 gi|282563602|gb|EFB69140.1| TIM-barrel protein, nifR3 family [Streptomyces sp. ACTE]
          Length = 383

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 102/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 28  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDASETPRSIQLYGV 87

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKAL 115
           D   + +A + IVE+   + I+LN GCP  +V     G+ L    P +      A+  A 
Sbjct: 88  DPVTVGKAVRMIVEEDLADHIDLNFGCPVPKVTRKGGGSALPFKRPLLRAILKEAVAGAG 147

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 148 DLPVTIKMRKGIDDD--HLTYLDAGRIAVEEGVTAVALHGRTTA--------QHYGGTAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 198 WEAIARLKEHVPEIPVLGNGDIWSADDALRMMRETGCDGVVVGRG 242


>gi|256832754|ref|YP_003161481.1| TIM-barrel protein, nifR3 family [Jonesia denitrificans DSM 20603]
 gi|256686285|gb|ACV09178.1| TIM-barrel protein, nifR3 family [Jonesia denitrificans DSM 20603]
          Length = 380

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 71/297 (23%), Positives = 121/297 (40%), Gaps = 33/297 (11%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV- 69
           F A ++T+ AL+       D  LR     I+ F   E+P + Q+ G D + +  A  I+ 
Sbjct: 41  FVAEMVTSRALVERN----DVSLR-----IVSFEDYEQPRSAQVYGVDPATVGAAVSIIA 91

Query: 70  -EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
            ED   + I+LN GCP  +V     GA L    ++    + A  +A S   +PVTVK R+
Sbjct: 92  GEDRA-DHIDLNFGCPVPKVTRKGGGAALPWKKELYTRIVDAAVRAASPHHVPVTVKMRM 150

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD    +      K  +  GV+ + +HAR A                 +D +  +K+ 
Sbjct: 151 GIDDD--HMTYLEAGKIAEDLGVSAVALHARTAA--------QHYSGQARWDAIKNLKEH 200

Query: 186 NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              + +  NG +     AL ++     DGV++GR       +   +   F+      +P 
Sbjct: 201 VTTIPVLGNGDIWSAEDALNMVAHTGCDGVVVGRGCQGRPWLFADLTAAFAGRDERVTPG 260

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILTV 299
              V +  +R       +Y        G+ L+ + +HM     G+      R  L +
Sbjct: 261 LGYVAETIYRH-----GEYLVEFFGDEGRGLRDLRKHMAWYLKGYAVGGEARQALAL 312


>gi|54309774|ref|YP_130794.1| putative regulator protein [Photobacterium profundum SS9]
 gi|46914212|emb|CAG20992.1| putative regulator protein [Photobacterium profundum SS9]
          Length = 301

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 89/184 (48%), Gaps = 19/184 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +T   P+ +Q+ G +   + E A    + G   I++N GCP+  V++   GA L+  P
Sbjct: 42  GKTTSGTPVRVQLLGQEPVWMAENAYRASNLGSAGIDINFGCPAKSVNKNRGGAVLLKEP 101

Query: 102 D----IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +    IV +  +A+C   + PVT K R+G DD         +V ++ ++G + I IHAR 
Sbjct: 102 EKIYQIVKEVRSAVCP--TKPVTAKVRLGWDDPTHCF---EIVDAVAQAGGDEIAIHART 156

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMI 215
            +       D  K   + +D ++++ KE   + I  NG + +    QA   +   D +MI
Sbjct: 157 KV-------DGYKAETIKWDYIHQV-KEKSSIPIIANGEVWNYQDGQACLNVTQTDALMI 208

Query: 216 GRAA 219
            R A
Sbjct: 209 CRGA 212


>gi|295098775|emb|CBK87864.1| tRNA-U20-dihydrouridine synthase [Eubacterium cylindroides T2-87]
          Length = 326

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 101/222 (45%), Gaps = 18/222 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
            L+  EM+   A+    KK  ++      E P++ Q+ G DI  +V AAK ++     + 
Sbjct: 36  GLVCNEMVSDKALYYDSKKTFSMCDVDPNEHPVSFQLFGHDIDTVVYAAKYLDTQTNCDI 95

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVA 135
           I+ N+GCP  +V +   G+ LM + D   + ++ + + ++ PVTVK RIG D D I  V 
Sbjct: 96  IDFNMGCPVNKVIKAKAGSYLMKDIDYAKELVSHIVENVNKPVTVKMRIGFDKDHINCV- 154

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K+++  GV  + +H R         +        D+  + ++K+      IG NG
Sbjct: 155 --EMAKAMEGVGVKAVAVHGR--------TRSQMYEGKADWSYIKQVKEAVSIPVIG-NG 203

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +    ++      D VMIGR    N  ++    +   N
Sbjct: 204 DVRSVDDFFRMQKETGCDAVMIGRGIIGNPFLIQECKDALYN 245


>gi|225076728|ref|ZP_03719927.1| hypothetical protein NEIFLAOT_01779 [Neisseria flavescens
           NRL30031/H210]
 gi|224952004|gb|EEG33213.1| hypothetical protein NEIFLAOT_01779 [Neisseria flavescens
           NRL30031/H210]
          Length = 328

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 87/186 (46%), Gaps = 12/186 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +
Sbjct: 71  PCTVQLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIV 130

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  + +G  P 
Sbjct: 131 HTLRQRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKV-EGYEPP 186

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   D VM+GR A     + 
Sbjct: 187 AHWEWVRKIRDAVSIPVTANGDVF-----SLQDYLD-IKTVSGCDSVMLGRGAVIRPDLA 240

Query: 227 TTVDEY 232
             + +Y
Sbjct: 241 RQIKQY 246


>gi|50294732|ref|XP_449777.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49529091|emb|CAG62755.1| unnamed protein product [Candida glabrata]
          Length = 344

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 108/236 (45%), Gaps = 16/236 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R  +  I   +T   + PL +Q+G  +
Sbjct: 37  MVRYSKLPFRQTCRQYDTD-IVYTPMILAREFVRNQQARIADLTTNKNDTPLIVQVGVNN 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L++ A++V  F  + I +N GCP   ++ EG  G  L+ NPD++ + + ++      
Sbjct: 96  VGDLMKFAEMVAPFC-DGIGINCGCPIREQIREG-IGCALIYNPDLLCEMVKSVKSKYGA 153

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I + D        NL + +  SGV+ I IH R    +   P +   I      
Sbjct: 154 KLRLETKIRIHDDWDVTV--NLCRRLCDSGVDWITIHGRTRTTRSSQPVNLEAIKY---- 207

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           IV +IK +N  + +  NG    M     I     V GVM  R    N A+    D+
Sbjct: 208 IVDKIKDKN--VPVVANGDCFTMKDFKHISDYTGVQGVMAVRGVLANPALFAGHDK 261


>gi|296137143|ref|YP_003644385.1| TIM-barrel protein, nifR3 family [Thiomonas intermedia K12]
 gi|295797265|gb|ADG32055.1| TIM-barrel protein, nifR3 family [Thiomonas intermedia K12]
          Length = 350

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 108/245 (44%), Gaps = 25/245 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR L       +EM+ + A LR   K         +  P+A+QI G D
Sbjct: 36  MAGVTDRPYRRLARQL-GAGYCVSEMVTSRADLRDTLKTSRRANHDGEAAPIAVQIVGTD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---DCIAAMCKAL 115
             ++ EA +   + G + I++N+GCP+ +V     G+ LM + D+     +   A  +  
Sbjct: 95  PEQIAEATRYNLERGADIIDINMGCPAKKVCNRWAGSALMQDEDLAARLVEAAVAAARPF 154

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG---IWIHARKAILKGLSPKDNRKIP 172
             PVT+K R G  +     A RN  +  +++   G   + +H R         ++     
Sbjct: 155 DAPVTLKMRAGWCE-----AARNAPRIARRAEAAGAAMLVVHGRT--------REQGYGG 201

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             +Y  + E+K+ +  + +  NG ++   +A  +L     D VMIGRAA     +   V 
Sbjct: 202 EAEYATLAEVKR-SVGIPVVANGDIDSPQKAAAVLRQSGADAVMIGRAAMGRPWLFGQVA 260

Query: 231 EYFSN 235
            Y  +
Sbjct: 261 AYLEH 265


>gi|254480827|ref|ZP_05094073.1| putative TIM-barrel protein, nifR3 family [marine gamma
           proteobacterium HTCC2148]
 gi|214038622|gb|EEB79283.1| putative TIM-barrel protein, nifR3 family [marine gamma
           proteobacterium HTCC2148]
          Length = 334

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/240 (23%), Positives = 112/240 (46%), Gaps = 29/240 (12%)

Query: 21  LLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           L+ +EMI ++  LR  +K    ++  F  +  P ++QI G++  +L  AA+     G   
Sbjct: 44  LVVSEMISSNPRLRDSRKTAWRSVHDFEVE--PRSVQIAGSEPLELAAAAQYNVSQGAQI 101

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ +V + + G+ L+ +  +V D +  + K++ +PVT+K R G +        
Sbjct: 102 IDINMGCPAKKVCKKAAGSALLADEALVKDILHTVVKSVDVPVTLKIRTGANP-----GE 156

Query: 137 R---NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           R   N+ +  + +G+  + +H R    K             +YD +  I     +  +  
Sbjct: 157 RNGINIARIAQDAGIAALAVHGRTRACKFEGAA--------EYDTIAAIVAAT-EFPVFA 207

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG ++   +A  ++      GVM+GRAA     +   +  +    L+G + +    +K F
Sbjct: 208 NGDIDTPEKAAAVIRRTGAAGVMVGRAAQGKPWLCGQIAAH----LSGETIVSVTPEKQF 263


>gi|260801020|ref|XP_002595394.1| hypothetical protein BRAFLDRAFT_119015 [Branchiostoma floridae]
 gi|229280640|gb|EEN51406.1| hypothetical protein BRAFLDRAFT_119015 [Branchiostoma floridae]
          Length = 212

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 90/185 (48%), Gaps = 19/185 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  A    R +   ++ +    +++PL +Q    D
Sbjct: 27  MVDQSELPWRLLSRR-HGCQLAYTPMFHAALFSREETYFRDAMQTCPEDRPLIVQFCAND 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV+AA + +D   + I+LN+GCP +    G +GA L  + D++   ++A+ +  S+P
Sbjct: 86  PDILVQAALLAQDHC-DAIDLNLGCPQSIARRGHYGAFLQDDWDLIRRLVSAVHERCSVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSP-------KD 167
           VT K R+  D +          + ++K+G   + +H R    K  L GL+        KD
Sbjct: 145 VTCKIRVFQDVKRTV----EYAQMLEKAGCQLLTVHGRTKEQKGSLTGLASWDHIKAVKD 200

Query: 168 NRKIP 172
           + KIP
Sbjct: 201 SVKIP 205


>gi|166033391|ref|ZP_02236220.1| hypothetical protein DORFOR_03117 [Dorea formicigenerans ATCC
           27755]
 gi|166027748|gb|EDR46505.1| hypothetical protein DORFOR_03117 [Dorea formicigenerans ATCC
           27755]
          Length = 338

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 89/204 (43%), Gaps = 30/204 (14%)

Query: 42  GFSTQEKP-----------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           GFST+EK            L  QI        +   + ++ +GY E+NLN+GCPS  V  
Sbjct: 42  GFSTKEKNDVMPEHSPGMNLVPQIMSNQADSFLHTVEKLKVYGYEEVNLNLGCPSKTVVS 101

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
              G+  + +PD +   +  + K   + +++K RIG DD  P    R L+    +  V  
Sbjct: 102 KGRGSGFLADPDGLDRFLDEIFKKCDVKISIKTRIGKDD--PEEFAR-LLDIYNQYPVEE 158

Query: 151 IWIHARKAILKGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGL---EDMSQALK 205
           + IH R  + K       +  PNL   +D V E K     + +  NG +   E   +  +
Sbjct: 159 LIIHPR--VQKDFY----KNQPNLGAFHDAVEESK-----IPLCYNGDIFTPESYEEMKR 207

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTV 229
             P VD  M+GR    N A+L  +
Sbjct: 208 EFPQVDTFMLGRGILMNPALLDLI 231


>gi|269860977|ref|XP_002650205.1| tRNA-dihydrouridine synthase 1 [Enterocytozoon bieneusi H348]
 gi|220066379|gb|EED43863.1| tRNA-dihydrouridine synthase 1 [Enterocytozoon bieneusi H348]
          Length = 309

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/224 (25%), Positives = 111/224 (49%), Gaps = 21/224 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQE--KPLALQIGG 56
           MV +++  +R   R    + + YTEM+        + D +    ++T +  +PL +QI G
Sbjct: 1   MVSFSEEAFRILVRRYAVD-VCYTEMVNCKVFNQNKADPRKNRWYTTNDNDRPLVIQICG 59

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D S+++     ++ +  + I++N+GCP     +G++G+ LM + + V + I+ + + L+
Sbjct: 60  NDPSEMLATCLQIQQYC-DAIDINLGCPQNIAKKGNYGSYLMDDFEKVKNIISTLAEQLT 118

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+   C+I V + I         K I+KSG + + +H R    KG      +    + +
Sbjct: 119 VPIF--CKIRVFESIEKTI--TYAKMIEKSGCSLLAVHGRTREQKG------QNTGYVSF 168

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGR 217
           D +  +K     + +  NGG+    D+  A++I    DG+MIG 
Sbjct: 169 DHIRAVKNA-LSIPVVSNGGVLTHRDIKNAVEIT-GCDGIMIGE 210


>gi|326773529|ref|ZP_08232812.1| tRNA-dihydrouridine synthase [Actinomyces viscosus C505]
 gi|326636759|gb|EGE37662.1| tRNA-dihydrouridine synthase [Actinomyces viscosus C505]
          Length = 440

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/294 (22%), Positives = 125/294 (42%), Gaps = 32/294 (10%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKI 68
           F   LL    L  TEM+   A++  +++ +    T   E+  ++Q+ G D + +  A +I
Sbjct: 80  FDGGLLAPAGLYVTEMVTTRALVERNERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRI 139

Query: 69  -VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD-----------CIAAMCKALS 116
            VE+   + I+LN GCP  +V     GA L    D++              + A+ +A  
Sbjct: 140 LVEEDLADHIDLNFGCPVPKVTRKGGGAALPWKRDLLAAILTEAVRASEAAVRAVGRARQ 199

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R+G+D++       +  ++ + +G+  + +HAR A           +I  L  
Sbjct: 200 VPVTMKMRLGIDEE--HETFLDAARAAENAGIAAVALHARSARQHYSGQARWEEIARL-- 255

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
                  KE  DL +  NG +     A++++ +   DGV++GR       +   +     
Sbjct: 256 -------KEATDLPVLGNGDVWLGDDAVRMMEATGCDGVVVGRGCQGRPWLFADIVAAMH 308

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                 SP +TR D D   ++        A  +     ++ + +H+     G+P
Sbjct: 309 G-----SPARTRPDLDAVIEVIRRHGRMLAEEMGEDRGVRDLRKHVGWYLKGYP 357


>gi|162452011|ref|YP_001614378.1| dihydrouridine synthase TIM-barrel protein nifR3 [Sorangium
           cellulosum 'So ce 56']
 gi|161162593|emb|CAN93898.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sorangium
           cellulosum 'So ce 56']
          Length = 328

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 75/307 (24%), Positives = 138/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   R L    L  TE +  + +LRG K  +  L  +  ++P A+QI GA+
Sbjct: 22  MEDVTDAVFRRIGRELGAE-LCVTEFVNVEGLLRGCKTARRKLALADGDQPTAIQIYGAN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA++ E+ G   +++N GC   ++     GA  + +P+ +      + +++++P
Sbjct: 81  PERLAEAARVAEEAGPAFLDINCGCWVPKIAGRGAGAGWLRDPEAMVAMARLVTRSVALP 140

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD------NRK 170
           VTVK RI  G +  +P V   +L + ++ +GV  + IH R A +      D       R+
Sbjct: 141 VTVKTRIGWGPESHMPIV---DLARRLEDAGVAALTIHCRTAQMGHSGAADWGWAARARE 197

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           + ++   +  +IK  +            D ++AL+      GVM+GRAA  +  +     
Sbjct: 198 VVSIPVVVNGDIKTAD------------DAARALRET-GCAGVMVGRAAIDHPWIFREAR 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               + +    P     ++      +  + +  AR    G ++ +  RH+ G   G P +
Sbjct: 245 ALLDDGVHLPPPT---AEERLALCRAHLIANTEARGEPHGVRVTR--RHLTGYLRGLPGA 299

Query: 291 RRCRHIL 297
              R  L
Sbjct: 300 SALRREL 306


>gi|198429785|ref|XP_002120440.1| PREDICTED: similar to MGC79829 protein [Ciona intestinalis]
          Length = 305

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 111/244 (45%), Gaps = 24/244 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   R    + + YT MIVA + L  D  ++N    S  + PL +Q    +
Sbjct: 21  MVRYSKHAFRLLVRKYDCD-IAYTPMIVAKSFLESDSCRQNEFITSKDDTPLIVQFAAKN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
             +  EA++++  F  + + LN GCP        +GA L+  P+ + D I    KAL   
Sbjct: 80  AKEFSEASELIYPFA-SGVGLNCGCPQRWAMAEGYGAKLLQKPEEIVDFI-RFTKALVSD 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
              T+  +I + +++       + + ++K+G + + +H R +          R  P + Y
Sbjct: 138 EKFTISVKIRLHEELARTV--EMCRGLEKAGASFVSVHGRTS--------KERHQP-VHY 186

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + +I KE+  + I  NGG+       K+  +   +GVM+ +    N A+      Y +
Sbjct: 187 DAI-KILKESVSIPIVANGGVNTYKDFDKVHKMTGANGVMVAQGLLNNPALF---QGYKT 242

Query: 235 NPLT 238
            PL+
Sbjct: 243 TPLS 246


>gi|331090015|ref|ZP_08338905.1| hypothetical protein HMPREF1025_02488 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330402929|gb|EGG82495.1| hypothetical protein HMPREF1025_02488 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 311

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 107/250 (42%), Gaps = 40/250 (16%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+IL    +      QI        V+ AK +E +GY EINLNVGCPS  V     GA
Sbjct: 47  EKKDILPEHNKGMHAVPQILTNCAEDFVQTAKKLEQYGYKEINLNVGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWI 153
             +  P+ +   +  + +   I ++VK RIG +  ++ P      L+    K  +  + I
Sbjct: 107 GFLAFPERLDLFLEEVFQNCPIDISVKTRIGTESGEEFP-----KLMDIYNKYPIKELII 161

Query: 154 HARKAILKGLSPKDNRK-IPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPS 209
           H R       + KD  K IP++D   V+E         I  NG L   ED+    +  P 
Sbjct: 162 HPR-------TQKDFYKNIPHMD---VFEKALGTGRHKICYNGDLTSEEDVRNLSEQFPE 211

Query: 210 VDGVMIGRAAYKNSAMLTTVD------------------EYFSNPLTGSSPIKTRVDKDF 251
           V+ +MIGR    + A+   +                   E +   ++G   +  ++ K+ 
Sbjct: 212 VESIMIGRGVLADPAIARKIKGGDGADKAEMRHFHDMLYEAYCEEMSGERTVLYKM-KEL 270

Query: 252 WRKISASMTD 261
           W  +++S T+
Sbjct: 271 WFYLASSFTN 280


>gi|300932473|ref|ZP_07147729.1| hypothetical protein CresD4_00255 [Corynebacterium resistens DSM
           45100]
          Length = 394

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 41/118 (34%), Positives = 64/118 (54%), Gaps = 6/118 (5%)

Query: 19  NALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYN 75
           + L   EM+ A A++  + K  ++  F   E+P +LQ+   D     EAAK IV++   +
Sbjct: 57  SGLYVCEMVTARALVERNPKTLHMTTFGPDEQPRSLQLYTTDPKYTYEAAKMIVDENMAD 116

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQ 130
            I++N GCP  +V     G+ L     + G+ +AA  KA     IPVTVK R+G+DD+
Sbjct: 117 HIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAAVKATEGTDIPVTVKFRVGIDDE 174


>gi|298291769|ref|YP_003693708.1| hypothetical protein Snov_1785 [Starkeya novella DSM 506]
 gi|296928280|gb|ADH89089.1| TIM-barrel protein, nifR3 family [Starkeya novella DSM 506]
          Length = 343

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 114/245 (46%), Gaps = 15/245 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD   R  A L    +L  +EM+ + A+  G ++ +L    +   L A+Q+ G + 
Sbjct: 27  MAGITDAPMRRMA-LRYGASLAVSEMVASAALETGHEETVLRAEGEGVALHAVQLAGNEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + +  AA+I E  G   I++N+GCP+ RV  G  G+ L+ + D+    I ++  A+ +PV
Sbjct: 86  ASMARAARIAEAAGAAIIDINMGCPAKRVTTGLAGSALLRDLDLATSIIESVVAAVKVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD +  +    L +  +  GV  + IH R         +        D+  +
Sbjct: 146 TLKTRLGWDDNV--LVAPELARRAEAIGVQLVTIHGRT--------RCQFYTGRADWAAI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K+    + +  NG L +   A  +L +   DG+MIGR A         V E   +  
Sbjct: 196 RQVKQAV-SIPVLANGDLVEAEDAPAMLAASGTDGLMIGRGAQGRPWFPGQVVERLRSGR 254

Query: 238 TGSSP 242
           T + P
Sbjct: 255 TPADP 259


>gi|145349324|ref|XP_001419086.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144579317|gb|ABO97379.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 307

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/248 (23%), Positives = 110/248 (44%), Gaps = 20/248 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   +      L YT MI A   +   K  + I   ST+++PL  Q    D
Sbjct: 23  MVDQSELAFRELCKRY-GATLGYTPMIHARLFVESPKYRREIFSTSTRDRPLLAQFCAND 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AA ++  +  + +++N GCP      G++GA LM +   V   I  + + L +P
Sbjct: 82  PEILLRAATMIAPYC-DGVDINFGCPQRIAKRGNYGAFLMDDWKTVEALIRKLDEELPVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +          K ++ +G   + +H R         ++ ++  ++  + 
Sbjct: 141 VTAKIRVYDDLE----TTLKYAKMVEAAGAQIVAVHGRT--------REQKRCADIRANW 188

Query: 179 VY-EIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            Y    K+   + +  NG +  +++A   L +   DGV+       N A+ +    +++ 
Sbjct: 189 AYIRAIKDALKVPVLANGDIRSLAEARACLEATGADGVLSAEPLLSNPALFSD-PPFYAA 247

Query: 236 PLTGSSPI 243
           P  G +PI
Sbjct: 248 PTDGYAPI 255


>gi|118099691|ref|XP_415637.2| PREDICTED: similar to DUS1L protein isoform 2 [Gallus gallus]
          Length = 486

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 81/166 (48%), Gaps = 10/166 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---DKKNILGFSTQE-KPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   LR     ++N+ G +  E +PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRRENLYGEACPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +P+T  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 142 VPIT--CKIRVFPEIDKTV--KYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|302518906|ref|ZP_07271248.1| dihydrouridine synthase [Streptomyces sp. SPB78]
 gi|318062752|ref|ZP_07981473.1| dihydrouridine synthase [Streptomyces sp. SA3_actG]
 gi|318080557|ref|ZP_07987889.1| dihydrouridine synthase [Streptomyces sp. SA3_actF]
 gi|302427801|gb|EFK99616.1| dihydrouridine synthase [Streptomyces sp. SPB78]
          Length = 402

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 102/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 47  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMRLVQFGPAETPRSIQLYGV 106

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +AA+++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 107 DPVTVGKAARMIRDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVAGAD 166

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +     G+  I +H R                  D
Sbjct: 167 GLPVTMKMRKGIDDD--HLTALDAGRIAVDEGITAIALHGRTTA--------QHYGGTAD 216

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P+L +  NG +     AL+++     DGV++GR 
Sbjct: 217 WDAIARLKEHVPELPVLGNGDIWTAEDALRMVRETGCDGVVVGRG 261


>gi|118099689|ref|XP_001232803.1| PREDICTED: similar to DUS1L protein isoform 1 [Gallus gallus]
          Length = 473

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 81/166 (48%), Gaps = 10/166 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---DKKNILGFSTQE-KPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   LR     ++N+ G +  E +PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRRENLYGEACPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +P+T  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 142 VPIT--CKIRVFPEIDKTV--KYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|325204077|gb|ADY99530.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M01-240355]
          Length = 333

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 93/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   + E A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAENALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|227833973|ref|YP_002835680.1| hypothetical protein cauri_2149 [Corynebacterium aurimucosum ATCC
           700975]
 gi|262183538|ref|ZP_06042959.1| hypothetical protein CaurA7_06061 [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454989|gb|ACP33742.1| hypothetical protein cauri_2149 [Corynebacterium aurimucosum ATCC
           700975]
          Length = 381

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/292 (23%), Positives = 121/292 (41%), Gaps = 25/292 (8%)

Query: 17  TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFG 73
           T + L   EM+ A A++  + K  ++  F  QE+P +LQ+   D     +AAK IV++  
Sbjct: 41  TVSGLYVCEMVTARALVERNPKTLHMTTFDPQEQPRSLQLYTVDPEYTYKAAKMIVDENL 100

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQ 130
            + I++N GCP  +V     G+ L     + G+ +AA  KA     IPVTVK R+G+D++
Sbjct: 101 ADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAAVKATEGTDIPVTVKMRVGIDEE 160

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                    +   + +      +H R A          R   + D+  +  +K+   D  
Sbjct: 161 HKTHLDAGRIAVAEGAAAVA--LHGRTAA--------QRYSGHADWGEIARLKEHLADTG 210

Query: 191 IGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           I +  NG +   + A  ++     DGV++GR       +   +  +         P    
Sbjct: 211 IPVLGNGDIFKATDAHDMMKQTGCDGVVVGRGCLGRPWLFAELSAHLRGEPVPEEPTLGE 270

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           V +   R       +  A+H       + I +H+     GFP   + R  L+
Sbjct: 271 VTRIMIRH-----AELLAQHEGEAQASRDIRKHIGWYLRGFPVGGQVRAGLS 317


>gi|227506387|ref|ZP_03936436.1| possible tRNA-dihydrouridine synthase [Corynebacterium striatum
           ATCC 6940]
 gi|227197038|gb|EEI77086.1| possible tRNA-dihydrouridine synthase [Corynebacterium striatum
           ATCC 6940]
          Length = 381

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/120 (35%), Positives = 66/120 (55%), Gaps = 6/120 (5%)

Query: 17  TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFG 73
           T + L   EM+ A A++  ++K  ++  F  +E P +LQ+   D     +AAK IV++  
Sbjct: 41  TVSGLYVCEMVTARALVERNEKTMHMTTFGPEENPRSLQLYTVDPEYTYKAAKMIVDENL 100

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQ 130
            + I++N GCP  +V     G+ L     + G+ IAA  KA     IPVTVK R+G+DD+
Sbjct: 101 ADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIIAAAVKATEGTDIPVTVKMRVGIDDE 160


>gi|164661924|ref|XP_001732084.1| hypothetical protein MGL_0677 [Malassezia globosa CBS 7966]
 gi|159105986|gb|EDP44870.1| hypothetical protein MGL_0677 [Malassezia globosa CBS 7966]
          Length = 473

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 54/184 (29%), Positives = 85/184 (46%), Gaps = 28/184 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQE---------- 47
           MVD ++  +R   R    + L+YT MI A   +   RG  +   GF  Q+          
Sbjct: 41  MVDQSELAWRILCRRYGAD-LVYTPMINAKIYVQQGRGTHRVREGFFNQDVGEEGAHTLD 99

Query: 48  ---------KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
                    +PL +Q    D   L+EAA+ V+D   + ++LN+GCP      G FGA LM
Sbjct: 100 LCDDRKDSDRPLIVQFCANDPDMLLEAAQAVQD-KCDAVDLNLGCPQQIAKRGKFGAFLM 158

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            + D+V   I  +   L +PVT K R+  D    ++A     + I+++G   + +H R  
Sbjct: 159 DDWDLVFRLINTLHLNLKVPVTAKFRV-YDSVEKSIA---YARMIQRAGAQIVTVHGRTR 214

Query: 159 ILKG 162
            +KG
Sbjct: 215 EMKG 218


>gi|325955982|ref|YP_004286592.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus 30SC]
 gi|325332547|gb|ADZ06455.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus 30SC]
          Length = 341

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 112/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ V+     +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYVDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+ +++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWGVLHDVAQVLDVPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y   
Sbjct: 207 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILQDMVHYLET 248


>gi|317501236|ref|ZP_07959441.1| dihydrouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897412|gb|EFV19478.1| dihydrouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 311

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 107/250 (42%), Gaps = 40/250 (16%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+IL    +      QI        V+ AK +E +GY EINLNVGCPS  V     GA
Sbjct: 47  EKKDILPEHNKGMHAVPQILTNCAEDFVQTAKKLEQYGYKEINLNVGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWI 153
             +  P+ +   +  + +   I ++VK RIG +  ++ P      L+    K  +  + I
Sbjct: 107 GFLAFPERLDLFLEEVFQNCPIDISVKTRIGTESGEEFP-----KLMDIYNKYPIKELII 161

Query: 154 HARKAILKGLSPKDNRK-IPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPS 209
           H R       + KD  K IP++D   V+E         I  NG L   ED+    +  P 
Sbjct: 162 HPR-------TQKDFYKNIPHMD---VFEKALGTGRHKICYNGDLTSEEDVRNLSEQFPE 211

Query: 210 VDGVMIGRAAYKNSAMLTTVD------------------EYFSNPLTGSSPIKTRVDKDF 251
           V+ +MIGR    + A+   +                   E +   ++G   +  ++ K+ 
Sbjct: 212 VESIMIGRGVLADPAIARKIKGGDGADKAEMRHFHDMLYEAYCEEMSGERTVLYKM-KEL 270

Query: 252 WRKISASMTD 261
           W  +++S T+
Sbjct: 271 WFYLASSFTN 280


>gi|116491410|ref|YP_810954.1| tRNA-dihydrouridine synthase [Oenococcus oeni PSU-1]
 gi|290890989|ref|ZP_06554053.1| hypothetical protein AWRIB429_1443 [Oenococcus oeni AWRIB429]
 gi|116092135|gb|ABJ57289.1| tRNA-dihydrouridine synthase [Oenococcus oeni PSU-1]
 gi|290479388|gb|EFD88048.1| hypothetical protein AWRIB429_1443 [Oenococcus oeni AWRIB429]
          Length = 330

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 111/223 (49%), Gaps = 31/223 (13%)

Query: 21  LLYTEMIVADAILRGDKK-NILGF----STQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L YTE   A ++     K +++G       +++P+ +Q+ G   S   +AA  V++ G+ 
Sbjct: 46  LFYTEFTNAISVTHPKAKFSVMGRLYVKKDEQRPI-VQLWGNHASDFAKAALSVKNQGFK 104

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQIP 132
            I++N+GCP + V +   G+ L+ +     + I A  K   +P++ K R+G   +D+   
Sbjct: 105 AIDINMGCPDSTVVKNGGGSDLIRHRSAAAEVIQA-SKEAGLPISAKTRLGFSKIDE--- 160

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PD 188
              + + +  + K  +  + +H R       + K+  K+P   ++++ EI K      P+
Sbjct: 161 ---MYDWLPWLLKQDLQVLTVHLR-------TRKEMSKVP-AHFELIDEIIKMRDQIAPE 209

Query: 189 LFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTT 228
             + +NG +++ S+ +++    P +DG+MIGR  ++N     T
Sbjct: 210 TLLQINGDIKNRSEGIELAKKHPGIDGIMIGRGVFENPYCFET 252


>gi|189425844|ref|YP_001953021.1| hypothetical protein Glov_2788 [Geobacter lovleyi SZ]
 gi|189422103|gb|ACD96501.1| TIM-barrel protein, nifR3 family [Geobacter lovleyi SZ]
          Length = 325

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/299 (23%), Positives = 128/299 (42%), Gaps = 27/299 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           T+  +R   R      L +TEMI  + ++R  +K +  L  S  ++PL +Q+ G     L
Sbjct: 27  TNHVFRLICRQ-AGACLAFTEMISVNGMVREGEKTLALLSSSPDDRPLGVQLFGNAPELL 85

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            +AA +V+D   + I++N+GCP  +V     G+ L+ +   + + + ++ +  ++P+T+K
Sbjct: 86  AQAASMVKD-NADLIDINMGCPVRKVVGTGAGSALLQDTARIAEIVRSVRRTTNLPLTIK 144

Query: 123 CRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            R G    DD    V      +  +  G + I +H R          D ++I  L   + 
Sbjct: 145 IRSGWQCGDDTWQEVG-----RIAEAEGCDAITLHPRSRAQMFNGQADWQQIGQLKQLVK 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLT 238
             +     DLF       +D  + L      DG+M+ R A  N  + +   E     P+T
Sbjct: 200 IPVIGSG-DLFTP-----QDCRRMLS-ETGCDGLMVARGALGNPWIFSQTCELLEGRPVT 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              P+          +  A  TDYA   +     ++++ +H+    HG P +   R  +
Sbjct: 253 ---PVSCADRMAMAEQHLALFTDYAGESV----AVREMKKHLGWYIHGVPGAAALRRTV 304


>gi|187925312|ref|YP_001896954.1| hypothetical protein Bphyt_3339 [Burkholderia phytofirmans PsJN]
 gi|187716506|gb|ACD17730.1| TIM-barrel protein, nifR3 family [Burkholderia phytofirmans PsJN]
          Length = 354

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 74/307 (24%), Positives = 140/307 (45%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWNRENKNAL--NVARLAESAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A ++L +   D +MIGRAA     +   + E
Sbjct: 187 AEYETIAAVKAA-VRIPVVANGDITSPHKAREVLAATGADAIMIGRAAQGRPWLFREI-E 244

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           YF    TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 245 YFLQ--TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 297

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 298 GANVFRH 304


>gi|147906386|ref|NP_001086550.1| dihydrouridine synthase 1-like [Xenopus laevis]
 gi|49903669|gb|AAH76792.1| MGC83715 protein [Xenopus laevis]
          Length = 464

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 83/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+     ++++PL +Q  
Sbjct: 18  MVDQSELAWRLLSRRHGVQLCYTPMLHAQVFVRDANYR--KENLYCERCSEDRPLIVQFC 75

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 76  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQDEWDLLEKMIQLAHQKL 134

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  ++         K ++K+G   + +H R    KG
Sbjct: 135 SVPVT--CKIRVFPEMEKTV--QYAKMLEKAGCQLLTVHGRTKEQKG 177


>gi|315037518|ref|YP_004031086.1| transcriptional regulator [Lactobacillus amylovorus GRL 1112]
 gi|312275651|gb|ADQ58291.1| transcriptional regulator [Lactobacillus amylovorus GRL 1112]
 gi|327182814|gb|AEA31261.1| tRNA-dihydrouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 341

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 112/222 (50%), Gaps = 20/222 (9%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  +++    +E P+++QI G     L++AA+ V+     +I 
Sbjct: 40  LVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGTEETLLQAAQYVDQHTDADII 99

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   + A+ + +  PV+VK RIG D +    A+ 
Sbjct: 100 DINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQKPVSVKMRIGWDRK-HIFAVE 158

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + I +H   RK + +G +          D+ +++++ +     F+  NG
Sbjct: 159 NALAA-QEAGASMIAMHGRTRKQMYQGEA----------DWGVLHDVAQVLDVPFVA-NG 206

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     A K L  +    VM+GRAA  N  +L  +  Y   
Sbjct: 207 DIRTPELAKKALDEIGCTAVMVGRAALGNPWILQDMVHYLET 248


>gi|171911693|ref|ZP_02927163.1| Dihydrouridine synthase, DuS [Verrucomicrobium spinosum DSM 4136]
          Length = 366

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 107/248 (43%), Gaps = 33/248 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNA---LLYTEMIVADA-------ILRGDKKNILGFSTQEKPL 50
           M D TD     F RL+ +     L YTE     A       ILR   +N  G     +P+
Sbjct: 39  MQDVTDLP---FWRLMADYGGADLYYTEYFRVHADSNLEKPILRSVTENPTG-----RPV 90

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           A Q+ G DI+ LV  A+ +++     ++LN+GCP+  V++   G  L+ +P  V   + A
Sbjct: 91  AAQMIGNDIASLVRTARELQEHPIAAVDLNLGCPAPVVYKKCAGGGLLRDPRHVDAILGA 150

Query: 111 MCKA-LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +  A +    TVK RIG DD   A      +    K  ++ + +H R       S     
Sbjct: 151 LRDAVVKCKFTVKTRIGFDD---AGVFEQFLPLFAKHDIDLLTVHGRTVAEMYRS----- 202

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
               + YD +     E     +  NG +   ++A +IL      G+MIGR A +N  M  
Sbjct: 203 ---EVHYDFIAR-AVEAMKCPVLANGNVSSAAKAEEILQLTGARGLMIGRGAIRNPWMFR 258

Query: 228 TVDEYFSN 235
            + ++ + 
Sbjct: 259 QIRQHLAR 266


>gi|256825031|ref|YP_003148991.1| TIM-barrel protein, nifR3 family [Kytococcus sedentarius DSM 20547]
 gi|256688424|gb|ACV06226.1| putative TIM-barrel protein, nifR3 family [Kytococcus sedentarius
           DSM 20547]
          Length = 419

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/279 (24%), Positives = 119/279 (42%), Gaps = 26/279 (9%)

Query: 19  NALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYN 75
           ++L  +EMI   A++        ++ F  +E+P ++Q+ G D + +  AA+ IVE+   +
Sbjct: 77  SSLYVSEMITTRALVERTPITMKLVEFDAEEQPRSMQLYGVDPATVRAAARDIVENDRAD 136

Query: 76  EINLNVGCPSARVHEGSFGACL----MLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQ 130
            I++N GCP  +V     GA +     L  DIV   +    KA  IPVTVK RIG+D D 
Sbjct: 137 HIDMNFGCPVPKVTRKGGGAAIPWKSTLFRDIVRSAVEEASKA-DIPVTVKMRIGIDEDH 195

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
              +    + + +   G   + +HAR A                 +  +  +K+    + 
Sbjct: 196 HTHLEAGRIAEDM---GAAAVALHARTA--------SQAYSGQARWGEIARLKQTVTTIP 244

Query: 191 IGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG +     AL+++     DGV++GR       + T +   F+      +P    V 
Sbjct: 245 VLGNGDIWSAEDALRMVAETGCDGVVVGRGCLGRPWLFTDLAAAFAGSDARVTPTLREVT 304

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               R+ +  + D+   H       + I +H+     GF
Sbjct: 305 ATL-RRHAEYLADF---HEDENHACRDIRKHITWYLKGF 339


>gi|324517466|gb|ADY46829.1| tRNA-dihydrouridine synthase-like protein [Ascaris suum]
          Length = 348

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 62/262 (23%), Positives = 113/262 (43%), Gaps = 31/262 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   RL   + L+YT MI A+  +  ++     F+T   + P  +Q    D
Sbjct: 63  MVRYSKLPFRSLVRLYGAD-LVYTPMINANNFITSEECRSSEFTTNKYDSPTIVQFASND 121

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSI 117
             +   A ++V  +  + ++LN GCP   V  G +G+ L+  P+ + D IA A  +    
Sbjct: 122 PVEFAAATELVYRYC-SGVDLNCGCPKRDVMRGGYGSSLLSTPERIADMIAHARRRIADT 180

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             T+  +I +++ I       L + ++ +G + I +H R    +   P ++  I      
Sbjct: 181 QFTISVKIRLNNDIRRTV--ELCRQVESAGASYICVHGRTPTQRS-EPANHEAI------ 231

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               + K    + I  NG +    +AL++      DGVM       N AM    D     
Sbjct: 232 ---ALVKSAMRIPIIANGAIGSYQEALQVAKRTQTDGVMAANGLLDNPAMFAGHD----- 283

Query: 236 PLTGSSPIKTRVDKDFWRKISA 257
               S+P++  +D   W +I+A
Sbjct: 284 ----STPVQCVLD---WLRITA 298


>gi|321261612|ref|XP_003195525.1| tRNA dihydrouridine synthase [Cryptococcus gattii WM276]
 gi|317461999|gb|ADV23738.1| tRNA dihydrouridine synthase, putative [Cryptococcus gattii WM276]
          Length = 725

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 106/238 (44%), Gaps = 24/238 (10%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL  +     T  EM +A  ++ G K+   ++     EK   LQ+ G   +++V AA+
Sbjct: 373 FRRLCVDYGATITISEMALAQPLVYGAKEEWALVRRHESEKMFGLQVAGGFPNRMVPAAE 432

Query: 68  IVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTV 121
           I+ +      G + +++N+GCP   V     G+ LM +P  +G  +  M +AL  IP+TV
Sbjct: 433 IIANTIGKGGGVDFVDVNMGCPIDLVFNQGAGSALMDSPGRLGKLLVGMNRALGEIPLTV 492

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV    P  A + + +   + GV  + IH R    +   P D   I      +   
Sbjct: 493 KFRTGVAHGKPN-AHKLIPRFATEWGVRALTIHGRSRQQRYSKPADWDYIKTCVTTLRES 551

Query: 182 IKKEN-PDLFIGLNGG-------LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   N P + I  NG         E+M ++      VDGVM+ R A     + T + E
Sbjct: 552 VADANLPPVPIFGNGDCFSAASYYEEMEKS-----GVDGVMVARGALIKPWIFTEIKE 604


>gi|66815915|ref|XP_641974.1| tRNA-dihydrouridine synthase 1-like protein [Dictyostelium
           discoideum AX4]
 gi|60470022|gb|EAL68003.1| tRNA-dihydrouridine synthase 1-like protein [Dictyostelium
           discoideum AX4]
          Length = 435

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 82/166 (49%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD T   +R   R    + ++YT M  +   A  +  +++      +++PL +Q  G +
Sbjct: 59  MVDHTFLAFRMLCRKYGAD-MVYTPMFHSKNFATCKTYRRDYWSTCPEDRPLVVQFCGNE 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V+AAK +ED   + I+LN+GCP      G++G+ L+  P I+   +  + K + +P
Sbjct: 118 PEWVVKAAKYIEDHC-DAIDLNLGCPQQIARRGNYGSFLLDKPHIILPIVQELHKHIKVP 176

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +  K R+   +DD I       L   ++++G   + IH R    KG
Sbjct: 177 IFCKIRLLPNLDDTI------KLALQLQEAGCQLLTIHGRTKEQKG 216


>gi|113968744|ref|YP_732537.1| nifR3 family TIM-barrel protein [Shewanella sp. MR-4]
 gi|114049112|ref|YP_739662.1| nifR3 family TIM-barrel protein [Shewanella sp. MR-7]
 gi|117918856|ref|YP_868048.1| nifR3 family TIM-barrel protein [Shewanella sp. ANA-3]
 gi|113883428|gb|ABI37480.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. MR-4]
 gi|113890554|gb|ABI44605.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. MR-7]
 gi|117611188|gb|ABK46642.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. ANA-3]
          Length = 322

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 78/332 (23%), Positives = 155/332 (46%), Gaps = 37/332 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK +  +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLC-LRYGAALAVSEMLSSNPEVWDTDKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G + I++N+GCP+ +V++   G+ LM NP +V + + A+  A+ +P
Sbjct: 76  PELMAQAAQFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKEILQAVVAAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN   + +  +  G+  + +H   R+ + +G          +
Sbjct: 136 VTLKIRTGWEPE-----HRNGVQIAQIAEDCGIASLAVHGRTRQCMYRG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K+N  + +  NG ++   +A  +L    VD +MIGR A     +   +  
Sbjct: 181 AEYDTIKAI-KQNVSIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQH 239

Query: 232 YFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           Y     TG+  +PI+    +    +    + D     L+   K  +  R  IG +    +
Sbjct: 240 YLD---TGNKLAPIEVAEQRQVMLEHLTKLYD-----LYGEYKGIRFARKHIGWYLDQED 291

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            R+ R     +   +   + ++E  F+ ++++
Sbjct: 292 QRQFRADFN-QLETAAEQYSLVEYYFDELVQN 322


>gi|327393212|dbj|BAK10634.1| tRNA-dihydrouridine synthase C DusC [Pantoea ananatis AJ13355]
          Length = 328

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 54/190 (28%), Positives = 91/190 (47%), Gaps = 16/190 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQ+ G     L E A      G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 67  LQLLGQHPDWLAENAARAVTLGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRAAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+  S+PVTVK R+G D    ++    +  +++++G + + +H R       + +D  
Sbjct: 127 RAAVPASLPVTVKVRLGWDSSARSM---EIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +   +++  + +I++      I  NG + D   A   L +   D VMIGR A  N   L+
Sbjct: 177 RAEAINWQAIGDIRQRLRIPVIA-NGEIWDWQTAQDCLRTTGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEYFSNPL 237
            V +Y   P+
Sbjct: 235 RVIKYNDAPM 244


>gi|325474572|gb|EGC77758.1| NifR3 family TIM-barrel protein [Treponema denticola F0402]
          Length = 334

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/307 (22%), Positives = 132/307 (42%), Gaps = 31/307 (10%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINL 79
           YTEM+ ++A++R   K  +++G +  EK  A+QI G++   + + A I+ E +    I++
Sbjct: 46  YTEMVSSEALVRDSDKTESLIGRAPNEKAYAVQIFGSNPEYMAKTAVIIAEKYSPECIDI 105

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVAL 136
           N GCP A++ +   G+ LM +  ++   + A+  A++   IPVT+K R G       +  
Sbjct: 106 NSGCPMAKITKNGAGSALMTDIPLLYRIVKAVNDAMAPYKIPVTLKIRSGFTAD--KLNW 163

Query: 137 RNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIG 192
           +    +   +GV  + +H   R  +  G            D++I+ E+ +  ++  + I 
Sbjct: 164 KEAASAAIDAGVKMLTLHPRTRSQVYSG----------KADWNILAELVQFAKSHQIPIF 213

Query: 193 LNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            +G L     A K+L      G+M  R A  N  + T   E  +N   G    + ++   
Sbjct: 214 GSGDLFSPEDAKKMLEETGCAGIMFARGAMGNPFIFTQTRELLTNGTYGEISTEQKIRTG 273

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           F   +      +           +++ +       G P+  R R  L V+A        I
Sbjct: 274 FKELV------FLCDEKGEEKGCREMRKRFATYTKGIPDGSRLRQEL-VQASTIAEYKTI 326

Query: 311 IETAFNL 317
           ++  F L
Sbjct: 327 VQNYFQL 333


>gi|291616786|ref|YP_003519528.1| DusC [Pantoea ananatis LMG 20103]
 gi|291151816|gb|ADD76400.1| DusC [Pantoea ananatis LMG 20103]
          Length = 328

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 54/190 (28%), Positives = 91/190 (47%), Gaps = 16/190 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQ+ G     L E A      G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 67  LQLLGQHPDWLAENAARAVTLGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRAAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+  S+PVTVK R+G D    ++    +  +++++G + + +H R       + +D  
Sbjct: 127 RAAVPASLPVTVKVRLGWDSSARSM---EIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +   +++  + +I++      I  NG + D   A   L +   D VMIGR A  N   L+
Sbjct: 177 RAEAINWQAIGDIRQRLRIPVIA-NGEIWDWQTAQDCLRTTGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEYFSNPL 237
            V +Y   P+
Sbjct: 235 RVIKYNDAPM 244


>gi|25029017|ref|NP_739071.1| putative transcription regulator [Corynebacterium efficiens YS-314]
 gi|259505993|ref|ZP_05748895.1| tRNA-dihydrouridine synthase [Corynebacterium efficiens YS-314]
 gi|23494304|dbj|BAC19271.1| putative transcription regulator [Corynebacterium efficiens YS-314]
 gi|259166474|gb|EEW51028.1| tRNA-dihydrouridine synthase [Corynebacterium efficiens YS-314]
          Length = 381

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 70/287 (24%), Positives = 121/287 (42%), Gaps = 29/287 (10%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R  T + L   EM+ A A++  ++K  ++  F+  E P +LQ+   D     EAAK IV+
Sbjct: 38  RTGTISGLYVCEMVTARALVERNEKTLHMTTFAPDENPRSLQLYTVDPQYTYEAAKMIVD 97

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V     G+ +     +  + ++A  +A     IPVTVK R+G+
Sbjct: 98  ENLADHIDMNFGCPVPKVTRRGGGSAIPYKRRLFENIVSAAVRATEGTDIPVTVKFRVGI 157

Query: 128 DDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           DD+      A R  V +  KS    + +HAR A          R     D++ +  +K+ 
Sbjct: 158 DDEHHTHLDAGRIAVDAGAKS----VALHARTAA--------QRYSGQADWNEIARLKEH 205

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             D  + +  NG +     A +++     DGV++GR       +   +            
Sbjct: 206 LADTGVPVLGNGDIFAAEDATRMMEQTGCDGVVVGRGCLGRPWLFAELSAAVRGEPIPEE 265

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           P    V +   R     M     +H      ++ + +HM     GFP
Sbjct: 266 PTLGEVTRIILRHAELLM-----QHDGELKGIRDLRKHMGWYLRGFP 307


>gi|330469566|ref|YP_004407309.1| TIM-barrel protein, nifR3 family [Verrucosispora maris AB-18-032]
 gi|328812537|gb|AEB46709.1| TIM-barrel protein, nifR3 family [Verrucosispora maris AB-18-032]
          Length = 389

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 70/289 (24%), Positives = 113/289 (39%), Gaps = 27/289 (9%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EMI   A++  + K +  + F   E P +LQ+ G D      A +IV E    + I+LN 
Sbjct: 50  EMITTVALVERNPKTLRMIAFGADESPRSLQLYGTDPEITAAAVRIVVEKDLADHIDLNF 109

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           GCP  +V     GA L     +    +           +PVTVK R G+DD         
Sbjct: 110 GCPVPKVTRRGGGAALPWRRRLFARLVKAAVDAAAPAGVPVTVKMRKGIDDDHLTYVEAG 169

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L  + + +GV  + +H R A          R     D+D +  +K+   D+ +  NG + 
Sbjct: 170 L--AAQDAGVAAVALHGRTAA--------QRYSGTADWDAIATLKQAL-DVPVLGNGDIW 218

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN------PLTGSSPIKTRVDKD 250
           +   AL+++    VDGV+IGR       +   ++  F+       P  G   +  R   +
Sbjct: 219 EADDALRMVTHTGVDGVVIGRGCLGRPWLFADLEAAFAGRTDRRLPTLGEVALTMRRHAE 278

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              +   +     AR    G       +H+     GFP     R  L +
Sbjct: 279 LLVEQFTAGARNPARGERDG--CTDFRKHVAWYLKGFPIGSELRRALAM 325


>gi|269140492|ref|YP_003297193.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda EIB202]
 gi|267986153|gb|ACY85982.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda EIB202]
 gi|304560282|gb|ADM42946.1| tRNA dihydrouridine synthase B [Edwardsiella tarda FL6-60]
          Length = 334

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  + A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GVGMAVSEMLSSNPEVWRTDKSRLRMVHMDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PDEMAAAARINADNGAQIIDINMGCPAKKVNRKLAGSALLQYPGLVEQILRAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      A RN V   +  ++ G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGWDP-----AHRNCVEIAQLAERCGIQALTIHGRTRACLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRTV-KQHVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|237809273|ref|YP_002893713.1| TIM-barrel protein, nifR3 family [Tolumonas auensis DSM 9187]
 gi|237501534|gb|ACQ94127.1| TIM-barrel protein, nifR3 family [Tolumonas auensis DSM 9187]
          Length = 322

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/251 (22%), Positives = 115/251 (45%), Gaps = 26/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +D+ +R    L     +  +EM+ A+       K++      ++P   A+QI G++
Sbjct: 17  MAGVSDQPFRQLC-LRMGAGMAVSEMMSANPDTWDTDKSLKRMYLADEPGIRAVQIVGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   +++N+GCP+ +++    G+ L+ +P +V + +  +  A+ +P
Sbjct: 76  PEWMADAARRSVSEGAQIVDINMGCPAKKINRRLAGSALLQDPALVREILQTVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D +      RN   + +  +  GV  + +H R    +  G           
Sbjct: 136 VTLKIRTGWDTE-----HRNGLEIAEIAESCGVQALTVHGRTRACLFNG----------Q 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K++  + +  NG ++   +A  +L     D +MIGRAA     + + +  
Sbjct: 181 AEYDTIRAI-KQHISIPVVANGDIDTPQKAQAVLEYTGADAIMIGRAAQGQPWLFSRIRH 239

Query: 232 YFSNPLTGSSP 242
           + ++     SP
Sbjct: 240 FLTHGSDLPSP 250


>gi|296157346|ref|ZP_06840182.1| TIM-barrel protein, nifR3 family [Burkholderia sp. Ch1-1]
 gi|295892682|gb|EFG72464.1| TIM-barrel protein, nifR3 family [Burkholderia sp. Ch1-1]
          Length = 352

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 74/308 (24%), Positives = 140/308 (45%), Gaps = 34/308 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             ++PVT+K R G + +   A+++  L +S   +G++ + +H R         + +    
Sbjct: 137 PDAVPVTLKIRTGWNRENRNALSVARLAES---AGISMLTVHGRT--------RADLYHG 185

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVD 230
             +YD +  +K     + +  NG +    +A ++L +   D +MIGRAA     +   + 
Sbjct: 186 EAEYDTIAAVKAA-VRIPVVANGDITSPQKAREVLAATGADAIMIGRAAQGRPWLFREIG 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGF 287
            +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G 
Sbjct: 245 HFLQ---TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGL 296

Query: 288 PNSRRCRH 295
             +   RH
Sbjct: 297 SGANVFRH 304


>gi|260582845|ref|ZP_05850630.1| RNA polymerase factor sigma-32 [Haemophilus influenzae NT127]
 gi|260094058|gb|EEW77961.1| RNA polymerase factor sigma-32 [Haemophilus influenzae NT127]
          Length = 310

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 103/226 (45%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G +   L E A    D G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQNPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ GV  I +H R   
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGVTEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + E+ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKADGYRADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+ V+K  W +I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNVEKMPWYEIQKILQKYA 257


>gi|312148418|gb|ADQ31077.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           JD1]
          Length = 329

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|323527305|ref|YP_004229458.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1001]
 gi|323384307|gb|ADX56398.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1001]
          Length = 357

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 73/307 (23%), Positives = 135/307 (43%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G+  + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENKNAL--NVARLAEAAGIAMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   ++ 
Sbjct: 187 AEYDTIAAVKAA-VRIPVVANGDITSPEKARHVLAVTGADAVMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 246 FLQ---TGELLSPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 297

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 298 GANVFRH 304


>gi|45549423|ref|NP_572950.2| CG1434 [Drosophila melanogaster]
 gi|45446950|gb|AAF48360.2| CG1434 [Drosophila melanogaster]
 gi|162944734|gb|ABY20436.1| GH10289p [Drosophila melanogaster]
          Length = 473

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 87/182 (47%), Gaps = 19/182 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+ +PD     + 
Sbjct: 97  LVLQMGTSDAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILR 155

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +C  L IPVT K RI  D +       +LV+ +  +G+  I IHAR         +D R
Sbjct: 156 TLCSGLDIPVTCKIRILPDVE----GTIDLVQKLAATGIAAIGIHART--------RDER 203

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNSA 224
                  +++  +  +  D+ I  NGG ++M      +  ++    D VM+ RAA  N +
Sbjct: 204 PQHPAHPEVLRAV-AQAVDIPIIANGGSKNMHCYDDLRKFQMECGADSVMVARAAQINVS 262

Query: 225 ML 226
           + 
Sbjct: 263 IF 264


>gi|195478541|ref|XP_002100554.1| GE17129 [Drosophila yakuba]
 gi|194188078|gb|EDX01662.1| GE17129 [Drosophila yakuba]
          Length = 473

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 88/182 (48%), Gaps = 19/182 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+ +PD     + 
Sbjct: 97  LVLQMGTSDAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAALILR 155

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +C  L IPVT K RI  D +       +LV+ +  +G+  I IHAR         +D R
Sbjct: 156 TLCSGLDIPVTCKIRILPDVE----GTIDLVQKLAATGIAAIGIHART--------RDER 203

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNSA 224
              +   +++  +  +  D+ I  NGG ++M      +  ++    D VM+ RAA  N +
Sbjct: 204 PQHSAHPEVLRAV-AQAVDIPIIANGGSKNMHCYEDLRKFQLECGADSVMVARAAQINVS 262

Query: 225 ML 226
           + 
Sbjct: 263 IF 264


>gi|256852018|ref|ZP_05557405.1| transcriptional regulator [Lactobacillus jensenii 27-2-CHN]
 gi|260661413|ref|ZP_05862326.1| transcriptional regulator [Lactobacillus jensenii 115-3-CHN]
 gi|282933690|ref|ZP_06339048.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
 gi|297205110|ref|ZP_06922506.1| tRNA-dihydrouridine synthase [Lactobacillus jensenii JV-V16]
 gi|256615430|gb|EEU20620.1| transcriptional regulator [Lactobacillus jensenii 27-2-CHN]
 gi|260547868|gb|EEX23845.1| transcriptional regulator [Lactobacillus jensenii 115-3-CHN]
 gi|281302180|gb|EFA94424.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
 gi|297149688|gb|EFH29985.1| tRNA-dihydrouridine synthase [Lactobacillus jensenii JV-V16]
          Length = 342

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 115/237 (48%), Gaps = 25/237 (10%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI- 77
           L+  EMI    I+  +KK  ++L  +  E P+++QI G     L+EAA+ ++     +I 
Sbjct: 42  LVVCEMISDHGIIYRNKKTLDMLQVAPGEHPMSIQIFGGTEDTLLEAAQYIDQHTAADII 101

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP  +V +   G+  +L+ + +   +  + + +  PV+VK R+G D +    A+ 
Sbjct: 102 DINMGCPVPKVTKTDAGSKWLLDANKIYQMVHKVVQNVEKPVSVKMRLGWDRK-HIFAVE 160

Query: 138 NLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           N + + +++G + + +H   RK + +G            D++ ++E+       F+G NG
Sbjct: 161 NALAA-QEAGASMLAMHGRTRKQMYQG----------EADWETLHEVANALTIPFVG-NG 208

Query: 196 GLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKT 245
            +     A K++  V    VMIGRAA  N   +  +  Y        P T    I+T
Sbjct: 209 DITSPELAKKMIDEVGATAVMIGRAALGNPWEIKDMVHYLETGEKLRPQTVREKIET 265


>gi|216264467|ref|ZP_03436459.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           156a]
 gi|224533271|ref|ZP_03673865.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           CA-11.2a]
 gi|225548971|ref|ZP_03769948.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           94a]
 gi|215980940|gb|EEC21747.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           156a]
 gi|224513436|gb|EEF83793.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           CA-11.2a]
 gi|225370574|gb|EEH00011.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           94a]
          Length = 329

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|195580071|ref|XP_002079879.1| GD24181 [Drosophila simulans]
 gi|194191888|gb|EDX05464.1| GD24181 [Drosophila simulans]
          Length = 396

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 58/246 (23%), Positives = 113/246 (45%), Gaps = 20/246 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVHQVVQEVRRTLPGD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G ++ +      +L + ++ +GV  + +H R    K    KD   IP++ 
Sbjct: 148 FSVSVKMRLLGGEESLQRTI--DLARQLEHAGVTFLTLHGRTPAQK--HSKDTLDIPSMS 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLT-TVDEY 232
                   +++  + + +NG +E    A  +       GVM  R    N A+   +  E 
Sbjct: 204 Q------VRQSLQIPLIVNGNVESYRDACDMHEQTGAAGVMAARGLLANPALFNRSYPEG 257

Query: 233 FSNPLT 238
            + PL+
Sbjct: 258 KTTPLS 263


>gi|17863006|gb|AAL39980.1| SD08006p [Drosophila melanogaster]
          Length = 460

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 21/183 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+ +PD     + 
Sbjct: 84  LVLQMGTSDAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAAHILR 142

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +C  L IPVT K RI     +P V    +LV+ +  +G+  I IHAR         +D 
Sbjct: 143 TLCSGLDIPVTCKIRI-----LPDVEGTIDLVQKLAATGIAAIGIHART--------RDE 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNS 223
           R       +++  +  +  D+ I  NGG ++M      +  ++    D VM+ RAA  N 
Sbjct: 190 RPQHPAHPEVLRAV-AQAVDIPIIANGGSKNMHCYDDLRKFQMECGADSVMVARAAQINV 248

Query: 224 AML 226
           ++ 
Sbjct: 249 SIF 251


>gi|225561353|gb|EEH09633.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus G186AR]
          Length = 583

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 58/202 (28%), Positives = 92/202 (45%), Gaps = 19/202 (9%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++PL +Q    +  +L++AA+ VE F  + ++LN+GCP     +G +GA L  +P
Sbjct: 110 GNPSFDRPLIVQFCANNPDELLQAARAVEPF-CDAVDLNLGCPQGIARKGHYGAFLQEHP 168

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++ + I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 169 DLIYELINTLHTQLSIPVTAKFRI----QETKEKTLEYARIILSAGASIITVHGRRREQK 224

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           G     N  + +  Y I Y  +    D  I  NG + +     K L +   DGVM    +
Sbjct: 225 G----HNTGLADWSY-IRYLRENLPADTVIFANGNILNHGDIEKCLEATGADGVMSAEGS 279

Query: 220 YKNSAMLTTVDEYFSNPLTGSS 241
             +  +       FS P   SS
Sbjct: 280 LCDPTI-------FSGPPPSSS 294


>gi|194770353|ref|XP_001967258.1| GF15959 [Drosophila ananassae]
 gi|190614534|gb|EDV30058.1| GF15959 [Drosophila ananassae]
          Length = 460

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 84/184 (45%), Gaps = 23/184 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+  PD     + 
Sbjct: 84  LVLQMGTSDADRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLSEPDKAAVILR 142

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +C  L IPVT K RI   VDD I       LV+ +  +G+  I IHAR         +D
Sbjct: 143 TLCSNLDIPVTCKIRILPDVDDTI------RLVQKLADTGIAAIGIHART--------RD 188

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKN 222
            R       D++  +  +   + I  NGG  DM +   +         D VM+ RAA  N
Sbjct: 189 ERPQHKPHPDVLRAV-AQAVSIPIIANGGSRDMHKYEDLRKFQEDCGADSVMVARAAQLN 247

Query: 223 SAML 226
            ++ 
Sbjct: 248 VSIF 251


>gi|223889346|ref|ZP_03623932.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           64b]
 gi|223885032|gb|EEF56136.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           64b]
          Length = 329

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|148223341|ref|NP_001085224.1| hypothetical protein LOC432319 [Xenopus laevis]
 gi|80477797|gb|AAI08778.1| MGC78973 protein [Xenopus laevis]
          Length = 465

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 18  MVDQSELAWRLLSRRHGVQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 75

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +G+ L    D++   I    + L
Sbjct: 76  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGSFLQDEWDLLEKMIQLAHQKL 134

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         K ++K+G   + +H R    KG
Sbjct: 135 SVPVT--CKIRVFPEIEKTV--EYAKMLEKAGCQLLTVHGRTKEQKG 177


>gi|146421120|ref|XP_001486511.1| hypothetical protein PGUG_02182 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 347

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 107/231 (46%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D      F+T   ++ + +Q+G  +
Sbjct: 38  MVRYSKLPFRELVRHY-NTDIVYTPMILAREFVRNDVARASDFTTNPADRLVIVQVGCNN 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L++  +++  +  + I LN GCP   +V EG  GA LM  P++V   + A+ +    
Sbjct: 97  VEDLLKFVEMIHPY-VDGIGLNCGCPIKEQVREG-IGAALMSEPELVSSMVKAVKQKYGD 154

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I +   I        VK +++SGV+ I +H R         K+ R    ++ D
Sbjct: 155 KICIETKIRIHPDIKETL--KFVKMVEESGVDFITVHGRT--------KNTRSSVPVNLD 204

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
            +  + KE   + +  NG    +  A  I     VDGVM  R    N A+ 
Sbjct: 205 AIKAV-KEAVLVPVVANGDCFSLQDAYDIAEYTGVDGVMAVRGILANPALF 254


>gi|47937507|gb|AAH72076.1| MGC78973 protein [Xenopus laevis]
          Length = 465

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 18  MVDQSELAWRLLSRRHGVQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 75

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +G+ L    D++   I    + L
Sbjct: 76  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGSFLQDEWDLLEKMIQLAHQKL 134

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         K ++K+G   + +H R    KG
Sbjct: 135 SVPVT--CKIRVFPEIEKTV--EYAKMLEKAGCQLLTVHGRTKEQKG 177


>gi|325479557|gb|EGC82653.1| TIM-barrel protein, nifR3 family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 326

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 68/279 (24%), Positives = 126/279 (45%), Gaps = 25/279 (8%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEI 77
           +TEM+  +A+L  +K    I+  S  EK   +QI G D   I K+V+  KI     + EI
Sbjct: 36  FTEMVSVNALLYDNKATHEIMYRSDLEKNCNIQIFGNDPAIIEKVVKE-KINPRDDFKEI 94

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           + N+GCP+ ++ +   G+ LM +     +    +  +    V +K R+G+D+   ++   
Sbjct: 95  SFNMGCPAPKIFKNGQGSALMGDIKKAQEIAKTLVGSTDKIVNIKFRLGIDEN--SINYI 152

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+++ +GV+ + +HAR    +  S K N       +D + ++ KE   + +  NG  
Sbjct: 153 DFGKALEDAGVDYVILHARTR-AQQYSGKAN-------WDDIRKL-KEALSIPVVANGDC 203

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             +   +KI+ +   DGVMI R A  N  +   + +Y         P    +     R+ 
Sbjct: 204 FSVDDYIKIIETTNADGVMIARGAMGNPFIFRQIKDYLKGKRI-KDPTYDDILDTIKRQY 262

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             S+T    R +     + Q+ +H+     G P +   R
Sbjct: 263 DLSLTYKEERLV-----INQMRKHVGWYIKGLPQAASYR 296


>gi|324510450|gb|ADY44369.1| tRNA-dihydrouridine synthase-like protein [Ascaris suum]
          Length = 560

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 62/262 (23%), Positives = 113/262 (43%), Gaps = 31/262 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   RL   + L+YT MI A+  +  ++     F+T   + P  +Q    D
Sbjct: 275 MVRYSKLPFRSLVRLYGAD-LVYTPMINANNFITSEECRSSEFTTNKYDSPTIVQFASND 333

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSI 117
             +   A ++V  +  + ++LN GCP   V  G +G+ L+  P+ + D IA A  +    
Sbjct: 334 PVEFAAATELVYRYC-SGVDLNCGCPKRDVMRGGYGSSLLSTPERIADMIAHARRRIADT 392

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             T+  +I +++ I       L + ++ +G + I +H R    +   P ++  I      
Sbjct: 393 QFTISVKIRLNNDIRRTV--ELCRQVESAGASYICVHGRTPTQRS-EPANHEAIA----- 444

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               + K    + I  NG +    +AL++      DGVM       N AM    D     
Sbjct: 445 ----LVKSAMRIPIIANGAIGSYQEALQVAKRTQTDGVMAANGLLDNPAMFAGHD----- 495

Query: 236 PLTGSSPIKTRVDKDFWRKISA 257
               S+P++  +D   W +I+A
Sbjct: 496 ----STPVQCVLD---WLRITA 510


>gi|291562170|emb|CBL40986.1| tRNA-dihydrouridine synthase [butyrate-producing bacterium SS3/4]
          Length = 385

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 55/189 (29%), Positives = 89/189 (47%), Gaps = 28/189 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  QI        + A+K + + GY EINLN+GCPS  V     G+  +L PD +    
Sbjct: 93  PVVPQILTNRAGDFLLASKKLAEMGYREINLNLGCPSGTVTAKKKGSGFLLYPDDLDRFF 152

Query: 109 AAMCKALSI-----PVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KA 158
             +    S+      ++VK RIG   V++    +A+ N      +  ++ + +H R  K 
Sbjct: 153 DEVFSDASVRNGEFQISVKTRIGKNEVEEWPEIMAIYN------RYPISELTVHPRIQKE 206

Query: 159 ILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
             KG        +P+LD   DI+ E +  NP ++ G     E M +  +  P+V+ VMIG
Sbjct: 207 FYKG--------VPHLDVFADILKESR--NPIVYNGDLFTAEHMKKFREKFPTVENVMIG 256

Query: 217 RAAYKNSAM 225
           R   +N A+
Sbjct: 257 RGLIRNPAL 265


>gi|304440037|ref|ZP_07399930.1| tRNA-dihydrouridine synthase B [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304371529|gb|EFM25142.1| tRNA-dihydrouridine synthase B [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 306

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 71/307 (23%), Positives = 134/307 (43%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGG-- 56
           M  +TD  YR        ++ + TEM+ A A+   DKK   ++  S +E+ + LQ+ G  
Sbjct: 8   MAGYTDFVYRSMCMDFGCDSTI-TEMVSAKALYYKDKKTLELMETSDKERDVHLQLFGYE 66

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            DI ++V A +I   F Y  IN+N+GCP+ ++ +   G+ L+ +P+     I A+  +  
Sbjct: 67  EDIFEIV-AKEIPNRFKY--ININMGCPAPKIVKNFSGSYLLNDPEKCKRLIYALKSSTD 123

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNL 174
           IP+++K R G++     +    + K  ++ G + + +H R  +    G++          
Sbjct: 124 IPISIKIRRGINGGNQGL---KVAKVAEEEGASMVIVHGRTKEEYYSGIA---------- 170

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D++ + E+        IG NG + D    L+      V GV IGR A  N  +   +   
Sbjct: 171 DWNFIEEVATSLNIPVIG-NGDITDYDSFLERTKDSKVSGVAIGRGAIGNPFIFKEIKSK 229

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
             N    + P +    + F   +   M  Y  +       + ++ +  +G  +G   ++ 
Sbjct: 230 I-NKEEYTPPTEKEKLETFLTHLKMMMEAYPKKVA-----INEMRKQFVGYSNGIYGAKE 283

Query: 293 CRHILTV 299
            R  L  
Sbjct: 284 LRQKLNT 290


>gi|309782621|ref|ZP_07677343.1| tRNA-dihydrouridine synthase C [Ralstonia sp. 5_7_47FAA]
 gi|308918596|gb|EFP64271.1| tRNA-dihydrouridine synthase C [Ralstonia sp. 5_7_47FAA]
          Length = 322

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 105/237 (44%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 54  GYTASGTPMTIQLLGSDPEWLARNAAYAATLTPHGIDLNFGCPAKVVNRHGGGAMLLATP 113

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++ D + A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 114 EVLYDIVHAVRAAVPANISVTAKMRLGVSDTSRAI---DCATALAEGGAESLVVHART-- 168

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                 +D+   P   +D +  I  +   + +  NG +  ++  +  + +     VMIGR
Sbjct: 169 ------RDHGYRPPAHWDWIARI-ADAVSIPVTANGEVWTVADWERCRAVSGCSDVMIGR 221

Query: 218 AAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +       P     PI      D+ +K+ A ++   A+H H   KL
Sbjct: 222 GAVSDPFLAQRIRGQMDEAPSAAEWPIVLGYLADYLKKLHARIS---AKHEHGRVKL 275


>gi|15595082|ref|NP_212871.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           B31]
 gi|2688667|gb|AAC67079.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           B31]
          Length = 335

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 23  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHVFLKPNELNRPLIA 82

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 83  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 142

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 143 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 194

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 195 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 250

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 251 NLFKPFSKHF 260


>gi|332289088|ref|YP_004419940.1| tRNA-dihydrouridine synthase C [Gallibacterium anatis UMN179]
 gi|330431984|gb|AEC17043.1| tRNA-dihydrouridine synthase C [Gallibacterium anatis UMN179]
          Length = 314

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 48/184 (26%), Positives = 92/184 (50%), Gaps = 15/184 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G     L E A +  + G + I+LN GCPS  V+    GA L+  P
Sbjct: 57  GYTDSGTPVRVQLLGQHPQWLAENANLAIELGSHGIDLNCGCPSKTVNGSCGGASLLKQP 116

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+S    V+VK R+G DD+  A+ + +   ++++ G + I IH R  +
Sbjct: 117 ELIYQATKAIRQAVSSEKTVSVKVRLGWDDKQKALEIAD---AVQQGGADEIAIHGRTKM 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  +   +D+  + E++++     I  NG + +  QA + L     + +M+ R
Sbjct: 174 -------DGYRADKIDWQKIGEVRQKLSIPVIA-NGEIFNAQQAQECLAVTGCEDLMVAR 225

Query: 218 AAYK 221
            A +
Sbjct: 226 GALQ 229


>gi|257126332|ref|YP_003164446.1| dihydrouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050271|gb|ACV39455.1| dihydrouridine synthase DuS [Leptotrichia buccalis C-1013-b]
          Length = 325

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 106/221 (47%), Gaps = 22/221 (9%)

Query: 21  LLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            L+TEM+ A+ + R D   I   L    +EK    QI G D ++LV     +++FG+ +I
Sbjct: 27  FLFTEMVNANLLNREDDTTINELLKCDNKEKT-GTQIFGGDKNELVSGILKLKNFGFRKI 85

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           N+N+GCP  ++ +   G+ L+ N ++V   +    + +   +++K R+G  D        
Sbjct: 86  NINMGCPQPKIVKNGAGSALLENYELVEQVLLE-TQNIDAKISIKIRVGYKDFDNPEIFL 144

Query: 138 NLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           NL     K  ++ I +H R  K +  G +          +++IV ++ K   ++    NG
Sbjct: 145 NLA---NKHNLDFICVHGRTQKQMYSGTA----------NWEIVEKLSKMPRNINFFGNG 191

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            L + S+  + + S  +DG+++ R    N  +++   E+  
Sbjct: 192 DLFEPSEIKRKIASCNLDGIILSRGIIGNPWLISQTREFLK 232


>gi|193699924|ref|XP_001951016.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Acyrthosiphon
           pisum]
          Length = 471

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 82/166 (49%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MV+ ++  +R  +R     L    +L+++  V D   R  +K       +++PL +Q  G
Sbjct: 21  MVEQSELPWRMLSRKHGVQLCFAPMLHSQNFVQD---RKYRKEFFTTCPEDRPLVVQFCG 77

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   ++EA K+VED   + I+LN+GCP A    G +G+ L     ++ D +  +   L 
Sbjct: 78  NDPKVILEAGKLVED-SCDVIDLNLGCPQAIAKRGFYGSFLQDEWKLIFDIVKTLRDNLK 136

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +PV+ K RI  +D    ++     K ++++G   + +H R    KG
Sbjct: 137 VPVSCKIRI-FEDLTKTIS---YAKMLEEAGCQMLSVHGRTRDQKG 178


>gi|322707292|gb|EFY98871.1| dihydrouridine synthase family protein, putative [Metarhizium
           anisopliae ARSEF 23]
          Length = 534

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 82/182 (45%), Gaps = 25/182 (13%)

Query: 1   MVDWTDRHYRFFAR-LLTNNA----LLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R  LT+      L YT M  A    +  K     F +          
Sbjct: 32  MVDQSEFAWRMLTRSFLTDEEKKKMLAYTPMFHARLFSQESKYRKAHFQSTKPDSQEPWL 91

Query: 47  ------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
                 ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  +
Sbjct: 92  DGNPSIDRPLFVQFCANDPEALLSAAKQVSPY-CDAVDLNLGCPQGIARKGHYGAFLQED 150

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + K LSIPVT K RI  D +      +N++    K+G + + +H R+   
Sbjct: 151 QDLIFRLINTLHKELSIPVTAKIRILEDKEKTLAYAQNVL----KAGASILTVHGRRREQ 206

Query: 161 KG 162
           KG
Sbjct: 207 KG 208


>gi|195345007|ref|XP_002039067.1| GM17321 [Drosophila sechellia]
 gi|194134197|gb|EDW55713.1| GM17321 [Drosophila sechellia]
          Length = 316

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 58/246 (23%), Positives = 113/246 (45%), Gaps = 20/246 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVHQVVQEVRRTLPGD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G ++ +      +L + ++ +GV  + +H R    K    KD   IP + 
Sbjct: 148 FSVSVKMRLLGGEESLQRTI--DLARQLEHAGVTFLTLHGRTPAQK--HSKDTLDIPAMS 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAML-TTVDEY 232
                   +++  + + +NG +E    A  +       GVM  R    N A+  ++  E 
Sbjct: 204 Q------VRQSLQIPLIVNGNVESYRDACDMHEQTGAAGVMAARGLLANPALFNSSYPEG 257

Query: 233 FSNPLT 238
            + PL+
Sbjct: 258 KTTPLS 263


>gi|261222286|ref|ZP_05936567.1| nitrogen regulation protein [Brucella ceti B1/94]
 gi|260920870|gb|EEX87523.1| nitrogen regulation protein [Brucella ceti B1/94]
          Length = 228

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 39/141 (27%), Positives = 74/141 (52%), Gaps = 11/141 (7%)

Query: 21  LLYTEMIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           ++ +EM+ +  +    ++++L     G  T      +Q+ G +   + EAAKI E  G +
Sbjct: 44  MVVSEMVASAELCNRHRESLLRLFGEGLGTH----VVQLAGREARWMGEAAKIAEGEGAD 99

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++ 
Sbjct: 100 IIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SIN 157

Query: 136 LRNLVKSIKKSGVNGIWIHAR 156
              L +  + +G+  + +H R
Sbjct: 158 APELARRAEDAGIAMVTVHGR 178


>gi|265998250|ref|ZP_06110807.1| nitrogen regulation protein [Brucella ceti M490/95/1]
 gi|262552718|gb|EEZ08708.1| nitrogen regulation protein [Brucella ceti M490/95/1]
          Length = 214

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 39/141 (27%), Positives = 74/141 (52%), Gaps = 11/141 (7%)

Query: 21  LLYTEMIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           ++ +EM+ +  +    ++++L     G  T      +Q+ G +   + EAAKI E  G +
Sbjct: 30  MVVSEMVASAELCNRHRESLLRLFGEGLGTH----VVQLAGREARWMGEAAKIAEGEGAD 85

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+   ++ 
Sbjct: 86  IIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDEN--SIN 143

Query: 136 LRNLVKSIKKSGVNGIWIHAR 156
              L +  + +G+  + +H R
Sbjct: 144 APELARRAEDAGIAMVTVHGR 164


>gi|311895936|dbj|BAJ28344.1| putative tRNA-dihydrouridine synthase [Kitasatospora setae KM-6054]
          Length = 395

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 105/226 (46%), Gaps = 18/226 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY-TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    LY +EMI   A++  + K   ++ F   EKP ++Q+ G 
Sbjct: 39  MAGITNAPFRTLCREQSGGRGLYVSEMITTRALVERNAKTMQLIKFDPSEKPRSIQLYGV 98

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +AA+++   G  + I+LN GCP  +V     G+ L    +++ D +  A+  A 
Sbjct: 99  DPETVGKAARMISAEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRDILRQAVANAG 158

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV+ I +H R A                D
Sbjct: 159 DLPVTMKMRKGIDDD--HLTYLDAGRIGAEEGVSAIALHGRTAA--------QHYGGTAD 208

Query: 176 YDIVYEIKKENPDLFIGL-NGGLEDMSQALKIL--PSVDGVMIGRA 218
           +  +  +++  P     L NG +     A++++     DGV++GR 
Sbjct: 209 WSAIARLRESVPAGIPVLGNGDIWSADDAVRMMRETGCDGVVVGRG 254


>gi|312962068|ref|ZP_07776564.1| NifR3/Smm1 family protein [Pseudomonas fluorescens WH6]
 gi|311283678|gb|EFQ62263.1| NifR3/Smm1 family protein [Pseudomonas fluorescens WH6]
          Length = 319

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 66/256 (25%), Positives = 110/256 (42%), Gaps = 31/256 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PLRVQLLGSDPVCLAENAALACELGSQVIDLNFGCPAKTVNKSRGGAVLLKEPELLNQIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+   IPVT K R+G D    A+       ++ + G   I +HAR        P 
Sbjct: 124 EHVRRAVPAHIPVTAKMRLGFDSPDGALV---CATALAEGGAAHIVVHARTKTDGYKPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               IP +  D+V      N DL+      +ED  +  +I  + D +M+GR       + 
Sbjct: 181 HWEWIPRVQ-DVVKVPVFANGDLW-----SVEDWQRCREISGAED-IMLGRGLVARPDLA 233

Query: 227 TTV------DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----I 276
             +      +E          P+     +DFW +  A +T+  A      G+L+Q    +
Sbjct: 234 RQIAAARAGEEVVEMTWAQMQPML----QDFWTQCVAQLTEKQA-----PGRLKQWLAML 284

Query: 277 TRHMIGLFHGFPNSRR 292
           TR+       F   RR
Sbjct: 285 TRNYPQAVELFTALRR 300


>gi|313212119|emb|CBY16141.1| unnamed protein product [Oikopleura dioica]
          Length = 250

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 68/116 (58%), Gaps = 9/116 (7%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +++ + LQ+G AD ++ V+AAK+ +D   + +++N+GCP A   +G  GA ++  PD+
Sbjct: 69  AKEKEKVILQLGTADPNRAVKAAKLCQDH-ISGVDVNMGCPKAYSTKGGMGAAMLKTPDL 127

Query: 104 VGDCIAAMCKALSIPVT--VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
               + A+ + L IPVT  ++C   +++ +         K ++K+G+  + IH R+
Sbjct: 128 AESILKALVQELDIPVTCKIRCLKTLEETV------EFAKRMEKTGIAALAIHGRQ 177


>gi|152990938|ref|YP_001356660.1| tRNA-dihydrouridine synthase [Nitratiruptor sp. SB155-2]
 gi|151422799|dbj|BAF70303.1| tRNA-dihydrouridine synthase [Nitratiruptor sp. SB155-2]
          Length = 308

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 110/225 (48%), Gaps = 20/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + L  +EMI ++A++   KK   +L  S +E P  +QI G D
Sbjct: 15  LAGYTDLPFRSVVKKFGAD-LTISEMISSNALVYDSKKTYKMLEKSPEENPYFVQIAGGD 73

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EA + + +  G + I+LN GCP  +V +   G+ L+ + D +G  +  + +    
Sbjct: 74  PLIVKEAVERLNEIEGIDGIDLNCGCPVPKVVKQGAGSALLDDLDRLGKIVQTIKETSEK 133

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             T VK R+G  +      +  +VK ++++G + I IH R       +     K P +DY
Sbjct: 134 NYTSVKIRLGFTEN----RVVEIVKVLEEAGADFITIHGR-------TRSGGFKAP-VDY 181

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           + +    KE+  + +  NG + +  +  ++L     DGVMIGR A
Sbjct: 182 EAIAR-AKESVSIPVIANGDITNFQKTQEVLFITKADGVMIGRGA 225


>gi|77458109|ref|YP_347614.1| dihydrouridine synthase, DuS [Pseudomonas fluorescens Pf0-1]
 gi|77382112|gb|ABA73625.1| tRNA-U20a,U20b-dihydrouridine synthase [Pseudomonas fluorescens
           Pf0-1]
          Length = 319

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 105/235 (44%), Gaps = 27/235 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PLRVQLLGSDPVCLAENAALACELGSEVIDLNFGCPAKTVNKSRGGAVLLKEPELLNRIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+   IPVT K R+G D    ++       ++ + G   I +HAR  +     P 
Sbjct: 124 EHVRRAVPAHIPVTAKMRLGFDSPDGSLV---CATALAEGGAEHIVVHARTKVDGYKPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               IP +  D+V      N D++      +ED  +  +I   V+ +M+GR       + 
Sbjct: 181 HWEWIPRVQ-DVVKVPVFANGDIW-----SVEDWRRCREI-SGVEDIMLGRGLVSRPDLA 233

Query: 227 TTV------DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
             +      +E          P+     +DFW +  A MT   AR   S G+L+Q
Sbjct: 234 RQIAAARAGEEVVEMTWAELMPLI----QDFWLQAKAQMT---AR--QSPGRLKQ 279


>gi|198428499|ref|XP_002130384.1| PREDICTED: similar to dihydrouridine synthase 1-like [Ciona
           intestinalis]
          Length = 626

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 65/255 (25%), Positives = 109/255 (42%), Gaps = 39/255 (15%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L  + +      V D   R      L  ST++ PL +Q   
Sbjct: 22  MVDQSELPWRLLSRRHGAQLCFSPMYSANTFVHDHTYRNKVVQDLS-STEDHPLIVQFCS 80

Query: 57  ADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
                 +EA+K+VE  G  E ++LN+GCP      G FGA L  + D++ + I+   + +
Sbjct: 81  NSAENFLEASKLVE--GLCEGVDLNLGCPQHIAKRGHFGAYLQEDWDLIIEIISTTKQHI 138

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            I VT K R+   +D  +    +      ++ +G + I +H R    KG         PN
Sbjct: 139 GIGVTAKIRVFNEIDKTVKYAQM------LETAGCDIITVHGRTREQKG---------PN 183

Query: 174 LDYDIVYEIK--KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT-- 227
                   IK  K+N D+ +  NG ++     ++ + +  VDGVM+      N  +    
Sbjct: 184 TGLASWDHIKAVKDNVDIPVFANGNIQYYCDIMRCMETTGVDGVMVAEGNLTNPMIFQDL 243

Query: 228 --------TVDEYFS 234
                    V+EYF+
Sbjct: 244 STPCNVYDVVEEYFA 258


>gi|313237639|emb|CBY12783.1| unnamed protein product [Oikopleura dioica]
          Length = 460

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 108/241 (44%), Gaps = 31/241 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----VADAILRGDKKNILGFSTQ-----EKPL 50
           MVD ++  +R  +R  +   L YT M      + DA  R +     G   Q     ++PL
Sbjct: 47  MVDASELPWRVLSRRYSAE-LCYTPMFHAANYIKDATYRRENFPDTGDLEQGSPEFDRPL 105

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q    DI+    AAK+VED   + ++LN+GCP      G +GA +M +   +   I  
Sbjct: 106 FVQFCANDINAFSTAAKMVED-RCDAVDLNLGCPQMIAKRGHYGAHMMEDWSNIRKMIEE 164

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             K   + +T K R   D+   ++ LR   K ++ +GV+ + IH R    +G        
Sbjct: 165 ARKVAKVRITAKIRKFEDE---SITLR-YAKMLENAGVSLLTIHGRTRDQRG-------- 212

Query: 171 IPNL---DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
            PN    D+ I+ ++ KE   + +  NG ++ +  A+  +    VDG+M       N A+
Sbjct: 213 -PNTGLADWQIIKKV-KEALRVPVVANGNIQCLQNAIDCMEQTGVDGIMTAEGNLYNPAL 270

Query: 226 L 226
            
Sbjct: 271 F 271


>gi|225551868|ref|ZP_03772811.1| putative histidine phosphokinase/phophatase [Borrelia sp. SV1]
 gi|225371663|gb|EEH01090.1| putative histidine phosphokinase/phophatase [Borrelia sp. SV1]
          Length = 329

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 58/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSTEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P+++K R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSIKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|222823251|ref|YP_002574824.1| tRNA-dihydrouridine synthase B [Campylobacter lari RM2100]
 gi|222538472|gb|ACM63573.1| tRNA-dihydrouridine synthase B [Campylobacter lari RM2100]
          Length = 308

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/203 (28%), Positives = 104/203 (51%), Gaps = 22/203 (10%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K +  L  +  E P  +QI G+D S + +A +I+  F + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLKMLEKAELENPYIVQIAGSDESVICKAVEILNRFDFIDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ + D +   +  + K  +   T VK R+G D + P      +
Sbjct: 96  CGCPVNKVIKQCAGSALLQDLDKLQRILELIKKTSNKKSTSVKVRLGFDKKDPIA----I 151

Query: 140 VKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K+ + +GV+ I +H   RK +  G          N DY+ +  + KEN  + +  NG +
Sbjct: 152 AKACENAGVDFISMHGRTRKQMYSG----------NADYEAI-ALAKENIKIPLVANGDI 200

Query: 198 -EDMSQALKILPSVDGVMIGRAA 219
            ED ++ +  + + D +MIGRA+
Sbjct: 201 SEDNAKEVFKITNCDALMIGRAS 223


>gi|184201291|ref|YP_001855498.1| putative dihydrouridine synthase [Kocuria rhizophila DC2201]
 gi|183581521|dbj|BAG29992.1| putative tRNA-dihydrouridine synthase [Kocuria rhizophila DC2201]
          Length = 394

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 100/211 (47%), Gaps = 15/211 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T++ +R   R      L  TEM+ A A++  R +   I+     E P ++QI G D
Sbjct: 37  MAGVTNKSFRKLCREY-GGGLYVTEMVTARALVERRPESLRIIHHDPGETPRSIQIYGVD 95

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + +A ++V ++   + I+LN GCP  +V +   G+ L    D+    ++ A+ +A  
Sbjct: 96  AVNVGKAVRMVAQEDRADHIDLNFGCPVPKVTKRGGGSALPWKTDLFRAIVSTAVREAGD 155

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK RIG+DD+       +  +  +  GV  + +H R          +       ++
Sbjct: 156 IPVTVKMRIGIDDE--HQTYLDAGRMARDEGVAAVALHGRTL--------EQHYSGTANW 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           D +  +++  PD+ +  NG +     A++++
Sbjct: 206 DAIARLREALPDIPVLGNGDIFSAEDAVRMV 236


>gi|73957464|ref|XP_546866.2| PREDICTED: similar to dihydrouridine synthase 2-like (SMM1, S.
           cerevisiae) [Canis familiaris]
          Length = 560

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 92/193 (47%), Gaps = 32/193 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           ++  +  Q+G +D  + +  AK+VE+     I++N+GCP     +G  GA L+ +PD + 
Sbjct: 147 EQSRVVFQMGTSDADRALAVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIE 205

Query: 106 DCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             ++ + K +  PVT K RI   ++D +      +LVK I+++G+  + +H RK      
Sbjct: 206 KILSTLVKGIRRPVTCKIRILPSLEDTL------SLVKRIERTGIAAVTVHGRK------ 253

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGV 213
             ++ R    +  + +  I  E   + +  NGG          +ED  QA     +   V
Sbjct: 254 --REERPQHPVSCEAIKAI-AETVSIPVIANGGSHDHIQKYLDIEDFRQAT----AASSV 306

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 307 MVARAAMWNPSIF 319


>gi|326779495|ref|ZP_08238760.1| TIM-barrel protein, nifR3 family [Streptomyces cf. griseus
           XylebKG-1]
 gi|326659828|gb|EGE44674.1| TIM-barrel protein, nifR3 family [Streptomyces cf. griseus
           XylebKG-1]
          Length = 382

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 102/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 86

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKAL 115
           D   + +A + IV++   + I+LN GCP  +V     G+ L    P +      A+  A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSNAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HLTFLDAGRIAVEEGVTAVALHGRTTA--------QHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWCADDALRMMRETGCDGVVVGRG 241


>gi|32266316|ref|NP_860348.1| hypothetical protein HH0817 [Helicobacter hepaticus ATCC 51449]
 gi|32262366|gb|AAP77414.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 328

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 101/202 (50%), Gaps = 18/202 (8%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLN 80
           +EMI + A++  + + +  +  S +E+P ++QI G+    + +A +I+    G + I+LN
Sbjct: 35  SEMISSHALVYNNARTLKMIEKSPEEQPYSVQISGSKEEVIKKAVEILNAQGGIDVIDLN 94

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ +  ++      +    + P T +K R+G D +IP      +
Sbjct: 95  CGCPAPKVANHGNGSGLLKDLHLLVKIANLIKDRATTPYTSLKVRLGFDKKIP----NEI 150

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +++K    + + +H R       +  D  K   +DYD +  IK+      I  NG ++ 
Sbjct: 151 AQALKDVRSDFVVVHGR-------TRADGYKKERIDYDAIAHIKQHISMPLIA-NGEIDS 202

Query: 200 MSQALKILP--SVDGVMIGRAA 219
           + +A K+      +GVMIGRAA
Sbjct: 203 VDKAQKVFSHTGANGVMIGRAA 224


>gi|154282457|ref|XP_001542024.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
 gi|150410204|gb|EDN05592.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
          Length = 584

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 83/175 (47%), Gaps = 12/175 (6%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++PL +Q    +   L++AA+ VE F  + ++LN+GCP     +G +GA L  +P
Sbjct: 110 GNPSFDRPLIVQFCANNPDDLLQAARAVEPF-CDAVDLNLGCPQGIARKGHYGAFLQEHP 168

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++ + I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 169 DLIYELINTLHTQLSIPVTAKFRI----QETKEKTLEYARMILSAGASIITVHGRRREQK 224

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
           G     N  + +  Y I Y  +    D  I  NG + +     K L +   DGVM
Sbjct: 225 G----HNTGLADWSY-IRYLRENLPADTVIFANGNILNHGDIEKCLEATGADGVM 274


>gi|321458641|gb|EFX69706.1| hypothetical protein DAPPUDRAFT_300841 [Daphnia pulex]
          Length = 459

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 99/232 (42%), Gaps = 39/232 (16%)

Query: 21  LLYTEMIVADAILRGDK--KNILG-------------FST---QEKPLALQIGGADISKL 62
           ++YTE IV   ++R  +    ILG             F T   +   +  Q+G +D    
Sbjct: 34  IVYTEEIVDKKMVRTKRVVNEILGTVDFIDEFDGSVVFRTCNEESSRVVFQVGTSDAELA 93

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  AK+VE       ++N+GCP     +G  GA L+  P+ V D +  +    SIP+T K
Sbjct: 94  LNVAKLVEK-DVAGFDVNMGCPKEFSIKGGMGAALLKQPEKVKDILTNLVSNTSIPITCK 152

Query: 123 CRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R+     +P +    +L   I+  GV  + +H R    +   P +N  I  +       
Sbjct: 153 MRL-----LPTIEETISLANIIQNCGVAAVAVHGRTKEERPQHPNNNEAIKTI------- 200

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKNSAMLTT 228
              EN  + +  NGG +++    +IL          VMI RAA  NS++  +
Sbjct: 201 --VENLKIPVIANGGSKEIETYEQILRFHKATGASSVMIARAAQYNSSVFRS 250


>gi|238921361|ref|YP_002934876.1| hypothetical protein NT01EI_3505 [Edwardsiella ictaluri 93-146]
 gi|238870930|gb|ACR70641.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 334

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +      E  + A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GVGMAVSEMLSSNPEVWRTDKSRLRMVHMDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PDEMAAAARINADNGAQIIDINMGCPAKKVNRKLAGSALLQYPGLVEQILRAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D      A RN V   +  ++ G+  + IH R    +  G +         
Sbjct: 136 VTLKIRTGWDP-----AHRNCVEIAQLAERCGIQALTIHGRTRACLFNGEA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + +  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 182 -EYDSIRTV-KQHVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|115680276|ref|XP_001190481.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115717833|ref|XP_784269.2| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 278

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 42/134 (31%), Positives = 69/134 (51%), Gaps = 12/134 (8%)

Query: 28  VADAILRGDKKNILGFSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           V D +    K +++ F T  K    L  Q+G AD  + +  AK+VE    + I++N+GCP
Sbjct: 56  VLDTVDYISKDDVVIFRTCSKETDRLVFQMGTADAQRALRVAKMVEK-DVSGIDINMGCP 114

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKS 142
                +G  GA L+  PD + + +  + + + IPVT K RI   ++D I       L K 
Sbjct: 115 KDFSLKGGMGAALLQKPDTIKEILTTLVQGVKIPVTCKIRILPKLEDTIA------LAKM 168

Query: 143 IKKSGVNGIWIHAR 156
           I+++GV  + +H R
Sbjct: 169 IEQTGVAALAVHGR 182


>gi|182438840|ref|YP_001826559.1| putative dihydrouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178467356|dbj|BAG21876.1| putative dihydrouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 382

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 102/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 86

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKAL 115
           D   + +A + IV++   + I+LN GCP  +V     G+ L    P +      A+  A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSNAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HLTFLDAGRIAVEEGVTAVALHGRTTA--------QHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWCADDALRMMRETGCDGVVVGRG 241


>gi|145299064|ref|YP_001141905.1| tRNA-dihydrouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142851836|gb|ABO90157.1| tRNA-dihydrouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 314

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 89/175 (50%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   ++LN GCP+  V++   GA L+  PD V   +
Sbjct: 64  PVRVQLLGQHPEWLAENAVRAIELGSPGVDLNFGCPAPTVNKSKGGAVLLKEPDAVYRIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   +PV+ K R+G DD+   + L N  +++ ++G N + +HAR       + +
Sbjct: 124 KAVREAVPAHLPVSAKIRLGYDDK--DLYLEN-AQAVYQAGANELAVHAR-------TKR 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
           +  K P   ++ V  I++  P + +  NG + D   AL    +   D +M+GR A
Sbjct: 174 EGYKAPA-HWEYVDAIRRALP-IPVTANGEIWDHQDALTCASVSGCDALMVGRGA 226


>gi|256396137|ref|YP_003117701.1| hypothetical protein Caci_7030 [Catenulispora acidiphila DSM 44928]
 gi|256362363|gb|ACU75860.1| TIM-barrel protein, nifR3 family [Catenulispora acidiphila DSM
           44928]
          Length = 379

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 99/220 (45%), Gaps = 21/220 (9%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYNEINLN 80
           EM++  A++  ++K +  + F++ EKP +LQ+ G D   + +A +++  ED   + +++N
Sbjct: 48  EMVMTRALVERNEKTLRMVKFASDEKPRSLQLYGVDPVTVRKAVEMIAAEDLA-DHVDMN 106

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            GCP  RV     GA L     + G  +           IPVTVK RIG+D++       
Sbjct: 107 FGCPVPRVTRKGGGAALPYKRRLFGQIVEAAVQAAAPAGIPVTVKMRIGIDEE--HHTFL 164

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              +  +++G   + +H R A          R     D+  +  +K E     +G NG +
Sbjct: 165 EAGRIAQEAGAAWVALHGRTAA--------QRYSGEADWSAIKALKDELEVPVLG-NGDI 215

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +   AL+++     DGV++GR       +   +   F  
Sbjct: 216 WEADDALRMIAETGADGVVVGRGCLGRPWLFADLAAAFDG 255


>gi|195941555|ref|ZP_03086937.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           80a]
 gi|218249652|ref|YP_002375235.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           ZS7]
 gi|225549995|ref|ZP_03770956.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           118a]
 gi|226321434|ref|ZP_03796961.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           Bol26]
 gi|218164840|gb|ACK74901.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           ZS7]
 gi|225369454|gb|EEG98906.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           118a]
 gi|226233230|gb|EEH31982.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           Bol26]
 gi|312148972|gb|ADQ29043.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           N40]
          Length = 329

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|332670826|ref|YP_004453834.1| TIM-barrel protein, nifR3 family [Cellulomonas fimi ATCC 484]
 gi|332339864|gb|AEE46447.1| TIM-barrel protein, nifR3 family [Cellulomonas fimi ATCC 484]
          Length = 396

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 103/225 (45%), Gaps = 19/225 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R  +   L   EM+ + A++    ++  I+ F+  E P ++Q+ G D
Sbjct: 37  MAGVTNAAFRRLCRE-SGAGLYVAEMLTSRALVERSPESFRIISFAPDEVPRSVQVYGVD 95

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            + +  A + +VE+   + ++LN GCP  +V     GA L    D+    + A   A   
Sbjct: 96  PATVGAAVRMLVEEDLADHVDLNFGCPVPKVTRRGGGAVLPWKRDLFSAIVHAAVDAARP 155

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+D++        L  + + +GV  + +H R A         +      
Sbjct: 156 SGVPVTVKMRKGIDEEHLTYVEAGL--TAQDAGVAAVALHGRTAA--------DYYSGTA 205

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           D+D +  +K+   D+ +  NG +     AL ++     DGV++GR
Sbjct: 206 DWDAIATLKEAVTDIPVLGNGDIWSAEDALAMVAHTGCDGVVVGR 250


>gi|147797460|emb|CAN64677.1| hypothetical protein VITISV_024917 [Vitis vinifera]
          Length = 326

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 96/200 (48%), Gaps = 15/200 (7%)

Query: 30  DAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSAR 87
           D + +G    +     +EK  +  Q+G ++  + + AA+IV +D     +++N+GCP + 
Sbjct: 57  DFVEKGTHNVVFRTCHEEKNRVVFQMGTSNAERALTAAQIVCKDVA--AVDINMGCPKSF 114

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G  GA L+  P+++ D +  + + L IPVT K R+    Q        L + I+K+G
Sbjct: 115 SISGGMGAALLTRPELIHDILTILKRNLDIPVTCKIRLLKSSQETV----ELAQQIEKTG 170

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V  + +H R+   +   P    +I ++   +   +   N D+F     G +D  Q +K+ 
Sbjct: 171 VAALAVHGRRIADRPRDPAKWNEIADVVAALSIPVIA-NGDVF-----GYDDF-QRIKVA 223

Query: 208 PSVDGVMIGRAAYKNSAMLT 227
                VM+ R A  N+++ +
Sbjct: 224 TGASSVMVARGALWNASVFS 243


>gi|224087931|ref|XP_002195720.1| PREDICTED: dihydrouridine synthase 3-like (S. cerevisiae)
           [Taeniopygia guttata]
          Length = 718

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/282 (23%), Positives = 121/282 (42%), Gaps = 40/282 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 403 EMAVCTNLLQGQSSEWALLKRHHTEDIFGVQLEGAFPDTMTKCAELLNRTIDVDF----V 458

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM   +     +  M   L +PVTVK R GV +++      
Sbjct: 459 DINVGCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPVTVKIRTGVQEKVNVA--H 516

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L+  I++ G + + +H R         ++ R   + D+  + E  +    + +  NG +
Sbjct: 517 KLIPRIREWGASMVTLHGRS--------REQRYTRSADWHYIAECARLASPMPLFGNGDI 568

Query: 198 ---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
              ED ++A+++   V G+MI R A     + T + E     ++ S   +  + KDF   
Sbjct: 569 LSYEDANRAMQM--GVSGIMIARGALIKPWLFTEIKEQRHWDISSSE--RFEILKDF--- 621

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                T+Y   H  S  +  + TR  +  +  F     CR+I
Sbjct: 622 -----TNYGLEHWGSDTQGVEKTRKFLLEWLSF----LCRYI 654


>gi|224532602|ref|ZP_03673224.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           WI91-23]
 gi|224512458|gb|EEF82837.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           WI91-23]
          Length = 329

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|126452924|ref|YP_001067633.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106a]
 gi|167847249|ref|ZP_02472757.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei B7210]
 gi|167912486|ref|ZP_02499577.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 112]
 gi|242318092|ref|ZP_04817108.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106b]
 gi|126226566|gb|ABN90106.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106a]
 gi|242141331|gb|EES27733.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106b]
          Length = 354

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 117/247 (47%), Gaps = 27/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV-----GDCIAAMCK 113
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V         A    
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGAG 136

Query: 114 ALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
           A ++PVT+K R G D D   A+ +  L ++   +G++ + +H R    + +G        
Sbjct: 137 ADAVPVTLKIRTGWDRDHKNALRIATLAEA---AGISMLTVHGRTRADLYRG-------- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
             + +YD +  +K     + +  NG +    +A  +L +   D +MIGRAA     +   
Sbjct: 186 --DAEYDTIAAVKAA-VRIPVVANGDITSPRKAKAVLDATRADALMIGRAAQGRPWLFRE 242

Query: 229 VDEYFSN 235
           +D +  +
Sbjct: 243 IDHFLQS 249


>gi|297242773|ref|ZP_06926711.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis AMD]
 gi|296888984|gb|EFH27718.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis AMD]
          Length = 377

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 79/162 (48%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 17  MAGITNWPFRVICREFGPDGLYVAEMITARALVARNPKALRLCRFAPSEKVRSLQLYGVN 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S + +AA+IV D    + ++LN GCP  +V     G+ L    D++ +    + ++C+ 
Sbjct: 77  PSIVEQAARIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCEP 136

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             IPVT K R+G+D+          +   ++ G   + +HAR
Sbjct: 137 AGIPVTAKFRVGIDENHETFIQAGHIA--QEEGCAAVTLHAR 176


>gi|195350041|ref|XP_002041550.1| GM16688 [Drosophila sechellia]
 gi|194123323|gb|EDW45366.1| GM16688 [Drosophila sechellia]
          Length = 503

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 111/237 (46%), Gaps = 25/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L++P
Sbjct: 94  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +     +R   K ++ +G   + +H R    K  L G++          
Sbjct: 153 VTCKIRIFEDLE---KTIR-YAKMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 198

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D++ +  +++  + P L  G    L+D+ + L     VDGVM       N A+   V
Sbjct: 199 DWNYIKNVRQHIKIPMLANGNILALDDVHRCLTET-GVDGVMSAEGNLHNPAIFKGV 254


>gi|91785159|ref|YP_560365.1| dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           xenovorans LB400]
 gi|91689113|gb|ABE32313.1| tRNA-U20-dihydrouridine synthase [Burkholderia xenovorans LB400]
          Length = 352

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 72/307 (23%), Positives = 137/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENRNAL--NVARLAESAGISMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A ++L +   D +MIGRAA     +   +  
Sbjct: 187 AEYDTIAAVKAA-VRIPVVANGDITSPQKAREVLAATGADALMIGRAAQGRPWLFREIGH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 246 FLQ---TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 297

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 298 GANVFRH 304


>gi|241895343|ref|ZP_04782639.1| tRNA-dihydrouridine synthase [Weissella paramesenteroides ATCC
           33313]
 gi|241871317|gb|EER75068.1| tRNA-dihydrouridine synthase [Weissella paramesenteroides ATCC
           33313]
          Length = 353

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 86/156 (55%), Gaps = 17/156 (10%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY  +++N+GCP+A V +   G+ L+ + D   + I A  KA  + V+VK R+G  +QI 
Sbjct: 112 GYEAVDINMGCPAATVVKNGGGSDLIRHFDKAEEIIVAAKKA-GLAVSVKTRLGF-NQID 169

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDY-DIVYEIKKE-NPDL 189
                  +  I K  V  + +H R       + K+  K+P + +Y D + +++ E  P+ 
Sbjct: 170 --TFEEWIPFILKQDVPLLTVHMR-------TRKEMSKVPAHFEYIDRLIQLRDEIAPNT 220

Query: 190 FIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
            + +NG ++D ++ L+++   P V+G+MIGR  ++N
Sbjct: 221 LLQINGDIKDRTEGLELVRQHPGVNGIMIGRGIFEN 256


>gi|163841639|ref|YP_001626044.1| tRNA-dihydrouridine synthase [Renibacterium salmoninarum ATCC
           33209]
 gi|162955115|gb|ABY24630.1| tRNA-dihydrouridine synthase [Renibacterium salmoninarum ATCC
           33209]
          Length = 393

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/297 (22%), Positives = 122/297 (41%), Gaps = 27/297 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EM+ + A++    ++  I+     EK  ++Q+ G D
Sbjct: 34  MAGITNTAFRRLCREY-GGGLYVAEMVTSRALVERTPESLRIISHDEDEKVRSVQLYGVD 92

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A + +VE+   + I+LN GCP A+V     GA L    ++    +    +  S 
Sbjct: 93  PITVGKAVRMLVEEDHADHIDLNFGCPVAKVTRRGGGAALPWKTELFASIVRTAVREASK 152

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             IP+T+K R G+DD    +      K  + SGV  + +H R A     G +        
Sbjct: 153 GDIPLTIKMRKGIDDD--HLTYLEAGKIARDSGVAAVALHGRTASQFYSGTA-------- 202

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             D+  +  +++   D+ +  NG +     A++++    +DGV+IGR       +   + 
Sbjct: 203 --DWSAIARLREAVTDIPVLGNGDIWSAEDAIRMVRETGIDGVVIGRGCQGRPWLFGDLM 260

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
             F        P   +V    +R     +  +       G  L+ I +HM   F G+
Sbjct: 261 AAFDGDSRRFRPGLKQVADTVYRHAQLLIETFG----EEGKALRDIRKHMAWYFKGY 313


>gi|225468696|ref|XP_002269969.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 326

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 96/200 (48%), Gaps = 15/200 (7%)

Query: 30  DAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSAR 87
           D + +G    +     +EK  +  Q+G ++  + + AA+IV +D     +++N+GCP + 
Sbjct: 57  DFVEKGTHNVVFRTCHEEKNRVVFQMGTSNAERALTAAQIVCKDVA--AVDINMGCPKSF 114

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G  GA L+  P+++ D +  + + L IPVT K R+    Q        L + I+K+G
Sbjct: 115 SISGGMGAALLTRPELIHDILTILKRNLDIPVTCKIRLLKSSQETV----ELAQQIEKTG 170

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V  + +H R+   +   P    +I ++   +   +   N D+F     G +D  Q +K+ 
Sbjct: 171 VAALAVHGRRIADRPRDPAKWNEIADVVAALSIPVIA-NGDVF-----GYDDF-QRIKVA 223

Query: 208 PSVDGVMIGRAAYKNSAMLT 227
                VM+ R A  N+++ +
Sbjct: 224 TGASSVMVARGALWNASVFS 243


>gi|313218109|emb|CBY41424.1| unnamed protein product [Oikopleura dioica]
          Length = 283

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 107/241 (44%), Gaps = 31/241 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----VADAILRGDKKNILGFSTQ-----EKPL 50
           MVD ++  +R  +R  +   L YT M      + DA  R +     G   Q     ++PL
Sbjct: 47  MVDASELPWRVLSRRYSAE-LCYTPMFHAANYIKDATYRRENFPDTGDLEQGSPEFDRPL 105

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q    DI+    AAK+VED   + ++LN+GCP      G +GA +M +   +   I  
Sbjct: 106 FVQFCANDINAFSTAAKMVED-RCDAVDLNLGCPQMIAKRGHYGAHMMEDWSNIRKMIEE 164

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             K   + +T K R   D+ I    LR   K ++ +GV+ + IH R    +G        
Sbjct: 165 ARKVAKVRITAKIRKFEDESI---TLR-YAKMLENAGVSLLTIHGRTRDQRG-------- 212

Query: 171 IPNL---DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
            PN    D+ I+ ++ KE   + +  NG ++ +  A+  +    VDG+M       N A+
Sbjct: 213 -PNTGLADWQIIKKV-KEALRVPVVANGNIQCLQNAIDCMEQTGVDGIMTAEGNLYNPAL 270

Query: 226 L 226
            
Sbjct: 271 F 271


>gi|77456843|ref|YP_346348.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           fluorescens Pf0-1]
 gi|77380846|gb|ABA72359.1| tRNA-U20-dihydrouridine synthase [Pseudomonas fluorescens Pf0-1]
          Length = 336

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 70/301 (23%), Positives = 136/301 (45%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ +        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRMRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVTEILNAVVAAVDVP 138

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G D D    +    + K  +++G+  + +H R         + +      +YD
Sbjct: 139 VTLKIRTGWDRDNKNGL---TVAKIAEQAGITALAVHGRT--------RADLYTGEAEYD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I K+   + +  NG +    +A  +L +   DG++IGRAA     +   ++ +   
Sbjct: 188 TIAAI-KQAVSIPVFANGDIVSPEKARYVLDATGADGLLIGRAAQGRPWIFREIEHFLRT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLFHG-FPNSRRC 293
                +P    V++         +   AA H   G  +  +I R  +G +    P +R  
Sbjct: 247 GEKLPAPELIEVERIL-------LEHLAALHAFYGDVMGVRIARKHVGWYLATLPGAREF 299

Query: 294 R 294
           R
Sbjct: 300 R 300


>gi|229846358|ref|ZP_04466466.1| hypothetical protein CGSHi7P49H1_06795 [Haemophilus influenzae
           7P49H1]
 gi|229810451|gb|EEP46169.1| hypothetical protein CGSHi7P49H1_06795 [Haemophilus influenzae
           7P49H1]
          Length = 310

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 102/226 (45%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    D G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ GV  I +H R   
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGVTEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + E+ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKADGYRADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+ V+K  W +I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNVEKMPWYEIQKILQKYA 257


>gi|139438091|ref|ZP_01771644.1| Hypothetical protein COLAER_00632 [Collinsella aerofaciens ATCC
           25986]
 gi|133776288|gb|EBA40108.1| Hypothetical protein COLAER_00632 [Collinsella aerofaciens ATCC
           25986]
          Length = 317

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 84/181 (46%), Gaps = 17/181 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   +  + V A +++ D GY E+NLN+GCPS  V     G+  + N D +   ++ +C
Sbjct: 65  QLMSKNADEFVWAVQVLADMGYREVNLNLGCPSGTVVAKGKGSGFLRNLDELEAFLSDVC 124

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD--N 168
           +   +PV+VK R+G+++      + +L   +    +  + +H R  K    GL  K+   
Sbjct: 125 ERSPLPVSVKTRLGLENDDEYERVLDLYCRMP---LAELIVHPRVQKDRYTGLPRKEFYG 181

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
             +    + + Y     N D+F      LEDM   ++  P    VM+GR    N A+   
Sbjct: 182 ETLERAPFPVAY-----NGDIF-----DLEDMDALVEAYPGTRHVMLGRGLLANPALARM 231

Query: 229 V 229
           V
Sbjct: 232 V 232


>gi|156387454|ref|XP_001634218.1| predicted protein [Nematostella vectensis]
 gi|156221299|gb|EDO42155.1| predicted protein [Nematostella vectensis]
          Length = 570

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 53/213 (24%), Positives = 94/213 (44%), Gaps = 15/213 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G +    ++   + E    +Q+ GA    + + A++++ +   + I++N 
Sbjct: 248 EMAMCTNLLQGQQSEWALVKRHSSEDIFGVQLCGAFPDTMTKCAELLQKETDVDFIDINT 307

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     G+ LM     +   +  M   + IP+TVK R G+ D+        LV 
Sbjct: 308 GCPIDLVFNKGAGSALMERKGKLQQIVQGMKSVIDIPLTVKIRAGIHDKKYTWNAHKLVG 367

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
           +++  G + + IH R         ++ R   + D+D + E+ K    + +  NG     E
Sbjct: 368 NLRDWGTDMVTIHGRS--------REQRYTKSADWDYISEVAKLASPMPVFGNGDILSFE 419

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  Q  K    V GVMI R A     + T + E
Sbjct: 420 DAMQHRK-QAGVAGVMIARGAIIKPWIFTEIKE 451


>gi|315268000|gb|ADT94853.1| dihydrouridine synthase DuS [Shewanella baltica OS678]
          Length = 327

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 105/231 (45%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P
Sbjct: 69  GNTPSGTPVRVQLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYP 128

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + V D + AM +A+ I   VT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 129 ESVHDIVKAMRQAVPIEHAVTAKIRLGYEDK--SLFMENAI-AVYEAGATELAIHARSKV 185

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                  D  K P   ++ + E++K  P   I  NG + +   A +   +   D +MIGR
Sbjct: 186 -------DGYKPPAY-WEYITEVRKRLPIPVIA-NGEIWNRDDAKRCIDITGCDSIMIGR 236

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W +    M  Y  R L+
Sbjct: 237 GAISLPNLADTIK-------TGATPYT-------WAQTLGLMLSYTQRELN 273


>gi|226355126|ref|YP_002784866.1| tRNA-dihydrouridine synthase [Deinococcus deserti VCD115]
 gi|226317116|gb|ACO45112.1| putative tRNA-dihydrouridine synthase [Deinococcus deserti VCD115]
          Length = 346

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 109/245 (44%), Gaps = 28/245 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADA-ILRGDKKNI-LGFSTQ-EKPLALQIG 55
           M  ++D   R   +L      L+T  EMI A   +L GD +N+ LG   + E    +Q+ 
Sbjct: 32  MAGYSDAPLR---QLAAEQGALWTVSEMISARGLVLGGDSENLSLGRPFEGETNRVVQLF 88

Query: 56  GADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           GA+   L  A + VE  F    I+LN+GCP  ++  G  GACL+  P++  + I AM  A
Sbjct: 89  GAESELLARAVQKVEAWFAPAAIDLNMGCPVPKIR-GKGGACLLQTPEVAFELIQAMKAA 147

Query: 115 LSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            ++ V+ K R+G D D+   VA     + +  +GVN I +H R +          R    
Sbjct: 148 TTLDVSAKIRLGWDHDRSVEVA-----QGLAAAGVNLITVHGRTSA--------QRYTGE 194

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS----AMLTTV 229
            D++ +  +        +G            +    V  VMIGR A  N     A+ T  
Sbjct: 195 ADWEAIARVAAAVDVPVVGSGDIRSAAQARARQALGVAAVMIGRGAVGNPWLFRALATGG 254

Query: 230 DEYFS 234
           D+Y S
Sbjct: 255 DQYPS 259


>gi|90083447|dbj|BAE90806.1| unnamed protein product [Macaca fascicularis]
          Length = 493

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 91/189 (48%), Gaps = 32/189 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++
Sbjct: 84  VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILS 142

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K +  PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 143 TLVKGIRRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------RE 188

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 189 ERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQRYSDIEDFRQAT----AASSVMVAR 243

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 244 AAMWNPSIF 252


>gi|221217908|ref|ZP_03589375.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           72a]
 gi|221192214|gb|EEE18434.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           72a]
          Length = 329

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             C   ++P++VK R G     P V   + +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACARFNLPLSVKTRHGF--SYPEVD--DWLGFLLGLEIDMLTVYPRLAVNQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K     +P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 189 ----VNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYCVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTVDEYF 233
            +     ++F
Sbjct: 245 NLFKPFSKHF 254


>gi|326934323|ref|XP_003213240.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Meleagris
           gallopavo]
          Length = 667

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 68/280 (24%), Positives = 120/280 (42%), Gaps = 36/280 (12%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM V   +L+G      +L     E    +Q+ GA    + + A+++ +    + +++NV
Sbjct: 352 EMAVCTNLLQGQSSEWALLKRHHTEDVFGVQLEGAFPDTMTKCAELLNQTIDVDFVDINV 411

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM   +     +  M   L +P+TVK R GV +++       ++ 
Sbjct: 412 GCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPLTVKIRTGVQEKMNVA--HKIIP 469

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---E 198
            I++ G + + +H R         ++ R     D+D + E  K    + +  NG +   E
Sbjct: 470 KIREWGASMVTLHGRS--------REQRYTRVADWDYIAECAKIASPMPLFGNGDILSYE 521

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD--KDFWRKIS 256
           D +QA++    V G+MI R A     + T + E     ++ S     R D  KDF     
Sbjct: 522 DANQAMQT--GVSGIMIARGALIKPWLFTEIKEQRHWDISSSE----RFDILKDF----- 570

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              T+Y   H  S  +  + TR  +  +  F     CR+I
Sbjct: 571 ---TNYGLEHWGSDTQGVEKTRKFLLEWLSF----LCRYI 603


>gi|320164949|gb|EFW41848.1| tRNA-dihydrouridine synthase 1-like protein [Capsaspora owczarzaki
           ATCC 30864]
          Length = 563

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 105/233 (45%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R  +R    + L YT M  A             FST  +++PL +Q    D
Sbjct: 39  MVDQSELAWRMLSRRYGAD-LCYTPMFNARLFAESQLYRDEMFSTCAEDRPLVVQFCAND 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE+   + ++LN+GCP      G +G+ LM   D++   +  + + L +P
Sbjct: 98  PDHLLAAAKLVEN-DCDAVDLNLGCPQHIARRGHYGSFLMEEWDLIERMVRKLHENLKVP 156

Query: 119 VTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT K RI      P+V       + ++++G   + +H R    KG       K    D+ 
Sbjct: 157 VTCKIRI-----FPSVEKTVQYAQMLERAGCQLLTVHGRLREQKG------HKTGLADWS 205

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            +  + +E   + +  NG +   E++ + ++    V GVM       N A+ +
Sbjct: 206 YIRAV-REAVKIPVFANGNILYNENVEECIRQT-GVQGVMTAEGNLYNPALFS 256


>gi|258405203|ref|YP_003197945.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
 gi|257797430|gb|ACV68367.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
          Length = 328

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 22/229 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           +  +TD  +R   R   N A + +TEMI    ++   +   ++L  +  + PL +Q+ GA
Sbjct: 24  LAGFTDLPFRLLCR--ENGARVAHTEMISVKGLIYNSQGTWDLLATAPADTPLVVQLFGA 81

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D     +  + + + G++ I+LN GCP  +V +   GA LM +P  +   +  + +A  +
Sbjct: 82  DPDCFAQPVRWLTERGFHWIDLNAGCPVRKVIKTGAGAALMEDPQRLVRIMQTIGRAAPV 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLD 175
              VK R+  D       L  L  ++ ++GV+ I +H R A     GL+           
Sbjct: 142 QAGVKLRLPADGSTD--GLLRLRDTLARAGVSWITLHPRTARQGYGGLA----------Q 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +  +  + + +P + I  +G L +   A +      VDG+M  R A  N
Sbjct: 190 WSALSRMAESSP-VPIVASGDLWNAQAARRCFEQTGVDGIMFARGALHN 237


>gi|302534306|ref|ZP_07286648.1| dihydrouridine synthase [Streptomyces sp. C]
 gi|302443201|gb|EFL15017.1| dihydrouridine synthase [Streptomyces sp. C]
          Length = 386

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 55/225 (24%), Positives = 105/225 (46%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   EKP ++Q+ G 
Sbjct: 30  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATEKPRSIQLYGV 89

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A + IVE+   + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 90  DPVTVGKAVRMIVEEDRADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 149

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+ D+   +   +  +   + G+  I +H R                  D
Sbjct: 150 GLPVTMKMRKGITDE--HLTYLDAGRIAVEEGITAIALHGRTTA--------QHYGGTAD 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 200 WEAIARLKEHVPEIPVLGNGDIWCAEDALRMVRETGCDGVVVGRG 244


>gi|313233300|emb|CBY24415.1| unnamed protein product [Oikopleura dioica]
          Length = 355

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 68/116 (58%), Gaps = 9/116 (7%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +++ + LQ+G AD ++ V+AAK+ +D   + +++N+GCP A   +G  GA ++  PD+
Sbjct: 69  AKEKEKVILQLGTADPNRAVKAAKLCQDH-ISGVDVNMGCPKAYSTKGGMGAAMLKTPDL 127

Query: 104 VGDCIAAMCKALSIPVT--VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
               + A+ + L IPVT  ++C   +++ +         K ++K+G+  + IH R+
Sbjct: 128 AESILKALVQELDIPVTCKIRCLKTLEETV------EFAKRMEKTGIAALAIHGRQ 177


>gi|239940987|ref|ZP_04692924.1| putative dihydrouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|239987465|ref|ZP_04708129.1| putative dihydrouridine synthase [Streptomyces roseosporus NRRL
           11379]
 gi|291444424|ref|ZP_06583814.1| dihydrouridine synthase [Streptomyces roseosporus NRRL 15998]
 gi|291347371|gb|EFE74275.1| dihydrouridine synthase [Streptomyces roseosporus NRRL 15998]
          Length = 382

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 102/225 (45%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 86

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKAL 115
           D   + +A + IV++   + I+LN GCP  +V     G+ L    P +      A+  A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSGAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HLTFLDAGRIAVEEGVTAVALHGRTTA--------QHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR 
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWCADDALRMMRETGCDGVVVGRG 241


>gi|319940882|ref|ZP_08015221.1| nifR3 family TIM-barrel protein [Sutterella wadsworthensis 3_1_45B]
 gi|319805764|gb|EFW02545.1| nifR3 family TIM-barrel protein [Sutterella wadsworthensis 3_1_45B]
          Length = 323

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 113/238 (47%), Gaps = 26/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M  ++DR +R   R    +  +  EM  +   LR   K++  +  +++P    +Q+ GAD
Sbjct: 17  MAGYSDRSFREIVREWGADYAV-AEMTASREDLRCRAKSLTRWVERDEPGLHVVQLLGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK  ED G + +++N+GCP+ +V     G+ LM N  +  + + A+  A+ IP
Sbjct: 76  PVVMAEAAKAAEDDGADVVDINMGCPAKKVLNTDCGSALMKNECLTAEILEAVRAAVEIP 135

Query: 119 VTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPN 173
           VT+K R G D +    P +A     +  ++ G+  + IH R      +G          +
Sbjct: 136 VTLKIRTGWDREHKNAPEIA-----RIAEECGIAMLVIHGRTRADGFRG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            +YD +  IK E   + +  NG +    +A  +L +   DG+MIGR A     +   V
Sbjct: 181 AEYDTIARIKAER-GIPVVANGDIVSGVKAQAVLRACGADGLMIGRGAVGRPWLFAEV 237


>gi|212711052|ref|ZP_03319180.1| hypothetical protein PROVALCAL_02121 [Providencia alcalifaciens DSM
           30120]
 gi|212686220|gb|EEB45748.1| hypothetical protein PROVALCAL_02121 [Providencia alcalifaciens DSM
           30120]
          Length = 325

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 109/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TD+ +R     +    +  +EM+ ++  + + DK  +      E  + ++QI G D
Sbjct: 17  MAGITDKPFRSLCYAM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHRDELGVRSVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P+IV   +  +  A+ +P
Sbjct: 76  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPEIVKSILETVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G   +      RN +   +  +  G+  + IH R    +  G           
Sbjct: 136 VTLKIRTGWSPE-----ERNCIEIAQLAEDCGIQALTIHGRTRACLFNG----------E 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K+   + +  NG + D  +A  +L     D +M+GRAA     +   +  
Sbjct: 181 AEYDNIRAV-KQTVSIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|19921524|ref|NP_609939.1| CG10495 [Drosophila melanogaster]
 gi|7298533|gb|AAF53752.1| CG10495 [Drosophila melanogaster]
 gi|17862030|gb|AAL39492.1| LD05576p [Drosophila melanogaster]
 gi|220942934|gb|ACL84010.1| CG10495-PA [synthetic construct]
 gi|220953160|gb|ACL89123.1| CG10495-PA [synthetic construct]
          Length = 396

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 107/235 (45%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVHQVVQEVRRTLPGD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G ++ +      +L + ++ +GV  + +H R    K    KD   IP + 
Sbjct: 148 FSVSVKMRLLGGEESLQRTI--DLARQLESAGVTFLTLHGRTPAQK--HSKDTLDIPAMS 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTT 228
                   +++  + + +NG +E    A  +       GVM  R    N A+  +
Sbjct: 204 Q------VRQSLQIPLIVNGNVESYRDACDMHEQTGAAGVMAARGLLANPALFNS 252


>gi|195575487|ref|XP_002077609.1| GD22975 [Drosophila simulans]
 gi|194189618|gb|EDX03194.1| GD22975 [Drosophila simulans]
          Length = 505

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 111/237 (46%), Gaps = 25/237 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L++P
Sbjct: 94  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           VT K RI  D +     +R   K ++ +G   + +H R    K  L G++          
Sbjct: 153 VTCKIRIFEDLE---KTIR-YAKMLEAAGCQLLTVHGRTREQKGPLTGVA---------- 198

Query: 175 DYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           D++ +  +++  + P L  G    L+D+ + L     VDGVM       N A+   V
Sbjct: 199 DWNYIKNVRQHIKIPMLANGNILALDDVHRCLTET-GVDGVMSAEGNLHNPAIFKGV 254


>gi|290982534|ref|XP_002673985.1| predicted protein [Naegleria gruberi]
 gi|284087572|gb|EFC41241.1| predicted protein [Naegleria gruberi]
          Length = 427

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 100/237 (42%), Gaps = 15/237 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI++D   +  K     F+T   + PL +Q    +
Sbjct: 131 MVRYSKLAFRLLCREYGCD-VVYTPMIMSDCFHKSQKARDSDFTTHYYDSPLVVQFAANN 189

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP----DIVGDCIAAMCKA 114
            +    A ++   +  + I+LN GCP   V + S GA L+  P    D+V +        
Sbjct: 190 PTDFSLACQLAAPYC-DGIDLNCGCPQPYVMKESLGAALVTKPQKIFDMVHEANNKFISG 248

Query: 115 LSIPVTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +S P+ VK R+   DD +       L + I+ +G + + +H R    +  + K N   P 
Sbjct: 249 MSRPIGVKIRLHPEDDTLEFRKTIELARQIEMAGASWVTVHGRTHKQRTKNTKVNPDGPK 308

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
               I+      N D+F      L D  +  K     DGVM  R    N A+ +  D
Sbjct: 309 TIKQILNVPVMHNGDIFT-----LGDSDRFAKET-GCDGVMSARGLLSNPALFSGYD 359


>gi|145352754|ref|XP_001420702.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580937|gb|ABO98995.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 287

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 79/173 (45%), Gaps = 15/173 (8%)

Query: 50  LALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
              QI    I + V AA I   +FG + ++LN GCP     +   GA L+  P  +   +
Sbjct: 62  FGAQIATNAIEEGVNAALIASGEFGADFVDLNCGCPIHETWKRGLGAALLKKPAKLERLV 121

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +   + +P+TVK R+G+D    A   R + + ++ +G + + +H R         K+ 
Sbjct: 122 EGIASRIDVPLTVKIRLGIDSSSQA---RRIAEGLENAGASAVVVHGRT--------KEQ 170

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           R     DYD++ +I +E     IG NG +     A   +    V  +M+GR A
Sbjct: 171 RYTKAADYDVIRDIVRERNIPIIG-NGDVLTWYDARDRMEHSGVAAMMVGRGA 222


>gi|114561641|ref|YP_749154.1| putative TIM-barrel protein, nifR3 family protein [Shewanella
           frigidimarina NCIMB 400]
 gi|114332934|gb|ABI70316.1| putative TIM-barrel protein, nifR3 family protein [Shewanella
           frigidimarina NCIMB 400]
          Length = 320

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 81/331 (24%), Positives = 150/331 (45%), Gaps = 39/331 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK +  +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLC-LRYGAALAVSEMLSSNPDVWDSDKSRQRMMHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G + I++N+GCP+ +V++   G+ LM +P +V + + A+  A+ +P
Sbjct: 76  PDLMANAAKFNVEQGAHIIDINMGCPAKKVNKKFAGSALMQSPSLVKEILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G + +      RN   + +  +  G+  + +H   R+ + KG +         
Sbjct: 136 VTLKIRTGWEPE-----HRNGVEIAQIAEDCGIVSLAVHGRTRQCMYKGFA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K+N  + +  NG ++   +A  +L     D +MIGR A     +   +  
Sbjct: 182 -EYDTIKAI-KQNVSIPVVANGDIDTPEKAKFVLDYTGADALMIGRGAQGRPWIFKEILH 239

Query: 232 YFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           Y     TG   +PIK    +    +    + D     L+   K  +  R  +G +     
Sbjct: 240 YLE---TGKKLAPIKAEEQRSVMLEHLKKLYD-----LYGEYKGVRFARKHVGWYLNHEE 291

Query: 290 SRRCRHILT-VEAGASTATHHIIETAFNLMI 319
            R+ R     +E  A    H ++E  F+ ++
Sbjct: 292 QRQFRADFNRLETAAQ--QHSLVECYFDELV 320


>gi|160875809|ref|YP_001555125.1| dihydrouridine synthase DuS [Shewanella baltica OS195]
 gi|160861331|gb|ABX49865.1| dihydrouridine synthase DuS [Shewanella baltica OS195]
          Length = 315

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 105/231 (45%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P
Sbjct: 57  GNTPSGTPVRVQLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + V D + AM +A+ I   VT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 ESVHDIVKAMRQAVPIEHAVTAKIRLGYEDK--SLFMENAI-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                  D  K P   ++ + E++K  P   I  NG + +   A +   +   D +MIGR
Sbjct: 174 -------DGYKPPAY-WEYITEVRKRLPIPVIA-NGEIWNRDDAKRCIDITGCDSIMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W +    M  Y  R L+
Sbjct: 225 GAISLPNLADTIK-------TGATPYT-------WAQTLGLMLSYTQRELN 261


>gi|294670948|ref|ZP_06735804.1| hypothetical protein NEIELOOT_02654 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307435|gb|EFE48678.1| hypothetical protein NEIELOOT_02654 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 313

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 88/186 (47%), Gaps = 12/186 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D  K+ E A     FG  +I+LN GCP+  V++   GA L+  P+ +   +
Sbjct: 57  PCTVQLLGSDEEKMAENALEAVRFGVRKIDLNFGCPAPTVNKHQGGAVLLKEPERIHRIV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +AL   IP++ K R+G +D+   +AL N  ++I + G   + +HAR  + +G  P 
Sbjct: 117 RTLRRALPDHIPLSGKMRLGFEDK--TLALEN-AQAIAEGGACSLTVHARTKV-EGYEPP 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            +        D V      N D+F      L D    +K     + VMIGR A     + 
Sbjct: 173 AHWSWVKKIADAVSIPVTANGDVFT-----LRDYLD-IKRESGCNSVMIGRGAVMCPDLA 226

Query: 227 TTVDEY 232
             + +Y
Sbjct: 227 RQIKQY 232


>gi|261758310|ref|ZP_06002019.1| nitrogen regulation protein NifR3 [Brucella sp. F5/99]
 gi|261738294|gb|EEY26290.1| nitrogen regulation protein NifR3 [Brucella sp. F5/99]
          Length = 189

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 42/143 (29%), Positives = 76/143 (53%), Gaps = 8/143 (5%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVAL 136
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+     P +A 
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDENSINAPELAR 162

Query: 137 R-NLVKSIKKSGV---NGIWIHA 155
           R    ++ ++ G    +G W HA
Sbjct: 163 RAGACQARRRCGYRHGDGAWPHA 185


>gi|223041930|ref|ZP_03612115.1| tRNA-dihydrouridine synthase C [Actinobacillus minor 202]
 gi|223017284|gb|EEF15711.1| tRNA-dihydrouridine synthase C [Actinobacillus minor 202]
          Length = 319

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 65/269 (24%), Positives = 122/269 (45%), Gaps = 32/269 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +P+++    
Sbjct: 68  PVRVQLLGQYPQWLAENAELAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPELIYRAT 127

Query: 109 AAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+     V+VK R+G D    A     +  ++++ G N I +H R       +  
Sbjct: 128 QAIRQAVPKEQVVSVKVRLGWDS---AEQCFEIADAVQRGGANEITVHGR-------TKT 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
           D  +   +++  + +I+K   ++ +  NG + D   A K   + +   +MIGR A  N+ 
Sbjct: 178 DGYRAERINWQAIGDIQK-RLNIPVIANGEIWDFESAKKCQEITACQALMIGRGAL-NTP 235

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGG--KLQQITRHMI 281
            L+ V + F+ P            K  WR++   +  Y    + H  G   + +I + + 
Sbjct: 236 NLSRVVK-FNQP------------KLAWREVLKLLFQYVNMENEHDSGFYHVARIKQWLH 282

Query: 282 GLFHGFPNSRRCRHILTVEAGASTATHHI 310
            L   +P +     IL  E G +    HI
Sbjct: 283 YLDKEYPEAIALFQILKTEHGYAGLKRHI 311


>gi|240128100|ref|ZP_04740761.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-93-1035]
 gi|268686488|ref|ZP_06153350.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-93-1035]
 gi|268626772|gb|EEZ59172.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-93-1035]
          Length = 333

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 93/205 (45%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+  K R+G +D+ PA+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLAGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +     +D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIHDTVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|268590285|ref|ZP_06124506.1| tRNA-dihydrouridine synthase [Providencia rettgeri DSM 1131]
 gi|291314193|gb|EFE54646.1| tRNA-dihydrouridine synthase [Providencia rettgeri DSM 1131]
          Length = 313

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  PD++     +M
Sbjct: 67  VQLLGQHPQWLAENASRAVELGSWGVDLNCGCPSKTVNGHGGGATLLKQPDLIYQAAKSM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +P++VK R+G D    A     +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPKELPISVKVRLGWDSSEFAY---EIADAVQQAGATELTVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K  ++++  + EI+++     I  NG + D + A + L     D VMIGR A  N+  L+
Sbjct: 177 KAESINWSAIGEIRRKLSIPVIA-NGEIWDYASAQRCLEITGCDAVMIGRGAL-NTPNLS 234

Query: 228 TVDEY 232
            V ++
Sbjct: 235 RVVKF 239


>gi|229591631|ref|YP_002873750.1| hypothetical protein PFLU4202 [Pseudomonas fluorescens SBW25]
 gi|229363497|emb|CAY50729.1| conserved hypothetical protein [Pseudomonas fluorescens SBW25]
          Length = 325

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 103/235 (43%), Gaps = 27/235 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PLRVQLLGSDPVCLAENAALACELGSQVIDLNFGCPAKTVNKSRGGAVLLKEPELLNQIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+   IPVT K R+G D    A+       ++ + G   I +HAR        P 
Sbjct: 124 EHVRRAVPAHIPVTAKMRLGFDSPDGALV---CATALAEGGAAHIVVHARTKTDGYKPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               IP +  D+V      N D++      +ED  +  +I   V+ +M+GR       + 
Sbjct: 181 HWEWIPRVQ-DVVKVPVFANGDIW-----SVEDWRRCREI-SGVEDIMLGRGLVARPDLA 233

Query: 227 TTV------DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
             +      +E          P+     +DFW +  A +T+  A      G+L+Q
Sbjct: 234 RQIAAARAGEEVVEMTWAEMQPML----QDFWTQSVAQLTERQA-----PGRLKQ 279


>gi|260436473|ref|ZP_05790443.1| probable tRNA-dihydrouridine synthase 1 [Synechococcus sp. WH 8109]
 gi|260414347|gb|EEX07643.1| probable tRNA-dihydrouridine synthase 1 [Synechococcus sp. WH 8109]
          Length = 334

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 74/305 (24%), Positives = 135/305 (44%), Gaps = 38/305 (12%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G     +   + +  P+ +Q+       + 
Sbjct: 31  SDRIFRGLVRRWAPDALLFTEMVNATSLEMGHGLCKVESLAEESGPIGVQLFDHRPQAMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++     G+ L+ NP++    + A+  A+++PVTVK 
Sbjct: 91  DAARRAEASGAFLIDINMGCPVRKIARKGGGSGLIRNPELAIQIVEAVADAVAVPVTVKT 150

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
           R+G    D  P     +  + ++++G   + +H   R+   KG +          D+  +
Sbjct: 151 RLGWCGSDADPV----HWCQQLEQAGAQLLTLHGRTREQGFKGAA----------DWSAI 196

Query: 180 YEIKKENPDLFIGL--NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            E+++    L I L  NG +     AL+ L   S  GVM+GR       ++  +D   + 
Sbjct: 197 TEVREA---LTIPLIANGDINSPDDALRCLKQTSAAGVMVGRGTMGAPWLVGQIDAALAG 253

Query: 236 ---PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P T +   +  + +D    +     D+          L    +HM     GFP + R
Sbjct: 254 RAIPTTPNPSARLALARDQLDGLVEDRGDHG---------LLIARKHMGWTCTGFPGASR 304

Query: 293 CRHIL 297
            RH L
Sbjct: 305 LRHAL 309


>gi|33152782|ref|NP_874135.1| putative nitrogen regulator protein [Haemophilus ducreyi 35000HP]
 gi|38604730|sp|Q7VKU5|DUSC_HAEDU RecName: Full=tRNA-dihydrouridine synthase C
 gi|33149006|gb|AAP96524.1| putative nitrogen regulator protein [Haemophilus ducreyi 35000HP]
          Length = 325

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 110/225 (48%), Gaps = 22/225 (9%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F R++       T   +A  +L+G      G +    P+ +Q+ G     L E A++  +
Sbjct: 38  FVRVVDQRLPKKTFYRLAPELLQG------GLTDSGTPIRVQLLGQYPQWLAENAQLAIE 91

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDD 129
            G   I+ N GCPS  V+    GA L+ +P+++     A+ +A+  + PV+VK R+G D 
Sbjct: 92  LGSYGIDFNCGCPSKTVNGSHGGAALLKDPELIYCATKAIREAVPKAQPVSVKMRLGWD- 150

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
              A     +  +I+++G + I +H R       + +D  +   +++  + +I ++  ++
Sbjct: 151 --CASQCFEIADAIQQAGADEITVHGR-------TKQDGYRAERINWQAIGQI-QQRLNI 200

Query: 190 FIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
            +  NG + D + A K   + +  G+MIGR A  N+  L+ V +Y
Sbjct: 201 PVIANGEILDFNSAQKCREITACCGLMIGRGAL-NTPNLSKVIKY 244


>gi|241663179|ref|YP_002981539.1| dihydrouridine synthase DuS [Ralstonia pickettii 12D]
 gi|240865206|gb|ACS62867.1| dihydrouridine synthase DuS [Ralstonia pickettii 12D]
          Length = 326

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 105/237 (44%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 58  GYTASGTPMTIQLLGSDPEWLARNAAYAATLTPHGIDLNFGCPAKVVNRHGGGAMLLATP 117

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++ D + A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 EVLYDIVRAVRAAVPANISVTAKMRLGVSDTSRAI---DCATALAEGGAESLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGR 217
                 +D+   P   +D +  I  +   + +  NG +  ++     + +     VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARI-ADAVSIPVTANGEVWTVADWARCRAVSGCSDVMIGR 225

Query: 218 AAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +  +    P     PI      D+ +K+ A ++   A+H H   KL
Sbjct: 226 GAVSDPFLAQRIRGQMDEAPSAAEWPIVLGYLADYLKKLHARIS---AKHEHGRVKL 279


>gi|258655080|ref|YP_003204236.1| hypothetical protein Namu_4974 [Nakamurella multipartita DSM 44233]
 gi|258558305|gb|ACV81247.1| TIM-barrel protein, nifR3 family [Nakamurella multipartita DSM
           44233]
          Length = 398

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 71/312 (22%), Positives = 128/312 (41%), Gaps = 30/312 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EMI   A++ GD K+  ++ F   E P ++Q+ G D
Sbjct: 44  MAGVTNAPFRSLCREF-GAGLYVCEMITTRALVAGDPKSRAMMRFEPDEHPRSVQLYGVD 102

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A + +VE    + I+LN GCP  +V     G+ +     +    + +     + 
Sbjct: 103 PVVVGQAVRLVVEQDLADHIDLNFGCPVPKVTRKGGGSAIPYKRRLFESIVRSAVDQATP 162

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D     +   +  +  + +GV  + +HAR AI               
Sbjct: 163 HGVPVTVKMRIGIDSD--HITYLDAGRIAEDAGVAAVALHARTAI--------QHYSGQA 212

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           D++ +  +K+    + +  NG +   S AL ++     DGV++GR       +   +   
Sbjct: 213 DWETIGRLKQAVTSVPVLGNGDIFAASDALTMMAMTGCDGVVVGRGCQGRPWLFAELAAA 272

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPN 289
           F        P  T  D    R ++  M  +A   +   G    ++++ +H      GF  
Sbjct: 273 FDG-----RPAPTPPD---LRAVAEVMRRHAVLLVAEMGADRGIRELRKHTAWYLRGFAV 324

Query: 290 SRRCRHILTVEA 301
             + R  L + A
Sbjct: 325 GSQVRRELGMVA 336


>gi|283782945|ref|YP_003373699.1| TIM-barrel protein, nifR3 family [Gardnerella vaginalis 409-05]
 gi|283441929|gb|ADB14395.1| TIM-barrel protein, nifR3 family [Gardnerella vaginalis 409-05]
          Length = 384

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 66/296 (22%), Positives = 117/296 (39%), Gaps = 22/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 24  MAGITNWPFRVICREFGPDGLYVAEMITARALVARNPKALRLCRFAPSEKVRSLQLYGVN 83

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S + +A +IV D    + ++LN GCP  +V     G+ L    D++ +    + ++C+ 
Sbjct: 84  PSIVEQATRIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCEP 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D+          +   ++ G   + +HAR          D ++I  L
Sbjct: 144 AGIPVTAKFRVGIDENHETFIQAGHIA--QEEGCAAVTLHARTTAEYYGGHSDWQRIGEL 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
                     E  D+ +  NG +     AL +       GV IGR       +   +   
Sbjct: 202 ---------VETLDIPVFGNGDIWGAEDALAMFKETGCAGVAIGRGCQGRPWLFADIRNA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                   +P    V     R ++  +  Y      +   +  + +H+     GFP
Sbjct: 253 CEGSDNRVNPTLAEVGSVILRHLNLLVEFYDGDERMA---VHDLRKHIAWYLKGFP 305


>gi|260834651|ref|XP_002612323.1| hypothetical protein BRAFLDRAFT_265495 [Branchiostoma floridae]
 gi|229297700|gb|EEN68332.1| hypothetical protein BRAFLDRAFT_265495 [Branchiostoma floridae]
          Length = 444

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 105/235 (44%), Gaps = 39/235 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G AD  + ++ AK+VE+     I++N+GCP     +G  GA L+ NP+ +   + 
Sbjct: 89  VVFQMGTADPERALKVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSNPEKIKQILT 147

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +   +SIPVT K RI   ++D +      +LV+ I+ +GV  + +H R         K+
Sbjct: 148 TLVNGVSIPVTCKIRILPKLEDTL------SLVQLIESTGVAAVAVHGRY--------KE 193

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG------LEDMSQALKILPSVDGVMIGRAAYK 221
            R    +  D++  I +      I  NGG       ED+ Q  +       VM+ RAA  
Sbjct: 194 ERPRHPVHADVIKAISQAVSIPVIA-NGGSGVINRYEDL-QRFREDTGASSVMVARAAQW 251

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           N ++             G  P+   V +D+ R       DY    L+S   LQQI
Sbjct: 252 NFSIFRP---------EGMLPVDD-VIRDYLR----YAVDYDNVALNSKYVLQQI 292


>gi|296118884|ref|ZP_06837457.1| putative tRNA-dihydrouridine synthase [Corynebacterium ammoniagenes
           DSM 20306]
 gi|295967982|gb|EFG81234.1| putative tRNA-dihydrouridine synthase [Corynebacterium ammoniagenes
           DSM 20306]
          Length = 400

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 66/123 (53%), Gaps = 6/123 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R  T + L   EM+ A A++  ++K +    F+  E P +LQ+   D     +AAK IV+
Sbjct: 57  RTGTVSGLYVCEMVTARALVERNEKTMKMTTFAPDEDPRSLQLYTVDPEYTYKAAKMIVD 116

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  ++     G+ L     + G+ +AA  KA     IPVTVK R+G+
Sbjct: 117 ENLADHIDMNFGCPVPKITRRGGGSALPYKRRLFGNIVAAAVKATEGTDIPVTVKFRVGI 176

Query: 128 DDQ 130
           DD+
Sbjct: 177 DDE 179


>gi|224002192|ref|XP_002290768.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974190|gb|EED92520.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 615

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 101/233 (43%), Gaps = 15/233 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           MV  ++  +R   R      L YT M+ +   ++     KN +  S   +PL        
Sbjct: 98  MVGASELAFRLLCRKY-GATLSYTPMMSSSQFVQEAASMKNTVADSNLYRPLVCHFSANQ 156

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCIAAMCKALS 116
                +AAK+VE +  + I+LN+GCP      G FG+ L+   D  +V   + A  KA+S
Sbjct: 157 PQDFAKAAKLVEKYC-DAIDLNLGCPQRTAFIGHFGSYLLGQKDRKLVLSIVRAGSKAVS 215

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLD 175
           IP+ VK R+   D +       L   ++ +G + I IHAR +A  +   P   R  P L 
Sbjct: 216 IPIFVKIRLL--DTVEETT--KLCHELRDAGASLIAIHARYRATWERTGP-GARDGPAL- 269

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAML 226
            D V  +K+  PD  I  NG +      +  K     DG+M       N A+ 
Sbjct: 270 LDQVAVVKQSMPDFPIIANGNVITYDDVISNKQSTGADGIMSAEGILDNPALF 322


>gi|115495449|ref|NP_001068887.1| tRNA-dihydrouridine synthase 2-like [Bos taurus]
 gi|111308646|gb|AAI20343.1| Dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae) [Bos
           taurus]
 gi|296477934|gb|DAA20049.1| dihydrouridine synthase 2-like, SMM1 homolog [Bos taurus]
          Length = 493

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 98/219 (44%), Gaps = 29/219 (13%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           + N AL   + +  D     D+        ++  +  Q+G +D  + +  A++VE+    
Sbjct: 55  VVNEALSTVDFVAPD-----DRVVFRTCEREQSKVVFQMGTSDAERALAVARLVEN-DVA 108

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPA 133
            I++N+GCP     +G  GA L+ +PD +   ++ + K    PVT K RI   ++D +  
Sbjct: 109 GIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTRRPVTCKIRILPSLEDTL-- 166

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
               +LVK I+++G+  I +H RK        ++ R    +  + +  I  E   + +  
Sbjct: 167 ----SLVKRIERTGIAAIAVHGRK--------REERPQHPVSCEAIKAI-AETLSIPVIA 213

Query: 194 NGGLEDMSQA------LKILPSVDGVMIGRAAYKNSAML 226
           NGG  D  Q        +   +   VM+ RAA  N ++ 
Sbjct: 214 NGGSHDHIQGYLDIEDFRRATAASSVMVARAAMWNPSIF 252


>gi|239979346|ref|ZP_04701870.1| putative dihydrouridine synthase [Streptomyces albus J1074]
          Length = 389

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 53/226 (23%), Positives = 106/226 (46%), Gaps = 19/226 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E+P ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIQFGETERPRSIQLYGV 93

Query: 58  DISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKA 114
           D + + +A +++  ED   + I+LN GCP  +V     G+ L    +++   +  A+  A
Sbjct: 94  DPATVGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGA 152

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD        +  +   + GV  + +H R A                
Sbjct: 153 GDLPVTIKMRKGIDDD--HTTYLDAGRIAVEEGVTAVALHGRTAA--------QHYSGTA 202

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
           D++ +  +K+   ++ +  NG +   + A++++     DGV++GR 
Sbjct: 203 DWEAIARLKEHVTEIPVLGNGDIWSAADAVRMMAETGCDGVVVGRG 248


>gi|332999337|gb|EGK18923.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-272]
 gi|333014706|gb|EGK34052.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-227]
          Length = 281

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 87/189 (46%), Gaps = 23/189 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+   ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSAPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPK 166
             A+ +PV +K R G      A   RN   + +  +  G+  + IH R    +  G    
Sbjct: 89  VNAVDVPVPLKIRTGW-----APVHRNCEEIAQLAEDCGIQALTIHGRTRACLFNG---- 139

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   +YD +  +K++     I  NG + D  +A  +L     D +MIGRAA     
Sbjct: 140 ------EAEYDSIRAVKQKVSIPVIA-NGDITDPLKARAVLDYTGADALMIGRAAQGRPW 192

Query: 225 MLTTVDEYF 233
           +   +  Y 
Sbjct: 193 IFREIQHYL 201


>gi|317509475|ref|ZP_07967091.1| dihydrouridine synthase [Segniliparus rugosus ATCC BAA-974]
 gi|316252227|gb|EFV11681.1| dihydrouridine synthase [Segniliparus rugosus ATCC BAA-974]
          Length = 386

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 56/214 (26%), Positives = 101/214 (47%), Gaps = 25/214 (11%)

Query: 16  LTNNA--LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-- 69
           LT  A  L   EMI+A +++  + K   ++ F  +E+P ++Q+   D   + EA +++  
Sbjct: 45  LTGQARGLYVNEMIMARSLVARNPKAMRMVEFGPEERPRSMQLYTVDPEAVGEAVRMIVA 104

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV 127
           ED   + ++LN GCP  +V     G+ L     +    I A  +     +PVTVK RIG+
Sbjct: 105 EDLA-DHVDLNFGCPVPKVTRNGGGSALPYKRRLFARIIEAAVRGADGVVPVTVKFRIGI 163

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           DD+       +  +  + SG   + +HAR A  +  G +          D+  +  +K+ 
Sbjct: 164 DDE--HHTYLDAGRIARDSGAAAVALHARTAAQLYSGTA----------DWSAIARLKEH 211

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
             D+ +  NG +     A +++     DGV++GR
Sbjct: 212 VTDIPVLGNGDIFAAEDAARMMAQTGCDGVVVGR 245


>gi|90410806|ref|ZP_01218821.1| putative regulator protein [Photobacterium profundum 3TCK]
 gi|90328437|gb|EAS44735.1| putative regulator protein [Photobacterium profundum 3TCK]
          Length = 322

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 88/184 (47%), Gaps = 19/184 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +T   P+ +Q+ G +   + E A    + G   I++N GCP+  V++   GA L+  P
Sbjct: 57  GKTTSGTPVRVQLLGQEPVWMAENAYRASNLGSAGIDINFGCPAKSVNKNRGGAVLLKEP 116

Query: 102 D----IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +    IV +  +A+C   + PVT K R+G DD         +V ++ ++G + I IHAR 
Sbjct: 117 EKIYQIVKEVRSAVCP--TKPVTAKVRLGWDDPTHCF---EIVDAVAQAGGDEIAIHART 171

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMI 215
            +       D  K   + +D + ++ KE   + I  NG + +    QA   +   D +MI
Sbjct: 172 KV-------DGYKAETIKWDYIRQV-KEKSSIPIIANGEVWNYQDGQACLNVTQTDALMI 223

Query: 216 GRAA 219
            R A
Sbjct: 224 CRGA 227


>gi|86160208|ref|YP_466993.1| dihydrouridine synthase TIM-barrel protein nifR3 [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85776719|gb|ABC83556.1| tRNA-U20-dihydrouridine synthase [Anaeromyxobacter dehalogenans
           2CP-C]
          Length = 352

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 38/127 (29%), Positives = 62/127 (48%), Gaps = 3/127 (2%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKL 62
           +DR +R   R +   +  YTEM+ A  ++ G     + L     E P A+QI  ++   L
Sbjct: 21  SDRPFRAICRRM-GASFAYTEMVSAHGLMHGALQTSSYLDREPDEDPFAVQIFASEPDVL 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              A +    G   I++N+ CP  +V     GA +  +P  V + + A+  A+ +PVTVK
Sbjct: 80  ARGAVVAVQAGAGMIDVNMACPVKKVCGSGAGAAMGRDPRKVEEAVRAIRAAVPVPVTVK 139

Query: 123 CRIGVDD 129
            R G D+
Sbjct: 140 IRAGWDE 146


>gi|218283931|ref|ZP_03489799.1| hypothetical protein EUBIFOR_02395 [Eubacterium biforme DSM 3989]
 gi|218215510|gb|EEC89048.1| hypothetical protein EUBIFOR_02395 [Eubacterium biforme DSM 3989]
          Length = 321

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 102/223 (45%), Gaps = 24/223 (10%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDK---KNILGFSTQEKPLALQIGGADISKLVEAA 66
           RF A L+ N        +V+D  L  D    K +      E P++ Q+ G DI  +V AA
Sbjct: 32  RFGAGLVCNE-------MVSDKALYYDSLKTKQMCAIDENEHPVSFQLFGHDIDTVVYAA 84

Query: 67  KIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K ++     + I+ N+GCP  +V +   G+ LM + D   + ++ + + +S PVTVK R+
Sbjct: 85  KYLDTQTDCDIIDFNMGCPVNKVIKAQAGSFLMKDIDYAKELVSNIVQNVSKPVTVKMRL 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D     +    + K+++  GV+ + +H R         ++       D+  + ++K  
Sbjct: 145 GFDTY--HINCVEMAKAMESVGVSAVAVHGR--------TRNQMYEGKADWSYIKQVKDA 194

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
                IG NG +  +    +++     D VM+GR    N  ++
Sbjct: 195 VSIPVIG-NGDVRSVEDFHRMMNETGCDAVMLGRGIVGNPFLI 236


>gi|118103122|ref|XP_425899.2| PREDICTED: similar to Dihydrouridine synthase 3-like protein
           [Gallus gallus]
          Length = 660

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 66/278 (23%), Positives = 118/278 (42%), Gaps = 32/278 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM V   +L+G      +L     E    +Q+ GA    + + A+++ +    + +++NV
Sbjct: 345 EMAVCTNLLQGQSSEWALLKRHHTEDIFGVQLEGAFPDTMTKCAELLNQTIDVDFVDINV 404

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM   +     +  M   L +P+TVK R GV +++       ++ 
Sbjct: 405 GCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPLTVKIRTGVQEKMNVA--HKIIP 462

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---E 198
            I++ G + + +H R         ++ R     D+D + E  K    + +  NG +   E
Sbjct: 463 KIREWGASMVTLHGRS--------REQRYTRVADWDYIAECAKIASPMPLFGNGDILSYE 514

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
           D +QA++    V G+MI R A     + T + E     ++ S     R D      I   
Sbjct: 515 DANQAMQT--GVSGIMIARGALIKPWLFTEIKEQRHWDISSSE----RFD------ILRD 562

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T+Y   H  S  +  + TR  +  +  F     CR+I
Sbjct: 563 FTNYGLEHWGSDTQGVEKTRKFLLEWLSF----LCRYI 596


>gi|253682545|ref|ZP_04863342.1| dihydrouridine synthase family protein [Clostridium botulinum D
           str. 1873]
 gi|253562257|gb|EES91709.1| dihydrouridine synthase family protein [Clostridium botulinum D
           str. 1873]
          Length = 319

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 57/254 (22%), Positives = 112/254 (44%), Gaps = 31/254 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +++L  + + K +  QI   D  + +  A+ +++ GYNEINLN+GCPS  V     G+  
Sbjct: 49  RDVLPENNEVKNIVPQILTNDSERFINIARKLQELGYNEINLNLGCPSGTVVSKYRGSGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   + +   +  + K  ++ +++K RIG D          L+K   K  +  + IH R 
Sbjct: 109 LAKREELDRFLDEIFKIDNMKISIKTRIGKDS---PEEFYELIKIFNKYPLEELIIHPR- 164

Query: 158 AILKGLSPKDNRK-IPNLDYDIVYEIKKE------NPDLFIGLNGGLEDMSQALKILPSV 210
                 + +D  K  PNLD      + K+      NP  + G      D  + ++    V
Sbjct: 165 ------TREDFYKNKPNLD------VFKDALSLSVNPICYNGDIFTATDYKKLIETFKEV 212

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
           + VMIGR    N  ++  + E           +  +V K+F  ++  +  +      ++ 
Sbjct: 213 ETVMIGRGILANPGLINEIKE--------DKTLDKKVLKEFHDEVLNNYRELFNEDRNAM 264

Query: 271 GKLQQITRHMIGLF 284
            +++++  +MI +F
Sbjct: 265 FRMKELWGYMIYIF 278


>gi|221065205|ref|ZP_03541310.1| TIM-barrel protein, nifR3 family [Comamonas testosteroni KF-1]
 gi|220710228|gb|EED65596.1| TIM-barrel protein, nifR3 family [Comamonas testosteroni KF-1]
          Length = 354

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 63/258 (24%), Positives = 110/258 (42%), Gaps = 37/258 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+A+QI
Sbjct: 20  MAGVTDRPFRQLCKAL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 74

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G +   + EAA    + G   I++N+GCP+ +V     G+ LM N  +   +   +   
Sbjct: 75  AGTEALMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMQNEPLAVEIAQAVVEA 134

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNR 169
            +  ++PVT+K R G  D      L  L +  ++ G+  + +H   R+   KG +     
Sbjct: 135 ARPYNVPVTLKMRTGWCDTHKNAVL--LARQFEEVGIQMLTVHGRTREQGYKGFA----- 187

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA------YK 221
                +YD +  +K+    + +  NG +    +A  +L     D +M+GRAA      ++
Sbjct: 188 -----EYDTIAAVKQAV-RVPVVANGDINSPEKARDVLAYTGADAIMVGRAAQGRPWIFR 241

Query: 222 NSAMLTTVDEYFSNPLTG 239
             A      E+ + PL  
Sbjct: 242 EIAHFLATGEHMAAPLVA 259


>gi|68535448|ref|YP_250153.1| hypothetical protein jk0383 [Corynebacterium jeikeium K411]
 gi|68263047|emb|CAI36535.1| hypothetical protein jk0383 [Corynebacterium jeikeium K411]
          Length = 389

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 66/123 (53%), Gaps = 6/123 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R+ +   L   EM+ A A++  + K  ++  F+  E P +LQ+   D     +AAK IV+
Sbjct: 46  RMGSVAGLYVCEMVTARALVERNPKTLHMTTFAPDEDPRSLQLYTTDPEYTYKAAKMIVD 105

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V     G+ L     + G+ +AA  KA     IPVTVK R+G+
Sbjct: 106 ENLADHIDMNFGCPVPKVTRRGGGSALPYKRKLFGNIVAAAVKATEGTDIPVTVKMRVGI 165

Query: 128 DDQ 130
           DD+
Sbjct: 166 DDE 168


>gi|260578340|ref|ZP_05846255.1| tRNA-dihydrouridine synthase [Corynebacterium jeikeium ATCC 43734]
 gi|258603521|gb|EEW16783.1| tRNA-dihydrouridine synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 374

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 69/293 (23%), Positives = 117/293 (39%), Gaps = 21/293 (7%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R+ +   L   EM+ A A++  + K  ++  F+  E P +LQ+   D     +AAK IV+
Sbjct: 31  RMGSVAGLYVCEMVTARALVERNPKTLHMTTFAPDEDPRSLQLYTTDPEYTYKAAKMIVD 90

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV 127
           +   + I++N GCP  +V     G+ L     + G+ +AA  KA     IPVTVK R+G+
Sbjct: 91  ENLADHIDMNFGCPVPKVTRRGGGSALPYKRKLFGNIVAAAVKATEGTDIPVTVKMRVGI 150

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--E 185
           DD+         +   + +      +H R A  +     D  +I  L   + +       
Sbjct: 151 DDEHHTHLDAGRIAVEEGAAAVA--LHGRTAAQRYSGHADWNEIARLKEHLAHTGIPVLG 208

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           N D+F   +      ++A+      DGV++GR       +   +          S P   
Sbjct: 209 NGDIFKATD------ARAMMEQTGCDGVVVGRGCLGRPWLFAELSAELRGLPIPSEPTLG 262

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            V +   R       +  A H       + + +HM     GFP     R  L+
Sbjct: 263 EVARIILRH-----AELLAAHDGEQKACRDLRKHMTWYLRGFPAGGELRRSLS 310


>gi|126308862|ref|XP_001379483.1| PREDICTED: similar to DUS1L protein [Monodelphis domestica]
          Length = 480

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVKAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+   +D  +    L      ++K+G   + +H R    KG
Sbjct: 141 SVPVTCKIRVFPEIDKTVKYAQL------LEKAGCQLLTVHGRTKEQKG 183


>gi|257784603|ref|YP_003179820.1| TIM-barrel protein, nifR3 family [Atopobium parvulum DSM 20469]
 gi|257473110|gb|ACV51229.1| TIM-barrel protein, nifR3 family [Atopobium parvulum DSM 20469]
          Length = 363

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 67/260 (25%), Positives = 115/260 (44%), Gaps = 31/260 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR      L Y+EM+    I  G +K   ++   + E  +A+Q+ G+ 
Sbjct: 44  MAGVSDGVYRTMARA-GGAGLAYSEMVSVAGIHFGGEKTWELVEPLSTEPDIAVQLFGSK 102

Query: 59  ISKLVEAA-KIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  EAA +I E  G     I++N+ CP  +V +   G+ L+  P++  + + A    +
Sbjct: 103 PEQFKEAAAQISERLGNKLALIDINMACPVPKVVKKGEGSALLDTPELAANLVKACLSEV 162

Query: 116 SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKI 171
           ++PVTVK R G   D+++         ++++ +G + I +H R A  + +G         
Sbjct: 163 TVPVTVKIRRGRRQDEEVAP----EFARAMEAAGASAIAVHGRFATQMYRG--------- 209

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              +++ V  +        IG    L  ED++ ALK    V  VMI R  Y N  +    
Sbjct: 210 -QAEWETVNRVCDAVSIPVIGSGDMLSAEDVAHALKET-GVTAVMIARGTYGNPWIFKNT 267

Query: 230 DEYFSNPLTGSSPIKTRVDK 249
                  L G +P    VD+
Sbjct: 268 QAL----LEGKTPFVPSVDQ 283


>gi|149055089|gb|EDM06906.1| PP3111 protein, isoform CRA_b [Rattus norvegicus]
 gi|149055090|gb|EDM06907.1| PP3111 protein, isoform CRA_b [Rattus norvegicus]
          Length = 326

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGRYGAFLQEEWDLLQRMILLAHERL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|291451221|ref|ZP_06590611.1| dihydrouridine synthase [Streptomyces albus J1074]
 gi|291354170|gb|EFE81072.1| dihydrouridine synthase [Streptomyces albus J1074]
          Length = 396

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 52/222 (23%), Positives = 105/222 (47%), Gaps = 19/222 (8%)

Query: 5   TDRHYRFFARLLTNN-ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISK 61
           T+  +R   R  +    L  +EMI   A++  ++K   ++ F   E+P ++Q+ G D + 
Sbjct: 45  TNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIQFGETERPRSIQLYGVDPAT 104

Query: 62  LVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
           + +A +++  ED   + I+LN GCP  +V     G+ L    +++   +  A+  A  +P
Sbjct: 105 VGKAVRMIVDEDLA-DHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGAGDLP 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G+DD        +  +   + GV  + +H R A                D++ 
Sbjct: 164 VTIKMRKGIDDD--HTTYLDAGRIAVEEGVTAVALHGRTAA--------QHYSGTADWEA 213

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
           +  +K+   ++ +  NG +   + A++++     DGV++GR 
Sbjct: 214 IARLKEHVTEIPVLGNGDIWSAADAVRMMAETGCDGVVVGRG 255


>gi|242822853|ref|XP_002487972.1| tRNA dihydrouridine synthase (Smm1), putative [Talaromyces
           stipitatus ATCC 10500]
 gi|218712893|gb|EED12318.1| tRNA dihydrouridine synthase (Smm1), putative [Talaromyces
           stipitatus ATCC 10500]
          Length = 787

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 58/221 (26%), Positives = 106/221 (47%), Gaps = 23/221 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F R+ +N++    ++     I R D +N      ++  L  QIG A     V+AAK+V  
Sbjct: 418 FTRIPSNSSKSADQLPKESVIYRIDPEN------EKGKLIFQIGTASPEFAVQAAKVVAG 471

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD +   + ++ + +  P    ++VK R+  
Sbjct: 472 -DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILESLVREVGTPYKIGISVKIRLLE 530

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
             ++     ++LV  +  +G+ G+ IH R   ++   P++ R I +    ++ E+ + N 
Sbjct: 531 TPEL----TKSLVTRLVATGITGLTIHCRTTPMR---PRE-RAIRD-QLSMIAEVCR-NA 580

Query: 188 DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +   +NG +    QAL+++   +VDG MI  AA  NS+  
Sbjct: 581 GVACVMNGDVTSRDQALELMKEYNVDGAMIATAAEANSSCF 621


>gi|240274458|gb|EER37974.1| dihydrouridine synthase [Ajellomyces capsulatus H143]
          Length = 545

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 83/175 (47%), Gaps = 12/175 (6%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++PL +Q    +   L++AA+ VE F  + ++LN+GCP     +G +GA L  +P
Sbjct: 72  GNPSFDRPLIVQFCANNPDDLLQAARAVEPF-CDAVDLNLGCPQGIARKGHYGAFLQEHP 130

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++ + I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 131 DLIYELINTLHTQLSIPVTAKFRI----QETKEKTLEYARIILSAGASIITVHGRRREQK 186

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
           G     N  + +  Y I Y  +    D  I  NG + +     K L +   DGVM
Sbjct: 187 G----HNTGLADWSY-IRYLRENLPADTVIFANGNILNHGDIEKCLEATGADGVM 236


>gi|210630809|ref|ZP_03296610.1| hypothetical protein COLSTE_00495 [Collinsella stercoris DSM 13279]
 gi|210160312|gb|EEA91283.1| hypothetical protein COLSTE_00495 [Collinsella stercoris DSM 13279]
          Length = 317

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 55/214 (25%), Positives = 93/214 (43%), Gaps = 27/214 (12%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   +    V AA+ + + GY E+NLN+GCPS  V     G+  + N D +   +  +C
Sbjct: 65  QLLTKNADAFVWAARELAELGYAEVNLNLGCPSGTVVSKGKGSGFLRNLDELEVFLRDVC 124

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPK---D 167
           +   IPV+VK R+G++D      +  L +S+    +  + +H R  K   +G  P+    
Sbjct: 125 ERSPIPVSVKTRLGLEDDAEYERILELYRSLP---LAELIVHPRVQKDRYQG-KPRWEPY 180

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              +    + + Y     N D+F     G ED +  +   P    +M+GR    N A+  
Sbjct: 181 GETLARAPFPVAY-----NGDIF-----GEEDQAALVAAYPQTRHIMLGRGLLANPAL-- 228

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
                 +  LTG +P      K F  K+  +  D
Sbjct: 229 ------ARMLTGGAPASASELKRFHDKLFCAYLD 256


>gi|289522351|ref|ZP_06439205.1| dihydrouridine synthase family protein [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289504187|gb|EFD25351.1| dihydrouridine synthase family protein [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 329

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 72/309 (23%), Positives = 129/309 (41%), Gaps = 46/309 (14%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKIVEDF---GYN 75
           L +TEM+ + A++ G             E PL LQ+   D++ L+EAA+  E F    + 
Sbjct: 33  LAHTEMVASRALMEGHSSAFYSLQRHHDEGPLVLQLFSGDVASLLEAAQ--EAFRISSFE 90

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            +++N+ CPS +V     GA L+  P +  + I    K L  P+ VK RI   +     +
Sbjct: 91  ALSINMACPSKKVMASGGGASLINRPHVAAEMI-RQAKNLGFPIWVKTRIPSRNLKDVAS 149

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
             +L+ S   +G   + +H R  + +G     +R       +I+ E+ +  P    G   
Sbjct: 150 WCDLLIS---AGAKNVALHGR-TVSQGYKGSSDR-------NIIGEVARAFP----GKIT 194

Query: 196 GLEDMSQALKILPSVD----GVMIGRAAYKNSAML--TTVDEYFSNPLTGSSPIKTRVDK 249
           G  D+  +  +L  ++    GV++ R A K+  ++        F N    +   +  + +
Sbjct: 195 GTGDVFTSDDVLDYLEKGCIGVLVARGALKDPFIVLDALAKLGFRNDRKATFEFQREIFR 254

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHH 309
            F   +   + D  A HL        + R +  +F G P + + R        +S A  H
Sbjct: 255 SFLSDL-CQVKDNLAMHL--------LRRFLSCIFKGMPGASQLR--------SSMARAH 297

Query: 310 IIETAFNLM 318
            I  AF + 
Sbjct: 298 GITQAFEIF 306


>gi|195566706|ref|XP_002106918.1| GD17163 [Drosophila simulans]
 gi|194204313|gb|EDX17889.1| GD17163 [Drosophila simulans]
          Length = 460

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 49/183 (26%), Positives = 88/183 (48%), Gaps = 21/183 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +    +++    + +++N+GCP     +G  GA L+ +PD   + + 
Sbjct: 84  LVLQMGTSDARRALAVGMLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAANILR 142

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +C  L IPVT K RI     +P V    +LV+ +  +G+  I IHAR         +D 
Sbjct: 143 TLCSGLDIPVTCKIRI-----LPDVERTIDLVQKLAATGIAAIGIHART--------RDE 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNS 223
           R       +++  +  +  D+ I  NGG ++M      +  ++    D VM+ RAA  N 
Sbjct: 190 RPQHPAHPEVLRAV-AQAVDIPIIANGGSKNMHCYEDLRKFQLECGADSVMVARAAQINV 248

Query: 224 AML 226
           ++ 
Sbjct: 249 SIF 251


>gi|145640201|ref|ZP_01795785.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|145274787|gb|EDK14649.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 22.4-21]
          Length = 310

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 102/226 (45%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G +   L E A    D G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQNPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ GV  I +H R   
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGVTEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + E+ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKADGYRADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  W +I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWYEIQKILQKYA 257


>gi|218887737|ref|YP_002437058.1| dihydrouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218758691|gb|ACL09590.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris str. 'Miyazaki
           F']
          Length = 383

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 59/203 (29%), Positives = 95/203 (46%), Gaps = 14/203 (6%)

Query: 21  LLYTEMIVADAIL--RGDKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEI 77
           LL+T M  A A+   R +K     +   E P L  Q+ GA+   + E A+ V+  G+  +
Sbjct: 74  LLFTGMCNARAVPTERPEKSEAFSWRAGEPPRLVCQLFGAEPEHMAEGARRVQAEGFFGV 133

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVAL 136
           +LN+GC  + + +   GA L+ +P+     +AA+ +A+ IPV VK R G   D  PAV  
Sbjct: 134 DLNMGCSVSAIIKRGCGADLLRDPERAVRMVAAVRRAVDIPVFVKFRTGWSPDPQPAV-- 191

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            +L +  + +G + +  H R A  +   P     I  +   +   +   N D+F      
Sbjct: 192 -DLARRFEDAGADCLVFHPRVAPDRRTQPPRRAHIGLVKAAVSIPVMG-NGDVFT----- 244

Query: 197 LEDMSQALKILPSVDGVMIGRAA 219
            ED +  L      DGV +GR A
Sbjct: 245 PEDCANLLDDT-GCDGVSLGRIA 266


>gi|149910034|ref|ZP_01898682.1| putative Dihydrouridine synthase [Moritella sp. PE36]
 gi|149806902|gb|EDM66863.1| putative Dihydrouridine synthase [Moritella sp. PE36]
          Length = 321

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 119/242 (49%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EM+ ++  +   +K+   +  + +    ++QI GAD
Sbjct: 17  MAGVTDRPFRQLCRDL-GVGMAVSEMLSSNPRVWSTEKSQQRMDHAGETGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +  AA+     G   I++N+GCP+ +V++   G+ LM +P  V   + A+  A+ +P
Sbjct: 76  PALMAAAAQHNVKNGAQIIDINMGCPAKKVNKKMAGSALMQHPAQVKLILDAVISAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D     +  RN   + +  +++G+  + +H R    + KG +         
Sbjct: 136 VTLKIRTGWD-----LENRNGIQIAEIAEQAGIQALAVHGRTRACLYKGTA--------- 181

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  IK  +  + +  NG ++   +A ++L    VDG+MIGR A  N  +   ++ 
Sbjct: 182 -EYDTIKAIKA-SISIPVIANGDIDSPEKAKQVLEYTGVDGLMIGRPAQGNPWIFREINH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|257791401|ref|YP_003182007.1| TIM-barrel protein, nifR3 family [Eggerthella lenta DSM 2243]
 gi|257475298|gb|ACV55618.1| TIM-barrel protein, nifR3 family [Eggerthella lenta DSM 2243]
          Length = 330

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 29/234 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L YTEM+ A  +   ++K  ++L  +  E  +A+Q+ G +
Sbjct: 18  MAGVSDEAFRTLCREQGAD-LTYTEMVSAKGLSYANEKTRHLLRLAPGEDQVAVQLFGHE 76

Query: 59  ISKLV-EAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  +AA I  + G +   +++N+GCP+ ++     G+ LM +P +    + A+  A+
Sbjct: 77  PDTMAAQAAWIEREMGQSLAYLDINMGCPARKIVSKGDGSALMKDPALAASIVRAVRAAV 136

Query: 116 SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
           S PVTVK R G    D+  P  A R     ++ +G   I +H R A  + +G +      
Sbjct: 137 SRPVTVKFRRGWAEGDETAPEFARR-----MEDAGACAIAVHGRYAEQLYRGRA------ 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
               ++  +  +K+      +G NG +   + A+ I      D VMI RAA  N
Sbjct: 186 ----EWGAIARVKEAVSVPVVG-NGDVRSGADAVAITERTGCDAVMIARAAEGN 234


>gi|195398221|ref|XP_002057721.1| GJ17945 [Drosophila virilis]
 gi|194141375|gb|EDW57794.1| GJ17945 [Drosophila virilis]
          Length = 399

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 64/261 (24%), Positives = 114/261 (43%), Gaps = 27/261 (10%)

Query: 12  FARLLTNNA--LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAK 67
           F RLL  N   L +T M+++D++   +K     F+T   ++PL  Q    D  + V +A+
Sbjct: 37  FRRLLRQNGVQLAFTPMMISDSVNNSEKARQNEFTTGPDDQPLIAQFAAKDAMEFVTSAQ 96

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI 125
           +V  +  + ++LN GCP        +G  L+  P+ V D +  + + L     V+VK R+
Sbjct: 97  LVYPY-VDGVDLNCGCPQGWAISKGYGCGLLRQPEQVRDIVQCLRRTLPTDFSVSVKMRL 155

Query: 126 --GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
               D Q        L + ++  GV  + +H R    K    KD   +  +  D+   ++
Sbjct: 156 LQSSDSQTSLQRTIQLAQQLEHCGVTFLTLHGRTPSQK--HSKDTLNVAAM-ADVCQSLQ 212

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                + + +NG +E    A ++       GVM  R    N A+  +  +Y   P   ++
Sbjct: 213 -----IPLIVNGNVESFQDACELHARTHAAGVMAARGLLANPALFNS--DY---PQATTT 262

Query: 242 PIKTRVDKDFWRKISASMTDY 262
           P K  V +  W  I+ S  D+
Sbjct: 263 P-KACVQQ--WLDIAQSAGDH 280


>gi|325134156|gb|EGC56806.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M13399]
 gi|325144337|gb|EGC66640.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M01-240013]
 gi|325206171|gb|ADZ01624.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M04-240196]
          Length = 333

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 51/207 (24%), Positives = 95/207 (45%), Gaps = 24/207 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K
Sbjct: 136 KTLRERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------K 184

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
                P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     
Sbjct: 185 AEAYEPPAHWEWIRKI-RDTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPD 243

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           +   + +Y         P+K   D DF
Sbjct: 244 LARQIKQY-----ENGGPVK---DTDF 262


>gi|254555542|ref|YP_003061959.1| hypothetical protein JDM1_0373 [Lactobacillus plantarum JDM1]
 gi|254044469|gb|ACT61262.1| conserved hypothetical protein [Lactobacillus plantarum JDM1]
          Length = 337

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 48/214 (22%), Positives = 97/214 (45%), Gaps = 26/214 (12%)

Query: 22  LYTEMIVADAILRGDKKN------ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
            ++E + A +I   + K        +  +  +KP+ +Q+ G + +    A   + D G+ 
Sbjct: 48  FFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPV-VQLWGNEAADFASATAELRDRGFE 106

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            +++N+GCP   V +   G+ L+ NP    D IAA  K   + V+ K R+G         
Sbjct: 107 AVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTSGLAVSAKTRLGYSK---VAE 162

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFI 191
             + + ++    V  + +H R       + ++  K+P   ++++ ++ K      P+  +
Sbjct: 163 YHDWIATLLSQHVAVLTVHLR-------TKQEMSKVP-AHFEVIDDLIKMRDAIAPETLL 214

Query: 192 GLNGGLEDMSQAL---KILPSVDGVMIGRAAYKN 222
            +NG + D    +   K  P +DG+MIGR  + N
Sbjct: 215 QINGDVADYQAGVALAKAHPGLDGIMIGRGVFAN 248


>gi|170693384|ref|ZP_02884543.1| TIM-barrel protein, nifR3 family [Burkholderia graminis C4D1M]
 gi|170141539|gb|EDT09708.1| TIM-barrel protein, nifR3 family [Burkholderia graminis C4D1M]
          Length = 374

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 71/307 (23%), Positives = 136/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 34  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 93  PDMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGVG 152

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 153 PDAVPVTLKIRTGWNRENKNAL--NVARLAEAAGISMLTVHGRT--------RADLYHGD 202

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ 
Sbjct: 203 AEYETIAAVKAA-VRIPVVANGDISSPEKARHVLAVTGADAIMIGRAAQGRPWLFREIEH 261

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 262 FLQ---TGELLPPPRID-----EIQQVMNEHLQDHYGFYGEFTGVRTARKHIGWYTRGLS 313

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 314 GANLFRH 320


>gi|73964669|ref|XP_848227.1| PREDICTED: similar to PP3111 protein isoform 2 [Canis familiaris]
          Length = 475

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--KYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|120597327|ref|YP_961901.1| nifR3 family TIM-barrel protein [Shewanella sp. W3-18-1]
 gi|146294528|ref|YP_001184952.1| nifR3 family TIM-barrel protein [Shewanella putrefaciens CN-32]
 gi|120557420|gb|ABM23347.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. W3-18-1]
 gi|145566218|gb|ABP77153.1| putative TIM-barrel protein, nifR3 family [Shewanella putrefaciens
           CN-32]
 gi|319427893|gb|ADV55967.1| TIM-barrel protein, nifR3 family [Shewanella putrefaciens 200]
          Length = 322

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 26/243 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK +  +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQVFRNLC-LRYGAALAVSEMLSSNPDVWETDKSRQRMMHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G + I++N+GCP+ +V++   G+ LM NP +V   + A+  A+++P
Sbjct: 76  PDLMAQAAQFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKAILQAVVAAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + +H   R+ + KG          +
Sbjct: 136 VTLKIRTGW-----APEHRNGVQIAQIAEDCGIASLAVHGRTRQCMYKG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K+N  + +  NG ++   +A  +L    VD +MIGR A     +   +  
Sbjct: 181 AEYDTIKAI-KQNVSIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQH 239

Query: 232 YFS 234
           Y  
Sbjct: 240 YLE 242


>gi|325831497|ref|ZP_08164751.1| tRNA-dihydrouridine synthase B [Eggerthella sp. HGA1]
 gi|325486751|gb|EGC89199.1| tRNA-dihydrouridine synthase B [Eggerthella sp. HGA1]
          Length = 330

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 29/234 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L YTEM+ A  +   ++K  ++L  +  E  +A+Q+ G +
Sbjct: 18  MAGVSDEAFRTLCREQGAD-LTYTEMVSAKGLSYANEKTRHLLRLAPGEDQVAVQLFGHE 76

Query: 59  ISKLV-EAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  +AA I  + G +   +++N+GCP+ ++     G+ LM +P +    + A+  A+
Sbjct: 77  PDTMAAQAAWIEREMGQSLAYLDINMGCPARKIVSKGDGSALMKDPALAASIVRAVRAAV 136

Query: 116 SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
           S PVTVK R G    D+  P  A R     ++ +G   I +H R A  + +G +      
Sbjct: 137 SRPVTVKFRRGWAEGDETAPEFARR-----MEDAGACAIAVHGRYAEQLYRGRA------ 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
               ++  +  +K+      +G NG +   + A+ I      D VMI RAA  N
Sbjct: 186 ----EWGAIARVKEAVSVPVVG-NGDVRSGADAVAITERTGCDAVMIARAAEGN 234


>gi|19920448|ref|NP_608507.1| CG3645, isoform A [Drosophila melanogaster]
 gi|24580595|ref|NP_722619.1| CG3645, isoform B [Drosophila melanogaster]
 gi|15292203|gb|AAK93370.1| LD42056p [Drosophila melanogaster]
 gi|22945600|gb|AAF51525.2| CG3645, isoform A [Drosophila melanogaster]
 gi|22945601|gb|AAN10512.1| CG3645, isoform B [Drosophila melanogaster]
 gi|220955978|gb|ACL90532.1| CG3645-PA [synthetic construct]
 gi|295293325|gb|ADF87928.1| MIP22167p [Drosophila melanogaster]
          Length = 505

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 108/233 (46%), Gaps = 17/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+      K  K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L++P
Sbjct: 94  AQQILDAALLAQDHC-DAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-- 176
           VT K RI  D +     +R   K ++ +G   + +H R    KG        + N +Y  
Sbjct: 153 VTCKIRIFEDLE---KTIR-YAKMLEAAGCQLLTVHGRTREQKGPL----TGVANWNYIK 204

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           ++   IK   P L  G    L+D+ + L     VDGVM       N A+   V
Sbjct: 205 NVRQHIKI--PMLANGNILALDDVHRCLTET-GVDGVMSAEGNLHNPAIFKGV 254


>gi|118151248|ref|NP_001071552.1| tRNA-dihydrouridine synthase 1-like [Bos taurus]
 gi|117306348|gb|AAI26847.1| Dihydrouridine synthase 1-like (S. cerevisiae) [Bos taurus]
          Length = 270

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAHLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+   +D  +         + ++K+G   + +H R    KG
Sbjct: 141 SVPVTCKIRVFPEIDKTV------RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|325090797|gb|EGC44107.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus H88]
          Length = 583

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 83/175 (47%), Gaps = 12/175 (6%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++PL +Q    +   L++AA+ VE F  + ++LN+GCP     +G +GA L  +P
Sbjct: 110 GNPSFDRPLIVQFCANNPDDLLQAARAVEPF-CDAVDLNLGCPQGIARKGHYGAFLQEHP 168

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++ + I  +   LSIPVT K RI    Q          + I  +G + I +H R+   K
Sbjct: 169 DLIYELINTLHTHLSIPVTAKFRI----QETKEKTLEYARIILSAGASIITVHGRRREQK 224

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
           G     N  + +  Y I Y  +    D  I  NG + +     K L +   DGVM
Sbjct: 225 G----HNTGLADWSY-IRYLRENLPADTVIFANGNILNHGDIEKCLEATGADGVM 274


>gi|194216507|ref|XP_001490768.2| PREDICTED: dihydrouridine synthase 1-like (S. cerevisiae) [Equus
           caballus]
          Length = 475

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|17232390|ref|NP_488938.1| transcriptional regulator [Nostoc sp. PCC 7120]
 gi|17134036|dbj|BAB76597.1| transcriptional regulator [Nostoc sp. PCC 7120]
          Length = 349

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 105/224 (46%), Gaps = 26/224 (11%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +P+  Q+ G  I  LV  AK  E  GYN   ++LN+GCP+ R++  + G  L+L+P  V 
Sbjct: 81  RPVFAQMIGESIPDLVRTAK--ELCGYNIAGVDLNMGCPAPRIYRKNVGGGLLLSPAKVE 138

Query: 106 DCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKG 162
             +  + +A++  P+TVK R+G ++         ++  + +  ++ + +H R  K +  G
Sbjct: 139 QILEELRQAVNDRPLTVKMRVGFEN---TDTFYEILDIVNRHNIDLLSLHGRTVKDMYHG 195

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAY 220
                      + YD++ E  +   D  +  NG +   + AL++L      GVM+GR A 
Sbjct: 196 ----------AVKYDLIAEAVRR-VDCPVLANGNIHSATTALEVLERTGAAGVMVGRWAI 244

Query: 221 KNSAMLTTVDEYFSNPLTGSSP---IKTRVDKDFWRKISASMTD 261
            N  +   + +          P   ++  +D+ +    +A+M +
Sbjct: 245 GNPWLFNQIRQALQGETITPVPLVEVRNYIDRLWQTPTAATMPE 288


>gi|118082096|ref|XP_001231946.1| PREDICTED: similar to Dihydrouridine synthase 4-like (S.
           cerevisiae) isoform 2 [Gallus gallus]
          Length = 301

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 105/242 (43%), Gaps = 38/242 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + L YT M+VA   +R  K     F+T   + PL +Q    +
Sbjct: 32  MVRYSKLAFRTLVRRYGCD-LCYTPMVVAADFVRSAKARDSEFTTNRGDNPLIVQFAAKE 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 91  AQVLCDAALLVCPFA-DGVDLNCGCPQRWAMAEGYGACLINKPELVRDMVRHVRNQIDNP 149

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L K  + +GV+ I +H R          + R  P + 
Sbjct: 150 RFSVSIKIRIHEDLKKTV----DLCKKAEATGVSWITVHGRNI--------EERHQP-VH 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           YD + ++ KE+  + +  NG ++ +  A                 +N   LT  D Y   
Sbjct: 197 YDAI-KVIKESIHIPVVANGDIKTLKDA-----------------ENVHHLTGADGYEET 238

Query: 236 PL 237
           PL
Sbjct: 239 PL 240


>gi|307730942|ref|YP_003908166.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1003]
 gi|307585477|gb|ADN58875.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1003]
          Length = 358

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 71/307 (23%), Positives = 136/307 (44%), Gaps = 32/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENRNAL--NVARLAEAAGISMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVKAA-VRIPVVANGDITSPEKARHVLAVTGADAIMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLF-HGFP 288
           +     TG      R+D     +I   M ++   H    G+   +   R  IG +  G  
Sbjct: 246 FLQ---TGELLPPPRID-----EIQQVMNEHLEDHYAFYGEFTGVRTARKHIGWYTRGLS 297

Query: 289 NSRRCRH 295
            +   RH
Sbjct: 298 GANVFRH 304


>gi|134114502|ref|XP_774081.1| hypothetical protein CNBH0060 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50256713|gb|EAL19434.1| hypothetical protein CNBH0060 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 725

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 106/238 (44%), Gaps = 24/238 (10%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL  +     T  EM +A  ++ G K+   ++     EK   +Q+ G   +++V AA+
Sbjct: 373 FRRLCVDYGATITVSEMALAQPLVYGAKEEWALVRRHESEKMFGVQVAGGFPNRMVPAAE 432

Query: 68  IVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           ++ +      G + +++N+GCP   V     G+ LM +P  +G  +  M +AL  IP+TV
Sbjct: 433 VIANTIGKGGGVDFVDVNMGCPIDLVFNQGAGSALMDSPGRLGKLLVGMNRALGDIPLTV 492

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV    P  A + + + + + G   + IH R    +   P D   I      +   
Sbjct: 493 KFRTGVAHGKPN-AHKLIPRFVTEWGAGALTIHGRSRQQRYSKPADWEYIKTCVTALRES 551

Query: 182 IKKEN-PDLFIGLNGG-------LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   N P + I  NG         E+M ++      VDGVM+ R A     + T + E
Sbjct: 552 VADANLPPVPIFGNGDCFSAASYYEEMDRS-----GVDGVMVARGALIKPWIFTEIKE 604


>gi|58271188|ref|XP_572750.1| tRNA dihydrouridine synthase [Cryptococcus neoformans var.
           neoformans JEC21]
 gi|74683549|sp|Q5KC68|DUS3_CRYNE RecName: Full=tRNA-dihydrouridine synthase 3
 gi|57229009|gb|AAW45443.1| tRNA dihydrouridine synthase, putative [Cryptococcus neoformans
           var. neoformans JEC21]
          Length = 725

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 106/238 (44%), Gaps = 24/238 (10%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL  +     T  EM +A  ++ G K+   ++     EK   +Q+ G   +++V AA+
Sbjct: 373 FRRLCVDYGATITVSEMALAQPLVYGAKEEWALVRRHESEKMFGVQVAGGFPNRMVPAAE 432

Query: 68  IVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           ++ +      G + +++N+GCP   V     G+ LM +P  +G  +  M +AL  IP+TV
Sbjct: 433 VIANTIGKGGGVDFVDVNMGCPIDLVFNQGAGSALMDSPGRLGKLLVGMNRALGDIPLTV 492

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV    P  A + + + + + G   + IH R    +   P D   I      +   
Sbjct: 493 KFRTGVAHGKPN-AHKLIPRFVTEWGAGALTIHGRSRQQRYSKPADWEYIKTCVTALRES 551

Query: 182 IKKEN-PDLFIGLNGG-------LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   N P + I  NG         E+M ++      VDGVM+ R A     + T + E
Sbjct: 552 VADANLPPVPIFGNGDCFSAASYYEEMDRS-----GVDGVMVARGALIKPWIFTEIKE 604


>gi|113461433|ref|YP_719502.1| tRNA-dihydrouridine synthase C [Haemophilus somnus 129PT]
 gi|170718461|ref|YP_001783677.1| dihydrouridine synthase [Haemophilus somnus 2336]
 gi|112823476|gb|ABI25565.1| tRNA-U20a,U20b-dihydrouridine synthase [Haemophilus somnus 129PT]
 gi|168826590|gb|ACA31961.1| dihydrouridine synthase DuS [Haemophilus somnus 2336]
          Length = 309

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 89/184 (48%), Gaps = 19/184 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G     L E A+   + G   I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTLSGTPVRVQLLGQYPQWLAENAQRAVELGSQGIDLNCGCPSKAVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +++     A+ +A+ +  PV+VK R+G D  DQ+  +A      ++++ G   I IH R 
Sbjct: 117 ELIYQATKAIRQAVPMEQPVSVKVRLGWDNVDQVFEIA-----DAVQQGGATEITIHGR- 170

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
                 +  D  +   +++  + E++K+   P +  G     +D    L I    D +MI
Sbjct: 171 ------TKSDGYRADRINWYKIAEVRKKLRIPVIANGEIWHWQDGQNCLAITGCQD-LMI 223

Query: 216 GRAA 219
           GR A
Sbjct: 224 GRGA 227


>gi|89900372|ref|YP_522843.1| dihydrouridine synthase TIM-barrel protein nifR3 [Rhodoferax
           ferrireducens T118]
 gi|89345109|gb|ABD69312.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodoferax
           ferrireducens T118]
          Length = 350

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/251 (25%), Positives = 109/251 (43%), Gaps = 27/251 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM+ +   L    +         +  P+A+QI G +
Sbjct: 17  MAGVTDRPFRQLCRRL-GAGYAVSEMLTSRPDLWHTPQTARRANHDGEAGPIAVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
            + + +AA    D G   I++N+GCP+ +V     G+ LM N  +   + + + A+C   
Sbjct: 76  AAMMAQAAAYNIDCGAQIIDINMGCPAKKVCSKWAGSALMQNEPLALSIIEAVVAVCTPR 135

Query: 116 SIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +PVT+K R G       AVA   L ++ + +GV  I +H R         ++       
Sbjct: 136 GVPVTLKMRTGWCQSHKNAVA---LARAAEGAGVQMITVHGRT--------REQGYSGTA 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA------YKNSAML 226
           +YD +  +K     + +  NG ++   QA  +L     D VM+GRAA      ++  A  
Sbjct: 185 EYDTIAAVKAAI-KVPVVANGDIDSPEQARHVLAVTRADAVMVGRAAQGRPWIFREMAHF 243

Query: 227 TTVDEYFSNPL 237
                + + PL
Sbjct: 244 LATGSHLAPPL 254


>gi|25282413|ref|NP_742015.1| tRNA-dihydrouridine synthase 1-like [Rattus norvegicus]
 gi|81866863|sp|Q8K582|DUS1L_RAT RecName: Full=tRNA-dihydrouridine synthase 1-like; AltName:
           Full=Liver regeneration-related protein LRRG08/LRRG09
 gi|21105480|gb|AAM34683.1|AF508021_1 embryo-related protein [Rattus norvegicus]
 gi|33187773|gb|AAP97740.1| liver regeneration-related protein LRRG08 [Rattus norvegicus]
 gi|33187775|gb|AAP97741.1| liver regeneration-related protein LRRG09 [Rattus norvegicus]
          Length = 438

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGRYGAFLQEEWDLLQRMILLAHERL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|31980834|ref|NP_081100.2| tRNA-dihydrouridine synthase 1-like [Mus musculus]
 gi|81898593|sp|Q8C2P3|DUS1L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 1-like
 gi|26353202|dbj|BAC40231.1| unnamed protein product [Mus musculus]
 gi|148702860|gb|EDL34807.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_b [Mus
           musculus]
          Length = 475

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|241759875|ref|ZP_04757975.1| tRNA-dihydrouridine synthase C [Neisseria flavescens SK114]
 gi|241319883|gb|EER56279.1| tRNA-dihydrouridine synthase C [Neisseria flavescens SK114]
          Length = 321

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 94/193 (48%), Gaps = 16/193 (8%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +T   P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD+
Sbjct: 59  TTAGTPCTVQLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDL 118

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   +  + + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  + +
Sbjct: 119 IYHIVHTLRQRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKV-E 174

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
           G  P  +       ++ V +I ++  ++ +  NG + ++   L I  +   + VM+GR A
Sbjct: 175 GYEPPAH-------WEWVRKI-RDAVNIPVTANGDVFNLQDYLDIKSVSGCNSVMLGRGA 226

Query: 220 YKNSAMLTTVDEY 232
                +   + +Y
Sbjct: 227 VIRPDLARQIKQY 239


>gi|269120324|ref|YP_003308501.1| dihydrouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268614202|gb|ACZ08570.1| dihydrouridine synthase DuS [Sebaldella termitidis ATCC 33386]
          Length = 309

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 106/237 (44%), Gaps = 28/237 (11%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F  ++  NAL Y+     D ILR           +    A+QI G      +EA K++ +
Sbjct: 29  FTEMVDVNALKYSNQRTQDEILR-----------KAGNEAVQIFGNKNEDFLEAVKLLIE 77

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDD 129
            G++ I++N+GCP  ++     G+ L+L  D V + +  + K     I +++K R G  +
Sbjct: 78  RGFDHIDINLGCPVKKIIRAGKGSALLLESDFVKELLLKLKKEFRNDIKLSMKIRTGYKN 137

Query: 130 -QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
              P       VK  ++ G+  I IH R         ++       D++I+ ++K+++ +
Sbjct: 138 FSDPEY----YVKLAEEYGLFQICIHGR--------TQEQLYSGQADWNIIKKMKQKHKN 185

Query: 189 LFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           + I  NG L D+    +   S   DG+M+ R    N  +L    +YF   +   S +
Sbjct: 186 VKIIGNGDLTDLKTIKEKTDSAKPDGIMLARGLLGNPWLLKEAKDYFKTGVFHESEV 242


>gi|298528412|ref|ZP_07015816.1| dihydrouridine synthase DuS [Desulfonatronospira thiodismutans
           ASO3-1]
 gi|298512064|gb|EFI35966.1| dihydrouridine synthase DuS [Desulfonatronospira thiodismutans
           ASO3-1]
          Length = 328

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 78/322 (24%), Positives = 132/322 (40%), Gaps = 31/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R L   A   TEMI A  +     +   +L    Q+ PL +Q+ G+D
Sbjct: 23  LAGYSDLSFRLLCRNLGCRAAC-TEMISAKGLFFSTANTMRLLETCDQDLPLVVQLYGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  A   +   G+   +LN GC   +V +   GA L+ +  ++   +AAM   ++ P
Sbjct: 82  PDIMGRAVSTLSSKGFRYFDLNCGCSVKKVVKTGAGAALLKDTGLLLQMVAAMAD-MAGP 140

Query: 119 --VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V VK R+G   +       +L   +  +G   I +H R A+ +     D + + NL  
Sbjct: 141 GRVGVKLRLGWSSEQKVYL--DLAAPLADAGAGWITLHPRTAVQQFTGKADWQALKNL-- 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  KE   + +  +G L     AL  +    VD VM  R A  + A    +   + 
Sbjct: 197 -------KEISPVPVVASGDLFTARDALDCVRQTGVDTVMFARGALMDPA----IGMRYK 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRR 292
           N L G   +    D++F  ++     D   RH  S    KL+ +   MI    G  + R+
Sbjct: 246 NLLQGLEDLPR--DQEFTLRLCMETIDTYRRHASSRAVLKLRTLLPRMIRGLPGAKDLRK 303

Query: 293 ----CRHILTVEAGASTATHHI 310
               CR    +E   ++A  H+
Sbjct: 304 KIILCRQWAELEEVMNSARKHL 325


>gi|28377345|ref|NP_784237.1| hypothetical protein lp_0443 [Lactobacillus plantarum WCFS1]
 gi|28270177|emb|CAD63076.1| unknown [Lactobacillus plantarum WCFS1]
          Length = 337

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/214 (22%), Positives = 97/214 (45%), Gaps = 26/214 (12%)

Query: 22  LYTEMIVADAILRGDKKN------ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
            ++E + A +I   + K        +  +  +KP+ +Q+ G + +    A   + D G+ 
Sbjct: 48  FFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPV-VQLWGNEAADFASATAELRDRGFE 106

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            +++N+GCP   V +   G+ L+ NP    D IAA  K   + V+ K R+G         
Sbjct: 107 AVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTSGLAVSAKTRLGYSK---VAE 162

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFI 191
             + + ++    V  + +H R       + ++  K+P   ++++ ++ K      P+  +
Sbjct: 163 YHDWIATLLSQHVAVLTVHLR-------TKQEMSKVP-AHFEVIDDLIKMRDAIAPETLL 214

Query: 192 GLNGGLEDMSQAL---KILPSVDGVMIGRAAYKN 222
            +NG + D    +   K  P +DG+MIGR  + N
Sbjct: 215 QINGDVADYQAGVALAKAHPGLDGIMIGRGVFAN 248


>gi|289705787|ref|ZP_06502170.1| TIM-barrel protein, nifR3 family [Micrococcus luteus SK58]
 gi|289557503|gb|EFD50811.1| TIM-barrel protein, nifR3 family [Micrococcus luteus SK58]
          Length = 436

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/300 (22%), Positives = 123/300 (41%), Gaps = 27/300 (9%)

Query: 12  FARLLTN--NALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       L   EM+ A A++  + +   I+     E P ++Q+   D      A +
Sbjct: 84  FRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVPRSVQLYSVDPVTTGAAVR 143

Query: 68  -IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL--SIPVTVKC 123
            +VE+   + I++N GCP  +V     G+ L    ++    + AA+ +A    IPVTVK 
Sbjct: 144 MLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVTEAAKRDIPVTVKM 203

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYE 181
           R G+D+    +   +  ++ +  GV  + +H R  +    G +           +D +  
Sbjct: 204 RRGIDED--HLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTAV----------WDDIAR 251

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++  PD+ +  NG +     A+ ++    VDGV+IGR       +   +   F      
Sbjct: 252 LREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAAFEGRQDR 311

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P    V    +R     +  +    L +   L+ I +H+   F G+P     R  L+ 
Sbjct: 312 FQPTLGMVADTLYRHAELLVGTFGGDELKA---LRDIRKHVAWYFKGYPVGSEIRTALST 368


>gi|209695593|ref|YP_002263522.1| tRNA-dihydrouridine synthase C [Aliivibrio salmonicida LFI1238]
 gi|208009545|emb|CAQ79837.1| tRNA-dihydrouridine synthase C [Aliivibrio salmonicida LFI1238]
          Length = 315

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 93/176 (52%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G + + + E A    D G + ++LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PIRLQLLGQEPNWMAENAARAIDLGSDGLDLNFGCPAKAVNKSRGGAALLKDPELIYQIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+     VT K R+G ++     A+ +   +IK++G N + IHAR       +  
Sbjct: 124 KACREAVPQDKKVTAKIRLGWENPEECFAIAD---AIKQAGANELTIHAR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           D  +   + +D + +++++  D+ I  NG + + +   + + +  +D +M+ R A+
Sbjct: 174 DGYRAEEIKWDYINQVRQK-IDIPIIANGEIWNYADGQRCIAATGIDSLMVCRGAF 228


>gi|302879006|ref|YP_003847570.1| dihydrouridine synthase DuS [Gallionella capsiferriformans ES-2]
 gi|302581795|gb|ADL55806.1| dihydrouridine synthase DuS [Gallionella capsiferriformans ES-2]
          Length = 309

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 111/245 (45%), Gaps = 38/245 (15%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   L E A  +   G   I+LN GCP+  V+    GA L+  P
Sbjct: 57  GCTPSGVPVRVQLLGSDPVCLAENAAFIASLGAPGIDLNFGCPAPTVNRHGGGAVLLAFP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   +AA  +A+   IPVT K R+G+ D   ++ L    ++I+  G + I +HAR   
Sbjct: 117 EQIHAIVAATRRAVPEGIPVTAKMRLGLSDT--SLTL-ECARAIEAGGADEITVHART-- 171

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
                 + +   P   ++ + +I +E   L + +NG +   ED  Q ++ +   + VM+G
Sbjct: 172 ------RSDGYRPPARWEWLSQI-REVVTLPMVVNGDVWTPED-GQNIRRVSGCEDVMVG 223

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY----AAR--HLHSG 270
           R       ++  + E       G   +        W  +   + DY     AR  H H+ 
Sbjct: 224 RGVILRPDLMRRIKE-------GGEAMS-------WEALRPWVLDYFDLLCARMEHRHAP 269

Query: 271 GKLQQ 275
           G+L+Q
Sbjct: 270 GRLKQ 274


>gi|168050219|ref|XP_001777557.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162671042|gb|EDQ57600.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 324

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 108/232 (46%), Gaps = 19/232 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGAD 58
           M+D ++  +R   R     A  YT M  +   A+  G ++       +++PL +Q G  D
Sbjct: 21  MMDQSELPFRMLCRKYGATAA-YTPMFHSRPFALQPGYRRVEFTTCPEDRPLFVQFGAND 79

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AA  V ED  Y  +++N+GCP      G +GA LM +  ++   +  +  +L+ 
Sbjct: 80  PELLVKAAMFVQEDCDY--VDINLGCPQRVAKRGFYGAFLMDDLPLIQLMVTQLVSSLTT 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K RI  D +      R L    + +G + + +H R         KD R     D++
Sbjct: 138 PVSCKIRIFPDLEDTLAYARML----ENAGCSLLAVHGRTR-----DQKDGRTT-RADWE 187

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            +  +K+    P L  G    LED+ + +++   VDGV+   +  +N A+ +
Sbjct: 188 AIKAVKEAVRIPVLANGNIRWLEDVHECIRMT-GVDGVLSAESLLENPALFS 238


>gi|195448673|ref|XP_002071763.1| GK10156 [Drosophila willistoni]
 gi|194167848|gb|EDW82749.1| GK10156 [Drosophila willistoni]
          Length = 458

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 83/183 (45%), Gaps = 21/183 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+  PD     ++
Sbjct: 84  LVLQMGTSDAERALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLAEPDKAAQILS 142

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +C  L IPVT K RI     +P VA    LV+ +  +G+  I IHAR         +D 
Sbjct: 143 TLCSNLEIPVTCKIRI-----LPDVADTIALVQKLAATGIAAIGIHART--------RDE 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNS 223
           R       D++ E+ +      I  NGG   M         ++      VM+ RAA  N 
Sbjct: 190 RPQHQPHPDVLREVAQSVTIPVIA-NGGSRHMHCYDDLLKFQLECGAASVMVARAAQLNV 248

Query: 224 AML 226
           ++ 
Sbjct: 249 SIF 251


>gi|322702122|gb|EFY93870.1| dihydrouridine synthase family protein, putative [Metarhizium
           acridum CQMa 102]
          Length = 543

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 79/321 (24%), Positives = 129/321 (40%), Gaps = 63/321 (19%)

Query: 1   MVDWTDRHYRFFAR-LLTNNA----LLYTEMIVADAILRGDKKNILGFST-----QE--- 47
           MVD ++  +R   R  LT+      L YT M  A    +  K     F +     QE   
Sbjct: 41  MVDQSEFAWRMLTRSFLTDEEKKKMLAYTPMFHARLFSQERKYRKTHFQSTKPDSQEPWL 100

Query: 48  -------KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
                  +PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  +
Sbjct: 101 DGNPSIDRPLFVQFCANDPEALLSAAKQVSPY-CDAVDLNLGCPQGIARKGHYGAFLQED 159

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + K LSIPVT K RI  D +      +N++    ++G + + +H R+   
Sbjct: 160 QDLIFRLINTLHKELSIPVTAKIRILEDKEKTLEYAQNVL----RAGASILTVHGRRREQ 215

Query: 161 KG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
           KG L+   + K+     D +       P+  I  NG +    D+ + L      DGVM  
Sbjct: 216 KGHLTGVADWKVLRFLRDSL------PPETVIFANGNILQGGDIDECLAAT-GADGVMSA 268

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                + A+          P  G         +++WR           +    G ++  I
Sbjct: 269 EGNLSDPALFAKA------PPVGEE------GREYWR----------GKDGRGGWRVDAI 306

Query: 277 TRHMIGLFHGF-----PNSRR 292
           TR  + + H +     P +RR
Sbjct: 307 TRRYLDILHRYALGVEPPARR 327


>gi|87309530|ref|ZP_01091665.1| hypothetical protein DSM3645_24550 [Blastopirellula marina DSM
           3645]
 gi|87287838|gb|EAQ79737.1| hypothetical protein DSM3645_24550 [Blastopirellula marina DSM
           3645]
          Length = 362

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 90/212 (42%), Gaps = 18/212 (8%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           R   K+ L  + +E P+  Q+ GA+  +    A  +   GY+ I++N GCP  +V     
Sbjct: 69  RSKNKHFLAIADEEHPVGGQLMGAEPIQFAAGAVKLAQAGYDVIDINFGCPVRKVLGRCR 128

Query: 94  GACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKS---GV 148
           G   +  P++  + I+    A    IPVTVK R G+DD   A +  N  + +  +   GV
Sbjct: 129 GGFHLSQPEVALEVISRTRDATPPEIPVTVKMRRGIDDT--AASRDNFFRILDGAFDLGV 186

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
             I +H R    + + P          ++ + E+K+      I  +G L      L ++ 
Sbjct: 187 AAITVHGRTVEQRYVGPS--------RWEFLREVKEHVGSRVILGSGDLFSAQDCLDMMR 238

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDE-YFSNPL 237
              VDGV + R A  N  +       Y   PL
Sbjct: 239 QTGVDGVTVARGAIGNPWIFQQCRALYAGEPL 270


>gi|225438161|ref|XP_002262652.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 349

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 96/200 (48%), Gaps = 15/200 (7%)

Query: 30  DAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSAR 87
           D + +G    +     +EK  +  Q+G ++  + + AA+IV +D     +++N+GCP + 
Sbjct: 57  DFVEKGTHNVVFRTCHEEKNRVVFQMGTSNAERALTAAQIVCKDVA--AVDINMGCPKSF 114

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G  GA L+  P+++ D +  + + L IPVT K R+    Q        L + I+K+G
Sbjct: 115 SISGGMGAALLTRPELIHDILTILKRNLDIPVTCKIRLLKSSQ----ETVELAQQIEKTG 170

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V  + +H R+   +   P    +I ++   +   +   N D+F     G +D  Q +K+ 
Sbjct: 171 VAALAVHGRRIADRPRDPAKWNEIADVVAALSIPVIA-NGDVF-----GYDDF-QRIKVA 223

Query: 208 PSVDGVMIGRAAYKNSAMLT 227
                VM+ R A  N+++ +
Sbjct: 224 TGASSVMVARGALWNASVFS 243


>gi|301754165|ref|XP_002912927.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Ailuropoda
           melanoleuca]
          Length = 475

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--KYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|88704576|ref|ZP_01102289.1| tRNA-dihydrouridine synthase B [Congregibacter litoralis KT71]
 gi|88700897|gb|EAQ98003.1| tRNA-dihydrouridine synthase B [Congregibacter litoralis KT71]
          Length = 327

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 105/234 (44%), Gaps = 38/234 (16%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-------PLAL 52
           M   TD  +R   AR      LL  EM+ +D  LR  +K     S Q +       P ++
Sbjct: 18  MAGVTDLPFRRLCARF--GAGLLVGEMVHSDPRLRESRK-----SRQRRRHDLEINPRSV 70

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D   + EAA+     G   I++N+GCP+ +V   + G+ L+ +  +V   + A+ 
Sbjct: 71  QIVGNDPLLMAEAARYNVACGAQIIDINMGCPAKKVCRKAAGSALLADEPLVAAILGAVV 130

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
            A+ +PVT+K R G D        RN   + +  + +G+  + +H R      KG     
Sbjct: 131 SAVDVPVTLKIRTGADP-----LHRNGTSIARIAEDAGIALLAVHGRTRACAFKG----- 180

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                 +++D    I  E+ D+ +  NG +     A  +L      GVM+GRAA
Sbjct: 181 -----EVEHDTTARI-VESVDIPVLANGDIASARDAQAVLNHTGAAGVMVGRAA 228


>gi|315187425|gb|EFU21181.1| dihydrouridine synthase DuS [Spirochaeta thermophila DSM 6578]
          Length = 334

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 105/224 (46%), Gaps = 14/224 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGD-KKNILGFSTQEKPLALQIGGAD 58
           M + T   +R         ++  TEMI A  +L +G  ++  L FS       +Q+ G D
Sbjct: 21  MAELTHSGFRTLIHTWGGCSVYATEMISAPGLLSKGPYERFYLDFSPDPSRTIVQLVGYD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  LV+AA I+ +     +++N+GC +  + +   GA  +L  +     +  + + L   
Sbjct: 81  MDSLVQAAGILAEHPILGVDINMGCAAPEIRKRGGGAGWLLRGEEAVRLVGEVRRLLPPH 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++  +I + + +P       ++ + K G++ I +H      KGL  K +R      +D+
Sbjct: 141 LSLSVKIRIPESLPLEEFILFLQRLAKQGLSFITVHP-----KGLKEKHDRPA---RWDL 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMS---QALKILPSVDGVMIGRAA 219
           +  + +E P   +G NG +  +    +  + LP + G+MIGR A
Sbjct: 193 IPPLLEEIPIPVVG-NGNITSLDVYRKKREELPRLAGIMIGRKA 235


>gi|296476150|gb|DAA18265.1| PP3111 protein [Bos taurus]
          Length = 266

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAHLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+   +D  +         + ++K+G   + +H R    KG
Sbjct: 141 SVPVTCKIRVFPEIDKTV------RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|8923374|ref|NP_060273.1| tRNA-dihydrouridine synthase 2-like [Homo sapiens]
 gi|73620832|sp|Q9NX74|DUS2L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 2-like; Short=hDUS2;
           AltName: Full=Up-regulated in lung cancer protein 8;
           Short=URLC8
 gi|7020473|dbj|BAA91143.1| unnamed protein product [Homo sapiens]
 gi|16306804|gb|AAH06527.1| Dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae) [Homo
           sapiens]
 gi|71006842|dbj|BAE07219.1| up-regulated in lung cancer 8 [Homo sapiens]
 gi|119603613|gb|EAW83207.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae),
           isoform CRA_a [Homo sapiens]
 gi|119603614|gb|EAW83208.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae),
           isoform CRA_a [Homo sapiens]
 gi|119603615|gb|EAW83209.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae),
           isoform CRA_a [Homo sapiens]
 gi|158254588|dbj|BAF83267.1| unnamed protein product [Homo sapiens]
 gi|312152458|gb|ADQ32741.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           [synthetic construct]
          Length = 493

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 90/189 (47%), Gaps = 32/189 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++
Sbjct: 84  VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILS 142

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K    PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 143 TLVKGTRRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------RE 188

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 189 ERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQQYSDIEDFRQAT----AASSVMVAR 243

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 244 AAMWNPSIF 252


>gi|308179559|ref|YP_003923687.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308045050|gb|ADN97593.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 337

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/214 (22%), Positives = 97/214 (45%), Gaps = 26/214 (12%)

Query: 22  LYTEMIVADAILRGDKKN------ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
            ++E + A +I   + K        +  +  +KP+ +Q+ G + +    A   + D G+ 
Sbjct: 48  FFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPV-VQLWGNEAADFASATAELRDRGFK 106

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            +++N+GCP   V +   G+ L+ NP    D IAA  K   + V+ K R+G         
Sbjct: 107 AVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTSGLAVSAKTRLGYSK---VAE 162

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFI 191
             + + ++    V  + +H R       + ++  K+P   ++++ ++ K      P+  +
Sbjct: 163 YHDWIATLLSQHVAVLTVHLR-------TKQEMSKVP-AHFEVIDDLIKMRDAIAPETLL 214

Query: 192 GLNGGLEDMSQAL---KILPSVDGVMIGRAAYKN 222
            +NG + D    +   K  P +DG+MIGR  + N
Sbjct: 215 QINGDVADYQAGVALAKAHPGLDGIMIGRGVFAN 248


>gi|123288584|emb|CAM27542.1| dihydrouridine synthase 1-like (S. cerevisiae) [Mus musculus]
          Length = 482

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|302876216|ref|YP_003844849.1| dihydrouridine synthase DuS [Clostridium cellulovorans 743B]
 gi|307686948|ref|ZP_07629394.1| dihydrouridine synthase DuS [Clostridium cellulovorans 743B]
 gi|302579073|gb|ADL53085.1| dihydrouridine synthase DuS [Clostridium cellulovorans 743B]
          Length = 321

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 103/233 (44%), Gaps = 19/233 (8%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    +   K +  FGY EINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNNSEYFIHTMKDLMKFGYKEINLNLGCPAGTVVAKNKGSGFLAQREQLDQFLEEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
                 +++K RIG D   P      L++   K  +  + IH R  I K L    N K P
Sbjct: 124 LKAETKISIKTRIGKDS--PG-EFYKLIEIFNKYPLEELIIHPR--IQKDLY---NNK-P 174

Query: 173 NLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           N+D +     + K NP  + G     +D ++ ++  P++D VM+GR    N A++  +  
Sbjct: 175 NMDVFKDAVSLSK-NPICYNGDIFNAKDYTELIETYPNLDAVMLGRGLIANPALIGEI-- 231

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                   ++    +V K+F  K+  S  +  +   +   K+ +   +MI LF
Sbjct: 232 ------KNNNSADKKVMKEFHDKVYNSYQEILSGERNVLFKMMEFWFYMIHLF 278


>gi|114663240|ref|XP_001166638.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 1
           [Pan troglodytes]
 gi|114663242|ref|XP_001166736.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 3
           [Pan troglodytes]
 gi|114663244|ref|XP_001166768.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 4 [Pan
           troglodytes]
 gi|114663246|ref|XP_001166835.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 6
           [Pan troglodytes]
 gi|114663248|ref|XP_001166866.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 7
           [Pan troglodytes]
 gi|114663250|ref|XP_001166896.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 8
           [Pan troglodytes]
 gi|114663252|ref|XP_001166928.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 9
           [Pan troglodytes]
          Length = 493

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 90/189 (47%), Gaps = 32/189 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++
Sbjct: 84  VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILS 142

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K    PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 143 TLVKGTHRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------RE 188

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 189 ERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQQYSDIEDFRQAT----AASSVMVAR 243

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 244 AAMWNPSIF 252


>gi|118581317|ref|YP_902567.1| dihydrouridine synthase, DuS [Pelobacter propionicus DSM 2379]
 gi|118504027|gb|ABL00510.1| tRNA-U20a,U20b-dihydrouridine synthase [Pelobacter propionicus DSM
           2379]
          Length = 342

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 96/230 (41%), Gaps = 25/230 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
            +DW      F   +  N A     +  AD    G   +       + PL +Q+ G    
Sbjct: 53  FIDWVRPDVVFTEFMRVNPAAAQRRLSAADLAEAGSAGD-------DVPLVVQLIGHGRE 105

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV  ++  +D G   INLN+GCP  R+  G  G  ++ +P  +   I A+ K +    +
Sbjct: 106 ALVSGSQAAQDAGAAHINLNMGCPYGRMTSGQTGGGMLRSPQELSSIIPALRKTIRGTFS 165

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK--GLSPKDNRKIPNLDYDI 178
           +K R G D+      + +L+   + SGV+ + +H R  + K  G +          D+ I
Sbjct: 166 IKLRSGYDN---PRQIFDLLPLFEASGVDFLVLHPRTVLQKYAGFA----------DHGI 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAML 226
             E  + +  L I  NG +  ++    +L      G+M+GR A  +  + 
Sbjct: 213 TAEAVQRS-TLPIIANGDIRSVATGRHVLRETGAAGLMLGRGAISDPLLF 261


>gi|51246252|ref|YP_066136.1| hypothetical protein DP2400 [Desulfotalea psychrophila LSv54]
 gi|50877289|emb|CAG37129.1| conserved hypothetical protein [Desulfotalea psychrophila LSv54]
          Length = 354

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 69/280 (24%), Positives = 125/280 (44%), Gaps = 28/280 (10%)

Query: 16  LTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           L    L YTEM+ A  +   +    + L  +  E+PL  Q+  AD+  +  A   +   G
Sbjct: 64  LGGCGLFYTEMLAARRLPHENPAVSSYLHTTPCERPLIYQLFIADVKYVAPALDKIHRLG 123

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + +++N+GCP+  V  G  GA L  + D V D +++  +   + ++ K R+G   +   
Sbjct: 124 GDGVDINLGCPAPSVRRGGAGAALAEDWDRVRDIVSSARRHTDLTLSAKIRVGHVGK--E 181

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             L +  K ++  GV+ + +HAR         K  RK P   + ++  I  E  D+ I  
Sbjct: 182 AHLLDFCKMLEAEGVDLLAVHARYH-----GEKFCRK-PR--WQLLAPI-CEQLDIPIFA 232

Query: 194 NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN---PLTGSSPIKTRVD 248
           NGG+  +  A +   L    G+M+GR A +   +   +         P+  S P++    
Sbjct: 233 NGGIFSVDDARRCLELSGAAGLMLGRGAVERPWLFNEIAREVYGLDLPVAESRPVEI--- 289

Query: 249 KDFWRKISASMTDYAA-RHLHSGGKLQQITRHMIGLFHGF 287
             ++R +   +  +A  R L   G++++ T H I   H F
Sbjct: 290 --YFRFVQKMVEIFAPERQL---GRIKEFT-HYIAKNHQF 323


>gi|332227763|ref|XP_003263057.1| PREDICTED: tRNA-dihydrouridine synthase 2 [Nomascus leucogenys]
          Length = 540

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 90/189 (47%), Gaps = 32/189 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++
Sbjct: 131 VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILS 189

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K    PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 190 TLVKGTRRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------RE 235

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 236 ERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQRYSDIEDFRQAT----AASSVMVAR 290

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 291 AAMWNPSIF 299


>gi|296231397|ref|XP_002761126.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 1
           [Callithrix jacchus]
 gi|296231399|ref|XP_002761127.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 2
           [Callithrix jacchus]
          Length = 493

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/193 (25%), Positives = 92/193 (47%), Gaps = 32/193 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           ++  +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD + 
Sbjct: 80  EQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIE 138

Query: 106 DCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             ++ + K    PVT K RI   ++D +      +LVK I+++G+  I +H RK      
Sbjct: 139 KILSTLVKGTHRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NGG          +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQRYSDIEDFRQAT----AASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|119026155|ref|YP_910000.1| NifR3-like protein [Bifidobacterium adolescentis ATCC 15703]
 gi|154488945|ref|ZP_02029794.1| hypothetical protein BIFADO_02254 [Bifidobacterium adolescentis
           L2-32]
 gi|118765739|dbj|BAF39918.1| possible NifR3-like protein [Bifidobacterium adolescentis ATCC
           15703]
 gi|154083082|gb|EDN82127.1| hypothetical protein BIFADO_02254 [Bifidobacterium adolescentis
           L2-32]
          Length = 409

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 104/242 (42%), Gaps = 19/242 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPSEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            S + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I     +C A
Sbjct: 109 PSIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +         +   ++ G   + +HAR          D  +I  L
Sbjct: 169 ANVPVTAKIRVGIDHEHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 226

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
               V E+     D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 227 ----VSEL-----DIPVFGNGDIWGANDALAMVAETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FS 234
           F+
Sbjct: 278 FA 279


>gi|326200913|ref|ZP_08190785.1| dihydrouridine synthase DuS [Clostridium papyrosolvens DSM 2782]
 gi|325988481|gb|EGD49305.1| dihydrouridine synthase DuS [Clostridium papyrosolvens DSM 2782]
          Length = 312

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/270 (23%), Positives = 113/270 (41%), Gaps = 30/270 (11%)

Query: 23  YTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++  I+A   D     D ++IL  + Q   L  Q+   +    +  +K +   GYNEINL
Sbjct: 31  FSPFIIANQIDGFKTRDLRDILPENNQGLVLVPQVLTNNAKDFIYTSKKINSMGYNEINL 90

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCPS  V   + G+  +   + +   +  +       ++VK RIG D         +L
Sbjct: 91  NLGCPSGTVVSKNRGSGFLAKKEELDAFLEEIFSQAMTKISVKTRIGKDH---PEEFYDL 147

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-YDIVYEIKKE----NPDLFIGLN 194
           +    K  V  + IH R  I K       +  PNL  +     + K     N D+F    
Sbjct: 148 INIFNKYPVEELIIHPR--IQKDFY----KNKPNLQIFKDALGLSKNTVCYNGDIFTS-- 199

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
              +D  +  +  PSVD +M+GR    N A++  +           + ++  + K+F  K
Sbjct: 200 ---KDYVKFHEDFPSVDTLMLGRGLLMNPALVHEI--------KNGTKLEKNLLKEFHNK 248

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           I     D  +   +   K++++  +MI +F
Sbjct: 249 IYNDYKDILSGERNVLFKMKELWFYMINVF 278


>gi|308389562|gb|ADO31882.1| NifR3/SMM1 family protein [Neisseria meningitidis alpha710]
          Length = 333

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|325972614|ref|YP_004248805.1| hypothetical protein SpiBuddy_2803 [Spirochaeta sp. Buddy]
 gi|324027852|gb|ADY14611.1| TIM-barrel protein, nifR3 family [Spirochaeta sp. Buddy]
          Length = 332

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 99/209 (47%), Gaps = 20/209 (9%)

Query: 23  YTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +TEM+ A+ + R  +K   ++  +  EK  A+Q+  ++   L +A + +  F    I++N
Sbjct: 47  FTEMVSAEGLSREGEKTMELMYRAPNEKQYAIQLFMSNTDSLKQALEQLLPFHPEVIDIN 106

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
            GCP  +V +   G+ +M  P ++ D +  +   + IPV+VK R G D Q  +       
Sbjct: 107 CGCPVPKVTKTGAGSAMMKTPSLITDVVRTITAEVDIPVSVKFRTGWDAQ--SENFLEFA 164

Query: 141 KSIKKSGVNGIWIHARKAILKGLSP-KDNRKIPNL-DYDIVYEIKKE---NPDLFIGLNG 195
           ++    G + + +HAR    +G +P  D  K+  L  Y + +        + DLFI    
Sbjct: 165 QAALDGGASALTLHARTRS-QGYAPFADWSKLRALKQYCLTHGYTVPVFGSGDLFIA--- 220

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ED   A+++L    +D VM  R A  N
Sbjct: 221 --ED---AIRMLQETGIDAVMFARGAIGN 244


>gi|291545851|emb|CBL18959.1| tRNA-U20a,U20b-dihydrouridine synthase [Ruminococcus sp. SR1/5]
          Length = 320

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 69/286 (24%), Positives = 115/286 (40%), Gaps = 47/286 (16%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGADISKLVEAAKIVED-FGYNEIN 78
           +T  I A    R   K I   S +   + P+  QI   +    V+ A I  D +G+ E+N
Sbjct: 31  FTPFITAKPNKRLSSKEIKEVSPETNGDLPVIPQILTNNAEDFVKTAHIFRDEYGHREVN 90

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCPS  V     GA  +  PD +   +  + +   + +++K R+G D +        
Sbjct: 91  LNLGCPSGTVTAKGKGAGFLGEPDKLERFLDEIFEKTGMEISIKTRVGTDYE---EDWER 147

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRK-IPNLDYDIVYEIKKENPDLFIGLNG-- 195
           L++   +  +  + IH R         KD+ K IP      +YE  +E   + +G NG  
Sbjct: 148 LLEIYGRYPLKELIIHPRLL-------KDHYKGIPRYG---LYEEAREKLKVPLGYNGDI 197

Query: 196 -GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV----------DEY------------ 232
             +E   +  +  P  D VM GR       +L  +          +EY            
Sbjct: 198 FSVEAYQEIREKFPDADSVMYGRGLIARPYLLDAIMQKEDGEDHREEYRKKLRQFHDRLY 257

Query: 233 --FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
             +   L+G   +  R+ K+ W  ++   T+Y AR+L    K Q  
Sbjct: 258 RDYQRYLSGERNVLFRM-KELWSYMAPGFTNY-ARYLKKIKKSQHF 301


>gi|149699255|ref|XP_001498775.1| PREDICTED: similar to tRNA-dihydrouridine synthase 2-like (hDUS2)
           (Up-regulated in lung cancer) (URLC8) isoform 1 [Equus
           caballus]
          Length = 493

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/187 (26%), Positives = 88/187 (47%), Gaps = 32/187 (17%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++ +
Sbjct: 86  FQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTL 144

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            K    PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++ R
Sbjct: 145 VKGTRRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------REER 190

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGRAA 219
               +  + +  I  E   + +  NGG          +ED  QA     +   VM+ RAA
Sbjct: 191 PQHPVSCEAIKAI-AETLSIPVIANGGSYDHIQEYLDIEDFRQAT----AASSVMVARAA 245

Query: 220 YKNSAML 226
             N ++ 
Sbjct: 246 MWNPSIF 252


>gi|281348632|gb|EFB24216.1| hypothetical protein PANDA_000684 [Ailuropoda melanoleuca]
          Length = 478

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--KYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|254496630|ref|ZP_05109495.1| nitrogen regulation protein [Legionella drancourtii LLAP12]
 gi|254354152|gb|EET12822.1| nitrogen regulation protein [Legionella drancourtii LLAP12]
          Length = 268

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/114 (28%), Positives = 64/114 (56%), Gaps = 5/114 (4%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + QE+ LA QI G +   L +AA+ ++  G + I++N GCP  ++ +   G+ L+  P+ 
Sbjct: 21  AAQEQILAYQISGTEPQVLAQAARQLQMQGADLIDINCGCPKPKIRKKGAGSALLERPEQ 80

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   + A+  A++IP+T+K RI  +D    +A     + I  +G + + +H R+
Sbjct: 81  LVSLVHAVRAAITIPLTIKIRIQGNDHDLLLA-----QKIAAAGADALIVHGRR 129


>gi|225155097|ref|ZP_03723593.1| dihydrouridine synthase DuS [Opitutaceae bacterium TAV2]
 gi|224804267|gb|EEG22494.1| dihydrouridine synthase DuS [Opitutaceae bacterium TAV2]
          Length = 360

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/247 (24%), Positives = 116/247 (46%), Gaps = 22/247 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +             YTE     +  R +K   + +  +   +P+  Q+ G D
Sbjct: 18  MQDVTDHAFMHVIARTGAPDYFYTEFFRVHSQSRPEKHILHAIDHNATGRPIFAQLIGED 77

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L   A +I+++     ++LN+GCP+ +V++ + G  L+ +P  + + +A +  AL  
Sbjct: 78  LQHLARTATEILKNHPAAALDLNLGCPAPKVYKKNVGGGLLRDPARIDEILATLRAALPP 137

Query: 118 P--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           P  +TVK RIG +D     A+ +L+ + +   V+ + +H R   ++ L   +      + 
Sbjct: 138 PRLLTVKMRIGFEDTSNYDAILDLINAHR---VDLLTVHGRT--VRELYRSE------VH 186

Query: 176 YD-IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
           YD I + +++    +    NG +   + A ++L      GVMIGR A +N  +     + 
Sbjct: 187 YDAIAHAVRRVRCPVLA--NGNITSAATATRVLAETGAAGVMIGRHAIRNPWIFAQCRQA 244

Query: 233 FS-NPLT 238
           F+  P+T
Sbjct: 245 FAGQPVT 251


>gi|15676890|ref|NP_274035.1| NifR3/SMM1 family protein [Neisseria meningitidis MC58]
 gi|38605055|sp|Q9JZL5|DUSC_NEIMB RecName: Full=tRNA-dihydrouridine synthase C
 gi|7226240|gb|AAF41402.1| NifR3/SMM1 family protein [Neisseria meningitidis MC58]
 gi|316985877|gb|EFV64818.1| dihydrouridine synthase (Dus) family protein [Neisseria
           meningitidis H44/76]
 gi|325140199|gb|EGC62725.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis CU385]
 gi|325200316|gb|ADY95771.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis H44/76]
          Length = 333

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|241955235|ref|XP_002420338.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223643680|emb|CAX41413.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 340

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 111/238 (46%), Gaps = 22/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R +      F+T +  K + +Q+G  +
Sbjct: 33  MVRYSKLPFRELCRFYDVD-IVYTPMILAREFVRNEVARSTDFTTNDSDKCVIVQVGVNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCI-AAMCK-AL 115
           +   ++  +++  F  + I +N GCP   +V EG  GA LM +PD+V + I  A CK   
Sbjct: 92  VEDFMKFIEMIHPF-VDGIGINCGCPIKEQVREG-IGAALMSDPDLVAELIKTAKCKYGD 149

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           SI +  K RI  D         + V  + ++G + + +H R         K+ R    ++
Sbjct: 150 SICIDTKIRIHRDIN----QTIDFVNKVVEAGTDMLTVHGRT--------KNTRSSVPVN 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            D +  I+     + +  NG    ++   KI+    VDGVM  R    N A+ T +++
Sbjct: 198 LDAIKIIRDNVSSIPVIANGDCFTLTDFQKIVAYTGVDGVMSARGVLANPALFTGLNK 255


>gi|161869911|ref|YP_001599080.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis 053442]
 gi|161595464|gb|ABX73124.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis 053442]
 gi|261392649|emb|CAX50215.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis 8013]
 gi|325130157|gb|EGC52936.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           OX99.30304]
 gi|325132113|gb|EGC54809.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M6190]
 gi|325136420|gb|EGC59028.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M0579]
 gi|325138046|gb|EGC60619.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           ES14902]
 gi|325202214|gb|ADY97668.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           M01-240149]
 gi|325208031|gb|ADZ03483.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis NZ-05/33]
          Length = 333

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|46125679|ref|XP_387393.1| hypothetical protein FG07217.1 [Gibberella zeae PH-1]
          Length = 510

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 84/182 (46%), Gaps = 25/182 (13%)

Query: 1   MVDWTDRHYRFFAR----------LLTNNALLYTEMIVADAILR----------GDKKNI 40
           MVD ++  +R   R          LL    +L+  +   D   R          G+   +
Sbjct: 35  MVDQSEFAWRMLTRSFISPTEQKSLLAYTPMLHARLFSQDDKYRKAHFQAVKTDGETPWL 94

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
            G  + ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  +
Sbjct: 95  DGNPSIDRPLFVQFCANDPDALLSAAKQVAPY-CDAVDLNLGCPQGIARKGKYGAFLQED 153

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + K L +PVT K RI +D +   +A     +++ K+G + + +H RK   
Sbjct: 154 QDLIFRLINILHKELPVPVTAKIRI-LDTKEETLA---YAQNVLKAGASILTVHGRKREQ 209

Query: 161 KG 162
           KG
Sbjct: 210 KG 211


>gi|156847371|ref|XP_001646570.1| hypothetical protein Kpol_1055p69 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156117248|gb|EDO18712.1| hypothetical protein Kpol_1055p69 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 346

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/215 (24%), Positives = 98/215 (45%), Gaps = 15/215 (6%)

Query: 21  LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           ++YT MI+A   +R     +  F+T   + PL +Q+G  +++ L++  ++V  +  + I 
Sbjct: 57  IVYTPMILAREFVRNGHARLADFTTCSTDSPLIVQVGVNNVADLLKFVEMVSPYC-DGIG 115

Query: 79  LNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +N GCP   ++ EG  G  L+ NP+++   ++A+ +     V ++ +I + D +      
Sbjct: 116 INCGCPIKEQIREG-IGCALIYNPELLASMVSAVKQKYGDKVRLETKIRIHDDLEQTV-- 172

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNG 195
            L   +  +GV+ I IH R    +   P       NLD    I+ +IK  N  +    + 
Sbjct: 173 ELCNKVCDAGVDWITIHGRTRTTRSSQPV------NLDAIKYIISQIKGRNVPVVANGDC 226

Query: 196 GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            +E     +      DGVM  R    N A+    D
Sbjct: 227 FVETDLAKISECTGADGVMAVRGLLANPALFAKYD 261


>gi|148378675|ref|YP_001253216.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. ATCC 3502]
 gi|153932290|ref|YP_001383059.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|153935524|ref|YP_001386608.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. Hall]
 gi|148288159|emb|CAL82227.1| putative dihydrouridine synthase (tRNA modification protein)
           [Clostridium botulinum A str. ATCC 3502]
 gi|152928334|gb|ABS33834.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|152931438|gb|ABS36937.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. Hall]
          Length = 319

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/279 (21%), Positives = 118/279 (42%), Gaps = 26/279 (9%)

Query: 12  FARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           + +   N    +T  IV +   ++   + ++IL  + +   +  QI   D    +  A+ 
Sbjct: 20  YEKFFNNIDKYFTPFIVPNKSTSLKTKELRDILPENNKGMNIVPQILTNDSEGFIITARK 79

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   + +++K RIG D
Sbjct: 80  LQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDDMKISIKTRIGKD 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVYEI--KKE 185
                     L+K   K  +  + IH R +    G  P         D D+  +      
Sbjct: 140 S---PEEFYELIKIYNKYPIEELIIHPRTQKDFYGHKP---------DLDVFKDALSLSS 187

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           NP  + G    + D ++ +K  P V  +M+GR    N  ++        N +  ++ I  
Sbjct: 188 NPICYNGDIFTVSDYNRLIKTFPKVKTIMLGRGILANPGLI--------NEIKNNTTIDK 239

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 240 EVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIHIF 278


>gi|300691378|ref|YP_003752373.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum PSI07]
 gi|299078438|emb|CBJ51090.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum PSI07]
          Length = 326

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 104/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 58  GYTASGTPMVIQLLGSDPEWLARNAAQAATVSPHGIDLNFGCPAKVVNRHGGGAMLLATP 117

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++++  A+   I VT K R+GV D   A+A      ++++ G   + +HAR   
Sbjct: 118 ELLHRIVSSVRAAVPAHIAVTAKMRLGVSDTSLAIA---CATALEEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I      P +  G    ++D  +  + +   D VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIADAVHVPVVANGEVWTVDDWERC-RAVSGCDDVMIGR 225

Query: 218 AAYKNSAM-LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  + L    +    P     P+  R   D+ +K+ A +   A  H H   KL
Sbjct: 226 GAVSDPFLALRIRGQMARAPSDAEWPLVLRCLVDYLKKLHARI---AVHHEHGRVKL 279


>gi|110806117|ref|YP_689637.1| tRNA-dihydrouridine synthase C [Shigella flexneri 5 str. 8401]
 gi|110615665|gb|ABF04332.1| putative regulator protein [Shigella flexneri 5 str. 8401]
          Length = 315

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +P    D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMPISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|329850670|ref|ZP_08265515.1| putative tRNA-dihydrouridine synthase [Asticcacaulis biprosthecum
           C19]
 gi|328840985|gb|EGF90556.1| putative tRNA-dihydrouridine synthase [Asticcacaulis biprosthecum
           C19]
          Length = 326

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 79/173 (45%), Gaps = 17/173 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G D   +   A++ E+ G + ++LN GCP+  V     G+ LM + D     + A 
Sbjct: 71  VQLVGRDPEHIAHGARLAEESGADIVDLNFGCPAKEVIGVLCGSALMRDLDQAERIMTAA 130

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNR 169
            KA S PVTVK R+G DD         L +  +K G+  + +H   R+   KG       
Sbjct: 131 LKATSRPVTVKMRLGWDDDSQNAP--ELAQRAEKLGIKALTVHGRTRQQFYKG------- 181

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
                ++  V  +K     + + +NG + D+  A   L     DG+MIGR  Y
Sbjct: 182 ---EANWHAVAHVKSA-VRIPVIVNGDIVDLGSARDALHQSGADGLMIGRGIY 230


>gi|121634803|ref|YP_975048.1| hypothetical protein NMC0986 [Neisseria meningitidis FAM18]
 gi|120866509|emb|CAM10257.1| hypothetical protein NMC0986 [Neisseria meningitidis FAM18]
          Length = 341

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 84  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 143

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 144 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTK-AEGYEPP 199

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 200 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 253

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 254 RQIKQY-----ENGGPVK---DTDF 270


>gi|187777797|ref|ZP_02994270.1| hypothetical protein CLOSPO_01389 [Clostridium sporogenes ATCC
           15579]
 gi|187774725|gb|EDU38527.1| hypothetical protein CLOSPO_01389 [Clostridium sporogenes ATCC
           15579]
          Length = 319

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/279 (21%), Positives = 118/279 (42%), Gaps = 26/279 (9%)

Query: 12  FARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           + +   N    +T  IV +   ++   + ++IL  + +   +  QI   D    +  A+ 
Sbjct: 20  YEKFFNNIDKYFTPFIVPNKSTSLKTKELRDILPENNKGMNIVPQILTNDSEGFIITARK 79

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   + +++K RIG D
Sbjct: 80  LQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDDMKISIKTRIGKD 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVYEI--KKE 185
                     L+K   K  +  + IH R +    G  P         D D+  +      
Sbjct: 140 S---PEEFYELIKIYNKYPIEELIIHPRTQKDFYGHKP---------DLDVFKDALSLSS 187

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           NP  + G    + D ++ +K  P V  +M+GR    N  ++        N +  ++ I  
Sbjct: 188 NPICYNGDIFTVSDYNRLIKTFPKVKTIMLGRGILANPGLI--------NEIKNNTTIDK 239

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 240 EVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIHIF 278


>gi|258578427|ref|XP_002543395.1| tRNA-dihydrouridine synthase 1 [Uncinocarpus reesii 1704]
 gi|237903661|gb|EEP78062.1| tRNA-dihydrouridine synthase 1 [Uncinocarpus reesii 1704]
          Length = 514

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 57/213 (26%), Positives = 98/213 (46%), Gaps = 20/213 (9%)

Query: 11  FFARLLTNNALLYTEMI--VADAILRGDKKNILGF----STQEKPLALQIGGADISKLVE 64
           F ARL  + A   ++    V  + + G+    + F       ++PL +Q    D  +L+ 
Sbjct: 48  FHARLFKDRAAYRSQHFEAVRPSPVAGETAEPVPFLDGNPAIDRPLIVQFCANDPDELLA 107

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AA++V+ +  + ++LN+GCP     +G +GA L  +P+++   I  +   LSIPVT K R
Sbjct: 108 AARLVQPY-CDAVDLNLGCPQGIAKKGHYGAFLQEDPELIYKLIHTLHTGLSIPVTAKFR 166

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           I    +       +  K I  +G + I +H R+   KG     N  + +  Y I Y    
Sbjct: 167 ILETRE----KTLDYAKMILSAGASFISVHGRRREQKG----HNTGVADWSY-IRYLRDN 217

Query: 185 ENPDLFIGLNGGL---EDMSQALKILPSVDGVM 214
             P+  I  NG +   +D+ + L+     D VM
Sbjct: 218 LPPETVIFANGNILNHDDIQKCLEAT-GADAVM 249


>gi|329295989|ref|ZP_08253325.1| tRNA-dihydrouridine synthase C [Plautia stali symbiont]
          Length = 315

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 107/237 (45%), Gaps = 16/237 (6%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  MQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKVRLGWDS---GARRFEIADAVQQAGASELVVHGR-------AKEDGY 176

Query: 170 KIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  ++++  + EI++    P +  G     +D    L+I    D VM+GR A  N   L 
Sbjct: 177 RAESINWQAIGEIRQRLTIPVIANGEIWNWQDAQDCLRI-TGCDAVMLGRGAL-NVPNLG 234

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            V +Y   P+  S  ++  +      K   +   + AR     G L++    + GLF
Sbjct: 235 RVVKYNEAPMPWSQVVELLLRYTQLEKQGDTGNYHVARIKQWLGYLRKAYHEVDGLF 291


>gi|317490541|ref|ZP_07949018.1| dihydrouridine synthase [Eggerthella sp. 1_3_56FAA]
 gi|316910356|gb|EFV31988.1| dihydrouridine synthase [Eggerthella sp. 1_3_56FAA]
          Length = 330

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 29/234 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L YTEM+ A  +   ++K  ++L  +  E  +A+Q+ G +
Sbjct: 18  MAGVSDEAFRTLCREQGAD-LTYTEMVSAKGLSYANEKTRHLLRLAPGEGQVAVQLFGHE 76

Query: 59  ISKLV-EAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  +AA I  + G +   +++N+GCP+ ++     G+ LM +P +    + A+  A+
Sbjct: 77  PDTMAAQAAWIEREMGQSLAYLDINMGCPARKIVSKGDGSALMKDPALAASIVRAVRAAV 136

Query: 116 SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRK 170
           S PVTVK R G    D+  P  A R     ++ +G   I +H R A  + +G +      
Sbjct: 137 SRPVTVKFRRGWAEGDETAPEFARR-----MEDAGACAIAVHGRYAEQLYRGRA------ 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKN 222
               ++  +  +K+      +G NG +   + A+ +      D VMI RAA  N
Sbjct: 186 ----EWGAIARVKEAVSVPVVG-NGDVRSGADAVAVTERTGCDAVMIARAAEGN 234


>gi|290982753|ref|XP_002674094.1| predicted protein [Naegleria gruberi]
 gi|284087682|gb|EFC41350.1| predicted protein [Naegleria gruberi]
          Length = 450

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 100/235 (42%), Gaps = 21/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILGFSTQ-EKPLALQIGGA 57
           MVD ++  +R  ++      L YT M   +  A  +  +     F+   E P+  Q    
Sbjct: 110 MVDQSEMAFRLLSKEY-GATLAYTPMFHGMYFAYHKKYRARFYQFNPDLEGPVFAQFCTN 168

Query: 58  DISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           D    V+  K V D    +I   +LN+GCP      G +G+ LM +   V   I      
Sbjct: 169 DPETFVQCGKRVWDLSKQKISAIDLNLGCPQRIARRGRYGSFLMEDLQTVHSIINKAHLE 228

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K RI  D ++      N VK++  +G   + +H R    KG +          
Sbjct: 229 LPMPVTAKIRIFEDLELTM----NYVKTVVDAGAQVLCVHGRTREQKGANQN------YA 278

Query: 175 DYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D+ ++  I+++ P + +  NG +   +D+   L+    VD VM G    +N A+ 
Sbjct: 279 DWTVIRAIREQFPQIPMIANGNIRTFQDVQDCLEYT-RVDAVMSGEGLLENPALF 332


>gi|257063743|ref|YP_003143415.1| putative TIM-barrel protein, nifR3 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256791396|gb|ACV22066.1| putative TIM-barrel protein, nifR3 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 341

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 66/286 (23%), Positives = 125/286 (43%), Gaps = 29/286 (10%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-- 76
           L +TEM+ + A+   ++K   +L  +  E  + +Q+ G +   +   A  VED    +  
Sbjct: 40  LTFTEMVSSKALSFANEKTRRLLDTAPNELHVGVQLFGHEPDTMAREAAWVEDSLGEKLV 99

Query: 77  -INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ ++ +   G+ L+  PD+    +  +   +S PVTVK R G         
Sbjct: 100 CIDVNMGCPARKIIKKGDGSALLNTPDVAQQIVRQIKSQVSCPVTVKFRKGFAAGEDVAC 159

Query: 136 LRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             +  K ++ +G + + +H R    +  G          + D+D++  +K+      IG 
Sbjct: 160 --DFAKRMEDAGADWMTVHGRTTAQMYSG----------DADWDVLGRVKRSVSVPVIG- 206

Query: 194 NGGLE--DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG ++  + ++A+     VDGVMI R A  N  +        +     + P  T  ++  
Sbjct: 207 NGDIKRGEDARAMVDATGVDGVMIARGAQGNPWIFPEAAAALAGEPAPAEP--TDEERVA 264

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +  ASM D      + G  +  + +H++    G P  R  R  L
Sbjct: 265 MARRHASMLDG-----YMGNTIVYMRKHVMWYLRGVPGVREARGAL 305


>gi|323136427|ref|ZP_08071509.1| TIM-barrel protein, nifR3 family [Methylocystis sp. ATCC 49242]
 gi|322398501|gb|EFY01021.1| TIM-barrel protein, nifR3 family [Methylocystis sp. ATCC 49242]
          Length = 331

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/222 (27%), Positives = 98/222 (44%), Gaps = 24/222 (10%)

Query: 24  TEMIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +EMI A  + RGD++  L  S         P  +QI   D +++  AA+  E  G   ++
Sbjct: 37  SEMITAAGVARGDRETALRLSGSNDEANSAPRVIQIAARDATEIAAAARHAEAAGAQWVD 96

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP  RV  G  GA LM + D     IAA   A+ IP+++K R+G DD     A RN
Sbjct: 97  INMGCPCKRVTGGLAGAALMRDLDQATSLIAAARAAIRIPLSIKMRLGWDD-----ASRN 151

Query: 139 ---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              L +  +  G   + +H R         +        D+  +  + K+   + +  NG
Sbjct: 152 APELARRAEGEGAALVTVHGRT--------RQQFYTGRADWAAIAAV-KQAVKIPVVANG 202

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                  A ++L     D VM+GRAA     ++  +  Y + 
Sbjct: 203 DCASAGDAAEMLRASGADAVMVGRAAQGRPWLVGDISHYLAT 244


>gi|300767086|ref|ZP_07076999.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300495624|gb|EFK30779.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 357

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/214 (22%), Positives = 97/214 (45%), Gaps = 26/214 (12%)

Query: 22  LYTEMIVADAILRGDKKN------ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
            ++E + A +I   + K        +  +  +KP+ +Q+ G + +    A   + D G+ 
Sbjct: 68  FFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPV-VQLWGNEAADFASATAELRDRGFK 126

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            +++N+GCP   V +   G+ L+ NP    D IAA  K   + V+ K R+G         
Sbjct: 127 AVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTSGLAVSAKTRLGYSK---VAE 182

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFI 191
             + + ++    V  + +H R       + ++  K+P   ++++ ++ K      P+  +
Sbjct: 183 YHDWIATLLSQHVAVLTVHLR-------TKQEMSKVP-AHFEVIDDLIKMRDAIAPETLL 234

Query: 192 GLNGGLEDMSQAL---KILPSVDGVMIGRAAYKN 222
            +NG + D    +   K  P +DG+MIGR  + N
Sbjct: 235 QINGDVADYQAGVALAKAHPGLDGIMIGRGVFAN 268


>gi|182415683|ref|YP_001820749.1| dihydrouridine synthase DuS [Opitutus terrae PB90-1]
 gi|177842897|gb|ACB77149.1| dihydrouridine synthase DuS [Opitutus terrae PB90-1]
          Length = 384

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 102/227 (44%), Gaps = 31/227 (13%)

Query: 22  LYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
            +TE     +  R +K  +  L  +T  +P+  Q+ G D+ +LV  A+ ++      I+L
Sbjct: 45  FFTEFFRVHSQSRLEKHIVRCLDDNTTGRPIFAQVIGEDLEQLVRTARELQQHPIAGIDL 104

Query: 80  NVGCPSARVHEGSFGACLMLN----PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           N+GCP+ +V++ + G  L+ +      I+G   AA    L    TVK RIG DD  P   
Sbjct: 105 NLGCPAPKVYKKNVGGGLLRDLAHVDRILGALRAATPGGL---FTVKMRIGFDDTTPFEP 161

Query: 136 LRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFI 191
           + +LV + +   V+ + +H R  K + +            + YD +     +   P L  
Sbjct: 162 MLDLVNAHR---VDLLSVHGRTVKEMYRS----------RVHYDFIARAVQRVRCPVL-- 206

Query: 192 GLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNP 236
             NG +    +A+ IL      GVMIGR A +N  +     E F  P
Sbjct: 207 -ANGNVTSAPRAVAILRETGAAGVMIGRHAIRNPWIFRQCRELFHPP 252


>gi|40807366|ref|NP_071439.3| tRNA-dihydrouridine synthase 1-like [Homo sapiens]
 gi|74749069|sp|Q6P1R4|DUS1L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 1-like
 gi|38511481|gb|AAH62566.1| DUS1L protein [Homo sapiens]
 gi|40787788|gb|AAH64918.1| Dihydrouridine synthase 1-like (S. cerevisiae) [Homo sapiens]
 gi|313883632|gb|ADR83302.1| dihydrouridine synthase 1-like (S. cerevisiae) [synthetic
           construct]
          Length = 473

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|66810311|ref|XP_638879.1| tRNA-dihydrouridine synthase 2-like protein [Dictyostelium
           discoideum AX4]
 gi|60467531|gb|EAL65553.1| tRNA-dihydrouridine synthase 2-like protein [Dictyostelium
           discoideum AX4]
          Length = 402

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 118/259 (45%), Gaps = 31/259 (11%)

Query: 37  KKNILGFSTQEKPL--ALQIGGADISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEG 91
           K   L + T EK +   LQ+G A     +EAAK+V     N+I   ++N+GCP     +G
Sbjct: 88  KDQTLCYRTSEKDVRNVLQLGTASSMTALEAAKVV----CNDICALDINMGCPKFFSVQG 143

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
             G+ L+  P+ + D +  + + L+ IP+T K R+   DQ       +L++ I+ +GV+ 
Sbjct: 144 GMGSALLSKPETIKDILTTLKRNLNGIPITCKIRLLSTDQ----ETIDLLRIIESTGVSA 199

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS 209
           I +H R    +   P    ++ N+  +  + +    N D+F   +  +E + +  K    
Sbjct: 200 IGVHCRMIPERPRDPAHWDRLENILSNASFSVPIIANGDIF--EHADIEKIKKQTK---- 253

Query: 210 VDGVMIGRAAYKNSAMLTT---------VDEYFSNPL-TGSSPIKTRVDKDFWRKISASM 259
           VD +MI R   KN ++ +          + EY      T +SP+ T+   +     +   
Sbjct: 254 VDSIMIARGVVKNVSIFSKPSPIDLKQIIQEYTEIAYQTNNSPVNTKYVINSMLNENNIT 313

Query: 260 TDYAARHLHSGGKLQQITR 278
           T+  A+ + S      IT+
Sbjct: 314 TNKEAKAMSSARDYDTITK 332


>gi|296237888|ref|XP_002763931.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Callithrix jacchus]
          Length = 471

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/167 (29%), Positives = 81/167 (48%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIG 55
           MVD ++  +R  +R     L     L+ ++ V DA  R  K+N+   +  E +PL +Q  
Sbjct: 24  MVDQSELGWRLLSRRHGAQLCCTPTLHAQVFVCDANYR--KENLYCEACPEDRPLIMQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    +++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQTIAKRGHYGAFLQDEWNLLQRIILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  CRI V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CRIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|114671084|ref|XP_001167358.1| PREDICTED: PP3111 protein isoform 1 [Pan troglodytes]
 gi|114671086|ref|XP_001167386.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 2 [Pan
           troglodytes]
          Length = 473

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|41054535|ref|NP_955911.1| tRNA-dihydrouridine synthase 1-like [Danio rerio]
 gi|37589069|gb|AAH58873.1| Dihydrouridine synthase 1-like (S. cerevisiae) [Danio rerio]
          Length = 479

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 80/167 (47%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  ++N+     QE +PL  Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAELCYTPMLHAQVFVRDANYR--RENLYSEVNQEDRPLITQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    ++AA + +D+  + I+LN+GCP      G +G  L    D++   I    + L
Sbjct: 82  ANDPEVFIQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGVFLQDEWDLLEKMIKLANEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+P+T  C+I V  +I         K ++K+G   + +H R    KG
Sbjct: 141 SVPIT--CKIRVFPEIEKTV--KYAKMLEKAGCQLLTVHGRTKDQKG 183


>gi|194895115|ref|XP_001978186.1| GG17837 [Drosophila erecta]
 gi|190649835|gb|EDV47113.1| GG17837 [Drosophila erecta]
          Length = 473

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/182 (26%), Positives = 86/182 (47%), Gaps = 19/182 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+  PD     + 
Sbjct: 97  LVLQMGTSDAGRALAVGKLLQR-DISGLDINMGCPKEFSIKGGMGAALLAVPDKAALILR 155

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +C  L IPVT K RI  D +    +  +LV+ +  +G+  I IHAR ++          
Sbjct: 156 TLCSGLDIPVTCKIRILPDVE----STIDLVQKLAATGIAAIGIHARTSV---------E 202

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNSA 224
           +  +  +  V     +  D+ I  NGG ++M      +  ++    D VM+ RAA  N +
Sbjct: 203 RPQHAAHPEVLRAVAQAVDIPIIANGGSKNMHCYEDLRKFQLECGADSVMVARAAQINVS 262

Query: 225 ML 226
           + 
Sbjct: 263 IF 264


>gi|309972569|gb|ADO95770.1| tRNA-dihydrouridine synthase YohI [Haemophilus influenzae R2846]
          Length = 310

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 101/226 (44%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    D G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ GV  I +H R   
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGVTEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + E+ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKADGYRADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  W +I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWYEIQKILQKYA 257


>gi|323495036|ref|ZP_08100125.1| tRNA-dihydrouridine synthase C [Vibrio brasiliensis LMG 20546]
 gi|323310693|gb|EGA63868.1| tRNA-dihydrouridine synthase C [Vibrio brasiliensis LMG 20546]
          Length = 317

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 86/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++ + +
Sbjct: 64  PIHVQLLGQDPHWMAENAVKAAELGAKGIDLNFGCPAKLVNKSKGGAALLQHPELIHNVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+  + PVT K R+G D+  P      +V +I+ +G N + +HAR       +  
Sbjct: 124 KACRDAVDPATPVTAKIRLGWDN--PEDCFE-IVDAIQTAGANELTVHAR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAY 220
              K   + +D + +I++      I  NG + +    QA      VD +M+ R A+
Sbjct: 174 GGYKASEIKWDYINQIRQRFSIPLIA-NGEIWNYQDGQACIETTGVDSLMVCRGAF 228


>gi|258542828|ref|YP_003188261.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256633906|dbj|BAH99881.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256636965|dbj|BAI02934.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-03]
 gi|256640018|dbj|BAI05980.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-07]
 gi|256643074|dbj|BAI09029.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-22]
 gi|256646129|dbj|BAI12077.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-26]
 gi|256649182|dbj|BAI15123.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-32]
 gi|256652169|dbj|BAI18103.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-01-42C]
 gi|256655226|dbj|BAI21153.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-12]
          Length = 356

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 111/233 (47%), Gaps = 23/233 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGADISKL 62
           TD  +R  AR L    L+ +EMI + A++R +   +      +   P A+Q+ G D   +
Sbjct: 30  TDLPFRRLARKL-GAGLVVSEMIASWAMVRENDTTLRMAEVADAGGPNAVQLAGCDPDAM 88

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIPVTV 121
            EAA+I    G + I++N GCP  +V  G   G+ LM +       +AA+ KA+ +PVT+
Sbjct: 89  AEAARIAVGRGADLIDINFGCPVKKVAVGQMAGSALMRDEGAAERLLAAVVKAVPVPVTL 148

Query: 122 KCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDI 178
           K R+G D + + A  L  + + +   G+  I +H   R+    G +          ++  
Sbjct: 149 KMRMGWDHEHLNAPVLARIAQDV---GIRMITVHGRTRQQFYNGTA----------NWAF 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           V  + KE  DL + +NG +  +  A + L     DGVMIGR  Y     L  V
Sbjct: 196 VKNV-KEAVDLPVIVNGDILTVGDAREALAQSGADGVMIGRGCYGRPWFLAQV 247


>gi|254229857|ref|ZP_04923262.1| dihydrouridine synthase (Dus) superfamily [Vibrio sp. Ex25]
 gi|262393748|ref|YP_003285602.1| tRNA-dihydrouridine synthase C [Vibrio sp. Ex25]
 gi|151937626|gb|EDN56479.1| dihydrouridine synthase (Dus) superfamily [Vibrio sp. Ex25]
 gi|262337342|gb|ACY51137.1| tRNA-dihydrouridine synthase C [Vibrio sp. Ex25]
          Length = 319

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 45/176 (25%), Positives = 91/176 (51%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G + + + E A      G   I++N GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHVQLLGQEPNWMAENAIKAASLGARGIDINFGCPAKMVNKSKGGAALLQHPELIHRVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+  +IPVT K R+G ++  P      +V +I+ +G N + +HAR       + +
Sbjct: 124 KACREAVPEAIPVTAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR-------TKQ 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + +D + +I +E  D+ +  NG + +     + + +  VD +M+ R A+
Sbjct: 174 GGYKASEIKWDYINQI-RERFDIPLIANGEIWNYEDGQRCIETTGVDSLMVCRGAF 228


>gi|320535329|ref|ZP_08035448.1| TIM-barrel protein, nifR3 family [Treponema phagedenis F0421]
 gi|320147829|gb|EFW39326.1| TIM-barrel protein, nifR3 family [Treponema phagedenis F0421]
          Length = 334

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/116 (32%), Positives = 66/116 (56%), Gaps = 8/116 (6%)

Query: 23  YTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINL 79
           YTEM+ ++A++R  +K  N+   +  E+  A+QI G++ + + E AK I+E    + I++
Sbjct: 47  YTEMVSSEAMVRDSQKTENLFKRAPNEQAYAVQIFGSNPNHMAETAKKILEKASPSCIDI 106

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVDDQ 130
           N GCP  ++ +   G+ LM NP  +     A+  A     +S+PVTVK R G + +
Sbjct: 107 NAGCPMPKITKTGAGSALMRNPQNLYTVTKAVRDAVDTVNISVPVTVKIRSGWNTE 162


>gi|295318114|gb|ADF98491.1| dihydrouridine synthase family protein [Clostridium botulinum F
           str. 230613]
          Length = 287

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/243 (22%), Positives = 102/243 (41%), Gaps = 23/243 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D  + +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSERFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKI 171
           K   + +++K RIG D          L+K   K  +  + IH R +    G  P      
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPRTQKDFYGNKP------ 174

Query: 172 PNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              D DI  +      NP  + G    +   ++ +K  P V  +M+GR    N  ++   
Sbjct: 175 ---DLDIFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLI--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                N +  ++ I   V K+F  +I     +      ++  +++++  +MI +F    N
Sbjct: 229 -----NEIKNNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIFSNIKN 283

Query: 290 SRR 292
             R
Sbjct: 284 MLR 286


>gi|169154846|emb|CAQ15427.1| dihydrouridine synthase 1-like (S. cerevisiae) [Danio rerio]
          Length = 496

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 80/167 (47%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  ++N+     QE +PL  Q  
Sbjct: 41  MVDQSELAWRLLSRRHGAELCYTPMLHAQVFVRDANYR--RENLYSEVNQEDRPLITQFC 98

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    ++AA + +D+  + I+LN+GCP      G +G  L    D++   I    + L
Sbjct: 99  ANDPEVFIQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGVFLQDEWDLLEKMIKLANEKL 157

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+P+T  C+I V  +I         K ++K+G   + +H R    KG
Sbjct: 158 SVPIT--CKIRVFPEIEKTV--KYAKMLEKAGCQLLTVHGRTKDQKG 200


>gi|121700723|ref|XP_001268626.1| dihydrouridine synthase family protein, putative [Aspergillus
           clavatus NRRL 1]
 gi|119396769|gb|EAW07200.1| dihydrouridine synthase family protein, putative [Aspergillus
           clavatus NRRL 1]
          Length = 538

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 92/210 (43%), Gaps = 26/210 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D    +EAA+ V  +  + ++LN+GCP     +G +GA L  + D++  
Sbjct: 120 DRPLFVQFCANDPDDFIEAARHVAPYC-DAVDLNLGCPQGIARKGHYGAFLQEDWDLIYK 178

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  + K LSIPVT K RI    Q          K I  +G + I +H R    KG    
Sbjct: 179 LINRLHKELSIPVTAKFRI----QESKEKTLEYAKMILSAGASIITLHGRTREQKG---- 230

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNS 223
            N  + +  Y I Y      P+  I  NG     +D+ + L+     DGVM       + 
Sbjct: 231 HNTGLADWSY-IRYLRDNLPPETVIFANGNNLNHDDLERCLEAT-GADGVMSAEGNLSDP 288

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           A+       FS P     P+ T   +++WR
Sbjct: 289 AI-------FSKP----PPVGTHT-REYWR 306


>gi|331268768|ref|YP_004395260.1| dihydrouridine synthase, DuS [Clostridium botulinum BKT015925]
 gi|329125318|gb|AEB75263.1| dihydrouridine synthase, DuS [Clostridium botulinum BKT015925]
          Length = 323

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/282 (22%), Positives = 119/282 (42%), Gaps = 32/282 (11%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGADISKLVEAAKI 68
           + +   N    +T  IV +  +R   K   ++L  + +   +  QI   D    +  +  
Sbjct: 20  YEKFFGNVDKYFTPFIVTNKNIRFKAKELRDVLPENNEGMNIVPQILTNDSEGFISISTK 79

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           ++  GYNEINLN+GCPS  V     G+  +   + +   +  + K  ++ +++K RIG D
Sbjct: 80  LQQLGYNEINLNLGCPSGTVVSKYRGSGFLAKREELDRFLDEIFKIDNMKISIKTRIGKD 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK-IPNLDYDIVYEIKKE-- 185
                     L+K   K  +  + IH R       + +D  K  PNL     Y  K    
Sbjct: 140 S---PEEFYELIKIFNKYPLEELIIHPR-------TREDFYKNKPNL-----YVFKDALS 184

Query: 186 ---NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
              NP  + G    + D  + ++  P V+ VMIGR    N  ++  + E        +  
Sbjct: 185 LSVNPVCYNGDIFTVTDYKKLIETFPEVETVMIGRGILANPGLINEIKE--------NKN 236

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +  +V +DF  +I  +  +      ++  +++++  +MI +F
Sbjct: 237 LDKKVLEDFHDEILNNYRELFNEDRNAMFRMKELWGYMIYIF 278


>gi|227489463|ref|ZP_03919779.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227090641|gb|EEI25953.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
          Length = 371

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 97/207 (46%), Gaps = 19/207 (9%)

Query: 19  NALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYN 75
           + L   EM+ A A++  ++K +    FS+ E+P +LQ+   D     +AAK I E+   +
Sbjct: 43  SGLYVCEMVTARALVERNEKTLHMAAFSSVEEPRSLQLYTTDPEYTYKAAKMIAEENLAD 102

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIP 132
            ++LN GCP  +V     GA L    ++    + A  + +S   IPVTVK RIG+D    
Sbjct: 103 HVDLNFGCPVPKVTRKGGGAALPYKRELFKRIVDATVRGVSGTDIPVTVKFRIGIDAD-- 160

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
              + +  +  ++ G   + +HAR A          R      ++ + E+K+   D+ + 
Sbjct: 161 HETMLDAGRIAQEEGAAAVTLHARTAA--------ERYSGQAHWERIAELKQAL-DVPVF 211

Query: 193 LNGGLEDMSQALKILPSV--DGVMIGR 217
            NG +   +  L +      DG+ IGR
Sbjct: 212 GNGDVFSAADGLAMFEQTGCDGIEIGR 238


>gi|302833555|ref|XP_002948341.1| hypothetical protein VOLCADRAFT_80128 [Volvox carteri f.
           nagariensis]
 gi|300266561|gb|EFJ50748.1| hypothetical protein VOLCADRAFT_80128 [Volvox carteri f.
           nagariensis]
          Length = 422

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 88/187 (47%), Gaps = 16/187 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGA 57
           MVD ++  +R   R        YT M+ A  I   D+K    +L   ++++PL +Q    
Sbjct: 54  MVDQSELPFRLLCRR-HGATCAYTPMLHAR-IFSQDRKYREEMLTTCSEDRPLLVQFCAH 111

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   L+ AA++V+D G  + I++N GCP      G +GA LM +   V   +  + + L 
Sbjct: 112 EPQHLLAAARLVQDSGVADAIDINFGCPQRIAKRGGYGAFLMDDLPRVESLVRVLAQNLR 171

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT K RI   D    VA   +V++   +G + + +H R      L  + +      D+
Sbjct: 172 IPVTAKIRI-FPDLAKTVAYARMVEA---AGASLVAVHGR------LREQKDNSSTRADW 221

Query: 177 DIVYEIK 183
           D +  +K
Sbjct: 222 DAIRAVK 228


>gi|308234685|ref|ZP_07665422.1| TIM-barrel protein, nifR3 family [Gardnerella vaginalis ATCC 14018]
 gi|311114396|ref|YP_003985617.1| dihydrouridine synthase [Gardnerella vaginalis ATCC 14019]
 gi|310945890|gb|ADP38594.1| dihydrouridine synthase [Gardnerella vaginalis ATCC 14019]
          Length = 384

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/162 (28%), Positives = 77/162 (47%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    + L   EMI A A++  + K   +  F+  EK  +LQ+ G D
Sbjct: 24  MAGITNWPFRVICREYGPDGLYVAEMITARALVARNPKALRLCRFAPNEKVRSLQLYGVD 83

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S +  AA+IV D    + ++LN GCP  +V     G+ L    D++ +    + ++C  
Sbjct: 84  PSIVELAARIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCDP 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             IPVT K R+G+D+          +   ++ G   + +HAR
Sbjct: 144 AGIPVTAKFRVGIDENHETFMQAGHIA--QEEGCAAVTLHAR 183


>gi|183220020|ref|YP_001838016.1| tRNA-dihydrouridine synthase C [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910141|ref|YP_001961696.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167774817|gb|ABZ93118.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167778442|gb|ABZ96740.1| tRNA-dihydrouridine synthase C [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 316

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/186 (25%), Positives = 94/186 (50%), Gaps = 16/186 (8%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +  + P+ +QI G+D +++ + A +V   G   I++N GCP+  V+    GA L+  P++
Sbjct: 59  TKSDTPVKIQILGSDPNRMADNAHLVASLGAYGIDINFGCPAPTVNRNRGGAALLKEPNL 118

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A+   +  +IPVT K R+G +    A+   +  K++++ G   I +HAR     
Sbjct: 119 MYSIVKAVRNVVPENIPVTAKMRLGYESTELAL---DCAKALEEGGAKEIVVHAR----- 170

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
             +  D  K P   ++ + +IK     + +  NG +  +  A++   +   D +MIGR A
Sbjct: 171 --TKTDGYKPPAY-WEWIAKIKS-ILKINVIANGEIWTVQDAIQCQKISGCDDIMIGRGA 226

Query: 220 YKNSAM 225
             N ++
Sbjct: 227 VTNPSI 232


>gi|19075762|ref|NP_588262.1| tRNA dihydrouridine synthase Dus4 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74626875|sp|O74553|DUS4_SCHPO RecName: Full=tRNA-dihydrouridine synthase 4
 gi|3560252|emb|CAA20719.1| tRNA dihydrouridine synthase Dus4 (predicted) [Schizosaccharomyces
           pombe]
          Length = 326

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 108/240 (45%), Gaps = 28/240 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   L   K     FST +    L LQ G  D
Sbjct: 27  MVRYSKLPFRQLVRDY-NTDIVYTPMILAKEFLH-PKGRYFDFSTNDADASLILQFGVDD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
              L +AA++V  +  + I +N GCP     +   G+ L+  P+ V   + A+   L  S
Sbjct: 85  PVILEKAAQLVGPY-VDGIGINCGCPQTWAIQEGIGSALLDEPEKVHKLVRAVKSTLGES 143

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLD 175
               VK RI  D        R+L++ I+KSG + I +H R       + +D    P NLD
Sbjct: 144 FCTEVKIRIAKDLN----KTRHLMQVIEKSGADIITVHGR-------TRQDRSSFPVNLD 192

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
                 I++  P + I +  NG ++ + + L+I       G+M  R   +N A+    +E
Sbjct: 193 -----AIREVRPCVQIPVVANGDVKSLRKGLEIAKYTETQGIMSARGLLENPALFAGYEE 247


>gi|119504827|ref|ZP_01626905.1| hypothetical protein MGP2080_09206 [marine gamma proteobacterium
           HTCC2080]
 gi|119459432|gb|EAW40529.1| hypothetical protein MGP2080_09206 [marine gamma proteobacterium
           HTCC2080]
          Length = 342

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 63/117 (53%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ LQ+ G +   +   A++ E  G   I+LN GCP+  V++   GA L+  P
Sbjct: 77  GRTPAGTPVFLQLLGNNPDLMARNAQVAEALGAPGIDLNFGCPAKTVNKSQGGAVLLKTP 136

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           D++G   A +  A++  IPVT K R+G +D     +   +VK+    GV+ + +HA+
Sbjct: 137 DLLGAVCAEVRAAVAPEIPVTAKIRLGFEDDD---SFEAIVKAAVDGGVSELTVHAK 190


>gi|119510895|ref|ZP_01630018.1| transcriptional regulator [Nodularia spumigena CCY9414]
 gi|119464423|gb|EAW45337.1| transcriptional regulator [Nodularia spumigena CCY9414]
          Length = 339

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/224 (25%), Positives = 108/224 (48%), Gaps = 30/224 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +P+  Q+ G  I  LV  AK  E  GYN   ++LN+GCP+ R++  + G  L+L+P+ V 
Sbjct: 71  RPVFAQMIGESIPDLVRTAK--ELCGYNIAGVDLNMGCPAPRIYRKNVGGGLLLSPEKVD 128

Query: 106 DCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKG 162
             +A + + ++  P+TVK R+G ++         ++  I +  ++ + +H R  K +  G
Sbjct: 129 RILAELRQTVNDRPLTVKMRLGFEN---TDTFYEILDIINRHSIDLLSLHGRTVKDMYHG 185

Query: 163 LSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRA 218
                      + YD++ E   + + P L    NG +     AL++L      GVM+GR 
Sbjct: 186 ----------AVKYDLIAEAVRRVQCPVL---ANGNIHSAKTALEVLSQTGAAGVMVGRW 232

Query: 219 AYKNSAMLTTVDEYFS-NPLTGSSPIKTR--VDKDFWRKISASM 259
           A  N  +   + +     P+T    ++ R  +D+ +    +A+M
Sbjct: 233 AIGNPWLFNQIRQALRFEPITPVPLVEVRNYIDRLWQTPAAATM 276


>gi|114563584|ref|YP_751097.1| dihydrouridine synthase, DuS [Shewanella frigidimarina NCIMB 400]
 gi|114334877|gb|ABI72259.1| dihydrouridine synthase, DuS [Shewanella frigidimarina NCIMB 400]
          Length = 314

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 107/231 (46%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + + A    + G N ++ N GCP+  V++   GA L+  P
Sbjct: 57  GLTASGTPVRVQLLGQEPEWMAQNAIRAIELGSNGVDANFGCPAKTVNKSKGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   + AM  A+    PVT K R+G +D+  ++ + N + ++ ++G   + IHAR   
Sbjct: 117 ENIYSIVKAMRDAVPSEHPVTAKIRLGYEDK--SLFMENAL-AVYEAGATELAIHAR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
               S  D  K P   ++ + E+++  P   I  NG + + + A + +     D +MIGR
Sbjct: 171 ----SKTDGYKPPAY-WEYITEVRQRLPIPVIA-NGEIWNAADAQRCMDVTGCDSIMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W++  + +  Y  + L+
Sbjct: 225 GAISLPNLGDTIK-------TGATPFS-------WQQTLSLLMAYTDKELN 261


>gi|327293319|ref|XP_003231356.1| dihydrouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326466472|gb|EGD91925.1| dihydrouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 456

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/121 (30%), Positives = 67/121 (55%), Gaps = 5/121 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G    ++PL +Q    D  +L++AA+ VE++  + ++LN+GCP     +G +GA L  +P
Sbjct: 40  GNPKYDRPLIVQFCANDPDELLKAARHVEEYC-DAVDLNLGCPQGIAKKGHYGAFLQEDP 98

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++   I  +   LSIPVT K RI ++ +   +    ++ S   +G + + +H R+   K
Sbjct: 99  DLIYKLINKLHNELSIPVTAKFRI-LETKEKTLEYARMILS---AGASILSVHGRRREQK 154

Query: 162 G 162
           G
Sbjct: 155 G 155


>gi|189460249|ref|ZP_03009034.1| hypothetical protein BACCOP_00886 [Bacteroides coprocola DSM 17136]
 gi|189433110|gb|EDV02095.1| hypothetical protein BACCOP_00886 [Bacteroides coprocola DSM 17136]
          Length = 313

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/224 (26%), Positives = 103/224 (45%), Gaps = 24/224 (10%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           DK+ +L        L  Q+  ++  +L + A  +   GY EI++N+GCP   +     G+
Sbjct: 51  DKREVLPRQNTVSHLIPQLVASEPEELNQLAGFLASKGYREIDVNMGCPFPLIANRGKGS 110

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++  P+ V   + AM +   I  +VK R+G    + A   + ++  +  SGV+ I +H 
Sbjct: 111 GILPYPEKVAALLDAMRQLPEIRFSVKMRLG---WLHADEWKQVLPLLNGSGVSQITLHP 167

Query: 156 R--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
           R  K   KG   + NR      YD       E P ++ G    LE + + L+  P + GV
Sbjct: 168 RIGKQQYKG---EVNRVAFKEFYDSC-----ELPLVYNGDLCTLETVQELLEEYPRLKGV 219

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           M+GR    + ++  +V +       G SP KT      +R++SA
Sbjct: 220 MLGRGLLADPSLALSVRK-------GQSPDKT----TLYRQVSA 252


>gi|315604759|ref|ZP_07879822.1| NifR3/Smm1 family transcriptional regulator [Actinomyces sp. oral
           taxon 180 str. F0310]
 gi|315313771|gb|EFU61825.1| NifR3/Smm1 family transcriptional regulator [Actinomyces sp. oral
           taxon 180 str. F0310]
          Length = 423

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 69/300 (23%), Positives = 123/300 (41%), Gaps = 29/300 (9%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R+     L  TEM+ + A++ G+++  +++     E+  +LQ+ G D + +  AA  +VE
Sbjct: 75  RVDAPAGLYVTEMVTSRALVEGNERTLDMVRPDPAERVRSLQLYGVDPAVMARAATMLVE 134

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---------SIPVTV 121
               + ++LN GCP  +V +   GA L    D+  D + ++ +A           IPVTV
Sbjct: 135 RDLTDHVDLNFGCPVPKVTKKGGGAALPWKRDLFVDLLDSVVRACRKAGERAGREIPVTV 194

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D         +   S ++ G   + +HAR              I  L       
Sbjct: 195 KIRIGIDSSHETAT--DAALSAQRLGAAALTLHARTQTQHYAGKAQWEHIARL------- 245

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             KE  D+ +  NG + + + AL +L     DG+ +GR A     +   +   +      
Sbjct: 246 --KELLDIPVFGNGDVFEGADALDMLERTGCDGISVGRGAQGRPWIFRDIVAAYHGAPIP 303

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P    V     R  +  + D           L+++ +H+     GF      RH L++
Sbjct: 304 AGPTLADVIAVIERHAAWCVADQGCEER----ALREMRKHIGWYLRGFAVGGAQRHALSM 359


>gi|269962061|ref|ZP_06176415.1| tRNA-dihydrouridine synthase C [Vibrio harveyi 1DA3]
 gi|269833145|gb|EEZ87250.1| tRNA-dihydrouridine synthase C [Vibrio harveyi 1DA3]
          Length = 319

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/200 (24%), Positives = 101/200 (50%), Gaps = 16/200 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G + + + E A    + G   I+LN GCP+  V++   GA L+ +P+++ + +
Sbjct: 64  PVHVQLLGQEPNWMAENAIKAAELGARGIDLNFGCPARLVNKSKGGAALLQHPELIHNVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G ++  P      +V +I+ +G N + +HAR       + +
Sbjct: 124 KACRDAVPSDIPVSAKIRLGWEN--PEDCF-EIVDAIQSAGANELTVHAR-------TKQ 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              K   + ++ + +I +E  D+ +  NG + +     + + +  VD +M+ R A+ N  
Sbjct: 174 GGYKASEIKWEYITQI-RERFDIPLIANGEIWNYEDGQRCIETTGVDSLMVCRGAF-NIP 231

Query: 225 MLTTVDEYFSNPLTGSSPIK 244
            L  + +Y   P+  +  ++
Sbjct: 232 NLGNMVKYNHKPMVWAEVVE 251


>gi|308485393|ref|XP_003104895.1| hypothetical protein CRE_24419 [Caenorhabditis remanei]
 gi|308257216|gb|EFP01169.1| hypothetical protein CRE_24419 [Caenorhabditis remanei]
          Length = 304

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 103/232 (44%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   RL   + + YT MI A   +  +K   + L    ++ PL +Q    D
Sbjct: 20  MVRYSKLAFRQLVRLYDVD-VCYTPMIYAKNFIESEKCRNSELSICERDSPLIVQFATDD 78

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              L EAA++V  +G +  +++N GCP   V    FG+ L+  P+++ D I      +S 
Sbjct: 79  PIVLAEAAEMV--YGCSTGVDVNCGCPKHDVRSKGFGSALLNKPELLADMIRQTRARISD 136

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
              +V  +I V+  I      +L +  + +GV  + +H R    +   P D + I     
Sbjct: 137 TEFSVSLKIRVNSDIERTV--DLCRKAESAGVTHLTVHGRTPS-QHAEPIDIQAI----- 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
                I KE+  + +  NGG+    +AL +     VDG+M       N A+ 
Sbjct: 189 ----RIVKESVSVPVIANGGITTREEALFLAEQTGVDGIMAANGLLDNPALF 236


>gi|264680133|ref|YP_003280042.1| hypothetical protein CtCNB1_4000 [Comamonas testosteroni CNB-2]
 gi|262210648|gb|ACY34746.1| putative TIM-barrel protein, nifR3 family [Comamonas testosteroni
           CNB-2]
          Length = 367

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/258 (24%), Positives = 109/258 (42%), Gaps = 37/258 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+++QI
Sbjct: 33  MAGVTDRPFRQLCKAL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPISVQI 87

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G +   + EAA    + G   I++N+GCP+ +V     G+ LM N  +   +   +   
Sbjct: 88  AGTEAPMMAEAAIYNIERGAQIIDINMGCPAKKVCNKWAGSALMQNEPLAVEIAQAVVEA 147

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNR 169
            +  ++PVT+K R G  D      L  L +  +  G+  + +H   R+   KG +     
Sbjct: 148 ARPYNVPVTLKMRTGWCDTHKNAVL--LARQFEDVGIQMLTVHGRTREQGYKGFA----- 200

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA------YK 221
                +YD +  +K+    + +  NG +    +A  +L     D +M+GRAA      ++
Sbjct: 201 -----EYDTIAAVKQAV-KVPVVANGDVNSPEKARDVLAYTGADAIMVGRAAQGRPWIFR 254

Query: 222 NSAMLTTVDEYFSNPLTG 239
             A      E+ + PL  
Sbjct: 255 EIAHFLATGEHLAPPLVA 272


>gi|16125983|ref|NP_420547.1| nitrogen regulation protein Nifr3 [Caulobacter crescentus CB15]
 gi|13423159|gb|AAK23715.1| nitrogen regulation protein Nifr3 [Caulobacter crescentus CB15]
          Length = 315

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 108/227 (47%), Gaps = 21/227 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLA-LQIGGAD 58
           M   +D  +R  A  L     + TEM+ +    +G    +   +  E  PL  +Q+ G D
Sbjct: 1   MTGVSDLPFRETASAL-GAPYVATEMVASAEFAKGRPDVVRRAAVGEGLPLTVIQLVGRD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSI 117
           +  + + A++ ++ G   I+LN GCP+  V  G+  G+ LM  PD+    +AA  +A+ +
Sbjct: 60  VDFMAQGARMAQEAGAEIIDLNFGCPAKEVAAGAACGSALMREPDLAEALVAAAVEAVDV 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G D  I  +   ++ +  + +G   + +H   R    KG++          D
Sbjct: 120 PVTVKMRLGWD--IDCLNAPDIARRAEAAGAKAVTVHGRTRNQFYKGVA----------D 167

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           +  V  +K+    + + +NG + D   A + L     DGVMIGR  Y
Sbjct: 168 WTAVAAVKQAV-SVPVLVNGDIVDGETARQALEQSGADGVMIGRGVY 213


>gi|239618483|ref|YP_002941805.1| dihydrouridine synthase DuS [Kosmotoga olearia TBF 19.5.1]
 gi|239507314|gb|ACR80801.1| dihydrouridine synthase DuS [Kosmotoga olearia TBF 19.5.1]
          Length = 314

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 110/240 (45%), Gaps = 30/240 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----EKPLALQIGG 56
           M  +TD   R  + L      +++EM+  + +LR D+      +TQ    E P  +Q+ G
Sbjct: 11  MAGYTDEAMRAIS-LEWGADFVFSEMLSVEGVLRNDR------TTQKIIPETPCRIQLFG 63

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            DI++L  AAK V D      ++N GCP  +V +   GA L+  P+ +   I  +     
Sbjct: 64  NDIARLAMAAKAVLDKA-TWFDINAGCPVKKVVKRGAGAALLREPEKLNAMIQTLKGISD 122

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G D       +  +V+ + +S    I +H R  +++G S          D+
Sbjct: 123 LPVSVKIRLGWDKN----EVVKIVERLVESRPFAIMVHGR-TVVQGYS-------GVADW 170

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-----VDGVMIGRAAYKNSAMLTTVDE 231
           + + ++ K      I + G   D+    KI+ +     VDGV++ R A  N  + +   E
Sbjct: 171 ESIGKVVKICKPHGIKVYGS-GDVFSPEKIVEAFEKYGVDGVLVARGAIGNPWIFSQYKE 229


>gi|194469675|ref|ZP_03075659.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194456039|gb|EDX44878.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
          Length = 331

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G N + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGANELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|297819610|ref|XP_002877688.1| FAD binding protein [Arabidopsis lyrata subsp. lyrata]
 gi|297323526|gb|EFH53947.1| FAD binding protein [Arabidopsis lyrata subsp. lyrata]
          Length = 543

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 98/191 (51%), Gaps = 21/191 (10%)

Query: 43  FST---QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST   +   +  Q+G +D  + ++AA+IV +     +++N+GCP A   +G  GA L+ 
Sbjct: 282 FSTCKEERNRVVFQMGTSDAVRALKAAEIVCN-DVATVDINMGCPKAFSIQGGMGAALLS 340

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D +A + + L +PVT K R+    + PA  +  L + I+K GV  + +H RK  
Sbjct: 341 KPELIHDILATLKRNLDVPVTCKIRLL---KSPADTVE-LARRIEKLGVPALAVHGRKIA 396

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
            +   P+D  K   +  D+V  +      + +  NG +   +D S+ +K       VM+ 
Sbjct: 397 DR---PRDPAKWDEI-ADVVAAL-----SIPVIANGDVLEYDDFSR-IKTATGAASVMVA 446

Query: 217 RAAYKNSAMLT 227
           R A  N+++ +
Sbjct: 447 RGAMWNASIFS 457


>gi|46579075|ref|YP_009883.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46448488|gb|AAS95142.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
          Length = 332

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 70/261 (26%), Positives = 115/261 (44%), Gaps = 34/261 (13%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGADISKLVEAAKIVEDF 72
           L    LL+T M  A A+   +      F+ + + L     Q+ GAD S++ EAA+ VE  
Sbjct: 32  LGGCGLLFTGMCNARAVPTENPARSNAFTWRAEELERCVCQLFGADPSEMAEAARRVEAE 91

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQI 131
           G+  +++N+GC  A +     GA L+ + +     + ++ +A+  PV VK R G   D  
Sbjct: 92  GFFGVDINMGCSVAAIVRRGCGADLLRDEERAVRMVESVRRAVDCPVLVKFRTGWSPDPQ 151

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
            AVA   L +  + +G + +  H R A        D R  P L + I   + KE   + +
Sbjct: 152 GAVA---LARRFEDAGADALVFHPRVA-------PDRRTRPPLRHHI--RLVKEAVAIPV 199

Query: 192 GLNGGLEDMSQALKILPSV--DGVMIGRAA----YKNSAMLTTVDEYFSNPLTGSSPIKT 245
             NG +     A  +L +   DG+ +GR A    +  +A    VD+   NP +       
Sbjct: 200 LGNGEVFTPGDAASMLETTGCDGISLGRIALGRPWVFAAWTGLVDD---NPAS------- 249

Query: 246 RVDKDFWRKISASMTDYAARH 266
             + D WR I  ++ D   R 
Sbjct: 250 --NPDLWRDIPLALLDALERR 268


>gi|296276940|ref|ZP_06859447.1| histidine phosphokinase/phophatase, putative [Staphylococcus aureus
           subsp. aureus MR1]
          Length = 193

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/149 (28%), Positives = 71/149 (47%), Gaps = 17/149 (11%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           FF       +  + E I +   +RG     L FS  E P+   I G    +  E +  + 
Sbjct: 40  FFTEFTNTESFCHPEGIHS---VRGR----LTFSEDEHPMVAHIWGDKPEQFRETSIQLA 92

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---V 127
             G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  +PV+VK R+G   +
Sbjct: 93  KMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQA-TKAGGLPVSVKTRLGYYEI 151

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           D+       ++ +K + +  +  + IH R
Sbjct: 152 DE------WKDWLKHVFEQDIANLSIHLR 174


>gi|294789807|ref|ZP_06755036.1| tRNA-dihydrouridine synthase C [Simonsiella muelleri ATCC 29453]
 gi|294482249|gb|EFG29947.1| tRNA-dihydrouridine synthase C [Simonsiella muelleri ATCC 29453]
          Length = 331

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 98/188 (52%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +QI G+D + +   A      G N+I++N GCP+  V++   GA L+  PD++   +
Sbjct: 76  PCTVQILGSDENMMAINALEAIKLGANKIDINFGCPAPTVNKHKGGAILLQEPDLIYQIV 135

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L  +IP+T K R+G +++   +AL N  ++I  +GV+ + +HAR  + +G  P 
Sbjct: 136 RTLRERLPENIPLTAKMRLGYENK--DLALEN-AQAIASAGVSALTVHARTKV-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
            +       ++ V +I +++ D+ +  NG +  +    A+K     + +M+GR A     
Sbjct: 192 AH-------WNWVKKI-QQSIDIPVIANGDVFSLDDFIAIKNETGCNQIMLGRGAVMRPD 243

Query: 225 MLTTVDEY 232
           +   + ++
Sbjct: 244 LARQIRQF 251


>gi|114650483|ref|XP_001146302.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Pan troglodytes]
          Length = 473

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTM--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|120553985|ref|YP_958336.1| dihydrouridine synthase, DuS [Marinobacter aquaeolei VT8]
 gi|120323834|gb|ABM18149.1| tRNA-U20a,U20b-dihydrouridine synthase [Marinobacter aquaeolei VT8]
          Length = 325

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/172 (29%), Positives = 84/172 (48%), Gaps = 14/172 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+A+Q+ G++   +        + G  ++++N GCP+  V++   G  LM  P+++ +  
Sbjct: 64  PVAVQLLGSNADMMGRHGAKAAELGAGQVDINFGCPAKTVNKHKGGCVLMREPELMYEIT 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ KA+   IPVT K R+G DD+   VA     ++++ +G + I IHAR  +       
Sbjct: 124 AAVRKAVPADIPVTAKMRLGYDDRSMGVACG---QALEAAGASEIVIHARSKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFI-GLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P    +I    K     +   G    +ED  +  K+    D VMIGR
Sbjct: 174 DGYKPPAYWEEIAKVCKAVKSHVIANGEIWTVEDYWRCRKV-SGCDDVMIGR 224


>gi|168229529|ref|ZP_02654587.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205335746|gb|EDZ22510.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
          Length = 312

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G N + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGANELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|171464157|ref|YP_001798270.1| TIM-barrel protein, nifR3 family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
 gi|171193695|gb|ACB44656.1| TIM-barrel protein, nifR3 family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
          Length = 338

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 119/247 (48%), Gaps = 29/247 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   TDR +R   + L  +  + +EM+ ++A+L   +K     N +G   + K +A+QI 
Sbjct: 17  MAGVTDRPFRQLCKKLGADYAV-SEMVASNALLWKSEKTQRRANHIG---EFKLIAVQIA 72

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           GAD + +  AAKI  D G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+
Sbjct: 73  GADPAMMAAAAKINVDHGAQIIDINMGCPAKKVCNVAAGSALLRDEPLVQQILEAVVNAV 132

Query: 116 -----SIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                ++PVT+K R G D Q   A+ +  L    +KSG++ + +H R         + + 
Sbjct: 133 GIGPDAVPVTLKIRTGWDRQNKNAIEIAQLA---EKSGISMLTVHGRT--------RADL 181

Query: 170 KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
                +Y+ +  +K     P +  G     E   Q LKI    D +MIGRAA     +  
Sbjct: 182 YHGEAEYETITTVKNYVRIPVVANGDINSPEKAEQVLKIT-GADAIMIGRAAQGRPWIFR 240

Query: 228 TVDEYFS 234
            ++ Y  
Sbjct: 241 EINHYLE 247


>gi|299534036|ref|ZP_07047388.1| putative TIM-barrel protein, nifR3 family [Comamonas testosteroni
           S44]
 gi|298717945|gb|EFI58950.1| putative TIM-barrel protein, nifR3 family [Comamonas testosteroni
           S44]
          Length = 354

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/256 (24%), Positives = 109/256 (42%), Gaps = 37/256 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST------QEKPLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S       +  P+++QI
Sbjct: 20  MAGVTDRPFRQLCKAL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPISVQI 74

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G +   + EAA    + G   I++N+GCP+ +V     G+ LM N  +   +   +   
Sbjct: 75  AGTEAPMMAEAAIYNIERGAQIIDINMGCPAKKVCNKWAGSALMQNEPLAVEIAQAVVEA 134

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNR 169
            +  ++PVT+K R G  D      L  L +  +  G+  + +H   R+   KG +     
Sbjct: 135 ARPYNVPVTLKMRTGWCDTHKNAVL--LARQFEDVGIQMLTVHGRTREQGYKGFA----- 187

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA------YK 221
                +YD +  +K+    + +  NG +    +A  +L     D +M+GRAA      ++
Sbjct: 188 -----EYDTIAAVKQAV-KVPVVANGDVNSPEKARDVLAYTGADAIMVGRAAQGRPWIFR 241

Query: 222 NSAMLTTVDEYFSNPL 237
             A      E+ + PL
Sbjct: 242 EIAHFLATGEHLAPPL 257


>gi|56751238|ref|YP_171939.1| nitrogen regulation protein NifR3-like protein [Synechococcus
           elongatus PCC 6301]
 gi|81299094|ref|YP_399302.1| dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus
           elongatus PCC 7942]
 gi|56686197|dbj|BAD79419.1| nitrogen regulation protein NifR3 homolog [Synechococcus elongatus
           PCC 6301]
 gi|81167975|gb|ABB56315.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus
           elongatus PCC 7942]
          Length = 334

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 108/233 (46%), Gaps = 17/233 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           +DR +R   R     +L++ EM  A   L G  ++   F   E+P+  Q+ G   + L  
Sbjct: 39  SDRSFRQLVRRSAPQSLIFAEMAHAGLQLAG--RDRWEFLPHEQPIGAQLFGDQPATLAA 96

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AA+  E  G   I+LN+GCP ++V     G+ L+  P++    + A+  A+SIPVTVK R
Sbjct: 97  AAQQAEAAGAVCIDLNMGCPVSKVTRKRGGSALLREPELAIAIVQAVAAAVSIPVTVKTR 156

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G +     V + +  + ++ +G   + +H R    +G S +        D++ +  +K 
Sbjct: 157 LGWEQ----VTILDFAQQLEAAGAQLLTLHGRSRS-QGYSGQ-------ADWNWITRVKS 204

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
                 I  NG +   + A+  L     DGVM GR +  N  ++  +D     
Sbjct: 205 RLSIPVIA-NGDINSPADAIACLQQTGADGVMCGRGSLGNPGLVGAIDRSLKT 256


>gi|325142309|gb|EGC64723.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           961-5945]
 gi|325198237|gb|ADY93693.1| dihydrouridine synthase, Dus family [Neisseria meningitidis G2136]
          Length = 333

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 92/205 (44%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKGRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|254669503|emb|CBA03423.1| tRNA-dihydrouridine synthase [Neisseria meningitidis alpha153]
          Length = 333

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 51/207 (24%), Positives = 94/207 (45%), Gaps = 24/207 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K
Sbjct: 136 KTLRGRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------K 184

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
                P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     
Sbjct: 185 AEAYEPPAHWEWIRKI-RDTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPD 243

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           +   + +Y         P+K   D DF
Sbjct: 244 LARQIKQY-----ENGGPVK---DTDF 262


>gi|145637129|ref|ZP_01792791.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           PittHH]
 gi|145269574|gb|EDK09515.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           PittHH]
          Length = 310

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 63/117 (53%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G +   L E A    D G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQNPECLAENAIRAIDLGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ G   I +H R
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGATEITVHGR 170


>gi|237746835|ref|ZP_04577315.1| tRNA-dihydrouridine synthase B [Oxalobacter formigenes HOxBLS]
 gi|229378186|gb|EEO28277.1| tRNA-dihydrouridine synthase B [Oxalobacter formigenes HOxBLS]
          Length = 335

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 74/302 (24%), Positives = 138/302 (45%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---DKKNILGFSTQEKPLALQIGGA 57
           M   TDR +R   + L       +EM  A+ +LR     +K I+    +  P A+QI G+
Sbjct: 1   MAGITDRPFRQLCKKL-GAGYAVSEMAAANPLLRDTLKSRKRII-HDGESGPHAIQIVGS 58

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             + + ++A+   D G + I++N+GCP+ +V     G+ L+ N  +VG  + A+  A+ +
Sbjct: 59  VPAIMADSARYHVDQGADIIDINMGCPAKKVCNNWCGSALLQNESLVGQILDAVVHAVPV 118

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVT+K R G D   I A A+  + +S   +G+  + +H R         + +      +Y
Sbjct: 119 PVTLKFRTGWDRSHINAPAIAKIAES---AGIAMLTLHGRT--------RADGYRGEAEY 167

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E+K     + +  NG ++   +A  +L     D +MIGRAA     +   +  +  
Sbjct: 168 ATIAEVKSL-VSIPVVANGDIDSPQKAKTVLDKTGADALMIGRAARGRPWIFREIGHF-- 224

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG-FPNSRRC 293
             L   +P+     ++ W+ +   + D+ A +  + G      R  IG + G  P+  + 
Sbjct: 225 --LQYGTPLLPPSLQEIWQILREHLEDHYAFYGETLGVRN--ARKHIGWYAGNLPDGEKL 280

Query: 294 RH 295
           R 
Sbjct: 281 RQ 282


>gi|68478245|ref|XP_716864.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68478366|ref|XP_716804.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46438488|gb|EAK97818.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46438550|gb|EAK97879.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|238882442|gb|EEQ46080.1| tRNA-dihydrouridine synthase 4 [Candida albicans WO-1]
          Length = 339

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 108/236 (45%), Gaps = 18/236 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R +      F+T +  K + +Q+G  +
Sbjct: 33  MVRYSKLPFRELCRFYDVD-IVYTPMILAREFVRNEVARSTDFTTNDSDKCVIVQVGVNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   ++  +++  F  + I +N GCP   +V EG  GA LM +PD+V + I         
Sbjct: 92  VDDFMKFIEMIHPF-VDGIGINCGCPIKEQVREG-IGAALMSDPDLVAELIKTAKDKYGD 149

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + +  +I +   I      + V  + ++G + + +H R         K+ R    ++ D
Sbjct: 150 SICIDTKIRIHRDINQTI--DFVNKVVEAGTDTLTVHGRT--------KNTRSSVPVNLD 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +  I++    + +  NG    ++   KI+    VDGVM  R    N A+ T +D+
Sbjct: 200 AIKIIRENVTTIPVIANGDCFTLTDFQKIVDYTGVDGVMSARGVLANPALFTGLDK 255


>gi|111021839|ref|YP_704811.1| tRNA-dihydrouridine synthase [Rhodococcus jostii RHA1]
 gi|110821369|gb|ABG96653.1| probable tRNA-dihydrouridine synthase [Rhodococcus jostii RHA1]
          Length = 380

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 71/308 (23%), Positives = 121/308 (39%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L      + + L   EM+ A A++       ++  F   E P +L
Sbjct: 20  MAGITNVAFRTLCRELETERAGSTSGLYVCEMVTARALVERQPATLHMTTFGPTETPRSL 79

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK IV++   + I++N GCP  +V     GA L     + G  +AA 
Sbjct: 80  QLYTVDPDTTYAAAKMIVDENMADHIDMNFGCPVPKVTRKGGGAALPYKRTLFGRIVAAA 139

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     +PVTVK R+G+D +       +  +     G   + +HAR A          
Sbjct: 140 VKATEGTDVPVTVKFRVGIDAE--HHTHLDAGRIAAGEGAAAVALHARTA--------SQ 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
           R     D++ +  +K+   D+ +  NG +     A +++     DGV++GR       + 
Sbjct: 190 RYSGTADWNEIARLKEHVTDVPVLGNGDIFAAEDAARMMEQTGCDGVVVGRGCLGRPWLF 249

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +    +     + P    V     R       +  A H      L+++ +H+     G
Sbjct: 250 AELSAALNGKPQPTPPNLGEVATIIRRH-----AELLADHHGEDKGLRELRKHVSWYLRG 304

Query: 287 FPNSRRCR 294
           FP     R
Sbjct: 305 FPAGSELR 312


>gi|149194756|ref|ZP_01871851.1| tRNA-dihydrouridine synthase B [Caminibacter mediatlanticus TB-2]
 gi|149135179|gb|EDM23660.1| tRNA-dihydrouridine synthase B [Caminibacter mediatlanticus TB-2]
          Length = 311

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/207 (24%), Positives = 105/207 (50%), Gaps = 24/207 (11%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEI 77
           + ++EMI A+AI   ++K   ++  S++E P  +QI   ++   ++A +I+ +  + + I
Sbjct: 37  MTFSEMINANAIAFNNEKTKKMMQKSSKETPYFIQIAANNVENAIKAVEIINEIPWIDGI 96

Query: 78  NLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           ++N+GCP  +     +G  L+   N + + + ++A+ K     V+ K R+G ++    V 
Sbjct: 97  DINLGCPVNKARRSGYGGVLLKDENKEKLKEIVSAIIKTSKKIVSAKMRLGYNE----VV 152

Query: 136 LRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             +  K ++  G+  + +H R  K + KG          N +Y  + ++ KE  ++ +  
Sbjct: 153 AVDRAKMLEDLGIKFLTVHGRTVKQMYKG----------NANYKEIKKVVKE-VNIPVIA 201

Query: 194 NGGLEDMSQALKILP--SVDGVMIGRA 218
           NG + D  +A ++L     +GV IGR 
Sbjct: 202 NGDITDYKKAKEVLEYTEANGVAIGRG 228


>gi|221234750|ref|YP_002517186.1| tRNA-dihydrouridine synthase [Caulobacter crescentus NA1000]
 gi|220963922|gb|ACL95278.1| tRNA-dihydrouridine synthase [Caulobacter crescentus NA1000]
          Length = 335

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 108/227 (47%), Gaps = 21/227 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLA-LQIGGAD 58
           M   +D  +R  A  L     + TEM+ +    +G    +   +  E  PL  +Q+ G D
Sbjct: 21  MTGVSDLPFRETASAL-GAPYVATEMVASAEFAKGRPDVVRRAAVGEGLPLTVIQLVGRD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSI 117
           +  + + A++ ++ G   I+LN GCP+  V  G+  G+ LM  PD+    +AA  +A+ +
Sbjct: 80  VDFMAQGARMAQEAGAEIIDLNFGCPAKEVAAGAACGSALMREPDLAEALVAAAVEAVDV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           PVTVK R+G D  I  +   ++ +  + +G   + +H   R    KG++          D
Sbjct: 140 PVTVKMRLGWD--IDCLNAPDIARRAEAAGAKAVTVHGRTRNQFYKGVA----------D 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           +  V  +K+    + + +NG + D   A + L     DGVMIGR  Y
Sbjct: 188 WTAVAAVKQAV-SVPVLVNGDIVDGETARQALEQSGADGVMIGRGVY 233


>gi|317125242|ref|YP_004099354.1| hypothetical protein Intca_2117 [Intrasporangium calvum DSM 43043]
 gi|315589330|gb|ADU48627.1| TIM-barrel protein, nifR3 family [Intrasporangium calvum DSM 43043]
          Length = 419

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 71/318 (22%), Positives = 126/318 (39%), Gaps = 33/318 (10%)

Query: 1   MVDWTDRHYRFFARLLTN-----------NALLYTEMIVADAILR--GDKKNILGFSTQE 47
           M   T+R +R   R   N            +L  +EMI   A++    +   ++     E
Sbjct: 48  MAGITNRAFRRLCREYGNEGAVTGGASGATSLYVSEMITTRALVERNAETMRLIEHDPDE 107

Query: 48  KPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P ++Q+   D +    AA+I V++   + I+LN GCP  +V     G+ L    D+   
Sbjct: 108 NPRSIQLYSVDPATARAAARILVQEDRADHIDLNFGCPVPKVTRKGGGSALPWKRDLFRS 167

Query: 107 CIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            + A+ +  +   IPVTVK R G+DD+        L  + +  G   + +H R A     
Sbjct: 168 IVGAVVEEGARRDIPVTVKMRKGIDDEHLTYLEAGL--AAEDEGAAAVALHGRTAA---- 221

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYK 221
                      D+  +  +K+    + +  NG +     AL+++     DGV++GR    
Sbjct: 222 ----QAYSGTADWAAIRLLKQTVTTVPVLGNGDIWSAEDALRMVAETGCDGVVVGRGCLG 277

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T +   F+      +P    V  D  R  +  +TD+      +    + I +H+ 
Sbjct: 278 RPWLFTDLAAAFAGSSARVTP-SLGVVADTLRTHTLYLTDFYGDEERA---CRDIRKHIA 333

Query: 282 GLFHGFPNSRRCRHILTV 299
               GFP     R  L +
Sbjct: 334 WYLKGFPAGSTLRSSLAL 351


>gi|296130021|ref|YP_003637271.1| TIM-barrel protein, nifR3 family [Cellulomonas flavigena DSM 20109]
 gi|296021836|gb|ADG75072.1| TIM-barrel protein, nifR3 family [Cellulomonas flavigena DSM 20109]
          Length = 442

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 98/217 (45%), Gaps = 20/217 (9%)

Query: 12  FARLL--TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL   +   L   EM+ + A++    ++  I+ F   E P ++Q+ G D + +  A +
Sbjct: 91  FRRLCRESGAGLYVAEMLTSRALVERSPESFRIIAFEPDEVPRSVQVYGVDPATVGAAVR 150

Query: 68  I-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKC 123
           + VE+   + ++LN GCP  +V     GA L    ++    + A   A     +PVTVK 
Sbjct: 151 LLVEEDRADHVDLNFGCPVPKVTRRGGGAVLPWKRELFASIVRAAVDAARPHGVPVTVKM 210

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G+D+         L  + + +GV  + +H R A         +      D+D +  +K
Sbjct: 211 RKGIDEDHLTYVEAGL--TAQDAGVAAVALHGRTAA--------DYYSGTADWDAIATLK 260

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
           +   D+ +  NG +     AL ++     DGV++GR 
Sbjct: 261 EAVTDIPVLGNGDIWSAEDALAMVAHTRCDGVVVGRG 297


>gi|297702082|ref|XP_002828013.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 2 [Pongo
           abelii]
 gi|297702084|ref|XP_002828014.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 3 [Pongo
           abelii]
          Length = 473

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 82/167 (49%), Gaps = 12/167 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + ++LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAVDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|225164984|ref|ZP_03727193.1| TIM-barrel protein, nifR3 family [Opitutaceae bacterium TAV2]
 gi|224800406|gb|EEG18793.1| TIM-barrel protein, nifR3 family [Opitutaceae bacterium TAV2]
          Length = 389

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 80/160 (50%), Gaps = 6/160 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           +  +T+   R   R L       T+++ A +++   K    ++  +  ++PLA+Q+ G+ 
Sbjct: 17  LAGYTNLPMRLTVRELGGLGWATTDLVNARSLIERSKGAMKLVETAPGDQPLAIQLFGSV 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
             ++ +AA I ++ G   +++N+GCP  +V     GA +M   +     +  M +A+   
Sbjct: 77  PEEMRDAAVICKELGAQSVDVNMGCPVKKVVGIGGGAAMMTELNKTAALVRGMVEAVGNK 136

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           IPVT K R+G DD    +   +L + +   GV  I++H R
Sbjct: 137 IPVTAKMRLGWDDA--NITAPDLARVLADVGVAAIFVHGR 174


>gi|70729433|ref|YP_259171.1| NifR3/Smm1 family protein [Pseudomonas fluorescens Pf-5]
 gi|68343732|gb|AAY91338.1| NifR3/Smm1 family protein [Pseudomonas fluorescens Pf-5]
          Length = 362

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 104/235 (44%), Gaps = 27/235 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 107 PLRVQLLGSDPVCLAENAALACELGSEVIDLNFGCPAKTVNKSRGGAVLLKEPELLNQIV 166

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+   IPVT K R+G D    ++       ++ + G   I +HAR  +     P 
Sbjct: 167 EHVRRAVPAHIPVTAKMRLGFDSPDGSLV---CATALAEGGAEHIVVHARTKVDGYKPPA 223

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               IP +  ++V      N D++      +ED  +  +I   V+ +M+GR       + 
Sbjct: 224 HWEWIPRVQ-EVVKVPVFANGDIW-----SVEDWRRCREI-SGVEDIMLGRGLVSRPDLA 276

Query: 227 TTV------DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
             +      +E          P+     +DFW ++   +T  +A      G+L+Q
Sbjct: 277 RQIAAARAGEEVVEMSWADLQPML----QDFWAQVVVQLTPRSA-----PGRLKQ 322


>gi|269956952|ref|YP_003326741.1| TIM-barrel protein, nifR3 family [Xylanimonas cellulosilytica DSM
           15894]
 gi|269305633|gb|ACZ31183.1| TIM-barrel protein, nifR3 family [Xylanimonas cellulosilytica DSM
           15894]
          Length = 400

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 69/314 (21%), Positives = 127/314 (40%), Gaps = 30/314 (9%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQ 53
           M   T+R +R   R        +  L   EM+ + A++  + +   I+ F   E P + Q
Sbjct: 35  MAGVTNRAFRTLCREAGASGGEHPGLYVAEMVTSRALVERNAEALRIVTFGADETPRSAQ 94

Query: 54  IGGADISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + G D + +  A +I+  ED   + ++LN GCP  +V     G  L     +  D + A 
Sbjct: 95  VYGVDPATVGAAVRIIASEDRA-DHVDLNFGCPVPKVTRKGGGGALPWKRQLFTDIVRAA 153

Query: 112 CKALS---IPVTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A +   +PVT+K R G+ DD +  +    + + +   GV  + +HAR  + +  S + 
Sbjct: 154 VDAAAPYGVPVTIKMREGIDDDHLTYLEAGTIAEGL---GVAAVALHART-VAQHYSGEA 209

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAM 225
                   +  +  +K+    + +  NG +     AL+++     DGV++GR       +
Sbjct: 210 R-------WPSIARLKEAVTSVPVLGNGDIWSADDALRMVAETGADGVVVGRGCQGRPWL 262

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +   F        P    V    +R     M +Y     H G  ++ + +HM     
Sbjct: 263 FADLAAAFHGQTVRVQPTLREVADTIYRH-GELMIEYYDGDEHKG--VRDLRKHMAWYLK 319

Query: 286 GFPNSRRCRHILTV 299
           G+      RH L +
Sbjct: 320 GYAVGGEARHALAL 333


>gi|309810988|ref|ZP_07704786.1| TIM-barrel protein, nifR3 family [Dermacoccus sp. Ellin185]
 gi|308434952|gb|EFP58786.1| TIM-barrel protein, nifR3 family [Dermacoccus sp. Ellin185]
          Length = 410

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 70/318 (22%), Positives = 129/318 (40%), Gaps = 33/318 (10%)

Query: 1   MVDWTDRHYRFFARLLTNN-----------ALLYTEMIVADAILRGDKKNILGFSTQ--E 47
           M   T+R +R   R   ++           +L  +EMI + A++      +    T   E
Sbjct: 39  MAGITNRAFRRLCRQYGDDGSVAAGASGATSLYVSEMITSRALVERVPLTMKLIETDPDE 98

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P ++Q+   D     +AA+I+   G  + I+LN GCP  +V     G+ L    ++   
Sbjct: 99  NPRSIQLYCTDPLNAGKAARILASEGRADHIDLNFGCPVPKVTRKGGGSALPWKTELFRG 158

Query: 107 CIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            ++A+ +  S   IPVTVK R G+D     +      +  +  GV  + +HAR A     
Sbjct: 159 IVSAVVREASPYDIPVTVKMRKGIDTD--HLTYLEAARIAEGEGVAAVALHARTAA---- 212

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYK 221
                    + D+  +  +K+    + +  NG +     A++++     DGV++GR    
Sbjct: 213 ----QAYSGHADWSAIRTLKETVTSIPVLGNGDIWSAEDAMRMVAETGCDGVVVGRGCLG 268

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T +   F+       P    V     R+ +  + ++    L      + I +H+ 
Sbjct: 269 RPWLFTDLAAAFAGSDARVDPTLGEVCATL-RRHAEYLVEFYDDELKG---CRDIRKHIA 324

Query: 282 GLFHGFPNSRRCRHILTV 299
             F GFP   + RH L +
Sbjct: 325 WYFKGFPVGSQLRHQLAL 342


>gi|154148885|ref|YP_001406121.1| NifR3 family protein [Campylobacter hominis ATCC BAA-381]
 gi|153804894|gb|ABS51901.1| NifR3 family protein [Campylobacter hominis ATCC BAA-381]
          Length = 310

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 100/205 (48%), Gaps = 20/205 (9%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EMI A+A++   +K++  +  S  E P  +QI G+D   + +A +I+    G + I+LN
Sbjct: 36  SEMISANALVFCSEKSLKMIKKSENETPYFVQIAGSDPKIIKQAVEILNKIDGIDGIDLN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V   + G+ L+ N D++   I  + K  +   T  K R+G D + P     N+
Sbjct: 96  CGCPVPKVVRQNAGSALLQNLDLLSKLIEIIKKTSNKKYTSAKVRLGFDTKNPV----NI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
             +++ +G + I +HAR     G S K        DY+ +   K       I  NG +  
Sbjct: 152 ALAVQNAGADFIAMHARTR-AGGYSAKP-------DYEAIAAAKSAVKIPLIA-NGNINS 202

Query: 198 EDMSQALKILPSVDGVMIGRAAYKN 222
           ++ +Q L  L   D +MIGRA   N
Sbjct: 203 QNANQILN-LTKADALMIGRATIGN 226


>gi|319775859|ref|YP_004138347.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae F3047]
 gi|329123704|ref|ZP_08252264.1| tRNA-dihydrouridine synthase C [Haemophilus aegyptius ATCC 11116]
 gi|317450450|emb|CBY86666.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae F3047]
 gi|327469903|gb|EGF15368.1| tRNA-dihydrouridine synthase C [Haemophilus aegyptius ATCC 11116]
          Length = 310

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 102/228 (44%), Gaps = 33/228 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    D G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPECLAENAIRAIDLGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ G   I +H R   
Sbjct: 117 ELIYRATQALRQAVPGEFPVSVKVRLGWDDISQAFEITD---AVEQGGATEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSV--DGVMI 215
               +  D  +   +++  + E+++    LFI +  NG +         L       +M+
Sbjct: 171 ----TKADGYRADRINWKKIGEVRER---LFIPVIANGEIWHWQDGQDCLSQTGCQDLMV 223

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
           GR A  N   L+ V             +K+  +K  W +I   +  YA
Sbjct: 224 GRGAL-NIPNLSHV-------------LKSNAEKMPWCEIQKILQKYA 257


>gi|293189559|ref|ZP_06608279.1| zinc-binding TIM-barrel protein, nifR3 family [Actinomyces
           odontolyticus F0309]
 gi|292821649|gb|EFF80588.1| zinc-binding TIM-barrel protein, nifR3 family [Actinomyces
           odontolyticus F0309]
          Length = 411

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 57/220 (25%), Positives = 104/220 (47%), Gaps = 25/220 (11%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R+     L  TEM+ + A++  +++ +  +     E+  +LQ+ G + + + +AA  +VE
Sbjct: 63  RVDAPAGLYVTEMVTSRALVEENERTLEMVRPDPAERVRSLQLYGVNPAVMAKAATMLVE 122

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---------SIPVTV 121
               + I+LN GCP  +V +   GA L    D+  D + A+ +A           IPVTV
Sbjct: 123 RDLTDHIDLNFGCPVPKVTKKGGGAALPWKRDLFSDLVGAVVRACDEAGERAGREIPVTV 182

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D +       +   S +K G   + +HAR         ++     +  +D +  
Sbjct: 183 KIRIGIDSEHETAT--DAALSAQKLGAAALTLHART--------QNQHYAGHAHWDEIAR 232

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           + K+  D+ +  NG + + + AL +L     DG+ +GR A
Sbjct: 233 L-KDLLDIPVFGNGDVFEAADALAMLEQTGCDGISVGRGA 271


>gi|239907298|ref|YP_002954039.1| putative tRNA-dihydrouridine synthase [Desulfovibrio magneticus
           RS-1]
 gi|239797164|dbj|BAH76153.1| putative tRNA-dihydrouridine synthase [Desulfovibrio magneticus
           RS-1]
          Length = 337

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/160 (27%), Positives = 77/160 (48%), Gaps = 4/160 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R  +R L   A+  TEM+ A  +    +  K +L     + PL +Q+ GA+
Sbjct: 22  LAGFSDLPFRLLSREL-GAAVAVTEMVSAKGLFYDSRNTKRLLDTCPADSPLVVQLFGAE 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA  + + GY   +LN GC   +V +   GA L+ +PD +  C  AM +A+  P
Sbjct: 81  PDYLERAAVALAEAGYTYFDLNCGCSVRKVVKTGAGAALLGDPDRLVACARAMVRAVG-P 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             V  ++ +  + PA     L   + ++G   + +H R A
Sbjct: 140 GRVGVKLRLGPKPPARVDLELAIRLAEAGAAWLALHPRHA 179


>gi|145632514|ref|ZP_01788248.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 3655]
 gi|144986709|gb|EDJ93261.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 3655]
          Length = 310

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 100/226 (44%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSSTPVRVQLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A     +  ++++ G   I +H R   
Sbjct: 117 ELIYRATQALRRAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + ++ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKSDGYRADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  WR+I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWREIQKILQKYA 257


>gi|119610149|gb|EAW89743.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
          Length = 415

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+   +D  +         + ++K+G   + +H R    KG
Sbjct: 141 SVPVTCKIRVFPEIDKTV------RYAQMLEKAGCQLLTVHGRTKEQKG 183


>gi|186510839|ref|NP_001118800.1| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|26452531|dbj|BAC43350.1| unknown protein [Arabidopsis thaliana]
 gi|332645049|gb|AEE78570.1| tRNA-dihydrouridine synthase 2 [Arabidopsis thaliana]
          Length = 290

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 100/191 (52%), Gaps = 21/191 (10%)

Query: 43  FST--QEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST  +EK  +  Q+G +D  + ++A++IV +     I++N+GCP A   +G  GA L+ 
Sbjct: 29  FSTCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLS 87

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D +A + + L +PVT K R+    + PA  +  L + I+K GV  + +H RK  
Sbjct: 88  KPELIHDILATLKRNLDVPVTCKIRLL---KSPADTVE-LARRIEKLGVPALAVHGRKIA 143

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
            +   P+D  K   +  D+V  +      + +  NG +   +D S+ +K       VM+ 
Sbjct: 144 DR---PRDPAKWDEI-ADVVAALS-----IPVIANGDVLEYDDFSR-IKTATGAASVMVA 193

Query: 217 RAAYKNSAMLT 227
           R A  N+++ +
Sbjct: 194 RGAMWNASIFS 204


>gi|84496809|ref|ZP_00995663.1| transcriptional regulator, NifR3/Smm1 family protein [Janibacter
           sp. HTCC2649]
 gi|84383577|gb|EAP99458.1| transcriptional regulator, NifR3/Smm1 family protein [Janibacter
           sp. HTCC2649]
          Length = 407

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/293 (21%), Positives = 121/293 (41%), Gaps = 23/293 (7%)

Query: 19  NALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD-ISKLVEAAKIVEDFGYN 75
            +L   EM+ + A++    +   ++    +E P ++Q+   D ++  + A  +V +   +
Sbjct: 64  TSLYVNEMVTSRALVERTPETMRLISHGPEEHPRSVQLYSVDPVTAGLAARMLVTEDRAD 123

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSIPVTVKCRIGVD-DQI 131
            I+LN GCP  +V     GA L    ++    ++A+ +     ++PVTVK RIG+D D I
Sbjct: 124 HIDLNFGCPVPKVTRKGGGAALPWKTELFRGIVSAVVREANPYNVPVTVKMRIGIDADHI 183

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
             +    + +     GV  + +H R A                D+  +  +K+    + +
Sbjct: 184 TYLDAGRIAEG---EGVAAVALHGRTAA--------QAYSGQADWSAIARLKEAVTTIPV 232

Query: 192 GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
             NG +     AL+++     DGV++GR       + T +   F+   T   P    V +
Sbjct: 233 LGNGDIWSAEDALEMVRQTGCDGVVVGRGCLGRPWLFTDLAAAFAGTPTRVQPGLREVTQ 292

Query: 250 DFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAG 302
              R     +  Y    L +    + I +H+     GFP     R+ L +  G
Sbjct: 293 TLSRHTRYLIDFYDGDELRA---CRDIRKHIAWYLKGFPAGSTVRNQLALVDG 342


>gi|16272228|ref|NP_438439.1| hypothetical protein HI0270 [Haemophilus influenzae Rd KW20]
 gi|260580847|ref|ZP_05848672.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae RdAW]
 gi|1176627|sp|P44606|DUSC_HAEIN RecName: Full=tRNA-dihydrouridine synthase C
 gi|1573236|gb|AAC21936.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092470|gb|EEW76408.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae RdAW]
          Length = 310

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 100/226 (44%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    D G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPKCLAENAIRAIDLGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ G   I +H R   
Sbjct: 117 ELIYRATQALRRAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGATEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + E+ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKADGYRADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  W +I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWYEIQKILQKYA 257


>gi|6561964|emb|CAB62468.1| putative protein [Arabidopsis thaliana]
          Length = 519

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 100/191 (52%), Gaps = 21/191 (10%)

Query: 43  FST--QEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST  +EK  +  Q+G +D  + ++A++IV +     I++N+GCP A   +G  GA L+ 
Sbjct: 284 FSTCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLS 342

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D +A + + L +PVT K R+    + PA  +  L + I+K GV  + +H RK  
Sbjct: 343 KPELIHDILATLKRNLDVPVTCKIRLL---KSPADTV-ELARRIEKLGVPALAVHGRKIA 398

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
            +   P+D  K   +  D+V  +      + +  NG +   +D S+ +K       VM+ 
Sbjct: 399 DR---PRDPAKWDEI-ADVVAAL-----SIPVIANGDVLEYDDFSR-IKTATGAASVMVA 448

Query: 217 RAAYKNSAMLT 227
           R A  N+++ +
Sbjct: 449 RGAMWNASIFS 459


>gi|220928485|ref|YP_002505394.1| dihydrouridine synthase [Clostridium cellulolyticum H10]
 gi|219998813|gb|ACL75414.1| dihydrouridine synthase DuS [Clostridium cellulolyticum H10]
          Length = 311

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/267 (24%), Positives = 111/267 (41%), Gaps = 24/267 (8%)

Query: 23  YTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++  I+A   D     D K+I   + QE  L  Q+   +    +  +K ++  GY EINL
Sbjct: 31  FSPFIIANQIDGFKTRDLKDISPENNQELVLIPQVLTNNAKDFIYTSKKIKSMGYTEINL 90

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCPS  V   + G+  +   + +   +  +       +++K RIG D         +L
Sbjct: 91  NLGCPSGTVVSKNRGSGFLAKKEELDVFLEEIFSQAITKISIKTRIGKDQ---PEEFYDL 147

Query: 140 VKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++   K  +N + IH R  K   K    K N KI     D + E K  NP  + G     
Sbjct: 148 IRIFNKYPINELIIHPRIQKDFYKN---KPNMKIFR---DALAESK--NPVCYNGDIFTA 199

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +D  +     P VD +M+GR    N A+   V             ++  + K F  K+  
Sbjct: 200 KDYKEFCNDFPGVDTLMLGRGLLMNPALAGYV--------KNGRKLEKSLLKKFHDKVYN 251

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLF 284
              D  +   +   K++++  +MI +F
Sbjct: 252 DYKDILSGERNVLFKMKELWFYMINVF 278


>gi|170077562|ref|YP_001734200.1| dihydrouridine synthase (Dus) [Synechococcus sp. PCC 7002]
 gi|169885231|gb|ACA98944.1| Dihydrouridine synthase (Dus) [Synechococcus sp. PCC 7002]
          Length = 353

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/234 (22%), Positives = 107/234 (45%), Gaps = 14/234 (5%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           TD  +R   R    ++++YTEM+ A  +        ++     E+P+++Q+       + 
Sbjct: 38  TDLVFRRLVRRYAPSSMMYTEMVRAQEVHHLQTLPRLMEIDPGEQPISIQLFDCRPDFMG 97

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           EAAK     G   I++N+GCP  ++     G+ L+  P++    + A+ +A+ +PVTVK 
Sbjct: 98  EAAKKAVAEGAQTIDINMGCPVNKITRKGGGSSLLRQPEVAVAIVKAVVEAVDVPVTVKT 157

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           RIG  D    + + +  + ++ +G   + +H R    +G + K         +  + ++ 
Sbjct: 158 RIGWADA--EIVIVDFARRLEDAGAQMLTVHGRTRA-QGYTGKAQ-------WQWIKKV- 206

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           KE   + +  NG +  +  A+  L +   DGVM  R       ++  +D +   
Sbjct: 207 KEVLSIPVIANGDIFSVDAAIACLEATGADGVMCSRGTLGYPFLVGEIDHFLKT 260


>gi|148825450|ref|YP_001290203.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           PittEE]
 gi|148715610|gb|ABQ97820.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           PittEE]
          Length = 310

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 100/226 (44%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSSTPVRVQLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A     +  ++++ G   I +H R   
Sbjct: 117 ELIYRATQALRRAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + ++ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKSDGYRADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  WR+I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWREIQKILQKYA 257


>gi|319896605|ref|YP_004134798.1| tRNA-dihydrouridine synthase c [Haemophilus influenzae F3031]
 gi|317432107|emb|CBY80458.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae F3031]
          Length = 310

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 63/117 (53%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G +   L E A    D G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQNPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +++     A+ KA+    PV+VK R+G DD   A  + +   ++++ G   I +H R
Sbjct: 117 ELIYCATQALRKAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGATEITVHGR 170


>gi|186510837|ref|NP_190533.3| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|332645048|gb|AEE78569.1| tRNA-dihydrouridine synthase 2 [Arabidopsis thaliana]
          Length = 329

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 55/191 (28%), Positives = 100/191 (52%), Gaps = 21/191 (10%)

Query: 43  FST--QEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST  +EK  +  Q+G +D  + ++A++IV +     I++N+GCP A   +G  GA L+ 
Sbjct: 68  FSTCDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLS 126

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D +A + + L +PVT K R+    + PA  +  L + I+K GV  + +H RK  
Sbjct: 127 KPELIHDILATLKRNLDVPVTCKIRLL---KSPADTVE-LARRIEKLGVPALAVHGRKIA 182

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
            +   P+D  K   +  D+V  +      + +  NG +   +D S+ +K       VM+ 
Sbjct: 183 DR---PRDPAKWDEI-ADVVAALS-----IPVIANGDVLEYDDFSR-IKTATGAASVMVA 232

Query: 217 RAAYKNSAMLT 227
           R A  N+++ +
Sbjct: 233 RGAMWNASIFS 243


>gi|38604692|sp|O52532|DUSB_SERMA RecName: Full=tRNA-dihydrouridine synthase B
 gi|3885440|gb|AAC77880.1| yhdG homolog [Serratia marcescens]
          Length = 334

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  + R DK  +    + E  + ++QI G D
Sbjct: 17  MAGITDRPFRTLCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAARINVASGAQLIDINMGCPAKKVNRKLAGSALLQYPDLVKRILHAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G      A   RN V   +  +  G+  + IH R    +  G          +
Sbjct: 136 VTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGRTRACLFNG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  + K++  + I  NG + D  +A  +L     D +MIGRAA     +   +  
Sbjct: 181 AEYDSIRAV-KQSVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|330938356|gb|EGH41984.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 216

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 93/189 (49%), Gaps = 19/189 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G D        RN   + K  +++G+  + +H R         + +      +
Sbjct: 139 VTLKIRTGWDRDN-----RNGLTVAKIAEQAGIQALAVHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKK 184
           YD + +IK+
Sbjct: 186 YDTIAQIKQ 194


>gi|328947505|ref|YP_004364842.1| dihydrouridine synthase DuS [Treponema succinifaciens DSM 2489]
 gi|328447829|gb|AEB13545.1| dihydrouridine synthase DuS [Treponema succinifaciens DSM 2489]
          Length = 331

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 102/215 (47%), Gaps = 29/215 (13%)

Query: 23  YTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           +TEMI A ++L     +K  ++     EK +  Q+ G     L +AA+IV + G   I+L
Sbjct: 30  FTEMINASSLLNMGPFEKYYLMNGPCPEK-IVWQLTGTSAESLAKAAEIVCEKGGIGIDL 88

Query: 80  NVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSI---------PVTVKCRIGVDD 129
           N+GC + ++++   G   ML P     + ++ + K+L +           +VKCR+G ++
Sbjct: 89  NMGCSAPQIYKIGAGIAWMLKPLKETAEAVSKVKKSLDLIEEKTQNHFRFSVKCRLG-NE 147

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                   N    + ++GV  I +HAR  K   +GL   +  K  +  Y+          
Sbjct: 148 NFTEQTFFNFTDMLVENGVELITLHARTIKEKYRGLPRYEFAKKLSQRYE---------K 198

Query: 188 DLFIGLNGGLEDMSQ---ALKILPSVDGVMIGRAA 219
            + + +NG ++D +    A++  P  DG+MI RAA
Sbjct: 199 KIKVYVNGCIKDTASAKFAIQKAPEADGIMIARAA 233


>gi|322417631|ref|YP_004196854.1| dihydrouridine synthase DuS [Geobacter sp. M18]
 gi|320124018|gb|ADW11578.1| dihydrouridine synthase DuS [Geobacter sp. M18]
          Length = 340

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 101/225 (44%), Gaps = 35/225 (15%)

Query: 16  LTNNAL--LYTEMIVADAIL--------RGDKKNILGFSTQE-------KPLALQIGGAD 58
           LTN AL  L+T+ +  DA+         + +KK ++    +E        PL +Q+ G  
Sbjct: 39  LTNRALRELFTKWVRPDAVWTEFMRVNAQSEKKLLMPGDLREIAPAENGVPLVVQLIGHG 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV AAK  +D G   INLN+GCP  R+  G  G  ++  P+++ + I A+   +   
Sbjct: 99  RDALVAAAKTAQDAGAVHINLNMGCPYGRMTSGLTGGGMLKRPELLEEIIPALRHVIQGS 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDY 176
            ++K R G ++     +L  L ++ +   V+ + +H R  +    G +          D+
Sbjct: 159 FSIKLRAGYEEPQQVFSLLPLFEAAR---VDFLVLHPRTVRQAYDGFA----------DH 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAA 219
            I  E+ K+     I  NG +      LK+L      G+M+GR  
Sbjct: 206 AITAEVVKQTSIPVIA-NGDIRSSRFGLKVLEETGAAGLMLGRGG 249


>gi|307130591|ref|YP_003882607.1| tRNA-dihydrouridine synthase C [Dickeya dadantii 3937]
 gi|306528120|gb|ADM98050.1| tRNA-dihydrouridine synthase C [Dickeya dadantii 3937]
          Length = 311

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKMVNGSGGGATLLKDPDLIYRAARAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+  S+PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPSSLPVTVKVRLGWDSGERQF---EIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A   + +   D VMIGR A  N   L+
Sbjct: 177 RAERINWAAIGEIRRRLRIPVIA-NGEIWDWQSAQDCMAATGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|261327635|emb|CBH10611.1| tRNA-dihydrouridine synthase 4, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 419

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 93/211 (44%), Gaps = 21/211 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL   + + YT MI+AD+    +      FS  + E  L  Q+  + 
Sbjct: 66  MVRCSRPAFRKLCRLWGTD-ISYTHMIMADSFACSEAARQAEFSIYSGETRLITQLASSS 124

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
                 AA IV  +  + I+LN GCP  RV     GA L+ NP++V D +  +  AL   
Sbjct: 125 GPTAATAAAIVAPW-CDAIDLNCGCPQRRVMADGLGAALLRNPEVVADTVRCVRNALEGG 183

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P  VK R+  D ++      +  +  + +G   I +H R       +P        +
Sbjct: 184 VELPCVVKMRVKDDVRLSV----DFARQCEAAGAAWITVHGRTPNCSAHAP--------V 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            +D +  I +E   + +  NGG+ D S AL+
Sbjct: 232 RFDAINTI-REALGVPVVANGGVRDPSTALQ 261


>gi|311232920|gb|ADP85774.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris RCH1]
          Length = 400

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 70/261 (26%), Positives = 115/261 (44%), Gaps = 34/261 (13%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGADISKLVEAAKIVEDF 72
           L    LL+T M  A A+   +      F+ + + L     Q+ GAD S++ EAA+ VE  
Sbjct: 100 LGGCGLLFTGMCNARAVPTENPARSNAFTWRAEELERCVCQLFGADPSEMAEAARRVEAE 159

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQI 131
           G+  +++N+GC  A +     GA L+ + +     + ++ +A+  PV VK R G   D  
Sbjct: 160 GFFGVDINMGCSVAAIVRRGCGADLLRDEERAVRMVESVRRAVDCPVLVKFRTGWSPDPQ 219

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
            AVA   L +  + +G + +  H R A        D R  P L + I   + KE   + +
Sbjct: 220 GAVA---LARRFEDAGADALVFHPRVA-------PDRRTRPPLRHHI--RLVKEAVAIPV 267

Query: 192 GLNGGLEDMSQALKILPSV--DGVMIGRAA----YKNSAMLTTVDEYFSNPLTGSSPIKT 245
             NG +     A  +L +   DG+ +GR A    +  +A    VD+   NP +       
Sbjct: 268 LGNGEVFTPGDAASMLETTGCDGISLGRIALGRPWVFAAWTGLVDD---NPAS------- 317

Query: 246 RVDKDFWRKISASMTDYAARH 266
             + D WR I  ++ D   R 
Sbjct: 318 --NPDLWRDIPLALLDALERR 336


>gi|295689377|ref|YP_003593070.1| NifR3 family TIM-barrel protein [Caulobacter segnis ATCC 21756]
 gi|295431280|gb|ADG10452.1| TIM-barrel protein, nifR3 family [Caulobacter segnis ATCC 21756]
          Length = 335

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 97/205 (47%), Gaps = 22/205 (10%)

Query: 24  TEMIVADAILRGDKKNILGFSTQEK-PLA-LQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           TEM+ +    +G    +   +  +  PL  +Q+ G DI  + + A++  + G   I+LN 
Sbjct: 43  TEMVASAEFAKGRPDVVRRAAVGDGLPLTVIQLVGRDIDCMAQGARMAAEAGAEIIDLNF 102

Query: 82  GCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALR 137
           GCP+  V  G+  G+ LM  PD+    +AA  +A+ +PVTVK R+G DD     P +A R
Sbjct: 103 GCPAKEVAAGAACGSALMREPDLAEALVAAAVRAVDVPVTVKMRLGWDDGSRNAPEIAAR 162

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                 K   V+G     R    KG++          D+  V ++KK    + + +NG +
Sbjct: 163 AEAVGAKAITVHG---RTRNQFYKGVA----------DWSAVAQVKKAV-SVPVLVNGDI 208

Query: 198 EDMSQALKIL--PSVDGVMIGRAAY 220
            D   A   L     DGVMIGR  Y
Sbjct: 209 VDGESARAALEQSGADGVMIGRGVY 233


>gi|271967481|ref|YP_003341677.1| hypothetical protein Sros_6205 [Streptosporangium roseum DSM 43021]
 gi|270510656|gb|ACZ88934.1| conserved hypothetical protein [Streptosporangium roseum DSM 43021]
          Length = 373

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 105/224 (46%), Gaps = 17/224 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EMI   A++  + K   ++ F   EKP ++Q+ G D
Sbjct: 20  MAGITNAPFRTLCRE-QGGGLFVCEMITTRALVERNAKTFKMIRFEPAEKPRSIQLYGVD 78

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALS 116
              + +A +++ D    + ++LN GCP  +V     G+ L    +++   +  A+  A +
Sbjct: 79  PVTVGKAVRMIADEDLADHVDLNFGCPVPKVTRRGGGSALPYKRNLLRAILREAVRNAGT 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G+DD    +   +  +   + GV+ I +H R A+               D+
Sbjct: 139 LPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVSAIALHGRTAV--------QHYGGTADW 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRA 218
           + +  +K+   ++ +  NG +   + AL+++     DGV++GR 
Sbjct: 189 EAIARLKEAVTEIPVLGNGDIWSAADALRMMDETGCDGVVVGRG 232


>gi|254579200|ref|XP_002495586.1| ZYRO0B14872p [Zygosaccharomyces rouxii]
 gi|238938476|emb|CAR26653.1| ZYRO0B14872p [Zygosaccharomyces rouxii]
          Length = 406

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 79/167 (47%), Gaps = 10/167 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    + + ++       R D    + G S  ++PL +Q  
Sbjct: 26  MVDQSELAWRILSRKYGATLAYTPMFHAKLFATSPKYRKDMWCEMDGDSKIDRPLVVQFC 85

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L++AA++V+D   + ++LN+GCP     +G +G+ LM   D+V   I  + + L
Sbjct: 86  ANDPEYLLQAARLVQD-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLVHKLIRNLHENL 144

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +PVT K RI  + +      R ++     +G   + +H R    KG
Sbjct: 145 DVPVTAKIRIFPEKEKSLQYARTVL----DAGAQFLTVHGRLREQKG 187


>gi|255576019|ref|XP_002528905.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
 gi|223531659|gb|EEF33485.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
          Length = 330

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/202 (25%), Positives = 97/202 (48%), Gaps = 19/202 (9%)

Query: 30  DAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSAR 87
           D + +G +  +     +EK  +  Q+G +D  + + AA++V +D     I++N+GCP + 
Sbjct: 57  DFVEKGTENVVFRTCNEEKNRVVFQMGTSDAVRALTAAQMVCKDVA--AIDINMGCPKSF 114

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G  GA L+  P+++ D +  + + L  PVT K R+    Q        L + I+K+G
Sbjct: 115 SISGGMGAALLTKPELIHDILTTLKRNLDSPVTCKIRLLKSPQDTV----ELARRIEKTG 170

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALK 205
           V+ + +H RK   +   P+D  K   +  DIV  +      + +  NG + D    + +K
Sbjct: 171 VSALAVHGRKVADR---PRDPAKWSEI-ADIVSTL-----SIPVIANGDVFDYGDFERIK 221

Query: 206 ILPSVDGVMIGRAAYKNSAMLT 227
                  VM+ R A  N+++ +
Sbjct: 222 AATGASSVMVARGALWNASIFS 243


>gi|72388074|ref|XP_844461.1| tRNA-dihydrouridine synthase 4 [Trypanosoma brucei TREU927]
 gi|62359403|gb|AAX79841.1| tRNA-dihydrouridine synthase 4, putative [Trypanosoma brucei]
 gi|70800994|gb|AAZ10902.1| tRNA-dihydrouridine synthase 4, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 419

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 93/211 (44%), Gaps = 21/211 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL   + + YT MI+AD+    +      FS  + E  L  Q+  + 
Sbjct: 66  MVRCSRPAFRKLCRLWGTD-ISYTHMIMADSFACSEAARQAEFSIYSGETRLITQLASSS 124

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
                 AA IV  +  + I+LN GCP  RV     GA L+ NP++V D +  +  AL   
Sbjct: 125 GPTAATAAAIVAPW-CDAIDLNCGCPQRRVMADGLGAALLRNPEVVADTVRCVRNALEGG 183

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P  VK R+  D ++      +  +  + +G   I +H R       +P        +
Sbjct: 184 VELPCVVKMRVKDDVRLSV----DFARQCEAAGAAWITVHGRTPNCSAHAP--------V 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            +D +  I +E   + +  NGG+ D S AL+
Sbjct: 232 RFDAINTI-REALGVPVVANGGVRDPSTALQ 261


>gi|290474025|ref|YP_003466899.1| tRNA-dihydrouridine synthase C [Xenorhabdus bovienii SS-2004]
 gi|289173332|emb|CBJ80109.1| tRNA-dihydrouridine synthase C [Xenorhabdus bovienii SS-2004]
          Length = 313

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/175 (28%), Positives = 82/175 (46%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRVQLLGQYPEWLAENAVRAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYRGA 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G   + +H R       + +
Sbjct: 124 KAMRDAVPEELPVTVKVRLGWDSGDHQF---EIADAVQQAGATELVVHGR-------TKE 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D  K   +D+  + EI++      I  NG + D   A + +     D VMIGR A
Sbjct: 174 DGYKAERIDWQAIGEIRRRLAIPVIA-NGEIWDWHSAQECMKVTGCDAVMIGRGA 227


>gi|258404616|ref|YP_003197358.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
 gi|257796843|gb|ACV67780.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
          Length = 341

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/202 (28%), Positives = 96/202 (47%), Gaps = 12/202 (5%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           L +TEM  A A+L+ D +   +  F   E   L  QI G++   +  AA+ ++D G+  +
Sbjct: 49  LHWTEMCSASAVLQEDPRISPVFRFHRDELATLVCQIMGSEPETMAAAARRIQDEGFFGV 108

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GC  A V +   GA L+ +       + A+ +A+ IP+ VK R G  DQ P V   
Sbjct: 109 DINMGCCVAAVRQQGAGAALLRDISRAAAIVDAVRQAVDIPLFVKLRSGWTDQGPVVV-- 166

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  ++  K+G + + +H R      L+P D R  P    DI    +  +  +F   N   
Sbjct: 167 HAARACAKAGADALIVHPR------LAP-DRRTRPPQWRDIRAVCEAVDLPVFGNGNVFT 219

Query: 198 EDMSQALKILPSVDGVMIGRAA 219
            D + A+       G+ +GR A
Sbjct: 220 ADDATAMLRQTGCQGIALGRMA 241


>gi|183602388|ref|ZP_02963754.1| possible NifR3-like protein [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|219683297|ref|YP_002469680.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis AD011]
 gi|241191258|ref|YP_002968652.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis Bl-04]
 gi|241196664|ref|YP_002970219.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis DSM
           10140]
 gi|183218307|gb|EDT88952.1| possible NifR3-like protein [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|219620947|gb|ACL29104.1| possible NifR3-like protein [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249650|gb|ACS46590.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis Bl-04]
 gi|240251218|gb|ACS48157.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis DSM
           10140]
 gi|295794251|gb|ADG33786.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis V9]
          Length = 417

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 42/162 (25%), Positives = 79/162 (48%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EM+ A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 57  MAGVTNWPFRVLCEEYGPDGLYVAEMVTARALVERNPKALRLCRFAPSERIRSLQLYGVN 116

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            S + +AA+ + D G  + ++LN GCP  +V     G+ L    D+  + +    A+C+ 
Sbjct: 117 PSIMEQAARFLVDNGMMDHLDLNFGCPVPKVTRRGGGSALPWKTDLFTEIVQRVVAVCEP 176

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            +IPVT K R+G+D +          +  ++ G + + +HAR
Sbjct: 177 ANIPVTAKIRVGLDHE--HETFLEAGRIAQEEGCSAVTLHAR 216


>gi|261364482|ref|ZP_05977365.1| tRNA-dihydrouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288567413|gb|EFC88973.1| tRNA-dihydrouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 321

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 91/188 (48%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +
Sbjct: 64  PCTVQLLGSDADNMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIHHIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I + G   + +HAR  I +G  P 
Sbjct: 124 KTLRQRLPEHIPLTGKMRLGYEDKSLAL---ECAAAIAEGGACALTVHARTKI-EGYEPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
            +       ++ + +I +E+  + I  NG +  +     +K +   + VM+GR A     
Sbjct: 180 AH-------WEWIRKI-REHVAIPITANGDVFSLKDYIGIKEMTGCNSVMLGRGAVIRPD 231

Query: 225 MLTTVDEY 232
           +   + +Y
Sbjct: 232 LARQIKQY 239


>gi|290969239|ref|ZP_06560764.1| TIM-barrel protein, nifR3 family [Megasphaera genomosp. type_1 str.
           28L]
 gi|290780745|gb|EFD93348.1| TIM-barrel protein, nifR3 family [Megasphaera genomosp. type_1 str.
           28L]
          Length = 331

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 103/241 (42%), Gaps = 16/241 (6%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLV 63
           D  YR  A+     AL+ TEM+    ++   G  + +L  +  E PL+LQ+ GAD + + 
Sbjct: 30  DLPYRRIAKA-HGAALVCTEMVSDKGLVYHNGHTQEMLQIAKDEHPLSLQLFGADPASMA 88

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA   E+ G + +++N+GCP  +V     GA L+ +       I A+ +A+SIPVTVK 
Sbjct: 89  YAAAAAEEAGADLVDINMGCPVKKVVRNGAGAALLQDLPRAEAIIRAVVQAVSIPVTVKM 148

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G D                 +    +    R+A   G            D+ ++ +  
Sbjct: 149 RAGWDAAHVVAPALAERAEAAGAAAVAVHGRTREAFYSG----------KADWRVIADTV 198

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +      IG NG + D   A  +L       VM+ RAA  N  + + +  Y +     + 
Sbjct: 199 QAVSIPVIG-NGDVVDGPSARDMLQQTGCAAVMVARAAQGNPWIFSQITHYLTTGEMAAP 257

Query: 242 P 242
           P
Sbjct: 258 P 258


>gi|56412912|ref|YP_149987.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197361843|ref|YP_002141479.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56127169|gb|AAV76675.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197093319|emb|CAR58767.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 312

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 88/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA   +   D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMAISGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|222054277|ref|YP_002536639.1| dihydrouridine synthase DuS [Geobacter sp. FRC-32]
 gi|221563566|gb|ACM19538.1| dihydrouridine synthase DuS [Geobacter sp. FRC-32]
          Length = 306

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 108/229 (47%), Gaps = 25/229 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA------ILRGDKKNILGFSTQEKPLALQI 54
           M   T+R  R     L     ++TE I  +A      I  GD K  +  + ++ PL +Q+
Sbjct: 5   MQGVTNRAMRSLFIELVRPDTVFTEFIRVNAAAPVRRISAGDLKE-MAAAEKDVPLVVQL 63

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G     LV AA+  +  G   INLN+GCP  R+  G  G  L+ +P+++ + I ++ + 
Sbjct: 64  IGHGRDALVSAAEAAQATGAIHINLNMGCPYGRMTSGPTGGGLLRHPEVLSEIIPSLRRV 123

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIP 172
           +    ++K R G DD  P   LR L+   + + V+ + +H R  +   +GL+        
Sbjct: 124 IKGTFSLKMRAGYDD--PEQILR-LLPLFEAAKVDFLVLHPRTVLQQYQGLA-------- 172

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAA 219
             D+ I   + +E  ++ +  NG +   S  L++L      G+M+GR A
Sbjct: 173 --DHAITARVVRET-EIPVIANGDIRTASAGLQLLEETGAAGLMLGRGA 218


>gi|186682399|ref|YP_001865595.1| dihydrouridine synthase, DuS [Nostoc punctiforme PCC 73102]
 gi|186464851|gb|ACC80652.1| dihydrouridine synthase, DuS [Nostoc punctiforme PCC 73102]
          Length = 340

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 109/235 (46%), Gaps = 25/235 (10%)

Query: 38  KNILGFSTQE---KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           +NIL   T+    +P+  Q+ G  I  LV  A  +  +    ++LN+GCP+ R++  + G
Sbjct: 59  RNILAAITENDTGRPVFAQMIGESIPDLVRTAIDLCRYNIAGVDLNMGCPAPRIYRKNVG 118

Query: 95  ACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
             L+L+P+ V   +A + +A++  P+TVK R+G ++         ++  I +  ++ + +
Sbjct: 119 GGLLLSPEKVDRILAELRQAVNDRPLTVKMRVGFEN---TDNFYKILDIINRHNIDLLSL 175

Query: 154 HAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
           H R  K +  G           + YD++ E  +   D  +  NG +     A+++L    
Sbjct: 176 HGRTVKDMYHG----------AVRYDLIAEAVRR-VDCPVLANGNINSAKTAIEVLSQTG 224

Query: 212 --GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP---IKTRVDKDFWRKISASMTD 261
             GVM+GR A  N  +   + +          P   ++  +D+ +    +A+M +
Sbjct: 225 AAGVMVGRWAIGNPWIFNQIRQALRFEPIAPVPLVEVRNYIDRLWQTPTAATMPE 279


>gi|189203793|ref|XP_001938232.1| hypothetical protein PTRG_07900 [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187985331|gb|EDU50819.1| hypothetical protein PTRG_07900 [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 434

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 94/181 (51%), Gaps = 17/181 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    V+AAK+V       I++N GCP      G  GA L+  PD++ + + 
Sbjct: 107 LIYQIGTANPELAVQAAKMVA-ADVAGIDVNSGCPKPFSTSGGMGAALLKTPDLLCNILT 165

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++ + +  P    ++VK RI +D      A   LVK + ++G+ G+ +H R   ++   P
Sbjct: 166 SLVEEVGKPYEIGISVKIRI-LDTPEETAA---LVKRLVRTGITGLTVHCRTTPMR---P 218

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++ R I +    ++ EI +E   +   +NG +   ++ALK++   +VDG MI   A KN 
Sbjct: 219 RE-RAIRH-QLKMIGEICREA-GVACVMNGDVTSRTEALKLMEEFNVDGAMIATEAEKNP 275

Query: 224 A 224
           +
Sbjct: 276 S 276


>gi|224094282|ref|XP_002310123.1| predicted protein [Populus trichocarpa]
 gi|222853026|gb|EEE90573.1| predicted protein [Populus trichocarpa]
          Length = 358

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 105/232 (45%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 91  MVDNSELPFRMLCRKYGAEAA-YTPMLHSRIFSENEKYRREEFTTCKEDRPLFVQFCAND 149

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AA+ VE +  + +++N+GCP      G +GA LM N  +V   +  +   L++P
Sbjct: 150 PDILLQAARRVEPYC-DYVDINLGCPQRIARRGYYGAFLMDNLLLVKSLVEKLAINLNVP 208

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   ++D I      N  + ++++G + + +H R         KD +K    D+
Sbjct: 209 VSCKIRVFPKLEDTI------NYARMLEEAGCSLLAVHGRTR-----DEKDGKKF-RADW 256

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
             +  +K     + +  NG +  M      L     DGV+      +N A+ 
Sbjct: 257 KAIKAVKSAL-RIPVLANGNIRHMDDVKTCLEETGTDGVLSAETLLENPALF 307


>gi|222099569|ref|YP_002534137.1| TIM-barrel protein, nifR3 family [Thermotoga neapolitana DSM 4359]
 gi|221571959|gb|ACM22771.1| TIM-barrel protein, nifR3 family [Thermotoga neapolitana DSM 4359]
          Length = 273

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 60/263 (22%), Positives = 110/263 (41%), Gaps = 20/263 (7%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           ++  +K   L  S +EK +A+QI G+D  +L  AA ++ D  Y  I+LN GCP  +V + 
Sbjct: 8   LMNSEKTRELLPSPEEKNVAVQIFGSDPEELSRAADVLSD-EYPWIDLNAGCPVRKVVKK 66

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             G  L+ + D+    +  + K +    TVK R+G ++      +  + + + + GV+ +
Sbjct: 67  GAGGGLLRDLDLFRAVVKELRKHVKGKFTVKTRLGWNEN----QISKIYEILVEEGVDEV 122

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
           +IH R          D + +  LD  I        P    G     ED  +AL+      
Sbjct: 123 FIHTRTVAQAFTGKADWKSLSVLDKKI--------PTFVSGDIFSPEDAKRALE-ESGCH 173

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           GV++ R A     +   + ++       S P    + + F   +S  + D          
Sbjct: 174 GVLVARGAIGRPWLFKQIKDFLERG-KYSEPSTDEILRSFEMHLSLLVEDKGEEKA---- 228

Query: 272 KLQQITRHMIGLFHGFPNSRRCR 294
            +++I + + G       +RR R
Sbjct: 229 -IKEIKKFVAGYTKNLKGARRFR 250


>gi|308186130|ref|YP_003930261.1| tRNA-dihydrouridine synthase [Pantoea vagans C9-1]
 gi|308056640|gb|ADO08812.1| tRNA-dihydrouridine synthase [Pantoea vagans C9-1]
          Length = 316

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 91/191 (47%), Gaps = 16/191 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 67  MQLLGQHPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D    ++    +  +++++G + + +H R       + ++  
Sbjct: 127 REAVPADLPVTVKVRLGWDSSARSL---EIADAVQQAGASELTVHGR-------TKEEGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + +I++      I  NG + D   A   +     D VMIGR A  N   L+
Sbjct: 177 RAEAINWQAIGDIRQRLRIPVIA-NGEIWDWQSAQNCMAVTGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEYFSNPLT 238
            V +Y   P+ 
Sbjct: 235 RVVKYNEPPMA 245


>gi|58041830|gb|AAW63417.1| Orf2 [Klebsiella pneumoniae]
          Length = 312

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPTHLPVTVKVRLGWDS---GERRFEIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +D+  + EI ++   + +  NG + D   A   L +   D VMIGR A  N   L+
Sbjct: 177 KAERIDWQAIGEI-RQRLTIPVVANGEIWDWQSAQDCLAATGCDSVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|327265085|ref|XP_003217339.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Anolis
           carolinensis]
          Length = 485

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 82/168 (48%), Gaps = 14/168 (8%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + ++LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEIFVQAALLAQDYC-DAVDLNLGCPQMIAKRGHYGAFLQEEWDLLRRMIMLANEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKG 162
           S+P+T K R+      P +A      + ++++G   + +H R    KG
Sbjct: 141 SVPITCKIRV-----FPEIAKTVKYAQLLEEAGCQLLTVHGRTKEQKG 183


>gi|332525538|ref|ZP_08401693.1| NifR3 family TIM-barrel protein [Rubrivivax benzoatilyticus JA2]
 gi|332109103|gb|EGJ10026.1| NifR3 family TIM-barrel protein [Rubrivivax benzoatilyticus JA2]
          Length = 346

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 71/316 (22%), Positives = 129/316 (40%), Gaps = 32/316 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EMI +   LR  +K       + +  P+A+QI G +
Sbjct: 18  MAGVTDRAFRKLCKRL-GAGYAVSEMITSRPDLRDSRKTSRRADHTGEGAPIAVQIAGTE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
            + + +AA+   D G   +++N+GCP+ +V     G+ LM +  +   + + +   C   
Sbjct: 77  PAMMADAARHEIDRGAQIVDINMGCPAKKVCNKWAGSALMQDEALALSIVEAVVGACAPR 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG---IWIHARKAILKGLSPKDNRKIP 172
            +PVT+K R G        A RN ++  + +   G   + +H R         ++     
Sbjct: 137 GVPVTLKMRTGW-----CAAERNALRLARAAEAAGVAMVTVHGRT--------REQGYQG 183

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
             +YD +  +K     + +  NG ++  ++A  +L     D +MIGRAA     +   + 
Sbjct: 184 QAEYDTIAAVKAALA-IPVVANGDIDSPAKAAAVLARTGADALMIGRAAQGRPWIFREIA 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
            Y +     + P    V       +      YA    H+G  ++   +H+     G P  
Sbjct: 243 HYLATGTLLAPPATHEVRGWLLEHLE---EHYALYGEHAG--VRSARKHIGWAVRGLPGG 297

Query: 291 RRCRHILTV--EAGAS 304
              R  +    EAGA 
Sbjct: 298 EDFRAAMNTIAEAGAQ 313


>gi|261219467|ref|ZP_05933748.1| nifR3 family TIM-barrel protein [Brucella ceti M13/05/1]
 gi|261321963|ref|ZP_05961160.1| nifR3 family TIM-barrel protein [Brucella ceti M644/93/1]
 gi|260924556|gb|EEX91124.1| nifR3 family TIM-barrel protein [Brucella ceti M13/05/1]
 gi|261294653|gb|EEX98149.1| nifR3 family TIM-barrel protein [Brucella ceti M644/93/1]
          Length = 171

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 62/110 (56%), Gaps = 1/110 (0%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ +EM+ +  +    ++++L  S +      +Q+ G +   + EAAKI E  G + I++
Sbjct: 43  MVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREARWMGEAAKIAEGEGADIIDI 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
           N+GCP+ +V  G  G+ LM N D     + A   A+ +PVT+K R+G D+
Sbjct: 103 NMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPVTLKMRLGWDE 152


>gi|159116295|ref|XP_001708369.1| Embryo-related protein [Giardia lamblia ATCC 50803]
 gi|157436480|gb|EDO80695.1| Embryo-related protein [Giardia lamblia ATCC 50803]
          Length = 406

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 102/232 (43%), Gaps = 34/232 (14%)

Query: 23  YTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE---- 76
           +T+M  ADA+L     +  +L  +   + + LQ+ G + S    AA+++ D         
Sbjct: 86  FTQMYTADALLHNSPLRDAVLSTAAPGEKIILQLCGNNPSTFRAAAELLHDSPIASQLVA 145

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAV 134
           +++N+GCP++      +G  +  N  +V   I+    A   PVT K R    ++  I  +
Sbjct: 146 LDINLGCPASCASSKGYGFYVAQNWPLVHQIISETSSARLFPVTCKIRPLNSIEKTIDYM 205

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV--------------- 179
            L      +  SG +GI IH R    +G   +  R       ++V               
Sbjct: 206 VL------LVMSGASGITIHMRHTTRQGKHAQAVRPAYQEFEELVRAFRQRLDTLFTGLG 259

Query: 180 -YEIKKENPDLF--IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
             E  +ENP ++  I LNGG+++  +A  +L +   DGVM+G    KN A L
Sbjct: 260 GSETAQENPHVYPVIILNGGIKNRQEADHLLATYPADGVMLGVGLLKNPACL 311


>gi|94987210|ref|YP_595143.1| tRNA-dihydrouridine synthase [Lawsonia intracellularis PHE/MN1-00]
 gi|94731459|emb|CAJ54822.1| tRNA-dihydrouridine synthase [Lawsonia intracellularis PHE/MN1-00]
          Length = 330

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 107/229 (46%), Gaps = 17/229 (7%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISK 61
           W+D  +R   R     A+ YTEMI A  ++  +   +++L    ++ PL +Q+ G++ S 
Sbjct: 22  WSDLPFRLLCRE-HGAAVCYTEMISAKGLIYNNPGTESLLKTIPEDNPLIVQLCGSEASC 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVT 120
           + +A  I+ + GY   + N+GC   ++     GA +M N D       AM   ++   + 
Sbjct: 81  MKDALTILLEKGYKWFDCNMGCSVPKITRTGSGASMMKNIDNSIKIAEAMIHTVNKKSIG 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+G D++     +  L K ++++G   I +H R A  +G +   N       ++ + 
Sbjct: 141 FKLRLGWDEKHETWPI--LAKLLEEAGAGWITLHPRTA-QQGFTGTAN-------WEKLL 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           E+K++     I  +G L   S  +  +    VD VM  R A K+  + T
Sbjct: 191 ELKQQVKIPVIA-SGDLLTASHGVDCIKKTHVDTVMYARGALKDPNIFT 238


>gi|289177373|gb|ADC84619.1| tRNA-dihydrouridine synthase [Bifidobacterium animalis subsp.
           lactis BB-12]
          Length = 502

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 42/162 (25%), Positives = 79/162 (48%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EM+ A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 142 MAGVTNWPFRVLCEEYGPDGLYVAEMVTARALVERNPKALRLCRFAPSERIRSLQLYGVN 201

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            S + +AA+ + D G  + ++LN GCP  +V     G+ L    D+  + +    A+C+ 
Sbjct: 202 PSIMEQAARFLVDNGMMDHLDLNFGCPVPKVTRRGGGSALPWKTDLFTEIVQRVVAVCEP 261

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            +IPVT K R+G+D +          +  ++ G + + +HAR
Sbjct: 262 ANIPVTAKIRVGLDHE--HETFLEAGRIAQEEGCSAVTLHAR 301


>gi|225351461|ref|ZP_03742484.1| hypothetical protein BIFPSEUDO_03056 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157805|gb|EEG71088.1| hypothetical protein BIFPSEUDO_03056 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 409

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 102/242 (42%), Gaps = 19/242 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCHFAPSEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I     +C A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +         +   ++ G   + +HAR          D  +I  L
Sbjct: 169 ANVPVTAKIRVGIDHEHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 226

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
                     E  D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 227 ---------VEALDIPVFGNGDIWGANDALAMVAETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FS 234
           F+
Sbjct: 278 FA 279


>gi|159465759|ref|XP_001691090.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158279776|gb|EDP05536.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 336

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 85/189 (44%), Gaps = 18/189 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           MVD ++  +R   R        YT M+ A  I   DKK      +L   T+++PL +Q  
Sbjct: 52  MVDQSELPFRMLCRN-HGATCAYTPMLHAR-IFTQDKKYRCAAEMLTTCTEDRPLFVQFC 109

Query: 56  GADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
             +   L++AA++VE  G  + I++N GCP      G +GA LM +   V   +  + + 
Sbjct: 110 SNEPQHLLKAARMVEAMGICDAIDINFGCPQRIAKRGGYGAFLMDDLPKVEAMVRGLAQG 169

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L IPVT K RI  D            + ++++G   + +H R    K LS          
Sbjct: 170 LRIPVTAKIRIFPD----LAKTVEYARMVERAGAWLVAVHGRLREQKDLSAT------RA 219

Query: 175 DYDIVYEIK 183
           D+D +  +K
Sbjct: 220 DWDAIRAVK 228


>gi|145631054|ref|ZP_01786829.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           R3021]
 gi|144983339|gb|EDJ90821.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           R3021]
          Length = 310

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 100/226 (44%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G     L E A    D G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQHPEYLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   A  + +   ++++ G   I +H R   
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDDISQAFEIAD---AVEQGGATEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + ++ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKTDGYRADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  WR+I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWREIQKILQKYA 257


>gi|126176129|ref|YP_001052278.1| nifR3 family TIM-barrel protein [Shewanella baltica OS155]
 gi|153002467|ref|YP_001368148.1| nifR3 family TIM-barrel protein [Shewanella baltica OS185]
 gi|160877184|ref|YP_001556500.1| NifR3 family TIM-barrel protein [Shewanella baltica OS195]
 gi|217975034|ref|YP_002359785.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS223]
 gi|304412483|ref|ZP_07394089.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS183]
 gi|307307142|ref|ZP_07586880.1| TIM-barrel protein, nifR3 family [Shewanella baltica BA175]
 gi|125999334|gb|ABN63409.1| putative TIM-barrel protein, nifR3 family [Shewanella baltica
           OS155]
 gi|151367085|gb|ABS10085.1| putative TIM-barrel protein, nifR3 family [Shewanella baltica
           OS185]
 gi|160862706|gb|ABX51240.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS195]
 gi|217500169|gb|ACK48362.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS223]
 gi|304349125|gb|EFM13537.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS183]
 gi|306910381|gb|EFN40812.1| TIM-barrel protein, nifR3 family [Shewanella baltica BA175]
 gi|315269388|gb|ADT96241.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS678]
          Length = 322

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 118/246 (47%), Gaps = 32/246 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK +  +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLC-LRYGAALAVSEMLSSNPEVWDTDKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA    + G + I++N+GCP+ +V++   G+ LM NP +V + + A+  A+++P
Sbjct: 76  PDLMAQAALFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKEILQAVVAAVNVP 135

Query: 119 VTVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRK 170
           VT+K R G +       QI  +A        +  G+  + +H   R+ + +G        
Sbjct: 136 VTLKIRTGWEPEHKNGVQIAQIA--------QDCGIASLAVHGRTRQCMYRG-------- 179

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
             + +YD +  I K+N  + +  NG ++   +A  +L     D +MIGR A     +   
Sbjct: 180 --DAEYDTIKAI-KQNVSIPVVANGDIDSPEKARFVLEYTGADALMIGRGAQGRPWIFRE 236

Query: 229 VDEYFS 234
           +  Y  
Sbjct: 237 IQHYLE 242


>gi|195352556|ref|XP_002042778.1| GM17665 [Drosophila sechellia]
 gi|194126809|gb|EDW48852.1| GM17665 [Drosophila sechellia]
          Length = 473

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 88/186 (47%), Gaps = 21/186 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G +D  + +    +++    + +++N+GCP     +G  GA L+ +PD   + + 
Sbjct: 97  LVLQMGTSDARRALAVGMLLQR-DISGLDINMGCPKEFSIKGGMGAALLADPDKAANILR 155

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +C  L IPVT K RI     +P V    +LV+ +  +G+  I IHAR         +D 
Sbjct: 156 TLCSGLDIPVTCKIRI-----LPDVERTIDLVQKLAATGIAAIGIHART--------RDE 202

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNS 223
           R       +++  + +   D+ I  NGG ++M      +  ++      VM+ RAA  N 
Sbjct: 203 RPQHPAHPEVLRAVAQAV-DIPIIANGGSKNMHCYEDLRKFQLECGAASVMVARAAQINV 261

Query: 224 AMLTTV 229
           ++   V
Sbjct: 262 SIFRPV 267


>gi|317025631|ref|XP_001389487.2| dihydrouridine synthase family protein [Aspergillus niger CBS
           513.88]
          Length = 542

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 59/215 (27%), Positives = 91/215 (42%), Gaps = 26/215 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++PL +Q    D    +EAA+ V  +  + ++LN+GCP      G +GA L  + 
Sbjct: 116 GNPSFDRPLFVQFCANDPDDFLEAARHVAPYC-DAVDLNLGCPQGIAKRGHYGAFLQEDW 174

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++   I  +   LSIPVT K RI    Q          K I  +G N I +H R+   K
Sbjct: 175 DLIYRLINRLHNELSIPVTAKFRI----QETKEKTLEYAKMILSAGANIITVHGRRREQK 230

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRA 218
           G     N  + +  Y I Y      P+  I  NG     ED+ + L+     DGVM    
Sbjct: 231 G----HNTGLADWSY-IRYLRDNLPPETVIFANGNNLNYEDLDRCLEET-GADGVMSAEG 284

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
              + ++ +        P  GS        +++WR
Sbjct: 285 NLSDPSIFS------KPPPVGSE------GREYWR 307


>gi|156933286|ref|YP_001437202.1| tRNA-dihydrouridine synthase C [Cronobacter sakazakii ATCC BAA-894]
 gi|156531540|gb|ABU76366.1| hypothetical protein ESA_01098 [Cronobacter sakazakii ATCC BAA-894]
          Length = 310

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 67  VQLLGQHPQWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDS---GARRFEIADAVQQAGATELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI +E   + +  NG + D + A   +     D +MIGR A  N   L+
Sbjct: 177 KAERINWAAIGEI-RERLTIPVIANGEIWDYASAQACMAETGCDAIMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|226364360|ref|YP_002782142.1| tRNA-dihydrouridine synthase [Rhodococcus opacus B4]
 gi|226242849|dbj|BAH53197.1| putative tRNA-dihydrouridine synthase [Rhodococcus opacus B4]
          Length = 380

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 72/309 (23%), Positives = 122/309 (39%), Gaps = 31/309 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L      + + L   EM+ A A++       ++  F   E P +L
Sbjct: 20  MAGITNVAFRTLCRELETERAGSTSGLYVCEMVTARALVERQPATLHMTTFGPTETPRSL 79

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK IV++   + I++N GCP  +V     GA L     + G  +AA 
Sbjct: 80  QLYTVDPDTTYAAAKMIVDENMADHIDMNFGCPVPKVTRKGGGAALPYKRTLFGRIVAAA 139

Query: 112 CKALS---IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            KA     +PVTVK R+G+D D    +   +  +     G   + +HAR A         
Sbjct: 140 VKATEGTDVPVTVKFRVGIDADHHTHL---DAGRIAAGEGAAAVALHARTA--------S 188

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAM 225
            R     D++ +  +K+   D+ +  NG +     A +++     DGV++GR       +
Sbjct: 189 QRYSGTADWNEIARLKEHVTDVPVLGNGDIFAAEDAARMMEQTGCDGVVVGRGCLGRPWL 248

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +    +     + P    V     R       +  A H      L+++ +H+     
Sbjct: 249 FAELSAALNGKPQPTPPNLGEVATIIRRH-----AELLADHHGEDKGLRELRKHVSWYLR 303

Query: 286 GFPNSRRCR 294
           GFP     R
Sbjct: 304 GFPAGSELR 312


>gi|134055604|emb|CAK37250.1| unnamed protein product [Aspergillus niger]
          Length = 466

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 95/225 (42%), Gaps = 22/225 (9%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILR--GDKKNIL-GFSTQEKPLAL 52
           MVD ++  +R   R           L Y+ M  A        D+   L G  + ++PL +
Sbjct: 50  MVDRSEFAWRMLTRSFMTPEDQKKVLAYSPMYHARLFREQANDESPYLDGNPSFDRPLFV 109

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q    D    +EAA+ V  +  + ++LN+GCP      G +GA L  + D++   I  + 
Sbjct: 110 QFCANDPDDFLEAARHVAPY-CDAVDLNLGCPQGIAKRGHYGAFLQEDWDLIYRLINRLH 168

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             LSIPVT K RI    Q          K I  +G N I +H R+   KG     N  + 
Sbjct: 169 NELSIPVTAKFRI----QETKEKTLEYAKMILSAGANIITVHGRRREQKG----HNTGLA 220

Query: 173 NLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVM 214
           +  Y I Y      P+  I  NG     ED+ + L+     DGVM
Sbjct: 221 DWSY-IRYLRDNLPPETVIFANGNNLNYEDLDRCLEET-GADGVM 263


>gi|329114574|ref|ZP_08243333.1| Putative tRNA-dihydrouridine synthase [Acetobacter pomorum DM001]
 gi|326696054|gb|EGE47736.1| Putative tRNA-dihydrouridine synthase [Acetobacter pomorum DM001]
          Length = 356

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 111/233 (47%), Gaps = 23/233 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGADISKL 62
           TD  +R  AR L    L+ +EMI + A++R +   +      +   P A+Q+ G D   +
Sbjct: 30  TDLPFRRLARKL-GAGLVVSEMIASWAMVRENDTTLRMAEVADAGGPNAVQLAGCDPDAM 88

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSIPVTV 121
            EAA+I    G + I++N GCP  +V  G   G+ LM +       +AA+ KA+ +PVT+
Sbjct: 89  AEAARIAVGRGADLIDINFGCPVKKVAVGQMAGSALMRDEGAAERLLAAVVKAVPVPVTL 148

Query: 122 KCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDI 178
           K R+G D + + A  L  + + +   G+  I +H   R+    G +          ++  
Sbjct: 149 KMRMGWDHEHLNAPVLARIAQDV---GIRMITVHGRTRQQFYNGTA----------NWAF 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           V  + K+  DL + +NG +  +  A + L     DGVMIGR  Y     L  V
Sbjct: 196 VKNV-KDAVDLPVIVNGDILTVGDAREALAQSGADGVMIGRGCYGRPWFLAQV 247


>gi|15642871|ref|NP_227912.1| hypothetical protein TM0096 [Thermotoga maritima MSB8]
 gi|4980586|gb|AAD35190.1|AE001696_4 conserved hypothetical protein [Thermotoga maritima MSB8]
          Length = 306

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 67/302 (22%), Positives = 132/302 (43%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M  +TD  +R  A         ++EM+ A   L   +K   L     E+ +A+QI G++ 
Sbjct: 10  MAGYTDSAFRTLA-FEWGADFAFSEMVSAKGFLMNSQKTEELLPQPHERNVAVQIFGSEP 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   
Sbjct: 69  NELSEAARILSE-KYKWIDLNAGCPVRKVVKKGAGGALLKDLRHFRYIVRELRKSVSGKF 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +        R LV    + GV+ ++IH R  +++  + +   K  ++     
Sbjct: 128 SVKTRLGWEKNEVEEIYRILV----EEGVDEVFIHTR-TVVQSFTGRAEWKALSV----- 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             ++K  P    G     ED  +AL+     DG+++ R A     +   + ++  +    
Sbjct: 178 --LEKRIPTFVSGDIFTPEDAKRALE-ESGCDGLLVARGAIGRPWIFKQIKDFLRSG-KY 233

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH-ILT 298
           S P +  + + F R +   +     R       + ++ + + G       +RR R  ++ 
Sbjct: 234 SEPSREEILRTFERHLELLIKTKGERKA-----VVEMRKFLAGYTKDLKGARRFREKVMK 288

Query: 299 VE 300
           +E
Sbjct: 289 IE 290


>gi|333002068|gb|EGK21634.1| dihydrouridine synthase family protein [Shigella flexneri K-218]
          Length = 315

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A+ N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISDCDAVMIGRGAF-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|221121780|ref|XP_002165230.1| PREDICTED: similar to tRNA-dihydrouridine synthase 2-like, partial
           [Hydra magnipapillata]
          Length = 246

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 82/184 (44%), Gaps = 23/184 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G  +  + +  A+++E    + I++N+GCP     +G  GA L+  PD V   + 
Sbjct: 79  LVFQMGTNNAERALSVAQMLEK-DIDGIDINMGCPKEFSVKGGMGAALLTQPDKVKQILT 137

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + + LSIPVT K RI   + D I       L K I+ +GV  I IH R    +  SP  
Sbjct: 138 GLVQNLSIPVTCKIRILPQLSDTI------ELAKLIEATGVKAIAIHGRTKDERSSSPCH 191

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKN 222
           N  I  +          +  ++ +  NGG +D+     I           VMI R+A  N
Sbjct: 192 NDYIKAV---------ADAVNIPVIANGGSQDIKTYFNIAKFKEETGCSSVMIARSAQWN 242

Query: 223 SAML 226
            ++ 
Sbjct: 243 PSVF 246


>gi|332754772|gb|EGJ85137.1| dihydrouridine synthase family protein [Shigella flexneri 4343-70]
          Length = 315

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A+ N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISDCDAVMIGRGAF-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|312882490|ref|ZP_07742231.1| tRNA-dihydrouridine synthase C [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309369890|gb|EFP97401.1| tRNA-dihydrouridine synthase C [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 317

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 85/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D + + E A      G   I++N GCP+  V++   GA L+ +PD++   +
Sbjct: 64  PVHIQLLGQDPNWMAENAVKAATLGAKGIDINFGCPAKLVNKSKGGAALLRHPDVIYQVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+  S PV+ K R+G +D  P      +V +I+ +G N + +HAR       +  
Sbjct: 124 KACREAVPSSTPVSAKIRLGWED--PEDCF-EIVDAIQSAGANELTVHAR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAY 220
              K   + +D + +I++      I  NG + +    Q    L   D +M+ R A+
Sbjct: 174 GGYKASEIKWDYIRQIRQRFSIPVIA-NGEIWNHQDGQDCMSLTGADSLMVCRGAF 228


>gi|302916105|ref|XP_003051863.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256732802|gb|EEU46150.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 509

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 85/182 (46%), Gaps = 26/182 (14%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVA--------------DAILRGDKKNIL 41
           MVD ++  +R   R        ++ L YT M+ A               A+   +   + 
Sbjct: 36  MVDQSEFAWRMLTRSFLSPTEQSSLLAYTPMLHARLFSQDEKYRQAHFQAVRSNEDPWLD 95

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  + 
Sbjct: 96  GNPSIDRPLFVQFCANDPDALLAAAKQVAPY-CDAVDLNLGCPQGIARKGKYGAFLQEDQ 154

Query: 102 DIVGDCIAAMCKALSIPVTVKCRI-GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           D++   I  + K L +PVT K RI   ++Q  A A     +++ K+G + + +H R+   
Sbjct: 155 DLIFRLINILHKELPVPVTAKIRILETEEQTLAYA-----QNVLKAGASILTVHGRRREQ 209

Query: 161 KG 162
           KG
Sbjct: 210 KG 211


>gi|227541059|ref|ZP_03971108.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227183319|gb|EEI64291.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 405

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 97/207 (46%), Gaps = 19/207 (9%)

Query: 19  NALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYN 75
           + L   EM+ A A++  + K +    FS+ E+P +LQ+   D     +AAK I E+   +
Sbjct: 77  SGLYVCEMVTARALVERNVKTLHMAAFSSVEEPRSLQLYTTDPEYTYKAAKMIAEENLAD 136

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIP 132
            +++N GCP  +V     GA L    ++    + A  + +S   IPVTVK RIG+D +  
Sbjct: 137 HLDMNFGCPVPKVTRKGGGAALPYKRELFKRIVDAAVRGVSGTDIPVTVKFRIGIDAE-- 194

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
              + +  +  ++ G   + +HAR A          R      ++ + E+K+   D+ + 
Sbjct: 195 HETMLDAGRIAQEEGAAAVTLHARTAA--------ERYSGQAHWERIAELKQAL-DVPVF 245

Query: 193 LNGGLEDMSQALKILPSV--DGVMIGR 217
            NG +   +  L +      DG+ IGR
Sbjct: 246 GNGDVFSAADGLAMFEQTGCDGIEIGR 272


>gi|326435349|gb|EGD80919.1| DUS4L protein [Salpingoeca sp. ATCC 50818]
          Length = 558

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/164 (28%), Positives = 81/164 (49%), Gaps = 18/164 (10%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +T MIV+D+ ++  +     F  STQ++P+  Q   A+      AA ++  +  + I+LN
Sbjct: 52  FTPMIVSDSFVQSWRAREADFATSTQDEPVVAQFAAANARDFAHAAALMAPYA-DAIDLN 110

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNL 139
            GCP     +   G+ L+  P++V D +    +ALS IPV++K R+    +        L
Sbjct: 111 CGCPQKWAMQDGLGSHLVSKPELVADMV-KQARALSGIPVSIKIRL----RNTTAETVEL 165

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
            +  ++ G   I +H R       SPK+ R+ P + YD +  +K
Sbjct: 166 CRRAEQMGAAWISVHGR-------SPKE-RRCP-VHYDEIAAVK 200


>gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or NifR3-like protein [Herbaspirillum
           seropedicae SmR1]
 gi|300072539|gb|ADJ61938.1| tRNA-dihydrouridine synthase protein or NifR3-like protein
           [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 63/253 (24%), Positives = 113/253 (44%), Gaps = 16/253 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  +D  L   +K    +    + +P A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMAASDPRLWQSEKTSRRINHDGEMEPKAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L + AK   + G   I++N+GCP  +V     G+ L+ + ++V   + A+  A+ +P
Sbjct: 76  PVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +      A +N +K   ++   GI +      L G +  D       +Y+ 
Sbjct: 136 VTLKFRTGWNR-----ANKNALKIAARAEAAGIAM----LTLHGRTRADGYS-GEAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +  L   D VM+GRAA     +   +D +    
Sbjct: 186 IAAVKAA-VKIPVVANGDITTPEKARDVLLLTKADAVMVGRAAQGRPWIFREIDHFLRTG 244

Query: 237 LTGSSPIKTRVDK 249
               +P+ + V++
Sbjct: 245 EHLPAPLVSEVEQ 257


>gi|189208310|ref|XP_001940488.1| tRNA-dihydrouridine synthase C [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187976581|gb|EDU43207.1| tRNA-dihydrouridine synthase C [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 801

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 90/186 (48%), Gaps = 16/186 (8%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR   +++ G    ++PL +Q    D    + AAK V  F  + ++LN+GCP      G 
Sbjct: 118 LRDSDRHLDGNPVFDRPLTVQFCSNDPDDFLRAAKHVAPF-CDAVDLNLGCPQGIAKRGK 176

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L  + D++   I  + + L +PVT K R+    + P   L    K++  +G + I 
Sbjct: 177 YGAFLQEDWDLISRMIRKLHEELDVPVTAKMRVL---ETPEKTL-AYAKTLLDAGASIIT 232

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILP 208
           +H R+   KG     N  +   D+ ++  +++  P +  I  NG +   ED+++ L+   
Sbjct: 233 VHGRRREQKG----HNTGL--ADWKMIRHLRENLPKETVIFANGNILQHEDIAKCLEAT- 285

Query: 209 SVDGVM 214
             DGVM
Sbjct: 286 GADGVM 291


>gi|149377033|ref|ZP_01894784.1| Dihydrouridine synthase, DuS [Marinobacter algicola DG893]
 gi|149358691|gb|EDM47162.1| Dihydrouridine synthase, DuS [Marinobacter algicola DG893]
          Length = 314

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 50/174 (28%), Positives = 88/174 (50%), Gaps = 18/174 (10%)

Query: 49  PLALQIGGADISKL-VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+A+Q+ G+D  ++    AK VE  G  ++++N GCP+  V++   G  LM  P+++   
Sbjct: 57  PVAVQLLGSDPVQMGRHGAKAVE-LGATQVDINFGCPAKTVNKHKGGCVLMREPELMQQI 115

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             A+  A+   +PVT K R+G DD+   VA     ++++ +G + I +HAR  +      
Sbjct: 116 TEAVRAAVPAHVPVTAKMRLGYDDRSMGVACG---QALEAAGASEIVVHARSKV------ 166

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
            D  K P    D+     +E  D  + +NG +  ++   +   +   D VMIGR
Sbjct: 167 -DGYKPPAYWEDVAR--VREAVDAHVIVNGEIWTVADYWRCREVSGCDDVMIGR 217


>gi|299742242|ref|XP_001832336.2| t-diRNAhydrouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|298405094|gb|EAU89497.2| t-diRNAhydrouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 349

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 105/233 (45%), Gaps = 24/233 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFST-QEKPLALQ 53
           MV+ +D  +R         +  YT+M++ + +L   +      +++  F+  + +P+ +Q
Sbjct: 1   MVNQSDLPFRLLVEQYGATST-YTQMLLPEKLLNDQEYLEFHLRDLQTFAKLKTRPVVVQ 59

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCIAAM 111
           +GG D   +V+A + ++ +  + I+LN+GCP     +  +GA L+   D  +V   +++M
Sbjct: 60  LGGNDPDLVVQAGRKMQQW-CDGIDLNLGCPQEAARDAHYGAYLLGQRDWPLVEQIVSSM 118

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             + ++P + K R+      P        + ++  G + I +HAR    +       R+ 
Sbjct: 119 ATSFTVPCSAKIRLCQ----PVGKTSEFSQRLEAQGASWITLHARTVSAR------RRRQ 168

Query: 172 PNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
              D  IV E+K     P +  G      D+   L      DG+M+G A   N
Sbjct: 169 GAADLSIVQELKSSLRVPVISNGNVRAFPDLQVNLDYT-GADGLMVGEALLDN 220


>gi|170759302|ref|YP_001786033.1| dihydrouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
 gi|169406291|gb|ACA54702.1| dihydrouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
          Length = 312

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/232 (23%), Positives = 98/232 (42%), Gaps = 17/232 (7%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GY+EINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFIITARKLQQLGYDEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           K   + +++K RIG D          L+K   K  +  + IH R    K     +    P
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPRTQ--KDFYGNE----P 174

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           NLD          NP  + G    + D ++ +K  P V  +M+GR    N  ++      
Sbjct: 175 NLDVFKDALSLSSNPICYNGDIFTISDYNRLIKTFPKVKTIMLGRGILANPGLI------ 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             N +  ++ I   V K+F  +I     +      ++  K++++  +MI  F
Sbjct: 229 --NEMKNNTNIDKEVLKEFHDEILNKYIELYNEDRNALFKMKELWGYMIYTF 278


>gi|322701013|gb|EFY92764.1| tRNA dihydrouridine synthase (Smm1), putative [Metarhizium acridum
           CQMa 102]
          Length = 413

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 88/183 (48%), Gaps = 21/183 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + VEAA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 104 LIFQIGTADPDRAVEAARLVA-ADVAGIDVNAGCPKPFSTSGGMGAALLRTPDKLVAILE 162

Query: 110 AMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K ++    I ++VK RI    + PA     LV+ +  +G+ G+ +H R   ++   P
Sbjct: 163 ALVKNITPEFDIGISVKIRI---LETPA-ETEALVRRLVATGITGLTVHCRTTPMR---P 215

Query: 166 KDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++   R    +  +I +E       +   +NG +E+  Q LK+      DG MI  AA K
Sbjct: 216 RERAIRDQLRMVANICHEA-----GVACIMNGDVENRDQGLKLAEKYGADGAMIAVAAEK 270

Query: 222 NSA 224
           N +
Sbjct: 271 NPS 273


>gi|330925066|ref|XP_003300902.1| hypothetical protein PTT_12265 [Pyrenophora teres f. teres 0-1]
 gi|311324785|gb|EFQ91034.1| hypothetical protein PTT_12265 [Pyrenophora teres f. teres 0-1]
          Length = 473

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 94/181 (51%), Gaps = 17/181 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    V+AAK+V       I++N GCP      G  GA L+  PD++ + + 
Sbjct: 107 LIYQIGTANPELAVQAAKMVA-ADVAGIDVNSGCPKPFSTSGGMGAALLKTPDLLCNILT 165

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++ + +  P    ++VK RI +D      A   LVK + ++G+ G+ +H R   ++   P
Sbjct: 166 SLVEEVGKPYEIGISVKIRI-LDTPEETAA---LVKRLVRTGITGLTVHCRTTPMR---P 218

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++ R I +    ++ EI +E   +   +NG +   ++ALK++   +VDG MI   A KN 
Sbjct: 219 RE-RAIRH-QLKMIGEICREA-GVACVMNGDVTSRTEALKLMEEFNVDGAMIATEAEKNP 275

Query: 224 A 224
           +
Sbjct: 276 S 276


>gi|296103788|ref|YP_003613934.1| tRNA-dihydrouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295058247|gb|ADF62985.1| tRNA-dihydrouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 310

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKVRLGWDSDARQF---EIADAVQQAGATELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI+K      I  NG + D   A   L +   + VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEIRKRLSIPVIA-NGEIWDYQSAQACLKATGCEAVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|242003652|ref|XP_002422814.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212505672|gb|EEB10076.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 540

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 41/164 (25%), Positives = 82/164 (50%), Gaps = 8/164 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  +      ++    G ++  +++PL +Q  G +
Sbjct: 19  MVDASELAWRLLSRR-HGAQLCYTPMFHSLIFANNERYRKEGLASVPEDRPLIVQFCGNE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +++AA++ E +  + +++N+GCP A    G +GA L  +  ++ + +  + K+L IP
Sbjct: 78  PDSILKAAQLAEPYC-DAVDINLGCPQAIAKRGHYGAFLQDDWPLLKEIVGTLKKSLKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           VT K R+  D +          K ++++G   + +H R    KG
Sbjct: 137 VTCKIRVFEDVKKTV----KYAKMLEEAGCQLLTVHGRTKEQKG 176


>gi|59712245|ref|YP_205021.1| tRNA-dihydrouridine synthase C [Vibrio fischeri ES114]
 gi|59480346|gb|AAW86133.1| tRNA-dihydrouridine synthase C [Vibrio fischeri ES114]
          Length = 315

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 90/176 (51%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G + + + E A    + G + I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PIRLQLLGQEPNWMAENAARAIELGSDGIDLNFGCPAKAVNKSRGGAALLKEPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+S    VT K R+G ++      + +   +IK++G + + IHAR  +       
Sbjct: 124 KACRDAVSKDKKVTAKIRLGWENPEECFVIAD---AIKQAGADELTIHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           D  K   + +D + +++++  D+ I  NG + +     + + +  +D +M+ R A+
Sbjct: 174 DGYKAEEIKWDYINQVRQK-IDIPIIANGEIWNYDDGQRCIAATGIDSLMVCRGAF 228


>gi|197336215|ref|YP_002156459.1| tRNA-dihydrouridine synthase C [Vibrio fischeri MJ11]
 gi|197317705|gb|ACH67152.1| tRNA-dihydrouridine synthase C [Vibrio fischeri MJ11]
          Length = 315

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 90/176 (51%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G + + + E A    + G + I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PIRLQLLGQEPNWMAENAARAIELGSDGIDLNFGCPAKAVNKSRGGAALLKEPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+S    VT K R+G ++      + +   +IK++G + + IHAR  +       
Sbjct: 124 KACRDAVSKDKKVTAKIRLGWENPEECFVIAD---AIKQAGADELTIHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           D  K   + +D + +++++  D+ I  NG + +     + + +  +D +M+ R A+
Sbjct: 174 DGYKAEEIKWDYINQVRQK-IDIPIIANGEIWNYDDGQRCIAATGIDSLMVCRGAF 228


>gi|3046395|gb|AAC38320.1| unknown [Ralstonia eutropha H16]
          Length = 322

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 105/237 (44%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+ NP
Sbjct: 58  GYTRSGTPMVIQLLGSDPEWLARNAAYAATLSPHGIDLNFGCPAKVVNRHGGGAMLLTNP 117

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   +A++  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 ELLNRIVASVRAAVPAHIAVTAKMRLGVSDASLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                 +D+   P   +D +  I     D+ +  NG +  ++  +  + +     VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIAAAV-DVPVIANGDVWTVADWERCRAVSGCADVMIGR 225

Query: 218 AAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +      +P     P+  R    + +K+ A +   A+ H H   KL
Sbjct: 226 GAVSDPFLALRIRGLMDGSPSDQEWPLVLRQIATYLKKLHARI---ASCHEHGRVKL 279


>gi|146277526|ref|YP_001167685.1| nifR3 family TIM-barrel protein [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555767|gb|ABP70380.1| putative TIM-barrel protein, nifR3 family [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 326

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 50/150 (33%), Positives = 77/150 (51%), Gaps = 12/150 (8%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           RF A L+ +  +   EM+ A    R   +        E   A+Q+ G D   + EAA++V
Sbjct: 33  RFGAGLVVSEMVASREMVCAGTEARARAE----IGAAEGRTAVQLAGCDPHWMAEAARLV 88

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
           E  G   I++N+GCP+ RV  G  G+ LM  PD     + A+  A+++PVT+K R+G D+
Sbjct: 89  EAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALVEAVVAAVTVPVTLKMRLGWDE 148

Query: 130 QI---PAVALRNLVKSIKKSGVNGIWIHAR 156
            +   P +A R      + +GV  I IH R
Sbjct: 149 GMLNAPEIARRA-----EAAGVAMITIHGR 173


>gi|261253437|ref|ZP_05946010.1| tRNA-dihydrouridine synthase C [Vibrio orientalis CIP 102891]
 gi|260936828|gb|EEX92817.1| tRNA-dihydrouridine synthase C [Vibrio orientalis CIP 102891]
          Length = 317

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 85/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++ + +
Sbjct: 64  PVHIQLLGQDPKWMAENAIRAAELGARGIDLNFGCPAKLVNKSKGGAALLQHPELIHNVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+    PVT K R+G ++         +V +I+ +G N + +HAR       +  
Sbjct: 124 KACREAVPQGTPVTAKIRLGWENPDDCF---EIVDAIQSAGANELTVHAR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAY 220
              K   + +D + +I++      I  NG + +    QA      VD +M+ R A+
Sbjct: 174 GGYKASEIKWDYINQIRQRFSIPLIA-NGEIWNYQDGQACIETTGVDSLMVCRGAF 228


>gi|332971837|gb|EGK10783.1| tRNA-dihydrouridine synthase C [Kingella kingae ATCC 23330]
          Length = 322

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 50/189 (26%), Positives = 93/189 (49%), Gaps = 16/189 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P   Q+ G+D   + + A      G N+I+LN GCP+  V++   GA L+  P+ V   +
Sbjct: 67  PCVTQLLGSDADMMAQNALEAVKLGANKIDLNFGCPAPTVNKHQGGAVLLREPERVRHIV 126

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           A +   L   I +T K R+G +++   +AL N  ++I++ G + + +HAR  + +G  P 
Sbjct: 127 ATLRDRLPSHITLTAKMRLGFENK--ELALEN-AQAIEQGGASLLTVHARTKV-EGYQPP 182

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSA 224
            +       +D V +I++    + +  NG +  +S  +A++       VMIGR A     
Sbjct: 183 AH-------WDWVNKIRQAV-QIPVVANGDVFTLSDYRAIREQSGCQDVMIGRGAVIRPD 234

Query: 225 MLTTVDEYF 233
           +   + +Y 
Sbjct: 235 LARQIKQYL 243


>gi|304395766|ref|ZP_07377649.1| dihydrouridine synthase DuS [Pantoea sp. aB]
 gi|304357060|gb|EFM21424.1| dihydrouridine synthase DuS [Pantoea sp. aB]
          Length = 309

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 50/197 (25%), Positives = 93/197 (47%), Gaps = 16/197 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 60  MQLLGQHPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAM 119

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D    ++    +  +++++G + + +H R       + ++  
Sbjct: 120 REAVPADLPVTVKVRLGWDSSARSL---EIADAVQQAGASELTVHGR-------TKEEGY 169

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A   +       VMIGR A  N   L+
Sbjct: 170 RAEAINWQAIGEIRQRLRIPVIA-NGEIWDWQSAQNCMAVTGCSAVMIGRGAL-NIPNLS 227

Query: 228 TVDEYFSNPLTGSSPIK 244
            V +Y   P+  +  ++
Sbjct: 228 RVVKYNEPPMAWTDVVR 244


>gi|213428225|ref|ZP_03360975.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
          Length = 331

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|120603342|ref|YP_967742.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
 gi|120563571|gb|ABM29315.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
          Length = 332

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 67/257 (26%), Positives = 109/257 (42%), Gaps = 26/257 (10%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGADISKLVEAAKIVEDF 72
           L    LL+T M  A A+   +      F+ + + L     Q+ GAD S++ EAA+ VE  
Sbjct: 32  LGGCGLLFTGMCNARAVPTENPARSNAFTWRAEELERCVCQLFGADPSEMAEAARRVEAE 91

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQI 131
           G+  +++N+GC  A +     GA L+ + +     + ++ +A+  PV VK R G   D  
Sbjct: 92  GFFGVDINMGCSVAAIVRRGCGADLLRDEERAVRMVESVRRAVDCPVLVKFRTGWSPDPQ 151

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
            AVA   L +  + +G + +  H R A        D R  P L + I   + KE   + +
Sbjct: 152 GAVA---LARRFEDAGADALVFHPRVA-------PDRRTRPPLRHHI--RLVKEAVAIPV 199

Query: 192 GLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
             NG +     A  +L +   DG+ +GR A     +            TG        + 
Sbjct: 200 LGNGEVFTPGDAASMLETTGCDGISLGRIALGRPWVFAG--------WTGLVDDNPASNP 251

Query: 250 DFWRKISASMTDYAARH 266
           D WR I  ++ D   R 
Sbjct: 252 DLWRDIPLALLDALERR 268


>gi|261330856|emb|CBH13841.1| tRNA-dihydrouridine synthase 1, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 520

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 47/168 (27%), Positives = 81/168 (48%), Gaps = 12/168 (7%)

Query: 8   HYR--FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA 65
           HYR  +F+   T     ++ M     +   D  +  G    + PL  Q  G D   ++ A
Sbjct: 115 HYRQRYFS---TTTFPPHSAMESGGNVAANDSTSNDGALDNDHPLFAQFCGNDPETILAA 171

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ VED+    ++ N+GCP      G +G+ LM + +++ + + A+   L +PVT K RI
Sbjct: 172 ARHVEDYC-EAVDFNIGCPQGIARRGHYGSFLMEDWELLHNILHALAVELRVPVTAKMRI 230

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG--LSPKDNRKI 171
             DD+  A+ L+   + ++ +G+  + +H R    KG    P D R I
Sbjct: 231 -FDDE--ALTLK-YAEMLRDTGIYVLCVHGRTRENKGQQQQPADLRMI 274


>gi|213648444|ref|ZP_03378497.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
          Length = 331

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|253742273|gb|EES99116.1| tRNA-dihydrouridine synthase [Giardia intestinalis ATCC 50581]
          Length = 409

 Score = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 108/233 (46%), Gaps = 36/233 (15%)

Query: 23  YTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE---- 76
           +T+M  ADA+L     +  +L  +   + + LQ+ G + S  + AAK++           
Sbjct: 86  FTQMYTADALLHNSLLRDTVLSAAAPGENIILQLCGNNPSNFLAAAKVLSSSSLAPQIIA 145

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR-IG-VDDQIPAV 134
           +++N+GCP++      +G  +  N  +V   ++ +  A   PVT K R +G +++ +  +
Sbjct: 146 LDVNLGCPASCASSRGYGLYIAQNWPLVHQILSEVSSAQLFPVTCKIRPLGTIEETVDYM 205

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIK---------- 183
            L  L      SG +GI IH R    +G   + + K   L++ +IVY  +          
Sbjct: 206 LLLAL------SGASGITIHMRHTTRQGKHAQ-SVKPAYLEFEEIVYAFRRRLDVFLDSI 258

Query: 184 ------KENPDLF--IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
                 K  P+L+  I LNGG++   +A  +L S   DG+MIG    K+   L
Sbjct: 259 GKRKPTKREPNLYPVIILNGGVKSRQEADDLLSSYPADGIMIGVGLLKDPTCL 311


>gi|268679177|ref|YP_003303608.1| dihydrouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268617208|gb|ACZ11573.1| dihydrouridine synthase DuS [Sulfurospirillum deleyianum DSM 6946]
          Length = 312

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 109/230 (47%), Gaps = 24/230 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +TD  +R   +    + + ++EMI A+A+    +K   +L  S  E P  +QI G+D
Sbjct: 17  LAGFTDLPFRSVVKKFGAD-VTFSEMISANALRFKSEKTFKMLTKSPLEIPYIVQIVGSD 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ + EA  I+ D  G   I+LN GCP  ++     G+ L+LN D +   I  + K  S 
Sbjct: 76  LTSIKEAVLILNDMEGIAGIDLNCGCPVPKMVAQEAGSSLLLNLDHMQRVIETI-KTYSN 134

Query: 118 P--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               + K R+G + +IP +    + K+ + +G + + +H R         +       +D
Sbjct: 135 KRYTSAKVRLGFNTKIPEL----IAKACENAGADFMSMHGR--------TRSGAYKAEVD 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG---VMIGRAAYKN 222
           Y  + E +       I  NG +  + +AL ++ SV G   +MIGR A  N
Sbjct: 183 YQAIAEARAAVKIPVIA-NGDITSLEKALHVM-SVTGCKNLMIGRGALGN 230


>gi|91227370|ref|ZP_01261759.1| putative regulator protein [Vibrio alginolyticus 12G01]
 gi|91188634|gb|EAS74924.1| putative regulator protein [Vibrio alginolyticus 12G01]
          Length = 319

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 91/176 (51%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G + + + E A    + G   I++N GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHVQLLGQEPNWMAENAIKAANLGARGIDINFGCPAKMVNKSKGGAALLQHPELIHRVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+  +IPVT K R+G ++  P      +V +I+ +G N + +HAR       + +
Sbjct: 124 KACREAVPEAIPVTAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR-------TKQ 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + +D + +I +E  D+ +  NG + +     + + +  V  +M+ R A+
Sbjct: 174 GGYKASEIKWDYINQI-RERFDIPLIANGEIWNYEDGQRCIETTGVSSLMVCRGAF 228


>gi|251790102|ref|YP_003004823.1| tRNA-dihydrouridine synthase C [Dickeya zeae Ech1591]
 gi|247538723|gb|ACT07344.1| dihydrouridine synthase DuS [Dickeya zeae Ech1591]
          Length = 311

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKMVNGSGGGATLLKDPDLIYRAAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+  S+PVTVK R+G D          +  ++ ++G + + +H R       + +D  
Sbjct: 127 REAVPSSLPVTVKVRLGWDSGERRF---EIADAVAQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A   + +   D VMIGR A  N   L+
Sbjct: 177 RAERINWAAIGEIRRRLRIPVIA-NGEIWDWQSAQDCMAATGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|156037856|ref|XP_001586655.1| hypothetical protein SS1G_12642 [Sclerotinia sclerotiorum 1980]
 gi|154698050|gb|EDN97788.1| hypothetical protein SS1G_12642 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 587

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 51/217 (23%), Positives = 98/217 (45%), Gaps = 28/217 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D  +L+E AK V  F  + ++LN+GCP      G +GA L  +  ++  
Sbjct: 131 DRPLFVQFCANDEKELLEGAKYVAPF-CDAVDLNLGCPQGIARRGKYGAFLQEDQGLIYK 189

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  + K L +PVT K RI ++ +   +    +V S   +G + + +H R   +KG    
Sbjct: 190 LINTLHKELDVPVTAKIRI-LETREKTLEYAKMVVS---AGASILTVHGRTREMKG---- 241

Query: 167 DNRKIPNLDYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
              K    D+ ++  +++  P ++ +  NG +   ED+ + LK+    DGVM       +
Sbjct: 242 --HKTGLADWAVLRFLRESLPKEVVLFANGNILSREDIDECLKVT-GADGVMSAEGNLYD 298

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
             + +             +P      +++WR +   +
Sbjct: 299 PTIFS------------DAPTLREEGREYWRSLDGKL 323


>gi|153940547|ref|YP_001390029.1| dihydrouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
 gi|152936443|gb|ABS41941.1| dihydrouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
          Length = 312

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 100/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D  + +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSERFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKI 171
           K   + +++K RIG D          L+K   K  +  + IH R +    G  P      
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPRTQKDFYGNKP------ 174

Query: 172 PNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              D DI  +      NP  + G    +   ++ +K  P V  +M+GR    N  ++   
Sbjct: 175 ---DLDIFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLI--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|149237573|ref|XP_001524663.1| tRNA-dihydrouridine synthase 4 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146451260|gb|EDK45516.1| tRNA-dihydrouridine synthase 4 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 342

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 101/229 (44%), Gaps = 14/229 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R +      F+T +K   + +Q+G  +
Sbjct: 36  MVRYSKLPFRELCRFY-NVDIIYTPMILAREFVRNEMARYSDFTTNDKDTCVIVQVGVNN 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   ++  +++  +  + I +N GCP   ++ EG  GA LM  PD+V + IA   K    
Sbjct: 95  VEDFMKFIEMIHPY-VDGIGINCGCPIRDQIREG-IGAALMSEPDLVAEMIATAKKQYGD 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + +  +I + + +        VK ++ +G + I IH R    +   P +   I  +   
Sbjct: 153 SICIDTKIRIHNDLSETI--EFVKKVEAAGTDIITIHGRTKTTRSSIPVNLDAIKLVRSH 210

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           I       N D F      LED  + +     V+GVM  R    N A+ 
Sbjct: 211 ITKVPVIANGDCFT-----LED-CERIADYTGVNGVMSARGILANPALF 253


>gi|254804888|ref|YP_003083109.1| putative dihydrouridine synthase [Neisseria meningitidis alpha14]
 gi|254668430|emb|CBA05633.1| putative dihydrouridine synthase [Neisseria meningitidis alpha14]
          Length = 333

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 91/205 (44%), Gaps = 20/205 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V+    GA L+  P ++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNRHKGGAILLKEPQLIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 192 AHWEWIRKIRDSVNIPVTANGDVF-----SLQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDF 251
             + +Y         P+K   D DF
Sbjct: 246 RQIKQY-----ENGGPVK---DTDF 262


>gi|156537077|ref|XP_001602214.1| PREDICTED: similar to tRNA-dihydrouridine synthase [Nasonia
           vitripennis]
          Length = 505

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 92/205 (44%), Gaps = 24/205 (11%)

Query: 30  DAILRGDKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           D I R D   +   S  E+  + LQ+G  D ++ ++ AK+VE      I++N+GCP    
Sbjct: 109 DYIDRTDGTIVFRTSPIERDRVVLQLGTCDANRALKVAKLVEQ-DVAGIDVNMGCPKRFS 167

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKS 146
             G  GA L+  P+   + +  +   LSIPVT K R+   V+D +       LV ++  +
Sbjct: 168 ILGGMGAALLKQPEKASEILRTLVGGLSIPVTCKIRVLGNVEDTL------KLVDTLVDT 221

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G++ I +H R    +   P  +  I  +          E+  + +  NGG +++ +   I
Sbjct: 222 GISAITVHGRTVDERPQHPNRSEFIKRV---------AEHAKIPVIANGGSKEIEKRADI 272

Query: 207 LP-----SVDGVMIGRAAYKNSAML 226
                      VMI RAA  N ++ 
Sbjct: 273 FKFKKETGCSSVMIARAAEWNCSIF 297


>gi|330721068|gb|EGG99210.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC2047]
          Length = 312

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 113/238 (47%), Gaps = 18/238 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR YR   R      L  +EM+ +D  L   +K+   L  + ++ P ++QI G+D
Sbjct: 1   MAGVTDRPYRALCRHY-GAGLAVSEMVTSDQSLWHTRKSQQRLNHAGEQTPRSVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA    + G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+++P
Sbjct: 60  PKMMAAAAVANVENGAQIIDINMGCPAKKVCNKAAGSALLRDEKLVSHILEAVVAAVNVP 119

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G   D   A+ + N+    ++SG+  + IH R         +  R     +YD
Sbjct: 120 VTLKIRTGWCPDSRNALTIANIA---EQSGIQALTIHGRT--------RACRYNGEAEYD 168

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
            +  + +++    I  NG +   ++A  ++     + +MIGR A     +   ++ + 
Sbjct: 169 TIAAVVQQSRIPIIA-NGDITTANKAHWVMQRTGANAIMIGRGAQGTPWIFAEINHFL 225


>gi|113867457|ref|YP_725946.1| hypothetical protein H16_A1443 [Ralstonia eutropha H16]
 gi|124106281|sp|O68273|DUSC_RALEH RecName: Full=tRNA-dihydrouridine synthase C
 gi|113526233|emb|CAJ92578.1| conserved hypothetical protein [Ralstonia eutropha H16]
          Length = 322

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 105/237 (44%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+ NP
Sbjct: 58  GYTRSGTPMVIQLLGSDPEWLARNAAYAATLSPHGIDLNFGCPAKVVNRHGGGAMLLTNP 117

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   +A++  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 ELLNRIVASVRAAVPAHIAVTAKMRLGVSDASLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                 +D+   P   +D +  I     D+ +  NG +  ++  +  + +     VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIAAAV-DVPVIANGDVWTVADWERCRAVSGCADVMIGR 225

Query: 218 AAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +      +P     P+  R    + +K+ A +   A+ H H   KL
Sbjct: 226 GAVSDPFLALRIRGLMDGSPSDQEWPLVLRQIATYLKKLHARI---ASCHEHGRVKL 279


>gi|302682790|ref|XP_003031076.1| hypothetical protein SCHCODRAFT_82562 [Schizophyllum commune H4-8]
 gi|300104768|gb|EFI96173.1| hypothetical protein SCHCODRAFT_82562 [Schizophyllum commune H4-8]
          Length = 701

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 100/229 (43%), Gaps = 37/229 (16%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVE-------DFGYN 75
           EM +A + L G K+  +++     EK   +Q+ G   + +V AA++++       DF   
Sbjct: 370 EMGLATSFLSGSKEEWSLVRRHPSEKMFGVQMAGNKPNTMVRAAELLKNEIGPHVDF--- 426

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAV 134
            +++N GCP   V++   G+ L+ +P  +G  I  M KAL   PV+VK R GV D     
Sbjct: 427 -VDINCGCPIDLVYKTGSGSALLDSPGKLGRIIVGMNKALGDTPVSVKLRTGVKDG--KN 483

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV---------YEIKKE 185
               L+  + + G   + +H R         +  R     D+D V         YE +K 
Sbjct: 484 NAHRLMPRVAEWGAGMMTLHGRT--------RQQRYTKLADWDYVRECVQAVRAYEAEKN 535

Query: 186 NPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDE 231
            P + I   GG    SQ          VDGVMIGR A     + T + E
Sbjct: 536 LPKVPI-FGGGDCYSSQDYWTDVETTGVDGVMIGRGALIKPWIFTEIKE 583


>gi|213852323|ref|ZP_03381855.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 316

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 68  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 128 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 178 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 235

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 236 NLSRVVKY 243


>gi|16761116|ref|NP_456733.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29141188|ref|NP_804530.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|289824273|ref|ZP_06543868.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|38604947|sp|Q8Z5B2|DUSC_SALTI RecName: Full=tRNA-dihydrouridine synthase C
 gi|25311313|pir||AD0779 conserved hypothetical protein STY2404 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16503414|emb|CAD02554.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29136814|gb|AAO68379.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
          Length = 312

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|114663256|ref|XP_001166706.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 2
           [Pan troglodytes]
          Length = 406

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 88/185 (47%), Gaps = 32/185 (17%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++ + K
Sbjct: 1   MGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVK 59

Query: 114 ALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
               PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++ R  
Sbjct: 60  GTHRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------REERPQ 105

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGRAAYK 221
             +  +++  I  +   + +  NGG          +ED  QA     +   VM+ RAA  
Sbjct: 106 HPVSCEVIKAI-ADTLSIPVIANGGSHDHIQQYSDIEDFRQAT----AASSVMVARAAMW 160

Query: 222 NSAML 226
           N ++ 
Sbjct: 161 NPSIF 165


>gi|332263179|ref|XP_003280632.1| PREDICTED: tRNA-dihydrouridine synthase 3 isoform 2 [Nomascus
           leucogenys]
          Length = 408

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 70/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 93  EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 148

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 149 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 207

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E +K  +P    G NG 
Sbjct: 208 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVKAASPMPLFG-NGD 257

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 258 ILSFEDANRAMQT--GVAGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 306

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 307 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 344


>gi|330810804|ref|YP_004355266.1| tRNA-dihydrouridine synthase C [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327378912|gb|AEA70262.1| tRNA-dihydrouridine synthase C [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 319

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 84/171 (49%), Gaps = 12/171 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++ + +
Sbjct: 64  PLRVQLLGSDPVCLAENAALACELGSEVIDLNFGCPAKTVNKSRGGAVLLKEPELLNEIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+   IPVT K R+G D    A+       ++ + G   I +HAR  +     P 
Sbjct: 124 EHVRRAVPKHIPVTAKMRLGFDSPDGALV---CATALAEGGAAHIVVHARTKVDGYKPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               IP +  ++V      N D++      +ED  +  +I   V+ +M+GR
Sbjct: 181 HWEWIPRVQ-EVVKVPVFANGDIW-----SVEDWRRCREI-SGVEDIMLGR 224


>gi|292487710|ref|YP_003530583.1| putative regulator protein [Erwinia amylovora CFBP1430]
 gi|292898945|ref|YP_003538314.1| tRNA-dihydrouridine synthase C [Erwinia amylovora ATCC 49946]
 gi|291198793|emb|CBJ45902.1| tRNA-dihydrouridine synthase C [Erwinia amylovora ATCC 49946]
 gi|291553130|emb|CBA20175.1| putative regulator protein [Erwinia amylovora CFBP1430]
          Length = 310

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 49/191 (25%), Positives = 91/191 (47%), Gaps = 16/191 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G + + +H R       + ++  
Sbjct: 127 RAAVPDHLPVTVKVRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEEGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEAINWQAIGEI-RQRLNIPVIANGEIRDWQSAQECMAMTGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEYFSNPLT 238
            V +Y   P+ 
Sbjct: 235 RVIKYREPPMA 245


>gi|270260822|ref|ZP_06189095.1| tRNA-dihydrouridine synthase C [Serratia odorifera 4Rx13]
 gi|270044306|gb|EFA17397.1| tRNA-dihydrouridine synthase C [Serratia odorifera 4Rx13]
          Length = 309

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQHPQWLGENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D    +     +  +++++G   + +H R       + +D  
Sbjct: 127 RAAVPDHLPVTVKVRLGWDSDSRSF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI+K      I  NG + D   A   L +   D VM+GR A  N   L+
Sbjct: 177 KAERINWAAIGEIRKRLTIPVIA-NGEIWDYQSAQDCLQTTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 QVVKY 239


>gi|194444008|ref|YP_002041446.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|200388326|ref|ZP_03214938.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|194402671|gb|ACF62893.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|199605424|gb|EDZ03969.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
          Length = 331

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|295110086|emb|CBL24039.1| tRNA-U20a,U20b-dihydrouridine synthase [Ruminococcus obeum A2-162]
          Length = 316

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 77/167 (46%), Gaps = 11/167 (6%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    +  A  +   GY EINLN+GCPS  V     GA  +   D +   +  + 
Sbjct: 64  QILTRNADDFLRTASQLAGLGYREINLNLGCPSKTVVTKGCGAGFLDRTDELERFLNHIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + +++K R+G+DD   A    +L++   +  +  + +H R      +     + +P
Sbjct: 124 ANTDLKISIKTRLGMDD---AEEFEDLLEIYNRFPLEELIVHPR------VQKDFYKNVP 174

Query: 173 NLDYDIVYEIKK-ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
           NL+    Y ++K +NP  + G     ED ++  +  PSVD  M+GR 
Sbjct: 175 NLE-AFEYAVQKSKNPLCYNGDIFSAEDFAKVQERFPSVDCFMMGRG 220


>gi|325265681|ref|ZP_08132370.1| tRNA-dihydrouridine synthase C [Kingella denitrificans ATCC 33394]
 gi|324982812|gb|EGC18435.1| tRNA-dihydrouridine synthase C [Kingella denitrificans ATCC 33394]
          Length = 330

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 96/194 (49%), Gaps = 26/194 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +V+ A +    G ++I+LN GCP+  V++   GA L+  P+ +   +
Sbjct: 74  PCVVQMLGSDAEMMVKNALVAVGLGAHQIDLNFGCPAPTVNKHQGGAVLLQTPERIYHIV 133

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +A+ + +   IP++ K R+G +++   +AL N   +I ++G + + +HAR  I +G  P 
Sbjct: 134 SAIRQGVPEHIPISAKMRLGFENK--DLALEN-ADAIAQAGASVLTVHARTKI-EGYRPP 189

Query: 167 DNRKIPNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
            +       +  V +I++        N D+F      L+D    ++     D VM+GR A
Sbjct: 190 AH-------WGWVDKIRRHVAIPVIANGDVFC-----LQDYID-IRAQSGCDDVMLGRGA 236

Query: 220 YKNSAMLTTVDEYF 233
                +   + +Y 
Sbjct: 237 VMRPDLARQIRQYL 250


>gi|168259485|ref|ZP_02681458.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205350920|gb|EDZ37551.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 312

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|289806468|ref|ZP_06537097.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 195

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 18  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 77

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 78  KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 127

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 128 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 185

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 186 NLSRVVKY 193


>gi|109119167|ref|XP_001113015.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Macaca mulatta]
          Length = 476

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 46/161 (28%), Positives = 80/161 (49%), Gaps = 12/161 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           S+PVT  C+I V  +I         + ++K+G   + +H R
Sbjct: 141 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGR 177


>gi|312880306|ref|ZP_07740106.1| tRNA-U20-dihydrouridine synthase [Aminomonas paucivorans DSM 12260]
 gi|310783597|gb|EFQ23995.1| tRNA-U20-dihydrouridine synthase [Aminomonas paucivorans DSM 12260]
          Length = 340

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 99/235 (42%), Gaps = 24/235 (10%)

Query: 10  RFFARLLTNNALLYTEMIVADAI-LRGDK-KNILGFSTQEKPLALQIGGADISKLVEAAK 67
           RF  RL     L +TEM+ A  +  RG K + +L     E PLA Q+ G D   L E A+
Sbjct: 38  RFHRRL--GAGLAHTEMVSALGLAYRGKKTRELLTVLEGEGPLAAQLFGPDAPSLAEGAR 95

Query: 68  I-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + +    +  + +N+ CP  +V     GA L+  PD     + + C AL +P+ VK R+ 
Sbjct: 96  LTLAVHPFQALEINMACPMPKVARKGAGAALLERPDEAVRAVRS-CAALGVPLWVKVRL- 153

Query: 127 VDDQIP---AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
               +P   A A     +++  +G   + +H R            R     D D V  + 
Sbjct: 154 ----LPGGAATATARFCEALLDAGAAFLLVHGRT--------PGQRYEGTADRDAVCALA 201

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           +  P L +G +G L     A   L      V++ R   K+  ++  + E    PL
Sbjct: 202 RLYPGL-LGASGDLFTPEDARAYLEGGCASVLVARGLLKDPLLVPRILEELGFPL 255


>gi|311744088|ref|ZP_07717894.1| NifR3 family TIM-barrel enzyme [Aeromicrobium marinum DSM 15272]
 gi|311313218|gb|EFQ83129.1| NifR3 family TIM-barrel enzyme [Aeromicrobium marinum DSM 15272]
          Length = 432

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/153 (28%), Positives = 72/153 (47%), Gaps = 8/153 (5%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV- 69
           AR      L   EMI +  ++ GD+ ++  L F+  E+  ++Q+ G D + +  A  I+ 
Sbjct: 88  ARTSGQAGLYVCEMITSRGVVEGDRTSLGMLTFAPNERVRSVQLYGIDPATVGRAVAILC 147

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKALSIPVTVKCRIG 126
            D G + ++LN GCP  +V     GA L     ++G  +    A      +PVT+K R G
Sbjct: 148 GDHGVDHVDLNFGCPVPKVTRKGGGAALPWKATLLGRILTEAVAAAAPFGVPVTMKTRKG 207

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +DD    +   +     + SG   I +H R A+
Sbjct: 208 IDDD--HLTYLDAGHIAEDSGCAAIALHGRTAV 238


>gi|255600129|ref|XP_002537390.1| tRNA-dihydrouridine synthase C, putative [Ricinus communis]
 gi|223516517|gb|EEF24993.1| tRNA-dihydrouridine synthase C, putative [Ricinus communis]
          Length = 329

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 110/231 (47%), Gaps = 23/231 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G+D   + E A      G   I++N GCP+  V+    GA L+  P+++ + +
Sbjct: 77  PVRLQLLGSDPVCMAENAAKAASLGAAGIDINFGCPAKIVNRHRGGAALLKEPELMREIV 136

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+  A+  S+ VT K R+G   ++P  A+    ++++  G + I +HAR       +  
Sbjct: 137 AAIRAAVPASVSVTAKMRLGY--EVPDYAV-ECAQALQDGGADEITVHAR-------TKT 186

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
           D  K P   ++ + +I +E   + +  NG +   + A +   +     +MIGR A  N A
Sbjct: 187 DGYKPPAY-WEWIAQI-REALQIPVIANGEIWTAADARRCREISGCTDIMIGRGAVANPA 244

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           +   +     +PL  S  I   +   +W  +S  +++      H  G+++Q
Sbjct: 245 LALMIRGELESPLPWSEVIV--LLHRYWATVSRHISER-----HRNGRIKQ 288


>gi|189239358|ref|XP_974445.2| PREDICTED: similar to tRNA-dihydrouridine synthase [Tribolium
           castaneum]
          Length = 401

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/238 (21%), Positives = 97/238 (40%), Gaps = 32/238 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +   N  L YT MI+AD+  +  K     F+T   + PL  Q     
Sbjct: 31  MVRYSKLQFRNLVKSY-NCDLCYTPMILADSFCKSGKARANEFTTNMNDTPLITQFAANK 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   V AA +V  F  + ++LN GCP         G  ++  P+++ D +      +  P
Sbjct: 90  VYDFVGAAYMVSPFC-DGVDLNCGCPQRWAKLQGLGCIMLEKPEVIYDLVKQCRNVIPKP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  ++ +   +       + + ++  GV+ + +H R       +P            +
Sbjct: 149 FTVSVKLRLQKDLRRSV--EICRQLEHCGVSFLTVHGR-------TPD----------QL 189

Query: 179 VYEIKKENPDLFIG-------LNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLT 227
             E+ KE  +L +G        NGG++ +   L++    +  GVM+      N  + T
Sbjct: 190 TGEVNKEALNLIVGSVNVPVVANGGVKSLEDCLELQEKTNCKGVMVANGLLTNPTLFT 247


>gi|121595495|ref|YP_987391.1| dihydrouridine synthase [Acidovorax sp. JS42]
 gi|120607575|gb|ABM43315.1| tRNA-U20a,U20b-dihydrouridine synthase [Acidovorax sp. JS42]
          Length = 342

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 45/188 (23%), Positives = 86/188 (45%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   + E A  + + G   I+LN GCP+  V+    GA L+  P+ +   +
Sbjct: 74  PVRAQLLGSDPVSMAENAARLAELGPEGIDLNFGCPAKTVNRHGGGAALLREPERIAAVV 133

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   +PV+ K R+G DD   A   R   +++ + G   + +HAR        P 
Sbjct: 134 EAVRRAVPAHVPVSAKMRLGYDD---AGLARECAQAMARGGACELVVHARTKADGYRPPA 190

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
              +IP +         +E   + +  NG +  +  AL+   +   D +M+GR    +  
Sbjct: 191 YWEQIPAI---------REAVGIPVVANGEIWTVQDALRCRSVSGCDALMLGRGIVADPG 241

Query: 225 MLTTVDEY 232
           +  ++  +
Sbjct: 242 LALSIRAH 249


>gi|269967333|ref|ZP_06181394.1| tRNA-dihydrouridine synthase C [Vibrio alginolyticus 40B]
 gi|269828041|gb|EEZ82314.1| tRNA-dihydrouridine synthase C [Vibrio alginolyticus 40B]
          Length = 319

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 91/176 (51%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G + + + E A    + G   I++N GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHVQLLGQEPNWMAENAIKAANLGARGIDINFGCPAKMVNKSKGGAALLQHPELIHRVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+  +IPVT K R+G ++  P      +V +I+ +G N + +HAR       + +
Sbjct: 124 KACREAVPEAIPVTAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR-------TKQ 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + +D + +I +E  D+ +  NG + +     + + +  V  +M+ R A+
Sbjct: 174 GGYKASEIKWDYINQI-RERFDIPLIANGEIWNYEDGQRCIETTGVSSLMVCRGAF 228


>gi|72393571|ref|XP_847586.1| tRNA-dihydrouridine synthase 1 [Trypanosoma brucei TREU927]
 gi|62176372|gb|AAX70483.1| tRNA-dihydrouridine synthase 1, putative [Trypanosoma brucei]
 gi|70803616|gb|AAZ13520.1| tRNA-dihydrouridine synthase 1, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 520

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 47/168 (27%), Positives = 81/168 (48%), Gaps = 12/168 (7%)

Query: 8   HYR--FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA 65
           HYR  +F+   T     ++ M     +   D  +  G    + PL  Q  G D   ++ A
Sbjct: 115 HYRQRYFS---TTTFPPHSAMESGGNVAANDSTSNDGALDNDHPLFAQFCGNDPETVLAA 171

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ VED+    ++ N+GCP      G +G+ LM + +++ + + A+   L +PVT K RI
Sbjct: 172 ARHVEDYC-EAVDFNIGCPQGIARRGHYGSFLMEDWELLHNILHALAVELRVPVTAKMRI 230

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG--LSPKDNRKI 171
             DD+  A+ L+   + ++ +G+  + +H R    KG    P D R I
Sbjct: 231 -FDDE--ALTLK-YAEMLRDTGIYVLCVHGRTRENKGQQQQPADLRMI 274


>gi|270007852|gb|EFA04300.1| hypothetical protein TcasGA2_TC014592 [Tribolium castaneum]
          Length = 548

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 63/269 (23%), Positives = 114/269 (42%), Gaps = 38/269 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM +  ++L+G  +   ++     E    +Q+   +   L +  ++++     DF    I
Sbjct: 231 EMAMCSSLLQGAPQEWALVKRHHSEDIFGVQLCANNPHLLTKCGQVLQQEAEIDF----I 286

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV--DDQIPAVA 135
           +LN+GCP   V++   G  L+    ++  CI  + + L+IP+TVK R GV  ++ +  + 
Sbjct: 287 DLNLGCPIELVYKEGGGCGLLRRQRVLESCIKNLSQLLTIPMTVKTRTGVYSNENLAHI- 345

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              L    +  G + I IH R         ++ R     D+  + ++ +    L +  NG
Sbjct: 346 ---LAPKFRDWGASLITIHGRS--------REQRYTKLADWTYIRQVAQAAAPLPVLGNG 394

Query: 196 GL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   ED   A +  P + GVMIGR A     + T + E     ++ S     R D    
Sbjct: 395 DVLSYEDYKIARETCPELAGVMIGRGALIKPWIFTEIKEQKLWDISSSE----RFD---- 446

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMI 281
             +    T+Y   H  S  K  + TR  +
Sbjct: 447 --LLKKYTNYGLEHWGSDNKGVENTRRFL 473


>gi|167551130|ref|ZP_02344885.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205324041|gb|EDZ11880.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
          Length = 312

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|288549865|ref|ZP_05968436.2| tRNA-dihydrouridine synthase [Enterobacter cancerogenus ATCC 35316]
 gi|288316988|gb|EFC55926.1| tRNA-dihydrouridine synthase [Enterobacter cancerogenus ATCC 35316]
          Length = 303

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 60  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYRGAKAM 119

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 120 REAVPSHLPVTVKVRLGWDS---GARQFEIADAVQQAGATELVVHGR-------TKEDGY 169

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   L     D VMIGR A  N   L+
Sbjct: 170 KAERINWQAIGEIRQRLTIPVIA-NGEIWDYESAQACLKETGCDAVMIGRGAL-NVPNLS 227

Query: 228 TVDEY 232
            V +Y
Sbjct: 228 RVVKY 232


>gi|163803826|ref|ZP_02197676.1| DNA-binding protein Fis [Vibrio sp. AND4]
 gi|159172369|gb|EDP57246.1| DNA-binding protein Fis [Vibrio sp. AND4]
          Length = 322

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 113/244 (46%), Gaps = 20/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L G  K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPKLWGTSKSKQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G + +       ++ K  +  G+  + +H R    + KG +          +Y
Sbjct: 136 VTLKTRTGWNTENKNCV--HVAKLAEDCGIQALALHGRTKACMYKGEA----------EY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  Y  
Sbjct: 184 DSIKAVKQAISIPVIA-NGDIDSPEKAKYVLEYTGADALMIGRPAQGRPWIFQEIHHYLE 242

Query: 235 NPLT 238
           N  T
Sbjct: 243 NGTT 246


>gi|117620179|ref|YP_856732.1| tRNA-dihydrouridine synthase C [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117561586|gb|ABK38534.1| tRNA-dihydrouridine synthase C [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 314

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 49/175 (28%), Positives = 87/175 (49%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   I+LN GCP+  V++   GA L+  P  +   +
Sbjct: 64  PVRVQLLGQHPEWLAENALRAIELGSPGIDLNFGCPAPTVNKSKGGAVLLKEPGTIYRIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   +PV+ K R+G DD+   + L N   ++ + G N + +HAR       + +
Sbjct: 124 KAVREAVPAHLPVSAKIRLGYDDK--ELYLEN-AHAVHQGGANELAVHAR-------TKR 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
           +  K P   ++ V  I++  P + +  NG + D + AL    +   D +M+GR A
Sbjct: 174 EGYKAPA-HWEYVDAIRRALP-IPVTANGEIWDHADALACAQVSGCDTLMVGRGA 226


>gi|312171823|emb|CBX80080.1| putative regulator protein [Erwinia amylovora ATCC BAA-2158]
          Length = 310

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 89/191 (46%), Gaps = 16/191 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G + + +H R       + ++  
Sbjct: 127 RAAVPDHLPVTVKVRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEEGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEAINWQAIGEIRQRLTIPVIA-NGEIRDWQSAQECMAMTGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEYFSNPLT 238
            V +Y   P+ 
Sbjct: 235 RVIKYREPPMA 245


>gi|284043141|ref|YP_003393481.1| dihydrouridine synthase [Conexibacter woesei DSM 14684]
 gi|283947362|gb|ADB50106.1| dihydrouridine synthase DuS [Conexibacter woesei DSM 14684]
          Length = 333

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 70/276 (25%), Positives = 118/276 (42%), Gaps = 33/276 (11%)

Query: 11  FFARLLTNN---ALLYTEMIVADAILRGDKK---NILGFSTQE------KPLALQIGGAD 58
           +F RL        L  +EM+ + AI  G++K    +L     E       P+++Q+ G D
Sbjct: 31  WFVRLQAKRYGAGLAVSEMVSSHAIHYGNEKTCTELLRVHPDEWRAGAGGPVSIQLFGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA    + G N I+LN+GCP  +V +   GA L+ +PD+  +   A  +   +P
Sbjct: 91  PDIMRSAAARAAETGANLIDLNMGCPVPKVCKTGAGAALVKDPDLAVEIARAAAEGSGLP 150

Query: 119 VTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VTVK R G+   D     +A R     +  +G+ G+ IH R A          +     D
Sbjct: 151 VTVKLRPGLRPGDRNGIELAYR----LVADAGIAGLCIHPRHA--------SQQHSGRPD 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV-DEY 232
           Y++   + +E P + + ++GGL       ++      + V++ R +  N  +   V  + 
Sbjct: 199 YELAKRLVEELP-VPVLISGGLRSAELVREVFEFTGAEAVLLARGSLGNPWLFEQVLGDR 257

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
              P      I T VD    R +       AAR+L 
Sbjct: 258 VGEPT--REEILTEVDWILDRAVEHLGEGRAARYLR 291


>gi|304414074|ref|ZP_07395442.1| fusion of tRNA-dihydrouridine synthase and subunit of Fis DNA
           binding transcriptional dual regulator [Candidatus
           Regiella insecticola LSR1]
 gi|304283288|gb|EFL91684.1| fusion of tRNA-dihydrouridine synthase and subunit of Fis DNA
           binding transcriptional dual regulator [Candidatus
           Regiella insecticola LSR1]
          Length = 440

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/253 (26%), Positives = 117/253 (46%), Gaps = 23/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPL-ALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  + + DK  +      E  +  +QI G+D
Sbjct: 25  MAGITDRPFRALC-LAMGAGMAVSEMLSSNLEVWQTDKSRLRRIHKDEAGIRTVQIAGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAKI    G   I++N+GCP+ +V+    G+ L+  P++V   I A+  A+ +P
Sbjct: 84  PDEMAAAAKINVANGAQIIDINMGCPAKKVNRKLAGSALLKYPNLVKQIITAVVDAVDVP 143

Query: 119 VTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLD 175
           VT+K R G V +    V +  L +     G+  + IH   R  +  G +          +
Sbjct: 144 VTLKIRTGWVPENRNCVEIAQLAEC---CGIQALTIHGRTRSCLFNGEA----------E 190

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + K+N  + +  NG + +  +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 191 YDSIRAV-KQNVTIPVIANGDITNPHKAKVVLDYTGADALMIGRAAQGRPWIFREIQHYL 249

Query: 234 -SNPLTGSSPIKT 245
            +  L    P++T
Sbjct: 250 DTGELLPPMPLET 262


>gi|330829416|ref|YP_004392368.1| tRNA-dihydrouridine synthase C [Aeromonas veronii B565]
 gi|328804552|gb|AEB49751.1| tRNA-dihydrouridine synthase C [Aeromonas veronii B565]
          Length = 314

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   ++LN GCP+  V++   GA L+  P+ +   +
Sbjct: 64  PVRVQLLGQHPEWLAENALRAIELGSPGVDLNFGCPAPTVNKSKGGAVLLKEPETIYRIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   +PV+ K R+G DD+   + L N  +++ + G N + +HAR       + +
Sbjct: 124 KAVREAVPAHLPVSAKIRLGYDDK--DLYLEN-AQAVFQGGANELAVHAR-------TKR 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
           +  K P   ++ V  I++  P + +  NG + D   AL    +   D +M+GR A
Sbjct: 174 EGYKAPA-HWEYVDAIRRALP-IPVTANGEIWDHKDALACARVSGCDALMVGRGA 226


>gi|260598603|ref|YP_003211174.1| tRNA-dihydrouridine synthase C [Cronobacter turicensis z3032]
 gi|260217780|emb|CBA32227.1| tRNA-dihydrouridine synthase C [Cronobacter turicensis z3032]
          Length = 320

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +PD++     AM
Sbjct: 77  VQLLGQHPQWLAENAARAVALGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAM 136

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 137 REAVPAHLPVTVKIRLGWDS---GARRFEIADAVQQAGATELVVHGR-------TKEDGY 186

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI +E   + +  NG + D + A   +     D VMIGR A  N   L+
Sbjct: 187 KAERINWAAIGEI-RERLTIPVIANGEIWDYASAQACMAETGCDAVMIGRGAL-NVPNLS 244

Query: 228 TVDEY 232
            V +Y
Sbjct: 245 RVIKY 249


>gi|253990396|ref|YP_003041752.1| tRNA -dihydrouridine synthase C [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253781846|emb|CAQ85009.1| tRNA-dihydrouridine synthase C [Photorhabdus asymbiotica]
          Length = 310

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   I IH R       + +D  
Sbjct: 127 REAVPSHLPVTVKVRLGWDSSERQF---EIADAVQQAGATEITIHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   +     + VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEIRRRLSIPVIA-NGEIWDWQSAQDCMDVTGCNAVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|328871537|gb|EGG19907.1| tRNA-dihydrouridine synthase 2-like protein [Dictyostelium
           fasciculatum]
          Length = 375

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 88/186 (47%), Gaps = 18/186 (9%)

Query: 46  QEKPLALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           Q++   LQ+G A  +S L  A  +V D     I++N+GCP     +G  G+ L+  P+ +
Sbjct: 64  QDRNNVLQLGTASSVSALKAAQHVVNDICA--IDINMGCPKFFSVQGGMGSALLSKPETI 121

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            D +  + + L +PVT K R+   DQ       +L+K I+ +GV+ I +H R+   +   
Sbjct: 122 KDILTTLIRNLPVPVTCKIRLLKTDQ----ETIDLLKIIESTGVSAIGVHMREIPERPKD 177

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYK 221
           P    ++  +  +  Y +        I  NG +   +D+   L      + VMI R A +
Sbjct: 178 PAHWDRLATILANSSYSVP-------IIANGDIYTHQDIDNVLN-QTKANSVMIARGAIR 229

Query: 222 NSAMLT 227
           N ++ +
Sbjct: 230 NVSVFS 235


>gi|322715236|gb|EFZ06807.1| Dihydrouridine synthase, DuS [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 312

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|62180761|ref|YP_217178.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|197264574|ref|ZP_03164648.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|62128394|gb|AAX66097.1| putative nitrogen regulation protein [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|197242829|gb|EDY25449.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
          Length = 312

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|254369301|ref|ZP_04985313.1| Nif3 family protein [Francisella tularensis subsp. holarctica
           FSC022]
 gi|157122251|gb|EDO66391.1| Nif3 family protein [Francisella tularensis subsp. holarctica
           FSC022]
          Length = 242

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 106/233 (45%), Gaps = 39/233 (16%)

Query: 76  EINLNVG-CPSARVHEGSF--GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-I 131
           EI  NV   P A   + +F  GA L+ + + + + + A+ KA+  PVTVK RIG D+Q I
Sbjct: 9   EIENNVVLAPMAGFCDSAFRAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQNI 68

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
            A+    + K+ + +GV+ I IH R         ++       ++DI+ +++K    + I
Sbjct: 69  NAI---EVAKACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAVDTVVI 117

Query: 192 GLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS-SPIKTRVD 248
           G NG +     ++A+     VD VM+GRA+  N  +   + EY +   TG   P  T V+
Sbjct: 118 G-NGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN---TGELIPPPTPVE 173

Query: 249 KDFWRKISASMTDYAARHLHSGGKL-------QQITRHMIGLFHGFPNSRRCR 294
           +           D    HL    KL       ++I  H        PNS+  R
Sbjct: 174 R----------VDVLGEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 216


>gi|312075878|ref|XP_003140612.1| hypothetical protein LOAG_05027 [Loa loa]
 gi|307764220|gb|EFO23454.1| hypothetical protein LOAG_05027 [Loa loa]
          Length = 463

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 83/169 (49%), Gaps = 18/169 (10%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R   R     L  + +++ ++ + DA  R   +  L  S  ++PL +Q   
Sbjct: 51  MVDQSELAFRMMLRKHGAHLCFSPMIHAQLFITDATYR---RTALSTSLDDRPLIVQFCA 107

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ A ++VE F  + ++LN+GCP      G +GA L  +  ++ + +A +   L 
Sbjct: 108 NDPVTLLTACQLVESFC-DGVDLNLGCPQLIAKRGHYGAYLQEDQKLICEMVALLHSRLQ 166

Query: 117 IPVTVKCRI--GVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +P++ K RI   +++ I  AVAL        K+G   + +H R    +G
Sbjct: 167 LPLSCKIRILQNINETIAYAVAL-------VKAGACMLTVHGRTREQRG 208


>gi|161613134|ref|YP_001587099.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|161362498|gb|ABX66266.1| hypothetical protein SPAB_00842 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 331

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|251793338|ref|YP_003008066.1| tRNA-dihydrouridine synthase C [Aggregatibacter aphrophilus NJ8700]
 gi|247534733|gb|ACS97979.1| tRNA-dihydrouridine synthase C [Aggregatibacter aphrophilus NJ8700]
          Length = 312

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/201 (25%), Positives = 96/201 (47%), Gaps = 16/201 (7%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQHPQWLAENAELAIQLGSHGVDLNCGCPSKTVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+     V+VK R+G D    A    ++  ++++ G   I IH R   
Sbjct: 117 ELIYQATKAIRQAVPQEQAVSVKVRLGWDSTEFAY---DIADAVQQGGATEIAIHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               +  D  +   +++  + EI+++   P +  G     ED  + L  +   D +M+GR
Sbjct: 171 ----TKTDGYRADRINWQKIGEIRQKLNIPVIANGEIWRWEDGQRCL-TMTGCDDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLT 238
            A  N   L+ V ++   PL+
Sbjct: 226 GAL-NMPNLSRVLKHNDVPLS 245


>gi|156972542|ref|YP_001443449.1| tRNA-dihydrouridine synthase B [Vibrio harveyi ATCC BAA-1116]
 gi|156524136|gb|ABU69222.1| hypothetical protein VIBHAR_00174 [Vibrio harveyi ATCC BAA-1116]
          Length = 331

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 113/244 (46%), Gaps = 20/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G + +       ++ K  +  G+  + +H R    + KG +          +Y
Sbjct: 145 VTLKTRTGWNTENKNCV--HIAKLAEDCGIQALALHGRTKACMYKGEA----------EY 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  Y  
Sbjct: 193 DSIKAVKQAISIPVIA-NGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLE 251

Query: 235 NPLT 238
           N  T
Sbjct: 252 NGTT 255


>gi|326435888|gb|EGD81458.1| DUS3L protein [Salpingoeca sp. ATCC 50818]
          Length = 612

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 75/301 (24%), Positives = 117/301 (38%), Gaps = 44/301 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT-------------EMIVADAILRGDKKN--ILGFST 45
            +DW D+ Y   A L T   L +              EM +A  +L G K    +L    
Sbjct: 256 QIDWKDKLY--LAPLTTVGNLPFRRLCKRLGADITCGEMAMARNLLEGQKSEWALLRRHE 313

Query: 46  QEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            E    +QI G      +K VE      D  +  I+LN GCP   V     G+ L+    
Sbjct: 314 SEDVFGVQICGNHPRLTTKCVELLSNETDVDF--IDLNCGCPIDLVFNHGSGSALLARKR 371

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +GD +  M  A  +P+TVK R GV +   +     L+   + +GV+ + IH R      
Sbjct: 372 RLGDILRGMSFASRVPITVKIRAGVTNT--SWTSHTLMPIFRDAGVSLVSIHGRS----- 424

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAY 220
              +  R     D+  V +  +E   L +  NG +    +A+  K    V G+M+ R A 
Sbjct: 425 ---RQQRYARLADWGYVRKCVEEAKGLPVYGNGDILSFEEAMQHKATTGVSGLMLARGAL 481

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               + T + E     ++ S   + +  KDF         DY   H  S  +  + TR  
Sbjct: 482 IKPWLFTEIKEQRHWDISSSE--RFQFLKDF--------ADYGLTHWGSDQQGVETTRRF 531

Query: 281 I 281
           +
Sbjct: 532 L 532


>gi|325579218|ref|ZP_08149174.1| tRNA-dihydrouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
 gi|325159453|gb|EGC71587.1| tRNA-dihydrouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
          Length = 307

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 109/249 (43%), Gaps = 35/249 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+  + P+ +Q+ G   + L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTPSKTPVRVQLLGQHPNCLAENANRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ + +   +PV+VK R+G D    A     +  ++++ G   I IH R   
Sbjct: 117 ELIYQATLALRQTVPSHLPVSVKVRLGWDCTSQAF---EIADAVQQGGATEITIHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               +  D  +   ++++ + E++     P +  G     ED    LK     D +M+GR
Sbjct: 171 ----TKADGYRADRINWEKIGEVRSRLTIPVIANGEIWRWEDGQACLKATGCED-LMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA-RHLHSGG----- 271
            A  N   L+ V             +K   +K  W  I   +  YA   + H  G     
Sbjct: 226 GAL-NIPNLSLV-------------LKQNCEKMPWVDIQKILQKYAEMENFHDSGFYHVA 271

Query: 272 KLQQITRHM 280
           +++Q  R++
Sbjct: 272 RIKQWLRYL 280


>gi|212634541|ref|YP_002311066.1| NifR3/Smm1 family protein [Shewanella piezotolerans WP3]
 gi|212556025|gb|ACJ28479.1| NifR3/Smm1 family protein [Shewanella piezotolerans WP3]
          Length = 311

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 108/230 (46%), Gaps = 31/230 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G   +++N GCP+  V+  + GA ++  P
Sbjct: 50  GETASGTPVRVQLLGQEPGWMAENAIRAIEMGSKGVDVNFGCPAKMVNRSNGGAVMLQYP 109

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + + + AM +A+    PVT K R+G +D+  ++ + N  ++I ++G + + +HAR  +
Sbjct: 110 EQLYNVVKAMREAVPEQHPVTAKIRLGFNDK--SLYMEN-AQAIYEAGASELAVHARSKV 166

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                  D  K P   ++ + +I  + P   I  NG + ++  A +   L   D +M+GR
Sbjct: 167 -------DGYKPPAY-WEYITDINAKLPIPVIA-NGEIWNVDDARRCMELTGCDSIMVGR 217

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
            A     +  ++         G++P         W++  A M +Y  R L
Sbjct: 218 GAISLPNLAASIK--------GAAPYT-------WQQSLALMLEYTNREL 252


>gi|261400872|ref|ZP_05986997.1| tRNA-dihydrouridine synthase C [Neisseria lactamica ATCC 23970]
 gi|269209349|gb|EEZ75804.1| tRNA-dihydrouridine synthase C [Neisseria lactamica ATCC 23970]
          Length = 333

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 86/188 (45%), Gaps = 12/188 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P ++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR    +G  P 
Sbjct: 136 KTLRERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKA-EGYEPP 191

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D V      N D+F      L+D    +K     + VM+GR A     + 
Sbjct: 192 AHWEWIKKIRDAVNIPVTANGDVF-----SLQDYI-GIKTASGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFS 234
             + +Y S
Sbjct: 246 RQIKQYES 253


>gi|224583325|ref|YP_002637123.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|224467852|gb|ACN45682.1| hypothetical protein SPC_1528 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
          Length = 316

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 68  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 128 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 178 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 235

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 236 NLSRVVKY 243


>gi|296392551|ref|YP_003657435.1| hypothetical protein Srot_0113 [Segniliparus rotundus DSM 44985]
 gi|296179698|gb|ADG96604.1| TIM-barrel protein, nifR3 family [Segniliparus rotundus DSM 44985]
          Length = 386

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 102/214 (47%), Gaps = 25/214 (11%)

Query: 16  LTNNA--LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-- 69
           LT  A  L   EM++A +++  + K   ++ F  +E+P ++Q+   D   + EA +++  
Sbjct: 45  LTGQARGLYVNEMVMARSLVNRNPKAMRMIEFGPEERPRSMQLYTVDPEAVGEAVRMIVA 104

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV 127
           ED   + ++LN GCP  +V     GA L     +    I A       ++P+TVK R+G+
Sbjct: 105 EDLA-DHVDLNFGCPVPKVTRNGGGAALPYKRRLFARIIEAAVNGAQGAVPITVKFRVGI 163

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           DD+       +  +  + SG   + +HAR A  +  G +          D+  +  +K+ 
Sbjct: 164 DDE--HHTYLDAGRIAQDSGAASVALHARTAAQLYSGTA----------DWSAIARLKEH 211

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
             ++ +  NG +   + A +++     DGV++GR
Sbjct: 212 VTEIPVLGNGDIFAAADAKRMMDQTGCDGVVVGR 245


>gi|195873972|ref|ZP_02700016.2| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|195631197|gb|EDX49757.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
          Length = 331

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|159473569|ref|XP_001694906.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158276285|gb|EDP02058.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 368

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 101/217 (46%), Gaps = 20/217 (9%)

Query: 12  FARLLTNN--ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           + RL T++  A+  +EM++A  +L  +++   +  F+  E+  ++Q+ G    +L +A +
Sbjct: 9   YRRLATSHGAAMATSEMVIASTLLVKNRRTRKLASFADDERVRSVQLYGVKPEQLEQAVR 68

Query: 68  I-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--IAAMCKALSIPVTVKCR 124
           + V + G   ++LN GCP  ++     G+ L L P +       A        PVTVK R
Sbjct: 69  LLVCEHGVQHVDLNFGCPVRKITARGGGSALPLRPRLFAKLVAAAVAGAGGEAPVTVKFR 128

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G+  ++P       +   +  G   + +HAR A     SP D   +  L   +   +  
Sbjct: 129 VGLTPELPTHLQAGRIA--EAEGAAALVLHARTADQLYASPVDWAAVRALVEAVRIPVVG 186

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAA 219
            N D+F G        + AL++L      GVM+GRAA
Sbjct: 187 -NGDVFEG--------ADALRLLRETGCAGVMVGRAA 214


>gi|154509409|ref|ZP_02045051.1| hypothetical protein ACTODO_01940 [Actinomyces odontolyticus ATCC
           17982]
 gi|153799043|gb|EDN81463.1| hypothetical protein ACTODO_01940 [Actinomyces odontolyticus ATCC
           17982]
          Length = 411

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 56/220 (25%), Positives = 104/220 (47%), Gaps = 25/220 (11%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK-IVE 70
           R+     L  TEM+ + A++  +++ +  +     E+  +LQ+ G + + + +AA  +VE
Sbjct: 63  RVDAPAGLYVTEMVTSRALVEENERTLEMVRPDPAERVRSLQLYGVNPAVMAKAATMLVE 122

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---------SIPVTV 121
               + I+LN GCP  +V +   GA L    D+  D + A+ +A           IPVTV
Sbjct: 123 RDLTDHIDLNFGCPVPKVTKKGGGAALPWKRDLFSDLVGAVVRACDEAGERAGREIPVTV 182

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D +       +   + +K G   + +HAR         ++     +  +D +  
Sbjct: 183 KIRIGIDSEHETAT--DAALNAQKLGAAALTLHART--------QNQHYAGHAHWDEIAR 232

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           + K+  D+ +  NG + + + AL +L     DG+ +GR A
Sbjct: 233 L-KDLLDIPVFGNGDVFEAADALAMLEQTGCDGISVGRGA 271


>gi|154505842|ref|ZP_02042580.1| hypothetical protein RUMGNA_03383 [Ruminococcus gnavus ATCC 29149]
 gi|153793860|gb|EDN76280.1| hypothetical protein RUMGNA_03383 [Ruminococcus gnavus ATCC 29149]
          Length = 312

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 51/197 (25%), Positives = 86/197 (43%), Gaps = 11/197 (5%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +IL    Q      QI        ++ A+ + ++GY E+NLN+GCPS  V     GA
Sbjct: 48  EKNDILPMHNQGMCAIPQILTNSAEDFIKTAERLGEYGYEEVNLNLGCPSKTVVSKGRGA 107

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  PD +   +  + +   I ++VK RIG +   P   +R L++   +  +  + IH 
Sbjct: 108 GFLAEPDRLNAFLEELFEKTPIRISVKTRIGKES--PEEWIR-LLEIYNQYPMEELIIHP 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           R      +     +  PNL+    Y +K  +NP  + G     E+          V  VM
Sbjct: 165 R------IQTDFYKNTPNLEM-FEYAVKNSKNPLCYNGDICTKEEYEIICNRFQEVPSVM 217

Query: 215 IGRAAYKNSAMLTTVDE 231
           IGR   KN  ++  + +
Sbjct: 218 IGRGILKNPGLVRKIRQ 234


>gi|322707013|gb|EFY98592.1| tRNA dihydrouridine synthase (Smm1), putative [Metarhizium
           anisopliae ARSEF 23]
          Length = 457

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 88/183 (48%), Gaps = 21/183 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + VEAA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 148 LIFQIGTADPDRAVEAARLVA-ADVAGIDVNAGCPKPFSTSGGMGAALLRTPDKLVAILE 206

Query: 110 AMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K ++    I ++VK RI    + PA     LV+ +  +G+ G+ +H R   ++   P
Sbjct: 207 ALVKNITPEFDIGISVKIRI---LETPA-ETEALVRRLVATGITGLTVHCRTTPMR---P 259

Query: 166 KDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++   R    +  +I +E       +   +NG +E+  Q +K+      DG MI  AA K
Sbjct: 260 RERAIRDQLRMVANICHEA-----GIACIMNGDVENRDQGIKLAGEYGADGAMIAVAAEK 314

Query: 222 NSA 224
           N +
Sbjct: 315 NPS 317


>gi|322378794|ref|ZP_08053223.1| Putative tRNA-dihydrouridine synthase [Helicobacter suis HS1]
 gi|322380643|ref|ZP_08054795.1| tRNA-dihydrouridine synthase [Helicobacter suis HS5]
 gi|321146965|gb|EFX41713.1| tRNA-dihydrouridine synthase [Helicobacter suis HS5]
 gi|321148824|gb|EFX43295.1| Putative tRNA-dihydrouridine synthase [Helicobacter suis HS1]
          Length = 350

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 101/202 (50%), Gaps = 18/202 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EMI + A++    K   +L  S +E P ++QI G+ +  + +A +++    G + ++ N
Sbjct: 58  SEMISSHALVHAFDKTSKMLQKSPEESPFSVQIAGSKMEVVKQAVELLNTTTGIDILDFN 117

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ +   +   +  +    + P T VK R+G D++IP      +
Sbjct: 118 CGCPAPKVANHGNGSGLLKDLKHLVKLLELIKTTTNKPYTSVKVRLGFDEKIPL----EI 173

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +HAR       +  D  K   +DYD V  +++      I  NG ++ 
Sbjct: 174 AHALNDAPVDFVVVHAR-------TRSDRYKKERIDYDSVRLMRQILHKPLIA-NGEIDS 225

Query: 200 MSQALKILP--SVDGVMIGRAA 219
             +A ++L     +GVMIGR++
Sbjct: 226 PKKAREVLEYTGANGVMIGRSS 247


>gi|301155565|emb|CBW15033.1| tRNA-dihydrouridine synthase C [Haemophilus parainfluenzae T3T1]
          Length = 303

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 109/249 (43%), Gaps = 35/249 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+  + P+ +Q+ G   + L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 50  GFTPSKTPVRVQLLGQHPNCLAENANRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 109

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ + +   +PV+VK R+G D    A     +  ++++ G   I IH R   
Sbjct: 110 ELIYQATLALRQTVPSHLPVSVKVRLGWDCTSQAF---EIADAVQQGGATEITIHGR--- 163

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               +  D  +   ++++ + E++     P +  G     ED    LK     D +M+GR
Sbjct: 164 ----TKADGYRADRINWEKIGEVRSRLTIPVIANGEIWRWEDGQACLKATGCED-LMVGR 218

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA-RHLHSGG----- 271
            A  N   L+ V             +K   +K  W  I   +  YA   + H  G     
Sbjct: 219 GAL-NIPNLSLV-------------LKQNCEKMPWVDIQKILQKYAEMENFHDSGFYHVA 264

Query: 272 KLQQITRHM 280
           +++Q  R++
Sbjct: 265 RIKQWLRYL 273


>gi|126174794|ref|YP_001050943.1| dihydrouridine synthase DuS [Shewanella baltica OS155]
 gi|217972939|ref|YP_002357690.1| dihydrouridine synthase DuS [Shewanella baltica OS223]
 gi|125997999|gb|ABN62074.1| dihydrouridine synthase, DuS [Shewanella baltica OS155]
 gi|217498074|gb|ACK46267.1| dihydrouridine synthase DuS [Shewanella baltica OS223]
          Length = 317

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 104/231 (45%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P
Sbjct: 57  GNTPSGTPVRVQLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + V D + AM +A+     VT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 ESVHDIVKAMRQAVPKEHAVTAKIRLGYEDK--SLFMENAI-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  + P   ++ + E++K  P   I  NG + +   A + +     D +MIGR
Sbjct: 174 -------DGYRPPAY-WEYITEVRKRLPIPVIA-NGEIWNSDDAKRCIEVTGCDSIMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W +    M  Y  R L+
Sbjct: 225 GAISLPNLADTIK-------TGATPYT-------WAQTLGLMLSYTQRELN 261


>gi|323213523|gb|EFZ98314.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
          Length = 331

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMAASGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|322514831|ref|ZP_08067850.1| tRNA-dihydrouridine synthase C [Actinobacillus ureae ATCC 25976]
 gi|322119213|gb|EFX91354.1| tRNA-dihydrouridine synthase C [Actinobacillus ureae ATCC 25976]
          Length = 319

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 70/287 (24%), Positives = 118/287 (41%), Gaps = 37/287 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ + 
Sbjct: 61  GLTDSGTPVRVQLLGQHPQWLAENAQLAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDL 120

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D++     AM +A+     V+VK R+G D  DQ   +A      ++ + G N I +H R 
Sbjct: 121 DLIYRATKAMREAVPQDQIVSVKVRLGWDSADQCFEIA-----DAVAQGGANEITVHGR- 174

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMI 215
                 + +D  +   +++  + EI+K      I  NG + D   A   +   +   +MI
Sbjct: 175 ------TKQDGYRAERINWQAIGEIQKRLSIPVIA-NGEIWDFESAKNCQNTTACSSLMI 227

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           GR A  N+  L+ V             +K    K  W ++   +  Y             
Sbjct: 228 GRGAL-NTPNLSRV-------------VKFNQPKMAWNEVLQLLFQYVNMENEDDSGFYH 273

Query: 276 ITRHMIGLFH---GFPNSRRCRHILTVEAGASTATHHIIETAFNLMI 319
           + R    L +    +P ++    IL  E G      H IE A N  I
Sbjct: 274 VARIKQWLHYLDKEYPEAKDLFQILKTEHGYDGLNAH-IERAVNQEI 319


>gi|304409222|ref|ZP_07390843.1| dihydrouridine synthase DuS [Shewanella baltica OS183]
 gi|307303225|ref|ZP_07582980.1| dihydrouridine synthase DuS [Shewanella baltica BA175]
 gi|304353043|gb|EFM17440.1| dihydrouridine synthase DuS [Shewanella baltica OS183]
 gi|306913585|gb|EFN44007.1| dihydrouridine synthase DuS [Shewanella baltica BA175]
          Length = 310

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 104/231 (45%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P
Sbjct: 50  GNTPSGTPVRVQLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYP 109

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + V D + AM +A+     VT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 110 ESVHDIVKAMRQAVPKEHAVTAKIRLGYEDK--SLFMENAI-AVYEAGATELAIHARSKV 166

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  + P   ++ + E++K  P   I  NG + +   A + +     D +MIGR
Sbjct: 167 -------DGYRPPAY-WEYIKEVRKRLPIPVIA-NGEIWNSDDAKRCIEVTGCDSIMIGR 217

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W +    M  Y  R L+
Sbjct: 218 GAISLPNLADTIK-------TGATPYT-------WAQTLGLMLSYTQRELN 254


>gi|302687524|ref|XP_003033442.1| hypothetical protein SCHCODRAFT_256941 [Schizophyllum commune H4-8]
 gi|300107136|gb|EFI98539.1| hypothetical protein SCHCODRAFT_256941 [Schizophyllum commune H4-8]
          Length = 467

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 49/176 (27%), Positives = 83/176 (47%), Gaps = 20/176 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQE---------KPL 50
           MVD ++  +R   R      + YT MI A      G K+    F   E         +PL
Sbjct: 43  MVDQSELAFRILCRRY-GAQVAYTPMINAHVFPFYGKKQQDKNFDVSEGEEGAQGLDRPL 101

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q  G +  +L+ +A+IVE    + ++LN+GCP     +G +G+ L    ++V   +  
Sbjct: 102 VVQFCGNNPDELLASARIVEAH-CDAVDLNLGCPQDIAKKGHYGSWLQDEWELVYKLVNT 160

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGIWIHARKAILKGLS 164
           + + LSIPVT K RI  D +      R L   K ++++G   + +H R    +G++
Sbjct: 161 LHENLSIPVTAKFRIFSDPE------RTLAYAKMLERAGAQILTVHGRTRDQRGVN 210


>gi|205353310|ref|YP_002227111.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207857608|ref|YP_002244259.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|238912616|ref|ZP_04656453.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|205273091|emb|CAR38045.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|206709411|emb|CAR33752.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
          Length = 312

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|294141562|ref|YP_003557540.1| tRNA-dihydrouridine synthase C [Shewanella violacea DSS12]
 gi|293328031|dbj|BAJ02762.1| tRNA-dihydrouridine synthase C [Shewanella violacea DSS12]
          Length = 310

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 83/175 (47%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G     + E A+   + G   ++LN GCP+  V+  + GA ++  P+ +   +
Sbjct: 64  PVRLQLLGQHPQWMAENAQRAIELGSLGVDLNFGCPAPMVNRSNGGAAMLKEPETIYRVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   +P T K R+G DD+   V    + ++I+ +G   + +HAR         K
Sbjct: 124 KAVREAVPEQLPATAKIRLGWDDKSRCV---EIAQAIEAAGATELTVHART--------K 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
           +    P   ++ + +IK+      I  NG +      LK   +   D VMIGR A
Sbjct: 173 EEGYRPPAHWEYIQQIKQAISIPVIA-NGEVWSREDYLKCQQVSQCDDVMIGRGA 226


>gi|326628399|gb|EGE34742.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 316

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 68  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 128 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 178 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 235

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 236 NLSRVVKY 243


>gi|161502677|ref|YP_001569789.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160864024|gb|ABX20647.1| hypothetical protein SARI_00724 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 305

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G + ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 60  IQLLGQHPGWLAENAVRAVELGSHGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 119

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 120 REAVPAHLPVTVKVRLGWDSDARQF---EIADAVQQAGATELVVHGR-------TKEDGY 169

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI+       I  NG + D   +QA       D VMIGR A  N   L+
Sbjct: 170 KAECINWSAIGEIRNRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLS 227

Query: 228 TVDEY 232
            V +Y
Sbjct: 228 RVVKY 232


>gi|124265679|ref|YP_001019683.1| tRNA-dihydrouridine synthase B [Methylibium petroleiphilum PM1]
 gi|124258454|gb|ABM93448.1| tRNA-dihydrouridine synthase B [Methylibium petroleiphilum PM1]
          Length = 349

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 63/255 (24%), Positives = 109/255 (42%), Gaps = 27/255 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G +
Sbjct: 20  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKELWHSLKTSRRANHDGEVAPIAVQIAGTE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKAL 115
              + EAA    D G   I++N+GCP+ +V     G+ LM +  +   + + +   C   
Sbjct: 79  PLMMAEAAAYNIDRGAQVIDINMGCPAKKVCNVWAGSALMRDESLALRIVEAVVTACAPH 138

Query: 116 SIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +PVT+K R G + Q   AVAL    +S+   G+  + +H R         ++     + 
Sbjct: 139 GVPVTLKMRTGWNMQNRNAVALARGAESL---GIAMLTVHGRT--------REQGYAGSA 187

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA------YKNSAML 226
           ++D V  +K     + +  NG ++   +A  +L +   D VM+GRAA      ++  A  
Sbjct: 188 EHDTVRAVKTAV-QVPVVANGDIDSPEKARDVLAATGADAVMVGRAAQGRPWIFREIAHF 246

Query: 227 TTVDEYFSNPLTGSS 241
               E    P T  +
Sbjct: 247 LATGERLPPPRTAQA 261


>gi|326624009|gb|EGE30354.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
          Length = 316

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 68  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 128 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 178 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 235

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 236 NLSRVVKY 243


>gi|168242260|ref|ZP_02667192.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194448667|ref|YP_002046228.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194406971|gb|ACF67190.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205338332|gb|EDZ25096.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 312

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|331091090|ref|ZP_08339932.1| hypothetical protein HMPREF9477_00575 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330405312|gb|EGG84848.1| hypothetical protein HMPREF9477_00575 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 314

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 76/171 (44%), Gaps = 15/171 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +  AK +E+ GY EINLN+GCPS  V     G+  +  P+ +   +  +   L + ++V
Sbjct: 73  FITTAKEIENMGYKEINLNLGCPSGTVVAKGKGSGFLAYPEELDRFLDNIYSKLDMKISV 132

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG   +        L++   K  +  + +H R      L     +  PNL    +++
Sbjct: 133 KTRIG---KTSPDEFYRLIEIYNKYPLEELIVHPR------LQTDFYKNKPNLQ---IFK 180

Query: 182 IKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              E     +  NG +   ED  +  +  P+V+ +M GR A  N ++   +
Sbjct: 181 EAVEMSRHSLCYNGDIYTVEDFQKFSEHFPTVEKIMCGRGAVANPSLFDAI 231


>gi|300722436|ref|YP_003711724.1| tRNA -dihydrouridine synthase C [Xenorhabdus nematophila ATCC
           19061]
 gi|297628941|emb|CBJ89524.1| tRNA-dihydrouridine synthase C [Xenorhabdus nematophila ATCC 19061]
          Length = 324

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 84/175 (48%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQYPEWLAENAVRAIELGSWGVDLNCGCPSKTVNGSGGGASLLKDPELIYRGA 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM +A+    PVTVK R+G D          +  +I+++G   + +H R       + +
Sbjct: 124 KAMREAVPDCFPVTVKVRLGWDS---GARQFEIADAIQQAGATELVVHGR-------TKE 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           D  K   ++++ + EI++    + +  NG + D   A   + +   + VMIGR A
Sbjct: 174 DGYKAERINWEAIGEIRR-RLSIPVVANGEIWDWQSAQACIKTTGCNAVMIGRGA 227


>gi|239788483|ref|NP_001155091.1| tRNA-dihydrouridine synthase 3-like isoform 2 [Homo sapiens]
 gi|13528705|gb|AAH04549.1| DUS3L protein [Homo sapiens]
 gi|119589550|gb|EAW69144.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
 gi|325463133|gb|ADZ15337.1| dihydrouridine synthase 3-like (S. cerevisiae) [synthetic
           construct]
          Length = 408

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 67/283 (23%), Positives = 118/283 (41%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 93  EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 148

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++      
Sbjct: 149 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERVNLA--H 206

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 207 RLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 257

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 258 ILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 306

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 307 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 344


>gi|239917156|ref|YP_002956714.1| putative TIM-barrel protein, nifR3 family [Micrococcus luteus NCTC
           2665]
 gi|281414375|ref|ZP_06246117.1| putative TIM-barrel protein, nifR3 family [Micrococcus luteus NCTC
           2665]
 gi|239838363|gb|ACS30160.1| putative TIM-barrel protein, nifR3 family [Micrococcus luteus NCTC
           2665]
          Length = 436

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 66/298 (22%), Positives = 121/298 (40%), Gaps = 27/298 (9%)

Query: 12  FARLLTN--NALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       L   EM+ A A++  + +   I+     E P ++Q+   D      A +
Sbjct: 84  FRRLCREYGGGLYVNEMVTARALVERKPESMRIIQHDPDEVPRSVQLYSVDPVTTGAAVR 143

Query: 68  -IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL--SIPVTVKC 123
            +VE+   + I++N GCP  +V     G+ L    ++    + AA+ +A    IPVTVK 
Sbjct: 144 MLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVTEAAKKDIPVTVKM 203

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYE 181
           R G+D+    +   +  ++ +  GV  + +H R  +    G +           +D +  
Sbjct: 204 RRGIDED--HLTFLDAGRTARDLGVAAVALHGRTTRQFYSGTA----------VWDDIAR 251

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++  PD+ +  NG +     A+ ++    VDGV+IGR       +   +   F      
Sbjct: 252 LREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGDLQAAFEGRQDR 311

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             P    V    +R     +  +      +   L+ I +H+   F G+P     R  L
Sbjct: 312 FHPTLGMVADTLYRHAELLVDTFGGDETKA---LRDIRKHVAWYFKGYPVGSEIRTAL 366


>gi|198242215|ref|YP_002216259.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|197936731|gb|ACH74064.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
          Length = 312

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|123288586|emb|CAM27544.1| dihydrouridine synthase 1-like (S. cerevisiae) [Mus musculus]
          Length = 166

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 67/130 (51%), Gaps = 8/130 (6%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 82  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERL 140

Query: 116 SIPVTVKCRI 125
           S+PVT K R+
Sbjct: 141 SVPVTCKIRV 150


>gi|153001139|ref|YP_001366820.1| dihydrouridine synthase DuS [Shewanella baltica OS185]
 gi|151365757|gb|ABS08757.1| dihydrouridine synthase DuS [Shewanella baltica OS185]
          Length = 317

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 104/231 (45%), Gaps = 30/231 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P
Sbjct: 57  GNTPSGTPVRVQLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYP 116

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + V D + AM +A+     VT K R+G +D+  ++ + N + ++ ++G   + IHAR  +
Sbjct: 117 ESVHDIVKAMRQAVPKEHAVTAKIRLGYEDK--SLFMENAI-AVYEAGATELAIHARSKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
                  D  + P   ++ + E++K  P   I  NG + +   A + +     D +MIGR
Sbjct: 174 -------DGYRPPAY-WEYITEVRKRLPIPVIA-NGEIWNSDDAKRCIEVTGCDSIMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A     +  T+        TG++P         W +    M  Y  R L+
Sbjct: 225 GAISLPNLADTIK-------TGATPYT-------WAQTLGLMLSYTQRELN 261


>gi|303247058|ref|ZP_07333333.1| dihydrouridine synthase DuS [Desulfovibrio fructosovorans JJ]
 gi|302491484|gb|EFL51369.1| dihydrouridine synthase DuS [Desulfovibrio fructosovorans JJ]
          Length = 331

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 49/162 (30%), Positives = 77/162 (47%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R L   A+  TEM+ A  +    +  K +L     + PL +Q+ GAD
Sbjct: 16  LAGFSDLPFRLLCREL-GAAVAMTEMVSAKGLFYDSRNTKRLLATLPPDSPLVVQLFGAD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              L  A   +   GY   +LN GC   +V +   GA L+ +PD +  C  AM +A    
Sbjct: 75  PDYLSRAVTALSGEGYGFFDLNCGCSVRKVVKTGAGAALLGDPDKLVACARAMVEAAGDA 134

Query: 118 PVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V VK R+G       A+ALR+    + ++GV  + +H R A
Sbjct: 135 HVGVKLRLGPKPPDFCALALRD---RLTEAGVAWLTLHPRHA 173


>gi|242774281|ref|XP_002478411.1| dihydrouridine synthase family protein, putative [Talaromyces
           stipitatus ATCC 10500]
 gi|218722030|gb|EED21448.1| dihydrouridine synthase family protein, putative [Talaromyces
           stipitatus ATCC 10500]
          Length = 524

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 89/205 (43%), Gaps = 17/205 (8%)

Query: 33  LRGDKKNIL---GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +R D  N+    G    ++PL +Q    D +  +EAA++V  +  + ++LN+GCP     
Sbjct: 83  VRRDDPNVPFLDGNPAIDRPLFVQFCANDPNDFLEAARLVAPYC-DAVDLNLGCPQGIAR 141

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +G +GA L  + D++   I  +   L +PVT K RI    Q          K I  +G +
Sbjct: 142 KGHYGAFLQEDWDLIYKLINRLHTELPVPVTAKFRI----QETKEKTLEYAKMILSAGAS 197

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKI 206
            I +H R+   KG     N  + +  Y I Y  +   P   I  NG +    D+   L+ 
Sbjct: 198 IITVHGRRREQKG----HNTGVADWSY-IKYLRENLPPKTVIFANGNILNHGDIEHCLEA 252

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDE 231
               DGVM       +  + + V E
Sbjct: 253 T-GADGVMSAEGNLSDPTIFSKVPE 276


>gi|254360707|ref|ZP_04976855.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|153091277|gb|EDN73251.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
          Length = 306

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 63/279 (22%), Positives = 116/279 (41%), Gaps = 38/279 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A +  + G + ++LN GCPS  V+  + GA L+ +P
Sbjct: 50  GLTDSGTPVRVQLLGQHPQWLAENAALAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDP 109

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     AM +A+     V+VK R+G D          +  ++++ G N I +H R  +
Sbjct: 110 ELIYRATKAMREAVPSDKIVSVKVRLGWDS---VSQCFEIADAVEQGGANEITVHGRTKV 166

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGR 217
                  D  +   +++  + EI++      I  NG + D   A   + + +   +M+GR
Sbjct: 167 -------DGYRAERINWQAIGEIQQRLSIPVIA-NGEIWDFESAKNCQKITACKALMMGR 218

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH------LHSGG 271
            A  N+  L+ V             +K  V K  W ++   +  Y           +   
Sbjct: 219 GAL-NTPNLSKV-------------VKYNVPKMAWNEVLQLLFKYVQMENQFDTGFYHVA 264

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           +++Q  R+   L   +P +     IL  E G      HI
Sbjct: 265 RIKQWLRY---LDKEYPQAVELFDILKTEHGYDGLKAHI 300


>gi|327348456|gb|EGE77313.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis ATCC 18188]
          Length = 508

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 95/219 (43%), Gaps = 23/219 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N     T       I R D         +   L  QIG A  +  V+AAKI+  
Sbjct: 91  FTRLPSNGGRQNTPNAKESVIYRIDPHR------ESGKLIFQIGTASPNLAVQAAKIIA- 143

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD++   + A+ + +  P    ++VK R+  
Sbjct: 144 ADVAGIDVNAGCPKPFSTSGGMGAALLQTPDLLVSILTALVQQIGNPYQIGISVKIRLLA 203

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 204 DPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRERAIRAQLP-----MIASICRAA- 253

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            + I +NG +E     L ++    VDG MI  +A  NS+
Sbjct: 254 GVAILMNGDVESRDHGLALMSEYGVDGAMIATSAEANSS 292


>gi|154175306|ref|YP_001408795.1| dihydrouridine synthase (Dus) superfamily protein [Campylobacter
           curvus 525.92]
 gi|112803746|gb|EAU01090.1| dihydrouridine synthase (Dus) superfamily [Campylobacter curvus
           525.92]
          Length = 307

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 61/203 (30%), Positives = 107/203 (52%), Gaps = 21/203 (10%)

Query: 24  TEMIVADAIL--RGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           +EMI A+A++   G K   +L  S  E P  +QI G+DI  + +A  I+  F G + I+L
Sbjct: 36  SEMISANALVYESGAKTLEMLKKSPNETPYIVQIAGSDIENIKKAVAIINKFDGIDGIDL 95

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRN 138
           N GCP  +V +   G+ L+ + + +   I A+ K  +  +T VK R+G +++       +
Sbjct: 96  NCGCPVPKVVKQCAGSALLNDLENLKRIIEAIKKISNKTMTSVKFRLGFNEKNQV----D 151

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           + K+ +++G + I IH R     G S K       +DY+ + +  K +  + +  NG + 
Sbjct: 152 IAKACEEAGADYIAIHGRTR-AGGYSAK-------VDYEAIAQ-AKASVKIPVVANGDIN 202

Query: 198 -EDMSQALKILPSVDGVMIGRAA 219
            ++ S+ L  L S D +MIGRA+
Sbjct: 203 SQNASEILA-LTSCDALMIGRAS 224


>gi|289621184|emb|CBI51967.1| unnamed protein product [Sordaria macrospora]
          Length = 614

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 95/219 (43%), Gaps = 24/219 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G  + ++ L +Q    D S L+ AAK+V  +  + ++LN+GCP      G +G+ L  N 
Sbjct: 129 GNPSIDRSLFVQFCANDPSYLLSAAKLVAPYC-DAVDLNLGCPQGIAKRGQYGSFLQENQ 187

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +++ + I  + K L IPVT K RI    +    A     +++ ++G + + +H R+   K
Sbjct: 188 ELIFELINTLHKELDIPVTAKIRILETKE----ATLKYAQNVLRAGASILTVHGRRREQK 243

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           G        + N +Y I Y  +    +  I  NG +   S   K L +   DGVM     
Sbjct: 244 G----HQTGLANWEY-IRYLRENLPKETVIFANGNILQYSDLEKCLEATGADGVMSAEGN 298

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
             +  +       F+ P     P      +++WR    S
Sbjct: 299 LSDPGL-------FAKP-----PAVGEEGREYWRSKDGS 325


>gi|261493422|ref|ZP_05989947.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
 gi|261496889|ref|ZP_05993257.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261307413|gb|EEY08748.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261310916|gb|EEY12094.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
          Length = 317

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 63/279 (22%), Positives = 116/279 (41%), Gaps = 38/279 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A +  + G + ++LN GCPS  V+  + GA L+ +P
Sbjct: 61  GLTDSGTPVRVQLLGQHPQWLAENAALAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDP 120

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     AM +A+     V+VK R+G D          +  ++++ G N I +H R  +
Sbjct: 121 ELIYRATKAMREAVPSDKIVSVKVRLGWDS---VSQCFEIADAVEQGGANEITVHGRTKV 177

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGR 217
                  D  +   +++  + EI++      I  NG + D   A   + + +   +M+GR
Sbjct: 178 -------DGYRAERINWQAIGEIQQRLSIPVIA-NGEIWDFESAKNCQKITACKALMMGR 229

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH------LHSGG 271
            A  N+  L+ V             +K  V K  W ++   +  Y           +   
Sbjct: 230 GAL-NTPNLSKV-------------VKYNVPKMAWNEVLQLLFKYVQMENQFDTGFYHVA 275

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           +++Q  R+   L   +P +     IL  E G      HI
Sbjct: 276 RIKQWLRY---LDKEYPQAVELFDILKTEHGYDGLKAHI 311


>gi|295093806|emb|CBK82897.1| tRNA-U20a,U20b-dihydrouridine synthase [Coprococcus sp. ART55/1]
          Length = 322

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 81/173 (46%), Gaps = 13/173 (7%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            V AAK +++ GYNE+N+N+GCPS  V     G+ L+ + + + + +  +  A  + V++
Sbjct: 78  FVTAAKFLKELGYNEVNINLGCPSKTVVTKYKGSGLIYDTERLDNFLYEVFAADVMDVSI 137

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG D    +V   ++++  KK  ++ + IH R      +     +  PN++      
Sbjct: 138 KTRIGRDS---SVEFEDIIEIYKKYPISELIIHPR------IQTDFYKNTPNMEVFAEGV 188

Query: 182 IKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                PD  +  NG +    D  +     P +  VMIGR    +  +   ++E
Sbjct: 189 ASYGRPDT-VCYNGDINSVADYDRFTGDFPDISKVMIGRGIIADPCLAERINE 240


>gi|239625676|ref|ZP_04668707.1| dihydrouridine synthase [Clostridiales bacterium 1_7_47_FAA]
 gi|239519906|gb|EEQ59772.1| dihydrouridine synthase [Clostridiales bacterium 1_7_47FAA]
          Length = 322

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 64/269 (23%), Positives = 112/269 (41%), Gaps = 42/269 (15%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV---HEGSFGACLMLNPDIVGDCIA 109
           QI        +  A+I++D+GY E+NLN+GCPS  V   H+G+    L    +     + 
Sbjct: 64  QILTNQAEDFLTVARILKDYGYQEVNLNLGCPSGTVVSKHKGAGFLALTCGLNSFLSTVT 123

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
              + L + ++VK R+G+   +       L+    +  +  + IH R      +     R
Sbjct: 124 EQLEVLGMELSVKTRLGM---VTPDEFYELLDIYNQYHLKRLIIHPR------IRTDYYR 174

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
             PN +   ++    EN    +  NG +   ED  +  +  P +D VM+GR    N  ++
Sbjct: 175 NTPNWE---MFRHGLENSANHVCYNGDIFTVEDFKRLSRSYPELDEVMLGRGIIANPGLV 231

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-----KLQQITRHMI 281
             +        TG       VDK   R+    + +   R + SG      K+++I   MI
Sbjct: 232 GEIR-------TGRP-----VDKKQLREFHQLLYE-GYRGIMSGDRNVLFKMKEIWASMI 278

Query: 282 GLF-----HGFPNSRRCRHILTVEAGAST 305
            +F     HG    ++ +H+   EA  S+
Sbjct: 279 QIFADSEKHG-KKIKKAQHLTEYEAAVSS 306


>gi|153835711|ref|ZP_01988378.1| tRNA-dihydrouridine synthase B [Vibrio harveyi HY01]
 gi|148867644|gb|EDL66932.1| tRNA-dihydrouridine synthase B [Vibrio harveyi HY01]
          Length = 331

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 113/244 (46%), Gaps = 20/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G + +       ++ K  +  G+  + +H R    + KG +          +Y
Sbjct: 145 VTLKTRTGWNTENKNCV--HIAKLAEDCGIQALALHGRTKACMYKGEA----------EY 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  Y  
Sbjct: 193 DSIKAVKQAISIPVIA-NGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLE 251

Query: 235 NPLT 238
           N  T
Sbjct: 252 NGTT 255


>gi|332701296|ref|ZP_08421384.1| TIM-barrel protein, nifR3 family [Desulfovibrio africanus str.
           Walvis Bay]
 gi|332551445|gb|EGJ48489.1| TIM-barrel protein, nifR3 family [Desulfovibrio africanus str.
           Walvis Bay]
          Length = 322

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 102/230 (44%), Gaps = 15/230 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           +  ++D  +R   R L   A+  TEMI A  ++  D +N   IL   + + PL  Q+ G+
Sbjct: 17  LAGFSDLPFRLLCREL-GAAVTVTEMISARGLVY-DSRNTQPILATDSADSPLVAQLFGS 74

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALS 116
           +   + +A  ++   G+   +LN GC   +V +   GA LM +PD++     AM  +A  
Sbjct: 75  EPKFMGQATDMLLARGFTWFDLNCGCSVPKVVKTGSGAALMKDPDLLLAVAKAMVERASP 134

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V VK R+G +          + K+++++GV  + +H R A        D   +  L  
Sbjct: 135 FRVGVKMRLGWNPS--GENYLEVAKALEQAGVGWLTLHPRYAQQGFSGQADWAAVARLRQ 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            +   +     DLF       ED  + L+      GVM  R A ++ A+ 
Sbjct: 193 SVSIPVLASG-DLFTA-----EDAVRCLQET-GASGVMFARGALRDPAVF 235


>gi|168236343|ref|ZP_02661401.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194735562|ref|YP_002115264.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|204929001|ref|ZP_03220144.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|194711064|gb|ACF90285.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197290619|gb|EDY29974.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|204321545|gb|EDZ06744.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|322615201|gb|EFY12123.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617792|gb|EFY14688.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322624614|gb|EFY21445.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322626935|gb|EFY23731.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322634121|gb|EFY30857.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322635688|gb|EFY32398.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322640177|gb|EFY36841.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322646400|gb|EFY42912.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322649367|gb|EFY45803.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322656488|gb|EFY52777.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322661464|gb|EFY57688.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322665648|gb|EFY61832.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667172|gb|EFY63339.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322671178|gb|EFY67306.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675182|gb|EFY71259.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322680790|gb|EFY76825.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322686965|gb|EFY82942.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323192729|gb|EFZ77956.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323198839|gb|EFZ83938.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323205151|gb|EFZ90129.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323208194|gb|EFZ93138.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323215781|gb|EGA00524.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323221280|gb|EGA05703.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323223854|gb|EGA08157.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323231227|gb|EGA15342.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233661|gb|EGA17753.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237731|gb|EGA21791.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323245714|gb|EGA29708.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323248921|gb|EGA32845.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323253007|gb|EGA36840.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323258683|gb|EGA42345.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323259515|gb|EGA43150.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323268298|gb|EGA51773.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323271913|gb|EGA55329.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
          Length = 312

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMAASGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|296411986|ref|XP_002835709.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295629498|emb|CAZ79866.1| unnamed protein product [Tuber melanosporum]
          Length = 459

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 92/212 (43%), Gaps = 18/212 (8%)

Query: 21  LLYTEMIVADAI--LRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           L YT M+    +  +   KK +L F+T   ++PL  Q G         AA++V+ +  + 
Sbjct: 55  LCYTPMVSLKRLYWIASAKKLLLDFTTNASDRPLIAQFGAHSSIDFSRAAELVKPYT-DG 113

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           ++LN GCP +   +   G  LM  P +V + + A          V  +I V   +     
Sbjct: 114 VDLNCGCPQSWAIQEGIGCRLMQQPQLVKEMVRAAKDRCGEDFCVSIKIRVHHDLRETV- 172

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            + VK ++ SGV+ I IH R+   +   P ++  I          + K    + I  NG 
Sbjct: 173 -DFVKMVESSGVDYITIHGRRRSQRSSEPVNSEAI---------ALVKSLAGVPIVANGD 222

Query: 197 LEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
           +  +  A +I  +  VDGVM  R   +N A+ 
Sbjct: 223 VFSLGDAERIVGITGVDGVMAARGLMENPALF 254


>gi|242239833|ref|YP_002988014.1| tRNA-dihydrouridine synthase C [Dickeya dadantii Ech703]
 gi|242131890|gb|ACS86192.1| dihydrouridine synthase DuS [Dickeya dadantii Ech703]
          Length = 320

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A+     G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAERAVSLGSWGVDLNCGCPSKMVNGSGGGATLLKDPELIYQAAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+  ++PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAALPVTVKIRLGWDS---GARRFEIADAVQQAGATELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A   L +   D VM+GR A  N   L+
Sbjct: 177 QAERINWAAIGEIRRRLTIPVIA-NGEIWDWQSAQDCLAATGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|89901795|ref|YP_524266.1| dihydrouridine synthase [Rhodoferax ferrireducens T118]
 gi|89346532|gb|ABD70735.1| dihydrouridine synthase, DuS [Rhodoferax ferrireducens T118]
          Length = 335

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 95/198 (47%), Gaps = 16/198 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+A Q+ G+D   L E A  +   G + I+LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PVAAQLLGSDPVCLAENAARLAALGPHGIDLNFGCPAKTVNRHGGGAALLDEPELLLAIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+  ++PV+ K R+GV D   A+       +++  G + + +HAR         +
Sbjct: 124 AAVRRAVPKTMPVSAKMRLGVHDDSRAL---ECALALEGGGASELVVHART--------R 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            +   P   ++ + +I+    ++ +  NG + ++  AL+       D +M+GR    N  
Sbjct: 173 ADAYRPPAYWERIADIRAVV-NIPVVANGEIWNVQDALRCREESGCDSLMLGRGMVTNPG 231

Query: 225 MLTTVDEYFSNPLTGSSP 242
           +   +    + P    +P
Sbjct: 232 LALAIRAAMAGPDASPAP 249


>gi|269102154|ref|ZP_06154851.1| tRNA-dihydrouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162052|gb|EEZ40548.1| tRNA-dihydrouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 314

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 40/175 (22%), Positives = 89/175 (50%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +QI G D + + E  +   + G   +++N GCP+  V++   GA L+  P+++   +
Sbjct: 64  PVRVQILGQDPNWMAENGRRAVELGSPGVDINFGCPAKLVNKSKGGAVLLKEPELIHQIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            ++ +A+  + PVT K R+G DD  P      +  +I ++G + I +H R       + +
Sbjct: 124 KSVRQAVDPTKPVTAKIRLGWDD--PNHCFE-IADAIAQAGADEITVHGR-------TKE 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           D  +   + +D ++++++ +P + I  NG + +     + + +     +M+ R A
Sbjct: 174 DGYRAEEIKWDYIHQLQQHSP-ISIVANGEVWNYQDGQQCIATTGTQSLMVCRGA 227


>gi|170755297|ref|YP_001780311.1| dihydrouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
 gi|169120509|gb|ACA44345.1| dihydrouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
          Length = 312

 Score = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 101/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NR 169
           K   + +++K RIG D          L+K   K  +  + IH R       + KD   N+
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPR-------TQKDFYGNK 173

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             PNLD          NP  + G    +   ++ +K  P V  +M+GR    N  ++   
Sbjct: 174 --PNLDVFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLI--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|261205036|ref|XP_002627255.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239592314|gb|EEQ74895.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239611532|gb|EEQ88519.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis ER-3]
          Length = 464

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 95/219 (43%), Gaps = 23/219 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N     T       I R D         +   L  QIG A  +  V+AAKI+  
Sbjct: 47  FTRLPSNGGRQNTPNAKESVIYRIDPHR------ESGKLIFQIGTASPNLAVQAAKIIA- 99

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD++   + A+ + +  P    ++VK R+  
Sbjct: 100 ADVAGIDVNAGCPKPFSTSGGMGAALLQTPDLLVSILTALVQQIGNPYQIGISVKIRLLA 159

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 160 DPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRERAIRAQLP-----MIASICRA-A 209

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            + I +NG +E     L ++    VDG MI  +A  NS+
Sbjct: 210 GVAILMNGDVESRDHGLALMSEYGVDGAMIATSAEANSS 248


>gi|90020951|ref|YP_526778.1| RecR protein [Saccharophagus degradans 2-40]
 gi|89950551|gb|ABD80566.1| dihydrouridine synthase, DuS [Saccharophagus degradans 2-40]
          Length = 318

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 58/199 (29%), Positives = 94/199 (47%), Gaps = 22/199 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G++ S L   A    + G   I+LN GCP+  V+    GACL+   D V D +
Sbjct: 69  PVRVQLLGSNPSALAANAARAAELGAVAIDLNFGCPAKTVNRHKGGACLLDETDTVFDIV 128

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ KA   S PVT K R+G  ++     LRN  K+I+ +G N + +HAR         K
Sbjct: 129 NAVRKATPASTPVTAKIRLGYLNR--DSYLRN-AKAIEAAGANELCVHARS--------K 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNS 223
            +   P   +  + +I ++N  + +  NG    LED  +  +     D  M+GR      
Sbjct: 178 TDGYQPPAYWHYIGDI-RDNLSIPVVANGEIWSLEDFKRCAEQSKCSD-FMLGRGLLAKP 235

Query: 224 AMLTTVDEYFS----NPLT 238
            +   + +Y +    NPL+
Sbjct: 236 DLALEIKQYMAGEAFNPLS 254


>gi|296082372|emb|CBI21377.3| unnamed protein product [Vitis vinifera]
          Length = 316

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/127 (29%), Positives = 65/127 (51%), Gaps = 4/127 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 75  MVDNSELPFRMLCRKYGAQAA-YTPMLHSRIFSENEKYRSQEFTTCKEDRPLFVQFCAND 133

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA+ VE +  + +++N+GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 134 PDTLLEAAQRVEPYC-DYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLHVP 192

Query: 119 VTVKCRI 125
           V+ K R+
Sbjct: 193 VSCKIRV 199


>gi|167526006|ref|XP_001747337.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774172|gb|EDQ87804.1| predicted protein [Monosiga brevicollis MX1]
          Length = 487

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 83/182 (45%), Gaps = 18/182 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQIG +D  +    A+++       I++N+GCP     +G  GA L+  PD V D + ++
Sbjct: 81  LQIGTSDPDRAARVAQMMA-ADVAGIDVNMGCPKPFSIKGDMGAALLRQPDRVRDILTSL 139

Query: 112 CKALSIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
               + P+T K R+     +P +    NLV  I+ +GV  + IH R    +   P     
Sbjct: 140 VATTTKPITCKIRV-----LPTLEETLNLVNIIQDAGVAALGIHGRVPNQRPREP----- 189

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD-----GVMIGRAAYKNSAM 225
           I +  Y+ +  + K    + +  NGG  DM     IL   D      VM+ RAA  N ++
Sbjct: 190 ITDYQYEAIRAVAKAC-RIPVICNGGSLDMDSYDDILAFRDKCGCSSVMVARAAQYNMSI 248

Query: 226 LT 227
            +
Sbjct: 249 FS 250


>gi|124023850|ref|YP_001018157.1| nitrogen regulation protein NifR3 family protein [Prochlorococcus
           marinus str. MIT 9303]
 gi|123964136|gb|ABM78892.1| putative nitrogen regulation protein NifR3 family protein
           [Prochlorococcus marinus str. MIT 9303]
          Length = 336

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 73/323 (22%), Positives = 139/323 (43%), Gaps = 27/323 (8%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           +D+ +R   R    +ALL+TEM+ A ++  G   + I   + +  P+ +Q+       + 
Sbjct: 28  SDQIFRSLVRRWAPDALLFTEMVNATSLELGHGLQKIDELANEAGPIGVQLFDHRPEAMA 87

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    ++ +  A+ IPVTVK 
Sbjct: 88  DAAQRAEAAGAFLIDINMGCPVRKIARKGGGSGLIRDPQLAAKIVSTVAAAVKIPVTVKT 147

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D  P        + ++++G   + +HAR         ++     + D+  +  
Sbjct: 148 RLGWCGSDASPV----RWCQWLEQAGAQMLTLHART--------REQGFKGSADWLAIAA 195

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN-PLT 238
           +K       I  NG ++    A + L     DGVM+GR +     ++  +D   S  P+ 
Sbjct: 196 VKSALQIPVIA-NGDVKSDMDAKRCLAITGADGVMVGRGSMGAPWLVGQIDAALSGIPVP 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +     R+     R+   ++      H      L    +HM     GF  + + RH L 
Sbjct: 255 ATPGAAERL--TIAREQLEALVQAKGEH-----GLLIARKHMGWTCSGFVGASKLRHAL- 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
           + A   T    ++E A   +I +
Sbjct: 307 MRAPTPTDAISLLEQASAELITA 329


>gi|239993480|ref|ZP_04714004.1| NifR3/Smm1 family protein [Alteromonas macleodii ATCC 27126]
          Length = 309

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 104/223 (46%), Gaps = 30/223 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A+   + G   ++LN GCP+  V++   GA L+     + D +
Sbjct: 61  PVRVQLLGQHPQWLAENAQTAIELGSPGVDLNFGCPAKTVNKSKGGAVLLKETQTLYDIV 120

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+  A+   IPV+ K R+G +D+  ++A+ N + +I ++G + + +HAR         K
Sbjct: 121 KAVRDAVPAEIPVSAKIRLGFEDK--SLAIENAI-AITEAGASELVVHART--------K 169

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSA 224
                P   +D + +IK+   D+ +  NG + +   A +     +   +MIGR A     
Sbjct: 170 TEGYKPPAYWDWIAKIKQHT-DIPLVANGEIWNAEDAQRCQSQSECTNLMIGRGALAMPN 228

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
           +  ++ E       G +P+        W +++A +  Y+   +
Sbjct: 229 LAMSIKE-------GVAPMP-------WSELAALLIQYSGYEI 257


>gi|307546327|ref|YP_003898806.1| dihydrouridine synthase, DuS [Halomonas elongata DSM 2581]
 gi|307218351|emb|CBV43621.1| dihydrouridine synthase, DuS [Halomonas elongata DSM 2581]
          Length = 344

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 66/259 (25%), Positives = 113/259 (43%), Gaps = 33/259 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G+D   L   A+     G   ++LN GCP+  V+    GA ++  P  +   +
Sbjct: 83  PVHLQLLGSDPVALAANARQALALGATSLDLNFGCPAKLVNRHDGGASMLRTPWRLRTAV 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +A+  A+   IPVT K R+G  D+  A+   +  ++ +  G + + +HAR         +
Sbjct: 143 SAVHDAVGDVIPVTAKIRLGFADRRLAL---DCARATEDGGASQLVVHART--------R 191

Query: 167 DNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
           +    P   ++ +  I++    P +  G    LED  +A + L     VM+GR A  +S 
Sbjct: 192 NEGYRPPAHWEWIGRIRRRLSIPVIANGDIWTLEDYWKA-RTLSGCRDVMLGRGALADSG 250

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA--RHLHSG----GKLQQITR 278
           +   +  +     TG     T      W   ++ + DYAA  R + S      +L+Q   
Sbjct: 251 LAPRIRHWQG---TGEHLPPT-----PWADKASLLLDYAAMQRSILSSKTVVARLKQWMN 302

Query: 279 HMIGLFHGFPNSRRCRHIL 297
           HM G     P + RC   L
Sbjct: 303 HMRGR---DPEAARCFQAL 318


>gi|300703947|ref|YP_003745549.1| tRNA-dihydrouridine synthase c [Ralstonia solanacearum CFBP2957]
 gi|299071610|emb|CBJ42934.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum CFBP2957]
          Length = 326

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 102/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 58  GCTASGTPMVIQLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLATP 117

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++A+  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 ELLHTIVSAVRAAVPADIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I    E P +  G    + D  +  + +   D VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIADAVEVPVVANGEVWTVADWERC-RAVSGCDDVMIGR 225

Query: 218 AAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +  +    P     P+  R   D+ + + A +   AA H H   KL
Sbjct: 226 GAVSDPFLAQRIRGQMEQTPSDAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKL 279


>gi|50303445|ref|XP_451664.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640796|emb|CAH02057.1| KLLA0B02959p [Kluyveromyces lactis]
          Length = 351

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 52/216 (24%), Positives = 102/216 (47%), Gaps = 15/216 (6%)

Query: 21  LLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           ++YT MI+A   +R     +  F+T  ++ PL +Q+G  ++  L++  ++V  +  + I 
Sbjct: 59  IVYTPMILAREFVRNGHARMADFTTCDEDSPLIVQVGVNNVPDLLKFTEMVYPYC-DGIG 117

Query: 79  LNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +N GCP   +V EG  G+ L+ N +++ D + A+       V ++ +I + D +      
Sbjct: 118 INCGCPIREQVREG-IGSALIYNGELLCDMVKAVKDKYRDSVRLETKIRIHDDVKDTV-- 174

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L   + ++GV+ I +H R    +   P +   I  +  ++ Y+      D+ +  NG  
Sbjct: 175 KLCDDLCEAGVDWITVHGRTRTTRSSVPVNLDAIKFIRENMKYQ------DVPLVANGDC 228

Query: 198 EDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
             ++   +I     VDGVM  R    N A+    D+
Sbjct: 229 FTLNDCYRISEYTKVDGVMAVRGLLCNPALFDGYDK 264


>gi|328861733|gb|EGG10836.1| hypothetical protein MELLADRAFT_60122 [Melampsora larici-populina
           98AG31]
          Length = 377

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 52/199 (26%), Positives = 97/199 (48%), Gaps = 15/199 (7%)

Query: 50  LALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           L  QIG AD    ++AA+ +++D   + I+LN GCP     +G  GA L+  P+ +   +
Sbjct: 173 LIYQIGSADPELALKAAQTVLQDV--SGIDLNCGCPKDFSLKGGMGAALLKEPEKLCGIL 230

Query: 109 AAMCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           + + K +   P++ K R+  D +       NLVK I  +G++ + +H R  +++   P  
Sbjct: 231 SHLVKNIPTHPISAKIRLLPDQE----DTLNLVKQISATGISCLTVHCRTQLMRSTEPAL 286

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSA 224
             ++  +  + V   +  +  L +  NG     +DM + +K L  V  +MI R A +N +
Sbjct: 287 LHRLKEI-VETVNRSRSSSVPLPVVANGDCFEYKDM-EKIKALTGVQRIMIARGAERNVS 344

Query: 225 MLTTVDEYFSNPLTGSSPI 243
             +      S+P+T   P+
Sbjct: 345 CFSPCG--LSDPVTQIIPL 361


>gi|257066133|ref|YP_003152389.1| TIM-barrel protein, nifR3 family [Anaerococcus prevotii DSM 20548]
 gi|256798013|gb|ACV28668.1| TIM-barrel protein, nifR3 family [Anaerococcus prevotii DSM 20548]
          Length = 326

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 103/227 (45%), Gaps = 19/227 (8%)

Query: 23  YTEMIVADAILRGDK--KNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEIN 78
           +TEM+  +A+   ++  + I+  +  EK   +QI G   DI + V   KI     + EI+
Sbjct: 36  FTEMVSVNALDFNNRATEEIMYTAYSEKNCNIQIFGKDCDIIERVIKDKINPREDFEEIS 95

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
            N+GCP+ ++     G+ LM +   V +    + ++    V VK R+G+DD   +V    
Sbjct: 96  FNMGCPAPKIFNNGQGSALMRDVKKVYEIGKCLKESTDKIVNVKIRMGIDDD--SVNYIE 153

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K+++ SG++ + +H R    +     + + I  L         KE   + +  NG + 
Sbjct: 154 VGKALEDSGIDYVILHGRTRKQQYSGKANWQAIRKL---------KETLSIPVIANGDVF 204

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
            +     IL     DGVMI R A  N  +   + +Y     T  SPI
Sbjct: 205 SVKDYKDILDETGADGVMIARGAMGNPFIFRQIKDYIQGKET--SPI 249


>gi|328877006|gb|EGG25369.1| CCCH-type zinc finger-containing protein [Dictyostelium
           fasciculatum]
          Length = 699

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 63/278 (22%), Positives = 117/278 (42%), Gaps = 31/278 (11%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKNILGFS--TQEKPLALQIGGADISKLVEAAK 67
           F RL  +  +  T  EM +A  I+ G +  +  F     E    +Q+ G  +  ++  A+
Sbjct: 367 FRRLCKDLGVDITCGEMALASNIVIGQQSELALFKRHASEDKFGVQVCGPHLDSMIHTAE 426

Query: 68  IVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
            + ++   + +++N GCP   V     GA +M  P+ +   +  M   L +P+T+K RIG
Sbjct: 427 FINEYMDVDFVDINSGCPIDLVCNMGAGAAMMERPNRMETLVRGMSSVLDVPLTIKIRIG 486

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
             ++ P      L+ ++K+ G   + +H R    +        ++ N +Y  + E    +
Sbjct: 487 KSEESPNA--HKLIPNLKEWGAQAVTLHGRSRAQRYT------RLANWEY--IRECADIS 536

Query: 187 PDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           P   I  NG + +     K+  S +  +M+ R A     + T + E     ++ S     
Sbjct: 537 PLPLIA-NGDIYNWRDIEKVKESKISSLMVARGALIKPWIFTEIKERRDWDISASE---- 591

Query: 246 RVD--KDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           R+D  KDF         +Y   H  S  +    TRH +
Sbjct: 592 RLDLIKDF--------VNYGLTHWGSDQQGVDNTRHFL 621


>gi|251780591|ref|ZP_04823511.1| dihydrouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243084906|gb|EES50796.1| dihydrouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 321

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 99/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +   + ++  GYNE+NLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFINTTRKLQQLGYNEVNLNLGCPAGTVVSKNRGSGFLAKREELDIFLEEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NR 169
           K   + +++K RIG D          L+K   K  +  + IH R       + KD   N+
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPLEELIIHPR-------TQKDFYGNK 173

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             PNLD          NP  + G    + D ++  +  P V  +M+GR    N  ++   
Sbjct: 174 --PNLDVFKDTLSLSNNPVCYNGDIFTVADHNKFEETFPKVKTLMLGRGILANPGLM--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  +  I   + KDF  +I     D      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNDFINKELLKDFHDEIFNKYIDLFNEEKNAMFRMKELWGYMIYIF 278


>gi|16765504|ref|NP_461119.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167991101|ref|ZP_02572200.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|38604956|sp|Q8ZNM4|DUSC_SALTY RecName: Full=tRNA-dihydrouridine synthase C
 gi|16420711|gb|AAL21078.1| putative nitrogen regulation protein [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|205330623|gb|EDZ17387.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261247388|emb|CBG25213.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994239|gb|ACY89124.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301158735|emb|CBW18247.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913164|dbj|BAJ37138.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321224828|gb|EFX49891.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. TN061786]
 gi|332989108|gb|AEF08091.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 312

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 124 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 174 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEILDWQSAQACMATSGCDAVMIGRGAL-NIP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|114704555|ref|ZP_01437463.1| nitrogen regulation protein nifr3 [Fulvimarina pelagi HTCC2506]
 gi|114539340|gb|EAU42460.1| nitrogen regulation protein nifr3 [Fulvimarina pelagi HTCC2506]
          Length = 344

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 104/219 (47%), Gaps = 20/219 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKL 62
           +D  +R  +R      L+ +EM+ +   ++G ++  L  + ++ P    +Q+ G D   +
Sbjct: 29  SDVPFRRLSRRF-GAGLVVSEMVASGEFVKGAEEGKL-RALRDGPGVHTVQLAGRDPIWM 86

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTV 121
            EAA+ + D G + I++N+GCP+ +V  G  G+ LM  PD+    + A  + A + PV++
Sbjct: 87  EEAARRLADEGADLIDINMGCPAKKVVGGLSGSALMREPDLAFSIVEATVRGAGATPVSL 146

Query: 122 KCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R+G   D + A     +    + +GV  I +H R          D R I ++      
Sbjct: 147 KMRLGWCRDSMNAA---EIAVRAEAAGVTMITVHGRTRAEFYEGTADWRAICSV------ 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
              K +  + +  NG L + +Q   IL +   D VM GR
Sbjct: 198 ---KRSVGVPVVANGDLTEANQLSAILAASGADAVMTGR 233


>gi|145628600|ref|ZP_01784400.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 22.1-21]
 gi|144979070|gb|EDJ88756.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 22.1-21]
          Length = 310

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 101/226 (44%), Gaps = 29/226 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+    PV+VK R+G DD   +  + +   ++++ G   I +H R   
Sbjct: 117 ELIYRATQALRRAVPSEFPVSVKVRLGWDDISQSFEIAD---AVEQGGATEITVHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGR 217
               +  D  +   +++  + ++ +E   + +  NG +         L       +M+GR
Sbjct: 171 ----TKTDGYRADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            A  N   L+ V             +K+  +K  WR+I   +  YA
Sbjct: 226 GAL-NIPNLSHV-------------LKSNAEKMPWREIQKILQKYA 257


>gi|207743024|ref|YP_002259416.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           IPO1609]
 gi|206594421|emb|CAQ61348.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           IPO1609]
          Length = 310

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 103/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 42  GCTASGTPMVIQLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLSTP 101

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 102 ELLHTIVSAVRAAVPANIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 156

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I    E P +  G    + D  +  + +   D VMIGR
Sbjct: 157 ------RDHGYRPPAHWDWIARIADAVEVPVIANGEVWTVADWERC-RAVSGCDDVMIGR 209

Query: 218 AAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +  +    P     P+  R   D+ + + A +   AA H H   KL
Sbjct: 210 GAVSDPFLAQRIRGQMERTPSNAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKL 263


>gi|197250762|ref|YP_002147146.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|205359500|ref|ZP_02830116.2| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|197214465|gb|ACH51862.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|205344872|gb|EDZ31636.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
          Length = 331

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQYPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 193 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 250

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 251 NLSRVVKY 258


>gi|323130501|gb|ADX17931.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
          Length = 316

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 68  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 128 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 178 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEILDWQSAQACMATSGCDAVMIGRGAL-NIP 235

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 236 NLSRVVKY 243


>gi|240949296|ref|ZP_04753639.1| putative nitrogen regulator protein [Actinobacillus minor NM305]
 gi|240296247|gb|EER46896.1| putative nitrogen regulator protein [Actinobacillus minor NM305]
          Length = 319

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 94/192 (48%), Gaps = 17/192 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +P+++    
Sbjct: 68  PVRVQLLGQYPQWLAENAELAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPELIYRAT 127

Query: 109 AAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+     V+VK R+G D    A     +  ++++ G N I +H R       +  
Sbjct: 128 QAIRQAVPQDQVVSVKVRLGWDS---AEQCFEIADAVQQGGANEITVHGR-------TKT 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
           D  +   +++  + +I+K      I  NG + D   A K   + +   +MIGR A  N+ 
Sbjct: 178 DGYRAERINWQAIGDIQKRLTIPVIA-NGEIWDFESAKKCQEITACQALMIGRGAL-NTP 235

Query: 225 MLTTVDEYFSNP 236
            L+ V + F+ P
Sbjct: 236 NLSRVVK-FNQP 246


>gi|328868434|gb|EGG16812.1| tRNA-dihydrouridine synthase 4-like protein [Dictyostelium
           fasciculatum]
          Length = 346

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 62/252 (24%), Positives = 113/252 (44%), Gaps = 27/252 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L ++ M++A++  R +      F+T +    L +Q    D  +L  A + V +     ++
Sbjct: 82  LTFSPMLLAESFNRSEFARDSDFTTNQFDNSLIVQFAANDGEELSAAVEKVANHCQG-VD 140

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALR 137
           +N GCP   +   + GA L+  P+ + + I    + ++ IP+++K RI  D         
Sbjct: 141 INCGCPQKWIIRENMGAGLLTTPEKIEEMIKTTTRRITNIPLSIKIRIQKD----MSQTI 196

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K  +++GV+ I +H R +  +   P        +DYD + ++ KE+  + +  NG +
Sbjct: 197 ELAKRAERAGVSWITVHGRTSSQRSSHP--------VDYDAI-KLVKESIGIPVFANGDI 247

Query: 198 EDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             + QA  ++    V+GVM  R    N A+      Y     T    IK  +D +   +I
Sbjct: 248 FTLDQANDIRDKTKVNGVMSARGILCNPAL------YMGYDTTPIECIKEFIDIN--SQI 299

Query: 256 SASMTDYAARHL 267
               TD   RHL
Sbjct: 300 GGLNTDIFHRHL 311


>gi|306822377|ref|ZP_07455756.1| possible dihydrouridine synthase [Bifidobacterium dentium ATCC
           27679]
 gi|309802137|ref|ZP_07696246.1| TIM-barrel protein, nifR3 family [Bifidobacterium dentium
           JCVIHMP022]
 gi|304554375|gb|EFM42283.1| possible dihydrouridine synthase [Bifidobacterium dentium ATCC
           27679]
 gi|308221217|gb|EFO77520.1| TIM-barrel protein, nifR3 family [Bifidobacterium dentium
           JCVIHMP022]
          Length = 409

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPGEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I     +C A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++PVT K R+G+D +         +   ++ G   + +HAR
Sbjct: 169 ANVPVTAKIRVGIDHEHETFLEAGHIA--QEEGCKAVTLHAR 208


>gi|207724169|ref|YP_002254567.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           MolK2]
 gi|206589379|emb|CAQ36341.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           MolK2]
          Length = 315

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 103/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 47  GCTASGTPMVIQLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLSTP 106

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 107 ELLHTIVSAVRAAVPANIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 161

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I    E P +  G    + D  +  + +   D VMIGR
Sbjct: 162 ------RDHGYRPPAHWDWIARIADAVEVPVIANGEVWTVADWERC-RAVSGCDDVMIGR 214

Query: 218 AAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +  +    P     P+  R   D+ + + A +   AA H H   KL
Sbjct: 215 GAVSDPFLAQRIRGQMERTPSDAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKL 268


>gi|297699046|ref|XP_002826610.1| PREDICTED: LOW QUALITY PROTEIN: tRNA-dihydrouridine synthase 2-like
           [Pongo abelii]
          Length = 493

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/189 (25%), Positives = 88/189 (46%), Gaps = 32/189 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++
Sbjct: 84  VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKLLS 142

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              K    PVT   RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 143 LFVKGTRRPVTCNIRILPSLEDTL------SLVKRIERTGIAAITVHGRK--------QE 188

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 189 ERPQHPVSCEVIKAI-ADTVSIPVIANGGSHDHIQRYSDIEDFRQAT----AASSVMVAR 243

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 244 AAMWNPSIF 252


>gi|254508473|ref|ZP_05120592.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus 16]
 gi|219548585|gb|EED25591.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus 16]
          Length = 317

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 86/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHVQLLGQDPVWMAENAIKAAELGARGVDLNFGCPAKLVNKSKGGAALLQHPELIHQVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+   IPVT K R+G ++         +V +I+K+G N + +HAR       +  
Sbjct: 124 KACREAVPSEIPVTAKIRLGWENPDDCF---EIVDAIEKAGANELTVHAR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
              K   + ++ + ++++    P +  G     ED  QA      VD +M+ R A+
Sbjct: 174 GGYKASEIKWEYIGQLRERFTIPLIANGEIWNYED-GQACIETTGVDSLMVCRGAF 228


>gi|83745889|ref|ZP_00942946.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
 gi|83727579|gb|EAP74700.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
          Length = 369

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 103/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 101 GCTASGTPMVIQLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLSTP 160

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 161 ELLHTIVSAVRAAVPANIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 215

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I    E P +  G    + D  +  + +   D VMIGR
Sbjct: 216 ------RDHGYRPPAHWDWIARIADAVEVPVIANGEVWTVADWERC-RAVSGCDDVMIGR 268

Query: 218 AAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  +   +  +    P     P+  R   D+ + + A +   AA H H   KL
Sbjct: 269 GAVSDPFLAQRIRGQMERTPSNAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKL 322


>gi|171742467|ref|ZP_02918274.1| hypothetical protein BIFDEN_01579 [Bifidobacterium dentium ATCC
           27678]
 gi|171278081|gb|EDT45742.1| hypothetical protein BIFDEN_01579 [Bifidobacterium dentium ATCC
           27678]
          Length = 409

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPGEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I     +C A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++PVT K R+G+D +         +   ++ G   + +HAR
Sbjct: 169 ANVPVTAKIRVGIDHEHETFLEAGHIA--QEEGCKAVTLHAR 208


>gi|39953378|ref|XP_363980.1| hypothetical protein MGG_08825 [Magnaporthe oryzae 70-15]
 gi|145021243|gb|EDK05372.1| hypothetical protein MGG_08825 [Magnaporthe oryzae 70-15]
          Length = 614

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 37/116 (31%), Positives = 61/116 (52%), Gaps = 5/116 (4%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D S L+EAAK V  +  + ++LN+GCP     +G +GA L  + +++  
Sbjct: 117 DRPLFVQFCANDPSALLEAAKHVAPY-CDAVDLNLGCPQGIARKGHYGAFLQEDQELIHK 175

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            I  +   LSIPVT K RI    +      RN++     +G + + +H R+   KG
Sbjct: 176 LIRQLHDGLSIPVTAKIRILDTPEATLAYARNVL----DAGASILTVHGRRREQKG 227


>gi|19112231|ref|NP_595439.1| tRNA dihydrouridine synthase Dus2 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74582543|sp|O74731|DUS2_SCHPO RecName: Full=tRNA-dihydrouridine synthase 2
 gi|3738144|emb|CAA21245.1| tRNA dihydrouridine synthase Dus2 (predicted) [Schizosaccharomyces
           pombe]
          Length = 479

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 56/182 (30%), Positives = 88/182 (48%), Gaps = 23/182 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDCI 108
           L  Q+G A     VEAAK+V +     I+LN GCP    VH G  GA L+ N D +   +
Sbjct: 84  LIFQLGSASPELAVEAAKLVAN-DVAGIDLNCGCPKHFSVHAG-MGAGLLKNQDRLVSIL 141

Query: 109 AAMCKALSIP--VTVKCRIGV----DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            A+   +  P  +++ C+I +    +D +       LV+ I  +GV  I +H R   ++ 
Sbjct: 142 DALVNEIGKPYKISISCKIRLLETKEDTL------KLVERICDTGVRAITVHCRTTPMRN 195

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
             P D   +     +IV   +  N D+ I +NG +   +  L ++    VDGV+I RAA 
Sbjct: 196 TEPADRSYLS----EIVGVCR--NKDVSILVNGDVLSYNDGLDVIEKYGVDGVLIARAAE 249

Query: 221 KN 222
           +N
Sbjct: 250 RN 251


>gi|17546354|ref|NP_519756.1| hypothetical protein RSc1635 [Ralstonia solanacearum GMI1000]
 gi|38604943|sp|Q8XYX1|DUSC_RALSO RecName: Full=tRNA-dihydrouridine synthase C
 gi|17428651|emb|CAD15337.1| probable trna-dihydrouridine synthase c protein [Ralstonia
           solanacearum GMI1000]
          Length = 326

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 102/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 58  GYTASGTPMVIQLLGSDPEWLARNAAQAATVSPHGIDLNFGCPAKVVNRHGGGAMLLATP 117

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++ +  A+   I VT K R+GV D   A+A      ++ + G   + +HAR   
Sbjct: 118 ELLHRIVSTVRAAVPARIAVTAKMRLGVSDTSLAIA---CATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I      P +  G    ++D ++  + +   D VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIADAVRVPVVANGEVWTVDDWARC-RAVSGCDDVMIGR 225

Query: 218 AAYKNSAM-LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  + L    +    P     P+      D+ +K+ A +   A  H H   KL
Sbjct: 226 GAVSDPFLALRIRGQMARQPSDAEWPLVLGCLADYLKKLRARI---AIHHEHGRVKL 279


>gi|223938646|ref|ZP_03630536.1| dihydrouridine synthase DuS [bacterium Ellin514]
 gi|223892634|gb|EEF59105.1| dihydrouridine synthase DuS [bacterium Ellin514]
          Length = 340

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 60/125 (48%), Gaps = 8/125 (6%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           IL    KN  G     +P+  Q+ G DI  LV +AK ++ +    ++LN+GCP+  V+  
Sbjct: 52  ILESITKNPTG-----QPVIAQMIGNDIPSLVRSAKELQQYPIVAVDLNLGCPAPIVYRK 106

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             G  L+  P  V   + A+  A+S+  TVK RIG D          L+    K  ++ +
Sbjct: 107 CAGGGLLREPKRVDSILGALRDAISVKFTVKTRIGFDS---TGVFDELLPIFAKHSIDLL 163

Query: 152 WIHAR 156
            +H R
Sbjct: 164 TVHGR 168


>gi|148702859|gb|EDL34806.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_a [Mus
           musculus]
          Length = 228

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 67/130 (51%), Gaps = 8/130 (6%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 40  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPLIVQFC 97

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 98  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERL 156

Query: 116 SIPVTVKCRI 125
           S+PVT K R+
Sbjct: 157 SVPVTCKIRV 166


>gi|197105195|ref|YP_002130572.1| tRNA-dihydrouridine synthase, nifR3 [Phenylobacterium zucineum
           HLK1]
 gi|196478615|gb|ACG78143.1| tRNA-dihydrouridine synthase, nifR3 [Phenylobacterium zucineum
           HLK1]
          Length = 334

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 42/142 (29%), Positives = 69/142 (48%), Gaps = 10/142 (7%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFSTQEK-PL-ALQIGGADISKLVEAAKIVEDFGYNEI 77
           A + TEM+      +G    +   +  E  PL  +Q+ G D   + + A++    G   +
Sbjct: 39  AYVATEMVACAEFSKGRPDVVRRAAVGEGLPLMVVQLVGRDPEHIRQGARLAAQAGAQIV 98

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN GCP+  V     G+ LM  P++    +AA  +A+ +PVTVK R+G DD     A R
Sbjct: 99  DLNFGCPAKEVTGVLSGSALMREPELAARLMAAAVEAVDVPVTVKMRLGWDD-----ASR 153

Query: 138 N---LVKSIKKSGVNGIWIHAR 156
           N   +  + +  GV  + +H R
Sbjct: 154 NAPEIAAAAEAIGVQAVTVHGR 175


>gi|320086613|emb|CBY96384.1| tRNA-dihydrouridine synthase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 316

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 68  PVRIQLLGQYPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGA 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 128 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 177

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSA 224
              +  ++D+  + EI++      I  NG + D   +QA       D VMIGR A  N  
Sbjct: 178 QGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSGCDAVMIGRGAL-NIP 235

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 236 NLSRVVKY 243


>gi|283456447|ref|YP_003361011.1| tRNA-dihydrouridine synthase [Bifidobacterium dentium Bd1]
 gi|283103081|gb|ADB10187.1| tRNA-dihydrouridine synthase [Bifidobacterium dentium Bd1]
          Length = 372

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 8/162 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 12  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPGEKIRSLQLYGVN 71

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I     +C A
Sbjct: 72  PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 131

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++PVT K R+G+D +         +   ++ G   + +HAR
Sbjct: 132 ANVPVTAKIRVGIDHEHETFLEAGHIA--QEEGCKAVTLHAR 171


>gi|229815921|ref|ZP_04446244.1| hypothetical protein COLINT_02976 [Collinsella intestinalis DSM
           13280]
 gi|229808474|gb|EEP44253.1| hypothetical protein COLINT_02976 [Collinsella intestinalis DSM
           13280]
          Length = 317

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/178 (26%), Positives = 81/178 (45%), Gaps = 19/178 (10%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   +  + V AA+ + + GY E+NLN+GCPS  V     G+  + N D +   +  +C
Sbjct: 65  QLLTKNADEFVWAARELAELGYREVNLNLGCPSGTVVSKGKGSGFLRNLDELEVFLRDVC 124

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPK---D 167
               +PV+VK R+G++D      +  L  S+    +  + +H R  K   +G  P+    
Sbjct: 125 DRSPLPVSVKTRLGLEDDAEYERILELYCSLP---LAELIVHPRVQKDRYQG-KPRWEPY 180

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
              +    + + Y     N D+F     G EDM   ++  P    VM+GR    N A+
Sbjct: 181 GETLARAPFPVAY-----NGDIF-----GTEDMDVLMEAHPRTRHVMLGRGLLANPAL 228


>gi|188589378|ref|YP_001920726.1| dihydrouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
 gi|188499659|gb|ACD52795.1| dihydrouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
          Length = 321

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 99/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +   + ++  GYNE+NLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFINTTRKLQQLGYNEVNLNLGCPAGTVVSKNRGSGFLAKREELDIFLEEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NR 169
           K   + +++K RIG D          L+K   K  +  + IH R       + KD   N+
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPLEELIIHPR-------TQKDFYGNK 173

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             PNLD          NP  + G    + D ++  +  P V  +M+GR    N  ++   
Sbjct: 174 --PNLDVFKDALSLSNNPVCYNGDIFTVADHNKFEETFPKVKTLMLGRGILANPGLM--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  +  I   + KDF  +I     D      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNDFINKELLKDFHDEIFNKYIDLFNEEKNAMFRMKELWGYMIYIF 278


>gi|281200935|gb|EFA75149.1| tRNA-dihydrouridine synthase 2-like protein [Polysphondylium
           pallidum PN500]
          Length = 437

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 40/147 (27%), Positives = 73/147 (49%), Gaps = 11/147 (7%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP     +G  G+ L+  PD + D +  + + L +PVT K R+  DD       
Sbjct: 142 IDINMGCPKFFSVQGGMGSALLSKPDTIKDILTTLIRNLPLPVTCKIRLLEDDN----KT 197

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNG 195
            +L++ I+ +GV  I +H R    +   P    ++ N+  +  + +    N D+F+    
Sbjct: 198 IDLMRIIENTGVKAIGVHMRTIPERPRDPAHWDRLKNILDNAKFSVPIIANGDIFVN--- 254

Query: 196 GLEDMSQALKILPSVDGVMIGRAAYKN 222
             ED+ + +K +   + VM+ R A KN
Sbjct: 255 --EDI-EKVKKMTGANSVMVARGAIKN 278


>gi|167760575|ref|ZP_02432702.1| hypothetical protein CLOSCI_02949 [Clostridium scindens ATCC 35704]
 gi|167661796|gb|EDS05926.1| hypothetical protein CLOSCI_02949 [Clostridium scindens ATCC 35704]
          Length = 279

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 74/176 (42%), Gaps = 9/176 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI   D    ++  K +ED+GY E+NLN+GCPS  V   + G+  +  PD +   + 
Sbjct: 35  LVPQILTNDAKGFLQTVKKLEDYGYEEVNLNLGCPSKTVVSKNRGSGFLAMPDELDRFLD 94

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     + +++K RIG   +        L++   +  V  + IH R      L     +
Sbjct: 95  EIYSGTQVRISIKTRIG---KHSPDEFGRLLEIYNQYPVEELIIHPR------LQQDFYK 145

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             PNL+       +  NP  + G    + D  +  +  P V   M+GR    N  +
Sbjct: 146 NTPNLEVFAEAVRESRNPLCYNGDIFSVTDRDRIKERFPEVKTYMMGRGILVNPGL 201


>gi|170085799|ref|XP_001874123.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164651675|gb|EDR15915.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 308

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 93/210 (44%), Gaps = 24/210 (11%)

Query: 35  GDKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           G  + I      EKP L  QIG +D    V+AAK+V     + I+LN GCP         
Sbjct: 85  GVSRAIFATHPVEKPYLIYQIGSSDPELAVQAAKMVMQ-DVSGIDLNCGCPKPFSTHAGM 143

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV----DDQIPAVALRNLVKSIKKSGVN 149
           GA L+ NPD++   + A+ + +   +TV  +I +    +D +       LV+ I  +G++
Sbjct: 144 GAALLTNPDLLCSILTALRREMPPEITVTAKIRLLPSQEDTL------KLVERIVNTGIS 197

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + +H R    + +  KD   I  L  +IV  ++     + +  NG       A ++  +
Sbjct: 198 ALTVHCRT---RNMREKDRAVIERL-REIVEFVEGLGRGIAVIENGDCMSWEDAKRVRET 253

Query: 210 VDG--VMIGRAAYKNSAMLTTVDEYFSNPL 237
                VMI R A  N +  +      SNPL
Sbjct: 254 TGAHSVMIARGAEANPSCFS------SNPL 277


>gi|320181530|gb|EFW56448.1| tRNA dihydrouridine synthase B [Shigella boydii ATCC 9905]
          Length = 109

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 47/75 (62%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEV 88

Query: 112 CKALSIPVTVKCRIG 126
             A+ +PVT+K R G
Sbjct: 89  VNAVDVPVTLKIRTG 103


>gi|157369580|ref|YP_001477569.1| tRNA-dihydrouridine synthase C [Serratia proteamaculans 568]
 gi|157321344|gb|ABV40441.1| dihydrouridine synthase DuS [Serratia proteamaculans 568]
          Length = 309

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D    +     +  +++++G   + +H R       + +D  
Sbjct: 127 RAAVPAHLPVTVKIRLGWDSDSRSF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   L +   D VM+GR A  N   L+
Sbjct: 177 KAERINWAAIGEIRQRLTIPVIA-NGEIWDYQSAQDCLQTTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|156975206|ref|YP_001446113.1| hypothetical protein VIBHAR_02933 [Vibrio harveyi ATCC BAA-1116]
 gi|156526800|gb|ABU71886.1| hypothetical protein VIBHAR_02933 [Vibrio harveyi ATCC BAA-1116]
          Length = 319

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 88/176 (50%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G + + + E A    + G   I+LN GCP+  V++   GA L+ +P+ + + +
Sbjct: 64  PVHVQLLGQEPNWMAENAVKAAELGARGIDLNFGCPAKLVNKSKGGAALLQHPEFIHNIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+  +IPVT K R+G ++  P      +V +I+ +G N + +HAR       + +
Sbjct: 124 KACRDAVPSNIPVTAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR-------TKQ 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + ++ + +I+       I  NG + +     + + +  VD +M+ R A+
Sbjct: 174 GGYKASEIKWEYITQIRDRFSIPLIA-NGEIWNYEDGQRCIETTGVDSLMVCRGAF 228


>gi|119386836|ref|YP_917891.1| nifR3 family TIM-barrel protein [Paracoccus denitrificans PD1222]
 gi|119377431|gb|ABL72195.1| tRNA-U20-dihydrouridine synthase [Paracoccus denitrificans PD1222]
          Length = 349

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/145 (28%), Positives = 71/145 (48%), Gaps = 4/145 (2%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
           A L+ +  +  TEM+      R   +     +    P+++QI G +   + E A+IV   
Sbjct: 41  AGLMVSEMVASTEMVTPRPSTRAAVR-AKALTEGALPVSVQIAGREAGAMAETARIVAGM 99

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQI 131
           G   +++N+GCP+ +V  G  GA LM + D     I A+  A+  +PVT+K R+G D   
Sbjct: 100 GARIVDINMGCPAKKVTGGLSGAALMRDLDHALGLIDAVVAAVPDLPVTLKMRLGWDGDC 159

Query: 132 PAVALRNLVKSIKKSGVNGIWIHAR 156
             +   +L +    +GV  + +H R
Sbjct: 160 --LNAPDLARRAAGAGVGMLTVHGR 182


>gi|315635015|ref|ZP_07890296.1| tRNA-dihydrouridine synthase C [Aggregatibacter segnis ATCC 33393]
 gi|315476277|gb|EFU67028.1| tRNA-dihydrouridine synthase C [Aggregatibacter segnis ATCC 33393]
          Length = 312

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 97/204 (47%), Gaps = 16/204 (7%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GCTPSGTPVRVQLLGQHPQWLAENAELAIQLGSHGVDLNCGCPSKTVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+     VTVK R+G D    A    ++  ++++ G   I IH R  +
Sbjct: 117 ELIYQATKAIRQAVPPEQAVTVKVRLGWDSTDFAF---DIADAVQQGGATEIAIHGRTKV 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                  D  +   +++  + EI+++   P +  G     ED  + L++    D +M+GR
Sbjct: 174 -------DGYRADRINWQKIGEIRQKLHIPVIANGEIWRWEDGQRCLEMTGCED-LMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSS 241
            A  N   L+ V ++   PL+ S 
Sbjct: 226 GAL-NMPNLSRVLKHNDAPLSWSE 248


>gi|325264707|ref|ZP_08131436.1| dihydrouridine synthase family protein [Clostridium sp. D5]
 gi|324029999|gb|EGB91285.1| dihydrouridine synthase family protein [Clostridium sp. D5]
          Length = 313

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 77/180 (42%), Gaps = 15/180 (8%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI        +  A  ++ +GY+E+NLN+GCPS  V     G+  +  PD +   +  + 
Sbjct: 64  QILTNSAEDFIRTAGKLKKYGYSEVNLNLGCPSKTVVSKGRGSGFLAFPDKLDRFLKEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +   + ++VK RIG D         +L+    +  ++ + IH R      L     R  P
Sbjct: 124 EYTDMKISVKTRIGKDG---PDEFESLLDIYNQYPISELIIHPR------LQADMYRNTP 174

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           N     V+    E     +  NG +   +D  +     P VD VM+GR    N  ++T++
Sbjct: 175 NWQ---VFGEALERCRCRVCYNGDIFTPQDFERFTVTFPKVDCVMLGRGILSNPGLVTSI 231


>gi|242002314|ref|XP_002435800.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215499136|gb|EEC08630.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 483

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 79/166 (47%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ A   L+  K  ++ L    +++PL +Q    D
Sbjct: 25  MVDQSELAWRLLGRR-HGAQLCYTPMLHASVFLKDPKYRRDALASCDEDQPLVVQFCAND 83

Query: 59  ISKLVEAAKIVEDFGYN-EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+A+++V   G+   ++LN+GCP A    G +GA L  + D++   +  +   + +
Sbjct: 84  PEVLVQASRLV--VGHCCAVDLNLGCPQAIARAGHYGAFLQDDWDLLARMVQRVHTQVDV 141

Query: 118 PVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKG 162
           P+T K R+      P V       + ++ +G   + +H R    KG
Sbjct: 142 PITCKVRV-----FPEVEKTVRYAQMLEAAGCQVLTVHGRTREQKG 182


>gi|212712155|ref|ZP_03320283.1| hypothetical protein PROVALCAL_03237 [Providencia alcalifaciens DSM
           30120]
 gi|212685202|gb|EEB44730.1| hypothetical protein PROVALCAL_03237 [Providencia alcalifaciens DSM
           30120]
          Length = 319

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/215 (25%), Positives = 95/215 (44%), Gaps = 29/215 (13%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  PD++     A+
Sbjct: 67  VQLLGQYPEWLAENANRAVELGSWGVDLNCGCPSKTVNGSGGGATLLKQPDLIYHAAKAI 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PV+VK R+G D    A     +  +++++G   + +H R       + +D  
Sbjct: 127 RAAVPKELPVSVKVRLGWDSSQFA---HEIADAVQQAGATELTVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI+++     I  NG + D   A + +     D +MIGR A  N+  L+
Sbjct: 177 KAECINWQAIGEIRQKLSIPVIA-NGEIWDYESAKRCMEMTGCDSIMIGRGAL-NTPNLS 234

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
            V             IK  V K  W ++   +  Y
Sbjct: 235 RV-------------IKHNVPKMPWEQVGKILFKY 256


>gi|260773041|ref|ZP_05881957.1| tRNA-dihydrouridine synthase C [Vibrio metschnikovii CIP 69.14]
 gi|260612180|gb|EEX37383.1| tRNA-dihydrouridine synthase C [Vibrio metschnikovii CIP 69.14]
          Length = 348

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/220 (22%), Positives = 103/220 (46%), Gaps = 29/220 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   +
Sbjct: 97  PIKVQLLGQEPQWMAENAVRAAELGAYGVDLNFGCPAKMVNKSKGGAALLQHPELIYQVV 156

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G +D        ++V ++ ++G + + +HAR       +  
Sbjct: 157 KACRDAVPKHIPVSAKIRLGWEDPNDCF---DIVDAVTQAGADELTVHAR-------TKA 206

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              K   + +D + +I++++    I  NG + + + A   + +  VD +M+ R A  N  
Sbjct: 207 GGYKASEIQWDYIDQIRQKSTIPLIA-NGEIWNYADAQACISTTGVDSLMVCRGAL-NIP 264

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            L  + +Y   P+              W ++   + +Y+A
Sbjct: 265 NLGNIVKYNHAPMP-------------WNQVVELLLEYSA 291


>gi|163802863|ref|ZP_02196752.1| putative regulator protein [Vibrio sp. AND4]
 gi|159173403|gb|EDP58226.1| putative regulator protein [Vibrio sp. AND4]
          Length = 319

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/194 (24%), Positives = 94/194 (48%), Gaps = 16/194 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G + + L E A      G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHVQLLGQEPNWLAENAIKAAKLGARGIDLNFGCPAKLVNKSKGGAALLQHPELIHSIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                A+  +IPV+ K R+G ++  P      +V +I+ +G N + +HAR       + +
Sbjct: 124 KTCRDAVPSNIPVSAKIRLGWEN--PEDCFE-IVDAIQAAGANELTVHAR-------TKQ 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              K   + +D + +I++      I  NG + +     + + +  VD +M+ R A+ N  
Sbjct: 174 GGYKASEIKWDYITQIRERFTIPLIA-NGEIWNFKDGQRCIETTGVDSLMVCRGAF-NIP 231

Query: 225 MLTTVDEYFSNPLT 238
            L  + +Y   P+ 
Sbjct: 232 NLGNMVKYNHQPMA 245


>gi|302915835|ref|XP_003051728.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256732667|gb|EEU46015.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 407

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 90/185 (48%), Gaps = 17/185 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + V+AA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 104 LIFQIGTADPDRAVQAARLVA-ADVAGIDVNAGCPKPFSTSGGMGAALLKTPDKLCAILE 162

Query: 110 AMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K ++    I ++VK RI +D    A     LV+ +  +G+ G+ +H R   ++   P
Sbjct: 163 ALVKNITPEFEIGISVKIRI-LDT---AAETEALVRRLCATGITGLTVHCRTTPMR---P 215

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           ++ R I      +V E+  E   +   +NG +E+  + LK+      DG MI  AA KN 
Sbjct: 216 RE-RAIRG-QLRMVAEVCHEY-GVACLMNGDVENRDEGLKLAEEFGADGAMIATAAEKNP 272

Query: 224 AMLTT 228
           +   +
Sbjct: 273 SCFRS 277


>gi|160880024|ref|YP_001558992.1| dihydrouridine synthase DuS [Clostridium phytofermentans ISDg]
 gi|160428690|gb|ABX42253.1| dihydrouridine synthase DuS [Clostridium phytofermentans ISDg]
          Length = 318

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/187 (24%), Positives = 83/187 (44%), Gaps = 29/187 (15%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    ++ ++ + +FGY+EINLN+GCPS  V     G+  ++  D +   +  + 
Sbjct: 64  QILTNNAQDFIQTSRKIAEFGYDEINLNLGCPSGTVVAKGKGSGFLVMKDELNRFLEEVF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +A    +++K RIG D+        +L+    +  +  + IH R  I K +     +  P
Sbjct: 124 QASVTKISIKTRIGRDN---PEEFHDLMSIFNQYPLEELIIHPR--IQKDMY----KNTP 174

Query: 173 NL----------DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           NL           +++ Y     N D+F      ++D    +   P V  VM+GR    N
Sbjct: 175 NLPVFAEGLLLSKHEVCY-----NGDIFT-----VDDYKNFIANFPQVKAVMLGRGIIAN 224

Query: 223 SAMLTTV 229
            A++  +
Sbjct: 225 PAIIQEI 231


>gi|293397165|ref|ZP_06641439.1| tRNA-dihydrouridine synthase C [Serratia odorifera DSM 4582]
 gi|291420636|gb|EFE93891.1| tRNA-dihydrouridine synthase C [Serratia odorifera DSM 4582]
          Length = 311

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D   P  +L  +  +++++G + + +H R       + +D  
Sbjct: 127 RAAVPAELPVTVKVRLGWDS--PQHSL-EIADAVQQAGASELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D + A + +     D VM+GR A  N   L+
Sbjct: 177 KAERINWAAIGEIRQRLTIPVIA-NGEIWDYASAQQCMQITGCDVVMLGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|328474591|gb|EGF45396.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus 10329]
          Length = 322

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 90/181 (49%), Gaps = 15/181 (8%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +T   P+ +Q+ G +   + E A    + G   I+LN GCP+  V++   GA L+ +P++
Sbjct: 59  TTSGVPVHVQLLGQEPHWMAENAIRAAELGARGIDLNFGCPAKMVNKSKGGAALLQHPEV 118

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A   A+  +IPV+ K R+G ++  P      +V +I+ +G N + +HAR     
Sbjct: 119 IHSVVKACRDAVPANIPVSAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR----- 170

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
             + +   K   + ++ + +I++      I  NG + +     + + +  VD +M+ R A
Sbjct: 171 --TKQGGYKASEIKWEYINKIRERFSIPLIA-NGEIWNFEDGQRCIETTGVDSLMVCRGA 227

Query: 220 Y 220
           +
Sbjct: 228 F 228


>gi|293390935|ref|ZP_06635269.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951469|gb|EFE01588.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 322

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 107/235 (45%), Gaps = 30/235 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQHPQWLAENAELAVQLGSHGVDLNCGCPSKTVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+ +A+     V+VK R+G D    A    ++  ++++ G   I IH R   
Sbjct: 117 ELIYQATKAIRQAVPQHHTVSVKVRLGWDSTEFAY---DIADAVQQGGATEIAIHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
               +  D  ++  +++  + EI+++     I  NG +   +  Q  + +   + +M+GR
Sbjct: 171 ----TKTDGYRVDRINWQKIGEIRQKLKIPVIA-NGEIWRWADGQQCRDVTGCEDLMVGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA-RHLHSGG 271
            A  N   L+ V +  + PL+             W +I   +  YAA  + H  G
Sbjct: 226 GAL-NIPNLSRVLKRNAAPLS-------------WAEIMPILRKYAALENCHDSG 266


>gi|269962458|ref|ZP_06176807.1| tRNA-dihydrouridine synthase B [Vibrio harveyi 1DA3]
 gi|269832754|gb|EEZ86864.1| tRNA-dihydrouridine synthase B [Vibrio harveyi 1DA3]
          Length = 331

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 112/244 (45%), Gaps = 20/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G + +       ++ K  +  G+  + +H R    + KG +          +Y
Sbjct: 145 VTLKTRTGWNTENKNCV--HIAKLAEDCGIQALALHGRTKACMYKGEA----------EY 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  Y  
Sbjct: 193 DSIKAVKHAISIPVIA-NGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLE 251

Query: 235 NPLT 238
           N  T
Sbjct: 252 NGTT 255


>gi|207727952|ref|YP_002256346.1| trna-dihydrouridine synthase c (partial sequence n terminus)
           protein [Ralstonia solanacearum MolK2]
 gi|206591195|emb|CAQ56807.1| probable trna-dihydrouridine synthase c (partial sequence n
           terminus) protein [Ralstonia solanacearum MolK2]
          Length = 146

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 68/131 (51%), Gaps = 6/131 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A  +     
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAGGRGAVGD 135

Query: 116 SIPVTVKCRIG 126
            +PVT+K R G
Sbjct: 136 RVPVTLKIRTG 146


>gi|145635178|ref|ZP_01790883.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittAA]
 gi|145267599|gb|EDK07598.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittAA]
          Length = 310

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPEYLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +++     A+ +A+    PV+VK R+G DD   +  + +   ++++ G   I +H R
Sbjct: 117 ELIYRATQALRRAVPSEFPVSVKVRLGWDDISQSFEIAD---AVEQGGATEITVHGR 170


>gi|15603745|ref|NP_246819.1| hypothetical protein PM1880 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|38605040|sp|Q9CJW1|DUSC_PASMU RecName: Full=tRNA-dihydrouridine synthase C
 gi|12722310|gb|AAK03964.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 312

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 85/182 (46%), Gaps = 15/182 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A+   + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GLTASGTPVRVQLLGQHPQWLAENAQRAIELGSHGIDLNCGCPSKTVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+  A+  ++PV+VK R+G D+   A     +  ++++ G   I IH R  +
Sbjct: 117 ELIYHATKALRAAVPKALPVSVKVRLGWDNSEQAF---EIADAVQQGGATEITIHGRTKM 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                  D  +   +++  + ++++      I  NG + D    QA         +MIGR
Sbjct: 174 -------DGYRADRINWAKINDVRQRLSIPVIA-NGEIWDWQSGQACLAETGCQDLMIGR 225

Query: 218 AA 219
            A
Sbjct: 226 GA 227


>gi|229828623|ref|ZP_04454692.1| hypothetical protein GCWU000342_00688 [Shuttleworthia satelles DSM
           14600]
 gi|229793217|gb|EEP29331.1| hypothetical protein GCWU000342_00688 [Shuttleworthia satelles DSM
           14600]
          Length = 338

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 92/212 (43%), Gaps = 33/212 (15%)

Query: 36  DKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           D +N +G S   KP L  Q+  +D    +   + + D GY E+NLN GCPS  V     G
Sbjct: 65  DPRNQIGLSATGKPRLVPQLMASDPDLFLWGCQYLSDLGYEEVNLNAGCPSPTVTAKGKG 124

Query: 95  ACLMLNPDI----VGDCIAAMCKALSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            C ML   +      D +    +   IPV  +VK R+G++D   A  + +L++      +
Sbjct: 125 -CGMLEDTLKLNRFFDRVFEGLERQRIPVRISVKTRLGMED---AGEMEDLMRVYTMYPI 180

Query: 149 NGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
             + IHAR  +A   G+  +D+             ++K N  L +  NG +       KI
Sbjct: 181 ARLMIHARVGRAAYSGMPDQDS---------FCKALEKNN--LPVSYNGDILTPEDGEKI 229

Query: 207 L---------PSVDGVMIGRAAYKNSAMLTTV 229
           L            +G+M+GR   ++ A+   V
Sbjct: 230 LVRAEGHDLQKHFNGLMLGRGVLRDPALFRKV 261


>gi|30063584|ref|NP_837755.1| tRNA-dihydrouridine synthase C [Shigella flexneri 2a str. 2457T]
 gi|56480050|ref|NP_708040.2| tRNA-dihydrouridine synthase C [Shigella flexneri 2a str. 301]
 gi|38604724|sp|Q7UC91|DUSC_SHIFL RecName: Full=tRNA-dihydrouridine synthase C
 gi|30041837|gb|AAP17564.1| putative regulator protein [Shigella flexneri 2a str. 2457T]
 gi|56383601|gb|AAN43747.2| putative regulator protein [Shigella flexneri 2a str. 301]
 gi|281601597|gb|ADA74581.1| tRNA-dihydrouridine synthase C [Shigella flexneri 2002017]
 gi|332756520|gb|EGJ86871.1| dihydrouridine synthase family protein [Shigella flexneri 2747-71]
 gi|332765951|gb|EGJ96161.1| tRNA dihydrouridine synthase [Shigella flexneri 2930-71]
 gi|333016719|gb|EGK36048.1| dihydrouridine synthase family protein [Shigella flexneri K-304]
          Length = 315

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|317047410|ref|YP_004115058.1| dihydrouridine synthase DuS [Pantoea sp. At-9b]
 gi|316949027|gb|ADU68502.1| dihydrouridine synthase DuS [Pantoea sp. At-9b]
          Length = 318

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 90/191 (47%), Gaps = 16/191 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQ+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  LQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G + + +H R       + ++  
Sbjct: 127 RAAVPDHLPVTVKVRLGWDSSDRRF---EIADAVQQAGASELVVHGR-------TKEEGY 176

Query: 170 KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  ++++  + EI++    P +  G     +D    L+I    D VM+GR A  N   L+
Sbjct: 177 RAESINWQAIGEIRQRLRIPVIANGEIWNWQDAQDCLRI-TGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEYFSNPLT 238
            V +Y   P+ 
Sbjct: 235 RVVKYNEAPMA 245


>gi|313651246|gb|EFS15644.1| dihydrouridine synthase (Dus) family protein [Shigella flexneri 2a
           str. 2457T]
 gi|332755178|gb|EGJ85542.1| dihydrouridine synthase family protein [Shigella flexneri K-671]
          Length = 313

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 65  VQLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 124

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 125 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 174

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 175 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 232

Query: 228 TVDEY 232
            V +Y
Sbjct: 233 RVVKY 237


>gi|294142602|ref|YP_003558580.1| tRNA-dihydrouridine synthase B [Shewanella violacea DSS12]
 gi|293329071|dbj|BAJ03802.1| tRNA-dihydrouridine synthase B [Shewanella violacea DSS12]
          Length = 325

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/190 (28%), Positives = 93/190 (48%), Gaps = 23/190 (12%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   +  AA +    G   I++N+GCP+ +V++   G+ L+ NP +V + + A
Sbjct: 71  SVQIAGADPELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQNPVLVKEILQA 130

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSP 165
           +  A+ +PVT+K R G D +      RN   + +  +  G+  + +H   R+ + KG   
Sbjct: 131 VVAAVDVPVTLKIRTGWDPE-----HRNGVQIAQIAEDCGIASLAVHGRTRQCMYKG--- 182

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                  N +YD +  IKK N  + +  NG +    +A  +L    VD +MIGR A    
Sbjct: 183 -------NAEYDTIKAIKK-NISIPVIANGDIVTPEKARYVLDHTGVDALMIGRGAQGRP 234

Query: 224 AMLTTVDEYF 233
            +   +  Y 
Sbjct: 235 WIFREIQHYL 244


>gi|221116753|ref|XP_002163197.1| PREDICTED: similar to tRNA-dihydrouridine synthase 3-like [Hydra
           magnipapillata]
          Length = 679

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 51/213 (23%), Positives = 103/213 (48%), Gaps = 17/213 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A  +L+G +    ++   + E    +Q+ G     + +A +++ ++   + I++N+
Sbjct: 363 EMAMATNLLQGHQSEWALVKRHSSEDIFGVQLCGGYPDSMAKAVEMLNKECQIDFIDINM 422

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V +   G+ LM     + + +  M +   +P+T+K R G+ +   ++A + ++ 
Sbjct: 423 GCPIDLVFKKGEGSALMGRMKKLEEVVKGMVQVSDVPITIKMRTGIQEN-KSIAHK-IIP 480

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK-ENPDLFIGLNGGLEDM 200
            +K+ GV+ I +H R         ++ R     D+D + +  K  +P  F G NG +   
Sbjct: 481 LVKEWGVDLITLHGRS--------REQRYTKAADWDYINQCAKLSHPVPFFG-NGDIFSY 531

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
             A+K   +  VDG+MI R A     + T + E
Sbjct: 532 EDAIKRQENFGVDGLMIARGALIKPWIFTEIKE 564


>gi|213514710|ref|NP_001133911.1| tRNA-dihydrouridine synthase 3-like [Salmo salar]
 gi|209155790|gb|ACI34127.1| tRNA-dihydrouridine synthase 3-like [Salmo salar]
          Length = 654

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 64/276 (23%), Positives = 115/276 (41%), Gaps = 28/276 (10%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNV 81
           EM +   +L+G      +L     E    +Q+ G     +   A+++ +    + +++N 
Sbjct: 339 EMAMCTNLLQGQSSEWALLKRHESEDLFGVQVEGCFPDTMTRCAELLNNKIDVDFVDINS 398

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM   +     I  M   L +P+TVK R GV ++  A     L+ 
Sbjct: 399 GCPIDLVYKKGGGCGLMTRTNKFEQIIRGMNSVLDVPLTVKIRTGVQEK--ANIAHKLIP 456

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +KK GV+ I +H R         ++ R   + D+D +    +    + +  NG +    
Sbjct: 457 EMKKWGVSMITLHGRS--------REQRYTKSADWDYINTCSQLASPIPLFGNGDILSYY 508

Query: 202 QALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMT 260
            A+K   + V G+M+ R A     + T + E     ++ S  +   V +DF        T
Sbjct: 509 DAMKARETDVSGIMLARGALIKPWVFTEIKERRDWDISSSERLD--VLRDF--------T 558

Query: 261 DYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            Y   H  S  +  + TR+ +  +  F     CR+I
Sbjct: 559 HYGLEHWGSDTQGLEKTRNFLLEWLSF----MCRYI 590


>gi|156058113|ref|XP_001594980.1| hypothetical protein SS1G_04788 [Sclerotinia sclerotiorum 1980]
 gi|154702573|gb|EDO02312.1| hypothetical protein SS1G_04788 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 513

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 90/183 (49%), Gaps = 17/183 (9%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L  QIG +D  K V+ A++V       I++N GCP      G  GA L+  PD +   
Sbjct: 189 KKLIFQIGTSDPEKAVQCARMVAA-DVAGIDVNAGCPKPFSTSGGMGAALLQTPDKLCAI 247

Query: 108 IAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + A+ K +     I ++VK R+    + P      LV+ +  +G+ G+ IH R   ++  
Sbjct: 248 LEALVKEIVPEFEIGISVKIRLL---ETPERT-EALVRKLCATGITGLTIHCRTTPMR-- 301

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
            P++ R I      ++ +I +E+  +   +NG +E+  QALK+      +G MI  AA  
Sbjct: 302 -PRE-RAIRG-QLKMIADICRES-GIACLMNGDVENRDQALKLAEEYGTNGAMIAVAAEA 357

Query: 222 NSA 224
           NS+
Sbjct: 358 NSS 360


>gi|157165335|ref|YP_001466365.1| phosphoribosylamine--glycine ligase [Campylobacter concisus 13826]
 gi|112800093|gb|EAT97437.1| tRNA-dihydrouridine synthase B [Campylobacter concisus 13826]
          Length = 307

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 68/256 (26%), Positives = 122/256 (47%), Gaps = 35/256 (13%)

Query: 24  TEMIVADAIL--RGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           +EMI A+A++    DK   +L  S  E+P  +QI G++I  + +A +I+  F G   ++L
Sbjct: 36  SEMISANALVYESSDKTLEMLKKSPNEEPYVVQIAGSEIENIKKAVQIINKFDGIYGLDL 95

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALR 137
           N GCP  +V     G+ L+ + D + + I+ + K++S    ++VK R+G +D+       
Sbjct: 96  NCGCPVPKVVRQGAGSALLNDLDKLQNIISDI-KSVSNKESLSVKFRLGFNDKNE----E 150

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+ +++G + I +H R     G S K       +DY+ +  +K  +  + +  NG +
Sbjct: 151 KIAKACEEAGADYIAVHGRTR-AGGYSAK-------VDYEAIARVKA-SVKIPVIANGDI 201

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
            +   A +IL     D +MIGRA+  N  +   +              K+ VDK   +KI
Sbjct: 202 -NAQNADEILNFTKCDALMIGRASIGNPWIFHEI------------KTKSSVDKALKQKI 248

Query: 256 SASMTDYAARHLHSGG 271
             +  D    H    G
Sbjct: 249 ILAHFDAMIEHYGEHG 264


>gi|293115531|ref|ZP_05791959.2| dihydrouridine synthase family protein [Butyrivibrio crossotus DSM
           2876]
 gi|292809467|gb|EFF68672.1| dihydrouridine synthase family protein [Butyrivibrio crossotus DSM
           2876]
          Length = 298

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/220 (23%), Positives = 95/220 (43%), Gaps = 12/220 (5%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVE 70
           + R   +    +T  I +  +   +K ++L    Q   +  QI      +    A+++ E
Sbjct: 13  YNRYFGDADRYFTPFIASRKLNSKEKNDVLPEHNQNMDVIPQILTNKSEEFCYIASRLKE 72

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
            +GY E+NLN+GCPS  V   + G+  +  PD +      +     + ++VK R GV++ 
Sbjct: 73  YYGYEEVNLNLGCPSGTVVAKNRGSGFLAVPDELNRFFEEVFSMTDVRISVKTRTGVENN 132

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPDL 189
                  N++K   +  ++ + IH R     G   K     PNL D+     I + +   
Sbjct: 133 ---ENWENILKIYNEYPISELIIHPR-CRKDGYGGK-----PNLEDFKKAVLISRHSL-C 182

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           + G    +ED +   K  P+VD +M GR    N  + + +
Sbjct: 183 YNGDINSVEDYNAITKEFPTVDKIMCGRGILMNPGLFSEI 222


>gi|126663428|ref|ZP_01734425.1| hypothetical protein FBBAL38_08769 [Flavobacteria bacterium BAL38]
 gi|126624376|gb|EAZ95067.1| hypothetical protein FBBAL38_08769 [Flavobacteria bacterium BAL38]
          Length = 314

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 104/238 (43%), Gaps = 46/238 (19%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D  + +  AK V+ FGY E+N N+GCP   V +   G+ L+ N D +   +  + 
Sbjct: 66  QIITNDAEEFLFVAKYVQQFGYKELNWNLGCPYPMVAKCGMGSGLIKNTDQIEHILKRVH 125

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRK 170
               I V++K R+G ++  P+  L ++   +++  +  I IHAR  K + KG    D+ +
Sbjct: 126 NETDIIVSMKMRMGYEN--PSEIL-DVFPILEQYPIKNIAIHARIGKQLYKGGVDLDSFQ 182

Query: 171 --IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAY----- 220
             + +  + + Y             NG +  +++  ++    PS+D  MIGR        
Sbjct: 183 KCLDHSKHKLYY-------------NGDITSVTKFKEMQERFPSIDHFMIGRGLIADPFL 229

Query: 221 ------------KNSAML-----TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
                       KN   L      T+ + +   L G +PI+ ++   FW   S S ++
Sbjct: 230 PSMIKNNTTEYPKNRYQLFEEFHDTIYQEYDAYLQGPTPIRMKM-LGFWEYFSESFSN 286


>gi|326492876|dbj|BAJ90294.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326526215|dbj|BAJ97124.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 320

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 74/151 (49%), Gaps = 11/151 (7%)

Query: 8   HYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGADISKLVEAA 66
           H     + +TN +L  T     D + RG    +     QE+  +  Q+G +D  + ++AA
Sbjct: 40  HKFVHCQRVTNESLGTT-----DFLERGTDSVVFRTCPQERDRVVFQMGTSDAVRALKAA 94

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +IV +     I++N+GCP A    G  G+ L+  P+++ D +  + + L+ PVT K R+ 
Sbjct: 95  EIVCN-DVAAIDINMGCPKAFSVSGGMGSALLSKPELIHDILTTLRRNLNTPVTCKIRLL 153

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
              Q        L + I+K GV  + +H RK
Sbjct: 154 NTRQDTV----ELARRIEKCGVPALAVHGRK 180


>gi|324509339|gb|ADY43931.1| tRNA-dihydrouridine synthase 1-like protein [Ascaris suum]
          Length = 503

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/168 (24%), Positives = 83/168 (49%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R   R     L  + +++ ++ V D   R   ++ L     ++PL +Q   
Sbjct: 59  MVDQSELAFRMMMRQHGADLCFSPMIHAQLFVKDLTYR---RSALSSCPSDRPLIVQFCA 115

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   L+ A  +VED   + ++LN+GCP      G +GA L  + D+V + ++ +     
Sbjct: 116 NEPHMLLTACLLVEDIC-DGVDLNLGCPQLIAKRGHYGAYLEEDLDLVCEMVSLVHSHCR 174

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +P++  C+I + D+I      N  ++++K+G   + +H R    +G S
Sbjct: 175 VPLS--CKIRILDEIGKTV--NYARALEKAGACMLTVHGRTRQQRGAS 218


>gi|66801291|ref|XP_629571.1| CCCH-type zinc finger-containing protein [Dictyostelium discoideum
           AX4]
 gi|74850928|sp|Q54CU9|DUS3L_DICDI RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|60462949|gb|EAL61146.1| CCCH-type zinc finger-containing protein [Dictyostelium discoideum
           AX4]
          Length = 671

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 91/212 (42%), Gaps = 16/212 (7%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L G K  +  L     E    +QI G+ +   V+ A+ +E +   + +++N 
Sbjct: 354 EMALTTKLLEGTKSELALLKRHPCEDKFGVQICGSYVDAAVKCAEFIENEIDADFVDINS 413

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     GA LM  P  V   +  +  +LS P T+K RIG  +  P      L+ 
Sbjct: 414 GCPIDLVCNMGAGAALMERPKKVEQLLRGISSSLSCPTTIKIRIGKSEDAPTA--HKLIP 471

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           S+ + G   + +H R    +        ++ N DY  V +  + +    IG NG + +  
Sbjct: 472 SLGEWGACAVTLHGRSRAQR------YSRLANWDY--VKQCSEVSSIPLIG-NGDIYNYQ 522

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
             + I  S  V  +MI R A     + T + E
Sbjct: 523 DVVNIYDSSKVSSIMIARGALIKPWIFTEIKE 554


>gi|325092392|gb|EGC45702.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus H88]
          Length = 495

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 94/219 (42%), Gaps = 23/219 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N     ++      I R D +   G       L  QIG A     V+AAKI+  
Sbjct: 90  FTRLPSNGGRENSQAAKESIIYRLDPRRESGK------LVFQIGTASPDLAVQAAKIIA- 142

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD +   + A+ + +  P    ++VK R+  
Sbjct: 143 ADVAGIDVNAGCPKPFSTTGGMGAALLQTPDRLVSILTALVQQVGTPYQIGISVKIRLLA 202

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 203 DPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRERAIRDQLP-----MIASICRAA- 252

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            + I +NG +E     L ++    VDG MI   A  NS+
Sbjct: 253 GVAILVNGDVESRDHGLALMAEYGVDGAMIATCAEANSS 291


>gi|224825374|ref|ZP_03698479.1| dihydrouridine synthase DuS [Lutiella nitroferrum 2002]
 gi|224602295|gb|EEG08473.1| dihydrouridine synthase DuS [Lutiella nitroferrum 2002]
          Length = 310

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 91/171 (53%), Gaps = 18/171 (10%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D   L + A    + G   ++LN GCP+  V+    GA L+  P+++   +AA+
Sbjct: 67  VQLLGSDPVCLADNAVRAVELGAPAVDLNFGCPAPTVNRHRGGAVLLTEPELLFQIVAAV 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             ++   +PVT K R+G +D+  ++AL    ++I+++G + + +H R  + +G  P  + 
Sbjct: 127 RASVPKEVPVTAKMRLGYEDK--SLAL-ECAQAIERAGADELVVHGRTKV-EGYRPPAH- 181

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGR 217
                 +D +  I +E+ +L +  NG    +ED   A++     D VMIGR
Sbjct: 182 ------WDWIARI-RESVNLPVIANGEVWTVEDY-HAIRRESGCDTVMIGR 224


>gi|224282569|ref|ZP_03645891.1| NifR3-like protein [Bifidobacterium bifidum NCIMB 41171]
 gi|310287030|ref|YP_003938288.1| TIM-barrel protein [Bifidobacterium bifidum S17]
 gi|309250966|gb|ADO52714.1| putative TIM-barrel protein [Bifidobacterium bifidum S17]
          Length = 426

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G + + +
Sbjct: 70  TNWPFRVLCEEYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVNPAIV 129

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKALSI 117
            +AA+IV  ED   + ++LN GCP  +V     G+ L    D+  + I     +C A +I
Sbjct: 130 EQAARIVVDEDMA-DHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCSAANI 188

Query: 118 PVTVKCRIGVD 128
           PVT K R+G+D
Sbjct: 189 PVTAKIRVGID 199


>gi|168183356|ref|ZP_02618020.1| dihydrouridine synthase family protein [Clostridium botulinum Bf]
 gi|237793992|ref|YP_002861544.1| dihydrouridine synthase family protein [Clostridium botulinum Ba4
           str. 657]
 gi|182673465|gb|EDT85426.1| dihydrouridine synthase family protein [Clostridium botulinum Bf]
 gi|229262625|gb|ACQ53658.1| dihydrouridine synthase family protein [Clostridium botulinum Ba4
           str. 657]
          Length = 319

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 98/232 (42%), Gaps = 17/232 (7%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           K   + +++K RIG D          L+K   K  +  + IH R    K     +    P
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPRTQ--KDFYGNE----P 174

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           NL           NP  + G    + D ++ +K  P V  +M+GR    N  ++      
Sbjct: 175 NLGVFKDALSLSSNPICYNGDIFTVSDYNRLIKTFPKVKTIMLGRGILANPGLI------ 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             N +  ++ +   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 229 --NEIKNNTTVDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|321249423|ref|XP_003191451.1| tRNA dihydrouridine synthase [Cryptococcus gattii WM276]
 gi|317457918|gb|ADV19664.1| tRNA dihydrouridine synthase, putative [Cryptococcus gattii WM276]
          Length = 623

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/194 (26%), Positives = 92/194 (47%), Gaps = 18/194 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D   L+ AAK VE    + +++N GCP      G +G+ L    +++  
Sbjct: 153 DRPLIVQFCANDPDILLAAAKKVE-HRCDAVDINFGCPQGIAKRGHYGSFLQDEWELIHK 211

Query: 107 CIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            I+ + + LS+PVT K RI  D D+  A A     + ++ +G   +  H R   +KG   
Sbjct: 212 LISTLHENLSVPVTAKFRIFADLDKTIAYA-----RMMEAAGAQILTCHGRTREMKG--- 263

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
             N  +   D++ + E+K     + +  NG +   ED+ + +++    DGVM       N
Sbjct: 264 -QNTGL--ADWEYIREVKNAV-KVPVFANGNILYREDVDRCMEVT-GCDGVMTAEGNLSN 318

Query: 223 SAMLTTVDEYFSNP 236
            A+    D  +++P
Sbjct: 319 PAIFMPPDHPYAHP 332


>gi|157375994|ref|YP_001474594.1| dihydrouridine synthase, DuS [Shewanella sediminis HAW-EB3]
 gi|157318368|gb|ABV37466.1| dihydrouridine synthase, DuS [Shewanella sediminis HAW-EB3]
          Length = 308

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 86/176 (48%), Gaps = 18/176 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G   S + E A    + G   ++LN GCP+  V+  + GA L+  PD +    
Sbjct: 64  PVRLQLLGQHPSWMAENALRAVELGSRGVDLNFGCPAPMVNRSNGGAALLKEPDTIYRVT 123

Query: 109 AAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            ++ +A+    PV+ K R+G DD+   V    + ++I+ +G   + +HAR         K
Sbjct: 124 HSVREAVPSNHPVSAKIRLGWDDKSRCV---EIAQAIEAAGATELTVHART--------K 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           +    P   ++ + +I KE   + +  NG +   ED  Q  +++   + VM+GR A
Sbjct: 173 EEGYRPPAHWEYINQI-KEAISIPVIANGEVWNREDY-QRCQVVSGCNDVMVGRGA 226


>gi|91092412|ref|XP_967539.1| PREDICTED: similar to t-diRNAhydrouridine synthase [Tribolium
           castaneum]
 gi|270004747|gb|EFA01195.1| hypothetical protein TcasGA2_TC010522 [Tribolium castaneum]
          Length = 461

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 103/238 (43%), Gaps = 33/238 (13%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L++ +   DA  R +    L     +KPL +Q  G
Sbjct: 18  MVDASELPWRLLSRKYGAQLCYTPMLHSAIFARDAKYRNEA---LASCEIDKPLIVQFCG 74

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   ++EAA + +D     I++N+GCP A    G +GA L     ++ + ++ + + L 
Sbjct: 75  NDPKVMLEAALLAQDHCC-AIDINLGCPQAIAKRGHYGAFLQDEWPLLHEIVSLLSQRLK 133

Query: 117 IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRK 170
           +P+T K R    V+  +      +  K +  +G   + +H R    K  L GL+      
Sbjct: 134 VPITCKVRRFESVEKTV------DYAKMLVSAGCKMLTVHGRTREQKGPLTGLA------ 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAML 226
               D+  V  + +E  D+ +  NG ++ M    + L      GVM       N A+ 
Sbjct: 182 ----DWSYVKAV-REAVDIPVISNGNIQCMQDVDRCLEETGAVGVMTAEGNLYNPALF 234


>gi|332140763|ref|YP_004426501.1| multifunctional fatty acid oxidation complex subunit alpha
           [Alteromonas macleodii str. 'Deep ecotype']
 gi|327550785|gb|AEA97503.1| multifunctional fatty acid oxidation complex subunit alpha
           [Alteromonas macleodii str. 'Deep ecotype']
          Length = 629

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 76/140 (54%), Gaps = 10/140 (7%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           NA+ Y+  I+   +    KK  +  S  +K LAL  G  D S   +   +VE   + +++
Sbjct: 356 NAMKYSYDILNKKV----KKRFMRNSEMQKQLALLTGTLDYSGYQDVDIVVEAV-FEDLD 410

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVAL 136
           LN GCP+  V++   GA L+     + D + A+  A+   IPV+ K R+G +D+  ++A+
Sbjct: 411 LNFGCPAKTVNKSKGGAVLLKETQTLYDIVKAVRDAVPAEIPVSAKIRLGFEDK--SLAV 468

Query: 137 RNLVKSIKKSGVNGIWIHAR 156
            N V +I ++G + + +HAR
Sbjct: 469 ENAV-AITEAGASELVVHAR 487


>gi|16081529|ref|NP_393883.1| dihydroorotate dehydrogenase 1B [Thermoplasma acidophilum DSM 1728]
 gi|13878694|sp|Q9HL35|PYRD_THEAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|10639575|emb|CAC11547.1| DIHYDROOROTATE DEHYDROGENASE B related protein [Thermoplasma
           acidophilum]
          Length = 300

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 83/187 (44%), Gaps = 28/187 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           KP+   +  +D    V   + ++++G + + LN+ CP    H   FG  +  +PD+V D 
Sbjct: 93  KPVIGSVFASDAESFVNLGRKMQEYGCDAVELNLSCP----HVKGFGLEVGSDPDLVEDI 148

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIP---------AVALRNLVKSIKKSGVNGIWIHARKA 158
           +  M   +S+PV  K    V D I          A  L N VK++K      I I AR  
Sbjct: 149 VNEMKSKISVPVFAKLSPNVSDIIEIAKAAEKADAYVLINTVKAMK------IDIRARMP 202

Query: 159 ILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           +L     GLS      I  +    VYE+KKE     IG+ GG+     A++ I+     V
Sbjct: 203 VLTNAYGGLS---GPAIKPVGVRYVYEVKKETGKDIIGV-GGITTYEDAVEYIMAGASAV 258

Query: 214 MIGRAAY 220
            IG A Y
Sbjct: 259 QIGTALY 265


>gi|331694352|ref|YP_004330591.1| TIM-barrel protein, nifR3 family [Pseudonocardia dioxanivorans
           CB1190]
 gi|326949041|gb|AEA22738.1| TIM-barrel protein, nifR3 family [Pseudonocardia dioxanivorans
           CB1190]
          Length = 391

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 73/154 (47%), Gaps = 10/154 (6%)

Query: 12  FARLLTNNALLY--TEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       Y   EMI +  ++  +   + ++ F   E P ++Q+ G D + +  A +
Sbjct: 47  FRRLCREQGAGYYVCEMITSRGLVERNPLTRRMIAFDADEHPRSMQLYGVDPATIGAAVR 106

Query: 68  IV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCR 124
           IV  ED   + ++ N GCP  +V     GA L     +    + AA+  A  IPVT+K R
Sbjct: 107 IVAEEDLA-DHLDFNFGCPVPKVTRRGGGAALPYKRRLFERIVRAAVDNAGGIPVTIKMR 165

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +G+DD+       ++ +     GV  I +HAR A
Sbjct: 166 VGIDDE--HHTFLDVARIAADCGVAAITLHARTA 197


>gi|329946913|ref|ZP_08294325.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328526724|gb|EGF53737.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 436

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/290 (22%), Positives = 124/290 (42%), Gaps = 32/290 (11%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKI-VED 71
           LL    L  TEM+   A++  +++ +    T   E+  ++Q+ G D + +  A +I VE+
Sbjct: 78  LLAPAGLYVTEMVTTRALVERNERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEE 137

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----------LSIPVT 120
              + I+LN GCP  +V     GA L    D++   +    +A             +PVT
Sbjct: 138 DLADHIDLNFGCPVPKVTRKGGGAALPWKRDLLAAILTEAVRASEAACRAAGRAREVPVT 197

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G+D++          ++ + +G+  + +HAR A           +I  L      
Sbjct: 198 MKMRLGIDEE--HETFLAAARTAENAGIAAVALHARSARQHYSGQARWEEIARL------ 249

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              KE  DL +  NG +     A++++ +   DGV++GR       +   +       + 
Sbjct: 250 ---KEATDLPVLGNGDIWLGDDAVRMMETTGCDGVVVGRGCQGRPWLFADI----VAAMH 302

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           GSS ++TR D D   ++        A  +     ++ + +H+     G+P
Sbjct: 303 GSS-MRTRPDLDAVIEVIRRHGRMLAAEMGEDRGVRDLRKHVGWYLKGYP 351


>gi|240281112|gb|EER44615.1| tRNA dihydrouridine synthase [Ajellomyces capsulatus H143]
          Length = 495

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 94/219 (42%), Gaps = 23/219 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N     ++      I R D +   G       L  QIG A     V+AAKI+  
Sbjct: 90  FTRLPSNGGRENSQAAKESIIYRLDPRRESGK------LVFQIGTASPDLAVQAAKIIA- 142

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD +   + A+ + +  P    ++VK R+  
Sbjct: 143 ADVAGIDVNAGCPKPFSTTGGMGAALLQTPDRLVSILTALVQQVGTPYQIGISVKIRLLA 202

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 203 DPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRERAIRDQLP-----MIASICRAA- 252

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            + I +NG +E     L ++    VDG MI   A  NS+
Sbjct: 253 GVAILVNGDVESRDHGLALMAEYGVDGAMIATCAEANSS 291


>gi|242278643|ref|YP_002990772.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
 gi|242121537|gb|ACS79233.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
          Length = 323

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/248 (24%), Positives = 107/248 (43%), Gaps = 19/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+    +    K  K +L    ++ PL +Q+ G +
Sbjct: 16  LAGYSDLPFRMLCRK-RGCAVACTEMVSVKGLKYDGKGTKALLATCPEDNPLVVQLFGGE 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSI 117
                +    + D GY+  +LN GCP  +V +   G+ L L+PD + +  +AM + A   
Sbjct: 75  PQDYSDTMPQLIDEGYSFFDLNSGCPVKKVLKTGGGSALHLDPDRLVETASAMVRVAGEG 134

Query: 118 PVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            V VK R+G    +D    +A     K ++ +GV  + +H R A        D  K+  L
Sbjct: 135 KVGVKIRLGFMNGEDNFLEIA-----KRLEDTGVAWLTMHPRYAKQMFSGQADWSKLAVL 189

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             ++   +     DLF   + G+E + Q       +DG+M  R A  +  +     +   
Sbjct: 190 KQNVSIPVIGSG-DLFTAED-GMECIKQT-----GIDGIMFARGALFDPEIFARYLKLLD 242

Query: 235 NPLTGSSP 242
           +P   + P
Sbjct: 243 DPKCATLP 250


>gi|255543897|ref|XP_002513011.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
 gi|223548022|gb|EEF49514.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
          Length = 686

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 95/230 (41%), Gaps = 18/230 (7%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAA 66
           +R   +LL  + +   EM +   +L+G      +L   + E    +QI GA    +    
Sbjct: 348 FRRLCKLLGAD-ITCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYSDTVARTV 406

Query: 67  KIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           +++ ++   + I++N+GCP   V     G+CL+  P  +   I A    +  P+TVK R 
Sbjct: 407 ELIDQECTVDFIDINMGCPIDIVVSKGAGSCLLTKPMRMKSIIHAASSTVDTPITVKVRT 466

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G  +      + +L+  I   G N + IH R         +  R     D++ +Y   K+
Sbjct: 467 GYFEG--KNRIDSLIADISNWGTNAVTIHGRS--------RQQRYSKLADWEYIYHCAKK 516

Query: 186 NPDLFIGLNGG----LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            P+ F  L  G      D ++     P +   MI R A     + T + E
Sbjct: 517 APESFQVLGNGDIFSYTDWNKHKSDCPELSSCMIARGALIKPWLFTEIKE 566


>gi|119469539|ref|ZP_01612443.1| tRNA-dihydrouridine synthase C [Alteromonadales bacterium TW-7]
 gi|119447074|gb|EAW28344.1| tRNA-dihydrouridine synthase C [Alteromonadales bacterium TW-7]
          Length = 326

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 92/198 (46%), Gaps = 16/198 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G + + L E A    D G + ++LN GCP+  V+    GA L+ +P
Sbjct: 57  GYTRAGTPVRIQLLGQEANPLAENAVRAIDLGSHGVDLNFGCPAKTVNRSRGGAVLLKDP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   I A+  A+     V+ K R+G DD   +   + ++ ++  +G N + IHAR   
Sbjct: 117 EHMYTIIKAVRDAVDSKHEVSAKIRLGFDDDSNS---QEIIDAVVSAGANSVAIHARTKR 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGR 217
                P    KIP +       IK +N  + +  NG +  +  A+  +       +M+GR
Sbjct: 174 DGYNPPAYWEKIPPI-------IKGKN--IAVVANGEIWQVEDAMLCQKRSGCSDLMLGR 224

Query: 218 AAYKNSAMLTTVDEYFSN 235
            A  +  +   +  + +N
Sbjct: 225 GALSHPDLAKKIKAHVNN 242


>gi|313668540|ref|YP_004048824.1| trna-dihydrouridine synthase c [Neisseria lactamica ST-640]
 gi|313006002|emb|CBN87461.1| trna-dihydrouridine synthase c (ec 1.-.-.-) [Neisseria lactamica
           020-06]
          Length = 333

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 84/188 (44%), Gaps = 12/188 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V+    GA L+  P ++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAIRFGADKIDLNFGCPAPTVNRHKGGAILLKEPQLIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR        P 
Sbjct: 136 KTLRERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHARTKAEAYEPPA 192

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               I  +  D V      N D+F      L+D    +K +   + VM+GR A     + 
Sbjct: 193 HWEWIKKI-RDAVNIPVTANGDVFT-----LQDYI-GIKTISGCNSVMLGRGAVIRPDLA 245

Query: 227 TTVDEYFS 234
             + +Y S
Sbjct: 246 RQIKQYES 253


>gi|329119847|ref|ZP_08248521.1| tRNA-dihydrouridine synthase C [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327464003|gb|EGF10314.1| tRNA-dihydrouridine synthase C [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 315

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 87/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D + +   A     FG  +I+LN GCP+  V++   GA L+  P  V   +
Sbjct: 57  PCTVQLLGSDAANMAANALEAVRFGAEKIDLNFGCPAPTVNKHQGGAVLLKEPQRVHAIV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +AL   I +T K R+G DD+   +AL N  ++I + G   + +HAR  + +G  P 
Sbjct: 117 KTLREALPAHILLTGKMRLGFDDKT--LALEN-AQAIAEGGACALTVHARTKV-EGYEPP 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
            +       +  V +I     D+ +  NG +  +   L I       GVMIGR A     
Sbjct: 173 AH-------WAWVKKIAAAV-DIPVTANGDVFTLQDYLAIRRESGCAGVMIGRGAVIRPG 224

Query: 225 MLTTVDEY 232
           +   +  Y
Sbjct: 225 LARQIKAY 232


>gi|313139725|ref|ZP_07801918.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
 gi|313132235|gb|EFR49852.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
          Length = 413

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/135 (30%), Positives = 68/135 (50%), Gaps = 8/135 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 53  MAGVTNWPFRVLCEEYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVN 112

Query: 59  ISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCK 113
            + + +AA+IV  ED   + ++LN GCP  +V     G+ L    D+  + I     +C 
Sbjct: 113 PAIVEQAARIVVDEDMA-DHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCS 171

Query: 114 ALSIPVTVKCRIGVD 128
           A +IPVT K R+G+D
Sbjct: 172 AANIPVTAKIRVGID 186


>gi|298368946|ref|ZP_06980264.1| tRNA-dihydrouridine synthase C [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282949|gb|EFI24436.1| tRNA-dihydrouridine synthase C [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 338

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 48/189 (25%), Positives = 91/189 (48%), Gaps = 18/189 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 80  PCTVQLLGSDADNMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPELIYRIV 139

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+ PA+     + +     +    +HAR         K
Sbjct: 140 RTLRRRLPPHIPLTAKMRLGYEDKSPALECAAAIAAAGACALT---VHART--------K 188

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNS 223
           +    P   ++ + +I +++ D+ +  NG    LED  + +K +   D VM+GR A    
Sbjct: 189 NEGYEPPAHWEWIRKI-RDSVDIPVTANGDVFTLEDYLE-IKAVSGCDSVMLGRGAVIRP 246

Query: 224 AMLTTVDEY 232
            +   + +Y
Sbjct: 247 YLARQIKQY 255


>gi|332558248|ref|ZP_08412570.1| tRNA-dihydrouridine synthase B [Rhodobacter sphaeroides WS8N]
 gi|332275960|gb|EGJ21275.1| tRNA-dihydrouridine synthase B [Rhodobacter sphaeroides WS8N]
          Length = 326

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 82/161 (50%), Gaps = 11/161 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A +     L+ +EM+ +  ++    + +        E   A+Q+ G D
Sbjct: 19  MAGITDLPFRRLA-VRFGAGLVVSEMVASREVVCAGAEARARAEIGATEGRTAVQLAGCD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     I A+  A+++P
Sbjct: 78  PHWMTEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALIEAVVGAVAVP 137

Query: 119 VTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHAR 156
           VT+K R+G D+ +   P +A R      + +GV  I IH R
Sbjct: 138 VTLKMRLGWDEGMLNAPEIARRA-----EAAGVAMITIHGR 173


>gi|271500980|ref|YP_003334005.1| dihydrouridine synthase DuS [Dickeya dadantii Ech586]
 gi|270344535|gb|ACZ77300.1| dihydrouridine synthase DuS [Dickeya dadantii Ech586]
          Length = 311

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYQAAKAM 126

Query: 112 CKA--LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A  LS+PVTVK R+G D          +  ++ ++G + + +H R       + +D  
Sbjct: 127 RDAVPLSLPVTVKVRLGWDSGERQF---EIADAVAQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A   +     D VMIGR A  N   L+
Sbjct: 177 RAERINWAAIGEIRQRLRIPVIA-NGEIWDWQSAQDCMAVTGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|195132199|ref|XP_002010531.1| GI14629 [Drosophila mojavensis]
 gi|193908981|gb|EDW07848.1| GI14629 [Drosophila mojavensis]
          Length = 458

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 86/188 (45%), Gaps = 19/188 (10%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           S +   + LQ+G +D ++ +   K+V++     +++N+GCP     +G  GA L+  P  
Sbjct: 77  SLETSRVVLQLGTSDAARALAVGKLVQN-DIAGLDINMGCPKEFSIKGGMGAALLSEPAK 135

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               +  +   L IP+T K RI + D +  +    LV+ +  +G+  I IHAR       
Sbjct: 136 AAHILRTLTTHLDIPITCKIRI-LPDTLETI---KLVQELAATGIAAIGIHART------ 185

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRA 218
             +D R   +   D++  +     D+ I  NGG  +M         + L   D VM+ RA
Sbjct: 186 --RDERPQHHPHPDVLRAVASA-VDIPIIANGGSRNMHTYEDLHKFQELCGADSVMVARA 242

Query: 219 AYKNSAML 226
           A  N ++ 
Sbjct: 243 AQLNVSIF 250


>gi|297571272|ref|YP_003697046.1| hypothetical protein Arch_0694 [Arcanobacterium haemolyticum DSM
           20595]
 gi|296931619|gb|ADH92427.1| TIM-barrel protein, nifR3 family [Arcanobacterium haemolyticum DSM
           20595]
          Length = 407

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 88/183 (48%), Gaps = 27/183 (14%)

Query: 51  ALQIGGADISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACL----MLNPDIV 104
           ++Q+ G +   +  A +I+  ED+  + I++N GCP  +V     G+ L     L  DIV
Sbjct: 93  SIQLYGVEPKNIAAAVEILVREDWA-DHIDINFGCPVPKVTRKGGGSALPWKHQLFSDIV 151

Query: 105 GDCIAAMCKAL-------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
              +AA  +A        +IPVT K RIG+DD       R++ K  + +G++ + +HAR 
Sbjct: 152 TGAVAASERASREAGRTHTIPVTAKFRIGIDDD--HTTFRDVAKMSEDAGISALTLHART 209

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMI 215
                    +        +D + E+K  + +L I  NG + +   A ++L   + DGV +
Sbjct: 210 T--------EQHYSGQAQWDYIRELKATS-NLPIFGNGDVFEAEDAARMLAHTAADGVCV 260

Query: 216 GRA 218
           GR 
Sbjct: 261 GRG 263


>gi|134093535|ref|YP_001098610.1| tRNA-dihydrouridine synthase B [Herminiimonas arsenicoxydans]
 gi|133737438|emb|CAL60481.1| tRNA-dihydrouridine synthase B [Herminiimonas arsenicoxydans]
          Length = 322

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 115/251 (45%), Gaps = 16/251 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K+        + +P A+QI GAD
Sbjct: 1   MAGVTDRPFRQLCKQL-GAGYAVSEMAASNPRLWATDKSTRRTNHDGEVEPKAVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK   D G   I++N+GCP  +V     G+ L+ +  +V + + A+  A+ +P
Sbjct: 60  PLMLAECAKFNVDRGAQIIDINMGCPVKKVCNSWCGSALLQHESLVAEILQAVVAAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D+    AL N+ +  ++SG+  + +H R     G S +        +Y++
Sbjct: 120 VTLKFRTGW-DRAHKNAL-NIARIAEQSGIAMLTLHGRTRA-DGYSGE-------AEYEM 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +L +   D +MIGRAA     +   +  Y    
Sbjct: 170 IAAVKA-AVSIPVVANGDITTPEKAKFVLEATGADAIMIGRAAQGRPWIFREIVHYLRTG 228

Query: 237 LTGSSPIKTRV 247
               +P+ + V
Sbjct: 229 THLPAPLISEV 239


>gi|308802842|ref|XP_003078734.1| putative protein involved in tRNA-dihydrouridine (ISS)
           [Ostreococcus tauri]
 gi|116057187|emb|CAL51614.1| putative protein involved in tRNA-dihydrouridine (ISS)
           [Ostreococcus tauri]
          Length = 424

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 88/180 (48%), Gaps = 16/180 (8%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL  QI G+D   L  AAK + ED     ++LN GCP++ V     G+ L+ +P  V D 
Sbjct: 116 PLGAQIMGSDAELLTLAAKHLGEDKNAPRVDLNCGCPASVVTGKGAGSSLLKDPKFVYDA 175

Query: 108 IAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           + A+ + +   +  VT+K R G DD   +  LR  + + + +G   I +HAR    +G S
Sbjct: 176 VRAVARGVEGTNAIVTMKLRTGYDD---SGLLRENLCAARDAGARFISLHARTRA-QGYS 231

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
            + N        DI +  +    D+ I  NG +    +  ++L   + DGV IGR A ++
Sbjct: 232 GRANWD------DIAFAKEVLGDDVPIIGNGDVTSPLRCAELLRVSNADGVGIGRGAVQD 285


>gi|288572811|ref|ZP_06391168.1| dihydrouridine synthase DuS [Dethiosulfovibrio peptidovorans DSM
           11002]
 gi|288568552|gb|EFC90109.1| dihydrouridine synthase DuS [Dethiosulfovibrio peptidovorans DSM
           11002]
          Length = 345

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 73/317 (23%), Positives = 129/317 (40%), Gaps = 41/317 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           R F RL     L +TEM+    + R ++K   +L  +  E PL LQ+   D   L+  A+
Sbjct: 40  RMFWRL--GAGLAHTEMVSCAGLTRKNRKTTEMLFRAPGEGPLVLQLFAGDSDTLMRGAE 97

Query: 68  IVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           I    G  ++ + +N+ CP  +V +   GA L+   D+  D +  + + L +PV  K R 
Sbjct: 98  IALSLGVPFDALGINMACPMPKVLKKGAGARLLSRLDLAVDMVRRLNR-LGLPVWPKIRK 156

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            V D      L     ++ ++G   + +H R A          R     D+D V  + + 
Sbjct: 157 IVPDGSGPDTL-EFASALVEAGAANVGVHGRTA--------SQRYEGTSDFDEVRRVARA 207

Query: 186 NPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV---------DEYF 233
            P + I  +G   G ED+S+AL        V + R    +  +L  +         D  +
Sbjct: 208 LPGV-ISASGDISGPEDVSKALA--GGCVSVFLARGGVTDPFVLPRILSHLGYNIGDSVY 264

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            +P +    I+TR     +  ++  ++ +    +     +  + R M G+F G P     
Sbjct: 265 DDPPS----IETRA--ALFSDLAEDLSTFHGERV----AMVLLKRLMSGVFRGVPGCSSY 314

Query: 294 RHILTVEAGASTATHHI 310
           R  +   +   T   HI
Sbjct: 315 RRAIASASDWGTMCAHI 331


>gi|45190681|ref|NP_984935.1| AER075Wp [Ashbya gossypii ATCC 10895]
 gi|44983660|gb|AAS52759.1| AER075Wp [Ashbya gossypii ATCC 10895]
          Length = 352

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 107/230 (46%), Gaps = 12/230 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   +  F+T  ++ PL +Q+G  +
Sbjct: 41  MVRYSKLPFRQLCRHF-NVDIVYSPMILAREFVRNEHARMADFTTNSRDTPLIVQVGVNN 99

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L+   ++V  +  + I +N GCP   +V EG  G+ L+ N  ++ + + A+ +    
Sbjct: 100 VVDLLRFVEMVSPYC-DGIGINCGCPIREQVREG-IGSALIYNQPLLCEMVRAVKEKYKD 157

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++ +I + D +       L  ++  +GV+ I IH R    +   P +   I  + Y 
Sbjct: 158 TVRLETKIRIHDDLAQTV--TLCNALASAGVDWITIHGRTRTTRSSVPAN---IAAIRYI 212

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
             +   KE P +  G    L+D  + +      DG+M  R    N A+ +
Sbjct: 213 KEHITDKELPIVANGDCFTLDDCHR-IAAETGADGIMAVRGLLANPALFS 261


>gi|42522830|ref|NP_968210.1| nitrogen regulation protein nifR3 [Bdellovibrio bacteriovorus
           HD100]
 gi|39574026|emb|CAE79203.1| Nitrogen regulation protein nifR3 [Bdellovibrio bacteriovorus
           HD100]
          Length = 352

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/188 (25%), Positives = 85/188 (45%), Gaps = 14/188 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E  L  QI G +   + E+ K + ++G   I++N+GCP  +  + ++G  LM +P    +
Sbjct: 74  EPGLVPQILGNEEDAIAESVKRLVEWGAEAIDINMGCPVQKALKHNYGVALMGDPAYAAE 133

Query: 107 CIAAMCKALSIPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            +    K  ++PV+VK R +G   +     L   V  +++SG   + +H R A  K    
Sbjct: 134 VVRMTVKNSTVPVSVKLRAVGSTKEFD--ELLTFVSGLRQSGAAWVCLHPRTAAQK---- 187

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNS 223
               +  N D++ + ++ K      IG NG ++    A+ +L     D  M GR      
Sbjct: 188 ----RRGNADWEQIKQLHKAVDFPVIG-NGDVQTYDDAINMLKETGCDMAMAGRGLAARP 242

Query: 224 AMLTTVDE 231
            M+  + E
Sbjct: 243 WMMWQLGE 250


>gi|28898849|ref|NP_798454.1| putative regulatory protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|153838187|ref|ZP_01990854.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
 gi|260364849|ref|ZP_05777427.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus K5030]
 gi|260879477|ref|ZP_05891832.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|260898224|ref|ZP_05906720.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|260903223|ref|ZP_05911618.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|38604770|sp|Q87N01|DUSC_VIBPA RecName: Full=tRNA-dihydrouridine synthase C
 gi|28807068|dbj|BAC60338.1| putative regulator protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|149748446|gb|EDM59305.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
 gi|308088364|gb|EFO38059.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|308093520|gb|EFO43215.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|308106538|gb|EFO44078.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|308113931|gb|EFO51471.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus K5030]
          Length = 322

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 90/181 (49%), Gaps = 15/181 (8%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +T   P+ +Q+ G +   + E A    + G   I+LN GCP+  V++   GA L+ +P++
Sbjct: 59  TTSGVPVHVQLLGQEPHWMAENAIRAAELGARGIDLNFGCPAKMVNKSKGGAALLQHPEL 118

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A   A+  +IPV+ K R+G ++  P      +V +I+ +G N + +HAR     
Sbjct: 119 IHSVVKACRDAVPANIPVSAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR----- 170

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
             + +   K   + ++ + +I++      I  NG + +     + + +  VD +M+ R A
Sbjct: 171 --TKQGGYKASEIKWEYINKIRERFSIPLIA-NGEIWNFEDGQRCIETTGVDSLMVCRGA 227

Query: 220 Y 220
           +
Sbjct: 228 F 228


>gi|146307749|ref|YP_001188214.1| dihydrouridine synthase, DuS [Pseudomonas mendocina ymp]
 gi|145575950|gb|ABP85482.1| tRNA-U20a,U20b-dihydrouridine synthase [Pseudomonas mendocina ymp]
          Length = 318

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/260 (23%), Positives = 115/260 (44%), Gaps = 30/260 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + +Q  G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++   + 
Sbjct: 65  MRVQFLGSDPQCLADNAAFACGLGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVR 124

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + + +   IPVT K R+G +D+  +VAL +  +++ + G + I +HAR  + +G  P  
Sbjct: 125 EVRRTVPAEIPVTAKMRLGFEDK--SVAL-DCARALAEGGASQIVVHARTKV-EGYKPPA 180

Query: 168 NRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +       ++ V  +++    P    G    L+D  +  +I   VD +M+GR       +
Sbjct: 181 H-------WEWVARVQEVVAVPVFANGEVWTLQDWRRCREI-SGVDDIMLGRGLVSRPGL 232

Query: 226 LTTVDEYFS--NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----ITR- 278
              +    +   P   S      + +DFWR+    +        ++ G+L+Q    +TR 
Sbjct: 233 ARQIAAVRAGEQPQEMSWEELQPLLQDFWRQARRKLAPR-----YAPGRLKQWLAMLTRT 287

Query: 279 --HMIGLFHGFPNSRRCRHI 296
               + LF      + C  I
Sbjct: 288 YPEAVTLFAEVRREQDCERI 307


>gi|321468855|gb|EFX79838.1| hypothetical protein DAPPUDRAFT_304378 [Daphnia pulex]
          Length = 663

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 67/272 (24%), Positives = 114/272 (41%), Gaps = 33/272 (12%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM +A+ ++ G ++   ++     E    +QI GA+   L + ++++E     DF    I
Sbjct: 347 EMAMAETLVGGGQQEWALVRKHKSEDLFGVQICGANPYILGKCSQLLEENTEIDF----I 402

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           +LN+GCP   V++   G+ LM     +   I  M + L IP TVK R+GV    P     
Sbjct: 403 DLNLGCPIDMVYQKGAGSGLMRRKGPLESSIKTMSQLLKIPFTVKMRMGVYTDHPFA--H 460

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            LV+  +  GV+ + +H R         ++ R     D+D +    K    + I  NG L
Sbjct: 461 QLVEKCRDWGVSMVTVHGRS--------REQRYTRLADWDYIGNCVKAADPMPIFGNGDL 512

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
                  +++      GVMI R A     + T + E     ++ S   + +  KDF    
Sbjct: 513 MSYEDYERVVDQSGAAGVMIARGALIKPWIFTEIKERRHWDISSSE--RFQYMKDF---- 566

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                +Y   H  S  +  + TR  +  +  F
Sbjct: 567 ----CNYGLEHWGSDSQGVERTRRFLLEWQSF 594


>gi|299066646|emb|CBJ37839.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum CMR15]
          Length = 319

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 103/237 (43%), Gaps = 20/237 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 50  GYTASGTPMVIQLLGSDPEWLARNAAQAATVSPHGIDLNFGCPAKVVNRHGGGAMLLSTP 109

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++A+   +   I VT K R+GV D   A+A      ++ + G   + +HAR   
Sbjct: 110 ELLHRIVSAVRATVPARIAVTAKMRLGVSDTSLAIA---CATALAEGGAASLVVHART-- 164

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 +D+   P   +D +  I      P +  G    ++D ++  + +   D VM+GR
Sbjct: 165 ------RDHGYRPPAHWDWIARIADAVRVPVVANGEVWTVDDWARC-RAVSGCDDVMVGR 217

Query: 218 AAYKNSAM-LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            A  +  + L    +    P     P+      D+ +K+ A +   A +H H   KL
Sbjct: 218 GAVSDPFLALRIRGQMAPQPSDAEWPLVLGCLADYLKKLRARI---AIQHEHGRVKL 271


>gi|77463371|ref|YP_352875.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides 2.4.1]
 gi|126462226|ref|YP_001043340.1| nifR3 family TIM-barrel protein [Rhodobacter sphaeroides ATCC
           17029]
 gi|77387789|gb|ABA78974.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides 2.4.1]
 gi|126103890|gb|ABN76568.1| putative TIM-barrel protein, nifR3 family [Rhodobacter sphaeroides
           ATCC 17029]
          Length = 326

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 82/161 (50%), Gaps = 11/161 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A +     L+ +EM+ +  ++    + +        E   A+Q+ G D
Sbjct: 19  MAGITDLPFRRLA-VRFGAGLVVSEMVASREVVCAGAEARARAEIGAAEGRTAVQLAGCD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     I A+  A+++P
Sbjct: 78  PHWMAEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALIEAVVGAVAVP 137

Query: 119 VTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHAR 156
           VT+K R+G D+ +   P +A R      + +GV  I IH R
Sbjct: 138 VTLKMRLGWDEGMLNAPEIARRA-----EAAGVAMITIHGR 173


>gi|51246763|ref|YP_066647.1| hypothetical protein DP2911 [Desulfotalea psychrophila LSv54]
 gi|50877800|emb|CAG37640.1| conserved hypothetical protein [Desulfotalea psychrophila LSv54]
          Length = 318

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/278 (20%), Positives = 110/278 (39%), Gaps = 44/278 (15%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K++L  +    P+  Q+   +    +  A  + + GY EIN N+GCP+  V +   G+ +
Sbjct: 53  KDVLPEANMVVPVIPQLLHNNAEDFIALAGRLAELGYKEINWNLGCPAPMVAKKKRGSGM 112

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR- 156
           + +PD++ + +  +   + + +++K R+G  +       + L+  + +  +  I IHAR 
Sbjct: 113 LAHPDLIVEFLEEVLPQIPVKLSIKTRLGYSN---TAQTKELLPRLDQFPLTEIIIHARL 169

Query: 157 -KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDG 212
            K + KG +  D        +    ++ +      I  NG    LE   +     P V+ 
Sbjct: 170 GKQMYKGTTDPDT-------FAECLQLSQHR----IAYNGDITTLEHFHELQTRFPQVEH 218

Query: 213 VMIGRAAYKNSAMLTTVD----------------------EYFSNPLTGSSPIKTRVDKD 250
            MIGR A  +  +   +                       E +   L+G S I  R+ K 
Sbjct: 219 WMIGRGALADPFLAERIKGIGKLTPTQELLRLEKFHAELFEIYREELSGPSHIVGRM-KM 277

Query: 251 FWRKISASMTDYAA--RHLHSGGKLQQITRHMIGLFHG 286
            W+ + AS        + +H     +Q    +  LF  
Sbjct: 278 LWQYLGASFPKQKKLLKKVHKAYNEEQFQESVSQLFQA 315


>gi|330875733|gb|EGH09882.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 344

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/171 (27%), Positives = 84/171 (49%), Gaps = 12/171 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +  G  P 
Sbjct: 124 SQVRRAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKV-DGYKPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
            + +      D+V      N +++      +ED  +  +I  + D +MIGR
Sbjct: 180 AHWEWIARIQDVVKVPVVANGEIWT-----VEDWRRCREICGARD-IMIGR 224


>gi|330951649|gb|EGH51909.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae Cit 7]
          Length = 321

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/252 (25%), Positives = 112/252 (44%), Gaps = 34/252 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPRPIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
           D  K P   ++ +  I++    P +  G    +ED  +  +I  + D +MIGR       
Sbjct: 174 DGYK-PPAHWEWIARIQEVVNVPVVANGEIWTVEDWRRCREICGARD-IMIGRGLVARPD 231

Query: 225 MLTTV------DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           +   +      DE          P+  RV   FW+   A MT      + + G+L+Q   
Sbjct: 232 LARQIAAAQKGDEVVPMTWNELQPM-LRV---FWQDCLAKMT-----LIQAPGRLKQ--- 279

Query: 279 HMIGLFHGFPNS 290
            ++ L   +P +
Sbjct: 280 WLVLLTKSYPEA 291


>gi|192360796|ref|YP_001981875.1| dihydrouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686961|gb|ACE84639.1| dihydrouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
          Length = 321

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 61/110 (55%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+    +   A+ +  +G   I+LN GCP+  V+    GACL+  PD V   I
Sbjct: 64  PVKVQLLGSKPEPMALNAQELVRYGAKAIDLNFGCPAKTVNSHEGGACLLRTPDRVYSII 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A+  A+  +IPV+ K R+G +D+    +     ++++ +G + + +HAR
Sbjct: 124 KAVRDAVPRAIPVSAKIRLGFEDR---TSYMENAQAVEAAGADELTVHAR 170


>gi|163750237|ref|ZP_02157479.1| NifR3/Smm1 family protein [Shewanella benthica KT99]
 gi|161330093|gb|EDQ01077.1| NifR3/Smm1 family protein [Shewanella benthica KT99]
          Length = 303

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 83/175 (47%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G     + E A    + G   ++LN GCP+  V+  + GA L+  P+ +   +
Sbjct: 57  PVRLQLLGQHPQWMAENALRAVELGSLGVDLNFGCPAPMVNRNNGGAALLKEPETIYRIV 116

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   +P T K R+G DD+   V    + ++I+ +G   + +HAR         K
Sbjct: 117 KAVREAVPEPLPATAKIRLGWDDKSRCV---EIAQAIEAAGATELTVHART--------K 165

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
           +    P   ++ + +IK+    P +  G     ED  +  ++    D VMIGR A
Sbjct: 166 EEGYKPPAHWEYIRQIKQAISIPVIANGEVWSREDYLECQQV-SQCDDVMIGRGA 219


>gi|150865372|ref|XP_001384560.2| hypothetical protein PICST_72127 [Scheffersomyces stipitis CBS
           6054]
 gi|149386628|gb|ABN66531.2| predicted protein [Scheffersomyces stipitis CBS 6054]
          Length = 390

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/198 (27%), Positives = 98/198 (49%), Gaps = 27/198 (13%)

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           L LQ+G +D    V+AA K+++D   + I+LN GCP +       GA L+  P+++   +
Sbjct: 82  LILQLGSSDPDLAVQAAEKVIKDV--DGIDLNCGCPKSFSTHSGMGAALLSTPELLCSVL 139

Query: 109 AAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + + IP    + C+I + D + A   R+LV  I ++G+  + IH R+  ++     
Sbjct: 140 RDLVQKVGIPNQKPISCKIRLLDDLEAT--RSLVDQICETGIANLTIHCRQRAMR----- 192

Query: 167 DNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVD-GVMIGRAAY 220
            NR+ P   Y  +I+  ++ +   + I  NG L+   D+     +  + D G MI  AA 
Sbjct: 193 -NRQEPIWHYLSEIIPRVQSKGISVVI--NGNLQSKADLCSLQDLFNNKDIGGMIAEAAE 249

Query: 221 KNSAMLTTVDEYFSNPLT 238
            N ++ +       +PLT
Sbjct: 250 ANPSVFS------DSPLT 261


>gi|332993814|gb|AEF03869.1| NifR3/Smm1 family protein [Alteromonas sp. SN2]
          Length = 312

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    D G   ++LN GCP+  V++   GA L+     + D +
Sbjct: 64  PVRVQLLGQHPQWLAENAHTAVDLGSPGVDLNFGCPAKTVNKSKGGAVLLKETQALYDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+  A+  S PV+ K R+G +D+  ++A+ N + +I ++G + + +HAR         K
Sbjct: 124 KAVRDAVPASQPVSAKIRLGFEDK--SLAVENAI-AITEAGASELVVHART--------K 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAA 219
                P   +D + +I K+N D+ +  NG +  E+  +  +   +   +M+GR A
Sbjct: 173 TEGYKPPAYWDWIAKI-KQNTDIPLVANGEIWNEEDGKRCQEQSACTNLMVGRGA 226


>gi|331006519|ref|ZP_08329818.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC1989]
 gi|330419687|gb|EGG94054.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC1989]
          Length = 333

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 108/237 (45%), Gaps = 21/237 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     +   A      G N I+LN GCP+  V++   GACL+  P  + D I
Sbjct: 64  PVRIQLLGGKPEPIALNAVKAVSIGANAIDLNFGCPAKTVNKSDGGACLLRTPHRLYDII 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+   IPVT K R+G +D+  +  L N + +  ++G   I +HAR       S  
Sbjct: 124 KATRQAVPAHIPVTAKMRLGFEDR--SNYLENALAAY-EAGATEITVHAR-------SKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSA 224
           D  + P   +D + +IK+   D+ +  NG +  +   +  K +   D  M+GR       
Sbjct: 174 DGYRPPAY-WDSLADIKQAI-DIPVIANGEIWTVDDFIRCKEVSQCDDFMLGRGLLSCPD 231

Query: 225 MLTTVDEYFSNPLTGSSPIK-TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           +   +    +   T   P++ + +     R   A+   Y+ RH+  G +L+Q   ++
Sbjct: 232 LALQIKAREAG--TDYQPMEWSAICHMLQRFFDATTEQYSPRHV--GNRLKQWLNYL 284


>gi|212715521|ref|ZP_03323649.1| hypothetical protein BIFCAT_00419 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660888|gb|EEB21463.1| hypothetical protein BIFCAT_00419 [Bifidobacterium catenulatum DSM
           16992]
          Length = 409

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 101/242 (41%), Gaps = 19/242 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E   +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCHFAPSENIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKA 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I     +C A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKMDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +         +   ++ G   + +HAR          D  +I  L
Sbjct: 169 ANVPVTAKIRVGIDHEHETFLEAGHIA--QEEGCKAVTLHARTTAEYYGGHSDWSRIGEL 226

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
                     E  D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 227 ---------VEALDIPVFGNGDIWGANDALAMVAETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FS 234
           F+
Sbjct: 278 FA 279


>gi|212531921|ref|XP_002146117.1| dihydrouridine synthase family protein, putative [Penicillium
           marneffei ATCC 18224]
 gi|210071481|gb|EEA25570.1| dihydrouridine synthase family protein, putative [Penicillium
           marneffei ATCC 18224]
          Length = 526

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 78/171 (45%), Gaps = 14/171 (8%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D    +EAA++   +  + ++LN+GCP     +G +GA L  + D++ +
Sbjct: 103 DRPLFVQFCANDPDDFLEAARLAAPYC-DAVDLNLGCPQGIARKGHYGAFLQEDWDLIYN 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  +   L IPVT K RI    Q          K I  +G + I +H R+   KG    
Sbjct: 162 LINKLHTELPIPVTAKFRI----QETKEKTLEYAKMILSAGASIITVHGRRREQKG---- 213

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVM 214
            N  + +  Y + Y      P+  I  NG   G  D+ + L+     DGVM
Sbjct: 214 HNTGVADWSY-VRYLRDNLPPETVIFANGNILGQADIERCLEAT-GADGVM 262


>gi|57505594|ref|ZP_00371521.1| NifR3 family protein [Campylobacter upsaliensis RM3195]
 gi|57016141|gb|EAL52928.1| NifR3 family protein [Campylobacter upsaliensis RM3195]
          Length = 305

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 113/239 (47%), Gaps = 25/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R   +    +  + +EMI ++A++   +K++  L  +  E P  +QI G D
Sbjct: 14  MAGFTDPPFRSVVKQFGADVTI-SEMISSNALVYESQKSLKMLEKTPFETPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A  I+ +  + + I+ N GCP  +V +   G+ L+ + D+    +  +      
Sbjct: 73  EDILKKAVLILNELDFIDGIDFNCGCPVNKVVKQCAGSALLEDLDLFKRLVGVIKTHNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNL 174
             T VK R+G +D+ P      + K  ++ GV+ I IH   RK +  G          + 
Sbjct: 133 QFTSVKFRLGFNDKYP----EKMAKICEELGVDFISIHGRTRKQLYSG----------SA 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           DY+ + + KK      I  NG +  ++  + LKI  + +G+MIGRA+  N  +   + E
Sbjct: 179 DYNSIAKAKKSVKIPVIA-NGDINAQNAKKVLKI-TACEGLMIGRASVGNPWIFYEIKE 235


>gi|323498303|ref|ZP_08103305.1| tRNA-dihydrouridine synthase C [Vibrio sinaloensis DSM 21326]
 gi|323316731|gb|EGA69740.1| tRNA-dihydrouridine synthase C [Vibrio sinaloensis DSM 21326]
          Length = 317

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 85/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    D G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHVQLLGQDPKWMAENAIRAADLGAKGIDLNFGCPAKLVNKSKGGAALLQHPELIHQVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +   A+  +IPVT K R+G ++         +V +I+ +G N + +HAR       +  
Sbjct: 124 KSCRDAVPSNIPVTAKIRLGWENPDDCF---EIVDAIELAGANELTVHAR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAY 220
              K   + ++ + +I++      I  NG + +    QA      VD +M+ R A+
Sbjct: 174 GGYKASEIKWEYIGQIRERFSIPLIA-NGEIWNHQDGQACIETTGVDSLMVCRGAF 228


>gi|226947931|ref|YP_002803022.1| dihydrouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
 gi|226843334|gb|ACO86000.1| dihydrouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
          Length = 312

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/235 (22%), Positives = 99/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKI 171
           K   + +++K RIG D          L+K   K  +  + IH R +    G  P      
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPRTQKDFYGNEP------ 174

Query: 172 PNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              D D+  +      NP  + G    +   ++ +K  P V  +M+GR    N  ++   
Sbjct: 175 ---DLDVFKDALSLSRNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLI--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|110835023|ref|YP_693882.1| dihydrouridine synthase (Dus) superfamily protein [Alcanivorax
           borkumensis SK2]
 gi|110648134|emb|CAL17610.1| Dihydrouridine synthase protein family, putative [Alcanivorax
           borkumensis SK2]
          Length = 314

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/110 (33%), Positives = 63/110 (57%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G+D + + + A+   + G   I+LN GCP+  V+    GA L+  PD+V    
Sbjct: 67  PVHLQLLGSDPACMADNAERAVELGAPAIDLNFGCPAKTVNRHRGGAVLLDEPDVVHAVT 126

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           AA+ +A+   +PV+VK R+G +D   A AL N  +++  +G   + +H R
Sbjct: 127 AAVRQAVPSQVPVSVKMRLGNEDD--ARALDN-ARAVVDAGAAWLTVHGR 173


>gi|312138334|ref|YP_004005670.1| tRNA-dihydrouridine synthase [Rhodococcus equi 103S]
 gi|325674749|ref|ZP_08154436.1| dihydrouridine synthase [Rhodococcus equi ATCC 33707]
 gi|311887673|emb|CBH46985.1| tRNA-dihydrouridine synthase [Rhodococcus equi 103S]
 gi|325554335|gb|EGD24010.1| dihydrouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 380

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 69/296 (23%), Positives = 121/296 (40%), Gaps = 31/296 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK-I 68
             R  + + L   EM+ A A++       ++  F   E P +LQ+   D     +AAK I
Sbjct: 37  LERAGSTSGLYVCEMVTARALVERHPVTMHMTTFGPTETPRSLQLYTVDPEITYQAAKMI 96

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
           V++   + I++N GCP  +V     G+ L     + G  +AA  KA     IPVTVK R+
Sbjct: 97  VDENLADHIDMNFGCPVPKVTRKGGGSALPYKRRLFGQIVAAAVKATEGTDIPVTVKMRV 156

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+D +       +  +     G   + +H R A          R     D+  +  +K+ 
Sbjct: 157 GIDAE--HHTHLDAGRIAAAEGAAAVALHGRTAA--------QRYSGQADWSEIARLKEH 206

Query: 186 NPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS-P 242
             D+ +  NG +     A K++     DGV++GR       +        S  L G+  P
Sbjct: 207 VTDVPVLGNGDIFAAEDAEKMMSETGCDGVVVGRGCLGRPWLFAE----LSAALNGTEMP 262

Query: 243 IKTRVDKDFWRKISASMTDYA---ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           +   +      +++A M  +    A H      ++++ +H+     GFP     R+
Sbjct: 263 VPPNLG-----EVAAIMMRHGRLLADHHGEDKGMREMRKHIAWYMRGFPAGSELRN 313


>gi|290991278|ref|XP_002678262.1| predicted protein [Naegleria gruberi]
 gi|284091874|gb|EFC45518.1| predicted protein [Naegleria gruberi]
          Length = 292

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 95/234 (40%), Gaps = 18/234 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  A+    + L YT M      ++ +  +K    F   E P+  Q    D
Sbjct: 19  MVDQSELAFRLLAQN-HGSTLAYTPMFHGRIFVQDETYQKTHFQFLESEGPVFAQFCAND 77

Query: 59  ISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            +  VE   +  +    +I   +LN+GCP     +G +G+ LM + D++   I    K L
Sbjct: 78  PNIFVECGWLAWELSNQKIAAVDLNLGCPQRIAKKGRYGSYLMEDIDLICSMIEKAHKEL 137

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D    A      V  I ++G   + +H R    +G +          D
Sbjct: 138 PVPVTAKIRIFED----AEHTLKYVDRILEAGAQVLCVHGRTRDQRGHNQN------YAD 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           + ++  I++  P + +  NG +      +  L     D VM       N A+  
Sbjct: 188 WKMIKLIREHVPHIPVIANGNIRMYQDVIDCLEFTGADAVMSADPLLCNPALFN 241


>gi|152987650|ref|YP_001347379.1| hypothetical protein PSPA7_2003 [Pseudomonas aeruginosa PA7]
 gi|150962808|gb|ABR84833.1| conserved hypothetical protein [Pseudomonas aeruginosa PA7]
          Length = 319

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/256 (23%), Positives = 108/256 (42%), Gaps = 20/256 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +
Sbjct: 64  PMRVQLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+    PVT K R+G D   P  AL +  +++   G   + +HAR  +       
Sbjct: 124 AAVRRAVPGETPVTSKMRLGYDS--PDGAL-DCARALADGGSVHVVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
           D  K P   ++ V  +  E   + +  NG +  +   L+   +  V+ +M+GR       
Sbjct: 174 DGYK-PPAHWEWVARV-AEAVRVPVFANGEVWTLDDYLRCREISGVEDIMLGRGLVSRPG 231

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVD--KDFWRKISASMTD-YAARHLHSG-GKLQQITRHM 280
           +   +  +         P    +   +DFW +    +   YA   L    G L +     
Sbjct: 232 LARQIAAWRDGGEIREMPWSELLPLLRDFWLQARRKLAPRYAPGRLKQWLGMLTRTYPEA 291

Query: 281 IGLFHGFPNSRRCRHI 296
           + LF        C  I
Sbjct: 292 VELFAQIRRESDCETI 307


>gi|319950652|ref|ZP_08024556.1| TIM-barrel protein, nifR3 family [Dietzia cinnamea P4]
 gi|319435694|gb|EFV90910.1| TIM-barrel protein, nifR3 family [Dietzia cinnamea P4]
          Length = 392

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/288 (22%), Positives = 116/288 (40%), Gaps = 20/288 (6%)

Query: 19  NALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYN 75
           + L   EM+ A A++       ++  F+  E P +LQ+   D      AA+ IV++   +
Sbjct: 52  SGLYVCEMVTARALVERQPATLHMATFAPDESPRSLQLYTVDAEYTYAAARMIVDENLAD 111

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIP 132
            I++N GCP  +V     G+ +     +    +AA  +A     IPVTVK R+G+DD+  
Sbjct: 112 HIDINFGCPVPKVTRRGGGSAIPYKRRLFRSIVAAAVRATEGTDIPVTVKMRVGIDDE-- 169

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                +  +   + G   + +HAR A  +     D  +I  L      E      D+ + 
Sbjct: 170 HHTHLDAGRIAVEEGAKAVALHARTAAQRYSGEADWSQISRL-----VEHVGAVSDVPVL 224

Query: 193 LNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG +     A+++       GV+IGR       + + +    +     + P    V + 
Sbjct: 225 GNGDIFSAQDAVRMREQTGCAGVVIGRGCLGRPWLFSELAARLAGREAPAPPTLGEVARI 284

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +R       +  A H      ++ I +H+     GFP     R  L+
Sbjct: 285 MYRH-----GELLAEHHGEDKGMRDIRKHVAWYLRGFPAGSEKRVALS 327


>gi|317152055|ref|YP_004120103.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
 gi|316942306|gb|ADU61357.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
          Length = 352

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/149 (30%), Positives = 78/149 (52%), Gaps = 7/149 (4%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGADISKLVEAAKIVEDFGYNEI 77
           L +TEM  A A+   +++    F  ++  L     QI GAD ++L  AA+ VED G+  +
Sbjct: 56  LAFTEMCSARAVPTENRRVSAVFRWRDPELDRLVCQIAGADPAELAVAARRVEDEGFFGV 115

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-PAVAL 136
           ++N+GC  + + +   GA L+ + D     + A+  A++IPV VK R G    I PA+  
Sbjct: 116 DINMGCSVSGIVKKGAGAALLRDHDAALAALDAVRSAVAIPVFVKFRTGWSADIAPAI-- 173

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            +L + ++ +G + +  H R A  K   P
Sbjct: 174 -SLARRLESAGADCLVFHPRVAPDKRTRP 201


>gi|88857879|ref|ZP_01132521.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas tunicata D2]
 gi|88819496|gb|EAR29309.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas tunicata D2]
          Length = 311

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 54/186 (29%), Positives = 87/186 (46%), Gaps = 18/186 (9%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N  G +    P+ +Q+ G D   L E A    + G + ++LN GCP+  V +   GA L+
Sbjct: 47  NQAGLTRSGTPVRIQLLGQDPDWLSENAVRAVELGSHGVDLNFGCPAKAVMKNKGGAVLL 106

Query: 99  LNPDIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             P+++   + A+  A+     VT K R+G DD   +  + + V S K S +    IHAR
Sbjct: 107 KEPEVIYQIVKAVRDAVPAHHEVTAKVRLGFDDDSLSQEIFDAVVSAKASSIA---IHAR 163

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGV 213
                  + KD  + P   ++ +  +K  + +L    NG    +ED +   KI    D V
Sbjct: 164 -------TKKDGYRPPAY-WEKIKPLKNSS-NLKTIANGEVWSVEDYT-LCKIRSGCDDV 213

Query: 214 MIGRAA 219
           M+GR A
Sbjct: 214 MLGRGA 219


>gi|229506911|ref|ZP_04396419.1| tRNA dihydrouridine synthase B [Vibrio cholerae BX 330286]
 gi|229356016|gb|EEO20935.1| tRNA dihydrouridine synthase B [Vibrio cholerae BX 330286]
          Length = 322

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 183 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 241

Query: 234 SNPLT 238
            +  T
Sbjct: 242 EHGTT 246


>gi|309379684|emb|CBX21673.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 333

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/190 (24%), Positives = 88/190 (46%), Gaps = 16/190 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P ++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K
Sbjct: 136 KTLRERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------K 184

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSA 224
                P   ++ + +I ++  ++ +  NG +  +     +K     + VM+GR A     
Sbjct: 185 AEAYEPPAHWEWIKKI-RDAVNIPVTANGDVFSLQDYIGIKTASGCNSVMLGRGAVIRPD 243

Query: 225 MLTTVDEYFS 234
           +   + +Y S
Sbjct: 244 LARQIKQYES 253


>gi|268598864|ref|ZP_06133031.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae MS11]
 gi|268582995|gb|EEZ47671.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae MS11]
          Length = 196

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 63/120 (52%), Gaps = 6/120 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 76  PCTVQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIV 135

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P+
Sbjct: 136 KTLRGRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHARTKA-EGYEPR 191


>gi|305680317|ref|ZP_07403125.1| TIM-barrel protein, nifR3 family [Corynebacterium matruchotii ATCC
           14266]
 gi|305659848|gb|EFM49347.1| TIM-barrel protein, nifR3 family [Corynebacterium matruchotii ATCC
           14266]
          Length = 384

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 95/217 (43%), Gaps = 20/217 (9%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            A+  T + L   EMI A A++ G++K  ++  F   E P +LQ    D     +AA++V
Sbjct: 39  LAKTGTVSGLYVCEMITARALVEGNEKTRHMTTFGPDEHPRSLQFYTTDPEYTYKAARMV 98

Query: 70  EDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKALSIPVTVKCRI 125
            D    + I++N GCP  +V     G+ L     + G+            +IP+TVK RI
Sbjct: 99  ADNNLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAAVKAVAGTNIPITVKFRI 158

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD        +  +     G   + +HAR A          R     D+  +  +K+ 
Sbjct: 159 GIDDD--HHTHLDAGRIAAAEGAAAVALHARTAA--------QRYSGTADWSQIAALKEH 208

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRA 218
             D  I +  NG +   + A K++     DGV++GR 
Sbjct: 209 LADTGIPVLGNGDIFQATDAQKMMTETGCDGVVVGRG 245


>gi|330959087|gb|EGH59347.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 317

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 87/173 (50%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVTVK R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPKDIPVTVKMRLGYENTDLAL---DCARALADGGAAQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    +ED  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVEDWRRCREICGARD-IMIGR 224


>gi|168178053|ref|ZP_02612717.1| dihydrouridine synthase family protein [Clostridium botulinum NCTC
           2916]
 gi|182671610|gb|EDT83584.1| dihydrouridine synthase family protein [Clostridium botulinum NCTC
           2916]
          Length = 319

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/235 (22%), Positives = 99/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKI 171
           K   + +++K RIG D          L+K   K  +  + IH R +    G  P      
Sbjct: 124 KIDDMKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPRTQKDFYGNEP------ 174

Query: 172 PNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              D D+  +      NP  + G    +   ++ +K  P V  +M+GR    N  ++   
Sbjct: 175 ---DLDVFKDALSLSRNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLI--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|70996530|ref|XP_753020.1| dihydrouridine synthase family protein [Aspergillus fumigatus
           Af293]
 gi|66850655|gb|EAL90982.1| dihydrouridine synthase family protein, putative [Aspergillus
           fumigatus Af293]
 gi|159131754|gb|EDP56867.1| dihydrouridine synthase family protein, putative [Aspergillus
           fumigatus A1163]
          Length = 541

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 89/210 (42%), Gaps = 26/210 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D    +EAA+ V  +  + ++LN+GCP     +G +GA L  + D++  
Sbjct: 124 DRPLIVQFCANDPDDFLEAARHVAPYC-DAVDLNLGCPQGIARKGHYGAFLQEDWDLIYK 182

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  + K L IPVT K RI    Q          K I  +G + I +H R    KG    
Sbjct: 183 LINRLHKELPIPVTAKFRI----QESKEKTLEYAKMILSAGASIITLHGRTREQKG---- 234

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNS 223
            N  + +  Y I Y      P+  I  NG     +D+ + L+     DGVM       + 
Sbjct: 235 HNTGLADWSY-IRYLRDNLPPETVIFANGNNLNHDDLERCLEAT-GADGVMSAEGNLSDP 292

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           A+ +        P  GS        +++WR
Sbjct: 293 AIFS------KPPPVGSE------GREYWR 310


>gi|229520989|ref|ZP_04410410.1| tRNA dihydrouridine synthase B [Vibrio cholerae TM 11079-80]
 gi|229341874|gb|EEO06875.1| tRNA dihydrouridine synthase B [Vibrio cholerae TM 11079-80]
          Length = 322

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG +++  +A  +L     D +MIGR A     +   +  + 
Sbjct: 183 YDSIKAVKAAVSIPVIA-NGDIDNPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 241

Query: 234 SNPLT 238
            +  T
Sbjct: 242 EHGTT 246


>gi|146312384|ref|YP_001177458.1| tRNA-dihydrouridine synthase C [Enterobacter sp. 638]
 gi|145319260|gb|ABP61407.1| tRNA-U20a,U20b-dihydrouridine synthase [Enterobacter sp. 638]
          Length = 310

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 83/172 (48%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPSHLPVTVKVRLGWDSGDRQF---EIADAVQQAGATELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           K   +++  + +I ++  ++ +  NG + D   A   L +   D VMIGR A
Sbjct: 177 KAERINWQAIRDI-RQRLNIPVIANGEIWDYESAQACLHATGCDSVMIGRGA 227


>gi|88705806|ref|ZP_01103515.1| tRNA-dihydrouridine synthase C [Congregibacter litoralis KT71]
 gi|88699877|gb|EAQ96987.1| tRNA-dihydrouridine synthase C [Congregibacter litoralis KT71]
          Length = 328

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 62/117 (52%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G ++   P+ LQI G D S + E A    + G   ++LN GCP+  V+    G+ ++  P
Sbjct: 63  GCTSSGVPVYLQILGGDPSVVAENASRAAELGAPGVDLNFGCPAKTVNRSDGGSIILREP 122

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           + V   +AA  +AL  S+P++VK R+G D    +    ++V  I  +  + + IHAR
Sbjct: 123 ERVHRIVAATRQALPPSVPLSVKIRLGFDS---SDRFLDIVSGIDAARPSELVIHAR 176


>gi|260770653|ref|ZP_05879584.1| tRNA-dihydrouridine synthase B [Vibrio furnissii CIP 102972]
 gi|260614379|gb|EEX39567.1| tRNA-dihydrouridine synthase B [Vibrio furnissii CIP 102972]
 gi|315178395|gb|ADT85309.1| NifR3/Smm1 family protein [Vibrio furnissii NCTC 11218]
          Length = 287

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 107/222 (48%), Gaps = 21/222 (9%)

Query: 24  TEMIVAD-AILRGDK-KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ ++ A+ + DK +N +    +    ++QI G+D   + +AA+   + G   I++N+
Sbjct: 4   SEMMSSNPALWKTDKSRNRMVHEGESGIRSVQIAGSDPQLMADAAQFSVENGAQIIDINM 63

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLV 140
           GCP+ +V++   G+ L+  P+++ D + A+  A+++PVT+K R G D D    V +  L 
Sbjct: 64  GCPAKKVNKKLAGSALLRYPNVIEDILKAVVNAVNVPVTLKTRTGWDTDNKNCVQIAKLA 123

Query: 141 KSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +     G+  + +H   R  + KG            +YD +  +K       I  NG ++
Sbjct: 124 ED---CGIQALALHGRTRTCMYKG----------EAEYDSIKAVKAAIQIPVIA-NGDID 169

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +A  +L     D +MIGR A     +   +  Y  N  T
Sbjct: 170 SPEKAKHVLEYTGADALMIGRPAQGRPWIFQEIQHYLENGTT 211


>gi|121586356|ref|ZP_01676145.1| NifR3/Smm1 family protein [Vibrio cholerae 2740-80]
 gi|147675018|ref|YP_001218564.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|153820017|ref|ZP_01972684.1| NifR3/Smm1 family protein [Vibrio cholerae NCTC 8457]
 gi|227080505|ref|YP_002809056.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|298500925|ref|ZP_07010727.1| NifR3/Smm1 family protein [Vibrio cholerae MAK 757]
 gi|121549476|gb|EAX59504.1| NifR3/Smm1 family protein [Vibrio cholerae 2740-80]
 gi|126509439|gb|EAZ72033.1| NifR3/Smm1 family protein [Vibrio cholerae NCTC 8457]
 gi|146316901|gb|ABQ21440.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|227008393|gb|ACP04605.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|227012150|gb|ACP08360.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|297540429|gb|EFH76488.1| NifR3/Smm1 family protein [Vibrio cholerae MAK 757]
          Length = 331

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 145 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|50310669|ref|XP_455356.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644492|emb|CAG98064.1| KLLA0F06094p [Kluyveromyces lactis]
          Length = 359

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/190 (29%), Positives = 89/190 (46%), Gaps = 26/190 (13%)

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPD----I 103
           L  QIG +  S  VEAA K++ED     I++N GCP    +H G  GA L+  PD    I
Sbjct: 85  LIFQIGTSTPSLAVEAALKVIEDVA--GIDVNAGCPKHFSIHSG-MGAALLQTPDKLCSI 141

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + + +  + K    P++VK RI  D++        LV+ +  +G+  + +H R       
Sbjct: 142 LIELVEKVGKIYGKPISVKIRILKDEE----DTLTLVEKLCATGITNLTVHCRT------ 191

Query: 164 SPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDGVMIGR 217
           +P  NR+ P   Y   +YEI + N    I +NG + D     ++     LP   G M+  
Sbjct: 192 TPMRNRESPIRAYIPKIYEICERNKVSLI-MNGAIRDKEHFEQLRSDLNLPKTIGGMMAD 250

Query: 218 AAYKNSAMLT 227
            A +N  + +
Sbjct: 251 CAERNPTVFS 260


>gi|190344922|gb|EDK36711.2| hypothetical protein PGUG_00809 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 362

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 84/185 (45%), Gaps = 16/185 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVG 105
           L  QIG A+    VEAAK+V     + I+LN GCP         GA L+ NPD    I+ 
Sbjct: 79  LIFQIGSANPELAVEAAKVVAR-DVDGIDLNCGCPKNFSTHSGMGAELLTNPDVLVSILK 137

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +  +     IP++VK R+ +D   P  +++ L+  I K+GV  + +H R   ++   P
Sbjct: 138 NLVEKIGNVYRIPISVKIRL-LDATDPEPSIK-LIDRICKTGVANLTLHCRTKPMRNRQP 195

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---GVMIGRAAYKN 222
                +P      + E    N   FI LNG + +  +  ++        G MI  +A  N
Sbjct: 196 PIRTFLPQ-----IIETVHSNNVSFI-LNGAIRNRQEFYELQARYGKQIGAMIAESAEAN 249

Query: 223 SAMLT 227
             + +
Sbjct: 250 PTVFS 254


>gi|119589547|gb|EAW69141.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
 gi|119589548|gb|EAW69142.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
          Length = 315

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/282 (23%), Positives = 117/282 (41%), Gaps = 42/282 (14%)

Query: 26  MIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEIN 78
           M V   +L+G      +L     E    +Q+ GA    + + A+++      DF    ++
Sbjct: 1   MAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----VD 56

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++       
Sbjct: 57  INVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERVNLA--HR 114

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG-- 195
           L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG  
Sbjct: 115 LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGDI 165

Query: 196 -GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
              ED ++A++    V G+MI R A     + T + E     ++ S     R+D      
Sbjct: 166 LSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD------ 213

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 214 ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 251


>gi|15640319|ref|NP_229946.1| NifR3/Smm1 family protein [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121727027|ref|ZP_01680218.1| NifR3/Smm1 family protein [Vibrio cholerae V52]
 gi|153801529|ref|ZP_01956115.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-3]
 gi|153822836|ref|ZP_01975503.1| NifR3/Smm1 family protein [Vibrio cholerae B33]
 gi|254286235|ref|ZP_04961194.1| NifR3/Smm1 family protein [Vibrio cholerae AM-19226]
 gi|254851428|ref|ZP_05240778.1| NifR3/Smm1 family protein [Vibrio cholerae MO10]
 gi|297581755|ref|ZP_06943677.1| NifR3/Smm1 family protein [Vibrio cholerae RC385]
 gi|9654702|gb|AAF93465.1| NifR3/Smm1 family protein [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121630538|gb|EAX62928.1| NifR3/Smm1 family protein [Vibrio cholerae V52]
 gi|124122934|gb|EAY41677.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-3]
 gi|126519654|gb|EAZ76877.1| NifR3/Smm1 family protein [Vibrio cholerae B33]
 gi|150423650|gb|EDN15592.1| NifR3/Smm1 family protein [Vibrio cholerae AM-19226]
 gi|254847133|gb|EET25547.1| NifR3/Smm1 family protein [Vibrio cholerae MO10]
 gi|297534162|gb|EFH73001.1| NifR3/Smm1 family protein [Vibrio cholerae RC385]
          Length = 331

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 145 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|302848343|ref|XP_002955704.1| hypothetical protein VOLCADRAFT_106923 [Volvox carteri f.
           nagariensis]
 gi|300259113|gb|EFJ43344.1| hypothetical protein VOLCADRAFT_106923 [Volvox carteri f.
           nagariensis]
          Length = 396

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 107/236 (45%), Gaps = 33/236 (13%)

Query: 20  ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
           +L  +EM++A A+L  +++ +    ++  E   ++Q+ G    ++ +A + +V +   + 
Sbjct: 19  SLSTSEMVIASALLLRNRRTLKLASYAPDESLRSVQLYGVRPDQVEQAVRMLVSERNVHH 78

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAV 134
           ++LN GCP  ++     G+ L L P +    +AA  +     +PVTVK R+G+  ++P  
Sbjct: 79  VDLNFGCPVRKITARGGGSALPLRPMLFARLVAAAVRGAGGQVPVTVKLRVGLTSELPT- 137

Query: 135 ALRNLVKSI-------------KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
              +L  S+             +  G   + +HAR A        D      + +  + +
Sbjct: 138 ---HLQASVGWCGDMVDAGRIAEAEGAAALTLHARTA--------DQLYSAPVMWHAIRD 186

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSN 235
           + K      IG NG + + S A++++      GVM+GRAA     +   V E   +
Sbjct: 187 LVKTVQIPVIG-NGDVYEASDAVQLMEQTGCAGVMVGRAALGRPWVFREVAEALHD 241


>gi|229524749|ref|ZP_04414154.1| tRNA dihydrouridine synthase B [Vibrio cholerae bv. albensis VL426]
 gi|229338330|gb|EEO03347.1| tRNA dihydrouridine synthase B [Vibrio cholerae bv. albensis VL426]
          Length = 322

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 183 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 241

Query: 234 SNPLT 238
            +  T
Sbjct: 242 EHGTT 246


>gi|91789280|ref|YP_550232.1| dihydrouridine synthase [Polaromonas sp. JS666]
 gi|91698505|gb|ABE45334.1| tRNA-U20a,U20b-dihydrouridine synthase [Polaromonas sp. JS666]
          Length = 344

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 64/259 (24%), Positives = 112/259 (43%), Gaps = 30/259 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D + + E A  +   G   I+LN GCP+A V+    GA L+  P+ +   +
Sbjct: 70  PVRAQLLGSDPACMAENAARLATLGPAGIDLNFGCPAAVVNRHGGGASLLKEPETLLAIV 129

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +A+ +A+   +PV+ K R+G +D   AV       +I + G   + +HAR         K
Sbjct: 130 SAVRRAVPAGMPVSAKMRLGYNDDSRAV---ECALAIAEGGAGELVVHART--------K 178

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                P   ++ + +I+     + +  NG +  +  A +   +     +MIGR A  +  
Sbjct: 179 AQAYKPPAYWERIADIRAAV-QIPVVANGEIWTVDDARRCREASGCSMLMIGRGAVADPG 237

Query: 225 MLTTVDEYFSNPLT-GSSPIKTRVD-----KDFWRKISASMTDYAARHLHSGGKLQQITR 278
           +   +    S+P   G  P  T  +      DFW  + A + D  AR     G+L+Q   
Sbjct: 238 LGLAIKAAMSHPAAGGQEPGITWAELVPLLADFWHVVCARL-DARARP----GRLKQWLN 292

Query: 279 HMIGLFHGFPNSRRCRHIL 297
               L   FP +     +L
Sbjct: 293 F---LRRRFPQAEAAYQVL 308


>gi|153827384|ref|ZP_01980051.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-2]
 gi|149738714|gb|EDM53056.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-2]
          Length = 331

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 145 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|52425959|ref|YP_089096.1| hypothetical protein MS1904 [Mannheimia succiniciproducens MBEL55E]
 gi|52308011|gb|AAU38511.1| unknown [Mannheimia succiniciproducens MBEL55E]
          Length = 311

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 86/182 (47%), Gaps = 15/182 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +T   P+ +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  P
Sbjct: 57  GKTTTGTPIRVQLLGQFPEWLAENAVRAVELGSFGVDLNCGCPSKTVNGSHGGASLLKQP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     A+  A+   +PV+VK R+G D    A    ++  ++++ G N I IH R   
Sbjct: 117 ELIYQATRAIRTAVPKHLPVSVKVRLGWDSADFAF---DIADAVQQGGANEITIHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               +  D  K   ++++ + E++++   P +  G     +D    L +    D +MIGR
Sbjct: 171 ----TKADGYKAERINWEKIGELRRKLAIPVIANGEIWNWQDGQNCLAVTGCED-LMIGR 225

Query: 218 AA 219
            A
Sbjct: 226 GA 227


>gi|229509284|ref|ZP_04398767.1| tRNA dihydrouridine synthase B [Vibrio cholerae B33]
 gi|229512700|ref|ZP_04402168.1| tRNA dihydrouridine synthase B [Vibrio cholerae TMA 21]
 gi|229516228|ref|ZP_04405676.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC9]
 gi|229527213|ref|ZP_04416606.1| tRNA dihydrouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229606424|ref|YP_002877072.1| tRNA dihydrouridine synthase B [Vibrio cholerae MJ-1236]
 gi|38605062|sp|Q9KV66|DUSB_VIBCH RecName: Full=tRNA-dihydrouridine synthase B
 gi|229335221|gb|EEO00705.1| tRNA dihydrouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229346654|gb|EEO11624.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC9]
 gi|229350210|gb|EEO15162.1| tRNA dihydrouridine synthase B [Vibrio cholerae TMA 21]
 gi|229353599|gb|EEO18536.1| tRNA dihydrouridine synthase B [Vibrio cholerae B33]
 gi|229369079|gb|ACQ59502.1| tRNA dihydrouridine synthase B [Vibrio cholerae MJ-1236]
          Length = 322

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 111/245 (45%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 136 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D +MIGR A     +   +  + 
Sbjct: 183 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFL 241

Query: 234 SNPLT 238
            +  T
Sbjct: 242 EHGTT 246


>gi|317027955|ref|XP_001400331.2| tRNA dihydrouridine synthase (Smm1) [Aspergillus niger CBS 513.88]
          Length = 454

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 85/190 (44%), Gaps = 21/190 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 113 LIYQIGTATPEIAVQAAKLVAG-DVAGIDVNSGCPKPFSTSGGMGAALLKTPDKLVAILE 171

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +  P    ++VK RI  D +      R LV  + K+G+ G+ +H R   ++   P
Sbjct: 172 ALVKEVGTPFQIGISVKIRILKDPE----ETRALVSRLVKTGITGLTVHCRTPPMR---P 224

Query: 166 KDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYK 221
           ++   R    +  DI +E       +   +NG +  +D   AL     VDG MI  AA  
Sbjct: 225 RERAIRDQVRMIADICHEA-----GVACVINGDVTSKDEGHALMKEFGVDGAMIATAAEA 279

Query: 222 NSAMLTTVDE 231
           N +   T  E
Sbjct: 280 NPSCFRTEAE 289


>gi|157144926|ref|YP_001452245.1| tRNA-dihydrouridine synthase C [Citrobacter koseri ATCC BAA-895]
 gi|157082131|gb|ABV11809.1| hypothetical protein CKO_00655 [Citrobacter koseri ATCC BAA-895]
          Length = 312

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVTVKVRLGWDSGERKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           K  ++D+  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 177 KAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQECMAVSGCDAVMMGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|153006747|ref|YP_001381072.1| nifR3 family TIM-barrel protein [Anaeromyxobacter sp. Fw109-5]
 gi|152030320|gb|ABS28088.1| putative TIM-barrel protein, nifR3 family [Anaeromyxobacter sp.
           Fw109-5]
          Length = 348

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 65/127 (51%), Gaps = 3/127 (2%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKL 62
           +DR +R   R +   +  YTEM+ A  ++ G    ++ L     E P A+QI  ++   L
Sbjct: 21  SDRPFRAICRSM-GASFAYTEMVSAHGLVHGTLQTESYLDRDPDEDPFAVQIFASEADVL 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              A++    G   I++N+ CP  +V     GA L  +P  V + + A+  A+++PVTVK
Sbjct: 80  ARGAEVAVRAGAGIIDVNMACPVKKVCGTGAGAALGRDPRRVEEAVRAIRAAVAVPVTVK 139

Query: 123 CRIGVDD 129
            R G DD
Sbjct: 140 IRAGWDD 146


>gi|119494427|ref|XP_001264109.1| dihydrouridine synthase family protein, putative [Neosartorya
           fischeri NRRL 181]
 gi|119412271|gb|EAW22212.1| dihydrouridine synthase family protein, putative [Neosartorya
           fischeri NRRL 181]
          Length = 527

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 89/210 (42%), Gaps = 26/210 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D    +EAA+ V  +  + ++LN+GCP     +G +GA L  + D++  
Sbjct: 114 DRPLFVQFCANDPDDFLEAARHVAPYC-DAVDLNLGCPQGIARKGHYGAFLQEDWDLIYK 172

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  + K L IPVT K RI    Q          K I  +G + I +H R    KG    
Sbjct: 173 LINRLHKELPIPVTAKFRI----QESKEKTLEYAKMILSAGASIITLHGRTREQKG---- 224

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNS 223
            N  + +  Y I Y      P+  I  NG     +D+ + L+     DGVM       + 
Sbjct: 225 HNTGLADWSY-IRYLRDNLPPETVIFANGNNLNHDDLERCLEAT-GADGVMSAEGNLSDP 282

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           A+ +        P  GS        +++WR
Sbjct: 283 AIFS------KPPPVGSE------GREYWR 300


>gi|319954975|ref|YP_004166242.1| tRNA-u20a,u20b-dihydrouridine synthase [Cellulophaga algicola DSM
           14237]
 gi|319423635|gb|ADV50744.1| tRNA-U20a,U20b-dihydrouridine synthase [Cellulophaga algicola DSM
           14237]
          Length = 342

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/238 (22%), Positives = 99/238 (41%), Gaps = 46/238 (19%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   D  + +   K ++D GY E+N N+GCP   V +   G+ L+   D +   +  + 
Sbjct: 90  QVMTNDADEFLFVVKYIQDLGYTELNWNLGCPYPMVTKRGMGSGLVKEADKIDHILDRVH 149

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD--N 168
              ++ V++K R+G +D   +  + +    ++K  +  I IHAR  K + KG    D   
Sbjct: 150 AETNVTVSMKMRMGYED---SSEILDTFPVLEKYPIKNIAIHARIGKQLYKGGVDLDAFQ 206

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKN--- 222
           R + +  + + Y             NG +  +    K+    PS+D  MIGR    +   
Sbjct: 207 RCVESTSHKLYY-------------NGDITTVDAFKKMQERFPSIDHWMIGRGLIADPFL 253

Query: 223 -------------------SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
                              S    T+ + +   L+G +PIK ++ + FW   + S ++
Sbjct: 254 PSMIKANTFEYPENRWAIFSEFHDTIYQDYDAFLSGPTPIKMKM-QGFWEFFANSFSN 310


>gi|311694289|gb|ADP97162.1| tRNA-dihydrouridine synthase C [marine bacterium HP15]
          Length = 323

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 45/173 (26%), Positives = 84/173 (48%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+A+Q+ G+D  ++        + G  ++++N GCP+  V++   G  LM  P+++ + +
Sbjct: 64  PVAVQLLGSDPHQMARHGVRAAELGATQVDINFGCPAKTVNKHKGGCVLMREPELMHEIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+   +PVT K R+G DD+   VA    +++   + +    IHAR  +       
Sbjct: 124 AAVRQAVPAHVPVTAKMRLGYDDRSMGVACAQALEAAGAAEIV---IHARSKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
           D  K P    +I     +E     +  NG +  ++   +   +   D VMIGR
Sbjct: 174 DGYKPPAYWEEIAR--AREAVKAHVIANGEIWSVADYWRCREVSGCDDVMIGR 224


>gi|289621262|emb|CBI52045.1| unnamed protein product [Sordaria macrospora]
          Length = 456

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 101/233 (43%), Gaps = 41/233 (17%)

Query: 2   VDWTDRHYRFFARLLTNNAL--LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           V+WT        R+ TNN    LY E I    I R D     G          QIG +D 
Sbjct: 86  VEWT--------RIPTNNVKKELYDESI----IYRVDPVREAGRHI------FQIGTSDP 127

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVGDCIAAMCKAL 115
           S+ VE AK+V     + I++N GCP         GA L+  PD    I+   +A +  A 
Sbjct: 128 SRAVECAKLVA-ADVSGIDVNAGCPKPFSTHAGMGAALLRTPDKLVSILEALVAEIKPAF 186

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN--RKIPN 173
            I ++VK R+    + PA     LV+ +  +G+ G+ IH R   ++   P++   R    
Sbjct: 187 DIGISVKIRLL---ETPA-ETETLVRRLCAAGITGLTIHCRTTPMR---PRERAIRGQLR 239

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           +  D+ +E       +   +NG +E     L+++     DG MI   A KN +
Sbjct: 240 MIADVCHEY-----GVACVVNGDVEGRDHGLELMAEYGTDGAMIATCAEKNGS 287


>gi|302039230|ref|YP_003799552.1| putative tRNA-dihydrouridine synthase [Candidatus Nitrospira
           defluvii]
 gi|300607294|emb|CBK43627.1| putative tRNA-dihydrouridine synthase [Candidatus Nitrospira
           defluvii]
          Length = 394

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 73/354 (20%), Positives = 137/354 (38%), Gaps = 90/354 (25%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           TD  +R          + +TE    + I RG    +  L +S  E+P+  Q+ G D  + 
Sbjct: 21  TDAAFRRVVASQGQPDITFTEFTNVNEICRGPDHLLESLIYSEAERPIVAQLYGKDPDQF 80

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------ 116
             AA++V + G++ +++N+GCPS  V     GA L+  PD+    + A  + L       
Sbjct: 81  YRAAQVVCELGFDGLDINMGCPSKSVAASGSGAALIKTPDLAHAIVRAARQGLEDWAAGQ 140

Query: 117 --------------------------------IPVTVKCRIGVDDQIPAVALRNLVKSIK 144
                                           +P+++K R+G D     V +   V+ + 
Sbjct: 141 SIHSQGFKPSRIEFIHTLNHSRSGVPVVPRRLLPLSIKTRLGFD----CVVVERWVEHLL 196

Query: 145 KSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYE---IKKENPDLFIGLNGGLED 199
           ++    I +H R  + + +G +          D+  + E   + +    L +G NG L  
Sbjct: 197 EARPAAITLHGRTLQQMYRGAA----------DWSAIAEAATVARGTGTLMLG-NGDLNT 245

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE---YFSN-------PLTGSSPIKTRV 247
           +  A++ +   +V GV++GR    +       ++    FS        P T   P     
Sbjct: 246 LVDAMRRVAESNVQGVLVGRGTLGSPWFFREKEQARRAFSERRDLAALPATAWEP----- 300

Query: 248 DKDFWRKISAS-----MTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCR 294
                 ++S S     M D+A ++    G  + + I +H+     GFP++   R
Sbjct: 301 ------QVSVSHRMQVMLDHARQYEAIAGLERFRSIRKHLGWYCKGFPHAAAMR 348


>gi|330899152|gb|EGH30571.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 314

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 57  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 117 SQVRRAVPKHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV------- 166

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    +ED  +  +I  + D +MIGR
Sbjct: 167 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVEDWQRCREICGARD-IMIGR 217


>gi|293415423|ref|ZP_06658066.1| tRNA-dihydrouridine synthase C [Escherichia coli B185]
 gi|291433071|gb|EFF06050.1| tRNA-dihydrouridine synthase C [Escherichia coli B185]
          Length = 316

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI+++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEIRQQ-LNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|225562406|gb|EEH10685.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus G186AR]
          Length = 495

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 93/219 (42%), Gaps = 23/219 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N      +      I R D +   G       L  QIG A     V+AAKI+  
Sbjct: 90  FTRLPSNGGRENNQAAKESIIYRLDPRRESGK------LVFQIGTASPDLAVQAAKIIA- 142

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD +   + A+ + +  P    ++VK R+  
Sbjct: 143 ADVAGIDVNAGCPKPFSTTGGMGAALLQTPDRLVSILTALVQQVGTPYQIGISVKIRLLA 202

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 203 DPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRERAIRDQLP-----MIASICRAA- 252

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            + I +NG +E     L ++    VDG MI   A  NS+
Sbjct: 253 GVAILVNGDVESRDHGLALMAEYGVDGAMIATCAEANSS 291


>gi|330801859|ref|XP_003288940.1| hypothetical protein DICPUDRAFT_34883 [Dictyostelium purpureum]
 gi|325080971|gb|EGC34504.1| hypothetical protein DICPUDRAFT_34883 [Dictyostelium purpureum]
          Length = 384

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/196 (26%), Positives = 92/196 (46%), Gaps = 18/196 (9%)

Query: 37  KKNILGFSTQ--EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           K N L + T   +K   +Q+G       +EAA IV       I++N+GCP     +G  G
Sbjct: 74  KDNNLVYRTSAIDKNNVMQLGTGSAVTALEAASIVAR-DVCAIDINMGCPKYFSIQGGMG 132

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           + L+  P+ + D +  + + L+ P+T K R+   DQ       +L++ I+ +GV+ I +H
Sbjct: 133 SALLSKPETIKDILTTLKRNLNKPITCKIRLLSTDQ----ETIDLLRVIESTGVSAIGVH 188

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVD 211
            R    +   P    ++ N+  +  + +        I  NG +   ED+   LK   + +
Sbjct: 189 CRMIPERPRDPAHWDRLENILSNASFSVP-------IIANGDIWKHEDIDACLKKTKA-N 240

Query: 212 GVMIGRAAYKNSAMLT 227
            VMI R A KN ++ +
Sbjct: 241 SVMIARGAIKNVSIFS 256


>gi|160893898|ref|ZP_02074677.1| hypothetical protein CLOL250_01452 [Clostridium sp. L2-50]
 gi|156864276|gb|EDO57707.1| hypothetical protein CLOL250_01452 [Clostridium sp. L2-50]
          Length = 325

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 83/178 (46%), Gaps = 21/178 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            ++AAK + D GY+EIN+N+GCPS  V     G+ ++ +P  +   +  +  A    ++V
Sbjct: 85  FIKAAKALADMGYDEININMGCPSGTVVSKGKGSGMLADPVKLDHFLEEIFAADICKISV 144

Query: 122 KCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD---Y 176
           K R+G++  D+ P     +++  + K     + IH R         +++    ++D   +
Sbjct: 145 KTRLGMEFADEFP-----DILDVLMKYPFTEVIIHPRT--------REDYYGGSVDLAMF 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDE 231
           D+  E   E  +  +  NG + D +    I    P VD +MIGR    N  +   + E
Sbjct: 192 DLAVERYGEQTESVLCYNGDITDAAGYKNIQERYPQVDKIMIGRGIIGNPFLPQEIAE 249


>gi|320583736|gb|EFW97949.1| Dihydrouridine synthase [Pichia angusta DL-1]
          Length = 618

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 63/230 (27%), Positives = 102/230 (44%), Gaps = 24/230 (10%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEA 65
           YR   R L  + + Y+EM +A  +++G            ++     +QI  A   +  +A
Sbjct: 265 YRRLMRTLGAD-VTYSEMALALPLIQGSNSEWALPRAHESEYPGFGVQIATAKHWQACKA 323

Query: 66  AKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALSIPVTVK 122
           A+ ++      +E+NLN GCP   ++    G+ L+ NP  +   +  M   +  IPVTVK
Sbjct: 324 AEAIQTLTSHVSELNLNCGCPIDMLYRKGEGSALLDNPSRMLRILKGMSYSSGEIPVTVK 383

Query: 123 CRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DY 176
            R+GV D  P     NLV+ +  ++ V  I +H R    +     D   I  +     DY
Sbjct: 384 IRMGVKDDKPVA--ENLVRRVLNETDVAAITLHGRSRQQRYTRAADWDYISRVGAVVKDY 441

Query: 177 DIVYEIKKEN----PDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           +   E  K+     P  F+G NG     ED  +A+     +D VM+ R A
Sbjct: 442 NEQQEEDKDKVDRPPVYFVG-NGDCFTHEDWHRAVSD-EGIDSVMVARGA 489


>gi|291060336|gb|ADD73071.1| probable tRNA-dihydrouridine synthase [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 351

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 38/134 (28%), Positives = 72/134 (53%), Gaps = 9/134 (6%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISK 61
           ++D  +R  A +    +  YTEM+ ++A++R   + K ++  ++ E   A+QI G++ + 
Sbjct: 40  YSDSAFRSIA-IEWEASFTYTEMVSSEAMVRDSLNTKRLIRRASNETHYAIQIFGSNPAV 98

Query: 62  LVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----- 115
           + E AK++ D      I++N GCP  ++ +   GA L   P  + + + A+  A+     
Sbjct: 99  MAETAKLIVDSAQPSCIDINAGCPMPKITKTGAGAALTREPTRLYEVVKAVADAVYAQDA 158

Query: 116 SIPVTVKCRIGVDD 129
            IPVTVK R G ++
Sbjct: 159 RIPVTVKIRAGWEE 172


>gi|227499305|ref|ZP_03929417.1| dihydrouridine--tRNA ligase [Anaerococcus tetradius ATCC 35098]
 gi|227218656|gb|EEI83890.1| dihydrouridine--tRNA ligase [Anaerococcus tetradius ATCC 35098]
          Length = 326

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 106/226 (46%), Gaps = 37/226 (16%)

Query: 23  YTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD---ISKLV-EAAKIVEDFGYNE 76
           +TEM+  +A+   ++  + I+  S  EK + +QI G D   I ++V E    +E+F   E
Sbjct: 36  FTEMVSVNALDFDNRATEEIMYRSKAEKNVNIQIFGKDTDIIERVVKEKINPIEEF--KE 93

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIV---GDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
           I+ N+GCP+ ++ +   G+ LM +   V   G C+      +   V VK R+G+DD   +
Sbjct: 94  ISFNMGCPAPKIFKNGQGSALMADLKKVYAIGKCLVDSTNKI---VNVKFRLGIDD--SS 148

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-------N 186
                + K+++ +GV+ + +HAR         ++ +     D+  + ++K         N
Sbjct: 149 KNYIEVAKALEDAGVDYVILHAR--------TRNQQYSGKADWTAIRKLKDSLGIPVIAN 200

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            D F      +ED    L++    DGVM+ R    N  +   + +Y
Sbjct: 201 GDCF-----SVEDYKNILEV-TGADGVMLARGVMGNPFLFRQIKDY 240


>gi|126667330|ref|ZP_01738303.1| hypothetical protein MELB17_15347 [Marinobacter sp. ELB17]
 gi|126628275|gb|EAZ98899.1| hypothetical protein MELB17_15347 [Marinobacter sp. ELB17]
          Length = 335

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 82/173 (47%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+A+Q+ G+D   +        + G  ++++N GCP+  V++   G  LM  P+++ +  
Sbjct: 64  PVAVQLLGSDPHMMARHGAKAAELGATQVDINFGCPAKTVNKHKGGCVLMREPELMHEIT 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+   I VT K R+G DD+   VA     +++  +G   I IHAR       S  
Sbjct: 124 AAVRQAVPADILVTAKMRLGYDDRSMGVA---CAQALDAAGAGEIVIHAR-------SKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
           D  K P    +I     +E     +  NG +  ++   +   +   D VMIGR
Sbjct: 174 DGYKPPAYWEEIAK--AREAVKAKVIANGDIFTVADYWRCREVSGCDDVMIGR 224


>gi|332028941|gb|EGI68959.1| tRNA-dihydrouridine synthase 3-like protein [Acromyrmex echinatior]
          Length = 665

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/213 (23%), Positives = 98/213 (46%), Gaps = 16/213 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A  IL+G ++   ++     E    +Q+ G +   L   A+++  +   + I+LN+
Sbjct: 340 EMALAPNILKGTQEEWALVKRHESEDIFGVQLCGNNPGVLARCAQLLNHEIDADYIDLNL 399

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   +++   G+ ++   +++   I ++ + L IP++VK R GV   I      NL+ 
Sbjct: 400 GCPIDMIYKNGGGSGMLNRLNVLETVIKSVSQVLDIPLSVKTRTGV--YIDKPIAHNLMP 457

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
             +  GV+ I +H R         ++ R     D++ + +       + +  NG     +
Sbjct: 458 RFRDWGVSMITVHGRS--------REQRYTKLADWEYIEKCAMAAQPIPVFGNGDILSFD 509

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  +A +   +V G+ IGR A     + T + E
Sbjct: 510 DYRRAKETYSTVQGITIGRGALIKPWIFTEIKE 542


>gi|225022204|ref|ZP_03711396.1| hypothetical protein CORMATOL_02238 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945137|gb|EEG26346.1| hypothetical protein CORMATOL_02238 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 384

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 94/217 (43%), Gaps = 20/217 (9%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV 69
            A+  T + L   EMI A A++ G++K  ++  F   E P +LQ    D     +AA++V
Sbjct: 39  LAKTGTVSGLYVCEMITARALVEGNEKTRHMTTFGPDEHPRSLQFYTTDPEYTYKAARMV 98

Query: 70  EDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKALSIPVTVKCRI 125
            D    + I++N GCP  +V     G+ L     + G+             IP+TVK RI
Sbjct: 99  ADNNLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAAVKAVAGTDIPITVKFRI 158

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+DD        +  +     G   + +HAR A          R     D+  +  +K+ 
Sbjct: 159 GIDDD--HHTHLDAGRIAAAEGAAAVALHARTAA--------QRYSGTADWSQITALKEH 208

Query: 186 NPDLFIGL--NGGLEDMSQALKILPSV--DGVMIGRA 218
             D  I +  NG +   + A K++     DGV++GR 
Sbjct: 209 LADTGIPVLGNGDVFQATDAQKMMTETGCDGVVVGRG 245


>gi|206577930|ref|YP_002237438.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae 342]
 gi|288934362|ref|YP_003438421.1| dihydrouridine synthase [Klebsiella variicola At-22]
 gi|206566988|gb|ACI08764.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae 342]
 gi|288889091|gb|ADC57409.1| dihydrouridine synthase DuS [Klebsiella variicola At-22]
          Length = 310

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPDHLPVTVKVRLGWDS---GERRFEIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI ++   + +  NG + D   A   +     D VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEI-RQRLTIPVVANGEIWDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|209520559|ref|ZP_03269315.1| dihydrouridine synthase DuS [Burkholderia sp. H160]
 gi|209498996|gb|EDZ99095.1| dihydrouridine synthase DuS [Burkholderia sp. H160]
          Length = 347

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/219 (24%), Positives = 96/219 (43%), Gaps = 28/219 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   +   A          I+LN GCP+  V++   GA L+ NP+++   +
Sbjct: 65  PMVIQLLGSDPEWMARNAAHAATLSPYGIDLNFGCPAKVVNQHGGGAMLLANPELLNRIV 124

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +A+  A+  ++ VT K R+GV D   A+      +++   G   + +HAR         +
Sbjct: 125 SAVRAAVPANVAVTAKMRLGVSDTSRAI---ECAQALADGGAASLVVHART--------R 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
           D+R  P   ++ +  I    E P +  G    + D  +   +    D VMIGR A     
Sbjct: 174 DDRYRPPAHWEWIARIDDAVEVPVIANGEVWSVADWERCRSVSGCAD-VMIGRGAVS--- 229

Query: 225 MLTTVDEYFSNPLTG-SSPIKTRVDKDFWRKISASMTDY 262
                D + +  + G   P  +    D W+++  S+  Y
Sbjct: 230 -----DPFLAQRIRGLMDPCPS---ADEWQQVLRSIVGY 260


>gi|146422997|ref|XP_001487432.1| hypothetical protein PGUG_00809 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 362

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 83/184 (45%), Gaps = 16/184 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVG 105
           L  QIG A+    VEAAK+V     + I+LN GCP         GA L+ NPD    I+ 
Sbjct: 79  LIFQIGSANPELAVEAAKVVAR-DVDGIDLNCGCPKNFSTHSGMGAELLTNPDVLVLILK 137

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +  +     IP++VK R+ +D   P  +++ L+  I K+GV  + +H R   ++   P
Sbjct: 138 NLVEKIGNVYRIPISVKIRL-LDATDPEPSIK-LIDRICKTGVANLTLHCRTKPMRNRQP 195

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---GVMIGRAAYKN 222
                +P      + E    N   FI LNG + +  +  ++        G MI  +A  N
Sbjct: 196 PIRTFLPQ-----IIETVHSNNVSFI-LNGAIRNRQEFYELQARYGKQIGAMIAESAEAN 249

Query: 223 SAML 226
             + 
Sbjct: 250 PTVF 253


>gi|317491241|ref|ZP_07949677.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316920788|gb|EFV42111.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 314

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 71  VQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKMVNGSGGGATLLKDPEMIYQGAKAM 130

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   I +H R       + +D  
Sbjct: 131 REAVPAHLPVTVKVRLGWDSGDRQF---EIADAVEQAGATEITVHGR-------TKEDGY 180

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + +I ++  ++ +  NG + D   A   + +   D VMIGR A  N   L+
Sbjct: 181 KAEKINWAAIGKI-RQRLNIPVIANGEIWDWQSAQDCMATTGCDSVMIGRGAL-NVPNLS 238

Query: 228 TVDEY 232
            V +Y
Sbjct: 239 RVIKY 243


>gi|332534960|ref|ZP_08410779.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332035633|gb|EGI72124.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 326

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 51/198 (25%), Positives = 91/198 (45%), Gaps = 16/198 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G + + L E A      G + ++LN GCP+  V+    GA L+ +P
Sbjct: 57  GFTRAGTPVRVQLLGQEANPLAENAIRAIALGSHGVDLNFGCPAKTVNRSRGGAVLLKDP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D +   I A+  A+     V+ K R+G DD   +   + +V ++  +G N + IHAR   
Sbjct: 117 DHMYTIIKAVRDAVDDEHEVSAKIRLGFDDDSNS---QEIVDAVVSAGANSVAIHARTKR 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGR 217
                P    KIP +       IK +N  + +  NG +  +  A+  +       +M+GR
Sbjct: 174 DGYNPPAYWEKIPPI-------IKGKN--IAVVANGEIWQVEDAMLCQKRSGCTDLMLGR 224

Query: 218 AAYKNSAMLTTVDEYFSN 235
            A  +  +   +  + +N
Sbjct: 225 GALSHPDLAKKIKAHVNN 242


>gi|289824091|ref|ZP_06543688.1| hypothetical protein Salmonellentericaenterica_02632 [Salmonella
           enterica subsp. enterica serovar Typhi str. E98-3139]
          Length = 164

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 59/108 (54%), Gaps = 8/108 (7%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D  ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +
Sbjct: 29  VQIAGSDPVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGV 88

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHAR 156
             A+ +PVT+K R G      A   RN V+  +     G+  + IH R
Sbjct: 89  VNAVDVPVTLKIRTGW-----APEHRNCVEIAQLAEDCGIQALTIHGR 131


>gi|187935292|ref|YP_001886306.1| dihydrouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
 gi|187723445|gb|ACD24666.1| dihydrouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
          Length = 321

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 101/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  +  ++  GYNE+NLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSEGFINTSGKLKQLGYNEVNLNLGCPAGTVVSKNRGSGFLAKREELDMFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NR 169
           K   I +++K RIG D          L+K   K  +  + IH R       + KD   N+
Sbjct: 124 KMDDIKISIKTRIGKDS---PEEFYELIKIYNKYPIEELIIHPR-------TQKDFYGNK 173

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             PNLD          NP  + G    ++D  +  +  P V  +M+GR    N  ++   
Sbjct: 174 --PNLDVFKDALSLSNNPICYNGDIFTVKDHDKLTRDFPEVKTLMLGRGILANPGLM--- 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  ++ I   + K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 229 -----NEIKNNTFIDKEILKEFHDEILSKYIELFNEDRNAIFRMKELWGYMIYMF 278


>gi|154299041|ref|XP_001549941.1| hypothetical protein BC1G_11833 [Botryotinia fuckeliana B05.10]
 gi|150857536|gb|EDN32728.1| hypothetical protein BC1G_11833 [Botryotinia fuckeliana B05.10]
          Length = 434

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L  QIG +D  + V+ A+IV       I++N GCP      G  GA L+  PD     
Sbjct: 110 KKLIFQIGTSDPERAVQCARIVA-ADVAGIDVNAGCPKPFSTSGGMGAALLQTPDK---- 164

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + A+ +AL   +  +  IG+  +I     A     LV+ +  +G+ G+ IH R   ++  
Sbjct: 165 LCAILEALVREIVPEFEIGISVKIRLLETAEKTEALVRKLCATGITGLTIHCRTTPMR-- 222

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
            P++ R I      ++ +I +E+  +   +NG +E+  QALK+      +G MI  AA  
Sbjct: 223 -PRE-RAIRE-QLKMIADICRES-GVACLMNGDVENRDQALKLAEEFGTNGGMIAVAAEA 278

Query: 222 NSA 224
           NS+
Sbjct: 279 NSS 281


>gi|50121723|ref|YP_050890.1| tRNA-dihydrouridine synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612249|emb|CAG75699.1| putative dihydrouridine synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 310

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   + +   D +M+GR A  N   L+
Sbjct: 177 KAECINWQAIGEIRQRLQIPVIA-NGEIWDWQSAQDCMATTGCDAIMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|315639099|ref|ZP_07894266.1| tRNA-dihydrouridine synthase B [Campylobacter upsaliensis JV21]
 gi|315480803|gb|EFU71440.1| tRNA-dihydrouridine synthase B [Campylobacter upsaliensis JV21]
          Length = 305

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 113/239 (47%), Gaps = 25/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  +R   +    +  + +EMI ++A++   +K++  L  +  E P  +QI G D
Sbjct: 14  MAGFTDPPFRSVVKQFGADVTI-SEMISSNALVYESQKSLKMLEKTPFETPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A  I+ +  + + I+ N GCP  +V +   G+ L+ N ++    +  +      
Sbjct: 73  EDILKKAVLILNELDFIDGIDFNCGCPVNKVVKQCAGSALLENLELFRKLVGVIKTHNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNL 174
             T VK R+G +D+ P      + +  ++ GV+ I IH   RK +  G          + 
Sbjct: 133 QFTSVKFRLGFNDKYP----EKMAQICEELGVDFISIHGRTRKQLYSG----------SA 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           DY+ + + KK      I  NG +  ++  + LKI  + +G+MIGRA+  N  +   + E
Sbjct: 179 DYNSIAKAKKSVKIPVIA-NGDINAQNAKEVLKI-TACEGLMIGRASVGNPWIFYEIKE 235


>gi|312215880|emb|CBX95832.1| hypothetical protein [Leptosphaeria maculans]
          Length = 448

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVG 105
           L  Q+G A+    V+AAK+V       I++N GCP      G  GA L+  PD    I+ 
Sbjct: 107 LIYQMGTANPELAVQAAKMVA-ADVAGIDVNSGCPKPFSTAGGMGAALLKTPDLLCSILT 165

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +  + K   I ++VK RI    ++P      LVK + ++G+ G+ +H R   ++   P
Sbjct: 166 RLVEEVGKPFEIGISVKIRIL---ELPE-ETEALVKRLVRTGITGLTVHCRTTPMR---P 218

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           ++ R I +    +V EI +E   +   +NG +   ++AL+++    VDG MI   A KN 
Sbjct: 219 RE-RAIRD-QLKMVGEICREA-GVACVMNGDVTSRTEALQLMQEFHVDGAMIATEAEKNP 275

Query: 224 A 224
           +
Sbjct: 276 S 276


>gi|227326968|ref|ZP_03830992.1| tRNA-dihydrouridine synthase C [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 310

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   + +   D VMIGR A  N   L+
Sbjct: 177 KAECINWQAIGEIRQRLRIPVIA-NGEIWDWQSAQDCMATTGCDAVMIGRGAL-NLPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|332707883|ref|ZP_08427898.1| tRNA-dihydrouridine synthase [Lyngbya majuscula 3L]
 gi|332353349|gb|EGJ32874.1| tRNA-dihydrouridine synthase [Lyngbya majuscula 3L]
          Length = 52

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/37 (59%), Positives = 31/37 (83%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK 37
          M+DWTDRH R F R+L+  ALL+TEM++ADA++ GD+
Sbjct: 14 MMDWTDRHCRAFHRVLSKRALLWTEMVIADAVIHGDR 50


>gi|223997918|ref|XP_002288632.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975740|gb|EED94068.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 378

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 43/160 (26%), Positives = 74/160 (46%), Gaps = 16/160 (10%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV---EDFGYNEINL 79
           EM +AD +L+G      +L   + E    +QI      +    A+++    +   + +++
Sbjct: 43  EMAIADQLLQGKPSEWALLKRHSSEDVFGVQIATGHADQYTRVAELIANEPEIEVDFVDM 102

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP   V E   GA LML    +   +  + K L+ PVT+K R G ++  P      L
Sbjct: 103 NLGCPIDLVCEKGAGASLMLRERKLKGSVEGLTKTLNCPVTIKIRTGWNENEPIA--HKL 160

Query: 140 VKSIKKSGVNGI---WIHARKAILKGLSPKDNRKIPNLDY 176
           V++I+  G +GI    IH R  + +        ++ N DY
Sbjct: 161 VQTIQAWGYDGIGAVMIHGRSRLQR------YSRLANWDY 194


>gi|15639964|ref|NP_219417.1| histidine phosphokinase/phophatase (ntrB) [Treponema pallidum
           subsp. pallidum str. Nichols]
 gi|189026203|ref|YP_001933975.1| histidine phosphokinase/phophatase [Treponema pallidum subsp.
           pallidum SS14]
 gi|6136586|sp|O83945|DUS_TREPA RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|3323302|gb|AAC65935.1| histidine phosphokinase/phophatase (ntrB) [Treponema pallidum
           subsp. pallidum str. Nichols]
 gi|189018778|gb|ACD71396.1| histidine phosphokinase/phophatase [Treponema pallidum subsp.
           pallidum SS14]
          Length = 340

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 38/134 (28%), Positives = 72/134 (53%), Gaps = 9/134 (6%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISK 61
           ++D  +R  A +    +  YTEM+ ++A++R   + K ++  ++ E   A+QI G++ + 
Sbjct: 29  YSDSAFRSIA-IEWEASFTYTEMVSSEAMVRDSLNTKRLIRRASNETHYAIQIFGSNPAV 87

Query: 62  LVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----- 115
           + E AK++ D      I++N GCP  ++ +   GA L   P  + + + A+  A+     
Sbjct: 88  MAETAKLIVDSAQPSCIDINAGCPMPKITKTGAGAALTREPTRLYEVVKAVADAVYAQDA 147

Query: 116 SIPVTVKCRIGVDD 129
            IPVTVK R G ++
Sbjct: 148 RIPVTVKIRAGWEE 161


>gi|332263177|ref|XP_003280631.1| PREDICTED: tRNA-dihydrouridine synthase 3 isoform 1 [Nomascus
           leucogenys]
          Length = 649

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 70/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 334 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 389

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 390 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 448

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E +K  +P    G NG 
Sbjct: 449 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVKAASPMPLFG-NGD 498

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 499 ILSFEDANRAMQT--GVAGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 547

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 548 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 585


>gi|310790767|gb|EFQ26300.1| dihydrouridine synthase [Glomerella graminicola M1.001]
          Length = 427

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 100/223 (44%), Gaps = 38/223 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVG 105
           L  QIG AD    V+AA++V       I++N GCP      G  GA L+  PD    I+ 
Sbjct: 113 LIFQIGTADPDLAVQAARLVAG-DVAGIDVNAGCPKPFSISGGMGAALLKTPDKLCAILE 171

Query: 106 DCIAAMCKALSIPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             +A +     I ++VK R +   +Q  A     LV+ +  +G+ G+ IH R   ++   
Sbjct: 172 ALVANIMPEFEIGISVKIRLLDTPEQTEA-----LVRKLCATGITGLTIHCRTTPMR--- 223

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           P++ R I      +V E+  E     I +NG +E    A+ ++    VDG MI  AA  N
Sbjct: 224 PRE-RAI-REQLRMVAEVCHEAGVACI-MNGDVESRDHAVDLIKEYGVDGAMIATAAEAN 280

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDF--WRKISASMTDYA 263
           S+                   +++VD     W++I+A+   YA
Sbjct: 281 SSCF-----------------RSKVDGGLASWQEIAATYVKYA 306


>gi|37681322|ref|NP_935931.1| tRNA-dihydrouridine synthase [Vibrio vulnificus YJ016]
 gi|326423811|ref|NP_760162.2| tRNA dihydrouridine synthase B [Vibrio vulnificus CMCP6]
 gi|38604853|sp|Q8CWL2|DUSB_VIBVU RecName: Full=tRNA-dihydrouridine synthase B
 gi|37200073|dbj|BAC95902.1| tRNA-dihydrouridine synthase [Vibrio vulnificus YJ016]
 gi|319999178|gb|AAO09689.2| tRNA dihydrouridine synthase B [Vibrio vulnificus CMCP6]
          Length = 322

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 109/244 (44%), Gaps = 20/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  L      K  +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELC-LRYGAGMAVSEMMSSNPQLWKTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+   + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLKYPDIIEQILKAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDY 176
           VT+K R G D +       ++ K  +  G+  + +H R    + KG            +Y
Sbjct: 136 VTLKTRTGWDTENKNCI--HIAKLAEDCGIQALALHGRTKACMYKG----------EAEY 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K+      I  NG ++   +A  +L     D +MIGR A     +   +  Y  
Sbjct: 184 DSIKAVKQAVSIPVIA-NGDIDSPEKAKYVLEYTGADALMIGRPAQGRPWIFQEIHHYLE 242

Query: 235 NPLT 238
           N  T
Sbjct: 243 NGTT 246


>gi|238798925|ref|ZP_04642390.1| tRNA-dihydrouridine synthase C [Yersinia mollaretii ATCC 43969]
 gi|238717235|gb|EEQ09086.1| tRNA-dihydrouridine synthase C [Yersinia mollaretii ATCC 43969]
          Length = 310

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 81/172 (47%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQ+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  LQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPEHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A
Sbjct: 177 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGA 227


>gi|93007131|ref|YP_581568.1| dihydrouridine synthase, DuS [Psychrobacter cryohalolentis K5]
 gi|92394809|gb|ABE76084.1| dihydrouridine synthase, DuS [Psychrobacter cryohalolentis K5]
          Length = 340

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 51/215 (23%), Positives = 93/215 (43%), Gaps = 22/215 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR D K   G      P+ +Q+ G++   + + A      G   I++N GCP+  V+   
Sbjct: 78  LRHDAKTACG-----TPIHIQLLGSEAQLMADNAAYACALGAPAIDINFGCPAKTVNSHR 132

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            G+ L+  P+ +   I+A+ +A+   IPV+ K R+G  D      + ++  +IK SG + 
Sbjct: 133 GGSVLLDEPETMYQIISAVRQAVPADIPVSAKIRLGYTD---TSLMDDIRGAIKDSGADW 189

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS- 209
           + +HAR        P    KI + +            D+ +  NG + +   A   +   
Sbjct: 190 LTVHARTKTQGYKPPAYWDKIQSFN----------ALDIPVIANGEIWNAEHAQNCMTQS 239

Query: 210 -VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
             + +M+GR A     ++  VD   S  L   + +
Sbjct: 240 GTEHLMLGRGAVTRPDLIAQVDREHSQTLNNETTL 274


>gi|157867470|ref|XP_001682289.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68125742|emb|CAJ03495.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 595

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 44/169 (26%), Positives = 74/169 (43%), Gaps = 19/169 (11%)

Query: 59  ISKLVEAAKIVE-----DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +S+  EAA   +      F Y+ +++N GCP  ++ +   G  L    + + D + ++  
Sbjct: 298 VSRPQEAATFAQALEASGFSYDFLDINCGCPVEKIVKSGCGCGLWQRTERLRDVVESLAI 357

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             S PV +KCRIG+D+ IP   L   +      G   + +H R         +  R    
Sbjct: 358 YQSRPVAIKCRIGLDEDIP--TLHQQIHRYSAWGAAAVTVHGRS--------RKQRYTKF 407

Query: 174 LDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
            ++D V +  +      IG NG    LED+ +  +  P +   MIGR A
Sbjct: 408 ANWDYVDQCAQLTSLPVIG-NGDIMSLEDVLEHRERQPHIASHMIGRGA 455


>gi|134057270|emb|CAK37884.1| unnamed protein product [Aspergillus niger]
          Length = 446

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 57/190 (30%), Positives = 85/190 (44%), Gaps = 21/190 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LIYQIGTATPEIAVQAAKLVAG-DVAGIDVNSGCPKPFSTSGGMGAALLKTPDKLVAILE 163

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +  P    ++VK RI  D +      R LV  + K+G+ G+ +H R   ++   P
Sbjct: 164 ALVKEVGTPFQIGISVKIRILKDPE----ETRALVSRLVKTGITGLTVHCRTPPMR---P 216

Query: 166 KDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYK 221
           ++   R    +  DI +E       +   +NG +  +D   AL     VDG MI  AA  
Sbjct: 217 RERAIRDQVRMIADICHEA-----GVACVINGDVTSKDEGHALMKEFGVDGAMIATAAEA 271

Query: 222 NSAMLTTVDE 231
           N +   T  E
Sbjct: 272 NPSCFRTEAE 281


>gi|315924890|ref|ZP_07921107.1| tRNA-dihydrouridine synthase B [Pseudoramibacter alactolyticus ATCC
           23263]
 gi|315621789|gb|EFV01753.1| tRNA-dihydrouridine synthase B [Pseudoramibacter alactolyticus ATCC
           23263]
          Length = 322

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 78/315 (24%), Positives = 138/315 (43%), Gaps = 38/315 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +++  +R  A+    +A+  TEMI A  +   DKK   ++    +E P  +Q+ G+D
Sbjct: 17  LAGYSNLPFRLMAKKYGADAVT-TEMISAKGLFYRDKKTAKLMATCPEEAPAGIQLFGSD 75

Query: 59  ---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              I ++V  A+ V    +  I+ N GCP+ ++ +   GA L+ +   + + I    K +
Sbjct: 76  PAIIERVV--AEQVNATPFAFIDFNAGCPAPKIVKNGDGAALLKDLSRL-EAIVCRMKTV 132

Query: 116 SI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIP 172
           SI PV VK R+G D     VA+    K I+ +G + + +H   R+A   G +        
Sbjct: 133 SIKPVHVKIRLGWDAGH-RVAV-EAAKRIEAAGADVLTVHGRTREAFYSGAA-------- 182

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
             D+  + E+K     L +  NG ++  + + A       DG+M+GR A  N  +   + 
Sbjct: 183 --DWPAIAEVKAAV-SLPVVANGDIDSPEAAAAALAATGADGLMVGRGAIGNPFIFREMK 239

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISAS--MTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +     L G +     VD+     I     +T  A R     G + ++ + ++    G P
Sbjct: 240 QA----LAGKTAAPPSVDERLQAAIDHVHLVTAMAERV----GPMVEMRKQLVAYTRGMP 291

Query: 289 NSRRCR-HILTVEAG 302
            S   R  I T   G
Sbjct: 292 GSAALRQQIFTRSTG 306


>gi|315453289|ref|YP_004073559.1| tRNA Dihydrouridine synthase [Helicobacter felis ATCC 49179]
 gi|315132341|emb|CBY82969.1| tRNA Dihydrouridine synthase [Helicobacter felis ATCC 49179]
          Length = 332

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 49/203 (24%), Positives = 102/203 (50%), Gaps = 20/203 (9%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EM+ + A++   +K   +L  S  E P ++QI G+ +  +  A +++    G + ++ N
Sbjct: 40  SEMVSSHALVHAFEKTAKMLEKSPHENPFSVQIAGSKVEIVQRAVELLNQVEGIDIVDFN 99

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  + P T VK R+G + +IP      +
Sbjct: 100 CGCPAPKVANHGNGSGLLKDLNHLVKLLKVVREHTNKPYTSVKVRLGFERKIP----EEI 155

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK-ENPDLFIGLNGGLE 198
             ++  + V+ + +HAR       +  D  K   +DY+ V  ++   N  L +  NG ++
Sbjct: 156 AHALNDAPVDFVVVHAR-------TRADRYKKEKIDYESVRLMRSILNKPLIV--NGEID 206

Query: 199 DMSQALKI--LPSVDGVMIGRAA 219
            +++A ++       GVMIGRA+
Sbjct: 207 SVAKAQEVRAYTGAQGVMIGRAS 229


>gi|290508567|ref|ZP_06547938.1| tRNA-dihydrouridine synthase C [Klebsiella sp. 1_1_55]
 gi|289777961|gb|EFD85958.1| tRNA-dihydrouridine synthase C [Klebsiella sp. 1_1_55]
          Length = 310

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPDHLPVTVKVRLGWDS---GERRFEIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI ++   + +  NG + D   A   +     D VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEI-RQRLTIPVVANGEIGDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|320176621|gb|EFW51663.1| tRNA-dihydrouridine synthase C [Shigella dysenteriae CDC 74-1112]
          Length = 326

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 77  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 136

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 137 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 186

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 187 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 244

Query: 228 TVDEY 232
            V +Y
Sbjct: 245 RVVKY 249


>gi|260913194|ref|ZP_05919676.1| tRNA-dihydrouridine synthase C [Pasteurella dagmatis ATCC 43325]
 gi|260632781|gb|EEX50950.1| tRNA-dihydrouridine synthase C [Pasteurella dagmatis ATCC 43325]
          Length = 312

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 46/182 (25%), Positives = 85/182 (46%), Gaps = 15/182 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A+   + G   ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GLTPSGTPVRVQLLGQYPEWLAENAQRAIELGSYGVDLNCGCPSKTVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++     ++  A+   +PV+VK R+G DD   A  + +   ++++ G   I IH R   
Sbjct: 117 ELIYRATTSLRAAVPAHLPVSVKVRLGWDDVNQAFEIAD---AVQQGGATEITIHGR--- 170

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
               +  D  +   +++  + E+++      I  NG + D    Q   +    + +MIGR
Sbjct: 171 ----TKADGYRADRINWRKINEVRQRLSIPVIA-NGEVWDWQSGQDCLVQTGCEDLMIGR 225

Query: 218 AA 219
            A
Sbjct: 226 GA 227


>gi|225572095|ref|ZP_03780959.1| hypothetical protein RUMHYD_00389 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040429|gb|EEG50675.1| hypothetical protein RUMHYD_00389 [Blautia hydrogenotrophica DSM
           10507]
          Length = 316

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 44/177 (24%), Positives = 77/177 (43%), Gaps = 15/177 (8%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI        +  AK + D GY+E+NLN+GCPS  V     G+  +  P  +   +  + 
Sbjct: 64  QIMTNKAEDFISTAKKLRDLGYDEVNLNLGCPSKTVVSKGRGSGFLAYPKELERFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           + L + ++VK R GV+++   + L ++        +  + +H R      L     +K  
Sbjct: 124 EKLDMKISVKTRAGVEEEEEFLTLLDIYNRFP---MEELIVHPR------LQTDYYKKPV 174

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
                +       NP   +  NG L   +D+ +  +  P VD VMIGR   +N  ++
Sbjct: 175 RFSVFLQASAASRNP---LCYNGDLIYAQDIERFAREFPQVDRVMIGRGLLRNPGLV 228


>gi|257093932|ref|YP_003167573.1| dihydrouridine synthase DuS [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
 gi|257046456|gb|ACV35644.1| dihydrouridine synthase DuS [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
          Length = 327

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 52/216 (24%), Positives = 100/216 (46%), Gaps = 18/216 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+A+Q+ G+D   L E A  + +     I+LN GCP+  V+    GA L+ +P+ +   +
Sbjct: 65  PVAVQLLGSDPGCLAENAAQLAELSPAGIDLNFGCPAPTVNRHGGGARLLADPEQLFRIV 124

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+   IP T K R+GV D    +   +  +++   G++ + +HAR    +G  P 
Sbjct: 125 AAVRRAVPAGIPFTAKMRLGVSDTARTL---DCARALAAGGIDSLVVHARTRA-EGYRPP 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      ++V      N +++        D ++   +  S D VMIGR A  +  ++
Sbjct: 181 AHWEWVARIGEVVQRPVTANGEVWT-----TADHARCCLVSGS-DDVMIGRGAVADPFLV 234

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                +  + + G +    R     WR++   +  Y
Sbjct: 235 ----RHIRSRVAGETIAADRSAD--WRQLQPLLASY 264


>gi|295098151|emb|CBK87241.1| tRNA-U20a,U20b-dihydrouridine synthase [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 311

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 94/207 (45%), Gaps = 21/207 (10%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPSHLPVTVKVRLGWDSDDKQF---EIADAVQQAGATELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI+K      I  NG + D   A   L     + VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEIRKRLTIPVIA-NGEIWDYESAQACLKETGCNAVMIGRGAL-NVPNLS 234

Query: 228 TVDEYFSNPLTGSSPIK-----TRVDK 249
            V +Y    +  +  +K     TR++K
Sbjct: 235 RVVKYNEPRMPWADVVKLLQKYTRLEK 261


>gi|25144369|ref|NP_498078.2| hypothetical protein C45G9.2 [Caenorhabditis elegans]
 gi|21431919|sp|Q09504|YQI2_CAEEL RecName: Full=Uncharacterized tRNA-dihydrouridine synthase-like
           protein C45G9.2
 gi|16259260|gb|AAA62547.2| Hypothetical protein C45G9.2 [Caenorhabditis elegans]
          Length = 284

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 57/233 (24%), Positives = 100/233 (42%), Gaps = 23/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   R+   + + +T MI A   +  +K   + L     + PL +Q    D
Sbjct: 1   MVRYSKLAFRQLVRVYDVD-VCFTPMIYAKNFIESEKCRSSELSVCEGDSPLIVQFATDD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++V       ++LN GCP   V    FG+ L+  P+++ D +      +  P
Sbjct: 60  PFVLSEAAEMVYKCSTG-VDLNCGCPKHDVRSKGFGSALLSKPELLADMVRQTRARIPDP 118

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV  + +H R    +   P D + +    
Sbjct: 119 DFSVSLKIRINHDIEKTV----DLCRKAEAAGVTHLTVHGRTPSQRA-EPIDIQAL---- 169

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
                 I K++  + I  NGG+    +AL +     VDG+M       N A+ 
Sbjct: 170 -----RIVKDSVSVPIIANGGITTREEALFLAEQTGVDGIMAANGLLDNPALF 217


>gi|330967041|gb|EGH67301.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 321

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    +ED  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVIKVPVVANGEIWTVEDWRRCREICGARD-IMIGR 224


>gi|311278876|ref|YP_003941107.1| dihydrouridine synthase DuS [Enterobacter cloacae SCF1]
 gi|308748071|gb|ADO47823.1| dihydrouridine synthase DuS [Enterobacter cloacae SCF1]
          Length = 345

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 94  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYQGAKAM 153

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 154 REAVPAHLPVTVKVRLGWDSGDKRF---EIADAVQQAGATELVVHGR-------TKEDGY 203

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           +   +++  + +I++    + +  NG + D   A   + +   D VMIGR A  N   L+
Sbjct: 204 RAERINWQAIGDIRRRL-SIPVVANGEIWDWQSAQDCMAATGCDAVMIGRGAL-NIPNLS 261

Query: 228 TVDEY 232
            V +Y
Sbjct: 262 RVVKY 266


>gi|324114444|gb|EGC08413.1| dihydrouridine synthase [Escherichia fergusonii B253]
          Length = 312

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENALRAVELGSFGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEQKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI++      I  NG + D   A +   L   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQQCMALSGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|218549553|ref|YP_002383344.1| tRNA-dihydrouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|218357094|emb|CAQ89727.1| tRNA-dihydrouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|325497953|gb|EGC95812.1| tRNA-dihydrouridine synthase C [Escherichia fergusonii ECD227]
          Length = 316

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 71  IQLLGQYPQWLAENALRAVELGSFGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 130

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 131 REAVPAHLPVSVKVRLGWDSGEQKF---EIADAVQQAGATELVVHGR-------TKEQGY 180

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI++      I  NG + D   A +   L   D VMIGR A  N   L+
Sbjct: 181 RAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQQCMALSGCDAVMIGRGAL-NIPNLS 238

Query: 228 TVDEY 232
            V +Y
Sbjct: 239 RVVKY 243


>gi|299472929|emb|CBN80498.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 569

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 53/199 (26%), Positives = 87/199 (43%), Gaps = 20/199 (10%)

Query: 34  RGDKKNILGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           RG K     F T    +   L  QIG  D +  + AA+ VE      +++N+GCP     
Sbjct: 70  RGKKGIATPFQTCPALERGRLVYQIGTGDATNALRAAQHVER-DVAAVDINMGCPKRFSL 128

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +G  GA L+  P +  D +  + + LS+PV+VK R+    + P   +    + ++K+G  
Sbjct: 129 QGGMGAALLKQPQVAADIVGTLRRNLSVPVSVKIRL---LETPGETV-EFARRMEKAGAC 184

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + +H RK    G +P    +   L    D V      N D++        DM+  +K L
Sbjct: 185 ALSVHVRKV---GDTPASKARWEELRPVVDAVNIPVIANGDVYT-----RADMA-GIKAL 235

Query: 208 PSVDGVMIGRAAYKNSAML 226
                VM+ R A  N ++ 
Sbjct: 236 SGCSSVMLARPALLNCSIF 254


>gi|167519230|ref|XP_001743955.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163777917|gb|EDQ91533.1| predicted protein [Monosiga brevicollis MX1]
          Length = 328

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 89/211 (42%), Gaps = 20/211 (9%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           L YT MIVAD+  +        F T E  +PL  Q    +   L  A +++  +  +   
Sbjct: 49  LAYTPMIVADSFTKSQWAREADFHTAEDDRPLVAQFAANNGPVLAHAVELMAPYA-DAFC 107

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSIPVTVKCRIGVDDQIPAVALR 137
           LN GCP     +   G  L LNPD + D +  A       PV+VK RI    +  A    
Sbjct: 108 LNCGCPQRWAIQDGLGCALTLNPDAMVDLVRHARAAVPHHPVSVKVRI----RDTAAETV 163

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            LV+  +  G   I +H R       +P +  +   + YD++ ++ K++  + +  NG +
Sbjct: 164 ELVRRAEAMGAAWISVHGR-------TPAERHQ--PVHYDML-KLVKDSVSVPVVANGDI 213

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
             +  A ++      DG+M  R    N  + 
Sbjct: 214 FTLKDADRVWNETGCDGIMAARGLLANPGLF 244


>gi|170767246|ref|ZP_02901699.1| tRNA-dihydrouridine synthase C [Escherichia albertii TW07627]
 gi|170123580|gb|EDS92511.1| tRNA-dihydrouridine synthase C [Escherichia albertii TW07627]
          Length = 316

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYLGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  D+ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLDIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|78213546|ref|YP_382325.1| dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9605]
 gi|78198005|gb|ABB35770.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9605]
          Length = 333

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 71/305 (23%), Positives = 133/305 (43%), Gaps = 38/305 (12%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G     +   + +  P+ +Q+       + 
Sbjct: 31  SDRVFRSLVRRWAPDALLFTEMVNATSLEMGHGLCKVESLAEESGPIGVQLFDHRPQAMA 90

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    + A+  A+++PVTVK 
Sbjct: 91  DAARRAEASGAFLIDINMGCPVRKIARKGGGSGLIRDPGLAIQIVEAVADAVAVPVTVKT 150

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIV 179
           R+G    D  P     +  + ++++G   + +H   R+   KG +          D+  +
Sbjct: 151 RLGWCGSDADPV----HWCQQLEQAGAQLLTLHGRTREQGFKGAA----------DWSSI 196

Query: 180 YEIKKENPDLFIGL--NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++    L I L  NG +     AL+ L      GVM+GR    +  ++  +D   + 
Sbjct: 197 RQVREA---LTIPLIANGDINSPDDALRCLKQTGAAGVMVGRGTMGSPWLVGQIDAALAG 253

Query: 236 ---PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P T     +  + +D    +     D+          L    +HM     GFP + R
Sbjct: 254 RSIPATPDPSARLALARDQLDGLVQDRGDHG---------LLIARKHMGWTCTGFPGASR 304

Query: 293 CRHIL 297
            RH L
Sbjct: 305 LRHDL 309


>gi|153831237|ref|ZP_01983904.1| NifR3/Smm1 family protein [Vibrio cholerae 623-39]
 gi|148873280|gb|EDL71415.1| NifR3/Smm1 family protein [Vibrio cholerae 623-39]
          Length = 331

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 110/245 (44%), Gaps = 22/245 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+  +  L      +N +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELC-LRYGAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLD 175
           VT+K R G D D    +++  L +     G+  + +H R    + KG            +
Sbjct: 145 VTLKTRTGWDTDNKNCLSIAQLAED---CGIQALALHGRTRACMYKG----------EAE 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K       I  NG ++   +A  +L     D  MIGR A     +   +  + 
Sbjct: 192 YDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADAXMIGRPAQGRPWIFQEIQHFL 250

Query: 234 SNPLT 238
            +  T
Sbjct: 251 EHGTT 255


>gi|238788774|ref|ZP_04632565.1| tRNA-dihydrouridine synthase C [Yersinia frederiksenii ATCC 33641]
 gi|238723079|gb|EEQ14728.1| tRNA-dihydrouridine synthase C [Yersinia frederiksenii ATCC 33641]
          Length = 310

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 88/188 (46%), Gaps = 16/188 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM +A+   +PVTVK R+G D          +  +++++G   + +H R       +  
Sbjct: 124 KAMREAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKD 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
           D  +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N  
Sbjct: 174 DGYQADRINWPAIGEIRQRLTIPVIA-NGEIWDYHSAQQCMKVTGCDAVMLGRGAL-NVP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVVKY 239


>gi|320155028|ref|YP_004187407.1| tRNA dihydrouridine synthase B [Vibrio vulnificus MO6-24/O]
 gi|319930340|gb|ADV85204.1| tRNA dihydrouridine synthase B [Vibrio vulnificus MO6-24/O]
          Length = 287

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 91/192 (47%), Gaps = 17/192 (8%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D   + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+   + A
Sbjct: 33  SVQIAGSDPQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLKYPDIIEQILKA 92

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDN 168
           +  A+ +PVT+K R G D +       ++ K  +  G+  + +H R    + KG      
Sbjct: 93  VVDAVDVPVTLKTRTGWDTENKNCI--HIAKLAEDCGIQALALHGRTKACMYKG------ 144

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
                 +YD +  +K+      I  NG ++   +A  +L     D +MIGR A     + 
Sbjct: 145 ----EAEYDSIKAVKQAVSIPVIA-NGDIDSPEKAKYVLEYTGADALMIGRPAQGRPWIF 199

Query: 227 TTVDEYFSNPLT 238
             +  Y  N  T
Sbjct: 200 QEIHHYLENGTT 211


>gi|127511264|ref|YP_001092461.1| nifR3 family TIM-barrel protein [Shewanella loihica PV-4]
 gi|126636559|gb|ABO22202.1| putative TIM-barrel protein, nifR3 family [Shewanella loihica PV-4]
          Length = 322

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 66/258 (25%), Positives = 119/258 (46%), Gaps = 29/258 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-AILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK +  +  + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLC-LRYGAALAVSEMLSSNPEVWDTDKSRQRMAHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 76  PDMMAHAALVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQQPELVKAILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + +H   R+ + KG          +
Sbjct: 136 VTLKIRTGW-----APEHRNGVHIAQIAQDCGIASLAVHGRTRQCMYKG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K+N  + +  NG +    +A  +L     D VMIGR A     +   +  
Sbjct: 181 AEYDTIRAI-KQNVSIPVVANGDICTPEKARSVLDYTGADAVMIGRGAQGRPWLFREIQH 239

Query: 232 YFSNPLTGSSPIKTRVDK 249
           Y     TG+      VD+
Sbjct: 240 YLE---TGNKLAPIEVDE 254


>gi|145297864|ref|YP_001140705.1| tRNA-dihydrouridine synthase B [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142850636|gb|ABO88957.1| tRNA-dihydrouridine synthase B [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 321

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 63/256 (24%), Positives = 116/256 (45%), Gaps = 26/256 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM++A+  +   +K  +    S +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELC-LRLGAGMAVSEMLLANPDVWDTQKTRMRMDHSAEGGLRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   +++N+GCP+ +V++   G+ L+ +PD+V     A+  A+ +P
Sbjct: 76  PEMMAFAARYNVEQGAQIVDINMGCPAKKVNKKLAGSALLRHPDLVRTICRAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
           VT+K R G D        RN   + +  +  G+  + +H R    + +G          +
Sbjct: 136 VTLKIRTGWDPDN-----RNGEEIARIAEDCGIAALAVHGRTRACLYRG----------H 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  I K+   + +  NG ++   +A  +L    VD VMIGRAA     +   +  
Sbjct: 181 AEYDTIKAI-KQAVSIPVVANGDIDSPEKARYVLDYTGVDAVMIGRAAQGRPWIFREIRH 239

Query: 232 YFSNPLTGSSPIKTRV 247
           +         P +  V
Sbjct: 240 FLETGTKLPPPEREEV 255


>gi|238794075|ref|ZP_04637692.1| tRNA-dihydrouridine synthase C [Yersinia intermedia ATCC 29909]
 gi|238726580|gb|EEQ18117.1| tRNA-dihydrouridine synthase C [Yersinia intermedia ATCC 29909]
          Length = 310

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 177 QAERINWQAISEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|261867320|ref|YP_003255242.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412652|gb|ACX82023.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 334

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 107/237 (45%), Gaps = 34/237 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTPSGTPVRVQLLGQHPQWLAENAELAVQLGSHGVDLNCGCPSKTVNGSNGGASLLKQP 116

Query: 102 DIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +++     A+   L++P    V+VK R+G D    A    ++  ++++ G   I IH R 
Sbjct: 117 ELIYQATKAI--RLAVPQHHTVSVKVRLGWDSTEFAY---DIADAVQQGGATEIAIHGR- 170

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMI 215
                 +  D  +   +++  + E++++     I  NG +   +  Q  + +   + +M+
Sbjct: 171 ------TKTDGYRADRINWQKIGEVRQKLKIPVIA-NGEIWRWADGQQCRDVTGCEDLMV 223

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA-RHLHSGG 271
           GR A  N   L+ V +  + PL+             W +I   +  YAA  + H  G
Sbjct: 224 GRGAL-NIPNLSRVLKRNAAPLS-------------WAEIMPILRKYAALENCHDSG 266


>gi|302670253|ref|YP_003830213.1| tRNA dihydrouridine synthase A DusA1 [Butyrivibrio proteoclasticus
           B316]
 gi|302394726|gb|ADL33631.1| tRNA dihydrouridine synthase A DusA1 [Butyrivibrio proteoclasticus
           B316]
          Length = 343

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 4/118 (3%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           I GF      +  QI    +   V AAK + + GYNE+NLN+GCP+A V     G+ L+ 
Sbjct: 72  IKGFEDYGNEIVPQIMSNRVDTFVWAAKEMWNLGYNEVNLNLGCPAATVTNSHKGSGLLT 131

Query: 100 NPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           + + +   +  + + L +  +++K R+G  D+  A     L++   K  ++ + IHAR
Sbjct: 132 DTEYLDSMLDGIFEDLGNKSISIKTRLGFSDESEA---DRLMEIYAKYPISELTIHAR 186


>gi|333001275|gb|EGK20843.1| dihydrouridine synthase family protein [Shigella flexneri VA-6]
          Length = 327

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|71411788|ref|XP_808128.1| dihydrouridine synthase (Dus) [Trypanosoma cruzi strain CL Brener]
 gi|70872267|gb|EAN86277.1| dihydrouridine synthase (Dus), putative [Trypanosoma cruzi]
          Length = 548

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 67/147 (45%), Gaps = 5/147 (3%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           R+F+       L  T     +     D          + PL +Q  G D   L+ AA+ V
Sbjct: 142 RYFSTTPHRAELAMTATASGEGEAAEDAGRTSDGEETDHPLFVQFCGNDADTLLAAARHV 201

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
           ED     +++N+GCP      G +G+ LM + D V + +  +   L +PVT K R+  DD
Sbjct: 202 ED-DCEAVDVNLGCPQGIARRGHYGSFLMEDWDRVHNILHCLAVELRVPVTAKMRVFDDD 260

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHAR 156
              A+ L+   + ++ +G+  + +H R
Sbjct: 261 ---ALTLK-YAEMLRDTGIAVLCVHGR 283


>gi|331647791|ref|ZP_08348883.1| tRNA-dihydrouridine synthase C [Escherichia coli M605]
 gi|330911973|gb|EGH40483.1| tRNA-dihydrouridine synthase C [Escherichia coli AA86]
 gi|331043515|gb|EGI15653.1| tRNA-dihydrouridine synthase C [Escherichia coli M605]
          Length = 316

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|328955422|ref|YP_004372755.1| tRNA-U20-dihydrouridine synthase [Coriobacterium glomerans PW2]
 gi|328455746|gb|AEB06940.1| tRNA-U20-dihydrouridine synthase [Coriobacterium glomerans PW2]
          Length = 328

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 96/229 (41%), Gaps = 23/229 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKP-LALQIGGAD 58
           M   TD  YR   R      L Y+EM+    +     + I L     E+P L++Q+ G+ 
Sbjct: 17  MAGVTDAAYRIMCRR-HGAVLAYSEMVSVAGLAFASARTIELAEPHAEEPQLSVQLFGSK 75

Query: 59  ISKLVEAAKIVEDFGYNEINL---NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            ++   A ++++      ++L   N+ CP  +V     GA LM  PD+    + A     
Sbjct: 76  PAQFAAAVEMIQQRVGERLSLVDINMACPVRKVVSKGEGAALMDKPDLAARIVRACVSVA 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPN 173
            +PVT K RIG            L + +++ G+  + +H R A  + +G           
Sbjct: 136 RVPVTAKIRIGTRSGTRTAP--ELARRLEQEGLAAVAVHGRTAAQLYRG----------R 183

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
            D+ I+ E+        IG +G +     A+ +L   +   VMI R +Y
Sbjct: 184 ADWSIIDEVACGVTIPVIG-SGDVLTAEAAVAMLRDTAASAVMIARGSY 231


>gi|164428803|ref|XP_956375.2| hypothetical protein NCU00065 [Neurospora crassa OR74A]
 gi|157072287|gb|EAA27139.2| conserved hypothetical protein [Neurospora crassa OR74A]
          Length = 576

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 51/215 (23%), Positives = 97/215 (45%), Gaps = 26/215 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++ L +Q    D + L+ AAK+V  +  + ++LN+GCP      G +G+ L  N +++ +
Sbjct: 81  DRSLFVQFCANDPAYLLSAAKLVAPY-CDAVDLNLGCPQGIAKRGQYGSFLQENQELIFE 139

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  + K L IPVT K RI +D +    A     +++ ++G + + +H R+   KG    
Sbjct: 140 LINTLHKELDIPVTAKIRI-LDTK---EATLKYAQNVLRAGASILTVHGRRREQKG---- 191

Query: 167 DNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNS 223
              +    D++ +  +++  P +  I  NG +   +   K L +   DGVM       + 
Sbjct: 192 --HQTGLADWEYIRYLRENLPKETVIFANGNILQHADLEKCLAATGADGVMSAEGNLSDP 249

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            +       F+ P     P      +++WR    S
Sbjct: 250 GL-------FARP-----PAVGEEGREYWRSKDGS 272


>gi|320196009|gb|EFW70633.1| tRNA-dihydrouridine synthase C [Escherichia coli WV_060327]
          Length = 315

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMTISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|127513170|ref|YP_001094367.1| dihydrouridine synthase, DuS [Shewanella loihica PV-4]
 gi|126638465|gb|ABO24108.1| dihydrouridine synthase, DuS [Shewanella loihica PV-4]
          Length = 309

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G + + + E A    + G   ++LN GCP+  V+    GA L+  P+ +    
Sbjct: 64  PVRLQLLGQEPNWMAENAIRAVELGSRGVDLNYGCPAPMVNRSKGGAALLKEPETIYRVT 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+    PV+ K R+G DD+        + ++I+ +G   + +HAR         K
Sbjct: 124 QAVRQAVPKDKPVSAKIRLGWDDKSRCT---EIAQAIEAAGATELTVHART--------K 172

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +    P   ++ + +IK     L I  NG +      LK   +   D VM+GR A
Sbjct: 173 EEAYRPPAHWEYIAQIKSVT-RLPIIANGEIWGREDYLKCREASGCDDVMLGRGA 226


>gi|315305585|ref|ZP_07875289.1| tRNA-dihydrouridine synthase B [Listeria ivanovii FSL F6-596]
 gi|313626046|gb|EFR95474.1| tRNA-dihydrouridine synthase B [Listeria ivanovii FSL F6-596]
          Length = 147

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 62  LVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           LVEAAK V E+   + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVT
Sbjct: 1   LVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVT 60

Query: 121 VKCRIGVDDQ 130
           VK RIG D++
Sbjct: 61  VKMRIGWDEE 70


>gi|310767077|gb|ADP12027.1| tRNA-dihydrouridine synthase C [Erwinia sp. Ejp617]
          Length = 310

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 RAAVPAHLPVTVKVRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   +Q    +   D VMIGR A  N   L+
Sbjct: 177 RAEAINWQAIGEIRQRLTIPVIA-NGEIWDWHSAQDCMAVTGCDAVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|237704605|ref|ZP_04535086.1| tRNA-dihydrouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|226900971|gb|EEH87230.1| tRNA-dihydrouridine synthase C [Escherichia sp. 3_2_53FAA]
          Length = 332

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 83  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 142

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 143 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 192

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 193 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 250

Query: 228 TVDEY 232
            V +Y
Sbjct: 251 RVVKY 255


>gi|323977672|gb|EGB72758.1| dihydrouridine synthase [Escherichia coli TW10509]
          Length = 316

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|283832436|ref|ZP_06352177.1| tRNA-dihydrouridine synthase [Citrobacter youngae ATCC 29220]
 gi|291072092|gb|EFE10201.1| tRNA-dihydrouridine synthase [Citrobacter youngae ATCC 29220]
          Length = 316

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D+         +  +++++G + + +H R       + +   
Sbjct: 127 REAVPDHLPVTVKVRLGWDNSDRQF---EIADAVQQAGASELAVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLT 227
           K  ++++  + EI++      I  NG + D   +Q    +   D VMIGR A  N   L+
Sbjct: 177 KAEHINWQAIGEIRQRLTIPVIA-NGEIWDWQSAQDCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|294655111|ref|XP_457209.2| DEHA2B05720p [Debaryomyces hansenii CBS767]
 gi|199429699|emb|CAG85204.2| DEHA2B05720p [Debaryomyces hansenii]
          Length = 446

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 15/132 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVG 105
           L  QIG AD    V+AAKIV     + I+LN GCP         GA L+  PD    I+ 
Sbjct: 151 LIFQIGSADPELAVQAAKIVAQ-DVDGIDLNCGCPKPFSTHSGMGAALLTTPDLLESILR 209

Query: 106 DCIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           + ++ + K   IP++ K R+  D D  P++    L+  + K+G++ + +H R   ++   
Sbjct: 210 NLVSEVGKVYDIPISAKIRLLDDTDVTPSL---ELIDRLCKTGISNLTLHCRTPRMR--- 263

Query: 165 PKDNRKIPNLDY 176
              NR  P  D+
Sbjct: 264 ---NRDTPVRDF 272


>gi|261822179|ref|YP_003260285.1| tRNA-dihydrouridine synthase C [Pectobacterium wasabiae WPP163]
 gi|261606192|gb|ACX88678.1| dihydrouridine synthase DuS [Pectobacterium wasabiae WPP163]
          Length = 310

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   + +   D +M+GR A  N   L+
Sbjct: 177 KAECINWQAIGEIRQRLRIPVIA-NGEIWDWQSAQDCMATTGCDAIMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|169845921|ref|XP_001829678.1| tRNA-dihydrouridine synthase 1 [Coprinopsis cinerea okayama7#130]
 gi|116509234|gb|EAU92129.1| tRNA-dihydrouridine synthase 1 [Coprinopsis cinerea okayama7#130]
          Length = 561

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 61/250 (24%), Positives = 113/250 (45%), Gaps = 28/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA----DAILRGDKKNILGFSTQE-------KP 49
           MVD ++  +R   R      L+YT MI A    D + +  + +    ++ E       +P
Sbjct: 41  MVDQSELAFRRLCRQY-GAQLIYTPMINAKMFTDPVNKSYRASAFDIASGEEGDMASDRP 99

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L +Q    D  +L+++AK+VE +  + +++N+GCP      G +G+ L  +  ++   I 
Sbjct: 100 LIVQFCANDPDQLLQSAKVVEKY-CDAVDINLGCPQDIAKRGRYGSFLQDDWPLIYSMIN 158

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +   LSIPVT K R+  D +          K ++++G   +  H R    +G     N 
Sbjct: 159 TLHVNLSIPVTAKFRVFPDVE----KTVEYAKMLERAGAQILTCHGRIREQRG----QNT 210

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
            +   D+  +  + KE   + +  NG +   +D+++ L+     DGVM       N A+ 
Sbjct: 211 GL--ADWSKIRAV-KEAVKVPVFANGNILFQDDIARCLEET-GCDGVMSAEGILYNPALF 266

Query: 227 TTVDEYFSNP 236
             +D   S+P
Sbjct: 267 YGLDAPSSSP 276


>gi|260828450|ref|XP_002609176.1| hypothetical protein BRAFLDRAFT_92533 [Branchiostoma floridae]
 gi|229294531|gb|EEN65186.1| hypothetical protein BRAFLDRAFT_92533 [Branchiostoma floridae]
          Length = 578

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 54/212 (25%), Positives = 92/212 (43%), Gaps = 15/212 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNV 81
           EM +A  +L+G      +L     E    +QI G+    +   A+++ D    + +++NV
Sbjct: 262 EMAMASNLLQGQSSEWALLKRHQSEDVFGVQICGSHPEVMSHVAELLNDTISVDFVDVNV 321

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V +   G  LM         +  M   L +P+TVK R G+ ++ P  A R +V 
Sbjct: 322 GCPIDLVFKRGGGCALMGRLTKFEQVVKGMIGMLDVPLTVKMRTGIYEEKP-FAYR-VVP 379

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            ++  GV+ + +H R         ++ R     D+D + E  K    + +  NG +    
Sbjct: 380 HLRDWGVSLVTLHGRS--------REQRYTKLADWDYISECAKAASPMPLFGNGDILSFE 431

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
            A +   S  V G+MI R A     + T + E
Sbjct: 432 DANRHRESTGVAGLMIARGALIKPWIFTEIKE 463


>gi|26248520|ref|NP_754560.1| tRNA-dihydrouridine synthase C [Escherichia coli CFT073]
 gi|91211426|ref|YP_541412.1| tRNA-dihydrouridine synthase C [Escherichia coli UTI89]
 gi|191169962|ref|ZP_03031516.1| tRNA-dihydrouridine synthase C [Escherichia coli F11]
 gi|218690289|ref|YP_002398501.1| tRNA-dihydrouridine synthase C [Escherichia coli ED1a]
 gi|227887195|ref|ZP_04005000.1| tRNA-dihydrouridine synthase C [Escherichia coli 83972]
 gi|300981485|ref|ZP_07175566.1| dihydrouridine synthase [Escherichia coli MS 200-1]
 gi|300982854|ref|ZP_07176318.1| dihydrouridine synthase [Escherichia coli MS 45-1]
 gi|306814745|ref|ZP_07448907.1| tRNA-dihydrouridine synthase C [Escherichia coli NC101]
 gi|26108925|gb|AAN81128.1|AE016763_87 Hypothetical protein yohI [Escherichia coli CFT073]
 gi|91073000|gb|ABE07881.1| hypothetical protein YohI [Escherichia coli UTI89]
 gi|190909478|gb|EDV69063.1| tRNA-dihydrouridine synthase C [Escherichia coli F11]
 gi|218427853|emb|CAR08768.2| tRNA-dihydrouridine synthase C [Escherichia coli ED1a]
 gi|227835545|gb|EEJ46011.1| tRNA-dihydrouridine synthase C [Escherichia coli 83972]
 gi|300307558|gb|EFJ62078.1| dihydrouridine synthase [Escherichia coli MS 200-1]
 gi|300408654|gb|EFJ92192.1| dihydrouridine synthase [Escherichia coli MS 45-1]
 gi|305852139|gb|EFM52591.1| tRNA-dihydrouridine synthase C [Escherichia coli NC101]
 gi|307626319|gb|ADN70623.1| tRNA-dihydrouridine synthase C [Escherichia coli UM146]
 gi|312946758|gb|ADR27585.1| tRNA-dihydrouridine synthase C [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315285789|gb|EFU45229.1| dihydrouridine synthase [Escherichia coli MS 110-3]
 gi|315294495|gb|EFU53843.1| dihydrouridine synthase [Escherichia coli MS 153-1]
 gi|324013979|gb|EGB83198.1| dihydrouridine synthase [Escherichia coli MS 60-1]
          Length = 338

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|331653569|ref|ZP_08354570.1| tRNA-dihydrouridine synthase C [Escherichia coli M718]
 gi|331048418|gb|EGI20494.1| tRNA-dihydrouridine synthase C [Escherichia coli M718]
          Length = 294

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|260903895|ref|ZP_05912217.1| putative TIM-barrel protein, nifR3 family [Brevibacterium linens
           BL2]
          Length = 396

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 72/314 (22%), Positives = 127/314 (40%), Gaps = 36/314 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  TEM+ + A++    K+  I+     E P ++Q+ G D
Sbjct: 36  MAGITNTAFRRLCREY-GAGLYVTEMVTSRALVERSPKSMRIIRHEPYETPRSVQLYGVD 94

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A + +VE+   + I+LN GCP  +V     G+ L    D+    +         
Sbjct: 95  PVTIGQAVRMLVEEDRADHIDLNFGCPVPKVTRKGGGSALPWKKDLFESIVTTAVTEADR 154

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             IP+TVK R G+D         +  ++ + +GV  + +H R A  +  G          
Sbjct: 155 GGIPLTVKMRKGIDKD--HQTFLDAGETARNAGVAAVALHGRSAADLYSG---------- 202

Query: 173 NLDYDIVYEIKKENPDLFIGL-NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
             D+D +  +K    D    L NG +     AL+++     DGV+IGR       +   +
Sbjct: 203 QADWDAIARLKDHLGDTVPVLGNGDIFAAEDALEMMRRTGCDGVVIGRGCQGRPWLFGDL 262

Query: 230 DEYFSNPLTGSS----PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
               +N L GS     P    V +  + K    + +Y     +    ++ + +H+   F 
Sbjct: 263 ----ANALNGSDERFRPGLAEVARAVY-KHGEYLAEYYEDEFYG---VRDLRKHIAWYFK 314

Query: 286 GFPNSRRCRHILTV 299
           G+P     R  L +
Sbjct: 315 GYPVGGDLRRQLAM 328


>gi|325275792|ref|ZP_08141661.1| tRNA-dihydrouridine synthase C [Pseudomonas sp. TJI-51]
 gi|324099063|gb|EGB97040.1| tRNA-dihydrouridine synthase C [Pseudomonas sp. TJI-51]
          Length = 322

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 112/233 (48%), Gaps = 23/233 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPLCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+   IPVT K R+G D   PA AL +   ++   G   + +HAR  + +G  P 
Sbjct: 124 HAVRRAVPAHIPVTAKMRLGFDS--PAGAL-DCAMALADGGSAHLVVHARTKV-EGYKPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D+V      N +++      ++D  +  ++  + D +M+GR       + 
Sbjct: 180 AHWEWVARVQDVVKVPVFANGEIWT-----VDDWRRCREVSGAED-IMLGRGLVSRPDLG 233

Query: 227 TTV----DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
             +    D     PL G   ++  + ++FWR+  A ++       ++ G+L+Q
Sbjct: 234 LQIAAARDGRDYQPL-GWQDLQPLL-REFWRQAQAKLSPR-----YAPGRLKQ 279


>gi|323968058|gb|EGB63468.1| dihydrouridine synthase [Escherichia coli M863]
 gi|327253266|gb|EGE64920.1| dihydrouridine synthase family protein [Escherichia coli STEC_7v]
          Length = 315

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|311063903|ref|YP_003970628.1| tRNA-dihydrouridine synthase [Bifidobacterium bifidum PRL2010]
 gi|310866222|gb|ADP35591.1| tRNA-dihydrouridine synthase [Bifidobacterium bifidum PRL2010]
          Length = 413

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 67/135 (49%), Gaps = 8/135 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 53  MAGVTNWPFRVLCEEYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVN 112

Query: 59  ISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCK 113
            + + +AA+IV  ED   + ++LN GCP  +V     G+ L    D+  + I     +C 
Sbjct: 113 PAIVEQAARIVVDEDMA-DHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCS 171

Query: 114 ALSIPVTVKCRIGVD 128
             +IPVT K R+G+D
Sbjct: 172 TANIPVTAKIRVGID 186


>gi|308470958|ref|XP_003097711.1| hypothetical protein CRE_14205 [Caenorhabditis remanei]
 gi|308239829|gb|EFO83781.1| hypothetical protein CRE_14205 [Caenorhabditis remanei]
          Length = 436

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 103/225 (45%), Gaps = 23/225 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLA-LQIGGADISKLVEAA 66
           +   + +  L+ +  ++ DA+   D +N    IL  + +EK    LQIG     K  + A
Sbjct: 35  YTEEIVDKKLIESTRVINDALGTIDYRNGDDIILRLAPEEKGRCILQIGTNSGEKAAKIA 94

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +IV D     I++N+GCP         GA L+   + + D + ++  A  +PVT  C+I 
Sbjct: 95  EIVGD-DVAGIDVNMGCPKPFSIHCGMGAALLTQTEKIIDILKSLKAAAKVPVT--CKIR 151

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK-- 184
           V D  P   L+ LV+ I+K GV+ + +H R+        +D R+      + + E+ +  
Sbjct: 152 VLDN-PEDTLK-LVREIEKCGVSALGVHGRR--------RDERQPDQCRIEEIREVSRTI 201

Query: 185 -ENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAML 226
              P +  G +G +E  S   K   + +   +MI R A    ++ 
Sbjct: 202 TTIPIIANGFSGEIEQFSDIEKWRSATETSSIMIARKALSTPSIF 246


>gi|209882371|ref|XP_002142622.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209558228|gb|EEA08273.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 405

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 80/165 (48%), Gaps = 7/165 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  YR   R    + L +T M  +     L G +         +KPL LQ  G +
Sbjct: 21  MVDASELAYRLLCRKYGCD-LAFTPMYHSGLFSKLSGYRNTNFQTCDDDKPLILQFCGNN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSI 117
              +++A+K +++     I+LN GCP      G +GA L+  P+++   ++ +  + L  
Sbjct: 80  PEVILQASKYIDN-KVQGIDLNFGCPQNIAKRGHYGAFLLEEPELMESLVSKLVNSDLKC 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           PV+ K R+   + +      N++  ++++G++ + +H R    KG
Sbjct: 139 PVSCKIRLVCKNDLQKTI--NIMYRLEQAGISMLTVHGRTLKDKG 181


>gi|300821757|ref|ZP_07101902.1| dihydrouridine synthase [Escherichia coli MS 119-7]
 gi|300924857|ref|ZP_07140792.1| dihydrouridine synthase [Escherichia coli MS 182-1]
 gi|301328613|ref|ZP_07221674.1| dihydrouridine synthase [Escherichia coli MS 78-1]
 gi|309793018|ref|ZP_07687446.1| dihydrouridine synthase [Escherichia coli MS 145-7]
 gi|331668839|ref|ZP_08369687.1| tRNA-dihydrouridine synthase C [Escherichia coli TA271]
 gi|331678088|ref|ZP_08378763.1| tRNA-dihydrouridine synthase C [Escherichia coli H591]
 gi|300418974|gb|EFK02285.1| dihydrouridine synthase [Escherichia coli MS 182-1]
 gi|300525599|gb|EFK46668.1| dihydrouridine synthase [Escherichia coli MS 119-7]
 gi|300845005|gb|EFK72765.1| dihydrouridine synthase [Escherichia coli MS 78-1]
 gi|308123304|gb|EFO60566.1| dihydrouridine synthase [Escherichia coli MS 145-7]
 gi|331064033|gb|EGI35944.1| tRNA-dihydrouridine synthase C [Escherichia coli TA271]
 gi|331074548|gb|EGI45868.1| tRNA-dihydrouridine synthase C [Escherichia coli H591]
          Length = 315

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|282856150|ref|ZP_06265433.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pyramidobacter
           piscolens W5455]
 gi|282585909|gb|EFB91194.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pyramidobacter
           piscolens W5455]
          Length = 333

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/151 (27%), Positives = 72/151 (47%), Gaps = 7/151 (4%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA- 66
           R F RL    AL +TEM+ +  +L    K   +   + +E+PL LQ+   D   L  +A 
Sbjct: 31  RLFRRL--GAALTHTEMVSSAGLLYAGTKTWQMTECTDEERPLVLQLFTGDADSLCRSAE 88

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR-I 125
           + ++   Y    +N+ CP  +VH+   G+ L+ NPD+    +  + K   +PV  K R I
Sbjct: 89  RCLQSRSYAAFGVNMACPMPKVHKKGAGSRLLQNPDVAFAMVREL-KKFGLPVWPKIRKI 147

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             D +   +      + + ++G + + IH R
Sbjct: 148 VPDGREYRLDTLQFAEGLLEAGADNVTIHGR 178


>gi|225374618|ref|ZP_03751839.1| hypothetical protein ROSEINA2194_00234 [Roseburia inulinivorans DSM
           16841]
 gi|225213543|gb|EEG95897.1| hypothetical protein ROSEINA2194_00234 [Roseburia inulinivorans DSM
           16841]
          Length = 326

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 59/262 (22%), Positives = 107/262 (40%), Gaps = 34/262 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           R+F   +TN  L +             KK+I     Q   +  QI        +     +
Sbjct: 29  RYFTPFITNKKLDFKV-----------KKDIDPEHNQGMEVVPQILTNQPDDFISIVNQL 77

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
           + +GY+E+NLN+GCPS  V   + GA  +  PD +   +  +  A    +++K R+G D 
Sbjct: 78  KQYGYDEVNLNLGCPSGTVVAKNRGAGFLAVPDELDSFLDKIFNACDCKISIKTRVGKDS 137

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                   NL+   +K  ++ + +H R  I K       +  P ++    Y+   E+   
Sbjct: 138 ---PDEWENLLAIYEKYPLSELIVHPR--IQKDFY----KYTPRME---TYQYAAEHSRH 185

Query: 190 FIGLNGGLEDM---SQALKILPSVDGVMIGRAAYKNSAM---LTTVDEYFSNPLTGSSPI 243
            +  NG +  +    +  +  P  + VM+GR   ++  +   L  V+  F+   TG +P+
Sbjct: 186 SLCFNGDIHSVGAYGRLRQTFPETEKVMLGRGILQDPGLVGELRMVEAQFAAKDTG-TPV 244

Query: 244 KTR----VDKDFWRKISASMTD 261
             +    VDK   R     + D
Sbjct: 245 GNKKCNVVDKQTLRAFHDDICD 266


>gi|210615986|ref|ZP_03290886.1| hypothetical protein CLONEX_03105 [Clostridium nexile DSM 1787]
 gi|210149991|gb|EEA81000.1| hypothetical protein CLONEX_03105 [Clostridium nexile DSM 1787]
          Length = 316

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 64/257 (24%), Positives = 101/257 (39%), Gaps = 33/257 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K IL    Q   +  QI   +    +  A+   ++GY EINLN+GCPS  V     G+  
Sbjct: 49  KEILPQHNQGLCVVPQILTNNAEDFIRTAQEFREYGYEEINLNLGCPSGTVTAKKKGSGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +  PD +   +  + +     +++K RIGV+          L+    K  +  + IH R 
Sbjct: 109 LGYPDELERFLYEIFERTESKISIKTRIGVEH---PEEFERLLNIYNKFEMEELIIHPR- 164

Query: 158 AILKGLSPKDNRKIPNLDY--DIVYEIKKE---NPDLFIGLNGGLEDMSQALKILPSVDG 212
                +     +  PN++     V E K     N DLFI             K  P V+ 
Sbjct: 165 -----VRADFYKNKPNMEVFGQAVKESKNRLCYNGDLFIK-----SHFEAFEKEYPQVER 214

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSS---PIKTRVDKDFWRKISASMTDYAARHLHS 269
           VM+GR    N  +L  + E       G S    +      +F+RK    ++   A     
Sbjct: 215 VMLGRGVMVNPGLLNLICE-------GKSLDKEVLRAFQDEFYRKNQEVLSGDRAVLF-- 265

Query: 270 GGKLQQITRHMIGLFHG 286
             K++++   MI LF G
Sbjct: 266 --KMKELWFFMIHLFEG 280


>gi|300918780|ref|ZP_07135349.1| dihydrouridine synthase [Escherichia coli MS 115-1]
 gi|300414023|gb|EFJ97333.1| dihydrouridine synthase [Escherichia coli MS 115-1]
          Length = 337

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|90407636|ref|ZP_01215816.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
 gi|90311227|gb|EAS39332.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
          Length = 313

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 56/200 (28%), Positives = 100/200 (50%), Gaps = 29/200 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IV 104
           P+ +Q+ G D   L   A+     G + I+LN GCP+  V++   GA L+ +P+    IV
Sbjct: 64  PVRIQLLGQDPQCLANNARKALLVGSDGIDLNFGCPAKAVNKSKGGAILLKSPETLYKIV 123

Query: 105 GDCIAAM--CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +  A+M  C+ LS    VK R+G  D+  ++A+ N  ++I ++G N + +HAR      
Sbjct: 124 KEVRASMHTCETLS----VKIRLGYADK--SLAIEN-AQAICEAGANELAVHART----- 171

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
              K+    P   +  + +I +E+ D+ +  NG +   ED  +  +I      +MIGR A
Sbjct: 172 ---KEEGYAPPAHWHWIAKI-RESIDIPVTANGDIFSAEDAKRCHEI-SGCHSLMIGRGA 226

Query: 220 YKN---SAMLTTVDEYFSNP 236
                 + ++  ++E +S P
Sbjct: 227 LATPNLAQVIKGIEEPYSWP 246


>gi|10436076|dbj|BAB14740.1| unnamed protein product [Homo sapiens]
          Length = 650

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 335 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 390

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 391 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 449

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 450 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 499

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 500 ILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 548

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 549 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 586


>gi|166364397|ref|YP_001656670.1| nitrogen regulation protein NifR3-like protein [Microcystis
           aeruginosa NIES-843]
 gi|166086770|dbj|BAG01478.1| nitrogen regulation protein NifR3 homolog [Microcystis aeruginosa
           NIES-843]
          Length = 258

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 86/189 (45%), Gaps = 18/189 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           V A K V++ G   I++N+GCP  ++ +   G+ L+  P+I    +  +  A+S+PVTVK
Sbjct: 13  VAAEKAVKE-GAMTIDINMGCPVNKITKKGGGSSLLRQPEIAEQIVREVVGAVSVPVTVK 71

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G + Q   + + +  + ++ +G   + +HAR        P D + I  +        
Sbjct: 72  TRLGWNAQ--EINIIDFARRLEDAGAQMLTLHARTREQGYHGPADWQWIKRV-------- 121

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            KE   + +  NG +  +  A+  L     DGVM  R       ++  +D Y     TG 
Sbjct: 122 -KEVLSIPVIANGDIVSVEAAINCLEFTRADGVMCSRGTLGYPYLVGEIDYYLK---TGK 177

Query: 241 S-PIKTRVD 248
             P  T +D
Sbjct: 178 KLPKPTSID 186


>gi|300935056|ref|ZP_07150087.1| dihydrouridine synthase [Escherichia coli MS 21-1]
 gi|331663636|ref|ZP_08364546.1| tRNA-dihydrouridine synthase C [Escherichia coli TA143]
 gi|300459637|gb|EFK23130.1| dihydrouridine synthase [Escherichia coli MS 21-1]
 gi|320199735|gb|EFW74324.1| tRNA-dihydrouridine synthase C [Escherichia coli EC4100B]
 gi|331059435|gb|EGI31412.1| tRNA-dihydrouridine synthase C [Escherichia coli TA143]
 gi|333002858|gb|EGK22414.1| dihydrouridine synthase family protein [Shigella flexneri K-272]
 gi|333016862|gb|EGK36186.1| dihydrouridine synthase family protein [Shigella flexneri K-227]
          Length = 315

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|229844973|ref|ZP_04465110.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           6P18H1]
 gi|229812107|gb|EEP47799.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           6P18H1]
          Length = 310

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 62/117 (52%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF++   P+ +Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P
Sbjct: 57  GFTSSGTPVRVQLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +++     A+ +A+    PV+VK R+G D+   A  + +   ++++ G   I +H R
Sbjct: 117 ELIYRATQALRQAVPSEFPVSVKVRLGWDNISQAFEIAD---AVEQGGATEITVHGR 170


>gi|110642349|ref|YP_670079.1| tRNA-dihydrouridine synthase C [Escherichia coli 536]
 gi|117624342|ref|YP_853255.1| tRNA-dihydrouridine synthase C [Escherichia coli APEC O1]
 gi|215487361|ref|YP_002329792.1| tRNA-dihydrouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218559058|ref|YP_002391971.1| tRNA-dihydrouridine synthase C [Escherichia coli S88]
 gi|312967433|ref|ZP_07781648.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           2362-75]
 gi|331683817|ref|ZP_08384413.1| tRNA-dihydrouridine synthase C [Escherichia coli H299]
 gi|38604879|sp|Q8FFV5|DUSC_ECOL6 RecName: Full=tRNA-dihydrouridine synthase C
 gi|110343941|gb|ABG70178.1| tRNA-dihydrouridine synthase C [Escherichia coli 536]
 gi|115513466|gb|ABJ01541.1| tRNA-dihydrouridine synthase C [Escherichia coli APEC O1]
 gi|215265433|emb|CAS09834.1| tRNA-dihydrouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218365827|emb|CAR03568.1| tRNA-dihydrouridine synthase C [Escherichia coli S88]
 gi|222033901|emb|CAP76642.1| tRNA-dihydrouridine synthase C [Escherichia coli LF82]
 gi|281179232|dbj|BAI55562.1| putative regulator protein [Escherichia coli SE15]
 gi|294493936|gb|ADE92692.1| tRNA-dihydrouridine synthase C [Escherichia coli IHE3034]
 gi|307554209|gb|ADN46984.1| tRNA-dihydrouridine synthase C [Escherichia coli ABU 83972]
 gi|312287630|gb|EFR15535.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           2362-75]
 gi|320186769|gb|EFW61491.1| tRNA-dihydrouridine synthase C [Shigella flexneri CDC 796-83]
 gi|323188135|gb|EFZ73430.1| dihydrouridine synthase family protein [Escherichia coli RN587/1]
 gi|323951936|gb|EGB47810.1| dihydrouridine synthase [Escherichia coli H252]
 gi|323955905|gb|EGB51658.1| dihydrouridine synthase [Escherichia coli H263]
 gi|331078769|gb|EGI49971.1| tRNA-dihydrouridine synthase C [Escherichia coli H299]
          Length = 316

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|194759368|ref|XP_001961921.1| GF14697 [Drosophila ananassae]
 gi|190615618|gb|EDV31142.1| GF14697 [Drosophila ananassae]
          Length = 395

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 108/238 (45%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     F+T   ++PL  Q    D
Sbjct: 29  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFTTGPDDQPLVAQFAAKD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  L+  P++V + +  + + L   
Sbjct: 88  ATEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGLLRQPEVVREVVQQVRRTLPSD 146

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G +  +       L + ++++G   + +H R       +P        LD
Sbjct: 147 FSVSVKMRLLGGESSLERTI--ELARQLEQAGATFLTLHGR-------TPAQKHSKDTLD 197

Query: 176 YDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTV 229
              + E+++    L I L  NG +E  + A ++       GVM  R    N A+  + 
Sbjct: 198 IGAMSEVRQ---SLRIPLIVNGNVESWADACELSEKTGAAGVMAARGLLANPALFNSA 252


>gi|189055070|dbj|BAG38054.1| unnamed protein product [Homo sapiens]
          Length = 650

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 335 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 390

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 391 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 449

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 450 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 499

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 500 ILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 548

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 549 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 586


>gi|239788462|ref|NP_064560.2| tRNA-dihydrouridine synthase 3-like isoform 1 [Homo sapiens]
 gi|110808212|sp|Q96G46|DUS3L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 3-like
          Length = 650

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 335 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 390

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 391 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 449

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 450 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 499

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 500 ILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 548

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 549 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 586


>gi|254519722|ref|ZP_05131778.1| dihydrouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226913471|gb|EEH98672.1| dihydrouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 319

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 46/183 (25%), Positives = 81/183 (44%), Gaps = 21/183 (11%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GY+EINLN+GCPS  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDSDGFITTARKLQQLGYSEINLNLGCPSGTVVSKNRGSGFLAKREELDKFLDEIY 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSP-----K 166
           K   + +++K RIG D    +     L+K   K  +  + IH R +    G  P     K
Sbjct: 124 KIDDMKISIKTRIGKD---SSEEFYELIKIYNKYPLEELIIHPRTREDFYGNKPNLEVFK 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D   + N    + Y     N D+F      L+D ++  K  P ++ +M+GR    N  ++
Sbjct: 181 DALTLSNS--PVCY-----NGDIFT-----LDDYNKLSKEFPELNTIMLGRGVLANPGLI 228

Query: 227 TTV 229
             +
Sbjct: 229 NEI 231


>gi|323152368|gb|EFZ38657.1| dihydrouridine synthase family protein [Escherichia coli EPECa14]
          Length = 306

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 57  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 116

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 117 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 166

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 167 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 224

Query: 228 TVDEY 232
            V +Y
Sbjct: 225 RVVKY 229


>gi|255744093|ref|ZP_05418047.1| tRNA dihydrouridine synthase B [Vibrio cholera CIRS 101]
 gi|262161983|ref|ZP_06031000.1| tRNA dihydrouridine synthase B [Vibrio cholerae INDRE 91/1]
 gi|262167985|ref|ZP_06035684.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC27]
 gi|262192555|ref|ZP_06050705.1| tRNA dihydrouridine synthase B [Vibrio cholerae CT 5369-93]
 gi|255738358|gb|EET93749.1| tRNA dihydrouridine synthase B [Vibrio cholera CIRS 101]
 gi|262023518|gb|EEY42220.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC27]
 gi|262028361|gb|EEY47017.1| tRNA dihydrouridine synthase B [Vibrio cholerae INDRE 91/1]
 gi|262031600|gb|EEY50188.1| tRNA dihydrouridine synthase B [Vibrio cholerae CT 5369-93]
 gi|327483164|gb|AEA77571.1| tRNA dihydrouridine synthase B [Vibrio cholerae LMA3894-4]
          Length = 287

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 93/193 (48%), Gaps = 19/193 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D   + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A
Sbjct: 33  SVQIAGSDPQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKA 92

Query: 111 MCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKD 167
           +  A+++PVT+K R G D D    +++  L +     G+  + +H R    + KG     
Sbjct: 93  VVNAVNVPVTLKTRTGWDTDNKNCLSIAQLAEDC---GIQALALHGRTRACMYKG----- 144

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                  +YD +  +K       I  NG ++   +A  +L     D +MIGR A     +
Sbjct: 145 -----EAEYDSIKAVKAAVSIPVIA-NGDIDSPEKARYVLEYTGADALMIGRPAQGRPWI 198

Query: 226 LTTVDEYFSNPLT 238
              +  +  +  T
Sbjct: 199 FQEIQHFLEHGTT 211


>gi|154279318|ref|XP_001540472.1| hypothetical protein HCAG_04312 [Ajellomyces capsulatus NAm1]
 gi|150412415|gb|EDN07802.1| hypothetical protein HCAG_04312 [Ajellomyces capsulatus NAm1]
          Length = 461

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 82/181 (45%), Gaps = 17/181 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAKI+       I++N GCP      G  GA L+  PD +   + 
Sbjct: 88  LVFQIGTASPDLAVQAAKIIA-ADVAGIDVNAGCPKPFSTTGGMGAALLQTPDRLVSILT 146

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H R   ++    
Sbjct: 147 ALVQQVGTPYQIGISVKIRLLADPE----RTRDLVTRLCATGITGLTVHCRTTPMRPRER 202

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    + I +NG +E     L ++    VDG MI   A  NS
Sbjct: 203 AIRDQLP-----MIASICRA-AGVAILVNGDVESRDHGLALMAEYGVDGAMIATCAEANS 256

Query: 224 A 224
           +
Sbjct: 257 S 257


>gi|312796562|ref|YP_004029484.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
 gi|312168337|emb|CBW75340.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
          Length = 150

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 57/117 (48%), Gaps = 9/117 (7%)

Query: 202 QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           +A + L  VDGVMIGR AY N  +L  VD  F  P   S+  +TR +      +  +M +
Sbjct: 27  KAHEHLHHVDGVMIGREAYHNPFLLADVDRRFYEP---SALARTRGE------VEQAMIE 77

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           Y       G  +  +TRHM+GL+   P +R  R +L+     +T    I + A  ++
Sbjct: 78  YIGAEQARGTYIGAVTRHMLGLYRDQPGARGWRRVLSDHRKLATGDSRIFDEARAML 134


>gi|154249065|ref|YP_001409890.1| dihydrouridine synthase DuS [Fervidobacterium nodosum Rt17-B1]
 gi|154153001|gb|ABS60233.1| dihydrouridine synthase DuS [Fervidobacterium nodosum Rt17-B1]
          Length = 322

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 107/226 (47%), Gaps = 20/226 (8%)

Query: 9   YRFFARLLTNNALL-YTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEA 65
           Y F    L + A   +TEMI A +++   K N + F  Q++   + +Q+ G+D ++L EA
Sbjct: 22  YPFRKLCLQHGAYFAFTEMISAKSVIINVKINEIYFPRQDEKDRVGVQLFGSDYAELSEA 81

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A IV++ G   ++LN GCP ++V +   G+ L+ +       + AM   L    TVK RI
Sbjct: 82  AAIVQEKGL-WVDLNAGCPVSKVIKKGAGSALLKDLGEFRKVVRAMRSVLK-RFTVKTRI 139

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G +          +   + +  V+ +++H R A  +  S K   KI N  +  +Y     
Sbjct: 140 GWEKD----EFEKIYNILLEENVDAVFVHGRTA-KQMYSGKATWKIYNPGFVPLY----I 190

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + D++       ED+  A++      GV++ R +  N  + + + E
Sbjct: 191 SGDIYTK-----EDIKNAME-QSGATGVIVARGSIGNPWIFSEIGE 230


>gi|227495968|ref|ZP_03926279.1| dihydrouridine synthase [Actinomyces urogenitalis DSM 15434]
 gi|226834456|gb|EEH66839.1| dihydrouridine synthase [Actinomyces urogenitalis DSM 15434]
          Length = 438

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 59/244 (24%), Positives = 103/244 (42%), Gaps = 27/244 (11%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKI-VED 71
           LL    L  TEM+   A++  + K +    T   E+  ++Q+ G D     +AA+I VE+
Sbjct: 82  LLAPAGLYVTEMVTTRALVERNDKTLAMVRTDPTERVRSIQLYGVDPVIAGKAARILVEE 141

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----------IPVT 120
              + I+LN GCP  +V     GA L    D++   +  + +              +PVT
Sbjct: 142 DLADHIDLNFGCPVPKVTRKGGGAALPWKKDLLHAILREVVRGAEEGVRLGRREREVPVT 201

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD++       +  ++ + +GV  + +H R A                D+  + 
Sbjct: 202 VKMRIGVDEE--HETYLDAARAAQDAGVAALALHGRTA--------RQHYAGKADWSAIA 251

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+      +G NG     S AL+++     DGV++GR       +   +    S  + 
Sbjct: 252 RLKEACRIPVLG-NGDTWTGSHALEMMRQTGCDGVVVGRGCQGRPWLFADIVHALSGSVE 310

Query: 239 GSSP 242
            + P
Sbjct: 311 RTHP 314


>gi|90579253|ref|ZP_01235063.1| putative regulator protein [Vibrio angustum S14]
 gi|90440086|gb|EAS65267.1| putative regulator protein [Vibrio angustum S14]
          Length = 313

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 85/176 (48%), Gaps = 17/176 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +QI G D + + E A+     G   +++N GCP+  V++   GA L+  P+ +   +
Sbjct: 64  PVRVQILGQDPNWMAENAQRACSLGSAGVDINFGCPAKAVNKSRGGAVLLKEPERIYQIV 123

Query: 109 AAMCKALSIPV---TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A C+A   PV   T K R+G DD  PA     +  +I ++G + + +HAR       + 
Sbjct: 124 KA-CRAAVNPVKPLTAKVRLGWDD--PAQCF-EIADAIAQAGADEMVVHAR-------TK 172

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
           +D  +   + +D + ++K+      I  NG + +    QA     + D +M+ R A
Sbjct: 173 EDGYRAETIKWDYIKQLKQSVAIPIIA-NGEVWNYQDGQACLSTTNTDALMVCRGA 227


>gi|328778500|ref|XP_393458.4| PREDICTED: tRNA-dihydrouridine synthase 3-like [Apis mellifera]
          Length = 642

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 50/213 (23%), Positives = 96/213 (45%), Gaps = 16/213 (7%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A  IL+G  ++  ++     E    +Q+ G +   L   A+++ E    + I+LN+
Sbjct: 325 EMALAPRILKGAHEEWALVKRHESEDIFGIQLCGNNPGVLTRCAQLLNEQIDVDFIDLNL 384

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   ++    G+ ++   +++   + ++ + ++IP+TVK R GV   I       L+ 
Sbjct: 385 GCPIDLIYRQGGGSGMLNRLNVLETVVKSVNQVMNIPLTVKTRTGV--YIDKPIAHTLMP 442

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
             +  GV+ I +H R         ++ R     D+D + +  K    + +  NG     +
Sbjct: 443 KFRDWGVSMITVHGRS--------REQRYTKLADWDYIEKCAKTAHPIPVYGNGDILSFD 494

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  +      S+ GV IGR A     + T + E
Sbjct: 495 DYQRVQDTYNSIYGVTIGRGALIKPWIFTEIKE 527


>gi|14249957|gb|AAH08362.1| DUS3L protein [Homo sapiens]
          Length = 613

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 298 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 353

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 354 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 412

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 413 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 462

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 463 ILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 511

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 512 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 549


>gi|149174914|ref|ZP_01853538.1| hypothetical protein PM8797T_11079 [Planctomyces maris DSM 8797]
 gi|148846251|gb|EDL60590.1| hypothetical protein PM8797T_11079 [Planctomyces maris DSM 8797]
          Length = 355

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 89/194 (45%), Gaps = 13/194 (6%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           +G + +++     E P+  Q+ G++  +   AA+ + + G++ I++N GCP  +V     
Sbjct: 60  QGKQHSMMYCHQDEFPVGGQLMGSEPEEFGPAARRLVEAGFHVIDINFGCPVKKVMSRCR 119

Query: 94  GACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVNG 150
           G   +  P++  D I+ +   +   IPVT+K R G+DD   +      +       G++ 
Sbjct: 120 GGYHLSQPEVALDIISRVRDTVPAEIPVTLKMRRGIDDSSESADNFFMIFDGAYARGLSA 179

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--P 208
           I +H R    K + P         +++ + ++K+   +  +  +G L      L +L   
Sbjct: 180 ITVHGRTVDQKYVGPS--------NWEFLKQVKQHAGEKTVIGSGDLFSPQSCLDMLRVT 231

Query: 209 SVDGVMIGRAAYKN 222
            VDGV I R A  N
Sbjct: 232 GVDGVSIARGAIGN 245


>gi|14602971|gb|AAH09973.1| Dihydrouridine synthase 3-like (S. cerevisiae) [Homo sapiens]
 gi|190690551|gb|ACE87050.1| dihydrouridine synthase 3-like (S. cerevisiae) protein [synthetic
           construct]
 gi|190691915|gb|ACE87732.1| dihydrouridine synthase 3-like (S. cerevisiae) protein [synthetic
           construct]
          Length = 650

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 335 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 390

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 391 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 449

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 450 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 499

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 500 ILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 548

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 549 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 586


>gi|254445896|ref|ZP_05059372.1| Dihydrouridine synthase superfamily [Verrucomicrobiae bacterium
           DG1235]
 gi|198260204|gb|EDY84512.1| Dihydrouridine synthase superfamily [Verrucomicrobiae bacterium
           DG1235]
          Length = 352

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 103/239 (43%), Gaps = 24/239 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY--TEMIVADAILRGDKKNILGFSTQE--KPLALQIGG 56
           M D TDR   F A +    A  Y  TE        R +K  +   +  E  +P+  Q+ G
Sbjct: 29  MQDVTDRP--FMAVIANCGAPDYFVTEYFRVHVQSRLEKHILEAVTENETGRPVFAQMIG 86

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            DI  L   AK ++      ++LN+GCP+  V++   G  L+ +P  +   + A+ + + 
Sbjct: 87  EDIHHLTRTAKDLQSHPIAGVDLNMGCPAPTVYKKHCGGGLLRDPQKIDQVLGALRQTIP 146

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNL 174
              TVK RIG ++         ++  + K  V+ + +H R  K + +            +
Sbjct: 147 GLFTVKMRIGFEN---TENFETILDLVNKHQVDLLSLHGRTVKEMYRS----------EV 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            YD +     E  +  +  NG +   ++A +IL      GVM+GR A +N  +   + E
Sbjct: 194 HYDFIKR-AAERINCPLLANGDVTSAAKARQILDYTGAAGVMVGRHAIRNPWIFRQIRE 251


>gi|126323260|ref|XP_001376181.1| PREDICTED: similar to Dihydrouridine synthase 3-like (S.
           cerevisiae) [Monodelphis domestica]
          Length = 666

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 52/213 (24%), Positives = 97/213 (45%), Gaps = 18/213 (8%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM V   +L+G      +L     E    +Q+ GA    + + A+++ +    + +++NV
Sbjct: 351 EMAVCTNLLQGQSSEWALLKRHHTEDLFGVQLEGAFPDTMTKCAELLNQTVEVDFVDINV 410

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM   +     +  M + L +P+TVK R GV +++  +A R L+ 
Sbjct: 411 GCPIDLVYKKGGGCALMNRSNKFEQIVRGMNQVLDVPLTVKIRTGVQEKV-NLAHR-LLP 468

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---E 198
            +++ GV    +H R         ++ R     D+  +    +    + +  NG +   E
Sbjct: 469 ELREWGVALATLHGRS--------REQRYTKGADWQYIQHCAEVAHPMPLFGNGDILSYE 520

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D ++AL+    V G+MI R A     + T + E
Sbjct: 521 DANRALQT--GVSGIMIARGALIKPWLFTEIKE 551


>gi|193071073|ref|ZP_03051999.1| tRNA-dihydrouridine synthase C [Escherichia coli E110019]
 gi|300902211|ref|ZP_07120211.1| dihydrouridine synthase [Escherichia coli MS 84-1]
 gi|301306542|ref|ZP_07212606.1| dihydrouridine synthase [Escherichia coli MS 124-1]
 gi|192955596|gb|EDV86073.1| tRNA-dihydrouridine synthase C [Escherichia coli E110019]
 gi|300405730|gb|EFJ89268.1| dihydrouridine synthase [Escherichia coli MS 84-1]
 gi|300838243|gb|EFK66003.1| dihydrouridine synthase [Escherichia coli MS 124-1]
 gi|315255348|gb|EFU35316.1| dihydrouridine synthase [Escherichia coli MS 85-1]
          Length = 325

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 77  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 136

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 137 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 186

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 187 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 244

Query: 228 TVDEY 232
            V +Y
Sbjct: 245 RVVKY 249


>gi|212546591|ref|XP_002153449.1| tRNA dihydrouridine synthase (Smm1), putative [Penicillium
           marneffei ATCC 18224]
 gi|210064969|gb|EEA19064.1| tRNA dihydrouridine synthase (Smm1), putative [Penicillium
           marneffei ATCC 18224]
          Length = 446

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 109 LIFQIGTASPELAVQAAKVVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILE 167

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +      + LV  +  +G+ G+ IH R   ++   P
Sbjct: 168 ALVREVGTPYKIGISVKIRLFSDPE----ETKALVTRLVATGITGLTIHCRTTPMR---P 220

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++ R I      ++  + +E   +   +NG +    QAL+++   +VDG MI  +A  NS
Sbjct: 221 RE-RAI-REQLSMIATVCREA-GVACVMNGDVTSRDQALELMKEYNVDGAMIATSAEANS 277

Query: 224 A 224
           +
Sbjct: 278 S 278


>gi|324006553|gb|EGB75772.1| dihydrouridine synthase [Escherichia coli MS 57-2]
          Length = 338

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDS---GERKFEIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|66045219|ref|YP_235060.1| dihydrouridine synthase, DuS [Pseudomonas syringae pv. syringae
           B728a]
 gi|63255926|gb|AAY37022.1| Dihydrouridine synthase, DuS [Pseudomonas syringae pv. syringae
           B728a]
          Length = 321

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    +ED  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVEDWRRCREICGARD-IMIGR 224


>gi|293371535|ref|ZP_06617953.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CMC 3f]
 gi|292633483|gb|EFF52048.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CMC 3f]
          Length = 314

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 51/246 (20%), Positives = 102/246 (41%), Gaps = 34/246 (13%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +A KI+  F   GY E ++N+GCP   + +   G+ ++  P+ V + +  + K   I  +
Sbjct: 75  KAEKILSLFIEKGYKEADINMGCPFPILTKRHNGSGILPYPEEVKELLNLVLKYPEISFS 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G ++    + L  ++  +    +  + +H R      L  +  +   NL+    +
Sbjct: 135 IKMRLGWENPDECLHLAPIINDLP---LRQVTMHPR------LGKQQYKGEVNLEGFSAF 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA---------------- 224
           +   ++P ++ G    LED+ +  K  P++ G+MIGR    N A                
Sbjct: 186 QEVCKHPLIYNGDIHSLEDIQRIQKQFPALAGIMIGRGLLANPALALEYKENRILTADEM 245

Query: 225 ------MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                 M T+V   ++  L G         K FW  ++        + +H  G L +  +
Sbjct: 246 REKFHSMHTSVYTQYAEQLEGGDEQLLNKMKTFWEYLTPQADRKLLKAIHKSGSLNKYNQ 305

Query: 279 HMIGLF 284
            ++  F
Sbjct: 306 AILAFF 311


>gi|322823915|gb|EFZ29514.1| dihydrouridine synthase (Dus), putative [Trypanosoma cruzi]
          Length = 548

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 40/151 (26%), Positives = 72/151 (47%), Gaps = 9/151 (5%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----EKPLALQIGGADISKLVEA 65
           ++ AR  +         + A A   G+     G ++     + PL +Q  G D   L+ A
Sbjct: 138 QYRARYFSTTPHRAEPAMTATASGEGEAAEDAGRTSDGEETDHPLFVQFCGNDADTLLAA 197

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ VED     +++N+GCP      G +G+ LM + D V + +  +   L +PVT K R+
Sbjct: 198 ARHVED-DCEAVDVNLGCPQGIARRGYYGSFLMEDWDRVHNILHCLAVELRVPVTAKMRV 256

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             DD   A+ L+   + ++ +G+  + +H R
Sbjct: 257 FDDD---ALTLK-YAEMLRDTGIAVLCVHGR 283


>gi|237732187|ref|ZP_04562668.1| tRNA-dihydrouridine synthase C [Citrobacter sp. 30_2]
 gi|226907726|gb|EEH93644.1| tRNA-dihydrouridine synthase C [Citrobacter sp. 30_2]
          Length = 314

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAIELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D+         +  +++++G + + +H R       + +   
Sbjct: 127 REAVPAHLPVTVKVRLGWDNSDRQF---EIADAVQQAGASELAVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLT 227
           K  ++++  + EI++      I  NG + D   +Q    +   D VMIGR A  N   L+
Sbjct: 177 KAEHINWQAIGEIRQRLSIPVIA-NGEIWDWQSAQDCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|189404356|ref|ZP_02788797.2| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189405202|ref|ZP_02813951.2| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC869]
 gi|189406070|ref|ZP_02826184.2| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC508]
 gi|189366104|gb|EDU84520.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189371342|gb|EDU89758.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC869]
 gi|189376618|gb|EDU95034.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC508]
          Length = 335

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 86  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 145

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 146 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 195

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 196 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQECMAISGCDSVMIGRGAL-NIPNLS 253

Query: 228 TVDEY 232
            V +Y
Sbjct: 254 RVVKY 258


>gi|320593632|gb|EFX06041.1| tRNA dihydrouridine synthase [Grosmannia clavigera kw1407]
          Length = 441

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 43/154 (27%), Positives = 73/154 (47%), Gaps = 16/154 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           I++N GCP     +G  GA L+  PD    I+   +A +  A  I ++VK R+  D    
Sbjct: 138 IDINAGCPKPFSTDGGMGAALLKTPDLLCAILERLVATITPAFGIGISVKIRLLAD---- 193

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A   + LV+ +  +G+ G+ +H R    + + P++ R I +    +  E +         
Sbjct: 194 AAETKTLVRRLVATGITGLTVHCRT---RNMRPRE-RAIRDQLRMVADECRAAGVACL-- 247

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           +NG +    QAL ++    VDG MI  AA +N +
Sbjct: 248 MNGDVTSRDQALSLMAEYGVDGAMIATAAERNPS 281


>gi|159039340|ref|YP_001538593.1| nifR3 family TIM-barrel protein [Salinispora arenicola CNS-205]
 gi|157918175|gb|ABV99602.1| putative TIM-barrel protein, nifR3 family [Salinispora arenicola
           CNS-205]
          Length = 391

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 83/189 (43%), Gaps = 17/189 (8%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EMI   A++  + K +  + F   E P +LQ+ G D      A +IV E    + I+LN 
Sbjct: 52  EMITTVALVERNPKTLRMIAFGGGESPRSLQLYGTDPEVTAAAVRIVVERDLADHIDLNF 111

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRN 138
           GCP  +V     GA L     +    + A   A S   +PVTVK R G+DD         
Sbjct: 112 GCPVPKVTRKGGGAALPWRRRLFARLVTAAVDAASPAGVPVTVKMRKGIDDDHLTYVEAG 171

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L  + + +GV  + +H R A          R     D+D +  +K    D+ +  NG + 
Sbjct: 172 L--AAQDAGVAAVALHGRTAA--------QRYSGTADWDAIATLKAAL-DVPVLGNGDIW 220

Query: 199 DMSQALKIL 207
           +   AL+++
Sbjct: 221 EADDALRMV 229


>gi|28869372|ref|NP_791991.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|213968214|ref|ZP_03396359.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato T1]
 gi|301383780|ref|ZP_07232198.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tomato
           Max13]
 gi|302060777|ref|ZP_07252318.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tomato
           K40]
 gi|302131876|ref|ZP_07257866.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|38604775|sp|Q884C6|DUSC_PSESM RecName: Full=tRNA-dihydrouridine synthase C
 gi|28852613|gb|AAO55686.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|213927194|gb|EEB60744.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato T1]
 gi|331018629|gb|EGH98685.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 317

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHTIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPKDIPVTAKMRLGYENTDGAL---DCARALADGGAAQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    +ED  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVEDWRRCREICGARD-IMIGR 224


>gi|15802690|ref|NP_288717.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 EDL933]
 gi|38604938|sp|Q8XEC6|DUSC_ECO57 RecName: Full=tRNA-dihydrouridine synthase C
 gi|12516448|gb|AAG57272.1|AE005445_9 putative regulator protein [Escherichia coli O157:H7 str. EDL933]
          Length = 316

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQECMAISGCDSVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|315297996|gb|EFU57266.1| dihydrouridine synthase [Escherichia coli MS 16-3]
          Length = 337

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDRQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|191165389|ref|ZP_03027231.1| tRNA-dihydrouridine synthase C [Escherichia coli B7A]
 gi|209919598|ref|YP_002293682.1| tRNA-dihydrouridine synthase C [Escherichia coli SE11]
 gi|218554705|ref|YP_002387618.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI1]
 gi|218695751|ref|YP_002403418.1| tRNA-dihydrouridine synthase C [Escherichia coli 55989]
 gi|293446490|ref|ZP_06662912.1| tRNA-dihydrouridine synthase C [Escherichia coli B088]
 gi|300818860|ref|ZP_07099065.1| dihydrouridine synthase [Escherichia coli MS 107-1]
 gi|190904552|gb|EDV64259.1| tRNA-dihydrouridine synthase C [Escherichia coli B7A]
 gi|209912857|dbj|BAG77931.1| putative regulator protein [Escherichia coli SE11]
 gi|218352483|emb|CAU98260.1| tRNA-dihydrouridine synthase C [Escherichia coli 55989]
 gi|218361473|emb|CAQ99062.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI1]
 gi|291323320|gb|EFE62748.1| tRNA-dihydrouridine synthase C [Escherichia coli B088]
 gi|300528479|gb|EFK49541.1| dihydrouridine synthase [Escherichia coli MS 107-1]
 gi|323944956|gb|EGB41021.1| dihydrouridine synthase [Escherichia coli H120]
 gi|324020608|gb|EGB89827.1| dihydrouridine synthase [Escherichia coli MS 117-3]
 gi|324118020|gb|EGC11919.1| dihydrouridine synthase [Escherichia coli E1167]
          Length = 315

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|323184237|gb|EFZ69614.1| dihydrouridine synthase family protein [Escherichia coli 1357]
          Length = 313

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 65  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 124

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 125 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 174

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 175 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 232

Query: 228 TVDEY 232
            V +Y
Sbjct: 233 RVVKY 237


>gi|293410501|ref|ZP_06654077.1| tRNA-dihydrouridine synthase C [Escherichia coli B354]
 gi|291470969|gb|EFF13453.1| tRNA-dihydrouridine synthase C [Escherichia coli B354]
          Length = 315

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKEPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|298253423|ref|ZP_06977215.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis 5-1]
 gi|297532818|gb|EFH71704.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis 5-1]
          Length = 336

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 62/271 (22%), Positives = 108/271 (39%), Gaps = 22/271 (8%)

Query: 26  MIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVG 82
           MI A A++  + K   +  F+  EK  +LQ+ G + S + +AA+IV D    + ++LN G
Sbjct: 1   MITARALVARNPKALRLCRFAPSEKVRSLQLYGVNPSIVEQAAQIVVDENMADHVDLNFG 60

Query: 83  CPSARVHEGSFGACLMLNPDIVGDC---IAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           CP  +V     G+ L    D++ +    + ++C+   IPVT K R+G+D+          
Sbjct: 61  CPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCEPAGIPVTAKFRVGIDENHETFIQAGH 120

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           +   ++ G   + +HAR          D  +I  L          E  D+ +  NG +  
Sbjct: 121 IA--QEEGCAAVTLHARTTAEYYGGHSDWTRIGEL---------VEALDIPVFGNGDIWG 169

Query: 200 MSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              AL +       GV IGR       +   +           +P  T V     R +  
Sbjct: 170 AEDALAMFKETGCAGVAIGRGCQGRPWLFADIRNACEGSDNRVNPTLTEVGSVILRHLKL 229

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
            +  Y      +   +  + +H+     GFP
Sbjct: 230 LVEFYDGDERMA---VHDLRKHVAWYLKGFP 257


>gi|259909025|ref|YP_002649381.1| tRNA-dihydrouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224964647|emb|CAX56161.1| tRNA-dihydrouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|283479041|emb|CAY74957.1| putative regulator protein [Erwinia pyrifoliae DSM 12163]
          Length = 310

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 81/172 (47%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 RAAVPAHLPVTVKVRLGWDS---GARQFEIADAVQQAGASELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAA 219
           +   +++  + EI++      I  NG + D   +Q    +   D VMIGR A
Sbjct: 177 RAEAINWQAIGEIRQRLTIPVIA-NGEIWDWHSAQDCMAVTGCDAVMIGRGA 227


>gi|294892129|ref|XP_002773909.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239879113|gb|EER05725.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 606

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 58/230 (25%), Positives = 107/230 (46%), Gaps = 37/230 (16%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV----EDFGYNEI 77
           +EM +A+++L+G++    +L     EK   +Q+ G     +   A+++    +DF +  +
Sbjct: 265 SEMALAESLLKGNRAEHALLKKHPDEKIFGIQVAGGFPDMMSRCAEMLCREMDDFDF--L 322

Query: 78  NLNVGCPSARVHEGSFGACLML---NPDIVGDCIAAMCKALSIPVTVKCRIG------VD 128
           ++N+GCP   +H+   G+ LM      + V   +A +C A    +TVK R        V 
Sbjct: 323 DINMGCPLEGLHKKGAGSALMTRLGKAEGVMSSMAKVCHAYDKNLTVKIRTAHYGQNHVY 382

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD----NRKIPNLDYDIVYEIKK 184
           D++ A A+         SGV+G+ +H R A  +   P D     +    +D  +      
Sbjct: 383 DKVAARAV--------SSGVDGVVLHGRTAQQRYSRPADWTFHTKCRTAMDSAV-----P 429

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            N    +G  G + D  +A++ +  P V+G+MIGR A     + T + E+
Sbjct: 430 GNAVPLVGC-GDIIDWREAIERMETPGVEGLMIGRGALIKPWIFTEIKEH 478


>gi|255071937|ref|XP_002499643.1| dihydrouridine synthase-like family protein [Micromonas sp. RCC299]
 gi|226514905|gb|ACO60901.1| dihydrouridine synthase-like family protein [Micromonas sp. RCC299]
          Length = 495

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/166 (27%), Positives = 79/166 (47%), Gaps = 14/166 (8%)

Query: 24  TEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +EM+ A  +LR +  +K  L     EK   +Q+    I + V AA +  D G + I+LN 
Sbjct: 140 SEMVFARFLLRRNPVEKARLRRHPSEKLFGVQLATNQIVEGVNAAALAADAGADFIDLNC 199

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVALRNLV 140
           GCP     +   GA L+  P  +   +  +     +P+TVK R+G    + PA   R L 
Sbjct: 200 GCPIHETWKRGLGAALLKKPKKLERLVRGIADGTRLPLTVKIRLGAGGSEAPA---RQLA 256

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           ++++ +G   + IH R         K+ R     ++D++ EI++E 
Sbjct: 257 EAVENAGAAAVIIHGRT--------KEQRYTRAANWDLIGEIQRER 294


>gi|224023532|ref|ZP_03641898.1| hypothetical protein BACCOPRO_00234 [Bacteroides coprophilus DSM
           18228]
 gi|224016754|gb|EEF74766.1| hypothetical protein BACCOPRO_00234 [Bacteroides coprophilus DSM
           18228]
          Length = 308

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 51/195 (26%), Positives = 86/195 (44%), Gaps = 19/195 (9%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           DK+ +L        L  QI  A+  +     + +  +GY EI+LN+GCP   +     G+
Sbjct: 47  DKRELLPAGNTVSRLIPQIIAAEPDEFRMLVEQISGWGYREIDLNMGCPFPLIVNRRKGS 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++  PD V   +  M     I  +VK R+G +    A   R ++  + +S V  I +H 
Sbjct: 107 GILPFPDKVAALLHEMETFPEIRFSVKMRLGWER---ADEWREILPLLNESCVRQITLHP 163

Query: 156 R--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSV 210
           R  +   KG   ++        +   YE  +    L +  NG L   E+M + L   P +
Sbjct: 164 RIGRQQYKGTVDREA-------FTAFYESCR----LPLVYNGDLRTQEEMQELLLAYPRL 212

Query: 211 DGVMIGRAAYKNSAM 225
           +G+M+GR    N A+
Sbjct: 213 EGLMLGRGLLANPAL 227


>gi|331658219|ref|ZP_08359181.1| tRNA-dihydrouridine synthase C [Escherichia coli TA206]
 gi|331056467|gb|EGI28476.1| tRNA-dihydrouridine synthase C [Escherichia coli TA206]
          Length = 315

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDRQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|226330863|ref|ZP_03806381.1| hypothetical protein PROPEN_04784 [Proteus penneri ATCC 35198]
 gi|225201658|gb|EEG84012.1| hypothetical protein PROPEN_04784 [Proteus penneri ATCC 35198]
          Length = 244

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 77/172 (44%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+  P+ +     AM
Sbjct: 1   MQLLGQHPQWLAENAFRAVSLGSWGVDLNCGCPSKTVNGSGGGASLLKQPETIYQATKAM 60

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+  ++PV+VK R+G D    +     +  ++ + G   I IH R       + +D  
Sbjct: 61  RDAVPSALPVSVKVRLGWDS---SAYSHEIADAVAQGGATEITIHGR-------TKEDGY 110

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
               +++  + +I++      I  NG + +   AL  L +   D +MIGR A
Sbjct: 111 NAEKINWQAIGDIRQRLSIPVIA-NGEIWNREDALACLATTGCDAIMIGRGA 161


>gi|256017692|ref|ZP_05431557.1| tRNA-dihydrouridine synthase C [Shigella sp. D9]
 gi|307311281|ref|ZP_07590925.1| dihydrouridine synthase DuS [Escherichia coli W]
 gi|332278706|ref|ZP_08391119.1| tRNA-dihydrouridine synthase C [Shigella sp. D9]
 gi|306908787|gb|EFN39284.1| dihydrouridine synthase DuS [Escherichia coli W]
 gi|315061449|gb|ADT75776.1| tRNA-dihydrouridine synthase C [Escherichia coli W]
 gi|323377970|gb|ADX50238.1| dihydrouridine synthase DuS [Escherichia coli KO11]
 gi|332101058|gb|EGJ04404.1| tRNA-dihydrouridine synthase C [Shigella sp. D9]
          Length = 316

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|194760465|ref|XP_001962460.1| GF14432 [Drosophila ananassae]
 gi|190616157|gb|EDV31681.1| GF14432 [Drosophila ananassae]
          Length = 606

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 64/272 (23%), Positives = 117/272 (43%), Gaps = 31/272 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++E+    + I+LN+
Sbjct: 289 EMACALPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNTISQAAQLIEETAKVDYIDLNI 348

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 349 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCSALSERLPFTVKMRTGIYADKSVAHELLP 407

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + +++ + E   +   + +  NG + 
Sbjct: 408 LVEEW---GASAVTLHGRS--------REQRYTKHANWNYIEECAAKAKQMPVIGNGDIL 456

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ED  +   + P V  VMIGR A     +   + E        SS  +  + + F    
Sbjct: 457 SYEDYLERRTLAPHVSSVMIGRGALIKPWIFQEIKE--QKAWAPSSSQRFELMRKF---- 510

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                +Y   H  S  K  + TR  +  +  F
Sbjct: 511 ----CNYGLEHWGSDTKGVETTRRFLLEWQSF 538


>gi|3859982|gb|AAC72941.1| unknown [Homo sapiens]
          Length = 223

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 96/224 (42%), Gaps = 31/224 (13%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++     
Sbjct: 14  VDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERVNLA-- 71

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG 195
             L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG
Sbjct: 72  HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NG 122

Query: 196 ---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
                ED ++A++    V G+MI R A     + T + E     ++ S  +   + +DF 
Sbjct: 123 DILSFEDANRAMQT--GVTGIMIARGALLKPWLFTEIKEQRHWDISSSERLD--ILRDF- 177

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                  T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 178 -------TNYGLEHWGSDTQGVEKTRRFLLEWLSFL----CRYV 210


>gi|325288142|ref|YP_004263932.1| dihydrouridine synthase DuS [Cellulophaga lytica DSM 7489]
 gi|324323596|gb|ADY31061.1| dihydrouridine synthase DuS [Cellulophaga lytica DSM 7489]
          Length = 315

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 78/175 (44%), Gaps = 21/175 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+  AD  + + A K ++  GY E+N N+GCP   V     G+ L+ NP+ +   + 
Sbjct: 63  LIPQVMTADADQFIFAIKYIQSLGYKELNWNLGCPYPMVTNSGMGSGLICNPEKIDHILD 122

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILK-GLSPK 166
                  + V++K R+G ++   +  +      + K  +  I IHAR  K + K G+  +
Sbjct: 123 RAHSETDVTVSMKMRLGYEN---SNEILESFSVLDKYPLKSIAIHARLGKQLYKGGVDLQ 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRA 218
             +K  ++    +Y             NG +  ++Q  K+    PS+   MIGR 
Sbjct: 180 GFQKCVDVAKHTLY------------YNGDITTVAQFKKMKEQFPSIQHFMIGRG 222


>gi|302188293|ref|ZP_07264966.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. syringae
           642]
          Length = 326

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 61/113 (53%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + +A+  +IPVT K R+G ++   A+   +  +++   G   I +HAR  +
Sbjct: 124 SQVRRAVPKAIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV 173


>gi|238753348|ref|ZP_04614711.1| tRNA-dihydrouridine synthase C [Yersinia ruckeri ATCC 29473]
 gi|238708301|gb|EEQ00656.1| tRNA-dihydrouridine synthase C [Yersinia ruckeri ATCC 29473]
          Length = 309

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D+         +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDNDSRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A + L     D VM+GR A  N   L+
Sbjct: 177 KAELINWAAIGEIRQRLTIPVIA-NGEIWDYQSAQECLKVTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|209766354|gb|ACI81489.1| putative regulator protein [Escherichia coli]
          Length = 316

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   +Q    +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSTQECMAISGCDSVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|85116943|ref|XP_965143.1| hypothetical protein NCU00950 [Neurospora crassa OR74A]
 gi|28926947|gb|EAA35907.1| hypothetical protein NCU00950 [Neurospora crassa OR74A]
 gi|38567022|emb|CAE76320.1| related to tRNA dihydrouridine synthase [Neurospora crassa]
          Length = 475

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 86/181 (47%), Gaps = 21/181 (11%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IVGDC 107
            QIG +D ++ VE AK+V     + I++N GCP         GA L+  P+    I+   
Sbjct: 125 FQIGTSDPARAVECAKLVA-ADVSGIDVNAGCPKPFSTHAGMGAALLRTPEKLVSILEAL 183

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +A +  A  I ++VK R+    + PA     LV+ +  +G+ G+ IH R   ++   P++
Sbjct: 184 VAEIKPAFDIGISVKIRLL---ETPA-ETEALVRRLCATGITGLTIHCRTTPMR---PRE 236

Query: 168 N--RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R    +  D+ +E       +   +NG +E+   AL+++     DG MI   A KN 
Sbjct: 237 RAIRGQLRMIADVCHEF-----GVACLVNGDVENRDHALELMAEYGTDGAMIATCAEKNG 291

Query: 224 A 224
           +
Sbjct: 292 S 292


>gi|332022994|gb|EGI63259.1| tRNA-dihydrouridine synthase 2-like protein [Acromyrmex echinatior]
          Length = 461

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 52/229 (22%), Positives = 100/229 (43%), Gaps = 37/229 (16%)

Query: 21  LLYTEMIVADAILRGDKK--NILG----------------FSTQEKPLALQIGGADISKL 62
           ++YTE ++   +LR  ++  ++LG                 S + + + LQIG +D ++ 
Sbjct: 41  IVYTEELIDRKLLRSIRRENDVLGTVDYIDKTDGTVVFRTCSREREHVVLQIGTSDPARA 100

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            + A++VE+     I++N+GCP      G  GA L+  P    D +  + + ++IP+T K
Sbjct: 101 AQVARMVEN-DVAGIDINMGCPKKFSILGGMGASLLREPQKAIDILRKLIETVTIPITCK 159

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RI  D +   +    L  ++  +G+  I +H R    +   P  N  +  +   +    
Sbjct: 160 IRILPDLEETLL----LCDTLASTGIAAIAVHGRTIEERPQHPNRNHVLKQISARL---- 211

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKNSAML 226
                 + +  NGG +D+ +   I           VM+ RAA  N ++ 
Sbjct: 212 -----SIPVIANGGSKDIQKHSDIFRFKKETGCSSVMLARAAEWNCSVF 255


>gi|332161013|ref|YP_004297590.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318604885|emb|CBY26383.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325665243|gb|ADZ41887.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859407|emb|CBX69752.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica W22703]
          Length = 310

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRAAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+    PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHFPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 177 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|74312663|ref|YP_311082.1| tRNA-dihydrouridine synthase C [Shigella sonnei Ss046]
 gi|73856140|gb|AAZ88847.1| putative regulator protein [Shigella sonnei Ss046]
 gi|323171791|gb|EFZ57435.1| dihydrouridine synthase family protein [Escherichia coli LT-68]
          Length = 315

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|15832280|ref|NP_311053.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           Sakai]
 gi|168750514|ref|ZP_02775536.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|168757716|ref|ZP_02782723.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|195935510|ref|ZP_03080892.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208809098|ref|ZP_03251435.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813928|ref|ZP_03255257.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208818944|ref|ZP_03259264.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209400918|ref|YP_002271543.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|217326717|ref|ZP_03442800.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254794033|ref|YP_003078870.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261223407|ref|ZP_05937688.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261259043|ref|ZP_05951576.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291283388|ref|YP_003500206.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str.
           CB9615]
 gi|13362495|dbj|BAB36449.1| putative regulator protein [Escherichia coli O157:H7 str. Sakai]
 gi|188015333|gb|EDU53455.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|189355352|gb|EDU73771.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|208728899|gb|EDZ78500.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735205|gb|EDZ83892.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208739067|gb|EDZ86749.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209162318|gb|ACI39751.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|209766348|gb|ACI81486.1| putative regulator protein [Escherichia coli]
 gi|209766350|gb|ACI81487.1| putative regulator protein [Escherichia coli]
 gi|209766352|gb|ACI81488.1| putative regulator protein [Escherichia coli]
 gi|209766356|gb|ACI81490.1| putative regulator protein [Escherichia coli]
 gi|217319084|gb|EEC27509.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254593433|gb|ACT72794.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|290763261|gb|ADD57222.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str.
           CB9615]
 gi|320192243|gb|EFW66888.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|320641205|gb|EFX10683.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           G5101]
 gi|320646593|gb|EFX15504.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320651848|gb|EFX20223.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H- str. H
           2687]
 gi|320657572|gb|EFX25370.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320663178|gb|EFX30487.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320667929|gb|EFX34832.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|326339484|gb|EGD63295.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str. 1125]
 gi|326343945|gb|EGD67706.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str. 1044]
          Length = 316

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQECMAISGCDSVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|116051125|ref|YP_790044.1| hypothetical protein PA14_23640 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|313108452|ref|ZP_07794456.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
 gi|115586346|gb|ABJ12361.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|310880958|gb|EFQ39552.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
          Length = 319

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 62/113 (54%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +
Sbjct: 64  PMRVQLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           AA+ +A+   I VT K R+G D   P  AL +  +++   G   + +HAR  +
Sbjct: 124 AAVRRAVPSEIAVTSKMRLGYDS--PDGAL-DCARALADGGSAHVVVHARTKV 173


>gi|15598325|ref|NP_251819.1| hypothetical protein PA3129 [Pseudomonas aeruginosa PAO1]
 gi|107102678|ref|ZP_01366596.1| hypothetical protein PaerPA_01003743 [Pseudomonas aeruginosa PACS2]
 gi|254236099|ref|ZP_04929422.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|254241823|ref|ZP_04935145.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|38605051|sp|Q9HZ95|DUSC_PSEAE RecName: Full=tRNA-dihydrouridine synthase C
 gi|9949242|gb|AAG06517.1|AE004737_3 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|126168030|gb|EAZ53541.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|126195201|gb|EAZ59264.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
          Length = 319

 Score = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 62/113 (54%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +
Sbjct: 64  PMRVQLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           AA+ +A+   I VT K R+G D   P  AL +  +++   G   + +HAR  +
Sbjct: 124 AAVRRAVPSEIAVTSKMRLGYDS--PDGAL-DCARALADGGSAHVVVHARTKV 173


>gi|260856113|ref|YP_003230004.1| tRNA-dihydrouridine synthase C [Escherichia coli O26:H11 str.
           11368]
 gi|260868842|ref|YP_003235244.1| tRNA-dihydrouridine synthase C [Escherichia coli O111:H- str.
           11128]
 gi|257754762|dbj|BAI26264.1| tRNA-dihydrouridine synthase C [Escherichia coli O26:H11 str.
           11368]
 gi|257765198|dbj|BAI36693.1| tRNA-dihydrouridine synthase C [Escherichia coli O111:H- str.
           11128]
 gi|323176964|gb|EFZ62554.1| dihydrouridine synthase family protein [Escherichia coli 1180]
          Length = 316

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|330919514|ref|XP_003298646.1| hypothetical protein PTT_09419 [Pyrenophora teres f. teres 0-1]
 gi|311328059|gb|EFQ93260.1| hypothetical protein PTT_09419 [Pyrenophora teres f. teres 0-1]
          Length = 578

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 88/186 (47%), Gaps = 16/186 (8%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR   +++ G    ++PL +Q    D    + AAK V  F  + ++LN+GCP      G 
Sbjct: 111 LRDSDRHLDGNPAFDRPLTVQFCSNDPEDFLRAAKHVAPF-CDAVDLNLGCPQGIAKRGK 169

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L  +  ++   I  + + L +PVT K R+    + P   L    K++  +G + I 
Sbjct: 170 YGAFLQEDWGLISSMIRKLHEELDVPVTAKMRVL---ETPEKTL-AYAKTLLDAGASIIT 225

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILP 208
           +H R+   KG     N  +   D+ ++  +++  P +  I  NG +   ED++  L+   
Sbjct: 226 VHGRRREQKG----HNTGL--ADWKMIRYLRENLPKETVIFANGNILQHEDIAACLEAT- 278

Query: 209 SVDGVM 214
             DGVM
Sbjct: 279 GADGVM 284


>gi|295676479|ref|YP_003605003.1| dihydrouridine synthase DuS [Burkholderia sp. CCGE1002]
 gi|295436322|gb|ADG15492.1| dihydrouridine synthase DuS [Burkholderia sp. CCGE1002]
          Length = 347

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 83/178 (46%), Gaps = 16/178 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   +   A          I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 65  PMVIQLLGSDPQWMARNAAYAATLSPYGIDLNFGCPAKVVNQHGGGAMLLATPELLNQIV 124

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +A+  A+   I VT K R+GV D   A+      +++   G   + +HAR         +
Sbjct: 125 SAVRAAVPADIAVTAKMRLGVSDTSRAI---ECAQALVDGGAASLVVHART--------R 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKN 222
           D+R  P   ++ V  I  +  D+ +  NG +  ++  Q  + +     VMIGR A  +
Sbjct: 174 DDRYRPPAHWEWVARI-DDAVDVPVIANGEVWTVADWQRCRSVSGCADVMIGRGAVSD 230


>gi|238483959|ref|XP_002373218.1| dihydrouridine synthase family protein, putative [Aspergillus
           flavus NRRL3357]
 gi|220701268|gb|EED57606.1| dihydrouridine synthase family protein, putative [Aspergillus
           flavus NRRL3357]
          Length = 474

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 95/227 (41%), Gaps = 27/227 (11%)

Query: 31  AILRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           A ++GD    L G    ++PL +Q    +    +EAA+ V  +  + ++LN+GCP     
Sbjct: 102 AAIKGDDTPYLDGNPAIDRPLFVQFCANNPDDFLEAARHVAPYC-DAVDLNLGCPQGIAR 160

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +GA L  + D++   I  +   L +PVT K RI    Q          K I  +G +
Sbjct: 161 RGHYGAFLQEDWDLIYKLINKLHTELDVPVTAKFRI----QETKEKTLEYAKMILSAGAS 216

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKI 206
            I +H R    KG     N  + +  Y I Y      P+  I  NG +   +D+ + L+ 
Sbjct: 217 IITLHGRTREQKG----HNTGVADWSY-IRYLRDNLPPETVIFANGNILNYDDLERCLEE 271

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               DGVM       + ++ +        P  GS        +++WR
Sbjct: 272 T-GADGVMSAEGNLSDPSVFS------KPPPVGSE------GREYWR 305


>gi|183598227|ref|ZP_02959720.1| hypothetical protein PROSTU_01611 [Providencia stuartii ATCC 25827]
 gi|188020396|gb|EDU58436.1| hypothetical protein PROSTU_01611 [Providencia stuartii ATCC 25827]
          Length = 320

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 44/172 (25%), Positives = 80/172 (46%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+  P+++     AM
Sbjct: 67  VQLLGQHPQWLAENAYRAVSLGSWGVDLNCGCPSKTVNGHGGGATLLKQPELIYRAAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D+   +     +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPEELPVSVKVRLGWDN---SQFCHEIADAVEQAGATELTVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           +   +++  + +I++      I  NG + D   A   L     D +MIGR A
Sbjct: 177 RAEKINWQAIGDIRRRLSIPVIA-NGEVWDYESAQHCLAITGCDAIMIGRGA 227


>gi|71402428|ref|XP_804129.1| dihydrouridine synthase (Dus) [Trypanosoma cruzi strain CL Brener]
 gi|70866933|gb|EAN82278.1| dihydrouridine synthase (Dus), putative [Trypanosoma cruzi]
          Length = 547

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL +Q  G D   L+ AA+ VED     +++N+GCP      G +G+ LM + D V +
Sbjct: 178 DHPLFVQFCGNDADTLLAAARHVED-DCEAVDVNLGCPQGIARRGHYGSFLMEDWDRVHN 236

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            +  +   L +PVT K R+  DD   A+ L+   + ++ +G+  + +H R
Sbjct: 237 ILHCLAVELRVPVTAKMRVFDDD---ALTLK-YAEMLRDTGIAVLCVHGR 282


>gi|322833772|ref|YP_004213799.1| dihydrouridine synthase DuS [Rahnella sp. Y9602]
 gi|321168973|gb|ADW74672.1| dihydrouridine synthase DuS [Rahnella sp. Y9602]
          Length = 310

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 47/172 (27%), Positives = 81/172 (47%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D    +     +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKVRLGWDSLEHSF---EIADAVQQAGATELTVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
           K   +++  + EI++      I  NG + D    QA       D VM+GR A
Sbjct: 177 KPERINWAAIGEIRQRLSIPVIA-NGEIWDYESGQACLHTTGCDAVMLGRGA 227


>gi|296388369|ref|ZP_06877844.1| tRNA-dihydrouridine synthase C [Pseudomonas aeruginosa PAb1]
          Length = 319

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 62/113 (54%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +
Sbjct: 64  PMRVQLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           AA+ +A+   I VT K R+G D   P  AL +  +++   G   + +HAR  +
Sbjct: 124 AAVRRAVPSEIAVTSKMRLGYDS--PDGAL-DCARALADGGSAHVVVHARTKV 173


>gi|188534377|ref|YP_001908174.1| tRNA-dihydrouridine synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029419|emb|CAO97296.1| Putative dihydrouridine synthase [Erwinia tasmaniensis Et1/99]
          Length = 310

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 81/175 (46%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 64  PVRIQLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGA 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       + +
Sbjct: 124 KAMRAAVPSHLPVTVKIRLGWDS---GSRQFEIADAVQQAGASELAVHGR-------TKE 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D  +   +++  +  I++      I  NG + D   A   +     D VMIGR A
Sbjct: 174 DGYRAEAINWQAIGAIRQRLSIPVIA-NGEIWDWQSAQDCMAITGCDAVMIGRGA 227


>gi|157961327|ref|YP_001501361.1| dihydrouridine synthase DuS [Shewanella pealeana ATCC 700345]
 gi|157846327|gb|ABV86826.1| dihydrouridine synthase DuS [Shewanella pealeana ATCC 700345]
          Length = 319

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 45/175 (25%), Positives = 89/175 (50%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   + E A    + G N +++N GCP+  V+  + GA ++  P+ + + +
Sbjct: 69  PVRVQLLGQNPDWMAENAVRAIELGSNGVDVNFGCPAKMVNRSNGGAVMLQYPEQLYNVV 128

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+    PVT K R+G +D+  ++ + N + +I ++G + + +HAR  +       
Sbjct: 129 KAMRDAVPSEQPVTAKIRLGFNDK--SLYMENAL-AIYEAGASELAVHARSKV------- 178

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D  K P   ++ + +I  + P   I  NG + +   A + +     D +M+GR A
Sbjct: 179 DGYKPPAY-WEYITDINAKLPIPVIA-NGEIWNRDDAERCMSVTGCDNIMVGRGA 231


>gi|295394807|ref|ZP_06805022.1| dihydrouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
 gi|294972403|gb|EFG48263.1| dihydrouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
          Length = 382

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 95/210 (45%), Gaps = 25/210 (11%)

Query: 20  ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNE 76
            L  TEM+   A++    K+  I+     E P ++Q+ G D   + +A + +VE+   + 
Sbjct: 42  GLYVTEMVTTRALVERSPKSMRIIHHEPYETPRSVQLYGVDPVTVGQAVRMLVEEDRADH 101

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCRIGVD-DQIPAV 134
           I+LN GCP  +V     G+ L    D+    +  A+ +A  IPVTVK R G+D D +  +
Sbjct: 102 IDLNFGCPVPKVTRKGGGSALPWKIDLFTAIVTTAVREAGDIPVTVKMRKGIDADHLTYL 161

Query: 135 ALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
               +     ++GV  + +H R    +  G +          D+D +  +K    D    
Sbjct: 162 DAGQIA---ARAGVAAMTLHGRTTADLYSGTA----------DWDAIARLKDTIGDAIPV 208

Query: 193 LNGG----LEDMSQALKILPSVDGVMIGRA 218
           L  G     ED +QA+      DGV+IGR 
Sbjct: 209 LGNGDIFSAED-AQAMMAKTGCDGVVIGRG 237


>gi|46124971|ref|XP_387039.1| hypothetical protein FG06863.1 [Gibberella zeae PH-1]
          Length = 416

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 85/187 (45%), Gaps = 21/187 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + VEAA++V       I++N GCP      G  GA L+  PD     + 
Sbjct: 104 LIFQIGTADPDRAVEAARLVA-ADVAGIDVNAGCPKPFSTSGGMGAALLQTPDK----LC 158

Query: 110 AMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ +AL   +T +  IG+  +I     A     LV+ +  +G+ G+ IH R   ++   P
Sbjct: 159 AILEALVKNITPEFEIGISVKIRLLDTAAETEALVRRLCATGITGLTIHCRTTPMR---P 215

Query: 166 KDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++   R    +  ++ +E       +   +NG +E     L++      DG MI  AA K
Sbjct: 216 RERAIRGQLRMIAEVCHEF-----GVACLVNGDVEGRDHGLQLAEEFGADGAMIAVAAEK 270

Query: 222 NSAMLTT 228
           N +   +
Sbjct: 271 NPSCFRS 277


>gi|170592763|ref|XP_001901134.1| PP3111 protein [Brugia malayi]
 gi|158591201|gb|EDP29814.1| PP3111 protein, putative [Brugia malayi]
          Length = 513

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 76/166 (45%), Gaps = 12/166 (7%)

Query: 1   MVDWTDRHYRFFARL----LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R   R     L  + +++ ++ V DA  R   +  L     ++PL +Q   
Sbjct: 67  MVDQSELAFRMMLRKHGAHLCFSPMIHAQLFVTDATYR---RTALSTCLDDRPLVVQFCA 123

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   L+ A ++VE F  + ++LN+GCP      G +GA L  +  ++ + I  +     
Sbjct: 124 NDPVILLNACQLVESFC-DGVDLNLGCPQLIAKRGHYGAYLQEDLKLICEMITLLHSHSR 182

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +P++ K RI  D        R LV    K+G   + +H R    +G
Sbjct: 183 LPLSCKIRILQDINETVAYARALV----KAGACMLTVHGRTREQRG 224


>gi|238784237|ref|ZP_04628249.1| tRNA-dihydrouridine synthase C [Yersinia bercovieri ATCC 43970]
 gi|238714804|gb|EEQ06804.1| tRNA-dihydrouridine synthase C [Yersinia bercovieri ATCC 43970]
          Length = 310

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPKWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 177 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMNVTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|325189578|emb|CCA24064.1| tRNAdihydrouridine synthase putative [Albugo laibachii Nc14]
          Length = 427

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 61/120 (50%), Gaps = 8/120 (6%)

Query: 40  ILGFSTQEKP-LALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +   S +EK  +  Q+G +D I  +  A K+  D     I++N+GCP     +G  GA L
Sbjct: 70  VFRTSKEEKDRVVFQMGTSDPILAIKAAQKVARDVA--AIDVNMGCPKHFSIQGGMGAAL 127

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +  P +  D I A+ + L IPV+ K R+  D      A    VK ++++G + I +H R+
Sbjct: 128 LQKPQLAFDIIKALKQNLEIPVSCKIRVLEDTN----ATIEFVKKMEQAGADAIGVHGRQ 183


>gi|323168721|gb|EFZ54401.1| dihydrouridine synthase family protein [Shigella sonnei 53G]
          Length = 315

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKAVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A +   +   D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|254428569|ref|ZP_05042276.1| Dihydrouridine synthase superfamily [Alcanivorax sp. DG881]
 gi|196194738|gb|EDX89697.1| Dihydrouridine synthase superfamily [Alcanivorax sp. DG881]
          Length = 315

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 108/227 (47%), Gaps = 23/227 (10%)

Query: 41  LGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           LG  T+   P+ LQ+ G++   + E A      G   I+LN GCP+  V+    GA L+ 
Sbjct: 58  LGARTRAGTPVHLQLLGSEPDCMAENAVRAVALGAPAIDLNFGCPAKTVNRHRGGAVLLD 117

Query: 100 NPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
            P++V    AA+  A+  ++PV+VK R+G +D   A AL N  +++ ++G   + +H R 
Sbjct: 118 EPEVVHAVTAAVRDAVPANVPVSVKMRLGNEDD--ARALDN-ARAVVEAGAAWLTVHGR- 173

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVM 214
                 + +   K P   +D +  I +E   + +  NG +   +D ++A +     D +M
Sbjct: 174 ------TKRQGYKPPAF-WDRIGHI-REVVSIPVIANGEIWTADDAARA-RQESGCDDLM 224

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           +GR A  N  +++ +            PI     + FW  ++ + TD
Sbjct: 225 LGRGAVANPRLVSVLRHGGEPGWDAILPIL----QQFWVDVAGTGTD 267


>gi|330446569|ref|ZP_08310221.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328490760|dbj|GAA04718.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 298

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 85/176 (48%), Gaps = 17/176 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +QI G D   + E A+     G   +++N GCP+  V++   GA L+  P+ +   +
Sbjct: 49  PVRVQILGQDPDWMAENAQRACSLGSAGVDINFGCPAKAVNKSRGGAVLLKEPERIYQIV 108

Query: 109 AAMCKALSIPV---TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A C+A   PV   T K R+G DD  P+     +  +I ++G + + +HAR       + 
Sbjct: 109 KA-CRAAVNPVKPLTAKVRLGWDD--PSQCFE-IADAIAQAGADELVVHAR-------TK 157

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +D  +   + +D + ++K++   L I  NG + +       L +   D +M+ R A
Sbjct: 158 EDGYRADTIKWDYINQLKQQ-VKLPIIANGEVWNYQDGQNCLTATDTDALMVCRGA 212


>gi|77918513|ref|YP_356328.1| tRNA-dihydrouridine synthase [Pelobacter carbinolicus DSM 2380]
 gi|77544596|gb|ABA88158.1| tRNA-U20a,U20b-dihydrouridine synthase [Pelobacter carbinolicus DSM
           2380]
          Length = 303

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 84/180 (46%), Gaps = 14/180 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G D   L  AA+  +  G   INLN+GCP  R+   + G  L+  P+ +   +
Sbjct: 55  PLVVQLIGHDDRSLAIAAQSAQQAGARHINLNLGCPHGRMTSAAVGGNLLAQPERIAPML 114

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           A + K +S   +VK R G +D      + +L+  ++ +GV+   +H R  +L+G   +  
Sbjct: 115 AGLRKVVSGSFSVKLRAGYED---PTQIFSLLPMLEDAGVDFFILHPR-TVLQGYDGQA- 169

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAML 226
                 D+ I   + K      I  NG +   +   ++L   D  G+M+GR A  +  + 
Sbjct: 170 ------DHAITAAVAKRTCLPLIA-NGDIRKPADGCRLLEQTDIAGLMLGRGAIADPLLF 222


>gi|320534182|ref|ZP_08034711.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320133603|gb|EFW26022.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 432

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 62/288 (21%), Positives = 120/288 (41%), Gaps = 28/288 (9%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKI-VED 71
           LL    L  TEM+   A++  +++ +    T   E+  ++Q+ G D + +  A +I VE+
Sbjct: 76  LLAPAGLYVTEMVTTRALVERNERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEE 135

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-----------AMCKALSIPVT 120
              + I+LN GCP  +V     GA L    D++   +            A  +   +PVT
Sbjct: 136 DLSDHIDLNFGCPVPKVTRKGGGAALPWKRDLLAAILTEAVRASEAAARAAGRVRQVPVT 195

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G+D+        +  ++ + +G+  + +HAR A           +I  L    V 
Sbjct: 196 MKMRLGIDEG--HETFLDAARAAENAGIAAVALHARSARQHYSGQARWEEIARLKESTVL 253

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +   N D+++G     +D  + ++     DGV++GR       +   +           
Sbjct: 254 PVLG-NGDIWLG-----DDAVRMMETT-GCDGVVVGRGCQGRPWLFADIVAAMHG----- 301

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           SP +TR D D   ++        A  +     ++ + +H+     G+P
Sbjct: 302 SPTRTRPDLDAVIEVIRRHGRMLAEEMGEDRGVRDLRKHVGWYLKGYP 349


>gi|315042544|ref|XP_003170648.1| hypothetical protein MGYG_06634 [Arthroderma gypseum CBS 118893]
 gi|311344437|gb|EFR03640.1| hypothetical protein MGYG_06634 [Arthroderma gypseum CBS 118893]
          Length = 420

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 100/214 (46%), Gaps = 20/214 (9%)

Query: 18  NNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
           NN + +T +    A    DK +++     + ++  L  Q+G A     VEAAK++ D   
Sbjct: 81  NNTVEFTRVPSHPAPDAKDKVSVIYRIDPAREKGKLIFQLGTASPDLAVEAAKVIAD-DV 139

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQ 130
           + I++N GCP      G  GA L+  PD +   + A+ + +  P    ++VK R+  D +
Sbjct: 140 SGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILEALVREVGQPWQIGISVKIRLLKDPK 199

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                   LV ++  +G+ G+ IH R   ++        ++P     ++  I + +  + 
Sbjct: 200 ----DTERLVTALCATGITGLTIHCRTTPMRPREAAIRDQLP-----MIAAICR-SAGVA 249

Query: 191 IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           + +NG ++    AL+++    VDG MI  +A  N
Sbjct: 250 VLMNGDVKSRDHALELMSQYDVDGAMIATSAESN 283


>gi|303232252|ref|ZP_07318951.1| TIM-barrel protein, nifR3 family [Atopobium vaginae PB189-T1-4]
 gi|302481662|gb|EFL44723.1| TIM-barrel protein, nifR3 family [Atopobium vaginae PB189-T1-4]
          Length = 456

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 101/244 (41%), Gaps = 23/244 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKK-NILGFSTQEKPLALQIGGAD 58
           M   +D+ YR            Y+EM+ VA      DK  +++  S  EKPL +Q+ G+ 
Sbjct: 76  MASVSDKSYRIVNEC-AGAGFAYSEMVSVAGLHYDSDKTWDLICPSDVEKPLVVQLFGSK 134

Query: 59  ISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   AA  + +   + +   ++N+ CP A+V +   G+ LM  P+   D + A+C   
Sbjct: 135 PDQFRAAAARIAERLSDRLLFFDVNMACPVAKVTKKGEGSALMCTPEKAADIVRALCAET 194

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPN 173
           S+ VT K R G +      +     + ++ +G   I +H R  K +  G S         
Sbjct: 195 SVAVTCKIRRGYEQGNETAS--EFARVLEDAGAAAITVHGRYAKQLYSGNS--------- 243

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              D   E       +    +G +    +A  L  +P V GVMI R  Y N  + +    
Sbjct: 244 --CDACIERVARAISVPTIASGDILTPERACTLASIPGVAGVMIARGTYGNPWIFSDAYT 301

Query: 232 YFSN 235
            FS 
Sbjct: 302 LFSQ 305


>gi|302843625|ref|XP_002953354.1| hypothetical protein VOLCADRAFT_105870 [Volvox carteri f.
           nagariensis]
 gi|300261451|gb|EFJ45664.1| hypothetical protein VOLCADRAFT_105870 [Volvox carteri f.
           nagariensis]
          Length = 307

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 40/172 (23%), Positives = 78/172 (45%), Gaps = 13/172 (7%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
              Q+    I+  + A+K+ ++ G   +++N GCP         G+ ++  P  +   +A
Sbjct: 2   FGFQVACKTIADGIAASKLAKEAGAQFLDINCGCPIHEATRRGMGSAMLRKPRALAKMVA 61

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +PVTVK R+G +D+   + + ++V+ ++++G   + +H R A        + R
Sbjct: 62  GIAAESELPVTVKVRLGENDK--KINVDSVVRFLERAGAAAVTVHGRTA--------EQR 111

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
                D+  V E+ + +    IG NG +    +A   L       VM GR A
Sbjct: 112 YKKAADWGRVGELARSSSVPIIG-NGDILTHYEARARLEESGCAAVMAGRGA 162


>gi|258564268|ref|XP_002582879.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
 gi|237908386|gb|EEP82787.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
          Length = 431

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/179 (26%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A  S  VEAAKIV     + I++N GCP      G  GA L+  PD +   + 
Sbjct: 106 LVFQLGTATPSLAVEAAKIVA-ADVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLVSILE 164

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK RI  + +       +LV  + K+G+ G+ +H R   ++    
Sbjct: 165 ALVEEVGKPYEIGISVKIRILAEPE----RTESLVTRLCKTGITGLTVHCRTTPMRPREA 220

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I ++   +   +NG +    +A+ ++    VDG MI  +A  N
Sbjct: 221 AIREQLP-----MIASICRKA-GVACVMNGDVTSRDEAMTLIREYGVDGAMIATSAESN 273


>gi|152971120|ref|YP_001336229.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|262040158|ref|ZP_06013411.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|329999116|ref|ZP_08303320.1| tRNA-dihydrouridine synthase [Klebsiella sp. MS 92-3]
 gi|150955969|gb|ABR77999.1| conserved protein, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|259042511|gb|EEW43529.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328538446|gb|EGF64564.1| tRNA-dihydrouridine synthase [Klebsiella sp. MS 92-3]
          Length = 310

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPEWLAENAARAVALGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPEHLPVTVKVRLGWDS---GERRFEIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI ++   + +  NG + D   A   +     D VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEI-RQRLTIPVVANGEIWDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|40889946|pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
           Flavin
          Length = 318

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 59/254 (23%), Positives = 114/254 (44%), Gaps = 17/254 (6%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKL 62
           +TD  +R  A         ++E + A   L   +K   L     E+ +A+QI G++ ++L
Sbjct: 15  YTDSAFRTLA-FEWGADFAFSEXVSAKGFLXNSQKTEELLPQPHERNVAVQIFGSEPNEL 73

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   +VK
Sbjct: 74  SEAARILSE-KYKWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVRELRKSVSGKFSVK 132

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G +        R LV    + GV+ ++IH R  +++  + +   K  ++       +
Sbjct: 133 TRLGWEKNEVEEIYRILV----EEGVDEVFIHTR-TVVQSFTGRAEWKALSV-------L 180

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           +K  P    G     ED  +AL+     DG+++ R A     +   + ++  +    S P
Sbjct: 181 EKRIPTFVSGDIFTPEDAKRALE-ESGCDGLLVARGAIGRPWIFKQIKDFLRSG-KYSEP 238

Query: 243 IKTRVDKDFWRKIS 256
            +  + + F R + 
Sbjct: 239 SREEILRTFERHLE 252


>gi|329903041|ref|ZP_08273353.1| tRNA-dihydrouridine synthase B [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548519|gb|EGF33185.1| tRNA-dihydrouridine synthase B [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 348

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 111/251 (44%), Gaps = 16/251 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L   +K    +    +  P A+QI GAD
Sbjct: 27  MAGVTDRPFRQLCKQL-GAGYAVSEMAASNPRLWQTEKTSRRINHDGEMAPRAVQIAGAD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L + A+   + G   I++N+GCP  +V     G+ L+ +  +VG  + A+  A+ +P
Sbjct: 86  PAMLADCARFNVERGAQVIDINMGCPVKKVCNSWCGSALLQDERLVGQILDAVVAAVDVP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q       N+ +  + +G+  + +H R         + +      +Y+ 
Sbjct: 146 VTLKFRTGWDRQHKNAL--NIARLAQSAGIAMLTLHGRT--------RADGYNGAAEYET 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +L     D +MIGRAA     +   V  +    
Sbjct: 196 IAAVKAA-VTIPVVANGDITTPEKARHVLAVTGADAIMIGRAAQGRPWIFREVVHFLKTG 254

Query: 237 LTGSSPIKTRV 247
              ++P+ + V
Sbjct: 255 THLAAPLVSEV 265


>gi|49083690|gb|AAT51107.1| PA3129 [synthetic construct]
          Length = 320

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 62/113 (54%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +
Sbjct: 64  PMRVQLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           AA+ +A+   I VT K R+G D   P  AL +  +++   G   + +HAR  +
Sbjct: 124 AAVRRAVPSEIAVTSKMRLGYDS--PDGAL-DCARALADGGSAHVVVHARTKV 173


>gi|328855959|gb|EGG05082.1| hypothetical protein MELLADRAFT_48857 [Melampsora larici-populina
           98AG31]
          Length = 448

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 86/199 (43%), Gaps = 24/199 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           EK   +Q+ G+    LV AA+++  +   + +++N GCP   V +   GA L+ +   +G
Sbjct: 141 EKIFGVQVAGSRPQLLVPAAEMIGNELKVDFVDVNCGCPIDLVFKKGSGAALLEHTQRLG 200

Query: 106 DCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             +  M K L  IP+T+K R G+ +         ++  ++  GV    +H R        
Sbjct: 201 KSLIGMSKVLKEIPLTIKLRTGITEG--KNLAHKIIPQLQHWGVGATTLHGRS------- 251

Query: 165 PKDNRKIPNLDYDIVYEIKK-------ENPDL---FIGLNGGLEDMSQALK--ILPSVDG 212
            +  R     D++ + E  K       E PDL    I  NG   D  +  +   +  VDG
Sbjct: 252 -RQQRYSKRADWNYISECVKTLHRTFEEEPDLPQIPIFGNGDCYDYREYYENMEMSGVDG 310

Query: 213 VMIGRAAYKNSAMLTTVDE 231
           +MI R A     + T + E
Sbjct: 311 IMIARGALTKPWIFTEIKE 329


>gi|227356698|ref|ZP_03841084.1| tRNA-dihydrouridine synthase C [Proteus mirabilis ATCC 29906]
 gi|227163206|gb|EEI48137.1| tRNA-dihydrouridine synthase C [Proteus mirabilis ATCC 29906]
          Length = 303

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 80/173 (46%), Gaps = 17/173 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G +   L E A      G   ++LN GCPS  V+    GA L+  P+ +     AM
Sbjct: 60  VQLLGQNPQWLAENAFRAVSLGSWGVDLNCGCPSKTVNGNGGGASLLKQPETIYQATKAM 119

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PV+VK R+G D    +     +  ++++ G   I IH R       + +D  
Sbjct: 120 RGAVPADLPVSVKVRLGWD---CSSYCHEIADAVEQGGATEITIHGR-------TKEDGY 169

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           +   +++  + EI+++     I  NG +   ED    LKI    D +MIGR A
Sbjct: 170 RADKINWQAIGEIRQKLTIPVIA-NGEIWCREDAISCLKIT-GCDAIMIGRGA 220


>gi|223038738|ref|ZP_03609031.1| tRNA-dihydrouridine synthase B [Campylobacter rectus RM3267]
 gi|222880140|gb|EEF15228.1| tRNA-dihydrouridine synthase B [Campylobacter rectus RM3267]
          Length = 512

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 98/201 (48%), Gaps = 20/201 (9%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EMI A+A++    K +  L  S  E P  +QI G+D   + +A +I+    G + I+LN
Sbjct: 37  SEMISANALVYEGSKTLEMLKKSPLETPYIVQIAGSDADIVKKAVEILNGIEGIDGIDLN 96

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V + S G+ L+ +   +   +  + K  +  +T VK R+G D++IP +    L
Sbjct: 97  CGCPVPKVVKQSAGSALLKDISNLKRIVETIKKTSNKQMTSVKLRLGFDEKIPEI----L 152

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
             + + +G + I  H R         +       +DY  +    KE   + +  NG +  
Sbjct: 153 ALAAQDAGADYIAFHGRT--------RAGGYTATVDYAAIGR-AKEAVTIPVIANGDISP 203

Query: 198 EDMSQALKILPSVDGVMIGRA 218
           E+ + AL  L + D +MIGRA
Sbjct: 204 ENAADALN-LTNADALMIGRA 223


>gi|47192407|emb|CAF87237.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 142

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 32/111 (28%), Positives = 57/111 (51%), Gaps = 4/111 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R  + + + +T MIVA   ++  K     F+T +  +PL +Q    +
Sbjct: 16  MVRYSKLAFRSLVRKYSCD-VCFTPMIVASDFIQSTKARDSEFTTNQHDRPLIVQFAADN 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
              L +AA +V  F  + +++N GCP        +GACL+  P++V D +A
Sbjct: 75  AQTLADAACVVAPFS-DGVDINCGCPQRWAMSAGYGACLINKPELVKDMVA 124


>gi|224105275|ref|XP_002313751.1| predicted protein [Populus trichocarpa]
 gi|222850159|gb|EEE87706.1| predicted protein [Populus trichocarpa]
          Length = 362

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 63/279 (22%), Positives = 110/279 (39%), Gaps = 31/279 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    +++ ++   + I++N+
Sbjct: 45  EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVTRTVELIDQECTVDFIDINM 104

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     G+ L+  P  +   I A    +  P+TVK R G  +      + +L+ 
Sbjct: 105 GCPIDIVVNKGAGSSLLTKPMRMKSIIEATSGTVEKPITVKVRTGYFEG--KSRIDSLIV 162

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----L 197
            I K G + + IH R         +  R     D+D +Y+  ++ PD    L  G     
Sbjct: 163 DIGKWGASAVTIHGRS--------RQQRYSKLADWDYIYQCARKAPDSLQVLGNGDVFSF 214

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
            D +      P +   MI R A     + T + E     +  SS  +  + KD+ R    
Sbjct: 215 VDWNNHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDI--SSGERLNILKDYVRS--- 269

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   H  S  K  + TRH +  +  +     CR++
Sbjct: 270 -----GLEHWGSDTKGVETTRHFLLEWLSYT----CRYV 299


>gi|300715941|ref|YP_003740744.1| tRNA-dihydrouridine synthase C [Erwinia billingiae Eb661]
 gi|299061777|emb|CAX58893.1| tRNA-dihydrouridine synthase C [Erwinia billingiae Eb661]
          Length = 320

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 86/188 (45%), Gaps = 22/188 (11%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             A+   +PVTVK R+G    D Q        +  +++++G   + +H R       + +
Sbjct: 127 RDAVPAHLPVTVKVRLGWESGDRQF------EIADAVQQAGATELAVHGR-------TKE 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
           D  K   +++  + EI++      I  NG + D   A   +     D VMIGR A  N  
Sbjct: 174 DGYKPERINWQAIGEIRQRLTIPVIA-NGEIWDWQSAQDCMQVTGCDAVMIGRGAL-NVP 231

Query: 225 MLTTVDEY 232
            L+ V +Y
Sbjct: 232 NLSRVIKY 239


>gi|156844300|ref|XP_001645213.1| hypothetical protein Kpol_1060p9 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156115872|gb|EDO17355.1| hypothetical protein Kpol_1060p9 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 383

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 110/219 (50%), Gaps = 38/219 (17%)

Query: 36  DKKNILGFST----QEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSA-RVH 89
           +K + L F T    ++  L  Q+G +  +  VEAA KIV D   + I++N GCP    +H
Sbjct: 67  NKPSTLVFRTFPKNEQGKLIFQMGTSSPTLAVEAALKIVNDV--DGIDINAGCPKHFSIH 124

Query: 90  EGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            G  GA L+  PD    I+ + ++ + K  + P++VK RI +DD+   VA   LV+ +  
Sbjct: 125 SG-MGAALLKTPDILCSILENLVSKVGKPYNKPISVKIRI-LDDKETTVA---LVERLCT 179

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGL------E 198
           +G++ + +H R       +P  NR+ P  DY   + EI ++N ++ + +NG +      +
Sbjct: 180 TGISNLTVHCR------TTPMRNREAPIRDYIPSIKEICEKN-NVSLIMNGAIKNKVHFK 232

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           ++ + L +   + G MI   A  N  + +       NPL
Sbjct: 233 ELREELGLSKDIGG-MIAECAETNPTVFS------QNPL 264


>gi|145351179|ref|XP_001419962.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580195|gb|ABO98255.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 361

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 71/150 (47%), Gaps = 5/150 (3%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F R+ T+    +  +EM +A  +L+GD+K   +L     EK   +Q+ G     +   A+
Sbjct: 23  FRRVCTDLGADITVSEMAMASNLLKGDRKEWALLRRHPSEKCYGIQVCGGYPDLMARCAE 82

Query: 68  IVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +++ +   + I++N+GCP   V     G+ LM + D + + +  M    S PVT+K R+G
Sbjct: 83  LIDNEVSCDFIDVNMGCPIDGVCAKGAGSSLMRDTDRLKNVVRTMAAVSSTPVTIKLRMG 142

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             D        +++   K  G     +H R
Sbjct: 143 YFDDPSKYVAHDIIPRAKAWGAFAATLHGR 172


>gi|89073254|ref|ZP_01159784.1| putative regulator protein [Photobacterium sp. SKA34]
 gi|89050964|gb|EAR56428.1| putative regulator protein [Photobacterium sp. SKA34]
          Length = 313

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 89/192 (46%), Gaps = 22/192 (11%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR D K   G      P+ +QI G D + + E A+     G   +++N GCP+  V++  
Sbjct: 53  LRQDGKTRSG-----TPVRVQILGQDPNWMAENAQRACSLGSAGVDINFGCPAKAVNKSR 107

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPV---TVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            GA L+  P+ +   + A C+A   P+   T K R+G DD  PA     +  +I ++G +
Sbjct: 108 GGAVLLKEPERIYQIVKA-CRAAVNPIKPLTAKVRLGWDD--PAQCF-EIADAIAQAGAD 163

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKIL 207
            + +HAR       + +D  +   + +D + ++K       I  NG + +    QA    
Sbjct: 164 EMVVHAR-------TKEDGYRAETIKWDYIKQLKNSVAIPIIA-NGEVWNYHDGQACLTA 215

Query: 208 PSVDGVMIGRAA 219
            + D +M+ R A
Sbjct: 216 TNTDALMVCRGA 227


>gi|326930780|ref|XP_003211519.1| PREDICTED: LOW QUALITY PROTEIN: tRNA-dihydrouridine synthase
           1-like, partial [Meleagris gallopavo]
          Length = 487

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/174 (27%), Positives = 81/174 (46%), Gaps = 19/174 (10%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADA--ILRGDKKN------ILGFSTQEK 48
           MVD ++  +R  +R     L    +L+ ++ + DA   LRG K N      ++ F +   
Sbjct: 21  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFLRDANYRLRGKKNNYCLLILLVXFCSSLS 80

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P   Q    D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I
Sbjct: 81  PS--QFCANDPEVFVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMI 137

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
               + LS+P+T  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 138 LLANEKLSVPIT--CKIRVFPEIDKTV--KYAQMLEKAGCQLLTVHGRTKEQKG 187


>gi|89272495|emb|CAJ83250.1| dihydrouridine synthase 3-like protein [Xenopus (Silurana)
           tropicalis]
          Length = 639

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 67/282 (23%), Positives = 120/282 (42%), Gaps = 40/282 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM +   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 324 EMAMCTNLLQGQPSEWALLKRHHSEDIFGVQLEGAFPDTMTKCAELLNRTIDVDF----V 379

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM   +     +  M   L +P+TVK R GV ++I      
Sbjct: 380 DINVGCPIDLVYKKGGGCGLMNRTNKFEQIVKGMNSVLDVPLTVKIRTGVQEKINIA--H 437

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L+ +++  GV+ + +H R         ++ R     D++ + +       L +  NG +
Sbjct: 438 KLIPNLRDWGVSLVTLHGRS--------REQRYTKLADWEYIAQCADIASPLPLFGNGDI 489

Query: 198 ---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
              ED ++AL+    V G+M+ R A     + T + E     +  SS  +  + KDF   
Sbjct: 490 ISYEDANRALQT--GVSGIMLARGALLKPWLFTEIKEQRHWDI--SSTERFDILKDF--- 542

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                T+Y   H  S  +  + TR  +  +  F     CR+I
Sbjct: 543 -----TNYGLEHWGSDCQGVEKTRRFMLEWLSF----LCRYI 575


>gi|268576246|ref|XP_002643103.1| Hypothetical protein CBG23028 [Caenorhabditis briggsae]
          Length = 279

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 99/223 (44%), Gaps = 19/223 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R   RL   + + YT MI A   +  +K   + L     + PL +Q    D   L EAA
Sbjct: 6   FRQLVRLYDVD-VCYTPMIYAKNFIESEKCRNSELSVCEGDSPLIVQFATDDPFVLAEAA 64

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRI 125
           ++V     + ++LN GCP   V    FG+ L+  P+++ D +      +S    +V  +I
Sbjct: 65  EMVYSCS-SGVDLNCGCPKHDVRSKGFGSALLSKPELLADMVRQTRARISDENFSVSLKI 123

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            V+ +I      +L +  + +GV  + +H R       +P  + +  +++      + K 
Sbjct: 124 RVNKEIEKTV--DLCRKAESAGVTHLTVHGR-------TPSQHAEPIDIE---AIRLVKS 171

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
              + I  NGG+ ++ +A+ +     VDG+M       N A+ 
Sbjct: 172 AVKVPIIANGGITNLQEAMNLAEKTGVDGIMAANGLLDNPALF 214


>gi|330974611|gb|EGH74677.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 178

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 60/113 (53%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +
Sbjct: 124 SQVRRAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKV 173


>gi|260220081|emb|CBA27263.1| tRNA-dihydrouridine synthase B [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 350

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 65/261 (24%), Positives = 114/261 (43%), Gaps = 29/261 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK------PLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S +        P+A+QI
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHDGEPGPIAVQI 71

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G + + + EAA    D G   I++N+GCP+ +V     G+ LM +  +   + D +   
Sbjct: 72  AGTEAAMMAEAAVYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQDEQLAIEIVDAVVKA 131

Query: 112 CKALSIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           C   ++PVT+K R G    +  AV    L ++ + +GV  + +H R         ++   
Sbjct: 132 CAPRNVPVTLKMRTGWCQAEKNAVV---LARAAEAAGVQMVTVHGRT--------REQGY 180

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               +YD +  +K     + +  NG +    +A  +L +   D +MIGRAA     +   
Sbjct: 181 KGAAEYDTIAAVKAA-LRIPVVANGDITTPEKARDVLAATGADAIMIGRAAQGYPWIFRE 239

Query: 229 VDEYFSNPLTGSSPIKTRVDK 249
           V  + +     + P+ + V K
Sbjct: 240 VAHFLATGTHLAPPLVSEVKK 260


>gi|197284518|ref|YP_002150390.1| tRNA-dihydrouridine synthase C [Proteus mirabilis HI4320]
 gi|194682005|emb|CAR41473.1| tRNA-dihydrouridine synthase C [Proteus mirabilis HI4320]
          Length = 310

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 80/173 (46%), Gaps = 17/173 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G +   L E A      G   ++LN GCPS  V+    GA L+  P+ +     AM
Sbjct: 67  VQLLGQNPQWLAENAFRAVSLGSWGVDLNCGCPSKTVNGNGGGASLLKQPETIYQATKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PV+VK R+G D    +     +  ++++ G   I IH R       + +D  
Sbjct: 127 RGAVPADLPVSVKVRLGWD---CSSYCHEIADAVEQGGATEITIHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           +   +++  + EI+++     I  NG +   ED    LKI    D +MIGR A
Sbjct: 177 RADKINWQAIGEIRQKLTIPVIA-NGEIWCREDAISCLKIT-GCDAIMIGRGA 227


>gi|327539746|gb|EGF26351.1| tRNA-dihydrouridine synthase [Rhodopirellula baltica WH47]
          Length = 374

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 87/193 (45%), Gaps = 10/193 (5%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           R   ++ L  + +E P+  Q+ GA+  +    A  + + G++ I++N GCP  +V     
Sbjct: 81  REKTRHFLDIADEEHPVGGQLMGAEPEQFSAGALKLVEAGFDVIDVNFGCPVKKVLGRCR 140

Query: 94  GACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA-VALRNLVKSIKKSGVNG 150
           G   +  P +  + +      +   IPVTVK R G+DD   +      ++     +G+ G
Sbjct: 141 GGFHLSQPAVAIEILRRTRDVVPDHIPVTVKMRRGMDDTPESREQFFEILDGAIDAGLAG 200

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS 209
           + +H R  + + + P     +  +   +   +K   + DLF  ++ GLE M Q       
Sbjct: 201 VTVHGRTVMQRYIGPSRWAFLKEVKQHVGDRLKILGSGDLFAAVD-GLEMMHQT-----G 254

Query: 210 VDGVMIGRAAYKN 222
           +DGV I R A  N
Sbjct: 255 IDGVTIARGAIGN 267


>gi|32471326|ref|NP_864319.1| NifR3 family protein [Rhodopirellula baltica SH 1]
 gi|32443167|emb|CAD71998.1| conserved hypothetical protein-putative NifR3 family protein
           [Rhodopirellula baltica SH 1]
          Length = 374

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 88/201 (43%), Gaps = 26/201 (12%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           R   ++ L  + +E P+  Q+ GA+  +    A  + + G++ I++N GCP  +V     
Sbjct: 81  REKTRHFLDIADEEHPVGGQLMGAEPEQFSAGALKLVEAGFDVIDVNFGCPVKKVLGRCR 140

Query: 94  GACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA-VALRNLVKSIKKSGVNG 150
           G   +  P +  + +      +   IPVTVK R G+DD   +      ++     +G+ G
Sbjct: 141 GGFHLSQPAVAIEILRRTRDVVPDHIPVTVKMRRGMDDTPESREQFFEILDGAIDAGLAG 200

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE---------NPDLFIGLNGGLEDMS 201
           + +H R  + + + P          +  + E+K+          + DLF  ++ GLE M 
Sbjct: 201 VTVHGRTVMQRYIGPS--------RWAFLKEVKQHVGDRLKILGSGDLFAAVD-GLEMMR 251

Query: 202 QALKILPSVDGVMIGRAAYKN 222
           Q       +DGV I R A  N
Sbjct: 252 QT-----GIDGVTIARGAIGN 267


>gi|309355062|emb|CAP39416.2| hypothetical protein CBG_23028 [Caenorhabditis briggsae AF16]
          Length = 283

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 99/223 (44%), Gaps = 19/223 (8%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAA 66
           +R   RL   + + YT MI A   +  +K   + L     + PL +Q    D   L EAA
Sbjct: 7   FRQLVRLYDVD-VCYTPMIYAKNFIESEKCRNSELSVCEGDSPLIVQFATDDPFVLAEAA 65

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRI 125
           ++V     + ++LN GCP   V    FG+ L+  P+++ D +      +S    +V  +I
Sbjct: 66  EMVYSCS-SGVDLNCGCPKHDVRSKGFGSALLSKPELLADMVRQTRARISDENFSVSLKI 124

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            V+ +I      +L +  + +GV  + +H R       +P  + +  +++      + K 
Sbjct: 125 RVNKEIEKTV--DLCRKAESAGVTHLTVHGR-------TPSQHAEPIDIE---AIRLVKS 172

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
              + I  NGG+ ++ +A+ +     VDG+M       N A+ 
Sbjct: 173 AVKVPIIANGGITNLQEAMNLAEKTGVDGIMAANGLLDNPALF 215


>gi|307110102|gb|EFN58339.1| hypothetical protein CHLNCDRAFT_16859 [Chlorella variabilis]
          Length = 308

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 57/233 (24%), Positives = 104/233 (44%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A   L         F+T  Q++PL  Q    D
Sbjct: 18  MVDQSELAFRQLTRRHGATGA-YTPMLHARLFLETPSYRAEHFTTTQQDRPLLAQFCAND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AA++V     + ++LN+GCP      G +G+ LM +  +V   +  +   L++P
Sbjct: 77  PDILLSAARLVAPH-VDGVDLNLGCPQRIAKRGKYGSFLMDDLPLVERLVRQLAANLAVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R    D +         + ++++G + + IH R         ++ ++   +  ++
Sbjct: 136 VTVKIRRF--DCVQRTV--QYAQMLERAGASLLAIHGRT--------REQKRASEVRAEV 183

Query: 179 VYEIKKENPDLFIGL--NGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLT 227
            Y I+     L I +  NG +  ++  +AL     VDGVM   +   + A+ +
Sbjct: 184 EY-IRAVKQGLRIPVLGNGNIRTLADCEALMAATGVDGVMSAESLLADPALFS 235


>gi|45361515|ref|NP_989334.1| tRNA-dihydrouridine synthase 3-like [Xenopus (Silurana) tropicalis]
 gi|110808214|sp|Q28BT8|DUS3L_XENTR RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|39850298|gb|AAH64263.1| dihydrouridine synthase 3-like protein [Xenopus (Silurana)
           tropicalis]
          Length = 639

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 67/282 (23%), Positives = 120/282 (42%), Gaps = 40/282 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM +   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 324 EMAMCTNLLQGQPSEWALLKRHHSEDIFGVQLEGAFPDTMTKCAELLNRTIDVDF----V 379

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM   +     +  M   L +P+TVK R GV ++I      
Sbjct: 380 DINVGCPIDLVYKKGGGCGLMNRTNKFEQIVKGMNSVLDVPLTVKIRTGVQEKINIA--H 437

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L+ +++  GV+ + +H R         ++ R     D++ + +       L +  NG +
Sbjct: 438 KLIPNLRDWGVSLVTLHGRS--------REQRYTKLADWEYIAQCADIASPLPLFGNGDI 489

Query: 198 ---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
              ED ++AL+    V G+M+ R A     + T + E     +  SS  +  + KDF   
Sbjct: 490 ISYEDANRALQT--GVSGIMLARGALLKPWLFTEIKEQRHWDI--SSTERFDILKDF--- 542

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                T+Y   H  S  +  + TR  +  +  F     CR+I
Sbjct: 543 -----TNYGLEHWGSDCQGVEKTRRFMLEWLSF----LCRYI 575


>gi|262274594|ref|ZP_06052405.1| tRNA-dihydrouridine synthase C [Grimontia hollisae CIP 101886]
 gi|262221157|gb|EEY72471.1| tRNA-dihydrouridine synthase C [Grimontia hollisae CIP 101886]
          Length = 317

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 36/135 (26%), Positives = 67/135 (49%), Gaps = 12/135 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     + E A +V + G + +++N GCPS  V+    GA L+  P+++   + A+
Sbjct: 60  VQLLGQSPHYMAENAALVAELGSSGVDINFGCPSKTVNGNKGGAALLKEPELMYQVVKAV 119

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+     V+ K R+G DD     A R +  +++  G N I +H R       S  D  
Sbjct: 120 REAVPYDQVVSAKVRLGFDD---VSAYREIADAVQSGGANEIVVHGR-------SKADAY 169

Query: 170 KIPNLDYDIVYEIKK 184
           K   + +D++ ++ K
Sbjct: 170 KAGTIRWDLIGDLTK 184


>gi|50290121|ref|XP_447492.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49526802|emb|CAG60429.1| unnamed protein product [Candida glabrata]
          Length = 371

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 55/194 (28%), Positives = 88/194 (45%), Gaps = 25/194 (12%)

Query: 44  STQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           S +   L  QIG AD +   EAA K+++D   + I+LN GCP         G+ L+  P+
Sbjct: 73  SLERGKLIFQIGSADPALAKEAALKVIQDV--DGIDLNCGCPKHFSIHAGMGSALLKKPE 130

Query: 103 ----IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
               I+ + +  +      P++ K R+  D+     +   LVK I  +G+  + +H R  
Sbjct: 131 KLCSILKELVEHVGTPHGKPISCKIRLLEDE----ASTLELVKMICDTGIRNLTVHCR-- 184

Query: 159 ILKGLSPKDNRKIPNLDY-DIVYEI-KKENPDLFIGLNGGL---EDMSQALKILPSVDGV 213
                +P  NR+ P  DY D ++ + KK    L I  NG +   E+  Q     P + G 
Sbjct: 185 ----TTPMRNRETPIRDYIDSIFSVCKKAGVSLLI--NGAIRHREEFEQLFSYNPEIGG- 237

Query: 214 MIGRAAYKNSAMLT 227
           MI  AA  N  + +
Sbjct: 238 MIAEAAESNPTVFS 251


>gi|238763826|ref|ZP_04624784.1| tRNA-dihydrouridine synthase C [Yersinia kristensenii ATCC 33638]
 gi|238697956|gb|EEP90715.1| tRNA-dihydrouridine synthase C [Yersinia kristensenii ATCC 33638]
          Length = 303

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 60  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 119

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 120 REAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 169

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 170 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLS 227

Query: 228 TVDEY 232
            V +Y
Sbjct: 228 RVVKY 232


>gi|150017944|ref|YP_001310198.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
 gi|149904409|gb|ABR35242.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
          Length = 321

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 50/238 (21%), Positives = 101/238 (42%), Gaps = 29/238 (12%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  ++ ++  GY+E+NLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNDAEGFINTSRKLQQLGYSEVNLNLGCPAKTVVSKNRGSGFLAKREELDSFLDEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSP-----K 166
           K   + +++K RIG ++         L+K   K  +  + IH R +    G  P     +
Sbjct: 124 KMDDMKISIKTRIGKEN---PEEFYELIKIYNKYPLEELIIHPRTQKDFYGNKPNLCVFR 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D   + N            NP  + G    + D ++ +   P V+ VM+GR    N  ++
Sbjct: 181 DALSLSN------------NPVCYNGDIFTINDYNKLVADFPEVNTVMLGRGILANPGLI 228

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             +     N +  S  I     KDF  +I     +     +++  +++++  +MI +F
Sbjct: 229 NVI----KNNINTSKNIL----KDFHDEILNRYIEVFPEDIYAINRMKELFGYMIYIF 278


>gi|241615739|ref|XP_002406800.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215500870|gb|EEC10364.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 449

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 89/195 (45%), Gaps = 26/195 (13%)

Query: 43  FSTQEKPLA---LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F T EK      LQIG     + V+ AK+VE      I++N+GCP     +G  GA L+ 
Sbjct: 71  FRTCEKERGKNILQIGTCSPERAVQVAKLVEK-DVAGIDVNMGCPKEFSLKGGMGAALLT 129

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKA 158
             D V   + A+ ++ ++PVT  C+I V D++   +AL  L++S   +GV  + +H R  
Sbjct: 130 QLDKVKAILTALVQSTTLPVT--CKIRVLDRLEDTLALGKLIES---TGVKALGVHGRTK 184

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG------LEDMSQALKILPSVDG 212
             +      N  I  L          E+  + +  NGG       ED+ +  ++      
Sbjct: 185 EERPQHKNRNATIKAL---------AEHLTIPVIANGGSSEIVDYEDIER-FRVATGATS 234

Query: 213 VMIGRAAYKNSAMLT 227
           VM+ R A  N ++ +
Sbjct: 235 VMLARQAESNCSIFS 249


>gi|299530726|ref|ZP_07044141.1| dihydrouridine synthase, DuS [Comamonas testosteroni S44]
 gi|298721242|gb|EFI62184.1| dihydrouridine synthase, DuS [Comamonas testosteroni S44]
          Length = 340

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 47/201 (23%), Positives = 92/201 (45%), Gaps = 21/201 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR   + + G      P+  Q+ G+D   + E A  +   G   I+LN GCP+  V+   
Sbjct: 46  LRNGSRTLAGV-----PVRAQLLGSDPVSMAENAANLARLGPEGIDLNFGCPAKVVNRHG 100

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            GA L+ +P+ +   + A+ +A+   +PV+ K R+G +D+     +    +++++ G   
Sbjct: 101 GGASLLQDPEQIVRVVDAVRRAVPAQLPVSAKMRLGFNDR---ALMTECAQAMEQGGACE 157

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LP 208
           I +HAR  +     P    +IP +         +E   + +  NG +  + +AL+   + 
Sbjct: 158 IVVHARTKLDGYRPPAYWEEIPRI---------REAVGVNVVANGEIWTVEEALRCREVS 208

Query: 209 SVDGVMIGRAAYKNSAMLTTV 229
             D +M+GR    +  +   V
Sbjct: 209 GCDDLMLGRGIVADPGLALAV 229


>gi|120609942|ref|YP_969620.1| dihydrouridine synthase [Acidovorax citrulli AAC00-1]
 gi|120588406|gb|ABM31846.1| tRNA-U20a,U20b-dihydrouridine synthase [Acidovorax citrulli
           AAC00-1]
          Length = 323

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 58/110 (52%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D S + E A  +   G   I+LN GCP+  V+    GA L+  P+ +   +
Sbjct: 68  PVRAQLLGSDPSSMAENAARLAALGPEGIDLNFGCPAKVVNRHGGGAALLREPERIAAVV 127

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +A+ +A+   +PV+ K R+G DD   A   R   ++ +  G   + +HAR
Sbjct: 128 SAVRRAVPPEMPVSAKMRLGYDDTSLA---RECAQAAEAGGACELVVHAR 174


>gi|170781947|ref|YP_001710279.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156515|emb|CAQ01666.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 408

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 56/224 (25%), Positives = 102/224 (45%), Gaps = 17/224 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +   ++     EK  ++Q+ G D
Sbjct: 43  MAGITNTAFRRLCREF-GAGLYVSEMITSRALVERTPESMRLITHHPSEKVRSIQLYGVD 101

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
              + EA   +V +   + I+LN GCP A+V     GA L     +  D +    KA  +
Sbjct: 102 PKTVREAVTMLVAEDRADHIDLNFGCPVAKVTRKGGGAALPWKLGLFTDIVEGAVKAAGN 161

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IP+TVK R G+D     +      ++ + +GV  I +HAR A         +    + D+
Sbjct: 162 IPLTVKMRKGIDAD--HLTYLEAGRAAEGAGVASIALHARTAA--------DYYSGHADW 211

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
             + ++K+   ++ +  NG +     A++++     DGV++GR 
Sbjct: 212 SAIAKLKQAIRNVPVLGNGDIWAAEDAIRMMDETGADGVVVGRG 255


>gi|238895707|ref|YP_002920442.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae NTUH-K2044]
 gi|238548024|dbj|BAH64375.1| tRNA-dihydrouridine synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 310

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPEWLAENAARAVALGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPEHLPVTVKVRLGWDS---GERRFEIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           K   +++  + EI ++   + +  NG + D   A   +     D VMIGR A  N   L+
Sbjct: 177 KAERINWQAIGEI-RQRLTIPVVANGEIWDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|255321994|ref|ZP_05363144.1| tRNA-dihydrouridine synthase B [Campylobacter showae RM3277]
 gi|255301098|gb|EET80365.1| tRNA-dihydrouridine synthase B [Campylobacter showae RM3277]
          Length = 306

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/201 (28%), Positives = 98/201 (48%), Gaps = 20/201 (9%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EMI A+A++    K +  L  S  E P  +QI G+D   + +A +I+    G + I+LN
Sbjct: 37  SEMISANALVYEGSKTLEMLKKSPLETPYIVQIAGSDADIVKKAVEILNGIDGIDGIDLN 96

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V + S G+ L+ +   +   +  + K  +  +T VK R+G D++IP +    L
Sbjct: 97  CGCPVPKVVKQSAGSALLKDISNLKRIVETIKKTSNKQMTSVKLRLGFDEKIPEI----L 152

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
             + + +G + I  H R         +       +DY  +    KE   + +  NG +  
Sbjct: 153 AIAAQDAGADYIAFHGRT--------RAGGYTTAVDYAAIGR-AKEAVTIPVIANGDISP 203

Query: 198 EDMSQALKILPSVDGVMIGRA 218
           E+ +Q L  L + D +MIGRA
Sbjct: 204 ENAAQTLN-LTNADALMIGRA 223


>gi|226940983|ref|YP_002796057.1| tRNA-dihydrouridine synthase C [Laribacter hongkongensis HLHK9]
 gi|226715910|gb|ACO75048.1| tRNA-dihydrouridine synthase C [Laribacter hongkongensis HLHK9]
          Length = 323

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/197 (25%), Positives = 98/197 (49%), Gaps = 17/197 (8%)

Query: 26  MIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           ++ A A  R   ++  G+ T    P+ LQ+ G+D + L + A    + G   ++LN GCP
Sbjct: 40  LLPAAAFRRIAPEHAHGWRTPAGTPVRLQLLGSDPASLADNAARGAELGAPVLDLNFGCP 99

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           +  V++   GA L+ NP  +    +A+  AL   +P+T K R+G+ D    +   +  ++
Sbjct: 100 APTVNKHGGGAALLDNPGQLYRIASAVRAALPAGVPLTAKMRLGLRDTELTL---DCARA 156

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS- 201
           +  +G++ + +HAR  + +G  P  +       +  V ++ KE     +  NG + ++  
Sbjct: 157 LDSAGISELVVHARTKV-EGYRPPAH-------WQWVAQV-KEVVAARVWANGEVWNLQD 207

Query: 202 -QALKILPSVDGVMIGR 217
            Q ++    VD +MIGR
Sbjct: 208 WQDIRRESGVDDIMIGR 224


>gi|118475725|ref|YP_891451.1| tRNA-dihydrouridine synthase B [Campylobacter fetus subsp. fetus
           82-40]
 gi|261885859|ref|ZP_06009898.1| tRNA-dihydrouridine synthase B [Campylobacter fetus subsp.
           venerealis str. Azul-94]
 gi|118414951|gb|ABK83371.1| tRNA-dihydrouridine synthase B [Campylobacter fetus subsp. fetus
           82-40]
          Length = 306

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/258 (24%), Positives = 117/258 (45%), Gaps = 35/258 (13%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
           + ++++NAL+Y        I    +KN L     E P  +Q+ G     + +A +I+ D 
Sbjct: 36  SEMISSNALVYENTKTVSMI----EKNPL-----ETPYIVQLAGNGSEIIKQAVQILNDI 86

Query: 73  -GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQ 130
            G + I+LN GCP  +V + + G+ L+ +   + + +  + K  +   T VK R+G + +
Sbjct: 87  EGIDGIDLNCGCPVPKVVKQNSGSALLNDIKTLCEIVETIKKTSNKHYTSVKIRLGFNSK 146

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                  N+ K I+ +G + I +H R     G S K       +DY+ +  + K++  + 
Sbjct: 147 ----TAHNIAKDIENAGADFICVHGRTR-AGGYSAK-------VDYEAI-GLVKQSVSIP 193

Query: 191 IGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG +  ++  + L+ L + DGVMIGRA+  N  +   +            P+   + 
Sbjct: 194 VIANGDINAKNADEILR-LTNCDGVMIGRASIGNPWIFYEIKH--------KKPVDKNIK 244

Query: 249 KDFWRKISASMTDYAARH 266
           K    +    M +Y   H
Sbjct: 245 KQIVLEHFNEMLNYYGEH 262


>gi|227547980|ref|ZP_03978029.1| possible dihydrouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227079991|gb|EEI17954.1| possible dihydrouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 393

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 36/119 (30%), Positives = 64/119 (53%), Gaps = 6/119 (5%)

Query: 17  TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFG 73
           T++ L   EMI A A++  ++K  ++  F+  E P +LQ+   D     +A + IVE+  
Sbjct: 53  TSSGLYVCEMITARALVARNQKTLHMTTFADVETPRSLQLYTVDPKFTYDAVRMIVEEDI 112

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDD 129
            + +++N GCP  +V     G+ +     +  + ++A  +A     IP+TVK RIG+DD
Sbjct: 113 ADHVDMNFGCPVPKVTRKGGGSAIPFKRRLYANIVSAAVRAAEGSGIPITVKFRIGIDD 171


>gi|209875549|ref|XP_002139217.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209554823|gb|EEA04868.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 716

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/247 (22%), Positives = 104/247 (42%), Gaps = 39/247 (15%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEI 77
           + ++EM + + IL G    +  L   ++E+   +Q+ G +   + +  + + ++  Y+ +
Sbjct: 357 ITFSEMTLCNEILAGKSSELALLRRHSEERCFGIQLAGGNFETIAKTGEFINEYCDYDFL 416

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV--- 134
           ++NV CP   +H+   G+ L+  P ++   I  + K +  P+T+K R+      P +   
Sbjct: 417 DINVACPLKSLHDRGAGSILIDRPKLLESIITGLKKVIDKPLTIKLRMANSASPPNLKFY 476

Query: 135 ------------------ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD------NRK 170
                             A   L+K +    +NGI IH R +  +     D        K
Sbjct: 477 ENTYINNPLNWDIIYSNMAAHKLIKPLVNYNINGIIIHGRTSSQRYNKSADWNYLRYCSK 536

Query: 171 IPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           I   +Y + Y+   +N    P L IG  G + +     K L    V+ VMIGR A     
Sbjct: 537 ILKNEY-LTYKDTNKNITYCPSL-IGC-GDVLNYCDYYKHLNEDDVNAVMIGRGALLKPW 593

Query: 225 MLTTVDE 231
           + T + E
Sbjct: 594 IFTEIKE 600


>gi|159127783|gb|EDP52898.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus
           fumigatus A1163]
          Length = 443

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    VEAAK+V       I+LN GCP      G  GA L+  PD +   + 
Sbjct: 104 LVFQIGSANPELAVEAAKLVAG-DVAGIDLNSGCPKPFSTSGGMGAALLRTPDKLVSILE 162

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++ + +  P    ++VK RI    +       +LVK +  +G+ G+ +H R   ++   P
Sbjct: 163 SLVREVGNPYQIGISVKIRILETPE----KTESLVKRLVATGITGLTVHCRTTPMR---P 215

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           ++ R I +    ++  I +E   +   +NG +    +AL ++    VDG MI  AA  N 
Sbjct: 216 RE-RAIRD-QLTMIARICREA-GVACVMNGDVTSRDEALALMKEFGVDGAMIATAAEANP 272

Query: 224 AMLTTVDE 231
           +   +  E
Sbjct: 273 SCFRSEAE 280


>gi|109128993|ref|XP_001097732.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Macaca mulatta]
          Length = 492

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 88/189 (46%), Gaps = 33/189 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GACL   P      ++
Sbjct: 84  VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGG-GACLKTLPQKKKKILS 141

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K +  PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 142 TLVKGIRRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------RE 187

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 188 ERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQRYSDIEDFRQAT----AASSVMVAR 242

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 243 AAMWNPSIF 251


>gi|332975732|gb|EGK12615.1| tRNA-dihydrouridine synthase C [Psychrobacter sp. 1501(2011)]
          Length = 347

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 88/202 (43%), Gaps = 22/202 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR D +   G      P+ +Q+ G++   + E A      G   I++N GCP+  V+   
Sbjct: 88  LRNDSRTNSG-----TPIHVQLLGSNPELMGENALAACALGAPAIDINFGCPAKTVNNHR 142

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            G+ L+  P ++ D I+A+       IPV+ K R+G  D      +  + K+I  SG N 
Sbjct: 143 GGSVLLDEPSLMRDIISAVRNKTPSHIPVSAKIRLGYTD---TSNMDGIKKAIADSGANW 199

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
           + IHAR        P    KI             E P + +  NG + +  QAL+ +   
Sbjct: 200 LTIHARTKTQGYKPPAYWEKITGF---------TELP-IPVVANGEIWNHEQALRCITQS 249

Query: 211 DG--VMIGRAAYKNSAMLTTVD 230
           +   +M+GR A     ++  +D
Sbjct: 250 NTPHLMLGRGAVTRPDLVAQID 271


>gi|198274061|ref|ZP_03206593.1| hypothetical protein BACPLE_00198 [Bacteroides plebeius DSM 17135]
 gi|198273139|gb|EDY97408.1| hypothetical protein BACPLE_00198 [Bacteroides plebeius DSM 17135]
          Length = 327

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 46/166 (27%), Positives = 77/166 (46%), Gaps = 17/166 (10%)

Query: 59  ISKLVEAAKIVEDF----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           I+   E  K++ DF    GY EI++N+GCP   +     GA ++ +P+ V   +  M   
Sbjct: 85  IASEPEELKVLTDFLASQGYREIDVNMGCPFPLIVRRGKGAGILSSPEKVEALLETMKVF 144

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIP 172
             +  +VK R+G  D   A   + LV  + +S V  + +H R  K   KG   ++     
Sbjct: 145 PEVRFSVKMRLGGQD---AEEWKALVPLLNRSCVTQVTLHPRIGKQQYKGTVDRET---- 197

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
              +   YE   E P ++ G    + D+ + L+  P + GVM+GR 
Sbjct: 198 ---FRAFYEA-CERPLVYNGDLLTVADIREVLEAFPRLKGVMLGRG 239


>gi|323452795|gb|EGB08668.1| hypothetical protein AURANDRAFT_13024 [Aureococcus anophagefferens]
          Length = 224

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/224 (24%), Positives = 98/224 (43%), Gaps = 32/224 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----VADAILRGDKKNILGFSTQEKPLALQIG 55
           +VD ++  YR   R      + +T M+     VADA  R         +  ++PL  Q  
Sbjct: 15  LVDQSELAYRLLCRSY-GAGICWTPMMDATRFVADAAYRRAVFEAGAGAPADRPLVAQFA 73

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D + ++ AA++VE    + + LN GCP      G FGA L+  P+++   + A+ + L
Sbjct: 74  GDDPAAILAAARLVEHR-VDVVELNCGCPQKVAKRGHFGAFLLDEPEVIVAVVRALKRGL 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +  V+              A   L + ++ +G + + +H R   +K          P  D
Sbjct: 133 ACAVS-------------AATVALARRLEAAGADLLTVHGRTRAMKKCG------FP-CD 172

Query: 176 YDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIG 216
           +  +  +K+    + +  NGG+E   D ++A + L   D VM G
Sbjct: 173 FAAIAAVKRAV-RVPVVANGGVERHADFARA-RELTGCDCVMSG 214


>gi|221068625|ref|ZP_03544730.1| dihydrouridine synthase DuS [Comamonas testosteroni KF-1]
 gi|220713648|gb|EED69016.1| dihydrouridine synthase DuS [Comamonas testosteroni KF-1]
          Length = 347

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 45/185 (24%), Positives = 85/185 (45%), Gaps = 16/185 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+ +P  +   +
Sbjct: 64  PVRAQLLGSDPVSMAENAANLARLGPEGIDLNFGCPAKVVNRHGGGASLLQDPMQIARVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ KA+   +PV+ K R+G +D+     +    ++++  G   I +HAR  +     P 
Sbjct: 124 EAVRKAVPAQLPVSAKMRLGFNDR---ALMTECAQAMESGGACEIVVHARTKLDGYRPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
              +IP +         +E   + +  NG +  + +AL+   +   D +M+GR    +  
Sbjct: 181 YWEEIPRI---------REAVGVNVVANGEIWTVEEALRCREVSGCDDLMLGRGIVADPG 231

Query: 225 MLTTV 229
           +   V
Sbjct: 232 LALAV 236


>gi|158320020|ref|YP_001512527.1| dihydrouridine synthase DuS [Alkaliphilus oremlandii OhILAs]
 gi|158140219|gb|ABW18531.1| dihydrouridine synthase DuS [Alkaliphilus oremlandii OhILAs]
          Length = 321

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/233 (21%), Positives = 100/233 (42%), Gaps = 19/233 (8%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    +  +K ++  GY EINLN+GCPS  V   + G+  +   + +   +  + 
Sbjct: 64  QILTNNSEGFISVSKKLKQLGYAEINLNLGCPSGTVVSKNRGSGFLAKREELDRFLEEIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKI 171
           K   + +++K RIG D          L+K   K  +  + IH R +    G         
Sbjct: 124 KIEDMKISIKTRIGKDH---PEEFYELIKIYNKYPLEELIIHPRTRQDFYG-------NQ 173

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           PNL+      +   NP  + G    + D ++ ++  P VD +M+GR    N  ++  +  
Sbjct: 174 PNLEVFKDALLLSTNPVCYNGDIFTVGDHNRLVETFPDVDTMMLGRGVLANPGLMKEIR- 232

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             +N L     ++  +D+  ++ +     +  A +     +++++  +M  +F
Sbjct: 233 --NNTLMEKEVLREFIDEVLYQYVELFQEERNALY-----RMKELWSYMAYIF 278


>gi|73541045|ref|YP_295565.1| dihydrouridine synthase, DuS [Ralstonia eutropha JMP134]
 gi|72118458|gb|AAZ60721.1| Dihydrouridine synthase, DuS [Ralstonia eutropha JMP134]
          Length = 324

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 90/193 (46%), Gaps = 18/193 (9%)

Query: 36  DKKNIL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           D   IL  G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    
Sbjct: 50  DTPEILQGGHTPSGTPMVIQLLGSDPEWLARNATYAATLSPHGIDLNFGCPAKVVNRHGG 109

Query: 94  GACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           GA L+ +P+ +   ++A+  A+   I VT K R+GV D   A+AL +   ++ + G   +
Sbjct: 110 GAMLLAHPEQLHSIVSAVRAAVPPHIAVTAKMRLGVSDT--ALAL-DCATALAEGGAASL 166

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPS 209
            +HAR         +D+   P   ++ +  I  +  D+ +  NG +  ++  +  + +  
Sbjct: 167 VVHART--------RDHGYRPPAHWEWIARI-ADTVDIPVIANGDVWSVADWERCRAVSG 217

Query: 210 VDGVMIGRAAYKN 222
              VMIGR A  +
Sbjct: 218 CADVMIGRGAVSD 230


>gi|84684884|ref|ZP_01012784.1| tRNA-dihydrouridine synthase, putative [Maritimibacter alkaliphilus
           HTCC2654]
 gi|84667219|gb|EAQ13689.1| tRNA-dihydrouridine synthase, putative [Rhodobacterales bacterium
           HTCC2654]
          Length = 327

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 111/246 (45%), Gaps = 27/246 (10%)

Query: 1   MVDWTDRHYR-----FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     F A L+ +  +   EM+ A    R  ++  LG        A+Q+ 
Sbjct: 20  MAGITDLPFRDLVSSFGAGLVVSEMVASQEMVQAKPGTR--ERAELGIEVANT--AVQLA 75

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   + EAA++VE  G   I++N+GCP+ +V  G  G+ L+ +  +    I A+ +A+
Sbjct: 76  GRDPYWIGEAARMVEANGARMIDINMGCPAKKVVGGLSGSALLRDLPLALRLIEAVVEAV 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPN 173
            +PVT+K R+G DD +  +    L    + +G+  I IH R      KG +         
Sbjct: 136 EVPVTLKTRLGWDDDL--MNAPTLAAQAEAAGIRMITIHGRTRCQFYKGRA--------- 184

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV-D 230
            D+  +  + K+  D+ +  NG +     A   L     DGVM+GR       ++  +  
Sbjct: 185 -DWGAIRAV-KDAVDIPVIANGDICSTPDARSALNASGADGVMVGRGTGGRPWLIAEIAS 242

Query: 231 EYFSNP 236
           E F  P
Sbjct: 243 ELFDAP 248


>gi|296232631|ref|XP_002761660.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Callithrix jacchus]
          Length = 651

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 70/283 (24%), Positives = 121/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 336 EMAVCTNLLQGQMSEWALLKRHQCEDVFGIQLEGAFPDTMTKCAELLNRTVEVDF----V 391

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 392 DINVGCPIDLVYKKGGGCALMNRLAKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 450

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D++ + + +K  +P    G NG 
Sbjct: 451 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWEYIAQCVKAASPMPLFG-NGD 500

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED + A++    V GVMI R A     + T + E     ++ S     R+D     
Sbjct: 501 ILSFEDANHAMQT--GVAGVMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 549

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 550 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLQWLSF----LCRYV 587


>gi|163815550|ref|ZP_02206923.1| hypothetical protein COPEUT_01715 [Coprococcus eutactus ATCC 27759]
 gi|158449187|gb|EDP26182.1| hypothetical protein COPEUT_01715 [Coprococcus eutactus ATCC 27759]
          Length = 322

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/159 (26%), Positives = 76/159 (47%), Gaps = 11/159 (6%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            V+AAK ++  GY E+N+N+GCPS  V     GA L+ + + + + +  +  A  + V++
Sbjct: 78  FVKAAKFLKKLGYGEVNINLGCPSKTVVTKYKGAGLLYDTERLDNFLYEVFAAGVMDVSI 137

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY--DIV 179
           K RIG D    +V   +++   KK  V+ + IH R      +     +  PN++   + V
Sbjct: 138 KTRIGRDS---SVEFEDIIDIYKKYPVSELIIHPR------VQTDFYKNTPNMEVFAEGV 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
               + +   + G    + D  + +   P +  VMIGR 
Sbjct: 189 AAYGRTDTVCYNGDINSVADYERFIGNYPDIMKVMIGRG 227


>gi|305663799|ref|YP_003860087.1| dihydroorotate oxidase B, catalytic subunit [Ignisphaera aggregans
           DSM 17230]
 gi|304378368|gb|ADM28207.1| dihydroorotate oxidase B, catalytic subunit [Ignisphaera aggregans
           DSM 17230]
          Length = 301

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 85/192 (44%), Gaps = 21/192 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + IGG+   + +E A + ++FG N I LN+ CP A+     +G  +  +P  V   +
Sbjct: 94  PIIISIGGSSEREFIEVASLADEFGANGIELNLSCPHAK----GYGIEIGADPSSVYSIV 149

Query: 109 AAMCKALSIPVTVK---CRIGVDDQIPAVA----LRNLVKSIKKSGVNGIWIHARKAILK 161
             +   + IP+  K   C   V+  I A++       L+ ++K   ++   ++  K IL 
Sbjct: 150 KEVSSVVKIPIIAKLGLCDRVVESSIKALSGGARALTLINTVKAMAID---VYTMKPILS 206

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               GLS      I  +   IVYE+ +E     IG  G     S A   L     V IG 
Sbjct: 207 NIFGGLS---GPPIHPIAVRIVYEVYRETEADIIGCGGVDSWESAAEFFLAGAKAVQIGT 263

Query: 218 AAYKNSAMLTTV 229
           A Y++  ++  +
Sbjct: 264 AIYRDENIVNNI 275


>gi|92112823|ref|YP_572751.1| dihydrouridine synthase, DuS [Chromohalobacter salexigens DSM 3043]
 gi|91795913|gb|ABE58052.1| tRNA-U20a,U20b-dihydrouridine synthase [Chromohalobacter salexigens
           DSM 3043]
          Length = 340

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 50/90 (55%), Gaps = 3/90 (3%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G+D   L   A   +  G  +++LN GCP+  V+    GA L+  P+ V   +
Sbjct: 71  PVHLQLLGSDPEALAANAVRAQALGARQVDLNFGCPAKTVNRHDGGASLLRQPERVHTVV 130

Query: 109 AAMCKALS---IPVTVKCRIGVDDQIPAVA 135
            A+ +AL+   I VT K R+G DD+  A+A
Sbjct: 131 RAVAEALAPLGIAVTAKIRLGFDDKHVALA 160


>gi|331673664|ref|ZP_08374427.1| tRNA-dihydrouridine synthase C [Escherichia coli TA280]
 gi|331068937|gb|EGI40329.1| tRNA-dihydrouridine synthase C [Escherichia coli TA280]
          Length = 315

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + +   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + L     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCLAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|310791648|gb|EFQ27175.1| dihydrouridine synthase [Glomerella graminicola M1.001]
          Length = 555

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 73/334 (21%), Positives = 136/334 (40%), Gaps = 82/334 (24%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVA--------------DAILRGDKKN-- 39
           MVD ++  +R  +R         N + YT M  A               A+  GD  +  
Sbjct: 43  MVDQSEFAWRMLSRSFIPPAEQKNLVAYTPMFHARLFKDTENYRQCHFQAVRPGDANDST 102

Query: 40  ------ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
                 + G  + ++PL +Q    D   L+ AA  V  +  + ++LN+GCP     +G +
Sbjct: 103 STPQAWLDGNPSIDRPLFVQFCANDPDALLGAALRVAPY-CDAVDLNLGCPQGIAKKGKY 161

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-VALRNLVKSIKKSGVNGIW 152
           GA L  + +++   I  + + L IPVT K RI     +P   A     K++  +G + + 
Sbjct: 162 GAFLQEDQELIFKLINTLHRNLPIPVTAKIRI-----LPTREATLAYAKNVLSAGASILT 216

Query: 153 IHAR----KAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGL---EDMSQAL 204
           +H R    K  L GL+          D+  +  ++++  P+  +  NG +   +D+ +AL
Sbjct: 217 VHGRLREQKGHLTGLA----------DWSTIKWLREQLPPETVLFANGNILQHDDLQRAL 266

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD-KDFWRKISASMTDYA 263
           +     DG+M             + +   S+P   S P +   + +++WR          
Sbjct: 267 EAT-GADGIM-------------SAEGNLSDPTIFSRPPEPGTETREYWR---------- 302

Query: 264 ARHLHSGGKLQQITRHMIGLFHGF-----PNSRR 292
            +    G ++  + R  + + H +     P SRR
Sbjct: 303 GKDGKGGYRVDAVMRRYMDILHKYAAGEEPPSRR 336


>gi|264677182|ref|YP_003277088.1| dihydrouridine synthase, DuS [Comamonas testosteroni CNB-2]
 gi|262207694|gb|ACY31792.1| dihydrouridine synthase, DuS [Comamonas testosteroni CNB-2]
          Length = 347

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/201 (23%), Positives = 92/201 (45%), Gaps = 21/201 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR   + + G      P+  Q+ G+D   + E A  +   G   I+LN GCP+  V+   
Sbjct: 53  LRNGSRTLAGV-----PVRAQLLGSDPVSMAENAANLARLGPEGIDLNFGCPAKVVNRHG 107

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            GA L+ +P+ +   + A+ +A+   +PV+ K R+G +D+     +    +++++ G   
Sbjct: 108 GGASLLQDPEQIVRVVDAVRRAVPAQMPVSAKMRLGFNDR---ALMTECAQAMEQGGACE 164

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LP 208
           I +HAR  +     P    +IP +         +E   + +  NG +  + +AL+   + 
Sbjct: 165 IVVHARTKLDGYRPPAYWEEIPRI---------REAVGVNVVANGEIWTVEEALRCREVS 215

Query: 209 SVDGVMIGRAAYKNSAMLTTV 229
             D +M+GR    +  +   V
Sbjct: 216 GCDDLMLGRGIVADPGLALAV 236


>gi|307169925|gb|EFN62434.1| tRNA-dihydrouridine synthase 2-like [Camponotus floridanus]
          Length = 467

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/231 (22%), Positives = 98/231 (42%), Gaps = 41/231 (17%)

Query: 21  LLYTEMIVADAILRGDKKNILGFST------------------QEKPLALQIGGADISKL 62
           ++YTE ++   +LR  ++     ST                  + + + LQIG +D  + 
Sbjct: 43  IVYTEELIDRKLLRSIRRENDVLSTIDYIDKTDGTVVFRTCPREREHVVLQIGTSDPLRA 102

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A++VE      I++N+GCP      G  GA L+ +P    + +  M + ++IPVT K
Sbjct: 103 AEVARMVEK-DVAGIDVNMGCPKKFSILGGMGASLLSDPRKATNILRKMIETVTIPVTCK 161

Query: 123 CRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            R+   +++ +       L  ++  +G+  I IH R    +   P  N+ +  +      
Sbjct: 162 IRVLFSLEETL------QLCDTLASTGIEAIAIHGRTIEERPQHPNRNQVLKQIS----- 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKNSAML 226
               +   + +  NGG +D+ Q   I           VM+ RAA  N ++ 
Sbjct: 211 ----DRLSIPVIANGGSKDIQQHSDIFRFKEKTGCSSVMLARAAQWNCSIF 257


>gi|300120824|emb|CBK21066.2| unnamed protein product [Blastocystis hominis]
          Length = 225

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 89/186 (47%), Gaps = 21/186 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL +Q+ G D   L +AA   E      ++LN+GCP     +G +G+ L+ N ++V  
Sbjct: 24  DSPLIVQLCGNDPEFLQKAALKFEG-KCMAVDLNLGCPQGIARKGKYGSYLLPNYNLVEQ 82

Query: 107 CIAAM-CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
              A+  + +  P TVK R+   ++D I       L K +++ G   I IH R       
Sbjct: 83  IAKALGGEEVQFPFTVKIRLLPSLEDTI------KLCKMLEREGAQMITIHGRT------ 130

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAY 220
             ++  +    D+  +  I+KE   + +  NGG   LED+++ ++    V GVM+G A  
Sbjct: 131 REQNKDRTGACDWQAIATIRKE-LSIPVFANGGICSLEDVTKCIE-ETGVCGVMVGEAIL 188

Query: 221 KNSAML 226
           +N A  
Sbjct: 189 ENPAFF 194


>gi|71004722|ref|XP_757027.1| hypothetical protein UM00880.1 [Ustilago maydis 521]
 gi|46096397|gb|EAK81630.1| hypothetical protein UM00880.1 [Ustilago maydis 521]
          Length = 527

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 9/118 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D   L++AAK+VED   + ++LN+GCP      G +G+ LM +  ++  
Sbjct: 132 DRPLFVQFCSNDPETLLKAAKVVED-RCDAVDLNLGCPQHIARRGHYGSYLMEDWSLIFS 190

Query: 107 CIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            I  +   L +PVT K R+   V+  I         + ++++G   I +H R   +KG
Sbjct: 191 LINILHVNLKVPVTAKMRVYESVEKTI------TYARLLERAGAQIITVHGRTRNMKG 242


>gi|169767132|ref|XP_001818037.1| dihydrouridine synthase family protein [Aspergillus oryzae RIB40]
 gi|83765892|dbj|BAE56035.1| unnamed protein product [Aspergillus oryzae]
          Length = 536

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 95/227 (41%), Gaps = 27/227 (11%)

Query: 31  AILRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           A ++GD    L G    ++PL +Q    +    +EAA+ V  +  + ++LN+GCP     
Sbjct: 102 AAIKGDDTPYLDGNPAIDRPLFVQFCANNPDDFLEAARHVAPYC-DAVDLNLGCPQGIAR 160

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +GA L  + D++   I  +   L +PVT K RI    Q          K I  +G +
Sbjct: 161 RGHYGAFLQEDWDLIYKLINKLHTELDVPVTAKFRI----QETKEKTLEYAKMILSAGAS 216

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKI 206
            I +H R    KG     N  + +  Y I Y      P+  I  NG +   +D+ + L+ 
Sbjct: 217 IITLHGRTREQKG----HNTGVADWSY-IRYLRDNLPPETVIFANGNILNYDDLERCLEE 271

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               DGVM       + ++ +        P  GS        +++WR
Sbjct: 272 T-GADGVMSAEGNLSDPSVFS------KPPPVGSE------GREYWR 305


>gi|121606249|ref|YP_983578.1| nifR3 family TIM-barrel protein [Polaromonas naphthalenivorans CJ2]
 gi|120595218|gb|ABM38657.1| tRNA-U20-dihydrouridine synthase [Polaromonas naphthalenivorans
           CJ2]
          Length = 356

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 109/231 (47%), Gaps = 29/231 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-----DAILRGDKKNILGFSTQEKPLALQIG 55
           M   TDR +R   + L       +EM+ +     D +    + N  G   +  P+A+QI 
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVTSRRDLWDTLKTSRRANHEG---EAAPIAVQIA 72

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMC 112
           G D   + +AA    D G   I++N+GCP+ +V     G+ LM +  +   + + + A C
Sbjct: 73  GTDARMMADAAAYNLDRGAQIIDINMGCPAKKVCNKWAGSALMQDETLALQIIEAVVAAC 132

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRK 170
               +PVT+K R G   Q    AL ++ ++ + +G+  + +H   R+   KGL+      
Sbjct: 133 LPHGVPVTLKMRTGW-AQSHKNAL-SIARAAESAGIQMLAVHGRTREQGYKGLA------ 184

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
               +YD + E+K     + +  NG ++   +A  +L   + D +M+GRAA
Sbjct: 185 ----EYDTIAEVKAA-LRIPVVANGDIDSPEKARDVLAYTAADALMVGRAA 230


>gi|320165665|gb|EFW42564.1| tRNA dihydrouridine synthase Dus2 [Capsaspora owczarzaki ATCC
           30864]
          Length = 503

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 83/182 (45%), Gaps = 17/182 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G AD ++ V  A++V       +++N+GCP +   +G  GA L+ +PD +   + 
Sbjct: 59  LVFQMGTADPARAVAVARLVM-HDVLAVDVNMGCPKSYSTDGGMGAALLKHPDKIHAILT 117

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+  A+   V V C+I V   +       L K I+ +GV+ + +H R    +   P    
Sbjct: 118 ALVAAVGEHVHVTCKIRVLATVEETVA--LAKMIESTGVSALAVHCRLTHERPREPGH-- 173

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAAYKNSA 224
             P++   IV  +      + +  NGG  D+      +A +       VM+ RAA  N +
Sbjct: 174 --PDMLKPIVDALS-----IPVIANGGSLDIVSHDDIEAFRQRTGCASVMVARAAQNNPS 226

Query: 225 ML 226
           + 
Sbjct: 227 VF 228


>gi|242005452|ref|XP_002423579.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212506727|gb|EEB10841.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 409

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 99/224 (44%), Gaps = 26/224 (11%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +++F  L     + + +      I R  KK       ++  + LQ+G  D  + ++  K+
Sbjct: 5   FKYFVFLEVLETVDFIDQTDGTIIFRTCKK-------EKGKVILQLGTNDPERALKVGKL 57

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VE+     I++N+GCP     +G  GA L+  PD   + +  +   L IPVT K R+ + 
Sbjct: 58  VEN-DVAGIDINMGCPKEFSIKGGMGAALLDKPDKAVEILEKLVNNLKIPVTCKVRV-LK 115

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           D+   +    L + ++K+G+  I IH R    +   P  N        DI+  +  E   
Sbjct: 116 DKNKTI---ELCQRLEKTGIAAIAIHGRTKDERPQHPNKN--------DIIKAV-AEVLK 163

Query: 189 LFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAMLT 227
           + +  NGG +++     IL          +M+ RAA  N ++ +
Sbjct: 164 IPVIANGGSKEIDNYNDILKFKEATGCSSIMLARAAEWNCSVFS 207


>gi|330941969|gb|EGH44666.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 321

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 85/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E      + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENGAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPKHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    +ED  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVEDWRRCREICGARD-IMIGR 224


>gi|148272765|ref|YP_001222326.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147830695|emb|CAN01635.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 410

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 100/223 (44%), Gaps = 17/223 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +   ++     EK  ++Q+ G D
Sbjct: 45  MAGITNTAFRRLCREF-GAGLYVSEMITSRALVERTPESMRLITHHPSEKVRSIQLYGVD 103

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + EA   +V +   + I+LN GCP A+V     GA L     +  D +    KA   
Sbjct: 104 PKTVREAVTMLVAEDRADHIDLNFGCPVAKVTRKGGGAALPWKLGLFTDIVEGAVKAAGD 163

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IP+TVK R G+D     +      ++ + +GV  I +HAR A         +    + D+
Sbjct: 164 IPLTVKMRKGIDAD--HLTYLEAGRAAEGAGVASIALHARTAA--------DYYSGHADW 213

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             + ++K+    + +  NG +     A++++     DGV++GR
Sbjct: 214 SAIAKLKQAIESVPVLGNGDIWAAEDAIRMMDETGADGVVVGR 256


>gi|88798296|ref|ZP_01113882.1| NifR3/Smm1 family protein [Reinekea sp. MED297]
 gi|88779072|gb|EAR10261.1| NifR3/Smm1 family protein [Reinekea sp. MED297]
          Length = 314

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 54/240 (22%), Positives = 104/240 (43%), Gaps = 31/240 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+    L E A    + G + ++LN GCPS  V+    GA L+  P+ +   +
Sbjct: 64  PVRVQLLGSHPQALAENALRAIELGSHGLDLNFGCPSKTVNASKGGAVLLTEPESIYAVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            ++  AL     ++ K R+G +D      +     +I+  G N I +HAR    +G +P 
Sbjct: 124 RSVRDALPGDQTLSAKMRLGFEDN---SLMWECAHAIRDGGANEIIVHARTK-QQGYTPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               +P       +E +   P +  G      D  +A +   +   +M+GR A +N    
Sbjct: 180 AYWHLP-----ADFEARLGIPMIINGEIWTPADAGRA-QHEANCSSIMLGRGAVRNP--- 230

Query: 227 TTVDEYFSNPLTGSSPIKTRVDK------DFWRKISASMTDYAARHLHSGGKLQQITRHM 280
                + ++ +TG    K+   +       FW++++  M+       +  G+L+Q   H+
Sbjct: 231 -----WLASEITGRHNQKSDWSQVHQLVVQFWQEVTQQMSPR-----YCAGRLKQWLNHL 280


>gi|225024872|ref|ZP_03714064.1| hypothetical protein EIKCOROL_01760 [Eikenella corrodens ATCC
           23834]
 gi|224942352|gb|EEG23561.1| hypothetical protein EIKCOROL_01760 [Eikenella corrodens ATCC
           23834]
          Length = 320

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 89/175 (50%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  LQ+ G+D   +   A+     G  +I+LN GCP+  V++   GA L+  P+ +   +
Sbjct: 64  PCTLQLLGSDPDNMAANAQAAVAAGAQKIDLNFGCPAPTVNKHQGGAILLREPERIRQIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           A + + L  +IP+T K R+G +D   ++AL    K+I + G + + +HAR  I +G  P 
Sbjct: 124 ATVRQRLPENIPLTAKMRLGYEDG--SLAL-ECAKAIAQGGASALAVHARTKI-EGYRPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            +       ++ +  I++   ++ +  NG +  ++  L I  +     VM+GR A
Sbjct: 180 AH-------WEQIAPIRQAL-NIPVVANGDVFSLADYLAIRQTSGCQHVMLGRGA 226


>gi|195156385|ref|XP_002019081.1| GL26174 [Drosophila persimilis]
 gi|194115234|gb|EDW37277.1| GL26174 [Drosophila persimilis]
          Length = 577

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 48/203 (23%), Positives = 95/203 (46%), Gaps = 19/203 (9%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++++    + I+LN+
Sbjct: 260 EMACAVPLLKGLGQEWALTKRHESEDIFGVQLCGNNPNVITQAAQVLQETAKVDYIDLNI 319

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNL 139
           GCP   +++   G+ LM   +I+ + +   C +LS  +P TVK R G+           L
Sbjct: 320 GCPIDLIYQQGGGSALMRRTNIL-ELVVRSCSSLSEQLPFTVKMRTGI--YADKSVAHEL 376

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
           V  +++ G + + +H R         ++ R   + +++ + +       + I  NG +  
Sbjct: 377 VPLVEEWGASAVTLHGRS--------REQRYTKHANWEYIEQCAATAKQMPIIGNGDILS 428

Query: 198 -EDMSQALKILPSVDGVMIGRAA 219
            ED  +   + P V  VMIGR A
Sbjct: 429 YEDYVERRALAPHVSSVMIGRGA 451


>gi|21430920|gb|AAM51138.1| SD26982p [Drosophila melanogaster]
          Length = 604

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 65/272 (23%), Positives = 116/272 (42%), Gaps = 31/272 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + L +AA+++ E    + I+LN+
Sbjct: 287 EMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMLNQAAQVIHETAQVDFIDLNI 346

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 347 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSDRLPFTVKMRTGIYADKSVAHELLP 405

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + ++  + E   +   + +  NG + 
Sbjct: 406 LVEEW---GASAVTLHGRS--------REQRYTKHANWAYIEECAAKAKRMPVIGNGDIL 454

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ED  +   + P V  VMIGR A     +   + E      + SS  +  + + F    
Sbjct: 455 SYEDYMERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWSPSSGQRYEMLQKF---- 508

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                +Y   H  S  K  + TR  +  +  F
Sbjct: 509 ----CNYGLEHWGSDTKGVETTRRFLLEWQSF 536


>gi|330888122|gb|EGH20783.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. mori str.
           301020]
          Length = 321

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLWLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    ++D  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVDDWRRCREICGARD-IMIGR 224


>gi|289626961|ref|ZP_06459915.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289650795|ref|ZP_06482138.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330869806|gb|EGH04515.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 321

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    ++D  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVDDWRRCREICGARD-IMIGR 224


>gi|220919018|ref|YP_002494322.1| TIM-barrel protein, nifR3 family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219956872|gb|ACL67256.1| TIM-barrel protein, nifR3 family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 348

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/127 (29%), Positives = 62/127 (48%), Gaps = 3/127 (2%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKL 62
           +DR +R   R +   +  YTEM+ A  ++ G     + L     E P A+QI  ++   L
Sbjct: 21  SDRPFRAICRRM-GASFAYTEMVSAHGLMHGALQTSSYLDREPDEDPFAVQIFASEPEVL 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              A +    G   I++N+ CP  +V     GA +  +P  V + + A+  A+ +PVTVK
Sbjct: 80  ARGAAVAVAAGAGMIDVNMACPVKKVCGSGAGAAMGRDPRRVEEAVRAIRAAVPVPVTVK 139

Query: 123 CRIGVDD 129
            R G D+
Sbjct: 140 IRAGWDE 146


>gi|168056695|ref|XP_001780354.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162668196|gb|EDQ54808.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 332

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/183 (24%), Positives = 84/183 (45%), Gaps = 16/183 (8%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           ++  +  Q+G AD  + ++ A +V        ++N+GCP +    G  G+ L+  P+++ 
Sbjct: 74  EKHRVVFQVGTADAVRCLKVANMVAG-DIAAFDVNMGCPKSFSTSGGMGSALLDKPELIH 132

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           D +  + + L+IPVT K R+             L + I+K+GV+ + +H R+   +   P
Sbjct: 133 DILTTLRRNLNIPVTCKVRL----LKTCGETVELSRRIEKTGVSALAVHGRRVADRPRDP 188

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNS 223
                    ++D + E+        I  NG + D S  Q +K       VM+ R A  N+
Sbjct: 189 A--------NWDGIREVVSALSIPVIA-NGDVFDYSDFQRMKDATGASSVMVARGAVWNA 239

Query: 224 AML 226
           ++ 
Sbjct: 240 SVF 242


>gi|169599118|ref|XP_001792982.1| hypothetical protein SNOG_02375 [Phaeosphaeria nodorum SN15]
 gi|160704540|gb|EAT90587.2| hypothetical protein SNOG_02375 [Phaeosphaeria nodorum SN15]
          Length = 491

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/216 (24%), Positives = 96/216 (44%), Gaps = 21/216 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKL 62
           ++ D H++     + +    Y    V D      ++++ G    ++PL +Q    D    
Sbjct: 7   NYRDAHFQPLKSGMASPPDAYHVSQVEDG-----ERHLDGNPAFDRPLTVQFCSNDPDDF 61

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + AAK V  F  + ++LN+GCP      G +GA L  +  ++   I  + + L +PVT K
Sbjct: 62  LRAAKHVAPF-CDAVDLNLGCPQGIAKRGKYGAFLQEDQGLIARMINKLHEELEVPVTAK 120

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+    +          K+I  +G + I +H R+   KG     N  +   D+ ++  +
Sbjct: 121 MRVLETKE----KTLEYAKTILDAGASIITVHGRRREQKG----HNTGL--ADWQMIRYL 170

Query: 183 KKENP-DLFIGLNGGL---EDMSQALKILPSVDGVM 214
           ++  P D  I  NG +   ED++  L+     DGVM
Sbjct: 171 RESLPKDTVIFANGNILQHEDIAACLEAT-GADGVM 205


>gi|220905344|ref|YP_002480656.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869643|gb|ACL49978.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 331

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/161 (26%), Positives = 75/161 (46%), Gaps = 6/161 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+ A  ++        +L    +++PL +Q+ GA+
Sbjct: 29  LAGYSDLPFRLLCRQY-GAAVCVTEMVSAKGLVYQSPGTNELLASLPEDQPLVVQLFGAE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  A  ++ D GY   +LN+GC  A+V     GA ++ +   + +    M  A    
Sbjct: 88  APFLSRAVSLLRDAGYGWFDLNMGCSVAKVLRQGAGAAMLGDTGNILEVARGMIAAAGPG 147

Query: 119 -VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V  K R+G+DD  P   L +L   ++ +G   + +H R A
Sbjct: 148 RVGFKLRLGLDDTRP--VLPDLALRLEDAGAGWLVLHPRTA 186


>gi|320178912|gb|EFW53875.1| tRNA-dihydrouridine synthase C [Shigella boydii ATCC 9905]
 gi|332093245|gb|EGI98305.1| dihydrouridine synthase family protein [Shigella boydii 5216-82]
          Length = 315

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 91/185 (49%), Gaps = 17/185 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+ GS GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVN-GSGGATLLKDPELIYQGAKAM 125

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 126 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 175

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 176 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 233

Query: 228 TVDEY 232
            V +Y
Sbjct: 234 RVVKY 238


>gi|170720730|ref|YP_001748418.1| dihydrouridine synthase DuS [Pseudomonas putida W619]
 gi|169758733|gb|ACA72049.1| dihydrouridine synthase DuS [Pseudomonas putida W619]
          Length = 323

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 64/272 (23%), Positives = 125/272 (45%), Gaps = 33/272 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+   IPVT K R+G D   P  AL +   ++ + G   + +HAR  + +G  P 
Sbjct: 124 REVRRAVPAHIPVTSKMRLGFD--TPDGAL-DCATALAEGGSAHLVVHARTKV-EGYKPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D+V      N +++      ++D  +  ++  + D +M+GR       + 
Sbjct: 180 AHWEWVARVQDVVKVPVFANGEIWT-----VDDWRRCREVSGAED-IMLGRGLVSRPDLA 233

Query: 227 TTV----DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----ITR 278
             +    D     P++  + +   + ++FWR+  A ++       ++ G+++Q    +TR
Sbjct: 234 LQIAAARDGREYQPMSWEALLP--LLREFWRQAQAKLSPR-----YAPGRMKQWLAMLTR 286

Query: 279 ---HMIGLFHGFPNSRRCRHI---LTVEAGAS 304
                + LF        C+ I   L VE  AS
Sbjct: 287 SYPEAVLLFAELRREDDCQRISRLLGVEVQAS 318


>gi|84393366|ref|ZP_00992125.1| putative regulator protein [Vibrio splendidus 12B01]
 gi|84375975|gb|EAP92864.1| putative regulator protein [Vibrio splendidus 12B01]
          Length = 303

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 86/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G   + + E A    + G   I+LN GCP+  V++ + GA L+  P+++   +
Sbjct: 49  PIHLQLLGQHPNWMAENAFQAANLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVV 108

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+   IPV+ K R+G +   P      +V +I+++  + + +HAR  +       
Sbjct: 109 NACREAVPAHIPVSAKIRLGWEH--PEECFE-IVDAIEQAKADELTVHARTKV------- 158

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + +D + +I +E   L +  NG + +       + +  VD +M+ R A+
Sbjct: 159 GGYKASEIKWDYINQI-REKTSLPLIANGEIWNYQDGQDCIEATGVDSLMVCRGAF 213


>gi|330980698|gb|EGH78801.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 321

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 86/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPKHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    ++D  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVDDWRRCREICGARD-IMIGR 224


>gi|71000116|ref|XP_754775.1| tRNA dihydrouridine synthase (Smm1) [Aspergillus fumigatus Af293]
 gi|66852412|gb|EAL92737.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus
           fumigatus Af293]
          Length = 443

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    VEAAK+V       I+LN GCP      G  GA L+  PD +   + 
Sbjct: 104 LVFQIGSANPELAVEAAKLVAG-DVAGIDLNSGCPKPFSTSGGMGAALLRTPDKLVSILE 162

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++ + +  P    ++VK RI    +       +LVK +  +G+ G+ +H R   ++   P
Sbjct: 163 SLVREVGNPYQIGISVKIRILETPE----KTESLVKRLVATGITGLTVHCRTTPMR---P 215

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           ++ R I +    ++  I +E   +   +NG +    +AL ++    VDG MI  AA  N 
Sbjct: 216 RE-RAIRD-QLAMIARICREA-GVACVMNGDVTSRDEALALMKEFGVDGAMIATAAEANP 272

Query: 224 AMLTTVDE 231
           +   +  E
Sbjct: 273 SCFRSEAE 280


>gi|227113025|ref|ZP_03826681.1| tRNA-dihydrouridine synthase C [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 310

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDS---GARQFEIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + EI++      I  NG + D   A   + +   D +MIGR A  N   L+
Sbjct: 177 KAECINWLAIGEIRQRLRIPVIA-NGEIWDWQSAQDCMATTGCDAMMIGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|328787042|ref|XP_393745.3| PREDICTED: tRNA-dihydrouridine synthase 2-like [Apis mellifera]
          Length = 460

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 77/154 (50%), Gaps = 23/154 (14%)

Query: 21  LLYTEMIVADAILRGDKK--NILG-------------FST---QEKPLALQIGGADISKL 62
           ++YTE ++   +LR  ++  ++LG             F T   ++  + LQIG  D ++ 
Sbjct: 39  VVYTEELIDWKLLRSFRRENDVLGTIDYIDKTDGTVTFRTCPKEKDKVVLQIGTCDAARA 98

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           ++ AK+VE      I+LN+GCP      G  GA L+  P+   + +  +   L+IPVT K
Sbjct: 99  LKVAKMVEQ-DVAGIDLNMGCPKLFSLIGKMGAALLKEPETATNILKTLVDNLNIPVTCK 157

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R+ + D    + L  L++S   +G+  I +H R
Sbjct: 158 IRV-LPDIDKTIELCELLQS---TGIAAIAVHGR 187


>gi|71668150|ref|XP_821014.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70886380|gb|EAN99163.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 428

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/209 (24%), Positives = 91/209 (43%), Gaps = 17/209 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL   + + YT MI+AD+    D      FS    E+ L  QI    
Sbjct: 83  MVRCSRPAFRKLCRLWGTD-VSYTHMIMADSFTCSDAARHADFSMYAGEERLVAQIASCS 141

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                EAA ++  +  + I+LN GCP   + +   G+ L+  P++V D +  +   LS  
Sbjct: 142 GPVAAEAATLLAPY-CDAIDLNCGCPQRWIIKEGLGSALLQKPEVVADMVRCIHNGLSGG 200

Query: 119 VTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V++ C  ++ VD+ +      +  +  + +G   I +H R       +P        +  
Sbjct: 201 VSLPCVVKMRVDNDVGRSV--DFARHCEAAGCGWITVHGRTPSCSAHAP--------VRL 250

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           D +  I +E   + +  NGG+ +   ALK
Sbjct: 251 DAIRTI-RECVSVPVVANGGVNNPQTALK 278


>gi|322804995|emb|CBZ02555.1| nitrogen regulation protein NIFR3 [Clostridium botulinum H04402
           065]
          Length = 300

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 100/235 (42%), Gaps = 23/235 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   D    +  A+ ++  GY+EINLN+GCP+  V   + G+  +   + +   +  + 
Sbjct: 45  QILTNDSEGFIITARKLQQLGYDEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIF 104

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NR 169
           K   + +++K RIG D          L+K      +  + IH R       + KD   N+
Sbjct: 105 KIDDMKISIKTRIGKDS---PEEFYELIKIYNNYPIEELIIHPR-------TQKDFYGNK 154

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             PNLD          NP  + G    +   ++ +K  P V  +M+GR    N  ++   
Sbjct: 155 --PNLDVFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLI--- 209

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                N +  ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 210 -----NEIKNNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 259


>gi|241952298|ref|XP_002418871.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223642210|emb|CAX44177.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 451

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 107/229 (46%), Gaps = 25/229 (10%)

Query: 14  RLLTNNALLYTEMIVADAIL----RGDKKNIL--GFSTQEKPLALQIGGADISKLVEAA- 66
           ++L +  ++  E+   D I+    + DKK ++      +   L LQ+G +D    VEAA 
Sbjct: 42  KILQSTRIINQELNTIDYIVSNHQQSDKKTVIFRKHPDETGKLILQLGSSDPQLAVEAAN 101

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP--VTVKCR 124
           K+++D   + I+LN GCP         GA L+  PD +   +  + + + IP   ++ C+
Sbjct: 102 KVIDDV--DGIDLNCGCPKNFSTHSGMGAELLKTPDKLCCILINLVEKIGIPKKKSISCK 159

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP--NLDYDIVYEI 182
           I + +       +NL++ I ++G++ + IH R  I++      NR+ P  N    ++  I
Sbjct: 160 IRLFNN--YYQSKNLIEKILQTGISNLTIHCRTPIMR------NRQDPIWNFLPKLIPII 211

Query: 183 KKENPDLFIGLN----GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +    +L I  N      L+++  AL        +MI  AA  N ++  
Sbjct: 212 ENSQVNLIINGNMQNVNDLKNLQMALNDNEKKLSIMIAEAAEANPSIFN 260


>gi|150020274|ref|YP_001305628.1| dihydrouridine synthase, DuS [Thermosipho melanesiensis BI429]
 gi|149792795|gb|ABR30243.1| dihydrouridine synthase, DuS [Thermosipho melanesiensis BI429]
          Length = 295

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/212 (27%), Positives = 102/212 (48%), Gaps = 24/212 (11%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           YTEMI A++I+R  K N   F    ++K +A+QI G++   + +AA +V+  G   I++N
Sbjct: 32  YTEMISAESIVRNLKINEKYFPKDIEKKRVAVQIFGSEPYIMSQAASMVDGKG-AWIDIN 90

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
            GCP  +V +   G+ L+ +   +   I  +   +   V+VK R+G D+         + 
Sbjct: 91  AGCPVKKVIKKGAGSALLKDLKKLKKIIEGVKNNVKSKVSVKVRLGFDED----NFERIY 146

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            +  ++G + I +H R A  +  S +   +I N  Y  +Y            +NG + + 
Sbjct: 147 DAAVEAGADMIAVHGRTA-KQMYSGRAKWQIKNKGYIPLY------------INGDIYN- 192

Query: 201 SQALKI---LPSVDGVMIGRAAYKNSAMLTTV 229
           S  +KI   L   DGV+I R A  N  + + +
Sbjct: 193 SDNIKIAMELSGADGVLIARGAIGNPWIFSNI 224


>gi|298486487|ref|ZP_07004547.1| tRNA-dihydrouridine synthase C [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298158964|gb|EFI00025.1| tRNA-dihydrouridine synthase C [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 321

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 60/113 (53%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +
Sbjct: 124 SQVRRAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV 173


>gi|212704120|ref|ZP_03312248.1| hypothetical protein DESPIG_02175 [Desulfovibrio piger ATCC 29098]
 gi|212672480|gb|EEB32963.1| hypothetical protein DESPIG_02175 [Desulfovibrio piger ATCC 29098]
          Length = 332

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 106/231 (45%), Gaps = 17/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+ A  ++        +L    +++PL +Q+ GA+
Sbjct: 30  LAGYSDLPFRLLCRR-YGAAVCVTEMVSAKGLVYRSPGTGELLQSLPEDQPLVVQLFGAE 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI- 117
            S L  + +++ D GY   +LN+GC  A+V +   GA ++ +     +   AM +A    
Sbjct: 89  ASFLQRSVEMLRDVGYGWFDLNMGCSVAKVLKQGAGAAMLGDVPNALEVARAMLRAAGPG 148

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V  K R+G+D +      R+L   ++  G   I +H R A  +G   +         ++
Sbjct: 149 RVGFKIRLGLDSR--RHVWRDLSLRLQDLGAGWITLHPRTA-RQGFGGEAA-------HE 198

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           ++ E+K+   D+ +  +G L      L++L    VD VM  R A    A+ 
Sbjct: 199 VLAELKQAL-DIPLIASGDLFSARDGLRVLDQTGVDTVMYARGAMHGPAIF 248


>gi|90419633|ref|ZP_01227543.1| nitrogen regulation protein Nifr3 [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90336570|gb|EAS50311.1| nitrogen regulation protein Nifr3 [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 341

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 36/129 (27%), Positives = 71/129 (55%), Gaps = 5/129 (3%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKL 62
           +D  +R  AR      ++ +EM+ +   ++G +++ L  + ++ P    +Q+ G D + +
Sbjct: 23  SDVPFRRLARRF-GAGMVVSEMVASGEFVKGCEESAL-RAMRDGPGLHVVQLAGRDPAWM 80

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTV 121
             AA  + D G + I++N+GCP+ +V  G  G+ LM  P++    + A +  A  +PVT+
Sbjct: 81  QRAAAQLADNGTDIIDINMGCPAKKVVGGLSGSALMREPELALRIVEATVAGAGGVPVTL 140

Query: 122 KCRIGVDDQ 130
           K R+G D +
Sbjct: 141 KMRLGWDRE 149


>gi|67517419|ref|XP_658560.1| hypothetical protein AN0956.2 [Aspergillus nidulans FGSC A4]
 gi|40746829|gb|EAA65985.1| hypothetical protein AN0956.2 [Aspergillus nidulans FGSC A4]
 gi|259488751|tpe|CBF88446.1| TPA: dihydrouridine synthase family protein, putative
           (AFU_orthologue; AFUA_1G16550) [Aspergillus nidulans
           FGSC A4]
          Length = 563

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/213 (27%), Positives = 87/213 (40%), Gaps = 20/213 (9%)

Query: 11  FFARLLTNNA-----LLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADISKLVE 64
           + ARL   +A       +      D   +GD    L G    ++PL +Q    D      
Sbjct: 80  YHARLFEEHAGYRAKAFHPTRAWGDTKCKGDDSPYLDGNPAIDRPLFVQFCANDPDDFFN 139

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AA+ V  +  + ++LN+GCP      G +GA L  + D++   I  +   L +PVT K R
Sbjct: 140 AARHVAPYC-DAVDLNLGCPQGIARRGHYGAFLQEDWDLIYKLINKLHMELEVPVTAKFR 198

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           I    Q          K I  +G + I +H R    KG     N  + +  Y I Y    
Sbjct: 199 I----QESKEKTLEYAKMILSAGASIITLHGRTREQKG----HNTGLADWSY-IRYLRDN 249

Query: 185 ENPDLFIGLNG---GLEDMSQALKILPSVDGVM 214
             PD  I  NG     +D+++ L+     DGVM
Sbjct: 250 LPPDTVIFANGNNLNHDDLARCLEAT-GADGVM 281


>gi|260768108|ref|ZP_05877042.1| tRNA-dihydrouridine synthase C [Vibrio furnissii CIP 102972]
 gi|260616138|gb|EEX41323.1| tRNA-dihydrouridine synthase C [Vibrio furnissii CIP 102972]
          Length = 308

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 42/175 (24%), Positives = 86/175 (49%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   I
Sbjct: 57  PVKVQLLGQEPHWMAENAVRAAELGACGVDLNFGCPAKMVNQSKGGAALLQHPELIYQVI 116

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G ++         +V +++++G + + +HAR       +  
Sbjct: 117 KACRDAVPADIPVSAKIRLGWENPDDCF---EIVDAVQQAGADELTVHAR-------TKA 166

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +D + +I+++     I  NG + + +  QA      +D +M+ R A
Sbjct: 167 GGYKASEIKWDYINQIRQKTHIPLIA-NGEIWNYADGQACIDTTGIDSLMVCRGA 220


>gi|301021095|ref|ZP_07185136.1| dihydrouridine synthase [Escherichia coli MS 69-1]
 gi|300398276|gb|EFJ81814.1| dihydrouridine synthase [Escherichia coli MS 69-1]
          Length = 337

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|237801118|ref|ZP_04589579.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331023975|gb|EGI04032.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 326

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 59/113 (52%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPGCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +
Sbjct: 124 NQVRRAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV 173


>gi|71734038|ref|YP_274172.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71554591|gb|AAZ33802.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|320324866|gb|EFW80938.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329231|gb|EFW85228.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330880875|gb|EGH15024.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 321

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 60/113 (53%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLYSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +
Sbjct: 124 SQVRRAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKV 173


>gi|119492469|ref|XP_001263600.1| tRNA dihydrouridine synthase (Smm1), putative [Neosartorya fischeri
           NRRL 181]
 gi|119411760|gb|EAW21703.1| tRNA dihydrouridine synthase (Smm1), putative [Neosartorya fischeri
           NRRL 181]
          Length = 443

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/188 (28%), Positives = 88/188 (46%), Gaps = 17/188 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    VEAAK+V       I+LN GCP      G  GA L+  PD +   + 
Sbjct: 104 LVFQIGSANPELAVEAAKLVAG-DVAGIDLNSGCPKPFSTSGGMGAALLRTPDKLVSILE 162

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++ + +  P    ++VK RI    +       +LVK +  +G+ G+ +H R   ++   P
Sbjct: 163 SLVREVGNPYQIGISVKIRILETPE----KTESLVKRLVATGITGLTVHCRTTPMR---P 215

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           ++ R I +    ++  I +E   +   +NG +    +AL ++    VDG MI  AA  N 
Sbjct: 216 RE-RAIRD-QLAMIARICREA-GVACVMNGDVTSRDEALALMKEFGVDGAMIATAAEANP 272

Query: 224 AMLTTVDE 231
           +   +  E
Sbjct: 273 SCFRSEAE 280


>gi|134106399|ref|XP_778210.1| hypothetical protein CNBA2100 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50260913|gb|EAL23563.1| hypothetical protein CNBA2100 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 407

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 82/184 (44%), Gaps = 12/184 (6%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q    +   L +AA+++  +  + I+LN GCP    +    G  L+  P++V D + 
Sbjct: 152 LIAQFASPNAKSLADAAELISPY-VDGIDLNCGCPQRWAYNEGIGCALLRKPELVRDMVR 210

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +   +    PV++K RI  + +        L+ +  ++G++ + IH R        P +
Sbjct: 211 GVKDRMGWGWPVSIKIRIDSEQE----KTEQLISNALQAGISHLTIHGRTRHQPSTDPVN 266

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              +P + +  V  +K E P +  G    LED  Q +++   V GVM  R    N A+  
Sbjct: 267 ---LPGIKF-AVDCVKGEVPCVANGDVWELEDARQ-MRLHTGVQGVMAARGLLANPALFA 321

Query: 228 TVDE 231
             D+
Sbjct: 322 GYDK 325


>gi|323961604|gb|EGB57210.1| dihydrouridine synthase [Escherichia coli H489]
          Length = 311

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|195484562|ref|XP_002090745.1| GE13280 [Drosophila yakuba]
 gi|194176846|gb|EDW90457.1| GE13280 [Drosophila yakuba]
          Length = 609

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/273 (23%), Positives = 116/273 (42%), Gaps = 33/273 (12%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 292 EMACAQPLLKGMGQEWALTKRHQSEDIFGVQLCGNNPNMINQAAQVIYETAQVDFIDLNI 351

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 352 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSNRLPFTVKMRTGIYADKSVAHELLP 410

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + ++  + E   +   + +  NG + 
Sbjct: 411 LVEEW---GASAVTLHGRS--------REQRYTKHANWAYIEECAAKAKRMPVIGNGDIL 459

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS-NPLTGSSPIKTRVDKDFWRK 254
             ED  +   + P V  VMIGR A     +   + E  S +P +G              +
Sbjct: 460 SYEDYIERRTLAPHVSSVMIGRGALIKPWIFQEIKEKHSWSPSSGQR-----------YE 508

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +     +Y   H  S  K  + TR  +  +  F
Sbjct: 509 MLQKFCNYGLEHWGSDTKGVETTRRFLLEWQSF 541


>gi|313679501|ref|YP_004057240.1| dihydrouridine synthase dus [Oceanithermus profundus DSM 14977]
 gi|313152216|gb|ADR36067.1| dihydrouridine synthase DuS [Oceanithermus profundus DSM 14977]
          Length = 313

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/163 (27%), Positives = 82/163 (50%), Gaps = 15/163 (9%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNV 81
           EM++A ++L+   +   +L    +E+   +Q+ GAD  ++  AA  V +  G   I+LN+
Sbjct: 41  EMVMAGSLLQESVEGWRLLRLHPEERSRVVQLAGADPGEVARAAARVRERVGPRAIDLNM 100

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V     GA LM +P      +A + +A  +PV+VK R+G   +  AV    + +
Sbjct: 101 GCPMPKVTARGAGAALMDDPARAARMVAGVREATGLPVSVKLRLGF-SRANAV---EVAR 156

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +++++G   + +H R A          R     D+D V E+ +
Sbjct: 157 ALEQAGAALLRVHGRTA--------QQRYGGRADWDAVREVAR 191


>gi|323144809|ref|ZP_08079382.1| putative tRNA-dihydrouridine synthase C [Succinatimonas hippei YIT
           12066]
 gi|322415429|gb|EFY06190.1| putative tRNA-dihydrouridine synthase C [Succinatimonas hippei YIT
           12066]
          Length = 320

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 96/219 (43%), Gaps = 43/219 (19%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV-- 127
            G   I++N GCPS  VH G  GA L+  PD++ + ++ +  AL   I ++VK R G   
Sbjct: 91  LGAKSIDINFGCPSRFVHHG--GAMLLKEPDLMHEIVSTVRDALLPEIFLSVKVRTGFLS 148

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++ P      +V +I   GV+ I +HAR       + KD      LD+ ++  +++   
Sbjct: 149 KEEAP-----EIVSAIAVDGVDEIIMHAR-------TRKDLYSEAALDWSVIGRVREYAH 196

Query: 188 DLFIGLNG---GLEDMSQALKILPSVDGVMIGRAA----------------YKNSAMLTT 228
            + +  NG     ED  Q  +   + D +M+GR A                Y  S +L  
Sbjct: 197 GIPMVANGDILSFEDGQQCSEAAKT-DRLMVGRGALSIPNAGAVLKDGAEPYTTSEVLKV 255

Query: 229 VDEYFSNPLTGSSPIKTRVDK-----DFWRKISASMTDY 262
           VDE+    ++     K+ +D+      F R+    + ++
Sbjct: 256 VDEFIQELISRRFQEKSVLDRAKQFLGFARRTDKKLVEF 294


>gi|238920710|ref|YP_002934225.1| tRNA-dihydrouridine synthase C [Edwardsiella ictaluri 93-146]
 gi|238870279|gb|ACR69990.1| tRNA-dihydrouridine synthase C [Edwardsiella ictaluri 93-146]
          Length = 318

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 83/177 (46%), Gaps = 19/177 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++ N GCPS  V+    GA L+ +P ++   +
Sbjct: 68  PVRIQLLGQSPHWLAENALRAVTLGSPGVDFNCGCPSKAVNGSGGGATLLKDPALIYAGV 127

Query: 109 AAMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            AM +A+   +P+TVK R+G   D Q   +A      ++++ G   + +H R       +
Sbjct: 128 QAMRQAIPAHLPLTVKVRLGWACDSQRFEIA-----DAVQQGGATELVVHGR-------T 175

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            +D  +   ++++ + EI++      I  NG + D + A   L     D +MIGR A
Sbjct: 176 KEDGYRADRINWEAIGEIRRRLRIPVIA-NGEIWDYASAQACLAQSGCDALMIGRGA 231


>gi|218890670|ref|YP_002439534.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
 gi|218770893|emb|CAW26658.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
          Length = 319

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 61/113 (53%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P ++ D +
Sbjct: 64  PMRVQLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPKLMHDIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           AA+ +A+   I VT K R+G D   P  AL +  +++   G   + +HAR  +
Sbjct: 124 AAVRRAVPSEIAVTSKMRLGYDS--PDGAL-DCARALADGGSAHVVVHARTKV 173


>gi|58258399|ref|XP_566612.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57222749|gb|AAW40793.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 407

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 82/184 (44%), Gaps = 12/184 (6%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q    +   L +AA+++  +  + I+LN GCP    +    G  L+  P++V D + 
Sbjct: 152 LIAQFASPNAKSLADAAELISPY-VDGIDLNCGCPQRWAYNEGIGCALLRKPELVRDMVR 210

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +   +    PV++K RI  + +        L+ +  ++G++ + IH R        P +
Sbjct: 211 GVKDRMGWGWPVSIKIRIDSEQE----KTEQLISNALQAGISHLTIHGRTRHQPSTDPVN 266

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              +P + +  V  +K E P +  G    LED  Q +++   V GVM  R    N A+  
Sbjct: 267 ---LPGIKF-AVDCVKGEVPCVANGDVWELEDARQ-MRLHTGVQGVMAARGLLANPALFA 321

Query: 228 TVDE 231
             D+
Sbjct: 322 GYDK 325


>gi|296807698|ref|XP_002844234.1| tRNA-dihydrouridine synthase 2 [Arthroderma otae CBS 113480]
 gi|238843717|gb|EEQ33379.1| tRNA-dihydrouridine synthase 2 [Arthroderma otae CBS 113480]
          Length = 425

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 83/179 (46%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     V+AA++V D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 115 LVFQLGTASPELAVQAARVVAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDRLVSILE 173

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK RI  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 174 ALVREVGQPWQIGISVKIRILKDPE----QTERLVTALCATGITGLTVHCRTTPMRPREA 229

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I + +  +   +NG ++    AL ++    VDG MI  +A  N
Sbjct: 230 AIRDQLP-----MIASICR-SAGVACLMNGDVKSRDHALALMSQYDVDGAMIATSAESN 282


>gi|254786760|ref|YP_003074189.1| tRNA-dihydrouridine synthase C [Teredinibacter turnerae T7901]
 gi|237685547|gb|ACR12811.1| tRNA-dihydrouridine synthase C [Teredinibacter turnerae T7901]
          Length = 320

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 51/86 (59%), Gaps = 2/86 (2%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G++ + L   A      G   ++LN GCP+  V++   GACL+    ++G+ +
Sbjct: 66  PVRVQLLGSNPATLASNANKAAQLGAPAVDLNFGCPAKTVNKSRGGACLLNETSLLGEIV 125

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIP 132
           +A+ +A+   IPVT K R+G +++ P
Sbjct: 126 SAVREAVPAEIPVTAKIRLGYENREP 151


>gi|72127067|ref|XP_793440.1| PREDICTED: similar to MGC53781 protein [Strongylocentrotus
           purpuratus]
 gi|115710885|ref|XP_001202768.1| PREDICTED: similar to MGC53781 protein [Strongylocentrotus
           purpuratus]
          Length = 655

 Score = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/214 (25%), Positives = 91/214 (42%), Gaps = 19/214 (8%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNV 81
           EM +   +L+G      +L     E    +Q+ G     +   A+++ D    + I++NV
Sbjct: 312 EMAMCTNLLQGQSSEWALLRRHPSEDIFGVQLCGGFPDTMTRCAELLNDRLDIDFIDINV 371

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V+    G+ LM       + +  M   L IP+TVK R GV +  P      +V+
Sbjct: 372 GCPIDLVYHKGAGSGLMNRMGKFQEIVRGMSSVLDIPLTVKMRTGVHNDNPVA--HKIVR 429

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGL--- 197
            I   G + + +H R         ++ R     D+D + + ++  +P  FIG NG +   
Sbjct: 430 RIYDWGASVVTVHGRT--------REQRYSKLADWDYLKDCVQAADPHPFIG-NGDILSY 480

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ED S   +      G MI R A     + T + E
Sbjct: 481 ED-SNFFREQSGATGQMIARGALIKPWIFTEIKE 513


>gi|256022176|ref|ZP_05436041.1| tRNA-dihydrouridine synthase C [Escherichia sp. 4_1_40B]
 gi|300950101|ref|ZP_07164048.1| dihydrouridine synthase [Escherichia coli MS 116-1]
 gi|300955838|ref|ZP_07168179.1| dihydrouridine synthase [Escherichia coli MS 175-1]
 gi|301024370|ref|ZP_07188059.1| dihydrouridine synthase [Escherichia coli MS 196-1]
 gi|301644157|ref|ZP_07244165.1| dihydrouridine synthase [Escherichia coli MS 146-1]
 gi|307138799|ref|ZP_07498155.1| tRNA-dihydrouridine synthase C [Escherichia coli H736]
 gi|331642765|ref|ZP_08343900.1| tRNA-dihydrouridine synthase C [Escherichia coli H736]
 gi|299880467|gb|EFI88678.1| dihydrouridine synthase [Escherichia coli MS 196-1]
 gi|300317305|gb|EFJ67089.1| dihydrouridine synthase [Escherichia coli MS 175-1]
 gi|300450591|gb|EFK14211.1| dihydrouridine synthase [Escherichia coli MS 116-1]
 gi|301077455|gb|EFK92261.1| dihydrouridine synthase [Escherichia coli MS 146-1]
 gi|331039563|gb|EGI11783.1| tRNA-dihydrouridine synthase C [Escherichia coli H736]
          Length = 337

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|195998315|ref|XP_002109026.1| hypothetical protein TRIADDRAFT_2009 [Trichoplax adhaerens]
 gi|190589802|gb|EDV29824.1| hypothetical protein TRIADDRAFT_2009 [Trichoplax adhaerens]
          Length = 300

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/224 (27%), Positives = 94/224 (41%), Gaps = 24/224 (10%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQ+G AD  + +  AK+VE+     I++N+GCP     +G  GA L+  P  V + +  +
Sbjct: 77  LQLGTADPERALLTAKLVEN-DVAGIDINMGCPKEYSTKGGMGAALLTEPQKVYNILKKL 135

Query: 112 CKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                 PVT K RI     +P +    +L K I+ +GV  + IH R  + +   P     
Sbjct: 136 VDNCLKPVTCKIRI-----LPKLQDTLDLAKVIESTGVAAVAIHGRLKVERPRQP----- 185

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMS----QALKILPSVDGVMIGRAAYKNSAML 226
              +  DI+  I        I   G LE  S    +  K   +   VMI RAA  + ++ 
Sbjct: 186 ---VHKDIIRTISNSLSIPVIANGGSLEIKSFSDIEKFKQETNSSSVMIARAAQWDPSIF 242

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
                  ++ +  S  IK  +D D     S S + Y   H   G
Sbjct: 243 RKEGSLPTDEIVKSY-IKYAIDYDN----SWSNSKYCITHFMRG 281


>gi|119945939|ref|YP_943619.1| dihydrouridine synthase, DuS [Psychromonas ingrahamii 37]
 gi|119864543|gb|ABM04020.1| dihydrouridine synthase, DuS [Psychromonas ingrahamii 37]
          Length = 314

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/173 (26%), Positives = 87/173 (50%), Gaps = 12/173 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   L E A      G + I+LN GCP+  V++   GA L+ +P+ +   +
Sbjct: 64  PVRIQLLGQNPQCLAENAHQAISIGSDGIDLNFGCPAKTVNKNKGGAVLLKSPEALYQIV 123

Query: 109 AAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + KA+ +   ++VK R+G +D+  ++A+ N  ++I+ +G + + +HAR        P 
Sbjct: 124 TEVRKAVPVFQTLSVKIRLGYEDK--SLAIEN-AQAIQAAGADELAVHARTKAEGYRPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
               I  +   I   +   N D+F      ++D  + ++I    + +MIGR A
Sbjct: 181 HWHWIAKIKDAITIPVTA-NGDIF-----SVDDAKRCMEIT-GCERLMIGRGA 226


>gi|193062350|ref|ZP_03043445.1| tRNA-dihydrouridine synthase C [Escherichia coli E22]
 gi|194427149|ref|ZP_03059700.1| tRNA-dihydrouridine synthase C [Escherichia coli B171]
 gi|260844746|ref|YP_003222524.1| tRNA-dihydrouridine synthase C [Escherichia coli O103:H2 str.
           12009]
 gi|192932016|gb|EDV84615.1| tRNA-dihydrouridine synthase C [Escherichia coli E22]
 gi|194414770|gb|EDX31041.1| tRNA-dihydrouridine synthase C [Escherichia coli B171]
 gi|257759893|dbj|BAI31390.1| tRNA-dihydrouridine synthase C [Escherichia coli O103:H2 str.
           12009]
 gi|323161767|gb|EFZ47648.1| dihydrouridine synthase family protein [Escherichia coli E128010]
          Length = 316

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|332293467|ref|YP_004432076.1| dihydrouridine synthase DuS [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171553|gb|AEE20808.1| dihydrouridine synthase DuS [Krokinobacter diaphorus 4H-3-7-5]
          Length = 318

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/234 (23%), Positives = 95/234 (40%), Gaps = 44/234 (18%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  A   + +   K +E  GY E+N N+GCP   V +   G+ L+ N + +   +    
Sbjct: 66  QVMTASADEFMFVIKYIESLGYTELNWNLGCPYPMVTKSGMGSGLICNTEKINHILDRAH 125

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILK-GLSPKDNR 169
              S+ +++K R+G +   P   L +  K + K  +  + IHAR  K + K G+  +  +
Sbjct: 126 SESSVTISMKMRLGYES--PNEILESF-KVLDKYPLKNVAIHARLGKQLYKGGVDLEGFQ 182

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNS--- 223
           K  ++    +Y             NG +  + Q  K+    PS+   MIGR    +    
Sbjct: 183 KCIDVAKHTLY------------YNGDITSVEQFRKMRERFPSIKHFMIGRGLIADPFLP 230

Query: 224 -------------------AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
                              A   T+ E +   L+G +PIK ++   FW   S S
Sbjct: 231 SMIKADTTEYPANRWETFRAFHDTIYEQYDAALSGPTPIKMKM-LGFWEFFSQS 283


>gi|221505283|gb|EEE30937.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 544

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 50/90 (55%), Gaps = 3/90 (3%)

Query: 37  KKNILGFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           +    G  +QE  +P+ +Q  G   + L+ AA++VED     +++NVGCP      G +G
Sbjct: 132 RSQWTGDESQEFDEPVFVQFCGDSPATLLAAAQLVED-EVEAVDVNVGCPQGIARRGHYG 190

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           A L+  P+++ D ++ + K L  PVT K R
Sbjct: 191 AFLLNEPELLVDIVSTLHKHLKTPVTCKMR 220


>gi|219128482|ref|XP_002184441.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404242|gb|EEC44190.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 323

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 75/322 (23%), Positives = 130/322 (40%), Gaps = 60/322 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK------------ 48
           MV  +D  +R   R    + L YT+MI A        KN+LG +T  K            
Sbjct: 4   MVGASDFAFRCLCRQHGVD-LTYTQMIHA--------KNLLGDNTFSKSHLDMHEHRSLP 54

Query: 49  ---------PLALQIGGADISKLVEAAKIV---EDFGYNEINLNVGCPSARVHEGSFGAC 96
                    PL +Q+ G  +  ++ AA+ V    D   +  +LN GCP     +G +GA 
Sbjct: 55  PELKPFTNGPLMVQLAGNSVDMVLRAAQYVLDQTDGKVDGFDLNCGCPQGIARKGRYGAF 114

Query: 97  LM-LNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIW 152
           LM  + D+V   ++A+ + L  +I V+ K R+ V D++    +  L+ + +    ++G  
Sbjct: 115 LMEEDTDLVCRILSALRQELPANIAVSAKIRLPVTDEMLVARMPKLLDTGVDFMTIHGRT 174

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
           +H  K  ++G+     R         +  + K+ P   I  NGG+E M     +      
Sbjct: 175 LHENKTKVRGVHTDRIRL-------AIETVHKQRPGFPIVANGGVEHMPDVANL-----Q 222

Query: 213 VMIGRAAYKNSAMLTTVDEYFS---NPLTGSSPIKTRVD--KDF--WRKISASMTDYAAR 265
              G  A  +S  L      FS     LT    ++ ++   +D+  W ++   +   A  
Sbjct: 223 ARTGAVAVMSSESLLEFPNIFSIDTRKLTPRQILEQQIGFARDYLGWCRVYPPLPGVAG- 281

Query: 266 HLHSGGKLQQITRHMIGLFHGF 287
              +GG    I  H+    H +
Sbjct: 282 ---NGGSFNAIKGHLYKFLHRY 300


>gi|197124236|ref|YP_002136187.1| hypothetical protein AnaeK_3847 [Anaeromyxobacter sp. K]
 gi|196174085|gb|ACG75058.1| TIM-barrel protein, nifR3 family [Anaeromyxobacter sp. K]
          Length = 348

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/127 (29%), Positives = 61/127 (48%), Gaps = 3/127 (2%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKL 62
           +DR +R   R +   +  YTEM+ A  ++ G     + L     E P A+QI  ++   L
Sbjct: 21  SDRPFRAICRRM-GASFAYTEMVSAHGLMHGALQTSSYLDREPDEDPFAVQIFASEPEVL 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              A +    G   I++N+ CP  +V     GA +   P  V + + A+  A+ +PVTVK
Sbjct: 80  ARGAAVAVAAGAGMIDVNMACPVKKVCGSGAGAAMGREPRRVEEAVRAIRAAVPVPVTVK 139

Query: 123 CRIGVDD 129
            R G D+
Sbjct: 140 IRAGWDE 146


>gi|315179807|gb|ADT86721.1| tRNA-dihydrouridine synthase C [Vibrio furnissii NCTC 11218]
          Length = 305

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/175 (24%), Positives = 86/175 (49%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   I
Sbjct: 54  PVKVQLLGQEPHWMAENAVRAAELGACGVDLNFGCPAKMVNQSKGGAALLQHPELIYQVI 113

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G ++         +V +++++G + + +HAR       +  
Sbjct: 114 KACRDAVPADIPVSAKIRLGWENPDDCF---EIVDAVQQAGADELTVHAR-------TKA 163

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +D + +I+++     I  NG + + +  QA      +D +M+ R A
Sbjct: 164 GGYKASEIKWDYIDQIRQKTHIPLIA-NGEIWNYADGQACIETTGIDSLMVCRGA 217


>gi|167623514|ref|YP_001673808.1| dihydrouridine synthase DuS [Shewanella halifaxensis HAW-EB4]
 gi|167353536|gb|ABZ76149.1| dihydrouridine synthase DuS [Shewanella halifaxensis HAW-EB4]
          Length = 327

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/175 (25%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   + E A    + G   +++N GCP+  V+  + GA ++  P+ + + +
Sbjct: 77  PVRVQLLGQNPDWMAENAARAIELGSKGVDVNFGCPAKMVNRSNGGAVMLQYPEQLYNVV 136

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+    PVT K R+G +D+  ++ + N + +I ++G + + +HAR  +       
Sbjct: 137 KAMRDAVPSDQPVTAKIRLGFNDK--SLYMENAL-AIYEAGASELAVHARSKV------- 186

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           D  K P   ++ + +I  + P   I  NG + +   A + +     D VM+GR A
Sbjct: 187 DGYKPPAY-WEYITDINAKLPIPVIA-NGEIWNRDDAERCMSITGCDSVMVGRGA 239


>gi|160938134|ref|ZP_02085490.1| hypothetical protein CLOBOL_03028 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438938|gb|EDP16694.1| hypothetical protein CLOBOL_03028 [Clostridium bolteae ATCC
           BAA-613]
          Length = 335

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 95/229 (41%), Gaps = 27/229 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA 65
           D+++  F     N+ L + E+            +IL    Q   +  QI        ++ 
Sbjct: 36  DKYFTPFLSPKANSKLSFREL-----------NDILPEHNQGMYVVPQILTNQAGDFIQT 84

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KALSIPVTVK 122
           AK ++++GY+EINLN+GCPS  V     GA  +  PD +   +  +C     + + V+VK
Sbjct: 85  AKELQEYGYSEINLNLGCPSGTVVSKHKGAGFLGRPDSLDRFLDEVCGKMDEMGMEVSVK 144

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL--DYDIVY 180
            R+G+   I       L++   +  +  + +H R   ++    K+   +P     +D   
Sbjct: 145 TRLGL---ISPDEFTGLLEIYNRYPLKELILHPR---VRTDYYKNTPNMPAFRGGFDGSR 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
                N D+F      + D        P +D VM+GR    N  +L  +
Sbjct: 199 SPVCYNGDIFT-----ISDYETLCGDYPELDRVMLGRGIISNPGLLDRI 242


>gi|88855014|ref|ZP_01129679.1| transcriptional regulator, NifR3/Smm1 family protein [marine
           actinobacterium PHSC20C1]
 gi|88815542|gb|EAR25399.1| transcriptional regulator, NifR3/Smm1 family protein [marine
           actinobacterium PHSC20C1]
          Length = 388

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 105/261 (40%), Gaps = 21/261 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +   ++     E   ++Q+ G D
Sbjct: 31  MAGITNTAFRRLCREY-GAGLYVSEMITSRALVERTPESMRLITHHESETTRSIQLYGVD 89

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + EA   +V +   + I+LN GCP  +V     GA L    D+  D +    KA   
Sbjct: 90  PKTVKEAVTMLVAENRADHIDLNFGCPVPKVTRKGGGAALPWKIDLFRDIVEGAVKAAGD 149

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIPNL 174
           +P+T+K R G+D     +      +    +GV  I +HAR A     G +          
Sbjct: 150 VPLTIKMRKGIDSD--HLTYLEAARVGAGAGVASIALHARTAAEFYSGTA---------- 197

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+  + ++K    D  I  NG +   + AL+++     DGV++GR       +   +   
Sbjct: 198 DWSAIEKLKNTITDTPILGNGDIWSAADALRMVDETGCDGVVVGRGCLGRPWLFGDLAAA 257

Query: 233 FSNPLTGSSPIKTRVDKDFWR 253
           F      + P    V   F R
Sbjct: 258 FRGETLKAEPSLGEVAAAFKR 278


>gi|300897804|ref|ZP_07116197.1| dihydrouridine synthase [Escherichia coli MS 198-1]
 gi|300358519|gb|EFJ74389.1| dihydrouridine synthase [Escherichia coli MS 198-1]
          Length = 337

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + +   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|238749854|ref|ZP_04611358.1| tRNA-dihydrouridine synthase C [Yersinia rohdei ATCC 43380]
 gi|238711783|gb|EEQ03997.1| tRNA-dihydrouridine synthase C [Yersinia rohdei ATCC 43380]
          Length = 310

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 RAAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D + A + +     D +M+GR A  N   L+
Sbjct: 177 QAERINWQAIGEIRQRLSIPVIA-NGEIWDYASAQECMKVTGCDALMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|238759753|ref|ZP_04620911.1| tRNA-dihydrouridine synthase C [Yersinia aldovae ATCC 35236]
 gi|238701985|gb|EEP94544.1| tRNA-dihydrouridine synthase C [Yersinia aldovae ATCC 35236]
          Length = 314

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 89/186 (47%), Gaps = 18/186 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 69  IQLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 128

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 129 REAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 178

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG---VMIGRAAYKNSAML 226
           +   +++  + EI++      I  NG + D   A + + SV G   VM+GR A  N   L
Sbjct: 179 QAERINWQAISEIRQRLTIPVIA-NGEIWDYRSAQECM-SVTGCNTVMLGRGAL-NVPNL 235

Query: 227 TTVDEY 232
           + V +Y
Sbjct: 236 SRVVKY 241


>gi|156553630|ref|XP_001600195.1| PREDICTED: similar to CG10463-PA [Nasonia vitripennis]
          Length = 584

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/202 (26%), Positives = 90/202 (44%), Gaps = 18/202 (8%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNV 81
           EM +A  +L+G ++   ++     E    +QI G +   L    +++ D    + ++LNV
Sbjct: 320 EMALAPRLLKGVREEWALVKRHESEDLFGVQIAGNNPGVLTRCCQLLNDETEVDFVDLNV 379

Query: 82  GCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           GCP   V++   G C MLN  +I+   + +  + L IP TVK R GV    P      L+
Sbjct: 380 GCPIDLVYKQG-GGCGMLNRLNILESVVKSATEVLDIPFTVKTRTGVYADKPIA--HKLM 436

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL--- 197
              K  G + I IH R         ++ R     D+D + +  +    + +   G +   
Sbjct: 437 SKFKDWGASMINIHGRS--------REQRYTKLADWDYIEKCAQVASPIPVYGTGDILSW 488

Query: 198 EDMSQALKILPSVDGVMIGRAA 219
           +D  +  K  P+V GV I R A
Sbjct: 489 DDYQRVRKTYPTVQGVSIARGA 510


>gi|229820271|ref|YP_002881797.1| TIM-barrel protein, nifR3 family [Beutenbergia cavernae DSM 12333]
 gi|229566184|gb|ACQ80035.1| TIM-barrel protein, nifR3 family [Beutenbergia cavernae DSM 12333]
          Length = 397

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/277 (22%), Positives = 118/277 (42%), Gaps = 22/277 (7%)

Query: 19  NALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYN 75
             L  +EM+ + A++    +   I+  +  E+  ++Q+ G D + +  AA+ +V +   +
Sbjct: 55  EGLYVSEMVTSRALVERTPESMRIITAAPDERVRSVQLYGVDPATVRLAARMLVTEDRAD 114

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIP 132
            I+LN GCP  +V     GA L    D+    + A     +   +PVTVK R+G+DD   
Sbjct: 115 HIDLNFGCPVPKVTRKGGGAVLPWKRDLFAAIVRAAVDEAAPSGVPVTVKMRMGIDDDHL 174

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 L+   +++G   + +HAR A        +        ++ +  +K+   D+ + 
Sbjct: 175 TYLDAGLLA--QEAGAAWVALHARTA--------EQYYSGEARWEAIARLKETVTDVPVL 224

Query: 193 LNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG +     AL ++     DGV++GR       + T +   F+       P    V   
Sbjct: 225 GNGDIWSAEDALAMVQQTGCDGVVVGRGCQGRPWLFTDLVAGFAGSARRVRPGLADVAAT 284

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           F R+ +  M D+      +   L+++ +H      G+
Sbjct: 285 F-RRHAELMVDHFGEEERA---LRELRKHASWYLKGY 317


>gi|170680883|ref|YP_001744334.1| tRNA-dihydrouridine synthase C [Escherichia coli SMS-3-5]
 gi|218700612|ref|YP_002408241.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI39]
 gi|170518601|gb|ACB16779.1| tRNA-dihydrouridine synthase C [Escherichia coli SMS-3-5]
 gi|218370598|emb|CAR18405.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI39]
          Length = 315

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + +   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWNWQSAQQCMTISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|294637389|ref|ZP_06715682.1| tRNA-dihydrouridine synthase [Edwardsiella tarda ATCC 23685]
 gi|291089436|gb|EFE21997.1| tRNA-dihydrouridine synthase [Edwardsiella tarda ATCC 23685]
          Length = 337

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/172 (27%), Positives = 80/172 (46%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A+     G   ++ N GCPS  V+    GA L+ +P  +   + AM
Sbjct: 90  IQLLGQSPHWLAENAQRAVALGSPGVDFNCGCPSKAVNGSGGGATLLKDPAQIYAGVLAM 149

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+  ++PVTVK R+G +    A     +  + +++G   + +H R       + +D  
Sbjct: 150 RQAVPAALPVTVKVRLGWES---ASQRFEIADAAQQAGATELVVHGR-------TKEDGY 199

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
           +   +D+  + EI++      I  NG + D + A   L     D VMIGR A
Sbjct: 200 RADRIDWVAIGEIRQRLTIPVIA-NGEIWDYASAQACLAQTGCDAVMIGRGA 250


>gi|218705668|ref|YP_002413187.1| tRNA -dihydrouridine synthase C [Escherichia coli UMN026]
 gi|293405608|ref|ZP_06649600.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1412]
 gi|298381290|ref|ZP_06990889.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1302]
 gi|218432765|emb|CAR13659.1| tRNA-dihydrouridine synthase C [Escherichia coli UMN026]
 gi|291427816|gb|EFF00843.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1412]
 gi|298278732|gb|EFI20246.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1302]
          Length = 315

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + +   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|16130078|ref|NP_416645.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           MG1655]
 gi|89108957|ref|AP_002737.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           W3110]
 gi|157161621|ref|YP_001458939.1| tRNA-dihydrouridine synthase C [Escherichia coli HS]
 gi|170019543|ref|YP_001724497.1| tRNA-dihydrouridine synthase C [Escherichia coli ATCC 8739]
 gi|170081763|ref|YP_001731083.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188495359|ref|ZP_03002629.1| tRNA-dihydrouridine synthase C [Escherichia coli 53638]
 gi|194436141|ref|ZP_03068243.1| tRNA-dihydrouridine synthase C [Escherichia coli 101-1]
 gi|238901322|ref|YP_002927118.1| tRNA-dihydrouridine synthase C [Escherichia coli BW2952]
 gi|253772933|ref|YP_003035764.1| tRNA-dihydrouridine synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162154|ref|YP_003045262.1| tRNA-dihydrouridine synthase C [Escherichia coli B str. REL606]
 gi|297521104|ref|ZP_06939490.1| tRNA-dihydrouridine synthase C [Escherichia coli OP50]
 gi|312973611|ref|ZP_07787783.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           1827-70]
 gi|466094|sp|P33371|DUSC_ECOLI RecName: Full=tRNA-dihydrouridine synthase C
 gi|405871|gb|AAA60503.1| yohI [Escherichia coli]
 gi|1788462|gb|AAC75201.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           MG1655]
 gi|85675254|dbj|BAE76617.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K12 substr.
           W3110]
 gi|157067301|gb|ABV06556.1| tRNA-dihydrouridine synthase C [Escherichia coli HS]
 gi|169754471|gb|ACA77170.1| dihydrouridine synthase DuS [Escherichia coli ATCC 8739]
 gi|169889598|gb|ACB03305.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188490558|gb|EDU65661.1| tRNA-dihydrouridine synthase C [Escherichia coli 53638]
 gi|194424869|gb|EDX40854.1| tRNA-dihydrouridine synthase C [Escherichia coli 101-1]
 gi|238863715|gb|ACR65713.1| tRNA-dihydrouridine synthase C [Escherichia coli BW2952]
 gi|242377782|emb|CAQ32545.1| tRNA dihydrouridine synthase [Escherichia coli BL21(DE3)]
 gi|253323977|gb|ACT28579.1| dihydrouridine synthase DuS [Escherichia coli 'BL21-Gold(DE3)pLysS
           AG']
 gi|253974055|gb|ACT39726.1| tRNA-dihydrouridine synthase C [Escherichia coli B str. REL606]
 gi|253978223|gb|ACT43893.1| tRNA-dihydrouridine synthase C [Escherichia coli BL21(DE3)]
 gi|260448766|gb|ACX39188.1| dihydrouridine synthase DuS [Escherichia coli DH1]
 gi|309702453|emb|CBJ01779.1| tRNA-dihydrouridine synthase C [Escherichia coli ETEC H10407]
 gi|310332206|gb|EFP99441.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           1827-70]
 gi|315136773|dbj|BAJ43932.1| tRNA-dihydrouridine synthase C [Escherichia coli DH1]
 gi|315615379|gb|EFU96011.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           3431]
 gi|323936754|gb|EGB33039.1| dihydrouridine synthase [Escherichia coli E1520]
 gi|323940791|gb|EGB36979.1| dihydrouridine synthase [Escherichia coli E482]
 gi|323972978|gb|EGB68175.1| dihydrouridine synthase [Escherichia coli TA007]
 gi|332343918|gb|AEE57252.1| dihydrouridine synthase [Escherichia coli UMNK88]
 gi|744179|prf||2014253AN yohI gene
          Length = 315

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|119716174|ref|YP_923139.1| nifR3 family TIM-barrel protein [Nocardioides sp. JS614]
 gi|119536835|gb|ABL81452.1| putative TIM-barrel protein, nifR3 family [Nocardioides sp. JS614]
          Length = 386

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 81/164 (49%), Gaps = 13/164 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNA--LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGG 56
           M   T+  YR   RL       L   EMI +  ++ GD+  K++L F   E   ++Q+ G
Sbjct: 31  MAGITNAAYR---RLCAEQGAGLYVCEMITSRGLVEGDQHTKDMLVFDELETIRSVQLYG 87

Query: 57  ADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           +D + + +AA+I+  ++G   I+LN GCP  +V     G  L     ++ + + +   A 
Sbjct: 88  SDPAYVGKAAEILCAEYGVAHIDLNFGCPVPKVTRKGGGGALPWKRGLLAEILESAVAAA 147

Query: 116 S---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +   +PVT+K R G+D+    +   +  +  ++SG   I +H R
Sbjct: 148 APYDVPVTMKTRKGIDED--HLTYLDAGRIAQESGCAAIALHGR 189


>gi|300930369|ref|ZP_07145778.1| dihydrouridine synthase [Escherichia coli MS 187-1]
 gi|300461691|gb|EFK25184.1| dihydrouridine synthase [Escherichia coli MS 187-1]
          Length = 337

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDS---GEKKFEIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + +I ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 199 RAEHIDWQAIGDI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 256

Query: 228 TVDEY 232
            V +Y
Sbjct: 257 RVVKY 261


>gi|260776361|ref|ZP_05885256.1| tRNA-dihydrouridine synthase C [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260607584|gb|EEX33849.1| tRNA-dihydrouridine synthase C [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 317

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/176 (24%), Positives = 85/176 (48%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   +++N GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVHIQLLGQDPHWMAENAVRAAELGAKGVDINFGCPAKLVNKSKGGAALLQHPELIHRVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+    P+T K R+G D+  P      +V +I+ +G + + +HAR       +  
Sbjct: 124 KACREAVPEGTPLTAKIRLGWDN--PEDCFE-IVDAIQSAGADELTVHAR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
              K   + ++ + +I++    P +  G     ED    +K    VD +M+ R A+
Sbjct: 174 GGYKASEIKWNYINQIRQRFTIPLIANGEIWNYEDGQACIKAT-GVDSLMVCRGAF 228


>gi|294102360|ref|YP_003554218.1| dihydrouridine synthase DuS [Aminobacterium colombiense DSM 12261]
 gi|293617340|gb|ADE57494.1| dihydrouridine synthase DuS [Aminobacterium colombiense DSM 12261]
          Length = 339

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/228 (25%), Positives = 101/228 (44%), Gaps = 19/228 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T    R F R L   A  +TEM+    ++R + K  N+L    +E+P+ LQ+   D
Sbjct: 23  MAGVTIPPLRLFFRKL-GAAATHTEMVSCAGLMRSNTKSGNMLEICHKEEPVILQLFAGD 81

Query: 59  ISKLVEAAK--IVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              L+ AA+  + E  G +  + +N+ CP  +V +   G+ L+ +P+     + ++ K L
Sbjct: 82  TKTLLTAAEKAMSEAPGRFAALGINMACPMPKVLKKGAGSRLLEDPEKATSMVKSL-KEL 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PV VK RI  +      A  +  + +  +G + + +H R            R     +
Sbjct: 141 GAPVWVKTRIYSERGFSMTA--SFCEKLLSAGADNVCVHGRT--------PSQRYAGVAN 190

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN 222
              V+++ +  PD+ I  +G +    +AL  L      V I R A K+
Sbjct: 191 RQSVFDLAETFPDM-ISASGDVFTPQEALDYLEKRCVSVFIARGALKD 237


>gi|255725494|ref|XP_002547676.1| hypothetical protein CTRG_01983 [Candida tropicalis MYA-3404]
 gi|240135567|gb|EER35121.1| hypothetical protein CTRG_01983 [Candida tropicalis MYA-3404]
          Length = 428

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 91/189 (48%), Gaps = 21/189 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G +D    VEAAK V D   + I+LN GCP         GA L+  P+I+   + 
Sbjct: 88  LICQLGSSDPELAVEAAKKVID-DVDGIDLNCGCPKNFSTHSGMGAELLKTPEILCSILT 146

Query: 110 AMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + + +  P    + C+I + +       + L++ I ++G+  + IH R  I++      
Sbjct: 147 NLVENVGKPKGKPISCKIRLFNNFDKS--KELIEKICQTGITNLTIHCRTPIMR------ 198

Query: 168 NRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVD----GVMIGRAAY 220
           NR+ P  +Y   ++  I+K    L   LNG  ++  Q LKI+  ++D     +M G AA 
Sbjct: 199 NRQDPVWNYLPKLIPIIEKSGVSLV--LNGNFQN-KQDLKIVQKALDNDKLSIMFGEAAE 255

Query: 221 KNSAMLTTV 229
            N ++ + V
Sbjct: 256 ANPSVFSDV 264


>gi|123443101|ref|YP_001007075.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090062|emb|CAL12925.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 312

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 86/185 (46%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAM 126

Query: 112 CKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+    PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 REAVPAHQPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 177 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|304319857|ref|YP_003853500.1| dihydrouridine synthase TIM-barrel protein [Parvularcula
           bermudensis HTCC2503]
 gi|303298760|gb|ADM08359.1| dihydrouridine synthase TIM-barrel protein [Parvularcula
           bermudensis HTCC2503]
          Length = 368

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 78/316 (24%), Positives = 127/316 (40%), Gaps = 37/316 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKL 62
           TD  +R  A L     L+ +EM+ ++  +R      L     T +    +Q+ G +   +
Sbjct: 39  TDLPFRRAA-LRAGAPLVVSEMVASEEWVRERPDVALRAALPTGDSLNVIQLAGREARWM 97

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A   E  G + I++N+GCP+ +V     G+ LM + D     I A     S PVT+K
Sbjct: 98  REGAAKAEALGADIIDINMGCPARKVTGLLSGSALMRDVDHALSLIKATLSGTSRPVTLK 157

Query: 123 CRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYD 177
            R+G D      P +A     K    +GV  I +H   R+   KG +          D+ 
Sbjct: 158 MRLGWDHGHLNAPEIA-----KGAADAGVAVITVHGRTRQQFYKGTA----------DWR 202

Query: 178 IVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V     E   + + +NG + D   ++A        GVMIGRAA     +   + E  ++
Sbjct: 203 AV-RATVEAVSVPVIVNGDIVDDVTARAALAQSGAAGVMIGRAAEGRPWLPAALAEALAS 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI-----TRHMIGLFHGFPNS 290
                +P      +   R    +++ YAA H  S  + +Q+      +H+     G P  
Sbjct: 262 GTPMIAPSFVDQIQGVRRLYDETLSHYAAGHGRSAAQGRQLGARMARKHLAAFIDGAPAP 321

Query: 291 ------RRCRHILTVE 300
                 R  R +L  E
Sbjct: 322 WSSAARREWRRVLCAE 337


>gi|58258725|ref|XP_566775.1| tRNA dihydrouridine synthase [Cryptococcus neoformans var.
           neoformans JEC21]
 gi|134106771|ref|XP_777927.1| hypothetical protein CNBA3960 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50260627|gb|EAL23280.1| hypothetical protein CNBA3960 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|57222912|gb|AAW40956.1| tRNA dihydrouridine synthase, putative [Cryptococcus neoformans
           var. neoformans JEC21]
          Length = 610

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 50/184 (27%), Positives = 88/184 (47%), Gaps = 18/184 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D   L+ AAK VE    + +++N GCP      G +G+ L    +++  
Sbjct: 149 DRPLIVQFCANDPDILLAAAKKVE-HRCDAVDINFGCPQGIAKRGHYGSFLQDEWELIHK 207

Query: 107 CIAAMCKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            I+ + + LS+PVT K RI  D D+  A A     + ++ +G   +  H R   +KG   
Sbjct: 208 LISTLHENLSVPVTAKFRIFPDLDKTIAYA-----RMMEAAGAQILTCHGRTREMKG--- 259

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
             N  +   D++ + E+KK    + +  NG +   ED+ + +++    DGVM       N
Sbjct: 260 -QNTGL--ADWEYIREVKKAV-KVPVFANGNILYREDVDRCMEVT-GCDGVMTAEGNLSN 314

Query: 223 SAML 226
            A+ 
Sbjct: 315 PAIF 318


>gi|145346004|ref|XP_001417487.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144577714|gb|ABO95780.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 371

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 66/272 (24%), Positives = 116/272 (42%), Gaps = 38/272 (13%)

Query: 44  STQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           +T   PL  QI G++   L  AA+ +  +     I+LN GCP+  V     G+ L+ +P+
Sbjct: 61  ATARVPLGAQIMGSEPWLLELAARHLATEKSAPRIDLNCGCPANVVTGKGAGSSLLRDPE 120

Query: 103 IVGDCIAAM---CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            V  C+ A+    +     VT+K R G DD   +  LR  + + +++G   + +HAR   
Sbjct: 121 YVYACVKAVADGARGSGAHVTMKLRSGYDD---SSLLRENLLAAREAGARFVSLHARTRA 177

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
            +G S + N +      D++        D+ +  NG +    +A ++L     DG+M+GR
Sbjct: 178 -QGYSGRANWEEIAFAKDVL--------DIPVLGNGDVTSPQRAAELLRVSDADGIMLGR 228

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK---------DFWRKISASMTDYAAR--- 265
            A ++  +   +    S    G   +   V +         DF R  +A +     +   
Sbjct: 229 GAVQDPLIFRRIAATVSRDAQGVVRVSDDVFEREFEVELVIDFLRTFAAEVFKTENKPNG 288

Query: 266 HLHSGGKLQQITRHMIG--------LFHGFPN 289
              SG + Q++    +G        LF G PN
Sbjct: 289 KRGSGVQAQELETFKVGKIKSIVKYLFAGNPN 320


>gi|302502698|ref|XP_003013310.1| hypothetical protein ARB_00495 [Arthroderma benhamiae CBS 112371]
 gi|291176873|gb|EFE32670.1| hypothetical protein ARB_00495 [Arthroderma benhamiae CBS 112371]
          Length = 476

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 160 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 218

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 219 ALVREVGQPWQIGISVKIRLLKDPK----DTERLVTALCATGITGLTVHCRTTPMRPREA 274

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I + +  +   +NG ++    AL+++    VDG MI  +A  N
Sbjct: 275 AIRDQLP-----MIASICR-SAGVACLMNGDVKSRDHALELMSQYDVDGAMIATSAESN 327


>gi|195118882|ref|XP_002003961.1| GI20204 [Drosophila mojavensis]
 gi|193914536|gb|EDW13403.1| GI20204 [Drosophila mojavensis]
          Length = 614

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 95/204 (46%), Gaps = 21/204 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 297 EMACAVPLLKGLGQEWALTKRHESENVFGVQLCGNNPNVISQAAQVLHETSRVDFIDLNI 356

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R GV  D+  A  L  
Sbjct: 357 GCPIDLIYQQGGGSALMHRTNIL-ELTVRSCSALSDRLPFTVKMRTGVYADKSVAHELLP 415

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R     ++  + E  K+   + +  NG + 
Sbjct: 416 LVEEW---GASAVTLHGRS--------REQRYTRQANWTYIEECAKQAKHIPVIGNGDIL 464

Query: 198 --EDMSQALKILPSVDGVMIGRAA 219
             ED  +   + P V  VMIGR A
Sbjct: 465 SYEDYVERRALAPHVSSVMIGRGA 488


>gi|153855570|ref|ZP_01996686.1| hypothetical protein DORLON_02704 [Dorea longicatena DSM 13814]
 gi|149751991|gb|EDM61922.1| hypothetical protein DORLON_02704 [Dorea longicatena DSM 13814]
          Length = 288

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/202 (23%), Positives = 89/202 (44%), Gaps = 23/202 (11%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +IL        L  QI   D    ++  + ++ +GY+E+NLN+GCPS  V     G+
Sbjct: 21  EKNDILPAHNPGMNLVPQILTNDAKGFLDTVEKLKGYGYDEVNLNLGCPSKTVVSKGRGS 80

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +++ + +   +  +     + +++K RIG   +  A     L++   +  +  + +H 
Sbjct: 81  GFLIHTEELNWFLDEIYAKADVKISIKTRIG---KFDADEWGELLRIYNQYPLEELIVHP 137

Query: 156 R--KAILKGLSPKDNRKIPNLD--YDIVYEIKKE---NPDLFIGLNGGLEDMSQALKILP 208
           R  +   KG         P+LD   D V E K     N D+F       EDM +  K  P
Sbjct: 138 RVQQQFYKGH--------PDLDAFADAVKECKHTLCYNGDIFT-----TEDMEKLKKRFP 184

Query: 209 SVDGVMIGRAAYKNSAMLTTVD 230
               +M+GR   +N  ++  ++
Sbjct: 185 EASCIMLGRGILRNPELIEIME 206


>gi|213407250|ref|XP_002174396.1| tRNA dihydrouridine synthase Dus2 [Schizosaccharomyces japonicus
           yFS275]
 gi|212002443|gb|EEB08103.1| tRNA dihydrouridine synthase Dus2 [Schizosaccharomyces japonicus
           yFS275]
          Length = 462

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 88/178 (49%), Gaps = 15/178 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDCI 108
           L  Q+G  +    VEAAK+V +   + I+LN GCP    VH G  GA L+ N D +   +
Sbjct: 70  LIFQLGSCNPELAVEAAKLVVN-DVSAIDLNCGCPKHFSVHAG-MGAGLLKNLDRLESIL 127

Query: 109 AAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ + +  P  + + C+I + D   A    ++V+ + K+G+  I +H R   ++   P 
Sbjct: 128 RALVEQVGQPNNIGISCKIRLLDTHEATL--DMVRRLCKTGIRAITVHCRTTPMRNTEPA 185

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               + ++  +I +        + I +NG +++   A ++     VDG +I RAA KN
Sbjct: 186 IRTSLRDI-AEICHSYH-----VSILVNGDVDNRKMAKELCEEYGVDGAVIARAAEKN 237


>gi|198471850|ref|XP_001355747.2| GA10329 [Drosophila pseudoobscura pseudoobscura]
 gi|198139493|gb|EAL32806.2| GA10329 [Drosophila pseudoobscura pseudoobscura]
          Length = 615

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/203 (23%), Positives = 95/203 (46%), Gaps = 19/203 (9%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++++    + I+LN+
Sbjct: 298 EMACAVPLLKGLGQEWALTKRHESEDIFGVQLCGNNPNVITQAAQVLQETAKVDYIDLNI 357

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNL 139
           GCP   +++   G+ LM   +I+ + +   C +LS  +P TVK R G+           L
Sbjct: 358 GCPIDLIYQQGGGSALMRRTNIL-ELVVRSCSSLSEQLPFTVKMRTGI--YADKSVAHEL 414

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
           V  +++ G + + +H R         ++ R   + +++ + +       + I  NG +  
Sbjct: 415 VPLVEEWGASAVTLHGRS--------REQRYTKHANWEYIEQCAATAKKMPIIGNGDILS 466

Query: 198 -EDMSQALKILPSVDGVMIGRAA 219
            ED  +   + P V  VMIGR A
Sbjct: 467 YEDYVEKRALSPHVSSVMIGRGA 489


>gi|147903417|ref|NP_001079662.1| tRNA-dihydrouridine synthase 3-like [Xenopus laevis]
 gi|82176436|sp|Q7ZWS1|DUS3L_XENLA RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|28436916|gb|AAH46730.1| MGC53781 protein [Xenopus laevis]
          Length = 640

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 70/282 (24%), Positives = 120/282 (42%), Gaps = 40/282 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM +   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 325 EMAMCTNLLQGQPSEWALLKRHHSEDIFGVQLEGAFPDTMTKCAELLNRTIDVDF----V 380

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM   +     +  M   L +P+TVK R GV +++      
Sbjct: 381 DINVGCPIDLVYKKGGGCGLMNRTNKFEQIVKGMNSVLDVPLTVKIRTGVQEKVNIA--H 438

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNR--KIPNLDY-DIVYEIKKENPDLFIGLN 194
            L+ +++  GV+ + +H R         ++ R  K+ N +Y D   +I    P    G  
Sbjct: 439 KLIPNLRDWGVSLVTLHGRS--------REQRYTKLANWEYIDQCAKIASPVPLFGNGDI 490

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
              ED ++AL+    V GVM+ R A     + T + E     +  SS  +  + KDF   
Sbjct: 491 ISYEDANRALQT--GVAGVMLARGALFKPWLFTEIKEQRHWDI--SSTERFDILKDF--- 543

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                T+Y   H  S  +  + TR  +  +  F     CR+I
Sbjct: 544 -----TNYGLEHWGSDCQGVEKTRKFMLEWLSF----LCRYI 576


>gi|307207077|gb|EFN84886.1| tRNA-dihydrouridine synthase 2-like [Harpegnathos saltator]
          Length = 512

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 100/230 (43%), Gaps = 39/230 (16%)

Query: 21  LLYTEMIVADAILRGDKK--NILG----------------FSTQEKPLALQIGGADISKL 62
           ++YTE ++   +LR  ++  ++LG                 S +   + LQIG +D ++ 
Sbjct: 88  IVYTEELIDWKLLRSIRRENDVLGTIDYIDKTDRTVAFRTCSRERDNVVLQIGTSDPTRA 147

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           V+ A +VE      I++N+GCP      G  GA L+ NP      +  + + +SIPVT K
Sbjct: 148 VQVASMVEK-DVAGIDVNMGCPKKFSILGGMGAALLTNPQQATSILRKLIETVSIPVTCK 206

Query: 123 CRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R+     +P +     L  ++  +G+  I +H R           + +  + + + V +
Sbjct: 207 IRV-----LPNLEETFQLCDTLTSTGIEAIAVHGRTI---------DERPQHSNRNHVLK 252

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKNSAML 226
           +  +   + +  NGG +D+     I           VM+ RAA  N ++ 
Sbjct: 253 LISDRLSIPVIANGGSKDVQNHSDIFRFKEETGCSSVMLARAAEWNCSVF 302


>gi|225390252|ref|ZP_03759976.1| hypothetical protein CLOSTASPAR_04003 [Clostridium asparagiforme
           DSM 15981]
 gi|225043677|gb|EEG53923.1| hypothetical protein CLOSTASPAR_04003 [Clostridium asparagiforme
           DSM 15981]
          Length = 322

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 83/196 (42%), Gaps = 19/196 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI        + AA  ++  GY E+NLN+GCPS  V     GA  +   + +   + 
Sbjct: 61  LVPQILTNRAEDFIWAAGEMKARGYREVNLNLGCPSGTVVSKYKGAGFLARQEALNRFLD 120

Query: 110 AMCKALSIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + + + + +++K RIG+   ++ P      L++   +  +  + +H R      L    
Sbjct: 121 QIFQEVDLEISIKTRIGIAAPEEFP-----ELMEIFNRYPIRELIVHPR------LRTDF 169

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSA 224
            +  P+ +    Y +K+    L    NG +   E    A    PSV+ VM+GR    N A
Sbjct: 170 YKNTPDRE-SFGYAVKESRASL--CYNGDIFTEEAFRSAASRFPSVERVMLGRGLLANPA 226

Query: 225 MLTTVDEYFSNPLTGS 240
           +   +      PLT S
Sbjct: 227 LAERIRGIEEAPLTAS 242


>gi|320095947|ref|ZP_08027566.1| tRNA-dihydrouridine synthase B [Actinomyces sp. oral taxon 178 str.
           F0338]
 gi|319977118|gb|EFW08842.1| tRNA-dihydrouridine synthase B [Actinomyces sp. oral taxon 178 str.
           F0338]
          Length = 441

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/304 (20%), Positives = 123/304 (40%), Gaps = 29/304 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAK 67
           R   R+     L  TEM+ + A++    +  +++     E+  ++Q+ G D + +  AA+
Sbjct: 89  RAVPRVDAPAGLYVTEMVTSRALVEEGARTLDMVRPDPVERVRSIQLYGVDPAVMGAAAR 148

Query: 68  IVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---------SI 117
           ++ + G  + I+LN GCP  +V     GA L    D+  D + ++ +A           I
Sbjct: 149 LLVERGLADHIDLNFGCPVPKVTRKGGGAALPWKRDLFVDLVGSVVRACQKAGERAGRQI 208

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG+D         +   + ++ G + + +HAR         +         +D
Sbjct: 209 PVTVKIRIGIDSAHETAT--DAALAAQRLGASALTLHART--------QAQHYAGRAHWD 258

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+      +G NG + +   A+ ++     DGV +GR A     +   +   +  
Sbjct: 259 EIARLKEALTIPVLG-NGDVFEARDAMAMMERTGCDGVCVGRGAQGRPWLFRDIVAAYHG 317

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    V     R  +  + D           ++++ +H+     GF      RH
Sbjct: 318 APVPPGPALAEVVAVIERHAAWVVADQG----DEARAMREMRKHVGWYLRGFAVGGAQRH 373

Query: 296 ILTV 299
            L++
Sbjct: 374 ALSM 377


>gi|71066558|ref|YP_265285.1| tRNA-dihydrouridine synthase [Psychrobacter arcticus 273-4]
 gi|71039543|gb|AAZ19851.1| possible tRNA-dihydrouridine synthase [Psychrobacter arcticus
           273-4]
          Length = 350

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 66/126 (52%), Gaps = 10/126 (7%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           L  D K   G S     + +Q+ G++   + E A    + G   I++N GCP+  V+   
Sbjct: 88  LHHDAKTASGTS-----IHIQLLGSEAQLMAENAAHACELGAPAIDINFGCPAKTVNSHR 142

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            G+ L+  P+++ D I+A+ +A+  +IPV+ K R+G  D      + ++  +I  SG + 
Sbjct: 143 GGSVLLDEPEVMYDIISAVRQAVPANIPVSAKIRLGYTD---TSRMDDIRGAIAASGADW 199

Query: 151 IWIHAR 156
           + IHAR
Sbjct: 200 LTIHAR 205


>gi|320155949|ref|YP_004188328.1| tRNA-dihydrouridine synthase C [Vibrio vulnificus MO6-24/O]
 gi|319931261|gb|ADV86125.1| tRNA-dihydrouridine synthase C [Vibrio vulnificus MO6-24/O]
          Length = 311

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/175 (24%), Positives = 85/175 (48%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A      G + I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 57  PVKVQLLGQDPRWMAENAIRAAQLGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G ++  P      +V ++++   + + +HAR       +  
Sbjct: 117 KACRDAVPSHIPVSAKIRLGWEN--PEDCF-EIVDAVEQGKADELTVHAR-------TKA 166

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +D + +I++ +    I  NG + + +  QA      +D +M+ R A
Sbjct: 167 GGYKASEIKWDYIDQIRQRSTIPLIA-NGEIWNYADGQACIETTGIDSLMVCRGA 220


>gi|149038073|gb|EDL92433.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           (predicted), isoform CRA_b [Rattus norvegicus]
          Length = 380

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 43/158 (27%), Positives = 72/158 (45%), Gaps = 31/158 (19%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRN 138
           +GCP     +G  GA L+ +PD +   ++ + K    PVT K RI   ++D +      N
Sbjct: 1   MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDTL------N 54

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG-- 196
           LVK I+++G++ I +H R         +D R    +  +++  I  E   + +  NGG  
Sbjct: 55  LVKRIERTGISAIAVHGRN--------RDERPQHPVSCEVIRAI-AETLSIPVIANGGSH 105

Query: 197 --------LEDMSQALKILPSVDGVMIGRAAYKNSAML 226
                   +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 106 DHIQQHLDIEDFRQAT----AASSVMVARAAMWNPSIF 139


>gi|154335122|ref|XP_001563801.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134060830|emb|CAM37846.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 590

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/169 (26%), Positives = 73/169 (43%), Gaps = 19/169 (11%)

Query: 59  ISKLVEAAKIVE-----DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +S+  EAA   +      F Y+ +++N GCP  ++ +   G  L      + D +  +  
Sbjct: 293 VSRPQEAATFAQVLEASGFSYDFLDINCGCPVEKLVKSGCGCGLWERTGRLRDVVENLAI 352

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             S PVT+KCRIG D+ +P   L   +      G   + +H R         +  R    
Sbjct: 353 HQSRPVTIKCRIGFDEAMP--TLHQQIHQYSTWGAAAVTVHGRS--------RKQRYTKF 402

Query: 174 LDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
            ++D V +  + +    IG NG    LED+ +  +  P +   MIGR A
Sbjct: 403 ANWDYVDQCAQLSLLPVIG-NGDIMSLEDVLEHRRRQPHITSHMIGRGA 450


>gi|312375539|gb|EFR22895.1| hypothetical protein AND_14041 [Anopheles darlingi]
          Length = 512

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 102/231 (44%), Gaps = 41/231 (17%)

Query: 21  LLYTEMIVADAILRGDKK--NILG-------------FST---QEKPLALQIGGADISKL 62
           L+YTE I+   +LR +++  ++LG             F T   +   + LQIG A   + 
Sbjct: 39  LVYTEEIIDWKLLRAERRVNDVLGTIDYIDTTDGTVVFRTCPAERGKVVLQIGTAAAERA 98

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
               +++++   + I++N+GCP     +G  G  L+ +       + A+ + +SIPVT K
Sbjct: 99  AAVGRMLQE-DVSAIDVNMGCPKDFSIKGGMGVALLYDLPRAKSILEALVQTVSIPVTCK 157

Query: 123 CRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            R+   VDD I       L + ++ +G++ I +H R    +   P +   I  +   +  
Sbjct: 158 IRLMPDVDDTI------KLARELQSTGISAIGVHGRTKTERPRDPVNEAAIARVAKSL-- 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAML 226
                  D+ +  NGG + +++   IL           M+ RAA  N ++ 
Sbjct: 210 -------DIPVIANGGSQSITRRCDILKFARQCGTGSAMVARAAEWNVSVF 253


>gi|149239919|ref|XP_001525835.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146449958|gb|EDK44214.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 504

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 66/130 (50%), Gaps = 13/130 (10%)

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           L  Q+G +     VEAA +++ED   + I+LN GCP +    G  GA L+  PDI+   +
Sbjct: 94  LIFQLGTSTPELAVEAALRVIEDV--DGIDLNCGCPKSFSTHGGMGAELLKTPDILCSIL 151

Query: 109 AAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ + +  P    + C+I +     A  L  L++ I ++G+  + IH R  I++     
Sbjct: 152 RALVEKVGNPNKKPISCKIRLLPNFEASKL--LIEQICQTGIRNLTIHCRTPIMR----- 204

Query: 167 DNRKIPNLDY 176
            NR+ P  +Y
Sbjct: 205 -NRQDPFWNY 213


>gi|195580263|ref|XP_002079972.1| GD24232 [Drosophila simulans]
 gi|194191981|gb|EDX05557.1| GD24232 [Drosophila simulans]
          Length = 605

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/272 (23%), Positives = 116/272 (42%), Gaps = 31/272 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 288 EMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMINQAAQVIHETAQVDFIDLNI 347

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 348 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSDRLPFTVKMRTGIYADKSVAHELLP 406

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + ++  + E   +   + +  NG + 
Sbjct: 407 LVEEW---GASAVTLHGRS--------REQRYTKHANWAYIEECAAKAKRMPVIGNGDIL 455

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ED  +   + P V  VMIGR A     +   + E      + SS  +  + + F    
Sbjct: 456 SYEDYVERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWSPSSGQRYEMLQKF---- 509

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                +Y   H  S  K  + TR  +  +  F
Sbjct: 510 ----CNYGMEHWGSDTKGVETTRRFLLEWQSF 537


>gi|153813385|ref|ZP_01966053.1| hypothetical protein RUMOBE_03804 [Ruminococcus obeum ATCC 29174]
 gi|149830562|gb|EDM85653.1| hypothetical protein RUMOBE_03804 [Ruminococcus obeum ATCC 29174]
          Length = 316

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/174 (24%), Positives = 77/174 (44%), Gaps = 11/174 (6%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    +  A  ++++GY E+NLN+GCPS  V     GA  +  P+ +   +  + 
Sbjct: 64  QILTRNADDFLRTANQLKEYGYQEVNLNLGCPSKTVVTKGCGAGFLARPEELEQFLDRIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + ++VK R+G++D   A     L++   +  +  + IH R  + K          P
Sbjct: 124 SKTDMKISVKTRLGMED---AEEFPRLMEIYNRFPMEELIIHPR--VQKDFY----NNTP 174

Query: 173 NLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           NL+ +     I K NP  + G     +D  +     P V+  M+GR    + ++
Sbjct: 175 NLEAFGEALAISK-NPVCYNGDIFSTDDFKRIQSQFPDVECFMMGRGVLADPSL 227


>gi|326482381|gb|EGE06391.1| tRNA-dihydrouridine synthase [Trichophyton equinum CBS 127.97]
          Length = 419

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 108 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 166

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 167 ALVREVGQPWQIGISVKIRLLKDPR----DTERLVTALCATGITGLTVHCRTTPMRPREA 222

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I + +  +   +NG ++    AL+++    VDG MI  +A  N
Sbjct: 223 AIRDQLP-----MIASICR-SAGVACLMNGDVKSRDHALELMSQYDVDGAMIATSAESN 275


>gi|255956875|ref|XP_002569190.1| Pc21g22200 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211590901|emb|CAP97117.1| Pc21g22200 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 536

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/155 (29%), Positives = 70/155 (45%), Gaps = 8/155 (5%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEAAK 67
           F ARL      + T+         G  K+ L   G    ++PL +Q    +  + +EAA+
Sbjct: 75  FHARLFGEQENVRTKHFQPTRKAIGGSKDELFLDGNPAIDRPLFVQFCTNNPDEFLEAAR 134

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V     + ++LN+GCP     +G +GA L  + D++   +  +   LSIPVTVK RI  
Sbjct: 135 HVAPH-CDAVDLNLGCPQGIAKKGHYGAFLQEDWDLIYRLVNRLHTELSIPVTVKFRI-- 191

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
             Q          K I  +G + I +H R+   KG
Sbjct: 192 --QETKEKTLEYAKMILSAGASIIAVHGRRREQKG 224


>gi|302665254|ref|XP_003024239.1| hypothetical protein TRV_01589 [Trichophyton verrucosum HKI 0517]
 gi|291188286|gb|EFE43628.1| hypothetical protein TRV_01589 [Trichophyton verrucosum HKI 0517]
          Length = 640

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 328 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 386

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 387 ALVREVGRPWQIGISVKIRLLKDPK----DTERLVTALCATGITGLTVHCRTTPMRPREA 442

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I + +  +   +NG ++    AL+++    VDG MI  +A  N
Sbjct: 443 AIRDQLP-----MIASICR-SAGVACLMNGDVKSRDHALELMSQYDVDGAMIATSAESN 495


>gi|238060527|ref|ZP_04605236.1| nifR3 family TIM-barrel protein [Micromonospora sp. ATCC 39149]
 gi|237882338|gb|EEP71166.1| nifR3 family TIM-barrel protein [Micromonospora sp. ATCC 39149]
          Length = 239

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 77/181 (42%), Gaps = 18/181 (9%)

Query: 12  FARLL--TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK 67
           F RL       +   EMI   A++  + K +  + F   E+P +LQ+ G D      A +
Sbjct: 39  FRRLCREQGGGIYVCEMITTVALVERNPKTLRMIAFGDDERPRSLQLYGTDPEITAAAVR 98

Query: 68  IV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKC 123
           IV E    + I+LN GCP  +V     G+ L     +    + A   A S   +PVTVK 
Sbjct: 99  IVVEKDLADHIDLNFGCPVPKVTRKGGGSALPWRRRLFARLVRAAVDAASPAGVPVTVKM 158

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G+DD         L  + + +GV  + +H R A          R     D+D +  +K
Sbjct: 159 RKGIDDDHLTYVEAGL--AAQDAGVAAVALHGRTAA--------QRYSGTADWDAIATLK 208

Query: 184 K 184
           +
Sbjct: 209 Q 209


>gi|67525019|ref|XP_660571.1| hypothetical protein AN2967.2 [Aspergillus nidulans FGSC A4]
 gi|40744362|gb|EAA63538.1| hypothetical protein AN2967.2 [Aspergillus nidulans FGSC A4]
 gi|259486087|tpe|CBF83649.1| TPA: tRNA dihydrouridine synthase (Smm1), putative (AFU_orthologue;
           AFUA_3G08390) [Aspergillus nidulans FGSC A4]
          Length = 437

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 85/181 (46%), Gaps = 17/181 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A+    V+A K+V     N I++N GCP      G  GA L+  PD +   + 
Sbjct: 102 LIFQMGTANPELAVQAGKLVA-ADVNGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILE 160

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +  P    ++VK R+    ++      +LV  + ++G+ G+ IH R   ++   P
Sbjct: 161 ALVKEVGEPYQIGISVKIRLLETPEL----TESLVSRLVRTGITGLTIHCRTTPMR---P 213

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           ++ R I +    IV      N  +   +NG +    +AL ++     DG MI  AA  NS
Sbjct: 214 RE-RAIRDQLRMIVSTC--HNAGVACIMNGDVTSRDEALALMQEYGADGAMIATAAEANS 270

Query: 224 A 224
           +
Sbjct: 271 S 271


>gi|284922125|emb|CBG35206.1| tRNA-dihydrouridine synthase C [Escherichia coli 042]
          Length = 315

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 85/172 (49%), Gaps = 17/172 (9%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           AA+ VE  G   ++LN GCPS  V+    GA L+ +P+++     AM + +   +PV+VK
Sbjct: 81  AARAVE-LGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREVVPAHLPVSVK 139

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G D          +  +++++G   + +H R       + +   +  ++D+  + EI
Sbjct: 140 VRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGYRAEHIDWQAIGEI 189

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            ++  ++ +  NG + D   A + +     D VMIGR A  N   L+ V +Y
Sbjct: 190 -RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSRVVKY 239


>gi|316974141|gb|EFV57667.1| tRNA-dihydrouridine synthase 2 [Trichinella spiralis]
          Length = 724

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 59/224 (26%), Positives = 97/224 (43%), Gaps = 41/224 (18%)

Query: 21  LLYTEMIVADAILRGDKK---------------NILGFSTQEKP---LALQIGGADISKL 62
           L++TE IV   I+   +K               N   F T  K    L  QIG +D  K 
Sbjct: 20  LVFTEEIVDQKIIGCRRKINEHLGTIDFCSEGDNFPRFRTSSKETNKLVFQIGTSDGEKA 79

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + AA++VE      I++N+GCP      G  GA L+   + V   +  + + +S PV+ K
Sbjct: 80  LAAARVVEQ-DVAGIDVNMGCPKPFSLLGGMGAALLEQREKVRSILTMLVENISKPVSCK 138

Query: 123 CRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            R+   V+D +      +L + I++ GV  I IH R       +  +  + PN D D + 
Sbjct: 139 IRVLPSVEDTV------DLCRLIEECGVQAITIHGR-------TTSERAQHPNRD-DFIA 184

Query: 181 EIKKENPDLFIGLNGGLEDMS-----QALKILPSVDGVMIGRAA 219
           E+ +    + +  NGG  ++      +  ++       MI RAA
Sbjct: 185 EVARA-VRIPVICNGGSSEIRHHTDIENFRLKCHATHAMIARAA 227


>gi|326423970|ref|NP_761082.2| tRNA-dihydrouridine synthase C [Vibrio vulnificus CMCP6]
 gi|38604855|sp|Q8DAH1|DUSC_VIBVU RecName: Full=tRNA-dihydrouridine synthase C
 gi|319999348|gb|AAO10609.2| tRNA-dihydrouridine synthase C [Vibrio vulnificus CMCP6]
          Length = 318

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/175 (24%), Positives = 85/175 (48%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A      G + I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAQLGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G ++  P      +V ++++   + + +HAR       +  
Sbjct: 124 KACRDAVPSHIPVSAKIRLGWEN--PEDCF-EIVDAVEQGKADELTVHAR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +D + +I++ +    I  NG + + +  QA      +D +M+ R A
Sbjct: 174 GGYKASEIKWDYIDQIRQRSTIPLIA-NGEIWNYADGQACIETTGIDSLMVCRGA 227


>gi|37680310|ref|NP_934919.1| putative regulator protein [Vibrio vulnificus YJ016]
 gi|37199057|dbj|BAC94890.1| putative regulator protein [Vibrio vulnificus YJ016]
          Length = 318

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/175 (24%), Positives = 85/175 (48%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A      G + I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAQLGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G ++  P      +V ++++   + + +HAR       +  
Sbjct: 124 KACRDAVPSHIPVSAKIRLGWEN--PEDCF-EIVDAVEQGKADELTVHAR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +D + +I++ +    I  NG + + +  QA      +D +M+ R A
Sbjct: 174 GGYKASEIKWDYIDQIRQRSTIPLIA-NGEIWNYADGQACIETTGIDSLMVCRGA 227


>gi|148679393|gb|EDL11340.1| mCG20459, isoform CRA_a [Mus musculus]
          Length = 380

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/158 (27%), Positives = 72/158 (45%), Gaps = 31/158 (19%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRN 138
           +GCP     +G  GA L+ +PD +   ++ + K    PVT K RI   ++D +      N
Sbjct: 1   MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDTL------N 54

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG-- 196
           LVK I+++G++ I +H R         +D R    +  +++  I  E   + +  NGG  
Sbjct: 55  LVKRIERTGISAIAVHGRN--------RDERPQHPVSCEVIRAI-AETLSIPVIANGGSH 105

Query: 197 --------LEDMSQALKILPSVDGVMIGRAAYKNSAML 226
                   +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 106 DHIQQHVDIEDFRQAT----AASSVMVARAAMWNPSIF 139


>gi|257460864|ref|ZP_05625965.1| tRNA-dihydrouridine synthase B [Campylobacter gracilis RM3268]
 gi|257442195|gb|EEV17337.1| tRNA-dihydrouridine synthase B [Campylobacter gracilis RM3268]
          Length = 308

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 72/137 (52%), Gaps = 8/137 (5%)

Query: 24  TEMIVADA-ILRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EMI A+A +  G+K   +L  +  E P  +QI G+D   + +A  ++  F G + I+LN
Sbjct: 38  SEMISANALVFEGEKTLKMLEKNAAETPFFVQIAGSDAEIIKKAVLLINKFDGIDGIDLN 97

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+L+   +   +  + K  +   T  K R+G      AV + N+
Sbjct: 98  CGCPVPKVVKQGAGSALLLDLPRLSRLVETIKKYSNKKFTSAKVRLG----FSAVDIENI 153

Query: 140 VKSIKKSGVNGIWIHAR 156
            ++++ +G + I IH R
Sbjct: 154 ARAVQSAGADFIAIHGR 170


>gi|50303455|ref|XP_451669.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|74637047|sp|Q6CWM0|DUS3_KLULA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49640801|emb|CAH02062.1| KLLA0B03069p [Kluyveromyces lactis]
          Length = 665

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 79/178 (44%), Gaps = 30/178 (16%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQI 131
           G +EINLN GCP   ++    G+ L+ NP  +  C+  M    + IPVTVK R G  +  
Sbjct: 380 GVSEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNGMNYVSNDIPVTVKIRTGTREGH 439

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI--------- 182
           P +AL    + + ++ V  I +H R         +  R   + D+D V E+         
Sbjct: 440 P-IALSITKRLVLETDVAAITLHGRT--------RQQRYTKSADWDYVGEVANAVRTYEA 490

Query: 183 -KKENPDL-------FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
            ++EN +L       F+G NG   +     K L   ++D VM+ R A     +   VD
Sbjct: 491 ERQENKNLRDGQKIQFVG-NGDCNNWEDWYKHLENKNMDSVMVARGALIKPWIFEEVD 547


>gi|261343438|ref|ZP_05971083.1| tRNA-dihydrouridine synthase [Providencia rustigianii DSM 4541]
 gi|282568584|gb|EFB74119.1| tRNA-dihydrouridine synthase [Providencia rustigianii DSM 4541]
          Length = 319

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/172 (26%), Positives = 79/172 (45%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  P+ +     AM
Sbjct: 67  VQLLGQHPEWLAENANRAIELGSWGVDLNCGCPSKTVNGSGGGATLLKQPESIYRAAKAM 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PV+VK R+G D    +     +  + +++GV  + +H R       + +D  
Sbjct: 127 RDAVPKELPVSVKVRLGWDS---SQFSHEIADAAQQAGVTELTVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
           K   +++  + +I++      I  NG + D   A + +     D +MIGR A
Sbjct: 177 KAECINWQAIGDIRQRLSIPVIA-NGEIWDYESAKRCMEITGCDSIMIGRGA 227


>gi|71660993|ref|XP_817524.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70882721|gb|EAN95673.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 428

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 88/211 (41%), Gaps = 21/211 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL   + + YT MI+AD+    D      FS    E+ L  QI    
Sbjct: 83  MVRCSRPAFRKLCRLWGTD-VSYTHMIMADSFTCSDAARHADFSMYAGEERLVAQIASCS 141

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                EAA ++  +  + I+LN GCP   + +   G+ L+  P++V D +  +   LS  
Sbjct: 142 GPVAAEAATLLAPY-CDAIDLNCGCPQRWIIKEGLGSALLQKPEVVADMVRCIHNGLSGG 200

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P  VK R+  D         +  +  + +G   I +H R       +P        +
Sbjct: 201 VDLPCVVKMRVSNDVGRSV----DFARQCEAAGCGWITVHGRTPSCSAHAP--------V 248

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
             D +  I +E   + +  NGG+ +   ALK
Sbjct: 249 RLDAIRTI-RECVSVPVVANGGVNNPQTALK 278


>gi|148654121|ref|YP_001281214.1| dihydrouridine synthase, DuS [Psychrobacter sp. PRwf-1]
 gi|148573205|gb|ABQ95264.1| dihydrouridine synthase, DuS [Psychrobacter sp. PRwf-1]
          Length = 323

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 89/193 (46%), Gaps = 17/193 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G++   +   A    + G   I+LN GCP+  V+    G+ L+  P
Sbjct: 72  GTTDSGTPIHVQLLGSEPKLMGANALAAAELGAPAIDLNFGCPAKTVNNHRGGSVLLDEP 131

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            ++ D I+A+ +A+   IPV+ K R+G +D      + ++ ++I  SG + + IHAR   
Sbjct: 132 RLMRDIISAVREAVPAHIPVSAKIRLGYND---TNNIDDIRQAIADSGADWLTIHARTKT 188

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
            +G  P      P     IV   +   P   I  NG + +   A + +       VM+GR
Sbjct: 189 -QGYKP------PAYWEKIVAFTELPIP---IIANGEIWNAQHAHQCIAQSHTSHVMLGR 238

Query: 218 AAYKNSAMLTTVD 230
            A     ++  +D
Sbjct: 239 GAVTRPDLVAQID 251


>gi|68482812|ref|XP_714632.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68483004|ref|XP_714536.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436113|gb|EAK95481.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436216|gb|EAK95582.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
          Length = 433

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 110/231 (47%), Gaps = 28/231 (12%)

Query: 14  RLLTNNALLYTEMIVADAIL----RGDKKNIL--GFSTQEKPLALQIGGADISKLVEAAK 67
           ++L +  ++  E+   D I+    + DKK ++      +   L LQ+G +D    V+AA+
Sbjct: 42  KILQSTRIINQELNTIDYIVSNHQQSDKKTVIFRKHPVETGRLILQLGSSDPQLAVDAAR 101

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP--VTVKCRI 125
            V D   + I+LN GCP         GA L+  PD +   +  + + + IP   ++ C+I
Sbjct: 102 KVID-DVDGIDLNCGCPKNFSTHSGMGAELLKTPDKLCSILINLVEKIGIPNKKSISCKI 160

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP--NLDYDIVYEIK 183
            + +       +NL++ I ++G++ + IH R  I++      NR+ P  N    ++  I+
Sbjct: 161 RLFNNYDQS--KNLIEKILQTGISNLTIHCRTPIMR------NRQDPVWNFLPKLIPIIQ 212

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVD-------GVMIGRAAYKNSAMLT 227
               +L I  NG +++++    +  +++        +MI  AA  N ++ +
Sbjct: 213 TAGVNLVI--NGNMQNVADLKNLQSALNDNGGGKLSIMIAEAAEANPSVFS 261


>gi|119476924|ref|ZP_01617205.1| hypothetical protein GP2143_10237 [marine gamma proteobacterium
           HTCC2143]
 gi|119449731|gb|EAW30968.1| hypothetical protein GP2143_10237 [marine gamma proteobacterium
           HTCC2143]
          Length = 321

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 84/181 (46%), Gaps = 18/181 (9%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   +   A      G   I++N GCP+  V+    G+ L+  P
Sbjct: 50  GMTPSGVPVYIQLLGGNAESMAINAAKAASLGAPGIDINFGCPAKSVNRNDGGSVLLKEP 109

Query: 102 DIVGDCIAAMCKA--LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + D +AA+  A  L IPVT K R+G +D   +  L ++ ++I  +  + + IHAR   
Sbjct: 110 QRLHDIVAAVRDAVPLDIPVTAKIRLGFND---SSLLTDISQAIFSANASELTIHAR--- 163

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIG 216
               +  D  K P   ++ + +I+  +P   I  NG +    D    +K     D VM+G
Sbjct: 164 ----TKSDGYKPPAY-WEAIADIQANSPVPVIA-NGEIWTVNDYHSCIK-QSGCDDVMLG 216

Query: 217 R 217
           R
Sbjct: 217 R 217


>gi|153950443|ref|YP_001401772.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|229841115|ref|ZP_04461274.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229843219|ref|ZP_04463365.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229894163|ref|ZP_04509349.1| tRNA-dihydrouridine synthase C [Yersinia pestis Pestoides A]
 gi|229903397|ref|ZP_04518510.1| tRNA-dihydrouridine synthase C [Yersinia pestis Nepal516]
 gi|38604952|sp|Q8ZGV2|DUSC_YERPE RecName: Full=tRNA-dihydrouridine synthase C
 gi|152961938|gb|ABS49399.1| tRNA-dihydrouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|229679167|gb|EEO75270.1| tRNA-dihydrouridine synthase C [Yersinia pestis Nepal516]
 gi|229689566|gb|EEO81627.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229697481|gb|EEO87528.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229704048|gb|EEO91061.1| tRNA-dihydrouridine synthase C [Yersinia pestis Pestoides A]
 gi|320015990|gb|ADV99561.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 312

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 85/185 (45%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  IQLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 127 RAAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 177 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|257485510|ref|ZP_05639551.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|331010686|gb|EGH90742.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 321

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 85/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++    +   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPRHIPVTAKMRLGYENTDGTL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    ++D  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVDDWRRCREICGARD-IMIGR 224


>gi|22126892|ref|NP_670315.1| tRNA-dihydrouridine synthase C [Yersinia pestis KIM 10]
 gi|45440801|ref|NP_992340.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51595560|ref|YP_069751.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|108806882|ref|YP_650798.1| tRNA-dihydrouridine synthase C [Yersinia pestis Antiqua]
 gi|108812963|ref|YP_648730.1| tRNA-dihydrouridine synthase C [Yersinia pestis Nepal516]
 gi|145599791|ref|YP_001163867.1| tRNA-dihydrouridine synthase C [Yersinia pestis Pestoides F]
 gi|149366830|ref|ZP_01888864.1| tRNA-dihydrouridine synthase C [Yersinia pestis CA88-4125]
 gi|162420578|ref|YP_001605884.1| tRNA-dihydrouridine synthase C [Yersinia pestis Angola]
 gi|165924670|ref|ZP_02220502.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165938395|ref|ZP_02226953.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166009907|ref|ZP_02230805.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166211701|ref|ZP_02237736.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167400320|ref|ZP_02305833.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167419917|ref|ZP_02311670.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167424368|ref|ZP_02316121.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167466751|ref|ZP_02331455.1| tRNA-dihydrouridine synthase [Yersinia pestis FV-1]
 gi|170025109|ref|YP_001721614.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis YPIII]
 gi|186894623|ref|YP_001871735.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis PB1/+]
 gi|218928338|ref|YP_002346213.1| tRNA-dihydrouridine synthase C [Yersinia pestis CO92]
 gi|270487207|ref|ZP_06204281.1| dihydrouridine synthase (Dus) [Yersinia pestis KIM D27]
 gi|294503193|ref|YP_003567255.1| hypothetical protein YPZ3_1083 [Yersinia pestis Z176003]
 gi|21959928|gb|AAM86566.1|AE013903_3 putative regulator protein [Yersinia pestis KIM 10]
 gi|45435659|gb|AAS61217.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Yersinia pestis biovar Microtus str. 91001]
 gi|51588842|emb|CAH20456.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108776611|gb|ABG19130.1| hypothetical protein YPN_2803 [Yersinia pestis Nepal516]
 gi|108778795|gb|ABG12853.1| hypothetical protein YPA_0885 [Yersinia pestis Antiqua]
 gi|115346949|emb|CAL19839.1| conserved hypothetical protein [Yersinia pestis CO92]
 gi|145211487|gb|ABP40894.1| hypothetical protein YPDSF_2522 [Yersinia pestis Pestoides F]
 gi|149291204|gb|EDM41279.1| tRNA-dihydrouridine synthase C [Yersinia pestis CA88-4125]
 gi|162353393|gb|ABX87341.1| tRNA-dihydrouridine synthase [Yersinia pestis Angola]
 gi|165913773|gb|EDR32392.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165923730|gb|EDR40862.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165991303|gb|EDR43604.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166207472|gb|EDR51952.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962658|gb|EDR58679.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167050269|gb|EDR61677.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167057217|gb|EDR66980.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169751643|gb|ACA69161.1| dihydrouridine synthase DuS [Yersinia pseudotuberculosis YPIII]
 gi|186697649|gb|ACC88278.1| dihydrouridine synthase DuS [Yersinia pseudotuberculosis PB1/+]
 gi|262361232|gb|ACY57953.1| hypothetical protein YPD4_1044 [Yersinia pestis D106004]
 gi|262365231|gb|ACY61788.1| hypothetical protein YPD8_1103 [Yersinia pestis D182038]
 gi|270335711|gb|EFA46488.1| dihydrouridine synthase (Dus) [Yersinia pestis KIM D27]
 gi|294353652|gb|ADE63993.1| hypothetical protein YPZ3_1083 [Yersinia pestis Z176003]
          Length = 314

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 85/185 (45%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 69  IQLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 128

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVTVK R+G D          +  +++++G   + +H R       + +D  
Sbjct: 129 RAAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGR-------TKEDGY 178

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI++      I  NG + D   A + +     D VM+GR A  N   L+
Sbjct: 179 QAERINWQAIGEIRQRLTIPVIA-NGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLS 236

Query: 228 TVDEY 232
            V +Y
Sbjct: 237 RVVKY 241


>gi|309788022|ref|ZP_07682631.1| dihydrouridine synthase (Dus) family protein [Shigella dysenteriae
           1617]
 gi|308924156|gb|EFP69654.1| dihydrouridine synthase (Dus) family protein [Shigella dysenteriae
           1617]
          Length = 225

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 42/160 (26%), Positives = 81/160 (50%), Gaps = 16/160 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAV 134
           ++LN GCPS  V+    GA L+ +P+++     AM +A+   +PV+VK R+G D      
Sbjct: 1   MDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKF 60

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               +  +++++G   + +H R       + +   +  ++D+  + EI+++  ++ +  N
Sbjct: 61  ---EIADAVQQAGATELVVHGR-------TKEQGYRAEHIDWQAIGEIRQQ-LNIPVIAN 109

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           G + D   A + +     D VMIGR A  N   L+ V +Y
Sbjct: 110 GEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSRVVKY 148


>gi|118581480|ref|YP_902730.1| nifR3 family TIM-barrel protein [Pelobacter propionicus DSM 2379]
 gi|118504190|gb|ABL00673.1| tRNA-U20-dihydrouridine synthase [Pelobacter propionicus DSM 2379]
          Length = 329

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 106/236 (44%), Gaps = 27/236 (11%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKL 62
           T+  +R   R +   AL +TEM+  + ++R     +  L  + ++ PL +Q+ G     L
Sbjct: 25  TNLPFRVICRRM-GAALAFTEMVSVNGLVRSGSNTLALLKSTPEDHPLGIQLFGDRPEDL 83

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            EAA+ VE  G   +++N+GCP  +V     G+ L+  P  V   I A+  A  +P++VK
Sbjct: 84  AEAARRVEGTG-ELLDINMGCPVRKVVGTGAGSALLREPLKVAAIIRAVRAATPLPLSVK 142

Query: 123 CRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYD 177
            R G    +D    +A     +  +  G + I +H  +R  +  G          + D+D
Sbjct: 143 IRSGWHCGEDSYLRIA-----QIAQSEGCDAITLHPRSRSQMFSG----------HADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            + E+K +     IG +G L       ++L     DGVM+ R A     +   V E
Sbjct: 188 QLRELKSQLSIPVIG-SGDLFTPQDCQRMLAETGCDGVMVARGALGTPWIFRQVLE 242


>gi|194212507|ref|XP_001916859.1| PREDICTED: similar to dihydrouridine synthase 3-like [Equus
           caballus]
          Length = 784

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 94/218 (43%), Gaps = 28/218 (12%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 469 EMAVCTNLLQGQTSEWALLRRHQCEDIFGVQLEGAFPDTMTKCAELLNRTVDVDF----V 524

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV ++ P     
Sbjct: 525 DINVGCPIDLVYKKGGGCALMQRSGKFQQIVRGMSQVLDVPLTVKLRTGVQERTPLA--H 582

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGG 196
            L+  ++  G   + +H R         ++ R     D+  + + +   +P    G NG 
Sbjct: 583 RLLPELRTWGAALVTLHGRS--------REQRYTKLADWRYIEQCVAAASPMPLFG-NGD 633

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   ED ++A++    V GVMI R A     + T + E
Sbjct: 634 ILSYEDANRAMQT--GVAGVMIARGALLKPWLFTEIKE 669


>gi|322822399|gb|EFZ28459.1| hypothetical protein TCSYLVIO_5308 [Trypanosoma cruzi]
          Length = 428

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 89/211 (42%), Gaps = 21/211 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL   + + YT MI+AD+    D      FS    E+ L  QI    
Sbjct: 83  MVRCSRPAFRKLCRLWGTD-VSYTHMIMADSFTCSDAARHADFSIYAGEERLVAQIASCS 141

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD---CI-AAMCKA 114
                EAA ++  +  + I+LN GCP   + +   G+ L+  P++V D   CI   +   
Sbjct: 142 GPVAAEAATLLAPY-CDAIDLNCGCPQRWIIKEGLGSALLQKPEVVADMVRCIHNGLSGG 200

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +S+P  VK R+  D         +  +  + +G   I +H R       +P        +
Sbjct: 201 VSLPCVVKMRVNNDVGRSV----DFARHCEAAGCGWITVHGRTPSCSAHAP--------V 248

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
             D +  I +E   + +  NGG+ +   ALK
Sbjct: 249 RLDAIRTI-RECVSVPVVANGGVNNPQTALK 278


>gi|289742295|gb|ADD19895.1| uncharacterized conserved protein [Glossina morsitans morsitans]
          Length = 582

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 88/180 (48%), Gaps = 19/180 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E    +Q+ G   + + +AA++V++    + ++LN+GCP   +++   G+ LM   +I+ 
Sbjct: 289 EDVFGIQLCGNSPNIVAQAAQLVQETTEVDYLDLNIGCPIDLIYQQGGGSALMRRTNIL- 347

Query: 106 DCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + I   C  L+  IP TVK R GV  D+  A    +L+  +++ G   + +H R      
Sbjct: 348 ELIVRSCANLNTKIPFTVKMRTGVYADKSTA---HDLMPLVEEWGAAAVTLHGRS----- 399

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
              ++ R   N ++  + E   +   + +  NG +   ED ++   I P V  VMIGR A
Sbjct: 400 ---REQRYTKNANWTYIEECAAKVKTIPVVGNGDILSYEDYNEKRDIAPHVSSVMIGRGA 456


>gi|157157351|ref|YP_001463486.1| tRNA-dihydrouridine synthase C [Escherichia coli E24377A]
 gi|157079381|gb|ABV19089.1| tRNA-dihydrouridine synthase C [Escherichia coli E24377A]
          Length = 315

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     A 
Sbjct: 67  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAT 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGR-------TKEQGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  ++D+  + EI ++  ++ +  NG + D   A + +     D VMIGR A  N   L+
Sbjct: 177 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVVKY 239


>gi|328851127|gb|EGG00285.1| hypothetical protein MELLADRAFT_93719 [Melampsora larici-populina
           98AG31]
          Length = 321

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 89/202 (44%), Gaps = 31/202 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+GG +   +  AA++++ +  + I++N GCP +  ++   G+ L+  PD+V D + 
Sbjct: 69  LVAQLGGNESFYMAHAAELLQPY-VDGIDINCGCPQSWAYKEGIGSALLRKPDLVRDLVR 127

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +      + PV++K R  VDD +   +   L+K+   + V+ I +H R        P  
Sbjct: 128 GIKTKCGETFPVSIKIR--VDDDLQHTS--RLIKTALAANVSFITVHGRTRHQASSEP-- 181

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM----------SQALKILPSVDGVMIGR 217
                 + YD    IK    +   G +GG+             +Q  + L  V GVM  R
Sbjct: 182 ------VSYD---SIKFAAEEATTGSDGGVPTAANGNVFTLADAQKTRELCGVKGVMSAR 232

Query: 218 AAYKNSAMLTTVDEYFSNPLTG 239
              +N A+    +     PL+G
Sbjct: 233 GLQENPALFAGYERI---PLSG 251


>gi|218132878|ref|ZP_03461682.1| hypothetical protein BACPEC_00739 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991751|gb|EEC57755.1| hypothetical protein BACPEC_00739 [Bacteroides pectinophilus ATCC
           43243]
          Length = 321

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 103/248 (41%), Gaps = 37/248 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD----IV 104
           P  L     D  K++ A  + +++GY+E+NLN+GCPS  V     GA  +  PD     +
Sbjct: 71  PQILSNNSCDCIKVIRA--LHDEYGYDEVNLNLGCPSPTVVTKHKGAGFLAFPDKLDSFL 128

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGL 163
            D   A  K   + V+VK R GV+     + + ++      S    + +H R +  L   
Sbjct: 129 NDVFVAAGKD-GVRVSVKTRTGVESHDEFIKILDIYNQYPLS---ELIVHPRVQKDLYKN 184

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG---VMIGRAAY 220
           SP         DYDI +E    N    +  NG +  +    +I    +G   VM GR   
Sbjct: 185 SP---------DYDI-FEYAYTNSKAPVCYNGDICSVDDYQRITSRFNGLNAVMCGRGMI 234

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITR 278
            N A+  T++        G   + +R  + F    +A   +Y A         K++++  
Sbjct: 235 TNPAIFATIN--------GGDKLSSRALRTFH---NAVFKEYCAVMGERNALFKMKELWY 283

Query: 279 HMIGLFHG 286
           +MI  F G
Sbjct: 284 YMIRNFDG 291


>gi|168053249|ref|XP_001779050.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162669612|gb|EDQ56196.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 336

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/190 (24%), Positives = 91/190 (47%), Gaps = 16/190 (8%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           ++  +  Q+G ++  + ++AA +V        ++N+GCP +    G  G+ L+  PD++ 
Sbjct: 78  EKHRVVFQVGTSEAVRCLKAANLVAG-DIAAFDVNMGCPKSFSTSGGMGSALLSKPDVIH 136

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           D +  + + L+IPVT K R+ +      V    L + I+K+GV+ + +H R+   +   P
Sbjct: 137 DILTTLKRNLNIPVTCKIRL-LKTYGETV---ELARRIEKTGVSALAVHGRRVPDR---P 189

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNS 223
           +D  +     +D + E+        I  NG + + S  Q +K       VM+ R A  N 
Sbjct: 190 RDPAQ-----WDGIQEVVSALSIPVIA-NGDVFEYSDFQRIKDATGAASVMVARGAMWNV 243

Query: 224 AMLTTVDEYF 233
           ++     ++F
Sbjct: 244 SVFRPEGKHF 253


>gi|313234425|emb|CBY24624.1| unnamed protein product [Oikopleura dioica]
          Length = 636

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 81/179 (45%), Gaps = 19/179 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
             +QI GA   +L + A+++ +F   + I++N GCP   + +   G  L   PD +  CI
Sbjct: 340 FGVQIAGAWPDELSKTAELISEFCDVDFIDINCGCPLDLICKTGGGCRLGKAPDKLAGCI 399

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           ++M     +PVT K R G + Q        L+  +K++    I +H R  I +       
Sbjct: 400 SSMKTTSGLPVTCKIRTGWEPQHDMA--HKLIAKLKEAQPALITLHGRSRICRYTG---- 453

Query: 169 RKIPNLDY-----DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
             +   DY     +   E+ KE    F G NG +    D ++A++     DG MIGR A
Sbjct: 454 --VARWDYINECSEASSEVAKEIDVPFFG-NGDVLSYSDYAEAIEKY-GTDGAMIGRGA 508


>gi|269139890|ref|YP_003296591.1| tRNA-dihydrouridine synthase C [Edwardsiella tarda EIB202]
 gi|267985551|gb|ACY85380.1| tRNA-dihydrouridine synthase C [Edwardsiella tarda EIB202]
 gi|304559726|gb|ADM42390.1| tRNA-dihydrouridine synthase C [Edwardsiella tarda FL6-60]
          Length = 318

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 82/177 (46%), Gaps = 19/177 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++ N GCPS  V+    GA L+ +P ++   +
Sbjct: 68  PVRIQLLGQSPHWLAENALRAVTLGSPGVDFNCGCPSKAVNGSGGGATLLKDPALIYAGV 127

Query: 109 AAMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            AM +A+   +P+TVK R+G   D Q   +A      ++++ G   + +H R       +
Sbjct: 128 QAMRQAIPAHLPLTVKVRLGWACDSQRVEIA-----DAVQQGGATELVVHGR-------T 175

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
            +D  +   +++  + EI++      I  NG + D + A   L     D +MIGR A
Sbjct: 176 KEDGYRADRINWAAIGEIRRRLRIPVIA-NGEIWDYASAQACLAQTGCDALMIGRGA 231


>gi|195995959|ref|XP_002107848.1| hypothetical protein TRIADDRAFT_49631 [Trichoplax adhaerens]
 gi|190588624|gb|EDV28646.1| hypothetical protein TRIADDRAFT_49631 [Trichoplax adhaerens]
          Length = 581

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 52/214 (24%), Positives = 92/214 (42%), Gaps = 17/214 (7%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLN 80
           +EM +   +L+G +    ++     E    LQ+ GA    L   ++ + D    + ++LN
Sbjct: 264 SEMALCTNLLQGQQSEWALVKRHESEDLFGLQVCGAWPDTLARLSEYINDRVNVDFVDLN 323

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP   V     G+ LM   + +   +  M   LS+P+TVK R G+  +        L+
Sbjct: 324 LGCPIDLVFHQGAGSALMGRANKLQQIVTGMSSILSVPLTVKLRTGILAK--KSTAHKLI 381

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGLED 199
             I++ G + + +H R         ++ R     D+  + E     +P   IG NG +  
Sbjct: 382 PQIREWGASLVTLHGRS--------REQRYTKLADWSYINECATAADPMPLIG-NGDILS 432

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
               L+ +   +V GVMI R A     + T + E
Sbjct: 433 FEDYLEHMNNTNVAGVMIARGALIKPWLFTEIKE 466


>gi|109947333|ref|YP_664561.1| putative transcriptional regulator [Helicobacter acinonychis str.
           Sheeba]
 gi|109714554|emb|CAJ99562.1| putative transcriptional regulator [Helicobacter acinonychis str.
           Sheeba]
          Length = 328

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 102/204 (50%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  ST E    +QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSTLEDHFMVQISGSKESVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  + P+T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKVIRENTNKPITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + ++ + +H R       +  D  +   +DY+ +  +K+      I  NG ++ 
Sbjct: 152 AHALNDAPIDYVVVHGR-------TRSDKYQKDKIDYESIALMKEILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|297626128|ref|YP_003687891.1| TIM-barrel enzyme, dihydrouridine synthase [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296921893|emb|CBL56453.1| TIM-barrel enzyme, dihydrouridine synthase [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 387

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 63/286 (22%), Positives = 111/286 (38%), Gaps = 24/286 (8%)

Query: 20  ALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNE 76
            L   EMI +  ++ G+ K  ++L F   E   ++Q  G +   L  A  ++   +  + 
Sbjct: 46  GLCVCEMITSRGLVVGNVKTDSMLTFFDDEPHRSVQTYGTNPRVLARAIDELCTHYRADH 105

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGVDDQIPA 133
           ++LN GCP  +V     G  L    D++ + I    +A     +P+TVK R+G+DD    
Sbjct: 106 VDLNFGCPVPKVTRKGGGGVLPWKLDLIREIIRQSVRAADAHGVPLTVKTRVGIDDD--H 163

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
               ++ +  ++ G   I +H R                +  +D + E+     D+ +  
Sbjct: 164 TTFLDVGRIAQEEGAAAICLHGRTVA--------EAYAGHAHWDRIGELVAAV-DIPVLG 214

Query: 194 NGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           NG + + S AL+++      GV IGR       +   +          + P    V    
Sbjct: 215 NGDIWEPSDALEMMARTGCAGVEIGRGCLGRPWLFRDLAAAMHGQQVQTLPTLGEVAAIV 274

Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            R     +     +H      L  + +HM   F GFP     RH L
Sbjct: 275 RRHGELLVRQMGVKH-----GLTDLRKHMSWYFKGFPVGGELRHSL 315


>gi|83766214|dbj|BAE56357.1| unnamed protein product [Aspergillus oryzae]
          Length = 444

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/187 (26%), Positives = 84/187 (44%), Gaps = 21/187 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LIFQLGTASPELAVQAAKVVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILE 163

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK RI    +I       LV  + K+G+ G+ +H R   ++   P
Sbjct: 164 ALVREIGEPYQIGISVKIRILEKPEI----TEALVSRLVKTGITGLTVHCRTPAMR---P 216

Query: 166 KDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++   R+   +  DI ++       +   +NG +    Q L ++    VDG MI  +A  
Sbjct: 217 RERAIREQLRMIRDICHDA-----GVACLMNGDVTSRDQGLALMEEFGVDGAMIATSAEA 271

Query: 222 NSAMLTT 228
           N +   +
Sbjct: 272 NPSCFQS 278


>gi|77360138|ref|YP_339713.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875049|emb|CAI86270.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 326

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 50/198 (25%), Positives = 89/198 (44%), Gaps = 16/198 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G ++   P+ +Q+ G     L E A      G + I+LN GCP+  V++   GA L+ +P
Sbjct: 57  GLTSAGTPVRIQLLGQVAGALAENAVKAISLGSHGIDLNFGCPAKTVNKSKGGAVLLKDP 116

Query: 102 DIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + + I A+  A+     V+ K R+G DD   +   + +V ++  +G + I IHAR   
Sbjct: 117 EHMYEIIKAVRDAVDSKHQVSAKIRLGFDDDSNS---QEIVDAVVSAGASSIAIHARTKR 173

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGR 217
                P    KIP L  D          D+ +  NG +  ++ A+  +       +M+GR
Sbjct: 174 DGYNPPAYWEKIPPLIKD---------KDIAVVANGEIWQVADAMLCQKRSGCTDLMLGR 224

Query: 218 AAYKNSAMLTTVDEYFSN 235
            A  +  +   +    +N
Sbjct: 225 GALSHPDLAKKIKANINN 242


>gi|330987411|gb|EGH85514.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 321

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 85/173 (49%), Gaps = 16/173 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL LQ+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +
Sbjct: 64  PLRLQLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +A+   IPVT K R+G ++    +   +  +++   G   I +HAR  +       
Sbjct: 124 SQVRRAVPRHIPVTAKMRLGYENTDGTL---DCARALADGGAEQIVVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D  K P   ++ +  I++  + P +  G    ++D  +  +I  + D +MIGR
Sbjct: 174 DGYK-PPAHWEWIARIQEVVKVPVVANGEIWTVDDWRRCREICGARD-IMIGR 224


>gi|312382630|gb|EFR28023.1| hypothetical protein AND_04540 [Anopheles darlingi]
          Length = 708

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 80/168 (47%), Gaps = 12/168 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +  K  K+ L    +++PL +Q  G D
Sbjct: 165 MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFSKDPKYRKDSLQTCPEDRPLIIQFCGND 223

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM----LNPDIVGDCIAAMCKA 114
              +++AA + +D   + I++N+GCP A    G +GA L     L  +I    ++ +   
Sbjct: 224 PKVMLQAALLAQDHC-DAIDINLGCPQAIAKRGHYGAFLQDEWELLREIGQQTMSTLHCH 282

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           L+IPVT K RI  +D    +      + ++ +G   + +H R    KG
Sbjct: 283 LAIPVTCKIRI-FEDMSKTI---RYARMLQDAGAQLLTVHGRTREQKG 326


>gi|270009693|gb|EFA06141.1| hypothetical protein TcasGA2_TC008984 [Tribolium castaneum]
          Length = 418

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 54/254 (21%), Positives = 98/254 (38%), Gaps = 47/254 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +   N  L YT MI+AD+  +  K     F+T   + PL  Q     
Sbjct: 31  MVRYSKLQFRNLVKSY-NCDLCYTPMILADSFCKSGKARANEFTTNMNDTPLITQFAANK 89

Query: 59  ISKLVEAAKIVED--FGYN--------------EINLNVGCPSARVHEGSFGACLMLNPD 102
           +   V AA +V    FG N               ++LN GCP         G  ++  P+
Sbjct: 90  VYDFVGAAYMVSPLVFGLNLANFYRFFIFSFCDGVDLNCGCPQRWAKLQGLGCIMLEKPE 149

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +      +  P TV  ++ +   +       + + ++  GV+ + +H R      
Sbjct: 150 VIYDLVKQCRNVIPKPFTVSVKLRLQKDLRRSV--EICRQLEHCGVSFLTVHGR------ 201

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIG-------LNGGLEDMSQALKILPSVD--GV 213
            +P            +  E+ KE  +L +G        NGG++ +   L++    +  GV
Sbjct: 202 -TPD----------QLTGEVNKEALNLIVGSVNVPVVANGGVKSLEDCLELQEKTNCKGV 250

Query: 214 MIGRAAYKNSAMLT 227
           M+      N  + T
Sbjct: 251 MVANGLLTNPTLFT 264


>gi|94984185|ref|YP_603549.1| dihydrouridine synthase, DuS [Deinococcus geothermalis DSM 11300]
 gi|94554466|gb|ABF44380.1| tRNA-U20-dihydrouridine synthase [Deinococcus geothermalis DSM
           11300]
          Length = 333

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 102/233 (43%), Gaps = 32/233 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADA-ILRGDKKNILGFSTQEKPLALQIG-- 55
           M  ++D   R   +L      L+T  EMI A   +L GD + +    T  +P   ++G  
Sbjct: 22  MAGYSDAPMR---QLAAEQGALWTVSEMISARGLVLGGDSEKL----TLGRPYPGEVGRV 74

Query: 56  ----GADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               GA+   L +A    E  F    ++LN+GCP  +V +G  GACL+  P++    + A
Sbjct: 75  VQLFGAEPDVLAQAVARAESWFAPAALDLNMGCPVPKV-KGRGGACLLQTPEVAYTLVRA 133

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           M  A ++ V+ K R+G D          + + +  +G   I +H R ++         R 
Sbjct: 134 MRSATTLDVSAKIRLGWDTDRSV----EIAQGLAAAGAALITVHGRTSV--------QRY 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKN 222
               D+D +  +        +G +G ++   QA  ++   V  VMIGR A  N
Sbjct: 182 SGEADWDAIARVAASVKVPVVG-SGDVKSAEQARARLNTGVAAVMIGRGAVGN 233


>gi|146083263|ref|XP_001464693.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134068787|emb|CAM59721.1| conserved hypothetical protein [Leishmania infantum JPCM5]
 gi|322498112|emb|CBZ33187.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 595

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/169 (25%), Positives = 72/169 (42%), Gaps = 19/169 (11%)

Query: 59  ISKLVEAAKIVE-----DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +S+  EAA   +      F Y+ +++N GCP  ++ +   G  L      + D + ++  
Sbjct: 298 VSRPQEAATFAQALEASGFSYDFLDINCGCPVEKIVKSGCGCGLWKRTGRLRDVVESLAI 357

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             S PV +KCRIG+D+  P   L   +      G   + +H R         +  R    
Sbjct: 358 HQSRPVAIKCRIGLDEDTP--TLHQQIHRYSTWGAAAVTVHGRS--------RKQRYTKF 407

Query: 174 LDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
            ++D V +  +      IG NG    LED+ +  +  P +   MIGR A
Sbjct: 408 ANWDYVDQCAQLTSLPVIG-NGDIMSLEDVLEHRERQPHITSHMIGRGA 455


>gi|255525292|ref|ZP_05392233.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
 gi|296187797|ref|ZP_06856191.1| dihydrouridine synthase (Dus) [Clostridium carboxidivorans P7]
 gi|255511057|gb|EET87356.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
 gi|296047754|gb|EFG87194.1| dihydrouridine synthase (Dus) [Clostridium carboxidivorans P7]
          Length = 313

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 52/218 (23%), Positives = 92/218 (42%), Gaps = 17/218 (7%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +++L  + Q   L  Q+   +       +K ++  GYNE+NLN+GCPS  V   + G+  
Sbjct: 49  RDVLPENNQGLVLIPQLLTNNAKDFTHMSKKLKQLGYNEVNLNLGCPSGTVVSKNRGSGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +     + + +  +       +++K RIG D         NL++   K  +  + IH R 
Sbjct: 109 LSKTKELDEFLEEIFSEAVTKISIKTRIGKDS---PEEFYNLIEIFNKYPMEELIIHPR- 164

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
            I K       +  PN++      I  +NP  + G    ++D     K   SV  +M+GR
Sbjct: 165 -IQKDFY----KNKPNMEIFKEALILSKNPICYNGDIFKVKDYENFSKDFTSVQTLMLGR 219

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
               N  ++  +          + P K ++ KDF  KI
Sbjct: 220 GLLANPGLIGDIK-------NNTKPEK-KLLKDFHDKI 249


>gi|238853381|ref|ZP_04643760.1| dihydroorotate dehydrogenase B, catalytic subunit [Lactobacillus
           gasseri 202-4]
 gi|282851814|ref|ZP_06261177.1| dihydroorotate dehydrogenase 1B [Lactobacillus gasseri 224-1]
 gi|238833953|gb|EEQ26211.1| dihydroorotate dehydrogenase B, catalytic subunit [Lactobacillus
           gasseri 202-4]
 gi|282557056|gb|EFB62655.1| dihydroorotate dehydrogenase 1B [Lactobacillus gasseri 224-1]
          Length = 307

 Score = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 99/225 (44%), Gaps = 32/225 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA++  DK   L  S  + P+   +GG D +  VE AK + D G  N + +NV CP+   
Sbjct: 80  DAVIE-DKLKPLRQSYPDLPIMASVGGEDEAGYVEVAKKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V      +    ++P+ VK    V D      +  + K+ +K G 
Sbjct: 139 GGMSFG----VHPDVVESLTKKIKAVTNVPIYVKLTPNVTD------ITQISKAAEKGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I I  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMDIDIKTRKPVLGHNIGGLS---GEAVKPVALRMVHQVRQSTSLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            GG+      +K +L   + V +G A +K+S     + +   N L
Sbjct: 246 -GGISSAQDVIKFMLAGANAVAVGTAHFKDSIASKHIADELPNEL 289


>gi|86153597|ref|ZP_01071800.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           HB93-13]
 gi|85842558|gb|EAQ59770.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           HB93-13]
          Length = 305

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 61/256 (23%), Positives = 118/256 (46%), Gaps = 36/256 (14%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +          DY+ +    K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSIHGRTRKQLYSGKA----------DYESIASA-KASVKIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ++  +  KI    DG+MIGRA+  N  +   +        +G S     VD+ F ++I
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGNPWIFHEIK-------SGKS-----VDEKFKKEI 247

Query: 256 SASMTDYAARHLHSGG 271
             +  D   +H    G
Sbjct: 248 ILTHFDEMIKHYKDQG 263


>gi|17510279|ref|NP_493554.1| hypothetical protein Y54E5A.6 [Caenorhabditis elegans]
 gi|3925277|emb|CAA21662.1| C. elegans protein Y54E5A.6, partially confirmed by transcript
           evidence [Caenorhabditis elegans]
          Length = 436

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 102/225 (45%), Gaps = 23/225 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLA-LQIGGADISKLVEAA 66
           +   + +  L+    +V +A+   D +N    IL  + +EK    LQIG     K  + A
Sbjct: 35  YTEEIVDKKLIEATRVVNEALGTIDYRNGDDIILRLAPEEKGRCILQIGTNSGEKAAKIA 94

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +IV D     I++N+GCP         GA L+   + + D + ++  A  +PVT K R+ 
Sbjct: 95  QIVGD-DVAGIDVNMGCPKPFSIHCGMGAALLTQTEKIVDILTSLKSAAKVPVTCKIRV- 152

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--- 183
           +DD  P   L+ LV+ I+K  V+ + +H R+        +D R+      D + ++    
Sbjct: 153 LDD--PEDTLK-LVQEIEKCRVSALGVHGRR--------RDERQPDKCRIDEIRDVAQAV 201

Query: 184 KENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAML 226
           +  P +  GL+  +E  S  +  ++L      MI R A    ++ 
Sbjct: 202 QSIPVISNGLSDEIEQYSDFEKYQLLTETSSTMIARKALSTPSIF 246


>gi|327292817|ref|XP_003231106.1| tRNA dihydrouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326466736|gb|EGD92189.1| tRNA dihydrouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 414

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 108 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLISILE 166

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 167 ALVREVGRPWQIGISVKIRLLKDPK----DTERLVTALCATGITGLTVHCRTTPMRPREA 222

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I + +  +   +NG ++    AL+++    VDG MI  +A  N
Sbjct: 223 AIRDQLP-----MIASICR-SAGVACLMNGDVKSRDHALELMSQYDVDGAMIATSAESN 275


>gi|212633320|ref|YP_002309845.1| dihydrouridine synthase [Shewanella piezotolerans WP3]
 gi|212554804|gb|ACJ27258.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Shewanella
           piezotolerans WP3]
          Length = 322

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 69/277 (24%), Positives = 120/277 (43%), Gaps = 33/277 (11%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI G+D   +  AA +    G   I++N+GCP+ +V++   G+ L+ +P  V   + A
Sbjct: 68  SVQIAGSDPELMANAAAVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQDPQQVEAILKA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSP 165
           +  A+ +PVT+K R G      A   RN   + +  +  G+  + +H   R+ + KG + 
Sbjct: 128 VVAAVDVPVTLKIRTGW-----APEHRNGVHIAQIAENCGIASLAVHGRTRQCMYKGEA- 181

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                    +YD +  IKK+   + +  NG +    +A  +L    VD +MIGR A    
Sbjct: 182 ---------EYDTIKAIKKQ-ISIPVVANGDILTPEKARFVLDYTGVDALMIGRGAQGRP 231

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +  Y     TG+       D+     +      YA   L+   K  +  R  +G 
Sbjct: 232 WIFREIQHYLD---TGNKLAPVETDEKRQLMLEHLKMLYA---LYGDYKGIRFARKHVGW 285

Query: 284 FHGFPNSRRCR----HILTVEAGASTATHHIIETAFN 316
           +    + R  R     ++TVE   S   H+  E A N
Sbjct: 286 YLNQESQRAFRAEFNRLVTVEEQCSMVEHYFDEFAAN 322


>gi|50294738|ref|XP_449780.1| hypothetical protein [Candida glabrata CBS 138]
 gi|74637232|sp|Q6FJ14|DUS3_CANGA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49529094|emb|CAG62758.1| unnamed protein product [Candida glabrata]
          Length = 640

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 102/243 (41%), Gaps = 43/243 (17%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIG---GADISKL 62
           YR   R L  + + Y+EM +A  +++G      +      E P   +Q+    G   SK 
Sbjct: 282 YRRLMRTLGAD-VTYSEMALAVPLVQGTNSEWALPKAHESEYPGFGVQVACSKGWQASKA 340

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTV 121
            EA       G +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  IP+TV
Sbjct: 341 AEALATYIPNGISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSGDIPITV 400

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G  +  P +A   + + + ++ V  I +H R         +  R     D+D V +
Sbjct: 401 KIRTGTKEGHP-IADTLVRRLVFETDVAAITLHGRS--------RQQRYTKVADWDYVSQ 451

Query: 182 IKK----------ENPD-------------LFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
           + K          E+P               F+G NG + + +   + L  P VD  M+ 
Sbjct: 452 VAKALRQAEADFMESPQGKESHHDEKTRHTQFVG-NGDIFNYTDWYQHLEDPEVDSCMVA 510

Query: 217 RAA 219
           R A
Sbjct: 511 RGA 513


>gi|195433972|ref|XP_002064980.1| GK14924 [Drosophila willistoni]
 gi|194161065|gb|EDW75966.1| GK14924 [Drosophila willistoni]
          Length = 579

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 95/204 (46%), Gaps = 21/204 (10%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNV 81
           EM  A  I++G  +   +      E    +Q+ G + + + +AA+++ D    + I+LN+
Sbjct: 262 EMACALPIVKGLSQEWALTKRHESEDFFGVQLCGNNPNIISQAAQVLHDTAKVDYIDLNI 321

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C  LS  +P TVK R G+  D+  A  L  
Sbjct: 322 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCSNLSPQLPFTVKMRTGIYADKSVAHELLP 380

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G   + +H R         ++ R   + +++ + E   +   + +  NG + 
Sbjct: 381 LVEEW---GAAAVTLHGRS--------REQRYTKHANWEYIEECASKAKSIPVIGNGDIL 429

Query: 198 --EDMSQALKILPSVDGVMIGRAA 219
             ED  +  +I P V  VMIGR A
Sbjct: 430 SYEDYVERRQIAPHVSSVMIGRGA 453


>gi|146282133|ref|YP_001172286.1| NifR3/Smm1 family protein [Pseudomonas stutzeri A1501]
 gi|145570338|gb|ABP79444.1| NifR3/Smm1 family protein [Pseudomonas stutzeri A1501]
          Length = 302

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 84/174 (48%), Gaps = 18/174 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L + A      G   I+LN GCP+  V++   GA L+  PD++    
Sbjct: 42  PVRVQLLGSDPICLADNAAFACTLGAPAIDLNFGCPAKTVNKSRGGAVLLKEPDLLH--- 98

Query: 109 AAMCKALS-----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           A +C+  S     IPVT K R+G D   P  AL +  +++   G   + +HAR  + +G 
Sbjct: 99  AILCEVRSAVPAHIPVTAKMRLGFDS--PDGAL-DCARALVAGGAEQLVVHARTKV-EGY 154

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
            P  + +      ++V      N D++      LED  +  ++  + D +M+GR
Sbjct: 155 KPPAHWEWVARVQEVVPVPVYANGDIW-----SLEDWRRCREVSGAED-IMLGR 202


>gi|297568054|ref|YP_003689398.1| dihydrouridine synthase DuS [Desulfurivibrio alkaliphilus AHT2]
 gi|296923969|gb|ADH84779.1| dihydrouridine synthase DuS [Desulfurivibrio alkaliphilus AHT2]
          Length = 335

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 101/220 (45%), Gaps = 17/220 (7%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           LL TEM+ A  +   +      L     E+PL+ Q+     +++  A    E+ G   I+
Sbjct: 45  LLSTEMLAAKRLPHENPTLSPYLVRHPSEQPLSFQLLLTSPAEVAAAVASAEELGAAAID 104

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCP+  +     G+ LM  P +V   +    +  ++P++ K R+G  +++ A  LR 
Sbjct: 105 LNLGCPAPDIRRQGGGSRLMEEPQMVRRLVQETRRRTALPLSAKIRLG--EELNAERLRA 162

Query: 139 LVKSIKKSGVNGIWIHAR-KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               ++ +GV+ + +HAR +    G  P+         ++ V ++K     + +  NGG+
Sbjct: 163 FCLLLEDAGVDLLTVHARLRGEPYGRKPR---------WEWVGKVKHWL-RIPVVANGGI 212

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                + A       DG+MIGRAA     +   + E ++ 
Sbjct: 213 FSAADAAACLAASGADGLMIGRAAAATPWLFRQLAEGWAT 252


>gi|253687922|ref|YP_003017112.1| dihydrouridine synthase DuS [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754500|gb|ACT12576.1| dihydrouridine synthase DuS [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 310

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 67  VQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAM 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  
Sbjct: 127 REAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGASELVVHGR-------TKEDGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLT 227
           K   +++  + +I++      I  NG + D   A   + +   D +M+GR A  N   L+
Sbjct: 177 KAECINWQAIGKIRQRLRIPVIA-NGEIWDWQSAQDCMATTGCDAIMLGRGAL-NVPNLS 234

Query: 228 TVDEY 232
            V +Y
Sbjct: 235 RVIKY 239


>gi|238883846|gb|EEQ47484.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 433

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 111/231 (48%), Gaps = 28/231 (12%)

Query: 14  RLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKP--LALQIGGADISKLVEAAK 67
           ++L +  ++  E+   D I+    + DKK ++     ++   L LQ+G +D    V+AA+
Sbjct: 42  KILQSTRIINQELNTIDYIVSNHQQSDKKTVIFRKHPDETGRLILQLGSSDPQLAVDAAR 101

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP--VTVKCRI 125
            V D   + I+LN GCP         GA L+  PD +   +  + + + IP   ++ C+I
Sbjct: 102 KVID-DVDGIDLNCGCPKNFSTHSGMGAELLKTPDKLCSILINLVEKIGIPNKKSISCKI 160

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP--NLDYDIVYEIK 183
            + +       +NL++ I ++G++ + IH R  I++      NR+ P  N    ++  I+
Sbjct: 161 RLFNNYDQS--KNLIEKILQTGISNLTIHCRTPIMR------NRQDPVWNFLPKLIPIIQ 212

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVD-------GVMIGRAAYKNSAMLT 227
               +L I  NG +++++    +  +++        +MI  AA  N ++ +
Sbjct: 213 TAGVNLVI--NGNMQNVADLKNLQSALNDNGGGKLSIMIAEAAEANPSVFS 261


>gi|308808596|ref|XP_003081608.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
 gi|116060073|emb|CAL56132.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
          Length = 639

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 71/150 (47%), Gaps = 5/150 (3%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F R+ T+    +  +EM +A  +L+GD+K   ++     EK   +QI G     +   A+
Sbjct: 284 FRRICTDLGADITVSEMAMASNLLKGDRKEWALVRRHPIEKCFGIQICGGYPDLMTRCAE 343

Query: 68  IVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           ++++  + + I++N+GCP   V     G  LM + D +   + +M    S PVT+K R+G
Sbjct: 344 LLDNEVHCDFIDVNMGCPIDGVCAKGAGGSLMRDTDRLKRVVRSMTSVSSTPVTIKLRMG 403

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             D        +++   K  G     +H R
Sbjct: 404 YFDDPSRYVAHDIISKAKSWGAYAATLHGR 433


>gi|301510952|ref|ZP_07236189.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB058]
          Length = 119

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 54/104 (51%), Gaps = 3/104 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   +       + +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYFGAGHAV-SEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDED 119


>gi|115397477|ref|XP_001214330.1| tRNA-dihydrouridine synthase 1 [Aspergillus terreus NIH2624]
 gi|114192521|gb|EAU34221.1| tRNA-dihydrouridine synthase 1 [Aspergillus terreus NIH2624]
          Length = 536

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 89/210 (42%), Gaps = 26/210 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    +    +EAA+ V  +  + ++LN+GCP      G +G+ L  + D++  
Sbjct: 116 DRPLFVQFCANNPDDFLEAAQHVAPYC-DAVDLNLGCPQGIAKRGHYGSFLQEDWDLIYK 174

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I  +   L IPVT K RI    +          K I  +G + I +H R    KG    
Sbjct: 175 LINKLHTELPIPVTAKFRILESKE----KTLEYAKMILSAGASIITLHGRTREQKG---- 226

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNS 223
            N  + +  Y I Y      P+  I  NG     +D+ + L+     DGVM       + 
Sbjct: 227 HNTGVADWSY-IRYLRDNLPPETVIFANGNNLNHDDLERCLEAT-GADGVMSAEGNLSDP 284

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           A+       FS P     PI +   +D+WR
Sbjct: 285 AI-------FSKP----PPIGSE-GRDYWR 302


>gi|116629731|ref|YP_814903.1| dihydroorotate dehydrogenase 1B [Lactobacillus gasseri ATCC 33323]
 gi|116095313|gb|ABJ60465.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus gasseri
           ATCC 33323]
          Length = 311

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 99/225 (44%), Gaps = 32/225 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA++  DK   L  S  + P+   +GG D +  VE AK + D G  N + +NV CP+   
Sbjct: 84  DAVIE-DKLKPLRQSYPDLPIMASVGGEDEAGYVEVAKKLSDSGLVNALEINVSCPNVNQ 142

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V      +    ++P+ VK    V D      +  + K+ +K G 
Sbjct: 143 GGMSFG----VHPDVVESLTKKIKAVTNVPIYVKLTPNVTD------ITQISKAAEKGGA 192

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I I  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 193 DGLSLINTLLGMDIDIKTRKPVLGHNIGGLS---GEAVKPVALRMVHQVRQSTSLPIIGM 249

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            GG+      +K +L   + V +G A +K+S     + +   N L
Sbjct: 250 -GGISSAQDVIKFMLAGANAVAVGTAHFKDSIASKHIADELPNEL 293


>gi|269792729|ref|YP_003317633.1| dihydrouridine synthase DuS [Thermanaerovibrio acidaminovorans DSM
           6589]
 gi|269100364|gb|ACZ19351.1| dihydrouridine synthase DuS [Thermanaerovibrio acidaminovorans DSM
           6589]
          Length = 318

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/128 (29%), Positives = 67/128 (52%), Gaps = 5/128 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-LRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   T    R F R +   +L++TEM+ A  +  RG+K + IL     E+P+  Q+ G  
Sbjct: 23  MAGITTPSVRLFQRRI-GVSLVHTEMVSALGLKYRGEKSRRILIPLPGEEPVIPQLFGPS 81

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+E A+I + ++ +  + +N+ CP  +V     GA ++ +PD+    + A+ K L +
Sbjct: 82  GEDLLEGARIALGEYPFRAVEVNMACPMPKVVSKGSGAAMLKDPDLAARAV-ALLKGLGV 140

Query: 118 PVTVKCRI 125
            V VK R+
Sbjct: 141 SVWVKARV 148


>gi|114615414|ref|XP_001164035.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 1 [Pan
           troglodytes]
 gi|114615416|ref|XP_001164118.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 2 [Pan
           troglodytes]
 gi|114615418|ref|XP_001164161.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 3 [Pan
           troglodytes]
 gi|114615420|ref|XP_001164233.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 4 [Pan
           troglodytes]
 gi|84627517|gb|AAI11775.1| DUS4L protein [Homo sapiens]
 gi|119603806|gb|EAW83400.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
 gi|119603809|gb|EAW83403.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
 gi|194386236|dbj|BAG59682.1| unnamed protein product [Homo sapiens]
          Length = 196

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 88/191 (46%), Gaps = 32/191 (16%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +GACL+  P++V D +  +   +  P   V++K RI  DD    V   +L +  + +GV+
Sbjct: 5   YGACLINKPELVQDMVKQVRNQVETPGFSVSIKIRIH-DDLKRTV---DLCQKAEATGVS 60

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--L 207
            I +H R A        + R  P + YD + +I KEN  + +  NG +  + +A  +  +
Sbjct: 61  WITVHGRTA--------EERHQP-VHYDSI-KIIKENMSIPVIANGDIRSLKEAENVWRI 110

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM-TDYAARH 266
              DGVM+ R    N AM    +E         +P+K   D   W  I+  + T Y   H
Sbjct: 111 TGTDGVMVARGLLANPAMFAGYEE---------TPLKCIWD---WVDIALELGTPYMCFH 158

Query: 267 LHSGGKLQQIT 277
            H    +++IT
Sbjct: 159 QHLMYMMEKIT 169


>gi|281204195|gb|EFA78391.1| CCCH-type zinc finger-containing protein [Polysphondylium pallidum
           PN500]
          Length = 664

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 45/210 (21%), Positives = 93/210 (44%), Gaps = 14/210 (6%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNV 81
           EM +A  I++G K  +  L     E    +Q+ G  +  ++ +A+ +ED    + +++N 
Sbjct: 348 EMALASNIVQGHKGELALLKRHPSEDKFGVQLCGPHLDSMMSSAEFIEDNLNVDFVDVNS 407

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   +     GA +M   + +   +  M   L+ P+T+K R+G  ++ P      ++ 
Sbjct: 408 GCPIDLICNMGAGAAMMDRQNRMEMILRGMSSVLTCPLTIKLRVGRTEENPNA--HKIIP 465

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           ++   G   + +H R    +        ++ N +Y  + +  + +P   IG NG + +  
Sbjct: 466 NLGSWGAQAVTVHGRSRTQRYT------RLANWEY--IKQCAEISPIPVIG-NGDIYNWR 516

Query: 202 QALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              K   S+  +M+ R A     + T + E
Sbjct: 517 DIEKSSDSISALMVARGALIKPWIFTEIKE 546


>gi|149924148|ref|ZP_01912526.1| Dihydrouridine synthase family protein [Plesiocystis pacifica
           SIR-1]
 gi|149814994|gb|EDM74553.1| Dihydrouridine synthase family protein [Plesiocystis pacifica
           SIR-1]
          Length = 321

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 79/180 (43%), Gaps = 26/180 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G +   +  AA+     G   I+LN GCP+  V+    GA L+ +P  V    
Sbjct: 61  PVFVQLLGGEPHWMARAAETAVALGAPGIDLNFGCPAKTVNSSDGGATLLKDPCRVEAVT 120

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+  A+   +PVTVK R+G +D  P V    + ++ +  G + + IH R         +
Sbjct: 121 RAVRAAVPAELPVTVKIRVGWEDPSPVV---EIARAAEAGGASWLTIHGRT--------R 169

Query: 167 DNRKIPNLDYDIVYEIKK-------ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
                P +DY+ +   +         N DLF     G+  + +A +        MIGR A
Sbjct: 170 RQLYKPPVDYEAIGRAQAAVSMAVVANGDLF-----GVPSLFEAAQ-RSGCTAFMIGRGA 223


>gi|148977641|ref|ZP_01814217.1| putative regulator protein [Vibrionales bacterium SWAT-3]
 gi|145963156|gb|EDK28424.1| putative regulator protein [Vibrionales bacterium SWAT-3]
          Length = 311

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 47/193 (24%), Positives = 92/193 (47%), Gaps = 16/193 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     + E A    + G   I+LN GCP+  V++ + GA L+  P+++   +
Sbjct: 57  PVHVQLLGQHPKWMAENAIQAANLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+   IPV+ K R+G +   P      +V +I+++  + + +HAR       +  
Sbjct: 117 KATREAVPKHIPVSAKIRLGWEH--PDECFE-IVDAIEQAKADELTVHAR-------TKT 166

Query: 167 DNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
              K   + +D + +I+++   P +  G     +D    +K    VD +M+ R A+ N  
Sbjct: 167 GGYKASEIKWDYINQIRQKTSLPLIANGEIWNYQDGQDCIKTT-GVDSLMVCRGAF-NVP 224

Query: 225 MLTTVDEYFSNPL 237
            L  V ++   P+
Sbjct: 225 NLGNVVKHNHQPM 237


>gi|149028167|gb|EDL83605.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_b
           [Rattus norvegicus]
          Length = 304

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 57/254 (22%), Positives = 109/254 (42%), Gaps = 30/254 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E    +Q+ GA    + + A+++      + +++NVGCP   V++   G  LM       
Sbjct: 13  EDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQ 72

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +  M + L +P+TVK R GV +++ ++A R L+  ++  GV  + +H R         
Sbjct: 73  QIVRGMNEVLDVPLTVKMRTGVQERV-SLAHR-LLPELRNWGVALVTLHGRS-------- 122

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKN 222
           ++ R     D+  + +  K    + +  NG     ED + A++    V G+M+ R A   
Sbjct: 123 REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFEDANCAMQT--GVAGIMVARGALLK 180

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             + T + E     ++ S   +  + +DF        T Y   H  S  +  + TR  + 
Sbjct: 181 PWLFTEIKEQRHWDISSSE--RLDILRDF--------THYGLEHWGSDTQGVERTRRFLL 230

Query: 283 LFHGFPNSRRCRHI 296
            +  F     CR++
Sbjct: 231 EWLSF----LCRYV 240


>gi|294788400|ref|ZP_06753643.1| tRNA-dihydrouridine synthase B [Simonsiella muelleri ATCC 29453]
 gi|294483831|gb|EFG31515.1| tRNA-dihydrouridine synthase B [Simonsiella muelleri ATCC 29453]
          Length = 218

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 37/139 (26%), Positives = 71/139 (51%), Gaps = 14/139 (10%)

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           ++ N  +V + +  + KA+ IPVT+K R+G +D+   ++   + K  +++G+  + IH R
Sbjct: 1   MLQNEPLVEEILNTVVKAVPIPVTLKTRLGWNDEHKNIS--TIAKIAEQAGIAALAIHGR 58

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVM 214
                    +         YD++ EI K++ +L I  NG +    +A+++L     DG+M
Sbjct: 59  T--------RTQMYNGEAQYDLIAEI-KQSVNLPIWANGDITSPQKAVQVLQQTGADGIM 109

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           IGR A     +   + +YF
Sbjct: 110 IGRGAQGQPWLFADI-QYF 127


>gi|145595944|ref|YP_001160241.1| nifR3 family TIM-barrel protein [Salinispora tropica CNB-440]
 gi|145305281|gb|ABP55863.1| putative TIM-barrel protein, nifR3 family [Salinispora tropica
           CNB-440]
          Length = 368

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/111 (34%), Positives = 54/111 (48%), Gaps = 6/111 (5%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EMI   A++  + K +  + F + E P +LQ+ G D      A +IV E    + I+LN 
Sbjct: 29  EMITTVALVERNPKTLRMIAFGSGESPRSLQLYGTDPDTTAAAVRIVVERDLADHIDLNF 88

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDD 129
           GCP  +V     GA L     +    + A   A S   +PVTVK R G+DD
Sbjct: 89  GCPVPKVTRRGGGAALPWRRRLFARLVRAAVDAASPAGVPVTVKMRKGIDD 139


>gi|328770050|gb|EGF80092.1| hypothetical protein BATDEDRAFT_35061 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 507

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 63/111 (56%), Gaps = 7/111 (6%)

Query: 50  LALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           L +Q+G ++ +  ++ A K+  D   + I+LN GCP      G  G+ L+ NPD +   +
Sbjct: 253 LVVQLGSSNPVFAVLAAQKVAGDV--DGIDLNCGCPKKFSVSGGMGSALLENPDTLEAIL 310

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHAR 156
            A+  ++SIPVT K R+ +D +    ++     L++ ++K+G++ I +H R
Sbjct: 311 TALVSSVSIPVTCKIRL-LDPREGKTSIERTIELMQRLEKTGISAIAVHCR 360


>gi|253698736|ref|YP_003019925.1| dihydrouridine synthase [Geobacter sp. M21]
 gi|251773586|gb|ACT16167.1| dihydrouridine synthase DuS [Geobacter sp. M21]
          Length = 341

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 102/226 (45%), Gaps = 37/226 (16%)

Query: 16  LTNNAL--LYTEMIVADAI----------------LRGDKKNILGFSTQEKPLALQIGGA 57
           LTN AL  L+T+ +  D +                + GD + I   S    PL +Q+ G 
Sbjct: 42  LTNRALRSLFTKWVRPDVVWTEFMRVNPVSAKKRLMPGDLREI-SASEDGIPLVVQLIGH 100

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
               LV AA+  +D G   +NLN+GCP  R+  G  G  ++  P+++ + I A+ +A+  
Sbjct: 101 GREALVSAAQAAQDAGAKHLNLNMGCPYGRMTSGLTGGGMLKKPELLEEIIPALREAIHG 160

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN--LD 175
             ++K R G +D     +L  L    ++SGV+ + +H          P+  R+  N   D
Sbjct: 161 SFSIKLRAGYEDPRQVFSLLPL---FERSGVDFLVLH----------PRTVRQAYNGWAD 207

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAA 219
           +++  E+ +      I  NG +   +  L +L      G+M+GR  
Sbjct: 208 HEVTAEVVRSTGIPVIA-NGDIRSAAGGLHLLEQTGAAGLMLGRGG 252


>gi|121609971|ref|YP_997778.1| nifR3 family TIM-barrel protein [Verminephrobacter eiseniae EF01-2]
 gi|121554611|gb|ABM58760.1| putative TIM-barrel protein, nifR3 family [Verminephrobacter
           eiseniae EF01-2]
          Length = 348

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 60/250 (24%), Positives = 103/250 (41%), Gaps = 25/250 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EMI A   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKAL-GAGYAVSEMITARKDLWSSLKTSRRANHDGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA    + G   I++N+GCP+ +V     G+ LM +  +      A+  A +  
Sbjct: 76  AAMMAEAALYNIERGAQIIDINMGCPAKKVCRQWAGSALMQDEALAVAIARAVVAACAPH 135

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   Q        L +  +  G+  + +H R         ++       +
Sbjct: 136 RVPVTLKMRTGWCQQHKNAP--QLARQFESVGIQMLTVHGRT--------REQGYGGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA------YKNSAMLT 227
           Y+ +  +K     + +  NG +    +A  +L +   D +MIGRAA      ++      
Sbjct: 186 YETIAAVKAAV-GVPVVANGDITTPEKARAVLAATGADAIMIGRAAQGRPWIFREVGHFL 244

Query: 228 TVDEYFSNPL 237
              E+ + PL
Sbjct: 245 ATGEHLAPPL 254


>gi|86147938|ref|ZP_01066242.1| putative regulator protein [Vibrio sp. MED222]
 gi|85834263|gb|EAQ52417.1| putative regulator protein [Vibrio sp. MED222]
          Length = 303

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 43/176 (24%), Positives = 84/176 (47%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G   + + E A      G   I+LN GCP+  V++ + GA L+  P+++   +
Sbjct: 49  PIHLQLLGQHPNWMAENAFQAASLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVV 108

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +   A+   IPV+ K R+G +   P      +V +I+++  + + +HAR  +       
Sbjct: 109 KSCRDAVPAHIPVSAKIRLGWEH--PEECFE-IVDAIEQAKADELTVHARTKV------- 158

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + +D + +I +E   L +  NG + +       + +  VD +M+ R A+
Sbjct: 159 GGYKASEIKWDYINQI-REKTSLPLIANGEIWNYQDGQDCIEATGVDSLMVCRGAF 213


>gi|258621727|ref|ZP_05716758.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM573]
 gi|258585958|gb|EEW10676.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM573]
          Length = 326

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPQWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPEHIPVSAKIRLGWED--PEDCFE-IVDAVAQAKADELTVHAR 170


>gi|330502905|ref|YP_004379774.1| dihydrouridine synthase, DuS [Pseudomonas mendocina NK-01]
 gi|328917191|gb|AEB58022.1| dihydrouridine synthase, DuS [Pseudomonas mendocina NK-01]
          Length = 316

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 61/273 (22%), Positives = 117/273 (42%), Gaps = 39/273 (14%)

Query: 42  GFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           G  TQ   P+ +Q  G+D   L + A      G   I+LN GCP+  V++   GA L+  
Sbjct: 56  GSRTQAGTPMRVQFLGSDPQCLADNAAFACTLGAPVIDLNFGCPAKTVNKSRGGAVLLKE 115

Query: 101 PDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           P+++   +  + + +   IPVT K R+G + +  A+   +  +++ + G + I +HAR  
Sbjct: 116 PELLHAIVREVRRTVPADIPVTAKMRLGFEGKEGAL---DCARALAEGGASQIVVHARTK 172

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
           + +G  P  +       ++ V  +++    P    G    L+D  +  +I   VD +M+G
Sbjct: 173 V-EGYKPPAH-------WEWVARVQEVVGVPVFANGEVWTLDDWHRCREI-SGVDDIMLG 223

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK------DFWRKISASMTDYAARHLHSG 270
           R       +   +    +    G +P +    +      DFW++    +        ++ 
Sbjct: 224 RGLVSRPGLARQIAAVRA----GEAPAEMSWAELQPLLLDFWQQARRKLAPR-----YAP 274

Query: 271 GKLQQ----ITR---HMIGLFHGFPNSRRCRHI 296
           G+L+Q    +TR     + LF      + C  I
Sbjct: 275 GRLKQWLAMLTRTYPEAVALFAEVRREQDCERI 307


>gi|47219443|emb|CAG10807.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 614

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 52/215 (24%), Positives = 88/215 (40%), Gaps = 22/215 (10%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM +   +L+G +    +L     E    +QI G     +   A+++      DF    +
Sbjct: 299 EMAMCTNLLQGQQSEWALLKRHESEDVFGVQIEGCFPDTMTRCAELINNNTEVDF----V 354

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N GCP   V +   G  LM       + +  M   L +P+TVK R GV ++       
Sbjct: 355 DINSGCPIDLVFKKGGGCGLMTRTRKFEEIVKGMNYVLDVPLTVKIRTGVQEKTNIA--H 412

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L+  +KK GV+ I +H R         ++ R     D+D +    K    + +  NG +
Sbjct: 413 KLIPEMKKWGVSMITLHGRS--------REQRYTKLADWDYISTCSKLASPVPLFGNGDI 464

Query: 198 EDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDE 231
                A+    + V G+MI R A     + T + E
Sbjct: 465 LSYEDAMMAKETGVSGIMIARGALIKPWIFTEIKE 499


>gi|268570080|ref|XP_002640687.1| Hypothetical protein CBG19749 [Caenorhabditis briggsae]
 gi|187023917|emb|CAP36964.1| hypothetical protein CBG_19749 [Caenorhabditis briggsae AF16]
          Length = 436

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 106/235 (45%), Gaps = 28/235 (11%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEK-PLALQIGGADISKLVEAA 66
           +   + +  L+    +V +A+   D +N    IL  + +EK    LQIG     K  + A
Sbjct: 35  YTEEIVDKKLIEATRVVNEALGTIDYRNGDDIILRLAPEEKGKCILQIGTNSGEKAAKIA 94

Query: 67  KIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           +IV D     I++N+GCP    +H G   A L     IVG  + A+  A  +PVT  C+I
Sbjct: 95  EIVGD-DVAGIDVNMGCPKPFSIHCGMGAALLTQTEKIVG-ILTALKAAAKVPVT--CKI 150

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK- 184
            V D  P   L+ LV+ I+K GV  + +H R+        +D R+     Y+ + E+ K 
Sbjct: 151 RVLDN-PEDTLK-LVREIEKCGVVALGVHGRR--------RDERQPDRCRYEEIREVVKT 200

Query: 185 --ENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTT---VDEY 232
               P +  G +G +E     +  +       +MI R A    ++  +   +D+Y
Sbjct: 201 IQSIPIIANGFSGEIERYEDIEKWRDAAGTSSIMIARKALSTPSIFRSEGVLDKY 255


>gi|270687218|ref|ZP_06222867.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae HK1212]
 gi|270316153|gb|EFA28138.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae HK1212]
          Length = 132

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 62/114 (54%), Gaps = 10/114 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++PVT+
Sbjct: 1   MAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVPVTL 60

Query: 122 KCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARK--AILKGLSPKDNRK 170
           K R G D      + RN V   K  ++ G+  + +H R    + +G +  DN K
Sbjct: 61  KIRTGWDK-----SNRNCVQIGKIAEQCGIQALTVHGRTRACLFEGEAEYDNIK 109


>gi|123288585|emb|CAM27543.1| dihydrouridine synthase 1-like (S. cerevisiae) [Mus musculus]
          Length = 194

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 80/167 (47%), Gaps = 23/167 (13%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL     
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCDVCPEDRPL----- 76

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
                 +V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + L
Sbjct: 77  ------IVQAALLAQDYC-DAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERL 129

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT  C+I V  +I         + ++K+G   + +H R    KG
Sbjct: 130 SVPVT--CKIRVFPEIDKTV--RYAQMLEKAGCQLLTVHGRTKEQKG 172


>gi|170724871|ref|YP_001758897.1| NifR3 family TIM-barrel protein [Shewanella woodyi ATCC 51908]
 gi|169810218|gb|ACA84802.1| TIM-barrel protein, nifR3 family [Shewanella woodyi ATCC 51908]
          Length = 322

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 95/206 (46%), Gaps = 26/206 (12%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   +  AA +    G   I++N+GCP+ +V+    G+ L+ +P  V   + A
Sbjct: 68  SVQIAGADPELMANAAVVNVQQGAQIIDINMGCPAKKVNRKLAGSALLQDPVQVKAILQA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSP 165
           +  A+ +PVT+K R G      A   RN   + +  +  G+  + +H   R+ + KG   
Sbjct: 128 VVAAVDVPVTLKIRTGW-----APEHRNGVQIAQIAEDCGIAALAVHGRTRQCMYKG--- 179

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                  N +YD +  IKK N  + +  NG +    +A  +L    VD +MIGR A    
Sbjct: 180 -------NAEYDTIKAIKK-NVSIPVVANGDITTPQKAQFVLEHTGVDALMIGRGAQGRP 231

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDK 249
            +   +  Y     TG+      VD+
Sbjct: 232 WIFREIQHYLE---TGNMLAPVEVDE 254


>gi|330720421|gb|EGG98739.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC2047]
          Length = 325

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/110 (31%), Positives = 56/110 (50%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   L + A      G + I+LN GCP+  V+    G+ L+  P  V   +
Sbjct: 68  PVYIQLLGGDPHWLSQNAAKAARLGAHGIDLNFGCPAKIVNRNDGGSVLLKEPSRVAGIV 127

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A+  A+  ++PVT K R+G  D   A  L  +   I+ +G + + IHAR
Sbjct: 128 RAVRDAVDPAVPVTAKIRLGFSD---ASLLPEIAGGIEAAGASELCIHAR 174


>gi|194879304|ref|XP_001974213.1| GG21206 [Drosophila erecta]
 gi|190657400|gb|EDV54613.1| GG21206 [Drosophila erecta]
          Length = 609

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 64/272 (23%), Positives = 116/272 (42%), Gaps = 31/272 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 292 EMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMINQAAQVIHETAQVDFIDLNI 351

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 352 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSDRLPFTVKMRTGIYADKSVAHELLP 410

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + ++  + E   +   + +  NG + 
Sbjct: 411 LVEEW---GASAVTLHGRS--------REQRYTKHANWAYIEECAAKAKRMPVIGNGDIL 459

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ED  +   + P V  VMIGR A     +   + E      + SS  +  + + F    
Sbjct: 460 SYEDYIERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWSPSSGQRYEMLQKF---- 513

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                +Y   H  S  K  + TR  +  +  F
Sbjct: 514 ----CNYGLEHWGSDTKGVETTRRFLLEWQSF 541


>gi|284007122|emb|CBA72398.1| tRNA-dihydrouridine synthase C [Arsenophonus nasoniae]
          Length = 313

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 48/197 (24%), Positives = 89/197 (45%), Gaps = 16/197 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++ N GCPS  V+    GA L+ +P+ +     A+
Sbjct: 67  IQLLGQHPQWLAENAARAVELGSWGVDFNCGCPSPTVNGHGGGATLLKDPERIYQAAKAI 126

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+  ++P +VK R+G DD+  A     +  +++++G   I IH R       +  +  
Sbjct: 127 RAAVPANLPTSVKVRLGWDDRCLAF---EIADAVQQAGATEIIIHGR-------TKAEGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLT 227
           +   +D   +  I+++     I  NG + D   A   + +   D +MIGR    +   L 
Sbjct: 177 RAEKIDSLTIGRIRQKLTIPVIA-NGEIWDWCSANECRTITGCDALMIGRGGL-HVPNLA 234

Query: 228 TVDEYFSNPLTGSSPIK 244
            V +Y + P+  S  ++
Sbjct: 235 QVIKYQTEPMAWSQVMQ 251


>gi|237836529|ref|XP_002367562.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211965226|gb|EEB00422.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
          Length = 540

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 37  KKNILGFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           +    G  +QE  +P+ +Q  G   + L+ AA++VED     +++N GCP      G +G
Sbjct: 128 RSQWTGDESQEFDEPVFVQFCGDSPATLLAAAQLVED-EVEAVDVNFGCPQGIARRGHYG 186

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           A L+  P+++ D ++ + K L  PVT K R
Sbjct: 187 AFLLNEPELLVDIVSTLHKHLKTPVTCKMR 216


>gi|187923837|ref|YP_001895479.1| dihydrouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187715031|gb|ACD16255.1| dihydrouridine synthase DuS [Burkholderia phytofirmans PsJN]
          Length = 340

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/239 (23%), Positives = 102/239 (42%), Gaps = 34/239 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   +   A        + ++LN GCP+  V++   GA L+ +P
Sbjct: 58  GHTPNGTPMVVQLLGSDPEWMALNAAHAATLSPHGVDLNFGCPAKVVNQHGGGAMLLADP 117

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   ++A+  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 EQLNRIVSAVRAAVPADILVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                 +D+   P   ++ +  I     D+ +  NG +  ++  +  + +   D VMIGR
Sbjct: 173 ------RDHGYRPPAHWEWIARIDAAV-DVPVIANGEVWTVTDWERCRAVSGCDDVMIGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY--------AARHLH 268
            A  +  +   +       L   SP       + WR +   M  Y        A+RH H
Sbjct: 226 GAVSDPFLALRI-----RGLMDRSP-----SNEDWRDVLGHMAGYLRKLQARVASRHEH 274


>gi|326794052|ref|YP_004311872.1| dihydrouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326544816|gb|ADZ90036.1| dihydrouridine synthase DuS [Marinomonas mediterranea MMB-1]
          Length = 319

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 43/178 (24%), Positives = 89/178 (50%), Gaps = 16/178 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G++  ++ ++A      G   I++N GCP+ RV+    G+ L+  P+ +   +
Sbjct: 62  PVHIQLLGSNAERIAQSAINAVAAGAKHIDMNFGCPAKRVNGHGGGSVLLQTPEQLHLIM 121

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +++ + L   I ++ K R+G +D+  ++   N V +I+++G + + +H R       + K
Sbjct: 122 SSLQQVLPSHIGLSAKIRLGYEDE--SLLFEN-VSAIEEAGTHALTVHGR-------TKK 171

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIGRAAYKN 222
           D  K P   ++ + EI   +    I  NG ++D    ++       V  MIGR +  N
Sbjct: 172 DGYK-PPARWEKIGEINARSKMRIIA-NGDIDDFETLMRCHEMTGCVDFMIGRGSLSN 227


>gi|300123558|emb|CBK24830.2| unnamed protein product [Blastocystis hominis]
          Length = 263

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 40/142 (28%), Positives = 64/142 (45%), Gaps = 11/142 (7%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G  G+ L+  PDI    +  + K+ S+PV+ K R+ +D  I      N +
Sbjct: 1   MGCPKQFSVQGHMGSALLKTPDIACSIVQGLSKSTSLPVSCKIRL-LDGPIENTI--NFM 57

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GL 197
           K +  SG + I +H R    +   P      P     ++  +K   P + +  NG     
Sbjct: 58  KRLVDSGASAITLHLRYTDDRPRVPCHKEFFPT----VLEAMKAYAPSVPVCYNGDIFSF 113

Query: 198 EDMSQALKILPSVDGVMIGRAA 219
           ED+    K  P+  G+MIGR A
Sbjct: 114 EDVCSLRKKFPTT-GLMIGRGA 134


>gi|76156838|gb|AAX27956.2| SJCHGC08364 protein [Schistosoma japonicum]
          Length = 170

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 32/112 (28%), Positives = 59/112 (52%), Gaps = 1/112 (0%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           R++ ++ +   E+   D IL          + ++  + +Q+G ++    ++AAK++E+  
Sbjct: 60  RVIRSSRIANDELNTVDFILPDGSVTFRTSAEEKNRVIVQLGTSNPETALKAAKVLEN-D 118

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
              I++N+GCP A   +G  GA L+  PD V + +  +   L IPVT K RI
Sbjct: 119 VMAIDVNMGCPKAYSVKGGMGAALLTKPDTVKEILTTLTTNLRIPVTCKMRI 170


>gi|262171859|ref|ZP_06039537.1| tRNA-dihydrouridine synthase C [Vibrio mimicus MB-451]
 gi|261892935|gb|EEY38921.1| tRNA-dihydrouridine synthase C [Vibrio mimicus MB-451]
          Length = 326

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPQWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCFE-IVDAVAQAKADELTVHAR 170


>gi|153824959|ref|ZP_01977626.1| conserved hypothetical protein [Vibrio cholerae MZO-2]
 gi|149741471|gb|EDM55501.1| conserved hypothetical protein [Vibrio cholerae MZO-2]
          Length = 323

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 60/113 (53%), Gaps = 5/113 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPDWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR  +
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHARTKV 173


>gi|229520462|ref|ZP_04409887.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TM 11079-80]
 gi|229342560|gb|EEO07553.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TM 11079-80]
          Length = 323

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 84/175 (48%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR  +       
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +  + +I+++     I  NG + + +  QA      VD +M+ R A
Sbjct: 174 GGYKASEIKWHYIDQIRQKCSIPLIA-NGEVWNYADGQACIQTTGVDSLMVCRGA 227


>gi|258626327|ref|ZP_05721174.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM603]
 gi|258581379|gb|EEW06281.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM603]
          Length = 326

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDSQWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCFE-IVDAVAQAKADELTVHAR 170


>gi|195345193|ref|XP_002039157.1| GM17377 [Drosophila sechellia]
 gi|194134287|gb|EDW55803.1| GM17377 [Drosophila sechellia]
          Length = 605

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 95/204 (46%), Gaps = 21/204 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 288 EMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMINQAAQVIHETAQVDFIDLNI 347

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 348 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSDRLPFTVKMRTGIYADKSVAHELLP 406

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + ++  + E   +   + +  NG + 
Sbjct: 407 LVEEW---GASAVTLHGRS--------REQRYTKHANWAYIEECAAKAKRMPVIGNGDIL 455

Query: 198 --EDMSQALKILPSVDGVMIGRAA 219
             ED  +   + P V  VMIGR A
Sbjct: 456 SYEDYIERRTLAPHVSSVMIGRGA 479


>gi|119603805|gb|EAW83399.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
          Length = 237

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 88/191 (46%), Gaps = 32/191 (16%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +GACL+  P++V D +  +   +  P   V++K RI  DD    V   +L +  + +GV+
Sbjct: 46  YGACLINKPELVQDMVKQVRNQVETPGFSVSIKIRIH-DDLKRTV---DLCQKAEATGVS 101

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--L 207
            I +H R A        + R  P + YD + +I KEN  + +  NG +  + +A  +  +
Sbjct: 102 WITVHGRTA--------EERHQP-VHYDSI-KIIKENMSIPVIANGDIRSLKEAENVWRI 151

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM-TDYAARH 266
              DGVM+ R    N AM    +E         +P+K   D   W  I+  + T Y   H
Sbjct: 152 TGTDGVMVARGLLANPAMFAGYEE---------TPLKCIWD---WVDIALELGTPYMCFH 199

Query: 267 LHSGGKLQQIT 277
            H    +++IT
Sbjct: 200 QHLMYMMEKIT 210


>gi|71908499|ref|YP_286086.1| dihydrouridine synthase, DuS [Dechloromonas aromatica RCB]
 gi|71848120|gb|AAZ47616.1| tRNA-U20a,U20b-dihydrouridine synthase [Dechloromonas aromatica
           RCB]
          Length = 319

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/110 (26%), Positives = 60/110 (54%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   + E A+ +       ++LN GCP+  V     G+ L+  P+++ +  
Sbjct: 65  PMRVQLLGSDPHFMAENARRLVALNPAGVDLNFGCPAPTVFRHRGGSALLGEPELLNEIT 124

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +A+   +   IP T K R+G+DD   A+   +  ++++ +G+N + +H R
Sbjct: 125 SAVRSVVPAHIPFTAKMRLGIDDTSRAI---DCAQALEAAGINELIVHGR 171


>gi|313204382|ref|YP_004043039.1| dihydrouridine synthase dus [Paludibacter propionicigenes WB4]
 gi|312443698|gb|ADQ80054.1| dihydrouridine synthase DuS [Paludibacter propionicigenes WB4]
          Length = 312

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/183 (24%), Positives = 80/183 (43%), Gaps = 10/183 (5%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +KP+  Q  G D +      ++    GY E+N+N+GCP   V     GA L+ +   V  
Sbjct: 59  QKPVP-QFLGRDAASFKVFEELCIAQGYTEVNINMGCPFPIVTGKQMGAGLLQHSADVDR 117

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +  +     + V+VKCR+G   Q  A     L+       +  I IH R      +  +
Sbjct: 118 LLEGVFSNSDLKVSVKCRLG---QQSADEFAPLIPVFNAYPLEEIIIHPR------VGKQ 168

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
             +   ++D  + Y+ + ++P  F G      D+ +  ++ P V   M+GR   +N  +L
Sbjct: 169 QYKGEVDIDAFVHYQSQLQHPVCFNGDIVTPADVERIRQLAPQVSRFMLGRGVLRNPFLL 228

Query: 227 TTV 229
           + +
Sbjct: 229 SEL 231


>gi|254291529|ref|ZP_04962320.1| conserved hypothetical protein [Vibrio cholerae AM-19226]
 gi|150422593|gb|EDN14549.1| conserved hypothetical protein [Vibrio cholerae AM-19226]
          Length = 323

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 84/175 (48%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR  +       
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +  + +I+++     I  NG + + +  QA      VD +M+ R A
Sbjct: 174 GGYKASEIKWHYIDQIRQKCSIPLIA-NGEVWNYADGQACIQTTGVDSLMVCRGA 227


>gi|319442510|ref|ZP_07991666.1| hypothetical protein CvarD4_12149 [Corynebacterium variabile DSM
           44702]
          Length = 402

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 64/301 (21%), Positives = 117/301 (38%), Gaps = 32/301 (10%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-E 70
           R  + + L   EMI A A++  + K  ++  F   E P +LQ+   D     +AA+++ E
Sbjct: 49  RTGSASGLYVCEMITARALVERNPKTLHMTTFGPDESPRSLQLYTTDPEYTYKAARMLAE 108

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----------IPVT 120
           +   + I++N GCP  +V     G+ L     +    + A  + ++          IPVT
Sbjct: 109 EDRADHIDMNFGCPVPKVTRRGGGSALPYKRKLFAAVVGAAVRGVADAGRASGPDAIPVT 168

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD----NRKIPNLDY 176
           VK R+G+DD+       +  +     G   + +H R A  +     D     R + ++D 
Sbjct: 169 VKFRVGIDDE--HHTHLDAGRIAADQGAAAVTLHGRTAAQRYSGTADWGEIARLVEHMDG 226

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             +  +   N D+F   +      + A+      DGV++GR       +   +  +    
Sbjct: 227 TGIPVLG--NGDIFKATD------AAAMMEQTGCDGVVVGRGCLGRPWLFAELSAHLRGE 278

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    V     R  +  + D+      S    + I +H+     GFP     R  
Sbjct: 279 EIPAEPTLGEVAHIILRH-AELLADHDGEKYAS----RDIRKHIAWYLRGFPAGGEMRRQ 333

Query: 297 L 297
           L
Sbjct: 334 L 334


>gi|331002215|ref|ZP_08325734.1| hypothetical protein HMPREF0491_00596 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411309|gb|EGG90725.1| hypothetical protein HMPREF0491_00596 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 311

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 85/194 (43%), Gaps = 35/194 (18%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  L     +  KL +    ++  GY+E N+N+GCPSA V     G+  + + D +    
Sbjct: 63  PQVLLNNAEEFLKLTDE---IKQMGYSEFNINLGCPSATVTSKKRGSGFLQDIDSLDKFF 119

Query: 109 AAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            A+  K  +I +++K RIG  D         L+K  KK   N I IH R   L+    K+
Sbjct: 120 YAIFEKRKNIKISIKTRIGFCD---YDEWDELLKVYKKYDFNEIIIHPR---LRSDFYKN 173

Query: 168 NRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV-----DGVMI 215
           N  +P        L+  ++Y             NG +  ++  +K+  ++     DG+M+
Sbjct: 174 NVYLPAFLDAGGRLNTKLIY-------------NGDINTLNDYIKLKENLKNNIADGIMV 220

Query: 216 GRAAYKNSAMLTTV 229
           GR   +N  +  ++
Sbjct: 221 GRGLVRNPLLAESI 234


>gi|326475386|gb|EGD99395.1| tRNA dihydrouridine synthase [Trichophyton tonsurans CBS 112818]
          Length = 419

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 45/177 (25%), Positives = 83/177 (46%), Gaps = 17/177 (9%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + A+
Sbjct: 110 FQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILEAL 168

Query: 112 CKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++      
Sbjct: 169 VREVGQPWQIGISVKIRLLKDPR----DTERLVTALCATGITGLTVHCRTTPMRPREAAI 224

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             ++P     ++  I + +  +   +NG ++    AL+++    VDG MI  +A  N
Sbjct: 225 RDQLP-----MIASICR-SAGVACLMNGDVKSRDHALELMSQYDVDGAMIATSAESN 275


>gi|195053116|ref|XP_001993476.1| GH13829 [Drosophila grimshawi]
 gi|193900535|gb|EDV99401.1| GH13829 [Drosophila grimshawi]
          Length = 582

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 51/204 (25%), Positives = 95/204 (46%), Gaps = 21/204 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 265 EMACAVPLLKGLGQEWALTKRHETEDIFGVQVCGNNPNVIAQAAQVLHETSRVDYIDLNI 324

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ + +   C +LS  +P TVK R G+  D+  A  L  
Sbjct: 325 GCPIDLIYQQGGGSALMRRTNIL-ELVVRSCSSLSPQLPFTVKMRTGIYADKSVAHELMP 383

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G   + +H R         ++ R +   ++  + +   +   + +  NG + 
Sbjct: 384 LVEEW---GAAAVTLHGRS--------REQRYMKQANWTYIEQCAAQAKQMPVIGNGDIL 432

Query: 198 --EDMSQALKILPSVDGVMIGRAA 219
             ED  +   + P V  VMIGR A
Sbjct: 433 SYEDYVEKRAMAPHVSSVMIGRGA 456


>gi|322490130|emb|CBZ25391.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 660

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 65/151 (43%), Gaps = 14/151 (9%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
           F Y+ +++N GCP  ++ +   G  L      + D + ++    S PV +KCRIG+D+  
Sbjct: 381 FSYDFLDINCGCPVEKIVKSGCGCGLWKRTGRLRDVVESLAIHQSRPVAIKCRIGLDEDT 440

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           P   L   +      G   + +H R         +  R     ++D V +  +      I
Sbjct: 441 P--TLHQQIHRYSTWGAAAVTVHGRS--------RKQRYTKLANWDYVDQCAQLTSLPVI 490

Query: 192 GLNG---GLEDMSQALKILPSVDGVMIGRAA 219
           G NG    LED+ +  +  P +   MIGR A
Sbjct: 491 G-NGDIMSLEDVLEHRERQPHITSHMIGRGA 520


>gi|37525463|ref|NP_928807.1| tRNA-dihydrouridine synthase C [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784891|emb|CAE13805.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 310

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 44/172 (25%), Positives = 81/172 (47%), Gaps = 15/172 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     A+
Sbjct: 67  IQLLGQYPQWLAENAARAIELGSYGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAI 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVTVK R+G D          +  +++++G   + +H R       + +   
Sbjct: 127 REAVPAHLPVTVKVRLGWDSGDRQF---EIADAVQQAGATEMTVHGR-------TKEHGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAA 219
           +   +++  + EI++      I  NG + D   +Q  + +   D VMIGR A
Sbjct: 177 RAERINWQAIGEIRQRLSIPVIA-NGEIWDWQSAQNCQSVTGCDAVMIGRGA 227


>gi|289449752|ref|YP_003474753.1| TIM-barrel protein [Clostridiales genomosp. BVAB3 str. UPII9-5]
 gi|289184299|gb|ADC90724.1| TIM-barrel protein, nifR3 family [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 367

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 101/243 (41%), Gaps = 34/243 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV----EDFGYNEINLNVGCPSARVHEGSFGAC 96
           L     E P A+Q+ G D +    A +++    E    + I++N+GCP  +V +   G+ 
Sbjct: 86  LRLGEDETPRAIQLFGYDPTDFAAAIELILKTAELPRPDIIDINMGCPVPKVTKTGAGSA 145

Query: 97  LMLNPDIVGDCIAAMCKALS---IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGI 151
           LML P++    I+A    L+   I VT K R G   D  I A        ++ ++G   I
Sbjct: 146 LMLRPELAAKIISACKNTLNGTDILVTCKFRRGYNKDSNIAA----EFALAMAEAGAAMI 201

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEI----------KKENPDLFIGLNGGLEDMS 201
            +H R         ++       D++ + E+           + +P   I  NG + D  
Sbjct: 202 TVHGRT--------REQGYSGTADWECIAEVVEAVHGFLARHRYSPIPVIA-NGDIIDGP 252

Query: 202 QALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            A K L +   DGVMIGRAA  +  +   +  Y        +P +  +    W +  A +
Sbjct: 253 TARKALETTGADGVMIGRAALGHPWIFREIANYLQGLPKPEAPTRQEIAAAIWGQYQAYL 312

Query: 260 TDY 262
           + Y
Sbjct: 313 SFY 315


>gi|303277773|ref|XP_003058180.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460837|gb|EEH58131.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 229

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/141 (24%), Positives = 65/141 (46%), Gaps = 12/141 (8%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            E    +QI    I++ V A ++  + G + ++LN GCP     +   GA L+  P  + 
Sbjct: 54  SETLFGVQIATNQITEGVNAGRLAHEAGADFVDLNCGCPIHETWKRGLGAALLKKPRKLE 113

Query: 106 DCIAAMCKALSIPVTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             +  +   + IP+TVK R+G    + PA A   L ++++ +G   + IH R        
Sbjct: 114 RLVRGIADGIPIPLTVKIRLGAGSSEAPAHA---LAEAVENAGAAAVVIHGRT------- 163

Query: 165 PKDNRKIPNLDYDIVYEIKKE 185
            K+ R     +++ +  I+ E
Sbjct: 164 -KEARYTKAANWETIGAIQAE 183


>gi|167646566|ref|YP_001684229.1| NifR3 family TIM-barrel protein [Caulobacter sp. K31]
 gi|167348996|gb|ABZ71731.1| TIM-barrel protein, nifR3 family [Caulobacter sp. K31]
          Length = 335

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 103/229 (44%), Gaps = 25/229 (10%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFSTQEK-PL-ALQIGGADISKLVEAAKIVEDFGYNEI 77
           A + TEM+      RG    +   +  +  PL  +Q+ G D + + + A++  + G   I
Sbjct: 39  AYVATEMVACAEFARGRPDAVRRAAVGDGLPLMVVQLVGRDPTFMGQGARMAAEAGAQII 98

Query: 78  NLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +LN GCPS +V  G + G+ LM  PD+    +AA  +A+ +PVTVK R+G DD     A 
Sbjct: 99  DLNFGCPSKQVTGGVASGSALMREPDLAEALVAAAVRAVDVPVTVKMRLGWDDDSRNAA- 157

Query: 137 RNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            ++ +    +G   I +H R      KG++          D+  V  +K       + +N
Sbjct: 158 -DIARRAVDAGAQAITVHGRTRCQFYKGVA----------DWSAVAAVKAAVSVPVL-VN 205

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD-----EYFSNP 236
           G + D   A   L     DGVMIGR  Y    +   ++     E F  P
Sbjct: 206 GDIIDGDTARLALEQSGADGVMIGRGVYGRPWIAQAIEAALNGEGFREP 254


>gi|296088965|emb|CBI38530.3| unnamed protein product [Vitis vinifera]
          Length = 160

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 31/105 (29%), Positives = 57/105 (54%), Gaps = 7/105 (6%)

Query: 54  IGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           +G ++  + + AA+IV +D     +++N+GCP +    G  GA L+  P+++ D +  + 
Sbjct: 1   MGTSNAERALTAAQIVCKDVA--AVDINMGCPKSFSISGGMGAALLTRPELIHDILTILK 58

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + L IPVT K R+    Q        L + I+K+GV  + +H R+
Sbjct: 59  RNLDIPVTCKIRLLKSSQETV----ELAQQIEKTGVAALAVHGRR 99


>gi|260589646|ref|ZP_05855559.1| dihydrouridine synthase family protein [Blautia hansenii DSM 20583]
 gi|260539886|gb|EEX20455.1| dihydrouridine synthase family protein [Blautia hansenii DSM 20583]
          Length = 314

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 78/184 (42%), Gaps = 15/184 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI        +  A+ + ++GY E+NLN+GCPS  V     G+  +  P  +   + 
Sbjct: 61  LVPQILTNQAQDFIRLAEELREYGYEEVNLNLGCPSGTVTAKKKGSGFLEFPAQLEKFLN 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + + L + ++VK RIG D+         L++   +  +  + +H R   ++    K+  
Sbjct: 121 EVFENLDMKISVKTRIGKDE---PEEFTELLRIYNRFPLEELIVHPR---IQSDYYKNEP 174

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAML 226
           ++      +            +  NG L   S+  K     PS++ VM+GR    N A++
Sbjct: 175 RMEQFQEAVRCSQNS------LCYNGDLFTRSKCEKFFEEYPSIEKVMLGRGLLVNPALV 228

Query: 227 TTVD 230
             V 
Sbjct: 229 QQVQ 232


>gi|322782637|gb|EFZ10516.1| hypothetical protein SINV_13804 [Solenopsis invicta]
          Length = 401

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 45/188 (23%), Positives = 87/188 (46%), Gaps = 19/188 (10%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           S + + + LQIG +D ++  + A++VE+     I++N+GCP      G  GA L+ + + 
Sbjct: 22  SREREHIVLQIGTSDPARAAQVARMVEN-DVAGIDVNMGCPKKFSMLGGMGAALLSDMEK 80

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             D +  + + ++IP++ K R+  D +     LR L  ++  +G+  I +H R    +  
Sbjct: 81  ATDILRKLIETVTIPISCKIRVLPDLE---ETLR-LCNTLASTGIAAIAVHGRTIEERPQ 136

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRA 218
            P  N  +  +   +          + +  NGG +D+ +   IL          VM+ RA
Sbjct: 137 HPNRNHILKQISTAL---------SIPVIANGGSKDIQKHSDILRFKTETGCSSVMLARA 187

Query: 219 AYKNSAML 226
           A  N ++ 
Sbjct: 188 AEWNCSVF 195


>gi|24585320|ref|NP_610000.1| CG10463 [Drosophila melanogaster]
 gi|7298625|gb|AAF53841.1| CG10463 [Drosophila melanogaster]
          Length = 604

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 65/272 (23%), Positives = 116/272 (42%), Gaps = 31/272 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + L +AA+++ E    + I+LN+
Sbjct: 287 EMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMLNQAAQVIHETAQVDFIDLNI 346

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV-DDQIPAVALRN 138
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D+  A  L  
Sbjct: 347 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSDRLPFTVKMRTGIYADKSVAHELLP 405

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           LV+     G + + +H R         ++ R   + ++  + E   +   + +  NG + 
Sbjct: 406 LVEEW---GASAVTLHGRS--------REQRYTKHANWAYIEECAAKAKCMPVIGNGDIL 454

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ED  +   + P V  VMIGR A     +   + E      + SS  +  + + F    
Sbjct: 455 SYEDYMERRTLAPHVCSVMIGRGALIKPWIFQEIKE--KQAWSPSSGQRYEMLQKF---- 508

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                +Y   H  S  K  + TR  +  +  F
Sbjct: 509 ----CNYGLEHWGSDTKGVETTRRFLLEWQSF 536


>gi|84999472|ref|XP_954457.1| hypothetical protein [Theileria annulata]
 gi|65305455|emb|CAI73780.1| hypothetical protein, conserved [Theileria annulata]
          Length = 359

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 98/233 (42%), Gaps = 31/233 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R  + + L YT M+ A      +    + F  S+ +KPL  Q  G D
Sbjct: 33  MVDQSELPFRLLCRRYSAD-LAYTPMLHAKIFSENENYRNIHFHTSSDDKPLIAQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S  + A+  +++   + I++N+GCP     +G +G+ L+  P ++    A+        
Sbjct: 92  PSAFILASSYIKN-DVSAIDINLGCPQGIAKKGRYGSFLLEYPQLITKGFAS-------- 142

Query: 119 VTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                   VD +        L  V+S + +G   + +H R         +   +I   D+
Sbjct: 143 --------VDTKFMLFTRGWLFSVQSCQANGCKALTVHGRH------RSETKTRISECDW 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           D + +I K   ++ +  NGG+E      + L     D VM   A  +N  + +
Sbjct: 189 DSI-KIIKSRVNIPVIANGGIETFEDVKRCLDYTGADAVMSSEAILENPYLFS 240


>gi|15645347|ref|NP_207521.1| transcriptional regulator, putative [Helicobacter pylori 26695]
 gi|39930813|sp|O25427|DUS_HELPY RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|2313849|gb|AAD07774.1| transcriptional regulator, putative [Helicobacter pylori 26695]
          Length = 328

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 99/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + N I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALEHVNGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  S  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTSKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|241763268|ref|ZP_04761325.1| dihydrouridine synthase DuS [Acidovorax delafieldii 2AN]
 gi|241367543|gb|EER61830.1| dihydrouridine synthase DuS [Acidovorax delafieldii 2AN]
          Length = 317

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 81/181 (44%), Gaps = 16/181 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+  P  +   +
Sbjct: 64  PVRAQLLGSDPVCMAENAARLAALGPEGIDLNFGCPAKVVNRHGGGAALLQEPQRIAAVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +A+ +A+   +PV+ K R+G +D   A   R   ++++  G   + +HAR        P 
Sbjct: 124 SAVRRAVPAHLPVSAKMRLGFND---ASLARECAQAMEAGGACELVVHARTKADGYRPPA 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
              +IP +   +   +           NG +  ++ AL+   +   D +M+GR    +  
Sbjct: 181 YWEQIPAIRAAVRIPVVA---------NGEIWTVADALRCREVSGCDALMLGRGMVADPG 231

Query: 225 M 225
           +
Sbjct: 232 L 232


>gi|313238054|emb|CBY13173.1| unnamed protein product [Oikopleura dioica]
          Length = 575

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 55/214 (25%), Positives = 100/214 (46%), Gaps = 27/214 (12%)

Query: 21  LLYTEMIVADAILRGDK--KNILG-FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           L YT M  A  I+   K  +N+L       +P+ +Q+   D+   +EA +IV+DF  + +
Sbjct: 44  LSYTPMHNAHLIVNDLKYRQNVLADLRNSPRPVFVQMAANDVKLFLEAIRIVKDFC-DAV 102

Query: 78  NLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +LN+GCP      G +GA +ML   +++ + I A  K   I V ++    ++  +     
Sbjct: 103 DLNLGCPQHIARRGGYGAFMMLGSWELISELIQAGSKIHRITVKIRVFEEIEKSVKYAKE 162

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           R L+       V+G  I  ++  L GL+          +++ +  +K++   + + LNG 
Sbjct: 163 RFLL------TVHGRTIEQKRE-LTGLA----------NWEHIKAVKRK-LTIPVILNGN 204

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +   ED+ +A +    VDGVM       N  + T
Sbjct: 205 IRYFEDIERAFQ-ETRVDGVMSAEGILSNPGIFT 237


>gi|327483810|gb|AEA78217.1| tRNA-dihydrouridine synthase C [Vibrio cholerae LMA3894-4]
          Length = 313

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 54  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 113

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 114 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 160


>gi|262158407|ref|ZP_06029523.1| tRNA-dihydrouridine synthase C [Vibrio cholerae INDRE 91/1]
 gi|262029848|gb|EEY48496.1| tRNA-dihydrouridine synthase C [Vibrio cholerae INDRE 91/1]
          Length = 313

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 54  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 113

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 114 KACRDAVPAHIPVSAKIRLGWED--PEDCFE-IVDAVAQAKADELTVHAR 160


>gi|169862298|ref|XP_001837779.1| zinc finger dihydrouridine synthase [Coprinopsis cinerea
           okayama7#130]
 gi|187471053|sp|A8NZY7|DUS3_COPC7 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|116501141|gb|EAU84036.1| zinc finger dihydrouridine synthase [Coprinopsis cinerea
           okayama7#130]
          Length = 676

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 103/225 (45%), Gaps = 28/225 (12%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDF--GYNEINL 79
           EM +A + L G K+  +++     EK   +Q+ G     LV  A+++ ++F  G + ++L
Sbjct: 341 EMGLATSFLAGSKEEWSLVRRHPSEKIFGIQVAGNKPHTLVPTAEVIAKEFPTGVDFVDL 400

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N GCP   V +   G+ L+ N   +G  I  M +AL  IP+TVK R GV +     A + 
Sbjct: 401 NCGCPIDLVFKAGSGSALLDNAGKLGKIIQGMNRALGEIPLTVKIRTGVKEGR-NNAHKL 459

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI------KKENPDL-FI 191
           + +   +   + I +H R         +  R     D+D + E       ++ + DL  +
Sbjct: 460 MPRISAEWSASAITLHGRT--------RQQRYTKLADWDYIKECVAAVRAREADEDLPPV 511

Query: 192 GLNGG-----LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            + GG      +D  + +     VDGVMIGR A     + T + E
Sbjct: 512 PIFGGGDCFSSQDYWEKINNY-GVDGVMIGRGALIKPWIFTEIKE 555


>gi|312073196|ref|XP_003139411.1| dihydrouridine synthase domain-containing protein [Loa loa]
 gi|307765423|gb|EFO24657.1| dihydrouridine synthase domain-containing protein [Loa loa]
          Length = 439

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 52/227 (22%), Positives = 99/227 (43%), Gaps = 34/227 (14%)

Query: 21  LLYTEMIVADAILRGDK--KNILGFS---------------TQEKPLALQIGGADISKLV 63
           L+YTE I+   +L   +   +ILG +                +++   LQIG  D  +  
Sbjct: 35  LVYTEEIIDQKLLGSQRTINDILGTTDYTYEDDVVLRICNRIEKQKCVLQIGTNDAQRAA 94

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
              K VE+     I++N+GCP      G  GA L+ +P+   + +       +IPV+ K 
Sbjct: 95  NVVKKVEN-DVAAIDINMGCPKPFSIAGGMGAALLGSPERAKEIVQTCVSISTIPVSCKM 153

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+ +D +   +     VK +++ GV+ I IH R+        +  R+      + ++E+ 
Sbjct: 154 RV-LDKREDTL---EFVKMLERCGVSAIGIHGRR--------RSERQSDMNRLNEIHEVT 201

Query: 184 K--ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           +    P +  G +G +++ +  ++         VMI R A  N ++ 
Sbjct: 202 RVVSVPVIANGFSGSIKEYADIMRFWKQSGASSVMIARKALSNPSIF 248


>gi|226322662|ref|ZP_03798180.1| hypothetical protein COPCOM_00434 [Coprococcus comes ATCC 27758]
 gi|225208999|gb|EEG91353.1| hypothetical protein COPCOM_00434 [Coprococcus comes ATCC 27758]
          Length = 311

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 41/78 (52%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI        +  A+ +++FGY E+NLN+GCPS  V     G+  +  PD +   +A + 
Sbjct: 64  QILTNRAEDFIRLARQLKEFGYEEVNLNLGCPSKTVVNRKRGSGFLFYPDELNHFLAEVF 123

Query: 113 KALSIPVTVKCRIGVDDQ 130
             L + +++K R G  DQ
Sbjct: 124 DQLDMKISIKTRSGKYDQ 141


>gi|91783478|ref|YP_558684.1| putative tRNA-dihydrouridine synthase C, DuS [Burkholderia
           xenovorans LB400]
 gi|91687432|gb|ABE30632.1| tRNA-U20a,U20b-dihydrouridine synthase [Burkholderia xenovorans
           LB400]
          Length = 340

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 42/185 (22%), Positives = 85/185 (45%), Gaps = 16/185 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   +   A        + I+LN GCP+  V++   GA L+ +P
Sbjct: 58  GHTPNGTPMVIQLLGSDPEWMARNAAHAASLSPHGIDLNFGCPAKVVNQHGGGAMLLADP 117

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   ++++  A+   +PVT K R+GV D   A+       ++ + G   + +HAR   
Sbjct: 118 EQLNRIVSSVRAAVPAGVPVTAKMRLGVSDTSLAI---ECAVALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
                 +D+   P   ++ +  I     D+ +  NG +  ++  +  + +     VM+GR
Sbjct: 173 ------RDHGYRPPAHWEWIARIDAAV-DVPVVANGEVWTVADWERCRAVSGCANVMLGR 225

Query: 218 AAYKN 222
            A  +
Sbjct: 226 GAVSD 230


>gi|237844349|ref|XP_002371472.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211969136|gb|EEB04332.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|221481251|gb|EEE19648.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii GT1]
          Length = 653

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 37/145 (25%), Positives = 71/145 (48%), Gaps = 6/145 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDF 72
           +LL +      +    D + + +K  +     +E+  + +Q+G +D ++ ++AA +V   
Sbjct: 290 KLLNSVRTFNEDFSTIDFLHKSEKTCVFSTCLEERGKVVMQLGTSDATRALKAAMLVAQ- 348

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               +++N+GCP +    G  GA L+  P I  D +  + + L IPVT  C+I + D I 
Sbjct: 349 DVAAVDVNMGCPKSFSINGGMGAALLKTPLIATDILKTLRRNLDIPVT--CKIRLLDTIH 406

Query: 133 AVALRNLVKSIKKSGVNGIWIHARK 157
                +  +  +  G+  I IHAR+
Sbjct: 407 KTI--DFARLCENCGIEAIAIHARE 429


>gi|255745518|ref|ZP_05419466.1| tRNA-dihydrouridine synthase C [Vibrio cholera CIRS 101]
 gi|255736593|gb|EET91990.1| tRNA-dihydrouridine synthase C [Vibrio cholera CIRS 101]
          Length = 316

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 57  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 117 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 163


>gi|170726139|ref|YP_001760165.1| dihydrouridine synthase DuS [Shewanella woodyi ATCC 51908]
 gi|169811486|gb|ACA86070.1| dihydrouridine synthase DuS [Shewanella woodyi ATCC 51908]
          Length = 315

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 88/186 (47%), Gaps = 19/186 (10%)

Query: 41  LGFSTQEK---PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           L + ++ K   P+ LQ+ G   + + E A    + G   ++LN GCP+  V+  + GA L
Sbjct: 53  LAYGSKTKAGTPVRLQLLGQHPNWMAENAIRAIELGSLGVDLNYGCPAPMVNRSNGGAAL 112

Query: 98  MLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
           +  P+ +     A+ +A+  S PV+ K R+G DD+   V    + ++I+ +G   + +HA
Sbjct: 113 LKEPETIYKVTKAVREAVPSSHPVSAKIRLGWDDKSRCV---EIAQAIESAGATELTVHA 169

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R    +G  P  + +  NL         +E   + +  NG +      LK   +   D V
Sbjct: 170 RTK-EEGYRPPAHWEYINLI--------REAIAIPVIANGEVWCHQDYLKCQAASGCDDV 220

Query: 214 MIGRAA 219
           MIGR A
Sbjct: 221 MIGRGA 226


>gi|320582810|gb|EFW97027.1| Dihydrouridine synthase [Pichia angusta DL-1]
          Length = 367

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 46/159 (28%), Positives = 79/159 (49%), Gaps = 19/159 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDCI 108
           L  Q+G A     V+AAKIV     + I++N GCP    VH G  GA L+  PD++   +
Sbjct: 87  LIFQLGTASPELAVQAAKIVA-ADVDGIDINAGCPKHFSVHSG-MGAALLKTPDVLCSIL 144

Query: 109 AAMC----KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +++     K    P++VK R+  + +       +LV+ + K+G+  + +H R   ++   
Sbjct: 145 SSLVEQVGKPFQKPISVKIRLLPEQE----QTLDLVRKLVKTGIANLTVHCRTREMRNGQ 200

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQ 202
           P      P  DY D + EI  E  D+ + +NGG++   +
Sbjct: 201 P------PIRDYIDKIKEICDE-ADVSLIINGGIKSYQE 232


>gi|260944248|ref|XP_002616422.1| hypothetical protein CLUG_03663 [Clavispora lusitaniae ATCC 42720]
 gi|238850071|gb|EEQ39535.1| hypothetical protein CLUG_03663 [Clavispora lusitaniae ATCC 42720]
          Length = 393

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 95/204 (46%), Gaps = 25/204 (12%)

Query: 38  KNILGFST----QEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGS 92
           KN L F T    +E  L  Q+G AD    VE A K+++D   + I+LN GCP        
Sbjct: 87  KNSLIFRTNRKYEEGKLIFQLGSADPDIAVEGALKVIQDV--DGIDLNCGCPKPFSTHAG 144

Query: 93  FGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            GA L+ NPD    I+ + +  + K    P++ K R+ +D +    +L  L+  +  +G+
Sbjct: 145 MGAALLSNPDLLCSILENLVEKVGKPYRKPISAKIRL-LDSKSAEPSL-ALIDRLCSTGI 202

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQA--LK 205
             + +H R   ++      NR+ P  DY   +Y++  +   + + +NG      +A   K
Sbjct: 203 TNLTVHCRTREMR------NRESPVRDYVSQIYDLTNKR-GVSLVINGAFRCRKEAEQFK 255

Query: 206 ILPSVD--GVMIGRAAYKNSAMLT 227
                D  G+M+  AA  N ++ +
Sbjct: 256 QFMGNDQIGIMMAEAAESNPSVFS 279


>gi|229525717|ref|ZP_04415122.1| tRNA-dihydrouridine synthase C [Vibrio cholerae bv. albensis VL426]
 gi|229339298|gb|EEO04315.1| tRNA-dihydrouridine synthase C [Vibrio cholerae bv. albensis VL426]
          Length = 323

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|221501948|gb|EEE27699.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 653

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 37/145 (25%), Positives = 71/145 (48%), Gaps = 6/145 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDF 72
           +LL +      +    D + + +K  +     +E+  + +Q+G +D ++ ++AA +V   
Sbjct: 290 KLLNSVRTFNEDFSTIDFLHKSEKTCVFSTCLEERGKVVMQLGTSDATRALKAAMLVAQ- 348

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               +++N+GCP +    G  GA L+  P I  D +  + + L IPVT  C+I + D I 
Sbjct: 349 DVAAVDVNMGCPKSFSINGGMGAALLKTPLIATDILKTLRRNLDIPVT--CKIRLLDTIH 406

Query: 133 AVALRNLVKSIKKSGVNGIWIHARK 157
                +  +  +  G+  I IHAR+
Sbjct: 407 KTI--DFARLCENCGIEAIAIHARE 429


>gi|317474612|ref|ZP_07933886.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|316909293|gb|EFV30973.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 318

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 103/229 (44%), Gaps = 18/229 (7%)

Query: 4   WTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEK-PLALQIGGADI 59
           +TD  YR   AR+       Y+  +  +   I R D ++I   + +E   L  Q+  +  
Sbjct: 16  YTDAVYRLAHARIFGGIDTYYSPFVRVEHGEIRRKDARDISSKNNREGIHLIPQLIASQP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            KL +   +  +  Y E ++N+GCP   + +   GA ++  PD V D + AA+ K   I 
Sbjct: 76  DKLEQIITLFIENNYQEADINLGCPFPMLAKRHNGAGMLPYPDEVKDLLTAAIEKYPQIH 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDY 176
            +VK R+G ++    +AL  L  ++    +  I +H R  K   KG       ++    +
Sbjct: 136 FSVKLRLGWENAEECLALLPLFNALP---LTHIILHPRLGKQQYKG-------EVDLSGF 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +  Y    E P L+ G    +ED+    +  P + GV+IGR    N A+
Sbjct: 186 EAFYN-GCEKPLLYNGDLHTVEDIQTITEHFPKLAGVVIGRGLLANPAL 233


>gi|218708996|ref|YP_002416617.1| tRNA-dihydrouridine synthase C [Vibrio splendidus LGP32]
 gi|218322015|emb|CAV18052.1| tRNA-dihydrouridine synthase C [Vibrio splendidus LGP32]
          Length = 318

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 43/176 (24%), Positives = 84/176 (47%), Gaps = 15/176 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+ G   + + E A      G   I+LN GCP+  V++ + GA L+  P+++   +
Sbjct: 64  PIHLQLLGQHPNWMAENAFQAASLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +   A+   IPV+ K R+G +   P      +V +I+++  + + +HAR  +       
Sbjct: 124 KSCRDAVPAHIPVSAKIRLGWER--PEECFE-IVDAIEQAKADELTVHARTKV------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
              K   + +D + +I +E   L +  NG + +       + +  VD +M+ R A+
Sbjct: 174 GGYKASEIKWDYINQI-REKTSLPLIANGEIWNYQDGQDCIEATGVDSLMVCRGAF 228


>gi|320100761|ref|YP_004176353.1| dihydroorotate oxidase B, catalytic subunit [Desulfurococcus
           mucosus DSM 2162]
 gi|319753113|gb|ADV64871.1| dihydroorotate oxidase B, catalytic subunit [Desulfurococcus
           mucosus DSM 2162]
          Length = 299

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 53/200 (26%), Positives = 88/200 (44%), Gaps = 31/200 (15%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           KPL L IGG  I + V+ A+   + G + + LN+ CP AR     +G  L  +P +V   
Sbjct: 92  KPLVLSIGGGGIDEFVKLAEAASEAGVDAVELNLSCPHAR----GYGLELGGDPALVYTI 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI------------PAVALRNLVKSIKKSGVNGIWIHA 155
           +       S PV  K  +G+ D+I             A+ L N VK++       I +++
Sbjct: 148 VKNTVSVSSAPVVAK--LGLSDRIMESAGKALEGGAKALTLINTVKAMA------IDVYS 199

Query: 156 RKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
           RK +L     GLS      I  +   +VY++ +E     IG+ G    +  A  IL    
Sbjct: 200 RKPVLSNKHGGLS---GPPIHPIAVRVVYDVYREYRAEVIGVGGVSSWIDAAELILAGAR 256

Query: 212 GVMIGRAAYKNSAMLTTVDE 231
            + +G A   N  ++  +++
Sbjct: 257 AIQVGTAVLFNEKVVEEINK 276


>gi|153814602|ref|ZP_01967270.1| hypothetical protein RUMTOR_00816 [Ruminococcus torques ATCC 27756]
 gi|145848096|gb|EDK25014.1| hypothetical protein RUMTOR_00816 [Ruminococcus torques ATCC 27756]
          Length = 211

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 38/123 (30%), Positives = 58/123 (47%), Gaps = 7/123 (5%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+IL    +      QI        V+ AK +E +GY EINLNVGCPS  V     GA
Sbjct: 47  EKKDILPEHNKGMHAVPQILTNCAEDFVQTAKKLEQYGYKEINLNVGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWI 153
             +  P+ +   +  + +   I ++VK RIG +  ++ P      L+    K  +  + I
Sbjct: 107 GFLAFPERLDLFLEEVFQNCPIDISVKTRIGTESGEEFP-----KLMDIYNKYPIKELII 161

Query: 154 HAR 156
           H R
Sbjct: 162 HPR 164


>gi|254572948|ref|XP_002493583.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|238033382|emb|CAY71404.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|328354589|emb|CCA40986.1| tRNA-dihydrouridine synthase 3 [Pichia pastoris CBS 7435]
          Length = 618

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 100/231 (43%), Gaps = 26/231 (11%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEA 65
           YR   + L  + + Y+EM ++  +++G           S++     +QI  +      +A
Sbjct: 266 YRRLMKTLGAD-ITYSEMALSLPLIQGTNSEWALPKAHSSEYPGFGVQIATSKHWTGAKA 324

Query: 66  AKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM--CKALSIPVTV 121
           A+ +       +EINLN GCP   ++    G+ LM  P  +   +  M  C    IPVT 
Sbjct: 325 AEAIAKLTPQVSEINLNCGCPIDLLYRQGQGSALMEQPPKLLRVLKGMNYCSG-EIPVTF 383

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNL-----D 175
           K RIG  D  P     NLVK + + G +  + +H R    +     D   I  +     D
Sbjct: 384 KLRIGTRDNHPLA--ENLVKRVCEEGDIGCVTLHGRTRQQRYTKEADWSYISKVGQVVRD 441

Query: 176 YDIVYEIKKE----NPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
           Y+      KE    +P  F+G NG     ED  +A+   P++D VM+ R A
Sbjct: 442 YNHNQLDDKEQSDRDPIYFVG-NGDCFTHEDWHKAVSD-PNIDSVMVARGA 490


>gi|218131773|ref|ZP_03460577.1| hypothetical protein BACEGG_03394 [Bacteroides eggerthii DSM 20697]
 gi|217986076|gb|EEC52415.1| hypothetical protein BACEGG_03394 [Bacteroides eggerthii DSM 20697]
          Length = 318

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 103/229 (44%), Gaps = 18/229 (7%)

Query: 4   WTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEK-PLALQIGGADI 59
           +TD  YR   AR+       Y+  +  +   I R D ++I   + +E   L  Q+  +  
Sbjct: 16  YTDAVYRLAHARIFGGIDTYYSPFVRVEHGEIRRKDARDISSKNNREGIHLIPQLIASQP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            KL +   +  +  Y E ++N+GCP   + +   GA ++  PD V D + AA+ K   I 
Sbjct: 76  DKLEQIITLFIENNYQEADINLGCPFPMLAKRHNGAGMLPYPDEVKDLLTAAIEKYPQIH 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDY 176
            +VK R+G ++    +AL  L  ++    +  I +H R  K   KG       ++    +
Sbjct: 136 FSVKLRLGWENAEECLALLPLFNALP---LTHIILHPRLGKQQYKG-------EVDLSGF 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +  Y    E P L+ G    +ED+    +  P + GV+IGR    N A+
Sbjct: 186 EAFYN-GCEKPLLYNGDLHTVEDIQTITERFPKLAGVVIGRGLLANPAL 233


>gi|15641118|ref|NP_230750.1| hypothetical protein VC1105 [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121591280|ref|ZP_01678575.1| conserved hypothetical protein [Vibrio cholerae 2740-80]
 gi|153816887|ref|ZP_01969554.1| conserved hypothetical protein [Vibrio cholerae NCTC 8457]
 gi|227081278|ref|YP_002809829.1| hypothetical protein VCM66_1061 [Vibrio cholerae M66-2]
 gi|229505299|ref|ZP_04394809.1| tRNA-dihydrouridine synthase C [Vibrio cholerae BX 330286]
 gi|229511031|ref|ZP_04400510.1| tRNA-dihydrouridine synthase C [Vibrio cholerae B33]
 gi|229518152|ref|ZP_04407596.1| tRNA-dihydrouridine synthase C [Vibrio cholerae RC9]
 gi|229608318|ref|YP_002878966.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254848235|ref|ZP_05237585.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MO10]
 gi|298498790|ref|ZP_07008597.1| conserved hypothetical protein [Vibrio cholerae MAK 757]
 gi|38605060|sp|Q9KT00|DUSC_VIBCH RecName: Full=tRNA-dihydrouridine synthase C
 gi|9655575|gb|AAF94264.1| conserved hypothetical protein [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121546864|gb|EAX57022.1| conserved hypothetical protein [Vibrio cholerae 2740-80]
 gi|126512474|gb|EAZ75068.1| conserved hypothetical protein [Vibrio cholerae NCTC 8457]
 gi|227009166|gb|ACP05378.1| conserved hypothetical protein [Vibrio cholerae M66-2]
 gi|229344867|gb|EEO09841.1| tRNA-dihydrouridine synthase C [Vibrio cholerae RC9]
 gi|229350996|gb|EEO15937.1| tRNA-dihydrouridine synthase C [Vibrio cholerae B33]
 gi|229357522|gb|EEO22439.1| tRNA-dihydrouridine synthase C [Vibrio cholerae BX 330286]
 gi|229370973|gb|ACQ61396.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254843940|gb|EET22354.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MO10]
 gi|297543123|gb|EFH79173.1| conserved hypothetical protein [Vibrio cholerae MAK 757]
          Length = 323

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|115384898|ref|XP_001208996.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
 gi|114196688|gb|EAU38388.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
          Length = 441

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 82/185 (44%), Gaps = 29/185 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAKIV       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LIFQIGTASPELAVQAAKIVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVAILE 163

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK RI    ++      +LV  + K+G+ G+ +H R   ++   P
Sbjct: 164 ALVREVGTPYQIGISVKIRILETPEL----TESLVSRLVKTGITGLTVHCRTTPMR---P 216

Query: 166 KDN------RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
           ++       R + N+ +         N  +   +NG +     AL ++    VDG MI  
Sbjct: 217 RERAIRDQLRMVANVCH---------NAGVACVMNGDVTSRDDALALMQEYGVDGAMIAT 267

Query: 218 AAYKN 222
           +A  N
Sbjct: 268 SAESN 272


>gi|121726268|ref|ZP_01679558.1| conserved hypothetical protein [Vibrio cholerae V52]
 gi|229529805|ref|ZP_04419195.1| tRNA-dihydrouridine synthase C [Vibrio cholerae 12129(1)]
 gi|121631214|gb|EAX63587.1| conserved hypothetical protein [Vibrio cholerae V52]
 gi|229333579|gb|EEN99065.1| tRNA-dihydrouridine synthase C [Vibrio cholerae 12129(1)]
          Length = 323

 Score = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|302785397|ref|XP_002974470.1| hypothetical protein SELMODRAFT_174143 [Selaginella moellendorffii]
 gi|300158068|gb|EFJ24692.1| hypothetical protein SELMODRAFT_174143 [Selaginella moellendorffii]
          Length = 319

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 63/122 (51%), Gaps = 10/122 (8%)

Query: 50  LALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +  Q+G +D  + +  A+++ +D     +++N+GCP      G  G+ L+  P++V + +
Sbjct: 82  VVFQMGTSDPYRALTVAQLLCKDIA--AVDINMGCPKPFSVTGGMGSALLSQPELVSEIL 139

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             + + L IPVT K R+    Q        L + I+K+GV+ I +H R+   +   PKD 
Sbjct: 140 TTLRRNLDIPVTCKIRLLKSTQ----ETVELARRIEKTGVSAIAVHGRRIPDR---PKDR 192

Query: 169 RK 170
            K
Sbjct: 193 AK 194


>gi|254225500|ref|ZP_04919110.1| conserved hypothetical protein [Vibrio cholerae V51]
 gi|125621970|gb|EAZ50294.1| conserved hypothetical protein [Vibrio cholerae V51]
          Length = 323

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|262402534|ref|ZP_06079095.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC586]
 gi|262351316|gb|EEZ00449.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC586]
          Length = 331

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|330983303|gb|EGH81406.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 67

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 22/43 (51%), Positives = 30/43 (69%)

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 4   SMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 46


>gi|297578707|ref|ZP_06940635.1| conserved hypothetical protein [Vibrio cholerae RC385]
 gi|297536301|gb|EFH75134.1| conserved hypothetical protein [Vibrio cholerae RC385]
          Length = 323

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|115459590|ref|NP_001053395.1| Os04g0531300 [Oryza sativa Japonica Group]
 gi|38346764|emb|CAD41143.2| OSJNBa0081C01.15 [Oryza sativa Japonica Group]
 gi|113564966|dbj|BAF15309.1| Os04g0531300 [Oryza sativa Japonica Group]
 gi|116312037|emb|CAJ86402.1| OSIGBa0125M19.5 [Oryza sativa Indica Group]
 gi|125549126|gb|EAY94948.1| hypothetical protein OsI_16753 [Oryza sativa Indica Group]
 gi|215737387|dbj|BAG96316.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 319

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 55/215 (25%), Positives = 98/215 (45%), Gaps = 24/215 (11%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGY 74
           +TN +L  T     D + RG    +     QE+  +  Q+G +D  + ++AA++V +   
Sbjct: 48  VTNESLGTT-----DFLERGTDTVVFRTCPQERDRVVFQMGTSDAVRALKAAQLVCN-DV 101

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
             I++N+GCP +    G  GA L+  P+++ D +  + + L   VT K R+    Q    
Sbjct: 102 AAIDINMGCPKSFSLSGGMGAALLSKPELIHDILTTLRRNLDTTVTCKIRLLNTRQDTV- 160

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK---KENPDLFI 191
               L + ++K GV  + +H RK   +   P+D  K   +  D+V  +      N D+F 
Sbjct: 161 ---ELARRVEKIGVPALAVHGRKVKDR---PRDPAKWDEI-ADVVSALSIPVIANGDVF- 212

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
                 ED  + +K       VM+ R A  N+++ 
Sbjct: 213 ----EYEDFKR-IKDATGAASVMVARGAMWNASIF 242


>gi|229515488|ref|ZP_04404947.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TMA 21]
 gi|229347257|gb|EEO12217.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TMA 21]
          Length = 323

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|197116498|ref|YP_002136925.1| tRNA dihydrouridine synthase-like flavin mononucleotide-binding
           domain-containing protein [Geobacter bemidjiensis Bem]
 gi|197085858|gb|ACH37129.1| tRNA dihydrouridine synthase-like flavin mononucleotide-binding
           domain protein [Geobacter bemidjiensis Bem]
          Length = 341

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 103/226 (45%), Gaps = 37/226 (16%)

Query: 16  LTNNAL--LYTEMIVADAI----------------LRGDKKNILGFSTQEKPLALQIGGA 57
           LTN AL  L+T+ +  D +                + GD + I   S    PL +Q+ G 
Sbjct: 42  LTNRALRSLFTKWVRPDVVWTEFMRVNPVSAKKRLMPGDLREI-SASEDGIPLVVQLIGH 100

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
               LV AA+  +D G   +NLN+GCP  R+  G  G  ++  P+++ + I A+ +A+  
Sbjct: 101 GREALVSAAQAAQDAGAVHLNLNMGCPYGRMTSGLTGGGMLKKPELLEEIIPALREAIHG 160

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN--LD 175
             ++K R G +D     +L  L    ++SGV+ + +H          P+  R+  N   D
Sbjct: 161 SFSIKLRAGYEDPQQVFSLLPL---FERSGVDFLVLH----------PRTVRQAYNGWAD 207

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAA 219
           +++  E+ ++     I  NG +   +   ++L      G+M+GR  
Sbjct: 208 HEVTAEVVRQTSIPVIA-NGDIRSAAGGQRLLEQTGAAGLMLGRGG 252


>gi|153802134|ref|ZP_01956720.1| conserved hypothetical protein [Vibrio cholerae MZO-3]
 gi|124122327|gb|EAY41070.1| conserved hypothetical protein [Vibrio cholerae MZO-3]
          Length = 323

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|260655068|ref|ZP_05860556.1| dihydrouridine synthase family protein [Jonquetella anthropi E3_33
           E1]
 gi|260630179|gb|EEX48373.1| dihydrouridine synthase family protein [Jonquetella anthropi E3_33
           E1]
          Length = 317

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 35/157 (22%), Positives = 70/157 (44%), Gaps = 6/157 (3%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEI 77
           L +TEM  A  ++RG ++   +L  +   +PL  Q+   D   LV  A++    G ++ +
Sbjct: 20  LTHTEMASATGLVRGGRQTLRVLDQTNDTRPLVAQLFAGDAESLVRGAEVALTCGPFDAL 79

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            +N+ CP  +V +   G+ L+  PD     +  +C+    PV  K R   +     +   
Sbjct: 80  GINMACPMPKVLKRGAGSALLDRPDEAASMVRELCR-FGFPVWPKVR--KEPAGSGITTE 136

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             V+ + ++G + + +H R    +     D + +  L
Sbjct: 137 EFVQILFEAGASCVAVHGRTPGQRYEGQADRKSVKEL 173


>gi|153213536|ref|ZP_01948826.1| conserved hypothetical protein [Vibrio cholerae 1587]
 gi|124115872|gb|EAY34692.1| conserved hypothetical protein [Vibrio cholerae 1587]
          Length = 323

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|300857022|ref|YP_003782006.1| putative tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
 gi|300437137|gb|ADK16904.1| putative tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
          Length = 313

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 58/273 (21%), Positives = 113/273 (41%), Gaps = 21/273 (7%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           +D     +  +IL  + Q   L  Q+   +    +  +K ++  GY E+NLN+GCPS  V
Sbjct: 40  SDKFKTKELNDILPENNQGIVLIPQLLTNNAKDFIHTSKKIKQMGYTEVNLNLGCPSGTV 99

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              + G+  +     +   +  +    +  ++VK RIG D         NL++   K  +
Sbjct: 100 VSKNRGSGFLSKTKELDAFLDEIFSEAATKISVKTRIGKDS---PEEFYNLIEIFNKYPI 156

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             + IH R  I K       +  PNL  +     + K NP  + G    ++D  +     
Sbjct: 157 EELIIHPR--IQKDFY----KNKPNLKVFKDALSLSK-NPICYNGDIFSVKDYKKFTTNF 209

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
            SV+ +M+GR    N  ++        N +  ++ +  ++ K+F  KI            
Sbjct: 210 HSVETLMLGRGLLINPGLI--------NDIKNNTKLDKKLLKNFHDKIYEDYKKVLFGDR 261

Query: 268 HSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +   +++++  +MI +F    N++  + I   E
Sbjct: 262 NVLFRMKELWSYMIQIFSN--NTKYAKKIKKSE 292


>gi|41056139|ref|NP_956968.1| tRNA-dihydrouridine synthase 3-like [Danio rerio]
 gi|34784014|gb|AAH58066.1| Zgc:63779 [Danio rerio]
          Length = 660

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 49/211 (23%), Positives = 89/211 (42%), Gaps = 14/211 (6%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +   +L+G      +L     E    +Q+ G     +   A+++ ++   + +++N 
Sbjct: 345 EMAMCTNLLQGQASEWALLKRHASEDLFGVQLEGCFPDTMTRCAELLNQNIDVDFVDINS 404

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM         +  M   L +P+TVK R GV  Q  +     L+ 
Sbjct: 405 GCPIDLVYKKGGGCGLMTRTSKFEQIVRGMNSVLDVPLTVKIRTGV--QQNSNIAHKLIP 462

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +KK GV+ I +H R         ++ R     D+D +    +    + +  NG +    
Sbjct: 463 EMKKWGVSLITLHGRS--------REQRYTKLADWDYINTCAQLAAPVPLFGNGDILSYE 514

Query: 202 QALKILPS-VDGVMIGRAAYKNSAMLTTVDE 231
            A+K   + V G+M+ R A     + T + E
Sbjct: 515 DAMKARETGVSGIMVARGALIKPWLFTEIKE 545


>gi|38605039|sp|Q9AMN9|DUSC_PSEAC RecName: Full=tRNA-dihydrouridine synthase C
 gi|12965136|gb|AAK11471.1|AF323438_3 unknown [Pseudomonas alcaligenes]
          Length = 315

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 58/261 (22%), Positives = 112/261 (42%), Gaps = 30/261 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q  G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQFLGSDPQCLADNAAFACTLGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + + +   IPVT K R+G + +  A+   +  +++ + G + I +HAR  + +G  P 
Sbjct: 124 REVRRTVPAEIPVTAKMRLGFEGKEGAL---DCARALAEGGASQIVVHARTKV-EGYKPP 179

Query: 167 DNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
            +       ++ V  +++    P    G    L+D  +  +I   VD +M+GR       
Sbjct: 180 AH-------WEWVARVQEVVGVPVFANGEVWTLDDWRRCREI-SGVDDIMLGRGLVSRPG 231

Query: 225 MLTTVDEYFS--NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----ITR 278
           +   +    +   P   S      +  DFW++    +        ++ G+L+Q    +TR
Sbjct: 232 LARQIAAVRAGEEPEDMSWAELQPLLLDFWQQARRKLAPR-----YAPGRLKQWLAMLTR 286

Query: 279 ---HMIGLFHGFPNSRRCRHI 296
                + LF      + C  I
Sbjct: 287 TYPEAVALFAEVRREQDCERI 307


>gi|307203528|gb|EFN82561.1| tRNA-dihydrouridine synthase 3-like [Harpegnathos saltator]
          Length = 660

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 46/213 (21%), Positives = 96/213 (45%), Gaps = 16/213 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A  IL+G ++   ++     E    +Q+ G +   L   A+++  +   + I+LN+
Sbjct: 343 EMALAPKILKGTQEEWALVKRHECEDVFGVQLCGNNPGVLTRCAQLLNREIDVDYIDLNL 402

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   ++    G+ ++   +++   + ++ + L IP+++K R GV   I      NL+ 
Sbjct: 403 GCPIDLIYRQGGGSGMLNRLNVLETVVKSVSQVLDIPLSIKTRTGV--YIDKPIAHNLMP 460

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
              + GV+ I +H R         ++ R     D++ + +       + +  NG     +
Sbjct: 461 KFHEWGVSMITVHGRS--------REQRYTKLADWEYIEKCAVAASPVPVFGNGDILSFD 512

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  +  +   +V G+ IGR A     + T + E
Sbjct: 513 DYQRMKETYSTVQGITIGRGALIKPWIFTEIKE 545


>gi|311110625|ref|ZP_07712022.1| dihydroorotate oxidase [Lactobacillus gasseri MV-22]
 gi|311065779|gb|EFQ46119.1| dihydroorotate oxidase [Lactobacillus gasseri MV-22]
          Length = 307

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 99/225 (44%), Gaps = 32/225 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA++  DK   L  S  + P+   +GG D +  VE AK + D G  N + +NV CP+   
Sbjct: 80  DAVIE-DKLKPLRQSYPDLPIMASVGGEDEAGYVEVAKKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V      +    ++P+ +K    V D      +  + K+ +K G 
Sbjct: 139 GGMSFG----VHPDVVESLTKKIKAVTNVPIYLKLTPNVTD------ITQISKAAEKGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I I  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMDIDIKTRKPVLGHNIGGLS---GEAVKPVALRMVHQVRQSTSLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            GG+      +K +L   + V +G A +K+S     + +   N L
Sbjct: 246 -GGISSAQDVIKFMLAGANAVAVGTAHFKDSIASKHIADELPNEL 289


>gi|153828105|ref|ZP_01980772.1| conserved hypothetical protein [Vibrio cholerae 623-39]
 gi|148876347|gb|EDL74482.1| conserved hypothetical protein [Vibrio cholerae 623-39]
          Length = 323

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A   A+   IPV+ K R+G +D  P      +V ++ ++  + + +HAR
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED--PEDCF-EIVDAVAQAKADELTVHAR 170


>gi|121604209|ref|YP_981538.1| dihydrouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593178|gb|ABM36617.1| tRNA-U20a,U20b-dihydrouridine synthase [Polaromonas
           naphthalenivorans CJ2]
          Length = 318

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 36/110 (32%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   L E A  + + G   I+LN GCP+  V+    GA L+  P+ V   +
Sbjct: 63  PVRAQLLGSDPVCLAENAGRLAELGPAGIDLNFGCPAKIVNRHGGGAALLDEPETVFAIV 122

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           AA+ +A+   +PV+ K R+G +D   AV       +I  +G + + +HAR
Sbjct: 123 AAVRRAVPNHMPVSAKMRLGFNDDSRAV---ECALAIAGAGADELVVHAR 169


>gi|149200474|ref|ZP_01877488.1| dihydrouridine synthase family protein [Lentisphaera araneosa
           HTCC2155]
 gi|149136436|gb|EDM24875.1| dihydrouridine synthase family protein [Lentisphaera araneosa
           HTCC2155]
          Length = 334

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 57/228 (25%), Positives = 99/228 (43%), Gaps = 27/228 (11%)

Query: 18  NNALLYTEMIVADAILR--GDKKNILGF--STQEKPL--------ALQIGGADISKLVEA 65
           N  ++++E I  D +    G  K I  F  S +E+ L          Q+ G +  K  EA
Sbjct: 38  NLQVVFSEFISTDGLCHPIGHDKVIHRFLISDEERKLLKEKNIKIVAQVWGKNPDKFSEA 97

Query: 66  -AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
            +K V+   ++ +++N+GCP A++ +    + L+  P+I  + + A   A  +PV+VK R
Sbjct: 98  ISKYVDPEVFDGVDINMGCPVAKIVKQGGCSALINTPEIAKELVLAAKAATKLPVSVKTR 157

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEI 182
            G    I A      +  + +     I +H R  K   +GL+  D         D     
Sbjct: 158 TG----ITAHKTEEWMTHLLEVEPAAIILHGRTQKQQSEGLASWDEIAKGARVRD----- 208

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            +  P +    NG +  + QA ++     +DG MIGR  + N  +  T
Sbjct: 209 -RLKPHIPFWGNGDVRSIEQAHQLCQEHKLDGAMIGRGVFHNPWIFNT 255


>gi|311248426|ref|XP_003123132.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Sus scrofa]
 gi|311248450|ref|XP_003123140.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Sus scrofa]
          Length = 652

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 68/283 (24%), Positives = 119/283 (42%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 337 EMAVCTNLLQGQTSEWALLKRHPCEDVFGVQLEGAFPDTMTKCAELLNRTIEVDF----V 392

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 393 DINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 451

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGG 196
            L+  ++  G   + +H R         ++ R     D+  + + +   +P    G NG 
Sbjct: 452 -LLPELRDWGAALVTLHGRS--------REQRYTKLADWQYIEQCVTAASPMPLFG-NGD 501

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +   ED ++A+K    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 502 ILSYEDANRAMKT--GVAGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 550

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 551 -ILRDFTHYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 588


>gi|71278711|ref|YP_267655.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
 gi|71144451|gb|AAZ24924.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
          Length = 310

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 67/119 (56%), Gaps = 6/119 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     + E A  V + G + I+LN GCPS  V++   G+ L+ +P+ +   I
Sbjct: 68  PVRVQLLGQYPEYMAENAAKVIELGSSGIDLNFGCPSKTVNKSRGGSILLKDPENLYQII 127

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A+ +A+     V+ K R+G +D+   +A+ N  ++++ +G N + IHAR   L+G  P
Sbjct: 128 KAVKEAVPSDTIVSAKIRLGYEDK--TLAIEN-GQAVEAAGANELTIHARTK-LEGYKP 182


>gi|255710875|ref|XP_002551721.1| KLTH0A06028p [Lachancea thermotolerans]
 gi|238933098|emb|CAR21279.1| KLTH0A06028p [Lachancea thermotolerans]
          Length = 397

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 95/190 (50%), Gaps = 26/190 (13%)

Query: 50  LALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDC 107
           L  Q+G +  S  VEAA +V +D   + I++N GCP    +H G  GA L+  P+ +   
Sbjct: 85  LIFQMGTSTPSLAVEAAMVVIKDV--DGIDVNAGCPKHFSIHSG-MGAALLKTPETLCSI 141

Query: 108 IAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           ++++ + +      P++VK RI   +++      NLVK +  +G++ + +H R       
Sbjct: 142 LSSLVEKVGRPHEKPISVKIRILDSEELTL----NLVKKLCGTGISNLTVHCR------T 191

Query: 164 SPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDGVMIGR 217
           +P  NR+ P  +Y   +Y+I + N ++ + +NG ++ +    ++     LP   G M+  
Sbjct: 192 TPMRNRQAPIRNYVPSIYKICQAN-NVSLIMNGAIQSLEHFRQLRKQMDLPETIGGMMAD 250

Query: 218 AAYKNSAMLT 227
            A  N  + +
Sbjct: 251 CAEANPTVFS 260


>gi|298710301|emb|CBJ31922.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 743

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 79/168 (47%), Gaps = 22/168 (13%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F R++ +     T  EM ++  +L+G+     +L     E    +Q+ GA   ++   A+
Sbjct: 370 FRRVMKDQGADITCGEMALSHHLLKGNGSEWALLRRHPSEDVFGVQVAGAHPDQMTRVAE 429

Query: 68  IVE-----DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           ++E     DF    +++N+GCP   V +   GA LM     +   IA M   L+ P+TVK
Sbjct: 430 LLEKNAKMDF----VDINMGCPIDLVCDKGMGAALMGRSRKLRGIIAGMSSQLTCPLTVK 485

Query: 123 CRIGVDDQIPA--VALRNLVKS---IKKSGVNG----IWIHARKAILK 161
            R+G D++ P   V +R + +     +K G  G    + IH R  + +
Sbjct: 486 MRVGWDEKKPNADVVVRTVQREADRCRKRGFPGSVARVMIHGRSRLQR 533


>gi|218883785|ref|YP_002428167.1| dihydroorotate dehydrogenase 1B [Desulfurococcus kamchatkensis
           1221n]
 gi|218765401|gb|ACL10800.1| Dihydroorotate dehydrogenase, PyrD [Desulfurococcus kamchatkensis
           1221n]
          Length = 302

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 88/200 (44%), Gaps = 28/200 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           KPL L IGG+ + + V+ A++  + G + + LN+ CP A  +    G+  ML   IV D 
Sbjct: 95  KPLILSIGGSSVEEFVKLAELASEAGVDAVELNLSCPHAEGYGLELGSDPMLVYRIVKDA 154

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI---------PAVALRNLVKSIKKSGVNGIWIHARKA 158
           ++      S+PV  K  +G+ D++           V    L+ ++K   ++   ++  K 
Sbjct: 155 VSVA----SLPVIAK--LGLTDRVIESAGKALEAGVKALTLINTVKAMSID---VYTLKP 205

Query: 159 ILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           +L     GLS      I  +   +VY++ +E     IG+ G    M  A  IL     V 
Sbjct: 206 VLSNKYGGLS---GPPIHPIAVRVVYDVYREYRAEIIGVGGVSSWMDVAELILAGARAVQ 262

Query: 215 IGRAAYKNSAMLTTVDEYFS 234
           +G A   N      VDE  S
Sbjct: 263 VGTALIWNE---NIVDEILS 279


>gi|327480372|gb|AEA83682.1| NifR3/Smm1 family protein [Pseudomonas stutzeri DSM 4166]
          Length = 324

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 84/174 (48%), Gaps = 18/174 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++    
Sbjct: 64  PVRVQLLGSDPICLADNAAFACTLGAPAIDLNFGCPAKTVNKSRGGAVLLKEPELLH--- 120

Query: 109 AAMCKALS-----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           A +C+  S     IPVT K R+G D   P  AL +  +++   G   + +HAR  + +G 
Sbjct: 121 AILCEVRSAVPAHIPVTAKMRLGFDS--PDGAL-DCARALVAGGAEQLVVHARTKV-EGY 176

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
            P  + +      +IV      N D++      LED  +  ++  + D +M+GR
Sbjct: 177 KPPAHWEWVARVQEIVPVPVYANGDIW-----SLEDWRRCREVSGAED-IMLGR 224


>gi|261210733|ref|ZP_05925025.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC341]
 gi|260840218|gb|EEX66798.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC341]
          Length = 323

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 31/110 (28%), Positives = 61/110 (55%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G + I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A  +A+   IPV+ K R+G ++  P      +V ++ ++  + + +HAR
Sbjct: 124 KACREAVPAHIPVSAKIRLGWEN--PEDCFE-IVDAVAQAKADELTVHAR 170


>gi|332653747|ref|ZP_08419491.1| dihydrouridine synthase family protein [Ruminococcaceae bacterium
           D16]
 gi|332516833|gb|EGJ46438.1| dihydrouridine synthase family protein [Ruminococcaceae bacterium
           D16]
          Length = 317

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 43/176 (24%), Positives = 77/176 (43%), Gaps = 15/176 (8%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   ++   + AA  +   GY+E+NLN+GCPS  V     GA L+   D + + +  + 
Sbjct: 57  QLLTRNVEDFLWAAGELAAMGYDEVNLNLGCPSGTVTAKGKGAGLLQRRDTLEELLEGIF 116

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + +++K R+G +D    V    L++   +  V+ + IH R         + +    
Sbjct: 117 AKTPVKLSIKTRLGWED---PVEFGPLLELFSRYPVSLLIIHPRV--------RQDFYRE 165

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAM 225
            +  D   +  +  P   +  NGGL   ED        P V+ VMIG+    + A+
Sbjct: 166 KVRLDAFAQALEVYPGP-VCFNGGLVTPEDCKAFHARFPQVEHVMIGQGLLADPAL 220


>gi|6323437|ref|NP_013509.1| Dus4p [Saccharomyces cerevisiae S288c]
 gi|2833204|sp|Q06063|DUS4_YEAST RecName: Full=tRNA-dihydrouridine synthase 4
 gi|625099|gb|AAB82341.1| Ylr405wp [Saccharomyces cerevisiae]
 gi|45271062|gb|AAS56912.1| YLR405W [Saccharomyces cerevisiae]
 gi|285813808|tpg|DAA09704.1| TPA: Dus4p [Saccharomyces cerevisiae S288c]
          Length = 367

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 103/229 (44%), Gaps = 12/229 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I   ST  ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L++  ++V  +  + I +N GCP   ++ EG  G  L+ N D++   + A+      
Sbjct: 105 VADLLKFVEMVAPYC-DGIGINCGCPIKEQIREG-IGCALIYNSDLLCSMVHAVKDKYGD 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I + + +       L + +  +GV+ I IH R    +   P +   +  + Y 
Sbjct: 163 KLRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRTRRTRSSQPAN---LDAIKYI 217

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           I     K  P +  G    L D+ +  K      GVM  R    N A+ 
Sbjct: 218 IENISDKNVPVIANGDCFKLSDLERITK-YTGAHGVMAVRGLLSNPALF 265


>gi|325116870|emb|CBZ52423.1| dihydrouridine synthase domain-containing protein [Neospora caninum
           Liverpool]
          Length = 568

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 97/243 (39%), Gaps = 44/243 (18%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G     L+ AA++VED   + ++LN GCP      G +GA L+   +++ D ++ + K 
Sbjct: 174 AGDSPETLLAAAQLVED-EVDAVDLNFGCPQGIARRGHYGAFLLHESELLIDIVSTLHKH 232

Query: 115 LSIPVTVKCR----------------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-- 156
           L  PVT K R                + +D++        L  + + +G   + IH R  
Sbjct: 233 LRTPVTCKMRKVSPRPTAALPRSTTALVLDEERRLQDTLRLCDAFEAAGCACLCIHGRTK 292

Query: 157 --KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDG 212
             KA L G  P D   I +          KE   + +  NGG+E    AL+ L     D 
Sbjct: 293 EEKASLVG--PCDWLAIRH---------AKERLSIPVIANGGVETYEDALRCLEFTGADA 341

Query: 213 VMIGRAAYKNSAMLT-------TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           VM       N  +         +V    S  L   SP+ +   +D  R+    ++  A R
Sbjct: 342 VMSAEGLLDNPLLFAPSRFAAPSVYALLSPSLFALSPLLSSSWRDHLRR---RLSLPARR 398

Query: 266 HLH 268
           HLH
Sbjct: 399 HLH 401


>gi|323303732|gb|EGA57518.1| Dus4p [Saccharomyces cerevisiae FostersB]
 gi|323307899|gb|EGA61159.1| Dus4p [Saccharomyces cerevisiae FostersO]
          Length = 367

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 103/229 (44%), Gaps = 12/229 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I   ST  ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L++  ++V  +  + I +N GCP   ++ EG  G  L+ N D++   + A+      
Sbjct: 105 VADLLKFVEMVAPYC-DGIGINCGCPIKEQIREG-IGCALIYNSDLLCSMVHAVKDKYGD 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I + + +       L + +  +GV+ I IH R    +   P +   +  + Y 
Sbjct: 163 KLRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRTRRTRSSQPAN---LDAIKYI 217

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           I     K  P +  G    L D+ +  K      GVM  R    N A+ 
Sbjct: 218 IENISDKNVPVIANGDCFKLSDLERITK-YTGAHGVMAVRGLLSNPALF 265


>gi|317153973|ref|YP_004122021.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
 gi|316944224|gb|ADU63275.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
          Length = 339

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 94/230 (40%), Gaps = 20/230 (8%)

Query: 20  ALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           A+  +EM+    +  G++  + ++    ++ P+ LQ+ GAD          + D GY   
Sbjct: 34  AVACSEMVSVKGMTFGNEGTQRLIATCPEDDPMVLQLFGADPDLFGPVMDWLVDLGYRNF 93

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-----ALSIPVTVKCRIGVDDQIP 132
           +LN GCP  +V +   G  LM +PD +    + M +     A    V VK R+G D    
Sbjct: 94  DLNAGCPVRKVLKSGSGVKLMEDPDTLVRIASVMVERATAHARGGQVGVKFRLGFDKGND 153

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 L + ++ +GV+ + +H R          D  K+  L   +   +     DLF  
Sbjct: 154 TYL--ELARRLEDAGVHWVTLHPRYGRQMFAGQADWSKLGLLKRAVSIPVVASG-DLFTA 210

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                ED  + ++    VD VM  R A  + A+     + +   L G  P
Sbjct: 211 -----EDGVRCVEET-GVDAVMFARGALYDPAIF----DRYRTLLAGGQP 250


>gi|151940924|gb|EDN59306.1| dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|256269148|gb|EEU04483.1| Dus4p [Saccharomyces cerevisiae JAY291]
          Length = 367

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 103/229 (44%), Gaps = 12/229 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I   ST  ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L++  ++V  +  + I +N GCP   ++ EG  G  L+ N D++   + A+      
Sbjct: 105 VADLLKFVEMVAPYC-DGIGINCGCPIKEQIREG-IGCALIYNSDLLCSMVHAVKDKYGD 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I + + +       L + +  +GV+ I IH R    +   P +   +  + Y 
Sbjct: 163 KLRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRTRRTRSSQPAN---LDAIKYI 217

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           I     K  P +  G    L D+ +  K      GVM  R    N A+ 
Sbjct: 218 IENISDKNVPVIANGDCFKLSDLERITK-YTGAHGVMAVRGLLSNPALF 265


>gi|78355436|ref|YP_386885.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
 gi|78217841|gb|ABB37190.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 378

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 111/244 (45%), Gaps = 21/244 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           +  +TD  +R   R      ++ +EM+ A  ++        +L    Q+ P+ LQ+ G +
Sbjct: 49  LAGFTDLAFRLLCREFGAR-VVCSEMVSAKGLVYRSPGTHALLETCPQDAPMVLQLFGNE 107

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSI 117
           +  +  A + + D GY   +LN+GC   +V +   GA ++ + P+ V    A    A + 
Sbjct: 108 VPIMDAAMRELVDKGYRWFDLNMGCSVRKVVKTGCGAGMLRDVPNAVRVARAMTAVAGAG 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V  K R+G +    A    +L + ++ +G   + +H R A  +G S          D+D
Sbjct: 168 RVGFKFRLGWEQG--AQVCMDLARRLEDAGAGWLTLHPRFA-RQGFS-------GTADWD 217

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KE+  + +  +G L     A++ + +  VDGVM  R A  N A+     E FS 
Sbjct: 218 ALARL-KEHVTIPVIASGDLFTAGDAVRCMRASGVDGVMFARGALANPAVF----EDFSA 272

Query: 236 PLTG 239
            ++G
Sbjct: 273 MMSG 276


>gi|190405444|gb|EDV08711.1| dihydrouridine synthase 4 [Saccharomyces cerevisiae RM11-1a]
 gi|259148383|emb|CAY81630.1| Dus4p [Saccharomyces cerevisiae EC1118]
 gi|323332436|gb|EGA73845.1| Dus4p [Saccharomyces cerevisiae AWRI796]
 gi|323336419|gb|EGA77687.1| Dus4p [Saccharomyces cerevisiae Vin13]
 gi|323347323|gb|EGA81596.1| Dus4p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 367

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 103/229 (44%), Gaps = 12/229 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I   ST  ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L++  ++V  +  + I +N GCP   ++ EG  G  L+ N D++   + A+      
Sbjct: 105 VADLLKFVEMVAPYC-DGIGINCGCPIKEQIREG-IGCALIYNSDLLCSMVHAVKDKYGD 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + ++ +I + + +       L + +  +GV+ I IH R    +   P +   +  + Y 
Sbjct: 163 KLRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRTRRTRSSQPAN---LDAIKYI 217

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           I     K  P +  G    L D+ +  K      GVM  R    N A+ 
Sbjct: 218 IENISDKNVPVIANGDCFKLSDLERITK-YTGAHGVMAVRGLLSNPALF 265


>gi|164659486|ref|XP_001730867.1| hypothetical protein MGL_1866 [Malassezia globosa CBS 7966]
 gi|159104765|gb|EDP43653.1| hypothetical protein MGL_1866 [Malassezia globosa CBS 7966]
          Length = 212

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 63/122 (51%), Gaps = 7/122 (5%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           ++N    + +  P  +Q+ G D  + V+AA+       + I+LN+GCP AR  +G +G  
Sbjct: 72  RENCDIVTGERAPQIVQLAGDDPEQFVQAARRFLPIA-DAIDLNLGCPQARARDGHYGGY 130

Query: 97  LMLNPD--IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           L+   +  ++   + A+CK+  +P+T K R+  D    A     L + +  +G + I +H
Sbjct: 131 LLKRREWPLLERIVQALCKSCDVPITTKIRL-CD---TASDTYELGQRLALAGSSVITLH 186

Query: 155 AR 156
           AR
Sbjct: 187 AR 188


>gi|300361819|ref|ZP_07057996.1| dihydroorotate oxidase [Lactobacillus gasseri JV-V03]
 gi|300354438|gb|EFJ70309.1| dihydroorotate oxidase [Lactobacillus gasseri JV-V03]
          Length = 307

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 99/225 (44%), Gaps = 32/225 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA+++ DK   L  S    P+   +GG D +  VE A+ + D G  N + +NV CP+   
Sbjct: 80  DAVIK-DKLAPLRQSYPALPIMASVGGEDEAGYVEVAQKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V      +    ++P+ VK    V D I       + K+ +K G 
Sbjct: 139 GGMSFG----VHPDVVESLTKKIKAVTNVPIYVKLTPNVTDII------QIAKAAEKGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I I  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMDIDIKTRKPVLGHNVGGLS---GEAVKPVALRMVHQVRQSTSLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            GG+      +K +L   + V +G A +K+S     + +   N L
Sbjct: 246 -GGISSAQDVIKFMLAGANAVAVGTAHFKDSIASKHIADELPNEL 289


>gi|304313177|ref|YP_003812775.1| Dihydrouridine synthase [gamma proteobacterium HdN1]
 gi|301798910|emb|CBL47146.1| Dihydrouridine synthase [gamma proteobacterium HdN1]
          Length = 313

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 56/110 (50%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q  G+D   L   A      G  EI+LN GCP+  V+    GA L+  P+++   +
Sbjct: 71  PLHVQFLGSDPEFLAANAVRAAKLGAKEIDLNFGCPAKAVNRHRGGAVLLEEPELLNTIV 130

Query: 109 AAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A+  A+  P  VT K R+G  D+     + +  +++ ++G   I +HAR
Sbjct: 131 TAVRAAVPEPIKVTAKMRLGYLDK---SLMLDCARALDEAGAARIVVHAR 177


>gi|139439601|ref|ZP_01773014.1| Hypothetical protein COLAER_02041 [Collinsella aerofaciens ATCC
           25986]
 gi|133774942|gb|EBA38762.1| Hypothetical protein COLAER_02041 [Collinsella aerofaciens ATCC
           25986]
          Length = 347

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 61/131 (46%), Gaps = 6/131 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R    N L Y+EM+    +     K   ++  + +E+ + +Q+ G+ 
Sbjct: 24  MAGVTDPAYRIMCRRRGAN-LAYSEMVSVAGLAYASNKTWRLVLPADEEQQICVQLFGSK 82

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A   VE+   +    I++N+ CP+ +V     G+ LM  PD+    + A   A 
Sbjct: 83  PEQFASAVAAVEERVGDRLSLIDINMACPARKVVTKGEGSALMRTPDLAEKIVEAAVGAA 142

Query: 116 SIPVTVKCRIG 126
            +PVTVK R G
Sbjct: 143 HVPVTVKIRKG 153


>gi|313499911|gb|ADR61277.1| TRNA-dihydrouridine synthase C [Pseudomonas putida BIRD-1]
          Length = 323

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 65/274 (23%), Positives = 124/274 (45%), Gaps = 33/274 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + +A+  +IPVT K R+G D   P  AL     ++ + G   + +HAR  + +G  P 
Sbjct: 124 REVRRAVPANIPVTSKMRLGFDS--PDGAL-ECATALAEGGSAHLVVHARTKV-EGYKPP 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + +      D+V      N +++      ++D  +  ++  + D +M+GR       + 
Sbjct: 180 AHWEWVARVQDVVKVPVFANGEIWT-----VDDWRRCREVSGAED-IMLGRGLVSRPDLG 233

Query: 227 TTV----DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----ITR 278
             +    D     P++    +   + ++FWR+  A ++       ++ G+++Q    +TR
Sbjct: 234 LQIAAARDGRDYQPMSWHDLLP--LLREFWRQAQAKLSPR-----YAPGRMKQWLAMLTR 286

Query: 279 ---HMIGLFHGFPNSRRCRHI---LTVEAGASTA 306
                + LF        C  I   L VEA A  A
Sbjct: 287 SYPEAVVLFAELRREDDCARITRLLGVEAQALEA 320


>gi|73987294|ref|XP_542144.2| PREDICTED: similar to dihydrouridine synthase 3-like [Canis
           familiaris]
          Length = 645

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/218 (25%), Positives = 98/218 (44%), Gaps = 28/218 (12%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 330 EMAVCTNLLQGQTSEWALLRRHPCEDVFGVQLEGAFPDTMTKCAELLNRTIEVDF----V 385

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 386 DINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 444

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGG 196
            L+  +++ G   + +H R         ++ R     D+  + + +   +P    G NG 
Sbjct: 445 -LLPELREWGAALVTLHGRS--------REQRYTKLADWQYIEQCVTAASPMPLFG-NGD 494

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   ED ++A++    V GVMI R A     + T + E
Sbjct: 495 ILSYEDANRAMQT--GVAGVMIARGALLKPWLFTEIKE 530


>gi|148548985|ref|YP_001269087.1| dihydrouridine synthase, DuS [Pseudomonas putida F1]
 gi|148513043|gb|ABQ79903.1| dihydrouridine synthase, DuS [Pseudomonas putida F1]
          Length = 323

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 64/119 (53%), Gaps = 6/119 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             + +A+  +IPVT K R+G D   P  AL     ++ + G   + +HAR  + +G  P
Sbjct: 124 REVRRAVPANIPVTSKMRLGFDS--PDGAL-ECATALAEGGSAHLVVHARTKV-EGYKP 178


>gi|221484010|gb|EEE22314.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii GT1]
          Length = 608

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 37  KKNILGFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           +    G  +QE  +P+ +Q  G   + L+ AA++VED     +++N GCP      G +G
Sbjct: 196 RSQWTGDESQEFDEPVFVQFCGDSPATLLAAAQLVED-EVEAVDVNFGCPQGIARRGHYG 254

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           A L+  P+++ D ++ + K L  PVT K R
Sbjct: 255 AFLLNEPELLVDIVSTLHKHLKTPVTCKMR 284


>gi|110003924|emb|CAK98264.1| probable trna-dihydrouridine synthase n-terminal truncated protein
           [Spiroplasma citri]
          Length = 262

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/209 (23%), Positives = 94/209 (44%), Gaps = 22/209 (10%)

Query: 52  LQIGGADISKLVEAAKIVE---DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +QI G DI   V A K V+   D    +IN+    P   +   + G+ L+ +P  V + +
Sbjct: 1   MQIFGTDIETFVAAEKYVDQHSDCDIIDINMGYSAPKIAIKSQA-GSYLLKHPQRVYEVV 59

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+ + ++ PVTVK RIG D++   +    + K  +++G   I +H R         ++ 
Sbjct: 60  KAVVENVTKPVTVKIRIGWDEE--NINCVEIAKYCEQAGAQAIAVHVR--------TRNQ 109

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAML 226
                 D++ + ++ KEN  + +  NG +     A ++L     D +M+ R A  N  + 
Sbjct: 110 FYSGKADWNWIRKV-KENVAIPVIGNGDVFTCEDAERMLKETGCDAIMLARGAQGNPWVF 168

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             +  +     TG    +  +D+  W+ I
Sbjct: 169 KQIQHFLD---TGEKIAQPPLDE--WQNI 192


>gi|315126902|ref|YP_004068905.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas sp. SM9913]
 gi|315015416|gb|ADT68754.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas sp. SM9913]
          Length = 326

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 64/138 (46%), Gaps = 5/138 (3%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G     L E A      G + ++LN GCP+  V++   GA L+ +P
Sbjct: 57  GLTRSGTPVRIQLLGQVADVLAENAVKAIGLGSHGVDLNFGCPAKTVNKSKGGAVLLKDP 116

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           D +   I  +  A+     V+ K R+G DD   +   + +V ++  +G N I IHAR   
Sbjct: 117 DHMYSIIKTVRDAVDDEHEVSAKIRLGFDDDSNS---QEIVDAVVSAGANSIAIHARTKR 173

Query: 160 LKGLSPKDNRKIPNLDYD 177
                P    KIP L  D
Sbjct: 174 DGYNPPAYWEKIPPLVKD 191


>gi|254579030|ref|XP_002495501.1| ZYRO0B12826p [Zygosaccharomyces rouxii]
 gi|238938391|emb|CAR26568.1| ZYRO0B12826p [Zygosaccharomyces rouxii]
          Length = 348

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 106/235 (45%), Gaps = 22/235 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R     +  FST   + PL +Q+G  +
Sbjct: 41  MVRYSKLPFRQVCRQYDTD-IVYTPMILAREFVRNPHARLADFSTNSSDSPLMVQVGTNN 99

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L++  ++V  +  + I +N GCP   +V EG  G  L+ N +++   + A+ +    
Sbjct: 100 VMDLLKFVEMVAPYC-DGIGINCGCPIKEQVREG-IGCALIYNRELLCSMVKAVKEKYGD 157

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++ +I + +         L + +  +GV+ I IH R         K+ R     +++
Sbjct: 158 LVRLETKIRIHEDWDQTV--KLCRDLCSAGVDWITIHGRT--------KNTRSSHTANFE 207

Query: 178 IVYEI-----KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            +  +      K+ P +  G     ED+ +  +I    DGVM  R    N A+ +
Sbjct: 208 AIRYVVDRIRDKQVPVVANGDCLQSEDVQKIAEIT-GADGVMAVRGVLSNPALFS 261


>gi|26988707|ref|NP_744132.1| NifR3/Smm1 family protein [Pseudomonas putida KT2440]
 gi|38604780|sp|Q88LF2|DUSC_PSEPK RecName: Full=tRNA-dihydrouridine synthase C
 gi|24983496|gb|AAN67596.1|AE016389_4 NifR3/Smm1 family protein [Pseudomonas putida KT2440]
          Length = 323

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 64/119 (53%), Gaps = 6/119 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             + +A+  +IPVT K R+G D   P  AL     ++ + G   + +HAR  + +G  P
Sbjct: 124 REVRRAVPANIPVTSKMRLGFDS--PDGAL-ECATALAEGGSAHLVVHARTKV-EGYKP 178


>gi|116192117|ref|XP_001221871.1| hypothetical protein CHGG_05776 [Chaetomium globosum CBS 148.51]
 gi|88181689|gb|EAQ89157.1| hypothetical protein CHGG_05776 [Chaetomium globosum CBS 148.51]
          Length = 464

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/115 (29%), Positives = 55/115 (47%), Gaps = 2/115 (1%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           F ARL + +   Y +          DK  + G    ++P  +Q    D   L+ AAKI  
Sbjct: 74  FHARLFSESQK-YRDQHFQPTKPDCDKLYLDGNPAIDRPFFVQFCANDPQALLNAAKIAA 132

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            +  + ++LN+GCP     +G +G+ L  + D++   I  + + L IPVT K RI
Sbjct: 133 PY-CDAVDLNLGCPQGIAKKGHYGSFLQEDQDLIHQLIKILHENLDIPVTAKIRI 186


>gi|121612695|ref|YP_999847.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|167004818|ref|ZP_02270576.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|87250431|gb|EAQ73389.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81-176]
          Length = 305

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 101/207 (48%), Gaps = 24/207 (11%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ I IH   RK +  G +          DY+ +    K +  + +  NG +
Sbjct: 152 AKICESLGVDFISIHGRTRKQLYSGKA----------DYESIASA-KASVSIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKN 222
             ++  +  KI    DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|13542001|ref|NP_111689.1| dihydroorotate dehydrogenase 1B [Thermoplasma volcanium GSS1]
 gi|30173362|sp|Q979G6|PYRD_THEVO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|14325433|dbj|BAB60337.1| dihydroorotate oxidase [Thermoplasma volcanium GSS1]
          Length = 301

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/164 (29%), Positives = 74/164 (45%), Gaps = 22/164 (13%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +E++G + I LN+ CP    H   FG  +  +PD+V D +  +   + +PV  K    V 
Sbjct: 114 MEEYGVDAIELNLSCP----HVKGFGLEVGSDPDLVEDIVNEIKSKVKVPVFAKLSPNVS 169

Query: 129 DQIP---------AVALRNLVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDI 178
           + I          A  L N VK++       I I++R  +L  L        I  +    
Sbjct: 170 NIIEIAKAAEKADAYVLINTVKAM------AIDIYSRSPVLSNLYGGLSGPAIKPVGIRY 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           VYE+KKE     IG+ GG+ +   A++ I+     V IG A YK
Sbjct: 224 VYEVKKETGKEIIGV-GGISNYKDAIEYIMAGASAVQIGTALYK 266


>gi|296421665|ref|XP_002840385.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295636600|emb|CAZ84576.1| unnamed protein product [Tuber melanosporum]
          Length = 386

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 83/180 (46%), Gaps = 11/180 (6%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDCI 108
           L  Q+G A     VEAAKI+       I++N GCP    +H G  GA L+ NPD + D +
Sbjct: 82  LIFQLGTASPELAVEAAKIIVG-DVAGIDVNSGCPKHFSIHSG-MGAALLKNPDKLIDIL 139

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            ++   + +P +V   + +    P      LV+ +  +G++ + +H R   ++   P   
Sbjct: 140 TSLVTEVGVPNSVPISVKIRLLEPHTDTIGLVQRLCTTGISRVTVHCRTIPMRPREP--- 196

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
             I  +  +I     +   + F   NG +   + A +++    VDG MI RAA  N ++ 
Sbjct: 197 -AIRGVLSEIANVCHEAGIECF--ANGDVTSRAHAEELIEKHGVDGCMIARAAETNPSVF 253


>gi|242210427|ref|XP_002471056.1| predicted protein [Postia placenta Mad-698-R]
 gi|220729846|gb|EED83713.1| predicted protein [Postia placenta Mad-698-R]
          Length = 513

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 44/165 (26%), Positives = 74/165 (44%), Gaps = 35/165 (21%)

Query: 21  LLYTEMIVADAILR-GDKKNIL--------------GFSTQ-------------EKPLAL 52
           L+YT MI A A +R     NIL              G+  Q             ++PL +
Sbjct: 38  LVYTPMINAKACMRYAGPHNILLSHHYQMFAEGARKGYRDQNFNITLGEEGGPEDRPLIV 97

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q       +L+++AK+VE +  + +++N+GCP      G +G+ L    D++ + I  + 
Sbjct: 98  QFCANSPEQLLKSAKVVEPY-CDAVDVNLGCPQDIARRGHYGSFLQDEWDLIYELINTLH 156

Query: 113 KALSIPVTVKCRIGVDDQIPAVALR-NLVKSIKKSGVNGIWIHAR 156
           + LSIPVT K R+      P V       K ++++G   +  H R
Sbjct: 157 RNLSIPVTAKFRV-----FPTVEKTVEYAKMLERAGAQILTCHGR 196


>gi|323359853|ref|YP_004226249.1| tRNA-dihydrouridine synthase [Microbacterium testaceum StLB037]
 gi|323276224|dbj|BAJ76369.1| tRNA-dihydrouridine synthase [Microbacterium testaceum StLB037]
          Length = 388

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 66/299 (22%), Positives = 122/299 (40%), Gaps = 27/299 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGDKK-NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI   A++ R D    ++     E P ++Q+ G D
Sbjct: 27  MAGITNTAFRRLCREY-GAGLYVSEMITTRALVERNDTTMRLIRHHESETPRSIQLYGVD 85

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
              +  A +I+ D  + + I+LN GCP  +V     GA L     +  + +    +A   
Sbjct: 86  PGTVEAAVRIIVDEDHADHIDLNFGCPVPKVTRRGGGAALPWKTSLFREIVERAVRAAGE 145

Query: 117 IPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            P+T+K R G+D D +  +    + +    +GV  I +HAR A              + D
Sbjct: 146 KPLTIKMRKGIDADHLTYLEAGRIAEG---AGVASIALHARTA--------SEFYSGHAD 194

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYF 233
           +  + ++K+    + +  NG +     A +++     DGV++GR       +   +    
Sbjct: 195 WSAITKLKETVTSVPVLGNGDIWSADDAARMMAETGCDGVVVGRGCLGRPWLFGDLARAL 254

Query: 234 SNPLTG-SSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             P      P+      V K F R+ +  + ++       G   + I +H+   F G+P
Sbjct: 255 GQPGAAHGEPVDATLGFVAKAF-RRHAELLVEF---FEDEGRGCRDIRKHVAWYFKGYP 309


>gi|226321186|ref|ZP_03796724.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           29805]
 gi|226233406|gb|EEH32149.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           29805]
          Length = 188

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/147 (27%), Positives = 70/147 (47%), Gaps = 16/147 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-- 110
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 111 -MCKALSIPVTVKCRIG-----VDDQI 131
             C   ++P++VK R G     VDD +
Sbjct: 137 EACARFNLPLSVKTRHGFSYPEVDDWL 163


>gi|157131542|ref|XP_001655871.1| tRNA-dihydrouridine synthase [Aedes aegypti]
 gi|108871488|gb|EAT35713.1| tRNA-dihydrouridine synthase [Aedes aegypti]
          Length = 461

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 62/258 (24%), Positives = 112/258 (43%), Gaps = 44/258 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           ++DW         +LL +   +   +   D + + D   I     QE+  + LQ+G A+ 
Sbjct: 41  IIDW---------KLLKSERRVNDVLKTVDYVDKTDGTIIFRTCEQERGKVVLQLGTANA 91

Query: 60  SKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + ++   K+  D     +++N+GCP     +G  G  L+ + +     +  +   LSIP
Sbjct: 92  ERALQVGLKLQGDIA--GLDVNMGCPKDFSIKGGMGVALLYDLERAKGILKTLVDNLSIP 149

Query: 119 VTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           VT K RI   ++D I        V+ ++ +G+  I +H R  + +   P        +  
Sbjct: 150 VTCKIRIMPQLEDTI------RTVQELESTGIAAIAVHGRTKVERPRHP--------VHP 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG-----VMIGRAAYKNSAMLTTVDE 231
           D++ E+ K      I  NGG ++M++   IL   D      VM+ RAA  N ++    DE
Sbjct: 196 DVIREVAKIAKIPVIA-NGGSQEMNKRSDILKFRDACGASSVMVARAAQWNCSIFR--DE 252

Query: 232 YFSNPLTGSSPIKTRVDK 249
                  G  PI+  +D+
Sbjct: 253 -------GPLPIEEIIDR 263


>gi|149028168|gb|EDL83606.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_c
           [Rattus norvegicus]
          Length = 640

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/213 (23%), Positives = 95/213 (44%), Gaps = 18/213 (8%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +   +L+G      +L     E    +Q+ GA    + + A+++      + +++NV
Sbjct: 325 EMAMCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINV 384

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM         +  M + L +P+TVK R GV +++ ++A R L+ 
Sbjct: 385 GCPIDLVYKKGGGCALMNRSAKFQQIVRGMNEVLDVPLTVKMRTGVQERV-SLAHR-LLP 442

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
            ++  GV  + +H R         ++ R     D+  + +  K    + +  NG     E
Sbjct: 443 ELRNWGVALVTLHGRS--------REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFE 494

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D + A++    V G+M+ R A     + T + E
Sbjct: 495 DANCAMQT--GVAGIMVARGALLKPWLFTEIKE 525


>gi|145616686|ref|XP_363722.2| hypothetical protein MGG_01648 [Magnaporthe oryzae 70-15]
 gi|145023291|gb|EDK06730.1| hypothetical protein MGG_01648 [Magnaporthe oryzae 70-15]
          Length = 428

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 84/186 (45%), Gaps = 16/186 (8%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----P 132
           I+LN GCP      G  GA L+ +PD     + A+ +AL   V     IG+  +I     
Sbjct: 128 IDLNAGCPKPFSTTGGMGAALLRDPDR----LVAILEALVREVAPAAEIGISVKIRLLET 183

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A     LV+ + K+G+  + +H R   ++   P++ R I      +V ++ +E   +   
Sbjct: 184 AAETEALVRRLVKTGITALTVHCRTTPMR---PRE-RAIRG-QLRMVADVCREA-GVACL 237

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           +NG ++D  + +++      DG MI RAA +N +      +    P T + P+  R   D
Sbjct: 238 MNGDVKDRDEGVRLAAEYGTDGAMIARAAEENPSCFRAGADGGLAPWTETVPLFMRFCLD 297

Query: 251 FWRKIS 256
              K S
Sbjct: 298 MENKFS 303


>gi|308801569|ref|XP_003078098.1| unnamed protein product [Ostreococcus tauri]
 gi|116056549|emb|CAL52838.1| unnamed protein product [Ostreococcus tauri]
          Length = 343

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/124 (27%), Positives = 62/124 (50%), Gaps = 6/124 (4%)

Query: 36  DKKNILGFST---QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           D K +L F T   +++ L  Q+G +  +  +++A++V       I++N+GCP      G 
Sbjct: 68  DSKGVLTFRTIPEEKERLVFQVGTSSAALALQSAQLVAG-DVAAIDVNMGCPKHFSTSGG 126

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
            GA L+  PD++ D +  + + L     V C+I + +   + A   L K I+  GV+   
Sbjct: 127 MGARLLSQPDLIRDILTTLRRNLPETTHVTCKIRLLECEKSTA--ELAKMIESCGVSAFA 184

Query: 153 IHAR 156
           +H R
Sbjct: 185 VHGR 188


>gi|302818315|ref|XP_002990831.1| hypothetical protein SELMODRAFT_132390 [Selaginella moellendorffii]
 gi|300141392|gb|EFJ08104.1| hypothetical protein SELMODRAFT_132390 [Selaginella moellendorffii]
          Length = 299

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 62/122 (50%), Gaps = 10/122 (8%)

Query: 50  LALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +  Q+G +D  + +  A+++  D     +++N+GCP      G  G+ L+  P++V + +
Sbjct: 82  VVFQMGTSDPYRALTVAQLLCRDIA--AVDINMGCPKPFSVTGGMGSALLSQPELVSEIL 139

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             + + L IPVT K R+    Q        L + I+K+GV+ I +H R+   +   PKD 
Sbjct: 140 TTLRRNLDIPVTCKIRLLKSTQ----ETVELARRIEKTGVSAIAVHGRRIPDR---PKDR 192

Query: 169 RK 170
            K
Sbjct: 193 AK 194


>gi|77917548|ref|NP_001030095.1| tRNA-dihydrouridine synthase 3-like [Rattus norvegicus]
 gi|110808213|sp|Q3KRC5|DUS3L_RAT RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|77415407|gb|AAI05781.1| Dihydrouridine synthase 3-like (S. cerevisiae) [Rattus norvegicus]
          Length = 640

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/213 (23%), Positives = 95/213 (44%), Gaps = 18/213 (8%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +   +L+G      +L     E    +Q+ GA    + + A+++      + +++NV
Sbjct: 325 EMAMCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINV 384

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM         +  M + L +P+TVK R GV +++ ++A R L+ 
Sbjct: 385 GCPIDLVYKKGGGCALMNRSAKFQQIVRGMNEVLDVPLTVKMRTGVQERV-SLAHR-LLP 442

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
            ++  GV  + +H R         ++ R     D+  + +  K    + +  NG     E
Sbjct: 443 ELRNWGVALVTLHGRS--------REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFE 494

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D + A++    V G+M+ R A     + T + E
Sbjct: 495 DANCAMQT--GVAGIMVARGALLKPWLFTEIKE 525


>gi|86151249|ref|ZP_01069464.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           260.94]
 gi|315123725|ref|YP_004065729.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|85841596|gb|EAQ58843.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           260.94]
 gi|315017447|gb|ADT65540.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
          Length = 308

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 100/207 (48%), Gaps = 24/207 (11%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +  D   I N          K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSIHGRTRKQLYSGKT--DYESIANA---------KASVKIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKN 222
             ++  +  KI    DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|156839540|ref|XP_001643460.1| hypothetical protein Kpol_483p21 [Vanderwaltozyma polyspora DSM
           70294]
 gi|187471051|sp|A7TQ73|DUS3_VANPO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|156114071|gb|EDO15602.1| hypothetical protein Kpol_483p21 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 664

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 68/253 (26%), Positives = 106/253 (41%), Gaps = 43/253 (16%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEA 65
           YR   R L  + + Y+EM +A  +++G           ST+     +QI  +   +  +A
Sbjct: 306 YRRLMRKLGAD-VTYSEMALAVPLIQGTNSEWALPKAHSTEIPGFGVQIACSKAWQAAKA 364

Query: 66  AKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVK 122
           A+ +  F    NEINLN GCP   ++    G+ L+ NP  +  C+ AM   + SIP+TVK
Sbjct: 365 AEALAKFTPDINEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSDSIPITVK 424

Query: 123 CRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R G  D  P      LVK  + ++ V  I +H R         +  R     D+D V  
Sbjct: 425 IRTGTRDSHPVAD--TLVKRLVYETDVAAITLHGRS--------RQQRYTRVADWDYVST 474

Query: 182 IKK----------ENPD-----------LFIGLNG---GLEDMSQALKILPSVDGVMIGR 217
           + K          E+ +            F+G NG     ED  + L    ++D +M+ R
Sbjct: 475 VAKSLRESEASFLESAEGKESRESKRRIQFVG-NGDVNNFEDWHRILNNDENIDSIMVAR 533

Query: 218 AAYKNSAMLTTVD 230
            A     +   VD
Sbjct: 534 GALIKPWVFEEVD 546


>gi|221508413|gb|EEE34000.1| tRNA-dihydrouridine synthase, putative [Toxoplasma gondii VEG]
          Length = 1220

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 19/217 (8%)

Query: 24   TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYNEINL 79
            +EM VA +I+ G +   ++L     E    +QI G     L     I+  ED   + I+L
Sbjct: 848  SEMAVAKSIVDGKQSELSLLKRHKSETFFGVQIAGGTPEVLNACTDILASEDVSCDFIDL 907

Query: 80   NVGCPSARVHEG-SFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALR 137
            N  CP  ++H     GAC++ +P  +   + +M  +   +PVTVK R    +Q     L 
Sbjct: 908  NAACPLVQLHRRFKAGACMLDHPKRLESLVESMTTRHPEVPVTVKLRTA--NQGKKQVLH 965

Query: 138  NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNG 195
            + ++ +  +G   + +H R A          R     D+  V + ++  ++    IG   
Sbjct: 966  SFIRRLGDAGAAALIVHGRTA--------QQRYTKAADWSYVAQCREALDSSTPLIGCGD 1017

Query: 196  GLEDMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDE 231
                     ++     DG+MI RAA     + T + E
Sbjct: 1018 IFSSPEFEFRLASGASDGLMIARAALVKPWVFTEISE 1054


>gi|221486656|gb|EEE24917.1| tRNA-dihydrouridine synthase, putative [Toxoplasma gondii GT1]
          Length = 1220

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 19/217 (8%)

Query: 24   TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYNEINL 79
            +EM VA +I+ G +   ++L     E    +QI G     L     I+  ED   + I+L
Sbjct: 848  SEMAVAKSIVDGKQSELSLLKRHKSETFFGVQIAGGTPEVLNACTDILASEDVSCDFIDL 907

Query: 80   NVGCPSARVHEG-SFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALR 137
            N  CP  ++H     GAC++ +P  +   + +M  +   +PVTVK R    +Q     L 
Sbjct: 908  NAACPLVQLHRRFKAGACMLDHPKRLESLVESMTTRHPEVPVTVKLRTA--NQGKKQVLH 965

Query: 138  NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNG 195
            + ++ +  +G   + +H R A          R     D+  V + ++  ++    IG   
Sbjct: 966  SFIRRLGDAGAAALIVHGRTA--------QQRYTKAADWSYVAQCREALDSSTPLIGCGD 1017

Query: 196  GLEDMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDE 231
                     ++     DG+MI RAA     + T + E
Sbjct: 1018 IFSSPEFEFRLASGASDGLMIARAALVKPWVFTEISE 1054


>gi|237834267|ref|XP_002366431.1| hypothetical protein TGME49_028080 [Toxoplasma gondii ME49]
 gi|211964095|gb|EEA99290.1| hypothetical protein TGME49_028080 [Toxoplasma gondii ME49]
          Length = 1220

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 19/217 (8%)

Query: 24   TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYNEINL 79
            +EM VA +I+ G +   ++L     E    +QI G     L     I+  ED   + I+L
Sbjct: 848  SEMAVAKSIVDGKQSELSLLKRHKSETFFGVQIAGGTPEVLNACTDILASEDVSCDFIDL 907

Query: 80   NVGCPSARVHEG-SFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALR 137
            N  CP  ++H     GAC++ +P  +   + +M  +   +PVTVK R    +Q     L 
Sbjct: 908  NAACPLVQLHRRFKAGACMLDHPKRLESLVESMTTRHPEVPVTVKLRTA--NQGKKQVLH 965

Query: 138  NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNG 195
            + ++ +  +G   + +H R A          R     D+  V + ++  ++    IG   
Sbjct: 966  SFIRRLGDAGAAALIVHGRTA--------QQRYTKAADWSYVAQCREALDSSTPLIGCGD 1017

Query: 196  GLEDMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDE 231
                     ++     DG+MI RAA     + T + E
Sbjct: 1018 IFSSPEFEFRLASGASDGLMIARAALVKPWVFTEISE 1054


>gi|148262356|ref|YP_001229062.1| dihydrouridine synthase, DuS [Geobacter uraniireducens Rf4]
 gi|146395856|gb|ABQ24489.1| tRNA-U20a,U20b-dihydrouridine synthase [Geobacter uraniireducens
           Rf4]
          Length = 333

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/228 (24%), Positives = 98/228 (42%), Gaps = 21/228 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
            +DW  R    F   +  NA      + A     GD + I   S    PL +Q+ G    
Sbjct: 44  FIDWV-RPDVVFTEFMRVNAAAPIRRLSA-----GDLREITA-SEGNVPLVVQLIGHGRE 96

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV AA+  +  G   INLN+GCP  R+  G  G  ++  P+ + + I A+ +A+    +
Sbjct: 97  ALVSAAQAAQAAGAVHINLNMGCPYGRMTSGLTGGGMLQRPEDLAEIIPALRRAIDGTFS 156

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G DD      + +L+   + + V+ + +H R  + K             D+ +  
Sbjct: 157 IKLRAGYDDH---GQIFDLLPLFETASVDFLVLHPRTVVQKYGGAA--------DHAVTA 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAML 226
           ++ +    L +  NG +   +  L++L      G+M+GR A  +  + 
Sbjct: 206 QVVRHT-RLPVIANGDIRSAAVGLRVLQETGAAGLMLGRGAIADPLLF 252


>gi|104780807|ref|YP_607305.1| tRNA-dihydrouridine synthase C [Pseudomonas entomophila L48]
 gi|95109794|emb|CAK14499.1| putative tRNA-dihydrouridine synthase C [Pseudomonas entomophila
           L48]
          Length = 323

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 97/215 (45%), Gaps = 29/215 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPVCLAENAVLACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP- 165
             + + +   IPVT K R+G   + P  AL +   ++ + G   + +HAR  + +G  P 
Sbjct: 124 REVRRQVPAHIPVTAKMRLGF--ETPDGAL-DCATALAEGGAEHLVVHARTKV-EGYKPP 179

Query: 166 ---------KDNRKIPNL---------DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                    +D  K+P           D+    E+     D+ +G  G +     AL+I 
Sbjct: 180 AHWEWVARVQDVVKVPVFANGEIWTVDDWRRCREVSGAT-DIMLG-RGLVSRPDLALQIA 237

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            + DGV     A+ +  +L  + E++       SP
Sbjct: 238 AARDGVEYQPMAWDD--LLPLLREFWRQAQDKLSP 270


>gi|332305787|ref|YP_004433638.1| dihydrouridine synthase DuS [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332173116|gb|AEE22370.1| dihydrouridine synthase DuS [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 310

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 2/91 (2%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G +   L E A    + G + ++LN GCP+  V++   GA L+  P
Sbjct: 57  GYTPNGTPVRVQLLGQNPQPLAENAVRAVELGSHGVDLNFGCPAKTVNKSKGGAVLLREP 116

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQ 130
             + D ++A+ +A+     VT K R+G DD+
Sbjct: 117 QTLYDIVSAVRQAVPSEHKVTAKMRLGFDDK 147


>gi|330797093|ref|XP_003286597.1| hypothetical protein DICPUDRAFT_31125 [Dictyostelium purpureum]
 gi|325083422|gb|EGC36875.1| hypothetical protein DICPUDRAFT_31125 [Dictyostelium purpureum]
          Length = 561

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/212 (23%), Positives = 88/212 (41%), Gaps = 16/212 (7%)

Query: 25  EMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   IL G +  +  L     E    +QI G+ +   +  A+ +E +   + +++N 
Sbjct: 244 EMALTTKILEGSRSELALLKKHPCEDKFGIQICGSYVDTAIRCAEFIENEVECDFVDINS 303

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     GA LM  P  V   +  +   LS P T+K RIG  +  P      ++ 
Sbjct: 304 GCPIDMVCNMGAGAALMEKPKKVEQLLKGISSTLSCPTTIKIRIGKLEDAPTA--HKIIP 361

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +   G + + +H R         ++ R     +++ V +  + +    IG NG + +  
Sbjct: 362 FLGDYGASAVTLHGRS--------RNQRYSRLANWEYVKQCSEVSKIPLIG-NGDIYNYR 412

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
             + I  +  V  VM+ R A     + T + E
Sbjct: 413 DVVNIYDTSKVSSVMVARGALIKPWIFTEIKE 444


>gi|323451531|gb|EGB07408.1| hypothetical protein AURANDRAFT_71832 [Aureococcus anophagefferens]
          Length = 557

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 74/165 (44%), Gaps = 14/165 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----VADAILRGDKKNILGFSTQEKPLALQIG 55
           MV  ++  +R   R     A  YT M+     V DA  R      L    +++PL     
Sbjct: 132 MVGGSELAFRLLCRRHGATAA-YTPMMEATRFVEDAAFRA---QYLQTHAEDRPLVAHFC 187

Query: 56  GADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMC 112
           G D   +  A  +    G  + ++LN+GCP      G +G+ LM   + D+V   +AAM 
Sbjct: 188 GNDPGVVGRACALAAATGGVDAVDLNLGCPQRVAFAGHYGSYLMREEDRDLVKSIVAAMR 247

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +++   + V  +I + D  PA     LV+ ++ +G   + IH RK
Sbjct: 248 RSVPREIAVCVKIRLMDDFPATL--KLVEDLRDAGAQVVAIHGRK 290


>gi|259148964|emb|CAY82208.1| Smm1p [Saccharomyces cerevisiae EC1118]
          Length = 384

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/195 (28%), Positives = 91/195 (46%), Gaps = 27/195 (13%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEK----PLALQIGGADISKLVEAA-KIVEDF 72
           N AL   + +V   +    +   L F T  K     L  QIG A  +   +AA K++ D 
Sbjct: 51  NTALQTVDYVVPSKV--QTRPETLVFRTYPKLESSKLIFQIGSASPALATQAALKVINDV 108

Query: 73  GYNEINLNVGCPSA-RVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGV 127
             + I++N GCP    +H G  G+ L+  PD    I+ + +  +    S P++VK R+  
Sbjct: 109 --SGIDINAGCPKHFSIHSG-MGSALLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLN 165

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKEN 186
             Q        LVK +  +G+  + +H RK  ++      NR+ P  DY   +YEI + N
Sbjct: 166 TKQ----DTLQLVKRLCATGITNLTVHCRKTEMR------NREQPITDYIAEIYEICQAN 215

Query: 187 PDLFIGLNGGLEDMS 201
            ++ + +NG + D S
Sbjct: 216 -NVSLIVNGAIRDRS 229


>gi|114799466|ref|YP_760712.1| putative tRNA-dihydrouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114739640|gb|ABI77765.1| putative tRNA-dihydrouridine synthase [Hyphomonas neptunium ATCC
           15444]
          Length = 345

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 82/174 (47%), Gaps = 20/174 (11%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AA 110
           +Q+       ++  A ++ + G + I++N+GCPS +V  G  G+ LM +  + G+ I AA
Sbjct: 80  VQLAARRPEDMLAGAVLMAEAGVDVIDINMGCPSKQVTGGQSGSALMRDLPLAGEIIDAA 139

Query: 111 MCKALSIPVTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  A   PVT+K R+G DD+    P +A+       +  GV  + +H R    +  +   
Sbjct: 140 LQGAAGRPVTLKMRLGWDDENLNAPELAV-----MAQDRGVQMLTVHGRTRC-QFYTGGA 193

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAA 219
           N        D V         L + +NG + D + A + L      GVM+GRAA
Sbjct: 194 NWAAVRATVDAV--------SLPVIVNGDISDTASAREALAQSGAYGVMLGRAA 239


>gi|257075749|ref|ZP_05570110.1| dihydroorotate dehydrogenase 1B [Ferroplasma acidarmanus fer1]
          Length = 298

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 90/189 (47%), Gaps = 28/189 (14%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           ++  KP+   I G    +    A+ ++ +G + + LN+ CP    H   +G  +  +P++
Sbjct: 87  TSSGKPVIGSIFGQTPEEFAMLAEKMQAYGASAVELNLSCP----HVKGYGTEIGSDPEL 142

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI-PAVA--------LRNLVKSIKKSGVNGIWIH 154
           V   ++A+   ++IPV  K      D +  A+A        L N +K++K      I I+
Sbjct: 143 VSAIVSAVKSRINIPVYAKLSPNTSDMLGQAIAAGKADGYVLINTIKAMK------IDIN 196

Query: 155 ARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
             KA+L     GLS K  + +  + Y  VYE+KKE     IG+ GG+ +   AL+ I+  
Sbjct: 197 TGKAVLSNIYGGLSGKSIKPV-GIRY--VYEVKKETGKTIIGV-GGINNFEDALEYIMAG 252

Query: 210 VDGVMIGRA 218
              V IG A
Sbjct: 253 ASAVQIGSA 261


>gi|325067270|ref|ZP_08125943.1| dihydrouridine synthase [Actinomyces oris K20]
          Length = 180

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 65/130 (50%), Gaps = 14/130 (10%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGADISKLVEAAKI-VED 71
           LL    L  TEM+   A++  +++ +    T   E+  ++Q+ G D + +  A +I VE+
Sbjct: 46  LLAPAGLYVTEMVTTRALVERNERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEE 105

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD-----------CIAAMCKALSIPVT 120
              + I+LN GCP  +V     GA L    D++              + A+ +A  +PVT
Sbjct: 106 DLADHIDLNFGCPVPKVTRKGGGAALPWKRDLLAAILTEAVRASEAAVRAVGRARQVPVT 165

Query: 121 VKCRIGVDDQ 130
           +K R+G+D++
Sbjct: 166 MKMRLGIDEE 175


>gi|321251331|ref|XP_003192028.1| hypothetical protein CGB_B2580W [Cryptococcus gattii WM276]
 gi|317458496|gb|ADV20241.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 408

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/183 (24%), Positives = 81/183 (44%), Gaps = 12/183 (6%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI- 108
           L  Q    +   L +AA+++  +  + I+LN GCP    +    G  L+  P++V D + 
Sbjct: 152 LIAQFASPNAKSLADAAELISPY-VDGIDLNCGCPQRWAYNEGIGCALLRKPELVRDMVR 210

Query: 109 -AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            A        PV++K RI  + +        L+ +  ++G++ + IH R        P +
Sbjct: 211 GAKDRMGWGWPVSIKIRIDSEQK----NTEQLISNALQAGISHLTIHGRTRHQPSTDPVN 266

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              +P + +  V  +K + P +  G    LED ++ +++   V GVM  R    N A+  
Sbjct: 267 ---LPGIKF-AVECVKGQVPCVANGDVWELED-ARRMRLQTGVQGVMAARGLLANPALFA 321

Query: 228 TVD 230
             D
Sbjct: 322 GYD 324


>gi|213023307|ref|ZP_03337754.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 213

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 35/138 (25%), Positives = 66/138 (47%), Gaps = 12/138 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR-------TKA 192

Query: 167 DNRKIPNLDYDIVYEIKK 184
              +  ++D+  + EI++
Sbjct: 193 QGYRAEHIDWQAIGEIRQ 210


>gi|157377250|ref|YP_001475850.1| nifR3 family TIM-barrel protein [Shewanella sediminis HAW-EB3]
 gi|157319624|gb|ABV38722.1| putative TIM-barrel protein, nifR3 family [Shewanella sediminis
           HAW-EB3]
          Length = 322

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 80/329 (24%), Positives = 139/329 (42%), Gaps = 36/329 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDK-KNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    A+  +EM+ ++  +   DK +  +  + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLC-LRYGAAMAVSEMLSSNPDVWDTDKSRQRMSHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V+    G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNRKLAGSALLQDPVQVKAILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + +H   R+ + KG          N
Sbjct: 136 VTLKIRTGW-----APEHRNGVQIAQIAEDCGIASLAVHGRTRQCMYKG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
            +YD +  IKK N  + +  NG +    +A  +L     D +MIGR A     +   +  
Sbjct: 181 AEYDTIKAIKK-NVSIPVVANGDIVTPEKARFVLDQTGADALMIGRGAQGRPWIFREIQH 239

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           Y     TG+      +D+     +      YA   L+   K  +  R  +G +      R
Sbjct: 240 YLE---TGNKLAPVEMDEKRLVMLEHLKNLYA---LYGEYKGIRFARKHVGWYLDQDEQR 293

Query: 292 RCR----HILTVEAGASTATHHIIETAFN 316
             R     + TVE   S    +  E A N
Sbjct: 294 PFRAEFNRLETVEEQGSMVERYFDEIAQN 322


>gi|256273339|gb|EEU08277.1| Smm1p [Saccharomyces cerevisiae JAY291]
          Length = 384

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 94/196 (47%), Gaps = 27/196 (13%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEK----PLALQIGGADISKLVEAA-KIVEDF 72
           N AL   + +V   +    +   L F T  K     L  QIG A  +   +AA K++ D 
Sbjct: 51  NTALQTVDYVVPSKV--QTRPETLVFRTYPKLESSKLIFQIGSASPALATQAALKVINDV 108

Query: 73  GYNEINLNVGCPSA-RVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGV 127
             + I++N GCP    +H G  G+ L+  PD    I+ + +  +    S P++VK R+ +
Sbjct: 109 --SGIDINAGCPKHFSIHSG-MGSALLRTPDTLCLILKELVKNVGNPHSKPISVKIRL-L 164

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKEN 186
           D +   +    LVK +  +G+  + +H RK  ++      NR+ P  DY   +YEI + N
Sbjct: 165 DTKQDTL---QLVKRLCATGITNLTVHCRKTEMR------NREQPITDYIAEIYEICQAN 215

Query: 187 PDLFIGLNGGLEDMSQ 202
            ++ + +NG + D S 
Sbjct: 216 -NVSLIVNGAIRDRSH 230


>gi|255522703|ref|ZP_05389940.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           J1-175]
          Length = 219

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 70/137 (51%), Gaps = 17/137 (12%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           GA  +L+P+ V D +AA+  A+  PVTVK RIG D++    A+ N + + +        +
Sbjct: 1   GAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEE-HVFAIENALAAERAGAAAVA-M 58

Query: 154 HARKAI--LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--S 209
           H R  +   +G          + ++D++ ++K+E    F+  NG +     A +IL    
Sbjct: 59  HGRTRVQMYEG----------SANWDVLRDVKRELKIPFMA-NGDVRTPEDAKRILEHTG 107

Query: 210 VDGVMIGRAAYKNSAML 226
            DGVMIGRAA  N  M+
Sbjct: 108 ADGVMIGRAALGNPWMI 124


>gi|224368002|ref|YP_002602165.1| Dhs1 [Desulfobacterium autotrophicum HRM2]
 gi|223690718|gb|ACN14001.1| Dhs1 [Desulfobacterium autotrophicum HRM2]
          Length = 320

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 40/196 (20%), Positives = 86/196 (43%), Gaps = 17/196 (8%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K++L  +    P+  QI G      +  A+ + D GY  +N N+GCP +++ +   G+ L
Sbjct: 51  KDVLPENNPLLPVVPQILGNVAEDFIFLARYLADKGYTRVNWNLGCPHSKITKKLRGSGL 110

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +  PD++   +  +  A+   ++VK R+G   +  +  + +L+    +  ++ I +H R 
Sbjct: 111 LCRPDLIDAFLEQVVPAIPCSLSVKVRLG---RKTSHEIFDLLPVFDRYPLDEIIVHPRT 167

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL----PSVDGV 213
            +               D D    +  ++  + +  NG + D  +  ++L    P +   
Sbjct: 168 GV--------QLYTGTADIDAFERVLAQSRHILV-YNGDITD-KKGFQVLVDRFPEIRSF 217

Query: 214 MIGRAAYKNSAMLTTV 229
           MIGR    +  +  T+
Sbjct: 218 MIGRGVLADPFLPATI 233


>gi|149372757|ref|ZP_01891778.1| hypothetical protein SCB49_12379 [unidentified eubacterium SCB49]
 gi|149354454|gb|EDM43019.1| hypothetical protein SCB49_12379 [unidentified eubacterium SCB49]
          Length = 317

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/237 (21%), Positives = 95/237 (40%), Gaps = 44/237 (18%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+  AD    +   K ++  GY E+N N+GCP   V +   G+ L+ N   +   + 
Sbjct: 63  LIPQVMTADADHFIFVIKYIQSLGYKELNWNLGCPYPMVTKSGMGSGLICNTTQIDHILD 122

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILK-GLSPK 166
                  + +++K R+G +     V      K + K  +  I IHAR  K + K G+  +
Sbjct: 123 RAHSETDVTISMKMRLGYESSSEIV---ESFKILDKYPIKNIAIHARLGKQLYKGGVDLE 179

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNS 223
             +K  ++    +Y             NG +  ++Q   +    PS++  MIGR    + 
Sbjct: 180 AFQKCIDVAKHTLY------------YNGDITSVAQFKAMQERFPSIEHFMIGRGLIADP 227

Query: 224 AMLT----------------------TVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            + +                      T+ + + + L+G +PIK ++   FW   S S
Sbjct: 228 FLPSMIKADTNQYPENRWEIFREFHDTIYQQYDSMLSGPTPIKMKM-LGFWEFFSQS 283


>gi|6324342|ref|NP_014412.1| Smm1p [Saccharomyces cerevisiae S288c]
 gi|1730664|sp|P53720|DUS2_YEAST RecName: Full=tRNA-dihydrouridine synthase 2; AltName: Full=Protein
           SMM1
 gi|1302496|emb|CAA96293.1| SMM1 [Saccharomyces cerevisiae]
 gi|1616627|emb|CAA62924.1| SMM1 protein [Saccharomyces cerevisiae]
 gi|151944543|gb|EDN62821.1| tRNA dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190408986|gb|EDV12251.1| tRNA-dihydrouridine synthase 2 [Saccharomyces cerevisiae RM11-1a]
 gi|207341587|gb|EDZ69599.1| YNR015Wp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|285814662|tpg|DAA10556.1| TPA: Smm1p [Saccharomyces cerevisiae S288c]
          Length = 384

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 94/196 (47%), Gaps = 27/196 (13%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEK----PLALQIGGADISKLVEAA-KIVEDF 72
           N AL   + +V   +    +   L F T  K     L  QIG A  +   +AA K++ D 
Sbjct: 51  NTALQTVDYVVPSKV--QTRPETLVFRTYPKLESSKLIFQIGSASPALATQAALKVINDV 108

Query: 73  GYNEINLNVGCPSA-RVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGV 127
             + I++N GCP    +H G  G+ L+  PD    I+ + +  +    S P++VK R+ +
Sbjct: 109 --SGIDINAGCPKHFSIHSG-MGSALLRTPDTLCLILKELVKNVGNPHSKPISVKIRL-L 164

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKEN 186
           D +   +    LVK +  +G+  + +H RK  ++      NR+ P  DY   +YEI + N
Sbjct: 165 DTKQDTL---QLVKRLCATGITNLTVHCRKTEMR------NREQPITDYIAEIYEICQAN 215

Query: 187 PDLFIGLNGGLEDMSQ 202
            ++ + +NG + D S 
Sbjct: 216 -NVSLIVNGAIRDRSH 230


>gi|291087414|ref|ZP_06571931.1| dihydrouridine synthase family protein [Clostridium sp. M62/1]
 gi|291075096|gb|EFE12460.1| dihydrouridine synthase family protein [Clostridium sp. M62/1]
          Length = 319

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/257 (21%), Positives = 107/257 (41%), Gaps = 41/257 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-----EGSFGACLMLNPDIV 104
           L  QI   D      A + + + GY E+NLN+GCPS  V       G   A L    +  
Sbjct: 54  LVPQILTNDAEAFCSAMRGLWELGYREVNLNLGCPSGTVAAKGKGSGFLAAQLRERLECF 113

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            D I    + + + V++K R+G +    +     L++   +  ++ + IH R      + 
Sbjct: 114 LDEIFDCAENMGMRVSIKTRLGKES---SEGFEELLELYLRFPLSELIIHPR------VQ 164

Query: 165 PKDNRKIPNLDYDIVYEIKKE---------NPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
               +  P+ +    + + KE         N D+F       E++S+     P  + VM+
Sbjct: 165 TDFYKNTPHWE---AFRLAKERACGVKLCYNGDIFTP-----EELSRFRAEFPETECVML 216

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           GR    N  +   ++       TG +P+  +  +DF   +     +  + + ++  K+++
Sbjct: 217 GRGVIANPGLAEWME-------TGKNPLDEKRFRDFHEDLLNGYREVMSGNRNTLFKMKE 269

Query: 276 ITRHMIGLFHGFPNSRR 292
           +  +M+ L   FP+S +
Sbjct: 270 LWTYMLTL---FPDSEK 283


>gi|212722480|ref|NP_001132459.1| hypothetical protein LOC100193915 [Zea mays]
 gi|194694448|gb|ACF81308.1| unknown [Zea mays]
          Length = 320

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/143 (27%), Positives = 72/143 (50%), Gaps = 11/143 (7%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGY 74
           +TN +L  T     D + +G    +     QE+  +  Q+G ++  + ++AA+IV     
Sbjct: 48  VTNESLGTT-----DFVEKGTDSVVFRTCPQERGRVVFQMGTSNAVRALKAAQIVCR-DV 101

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
           + I++N+GCP +    G  GA L+  P+++ D +  + + L   VT K R+      P  
Sbjct: 102 SAIDINMGCPKSFSLSGGMGAALLSKPELIHDILTTLRRNLDTTVTCKIRLL---NTPKD 158

Query: 135 ALRNLVKSIKKSGVNGIWIHARK 157
            +  L + I+K+GV  + +H RK
Sbjct: 159 TV-ELARRIEKTGVPALAVHGRK 180


>gi|157414436|ref|YP_001481692.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81116]
 gi|157385400|gb|ABV51715.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81116]
 gi|307747080|gb|ADN90350.1| Probable tRNA-dihydrouridine synthase [Campylobacter jejuni subsp.
           jejuni M1]
 gi|315931517|gb|EFV10484.1| dihydrouridine synthase (Dus) family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 305

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/207 (25%), Positives = 101/207 (48%), Gaps = 24/207 (11%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +          DY+ +    K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSIHGRTRKQLYSGKA----------DYESIASA-KASVSIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKN 222
             ++  +  KI    DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|86130500|ref|ZP_01049100.1| dihydrouridine synthase [Dokdonia donghaensis MED134]
 gi|85819175|gb|EAQ40334.1| dihydrouridine synthase [Dokdonia donghaensis MED134]
          Length = 315

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/235 (21%), Positives = 96/235 (40%), Gaps = 46/235 (19%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  AD    +   K ++  GY E+N N+GCP   V +   G+ L+ N + +   +    
Sbjct: 66  QVMTADPDDFIFVIKYIQSLGYKELNWNLGCPYPMVTKSGMGSGLICNTEKIDHILDRAH 125

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD--N 168
               + +++K R+G +       + N    ++K  +  + IHAR  K + KG    +   
Sbjct: 126 TETDVTISMKMRLGYES---PEEIINSFPILEKYPLKSVAIHARLGKQLYKGGVDLEGFQ 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAM 225
           + I    + + Y             NG +  ++Q  K+    PS++  MIGR    +  +
Sbjct: 183 KCIDTAKHKLYY-------------NGDITTVAQFRKMRARFPSIEHFMIGRGLIADPFL 229

Query: 226 LTTV-------------------DEYFSN---PLTGSSPIKTRVDKDFWRKISAS 258
            + +                   DE ++     L+G +PIK ++ + FW   + S
Sbjct: 230 PSMIKADTTAYPENRWAIFREFHDEIYTQYDAALSGPTPIKMKM-QGFWEFFAQS 283


>gi|326791078|ref|YP_004308899.1| dihydrouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326541842|gb|ADZ83701.1| dihydrouridine synthase DuS [Clostridium lentocellum DSM 5427]
          Length = 324

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/163 (22%), Positives = 68/163 (41%), Gaps = 15/163 (9%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
           FGY E+NLN+GCPS  V   + G+  +   + +   +  +       +++K RIG +   
Sbjct: 83  FGYEEVNLNLGCPSGTVVSKNKGSGFLAEKEALDQFLEEIFSKAITKISIKTRIGKER-- 140

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                  L+    K  +  + IH R      +     R  PN +    +    +  +  +
Sbjct: 141 -PEEFEELIHIFNKYPLEELIIHPR------VQKDYYRNTPNWE---SFSTGVQLSNNSV 190

Query: 192 GLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           G NG +   +      K  PSVD +M+GR    N  +++ + +
Sbjct: 191 GYNGDIFTAQRYELFAKQFPSVDTIMLGRGLVANPGLISDIKD 233


>gi|57237130|ref|YP_178142.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni RM1221]
 gi|57165934|gb|AAW34713.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni RM1221]
 gi|284925416|gb|ADC27768.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           IA3902]
 gi|315057563|gb|ADT71892.1| tRNA dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           S3]
          Length = 308

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 99/212 (46%), Gaps = 34/212 (16%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKG-------LSPKDNRKIPNLDYDIVYEIKKENPDLF 190
            K  +  GV+ I IH   RK +  G        S K + KIP +           N D+ 
Sbjct: 152 AKICESLGVDFISIHGRTRKQLYSGKADYGSIASAKASVKIPVI----------ANGDI- 200

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
                  ++  +  KI    DG+MIGRA+  N
Sbjct: 201 -----NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|205356497|ref|ZP_03223261.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|205345684|gb|EDZ32323.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8421]
          Length = 308

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 99/212 (46%), Gaps = 34/212 (16%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKG-------LSPKDNRKIPNLDYDIVYEIKKENPDLF 190
            K  +  GV+ I IH   RK +  G        S K + KIP +           N D+ 
Sbjct: 152 AKICESLGVDFISIHGRTRKQLYSGKADYGSIASAKASVKIPVI----------ANGDI- 200

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
                  ++  +  KI    DG+MIGRA+  N
Sbjct: 201 -----NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|86149700|ref|ZP_01067930.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88597178|ref|ZP_01100413.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|218561804|ref|YP_002343583.1| putative tRNA-dihydrouridine synthase [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|85839968|gb|EAQ57227.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88190239|gb|EAQ94213.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|112359510|emb|CAL34294.1| putative tRNA-dihydrouridine synthase [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|315926939|gb|EFV06301.1| dihydrouridine synthase (Dus) family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
          Length = 308

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 99/212 (46%), Gaps = 34/212 (16%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKG-------LSPKDNRKIPNLDYDIVYEIKKENPDLF 190
            K  +  GV+ I IH   RK +  G        S K + KIP +           N D+ 
Sbjct: 152 AKICESLGVDFISIHGRTRKQLYSGKADYGSIASAKASVKIPVI----------ANGDI- 200

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
                  ++  +  KI    DG+MIGRA+  N
Sbjct: 201 -----NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|121705192|ref|XP_001270859.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus clavatus
           NRRL 1]
 gi|119399005|gb|EAW09433.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus clavatus
           NRRL 1]
          Length = 444

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 86/188 (45%), Gaps = 17/188 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     VEAAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LVFQIGTASPELAVEAAKLVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILE 163

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++ + +  P    ++VK RI    +     +R LV     +G+ G+ +H R   ++   P
Sbjct: 164 SLVREVGNPFQIGISVKIRILETPEKTEALVRRLV----ATGITGLTVHCRTTPMR---P 216

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++ R I +    +V  I ++   +   +NG +    +AL ++    VDG MI  AA  N 
Sbjct: 217 RE-RAIRD-QLRMVASICRDA-GVACVMNGDVTSRDEALALMKEFEVDGAMIATAAESNP 273

Query: 224 AMLTTVDE 231
           +   +  E
Sbjct: 274 SCFRSEAE 281


>gi|168702483|ref|ZP_02734760.1| dihydrouridine synthase DuS [Gemmata obscuriglobus UQM 2246]
          Length = 326

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D  ++ E+A    + G   +++N GCP+  V+    GA L+ +P  + + +
Sbjct: 49  PVQVQLLGGDSGRMAESAVRAHELGATAVDVNFGCPAPTVNRHDGGAALLRHPLRIREIV 108

Query: 109 AAMCKALS--IPVTVKCRIGVD 128
            A+  AL   +PV+ K R+G D
Sbjct: 109 GAIRAALPPHVPVSAKLRLGWD 130


>gi|315651846|ref|ZP_07904849.1| dihydrouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315485848|gb|EFU76227.1| dihydrouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 310

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 76/181 (41%), Gaps = 22/181 (12%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI    +    + +  ++  GYNE+N+N+GCPSA V     G+  + +   +      + 
Sbjct: 64  QILTNSVQDFFKLSGEIKQMGYNELNINIGCPSATVTSKGRGSGFLQDTKAIDKFFYEIF 123

Query: 113 -KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            K + I +++K RIG  D        +LVK  +K     I IH R   L+    K+   I
Sbjct: 124 EKTVDIKISIKTRIGFCD---YSEWDDLVKVYEKYNFCEIIIHPR---LRSDFYKNKVYI 177

Query: 172 PN-------LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
           P        L   +VY       D F  LN  L++          VD VMIGR   +N  
Sbjct: 178 PAFIEACKILKSKLVYNGDINTMDDFKILNEQLKE--------NKVDTVMIGRGLVRNPL 229

Query: 225 M 225
           +
Sbjct: 230 L 230


>gi|331083077|ref|ZP_08332194.1| hypothetical protein HMPREF0992_01118 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330405079|gb|EGG84616.1| hypothetical protein HMPREF0992_01118 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 314

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 78/184 (42%), Gaps = 15/184 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI        +  A+ + ++GY E+NLN+GCPS  V     G+  +  P  +   + 
Sbjct: 61  LVPQILTNQAQDFIRLAEELREYGYEEVNLNLGCPSGTVTAKKKGSGFLEFPAQLEKFLD 120

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + + L + ++VK RIG D+         L++   +  +  + +H R   ++    K+  
Sbjct: 121 EVFENLDMKISVKTRIGKDE---PEEFTELLRIYNRFPLEELIVHPR---IQSDYYKNEP 174

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAML 226
           ++      +            +  NG L   ++  K     PS++ VM+GR    N A++
Sbjct: 175 RMEQFQEAVRCSQNS------LCYNGDLFTKARCEKFFEEYPSIEKVMLGRGLLVNPALV 228

Query: 227 TTVD 230
             V 
Sbjct: 229 QQVQ 232


>gi|302854216|ref|XP_002958618.1| hypothetical protein VOLCADRAFT_108215 [Volvox carteri f.
           nagariensis]
 gi|300256079|gb|EFJ40355.1| hypothetical protein VOLCADRAFT_108215 [Volvox carteri f.
           nagariensis]
          Length = 508

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 60/111 (54%), Gaps = 6/111 (5%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL +QI G++   +  AAK +V+  G   ++LN GCP+  V     G+ L+  P ++G  
Sbjct: 148 PLGVQIMGSNPELMGLAAKYLVQVRGAPRVDLNCGCPANTVTGRGAGSSLLRTPHLLGQV 207

Query: 108 IAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +A M + +  + PV+VK R G DD      L + + + +++G   + +H R
Sbjct: 208 VAEMVRQVDGAAPVSVKLRAGFDD---TSLLEDNLLAAQEAGAAFVTLHPR 255


>gi|323335734|gb|EGA77015.1| Smm1p [Saccharomyces cerevisiae Vin13]
          Length = 361

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/195 (28%), Positives = 91/195 (46%), Gaps = 27/195 (13%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEK----PLALQIGGADISKLVEAA-KIVEDF 72
           N AL   + +V   +    +   L F T  K     L  QIG A  +   +AA K++ D 
Sbjct: 28  NTALQTVDYVVPSKV--QTRPETLVFRTYPKLESSKLIFQIGSASPALATQAALKVINDV 85

Query: 73  GYNEINLNVGCPSA-RVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGV 127
             + I++N GCP    +H G  G+ L+  PD    I+ + +  +    S P++VK R+  
Sbjct: 86  --SGIDINAGCPKHFSIHSG-MGSALLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLN 142

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKEN 186
             Q        LVK +  +G+  + +H RK  ++      NR+ P  DY   +YEI + N
Sbjct: 143 TKQ----DTLQLVKRLCATGITNLTVHCRKTEMR------NREQPITDYIAEIYEICQAN 192

Query: 187 PDLFIGLNGGLEDMS 201
            ++ + +NG + D S
Sbjct: 193 -NVSLIVNGAIRDRS 206


>gi|281348023|gb|EFB23607.1| hypothetical protein PANDA_017628 [Ailuropoda melanoleuca]
          Length = 610

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 98/218 (44%), Gaps = 28/218 (12%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 298 EMAVCTNLLQGQTSEWALLRRHPCEDVFGVQLEGAFPDTMTKCAELLNRTIEVDF----V 353

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 354 DINVGCPIDLVYKKGGGCALMNRAAKFQQIVRGMNQVLDVPLTVKIRTGVQERM-NLAHR 412

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGG 196
            L+  ++  G   + +H R         ++ R     D++ + + +   +P    G NG 
Sbjct: 413 -LLPELRDWGAALVTLHGRS--------REQRYTKLADWEYIAQCVTAASPMPLFG-NGD 462

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   ED ++A++    V GVM+ R A     + T + E
Sbjct: 463 ILSYEDANRAMQT--GVAGVMVARGALLKPWLFTEIKE 498


>gi|254282370|ref|ZP_04957338.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR51-B]
 gi|219678573|gb|EED34922.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR51-B]
          Length = 319

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 118/254 (46%), Gaps = 22/254 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R    L    A+  +EMI  D  L   +K  L    S +    ++QI G D
Sbjct: 1   MAGVTDRPFRELC-LDLGAAMAVSEMISDDPELAQSRKTRLRREHSPRAALRSVQIVGND 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA      G + I++N+GCP+ +V + + G+ L+ +  +V   + A+   +S+P
Sbjct: 60  PERMAAAALRNAKDGADIIDINMGCPAKKVCKKAAGSALLGDEALVTAILEAVVSTVSVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           VT+K R G+D      + RN V+  K    +GV  + +H R         + ++   + +
Sbjct: 120 VTLKIRTGLDR-----SRRNGVRIAKIAEDAGVQMLAVHGRT--------RADKFAGDAE 166

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYF 233
           Y  + +I  +   + +  NG +  +++A ++L +    GVMIGR A     +   +    
Sbjct: 167 YHTIEQI-VDAVTIPVLANGDINSITRARRVLETTGAAGVMIGRGAQGQPWLPGMIARAL 225

Query: 234 SNPLTGSSPIKTRV 247
               T +   +T+V
Sbjct: 226 RGQSTAAPSPETQV 239


>gi|163748710|ref|ZP_02155963.1| hypothetical protein KT99_18942 [Shewanella benthica KT99]
 gi|161331820|gb|EDQ02624.1| hypothetical protein KT99_18942 [Shewanella benthica KT99]
          Length = 322

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 51/190 (26%), Positives = 90/190 (47%), Gaps = 23/190 (12%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ++QI GAD   +  AA +    G   I++N+GCP+ +V++   G+ L+ NP+ V   + A
Sbjct: 68  SVQIAGADPELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQNPEQVKAILQA 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSP 165
           +  A+ +PVT+K R G      A   RN   + +  +  G+  + +H   R+ + KG   
Sbjct: 128 VVAAVDVPVTLKIRTGW-----APEHRNGVQIAQIAEDCGIASLAVHGRTRQCMYKG--- 179

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                  + +YD +  I K+N  + +  NG +    +A  +L     D +MIGR A    
Sbjct: 180 -------DAEYDTIKAI-KQNISIPVIANGDIVTPEKARYVLDHTGADALMIGRGAQGRP 231

Query: 224 AMLTTVDEYF 233
            +   +  Y 
Sbjct: 232 WIFREIQHYL 241


>gi|42522835|ref|NP_968215.1| dihydrouridine synthase family protein [Bdellovibrio bacteriovorus
           HD100]
 gi|39574031|emb|CAE79208.1| Dihydrouridine synthase family protein [Bdellovibrio bacteriovorus
           HD100]
          Length = 323

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/223 (24%), Positives = 102/223 (45%), Gaps = 20/223 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L   A+     G   ++LN GCP+  V+    GA L+ + D V + +
Sbjct: 64  PVFVQLLGGQAEPLALNAQRAVKLGALGVDLNFGCPAKTVNRHDGGASLLKSCDRVFNIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             + KA+   +PVT K R+G DD  P   L  + ++++++    + +H R       +  
Sbjct: 124 DTVRKAVPADVPVTAKIRLGFDD--PTKCL-EIAQAVEEANATWLTVHCR-------TKT 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNS 223
           D  K P   +D + +IK++     I  NG    + D ++ +++    D  MIGR    N 
Sbjct: 174 DGYKPPAY-WDWIPKIKEKTKIKLIA-NGEIWNVADFNRCVEVTQCED-YMIGRGVMSNP 230

Query: 224 AMLTTVDEYFS-NPLTGSSPIKTR-VDKDFWRKISASMTDYAA 264
            + + + +  +  P+   S  + R +   F+   +  + DY A
Sbjct: 231 FIFSQIKQSLNQQPVEDMSWERARPLLPQFFESSTLYINDYFA 273


>gi|262165382|ref|ZP_06033119.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM223]
 gi|262025098|gb|EEY43766.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM223]
          Length = 326

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/175 (24%), Positives = 86/175 (49%), Gaps = 15/175 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G + I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPLWMAENAIRAAELGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A  +A+   IPV+ K R+G ++  P      +V ++ ++  + + +HAR       +  
Sbjct: 124 KACREAVPAHIPVSAKIRLGWEN--PEDCFE-IVDAVVQAKADELTVHAR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
              K   + +  + +I+++     I  NG + + +  QA      VD +M+ R A
Sbjct: 174 GGYKASEIKWHYIDQIRQKCSIPLIA-NGEVWNYTDGQACIQTTGVDSLMVCRGA 227


>gi|317177444|dbj|BAJ55233.1| transcriptional regulator [Helicobacter pylori F16]
          Length = 328

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 49/204 (24%), Positives = 100/204 (49%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S+ E    +QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSSLEDHFMVQISGSKESVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ I +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYIVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|148926294|ref|ZP_01809978.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|145844686|gb|EDK21791.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8486]
          Length = 300

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 99/212 (46%), Gaps = 34/212 (16%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKG-------LSPKDNRKIPNLDYDIVYEIKKENPDLF 190
            K  +  GV+ I IH   RK +  G        S K + KIP +           N D+ 
Sbjct: 152 AKICESLGVDFISIHGRTRKQLYSGKADYGSIASAKASVKIPVI----------ANGDI- 200

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
                  ++  +  KI    DG+MIGRA+  N
Sbjct: 201 -----NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|254579020|ref|XP_002495496.1| ZYRO0B12716p [Zygosaccharomyces rouxii]
 gi|238938386|emb|CAR26563.1| ZYRO0B12716p [Zygosaccharomyces rouxii]
          Length = 645

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 73/178 (41%), Gaps = 34/178 (19%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +E+NLN GCP   ++    G+ L+ NP  +  C+ AM   +  IPV+VK R G  D  P 
Sbjct: 365 SEVNLNCGCPIDLLYRQGSGSALLDNPARMIRCLNAMSYVSGEIPVSVKIRTGTKDGHPV 424

Query: 134 VAL--RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE------ 185
             L  R LV    ++ V  + +H R         +  R   N D+D V  + +E      
Sbjct: 425 AGLLARRLV---NETDVAAMTLHGRS--------RAQRYTKNADWDYVVRVAEELRSCED 473

Query: 186 ----------NPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                         F+G NG     ED    +    ++D VM+ R A     +   VD
Sbjct: 474 EYDREGRQRSQRIQFVG-NGDVNNFEDWYAHVNRSDAIDSVMVARGALIKPWIFEEVD 530


>gi|207342736|gb|EDZ70406.1| YLR405Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 247

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 40/168 (23%), Positives = 82/168 (48%), Gaps = 8/168 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I   ST  ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L++  ++V  +  + I +N GCP   ++ EG  G  L+ N D++   + A+      
Sbjct: 105 VADLLKFVEMVAPYC-DGIGINCGCPIKEQIREG-IGCALIYNSDLLCSMVHAVKDKYGD 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            + ++ +I + + +       L + +  +GV+ I IH R    +   P
Sbjct: 163 KLRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRTRRTRSSQP 208


>gi|241766789|ref|ZP_04764615.1| TIM-barrel protein, nifR3 family [Acidovorax delafieldii 2AN]
 gi|241362823|gb|EER58579.1| TIM-barrel protein, nifR3 family [Acidovorax delafieldii 2AN]
          Length = 349

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/261 (23%), Positives = 111/261 (42%), Gaps = 29/261 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK------PLALQI 54
           M   TDR +R   + L       +EM+ +    R D  N L  S +        P+A+QI
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVTS----RKDLWNSLKTSRRANHEGEPGPIAVQI 71

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAM 111
            G + + + EAA    + G   I++N+GCP+ +V     G+ LM +  +   +   +   
Sbjct: 72  AGTEAAMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMQDEVLAVSIARAVVDA 131

Query: 112 CKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           C   ++PVT+K R G   Q   AVA   L +  +  G+  + +H R         ++   
Sbjct: 132 CAPRNVPVTLKMRTGWCQQHKNAVA---LARQFEAVGIQMLTVHGRT--------REQGY 180

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
               +YD +  +K     + +  NG +    +A ++L     D +M+GRAA     +   
Sbjct: 181 KGQAEYDTIAAVKAAV-QVPVVANGDIASPEKAREVLAYTGADAIMVGRAAQGRPWIFRE 239

Query: 229 VDEYFSNPLTGSSPIKTRVDK 249
           +  + +     + P+   V +
Sbjct: 240 IGHFLATGEHLAPPLVAEVRR 260


>gi|170579239|ref|XP_001894741.1| dihydrouridine synthase domain containing protein [Brugia malayi]
 gi|158598545|gb|EDP36417.1| dihydrouridine synthase domain containing protein [Brugia malayi]
          Length = 832

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 53/215 (24%), Positives = 94/215 (43%), Gaps = 17/215 (7%)

Query: 24  TEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EM +    L G   + ++L     EK   +Q+ G     +  AA+I+ E+   + I++N
Sbjct: 496 SEMGICTNYLNGTSSEWSLLKRHPNEKYFGVQLAGGYPDSMSRAAQIIAENEQIDFIDIN 555

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNL 139
            GCP   V+E   G  L L  + + + +  M K + + P+T+K R G+ + +   A + +
Sbjct: 556 CGCPIDLVNEKGGGCSLALRSNKLVEVMKTMSKVIGNTPLTLKLRTGIKEGV-YTAHQTI 614

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-- 197
            K +K      I +H R         K  R     D+    +  +   ++     G +  
Sbjct: 615 SKVVKYCPPQLITLHPRS--------KAQRYTKLADWSYTQQCSEACQNIPFWACGDVLS 666

Query: 198 -EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
             D  + L+  P V+GVMIGR A     + T + E
Sbjct: 667 YTDYYEKLEKYP-VNGVMIGRGALMKPWIFTEIKE 700


>gi|283955568|ref|ZP_06373062.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           1336]
 gi|283792911|gb|EFC31686.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           1336]
          Length = 305

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/256 (23%), Positives = 116/256 (45%), Gaps = 36/256 (14%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKNLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +  D   I N          K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSIHGRTRKQLYSGKA--DYESIANA---------KASVKIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             ++  +  KI    DG+MIGRA+  N  +   +        +G S     VD+   ++I
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGNPWIFYEIK-------SGKS-----VDEKLKKEI 247

Query: 256 SASMTDYAARHLHSGG 271
             +  D   +H    G
Sbjct: 248 ILTHFDEMIKHYKDQG 263


>gi|315929909|gb|EFV09068.1| dihydrouridine synthase (Dus) family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 308

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 53/207 (25%), Positives = 100/207 (48%), Gaps = 24/207 (11%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ I IH   RK +  G +          DY  +    K +  + +  NG +
Sbjct: 152 AKICESLGVDFISIHGRTRKQLYSGKA----------DYGSIASA-KASVSIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKN 222
             ++  +  KI    DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|312214198|emb|CBX94192.1| hypothetical protein [Leptosphaeria maculans]
          Length = 623

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 59/116 (50%), Gaps = 5/116 (4%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           ++PL +Q    D   L+ AAK V  F  + ++LN+GCP      G +GA L  + D++  
Sbjct: 125 DRPLTVQFCSNDPDDLLAAAKHVAPF-CDAVDLNLGCPQGIAKRGKYGAFLQEDWDLIAR 183

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            I    + L +P+T K RI ++ +   +      K++  +G + + +H R+   KG
Sbjct: 184 MIRKCHEELDVPITAKMRI-LETREKTL---EYAKTLLDAGASILTVHGRQREQKG 235


>gi|149909476|ref|ZP_01898130.1| hypothetical protein PE36_16760 [Moritella sp. PE36]
 gi|149807381|gb|EDM67332.1| hypothetical protein PE36_16760 [Moritella sp. PE36]
          Length = 312

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 44/193 (22%), Positives = 92/193 (47%), Gaps = 16/193 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     + E A    D G + +++N GCP+ +V++ S GA  +  P++V   +
Sbjct: 64  PVRIQLLGQHPQWMAENAVRAIDLGSHGLDINFGCPAKQVNKSSGGAACLREPELVYQIV 123

Query: 109 AAMCKALSIPVTV--KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +  A+    TV  K R+G +D    +    +  +++++G N + +H R       +  
Sbjct: 124 KQVRDAVPAEHTVSAKIRLGWEDSNQKL---EIADAVQQAGANELTVHGR-------TKA 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
           D  +   +++  + EI +++  + +  NG +   + A + L     + +M+GR A  N  
Sbjct: 174 DGYRAAAINWQAIAEI-RQHVSIPVIANGEIWSHADAQRCLEVTGCNDLMVGRGAL-NLP 231

Query: 225 MLTTVDEYFSNPL 237
            L  V +Y   P+
Sbjct: 232 NLGEVVKYNKAPM 244


>gi|153846110|ref|ZP_01993830.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
 gi|149744985|gb|EDM56303.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
          Length = 158

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/107 (29%), Positives = 59/107 (55%), Gaps = 5/107 (4%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G +   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A 
Sbjct: 2   VQLLGQEPHWMAENAIRAAELGARGIDLNFGCPAKMVNKSKGGAALLQHPELIHSVVKAC 61

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             A+  +IPV+ K R+G ++  P      +V +I+ +G N + +HAR
Sbjct: 62  RDAVPANIPVSAKIRLGWEN--PEDCFE-IVDAIQSAGANELTVHAR 105


>gi|329667277|gb|AEB93225.1| dihydroorotate dehydrogenase [Lactobacillus johnsonii DPC 6026]
          Length = 307

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 95/211 (45%), Gaps = 32/211 (15%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA+++ DK   L     + P+   +GG D +  +E AK + D G  N + +NV CP+   
Sbjct: 80  DAVIK-DKLTPLRNEYPDLPIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V +    +   + IP+ VK    V D      +  + K+ +  G 
Sbjct: 139 GGMSFG----VHPDVVEELTKKIKSVVKIPIYVKLTPNVTD------ITQIAKAAENGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I +  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMEIDVETRKPVLGHNIGGLS---GEAVKPIAIRMVHQVRESTTLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
            GG+      ++ IL   + V +G A +K+S
Sbjct: 246 -GGISSAKDVIEFILAGANAVAVGTAHFKDS 275


>gi|255003775|ref|NP_659107.2| tRNA-dihydrouridine synthase 3-like [Mus musculus]
 gi|74186083|dbj|BAE34157.1| unnamed protein product [Mus musculus]
 gi|148706257|gb|EDL38204.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_d [Mus
           musculus]
          Length = 637

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/278 (22%), Positives = 117/278 (42%), Gaps = 32/278 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      + +++NV
Sbjct: 322 EMAVCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINV 381

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM         +  + + L +P+TVK R GV +++ ++A R L+ 
Sbjct: 382 GCPIDLVYKKGGGCALMNRSAKFQQIVRGVNEVLDVPLTVKMRTGVQERV-SLAHR-LLP 439

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
            ++  GV  + +H R         ++ R     D+  + +  K    + +  NG     E
Sbjct: 440 ELRDWGVALVTLHGRS--------REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFE 491

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
           D + A++    V G+M+ R A     + T + E     ++ S     R+D      I   
Sbjct: 492 DANCAMQT--GVAGIMVARGALLKPWLFTEIKEQRHWDISSSE----RLD------ILRD 539

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 540 FTHYGLEHWGSDTQGVERTRRFLLEWLSF----LCRYV 573


>gi|301784767|ref|XP_002927798.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Ailuropoda
           melanoleuca]
          Length = 646

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 98/218 (44%), Gaps = 28/218 (12%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 334 EMAVCTNLLQGQTSEWALLRRHPCEDVFGVQLEGAFPDTMTKCAELLNRTIEVDF----V 389

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 390 DINVGCPIDLVYKKGGGCALMNRAAKFQQIVRGMNQVLDVPLTVKIRTGVQERM-NLAHR 448

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGG 196
            L+  ++  G   + +H R         ++ R     D++ + + +   +P    G NG 
Sbjct: 449 -LLPELRDWGAALVTLHGRS--------REQRYTKLADWEYIAQCVTAASPMPLFG-NGD 498

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   ED ++A++    V GVM+ R A     + T + E
Sbjct: 499 ILSYEDANRAMQT--GVAGVMVARGALLKPWLFTEIKE 534


>gi|323331765|gb|EGA73178.1| Smm1p [Saccharomyces cerevisiae AWRI796]
          Length = 372

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 94/195 (48%), Gaps = 27/195 (13%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEK----PLALQIGGADISKLVEAA-KIVEDF 72
           N AL   + +V   +    +   L F T  K     L  QIG A  +   +AA K++ D 
Sbjct: 39  NTALQTVDYVVPSKV--QTRPETLVFRTYPKLESSKLIFQIGSASPALATQAALKVINDV 96

Query: 73  GYNEINLNVGCPSA-RVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGV 127
             + I++N GCP    +H G  G+ L+  PD    I+ + +  +    S P++VK R+ +
Sbjct: 97  --SGIDINAGCPKHFSIHSG-MGSALLRTPDTLCLILKELVKNVGNPHSKPISVKIRL-L 152

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKEN 186
           D +   +    L+K +  +G+  + +H RK  ++      NR+ P  DY   +YEI + N
Sbjct: 153 DTKQDTL---QLIKRLCATGITNLTVHCRKTEMR------NREQPITDYIAEIYEICQAN 203

Query: 187 PDLFIGLNGGLEDMS 201
            ++ + +NG + D S
Sbjct: 204 -NVSLIVNGAIRDRS 217


>gi|158296416|ref|XP_316826.3| AGAP000856-PA [Anopheles gambiae str. PEST]
 gi|157015286|gb|EAA12065.3| AGAP000856-PA [Anopheles gambiae str. PEST]
          Length = 469

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 100/230 (43%), Gaps = 39/230 (16%)

Query: 21  LLYTEMIVADAILRGDK--KNILG-------------FST---QEKPLALQIGGADISKL 62
           L+YTE I+   +LR ++    +LG             F T   +   + LQIG A   + 
Sbjct: 35  LVYTEEIIDWKLLRAERHTNEVLGTIDYIDTTDGTVVFRTCPHERGKVVLQIGTASAERA 94

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           V   +++++     I++N+GCP     +G  G  L+ +       +  + + + IPVT K
Sbjct: 95  VAVGQMMQN-DVAAIDVNMGCPKDFSIKGGMGVALLYDLPRAKAILEGLVQGVRIPVTCK 153

Query: 123 CRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R+  D D+  A+A     K ++ +G+  I +H R  + +   P +   I  +   +   
Sbjct: 154 IRVMPDLDETVALA-----KELQSTGIRAIGVHGRTKMERPRDPVNEGAIARVANAL--- 205

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAML 226
                  + +  NGG + +++   IL      S   VM+ RAA  N ++ 
Sbjct: 206 ------HIPVIANGGSQSITRRHDILRFAQRCSTTSVMVARAAEWNCSVF 249


>gi|157960219|ref|YP_001500253.1| nifR3 family TIM-barrel protein [Shewanella pealeana ATCC 700345]
 gi|157845219|gb|ABV85718.1| putative TIM-barrel protein, nifR3 family [Shewanella pealeana ATCC
           700345]
          Length = 322

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNI-LGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK  + +  + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLC-LRYGAALAVSEMLSSNPDVWDTDKSRLRMTHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQDPVQVEAILRAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + +H   R+ + KG          N
Sbjct: 136 VTLKIRTGW-----APEHRNGVHIAQIAEDCGIASLAVHGRTRQCMYKG----------N 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  IKK+   + +  NG +    +A  +L    VD +MIGR A     +   +  
Sbjct: 181 AEYDTIKAIKKQ-ISIPVVANGDILTPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|332879624|ref|ZP_08447319.1| dihydrouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
 gi|332682590|gb|EGJ55492.1| dihydrouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
          Length = 313

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/265 (20%), Positives = 107/265 (40%), Gaps = 41/265 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QI  A   +  +    V  +GY E++LN+GC    + +   G  L+  P+ V   + 
Sbjct: 63  LVPQIIAASAEEAEQILAQVVPYGYQEVDLNMGCAFPMLVKKGKGCGLLPEPERVRGLLQ 122

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD 167
            + +   I  +VK R+G ++   A     L+  + ++ ++ + +HAR  +   KG     
Sbjct: 123 VVERYPDISFSVKMRLGYEN---AAECMELLSVLNETRLSRVVVHARTGRQQYKG----- 174

Query: 168 NRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA------- 218
                  D +      +E  +P ++ G    +E +S+  + +P ++GVM+GR        
Sbjct: 175 -----ECDREAFLRFARECRHPVVYNGDVTTVESLSELQQGMPFLEGVMMGRGLLAAPWV 229

Query: 219 --------AYKNSAMLTT--------VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                   A+     +++        +D Y      G   + T++ K FW  I       
Sbjct: 230 AIEYHEGTAWSMERRMSSLRALHADLLDHYVQTLEGGEKQLLTKM-KAFWEYIYPEGDRK 288

Query: 263 AARHLHSGGKLQQITRHMIGLFHGF 287
             + +H   K+   T+ +  L  G+
Sbjct: 289 CRKKIHKAQKMADYTQAVFQLLSGY 313


>gi|260172570|ref|ZP_05758982.1| dihydrouridine synthase [Bacteroides sp. D2]
 gi|315920863|ref|ZP_07917103.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313694738|gb|EFS31573.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 314

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 50/247 (20%), Positives = 100/247 (40%), Gaps = 34/247 (13%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +A KI+  F   GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  +
Sbjct: 75  KAEKILSLFIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQALLSLITEYPQISFS 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G +D  P   L+ L   I +  +  + +H R      L  +  +   +L     +
Sbjct: 135 IKMRLGWED--PEECLK-LAPIINELPLRQVVMHPR------LGKQQYKGEVDLKAFEAF 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA---------------- 224
           +   ++P ++ G    +ED+ +  +  P + G+MIGR    N A                
Sbjct: 186 QNACKHPLIYNGDINSVEDIHRIQEQFPGLAGIMIGRGLLANPALALEYRQNRALEFDEM 245

Query: 225 ------MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                 M   V   ++  L G         K FW  +         + +H  G L +  +
Sbjct: 246 REKLQSMHKCVYNQYAEQLEGGDEQLLNKMKTFWEYLMPQADRKLLKAIHKSGNLNKYNQ 305

Query: 279 HMIGLFH 285
            ++  F+
Sbjct: 306 AILAFFN 312


>gi|308161253|gb|EFO63708.1| Embryo-related protein [Giardia lamblia P15]
          Length = 406

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 102/231 (44%), Gaps = 32/231 (13%)

Query: 23  YTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE---- 76
           +T+M  ADA+L     +  +L  +   + + LQ+ G +      AA+++ D         
Sbjct: 86  FTQMYTADALLHNSLLRDVVLSTAASGEKVILQLCGNNPFSFRTAAELLYDSPIASQLIA 145

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N+GCP++      +G  +  N  +V   I+        PVT  C+I   + I     
Sbjct: 146 LDINLGCPASCASSRGYGFYVTQNWPLVHRIISETSSTRLFPVT--CKIRPLNSIEKTVD 203

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-----------DIVY----- 180
             L+  +  SG +GI IH R    +G   + + K   L++           D ++     
Sbjct: 204 YMLL--LVMSGASGITIHMRHTTRQGKHAQ-SVKPAYLEFEKLVHTFRQKLDTLFNSLDR 260

Query: 181 -EIKKENPDLF--IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
            EI +E   L+  I LNGG+++  +A  +L +   DGVM+G    KN   L
Sbjct: 261 SEIAREKSHLYPVIILNGGIKNRQEADHLLTTYPADGVMLGVGLLKNPTCL 311


>gi|167032522|ref|YP_001667753.1| dihydrouridine synthase DuS [Pseudomonas putida GB-1]
 gi|166859010|gb|ABY97417.1| dihydrouridine synthase DuS [Pseudomonas putida GB-1]
          Length = 323

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 63/119 (52%), Gaps = 6/119 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +
Sbjct: 64  PMRVQLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +  A+  +IPVT K R+G D   P  AL     ++ + G   + +HAR  + +G  P
Sbjct: 124 REVRHAVPANIPVTSKMRLGFDS--PDGAL-ECATALAEGGSAHLVVHARTKV-EGYKP 178


>gi|123469809|ref|XP_001318114.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121900865|gb|EAY05891.1| hypothetical protein TVAG_353310 [Trichomonas vaginalis G3]
          Length = 321

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/128 (26%), Positives = 70/128 (54%), Gaps = 8/128 (6%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           ++  + +S +++PL +QI G+    L+  AK + +FG   I++N+GC       G +G  
Sbjct: 57  RQQQIEYSEEDRPLVIQISGSIDVDLLTTAKSMSEFGV-PIDINLGCCQKVAKRGEYGY- 114

Query: 97  LMLNPDI----VGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVALR-NLVKSIKKSGVNG 150
            M++ +     V + I ++   +++P+ VK R   D+  IP++ +  +  K ++++G + 
Sbjct: 115 FMVDSEQKRQNVVNLIKSIPSEITVPLYVKIRALTDESGIPSIPITVDFAKHLEEAGASL 174

Query: 151 IWIHARKA 158
           I IH R A
Sbjct: 175 ITIHGRSA 182


>gi|319763927|ref|YP_004127864.1| dihydrouridine synthase dus [Alicycliphilus denitrificans BC]
 gi|330823809|ref|YP_004387112.1| dihydrouridine synthase DuS [Alicycliphilus denitrificans K601]
 gi|317118488|gb|ADV00977.1| dihydrouridine synthase DuS [Alicycliphilus denitrificans BC]
 gi|329309181|gb|AEB83596.1| dihydrouridine synthase DuS [Alicycliphilus denitrificans K601]
          Length = 339

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 105/237 (44%), Gaps = 31/237 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+  P+++   +
Sbjct: 72  PVRAQLLGSDPVSMAENAARLAALGPEGIDLNFGCPARTVNRHGGGAALLREPEVIAAVV 131

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+   +PV+ K R+G DD   A   R   +++++ G   + +HAR         K
Sbjct: 132 AAVRRAVPAHLPVSAKMRLGYDD---AGRARECAQAMEQGGACELVVHART--------K 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
            +   P   ++ + EI +E   + +  NG +  ++ AL+   +   D +M+GR    +  
Sbjct: 181 ADGYRPPAYWERIPEI-REAVAIPVVANGEIWTVADALRCRGVSGCDALMLGRGMVADPG 239

Query: 225 MLTTVDEY------FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           +   +         F+ P     P   R    FW+ +   +           G+L+Q
Sbjct: 240 LALAIRAQDVGQGAFALPWAALLPQLAR----FWQLVCEDLEPR-----QRAGRLKQ 287


>gi|154336333|ref|XP_001564402.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134061437|emb|CAM38463.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 512

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 99/236 (41%), Gaps = 49/236 (20%)

Query: 23  YTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           YT M++A++ ++        F+    E  L +Q+     +   EAA ++  +  + I+LN
Sbjct: 143 YTHMLIAESFVKSPHARHAEFALYEGENRLVVQLAAKSGTDAAEAALLLRPY-CDAIDLN 201

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAM----------------------CKALS-- 116
            GCP     +   GA L+  P+ V D + ++                      C A +  
Sbjct: 202 CGCPQRWAMKDGIGAVLLDQPERVADMVRSIRNAMPDGNTAPMMVSIGGACSSCPATAPP 261

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            +P  VK RI  D       LRN V   +  + +G + + +H R A         ++   
Sbjct: 262 FLPCVVKMRIKDD-------LRNSVDFARQCEAAGASWLTVHGRSAT--------SQPSA 306

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
            + ++ V ++ +EN  + + LNGG+ D+S A++  +     G+M       N AM 
Sbjct: 307 AVQFEAV-KLIRENLSVPVVLNGGVRDVSTAMEAALRTGCGGLMSANGLLDNPAMF 361


>gi|109899222|ref|YP_662477.1| dihydrouridine synthase, DuS [Pseudoalteromonas atlantica T6c]
 gi|109701503|gb|ABG41423.1| tRNA-U20a,U20b-dihydrouridine synthase [Pseudoalteromonas atlantica
           T6c]
          Length = 310

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 2/91 (2%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           GF+    P+ +Q+ G +   L E A    + G + ++LN GCP+  V++   GA L+  P
Sbjct: 57  GFTPNGTPVRVQLLGQNPQPLAENAVRAVELGSHGVDLNFGCPAKTVNKSKGGAILLREP 116

Query: 102 DIVGDCIAAMCKALSIP--VTVKCRIGVDDQ 130
             + D ++A+ +A+     VT K R+G +D+
Sbjct: 117 QALYDIVSAVREAVPKEHKVTAKMRLGFEDK 147


>gi|296419375|ref|XP_002839286.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295635409|emb|CAZ83477.1| unnamed protein product [Tuber melanosporum]
          Length = 483

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 75/333 (22%), Positives = 131/333 (39%), Gaps = 27/333 (8%)

Query: 1   MVDWTDRHYRFFARLLTN-NALLYTEMI-----VADAILRGDK-KNILGFSTQEKPLALQ 53
           MV+ ++  +R  +R  +  N L YT M          I R       L  S  ++PL +Q
Sbjct: 32  MVEQSELAWRLLSRRHSPPNTLCYTPMFHSRLFATTPIYRSQSFYPPLDGSKPDRPLFVQ 91

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
                   L  AA+ V     + ++LN+GCP     +G +GA L  +  ++   ++ + K
Sbjct: 92  FCSNTPEDLFSAAQHVAPH-CDGVDLNLGCPQGIARKGKYGAFLQEDWGLIRSLVSKLHK 150

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L +PVT K RI    +      R +V     +G   + +H R    KG           
Sbjct: 151 DLEVPVTAKIRILETRERSLEYARMVV----DAGAQVLTVHGRTRDQKG------HNTGM 200

Query: 174 LDYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
            D+ ++  I+   P ++ +  NG +   ED+ + L      DGVM       N A+  + 
Sbjct: 201 ADWGVIRYIRDNLPKEVVLFANGNILWHEDVQRCLDAT-GADGVMSAEGNLYNPAIFQS- 258

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRK-ISASMTDYAARHLHSGGKLQQITRHMIGLFHG-F 287
           DE +         I  R   D  RK +   + +   + L     +  I  H+  L+H   
Sbjct: 259 DEDWEKRFPRMD-ILGREYLDIVRKEVLPGLEERGRKLLLQDPSITAIKPHLFKLWHALL 317

Query: 288 PNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           P     R +L   +  ++    ++E     ++E
Sbjct: 318 PKYTDVRALLAKSSARASEGGDVLEPYETCLME 350


>gi|148706255|gb|EDL38202.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_b [Mus
           musculus]
          Length = 351

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 57/254 (22%), Positives = 108/254 (42%), Gaps = 30/254 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E    +Q+ GA    + + A+++      + +++NVGCP   V++   G  LM       
Sbjct: 60  EDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQ 119

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +  + + L +P+TVK R GV +++ ++A R L+  ++  GV  + +H R         
Sbjct: 120 QIVRGVNEVLDVPLTVKMRTGVQERV-SLAHR-LLPELRDWGVALVTLHGRS-------- 169

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAYKN 222
           ++ R     D+  + +  K    + +  NG     ED + A++    V G+M+ R A   
Sbjct: 170 REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFEDANCAMQT--GVAGIMVARGALLK 227

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             + T + E     ++ S     R+D      I    T Y   H  S  +  + TR  + 
Sbjct: 228 PWLFTEIKEQRHWDISSSE----RLD------ILRDFTHYGLEHWGSDTQGVERTRRFLL 277

Query: 283 LFHGFPNSRRCRHI 296
            +  F     CR++
Sbjct: 278 EWLSF----LCRYV 287


>gi|45946028|gb|AAH17081.4| DUS1L protein [Homo sapiens]
          Length = 406

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/119 (28%), Positives = 59/119 (49%), Gaps = 9/119 (7%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +++PL +Q    D    V+AA + +D+  + I+LN+GCP      G +GA L    D++ 
Sbjct: 5   EDRPLIVQFCANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQ 63

Query: 106 DCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
             I    + LS+PVT K R+   +D  +         + ++K+G   + +H R    KG
Sbjct: 64  RMILLAHEKLSVPVTCKIRVFPEIDKTV------RYAQMLEKAGCQLLTVHGRTKEQKG 116


>gi|284990203|ref|YP_003408757.1| TIM-barrel protein, nifR3 family [Geodermatophilus obscurus DSM
           43160]
 gi|284063448|gb|ADB74386.1| TIM-barrel protein, nifR3 family [Geodermatophilus obscurus DSM
           43160]
          Length = 400

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 71/313 (22%), Positives = 121/313 (38%), Gaps = 34/313 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R      L   EMI   A++   +K    +     +E   ++Q+ G 
Sbjct: 45  MAGITNPAFRTLCREF-GAGLYVCEMITTRALVERTEKTLSMVRATPDEEDAFSVQLYGV 103

Query: 58  DISKLVEAAKIVEDFGYN-----EINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAM 111
           D + +  A +++ D G        ++LN GCP  +V     G+ L     +  D + AA+
Sbjct: 104 DPATVGRAVEMLVDEGVAGTRPAHVDLNFGCPVPKVTRKGGGSALPWRRVLFRDIVRAAV 163

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A  +PVTVK RIG+D     V   +  +  +  G   I +H R A        D    
Sbjct: 164 RAARDVPVTVKTRIGIDAD--HVTYLDAGRIAQDEGAAAITLHGRTA--------DQLYS 213

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTV 229
              D+  +  +  E  D+ +  NG + +   AL+++      GV+IGR       +   +
Sbjct: 214 GTADWAPIARL-VEAVDIPVLGNGDIWEADDALRMVAETGCAGVVIGRGCLGRPWLFGDL 272

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT---RHMIGLFHG 286
              F+          TR      R+++A M  +A       G+    T   +H+     G
Sbjct: 273 AAAFAG--------GTRRALPTLREVAAVMHRHATLLSEEQGERHGCTDFRKHVAWYLKG 324

Query: 287 FPNSRRCRHILTV 299
           F      R  L +
Sbjct: 325 FSVGSDVRRALAM 337


>gi|320168070|gb|EFW44969.1| tRNA-dihydrouridine synthase 3 [Capsaspora owczarzaki ATCC 30864]
          Length = 741

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 46/214 (21%), Positives = 96/214 (44%), Gaps = 17/214 (7%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLN 80
           +EM +A  +++G+ +   +      E    +Q+ G ++  +  AA+++ +    + I++N
Sbjct: 423 SEMAMAVKLIQGEAQEWALTKRHASEDIFGVQLCGGNVEVMGNAAELLSNHCELDFIDVN 482

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVALRNL 139
            GCP   V E   G+ L+  P  +      M +  ++P+T+K R G  +D++ A     L
Sbjct: 483 CGCPIDLVVERGQGSALLSRPSRLETIAKGMLQVSTVPITIKLRTGFSEDRLVA---HTL 539

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           +  +   GV+ + +H R         +  R     D+  + +  +  P L +  NG +  
Sbjct: 540 IPRLANLGVSLVTLHGRT--------RAQRYSRLADWQYINQCAEAAPTLPVYGNGDIMS 591

Query: 200 MSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
             +A+  +    V G+M+ R A     + T + E
Sbjct: 592 YQEAMEHREKTKVSGLMLARGALIKPWVFTEIKE 625


>gi|330995636|ref|ZP_08319534.1| dihydrouridine synthase [Paraprevotella xylaniphila YIT 11841]
 gi|329574695|gb|EGG56256.1| dihydrouridine synthase [Paraprevotella xylaniphila YIT 11841]
          Length = 313

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 50/256 (19%), Positives = 110/256 (42%), Gaps = 37/256 (14%)

Query: 59  ISKLVEAAKIVED----FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           I+   E A+++ D    +GY E++LN+GC    + +   G  L+  P+ V   +  + + 
Sbjct: 68  IAASAEEAELILDQVVSYGYQEVDLNMGCAFPMLVKKGKGCGLLPEPERVRGLLQVVERY 127

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I  +VK R+G ++   A     L+  + ++ ++ + +HAR         +  + + + 
Sbjct: 128 PDISFSVKMRLGYEN---AAECMELLPVLNETRLSRVVVHARTG------RQQYKGVCDR 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR---------------AA 219
           +  + +  +  +P ++ G    +E +S+  + +P ++GVM+GR               AA
Sbjct: 179 EAFLRFARECRHPVVYNGDVTTVEFLSELQRGMPFLEGVMMGRGLLAAPWVAIEYHEGAA 238

Query: 220 YKNSAMLTT--------VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           +     +++        +D Y      G   + T++ K FW  I         + +H   
Sbjct: 239 WSMERRMSSLRALHADLLDHYVQTLEGGEKQLLTKM-KAFWEYIYPEGDRKCRKKIHKVQ 297

Query: 272 KLQQITRHMIGLFHGF 287
           K+   T+ +  L  G+
Sbjct: 298 KVADYTQAVFQLLSGY 313


>gi|193788568|ref|NP_001123329.1| zinc finger protein ZF(C3H)-5 [Ciona intestinalis]
 gi|93003036|tpd|FAA00101.1| TPA: zinc finger protein [Ciona intestinalis]
          Length = 609

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 48/216 (22%), Positives = 94/216 (43%), Gaps = 23/216 (10%)

Query: 25  EMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM VA  +L  +G +  ++     E    +Q+ GA    +   A+++      DF    I
Sbjct: 293 EMAVATNVLQAKGGEWALMKRHPCEDIFGVQLCGAFPDTMSRCAELISKTCEVDF----I 348

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP   +++   G+ LM   + + D +  M +++ +P+T K R GV+ +       
Sbjct: 349 DINMGCPIDLIYKKGAGSALMRRTNKLFDIVNCMNRSIDVPLTCKVRAGVETK--KNCAH 406

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N++  ++  GV    +H R         ++ R     D+  + E       + +  NG +
Sbjct: 407 NILPKLRDYGVAMTTVHGRS--------REARYTKAADWGYISECAALADPMPVFGNGDI 458

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
                 + ++   +V GVMI R A     + T + E
Sbjct: 459 LSYHDYMSVMENTTVSGVMIARGALIKPWVFTEIKE 494


>gi|152978301|ref|YP_001343930.1| dihydrouridine synthase DuS [Actinobacillus succinogenes 130Z]
 gi|150840024|gb|ABR73995.1| dihydrouridine synthase DuS [Actinobacillus succinogenes 130Z]
          Length = 326

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 60/112 (53%), Gaps = 9/112 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A    + G + I+ N GCPS  V+  + GA L+ NP+++    
Sbjct: 75  PVRVQLLGQYPDWLAENAVRAIELGSHGIDFNCGCPSKTVNGSNGGASLLKNPELIYRAT 134

Query: 109 AAMCKALSIP--VTVKCRIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A+ +A++    V+VK R+G DD  Q+  +A      ++++ G + I +H R
Sbjct: 135 RAIRQAVTPEQTVSVKVRLGWDDISQVFEIA-----DAVQQGGADEIAVHGR 181


>gi|42519206|ref|NP_965136.1| dihydroorotate dehydrogenase 1B [Lactobacillus johnsonii NCC 533]
 gi|81832219|sp|Q74J29|PYRD_LACJO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|41583494|gb|AAS09102.1| dihydroorotate dehydrogenase [Lactobacillus johnsonii NCC 533]
          Length = 307

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 94/211 (44%), Gaps = 32/211 (15%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA+++ DK   L       P+   +GG D +  +E AK + D G  N + +NV CP+   
Sbjct: 80  DAVIK-DKLTPLRSEYPNLPIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V +    +   + IP+ VK    V D      +  + K+ +  G 
Sbjct: 139 GGMSFG----VHPDVVEELTKKIKSLVKIPIYVKLTPNVTD------ITQIAKAAENGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I +  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMEIDVETRKPVLGHNIGGLS---GEAVKPIAIRMVHQVRESTTLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
            GG+      ++ IL   + V +G A +K+S
Sbjct: 246 -GGISSAKDVIEFILAGANAVAVGTAHFKDS 275


>gi|255714134|ref|XP_002553349.1| KLTH0D14696p [Lachancea thermotolerans]
 gi|238934729|emb|CAR22911.1| KLTH0D14696p [Lachancea thermotolerans]
          Length = 667

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 76/169 (44%), Gaps = 36/169 (21%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +EINLN GCP   ++    G+ L+ NP  +  C+ +M   +  IPVTVK R G  D  P 
Sbjct: 383 SEINLNSGCPIDLLYRQGSGSALLDNPARMFRCLNSMSYVSGDIPVTVKIRTGTKDGHPM 442

Query: 134 VA--LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-----------Y 180
               +R LV    ++ V  I +H R         +  R   N D+D +           +
Sbjct: 443 AEGLVRRLV---SETDVAAITLHGRT--------RQQRYTRNADWDYISKVASTLREAEH 491

Query: 181 EIKKENPD--------LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           E+++++ +         F+G NG + +     K +   ++D VM+ R A
Sbjct: 492 EVEEKDKERREGKLRTQFVG-NGDVNNFEDWYKHVEDENIDSVMVARGA 539


>gi|227890081|ref|ZP_04007886.1| dihydroorotate dehydrogenase 1B [Lactobacillus johnsonii ATCC
           33200]
 gi|227849525|gb|EEJ59611.1| dihydroorotate dehydrogenase 1B [Lactobacillus johnsonii ATCC
           33200]
          Length = 307

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 94/211 (44%), Gaps = 32/211 (15%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA+++ DK   L       P+   +GG D +  +E AK + D G  N + +NV CP+   
Sbjct: 80  DAVIK-DKLTPLRNEYPALPIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG    ++PD+V +    +   + IP+ VK    V D      +  + K+ +  G 
Sbjct: 139 GGMSFG----VHPDVVEELTKKIKSVVKIPIYVKLTPNVTD------ITQIAKAAENGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I +  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMEIDVETRKPVLGHNIGGLS---GEAVKPIAIRMVHQVRESTTLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
            GG+      ++ IL   + V +G A +K+S
Sbjct: 246 -GGISSAKDVIEFILAGANAVAVGTAHFKDS 275


>gi|217970411|ref|YP_002355645.1| dihydrouridine synthase [Thauera sp. MZ1T]
 gi|217507738|gb|ACK54749.1| dihydrouridine synthase DuS [Thauera sp. MZ1T]
          Length = 336

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 35/110 (31%), Positives = 57/110 (51%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC- 107
           P+A+Q+ G+D   L E A  +     + I+LN GCP+  V+    GA L+  P ++ D  
Sbjct: 64  PVAVQLLGSDPVLLAENAARLAALSPHGIDLNFGCPAKVVNRHGGGAMLLDRPRLLHDIA 123

Query: 108 -IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                    +IPV+ K R+G+ D  P+ AL +  +++   G   I +HAR
Sbjct: 124 AAVRAAVPAAIPVSAKMRLGIAD--PSRAL-DCAQALADGGAQAIVVHAR 170


>gi|299771376|ref|YP_003733402.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. DR1]
 gi|298701464|gb|ADI92029.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. DR1]
          Length = 307

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 42/127 (33%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 46  LKNDGKTAAG-----TPVHVQFLGNNPDMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 99

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  AL   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 100 RGGSVLLDEPDVVHMLIKAVRDALPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 156

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 157 WLTVHAR 163


>gi|207342565|gb|EDZ70296.1| YML080Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 135

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 51/99 (51%), Gaps = 5/99 (5%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R     L    +L+ ++       R D  + L  S+ ++PL +Q   
Sbjct: 36  MVDQSELAWRILSRRYGATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
            D   L+ AAK+VED   + ++LN+GCP     +G +G+
Sbjct: 96  NDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGS 133


>gi|257456062|ref|ZP_05621265.1| tRNA-dihydrouridine synthase B [Treponema vincentii ATCC 35580]
 gi|257446520|gb|EEV21560.1| tRNA-dihydrouridine synthase B [Treponema vincentii ATCC 35580]
          Length = 340

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 68/131 (51%), Gaps = 9/131 (6%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISK 61
           ++DR +R    +       YTEM+ ++A +R   K   ++  +  E+  A+QI GA+   
Sbjct: 36  YSDRSFRSVC-VDWGADFTYTEMVSSEAYIRNSVKTEKLIARAYNEQRYAVQIFGANPDY 94

Query: 62  LVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----KAL 115
           + E A +I+E +  + I++N GCP  ++ +   G+ LM  P+ +   + A+       + 
Sbjct: 95  MAETAVRIIERYRPDCIDINAGCPMPKITKTGAGSALMRKPERLYAVVKAVAEAAGKTSS 154

Query: 116 SIPVTVKCRIG 126
            IPVTVK R G
Sbjct: 155 GIPVTVKIRSG 165


>gi|195384997|ref|XP_002051195.1| GJ13589 [Drosophila virilis]
 gi|194147652|gb|EDW63350.1| GJ13589 [Drosophila virilis]
          Length = 590

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 49/205 (23%), Positives = 93/205 (45%), Gaps = 23/205 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM  A  +L+G   +  +      E    +Q+ G + + + +AA+++ E    + I+LN+
Sbjct: 273 EMACAVPLLKGLGQEWALTKRHESEDIFGVQVCGNNPNVITQAAEVLHETARVDYIDLNI 332

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV--DDQIPAVALR 137
           GCP   +++   G+ LM   +I+ +     C ALS  +P TVK R G+  D  +      
Sbjct: 333 GCPIDLIYQQGGGSALMRRTNIL-ELTVRSCAALSDRLPFTVKMRTGIYADKSV----AH 387

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L+  +++ G   + +H R         ++ R     ++  + +   +   + +  NG +
Sbjct: 388 ELLPLVEQWGAAAVTLHGRS--------REQRYTRQANWAYIEQCAAQARHMPVIGNGDI 439

Query: 198 ---EDMSQALKILPSVDGVMIGRAA 219
              ED  +   + P V  VMIGR A
Sbjct: 440 ISYEDYVERRALAPHVSSVMIGRGA 464


>gi|220912142|ref|YP_002487451.1| hypothetical protein Achl_1372 [Arthrobacter chlorophenolicus A6]
 gi|219859020|gb|ACL39362.1| TIM-barrel protein, nifR3 family [Arthrobacter chlorophenolicus A6]
          Length = 392

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 48/215 (22%), Positives = 93/215 (43%), Gaps = 21/215 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    ++  I+     EK  ++Q+ G D
Sbjct: 33  MAGITNSAFRRLCREY-GGGMYVAEMVTSRALVERTPESLRIISHDDDEKVRSVQLYGVD 91

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              +  A + +VE+   + I+LN GCP  +V     G+ L    D+    +    +  S 
Sbjct: 92  AGTVGAAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTAIVQTAVREASK 151

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             IP+T+K R G+DD    +   +  +  + SGV  + +H R A     G          
Sbjct: 152 GNIPLTIKMRKGIDDD--HLTYLDAGRIARDSGVAAVALHGRTAAQFYSG---------- 199

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             D+  +  +++  PD+ +  NG +     A++++
Sbjct: 200 QADWSAIARLREALPDIPVLGNGDIWSAEDAVRMV 234


>gi|283955300|ref|ZP_06372800.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           414]
 gi|283793214|gb|EFC31983.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           414]
          Length = 311

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 50/206 (24%), Positives = 100/206 (48%), Gaps = 22/206 (10%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++    +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFTSLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +          DY+ + +  K +  + +  NG +
Sbjct: 152 TKICESLGVDFVSIHGRTRKQLYSGKA----------DYNSIAK-AKASVKIPVIANGDI 200

Query: 198 EDM-SQALKILPSVDGVMIGRAAYKN 222
               ++ +  +   DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYEITKCDGLMIGRASVGN 226


>gi|213052349|ref|ZP_03345227.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
          Length = 200

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 55/110 (50%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++    
Sbjct: 83  PVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGA 142

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            AM  A+   +PVTVK R+G D          +  +++++G + + +H R
Sbjct: 143 KAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGR 189


>gi|260223243|emb|CBA33610.1| tRNA-dihydrouridine synthase C [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 345

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 57/110 (51%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC- 107
           P+  Q+ G+D   + E A  + + G   I+LN GCP+  V+    GA L+ +P+I+    
Sbjct: 85  PVWPQLLGSDAPCMAENAARLAEMGSPGIDLNFGCPAKVVNRHGGGATLLQDPEILHTIV 144

Query: 108 -IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                     IPVT K R+G +D   ++AL +  ++++  G   I +HAR
Sbjct: 145 AAVRAAVPAQIPVTAKMRLGYNDD--SLAL-DCARALEAGGAAEIVVHAR 191


>gi|153952282|ref|YP_001397382.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. doylei
           269.97]
 gi|152939728|gb|ABS44469.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. doylei
           269.97]
          Length = 308

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 51/207 (24%), Positives = 100/207 (48%), Gaps = 24/207 (11%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++    + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNKMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++  + +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + +H   RK +  G +          DY+ +    K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSVHGRTRKQLYSGKA----------DYESIASA-KASVKIPVIANGDI 200

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKN 222
             ++  +  KI    DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYKI-TKCDGLMIGRASVGN 226


>gi|291535651|emb|CBL08763.1| tRNA-U20a,U20b-dihydrouridine synthase [Roseburia intestinalis
           M50/1]
          Length = 335

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 36/146 (24%), Positives = 64/146 (43%), Gaps = 14/146 (9%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           +F   + N  + Y E+           K+IL    +   +  QI        +  AK + 
Sbjct: 33  YFTPFINNKKMNYKEI-----------KDILPEHNEGMHVVPQILTNRAEDFLAIAKELG 81

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           ++GY  +NLN+GCPS  V     GA  +  P+ +   +  +     + ++VK R+GV+D 
Sbjct: 82  NYGYESVNLNLGCPSGTVVAKHRGAGFLAVPEELDHFLEEIFAECPLRISVKTRVGVND- 140

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHAR 156
             A    +L+   +K  +  + IH R
Sbjct: 141 --AGEWEHLLSIYEKYPMEELIIHPR 164


>gi|242073810|ref|XP_002446841.1| hypothetical protein SORBIDRAFT_06g023500 [Sorghum bicolor]
 gi|241938024|gb|EES11169.1| hypothetical protein SORBIDRAFT_06g023500 [Sorghum bicolor]
          Length = 320

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 38/144 (26%), Positives = 73/144 (50%), Gaps = 13/144 (9%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIV-EDFG 73
           +TN +L  T     D + +G    +     +E+  +  Q+G ++  + ++AA++V +D  
Sbjct: 48  VTNESLGTT-----DFVEKGTDSVVFRTCPEERGRVVFQMGTSNAVRALKAAQLVCQDV- 101

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
              I++N+GCP +    G  GA L+  P+++ D +  + + L   VT K R+      P 
Sbjct: 102 -TAIDINMGCPKSFSLSGGMGAALLSKPELIHDILTTLRRNLDTTVTCKIRLL---NTPK 157

Query: 134 VALRNLVKSIKKSGVNGIWIHARK 157
             +  L + I+K+GV  + +H RK
Sbjct: 158 DTV-ELARRIEKTGVPALAVHGRK 180


>gi|169623807|ref|XP_001805310.1| hypothetical protein SNOG_15147 [Phaeosphaeria nodorum SN15]
 gi|111056252|gb|EAT77372.1| hypothetical protein SNOG_15147 [Phaeosphaeria nodorum SN15]
          Length = 442

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 43/154 (27%), Positives = 78/154 (50%), Gaps = 16/154 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIP 132
           I++N GCP      G  GA L+  PD++ + + ++ + +  P    ++VK RI +D    
Sbjct: 133 IDVNSGCPKPFSTAGGMGAALLKTPDLLCNILTSLVEEVGKPYEIGISVKIRI-LDTPEE 191

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
             A   LV  + K+G+ G+ +H R   ++   P++ R I      ++  I +E   +   
Sbjct: 192 TAA---LVSRLVKTGITGLTVHCRTTPMR---PRE-RAI-RHQLKMIGNICREA-GVACV 242

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
           +NG +   ++ALK++   +VDG MI   A KN +
Sbjct: 243 MNGDVTSRTEALKLMEEFNVDGAMIATEAEKNPS 276


>gi|50084050|ref|YP_045560.1| hypothetical protein ACIAD0837 [Acinetobacter sp. ADP1]
 gi|49530026|emb|CAG67738.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. ADP1]
          Length = 310

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 60/117 (51%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q  G +   L   A+ V   G   I+LN GCP+  V+    G+ L+  P
Sbjct: 57  GKTAAGTPVHVQFLGNNPDMLAANAEKVVALGAPAIDLNFGCPAKTVNRHRGGSILLDEP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           D+V   + A+  A+   IPV+ K R+G  D+   +   +   +I+++G N + +HAR
Sbjct: 117 DVVHLLVKAVRDAVPAHIPVSAKMRLGYLDENHTM---DNAYAIQEAGANWLTVHAR 170


>gi|312377328|gb|EFR24184.1| hypothetical protein AND_11402 [Anopheles darlingi]
          Length = 633

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 46/189 (24%), Positives = 82/189 (43%), Gaps = 17/189 (8%)

Query: 50  LALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
             +Q+ G     +  AA+I+ E    + I+LN+GCP   +     G+ L+   +++   +
Sbjct: 326 FGVQLCGHKPKLVTYAAQIIAEKADVDFIDLNIGCPIDLIFNQGGGSALLRRQNVLQVMV 385

Query: 109 AAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            +  + L+      TVK RIG+ +  P      LV   ++ G + I IH R         
Sbjct: 386 QSCSRLLADYGKEFTVKTRIGIYNNKPIA--HELVPRFEEWGASLITIHGRT-------- 435

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
           K+ R   + D++ V     +   + +  NG +    D   A +  P+V GVM+GR A   
Sbjct: 436 KEQRYTKHADWEFVQRCAAQASSVPVYGNGDIYCYSDYESARERCPNVGGVMVGRGALIK 495

Query: 223 SAMLTTVDE 231
             +   + E
Sbjct: 496 PWVFQEIKE 504


>gi|15896694|ref|NP_350043.1| hypothetical protein CA_C3454 [Clostridium acetobutylicum ATCC 824]
 gi|15026545|gb|AAK81383.1|AE007843_1 Predicted TIM-barrel enzyme, nifR3 family [Clostridium
           acetobutylicum ATCC 824]
 gi|325510859|gb|ADZ22495.1| TIM-barrel enzyme, nifR3 family [Clostridium acetobutylicum EA
           2018]
          Length = 311

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 55/250 (22%), Positives = 103/250 (41%), Gaps = 23/250 (9%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K++L  + +   L  QI   D +K +   + + + GY+E+NLN+GCPS  V     GA  
Sbjct: 49  KDVLPENNKVTFLVPQILTNDANKFIFTTEKLMNLGYSEVNLNLGCPSGTVVSKGRGAGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +     + + +  +       +++K RIG D          L+K   K  +  + IH R 
Sbjct: 109 LKKRQELDEFLEKIFSKSPAKISIKTRIGKDS---PDEFYELIKIFNKYPLEELIIHPRI 165

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG---VM 214
                 + K N K+    +    E+ K      +  NG +   +  +K++        VM
Sbjct: 166 QT-DFYNNKPNMKV----FKDALELSKST----VCYNGDIFQSNDYIKLIEEFSNLGVVM 216

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +GR    N  ++  ++         ++ ++  V K F   I     D  +   +   K++
Sbjct: 217 LGRGIISNPNIIKKIN--------SNNVLEKEVLKKFHDAIYEEYQDILSGEKNVLFKMK 268

Query: 275 QITRHMIGLF 284
           +I  +MI LF
Sbjct: 269 EIWFYMIHLF 278


>gi|150016954|ref|YP_001309208.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
 gi|149903419|gb|ABR34252.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
          Length = 318

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 39/177 (22%), Positives = 73/177 (41%), Gaps = 9/177 (5%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI   +    ++    +  FG NE+NLN+GCPS  V     G+  +     + + +  + 
Sbjct: 64  QILTNNSEYFIDTVNQLGKFGNNEVNLNLGCPSGTVVAKHKGSGFLAQRKQLDEFLEDIF 123

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
              S  +++K RIG D          L++   K  +  + IH R      +     +  P
Sbjct: 124 SNASTKISIKTRIGKDS---PDEFYELIEIFNKYPLEELIIHPR------IQTDFYKNKP 174

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           N++         +NP  + G    +ED  +  +  P ++ VM+GR    N  ++  +
Sbjct: 175 NMEVFKDALALSKNPVCYNGDIFNIEDYKKLSEAYPKLETVMLGRGLIANPGLIEEI 231


>gi|305432665|ref|ZP_07401826.1| tRNA-dihydrouridine synthase B [Campylobacter coli JV20]
 gi|304444376|gb|EFM37028.1| tRNA-dihydrouridine synthase B [Campylobacter coli JV20]
          Length = 308

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 98/206 (47%), Gaps = 22/206 (10%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +QI G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQIAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++    +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKSLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +  D   I N          K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSIHGRTRKQLYSGKA--DYESIANA---------KASVKIPVIANGDI 200

Query: 198 EDM-SQALKILPSVDGVMIGRAAYKN 222
               ++ +  +   DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYEITKCDGLMIGRASVGN 226


>gi|323700791|ref|ZP_08112703.1| dihydrouridine synthase DuS [Desulfovibrio sp. ND132]
 gi|323460723|gb|EGB16588.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans ND132]
          Length = 339

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 54/238 (22%), Positives = 105/238 (44%), Gaps = 25/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R  AR     A+  +EM+     A      + ++    ++ P+ LQ+ G++
Sbjct: 16  LAGYSDLPFRLLARRF-GCAVACSEMVSVKGMAFKNSGTRRLIATCPEDDPMVLQLFGSE 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-IVGDCIAAMCKALSI 117
                   + +   GY   +LN GCP  +V +   G  LM + D +VG     + KA   
Sbjct: 75  PQYFPPVMEKLVSLGYRNFDLNAGCPVRKVLKSGSGVQLMEDLDRLVGLAAIMVAKAAEH 134

Query: 118 P----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKI 171
           P    V VK R+G  ++   V L +L + ++ +GVN + +H R  + +  G         
Sbjct: 135 PEGGRVGVKFRLGF-NKGEDVYL-DLARRLEDAGVNWVTLHPRYGRQMFGG--------- 183

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
            + D+  + E+K+      IG +G L      ++ +    +D +M  R A  + ++ +
Sbjct: 184 -SADWSKLAELKRAVSIPVIG-SGDLFSAEDGVRCIEETGIDAIMFARGALYDPSIFS 239


>gi|262280104|ref|ZP_06057889.1| tRNA-dihydrouridine synthase C [Acinetobacter calcoaceticus
           RUH2202]
 gi|262260455|gb|EEY79188.1| tRNA-dihydrouridine synthase C [Acinetobacter calcoaceticus
           RUH2202]
          Length = 314

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 95/210 (45%), Gaps = 23/210 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 53  LKNDGKTAAG-----TPVHVQFLGNNPDMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 106

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 107 RGGSVLLDEPDVVHMLIKAVRDAVPPHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 163

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKIL 207
            + +HAR         K +   P   ++ +  I KE   + +  NG +   S  +A +  
Sbjct: 164 WLTVHART--------KADGYTPPAYWEKILPI-KEALKINVIANGEIWSNSDARACQQQ 214

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              + +MIGR A     +   + E  +  L
Sbjct: 215 SGCEDLMIGRGAVTTPDLTQCIRENMNEAL 244


>gi|254168949|ref|ZP_04875788.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|197622055|gb|EDY34631.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
          Length = 299

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 91/183 (49%), Gaps = 22/183 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I G++  +    AK +ED+G + + LN+ CP A+     +G  +  + D+V + I
Sbjct: 92  PIIGSIFGSNAEEFSYLAKKMEDYGADAVELNLSCPHAK----GYGMEVGTDLDLVEEII 147

Query: 109 AAMCKALSIPVTVKCRIGVDDQIP-AVALRN-----LVKSIKKSGVNGIWIHARKAILK- 161
            ++ +A+ IPV  K     ++ +  A A  N     L+ ++K   ++   I A++ +LK 
Sbjct: 148 NSVKRAVKIPVWAKLTPNTNNIVEIAKAAENADAFVLINTLKAMAID---IDAKRPVLKN 204

Query: 162 ---GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGR 217
              GLS K    I  +    VYE+ +E     IG+ GG+E+   A++ ++     V IG 
Sbjct: 205 VFGGLSGK---AIKPIGVRAVYEVYREVEKPIIGV-GGIENGRDAIEYMMAGASAVEIGT 260

Query: 218 AAY 220
           A Y
Sbjct: 261 ALY 263


>gi|160884027|ref|ZP_02065030.1| hypothetical protein BACOVA_02001 [Bacteroides ovatus ATCC 8483]
 gi|156110757|gb|EDO12502.1| hypothetical protein BACOVA_02001 [Bacteroides ovatus ATCC 8483]
          Length = 314

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 39/165 (23%), Positives = 80/165 (48%), Gaps = 12/165 (7%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +A KI+  F   GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  +
Sbjct: 75  KAEKILSLFIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQTLLSLITEYPQISFS 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G +D  P   L+ L   I +  +  + +H R      L  +  +   +L     +
Sbjct: 135 IKMRLGWED--PEECLK-LAPIINELPLRQVVMHPR------LGKQQYKGEVDLKAFEAF 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +   ++P ++ G    +ED+ +  +  P + G+MIGR    N A+
Sbjct: 186 QNACKHPLIYNGDINSVEDIHRIQEQFPGLAGIMIGRGLLANPAL 230


>gi|262369265|ref|ZP_06062593.1| tRNA-dihydrouridine synthase C [Acinetobacter johnsonii SH046]
 gi|262315333|gb|EEY96372.1| tRNA-dihydrouridine synthase C [Acinetobacter johnsonii SH046]
          Length = 317

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 49/200 (24%), Positives = 88/200 (44%), Gaps = 16/200 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q  G D   L   A      G   I++N GCP+  V+    G+ L+  P
Sbjct: 63  GKTAAGTPVHVQFLGNDPEMLAANAIRAVKLGAPAIDMNFGCPAKTVNRHRGGSVLLDEP 122

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           ++V + + A+  A+   IPV+ K R+G  D+     L N   +I+ +G   + +HAR   
Sbjct: 123 EVVHELVKAVRDAVPAHIPVSAKMRLGYMDR--HFMLDN-AHAIEDAGAAWVTVHART-- 177

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGR 217
                 K +   P   +D +  I +E   + +  NG + + + A   ++    + +MIGR
Sbjct: 178 ------KADGYTPPAFWDQLRPI-REALKINVIANGEIWNNADAKQCRLESGCEDLMIGR 230

Query: 218 AAYKNSAMLTTVDEYFSNPL 237
            A     +   + +    PL
Sbjct: 231 GAVTTPDLTQCIRQNIDTPL 250


>gi|81902404|sp|Q91XI1|DUS3L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|15192726|gb|AAK84684.1| putative zinc finger protein [Mus musculus]
          Length = 637

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 63/278 (22%), Positives = 116/278 (41%), Gaps = 32/278 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      + +++NV
Sbjct: 322 EMAVCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINV 381

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V++   G  LM         +  +   L +P+TVK R GV +++ ++A R L+ 
Sbjct: 382 GCPIDLVYKKGGGCALMNRSAKFQQIVRGVNGVLDVPLTVKMRTGVQERV-SLAHR-LLP 439

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
            ++  GV  + +H R         ++ R     D+  + +  K    + +  NG     E
Sbjct: 440 ELRDWGVALVTLHGRS--------REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFE 491

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
           D + A++    V G+M+ R A     + T + E     ++ S     R+D      I   
Sbjct: 492 DANCAMQT--GVAGIMVARGALLKPWLFTEIKEQRHWDISSSE----RLD------ILRD 539

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 540 FTHYGLEHWGSDTQGVERTRRFLLEWLSF----LCRYV 573


>gi|167625806|ref|YP_001676100.1| nifR3 family TIM-barrel protein [Shewanella halifaxensis HAW-EB4]
 gi|167355828|gb|ABZ78441.1| putative TIM-barrel protein, nifR3 family [Shewanella halifaxensis
           HAW-EB4]
          Length = 322

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 62/242 (25%), Positives = 113/242 (46%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA-ILRGDKKNI-LGFSTQEKPLALQIGGAD 58
           M   TD+ +R    L    AL  +EM+ ++  +   DK  + +  + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLC-LRYGAALAVSEMLSSNPDVWDTDKSRLRMTHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQDPAQVEAILRAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPN 173
           VT+K R G      A   RN   + +  +  G+  + +H   R+ + KG          +
Sbjct: 136 VTLKIRTGW-----APEHRNGVHIAQIAEDCGIASLAVHGRTRQCMYKG----------D 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  IKK+   + +  NG +    +A  +L    VD +MIGR A     +   +  
Sbjct: 181 AEYDTIKAIKKQ-ISIPVVANGDILTPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQH 239

Query: 232 YF 233
           Y 
Sbjct: 240 YL 241


>gi|322828617|gb|EFZ32349.1| hypothetical protein TCSYLVIO_1313 [Trypanosoma cruzi]
          Length = 529

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 78/190 (41%), Gaps = 10/190 (5%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHE 90
           L+  + ++L     E    LQI  +        AK +E  GY+   I++N GCP   +  
Sbjct: 210 LQKSEWSLLRRHESEDVFGLQIAVSQPQSAQTWAKAIEASGYSYDFIDINCGCPVQMIMS 269

Query: 91  GSFGACLMLNPD-IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              G  L    D  + D ++++ +  S PV++KCRIG      A +L   +   +  G +
Sbjct: 270 AGCGCGLWERRDNRLRDIVSSLVQHQSKPVSIKCRIGAGANSNA-SLHEKIGDYEGWGAD 328

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + IH R         +   K+ N +Y      +   P +  G     ED+    +  P 
Sbjct: 329 AVTIHGR------FRAQRYTKLANWEYIDSCAARTSLPVIGNGDIFSYEDIIDHRERYPH 382

Query: 210 VDGVMIGRAA 219
           V   MIGR A
Sbjct: 383 VSSYMIGRGA 392


>gi|222111715|ref|YP_002553979.1| dihydrouridine synthase dus [Acidovorax ebreus TPSY]
 gi|221731159|gb|ACM33979.1| dihydrouridine synthase DuS [Acidovorax ebreus TPSY]
          Length = 338

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/217 (23%), Positives = 96/217 (44%), Gaps = 18/217 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   + E A  + + G   I+LN GCP+  V+    GA L+  P+ +   +
Sbjct: 68  PVRAQLLGSDPVSMAENAARLAELGPEGIDLNFGCPARTVNRHGGGAALLREPEAIAAVV 127

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +A+   +PV+ K R+G DD   A   R   +++++ G   + +HAR        P 
Sbjct: 128 AAVRRAVPAHLPVSAKMRLGYDD---ASLARECAQAMEQGGACELVVHARTKADGYRPPA 184

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              +IP +   +   +           NG +  +  AL+   +   D +M+GR    +  
Sbjct: 185 YWEQIPAIRAAVRIPLVA---------NGEIWTVQDALRCRAASGCDALMLGRGIVADPG 235

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDK--DFWRKISASM 259
           +   +  +     T + P    + +   FW+ + A +
Sbjct: 236 LALAIRAHDVGRHTIALPWAALLPQLERFWQLVCADL 272


>gi|240144438|ref|ZP_04743039.1| dihydrouridine synthase family protein [Roseburia intestinalis
           L1-82]
 gi|257203546|gb|EEV01831.1| dihydrouridine synthase family protein [Roseburia intestinalis
           L1-82]
          Length = 335

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 36/146 (24%), Positives = 64/146 (43%), Gaps = 14/146 (9%)

Query: 11  FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           +F   + N  + Y E+           K+IL    +   +  QI        +  AK + 
Sbjct: 33  YFTPFINNKKMNYKEI-----------KDILPEHNEGMHVVPQILTNRAEDFLAIAKELG 81

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           ++GY  +NLN+GCPS  V     GA  +  P+ +   +  +     + ++VK R+GV+D 
Sbjct: 82  NYGYESVNLNLGCPSGTVVAKHRGAGFLAVPEELDHFLEEIFAECPLRISVKTRVGVND- 140

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHAR 156
             A    +L+   +K  +  + IH R
Sbjct: 141 --AGEWEHLLSIYEKFPMEELIIHPR 164


>gi|254514890|ref|ZP_05126951.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR5-3]
 gi|219677133|gb|EED33498.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR5-3]
          Length = 315

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 59/117 (50%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G ++   P+ LQI G D + + E A    + G   I+LN GCP+  V+    G+ ++  P
Sbjct: 50  GRTSSGAPVFLQILGGDATLVAENAARAAELGGLGIDLNFGCPAKTVNRSDGGSIILREP 109

Query: 102 DIV--GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           + V      A     +S+P++VK R+G +D+       ++V  I  +  + + IHAR
Sbjct: 110 ERVHAIVAAARRAVPVSVPLSVKIRLGFEDRD---RFLDIVSGIDAAKPSELVIHAR 163


>gi|71422193|ref|XP_812059.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70876795|gb|EAN90208.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 529

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 78/190 (41%), Gaps = 10/190 (5%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHE 90
           L+  + ++L     E    LQI  +        AK +E  GY+   I++N GCP   +  
Sbjct: 210 LQKGEWSLLRRHESEDVFGLQIAVSQPQSAQTWAKAIEASGYSYDFIDINCGCPVQMIMS 269

Query: 91  GSFGACLMLNPD-IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              G  L    D  + D ++++ +  S PV++KCRIG      A +L   +   +  G +
Sbjct: 270 AGCGCGLWERRDNRLRDIVSSLVQHQSKPVSIKCRIGAGANSSA-SLHEKIGDYEGWGAD 328

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + IH R         +   K+ N +Y      +   P +  G     ED+    +  P 
Sbjct: 329 AVTIHGR------FRAQRYTKLANWEYIDSCAARTSLPVIGNGDIFSYEDIIDHRERYPH 382

Query: 210 VDGVMIGRAA 219
           V   MIGR A
Sbjct: 383 VSSYMIGRGA 392


>gi|301091909|ref|XP_002896129.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262094949|gb|EEY53001.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 480

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 33/126 (26%), Positives = 62/126 (49%), Gaps = 11/126 (8%)

Query: 35  GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSF 93
           GD       S +   +  QIG AD    ++AA+ V  D     +++N+GCP     +G  
Sbjct: 65  GDSVVFRTCSEEAGKVVFQIGTADAVLALKAAEAVARDVA--AVDINMGCPKHFSVQGGM 122

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGI 151
           GA L+  P++  D +  + + L+IPV+ K R+   + D +      +L + ++ +G   +
Sbjct: 123 GAALLRKPEVACDIMKTLRRNLNIPVSCKIRLLPEIQDTV------DLARRLEDAGACAV 176

Query: 152 WIHARK 157
            +H R+
Sbjct: 177 GVHMRQ 182


>gi|159489528|ref|XP_001702749.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158280771|gb|EDP06528.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 198

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/145 (24%), Positives = 63/145 (43%), Gaps = 13/145 (8%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N GCP         G+ ++  P  +   +A +     +PVTVK R+G +D+   + +
Sbjct: 2   LDINCGCPIYEATRRGMGSAMLRKPRALAKMVAGIAADSELPVTVKIRLGENDK--KIVV 59

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             +V  + ++G   + +H R A        + R     D+  V E+ +  P   IG NG 
Sbjct: 60  DTVVDYLHRAGAAAVTVHGRTA--------EQRYKKAADWAKVGEVARSTPVPIIG-NGD 110

Query: 197 L--EDMSQALKILPSVDGVMIGRAA 219
           +     + A +       VM GR A
Sbjct: 111 ILTHYEAHARRTESGCTAVMAGRGA 135


>gi|307171073|gb|EFN63116.1| tRNA-dihydrouridine synthase 3-like [Camponotus floridanus]
          Length = 592

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 46/213 (21%), Positives = 94/213 (44%), Gaps = 16/213 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A  IL+  ++   ++     E    +Q+ G +   L   A+++ ++   + I+LN+
Sbjct: 307 EMALAPKILKAAQEEWALVKRHESEDIFGVQLCGNNPGVLTRCAQLLNQEIDVDFIDLNL 366

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   ++    G+ ++    ++   + ++ + L IP+TVK R GV   I       L+ 
Sbjct: 367 GCPIDLIYRKGGGSGMLNRLHVLESVVKSISQVLDIPLTVKTRTGV--YIDKPIAHKLMP 424

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLE 198
             +  G + I +H R         ++ R     +++ + +       + +  NG     +
Sbjct: 425 RFRDWGASMITVHGRS--------REQRYTKLANWEYIEKCALAAQPIPVFGNGDVLSFD 476

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  +  KI  +V G+ IGR A     + T + E
Sbjct: 477 DYQRMKKICGTVQGITIGRGALIKPWIFTEIKE 509


>gi|207093032|ref|ZP_03240819.1| transcriptional regulator, putative [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 323

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 49/204 (24%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + N I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALEHVNGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  S  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTSKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|291242586|ref|XP_002741186.1| PREDICTED: CG3645-like [Saccoglossus kowalevskii]
          Length = 599

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 94/239 (39%), Gaps = 25/239 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E    +Q+ G+    + + A+I+ D    + I++NVGCP   V +   G  LM       
Sbjct: 307 EDLFGVQLCGSFPDTMTKCAEILNDKMDIDFIDVNVGCPIDLVFKKGGGCALMGRLSRFE 366

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             I  M   + IP+TVK R G+ D         ++  ++  GV+ + +H R         
Sbjct: 367 HIITGMSSVMDIPITVKMRAGIQDN--NFTAHKVLPRLRDWGVSMVTLHGRS-------- 416

Query: 166 KDNRKIPNLDYDIVY---EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           ++ R     D+D +    EI K  P    G     ED ++  +    V GVMI R A   
Sbjct: 417 REQRYTKIADWDYISKCAEIAKPMPLYGNGDILSYEDANRQ-RQHTGVSGVMIARGALIK 475

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             + T + E     ++ S     R D      I    T+Y   H  S  +    TR  +
Sbjct: 476 PWVFTEIKEQRHWDISSSE----RFD------ILRDFTNYGLEHWGSDQQGVDRTRRFL 524


>gi|57168706|ref|ZP_00367838.1| probable transcription regulator Cj0123c [Campylobacter coli
           RM2228]
 gi|57019987|gb|EAL56667.1| probable transcription regulator Cj0123c [Campylobacter coli
           RM2228]
          Length = 308

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/206 (24%), Positives = 98/206 (47%), Gaps = 22/206 (10%)

Query: 24  TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EMI ++A++    K  ++L  +  E P  +Q+ G D   L +A +++ +  + + I+ N
Sbjct: 36  SEMISSNALVYESSKTLHMLERAELENPYIVQVAGGDKEVLKKAVQMLNEMDFVDGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP  +V +   G+ L+ N ++    +  + +     +T VK R+G +++ P      +
Sbjct: 96  CGCPVNKVVKQCAGSALLENLELFKSLVGVIKENNKKSLTSVKFRLGFNEKYP----EKM 151

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K  +  GV+ + IH   RK +  G +  D   I N          K +  + +  NG +
Sbjct: 152 AKICESLGVDFVSIHGRTRKQLYSGKA--DYESIANA---------KASVKIPVIANGDI 200

Query: 198 EDM-SQALKILPSVDGVMIGRAAYKN 222
               ++ +  +   DG+MIGRA+  N
Sbjct: 201 NAQNAKEVYEITKCDGLMIGRASVGN 226


>gi|268319399|ref|YP_003293055.1| hypothetical protein FI9785_918 [Lactobacillus johnsonii FI9785]
 gi|262397774|emb|CAX66788.1| pyrD [Lactobacillus johnsonii FI9785]
          Length = 307

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 92/211 (43%), Gaps = 32/211 (15%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA+++ DK   L       P+   +GG D +  +E AK + D G  N + +NV CP+   
Sbjct: 80  DAVIK-DKLTPLRNEYPALPIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCPNVNQ 138

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              SFG      PD+V +    +   + IP+ VK    V D      +  + K+ +  G 
Sbjct: 139 GGMSFGVY----PDVVEELTKKIKSVVKIPIYVKLTPNVTD------ITQIAKAAENGGA 188

Query: 149 NG-----------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G           I +  RK +L     GLS      +  +   +V+++++      IG+
Sbjct: 189 DGLSLINTLLGMEIDVETRKPVLGHNIGGLS---GEAVKPIAIRMVHQVRESTTLPIIGM 245

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
            GG+      ++ IL   + V +G A +K+S
Sbjct: 246 -GGISSAKDVIEFILAGANAVAVGTAHFKDS 275


>gi|325849659|ref|ZP_08170862.1| dihydrouridine synthase (Dus) [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325480000|gb|EGC83078.1| dihydrouridine synthase (Dus) [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 220

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 46/204 (22%), Positives = 90/204 (44%), Gaps = 25/204 (12%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           G+ LM NP +V +    + K+    + +K R+G+DD+   +   ++ K  + +G++ + +
Sbjct: 10  GSQLMANPKLVEEICKTLRKSTDKKLNIKFRLGIDDK--HINYLDIGKIAQDTGIDYVIL 67

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVD 211
           HAR         KD     + ++D + ++ KEN  + +  NG +  +   +K+  L   D
Sbjct: 68  HAR--------TKDQMYSGHANWDHIRKL-KENLQIPVIANGDIFSVEDFIKVIDLTKAD 118

Query: 212 GVMIGRAAYKNSAMLTTVDEYF-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
           GVM+ R A  N  +   + +Y  +      SPI+          +   +  Y     +  
Sbjct: 119 GVMLARGAMGNPFLFKEIKDYIKTGNYNKPSPIEI---------VDQLIDQYKLELKYKE 169

Query: 271 GKL--QQITRHMIGLFHGFPNSRR 292
            KL   Q+ +H+     G  NS +
Sbjct: 170 EKLVVTQMRKHLSWYIKGLENSSK 193


>gi|299146981|ref|ZP_07040048.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 3_1_23]
 gi|298514866|gb|EFI38748.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 3_1_23]
          Length = 314

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 39/165 (23%), Positives = 80/165 (48%), Gaps = 12/165 (7%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +A KI+  F   GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  +
Sbjct: 75  KAEKILSLFIEKGYKEVDINIGCPFPMLAKRHNGSGILPYPEEVQALLSLITEYPQISFS 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G +D  P   L+ L   I +  +  + +H R      L  +  +   +L     +
Sbjct: 135 IKMRLGWED--PEECLK-LAPIINELPLRQVVMHPR------LGKQQYKGEVDLKAFEAF 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +   ++P ++ G    +ED+ +  +  P + G+MIGR    N A+
Sbjct: 186 QNACKHPLIYNGDINSVEDIHRIQEQFPGLAGMMIGRGLLANPAL 230


>gi|328851782|gb|EGG00933.1| hypothetical protein MELLADRAFT_39468 [Melampsora larici-populina
           98AG31]
          Length = 224

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 107/248 (43%), Gaps = 52/248 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNA--LLYTEMIVADAILRGD--------------KKNILGFS 44
           M+D  D+    F  L+  +   ++YT+MI AD  L                 K+  +   
Sbjct: 1   MIDQVDQSDLPFRILVARHGATMVYTQMIWADRFLSDPQYHDFHLNDVKAWCKRKDIEQD 60

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML--NPD 102
             + PL +Q+GG D+ +++  AK  E +  + I+LN+GCP     +  +GA L+   N D
Sbjct: 61  LTKIPLIVQLGGNDVERVLRTAKCFEPWC-DGIDLNMGCPQTHALQNGYGASLLFRKNHD 119

Query: 103 IVGDCIAAMCKALSIPVTV-----KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
                     +A+SI ++      KC+           + NLV   +++G + I +H R 
Sbjct: 120 ----------QAISIGISTSSLSYKCK-------EKAHIWNLVLLSRQAGASWITLHPR- 161

Query: 158 AILKGLSPKDNRK-IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
                +S +  RK  P L +  V E+K+      I  NGG+   S   K L     DG+M
Sbjct: 162 ----FISCRRRRKGSPFLRF--VKELKQAVKIPVIS-NGGVRSYSDFEKNLNETGADGLM 214

Query: 215 IGRAAYKN 222
           +G     N
Sbjct: 215 VGEPLLTN 222


>gi|221127160|ref|XP_002167936.1| PREDICTED: similar to predicted protein, partial [Hydra
           magnipapillata]
          Length = 156

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 33/111 (29%), Positives = 56/111 (50%), Gaps = 8/111 (7%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGY 74
           + N  L  T+ ++AD  +      +     +EK  L  Q+G  +  + +  A+++E    
Sbjct: 50  IENKLLDTTDFLLADGTV------VFRTCKEEKGKLVFQMGTNNAERALSVAQMLEK-DI 102

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           + I++N+GCP     +G  GA L+  PD V   +  + + LSIPVT K RI
Sbjct: 103 DGIDINMGCPKEFSVKGGMGAALLTQPDKVKQILTGLVQNLSIPVTCKIRI 153


>gi|323484713|ref|ZP_08090072.1| dihydrouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401950|gb|EGA94289.1| dihydrouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 325

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 58/261 (22%), Positives = 102/261 (39%), Gaps = 30/261 (11%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +IL        L  QI        + AAK +  +GY E+NLN+GCPSA V   + GA
Sbjct: 47  EKNDILPGHNAGISLVPQILTNKAEDFIWAAKELSSYGYREVNLNLGCPSATVTAKNKGA 106

Query: 96  CLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
             +  P+ +   +  +   L   ++ V+VK R G++          L+K   +  +  + 
Sbjct: 107 GFLSVPNELDRFLEQVFSGLETEAVQVSVKTRTGMESHD---EFEELLKIYNRYPLKELI 163

Query: 153 IHAR-KAILKGLSPKDN---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           IH R ++      P+     R +   +  + Y     N D+F                 P
Sbjct: 164 IHPRVRSDFYANKPEREVFCRGVRGSNNPVCY-----NGDIFTKEECARFRSDFPEDEFP 218

Query: 209 SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            +  +M+GR A  N  +   V           + ++   D+ F          Y  + + 
Sbjct: 219 MLKSIMLGRGAVANPWLFAEVKGIKERSKPDKATLRAFHDQIF----------YGYQEIM 268

Query: 269 SGG-----KLQQITRHMIGLF 284
           SG      K++++  +M GLF
Sbjct: 269 SGDRNTLFKMKELWFYMAGLF 289


>gi|195392594|ref|XP_002054942.1| GJ19062 [Drosophila virilis]
 gi|194149452|gb|EDW65143.1| GJ19062 [Drosophila virilis]
          Length = 137

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 43/148 (29%), Positives = 64/148 (43%), Gaps = 17/148 (11%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN 138
           +GCP     +G  GA L+ +P      +  +   L IPVT K RI  D  D I       
Sbjct: 1   MGCPKEFSIKGGMGAALLADPAKAAHILRTLSSQLDIPVTCKIRILPDLLDTI------R 54

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           LV+ +  +G+  I IHAR         +D R       D+++ +     D+ I  NGG  
Sbjct: 55  LVQQLAVTGIAAIGIHART--------RDERPQHRPHPDVLHAVASAV-DIPIIANGGSR 105

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAML 226
           DM    +    V  V++G  + K + ML
Sbjct: 106 DMHTFARFGIWVTTVVVGSKSLKIAEML 133


>gi|329663208|ref|NP_001193247.1| tRNA-dihydrouridine synthase 3-like [Bos taurus]
 gi|297476780|ref|XP_002688932.1| PREDICTED: Dihydrouridine synthase 3-like (S. cerevisiae)-like [Bos
           taurus]
 gi|296485774|gb|DAA27889.1| Dihydrouridine synthase 3-like protein [Bos taurus]
          Length = 650

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 117/283 (41%), Gaps = 42/283 (14%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 335 EMAVCTNLLQGQTSEWALLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIEVDF----V 390

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V +   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 391 DINVGCPIDLVFKKGGGCALMNRLAKFQQIVRGMNQVLDVPLTVKLRTGVQERV-NLAHR 449

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGG 196
            L+  ++  G   + +H R         ++ R     D+  + + +    P    G NG 
Sbjct: 450 -LLPDLRDWGAALVTLHGRS--------REQRYTKLADWQYIEQCVAAARPMPLFG-NGD 499

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +   ED ++AL+    V GVMI R A     + T + E     ++ S     R+D     
Sbjct: 500 VLSYEDANRALQT--GVAGVMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 548

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 549 -ILRDFTHYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 586


>gi|332852106|ref|ZP_08433933.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013150]
 gi|332867504|ref|ZP_08437657.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013113]
 gi|332872645|ref|ZP_08440613.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6014059]
 gi|332729478|gb|EGJ60817.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013150]
 gi|332733921|gb|EGJ65066.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013113]
 gi|332739174|gb|EGJ70033.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6014059]
          Length = 318

 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 57  LKNDGKTAAG-----TPVHVQFLGNNPEMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 110

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 111 RGGSVLLDEPDVVHMLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 167

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 168 WLTVHAR 174


>gi|323691781|ref|ZP_08106038.1| dihydrouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323504147|gb|EGB19952.1| dihydrouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 325

 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 59/261 (22%), Positives = 103/261 (39%), Gaps = 30/261 (11%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +IL        L  QI        + AAK +  +GY E+NLN+GCPSA V   + GA
Sbjct: 47  EKNDILPGHNAGISLVPQILTNKAEDFIWAAKELSSYGYREVNLNLGCPSATVTAKNKGA 106

Query: 96  CLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
             +  P+ +   +  +   L   ++ V+VK R G++     V    L+K   +  +  + 
Sbjct: 107 GFLSVPNELDRFLEQVFSGLETEAVQVSVKTRTGMESHDEFV---ELLKIYNRYPLKELI 163

Query: 153 IHAR-KAILKGLSPKDN---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           IH R ++      P+     R +   +  + Y     N D+F                 P
Sbjct: 164 IHPRVRSDFYANKPEREVFCRGVRGSNNPVCY-----NGDIFTKEECARFRSDFPEDEFP 218

Query: 209 SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            +  +M+GR A  N  +   V           + ++   D+ F          Y  + + 
Sbjct: 219 MLKSIMLGRGAVANPWLFAEVKGIKERSKPDKATLRAFHDQIF----------YGYQEIM 268

Query: 269 SGG-----KLQQITRHMIGLF 284
           SG      K++++  +M GLF
Sbjct: 269 SGDRNTLFKMKELWFYMAGLF 289


>gi|255690639|ref|ZP_05414314.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides finegoldii DSM 17565]
 gi|260623662|gb|EEX46533.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides finegoldii DSM 17565]
          Length = 313

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 47/234 (20%), Positives = 94/234 (40%), Gaps = 31/234 (13%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY E ++N+GCP   + +   G+ ++  P+ V   +  + K   I  +VK R+G ++   
Sbjct: 86  GYGEADINLGCPFPILAKRHNGSGILPYPEEVKTLLGIVVKYPQIRFSVKMRLGWENPEE 145

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            +A+  L+  +    +  + +H R      L  +  +   +L+    ++   ++P ++ G
Sbjct: 146 CLAIAPLLNDLP---LRQVTMHPR------LGKQQYKGDVDLEGFAAFQSVCKHPLIYNG 196

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSA----------------------MLTTVD 230
                ED+ +  +  P + GVMIGR    N A                      M T+V 
Sbjct: 197 DIKRREDILRIQEQFPMLAGVMIGRGLLANPALALEYKENRTLSADEMRNKLHSMHTSVY 256

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             ++  L G         K FW  ++        + +H  G  Q+  + ++  F
Sbjct: 257 SQYAAQLEGGEGQLLNKMKTFWEYLAPEADRKLLKAIHKSGTFQKYNQAVLSFF 310


>gi|169634141|ref|YP_001707877.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii SDF]
 gi|169152933|emb|CAP01974.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii]
          Length = 321

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 53  LKNDGKTAAG-----TPVHVQFLGNNPEMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 106

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 107 RGGSVLLDEPDVVHMLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 163

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 164 WLTVHAR 170


>gi|217033055|ref|ZP_03438523.1| hypothetical protein HPB128_5g8 [Helicobacter pylori B128]
 gi|298736427|ref|YP_003728953.1| tRNA-dihydrouridine synthase B [Helicobacter pylori B8]
 gi|216945227|gb|EEC23910.1| hypothetical protein HPB128_5g8 [Helicobacter pylori B128]
 gi|298355617|emb|CBI66489.1| tRNA-dihydrouridine synthase B [Helicobacter pylori B8]
          Length = 328

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 99/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKILKVIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDRYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|45190676|ref|NP_984930.1| AER070Cp [Ashbya gossypii ATCC 10895]
 gi|74693589|sp|Q757E3|DUS3_ASHGO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|44983655|gb|AAS52754.1| AER070Cp [Ashbya gossypii ATCC 10895]
          Length = 647

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 77/179 (43%), Gaps = 31/179 (17%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQI 131
           G +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  +PV+VK R G  D  
Sbjct: 359 GLSEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDVPVSVKLRTGTRDGH 418

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV---------YE- 181
           P +AL    + + ++ V  I +H R         +  R   + D+D V         YE 
Sbjct: 419 P-IALGLCKRLVMETDVAAITLHGRT--------RQQRYTRSADWDYVGQVADALRSYET 469

Query: 182 -----IKKENPDL---FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                +K     L   F+G NG   +     + L   +VD VM+ R A     +   VD
Sbjct: 470 ERAEKLKDREGKLRIQFVG-NGDCNNWEDWYRHLENENVDSVMVARGALIKPWIFEEVD 527


>gi|327288843|ref|XP_003229134.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Anolis
           carolinensis]
          Length = 624

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 20/237 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF---STQEKPLALQIGGA 57
           +  W +  +R   +    + +  +E+I +  + +GD +    F      E    +Q+ G+
Sbjct: 260 LAKWGNLPFRRICKRFGAD-ITCSEVISSQDLCQGDLEKCAEFFHRHESEDFFGIQVEGS 318

Query: 58  DISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +V+ A+ + E    + +++N   P   + E   G+ LM++P+   + +  M    +
Sbjct: 319 APEHMVKCAEFLNERIQVDFVDINAEGPV--LFEKGSGSALMMHPNTFENIVRGMDYVSN 376

Query: 117 IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +P+TVK R G+  D+ +       L+  + + G   + +H R       SP D   I + 
Sbjct: 377 VPITVKLRSGISLDENL----AHTLIPDLHRWGAAMVTLHGRVKESTFRSPADWNYISH- 431

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                 +I K  P    G     ED+ +A +    V GVMIGR A     + T + E
Sbjct: 432 ----CAQIAKPMPLFGCGDIFSFEDVLKAKQT--GVSGVMIGRGALVKPWIFTEIKE 482


>gi|169797018|ref|YP_001714811.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AYE]
 gi|213156578|ref|YP_002318239.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB0057]
 gi|215484478|ref|YP_002326713.1| Dihydrouridine synthase (Dus) family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260555690|ref|ZP_05827910.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii ATCC 19606]
 gi|301347725|ref|ZP_07228466.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB056]
 gi|301512473|ref|ZP_07237710.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB058]
 gi|301594395|ref|ZP_07239403.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB059]
 gi|169149945|emb|CAM87839.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AYE]
 gi|213055738|gb|ACJ40640.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB0057]
 gi|213987092|gb|ACJ57391.1| Dihydrouridine synthase (Dus) family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260410601|gb|EEX03899.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii ATCC 19606]
          Length = 314

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 53  LKNDGKTAAG-----TPVHVQFLGNNPEMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 106

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 107 RGGSVLLDEPDVVHMLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 163

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 164 WLTVHAR 170


>gi|184157069|ref|YP_001845408.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|239501250|ref|ZP_04660560.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii AB900]
 gi|183208663|gb|ACC56061.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|322506968|gb|ADX02422.1| dusC [Acinetobacter baumannii 1656-2]
 gi|323516835|gb|ADX91216.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii TCDC-AB0715]
          Length = 307

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 46  LKNDGKTAAG-----TPVHVQFLGNNPEMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 99

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 100 RGGSVLLDEPDVVHMLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 156

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 157 WLTVHAR 163


>gi|169836870|ref|ZP_02870058.1| hypothetical protein cdivTM_07144 [candidate division TM7
           single-cell isolate TM7a]
          Length = 79

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 2/79 (2%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           ST E P+  QI G + + +   A    + G++ I++N+GCP A+    S GA L+ NP++
Sbjct: 1   STDEDPIVAQIWGGNPNDMQNLASYCRELGFHGIDINMGCP-AKSAIKSGGAALIRNPEL 59

Query: 104 VGDCIAAMCKALSIPVTVK 122
             + I A  KA ++PV+VK
Sbjct: 60  AIESIKA-AKAANLPVSVK 77


>gi|254481818|ref|ZP_05095061.1| Dihydrouridine synthase superfamily protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037947|gb|EEB78611.1| Dihydrouridine synthase superfamily protein [marine gamma
           proteobacterium HTCC2148]
          Length = 325

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 33/110 (30%), Positives = 56/110 (50%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--D 106
           P+ +Q+ G D + + E A    + G   I+LN GCP+  V+    G+ L+  P+ V    
Sbjct: 64  PVYIQLLGGDPTVVAENAARAAELGAPGIDLNFGCPAKTVNRSDGGSILLRQPERVAAIT 123

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                    ++PVTVK R+G +DQ+      ++V  I ++G   + +HAR
Sbjct: 124 AAVRRAVPAAVPVTVKTRLGYEDQL---QFLDIVAGIAEAGATELTVHAR 170


>gi|316968258|gb|EFV52559.1| dihydrouridine synthase (Dus) superfamily [Trichinella spiralis]
          Length = 355

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 2/80 (2%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +++PL  Q    +   L  AA +V +   + I++N+GCP      G +GA L  + D+V 
Sbjct: 23  EDRPLIAQFCANEPETLFNAASLVAN-QCDAIDINLGCPQTIARRGKYGAYLQDDWDLVS 81

Query: 106 DCIAAMCKALSIPVTVKCRI 125
             I + C+ L IPVT K RI
Sbjct: 82  SLIKSACR-LPIPVTCKIRI 100


>gi|210633854|ref|ZP_03297869.1| hypothetical protein COLSTE_01786 [Collinsella stercoris DSM 13279]
 gi|210159023|gb|EEA89994.1| hypothetical protein COLSTE_01786 [Collinsella stercoris DSM 13279]
          Length = 330

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 61/131 (46%), Gaps = 6/131 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEKP-LALQIGGAD 58
           M   TD  YR   R      L YTEM+ VA    +  K  +L     E+P + +Q+ G  
Sbjct: 18  MAGVTDAAYRIMCRR-RGAELAYTEMVSVAGLSYKSAKTWVLVEPEPEEPQICVQLFGTK 76

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A   V++   ++   I++N+ CP+ +V     G+ LM  P++    + A  +  
Sbjct: 77  PEQFAYAVDSVQERVGDKLSLIDINMACPARKVITKGEGSALMKTPELAASLVEASVREA 136

Query: 116 SIPVTVKCRIG 126
            +PVTVK R G
Sbjct: 137 RVPVTVKIRRG 147


>gi|260550991|ref|ZP_05825196.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. RUH2624]
 gi|260405939|gb|EEW99426.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. RUH2624]
          Length = 314

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 53  LKNDGKTAAG-----TPVHVQFLGNNPDMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 106

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 107 RGGSVLLDEPDVVHILIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 163

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 164 WLTVHAR 170


>gi|313611217|gb|EFR86015.1| probable tRNA-dihydrouridine synthase 1 [Listeria monocytogenes FSL
           F2-208]
          Length = 123

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 51/87 (58%), Gaps = 3/87 (3%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIV 104
           ++N+GCP  ++ +   GA  +L+P+ V
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPNKV 123


>gi|193076570|gb|ABO11229.2| hypothetical protein A1S_0789 [Acinetobacter baumannii ATCC 17978]
          Length = 307

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 46  LKNDGKTAAG-----TPVHVQFLGNNPEMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 99

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 100 RGGSVLLDEPDVVHMLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AYAVEDAGAS 156

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 157 WLTVHAR 163


>gi|325118549|emb|CBZ54100.1| Dihydrouridine synthase, related [Neospora caninum Liverpool]
          Length = 1295

 Score = 48.9 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 39/141 (27%), Positives = 67/141 (47%), Gaps = 8/141 (5%)

Query: 24   TEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYNEINL 79
            +EM VA +I+ G +   ++L     EK   +QI G     L   A ++  E+   + I+L
Sbjct: 922  SEMAVAKSIVEGKQSELSLLKRHKSEKFFGVQIAGGTPEVLNACADVLASEEVSCDFIDL 981

Query: 80   NVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALR 137
            N  CP  ++H     GAC++ +P  +   I  +  +   I +TVK R    +Q     L 
Sbjct: 982  NAACPLVQLHRRFKAGACMLDHPARLESLIEGVTMRQPEIALTVKLRTA--NQGKKQVLH 1039

Query: 138  NLVKSIKKSGVNGIWIHARKA 158
            N ++ + ++G   + IH R A
Sbjct: 1040 NFIQRLGQAGAAALIIHGRTA 1060


>gi|149247657|ref|XP_001528237.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|187471054|sp|A5DTS1|DUS3_LODEL RecName: Full=tRNA-dihydrouridine synthase 3
 gi|146448191|gb|EDK42579.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 642

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 49/168 (29%), Positives = 75/168 (44%), Gaps = 35/168 (20%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGV-DDQIP 132
           +EINLN GCP   + +   G+ L+ +P  +   + AM   +  IPVT+K R GV +++  
Sbjct: 359 SEINLNCGCPIDLLFKQGQGSALLDSPPRLIRIVKAMNASSGDIPVTIKIRTGVKENKNT 418

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK-------- 184
           AV L N V  ++++ V  I +H R         +  R     D+D + E+ K        
Sbjct: 419 AVHLVNRV--LEETQVAAITLHGRS--------RQQRYTKEADWDYIEEVGKVVKTWNEK 468

Query: 185 ----------ENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
                      NP  F+G NG +   ED    +     VD VM+ R A
Sbjct: 469 REDEDKEGRDTNPTWFVG-NGDVYSHEDWYNGVN-REGVDSVMVARGA 514


>gi|116669897|ref|YP_830830.1| nifR3 family TIM-barrel protein [Arthrobacter sp. FB24]
 gi|116610006|gb|ABK02730.1| putative TIM-barrel protein, nifR3 family [Arthrobacter sp. FB24]
          Length = 392

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 58/297 (19%), Positives = 118/297 (39%), Gaps = 27/297 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    ++  I+     EK  ++Q+ G D
Sbjct: 33  MAGITNSAFRRLCREY-GGGMYVAEMVTSRALVERTPESLRIISHDDDEKVRSVQLYGVD 91

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A + +VE+   + I+LN GCP  +V     G+ L    D+    +    K  S 
Sbjct: 92  PVTVGQAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTSIVQTAVKEASK 151

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             +P+T+K R G+D+    +   +  +  + +GV  + +H R A     G          
Sbjct: 152 GNVPLTIKMRKGIDED--HLTYLDAGRIARDAGVAAVALHGRTAAQFYSG---------- 199

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA--YKNSAMLTTVD 230
             D+  +  +++  PD+ +  NG +     A++++       +           +   + 
Sbjct: 200 QADWSAIARLREALPDIPVLGNGDIWSAEDAVRMVRETGVDGVVVGRGCQGRPWLFGDLQ 259

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
             F    T   P   +V +  +R     +  +       G  L++I +HM   F G+
Sbjct: 260 AAFEGSDTRHRPNLRQVAEGVYRHAELMVETFG----DEGKALREIRKHMAWYFKGY 312


>gi|242072234|ref|XP_002446053.1| hypothetical protein SORBIDRAFT_06g001050 [Sorghum bicolor]
 gi|241937236|gb|EES10381.1| hypothetical protein SORBIDRAFT_06g001050 [Sorghum bicolor]
          Length = 679

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 62/283 (21%), Positives = 106/283 (37%), Gaps = 39/283 (13%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM ++  +L+G      +L     E    +QI G     +    ++V+ +   + I++N+
Sbjct: 356 EMAMSTNLLQGQASEWALLRRHPSEDLFGVQICGPYPDTVARTVELVDNECPVDFIDINM 415

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--- 138
           GCP   V     G+ L+  P  +   + A       P+TVK R            RN   
Sbjct: 416 GCPIDIVVNKGAGSSLLTKPMRIRSIVQAASSVTEKPLTVKVRTAF------FEGRNRAD 469

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG- 196
            +V  I   G + I IH R         +  R     D+D +Y+  ++ PD    +  G 
Sbjct: 470 SIVSDIYDWGASAITIHGRS--------RQQRYSKLADWDYIYQCAQKAPDYLHVIGNGD 521

Query: 197 ---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D ++ +     +   MI R A     + T + E     +T     +  + KDF R
Sbjct: 522 VFSFTDWNKHVSDCSKISTCMIARGALIKPWLFTEIKEQRHWDITSGE--RLNILKDFVR 579

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   H  S  K  + TRH +  +  +     CR+I
Sbjct: 580 --------FGLEHWGSDSKGVETTRHFLLEWLSY----TCRYI 610


>gi|307637408|gb|ADN79858.1| tRNA di hydro uridine synthase B [Helicobacter pylori 908]
 gi|325995999|gb|ADZ51404.1| tRNA dihydrouridine synthase B [Helicobacter pylori 2018]
 gi|325997594|gb|ADZ49802.1| putative tRNA dihydrouridine synthase B [Helicobacter pylori 2017]
          Length = 328

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 99/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDRYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|293609101|ref|ZP_06691404.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292829674|gb|EFF88036.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 307

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 46  LKNDGKTAAG-----TPVHVQFLGNNPDMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 99

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 100 RGGSVLLDEPDVVHLLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 156

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 157 WLTVHAR 163


>gi|219121577|ref|XP_002181140.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407126|gb|EEC47063.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 545

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 37/143 (25%), Positives = 65/143 (45%), Gaps = 8/143 (5%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM VA  +L G      +L    +E    +QI            +++E +   + ++LN+
Sbjct: 217 EMAVATNLLSGQSSEWALLKRHPEEDIFGVQIAAGYPDVFARTCELIENEMNVDFVDLNL 276

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     GA LM+    +   +  + + L+ P+++K R G +   P     NLV+
Sbjct: 277 GCPLDIVCNKGSGAALMMRDKRLRSSVEGILETLTCPISIKMRTGWEMTKPFA--HNLVQ 334

Query: 142 SIKKSGVNGI---WIHARKAILK 161
            I+  G++GI    IH R  + +
Sbjct: 335 KIQSWGLDGISAVMIHGRSRLQR 357


>gi|108563136|ref|YP_627452.1| transcriptional regulator [Helicobacter pylori HPAG1]
 gi|107836909|gb|ABF84778.1| transcriptional regulator [Helicobacter pylori HPAG1]
          Length = 328

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + D +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLDHLVKLLKIIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|325121123|gb|ADY80646.1| tRNA-dihydrouridine synthase C [Acinetobacter calcoaceticus PHEA-2]
          Length = 307

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 65/127 (51%), Gaps = 12/127 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEG 91
           L+ D K   G      P+ +Q  G +   L   AAK+VE  G   I+LN GCP+  V+  
Sbjct: 46  LKNDGKTAAG-----TPVHVQFLGNNPDMLAANAAKVVE-LGAPAIDLNFGCPAKTVNRH 99

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             G+ L+  PD+V   I A+  A+   IPV+ K R+G  D+     + N   +++ +G +
Sbjct: 100 RGGSVLLDEPDVVHLLIKAVRDAVPAHIPVSAKMRLGYLDE--NHTMEN-AHAVEDAGAS 156

Query: 150 GIWIHAR 156
            + +HAR
Sbjct: 157 WLTVHAR 163


>gi|255023090|ref|ZP_05295076.1| hypothetical protein LmonocyFSL_05790 [Listeria monocytogenes FSL
           J1-208]
          Length = 122

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 50/85 (58%), Gaps = 3/85 (3%)

Query: 21  LLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEI 77
           L+  EMI    I   + K  ++L    +EKPL+LQI G +   LVEAAK V E+   + I
Sbjct: 37  LVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGEKETLVEAAKFVAENTTADII 96

Query: 78  NLNVGCPSARVHEGSFGACLMLNPD 102
           ++N+GCP  ++ +   GA  +L+P+
Sbjct: 97  DINMGCPVNKIIKCEAGAKWLLDPN 121


>gi|313235191|emb|CBY25064.1| unnamed protein product [Oikopleura dioica]
          Length = 286

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 63/286 (22%), Positives = 120/286 (41%), Gaps = 38/286 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  + ++ M+++D+ +     +   L  + ++ PL +Q     
Sbjct: 1   MVRYSRLPFRALCRKF-NVDVCFSPMLISDSFINSASARDADLRSNAEDGPLVVQFAANK 59

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
                + A+++  +G+ E I+LN GCP   V+  ++G  LM  P+++ D +    +A+  
Sbjct: 60  GEDFAKVAQML--YGHCEGIDLNCGCPQRWVNALNYGDILMKQPELLADIVLQARRAIPD 117

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
               ++VK R+  DD    +    + + I+K+G   + IH R            R  P +
Sbjct: 118 SEFSISVKTRV-FDDLHTTI---EMARRIEKAGATMLSIHGRT--------HGERDHP-V 164

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
             + +  I  E   + +  NG +     A     S  V GVM+ R    N  +       
Sbjct: 165 RIETISTI-VETLSIPVNYNGSIRTREDAQLAYESTGVGGVMVARGLLHNPGL------- 216

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
           F +   G   + T      W KI+  +   Y++ H H    L ++T
Sbjct: 217 FDDRRLGDPEVLTE-----WTKIALELGIPYSSYHKHLMYMLDKVT 257


>gi|15611731|ref|NP_223382.1| putative transcriptional regulator [Helicobacter pylori J99]
 gi|39930913|sp|Q9ZLB6|DUS_HELPJ RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|4155212|gb|AAD06235.1| putative TRANSCRIPTIONAL REGULATOR [Helicobacter pylori J99]
          Length = 328

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 99/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + + + +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVEILKVIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDRYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRA  +
Sbjct: 204 VKKAFEVLQITQADGLMIGRATLR 227


>gi|70930687|ref|XP_737208.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56512402|emb|CAH78878.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 141

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 34/111 (30%), Positives = 57/111 (51%), Gaps = 4/111 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M  +   +   K     F T  Q+KPL +Q  G D
Sbjct: 32  MVDLSELPFRLLCRNY-NCDLAFTPMFHSKNFVEHSKYRTGYFKTCDQDKPLIVQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
            S +++A   ++D   N +++N+GCP     +G++GA L+   D V + I+
Sbjct: 91  PSIILKAIDYIKD-EVNGVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLIS 140


>gi|254166940|ref|ZP_04873794.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|289596507|ref|YP_003483203.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|197624550|gb|EDY37111.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|289534294|gb|ADD08641.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
          Length = 299

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 91/183 (49%), Gaps = 22/183 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I G++  +    AK +ED+G + + LN+ CP A+     +G  +  + ++V + I
Sbjct: 92  PIIGSIFGSNPEEFSYLAKKMEDYGADAVELNLSCPHAK----GYGMEVGTDLELVEEII 147

Query: 109 AAMCKALSIPVTVKCRIGVDDQIP-AVALRN-----LVKSIKKSGVNGIWIHARKAILK- 161
            ++ +A+ IPV  K     ++ +  A A  N     L+ ++K   ++   I A++ +LK 
Sbjct: 148 NSVKRAVKIPVWAKLTPNTNNIVEIAKAAENADAFVLINTLKAMAID---IDAKRPVLKN 204

Query: 162 ---GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGR 217
              GLS    + I  +    VYE+ +E     IG+ GG+E+   A++ I+     V IG 
Sbjct: 205 VFGGLS---GKAIKPIGVRAVYEVYREIEKPIIGV-GGIENGRDAIEYIMAGASAVEIGT 260

Query: 218 AAY 220
           A Y
Sbjct: 261 ALY 263


>gi|296421752|ref|XP_002840428.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295636644|emb|CAZ84619.1| unnamed protein product [Tuber melanosporum]
          Length = 707

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 46/161 (28%), Positives = 71/161 (44%), Gaps = 18/161 (11%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKLVEAA 66
           F RL +    AL Y+EM ++  +L+G K    +L     E P    QI G  I   V A 
Sbjct: 339 FRRLCSRLGAALTYSEMAMSVPLLQGHKPEWALLRAHASEIPNFGAQICGTKIGTAVRAT 398

Query: 67  KIVEDF---------GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
           +++            G + ++LN GCP   V+    G+ L+  P  +   +  M   +  
Sbjct: 399 EVLTTLFPSAASSRHGLSLVDLNCGCPIDLVYRQGGGSALLDQPSKLIKMLKGMNYVSGE 458

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHAR 156
            P+T K R+G  D  P    + LV+ I  +G V  I +H R
Sbjct: 459 TPITCKIRLGTRDSSPVA--KKLVQRIYDAGDVQAITLHGR 497


>gi|160900633|ref|YP_001566215.1| dihydrouridine synthase DuS [Delftia acidovorans SPH-1]
 gi|160366217|gb|ABX37830.1| dihydrouridine synthase DuS [Delftia acidovorans SPH-1]
          Length = 329

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/159 (24%), Positives = 77/159 (48%), Gaps = 14/159 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D   +   A  +   G   I+LN GCP+  V+    GA L+ +P+ +   +
Sbjct: 64  PVRAQLLGSDPDSMAANAANLARLGPEGIDLNFGCPAKVVNRHGGGAALLQDPEQIARVV 123

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+  A+  ++PV+ K R+G +D      +    ++++  G   I +HAR  +       
Sbjct: 124 GAVRAAVPAAMPVSAKMRLGFND---TTLMTECAQAMQAGGACEIVVHARTKL------- 173

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           D  + P   +D++  I +E+  + +  NG +  +  AL+
Sbjct: 174 DGYRPPAY-WDMIPRI-RESVTVPVVANGEIWTVEDALR 210


>gi|254581674|ref|XP_002496822.1| ZYRO0D08932p [Zygosaccharomyces rouxii]
 gi|238939714|emb|CAR27889.1| ZYRO0D08932p [Zygosaccharomyces rouxii]
          Length = 373

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 51/197 (25%), Positives = 98/197 (49%), Gaps = 27/197 (13%)

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDC 107
           +  QIG +  S  ++AA  +++D   + I++N GCP    +H G  GA L+  PD + + 
Sbjct: 80  IVFQIGTSTPSLAIQAALTVIQDV--DGIDINAGCPKHFSIHSG-MGAALLRTPDKLCEI 136

Query: 108 IAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +  + + +  P    ++VK R+ +D++   +    L+  + ++G++ + +H R       
Sbjct: 137 LCELVEKVGRPYGKTISVKIRL-LDNREDTL---QLINRLCQTGISHLTVHCRT------ 186

Query: 164 SPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDGVMIGR 217
           +P  NR+ P   Y   +YE+ + N    I +NGG++  S   +I     LP   G M+  
Sbjct: 187 TPMRNREQPIRGYIKEIYEVCQTNGVTLI-INGGIKSRSHFQEIQRDLELPKEIGGMMAD 245

Query: 218 AAYKN-SAMLTTVDEYF 233
            A +N +  L +  E+F
Sbjct: 246 CAEQNPTVFLDSPIEWF 262


>gi|182417542|ref|ZP_02948869.1| dihydrouridine synthase family protein [Clostridium butyricum 5521]
 gi|237665938|ref|ZP_04525926.1| dihydrouridine synthase, DuS [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182378711|gb|EDT76238.1| dihydrouridine synthase family protein [Clostridium butyricum 5521]
 gi|237658885|gb|EEP56437.1| dihydrouridine synthase, DuS [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 311

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/222 (21%), Positives = 98/222 (44%), Gaps = 27/222 (12%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +++ GY+E+NLN+GCPS  V     G+  + + D +   + A+     I +++K RIGV+
Sbjct: 80  MKNMGYDEVNLNLGCPSGTVVAKGRGSGFLAHKDELDRFLEAIFSKTEIKISIKTRIGVN 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--EN 186
               +    +++    K  +  + IH R  I K       +  PN+  D+  E  K  +N
Sbjct: 140 S---SDDFNDIMNIYNKYPLEELIIHPR--IQKDFY----KNTPNM--DVFKEALKSSKN 188

Query: 187 PDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           P   +  NG + +     +++     ++ VM+GR    N  ++  + +   N  T    +
Sbjct: 189 P---VCYNGDIFNSHHYKRVVDECSDINAVMLGRGIITNPGLIKEITD---NEFTDKKNL 242

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           K      F  ++     +  +   +   K+++   +MI +F 
Sbjct: 243 KK-----FHNQVYLGYKEILSGDKNVLFKMKEFWFYMINIFE 279


>gi|325960157|ref|YP_004291623.1| TiM-barrel protein [Methanobacterium sp. AL-21]
 gi|325331589|gb|ADZ10651.1| TIM-barrel protein [Methanobacterium sp. AL-21]
          Length = 238

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/146 (26%), Positives = 70/146 (47%), Gaps = 17/146 (11%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           + +N  C  A + +  +G  LM  PD + + +    +  S  V+VK R  V+     V  
Sbjct: 99  VEINAHCRQAELVKSGYGQALMNYPDELYNLVHGTVEGCSKQVSVKIRANVE----GVNY 154

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             ++++I+ +G + I + A K               + DYD +  +K+ N D F+  N  
Sbjct: 155 LKVLEAIENAGAHYIHVDAMKP-----------GYDSADYDFITWVKR-NTDSFVIGNNS 202

Query: 197 LEDMSQALKILPS-VDGVMIGRAAYK 221
           ++D++ A K+L S  DG+ I RAA +
Sbjct: 203 IKDIASARKMLSSGADGISIARAAIR 228


>gi|308182888|ref|YP_003927015.1| putative transcriptional regulator [Helicobacter pylori PeCan4]
 gi|308065073|gb|ADO06965.1| putative transcriptional regulator [Helicobacter pylori PeCan4]
          Length = 328

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSLLEDHFMAQISGSKESVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKEKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|254566505|ref|XP_002490363.1| Dihydrouridine synthase, member of a family of dihydrouridine
           synthases [Pichia pastoris GS115]
 gi|238030159|emb|CAY68082.1| Dihydrouridine synthase, member of a family of dihydrouridine
           synthases [Pichia pastoris GS115]
 gi|328350757|emb|CCA37157.1| tRNA-dihydrouridine synthase 2 [Pichia pastoris CBS 7435]
          Length = 366

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 98/232 (42%), Gaps = 43/232 (18%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNP----DIV 104
           L  Q+G A+    V AAKIV +   + I++N GCP    +H G  GA L+  P    +I+
Sbjct: 87  LIFQMGTANPELAVRAAKIVVN-DVSGIDVNAGCPKHFSIHSG-MGAALLSTPALLEEIL 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
              +  + +    P++VK R+  ++Q        LV+ + K+G++ + +H R   ++   
Sbjct: 145 TRLVTEVGRPNGKPISVKIRVLENEQ----KTLELVERLVKTGISNLTVHCRTKNMR--- 197

Query: 165 PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---GVMIGRAA 219
              NR+ P  DY   I+   +     L I  NGG++D +  + I        G M+   A
Sbjct: 198 ---NREAPIRDYLEGILDHCRSNKVSLVI--NGGIKDRNDFIAIQEKYGMDVGAMVASEA 252

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
             N      V      PL              WR++     ++A R  +  G
Sbjct: 253 ELNPTCFRKV------PLP-------------WREVCKEFLEFADRFANWKG 285


>gi|317180488|dbj|BAJ58274.1| transcriptional regulator [Helicobacter pylori F32]
          Length = 328

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + N I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVNGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|71414125|ref|XP_809176.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70873517|gb|EAN87325.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 529

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/190 (25%), Positives = 78/190 (41%), Gaps = 10/190 (5%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHE 90
           L+  + ++L     E    LQI  +        AK +E  GY+   I++N GCP   +  
Sbjct: 210 LQKGEWSLLRRHESEDVFGLQIAVSQPQSAQTWAKAIEASGYSYDFIDINCGCPVQMIMS 269

Query: 91  GSFGACLMLNPD-IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              G  L    D  + D ++++ +  S PV++KCRIG      A +L   +   +  G +
Sbjct: 270 AGCGCGLWERRDNRLRDIVSSLVQHQSKPVSIKCRIGAGANSNA-SLHEKIGDYEGWGAD 328

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + IH R         +   K+ N +Y      +   P +  G     ED+    +  P 
Sbjct: 329 AVTIHGR------FRAQRYTKLANWEYIDSCAARTSLPVIGNGDIFSYEDIIGHRERYPH 382

Query: 210 VDGVMIGRAA 219
           V   MIGR A
Sbjct: 383 VSSYMIGRGA 392


>gi|164663047|ref|XP_001732645.1| hypothetical protein MGL_0420 [Malassezia globosa CBS 7966]
 gi|190359304|sp|A8PTG4|DUS3_MALGO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|159106548|gb|EDP45431.1| hypothetical protein MGL_0420 [Malassezia globosa CBS 7966]
          Length = 766

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 100/227 (44%), Gaps = 23/227 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE---DFGYNEINL 79
           EM +A++ L+G   + +++     E+    Q+ GA    LV  A+++      G + +++
Sbjct: 425 EMGMAESFLQGHASEWSLVRRWEGERIFGTQVCGAKPELLVPTAEVLAREVGRGLDFVDV 484

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N GCP   V+    G+ L+ + + +G  +  M +AL  IP+T+K R G   +      + 
Sbjct: 485 NCGCPIDLVYNKGAGSALLDHANKLGRIVRGMSEALGEIPLTIKLRTGTTSK--PTTHKI 542

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDN---RKIPNLDYDIVYEIKKE-----NPDLF 190
             ++  + GV G+ +H R    +  +  D    R   +  +D V    +E      PD+ 
Sbjct: 543 FARAQTEWGVGGLSLHGRSRKQRYKNDADWAYIRTCVDTLHDAVRTWNEEPQHADEPDMV 602

Query: 191 ---IGLNG---GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              +  NG   G  D    L+    VDG MI R A     + T + E
Sbjct: 603 PVPVYGNGDVYGWRDYYDHLEHA-HVDGTMIARGALIKPWIFTEIKE 648


>gi|298245190|ref|ZP_06968996.1| dihydrouridine synthase DuS [Ktedonobacter racemifer DSM 44963]
 gi|297552671|gb|EFH86536.1| dihydrouridine synthase DuS [Ktedonobacter racemifer DSM 44963]
          Length = 404

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/273 (21%), Positives = 103/273 (37%), Gaps = 66/273 (24%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKL 62
           TD   R    L     ++ TE    + + +G  +    F  +  E+P   QI G      
Sbjct: 24  TDAPCRTMHGLHGRPDIVLTEFTNVEGLWKGSDRIFRDFLYTPAERPAIAQIFGCRPEYF 83

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------ 116
             AA +  + G++ +++N+GCP+ ++     GA L+  PD     I A    +       
Sbjct: 84  YLAAHVACELGFDGVDINMGCPATKIANKGGGAALIRVPDTAKAIIRATQAGVRDWANGQ 143

Query: 117 ------------------------------------IPVTVKCRIGVDDQIPAVALRNLV 140
                                               +PV+VK R+G D    ++ + + V
Sbjct: 144 TLEELGMEPERIQRIRQMNEERVRIWGDKAVIERRLLPVSVKTRLGYD----SITITDWV 199

Query: 141 KSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIPNLDYDIV---YEIKKENPDLFIGLNG 195
           K + +     I +H R      KG +          ++D +    EI ++   L +G NG
Sbjct: 200 KDLLEMEPANISLHGRTLAQHYKGEA----------NWDAIAQAAEIVRQTDTLILG-NG 248

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            + ++  A K +    V GV+IGRA Y N  + 
Sbjct: 249 DIHNLYDAAKRIRETGVHGVLIGRATYGNPWLF 281


>gi|210134928|ref|YP_002301367.1| transcriptional regulator [Helicobacter pylori P12]
 gi|210132896|gb|ACJ07887.1| transcriptional regulator [Helicobacter pylori P12]
          Length = 328

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 48/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKEGVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  S  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTSKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDRYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|45184895|ref|NP_982613.1| AAR072Cp [Ashbya gossypii ATCC 10895]
 gi|44980504|gb|AAS50437.1| AAR072Cp [Ashbya gossypii ATCC 10895]
          Length = 384

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/187 (26%), Positives = 86/187 (45%), Gaps = 24/187 (12%)

Query: 52  LQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            Q+G A  +  V AA  ++ D     I++N GCP         GA L+  PD +   + A
Sbjct: 87  FQLGTASPTLAVRAANTVIGDVA--GIDVNAGCPKHFSIHAGMGAALLRTPDTLCGILRA 144

Query: 111 MCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +    S P++VK R+ +DD     A  +LV+ +  +G++ + +H R       +P 
Sbjct: 145 LVDEVGRPHSKPISVKIRL-LDD---LAATLDLVEKLCATGISNLTVHCRT------TPM 194

Query: 167 DNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDGVMIGRAAY 220
            NR+ P   Y   ++E+ + +    I +NG LE      ++     LP+  G MI  AA 
Sbjct: 195 RNREAPIRSYLASIFELCQASKVSLI-MNGALEGRKHFEEVRAELKLPTDVGGMIAEAAE 253

Query: 221 KNSAMLT 227
            N  + +
Sbjct: 254 ANPTVFS 260


>gi|255944963|ref|XP_002563249.1| Pc20g07240 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211587984|emb|CAP86053.1| Pc20g07240 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 463

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 42/166 (25%), Positives = 73/166 (43%), Gaps = 16/166 (9%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIP 132
           I+LN GCP      G  GA L+  PD++   + A+ K +  P    ++VK RI    +  
Sbjct: 141 IDLNSGCPKPFSTSGGMGAALLRTPDLLVSILEALVKEVGQPFQIGISVKIRILSKPE-- 198

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 LV  + K+G+ G+ +H R   ++        ++P     +V  I  E   +   
Sbjct: 199 --ETEALVSRLVKTGITGLTVHCRTTPMRPRERAIRDQLP-----MVARICHEA-GVACL 250

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +NG +    + L ++    VDG MI  +A  NS+     ++  + P
Sbjct: 251 MNGDVTSRDEGLALMAEYGVDGAMIATSAETNSSCFRAKEDGGAAP 296


>gi|15234862|ref|NP_195600.1| dihydrouridine synthase family protein [Arabidopsis thaliana]
 gi|75266821|sp|Q9T0J6|DUS3L_ARATH RecName: Full=tRNA-dihydrouridine synthase 3-like; AltName:
           Full=Zinc finger CCCH domain-containing protein 50;
           Short=AtC3H50
 gi|4490341|emb|CAB38623.1| putative protein [Arabidopsis thaliana]
 gi|7270872|emb|CAB80552.1| putative protein [Arabidopsis thaliana]
          Length = 700

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/266 (22%), Positives = 108/266 (40%), Gaps = 31/266 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA---DISKLVEAAKIVEDFGYNEINL 79
           EM +   +L+G      +L   + E    +QI G+    +S++VE   I  +   + I++
Sbjct: 377 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGSYPDTVSRVVEL--IDRECTVDFIDI 434

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP   V   S G+ L+  P  + + +      +  P+T+K R    +      + +L
Sbjct: 435 NMGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSIVETPITIKVRTAFFEG--KNRIDSL 492

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLE 198
           +  I   G   + IH R         +  R   + D+D +Y+  K    +L +  NG + 
Sbjct: 493 IADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQCTKNATTNLQVIGNGDVY 544

Query: 199 ---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              D ++     P +   MI R A     + T + E     +T     +  + KDF R  
Sbjct: 545 SYLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDITSGE--RLNIMKDFVR-- 600

Query: 256 SASMTDYAARHLHSGGKLQQITRHMI 281
                 +  +H  S  K  + TRH +
Sbjct: 601 ------FGLQHWGSDTKGVETTRHFL 620


>gi|297801970|ref|XP_002868869.1| dihydrouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297314705|gb|EFH45128.1| dihydrouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 691

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 61/266 (22%), Positives = 108/266 (40%), Gaps = 31/266 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA---DISKLVEAAKIVEDFGYNEINL 79
           EM +   +L+G      +L   + E    +QI G+    +S+ VE   I  +   + I++
Sbjct: 368 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGSYPDTVSRTVEL--IDRECTVDFIDI 425

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP   V   S G+ L+  P  + + +      L  P+T+K R    +      + +L
Sbjct: 426 NMGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSILETPITIKVRTAFFEG--KNRIDSL 483

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLE 198
           +  I   G   + IH R         +  R   + D+D +Y+  K  + +L +  NG + 
Sbjct: 484 IADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQCTKNASTNLQVIGNGDVY 535

Query: 199 ---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              D ++     P +   MI R A     + T + E     +T     +  + KDF R  
Sbjct: 536 SYLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDITSGE--RLNIMKDFVR-- 591

Query: 256 SASMTDYAARHLHSGGKLQQITRHMI 281
                 +  +H  S  K  + TRH +
Sbjct: 592 ------FGLQHWGSDTKGVETTRHFL 611


>gi|229815224|ref|ZP_04445560.1| hypothetical protein COLINT_02270 [Collinsella intestinalis DSM
           13280]
 gi|229809234|gb|EEP45000.1| hypothetical protein COLINT_02270 [Collinsella intestinalis DSM
           13280]
          Length = 330

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 61/131 (46%), Gaps = 6/131 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEKP-LALQIGGAD 58
           M   TD  YR   R      + YTEM+ VA    +  K  +L     E+P + +Q+ G  
Sbjct: 18  MAGVTDAAYRIMCRR-RGAEMAYTEMVSVAGLSYKSAKTWVLVEPEPEEPQICVQLFGTK 76

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A   V++   ++   I++N+ CP+ +V     G+ LM  P++    + A  +  
Sbjct: 77  PEQFAFAVNAVQERVGDKLTLIDINMACPARKVITKGEGSALMKEPELAASLVEACVREA 136

Query: 116 SIPVTVKCRIG 126
            +PVTVK R G
Sbjct: 137 RVPVTVKIRRG 147


>gi|301048876|ref|ZP_07195869.1| dihydrouridine synthase [Escherichia coli MS 185-1]
 gi|300299252|gb|EFJ55637.1| dihydrouridine synthase [Escherichia coli MS 185-1]
          Length = 236

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 37/158 (23%), Positives = 76/158 (48%), Gaps = 13/158 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM
Sbjct: 89  VQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAM 148

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+VK R+G D          +  +++++G   + +H R       + +   
Sbjct: 149 REAVPAHLPVSVKVRLGWDS---GEKKFEIADAVQQAGATELVVHGR-------TKEQGY 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +  ++D+  + EI ++  ++ +  NG + D   A + +
Sbjct: 199 RAEHIDWQAIGEI-RQRLNIPVIANGEIWDWQSAQQCM 235


>gi|226492326|ref|NP_001145737.1| hypothetical protein LOC100279244 [Zea mays]
 gi|219884231|gb|ACL52490.1| unknown [Zea mays]
 gi|224031411|gb|ACN34781.1| unknown [Zea mays]
          Length = 686

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 63/283 (22%), Positives = 105/283 (37%), Gaps = 39/283 (13%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L     E    +QI G     +    ++V+ +   + I++N+
Sbjct: 363 EMAMCTNLLQGQASEWALLRRHPSEDLFGVQICGPYPDTVARTVELVDNECSVDFIDINM 422

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--- 138
           GCP   V     G+ L+  P  +   + A       P+TVK R            RN   
Sbjct: 423 GCPIDIVVNKGAGSSLLTKPMRIRSIVQAASTVTEKPLTVKVRTAF------FEGRNRAD 476

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG- 196
            LV  I   G + I IH R         +  R     D+D +Y+  ++ PD    +  G 
Sbjct: 477 SLVSDIYNWGASAITIHGRS--------RQQRYSKLADWDYIYQCAQKAPDYLHVIGNGD 528

Query: 197 ---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D ++ +     +   MI R A     + T + E     +T     +  + KDF R
Sbjct: 529 VFSFTDWNKHVSDCSKISTCMIARGALIKPWLFTEIKEQRHWDITSGE--RLNILKDFVR 586

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   H  S  K  + TRH +  +  +     CR+I
Sbjct: 587 --------FGLEHWGSDFKGVETTRHFLLEWLSY----TCRYI 617


>gi|317014140|gb|ADU81576.1| tRNA-dihydrouridine synthase B [Helicobacter pylori Gambia94/24]
          Length = 328

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 99/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + + + +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVEILKVIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +KK      I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDRYQKDKIDYESIALMKKILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|50420831|ref|XP_458956.1| DEHA2D11286p [Debaryomyces hansenii CBS767]
 gi|74631711|sp|Q6BS64|DUS3_DEBHA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49654623|emb|CAG87117.1| DEHA2D11286p [Debaryomyces hansenii]
          Length = 622

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 48/159 (30%), Positives = 75/159 (47%), Gaps = 18/159 (11%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGV-DDQIP 132
           +E+NLN GCP   ++    G+ LM  P  +   +  M   +  IPVTVK R G  +++  
Sbjct: 339 SELNLNCGCPIDLLYRQGQGSALMEQPARLLRILKGMNASSGDIPVTVKIRTGTKENKNT 398

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DYDIVYEIKKE-- 185
           A AL  + + + ++ V  I +H R    +     D   + ++     D++   E  KE  
Sbjct: 399 AKAL--VERILSENEVAAITLHGRSRQQRYTKEADWSYVQDVANIVQDWNNKKEDNKELR 456

Query: 186 --NPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
              P  F+G NG +   ED   A+ I P VD VM+ R A
Sbjct: 457 DTQPTCFVG-NGDVYTHEDWYNAVNI-PGVDSVMVARGA 493


>gi|308233986|ref|ZP_07664723.1| TIM-barrel protein, nifR3 family [Atopobium vaginae DSM 15829]
 gi|328944005|ref|ZP_08241470.1| tRNA-dihydrouridine synthase [Atopobium vaginae DSM 15829]
 gi|327491974|gb|EGF23748.1| tRNA-dihydrouridine synthase [Atopobium vaginae DSM 15829]
          Length = 390

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 55/233 (23%), Positives = 101/233 (43%), Gaps = 27/233 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFS-TQEKPLALQIGGAD 58
           M   T+  YR   RL       Y+EM+ VA   ++      L    T E  L +Q+ G+D
Sbjct: 42  MAGVTNSAYRIMNRL-GGAQYAYSEMVSVAGLCMKNQATRELCLPHTAEPNLIVQLFGSD 100

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A  +V +   ++   I++N+ CP  +V +   G+ LM +P      + A  + +
Sbjct: 101 PVQFQRACALVGELLGDKLSCIDINMACPVPKVTKRGEGSALMCDPHRACALVRACLREV 160

Query: 116 SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKI 171
            +PVT K R G  +D +  A       ++++ +G + + +H R  K + KG         
Sbjct: 161 RVPVTCKIRRGYYMDHESAA----EFGRALQDAGASALAVHGRFAKQLYKG--------- 207

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
              +++ +  +  E  D+ +  +G +     A +IL       V+I R  Y N
Sbjct: 208 -EANWESIKRV-VEAVDIPVIASGDVMSAEDACRILYKTQAHAVLIARGTYGN 258


>gi|238916319|ref|YP_002929836.1| tRNA-dihydrouridine synthase C [Eubacterium eligens ATCC 27750]
 gi|238871679|gb|ACR71389.1| tRNA-dihydrouridine synthase C [Eubacterium eligens ATCC 27750]
          Length = 333

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 57/239 (23%), Positives = 102/239 (42%), Gaps = 34/239 (14%)

Query: 52  LQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           +Q+   +    +  AK++ E +GY+EINLN GCPS  V     G+ ++ + + +   +  
Sbjct: 61  VQVMTNEAKDFIWTAKMLYEKYGYSEINLNAGCPSGTVVSKDKGSGMLRDTEKLDRFLDE 120

Query: 111 MCKAL----SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           + +      +I V+VK RIGV  DD  P +     ++      +  + +H R      + 
Sbjct: 121 VFEDAFIRENIKVSVKTRIGVEDDDSFPQI-----MEVYNSYPLEELIVHPR------VR 169

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYK 221
               R   +LD    +    +N    + LNG +   ++  +  ++ P VD  M+GR    
Sbjct: 170 TDYYRNELHLD---AFRYAVDNSRNKLVLNGDIFTRKNFLEMKEMFPEVDTFMLGRGLIA 226

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITR 278
           +  ++        N LT  +P     D +  +K+   + D  YAAR     G    I R
Sbjct: 227 DPGLI--------NVLTDDNPQAMVRDLNADKKLMKELHDLVYAARTAIMPGDTHAIHR 277


>gi|89891167|ref|ZP_01202674.1| conserved hypothetical protein [Flavobacteria bacterium BBFL7]
 gi|89516479|gb|EAS19139.1| conserved hypothetical protein [Flavobacteria bacterium BBFL7]
          Length = 316

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 29/115 (25%), Positives = 52/115 (45%), Gaps = 5/115 (4%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+      + + A K +   GY E+N N+GCP   V +   G+ L+  P  +   + 
Sbjct: 63  LIPQVMTNSADEFITAVKYIRSLGYKELNWNLGCPYPMVTKKGMGSGLICEPSKIDAILD 122

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKG 162
            +     + V++K R+G    +    + +    ++K  +  I IHAR  K + KG
Sbjct: 123 RVHNETDVIVSMKMRMGY---LEPTEILDTFPILEKYPIKSIAIHARIGKQLYKG 174


>gi|332661587|gb|AEE86987.1| tRNA-dihydrouridine synthase 3-like protein [Arabidopsis thaliana]
          Length = 691

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 60/266 (22%), Positives = 108/266 (40%), Gaps = 31/266 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA---DISKLVEAAKIVEDFGYNEINL 79
           EM +   +L+G      +L   + E    +QI G+    +S++VE   I  +   + I++
Sbjct: 368 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGSYPDTVSRVVEL--IDRECTVDFIDI 425

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP   V   S G+ L+  P  + + +      +  P+T+K R    +      + +L
Sbjct: 426 NMGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSIVETPITIKVRTAFFEG--KNRIDSL 483

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLE 198
           +  I   G   + IH R         +  R   + D+D +Y+  K    +L +  NG + 
Sbjct: 484 IADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQCTKNATTNLQVIGNGDVY 535

Query: 199 ---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              D ++     P +   MI R A     + T + E     +T     +  + KDF R  
Sbjct: 536 SYLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDITSGE--RLNIMKDFVR-- 591

Query: 256 SASMTDYAARHLHSGGKLQQITRHMI 281
                 +  +H  S  K  + TRH +
Sbjct: 592 ------FGLQHWGSDTKGVETTRHFL 611


>gi|219123999|ref|XP_002182301.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|219128682|ref|XP_002184536.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403986|gb|EEC43935.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406262|gb|EEC46202.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 229

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 47/162 (29%), Positives = 79/162 (48%), Gaps = 21/162 (12%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCIAAMCKALSIPVTVKCRI--GVDDQ 130
           + I+LN+GCP    + G FG+ L+   D  ++ D + A   A+SIP+ VK R+   V++ 
Sbjct: 79  DAIDLNLGCPQRTAYLGHFGSYLLDRKDRSLICDIVRAGAAAVSIPIFVKIRLLDKVEET 138

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAI---LKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           I       L + ++++G + I +HAR       KG   +D    P L  D +  +K+   
Sbjct: 139 I------ELCQQLERAGASLIAVHARYRASWERKGAGARDG---PAL-LDQIAVLKQHIT 188

Query: 188 DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
            + I  NG +   +D+ + L+ L   DGVM       N A+ 
Sbjct: 189 SIPIIANGNVITYDDVEKNLE-LTGADGVMSAEGILDNPALF 229


>gi|302769496|ref|XP_002968167.1| hypothetical protein SELMODRAFT_89139 [Selaginella moellendorffii]
 gi|300163811|gb|EFJ30421.1| hypothetical protein SELMODRAFT_89139 [Selaginella moellendorffii]
          Length = 540

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 46/214 (21%), Positives = 89/214 (41%), Gaps = 17/214 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L     E    +QI G+    L +  +++E +   + I++N+
Sbjct: 217 EMAMCTNLLQGHASEWALLRRHPVEDCFGVQICGSYADSLTKTVELIERECTVDFIDINL 276

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V +   G+CL+  P  +   + A    +  P+T+K R G  +        +++ 
Sbjct: 277 GCPIDIVVKKGAGSCLLTKPTRLEQIVRATASIVEKPLTLKMRTGYFEG--KNCAHSMIS 334

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----L 197
            +   GV+ + +H R         +  R     D+  +Y+  K  PD    L  G     
Sbjct: 335 ELSNWGVSAVTVHGRT--------RQQRYSKLADWVYIYDCAKRAPDDLQVLGNGDIFSY 386

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            D ++ +    ++   M+ R A     +LT + E
Sbjct: 387 SDWNEHMLPDLNLSSCMLARGALIKPWLLTEIKE 420


>gi|15668835|ref|NP_247638.1| dihydroorotate dehydrogenase 1B [Methanocaldococcus jannaschii DSM
           2661]
 gi|2500041|sp|Q58070|PYRD_METJA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|1591367|gb|AAB98649.1| dihydroorotase dehydrogenase (pyrD) [Methanocaldococcus jannaschii
           DSM 2661]
          Length = 306

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 55/184 (29%), Positives = 85/184 (46%), Gaps = 31/184 (16%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            I G D  +  E AK +E +  + I LN+ CP A+     +GA +  NPD+  D   A+ 
Sbjct: 104 SIYGKDEEEFAEVAKKMERY-VDIIELNISCPHAK----GYGATIGQNPDLSYDVCKAVK 158

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK 161
           KA+ IPV  K    V D I       + +++  +GV+G           I I A+K IL 
Sbjct: 159 KAVKIPVFAKLTPNVTDII------EIAQAVVDAGVDGLVAINTVRGMAIDIRAKKPILA 212

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
               GLS K    I ++   +V+++  EN D+ I   GG+     A++ ++     V IG
Sbjct: 213 NKFGGLSGK---AIKSIGIKVVWDL-YENFDVPIIGVGGIMSGEDAIEYMMAGASAVQIG 268

Query: 217 RAAY 220
              Y
Sbjct: 269 SGVY 272


>gi|302773960|ref|XP_002970397.1| hypothetical protein SELMODRAFT_267436 [Selaginella moellendorffii]
 gi|300161913|gb|EFJ28527.1| hypothetical protein SELMODRAFT_267436 [Selaginella moellendorffii]
          Length = 634

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/214 (22%), Positives = 93/214 (43%), Gaps = 17/214 (7%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L     E    +QI G+    L +  +++E +   + I++N+
Sbjct: 311 EMAMCTNLLQGHASEWALLRRHPVEDCFGVQICGSYADSLTKTVELIERECTVDFIDINL 370

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V +   G+CL+  P  +   + A    +  P+T+K R G  +        +++ 
Sbjct: 371 GCPIDIVVKKGAGSCLLTKPTRLEQIVRATASIMEKPLTLKMRTGYFEG--KNCAHSMIS 428

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDM 200
            +   GV+ + +H R         +  R     D+  +Y+  K  P DL +  NG +   
Sbjct: 429 ELSNWGVSAVTVHGRT--------RQQRYSKLADWVYIYDCAKRAPDDLQVLGNGDIFSY 480

Query: 201 SQALK-ILPSVD--GVMIGRAAYKNSAMLTTVDE 231
           S   + +LP ++    M+ R A     +LT + E
Sbjct: 481 SDWNEHMLPDLNLSSCMLARGALIKPWLLTEIKE 514


>gi|256829559|ref|YP_003158287.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
 gi|256578735|gb|ACU89871.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
          Length = 340

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 60/272 (22%), Positives = 115/272 (42%), Gaps = 28/272 (10%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEK---PLALQIGGADISKLVEAAKIVEDFGYNEI 77
            + TEM  A A+ +  + +   F  +++    L  QI G +   +  AA+ +E  G   +
Sbjct: 48  FMVTEMCNARAVPQESRHHSPVFRWRDEEAASLVCQIFGGEPEVMAAAARRIEAEGLMGV 107

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GC  A + +  +GA L+ +P+     + A+ +A+  PV VK R G ++  P +A+ 
Sbjct: 108 DINMGCSVAAICKKGYGAALLKDPERAVAMVRAVRRAVRCPVMVKFRSGWENS-PDLAV- 165

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +L +  + +G + +  H R A        D R  P     I   +  E   + +  NG  
Sbjct: 166 DLARRFEDAGADLLTFHPRIA-------PDRRSRPPKWAHIRAVV--EAVSIPVLGNGNA 216

Query: 198 EDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              +  L+++     DGV IGR A     +   +   F              D+D + + 
Sbjct: 217 FCAADCLRMMEETGCDGVSIGRMAIARPWIFAQLAHGFEP------------DEDIFLRT 264

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +  + D   RH      ++   +++  L   F
Sbjct: 265 ALELIDAIWRHFEQARAIKMYKKYLPYLAANF 296


>gi|262375633|ref|ZP_06068865.1| tRNA-dihydrouridine synthase C [Acinetobacter lwoffii SH145]
 gi|262309236|gb|EEY90367.1| tRNA-dihydrouridine synthase C [Acinetobacter lwoffii SH145]
          Length = 311

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/200 (24%), Positives = 90/200 (45%), Gaps = 16/200 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q  G +   L   A  V   G   I++N GCP+  V+    G+ L+  P
Sbjct: 57  GKTAAGTPVHVQFLGNNPEMLAANAAKVAAMGAPAIDMNFGCPAKTVNRHRGGSVLLDEP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           ++V + + A+  A+   IPV+ K R+G  D+     L N   +I+ +G + + +HAR   
Sbjct: 117 EVVHELVKAVRDAVPAHIPVSAKMRLGYMDR--NFMLEN-AHAIEDAGASWVTVHART-- 171

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGR 217
                 K +   P   +D +  I +E   + +  NG + + + A   ++    + +MIGR
Sbjct: 172 ------KADGYTPPAFWDQLQPI-REALKINVIANGEIWNNADAKQCRLESGCEDLMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPL 237
            A     +   + +    PL
Sbjct: 225 GAVTTPDLTQCIRQNSDAPL 244


>gi|318042395|ref|ZP_07974351.1| nitrogen regulation protein NifR3 family protein [Synechococcus sp.
           CB0101]
          Length = 331

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 73/297 (24%), Positives = 132/297 (44%), Gaps = 22/297 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G     +   +++  P+ +Q+     + + 
Sbjct: 32  SDRIFRGLVRRWAPDALLFTEMVNATSLELGHGLIKVEELASEPGPIGVQLFDHRPAAMA 91

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++ +   G+ L+ +P +    + A+  A++IPVTVK 
Sbjct: 92  DAARRAEAAGAFLIDINMGCPVKKIAKKGGGSGLIRDPSLAARIVEAVAAAVAIPVTVKT 151

Query: 124 RIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           R+G     +  V      + ++ +G   + +H R         ++       D+D +  +
Sbjct: 152 RLGWCGSSLDPV---GWCRELEDAGAQLLTLHGRT--------REQGFKGQADWDAIAAV 200

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           K+      I  NG +     AL+ L     DGVM+GR A     ++  +D   S      
Sbjct: 201 KQALQIPVIA-NGDVNSADDALRCLAHTGADGVMVGRGAMGAPWLVGQIDAALSGRPVPP 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           SP      +    ++ A +   AAR  H    L    +HM     GF  + + RH L
Sbjct: 260 SPGALERIQLASEQLQALV---AARGDHG---LLIARKHMSWTCTGFSGAPQLRHAL 310


>gi|88801417|ref|ZP_01116945.1| hypothetical protein PI23P_02122 [Polaribacter irgensii 23-P]
 gi|88782075|gb|EAR13252.1| hypothetical protein PI23P_02122 [Polaribacter irgensii 23-P]
          Length = 317

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/254 (22%), Positives = 105/254 (41%), Gaps = 46/254 (18%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           +K++L  +  E  +  QI   D  + +  +K V   GY E+N N+GCP   V +   G+ 
Sbjct: 50  QKDLLLENNSELEVIPQIITNDAEEFLFVSKYVRALGYKELNWNLGCPYPMVTKRGMGSG 109

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L+ + + +   +  +     I V++K R+G ++    + +  ++ +     +  I IHAR
Sbjct: 110 LISDAEKINSILHKVHNESDILVSMKMRMGYENPEEILGVLPILDTYP---LKNIAIHAR 166

Query: 157 --KAILKGLSPKD--NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPS 209
             K + KG +  +   + + N  + + Y             NG +  +    K+    PS
Sbjct: 167 IGKQLYKGGTDLEAFQKCLDNSKHKMYY-------------NGDITSVVAFHKLQERFPS 213

Query: 210 VDGVMIGRA----AYKNSAMLTTVDEY------------------FSNPLTGSSPIKTRV 247
           +D  MIGR      +  S +     EY                  +   L+G +PIK ++
Sbjct: 214 IDHWMIGRGLIGDPFLPSMIKADTTEYPKERFDVFREFHDRIYQEYDAALSGPTPIKMKM 273

Query: 248 DKDFWRKISASMTD 261
              FW   S S ++
Sbjct: 274 -LGFWEFFSQSFSN 286


>gi|294054269|ref|YP_003547927.1| dihydrouridine synthase DuS [Coraliomargarita akajimensis DSM
           45221]
 gi|293613602|gb|ADE53757.1| dihydrouridine synthase DuS [Coraliomargarita akajimensis DSM
           45221]
          Length = 356

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 89/194 (45%), Gaps = 20/194 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           ++P+  Q+ G     L    K + D       I+LN+GCP+ +V++ + G  L+  P+ +
Sbjct: 70  DRPVFAQLIGESHPDLKRTVKAIHDAQLPVAGIDLNMGCPAPKVYKKNVGGGLLREPEKI 129

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
              +  + +++    TVK RIG +D     A+ +L   I+K  V+ + +HAR        
Sbjct: 130 DGILGLLRESVEGRFTVKMRIGFEDDRHFEAILDL---IEKHEVDLLSLHARTV------ 180

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSVD--GVMIGRAAY 220
               ++    +    Y IK+    L   +  NG +  +++   +L      G+MIGR+  
Sbjct: 181 ----KEAYRSEVHYAY-IKRAAERLACPVLANGNVTSVAKGQWVLDETKCAGLMIGRSCI 235

Query: 221 KNSAMLTTVDEYFS 234
           +N  +     E+F+
Sbjct: 236 RNPWIFRQHREHFA 249


>gi|294940939|ref|XP_002782932.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
 gi|239895114|gb|EER14728.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
          Length = 413

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 47/217 (21%), Positives = 89/217 (41%), Gaps = 30/217 (13%)

Query: 30  DAILRGDKKNILGFSTQEKP-LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSAR 87
           D I + D   +   + +EKP L  Q+G        +AA  +++D      ++N+GCP + 
Sbjct: 72  DYISQRDNSLVFQTAEEEKPKLIFQMGTNSGPGAQKAAMALLQDVA--GFDVNMGCPKSF 129

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVA--------LR 137
             +G  G+ L+  P++  D +  + + +  ++PVT K R+  D Q P             
Sbjct: 130 SIKGGMGSALLKKPEVAVDILKTLRRTVPETMPVTCKVRLICDTQQPTEEELQDATKRTS 189

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
             +K    +G   + +H R   ++  +P          +    ++++  PD+ +  NG  
Sbjct: 190 EFIKGCSDAGACAVALHTRTIPMRPRNPA--------IWPTFAQVQRLCPDVLLIPNGDF 241

Query: 198 EDMS--QALKIL------PSVDGVMIGRAAYKNSAML 226
            D    +A + L      P  +  MI R    N  M 
Sbjct: 242 FDRKAIEAFRALMDQTGVPWSNSFMIARGGLYNPQMF 278


>gi|167394491|ref|XP_001740985.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165894630|gb|EDR22551.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 515

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/213 (23%), Positives = 87/213 (40%), Gaps = 19/213 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           TEMI+A++++ G      ++     E    +Q+   +     +A +++     +   LN 
Sbjct: 199 TEMIMAESLVEGKTSEWALVKRDPSEDIFGIQLCVGNSLLAAKACQVLNSVDCDFYELNC 258

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALRNLV 140
            CP   V++   GA L+  P  +   + AM      PV +K R G   + I  V L N  
Sbjct: 259 ACPIDYVYKKGMGAQLIERPKRIESLLHAMRSVTERPVAIKVRTGKSSNTIQDVLLPNCA 318

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLE 198
                 G   + IH R         +D R   + D+D + +     + P + +G   G +
Sbjct: 319 ----NYGAAMVSIHGRT--------RDQRYTKSADWDFIKQATTITQCPVIGVGDIYGYK 366

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  +AL+    V  V IGR A     + T + E
Sbjct: 367 DYQKALEC--GVATVAIGRGALIKPWIYTEIKE 397


>gi|73964671|ref|XP_533136.2| PREDICTED: similar to PP3111 protein isoform 1 [Canis familiaris]
          Length = 507

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 8/109 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
             D    V+AA + +D+  + I+LN+GCP      G +GA L    D++
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLL 129


>gi|186703885|emb|CAQ43570.1| tRNA-dihydrouridine synthase 2 [Zygosaccharomyces rouxii]
          Length = 373

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/197 (25%), Positives = 98/197 (49%), Gaps = 27/197 (13%)

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDC 107
           +  QIG +  S  ++AA  +++D   + I++N GCP    +H G  GA L+  PD + + 
Sbjct: 80  IVFQIGTSTPSLAIQAALTVIQDV--DGIDINAGCPKHFSIHSG-MGAALLRTPDKLCEI 136

Query: 108 IAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +  + + +  P    ++VK R+ +D++   +    L+  + ++G++ + +H R       
Sbjct: 137 LCELVEKVGRPYGKTISVKIRL-LDNREDTL---QLINRLCQNGISHLTVHCRT------ 186

Query: 164 SPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDGVMIGR 217
           +P  NR+ P   Y   +YE+ + N    I +NGG++  S   +I     LP   G M+  
Sbjct: 187 TPMRNREQPIRGYIKEIYEVCQTNGVTLI-INGGIKSRSHFQEIQRDLELPKEIGGMMAD 245

Query: 218 AAYKN-SAMLTTVDEYF 233
            A +N +  L +  E+F
Sbjct: 246 CAEQNPTVFLDSPIEWF 262


>gi|625116|gb|AAB82358.1| Ylr401cp [Saccharomyces cerevisiae]
          Length = 609

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 73/171 (42%), Gaps = 37/171 (21%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  IP+TVK R G  +  P 
Sbjct: 378 SEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPITVKIRTGTKEGHPI 437

Query: 134 VALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--------- 183
                LVK  + ++ V  I +H R         +  R   + D+D V ++          
Sbjct: 438 A--EGLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDYVSQVADTLRSAEAD 487

Query: 184 -------KENPD-----LFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
                  KE  D      F+G NG     ED  + L    ++D VM+ R A
Sbjct: 488 FIETEQGKEGRDSKNRIQFVG-NGDVNNFEDWYRYLNGNENIDSVMVARGA 537


>gi|147674360|ref|YP_001216574.1| tRNA-dihydrouridine synthase C [Vibrio cholerae O395]
 gi|146316243|gb|ABQ20782.1| tRNA-dihydrouridine synthase C [Vibrio cholerae O395]
          Length = 158

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   +
Sbjct: 64  PVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVV 123

Query: 109 AAMCKALS--IPVTVKCRIGVDD 129
            A   A+   IPV+ K R+G +D
Sbjct: 124 KACRDAVPAHIPVSAKIRLGWED 146


>gi|67471577|ref|XP_651736.1| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|56468508|gb|EAL46349.1| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 515

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/213 (23%), Positives = 87/213 (40%), Gaps = 19/213 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           TEMI+A++++ G      ++   + E    +Q+   +     +A +++     +   LN 
Sbjct: 199 TEMIMAESLVEGKTSEWALVKRDSSEDIFGIQLCVGNSMLAAKACQVLNSVDCDFYELNC 258

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALRNLV 140
            CP   V++   GA L+  P  +   + AM      PV +K R G   + I  V L N  
Sbjct: 259 ACPIDYVYKKGMGAQLIERPKRIESLLHAMRSVTERPVAIKVRTGKSSNTIQDVLLPNCA 318

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLE 198
                 G   + IH R         +D R   + D+D + +     + P + +G   G +
Sbjct: 319 ----DYGAAMVSIHGRT--------RDQRYTKSADWDFIKQATTITQCPVIGVGDIYGYK 366

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D  +AL     V  V IGR A     + T + E
Sbjct: 367 DYQKALDC--GVATVAIGRGALIKPWIYTEIKE 397


>gi|313217157|emb|CBY38320.1| unnamed protein product [Oikopleura dioica]
          Length = 163

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 38/162 (23%), Positives = 79/162 (48%), Gaps = 13/162 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  + ++ M+++D+ +     +   L  + ++ PL +Q     
Sbjct: 1   MVRYSRLPFRALCRKF-NVDVCFSPMLISDSFINSASARDADLRSNAEDGPLVVQFAANK 59

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
                + A+++  +G+ E I+LN GCP   V+  ++G  LM  P+++ D +    +A+  
Sbjct: 60  GEDFAKVAQML--YGHCEGIDLNCGCPQRWVNALNYGDILMKQPELLADIVLQARRAIPD 117

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
               ++VK R+  DD    +    + + I+K+G   + IH R
Sbjct: 118 SEFSISVKTRV-FDDLHTTI---EMARRIEKAGATMLSIHGR 155


>gi|119963532|ref|YP_947259.1| IMP dehydrogenase/GMP reductase domain-containing protein
           [Arthrobacter aurescens TC1]
 gi|119950391|gb|ABM09302.1| putative IMP dehydrogenase / GMP reductase domain protein
           [Arthrobacter aurescens TC1]
          Length = 401

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 47/215 (21%), Positives = 93/215 (43%), Gaps = 21/215 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    ++  I+     EK  ++Q+ G D
Sbjct: 41  MAGITNSAFRRLCREY-GGGMYVAEMVTSRALVERTPESLRIISHDEDEKVRSVQLYGVD 99

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              +  A + +VE+   + I+LN GCP  +V     G+ L    D+    +    K  S 
Sbjct: 100 PVTVGAAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTSIVQTAVKEASK 159

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             IP+T+K R G+D+    +   +  +  + +GV  + +H R A     G          
Sbjct: 160 GGIPLTIKMRKGIDED--HLTYLDAGRIARDAGVAAVALHGRTAAQFYSG---------- 207

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             D+  +  +++  PD+ +  NG +     A++++
Sbjct: 208 QADWSAIARLREALPDIPVLGNGDIWSAEDAVRMV 242


>gi|303325730|ref|ZP_07356173.1| dihydrouridine synthase family protein [Desulfovibrio sp. 3_1_syn3]
 gi|302863646|gb|EFL86577.1| dihydrouridine synthase family protein [Desulfovibrio sp. 3_1_syn3]
          Length = 334

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 43/164 (26%), Positives = 77/164 (46%), Gaps = 12/164 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+ A  ++       ++L    +++PL +Q+ GA+
Sbjct: 29  LAGYSDLPFRLLCREY-GAAVCVTEMVSAKGLVYQSPGTNDLLVSLPEDQPLVVQLFGAE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSI 117
              L  A  ++ + GY   +LN+GC   +V     GA ++ + +       AM K A   
Sbjct: 88  ADFLRRAVGLLREAGYGWFDLNMGCSVPKVLRQGAGAAMLGDLENSLAVAGAMLKEAGPG 147

Query: 118 PVTVKCRIGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V  K R+G+DD    +P +ALR     ++  G   + +H R A
Sbjct: 148 RVGFKLRLGLDDARTVLPDLALR-----LEDLGAGWLTLHPRTA 186


>gi|303258014|ref|ZP_07344023.1| dihydrouridine synthase family protein [Burkholderiales bacterium
           1_1_47]
 gi|302859357|gb|EFL82439.1| dihydrouridine synthase family protein [Burkholderiales bacterium
           1_1_47]
          Length = 315

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+     +  + AAK ++D GY E+NLN+GCPS  V     G+  + +   +   +
Sbjct: 53  PVVPQLLSNRSADFIWAAKALQDLGYKEVNLNLGCPSGTVVAKGKGSGFLRDLYALERFL 112

Query: 109 AAMCKA-LSIPVTVKCRIG 126
             +  A + IP+++K R+G
Sbjct: 113 DEIFSAGIDIPISIKTRLG 131


>gi|225427796|ref|XP_002275411.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 692

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 60/264 (22%), Positives = 106/264 (40%), Gaps = 27/264 (10%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    +++ ++   + I++N+
Sbjct: 369 EMAMCTNLLQGQASEWALLRRHSAEDLFGVQICGAYPDTVARTVELIDQECEVDFIDINM 428

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     G+ L+  P  + + I A    +  P+TVK R G  +    V   +L+ 
Sbjct: 429 GCPIDIVVNKGAGSALLTKPMRMKNIIEAASGIVDKPITVKVRTGFLEGRNRV--DSLIA 486

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----L 197
            I + G N + IH R         +  R     D++ +Y+  ++ P+    L  G     
Sbjct: 487 DIGQWGANVVTIHGRS--------RQQRYSKLADWEYIYQCARKAPEALQVLGNGDIFSY 538

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
            D ++     P +   MI R A     + T + E     +  SS  +  + KD+ R    
Sbjct: 539 LDWNKHKSGCPELSTCMIARGALVKPWIFTEIKEQRHWDI--SSGERLNILKDYVR---- 592

Query: 258 SMTDYAARHLHSGGKLQQITRHMI 281
                   H  S  K  + TRH +
Sbjct: 593 ----CGLEHWGSDTKGVETTRHFM 612


>gi|298387098|ref|ZP_06996652.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 1_1_14]
 gi|298260248|gb|EFI03118.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 1_1_14]
          Length = 314

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 39/163 (23%), Positives = 73/163 (44%), Gaps = 17/163 (10%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  +VK R+G +    
Sbjct: 87  GYQEVDINLGCPFPLLAKRHNGSGILPYPEEVKALLSIVTRYPQISFSVKMRLGWEQPDE 146

Query: 133 AVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPD 188
            +AL  ++  +    +  I +H R  K   KG           +D  +    ++    P 
Sbjct: 147 CLALAPILNDLP---LRQITMHPRLGKQGYKG----------EVDLQVFSAFREVCRLPL 193

Query: 189 LFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ G    LED+ +     PS+ G+MIGR    N A+     E
Sbjct: 194 VYNGDIHNLEDIQRISAQFPSLAGIMIGRGLLANPALALEYKE 236


>gi|85666121|ref|NP_013505.2| Dus3p [Saccharomyces cerevisiae S288c]
 gi|187471052|sp|A7A1S5|DUS3_YEAS7 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|187608869|sp|Q06053|DUS3_YEAST RecName: Full=tRNA-dihydrouridine synthase 3
 gi|151940921|gb|EDN59303.1| dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|285813805|tpg|DAA09701.1| TPA: Dus3p [Saccharomyces cerevisiae S288c]
          Length = 668

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 73/171 (42%), Gaps = 37/171 (21%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  IP+TVK R G  +  P 
Sbjct: 378 SEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPITVKIRTGTKEGHPI 437

Query: 134 VALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--------- 183
                LVK  + ++ V  I +H R         +  R   + D+D V ++          
Sbjct: 438 A--EGLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDYVSQVADTLRSAEAD 487

Query: 184 -------KENPD-----LFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
                  KE  D      F+G NG     ED  + L    ++D VM+ R A
Sbjct: 488 FIETEQGKEGRDSKNRIQFVG-NGDVNNFEDWYRYLNGNENIDSVMVARGA 537


>gi|291519623|emb|CBK74844.1| tRNA-U20a,U20b-dihydrouridine synthase [Butyrivibrio fibrisolvens
           16/4]
          Length = 245

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 40/164 (24%), Positives = 71/164 (43%), Gaps = 13/164 (7%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           AA  +   G+ EIN N+GCPS  V     G+ L+  P+ +   +  +   L   I V++K
Sbjct: 80  AAGEIASLGFKEINFNLGCPSGTVVAKKKGSGLLYYPEELDSMLYEIFAGLKNDIQVSIK 139

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-NLDYDIVYE 181
            R+G   ++ +     +++   K  ++ + IH R         KD  + P + D+     
Sbjct: 140 TRLG---KLESDEFYEILEIYNKYPISELTIHPRVQ-------KDFYREPIHPDFFQYAY 189

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
              + P +F G    + D+       P ++ VMIGR    N  +
Sbjct: 190 SNAKAPLVFNGDVKTISDIDDTFNNYPLINAVMIGRGLISNPKL 233


>gi|72391948|ref|XP_846268.1| tRNA-dihydrouridine synthase 3 [Trypanosoma brucei TREU927]
 gi|62359888|gb|AAX80315.1| tRNA-dihydrouridine synthase 3, putative [Trypanosoma brucei]
 gi|70802804|gb|AAZ12709.1| tRNA-dihydrouridine synthase 3, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 528

 Score = 47.8 bits (112), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 34/127 (26%), Positives = 60/127 (47%), Gaps = 5/127 (3%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED--FGYNEINLNVGCPSARVHE 90
           L+  + ++L   + E    LQI  +     +  A+ VE+  F Y+ +++N GCP  +V  
Sbjct: 206 LQKSEWSLLRRHSSEDIFGLQIAVSRPHDAITWAQAVEESGFSYDFVDINCGCPVDKVVL 265

Query: 91  GSFGACLMLNP-DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              G  L     + + D + ++    S PVT+KCR+G D++ P   L   +   +  G  
Sbjct: 266 SGCGCGLWERKGNRLRDVVQSLVAHQSKPVTIKCRMGPDEENP--ELHKHIADYETWGAA 323

Query: 150 GIWIHAR 156
            + IH R
Sbjct: 324 AVTIHGR 330


>gi|327404377|ref|YP_004345215.1| dihydrouridine synthase DuS [Fluviicola taffensis DSM 16823]
 gi|327319885|gb|AEA44377.1| dihydrouridine synthase DuS [Fluviicola taffensis DSM 16823]
          Length = 309

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 35/159 (22%), Positives = 69/159 (43%), Gaps = 7/159 (4%)

Query: 4   WTDRHYRFFARLLTNNA----LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           +TD H+R   + + +N       Y ++     I    K +IL  +   + +  Q+   + 
Sbjct: 11  YTDYHFRNAHQQVYSNVDKFYAPYLKLNNDGTIKNNPKIDILVKNNPFQKIVPQLMACNK 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
                 A  +E  GY E+N N+GCP   V   + GA ++  PD +   + ++     + +
Sbjct: 71  DDFFVMADYIESLGYTEVNWNMGCPYPMVTNKNLGAGILNKPDEILRLLDSILPKTKLGI 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            +K R+G++     +     + ++    +  I IHAR A
Sbjct: 131 GIKMRMGLESTQEIIE---FLPALNNYPLTEIIIHARNA 166


>gi|330999429|ref|ZP_08323143.1| dihydrouridine synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329574855|gb|EGG56414.1| dihydrouridine synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 325

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 1/79 (1%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+     +  + AAK ++D GY E+NLN+GCPS  V     G+  + +   +   +
Sbjct: 63  PVVPQLLSNRSADFIWAAKALQDLGYKEVNLNLGCPSGTVVAKGKGSGFLRDLYALERFL 122

Query: 109 AAMCKA-LSIPVTVKCRIG 126
             +  A + IP+++K R+G
Sbjct: 123 DEIFSAGIDIPISIKTRLG 141


>gi|207342739|gb|EDZ70408.1| YLR401Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 668

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 73/171 (42%), Gaps = 37/171 (21%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  IP+TVK R G  +  P 
Sbjct: 378 SEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPITVKIRTGTKEGHPI 437

Query: 134 VALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--------- 183
                LVK  + ++ V  I +H R         +  R   + D+D V ++          
Sbjct: 438 A--EGLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDYVSQVADTLRSAEAD 487

Query: 184 -------KENPD-----LFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
                  KE  D      F+G NG     ED  + L    ++D VM+ R A
Sbjct: 488 FIETEQGKEGRDSKNRIQFVG-NGDVNNFEDWYRYLDGNENIDSVMVARGA 537


>gi|326316090|ref|YP_004233762.1| dihydrouridine synthase duS [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323372926|gb|ADX45195.1| dihydrouridine synthase DuS [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 323

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 85/180 (47%), Gaps = 16/180 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+  Q+ G+D S + E A  +   G   I+LN GCP+  V+    GA L+  P
Sbjct: 61  GRTAAGVPVRAQLLGSDPSSMAENAARLAALGPEGIDLNFGCPANVVNRHGGGAALLREP 120

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   +AA+ +A+   +PV+ K R+G DD   A   R   ++ +  G   + +HAR   
Sbjct: 121 ERIAAVVAAVRRAVPAGMPVSAKMRLGYDDTSLA---RECAQAAEAGGACELVVHART-- 175

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                 K +   P   +++V  ++       I  NG +  ++ A++   L   D +M+GR
Sbjct: 176 ------KADGYRPPAYWELVAPLRAAVHIPVIA-NGEIWTVADAMRCRALSGGDALMLGR 228


>gi|256075605|ref|XP_002574108.1| tRNA-dihydrouridine synthase [Schistosoma mansoni]
 gi|238659304|emb|CAZ30341.1| tRNA-dihydrouridine synthase, putative [Schistosoma mansoni]
          Length = 370

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 29/112 (25%), Positives = 58/112 (51%), Gaps = 4/112 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV +T   +R   R   N  L++T MI+A++ ++ +K   + F+T   ++PL +Q+   D
Sbjct: 21  MVRYTKLPFRLLLRQ-HNVDLVHTPMILANSFIQSEKARNIEFTTCPNDRPLIVQLASND 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             +   A +++  +  + I+LN GCP         G+ L+  P+ + + + A
Sbjct: 80  PCEFAIATEMLAPYC-DGIDLNCGCPQPWAIGSGLGSALLKEPEKIANIVHA 130


>gi|281208917|gb|EFA83092.1| chaperonin containing TCP1 beta subunit [Polysphondylium pallidum
           PN500]
          Length = 853

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 31/127 (24%), Positives = 63/127 (49%), Gaps = 13/127 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N GCP   V +  +GA L+ +P  + D +  +   + IP ++K R+  + Q      
Sbjct: 150 VDINCGCPQKWVMKEGYGANLLQHPQKITDMVKQVNNRVGIPCSIKIRVDKNLQKTV--- 206

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             LV+  + SGV+ + +H R +  +   P        +DY+ + ++ KE+  + +  NG 
Sbjct: 207 -ELVRQAEASGVSWLAVHGRTSSQRSSHP--------VDYEAI-KLVKESVSIPVFANGD 256

Query: 197 LEDMSQA 203
           +  + QA
Sbjct: 257 IFTLEQA 263


>gi|158522669|ref|YP_001530539.1| dihydrouridine synthase DuS [Desulfococcus oleovorans Hxd3]
 gi|158511495|gb|ABW68462.1| dihydrouridine synthase DuS [Desulfococcus oleovorans Hxd3]
          Length = 324

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 60/253 (23%), Positives = 102/253 (40%), Gaps = 26/253 (10%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K++L       P+  QI        V  A  + D GY+  N N+GCP   V +   GA L
Sbjct: 51  KDLLPEYNTALPVVPQILSNSGEDFVYLADHLYDLGYSVTNWNLGCPYPMVAKKYRGAGL 110

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + + D + + +  +   +   ++VK R+G  D      L  L+  + +  +  + +H R 
Sbjct: 111 LPHTDRIAEFLDTVMSRMKGGLSVKIRLGWAD---TTELMGLLPVLHRYPLAELIVHPRT 167

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVM 214
            I         R    +D    +E   EN  L +  NG ++   D +       +VD  M
Sbjct: 168 GI--------QRYEGTVDL-AAFERVLENTGLPVMYNGDIQTVADFAYLSGRFKAVDRWM 218

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSP-IKTRVD--KDFWRKISASMTDYAARHLHSGG 271
           IGR A          D +    + GS P  K +V   ++F   + A  T      +H   
Sbjct: 219 IGRGA--------LADPFLPAAIGGSQPEEKEKVARMRNFHDDLMARYTLRLNGPVHLLD 270

Query: 272 KLQQITRHMIGLF 284
           +++ + R+ I LF
Sbjct: 271 RMKGLWRYFILLF 283


>gi|256269134|gb|EEU04469.1| Dus3p [Saccharomyces cerevisiae JAY291]
          Length = 668

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 73/171 (42%), Gaps = 37/171 (21%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  IP+TVK R G  +  P 
Sbjct: 378 SEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPITVKIRTGTKEGHPI 437

Query: 134 VALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--------- 183
                LVK  + ++ V  I +H R         +  R   + D+D V ++          
Sbjct: 438 A--EGLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDYVSQVADTLRSAEAD 487

Query: 184 -------KENPD-----LFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
                  KE  D      F+G NG     ED  + L    ++D VM+ R A
Sbjct: 488 FIETEQGKEGRDSKNRIQFVG-NGDVNNFEDWYRYLNGNDNIDSVMVARGA 537


>gi|260949371|ref|XP_002618982.1| hypothetical protein CLUG_00141 [Clavispora lusitaniae ATCC 42720]
 gi|238846554|gb|EEQ36018.1| hypothetical protein CLUG_00141 [Clavispora lusitaniae ATCC 42720]
          Length = 611

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 62/249 (24%), Positives = 103/249 (41%), Gaps = 40/249 (16%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEA 65
           YR   + L  + + Y+EM +A  +L+G K         +++     +Q+      +  +A
Sbjct: 258 YRRLMKTLGAD-VTYSEMALALPLLQGTKPEWALPKAHASEYPGFGIQLATNHHQQASKA 316

Query: 66  AKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM--CKALSIPVTV 121
           A+ +     N  E+NLN GCP   ++    G+ L+  P  +   +  M  C    IPVT+
Sbjct: 317 AEAISREAPNVSELNLNCGCPIDLLYRQGQGSALLDQPSKMVRILNGMNACSG-DIPVTL 375

Query: 122 KCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R G  D++  A+ L N  + +  + V  I +H R         +  R     D++ + 
Sbjct: 376 KIRTGTKDNKNTAIPLIN--RMLADTHVAAITLHGRS--------RQQRYTREADWNYIA 425

Query: 181 EI---------KKE--------NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           E+         KKE        NP  FIG NG      Q    + +  +D VM+ R A  
Sbjct: 426 EVGKTVQEWNHKKEEDKDSSETNPTWFIG-NGDCFTYEQWHNAVNTEGIDSVMVARGALI 484

Query: 222 NSAMLTTVD 230
              +   VD
Sbjct: 485 KPWIFEEVD 493


>gi|297744713|emb|CBI37975.3| unnamed protein product [Vitis vinifera]
          Length = 678

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 60/264 (22%), Positives = 106/264 (40%), Gaps = 27/264 (10%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    +++ ++   + I++N+
Sbjct: 355 EMAMCTNLLQGQASEWALLRRHSAEDLFGVQICGAYPDTVARTVELIDQECEVDFIDINM 414

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     G+ L+  P  + + I A    +  P+TVK R G  +    V   +L+ 
Sbjct: 415 GCPIDIVVNKGAGSALLTKPMRMKNIIEAASGIVDKPITVKVRTGFLEGRNRVD--SLIA 472

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----L 197
            I + G N + IH R         +  R     D++ +Y+  ++ P+    L  G     
Sbjct: 473 DIGQWGANVVTIHGRS--------RQQRYSKLADWEYIYQCARKAPEALQVLGNGDIFSY 524

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
            D ++     P +   MI R A     + T + E     +  SS  +  + KD+ R    
Sbjct: 525 LDWNKHKSGCPELSTCMIARGALVKPWIFTEIKEQRHWDI--SSGERLNILKDYVR---- 578

Query: 258 SMTDYAARHLHSGGKLQQITRHMI 281
                   H  S  K  + TRH +
Sbjct: 579 ----CGLEHWGSDTKGVETTRHFM 598


>gi|307105362|gb|EFN53612.1| hypothetical protein CHLNCDRAFT_25754 [Chlorella variabilis]
          Length = 385

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 50/215 (23%), Positives = 81/215 (37%), Gaps = 18/215 (8%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNV 81
           EM +A  +L+G      +L     E    +Q+ G     L   A++VE+    + +++N 
Sbjct: 21  EMALATNLLQGQPSEWALLKRHPSEDCFGVQLCGGYADSLARCAQLVEEQCCVDFVDVNF 80

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP   V     G+  +L P  +   +  M   LS PVT K R G  D         L+ 
Sbjct: 81  GCPIDVVCSKGAGSACLLKPQRMQAIVRGMSSVLSCPVTFKSRKGYHDGQDMA--HTLIP 138

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNG---G 196
                G   + +H R         ++ R     D+  +    +  E   L +  NG    
Sbjct: 139 QAAGWGAAAVTLHGRT--------REQRYSRLADWPYIKRCVEAAEGTGLQVVGNGDVFS 190

Query: 197 LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            ED  + L+  P +    I R A     + T + E
Sbjct: 191 FEDHYRHLEECPGLATTYIARGALIKPWIFTEIKE 225


>gi|255088371|ref|XP_002506108.1| predicted protein [Micromonas sp. RCC299]
 gi|226521379|gb|ACO67366.1| predicted protein [Micromonas sp. RCC299]
          Length = 353

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 71/156 (45%), Gaps = 10/156 (6%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKI-VED 71
           + + N A    + I  DA    D   +   + +EK  L +Q+G  D ++ +++A + V D
Sbjct: 50  KRVENTAWGTVDFIDPDAT-NDDTAVVFQTTPEEKNRLVMQLGTGDATRALQSAMVAVND 108

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
                I++N+GCP         G+ L+  P+ V D +  + + L     V C+I + + I
Sbjct: 109 VAA--IDINMGCPLKFSTASGAGSALLKKPETVHDILTTLRRNLPAETHVTCKIRLLETI 166

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                  L + I+K GV+   +H R     G  P+D
Sbjct: 167 EQTV--ELARVIEKCGVSAFGVHGRYV---GQRPRD 197


>gi|261329882|emb|CBH12865.1| tRNA-dihydrouridine synthase 3, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 528

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 34/127 (26%), Positives = 60/127 (47%), Gaps = 5/127 (3%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED--FGYNEINLNVGCPSARVHE 90
           L+  + ++L   + E    LQI  +     +  A+ VE+  F Y+ +++N GCP  +V  
Sbjct: 206 LQKSEWSLLRRHSSEDIFGLQIAVSRPHDAITWAQAVEESGFSYDFVDINCGCPVDKVVL 265

Query: 91  GSFGACLMLNP-DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              G  L     + + D + ++    S PVT+KCR+G D++ P   L   +   +  G  
Sbjct: 266 SGCGCGLWERKGNRLRDVVQSLVAHQSKPVTIKCRMGPDEENP--DLHKHIADYETWGAA 323

Query: 150 GIWIHAR 156
            + IH R
Sbjct: 324 AVTIHGR 330


>gi|303282165|ref|XP_003060374.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
 gi|226457845|gb|EEH55143.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
          Length = 424

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 95/202 (47%), Gaps = 22/202 (10%)

Query: 29  ADAILRGDKKNILGFSTQE--KPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPS 85
           A+ +LRG   N  G+  +E  +P    + G++   L   A+++  +     ++LN GCP+
Sbjct: 82  AEKLLRGIALN--GYDAEELSRPANASLMGSNPDLLEHCARVLARETRAPRVDLNCGCPA 139

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAM---CKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
             V     G+ L+ +P+ V  C++A+   C+      T+K R G DD      LR  + +
Sbjct: 140 NVVTGKGAGSSLLRDPNDVYACVSAIRRGCEGTGCVPTLKLRSGYDDD---SLLRENLLA 196

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE--DM 200
            ++ G   + +H R    +G S + N K      DI   I  E  D+ +  NG +   + 
Sbjct: 197 AQEGGAAFVTLHPRTR-RQGYSGRANWK------DIA--IAVETLDVPVIGNGDVTSPER 247

Query: 201 SQALKILPSVDGVMIGRAAYKN 222
           ++AL       G+M+GR A ++
Sbjct: 248 ARALLFETGCAGIMVGRGAVQD 269


>gi|217033784|ref|ZP_03439210.1| hypothetical protein HP9810_7g65 [Helicobacter pylori 98-10]
 gi|216943833|gb|EEC23273.1| hypothetical protein HP9810_7g65 [Helicobacter pylori 98-10]
          Length = 328

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 47/206 (22%), Positives = 99/206 (48%), Gaps = 22/206 (10%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGL 197
             ++  + V+ + +H R       +  D  +   +DY+ +  +K   + P   +  NG +
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKP---VVANGEI 201

Query: 198 EDMSQALKILP--SVDGVMIGRAAYK 221
           + + +A ++L     DG+MIGRAA +
Sbjct: 202 DSVKKAFEVLQITQADGLMIGRAALR 227


>gi|229825556|ref|ZP_04451625.1| hypothetical protein GCWU000182_00917 [Abiotrophia defectiva ATCC
           49176]
 gi|229790119|gb|EEP26233.1| hypothetical protein GCWU000182_00917 [Abiotrophia defectiva ATCC
           49176]
          Length = 323

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 86/220 (39%), Gaps = 29/220 (13%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD---CIAAMCKALSIPVTV 121
           AA+ +   GY E+NLN+GCPS  V     G+  + + D +      I +      + ++V
Sbjct: 79  AAEKLMRLGYKEVNLNLGCPSGTVVNKGRGSGALKDLDSLEKLLTLIYSKSANTGLKISV 138

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIV 179
           K RIG +    A    N++   KK  V  + IH  +R    KG   K++     L  D  
Sbjct: 139 KTRIGYEK---AEEFENILSLYKKFPVEKLIIHPRSRTEFYKGEVHKESFA---LAVDEY 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV---------- 229
            +I   +   F G    + D+    +  P +  +MIGR   ++  ++  V          
Sbjct: 193 LKIGAADRLCFNGELNTVADIKNLNEEFPDISRIMIGRGLLRHPFLIEGVLEKESEDRKV 252

Query: 230 ------DEYFSNPLT--GSSPIKTRVDKDFWRKISASMTD 261
                 DE F    T    SP      K+ W  I  S  D
Sbjct: 253 RLKNYLDELFYTYFTEFNGSPAAVLKMKELWYYIKESFRD 292


>gi|119610150|gb|EAW89744.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
          Length = 378

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 41/169 (24%), Positives = 76/169 (44%), Gaps = 33/169 (19%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + I+LN+GCP                  ++   +    + L
Sbjct: 82  ANDPEVFVQAALLAQDYC-DAIDLNLGCPQ-----------------MIAKRVLLAHEKL 123

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+   +D  +         + ++K+G   + +H R    KG
Sbjct: 124 SVPVTCKIRVFPEIDKTV------RYAQMLEKAGCQLLTVHGRTKEQKG 166


>gi|315586603|gb|ADU40984.1| tRNA-dihydrouridine synthase B [Helicobacter pylori 35A]
 gi|332673473|gb|AEE70290.1| tRNA-dihydrouridine synthase B [Helicobacter pylori 83]
          Length = 328

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|126640847|ref|YP_001083831.1| hypothetical protein A1S_0789 [Acinetobacter baumannii ATCC 17978]
          Length = 239

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 53/94 (56%), Gaps = 6/94 (6%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVK 122
           AAK+VE  G   I+LN GCP+  V+    G+ L+  PD+V   I A+  A+   IPV+ K
Sbjct: 6   AAKVVE-LGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVRDAVPAHIPVSAK 64

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R+G  D+     + N   +++ +G + + +HAR
Sbjct: 65  MRLGYLDE--NHTMEN-AYAVEDAGASWLTVHAR 95


>gi|164655383|ref|XP_001728821.1| hypothetical protein MGL_3988 [Malassezia globosa CBS 7966]
 gi|159102707|gb|EDP41607.1| hypothetical protein MGL_3988 [Malassezia globosa CBS 7966]
          Length = 395

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 66/139 (47%), Gaps = 13/139 (9%)

Query: 34  RGDKKNILGFSTQ--EKP-LALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVH 89
           +GDK     FST   E+P L  Q+G A      EA +IV        ++LN GCP     
Sbjct: 97  KGDKPV---FSTHPIERPYLIYQLGSATPEFAAEAVRIVTQHDDVAGVDLNCGCPKPFST 153

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGV 148
            G  G+ L+  PD++ D I AM +A    V+V C+I  +  Q    +L  + K ++   +
Sbjct: 154 LGGMGSNLLSTPDLLCDIIKAMRRAAPPHVSVSCKIRLLPTQEETFSL--VEKIVRARAI 211

Query: 149 NGIWIHARKAILKGLSPKD 167
             + IH R    K + P++
Sbjct: 212 RVLTIHCRT---KPMRPRE 227


>gi|317182037|dbj|BAJ59821.1| transcriptional regulator [Helicobacter pylori F57]
          Length = 328

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 47/206 (22%), Positives = 99/206 (48%), Gaps = 22/206 (10%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGL 197
             ++  + V+ + +H R       +  D  +   +DY+ +  +K   + P   +  NG +
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDRIDYESIALMKGILKKP---VVANGEI 201

Query: 198 EDMSQALKILP--SVDGVMIGRAAYK 221
           + + +A ++L     DG+MIGRAA +
Sbjct: 202 DSVKKAFEVLQITQADGLMIGRAALR 227


>gi|29348735|ref|NP_812238.1| dihydrouridine synthase [Bacteroides thetaiotaomicron VPI-5482]
 gi|253568922|ref|ZP_04846332.1| dihydrouridine synthase [Bacteroides sp. 1_1_6]
 gi|29340641|gb|AAO78432.1| putative nifR3 family TIM-barrel enzyme with dihydrouridine
           synthase domain [Bacteroides thetaiotaomicron VPI-5482]
 gi|251840941|gb|EES69022.1| dihydrouridine synthase [Bacteroides sp. 1_1_6]
          Length = 314

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 37/159 (23%), Positives = 72/159 (45%), Gaps = 9/159 (5%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  +VK R+G +    
Sbjct: 87  GYQEVDINLGCPFPLLAKRHNGSGILPYPEEVKALLSIVTRYPQISFSVKMRLGWEQPDE 146

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            +AL  ++  +    +  I +H R      L  +  +   +L     +    + P ++ G
Sbjct: 147 CLALAPILNDLP---LRQITMHPR------LGKQGYKGEVDLQGFSAFREVCQLPLVYNG 197

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
               LED+ +     PS+ G+MIGR    N A+     E
Sbjct: 198 DIHNLEDIQRISTQFPSLAGIMIGRGLLANPALALEYKE 236


>gi|219118875|ref|XP_002180204.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408461|gb|EEC48395.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 231

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 52/217 (23%), Positives = 95/217 (43%), Gaps = 25/217 (11%)

Query: 22  LYTEMIVADAI---LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +YTE +V  A+   +R + K +     +   L  Q+G  +    + AA  V     + I+
Sbjct: 24  VYTEELVDRALTGTIRVENKELGTIDYERGKLVCQLGSGEPDLALAAALHVHQ-DVDAID 82

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVA 135
           LN+GCP      G  G+ L+ +P+     I  + + LS   IPV+ K R+ + D    VA
Sbjct: 83  LNMGCPKKFSVSGGMGSALLSDPERACRIIRTLTENLSSKGIPVSAKIRL-LKDVSSTVA 141

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----PDLFI 191
               +  + ++G   I +H R+         D+  +P   + ++ E+ KE     P +  
Sbjct: 142 ---FIAGLVEAGAKAIAVHGRQV-------SDDCTVPA-RWSMLREVIKEAVHRFPHIPF 190

Query: 192 GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            LNG      + +  +      GV++ R A  N+++ 
Sbjct: 191 LLNGDFYTRDEFVSFMRDTGARGVLLARPALFNTSIF 227


>gi|255010234|ref|ZP_05282360.1| nifR3 family TIM-barrel protein [Bacteroides fragilis 3_1_12]
 gi|313148028|ref|ZP_07810221.1| dihydrouridine synthase [Bacteroides fragilis 3_1_12]
 gi|313136795|gb|EFR54155.1| dihydrouridine synthase [Bacteroides fragilis 3_1_12]
          Length = 311

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 45/190 (23%), Positives = 85/190 (44%), Gaps = 9/190 (4%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           D ++IL  + +   L  Q+  ++  K      +  + GY EI++N+GCP   + +   G+
Sbjct: 50  DVRDILPENNRVARLIPQLIASEADKTERMIALFIEQGYREIDINLGCPFPMLAKRQCGS 109

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++  PD V   +    +   I  +VK R+G +   P   L +L+  +  + +  I +H 
Sbjct: 110 GMLPYPDKVEALLKQTEQFPDIRFSVKMRLGWEK--PDECL-SLIPLLNAAPLTEITLHP 166

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
           R  I +     D        +   YE  + +P ++ G    + D+ +     P++ GVMI
Sbjct: 167 RLGIQQYKGEVDME-----GFTSFYEACR-HPVVYNGDILTIADIHRITDRFPNLAGVMI 220

Query: 216 GRAAYKNSAM 225
           GR    N A+
Sbjct: 221 GRGLLTNPAL 230


>gi|317012537|gb|ADU83145.1| putative transcriptional regulator [Helicobacter pylori
           Lithuania75]
          Length = 328

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 99/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + + + +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVNLLKIIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|332251618|ref|XP_003274943.1| PREDICTED: tRNA-dihydrouridine synthase 1 [Nomascus leucogenys]
          Length = 438

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 53/103 (51%), Gaps = 8/103 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             D    V+AA + +D+  + I+LN+GCP      G +GA L 
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQ 123


>gi|85713392|ref|ZP_01044397.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
 gi|85692787|gb|EAQ30780.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
          Length = 97

 Score = 47.0 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 11/90 (12%)

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           Y SNP        T + ++    ++  M  Y  +H+ +GG+   + RHM+GLF G P  +
Sbjct: 11  YTSNP--------TSISRE---SVARQMIPYIQQHIAAGGRAWHVVRHMLGLFQGQPGGK 59

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMIES 321
           + R  L+++         +IE A     +S
Sbjct: 60  KWRQFLSIKGPRLNDAEALIEGAIEFRTDS 89


>gi|257455770|ref|ZP_05620996.1| tRNA-dihydrouridine synthase C [Enhydrobacter aerosaccus SK60]
 gi|257446784|gb|EEV21801.1| tRNA-dihydrouridine synthase C [Enhydrobacter aerosaccus SK60]
          Length = 337

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 44/187 (23%), Positives = 83/187 (44%), Gaps = 16/187 (8%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           K  + G +    P+ +Q+ G++   +   A    + G   I++N GCP+  V+    G+ 
Sbjct: 70  KDGLKGKTIHGTPVHVQLLGSEPDLMAGNAVRAVELGALAIDINFGCPAKTVNSHRGGSV 129

Query: 97  LMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           L+  P+ +   I A+ +A+    PV+ K R+G +D      + + V+S   S +    IH
Sbjct: 130 LLTEPETLYQIIHAVRQAVPSDTPVSAKIRLGYEDTSLTQEIGDAVQSANASWLT---IH 186

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG-- 212
           AR         K     P   ++++  +  +   L I  NG +    QA++     +   
Sbjct: 187 ART--------KTQGYKPPAYWELIAPL-TQRLSLPIIANGEIWQTEQAMRCRKQANTPH 237

Query: 213 VMIGRAA 219
           +M+GR A
Sbjct: 238 IMLGRGA 244


>gi|261838041|gb|ACX97807.1| transcriptional regulator [Helicobacter pylori 51]
          Length = 328

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|153807233|ref|ZP_01959901.1| hypothetical protein BACCAC_01511 [Bacteroides caccae ATCC 43185]
 gi|149130353|gb|EDM21563.1| hypothetical protein BACCAC_01511 [Bacteroides caccae ATCC 43185]
          Length = 314

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 46/203 (22%), Positives = 86/203 (42%), Gaps = 11/203 (5%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D     D + I   S Q   L  Q+    I K      +  + GY E ++N+GCP   + 
Sbjct: 44  DGFRNKDVREIAPESNQVPHLVPQLIATSIEKAETILSLFIEKGYKEADINLGCPFPLLA 103

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +   G+ ++  PD V   +    K   I  +VK R+G ++    + L  ++  +    + 
Sbjct: 104 KRHNGSGILPYPDEVKTLLGLTLKYPQISFSVKMRLGWENPDECLQLAPILNDLP---LR 160

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I +H R      L  +  +   +L+ +D    +  ++P ++ G     +D+ +  +  P
Sbjct: 161 HITMHPR------LGKQQYKGSVDLNGFDAFLNV-CQHPLIYNGDINCPDDVHRIRQQFP 213

Query: 209 SVDGVMIGRAAYKNSAMLTTVDE 231
           ++ GVMIGR    N A+     E
Sbjct: 214 ALAGVMIGRGLLANPALALEYKE 236


>gi|170095681|ref|XP_001879061.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164646365|gb|EDR10611.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 632

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 96/224 (42%), Gaps = 26/224 (11%)

Query: 25  EMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF---GYNEINL 79
           EM +A++ L G K+  +++     E    +Q+ G   + LV  A+++      G + +++
Sbjct: 290 EMGLANSFLAGSKEEWSLVRRHPSESIFGVQVAGNKPANLVPTAEVIAKECAGGIDFVDV 349

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N GCP   V     G+ L+     +G  +  M KAL  IPVTVK R GV D     A + 
Sbjct: 350 NCGCPIDLVFRTGSGSALLDTVGKLGKILIGMNKALGEIPVTVKLRTGVKDG-KNTAHKL 408

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI------KKENPDL-FI 191
           + +   +     I +H R         +  R     D+D + E       ++ + DL  +
Sbjct: 409 MPRLSTEWNAGCITLHGRT--------RQQRYTKLADWDYIKECVRAVRAQEADEDLPPV 460

Query: 192 GLNGGLEDMSQALKIL----PSVDGVMIGRAAYKNSAMLTTVDE 231
            + GG +  S            VDG+M+GR A     + T + E
Sbjct: 461 PIFGGGDCFSSYDYWTNVENTGVDGIMVGRGALIKPWIFTEIKE 504


>gi|167957490|ref|ZP_02544564.1| tRNA-dihydrouridine synthase [candidate division TM7 single-cell
           isolate TM7c]
          Length = 278

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 43/158 (27%), Positives = 76/158 (48%), Gaps = 24/158 (15%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG---VDDQ 130
           ++ I++N+GCP A+    S GA L+  PD V     A  K   +PV+VK R+G   VD+ 
Sbjct: 14  FDGIDINMGCP-AKSAIKSGGAALIRRPD-VAVAAIAAAKTAGLPVSVKTRLGYTYVDE- 70

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP---NLDYDIVYEIKKENP 187
                 R  + +I +  +  + IH R       + K+  K+P    L  DI+    +  P
Sbjct: 71  -----WREWLTTILQQDIVNLTIHLR-------TKKEMSKVPAHYELTDDIIKLRDEIAP 118

Query: 188 DLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKN 222
              + +NG + + +   ++    P ++G+MIGR  + +
Sbjct: 119 QTLLTINGDIRNRAHGEELFATHPGLNGLMIGRGVFSD 156


>gi|154501072|ref|ZP_02039110.1| hypothetical protein BACCAP_04760 [Bacteroides capillosus ATCC
           29799]
 gi|150269900|gb|EDM97428.1| hypothetical protein BACCAP_04760 [Bacteroides capillosus ATCC
           29799]
          Length = 311

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 95/230 (41%), Gaps = 37/230 (16%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AA  +   GY E+NLN+GCPS  V     G+ L+   + +   +  +  A  + +++K R
Sbjct: 69  AAGELAAMGYREVNLNLGCPSGTVTAKGKGSGLLARREELEQLLDGIFAAAPMAISIKTR 128

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G+ D        +L++   +  V  + +H R   ++G    D  K P         ++ 
Sbjct: 129 LGMHD---PEEFGHLLELYNRYPVAELTVHPR---IRG----DFYKKP---------VRP 169

Query: 185 ENPDLFIGL-------NGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           E  DL + +       NG +    D  +A +  P V+ VMIGR            D   +
Sbjct: 170 EYFDLAVRMSRAPLCYNGDIITPGDWEKASQRWPGVETVMIGRG--------LVADPSLA 221

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             L G  P      + F  ++  +         ++  ++++I  ++I LF
Sbjct: 222 GRLKGEQPAGLDTLRAFHHELYETYAQAFGSRRNAMLRMKEIWVYLIHLF 271


>gi|317010947|gb|ADU84694.1| putative transcriptional regulator [Helicobacter pylori
           SouthAfrica7]
          Length = 328

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSALEDHFMAQISGSKESVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKVIRENTNKKITSVKVRLGFEKKIP----QEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLEITQADGLMIGRAALR 227


>gi|308062049|gb|ADO03937.1| transcriptional regulator [Helicobacter pylori Cuz20]
          Length = 328

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKEKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|331211843|ref|XP_003307191.1| up-regulated in lung cancer 8 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309297594|gb|EFP74185.1| up-regulated in lung cancer 8 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 464

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 91/202 (45%), Gaps = 29/202 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-IVGDCI 108
           L  QIG A+    ++AA+ V +   + I+LN GCP     +G  GA L+  PD + G   
Sbjct: 179 LIYQIGSANKELALQAAQTVAN-DVSGIDLNCGCPKDFSLKGGMGAALLKEPDKLCGVRF 237

Query: 109 AAMCKALSI--------PVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +    + S+        P++VK R+    +D +      +LVK I  +GV+ + +H R  
Sbjct: 238 SHPINSNSLEIQNLPTHPISVKIRLLPSQEDTL------SLVKKICDTGVSCLTVHCRTQ 291

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMI 215
            ++   P    ++  +  D V  I+     L +  NG     +D+ +  K L  V  VMI
Sbjct: 292 PMRSTEPALLHRLREI-VDFVNGIRTSENPLPVVANGDCFSAQDLPK-FKELTGVSRVMI 349

Query: 216 GRAA------YKNSAMLTTVDE 231
            R A      ++   +L  ++E
Sbjct: 350 ARGAESNVSCFRQDGLLNPIEE 371


>gi|325116599|emb|CBZ52152.1| GH10224, related [Neospora caninum Liverpool]
          Length = 663

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/145 (27%), Positives = 72/145 (49%), Gaps = 6/145 (4%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDF 72
           +LL +   +  +    D + +G+K  +     +E+  + +Q+G +D ++ + AA +V   
Sbjct: 301 KLLNSVRKINEDFSTIDFVHKGEKTCVFSTCLEERGKVVMQLGTSDATRALRAAALVAQ- 359

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I++N+GCP +    G  GA L+  P I  D +  + + L IPVT  C+I + D I 
Sbjct: 360 DVAAIDVNMGCPKSFSINGGMGAALLKTPLIATDILKTLRRNLDIPVT--CKIRLLDTIH 417

Query: 133 AVALRNLVKSIKKSGVNGIWIHARK 157
                +  +  +  GV  I IHAR+
Sbjct: 418 KTI--DFARMCENCGVEAIAIHARE 440


>gi|237808200|ref|YP_002892640.1| dihydrouridine synthase DuS [Tolumonas auensis DSM 9187]
 gi|237500461|gb|ACQ93054.1| dihydrouridine synthase DuS [Tolumonas auensis DSM 9187]
          Length = 327

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 40/184 (21%), Positives = 84/184 (45%), Gaps = 15/184 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +T   P+ +Q+ G     L E A +  + G   I++N GCP+ RV+    GA L+  P
Sbjct: 69  GKTTSGTPVRVQLLGQHPQWLAENAVLATELGSPGIDINFGCPARRVNNSCGGAALLKEP 128

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +   +  +  AL     +  ++ +    P      ++ ++ + G   + IHAR     
Sbjct: 129 ESIYRILRTVRDALPAEQLLSAKVRLGWSSPD-ECHEIIDAVIQGGAGELAIHAR----- 182

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKI--LPSVDGVMIGR 217
             + +D  K   + ++ +  ++   P + I L  NG + + + A++   +   + +M+GR
Sbjct: 183 --TKEDGYKADAIKWEWINTLR---PKINIPLIANGEIWNAADAMRCRQITGCNDLMVGR 237

Query: 218 AAYK 221
            A +
Sbjct: 238 GALQ 241


>gi|241649968|ref|XP_002411233.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215503863|gb|EEC13357.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 326

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 29/122 (23%), Positives = 62/122 (50%), Gaps = 5/122 (4%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNV 81
           EM +A  +L+G +    +L     E    +Q+ GA   ++   A+++ E    + +++N+
Sbjct: 55  EMAMASNLLQGQQSEWALLKRHASEDLFGVQVCGAHADQMTRCAQLLTEKCSVDFVDINM 114

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD--QIPAVALRNL 139
           GCP   V++   G+ LM     + + +  M   + +P+T+K R G+ +  QI    +++L
Sbjct: 115 GCPIDFVYKKGAGSGLMGRAKKLSEIVFGMSSVMDVPLTLKMRAGIQEGRQIAHQVIQDL 174

Query: 140 VK 141
            +
Sbjct: 175 KR 176


>gi|315655777|ref|ZP_07908675.1| tRNA-dihydrouridine synthase B [Mobiluncus curtisii ATCC 51333]
 gi|315489841|gb|EFU79468.1| tRNA-dihydrouridine synthase B [Mobiluncus curtisii ATCC 51333]
          Length = 438

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 39/132 (29%), Positives = 59/132 (44%), Gaps = 20/132 (15%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP----LALQIGGADISKLVEAAK--I 68
           L +   +   EMI A A++    ++ +    Q  P     ALQ+ G   + L  AA+  I
Sbjct: 66  LCSVEGMFVNEMITAKALMMNSTRSWV--MAQSGPGQTVRALQLYGVVGADLAWAARELI 123

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----------LSI 117
             D   + I+LN GCP  +V     GA L       GD I  + +A           + +
Sbjct: 124 ARDL-VDVIDLNFGCPVPKVTRKGGGAALPWKTTYFGDLIGQVVQAAQESSQAARREVEV 182

Query: 118 PVTVKCRIGVDD 129
           PVTVK R+G+D+
Sbjct: 183 PVTVKIRVGIDE 194


>gi|146422829|ref|XP_001487349.1| hypothetical protein PGUG_00726 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 607

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 100/242 (41%), Gaps = 48/242 (19%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEA 65
           YR   + L  + + Y+EM ++  +L+            S++     +QI  +      +A
Sbjct: 254 YRRLMKTLGAD-VTYSEMALSLPLLQATNSEWALPKAHSSEYPGFGVQIATSKHWAAAKA 312

Query: 66  AKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVK 122
           A+++  E    +E+NLN GCP   ++    G+ LM  P  +   +  M   +  IPVTVK
Sbjct: 313 AEVIYKETTHVSELNLNCGCPIDLLYRQGQGSALMEQPARLLRILKGMNASSGDIPVTVK 372

Query: 123 CRIGVDDQIPAVALRNLVKS-----IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            R G  D       +N  KS     + ++ V  I +H R         +  R   + D++
Sbjct: 373 IRTGTKDN------KNTAKSLVERVLAENDVAAITLHGRS--------RQQRYTKDADWE 418

Query: 178 IVYEI---------KKE--------NPDLFIGLNGGL---EDMSQALKILPSVDGVMIGR 217
            + E+         KKE        N   F+G NG +   ED   A+     VD VM+ R
Sbjct: 419 YIKEVGAVVTEWNNKKEEDKESSETNRTNFVG-NGDVFTHEDWYNAVNT-EGVDSVMVAR 476

Query: 218 AA 219
            A
Sbjct: 477 GA 478


>gi|125547021|gb|EAY92843.1| hypothetical protein OsI_14644 [Oryza sativa Indica Group]
          Length = 685

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 63/283 (22%), Positives = 108/283 (38%), Gaps = 39/283 (13%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    ++V+ +   + I++N+
Sbjct: 362 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVARTVELVDNECSVDFIDINM 421

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--- 138
           GCP   V     G+ L+  P  +   + A       P+TVK R            RN   
Sbjct: 422 GCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVKVRTAF------FEGRNRAD 475

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNG- 195
            +V  I   G + I +H R         +  R     D+D +Y+  ++ PD L +  NG 
Sbjct: 476 SIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQCAQKAPDQLHVVGNGD 527

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D ++ +     +   MI R A     + T V E     +T     +  + KDF  
Sbjct: 528 VFSFTDWNKHVSGCSKISTCMIARGALIKPWIFTEVKEQRHWDITSGE--RFNILKDF-- 583

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   H  S  K  + TR+ +  +  +     CR+I
Sbjct: 584 ------VSFGLEHWGSDSKGVETTRYFLLEWLSY----TCRYI 616


>gi|223590199|sp|A5DBS1|DUS3_PICGU RecName: Full=tRNA-dihydrouridine synthase 3
 gi|190344863|gb|EDK36628.2| hypothetical protein PGUG_00726 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 607

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 100/242 (41%), Gaps = 48/242 (19%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEA 65
           YR   + L  + + Y+EM ++  +L+            S++     +QI  +      +A
Sbjct: 254 YRRLMKTLGAD-VTYSEMALSLPLLQATNSEWALPKAHSSEYPGFGVQIATSKHWAAAKA 312

Query: 66  AKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVK 122
           A+++  E    +E+NLN GCP   ++    G+ LM  P  +   +  M   +  IPVTVK
Sbjct: 313 AEVIYKETTHVSELNLNCGCPIDLLYRQGQGSALMEQPARLLRILKGMNASSGDIPVTVK 372

Query: 123 CRIGVDDQIPAVALRNLVKS-----IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            R G  D       +N  KS     + ++ V  I +H R         +  R   + D++
Sbjct: 373 IRTGTKDN------KNTAKSLVERVLAENDVAAITLHGRS--------RQQRYTKDADWE 418

Query: 178 IVYEI---------KKE--------NPDLFIGLNGGL---EDMSQALKILPSVDGVMIGR 217
            + E+         KKE        N   F+G NG +   ED   A+     VD VM+ R
Sbjct: 419 YIKEVGAVVTEWNNKKEEDKESSETNRTNFVG-NGDVFTHEDWYNAVNT-EGVDSVMVAR 476

Query: 218 AA 219
            A
Sbjct: 477 GA 478


>gi|256831223|ref|YP_003159951.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
 gi|256580399|gb|ACU91535.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
          Length = 324

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 46/208 (22%), Positives = 86/208 (41%), Gaps = 14/208 (6%)

Query: 24  TEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           TEM+ A  ++        +L    Q+ PL +Q+ G++   LV++ + +   G+   +LN 
Sbjct: 40  TEMVSAKGLIYDSPGTNELLQTCDQDSPLVVQLFGSEEPFLVQSIERLRKAGFRYFDLNC 99

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP  +V +   GA L+  P+ +     +M  A   P  +  +I +   +       +  
Sbjct: 100 GCPVRKVIKTGSGAALLKEPENLLKIAKSMIDAAE-PGCMGFKIRLGWYVGQPVYLQVAT 158

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +++ G   + +H R          D   +  L         KE   L +  +G L    
Sbjct: 159 KLEELGAGWVTMHPRFGAQGFTGHADWSHLKTL---------KERVTLPVIASGDLFHAE 209

Query: 202 QALKILP--SVDGVMIGRAAYKNSAMLT 227
            A+K +   SVD +M  R A  + ++ T
Sbjct: 210 DAIKCIEQTSVDSIMFARGALNDPSIFT 237


>gi|164657526|ref|XP_001729889.1| hypothetical protein MGL_2875 [Malassezia globosa CBS 7966]
 gi|159103783|gb|EDP42675.1| hypothetical protein MGL_2875 [Malassezia globosa CBS 7966]
          Length = 308

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 3/107 (2%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+  +  S L +AA++V  +  + I+LN GCP    +E   G+ L+  P++V D I 
Sbjct: 45  LVCQLAASHSSPLADAAELVSPY-VDGIDLNCGCPQPWAYEERVGSYLLEEPELVADMIR 103

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            +   L     V  +I +D  +       LV++   +G + I IH R
Sbjct: 104 TVKGRLGDAYCVSVKIRIDPDLRRT--DTLVRNALHAGASFITIHGR 148


>gi|19115484|ref|NP_594572.1| tRNA dihydrouridine synthase Dus3 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74638894|sp|Q9UTH9|DUS3_SCHPO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|6013094|emb|CAB57402.1| tRNA dihydrouridine synthase Dus3 (predicted) [Schizosaccharomyces
           pombe]
          Length = 617

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 42/156 (26%), Positives = 74/156 (47%), Gaps = 25/156 (16%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF--GYNEINLNVGCPSARVH 89
           ++RG ++ ILG         +Q+    + +  + A+++ +   G + ++LN GCP   V 
Sbjct: 296 MMRGGRRGILG---------VQLATGKLWQATKTAQVIAEQCDGVDFLDLNCGCPIDLVF 346

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSI-KKS 146
               G+ L+ NP  +   +  M  A+S  IPVTVK R+G  D  P V  +NL+  I  ++
Sbjct: 347 RQGAGSSLLENPGRLLRNLQGM-DAVSGQIPVTVKLRMGNKDDHPVV--KNLIGRIFNET 403

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
             +   +H R         +  R   N ++D + EI
Sbjct: 404 NTSAATLHGRS--------RQQRYSKNANWDYIGEI 431


>gi|324504592|gb|ADY41982.1| tRNA-dihydrouridine synthase 2-like protein [Ascaris suum]
          Length = 454

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 63/267 (23%), Positives = 112/267 (41%), Gaps = 40/267 (14%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           RLL +  ++   +   D ++  D    +    +     LQ+G  +  ++   AK V D  
Sbjct: 62  RLLNSRRIVNDVLHTVDYVIEEDVVLRVATERERNKCVLQVGTNNGDRIAAVAKKVHD-D 120

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
              I++N+GCP      G  GA L+  PD + + + ++       V V C+I V D++  
Sbjct: 121 IAAIDVNMGCPKPFSLTGGMGAALLTQPDKIKEILTSL--VSVSSVPVSCKIRVLDKLED 178

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI-- 191
                LV+ I+K GV  + +H R+        +D R+    D + V EI++    L I  
Sbjct: 179 TLA--LVRLIEKCGVAAVGVHGRR--------RDERQ---GDANRVNEIREVVRALSIPV 225

Query: 192 ------GLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM-----LTTVDEYFSNPLTGS 240
                 G+    +D+ Q  K       +M+ R A  N ++     L T+ E  +N L   
Sbjct: 226 IANGASGMVKEFKDVEQFRK-ESEASSIMLARRALSNPSIFRPQGLLTMQEEVTNFLK-- 282

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL 267
             +    D++F      +MT Y  + +
Sbjct: 283 --LACEFDENF------TMTKYVVQRI 301


>gi|298480434|ref|ZP_06998631.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. D22]
 gi|298273255|gb|EFI14819.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. D22]
          Length = 314

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 38/165 (23%), Positives = 79/165 (47%), Gaps = 12/165 (7%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +A KI+  F    Y E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  +
Sbjct: 75  KAEKILSLFIEKEYKEVDINIGCPFPMLAKRHNGSGILPYPEEVQALLSLITEYPQISFS 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G +D  P   L+ L   I +  +  + +H R      L  +  +   +L     +
Sbjct: 135 IKMRLGWED--PEECLK-LAPIINELPLRQVVMHPR------LGKQQYKGEVDLKAFEAF 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +   ++P ++ G    +ED+ +  +  P + G+MIGR    N A+
Sbjct: 186 QNACKHPLIYNGDINSVEDIHRIQEQFPGLAGMMIGRGLLANPAL 230


>gi|317009261|gb|ADU79841.1| transcriptional regulator [Helicobacter pylori India7]
          Length = 328

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|226945483|ref|YP_002800556.1| tRNA-dihydrouridine synthase C [Azotobacter vinelandii DJ]
 gi|226720410|gb|ACO79581.1| tRNA-dihydrouridine synthase C [Azotobacter vinelandii DJ]
          Length = 326

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 39/127 (30%), Positives = 68/127 (53%), Gaps = 7/127 (5%)

Query: 42  GFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           G+ T+   P+ LQ+ G+D + L E A +  + G   I+LN GCP+  V+    GA L+  
Sbjct: 56  GWRTRAGTPMHLQLLGSDPACLAENAALAAELGAPAIDLNFGCPAKTVNRSRGGAVLLDE 115

Query: 101 PDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           P+++   +  + +A+   +PVT K R+G     P  AL    +++ + GV  + +HAR  
Sbjct: 116 PELLHAIVREVRRAVPAHVPVTAKMRLGYAR--PEGAL-ECARALVEGGVAHLVVHARTK 172

Query: 159 ILKGLSP 165
           + +G  P
Sbjct: 173 V-EGYRP 178


>gi|158299928|ref|XP_319936.4| AGAP009171-PA [Anopheles gambiae str. PEST]
 gi|157013754|gb|EAA14958.4| AGAP009171-PA [Anopheles gambiae str. PEST]
          Length = 599

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 55/250 (22%), Positives = 100/250 (40%), Gaps = 27/250 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + E    +Q+ G +   +  AA+I+ E    + I+LN GCP   +     G+ L+   ++
Sbjct: 302 SSEDLFGVQLCGHNPKLVTYAAQIIAEKADVDFIDLNTGCPIDLIFNQGGGSALLRRQNV 361

Query: 104 VGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           +   + +  + L+      TVK RIG+ +    +    +V   +  G + I IH R    
Sbjct: 362 LKVMVQSCSRLLADYGKEFTVKTRIGIYNN--KLIAHEMVPKFEDWGASLITIHGRT--- 416

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGR 217
                K+ R     D++ + +   +   + +  NG   G ED        P++ GVM+GR
Sbjct: 417 -----KEQRYTKRADWEYLQQCATQAQSVPVFGNGDIFGYEDYEHIRTKCPNIAGVMVGR 471

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            A     +   + E     L  SS  +  + K +         +Y   H  S  K  + T
Sbjct: 472 GALIKPWVFQEIKE--RKTLDPSSGERFEMLKRY--------VNYGLEHWGSDTKGVETT 521

Query: 278 RHMIGLFHGF 287
           R  +  +  F
Sbjct: 522 RRFLLEWQSF 531


>gi|116308867|emb|CAH66003.1| H0613H07.1 [Oryza sativa Indica Group]
          Length = 685

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 63/283 (22%), Positives = 108/283 (38%), Gaps = 39/283 (13%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    ++V+ +   + I++N+
Sbjct: 362 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVARTVELVDNECSVDFIDINM 421

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--- 138
           GCP   V     G+ L+  P  +   + A       P+TVK R            RN   
Sbjct: 422 GCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVKVRTAF------FEGRNRAD 475

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNG- 195
            +V  I   G + I +H R         +  R     D+D +Y+  ++ PD L +  NG 
Sbjct: 476 SIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQCAQKAPDQLHVVGNGD 527

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D ++ +     +   MI R A     + T V E     +T     +  + KDF  
Sbjct: 528 VFSFTDWNKHVSGCSKISTCMIARGALIKPWIFTEVKEQRHWDITSGE--RFNILKDF-- 583

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   H  S  K  + TR+ +  +  +     CR+I
Sbjct: 584 ------VTFGLEHWGSDSKGVETTRYFLLEWLSY----TCRYI 616


>gi|297702080|ref|XP_002828012.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 1 [Pongo
           abelii]
          Length = 456

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 40/169 (23%), Positives = 76/169 (44%), Gaps = 33/169 (19%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIG 55
           MVD ++  +R  +R     L    +L+ ++ V DA  R  K+N+      +++PL +Q  
Sbjct: 24  MVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYR--KENLYCEVCPEDRPLIVQFC 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D    V+AA + +D+  + ++LN+GC                 P ++   +    + L
Sbjct: 82  ANDPEVFVQAALLAQDY-CDAVDLNLGC-----------------PQMIAKRVLLAHEKL 123

Query: 116 SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           S+PVT K R+   +D  +         + ++K+G   + +H R    KG
Sbjct: 124 SVPVTCKIRVFPEIDKTV------RYAQMLEKAGCQLLTVHGRTKEQKG 166


>gi|224160043|ref|XP_002338164.1| predicted protein [Populus trichocarpa]
 gi|222871075|gb|EEF08206.1| predicted protein [Populus trichocarpa]
          Length = 335

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 41/194 (21%), Positives = 84/194 (43%), Gaps = 19/194 (9%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ 130
           G   I+LN GCP+  V+    GA L+ +P+ +   + A+  A+  ++PV+ K R+G +D 
Sbjct: 12  GPEGIDLNFGCPAKVVNRHGGGAALLQDPEQIARVVGAVRAAVPAAMPVSAKMRLGFND- 70

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                +    ++++  G   I +HAR  +       D  + P   +D++  I +E+  + 
Sbjct: 71  --TALMTECAQAMQAGGACEIVVHARTKL-------DGYRPPAY-WDMIPRI-RESVTVP 119

Query: 191 IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG +  +  AL+         +M+GR    +  +   +         G  P +    
Sbjct: 120 VVANGEIWTVEDALRCREQSGCGDLMLGRGIVADPGLALAIRAAVEG---GRMPAEHVAA 176

Query: 249 KDFWRKISASMTDY 262
           + FW  +   +  +
Sbjct: 177 QVFWSDLVPQVQRF 190


>gi|261839452|gb|ACX99217.1| transcriptional regulator [Helicobacter pylori 52]
          Length = 328

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFIAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLTIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|50954563|ref|YP_061851.1| NifR3/Smm1 family transcriptional regulator [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50951045|gb|AAT88746.1| transcriptional regulator, NifR3/Smm1 family [Leifsonia xyli subsp.
           xyli str. CTCB07]
          Length = 408

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 62/132 (46%), Gaps = 5/132 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +++  +     E P ++Q+ G D
Sbjct: 41  MAGITNTAFRRLCREF-GAGLYVSEMITSRALVERTPESLRLIAHHESETPRSIQLYGVD 99

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALS 116
              + EA  + V +   + I+LN GCP  +V     GA L     +  + +  A+  A  
Sbjct: 100 PKTVREAVTLLVAEDRADHIDLNFGCPVPKVTRKGGGAALPWKLGLFREIVEGAVAAAGD 159

Query: 117 IPVTVKCRIGVD 128
           IP+TVK R G+D
Sbjct: 160 IPLTVKMRKGID 171


>gi|254431919|ref|ZP_05045622.1| tRNA-dihydrouridine synthase B [Cyanobium sp. PCC 7001]
 gi|197626372|gb|EDY38931.1| tRNA-dihydrouridine synthase B [Cyanobium sp. PCC 7001]
          Length = 342

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 70/301 (23%), Positives = 133/301 (44%), Gaps = 30/301 (9%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISKLV 63
           +DR +R   R    +ALL+TEM+ A ++  G   + +    ++  P+ +Q+     + + 
Sbjct: 44  SDRIFRSLVRRWAPDALLFTEMVNATSLELGHGVQKVEELGSESGPIGVQLFDHRPAAMA 103

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    + A+  A++IPVTVK 
Sbjct: 104 DAARRAEAAGAFLIDINMGCPVKKIARKGGGSGLIRDPHLAARIVEAVAAAVAIPVTVKT 163

Query: 124 RIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           R+G    D  P    R L    + +G   + +H R         ++       D+  +  
Sbjct: 164 RLGWCGSDADPVSWCRQL----QDAGAQLLTLHGRT--------REQGFRGRADWGAIAA 211

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN---P 236
           +K+    + +  NG +     AL  L +   DG+M+GR +     ++  +D   S    P
Sbjct: 212 VKRAL-TIPVVANGDVNTPEGALHCLAATGCDGLMVGRGSMGAPWLVGQIDAALSGQPIP 270

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +  +  +  +  + + A+  D+          L    +HM     GFP + + RH 
Sbjct: 271 PTPGAAERIALAAEQLQALVAAKGDHG---------LLIARKHMGWTCTGFPGAPQLRHD 321

Query: 297 L 297
           L
Sbjct: 322 L 322


>gi|116181790|ref|XP_001220744.1| hypothetical protein CHGG_01523 [Chaetomium globosum CBS 148.51]
 gi|88185820|gb|EAQ93288.1| hypothetical protein CHGG_01523 [Chaetomium globosum CBS 148.51]
          Length = 655

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 73/154 (47%), Gaps = 16/154 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK----ALSIPVTVKCRIGVDDQIP 132
           I++N GCP      G  GA L+  P+ +   + A+ +    A  + V+VK R+       
Sbjct: 160 IDVNAGCPKPFSVSGGMGAALLRTPEKLAGILEALVRDITPAYGLGVSVKIRLLET---- 215

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A     LV+ + ++G+ G+ +H R   ++   P++ R I      +V E+  E   +   
Sbjct: 216 AAETEALVRRLVRTGITGLTVHCRTTPMR---PRE-RAI-RGQLRMVREVCHEA-GVACL 269

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           +NG +E   QA  ++    VDG MI  AA +N +
Sbjct: 270 MNGDVESRDQADALVEEFGVDGAMIATAAERNPS 303


>gi|308184510|ref|YP_003928643.1| putative transcriptional regulator [Helicobacter pylori SJM180]
 gi|308060430|gb|ADO02326.1| putative transcriptional regulator [Helicobacter pylori SJM180]
          Length = 328

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|254779294|ref|YP_003057399.1| putative transcriptional regulator [Helicobacter pylori B38]
 gi|254001205|emb|CAX29173.1| Putative transcriptional regulator [Helicobacter pylori B38]
          Length = 328

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 98/204 (48%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+  S + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKESVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|115456906|ref|NP_001052053.1| Os04g0117600 [Oryza sativa Japonica Group]
 gi|75233055|sp|Q7XT07|DUS3L_ORYSJ RecName: Full=tRNA-dihydrouridine synthase 3-like; AltName:
           Full=Zinc finger CCCH domain-containing protein 26;
           Short=OsC3H26
 gi|38344118|emb|CAE01725.2| OSJNBb0050O03.15 [Oryza sativa Japonica Group]
 gi|113563624|dbj|BAF13967.1| Os04g0117600 [Oryza sativa Japonica Group]
          Length = 685

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 63/283 (22%), Positives = 108/283 (38%), Gaps = 39/283 (13%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    ++V+ +   + I++N+
Sbjct: 362 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVARTVELVDNECSVDFIDINM 421

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--- 138
           GCP   V     G+ L+  P  +   + A       P+TVK R            RN   
Sbjct: 422 GCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVKVRTAF------FEGRNRAD 475

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNG- 195
            +V  I   G + I +H R         +  R     D+D +Y+  ++ PD L +  NG 
Sbjct: 476 SIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQCAQKAPDQLHVVGNGD 527

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D ++ +     +   MI R A     + T V E     +T     +  + KDF  
Sbjct: 528 VFSFTDWNKHVSGCSKISTSMIARGALIKPWIFTEVKEQRHWDITSGE--RFNILKDF-- 583

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   H  S  K  + TR+ +  +  +     CR+I
Sbjct: 584 ------VSFGLEHWGSDSKGVETTRYFLLEWLSY----TCRYI 616


>gi|290985846|ref|XP_002675636.1| dihydrouridine synthase, DuS [Naegleria gruberi]
 gi|284089233|gb|EFC42892.1| dihydrouridine synthase, DuS [Naegleria gruberi]
          Length = 388

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 67/128 (52%), Gaps = 13/128 (10%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           DK++    ++Q+ P  LQ+G +     ++ A+++ D GY+ I++N+GCP     +G  G+
Sbjct: 102 DKESDSPTASQKVPTVLQLGTSSPELALQVAELMID-GYDAIDVNMGCPKKFSVKGGMGS 160

Query: 96  CLMLNPDIVGDCIA---AMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            L L P+   +  A   A+ K +      PVT K R+ +D     +    L + ++ +GV
Sbjct: 161 AL-LRPENQENAFAILRALVKGIQEKHGKPVTCKIRL-LDTTENTI---ELYEKLQATGV 215

Query: 149 NGIWIHAR 156
             I +HAR
Sbjct: 216 TAICVHAR 223


>gi|262373327|ref|ZP_06066606.1| tRNA-dihydrouridine synthase C [Acinetobacter junii SH205]
 gi|262313352|gb|EEY94437.1| tRNA-dihydrouridine synthase C [Acinetobacter junii SH205]
          Length = 310

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 38/126 (30%), Positives = 61/126 (48%), Gaps = 10/126 (7%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           L+ D K   G      P+ +Q  G +   L   A  V + G   I+LN GCP+  V+   
Sbjct: 53  LKTDGKTAAG-----TPVHVQFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHR 107

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            G+ L+  P+ V   + A+  A+   IPV+ K R+G  D+     L N   +I+ +G + 
Sbjct: 108 GGSVLLDEPETVHLLVKAVRDAVPKHIPVSAKMRLGYLDE--NHTLDN-AHAIEDAGASW 164

Query: 151 IWIHAR 156
           + +HAR
Sbjct: 165 LTVHAR 170


>gi|255318636|ref|ZP_05359867.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SK82]
 gi|262379139|ref|ZP_06072295.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SH164]
 gi|255304318|gb|EET83504.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SK82]
 gi|262298596|gb|EEY86509.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SH164]
          Length = 313

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 48/200 (24%), Positives = 88/200 (44%), Gaps = 16/200 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q  G +   L   A      G   I++N GCP+  V+    G+ L+  P
Sbjct: 57  GKTAAGTPVHVQFLGNNPEMLAANAVRAAILGAPAIDMNFGCPAKTVNRHRGGSVLLDEP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           ++V + + A+  A+   IPV+ K R+G  D+     L N   +I+ +G + + +HAR   
Sbjct: 117 EVVYELVKAVRDAVPAHIPVSAKMRLGYMDR--NFMLDN-AHAIEDAGASWVTVHART-- 171

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGR 217
                 K +   P   +D +  I +E   + +  NG + + + A   ++    + +MIGR
Sbjct: 172 ------KADGYTPPAFWDQLQPI-REALKINVIANGEIWNNTDARQCQLESGCEDLMIGR 224

Query: 218 AAYKNSAMLTTVDEYFSNPL 237
            A     +   +      PL
Sbjct: 225 GAVTTPDLTQCIRNNSDEPL 244


>gi|332526992|ref|ZP_08403077.1| dihydrouridine synthase, DuS [Rubrivivax benzoatilyticus JA2]
 gi|332111427|gb|EGJ11410.1| dihydrouridine synthase, DuS [Rubrivivax benzoatilyticus JA2]
          Length = 311

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 55/238 (23%), Positives = 98/238 (41%), Gaps = 25/238 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+  Q+ G D   L E A  + +     I+LN GCP+  V+    GA L+  P
Sbjct: 50  GRTAAGTPVRAQLLGGDPVCLAENAARLAELSPAGIDLNFGCPAPVVNRHRGGAVLLDEP 109

Query: 102 DIVG--DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           ++V             ++PVT K R+G    +    + +   +I   G   + +HAR   
Sbjct: 110 ELVHAIVAAVRRAVPAAVPVTAKMRLG---HLDTSRMLDCAHAIADGGAAELVVHART-- 164

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
                 K     P   +  + EI +E   L +  NG +  +  A + L     D +M+GR
Sbjct: 165 ------KAEGYRPPAHWHRIAEI-REAVALPVVANGEVWTVDDARRCLAESGCDALMLGR 217

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
               +  +   +    + P+ G + ++  + + FW  +SA +        H  G+L+Q
Sbjct: 218 GMVADPGLARAIR---AEPVPGWAALQPEL-RRFWASVSARVEPR-----HRAGRLKQ 266


>gi|125589164|gb|EAZ29514.1| hypothetical protein OsJ_13588 [Oryza sativa Japonica Group]
          Length = 685

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 63/283 (22%), Positives = 108/283 (38%), Gaps = 39/283 (13%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNV 81
           EM +   +L+G      +L   + E    +QI GA    +    ++V+ +   + I++N+
Sbjct: 362 EMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVARTVELVDNECSVDFIDINM 421

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--- 138
           GCP   V     G+ L+  P  +   + A       P+TVK R            RN   
Sbjct: 422 GCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVKVRTAF------FEGRNRAD 475

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNG- 195
            +V  I   G + I +H R         +  R     D+D +Y+  ++ PD L +  NG 
Sbjct: 476 SIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQCAQKAPDQLHVVGNGD 527

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D ++ +     +   MI R A     + T V E     +T     +  + KDF  
Sbjct: 528 VFSFTDWNKHVSGCSKISTSMIARGALIKPWIFTEVKEQRHWDITSGE--RFNILKDF-- 583

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   H  S  K  + TR+ +  +  +     CR+I
Sbjct: 584 ------VSFGLEHWGSDSKGVETTRYFLLEWLSY----TCRYI 616


>gi|294649504|ref|ZP_06726925.1| tRNA-dihydrouridine synthase C [Acinetobacter haemolyticus ATCC
           19194]
 gi|292824565|gb|EFF83347.1| tRNA-dihydrouridine synthase C [Acinetobacter haemolyticus ATCC
           19194]
          Length = 309

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 58/117 (49%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  P
Sbjct: 57  GKTAAGTPVHVQFLGNNPDMLAANASKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           + V   + A+  A+   IPV+ K R+G  D+     + N   +I+ +G + + +HAR
Sbjct: 117 ETVHLLVKAVRDAVPSHIPVSAKMRLGYLDE--NHTMEN-AHAIEDAGASWLTVHAR 170


>gi|308063487|gb|ADO05374.1| transcriptional regulator [Helicobacter pylori Sat464]
          Length = 328

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN-EINLN 80
           +EM+ + +++    K   +L  S  E    +QI G+    + EA + +    +   I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMVQISGSKEGVVKEAVEKINALEHVIGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKEKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|265764875|ref|ZP_06093150.1| nifR3 family TIM-barrel protein [Bacteroides sp. 2_1_16]
 gi|263254259|gb|EEZ25693.1| nifR3 family TIM-barrel protein [Bacteroides sp. 2_1_16]
          Length = 310

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 44/191 (23%), Positives = 86/191 (45%), Gaps = 11/191 (5%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           D ++IL  + +   L  Q+  +++ K      +  + GY E+++N+GCP   + +   G+
Sbjct: 49  DVRDILPENNRVPHLIPQLIASEMDKTERIIALFIEQGYREMDINLGCPFPMLAKRQCGS 108

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++ +PD V   +  + +   +  +VK R+G +   P   L  L           I +H 
Sbjct: 109 GMLPHPDKVETLLKQIEQYPGVSFSVKMRLGWEK--PDECLTLLPLLNAAPLTE-IIVHP 165

Query: 156 RKAILKGLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           R  I      +  +   N++ +   YE  + +P ++ G    +ED+    +  P + GVM
Sbjct: 166 RLGI------QQYKGEVNMEGFTAFYEACR-HPVIYNGDILTIEDIRCITEKFPKLTGVM 218

Query: 215 IGRAAYKNSAM 225
           IGR    N A+
Sbjct: 219 IGRGLLANPAL 229


>gi|227872442|ref|ZP_03990784.1| dihydrouridine synthase, DuS [Oribacterium sinus F0268]
 gi|227841702|gb|EEJ51990.1| dihydrouridine synthase, DuS [Oribacterium sinus F0268]
          Length = 323

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 52/228 (22%), Positives = 87/228 (38%), Gaps = 61/228 (26%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKALSIPVTVKC 123
           K +E  GY E NLN+GCPS  V     G+ ++  P ++ D      ++ K   + V++K 
Sbjct: 78  KYMESLGYQECNLNLGCPSGTVVAKGKGSGMLRIPLLLEDFFQELFSLLKDSKMRVSIKT 137

Query: 124 RIGVD------------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           RIG++            +  P   +    ++ K+     + +H  + I K        K+
Sbjct: 138 RIGLNTDGEWEELFAVFNHFPFSEIIVHPRTQKQYYSGRVNLHCFQNICK------YSKL 191

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAM--- 225
           P     +VY             NG +E     L +    P + G+M GR    N A+   
Sbjct: 192 P-----LVY-------------NGDVETREDILFLQEQFPEIQGIMCGRGLLSNPALFRE 233

Query: 226 ---------------LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
                          L  V+E F+  + G   I  +  K+FW   + S
Sbjct: 234 ARGGKALQEGEFKEFLRLVEENFAKEIQGERNILAKY-KEFWSYFAKS 280


>gi|53711476|ref|YP_097468.1| nifR3 family TIM-barrel protein [Bacteroides fragilis YCH46]
 gi|253564462|ref|ZP_04841919.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_2_5]
 gi|52214341|dbj|BAD46934.1| putative nifR3 family TIM-barrel enzyme [Bacteroides fragilis
           YCH46]
 gi|251948238|gb|EES88520.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_2_5]
 gi|301161208|emb|CBW20746.1| conserved hypothetical protein [Bacteroides fragilis 638R]
          Length = 310

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 44/191 (23%), Positives = 90/191 (47%), Gaps = 11/191 (5%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           D ++IL  + +   L  Q+  +++ K      +  + GY E+++N+GCP   + +   G+
Sbjct: 49  DVRDILPENNRVPHLIPQLIASEMDKTERIIALFIEQGYREMDINLGCPFPMLAKRQCGS 108

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++ +PD V   +  + +   +  +VK R+G +   P   L  L+  +  + +  I +H 
Sbjct: 109 GMLPHPDKVETLLKQIEQYPDVSFSVKMRLGWEK--PDECL-TLLPLLNAAPLTEIIVHP 165

Query: 156 RKAILKGLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           R  I      +  +   N++ +   YE  + +P ++ G    +ED+    +  P + GVM
Sbjct: 166 RLGI------QQYKGEVNMEGFTAFYEACR-HPVIYNGDILTIEDIRCITEKFPKLTGVM 218

Query: 215 IGRAAYKNSAM 225
           IGR    N A+
Sbjct: 219 IGRGLLANPAL 229


>gi|269219506|ref|ZP_06163360.1| putative tRNA-dihydrouridine synthase [Actinomyces sp. oral taxon
           848 str. F0332]
 gi|269211085|gb|EEZ77425.1| putative tRNA-dihydrouridine synthase [Actinomyces sp. oral taxon
           848 str. F0332]
          Length = 432

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 47/213 (22%), Positives = 93/213 (43%), Gaps = 25/213 (11%)

Query: 19  NALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEA-AKIVEDFGYN 75
             L   EM+ + A++  + +  N++     +   ++Q+ G +      A A +V +   +
Sbjct: 85  GGLWVCEMVTSRALVERNPEAMNMIKPDPGDPVRSIQLYGVEPKTSAAAVAMLVGENRAD 144

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---------LSIPVTVKCRIG 126
            I+LN GCP+ +V     G+ L    D+  + ++A  +A         + +PVT K R+G
Sbjct: 145 HIDLNFGCPAPKVTRKGGGSALPWKLDLFREIVSAAVEAARRASADRDVEVPVTAKIRVG 204

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +DD        +  +  + +G+ G+ +HAR          D  +I  L          E 
Sbjct: 205 IDDG--HTTFLDAARIAEDAGIAGLTLHARTTAQHYSGSADWGRIAEL---------AEA 253

Query: 187 PDLFIGLNGGLEDMSQALKILPSVD--GVMIGR 217
             L +  NG + ++  A++++      GV +GR
Sbjct: 254 TSLPVLGNGDVFEVEDAVRLMAETGCAGVAVGR 286


>gi|221194516|ref|ZP_03567573.1| tRNA-dihydrouridine synthase B [Atopobium rimae ATCC 49626]
 gi|221185420|gb|EEE17810.1| tRNA-dihydrouridine synthase B [Atopobium rimae ATCC 49626]
          Length = 361

 Score = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 35/109 (32%), Positives = 56/109 (51%), Gaps = 5/109 (4%)

Query: 23  YTEMI-VADAILRGDKKNILGFSTQEKP-LALQIGGADISKLVEAA-KIVEDFG--YNEI 77
           YTEM+ VA     G+K   L +    +P +A+Q+ G+   +  EAA +I E  G     I
Sbjct: 66  YTEMVSVAGIHFGGEKTWQLVYPLDPEPDIAVQLFGSKPEQFREAASQIAERLGPKLALI 125

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           ++N+ CP  +V +   G+ L+ NP    + + A    + +PVT K R G
Sbjct: 126 DINMACPVPKVVKKGEGSALLDNPVRAAEIVRACISEVDVPVTAKIRRG 174


>gi|167381618|ref|XP_001735786.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165902070|gb|EDR27991.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 366

 Score = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 55/236 (23%), Positives = 101/236 (42%), Gaps = 38/236 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q+    LQ+G  D+   ++   ++++     I++N+GC      +G  G  L+ N D + 
Sbjct: 90  QQSKTILQLGTFDVESSIKCVSLIKEVC--GIDINLGCGMWFSTKGEMGQALVSNRDKLE 147

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             + A+ K L  P++ K R+    Q         ++ +   G++ I +H R         
Sbjct: 148 KIVKALVK-LGKPISAKIRL----QQTHEETLEFIQWLYSLGISIISLHGR--------- 193

Query: 166 KDNRKIPNLDYDIVY--EIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAY 220
             ++++  +D D V   ++ K+ P   I LNG +   ED+++ L    +V GVMIGRA+ 
Sbjct: 194 -HHKELYGVDCDWVELEKVVKDCPYDLI-LNGDICKQEDITKLLSFGKNVRGVMIGRASG 251

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
            +  +         NP  G              K    MTD+  R +  G +  +I
Sbjct: 252 IHLGLF--------NPQGGDYVFDE-------NKTKMRMTDFVQRAIRDGLRFTKI 292


>gi|325962747|ref|YP_004240653.1| hypothetical protein Asphe3_13420 [Arthrobacter phenanthrenivorans
           Sphe3]
 gi|323468834|gb|ADX72519.1| putative TIM-barrel protein, nifR3 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 392

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 44/215 (20%), Positives = 93/215 (43%), Gaps = 21/215 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    ++  I+     E+  ++Q+ G D
Sbjct: 33  MAGITNSAFRRLCREY-GGGMYVAEMVTSRALVERTPESLRIISHDEDEQVRSVQLYGVD 91

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              +  A + +VE+   + I+LN GCP  +V     G+ L    D+    +    +  + 
Sbjct: 92  PVTVGAAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTSIVQTAVREAAK 151

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA--ILKGLSPKDNRKIP 172
             +P+T+K R G+DD    +   +  +  + +GV  + +H R A     G          
Sbjct: 152 GNVPLTIKMRKGIDDD--HLTYLDAGRIARDAGVAAVALHGRTAAQFYSG---------- 199

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             D+  +  +++  PD+ +  NG +     A++++
Sbjct: 200 QADWSAIARLREALPDIPVLGNGDIWSAEDAVRMV 234


>gi|167540353|ref|XP_001741843.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165893431|gb|EDR21688.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 355

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 55/236 (23%), Positives = 101/236 (42%), Gaps = 38/236 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q+    LQ+G  D+   ++   ++++     I++N+GC      +G  G  L+ N D + 
Sbjct: 79  QQSKTILQLGTFDVESSIKCVSLIKEVC--GIDINLGCGMWFSTKGEMGQALVSNRDKLE 136

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             + A+ K L  P++ K R+    Q         ++ +   G++ I +H R         
Sbjct: 137 KIVKALVK-LGKPISAKIRL----QQTHEETLEFIQWLYSLGISIISLHGR--------- 182

Query: 166 KDNRKIPNLDYDIVY--EIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAY 220
             ++++  +D D V   ++ K+ P   I LNG +   ED+++ L    +V GVMIGRA+ 
Sbjct: 183 -HHKELYGVDCDWVELEKVVKDCPYDLI-LNGDICKQEDITKLLSFGKNVRGVMIGRASG 240

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
            +  +         NP  G              K    MTD+  R +  G +  +I
Sbjct: 241 IHLGLF--------NPQGGDYVFDE-------NKTKMRMTDFVQRAIKDGLRFTKI 281


>gi|226953507|ref|ZP_03823971.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. ATCC 27244]
 gi|226835748|gb|EEH68131.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. ATCC 27244]
          Length = 309

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 58/117 (49%), Gaps = 5/117 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  P
Sbjct: 57  GKTAAGTPVHVQFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEP 116

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           + V   + A+  A+   IPV+ K R+G  D+     + N   +I+ +G + + +HAR
Sbjct: 117 ETVHLLVKAVRDAVPSHIPVSAKMRLGYLDE--NHTMEN-AHAIEDAGASWLTVHAR 170


>gi|257440871|ref|ZP_05616626.1| dihydrouridine synthase family protein [Faecalibacterium
           prausnitzii A2-165]
 gi|257196651|gb|EEU94935.1| dihydrouridine synthase family protein [Faecalibacterium
           prausnitzii A2-165]
          Length = 313

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 66/154 (42%), Gaps = 9/154 (5%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY E+NLN GCPS  V     G+ ++ +P  +   + A+       V+VK R+GV     
Sbjct: 87  GYTEVNLNFGCPSGTVTAKGKGSGMLRDPQKLDAFLDAVFSQAGGSVSVKTRLGVAR--- 143

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A     ++    K  +  + IH R  ++K L     R   + +    Y      P  + G
Sbjct: 144 AEEFGEILDVYNKYPLCELTIHPR--VMKQLY----RGQADREAFAAYLPACTAPVCYNG 197

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
               ++D+       P + G+M+GR    + A+L
Sbjct: 198 DVTTVDDLRALEAAFPELSGIMVGRGLIADPALL 231


>gi|313114319|ref|ZP_07799854.1| dihydrouridine synthase [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310623374|gb|EFQ06794.1| dihydrouridine synthase [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 314

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            GY E+NLN+GCPS  V     G+ ++ +P  +   +AA+      P++VK R+GV+
Sbjct: 86  LGYTEVNLNLGCPSGTVTAKGKGSGMLRDPVKLDAFLAAVFANAEGPISVKTRLGVE 142


>gi|134112079|ref|XP_775575.1| hypothetical protein CNBE2890 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50258234|gb|EAL20928.1| hypothetical protein CNBE2890 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 491

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 87/189 (46%), Gaps = 16/189 (8%)

Query: 43  FSTQ--EKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST   EKP L  QIG ++    V+AA+ V+      I+LN GCP         GA L+ 
Sbjct: 169 FSTHPAEKPFLIFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLS 227

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D + A+    SIP+ + C+I +    P+     L   I ++GV  + +H R   
Sbjct: 228 TPELLLDILRALLD--SIPLPISCKIRLLPTQPSTLY--LASRILRTGVRNLTVHCRT-- 281

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
            + + P +      L    + E+ K    + +  NG  E  S   +I      D VM+ R
Sbjct: 282 -RQMRPGERALWERLSS--IVELGKRR-GISVICNGDGEGWSNWDRIRNETGADSVMLAR 337

Query: 218 AAYKNSAML 226
           +A +N ++ 
Sbjct: 338 SAERNPSVF 346


>gi|170572085|ref|XP_001891977.1| dihydrouridine synthase domain containing protein [Brugia malayi]
 gi|158603180|gb|EDP39210.1| dihydrouridine synthase domain containing protein [Brugia malayi]
          Length = 437

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 36/156 (23%), Positives = 69/156 (44%), Gaps = 16/156 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP      G  GA L+ NP+   + +       +IP++ K R+ +D Q   +  
Sbjct: 106 IDINMGCPKPFSIAGGMGAALLGNPERAKEIVQTCVSVSTIPISCKIRV-LDKQEDTL-- 162

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLN 194
              VK +++ G++ I +H R+        +  R+      + + EI +    P +  G +
Sbjct: 163 -EFVKMLERCGISAIGVHGRR--------RSERQSNMNRLNEIREITRVVSVPVIANGFS 213

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           G ++     +K         VMI R A  N ++  +
Sbjct: 214 GSIKKYEDIIKFWEQSXASSVMIARKALSNPSIFCS 249


>gi|299143799|ref|ZP_07036879.1| dihydroorotate oxidase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
 gi|298518284|gb|EFI42023.1| dihydroorotate oxidase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
          Length = 299

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 34/115 (29%), Positives = 58/115 (50%), Gaps = 11/115 (9%)

Query: 38  KNILG-FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           +NILG  +T E  + + +GG  + + VEAAKI+ D+ +  I LN+ CP+ +    +FG  
Sbjct: 83  ENILGKMNTLETNVIVNLGGNTVEEYVEAAKILNDYEFFAIELNISCPNVKHGGMAFG-- 140

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             +  D       A+ KA    + VK      D + +       K+++K+G +GI
Sbjct: 141 --IEADSAALVTEAVKKATRHRLIVKLSPNARDIVES------AKAVEKAGADGI 187


>gi|159110447|ref|XP_001705482.1| tRNA dihydrouridine synthase, putative [Giardia lamblia ATCC 50803]
 gi|157433567|gb|EDO77808.1| tRNA dihydrouridine synthase, putative [Giardia lamblia ATCC 50803]
          Length = 462

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 103/250 (41%), Gaps = 29/250 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLALQI 54
           MVD ++  YR   R      L +T M   + ++   K        +    + ++PL LQ+
Sbjct: 24  MVDGSELPYRLLTRRY-GVELAWTPMHSTNTLVTSSKAMTQLVDELKHGESIDRPLVLQL 82

Query: 55  GGADISKLVEAAKIVEDFG----YNEINLNVGCPSARVHEGSFGACLM----LNPDIVGD 106
            G + S    A   +   G    ++ + LN+GCP A    G +GA LM    L  +I+  
Sbjct: 83  SGNNPSNFELAYNTLVQMGAGCCFDVVELNMGCPQAVALRGKYGAYLMGHLDLAEEILRT 142

Query: 107 CIAAMCKA-LSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            +A   ++ L   V VK R+ + D+    + LR     +  +G+    +H R  + +  S
Sbjct: 143 LVAVTARSGLGHKVAVKTRLDISDKDTVKMCLR-----LCSTGIAMFTLHGRTRLQRTGS 197

Query: 165 PKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAY 220
                 +P+      I+  ++   P L    NGG+ ++   + L+ L    G M      
Sbjct: 198 AVG---LPDWQALASILNNLRASYPHLIFFANGGVWNLETHEHLRSLTGCHGTMSASMLT 254

Query: 221 KNSAMLTTVD 230
           +N+ +    D
Sbjct: 255 ENAGVYNCRD 264


>gi|58268108|ref|XP_571210.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57227444|gb|AAW43903.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 491

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 87/189 (46%), Gaps = 16/189 (8%)

Query: 43  FSTQ--EKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST   EKP L  QIG ++    V+AA+ V+      I+LN GCP         GA L+ 
Sbjct: 169 FSTHPAEKPFLIFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLS 227

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D + A+    SIP+ + C+I +    P+     L   I ++GV  + +H R   
Sbjct: 228 TPELLLDILRALLD--SIPLPISCKIRLLPTQPSTLY--LASRILRTGVRNLTVHCRT-- 281

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
            + + P +      L    + E+ K    + +  NG  E  S   +I      D VM+ R
Sbjct: 282 -RQMRPGERALWERLSS--IVELGKRR-GISVICNGDGEGWSNWDRIRNETGADSVMLAR 337

Query: 218 AAYKNSAML 226
           +A +N ++ 
Sbjct: 338 SAERNPSVF 346


>gi|296112348|ref|YP_003626286.1| dihydrouridine synthase [Moraxella catarrhalis RH4]
 gi|295920042|gb|ADG60393.1| dihydrouridine synthase [Moraxella catarrhalis RH4]
 gi|326561856|gb|EGE12191.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 7169]
 gi|326563291|gb|EGE13558.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 46P47B1]
 gi|326563404|gb|EGE13669.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 12P80B1]
 gi|326565945|gb|EGE16106.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 103P14B1]
 gi|326568920|gb|EGE18989.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis BC1]
 gi|326569221|gb|EGE19282.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis BC7]
 gi|326571895|gb|EGE21900.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis BC8]
 gi|326575406|gb|EGE25331.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 101P30B1]
 gi|326576507|gb|EGE26415.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis CO72]
 gi|326577976|gb|EGE27840.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis O35E]
          Length = 323

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 5/120 (4%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G +   +  +A +    G   I+LN GCP+  V+    G+ L+  P
Sbjct: 71  GCTASGTPVHVQLLGNNPETMAASALVAVSLGAKAIDLNFGCPAKTVNNHKGGSVLLEEP 130

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             +   I  +  A+   IPV+ K R+G  D   +  + + V   +   +    +HAR  +
Sbjct: 131 KTLYTIIRTVRDAIPTQIPVSAKIRLGYTDTSQSAEIGHAVADARADWLT---VHARTKV 187


>gi|47216250|emb|CAG05946.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 505

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 50/103 (48%), Gaps = 8/103 (7%)

Query: 1   MVDWTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIG 55
           MVD ++  +R  +R     L    + + ++ V DA  R D  N+     +E +PL  Q  
Sbjct: 1   MVDQSELAWRLLSRRHGAQLCYTPMFHAQVFVRDANYRRD--NLYNEVCEEDRPLITQFC 58

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             D    V+AA + +D+  + I+LN+GCP      G +GA L 
Sbjct: 59  ANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQ 100


>gi|328771087|gb|EGF81127.1| hypothetical protein BATDEDRAFT_10653 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 624

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 37/164 (22%), Positives = 71/164 (43%), Gaps = 13/164 (7%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EM +A  +LRG  +   +      E    +Q+   D ++  +  +I+ +    + I+LN
Sbjct: 291 SEMAIARQLLRGSPQEWALTRRHASEDMFGIQLASNDPTQFTQTVEILSQKVDCDFIDLN 350

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP   + +   G+ L+   + V   +       S+P+T+K RIG+ ++        ++
Sbjct: 351 MGCPIDTMTKSGNGSALLERKNKVRGMLLGAVHVSSVPITIKMRIGLSNK--KKIGHKII 408

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
              +  GV  I +H R         K+ R     D+D   E  K
Sbjct: 409 PLARDCGVAAITVHGRS--------KEQRYTKLSDWDYTMECAK 444


>gi|109126451|ref|XP_001113869.1| PREDICTED: tRNA-dihydrouridine synthase 3-like, partial [Macaca
           mulatta]
          Length = 246

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 51/208 (24%), Positives = 89/208 (42%), Gaps = 32/208 (15%)

Query: 94  GACLMLNPDI-VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           G C ++N        +  M + L +P+TVK R GV +++  +A R L+  ++  GV  + 
Sbjct: 2   GGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR-LLPELRDWGVALVT 59

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG---GLEDMSQALKILP 208
           +H R         ++ R     D+  + E +K  +P    G NG     ED ++A++   
Sbjct: 60  LHGRS--------REQRYTKLADWQYIEECVKAASPMPLFG-NGDILSFEDANRAMQT-- 108

Query: 209 SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            V G+MI R A     + T + E     ++ S     R+D      I    T+Y   H  
Sbjct: 109 GVAGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD------ILRDFTNYGLEHWG 158

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           S  +  + TR  +  +  F     CR++
Sbjct: 159 SDTQGVEKTRRFLLEWLSF----LCRYV 182


>gi|303243957|ref|ZP_07330296.1| dihydroorotate dehydrogenase family protein [Methanothermococcus
           okinawensis IH1]
 gi|302485609|gb|EFL48534.1| dihydroorotate dehydrogenase family protein [Methanothermococcus
           okinawensis IH1]
          Length = 304

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 10/96 (10%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D  +  E A+I+E +    I LN+ CP A    G +GA +  NPD+    ++A+  A+
Sbjct: 103 GKDQKEFSEVAEIIEPY-VELIELNISCPHAG---GGYGAQIGQNPDLSYKVVSAVKDAV 158

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           +IPV  K    V D      ++ + K++ ++G +GI
Sbjct: 159 NIPVIAKLTPNVVD------IKEIAKTVVEAGADGI 188


>gi|71017671|ref|XP_759066.1| hypothetical protein UM02919.1 [Ustilago maydis 521]
 gi|46098858|gb|EAK84091.1| hypothetical protein UM02919.1 [Ustilago maydis 521]
          Length = 766

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 83/198 (41%), Gaps = 15/198 (7%)

Query: 36  DKKNILGFSTQEKP-LALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSF 93
           D K I      E+P L  Q+G AD     +A K I +      ++LN GCP         
Sbjct: 132 DHKQIFSCHPIERPYLVYQLGSADPHLAFQAIKTITQADDVAAVDLNCGCPKPFSTHAGM 191

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV--ALRNLVKSIKKSGVNGI 151
           GA ++  P ++ + + AM +A    V V C+I +   +P     L  + K ++   +  +
Sbjct: 192 GANMLSTPILLCNTLKAMRRAAPAHVAVTCKIRL---LPTQEKTLELVDKIVRTGAIECL 248

Query: 152 WIHARKAILKGLSP---KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-- 206
            +H R   ++   P      R+I +    +  E+ +  P   +  NG + D +   +I  
Sbjct: 249 TVHCRTKDMRPREPALLHRLREIVDHVNSVATEMGRTIP---VVCNGDVWDAATVPRIKE 305

Query: 207 LPSVDGVMIGRAAYKNSA 224
           L  V   MI R A  N +
Sbjct: 306 LTGVTSTMIARGAEANPS 323


>gi|259148380|emb|CAY81627.1| Dus3p [Saccharomyces cerevisiae EC1118]
          Length = 668

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 72/171 (42%), Gaps = 37/171 (21%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA 133
           +EINLN GCP   ++    G+ L+ NP  +  C+ AM   +  IP+TVK R    +  P 
Sbjct: 378 SEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPITVKIRTSTKEGHPI 437

Query: 134 VALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--------- 183
                LVK  + ++ V  I +H R         +  R   + D+D V ++          
Sbjct: 438 A--EGLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDYVSQVADTLRSAEAD 487

Query: 184 -------KENPD-----LFIGLNG---GLEDMSQALKILPSVDGVMIGRAA 219
                  KE  D      F+G NG     ED  + L    ++D VM+ R A
Sbjct: 488 FIETEQGKEGRDSKNRIQFVG-NGDVNNFEDWYRYLDGNENIDSVMVARGA 537


>gi|194765699|ref|XP_001964964.1| GF22896 [Drosophila ananassae]
 gi|190617574|gb|EDV33098.1| GF22896 [Drosophila ananassae]
          Length = 148

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 50/98 (51%), Gaps = 7/98 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R    + L YT M  A+      K  K+ L     ++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRYGAH-LCYTPMYHANLFATDPKYRKDALQTCAGDRPLVIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSA---RVHEGSF 93
             ++++AA   +D   + +++N+GCP A   R H GSF
Sbjct: 94  AQQILDAALAAQDHC-DAVDINLGCPQAIAKRGHYGSF 130


>gi|120603945|ref|YP_968345.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
 gi|120564174|gb|ABM29918.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
          Length = 449

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 37/161 (22%), Positives = 76/161 (47%), Gaps = 6/161 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+ A  ++      +++L  + ++ PL +Q+ G D
Sbjct: 39  LAGYSDLSFRLLCRK-AGAAVCCTEMVSAKGLIYYSPGTRDLLATTPEDAPLVVQLFGCD 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSI 117
              +V A + + + G+   +LN+GC   +V +   GA ++ + P  +    A +  A + 
Sbjct: 98  PDIMVRAMEPLLEQGFRWFDLNMGCSVPKVVKTGCGAAMLRDVPQALAVARAMLRTAGAG 157

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V  K R+G D  +      +L +++   G   + +H R A
Sbjct: 158 RVGFKFRLGWD--VGQEVWADLGRALADLGAGWVTLHPRYA 196


>gi|225570267|ref|ZP_03779292.1| hypothetical protein CLOHYLEM_06363 [Clostridium hylemonae DSM
           15053]
 gi|225161062|gb|EEG73681.1| hypothetical protein CLOHYLEM_06363 [Clostridium hylemonae DSM
           15053]
          Length = 319

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 92/222 (41%), Gaps = 29/222 (13%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           ++++GY E+NLN+GCPS  V     G+  +  P+ +   +  + +     ++VK R G D
Sbjct: 80  LKEYGYREVNLNLGCPSRTVVSKYRGSGFLARPEELDRFLYEVFEKTETDISVKTRTGRD 139

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK-IPNLDYDIVYEIKKENP 187
              P   +R L++   K  +  + IH R       + +D  K  P+L            P
Sbjct: 140 S--PQEFVR-LMEIYNKYPLKELIIHPR-------TQQDFYKNTPDLSVFAQALSVSRCP 189

Query: 188 DLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
             + G     ED+        +VD VM+GR    N  ++   ++             T +
Sbjct: 190 VCYNGDIFTTEDLKVFRARFANVDKVMLGRGLLVNPMLIEMAED------------GTAI 237

Query: 248 DKDFWRKISASMTDYAARHLHSGG-----KLQQITRHMIGLF 284
           D +  RK    M     R + SG      K++++  +MI LF
Sbjct: 238 DMERIRKFH-DMVYGGYREVLSGDKVILFKMKELWSYMIHLF 278


>gi|303278930|ref|XP_003058758.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459918|gb|EEH57213.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 440

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 51/220 (23%), Positives = 92/220 (41%), Gaps = 21/220 (9%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLN 80
           +EM +A  +L+GD+    +L     EK    Q+ G     L    ++++D    + +++N
Sbjct: 81  SEMAMASNVLKGDRGEWALLRRHPSEKLFGAQVCGGWPDLLARCGELLDDELDCDFVDVN 140

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGD---CIAAMCKALS-IPVTVKCRIGVDDQIPAVAL 136
           +GCP   V     G+ L+ + + V      + A  +++   P+T+K R+G DD       
Sbjct: 141 MGCPIDGVCAKGAGSSLLRDAEGVARMERVVRAASRSMRRAPLTIKLRMGYDDDPSKHVA 200

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI---KKENPDLFIGL 193
             +V   K  G + + +H R         +  R     D+  V       +E     IG 
Sbjct: 201 HEIVARAKSWGAHAVTLHGRT--------RQQRYSRAADWAYVERCAAAARETSTPLIG- 251

Query: 194 NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           NG +   +   + +   S+   MIGR A     +LT + E
Sbjct: 252 NGDVFSSADYERHMSSGSLATCMIGRGALIKPWVLTEIKE 291


>gi|317178919|dbj|BAJ56707.1| transcriptional regulator [Helicobacter pylori F30]
          Length = 328

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 47/204 (23%), Positives = 96/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY  +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYKSIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|320587574|gb|EFX00049.1| dihydrouridine synthase family [Grosmannia clavigera kw1407]
          Length = 556

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 48/88 (54%), Gaps = 4/88 (4%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
           + ++LN+GCP     +G +GA L  + +++   I A+ + L +PVT K RI +D +    
Sbjct: 139 DAVDLNLGCPQGIARKGRYGAFLQEDRELIVRLIRALHEGLDVPVTAKIRI-LDTR---E 194

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKG 162
           A     +++  +G + + +H R+   KG
Sbjct: 195 ATLQYAQAVLAAGASILTVHGRRRDQKG 222


>gi|296418297|ref|XP_002838778.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295634739|emb|CAZ82969.1| unnamed protein product [Tuber melanosporum]
          Length = 689

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 93/226 (41%), Gaps = 22/226 (9%)

Query: 12  FARLLTN--NALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKLVEAA 66
           F RL +    AL Y+EM ++  +L+G K    +L     E P    QI G  I   V A 
Sbjct: 337 FRRLCSRLGAALTYSEMAMSVPLLQGHKPEWALLRAHASEIPNFGAQICGTKIGTAVRAT 396

Query: 67  KIVEDF---------GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
           +++            G + ++LN GCP   V+    G+ L+  P  +   +  M   +  
Sbjct: 397 EVLTTLFPSAASSRHGLSLVDLNCGCPVDLVYRQGGGSALLDQPSKLIKMLKGMNYVSGE 456

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            P+T K RI     + A+ L    +  + S   +  +I    A++K L     R     D
Sbjct: 457 TPITCKIRIYDAGDVQAITLHGRSRQQRYSRDADWTYIAETAALIKDLK---RRSDTTAD 513

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             I  E  ++ P++F   NG           +   +VDGVM+ R A
Sbjct: 514 TAIDKEA-RDKPNVFFVGNGDCYSHVDYYNSIDQGNVDGVMLARGA 558


>gi|119177354|ref|XP_001240465.1| hypothetical protein CIMG_07628 [Coccidioides immitis RS]
          Length = 453

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 43/179 (24%), Positives = 81/179 (45%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A+ S L   A  V     + I++N GCP      G  GA L+  PD +   + 
Sbjct: 106 LIFQLGTANPS-LAVEAAKVVAADVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLVSILE 164

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  + +        LV  + ++G+ G+ +H R   ++    
Sbjct: 165 ALVEEIGKPYEIGISVKIRLLAEPE----RTEALVTRVCRTGITGLTVHCRTTPMRPREA 220

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I ++   +   +NG +    +A+K++    VDG MI  +A  N
Sbjct: 221 AIREQLP-----MIASICRKA-GVACLMNGDVRSRDEAMKLIREYGVDGAMIATSAESN 273


>gi|257456040|ref|ZP_05621245.1| putative dihydrouridine synthase [Treponema vincentii ATCC 35580]
 gi|257446563|gb|EEV21601.1| putative dihydrouridine synthase [Treponema vincentii ATCC 35580]
          Length = 347

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 90/215 (41%), Gaps = 26/215 (12%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +TEMI A +++ G +       T   P  L  Q+        V+A  +V   G   ++LN
Sbjct: 30  FTEMIHAPSLIAGGRFEQWYLRTNPVPEKLVWQLTSPKGEAFVQAVPLVLQQGGIGVDLN 89

Query: 81  VGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKAL---------SIPVTVKCRIGVDDQ 130
           +GC +  +     GA  ML P +   + + ++ +AL         S  ++VK RIG    
Sbjct: 90  MGCSAPPIVRTGAGAAWMLKPLNETAEAVRSVKQALDVYAAAQSRSFRLSVKLRIGAAAD 149

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
             A  LR     + + GV  I IH R         + +   P L ++    + K+ P   
Sbjct: 150 Y-AYLLR-FCTMLVEEGVQLITIHPRLQ-------RQSYARPAL-HEYTAALAKDLPIPV 199

Query: 191 IGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
            G NG +   E +  A    P+  G MIGRAA + 
Sbjct: 200 YG-NGDIDSAEKLQTAAARYPACTGWMIGRAAVQK 233


>gi|46578471|ref|YP_009279.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46447882|gb|AAS94538.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
          Length = 419

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 37/161 (22%), Positives = 76/161 (47%), Gaps = 6/161 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+ A  ++      +++L  + ++ PL +Q+ G D
Sbjct: 17  LAGYSDLSFRLLCRE-AGAAVCCTEMVSAKGLIYCSPGTRDLLATTPEDAPLVVQLFGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSI 117
              +V A + + + G+   +LN+GC   +V +   GA ++ + P  +    A +  A + 
Sbjct: 76  PDIMVRAMEPLLEQGFRWFDLNMGCSVPKVVKTGCGAAMLRDVPQALAVARAMLRTAGAG 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V  K R+G D  +      +L +++   G   + +H R A
Sbjct: 136 RVGFKFRLGWD--VGQEVWADLGRALADLGAGWVTLHPRYA 174


>gi|311232399|gb|ADP85253.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris RCH1]
          Length = 441

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 37/161 (22%), Positives = 76/161 (47%), Gaps = 6/161 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A+  TEM+ A  ++      +++L  + ++ PL +Q+ G D
Sbjct: 39  LAGYSDLSFRLLCRE-AGAAVCCTEMVSAKGLIYCSPGTRDLLATTPEDAPLVVQLFGCD 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSI 117
              +V A + + + G+   +LN+GC   +V +   GA ++ + P  +    A +  A + 
Sbjct: 98  PDIMVRAMEPLLEQGFRWFDLNMGCSVPKVVKTGCGAAMLRDVPQALAVARAMLRTAGAG 157

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V  K R+G D  +      +L +++   G   + +H R A
Sbjct: 158 RVGFKFRLGWD--VGQEVWADLGRALADLGAGWVTLHPRYA 196


>gi|209880479|ref|XP_002141679.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209557285|gb|EEA07330.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 330

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 61/258 (23%), Positives = 108/258 (41%), Gaps = 43/258 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--------------DKKNILGFSTQ 46
           MV++T+  +R    L     +++TE I+   IL+               D +N + FST 
Sbjct: 12  MVNFTNLPFRLTC-LDYGADIVFTEEIMDFNILKTNRIFNEKSGIYEYTDDRNSVIFSTN 70

Query: 47  EKP---LALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           +     +  QIG    ++ L     I+ DF   +IN+  GCP         G+ L+L P+
Sbjct: 71  QNENGKVIFQIGTFCSVNALKACEHIINDFCAFDINM--GCPKLYNIRRGMGSALLLKPE 128

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           I  D +  + + L    ++ C+I + D        + ++      ++GI +HAR      
Sbjct: 129 IAEDILKCLNRNLP-KCSITCKIRLLDDFKKTL--DFIRLCSNCNISGITVHAR------ 179

Query: 163 LSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-------LKILPSVDGVM 214
            +PK+   + P+  +DI   IK E       +  G  D S A        K   +VD  M
Sbjct: 180 -TPKEKYDVFPH--WDIFPLIKSELSSCIPVIANG--DFSSASLINSFESKFPNAVDSFM 234

Query: 215 IGRAAYKNSAMLTTVDEY 232
           + R+A  + ++     E+
Sbjct: 235 LSRSARHDPSIFLQKLEW 252


>gi|224160922|ref|XP_002199744.1| PREDICTED: hypothetical protein, partial [Taeniopygia guttata]
          Length = 435

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 36/139 (25%), Positives = 63/139 (45%), Gaps = 13/139 (9%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 302 EMAVCTNLLQGQSSEWALLKRHHTEDIFGVQLEGAFPDTMTKCAELLNRTIDVDF----V 357

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM   +     +  M   L +PVTVK R GV +++      
Sbjct: 358 DINVGCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPVTVKIRTGVQEKVNVA--H 415

Query: 138 NLVKSIKKSGVNGIWIHAR 156
            L+  I++ G + + +  R
Sbjct: 416 KLIPRIREWGASMVTVRGR 434


>gi|208434637|ref|YP_002266303.1| transcriptional regulator [Helicobacter pylori G27]
 gi|208432566|gb|ACI27437.1| transcriptional regulator [Helicobacter pylori G27]
          Length = 328

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 46/204 (22%), Positives = 97/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKEGVVKEAVEKINALDHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G + +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKVIRENTNKKITSVKVRLGFEKKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGRAA +
Sbjct: 204 VKKAFEVLQITQADGLMIGRAALR 227


>gi|297703228|ref|XP_002828550.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Pongo abelii]
          Length = 645

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 69/283 (24%), Positives = 121/283 (42%), Gaps = 51/283 (18%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 339 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 394

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++    A L    D+   C+      L +P+TVK R GV +++  +A R
Sbjct: 395 DINVGCPIDLVYKKV--AAL----DV---CLGFPIWVLDVPLTVKIRTGVQERV-NLAHR 444

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNG- 195
            L+  ++  GV  + +H R         ++ R     D+  + E ++  +P    G NG 
Sbjct: 445 -LLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG-NGD 494

Query: 196 --GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               ED ++A++    V G+MI R A     + T + E     ++ S     R+D     
Sbjct: 495 ILSFEDANRAMQT--GVAGIMIARGALLKPWLFTEIKEQRHWDISSSE----RLD----- 543

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            I    T+Y   H  S  +  + TR  +  +  F     CR++
Sbjct: 544 -ILRDFTNYGLEHWGSDTQGVEKTRRFLLEWLSF----LCRYV 581


>gi|288871174|ref|ZP_06116619.2| dihydrouridine synthase family protein [Clostridium hathewayi DSM
           13479]
 gi|288864521|gb|EFC96819.1| dihydrouridine synthase family protein [Clostridium hathewayi DSM
           13479]
          Length = 192

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 45/92 (48%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           ++ +IL    +   L  QI        +  A  +E  GY+E+NLN+GCPS  V     GA
Sbjct: 40  ERNDILPEHNKGITLIPQILTNRAEDFIWMAGELEALGYDEVNLNLGCPSGTVVSKYKGA 99

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
             +   + +   +  +C  + I ++VK R+G+
Sbjct: 100 GFLAKKEELDAFLDEVCSGIRIRLSVKTRLGM 131


>gi|60679746|ref|YP_209890.1| hypothetical protein BF0150 [Bacteroides fragilis NCTC 9343]
 gi|60491180|emb|CAH05928.1| conserved hypothetical protein [Bacteroides fragilis NCTC 9343]
          Length = 310

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 44/191 (23%), Positives = 89/191 (46%), Gaps = 11/191 (5%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           D ++IL  + +   L  Q+  +++ K      +  + GY E+++N+GCP   + +   G+
Sbjct: 49  DVRDILPENNRVPHLIPQLIASEMDKTERIIALFIEQGYREMDINLGCPFPMLAKRQCGS 108

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            ++ +PD V   +  + +   +  +VK R+G     P   L  L+  +  + +  I +H 
Sbjct: 109 GMLPHPDKVETLLKQIEQYPDVSFSVKMRLGWKK--PDECL-TLLPLLNAAPLTEIIVHP 165

Query: 156 RKAILKGLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           R  I      +  +   N++ +   YE  + +P ++ G    +ED+    +  P + GVM
Sbjct: 166 RLGI------QQYKGEVNMEGFTAFYEACR-HPVIYNGDILTIEDIRCITEKFPKLTGVM 218

Query: 215 IGRAAYKNSAM 225
           IGR    N A+
Sbjct: 219 IGRGLLANPAL 229


>gi|297379926|gb|ADI34813.1| tRNA-dihydrouridine synthase B [Helicobacter pylori v225d]
          Length = 328

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 46/204 (22%), Positives = 96/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY+ +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYESIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     DG+MIGR A +
Sbjct: 204 VKKAFEVLQITQADGLMIGRTALR 227


>gi|170049778|ref|XP_001870922.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
 gi|167871506|gb|EDS34889.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
          Length = 590

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 93/230 (40%), Gaps = 34/230 (14%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCR 124
           I E+   + +++N+GCP   +     G+ L+    ++   + +  + L+      TVK R
Sbjct: 317 IAENADVDFVDINLGCPIELIFNQGGGSALLRREKVLEVLVQSCSRLLADYGKEFTVKTR 376

Query: 125 IGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            GV       A +N    LV   ++ G + + IH R         K+ R     D++ ++
Sbjct: 377 TGV------YAGKNVAHELVPKFEEWGASLVTIHGRT--------KEQRYTKRADWNYIW 422

Query: 181 EIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           +  +    + I  NG +   ED  +A K  P + GVMIGR A     +   + E     L
Sbjct: 423 QCAQTVKSVPIYGNGDIFSYEDYVEAKKCAPELAGVMIGRGALVKPWIFQEIKE--QKAL 480

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
             SS  +  + K +         +Y   H  S  K  + TR  +  +  F
Sbjct: 481 DPSSSERMEMLKRY--------VNYGLEHWGSDTKGVENTRRFLLEWQSF 522


>gi|329960701|ref|ZP_08299044.1| dihydrouridine synthase [Bacteroides fluxus YIT 12057]
 gi|328532574|gb|EGF59368.1| dihydrouridine synthase [Bacteroides fluxus YIT 12057]
          Length = 316

 Score = 44.7 bits (104), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 98/226 (43%), Gaps = 36/226 (15%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALSIPV 119
           +A +I+  F   GY E+++N+GCP   + +   GA ++  P+ V   ++ +  K   I  
Sbjct: 76  KAERIISLFIEKGYREVDINLGCPFPVLAKRHNGAGMLPYPEEVRTLLSTITGKHPDIRF 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYD 177
           +VK R+G +    ++AL  L   +    ++ I +H R  K   KG +  +        + 
Sbjct: 136 SVKLRLGWERPEESLALLPLFNELP---LSHIILHPRLGKQQYKGETDPEG-------FK 185

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             YE    N  LF   NG L   ED+       P + G++IGR    N A+     +   
Sbjct: 186 AFYE--GCNKPLFY--NGDLLTVEDIRSVTTRFPRLAGLVIGRGLLANPALALEYRQ--G 239

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGKLQQITR 278
            PL+           +  RK+S   T+   + R    GG+LQ + +
Sbjct: 240 EPLSAD---------EMARKVSRLHTEVYESYREQLQGGELQLLMK 276


>gi|31789402|gb|AAP58518.1| hypothetical protein [uncultured Acidobacteria bacterium]
          Length = 355

 Score = 44.7 bits (104), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 49/194 (25%), Positives = 80/194 (41%), Gaps = 21/194 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E    +Q+ G    +   AA +VE  G + +++N GCP         GA +   P  +  
Sbjct: 51  EPCFGVQLAGNKPDETAWAAALVESRGADFVDINFGCPIDYFTRKGLGASIGRQPQRMRR 110

Query: 107 CIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKG 162
            + A+  +++ IPVT K R+G +D       RN ++  + +   G   +++H R      
Sbjct: 111 LVEAIKGSVTNIPVTAKIRLGWNDDD-----RNYLQQAQAAVDGGAAALFVHGRT----- 160

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAY 220
              ++ R     D+D +  I    P   IG NG L       A +       VM+ RAA 
Sbjct: 161 ---RNARYRFAADWDAIARIVAAVPVPVIG-NGDLLFPHEIAAARERSGCAAVMVARAAL 216

Query: 221 -KNSAMLTTVDEYF 233
            K       VD Y+
Sbjct: 217 IKPWIFREAVDGYW 230


>gi|213407258|ref|XP_002174400.1| tRNA dihydrouridine synthase Dus3 [Schizosaccharomyces japonicus
           yFS275]
 gi|212002447|gb|EEB08107.1| tRNA dihydrouridine synthase Dus3 [Schizosaccharomyces japonicus
           yFS275]
          Length = 617

 Score = 44.7 bits (104), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 48/225 (21%), Positives = 99/225 (44%), Gaps = 30/225 (13%)

Query: 22  LYTEMIVADAILRGDKKN---ILGFSTQEKPL--------ALQIGGADISKLVEAAKIVE 70
            Y+EM +   +++G +     + G  ++ + +         +Q+    + + V+ A+++ 
Sbjct: 264 FYSEMALCYPLMQGHQPEWALVRGVESERQTMKTGRRGIFGIQLACGKLWQGVKTAQVLS 323

Query: 71  DF--GYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSIPVTVKCRIGV 127
           ++  G + ++LN GCP   V+    G+ L+ N   ++         + S+P TVK R+G 
Sbjct: 324 EYCDGLDFLDLNCGCPIDLVYRQGAGSALLDNHTRLIRSLQGIDTISGSLPTTVKLRMGC 383

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            D  P +A R + +   ++ V+ + +H  +R+     L+  D  +    +   + E  +E
Sbjct: 384 RDDHP-IAKRLMTRIFHETNVSAVTLHGRSRQQRYSKLADWDYVRQCATEIRTLNEALEE 442

Query: 186 NPDLFIGLNGGL-----------EDMSQALKILPSVDGVMIGRAA 219
            PD F   N  +           +D    ++    VD VMI R A
Sbjct: 443 KPDAFPMRNQRMAVIGNGDCFTYKDWYDGMET--GVDTVMIARGA 485


>gi|308159955|gb|EFO62469.1| tRNA dihydrouridine synthase, putative [Giardia lamblia P15]
          Length = 471

 Score = 44.7 bits (104), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 55/248 (22%), Positives = 106/248 (42%), Gaps = 31/248 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQ-EKPLALQI 54
           MVD ++  YR   R   N  L +T M   + ++   K      + L +    ++PL LQ+
Sbjct: 36  MVDGSELPYRLLTRRY-NVELSWTPMYNTNTLVMSPKAMTQLVDELKYGESIDRPLVLQL 94

Query: 55  GGADISKLVEAAKIVEDFG----YNEINLNVGCPSARVHEGSFGACLM----LNPDIVGD 106
            G + S    A   +   G    ++ + LN+GCP A    G +G+ LM    L  +I+  
Sbjct: 95  SGNNPSNFELAYSTLVQMGAGCCFDIVELNMGCPQAVALRGKYGSYLMEHLELAEEILHT 154

Query: 107 CIAAMCK-ALSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILK--- 161
            +AA  +  L   V VK R+    +    + LR     +  +G+    +H R  + +   
Sbjct: 155 LVAATTRFGLGHKVAVKTRLETSSKDTLKMCLR-----LCNTGIAMFTLHGRTRLQRTGS 209

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAA 219
            + P + + + +    ++ +++   P L    NGG+ ++   + L+ L    G M     
Sbjct: 210 AVGPPNWQMLAS----VLKDLRASYPHLIFFANGGVWNLETHERLRSLTGCHGTMSASML 265

Query: 220 YKNSAMLT 227
            +N+ + +
Sbjct: 266 TENAGVYS 273


>gi|323450369|gb|EGB06251.1| hypothetical protein AURANDRAFT_72033 [Aureococcus anophagefferens]
          Length = 2222

 Score = 44.7 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 30/99 (30%), Positives = 54/99 (54%), Gaps = 7/99 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGG 56
           MVD ++R +R  AR      L Y+ M+VA A+  GD      +      +++PL +Q+GG
Sbjct: 22  MVDQSERAFRAVARR-HGVGLCYSPMLVASAL--GDASYRAAYLDAPDARDRPLFVQVGG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +  + +  AA++    G + +++N+GCP +    G +GA
Sbjct: 79  SGEAFVAAAARVARAGGCDAVDVNLGCPQSCARRGGYGA 117


>gi|256827198|ref|YP_003151157.1| putative TIM-barrel protein, nifR3 family [Cryptobacterium curtum
           DSM 15641]
 gi|256583341|gb|ACU94475.1| putative TIM-barrel protein, nifR3 family [Cryptobacterium curtum
           DSM 15641]
          Length = 331

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 58/243 (23%), Positives = 115/243 (47%), Gaps = 23/243 (9%)

Query: 15  LLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLV-EAAKIVED 71
           L    +L +TEM+ A  +   +++  ++L  S  E  + +Q+ G + + +  +AA++ E 
Sbjct: 30  LEQGASLTFTEMVSAKGLSYENQRTEDLLTLSPDETQVGVQLFGHEPATMAHQAARVREM 89

Query: 72  FG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            G     I++N+GCP+ ++     G+ LM  PD     +AA+  A+ +PVTVK R G   
Sbjct: 90  LGEALAVIDINMGCPARKIITKGDGSALMQQPDRAVHIVAAVVDAVDVPVTVKMRRGF-- 147

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            +      +L + ++++G  G+ +H R  + + +G S           +  +  +K+   
Sbjct: 148 ALGCETAGDLARRVEQAGAAGVTVHGRFAQQLYRGTS----------CHATIRRVKEAVA 197

Query: 188 DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS-NPLTGSSPIK 244
              +G NG +   + A+ ++   + D +MI RAA  N  +   V    +  P      ++
Sbjct: 198 IPVVG-NGDVCCGADAVTLMRETACDAIMIARAAEGNPWVFADVAAALAGKPAPQPPSLR 256

Query: 245 TRV 247
            RV
Sbjct: 257 ERV 259


>gi|119897813|ref|YP_933026.1| hypothetical protein azo1522 [Azoarcus sp. BH72]
 gi|119670226|emb|CAL94139.1| conserved hypothetical protein [Azoarcus sp. BH72]
          Length = 366

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 30/110 (27%), Positives = 59/110 (53%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL +Q+ G+D + L   A ++       ++LN GCP+  V+    GA L+  P+++ +  
Sbjct: 102 PLRVQLLGSDPALLAANAAVLARLAPTAVDLNFGCPAPTVNRHRGGAALLDEPELLHEIA 161

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++  AL   +P+T K R+G+ D   A+   +  +++   G+  + +HAR
Sbjct: 162 CSVRAALPPEMPLTAKMRLGIADAGRAL---DCARALADGGIAELVVHAR 208


>gi|48477247|ref|YP_022953.1| dihydroorotate dehydrogenase 1B [Picrophilus torridus DSM 9790]
 gi|48429895|gb|AAT42760.1| dihydroorotate dehydrogenase [Picrophilus torridus DSM 9790]
          Length = 297

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 92/207 (44%), Gaps = 44/207 (21%)

Query: 32  ILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           ILRG   N++G  F T         G  D S L   AK +ED+G   + LN+ CP    H
Sbjct: 86  ILRGS--NVIGSIFGT---------GPEDFSYL---AKRMEDYGAIAVELNLSCP----H 127

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---------QIPAVALRNLV 140
              FG  +  +  +V   ++ +   ++IPV  K      D         +  A+ L N +
Sbjct: 128 VKGFGLEVGSDSGLVESIVSEVKSKVNIPVFAKLSPNTHDILEEARAAEKADALVLINTL 187

Query: 141 KSIKKSGVNGIWIHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           K++K      I I+AR  +L     GLS    R I  +    VYE+ +E     IG+ GG
Sbjct: 188 KAMK------IDINARMPVLSNIYGGLS---GRSIKPVGIRYVYEVSRELKIPVIGV-GG 237

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKN 222
           +E+   A++ I+     V IG   Y++
Sbjct: 238 IENYEDAIEYIMAGASAVEIGTGIYRH 264


>gi|303316025|ref|XP_003068017.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
 gi|240107693|gb|EER25872.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
          Length = 453

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 43/179 (24%), Positives = 81/179 (45%), Gaps = 17/179 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A+ S L   A  V     + I++N GCP      G  GA L+  PD +   + 
Sbjct: 106 LIFQLGTANPS-LAVEAAKVVAADVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLVSILE 164

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  + +        LV  + ++G+ G+ +H R   ++    
Sbjct: 165 ALVEEIGKPYEIGISVKIRLLAEPE----RTEALVTRLCRTGITGLTVHCRTTPMRPREA 220

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               ++P     ++  I ++   +   +NG +    +A+K++    VDG MI  +A  N
Sbjct: 221 AIREQLP-----MIASICRKA-GVACLMNGDVRSRDEAMKLIREYGVDGAMIATSAESN 273


>gi|298345359|ref|YP_003718046.1| putative dihydrouridine synthase [Mobiluncus curtisii ATCC 43063]
 gi|298235420|gb|ADI66552.1| possible dihydrouridine synthase [Mobiluncus curtisii ATCC 43063]
          Length = 367

 Score = 44.3 bits (103), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 56/126 (44%), Gaps = 20/126 (15%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP----LALQIGGADISKLVEAAK--IVEDFGY 74
           +   EMI A A++    ++ +    Q  P      LQ+ G   + L  AA+  I  D   
Sbjct: 1   MFVNEMITAKALMMNSTRSWV--MAQSGPGQTVRVLQLYGVVGADLAWAARELIARDL-V 57

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----------LSIPVTVKC 123
           + I+LN GCP  +V     GA L       GD I  + +A           + +PVTVK 
Sbjct: 58  DVIDLNFGCPVPKVTRKGGGAALPWKTAYFGDLIGQVVQAAQESSQAARREVEVPVTVKI 117

Query: 124 RIGVDD 129
           R+G+D+
Sbjct: 118 RVGIDE 123


>gi|58268106|ref|XP_571209.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57227443|gb|AAW43902.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 496

 Score = 44.3 bits (103), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 38/117 (32%), Positives = 59/117 (50%), Gaps = 8/117 (6%)

Query: 43  FSTQ--EKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST   EKP L  QIG ++    V+AA+ V+      I+LN GCP         GA L+ 
Sbjct: 169 FSTHPAEKPFLIFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLS 227

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            P+++ D + A+    SIP+ + C+I +    P+     L   I ++GV  + +H R
Sbjct: 228 TPELLLDILRALLD--SIPLPISCKIRLLPTQPSTLY--LASRILRTGVRNLTVHCR 280


>gi|316965778|gb|EFV50452.1| dihydrouridine synthase (Dus) superfamily [Trichinella spiralis]
          Length = 787

 Score = 44.3 bits (103), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 51/236 (21%), Positives = 104/236 (44%), Gaps = 36/236 (15%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQ--IGGADISKL 62
           +HYR +         ++  +I++   +  D  K NI    +   PL +   +   +    
Sbjct: 3   KHYRGYT--------IWLLLIISRDTMTNDRTKINIAELFSNSAPLKISAPMVPDNCDDF 54

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-----MCKALSI 117
           V+AA+IV     + ++LN GCP  +  + + G+ L+ N   + + I       +    SI
Sbjct: 55  VKAAEIVYT-QCDGVDLNCGCPKRKTLDANCGSALLDNASHLAELIKQSRLRILDSKFSI 113

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++    + D +      +L + ++ +G+  I +H R          + R  P +D +
Sbjct: 114 SVKIRIYENLKDTV------DLCQKLQSAGITFINVHGRTV--------EQRHEP-VDVE 158

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            V+++ K++  + +  NG +  +S          V+GVM+ RA  +N A+ T  D+
Sbjct: 159 -VFKVIKDSLQIPVVANGDVRSLSDVHYYHQHAGVEGVMVARALLENPALFTGADK 213


>gi|146098870|ref|XP_001468493.1| hypothetical protein [Leishmania infantum]
 gi|134072861|emb|CAM71577.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 493

 Score = 44.3 bits (103), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 49/233 (21%), Positives = 96/233 (41%), Gaps = 43/233 (18%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           YT M++A++ ++        F+  E    L +Q+         +AA ++  +  + I+LN
Sbjct: 124 YTHMLIAESFVKSPHARHAEFARYEGEDRLVVQLAAKSGPAAAQAAVLLRPY-CDGIDLN 182

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------------------------ 116
            GCP     +   G+ L+  P+ V D + ++  A+                         
Sbjct: 183 CGCPQRWAMKEGIGSALLDQPERVADMVRSIRNAMPDGSTASTIVGNGCEYGSCTSTVPP 242

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +P  VK RI  DD   +V   +  +  + +GV+ + +H R       +         + 
Sbjct: 243 FLPCVVKMRIK-DDLRRSV---DFARQCEAAGVSWLTVHGRTPTCHPSA--------AVQ 290

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
           ++ V ++ +EN  + + LNGG+ D+S A++  +     G+M       N AM 
Sbjct: 291 FEAV-KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCGGLMSANGLLDNPAMF 342


>gi|50557204|ref|XP_506010.1| YALI0F29205p [Yarrowia lipolytica]
 gi|49651880|emb|CAG78822.1| YALI0F29205p [Yarrowia lipolytica]
          Length = 394

 Score = 43.9 bits (102), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 51/195 (26%), Positives = 84/195 (43%), Gaps = 15/195 (7%)

Query: 36  DKKNILGFSTQEKP---LALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEG 91
           +KK I+ F T E     +  Q+G A+    V A K+V +D     I+LN GCP       
Sbjct: 70  EKKAII-FRTSEAERDKIIFQVGSANPEIAVAACKMVAKDVAG--IDLNCGCPKHFSMHA 126

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             GA L+  PD +   + A+ K +  P  V   + +           LV  + ++GV  +
Sbjct: 127 GMGAALLKTPDKLVAILEALVKEVGEPFNVSISVKIRLLETEEKTLELVDRLAQTGVKNL 186

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPS 209
            IH R   ++   P     +       V E+  ++  +   +NG +E   +   L+    
Sbjct: 187 TIHCRTTPMRPREPVIRDTLAK-----VAEVCHKH-GITCLVNGDVEGRHELADLQEKYG 240

Query: 210 VDGVMIGRAAYKNSA 224
           +DG MI RAA  N++
Sbjct: 241 IDGAMIARAAEANAS 255


>gi|171696070|ref|XP_001912959.1| hypothetical protein [Podospora anserina S mat+]
 gi|170948277|emb|CAP60441.1| unnamed protein product [Podospora anserina S mat+]
          Length = 516

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 43/152 (28%), Positives = 67/152 (44%), Gaps = 16/152 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPD----IVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           I++N GCP      G  GA L+  PD    I+ +    +     I V+VK R+    +  
Sbjct: 227 IDVNAGCPKPFSTSGGMGAALLQTPDKLVAILENLTRHIIPEFGIGVSVKIRLLETPEKT 286

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
              +R LV     +G+ G+ IH R   ++   P++ R I      I Y  ++    +   
Sbjct: 287 EALVRRLV----GTGITGLTIHCRTTPMR---PRE-RAIRGQLRMIGYICREAG--VACV 336

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +NG + D     K++    VDG MI  AA KN
Sbjct: 337 VNGDVADRRDGYKLMEEFRVDGAMIATAAEKN 368


>gi|322502519|emb|CBZ37602.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 493

 Score = 43.9 bits (102), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 49/233 (21%), Positives = 96/233 (41%), Gaps = 43/233 (18%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           YT M++A++ ++        F+  E    L +Q+         +AA ++  +  + I+LN
Sbjct: 124 YTHMLIAESFVKSPHARHAEFARYEGEDRLVVQLAAKSGPAAAQAAVLLRPY-CDGIDLN 182

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------------------------ 116
            GCP     +   G+ L+  P+ V D + ++  A+                         
Sbjct: 183 CGCPQRWAMKEGIGSALLDQPERVADMVRSIRNAMPDGSTASTIVGNGCEYGSCTSTVPP 242

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +P  VK RI  DD   +V   +  +  + +GV+ + +H R       +         + 
Sbjct: 243 FLPCVVKMRIK-DDLRRSV---DFARQCEAAGVSWLTVHGRTPTCHPSA--------AVQ 290

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
           ++ V ++ +EN  + + LNGG+ D+S A++  +     G+M       N AM 
Sbjct: 291 FEAV-KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCGGLMSANGLLDNPAMF 342


>gi|157115267|ref|XP_001658172.1| tRNA-dihydrouridine synthase [Aedes aegypti]
 gi|108883495|gb|EAT47720.1| tRNA-dihydrouridine synthase [Aedes aegypti]
          Length = 578

 Score = 43.9 bits (102), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 47/190 (24%), Positives = 81/190 (42%), Gaps = 19/190 (10%)

Query: 50  LALQIGGADISKLVEAAK--IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
             +QI G +  KLV  A   I E    + ++LN+GCP   +     G+ L+   +I+   
Sbjct: 286 FGVQICGHN-QKLVSYATQVIAEHADVDFVDLNLGCPIDLIFNQGGGSALLRRRNILEVM 344

Query: 108 IAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           I +  + L+      TVK R+G+           LV   ++ G + + IH R        
Sbjct: 345 IQSCSRILADYDKEFTVKTRMGI--YANKYVAHELVPKFEEWGASLVTIHGRT------- 395

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYK 221
            K+ R     D+D + +  ++   + I  NG +   +D   A +  P + GVM+GR A  
Sbjct: 396 -KEQRYTKKADWDYIRQCAQQAKSIPIYGNGDIFCYQDYLDAKERAPELAGVMVGRGALI 454

Query: 222 NSAMLTTVDE 231
              +   + E
Sbjct: 455 KPWVFQEIKE 464


>gi|304390914|ref|ZP_07372866.1| possible dihydrouridine synthase [Mobiluncus curtisii subsp.
           curtisii ATCC 35241]
 gi|315656297|ref|ZP_07909188.1| dihydrouridine synthase [Mobiluncus curtisii subsp. holmesii ATCC
           35242]
 gi|304325797|gb|EFL93043.1| possible dihydrouridine synthase [Mobiluncus curtisii subsp.
           curtisii ATCC 35241]
 gi|315493299|gb|EFU82899.1| dihydrouridine synthase [Mobiluncus curtisii subsp. holmesii ATCC
           35242]
          Length = 438

 Score = 43.9 bits (102), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 37/128 (28%), Positives = 56/128 (43%), Gaps = 20/128 (15%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKP----LALQIGGADISKLVEAAK--IVEDF 72
             +   EMI A A++    ++ +    Q  P      LQ+ G   + L  AA+  I  D 
Sbjct: 70  EGMFVNEMITAKALMMNSTRSWV--MAQSGPGQTVRVLQLYGVVGADLAWAARELIARDL 127

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----------LSIPVTV 121
             + I+LN GCP  +V     GA L       GD I  + +A           + +PVTV
Sbjct: 128 -VDVIDLNFGCPVPKVTRKGGGAALPWKTAYFGDLIGQVVQAAQESSQAARREVEVPVTV 186

Query: 122 KCRIGVDD 129
           K R+G+D+
Sbjct: 187 KIRVGIDE 194


>gi|321259143|ref|XP_003194292.1| hypothetical protein CGB_E3650W [Cryptococcus gattii WM276]
 gi|317460763|gb|ADV22505.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 493

 Score = 43.5 bits (101), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 16/189 (8%)

Query: 43  FSTQ--EKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           FST   EKP L  QIG ++    V+AA+ V+      I+LN GCP         GA L+ 
Sbjct: 172 FSTHPAEKPFLIFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLS 230

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+++ D + A+    SIP+ + C+I +    P+     L   I ++G+  + +H R   
Sbjct: 231 TPELLLDILRALLD--SIPLPISCKIRLLPTQPSTLY--LASRIIRTGIRNLTVHCRTRQ 286

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGR 217
           ++       R +      IV   K+    + +  NG  E  S  + +K     D VM+ R
Sbjct: 287 MR----PGERALWERLGSIVDLGKRRG--ISVICNGDGEGWSNWERIKNETGADSVMLAR 340

Query: 218 AAYKNSAML 226
           +A +N ++ 
Sbjct: 341 SAERNPSVF 349


>gi|256422463|ref|YP_003123116.1| dihydropyrimidine dehydrogenase [Chitinophaga pinensis DSM 2588]
 gi|256037371|gb|ACU60915.1| dihydroorotate dehydrogenase family protein [Chitinophaga pinensis
           DSM 2588]
          Length = 422

 Score = 43.5 bits (101), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 14/97 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP      G  GA +  +P+I G  +A + +  SIPV  K 
Sbjct: 116 ELIKKVEDTGAHGLELNFGCPHGMTERG-MGAAVGQDPEIAGRVVAWVMEVASIPVITKL 174

Query: 124 RIGVDDQIP-----------AVALRNLVKSIKKSGVN 149
              V   +P           A++L N ++S+  +GVN
Sbjct: 175 TPNVHSVVPTGRASVLAGCHALSLINTIQSV--TGVN 209


>gi|188527429|ref|YP_001910116.1| transcriptional regulator [Helicobacter pylori Shi470]
 gi|188143669|gb|ACD48086.1| transcriptional regulator [Helicobacter pylori Shi470]
          Length = 328

 Score = 43.5 bits (101), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 46/204 (22%), Positives = 96/204 (47%), Gaps = 18/204 (8%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLN 80
           +EM+ + +++    K   +L  S  E     QI G+    + EA + +    + + I+ N
Sbjct: 36  SEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKEGVVKEAVEKINALEHVSGIDFN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT-VKCRIGVDDQIPAVALRNL 139
            GCP+ +V     G+ L+ + + +   +  + +  +  +T VK R+G D +IP    + +
Sbjct: 96  CGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKKITSVKVRLGFDQKIP----KEI 151

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             ++  + V+ + +H R       +  D  +   +DY  +  +K       I  NG ++ 
Sbjct: 152 AHALNDAPVDYVVVHGR-------TRSDKYQKDKIDYKSIALMKGILKKPVIA-NGEIDS 203

Query: 200 MSQALKILP--SVDGVMIGRAAYK 221
           + +A ++L     +G+MIGRAA +
Sbjct: 204 VKKAFEVLQITQAEGLMIGRAALR 227


>gi|227891887|ref|ZP_04009692.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius ATCC
           11741]
 gi|227866350|gb|EEJ73771.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius ATCC
           11741]
          Length = 319

 Score = 43.5 bits (101), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 90/196 (45%), Gaps = 35/196 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG--SFGACLMLNPDI 103
           E P+   +GGA     VE A  +   G  N + LN+ CP+  VHEG  +FG      P++
Sbjct: 103 ELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCPN--VHEGGMAFGTV----PEV 156

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-------WIHAR 156
                  + +  ++PV VK    V D I A+A     K++++ G +GI        +H  
Sbjct: 157 AERLTKKVKEVSTVPVYVKLSPNVTD-IVAIA-----KAVERGGADGISMINTVLGMHID 210

Query: 157 KA--------ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-L 207
            A        I+ GLS K  + I      ++Y++  +N DL I   GG+E +   L++ +
Sbjct: 211 VASGKPVLGNIMGGLSGKAVKAI---AIRMIYQV-SQNTDLPIIGMGGVETVDDVLEMYM 266

Query: 208 PSVDGVMIGRAAYKNS 223
                V +G A + +S
Sbjct: 267 AGASAVAVGTAHFHDS 282


>gi|308048892|ref|YP_003912458.1| tRNA-U20a,U20b-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
 gi|307631082|gb|ADN75384.1| tRNA-U20a,U20b-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
          Length = 310

 Score = 43.5 bits (101), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 26/108 (24%), Positives = 55/108 (50%), Gaps = 1/108 (0%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D   L   A+     G   +++N GCP+  V++   GA L+  P+ +   +
Sbjct: 64  PVRVQLLGQDPDWLAYNAERAIALGSPGVDINFGCPAKTVNKSKGGAVLLKEPETLYRIV 123

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +AM +A+     +  +I +  +  +  +  + ++I+ +G N + IH R
Sbjct: 124 SAMRQAVPADQVLSAKIRLGWECTSQTM-EIAQAIESAGANELAIHGR 170


>gi|296157786|ref|ZP_06840620.1| dihydrouridine synthase DuS [Burkholderia sp. Ch1-1]
 gi|295892032|gb|EFG71816.1| dihydrouridine synthase DuS [Burkholderia sp. Ch1-1]
          Length = 340

 Score = 43.5 bits (101), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 2/90 (2%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   +   A        + I+LN GCP+  V++   GA L+ +P
Sbjct: 58  GHTPCGTPMVIQLLGSDPEWMALNAAHAASLSPHGIDLNFGCPAKVVNQHGGGAMLLADP 117

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDD 129
           + +   ++++  A+   I VT K R+GV D
Sbjct: 118 EQLNRIVSSVRAAVPAGIAVTAKMRLGVSD 147


>gi|123475588|ref|XP_001320971.1| dihydrouridine synthase [Trichomonas vaginalis G3]
 gi|121903787|gb|EAY08748.1| dihydrouridine synthase, putative [Trichomonas vaginalis G3]
          Length = 318

 Score = 43.5 bits (101), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 52/226 (23%), Positives = 102/226 (45%), Gaps = 30/226 (13%)

Query: 14  RLLTNN---ALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGA--DISKLVEAA 66
           R+L  N    + +T M+ A    +G       F+T  ++ PL  QI G+  D   +V AA
Sbjct: 34  RMLIRNHGVKVCWTGMLNAHQWSQGSGYQNKFFNTCPEDHPLIAQIAGSNEDQDLIVAAA 93

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN---PDIVGDCIAAMCKALSIPVTVKC 123
           K +  +  + +++N+GC         +G  ++ N    +   +    +CK ++ P+  K 
Sbjct: 94  KDLAKYA-DGVDVNLGCTQKIASRSEYGYFMVDNCQKREKTLELFRRLCKEVNCPICAKI 152

Query: 124 RIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           RI +DD  ++      +  K ++++GV+ + +H R          ++R   N   D+  E
Sbjct: 153 RIFIDDSGEVSEKITIDFAKKLEEAGVSLLQVHGR---------AEHR---NKQADVYNE 200

Query: 182 IKK---ENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKN 222
           I K   +  ++ +  NGG+  +  A K +      GV + +A  K+
Sbjct: 201 IIKHIVQAVNIPVVANGGINTVEDAHKFMEETGAAGVSVAQALLKD 246


>gi|253744195|gb|EET00435.1| tRNA dihydrouridine synthase, putative [Giardia intestinalis ATCC
           50581]
          Length = 459

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 61/252 (24%), Positives = 105/252 (41%), Gaps = 33/252 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQ-----EKPLALQI 54
           MVD ++  YR   R      L +T M   + ++   K  N L    +     ++PL LQ+
Sbjct: 24  MVDGSELPYRLLTRRY-GVELAWTPMYNTNNLVTSSKAMNQLVAELKYGGSIDRPLVLQL 82

Query: 55  GGADISKLVEAAKIVEDFG----YNEINLNVGCPSARVHEGSFGACLM----LNPDIVGD 106
            G + S    A   +   G    ++ + LN+GCP A    G +GA LM    L  +I+  
Sbjct: 83  SGNNPSNFEIAYNTLIQMGAGHCFDVVELNMGCPQAVALRGKYGAYLMGHLSLAEEILKI 142

Query: 107 CIAAMC-KALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK-- 161
            +A      L   V VK R+   V D + A+ LR     +  +GV  + +H R  + +  
Sbjct: 143 LVAVTTLSGLGHKVAVKTRLDTSVADTV-AMCLR-----LCSTGVAMLTLHGRTKVQRTG 196

Query: 162 -GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRA 218
             + P D + + ++  D    ++   P +    NGG+ ++   + L       G M    
Sbjct: 197 SAVGPPDWQALASVFKD----LRAAYPQMVFFANGGVWNIETHERLCTFTGCHGTMSASM 252

Query: 219 AYKNSAMLTTVD 230
             +N+ + T  D
Sbjct: 253 LTENAGVYTCRD 264


>gi|145344190|ref|XP_001416620.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576846|gb|ABO94913.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 345

 Score = 43.5 bits (101), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 38/146 (26%), Positives = 67/146 (45%), Gaps = 9/146 (6%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFST---QEKPLALQIGGADISKLVEAAKIVE 70
           R +    +L  E+   D I   D K  L F T   + + +  Q+G +  +  +++A++V 
Sbjct: 49  RFMHCRRILNKELGSVDFI---DAKGTLTFRTVPEERERVVFQVGTSSAASALKSAELVA 105

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
                 I++N+GCP      G  GA L+  P++V D +  + + L     V C+I + + 
Sbjct: 106 R-DVAAIDVNMGCPKHFSTSGGMGARLLSQPELVRDILTTLRRNLPSTTHVTCKIRLLES 164

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHAR 156
               A   L K I+  GV+   +H R
Sbjct: 165 ERETA--ELAKMIESCGVSAFAVHGR 188


>gi|301168352|emb|CBW27942.1| putative tRNA-dihydrouridine synthease [Bacteriovorax marinus SJ]
          Length = 345

 Score = 43.5 bits (101), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 42/148 (28%), Positives = 66/148 (44%), Gaps = 16/148 (10%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           ++LN+GCPS +V+    GA L+   D + + I  + +      TVK RIG  +       
Sbjct: 118 LDLNLGCPSKKVNAHKGGAYLLSEMDELREIIKIIRENFKRTFTVKIRIGYKN---TDRF 174

Query: 137 RNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGL 193
            + +K  +  GV  I IH   R  + +GL+        N DY I   +K  N P +  G 
Sbjct: 175 LDSLKLFEDEGVEAITIHGRTRDQLYRGLA--------NWDY-IKQAVKSVNIPIIGNGD 225

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAYK 221
              + D+ +        D +M+GR A K
Sbjct: 226 VWTVHDIDRMFDYC-ECDSIMLGRGALK 252


>gi|254674273|emb|CBA10057.1| tRNA-dihydrouridine synthase [Neisseria meningitidis alpha275]
          Length = 272

 Score = 43.5 bits (101), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 75/175 (42%), Gaps = 20/175 (11%)

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVAL 136
              GCP+  V++   GA L+  P+++   +  +   L   IP+T K R+G +D+  A+  
Sbjct: 45  FEFGCPAPTVNKHKGGAILLKEPELIFHIVKTLRGRLPAHIPLTAKMRLGYEDKSRAL-- 102

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
                +I + G  G+ +HAR    +G  P  + +      D V      N D+F      
Sbjct: 103 -ECACAIAEGGACGLTVHARTKA-EGYEPPAHWEWIRKIRDSVNIPVTANGDVF-----S 155

Query: 197 LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           L+D    +K +   + VM+GR A     +   + +Y         P+K   D DF
Sbjct: 156 LQDYI-GIKTISGCNSVMLGRGAVIRPDLARQIKQY-----ENGGPVK---DTDF 201


>gi|15921375|ref|NP_377044.1| dihydropyrimidine dehydrogenase [Sulfolobus tokodaii str. 7]
 gi|15622161|dbj|BAB66153.1| 350aa long hypothetical dihydroorotate dehydrogenase [Sulfolobus
           tokodaii str. 7]
          Length = 350

 Score = 43.5 bits (101), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 36/133 (27%), Positives = 60/133 (45%), Gaps = 16/133 (12%)

Query: 25  EMIVADAILRGDK-----KNILGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEIN 78
           E+I  D +   DK     K+ +G S    P+ + I GG D S+ +  A+  ED G + + 
Sbjct: 76  ELITEDPLEVWDKYLRVIKSEIGKSA---PIIVSIMGGPDYSEWIRLARWAEDRGADMLE 132

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN GCP     E   GA +  + D+V +    +  ++ IPV  K    + D      +R 
Sbjct: 133 LNFGCPHGE-PEKRTGAFIGQHADLVQEYTKEVVSSVGIPVIAKLTPNITD------IRE 185

Query: 139 LVKSIKKSGVNGI 151
             K+ + +G   +
Sbjct: 186 TAKAAENAGAKAV 198


>gi|300214100|gb|ADJ78516.1| Dihydroorotate dehydrogenase [Lactobacillus salivarius CECT 5713]
          Length = 314

 Score = 43.5 bits (101), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 90/196 (45%), Gaps = 35/196 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG--SFGACLMLNPDI 103
           E P+   +GGA     VE A  +   G  N + LN+ CP+  VHEG  +FG      P++
Sbjct: 98  ELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCPN--VHEGGMAFGTV----PEV 151

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-------WIHAR 156
                  + +  ++PV VK    V D I A+A     K++++ G +GI        +H  
Sbjct: 152 AERLTKKVKEVSTVPVYVKLSPNVTD-IVAIA-----KAVERGGADGISMINTVLGMHID 205

Query: 157 KA--------ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-L 207
            A        I+ GLS K  + I      ++Y++  +N DL I   GG+E +   L++ +
Sbjct: 206 VASGKPVLGNIMGGLSGKAVKAI---AIRMIYQV-AQNTDLPIIGMGGVETVDDVLEMYM 261

Query: 208 PSVDGVMIGRAAYKNS 223
                V +G A + +S
Sbjct: 262 AGASAVAVGTAHFHDS 277


>gi|301299460|ref|ZP_07205736.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852942|gb|EFK80550.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 314

 Score = 43.5 bits (101), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 90/196 (45%), Gaps = 35/196 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG--SFGACLMLNPDI 103
           E P+   +GGA     VE A  +   G  N + LN+ CP+  VHEG  +FG      P++
Sbjct: 98  ELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCPN--VHEGGMAFGTV----PEV 151

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-------WIHAR 156
                  + +  ++PV VK    V D I A+A     K++++ G +GI        +H  
Sbjct: 152 AERLTKKVKEVSTVPVYVKLSPNVTD-IVAIA-----KAVERGGADGISMINTVLGMHID 205

Query: 157 KA--------ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-L 207
            A        I+ GLS K  + I      ++Y++  +N DL I   GG+E +   L++ +
Sbjct: 206 VASGKPVLGNIMGGLSGKAVKAI---AIRMIYQV-AQNTDLPIIGMGGVETVDDVLEMYM 261

Query: 208 PSVDGVMIGRAAYKNS 223
                V +G A + +S
Sbjct: 262 AGASAVAVGTAHFHDS 277


>gi|90961176|ref|YP_535092.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius UCC118]
 gi|90820370|gb|ABD99009.1| Dihydroorotate dehydrogenase [Lactobacillus salivarius UCC118]
          Length = 314

 Score = 43.1 bits (100), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 90/196 (45%), Gaps = 35/196 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG--SFGACLMLNPDI 103
           E P+   +GGA     VE A  +   G  N + LN+ CP+  VHEG  +FG      P++
Sbjct: 98  ELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCPN--VHEGGMAFGTV----PEV 151

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-------WIHAR 156
                  + +  ++PV VK    V D I A+A     K++++ G +GI        +H  
Sbjct: 152 AERLTKKVKEVSTVPVYVKLSPNVTD-IVAIA-----KAVERGGADGISMINTVLGMHID 205

Query: 157 KA--------ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-L 207
            A        I+ GLS K  + I      ++Y++  +N DL I   GG+E +   L++ +
Sbjct: 206 VASGKPVLGNIMGGLSGKAVKAI---AIRMIYQV-AQNTDLPIIGMGGVETVDDVLEMYM 261

Query: 208 PSVDGVMIGRAAYKNS 223
                V +G A + +S
Sbjct: 262 AGASAVAVGTAHFHDS 277


>gi|296231401|ref|XP_002761128.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 3
           [Callithrix jacchus]
          Length = 458

 Score = 43.1 bits (100), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 38/148 (25%), Positives = 67/148 (45%), Gaps = 31/148 (20%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGV 148
           G  GA L+ +PD +   ++ + K    PVT K RI   ++D +      +LVK I+++G+
Sbjct: 89  GGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDTL------SLVKRIERTGI 142

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LE 198
             I +H RK        ++ R    +  +++  I  +   + +  NGG          +E
Sbjct: 143 AAIAVHGRK--------REERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQRYSDIE 193

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAML 226
           D  QA     +   VM+ RAA  N ++ 
Sbjct: 194 DFRQAT----AASSVMVARAAMWNPSIF 217


>gi|15643101|ref|NP_228144.1| dihydroorotate dehydrogenase [Thermotoga maritima MSB8]
 gi|148269723|ref|YP_001244183.1| dihydroorotate dehydrogenase family protein [Thermotoga petrophila
           RKU-1]
 gi|9297058|sp|Q9WYG8|PYRD_THEMA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|166215966|sp|A5IK84|PYRD_THEP1 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|4980834|gb|AAD35420.1|AE001714_11 dihydroorotate dehydrogenase [Thermotoga maritima MSB8]
 gi|147735267|gb|ABQ46607.1| dihydroorotate oxidase B, catalytic subunit [Thermotoga petrophila
           RKU-1]
          Length = 270

 Score = 43.1 bits (100), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 47/199 (23%), Positives = 91/199 (45%), Gaps = 28/199 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+   +GG    + +E A++ +     +  +  N  CP+  V EG  G  ++ N +    
Sbjct: 81  PMIASLGGDSFEEYLEVARVFKKVADRFYAVEFNFSCPN--VKEG--GLSIVKNAEEWKK 136

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-------WIHARK-- 157
            +  + K L     +  ++GV+     + + +  + + K+G +GI        +H  K  
Sbjct: 137 LLNTLRKELPDSFLI-AKVGVE----GIFVEDAAEFVMKTGWDGITLVNTVRGLHFEKDT 191

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVM 214
            IL GLS    + I       VYE+KK  P+LF+  +GG   ++D  + LK+    D + 
Sbjct: 192 MILGGLSGPVLKPI---ALRAVYEVKKRFPELFVIASGGVYSVKDAEEFLKV--GADVIG 246

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A +K+  ++  + +Y 
Sbjct: 247 VGSALFKDPGVVEEIGKYL 265


>gi|56807747|ref|ZP_00365610.1| COG0042: tRNA-dihydrouridine synthase [Streptococcus pyogenes M49
           591]
          Length = 191

 Score = 43.1 bits (100), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 60/122 (49%), Gaps = 15/122 (12%)

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IP+TVK R G  D   ++A+ N + + + +GV+ + +H R         ++       D+
Sbjct: 8   IPLTVKMRTGWADS--SLAVENALAA-ESAGVSALAMHGRT--------REQMYTGTCDH 56

Query: 177 DIVYEIKKENPDL-FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  + K    + FIG NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F
Sbjct: 57  ETLARVSKAITKIPFIG-NGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFF 115

Query: 234 SN 235
             
Sbjct: 116 ET 117


>gi|189465014|ref|ZP_03013799.1| hypothetical protein BACINT_01358 [Bacteroides intestinalis DSM
           17393]
 gi|189437288|gb|EDV06273.1| hypothetical protein BACINT_01358 [Bacteroides intestinalis DSM
           17393]
          Length = 313

 Score = 43.1 bits (100), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 61/283 (21%), Positives = 122/283 (43%), Gaps = 30/283 (10%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADIS 60
           +T+  YR   AR+       YT  +  +   I + D + I   + +   L  Q+   D+ 
Sbjct: 15  YTEAIYRQAHARIFGGIESYYTPFVRVEHGEIRKKDMREITLENNRGVQLIPQLIAPDVD 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPV 119
           K+ +   +  + GY  +++N+GCP   + +   G+ ++  P+ V + + A  K    +  
Sbjct: 75  KMEQIIALFIEKGYKNVDINLGCPFPLLAKRHNGSGMLPYPEEVRELLTAAIKNHPDLQF 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYD 177
           +VK R+G ++   A     L+  + +  +  I +H R  K   KG       ++    ++
Sbjct: 135 SVKMRLGWEN---AEECLALLPLLNELPLTHIIMHPRLGKQQYKG-------EVDLKGFE 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             Y  +  +P ++ G    +ED+    +  P + G+MIGR    N A+     +   +PL
Sbjct: 185 TFYN-ECRHPLMYNGDLLTIEDIQAIRERFPQLAGIMIGRGLLANPALALEYQQ--GHPL 241

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITR 278
           +         +KD   ++     D  A++  L  GG  Q +T+
Sbjct: 242 S---------EKDMQERLRLFHADVFAQYGNLLEGGDKQLLTK 275


>gi|255524904|ref|ZP_05391852.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
 gi|255511382|gb|EET87674.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
          Length = 236

 Score = 43.1 bits (100), Expect = 0.054,   Method: Compositional matrix adjust.
 Identities = 43/160 (26%), Positives = 71/160 (44%), Gaps = 18/160 (11%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIP 132
           ++ I++N+GCP   V +   G+ L+ +       I   CK     +TVK R+G+ +D++ 
Sbjct: 13  FDIIDINMGCPVPNVFKSGQGSALLGDLKKASSIIKG-CKKSGKVITVKFRVGIKEDEMI 71

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A     + ++   SG + I IH R           N       Y    E  K    + + 
Sbjct: 72  AAEFAKMCEA---SGADMITIHGRTR---------NMMYHGTPYFDQIEQAKSVVRIPVI 119

Query: 193 LNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
            NGG+   ED  + +K L   DGVMI R A +N  + + +
Sbjct: 120 ANGGIFSKEDADKMMK-LTGADGVMIARYAIENPFIFSEL 158


>gi|295086114|emb|CBK67637.1| tRNA-U20a,U20b-dihydrouridine synthase [Bacteroides xylanisolvens
           XB1A]
          Length = 315

 Score = 43.1 bits (100), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 39/166 (23%), Positives = 78/166 (46%), Gaps = 13/166 (7%)

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
           +A KI+  F   GY E+++N+GCP   + +   G+ ++  P+ V   ++ +      I  
Sbjct: 75  KADKILSLFIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQALLSLLITEYPQISF 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +D  P   L+ L   I +  +  + +H R      L  +  +   +L     
Sbjct: 135 SIKMRLGWED--PKECLK-LAPIINELPLRQVVMHPR------LGKQQYKGEVDLKAFEA 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           ++   ++P ++ G    +ED+    +  P + G+MIGR    N A+
Sbjct: 186 FQGVCKHPLIYNGDINSVEDIHHIQEQFPGLAGMMIGRGLLANPAL 231


>gi|319900465|ref|YP_004160193.1| tRNA-U20a,U20b-dihydrouridine synthase [Bacteroides helcogenes P
           36-108]
 gi|319415496|gb|ADV42607.1| tRNA-U20a,U20b-dihydrouridine synthase [Bacteroides helcogenes P
           36-108]
          Length = 323

 Score = 43.1 bits (100), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 52/228 (22%), Positives = 98/228 (42%), Gaps = 17/228 (7%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADIS 60
           +TD  YR    R+       Y+  +  +   I R D ++IL  +  +  L  Q+  ++  
Sbjct: 22  YTDAVYRRAHVRIFGGIETYYSPFVRIEHGEIRRKDIRDILPENNPDLHLIPQLIASEAD 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSIPV 119
           K      +  + GY E ++N+GCP   + +   GA ++  P+ V   +   + K  +I  
Sbjct: 82  KAERITALFTEKGYQEADINLGCPFPMLAKRHNGAGMLPYPEEVKALLTDTVKKHPNISF 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYD 177
           +VK R+G D+    +AL  +   +    ++ I +H R  +   KG       +I    ++
Sbjct: 142 SVKLRLGWDNPEECLALLPIFNELP---LSHIILHPRLGRQQYKG-------EIDLKGFE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             Y      P L+ G     ED+    +  P + G++IGR    + A+
Sbjct: 192 AFYN-GCSKPLLYNGDLNTPEDIHSIARRFPQLAGIVIGRGLLASPAL 238


>gi|270294956|ref|ZP_06201157.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270274203|gb|EFA20064.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 322

 Score = 43.1 bits (100), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 93/230 (40%), Gaps = 21/230 (9%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADIS 60
           +TD  YR   AR+       Y+  +  +   I R D ++I      +  L  Q+   D  
Sbjct: 22  YTDAVYRRAHARIFGGIETYYSPFVRMEHGEIRRKDARDIEPDHNPDLHLIPQLIAPDTD 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSIPV 119
           KL     +  + GY E ++N+GCP   +     G+ ++  P+ V   ++ A+ +   I  
Sbjct: 82  KLEHIMSLFIEKGYRETDINLGCPFPMLARRHNGSGMLPYPEEVKALLSEAIDRHPDIRF 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYD 177
           +VK R+G +     +AL  L   +    +  I +H R  K   KG           +D +
Sbjct: 142 SVKLRLGWEQAEECLALLPLFNELP---LAHIILHPRLGKQQYKG----------EVDLE 188

Query: 178 IVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
                 KE  +P  + G      D+       P + G++IGR    N A+
Sbjct: 189 GFEAFYKECTHPLFYNGDLHTANDIRSITTRFPRLAGIVIGRGLLANPAL 238


>gi|302344296|ref|YP_003808825.1| dihydroorotate dehydrogenase family protein [Desulfarculus baarsii
           DSM 2075]
 gi|301640909|gb|ADK86231.1| dihydroorotate dehydrogenase family protein [Desulfarculus baarsii
           DSM 2075]
          Length = 307

 Score = 42.7 bits (99), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 49/201 (24%), Positives = 85/201 (42%), Gaps = 19/201 (9%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNP 101
            + Q+ P A+ + G  I + V+ A+ ++   G   + LNV CP+ +    +FG     NP
Sbjct: 92  LAGQDTPAAVNLYGESIDEFVQLAQRLDGLAGVAALELNVSCPNVKAGGMAFGT----NP 147

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---GIWIHARKA 158
             V    AA+ +  S+P+ VK    V D +          +     +N   G+ I AR+ 
Sbjct: 148 QAVAQVTAAVRRVTSLPLWVKLTPNVTDPVAVAGAAMEAGADALCLINTLLGMAIDARRR 207

Query: 159 ------ILKGLSPKDNRKIPNLDYDIVYEIKKENPDL-FIGLNGGLEDMSQALKILPSVD 211
                 ++ GLS      I  +   +V+++ +  P    IGL G       A  +L    
Sbjct: 208 APRLANVVGGLS---GPAIKPVGLRMVWQVARALPGAPIIGLGGICCGEDAAEYLLAGAS 264

Query: 212 GVMIGRAAYKN-SAMLTTVDE 231
            V +G A++ + +A     DE
Sbjct: 265 AVQVGTASFADPTACARVADE 285


>gi|289192997|ref|YP_003458938.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus sp.
           FS406-22]
 gi|288939447|gb|ADC70202.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus sp.
           FS406-22]
          Length = 302

 Score = 42.7 bits (99), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 82/181 (45%), Gaps = 31/181 (17%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +  +  E AK +E +  + I LN+ CP A+     +GA +  NPD+      A+ KA+
Sbjct: 103 GKNEEEFAEVAKRMEKY-VDIIELNISCPHAK----GYGATIGQNPDLSYSVCKAVKKAV 157

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAIL---- 160
            +PV  K    V D +       + +++  +GV+G           I I A+K IL    
Sbjct: 158 KVPVFAKLTPNVTDIV------EIAQAVVDAGVDGLVAINTVRGMAIDIKAKKPILGNKF 211

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            GLS    R I  +   +V+++  EN D+ I   GG+     A++ ++     V IG   
Sbjct: 212 GGLS---GRAIKPIGIKVVWDL-YENFDVPIIGVGGIMSGEDAIEYMMAGASAVQIGSGV 267

Query: 220 Y 220
           Y
Sbjct: 268 Y 268


>gi|224013536|ref|XP_002296432.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968784|gb|EED87128.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 242

 Score = 42.7 bits (99), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 41/144 (28%), Positives = 69/144 (47%), Gaps = 9/144 (6%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP      G  G+ L+ +     D I+ + + L+ PV+ K R+ +D   P   L + V
Sbjct: 100 MGCPKKFSVTGGMGSALLSDVKRACDIISTLRRNLNKPVSAKIRL-LDPDNPKPTL-DFV 157

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +++ K+G N I IH R   + G       +   L  ++V ++ K+   + I +NG L   
Sbjct: 158 RALIKAGANAIAIHGR---IVGDESHTMARWETL-IEVVRQL-KQTESVPIIVNGDLYTR 212

Query: 201 S--QALKILPSVDGVMIGRAAYKN 222
           +  Q +K     DGVM+ R A  N
Sbjct: 213 ADIQEMKSRTGCDGVMLARPALYN 236


>gi|183230428|ref|XP_648510.2| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
 gi|169802927|gb|EAL43123.2| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
          Length = 366

 Score = 42.7 bits (99), Expect = 0.074,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 98/234 (41%), Gaps = 34/234 (14%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q+    LQ+G  D+   V+   ++++     I++N+GC      +G  G  L+ N D + 
Sbjct: 90  QQSKTILQLGTFDVESSVKCVSLIQEVC--GIDINLGCGMWFSTKGEMGQALVDNRDKLE 147

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             + A+   LS P++ K R+    Q         ++ +   G++ I +H R    K L  
Sbjct: 148 KIVKALV-GLSKPISAKIRL----QQTHEETLEFIQWLYSLGISIISLHGRHH--KELYG 200

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
            D       D+  + ++ K+ P   I LNG +   ED+++ L    +V GVMIGR +  +
Sbjct: 201 VD------CDWAELEKLVKDCPYDLI-LNGDICKQEDITKLLSFGKNVRGVMIGRGSGIH 253

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
             +         NP  G              K    MTD+  R +  G +  +I
Sbjct: 254 LGLF--------NPQGGDYVFDE-------SKTKMRMTDFIQRAIKDGLRFTKI 292


>gi|238021955|ref|ZP_04602381.1| hypothetical protein GCWU000324_01860 [Kingella oralis ATCC 51147]
 gi|237866569|gb|EEP67611.1| hypothetical protein GCWU000324_01860 [Kingella oralis ATCC 51147]
          Length = 320

 Score = 42.7 bits (99), Expect = 0.078,   Method: Compositional matrix adjust.
 Identities = 45/189 (23%), Positives = 82/189 (43%), Gaps = 16/189 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P   Q+ G+D   + + A      G   I+LN GCP+  V++   GA L+  P+ +   +
Sbjct: 65  PCTTQLLGSDADMMAKNALEAVRLGVQTIDLNFGCPAPTVNKHQGGAILLREPERIHQIV 124

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +   L   I +T K R+G ++           ++I   G + I IHAR  + +G  P 
Sbjct: 125 HELRFRLPEHINLTAKMRLGFEN---TDLAVANAQAIAAGGASQITIHARTKV-QGYEPP 180

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            +       +  +  I +E+ ++ +  NG +  +   L I  +   D VMIGR A     
Sbjct: 181 AH-------WHWLKTI-REHVNIPVIANGDVFTLDDYLAIRQTSGCDDVMIGRGAVMRPD 232

Query: 225 MLTTVDEYF 233
           +   + ++ 
Sbjct: 233 LARQIKQHL 241


>gi|237716774|ref|ZP_04547255.1| dihydrouridine synthase [Bacteroides sp. D1]
 gi|237720529|ref|ZP_04551010.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|262405549|ref|ZP_06082099.1| dihydrouridine synthase [Bacteroides sp. 2_1_22]
 gi|294644573|ref|ZP_06722327.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CC 2a]
 gi|294809605|ref|ZP_06768298.1| dihydrouridine synthase (Dus) [Bacteroides xylanisolvens SD CC 1b]
 gi|229442757|gb|EEO48548.1| dihydrouridine synthase [Bacteroides sp. D1]
 gi|229450280|gb|EEO56071.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|262356424|gb|EEZ05514.1| dihydrouridine synthase [Bacteroides sp. 2_1_22]
 gi|292640126|gb|EFF58390.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CC 2a]
 gi|294443217|gb|EFG11991.1| dihydrouridine synthase (Dus) [Bacteroides xylanisolvens SD CC 1b]
          Length = 315

 Score = 42.7 bits (99), Expect = 0.078,   Method: Compositional matrix adjust.
 Identities = 35/154 (22%), Positives = 73/154 (47%), Gaps = 10/154 (6%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQI 131
           GY E+++N+GCP   + +   G+ ++  P+ V   ++ +      I  ++K R+G +D  
Sbjct: 87  GYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQALLSWLITEYPQISFSIKMRLGWED-- 144

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           P   L+ L   I +  +  + +H R      L  +  +   +L     ++   ++P ++ 
Sbjct: 145 PEECLK-LAPIINELPLRQVVMHPR------LGKQQYKGEVDLKAFEAFQGVCKHPLIYN 197

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           G    +ED+ +  +  P + G+MIGR    N A+
Sbjct: 198 GDINSVEDIHRIQEQFPGLAGMMIGRGLLANPAL 231


>gi|159474720|ref|XP_001695473.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158275956|gb|EDP01731.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 241

 Score = 42.7 bits (99), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 49/195 (25%), Positives = 87/195 (44%), Gaps = 25/195 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL  Q+ G+    +  AA+ + +     I+LN GCP+  V     G+ L+  P  + D +
Sbjct: 60  PLGAQVMGSSPELMGLAAQYLAERA-PRIDLNCGCPANTVTGNGAGSSLLRTPQRIHDIV 118

Query: 109 AAM------CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +AM        A   PV+VK R G DD   ++   NL+ + +++G + I +H        
Sbjct: 119 SAMVAGVRASAAPHTPVSVKLRAGFDDT--SLFEDNLLAA-QEAGASFITLH-------- 167

Query: 163 LSPKDNRKIPN--LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
             P+  R+  +   D+ +     +      IG NG +  + +A  +L      GVM+GR 
Sbjct: 168 --PRTKRQCYDGAADWSLTARAVQLLRVPVIG-NGDVVCVERAHALLRQTGCHGVMVGRG 224

Query: 219 AYKNSAMLTTVDEYF 233
           A ++  +   +   F
Sbjct: 225 AVQDPLLFHRIRHSF 239


>gi|296820214|ref|XP_002849907.1| tRNA-dihydrouridine synthase 1 [Arthroderma otae CBS 113480]
 gi|238837461|gb|EEQ27123.1| tRNA-dihydrouridine synthase 1 [Arthroderma otae CBS 113480]
          Length = 573

 Score = 42.7 bits (99), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 50/228 (21%), Positives = 87/228 (38%), Gaps = 34/228 (14%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKL 62
           +W  + +    + + N+ +   +   +DA +   +  + G    ++PL +Q    +  +L
Sbjct: 120 EWMSQQHHDDRKNIENDEVAADDRASSDAAVTATEPYLDGNPKYDRPLIVQFCANNPDEL 179

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + AA+ VE                       G C   +PD++   I  +   LSIPVT K
Sbjct: 180 LRAARHVE-----------------------GYCDAEDPDLIYKLINKLHAELSIPVTAK 216

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RI    +          K I  +G + + +H R+   KG     N  + N +Y I Y  
Sbjct: 217 FRILETKE----KTLEYAKMILSAGASILSVHGRRREQKG----HNTGVANWEY-IRYLR 267

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
               P+  I  NG + +       L S   DGVM       +  + +T
Sbjct: 268 DNLPPETVIFANGNILNHGDIRDCLESTGADGVMSAEGNLSDPTIFST 315


>gi|323449937|gb|EGB05821.1| hypothetical protein AURANDRAFT_1138 [Aureococcus anophagefferens]
          Length = 367

 Score = 42.4 bits (98), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 56/123 (45%), Gaps = 5/123 (4%)

Query: 12  FARLLTNNALLYT--EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           F R+LT      T  EM +   +  G      +L     EK   +Q+  A   +   A +
Sbjct: 24  FRRVLTKYGADITCGEMALCPNLNDGQSSEWALLRRHKDEKCFGVQLSAAHGDQFGRACE 83

Query: 68  IVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +V+ +G  + ++LN+GCP   V     GA LM     V   +    + LS+P+T+K R G
Sbjct: 84  VVDKYGDVDFVDLNMGCPIDLVCSKGGGAALMRRNKKVRSILEMGLERLSVPMTLKMRTG 143

Query: 127 VDD 129
            D+
Sbjct: 144 WDE 146


>gi|329954094|ref|ZP_08295189.1| dihydrouridine synthase [Bacteroides clarus YIT 12056]
 gi|328528071|gb|EGF55051.1| dihydrouridine synthase [Bacteroides clarus YIT 12056]
          Length = 316

 Score = 42.4 bits (98), Expect = 0.083,   Method: Compositional matrix adjust.
 Identities = 64/296 (21%), Positives = 118/296 (39%), Gaps = 35/296 (11%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADIS 60
           +TD  YR   AR+       Y+  +  +   I R D ++I   + +   L  Q+  +  +
Sbjct: 15  YTDAAYRQAHARIFGGIDTYYSPFVRVEHGEIRRKDARDIHPENNRNIHLIPQLIASCPN 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPV 119
           KL +   ++ +  Y E ++N+GCP   + +   GA ++  P+ V D + AA+ +   I  
Sbjct: 75  KLEQIMSLLTEHNYQEADINLGCPFPMLAKRHNGAGMLPYPEEVKDLLTAAIEQYPQIRF 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G ++    +A   L+  +    +  I +H R      L  +  +   +L+    
Sbjct: 135 SVKLRLGWENASECIA---LLPLLNALPLAHIILHPR------LGKQQYKGEVDLNGFEA 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML------------- 226
           +    + P L+ G    +ED+    +  P + G++IGR    N A+              
Sbjct: 186 FYDGCDKPLLYNGDLHTIEDIQIITERFPKLAGLVIGRGLLANPALAWEYRQGRKLSPSE 245

Query: 227 ---------TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
                    T V   +   L G         K FW  +       A + +H  GKL
Sbjct: 246 MAAKVKQLHTAVYNSYEEQLQGGEMQLLMKMKSFWEYLLPDGDRKAKKVIHKTGKL 301


>gi|303286323|ref|XP_003062451.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
 gi|226455968|gb|EEH53270.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
          Length = 346

 Score = 42.4 bits (98), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 27/107 (25%), Positives = 52/107 (48%), Gaps = 3/107 (2%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L LQ+G  D ++ ++ A ++     + +++N+GCP         G+ L+  P+ V D + 
Sbjct: 88  LVLQLGTGDATRALKCA-LLAAKDISAVDINMGCPLKFSTSSGAGSALLKKPEQVRDIMT 146

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            + + L   V V C+I + +         L + I+  GV+   +HAR
Sbjct: 147 TLRRNLPSEVHVTCKIRLLETTEKTI--ELARVIEACGVSAFGVHAR 191


>gi|159485198|ref|XP_001700634.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158272158|gb|EDO97963.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 364

 Score = 42.4 bits (98), Expect = 0.097,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 20/89 (22%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  +CR+GVD+      L   VK                    GLSP  NR +P L +  
Sbjct: 74  VGSRCRLGVDECDSYAQLHEFVK--------------------GLSPHQNRTVPPLRHQW 113

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + + ++ P L   LNGGL+    A   L
Sbjct: 114 AWALARDFPHLQFSLNGGLQTCHDARAAL 142


>gi|295425253|ref|ZP_06817956.1| dihydroorotate oxidase [Lactobacillus amylolyticus DSM 11664]
 gi|295065029|gb|EFG55934.1| dihydroorotate oxidase [Lactobacillus amylolyticus DSM 11664]
          Length = 318

 Score = 42.4 bits (98), Expect = 0.100,   Method: Compositional matrix adjust.
 Identities = 30/106 (28%), Positives = 51/106 (48%), Gaps = 11/106 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG D +  VE A+ +   G  N + +NV CP+      SFG    ++PD++ 
Sbjct: 107 ELPIMASVGGDDEAGYVEVARKLSASGLVNTLEINVSCPNVARGGMSFG----VHPDVIE 162

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           D    +   ++IP+ VK    V D +       + K+ +  G +GI
Sbjct: 163 DLTKKIKDVVNIPIYVKLTPNVTDIV------EIAKAAQAGGADGI 202


>gi|237724433|ref|ZP_04554914.1| nifR3 family TIM-barrel protein [Bacteroides sp. D4]
 gi|229437302|gb|EEO47379.1| nifR3 family TIM-barrel protein [Bacteroides dorei 5_1_36/D4]
          Length = 305

 Score = 42.4 bits (98), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 52/223 (23%), Positives = 93/223 (41%), Gaps = 21/223 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  +   +L   A +  + GY E + N+GCP   V     G+ ++  P  V   +  + 
Sbjct: 63  QLIASTPVELERLAALFTEKGYKEADFNMGCPFPLVARKHKGSGILPYPAEVEALLKELT 122

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRK 170
               +  +VK R+G +    A   R L+  +  + +  I +H R  K   KG       +
Sbjct: 123 HYPELSFSVKMRLGWES---ADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-------E 172

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +    +   YE +  +P ++ G    +ED+ +  +  P ++GVM+GR    N A+     
Sbjct: 173 VDLAAFTAFYE-ECAHPLVYNGDLLTVEDIRKVEEKFPCLEGVMLGRGLLANPALAW--- 228

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           EY +   T  SP K        + + A +  Y   HL    +L
Sbjct: 229 EYVNG--TSFSPDKLHEKV---KALHARLLQYYEAHLQGEAQL 266


>gi|258615864|ref|ZP_05713634.1| dihydrouridine synthase family protein [Enterococcus faecium DO]
          Length = 116

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 25/94 (26%), Positives = 42/94 (44%), Gaps = 4/94 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
                  E +  + + G+  I++N+GCP   V E
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAE 112


>gi|315038743|ref|YP_004032311.1| dihydroorotate dehydrogenase 1B [Lactobacillus amylovorus GRL 1112]
 gi|325957179|ref|YP_004292591.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus 30SC]
 gi|312276876|gb|ADQ59516.1| dihydroorotate dehydrogenase 1B [Lactobacillus amylovorus GRL 1112]
 gi|325333744|gb|ADZ07652.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus 30SC]
 gi|327183884|gb|AEA32331.1| dihydroorotate dehydrogenase 1B [Lactobacillus amylovorus GRL 1118]
          Length = 307

 Score = 42.0 bits (97), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 29/106 (27%), Positives = 51/106 (48%), Gaps = 11/106 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG      VE AK + D G  N + +NV CP+      SFG    ++PD+V + 
Sbjct: 98  PIMASVGGDSEDDYVEVAKKLSDSGLVNALEINVSCPNVDRGGMSFG----VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
              +   +++P+ VK    V D +       + K+ +K G +G+ +
Sbjct: 154 TQKIKNVVNVPIYVKLTPNVTDVV------TIAKAAEKGGADGLSM 193


>gi|255074587|ref|XP_002500968.1| predicted protein [Micromonas sp. RCC299]
 gi|226516231|gb|ACO62226.1| predicted protein [Micromonas sp. RCC299]
          Length = 662

 Score = 42.0 bits (97), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 49/216 (22%), Positives = 86/216 (39%), Gaps = 20/216 (9%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-----GYNEI 77
           EM +   +L+G      +L     E     Q+ G     +    +++ED      G + I
Sbjct: 335 EMAMVTNLLQGQPAEWALLRRHPSEDIFGAQVCGGYSDSMSRCMQLLEDEVVSKGGLDFI 394

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP   V     G+ L+  P  +   + A    LS P+T+K R+G  D        
Sbjct: 395 DINMGCPIDLVCNKGAGSMLLEKPARMEQLVRASAPLLSCPLTLKTRMGYFDN--KRVAH 452

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            ++  +   G+ G+ +H R         +  R     D+D + +  + +P   IG NG +
Sbjct: 453 EIIPKMVDWGLAGMTLHGRS--------RQQRYSRLADWDYINQCARASPIQLIG-NGDV 503

Query: 198 EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
                 +K +    V   MI R A     + T + E
Sbjct: 504 FSYHDYVKNVEGQGVATCMIARGALIKPWIFTEIKE 539


>gi|160888611|ref|ZP_02069614.1| hypothetical protein BACUNI_01028 [Bacteroides uniformis ATCC 8492]
 gi|317477952|ref|ZP_07937135.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
 gi|156861925|gb|EDO55356.1| hypothetical protein BACUNI_01028 [Bacteroides uniformis ATCC 8492]
 gi|316905866|gb|EFV27637.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
          Length = 322

 Score = 41.6 bits (96), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 93/230 (40%), Gaps = 21/230 (9%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADIS 60
           +TD  YR   AR+       Y+  +  +   I R D ++I   +  +  L  Q+   D  
Sbjct: 22  YTDAVYRRAHARIFGGIETYYSPFVRMEHGEIRRKDARDIEPDNNPDLHLIPQLIAPDAD 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSIPV 119
           KL     +  + GY E ++N+GCP   +     G  ++  P+ V   ++ A+ +   I  
Sbjct: 82  KLEHIMSLFIEKGYQEADINLGCPFPMLARRHNGCGMLPYPEEVKALLSEAIDRHPDIRF 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYD 177
           +VK R+G +     +AL  L   +    +  I +H R  K   KG           +D +
Sbjct: 142 SVKLRLGWEQAEECLALLPLFNELP---LAHIILHPRLGKQQYKG----------EVDLE 188

Query: 178 IVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
                 KE  +P  + G      D+       P + G++IGR    N A+
Sbjct: 189 GFEAFYKECTHPLFYNGDLHTANDIRSITTRFPRLAGIVIGRGLLANPAL 238


>gi|26451942|dbj|BAC43063.1| unknown protein [Arabidopsis thaliana]
 gi|30017287|gb|AAP12877.1| At4g38890 [Arabidopsis thaliana]
          Length = 265

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 45/205 (21%), Positives = 79/205 (38%), Gaps = 24/205 (11%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP   V   S G+ L+  P  + + +      +  P+T+K R    +      + +L+
Sbjct: 1   MGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSIVETPITIKVRTAFFEG--KNRIDSLI 58

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLE- 198
             I   G   + IH R         +  R   + D+D +Y+  K    +L +  NG +  
Sbjct: 59  ADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQCTKNATTNLQVIGNGDVYS 110

Query: 199 --DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             D ++     P +   MI R A     + T + E     +T     +  + KDF R   
Sbjct: 111 YLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDITSGE--RLNIMKDFVR--- 165

Query: 257 ASMTDYAARHLHSGGKLQQITRHMI 281
                +  +H  S  K  + TRH +
Sbjct: 166 -----FGLQHWGSDTKGVETTRHFL 185


>gi|163790400|ref|ZP_02184831.1| dihydroorotate dehydrogenase [Carnobacterium sp. AT7]
 gi|159874304|gb|EDP68377.1| dihydroorotate dehydrogenase [Carnobacterium sp. AT7]
          Length = 309

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 48/193 (24%), Positives = 86/193 (44%), Gaps = 31/193 (16%)

Query: 47  EKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G  I +  E  K + +      + +NV CP+ +    +FGA    +P++V 
Sbjct: 93  DTPVIASVAGTTIEEYCEVTKRLCQSPTVRALEINVSCPNVKEGGLTFGA----SPELVY 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           D   A+    ++P+ +K    V D I A+A     ++ +K+G +GI            + 
Sbjct: 149 DITKAVKAVATVPIYIKLTPNVTD-IVAIA-----QAAEKAGADGISMINTVLGMSINLE 202

Query: 155 ARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPS 209
           +RK +L     GLS      I  +   +VY++ +      IG+ GG+  +   L++ L  
Sbjct: 203 SRKPVLANKTGGLS---GAAIKPIAIRMVYQVARAVSIPIIGM-GGISTVDDVLEMFLAG 258

Query: 210 VDGVMIGRAAYKN 222
              V IG A Y N
Sbjct: 259 ASAVAIGTANYAN 271


>gi|213419249|ref|ZP_03352315.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
 gi|213861619|ref|ZP_03386089.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 52

 Score = 41.6 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           L  ITRHM+GLF G P +R+ R  L+  A  + A   ++E A  L+ +
Sbjct: 3   LGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADAAVLEQALKLIAD 50


>gi|308810258|ref|XP_003082438.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
 gi|116060906|emb|CAL57384.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
          Length = 295

 Score = 41.6 bits (96), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 30/104 (28%), Positives = 49/104 (47%), Gaps = 14/104 (13%)

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G++   PA     + + ++ +G   I +H R         K+ R   + DYD
Sbjct: 36  PLTVKIRLGIESSSPAT---KIAERLENAGAAAIIVHGRT--------KEQRYTKSADYD 84

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           ++ +I  E     IG NG +     A + L      G+M+GR A
Sbjct: 85  VIRQIVSERAIPVIG-NGDVLTWYDAQQRLDYSGCAGIMVGRGA 127


>gi|300122290|emb|CBK22863.2| unnamed protein product [Blastocystis hominis]
          Length = 516

 Score = 41.2 bits (95), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 45/183 (24%), Positives = 75/183 (40%), Gaps = 28/183 (15%)

Query: 69  VEDFGY-----------NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
           VED GY           + ++LN GCP   V +   GA L+     +   +  M  +L +
Sbjct: 223 VEDAGYVCELLRREGTVDFVDLNAGCPIDAVEKAGAGAGLLTKVGRLKRIVRCMLGSLEN 282

Query: 117 IPVTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +P+ VK R G  +      +  L  ++  + + V+G+ IH R         K  R   + 
Sbjct: 283 VPLMVKVRTGDHENTSHRLVPQLQRIRGNRGNRVSGVIIHGRT--------KQGRYTKSA 334

Query: 175 DYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           D++ +    K      P L +  NG + D       +    +DG+MIGR A     + T 
Sbjct: 335 DWEYIKACAKSQDADLPRLQVIGNGDVFDNEDYWNRMEDGVLDGIMIGRGALIKPWICTE 394

Query: 229 VDE 231
           + E
Sbjct: 395 IKE 397


>gi|294496112|ref|YP_003542605.1| dihydroorotate oxidase B, catalytic subunit [Methanohalophilus
           mahii DSM 5219]
 gi|292667111|gb|ADE36960.1| dihydroorotate oxidase B, catalytic subunit [Methanohalophilus
           mahii DSM 5219]
          Length = 299

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 52/198 (26%), Positives = 85/198 (42%), Gaps = 18/198 (9%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           S  + PL   I G D ++  E A  +     +   LNV CP    H   +GA +  +PD+
Sbjct: 85  SKTDAPLIASIFGGDAAEFTEVANGLLSSKPDCFELNVSCP----HAEGYGASVGTDPDL 140

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           V +  A++  A+ +PV VK    V D     +    A  + V +I       I IH+   
Sbjct: 141 VHEITASVVDAVDVPVWVKLTPNVTDITSIGRAAESAGASAVVAINTVRGMAIDIHSGYP 200

Query: 159 IL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           IL     GLS      +  +    VY++ +      IG+ GG+     A++ IL     V
Sbjct: 201 ILGNRFGGLS---GPAVKPVAVKCVYDLYEALDIPVIGV-GGITCPQDAIEMILAGASAV 256

Query: 214 MIGRAAYKNSAMLTTVDE 231
            IG A + ++ +  T+ +
Sbjct: 257 EIGSAVHDDTQIFETISK 274


>gi|116512185|ref|YP_809401.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. cremoris
           SK11]
 gi|116107839|gb|ABJ72979.1| dihydroorotate oxidase B, catalytic subunit [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 311

 Score = 41.2 bits (95), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 30/107 (28%), Positives = 56/107 (52%), Gaps = 13/107 (12%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++ +  V   AKI +      I LN+ CP+ +    +FG    ++P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFG----IDPEVAA 153

Query: 106 DCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           D + A CKA+S +P+ VK    V D +P      + K+++ +G +G+
Sbjct: 154 DLVKA-CKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGL 193


>gi|146095124|ref|XP_001467487.1| dihydrouridine synthase (Dus) [Leishmania infantum JPCM5]
 gi|134071852|emb|CAM70545.1| putative dihydrouridine synthase (Dus) [Leishmania infantum JPCM5]
          Length = 660

 Score = 41.2 bits (95), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 28/109 (25%), Positives = 48/109 (44%), Gaps = 12/109 (11%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISK----------LVEAAKIVEDFGY--NE 76
           AD +LR  +  +LG            GGA ++           L  + K  E   Y  + 
Sbjct: 224 ADTVLRAARFAVLGEQAAAAEQTSGSGGASVAPVYPVHVRVNGLSSSEKAPEHLLYQCDA 283

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           ++LN+GCP      G +G+ LM + +++   +  +   L +PVT K R+
Sbjct: 284 VDLNLGCPQGIARRGHYGSFLMEDWELIHTIVHTLHVELEVPVTAKIRV 332


>gi|322501518|emb|CBZ36597.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 660

 Score = 41.2 bits (95), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 28/109 (25%), Positives = 48/109 (44%), Gaps = 12/109 (11%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISK----------LVEAAKIVEDFGY--NE 76
           AD +LR  +  +LG            GGA ++           L  + K  E   Y  + 
Sbjct: 224 ADTVLRAARFAVLGEQAAAAEQTSGSGGASVAPVYPVHVRVNGLSSSEKAPEHLLYQCDA 283

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           ++LN+GCP      G +G+ LM + +++   +  +   L +PVT K R+
Sbjct: 284 VDLNLGCPQGIARRGHYGSFLMEDWELIHTIVHTLHVELEVPVTAKIRV 332


>gi|291523511|emb|CBK81804.1| tRNA-dihydrouridine synthase [Coprococcus catus GD/7]
          Length = 329

 Score = 41.2 bits (95), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 37/67 (55%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +  A  ++  GY+E+NLN+GCPS+ V     G+  +   + +   +A +     + +++
Sbjct: 76  FIATAHTLKGLGYDEVNLNLGCPSSTVASKGRGSGFLGEKEALKAFLADIFDKTDMKISL 135

Query: 122 KCRIGVD 128
           K RIG++
Sbjct: 136 KTRIGLN 142


>gi|212692604|ref|ZP_03300732.1| hypothetical protein BACDOR_02101 [Bacteroides dorei DSM 17855]
 gi|237709084|ref|ZP_04539565.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|265752608|ref|ZP_06088177.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_1_33FAA]
 gi|212664889|gb|EEB25461.1| hypothetical protein BACDOR_02101 [Bacteroides dorei DSM 17855]
 gi|229456780|gb|EEO62501.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|263235794|gb|EEZ21289.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_1_33FAA]
          Length = 305

 Score = 41.2 bits (95), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 41/175 (23%), Positives = 77/175 (44%), Gaps = 13/175 (7%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  +   +L   A +  + GY E + N+GCP   V     G+ ++  P  V   +  + 
Sbjct: 63  QLIASTPVELERLAALFTEKGYKEADFNMGCPFPLVARKHKGSGILPYPAEVEALLKELT 122

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRK 170
               +  +VK R+G +    A   R L+  +  + +  I +H R  K   KG       +
Sbjct: 123 HYPELSFSVKMRLGWES---ADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-------E 172

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           +    +   YE +  +P ++ G    +ED+ +  +  P ++GVM+GR    N A+
Sbjct: 173 VDLAAFTAFYE-ECAHPLVYNGDLLTVEDIRKVEEKFPCLEGVMLGRGLLANPAL 226


>gi|171058809|ref|YP_001791158.1| dihydrouridine synthase DuS [Leptothrix cholodnii SP-6]
 gi|170776254|gb|ACB34393.1| dihydrouridine synthase DuS [Leptothrix cholodnii SP-6]
          Length = 339

 Score = 41.2 bits (95), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 57/110 (51%), Gaps = 5/110 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+  Q+ G+D + L + A  +   G   ++LN GCP+  V+    GA L+  P  +   +
Sbjct: 57  PVRPQLMGSDAACLADNAARLAQMGAEGVDLNFGCPAQVVNRHGGGAALLREPQRLAAIV 116

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           AA+ +A+   +PV+ K R+G D    AV   +  +++   G   + +HAR
Sbjct: 117 AAVRRAVPAHLPVSAKMRLGYDHDEHAV---DCAQALVDGGAAELVVHAR 163


>gi|296331130|ref|ZP_06873604.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674285|ref|YP_003865957.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151774|gb|EFG92649.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412529|gb|ADM37648.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 311

 Score = 41.2 bits (95), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 54/243 (22%), Positives = 104/243 (42%), Gaps = 35/243 (14%)

Query: 1   MVDWTDRHYRF---FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGG 56
           M+  T +  RF     R+    A +   + + +  L    +N L +  Q + P+   + G
Sbjct: 41  MIKATTKEPRFGNPTPRVAETGAGMLNAIGLQNPGLESVLQNELPWLEQFDTPIIANVAG 100

Query: 57  ADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           + +   VE A+ I +    + + LN+ CP+ +    +FG     NP++  D   A+ +  
Sbjct: 101 SQVEDYVEVAEHISKAPNVHALELNISCPNVKTGGIAFGT----NPEMAADLTKAVKEVS 156

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK--- 161
            +PV VK    V +      +  +  +I+++G +G+            + + K IL    
Sbjct: 157 DVPVYVKLSPNVAN------ITEIASAIEEAGADGLTMINTLIGMRLDLKSGKPILANKT 210

Query: 162 -GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            GLS      +  +   +VYE+ +      IG+ GG++    AL+ +L     V +G A 
Sbjct: 211 GGLS---GPAVKPVAIRMVYEVSQAVNIPIIGM-GGVQTAEDALEFLLAGASAVAVGTAN 266

Query: 220 YKN 222
           + N
Sbjct: 267 FVN 269


>gi|150391898|ref|YP_001321947.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           metalliredigens QYMF]
 gi|189038413|sp|A6TVS0|PYRD_ALKMQ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|149951760|gb|ABR50288.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           metalliredigens QYMF]
          Length = 302

 Score = 41.2 bits (95), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 45/185 (24%), Positives = 72/185 (38%), Gaps = 22/185 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I    E  K + D   + + LN+ CP+ +    + G C   +P +V +   
Sbjct: 98  IIVNIAGRTIEDYCEVVKKLGDADVDLLELNISCPNVK----AGGVCFGTDPFMVEEVTK 153

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
           A+ K    P+ VK    V D +P      + K+    G +GI            IH RK 
Sbjct: 154 AVKKVAKQPLIVKLTPNVTDIVP------IAKAAVAGGADGISLINTLLGMAIDIHKRKP 207

Query: 159 ILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           IL   +       I  +   +VY++        IG+ G +        IL    GV +G 
Sbjct: 208 ILANVMGGFSGPAIKPVALRMVYQVANAVDVPIIGMGGIMTGEDAVEFILAGASGVAVGT 267

Query: 218 AAYKN 222
           A + N
Sbjct: 268 ANFIN 272


>gi|295102082|emb|CBK99627.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii L2-6]
          Length = 313

 Score = 41.2 bits (95), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 39/166 (23%), Positives = 72/166 (43%), Gaps = 25/166 (15%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +   GY E+NLN GCPS  V     GA ++ +   +   +  +      P++VK R+GV 
Sbjct: 83  LRKMGYTEVNLNFGCPSGTVTAKGKGAGMLRDLSKLEVFLDEVFSQAEGPISVKTRLGVT 142

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD--NRKIPNLDYDIVYEIKK 184
                 A+ +L        +  + +H R  + + +G + +    + +P+    + Y    
Sbjct: 143 SPEEFEAILDLYDRFP---ICELTVHPRVMRQLYRGEADRAAFAKYLPHCRMPVCY---- 195

Query: 185 ENPDLFIGLNGGLEDMSQALKIL----PSVDGVMIGRAAYKNSAML 226
                    NG +   +Q LK L    P++ G+M+GR    + A+L
Sbjct: 196 ---------NGDITTPAQ-LKALEAEFPNLSGIMVGRGIIADPALL 231


>gi|322490625|emb|CBZ25887.1| dihydrouridine synthase domain protein-like protein [Leishmania
           mexicana MHOM/GT/2001/U1103]
          Length = 440

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 54/199 (27%), Positives = 88/199 (44%), Gaps = 35/199 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA-RVHEGSFGACLMLNPDIVGDCI 108
           + LQ+G AD  +   AA +  +   + I++N+GCP    VH G FGA LM  P++ G  +
Sbjct: 106 IVLQLGVADPVRGAAAALVCSN-DIDGIDINMGCPKKFSVHNG-FGAALMKRPEVGGAIV 163

Query: 109 AAMCKALS------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----GIW 152
            A+  A++            I V++K R+    +     LR ++ + + +  N     I 
Sbjct: 164 RAVHDAVNSDSNVDARGGKRIAVSLKTRLKDTAEATVGMLRAMLTAAQHTPANPALHAIT 223

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIG----LNGGL--EDMSQAL 204
           IHAR       +P+   +   L YD   E+ +       F G    LNG +      +A 
Sbjct: 224 IHAR-------TPEQRSEQAPL-YDRAAEVVRICRANAAFEGICLVLNGSVLSRQDGEAK 275

Query: 205 KILPSVDGVMIGRAAYKNS 223
             L   D  MI RAA +++
Sbjct: 276 CALYGFDAAMIARAALEDA 294


>gi|281412393|ref|YP_003346472.1| dihydroorotate dehydrogenase family protein [Thermotoga
           naphthophila RKU-10]
 gi|281373496|gb|ADA67058.1| dihydroorotate dehydrogenase family protein [Thermotoga
           naphthophila RKU-10]
          Length = 270

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 50/200 (25%), Positives = 91/200 (45%), Gaps = 30/200 (15%)

Query: 49  PLALQIGGADISKLVEAA---KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           P+   +GG    + +E A   K V D  Y  +  N  CP+  V EG  G  ++ N +   
Sbjct: 81  PMIASLGGDSFEEYLEVAHAFKKVADRFYA-VEFNFSCPN--VKEG--GLSIVKNVEEWE 135

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-------WIHARK- 157
             +A + K L     +  ++G++     + + +  + + K+G +GI        +H  K 
Sbjct: 136 KLLATLRKELPDTFLI-AKVGIE----GIFVEDAAEFVMKAGWDGITLVNTVRGLHFEKD 190

Query: 158 -AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGV 213
             IL GLS      +  +    VYE+KK  P LF+  +GG   ++D  + LK+    D +
Sbjct: 191 TMILGGLS---GPLLKPIALRTVYEVKKRFPKLFVIASGGVYSVKDAEEFLKV--GADVI 245

Query: 214 MIGRAAYKNSAMLTTVDEYF 233
            +G A +K+  ++  + +Y 
Sbjct: 246 GVGSALFKDPGVVEEIGKYL 265


>gi|221120394|ref|XP_002167268.1| PREDICTED: similar to GH10224 [Hydra magnipapillata]
          Length = 136

 Score = 40.8 bits (94), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 49/108 (45%), Gaps = 4/108 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MV+ ++  +R   R      L YT M  A   +  +K  K  +  +  ++PL  Q    D
Sbjct: 26  MVEQSELAFRSLCREYGAQ-LCYTPMWHAALFVNNEKYRKAAIETAFHDRPLLFQFCAND 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
                EA  + E +  + ++LN+GCP      G +G+ LM   D+V +
Sbjct: 85  PQIFAEACALAEPYC-DGVDLNLGCPQVIAARGHYGSYLMEELDLVEE 131


>gi|331238599|ref|XP_003331954.1| tRNA dihydrouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309310944|gb|EFP87535.1| tRNA dihydrouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 1548

 Score = 40.8 bits (94), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 59/138 (42%), Gaps = 31/138 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI------LGFSTQE------- 47
           MVD ++  +R  +R      L YT MI A   L  D + I      L   + E       
Sbjct: 92  MVDGSELAWRILSRYY-GAELCYTPMIHAG--LYSDDRQIKYRVEQLDLDSHEEGSEGLD 148

Query: 48  KPLALQIGGADISKLVEAAKIV-------EDF--------GYNEINLNVGCPSARVHEGS 92
           +PL +Q        L++AA +V        DF          + ++LN+GCP     +G 
Sbjct: 149 RPLIVQFCANHPDTLLKAANLVINHPSSSSDFLAGNMDRLPVDAVDLNLGCPQGIAKKGK 208

Query: 93  FGACLMLNPDIVGDCIAA 110
           +GA LM +PD++   + A
Sbjct: 209 YGAFLMDHPDLITQLMTA 226


>gi|255724312|ref|XP_002547085.1| hypothetical protein CTRG_01391 [Candida tropicalis MYA-3404]
 gi|240134976|gb|EER34530.1| hypothetical protein CTRG_01391 [Candida tropicalis MYA-3404]
          Length = 619

 Score = 40.8 bits (94), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 99/241 (41%), Gaps = 46/241 (19%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKLVEA 65
           YR   + L  + + Y+EM ++  +++G      +      E P   +QI     S+   A
Sbjct: 266 YRRLMKTLGAD-VTYSEMALSVPLIQGHNPEWALPKAHISEYPGFGVQIAS---SRHWPA 321

Query: 66  AKIVEDFGYN-----EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
           AK  E    N     E+NLN GCP   +++   G+ LM  P  +   +  M  +   IPV
Sbjct: 322 AKAAEAIYRNTNHVSELNLNCGCPIDLLYKQGQGSALMDQPSKLLRILHGMSASSGDIPV 381

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R GV +       + LV+ + + G    I +H R         +  R     D+D 
Sbjct: 382 TVKIRTGVREG--KNTAKTLVRRVLQEGNTAAITLHGRS--------RQQRYSREADWDY 431

Query: 179 VYEI----------KKENPD-------LFIGLNGGL---EDMSQALKILPSVDGVMIGRA 218
           + E+          +KE+ D        F+G NG +   ED    +     +D VM+ R 
Sbjct: 432 IAEVGSVVKEWNENQKEDKDATDIQPVYFVG-NGDVYSHEDWYNHVNT-DGIDSVMVARG 489

Query: 219 A 219
           A
Sbjct: 490 A 490


>gi|115680274|ref|XP_001190439.1| PREDICTED: similar to tRNA-dihydrouridine synthase
           [Strongylocentrotus purpuratus]
 gi|115717831|ref|XP_001201154.1| PREDICTED: similar to tRNA-dihydrouridine synthase
           [Strongylocentrotus purpuratus]
          Length = 499

 Score = 40.8 bits (94), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 37  KKNILGFSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           K +++ F T  K    L  Q+G AD  + +  AK+VE    + I++N+GCP     +G  
Sbjct: 96  KDDVVIFRTCSKETDRLVFQMGTADAQRALRVAKMVEK-DVSGIDINMGCPKDFSLKGGM 154

Query: 94  GACLMLNPDIVGD 106
           GA L+  PD + +
Sbjct: 155 GAALLQKPDTIKE 167


>gi|295103975|emb|CBL01519.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii SL3/3]
          Length = 316

 Score = 40.4 bits (93), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 36/165 (21%), Positives = 70/165 (42%), Gaps = 23/165 (13%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            GY E+NLN+GCP+  V     G+ ++ +   V   +  +      PV+VK R+GV+   
Sbjct: 86  LGYTEVNLNLGCPAGTVTAKGKGSGMLRDLAKVDAFLDGVFSRTEGPVSVKTRLGVEKPE 145

Query: 132 PAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKI--PNLDYDIVYEIKKENP 187
              A   +++   +  ++ + IH R  +   +G + +    +  P     + Y       
Sbjct: 146 EFAA---ILEIYSRYPISELTIHPRVMRQQYRGQADRAAFAVALPRCTMPVCY------- 195

Query: 188 DLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTV 229
                 NG +   +Q   +    P++ G+M+GR    + A+   V
Sbjct: 196 ------NGDVTTAAQLHALEEEFPALSGIMVGRGLIADPALFRRV 234


>gi|213615509|ref|ZP_03371335.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
          Length = 210

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 38/143 (26%), Positives = 67/143 (46%), Gaps = 16/143 (11%)

Query: 94  GACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           GA L+ +P+++     AM  A+   +PVTVK R+G D          +  +++++G + +
Sbjct: 7   GATLLTDPELIYQGAKAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASEL 63

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPS 209
            +H R       +     +  ++D+  + EI++      I  NG + D   +QA      
Sbjct: 64  VVHGR-------TKAQGYRAEHIDWQAIGEIRQRLTIPVIA-NGEIWDWQSAQACMATSG 115

Query: 210 VDGVMIGRAAYKNSAMLTTVDEY 232
            D VMIGR A  N   L+ V +Y
Sbjct: 116 CDAVMIGRGAL-NIPNLSRVVKY 137


>gi|32489914|emb|CAE05107.1| OSJNBa0009K15.27 [Oryza sativa Japonica Group]
 gi|39546255|emb|CAD39832.3| OSJNBa0079F16.3 [Oryza sativa Japonica Group]
          Length = 481

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 58/121 (47%), Gaps = 9/121 (7%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNS-AMLTTVD 230
           +L Y+  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD
Sbjct: 290 SLGYEYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVD 349

Query: 231 -EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            E +  P   SS  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P 
Sbjct: 350 SEVYGMPTRRSS--RRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEPG 403

Query: 290 S 290
           +
Sbjct: 404 N 404


>gi|218887109|ref|YP_002436430.1| dihydrouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218758063|gb|ACL08962.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris str. 'Miyazaki
           F']
          Length = 351

 Score = 40.4 bits (93), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 39/161 (24%), Positives = 70/161 (43%), Gaps = 6/161 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           +  ++D  +R   R     A   TEM+ A  +L      +++L  + ++ PL LQ+ GAD
Sbjct: 27  LAGYSDLPFRLLCRE-HGAAACCTEMVSAKGLLYHSPGTRDLLASTPEDAPLVLQLFGAD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSI 117
              +      + + G+   +LN+GC   +V +   G+ +  + D       AM + A   
Sbjct: 86  ADIMRTVMPGLLEQGFRWFDLNMGCSVPKVVKTGCGSAMSRDMDNALSVARAMVEVAGEG 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            V  K R+G   Q      R +   ++ +G   I +H R A
Sbjct: 146 RVGFKMRLGW--QAGEETWREMALRLQDAGAGWITLHPRFA 184


>gi|261403127|ref|YP_003247351.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           vulcanius M7]
 gi|261370120|gb|ACX72869.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           vulcanius M7]
          Length = 302

 Score = 40.4 bits (93), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 49/184 (26%), Positives = 83/184 (45%), Gaps = 31/184 (16%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            I G D  + ++ AK +E F  + I LN+ CP A+     +GA +  NP++  +  AA+ 
Sbjct: 100 SIYGKDEKEFMDVAKKIESF-VDAIELNISCPHAK----GYGATIGQNPEMSYNVCAAVK 154

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK 161
             + IPV  K    V D      +  +  ++ ++GV+G           I I A+K IL 
Sbjct: 155 DVVKIPVFAKLTPNVSD------IVEIAGAVVEAGVDGLVAINTVRGMVIDIKAKKPILS 208

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
               GLS    + I  +    V+++  EN D+ I   GG+     A++ ++     V +G
Sbjct: 209 NKFGGLS---GKAIKPVGIKAVWDL-YENFDVPIIGVGGIMSGEDAIEYMMAGASAVQVG 264

Query: 217 RAAY 220
              Y
Sbjct: 265 SGVY 268


>gi|322494951|emb|CBZ30254.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 493

 Score = 40.4 bits (93), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 51/232 (21%), Positives = 93/232 (40%), Gaps = 41/232 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNV 81
           YT M++A++ ++        F+  E    L +  A  S    A   +    Y + I+LN 
Sbjct: 124 YTHMLIAESFVKSPHARHAEFARYEGEDRLVVQLAAKSGPAAAQAALLLRPYCDGIDLNC 183

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------------------------- 116
           GCP     +   GA L+  P+ V D + ++  A+                          
Sbjct: 184 GCPQRWAMKEGIGAALLDQPERVADIVRSIRNAMPDGSTAPTIVGNGGEHSSCTSAAPPF 243

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P  VK RI  DD   +V   +  +  + +GV+ + +H R       +         + +
Sbjct: 244 LPCVVKMRIK-DDLRRSV---DFARQCEAAGVSWLTVHGRTPTCHPSA--------AVQF 291

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
           + V ++ +EN  + + LNGG+ D+S A++  +     G+M       N AM 
Sbjct: 292 EAV-KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCGGLMSANGLLDNPAMF 342


>gi|119476356|ref|ZP_01616707.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding protein
           [marine gamma proteobacterium HTCC2143]
 gi|119450220|gb|EAW31455.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding protein
           [marine gamma proteobacterium HTCC2143]
          Length = 541

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 45/77 (58%), Gaps = 5/77 (6%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +++ L + I G ++ + V+ AKI+  F  + + LN+ CP A+     +G  +  +PD+V 
Sbjct: 92  EDRFLLISIFGGNVDEYVQVAKIMAPFA-DGLELNLSCPHAK----GYGMAMGQDPDLVR 146

Query: 106 DCIAAMCKALSIPVTVK 122
           +  AA+  A++IPV  K
Sbjct: 147 EITAAVKAAVTIPVIPK 163


>gi|167764072|ref|ZP_02436199.1| hypothetical protein BACSTE_02455 [Bacteroides stercoris ATCC
           43183]
 gi|167698188|gb|EDS14767.1| hypothetical protein BACSTE_02455 [Bacteroides stercoris ATCC
           43183]
          Length = 317

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 57/265 (21%), Positives = 105/265 (39%), Gaps = 32/265 (12%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           I R D ++I   + +   L  Q+     S L +   +  +  Y E ++N+GCP   + + 
Sbjct: 47  IRRKDIRDINPENNRNIHLIPQLIAPQPSTLEQIVSLFIEHNYQEADINLGCPFPMLAKR 106

Query: 92  SFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
             GA ++  P+ + + + AA  K   I  +VK R+G ++   A     L+  +    ++ 
Sbjct: 107 HNGAGMLPYPEEIKELLTAATEKYPQIRFSVKLRLGWEN---ANECLALLPLLNTLPLSH 163

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
           I +H R      L  +  +   +L+    +    + P L+ G    +ED+    +  P +
Sbjct: 164 IILHPR------LGKQQYKGEVDLNGFEAFYHGCDKPLLYNGDLHTIEDIQTVTERFPRL 217

Query: 211 DGVMIGRAAYKNSA---------------MLTTVDEY-------FSNPLTGSSPIKTRVD 248
            GV+IGR    N A               ML+ V +        +   L G         
Sbjct: 218 AGVVIGRGLLANPALAWEYQQNRKLSPDEMLSKVKQLHTAIYNSYEEQLQGGETQLLMKM 277

Query: 249 KDFWRKISASMTDYAARHLHSGGKL 273
           K+FW  +  +    A + +H   KL
Sbjct: 278 KNFWEYLLPNGNRKAKKTIHKTSKL 302


>gi|222099309|ref|YP_002533877.1| Dihydroorotate dehydrogenase [Thermotoga neapolitana DSM 4359]
 gi|221571699|gb|ACM22511.1| Dihydroorotate dehydrogenase [Thermotoga neapolitana DSM 4359]
          Length = 270

 Score = 40.0 bits (92), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 45/195 (23%), Positives = 86/195 (44%), Gaps = 20/195 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+   +GG    + +E A++ +     +  +  N  CP+  V EG  G  ++ N +    
Sbjct: 81  PMIASLGGDSFEEYLEVARVFKKVADRFYAVEFNFSCPN--VKEG--GLSIVKNAEEWKK 136

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS-----IKKSGVNGIWIHARKAILK 161
            +  + K L     +  ++GV+      A   ++K+        + V G+       IL 
Sbjct: 137 LLNTLRKELPDSFLI-AKVGVEGIFVEDAAEFVMKAEWDGITLVNTVRGLHFEKDTMILG 195

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRA 218
           GLS    + I       VYE+KK  P+LF+  +GG   ++D  + LK+    D + +G A
Sbjct: 196 GLSGPVLKPI---ALRAVYEVKKRFPELFVIASGGVYSVKDAEEFLKV--GADVIGVGSA 250

Query: 219 AYKNSAMLTTVDEYF 233
            +K+  ++  + +Y 
Sbjct: 251 LFKDPGVVEEIGKYL 265


>gi|154482706|ref|ZP_02025154.1| hypothetical protein EUBVEN_00382 [Eubacterium ventriosum ATCC
           27560]
 gi|149736482|gb|EDM52368.1| hypothetical protein EUBVEN_00382 [Eubacterium ventriosum ATCC
           27560]
          Length = 326

 Score = 40.0 bits (92), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 43/199 (21%), Positives = 82/199 (41%), Gaps = 33/199 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYN-EINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           L  QI        ++AA  + + GY+ EINLN GCPS  V   + GA  + + + +    
Sbjct: 62  LVPQILANRADYFIKAANQLIELGYDKEINLNAGCPSGTVVSKNKGAGFLKDTEAMDRFF 121

Query: 109 AAMCKAL--------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH--ARKA 158
                 L        ++ ++VK RIG+          N+++   K  ++ + +H   R+ 
Sbjct: 122 DETFNWLEKKNSEGHNLSISVKTRIGM---YEPDEFENILEVYNKYPISQLIVHPRTREQ 178

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD------- 211
           + KG         PN++    ++   EN    +  NG +  +    +I+  ++       
Sbjct: 179 LYKG--------TPNME---AFKYALENSKNPVCYNGDINTVENYHRIIEKINDDSEMKI 227

Query: 212 -GVMIGRAAYKNSAMLTTV 229
             +MIGR    N  ++  +
Sbjct: 228 GSIMIGRGLIGNPNLVNEI 246


>gi|315612974|ref|ZP_07887885.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis ATCC 49296]
 gi|315315084|gb|EFU63125.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis ATCC 49296]
          Length = 328

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 119 NVAGFSKQEY--------AAVSRGISKATNVK-----AIELNISCPN--VDHGNHGLLIG 163

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 164 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------TIAKAAEDAGASGLTMINTLV 217

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 218 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 276

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 277 YLAGASAIGVGTANFTN 293


>gi|9187612|emb|CAB96955.1| hypothetical protein, similar to (AF091072.1) predicted protein
           [Homo sapiens]
          Length = 465

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 39/156 (25%), Positives = 72/156 (46%), Gaps = 15/156 (9%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-----DFGYNEI 77
           EM V   +L+G      +L     E    +Q+ GA    + + A+++      DF    +
Sbjct: 318 EMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDF----V 373

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  +A R
Sbjct: 374 DINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERV-NLAHR 432

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L+  ++  GV  + +       + L P+   ++P+
Sbjct: 433 -LLPELRDWGVALVTVGL--GTPRALGPRGRPRVPS 465


>gi|170288398|ref|YP_001738636.1| dihydroorotate dehydrogenase family protein [Thermotoga sp. RQ2]
 gi|170175901|gb|ACB08953.1| dihydroorotate dehydrogenase family protein [Thermotoga sp. RQ2]
          Length = 270

 Score = 40.0 bits (92), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 45/195 (23%), Positives = 86/195 (44%), Gaps = 20/195 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+   +GG    + +E A++ +     +  +  N  CP+  V EG  G  ++ N +    
Sbjct: 81  PMIASLGGDSFEEYLEVARVFKKVADRFYAVEFNFSCPN--VKEG--GLSIVKNAEEWKK 136

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS-----IKKSGVNGIWIHARKAILK 161
            +  + K L     +  ++GV+      A   ++K+        + V G+       IL 
Sbjct: 137 LLNTLRKELPDSFLI-AKVGVEGIFVEDAAEFVMKAEWDGITLVNTVRGLHFEKDTMILG 195

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRA 218
           GLS    + I       VYE+KK  P+LF+  +GG   ++D  + LK+    D + +G A
Sbjct: 196 GLSGPVLKPI---ALRAVYEVKKRFPELFVIASGGVYSVKDAEEFLKV--GADVIGVGSA 250

Query: 219 AYKNSAMLTTVDEYF 233
            +K+  ++  + +Y 
Sbjct: 251 LFKDPGVVEEIGKYL 265


>gi|322374500|ref|ZP_08049014.1| dihydroorotate dehydrogenase B [Streptococcus sp. C300]
 gi|321280000|gb|EFX57039.1| dihydroorotate dehydrogenase B [Streptococcus sp. C300]
          Length = 330

 Score = 40.0 bits (92), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 85/197 (43%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 121 NVAGFSKQEY--------AAVSRGISKAANVK-----AIELNISCPN--VDHGNHGLLIG 165

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +      ++ K+ + +G +G+       
Sbjct: 166 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------SIAKAAEDAGASGLTMINTLV 219

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 220 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTGLPIIGM-GGVDSAEAALEM 278

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 279 YLAGASAIGVGTANFTN 295


>gi|328949335|ref|YP_004366672.1| dihydroorotate dehydrogenase family protein [Treponema
           succinifaciens DSM 2489]
 gi|328449659|gb|AEB15375.1| dihydroorotate dehydrogenase family protein [Treponema
           succinifaciens DSM 2489]
          Length = 591

 Score = 40.0 bits (92), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 87/198 (43%), Gaps = 31/198 (15%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           + G D+   ++ A++++      I LN+ CP+ +    ++G    +NP+    C++A+ K
Sbjct: 382 LAGHDLDSYIKGAELLDKTPVPAIELNISCPNVKAGGMAWG----INPEAAFTCVSAVRK 437

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKA----ILKGLSPKDN 168
           A S P+ VK      D + +VAL  +     K+G N +  I+  +A    I  G    DN
Sbjct: 438 ATSKPLIVKLSPNAPDLV-SVALACI-----KAGANALSLINTIQAVAIDIESGRPVFDN 491

Query: 169 RKIP-----------NLDYDIVYEIK---KENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            K              + YD+V  +    KE     IGL GG+     A++ I+     +
Sbjct: 492 IKAGLCGPAVKPIALRMVYDVVKAVNSLPKEQQIPVIGL-GGISKWQDAVEFIMAGASAI 550

Query: 214 MIGRAAYKNSAMLTTVDE 231
            +G A + N   +  + E
Sbjct: 551 QVGTATFSNPKTMIEIIE 568


>gi|194383804|dbj|BAG59260.1| unnamed protein product [Homo sapiens]
          Length = 458

 Score = 40.0 bits (92), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 37/148 (25%), Positives = 66/148 (44%), Gaps = 31/148 (20%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGV 148
           G  GA L+ + D +   ++ + K    PVT K RI   ++D +      +LVK I+++G+
Sbjct: 89  GGMGAALLSDSDKIEKILSTLVKGTRRPVTCKIRILPSLEDTL------SLVKRIERTGI 142

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LE 198
             I +H RK        ++ R    +  +++  I  +   + +  NGG          +E
Sbjct: 143 AAIAVHGRK--------REERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQQYSDIE 193

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAML 226
           D  QA     +   VM+ RAA  N ++ 
Sbjct: 194 DFRQAT----AASSVMVARAAMWNPSIF 217


>gi|294788397|ref|ZP_06753640.1| dihydrouridine synthase (Dus) [Simonsiella muelleri ATCC 29453]
 gi|294483828|gb|EFG31512.1| dihydrouridine synthase (Dus) [Simonsiella muelleri ATCC 29453]
          Length = 175

 Score = 40.0 bits (92), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 24/90 (26%), Positives = 51/90 (56%), Gaps = 3/90 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R  A+    +  + +EM+ +D  L+  +K++     + +   +A+QI G++
Sbjct: 22  MAGITDNPFRQIAKQFGADWTV-SEMLSSDPTLQQTRKSLQRRNHTGESGVIAVQIAGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
             +L +AA++  + G   I++N+GCP+ +V
Sbjct: 81  PHELAKAAQLNYENGAQVIDINMGCPAKKV 110


>gi|218509228|ref|ZP_03507106.1| tRNA-dihydrouridine synthase protein [Rhizobium etli Brasil 5]
          Length = 117

 Score = 40.0 bits (92), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +RF A L+    +   E+ V D      +    GF    +P  +Q+ G +   + EAAKI
Sbjct: 47  WRFGAGLVVTEMVASREL-VNDTAESWSRLKAAGF----RPHMVQLAGREAHWMAEAAKI 101

Query: 69  VEDFGYNEINLNVGCP 84
             D G + I++N+GCP
Sbjct: 102 AADHGADIIDINMGCP 117


>gi|331266573|ref|YP_004326203.1| dihydroorotate dehydrogenase [Streptococcus oralis Uo5]
 gi|326683245|emb|CBZ00863.1| dihydroorotate dehydrogenase [Streptococcus oralis Uo5]
          Length = 312

 Score = 40.0 bits (92), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSRGISKAANVK-----AIELNISCPN--VDHGNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------TIAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|198427128|ref|XP_002120497.1| PREDICTED: similar to tRNA-dihydrouridine synthase 2-like (hDUS2)
           (Up-regulated in lung cancer) (URLC8) [Ciona
           intestinalis]
          Length = 482

 Score = 39.7 bits (91), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 36/142 (25%), Positives = 63/142 (44%), Gaps = 20/142 (14%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVN 149
           G  GA L+  P+ V + +  +   LSIPVT K RI     +P +     LV+ I+ +GV 
Sbjct: 170 GGMGAALITQPENVKEILTTLVNGLSIPVTCKIRI-----LPEIDKTLELVRIIESTGVA 224

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QAL 204
            + +H R         K  R    +  D++  I  E   + +  NGG  +++     +  
Sbjct: 225 ALAVHGRY--------KHERPRHPVHCDVIKAI-TETVKIPVIANGGSSNIACYDDIEKF 275

Query: 205 KILPSVDGVMIGRAAYKNSAML 226
           +   +   VM+ R+A  N ++ 
Sbjct: 276 RASTNASSVMLARSAQWNCSVF 297


>gi|160942572|ref|ZP_02089819.1| hypothetical protein FAEPRAM212_00047 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446156|gb|EDP23159.1| hypothetical protein FAEPRAM212_00047 [Faecalibacterium prausnitzii
           M21/2]
          Length = 316

 Score = 39.7 bits (91), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 38/162 (23%), Positives = 68/162 (41%), Gaps = 23/162 (14%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            GY E+NLN+GCP+  V     G+ ++ +   V   +  +      PV+VK R+GV+   
Sbjct: 86  LGYTEVNLNLGCPAGTVTAKGKGSGMLRDLAKVDAFLDGVFSHAEGPVSVKTRLGVEKPE 145

Query: 132 PAVALRNLVKSIKKSGVNGIWIHAR--KAILKG--LSPKDNRKIPNLDYDIVYEIKKENP 187
              A+  +     +  ++ + IH R  +   +G          +P     + Y       
Sbjct: 146 EFAAILEIY---SRYPISELTIHPRVMRQQYRGQADRAAFAAALPRCTMPVCY------- 195

Query: 188 DLFIGLNGGLEDMSQ--AL-KILPSVDGVMIGRAAYKNSAML 226
                 NG +   +Q  AL K  P++ G+M+GR    + A+ 
Sbjct: 196 ------NGDVTTAAQLHALEKEFPALSGIMVGRGLIADPALF 231


>gi|114663254|ref|XP_001166802.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 5
           [Pan troglodytes]
          Length = 477

 Score = 39.7 bits (91), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 43/189 (22%), Positives = 80/189 (42%), Gaps = 48/189 (25%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+G +D  + +  A++VE+     I++N+GCP                       ++
Sbjct: 84  VVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPK----------------QYSTKILS 126

Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + K    PVT K RI   ++D +      +LVK I+++G+  I +H RK        ++
Sbjct: 127 TLVKGTHRPVTCKIRILPSLEDTL------SLVKRIERTGIAAIAVHGRK--------RE 172

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGG----------LEDMSQALKILPSVDGVMIGR 217
            R    +  +++  I  +   + +  NGG          +ED  QA     +   VM+ R
Sbjct: 173 ERPQHPVSCEVIKAI-ADTLSIPVIANGGSHDHIQQYSDIEDFRQAT----AASSVMVAR 227

Query: 218 AAYKNSAML 226
           AA  N ++ 
Sbjct: 228 AAMWNPSIF 236


>gi|256810615|ref|YP_003127984.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           fervens AG86]
 gi|256793815|gb|ACV24484.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           fervens AG86]
          Length = 302

 Score = 39.7 bits (91), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 83/181 (45%), Gaps = 31/181 (17%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +  +  E AK +E +  + I LN+ CP A+     +GA +  NP++      A+ K++
Sbjct: 103 GKNEEEFAEVAKRMEKY-VDIIELNISCPHAK----GYGATIGQNPELSYSVCKAVKKSV 157

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAIL---- 160
            +PV  K    V D I       + +++  +GV+G           I I A+K IL    
Sbjct: 158 KVPVFAKLTPNVTDII------EIAQAVVDAGVDGLVAINTVRGMAIDIKAKKPILGNKF 211

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            GLS    + I  +   +V+++  EN D+ I   GG+ +   A++ ++     V IG   
Sbjct: 212 GGLS---GKAIKPIGIKVVWDL-YENFDVPIIGVGGIMNGEDAIEYMMAGASAVQIGSGV 267

Query: 220 Y 220
           Y
Sbjct: 268 Y 268


>gi|306829318|ref|ZP_07462508.1| dihydroorotate dehydrogenase B [Streptococcus mitis ATCC 6249]
 gi|304428404|gb|EFM31494.1| dihydroorotate dehydrogenase B [Streptococcus mitis ATCC 6249]
          Length = 328

 Score = 39.7 bits (91), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 119 NVAGFSKQEY--------AAVSRGISKAANVK-----AIELNISCPN--VDHGNHGLLIG 163

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 164 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------TIAKAAEDAGASGLTMINTLV 217

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 218 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 276

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 277 YLAGASAIGVGTANFTN 293


>gi|295695968|ref|YP_003589206.1| dihydroorotate dehydrogenase family protein [Bacillus tusciae DSM
           2912]
 gi|295411570|gb|ADG06062.1| dihydroorotate dehydrogenase family protein [Bacillus tusciae DSM
           2912]
          Length = 309

 Score = 39.7 bits (91), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 48/201 (23%), Positives = 88/201 (43%), Gaps = 32/201 (15%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + + G+ + + VE A+ +        + LN+ CP+ R     FG     +PD+  + 
Sbjct: 97  PVIVNVAGSVVEEYVETARRLSGSRDVAALELNISCPNVRCGGMHFGT----DPDMAAEV 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
            AA+     +PV VK    V D +       L ++++++G +G           I I  R
Sbjct: 153 TAAVKAVSRVPVFVKLSPNVTDIV------ALAQAVERAGADGLSMINTLVGMRIDIERR 206

Query: 157 KAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
           + IL     GLS      I  +   ++YE+ +      IG+ GG+     A++  +    
Sbjct: 207 RPILANFFGGLS---GPAIKPVALRMIYEVSRVVRIPIIGM-GGITSGEDAVEFFMAGAS 262

Query: 212 GVMIGRAAY-KNSAMLTTVDE 231
            V +G A + K +A +  +DE
Sbjct: 263 AVAVGTANFIKPTACVDILDE 283


>gi|293365211|ref|ZP_06611928.1| dihydroorotate dehydrogenase B [Streptococcus oralis ATCC 35037]
 gi|291316661|gb|EFE57097.1| dihydroorotate dehydrogenase B [Streptococcus oralis ATCC 35037]
          Length = 328

 Score = 39.7 bits (91), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 119 NVAGFSKQEY--------AAVSQGISKATNVK-----AIELNISCPN--VDHGNHGLLIG 163

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 164 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------TIAKAAEDAGASGLTMINTLV 217

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 218 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 276

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 277 YLAGASAIGVGTANFTN 293


>gi|295398020|ref|ZP_06808076.1| dihydroorotate oxidase [Aerococcus viridans ATCC 11563]
 gi|294973778|gb|EFG49549.1| dihydroorotate oxidase [Aerococcus viridans ATCC 11563]
          Length = 307

 Score = 39.7 bits (91), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 43/188 (22%), Positives = 82/188 (43%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+ +   VEA + + +      I LN+ CP+ ++    FG     +P++  D 
Sbjct: 95  PIIQSVAGSTVEDYVEATRALSQPENVKAIELNISCPNVKLGGLQFGT----DPEVAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
              +  A  +PV VK    V D I A+A     K+++ +G + I            +  R
Sbjct: 151 TKQVKAATDLPVYVKLTPNVTD-ITAIA-----KAVEAAGADAIVMINTITGQTFDLETR 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + +L G++       +  +   +V ++ +      IG+ GG+E +   L+ I+     V 
Sbjct: 205 QPVLGGITGGLSGSSVKYVALRMVRQVAQVVDIPIIGV-GGIESIDDVLEMIIAGATAVQ 263

Query: 215 IGRAAYKN 222
           +G A Y N
Sbjct: 264 VGSANYAN 271


>gi|312137365|ref|YP_004004702.1| dihydroorotate oxidase b, catalytic subunit [Methanothermus
           fervidus DSM 2088]
 gi|311225084|gb|ADP77940.1| dihydroorotate oxidase B, catalytic subunit [Methanothermus
           fervidus DSM 2088]
          Length = 301

 Score = 39.7 bits (91), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I G+   +  E +K V D   + I +NV CP A    GSF   +  +P +  + +
Sbjct: 92  PIIASIAGSSPKEFAEVSKEVSDL-VDMIEINVSCPHAGEGYGSF---IGQDPKLTYEVV 147

Query: 109 AAMCKALSIPVTVKCRIGVDD 129
            A+ KA+++PV+VK    V D
Sbjct: 148 KAVKKAVNLPVSVKLTANVAD 168


>gi|212533435|ref|XP_002146874.1| tRNA dihydrouridine synthase, putative [Penicillium marneffei ATCC
           18224]
 gi|210072238|gb|EEA26327.1| tRNA dihydrouridine synthase, putative [Penicillium marneffei ATCC
           18224]
          Length = 716

 Score = 39.7 bits (91), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 71/183 (38%), Gaps = 50/183 (27%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAV 134
           I+LN GCP   V +   G+ L+ +P  +   +  M  A+S  IP+TVK R+G  D  P  
Sbjct: 412 IDLNCGCPIDLVFKEGSGSALLDSPSKLEKILRGM-NAVSGEIPITVKIRMGTKDNQPTA 470

Query: 135 ----------ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE--- 181
                      + +    I   G+  I +H R         +  R   N D+  + E   
Sbjct: 471 LKLAERLVLGGIDSQTMGIGPPGIAAITLHGRS--------RQQRYTKNADWGYISECAA 522

Query: 182 -IKK------------ENPDLFIGLNGGL------------EDMSQALKILPSVDGVMIG 216
            +K+              PD  +  NGG             ED +  ++   +VD VMIG
Sbjct: 523 LVKRLRSESDVLADTVREPDERLQPNGGKIYFLGNGDCYSHEDYNDHVQNA-NVDTVMIG 581

Query: 217 RAA 219
           R A
Sbjct: 582 RGA 584


>gi|157875645|ref|XP_001686207.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68129281|emb|CAJ07821.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 493

 Score = 39.7 bits (91), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 50/229 (21%), Positives = 96/229 (41%), Gaps = 35/229 (15%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           YT M++A++ ++        F+  E    L  Q+         +AA ++  +  + I+LN
Sbjct: 124 YTHMLMAESFVKSPHARHAEFARYEGENRLVAQLAAKSGPAAAQAALLLRPY-CDGIDLN 182

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----SIPVTV-------KCRIGVDD 129
            GCP     +   GA L+  P+ V D + ++  A+    + P+ V        C   V  
Sbjct: 183 CGCPQRWAMKEGIGAALLDQPERVADMVRSIRNAMPDGSTAPMIVGNGGEYSSCTSAVPP 242

Query: 130 QIPAVA-------LR---NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            +P V        LR   +  +  + +GV+ + +H R       +         + ++ V
Sbjct: 243 FLPCVVKMRIKDDLRRSVDFARQCEAAGVSWLTVHGRTPTCHSST--------AVQFEAV 294

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
            ++ +EN  + + LNGG+ D+S A++  +     G+M       N AM 
Sbjct: 295 -KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCGGLMSANGLLDNPAMF 342


>gi|224536765|ref|ZP_03677304.1| hypothetical protein BACCELL_01641 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521623|gb|EEF90728.1| hypothetical protein BACCELL_01641 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 313

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 64/289 (22%), Positives = 119/289 (41%), Gaps = 42/289 (14%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADIS 60
           +T+  YR   AR+       YT  +  +   I + D + I   + +   L  Q+   D+ 
Sbjct: 15  YTEAIYRQAHARIFGGVESYYTPFVRVEHGEIRKKDMREITLENNRGVQLIPQLIAPDVD 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPV 119
           K+     +  + GY  +++N+GCP   + +   G+ ++  P+ V + + A  K    +  
Sbjct: 75  KMELIIALFIEKGYKNVDINLGCPFPLLAKRHNGSGMLPYPEEVRELLTAAIKNHPDLQF 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------KAILKGLSPKDNRKI 171
           +VK R+G ++  P  +L  L    +    + I +H R        +  LKG     N   
Sbjct: 135 SVKMRLGWEN--PEESLALLPLLNELPLTH-IIMHPRLGKQQYKGEVDLKGFEAFYN--- 188

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
               + ++Y     N DL       +ED+    +  P + G+MIGR    N A+     +
Sbjct: 189 -ECSHPLIY-----NGDLLT-----VEDIQTISERFPRLAGIMIGRGLLANPALALEYQQ 237

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITR 278
              +PL+         +KD   ++     D  A++  L  GG  Q +T+
Sbjct: 238 --GHPLS---------EKDMQERLRLFHADVFAQYGNLLEGGDKQLLTK 275


>gi|67587982|ref|XP_665290.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54655895|gb|EAL35060.1| hypothetical protein Chro.50134 [Cryptosporidium hominis]
          Length = 677

 Score = 39.7 bits (91), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 57/253 (22%), Positives = 100/253 (39%), Gaps = 52/253 (20%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EM++ + IL G    +  L  S +EK   +Q+ G + S +++  + + E   ++ I++N
Sbjct: 315 SEMVLCNEILSGKASELALLKKSPEEKHFGIQLAGGNKSTIIKTGEFINEHCEFDFIDIN 374

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-----VTVKCRIGVD------- 128
             CP   +H+   G+ L+   D V + +  M K L        VTVK R+          
Sbjct: 375 AACPLKSLHDKGAGSILV---DRVSE-LETMVKGLKKVMDGKLVTVKVRMSHGGSPINKN 430

Query: 129 ----------DQIPAV----ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD------- 167
                     +  P +        ++  +  SG++ + IH R +  +     D       
Sbjct: 431 LSEKDYFENFENWPVIYHNMKTHKILNILCDSGIDALTIHGRTSFQRYTKEADWSYIKYC 490

Query: 168 ---NRKIPNLDYDIVYEIKKENPDLF----IGLNG--GLEDMSQALKILPSVDGVMIGRA 218
              N K+      +   I+  N  LF    IG       +D  Q ++    VD VMIGR 
Sbjct: 491 SVLNSKL--YSNKVANNIQSSNHSLFCPSIIGCGDIINFQDYQQHIQN-DLVDSVMIGRG 547

Query: 219 AYKNSAMLTTVDE 231
           A     + T + E
Sbjct: 548 ALLKPWIFTEIKE 560


>gi|322493958|emb|CBZ29249.1| putative dihydrouridine synthase (Dus) [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 660

 Score = 39.7 bits (91), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 12/109 (11%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE------------ 76
           AD +LR  +  +LG            GGA  + +      V     +E            
Sbjct: 224 ADTVLRAARFAVLGEQAAATEQTGDNGGASAAPVYPVHVRVNGLSSSEKAPAHLLYQCDA 283

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           ++LN+GCP      G +G+ LM + +++   +  +   L +PVTVK R+
Sbjct: 284 VDLNLGCPQGIARRGHYGSFLMEDWELIHTIVHTLHVELEVPVTVKIRV 332


>gi|118776473|gb|ABL14244.1| dihydroprimidine dehydrogenase [Bacillus fordii]
          Length = 426

 Score = 39.7 bits (91), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 84/196 (42%), Gaps = 25/196 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K  E  K V+D G +   LN+GCP      G  G+ +  +PD+V        +A  +PV 
Sbjct: 113 KWHEIVKRVQDVGVDGFELNLGCPHGMSERG-MGSAVGQHPDLVEKTTLYAKEASEVPVI 171

Query: 121 VKCRIGVDD-----------QIPAVALRNLVKSIKKSGVNGIWIHA-RKAILKGLSPKDN 168
            K    + D              A+++ N + S+ +S    IWIH  R  ++ GL     
Sbjct: 172 TKLTPNITDITATARAAQRGGADAISMINTINSLMES----IWIHGIRSRMINGLGAHGG 227

Query: 169 RKIPNLD---YDIVYEIKKENPDLFIGLN--GGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
              P +     +++ E  ++  D+ I ++  GG+      ++ +L    GV I  AA  +
Sbjct: 228 YSGPAVKPIALNMIGECARQK-DITIPISGIGGVSTWQDTVEFMLMGAGGVQICTAAMHH 286

Query: 223 S-AMLTTVDEYFSNPL 237
             +++  + E  SN L
Sbjct: 287 GFSIIDDLTEGLSNHL 302


>gi|111221342|ref|YP_712136.1| putative dihydroorotate dehydrogenase A [Frankia alni ACN14a]
 gi|111148874|emb|CAJ60552.1| putative Dihydroorotate dehydrogenase A (Dihydroorotate oxidase A)
           (DHOdehase A) (DHODase A) (DHOD A) [Frankia alni ACN14a]
          Length = 318

 Score = 39.7 bits (91), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           V W  R Y   A  L N  L Y    +   + R  +          KPL + + G D+ +
Sbjct: 54  VYWPGRVYSINALGLPNRGLAYYGEHLPGMVERAHEAG--------KPLIVSVAGFDVGE 105

Query: 62  LVEAAKIVEDFGYNEINLNVGCPS 85
             E A++V D G + + LN+ CP+
Sbjct: 106 YQEIAEVVADAGVDLVELNLACPN 129


>gi|126135514|ref|XP_001384281.1| dihydrouridine synthase of tRNA [Scheffersomyces stipitis CBS 6054]
 gi|187471049|sp|A3LUK5|DUS3_PICST RecName: Full=tRNA-dihydrouridine synthase 3
 gi|126091479|gb|ABN66252.1| dihydrouridine synthase of tRNA [Scheffersomyces stipitis CBS 6054]
          Length = 613

 Score = 39.7 bits (91), Expect = 0.69,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 100/257 (38%), Gaps = 53/257 (20%)

Query: 60  SKLVEAAKIVEDFG-----YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CK 113
           SK   AAK+ E         +E+NLN GCP   ++    G+ L+  P  +   + AM   
Sbjct: 309 SKHWAAAKVAEIISRETEHVSELNLNCGCPIDLLYRQGQGSALLEQPARLVRILKAMNAS 368

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +  IPVTVK R G  +       + LV+  + ++ V  I +H R         +  R   
Sbjct: 369 SGDIPVTVKIRTGSKENKNTA--KTLVERLLAENDVAAITLHGRS--------RQQRYTK 418

Query: 173 NLDYDIVYEI----------KKENPD-------LFIGLNGGL---EDMSQALKILPSVDG 212
             D++ + E+          K+EN D        F+G NG +    D   A+     +D 
Sbjct: 419 EADWNYIAEVGQVVQQWNDKKEENKDSRDTQRTCFVG-NGDVFSHVDWYNAVNT-DGIDS 476

Query: 213 VMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
           VM+ R A     +   V+  +Y     T       R+D      I  + +DYA  H  + 
Sbjct: 477 VMVARGALIKPWIFEEVEAQQYLDKTAT------ERLD------ILKTFSDYALEHWGTD 524

Query: 271 GKLQQITRHMIGLFHGF 287
                + R  +  F  F
Sbjct: 525 EYGVGLARRFMCEFLSF 541


>gi|322391869|ref|ZP_08065334.1| dihydroorotate dehydrogenase B [Streptococcus peroris ATCC 700780]
 gi|321145349|gb|EFX40745.1| dihydroorotate dehydrogenase B [Streptococcus peroris ATCC 700780]
          Length = 327

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 52/113 (46%), Gaps = 21/113 (18%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 119 NVAGFSKQEY--------ASVSHGISKANNVK-----AIELNISCPN--VDHGNHGLLIG 163

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+
Sbjct: 164 QDPDLAFDVVKAAVEASDVPVYVKLTPSVTDIV------TIAKAAEDAGASGL 210


>gi|307703749|ref|ZP_07640690.1| dihydroorotate dehydrogenase family protein [Streptococcus oralis
           ATCC 35037]
 gi|307622584|gb|EFO01580.1| dihydroorotate dehydrogenase family protein [Streptococcus oralis
           ATCC 35037]
          Length = 312

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSQGISKATNVK-----AIELNISCPN--VDHGNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------TIAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|58337655|ref|YP_194240.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus NCFM]
 gi|81311432|sp|Q5FJB5|PYRD_LACAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|58254972|gb|AAV43209.1| dihydroorotate dehydrogenase B, catalytic unit [Lactobacillus
           acidophilus NCFM]
          Length = 307

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 52/106 (49%), Gaps = 11/106 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG   S  VE AK + D    N + +NV CP+      SFG    ++PD+V + 
Sbjct: 98  PIMASVGGDSESDYVEVAKKLSDSDLVNALEINVSCPNVAQGGMSFG----VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
              +   + +P+ VK    V D I A+A     ++ +K G +GI +
Sbjct: 154 TKKIKDVVDVPIYVKLTPNVTD-IVAIA-----QAAEKGGADGISM 193


>gi|227904296|ref|ZP_04022101.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus ATCC
           4796]
 gi|227867944|gb|EEJ75365.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus ATCC
           4796]
          Length = 307

 Score = 39.3 bits (90), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 52/106 (49%), Gaps = 11/106 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG   S  VE AK + D    N + +NV CP+      SFG    ++PD+V + 
Sbjct: 98  PIMASVGGDSESDYVEVAKKLSDSDLVNALEINVSCPNVAQGGMSFG----VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
              +   + +P+ VK    V D I A+A     ++ +K G +GI +
Sbjct: 154 TKKIKDVVDVPIYVKLTPNVTD-IVAIA-----QAAEKGGADGISM 193


>gi|270292932|ref|ZP_06199143.1| dihydroorotate dehydrogenase B [Streptococcus sp. M143]
 gi|270278911|gb|EFA24757.1| dihydroorotate dehydrogenase B [Streptococcus sp. M143]
          Length = 330

 Score = 39.3 bits (90), Expect = 0.73,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 121 NVAGFSKQEY--------AAVSRGISKAANVK-----AIELNISCPN--VDHGNHGLLIG 165

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 166 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 219

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 220 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 278

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 279 YLAGASAIGVGTANFTN 295


>gi|306825429|ref|ZP_07458769.1| dihydroorotate dehydrogenase B [Streptococcus sp. oral taxon 071
           str. 73H25AP]
 gi|304432367|gb|EFM35343.1| dihydroorotate dehydrogenase B [Streptococcus sp. oral taxon 071
           str. 73H25AP]
          Length = 319

 Score = 39.3 bits (90), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 84/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S+ +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 110 NVAGFSKQEY--------AAVSQGISKAANVK-----AIELNISCPN--VDHGNHGLLIG 154

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  + + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 155 QDPDLAYEVVKAAVEASDVPVYVKLTPSVTDVV------TIAKAAEDAGASGLTMINTLV 208

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 209 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 267

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 268 YLAGASAIGVGTANFTN 284


>gi|323457319|gb|EGB13185.1| hypothetical protein AURANDRAFT_19510 [Aureococcus anophagefferens]
          Length = 217

 Score = 39.3 bits (90), Expect = 0.82,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 55/119 (46%), Gaps = 5/119 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGGA 57
           +V +++  +R   R L       T MI A    A  R   +        ++PL  Q+GG+
Sbjct: 45  LVGYSEPAFRVLCRTLGAQ-CCSTPMIDAAGYAASPRYRAEYAFSGGAADRPLTAQLGGS 103

Query: 58  DISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           D + L  AA +V   G+ + + LN+GCP     +   GA LM +P     CI AM  AL
Sbjct: 104 DPAALARAAALVAATGHCDAVELNMGCPQRCAKKTGSGAFLMEDPARAVACIKAMRAAL 162


>gi|156052667|ref|XP_001592260.1| hypothetical protein SS1G_06500 [Sclerotinia sclerotiorum 1980]
 gi|154704279|gb|EDO04018.1| hypothetical protein SS1G_06500 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 342

 Score = 39.3 bits (90), Expect = 0.82,   Method: Compositional matrix adjust.
 Identities = 47/171 (27%), Positives = 67/171 (39%), Gaps = 25/171 (14%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-------SIPVTVKCRIGV 127
           N I++N GCP +     S GA LM   ++V + +     AL          V+VK RI  
Sbjct: 111 NGIDINCGCPQSWACACSIGAALMHKRELVAEMVKEAKSALKREGYEGKKTVSVKIRIHR 170

Query: 128 D--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           D  D +      + +K+++ +GV+ I IH R        P +   I  L+          
Sbjct: 171 DLRDTV------DFIKTVQDAGVDFITIHGRMRSTPSSHPVNLEAIKLLNTHTTVPTVS- 223

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           N D+   L    E   Q      SV GVM  R    N A+      Y S P
Sbjct: 224 NGDI-TSLRSAHEHTQQT-----SVSGVMSARGLLSNPALFAG---YVSTP 265


>gi|320032373|gb|EFW14326.1| tRNA dihydrouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 310

 Score = 39.3 bits (90), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 34/143 (23%), Positives = 64/143 (44%), Gaps = 10/143 (6%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A+ S L   A  V     + I++N GCP      G  GA L+  PD +   + 
Sbjct: 114 LIFQLGTANPS-LAVEAAKVVAADVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLVSILE 172

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  + +        LV  + ++G+ G+ +H R   ++    
Sbjct: 173 ALVEEIGKPYEIGISVKIRLLAEPE----RTEALVTRLCRTGITGLTVHCRTTPMRPREA 228

Query: 166 KDNRKIPNLDYDIVYEIKKENPD 188
               ++P +   I  + ++  PD
Sbjct: 229 AIREQLPMIA-SICRKSRRGMPD 250


>gi|227892690|ref|ZP_04010495.1| dihydroorotate dehydrogenase 1B [Lactobacillus ultunensis DSM
           16047]
 gi|227865467|gb|EEJ72888.1| dihydroorotate dehydrogenase 1B [Lactobacillus ultunensis DSM
           16047]
          Length = 307

 Score = 39.3 bits (90), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 50/205 (24%), Positives = 88/205 (42%), Gaps = 39/205 (19%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG 91
           LRG   N+        P+   +GG      VE AK + +    N + +NV CP+      
Sbjct: 90  LRGKYPNL--------PIMASVGGDSEDDYVEVAKKLSNSKLVNALEINVSCPNVARGGM 141

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           SFG    ++PD+V +    + K ++IP+ VK    V D      +  + ++ +K G +GI
Sbjct: 142 SFG----VHPDVVEELTRNIKKVVNIPIYVKLTPNVTD------ITVIARAAEKGGADGI 191

Query: 152 W-----------IHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
                       +  RK IL     GLS      I  +   ++ ++++      IG+ GG
Sbjct: 192 SMINTVLGMEIDVKTRKPILGHNMGGLS---GEAIKPIAIRMISQVRQATDLPIIGM-GG 247

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAY 220
           +E     ++ +L   + V +G A +
Sbjct: 248 IESAQDVVEFMLAGANAVAVGTAHF 272


>gi|257898603|ref|ZP_05678256.1| dihydroorotate dehydrogenase [Enterococcus faecium Com15]
 gi|257836515|gb|EEV61589.1| dihydroorotate dehydrogenase [Enterococcus faecium Com15]
          Length = 310

 Score = 38.9 bits (89), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 13/109 (11%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     VE  +KI E      I LN+ CP+ + H G +FG     +PD+ 
Sbjct: 96  ELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCPNVK-HGGIAFGT----DPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +
Sbjct: 151 FQLTQAVKKVASVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTM 193


>gi|238882041|gb|EEQ45679.1| hypothetical protein CAWG_04010 [Candida albicans WO-1]
          Length = 613

 Score = 38.9 bits (89), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 41/167 (24%), Positives = 70/167 (41%), Gaps = 34/167 (20%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPA 133
           +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPVTVK R G+ +    
Sbjct: 330 SELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPVTVKIRTGIKEGKNT 389

Query: 134 VALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI---------- 182
               NLV  + + G    I +H R         +  R     D++ + E+          
Sbjct: 390 AV--NLVSRVLEEGNAAAITLHGRS--------RQQRYSKEADWNYIAEVGTVVKNWNEQ 439

Query: 183 -------KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
                  +  +P  F+G NG +   ED  + +     +D VM+ R A
Sbjct: 440 QKEDKEGRDRDPVYFVG-NGDVYSHEDWYEHVNT-DGIDSVMVARGA 484


>gi|68466823|ref|XP_722607.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68467102|ref|XP_722466.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|74587613|sp|Q5ALL3|DUS3_CANAL RecName: Full=tRNA-dihydrouridine synthase 3
 gi|46444444|gb|EAL03719.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46444594|gb|EAL03868.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
          Length = 613

 Score = 38.9 bits (89), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 41/167 (24%), Positives = 70/167 (41%), Gaps = 34/167 (20%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPA 133
           +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPVTVK R G+ +    
Sbjct: 330 SELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPVTVKIRTGIKEGKNT 389

Query: 134 VALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI---------- 182
               NLV  + + G    I +H R         +  R     D++ + E+          
Sbjct: 390 AV--NLVSRVLEEGNAAAITLHGRS--------RQQRYSKEADWNYIAEVGTVVKNWNEQ 439

Query: 183 -------KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
                  +  +P  F+G NG +   ED  + +     +D VM+ R A
Sbjct: 440 QKEDKEGRDRDPVYFVG-NGDVYSHEDWYEHVNT-DGIDSVMVARGA 484


>gi|322505439|emb|CAM42636.2| putative dihydrouridine synthase (Dus) [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 666

 Score = 38.9 bits (89), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +++ G+ +    E   +   +  + ++LN+GCP      G +G+ LM + + +   +
Sbjct: 259 PVPVRVNGSSL----EEEPVHRLYQCDAVDLNLGCPQGIARRGHYGSFLMEDWESIHTIV 314

Query: 109 AAMCKALSIPVTVKCRI 125
             +   L +PVTVK R+
Sbjct: 315 HTLHVELEVPVTVKIRV 331


>gi|291484106|dbj|BAI85181.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. natto
           BEST195]
          Length = 311

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 51/210 (24%), Positives = 94/210 (44%), Gaps = 34/210 (16%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARV 88
           D++L  +   +  F T   P+   + G+ +   VE A+ I +    + + LN+ CP+ + 
Sbjct: 77  DSVLHNELPWLEQFDT---PIIANVAGSQVEDYVEVAEHISKAPNVHALELNISCPNVKT 133

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              +FG     NP++  D   A+ +  ++PV VK    V + I  +AL     +I+++G 
Sbjct: 134 GGIAFGT----NPEMAADLTKAVKEVSNVPVYVKLSPNVAN-ITEIAL-----AIEEAGA 183

Query: 149 NGIW-----------IHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G+            +   K IL     GLS      +  +   +VYE+ +      IG+
Sbjct: 184 DGLTMINTLIGMRLDLKTGKPILANKTGGLS---GPAVKPVAIRMVYEVSQVVNIPIIGM 240

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
            GG++    AL+ +L     V +G A + N
Sbjct: 241 -GGVQTAEDALEFLLAGASAVAVGTANFVN 269


>gi|281356662|ref|ZP_06243153.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
 gi|281316789|gb|EFB00812.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
          Length = 288

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 41/189 (21%), Positives = 86/189 (45%), Gaps = 18/189 (9%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     +  AA    + G   INLN GCPS +V  G  G   + +   +   +
Sbjct: 48  PVTVQLMGNRPEVIAAAAARFMELGAAGINLNFGCPSRQVTSGGAGGGALRDLAGMVTTV 107

Query: 109 AAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHAR--KAILKGLS 164
             + KA+ + P++VK R G +       ++ ++ ++ ++G V+  ++H R  +   + +S
Sbjct: 108 ETVKKAIPASPLSVKLRTGWESPD---EMQRILPALAETGCVSAFFLHFRTVREQYRPVS 164

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKN 222
            ++ R      ++    +    P   + LNG ++    A ++L      GVM  R   ++
Sbjct: 165 GREER------FEAGLRLAAPVP---VVLNGDIDSPDDASELLERTGAAGVMCARGWLRD 215

Query: 223 SAMLTTVDE 231
             +L  + +
Sbjct: 216 PLLLNRIRQ 224


>gi|71013186|ref|XP_758561.1| hypothetical protein UM02414.1 [Ustilago maydis 521]
 gi|46098219|gb|EAK83452.1| hypothetical protein UM02414.1 [Ustilago maydis 521]
          Length = 477

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 27/108 (25%), Positives = 52/108 (48%), Gaps = 5/108 (4%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q   +      +A++++  F  + ++LN GCP    +E   G+ L+  P+ V D + 
Sbjct: 169 LVAQFASSKPEPFADASELIGRF-VDGVDLNCGCPQPWAYEELLGSYLLRQPETVRDMVR 227

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRN-LVKSIKKSGVNGIWIHAR 156
           A+   +     V  +I +D   P + L + LV++   +G + + IH R
Sbjct: 228 AVKARMGSDFCVSVKIRID---PDLRLTDALVRNALHAGASILQIHGR 272


>gi|227551412|ref|ZP_03981461.1| dihydroorotate oxidase [Enterococcus faecium TX1330]
 gi|257887479|ref|ZP_05667132.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,141,733]
 gi|257895974|ref|ZP_05675627.1| dihydroorotate dehydrogenase [Enterococcus faecium Com12]
 gi|293377432|ref|ZP_06623634.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium PC4.1]
 gi|293570484|ref|ZP_06681539.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E980]
 gi|227179421|gb|EEI60393.1| dihydroorotate oxidase [Enterococcus faecium TX1330]
 gi|257823533|gb|EEV50465.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,141,733]
 gi|257832539|gb|EEV58960.1| dihydroorotate dehydrogenase [Enterococcus faecium Com12]
 gi|291609430|gb|EFF38697.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E980]
 gi|292643950|gb|EFF62058.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium PC4.1]
          Length = 310

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 13/109 (11%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     VE  +KI E      I LN+ CP+ + H G +FG     +PD+ 
Sbjct: 96  ELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCPNVK-HGGIAFGT----DPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +
Sbjct: 151 FQLTQAVKKVASVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTM 193


>gi|300175488|emb|CBK20799.2| unnamed protein product [Blastocystis hominis]
          Length = 562

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 95/224 (42%), Gaps = 28/224 (12%)

Query: 24  TEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLN 80
           +EM +   +L+G      +L     E+   +QI      +  + A+++  +F  + ++LN
Sbjct: 236 SEMAITTNLLKGQVSEWALLRRHPCERVFGVQIATGRPDEARKTAELLRREFRCDFLDLN 295

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNL 139
            GCP   + +   GA LM +P  +   +  +   A ++PV  K R G  +     +L   
Sbjct: 296 CGCPIDVLDKMGAGAALMGHPSKLRRILTGVLDGAETLPVVCKLRTGDREN----SLEKF 351

Query: 140 VKSI------KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI----KKENPDL 189
           V S+      + + V+ + IH R  +         R     D++ V +     K+   D+
Sbjct: 352 VGSLAALQGRRGNRVSALTIHGRTKV--------GRYTKLADWEYVEKCAALAKQSASDV 403

Query: 190 FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
            +  NG + D     + L S  + GVMIGR A     + T + E
Sbjct: 404 QVIGNGDVFDHEMYYEHLQSGVLSGVMIGRGALIKPWICTEIKE 447


>gi|50554001|ref|XP_504409.1| YALI0E26048p [Yarrowia lipolytica]
 gi|74633334|sp|Q6C4K3|DUS3_YARLI RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49650278|emb|CAG80010.1| YALI0E26048p [Yarrowia lipolytica]
          Length = 622

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 3/86 (3%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           T+     +Q+      + ++AA+ V +   G +EINLN GCP   V+    G+ LM    
Sbjct: 303 TEGNHFGVQVTAPKHWQAIKAAQAVSELCTGISEINLNCGCPIDLVYRQGAGSALMDQQG 362

Query: 103 IVGDCIAAMCK-ALSIPVTVKCRIGV 127
                +  M   +  +P+TVK R G 
Sbjct: 363 KTARIVRGMSMVSGDVPITVKMRTGT 388


>gi|296109015|ref|YP_003615964.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           infernus ME]
 gi|295433829|gb|ADG13000.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           infernus ME]
          Length = 302

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 45/183 (24%), Positives = 75/183 (40%), Gaps = 29/183 (15%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            I G D  +  E AK +ED+  + I LN+ CP A+     +GA +  +P++      A+ 
Sbjct: 100 SIYGKDEDEFREVAKKIEDY-VDIIELNISCPHAK----GYGATIGQDPELSYKVCKAVK 154

Query: 113 KALSIPVTVK-----------CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + +PV  K               VD ++      N V+ +K      I I A++ IL 
Sbjct: 155 EEVKVPVFAKLTPNVSNILEIAEALVDAKVDGFVAINTVRGMK------IDIKAKRPILS 208

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               GLS    + I  +   IVY++ +      IG+ G          ++     V +G 
Sbjct: 209 NKFGGLS---GKAIKPIGVKIVYDLYENFDKPIIGVGGIFTGEDAIEYMMAGASAVQVGS 265

Query: 218 AAY 220
           A Y
Sbjct: 266 AVY 268


>gi|323339843|ref|ZP_08080112.1| dihydroorotate oxidase [Lactobacillus ruminis ATCC 25644]
 gi|323092716|gb|EFZ35319.1| dihydroorotate oxidase [Lactobacillus ruminis ATCC 25644]
          Length = 311

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 34/128 (26%), Positives = 59/128 (46%), Gaps = 22/128 (17%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG+     VE A  +   GY + + LN+ CP+ +    +FG      P++    
Sbjct: 97  PIIGSVGGSSEEDYVEVASRLSQSGYVDALELNISCPNVKKGGMAFGTV----PEVAKKL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              + KA S+PV VK    V D + A+A     K++++ G +G           I +  R
Sbjct: 153 TEEVKKASSVPVYVKLSPNVTD-VCAIA-----KAVEEGGADGLTMINTLLGMHIDLKTR 206

Query: 157 KAILKGLS 164
           K++L  L+
Sbjct: 207 KSVLGNLT 214


>gi|148544533|ref|YP_001271903.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri DSM 20016]
 gi|184153896|ref|YP_001842237.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri JCM 1112]
 gi|227363039|ref|ZP_03847176.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri MM2-3]
 gi|325682854|ref|ZP_08162370.1| dihydroorotate dehydrogenase [Lactobacillus reuteri MM4-1A]
 gi|148531567|gb|ABQ83566.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           DSM 20016]
 gi|183225240|dbj|BAG25757.1| putative oxidoreductase [Lactobacillus reuteri JCM 1112]
 gi|227071923|gb|EEI10209.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri MM2-3]
 gi|324977204|gb|EGC14155.1| dihydroorotate dehydrogenase [Lactobacillus reuteri MM4-1A]
          Length = 432

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 34/129 (26%), Positives = 58/129 (44%), Gaps = 10/129 (7%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G  +      AK+V + G + I LN  CP    H  + G+ +  NP++    
Sbjct: 104 KVLIASIMGETLEDWTNLAKLVTETGADMIELNFSCPQMTSH--TMGSDVGTNPELCKKN 161

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILKGLSPK 166
             A+ +  S+PV  K    +   +P      +VK+  + G +G   I+  K+I+  +  K
Sbjct: 162 CEAVKRGTSLPVLAKMTPNITTMVP------VVKACLEGGADGFSAINTVKSIVD-VDLK 214

Query: 167 DNRKIPNLD 175
               +PN+D
Sbjct: 215 KKVGLPNID 223


>gi|221119232|ref|XP_002164620.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 556

 Score = 38.9 bits (89), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 10/87 (11%)

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVD---KDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           ++   +E F N  T ++  + R+D   K FWRK   +  D+  RH++S    +Q T+H  
Sbjct: 363 LIPLTNEKF-NFKTANTNDEARLDIKAKGFWRKEETAFFDFRVRHVNSKSSKKQPTKH-- 419

Query: 282 GLFHGFPNSRRCRH---ILTVEAGAST 305
            +F    ++++C +   +L VE G  T
Sbjct: 420 -IFRRHEDAKKCEYLERVLEVEHGTFT 445


>gi|255078812|ref|XP_002502986.1| predicted protein [Micromonas sp. RCC299]
 gi|226518252|gb|ACO64244.1| predicted protein [Micromonas sp. RCC299]
          Length = 361

 Score = 38.9 bits (89), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 34/142 (23%), Positives = 65/142 (45%), Gaps = 11/142 (7%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLN 80
           +EM +A  IL+G++  +  L     E+   +Q+ G     +    + ++ D   + +++N
Sbjct: 36  SEMAMASNILKGERSELALLRRHPSERLFGVQVCGGHPDLMARCGEFLDNDVDCDFVDVN 95

Query: 81  VGCPSARVHEGSFGACLMLNPDIVG-----DCIAAMCKALS-IPVTVKCRIGVDDQIPAV 134
           +GCP   V     G+ L+   D VG       + AM  ++   P+T+K R+G DD     
Sbjct: 96  MGCPIDGVCAKGAGSTLLR--DEVGLARMKKLVQAMSGSMQRTPLTIKVRMGYDDDPSKY 153

Query: 135 ALRNLVKSIKKSGVNGIWIHAR 156
              +++K  +  G     +H R
Sbjct: 154 VAHDVLKDARAWGAAAATLHGR 175


>gi|194466721|ref|ZP_03072708.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
 gi|227543869|ref|ZP_03973918.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           CF48-3A]
 gi|300909615|ref|ZP_07127076.1| dihydroorotate dehydrogenase [Lactobacillus reuteri SD2112]
 gi|157805448|gb|ABV80266.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri]
 gi|194453757|gb|EDX42654.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
 gi|227186130|gb|EEI66201.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           CF48-3A]
 gi|300893480|gb|EFK86839.1| dihydroorotate dehydrogenase [Lactobacillus reuteri SD2112]
          Length = 432

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 34/129 (26%), Positives = 58/129 (44%), Gaps = 10/129 (7%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G  +      AK+V + G + I LN  CP    H  + G+ +  NP++    
Sbjct: 104 KVLIASIMGETLEDWTNLAKLVTEAGADMIELNFSCPQMTSH--TMGSDVGTNPELCKKN 161

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILKGLSPK 166
             A+ +  S+PV  K    +   +P      +VK+  + G +G   I+  K+I+  +  K
Sbjct: 162 CEAVKRGTSLPVLAKMTPNITTMVP------VVKACLEGGADGFSAINTVKSIVD-VDLK 214

Query: 167 DNRKIPNLD 175
               +PN+D
Sbjct: 215 KKVGLPNID 223


>gi|293553495|ref|ZP_06674123.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1039]
 gi|291602372|gb|EFF32596.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1039]
          Length = 310

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 13/109 (11%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     VE  +KI E      I LN+ CP+ + H G +FG     +PD+ 
Sbjct: 96  ELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCPNVK-HGGIAFGT----DPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTM 193


>gi|241950946|ref|XP_002418195.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223641534|emb|CAX43495.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 613

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 40/166 (24%), Positives = 68/166 (40%), Gaps = 32/166 (19%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPA 133
           +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPVTVK R G+ +    
Sbjct: 330 SELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPVTVKIRTGIKEGKNT 389

Query: 134 VALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI---------- 182
               NLV  +   G    I +H R         +  R     D++ + E+          
Sbjct: 390 AV--NLVSRVLDEGNAAAITLHGRS--------RQQRYSKEADWNYIAEVGTVVKNWNEQ 439

Query: 183 -------KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
                  +  +P  F+G NG +       K + +  +D VM+ R A
Sbjct: 440 QKEDKEARDRDPVYFVG-NGDVYSHEDWYKHVNTEGIDSVMVARGA 484


>gi|261207811|ref|ZP_05922496.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium TC 6]
 gi|289566263|ref|ZP_06446695.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium D344SRF]
 gi|294616602|ref|ZP_06696378.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1636]
 gi|294617882|ref|ZP_06697491.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1679]
 gi|260078194|gb|EEW65900.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium TC 6]
 gi|289161970|gb|EFD09838.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium D344SRF]
 gi|291590552|gb|EFF22285.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1636]
 gi|291595827|gb|EFF27111.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1679]
          Length = 310

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 13/109 (11%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     VE  +KI E      I LN+ CP+ + H G +FG     +PD+ 
Sbjct: 96  ELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCPNVK-HGGIAFGT----DPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTM 193


>gi|297792133|ref|XP_002863951.1| hypothetical protein ARALYDRAFT_917859 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297309786|gb|EFH40210.1| hypothetical protein ARALYDRAFT_917859 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 758

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 36/59 (61%), Gaps = 1/59 (1%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +  Q+G +D  + ++AA+IV +     +++N+GCP A   +G  GA L+  P+++ D I
Sbjct: 78  VVFQMGTSDAVRALKAAEIVCN-DVATVDINMGCPKAFSIQGGMGAALLSKPELIHDPI 135


>gi|194467523|ref|ZP_03073510.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
 gi|194454559|gb|EDX43456.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
          Length = 308

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 44/178 (24%), Positives = 80/178 (44%), Gaps = 35/178 (19%)

Query: 64  EAAKIVEDF----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
           E  K+V +F    G   I LNV CP+ +      G  +  +P+++   +  + K AL IP
Sbjct: 112 EYVKVVSEFANTAGVKAIELNVSCPNVK----HGGMAMGTDPEVLQRLVKQVVKAALGIP 167

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK----GL 163
           + VK    V + +P      L ++ ++ G NG           I +  R+  L     GL
Sbjct: 168 IYVKLTPNVTNIVP------LAQAAEQGGANGLTMINTLTGLSIDLKTRRPALANVTGGL 221

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           S      I  L   +++++++ +    IG+ GG+E     L+ ++   + V IG A++
Sbjct: 222 S---GPAIKPLALRMIHQVRQVSSLPIIGV-GGIESAEDVLEFMMAGANAVQIGAASF 275


>gi|332297694|ref|YP_004439616.1| dihydrouridine synthase DuS [Treponema brennaborense DSM 12168]
 gi|332180797|gb|AEE16485.1| dihydrouridine synthase DuS [Treponema brennaborense DSM 12168]
          Length = 345

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 53/115 (46%), Gaps = 12/115 (10%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY--D 177
           +VK R+G D+        + +  +  +GV  I +H R    +  +P      P L+Y   
Sbjct: 153 SVKIRLG-DEDFTDDRFFSFIDMLVGTGVRQITLHPRTRKERYRTP------PRLEYVRK 205

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK---ILPSVDGVMIGRAAYKNSAMLTTV 229
           +   +     D+ + LNG + D + A K   I P+VDG+MI RAA +   +   +
Sbjct: 206 LCDYLNARGSDVKVVLNGAVCDAASARKAYEIAPAVDGIMIARAAIRKPWVFAEI 260


>gi|15679224|ref|NP_276341.1| dihydroorotate dehydrogenase 1B [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|3914506|sp|O27281|PYRD_METTH RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|2622323|gb|AAB85702.1| dihydroorotate oxidase [Methanothermobacter thermautotrophicus str.
           Delta H]
          Length = 303

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +E PL   + GA   +   AA  VE++  + I LNV CP A       GA +  +P++  
Sbjct: 91  EEVPLIASVYGASPEEFASAAASVEEYA-DMIELNVSCPHAM---AGCGASIGQDPELTF 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQI 131
             ++A+  A+ +P++ K    V D +
Sbjct: 147 RVVSAVKDAVDVPISTKLTPNVTDIV 172


>gi|91773205|ref|YP_565897.1| dihydroorotate dehydrogenase 1B [Methanococcoides burtonii DSM
           6242]
 gi|91712220|gb|ABE52147.1| Dihydroorotate dehydrogenase, catalytic subunit [Methanococcoides
           burtonii DSM 6242]
          Length = 300

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 47/107 (43%), Gaps = 14/107 (13%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           S  + P+   I G +    V+ A+ + D       LNV CP    H   +GA +  +  +
Sbjct: 86  SGTDVPVIASIFGGNAEDFVKVAEGLADSEPAAFELNVSCP----HAEGYGATIGTDTCM 141

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           V    AA+C A+ +PV VK    V D          +K+I K+  NG
Sbjct: 142 VESITAAVCDAVDVPVWVKLTPNVTD----------IKAIGKAAQNG 178


>gi|148543364|ref|YP_001270734.1| dihydroorotate dehydrogenase 1B [Lactobacillus reuteri DSM 20016]
 gi|184152774|ref|YP_001841115.1| dihydroorotate dehydrogenase 1B [Lactobacillus reuteri JCM 1112]
 gi|227364438|ref|ZP_03848528.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           MM2-3]
 gi|325683637|ref|ZP_08163153.1| dihydroorotate oxidase [Lactobacillus reuteri MM4-1A]
 gi|189038428|sp|A5VHS3|PYRD_LACRD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|229470318|sp|B2G5A3|PYRD_LACRJ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|148530398|gb|ABQ82397.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           DSM 20016]
 gi|183224118|dbj|BAG24635.1| dihydroorotate dehydrogenase [Lactobacillus reuteri JCM 1112]
 gi|227070531|gb|EEI08864.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           MM2-3]
 gi|324977987|gb|EGC14938.1| dihydroorotate oxidase [Lactobacillus reuteri MM4-1A]
          Length = 308

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 81/178 (45%), Gaps = 35/178 (19%)

Query: 64  EAAKIVEDF----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
           E  K+V +F    G   I LNV CP+  V  G  G  +  +P+++   +  + K AL IP
Sbjct: 112 EYVKVVSEFANTAGVKAIELNVSCPN--VKHG--GMAMGTDPEVLQRLVKQVVKAALGIP 167

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK----GL 163
           + VK    V + +P      L ++ ++ G NG           I +  R+  L     GL
Sbjct: 168 IYVKLTPNVTNIVP------LAQAAEQGGANGLTMINTLTGLSIDLKTRRPALANVTGGL 221

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           S      I  L   +++++++ +    IG+ GG+E     L+ ++   + V IG A++
Sbjct: 222 S---GPAIKPLALRMIHQVRQVSSLPIIGV-GGIESAEDVLEFMMAGANAVQIGAASF 275


>gi|66358006|ref|XP_626181.1| Ylr401cp-like protein with 2 CCCH domains plus Dus1p tRNA
           dihydrouridine synthase Tim barrel [Cryptosporidium
           parvum Iowa II]
 gi|46227017|gb|EAK87967.1| Ylr401cp-like protein with 2 CCCH domains plus Dus1p tRNA
           dihydrouridine synthase Tim barrel [Cryptosporidium
           parvum Iowa II]
          Length = 707

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 30/111 (27%), Positives = 55/111 (49%), Gaps = 12/111 (10%)

Query: 24  TEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLN 80
           +EM++ + IL G    +  L  S +EK   +Q+ G + S +++  + + E   ++ I++N
Sbjct: 345 SEMVLCNEILSGKASELALLKKSPEEKYFGIQLAGGNKSTIIKTGEFINEHCEFDFIDIN 404

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-----VTVKCRIG 126
             CP   +H+   G+ L+   D V + +  M K L        VTVK R+ 
Sbjct: 405 AACPLKSLHDKGAGSILV---DRVSE-LETMVKGLKKVMDGKLVTVKVRMS 451


>gi|321315319|ref|YP_004207606.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis BSn5]
 gi|320021593|gb|ADV96579.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis BSn5]
          Length = 311

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 50/206 (24%), Positives = 92/206 (44%), Gaps = 32/206 (15%)

Query: 47  EKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +   VE A+ I +    + + LN+ CP+ +    +FG     NP++  
Sbjct: 91  DTPIIANVAGSQVDDYVEVAEHISKAPNVHALELNISCPNVKTGGIAFGT----NPEMAA 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           D   A+ +   +PV VK    V + I  +AL     +I+++G +G+            + 
Sbjct: 147 DLTKAVKEVSDVPVYVKLSPNVAN-ITEIAL-----AIEEAGADGLTMINTLIGMRLDLK 200

Query: 155 ARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
             K IL     GLS      +  +   +VYE+ +      IG+ GG++    AL+ +L  
Sbjct: 201 TGKPILANKTGGLS---GPAVKPVAIRMVYEVSQAVNIPIIGM-GGVQTAEDALEFLLAG 256

Query: 210 VDGVMIGRAAYKNS-AMLTTVDEYFS 234
              V +G A + N  A L  +++  S
Sbjct: 257 ASAVAVGTANFVNPFACLEIIEQLPS 282


>gi|303278554|ref|XP_003058570.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459730|gb|EEH57025.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 430

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 32/139 (23%), Positives = 60/139 (43%), Gaps = 9/139 (6%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-----GYNEI 77
           EM +   +L+G      +L     E    +QI G     +   +++++D      G + +
Sbjct: 93  EMAMCTNLLQGQPNEWALLRRHPSEDLFGVQICGGYSDSVARCSQLIDDVIVSQGGCDFV 152

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
           ++N+GCP   V     G+ L+   + +     +    LS P+T+K R G  D        
Sbjct: 153 DINMGCPIDLVCNKGGGSMLLERHNRMEQIARSASSLLSCPLTLKTRTGYYDN--KRVAH 210

Query: 138 NLVKSIKKSGVNGIWIHAR 156
           ++V  +K  GV  + +H R
Sbjct: 211 DIVPKLKDWGVAAVTLHGR 229


>gi|227543831|ref|ZP_03973880.1| dihydroorotate oxidase [Lactobacillus reuteri CF48-3A]
 gi|300908899|ref|ZP_07126362.1| dihydroorotate oxidase [Lactobacillus reuteri SD2112]
 gi|112943111|gb|ABI26297.1| dihydroorotate dehydrogenase [Lactobacillus reuteri]
 gi|227186208|gb|EEI66279.1| dihydroorotate oxidase [Lactobacillus reuteri CF48-3A]
 gi|300894306|gb|EFK87664.1| dihydroorotate oxidase [Lactobacillus reuteri SD2112]
          Length = 308

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 44/178 (24%), Positives = 80/178 (44%), Gaps = 35/178 (19%)

Query: 64  EAAKIVEDF----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
           E  K+V +F    G   I LNV CP+ +      G  +  +P+++   +  + K AL IP
Sbjct: 112 EYVKVVSEFANTAGVKAIELNVSCPNVK----HGGMAMGTDPEVLQRLVKQVVKAALGIP 167

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK----GL 163
           + VK    V + +P      L ++ ++ G NG           I +  R+  L     GL
Sbjct: 168 IYVKLTPNVTNIVP------LAQAAEEGGANGLTMINTLTGLSIDLKTRRPALANVTGGL 221

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           S      I  L   +++++++ +    IG+ GG+E     L+ ++   + V IG A++
Sbjct: 222 S---GPAIKPLALRMIHQVRQVSSLPIIGV-GGIESAEDVLEFMMAGANAVQIGAASF 275


>gi|213029657|ref|ZP_03344104.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 153

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 37/147 (25%), Positives = 63/147 (42%), Gaps = 23/147 (15%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNG 150
           G+ L+  PD+V   +  +  A+ +PVT+K R G      A   RN V+  + +   G+  
Sbjct: 7   GSALLQYPDLVKSILIGVVNAVDVPVTLKIRTGW-----APEHRNCVEIAQLAEDCGIQA 61

Query: 151 IWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + IH R    +  G            +YD +  +K++     I  NG + +  +A  +L 
Sbjct: 62  LTIHGRTRACLFNG----------EAEYDSIRAVKQKVSIPIIA-NGDITNPHKARAVLD 110

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
               D +MIGRAA     +   +  Y 
Sbjct: 111 YTGADALMIGRAAQGRPWIFREIQHYL 137


>gi|119720067|ref|YP_920562.1| dihydroorotate dehydrogenase family protein [Thermofilum pendens
           Hrk 5]
 gi|119525187|gb|ABL78559.1| dihydroorotate oxidase B, catalytic subunit [Thermofilum pendens
           Hrk 5]
          Length = 299

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 89/200 (44%), Gaps = 33/200 (16%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           ILR + + +LG      P+   IG +   + +  A+ +E  G++ + LN  CP    H  
Sbjct: 84  ILR-EARRVLGI-----PVIASIGASTPDEALRIAEALE--GFDALELNASCP----HVK 131

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG- 150
             GA LM +PD V   ++A+ K+    V +K         P      + +    +GV+G 
Sbjct: 132 GLGADLMSDPDAVYGIVSAL-KSSGYRVFLKLS-------PHGDYLAVARKAYSAGVDGF 183

Query: 151 ----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
                     I ++ARK  +   +     R I  +   +VYE+ +E P++ +   GG+E 
Sbjct: 184 TAINTAKAMVIDVYARKPVLGGVVGGLSGRAIHPIAVRVVYELHREFPEVPVIGTGGVEG 243

Query: 200 MSQALK-ILPSVDGVMIGRA 218
             +A++ IL     V +G A
Sbjct: 244 WVEAVELILAGASAVGVGTA 263


>gi|322387775|ref|ZP_08061384.1| dihydroorotate dehydrogenase B [Streptococcus infantis ATCC 700779]
 gi|321141642|gb|EFX37138.1| dihydroorotate dehydrogenase B [Streptococcus infantis ATCC 700779]
          Length = 327

 Score = 38.1 bits (87), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 52/113 (46%), Gaps = 21/113 (18%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 119 NVAGFSKQEY--------AAVSSGISKAPNVK-----AIELNISCPN--VDHGNHGLLIG 163

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            +PD+    + A   A S+PV VK    V D +       + K+++ +G +G+
Sbjct: 164 QDPDLAYVVVKAAVGASSVPVYVKLTPSVTDIV------TIAKAVEDAGASGL 210


>gi|157692234|ref|YP_001486696.1| dihydroorotate dehydrogenase 1B [Bacillus pumilus SAFR-032]
 gi|167011966|sp|A8FD19|PYRD_BACP2 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|157680992|gb|ABV62136.1| dihydroorotate oxidase [Bacillus pumilus SAFR-032]
          Length = 310

 Score = 38.1 bits (87), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 59/276 (21%), Positives = 115/276 (41%), Gaps = 38/276 (13%)

Query: 1   MVDWTDRHYRF---FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGG 56
           M+  T    RF     R+    A +   + + +  L+G  +N L +  Q + P+   + G
Sbjct: 41  MIKATTLEPRFGNPTPRVAETGAGMLNAIGLQNPGLKGVLENELPWLEQFDTPIIANVAG 100

Query: 57  ADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           + +   VE A +I +    + + LN+ CP+ +    +FG     +P +      A+    
Sbjct: 101 SQVDDYVEVAEQISQAKNVHALELNISCPNVKTGGIAFGT----DPQMAAALTKAVKDVS 156

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK--- 161
           S+PV VK    V + +       + ++I+ +G +G+            +   K IL    
Sbjct: 157 SVPVYVKLSPNVANIV------EIAQAIESAGADGLTMINTLIGMRLDLKTGKPILANKT 210

Query: 162 -GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            GLS      I  +   +V+E+ +      IG+ GG+++    L+ +L     V +G A 
Sbjct: 211 GGLS---GPAIKPVAVRMVHEVSQAVSIPIIGM-GGVQNAEDVLEFLLAGASAVAVGTAN 266

Query: 220 YKNSAMLTTVDEYFSNPLT--GSSPIKTRVDKDFWR 253
           + N  +   + E   N L   G S ++  + +  W+
Sbjct: 267 FVNPFICPEIIEELPNVLAAYGYSSVEECIGRS-WK 301


>gi|47207088|emb|CAF94223.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 176

 Score = 38.1 bits (87), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 4/63 (6%)

Query: 43  FSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           F T EK    +  Q+G AD  + +  A++VE      I++N+GCP     +G  GA L+ 
Sbjct: 72  FRTCEKEKNKVVFQMGTADPDRALTVAQLVER-DVAAIDVNMGCPKEYSTKGGMGAALLS 130

Query: 100 NPD 102
           +PD
Sbjct: 131 DPD 133


>gi|154342528|ref|XP_001567212.1| dihydrouridine synthase (Dus) [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 666

 Score = 38.1 bits (87), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +++ G+ + +  E       +  + ++LN+GCP      G +G+ LM + + +   +
Sbjct: 259 PVPVRVNGSSLEEEPEHRL----YQCDAVDLNLGCPQGIARRGHYGSFLMEDWESIHTIV 314

Query: 109 AAMCKALSIPVTVKCRI 125
             +   L +PVTVK R+
Sbjct: 315 HTLHVELEVPVTVKIRV 331


>gi|218512468|ref|ZP_03509308.1| tRNA-dihydrouridine synthase protein [Rhizobium etli 8C-3]
          Length = 204

 Score = 38.1 bits (87), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 33/112 (29%), Positives = 53/112 (47%), Gaps = 13/112 (11%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I A  KA+ IPVT+K R+G D+   ++   ++ +  + +G+  + IH R      +   D
Sbjct: 6   IEATVKAVDIPVTLKMRLGWDEN--SINAPDIARRAEAAGIQLVTIHGRTR----MQFYD 59

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
            R     D+D +  ++       I  NG +E    A +IL     D VMIGR
Sbjct: 60  GRA----DWDAIRAVRDVISIPLIA-NGDVETAEDAQEILRRSGADAVMIGR 106


>gi|310780263|ref|YP_003968595.1| dihydroorotate oxidase B, catalytic subunit [Ilyobacter polytropus
           DSM 2926]
 gi|309749586|gb|ADO84247.1| dihydroorotate oxidase B, catalytic subunit [Ilyobacter polytropus
           DSM 2926]
          Length = 306

 Score = 37.7 bits (86), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G  I + VE AK VE       I LN+ CP+ +    +FGA     P++ G  
Sbjct: 96  PIITNINGRTIEEYVEIAKRVESIEAVKAIELNISCPNVKDGGMAFGA----RPEVAGAV 151

Query: 108 IAAMCKALSIPVTVKCRIGVDD 129
             A+ +  + PV VK    V D
Sbjct: 152 TKAVKEVTTKPVIVKLSPNVTD 173


>gi|56964096|ref|YP_175827.1| dihydroorotate dehydrogenase catalytic subunit [Bacillus clausii
           KSM-K16]
 gi|81822095|sp|Q5WFJ4|PYRD_BACSK RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|56910339|dbj|BAD64866.1| dihydroorotate dehydrogenase catalytic subunit [Bacillus clausii
           KSM-K16]
          Length = 304

 Score = 37.7 bits (86), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 30/110 (27%), Positives = 54/110 (49%), Gaps = 11/110 (10%)

Query: 43  FSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           F   + P+   I G+ +   +E AA++ +    + I LN+ CP+ +    +FG      P
Sbjct: 89  FDDYDVPILANIAGSTMDDYIEVAAELSQQRNVSAIELNISCPNVKQGGIAFGTV----P 144

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           +I  +    +    ++PV VK    V D I A+A     K+I+K+G +G+
Sbjct: 145 EIAAELTKEVKAVSAVPVYVKLSPNVAD-IVAIA-----KAIEKAGADGL 188


>gi|302853480|ref|XP_002958255.1| hypothetical protein VOLCADRAFT_69189 [Volvox carteri f.
           nagariensis]
 gi|300256443|gb|EFJ40709.1| hypothetical protein VOLCADRAFT_69189 [Volvox carteri f.
           nagariensis]
          Length = 252

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 34/137 (24%), Positives = 57/137 (41%), Gaps = 28/137 (20%)

Query: 35  GDKKNILGFSTQ--EKP-LALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHE 90
           G++   L F T   E+P L  Q+G A+    + A  +V  D G   +++N+GCP     +
Sbjct: 63  GEQGGRLMFRTSASERPRLVFQLGTAEAVGALRAVSVVAGDVG--ALDVNMGCPKQFSLQ 120

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G  GA L+  P++                     +G+DD    V    L + +   GV+ 
Sbjct: 121 GGMGAALLRKPEVA-------------------EVGLDDPRDTV---ELARRLGACGVSA 158

Query: 151 IWIHARKAILKGLSPKD 167
           I +H R    +   P +
Sbjct: 159 IAVHGRTTQQRPRDPAN 175


>gi|51892398|ref|YP_075089.1| dihydroorotate dehydrogenase catalytic subunit [Symbiobacterium
           thermophilum IAM 14863]
 gi|51856087|dbj|BAD40245.1| dihydroorotate dehydrogenase catalytic subunit [Symbiobacterium
           thermophilum IAM 14863]
          Length = 306

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 41/204 (20%), Positives = 82/204 (40%), Gaps = 28/204 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q   + + I G  + + V  A+ +E  G   + LN+ CP+ +    +FG      P    
Sbjct: 96  QGATVIVNIVGRTVEEYVAVARRLEGTGVAAVELNISCPNVKEGGMAFGT----TPGSAA 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
              AA+ KA ++P+ VK    V D +       + ++++ +G +G+ +      L+G+S 
Sbjct: 152 AVTAAVRKATTLPLIVKLSPNVADVV------AIARAVEDAGADGLSV---INTLQGMSI 202

Query: 166 KDNRKIPNLD---------------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
              R  P+L                  +V+++        IG+ G +     A  ++   
Sbjct: 203 DIRRGRPHLGNVFGGLSGPAIKPVALRMVWQVAGAVKVPVIGVGGIMSGEDAAEFLMAGA 262

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFS 234
             V +G A + +     T+ E  +
Sbjct: 263 SAVQVGTACFIDPRAPLTIAEELA 286


>gi|254880956|ref|ZP_05253666.1| nifR3 family TIM-barrel protein [Bacteroides sp. 4_3_47FAA]
 gi|319639964|ref|ZP_07994691.1| nifR3 family TIM-barrel enzyme [Bacteroides sp. 3_1_40A]
 gi|254833749|gb|EET14058.1| nifR3 family TIM-barrel protein [Bacteroides sp. 4_3_47FAA]
 gi|317388242|gb|EFV69094.1| nifR3 family TIM-barrel enzyme [Bacteroides sp. 3_1_40A]
          Length = 305

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 51/242 (21%), Positives = 105/242 (43%), Gaps = 23/242 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  +  ++L   A +  + GY E ++N+GCP   +     G+ ++  P  V   +  + 
Sbjct: 63  QLIASTPAELERLAGLFIEKGYKEADINMGCPFPLMTGKHKGSGILPYPAEVEALLKELV 122

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRK 170
               +  +VK R+G +    A   R L+  +  + +  I +H R  K   KG       +
Sbjct: 123 HYPELGFSVKMRLGWEC---ADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-------E 172

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +    +   YE +  +P ++ G    +ED+ +  +  P ++GVM+GR    N A+     
Sbjct: 173 VDLAAFTAFYE-ECAHPLVYNGDLLTVEDIRKVDEEFPRLEGVMLGRGLLANPALAW--- 228

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           EY +  +     +  +V     + + A +  Y   HL   G++Q +++      +  P++
Sbjct: 229 EYANGAVFSPDELHEKV-----KALHARLLQYYEAHLQ--GEVQLLSKMKPYWEYLLPDA 281

Query: 291 RR 292
            R
Sbjct: 282 DR 283


>gi|157873334|ref|XP_001685179.1| dihydrouridine synthase (Dus) [Leishmania major strain Friedlin]
 gi|68128250|emb|CAJ08381.1| putative dihydrouridine synthase (Dus) [Leishmania major strain
           Friedlin]
          Length = 661

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 28/112 (25%), Positives = 52/112 (46%), Gaps = 18/112 (16%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGAD-------------ISKLVEAAKIVEDFGY- 74
           AD +LR  +  +LG   ++   A Q G +              ++ L  + K  E   Y 
Sbjct: 224 ADTVLRAARFAVLG---EQAAAAEQTGSSRGASAAPVYPVHVRVNGLSCSEKAPEHLLYQ 280

Query: 75  -NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            + +++N+GCP      G +G+ LM + +++   +  +   L +PVTVK R+
Sbjct: 281 CDAVDVNLGCPQGIARRGHYGSFLMEDWELIHTIVHTLHVELEVPVTVKIRV 332


>gi|16078618|ref|NP_389437.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309428|ref|ZP_03591275.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313753|ref|ZP_03595558.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318677|ref|ZP_03599971.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322949|ref|ZP_03604243.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|131720|sp|P25996|PYRD_BACSU RecName: Full=Dihydroorotate dehydrogenase, catalytic subunit;
           AltName: Full=DHOdehase; Short=DHOD; Short=DHODase;
           AltName: Full=Dihydroorotate oxidase
 gi|143392|gb|AAA21272.1| dihydroorotase dehydrogenase [Bacillus subtilis]
 gi|2633927|emb|CAB13428.1| dihydroorotate dehydrogenase (catalytic subunit) [Bacillus subtilis
           subsp. subtilis str. 168]
          Length = 311

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 51/210 (24%), Positives = 93/210 (44%), Gaps = 34/210 (16%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARV 88
           D++L  +   +  F T   P+   + G+ +   VE A+ I +    + + LN+ CP+ + 
Sbjct: 77  DSVLHHELPWLEQFDT---PIIANVAGSQVDDYVEVAEHISKAPNVHALELNISCPNVKT 133

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              +FG     NP++  D   A+ +   +PV VK    V + I  +AL     +I+++G 
Sbjct: 134 GGIAFGT----NPEMAADLTKAVKEVSDVPVYVKLSPNVAN-ITEIAL-----AIEEAGA 183

Query: 149 NGIW-----------IHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G+            +   K IL     GLS      +  +   +VYE+ +      IG+
Sbjct: 184 DGLTMINTLIGMRLDLKTGKPILANKTGGLS---GPAVKPVAIRMVYEVSQMVNIPIIGM 240

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
            GG++    AL+ +L     V +G A + N
Sbjct: 241 -GGVQTAEDALEFLLAGASAVAVGTANFVN 269


>gi|307708598|ref|ZP_07645062.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis NCTC 12261]
 gi|307615347|gb|EFN94556.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis NCTC 12261]
          Length = 312

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 47/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKAANVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            NPD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QNPDLAYDVVKAAVEASDVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|255085626|ref|XP_002505244.1| dihydrouridine synthase [Micromonas sp. RCC299]
 gi|226520513|gb|ACO66502.1| dihydrouridine synthase [Micromonas sp. RCC299]
          Length = 465

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 50/205 (24%), Positives = 87/205 (42%), Gaps = 23/205 (11%)

Query: 50  LALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           LA Q+ G++   L   A+ +    G   ++LN GCP+  V     G+ L+ +P  V    
Sbjct: 134 LAAQLMGSNEDLLERCARFLAHQGGAPRVDLNCGCPANVVTGKGAGSSLLRDPRDVEAMT 193

Query: 109 AAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A+ + ++     VTVK R G DD+     LR  + + +  G + + +H R    +G S 
Sbjct: 194 RAVARGVAGTGCAVTVKLRSGFDDR---GLLRENLLAAQAGGASFVTLHPRTRA-QGYSG 249

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNS 223
               +      D++         + +  NG +   + A K+L      GVMIGR A ++ 
Sbjct: 250 HAAWEDIGFAVDLL--------SVPVVGNGDVTSAALASKMLRDTGCAGVMIGRGAVQDP 301

Query: 224 AMLTTV-----DEYFSNPLTGSSPI 243
            +         DE F    +G + +
Sbjct: 302 LVFRRCRAALSDENFRRGTSGDASV 326


>gi|261332512|emb|CBH15507.1| tRNA-dihydrouridine synthase 2, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 435

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 57/119 (47%), Gaps = 12/119 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+G A+ +    AA +  D   + I++N+GCP     +   GA LM +P      +
Sbjct: 95  PVVLQLGVAEPAIGARAALLCVD-DVDGIDVNMGCPKKFSVDNGMGAALMRDPARAAAIL 153

Query: 109 AAMCKALS-----------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A+ +A++           +P++ K R+       A  L ++++ +    V+ I +HAR
Sbjct: 154 VAVDEAVNSPEKVVARRRRVPISFKTRLLDTADATAQMLLSVMEGVGPDRVHAITLHAR 212


>gi|511017|emb|CAA52280.1| dihydroorotate dehydrogenase B [Lactococcus lactis subsp. cremoris
           MG1363]
          Length = 311

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 29/107 (27%), Positives = 54/107 (50%), Gaps = 13/107 (12%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++ +  V   AKI +      I LN+ CP+ +    +FG     +P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDRANVKAIELNISCPNVKHGGQAFGT----DPEVAA 153

Query: 106 DCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             + A CKA+S +P+ VK    V D +P      + K+++ +G +G+
Sbjct: 154 ALVKA-CKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGL 193


>gi|71747358|ref|XP_822734.1| tRNA-dihydrouridine synthase 2 [Trypanosoma brucei TREU927]
 gi|70832402|gb|EAN77906.1| tRNA-dihydrouridine synthase 2, putative [Trypanosoma brucei]
          Length = 435

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 57/119 (47%), Gaps = 12/119 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ LQ+G A+ +    AA +  D   + I++N+GCP     +   GA LM +P      +
Sbjct: 95  PVVLQLGVAEPAIGARAALLCVD-DVDGIDVNMGCPKKFSVDNGMGAALMRDPARAAAIL 153

Query: 109 AAMCKALS-----------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            A+ +A++           +P++ K R+       A  L ++++ +    V+ I +HAR
Sbjct: 154 VAVDEAVNSPEKVVARRRRVPISFKTRLLDTADATAQMLLSVMEGVGPDRVHAITLHAR 212


>gi|257884643|ref|ZP_05664296.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,501]
 gi|257820481|gb|EEV47629.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,501]
          Length = 310

 Score = 37.7 bits (86), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 51/109 (46%), Gaps = 13/109 (11%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     VE  +KI E      I LN+ CP+ + H G +FG     +P++ 
Sbjct: 96  ELPIIANVAGACEEDYVEVCSKISEAPNVKAIELNISCPNVK-HGGIAFGT----DPEVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTM 193


>gi|150003817|ref|YP_001298561.1| nifR3 family TIM-barrel protein [Bacteroides vulgatus ATCC 8482]
 gi|149932241|gb|ABR38939.1| putative nifR3 family TIM-barrel enzyme [Bacteroides vulgatus ATCC
           8482]
          Length = 305

 Score = 37.7 bits (86), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 48/223 (21%), Positives = 95/223 (42%), Gaps = 21/223 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  +  ++L   A +  + GY E ++N+GCP   +     G+ ++  P  V   +  + 
Sbjct: 63  QLIASTPAELERLAGLFIEKGYKEADINMGCPFPLMTGKHKGSGILPYPAEVEALLKELV 122

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRK 170
               +  +VK R+G +    A   R L+  +  + +  I +H R  K   KG       +
Sbjct: 123 HYPELGFSVKMRLGWEC---ADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-------E 172

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +    +   YE +  +P ++ G    +ED+ +  +  P ++GVM+GR    N A+     
Sbjct: 173 VDLAAFTAFYE-ECAHPLVYNGDLLTVEDIRKVDEEFPRLEGVMLGRGLLANPALAW--- 228

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           EY +  +     +  +V     + + A +  Y   HL    +L
Sbjct: 229 EYANGTVFSPDELHEKV-----KALHARLLQYYEAHLQGEAQL 266


>gi|254419655|ref|ZP_05033379.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Brevundimonas sp. BAL3]
 gi|196185832|gb|EDX80808.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Brevundimonas sp. BAL3]
          Length = 243

 Score = 37.7 bits (86), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 36/126 (28%), Positives = 63/126 (50%), Gaps = 18/126 (14%)

Query: 108 IAAMCKALSIP-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---HARKAILKGL 163
           +AA  K      +T+   + ++D +P  AL+   +S   SGV+ +W       K + K L
Sbjct: 113 VAAWLKGFGAEHITLAFDVKIEDGVPVPALKGWTQS---SGVD-LWTALDRYPKGLFKHL 168

Query: 164 SPKDNRKI-----PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIG 216
              D  +      PNL+  ++ EI++  PDL +  +GG+  +    A+K L   +G ++G
Sbjct: 169 LVTDVGRDGAMTGPNLE--LLAEIRRRRPDLVLQASGGVSSLDDIAAVKSL-GCNGAIVG 225

Query: 217 RAAYKN 222
           RA Y+N
Sbjct: 226 RALYEN 231


>gi|68491772|ref|XP_710328.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
 gi|68491789|ref|XP_710320.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
 gi|46431504|gb|EAK91057.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
 gi|46431513|gb|EAK91065.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
          Length = 487

 Score = 37.7 bits (86), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPA 133
           +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPVTVK R G+ +    
Sbjct: 386 SELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPVTVKIRTGIKEGKNT 445

Query: 134 VALRNLVKSIKKSG-VNGIWIHAR 156
               NLV  + + G    I +H R
Sbjct: 446 AV--NLVSRVLEEGNAAAITLHGR 467


>gi|223992807|ref|XP_002286087.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977402|gb|EED95728.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 451

 Score = 37.7 bits (86), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 44/147 (29%), Positives = 60/147 (40%), Gaps = 27/147 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQE----KPLALQI 54
           MV  +D  +R     L N  L YT+MI A   A + G+      F T      KP  +QI
Sbjct: 31  MVAQSDLPFRLMCEQLYNVDLSYTQMIHASNFADVNGEP-----FRTNHLDVIKPTVVQI 85

Query: 55  GGADISKLVEAAKIV----EDFGYN---------EINLNVGCPSARVHEGSFGACLMLN- 100
              D    VEAA ++    E  G +           +LN+GCP     +G +GA L    
Sbjct: 86  AAHDPDVAVEAALMILEKSESTGSSVNGSISPVVAFDLNLGCPQGIARKGKYGAFLHDEY 145

Query: 101 PDIVGDCIAAMCKAL--SIPVTVKCRI 125
           P    D +  +   L   I VT K R+
Sbjct: 146 PQSAYDVLIKLRAMLPREIGVTAKVRL 172


>gi|125623937|ref|YP_001032420.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|146345500|sp|P54322|PYRDB_LACLM RecName: Full=Dihydroorotate dehydrogenase B, catalytic subunit;
           AltName: Full=DHOdehase B; Short=DHOD B; Short=DHODase
           B; AltName: Full=Dihydroorotate oxidase B
 gi|124492745|emb|CAL97700.1| PyrDB protein [Lactococcus lactis subsp. cremoris MG1363]
 gi|300070711|gb|ADJ60111.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 311

 Score = 37.7 bits (86), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 29/107 (27%), Positives = 54/107 (50%), Gaps = 13/107 (12%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++ +  V   AKI +      I LN+ CP+ +    +FG     +P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFGT----DPEVAA 153

Query: 106 DCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             + A CKA+S +P+ VK    V D +P      + K+++ +G +G+
Sbjct: 154 ALVKA-CKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGL 193


>gi|227874944|ref|ZP_03993095.1| possible tRNA-dihydrouridine synthase [Mobiluncus mulieris ATCC
           35243]
 gi|227844464|gb|EEJ54622.1| possible tRNA-dihydrouridine synthase [Mobiluncus mulieris ATCC
           35243]
          Length = 471

 Score = 37.7 bits (86), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 70/154 (45%), Gaps = 20/154 (12%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPL----ALQIGGADISKLVEAA-KIVEDFG 73
             +   EM+ A A+  G +++ +    +  PL    ++Q+ G     L  AA ++V    
Sbjct: 117 EGMFVGEMVTAKALRMGSERSWV--MVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGL 174

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVK 122
            + I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK
Sbjct: 175 ADHIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVK 234

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R G+D +       ++ +  + +GV  + +HAR
Sbjct: 235 IRSGIDAE--HRIFLDVARVAEDNGVAAVTLHAR 266


>gi|306818269|ref|ZP_07451998.1| dihydrouridine synthase [Mobiluncus mulieris ATCC 35239]
 gi|304648914|gb|EFM46210.1| dihydrouridine synthase [Mobiluncus mulieris ATCC 35239]
          Length = 471

 Score = 37.7 bits (86), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 70/154 (45%), Gaps = 20/154 (12%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPL----ALQIGGADISKLVEAA-KIVEDFG 73
             +   EM+ A A+  G +++ +    +  PL    ++Q+ G     L  AA ++V    
Sbjct: 117 EGMFVGEMVTAKALRMGSERSWV--MVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGL 174

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVK 122
            + I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK
Sbjct: 175 ADHIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVK 234

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R G+D +       ++ +  + +GV  + +HAR
Sbjct: 235 IRSGIDAE--HRIFLDVARVAEDNGVAAVTLHAR 266


>gi|13096500|pdb|1EP1|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase B
 gi|13096502|pdb|1EP2|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase B Complexed With Orotate
 gi|13096504|pdb|1EP3|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase B. Data Collected Under Cryogenic
           Conditions
          Length = 311

 Score = 37.7 bits (86), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 29/107 (27%), Positives = 54/107 (50%), Gaps = 13/107 (12%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++ +  V   AKI +      I LN+ CP+ +    +FG     +P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCPNVKHGGQAFGT----DPEVAA 153

Query: 106 DCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             + A CKA+S +P+ VK    V D +P      + K+++ +G +G+
Sbjct: 154 ALVKA-CKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGL 193


>gi|313889165|ref|ZP_07822821.1| dihydroorotate oxidase, catalytic subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844905|gb|EFR32310.1| dihydroorotate oxidase, catalytic subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 301

 Score = 37.4 bits (85), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 10/100 (10%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + +GG  I + +E+A+I+ D+ +  I LN+ CP+  V EG  G    ++ D     +  +
Sbjct: 99  VNLGGNTIEEYIESAEILNDYDFAAIELNISCPN--VKEG--GMAFGMDKDSAAKVVREV 154

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            K  +  V VK      D +       + K+++  G  G+
Sbjct: 155 MKVTNKKVFVKLSPNAGDIV------GIAKAVEAEGATGL 188


>gi|118430958|ref|NP_147090.2| dihydroorotate dehydrogenase 1B [Aeropyrum pernix K1]
 gi|150421637|sp|Q9YFI6|PYRD_AERPE RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116062284|dbj|BAA79175.2| probable dihydroorotate dehydrogenase [Aeropyrum pernix K1]
          Length = 306

 Score = 37.4 bits (85), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 81/185 (43%), Gaps = 29/185 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I G    + VE A  +E+ G + + LN+ CP    H    G  L  +P  V   +
Sbjct: 98  PVIASIAGGAPGEWVEMASTLEEAGVSAVELNLSCP----HFAGGGLELGQDPAAVASVV 153

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALR---------NLVKSIKKSGVNGIWIHARKAI 159
           +A+   L IPV  K  +G  D++   A +          L+ S++   ++   ++A+K +
Sbjct: 154 SAVASTLRIPVIAK--LGYSDRLVDAASKALEAGARGLTLINSMRAMKID---VYAKKPV 208

Query: 160 L----KGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           L     GLS    + I  +    VYE+  E   D+F    GG+E    A++  L     V
Sbjct: 209 LGNRVGGLS---GKPIHPIAVRAVYEVYGETRADIFAA--GGVESWEDAVEFYLAGAKAV 263

Query: 214 MIGRA 218
            +G A
Sbjct: 264 QVGAA 268


>gi|254482153|ref|ZP_05095394.1| Dihydroorotate dehydrogenase family protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037478|gb|EEB78144.1| Dihydroorotate dehydrogenase family protein [marine gamma
           proteobacterium HTCC2148]
          Length = 552

 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +++ L   I G  I + VE AKI+     + + LN+ CP A+     +G  +  +PD+V 
Sbjct: 105 EDRFLLTSIFGGSIDEFVEVAKILAPVS-DGLELNLSCPHAK----GYGMAMGQDPDMVR 159

Query: 106 DCIAAMCKALSIPVTVK 122
           + +AA+   + IPV  K
Sbjct: 160 EIVAAVKAVVDIPVIPK 176


>gi|67517075|ref|XP_658422.1| hypothetical protein AN0818.2 [Aspergillus nidulans FGSC A4]
 gi|74598677|sp|Q5BF62|DUS3_EMENI RecName: Full=tRNA-dihydrouridine synthase 3
 gi|40746492|gb|EAA65648.1| hypothetical protein AN0818.2 [Aspergillus nidulans FGSC A4]
 gi|259488899|tpe|CBF88723.1| TPA: tRNA-dihydrouridine synthase 3 (EC 1.-.-.-)
           [Source:UniProtKB/Swiss-Prot;Acc:Q5BF62] [Aspergillus
           nidulans FGSC A4]
          Length = 714

 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 17/122 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
              QI G     +++A +++     N   I+LN GCP   ++    G+ L+  P  +   
Sbjct: 383 FGAQIAGNKYRWVMKATEVLSSLTPNLRVIDLNCGCPIDLLYREGSGSALLDAPSKLEKM 442

Query: 108 IAAM-CKALSIPVTVKCRIGVDDQIPAVALRNLVKSI------------KKSGVNGIWIH 154
           +  M   +  IP+TVK R G  D  P    + LV+ +              SGV  I +H
Sbjct: 443 LRGMNAVSEQIPITVKIRTGTRDNTPNA--QKLVERLILGGHEASMLNCGPSGVAAITLH 500

Query: 155 AR 156
            R
Sbjct: 501 GR 502


>gi|145230842|ref|XP_001389685.1| tRNA-dihydrouridine synthase 3 [Aspergillus niger CBS 513.88]
 gi|187471046|sp|A2QAU6|DUS3_ASPNC RecName: Full=tRNA-dihydrouridine synthase 3
 gi|134055808|emb|CAK37330.1| unnamed protein product [Aspergillus niger]
          Length = 748

 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIP 132
           I+LN GCP   V +   G+ L+ +P  +   I  M   +  IP+TVK R+G  D  P
Sbjct: 444 IDLNCGCPIDLVFKDGAGSALLEHPSKLEKIIRGMNTVSDQIPITVKIRMGTKDNNP 500


>gi|307701794|ref|ZP_07638808.1| TIM-barrel protein, nifR3 family [Mobiluncus mulieris FB024-16]
 gi|307613052|gb|EFN92307.1| TIM-barrel protein, nifR3 family [Mobiluncus mulieris FB024-16]
          Length = 458

 Score = 37.4 bits (85), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 70/154 (45%), Gaps = 20/154 (12%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPL----ALQIGGADISKLVEAA-KIVEDFG 73
             +   EM+ A A+  G +++ +    +  PL    ++Q+ G     L  AA ++V    
Sbjct: 104 EGMFVGEMVTAKALRMGSERSWV--MVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGL 161

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVK 122
            + I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK
Sbjct: 162 ADHIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVK 221

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R G+D +       ++ +  + +GV  + +HAR
Sbjct: 222 IRSGIDAE--HRIFLDVARVAEDNGVAAVTLHAR 253


>gi|194014711|ref|ZP_03053328.1| dihydroorotate dehydrogenase [Bacillus pumilus ATCC 7061]
 gi|194013737|gb|EDW23302.1| dihydroorotate dehydrogenase [Bacillus pumilus ATCC 7061]
          Length = 310

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 56/258 (21%), Positives = 107/258 (41%), Gaps = 35/258 (13%)

Query: 1   MVDWTDRHYRF---FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGG 56
           M+  T    RF     R+    A +   + + +  L+G  +N L +  Q + P+   + G
Sbjct: 41  MIKATTLEPRFGNPTPRVAETGAGMLNAIGLQNPGLKGVLENELPWLEQFDTPIIANVAG 100

Query: 57  ADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           + +   VE AK I +    + + LN+ CP+ +    +FG     +P +      A+    
Sbjct: 101 SQVDDYVEVAKQISQAKNVHALELNISCPNVKTGGIAFGT----DPHMAAALTKAVKDVS 156

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK--- 161
           S+PV VK    V + +       + ++I+ +G +G+            +   K IL    
Sbjct: 157 SVPVYVKLSPNVANIV------EIAQAIEYAGADGLTMINTLIGMRLDLKTGKPILANKT 210

Query: 162 -GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            GLS      +  +   +V+E+ +      IG+ GG+++    L+ +L     V +G A 
Sbjct: 211 GGLS---GPAVKPVAVRMVHEVSQAVSIPIIGM-GGVQNAEDVLEFLLAGASAVAVGTAN 266

Query: 220 YKNSAMLTTVDEYFSNPL 237
           + N  +   + E   N L
Sbjct: 267 FVNPFICPEIIEELPNVL 284


>gi|70996182|ref|XP_752846.1| tRNA dihydrouridine synthase [Aspergillus fumigatus Af293]
 gi|74672269|sp|Q4WRX4|DUS3_ASPFU RecName: Full=tRNA-dihydrouridine synthase 3
 gi|66850481|gb|EAL90808.1| tRNA dihydrouridine synthase, putative [Aspergillus fumigatus
           Af293]
 gi|159131599|gb|EDP56712.1| tRNA dihydrouridine synthase, putative [Aspergillus fumigatus
           A1163]
          Length = 726

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 7/105 (6%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
              QI G      ++A +++     N   I+LN GCP  +V     G+ L+ +P  +   
Sbjct: 395 FGAQIAGNKPWHAIKATELLSRLTPNLRVIDLNCGCPIDQVFREGAGSALLDHPSKLEKM 454

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVA--LRNLVKSIKKSGV 148
           +  M  A+S  IP+TVK R G  D  P     +  LV    +SG+
Sbjct: 455 LRGM-NAVSEMIPITVKIRTGTRDNSPNATKLIERLVLGGHESGI 498


>gi|294777363|ref|ZP_06742814.1| dihydrouridine synthase (Dus) [Bacteroides vulgatus PC510]
 gi|294448431|gb|EFG16980.1| dihydrouridine synthase (Dus) [Bacteroides vulgatus PC510]
          Length = 305

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 48/223 (21%), Positives = 95/223 (42%), Gaps = 21/223 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+  +  ++L   A +  + GY E ++N+GCP   +     G+ ++  P  V   +  + 
Sbjct: 63  QLIASTPAELERLAGLFIEKGYKEADINMGCPFPLMTGKHKGSGILPYPAEVEALLKELV 122

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRK 170
               +  +VK R+G +    A   R L+  +  + +  I +H R  K   KG       +
Sbjct: 123 HYPELGFSVKMRLGWEC---ADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-------E 172

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +    +   YE +  +P ++ G    +ED+ +  +  P ++GVM+GR    N A+     
Sbjct: 173 VDLAAFTAFYE-ECAHPLVYNGDLLTVEDIRKVDEEFPRLEGVMLGRGLLANPALAW--- 228

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           EY +  +     +  +V     + + A +  Y   HL    +L
Sbjct: 229 EYANGTVFSPDELYEKV-----KALHARLLQYYEAHLQGEAQL 266


>gi|328553552|gb|AEB24044.1| dihydroorotate dehydrogenase 1B [Bacillus amyloliquefaciens TA208]
          Length = 311

 Score = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 45/204 (22%), Positives = 87/204 (42%), Gaps = 31/204 (15%)

Query: 47  EKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +    E A+ I +    + + LN+ CP+ +    +FG     +P +  
Sbjct: 91  DTPIIANVAGSQVEDYKEVAEHISKAPNVHALELNISCPNVKTGGIAFGT----DPAMAA 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           D I A+ +  ++PV VK    V +      +  + K+I+ +G +G+            + 
Sbjct: 147 DLIKAVKEVSAVPVYVKLSPNVAN------ITEIAKAIEAAGADGLTMINTLVGMRLDLK 200

Query: 155 ARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
             + IL     GLS      I  +   +VYE+ +      IG+ GG++    AL+ +L  
Sbjct: 201 TGRPILANKTGGLS---GPAIKPVAIRMVYEVSQAVQIPIIGM-GGVQTAEDALEFLLAG 256

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYF 233
              V +G A + N  +   + E  
Sbjct: 257 ASAVAVGTANFVNPFVCPEIIEQL 280


>gi|309800244|ref|ZP_07694421.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           infantis SK1302]
 gi|308116126|gb|EFO53625.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           infantis SK1302]
          Length = 312

 Score = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 45/197 (22%), Positives = 83/197 (42%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V  G+ G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHGNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +P++  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPELAYDVVKAAVEASEVPVYVKLTPSVTDIV------TIAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK I+  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQTTKLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|261416953|ref|YP_003250636.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261373409|gb|ACX76154.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302325599|gb|ADL24800.1| conserved hypothetical protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 330

 Score = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 47/188 (25%), Positives = 81/188 (43%), Gaps = 29/188 (15%)

Query: 59  ISKLVEAAKIVEDF----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK- 113
           I+  V+  KI+ D     GY EI+ N+GCP         GA ++ +   V + +  + K 
Sbjct: 77  IANSVDEFKILADALIAKGYTEIDFNMGCPFPMQVNRHRGAGILNDKQTVQEIMDEIRKI 136

Query: 114 -----ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPK 166
                   +  +VK R+G D    A A   ++  + ++ ++ I +H R  K   KG    
Sbjct: 137 SNANGTAPVKFSVKMRLGQDTPDEAFA---ILPILNEAPLSQITLHPRLGKQQYKG---- 189

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNS 223
               I    ++  YE +  +P ++   NG +  +SQ  ++    P + GVMIGR      
Sbjct: 190 ---TIDFKSFEKFYE-ECRHPLVY---NGDITSVSQICEMERRYPKLAGVMIGRGMLARP 242

Query: 224 AMLTTVDE 231
           +M     E
Sbjct: 243 SMAADYKE 250


>gi|311068075|ref|YP_003972998.1| dihydroorotate dehydrogenase 1B [Bacillus atrophaeus 1942]
 gi|310868592|gb|ADP32067.1| dihydroorotate dehydrogenase 1B [Bacillus atrophaeus 1942]
          Length = 311

 Score = 37.4 bits (85), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 52/240 (21%), Positives = 99/240 (41%), Gaps = 29/240 (12%)

Query: 1   MVDWTDRHYRF---FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGG 56
           M+  T +  RF     R+    A +   + + +  L     N L +  Q + P+   + G
Sbjct: 41  MIKATTKEPRFGNPTPRVAETGAGMLNAIGLQNPGLESVLHNELTWLEQFDTPIIANVAG 100

Query: 57  ADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           + +   VE A +I +    N + LN+ CP+ +    +FG     NP +  +   A+ K  
Sbjct: 101 SQVEDYVEVAEQISKAPNVNALELNISCPNVKTGGIAFGT----NPAMAAELTKAVKKVS 156

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-----WIHARKAILKGLSPKDNRK 170
            +PV VK    V +      +  +  +I+++G +G+      I  R  +  G     N+ 
Sbjct: 157 QVPVYVKLSPNVAN------IAEIAVAIEEAGADGLTMINTLIGMRLDLKTGQPILANKT 210

Query: 171 -------IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
                  +  +   +VYE+ +      IG+ GG++    A + +L     V +G A + N
Sbjct: 211 GGLSGPAVKPVAIRMVYEVSQAVNIPIIGM-GGVQTAEDAFEFLLAGASAVAVGTANFVN 269


>gi|39950340|ref|XP_363279.1| hypothetical protein MGG_01205 [Magnaporthe oryzae 70-15]
 gi|187471055|sp|A4RLF4|DUS3_MAGO7 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|145020996|gb|EDK05125.1| hypothetical protein MGG_01205 [Magnaporthe oryzae 70-15]
          Length = 739

 Score = 37.4 bits (85), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 29/103 (28%), Positives = 49/103 (47%), Gaps = 14/103 (13%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAV 134
           I+LN GCP   +++   G+ L+   + +   I  M  A+S  +P+T K RIGV +  P +
Sbjct: 436 IDLNCGCPIDMIYKAGAGSALLEQHNKIERIIRGM-NAVSGEVPITCKLRIGVKENHP-L 493

Query: 135 ALRNLVKSIKKS----------GVNGIWIHARKAILKGLSPKD 167
           A +N+ +++  S          G   I +H R    +   P D
Sbjct: 494 AKKNIERAVFGSPDFRNQLGAPGCAAITLHGRTRQQRYKKPAD 536


>gi|167750622|ref|ZP_02422749.1| hypothetical protein EUBSIR_01599 [Eubacterium siraeum DSM 15702]
 gi|167656301|gb|EDS00431.1| hypothetical protein EUBSIR_01599 [Eubacterium siraeum DSM 15702]
          Length = 432

 Score = 37.0 bits (84), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 15/122 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           AIL+  K+N        K +   I G    +    A++ E+ G + I  N  CP    H 
Sbjct: 119 AILKKLKENY-----PTKIIVSSIMGESEDEWTALARLSEEAGVDMIECNFSCPQMTSH- 172

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVN 149
            S G+ +  NP++V    AA+ +   +PV  K    + + +IPA+A  N       +G +
Sbjct: 173 -SMGSDVGTNPELVAKYTAAVKRGTKLPVLAKMTPNITNMEIPAIAAVN-------AGAD 224

Query: 150 GI 151
           GI
Sbjct: 225 GI 226


>gi|220672921|emb|CAX13644.1| novel protein similar to H.sapiens DUS3L, dihydrouridine synthase
           3-like (S. cerevisiae) (DUS3L, zgc:63779) [Danio rerio]
          Length = 224

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 44/183 (24%), Positives = 76/183 (41%), Gaps = 25/183 (13%)

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +P+TVK R GV  Q  +     L+  +KK GV+ I +H R         ++ R     
Sbjct: 2   LDVPLTVKIRTGV--QQNSNIAHKLIPEMKKWGVSLITLHGRS--------REQRYTKLA 51

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYF 233
           D+D +    +    + +  NG +     A+K   + V G+M+ R A     + T + E  
Sbjct: 52  DWDYINTCAQLAAPVPLFGNGDILSYEDAMKARETGVSGIMVARGALIKPWLFTEIKE-- 109

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     SS  +  + +DF        T +   H  S  +  + TR+ +  +  F     C
Sbjct: 110 TRHWDISSTERLDILRDF--------THFGLEHWGSDTQGVEKTRNFLLEWLSF----LC 157

Query: 294 RHI 296
           R+I
Sbjct: 158 RYI 160


>gi|281491891|ref|YP_003353871.1| dihydroorotate dehydrogenase catalytic subunit [Lactococcus lactis
           subsp. lactis KF147]
 gi|281375602|gb|ADA65108.1| Dihydroorotate dehydrogenase, catalytic subunit [Lactococcus lactis
           subsp. lactis KF147]
          Length = 311

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 13/105 (12%)

Query: 49  PLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G++    V   AKI +      I LN+ CP+ +    +FG     +PD+    
Sbjct: 100 PIIANVAGSEEDDYVAVCAKIGDAPNVKAIELNISCPNVKHGGQAFGT----DPDVAAAL 155

Query: 108 IAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           + A CKA+S +P+ VK    V D +P      + K+++ +G +G+
Sbjct: 156 VKA-CKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGL 193


>gi|156937022|ref|YP_001434818.1| dihydroorotate dehydrogenase 1B [Ignicoccus hospitalis KIN4/I]
 gi|156566006|gb|ABU81411.1| dihydroorotate oxidase B, catalytic subunit [Ignicoccus hospitalis
           KIN4/I]
          Length = 302

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 46/185 (24%), Positives = 77/185 (41%), Gaps = 29/185 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + I G D  +  EAA    D G + + LN+ CP    H    G  L ++ + V   +
Sbjct: 95  PVVVSIAGKDEREFAEAAWASVDAGASALELNLSCP----HAKGLGLELGMDINAVRKVV 150

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-IWIHARKAI-------- 159
            A+   +++PV  K  +G+ D+     L +   +   +G +G + I+  +A+        
Sbjct: 151 EAVATTVNVPVFAK--LGLVDK-----LVDTASAALDAGASGLVLINTIRAMVIDIDVME 203

Query: 160 ------LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
                 + GLS    R I  +    VYE+ KE     +G+ G  E       +L     V
Sbjct: 204 PVLTNKVGGLS---GRAIHPIAVRAVYEVYKELKAPIVGVGGVYEWRDAVELVLAGASAV 260

Query: 214 MIGRA 218
            IG A
Sbjct: 261 QIGSA 265


>gi|204929087|ref|ZP_03220230.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
 gi|204321631|gb|EDZ06830.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
          Length = 411

 Score = 37.0 bits (84), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 74/175 (42%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +    ++  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLQMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|291333815|gb|ADD93498.1| dihydroorotate dehydrogenase/oxidoreductase FAD binding protein
           [uncultured marine bacterium MedDCM-OCT-S04-C13]
          Length = 546

 Score = 37.0 bits (84), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +++ L + I G  + + VE AKI+     N + LN+ CP A+     +G  +  +P++V 
Sbjct: 92  EDRFLLVSIFGGSVEEFVEVAKIMAPVA-NGLELNLSCPHAK----GYGMAMGQDPELVR 146

Query: 106 DCIAAMCKALSIPVTVK 122
           +  AA+   + IPV  K
Sbjct: 147 EVTAAVKAVVEIPVIPK 163


>gi|307244502|ref|ZP_07526609.1| dihydroorotate dehydrogenase 1B [Peptostreptococcus stomatis DSM
           17678]
 gi|306492120|gb|EFM64166.1| dihydroorotate dehydrogenase 1B [Peptostreptococcus stomatis DSM
           17678]
          Length = 300

 Score = 37.0 bits (84), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 38/192 (19%), Positives = 80/192 (41%), Gaps = 22/192 (11%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           FS  +    + +GG      VE A++++D  ++ + LN+ CP+ +    +FG    +  +
Sbjct: 89  FSKIDTCRIVNLGGGCEDDYVEGARLLDDKDFDIVELNISCPNVKHGGMAFG----IKSE 144

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---------- 152
           +  + + ++ KA   P+ VK     +D +       + K  ++ G +GI           
Sbjct: 145 VAREVVRSVRKATKKPLIVKLSPNAEDIV------EMAKVCQEEGADGISLVNTFKAMAI 198

Query: 153 -IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
            IH R+ +   ++       I  +   +VYE+ +      +G+ G +        I+   
Sbjct: 199 DIHKRRPVFNNVTAGLSGPAIKPIALRMVYEVCQAVTIPVVGMGGIMTAEDVIEFIMAGA 258

Query: 211 DGVMIGRAAYKN 222
             + IG A + N
Sbjct: 259 TCIQIGTANFTN 270


>gi|149376056|ref|ZP_01893822.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter algicola
           DG893]
 gi|149359693|gb|EDM48151.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter algicola
           DG893]
          Length = 245

 Score = 37.0 bits (84), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 31/97 (31%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYF-S 234
           +IV  I ++ PDL I + GG+   S     L + V  V+IG  A K    +T + + F  
Sbjct: 64  EIVQAIARKYPDLPIQIGGGIRSASTIEAYLKAGVQWVIIGTKAVKEPEFVTDMCKRFPG 123

Query: 235 NPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSG 270
           + + G      RV  D W ++S  M TD A R  + G
Sbjct: 124 HIIVGLDAKDGRVATDGWAEVSEVMATDLAKRFANDG 160


>gi|289423365|ref|ZP_06425173.1| dihydroorotate dehydrogenase, catalytic subunit [Peptostreptococcus
           anaerobius 653-L]
 gi|289156296|gb|EFD04953.1| dihydroorotate dehydrogenase, catalytic subunit [Peptostreptococcus
           anaerobius 653-L]
          Length = 300

 Score = 37.0 bits (84), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 42/199 (21%), Positives = 89/199 (44%), Gaps = 24/199 (12%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           +K +  FS  +    + +GG  +   V+ A+++E   ++ I LN+ CP+ +    ++G  
Sbjct: 83  EKELDNFSKLDLCRIVNLGGGCLEDYVKGAELLEGKDFDMIELNISCPNVKHGGMAYG-- 140

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKK 145
             +  ++  + + A+ KA + P+ VK     +D +            A++L N  K++  
Sbjct: 141 --IKSEVAREVVRAVKKATTKPLMVKLSPNAEDIVAMAIACQEEGADAISLVNTFKAM-- 196

Query: 146 SGVNGIWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                I I  +K +   ++       I  +   +VYE+ K      +G+ GG+ D +  +
Sbjct: 197 ----AIDIRNKKPVFNNVTAGLSGPAIKPIALRMVYEVAKAVTIPVVGM-GGIMDANDVI 251

Query: 205 K-ILPSVDGVMIGRAAYKN 222
           + I+     V +G A + N
Sbjct: 252 EFIMAGATCVQVGTANFVN 270


>gi|282882167|ref|ZP_06290806.1| dihydroorotate oxidase [Peptoniphilus lacrimalis 315-B]
 gi|281297932|gb|EFA90389.1| dihydroorotate oxidase [Peptoniphilus lacrimalis 315-B]
          Length = 300

 Score = 37.0 bits (84), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           + +GG  + + VE A+I+ED  +N + LNV CP+      +FG
Sbjct: 98  VNLGGNTLDEYVEGAEILEDLDFNFLELNVSCPNVSKGGMAFG 140


>gi|312978330|ref|ZP_07790073.1| dihydroorotate oxidase [Lactobacillus crispatus CTV-05]
 gi|310894849|gb|EFQ43920.1| dihydroorotate oxidase [Lactobacillus crispatus CTV-05]
          Length = 307

 Score = 37.0 bits (84), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 11/108 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG   +  VE A+ + + G  N + +NV CP+      SFG    ++ D+V 
Sbjct: 96  ELPIVASVGGDSEADYVEVAQKLSNSGLVNALEINVSCPNVAQGGMSFG----VHADVVE 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +    +   ++IP+ VK    V D      +  + K+ +K G +G+ +
Sbjct: 152 ELTRKIKAVVNIPIYVKLTPNVTD------ITVIAKAAEKGGADGLSM 193


>gi|300814247|ref|ZP_07094523.1| dihydroorotate dehydrogenase 1B [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300511671|gb|EFK38895.1| dihydroorotate dehydrogenase 1B [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 300

 Score = 36.6 bits (83), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           + +GG  + + VE A+I+ED  +N + LNV CP+      +FG
Sbjct: 98  VNLGGNTLDEYVEGAEILEDLDFNFLELNVSCPNVSKGGMAFG 140


>gi|309388710|gb|ADO76590.1| dihydroorotate oxidase B, catalytic subunit [Halanaerobium
           praevalens DSM 2228]
          Length = 411

 Score = 36.6 bits (83), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           I G +  +  E A++V + G + I  N  CP  ++  G+ G+ +  NP++V    AA+ +
Sbjct: 108 IMGENEKEWAELAEMVTEAGADLIECNFSCP--QMTSGAMGSDVGQNPELVKKYSAAVSQ 165

Query: 114 ALSIPVTVKCRIGVDD-QIPAVALRN 138
              +PV  K    + + +IPA+A  N
Sbjct: 166 VTDLPVIAKMTPNIGNMEIPAIAAVN 191


>gi|71408629|ref|XP_806706.1| tRNA-dihydrouridine synthase 2 [Trypanosoma cruzi strain CL Brener]
 gi|70870530|gb|EAN84855.1| tRNA-dihydrouridine synthase 2, putative [Trypanosoma cruzi]
          Length = 430

 Score = 36.6 bits (83), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 34/131 (25%), Positives = 63/131 (48%), Gaps = 14/131 (10%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           +++   S +  P+ LQ+G +D +  V AA    ED   + I++N+GCP     +   GA 
Sbjct: 84  RDMTSRSGEGAPVVLQLGVSDAAVGVAAALLCCEDV--DGIDVNMGCPKKFSVDNGMGAA 141

Query: 97  LMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
           LM +       + A+  AL+           +P++ K R+    +  A  L ++++ +  
Sbjct: 142 LMRDTSKAASILFALDDALNAPDKLAARGRRVPLSFKTRLLETAEATADMLISIMEKVGA 201

Query: 146 SGVNGIWIHAR 156
           + VN I +HAR
Sbjct: 202 NRVNAITLHAR 212


>gi|295693236|ref|YP_003601846.1| dihydroorotate dehydrogenase [Lactobacillus crispatus ST1]
 gi|295031342|emb|CBL50821.1| Dihydroorotate dehydrogenase [Lactobacillus crispatus ST1]
          Length = 307

 Score = 36.6 bits (83), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 11/108 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG   +  VE A+ + + G  N + +NV CP+      SFG    ++ D+V 
Sbjct: 96  ELPIVASVGGDSEADYVEVAQKLSNSGLVNALEINVSCPNVAQGGMSFG----VHADVVE 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +    +   ++IP+ VK    V D      +  + K+ +K G +G+ +
Sbjct: 152 ELTRKIKAVVNIPIYVKLTPNVTD------ITVIAKAAEKGGADGLSM 193


>gi|322661451|gb|EFY57675.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
          Length = 366

 Score = 36.6 bits (83), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|312868661|ref|ZP_07728854.1| dihydropyrimidine dehydrogenase [Lactobacillus oris PB013-T2-3]
 gi|311095775|gb|EFQ54026.1| dihydropyrimidine dehydrogenase [Lactobacillus oris PB013-T2-3]
          Length = 431

 Score = 36.6 bits (83), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 45/105 (42%), Gaps = 8/105 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G       + AK+V   G + I LN  CP    H  + G+ +  NP++   
Sbjct: 103 DKVLIASIMGETPQDWTDLAKLVTAAGADMIELNFSCPQMTSH--TMGSDVGTNPELCKT 160

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             AA+ K   +PV  K    +   IP      +VK+    G +G+
Sbjct: 161 NCAAVKKGTDLPVLAKMTPNITTMIP------VVKACLAGGADGV 199


>gi|253682030|ref|ZP_04862827.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           D str. 1873]
 gi|253561742|gb|EES91194.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           D str. 1873]
          Length = 411

 Score = 36.6 bits (83), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 3/89 (3%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G + S+  + AK+V + G + I  N  CP    H+   G+ +  NP++V   
Sbjct: 102 KVLVASIMGQNESEWTKLAKLVTEIGADIIECNFSCPQMTSHD--MGSDVGQNPELVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQ-IPAVA 135
             A+ K  ++P+  K    + +  IPA+A
Sbjct: 160 CQAVRKGTNLPILAKMTPNIGNMTIPAIA 188


>gi|323700196|ref|ZP_08112108.1| dihydroorotate dehydrogenase family protein [Desulfovibrio sp.
           ND132]
 gi|323460128|gb|EGB15993.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           desulfuricans ND132]
          Length = 300

 Score = 36.6 bits (83), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 93/221 (42%), Gaps = 32/221 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA  + D   + GF T+   +A+ I G  I + VE A+ +     + + LN+ CP+  V 
Sbjct: 78  DAFCQDDIPFLRGFDTK---IAVNIAGRTIDEYVEVAERLASADVDLLELNISCPN--VK 132

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           EG  G    ++P +      A+      P+ VK    V D I A+A     ++++  G +
Sbjct: 133 EG--GVAFGVDPAMAEAVTRAVKAVAGQPLIVKLSPNVTD-IAAIA-----RAVEAGGAD 184

Query: 150 GIW-----------IHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +            +H R  +L     GLS      I  +   +VY++ +      IG+ 
Sbjct: 185 AVSLINTLLGARIDVHRRAFVLSTKQGGLS---GPAIKPVAVRMVYQVARAVHLPIIGMG 241

Query: 195 GGLEDMSQALKILPSVDGVMIGRA-AYKNSAMLTTVDEYFS 234
           G +     A  ++     V +G A  +K +A +  +DE  +
Sbjct: 242 GIMTGEDAAEFLMAGATAVAVGTANLFKPTATMDILDELIT 282


>gi|227878925|ref|ZP_03996828.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus JV-V01]
 gi|256843503|ref|ZP_05548991.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus 125-2-CHN]
 gi|256849737|ref|ZP_05555168.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-1A-US]
 gi|262046689|ref|ZP_06019650.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-3A-US]
 gi|293380101|ref|ZP_06626190.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus 214-1]
 gi|227861471|gb|EEJ69087.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus JV-V01]
 gi|256614923|gb|EEU20124.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus 125-2-CHN]
 gi|256713226|gb|EEU28216.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-1A-US]
 gi|260573138|gb|EEX29697.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-3A-US]
 gi|290923314|gb|EFE00228.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus 214-1]
          Length = 307

 Score = 36.6 bits (83), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 11/108 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG   +  VE A+ + + G  N + +NV CP+      SFG    ++ D+V 
Sbjct: 96  ELPIVASVGGDSEADYVEVAQKLSNSGLVNALEINVSCPNVAQGGMSFG----VHADVVE 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +    +   ++IP+ VK    V D      +  + K+ +K G +G+ +
Sbjct: 152 ELTRKIKAVVNIPIYVKLTPNVTD------ITVIAKAAEKGGADGLSM 193


>gi|319947135|ref|ZP_08021369.1| dihydroorotate dehydrogenase B [Streptococcus australis ATCC
           700641]
 gi|319747183|gb|EFV99442.1| dihydroorotate dehydrogenase B [Streptococcus australis ATCC
           700641]
          Length = 312

 Score = 36.6 bits (83), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 21/113 (18%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS +E         A +S      KI +      I LN+ CP+  V  G+ G  + 
Sbjct: 103 NVAGFSNEEY--------ATVS-----GKISQAPNVKAIELNISCPN--VDHGNNGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             P++  D + A  +A S+PV VK    V D      +  + K+ + +G +G+
Sbjct: 148 QVPELAYDAVKAAVEASSVPVYVKLTPSVAD------ITQVAKAAEDAGASGL 194


>gi|154150653|ref|YP_001404271.1| dihydroorotate dehydrogenase 1B [Candidatus Methanoregula boonei
           6A8]
 gi|153999205|gb|ABS55628.1| dihydroorotate dehydrogenase family protein [Methanoregula boonei
           6A8]
          Length = 296

 Score = 36.6 bits (83), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           KP+ + I G D  +  E A   +      + LN+ CP    H   +GA + +NPD+V  C
Sbjct: 93  KPVIVSIFGGDPEEFAEVAGWFKGMAAG-LELNLSCP----HAEGYGASIGVNPDLVEKC 147

Query: 108 IAAMCKALSIPVTVKCRIGVDD 129
             A+   L +P  VK    V D
Sbjct: 148 TRAV-STLGMPTWVKLTPNVTD 168


>gi|289167808|ref|YP_003446077.1| dihydroorotate dehydrogenase [Streptococcus mitis B6]
 gi|288907375|emb|CBJ22212.1| dihydroorotate dehydrogenase [Streptococcus mitis B6]
          Length = 312

 Score = 36.2 bits (82), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 48/210 (22%), Positives = 85/210 (40%), Gaps = 35/210 (16%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKAANVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASDVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFNLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            L     + +G A + N      + E   N
Sbjct: 261 YLAGASAIGVGTANFTNPYACPDIIENLPN 290


>gi|15673328|ref|NP_267502.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. lactis
           Il1403]
 gi|18202791|sp|Q9CFW8|PYRDB_LACLA RecName: Full=Dihydroorotate dehydrogenase B, catalytic subunit;
           AltName: Full=DHOdehase B; Short=DHOD B; Short=DHODase
           B; AltName: Full=Dihydroorotate oxidase B
 gi|12724328|gb|AAK05444.1|AE006366_13 dihydroorotate dehydrogenase B [Lactococcus lactis subsp. lactis
           Il1403]
 gi|326406882|gb|ADZ63953.1| dihydroorotate dehydrogenase catalytic subunit [Lactococcus lactis
           subsp. lactis CV56]
          Length = 311

 Score = 36.2 bits (82), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 13/105 (12%)

Query: 49  PLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G++    V   AKI +      I LN+ CP+ +    +FG     +PD+    
Sbjct: 100 PIIANVAGSEEDDYVAVCAKIGDAPNVKVIELNISCPNVKHGGQAFGT----DPDVAAAL 155

Query: 108 IAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           + A CKA+S +P+ VK    V D +P      + K+++ +G +G+
Sbjct: 156 VKA-CKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGL 193


>gi|226224436|ref|YP_002758543.1| dihydroorotase dehydrogenase [Listeria monocytogenes Clip81459]
 gi|254933305|ref|ZP_05266664.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes HPB2262]
 gi|259547529|sp|C1KWD2|PYRD_LISMC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|225876898|emb|CAS05607.1| Putative dihydroorotase dehydrogenase [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|293584865|gb|EFF96897.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes HPB2262]
 gi|328473555|gb|EGF44392.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 220]
 gi|332312274|gb|EGJ25369.1| Dihydroorotate dehydrogenase [Listeria monocytogenes str. Scott A]
          Length = 304

 Score = 36.2 bits (82), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 44/191 (23%), Positives = 84/191 (43%), Gaps = 27/191 (14%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     V+  A+I E      I LN+ CP+ + H G +FG     +PD+ 
Sbjct: 93  ETPIIANVAGATEDDYVQVCARIGESKAVKAIELNISCPNVK-HGGIAFGT----DPDVA 147

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWI 153
                A+    ++PV VK    V D +      ++ ++I+ +G +G           I +
Sbjct: 148 HRLTKAVKNVATVPVYVKLSPNVADIV------SIAQAIEAAGADGLTMINTLLGMRIDL 201

Query: 154 HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVD 211
             RK I+  G        I  +   +++++++ +    IG+ GG++ +   L+ L    D
Sbjct: 202 KTRKPIIANGTGGLSGPAIKPVAIRMIHQVREVSNIPIIGM-GGVQTVDDVLEFLIAGAD 260

Query: 212 GVMIGRAAYKN 222
            V +G   + +
Sbjct: 261 AVAVGTMNFTD 271


>gi|259502930|ref|ZP_05745832.1| dihydroorotate dehydrogenase [Lactobacillus antri DSM 16041]
 gi|259169123|gb|EEW53618.1| dihydroorotate dehydrogenase [Lactobacillus antri DSM 16041]
          Length = 431

 Score = 36.2 bits (82), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 29/104 (27%), Positives = 45/104 (43%), Gaps = 8/104 (7%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G       + AK+V   G + I LN  CP    H  + G+ +  NP++    
Sbjct: 104 KVLIASIMGETPQDWTDLAKLVTAAGADMIELNFSCPQMTSH--TMGSDVGTNPELCKSN 161

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            AA+ +  ++PV  K    +   IP      +VK+    G +GI
Sbjct: 162 CAAVKRGTNLPVLAKMTPNITTMIP------VVKACLAGGADGI 199


>gi|291085135|ref|ZP_06352165.2| dihydroorotate dehydrogenase family protein [Citrobacter youngae
           ATCC 29220]
 gi|291072078|gb|EFE10187.1| dihydroorotate dehydrogenase family protein [Citrobacter youngae
           ATCC 29220]
          Length = 380

 Score = 36.2 bits (82), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 70  DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 127

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 128 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 187

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 188 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 241


>gi|116517057|ref|YP_816334.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae D39]
 gi|161410749|ref|NP_358460.2| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae R6]
 gi|116077633|gb|ABJ55353.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae D39]
          Length = 312

 Score = 36.2 bits (82), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSTEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|46908065|ref|YP_014454.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47093070|ref|ZP_00230848.1| dihydroorotate dehydrogenase [Listeria monocytogenes str. 4b H7858]
 gi|254826125|ref|ZP_05231126.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J1-194]
 gi|254852739|ref|ZP_05242087.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL R2-503]
 gi|254994290|ref|ZP_05276480.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J2-064]
 gi|255522430|ref|ZP_05389667.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J1-175]
 gi|300763854|ref|ZP_07073851.1| dihydroorotate dehydrogenase [Listeria monocytogenes FSL N1-017]
 gi|67460857|sp|Q71YI3|PYRD_LISMF RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|46881335|gb|AAT04631.1| dihydroorotate dehydrogenase [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47018571|gb|EAL09326.1| dihydroorotate dehydrogenase [Listeria monocytogenes str. 4b H7858]
 gi|258606063|gb|EEW18671.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL R2-503]
 gi|293595365|gb|EFG03126.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J1-194]
 gi|300515590|gb|EFK42640.1| dihydroorotate dehydrogenase [Listeria monocytogenes FSL N1-017]
          Length = 304

 Score = 36.2 bits (82), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 44/191 (23%), Positives = 84/191 (43%), Gaps = 27/191 (14%)

Query: 47  EKPLALQIGGADISKLVEA-AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIV 104
           E P+   + GA     V+  A+I E      I LN+ CP+ + H G +FG     +PD+ 
Sbjct: 93  ETPIIANVAGATEDDYVQVCARIGESKAVKAIELNISCPNVK-HGGIAFGT----DPDVA 147

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWI 153
                A+    ++PV VK    V D +      ++ ++I+ +G +G           I +
Sbjct: 148 HRLTKAVKNVATVPVYVKLSPNVADIV------SIAQAIEAAGADGLTMINTLLGMRIDL 201

Query: 154 HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVD 211
             RK I+  G        I  +   +++++++ +    IG+ GG++ +   L+ L    D
Sbjct: 202 KTRKPIIANGTGGLSGPAIKPVAIRMIHQVREVSNIPIIGM-GGVQTVDDVLEFLIAGAD 260

Query: 212 GVMIGRAAYKN 222
            V +G   + +
Sbjct: 261 AVAVGTMNFTD 271


>gi|298503026|ref|YP_003724966.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae TCH8431/19A]
 gi|298238621|gb|ADI69752.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae TCH8431/19A]
          Length = 328

 Score = 36.2 bits (82), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 119 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 163

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 164 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 217

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 218 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 276

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 277 YLAGASAIGVGTANFTN 293


>gi|149006359|ref|ZP_01830071.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP18-BS74]
 gi|225861149|ref|YP_002742658.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|307127485|ref|YP_003879516.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae 670-6B]
 gi|147762136|gb|EDK69098.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP18-BS74]
 gi|225728081|gb|ACO23932.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|306484547|gb|ADM91416.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae 670-6B]
 gi|327389242|gb|EGE87587.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA04375]
 gi|332075580|gb|EGI86048.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA17545]
 gi|332201430|gb|EGJ15500.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA47368]
          Length = 312

 Score = 36.2 bits (82), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSTEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|15458470|gb|AAK99670.1| Dihydroorotate dehydrogenase [Streptococcus pneumoniae R6]
          Length = 330

 Score = 36.2 bits (82), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 121 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 165

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 166 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 219

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 220 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSTEAALEM 278

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 279 YLAGASAIGVGTANFTN 295


>gi|194446223|ref|YP_002041458.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194404886|gb|ACF65108.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Newport str. SL254]
          Length = 411

 Score = 36.2 bits (82), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|322615214|gb|EFY12136.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322617805|gb|EFY14701.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624602|gb|EFY21433.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626948|gb|EFY23744.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322634134|gb|EFY30870.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322635675|gb|EFY32385.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640190|gb|EFY36854.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646387|gb|EFY42899.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649354|gb|EFY45790.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656475|gb|EFY52764.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322665661|gb|EFY61845.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667185|gb|EFY63352.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671191|gb|EFY67319.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675169|gb|EFY71246.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680777|gb|EFY76812.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686952|gb|EFY82929.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323192716|gb|EFZ77943.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323198852|gb|EFZ83951.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323205138|gb|EFZ90116.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323208181|gb|EFZ93125.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323213535|gb|EFZ98326.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215794|gb|EGA00537.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323221293|gb|EGA05716.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223841|gb|EGA08144.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231240|gb|EGA15355.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323233674|gb|EGA17766.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323237744|gb|EGA21804.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245727|gb|EGA29721.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323246535|gb|EGA30514.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2009159199]
 gi|323253020|gb|EGA36853.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008282]
 gi|323254772|gb|EGA38575.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008283]
 gi|323259528|gb|EGA43163.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323268311|gb|EGA51786.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008285]
          Length = 411

 Score = 36.2 bits (82), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|224583312|ref|YP_002637110.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|224467839|gb|ACN45669.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
          Length = 411

 Score = 36.2 bits (82), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITSIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|187935649|ref|YP_001886506.1| dihydropyrimidine dehydrogenase [Clostridium botulinum B str.
           Eklund 17B]
 gi|187723802|gb|ACD25023.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           B str. Eklund 17B]
          Length = 412

 Score = 36.2 bits (82), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 38/173 (21%), Positives = 71/173 (41%), Gaps = 15/173 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G +  +  + AK+V + G + I  N  CP    HE   G+ +  NP++V   
Sbjct: 103 KIVVASIMGENEKEWEDLAKLVTEAGADMIECNFSCPQMTSHE--MGSDVGQNPELVKKY 160

Query: 108 IAAMCKALSIPVTVKCRIGVDD-QIPAVALR----------NLVKSIKKSGVNGIWIHAR 156
             A  +  ++P+  K    + D  +PA+A            N +KSI    +N +     
Sbjct: 161 CEATRRGTNLPILAKMTPNIGDMSVPAIASMEGGATGLATINTIKSITGIDINSMTAKPV 220

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQALKIL 207
                 +S    + +  +    +YE+ K      + ++  GG+E    AL+ +
Sbjct: 221 VNAKSSVSGYSGKAVKPIALRFIYELAKNEKLKGVPISGIGGIETWEDALEFI 273


>gi|168242273|ref|ZP_02667205.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL486]
 gi|194448536|ref|YP_002046240.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|197261723|ref|ZP_03161797.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|200387718|ref|ZP_03214330.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|194406840|gb|ACF67059.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL476]
 gi|197239978|gb|EDY22598.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|199604816|gb|EDZ03361.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|205338639|gb|EDZ25403.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL486]
          Length = 411

 Score = 36.2 bits (82), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|188590495|ref|YP_001921441.1| dihydropyrimidine dehydrogenase [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500776|gb|ACD53912.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E3 str. Alaska E43]
          Length = 412

 Score = 36.2 bits (82), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 38/173 (21%), Positives = 71/173 (41%), Gaps = 15/173 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G +  +  + AK+V + G + I  N  CP    HE   G+ +  NP++V   
Sbjct: 103 KIVVASIMGENEKEWEDLAKLVTEAGADMIECNFSCPQMTSHE--MGSDVGQNPELVKKY 160

Query: 108 IAAMCKALSIPVTVKCRIGVDD-QIPAVALR----------NLVKSIKKSGVNGIWIHAR 156
             A  +  ++P+  K    + D  +PA+A            N +KSI    +N +     
Sbjct: 161 CEATRRGTNLPILAKMTPNIGDMSVPAIASMEGGATGLATINTIKSITGIDINSMTAKPV 220

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQALKIL 207
                 +S    + +  +    +YE+ K      + ++  GG+E    AL+ +
Sbjct: 221 VNAKSSVSGYSGKAVKPIALRFIYELAKNEKLKGVPISGIGGIETWEDALEFI 273


>gi|148992901|ref|ZP_01822520.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae SP9-BS68]
 gi|168490217|ref|ZP_02714416.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae SP195]
 gi|169833969|ref|YP_001694409.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           Hungary19A-6]
 gi|194398689|ref|YP_002037599.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae G54]
 gi|225856622|ref|YP_002738133.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae P1031]
 gi|225858757|ref|YP_002740267.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae 70585]
 gi|147928353|gb|EDK79369.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae SP9-BS68]
 gi|168996471|gb|ACA37083.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae Hungary19A-6]
 gi|183571422|gb|EDT91950.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae SP195]
 gi|194358356|gb|ACF56804.1| dihydroorotate dehydrogenase B [Streptococcus pneumoniae G54]
 gi|225721785|gb|ACO17639.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae 70585]
 gi|225725581|gb|ACO21433.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae P1031]
 gi|301794102|emb|CBW36508.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae INV104]
 gi|332073297|gb|EGI83776.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA17570]
 gi|332204967|gb|EGJ19032.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA47901]
          Length = 312

 Score = 36.2 bits (82), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|225854468|ref|YP_002735980.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae JJA]
 gi|225723113|gb|ACO18966.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae JJA]
          Length = 312

 Score = 36.2 bits (82), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|251777769|ref|ZP_04820689.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
 gi|243082084|gb|EES47974.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
          Length = 412

 Score = 36.2 bits (82), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 38/173 (21%), Positives = 71/173 (41%), Gaps = 15/173 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G +  +  + AK+V + G + I  N  CP    HE   G+ +  NP++V   
Sbjct: 103 KIVVASIMGENEKEWEDLAKLVTEAGADMIECNFSCPQMTSHE--MGSDVGQNPELVKKY 160

Query: 108 IAAMCKALSIPVTVKCRIGVDD-QIPAVALR----------NLVKSIKKSGVNGIWIHAR 156
             A  +  ++P+  K    + D  +PA+A            N +KSI    +N +     
Sbjct: 161 CEATRRGTNLPILAKMTPNIGDMSVPAIASMEGGATGLATINTIKSITGIDINSMTAKPV 220

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQALKIL 207
                 +S    + +  +    +YE+ K      + ++  GG+E    AL+ +
Sbjct: 221 VNAKSSVSGYSGKAVKPIALRFIYELAKNEKLKGVPISGIGGIETWEDALEFI 273


>gi|182683910|ref|YP_001835657.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae CGSP14]
 gi|182629244|gb|ACB90192.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae CGSP14]
          Length = 330

 Score = 36.2 bits (82), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 121 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 165

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 166 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 219

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 220 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 278

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 279 YLAGASAIGVGTANFTN 295


>gi|15900841|ref|NP_345445.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae TIGR4]
 gi|148988405|ref|ZP_01819852.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP6-BS73]
 gi|168485916|ref|ZP_02710424.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC1087-00]
 gi|168494393|ref|ZP_02718536.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC3059-06]
 gi|221231727|ref|YP_002510879.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae ATCC 700669]
 gi|237650887|ref|ZP_04525139.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae CCRI
           1974]
 gi|237821895|ref|ZP_04597740.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298229842|ref|ZP_06963523.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298254541|ref|ZP_06978127.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|303259876|ref|ZP_07345851.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP-BS293]
 gi|303262290|ref|ZP_07348234.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP14-BS292]
 gi|303264712|ref|ZP_07350630.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS397]
 gi|303267241|ref|ZP_07353106.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS457]
 gi|303269527|ref|ZP_07355292.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS458]
 gi|14972438|gb|AAK75085.1| dihydroorotate dehydrogenase B [Streptococcus pneumoniae TIGR4]
 gi|147926086|gb|EDK77160.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP6-BS73]
 gi|183571069|gb|EDT91597.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC1087-00]
 gi|183575702|gb|EDT96230.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674187|emb|CAR68715.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae ATCC 700669]
 gi|302636613|gb|EFL67104.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP14-BS292]
 gi|302639081|gb|EFL69541.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP-BS293]
 gi|302640963|gb|EFL71345.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS458]
 gi|302643250|gb|EFL73532.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS457]
 gi|302645799|gb|EFL76028.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS397]
 gi|332076238|gb|EGI86704.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA41301]
          Length = 312

 Score = 36.2 bits (82), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|229578456|ref|YP_002836854.1| hypothetical protein YG5714_0639 [Sulfolobus islandicus Y.G.57.14]
 gi|228009170|gb|ACP44932.1| conserved hypothetical protein [Sulfolobus islandicus Y.G.57.14]
          Length = 839

 Score = 36.2 bits (82), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 53/113 (46%), Gaps = 6/113 (5%)

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +YD +  I +E+P+L IG N   E     + I+  + G +  +  Y  S     +D Y S
Sbjct: 141 EYDRISSIAEESPEL-IGYNEE-EKEKYPVAIVSPIFGEI--KVIYP-SGDTKDLDNYIS 195

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           N L  +S  K  +DK+ W  I+ S+     R   SG  +  I  H+ G F+ +
Sbjct: 196 NKLNVTSSPKELIDKEKWDVIAKSLLLKPQRTWFSGNDI-AIIAHLRGAFYAY 247


>gi|16765517|ref|NP_461132.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|62180774|ref|YP_217191.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|161613121|ref|YP_001587086.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167991114|ref|ZP_02572213.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|168229542|ref|ZP_02654600.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CDC 191]
 gi|168259472|ref|ZP_02681445.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|168466133|ref|ZP_02700003.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|168818103|ref|ZP_02830103.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Weltevreden str. HI_N05-537]
 gi|194470352|ref|ZP_03076336.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|197248087|ref|YP_002147158.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|198241985|ref|YP_002216271.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205353322|ref|YP_002227123.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207857621|ref|YP_002244272.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|238912629|ref|ZP_04656466.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|16420724|gb|AAL21091.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|62128407|gb|AAX66110.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Choleraesuis str. SC-B67]
 gi|161362485|gb|ABX66253.1| hypothetical protein SPAB_00829 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194456716|gb|EDX45555.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|195631189|gb|EDX49749.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|197211790|gb|ACH49187.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Agona str. SL483]
 gi|197936501|gb|ACH73834.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|205273103|emb|CAR38058.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205330434|gb|EDZ17198.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205335946|gb|EDZ22710.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CDC 191]
 gi|205345012|gb|EDZ31776.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Weltevreden str. HI_N05-537]
 gi|205351177|gb|EDZ37808.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|206709424|emb|CAR33765.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|261247401|emb|CBG25226.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994252|gb|ACY89137.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158748|emb|CBW18260.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913177|dbj|BAJ37151.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320086627|emb|CBY96398.1| Dihydropyrimidine dehydrogenase [NADP+] DHPDHase; DPD;
           Dihydrouracil dehydrogenase; Dihydrothymine
           dehydrogenase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|321224841|gb|EFX49904.1| Dihydropyrimidine [Salmonella enterica subsp. enterica serovar
           Typhimurium str. TN061786]
 gi|322715249|gb|EFZ06820.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130514|gb|ADX17944.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326624022|gb|EGE30367.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326628411|gb|EGE34754.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
 gi|332989121|gb|AEF08104.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 411

 Score = 36.2 bits (82), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|168491053|ref|ZP_02715196.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183574652|gb|EDT95180.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC0288-04]
          Length = 312

 Score = 36.2 bits (82), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|315221729|ref|ZP_07863645.1| dihydroorotate dehydrogenase 1B [Streptococcus anginosus F0211]
 gi|315189216|gb|EFU22915.1| dihydroorotate dehydrogenase 1B [Streptococcus anginosus F0211]
          Length = 313

 Score = 36.2 bits (82), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 30/112 (26%), Positives = 47/112 (41%), Gaps = 21/112 (18%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS +E                 A KI +      I LN+ CP+  V  G+ G  + 
Sbjct: 103 NVAGFSNEEYAFV-------------AGKISQAPNVKAIELNISCPN--VDHGNGGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
             PD+  +   A  +A S+PV VK    V D      +  + K+++ +G  G
Sbjct: 148 QVPDLAYNATKAAVEASSVPVYVKLTPSVAD------ITEISKAVEAAGATG 193


>gi|168236356|ref|ZP_02661414.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|197290436|gb|EDY29791.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
          Length = 411

 Score = 36.2 bits (82), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|194736993|ref|YP_002115276.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|194712495|gb|ACF91716.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. CVM19633]
          Length = 411

 Score = 36.2 bits (82), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSGKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|146103428|ref|XP_001469559.1| dihydrouridine synthase domain protein-like protein [Leishmania
           infantum]
 gi|134073929|emb|CAM72668.1| dihydrouridine synthase domain protein-like protein [Leishmania
           infantum JPCM5]
 gi|322503403|emb|CBZ38488.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 439

 Score = 35.8 bits (81), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 49/172 (28%), Positives = 73/172 (42%), Gaps = 34/172 (19%)

Query: 77  INLNVGCPSA-RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG--------- 126
           I++N+GCP    VH G FGA LM  P++ G  + A+  A++    V+ R G         
Sbjct: 132 IDINMGCPKKFSVHNG-FGAALMKRPEVGGAIVRAVHDAVNSDSNVEARGGKRVAMSLKT 190

Query: 127 -VDDQIPAVA--LRNLVKSIKKSGVN----GIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            + D   A    LR ++ + + +  N     I IHAR       +P D R      YD  
Sbjct: 191 RLQDTAEATVGMLRAILAAAQHTPTNPILHAITIHAR-------TP-DQRSEQAPLYDRA 242

Query: 180 YEIKK--ENPDLFIG----LNGGL--EDMSQALKILPSVDGVMIGRAAYKNS 223
            E+ +       F G    LNG +      +A   L   D  MI RAA +++
Sbjct: 243 AEVVRTCRADAAFEGICLVLNGSVLSRQDGEAKCALYGFDAAMIARAALEDA 294


>gi|149019555|ref|ZP_01834874.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP23-BS72]
 gi|147930930|gb|EDK81910.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP23-BS72]
          Length = 312

 Score = 35.8 bits (81), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|56412899|ref|YP_149974.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197361830|ref|YP_002141466.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56127156|gb|AAV76662.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|197093306|emb|CAR58754.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
          Length = 411

 Score = 35.8 bits (81), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 73/175 (41%), Gaps = 17/175 (9%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +K L   I G +  +  E A++VE+ G + I  N  CP    H  + G+ +  +P++V  
Sbjct: 101 DKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQMTSH--AMGSDVGQSPELVEK 158

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----------AVALRNLVKSIKKSGVN---GIW 152
              A+ +  S+P+  K    + D               +A  N VKSI    +N   G+ 
Sbjct: 159 YCRAVKRGSSLPMLAKMTPNIGDMCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMP 218

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +   K+ + G S K  + I  L +     +  E  D  I   GG+E    A + L
Sbjct: 219 VVNGKSSISGYSRKAVKPIA-LRFIQQLRMHPELRDFPISGIGGIETWEDAAEFL 272


>gi|111658035|ref|ZP_01408737.1| hypothetical protein SpneT_02000768 [Streptococcus pneumoniae
           TIGR4]
          Length = 319

 Score = 35.8 bits (81), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 110 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 154

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 155 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 208

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 209 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 267

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 268 YLAGASAIGVGTANFTN 284


>gi|331270656|ref|YP_004397148.1| mccF-like protein [Clostridium botulinum BKT015925]
 gi|329127206|gb|AEB77151.1| mccF-like protein [Clostridium botulinum BKT015925]
          Length = 305

 Score = 35.8 bits (81), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 10/76 (13%)

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNSAML 226
           R +P LDYDI+    K+NP LF+G +    D++  L  + S  G++   G  A  +   L
Sbjct: 87  RILPLLDYDII----KKNPKLFVGFS----DITVLLNTINSYCGLITFHGPMATSDFTGL 138

Query: 227 TTVDEYFSNPLTGSSP 242
            T   +FS  + G+ P
Sbjct: 139 DTCQSFFSTLMNGTRP 154


>gi|307701802|ref|ZP_07638816.1| dihydrouridine synthase (Dus) [Mobiluncus mulieris FB024-16]
 gi|307613060|gb|EFN92315.1| dihydrouridine synthase (Dus) [Mobiluncus mulieris FB024-16]
          Length = 292

 Score = 35.8 bits (81), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 69/154 (44%), Gaps = 20/154 (12%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPL----ALQIGGADISKLVEAA-KIVEDFG 73
             +   EM+ A A+  G  ++ +    +  PL    ++Q+ G     L  AA ++V    
Sbjct: 121 EGMFVGEMVTAKALRMGSARSWV--MVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGL 178

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVK 122
            + I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK
Sbjct: 179 ADHIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVK 238

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R G+D +       ++ +  + +GV  + +HAR
Sbjct: 239 IRSGIDAE--HRIFLDVARVAEDNGVAAVTLHAR 270


>gi|307706462|ref|ZP_07643271.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis SK321]
 gi|307618172|gb|EFN97330.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis SK321]
          Length = 312

 Score = 35.8 bits (81), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASDVPVYVKLTPSVTDIV------TVAKAAEDAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVLPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|148998601|ref|ZP_01826041.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP11-BS70]
 gi|168575626|ref|ZP_02721562.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae MLV-016]
 gi|307067621|ref|YP_003876587.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae AP200]
 gi|147755599|gb|EDK62646.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP11-BS70]
 gi|183578496|gb|EDT99024.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae MLV-016]
 gi|306409158|gb|ADM84585.1| Dihydroorotate dehydrogenase [Streptococcus pneumoniae AP200]
 gi|332202819|gb|EGJ16888.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA41317]
          Length = 312

 Score = 35.8 bits (81), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 35/197 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           N+ GFS QE         A +S  +  A  V+      I LN+ CP+  V   + G  + 
Sbjct: 103 NVAGFSKQEY--------AAVSHGISKATNVK-----AIELNISCPN--VDHCNHGLLIG 147

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +PD+  D + A  +A  +PV VK    V D +       + K+ + +G +G+       
Sbjct: 148 QDPDLAYDVVKAAVEASEVPVYVKLTPSVTDIV------TVAKAAEYAGASGLTMINTLV 201

Query: 153 -----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +  RK IL  G        +  +   ++ ++ +      IG+ GG++    AL++
Sbjct: 202 GMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQTTDLPIIGM-GGVDSAEAALEM 260

Query: 207 -LPSVDGVMIGRAAYKN 222
            L     + +G A + N
Sbjct: 261 YLAGASAIGVGTANFTN 277


>gi|291558287|emb|CBL35404.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium siraeum
           V10Sc8a]
          Length = 494

 Score = 35.8 bits (81), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 15/122 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           AIL+  K+N        K +   I G    +    A++ E+ G + I  N  CP    H 
Sbjct: 181 AILKKLKENY-----PTKIIVSSIMGESEDEWTALARLSEEAGVDMIECNFSCPQMTSH- 234

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVN 149
            S G+ +  NP++V    AA+ +   +PV  K    + + +IPA+A  N       +G +
Sbjct: 235 -SMGSDVGTNPELVAKYTAAVRRGTKLPVLAKMTPNITNMEIPAIAAVN-------AGAD 286

Query: 150 GI 151
           GI
Sbjct: 287 GI 288


>gi|154345488|ref|XP_001568681.1| dihydrouridine synthase domain protein-like protein [Leishmania
           braziliensis MHOM/BR/75/M2904]
 gi|134066023|emb|CAM43808.1| dihydrouridine synthase domain protein-like protein [Leishmania
           braziliensis MHOM/BR/75/M2904]
          Length = 440

 Score = 35.8 bits (81), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 41/172 (23%), Positives = 71/172 (41%), Gaps = 34/172 (19%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP     +  FGA LM  P++ G  + A+  A++   +V+ R G   +  AV+L
Sbjct: 132 IDVNMGCPKKFSVQNGFGAALMKRPEVGGAIVRAVHDAVNSNASVEARGG---RRVAVSL 188

Query: 137 RNLVKSIKKSGV-------------------NGIWIHAR----KAILKGLSPKDNRKIPN 173
           +  +K   +  V                   + I +HAR    ++    L  +    +  
Sbjct: 189 KTRLKETTEDTVEMLRAMLTAAHHTPTSPVLHAITVHARTPNQRSEQAPLYSRAAEVVRT 248

Query: 174 LDYDIVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNS 223
              D  +E       +   LNG +      +A   L   DG MI RAA +++
Sbjct: 249 CRSDTAFE------GICFVLNGSILSRQDGEAKCALYGFDGAMIARAALEDA 294


>gi|311695901|gb|ADP98774.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [marine bacterium
           HP15]
          Length = 245

 Score = 35.8 bits (81), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 32/99 (32%), Positives = 47/99 (47%), Gaps = 7/99 (7%)

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +IV  I ++ PDL I + GG+   E +   LK    V  V+IG  A K    +T + + F
Sbjct: 64  EIVQAIARKYPDLPIQIGGGIRSAETIEAYLK--AGVQWVIIGTKAVKEPEFVTEMCKKF 121

Query: 234 -SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSG 270
             + + G      RV  D W ++S  M TD A R  + G
Sbjct: 122 PGHIIVGLDAKDGRVATDGWAEVSEVMATDLAKRFANDG 160


>gi|20089578|ref|NP_615653.1| hypothetical protein MA0693 [Methanosarcina acetivorans C2A]
 gi|19914494|gb|AAM04133.1| hypothetical protein (multi-domain) [Methanosarcina acetivorans
           C2A]
          Length = 379

 Score = 35.8 bits (81), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 45/183 (24%), Positives = 82/183 (44%), Gaps = 22/183 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +A+ +    +  L+EAAKIV++ G   + LN  C    + E   G  L+ +   +   I 
Sbjct: 91  VAVNVRSTTLEPLIEAAKIVKEEGAI-LELNAHCKQPEMLEAGIGEALLRDLPRLSAWIK 149

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ K   + ++VK R  V + I       L + I K+G + I +    A+L+G       
Sbjct: 150 AI-KETGVVLSVKVRANVINDI------ELARLIDKAGADIIHVD---AMLEGFG----- 194

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTT 228
              +LD  + Y   ++   LF+  N  + D + A  +     D V + R A +N  +++ 
Sbjct: 195 --ADLDAIVNY---RDATRLFLIGNNSVTDFATAKDMFSRGADMVSVARGAMENPELISQ 249

Query: 229 VDE 231
           + E
Sbjct: 250 LVE 252


>gi|220928070|ref|YP_002504979.1| dihydroorotate dehydrogenase [Clostridium cellulolyticum H10]
 gi|219998398|gb|ACL74999.1| dihydroorotate dehydrogenase family protein [Clostridium
           cellulolyticum H10]
          Length = 307

 Score = 35.8 bits (81), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 48/203 (23%), Positives = 86/203 (42%), Gaps = 34/203 (16%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            I G  I +  E A+I+   G + I +NV CP+ +    +FG      P  + +  +A+ 
Sbjct: 102 NIAGNTIEEYCEMAEILASSGVDAIEMNVSCPNVKAGCLAFGT----TPKGIEEITSAVK 157

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILK 161
           K    P+ VK    V D      +R++  + + +G +            I I+ +K IL 
Sbjct: 158 KYCKQPLIVKLTPNVSD------IRSIAVAAEGAGADCISLINTILGLAIDINKKKPILA 211

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
               GLS    + I      +VYE         IG+ GG+     A++ IL     +M+G
Sbjct: 212 NNFGGLSGPAVKPIA---LRMVYEAAHSVKIPVIGM-GGISSWEDAIEFILAGASAIMVG 267

Query: 217 RAAYKNS----AMLTTVDEYFSN 235
            A + N      +++ +++Y  +
Sbjct: 268 TANFVNPIVPIEIISGIEKYLQS 290


>gi|239928591|ref|ZP_04685544.1| hypothetical protein SghaA1_10230 [Streptomyces ghanaensis ATCC
           14672]
          Length = 758

 Score = 35.8 bits (81), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 25/103 (24%), Positives = 51/103 (49%), Gaps = 4/103 (3%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +  R+    ++ A  L  L ++ + +  + ++    +A+LKGL P    K+ N    + Y
Sbjct: 206 IATRLADGKKVSAAELAELDRAFRDNSDSKVF---SQALLKGLGPDGTIKLTNELNQLAY 262

Query: 181 EIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKN 222
           +  K+N   ++ L GGL D +++A ++  SV     G   +K+
Sbjct: 263 DDDKKNKAQYLELQGGLADTIAKATQVPGSVTDAPPGSQKFKD 305


>gi|269976450|ref|ZP_06183435.1| tRNA-dihydrouridine synthase B [Mobiluncus mulieris 28-1]
 gi|269935251|gb|EEZ91800.1| tRNA-dihydrouridine synthase B [Mobiluncus mulieris 28-1]
          Length = 462

 Score = 35.8 bits (81), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 69/154 (44%), Gaps = 20/154 (12%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPL----ALQIGGADISKLVEAA-KIVEDFG 73
             +   EM+ A A+  G  ++ +    +  PL    ++Q+ G     L  AA ++V    
Sbjct: 108 EGMFVGEMVTAKALRMGSARSWV--MVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGL 165

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVK 122
            + I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK
Sbjct: 166 ADHIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVK 225

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R G+D +       ++ +  + +GV  + +HAR
Sbjct: 226 IRSGIDAE--HRIFLDVARVAEDNGVVAVTLHAR 257


>gi|257416234|ref|ZP_05593228.1| pyrimidine biosynthesis D protein [Enterococcus faecalis AR01/DG]
 gi|257158062|gb|EEU88022.1| pyrimidine biosynthesis D protein [Enterococcus faecalis ARO1/DG]
          Length = 312

 Score = 35.8 bits (81), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 12/86 (13%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AKI +      I LN+ CP+ + H G +FG     +PDI      A+ K  S+P+ VK  
Sbjct: 116 AKIGQAPNVKAIELNISCPNVK-HGGIAFGT----DPDIAFQLTQAVKKVASVPIYVKLS 170

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNG 150
             V D +P      + ++I+  G +G
Sbjct: 171 PNVTDIVP------IAQAIEAGGADG 190


>gi|291436919|ref|ZP_06576309.1| predicted protein [Streptomyces ghanaensis ATCC 14672]
 gi|291339814|gb|EFE66770.1| predicted protein [Streptomyces ghanaensis ATCC 14672]
          Length = 834

 Score = 35.8 bits (81), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 25/103 (24%), Positives = 51/103 (49%), Gaps = 4/103 (3%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +  R+    ++ A  L  L ++ + +  + ++    +A+LKGL P    K+ N    + Y
Sbjct: 282 IATRLADGKKVSAAELAELDRAFRDNSDSKVF---SQALLKGLGPDGTIKLTNELNQLAY 338

Query: 181 EIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKN 222
           +  K+N   ++ L GGL D +++A ++  SV     G   +K+
Sbjct: 339 DDDKKNKAQYLELQGGLADTIAKATQVPGSVTDAPPGSQKFKD 381


>gi|291531974|emb|CBK97559.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium siraeum
           70/3]
          Length = 494

 Score = 35.8 bits (81), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 15/122 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           AIL+  K+N        K +   I G    +    A++ E+ G + I  N  CP    H 
Sbjct: 181 AILKKLKENY-----PSKIIVSSIMGESEDEWTALARLSEEAGVDMIECNFSCPQMTSH- 234

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVN 149
            S G+ +  NP++V    AA+ +   +PV  K    + + +IPA+A  N       +G +
Sbjct: 235 -SMGSDVGTNPELVTKYTAAVRRGTKLPVLAKMTPNITNMEIPAIAAVN-------AGAD 286

Query: 150 GI 151
           GI
Sbjct: 287 GI 288


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


Results from round 2




>gi|254781167|ref|YP_003065580.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254040844|gb|ACT57640.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 322

 Score =  457 bits (1177), Expect = e-127,   Method: Composition-based stats.
 Identities = 322/322 (100%), Positives = 322/322 (100%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS
Sbjct: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT
Sbjct: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY
Sbjct: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS
Sbjct: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE
Sbjct: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300

Query: 301 AGASTATHHIIETAFNLMIESL 322
           AGASTATHHIIETAFNLMIESL
Sbjct: 301 AGASTATHHIIETAFNLMIESL 322


>gi|315122552|ref|YP_004063041.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313495954|gb|ADR52553.1| tRNA-dihydrouridine synthase A [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 352

 Score =  424 bits (1090), Expect = e-117,   Method: Composition-based stats.
 Identities = 258/322 (80%), Positives = 292/322 (90%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVDWTDRHYRFFARLLTNNA+LYTEMIVADAIL G+++NILGFST+EKPLALQIGG+DI+
Sbjct: 29  MVDWTDRHYRFFARLLTNNAILYTEMIVADAILYGNRQNILGFSTEEKPLALQIGGSDIA 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KLVE+AKIVEDFGYNEIN NVGCPS  VH GSFGACLML P+ VGDCIAAM  ALSIPVT
Sbjct: 89  KLVESAKIVEDFGYNEINFNVGCPSPNVHAGSFGACLMLTPESVGDCIAAMQNALSIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+QIPA+ALRNL+KSIK+SGV GIWIHARKAIL GLSPKDNRKIP LDYDI+Y
Sbjct: 149 VKCRIGVDNQIPAIALRNLIKSIKQSGVKGIWIHARKAILGGLSPKDNRKIPKLDYDIIY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKKENPDLFIGLNGGL++M Q L++LP VDGVM+GR+AY+NS +L +VDEYF NPLTGS
Sbjct: 209 EIKKENPDLFIGLNGGLDNMQQILQVLPHVDGVMVGRSAYQNSIILASVDEYFMNPLTGS 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P K  +DKDFW++IS SM+ YA RH+ +GGKL  ITRHMIGLFHGFP++RRCRHILTVE
Sbjct: 269 APKKKTIDKDFWKQISDSMSKYADRHIKAGGKLSHITRHMIGLFHGFPHARRCRHILTVE 328

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A A TATH +I+TAFNLMIESL
Sbjct: 329 ANAPTATHQLIKTAFNLMIESL 350


>gi|37528192|ref|NP_931537.1| tRNA-dihydrouridine synthase A [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787629|emb|CAE16736.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 345

 Score =  386 bits (991), Expect = e-105,   Method: Composition-based stats.
 Identities = 142/323 (43%), Positives = 200/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S QE P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEQEHPIALQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AKI ++ GY+EINLNVGCPS RV  G FGACLM   ++V DC+ AM   +++PVT
Sbjct: 92  ALAHCAKIAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAELVADCVKAMQDVVNVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + +   ++ SG N   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDEQDSYQFLCDFIDIVVQHSGCNIFTMHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L I +NGG++ + +A + L  VDG+MIGR AY+N ++L  VD    +    
Sbjct: 212 YQLKKDFPQLTIAINGGIKSLEEAKQHLQHVDGIMIGREAYQNPSILAQVDHELFD---A 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S P+   V       +  ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 SMPVVNTV------AVVKALYPYIEQELSKGTYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  ++ E +
Sbjct: 323 NAHKPGADISVVEQALAMVTERM 345


>gi|323492300|ref|ZP_08097456.1| tRNA-dihydrouridine synthase A [Vibrio brasiliensis LMG 20546]
 gi|323313464|gb|EGA66572.1| tRNA-dihydrouridine synthase A [Vibrio brasiliensis LMG 20546]
          Length = 333

 Score =  386 bits (991), Expect = e-105,   Method: Composition-based stats.
 Identities = 143/323 (44%), Positives = 194/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIHGKG-DFLAYNQEEHPVALQLGGSNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 78  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMGEPQLVADCVAAMRDVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+      T 
Sbjct: 198 YQLKKDFSHLVIAVNGGVKTLQETKEHLQHLDGVMVGREAYQNPYILAEVDQQIFGLDT- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 257 --PIKKR------SQVVEEMYPYIEQQLSKGAYLGHITRHMLGLFQNMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   ++E A   + + L
Sbjct: 309 NAHKPGSGIEVVEAALAKIPKEL 331


>gi|117919170|ref|YP_868362.1| tRNA-dihydrouridine synthase A [Shewanella sp. ANA-3]
 gi|117611502|gb|ABK46956.1| TIM-barrel protein, yjbN family [Shewanella sp. ANA-3]
          Length = 334

 Score =  384 bits (987), Expect = e-105,   Method: Composition-based stats.
 Identities = 144/322 (44%), Positives = 204/322 (63%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++ +
Sbjct: 21  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM +A+ IPVT
Sbjct: 80  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQAVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 140 VKTRIGIDEQDSYEFLTHFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 200 QLKRDYPTLNISINGGITSLEQAKTHLQHLDGVMVGREAYQNPYILAQVDQLLCG----- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 255 ----SQKAVMSREAVIETMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 310

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ A+  +   +
Sbjct: 311 AHKNGAGIEVVKQAYQSIQSEI 332


>gi|152999313|ref|YP_001364994.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS185]
 gi|151363931|gb|ABS06931.1| TIM-barrel protein, yjbN family [Shewanella baltica OS185]
          Length = 339

 Score =  383 bits (983), Expect = e-104,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 200/322 (62%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 205 QLKRDYPTLNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQVLCG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 260 ----SQKAVISREDVIEAMLPYIEAHLQSGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ AF  +   +
Sbjct: 316 AHKNGAGIEVVKQAFQNIQAEV 337


>gi|37681156|ref|NP_935765.1| tRNA-dihydrouridine synthase A [Vibrio vulnificus YJ016]
 gi|326423833|ref|NP_760320.2| tRNA dihydrouridine synthase A [Vibrio vulnificus CMCP6]
 gi|38604852|sp|Q8CWK7|DUSA_VIBVU RecName: Full=tRNA-dihydrouridine synthase A
 gi|37199907|dbj|BAC95736.1| NifR3/Smm1 family protein [Vibrio vulnificus YJ016]
 gi|319999203|gb|AAO09847.2| tRNA dihydrouridine synthase A [Vibrio vulnificus CMCP6]
          Length = 326

 Score =  382 bits (981), Expect = e-104,   Method: Composition-based stats.
 Identities = 142/323 (43%), Positives = 198/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEMI   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMITTGAIIHGKG-DFLAYNQEEHPVALQLGGSNPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P +V DC+AAM + + IPVT
Sbjct: 71  DLATCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A + L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKKDFSHLTIAINGGVKSLEEAKEHLQHLDGVMIGREAYQSPYLLASVDQELFGSQ-- 248

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SPIK R      R+I   M  Y  + L +G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 249 -SPIKKR------RQIVEEMYPYIEQQLANGAYLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGIEVLQQALAKIPQEL 324


>gi|160873928|ref|YP_001553244.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS195]
 gi|160859450|gb|ABX47984.1| TIM-barrel protein, yjbN family [Shewanella baltica OS195]
 gi|315266160|gb|ADT93013.1| TIM-barrel protein, yjbN family [Shewanella baltica OS678]
          Length = 339

 Score =  382 bits (981), Expect = e-104,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 200/322 (62%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 205 QLKRDYPTLNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQVLCG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 260 ----SQKAVISREDVIEAMLPYIEAHLQSGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ AF  +   +
Sbjct: 316 AHKNGAGIEVVKQAFQNIQAEV 337


>gi|86148209|ref|ZP_01066506.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
 gi|218708347|ref|YP_002415968.1| tRNA-dihydrouridine synthase A [Vibrio splendidus LGP32]
 gi|85833979|gb|EAQ52140.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
 gi|218321366|emb|CAV17316.1| tRNA-dihydrouridine synthase A [Vibrio splendidus LGP32]
          Length = 333

 Score =  381 bits (980), Expect = e-104,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AIL G   + L ++ QE PLALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLSQQTLLYTEMVTTGAILHGKG-DFLEYNEQEHPLALQLGGSNPV 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V DC++AM +   IP+T
Sbjct: 78  DLAACAKLAGERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVADCVSAMKEVTDIPIT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G     IHARKA L GLSPK+NR+IP LDYD  
Sbjct: 138 VKTRIGIDDQDSYEFLTKFVSTVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYDRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+  DL I +NGG+  + Q  + L  +DGVMIGR AY +  +L  VD+      T 
Sbjct: 198 YQIKKDFSDLVIAVNGGITTLEQTKEHLQHLDGVMIGREAYHSPFILAEVDQQIFGLDT- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y  R L +G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 257 --PIKKR------SQVVEEMYPYIERQLSNGASLGHISRHMLGLFQSMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   +I+TA   + + L
Sbjct: 309 NAHKKGAGIEVIQTALAKIPKEL 331


>gi|320155187|ref|YP_004187566.1| tRNA dihydrouridine synthase A [Vibrio vulnificus MO6-24/O]
 gi|319930499|gb|ADV85363.1| tRNA dihydrouridine synthase A [Vibrio vulnificus MO6-24/O]
          Length = 326

 Score =  381 bits (980), Expect = e-104,   Method: Composition-based stats.
 Identities = 141/323 (43%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEMI   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMITTGAIIHGKG-DFLSYNQEEHPVALQLGGSNPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P +V DC+A M + + IPVT
Sbjct: 71  DLATCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVATMKEVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A + L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKKDFSHLTIAINGGVKSLEEAKEHLQHLDGVMIGREAYQSPYLLASVDQELFGSQ-- 248

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SPIK R      R+I   M  Y  + L +G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 249 -SPIKKR------RQIVEEMYPYIEQQLANGAYLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGIEVLQQALAKIPQEL 324


>gi|253991388|ref|YP_003042744.1| tRNA -dihydrouridine synthase A [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782838|emb|CAQ86003.1| tRNA-dihydrouridine synthase A [Photorhabdus asymbiotica]
          Length = 341

 Score =  381 bits (979), Expect = e-104,   Method: Composition-based stats.
 Identities = 144/323 (44%), Positives = 200/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   N L ++ +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFHRLLSKQTLLYTEMVTTGAIIHGKG-NYLAYNEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AKI ++ GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +++PVT
Sbjct: 88  ALAHCAKIAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAKLVADCVKAMQDVVNVPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + + ++ SG N   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDEQDSYEFLCDFIDTVVQHSGCNIFTIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L I +NGG++ + +A + L  VDGVMIGR AY+N A+L  VD    + +  
Sbjct: 208 YQLKKDFPQLTIAINGGIKSLEEAKQHLQYVDGVMIGREAYQNPAILAQVDHELFDAVI- 266

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+   V       +  ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 267 --PVVDTV------AVIRALYPYIEQALSQGTYLGHITRHILGIFQGIPGARQWRRHLSE 318

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  ++ E +
Sbjct: 319 NAHKPGADISVVEQALAMVTERM 341


>gi|254230410|ref|ZP_04923791.1| TIM-barrel protein, YjbN family [Vibrio sp. Ex25]
 gi|151937069|gb|EDN55946.1| TIM-barrel protein, YjbN family [Vibrio sp. Ex25]
          Length = 354

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 40  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+E+NLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 99  DLAKCAKLAQERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKGVVDIPVT 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 159 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 218

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 219 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 276 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 329

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 330 NAHKPGSGLEVLQDALAKIPKEL 352


>gi|308125855|ref|ZP_07663540.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus K5030]
 gi|308113305|gb|EFO50845.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus K5030]
          Length = 315

 Score =  381 bits (978), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + +PVT
Sbjct: 60  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDVPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 180 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 291 NAHKPGSGLEVLQDALAKIPKEL 313


>gi|261250374|ref|ZP_05942949.1| tRNA dihydrouridine synthase A [Vibrio orientalis CIP 102891]
 gi|260938943|gb|EEX94930.1| tRNA dihydrouridine synthase A [Vibrio orientalis CIP 102891]
          Length = 333

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIHGKG-DFLAYNQEEHPVALQLGGSNPK 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + +PVT
Sbjct: 78  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMGEPQLVADCVAAMRDVVDVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +++  + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLAIAVNGGVKTLAETKEHLQHLDGVMVGREAYQNPYILAEVDQQIFG---L 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 255 DKPVKKRT------QVVEEMYPYIEQQLSNGAYLGHITRHMLGLFQNMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   ++E A   + + L
Sbjct: 309 NAHKPGSGIEVVEAALAKIPKEL 331


>gi|262393119|ref|YP_003284973.1| tRNA dihydrouridine synthase A [Vibrio sp. Ex25]
 gi|262336713|gb|ACY50508.1| tRNA dihydrouridine synthase A [Vibrio sp. Ex25]
          Length = 315

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+E+NLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 60  DLAKCAKLAQERGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKGVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 180 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 291 NAHKPGSGLEVLQDALAKIPKEL 313


>gi|197334068|ref|YP_002155065.1| tRNA-dihydrouridine synthase A [Vibrio fischeri MJ11]
 gi|197315558|gb|ACH65005.1| tRNA-dihydrouridine synthase A [Vibrio fischeri MJ11]
          Length = 328

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 148/323 (45%), Positives = 202/323 (62%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +ALLYTEM+   AI+ G   + L ++ +E P+ALQ+GG+++ 
Sbjct: 14  MLDWTDRHCRYFHRQLSEHALLYTEMVTTGAIIHGKG-DFLAYNEEEHPVALQLGGSNVK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV  AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+A M   + IPVT
Sbjct: 73  DLVHCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAECVAEMKAVVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 133 VKTRIGIDDQDSYEFLTKFVSTVHEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ +++A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 193 YQIKKDFPQLIIAVNGGIKTLAEAKEHLAHLDGVMIGREAYQSPYLLAEVDQQLFGSD-- 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R      R+I  SM  Y  R L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 251 -KPIKKR------REIVESMYPYIERQLENGAYLGHITRHMLGLFQSMPGARQWRRYISE 303

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++ETA   +   L
Sbjct: 304 NAHKPGAGIEVVETALAKIPSEL 326


>gi|312884652|ref|ZP_07744353.1| tRNA-dihydrouridine synthase A [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367565|gb|EFP95116.1| tRNA-dihydrouridine synthase A [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 333

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 198/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLTN ALLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRFFHRLLTNEALLYTEMVTTGAIIHGKG-DFLAYNQEEHPVALQLGGSNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + IPVT
Sbjct: 78  DLAQCAKLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMREVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYQFLTDFVSIVAEKGGCEQFTIHARKAWLSGLSPKQNREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + ++ + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLNIAINGGVKTLQESQEHLVHLDGVMMGREAYQNPYILAQVDQLIFG---A 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SPIK R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 255 DSPIKKR------SQVVEEMYPYIEQQLSQGAYLGHITRHMLGLFQNMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++TA   + + L
Sbjct: 309 NAHKPGSGIEVVQTALAKIPQEL 331


>gi|262163875|ref|ZP_06031615.1| tRNA-dihydrouridine synthase [Vibrio mimicus VM223]
 gi|262027855|gb|EEY46520.1| tRNA-dihydrouridine synthase [Vibrio mimicus VM223]
          Length = 335

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 196/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++ ALLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLSSQALLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 79  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 139 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+      T 
Sbjct: 199 YQIKRDLPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQIFGLDT- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 258 --PVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 309

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 310 NAHKPGAGLEVVEQALAKIP 329


>gi|59710914|ref|YP_203690.1| tRNA-dihydrouridine synthase A [Vibrio fischeri ES114]
 gi|59479015|gb|AAW84802.1| NifR3/Smm1 family protein [Vibrio fischeri ES114]
          Length = 328

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 148/323 (45%), Positives = 202/323 (62%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +ALLYTEM+   AI+ G   + L ++ +E P+ALQ+GG+++ 
Sbjct: 14  MLDWTDRHCRYFHRQLSEHALLYTEMVTTGAIIHGKG-DFLAYNEEEHPVALQLGGSNVK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV  AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+A M   + IPVT
Sbjct: 73  DLVHCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAECVAEMKAVVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 133 VKTRIGIDDQDSYEFLTKFVSTVHEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ +S+A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 193 YQIKKDFPQLIIAVNGGIKTLSEAKEHLEHLDGVMIGREAYQSPYLLAEVDQQLFGSD-- 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R      R+I  SM  Y  R L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 251 -KPIKKR------REIVESMYPYIERQLENGAYLGHITRHMLGLFQSMPGARQWRRYISE 303

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   +++TA   +   L
Sbjct: 304 NAHKPGAGIEVVKTALAKIPSEL 326


>gi|126175780|ref|YP_001051929.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS155]
 gi|125998985|gb|ABN63060.1| TIM-barrel protein, yjbN family [Shewanella baltica OS155]
          Length = 339

 Score =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 200/322 (62%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 205 QLKRDYPALNIGINGGITTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQVLCG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 260 ----SQKAVISREDVIEAMLPYIEAHLLSGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ AF  +   +
Sbjct: 316 AHKNGAGIEVVKQAFQNIQAEV 337


>gi|149190495|ref|ZP_01868765.1| NifR3/Smm1 family protein [Vibrio shilonii AK1]
 gi|148835619|gb|EDL52586.1| NifR3/Smm1 family protein [Vibrio shilonii AK1]
          Length = 315

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 202/323 (62%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGKG-DFLAYNEEEHPVALQLGGSNPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM + + +PVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMKEVVDVPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V  + +K+G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTRFVSLVSEKAGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ + ++L+ L  +DGVMIGR AY+N  +L  VD+      T 
Sbjct: 180 YQIKKDFPHLQIAVNGGVKTLEESLEHLKHLDGVMIGREAYQNPYILAQVDQLIFGLDT- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R      +++   M  Y  R L +G  L  I+RHMIGLF   P +R+ R  ++ 
Sbjct: 239 --PVKKR------KQVVEEMYPYIERQLANGSYLGHISRHMIGLFQAMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++ETA   +   L
Sbjct: 291 NAHKKGAGIEVLETALAKIPAEL 313


>gi|258622397|ref|ZP_05717420.1| NifR3/Smm1 family protein [Vibrio mimicus VM573]
 gi|258585311|gb|EEW10037.1| NifR3/Smm1 family protein [Vibrio mimicus VM573]
          Length = 339

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 142/320 (44%), Positives = 195/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 24  MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 83  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 143 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+      T 
Sbjct: 203 YQIKRDFPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQIFGLDT- 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 262 --PVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 313

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 314 NAHKPGAGLEVVEQALAKIP 333


>gi|28899501|ref|NP_799106.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260879420|ref|ZP_05891775.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AN-5034]
 gi|260894695|ref|ZP_05903191.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus Peru-466]
 gi|260902033|ref|ZP_05910428.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ4037]
 gi|38604768|sp|Q87L85|DUSA_VIBPA RecName: Full=tRNA-dihydrouridine synthase A
 gi|28807737|dbj|BAC60990.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|308087465|gb|EFO37160.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus Peru-466]
 gi|308089701|gb|EFO39396.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AN-5034]
 gi|308109416|gb|EFO46956.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ4037]
          Length = 326

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + +PVT
Sbjct: 71  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 248 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGLEVLQDALAKIPKEL 324


>gi|260779457|ref|ZP_05888347.1| tRNA dihydrouridine synthase A [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260604266|gb|EEX30570.1| tRNA dihydrouridine synthase A [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 315

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT+  LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLTSETLLYTEMVTTGAIIHGKG-DFLAYNQEEHPVALQLGGSNPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM   + +PVT
Sbjct: 60  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPLLVAECVAAMRDVVDVPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGSDQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +    + L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 180 YQLKKDFAHLNIAINGGVKTLDDTKEHLTHLDGVMVGREAYQNPYILAEVDQQIFG---L 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 DKPVKKRT------QVVQEMYPYIESQLEKGAYLGHITRHMLGLFQNMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   ++ETA + + + L
Sbjct: 291 NAHKPGSGIEVVETALSKIPKEL 313


>gi|188025481|ref|ZP_02958806.2| hypothetical protein PROSTU_00565 [Providencia stuartii ATCC 25827]
 gi|188023335|gb|EDU61375.1| hypothetical protein PROSTU_00565 [Providencia stuartii ATCC 25827]
          Length = 336

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 198/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L FS +E+P+ALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRLLSKNTLLYTEMVTTGAIIHGKG-DYLAFSEEEQPVALQLGGSDPE 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   +SIPVT
Sbjct: 83  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMADAQLVADCVKAMQDVVSIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++  K G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 143 VKTRIGIDEQDSYEFLCDFIDTVSTKGGCEMFIIHARKAWLSGLSPKENREIPPLDYPRV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 203 YQLKRDFPHLTMAINGGIKTLEEAKEHLRHLDGVMVGREAYQNPSILTAVDNQLFDSQL- 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+   VD          M  Y  + L  G  L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 262 --PVVNAVDA------VRQMFPYIEKELSQGTYLGHITRHMLGIFQGIPGARQWRRYLSE 313

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 314 NAHKKGADLAVVEQALAFVT 333


>gi|328472365|gb|EGF43235.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus 10329]
          Length = 326

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 138/323 (42%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM + + +PVT
Sbjct: 71  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVAECVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 248 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGLEVLQDALAKIPKEL 324


>gi|153839570|ref|ZP_01992237.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ3810]
 gi|149746903|gb|EDM57891.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus AQ3810]
          Length = 326

 Score =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + +PVT
Sbjct: 71  DLAKCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 191 YQLKQDFSHLTIAINGGVKSLEEAKVHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 248 NAPVKKR------SEIVEEMYPYIETQLAKGAYLGHITRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 302 NAHKPGSGLEVLQDALAKIPKEL 324


>gi|84393138|ref|ZP_00991902.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
 gi|84376190|gb|EAP93074.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
          Length = 334

 Score =  379 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 148/323 (45%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEMI   AIL G   + L ++ QE PLALQ+GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLSQQTLLYTEMITTGAILHGKG-DFLEYNEQEHPLALQLGGSNPV 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V DC++AM +   IP+T
Sbjct: 79  DLAACAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVADCVSAMKEVTDIPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G     IHARKA L GLSPK+NR+IP LDYD  
Sbjct: 139 VKTRIGIDDQDSYEFLTKFVSTVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYDRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+  DL I +NGG+  + Q  + L  +DGVMIGR AY +  +L  VD+      T 
Sbjct: 199 YQIKKDFSDLVIAVNGGVTTLEQTKEHLQHLDGVMIGREAYHSPFILAEVDQQIFGLDT- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y  R L +G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 258 --PIKKR------SQVVEEMYPYIERELSNGASLGHISRHMLGLFQSMPGARQWRRYISE 309

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   +++TA   + + L
Sbjct: 310 NAHKKGAGIEVMQTALAKIPKEL 332


>gi|269964431|ref|ZP_06178672.1| NifR3/Smm1 family protein [Vibrio alginolyticus 40B]
 gi|269830769|gb|EEZ84987.1| NifR3/Smm1 family protein [Vibrio alginolyticus 40B]
          Length = 354

 Score =  379 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++ +
Sbjct: 40  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPA 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 99  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDIPVT 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 159 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 218

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 219 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 276 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 329

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 330 NAHKPGSGLEVLQDALAKIPKEL 352


>gi|258625982|ref|ZP_05720847.1| NifR3/Smm1 family protein [Vibrio mimicus VM603]
 gi|258581730|gb|EEW06614.1| NifR3/Smm1 family protein [Vibrio mimicus VM603]
          Length = 339

 Score =  379 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 196/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 24  MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 83  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 143 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+      T 
Sbjct: 203 YQIKRDFPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQIFGLDT- 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 262 --PVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 313

Query: 300 EAGASTATHHIIETAFNLMI 319
            A  S A   ++E A   + 
Sbjct: 314 NAHKSGAGLEVVEQALAKIP 333


>gi|217971989|ref|YP_002356740.1| tRNA-dihydrouridine synthase A [Shewanella baltica OS223]
 gi|217497124|gb|ACK45317.1| TIM-barrel protein, yjbN family [Shewanella baltica OS223]
          Length = 339

 Score =  379 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 199/322 (61%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 205 QLKRDYPALNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQVLCG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +   M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 260 ----SQKAVISREDVIEVMLPYIEAHLLSGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ AF  +   +
Sbjct: 316 AHKNGAGIEVVKQAFQNIQAEV 337


>gi|323495575|ref|ZP_08100649.1| tRNA-dihydrouridine synthase A [Vibrio sinaloensis DSM 21326]
 gi|323319456|gb|EGA72393.1| tRNA-dihydrouridine synthase A [Vibrio sinaloensis DSM 21326]
          Length = 333

 Score =  379 bits (974), Expect = e-103,   Method: Composition-based stats.
 Identities = 143/323 (44%), Positives = 194/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 19  MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIHGKG-DFLAYNQEEHPVALQLGGSNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V  C+A+M + + IPVT
Sbjct: 78  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVASMREVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 138 VKTRIGIDDQDSYEFLTDFVSIVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +  +L  L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 198 YQLKKDFSHLNIAVNGGVKTLEDSLVHLEHLDGVMVGREAYQNPYLLAQVDQQIFG---L 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y    L  G  L  ITRHMIGLF   P +R+ R  ++ 
Sbjct: 255 DKPVKKR------SQVVEEMYPYIEAQLSKGAYLGHITRHMIGLFQAMPGARQWRRYISE 308

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++ETA   + + L
Sbjct: 309 NAHKPGAGIEVVETALAKIPQEL 331


>gi|91227265|ref|ZP_01261690.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
 gi|91188659|gb|EAS74948.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
          Length = 315

 Score =  379 bits (974), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++ +
Sbjct: 1   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 60  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 180 YQLKQDFSHLTIAINGGVKSLEEAKAHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 237 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 291 NAHKPGSGLEVLQDALAKIPKEL 313


>gi|304411176|ref|ZP_07392791.1| TIM-barrel protein, yjbN family [Shewanella baltica OS183]
 gi|307306471|ref|ZP_07586214.1| TIM-barrel protein, yjbN family [Shewanella baltica BA175]
 gi|304350369|gb|EFM14772.1| TIM-barrel protein, yjbN family [Shewanella baltica OS183]
 gi|306910762|gb|EFN41190.1| TIM-barrel protein, yjbN family [Shewanella baltica BA175]
          Length = 339

 Score =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 200/322 (62%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPV 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVIDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 145 VKTRIGIDEQDSYAFLTQFIDVVSAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 205 QLKRDYPTLNIGINGGVTTLEQAQLHLAQLDGVMMGREAYQNPYILAQVDQVLCG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL SGG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 260 ----SQKAVISREDVIEAMLPYIEAHLLSGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ AF  +   +
Sbjct: 316 AHKNGAGIEVVKQAFQNIQAEV 337


>gi|148981615|ref|ZP_01816472.1| tRNA-dihydrouridine synthase A [Vibrionales bacterium SWAT-3]
 gi|145960800|gb|EDK26135.1| tRNA-dihydrouridine synthase A [Vibrionales bacterium SWAT-3]
          Length = 315

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 194/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AIL G   + L +S QE PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSQQTLLYTEMVTTGAILHGKG-DFLEYSEQEHPLALQLGGSNPV 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V DC+ AM +   IP+T
Sbjct: 60  DLAACAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVADCVLAMKEVTDIPIT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDYD  
Sbjct: 120 VKTRIGIDDQDSYEFLTKFISTVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYDRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+  DL I +NGG+  + Q  + L  +DGVMIGR AY +  +L  VD+      T 
Sbjct: 180 YQIKKDFSDLVIAVNGGITTLEQTKEHLQHLDGVMIGREAYHSPFILAEVDQQIFGLDT- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y  R L  G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 239 --PIKKR------SQVVEEMYPYIERELSKGASLGHISRHMLGLFQSMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   +++TA   + + L
Sbjct: 291 NAHKKGAGIEVMQTALAKIPKEL 313


>gi|260773671|ref|ZP_05882587.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
 gi|260612810|gb|EEX38013.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
          Length = 335

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 196/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT+  LLYTEM+   AI+ G   + L ++ +E P++LQ+GG++ +
Sbjct: 20  MLDWTDRHCRYFHRLLTSQTLLYTEMVTTGAIIHGKG-DFLTYNQEEHPVSLQLGGSNPT 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ +D GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM + + IPVT
Sbjct: 79  DLAHCAKLAQDRGYDEINLNVGCPSDRVQNGKFGACLMAEPQLVADCVAAMREVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V+ + ++ G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 139 VKTRIGIDDQDSYEFLTRFVQLVSEQGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++ L  L  +DGVM+GR AY+N  +L   D+        
Sbjct: 199 YQLKQDFPHLTIAINGGVKSLTEVLDHLQHLDGVMVGREAYQNPYLLAEADQQIFG---L 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 256 DKPIKKR------SQVVQEMYPYIEQQLTQGAYLGHITRHMLGLFQSMPGARQWRRYISE 309

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    +   ++ETA   + 
Sbjct: 310 NAHKPGSGVEVVETALAKIP 329


>gi|260767137|ref|ZP_05876081.1| tRNA-dihydrouridine synthase [Vibrio furnissii CIP 102972]
 gi|260617858|gb|EEX43033.1| tRNA-dihydrouridine synthase [Vibrio furnissii CIP 102972]
          Length = 316

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 197/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPV 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P++V  C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVAAMKAVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + ++ G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTHFVTVVSEQGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVMIGR AY++  +L  VD+      T 
Sbjct: 180 YQLKQDFPQLTIAVNGGVKSLAEAKEHLQHLDGVMIGREAYQSPYLLAEVDQQIFGLDT- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 239 --PVKKR------SQVVQEMYPYIEQQLAQGSYLGHITRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMI 319
            A  + A   ++E A   + 
Sbjct: 291 NAHKAGAGIEVVEQALAKIP 310


>gi|119776187|ref|YP_928927.1| tRNA-dihydrouridine synthase A [Shewanella amazonensis SB2B]
 gi|119768687|gb|ABM01258.1| TIM-barrel protein, yjbN family [Shewanella amazonensis SB2B]
          Length = 326

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 144/318 (45%), Positives = 202/318 (63%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G   + L ++ +E PLALQ+GG+D  
Sbjct: 14  MLDWTDRHYRYFARLMSKEALLYTEMVTTGAILHGKG-DYLAYNQEEHPLALQLGGSDPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+N+NVGCPS RV  G FGACLM  P +V +C+ AM + +S+PVT
Sbjct: 73  DLATCAKLAEARGYDEVNINVGCPSDRVQNGRFGACLMAEPKLVAECVDAMRQQVSVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + V+++  +G +   IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 133 VKTRIGIDEQDSYGFLTDFVETVSAAGCDTFIIHARKAWLQGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L +VD          
Sbjct: 193 QLKRDYPQLSISINGGVTSIEQAKTHLAQLDGVMVGREAYQNPYILASVDTELCG---KP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + +R       ++   +  Y  +HL  GG+L  I+RH+IGL+ G P SR  R  L+  
Sbjct: 250 AVVSSR------EEVIGKLLPYIGKHLADGGRLNHISRHIIGLYQGLPGSRAWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IE A   M
Sbjct: 304 AHKPGAGIEVIENAIKAM 321


>gi|315181327|gb|ADT88241.1| tRNA-dihydrouridine synthase A [Vibrio furnissii NCTC 11218]
          Length = 319

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 197/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 4   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPV 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P++V  C+AAM   + IPVT
Sbjct: 63  DLARCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVAAMKAVVDIPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + ++ G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 123 VKTRIGIDDQDSYEFLTHFVTVVSEQGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 182

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVMIGR AY++  +L  VD+      T 
Sbjct: 183 YQLKQDFPQLTIAVNGGVKSLAEAKEHLQHLDGVMIGREAYQSPYLLAEVDQQIFGLDT- 241

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  + L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 242 --PVKKR------SQVVQEMYPYIEQQLAQGSYLGHITRHMLGLFQNMPGARQWRRHISE 293

Query: 300 EAGASTATHHIIETAFNLMI 319
            A  + A   ++E A   + 
Sbjct: 294 NAHKAGAGIEVVEQALAKIP 313


>gi|114046253|ref|YP_736803.1| tRNA-dihydrouridine synthase A [Shewanella sp. MR-7]
 gi|113887695|gb|ABI41746.1| TIM-barrel protein, yjbN family [Shewanella sp. MR-7]
          Length = 340

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 142/322 (44%), Positives = 202/322 (62%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++ +
Sbjct: 26  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 85  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 145 VKTRIGIDEQDSYEFLTHFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++   L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 205 QLKRDYSTLNISINGGITSLEQAKTHLQHLDGVMVGREAYQNPYILAQVDQLLCG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 260 ----SQKAVISREAVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ A+  +   +
Sbjct: 316 AHKNGAGIEVVKQAYQSIQSEI 337


>gi|255747176|ref|ZP_05421119.1| tRNA dihydrouridine synthase A [Vibrio cholera CIRS 101]
 gi|262147248|ref|ZP_06028049.1| tRNA dihydrouridine synthase A [Vibrio cholerae INDRE 91/1]
 gi|262166864|ref|ZP_06034586.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC27]
 gi|262190629|ref|ZP_06048865.1| tRNA dihydrouridine synthase A [Vibrio cholerae CT 5369-93]
 gi|255735225|gb|EET90627.1| tRNA dihydrouridine synthase A [Vibrio cholera CIRS 101]
 gi|262024694|gb|EEY43373.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC27]
 gi|262031308|gb|EEY49921.1| tRNA dihydrouridine synthase A [Vibrio cholerae INDRE 91/1]
 gi|262033494|gb|EEY51996.1| tRNA dihydrouridine synthase A [Vibrio cholerae CT 5369-93]
 gi|327483237|gb|AEA77644.1| tRNA dihydrouridine synthase A [Vibrio cholerae LMA3894-4]
          Length = 316

 Score =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 193/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 180 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---L 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 237 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 291 NAHKPGAGLEVVEQALAKIP 310


>gi|254508997|ref|ZP_05121103.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus 16]
 gi|219548101|gb|EED25120.1| tRNA-dihydrouridine synthase A [Vibrio parahaemolyticus 16]
          Length = 315

 Score =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 193/323 (59%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLTN  LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLTNETLLYTEMVTTGAIIYGKG-DFLAYNEEEHPVALQLGGSNPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMRDVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ +  +L  L  VDGVM+GR AY+N  +L  VD+        
Sbjct: 180 YQLKKDFAHLNIAVNGGVKTLGDSLSHLEHVDGVMVGREAYQNPYLLAEVDQQIFG---L 236

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R       ++   M  Y    L  G  L  ITRHMIGLF   P +R+ R  ++ 
Sbjct: 237 DKPIKKR------SQVVKEMYPYIEAQLSKGAYLGHITRHMIGLFQAMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A   + + L
Sbjct: 291 NAHKPGAGIEVVEAALAKIPQEL 313


>gi|153803249|ref|ZP_01957835.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-3]
 gi|229519914|ref|ZP_04409345.1| tRNA dihydrouridine synthase A [Vibrio cholerae TM 11079-80]
 gi|124121229|gb|EAY39972.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-3]
 gi|229343042|gb|EEO08029.1| tRNA dihydrouridine synthase A [Vibrio cholerae TM 11079-80]
          Length = 327

 Score =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 194/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++ +
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPN 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---L 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 302 NAHKPGAGLEVVEQALAKIP 321


>gi|163803123|ref|ZP_02197007.1| tRNA-dihydrouridine synthase A [Vibrio sp. AND4]
 gi|159173115|gb|EDP57947.1| tRNA-dihydrouridine synthase A [Vibrio sp. AND4]
          Length = 318

 Score =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L  + +E PLALQ+GG++ +
Sbjct: 4   MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAHNEEEHPLALQLGGSNPA 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + +PVT
Sbjct: 63  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDVPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DD      L + V  + +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 123 VKTRIGIDDHDSYQFLTDFVSIVSEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 182

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 183 YQLKKDFSHLTIAINGGVKSLEEAKEHLQHLDGVMIGREAYQSPYLLAFVDQELFGS--- 239

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 240 NAPVKKR------SQIVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRYISE 293

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 294 NAHKPGSGLEVLQAALAKIPKEL 316


>gi|15640406|ref|NP_230033.1| tRNA-dihydrouridine synthase A [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590952|ref|ZP_01678272.1| TIM-barrel protein, yjbN family [Vibrio cholerae 2740-80]
 gi|121729744|ref|ZP_01682184.1| TIM-barrel protein, yjbN family [Vibrio cholerae V52]
 gi|147675235|ref|YP_001218647.1| tRNA-dihydrouridine synthase A [Vibrio cholerae O395]
 gi|153820423|ref|ZP_01973090.1| TIM-barrel protein, yjbN family [Vibrio cholerae NCTC 8457]
 gi|153823513|ref|ZP_01976180.1| TIM-barrel protein, yjbN family [Vibrio cholerae B33]
 gi|153827262|ref|ZP_01979929.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-2]
 gi|153830467|ref|ZP_01983134.1| TIM-barrel protein, yjbN family [Vibrio cholerae 623-39]
 gi|227080591|ref|YP_002809142.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|229504962|ref|ZP_04394473.1| tRNA dihydrouridine synthase A [Vibrio cholerae BX 330286]
 gi|229508600|ref|ZP_04398096.1| tRNA dihydrouridine synthase A [Vibrio cholerae B33]
 gi|229516011|ref|ZP_04405462.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC9]
 gi|229526966|ref|ZP_04416363.1| tRNA dihydrouridine synthase A [Vibrio cholerae 12129(1)]
 gi|229606339|ref|YP_002876987.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MJ-1236]
 gi|254286198|ref|ZP_04961157.1| TIM-barrel protein, yjbN family [Vibrio cholerae AM-19226]
 gi|254851689|ref|ZP_05241039.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MO10]
 gi|298501275|ref|ZP_07011073.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MAK 757]
 gi|38605061|sp|Q9KUX9|DUSA_VIBCH RecName: Full=tRNA-dihydrouridine synthase A
 gi|9654797|gb|AAF93552.1| NifR3/Smm1 family protein [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121547178|gb|EAX57305.1| TIM-barrel protein, yjbN family [Vibrio cholerae 2740-80]
 gi|121628529|gb|EAX61013.1| TIM-barrel protein, yjbN family [Vibrio cholerae V52]
 gi|126509034|gb|EAZ71628.1| TIM-barrel protein, yjbN family [Vibrio cholerae NCTC 8457]
 gi|126518958|gb|EAZ76181.1| TIM-barrel protein, yjbN family [Vibrio cholerae B33]
 gi|146317118|gb|ABQ21657.1| TIM-barrel protein, yjbN family [Vibrio cholerae O395]
 gi|148874069|gb|EDL72204.1| TIM-barrel protein, yjbN family [Vibrio cholerae 623-39]
 gi|149738810|gb|EDM53152.1| TIM-barrel protein, yjbN family [Vibrio cholerae MZO-2]
 gi|150423613|gb|EDN15555.1| TIM-barrel protein, yjbN family [Vibrio cholerae AM-19226]
 gi|227008479|gb|ACP04691.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|227012235|gb|ACP08445.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|229335578|gb|EEO01058.1| tRNA dihydrouridine synthase A [Vibrio cholerae 12129(1)]
 gi|229346914|gb|EEO11881.1| tRNA dihydrouridine synthase A [Vibrio cholerae RC9]
 gi|229354368|gb|EEO19295.1| tRNA dihydrouridine synthase A [Vibrio cholerae B33]
 gi|229358020|gb|EEO22936.1| tRNA dihydrouridine synthase A [Vibrio cholerae BX 330286]
 gi|229368994|gb|ACQ59417.1| tRNA dihydrouridine synthase A [Vibrio cholerae MJ-1236]
 gi|254847394|gb|EET25808.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MO10]
 gi|297540029|gb|EFH76092.1| tRNA-dihydrouridine synthase A [Vibrio cholerae MAK 757]
          Length = 327

 Score =  378 bits (970), Expect = e-103,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 193/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---L 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 302 NAHKPGAGLEVVEQALAKIP 321


>gi|226326586|ref|ZP_03802104.1| hypothetical protein PROPEN_00436 [Proteus penneri ATCC 35198]
 gi|225205011|gb|EEG87365.1| hypothetical protein PROPEN_00436 [Proteus penneri ATCC 35198]
          Length = 344

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 196/322 (60%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ N LLYTEM+   AI+ G   + L +S +E P++LQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFFRQLSKNTLLYTEMVTTGAIIHGKG-DYLKYSEEEHPVSLQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM +  +V +C+ AM   + IPVT
Sbjct: 92  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGDAQLVANCVKAMRDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + +  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIETVSRDNNCDTFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++ + +A + L  +DGVM+GR AY+N ++L  VD    +    
Sbjct: 212 YQLKRDFSHLTMAINGGIKSLEEAKEHLKHMDGVMVGREAYQNPSILAHVDHELFDNQL- 270

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PI   V          +M  Y  + L  G  L  +TRHM+G+F G P +R+ R  L+ 
Sbjct: 271 --PIADAV------AAVRAMYPYIEKELSQGTYLGHVTRHMLGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   + + 
Sbjct: 323 NAHKQGADLSVLENALKFVTDK 344


>gi|54310405|ref|YP_131425.1| tRNA-dihydrouridine synthase A [Photobacterium profundum SS9]
 gi|46914846|emb|CAG21623.1| putative NifR3/Smm1 family protein [Photobacterium profundum SS9]
          Length = 346

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 205/323 (63%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AI+ G   + L F+ +E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRLLSDNALLYTEMVTTGAIIHGKG-DFLTFNEEENPVALQLGGSNPV 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   D+V  C+++M + + IPVT
Sbjct: 91  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEADLVALCVSSMREVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ +KSG +   +HARKA LKGLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDEQDSYQFLVDFIGTVNEKSGCDNFTVHARKAWLKGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P++ + +NGG++   +  + L  +DGVM+GR AY+N  ++  VD+        
Sbjct: 211 YQLKRDFPNIIMAINGGIKTFDEMEEHLKHMDGVMVGREAYQNPYLMAEVDQRLFGS--- 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S PI  R      R+ + +M  Y  R L +G KL  ITRHM+GLF G P  R+ R  ++ 
Sbjct: 268 SKPIIKR------REAAEAMFPYIERQLANGSKLGHITRHMLGLFQGIPGGRQWRRYISE 321

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   +   L
Sbjct: 322 NAHKPGSGIEVVQRALEKISNDL 344


>gi|153216666|ref|ZP_01950573.1| TIM-barrel protein, yjbN family [Vibrio cholerae 1587]
 gi|124114177|gb|EAY32997.1| TIM-barrel protein, yjbN family [Vibrio cholerae 1587]
          Length = 327

 Score =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 192/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+A M   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVATMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---L 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 302 NAHKPGAGLEVVEQALAKIP 321


>gi|331650053|ref|ZP_08351126.1| tRNA-dihydrouridine synthase A [Escherichia coli M605]
 gi|331040998|gb|EGI13155.1| tRNA-dihydrouridine synthase A [Escherichia coli M605]
          Length = 345

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|237809463|ref|YP_002893903.1| TIM-barrel protein, yjbN family [Tolumonas auensis DSM 9187]
 gi|237501724|gb|ACQ94317.1| TIM-barrel protein, yjbN family [Tolumonas auensis DSM 9187]
          Length = 338

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 152/320 (47%), Positives = 201/320 (62%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AIL G   + L +ST+E P+ALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAILFGKG-DYLQYSTEEHPIALQLGGSDPV 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I ED GY+EINLNVGCPS RV  G FGACLM +  +V DC+AAM   + IPVT
Sbjct: 83  DLAKCARIAEDRGYDEINLNVGCPSDRVQNGRFGACLMASAQLVADCVAAMRAEVQIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + +++++++G N   +HARKA L GLSPK+NR IP LDY+ VY
Sbjct: 143 VKTRIGIDELDSYAFLCDFIETVQQTGCNTFIVHARKAWLSGLSPKENRDIPPLDYERVY 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+ D++QA   L  VDGVM+GR AY+N  ML  VD          
Sbjct: 203 QLKRDYPHLTIAINGGITDLAQAKHHLQYVDGVMVGREAYQNPYMLAQVDAQL---FADP 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       +    M  Y   HL +GG L  ITRHM+GLF G P +R  R  L+  
Sbjct: 260 HPVLSR------HETVMQMLPYIDAHLQAGGYLSHITRHMLGLFQGVPGARAWRRHLSEN 313

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   I+  A + + E
Sbjct: 314 ATRKGADTKIVLDALSHVQE 333


>gi|292490501|ref|YP_003525940.1| TIM-barrel protein, yjbN family [Nitrosococcus halophilus Nc4]
 gi|291579096|gb|ADE13553.1| TIM-barrel protein, yjbN family [Nitrosococcus halophilus Nc4]
          Length = 340

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 136/320 (42%), Positives = 200/320 (62%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RL++++ALLYTEM+   A++ GD++  L +   E PLA+Q+GG++  
Sbjct: 27  MMEWTDRHCRYFLRLISHHALLYTEMVTTGALIHGDRERFLAYHPTEHPLAVQLGGSNPE 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ ED G++E+NLNVGCPS RV  G FGACLM+ P++V +C+AAM + + +PVT
Sbjct: 87  ELAFCARLAEDHGFDEVNLNVGCPSDRVQSGRFGACLMMEPELVAECVAAMAQTVQLPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+Q    AL   + ++ ++G     +HARKA L+GLSPK+NR+ P L Y++V 
Sbjct: 147 VKTRIGVDEQDSYEALTRFINTVSQAGCRTFILHARKAWLQGLSPKENREKPPLRYEVVR 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK++ P L + +NGG+  + +A + L  +DG+MIGRAAY N  +L  VD YF       
Sbjct: 207 AIKQDFPHLEVVINGGIATLEEAQEQLTLLDGIMIGRAAYHNPYLLAQVDRYFYGDFH-- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ TR        I  +   Y    L  G  L +ITRH++GLF G P +R  R  L+  
Sbjct: 265 -PLPTR------HGIMEAFLPYVEEQLAQGIYLSRITRHILGLFQGQPGARAWRRYLSEN 317

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   +I  A   + +
Sbjct: 318 AHRPGAGIEVIREALRRVPQ 337


>gi|197286568|ref|YP_002152440.1| tRNA-dihydrouridine synthase A [Proteus mirabilis HI4320]
 gi|194684055|emb|CAR45390.1| tRNA-dihydrouridine synthase A [Proteus mirabilis HI4320]
          Length = 344

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 193/322 (59%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT N LLYTEM+   AI+ G   + L +S +E P++LQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFFRQLTKNTLLYTEMVTTGAIIHGKG-DYLKYSNEEHPISLQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   + IPVT
Sbjct: 92  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ + +  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDNQDSYQFLCDFIDTVSRDNNCDTFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++ + +A + L  +DGVM+GR AY+N ++L  VD    +    
Sbjct: 212 YQLKRDFSHLTMAINGGIKSLEEAQEHLKYMDGVMVGREAYQNPSILAHVDHVLFDN--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 ++          +M  Y  + L  G  L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 269 ------QLPVANAVAAVKAMYPYIEKELSQGTYLGHITRHMLGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   + E 
Sbjct: 323 NAHKQGADLTVLENALKFVTEK 344


>gi|77166407|ref|YP_344932.1| tRNA-dihydrouridine synthase A [Nitrosococcus oceani ATCC 19707]
 gi|254435191|ref|ZP_05048698.1| TIM-barrel protein, yjbN family [Nitrosococcus oceani AFC27]
 gi|76884721|gb|ABA59402.1| tRNA-U16,U17-dihydrouridine synthase [Nitrosococcus oceani ATCC
           19707]
 gi|207088302|gb|EDZ65574.1| TIM-barrel protein, yjbN family [Nitrosococcus oceani AFC27]
          Length = 337

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 196/319 (61%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RL+++ ALLYTEM+ A A++ G++   L +   E PLALQ+GG+   
Sbjct: 27  MMEWTDRHCRYFLRLISHRALLYTEMVTAGALIHGNRARFLAYHKSEHPLALQLGGSHPE 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ ED+G++E+NLNVGCPS RV  G FGACLM  P++V +C+AAM +A  IPVT
Sbjct: 87  ELALCAQMAEDYGFDEVNLNVGCPSNRVQSGRFGACLMAEPELVAECVAAMAQATQIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q    AL + + ++ ++G     IHARKA L+GLSPK+NR+ P L YD+V 
Sbjct: 147 VKTRIGIDEQDSYEALDHFISTVAQAGCRTFIIHARKAWLQGLSPKENREKPPLRYDVVR 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK++ P L + +NGG+  + +  + L  +DGVMIGRAAY N  +L  VD  F       
Sbjct: 207 TIKQDFPQLTVIINGGITTLEEISEHLELLDGVMIGRAAYHNPYLLAQVDRNFYGDFH-- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  TR       +I  +   Y A  L  G  L  +TRH++GLF G P +R  R  L+  
Sbjct: 265 -PFLTR------HEIIEAFLPYVAEQLVQGVYLNHMTRHILGLFQGQPGARAWRRHLSEN 317

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   II  A   M 
Sbjct: 318 AHRPGAGIEIIREALRQMP 336


>gi|319425100|gb|ADV53174.1| TIM-barrel protein, yjbN family [Shewanella putrefaciens 200]
          Length = 343

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 142/322 (44%), Positives = 196/322 (60%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 30  MLDWTDRHYRYFARLMSAKALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 89  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 149 VKTRIGIDEQDSYEFLTYFIDIVNAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 209 QLKRDYPVLNISINGGVTTLEQAQGHLSQLDGVMMGREAYQNPYILARVDQVLCG----- 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 264 ----SQRAVISREDVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 319

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A    +  AF  +   +
Sbjct: 320 AHKNGAGIETVRQAFQSIQTEM 341


>gi|262172527|ref|ZP_06040205.1| tRNA-dihydrouridine synthase [Vibrio mimicus MB-451]
 gi|261893603|gb|EEY39589.1| tRNA-dihydrouridine synthase [Vibrio mimicus MB-451]
          Length = 316

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 194/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D Q     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDAQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A + L  +DGVMIGR AY+N  +L  VD+      T 
Sbjct: 180 YQIKRDFPHLTIAVNGGVKTLEEAQQHLQYLDGVMIGREAYQNPYLLAEVDQQIFGLDT- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  R L  G  L  +TRH++GLF   P +R+ R  ++ 
Sbjct: 239 --PVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHILGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 291 NAHKPGAGLEVVEQALTKIP 310


>gi|193067849|ref|ZP_03048815.1| tRNA-dihydrouridine synthase A [Escherichia coli E110019]
 gi|192958824|gb|EDV89261.1| tRNA-dihydrouridine synthase A [Escherichia coli E110019]
          Length = 339

 Score =  376 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ LQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVVLQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|293417553|ref|ZP_06660175.1| tRNA-dihydrouridine synthase A [Escherichia coli B185]
 gi|291430271|gb|EFF03269.1| tRNA-dihydrouridine synthase A [Escherichia coli B185]
          Length = 345

 Score =  376 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 202/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E+ GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSYT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|209694000|ref|YP_002261928.1| tRNA-dihydrouridine synthase A [Aliivibrio salmonicida LFI1238]
 gi|208007951|emb|CAQ78084.1| tRNA-dihydrouridine synthase A [Aliivibrio salmonicida LFI1238]
          Length = 338

 Score =  376 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 199/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +ALLY+EMI   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 24  MLDWTDRHCRYFHRQLSEHALLYSEMITTGAIIHGKG-DFLAYNEEEHPLALQLGGSNAK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  D GY+EINLNVGCPS RV  G FGACLM +P++V +CIA M   + IPVT
Sbjct: 83  DLAHCAKLAADRGYDEINLNVGCPSDRVQNGRFGACLMADPELVAECIAEMKAVVDIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V ++ +K G +   IHARKA L GLSPK+NR+IP LDY   
Sbjct: 143 VKTRIGIDDQDSYEFLTKFVSTVHEKGGCDQFTIHARKAWLSGLSPKENREIPPLDYPRA 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ + +A + L  +DGVMIGR AY++  +L  VD+        
Sbjct: 203 YQIKKDFPQLIIAVNGGIKTLEEAKEHLAHLDGVMIGREAYQSPYLLAEVDQQLFGSD-- 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PIK R      R+I  SM  Y  R L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 261 -KPIKKR------REIVESMYPYIERQLENGAHLGHITRHMLGLFQSMPGARQWRRYISE 313

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   +   L
Sbjct: 314 NAHKPGSGIEVVQAALAKIPAEL 336


>gi|227357643|ref|ZP_03841996.1| tRNA-dihydrouridine synthase A [Proteus mirabilis ATCC 29906]
 gi|227162353|gb|EEI47357.1| tRNA-dihydrouridine synthase A [Proteus mirabilis ATCC 29906]
          Length = 344

 Score =  376 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 134/322 (41%), Positives = 192/322 (59%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT N LLYTEM+   AI+ G   + L +S +E P++LQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFFRQLTKNTLLYTEMVTTGAIIHGKG-DYLKYSNEEHPISLQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   + IPVT
Sbjct: 92  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ + +  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDNQDSYQFLCDFIDTVSRDNNCDTFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++ + +A + L  +DGVM+GR AY+N ++L  VD    +    
Sbjct: 212 YQLKRDFSHLTMAINGGIKSLEEAQEHLKYMDGVMVGREAYQNPSILAHVDHVLFDNQLP 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +     V           M  Y  + L  G  L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 272 VTNAVAAVKA---------MYPYIEKELSQGTYLGHITRHMLGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   + E 
Sbjct: 323 NAHKQGADLTVLENALKFVTEK 344


>gi|269961484|ref|ZP_06175848.1| NifR3/Smm1 family protein [Vibrio harveyi 1DA3]
 gi|269833861|gb|EEZ87956.1| NifR3/Smm1 family protein [Vibrio harveyi 1DA3]
          Length = 369

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++ +
Sbjct: 55  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNAA 113

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + IPVT
Sbjct: 114 DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDIPVT 173

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 174 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 233

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+   L I +NGG++ + +A   L  +DGVMIGR AY++  +L +VD+        
Sbjct: 234 YQLKKDFSHLTIAINGGVKSLEEAKDHLQHLDGVMIGREAYQSPYLLASVDQELFGS--- 290

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+K R       +I   M  Y    L  G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 291 NAPVKKR------SEIVEEMYPYIEAQLAKGAYLGHISRHMLGLFQNMPGARQWRRHISE 344

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A   + + L
Sbjct: 345 NAHKPGSGLEVLQDALAKIPKEL 367


>gi|146291866|ref|YP_001182290.1| tRNA-dihydrouridine synthase A [Shewanella putrefaciens CN-32]
 gi|145563556|gb|ABP74491.1| TIM-barrel protein, yjbN family [Shewanella putrefaciens CN-32]
          Length = 343

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 143/322 (44%), Positives = 196/322 (60%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 30  MLDWTDRHYRYFARLMSAKALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+ AM + + IPVT
Sbjct: 89  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAECVDAMKQVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 149 VKTRIGIDEQDSYEFLTYFIDIVNAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 209 QLKRDYPVLNISINGGVTTLEQAQGHLAQLDGVMMGREAYQNPYILARVDQVLCG----- 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 264 ----SQRAVISREDVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 319

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A    +  AF  +   +
Sbjct: 320 AHKNGAGIETVRQAFQSIQTEM 341


>gi|194426795|ref|ZP_03059348.1| tRNA-dihydrouridine synthase A [Escherichia coli B171]
 gi|194415131|gb|EDX31400.1| tRNA-dihydrouridine synthase A [Escherichia coli B171]
 gi|195183268|dbj|BAG66809.1| tRNA-dihydrouridine synthase A [Escherichia coli O111:H-]
          Length = 345

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEAHGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|212710291|ref|ZP_03318419.1| hypothetical protein PROVALCAL_01350 [Providencia alcalifaciens DSM
           30120]
 gi|212687098|gb|EEB46626.1| hypothetical protein PROVALCAL_01350 [Providencia alcalifaciens DSM
           30120]
          Length = 341

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 142/320 (44%), Positives = 195/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AI+ G   + L +S +E P++LQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAIIYGKG-DYLAYSEEEHPVSLQLGGSDPV 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E+ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   +SIPVT
Sbjct: 88  ALAQCAKLAEERGYDEINLNVGCPSDRVQNGRFGACLMADAQLVADCVKAMRDVVSIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L   + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDEQDSYEFLCEFIDTVSTKGDCEMFIIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 208 YQLKRDFPHLTMAINGGIKTLEEAKEHLKYLDGVMVGREAYQNPSILTAVDNQLFDE--- 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + PI   V          SM  Y    L  G  L  +TRHM+G+F G P +R+ R  L+ 
Sbjct: 265 NMPIVDSV------AAVRSMYPYIENELSKGAYLGHMTRHMLGIFQGIPGARQWRRHLSE 318

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 319 NAHKQGADLSVVEQALAFVT 338


>gi|229525073|ref|ZP_04414478.1| tRNA dihydrouridine synthase A [Vibrio cholerae bv. albensis VL426]
 gi|229338654|gb|EEO03671.1| tRNA dihydrouridine synthase A [Vibrio cholerae bv. albensis VL426]
          Length = 327

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 192/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L ++ +E P ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPAALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---L 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 302 NAHKPGAGLEVVEQALAKIP 321


>gi|261210364|ref|ZP_05924658.1| tRNA-dihydrouridine synthase [Vibrio sp. RC341]
 gi|260840422|gb|EEX66988.1| tRNA-dihydrouridine synthase [Vibrio sp. RC341]
          Length = 335

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 194/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM   + IPVT
Sbjct: 79  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMRSVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 139 VKTRIGIDDQDSYEFLTQFISTVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYSRA 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY++  +L  VD+      T 
Sbjct: 199 YQIKRDFPHLTIAVNGGVKTLEEAKLHLQHLDGVMIGREAYQSPYLLAEVDQQIFELDT- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 258 --PVKKR------SQVIHEMLPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 309

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 310 NAHKQGAGLEVVEQALAKIP 329


>gi|260870808|ref|YP_003237210.1| tRNA-dihydrouridine synthase A [Escherichia coli O111:H- str.
           11128]
 gi|257767164|dbj|BAI38659.1| tRNA-dihydrouridine synthase A [Escherichia coli O111:H- str.
           11128]
 gi|323175935|gb|EFZ61527.1| tRNA-dihydrouridine synthase A [Escherichia coli 1180]
          Length = 345

 Score =  376 bits (966), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|320644173|gb|EFX13238.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H- str.
           493-89]
 gi|320665665|gb|EFX32702.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 339

 Score =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|24375400|ref|NP_719443.1| tRNA-dihydrouridine synthase A [Shewanella oneidensis MR-1]
 gi|38604868|sp|Q8EAJ0|DUSA_SHEON RecName: Full=tRNA-dihydrouridine synthase A
 gi|24350234|gb|AAN56887.1|AE015823_9 TIM-barrel protein, yjbN family [Shewanella oneidensis MR-1]
          Length = 335

 Score =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 199/322 (61%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 21  MLDWTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLTYNQEEHPLALQLGGSNPV 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 80  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 140 VKTRIGIDEQDSYEFLTHFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  ML  VD+         
Sbjct: 200 QLKRDYPALNISINGGITSLEQAQTHLQHLDGVMVGREAYQNPYMLAQVDQVLCGSTKA- 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  +M  Y   HL  GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 259 --------VMSREAVIEAMLPYIEAHLQVGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 310

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ A+  +   L
Sbjct: 311 AHKNGAGIEVVKLAYQSVQTDL 332


>gi|260858159|ref|YP_003232050.1| tRNA-dihydrouridine synthase A [Escherichia coli O26:H11 str.
           11368]
 gi|257756808|dbj|BAI28310.1| tRNA-dihydrouridine synthase A [Escherichia coli O26:H11 str.
           11368]
          Length = 345

 Score =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|309704516|emb|CBJ03865.1| tRNA-dihydrouridine synthase A [Escherichia coli ETEC H10407]
          Length = 345

 Score =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 148/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L N + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCNFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|320638805|gb|EFX08451.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           G5101]
          Length = 339

 Score =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|120600206|ref|YP_964780.1| tRNA-dihydrouridine synthase A [Shewanella sp. W3-18-1]
 gi|120560299|gb|ABM26226.1| TIM-barrel protein, yjbN family [Shewanella sp. W3-18-1]
          Length = 343

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 142/322 (44%), Positives = 196/322 (60%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 30  MLDWTDRHYRYFARLMSAKALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 89  DLARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   +  +   G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 149 VKTRIGIDEQDSYEFLTYFIDIVNAKGCTDFTIHARKAWLQGLSPKENREIPPLDYERVY 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 209 QLKRDYPVLNISINGGVTTLEQAQGHLAQLDGVMMGREAYQNPYILARVDQVLCG----- 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               ++        +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 264 ----SQRAVISREDVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 319

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A    +  AF  +   +
Sbjct: 320 AHKNGAGIETVRQAFQSIQTEM 341


>gi|256019697|ref|ZP_05433562.1| tRNA-dihydrouridine synthase A [Shigella sp. D9]
 gi|332280828|ref|ZP_08393241.1| tRNA-dihydrouridine synthase A [Shigella sp. D9]
 gi|323171192|gb|EFZ56840.1| tRNA-dihydrouridine synthase A [Escherichia coli LT-68]
 gi|324014847|gb|EGB84066.1| tRNA dihydrouridine synthase A [Escherichia coli MS 60-1]
 gi|332103180|gb|EGJ06526.1| tRNA-dihydrouridine synthase A [Shigella sp. D9]
          Length = 345

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|127511470|ref|YP_001092667.1| tRNA-dihydrouridine synthase A [Shewanella loihica PV-4]
 gi|126636765|gb|ABO22408.1| TIM-barrel protein, yjbN family [Shewanella loihica PV-4]
          Length = 329

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 143/318 (44%), Positives = 198/318 (62%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++  LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 19  MLDWTDRHYRYFARLMSSELLLYTEMVTTGAIIHGKG-DYLAYNQEEHPLALQLGGSNPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+E+NLNVGCPS RV  G FGACLM  PD+V  C+AAM + + IPVT
Sbjct: 78  DLAKCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPDLVAQCVAAMNEVVDIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   V  +  +G +   IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 138 VKTRIGIDEQDSYEFLTEFVDKVSAAGCDTFIIHARKAWLQGLSPKENREIPELDYDRVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 198 RLKQDYPQLSISINGGVKTLEECGEHLKQLDGVMVGREAYQNPYLLAQVDQQLCG---LD 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R        +  +M  Y  +HL SGG+L  ITRHM GL+ G   SR  R  L+  
Sbjct: 255 KPVLSR------DAVLENMIPYIEKHLVSGGRLNHITRHMTGLYQGEAGSRAWRRYLSEN 308

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   M
Sbjct: 309 AHKPGAGIAVVHEARASM 326


>gi|300724718|ref|YP_003714043.1| tRNA -dihydrouridine synthase A [Xenorhabdus nematophila ATCC
           19061]
 gi|297631260|emb|CBJ91955.1| tRNA-dihydrouridine synthase A [Xenorhabdus nematophila ATCC 19061]
          Length = 342

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 198/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  ALLYTEM+   AI+ G   + L ++ QE PLALQ+GG++  
Sbjct: 30  MLDWTDRHCRYFHRLLSKEALLYTEMVTTGAIIHGKG-DYLAYNEQEHPLALQLGGSEPQ 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I ++ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   + IPVT
Sbjct: 89  ALAQCARIAQEKGYDEINLNVGCPSDRVQNGRFGACLMGDAALVADCVKAMQDVVDIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + +++ +K S  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 149 VKTRIGIDEQDSYEFLCDFIETVVKNSDCDNFVIHARKAWLSGLSPKENREIPPLDYPRV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K + P L   +NGG++ + +A + L  VDGVMIGR AY+N +ML  VD    N  + 
Sbjct: 209 YQLKNDFPQLTFSINGGIKSLEEAKQHLQYVDGVMIGREAYQNPSMLAHVDRELFNQTSP 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +            +   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 VTNTV---------EAVQALYPYIEQELSKGTYLGHITRHILGIFQGIPGARQWRRHLSE 319

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   ++E A  ++ E +
Sbjct: 320 NAHKPGSDIRVVEKALEMVTERI 342


>gi|292489772|ref|YP_003532662.1| tRNA-dihydrouridine synthase A [Erwinia amylovora CFBP1430]
 gi|292898020|ref|YP_003537389.1| tRNA-dihydrouridine synthase A [Erwinia amylovora ATCC 49946]
 gi|291197868|emb|CBJ44967.1| tRNA-dihydrouridine synthase A [Erwinia amylovora ATCC 49946]
 gi|291555209|emb|CBA23447.1| tRNA-dihydrouridine synthase A [Erwinia amylovora CFBP1430]
          Length = 349

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 143/324 (44%), Positives = 199/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLYTEM+   AI+ G   + L FS++E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRQLTRQTLLYTEMVTTGAIIHGKG-DYLAFSSEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 92  ALAQCAKLAERRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G     IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFMRTVSEQGGCEMFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD       + 
Sbjct: 212 YQLKRDFPHLTLSINGGVKSLAEAKIHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTSP 271

Query: 240 S-SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  PI           +  SM  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 272 SIDPI----------AVVRSMYPYIERELAGGTYLGHVTRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +++ E +
Sbjct: 322 ENAHKAGAGIDVVEKALSMVAEKV 345


>gi|312965642|ref|ZP_07779871.1| tRNA-dihydrouridine synthase A [Escherichia coli 2362-75]
 gi|312289616|gb|EFR17507.1| tRNA-dihydrouridine synthase A [Escherichia coli 2362-75]
          Length = 345

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|194437343|ref|ZP_03069441.1| tRNA-dihydrouridine synthase A [Escherichia coli 101-1]
 gi|194423899|gb|EDX39888.1| tRNA-dihydrouridine synthase A [Escherichia coli 101-1]
          Length = 345

 Score =  375 bits (963), Expect = e-102,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|323155612|gb|EFZ41787.1| tRNA-dihydrouridine synthase A [Escherichia coli EPECa14]
          Length = 347

 Score =  375 bits (963), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNTQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 324 ENAHKAGADINVLEHALKLVADK 346


>gi|297582262|ref|ZP_06944177.1| TIM-barrel protein [Vibrio cholerae RC385]
 gi|297533520|gb|EFH72366.1| TIM-barrel protein [Vibrio cholerae RC385]
          Length = 327

 Score =  375 bits (963), Expect = e-102,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 193/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 12  MLDWTDRHCRYFHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 71  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+        
Sbjct: 191 YQIKRDFPHLTIAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---L 247

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+K R       ++   M  Y  R L  G  L  +TRHM+G+F   P +R+ R  ++ 
Sbjct: 248 ETPVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGVFQNMPGARQWRRHISE 301

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 302 NAHKPGAGLEVVEQALAKIP 321


>gi|168784662|ref|ZP_02809669.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC869]
 gi|168798291|ref|ZP_02823298.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC508]
 gi|261225167|ref|ZP_05939448.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261255581|ref|ZP_05948114.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           FRIK966]
 gi|189375043|gb|EDU93459.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC869]
 gi|189379226|gb|EDU97642.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC508]
 gi|320190826|gb|EFW65476.1| tRNA dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC1212]
 gi|326341906|gb|EGD65689.1| tRNA dihydrouridine synthase A [Escherichia coli O157:H7 str. 1125]
          Length = 345

 Score =  375 bits (963), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|323162189|gb|EFZ48052.1| tRNA-dihydrouridine synthase A [Escherichia coli E128010]
          Length = 330

 Score =  375 bits (963), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 307 ENAHKAGADINVLEHALKLVADK 329


>gi|168760895|ref|ZP_02785902.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4501]
 gi|170682797|ref|YP_001746438.1| tRNA-dihydrouridine synthase A [Escherichia coli SMS-3-5]
 gi|191167463|ref|ZP_03029277.1| tRNA-dihydrouridine synthase A [Escherichia coli B7A]
 gi|209921533|ref|YP_002295617.1| tRNA-dihydrouridine synthase A [Escherichia coli SE11]
 gi|217325395|ref|ZP_03441479.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14588]
 gi|256024922|ref|ZP_05438787.1| tRNA-dihydrouridine synthase A [Escherichia sp. 4_1_40B]
 gi|301019187|ref|ZP_07183385.1| tRNA dihydrouridine synthase A [Escherichia coli MS 196-1]
 gi|307140739|ref|ZP_07500095.1| tRNA-dihydrouridine synthase A [Escherichia coli H736]
 gi|170520515|gb|ACB18693.1| tRNA-dihydrouridine synthase A [Escherichia coli SMS-3-5]
 gi|189368570|gb|EDU86986.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4501]
 gi|190902505|gb|EDV62240.1| tRNA-dihydrouridine synthase A [Escherichia coli B7A]
 gi|209914792|dbj|BAG79866.1| conserved hypothetical protein [Escherichia coli SE11]
 gi|217321616|gb|EEC30040.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14588]
 gi|299882344|gb|EFI90555.1| tRNA dihydrouridine synthase A [Escherichia coli MS 196-1]
 gi|320200820|gb|EFW75406.1| tRNA dihydrouridine synthase A [Escherichia coli EC4100B]
 gi|320654888|gb|EFX22849.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320660736|gb|EFX28193.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str. USDA
           5905]
 gi|323940232|gb|EGB36425.1| tRNA dihydrouridine synthase A [Escherichia coli E482]
 gi|324118621|gb|EGC12513.1| tRNA dihydrouridine synthase A [Escherichia coli E1167]
 gi|326346520|gb|EGD70254.1| tRNA dihydrouridine synthase A [Escherichia coli O157:H7 str. 1044]
          Length = 339

 Score =  375 bits (963), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|91794580|ref|YP_564231.1| tRNA-dihydrouridine synthase A [Shewanella denitrificans OS217]
 gi|91716582|gb|ABE56508.1| TIM-barrel protein, yjbN family [Shewanella denitrificans OS217]
          Length = 327

 Score =  374 bits (962), Expect = e-102,   Method: Composition-based stats.
 Identities = 143/314 (45%), Positives = 199/314 (63%), Gaps = 10/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+HYR+FAR+++  ALLYTEM+   AIL G   + L ++T+E PLALQ+GG++  
Sbjct: 11  MLDWTDKHYRYFARIMSTKALLYTEMVTTGAILHGRG-DYLAYNTEEHPLALQLGGSNPV 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 70  DLAACAKLAFERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   ++++   G +   IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 130 VKTRIGIDEQDSYEFLTKFIETVAAKGCDDFTIHARKAWLQGLSPKENREIPLLDYDRVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L IG+NGG++ +++A   L  +DGVM+GR AY+N  +L  VD          
Sbjct: 190 QLKRDFPKLNIGINGGIKTLAEAKLHLTQLDGVMVGREAYQNPYLLAEVDTQLYG----- 244

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                + D     ++   M  Y   HL +GG+L  ITRHMIGLF G   SR+ R  L+  
Sbjct: 245 ----VKRDIISREQVIEKMLPYIEAHLKTGGRLNHITRHMIGLFQGLAGSRQWRRHLSEN 300

Query: 301 AGASTATHHIIETA 314
           A    A   ++  A
Sbjct: 301 AHKPNAGIEVVREA 314


>gi|90414453|ref|ZP_01222429.1| putative NifR3/Smm1 family protein [Photobacterium profundum 3TCK]
 gi|90324458|gb|EAS41017.1| putative NifR3/Smm1 family protein [Photobacterium profundum 3TCK]
          Length = 346

 Score =  374 bits (962), Expect = e-102,   Method: Composition-based stats.
 Identities = 141/323 (43%), Positives = 206/323 (63%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AI+ G   + L F+ +E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRLLSDNALLYTEMVTTGAIIHGKG-DFLTFNEEENPVALQLGGSNPV 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   D+V  C+++M + + IPVT
Sbjct: 91  DLAHCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMGEADLVALCVSSMREVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++ +KSG +   +HARKA LKGLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDEQDSYQFLVDFIGTVNEKSGCDNFTVHARKAWLKGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P+L + +NGG++   +  + L  +DGVM+GR AY+N  ++  VD+        
Sbjct: 211 YQLKRDFPNLIMAINGGIKTFDEMEEHLNHMDGVMVGREAYQNPYLMAEVDQRLFG---C 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S PI  R      R+ + +M  Y  R L +G KL  ITRHM+GLF G P  R+ R  ++ 
Sbjct: 268 SKPIIKR------REAAEAMFPYIERQLANGSKLGHITRHMLGLFQGIPGGRQWRRYISE 321

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    +   +++ A + +   L
Sbjct: 322 NAHKPGSGIEVVQYALDKVPHDL 344


>gi|15834285|ref|NP_313058.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           Sakai]
 gi|74314543|ref|YP_312962.1| tRNA-dihydrouridine synthase A [Shigella sonnei Ss046]
 gi|89110770|ref|AP_004550.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           W3110]
 gi|170083506|ref|YP_001732826.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           DH10B]
 gi|193063063|ref|ZP_03044155.1| tRNA-dihydrouridine synthase A [Escherichia coli E22]
 gi|218556606|ref|YP_002389520.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI1]
 gi|218697757|ref|YP_002405424.1| tRNA-dihydrouridine synthase A [Escherichia coli 55989]
 gi|218707670|ref|YP_002415189.1| tRNA -dihydrouridine synthase A [Escherichia coli UMN026]
 gi|254163985|ref|YP_003047093.1| tRNA-dihydrouridine synthase A [Escherichia coli B str. REL606]
 gi|260846843|ref|YP_003224621.1| tRNA-dihydrouridine synthase A [Escherichia coli O103:H2 str.
           12009]
 gi|291285465|ref|YP_003502283.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str.
           CB9615]
 gi|300817967|ref|ZP_07098180.1| tRNA dihydrouridine synthase A [Escherichia coli MS 107-1]
 gi|300823590|ref|ZP_07103718.1| tRNA dihydrouridine synthase A [Escherichia coli MS 119-7]
 gi|300899835|ref|ZP_07118049.1| tRNA dihydrouridine synthase A [Escherichia coli MS 198-1]
 gi|300906360|ref|ZP_07124058.1| tRNA dihydrouridine synthase A [Escherichia coli MS 84-1]
 gi|300917303|ref|ZP_07133976.1| tRNA dihydrouridine synthase A [Escherichia coli MS 115-1]
 gi|300924312|ref|ZP_07140291.1| tRNA dihydrouridine synthase A [Escherichia coli MS 182-1]
 gi|300938186|ref|ZP_07152956.1| tRNA dihydrouridine synthase A [Escherichia coli MS 21-1]
 gi|300946621|ref|ZP_07160880.1| tRNA dihydrouridine synthase A [Escherichia coli MS 116-1]
 gi|300957541|ref|ZP_07169748.1| tRNA dihydrouridine synthase A [Escherichia coli MS 175-1]
 gi|301021575|ref|ZP_07185575.1| tRNA dihydrouridine synthase A [Escherichia coli MS 69-1]
 gi|301302728|ref|ZP_07208857.1| tRNA dihydrouridine synthase A [Escherichia coli MS 124-1]
 gi|301330578|ref|ZP_07223186.1| tRNA dihydrouridine synthase A [Escherichia coli MS 78-1]
 gi|301645037|ref|ZP_07245000.1| tRNA dihydrouridine synthase A [Escherichia coli MS 146-1]
 gi|307312109|ref|ZP_07591746.1| TIM-barrel protein, yjbN family [Escherichia coli W]
 gi|309795855|ref|ZP_07690269.1| tRNA dihydrouridine synthase A [Escherichia coli MS 145-7]
 gi|331644790|ref|ZP_08345907.1| tRNA-dihydrouridine synthase A [Escherichia coli H736]
 gi|331665718|ref|ZP_08366612.1| tRNA-dihydrouridine synthase A [Escherichia coli TA143]
 gi|331670912|ref|ZP_08371746.1| tRNA-dihydrouridine synthase A [Escherichia coli TA271]
 gi|331680179|ref|ZP_08380838.1| tRNA-dihydrouridine synthase A [Escherichia coli H591]
 gi|13364508|dbj|BAB38454.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|73858020|gb|AAZ90727.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|85676801|dbj|BAE78051.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K12 substr.
           W3110]
 gi|169891341|gb|ACB05048.1| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           DH10B]
 gi|192931322|gb|EDV83924.1| tRNA-dihydrouridine synthase A [Escherichia coli E22]
 gi|218354489|emb|CAV01337.1| tRNA-dihydrouridine synthase A [Escherichia coli 55989]
 gi|218363375|emb|CAR01028.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI1]
 gi|218434767|emb|CAR15700.1| tRNA-dihydrouridine synthase A [Escherichia coli UMN026]
 gi|253975886|gb|ACT41557.1| tRNA-dihydrouridine synthase A [Escherichia coli B str. REL606]
 gi|257761990|dbj|BAI33487.1| tRNA-dihydrouridine synthase A [Escherichia coli O103:H2 str.
           12009]
 gi|260451122|gb|ACX41544.1| TIM-barrel protein, yjbN family [Escherichia coli DH1]
 gi|290765338|gb|ADD59299.1| tRNA-dihydrouridine synthase A [Escherichia coli O55:H7 str.
           CB9615]
 gi|300315715|gb|EFJ65499.1| tRNA dihydrouridine synthase A [Escherichia coli MS 175-1]
 gi|300356606|gb|EFJ72476.1| tRNA dihydrouridine synthase A [Escherichia coli MS 198-1]
 gi|300397973|gb|EFJ81511.1| tRNA dihydrouridine synthase A [Escherichia coli MS 69-1]
 gi|300401808|gb|EFJ85346.1| tRNA dihydrouridine synthase A [Escherichia coli MS 84-1]
 gi|300415447|gb|EFJ98757.1| tRNA dihydrouridine synthase A [Escherichia coli MS 115-1]
 gi|300419477|gb|EFK02788.1| tRNA dihydrouridine synthase A [Escherichia coli MS 182-1]
 gi|300453720|gb|EFK17340.1| tRNA dihydrouridine synthase A [Escherichia coli MS 116-1]
 gi|300456844|gb|EFK20337.1| tRNA dihydrouridine synthase A [Escherichia coli MS 21-1]
 gi|300523922|gb|EFK44991.1| tRNA dihydrouridine synthase A [Escherichia coli MS 119-7]
 gi|300529377|gb|EFK50439.1| tRNA dihydrouridine synthase A [Escherichia coli MS 107-1]
 gi|300841948|gb|EFK69708.1| tRNA dihydrouridine synthase A [Escherichia coli MS 124-1]
 gi|300843456|gb|EFK71216.1| tRNA dihydrouridine synthase A [Escherichia coli MS 78-1]
 gi|301076659|gb|EFK91465.1| tRNA dihydrouridine synthase A [Escherichia coli MS 146-1]
 gi|306907916|gb|EFN38417.1| TIM-barrel protein, yjbN family [Escherichia coli W]
 gi|308120516|gb|EFO57778.1| tRNA dihydrouridine synthase A [Escherichia coli MS 145-7]
 gi|315063373|gb|ADT77700.1| tRNA-dihydrouridine synthase A [Escherichia coli W]
 gi|315138603|dbj|BAJ45762.1| tRNA-dihydrouridine synthase A [Escherichia coli DH1]
 gi|315254721|gb|EFU34689.1| tRNA dihydrouridine synthase A [Escherichia coli MS 85-1]
 gi|315617417|gb|EFU98023.1| tRNA-dihydrouridine synthase A [Escherichia coli 3431]
 gi|323164554|gb|EFZ50355.1| tRNA-dihydrouridine synthase A [Shigella sonnei 53G]
 gi|323182152|gb|EFZ67562.1| tRNA-dihydrouridine synthase A [Escherichia coli 1357]
 gi|323380563|gb|ADX52831.1| TIM-barrel protein, yjbN family [Escherichia coli KO11]
 gi|323946182|gb|EGB42216.1| tRNA dihydrouridine synthase A [Escherichia coli H120]
 gi|324017108|gb|EGB86327.1| tRNA dihydrouridine synthase A [Escherichia coli MS 117-3]
 gi|331035765|gb|EGI08003.1| tRNA-dihydrouridine synthase A [Escherichia coli H736]
 gi|331056769|gb|EGI28763.1| tRNA-dihydrouridine synthase A [Escherichia coli TA143]
 gi|331061826|gb|EGI33751.1| tRNA-dihydrouridine synthase A [Escherichia coli TA271]
 gi|331071642|gb|EGI42978.1| tRNA-dihydrouridine synthase A [Escherichia coli H591]
          Length = 345

 Score =  374 bits (962), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|323965711|gb|EGB61163.1| tRNA dihydrouridine synthase A [Escherichia coli M863]
 gi|327250393|gb|EGE62106.1| tRNA-dihydrouridine synthase A [Escherichia coli STEC_7v]
          Length = 345

 Score =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAETRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|271501941|ref|YP_003334967.1| yjbN family TIM-barrel protein [Dickeya dadantii Ech586]
 gi|270345496|gb|ACZ78261.1| TIM-barrel protein, yjbN family [Dickeya dadantii Ech586]
          Length = 344

 Score =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 145/319 (45%), Positives = 201/319 (63%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AIL G   + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRLLSHNALLYTEMVTTGAILHGKG-DYLAYSDEEHPLALQLGGSDPT 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM + +SIPVT
Sbjct: 92  ALAQCAVLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAQLVADCVTAMRERVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIRTVSEQGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A + L  VDGVM+GR AY+N  ML  VD    +  + 
Sbjct: 212 YQLKRDFPSLTLAINGGIKTLAEAKQHLEHVDGVMVGREAYQNPGMLAQVDRDLFDATSV 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 272 VP---------NQAAVVQAMYPYIERELSGGAALGHITRHMLGLFQGIPGARQWRRYLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A +L+
Sbjct: 323 NAHKPGADASVVEHALSLV 341


>gi|262401531|ref|ZP_06078098.1| tRNA-dihydrouridine synthase [Vibrio sp. RC586]
 gi|262352246|gb|EEZ01375.1| tRNA-dihydrouridine synthase [Vibrio sp. RC586]
          Length = 316

 Score =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 142/320 (44%), Positives = 194/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++  
Sbjct: 1   MLDWTDRHCRYFHRLLSSQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPK 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ +D GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVT
Sbjct: 60  DLAHCAKLAQDRGYDEINLNVGCPSDRVQNGRFGACLMAEPDLVAECVAAMRSVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 120 VKTRIGIDDQDSYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYSRA 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I +NGG++ + +A   L  +DGVMIGR AY++  +L  VD+      T 
Sbjct: 180 YQIKRDFPHLTIAVNGGVKTLEEAKLHLQHLDGVMIGREAYQSPYLLAEVDQQIFGLDT- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+K R       ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++ 
Sbjct: 239 --PVKKR------SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISE 290

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 291 NAHKLGAGLEVVEQALAKIP 310


>gi|238754677|ref|ZP_04616030.1| tRNA-dihydrouridine synthase A [Yersinia ruckeri ATCC 29473]
 gi|238707136|gb|EEP99500.1| tRNA-dihydrouridine synthase A [Yersinia ruckeri ATCC 29473]
          Length = 343

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/319 (46%), Positives = 199/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKEALLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DC+ AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   V+ + ++ G +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCEFVQKVAEQGGCDMFTIHARKAWLSGLSPKENREVPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 206 YQLKRDFPALTMAINGGVKTLEEAKEHLKYLDGVMMGREAYQNPSILTQVDRELFDPQA- 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                  V  D    I A +  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 265 -------VVTDSVAAIEA-LYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRYLSE 316

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A +L+
Sbjct: 317 NAHKPGAGVSVVEKALSLV 335


>gi|153009692|ref|YP_001370907.1| tRNA-dihydrouridine synthase A [Ochrobactrum anthropi ATCC 49188]
 gi|151561580|gb|ABS15078.1| TIM-barrel protein, yjbN family [Ochrobactrum anthropi ATCC 49188]
          Length = 337

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 160/315 (50%), Positives = 210/315 (66%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADAI+ G +  +LGF T E P+ALQ+GG+D  
Sbjct: 21  MIDWSDRHCRYFHRLFSKQALLYTEMVVADAIIHGPRDRLLGFDTAEHPVALQLGGSDPV 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAAKI  D+GY+EINLNVGCPS RV  G+FGACLM  PD+V  C++AM +A+S+PVT
Sbjct: 81  KLKEAAKIGADYGYDEINLNVGCPSDRVQSGTFGACLMQTPDVVARCVSAMKEAVSVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   VAL  L      +G + +W+HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 141 VKCRIGVDDQDVEVALDTLADLTLDAGADALWVHARKAWLKGLSPKENREIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K    D+F+G+NGG+  + +A + L +VD VM+GRAAY N  +L  VD          
Sbjct: 201 RLKARLGDVFVGINGGINTLDEAEQHLQTVDAVMLGRAAYHNPEILAEVDARLYGGDQAD 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + I           I   M  Y  RH+ +GG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 261 TSIA---------DIIDDMCAYTDRHIATGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 311

Query: 301 AGASTATHHIIETAF 315
           A    A   ++  A+
Sbjct: 312 ATKPGANSDVLRQAY 326


>gi|307321239|ref|ZP_07600641.1| dihydrouridine synthase DuS [Sinorhizobium meliloti AK83]
 gi|306893141|gb|EFN23925.1| dihydrouridine synthase DuS [Sinorhizobium meliloti AK83]
          Length = 385

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 192/352 (54%), Positives = 246/352 (69%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 27  MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 87  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL----------PSV----------DGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL  L                       DGVM+GRAAY
Sbjct: 207 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD----------KDFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 267 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+ EA    A   +I  AF+ + E++
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQILSTEATRKDAGPQVIHAAFDAVFEAV 378


>gi|145698340|ref|NP_418473.2| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           MG1655]
 gi|238903158|ref|YP_002928954.1| tRNA-dihydrouridine synthase A [Escherichia coli BW2952]
 gi|293402687|ref|ZP_06646784.1| tRNA dihydrouridine synthase A [Escherichia coli FVEC1412]
 gi|293407781|ref|ZP_06651621.1| tRNA-dihydrouridine synthase A [Escherichia coli B354]
 gi|293476353|ref|ZP_06664761.1| tRNA-dihydrouridine synthase A [Escherichia coli B088]
 gi|298378215|ref|ZP_06988099.1| tRNA-dihydrouridine synthase A [Escherichia coli FVEC1302]
 gi|3183570|sp|P32695|DUSA_ECOLI RecName: Full=tRNA-dihydrouridine synthase A
 gi|38604936|sp|Q8X5V6|DUSA_ECO57 RecName: Full=tRNA-dihydrouridine synthase A
 gi|145693211|gb|AAC77019.2| tRNA-dihydrouridine synthase A [Escherichia coli str. K-12 substr.
           MG1655]
 gi|238863713|gb|ACR65711.1| tRNA-dihydrouridine synthase A [Escherichia coli BW2952]
 gi|284924142|emb|CBG37241.1| tRNA-dihydrouridine synthase A [Escherichia coli 042]
 gi|291320806|gb|EFE60248.1| tRNA-dihydrouridine synthase A [Escherichia coli B088]
 gi|291429602|gb|EFF02616.1| tRNA dihydrouridine synthase A [Escherichia coli FVEC1412]
 gi|291472032|gb|EFF14514.1| tRNA-dihydrouridine synthase A [Escherichia coli B354]
 gi|298280549|gb|EFI22050.1| tRNA-dihydrouridine synthase A [Escherichia coli FVEC1302]
          Length = 330

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 307 ENAHKAGADINVLEHALKLVADK 329


>gi|301046994|ref|ZP_07194104.1| tRNA dihydrouridine synthase A [Escherichia coli MS 185-1]
 gi|300301082|gb|EFJ57467.1| tRNA dihydrouridine synthase A [Escherichia coli MS 185-1]
 gi|323190088|gb|EFZ75366.1| tRNA-dihydrouridine synthase A [Escherichia coli RN587/1]
          Length = 313

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 180 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 290 ENAHKAGADINVLEHALKLVADK 312


>gi|157157144|ref|YP_001465549.1| tRNA-dihydrouridine synthase A [Escherichia coli E24377A]
 gi|157163519|ref|YP_001460837.1| tRNA-dihydrouridine synthase A [Escherichia coli HS]
 gi|254037046|ref|ZP_04871123.1| tRNA-dihydrouridine synthase A [Escherichia sp. 1_1_43]
 gi|157069199|gb|ABV08454.1| tRNA-dihydrouridine synthase A [Escherichia coli HS]
 gi|157079174|gb|ABV18882.1| tRNA-dihydrouridine synthase A [Escherichia coli E24377A]
 gi|226840152|gb|EEH72154.1| tRNA-dihydrouridine synthase A [Escherichia sp. 1_1_43]
          Length = 347

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 324 ENAHKAGADINVLEHALKLVADK 346


>gi|331675581|ref|ZP_08376328.1| tRNA-dihydrouridine synthase A [Escherichia coli TA280]
 gi|331067189|gb|EGI38597.1| tRNA-dihydrouridine synthase A [Escherichia coli TA280]
          Length = 345

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DVDPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|331680980|ref|ZP_08381617.1| tRNA-dihydrouridine synthase A [Escherichia coli H299]
 gi|331081201|gb|EGI52362.1| tRNA-dihydrouridine synthase A [Escherichia coli H299]
          Length = 345

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|237728132|ref|ZP_04558613.1| tRNA-dihydrouridine synthase A [Citrobacter sp. 30_2]
 gi|226910143|gb|EEH96061.1| tRNA-dihydrouridine synthase A [Citrobacter sp. 30_2]
          Length = 331

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 202/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++  LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSSQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDYD V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYDRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F+    
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKIHLQHMDGVMVGREAYQNPGILASVDREIFAATTE 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 258 DTDPV----------AVVRAMYPYIERELSKGTYLGHVTRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 308 ENAHKAGADINVLEHALKLVADK 330


>gi|218551359|ref|YP_002385151.1| tRNA-dihydrouridine synthase A [Escherichia fergusonii ATCC 35469]
 gi|218358901|emb|CAQ91560.1| tRNA-dihydrouridine synthase A [Escherichia fergusonii ATCC 35469]
          Length = 331

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 202/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F++  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKMHLQHMDGVMVGREAYQNPGILAAVDREIFASTDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A  +++E A  L+ ++
Sbjct: 308 ENAHKPGADINVLEHALKLVADN 330


>gi|329296553|ref|ZP_08253889.1| TIM-barrel protein, yjbN family [Plautia stali symbiont]
          Length = 331

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/321 (44%), Positives = 190/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L  + LLYTEM+   AI+ G   + L +S  E PLALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLGGDTLLYTEMVTTGAIIHGKG-DYLAYSEAEHPLALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 74  ALATCAKLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMRDVVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+N +IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLCDFVGTVAQQGGCDTFIIHARKAWLSGLSPKENSEIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD       T 
Sbjct: 194 YQLKRDFPALTVAINGGIKTLDEAKAHLQHLDGVMMGREAYQNPGILAQVDRQLFGRETP 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +             +  SM  Y    L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 254 VADPV---------AVVRSMYPYIEVELAQGTYLGHITRHMLGLFQGIPGARQWRRHLSE 304

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A    A   ++E A  L+ +
Sbjct: 305 NAHKPGADVRVLEAALALVAD 325


>gi|320174478|gb|EFW49618.1| tRNA dihydrouridine synthase A [Shigella dysenteriae CDC 74-1112]
 gi|320185261|gb|EFW60037.1| tRNA dihydrouridine synthase A [Shigella flexneri CDC 796-83]
          Length = 339

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECGMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DAYPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|312173953|emb|CBX82207.1| tRNA-dihydrouridine synthase A [Erwinia amylovora ATCC BAA-2158]
          Length = 349

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 142/324 (43%), Positives = 198/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLYTEM+   AI+ G   + L F ++E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRQLTRQTLLYTEMVTTGAIIHGKG-DYLAFGSEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 92  ALAQCAKLAERRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G     IHARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFMRTVSEQGGCEMFIIHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD       + 
Sbjct: 212 YQLKRDFPHLTLSINGGVKSLAEAKIHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTSP 271

Query: 240 S-SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S  PI           +  SM  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 272 SIDPI----------AVVRSMYPYIERELAGGTYLGHVTRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +++ E +
Sbjct: 322 ENAHKAGAGIDVVEKALSMVAEKV 345


>gi|218702713|ref|YP_002410342.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI39]
 gi|218372699|emb|CAR20575.1| tRNA-dihydrouridine synthase A [Escherichia coli IAI39]
          Length = 345

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGVPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|261346564|ref|ZP_05974208.1| tRNA-dihydrouridine synthase A [Providencia rustigianii DSM 4541]
 gi|282565268|gb|EFB70803.1| tRNA-dihydrouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 341

 Score =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 199/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AI+ G   + L +S +E P++LQ+GG+D +
Sbjct: 29  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAIIFGKG-DYLAYSEEEHPVSLQLGGSDPA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ++ GY+EINLNVGCPS RV  G FGACLM +  +V DC+ AM   +SIPVT
Sbjct: 88  ALAQCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMADAQLVADCVKAMRDVVSIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++   G  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDEQDSYEFLCDFIDTVSTKGDCDTFVIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 208 YQLKRDFPHLTMAINGGVKTLEEAKEHLKYLDGVMMGREAYQNPSILTAVDNQLFDETM- 266

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             PI   ++          M  Y  + L +G  L  +TRHM+G+F G P +R+ R  L+ 
Sbjct: 267 --PIVDNIEA------VRRMYPYIEKELSNGAYLGHMTRHMLGIFQGIPGARQWRRHLSE 318

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 319 NAHKKGADLTVVEQALAFVT 338


>gi|26250830|ref|NP_756870.1| tRNA-dihydrouridine synthase A [Escherichia coli CFT073]
 gi|91213570|ref|YP_543556.1| tRNA-dihydrouridine synthase A [Escherichia coli UTI89]
 gi|110644384|ref|YP_672114.1| tRNA-dihydrouridine synthase A [Escherichia coli 536]
 gi|117626314|ref|YP_859637.1| tRNA-dihydrouridine synthase A [Escherichia coli APEC O1]
 gi|191172024|ref|ZP_03033569.1| tRNA-dihydrouridine synthase A [Escherichia coli F11]
 gi|215489385|ref|YP_002331816.1| tRNA-dihydrouridine synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218561117|ref|YP_002394030.1| tRNA-dihydrouridine synthase A [Escherichia coli S88]
 gi|218692332|ref|YP_002400544.1| tRNA-dihydrouridine synthase A [Escherichia coli ED1a]
 gi|227886947|ref|ZP_04004752.1| tRNA-dihydrouridine synthase A [Escherichia coli 83972]
 gi|237703603|ref|ZP_04534084.1| tRNA-dihydrouridine synthase A [Escherichia sp. 3_2_53FAA]
 gi|306815840|ref|ZP_07449985.1| tRNA-dihydrouridine synthase A [Escherichia coli NC101]
 gi|331660615|ref|ZP_08361547.1| tRNA-dihydrouridine synthase A [Escherichia coli TA206]
 gi|38604877|sp|Q8FB30|DUSA_ECOL6 RecName: Full=tRNA-dihydrouridine synthase A
 gi|26111261|gb|AAN83444.1|AE016770_244 Hypothetical protein yjbN [Escherichia coli CFT073]
 gi|91075144|gb|ABE10025.1| hypothetical protein YjbN [Escherichia coli UTI89]
 gi|110345976|gb|ABG72213.1| hypothetical protein YjbN (putative tRNA-dihydrouridine synthase)
           [Escherichia coli 536]
 gi|115515438|gb|ABJ03513.1| tRNA-dihydrouridine synthase A [Escherichia coli APEC O1]
 gi|190907789|gb|EDV67383.1| tRNA-dihydrouridine synthase A [Escherichia coli F11]
 gi|215267457|emb|CAS11910.1| tRNA-dihydrouridine synthase A [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218367886|emb|CAR05681.1| tRNA-dihydrouridine synthase A [Escherichia coli S88]
 gi|218429896|emb|CAR10723.1| tRNA-dihydrouridine synthase A [Escherichia coli ED1a]
 gi|222035761|emb|CAP78506.1| tRNA-dihydrouridine synthase A [Escherichia coli LF82]
 gi|226901515|gb|EEH87774.1| tRNA-dihydrouridine synthase A [Escherichia sp. 3_2_53FAA]
 gi|227836088|gb|EEJ46554.1| tRNA-dihydrouridine synthase A [Escherichia coli 83972]
 gi|281181113|dbj|BAI57443.1| conserved hypothetical protein [Escherichia coli SE15]
 gi|294489479|gb|ADE88235.1| tRNA-dihydrouridine synthase A [Escherichia coli IHE3034]
 gi|305850815|gb|EFM51271.1| tRNA-dihydrouridine synthase A [Escherichia coli NC101]
 gi|307556192|gb|ADN48967.1| tRNA-dihydrouridine synthase A [Escherichia coli ABU 83972]
 gi|307629096|gb|ADN73400.1| tRNA-dihydrouridine synthase A [Escherichia coli UM146]
 gi|312948626|gb|ADR29453.1| tRNA-dihydrouridine synthase A [Escherichia coli O83:H1 str. NRG
           857C]
 gi|323950409|gb|EGB46290.1| tRNA dihydrouridine synthase A [Escherichia coli H252]
 gi|323954491|gb|EGB50275.1| tRNA dihydrouridine synthase A [Escherichia coli H263]
 gi|330908368|gb|EGH36887.1| tRNA dihydrouridine synthase A [Escherichia coli AA86]
 gi|331051657|gb|EGI23696.1| tRNA-dihydrouridine synthase A [Escherichia coli TA206]
          Length = 331

 Score =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 308 ENAHKAGADINVLEHALKLVADK 330


>gi|325499627|gb|EGC97486.1| tRNA-dihydrouridine synthase A [Escherichia fergusonii ECD227]
          Length = 331

 Score =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNMLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYSRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F++  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKMHLQHMDGVMVGREAYQNPGILAAVDREIFASTDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A  +++E A  L+ + 
Sbjct: 308 ENAHKPGADINVLEHALKLVADK 330


>gi|82546382|ref|YP_410329.1| tRNA-dihydrouridine synthase A [Shigella boydii Sb227]
 gi|81247793|gb|ABB68501.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|332087840|gb|EGI92966.1| tRNA-dihydrouridine synthase A [Shigella boydii 3594-74]
          Length = 345

 Score =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECGMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DAYPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|307132468|ref|YP_003884484.1| tRNA dihydrouridine synthase A [Dickeya dadantii 3937]
 gi|306529997|gb|ADM99927.1| tRNA dihydrouridine synthase A [Dickeya dadantii 3937]
          Length = 346

 Score =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 144/319 (45%), Positives = 200/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AIL G   + L +S +E PLALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFHRLLSHNALLYTEMVTTGAILHGKG-DYLAYSDEEHPLALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM + + IPVT
Sbjct: 94  ALAQCAVLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAQLVADCVTAMRERVDIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYAFLCDFIRTVSEQGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A + L  VDGVM+GR AY+N  ML  VD       + 
Sbjct: 214 YQLKRDFPSLTLAINGGVKTLAEARQHLQHVDGVMVGREAYQNPGMLAQVDRELFGADSA 273

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +              +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 274 APDQA---------DVVRAMYPYIERELSAGASLGHITRHMLGLFQGLPGARQWRRYLSE 324

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 325 NAHKPGADAAVVERALALV 343


>gi|113971575|ref|YP_735368.1| tRNA-dihydrouridine synthase A [Shewanella sp. MR-4]
 gi|113886259|gb|ABI40311.1| TIM-barrel protein, yjbN family [Shewanella sp. MR-4]
          Length = 335

 Score =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 142/322 (44%), Positives = 199/322 (61%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRHYR+FARL++ NALLYTEM+   AIL G   + L ++ +E PLALQ+GG++ +
Sbjct: 21  MLDLTDRHYRYFARLMSANALLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 80  ELARCAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVDAMKQVVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++   G     IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 140 VKTRIGIDEQDSYEFLTYFIDTVMAKGCGEFIIHARKAWLQGLSPKENREIPPLDYDRVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + QA   L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 200 QLKRDYPMLNISINGGITSLEQAKTHLQYLDGVMVGREAYQNPYILAQVDQLLCG----- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  +M  Y   HL +GG+L  ITRHMIGLF G P +R  R  L+  
Sbjct: 255 ----CEKAVISREAVIEAMLPYIEAHLQAGGRLNHITRHMIGLFQGLPGARAWRRYLSEN 310

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A  + A   +++ A+  +   +
Sbjct: 311 AHKNGAGIEVVKQAYQSIQSEI 332


>gi|163749318|ref|ZP_02156567.1| TIM-barrel protein, yjbN family [Shewanella benthica KT99]
 gi|161331037|gb|EDQ01963.1| TIM-barrel protein, yjbN family [Shewanella benthica KT99]
          Length = 310

 Score =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 139/318 (43%), Positives = 194/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR+++   LLYTEM+   AI+ G   + L ++++E PLALQ+GG++  
Sbjct: 1   MLDWTDRHYRYLARIMSTELLLYTEMVTTGAIIHGKG-DYLAYNSEENPLALQLGGSNPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM +P +V +C+ AM + + IPVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQSGRFGACLMADPKLVAECVTAMKQVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V ++   G +   +HARKA L+GLSPK NR+IP LDY  VY
Sbjct: 120 VKTRIGIDDQDSYEFLTEFVDTVSDVGCDTFIVHARKAWLQGLSPKQNREIPPLDYQRVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 180 RLKQDYPKLHISINGGVKTLDECRQHLLHIDGVMVGREAYQNPYILAEVDQRLCGS---- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K+ + +D    +      Y  +HL  GG+L  ITRHM G+F G P SR  R  ++  
Sbjct: 236 --NKSVLSRD---AVLEKFIPYIEKHLVEGGRLNHITRHMTGMFQGEPGSRAWRRYISEN 290

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IE A   M
Sbjct: 291 AHKQGAGIEVIEQARKKM 308


>gi|332346048|gb|AEE59382.1| tRNA-dihydrouridine synthase A DusA [Escherichia coli UMNK88]
          Length = 339

 Score =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L N + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCNFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|170728528|ref|YP_001762554.1| tRNA-dihydrouridine synthase A [Shewanella woodyi ATCC 51908]
 gi|169813875|gb|ACA88459.1| TIM-barrel protein, yjbN family [Shewanella woodyi ATCC 51908]
          Length = 331

 Score =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 140/319 (43%), Positives = 194/319 (60%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ ARL++   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 22  MLDWTDRHYRYLARLMSAELLLYTEMVTTGAIIHGKG-DYLAYNEEEHPLALQLGGSNPH 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK   + GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM     IPVT
Sbjct: 81  DLAICAKQAVERGYDEINLNVGCPSDRVQSGRFGACLMAEPSLVAECVTAMRAVADIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   V++++ +G +   +HARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 141 VKTRIGIDEQDSYEFLTEFVETVRDAGCDTFIVHARKAWLQGLSPKENREIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I +NGG++ + +    L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 201 QLKRDYPDLSISINGGVKSLEECKVHLVKLDGVMVGREAYQNPYILAKVDQQLCG---LD 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R        +      Y  +HL +GG+L  ITRHM GLF G   SR  R  ++  
Sbjct: 258 KPVLSR------DAVLEKFIPYIEKHLQAGGRLNHITRHMTGLFQGEVGSRIWRRYISEN 311

Query: 301 AGASTATHHIIETAFNLMI 319
           A    +   +IE A   M 
Sbjct: 312 AHKPGSGIEVIEQARKNMT 330


>gi|170769561|ref|ZP_02904014.1| tRNA-dihydrouridine synthase A [Escherichia albertii TW07627]
 gi|170121618|gb|EDS90549.1| tRNA-dihydrouridine synthase A [Escherichia albertii TW07627]
          Length = 331

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 198 YQLKRDFPHLTMAINGGIKSLEEAKAHLQYMDGVMVGREAYQNPGILAAVDREIFGSSDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 308 ENAHKAGADINVLEHALRLVADK 330


>gi|309787535|ref|ZP_07682147.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1617]
 gi|308925113|gb|EFP70608.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1617]
          Length = 339

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCGFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|187731116|ref|YP_001882727.1| tRNA-dihydrouridine synthase A [Shigella boydii CDC 3083-94]
 gi|187428108|gb|ACD07382.1| tRNA-dihydrouridine synthase A [Shigella boydii CDC 3083-94]
          Length = 347

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECGMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DAYPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 324 ENAHKAGADINVLEHALKLVADK 346


>gi|323975321|gb|EGB70424.1| tRNA dihydrouridine synthase A [Escherichia coli TW10509]
          Length = 345

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAETRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DD      L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDLDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|168236934|ref|ZP_02661992.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194736682|ref|YP_002117177.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194712184|gb|ACF91405.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197289961|gb|EDY29320.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 345

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPVT----------VVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 322 ENAHKAGADVAVLEQALKLVADK 344


>gi|170021953|ref|YP_001726907.1| tRNA-dihydrouridine synthase A [Escherichia coli ATCC 8739]
 gi|253775323|ref|YP_003038154.1| tRNA-dihydrouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|300929788|ref|ZP_07145240.1| tRNA dihydrouridine synthase A [Escherichia coli MS 187-1]
 gi|312974158|ref|ZP_07788329.1| tRNA-dihydrouridine synthase A [Escherichia coli 1827-70]
 gi|169756881|gb|ACA79580.1| TIM-barrel protein, yjbN family [Escherichia coli ATCC 8739]
 gi|242379577|emb|CAQ34398.1| tRNA-dihydrouridine synthase A [Escherichia coli BL21(DE3)]
 gi|253326367|gb|ACT30969.1| TIM-barrel protein, yjbN family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253980042|gb|ACT45712.1| tRNA-dihydrouridine synthase A [Escherichia coli BL21(DE3)]
 gi|300462294|gb|EFK25787.1| tRNA dihydrouridine synthase A [Escherichia coli MS 187-1]
 gi|310331692|gb|EFP98948.1| tRNA-dihydrouridine synthase A [Escherichia coli 1827-70]
 gi|323935538|gb|EGB31869.1| tRNA dihydrouridine synthase A [Escherichia coli E1520]
 gi|323960455|gb|EGB56088.1| tRNA dihydrouridine synthase A [Escherichia coli H489]
 gi|323969817|gb|EGB65098.1| tRNA dihydrouridine synthase A [Escherichia coli TA007]
          Length = 345

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|15965658|ref|NP_386011.1| tRNA-dihydrouridine synthase A [Sinorhizobium meliloti 1021]
 gi|15074839|emb|CAC46484.1| Conserved hypothetical protein [Sinorhizobium meliloti 1021]
          Length = 359

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 192/352 (54%), Positives = 246/352 (69%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 1   MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 61  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 121 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL----------PSV----------DGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL  L                       DGVM+GRAAY
Sbjct: 181 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 240

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD----------KDFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 241 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 300

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+ EA    A   +I  AF+ + E++
Sbjct: 301 GRLIHVTRHMVGLFQGWPGARRYRQILSTEATRKDAGPQVIHAAFDAVFEAV 352


>gi|307315973|ref|ZP_07595462.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
 gi|306898376|gb|EFN29074.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
          Length = 361

 Score =  372 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 192/352 (54%), Positives = 246/352 (69%), Gaps = 30/352 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 3   MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 63  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 123 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 182

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL----------PSV----------DGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL  L                       DGVM+GRAAY
Sbjct: 183 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 242

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD----------KDFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 243 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 302

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
           G+L  +TRHM+GLF G+P +RR R IL+ EA    A   +I  AF+ + E++
Sbjct: 303 GRLIHVTRHMVGLFQGWPGARRYRQILSTEATRKDAGPQVIHAAFDAVFEAV 354


>gi|204927346|ref|ZP_03218548.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|204324011|gb|EDZ09206.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPVT----------VVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|15804641|ref|NP_290682.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 EDL933]
 gi|12519000|gb|AAG59247.1|AE005638_1 orf, hypothetical protein [Escherichia coli O157:H7 str. EDL933]
          Length = 345

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFXGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|254796068|ref|YP_003080905.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14359]
 gi|254595468|gb|ACT74829.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           TW14359]
          Length = 330

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++   L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFLHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 307 ENAHKAGADINVLEHALKLVADK 329


>gi|168748106|ref|ZP_02773128.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755216|ref|ZP_02780223.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4401]
 gi|168766306|ref|ZP_02791313.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4486]
 gi|168774404|ref|ZP_02799411.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4196]
 gi|168780459|ref|ZP_02805466.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4076]
 gi|195935832|ref|ZP_03081214.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807897|ref|ZP_03250234.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814168|ref|ZP_03255497.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821033|ref|ZP_03261353.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4042]
 gi|209398005|ref|YP_002273589.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4115]
 gi|187769933|gb|EDU33777.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4196]
 gi|188017450|gb|EDU55572.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4113]
 gi|189001854|gb|EDU70840.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357455|gb|EDU75874.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4401]
 gi|189364132|gb|EDU82551.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4486]
 gi|208727698|gb|EDZ77299.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735445|gb|EDZ84132.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741156|gb|EDZ88838.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4042]
 gi|209159405|gb|ACI36838.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H7 str.
           EC4115]
          Length = 345

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++   L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFLHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|22124488|ref|NP_667911.1| tRNA-dihydrouridine synthase A [Yersinia pestis KIM 10]
 gi|45440326|ref|NP_991865.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108809958|ref|YP_653874.1| tRNA-dihydrouridine synthase A [Yersinia pestis Antiqua]
 gi|108813513|ref|YP_649280.1| tRNA-dihydrouridine synthase A [Yersinia pestis Nepal516]
 gi|145600902|ref|YP_001164978.1| tRNA-dihydrouridine synthase A [Yersinia pestis Pestoides F]
 gi|150260637|ref|ZP_01917365.1| tRNA-dihydrouridine synthase A [Yersinia pestis CA88-4125]
 gi|162420841|ref|YP_001605835.1| tRNA-dihydrouridine synthase A [Yersinia pestis Angola]
 gi|165926732|ref|ZP_02222564.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165936521|ref|ZP_02225089.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166010496|ref|ZP_02231394.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166213918|ref|ZP_02239953.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167402469|ref|ZP_02307926.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167418732|ref|ZP_02310485.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167426194|ref|ZP_02317947.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167467147|ref|ZP_02331851.1| tRNA-dihydrouridine synthase A [Yersinia pestis FV-1]
 gi|218927522|ref|YP_002345397.1| tRNA-dihydrouridine synthase A [Yersinia pestis CO92]
 gi|229836573|ref|ZP_04456739.1| tRNA-dihydrouridine synthase A [Yersinia pestis Pestoides A]
 gi|229840181|ref|ZP_04460340.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229842263|ref|ZP_04462418.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229903999|ref|ZP_04519112.1| tRNA-dihydrouridine synthase A [Yersinia pestis Nepal516]
 gi|270489016|ref|ZP_06206090.1| tRNA dihydrouridine synthase A [Yersinia pestis KIM D27]
 gi|294502383|ref|YP_003566445.1| hypothetical protein YPZ3_0273 [Yersinia pestis Z176003]
 gi|38604954|sp|Q8ZJ14|DUSA_YERPE RecName: Full=tRNA-dihydrouridine synthase A
 gi|21957280|gb|AAM84162.1|AE013659_6 hypothetical protein y0574 [Yersinia pestis KIM 10]
 gi|45435182|gb|AAS60742.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Yersinia pestis biovar Microtus str. 91001]
 gi|108777161|gb|ABG19680.1| hypothetical protein YPN_3353 [Yersinia pestis Nepal516]
 gi|108781871|gb|ABG15929.1| hypothetical protein YPA_3968 [Yersinia pestis Antiqua]
 gi|115346133|emb|CAL19001.1| conserved hypothetical protein [Yersinia pestis CO92]
 gi|145212598|gb|ABP42005.1| hypothetical protein YPDSF_3655 [Yersinia pestis Pestoides F]
 gi|149290045|gb|EDM40122.1| tRNA-dihydrouridine synthase A [Yersinia pestis CA88-4125]
 gi|162353656|gb|ABX87604.1| tRNA-dihydrouridine synthase A [Yersinia pestis Angola]
 gi|165915637|gb|EDR34246.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165921355|gb|EDR38579.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165990586|gb|EDR42887.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166204893|gb|EDR49373.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962726|gb|EDR58747.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167048157|gb|EDR59565.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167054905|gb|EDR64707.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|229679769|gb|EEO75872.1| tRNA-dihydrouridine synthase A [Yersinia pestis Nepal516]
 gi|229690573|gb|EEO82627.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229696547|gb|EEO86594.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229706257|gb|EEO92265.1| tRNA-dihydrouridine synthase A [Yersinia pestis Pestoides A]
 gi|262360466|gb|ACY57187.1| hypothetical protein YPD4_0278 [Yersinia pestis D106004]
 gi|262364412|gb|ACY60969.1| hypothetical protein YPD8_0279 [Yersinia pestis D182038]
 gi|270337520|gb|EFA48297.1| tRNA dihydrouridine synthase A [Yersinia pestis KIM D27]
 gi|294352842|gb|ADE63183.1| hypothetical protein YPZ3_0273 [Yersinia pestis Z176003]
 gi|320013820|gb|ADV97391.1| tRNA-dihydrouridine synthase A [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 345

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/322 (45%), Positives = 201/322 (62%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G      IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|168263436|ref|ZP_02685409.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205348025|gb|EDZ34656.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L +VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILASVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DTDPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|157148055|ref|YP_001455374.1| tRNA-dihydrouridine synthase A [Citrobacter koseri ATCC BAA-895]
 gi|157085260|gb|ABV14938.1| hypothetical protein CKO_03862 [Citrobacter koseri ATCC BAA-895]
          Length = 345

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 142/322 (44%), Positives = 193/322 (59%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ +  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAQARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVAGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG+  + +A   L  +DGVMIGR AY+N  +L +VD       T 
Sbjct: 212 YQLKRDFPHLTMSINGGITSLEEAKAHLEHMDGVMIGREAYQNPGILASVDREIFGATTA 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +             +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 272 DADPV---------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSE 322

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A  + A   ++E A   + + 
Sbjct: 323 NAHKAGADIDVLEHALKRVADK 344


>gi|322834778|ref|YP_004214805.1| TIM-barrel protein, yjbN family [Rahnella sp. Y9602]
 gi|321169979|gb|ADW75678.1| TIM-barrel protein, yjbN family [Rahnella sp. Y9602]
          Length = 335

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 142/321 (44%), Positives = 196/321 (61%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RL+T   LLYTEM+   AI+ G   + LGF   E P++LQ+GG++ +
Sbjct: 17  MLDWTDRHCRHFHRLMTGQTLLYTEMVTTGAIIHGKG-DYLGFGDAEHPVSLQLGGSNPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 76  DLAHCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGQASLVADCIKAMRDVVSIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++ + +  G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 136 VKTRIGIDDQDSYEFLCDFIRQVSENGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 196 YQLKRDFPHLTLAINGGIKTLEEAKTHLQYMDGVMVGREAYQNPGLLLNVDRELFGSD-- 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+KT  D      I  ++  Y    L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 254 -APLKTGPD------IIRALYPYIEAELSKGTYLGHITRHILGLFQGVPGARQFRRHLSE 306

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A  + A   ++E A  ++ +
Sbjct: 307 NAHKAGAGIDVVEQALQMVAQ 327


>gi|82779541|ref|YP_405890.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae Sd197]
 gi|81243689|gb|ABB64399.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
          Length = 345

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCGFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|197263333|ref|ZP_03163407.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197241588|gb|EDY24208.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPVT----------VVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|168243640|ref|ZP_02668572.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194448858|ref|YP_002048234.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194407162|gb|ACF67381.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205337347|gb|EDZ24111.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|56416043|ref|YP_153118.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|161617371|ref|YP_001591336.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167552533|ref|ZP_02346286.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|197364970|ref|YP_002144607.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56130300|gb|AAV79806.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|161366735|gb|ABX70503.1| hypothetical protein SPAB_05226 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|197096447|emb|CAR62053.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|205322837|gb|EDZ10676.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|322615399|gb|EFY12319.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322618459|gb|EFY15348.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322622129|gb|EFY18979.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322627200|gb|EFY23992.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322631160|gb|EFY27924.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322637622|gb|EFY34323.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643604|gb|EFY40159.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322648339|gb|EFY44798.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322654648|gb|EFY50968.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659608|gb|EFY55851.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322662183|gb|EFY58399.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322666071|gb|EFY62249.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322672491|gb|EFY68602.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675920|gb|EFY71991.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322680405|gb|EFY76443.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322684701|gb|EFY80705.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323195965|gb|EFZ81131.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323197105|gb|EFZ82246.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323201777|gb|EFZ86841.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323206291|gb|EFZ91253.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323213302|gb|EFZ98104.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323215672|gb|EGA00416.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222095|gb|EGA06481.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323226506|gb|EGA10712.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323229131|gb|EGA13260.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323236259|gb|EGA20335.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237621|gb|EGA21682.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323241713|gb|EGA25742.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323248140|gb|EGA32077.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323254530|gb|EGA38341.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323258410|gb|EGA42087.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323259690|gb|EGA43324.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323265963|gb|EGA49459.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323270405|gb|EGA53853.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|200388599|ref|ZP_03215211.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|199605697|gb|EDZ04242.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|168231239|ref|ZP_02656297.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|194470364|ref|ZP_03076348.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194456728|gb|EDX45567.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|205334267|gb|EDZ21031.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSCQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|197247584|ref|YP_002149157.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197211287|gb|ACH48684.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|62182692|ref|YP_219109.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|168821313|ref|ZP_02833313.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|224586008|ref|YP_002639807.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|62130325|gb|AAX68028.1| putative TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|205342153|gb|EDZ28917.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|224470536|gb|ACN48366.1| hypothetical protein SPC_4304 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|320088651|emb|CBY98409.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|322717191|gb|EFZ08762.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 332

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSCQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|194432327|ref|ZP_03064615.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1012]
 gi|194419530|gb|EDX35611.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 1012]
 gi|320179045|gb|EFW54004.1| tRNA dihydrouridine synthase A [Shigella boydii ATCC 9905]
 gi|332083541|gb|EGI88761.1| tRNA-dihydrouridine synthase A [Shigella boydii 5216-82]
          Length = 339

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+VE  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLVEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIEHELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 316 ENAHKAGADINVLEHALKLVAD 337


>gi|167625570|ref|YP_001675864.1| tRNA-dihydrouridine synthase A [Shewanella halifaxensis HAW-EB4]
 gi|167355592|gb|ABZ78205.1| TIM-barrel protein, yjbN family [Shewanella halifaxensis HAW-EB4]
          Length = 328

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 139/318 (43%), Positives = 200/318 (62%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++  LLYTEM+   AIL G   + L ++ +E PLALQ+GG++ +
Sbjct: 15  MLDWTDRHYRYFARLMSSQVLLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P++V +C++AM + + IP+T
Sbjct: 74  DLAACAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVSAMKQVVDIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++K +G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKTRIGIDEQDSYEFLTQFIDTVKAAGCEEFTIHARKAWLQGLSPKENREIPPLDYERVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  +DGVM+GR AY+N  +L  VD+      T  
Sbjct: 194 QLKRDYPQLNISINGGIKTLEECQTHLQHLDGVMVGREAYQNPYILAEVDQKLCGIDT-- 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R        +   +  Y  +HL  GG+L  ITRH+IGL+ G   SR  R  L+  
Sbjct: 252 -PVISR------DAVLEKLLPYIEKHLQQGGRLNHITRHIIGLYQGEVGSRVWRRYLSEN 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   M
Sbjct: 305 AHKQGAGIEVVTQARAEM 322


>gi|283787222|ref|YP_003367087.1| tRNA-dihydrouridine synthase A [Citrobacter rodentium ICC168]
 gi|282950676|emb|CBG90350.1| putative tRNA-dihydrouridine synthase A [Citrobacter rodentium
           ICC168]
          Length = 345

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 202/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSGEEHPLALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  QLAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRNTVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIDTVSGHGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLAEAKAHLEHMDGVMVGREAYQNPGILASVDREIFGVDSP 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|238798490|ref|ZP_04641969.1| tRNA-dihydrouridine synthase A [Yersinia mollaretii ATCC 43969]
 gi|238717652|gb|EEQ09489.1| tRNA-dihydrouridine synthase A [Yersinia mollaretii ATCC 43969]
          Length = 343

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 199/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHGKG-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK  E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAQCAKQAEFRGYNEINLNVGCPSDRVQNGRFGACLMAEANLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G  +   IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAEQGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDS--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 317 NAHKPGADVSVVEQALALVT 336


>gi|294139225|ref|YP_003555203.1| tRNA-dihydrouridine synthase A [Shewanella violacea DSS12]
 gi|293325694|dbj|BAJ00425.1| tRNA-dihydrouridine synthase A [Shewanella violacea DSS12]
          Length = 329

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 193/314 (61%), Gaps = 10/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR+++   LLYTEM+   AI+ G   + L ++++E PLALQ+GG++  
Sbjct: 20  MLDWTDRHYRYLARIMSTELLLYTEMVTTGAIIHGKG-DYLAYNSEENPLALQLGGSNHH 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM + + IPVT
Sbjct: 79  DLATCAKLAAERGYDEINLNVGCPSDRVQSGRFGACLMAEPKLVAECVTAMKQVVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V ++   G +   +HARKA L+GLSPK NR+IP LDY  VY
Sbjct: 139 VKTRIGIDDQDSYEFLSEFVDTVSDVGCDTFIVHARKAWLQGLSPKQNREIPPLDYQRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ PDL I +NGG++ + +  + L  +DGVM+GR AY+N  +L  VD+        +
Sbjct: 199 RLKKDYPDLHISINGGVKTLDECHEHLQHIDGVMVGREAYQNPYILAEVDQRLCGS---N 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R        +      Y  +HL  GG+L  ITRHM G++ G P SR  R  ++  
Sbjct: 256 KPVLSR------DAVLDKFIPYIEKHLMDGGRLNHITRHMTGMYQGEPGSRAWRRYISEN 309

Query: 301 AGASTATHHIIETA 314
           A    A   +IE A
Sbjct: 310 AHKPGAGIEVIEQA 323


>gi|16762924|ref|NP_458541.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29144411|ref|NP_807753.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213051927|ref|ZP_03344805.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213424511|ref|ZP_03357308.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213582871|ref|ZP_03364697.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
 gi|213614451|ref|ZP_03371277.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213647516|ref|ZP_03377569.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|289824651|ref|ZP_06544178.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|38604946|sp|Q8Z1T1|DUSA_SALTI RecName: Full=tRNA-dihydrouridine synthase A
 gi|25329941|pir||AB1016 conserved hypothetical protein STY4439 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16505231|emb|CAD09227.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29140049|gb|AAO71613.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
          Length = 332

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DTDPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADAAVLEQALKLIADK 331


>gi|188494852|ref|ZP_03002122.1| tRNA-dihydrouridine synthase A [Escherichia coli 53638]
 gi|188490051|gb|EDU65154.1| tRNA-dihydrouridine synthase A [Escherichia coli 53638]
          Length = 347

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +   
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDI 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 324 ENAHKAGADINVLEHALKLVADK 346


>gi|332084336|gb|EGI89539.1| tRNA-dihydrouridine synthase A [Shigella dysenteriae 155-74]
          Length = 345

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/322 (45%), Positives = 201/322 (62%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+VE  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLVEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIEHELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A  + A  +++E A  L+ +
Sbjct: 322 ENAHKAGADINVLEHALKLVAD 343


>gi|157373905|ref|YP_001472505.1| tRNA-dihydrouridine synthase A [Shewanella sediminis HAW-EB3]
 gi|157316279|gb|ABV35377.1| TIM-barrel protein, YjbN family [Shewanella sediminis HAW-EB3]
          Length = 327

 Score =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/318 (44%), Positives = 198/318 (62%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ ARL++   LLYTEM+   AI+ G   + L ++++E  LALQ+GG++  
Sbjct: 18  MLDWTDRHYRYMARLMSAELLLYTEMVTTGAIIHGKG-DYLAYNSEEHALALQLGGSNAH 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  D GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM + + IPVT
Sbjct: 77  DLAICAKLAADRGYDEINLNVGCPSDRVQNGRFGACLMAEPKLVAECVTAMREVVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   V++++ +G +   +HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 137 VKTRIGIDEQDSYPFLTEFVETVRDAGCDTFIVHARKAWLKGLSPKENREIPPLDYDRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I +NGG++ + +    L  +DGVM+GR AY+N  ML  VD+         
Sbjct: 197 QLKQDYPELSISINGGVKSLDECRTHLTKLDGVMVGREAYQNPYMLAEVDQQLCGSD--- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R        +      Y  +HL SGG+L  I+RHM GLF G P SR  R  ++  
Sbjct: 254 RPVLSR------DAVLEKFIPYIEKHLQSGGRLNHISRHMTGLFQGEPGSRVWRRYISEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IE A   M
Sbjct: 308 AHKPGAGIEVIEQARKNM 325


>gi|209549798|ref|YP_002281715.1| tRNA-dihydrouridine synthase A [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209535554|gb|ACI55489.1| TIM-barrel protein, yjbN family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 333

 Score =  371 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 172/318 (54%), Positives = 220/318 (69%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D S
Sbjct: 13  MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E +GY+EINLNVGCPS RV  G+FGACLML P+ V DCIAAM K  ++PVT
Sbjct: 73  KLAEAVKISEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVADCIAAMKKVATVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEQALPELITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD+ F     G 
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAAAHLAHVDGVMLGRAAYQNAAILAEVDQRFFGAPAGE 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+ SGG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 253 PD---------WEGLRDRMMAYAERHIASGGRLQHVARHMVGLFTGLPGARRYRQILSTD 303

Query: 301 AGASTATHHIIETAFNLM 318
           A  S A   ++  AF  +
Sbjct: 304 AAKSGAGPEVLAAAFAAV 321


>gi|239831743|ref|ZP_04680072.1| TIM-barrel protein, yjbN family [Ochrobactrum intermedium LMG 3301]
 gi|239824010|gb|EEQ95578.1| TIM-barrel protein, yjbN family [Ochrobactrum intermedium LMG 3301]
          Length = 337

 Score =  371 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 158/314 (50%), Positives = 213/314 (67%), Gaps = 9/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +++ALLYTEM+VADAI+ G +  +LGF   E P+ALQ+GG+D +
Sbjct: 21  MIDWSDRHCRYFHRLFSSHALLYTEMVVADAIIHGPRDRLLGFDAAEHPVALQLGGSDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAAKI  D+GY+EINLNVGCPS RV  G+FGACLM  PD+V  C++AM +A+S+PVT
Sbjct: 81  KLKEAAKIGADYGYDEINLNVGCPSDRVQSGTFGACLMQTPDVVARCVSAMKEAVSVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR GVDDQ   VAL  L      +G + +W+HARKA LKGLSPK+NR+IP LDYD VY
Sbjct: 141 VKCRTGVDDQDVEVALDTLADMTLDAGADALWVHARKAWLKGLSPKENREIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K    D+F+G+NGG+  + +A + L +VD VM+GRAAY N  +L  VD          
Sbjct: 201 RLKARLGDVFVGINGGITTLDEAEQHLQTVDAVMLGRAAYHNPELLAEVDVRLYGGEQRD 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +   +D+         M  Y  RH+ +GG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 261 TSMAGIIDE---------MCAYIDRHIAAGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 311

Query: 301 AGASTATHHIIETA 314
           A    AT  ++  A
Sbjct: 312 ATRPGATSDVLRQA 325


>gi|396384|gb|AAC43143.1| ORF_o345 [Escherichia coli str. K-12 substr. MG1655]
          Length = 345

 Score =  371 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N   V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAXXVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|188535214|ref|YP_001909011.1| tRNA-dihydrouridine synthase A [Erwinia tasmaniensis Et1/99]
 gi|188030256|emb|CAO98143.1| tRNA-dihydrouridine synthase A [Erwinia tasmaniensis Et1/99]
          Length = 332

 Score =  371 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/324 (45%), Positives = 199/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLYTEM+   AI+ G   + L FS +E+P+ALQ+GG+D +
Sbjct: 16  MLDWTDRHCRYFHRQLTRQTLLYTEMVTTGAIIHGKG-DYLAFSREEQPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM    S+PVT
Sbjct: 75  ALAQCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEARLVADGIKAMRDVTSLPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 135 VKTRIGIDDQDSYAFLCDFIRTVSEQGGCEMFIIHARKAWLSGLSPKENREIPPLDYPRV 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + LNGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F   L 
Sbjct: 195 YQLKRDFPHLTLSLNGGVKTLEEAKVHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTLP 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  SM  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 255 DTDPV----------AVVRSMYPYIERELAKGTYLGHVTRHMLGLFQGVPGARQWRRYLS 304

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A  + A   ++E A +L+ + +
Sbjct: 305 ENAHKAGAGVEVVEKALSLVADKV 328


>gi|51594726|ref|YP_068917.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis IP
           32953]
 gi|186893729|ref|YP_001870841.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis PB1/+]
 gi|51588008|emb|CAH19612.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|186696755|gb|ACC87384.1| TIM-barrel protein, yjbN family [Yersinia pseudotuberculosis PB1/+]
          Length = 345

 Score =  371 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/322 (45%), Positives = 200/322 (62%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G      IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 HAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|290476894|ref|YP_003469805.1| tRNA-dihydrouridine synthase A [Xenorhabdus bovienii SS-2004]
 gi|289176238|emb|CBJ83043.1| tRNA-dihydrouridine synthase A [Xenorhabdus bovienii SS-2004]
          Length = 345

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 142/323 (43%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  ALLYTEM+   AI+ G   N L ++ +E PLALQ+GG++  
Sbjct: 33  MLDWTDRHCRYFHRLLSKEALLYTEMVTTGAIIHGKG-NYLTYNEEEHPLALQLGGSEPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AKI ++ GY+EINLNVGCPS RV  G FGACLM    +V D I AM   + IPVT
Sbjct: 92  ALAQCAKIAQERGYDEINLNVGCPSDRVQNGRFGACLMGEAKLVADGIKAMQDVVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + + +K S  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDEQDSYEFLCDFIDTVVKNSDCDNFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L + +NGG++ + +A + L  VDGVMIGR AY+N ++L  VD    N    
Sbjct: 212 YQLKKDFPQLTLSINGGIKSLEEAKQHLQYVDGVMIGREAYQNPSILAHVDRELFNETAL 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                  +           +  Y  R L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 272 VVNTINAIKA---------LYPYIERELSKGTYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A  + A   ++E A  ++ E +
Sbjct: 323 NAHKAGADIMVVEKALEMVTERM 345


>gi|324112315|gb|EGC06293.1| tRNA dihydrouridine synthase A [Escherichia fergusonii B253]
          Length = 333

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 197/322 (61%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GL+PK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLNPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L+ VD         
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKMHLQHMDGVMVGREAYQNPGILSAVDREIFASTD- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                T  D D    +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 257 -----TDTDADPV-AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSE 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A  +++E A  L+ + 
Sbjct: 311 NAHKPGADINVLEHALKLVADK 332


>gi|260599558|ref|YP_003212129.1| tRNA-dihydrouridine synthase A [Cronobacter turicensis z3032]
 gi|260218735|emb|CBA34083.1| tRNA-dihydrouridine synthase A [Cronobacter turicensis z3032]
          Length = 349

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 139/322 (43%), Positives = 192/322 (59%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L++ ALLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 37  MLDWTDRHCRYFLRQLSSQALLYTEMVTTGAIIHGKG-DYLAYSDEEHPVALQLGGSDPA 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 96  ALAHCAKLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 156 VKTRIGIDDQDSYEFLCDFVGTVAEQGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 215

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +      L  +DGVM+GR AY+N  +L +VD       T 
Sbjct: 216 YQLKRDFPQLTMSINGGIKTLDDVKAHLAHMDGVMVGREAYQNPGLLASVDREIFGLDTP 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +             +  +M  Y       G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 276 DADPV---------AVVRAMYPYIEGERAKGTYLGHVTRHMLGLFQGIPGARQWRRYLSE 326

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+ + 
Sbjct: 327 NAHKPGAGIDVLEQALKLVADK 348


>gi|330828271|ref|YP_004391223.1| tRNA-dihydrouridine synthase A [Aeromonas veronii B565]
 gi|328803407|gb|AEB48606.1| tRNA-dihydrouridine synthase A [Aeromonas veronii B565]
          Length = 328

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 138/320 (43%), Positives = 192/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++   LLYTEM+   AI+ G   + LG+S QE P++LQ+GG++ +
Sbjct: 11  MLDWTDRHCRYFHRLMSRQTLLYTEMVTTGAIIHGKG-DYLGYSEQEHPISLQLGGSNPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+E+N+NVGCPS RV  G FGACLM  P +V DC+ AM   + IPVT
Sbjct: 70  DLARCAKLAEERGYDEVNINVGCPSDRVQNGRFGACLMGEPALVADCVKAMRDVVDIPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  ++ ++ +G +   +HARKA L GLSPK+NR+IP LDY  VY
Sbjct: 130 VKTRIGIDDQDSYEFLQAFIEQVRDAGCDTFIVHARKAWLSGLSPKENREIPPLDYPRVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I LNGG+  M Q L+ L  VDGVM+GR AY+N  +L  VD          
Sbjct: 190 RVKQDYPELTIALNGGVTSMEQTLEHLQHVDGVMMGREAYQNPYILAQVDNLVFGQNNA- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + +R       ++   M  Y  + L  G  L  +TRHM+GLF     +R  R  L+  
Sbjct: 249 --VPSR------HEVVRMMLPYIEQELAKGNYLSHMTRHMLGLFQNMQGARAWRRHLSEN 300

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++  A   + E
Sbjct: 301 ACKPGADIQVVLDAMAKVPE 320


>gi|320193408|gb|EFW68045.1| tRNA dihydrouridine synthase A [Escherichia coli WV_060327]
          Length = 331

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 201/323 (62%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLGEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 308 ENAHKAGADINVLEHALKLVADK 330


>gi|117618436|ref|YP_858131.1| tRNA-dihydrouridine synthase A [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559843|gb|ABK36791.1| tRNA-dihydrouridine synthase A [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 328

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 138/320 (43%), Positives = 192/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + LG+S QE P++LQ+GG++ +
Sbjct: 11  MLDWTDRHCRYFHRLMTRQTLLYTEMVTTGAIIHGKG-DYLGYSEQEHPISLQLGGSNPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+E+N+NVGCPS RV  G FGACLM  P +V DC+ AM   + IPVT
Sbjct: 70  DLARCAKLAEERGYDEVNINVGCPSDRVQNGRFGACLMGEPALVADCVKAMRDVVDIPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  ++ ++ +G +   +HARKA L GLSPK+NR+IP LDY  VY
Sbjct: 130 VKTRIGIDDQDSYEFLQAFIEQVRDAGCDTFIVHARKAWLSGLSPKENREIPPLDYPRVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG+  M Q L+ L  +DGVM+GR AY+N  +L  VD          
Sbjct: 190 RVKQDYPDLTIAINGGVTSMEQTLEHLQHLDGVMMGREAYQNPYILAQVDNLVFGQNNA- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + +R       ++   M  Y  + L  G  L  +TRHM+GLF     +R  R  L+  
Sbjct: 249 --VPSR------HEVVRMMLPYIEQELAKGNYLSHMTRHMLGLFQNMQGARAWRRHLSEN 300

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++  A   + E
Sbjct: 301 ACKPGADIQVVLDAMAKVPE 320


>gi|242238196|ref|YP_002986377.1| TIM-barrel protein, yjbN family [Dickeya dadantii Ech703]
 gi|242130253|gb|ACS84555.1| TIM-barrel protein, yjbN family [Dickeya dadantii Ech703]
          Length = 335

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 142/319 (44%), Positives = 195/319 (61%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL++NALLYTEM+   AIL G   + L ++ +E PLALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRLLSHNALLYTEMVTTGAILHGRG-DYLAYNDEEHPLALQLGGSDPQ 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I E  GY+EINLNVGCPS RV  G FGACLM   ++V DC+ AM   + +PVT
Sbjct: 83  ALAQCAEIAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAELVADCVDAMRGRVRLPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 143 VKTRIGIDDQDSYDFLCAFIRTVAERGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + QA + L  +DGVM+GR AY+N  +L  VD         
Sbjct: 203 YQLKRDFPALTIAINGGIKTLEQAQQHLQHLDGVMVGREAYQNPGVLAQVDSQLFGVTAP 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              +           +   M  Y  R L  G +L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 263 VPDLF---------AVVEGMYPYIERELSRGAQLGHITRHMLGLFQGLPGARQWRRFLSE 313

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 314 NAHRPGADVSVVEQALTRV 332


>gi|260914683|ref|ZP_05921149.1| tRNA-dihydrouridine synthase A [Pasteurella dagmatis ATCC 43325]
 gi|260631282|gb|EEX49467.1| tRNA-dihydrouridine synthase A [Pasteurella dagmatis ATCC 43325]
          Length = 328

 Score =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 136/321 (42%), Positives = 196/321 (61%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+     + L FS +E P+ALQ+GG++ +
Sbjct: 18  MLDWTTRHCRYFHRQFSQHALLYTEMVTTGAIIHAKY-DHLAFSPEENPVALQLGGSNPT 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AKI E  GY EINLNVGCPS RV  G FGACLM   D+V +CI AM + + IPVT
Sbjct: 77  QLAQCAKIAEQRGYAEINLNVGCPSDRVQNGMFGACLMGKADLVAECINAMQEVVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V+ + ++G     IHARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDLDSYEFLCDFVQKVHQAGCQEFIIHARKAWLSGLSPKENREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG++ + +  + L  +DGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPQLIMSINGGIKTIEEMQQHLQYMDGVMVGREAYQNPSLLGYIDQALFDP---T 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SPI T       R+    M  Y  + L  G  L  + RHM+G F     +R+ R  L+  
Sbjct: 254 SPIVTP------REAVEKMFPYIEQQLTQGVYLNHMVRHMLGAFQSCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   ++E A + +   
Sbjct: 308 AHKAGAGLEVVEQALSFIENE 328


>gi|114564502|ref|YP_752016.1| tRNA-dihydrouridine synthase A [Shewanella frigidimarina NCIMB 400]
 gi|114335795|gb|ABI73177.1| TIM-barrel protein, yjbN family protein [Shewanella frigidimarina
           NCIMB 400]
          Length = 349

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 196/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++ ALLYTEMI   AIL+G   + L ++ QE P+ALQ+GG++  
Sbjct: 29  MLDWTDRHYRYFARLMSSKALLYTEMITTGAILQGKG-DYLAYNEQEHPVALQLGGSNAV 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+E+NLNVGCPS RV  G FGACLM  P +V  C+ AM +   IP+T
Sbjct: 88  DLAACAKLAAERGYDEVNLNVGCPSDRVQNGRFGACLMAEPALVAQCVDAMKQVTDIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L + ++++   G +   IHARKA L+GLSPK+NR+IP LDYD VY
Sbjct: 148 VKTRIGIDEQDSYQFLTDFIETVSAQGCSAFTIHARKAWLQGLSPKENREIPPLDYDRVY 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++   L I +NGG++ + ++   L  +DGVM+GR AY+N  +L  VD+      T  
Sbjct: 208 QLKRDYQHLNISINGGIKTLEESKLHLALLDGVMVGREAYQNPYILAQVDQQLCGLDTA- 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       +++   M  Y   HL  GG+L  ITRHMIGLF G P SR  R  L+  
Sbjct: 267 --------VITRQQVIEQMLPYIEAHLAQGGRLNHITRHMIGLFQGLPGSRGWRRHLSEN 318

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   +
Sbjct: 319 AHKPNADIGVVLKAAEFV 336


>gi|238764115|ref|ZP_04625069.1| tRNA-dihydrouridine synthase A [Yersinia kristensenii ATCC 33638]
 gi|238697652|gb|EEP90415.1| tRNA-dihydrouridine synthase A [Yersinia kristensenii ATCC 33638]
          Length = 343

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 200/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHGKG-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMAEANLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L   V+++   G  +   IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDELDSYEFLCEFVQTVAGRGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 317 NAHKPGADVSVVEQALALVT 336


>gi|194446261|ref|YP_002043494.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194404924|gb|ACF65146.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
          Length = 332

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPVT----------VVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|198244614|ref|YP_002218138.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|207859397|ref|YP_002246048.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|197939130|gb|ACH76463.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|206711200|emb|CAR35576.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|326625935|gb|EGE32280.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
          Length = 332

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|331655869|ref|ZP_08356857.1| tRNA-dihydrouridine synthase A [Escherichia coli M718]
 gi|331046223|gb|EGI18313.1| tRNA-dihydrouridine synthase A [Escherichia coli M718]
          Length = 345

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPALDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIECELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|170026071|ref|YP_001722576.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis YPIII]
 gi|169752605|gb|ACA70123.1| TIM-barrel protein, yjbN family [Yersinia pseudotuberculosis YPIII]
          Length = 345

 Score =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 147/322 (45%), Positives = 199/322 (61%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G      IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K + P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKCDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 HAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|295095415|emb|CBK84505.1| tRNA-U16,U17-dihydrouridine synthase [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 331

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E+ GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGNAHLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG+  + +A   L  +DGVM+GR AY+N  +L TVD E F     
Sbjct: 198 YQLKRDFPHLTMSINGGITSLDEAKAHLEHMDGVMVGREAYQNPGILATVDREIFGVDGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DTDPV----------AVVRAMYPYIERELSHGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 308 ENAHKAGADIEVLEHALRLVADK 330


>gi|296100676|ref|YP_003610822.1| tRNA-dihydrouridine synthase A [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295055135|gb|ADF59873.1| tRNA-dihydrouridine synthase A [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 331

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAHCAKLAEERGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFINTVAGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +LTTVD E F     
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLDEAKTHLAHMDGVMVGREAYQNPGILTTVDREIFGVEGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DTDPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 308 ENAHKAGADIEVLEQALRLVADK 330


>gi|304398443|ref|ZP_07380316.1| TIM-barrel protein, yjbN family [Pantoea sp. aB]
 gi|304353948|gb|EFM18322.1| TIM-barrel protein, yjbN family [Pantoea sp. aB]
          Length = 330

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 138/323 (42%), Positives = 191/323 (59%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G   + L +S  E P+ALQ+GG+D +
Sbjct: 14  MLDWTDRHCRYFHRQLTGDTLLYTEMVTTGAIIHGKG-DYLAYSEAEHPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM   ++V D I AM   +SIPVT
Sbjct: 73  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEANLVADAIKAMRDVVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 133 VKTRIGIDELDSYEFLTDFIGTVAGRGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I LNGG++ + +A   L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 193 YQLKRDFPHLTIALNGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDQTLFGRQHP 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++             +  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 253 AANPV---------DVVRAMYPYIEAELAKGTYLGHVTRHMLGLFQGIPGARQWRRHLSE 303

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  L+ + +
Sbjct: 304 NAHKPGADVRVLEAALALVADKI 326


>gi|308188956|ref|YP_003933087.1| tRNA-dihydrouridine synthase A [Pantoea vagans C9-1]
 gi|308059466|gb|ADO11638.1| tRNA-dihydrouridine synthase A [Pantoea vagans C9-1]
          Length = 330

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 138/323 (42%), Positives = 192/323 (59%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G   + L +S  E P+ALQ+GG+D +
Sbjct: 14  MLDWTDRHCRYFHRQLTGDTLLYTEMVTTGAIIHGKG-DYLAYSEAEHPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM   ++V D I AM   +SIPVT
Sbjct: 73  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEANLVADAIKAMRDVVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 133 VKTRIGIDELDSYEFLTDFIGTVAGRGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I LNGG++ + +A   L  +DGVM+GR AY+N  +L  VD+        
Sbjct: 193 YQLKRDFPHLTIALNGGVKTLEEAQTHLQHLDGVMMGREAYQNPGILAQVDQTLFGRQHP 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++            ++  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 253 AANPV---------EVVRAMYPYIEAELAKGTYLGHVTRHMLGLFQGIPGARQWRRHLSE 303

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  L+ + +
Sbjct: 304 NAHKPGADVRVLEAALALVADKI 326


>gi|220935021|ref|YP_002513920.1| tRNA-dihydrouridine synthase A [Thioalkalivibrio sp. HL-EbGR7]
 gi|219996331|gb|ACL72933.1| tRNA-dihydrouridine synthase A [Thioalkalivibrio sp. HL-EbGR7]
          Length = 336

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 138/319 (43%), Positives = 194/319 (60%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + LLYTEM+   A+L GD++  L F   E PLALQ+GG++  
Sbjct: 26  MMDWTDRHCRYFLRLISRHTLLYTEMVTTGALLHGDRERFLAFHPDEHPLALQLGGSEPG 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ ED GY+E+NLNVGCPS RV  G FGACLM  P +V DC+ AM  A  +PVT
Sbjct: 86  ELAACARMAEDHGYDEVNLNVGCPSDRVQSGRFGACLMAEPQLVADCVEAMRSACGLPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L   + ++++SG     IHARKA L+GLSP++NR++P L +D VY
Sbjct: 146 VKTRIGIDDRDSYPELTAFIDTVQRSGCRTFIIHARKAWLQGLSPRENREVPPLRHDWVY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I LNGG++D+      L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 206 RLKQDFPALEIILNGGVKDLDTVSDALRQVDGVMLGREAYHNPYVLAQVDARFYGD---A 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       ++      Y    L  G  LQ +TRH++GLF G P +R  R  ++  
Sbjct: 263 HPVPSR------HQVVERFLPYVEARLAQGVPLQAMTRHILGLFQGVPGARAWRRTISEN 316

Query: 301 AGASTATHHIIETAFNLMI 319
           A  + A   +I+ A   + 
Sbjct: 317 AHRAGAGVEVIQAAAQRVP 335


>gi|259909942|ref|YP_002650298.1| tRNA-dihydrouridine synthase A [Erwinia pyrifoliae Ep1/96]
 gi|224965564|emb|CAX57096.1| tRNA-dihydrouridine synthase A [Erwinia pyrifoliae Ep1/96]
          Length = 331

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLY+EM+   AI+ G   + L FS++E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTQQTLLYSEMVTTGAIIHGKG-DYLAFSSEEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 74  ALAHCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYEFLCDFIHTVSEQGGCEVFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD       + 
Sbjct: 194 YQLKRDFPHLTLSINGGVKSLAEAKIHLQYLDGVMMGREAYQNPGLLAQVDRELFGCTSP 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++             +  SM  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 254 AADPI---------AVVRSMYPYIERELANGTYLGHVTRHMLGLFQGIPGARQWRRYLSE 304

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A  + A   ++E A +++ E +
Sbjct: 305 NAHKAGAGIEVVEKALSMVAEKV 327


>gi|317493445|ref|ZP_07951866.1| tRNA dihydrouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918388|gb|EFV39726.1| tRNA dihydrouridine synthase A [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 337

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 189/322 (58%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+   LLYTEM+   AI+ G   + L +S +E PLALQ+GG+D  
Sbjct: 24  MLDWTDRHCRYFHRKLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPLALQLGGSDPE 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV  G FGACLM    +V D I AM   +SIPVT
Sbjct: 83  ALAHCARLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + +  +   G  N   +HARKA L GLSPK+NR+IP LDY+ V
Sbjct: 143 VKTRIGIDDQDSYEFLCDFIDIVSGKGECNSFTVHARKAWLSGLSPKENREIPPLDYERV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY++ ++L  VD    +    
Sbjct: 203 YQLKRDFPHLNIAINGGVKTLEEAKIHLQHLDGVMMGREAYQSPSILAHVDRELFDSTAD 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  S+  Y  R L +G  L  ITRH++GLF   P +R+ R  L+ 
Sbjct: 263 VPNSI---------DVVRSLYPYIERELSNGTYLGHITRHILGLFQSIPGARQWRRHLSE 313

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   + +S
Sbjct: 314 NAHKPGAGVEVVEAALQFVSQS 335


>gi|320649492|gb|EFX18016.1| tRNA-dihydrouridine synthase A [Escherichia coli O157:H- str. H
           2687]
          Length = 339

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDRTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|238752153|ref|ZP_04613635.1| tRNA-dihydrouridine synthase A [Yersinia rohdei ATCC 43380]
 gi|238709626|gb|EEQ01862.1| tRNA-dihydrouridine synthase A [Yersinia rohdei ATCC 43380]
          Length = 348

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 201/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKG-DYLAYSEQDHPVALQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM    +V DCI AM  A++IPVT
Sbjct: 92  ALAHCAKLAELRGYNEINLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDAVTIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G  +   IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 152 VKTRIGIDQLDSYEFLCEFVQTVAEQGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDP--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      +   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 NAPVIDPV------QAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 323 NAHKPGADVSVVEQALALVT 342


>gi|50122581|ref|YP_051748.1| tRNA-dihydrouridine synthase A [Pectobacterium atrosepticum
           SCRI1043]
 gi|49613107|emb|CAG76558.1| putative dihydrouridine synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 340

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 192/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G   + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHGKG-DYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM +  +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGDAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++ + G  +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCEFIQTVAERGECDTFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKMHLQHLDGVMMGREAYQNPGILAQVDRELFGIDAA 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +  +           +  SM  Y  R L     L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 268 TQDLAG---------VVRSMYPYIERELSGDASLGHITRHMLGMFQGIPGARQWRRYLSE 318

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 319 NAHKPGADSAVVERALALV 337


>gi|30064638|ref|NP_838809.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2a str. 2457T]
 gi|56480527|ref|NP_709871.2| tRNA-dihydrouridine synthase A [Shigella flexneri 2a str. 301]
 gi|30042897|gb|AAP18620.1| hypothetical protein S3574 [Shigella flexneri 2a str. 2457T]
 gi|56384078|gb|AAN45578.2| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
          Length = 339

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 86  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 146 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 206 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 266 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 315

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 316 ENAHKAGADINVLEHALKLVADK 338


>gi|238913008|ref|ZP_04656845.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
          Length = 332

 Score =  369 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++          IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQDECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|157372686|ref|YP_001480675.1| tRNA-dihydrouridine synthase A [Serratia proteamaculans 568]
 gi|157324450|gb|ABV43547.1| TIM-barrel protein, yjbN family [Serratia proteamaculans 568]
          Length = 336

 Score =  369 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/319 (44%), Positives = 196/319 (61%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFHRLLTKDTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 79  ALAHCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGQATLVADCIKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCDFIATVAGRGECDMFTIHARKAWLSGLSPKENREVPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P+L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD       T 
Sbjct: 199 YQLKRDFPELTLAINGGVKTLEEAKQHLQHLDGVMMGREAYQNPGILARVDSELFGRQT- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                   +      I  S+  Y  R L +G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 258 --------EVMDSVAIIESLYPYIERELSNGTYLGHITRHILGLFQGVPGARQWRRHLSE 309

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A +L+
Sbjct: 310 NAHKPGADARVVEQALDLV 328


>gi|161505294|ref|YP_001572406.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160866641|gb|ABX23264.1| hypothetical protein SARI_03435 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 345

 Score =  369 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPLALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  QLTHCAKLAEVRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 212 YQLKRDFPHLNMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 322 ENAHKAGADIGVLEQALKLVADK 344


>gi|168466925|ref|ZP_02700773.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|195630652|gb|EDX49264.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
          Length = 332

 Score =  369 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQMLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPVT----------VVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|313648753|gb|EFS13193.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2a str. 2457T]
 gi|332751993|gb|EGJ82386.1| tRNA-dihydrouridine synthase A [Shigella flexneri 4343-70]
 gi|332752162|gb|EGJ82554.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-671]
 gi|332753251|gb|EGJ83632.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2747-71]
 gi|332764755|gb|EGJ94984.1| tRNA-dihydrouridine synthase A [Shigella flexneri 2930-71]
 gi|332999047|gb|EGK18636.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-272]
 gi|332999143|gb|EGK18730.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-218]
 gi|333014208|gb|EGK33564.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-304]
 gi|333014419|gb|EGK33770.1| tRNA-dihydrouridine synthase A [Shigella flexneri K-227]
          Length = 345

 Score =  369 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 92  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 212 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 272 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 321

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 322 ENAHKAGADINVLEHALKLVADK 344


>gi|149907717|ref|ZP_01896464.1| TIM-barrel protein, yjbN family [Moritella sp. PE36]
 gi|149809387|gb|EDM69316.1| TIM-barrel protein, yjbN family [Moritella sp. PE36]
          Length = 330

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 200/321 (62%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT N LLYTEM+   AI+ G   + L ++ +E P++LQ+GG++  
Sbjct: 20  MLDWTDRHCRYFHRLLTKNTLLYTEMVTTGAIIHGRG-DYLAYNKEEHPVSLQLGGSNPI 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V DC+ AM   + IP+T
Sbjct: 79  DLAQSAKLAQERGYDEINLNVGCPSDRVQSGKFGACLMAEPTLVADCVKAMQDVVDIPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  + ++  +G     +HARKA L GLSPK+NR+IP L+Y  VY
Sbjct: 139 VKTRIGIDDQDSYEFLQTFIDTVAATGCKDFTLHARKAWLSGLSPKENREIPELNYQRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P LFI +NGG++ +++    L +VDGVM+GR AY N  +L+ +DE       G 
Sbjct: 199 DIKQDFPALFIAINGGVKTLAETQLHLGNVDGVMMGREAYHNPFLLSQIDELVYG---GE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R         +  M  Y   H+ +GG L  I RHM+GLF G P +R  +  L+ +
Sbjct: 256 KSIHSR------HDYAEMMLPYIDNHIRNGGSLTHIYRHMLGLFLGLPGARAWKRHLSEQ 309

Query: 301 AGASTATHHIIETAFNLMIES 321
                A   ++E A  L+ +S
Sbjct: 310 GHKKGAGVEVVEAALLLVPKS 330


>gi|306844081|ref|ZP_07476675.1| TIM-barrel protein, yjbN family [Brucella sp. BO1]
 gi|306275524|gb|EFM57256.1| TIM-barrel protein, yjbN family [Brucella sp. BO1]
          Length = 340

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 159/321 (49%), Positives = 215/321 (66%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML+PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLSPDVVARCVAAMKETVSIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD          
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGEGQEP 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +   +D          M  Y  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 264 PAMPEIIDA---------MCAYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYAAVVEA 335


>gi|238794664|ref|ZP_04638270.1| tRNA-dihydrouridine synthase A [Yersinia intermedia ATCC 29909]
 gi|238726053|gb|EEQ17601.1| tRNA-dihydrouridine synthase A [Yersinia intermedia ATCC 29909]
          Length = 343

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 198/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEAELVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++   G  +   IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVADRGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 206 YQLKRDFPTLTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFD---A 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 317 NAHKPGAGVAVVEQALALVT 336


>gi|16767493|ref|NP_463108.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167991432|ref|ZP_02572531.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|38604955|sp|Q8ZKH4|DUSA_SALTY RecName: Full=tRNA-dihydrouridine synthase A
 gi|16422801|gb|AAL23067.1| putative TIM-barrel enzyme [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|205330107|gb|EDZ16871.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261249341|emb|CBG27204.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267996554|gb|ACY91439.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301160735|emb|CBW20266.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312915348|dbj|BAJ39322.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321223111|gb|EFX48181.1| tRNA dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. TN061786]
 gi|323132582|gb|ADX20012.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332991059|gb|AEF10042.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 332

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+    LYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTQLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|330721563|gb|EGG99595.1| tRNA dihydrouridine synthase A [gamma proteobacterium IMCC2047]
          Length = 351

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 144/317 (45%), Positives = 200/317 (63%), Gaps = 9/317 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRHYR+F RL++ +ALLY+EM+   AI+ GD+ ++LGF   E+P+ALQ+GG+  S
Sbjct: 42  MLDWSDRHYRYFMRLISQHALLYSEMVTTGAIIHGDRDHLLGFDNHEQPVALQLGGSSPS 101

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E +KI ED GYNEINLNVGCPS RV  G+FGACLM  P++V  C+ +M +A++IPVT
Sbjct: 102 DLAECSKIGEDRGYNEINLNVGCPSDRVQNGAFGACLMAKPELVAACLESMQRAVNIPVT 161

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L+  ++ +  SG +   IHARKA L+GLSPK+NR IP L YD VY
Sbjct: 162 VKHRIGIDDLDSYELLQRFIEIVSHSGCSTFIIHARKAFLQGLSPKENRDIPPLKYDWVY 221

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P L I +NGG++ ++++ K L  VDGVMIGR AY N   L   D    +     
Sbjct: 222 QIKEQFPHLEIIINGGIKSLTESQKHLEQVDGVMIGREAYHNPYSLAQADAQLFDD---H 278

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R        I      Y  + L    +L  I++H++GLFHG P  R+ R  ++  
Sbjct: 279 HQIASR------HDILQQFLPYIEQQLTQDVRLTHISKHILGLFHGQPGGRKFRQYISEN 332

Query: 301 AGASTATHHIIETAFNL 317
           A    A   ++E A  L
Sbjct: 333 AYKPGAGIEVLENAAKL 349


>gi|256369291|ref|YP_003106799.1| TIM-barrel protein, yjbN family [Brucella microti CCM 4915]
 gi|255999451|gb|ACU47850.1| TIM-barrel protein, yjbN family [Brucella microti CCM 4915]
          Length = 340

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|153949073|ref|YP_001402722.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
 gi|152960568|gb|ABS48029.1| tRNA-dihydrouridine synthase A [Yersinia pseudotuberculosis IP
           31758]
          Length = 345

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/322 (45%), Positives = 199/322 (61%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM   D+V DCI AM  A++IPVT
Sbjct: 86  ALAHCAKLAEQRGYNEINLNVGCPSDRVQNGRFGACLMGEADLVADCIKAMRDAVAIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G      IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECEIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K + P L I +NGG++ +++A + L  +DGVM+GR AY+N  +LT VD    +    
Sbjct: 206 YQLKCDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPGILTQVDRELFDS--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSQGAYLGHITRHVLGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A  L+  S
Sbjct: 317 NAHKPGAGVSVVEEALALVSPS 338


>gi|23501749|ref|NP_697876.1| tRNA-dihydrouridine synthase A [Brucella suis 1330]
 gi|62289809|ref|YP_221602.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 1 str. 9-941]
 gi|82699735|ref|YP_414309.1| tRNA-dihydrouridine synthase A [Brucella melitensis biovar Abortus
           2308]
 gi|148560730|ref|YP_001258838.1| tRNA-dihydrouridine synthase A [Brucella ovis ATCC 25840]
 gi|161618824|ref|YP_001592711.1| tRNA-dihydrouridine synthase A [Brucella canis ATCC 23365]
 gi|163843134|ref|YP_001627538.1| tRNA-dihydrouridine synthase A [Brucella suis ATCC 23445]
 gi|189024050|ref|YP_001934818.1| tRNA-dihydrouridine synthase A [Brucella abortus S19]
 gi|225627352|ref|ZP_03785389.1| TIM-barrel protein, yjbN family protein [Brucella ceti str. Cudo]
 gi|237815294|ref|ZP_04594292.1| TIM-barrel protein, yjbN family [Brucella abortus str. 2308 A]
 gi|254689114|ref|ZP_05152368.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|254693597|ref|ZP_05155425.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|254697247|ref|ZP_05159075.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254704172|ref|ZP_05166000.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|254706926|ref|ZP_05168754.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|254709966|ref|ZP_05171777.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis B2/94]
 gi|254713966|ref|ZP_05175777.1| tRNA-dihydrouridine synthase A [Brucella ceti M644/93/1]
 gi|254716976|ref|ZP_05178787.1| tRNA-dihydrouridine synthase A [Brucella ceti M13/05/1]
 gi|254730146|ref|ZP_05188724.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|256031459|ref|ZP_05445073.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|256060968|ref|ZP_05451126.1| tRNA-dihydrouridine synthase A [Brucella neotomae 5K33]
 gi|256159585|ref|ZP_05457347.1| tRNA-dihydrouridine synthase A [Brucella ceti M490/95/1]
 gi|256254865|ref|ZP_05460401.1| tRNA-dihydrouridine synthase A [Brucella ceti B1/94]
 gi|256257363|ref|ZP_05462899.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|260168593|ref|ZP_05755404.1| tRNA-dihydrouridine synthase A [Brucella sp. F5/99]
 gi|260545444|ref|ZP_05821185.1| TIM-barrel protein [Brucella abortus NCTC 8038]
 gi|260566579|ref|ZP_05837049.1| TIM-barrel protein [Brucella suis bv. 4 str. 40]
 gi|260754612|ref|ZP_05866960.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|260757835|ref|ZP_05870183.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|260761658|ref|ZP_05874001.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260883639|ref|ZP_05895253.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|261213862|ref|ZP_05928143.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|261218781|ref|ZP_05933062.1| tRNA-dihydrouridine synthase A [Brucella ceti M13/05/1]
 gi|261222048|ref|ZP_05936329.1| tRNA-dihydrouridine synthase A [Brucella ceti B1/94]
 gi|261314391|ref|ZP_05953588.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|261317513|ref|ZP_05956710.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis B2/94]
 gi|261321720|ref|ZP_05960917.1| tRNA-dihydrouridine synthase A [Brucella ceti M644/93/1]
 gi|261324970|ref|ZP_05964167.1| tRNA-dihydrouridine synthase A [Brucella neotomae 5K33]
 gi|261754840|ref|ZP_05998549.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|261758066|ref|ZP_06001775.1| TIM-barrel protein [Brucella sp. F5/99]
 gi|265988548|ref|ZP_06101105.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|265998013|ref|ZP_06110570.1| tRNA-dihydrouridine synthase A [Brucella ceti M490/95/1]
 gi|297248212|ref|ZP_06931930.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 5 str. B3196]
 gi|23347676|gb|AAN29791.1| TIM-barrel protein, yjbN family [Brucella suis 1330]
 gi|62195941|gb|AAX74241.1| TIM-barrel protein, yjbN family [Brucella abortus bv. 1 str. 9-941]
 gi|82615836|emb|CAJ10838.1| Protein of unknown function UPF0034:TIM-barrel protein yjbN family
           [Brucella melitensis biovar Abortus 2308]
 gi|148371987|gb|ABQ61966.1| TIM-barrel protein, yjbN family [Brucella ovis ATCC 25840]
 gi|161335635|gb|ABX61940.1| TIM-barrel protein, yjbN family [Brucella canis ATCC 23365]
 gi|163673857|gb|ABY37968.1| TIM-barrel protein, yjbN family [Brucella suis ATCC 23445]
 gi|189019622|gb|ACD72344.1| TIM-barrel protein, yjbN family [Brucella abortus S19]
 gi|225617357|gb|EEH14402.1| TIM-barrel protein, yjbN family protein [Brucella ceti str. Cudo]
 gi|237790131|gb|EEP64341.1| TIM-barrel protein, yjbN family [Brucella abortus str. 2308 A]
 gi|260096851|gb|EEW80726.1| TIM-barrel protein [Brucella abortus NCTC 8038]
 gi|260156097|gb|EEW91177.1| TIM-barrel protein [Brucella suis bv. 4 str. 40]
 gi|260668153|gb|EEX55093.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 4 str. 292]
 gi|260672090|gb|EEX58911.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260674720|gb|EEX61541.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 6 str. 870]
 gi|260873167|gb|EEX80236.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 9 str. C68]
 gi|260915469|gb|EEX82330.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 3 str. Tulya]
 gi|260920632|gb|EEX87285.1| tRNA-dihydrouridine synthase A [Brucella ceti B1/94]
 gi|260923870|gb|EEX90438.1| tRNA-dihydrouridine synthase A [Brucella ceti M13/05/1]
 gi|261294410|gb|EEX97906.1| tRNA-dihydrouridine synthase A [Brucella ceti M644/93/1]
 gi|261296736|gb|EEY00233.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis B2/94]
 gi|261300950|gb|EEY04447.1| tRNA-dihydrouridine synthase A [Brucella neotomae 5K33]
 gi|261303417|gb|EEY06914.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M163/99/10]
 gi|261738050|gb|EEY26046.1| TIM-barrel protein [Brucella sp. F5/99]
 gi|261744593|gb|EEY32519.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 3 str. 686]
 gi|262552481|gb|EEZ08471.1| tRNA-dihydrouridine synthase A [Brucella ceti M490/95/1]
 gi|264660745|gb|EEZ31006.1| tRNA-dihydrouridine synthase A [Brucella pinnipedialis M292/94/1]
 gi|297175381|gb|EFH34728.1| tRNA-dihydrouridine synthase A [Brucella abortus bv. 5 str. B3196]
          Length = 340

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|238782919|ref|ZP_04626947.1| tRNA-dihydrouridine synthase A [Yersinia bercovieri ATCC 43970]
 gi|238716122|gb|EEQ08106.1| tRNA-dihydrouridine synthase A [Yersinia bercovieri ATCC 43970]
          Length = 339

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 198/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHGKG-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKQAELRGYNEINLNVGCPSDRVQNGRFGACLMAEANLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G  +   IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAEQGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +    
Sbjct: 206 YQLKRDFPVLTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPSILTQVDRELFDS--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 317 NAHKPGADVSVVEQALALVT 336


>gi|283480036|emb|CAY75952.1| tRNA-dihydrouridine synthase A [Erwinia pyrifoliae DSM 12163]
          Length = 332

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 197/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLY+EM+   AI+ G   + L FS++E P+ALQ+GG+D +
Sbjct: 16  MLDWTDRHCRYFHRQLTQQTLLYSEMVTTGAIIHGKG-DYLAFSSEEHPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 75  ALAHCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 135 VKTRIGIDDQDSYEFLCDFIHTVSEQGGCEVFIIHARKAWLSGLSPKENREIPPLDYPRV 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD       + 
Sbjct: 195 YQLKRDFPHLTLSINGGVKSLAEAKIHLQYLDGVMMGREAYQNPGLLAQVDRELFGCTSP 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++             +  SM  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 255 AADPI---------AVVRSMYPYIERELANGTYLGHVTRHMLGLFQGIPGARQWRRYLSE 305

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A  + A   ++E A +++ E +
Sbjct: 306 NAHKAGAGIEVVEKALSMVAEKV 328


>gi|38604722|sp|Q7UBC5|DUSA_SHIFL RecName: Full=tRNA-dihydrouridine synthase A
          Length = 330

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 18  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 77  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 137 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 197 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 257 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 307 ENAHKAGADINVLEHALKLVADK 329


>gi|254701628|ref|ZP_05163456.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|261752180|ref|ZP_05995889.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 5 str. 513]
 gi|261741933|gb|EEY29859.1| tRNA-dihydrouridine synthase A [Brucella suis bv. 5 str. 513]
          Length = 340

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|254449021|ref|ZP_05062475.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HTCC5015]
 gi|198261415|gb|EDY85706.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HTCC5015]
          Length = 315

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 195/318 (61%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A+L G+    L F + E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRYFHRLLSPHALLYTEMVTTGALLHGNVSRHLAFHSDEHPVALQLGGSEPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A++ E +GY+E+N+NVGCPS RV  G+FGACLM  PD V  C+AAM  A+SIPVT
Sbjct: 61  AMARCAELAERWGYDEVNINVGCPSDRVQSGAFGACLMAEPDTVASCVAAMKSAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L +    +  +  + + +HARKA LKGLSPK+NR IP L YD VY
Sbjct: 121 VKTRIGIDDMDDYQNLFDFTAKVIAANCDNLTVHARKAWLKGLSPKENRDIPPLMYDKVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L + +NGG+ D +   + L   DGVMIGRAAY+N   L  +++   + L   
Sbjct: 181 QLKRDYPELEVCINGGITDSASVSEHLRHTDGVMIGRAAYQNPWWLVELEQNLFDELHRP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            ++   M +Y    L +GG+L+ ITRHM+GLF   P +++ R  L+  
Sbjct: 241 T----------QHEVVEGMLEYIEAELLAGGQLKHITRHMLGLFQAVPGAKQWRRHLSEN 290

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   +
Sbjct: 291 AHLPGAGPELLRAAAAKV 308


>gi|156932320|ref|YP_001436236.1| tRNA-dihydrouridine synthase A [Cronobacter sakazakii ATCC BAA-894]
 gi|156530574|gb|ABU75400.1| hypothetical protein ESA_00095 [Cronobacter sakazakii ATCC BAA-894]
          Length = 313

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/323 (43%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L++  LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRQLSSQVLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 60  ALAHCAKLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFVGTVAEQGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ +      L  +DGVM+GR AY+N  +L +VD E F   + 
Sbjct: 180 HQLKRDFPKLTMSINGGIKTLDDVKTHLEHMDGVMVGREAYQNPGILASVDREIFGLDVP 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELAKGTYLGHVTRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A  +++E A  L+ + 
Sbjct: 290 ENAHKPGADINVLEQALKLVADK 312


>gi|293394136|ref|ZP_06638436.1| tRNA-dihydrouridine synthase A [Serratia odorifera DSM 4582]
 gi|291423114|gb|EFE96343.1| tRNA-dihydrouridine synthase A [Serratia odorifera DSM 4582]
          Length = 349

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/321 (43%), Positives = 196/321 (61%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRLLSKETLLYTEMVTTGAIVHGKG-DYLAYSEEEHPIALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 92  ALAHCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGQATLVADCIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + ++++   G      IHARKA L GLSPK NR++P LDY  V
Sbjct: 152 VKTRIGIDEQDSYAFLCDFIETVAGRGECEMFTIHARKAWLSGLSPKQNREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD         
Sbjct: 212 YQLKRDFPALTIAINGGVKTLDEARQHLQHLDGVMMGREAYQNPGILLQVDRELFGSQ-- 269

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P++  V          ++  Y  R L +G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 270 -APLQDSV------AAIEALYPYIERELANGTYLGHITRHILGLFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A    A   ++E A +L+ +
Sbjct: 323 NAHKPGADVRVVEQALSLVRQ 343


>gi|110807934|ref|YP_691454.1| tRNA-dihydrouridine synthase A [Shigella flexneri 5 str. 8401]
 gi|110617482|gb|ABF06149.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|281603466|gb|ADA76450.1| TIM-barrel protein, yjbN family [Shigella flexneri 2002017]
 gi|332998117|gb|EGK17721.1| tRNA-dihydrouridine synthase A [Shigella flexneri VA-6]
          Length = 347

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 94  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 154 VKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 213

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F +  T
Sbjct: 214 YQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDT 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y    L  G  L  I RHM+GLF G P +R+ R  L+
Sbjct: 274 DADPV----------AVVRAMYPYIEHELSQGTYLGHIIRHMLGLFQGIPGARQWRRYLS 323

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 324 ENAHKAGADINVLEHALKLVADK 346


>gi|254718967|ref|ZP_05180778.1| tRNA-dihydrouridine synthase A [Brucella sp. 83/13]
 gi|306838802|ref|ZP_07471633.1| TIM-barrel protein, yjbN family [Brucella sp. NF 2653]
 gi|306406086|gb|EFM62334.1| TIM-barrel protein, yjbN family [Brucella sp. NF 2653]
          Length = 340

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 159/321 (49%), Positives = 214/321 (66%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETVSIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            KCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 AKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD          
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGEGQEP 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +   +D          M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 264 PAMPEIIDA---------MCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|300115485|ref|YP_003762060.1| TIM-barrel protein [Nitrosococcus watsonii C-113]
 gi|299541422|gb|ADJ29739.1| TIM-barrel protein, yjbN family [Nitrosococcus watsonii C-113]
          Length = 325

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/319 (44%), Positives = 199/319 (62%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++++ALLYTEM+   A++ GD+   L   + E PLALQ+GG+   
Sbjct: 15  MMDWTDRHCRYFLRLISHHALLYTEMVTTGALVHGDRIRFLAHHSSEHPLALQLGGSHPE 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A+I ED+G++E+NLNVGCPS RV  G FGACLM  P +V +C+AAM +A  IPVT
Sbjct: 75  ELALCAQIAEDYGFDEVNLNVGCPSNRVQSGRFGACLMAEPQLVAECVAAMAQATQIPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q    AL + + ++ ++G     IHARKA L+GLSPK+NR+ P L YD+V 
Sbjct: 135 VKTRIGIDEQDSYEALSSFISTVAQAGCRTFIIHARKAWLQGLSPKENREKPPLRYDVVR 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK++ P L + +NGG+  + +  + L  +DGVMIGRAAY N  +L  VD+ F       
Sbjct: 195 AIKRDFPQLEVMINGGITTLKEVSEHLELLDGVMIGRAAYHNPYLLAPVDQRFYGDFRA- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + TR       +I  +   YAA  L  G  L ++TRH++GLF G P +R  R  L+  
Sbjct: 254 --LPTR------HEIIEAFLPYAAEQLARGVYLSRMTRHILGLFQGQPGARAWRRYLSEN 305

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   II  A   ++
Sbjct: 306 AHRPGAGIEIIREALQRVL 324


>gi|146309919|ref|YP_001174993.1| tRNA-dihydrouridine synthase A [Enterobacter sp. 638]
 gi|145316795|gb|ABP58942.1| tRNA-U16,U17-dihydrouridine synthase [Enterobacter sp. 638]
          Length = 331

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V D I AM   +SIPVT
Sbjct: 78  ALAECAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADGIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFIDTVAGKGECETFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L TVD E F     
Sbjct: 198 YQLKRDFPHLTMSINGGIKSLEEAKTHLQHMDGVMVGREAYQNPGILATVDREIFGIEGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+           +  +M  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 258 DSDPV----------AVVRAMYPYIERELSNGTYLGHVTRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 308 ENAHKAGADIEVLEHALRLVADK 330


>gi|238789911|ref|ZP_04633691.1| tRNA-dihydrouridine synthase A [Yersinia frederiksenii ATCC 33641]
 gi|238721984|gb|EEQ13644.1| tRNA-dihydrouridine synthase A [Yersinia frederiksenii ATCC 33641]
          Length = 343

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 200/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNE+NLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAEQRGYNEVNLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G  +   IHARKA L GLSPK+NR++P LDY+ V
Sbjct: 146 VKTRIGIDQLDSYEFLCEFVQTVAERGECDIFTIHARKAWLSGLSPKENREVPPLDYERV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N ++LT VD    +P   
Sbjct: 206 YQLKRDFPALTIAINGGVKTLAEAKEHLKYLDGVMMGREAYQNPSILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 317 NAHKPGADVSVVEQALALVT 336


>gi|332163190|ref|YP_004299767.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318603925|emb|CBY25423.1| tRNA dihydrouridine synthase A [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325667420|gb|ADZ44064.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330861940|emb|CBX72109.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica W22703]
          Length = 348

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 199/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLTKQTLLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 92  ALAHCAKLAELRGYNEINLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L   V+++ + G  +   IHARKA L GLSPK+NR++P L+Y+ V
Sbjct: 152 VKTRIGIDELDSYEFLCEFVQTVAERGECDIFTIHARKAWLSGLSPKENREVPPLNYERV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  VDGVM+GR AY+N  +LT VD    +P   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLAEAKEHLKHVDGVMMGREAYQNPTILTQVDRELFDP--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 NAPVVDSV------KAIETLFPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 323 NAHKPGADVSVVEQALALVT 342


>gi|294634339|ref|ZP_06712877.1| tRNA dihydrouridine synthase A [Edwardsiella tarda ATCC 23685]
 gi|291092236|gb|EFE24797.1| tRNA dihydrouridine synthase A [Edwardsiella tarda ATCC 23685]
          Length = 345

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 138/319 (43%), Positives = 187/319 (58%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S QE PLALQ+GG++ +
Sbjct: 32  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEQEHPLALQLGGSNPA 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 91  DLARCAALAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++   G  +   +HARKA L GLSPK+NR++P LDY  V
Sbjct: 151 VKTRIGIDEQDSYAFLCDFIGTVAGQGECDTFIVHARKAWLSGLSPKENREVPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P L I +NGG++ +++A   L  VDGVM+GR AY N  ML  VD    +    
Sbjct: 211 YRLKQDFPQLTIAINGGVKSLAEAQAHLCHVDGVMVGREAYHNPGMLAQVDRQLFDATAA 270

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y  R L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 271 VPDSI---------AVVRALYPYIERELAQGTYLGHITRHILGLFQGIPGARQWRRHLSE 321

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 322 NAHRPGADIAVVEQALRFV 340


>gi|253689857|ref|YP_003019047.1| TIM-barrel protein, yjbN family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251756435|gb|ACT14511.1| TIM-barrel protein, yjbN family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 340

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/319 (43%), Positives = 192/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L++  LLYTEM+   AIL G   + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLSSQTLLYTEMVTTGAILHGKG-DYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEASLVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + G      +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYAFLCDFIQTVAELGECETFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGIDAA 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +  +           +  +M  Y  R L  G  L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 268 TPDLAG---------VVRTMYPYIERELSGGAALGHITRHMLGMFQGIPGARQWRRYLSE 318

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 319 NAHKPGADAAVVERALALV 337


>gi|227326002|ref|ZP_03830026.1| tRNA-dihydrouridine synthase A [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 340

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 194/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G   + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHGKG-DYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + G  +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCDFIQTVAERGECDTFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 208 YQLKRDFPALTLAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGIDAA 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +  +           +  +M  Y  R L SG  L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 268 TPDLAG---------VVRAMYPYIERELSSGASLGHITRHMLGMFQGIPGARQWRRYLSE 318

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 319 NAHKPGADAAVVERALALV 337


>gi|145300509|ref|YP_001143350.1| tRNA-dihydrouridine synthase A [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853281|gb|ABO91602.1| tRNA-dihydrouridine synthase A [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 331

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 192/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + LG+S QE+P++LQ+GG++ +
Sbjct: 14  MLDWTDRHCRYFHRLMTRQTLLYTEMVTTGAIIHGKG-DYLGYSEQERPVSLQLGGSNPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+ AM   + IPVT
Sbjct: 73  DLAHCAKLARERGYDEINLNVGCPSDRVQNGRFGACLMGEPALVADCVKAMRDVVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L+  ++ ++ +G +   +HARKA L GLSP++NR+IP LDY  VY
Sbjct: 133 VKTRIGIDDQDSYEFLQTFIEQVRDAGCDTFIVHARKAWLSGLSPRENREIPPLDYPRVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I LNGG+  + Q L+ L  VDGVM+GR AY+N  +L  VD      L   
Sbjct: 193 RVKQDYPELTIALNGGVTSLEQTLEHLQQVDGVMMGREAYQNPYILAQVDSQLFG-LASE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +         ++   M  Y  + L  G  L  +TRHM+GLF     +R  R  L+  
Sbjct: 252 IPSR--------HEVVRMMLPYMEQELAKGNYLSHMTRHMLGLFQNMQGARAWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++  A   + E
Sbjct: 304 ACKQGAGIQVVLDAMAKVPE 323


>gi|90581341|ref|ZP_01237137.1| putative NifR3/Smm1 family protein [Vibrio angustum S14]
 gi|90437451|gb|EAS62646.1| putative NifR3/Smm1 family protein [Vibrio angustum S14]
          Length = 346

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 132/320 (41%), Positives = 195/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++  ALLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRLMSKEALLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPI 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   ++V  C+ AM   + IPVT
Sbjct: 91  DLARCAKLAQERGYDEINLNVGCPSDRVQNGMFGACLMGEAELVAQCVTAMRDVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L++ +  + +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDDQDSYEFLKDFIHVVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++   +  + L  +DGVM+GR AY++  ++  VD+        
Sbjct: 211 YQLKQDFAHLTMAINGGIKTFEEMEEHLKHMDGVMVGREAYQSPYLMAEVDQRLFGS--- 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+  R      R++  +M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 268 ERPVMKR------REVVEAMYPYIEKQLANGSYLGHITRHMLGLFQSMPGARQWRRHISE 321

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   +++ A + + 
Sbjct: 322 NAHKPGAGIEVVQQALDKIP 341


>gi|145633883|ref|ZP_01789604.1| hypothetical protein CGSHi3655_08484 [Haemophilus influenzae 3655]
 gi|145635660|ref|ZP_01791356.1| hypothetical protein CGSHiAA_01434 [Haemophilus influenzae PittAA]
 gi|144985255|gb|EDJ92098.1| hypothetical protein CGSHi3655_08484 [Haemophilus influenzae 3655]
 gi|145267055|gb|EDK07063.1| hypothetical protein CGSHiAA_01434 [Haemophilus influenzae PittAA]
          Length = 329

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 194/321 (60%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYTRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++ETA + + + 
Sbjct: 308 AFKQGAGVEVVETALSFVEKE 328


>gi|308051003|ref|YP_003914569.1| tRNA-U16,U17-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
 gi|307633193|gb|ADN77495.1| tRNA-U16,U17-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
          Length = 324

 Score =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/321 (43%), Positives = 198/321 (61%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++  ALLYTEM+   AI+ G   + LGF+ +E P+ALQ+GG++ +
Sbjct: 10  MLDWTDRHYRYFARLISRQALLYTEMVTTGAIIHGKG-DYLGFNEEEHPVALQLGGSNPA 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV  G FGACLM  P +V DC+ AM   +SIPVT
Sbjct: 69  DLAHCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEPQLVADCVKAMQDVVSIPVT 128

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++  +G +   IHARKA L+GLSPK+NR+IP L YD  Y
Sbjct: 129 VKTRIGIDEQDSYEFLTRFIDTVASAGCDIFTIHARKAWLQGLSPKENREIPELIYDRAY 188

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++   L I +NGG+  + Q    L  +DGVM+GR AY+N  M+  VD+         
Sbjct: 189 QVKRDFAHLNISVNGGITTLEQCEAHLQHLDGVMVGREAYQNPYMMAEVDQRLYGDD--- 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       ++   M  Y  RH+ +GG+   +TRHM+GLF+G P +R+ R  L   
Sbjct: 246 RPVLSRA------EVVEQMIPYLERHISNGGRANHVTRHMLGLFNGMPGARQWRRYLAQN 299

Query: 301 AGASTATHHIIETAFNLMIES 321
           A        ++  A   M E+
Sbjct: 300 AHLPGMGAELLADALASMPEA 320


>gi|56752036|ref|YP_172737.1| tRNA-dihydrouridine synthase A [Synechococcus elongatus PCC 6301]
 gi|81300875|ref|YP_401083.1| tRNA-dihydrouridine synthase A [Synechococcus elongatus PCC 7942]
 gi|56686995|dbj|BAD80217.1| hypothetical protein [Synechococcus elongatus PCC 6301]
 gi|81169756|gb|ABB58096.1| TIM-barrel protein, yjbN family [Synechococcus elongatus PCC 7942]
          Length = 343

 Score =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 195/321 (60%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F R ++   LLYTEMIVA AI  GD+  +L +  QE P+ALQ+GG +  
Sbjct: 24  MLDRTDRHCRYFLRQISRRTLLYTEMIVAQAIQYGDRARLLDYDPQEHPVALQVGGDNPQ 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I ED+GY+EINLNVGCPS RV +G FGACLM  P+ V  C+ AM  A ++PVT
Sbjct: 84  WLADCARIAEDWGYDEINLNVGCPSDRVQKGQFGACLMARPEQVAQCVEAMRSASTLPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L++ V+ + +SG +   +HARKA L+GL PK NR IP L YD+VY
Sbjct: 144 VKHRIGIDDRDSYEELQDFVRIVAESGCDRFSVHARKAWLQGLDPKQNRTIPPLRYDVVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+ D+ QA + L  VD VM+GRA Y N  +L   D          
Sbjct: 204 QLKQDFPQLVIEINGGILDLDQAQQHLQQVDAVMMGRAIYDNPYLLAAADAQLYGD---- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++     ++  +M  Y  + L  G +L  ITRH++ LFHG P SR  + +LT +
Sbjct: 260 -----HLEPRSRLQVVLAMMPYIEQQLSQGVRLHSITRHLLQLFHGCPGSRAWKRVLTEQ 314

Query: 301 AGASTATHHIIETAFNLMIES 321
                A   ++  A   + ES
Sbjct: 315 GCKPGAGPEVLLAALEQVSES 335


>gi|157963384|ref|YP_001503418.1| tRNA-dihydrouridine synthase A [Shewanella pealeana ATCC 700345]
 gi|157848384|gb|ABV88883.1| TIM-barrel protein, yjbN family [Shewanella pealeana ATCC 700345]
          Length = 328

 Score =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/318 (44%), Positives = 199/318 (62%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL+++  LLYTEM+   AIL G   + L ++ +E PLALQ+GG++  
Sbjct: 15  MLDWTDRHYRYFARLMSSQTLLYTEMVTTGAILHGRG-DYLAYNQEEHPLALQLGGSNPV 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+ AM + + IPVT
Sbjct: 74  DLAACAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVTAMKQVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++K +G     IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKTRIGIDEQDSYEFLTQFIDTVKAAGCEEFIIHARKAWLQGLSPKENREIPPLDYERVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I +NGG++ + +    L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 194 QLKRDYPELNISINGGVKTLEECQTHLQHLDGVMVGREAYQNPYILAEVDQKLCGID--- 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R        +   +  Y  +HL  GG+L  I+RH+IGLF G   SR  R  ++  
Sbjct: 251 APVMSR------DAVLEKLLPYIEKHLQQGGRLNHISRHIIGLFQGEVGSRVWRRYISEN 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  A   M
Sbjct: 305 AHKQGAGIEVITQARAEM 322


>gi|270263331|ref|ZP_06191601.1| tRNA-dihydrouridine synthase A [Serratia odorifera 4Rx13]
 gi|270043019|gb|EFA16113.1| tRNA-dihydrouridine synthase A [Serratia odorifera 4Rx13]
          Length = 336

 Score =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/319 (44%), Positives = 194/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFHRLLTKETLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 79  ALAHCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGQATLVADCIKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCDFIATVAGRGECDMFTIHARKAWLSGLSPKENREVPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD       T 
Sbjct: 199 YQLKRDFPQLTLAINGGVKTLEEAKQHLEHLDGVMMGREAYQNPGILARVDSELFGRQT- 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                   +      I  S+  Y  R L +G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 258 --------EVMDSVAIIESLYPYIERELSNGTYLGHITRHILGLFQGVPGARQWRRHLSE 309

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A +L+
Sbjct: 310 NAHKPGADARVVEAALDLV 328


>gi|310765537|gb|ADP10487.1| tRNA-dihydrouridine synthase A [Erwinia sp. Ejp617]
          Length = 331

 Score =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 139/322 (43%), Positives = 195/322 (60%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT   LLY+EM+   AI+ G   + L FS++E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTQQTLLYSEMVTTGAIIHGKG-DYLAFSSEEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY EINLNVGCPS RV  G FGACLM    +V D I AM   +S+PVT
Sbjct: 74  ALAHCAKLAEQRGYQEINLNVGCPSDRVQNGRFGACLMGEAQLVADGIKAMRDVVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G     IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYEFLCDFIHTVSEQGGCEVFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD       + 
Sbjct: 194 YQLKRDFPHLTLSINGGVKSLAEAKIHLQHLDGVMMGREAYQNPGLLAQVDRELFGCTSP 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++             +  SM  Y  R L +G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 254 AADPI---------AVVRSMYPYIERELANGTYLGHVTRHMLGLFQGIPGARQWRRYLSE 304

Query: 300 EAGASTATHHIIETAFNLMIES 321
               + A   ++E A +L+ + 
Sbjct: 305 NTHKAGAGVEVVEKALSLVADK 326


>gi|192359553|ref|YP_001981977.1| tRNA-dihydrouridine synthase A [Cellvibrio japonicus Ueda107]
 gi|190685718|gb|ACE83396.1| tRNA-dihydrouridine synthase A [Cellvibrio japonicus Ueda107]
          Length = 341

 Score =  367 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 198/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++W+    R F R+LT  A+LY+EM+   A+L GD+K  L ++  E PLALQ+GG+D  
Sbjct: 22  MMEWSTSDCRTFWRILTQRAVLYSEMVTTGALLYGDRKRFLDYNACEHPLALQLGGSDPR 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I E +GY+E+NLN GCPS RV  G  GACLM  P +V +CIAAM +A+SIPVT
Sbjct: 82  ALAECARIAEGWGYDEVNLNCGCPSDRVQNGMIGACLMAEPQLVAECIAAMQQAVSIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V++I  +G N   +HARKA LKGLSPK+NR+IP L YD VY
Sbjct: 142 VKHRIGIDDMDDYEGLETFVRTIAATGCNTFIVHARKAWLKGLSPKENREIPPLQYDKVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + Q+  +L  VDGVM+GR AY N  +L  VD+        S
Sbjct: 202 QLKQDFPHLNIIINGGITTLEQSQALLEHVDGVMVGREAYSNPYLLAQVDQTLYGE---S 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       +++ +   Y    L  G +L  +TRH++GL+ G P +R+ R +++  
Sbjct: 259 RPVISR------DQVTQAFIAYCEEQLAKGARLNHLTRHILGLYQGQPGARQFRRVISEH 312

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   +IE A   + E
Sbjct: 313 AHKPGAGIEVIERALAALNE 332


>gi|83645166|ref|YP_433601.1| tRNA-dihydrouridine synthase A [Hahella chejuensis KCTC 2396]
 gi|83633209|gb|ABC29176.1| tRNA-dihydrouridine synthase [Hahella chejuensis KCTC 2396]
          Length = 349

 Score =  367 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/318 (45%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ ARLL+ +  LYTEM+   AI+ GD+   L F+ +E P+A+Q+GG++  
Sbjct: 25  MMDWTDRHYRYLARLLSRHTYLYTEMVTTGAIIHGDRNRFLDFNAEEHPIAVQLGGSNPD 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E AKI ED+GY+EINLNVGCPS RV     GACLM  P+ V +C+AAMC A+SIPVT
Sbjct: 85  ELKECAKICEDWGYDEINLNVGCPSDRVQNNMIGACLMGYPERVAECVAAMCSAVSIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L N V+++K +G +   IHARKAILKGLSPK+NR+IP L Y   Y
Sbjct: 145 VKHRIGIDDQDSEEFLLNFVRTVKAAGCSTFIIHARKAILKGLSPKENREIPPLIYPRAY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK+  P+L I +NGG++ M ++   L  VDGVMIGR AY+   ML  VD    +     
Sbjct: 205 LIKQTFPELEIIINGGIKTMDESESHLQEVDGVMIGREAYQRPWMLADVDHRLFH---CP 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  +  D  +         +Y  R+  +G  +  + RH +GLFHG    ++ R  L+  
Sbjct: 262 PPSFSATDIGY------QFLEYIERNYQNGVAVWHMARHALGLFHGQKGGKQFRRYLSEN 315

Query: 301 AGASTATHHIIETAFNLM 318
           A   TA+  +   A +++
Sbjct: 316 AIKRTASPTVFRDALDIV 333


>gi|205355015|ref|YP_002228816.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205274796|emb|CAR39855.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|326630167|gb|EGE36510.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 332

 Score =  367 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFIDTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DG M+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGAMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADVAVLEQALKLVADK 331


>gi|265983957|ref|ZP_06096692.1| tRNA-dihydrouridine synthase A [Brucella sp. 83/13]
 gi|264662549|gb|EEZ32810.1| tRNA-dihydrouridine synthase A [Brucella sp. 83/13]
          Length = 329

 Score =  367 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 159/321 (49%), Positives = 214/321 (66%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 13  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 73  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            KCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 133 AKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD          
Sbjct: 193 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGEGQEP 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +   +D          M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 253 PAMPEIIDA---------MCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 304 ATKPGATSDVVRQAYATVVEA 324


>gi|17987386|ref|NP_540020.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str. 16M]
 gi|225852375|ref|YP_002732608.1| tRNA-dihydrouridine synthase A [Brucella melitensis ATCC 23457]
 gi|256044537|ref|ZP_05447441.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256113397|ref|ZP_05454251.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|256264126|ref|ZP_05466658.1| TIM-barrel protein [Brucella melitensis bv. 2 str. 63/9]
 gi|260563890|ref|ZP_05834376.1| TIM-barrel protein [Brucella melitensis bv. 1 str. 16M]
 gi|265990962|ref|ZP_06103519.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265994799|ref|ZP_06107356.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|17983074|gb|AAL52284.1| nifr3-like protein [Brucella melitensis bv. 1 str. 16M]
 gi|225640740|gb|ACO00654.1| TIM-barrel protein, yjbN family protein [Brucella melitensis ATCC
           23457]
 gi|260153906|gb|EEW88998.1| TIM-barrel protein [Brucella melitensis bv. 1 str. 16M]
 gi|262765912|gb|EEZ11701.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 3 str.
           Ether]
 gi|263001746|gb|EEZ14321.1| tRNA-dihydrouridine synthase A [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263094345|gb|EEZ18190.1| TIM-barrel protein [Brucella melitensis bv. 2 str. 63/9]
          Length = 340

 Score =  367 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 24  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 84  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 144 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKACLKGLSPKENREIPPLDYERVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 204 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 262 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 314

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 315 ATKPGATSDVVRQAYATVVEA 335


>gi|15888840|ref|NP_354521.1| tRNA-dihydrouridine synthase A [Agrobacterium tumefaciens str. C58]
 gi|15156601|gb|AAK87306.1| conserved hypothetical protein [Agrobacterium tumefaciens str. C58]
          Length = 336

 Score =  367 bits (943), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 158/318 (49%), Positives = 218/318 (68%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   RF  R L+  ALL+TEMIVADAI+ G ++ +LG+  QE P+ALQ+GG++ +
Sbjct: 18  MIDWTDTRCRFLHRQLSKRALLFTEMIVADAIIHGQREKLLGYHPQEHPVALQLGGSNPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  D+GY+EINLNVGCPS RV  G+FGACLM  P++V  CI+AM    ++PVT
Sbjct: 78  KLAEAVRIAGDYGYDEINLNVGCPSDRVQSGTFGACLMREPEVVAQCISAMKAVAAVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  +  +G + +W+HARKA L+GLSPK+NR++P LDYD+VY
Sbjct: 138 VKCRIGVDDQEPETVLPDFLARVVAAGADAVWVHARKAWLQGLSPKENREVPPLDYDLVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++NPD+FIG+NGG+ D+ QA + L  VDGVM+GRAAY N+++L  VD          
Sbjct: 198 RMKRDNPDVFIGINGGIADLDQAGEHLKYVDGVMLGRAAYHNTSILADVDHRIHGE---- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +  W  +  +M  YAA ++ +GG+L  +TRHM+GLF G P +RR R IL+ +
Sbjct: 254 -----EALQYDWMALRDTMMAYAADYIATGGRLNHVTRHMVGLFQGMPGARRFRQILSSD 308

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IE AF  +
Sbjct: 309 ATRPGAGPEVIEAAFAAI 326


>gi|148827810|ref|YP_001292563.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae PittGG]
 gi|148719052|gb|ABR00180.1| hypothetical protein CGSHiGG_06425 [Haemophilus influenzae PittGG]
          Length = 327

 Score =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKHCARLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYTRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T  +         SM  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTAYEA------VQSMLPYIEQQLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|330445027|ref|ZP_08308681.1| tRNA-dihydrouridine synthase A [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328493145|dbj|GAA03178.1| tRNA-dihydrouridine synthase A [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 346

 Score =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 130/320 (40%), Positives = 196/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+++  ALLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRYFHRIMSKEALLYTEMVTTGAIIHGKG-DFLAYNEEEHPVALQLGGSNPI 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   ++V  C+ AM   + IPVT
Sbjct: 91  DLARCAKLAQERGYDEINLNVGCPSDRVQNGMFGACLMGEAELVAQCVTAMRDVVDIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L++ +  + +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 151 VKTRIGIDDQDSYEFLKDFIHVVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++   +  + L  +DGVM+GR AY++  +++ VD+        
Sbjct: 211 YQLKQDFAHLTMAINGGIKTFEEMEEHLKHMDGVMVGREAYQSPYLMSEVDQRLFGSD-- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+  R      R++  +M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 269 -RPVMKR------REVVEAMYPYIEKQLANGSYLGHITRHMLGLFQNMPGARQWRRHISE 321

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   +++ A + + 
Sbjct: 322 NAHKPGAGIEVVQQALDKIP 341


>gi|288940773|ref|YP_003443013.1| TIM-barrel protein, yjbN family [Allochromatium vinosum DSM 180]
 gi|288896145|gb|ADC61981.1| TIM-barrel protein, yjbN family [Allochromatium vinosum DSM 180]
          Length = 310

 Score =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 137/311 (44%), Positives = 195/311 (62%), Gaps = 9/311 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + LLYTEMI   A++ GD++  L +   E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRYFLRLISRHTLLYTEMITTGALIHGDRERFLRYDPAEHPVALQLGGSDSE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E++GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM  A+ +PVT
Sbjct: 61  DLARCARMAEEWGYDEINLNVGCPSDRVQNGRFGACLMAEPVLVAECVTAMRAAVRVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     L + V  + ++G + I +HARKA LKGLSPK+NR IP L Y+IV 
Sbjct: 121 VKHRIGIDERDSYAELVDFVGRLSEAGCDAIIVHARKAWLKGLSPKENRDIPPLRYEIVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+E +  A+  L  +DGVMIGRAAY N  +L   D          
Sbjct: 181 DLKRDFPQLPIVINGGIETLDAAVDFLSDLDGVMIGRAAYHNPWILAEADRRVFGDTH-- 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  TR      R++  +   YA R L +G  L  ++RH++GLF G P +R  R  ++ +
Sbjct: 239 -PAPTR------RQVLEAFIPYAERQLAAGVPLNAMSRHLLGLFQGQPGARAWRRRISEQ 291

Query: 301 AGASTATHHII 311
           A    A   ++
Sbjct: 292 AHRPGAGVEVL 302


>gi|123444030|ref|YP_001008000.1| tRNA-dihydrouridine synthase A [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090991|emb|CAL13874.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 342

 Score =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 145/320 (45%), Positives = 199/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  +LLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 27  MLDWTDRHCRYFHRLLTKQSLLYTEMVTTGAIIHGKA-DYLAYSEQDHPVALQLGGSDPQ 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GYNEINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 86  ALAHCAKLAELRGYNEINLNVGCPSDRVQNGRFGACLMAEASLVADCIKAMRDVVSIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+      L   V+++ + G  +   IHARKA L GLSPK+NR++P LDY  V
Sbjct: 146 VKTRIGIDELDSYEFLCEFVQTVAERGECDIFTIHARKAWLSGLSPKENREVPPLDYARV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  VDGVM+GR AY+N  +LT VD    +P   
Sbjct: 206 YQLKRDFPTLTIAINGGVKTLAEAKEHLKYVDGVMMGREAYQNPTILTQVDRELFDP--- 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 263 NAPVVDSV------KAIEALFPYIEQELSRGAYLGHITRHILGIFQGIPGARQWRRHLSE 316

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  L+ 
Sbjct: 317 NAHKPGADVSVVEQALALVT 336


>gi|294852216|ref|ZP_06792889.1| tRNA-dihydrouridine synthase A [Brucella sp. NVSL 07-0026]
 gi|294820805|gb|EFG37804.1| tRNA-dihydrouridine synthase A [Brucella sp. NVSL 07-0026]
          Length = 329

 Score =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 13  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 73  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 133 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAWLKGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 193 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 251 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 304 ATKPGATSDVVRQAYATVVEA 324


>gi|227112414|ref|ZP_03826070.1| tRNA-dihydrouridine synthase A [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 340

 Score =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 192/319 (60%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G   + L +S +E PLALQ+GG+D  
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHGKG-DYLAYSEEEHPLALQLGGSDPQ 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+E+NLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEVNLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ + G      +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCDFIQTVAERGECETFIVHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGIDAA 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +  +           +  +M  Y  R L  G  L  ITRHM+G+F G P +R+ R  L+ 
Sbjct: 268 TPDLAG---------VVRAMYPYIERELSGGASLGHITRHMLGMFQGIPGARQWRRYLSE 318

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 319 NAHKPGADAAVVERALALV 337


>gi|326538599|gb|ADZ86814.1| TIM-barrel protein, yjbN family protein [Brucella melitensis M5-90]
          Length = 317

 Score =  367 bits (942), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 1   MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 61  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 121 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKACLKGLSPKENREIPPLDYERVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 181 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 239 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 291

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 292 ATKPGATSDVVRQAYATVVEA 312


>gi|291086669|ref|ZP_06356403.2| tRNA-dihydrouridine synthase A [Citrobacter youngae ATCC 29220]
 gi|291067402|gb|EFE05511.1| tRNA-dihydrouridine synthase A [Citrobacter youngae ATCC 29220]
          Length = 313

 Score =  367 bits (942), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 143/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIVHGKG-DYLAYSEEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 60  ALAQCAKLAEQRGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DD      L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDLDSYEFLCDFINTVAGKGECEMFIIHARKAWLSGLSPKENREIPPLDYARV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F+    
Sbjct: 180 YQLKRDFPHLTMSINGGIKSLEEAKIHLQHMDGVMVGREAYQNPGILASVDREIFAAATH 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSQGTYLGHVTRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A  +++E A  L+ + 
Sbjct: 290 ENAHKAGADINVLEHALKLVADK 312


>gi|15603283|ref|NP_246357.1| tRNA-dihydrouridine synthase A [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|38605041|sp|Q9CL29|DUSA_PASMU RecName: Full=tRNA-dihydrouridine synthase A
 gi|12721794|gb|AAK03502.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 327

 Score =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+     + L FS  E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSQHALLYTEMVTTGAIIHAKY-DHLEFSPAENPVALQLGGSDPT 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AKI +  GY EINLNVGCPS RV  G FGACLM   D+V DC++AM   +SIPVT
Sbjct: 77  QLAQCAKIAQQRGYTEINLNVGCPSDRVQNGMFGACLMAKADLVADCVSAMQTEVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+ + ++G     IHARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDLDSYEFLCEFVQKVHEAGCQEFIIHARKAWLSGLSPKENREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG++ + +  + L  +DGVM+GR AY+N ++L  +D+   +P    
Sbjct: 197 QLKRDFPHLLMSINGGIKTLEEMQQHLQYMDGVMVGREAYQNPSLLGYIDQALFDPTC-- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y  + L  G  L  + RHM+G F     +R+ R  L+  
Sbjct: 255 -PVVTP------REAVEKMFPYIEQQLSQGVYLNHVVRHMLGAFQSCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++E A + +
Sbjct: 308 AHKAGAGLEVVEKALSFV 325


>gi|126658190|ref|ZP_01729341.1| tRNA-dihydrouridine synthase A [Cyanothece sp. CCY0110]
 gi|126620561|gb|EAZ91279.1| tRNA-dihydrouridine synthase A [Cyanothece sp. CCY0110]
          Length = 341

 Score =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 143/318 (44%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R +T + LLYTEMIV  AI  GD+  +L FS +EKPL+LQ+GG    
Sbjct: 17  MMDYTDRHFRYFMRQITRHTLLYTEMIVTAAIKHGDRSKLLDFSPEEKPLSLQLGGDKPH 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I ED+GY+E+NLNVGCPS RV  G FGACLM NPD+V  C+  M KA++IPVT
Sbjct: 77  ELAECAIIAEDWGYDEVNLNVGCPSDRVQSGHFGACLMANPDLVAQCVEKMQKAVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     +   VK +  +G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 137 VKHRIGIDDQDSYENMAQFVKVVSDAGCQRFTVHARKAWLKGLSPKENRNIPPLRYEAVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P LFI +NGG+ ++ Q    L  VD VMIGRAAY N  +  TVD          
Sbjct: 197 RLKQEFPHLFIEINGGITNLEQVRNHLELVDAVMIGRAAYDNPYLFATVDRDIY------ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + ++ +    +I   M  Y    +  G KL +I+RH++ +F G P ++  +  ++  
Sbjct: 251 ---QDKIIQLTRHEIIEKMLPYIDDWVSRGHKLHKISRHLLAIFSGIPGTKAWKRHISEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  A   +
Sbjct: 308 AHLPDADSKVIVEALKKV 325


>gi|311281407|ref|YP_003943638.1| TIM-barrel protein, yjbN family [Enterobacter cloacae SCF1]
 gi|308750602|gb|ADO50354.1| TIM-barrel protein, yjbN family [Enterobacter cloacae SCF1]
          Length = 332

 Score =  366 bits (940), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 146/320 (45%), Positives = 198/320 (61%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ +  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM  A SIPVT
Sbjct: 79  ALAQCAKLAQARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDAASIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCEFINTVSGRGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR  Y+N  +L TVD E F     
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLAEAKAHLQHMDGVMVGREVYQNPGILATVDREIFGASAA 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + PI           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPI----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLM 318
             A  + A  +++E A  L+
Sbjct: 309 ENAHKAGADINVLEQALQLV 328


>gi|260583380|ref|ZP_05851150.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae NT127]
 gi|260093566|gb|EEW77484.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae NT127]
          Length = 327

 Score =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYTRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVRSMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|229845624|ref|ZP_04465749.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 6P18H1]
 gi|229811424|gb|EEP47128.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 6P18H1]
          Length = 327

 Score =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APVVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|16272577|ref|NP_438794.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae Rd KW20]
 gi|260581551|ref|ZP_05849356.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae RdAW]
 gi|1176344|sp|P44794|DUSA_HAEIN RecName: Full=tRNA-dihydrouridine synthase A
 gi|1573630|gb|AAC22293.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260091796|gb|EEW75754.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae RdAW]
          Length = 327

 Score =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|145642466|ref|ZP_01798016.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
 gi|145272834|gb|EDK12730.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 22.4-21]
          Length = 327

 Score =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|300714901|ref|YP_003739704.1| tRNA-dihydrouridine synthase A [Erwinia billingiae Eb661]
 gi|299060737|emb|CAX57844.1| tRNA-dihydrouridine synthase A [Erwinia billingiae Eb661]
          Length = 331

 Score =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 146/324 (45%), Positives = 199/324 (61%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT ++LLYTEM+   AI+ G   + L ++  E+P+ALQ+GG D +
Sbjct: 15  MLDWTDRHCRYFLRQLTRHSLLYTEMVTTGAIVHGKG-DYLAWNQAEQPVALQLGGYDAA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AK  E  GYNEINLNVGCPS RV  G FGACLM  P +V D I AM   +SIPVT
Sbjct: 74  ALAECAKQAEARGYNEINLNVGCPSDRVQNGRFGACLMGEPALVADGIKAMRDQVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L   ++ + ++ G +   IHARKA L GLSPK+NR+IP LDY+ V
Sbjct: 134 VKTRIGIDEQDSYEFLCEFIRQVSEQGGCDSFIIHARKAWLSGLSPKENREIPPLDYERV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ +++A   L  VDGVM+GR AY+N  +L  VD E F + L 
Sbjct: 194 YQLKRDFPHLTMSINGGIKSLAEAKVHLQHVDGVMMGREAYQNPGLLAQVDRELFGSELP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y    L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 254 APDPV----------AVVRAMYPYIEAELANGTYLGHITRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A    +E A  L+ + +
Sbjct: 304 ENAHKPGANIETVEQALALVADKI 327


>gi|262275131|ref|ZP_06052942.1| tRNA dihydrouridine synthase A [Grimontia hollisae CIP 101886]
 gi|262221694|gb|EEY73008.1| tRNA dihydrouridine synthase A [Grimontia hollisae CIP 101886]
          Length = 315

 Score =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 196/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+L+ NALLYTEM+   AI+ G   + L F+ +E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHCRYFHRILSKNALLYTEMVTTGAIIHGKG-DFLAFNEEEHPVALQLGGSNPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM   ++V  C+AAM + + IPVT
Sbjct: 60  DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMGEAELVAQCVAAMKEVVDIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V+++ +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLVDFVRTVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ P L + +NGG++ + +A   L  +DGVMIGR AY++  +L  VD         
Sbjct: 180 YQLKKDFPHLTMAINGGIKSLEEAEAHLKFMDGVMIGREAYQSPYLLAEVDSRLFGSD-- 237

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +PI  R       +   ++  Y    L  G  L  I+RHM+GLF   P +R+ R  ++ 
Sbjct: 238 -APIIKR------SEAVRAIFPYIEAELSKGTYLNHISRHMLGLFQNMPGARQWRRYISE 290

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A   + 
Sbjct: 291 NAHKPGAGTEVLEAALANIP 310


>gi|238892522|ref|YP_002917256.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae NTUH-K2044]
 gi|238544838|dbj|BAH61189.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 331

 Score =  366 bits (939), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D  
Sbjct: 19  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 198 WQLKRDFPHLTMAINGGIKSLDEARAQLEHMDGVMVGREAYQNPGILASVDREIFGVAGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 308 ENAHKAGADIAVLEHALKLVADK 330


>gi|326408882|gb|ADZ65947.1| tRNA-dihydrouridine synthase A [Brucella melitensis M28]
          Length = 329

 Score =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 218/321 (67%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RL +  ALLYTEM+VADA + G +  +LGF   E P+ALQ+GG+D +
Sbjct: 13  MIDWSDRHCRYFHRLFSKRALLYTEMVVADAAIFGPRDRLLGFDPAENPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML PD+V  C+AAM + +SIPVT
Sbjct: 73  KLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLMLTPDVVARCVAAMKETISIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L   + ++G + +W+HARKA LKGLSPK+NR+IP LDY+ VY
Sbjct: 133 VKCRIGVDDQDTETALDALADQVLEAGADALWVHARKACLKGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+   + F+G+NGG+  + +A   L  VD VM+GRAAY N A+L  VD        G 
Sbjct: 193 RLKQRLGETFVGINGGIATLEEAQVHLQKVDAVMLGRAAYHNPALLADVDARLYGE--GQ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+          +I  +M DY  RH+ SGG+L  ++RHM+GLF G P +RR R IL+ +
Sbjct: 251 EPLAMP-------EIIDAMCDYIDRHIASGGRLSHVSRHMVGLFTGQPGARRWRQILSTD 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    AT  ++  A+  ++E+
Sbjct: 304 ATKPGATSDVVRQAYATVVEA 324


>gi|238918205|ref|YP_002931719.1| hypothetical protein NT01EI_0241 [Edwardsiella ictaluri 93-146]
 gi|238867773|gb|ACR67484.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 349

 Score =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 186/319 (58%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +  +E PLALQ+GG++ +
Sbjct: 36  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYCEEEHPLALQLGGSNPA 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 95  DLARCARLAETRGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L + + ++   G  +   +HARKA L GLSP++NR++P LDY  V
Sbjct: 155 VKTRIGIDEQDSYPFLCDFIGTVAGQGECDTFIVHARKAWLSGLSPRENREVPPLDYPRV 214

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P L I LNGG++ + +A   L  VDGVM+GR AY N  +L  VD    +    
Sbjct: 215 YRLKQDFPHLTIALNGGVKRLDEARAHLQHVDGVMVGREAYHNPGILAQVDSQLFDADAA 274

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y  R L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 275 VPDSV---------AVVRALYPYIGRELAQGTYLGHITRHILGLFQGIPGARQWRRHLSE 325

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 326 NAHRPGAGIDVVEQALRFV 344


>gi|145638041|ref|ZP_01793669.1| hypothetical protein CGSHiHH_03013 [Haemophilus influenzae PittHH]
 gi|145268759|gb|EDK08734.1| hypothetical protein CGSHiHH_03013 [Haemophilus influenzae PittHH]
          Length = 327

 Score =  365 bits (938), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYIRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGVEVVETALSFV 325


>gi|212633607|ref|YP_002310132.1| tRNA-dihydrouridine synthase A [Shewanella piezotolerans WP3]
 gi|212555091|gb|ACJ27545.1| TIM-barrel protein, yjbN family [Shewanella piezotolerans WP3]
          Length = 370

 Score =  365 bits (938), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 140/318 (44%), Positives = 198/318 (62%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARL++   LLYTEM+   AI+ G   + L ++ +E P+ALQ+GG++  
Sbjct: 57  MLDWTDRHYRYFARLMSAEVLLYTEMVTTGAIIHGRG-DYLAYNQEEHPVALQLGGSNAV 115

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V +C+ AM + + IPVT
Sbjct: 116 DLATCAKLAAERGYDEINLNVGCPSDRVQNGRFGACLMAEPTLVAECVDAMKQVVDIPVT 175

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L   + ++K  G N   IHARKA L+GLSPK+NR+IP LDY+ VY
Sbjct: 176 VKTRIGIDEQDSYEFLTEFIDTVKAVGCNDFIIHARKAWLQGLSPKENREIPELDYERVY 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++  DL I +NGG++ +++    L  +DGVM+GR AY+N  +L  VD+         
Sbjct: 236 QLKRDYADLSISINGGVKTLAECKTHLQQLDGVMVGREAYQNPYILAEVDQQLCGID--- 292

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R        +   +  Y  +HL +GGKL  +TRH+IGLF G   SR  R  ++  
Sbjct: 293 KPVMSR------DAVLEKLLPYIEKHLQAGGKLNHVTRHIIGLFQGEVGSRVWRRYISEN 346

Query: 301 AGASTATHHIIETAFNLM 318
           A  S A   ++  A   M
Sbjct: 347 AHKSGAGIEVVTQARQEM 364


>gi|145639381|ref|ZP_01794986.1| hypothetical protein CGSHiII_04387 [Haemophilus influenzae PittII]
 gi|145271428|gb|EDK11340.1| hypothetical protein CGSHiII_04387 [Haemophilus influenzae PittII]
          Length = 327

 Score =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKHDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVESMLPYIEQQLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGVEVVETALSFV 325


>gi|251793819|ref|YP_003008551.1| tRNA-dihydrouridine synthase A [Aggregatibacter aphrophilus NJ8700]
 gi|247535218|gb|ACS98464.1| tRNA-dihydrouridine synthase A [Aggregatibacter aphrophilus NJ8700]
          Length = 327

 Score =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 194/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + + LLYTEM+ A AI+     + L F   E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRHTLLYTEMVTAQAIIHAKY-DHLDFDAAEHPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E  GY EINLNVGCPS RV  G FGACLM  P++V +C+  M  A+ IPVT
Sbjct: 77  QLKHCAQLAEQRGYQEINLNVGCPSDRVQNGMFGACLMAKPNLVAECVQQMQSAVQIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L N V+++K+ G     +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLYNFVQTVKQVGCREFIVHARKAWLSGLSPKQNREIPLLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPDLLISINGGIKTIEEIQQHLQHVDGVMVGREAYQNPSLLGHIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+  A M  Y    L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIITP------RQAVARMLPYIESQLSQGVYLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++ETA   + E
Sbjct: 308 AYKEGAGIEMVETALGFVEE 327


>gi|322642507|gb|EFY39107.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
          Length = 310

 Score =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 196/320 (61%), Gaps = 13/320 (4%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           WTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D ++L 
Sbjct: 1   WTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPAQLA 59

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
             AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVTVK 
Sbjct: 60  HCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKT 119

Query: 124 RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  VY++
Sbjct: 120 RIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQL 179

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSS 241
           K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T + 
Sbjct: 180 KRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTTDAD 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+  A
Sbjct: 240 PV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLSENA 289

Query: 302 GASTATHHIIETAFNLMIES 321
             + A   ++E A  L+ + 
Sbjct: 290 HKAGADVAVLEQALKLVADK 309


>gi|261822868|ref|YP_003260974.1| tRNA-dihydrouridine synthase A [Pectobacterium wasabiae WPP163]
 gi|261606881|gb|ACX89367.1| TIM-barrel protein, yjbN family [Pectobacterium wasabiae WPP163]
          Length = 340

 Score =  365 bits (937), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 142/319 (44%), Positives = 189/319 (59%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT+  LLYTEM+   AIL G   + L +S  E PLALQ+GG+D +
Sbjct: 29  MLDWTDRHCRYFLRQLTSQTLLYTEMVTTGAILHGKG-DYLAYSEDEHPLALQLGGSDPT 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM  + SIP+T
Sbjct: 88  ALAQCAKLAEQRGYDEINLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMKDSTSIPIT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++   G  +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 148 VKTRIGIDDQDSYEFLCEFIQTVAGRGECDTFIIHARKAWLSGLSPKENREIPPLDYPRV 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD         
Sbjct: 208 YQLKRDFPALTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGIDAA 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              +           +  +M  Y  R L  G  L  ITRHM+G+F G   +R+ R  L+ 
Sbjct: 268 EPDLAG---------VVRAMYPYIERELSGGASLGHITRHMLGMFQGITGARQWRRYLSE 318

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A  L+
Sbjct: 319 NAHKPGADAAVVERALTLV 337


>gi|254482016|ref|ZP_05095258.1| tRNA dihydrouridine synthase A subfamily protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037706|gb|EEB78371.1| tRNA dihydrouridine synthase A subfamily protein [marine gamma
           proteobacterium HTCC2148]
          Length = 315

 Score =  364 bits (936), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 131/321 (40%), Positives = 190/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+D H R+F RLL+  ALLYTEM+   A++ GD++  L F+ +E P+ALQ+GG++ +
Sbjct: 1   MMDWSDHHCRYFWRLLSKQALLYTEMVTTGALIHGDRERFLRFNAEEHPVALQLGGSNPN 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+  +++ Y+E+NLN GCPS RV  G FGACLM  P++V D + AM  A  +PVT
Sbjct: 61  DLAQCARWAQEWHYDEVNLNCGCPSDRVQSGMFGACLMAQPELVADGVKAMRDATLLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V  +  +G     +HARKA LKGLSPK+NR+IP L YD VY
Sbjct: 121 VKHRIGIDDMDSYEQMLDFVGPVADAGCEVFIVHARKAWLKGLSPKENREIPPLVYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG++ +      L  VDGVMIGR AY+N  ML  VD          
Sbjct: 181 RLKRDLPDLEIVINGGIQTIEDCEDHLAHVDGVMIGREAYQNPWMLAEVDSRLFG----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                    +    +   +  Y  + L  G  L  ITRH++GL+ G P +R+ R  L+  
Sbjct: 236 ----IDKVAESRDDVLLGLLPYVEQQLALGTHLNHITRHILGLYQGVPGARKFRRHLSEN 291

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A  +++  AF  + ++
Sbjct: 292 AYKKDAGLNVLIDAFEKVRQA 312


>gi|89075955|ref|ZP_01162327.1| putative NifR3/Smm1 family protein [Photobacterium sp. SKA34]
 gi|89048304|gb|EAR53883.1| putative NifR3/Smm1 family protein [Photobacterium sp. SKA34]
          Length = 348

 Score =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 132/320 (41%), Positives = 194/320 (60%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++  ALLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 34  MLDWTDRHCRYFHRLMSKEALLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNSI 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   ++V  C+ AM   + IPVT
Sbjct: 93  DLARCAKLAQERGYDEINLNVGCPSDRVQNGMFGACLMGEAELVAQCVTAMRDVVDIPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L++ +  + +K G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 153 VKTRIGIDDQDSYEFLKDFIHVVSEKGGCDNFTIHARKAWLSGLSPKENREIPPLDYPRV 212

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++   L + +NGG++   +    L  +DGVM+GR AY++  ++  VD+        
Sbjct: 213 YQLKQDFAHLTMAINGGIKTFEEMEAHLKHMDGVMVGREAYQSPYLMAEVDQRLFGS--- 269

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P+  R      R++  +M  Y  + L +G  L  ITRHM+GLF   P +R+ R  ++ 
Sbjct: 270 ERPVMKR------REVVEAMYPYIEKQLANGSYLGHITRHMLGLFQSMPGARQWRRHISE 323

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   +++ A + + 
Sbjct: 324 NAHKPGAGIEVVQQALDKIP 343


>gi|309973873|gb|ADO97074.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R2846]
          Length = 327

 Score =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G+D+      L + ++ ++  G     IHARKA L GLS K+NR+IP LDY  VY
Sbjct: 137 VKTRTGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSAKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L+ G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVQSMLPYIEQQLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IETA + +
Sbjct: 308 AFKQGAGVEVIETALSFV 325


>gi|116252712|ref|YP_768550.1| tRNA-dihydrouridine synthase A [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115257360|emb|CAK08455.1| putative tRNA-dihydrouridine synthase A [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 333

 Score =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 166/318 (52%), Positives = 218/318 (68%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G +  +LG    E PLALQ+GG+D +
Sbjct: 13  MIDWTDRHCRYFHRQISREALLYTEMVVADAIIHGPRDRLLGHDAAEHPLALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E + Y+EINLNVGCPS RV  G+FGACLML P++V +CIAAM +  ++PVT
Sbjct: 73  KLAEAVKIAEPYFYDEINLNVGCPSDRVQSGTFGACLMLTPEMVAECIAAMKRVATVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEQALPELITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  +D+ F       
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAATHLAHVDGVMLGRAAYQNAAILADIDQRFFGAPASE 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+ SGG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 253 PD---------WEALRDRMMAYAERHIASGGRLQHVARHMVGLFTGLPGARRYRQILSTD 303

Query: 301 AGASTATHHIIETAFNLM 318
           A  S A   ++  AF  +
Sbjct: 304 AAKSGAGPEVLAAAFAAV 321


>gi|68249213|ref|YP_248325.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 86-028NP]
 gi|68057412|gb|AAX87665.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 86-028NP]
          Length = 327

 Score =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 189/318 (59%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P    
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDPNAA- 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        +   SM  Y  + L+ G  L  I RHM+G F     +R+ R  L+  
Sbjct: 256 --------IVTAHEAVQSMLPYIEQQLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IETA + +
Sbjct: 308 AFKQGAGVEVIETALSFV 325


>gi|159029932|emb|CAO90311.1| dus2 [Microcystis aeruginosa PCC 7806]
          Length = 352

 Score =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 146/318 (45%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R ++   LLYTEMI   AI  GD+  +LGFS  EKPLALQ+GG +  
Sbjct: 34  MMDYTDRHFRYFLRQISRRPLLYTEMITTMAIKHGDRYKLLGFSLAEKPLALQLGGDNPY 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AKI E  GY+E+NLNVGCPS+RV EG+FGACLM NP++V   I+AM +A+SIPVT
Sbjct: 94  LLAECAKIAEYMGYDEVNLNVGCPSSRVKEGNFGACLMANPELVARGISAMNQAVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     + N V+ +  +G     IHARKA L+GLSPK+NR +P L YD VY
Sbjct: 154 VKQRIGIDDQDSYENMANFVRIVADAGCQRFTIHARKAWLQGLSPKENRTVPPLRYDDVY 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P LFI +NGG+ ++ QA + L  VD VMIGRAAY N  +  TVD  F      +
Sbjct: 214 RLKNQFPHLFIEINGGIINLEQARQHLQLVDAVMIGRAAYDNPYLFATVDRDFYGESV-T 272

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +         +I   M  Y    +  G KL QI++H++ LF G P ++  +  ++  
Sbjct: 273 PPTR--------EEIIKKMLPYIDEWVSKGYKLHQISKHLLQLFAGQPGTKAWKRYISEN 324

Query: 301 AGASTATHHIIETAFNLM 318
           +    A   +I  A   +
Sbjct: 325 SHFPGADSGVIWQALQQV 342


>gi|148826732|ref|YP_001291485.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae PittEE]
 gi|229847414|ref|ZP_04467514.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 7P49H1]
 gi|148716892|gb|ABQ99102.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae PittEE]
 gi|229809652|gb|EEP45378.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 7P49H1]
 gi|309751771|gb|ADO81755.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R2866]
          Length = 327

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 193/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M  A+ IPVT
Sbjct: 77  QLKYCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLS K+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSAKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L+ G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVQSMLPYIEQQLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IETA + +
Sbjct: 308 AFKQGAGVEVIETALSFV 325


>gi|325292867|ref|YP_004278731.1| tRNA-dihydrouridine synthase A [Agrobacterium sp. H13-3]
 gi|325060720|gb|ADY64411.1| tRNA-dihydrouridine synthase A [Agrobacterium sp. H13-3]
          Length = 319

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 161/318 (50%), Positives = 213/318 (66%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   RF  R L+  ALLYTEMIVADAI+ G +  +L + TQE P+ALQ+GG+D  
Sbjct: 1   MIDWTDTRCRFLHRQLSKRALLYTEMIVADAIIHGQRDRLLNYHTQEHPVALQLGGSDPV 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  D+GY+EINLNVGCPS RV  G+FGACLM  P+IV  C+AAM     +PVT
Sbjct: 61  KLSEAVRIASDYGYDEINLNVGCPSDRVQSGTFGACLMREPEIVAQCVAAMKAVAKVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  +  +G + +WIHARKA L+GLSPK+NR++P LDYD+VY
Sbjct: 121 VKCRIGVDDQEPEAVLPDFLSRVVAAGADAVWIHARKAWLQGLSPKENREVPPLDYDLVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ NPD+FIG+NGG+ D+ QA   L  +DGVM+GRAAY N+++L  VD          
Sbjct: 181 RMKRANPDIFIGINGGISDLDQASLHLHHMDGVMLGRAAYHNTSILADVDHRIYGE---- 236

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +  W  +  +M  YAA ++ +GG+L  +TRHM+GLF G P +RR R IL+ +
Sbjct: 237 -----EARQADWMGLRDAMMAYAADYIAAGGRLNHVTRHMVGLFQGMPGARRFRQILSSD 291

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +IE AF  +
Sbjct: 292 ATRPGAGTEVIEAAFAAV 309


>gi|288937656|ref|YP_003441715.1| TIM-barrel protein, yjbN family [Klebsiella variicola At-22]
 gi|288892365|gb|ADC60683.1| TIM-barrel protein, yjbN family [Klebsiella variicola At-22]
          Length = 331

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D  
Sbjct: 19  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 198 WQLKRDFPHLTMAINGGIKSLDEARLQLEHMDGVMVGREAYQNPGILASVDREIFGIAGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 308 ENAHKAGADIAVLEHALKLVADK 330


>gi|13470773|ref|NP_102342.1| tRNA-dihydrouridine synthase A [Mesorhizobium loti MAFF303099]
 gi|14021516|dbj|BAB48128.1| mll0566 [Mesorhizobium loti MAFF303099]
          Length = 332

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 163/318 (51%), Positives = 218/318 (68%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT+ ALLYTEM+VADA++ G ++ +LGF   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRFFHRQLTSRALLYTEMVVADAVIHGARERLLGFDDAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E FGY+E+NLNVGCPS RV  G+FGACLM  PD+V  C+ AM  A++IPVT
Sbjct: 74  KLAEAARIGEAFGYDEVNLNVGCPSDRVQSGTFGACLMKVPDLVAGCVTAMKAAVAIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L   +  +G + +W+HARKA L+GLSPK+NR IP LDY+ VY
Sbjct: 134 VKCRIGVDEQNPEPALDALADGVFNAGADALWVHARKAWLEGLSPKENRDIPPLDYNRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P+ FIG+NGG++ + +A   L  VDG M+GRAAY    +L  VD  F       
Sbjct: 194 RLKAKKPNEFIGINGGIQSLEEARAHLDHVDGAMLGRAAYHTPGILAGVDAGFYGA---- 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                + +   +  +  +M DYAARH+  GG+L  +TRHM+GLFHG P +RR R IL+ +
Sbjct: 250 -----KPEAFDFAALIDAMADYAARHIEQGGRLGHVTRHMVGLFHGLPGARRYRQILSTD 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +++TAF  +
Sbjct: 305 ANRPGAGPDVLKTAFAAV 322


>gi|16329480|ref|NP_440208.1| tRNA-dihydrouridine synthase A [Synechocystis sp. PCC 6803]
 gi|2829606|sp|P72872|DUS2_SYNY3 RecName: Full=Probable tRNA-dihydrouridine synthase 2
 gi|1651962|dbj|BAA16888.1| sll0926 [Synechocystis sp. PCC 6803]
          Length = 334

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 147/317 (46%), Positives = 200/317 (63%), Gaps = 9/317 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R LT + LLYTEMI A AIL GD++ +L FS +EKP+ALQ+GG D  
Sbjct: 18  MMDHTDRHFRYFLRQLTRHTLLYTEMITAQAILHGDRQRLLNFSPEEKPVALQLGGDDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I +D+GY+EINLNVGCPS RV  G+FGACLM  PD+V  C++AM KA+ IPVT
Sbjct: 78  LLAECARIGQDWGYDEINLNVGCPSDRVQSGNFGACLMAQPDLVAQCVSAMQKAVEIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     L + V+ +  +G     +HARKA L+GLSPK+NR IP L Y+ VY
Sbjct: 138 VKHRIGIDHRDSYEDLVHFVEIVANAGCQRFTVHARKAWLQGLSPKENRTIPPLRYEDVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG+    Q  + L  VD VM+GRAAY+N  +  TVD    +  T  
Sbjct: 198 QLKKDFPQLLIEINGGITQTEQIQQHLSHVDAVMVGRAAYENPYLFATVDRDIYHK-TNL 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +         +I   M  Y    L  G +L QITRH++ LF+G P ++  R  L+  
Sbjct: 257 VPSRA--------EIIERMLPYVEERLRHGDRLNQITRHLLSLFNGQPRAKFWRRTLSDS 308

Query: 301 AGASTATHHIIETAFNL 317
              ++A   +++TA   
Sbjct: 309 TLLASAGPELLQTALQA 325


>gi|288550133|ref|ZP_05969393.2| tRNA-dihydrouridine synthase A [Enterobacter cancerogenus ATCC
           35316]
 gi|288316334|gb|EFC55272.1| tRNA-dihydrouridine synthase A [Enterobacter cancerogenus ATCC
           35316]
          Length = 313

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRYFLRQLSRHTLLYTEMVTTGAIIHGKG-DYLAYSDEEHPVALQLGGSDPA 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V D I AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADSIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFIDTVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L TVD E F     
Sbjct: 180 YQLKRDFPHLTMSINGGIKSLEEAKTHLAHMDGVMVGREAYQNPGILATVDREIFGVEGA 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DTDPVS----------VVRAMYPYIERELSNGTWLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 290 ENAHKAGADIDVLEHALRLVADK 312


>gi|290512395|ref|ZP_06551762.1| tRNA-dihydrouridine synthase A [Klebsiella sp. 1_1_55]
 gi|289775390|gb|EFD83391.1| tRNA-dihydrouridine synthase A [Klebsiella sp. 1_1_55]
          Length = 331

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D  
Sbjct: 19  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 78  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 138 VKTRIGIDDQDSYEFLCEFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 198 WQLKRDFPHLTMAINGGIKSLDEARLQLEHMDGVMVGREAYQNPGILASVDREIFGIAGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 258 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 308 ENAHKAGADIAVLEHALKLVADK 330


>gi|262045546|ref|ZP_06018567.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330004874|ref|ZP_08305056.1| tRNA dihydrouridine synthase A [Klebsiella sp. MS 92-3]
 gi|259037105|gb|EEW38355.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328536493|gb|EGF62835.1| tRNA dihydrouridine synthase A [Klebsiella sp. MS 92-3]
          Length = 313

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 180 WQLKRDFPHLTMAINGGIKSLDEARVQLEHMDGVMVGREAYQNPGILASVDREIFGVAGA 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 290 ENAHKAGADIAVLEHALKLVADK 312


>gi|114765460|ref|ZP_01444570.1| tRNA-dihydrouridine synthase A [Pelagibaca bermudensis HTCC2601]
 gi|114542170|gb|EAU45201.1| tRNA-dihydrouridine synthase A [Roseovarius sp. HTCC2601]
          Length = 315

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 204/323 (63%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLY+EM+ A A++RG   ++L ++ +E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSRRALLYSEMVTAPALVRGGALHLLDYNPEEHPVALQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA + E  GY++I+LN GCPS RV  G+FGA LM +P++V DC+AAM +A+ I VT
Sbjct: 61  ELARAATLGEQAGYDQIDLNCGCPSDRVQSGTFGAVLMRSPELVADCVAAMREAVKIDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L + ++ I  +G   + IHARKA L+GLSPK+NR IP LDY+IV 
Sbjct: 121 VKCRIGVDEQEPRDVLPDFLQKISGAGCERVVIHARKAWLQGLSPKENRDIPPLDYEIVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           E+K+  P L + +NGG+ D+  A  +L   +DGVMIGRAAY     +L   D        
Sbjct: 181 EMKRAFPQLHVSINGGITDLDTAEALLADGLDGVMIGRAAYHQPWDILANADARIYGEAA 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G              +   +M  Y  RHL SGG+L QITRHM+GLF G P +R+ R +L+
Sbjct: 241 GPVSP---------EEAVQAMLPYIGRHLASGGRLHQITRHMLGLFAGRPGARQWRRVLS 291

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++E A + +  +
Sbjct: 292 EGATRDGAGPELVEEALSRVPAA 314


>gi|241205218|ref|YP_002976314.1| tRNA-dihydrouridine synthase A [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859108|gb|ACS56775.1| TIM-barrel protein, yjbN family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 333

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 164/318 (51%), Positives = 216/318 (67%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G +  +LG    E PLALQ+GG+D +
Sbjct: 13  MIDWTDRHCRYFHRQISREALLYTEMVVADAIIHGPRDRLLGHDAAEHPLALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI + +GY+EINLNVGCPS RV  G+FGACLML P+ V +CIAAM +  + PVT
Sbjct: 73  KLTEAVKIAQPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAECIAAMKRVATAPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEQALPELISRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  +D+ F       
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAAVHLEHVDGVMLGRAAYQNAAILADIDQRFFGAPAAE 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 253 PD---------WEALCNRMMAYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSTD 303

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++  AF  +
Sbjct: 304 AAKTGAGPEVLAAAFAAV 321


>gi|284006504|emb|CBA71765.1| tRNA-dihydrouridine synthase A [Arsenophonus nasoniae]
          Length = 344

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 145/321 (45%), Positives = 192/321 (59%), Gaps = 13/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   A++ G   + L +S +E P+ALQ+GG + +
Sbjct: 33  MLDWTDRHCRYFHRLLTKEALLYTEMVTTGALIYGKG-DYLAYSEEEHPVALQLGGNEPT 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ +  GY+EINLN+GCPS RV  G FGACLM    +V DCI AM  A +IP+T
Sbjct: 92  ALAYCAKMAQQSGYDEINLNIGCPSDRVQNGRFGACLMREGGLVADCIKAMQDAATIPIT 151

Query: 121 VKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVDD      L + + K +  S      IHARKA L GLSPK NR+IP LDY  V
Sbjct: 152 VKTRIGVDDDDSYAFLTDFIDKIVTDSQCRLFIIHARKAWLSGLSPKQNREIPPLDYLRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++KK+ P L I +NGG++++ +A + L  +DGVMIGR AY+N A+LT VD E+F     
Sbjct: 212 YQLKKDFPQLTIVVNGGIKNIDEAKQHLHHLDGVMIGREAYQNPALLTQVDVEFFDQRSL 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              PI              +M  Y  R L  G  L  ITRHM+G+F   P +R+ R  L+
Sbjct: 272 VIDPII----------AVQTMYPYIERELKQGTYLGHITRHMLGIFQAIPGARQWRRHLS 321

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   +++ A   + 
Sbjct: 322 ENAHKKGADVTVVKQALEFIT 342


>gi|319783627|ref|YP_004143103.1| TIM-barrel protein, yjbN family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169515|gb|ADV13053.1| TIM-barrel protein, yjbN family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 332

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 164/318 (51%), Positives = 216/318 (67%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+++ALLYTEM+VADA++ G ++ +LGF   E P+ALQ+GG+D  
Sbjct: 14  MMDWTDRHCRFFHRQLSSHALLYTEMVVADAVIHGARERLLGFDASEHPVALQLGGSDRE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E FGY+EINLNVGCPS RV  G+FGACLM  PD+V  C+AAM  A++IPVT
Sbjct: 74  KLAEAARIGEAFGYDEINLNVGCPSDRVQSGTFGACLMKVPDLVAGCVAAMKAAVTIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L   +  +G + +W+HARKA L+GLSPK+NR IP LDY+ VY
Sbjct: 134 VKCRIGVDEQDPEPALDALADGVFDAGADALWVHARKAWLEGLSPKENRDIPPLDYNRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K    + FIG+NGG++ + +AL  L  VDG M+GRAAY    +L  VD  F      S
Sbjct: 194 RLKARKHNEFIGINGGIQTIEEALAHLDHVDGAMLGRAAYHTPGILAGVDAAFYG--VQS 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P         +  +  +M DYAARH+  GG+L  +TRHM+GLFHG   +RR R IL+ +
Sbjct: 252 EPFD-------FAALIDTMADYAARHIEQGGRLGHVTRHMVGLFHGLSGARRYRQILSTD 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +++ AF  +
Sbjct: 305 ATKPGAGPDVLKAAFAAV 322


>gi|152978183|ref|YP_001343812.1| tRNA-dihydrouridine synthase A [Actinobacillus succinogenes 130Z]
 gi|150839906|gb|ABR73877.1| TIM-barrel protein, yjbN family [Actinobacillus succinogenes 130Z]
          Length = 326

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 133/318 (41%), Positives = 189/318 (59%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+     + L F T E P+ALQ+GG+D  
Sbjct: 17  MLDWTTRHCRYFHRQFSRHALLYTEMVTTQAIVHAGY-DHLAFDTAENPVALQLGGSDPV 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY EINLNVGCPS RV  G FGACLM   D+V +C+  M  A+SIPVT
Sbjct: 76  QLAHCAKLAEERGYREINLNVGCPSDRVQNGMFGACLMAKADLVAECVTKMQAAVSIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + V  I  +G   + +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 136 VKTRIGIDELDSYEFLYDFVHKITNAGCQELIVHARKAWLSGLSPKENREIPPLDYERVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P + I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D+   +P    
Sbjct: 196 QLKRDFPHILISINGGIKTIEEMTAHLQQVDGVMVGREAYQNPSLLGYIDQALFDPTAR- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R+   +M  Y  + L+ G  L  I RH++G F G   +R+ R  L+  
Sbjct: 255 --------IVTAREAVENMFPYIEQQLNRGVYLNHIVRHILGAFQGCKGARQWRRYLSEN 306

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ TA + +
Sbjct: 307 AYKPGADAEVVRTALSFV 324


>gi|145629754|ref|ZP_01785549.1| hypothetical protein CGSHi22121_00292 [Haemophilus influenzae
           22.1-21]
 gi|145632012|ref|ZP_01787761.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
 gi|144977993|gb|EDJ87777.1| hypothetical protein CGSHi22121_00292 [Haemophilus influenzae
           22.1-21]
 gi|144982331|gb|EDJ89920.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
          Length = 327

 Score =  362 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSKHALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+EINLNVGCPS RV  G FGACLM   D+V DC+  M   + IPVT
Sbjct: 77  QLKYCARLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVADCVEQMQGVVKIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ ++  G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDELDSYEFLCDFIEKVQGKGCQEFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P   +
Sbjct: 197 QLKRDFPHLTIAINGGIKTIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T        +   SM  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 254 APIVTA------HEAVQSMLPYIEQQLSQGIHLNHIVRHILGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|206576636|ref|YP_002241010.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae 342]
 gi|206565694|gb|ACI07470.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae 342]
          Length = 332

 Score =  362 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D  
Sbjct: 20  MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPQ 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 79  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L   ++++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYEFLCEFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 199 WQLKRDFPHLTMAINGGIKSLDEARLQLEHMDGVMVGREAYQNPGILASVDREIFGIAGA 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L +G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 259 DADPV----------AVVRAMYPYIERELSNGTYLGHITRHMLGLFQGIPGARQWRRYLS 308

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 309 ENAHKAGADIAVLEHALKLVADK 331


>gi|310818800|ref|YP_003951158.1| tRNA-dihydrouridine synthase a [Stigmatella aurantiaca DW4/3-1]
 gi|309391872|gb|ADO69331.1| tRNA-dihydrouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 344

 Score =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 142/319 (44%), Positives = 186/319 (58%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD+  +LGF   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDRHCRFFHRQLSRHTLLYTEMLTTGAVLHGDRDRLLGFEPAEHPVALQLGGSEPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E +GY+EINLNVGCPS RV  G FGACLM  P++V   +AAM +A+ IPVT
Sbjct: 74  ALAEAARIGEAWGYDEINLNVGCPSDRVQSGRFGACLMAEPELVARLVAAMREAVRIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +DD      L   V+ I   G +   +HARKA L+GLSPK+NR IP L Y++VY
Sbjct: 134 VKSRIAIDDMEEWPTLERFVRLISAEGCSRFIVHARKAWLQGLSPKENRDIPPLRYELVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG++ +  A + L  VDGVMIGRAAY+N  +L   D          
Sbjct: 194 RLKAEFPSLDISINGGIKTLEAAAEHLRHVDGVMIGRAAYENPYLLAEADSRLFGASEAP 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  +M  Y       G  L  ITRHM+GLF G P +R  R  L+  
Sbjct: 254 RD---------RHDVVEAMLPYMEARRSQGAPLNAITRHMLGLFQGLPGARAWRRHLSEN 304

Query: 301 AGASTATHHIIETAFNLMI 319
                A   ++  A  L+ 
Sbjct: 305 IHKPGAGPEVVTAALALVP 323


>gi|166365548|ref|YP_001657821.1| tRNA-dihydrouridine synthase A [Microcystis aeruginosa NIES-843]
 gi|166087921|dbj|BAG02629.1| dihydrouridine synthase TIM-barrel protein [Microcystis aeruginosa
           NIES-843]
          Length = 342

 Score =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 145/318 (45%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R ++   LLYTEMI   AI  GD+  +LGFS  EKPLALQ+GG +  
Sbjct: 21  MMDYTDRHFRYFWRQISLRPLLYTEMITTMAIKHGDRYKLLGFSLAEKPLALQLGGDNPY 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AKI ED GY+E+NLNVGCPS+RV EG+FGACLM NP++V   I+AM +A+SIPVT
Sbjct: 81  LLAECAKIAEDMGYDEVNLNVGCPSSRVKEGNFGACLMANPELVARGISAMNQAVSIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D Q     + N V+ +  +G     IHARKA L+GLSPK+NR +P L YD VY
Sbjct: 141 VKQRIGIDHQDSYENMANFVRIVADAGCQRFTIHARKAWLQGLSPKENRTVPPLRYDDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P LFI +NGG+ ++ QA + L  VD VMIGRAAY N  +  TVD  F      +
Sbjct: 201 RLKNQFPHLFIEINGGIINLEQARQHLQLVDAVMIGRAAYDNPYLFATVDRDFYGESV-T 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +         ++   M  Y    +  G KL QI++H++ LF G P ++  +  ++  
Sbjct: 260 PPTR--------EEVIKKMLPYIDEWVSKGYKLHQISKHLLQLFAGQPGTKAWKRYISEN 311

Query: 301 AGASTATHHIIETAFNLM 318
           +    A   +I  A   +
Sbjct: 312 SHFPGADSGVIWQALQQV 329


>gi|320539402|ref|ZP_08039071.1| putative tRNA-dihydrouridine synthase A [Serratia symbiotica str.
           Tucson]
 gi|320030527|gb|EFW12537.1| putative tRNA-dihydrouridine synthase A [Serratia symbiotica str.
           Tucson]
          Length = 342

 Score =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 138/319 (43%), Positives = 187/319 (58%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLYTEM+   AI+ G   + L  + +E P+ALQ+G +D +
Sbjct: 33  MLDWTDRHCRYFHRLLTKETLLYTEMVTTGAIIHGKG-DYLAHNKEEHPVALQLGASDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+EINLNVGCPS RV  G FGACLM    +V D I AM   +SIPVT
Sbjct: 92  ALAHCAKLAEQRGYDEINLNVGCPSGRVQNGMFGACLMAQAALVADGIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      +HARKA L GLSPK+NR++P LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFISTVAGRGECAMFTLHARKAWLSGLSPKENREVPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD         
Sbjct: 212 YQLKRDFPALTIAINGGVKTLEEAQQHLQHLDGVMMGREAYQNPGILARVDNELFGVQGA 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          I  S+  Y  R L +G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 272 VKDSV---------AIIESLYPYIERELSNGTYLGHITRHILGLFQGVPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A + +
Sbjct: 323 NAHKPGADVQVVEQALDWV 341


>gi|152972912|ref|YP_001338058.1| tRNA-dihydrouridine synthase A [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|150957761|gb|ABR79791.1| conserved protein, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 313

 Score =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DCI AM   +SIPVT
Sbjct: 60  ALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNALLVADCIKAMRDVVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 120 VKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           +++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L +VD E F     
Sbjct: 180 WQLKRDFPHLTMAINGGIKSLDEARVQLEHMDGVMVGREAYQNPGILASVDREIFGVAGA 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+
Sbjct: 240 DADPV----------AVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLS 289

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A  + A   ++E A  L+ + 
Sbjct: 290 ENAHKAGADIAVLEHALKLVADK 312


>gi|307244957|ref|ZP_07527054.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307253910|ref|ZP_07535762.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307258364|ref|ZP_07540105.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306854122|gb|EFM86330.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306863114|gb|EFM95056.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306867548|gb|EFM99395.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 325

 Score =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYECVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 QPLVTA------REAVEKMLPYIAAQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 304 ATKQGAGVEVVEQALSFVQES 324


>gi|190149417|ref|YP_001967942.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|307262734|ref|ZP_07544361.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|189914548|gb|ACE60800.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|306871879|gb|EFN03596.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 329

 Score =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYECVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 197 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 QPLVTA------REAVEKMLPYIAAQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|307256171|ref|ZP_07537958.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865352|gb|EFM97248.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 334

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 24  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 83  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 143 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 202 QLKRDFPHLNISINGGIKTIEEIKQHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 259 QPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 312

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 313 ATKQGAGVEVVEQALSFVQES 333


>gi|315633448|ref|ZP_07888738.1| tRNA-dihydrouridine synthase A [Aggregatibacter segnis ATCC 33393]
 gi|315477490|gb|EFU68232.1| tRNA-dihydrouridine synthase A [Aggregatibacter segnis ATCC 33393]
          Length = 327

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 135/320 (42%), Positives = 191/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+     + L F T E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSRHALLYTEMVTTQAIIHAKY-DHLDFDTAENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ +  GY EINLNVGCPS RV  G FGACLM N ++V +C+  M  A+ IPVT
Sbjct: 77  QLQHCAQLAQQRGYQEINLNVGCPSDRVQNGMFGACLMANAELVAECVQQMQSAVHIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V+ + ++G     +HARKA L GLSPK NR+IP L+Y+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLCDFVQKVHQAGCQEFIVHARKAWLSGLSPKQNREIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++   +  + L  VDGVM+GR AY+N A+L  +D    +    +
Sbjct: 197 QLKQDFPHLLISINGGIKTTEEMQQHLKYVDGVMVGREAYQNPALLGHIDHTLFD---AN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+   +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 APIITP------RQAVENMFPYIEQQLSQGVYLNHIVRHMLGAFQHCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
           A  + A   ++ETA   + E
Sbjct: 308 AYKAGAGIDVVETALGFVEE 327


>gi|307249353|ref|ZP_07531347.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306858647|gb|EFM90709.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 329

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 190/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NNFIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 197 QLKRDFPHLNISINGGIKTVEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y       G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 RPLVTA------REAVEKMLPYIETQTKKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|307822581|ref|ZP_07652812.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
 gi|307826605|ref|ZP_07656722.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
 gi|307732393|gb|EFO03309.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
 gi|307736185|gb|EFO07031.1| TIM-barrel protein, yjbN family [Methylobacter tundripaludum SV96]
          Length = 312

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 141/317 (44%), Positives = 194/317 (61%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +A LYTEM+   A++ GD    L FS  E+P+A Q+GG++  
Sbjct: 1   MLDWTDRHCRYFHRLISQHAFLYTEMVTTGALIHGDHHRFLQFSAAERPVAFQLGGSNPR 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK++ED+GY+E+NLNVGCPS RV  G FGACLM  P++V +C+AAM +A+SIPVT
Sbjct: 61  ELAICAKMIEDYGYDEVNLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMAQAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     L + V ++  +G     IHARKA L GLSPK NR +P L YD+ Y
Sbjct: 121 VKSRIGIDERDSYEELVHFVSTVADAGCETFIIHARKAWLSGLSPKQNRDVPPLRYDVAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P L I LNGG+  + QA  +L  VDGVM+GR AY N  +L  VD  F       
Sbjct: 181 QIKQDFPQLEIILNGGITTLDQAEAVLAHVDGVMVGREAYHNPYLLAEVDRRFYGESKEP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLH--SGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              +  +D          +  Y  + L    G +L  I+RH++GLFHG P +R  R  L+
Sbjct: 241 RSREMIMDL---------LIPYIQQQLELNDGVRLNNISRHILGLFHGEPGARGWRRHLS 291

Query: 299 VEAGASTATHHIIETAF 315
             A    A   +I  A 
Sbjct: 292 ENACKPGADIKVILEAL 308


>gi|304415193|ref|ZP_07395906.1| tRNA-dihydrouridine synthase A [Candidatus Regiella insecticola
           LSR1]
 gi|304282951|gb|EFL91401.1| tRNA-dihydrouridine synthase A [Candidatus Regiella insecticola
           LSR1]
          Length = 344

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 191/319 (59%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT   LLY+EM+   AI+ G   + L +S Q+ P+ LQ+GG+D  
Sbjct: 34  MLDWTDRHCRYFHRLLTKQTLLYSEMVTTGAIIHGKA-DYLAYSEQDHPVVLQLGGSDPK 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ +  GYNEINLN+GCPS RV  G FGACLM   D+V DCI AM   +SIPVT
Sbjct: 93  ILADCAKLGQQRGYNEINLNIGCPSDRVQNGRFGACLMGEADLVADCIKAMNDGVSIPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L + V +I  K G +   IHARKA L GLSPK+NR++P L+Y  V
Sbjct: 153 VKTRIGIDSHDSYEFLCDFVDTIANKGGCHIFIIHARKAWLSGLSPKENREVPPLNYPRV 212

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG+  +  A   L  VDGVMIGR AY+N A+L  VD    +P   
Sbjct: 213 YQLKRDFPQLTIVINGGITTLEDAADHLKYVDGVMIGREAYQNPAILAEVDRKLFDPQAA 272

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +             +  ++  Y  + L  G +L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 273 ITDKV---------AVIKALYPYIEQELSRGARLGHITRHILGLFQGTPGARQWRRYLSE 323

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A + +
Sbjct: 324 HAHQPRADAAVVERALSFV 342


>gi|238760286|ref|ZP_04621429.1| tRNA-dihydrouridine synthase A [Yersinia aldovae ATCC 35236]
 gi|238701488|gb|EEP94062.1| tRNA-dihydrouridine synthase A [Yersinia aldovae ATCC 35236]
          Length = 349

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 198/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT  ALLYTEM+   AI+ G   + L +S Q+ P+ALQ+GG+D  
Sbjct: 33  MLDWTDRHCRYFHRLLTKQALLYTEMVTTGAIIHGKG-DYLAYSEQDHPVALQLGGSDPL 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  E  GYNEINLNVGCPS RV  G FGACLM   ++V DCI AM   +SIPVT
Sbjct: 92  ALAHCAKSAELRGYNEINLNVGCPSDRVQNGRFGACLMGEAELVADCIKAMRDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D       L   V+++ + G  N   IHARKA L GLSPK+NR++P L+Y+ V
Sbjct: 152 VKTRIGIDQLDSYEFLCEFVQTVAERGECNIFTIHARKAWLSGLSPKENREVPPLNYERV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L I +NGG++ +++A + L  +DGVM+GR AY+N  +L  VD    +P   
Sbjct: 212 YQLKRDFPALTIAINGGVKTLAEAKEHLKHLDGVMMGREAYQNPCILAQVDRELFDP--- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P+   V      K   ++  Y  + L  G  L  ITRH++G+F G P +R+ R  L+ 
Sbjct: 269 NAPVMDSV------KAIEALYPYIEQELSRGAYLGHITRHILGIFQGVPGARQWRRHLSE 322

Query: 300 EAGASTATHHIIETAFNLMI 319
            A    A   ++E A  ++ 
Sbjct: 323 NAHKPGADVSVVEQALAMVT 342


>gi|269137592|ref|YP_003294292.1| tRNA-dihydrouridine synthase [Edwardsiella tarda EIB202]
 gi|267983252|gb|ACY83081.1| tRNA-dihydrouridine synthase [Edwardsiella tarda EIB202]
 gi|304557663|gb|ADM40327.1| tRNA dihydrouridine synthase A [Edwardsiella tarda FL6-60]
          Length = 352

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 137/319 (42%), Positives = 185/319 (57%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E PLALQ+GG++ +
Sbjct: 39  MLDWTDRHCRYFHRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPLALQLGGSNPA 97

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+ AM   +SIPVT
Sbjct: 98  DLARCAHLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAQLVADCVKAMRDVVSIPVT 157

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D Q     L + + ++   G  +   +HARKA L GLSPK+NR++P LDY  V
Sbjct: 158 VKTRIGIDAQDSYPFLCDFIGTVAGQGECDTFIVHARKAWLSGLSPKENREVPPLDYPRV 217

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P   I LNGG++ + +AL  L  VDGVM+GR AY N  +L  VD    +    
Sbjct: 218 YRLKQDFPQFTIALNGGVKRLDEALTHLQHVDGVMMGREAYHNPGILAQVDRQLFDADAA 277

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y  R L  G  L  ITRH++GLF G P +R+ R  L+ 
Sbjct: 278 VPDSV---------AVVRALYPYIERELAQGTYLGHITRHILGLFQGIPGARQWRRHLSE 328

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++E A   +
Sbjct: 329 NAHRPGAGIDVVEQALRFV 347


>gi|163759729|ref|ZP_02166814.1| tRNA-dihydrouridine synthase A [Hoeflea phototrophica DFL-43]
 gi|162283326|gb|EDQ33612.1| tRNA-dihydrouridine synthase A [Hoeflea phototrophica DFL-43]
          Length = 336

 Score =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 171/319 (53%), Positives = 220/319 (68%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RF  R LT +ALLYTEM+VADA + GD++ +LGF   E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRFLHRQLTRHALLYTEMVVADAAIHGDRERLLGFDAVEHPVALQLGGSDPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
           KL EA +I   FGY+EINLNVGCPS RV  G+FGACLM  PD+V  CIAAM  A   +PV
Sbjct: 78  KLAEAVRIAGGFGYDEINLNVGCPSDRVQSGTFGACLMREPDLVARCIAAMKAASGDVPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIGVD+Q P +AL  L +++ + G + IW+HARKA L+GLSPK+NR +P LDYD V
Sbjct: 138 TVKCRIGVDEQDPEIALSALTEAVIQVGADAIWVHARKAWLEGLSPKENRDVPPLDYDRV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P++FIGLNGG+ED++QAL+ L  VDGVMIGRAAY N+ MLT VD         
Sbjct: 198 YRLKQDYPNVFIGLNGGVEDLNQALEHLNHVDGVMIGRAAYHNAQMLTGVDRLIYGDD-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                  V    WR +  +M  +A  H+ SGG+L  +TRHM+GLF G   +RR R IL+ 
Sbjct: 256 -------VAAVDWRAVCEAMMAHADAHVASGGRLNHVTRHMVGLFQGVRGARRFRQILST 308

Query: 300 EAGASTATHHIIETAFNLM 318
           E+    A   +I  AF+ +
Sbjct: 309 ESTKPGAGPDVIARAFDEI 327


>gi|303249850|ref|ZP_07336054.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|303251970|ref|ZP_07338141.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302649400|gb|EFL79585.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302651417|gb|EFL81569.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 325

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLANCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 304 ATKQGAGVEVVEQALSFVQES 324


>gi|254473354|ref|ZP_05086751.1| tRNA-dihydrouridine synthase A [Pseudovibrio sp. JE062]
 gi|211957470|gb|EEA92673.1| tRNA-dihydrouridine synthase A [Pseudovibrio sp. JE062]
          Length = 348

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 155/318 (48%), Positives = 205/318 (64%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+ N+LLYTEM+   A++ GD+   L FS QE+P+A Q+GG+D  
Sbjct: 21  MLDWTDRHCRAFHRVLSKNSLLYTEMVTTGALIHGDRDRHLNFSRQEQPVACQLGGSDPK 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AK+VED+GY+E+NLNVGCPS RV  G FGACLML PD+V +CIAAM   +SIPVT
Sbjct: 81  ALAECAKMVEDWGYDEVNLNVGCPSDRVQSGKFGACLMLEPDLVAECIAAMKDVVSIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            KCRIGVDDQ P  AL  L   +  +G + +W+HARKA LKGLSPK+NR +P LDYD+VY
Sbjct: 141 TKCRIGVDDQEPEEALNALADKVIAAGTDALWVHARKAWLKGLSPKENRDVPPLDYDLVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +    L  +DGVM+GRAAY+N  +L  VD         +
Sbjct: 201 RLKQRLPDVFIGINGGVATLEETSAHLEKLDGVMMGRAAYQNPMLLAEVDRVVYGEDGTA 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D             Y    L +G KL  ITRH++G + G P +R  R I+TVE
Sbjct: 261 ITPVEAMD---------VYRGYIENELTAGTKLASITRHILGTYQGVPGARHFRRIMTVE 311

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++E A   +
Sbjct: 312 ANKTGAGIEVLEEALAAV 329


>gi|307247131|ref|ZP_07529183.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307251674|ref|ZP_07533579.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306856380|gb|EFM88531.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306860871|gb|EFM92879.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 329

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLANCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    N   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYS-NDFIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 197 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|307945371|ref|ZP_07660707.1| tRNA-dihydrouridine synthase A [Roseibium sp. TrichSKD4]
 gi|307771244|gb|EFO30469.1| tRNA-dihydrouridine synthase A [Roseibium sp. TrichSKD4]
          Length = 353

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 153/318 (48%), Positives = 205/318 (64%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R L++ ALLYTEM+   A++ GD++ +LGFS  E P+A Q+GG+D +
Sbjct: 20  MMEWTDRNCRAFHRQLSSRALLYTEMVTTGAVIHGDREKLLGFSDLEHPIACQLGGSDPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +  +AKIVED+GY+E+N+NVGCPS RV  GSFGACLM  PD+V +C+AAM  A+SIPVT
Sbjct: 80  DMATSAKIVEDWGYDEVNINVGCPSDRVQSGSFGACLMREPDLVAECVAAMKAAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  +   +  +G + +W+HARKA L+GLSPK NR +P LDYD V 
Sbjct: 140 VKCRIGVDDQDPEEALDAVADKVFAAGSDALWVHARKAWLQGLSPKQNRDVPPLDYDRVL 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+ FIGLNGGL D+ QA   L ++DGVM+GRAAY N  ++  VD          
Sbjct: 200 RLKARFPEKFIGLNGGLADLDQAEPFLDTLDGVMLGRAAYHNPGLMGEVDRRLYGED--- 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 V+     +       Y    L  G +L  +TRHM+GLFHG P ++  R ILTVE
Sbjct: 257 ------VEDVSPWQAVGKYIPYIEDGLARGVRLPHMTRHMLGLFHGRPGAKAWRRILTVE 310

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +++ A   +
Sbjct: 311 AIKPEAGIEVVQKALEAV 328


>gi|126207634|ref|YP_001052859.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           L20]
 gi|165975602|ref|YP_001651195.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|307260603|ref|ZP_07542295.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|126096426|gb|ABN73254.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
 gi|165875703|gb|ABY68751.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|306869680|gb|EFN01465.1| tRNA-dihydrouridine synthase A [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 325

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    +   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYSND-FIVHARKAWLSGLSPKQNREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 304 ATKQGAGVEVVEQALSFVQES 324


>gi|32034537|ref|ZP_00134701.1| COG0042: tRNA-dihydrouridine synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
          Length = 329

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 19  MLDWTTRHCRYFHRQFSRHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 78  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVQIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    +   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 138 VKHRIGIDDLDSYEFLCDFIEKVQPYSND-FIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 197 QLKRDFPHLNISINGGIKTIEEIKRHLAFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y A     G  L  I RHM+G F     +R+ R  L+  
Sbjct: 254 RPLVTA------REAVEKMLPYIAVQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + + ES
Sbjct: 308 ATKQGAGVEVVEQALSFVQES 328


>gi|240950331|ref|ZP_04754601.1| tRNA-dihydrouridine synthase A [Actinobacillus minor NM305]
 gi|240295142|gb|EER45961.1| tRNA-dihydrouridine synthase A [Actinobacillus minor NM305]
          Length = 329

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 194/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQHALLYTEMITAPAIIHAKY-DLLEYDPAENPVALQLGGSDPT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V++ GY E+NLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVQERGYAEVNLNVGCPSDRVQNGMFGACLMGKADLVADCIKAMQDAVEIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDELDSYAFLCDFIEKIQPYS-NDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D    N    +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKHHLQFVDGVMVGREAYQNPSLLGEIDSQIFNE---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 KPLVTA------REAVEKMLPYIEKELAKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   ++E A + + ES
Sbjct: 304 ACKAGAGVEVVEQALSFVQES 324


>gi|325576762|ref|ZP_08147377.1| tRNA-dihydrouridine synthase A [Haemophilus parainfluenzae ATCC
           33392]
 gi|325160968|gb|EGC73086.1| tRNA-dihydrouridine synthase A [Haemophilus parainfluenzae ATCC
           33392]
          Length = 328

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 139/318 (43%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + NALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSKNALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V +CIA M + ++IPVT
Sbjct: 77  QLKHCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVAECIAEMQRVVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + +K +  +G     +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKTRIGIDDLDSYQFLCDFIKKVHHAGCQEFIVHARKAWLSGLSPKENREIPPLDYDRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  VD+   +     
Sbjct: 197 QLKKDFPQLTIAINGGIKTIEEMKHHLQFVDGVMVGREAYQNPSLLGYVDQMLFDA---- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D    ++   +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 253 -----NADIVTPKQAVEAMFPYIEKQLSQGVYLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|120554835|ref|YP_959186.1| tRNA-dihydrouridine synthase A [Marinobacter aquaeolei VT8]
 gi|120324684|gb|ABM18999.1| tRNA-U16,U17-dihydrouridine synthase [Marinobacter aquaeolei VT8]
          Length = 337

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 124/320 (38%), Positives = 183/320 (57%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  H+R+ AR+L+  ALLYTEM+   A++ GD +  L     E PLALQ+GG+D +
Sbjct: 20  MMDWTTPHFRYLARILSKRALLYTEMVTTGALIHGDTERFLRHDVSEYPLALQLGGSDAN 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ + FG++E+NLNVGCPS RV     GACLM +PD V + ++AM +A  +PVT
Sbjct: 80  ELAHCARLAQQFGFSEVNLNVGCPSDRVQNNMIGACLMGHPDKVAEGVSAMIEATDLPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L   ++++  +G     +HAR A+L+GLSPK+NR IP L YD VY
Sbjct: 140 VKHRIGINGRESWEELCEFIETVAAAGCKTFIVHARIAVLEGLSPKENRDIPPLKYDWVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P L I +NGG++   +  + L   DGVM+GR AY N  +L  VD          
Sbjct: 200 RLKQAYPHLEIIINGGIKTFGECHEHLTHTDGVMLGREAYHNPWLLAEVDAALFGEPPAV 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            +   +M  +  + L  G  L  ITRH++GLF G P  R+ R  L+  
Sbjct: 260 T---------SRHEALRAMFPFIQQELDRGVYLTHITRHIMGLFLGQPGGRQFRRHLSEN 310

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    +   ++E A   + E
Sbjct: 311 ANKPGSGLEVVEQALAKVRE 330


>gi|254490145|ref|ZP_05103336.1| TIM-barrel protein, yjbN family [Methylophaga thiooxidans DMS010]
 gi|224464631|gb|EEF80889.1| TIM-barrel protein, yjbN family [Methylophaga thiooxydans DMS010]
          Length = 327

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R+  RL++ ++LLYTEM+   A++ GD+   L     E PLALQ+GG++ +
Sbjct: 18  MLDWTDRDCRYMLRLISRHSLLYTEMVTTGALIYGDRDRFLAHEALEYPLALQLGGSEPN 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+ ED GY+EINLNVGCPS RV  G FGACL+  PD+V + +AAM   +SIPVT
Sbjct: 78  DLAQCAKMGEDAGYDEINLNVGCPSDRVQSGRFGACLLAEPDVVAEGVAAMQNQVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L + +K +  +G +   +HARKA LKGLSPK+NR +P L+YD VY
Sbjct: 138 VKTRLGIDEHDSYEFLTDFIKKVSAAGCDTFILHARKAWLKGLSPKENRDVPPLNYDRVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + +A   L  VDGVM+GRA Y N  +L   DE         
Sbjct: 198 QVKQDFPHLHIDINGGINTLEEAQLHLQHVDGVMMGRAIYHNPFLLAQADEAIFG---HD 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + TR       ++  +M  Y  + +  G  L+ ITRHM+G+F G   +RR R  ++  
Sbjct: 255 ASVLTR------HQVVEAMLPYIEKRMAQGRPLKSITRHMLGVFQGQAGARRWRRHISEN 308

Query: 301 AGASTATHHIIETAFNLM 318
           A    A  HI++ A +L+
Sbjct: 309 AHLPGAGIHILQQALDLV 326


>gi|86358178|ref|YP_470070.1| tRNA-dihydrouridine synthase A [Rhizobium etli CFN 42]
 gi|86282280|gb|ABC91343.1| putative tRNA-dihydrouridine synthase (nifR3-like) protein
           [Rhizobium etli CFN 42]
          Length = 321

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 164/318 (51%), Positives = 214/318 (67%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 1   MIDWTDRHCRYFHRQISREALLYTEMVVADAIIHGPRERLLGHDATEHPLALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E + Y+EINLNVGCPS RV  G+FGACLML P+ V +C+AAM    + PVT
Sbjct: 61  KLAEAVKIAEPYRYDEINLNVGCPSDRVQSGTFGACLMLTPETVAECVAAMKAVATAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 121 VKCRIGVDEQEPEEALPELITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  F       
Sbjct: 181 RMKQRWPDVFIGINGGIRTLDEAASHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 241 PD---------WEALRDRMMVYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSSD 291

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++  AF  +
Sbjct: 292 AVKNGAGPEVLAAAFAAV 309


>gi|52426107|ref|YP_089244.1| tRNA-dihydrouridine synthase A [Mannheimia succiniciproducens
           MBEL55E]
 gi|52308159|gb|AAU38659.1| unknown [Mannheimia succiniciproducens MBEL55E]
          Length = 327

 Score =  359 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 138/320 (43%), Positives = 190/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+ A AI+     + L F   E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRYFHRQFSRHALLYTEMVTAPAIIHAKY-DHLEFDPAENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY EINLNVGCPS RV  G FGACLM   D+V +C+  M   + IPVT
Sbjct: 77  QLQHCAKLAEQRGYTEINLNVGCPSDRVQNGMFGACLMAKADLVAECVEKMQAEVEIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ +   G N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDNLDSYQFLCDFIQKVHSKGCNEFIVHARKAWLSGLSPKENREIPPLDYNRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY+N A+L  +D    +    +
Sbjct: 197 QLKRDFPQLSISINGGIKTIEEMTAHLQYVDGVMVGREAYQNPALLGQIDRALFD---LN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+    M  Y  R L  G  L  I RHM+G F     +R+ R +L+  
Sbjct: 254 APIVTP------REAVEKMFPYIERQLSRGVHLNHIVRHMLGAFQNCKGARQWRRLLSEN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
           A  + A   I+ETA + + E
Sbjct: 308 AHKTGAGIEILETALHFVEE 327


>gi|89093370|ref|ZP_01166319.1| NIFR3-like protein [Oceanospirillum sp. MED92]
 gi|89082349|gb|EAR61572.1| NIFR3-like protein [Oceanospirillum sp. MED92]
          Length = 328

 Score =  359 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 129/321 (40%), Positives = 192/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+L+ NA+LYTEM+   A++  +    L ++ +E+P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRYFHRILSQNAVLYTEMVTTGALIHAEADRFLRYNREEQPVALQLGGSNPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +  K+ ED+GYNE+NLNVGCPS RV     GACLM +P +V +C+  M  A+ IPVT
Sbjct: 77  DLAQCTKMAEDYGYNEVNLNVGCPSDRVQNNMIGACLMAHPQLVSECLEKMQAAVDIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G+DD      L   V ++++SG     IHARKAIL+GLSPK+NR IP L Y+ VY
Sbjct: 137 VKHRQGIDDMDSYEELVQFVDTVRQSGCKVFIIHARKAILQGLSPKENRDIPPLKYEWVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK+E P+L + +NGG++ + +    L  VDGVM+GR AY+N  +L  VD  F    +  
Sbjct: 197 QIKQEFPELEVHINGGIKTIDECHTHLQHVDGVMLGREAYQNPYLLADVDREFYGADS-- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  +K   +  + +M  Y  + +  G  L  + RHM+GLFH     ++ R  ++  
Sbjct: 255 -------EKISRKAAALAMVPYIEQQMEQGVPLNHVVRHMLGLFHAQRGGKQFRRFISEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++  A   + + 
Sbjct: 308 AHKPGAGIEVLLNALERVADE 328


>gi|251788352|ref|YP_003003073.1| TIM-barrel protein, yjbN family [Dickeya zeae Ech1591]
 gi|247536973|gb|ACT05594.1| TIM-barrel protein, yjbN family [Dickeya zeae Ech1591]
          Length = 344

 Score =  359 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 145/321 (45%), Positives = 199/321 (61%), Gaps = 15/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   AIL G   + L +S +E PLALQ+GG+D +
Sbjct: 33  MLDWTDRHCRYFHRLLSQHALLYTEMVTTGAILHGKG-DYLAYSDEEHPLALQLGGSDPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+EINLNVGCPS RV  G FGACLM    +V DC+AAM + + IPVT
Sbjct: 92  ALAQCALLAEQRGYDEINLNVGCPSDRVQNGRFGACLMAEAQLVADCVAAMRERVGIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + ++++ ++ G +   +HARKA L GLSPK+NR+IP LDY  V
Sbjct: 152 VKTRIGIDDQDSYEFLCDFIRTVSEQGGCDTFIVHARKAWLSGLSPKENREIPPLDYPRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ ++ A + L  VDGVM+GR AY+N  ML  VD         
Sbjct: 212 YQLKRDFPSLTVAINGGIKTLADAQQHLQHVDGVMVGREAYQNPGMLAQVDSELFG---- 267

Query: 240 SSPIKTRVDKDFWRK--ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                  VD+    +  +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L
Sbjct: 268 -------VDRAVPDQVAVVQAMYPYIERELSGGASLGHITRHMLGLFQGIPGARQWRRYL 320

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +  A    A   ++E A   +
Sbjct: 321 SENAHKPGADAAVVERALAQV 341


>gi|332289875|ref|YP_004420727.1| tRNA-dihydrouridine synthase A [Gallibacterium anatis UMN179]
 gi|330432771|gb|AEC17830.1| tRNA-dihydrouridine synthase A [Gallibacterium anatis UMN179]
          Length = 326

 Score =  359 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 188/318 (59%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH RFF R  + + LLYTEM+ A AI+     ++L +  QE PLALQ+GG+D  
Sbjct: 18  MLDWTTRHCRFFHRQFSRHTLLYTEMVTAPAIIYAKYDHLL-YHPQELPLALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A + E  GY+E+NLNVGCPS RV  G FGACLM   D+V  CI AM + ++IPVT
Sbjct: 77  QLADCAALAEQRGYSEVNLNVGCPSDRVQNGFFGACLMAKADLVAQCIDAMQQRINIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V+ +   G     IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 137 VKTRIGIDDLDSYEFLCDFVEKVAAVGCQDFIIHARKAWLSGLSPKENREIPPLDYARVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N  +L  +D+   +P    
Sbjct: 197 QLKRDFPQLKIAINGGIKTIEEIQQHLQYVDGVMVGREAYQNPQLLGYIDQALFDPNAAI 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 V+K         M  Y  R L  G  L  ITRHM+G F     +R+ R  L+  
Sbjct: 257 VTPLEAVEK---------MFPYIERELQQGVPLGAITRHMLGAFQNQRGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++E A + +
Sbjct: 308 AHKTGAGIEVVEKALSFV 325


>gi|257464833|ref|ZP_05629204.1| tRNA-dihydrouridine synthase A [Actinobacillus minor 202]
 gi|257450493|gb|EEV24536.1| tRNA-dihydrouridine synthase A [Actinobacillus minor 202]
          Length = 324

 Score =  359 bits (923), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 137/321 (42%), Positives = 194/321 (60%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQHALLYTEMITAPAIIHAKY-DLLEYDPAENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V++ GY E+NLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 74  QLAHCAKLVQERGYAEVNLNVGCPSDRVQNGMFGACLMGKADLVADCIKAMQDAVEIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + ++ I+    +   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDELDSYAFLCDFIEKIQPYSND-FIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVMIGR AY+N ++L  +D    N    +
Sbjct: 193 QLKRDFPHLNISINGGIKTIEEIKHHLQFVDGVMIGREAYQNPSLLGEIDSQIFNE---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 KPLVTA------REAVEKMLPYIEKELAKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   ++E A + + E+
Sbjct: 304 ACKAGAGVEVVEQALSFVQEN 324


>gi|260459398|ref|ZP_05807653.1| TIM-barrel protein, yjbN family [Mesorhizobium opportunistum
           WSM2075]
 gi|259034952|gb|EEW36208.1| TIM-barrel protein, yjbN family [Mesorhizobium opportunistum
           WSM2075]
          Length = 332

 Score =  359 bits (923), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 164/313 (52%), Positives = 213/313 (68%), Gaps = 9/313 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT  ALLYTEM+VADA+++G +  +LGF   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRFFHRQLTTCALLYTEMVVADAVIQGARDRLLGFDQAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E FGY+EINLNVGCPS RV  G+FGACLM  PD+V DC+AAM   + IPVT
Sbjct: 74  KLAEAARIGEAFGYDEINLNVGCPSDRVQSGTFGACLMKVPDLVADCVAAMKATVKIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L   + ++G + +W+HARKA L+GLSPK+NR IP LDY+ VY
Sbjct: 134 VKCRIGVDEQDPEPALDALANGVFEAGTDALWVHARKAWLEGLSPKENRDIPPLDYNRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+ FIG+NGG++ + +A   L  VDG M+GRAAY    +L  VD  F       
Sbjct: 194 RLKAGKPNKFIGINGGIQSLDEARGHLDHVDGAMLGRAAYHTPGILAGVDAAFYG----- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               T      +  +  +M DYAARH+  GG+L  +TRHM+GLFHG P +RR R IL+ +
Sbjct: 249 ----TEPAAFDFAALIDAMADYAARHIEQGGRLGHVTRHMVGLFHGLPGARRYRQILSTD 304

Query: 301 AGASTATHHIIET 313
           A    A   +++T
Sbjct: 305 ATRPGAGPDVLKT 317


>gi|317046530|ref|YP_004114178.1| TIM-barrel protein, yjbN family [Pantoea sp. At-9b]
 gi|316948147|gb|ADU67622.1| TIM-barrel protein, yjbN family [Pantoea sp. At-9b]
          Length = 331

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 142/323 (43%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ + LLYTEM+   AI+ G   + L FS  E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLSGDTLLYTEMVTTGAIIHGKG-DYLAFSEDEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A++ E  GY+EINLNVGCPS RV  G FGACLM    +V DCI AM   +SIPVT
Sbjct: 74  ALAQCAQLAEARGYDEINLNVGCPSDRVQNGRFGACLMGEAALVADCIKAMRDVVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLCDFVGTVAQQGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + +NGG++ +++A   L  +DGVM+GR AY+N  +L  VD       T 
Sbjct: 194 YQLKRDFPQLTMAINGGIKSLAEAKVHLQHMDGVMMGREAYQNPGILAQVDRELFGRDTP 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +              +  SM  Y    L  G  L  +TRHM+GLF G P +R+ R  L+ 
Sbjct: 254 AVDPV---------AVVRSMYPYIEAELAKGTYLGHVTRHMLGLFQGIPGARQWRRYLSE 304

Query: 300 EAGASTATHHIIETAFNLMIESL 322
            A    A   ++E A  L+ + +
Sbjct: 305 NAHKPGADVRVLEAALALVADKI 327


>gi|209527420|ref|ZP_03275926.1| TIM-barrel protein, yjbN family [Arthrospira maxima CS-328]
 gi|209492155|gb|EDZ92504.1| TIM-barrel protein, yjbN family [Arthrospira maxima CS-328]
          Length = 338

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 139/319 (43%), Positives = 187/319 (58%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +L FS +EKPLALQ+GG D +
Sbjct: 29  MMDRTDRHFRYFMRQITRRPLLYTEMVTSAAIINGDRHKLLDFSPEEKPLALQVGGDDPN 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+EINLNVGCPSARV  G+FGACLM  P+ V   I+AM KA++IPVT
Sbjct: 89  ELATCAKIAEDWGYDEINLNVGCPSARVQNGNFGACLMAEPERVAQAISAMKKAVNIPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     +   V+ +  SG     +HARKA L+GLSPKDNR IP L Y  V+
Sbjct: 149 VKHRIGIDNRDRYEDMAAFVRVVAASGCQRFTVHARKAWLQGLSPKDNRNIPPLRYGDVH 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E PDL I +NGG   + Q  + L  VD VMIGRAAY N  +    D          
Sbjct: 209 RLKAEFPDLTIEINGGFTTLEQVKQQLTKVDAVMIGRAAYDNPYLFAIADREIYGENINP 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++   M  Y    L  GG+L  + RH++ LF G P ++  +  L+  
Sbjct: 269 P---------TRHQVVEQMLPYIENWLSQGGRLNSVVRHILQLFAGQPGTKAWKRYLSEN 319

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +++ A   + 
Sbjct: 320 AHLPGAGVEVVKAALAEVP 338


>gi|315497697|ref|YP_004086501.1| tim-barrel protein, yjbn family [Asticcacaulis excentricus CB 48]
 gi|315415709|gb|ADU12350.1| TIM-barrel protein, yjbN family [Asticcacaulis excentricus CB 48]
          Length = 343

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 153/322 (47%), Positives = 206/322 (63%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+ + AI+ GD++ +LGFS  E P+ALQ+GG++  
Sbjct: 14  MMDWTDRHCRAFHRTLTKGALLYTEMVTSRAIINGDRQKLLGFSEVEHPVALQLGGSEPD 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+E+NLN GCPS RV  GSFGACLM  P +V DC+ AM +A  +PVT
Sbjct: 74  ELAACAKIAEDWGYDEVNLNCGCPSDRVQSGSFGACLMREPQLVADCMQAMGEATRLPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  LV++ +++GV    +HARKA LKGLSPK+NR IP L+Y++VY
Sbjct: 134 VKCRIGVDDQDEETALFALVEACRQAGVRTFIVHARKAWLKGLSPKENRDIPPLNYELVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ +PDL I +NGG+  + +A   L  VDGVM+GRAAY   A+L  VD    +     
Sbjct: 194 ALKRAHPDLTISINGGIGTLQEAETHLKHVDGVMLGRAAYHEPALLGQVDRRIFSGEADV 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P           +   + + Y    L +G  L  ITRHM+GL HG P +R  R ILTV 
Sbjct: 254 GPF----------EALEAYSPYVQAQLAAGVHLPAITRHMLGLMHGLPGARAFRRILTVG 303

Query: 301 AGASTATHHIIETAFNLMIESL 322
           +    A   +++ A   + +++
Sbjct: 304 SIQPGAGIEVLDQAIEAVRDAM 325


>gi|167855851|ref|ZP_02478602.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis 29755]
 gi|167853001|gb|EDS24264.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis 29755]
          Length = 323

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 136/319 (42%), Positives = 191/319 (59%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  T ++LLY+EMI+A AIL     ++L +   E P+ALQ+GG+D  
Sbjct: 15  MLDWTTRHCRYFHRQFTQHSLLYSEMIIAPAILHAKY-DLLAYDPTENPVALQLGGSDPE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V  C+ AM K +SIPVT
Sbjct: 74  QLAKCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMGKADLVARCVEAMKKEVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKIQPY-CNDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D+   +P    
Sbjct: 193 QLKRDFPHLKISINGGIKTIEEIKHHLQFVDGVMVGREAYQNPSLLGYIDQELFDP---- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D    ++    M  Y  + L  G  L  I RH++G F     +RR R  L+  
Sbjct: 249 -----NADIVTPKQAVEKMLPYIEQQLSQGVYLNHIVRHILGAFQNCKGARRWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   ++E A + + 
Sbjct: 304 ACKQGAGVEVVEQALSFLP 322


>gi|150396830|ref|YP_001327297.1| tRNA-dihydrouridine synthase A [Sinorhizobium medicae WSM419]
 gi|150028345|gb|ABR60462.1| dihydrouridine synthase DuS [Sinorhizobium medicae WSM419]
          Length = 385

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 186/351 (52%), Positives = 241/351 (68%), Gaps = 30/351 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR+L+ +ALLYTEMIVADA+LRGD+  +LG    E P+ALQ+GG D  
Sbjct: 27  MIDWTDRHYRFFARVLSRHALLYTEMIVADAVLRGDRAKLLGHDASEHPVALQLGGNDPV 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E +GY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 87  KMAEAARIGEAYGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVEIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LVK  K +G +G+W+HARKA L+GLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRDLVKCAKDAGTDGVWVHARKAWLQGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--------------------SVDGVMIGRAAY 220
            +K EN  LFIG+NGGL+ + QAL  L                      +DGVM+GRAAY
Sbjct: 207 RLKAENESLFIGINGGLQGLDQALSHLDPRSLPAGEAMKAATEIKSGAPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD----------KDFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG++ + T  D           +FW  +   M DYAA H+ +G
Sbjct: 267 HDSGLLTAADGYFRHPLTGAAAVPTDPDGFSDRDHNLSLEFWSGVRDVMEDYAAAHIENG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           G+L  +TRHM+GLF G+P +RR R IL+  A    A   +I TAF+ + ++
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQILSTRATRKDAGPEVIHTAFDAVFQA 377


>gi|222086273|ref|YP_002544805.1| tRNA-dihydrouridine synthase (nifR3-like) protein [Agrobacterium
           radiobacter K84]
 gi|221723721|gb|ACM26877.1| tRNA-dihydrouridine synthase (nifR3-like) protein [Agrobacterium
           radiobacter K84]
          Length = 337

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 163/318 (51%), Positives = 210/318 (66%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  R ++ +ALLYTEM+VADAI+ G +  +LG    E P+ALQ+GG+D +
Sbjct: 18  MIDWTDRHCRYLHRQISRHALLYTEMVVADAIIHGPRDRLLGHDVSEHPVALQLGGSDPA 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL  A +I E + Y+EINLNVGCPS RV  G+FGACLML P+ V +CIAAM      PVT
Sbjct: 78  KLSNALQIAEAYNYDEINLNVGCPSDRVQSGTFGACLMLTPETVAECIAAMKAVSKAPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDYDIVY
Sbjct: 138 VKCRIGVDEQEPEQALPELIARVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYDIVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG++ + QA   L  VDGVM+GRAAY+N+A+L  VD  F       
Sbjct: 198 RMKQRWPDVFIGINGGIQTLDQAEAHLAHVDGVMLGRAAYQNAAILADVDHRFFGEAAVE 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  Y  RH+ SGG++  + RHM+GLF G P SRR R IL+ +
Sbjct: 258 PD---------WNDLRDRMMAYTERHIASGGRVHHVARHMVGLFTGLPGSRRYRQILSTD 308

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  AF  +
Sbjct: 309 ANKPGAEPEVIAAAFAAV 326


>gi|115372138|ref|ZP_01459449.1| tRNA-dihydrouridine synthase A [Stigmatella aurantiaca DW4/3-1]
 gi|115370840|gb|EAU69764.1| tRNA-dihydrouridine synthase A [Stigmatella aurantiaca DW4/3-1]
          Length = 330

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 185/318 (58%), Gaps = 9/318 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH RFF R L+ + LLYTEM+   A+L GD+  +LGF   E P+ALQ+GG++ + 
Sbjct: 1   MDWTDRHCRFFHRQLSRHTLLYTEMLTTGAVLHGDRDRLLGFEPAEHPVALQLGGSEPAA 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA+I E +GY+EINLNVGCPS RV  G FGACLM  P++V   +AAM +A+ IPVTV
Sbjct: 61  LAEAARIGEAWGYDEINLNVGCPSDRVQSGRFGACLMAEPELVARLVAAMREAVRIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RI +DD      L   V+ I   G +   +HARKA L+GLSPK+NR IP L Y++VY 
Sbjct: 121 KSRIAIDDMEEWPTLERFVRLISAEGCSRFIVHARKAWLQGLSPKENRDIPPLRYELVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K E P L I +NGG++ +  A + L  VDGVMIGRAAY+N  +L   D           
Sbjct: 181 LKAEFPSLDISINGGIKTLEAAAEHLRHVDGVMIGRAAYENPYLLAEADSRLFGASEAPR 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
                        +  +M  Y       G  L  ITRHM+GLF G P +R  R  L+   
Sbjct: 241 D---------RHDVVEAMLPYMEARRSQGAPLNAITRHMLGLFQGLPGARAWRRHLSENI 291

Query: 302 GASTATHHIIETAFNLMI 319
               A   ++  A  L+ 
Sbjct: 292 HKPGAGPEVVTAALALVP 309


>gi|301155106|emb|CBW14569.1| tRNA-dihydrouridine synthase A [Haemophilus parainfluenzae T3T1]
          Length = 328

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 191/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + NALLYTEM+ A AI+     + L F  QE P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSKNALLYTEMVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E+ GY+EINLNVGCPS RV  G FGACLM   D+V +CIA M + ++IPVT
Sbjct: 77  QLKHCAKLAEERGYHEINLNVGCPSDRVQNGMFGACLMAKADLVAECIAEMQRVVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ +   G     +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKTRIGIDDLDSYEFLCDFIEKVHHDGCQEFIVHARKAWLSGLSPKENREIPPLDYDRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  VDGVM+GR AY+N ++L  +D+   +     
Sbjct: 197 QLKKDFPQLTIAINGGIKTIEEMKYHLQFVDGVMVGREAYQNPSLLGYIDQMLFDA---- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D    ++   +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 253 -----NADIVTPKQAVEAMFPYIEKQLSQGVYLNHIVRHMLGAFQNCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA + +
Sbjct: 308 AFKQGAGIEVVETALSFV 325


>gi|118590253|ref|ZP_01547656.1| tRNA-dihydrouridine synthase A [Stappia aggregata IAM 12614]
 gi|118437225|gb|EAV43863.1| tRNA-dihydrouridine synthase A [Stappia aggregata IAM 12614]
          Length = 351

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 156/321 (48%), Positives = 205/321 (63%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R LT +ALLYTEM+   A++ GD++ +LGFS  E P+A Q+GG+D  
Sbjct: 32  MMEWTDRHCRAFHRQLTRHALLYTEMVTTGAVIHGDREYLLGFSDIEHPVACQLGGSDPQ 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+IV +FGY+E+N+NVGCPS RV  G FGACLM  P +V  C+ AM  A+ IPVT
Sbjct: 92  DMAEAARIVAEFGYDEVNINVGCPSDRVQSGRFGACLMEEPALVAACVEAMKAAVDIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P VAL  +  ++  +G + +W+HARKA LKGLSPK+NR IP LDY+ V 
Sbjct: 152 VKCRIGVDEQDPEVALDTMADAVFAAGADALWVHARKAWLKGLSPKENRDIPPLDYERVL 211

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD FIGLNGGL+ + QA   L ++DG+M GRAAY    ++  VD          
Sbjct: 212 RLKQRLPDRFIGLNGGLQTLDQAEPFLETLDGLMFGRAAYHTPQIMGEVDRRLYGASGP- 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D   W  + A M  Y    L +G KL  +TRHM+GLFHG P +R  R ILTVE
Sbjct: 271 -------DITPWDAVKAHM-PYLEAQLTNGVKLAHMTRHMLGLFHGRPGARSWRRILTVE 322

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A   +  +
Sbjct: 323 AIKPGAGLEVVEKALAAVSPA 343


>gi|88706546|ref|ZP_01104250.1| tRNA-dihydrouridine synthase A [Congregibacter litoralis KT71]
 gi|88699258|gb|EAQ96373.1| tRNA-dihydrouridine synthase A [Congregibacter litoralis KT71]
          Length = 359

 Score =  358 bits (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 193/319 (60%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RLL+  A LYTEM+   A++ GD++  L F  +E P+ALQ+GG++  
Sbjct: 46  MMDWSDRHCRYFWRLLSRRARLYTEMVTTGALIHGDRQRFLQFHEEEAPIALQLGGSNPG 105

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  ED+GY+E+NLN GCPS RV  G+FGACLM    +V DCI+AM  A +I VT
Sbjct: 106 DLARCAKWAEDWGYDEVNLNCGCPSDRVQNGAFGACLMGEASLVRDCISAMRSACAIDVT 165

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L + V ++ + G     +HARKA LKGLSPK+NR++P L+Y  VY
Sbjct: 166 VKHRIGIDHMESYEELCDFVGTVAEGGSEVFIVHARKAWLKGLSPKENREVPPLNYPWVY 225

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I +NGG+E +  +   L  VDGVM+GR+AY N  +L  VD      +   
Sbjct: 226 QLKEDFPELTIVMNGGIESLEDSQTHLGHVDGVMLGRSAYHNPWVLAEVDHRLFGDVKQP 285

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                     +   I  +M  Y  + L  G +L QITRH++GL+   P +RR R +L+ +
Sbjct: 286 R---------YREDIIEAMLPYVEKELAHGARLNQITRHLLGLYQEVPGARRYRRLLSEQ 336

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   ++  A N + 
Sbjct: 337 AHRPGAGADVLRAAVNEVT 355


>gi|218463688|ref|ZP_03503779.1| tRNA-dihydrouridine synthase A [Rhizobium etli Kim 5]
          Length = 333

 Score =  358 bits (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 164/318 (51%), Positives = 213/318 (66%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D  
Sbjct: 13  MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDVAEHPLALQLGGSDPG 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA KI E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 73  KLAEAVKIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAACVAAMKAVATAPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+I Y
Sbjct: 133 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIAY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  F       
Sbjct: 193 RMKQRWPDVFIGINGGIRTLDEAASHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+ +GG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 253 PD---------WPALCERMMTYAERHIAAGGRLQHVARHMVGLFTGLPGARRYRQILSTD 303

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++  AF  +
Sbjct: 304 AAKTGAGPEVLAAAFAAV 321


>gi|218246535|ref|YP_002371906.1| tRNA-dihydrouridine synthase A [Cyanothece sp. PCC 8801]
 gi|218167013|gb|ACK65750.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 8801]
          Length = 331

 Score =  358 bits (919), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 143/319 (44%), Positives = 196/319 (61%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+F R +T + LLYTEMIV  AI  GD+  +LGFS +EKPL+LQ+GG D  
Sbjct: 14  MMERTDRHFRYFMRQITQDTLLYTEMIVTQAIRYGDRTKLLGFSPEEKPLSLQLGGDDPQ 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I EDFGY+E+NLNVGCPS RV  G+FGACLML P++V  C+ AM K ++IP+T
Sbjct: 74  ELAECAMIAEDFGYDEVNLNVGCPSDRVQSGNFGACLMLQPELVARCVEAMQKKVNIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIGVD++     L N VK +  +G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 134 IKHRIGVDERDRYEDLANFVKIVSDAGCQRFTVHARKAWLKGLSPKENRTIPPLKYEEVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E   LFI +NGG+  + Q    L  VDGVMIGRAAY N  +  TVD          
Sbjct: 194 QLKQEFSQLFIEINGGIITLDQIEHHLQFVDGVMIGRAAYDNPYLFATVDRDIYG----- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +      ++   M  Y    +++G KL  I+RH++ +F G P ++  +  ++  
Sbjct: 249 ----QNIIPPTRHQVVEKMLPYIDYWVNNGLKLHAISRHILAIFGGVPGTKAWKRHISEN 304

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +IE A   + 
Sbjct: 305 AHLPGAGVKVIEEALGKVP 323


>gi|227822301|ref|YP_002826272.1| tRNA-dihydrouridine synthase A [Sinorhizobium fredii NGR234]
 gi|227341301|gb|ACP25519.1| putative tRNA-dihydrouridine synthase A [Sinorhizobium fredii
           NGR234]
          Length = 385

 Score =  358 bits (919), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 182/348 (52%), Positives = 238/348 (68%), Gaps = 30/348 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+ +ALLYTEMIVADAILRGD+  +LG    E P+ALQ+GG D +
Sbjct: 27  MIDWTDRHYRFFARQLSRHALLYTEMIVADAILRGDRDRLLGHDAAEHPVALQLGGNDPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V +C+AAM +A++IPVT
Sbjct: 87  KMAEAARIAEAFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVAECVAAMKEAVTIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR LV  +K +G + +W+HARKA L+GLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRALVARVKSAGADAVWVHARKAWLQGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--------------------SVDGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL  L                      +DGVM+GRAAY
Sbjct: 207 RLKSENKNLFIGLNGGLQTLDQALAHLDPRLLPAHAPKLAVAEAEHEVPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD----------KDFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF++PLTG+ P+    D            FW  +  +M  YAA H+ +G
Sbjct: 267 HDSGLLTAADGYFAHPLTGAPPVPLDPDSFSERGHCLSLTFWADVRDAMAAYAAAHIDNG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           G+L  +TRHM+GLF G+P +RR R +L+ +A    A   +I  AF  +
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQMLSADATRKGAGPEVIHAAFEAV 374


>gi|110633902|ref|YP_674110.1| tRNA-dihydrouridine synthase A [Mesorhizobium sp. BNC1]
 gi|110284886|gb|ABG62945.1| tRNA-U16,U17-dihydrouridine synthase [Chelativorans sp. BNC1]
          Length = 342

 Score =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 154/318 (48%), Positives = 210/318 (66%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEMIVADAI+ G ++ +L +   E P+ALQ+GG++  
Sbjct: 25  MMDWTDRHCRFFHRQLSKDALLYTEMIVADAIIHGSRERLLAYDPAEHPVALQLGGSEPG 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I   FGY+EINLNVGCPS RV  G+FGACLM  P++V  C+AAM + + +PVT
Sbjct: 85  KLGEAARIAASFGYDEINLNVGCPSDRVQSGTFGACLMKTPELVSACVAAMKECVDVPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  + + +  +G + +W+HARKA L+GLSP++NR+IP LDYD VY
Sbjct: 145 VKCRIGVDDQDPEEALDRIAELVFAAGADALWVHARKAWLQGLSPRENREIPPLDYDRVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P  F+G+NGG++ + +A+  L  +DGVM+GRAAY    +L  VD          
Sbjct: 205 RLKKKYPGKFVGINGGIQTIDEAVNHLAHMDGVMLGRAAYHTPGILAEVDSRIYGGQNEP 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      + ++  +M  YA RH+  GG+L  +TRHM GLFHG   +RR R IL+ E
Sbjct: 265 ---------VSFAEVVEAMAAYAQRHIERGGRLAHVTRHMTGLFHGRAGARRFRQILSTE 315

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   +
Sbjct: 316 ATRPRAGPDVLLRALAEI 333


>gi|56697231|ref|YP_167596.1| tRNA-dihydrouridine synthase A [Ruegeria pomeroyi DSS-3]
 gi|56678968|gb|AAV95634.1| tRNA-dihydrouridine synthase A [Ruegeria pomeroyi DSS-3]
          Length = 344

 Score =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 146/320 (45%), Positives = 201/320 (62%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L +S +E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRYLHRLLSRQTLLYTEMVTAPALVRGGALHLLEYSVEEHPVALQLGGSDPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM +P +V DC+ AM +A+ + VT
Sbjct: 78  ELAQAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMKHPGLVADCVTAMREAVDVEVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I  +G   + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 138 VKCRIGVDDQDPETVLPEFLEQIAGAGCQRVIIHARKAWLQGLSPKENRDIPPLDYDLVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P + I +NGG++ ++ A   L   +DGVMIGRAAY   A +L   D       T
Sbjct: 198 RMKARFPGMHISINGGIDTLAAARAHLDAGLDGVMIGRAAYHQPADILCKADPLIYGTGT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+              +M  Y   HL +GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 258 ASDPVT----------AVRAMLPYIEAHLATGGRLHQITRHMLGLFAGRPGARGWRRMLS 307

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A + +
Sbjct: 308 EGAVRPGAGPELVEAALDQV 327


>gi|260433272|ref|ZP_05787243.1| tRNA-dihydrouridine synthase A [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417100|gb|EEX10359.1| tRNA-dihydrouridine synthase A [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 345

 Score =  357 bits (918), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 147/318 (46%), Positives = 202/318 (63%), Gaps = 12/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL++NALLYTEM+ A A++RG   ++L FS +E P+ALQ+GG+D  
Sbjct: 26  MMDWTDRHCRYLHRLLSSNALLYTEMVTAPALVRGGALHLLEFSPEEHPVALQLGGSDPE 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM +P  V DC+AA   A+ + VT
Sbjct: 86  ELAQAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMKDPARVADCVAATRAAVRVEVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L + +  I+ +G   + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 146 VKCRIGVDEQTPEEVLPDFLDKIRAAGCQRVTIHARKAWLQGLSPKENRDIPPLDYDLVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   PD+ I +NGG+  +++A   L   +DGVMIGRAAY     +L   D       T
Sbjct: 206 RMKAAFPDMHISINGGIASLAEARAHLEAGLDGVMIGRAAYHQPTDILAEADPLIFGTGT 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y  RHL +GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 266 AADPV----------DVVHQMLPYIDRHLAAGGRLHQITRHMLGLFAGRPGARGWRRVLS 315

Query: 299 VEAGASTATHHIIETAFN 316
             A    A   ++  A +
Sbjct: 316 EGAVRDNAGPEVVLEALD 333


>gi|329849777|ref|ZP_08264623.1| tRNA-dihydrouridine synthase A [Asticcacaulis biprosthecum C19]
 gi|328841688|gb|EGF91258.1| tRNA-dihydrouridine synthase A [Asticcacaulis biprosthecum C19]
          Length = 340

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 156/321 (48%), Positives = 210/321 (65%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+   A++ GD++ ++GFS  E P+ALQ+GG+D +
Sbjct: 13  MMDWTDRHCRAFHRALTKRALLYTEMVTTKAVIHGDRERLIGFSDIEHPVALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AKI ED+GY+EINLN GCPS RV  G+FGACLM +P +V D + AM +A  +P T
Sbjct: 73  ELAQCAKIAEDWGYDEINLNCGCPSDRVQSGAFGACLMRDPQLVADGMQAMIEASKLPAT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  LV++ +K+GV    +HARKA LKGLSPK+NR IP LDY++VY
Sbjct: 133 VKCRIGVDDQDPRDALFTLVEACRKAGVTTFIVHARKAWLKGLSPKENRDIPPLDYELVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+ +PDLFI +NGG+ ++  A + L  VDGVM+GRAAY   A+L  VD          
Sbjct: 193 ELKRSHPDLFISINGGIANLDDAQRHLQHVDGVMLGRAAYHEPALLGQVDTSVFGGSKDV 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P           +   +   Y A  L  G  L  +TRH++GL HG P +R  R ILTVE
Sbjct: 253 APF----------EALDAYRPYIAARLDEGVPLTHMTRHILGLMHGLPGARAFRRILTVE 302

Query: 301 AGASTATHHIIETAFNLMIES 321
           +    A   +I+ A + + ++
Sbjct: 303 SIVPGAGTEVIDRAAHAVRDA 323


>gi|33151604|ref|NP_872957.1| tRNA-dihydrouridine synthase A [Haemophilus ducreyi 35000HP]
 gi|38604736|sp|Q7VNV2|DUSA_HAEDU RecName: Full=tRNA-dihydrouridine synthase A
 gi|33147824|gb|AAP95346.1| conserved hypothetical protein [Haemophilus ducreyi 35000HP]
          Length = 323

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 137/320 (42%), Positives = 189/320 (59%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  +  ALLYTEMI A AIL     ++L +   E+P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQQALLYTEMITAPAILHAKY-DLLEYDPAEQPVALQLGGSDPT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V+  GY EINLNVGCPS RV  G FGACLM N D+V DCI AM   + IPVT
Sbjct: 74  QLANCAKLVQARGYTEINLNVGCPSDRVQNGMFGACLMANADLVADCIKAMQDVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+D       L + +  I+        +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 IKHRIGIDTLDSYAFLCDFIDKIQPYS-QDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N A+L  +D+   +    +
Sbjct: 193 QLKRDFPQLNISINGGIKTIDEIKQHLTKVDGVMVGREAYQNPALLGEIDQQLFDQ---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R    +M  Y  + L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 QPLITA------RIAVENMLPYIEQQLSKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++E A   + E
Sbjct: 304 ACKQGAGIEVVEQALRFVTE 323


>gi|288957792|ref|YP_003448133.1| tRNA-dihydrouridine synthase A [Azospirillum sp. B510]
 gi|288910100|dbj|BAI71589.1| tRNA-dihydrouridine synthase A [Azospirillum sp. B510]
          Length = 335

 Score =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 140/318 (44%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ + LLYTEM+   A+L GD++ +LGF   E P+ALQ+GG+D +
Sbjct: 11  MMDWTDRHCRYFHRLLSASTLLYTEMVTTGAVLHGDRERLLGFDAAEHPVALQLGGSDPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A+I E++GY+E+NLNVGCPS RV  G FGACLM  PD+V   + AM  A++IPVT
Sbjct: 71  DLAACARIAEEWGYDEVNLNVGCPSDRVQSGRFGACLMAEPDLVARLVGAMRDAVAIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +D+      L + V+++  +G     +HARKA LKGLSPK+NR IP L YD+V+
Sbjct: 131 VKSRIAIDEMEEWPTLDHFVRTVSAAGCTHFIVHARKAWLKGLSPKENRDIPPLRYDLVH 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K ENP L I +NGG+  + +A + L  VD VMIGRAAY+   +L   D   +    G 
Sbjct: 191 RLKAENPHLTIAINGGIRTLDEAEEHLGKVDSVMIGRAAYETPYLLADADRRLTGGAPGP 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         + A+M  +    +  G  L  ITRHM+GLF G P +R  R  +   
Sbjct: 251 D----------RHAVIAAMLPFIEARMALGTPLSAITRHMLGLFQGLPGARAYRRHIAEN 300

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A  L+
Sbjct: 301 AHRPGAGPEVLECAAALV 318


>gi|70729357|ref|YP_259094.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens Pf-5]
 gi|68343656|gb|AAY91262.1| TIM-barrel protein, yjbN family [Pseudomonas fluorescens Pf-5]
          Length = 336

 Score =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ + LLYTEM+   A+L GD +  L +   E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKHTLLYTEMVTTGALLNGDHERFLRYHPSEHPLALQLGGSTPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 85  DLAACARMAQEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMRDAVSIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G +   +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAELCDFVGQVMEAGCSSFTVHARIAILEGLSPKENRDIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I LNGG++ +    + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 205 QLKADFPQLEIILNGGIKTLEACHEHLQTFDGVMLGREAYHNPYLLAEVDQQLFGS---T 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R +        A +  Y A HL +GG +  ITRH++GL  GFP +R+ R +L+V+
Sbjct: 262 EPVISRAEA------LARLRPYIAEHLAAGGAMHHITRHVLGLGTGFPGARKFRQLLSVD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 316 IHKTQDPLALLDQAGQLL 333


>gi|67921570|ref|ZP_00515088.1| Dihydrouridine synthase TIM-barrel protein yjbN [Crocosphaera
           watsonii WH 8501]
 gi|67856682|gb|EAM51923.1| Dihydrouridine synthase TIM-barrel protein yjbN [Crocosphaera
           watsonii WH 8501]
          Length = 334

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 188/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+  R +T + LLYTEMIV+ AI  GD+  +L FS +EKPL+LQ+GG +  
Sbjct: 9   MMDYTDRHFRYLMRQITRHTLLYTEMIVSAAIKHGDRPKLLDFSPEEKPLSLQLGGDNPQ 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I ED+GY+EINLNVGCPS RV  G FGACLM  P++V  C+  M + ++IPVT
Sbjct: 69  ELAECAIIAEDWGYDEINLNVGCPSDRVQSGHFGACLMAKPELVAQCVQKMQQGVNIPVT 128

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     +   V  + ++G     IHARKA LKGLSPK+NR IP L Y  VY
Sbjct: 129 VKQRIGIDDQDSYEEMARFVAIVAEAGCQRFTIHARKAWLKGLSPKENRNIPPLRYQDVY 188

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+ ++ Q    L  VD VMIGRAAY N  +  TVD          
Sbjct: 189 RLKQDFPHLLIEINGGITNLEQVDNHLKIVDAVMIGRAAYDNPYLFATVDRDIYQED--- 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +      +I   M  Y    +  G KL +I+RH++ +F G P ++  +  ++  
Sbjct: 246 ------IIPATRHEIIEKMLPYIDHWVSRGHKLHRISRHLLAMFAGIPGTKAWKRYISEN 299

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  A   +
Sbjct: 300 AHLPGADSQVIIEALKRV 317


>gi|326795079|ref|YP_004312899.1| TIM-barrel protein, yjbN family [Marinomonas mediterranea MMB-1]
 gi|326545843|gb|ADZ91063.1| TIM-barrel protein, yjbN family [Marinomonas mediterranea MMB-1]
          Length = 348

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 139/322 (43%), Positives = 191/322 (59%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWT R YR FAR LT + LLYTEM+   AIL+GD  +  L +   E P+ALQ+GG+D 
Sbjct: 29  MLDWTTRDYRVFARTLTKHTLLYTEMVTTGAILQGDNPERFLKYDDCEHPIALQLGGSDA 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   AKI E F Y+E+NLNVGCPS RV     GACLM  PD V D + AM  A SIPV
Sbjct: 89  VALATCAKIAETFHYDEVNLNVGCPSDRVQNSLIGACLMAYPDKVADILKAMQDATSIPV 148

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+DDQ     LR+ V ++  +G+    +HAR AIL+GLSPK+NR+IP L YD V
Sbjct: 149 TIKHRIGLDDQQEYSILRDFVGTVADTGIQTFIVHARNAILQGLSPKENREIPPLKYDYV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ PDL I +NGG++ + + +  L  VDGVM+GR AY N  +L+ +D         
Sbjct: 209 YQLKKDFPDLEIIINGGIKTIDETISHLDHVDGVMMGREAYNNPWILSDIDTKVYG---A 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S+ +  R +             Y    L  G +L  +TRH++G+FHG P  ++ R  L+ 
Sbjct: 266 SACVNNRFEA------LERFVPYVEEQLAKGERLMHMTRHILGIFHGLPGGKQFRRYLSE 319

Query: 300 EAGASTATHHIIETAFNLMIES 321
               + A   I+  A  ++ + 
Sbjct: 320 NGHKTDAKIDILLEAIEIVRKQ 341


>gi|307154453|ref|YP_003889837.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 7822]
 gi|306984681|gb|ADN16562.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 7822]
          Length = 329

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 142/319 (44%), Positives = 192/319 (60%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+  R +T   LLYTEMI   AI+ GD+  +L FST+EKPLALQ+GG +  
Sbjct: 17  MMERTDRHFRYLMRQITRRTLLYTEMITTAAIIHGDRHKLLDFSTEEKPLALQLGGDNPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A I  D+GY+E+NLNVGCPS RV  G+FGACLM  P+ V  C+AAM KA++IPVT
Sbjct: 77  ELALCASIAADWGYDEVNLNVGCPSDRVQNGNFGACLMAQPEKVAHCVAAMQKAVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L N V+ + ++G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 137 VKHRIGIDDRDRYEDLANFVRIVSEAGCCRFSVHARKAWLKGLSPKENRTIPPLRYEDVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P LFI +NGG+  + Q  + L  VDGVMIGRAAY N  +  TVD       T  
Sbjct: 197 RLKQEFPHLFIEINGGITTLEQVHQQLQWVDGVMIGRAAYDNPYLFATVDRDIYGEETIP 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        +++  M  Y    +  G KL  I+RH++ LF G P ++  +  ++  
Sbjct: 257 P---------TRHQVAEKMLPYIEDIVSQGIKLHAISRHLLQLFSGQPGTKAWKRYISEN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                A   +IE A   + 
Sbjct: 308 VHHQAAGAEVIEAALAQVP 326


>gi|219871369|ref|YP_002475744.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis SH0165]
 gi|219691573|gb|ACL32796.1| tRNA-dihydrouridine synthase A [Haemophilus parasuis SH0165]
          Length = 323

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 134/319 (42%), Positives = 188/319 (58%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  T ++LLY+EMI A AIL     ++L +   E P+ALQ+GG+D  
Sbjct: 15  MLDWTTRHCRYFHRQFTQHSLLYSEMITAPAILHAKY-DLLAYDPTENPVALQLGGSDPE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+VE+ GY EINLNVGCPS RV  G FGACLM   D+V  C+ AM K +SIPVT
Sbjct: 74  QLAKCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMGKADLVARCVEAMKKEVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ I+    N   +HARKA L GLSPK+NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKIQPY-CNDFIVHARKAWLSGLSPKENREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG++ + +    L  VDGVM+GR AY+N ++L  +D    +P    
Sbjct: 193 QLKRDFPHLKMSINGGIKTIEEIKHHLQFVDGVMVGREAYQNPSLLGYIDRELFDPNAEI 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              K         +    M  Y  + L  G  L  I RH++G F     +R+ R  L+  
Sbjct: 253 VTPK---------QAVEKMLPYIEQQLSQGVYLNHIVRHILGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   ++E A + + 
Sbjct: 304 ACKQGAGVEVVEQALSFLP 322


>gi|149376568|ref|ZP_01894328.1| tRNA-dihydrouridine synthase A [Marinobacter algicola DG893]
 gi|149359086|gb|EDM47550.1| tRNA-dihydrouridine synthase A [Marinobacter algicola DG893]
          Length = 320

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 128/320 (40%), Positives = 180/320 (56%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  HYR+ AR L+ + LLYTEM+   A++ GD    L     E PLALQ+GG++  
Sbjct: 1   MMDWTTSHYRYLARQLSRHTLLYTEMVTTGALIHGDTARFLRHDPTEYPLALQLGGSNPQ 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A + E +G++E+NLNVGCPS RV     GACLM +PD V + + AM  A S+PVT
Sbjct: 61  ELAHCANLAEQYGFDEVNLNVGCPSDRVQNNMIGACLMAHPDKVAEGVQAMIAATSLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     L   ++ + ++G     +HAR A+L+GLSPK+NR IP L YD VY
Sbjct: 121 VKHRIGIDGRESWDDLCEFIEKVSEAGCRTFIVHARIAVLEGLSPKENRDIPPLKYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L I +NGG++  ++  + L   DGVM+GR AY N  +L  VD  F       
Sbjct: 181 RLKARYPHLEIIINGGIKTFAECREHLEHTDGVMLGREAYHNPWLLAGVDTEFFG----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+      D  R +      +    L  G  L  I+RH++GLFHG P  R+ R  ++  
Sbjct: 236 RPMPISSRHDALRAVL----PFIQSELDRGVYLSHISRHLMGLFHGQPGGRQFRRYISEN 291

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    +   +IE A   + E
Sbjct: 292 AHKPGSGIEVIEQAMAKVPE 311


>gi|329896416|ref|ZP_08271515.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC3088]
 gi|328921836|gb|EGG29207.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC3088]
          Length = 319

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 128/321 (39%), Positives = 179/321 (55%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++W+DRH R+F RL+   ALLYTEM+   A+L GDK   L F   E P+ALQ+GG +  
Sbjct: 1   MMEWSDRHCRYFWRLIAPQALLYTEMVTTGALLFGDKPYHLDFHDSEHPVALQLGGNEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ + +GY+E+NLN GCPS RV  G FGA LM  P  V  C+ AM  A  +PVT
Sbjct: 61  ALARCAELAQQWGYDEVNLNCGCPSDRVQSGGFGAYLMGEPKTVSACVQAMRNATDLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D Q     L   V+++ ++G     +HARKA LKGLSPK NR IP L+Y+ VY
Sbjct: 121 VKHRLGIDHQDSYEELLEFVQTVAEAGCRHFVVHARKAWLKGLSPKQNRDIPPLNYEWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG+    + ++ L  VDGVMIGR AY +   L  + E         
Sbjct: 181 RLKQTLPELTIVINGGITQPQECVEHLQHVDGVMIGREAYYHPWHLRAISEAVFGKQNLL 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            +I   M  Y+   L  G KL  +TRH+I  + G   +++ R  L+  
Sbjct: 241 SQP----------EIMTEMVRYSKEQLEKGVKLNHVTRHLINFYQGCRGAKQFRRYLSEN 290

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   I+  A  L+ ++
Sbjct: 291 AHRPGANEQILVDALALVEQA 311


>gi|257059573|ref|YP_003137461.1| tRNA-dihydrouridine synthase A [Cyanothece sp. PCC 8802]
 gi|256589739|gb|ACV00626.1| TIM-barrel protein, yjbN family [Cyanothece sp. PCC 8802]
          Length = 331

 Score =  356 bits (914), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 144/319 (45%), Positives = 199/319 (62%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+F R +T++ LLYTEMIV  AI  GD+  +LGFS +EKPL+LQ+GG D  
Sbjct: 14  MMERTDRHFRYFMRQITHHTLLYTEMIVTQAIRYGDRTKLLGFSPEEKPLSLQLGGDDPL 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I EDFGY+E+NLNVGCPS RV  G+FGACLML P++V  C+ AM K ++IP+T
Sbjct: 74  ELAECAIIAEDFGYDEVNLNVGCPSDRVQSGNFGACLMLQPELVARCVEAMQKRVNIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIGVD++     L N VK + ++G     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 134 IKHRIGVDERDRYEDLVNFVKIVSEAGCQRFTVHARKAWLKGLSPKENRTIPPLRYEEVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P LFI +NGG+  + Q    L  VDGVMIGRAAY N  +  TVD          
Sbjct: 194 QLKKDFPQLFIEINGGIITLDQIEHHLQFVDGVMIGRAAYDNPYLFATVDRDIYG----- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +      ++   M  Y    +++G KL  I+RH++ +F G P ++  +  ++  
Sbjct: 249 ----QNIIPPTRHQVVEKMLPYIDYWVNNGLKLHAISRHILAIFGGVPGTKAWKRHISEN 304

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +IE A   + 
Sbjct: 305 AHLPGAGVKVIEEALGKVP 323


>gi|113460197|ref|YP_718254.1| tRNA-dihydrouridine synthase A [Haemophilus somnus 129PT]
 gi|112822240|gb|ABI24329.1| tRNA-U16,U17-dihydrouridine synthase [Haemophilus somnus 129PT]
          Length = 328

 Score =  356 bits (914), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 132/321 (41%), Positives = 185/321 (57%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH RFF R  +   LLYTEM+   AI+     + L +   E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRFFHRQFSQYTLLYTEMVTTGAIIHAKY-DHLAYDVSENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL   AK  E+ GY EINLNVGCPS RV  G FGACLM   D+V +C+ AM  A++IPVT
Sbjct: 77  KLQYCAKKAEERGYQEINLNVGCPSDRVQNGMFGACLMARADLVAECVNAMQSAVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L + ++ +   G     IHARKA L GLSPK+NR+IP L+Y+ VY
Sbjct: 137 VKTRLGIDEFDSYEFLCDFIEKVHNIGCQEFIIHARKAWLSGLSPKENREIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P    
Sbjct: 197 QLKKDFPDLLISINGGIKTLEEIQRHLNYVDGVMVGREAYQNPSLLGYIDQALFDPSCAI 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R+   +M  Y  + L  G  L  I RH++G F     +R+ R  ++  
Sbjct: 257 ITP---------RQAIENMFPYIEQQLSQGVYLNHIARHLLGAFQQCKGARQWRRYMSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
              S A   +IE A   + E 
Sbjct: 308 IHKSHAGVEVIEKALTFIEEK 328


>gi|146306962|ref|YP_001187427.1| tRNA-dihydrouridine synthase A [Pseudomonas mendocina ymp]
 gi|145575163|gb|ABP84695.1| tRNA-U16,U17-dihydrouridine synthase [Pseudomonas mendocina ymp]
          Length = 331

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A++ GD++  L +S  E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRFFLRQLSRHALLYTEMVTTGALIHGDRERFLRYSECEHPIALQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 80  DLAACAKMAEQHGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 140 VKHRIGINGRDSYSELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +  + L + DGVM+GR AY N  +L  VD         +
Sbjct: 200 QLKRDFPDLEIILNGGIKTLEECEQHLQTFDGVMLGREAYHNPYLLAQVDNRLFG---AA 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R+D         ++  Y  +HL  GG L  ++RH++GL  GFP +RR R +L+V+
Sbjct: 257 APSISRMDA------LLALKPYVEQHLREGGTLHHVSRHVLGLAQGFPGARRFRQLLSVD 310

Query: 301 AGASTATHHIIETAFNLM 318
                    +++ A  L+
Sbjct: 311 IHKVQDPLGLLDQAAELL 328


>gi|256821809|ref|YP_003145772.1| TIM-barrel protein, yjbN family [Kangiella koreensis DSM 16069]
 gi|256795348|gb|ACV26004.1| TIM-barrel protein, yjbN family [Kangiella koreensis DSM 16069]
          Length = 330

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 141/322 (43%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RL+T +A+LYTEMI   AI+ G  +  L F+ +E P+A+Q+GG+D  
Sbjct: 14  MLDWTDRHQRRFMRLITKHAVLYTEMITTGAIIHGGAERHLKFNQEEHPVAVQLGGSDPK 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AKI EDFGY+EINLNVGCPS RV  G FGACLM  P++V +C++AM   + +PVT
Sbjct: 74  DLAHCAKICEDFGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECMSAMANVVDVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      L + + +++ +GV    IHARKA L GLSPK NR+IP L YDI Y
Sbjct: 134 VKSRIGIDELDSYEHLHHFINTVQSAGVKTFIIHARKAWLSGLSPKQNREIPPLRYDIAY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P+L I +NGG+  + QA   +   DGVMIGR AY N   L  VD  F       
Sbjct: 194 QVKKDFPELEIIVNGGVNTLDQAEDHMKHADGVMIGREAYHNPYFLAEVDNRFYGKDYD- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R+      +I+     Y    L     L  +TRH++GLF   P  +  R  L+  
Sbjct: 253 --IPSRI------EIAREYMVYIQSQLDQDVYLGHMTRHILGLFFAQPKGKLWRRYLSEN 304

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A    A   ++E A  +  E +
Sbjct: 305 AYQKGAGLEVLEGALAIYEEDI 326


>gi|170077369|ref|YP_001734007.1| dihydrouridine synthase A [Synechococcus sp. PCC 7002]
 gi|169885038|gb|ACA98751.1| Dihydrouridine synthase A [Synechococcus sp. PCC 7002]
          Length = 344

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 193/321 (60%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+  R +T   LLYTEMI   AI+ GD+  +L F   E P++LQ+GG +  
Sbjct: 19  MMDRTDRHFRYLMRRITRRTLLYTEMITTQAIIHGDRPKLLDFDAAEHPISLQLGGDNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E AK+ ED+GY+EINLNVGCPS RV +G+FGACLM  P++V DC+AAM  A++IPVT
Sbjct: 79  ELAECAKVGEDWGYDEINLNVGCPSPRVQQGNFGACLMTQPELVADCVAAMQGAVNIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+Q     L   ++ +  +G +   +HARKA L+GLSPK+NR +P L Y  VY
Sbjct: 139 VKHRIGVDEQDSYADLCRFIEIVSATGCDRFSVHARKAWLQGLSPKENRTVPPLRYADVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L+I +NGG+  +      L  VD VM+GRAAY N  +  TVD          
Sbjct: 199 RLKQDFPHLWIEINGGITTLEHIQTHLTQVDAVMVGRAAYDNPYLFATVDRDIYGEA--- 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +      +I   M  Y  R   +G KL  I+RHM+ LF G P ++  +  +T E
Sbjct: 256 ------IQPKSRHEIVEEMLPYIERATKAGVKLHSISRHMLSLFLGQPGTKAWKRFITEE 309

Query: 301 AGASTATHHIIETAFNLMIES 321
              +T    IIE A  L+ ++
Sbjct: 310 GRGTTVGREIIEQALALVSQT 330


>gi|119476488|ref|ZP_01616839.1| Dihydrouridine synthase TIM-barrel protein yjbN [marine gamma
           proteobacterium HTCC2143]
 gi|119450352|gb|EAW31587.1| Dihydrouridine synthase TIM-barrel protein yjbN [marine gamma
           proteobacterium HTCC2143]
          Length = 341

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 137/321 (42%), Positives = 192/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ W+DRH R F R LT +A++YTEM+   AIL       L ++T E PLALQ+GG++  
Sbjct: 13  MMAWSDRHCRMFWRQLTQHAVMYTEMVTTGAILHAGADRFLTYNTGEHPLALQLGGSNPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    KI  DFGY+E+NLN GCPS RV  G FGACLM +P  V DCI+AM  A S+P+T
Sbjct: 73  DLASCTKIAADFGYDEVNLNCGCPSDRVQNGMFGACLMAHPQRVADCISAMQDASSLPIT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +   VK I  +G +   +HARKA L+GLSPK NR IP L YD+V+
Sbjct: 133 VKHRIGIDEMESYDEMLEFVKPIADTGCSTFIVHARKAWLQGLSPKQNRDIPPLHYDMVH 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L + +NGG+  +   +  L  VDGVM+GRAAY+N  +L  VD    N     
Sbjct: 193 QLKQDFPSLNVIINGGITSIEHCVSHLQLVDGVMLGRAAYQNPYLLAEVDSLIYN---AP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + IKTR       ++      Y    L +   L  +TRH++GLF G P ++  R  ++ +
Sbjct: 250 TVIKTR------DQVLLDYIPYIEEQLQNNVALNHMTRHILGLFQGIPGAKLFRRHISEQ 303

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  S A  +++  A  LM+E+
Sbjct: 304 AHRSDAGINVVYQARELMLEA 324


>gi|254415230|ref|ZP_05028992.1| TIM-barrel protein, yjbN family [Microcoleus chthonoplastes PCC
           7420]
 gi|196178036|gb|EDX73038.1| TIM-barrel protein, yjbN family [Microcoleus chthonoplastes PCC
           7420]
          Length = 338

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 136/321 (42%), Positives = 191/321 (59%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +LGFS +EKPL LQ+GG +  
Sbjct: 26  MMDRTDRHFRYFMRQITRRTLLYTEMVTSAAIIHGDRDRLLGFSAEEKPLVLQVGGDNPL 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A+I E  GY++INLNVGCPS RV  G+FGACLM  P+ V   + AM KA++IPVT
Sbjct: 86  ELAECARIAEGMGYDQINLNVGCPSDRVQNGNFGACLMAQPERVARGVEAMIKAVTIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      + N V+ + ++G     +HARKA L+GLSPK+NR +P L Y  V+
Sbjct: 146 VKHRIGIDECDRYEDMANFVRIVSEAGCQHFSVHARKAWLQGLSPKENRTVPPLRYSDVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K+E P LFI +NGG   + Q  + L  VD VMIGRAAY N  +    D + F      
Sbjct: 206 RLKQEFPQLFIEINGGFTSLEQVQEQLKFVDAVMIGRAAYDNPYLFAQADCQIFEEECIP 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +            +++  M DY    +  G KL +ITRH++ LF G P SR  +  LT 
Sbjct: 266 PT----------RHQVAEGMLDYIDHWVAKGLKLNKITRHILQLFSGQPGSRAWKRHLTE 315

Query: 300 EAGASTATHHIIETAFNLMIE 320
           ++        ++  A   + +
Sbjct: 316 KSCIPGVGSEVVREALAKVPD 336


>gi|83945621|ref|ZP_00957967.1| TIM-barrel protein, yjbN family protein [Oceanicaulis alexandrii
           HTCC2633]
 gi|83850987|gb|EAP88846.1| TIM-barrel protein, yjbN family protein [Oceanicaulis alexandrii
           HTCC2633]
          Length = 332

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 151/321 (47%), Positives = 199/321 (61%), Gaps = 8/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+LT  A+LYTEM V  A++ GD   ++GF   E P+A+Q+GG+D  
Sbjct: 17  MMDWTDRHCRAFHRVLTRRAVLYTEMAVDQALIHGDVPRLIGFDASEHPVAIQLGGSDPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  A+KI E FGY EINLNVGCPS RV  G FGACLM  P++V DC+ AM +A+S+PVT
Sbjct: 77  ILARASKIAEGFGYLEINLNVGCPSDRVQSGKFGACLMREPELVRDCLTAMREAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+GVDDQ P   L   V+++++SGV    +HARKA LKGLSPK+NR +P LDYD+V 
Sbjct: 137 VKHRLGVDDQDPEKTLFGFVETVRESGVKTFIVHARKAWLKGLSPKENRDVPPLDYDLVR 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E+PDL + LNGGLE +   +  +   DG+M+GRAAY     L  VD         S
Sbjct: 197 RMKAEHPDLEVLLNGGLETLEHGMAEIHGADGIMLGRAAYHTPWTLAEVDTRIYGE--AS 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  T  +         +   Y  R L  G KL  ITRHM+GLF G P +R+ R +L+  
Sbjct: 255 DPCATPFEA------VEAYRPYVERQLDQGVKLHAITRHMLGLFAGRPGARKWRQVLSER 308

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + +  +
Sbjct: 309 ANRPGAGWEVLEDALDAVRPA 329


>gi|261494145|ref|ZP_05990648.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
 gi|261496014|ref|ZP_05992424.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261308264|gb|EEY09557.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261310311|gb|EEY11511.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
          Length = 325

 Score =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 189/318 (59%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  +  ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRQALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V + GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 77  QLAHCAKLVAERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVEIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    +   +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKHRIGIDDLDSYEFLCDFIEKVQPYSND-FIVHARKAWLTGLSPKENREIPPLDYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N +ML  +D    N    +
Sbjct: 196 QLKRDFPHLKISINGGIKTIEEIKQHLQFVDGVMVGREAYQNPSMLGEIDSQIFNE---N 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       ++    M  Y  R L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 253 RPLVTA------KEAVEKMFPYIERELAKGVYLNHIVRHMLGAFQHCKGARQWRRHLSEN 306

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++E A   +
Sbjct: 307 ATKPGAGVEVVEQALAFI 324


>gi|260428471|ref|ZP_05782450.1| tRNA-dihydrouridine synthase A [Citreicella sp. SE45]
 gi|260422963|gb|EEX16214.1| tRNA-dihydrouridine synthase A [Citreicella sp. SE45]
          Length = 372

 Score =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 150/320 (46%), Positives = 205/320 (64%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ NALLYTEM+ A A++RG   ++L F+ +E P+ALQ+GG+D  
Sbjct: 58  MMDWTDRHCRYLHRLLSRNALLYTEMVTAPALVRGGAVHLLDFNPEEHPVALQLGGSDPD 117

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AAK+    GY++I+LN GCPS RV  G+FGA LM  P++V DC+AAM +A ++ VT
Sbjct: 118 ELAQAAKLGGAAGYDQIDLNCGCPSDRVQSGTFGAVLMKTPELVADCVAAMQEATAVEVT 177

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  ++ +G   I IHARKA L+GLSPK+NR+IP LDY IV+
Sbjct: 178 VKCRIGVDDQKPREVLPAFIDKVRGAGCRRIAIHARKAWLQGLSPKENREIPPLDYAIVH 237

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           E+K   PDL + LNGG+E ++   K+L   +DGVM+GRAAY     +L   D        
Sbjct: 238 EMKAAFPDLHVSLNGGVESLATVEKLLDEGLDGVMVGRAAYHQPWDILAEADARI-WGEE 296

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +P           +I+ +M  Y  RHL  GGKL Q+TRHM+GLF G P +R  R +L+
Sbjct: 297 RETPSP--------EEIARAMLPYIERHLSDGGKLHQVTRHMLGLFAGRPGARGWRRVLS 348

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++E A   +
Sbjct: 349 ERATRDGAGPEVVEAALERI 368


>gi|311695131|gb|ADP98004.1| tRNA-dihydrouridine synthase, TIM-barrel, YjbN [marine bacterium
           HP15]
          Length = 344

 Score =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 131/320 (40%), Positives = 189/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  HYR+ AR L+ + LLYTEM+   A++ GD    L     E PLALQ+GG+D  
Sbjct: 25  MMDWTTSHYRYLARQLSRHTLLYTEMVTTGALIHGDTARFLRHDEAEYPLALQLGGSDAG 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ + +G++E+NLNVGCPS RV     GACLM +PD V + + AM +A  +PVT
Sbjct: 85  ELAHCARLAQQYGFDEVNLNVGCPSDRVQNNMIGACLMGHPDKVAEGVRAMIEATDLPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     L   V+ + ++G     +HAR AIL+GLSPK+NR++P L YD VY
Sbjct: 145 VKHRIGIDGRESWDDLCEFVEKVSEAGCRTFIVHARIAILEGLSPKENREVPPLKYDWVY 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG++   +  + L   DGVM+GR AY N  +L  VD  F      +
Sbjct: 205 RLKAKYPHLEIIINGGIKTFGECHEHLRHTDGVMLGREAYHNPWLLAGVDPEFFGQ---A 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++TR       +   +M  +    L  G  L  ++RH++GLFHG P  R+ R  ++  
Sbjct: 262 APVETR------HQALRAMLPFIGSELERGVFLTHMSRHLLGLFHGQPGGRQFRRYISEN 315

Query: 301 AGASTATHHIIETAFNLMIE 320
           A  S A   +IETA   + E
Sbjct: 316 AHKSGAGLEVIETALEKVRE 335


>gi|224588182|gb|ACN58806.1| tRNA dihydrouridine synthase A [uncultured bacterium BLR9]
          Length = 334

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 154/318 (48%), Positives = 204/318 (64%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R   RLL+ +ALLYTEM+ A+A++RGD+  +LGFS  E P+ALQ+GGA+ +
Sbjct: 20  MMDCTDRHCRVLHRLLSRHALLYTEMVTAEAVIRGDRARLLGFSPAEHPVALQLGGAEPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAKI  DFGY+EINLNVGCPS RV  G FGA LM  P  VGDC+AAM  A+S+PVT
Sbjct: 80  RLAEAAKIGADFGYDEINLNVGCPSDRVQSGCFGAALMKEPLRVGDCVAAMRAAVSVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+++  ++GV    +HARKA L GLSPK+NR++P LDY +VY
Sbjct: 140 VKCRIGVDEQEPREALPALIEACTRAGVTAFAVHARKAWLSGLSPKENREVPPLDYSLVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG+  + +A   LP VDGVM+GRAAY+  A+L  VD  F       
Sbjct: 200 ALKRARPELTIVINGGIGSLDEAEAHLPHVDGVMLGRAAYQTPAILAEVDSRFFG----- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +D    + A    Y    L  G  L  +T+HM+GLF+G P +R+ R  L+  
Sbjct: 255 -----EGARDIGEAVEA-YAAYIGARLAEGVPLNAMTKHMLGLFNGIPGARQFRRHLSEN 308

Query: 301 AGASTATHHIIETAFNLM 318
           A    A    +  A   +
Sbjct: 309 ATKKGAGLQTLRDALAFV 326


>gi|154251505|ref|YP_001412329.1| tRNA-dihydrouridine synthase A [Parvibaculum lavamentivorans DS-1]
 gi|154155455|gb|ABS62672.1| TIM-barrel protein, yjbN family [Parvibaculum lavamentivorans DS-1]
          Length = 335

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 142/320 (44%), Positives = 198/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T  +LLYTEM+   AIL G ++ +L F   E P+A+Q+GG++ +
Sbjct: 13  MMDWTDRHDRYFLRLITRRSLLYTEMVTTGAILHGPRERLLKFDLSEHPVAVQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+A+I  DFGY+EINLNVGCPS RV  G FGACLM  PD+V  C+ AM  A+S+PVT
Sbjct: 73  DLAESARIAADFGYDEINLNVGCPSDRVQSGRFGACLMREPDLVARCVEAMKNAVSVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  + K+++ +G   + +HARKA L+GLSPK+NR +P LDY +VY
Sbjct: 133 VKCRIGVDEQEPEEALPAMAKAVRGAGCETLIVHARKAWLEGLSPKENRDVPPLDYPLVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+ I +NGG+  + +A   L  VDGVM+GRAAY++  +L   D  F       
Sbjct: 193 RLKQAMPDMEIIINGGIATLDEAEAHLAHVDGVMLGRAAYQHPYILAEADRRFYGDGH-- 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D     ++      Y    +  G  L  +TRH++GLF G P +R  R  ++  
Sbjct: 251 -------DVPSRHEVLEGFVLYVQEEMAHGTHLHAMTRHILGLFQGCPGARAFRRHISEN 303

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   +I  A  L+ +
Sbjct: 304 APRPGAGAEVIREAMALVRD 323


>gi|172037930|ref|YP_001804431.1| tRNA-dihydrouridine synthase A [Cyanothece sp. ATCC 51142]
 gi|171699384|gb|ACB52365.1| putative dihydrouridine synthase TIM-barrel protein nifR3
           [Cyanothece sp. ATCC 51142]
          Length = 342

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 139/319 (43%), Positives = 195/319 (61%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R+F R +T + LLYTEMIV+ AI+ GD+  +L FS +EKPL+LQIGG +  
Sbjct: 22  MMDYTDRHFRYFMRQITRHTLLYTEMIVSAAIINGDRPKLLDFSPEEKPLSLQIGGDNPQ 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E A I ED+GY+E+NLNVGCPS RV  G FGACLM NP++V  C+  M + ++IPVT
Sbjct: 82  ELAECAIIGEDWGYDEVNLNVGCPSDRVQSGHFGACLMANPELVAQCVEKMQQGVTIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D Q     +   VK + ++G     +HARKA L+GLSPK+NR IP L Y  VY
Sbjct: 142 VKHRIGIDHQDSYEDMARFVKIVSEAGCQRFTVHARKAWLQGLSPKENRNIPPLRYQEVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P LFI +NGG+ ++ Q    L  VD VMIGR+AY N  +L TVD          
Sbjct: 202 RLKQEFPQLFIEINGGITNLEQVRNHLKLVDAVMIGRSAYDNPYLLATVDRDIY------ 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + +V +    +I   M  Y    +  G KL +I+RH++ +F G P ++  +  ++  
Sbjct: 256 ---RDKVTQLTRHQIIEKMLPYIDDWVSRGHKLHKISRHLLAIFSGIPGTKAWKRHISEN 312

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +I      + 
Sbjct: 313 AHLPGADSQVIVQGLKKVP 331


>gi|261866807|ref|YP_003254729.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412139|gb|ACX81510.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 327

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 131/318 (41%), Positives = 191/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEM+   AI+     + L F   E+P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRHALLYTEMVTTQAIIHAKY-DHLDFDPAEQPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E  GY EINLNVGCPS RV  G FGACLM   ++V +C+  M +A+ IPVT
Sbjct: 77  QLKHCAQLAEQRGYQEINLNVGCPSDRVQNGMFGACLMAKAELVAECVQQMQEAVRIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++++G     +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLCDFIEKVQQAGCREFIVHARKAWLSGLSPKQNREIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   N    +
Sbjct: 197 QLKRDFPHLLISINGGIKTIDEMQQHLQRVDGVMVGREAYQNPSLLGYIDQALFN---AN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+    M  Y  + L  G  L  I RH++  F     +R+ R  L+  
Sbjct: 254 APIVTP------REAVEKMLPYIEQQLSRGVYLNHIVRHILSAFQHCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++ETA   +
Sbjct: 308 AYKEGAGIEVVETALGFV 325


>gi|94986095|ref|YP_605459.1| tRNA-dihydrouridine synthase A [Deinococcus geothermalis DSM 11300]
 gi|94556376|gb|ABF46290.1| tRNA-U16,U17-dihydrouridine synthase [Deinococcus geothermalis DSM
           11300]
          Length = 344

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 187/322 (58%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT   LLYTEM+   AIL GD+   LGFS  E P+ALQ+GG+D +
Sbjct: 16  MMDWTDRHCRAFHRTLTRRTLLYTEMVTTGAILHGDRARHLGFSPAEHPVALQLGGSDPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I +D+GY+E+NLN GCPS RV  GSFGACLM  PD+V   + AM  A ++PVT
Sbjct: 76  ALAECARIAQDWGYDEVNLNCGCPSDRVQNGSFGACLMATPDVVARAVEAMRGATTLPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+++ ++G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 136 VKHRIGIDDLDSYEHLTRFVRTVAEAGCQTFIVHARKAWLSGLSPKENREIPPLRYEVVR 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L + LNGG+  ++ A + L   DGVM+GRAAY++  +L   D          
Sbjct: 196 QLKADFPHLTVVLNGGVLTLAAAQEHLAWADGVMVGRAAYQDPYLLAAADRDLFGEDVTP 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R+   +   Y A  L  G  L ++ RH +GLF G P +R  +  L+  
Sbjct: 256 P---------TRREAIEAFLPYVAAQLAEGQPLHRMMRHTLGLFAGQPGARHWKRTLSER 306

Query: 301 AGASTATHHIIETAFNLMIESL 322
                A   ++  A   + ES+
Sbjct: 307 GHRPGAGLEVVREALAGVPESV 328


>gi|163868285|ref|YP_001609494.1| tRNA-dihydrouridine synthase A [Bartonella tribocorum CIP 105476]
 gi|161017941|emb|CAK01499.1| tRNA-dihydrouridine synthase A [Bartonella tribocorum CIP 105476]
          Length = 327

 Score =  354 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 167/319 (52%), Positives = 219/319 (68%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VADAI+ G ++ +L FS +E P+ALQ+GGAD  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMMVADAIIHGVREQLLAFSHKECPVALQLGGADPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGYNEINLNVGCPS RV  G FGACLML+PDIV + + +M KA++IPVT
Sbjct: 77  KLAEAARIAEDFGYNEINLNVGCPSNRVQAGVFGACLMLHPDIVANAVESMKKAVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q   +AL  L   +  +G + +WIHARKA LKGLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRIGVDEQDEELALDLLADKVWDAGCDALWIHARKAWLKGLSPKENRNIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P  FIG+NGG++ + +  + L   D  M+GR  Y +  +L  +D  F      +
Sbjct: 197 KLKRKYPHKFIGINGGIKSIDEIKEHLVFCDATMVGRQVYHDPTLLKHIDFEFYGESQNN 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  +M DYAARH+ SGG+L  +TRHMIGLFHG   +RR R IL+ +
Sbjct: 257 LSES---------DLIETMCDYAARHIASGGRLSHVTRHMIGLFHGRSGARRWRQILSND 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A  S A  +I+  AF+ +I
Sbjct: 308 ATKSNADIYILREAFSALI 326


>gi|222106594|ref|YP_002547385.1| hypothetical protein Avi_5568 [Agrobacterium vitis S4]
 gi|221737773|gb|ACM38669.1| conserved hypothetical protein [Agrobacterium vitis S4]
          Length = 341

 Score =  354 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 169/318 (53%), Positives = 212/318 (66%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   R F RLLT +ALLYTEMIVADAIL G +  +L F   E PLALQ+GG+D  
Sbjct: 23  MIDWTDTFCRRFHRLLTRHALLYTEMIVADAILHGKRDRLLAFDASEHPLALQLGGSDPH 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  D+GY+EINLNVGCPS RV  G+FGACLM  P  V  CI AM  A ++PVT
Sbjct: 83  KLAEAVRIANDWGYDEINLNVGCPSDRVQAGTFGACLMREPQTVEACIQAMKAASTVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +K +  +G + +WIHARKA L+GLSPK+NR IP LDY +V+
Sbjct: 143 VKCRIGVDDQEPGDVLPDFIKRMIGAGADALWIHARKAWLQGLSPKENRDIPPLDYPLVH 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ENPD+FIG+NGG+ D+ QA   L  +DGVM+GRAAY N+ MLT VD         +
Sbjct: 203 LMKQENPDIFIGINGGVTDLDQASAHLQVMDGVMVGRAAYNNATMLTEVDARIYGEPLQA 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +    DK         M DYAARH+  GG+L  +TRHM+GLF G+  +RR R IL+ +
Sbjct: 263 QNMDIVRDK---------MMDYAARHIAEGGRLVHLTRHMVGLFQGYAGARRFRQILSAD 313

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   +I  AF  +
Sbjct: 314 APKPGAGPDVIAAAFAAV 331


>gi|254362517|ref|ZP_04978621.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|153094117|gb|EDN75017.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
          Length = 325

 Score =  354 bits (909), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 139/318 (43%), Positives = 190/318 (59%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  +  ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 18  MLDWTTRHCRYFHRQFSRQALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+V + GY EINLNVGCPS RV  G FGACLM   D+V DCI AM  A+ IPVT
Sbjct: 77  QLAHCAKLVAERGYAEINLNVGCPSDRVQNGMFGACLMAKADLVADCIKAMQDAVEIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    +   +HARKA L GLSPK+NR+IP LDYD VY
Sbjct: 137 VKHRIGIDDLDSYEFLCDFIEKVQPYSND-FIVHARKAWLTGLSPKENREIPPLDYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N +ML  +D    N    +
Sbjct: 196 QLKRDFPHLKISINGGIKTIEEIKQHLQFVDGVMVGREAYQNPSMLGEIDSQIFNE---N 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       ++    M  Y  R L  G  L  I RHM+G F     +R+ R  L+  
Sbjct: 253 RPLVTA------KEAVEKMFPYIERELAKGIYLNHIVRHMLGAFQHCKGARQWRRHLSEN 306

Query: 301 AGASTATHHIIETAFNLM 318
           A  S A   ++E A   +
Sbjct: 307 ATKSGAGVEVVEQALAFI 324


>gi|291615814|ref|YP_003518556.1| DusA [Pantoea ananatis LMG 20103]
 gi|291150844|gb|ADD75428.1| DusA [Pantoea ananatis LMG 20103]
          Length = 331

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 141/324 (43%), Positives = 194/324 (59%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G   + L +S QE P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTADTLLYTEMVTTGAIIHGKG-DYLAYSEQEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+E+NLNVGCPS RV  G FGACLM    +V D I AM   + IPVT
Sbjct: 74  ALAQCAALAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEAGLVADGIKAMRDVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLTDFIGTVAERGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPQLTIAINGGVKTLEEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGRDRP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AVDPV----------AVVRAMYPYIEAELSKGTYLGHVTRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 304 ENAHKPGADVRVLEAALALVADKI 327


>gi|254282686|ref|ZP_04957654.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR51-B]
 gi|219678889|gb|EED35238.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR51-B]
          Length = 311

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 193/315 (61%), Gaps = 9/315 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+F RLLT  A LYTEM+   A+L GD    L F+  E P+ALQ+GG++  +
Sbjct: 1   MDWTDRHCRYFWRLLTRRARLYTEMVTTGALLHGDVARHLQFNDCEHPIALQLGGSNPEE 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L   A++ ED+GY+E+NLN GCPS RV  G FGACLM   ++V DC+AAMC A ++PVTV
Sbjct: 61  LASCARMAEDWGYDEVNLNCGCPSDRVQNGRFGACLMAEAELVRDCVAAMCDASALPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D Q     LR+ V ++   G     +HARKA L+GLSPK+NR+IP L+Y  VY 
Sbjct: 121 KHRIGIDHQESYNELRDFVGTVASGGARVFIVHARKAWLQGLSPKENREIPPLNYPWVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P L I LNGG+ D+      L  VDGVM+GRAAY+N  +L +VD+          
Sbjct: 181 LKQDFPHLTIVLNGGVTDIPACESHLGKVDGVMLGRAAYQNPWLLASVDQALFGDAPRGQ 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
              +         +  ++  Y  R L  GG+L  +TRH++GL+ G P  +R R +++  A
Sbjct: 241 SRAS---------VLEALMPYIDRELARGGRLNHVTRHVLGLYQGIPGGKRFRRVISENA 291

Query: 302 GASTATHHIIETAFN 316
               AT  ++  A +
Sbjct: 292 HLPNATSDVLRAAMD 306


>gi|254514697|ref|ZP_05126758.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR5-3]
 gi|219676940|gb|EED33305.1| tRNA-dihydrouridine synthase A [gamma proteobacterium NOR5-3]
          Length = 343

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 133/320 (41%), Positives = 194/320 (60%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW++RH R+F RLL+ +A LYTEM+   A++ GD++  L F+ +E P+ALQ+GG++  
Sbjct: 30  MMDWSNRHCRYFWRLLSQHARLYTEMVTTGALIHGDRQRFLQFNAEETPIALQLGGSNPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A   E +GY+E+NLN GCPS RV  G+FGACLM  P++V D ++AM  A  I VT
Sbjct: 90  DLARCAAWAEAWGYDEVNLNCGCPSDRVQNGAFGACLMAEPELVRDAVSAMRSACEIDVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L + V ++   G +   +HARKA LKGLSPK+NR++P L Y  VY
Sbjct: 150 VKHRIGIDHMESYEELCHFVGTVADGGCSVFIVHARKAWLKGLSPKENREVPPLTYPWVY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+E +      L  VDGVM+GR+AY N  +L  VD          
Sbjct: 210 RLKRDFPALTIVINGGIESIDDCEPHLARVDGVMLGRSAYHNPWVLAEVDRRLFG----- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R  +D    I  ++  Y  + L SG +L QITRH++GL+   P ++R R +L+ +
Sbjct: 265 EPQQPRCRED----IIDALMPYVEKELASGTRLNQITRHILGLYQEVPGAKRYRRLLSEQ 320

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++  A N + +
Sbjct: 321 AHRPDAGADVLRAAVNEVTQ 340


>gi|322515077|ref|ZP_08068085.1| tRNA dihydrouridine synthase A [Actinobacillus ureae ATCC 25976]
 gi|322118957|gb|EFX91134.1| tRNA dihydrouridine synthase A [Actinobacillus ureae ATCC 25976]
          Length = 323

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 133/320 (41%), Positives = 188/320 (58%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH R+F R  + +ALLYTEMI A AI+     ++L +   E P+ALQ+GG+D +
Sbjct: 15  MLDWTTRHCRYFHRQFSQHALLYTEMITAPAIIHAKY-DLLEYDPSENPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+VE+ GY EINLNVGCPS RV  G FGACLM   ++V DCI AM   + IPVT
Sbjct: 74  QLAHCAKLVEERGYAEINLNVGCPSDRVQNGMFGACLMAKANLVADCIKAMQDTVQIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++    +   +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 134 VKHRIGIDDLDSYEFLCDFIEKVQPYSND-FIVHARKAWLSGLSPKQNREIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D         +
Sbjct: 193 QLKRDFPHLNISINGGIKTVDEIKQHLVFVDGVMVGREAYQNPSLLGEIDSQIFGE---N 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ T       R+    M  Y       G  L  I RHM+G F     +R+ R  L+  
Sbjct: 250 RPLVTA------REAVEKMLPYIEAQTQKGVYLNHIVRHMLGAFQNCKGARQWRRHLSEN 303

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++E A + + +
Sbjct: 304 ATKQGAGVEVVEQALSFVQK 323


>gi|330967777|gb|EGH68037.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 336

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 85  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++ ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 145 VKHRIGINGRDSYAELCDFVGTVHEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     +   
Sbjct: 205 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQLFGSV--- 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 262 APVISR------HEALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 316 IHKAENPLLLLDQAAKFL 333


>gi|119492928|ref|ZP_01623958.1| hypothetical protein L8106_26412 [Lyngbya sp. PCC 8106]
 gi|119452854|gb|EAW34028.1| hypothetical protein L8106_26412 [Lyngbya sp. PCC 8106]
          Length = 338

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 198/321 (61%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD++ +LGFS +EKPL LQIGG    
Sbjct: 25  MMDRTDRHFRYFMRQITKRTLLYTEMVTSAAIIHGDREKLLGFSPEEKPLVLQIGGDQPQ 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A+I ED GY+++NLNVGCPS+RV +G+FGACLM  P  V + ++ M + + IPVT
Sbjct: 85  ELAICAEIAEDMGYDQVNLNVGCPSSRVQDGNFGACLMAQPQRVAEAVSKMQQRVKIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD+     + N V+ + +SG     +HARKA L+GLSPKDNR IP L Y+ V+
Sbjct: 145 IKHRIGIDDRDRYEDMANFVEIVSQSGCQQFTVHARKAWLQGLSPKDNRNIPPLRYEDVH 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E P LFI +NGGL   SQ  + L SVD VM+GRAAY N  +  T D+ F    T  
Sbjct: 205 QLKQEFPHLFIEINGGLTIFSQVHEQLKSVDAVMLGRAAYDNPYLFATADQEFYGEKT-- 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+          ++  SM  Y    L  G KL  I RH++ LF G P ++  +  L+  
Sbjct: 263 TPLTR-------HQVVESMFPYLEYWLSRGVKLNSIMRHVLQLFSGQPGTKAWKRYLSEN 315

Query: 301 AGASTATHHIIETAFNLMIES 321
              + A   ++  A   + ++
Sbjct: 316 GYLAGAGVEVVREALTQVPQN 336


>gi|90408335|ref|ZP_01216499.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
 gi|90310566|gb|EAS38687.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
          Length = 333

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 183/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+   LLYTEM+   AIL G   + L     E P+ALQ+GG    
Sbjct: 20  MLDWTDRHCRHFHRILSKETLLYTEMVTTGAILYGKG-DYLQKGDAEHPVALQLGGFAAV 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA   ++ GY+EINLN+GCPS RV  G FGACLM  P++V D +AAM  A  +P+T
Sbjct: 79  DLAKAALAGKERGYDEINLNIGCPSDRVQNGRFGACLMAEPELVADAVAAMRDATGLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + +  +   G +   IHARKA L GLSPK NR +P LD+D VY
Sbjct: 139 VKTRIGIDDLDSYEFLCDFISKVHAKGCDNFIIHARKAWLSGLSPKQNRDVPPLDHDRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  +DGVM+GR AY N  +L+ VD+         
Sbjct: 199 QLKKDFPQLMIAINGGIKTLDECKTHLQHLDGVMLGREAYANPYLLSQVDKALFGCTKKP 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               TR       ++   M  Y  + L +G  L  + RHM+GLF G P +R  R  L+  
Sbjct: 259 ---LTRF------EVLEQMYPYIEQQLSNGSYLNHMGRHMLGLFQGLPGARAWRRHLSEN 309

Query: 301 AGASTATHHIIETAFNLMIESL 322
                +   +++ A + + E +
Sbjct: 310 GHLPGSGIEVMQKAASFVTEEI 331


>gi|229512584|ref|ZP_04402054.1| tRNA dihydrouridine synthase A [Vibrio cholerae TMA 21]
 gi|229350366|gb|EEO15316.1| tRNA dihydrouridine synthase A [Vibrio cholerae TMA 21]
          Length = 315

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 133/309 (43%), Positives = 183/309 (59%), Gaps = 11/309 (3%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RLL+   LLYTEM+   AI+ G   + L ++ +E P+ALQ GG++   L   AK+ ++
Sbjct: 11  FHRLLSAQTLLYTEMVTTGAIIHGRG-DFLAYNQEEHPVALQFGGSNPKDLAHCAKLAQE 69

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            GY+EINLNVGCPS RV  G FGACLM  PD+V +C+AAM   + IPVTVK RIG+DDQ 
Sbjct: 70  RGYDEINLNVGCPSDRVQNGRFGACLMGEPDLVAECVAAMRAVVDIPVTVKTRIGIDDQD 129

Query: 132 PAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
               L   + ++ +K G     IHARKA L GLSPK+NR+IP LDY   Y+IK++ P L 
Sbjct: 130 SYEFLTQFIATVAEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRAYQIKRDFPHLT 189

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           I +NGG++ + +A   L  +DGVMIGR AY+N  +L  VD+         +P+K R    
Sbjct: 190 IAVNGGVKSLEEAKLHLQHLDGVMIGREAYQNPYLLAEVDQQIFG---LETPVKKR---- 242

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
              ++   M  Y  R L  G  L  +TRHM+GLF   P +R+ R  ++  A    A   +
Sbjct: 243 --SQVIHEMMPYIERELSQGTHLGHMTRHMLGLFQNMPGARQWRRHISENAHKPGAGLEV 300

Query: 311 IETAFNLMI 319
           +E A   + 
Sbjct: 301 VEQALAKIP 309


>gi|53804232|ref|YP_114112.1| tRNA-dihydrouridine synthase A [Methylococcus capsulatus str. Bath]
 gi|53757993|gb|AAU92284.1| TIM-barrel protein, yjbN family [Methylococcus capsulatus str.
           Bath]
          Length = 360

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 141/306 (46%), Positives = 189/306 (61%), Gaps = 8/306 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL++ + LLYTEM+   AIL GD++ +LGF   E PLA+Q+GG+D  
Sbjct: 35  MMDWTDRHCRFFLRLISRHTLLYTEMVTTAAILHGDRERLLGFHPAEHPLAIQLGGSDPE 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E AKI E  G++E+NLNVGCPS RV  G FGACLM  P+ V DC+ AMC+A+S+PVT
Sbjct: 95  ALAECAKIAEFRGFDEVNLNVGCPSPRVQTGRFGACLMAEPERVADCVRAMCEAVSVPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L + V  + ++G     +HARKA L+GLSPK+NR+ P L YD+V 
Sbjct: 155 VKTRIGIDDRDSYEDLLHFVTIVAEAGCRTFIVHARKAWLQGLSPKENRQTPPLRYDVVR 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L I LNGG++ + +A + L   DGVMIGRAAY N  +L   D          
Sbjct: 215 RLKSELPELAIVLNGGIQTLDEAERHLSWCDGVMIGRAAYHNPYLLAEADRRCYGHSDVR 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              +  V +DF          Y    L  G +L  +TRH++GL+H  P  +R R  ++  
Sbjct: 275 PRTREEVIEDFM--------PYVRNELSKGSRLHALTRHILGLYHATPGGKRWRRHISEG 326

Query: 301 AGASTA 306
           A    A
Sbjct: 327 ASRRGA 332


>gi|330878546|gb|EGH12695.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 339

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++ ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVHEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     +   
Sbjct: 208 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQLFGSV--- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISR------HEALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPLLLLDQAAKFL 336


>gi|213970480|ref|ZP_03398608.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           T1]
 gi|301383868|ref|ZP_07232286.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tomato
           Max13]
 gi|302060592|ref|ZP_07252133.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tomato
           K40]
 gi|213924798|gb|EEB58365.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           T1]
          Length = 339

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     +   
Sbjct: 208 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQLFGSV--- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPLLLLDQAAKFL 336


>gi|332709415|ref|ZP_08429376.1| tRNA dihydrouridine synthase A [Lyngbya majuscula 3L]
 gi|332351674|gb|EGJ31253.1| tRNA dihydrouridine synthase A [Lyngbya majuscula 3L]
          Length = 340

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 140/319 (43%), Positives = 187/319 (58%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRHYR+F R +T   LLYTEM+ + AIL GD++ +LGFS QEKPL LQ+GG   S
Sbjct: 31  MMDRTDRHYRYFMRQITGRTLLYTEMVTSAAILHGDRERLLGFSPQEKPLVLQVGGDTPS 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I E   Y++INLNVGCPS+RV  G+FGACLM  PD V  C+  M K ++IPVT
Sbjct: 91  DLAECARIAEAMDYDQINLNVGCPSSRVQNGNFGACLMAQPDQVARCVEDMVKVVNIPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + N V+ + ++G     +HARKA L+GLSPK+NR +P L Y  V+
Sbjct: 151 VKHRIGIDDLDRYEDMANFVRIVSEAGCQHFTVHARKAWLQGLSPKENRNVPPLRYSDVH 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDLF+ +NGG   + Q  +    VDGVMIGRAAY N  +    D    +     
Sbjct: 211 RLKQELPDLFVEINGGFTSLEQVREQRKYVDGVMIGRAAYDNPYLFAKADCDIYSDT--- 267

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 V      ++  +M  Y    +  G KL +ITRHM+ LF G P SR  +  LT  
Sbjct: 268 ------VIPPTRHQVVEAMFSYIDHWVGKGIKLNKITRHMLQLFAGQPGSRAWKRHLTEN 321

Query: 301 AGASTATHHIIETAFNLMI 319
           +        ++  A   + 
Sbjct: 322 SCLVGVGSDVVREALAKIP 340


>gi|254293797|ref|YP_003059820.1| TIM-barrel protein, yjbN family [Hirschia baltica ATCC 49814]
 gi|254042328|gb|ACT59123.1| TIM-barrel protein, yjbN family [Hirschia baltica ATCC 49814]
          Length = 327

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 153/323 (47%), Positives = 198/323 (61%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R  T  ALLYTEM+ ADA+L GD + ++GF+  E+PLALQ+GG+D  
Sbjct: 14  MMDWTDRHCRMFHRAFTKRALLYTEMVTADALLHGDLEYLIGFNPDEQPLALQLGGSDPI 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL +A+K+ ED+GY+EINLN GCPS RV  G+FGACLM  P+ V +CI+AM  A+ IPVT
Sbjct: 74  KLAQASKVGEDYGYSEINLNCGCPSDRVQSGAFGACLMAQPERVAECISAMQNAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DD  P   L + V ++  +G     +HARKA LKGLSPK+NR IP LDYD+V 
Sbjct: 134 VKCRIGIDDDDPNERLFSFVNTVADAGCQVFIVHARKAWLKGLSPKENRDIPPLDYDLVV 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK  PDL I LNGGL DM  +L  L  +DGVM+GRAAY    +L  VD       T  
Sbjct: 194 RLKKARPDLTISLNGGLVDMEASLDQLSCLDGVMLGRAAYHTPHILGQVDRLVFGETTP- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        +  A+   Y    L  G  L  ITRHM+GLF+G   +++ R  L+  
Sbjct: 253 --------DVSEHQALATYRPYIKAQLEKGTHLHAITRHMMGLFNGKRGAKKWRRYLSEN 304

Query: 301 AGAST--ATHHIIETAFNLMIES 321
           A  +       I++ A   + E 
Sbjct: 305 APGAKGVEAISIVDEAAGFVAEE 327


>gi|289679765|ref|ZP_06500655.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. syringae
           FF5]
          Length = 339

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDESEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ ++ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFGS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|190892270|ref|YP_001978812.1| tRNA-dihydrouridine synthase [Rhizobium etli CIAT 652]
 gi|190697549|gb|ACE91634.1| putative tRNA-dihydrouridine synthase protein [Rhizobium etli CIAT
           652]
          Length = 321

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 163/308 (52%), Positives = 209/308 (67%), Gaps = 9/308 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 1   MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 61  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAGCVAAMKAVSTAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 121 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  F       
Sbjct: 181 RMKQRWPDVFIGINGGIRTLDEAADHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 241 PD---------WPALCERMMAYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSTD 291

Query: 301 AGASTATH 308
           A  S A  
Sbjct: 292 AAKSGAGP 299


>gi|284051988|ref|ZP_06382198.1| tRNA-dihydrouridine synthase A [Arthrospira platensis str. Paraca]
          Length = 331

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 137/319 (42%), Positives = 185/319 (57%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +L FS  EKPLALQ+GG D  
Sbjct: 22  MMDRTDRHFRYFMRQITRRPLLYTEMVTSAAIINGDRHKLLDFSPVEKPLALQVGGDDPE 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+EINLNVGCPSARV  G+FGACLM  P+ V + I+AM KA++IPVT
Sbjct: 82  QLATCAKIAEDWGYDEINLNVGCPSARVQNGNFGACLMAEPERVAEAISAMKKAVNIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     +   V+ +  SG     +HARKA L+GLSPKDNR IP L Y  V+
Sbjct: 142 VKHRIGIDNRDRYEDMTAFVRVVAASGCQRFTVHARKAWLQGLSPKDNRNIPPLRYGDVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG   + Q  + L  VD VM+GRAAY N  +    D          
Sbjct: 202 RLKAEFPHLTIEINGGFTTLEQVKQQLKKVDAVMMGRAAYDNPYLFAIADREIYGDNINP 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++   M  Y    L  GG+L  + RH++ LF G P ++  +  L+  
Sbjct: 262 P---------TRHQVVEQMLPYIENWLSQGGRLNSVVRHILQLFAGQPGTKAWKRHLSEN 312

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +++ A   + 
Sbjct: 313 AHLPGAGVEVVKAALAEVP 331


>gi|254501102|ref|ZP_05113253.1| TIM-barrel protein, yjbN family [Labrenzia alexandrii DFL-11]
 gi|222437173|gb|EEE43852.1| TIM-barrel protein, yjbN family [Labrenzia alexandrii DFL-11]
          Length = 327

 Score =  353 bits (906), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 157/321 (48%), Positives = 206/321 (64%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R L+ +ALLYTEM+   A++ GD+++ILGFS  E P+A Q+GG+D  
Sbjct: 8   MMEWTDRHCRAFHRHLSAHALLYTEMVTTGAVIHGDREHILGFSDLEHPVACQLGGSDPQ 67

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+IVE FGY+E+N+NVGCPS RV  G FGACLM  P +V DC++AM  A++IPVT
Sbjct: 68  AMAEAAQIVEGFGYDEVNINVGCPSDRVQSGRFGACLMEEPQLVADCVSAMKAAVAIPVT 127

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  +      +G + +W+HARKA L+GLSPK+NR +P LDYD V 
Sbjct: 128 VKCRIGVDDQDPEPALDAVADLTFAAGSDALWVHARKAWLQGLSPKENRDVPPLDYDRVV 187

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD FIGLNGGL+ + Q    L  +DG+M GRAAY +  +L  VD       T +
Sbjct: 188 RLKQRLPDKFIGLNGGLDTLEQGEPYLKPLDGLMYGRAAYHSPEILGEVDARLYGAETET 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   MT Y    L  G KL  +TRHM+GLFHG P +R  R ILTVE
Sbjct: 248 ISP--------WDAVRGHMT-YLEDQLSQGVKLAHMTRHMLGLFHGRPGARSWRRILTVE 298

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++E A + +  +
Sbjct: 299 AIKPGAGLEVVEKALDAVSPA 319


>gi|99080805|ref|YP_612959.1| tRNA-dihydrouridine synthase A [Ruegeria sp. TM1040]
 gi|99037085|gb|ABF63697.1| TIM-barrel protein yjbN family [Ruegeria sp. TM1040]
          Length = 336

 Score =  353 bits (906), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 145/321 (45%), Positives = 202/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R  R+  RLL+   LLYTEM+ A A++RG   ++L     E P+ALQ+GG+D  
Sbjct: 22  MMDWTTRECRYLHRLLSRETLLYTEMVTAPALVRGGALHLLDHDPSEHPVALQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++  + GY+EINLN GCPS RV  G+FGA LM  P++V DC+AAM +A+S+ VT
Sbjct: 82  ELAEAARLGAEAGYDEINLNCGCPSDRVQSGAFGAVLMQTPELVADCVAAMAEAVSVEVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  I+ +GV  + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 142 VKCRIGVDDQTPDEILPDFLDKIRAAGVKRVTIHARKAWLQGLSPKENRDIPPLDYELVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K    D+ I LNGG+  + +A   L   +DGVM+GRAAY   A +L   D       T
Sbjct: 202 AMKSAFADMHISLNGGITSLDEAQAQLARGLDGVMVGRAAYHQPADVLCAADPRIYGTGT 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+          ++   M  Y  + + SG +L QITRHM+GLF G P +R+ R  L+
Sbjct: 262 ASDPL----------EVVRQMLPYIEQQMQSGSRLHQITRHMLGLFAGRPGARQWRRHLS 311

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A  + A   ++E A +L++
Sbjct: 312 EGAHRTGAGPELVEEALSLVL 332


>gi|302184838|ref|ZP_07261511.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. syringae
           642]
          Length = 312

 Score =  352 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 61  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 121 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 181 QLKSDFPDLEIVLNGGIKTLEQCSEHLQAFDGVMLGREAYHNPYLLAHVDQQLFGS---T 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 238 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 291

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 292 IHKAGNPMLLLDQAAAFL 309


>gi|295689004|ref|YP_003592697.1| YjbN family TIM-barrel protein [Caulobacter segnis ATCC 21756]
 gi|295430907|gb|ADG10079.1| TIM-barrel protein, yjbN family [Caulobacter segnis ATCC 21756]
          Length = 339

 Score =  352 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 152/323 (47%), Positives = 210/323 (65%), Gaps = 10/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+L++ ALLYTEM+ + A++ GD++ +LGF   + P+ALQ+GG+D +
Sbjct: 15  MMDWTDRHCRSLHRVLSSRALLYTEMVTSGAVVHGDREKLLGFDAGQHPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I ED+GY+EINLNVGCPS RV  G FGACLM  P++V +C+AA+  A+ +P T
Sbjct: 75  DLAQAARIGEDWGYDEINLNVGCPSDRVQSGRFGACLMREPNLVAECMAAIKDAVKVPAT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV     +G++   +HARKA L+GLSPK+NR IP LDY++VY
Sbjct: 135 VKCRIGVDDQDPEESLFTLVDRCAAAGIDNFIVHARKAWLQGLSPKENRDIPPLDYELVY 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+E P+L I +NGG+  +  AL+ L   VDGVM+GRAAY  + +L  VD         
Sbjct: 195 RLKRERPNLTIAINGGVPSVDAALEHLANGVDGVMLGRAAYHEAGLLGEVDRRVFG---- 250

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                   D D +  +      Y AR L +G  L  +TRHM+GLFHG P +R  R ILTV
Sbjct: 251 ----LDVADVDSFEAV-ERYRPYLARELAAGTHLAAMTRHMLGLFHGLPGARAWRRILTV 305

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           E     A   +++ A + +  +L
Sbjct: 306 EGVKPGAGLDVVDRALDAVRAAL 328


>gi|293391683|ref|ZP_06636017.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952217|gb|EFE02336.1| tRNA-dihydrouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 327

 Score =  352 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 130/318 (40%), Positives = 192/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WT RH R+F R  + +ALLYTEM+   AI+     + L F   E+P+ALQ+GG+D +
Sbjct: 18  MLNWTTRHCRYFHRQFSRHALLYTEMVTTQAIIHAKY-DHLDFDPAEQPVALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E  GY EINLNVGCPS RV  G FGACLM   ++V +C+  M +A+ IPVT
Sbjct: 77  QLKHCAQLAEQRGYQEINLNVGCPSDRVQNGMFGACLMAKAELVAECVQQMQEAVRIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ ++++G     +HARKA L GLSPK NR+IP LDY+ VY
Sbjct: 137 VKTRIGIDDFDSYDFLCDFIEKVQQAGCREFIVHARKAWLSGLSPKQNREIPPLDYEQVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   N    +
Sbjct: 197 QLKRDFPHLLISINGGIKTIDEMQQHLQLVDGVMVGREAYQNPSLLGYIDQALFN---AN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PI T       R+    M  Y  + L  G  L  I RH++  F     +R+ R  L+  
Sbjct: 254 APIVTP------REAVEKMLPYIEQQLSRGVYLNHIVRHILSAFQHCKGARQWRRYLSEN 307

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   ++ETA   +
Sbjct: 308 AYKAGAGIEVVETALGFV 325


>gi|300023380|ref|YP_003755991.1| TIM-barrel protein, yjbN family [Hyphomicrobium denitrificans ATCC
           51888]
 gi|299525201|gb|ADJ23670.1| TIM-barrel protein, yjbN family [Hyphomicrobium denitrificans ATCC
           51888]
          Length = 335

 Score =  352 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 153/318 (48%), Positives = 204/318 (64%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+ ADA++ GD+  +LG+S  E P+ALQ+GG+D +
Sbjct: 13  MMDWTDRHCRVFHRQLTTRALLYTEMVTADAVIHGDRARLLGYSEVEHPIALQLGGSDPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I  + GY+EINLNVGCPS RV EG FGACLM  P++V  C+AAM     +PVT
Sbjct: 73  KLAEAARIGAELGYDEINLNVGCPSDRVQEGRFGACLMSEPELVAACVAAMRAHQPVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ     LR  +  +  +G     +HARKA LKGLSPK+NR++P LDY+ VY
Sbjct: 133 VKCRIGIDDQDAEEDLRRFIDVVADAGCTRFVVHARKAWLKGLSPKENREVPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   PDL I +NGG+E + +A   L  VDGVM+GRAAY+N A+L  VD    +  T S
Sbjct: 193 RLKAARPDLEIVINGGIETIEEARAHLDHVDGVMLGRAAYQNPAILADVDRLIFDADTES 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                            +M  Y  +HL  GG+L  +TRH++GL+HG P  +  R  L+  
Sbjct: 253 P---------TRAAALEAMLPYIEQHLKRGGRLSNVTRHVLGLYHGQPRGKTFRRHLSEG 303

Query: 301 AGASTATHHIIETAFNLM 318
           A ++ AT  ++  A  ++
Sbjct: 304 ATSADATADVLREAIAIV 321


>gi|146282034|ref|YP_001172187.1| tRNA-dihydrouridine synthase A [Pseudomonas stutzeri A1501]
 gi|145570239|gb|ABP79345.1| TIM-barrel protein, yjbN family [Pseudomonas stutzeri A1501]
          Length = 334

 Score =  352 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L GD    L +   E PLALQ+GG+   
Sbjct: 23  MMDWTDRHCRFFLRQLSKHALLYTEMVTTGALLHGDTARFLRYDESEHPLALQLGGSVPG 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ + VT
Sbjct: 83  DLAACAKLAEVAGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCVKAMRDAVGVEVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK NR++P L YD+  
Sbjct: 143 VKHRIGINGRDSYSQLCDFVGQVREAGCRSFTVHARIAILEGLSPKQNREVPPLRYDVAA 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +  + L + DGVM+GR AY N  +L  VD         +
Sbjct: 203 QLKRDFPDLEIILNGGIKTLEECREHLQTFDGVMLGREAYHNPYLLAQVDSSLFG---NN 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   +M  Y  RHL  GG +  +TRH++GL  GFP +RR R +L+V+
Sbjct: 260 APVISRA------QALRNMRPYIERHLAEGGAMHHVTRHVLGLGQGFPGARRFRQLLSVD 313

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 314 IHKTDEPLALLDQATALL 331


>gi|218510078|ref|ZP_03507956.1| tRNA-dihydrouridine synthase A [Rhizobium etli Brasil 5]
          Length = 301

 Score =  352 bits (904), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 163/310 (52%), Positives = 210/310 (67%), Gaps = 9/310 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 1   MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 61  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAGCVAAMKAVSTAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 121 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+FIG+NGG+  + +A   L  VDGVM+GRAAY+N+A+L  VD  F       
Sbjct: 181 RMKQRWPDVFIGINGGIRTLDEAADHLARVDGVMLGRAAYQNAAVLADVDHRFFGAPAAE 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                      W  +   M  YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ +
Sbjct: 241 PD---------WPALCERMMAYAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSTD 291

Query: 301 AGASTATHHI 310
           A  S A   +
Sbjct: 292 AAKSGAGPEV 301


>gi|163743186|ref|ZP_02150568.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis 2.10]
 gi|161383603|gb|EDQ07990.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis 2.10]
          Length = 390

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 147/321 (45%), Positives = 201/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL++  LLYTEM+ A A++RG   ++L  S QE P+ALQ+GG+D +
Sbjct: 76  MMDWTDRHCRYLHRLLSHETLLYTEMVTAPALVRGGALHLLDHSPQEHPVALQLGGSDPA 135

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+   + GY+EINLN GCPS RV  G+FGA LM +PD+V +C+AAM   + + VT
Sbjct: 136 ELAQAAEFGAEAGYDEINLNCGCPSDRVQSGAFGAVLMKSPDLVAECVAAMQAKVDVEVT 195

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I  +G   + IHARKA LKGLSPK+NR IP LDY+IV+
Sbjct: 196 VKCRIGVDDQDPQEVLPVFLERIAAAGCERVTIHARKAWLKGLSPKENRDIPPLDYEIVH 255

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K E P L I LNGG+  + +AL  L   +DGVMIGRAAY   + +L+  D       +
Sbjct: 256 QMKAEFPQLHISLNGGVASLDEALPHLERGLDGVMIGRAAYHQPSDILSQADPLIFGTGS 315

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 316 ATDPV----------AVVGHMLGYIDDQMAQGARLHQITRHMLGLFAGRPGARNWRRVLS 365

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   ++ETA   + 
Sbjct: 366 EGASRPGADTRLVETALEQVT 386


>gi|104782703|ref|YP_609201.1| tRNA-dihydrouridine synthase A [Pseudomonas entomophila L48]
 gi|95111690|emb|CAK16414.1| tRNA-dihydrouridine synthase A [Pseudomonas entomophila L48]
          Length = 333

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ +ALLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 22  MMDWTDRHCRFFLRLLSKHALLYTEMVTTGALLHNDAHRFLRHDDSEHPLALQLGGSVPA 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 82  DLAACARLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMQDAVSIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 142 VKHRIGINGRDSYAELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL + LNGG++ + +    L + DGVM+GR AY N  +L  VD+        S
Sbjct: 202 QLKADFPDLELVLNGGIKTLEECRTHLETFDGVMLGREAYHNPYLLAEVDQQLFGS---S 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R +        A +  Y   H+ SGG +  ITRH++GL  GFP +RR R +L+ +
Sbjct: 259 EPVISRAEAM------AKLRPYIVAHMESGGAMHHITRHILGLGQGFPGARRFRQLLSAD 312

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 313 IHKTDTPLAVLDQAAELL 330


>gi|197105805|ref|YP_002131182.1| tRNA-dihydrouridine synthase [Phenylobacterium zucineum HLK1]
 gi|196479225|gb|ACG78753.1| tRNA-dihydrouridine synthase [Phenylobacterium zucineum HLK1]
          Length = 343

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 150/320 (46%), Positives = 198/320 (61%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R L++ ALLYTEM+   A+L GD++ +L +   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDRHCRVLHRTLSSRALLYTEMLTTGAVLHGDRERLLAYDPVEHPVALQLGGSEPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA+I E  GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM  A+ +PVT
Sbjct: 74  ELAAAARIGEAEGYDEINLNVGCPSDRVQSGRFGACLMREPELVAECMAAMGAAVKVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV    ++GV    +HARKA LKGLSPK+NR +P LDY +V+
Sbjct: 134 VKCRIGVDDQDPEESLFTLVDLCAEAGVTSFVVHARKAWLKGLSPKENRDVPPLDYPLVW 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E PDL I +NGG+  + +A   L  VDGVM+GRAAY    +L   D          
Sbjct: 194 RLKAERPDLTIVINGGIGSLDEAEDHLRHVDGVMLGRAAYHTPDLLGQADARIFGEDRRV 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SP           +   +   Y A  L  G  L  +TRHM+GLFHG P +R  R ILTV+
Sbjct: 254 SPF----------EAVEAFRPYVAGQLARGTHLAAMTRHMLGLFHGVPGARAWRRILTVD 303

Query: 301 AGASTATHHIIETAFNLMIE 320
              + A   +I+ A   + E
Sbjct: 304 GVKAGAGLEVIDRALAAVSE 323


>gi|327396079|dbj|BAK13501.1| tRNA-dihydrouridine synthase A DusA [Pantoea ananatis AJ13355]
          Length = 331

 Score =  352 bits (903), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 141/324 (43%), Positives = 194/324 (59%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT + LLYTEM+   AI+ G   + L +S QE P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHCRYFHRQLTADTLLYTEMVTTGAIIHGKG-DYLAYSEQEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A + E  GY+E+NLNVGCPS RV  G FGACLM    +V D I AM   + IPVT
Sbjct: 74  ALAQCAALAEQRGYDEVNLNVGCPSDRVQNGRFGACLMAEAGLVADGIKAMRDVVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++ ++ G +   IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 134 VKTRIGIDDQDSYAFLTDFIGTVAERGGCDTFIIHARKAWLSGLSPKENREIPPLDYPRV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L I +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E F     
Sbjct: 194 YQLKRDFPQLTIAINGGVKTLGEAKTHLQHLDGVMMGREAYQNPGILAQVDRELFGRDRP 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P+           +  +M  Y    L  G  L  +TRHM+GLF G P +R+ R  L+
Sbjct: 254 AVDPV----------AVVRAMYPYIEAELSKGTYLGHVTRHMLGLFQGIPGARQWRRHLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A  L+ + +
Sbjct: 304 ENAHKPGADVRVLEAALALVADKI 327


>gi|240850670|ref|YP_002972070.1| tRNA-dihydrouridine synthase A [Bartonella grahamii as4aup]
 gi|240267793|gb|ACS51381.1| tRNA-dihydrouridine synthase A [Bartonella grahamii as4aup]
          Length = 326

 Score =  352 bits (903), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 163/319 (51%), Positives = 218/319 (68%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VAD+++ G ++ +L FS +E+P+ALQ+GGAD  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMMVADSVIHGVREQLLAFSDKERPVALQLGGADPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGYNEINLNVGCPS RV  G FGACLM +PDIV + + AM + ++IPVT
Sbjct: 77  KLAEAARIAEDFGYNEINLNVGCPSNRVQAGVFGACLMRHPDIVANAVEAMKREVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q   +AL  L   +  +G + +WIHARKA L+GLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRIGVDEQDEELALDLLANQVWNAGCDALWIHARKAWLQGLSPKENRNIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P  FIG+NGG++ + +  + L   D VM+GR  Y + A+L  +D    +    +
Sbjct: 197 KLKRKYPHKFIGINGGIKSIDEIKEHLTFCDAVMLGRQVYHDPALLKHIDFELYDEARNN 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +   M DYAARH+ SGG+L  +TRHMIGLFHG   +RR R IL+ +
Sbjct: 257 LSES---------DLIEVMCDYAARHIASGGRLSHVTRHMIGLFHGRGGARRWRQILSND 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A  S A   I++ AF  +I
Sbjct: 308 ATKSNADICILKEAFYALI 326


>gi|291568895|dbj|BAI91167.1| hypothetical protein [Arthrospira platensis NIES-39]
          Length = 337

 Score =  351 bits (902), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 137/319 (42%), Positives = 185/319 (57%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AI+ GD+  +L FS  EKPLALQ+GG D  
Sbjct: 28  MMDRTDRHFRYFMRQITRRPLLYTEMVTSAAIINGDRHKLLDFSPVEKPLALQVGGDDPE 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI ED+GY+EINLNVGCPSARV  G+FGACLM  P+ V + I+AM KA++IPVT
Sbjct: 88  QLATCAKIAEDWGYDEINLNVGCPSARVQNGNFGACLMAEPERVAEAISAMKKAVNIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     +   V+ +  SG     +HARKA L+GLSPKDNR IP L Y  V+
Sbjct: 148 VKHRIGIDNRDRYEDMTAFVRVVAASGCQRFTVHARKAWLQGLSPKDNRNIPPLRYGDVH 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG   + Q  + L  VD VM+GRAAY N  +    D          
Sbjct: 208 RLKAEFPHLTIEINGGFTTLEQVKQQLKKVDAVMMGRAAYDNPYLFAIADREIYGDNINP 267

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++   M  Y    L  GG+L  + RH++ LF G P ++  +  L+  
Sbjct: 268 P---------TRHQVVEQMLPYIENWLSQGGRLNSVVRHILQLFAGQPGTKAWKRHLSEN 318

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +++ A   + 
Sbjct: 319 AHLPGAGVEVVKAALAEVP 337


>gi|108761431|ref|YP_630504.1| tRNA-dihydrouridine synthase A [Myxococcus xanthus DK 1622]
 gi|108465311|gb|ABF90496.1| tRNA-dihydrouridine synthase A [Myxococcus xanthus DK 1622]
          Length = 332

 Score =  351 bits (902), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR+ R+F R L+ + LLYTEM+   AIL GD++ +LG+   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDRNCRYFHRQLSRHTLLYTEMVTTGAILHGDRERLLGYDAAEHPVALQLGGSEPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+A+I E +GY+EINLNVGCPS RV  G FGACLM  PD+V   + AM +A+SIPVT
Sbjct: 74  ALAESARIGEQWGYDEINLNVGCPSDRVQSGRFGACLMAEPDLVARLVGAMREAVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +D+      L   ++ +  +G     +HARKA L+GLSPK+NR +P L YD+V+
Sbjct: 134 VKSRIAIDELEEWPTLEGFIRKVSAAGCTRFIVHARKAWLQGLSPKENRDVPPLRYDLVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG++ +  A + L  VDGVM+GRA Y+N  +L   D  F    T  
Sbjct: 194 RLKVEFPHLDISINGGIKTLDAAAEQLRHVDGVMMGRAPYENPYLLAEADRRFFGATT-- 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+  R       ++  +M  Y  + +  G  L  ITRHM+GLF G P +R  R  L+  
Sbjct: 252 -PVPQR------HEVVEAMLPYIEKAMLRGAPLGAITRHMLGLFQGLPGARAWRRHLSEN 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   +
Sbjct: 305 AHKQGAGPEVVVAALAKV 322


>gi|330954517|gb|EGH54777.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae Cit 7]
          Length = 312

 Score =  351 bits (902), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSKAA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 61  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 121 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L S DGVM+GR AY N  +L  VD+        +
Sbjct: 181 QLKSDFPDLEIVLNGGIKTLEQCSEHLQSFDGVMLGREAYHNPYLLAHVDQQLFGS---T 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 238 APVISRYDA------LESMRPYIAEHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 291

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 292 IHKAENPMLLLDQAAAFL 309


>gi|152987423|ref|YP_001347729.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PA7]
 gi|150962581|gb|ABR84606.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PA7]
          Length = 334

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 23  MMDWTDRHCRFFLRQLSRHALLYTEMVTTGALLHGDRQRFLRHDECEHPLALQLGGSVPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 83  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMRDAVEIPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     LR+ V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 143 VKHRIGINGRDSYAELRDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 203 QLKKDFPDLEIVLNGGIKTLEDCREHLRTFDGVMLGREAYHNPYLLAAVDSQLFGSQV-- 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 261 -PPPSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 313

Query: 301 AGASTATHHIIETAFNLM 318
              S     + + A  L+
Sbjct: 314 VHKSADPLRVFDQALELL 331


>gi|66045176|ref|YP_235017.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. syringae
           B728a]
 gi|63255883|gb|AAY36979.1| Dihydrouridine synthase TIM-barrel protein yjbN [Pseudomonas
           syringae pv. syringae B728a]
          Length = 339

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ ++ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPGLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFGS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|170718234|ref|YP_001785255.1| tRNA-dihydrouridine synthase A [Haemophilus somnus 2336]
 gi|168826363|gb|ACA31734.1| TIM-barrel protein, yjbN family [Haemophilus somnus 2336]
          Length = 328

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 130/321 (40%), Positives = 183/321 (57%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT RH RFF R  +   LLYTEM+   AI+     + L +   E P+ALQ+GG+D  
Sbjct: 18  MLDWTTRHCRFFHRQFSRYTLLYTEMVTTGAIIHAKY-DHLAYDVSENPVALQLGGSDPE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL   AK  E+ GY EINLNVGCPS RV  G FGACLM    +V +C+ AM  A++IPVT
Sbjct: 77  KLQYCAKKGEERGYQEINLNVGCPSDRVQNGMFGACLMARAALVAECVNAMQSAVNIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L + ++ +   G     IHARKA L GLSPK+NR+IP L+Y+ VY
Sbjct: 137 VKTRLGIDEFDSYEFLCDFIEKVHNIGCQEFIIHARKAWLSGLSPKENREIPPLNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +  + L  VDGVM+GR AY+N ++L  +D+   +P    
Sbjct: 197 QLKKDFPHLLISINGGIKTLEEIQQHLNYVDGVMVGREAYQNPSLLGYIDQALFDPSCAI 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R+   +M  Y  + L  G  L  I RH++G F     +R+ R  ++  
Sbjct: 257 ITP---------RQAIENMFPYIEQQLSQGVYLNHIARHLLGAFQQCKGARQWRRYMSEN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
              S A   +IE A   + E 
Sbjct: 308 IHKSHAGVEVIEKALTFIEEK 328


>gi|328544451|ref|YP_004304560.1| TRNA-dihydrouridine synthase A [polymorphum gilvum SL003B-26A1]
 gi|326414193|gb|ADZ71256.1| TRNA-dihydrouridine synthase A [Polymorphum gilvum SL003B-26A1]
          Length = 320

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 160/317 (50%), Positives = 211/317 (66%), Gaps = 9/317 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F R  T+ ALLYTEM+   A+L GD++ +LGFS  E PLA Q+GGA+ + 
Sbjct: 1   MDWTDRHCRAFHRQFTHRALLYTEMVTTGAVLHGDRERLLGFSAVEHPLACQLGGAEPAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L +AA+IVE FGY+E+NLNVGCPS RV  G FGACLM  P +VGDC+AAM  A++IPVTV
Sbjct: 61  LAQAARIVEAFGYDEVNLNVGCPSDRVQSGRFGACLMHEPQLVGDCVAAMKAAVAIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIGVDDQ   +AL  L  ++  +GV+G+W+HARKA L+GLSPK+NR +P LDY  V  
Sbjct: 121 KCRIGVDDQDAEIALDTLADAVVAAGVDGLWVHARKAWLQGLSPKENRDVPPLDYGRVIR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K+  PDLF+G+NGG+ D+ QA  +L  +DGVM+GRAAY +  +L  VD          +
Sbjct: 181 LKRRLPDLFVGVNGGIADLDQAETLLADLDGVMLGRAAYHDPGLLGAVDRRLYGD---EA 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P +T V+         +   Y A  L  G +L  +TRHM+G FHG P +R  R ILTVEA
Sbjct: 238 PDRTPVEA------VEAFLPYVADRLAEGVRLSHMTRHMLGAFHGRPGARAFRRILTVEA 291

Query: 302 GASTATHHIIETAFNLM 318
               A   ++  A + +
Sbjct: 292 VRPGAGIEVVHRALDAV 308


>gi|90416108|ref|ZP_01224041.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2207]
 gi|90332482|gb|EAS47679.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2207]
          Length = 322

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 194/316 (61%), Gaps = 9/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + +LYTEM+   AI+ GD    L     E P+ALQ+GG+  +
Sbjct: 11  MLDWTDRHCRYFLRLISQHTMLYTEMLTTGAIIHGDSDYHLQMDAFEHPVALQLGGSSPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  A K+   + Y EINLN GCPS RV  G FGA +M + +I  +C++AM +A+ +P+T
Sbjct: 71  DLATACKMAAQYDYAEINLNCGCPSDRVQNGMFGAVMMKDAEITANCVSAMREAVDLPIT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      LR+ V  + +SG     +HARKA LKGLSPK NR+IP L+YD VY
Sbjct: 131 VKHRIGVDEYDSYEFLRDFVGRVTESGCEVFLVHARKAWLKGLSPKQNREIPELNYDRVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P L I +NGG+  + Q+ + L  +DGVM+GR  Y N  +L +VD+       G 
Sbjct: 191 RLKKDFPQLEIIINGGVTTLEQSKEHLQHLDGVMVGREVYSNPYLLASVDQDIYGASHG- 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +KTR      R+I+     YA   L  G KL  +TRH++GLFHG P +R+ R  ++  
Sbjct: 250 --VKTR------RQIAEEFLQYADNELSKGTKLNAMTRHILGLFHGMPGARQFRRHISEN 301

Query: 301 AGASTATHHIIETAFN 316
           A   +AT  ++ TA +
Sbjct: 302 AHKPSATIEVLSTALS 317


>gi|154248170|ref|YP_001419128.1| tRNA-dihydrouridine synthase A [Xanthobacter autotrophicus Py2]
 gi|154162255|gb|ABS69471.1| TIM-barrel protein, yjbN family [Xanthobacter autotrophicus Py2]
          Length = 330

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 150/318 (47%), Positives = 203/318 (63%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  A LYTEM+ A AIL GD+  +LGFS +E P+A+Q+GG+D +
Sbjct: 14  MMDWTDRHCRAFHRTLSRRARLYTEMVTAPAILHGDRARLLGFSPEEHPVAVQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I  D+GY+EINLNVGCPS RV  G+FGACLM  PD+V DC+AAM   ++IPVT
Sbjct: 74  ELAQAARICADYGYDEINLNVGCPSDRVQGGNFGACLMREPDLVADCVAAMKAVVAIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  ++  +G + + +HARKA LKGLSP++NR IP LDYD V 
Sbjct: 134 VKCRIGVDDQDPEEALDRLADAVVAAGTDALIVHARKAWLKGLSPRENRDIPPLDYDRVR 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + I +NGG+  ++Q L+    +DG+M+GRAAY++  +L  VD          
Sbjct: 194 RLKARLPHVPIAVNGGIASIAQGLEEARGLDGMMLGRAAYQDPELLLGVDPLLFGTPAPH 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     V+             Y A HL +GG+L  ITRHM+GLF G   +R  R  L+ E
Sbjct: 254 ADGFAAVEA---------FEPYVAHHLEAGGRLSDITRHMLGLFTGRKGARIFRRHLSTE 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A + +
Sbjct: 305 AIRPGAGLDVLRAAVDEV 322


>gi|330973923|gb|EGH73989.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 339

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ ++ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAQEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPGLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFGS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|312114498|ref|YP_004012094.1| TIM-barrel protein, yjbN family [Rhodomicrobium vannielii ATCC
           17100]
 gi|311219627|gb|ADP70995.1| TIM-barrel protein, yjbN family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 343

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 148/319 (46%), Positives = 198/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+  A LYTEM+ + AI+ GD++ +LGF   E P+ALQ+GG+D  
Sbjct: 22  MMDWTDRHCRFFHRQLSRRARLYTEMVTSGAIMFGDRERLLGFDASEHPVALQLGGSDPV 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
           +L  AA+I   FGY+EINLN GCPS RV  G FGACLM  P++V  C+AA+  A+   IP
Sbjct: 82  ELARAAEIGAGFGYDEINLNCGCPSDRVQSGRFGACLMAEPELVASCVAAIKSAVGGQIP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG+D+Q     L   ++++  SG     +HARKA LKGLSP++NR +P LDY+ 
Sbjct: 142 VTVKNRIGIDEQDSEADLTRFIETVAASGCEIFIVHARKAWLKGLSPRENRDVPPLDYER 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K   P+L I +NGG+E ++Q+ K L  VDGVM+GRAAYKN A+L  VD        
Sbjct: 202 VYRLKAAFPELTIIINGGIETIAQSAKHLEMVDGVMLGRAAYKNPALLLEVDAALYGET- 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P++         +    M  Y  R L  G +L  I RHM+GL +G P +R  R +LT
Sbjct: 261 -AAPLRP-------HEALERMLPYIERELERGTRLSAIARHMLGLVNGRPGARPFRRLLT 312

Query: 299 VEAGASTATHHIIETAFNL 317
            E+    A   II  A   
Sbjct: 313 EESVKPGAGLDIIHAAIEA 331


>gi|148254870|ref|YP_001239455.1| tRNA-dihydrouridine synthase A [Bradyrhizobium sp. BTAi1]
 gi|146407043|gb|ABQ35549.1| tRNA-U16,U17-dihydrouridine synthase [Bradyrhizobium sp. BTAi1]
          Length = 318

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 146/319 (45%), Positives = 198/319 (62%), Gaps = 9/319 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F RLL+  ALLYTEM+   A++ GD+K +LGF   E P+ALQ+GG+D + 
Sbjct: 1   MDWTDRHCRVFHRLLSRRALLYTEMVTTGAVIHGDRKRLLGFDASEHPVALQLGGSDPAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  +A+I EDFGY+EINLNVGCPS RV +G FGACLM  P++V  C+AAM +A+ IPVTV
Sbjct: 61  LATSARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPELVAACVAAMKRAVRIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIG+DDQ P +AL  L  ++  +G + + +HARKA L GLSPK+NR+IP LDYD VY 
Sbjct: 121 KCRIGIDDQDPELALDTLADAVVDAGADALIVHARKAWLNGLSPKENREIPPLDYDRVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K   P++ + +NGG+  ++ A   L  VDGVM+GRAAY+    L  VD           
Sbjct: 181 LKARLPNVPVIINGGITSIAAAQAHLAHVDGVMLGRAAYQEPWQLLDVDPMLFGDAAPHR 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
            +K            A++  Y  R L  G +L  ITRH++G +H  P +R  R  L    
Sbjct: 241 SMK---------DALAALEPYIERQLREGSRLHAITRHLVGAYHAVPGARAFRRHLAERG 291

Query: 302 GASTATHHIIETAFNLMIE 320
               A   ++  A  ++ E
Sbjct: 292 VKPDAGIEVLREAVAMVEE 310


>gi|297565479|ref|YP_003684451.1| TIM-barrel protein, yjbN family [Meiothermus silvanus DSM 9946]
 gi|296849928|gb|ADH62943.1| TIM-barrel protein, yjbN family [Meiothermus silvanus DSM 9946]
          Length = 345

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 135/321 (42%), Positives = 188/321 (58%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+  RL +    LYTEM+   AIL G++  +L F   E P+ALQ+GG+D +
Sbjct: 15  MLDWTDRHFRYLVRLCSRGVRLYTEMVTDRAILHGNRPRLLDFDPSEHPVALQLGGSDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I +D+GY+EINLN+GCPS RV  G FGACLM  PD+V +C AAM +A+ +PVT
Sbjct: 75  LLAEAARIGQDWGYDEINLNLGCPSERVQGGGFGACLMKEPDLVAECFAAMREAVQLPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+GVDD      L   V+ +   GV    +HARKA L+GLSPK+NR+IP L Y  VY
Sbjct: 135 AKHRLGVDDLEDYGYLARFVEKLASVGVEVFIVHARKAWLQGLSPKENREIPELRYGWVY 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L   LNGG++ + +A   L  VDGVM+GRA Y++  +L   D  F       
Sbjct: 195 RLKEDFPHLIFVLNGGVKTLDEAGAHLEHVDGVMLGRAVYEDPFVLEEADRRFFGLEHRP 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +          +++ +M  YA   L  G  L  I RHM+ LF G    +R R  L+  
Sbjct: 255 QRL----------QVAQAMIAYAEARLEEGVPLWSIARHMLNLFKGQRGGKRWRRYLSEH 304

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   ++  A   + ++
Sbjct: 305 AIRPQAKAQVLWEALEQVTKT 325


>gi|90418092|ref|ZP_01226004.1| tRNA-dihydrouridine synthase A [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90337764|gb|EAS51415.1| tRNA-dihydrouridine synthase A [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 351

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 171/318 (53%), Positives = 215/318 (67%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT +ALLYTEM+VADAIL GD+  +LG    E PLALQIGG++  
Sbjct: 33  MIDWTDRHCRFFHRQLTWHALLYTEMVVADAILHGDRDRLLGHDAVESPLALQIGGSEPQ 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I  DFGY+EINLNVGCPS RV  G+FGACLM  PD+VG C+AAM +A  +PVT
Sbjct: 93  KLAEACRIAADFGYDEINLNVGCPSDRVQSGAFGACLMREPDLVGRCLAAMAEASDVPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL +L  +   +GV  IW+HARKA L+GLSPK+NR IP LDYD V+
Sbjct: 153 VKCRIGVDEQDPEPALDDLADAAIAAGVTTIWVHARKAWLQGLSPKENRDIPPLDYDRVH 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+ F+GLNGGL  +  A++ L  VDGVM+GRAAY+    L  VD          
Sbjct: 213 RLKQRLPEAFVGLNGGLTTLDAAVEELDRVDGVMMGRAAYQTPDRLAEVDARVFG--AAP 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+        +  +  +M DYAARHL  GG+L Q+TRHM+GLF+G P +RR R IL+  
Sbjct: 271 RPVD-------YAALIDTMADYAARHLERGGRLGQVTRHMLGLFNGMPGARRWRQILSDG 323

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  AF  +
Sbjct: 324 AVRPNAGPQLLREAFAAV 341


>gi|254509778|ref|ZP_05121845.1| tRNA-dihydrouridine synthase A [Rhodobacteraceae bacterium KLH11]
 gi|221533489|gb|EEE36477.1| tRNA-dihydrouridine synthase A [Rhodobacteraceae bacterium KLH11]
          Length = 320

 Score =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 144/321 (44%), Positives = 194/321 (60%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L  + QE P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSAQTLLYTEMVTAPALVRGGALHLLKHNPQEHPVALQLGGSDPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM  P  V DC+ AM +A+ + VT
Sbjct: 61  ELAKAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMREPTRVADCVRAMQEAVDVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L   ++ I  +G   + IHARKA L+GLSPK+NR IP LDY +V+
Sbjct: 121 VKCRIGVDEQEPHAVLPAFLEQISAAGCQRVTIHARKAWLQGLSPKENRDIPPLDYALVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   P L I +NGG+  ++QA + L   +DGVMIGRAAY     +L   D        
Sbjct: 181 RMKAAFPALHISINGGITSLAQAQEQLEAGLDGVMIGRAAYHQPTDILAAADAQIFGTGR 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P           ++   M  Y   HL  GG+L QITRHM+GLF G P +R  R IL+
Sbjct: 241 IVDPT----------EVVQEMLPYVEAHLTEGGRLHQITRHMLGLFAGRPGARHWRRILS 290

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   +I  A + ++
Sbjct: 291 EGAVRDQAGPEVILQALDAIM 311


>gi|320329184|gb|EFW85181.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 339

 Score =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 200/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|167032718|ref|YP_001667949.1| tRNA-dihydrouridine synthase A [Pseudomonas putida GB-1]
 gi|166859206|gb|ABY97613.1| TIM-barrel protein, yjbN family [Pseudomonas putida GB-1]
          Length = 336

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 192/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D +  L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKQTLLYTEMVTTGALLHNDAQRFLRHDASEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ED GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 85  DLAACARLAEDAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + +  K L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKADFPDLEIVLNGGIKTLDECQKHLETFDGVMLGREAYHNPYLLAEVDQQL---FASD 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +  A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 262 APVVSR------SEALAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKAAEPLAVFDQAMELL 333


>gi|217978983|ref|YP_002363130.1| TIM-barrel protein, yjbN family [Methylocella silvestris BL2]
 gi|217504359|gb|ACK51768.1| TIM-barrel protein, yjbN family [Methylocella silvestris BL2]
          Length = 335

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 151/318 (47%), Positives = 196/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT  A LYTEM+   A+L G +  +LGF   E PLA Q+GG+D +
Sbjct: 14  MMDWTDRHCRSFHRLLTRRARLYTEMVTTGAVLHGQRDRLLGFDAAEHPLAAQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY+EINLN GCPS RV  G+FGACLM  P++VGDC+AAM  A+S PVT
Sbjct: 74  DLAAAARICADFGYDEINLNAGCPSKRVQNGAFGACLMREPELVGDCVAAMKAAVSAPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL    +++  +G + + +HARKA L+GLSPKDNR IP LDY +V+
Sbjct: 134 VKCRIGVDEQEPREALFAFAETVLGAGADALIVHARKAWLEGLSPKDNRHIPPLDYALVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+  PD  I +NGGL+ +      L  VDGVMIGRAAY++ A+L  VD  F       
Sbjct: 194 ELKRRFPDTPIAINGGLDTIDAMRAQLDHVDGVMIGRAAYQDPALLLEVDPVFFGEDAPF 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            +   + T Y A  L  G  L  + RH++G F+G P +R  R  L  E
Sbjct: 254 S---------EMAQAIEAFTPYIAARLTEGVPLNAMVRHLLGAFNGRPGARAFRRHLATE 304

Query: 301 AGASTATHHIIETAFNLM 318
           +    A   ++  A  L+
Sbjct: 305 SVKPGAGLEVLRAALALI 322


>gi|114569505|ref|YP_756185.1| tRNA-dihydrouridine synthase A [Maricaulis maris MCS10]
 gi|114339967|gb|ABI65247.1| tRNA-U16,U17-dihydrouridine synthase [Maricaulis maris MCS10]
          Length = 353

 Score =  349 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 158/318 (49%), Positives = 204/318 (64%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+LT  ALLYTEM V  AI+ GD   ++GF   E P+A+Q+GG+D  
Sbjct: 38  MMDWTDRHCRAFHRVLTRRALLYTEMAVDKAIIHGDTARLIGFDAAEHPVAIQLGGSDPG 97

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A+K  E FGY EINLNVGCPS RV  G FGACLM  PD+V DC+AAM  A+S+PVT
Sbjct: 98  ELAQASKTAEGFGYCEINLNVGCPSDRVQSGRFGACLMQEPDLVADCVAAMQDAVSVPVT 157

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  LV ++   GV    +HARKA LKGLSPK+NR +P LDY +V+
Sbjct: 158 VKCRIGVDDQEPEQALFTLVDTVAARGVTSFAVHARKAWLKGLSPKENRSVPPLDYALVH 217

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L I LNGGL+D+  A+     +DG MIGRAAY    +L  VD         +
Sbjct: 218 RLKAERPELEIILNGGLQDLDHAISESTGLDGAMIGRAAYHTPWILARVDSAVFGE---T 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ TR       +  A+   Y A  L  GG+L  ITRHM+GL+ G P +R+ R IL+ +
Sbjct: 275 DPVATR------SQALAAFRPYIAACLDEGGRLHDITRHMMGLYAGEPGARQWRRILSEK 328

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   +++ A   +
Sbjct: 329 ATRAGAGLDVLDEAQAAV 346


>gi|298486443|ref|ZP_07004503.1| tRNA dihydrouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298158920|gb|EFH99980.1| tRNA dihydrouridine synthase A [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 339

 Score =  349 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 200/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|77460046|ref|YP_349553.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens Pf0-1]
 gi|77384049|gb|ABA75562.1| tRNA-U16,U17-dihydrouridine synthase [Pseudomonas fluorescens
           Pf0-1]
          Length = 331

 Score =  349 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+L+ NALLYTEM+   A+L GD +  L  +  E PLALQ+GG+   
Sbjct: 20  MMDWTDRHCRYFLRILSKNALLYTEMVTTGALLNGDHERFLRHNEAEHPLALQLGGSVPL 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 80  DLAACARMAQEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V +++ +G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 140 VKHRIGINGRDSYEELCDFVGTVRDAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P+L   LNGG++ M    + L + DGVM+GR AY N  +L  VD+        S
Sbjct: 200 RLKADFPELEFILNGGIKTMEACHEHLQTFDGVMLGREAYHNPYLLAEVDQQLFGS---S 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +        A +  Y A HL +GG +  ITRH++GL  GFP +R+ R +L+V+
Sbjct: 257 APVISRAEA------LAQLRPYIAEHLLAGGAMHHITRHVLGLGTGFPGARKFRQLLSVD 310

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 311 IHKAKDPLALLDQAAELL 328


>gi|85060114|ref|YP_455816.1| tRNA-dihydrouridine synthase A [Sodalis glossinidius str.
           'morsitans']
 gi|84780634|dbj|BAE75411.1| conserced hypothetical protein [Sodalis glossinidius str.
           'morsitans']
          Length = 343

 Score =  349 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 139/319 (43%), Positives = 186/319 (58%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H RFF R L+  ALLYTEM+   A+L G   + L +   E PLALQ+GG++  
Sbjct: 33  MLDWTDSHCRFFLRQLSRRALLYTEMVTTGALLFGKG-DYLAYHDAEHPLALQLGGSEPD 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM   D V  CIAAM +A+++P+T
Sbjct: 92  ALARCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEKDRVAACIAAMREAVTLPIT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+D+Q     L   + ++    G     IHARKA L GLSPK+NR+IP LDYD V
Sbjct: 152 VKTRIGIDEQDSYAFLCEFIDTVATHGGCETFIIHARKAWLNGLSPKENREIPPLDYDRV 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++K++ P L + LNGG++ +  A + L  +DGVM+GR AY+N  +L  VD         
Sbjct: 212 YQLKRDFPALRLMLNGGIKTLHDAREHLQKLDGVMMGREAYQNPGILARVDSELFGDADT 271

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                  +D          M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 272 LPNQAAVID---------VMLPYIERELSQGAALGHITRHMLGLFQGMPGARQWRRYLSE 322

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   ++  A + +
Sbjct: 323 HAHRPGAGIDVVIKALSCI 341


>gi|148548779|ref|YP_001268881.1| tRNA-dihydrouridine synthase A [Pseudomonas putida F1]
 gi|148512837|gb|ABQ79697.1| TIM-barrel protein, yjbN family [Pseudomonas putida F1]
          Length = 336

 Score =  349 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 133/318 (41%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSRQTLLYTEMVTTGALLHNDAHRFLRHDASEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 85  DLAACARLAEETGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YDI  
Sbjct: 145 VKHRIGINGRDSYAELSDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDIAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKRDFPDLEIVLNGGIKTLDECQAHLETFDGVMLGREAYHNPYLLAEVDQQLFGSD--- 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +  A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 262 APVVSR------SEALAQLRPYIVTHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKAAEPLAVFDQAVELL 333


>gi|330989295|gb|EGH87398.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 339

 Score =  349 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCGEHLQTFDGVMLGREAYHNPYLLAQVDQQLFDS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|126725475|ref|ZP_01741317.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2150]
 gi|126704679|gb|EBA03770.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2150]
          Length = 337

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 150/322 (46%), Positives = 198/322 (61%), Gaps = 12/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ N+LLYTEM+ A AI+ GD++ +LGF   E P+A+Q+GG++ +
Sbjct: 22  MMDWTDRHCRYFHRQLSKNSLLYTEMVTAPAIINGDRERLLGFDATEHPVAVQLGGSNPA 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A  I  DFGY+E+NLN GCPS RV  G FGA LM  PD+V +C++ M  A ++ +T
Sbjct: 82  QLQQATAISCDFGYDEVNLNCGCPSDRVQSGYFGAVLMAKPDLVAECVSEMKAAANVEIT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L N +  +  +GV    IHARKA L+GLSPK+NR IP LDYDIV+
Sbjct: 142 VKCRIGVDDQDPQTVLPNFLAKVSAAGVTRFTIHARKAWLQGLSPKENRDIPPLDYDIVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K E P L I +NGG+  + QA  ++   +DGVMIGRAAY   A +L   DE   +   
Sbjct: 202 QMKAEFPHLHISINGGVTTLEQASGLIEQGLDGVMIGRAAYHQPADILCDADELIFSDEK 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G                  +M  Y   HL  GG+L QITRHM+G F G P +RR R  L+
Sbjct: 262 G----------QGVDAAIQTMLPYIENHLLKGGRLNQITRHMLGAFAGKPGARRWRRHLS 311

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A    +  A   M E
Sbjct: 312 EFAHKDGAGPETVLEALAKMRE 333


>gi|330503878|ref|YP_004380747.1| tRNA-dihydrouridine synthase A [Pseudomonas mendocina NK-01]
 gi|328918165|gb|AEB58996.1| tRNA-dihydrouridine synthase A [Pseudomonas mendocina NK-01]
          Length = 312

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 198/319 (62%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A++ GD++  L +S  E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRFFLRQLSRHALLYTEMVTTGALIHGDRERFLRYSECEHPIALQLGGSNPQ 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 61  DLATCTKMAEEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPALVADCVKAMQDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR++P L YD+  
Sbjct: 121 VKHRIGINGRDSYAELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREVPPLRYDVAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ PDL I LNGG++ + +  + L S DGVM+GR AY N  +L  VD   F    TG
Sbjct: 181 QLKQDFPDLEIILNGGIKTIEECEQHLQSFDGVMLGREAYHNPYLLAQVDSRLFGTADTG 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + +          +   ++  Y  +HL  GG L  ++RH++GL  GFP +RR R +L+V
Sbjct: 241 ITRM----------EALLALKPYVEQHLREGGTLHHVSRHVLGLAQGFPGARRFRQLLSV 290

Query: 300 EAGASTATHHIIETAFNLM 318
           +         +++ A  L+
Sbjct: 291 DIHKVQDPLGLLDQAAELL 309


>gi|238899063|ref|YP_002924745.1| tRNA-dihydrouridine synthase A [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229466823|gb|ACQ68597.1| tRNA-dihydrouridine synthase A [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 343

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 195/318 (61%), Gaps = 11/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT NA LYTEM+   A++ G   + L +S +E+P+ALQ+GG +  
Sbjct: 33  MLDWTDRHCRYFHRLLTKNAFLYTEMVTTGALIYGQA-DYLDYSEEEQPVALQLGGHNPF 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A++ E  GY EINLN+GCPS RV +G+FGA LM + + V  C+ AMC  +SIPVT
Sbjct: 92  ELAQCAQLGEQRGYQEINLNLGCPSPRVKKGAFGAALMQDIEQVCVCLKAMCDVVSIPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIGVD+Q     L   ++ I +  ++ + IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 152 IKIRIGVDEQDSYEFLSQFIEKISR-EIDTVIIHARKAWLSGLSPKENREIPPLDYPRVY 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG+  + +A + L  V+GVMIGRAAY+N  +LT VD    N     
Sbjct: 211 QLKKDFPKLNIVINGGISTLEEAKQHLQYVEGVMIGRAAYQNPTLLTQVDSELFNAQDPL 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I   +   +          Y  + L  G  L+ + R M+GLF G   +R+ R  L+  
Sbjct: 271 IDITASIKAFY---------PYIEQELSRGTFLKHLIRPMLGLFQGCAGARQWRRYLSEN 321

Query: 301 AGASTATHHIIETAFNLM 318
           A  S A   +I+ A + +
Sbjct: 322 AYQSGADVSVIDRALSFV 339


>gi|319405737|emb|CBI79360.1| tRNA-dihydrouridine synthase A [Bartonella sp. AR 15-3]
          Length = 331

 Score =  349 bits (896), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 161/318 (50%), Positives = 211/318 (66%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEM VAD ++ G +K +L FS +E P+ALQ+GG+D  
Sbjct: 22  MLGWTDRHCRFFYRLLTKKALLYTEMFVADTVIHGIRKKLLAFSDEEHPIALQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML+PD+V   + AM + ++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGACLMLHPDVVAQLVEAMKRTVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEELALDFLADRVWNAGCDALWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++  + FIGLNGG++ +S+  + L S D VM+GR  Y N   L  +D          
Sbjct: 202 NLKRKYENNFIGLNGGIKSISEIKEHLRSCDAVMVGRQVYHNPIWLCLIDSEIYG----- 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P     D D    +  +M +Y+A+H+ SGG+L  ITRHM+GLF G   +RR R IL+  
Sbjct: 257 EPQNNLSDYD----LINAMCEYSAKHIASGGRLSHITRHMLGLFQGRDGARRWRQILSHN 312

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A  HI++ AF  +
Sbjct: 313 ATKTDANTHILKEAFAAI 330


>gi|119946739|ref|YP_944419.1| tRNA-dihydrouridine synthase A [Psychromonas ingrahamii 37]
 gi|119865343|gb|ABM04820.1| tRNA-dihydrouridine synthase [Psychromonas ingrahamii 37]
          Length = 330

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 130/320 (40%), Positives = 186/320 (58%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R+++ N LLY+EM+   AIL G   + L     E P+ LQ+GG+   
Sbjct: 20  MLDWTDRHCRYFHRVMSKNTLLYSEMVTTGAILYGKG-DYLQKDAAEHPVCLQLGGSAPV 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A   ++ G++EINLNVGCPS RV  G FGACLM   ++VGD I AM  A  +PV+
Sbjct: 79  DLATSALAGKERGFDEINLNVGCPSDRVQNGRFGACLMSEGELVGDAIKAMKDATGLPVS 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + V  + + G +   +HARKA L GLSPK NR +P LDY+ VY
Sbjct: 139 VKTRIGIDDLDSYAFLCDFVGKVAEKGCDTFVVHARKAWLSGLSPKQNRDVPPLDYERVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +    L  +DGVM+GR  Y N  +L++VD+       G+
Sbjct: 199 QLKKDFPQLTIAINGGIKTLDECETHLQYLDGVMLGREIYTNPYLLSSVDQRL---FAGN 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I TR       ++   M  Y  + L +G   + + RHM+GLF G P +R  R  L+  
Sbjct: 256 EKILTRF------EVLEKMYPYIEQQLSNGAYFKHVARHMLGLFQGLPGARAWRRHLSEN 309

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++E A   ++E
Sbjct: 310 GHLPGAGIEVMEKAAAFVVE 329


>gi|121602008|ref|YP_989139.1| tRNA-dihydrouridine synthase A [Bartonella bacilliformis KC583]
 gi|120614185|gb|ABM44786.1| tRNA-dihydrouridine synthase A [Bartonella bacilliformis KC583]
          Length = 326

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 164/319 (51%), Positives = 217/319 (68%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VADAI+ G ++++L F+ QE P+ALQIGG+D  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMVVADAIIHGIRESLLAFNDQEHPVALQIGGSDPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G+FGACLMLNPDIV + + AM + ++IPVT
Sbjct: 77  KLAEAAQIAEDFGYDEINLNVGCPSNRVQSGTFGACLMLNPDIVANAVEAMKRVVTIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 137 VKCRIGVDEQDEELALDFLADRVWNAGCDALWVHARKAWLKGLSPKENRDIPQLNYKRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K +  + FIG+NGG++ + +  + L   D VM+GR  Y N ++L  +D  F       
Sbjct: 197 KLKNKFYNKFIGINGGIKSIYEMKEHLKLCDAVMVGRQVYYNPSLLQLID--FEIYSESQ 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +K          +   M DYAA+H+ SGG L  +TRHMI  FHG   +RR R IL+ +
Sbjct: 255 SNLKD-------CDVIDIMCDYAAKHIASGGHLSHVTRHMISFFHGRDGARRWRQILSND 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   I++ AF+ +I
Sbjct: 308 ARGKDADVRILKEAFSALI 326


>gi|323137432|ref|ZP_08072510.1| TIM-barrel protein, yjbN family [Methylocystis sp. ATCC 49242]
 gi|322397419|gb|EFX99942.1| TIM-barrel protein, yjbN family [Methylocystis sp. ATCC 49242]
          Length = 358

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 143/322 (44%), Positives = 204/322 (63%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  A LYTEM+   A++ GD+  ++GF   E+P+A Q+GG++ +
Sbjct: 36  MMDWTDRHCRYFHRLLSRRARLYTEMLTTGAVIHGDRLRLMGFDAFEQPVAFQLGGSEPA 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+IVE+FGY E+NLNVGCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 96  DLGRAARIVEEFGYAEVNLNVGCPSDRVQNGAFGACLMQCPALVADCVKAMKDAVALPVT 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL ++ +   ++GV+ + +HARKA L+GLSPK+NR IP LDY +V+
Sbjct: 156 VKCRIGVDDQEPERALFDIAERCVEAGVDALIVHARKAWLQGLSPKENRDIPPLDYALVH 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P   I +NGG+  ++Q  + L  VDGVM+GRAAY + A+L  VD    +  +  
Sbjct: 216 RLKRALPATPIAINGGIATLAQMREQLTEVDGVMVGRAAYHDPALLLQVDAELFDAPSPL 275

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            +   +   Y  R L  G +L  ITRH++GLF G P +R  R  L +E
Sbjct: 276 ADCF---------QAVEAFLPYIERELSKGERLSSITRHLLGLFAGLPGARSYRRRLALE 326

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A    A   ++  A   +  ++
Sbjct: 327 AVRPGAGVEVLLDAVGEVRAAM 348


>gi|183221906|ref|YP_001839902.1| tRNA-dihydrouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189911975|ref|YP_001963530.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167776651|gb|ABZ94952.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167780328|gb|ABZ98626.1| tRNA-dihydrouridine synthase A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 323

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 144/317 (45%), Positives = 192/317 (60%), Gaps = 10/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH+R+F RL++ +ALLYTEM+   AILRG D    L FS +E P+ALQ+GG   
Sbjct: 15  MMDWTDRHFRYFIRLISKHALLYTEMVTTGAILRGKDNHRYLDFSKEEHPIALQLGGDSP 74

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L E AKI ED+GY+EINLNVGCPS RV  GSFGACLM  PD+V + +A     + IPV
Sbjct: 75  KALAECAKIGEDYGYDEINLNVGCPSDRVQSGSFGACLMKEPDLVAEMVAFCKSKVKIPV 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIGV+ +     L   V  I+K+GV+   +HAR AIL+GLSPK+NR IP L Y+ V
Sbjct: 135 TVKHRIGVNGKESYEDLHQFVSKIQKAGVDHCIVHARIAILEGLSPKENRTIPPLRYEDV 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K + P+L I +NGG++  ++    L   DGVM+GRAAY N  +   VD  +     G
Sbjct: 195 YRLKSDFPNLPITINGGIKTHAEIKTHLTKADGVMVGRAAYDNPFLFADVDSLYFGSKEG 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +   ++         I   M  Y      SGGK+  I RH++GL+HG   +R  R   T 
Sbjct: 255 TITRES---------ILQKMIPYVQSVRMSGGKVSHILRHILGLYHGEKGAREFRRYFTN 305

Query: 300 EAGASTATHHIIETAFN 316
               ++AT  I+E+   
Sbjct: 306 GMHLTSATESILESYLQ 322


>gi|26988893|ref|NP_744318.1| tRNA-dihydrouridine synthase A [Pseudomonas putida KT2440]
 gi|38604779|sp|Q88KX0|DUSA_PSEPK RecName: Full=tRNA-dihydrouridine synthase A
 gi|24983702|gb|AAN67782.1|AE016409_8 TIM-barrel protein, yjbN family [Pseudomonas putida KT2440]
          Length = 336

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 133/318 (41%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSRQTLLYTEMVTTGALLHNDAHRFLRHDASEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 85  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YDI  
Sbjct: 145 VKHRIGINGRDSYAELSDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDIAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKRDFPDLEIVLNGGIKTLDECQAHLETFDGVMLGREAYHNPYLLAEVDQQLFGSD--- 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +  A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 262 APVVSR------SEALAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKAAEPLAVFDQAVELL 333


>gi|319408524|emb|CBI82177.1| tRNA-dihydrouridine synthase A [Bartonella schoenbuchensis R1]
          Length = 326

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 162/319 (50%), Positives = 214/319 (67%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLLT  ALLYTEM+VADA + G ++ +LGFS +E P+ALQ+GG+D  
Sbjct: 17  MLDWTDRHCRFFYRLLTKKALLYTEMVVADAAIHGIRERLLGFSDEEHPIALQLGGSDSQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML+PDIV   + AM +A++I VT
Sbjct: 77  KLAEAARIAEDFGYDEINLNVGCPSNRVQAGMFGACLMLHPDIVARAVEAMKQAVTISVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD Q   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRIGVDKQDEELALDILADQVWNAGCDALWVHARKAWLKGLSPKENRGIPELNYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P  FIG+NGG++ + +  + L   D  M+GR  Y N A+L ++D          
Sbjct: 197 RLKRKYPHKFIGINGGIQSIDEVKEHLKLCDATMVGRQVYHNPALLMSIDSKIYG----- 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P     D D    +  +M DYAA+H+ SGG+L  +TRHMI LFHG   +RR R IL+ +
Sbjct: 252 QPHSDLSDCD----LIDAMCDYAAKHIASGGRLSHVTRHMINLFHGRNGARRWRQILSND 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A   +++ AF   +
Sbjct: 308 ATRRDADVSVLKEAFAAFV 326


>gi|119469148|ref|ZP_01612132.1| tRNA-dihydrouridine synthase A [Alteromonadales bacterium TW-7]
 gi|119447400|gb|EAW28668.1| tRNA-dihydrouridine synthase A [Alteromonadales bacterium TW-7]
          Length = 329

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 190/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G   + L F+  E P+ALQ+GG+D  
Sbjct: 20  MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFGRG-DYLHFNQHEGPVALQLGGSDPE 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V  C+AAM   +SIPVT
Sbjct: 79  ALAKCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAQCVAAMKNEVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++  K G +   IHARKA L GLSPK+NR++P LDY  VY
Sbjct: 139 VKTRIGIDEQDSYEFLCALIEASHKVGCDDFIIHARKAWLNGLSPKENREVPPLDYPRVY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + +NGG++ + Q+L+ L  +DGVM+GR AY N  ML  VDE        +
Sbjct: 199 QLKKDYPQLDLSINGGVKTVEQSLEHLQYIDGVMVGREAYSNPFMLNEVDEKIYGDTANT 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  SM DY    +  G     + RHM+G+F G P +R  R  L+  
Sbjct: 259 Q---------TRHDVVRSMYDYIEEEMRLGANFWHVARHMLGIFQGQPGARGFRRHLSEN 309

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 310 GHGKQADLSVMDKALSFVPE 329


>gi|27378845|ref|NP_770374.1| tRNA-dihydrouridine synthase A [Bradyrhizobium japonicum USDA 110]
 gi|27351994|dbj|BAC48999.1| blr3734 [Bradyrhizobium japonicum USDA 110]
          Length = 331

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 145/318 (45%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+   AI+ GD++ +LGF   E P+ALQ+GG+D S
Sbjct: 13  MMDWTDRHCRVFHRQLTRRALLYTEMLTTGAIIHGDRERLLGFDACENPVALQLGGSDPS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I E FGY+EINLNVGCPS RV +G FGACLM  P++V  C+ AM +A+++PVT
Sbjct: 73  ELAQAARIGEAFGYDEINLNVGCPSDRVKDGRFGACLMAEPELVARCVDAMKRAVAVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDY+ VY
Sbjct: 133 VKCRIGIDDQDPEVALDTLARAVVAAGCDALIVHARKAWLNGLSPKENRDIPPLDYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PD+ + +NGG+  + +A   L  VDGVM+GRAAY+    L +VD          
Sbjct: 193 RLKRAMPDVPVIINGGIPGIDEAKAHLEHVDGVMLGRAAYQEPWRLLSVDSDIFGETAPH 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +           +    +M  Y    L  G +L  ITRH +G FH  P +R  R  L  +
Sbjct: 253 A---------TMQDALEAMMPYIEAQLARGTRLHAITRHFVGAFHAVPGARAFRRHLAEQ 303

Query: 301 AGASTATHHIIETAFNLM 318
                A   ++  A   +
Sbjct: 304 GVKPGAGLDVLRDAIARV 321


>gi|320324818|gb|EFW80890.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. glycinea
           str. B076]
          Length = 339

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPGLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|330808532|ref|YP_004352994.1| tRNA-dihydrouridine synthase A [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327376640|gb|AEA67990.1| tRNA-dihydrouridine synthase A [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 312

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H RFF R+L+ +ALLYTEM+   A+L GD +  L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDAHCRFFLRILSKHALLYTEMVTTGALLNGDHERFLRHHESEHPLALQLGGSVPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ ++ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAACARMAQEHGYDEVNLNVGCPSDRVQNNMIGACLMGHPHLVADCVKAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L   V +++++G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 121 VKHRIGINGRDSYEQLCEFVGTVREAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P+L I LNGG++ +    + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 181 RLKADFPELEIVLNGGIKTLEACHEHLQTFDGVMLGREAYHNPYLLAEVDQQLFGS---T 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ TR +        A +  Y A HL +GG +  ITRH++GL  GFP +RR R +L+V+
Sbjct: 238 APVITRAEA------LAQLRPYIADHLAAGGAMHHITRHVLGLGTGFPGARRFRQLLSVD 291

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 292 IHKTKDPLALLDQAGQLL 309


>gi|302134770|ref|ZP_07260760.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tomato
           NCPPB 1108]
          Length = 311

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 136/317 (42%), Positives = 196/317 (61%), Gaps = 9/317 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  + 
Sbjct: 1   MDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVTV
Sbjct: 61  LAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V +
Sbjct: 121 KHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVAQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     +   +
Sbjct: 181 LKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQLFGSV---A 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+ 
Sbjct: 238 PVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVDI 291

Query: 302 GASTATHHIIETAFNLM 318
             +     +++ A   +
Sbjct: 292 HKAENPLLLLDQAAKFL 308


>gi|149913943|ref|ZP_01902475.1| tRNA-dihydrouridine synthase A [Roseobacter sp. AzwK-3b]
 gi|149812227|gb|EDM72058.1| tRNA-dihydrouridine synthase A [Roseobacter sp. AzwK-3b]
          Length = 337

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLY+EM+ A A++RG   ++L +S QE P+ALQ+GG+D  
Sbjct: 17  MMDWTDRHCRYLHRLLSRRALLYSEMVTAAALVRGGALHLLDYSPQEHPVALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLNVGCPS RV  G+FGA LM +P +V +C AAM +A ++ VT
Sbjct: 77  ELAQAARMGAEAGYDEINLNVGCPSDRVQSGTFGAVLMKDPGLVSECCAAMIEASAVEVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  +  +GV    IHARKA L+GLSPK NR IP LDYD+V 
Sbjct: 137 VKCRIGVDDQDPETVLPEFLARVSAAGVQRFTIHARKAWLQGLSPKQNRDIPPLDYDLVL 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P L + +NGG+  + Q    L   +DGVM+GRAAY   A +L   D        
Sbjct: 197 RMKALFPGLHLSINGGITTLDQVRDFLEAGLDGVMVGRAAYHQPADILCAADRLIFGEEG 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +     V K         M  Y   HL  GG+L QITRHM+GLF G P +R  R IL+
Sbjct: 257 PDTTPDDAVLK---------MLPYIEAHLAQGGRLHQITRHMLGLFAGRPGARAWRRILS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++  A   + +S
Sbjct: 308 EGATRPDAGPDLVLDALAEVSQS 330


>gi|126664937|ref|ZP_01735920.1| Dihydrouridine synthase TIM-barrel protein yjbN [Marinobacter sp.
           ELB17]
 gi|126630307|gb|EBA00922.1| Dihydrouridine synthase TIM-barrel protein yjbN [Marinobacter sp.
           ELB17]
          Length = 321

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 124/320 (38%), Positives = 183/320 (57%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  HYR+ AR L+ +ALLYTEM+   A++ GD +  L  +  E PLALQ+GG++  
Sbjct: 1   MMDWTTPHYRYMARQLSKHALLYTEMVTTGALIHGDTERFLHHNAAEYPLALQLGGSNAG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A + + FG++E+NLNVGCPS +V     GACLM +PDIV +   AM  A  IPVT
Sbjct: 61  ELAHCADLAQQFGFSEVNLNVGCPSDKVQNNMIGACLMGHPDIVAEGFKAMQAATDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G++ +     L   ++++  +G     +HAR A+L+GLSPK+NR +P L YD VY
Sbjct: 121 VKHRTGINGRESWDELCGFIETVAAAGCKTFIVHARIAVLEGLSPKENRDVPPLKYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG++ +++  + L   DGVM+GR AY N  +LT VD  F      +
Sbjct: 181 HLKAKYPQLEIIINGGIKTVNECHQHLAHTDGVMLGREAYHNPWILTQVDSEFFGEPEKA 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        +   +M  +  + L  G  L  I+RHM+GLFHG P  R+ R  ++  
Sbjct: 241 ---------VNRHEALEAMYPFIEQELARGVYLGHISRHMLGLFHGVPGGRQFRRYISEN 291

Query: 301 AGASTATHHIIETAFNLMIE 320
           A    A   ++  A   + +
Sbjct: 292 AHKPGAGLDVLRQALAKVPQ 311


>gi|114799763|ref|YP_759023.1| tRNA-dihydrouridine synthase A [Hyphomonas neptunium ATCC 15444]
 gi|114739937|gb|ABI78062.1| tRNA-dihydrouridine synthase A [Hyphomonas neptunium ATCC 15444]
          Length = 328

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 143/318 (44%), Positives = 191/318 (60%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALL+TEM+ ADA++ GD++ ++GFS  E PL LQ+GG++  
Sbjct: 14  MMDWTDRHCRAFHRTLTKRALLWTEMVTADAVIHGDRQRLIGFSDVEHPLVLQLGGSEPG 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E +GY+E+NLN GCPS RV  G+FGACLM  PD+V DC+AAM  A+SIPVT
Sbjct: 74  KLAEAARIAEGYGYDEVNLNCGCPSERVQSGAFGACLMAEPDLVADCVAAMRAAVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RI +DD      L   ++ +  +G +   +HARKA LKGLSPK+NR++P LDY +V 
Sbjct: 134 VKNRIAIDDLPARETLFTFIEKVSVAGCSVFTVHARKAWLKGLSPKENREVPPLDYGLVA 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K   PDL I LNGG+  + Q    +   DGVM+GRAAY+   +L  VD          
Sbjct: 194 ELKTARPDLTIILNGGIATIDQCRDHIGVFDGVMLGRAAYQTPGLLGQVDSDLFG----- 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                            +   Y A  L  G  L  +TRHM+GLF G P +R+ R IL+ +
Sbjct: 249 -----EGAMIAAGDAVRAYEPYIAARLAEGSNLHAMTRHMLGLFAGQPGARQWRRILSEQ 303

Query: 301 AGASTATHHIIETAFNLM 318
                A   ++  A   +
Sbjct: 304 GVKKGAGLDVLRAALGAV 321


>gi|126735535|ref|ZP_01751280.1| TIM-barrel protein, yjbN family [Roseobacter sp. CCS2]
 gi|126714722|gb|EBA11588.1| TIM-barrel protein, yjbN family [Roseobacter sp. CCS2]
          Length = 331

 Score =  347 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 149/321 (46%), Positives = 205/321 (63%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL++ + LLYTEM+ A A++ GD+  +LGF   E+PLALQ+GG+D +
Sbjct: 17  MMDWTDRHCRYLHRLMSRHTLLYTEMVTAPAVIHGDRDRLLGFHVDEQPLALQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I E +GY EINLN GCPS RV  G FGA LM +P +V DC+AAM  A+ +PVT
Sbjct: 77  QLAEAARIAEGYGYAEINLNCGCPSDRVQSGHFGAVLMESPVLVADCVAAMIAAVRVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P V L + +  +  +GV+   +HARKA L+GLSPK+NR++P L+YD+V 
Sbjct: 137 VKCRIGVDDQDPHVILPDFLARVSAAGVDRFSVHARKAWLQGLSPKENREVPPLNYDLVM 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K   P L + +NGG+  + QA   L   +DGVMIGRAAY   A +L   D        
Sbjct: 197 KMKGLFPHLHVSINGGIATLDQAEDFLARGLDGVMIGRAAYHTPADILLQADARIYGD-- 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                + R  +D    +   M  Y A H+  GG+L Q+TRHM+GLF G P +R  R  L+
Sbjct: 255 ----PRERTAED----VVHLMLPYIADHIAQGGRLGQVTRHMLGLFQGRPGARGWRRHLS 306

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A A  A   ++ +A + + 
Sbjct: 307 ENAHADGAGPAVVLSALDHVT 327


>gi|16125555|ref|NP_420119.1| tRNA-dihydrouridine synthase A [Caulobacter crescentus CB15]
 gi|221234301|ref|YP_002516737.1| tRNA-dihydrouridine synthase A [Caulobacter crescentus NA1000]
 gi|13422645|gb|AAK23287.1| TIM-barrel protein, yjbN family [Caulobacter crescentus CB15]
 gi|220963473|gb|ACL94829.1| NIFR3-like protein [Caulobacter crescentus NA1000]
          Length = 341

 Score =  347 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 150/323 (46%), Positives = 208/323 (64%), Gaps = 10/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R L++ ALLYTEM+ + A++ GD+  +LG+   + P+A+Q+GG+D +
Sbjct: 17  MMDWTDRHCRSLHRGLSSRALLYTEMVTSGAVVHGDRNKLLGYDPGQHPVAVQLGGSDPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I ED+GY+E+NLNVGCPS RV  G FGACLM  PD+V +C+AA+  A+ +P T
Sbjct: 77  ELAQAARIAEDYGYDEVNLNVGCPSDRVQSGRFGACLMREPDLVAECMAAIKNAVRVPAT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV     +G++   +HARKA L+GLSPK+NR IP LDY +VY
Sbjct: 137 VKCRIGVDDQDPEESLFTLVDRCAAAGIDTFVVHARKAWLQGLSPKENRDIPPLDYALVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+E P L I +NGG+  +  AL+ L   VDGVM+GRAAY  + +L  VD         
Sbjct: 197 RLKRERPALTIAINGGVPSVDAALEHLANGVDGVMLGRAAYHEAGLLGEVDRRVFG---- 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                   D D +  +      Y AR L +G  L  ++RHM+GLFHG P +R  R ILTV
Sbjct: 253 ----LDVADVDSFEAV-ERYRPYLARELAAGTHLAAMSRHMLGLFHGLPGARAWRRILTV 307

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           E   S A   +++ A + +  +L
Sbjct: 308 EGVKSGAGLDVVDRALDAVRAAL 330


>gi|83943001|ref|ZP_00955461.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. EE-36]
 gi|83846009|gb|EAP83886.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. EE-36]
          Length = 337

 Score =  347 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 145/320 (45%), Positives = 192/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL +   LLYTEM+ + A++RG   ++L   T E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRYMHRLFSKQTLLYTEMVTSPALVRGGALHLLDHDTSEHPVALQLGGSDPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I    GY+EINLNVGCPS RV  G FGA LM  P +V   +AAM +A+ + VT
Sbjct: 78  ELAEAARIGAQAGYDEINLNVGCPSDRVQSGCFGAVLMEQPALVAKSVAAMRRAVDVDVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PA  L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 138 VKCRIGVDDQNPAEVLPEFLAQIVGAGCERVTIHARKAWLQGLSPKENRDIPPLDYELVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  + QA   L   +DGVMIGR+AY N   +L   D        
Sbjct: 198 RMKGLFPNLHISINGGITSLDQAEAFLDAGLDGVMIGRSAYHNPTDILAQADRRIYGTGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P            + A M  Y   H+  GGKL QITRHM+GLF G   +R  R  L+
Sbjct: 258 DTTP----------EDVVAQMLPYIDAHIDGGGKLNQITRHMMGLFAGRTGARVWRRTLS 307

Query: 299 VEAGASTATHHIIETAFNLM 318
            +A    A   ++  A + M
Sbjct: 308 EQASRPGADRQVLLEALDTM 327


>gi|289627280|ref|ZP_06460234.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289650430|ref|ZP_06481773.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330869475|gb|EGH04184.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 339

 Score =  347 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|83954176|ref|ZP_00962896.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. NAS-14.1]
 gi|83841213|gb|EAP80383.1| tRNA-dihydrouridine synthase A [Sulfitobacter sp. NAS-14.1]
          Length = 337

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 145/320 (45%), Positives = 192/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL +   LLYTEM+ + A++RG   ++L   T E P+ALQ+GG+D  
Sbjct: 18  MMDWTDRHCRYMHRLFSKQTLLYTEMVTSPALVRGGALHLLDHDTSEHPVALQLGGSDPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I    GY+EINLNVGCPS RV  G FGA LM  P +V   +AAM +A+ + VT
Sbjct: 78  ELAEAARIGAQAGYDEINLNVGCPSDRVQSGCFGAVLMEQPALVAKSVAAMRRAVDVDVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PA  L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 138 VKCRIGVDDQNPAEVLPEFLAQIVGAGCERVTIHARKAWLQGLSPKENRDIPPLDYELVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  + QA   L   +DGVMIGR+AY N   +L   D        
Sbjct: 198 RMKGLFPNLHISINGGITSLDQAEAFLDAGLDGVMIGRSAYHNPTDILAQADRRIYGTGA 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P            + A M  Y   H+  GGKL QITRHM+GLF G   +R  R  L+
Sbjct: 258 DTTP----------EDVVAQMLPYIDAHIDGGGKLNQITRHMMGLFAGRTGARVWRRTLS 307

Query: 299 VEAGASTATHHIIETAFNLM 318
            +A    A   ++  A + M
Sbjct: 308 EQASRPGADRQVLLEALDAM 327


>gi|254466832|ref|ZP_05080243.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium Y4I]
 gi|206687740|gb|EDZ48222.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium Y4I]
          Length = 316

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 142/320 (44%), Positives = 200/320 (62%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L F+ +E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSRETLLYTEMVTAPALVRGGALHLLEFNAEEHPVALQLGGSDPG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++  + GY+EINLN GCPS RV  G+FGA LM  P++V DC+AAM + + + VT
Sbjct: 61  ELAEAARLGAEAGYDEINLNCGCPSDRVQSGAFGAVLMQTPELVADCVAAMRETVDVDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L   ++ I+ +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 121 VKCRIGVDEQEPEEVLPEFLEKIRAAGCGRVTIHARKAWLQGLSPKENRDIPPLDYELVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   PDL + +NGG+  +++A   L   +DGVM+GRAAY   A +L   D       T
Sbjct: 181 RMKAAFPDLHVSINGGIATLAEAKAHLDRGLDGVMVGRAAYHQPADVLCAADPEIYGTGT 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P           +    M  Y    L  G +L QITRHM+GLF G P +R+ R +L+
Sbjct: 241 VSDPA----------EAVRQMLPYIEARLSEGARLNQITRHMLGLFAGKPGARQWRRMLS 290

Query: 299 VEAGASTATHHIIETAFNLM 318
             A  + A   +++ A   +
Sbjct: 291 EGACRAGAGPELVQEALAQV 310


>gi|313499712|gb|ADR61078.1| TRNA-dihydrouridine synthase A [Pseudomonas putida BIRD-1]
          Length = 312

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 133/318 (41%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 1   MMDWTDRHCRFFLRLLSRQTLLYTEMVTTGALLHNDAHRFLRHDASEHPLALQLGGSVPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 61  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YDI  
Sbjct: 121 VKHRIGINGRDSYAELSDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDIAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+         
Sbjct: 181 QLKRDFPDLEIVLNGGIKSLDECQAHLETFDGVMLGREAYHNPYLLAEVDQQLFGSD--- 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +  A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 238 APVVSR------SEALAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 291

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 292 IHKAAEPLAVFDQAVELL 309


>gi|77359457|ref|YP_339032.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874368|emb|CAI85589.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 310

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 190/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G   + L F+  E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFGRG-DYLHFNQHEGPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM   ++IPVT
Sbjct: 60  ALAQCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMGEPQLVADCVAAMKAEVNIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++    G +   IHARKA LKGLSPK+NR++P LDY  VY
Sbjct: 120 VKTRIGIDEQDSYEFLCALIEASHNVGCDDFIIHARKAWLKGLSPKENREVPPLDYPRVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + LNGG++ + Q+L+ L  +DGVMIGR AY N  +L  VDE     +  +
Sbjct: 180 QLKKDYPQLDLSLNGGVKTIEQSLEHLQHIDGVMIGREAYSNPFILNEVDEKIYGDIANT 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  SM  Y    +  G     + RHM+G+F G P +R  R  L+  
Sbjct: 240 Q---------SRHDVVRSMYSYIEDEMRLGANFWHVARHMLGIFQGQPGARGFRRHLSEN 290

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 291 GHGKQADLSVMDKALSFVPE 310


>gi|189350413|ref|YP_001946041.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans ATCC
           17616]
 gi|189334435|dbj|BAG43505.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans ATCC
           17616]
          Length = 344

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 191/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 197 RLKREFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 256 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     + + A   + +
Sbjct: 308 KKLARGDLAVFDEARAHLND 327


>gi|94499718|ref|ZP_01306255.1| Dihydrouridine synthase TIM-barrel protein yjbN [Oceanobacter sp.
           RED65]
 gi|94428472|gb|EAT13445.1| Dihydrouridine synthase TIM-barrel protein yjbN [Oceanobacter sp.
           RED65]
          Length = 330

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 140/322 (43%), Positives = 194/322 (60%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M+DW+D H R F R L+ +A LYTEM+   A++ GD      + +  +E P+ALQ+GG++
Sbjct: 18  MMDWSDSHCRLFWRTLSKDAFLYTEMVTTGALIHGDGGPDRFIRYRDEEHPVALQLGGSN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L + AKI +DFGY+E+NLNVGCPS RV     GACLM +P +V DCI AM  A+ IP
Sbjct: 78  PKDLAQCAKIAQDFGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCIKAMQDAVEIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG+DDQ     L + V ++  +G     IH RKAIL GLSPK+NR+IP L Y++
Sbjct: 138 VTVKHRIGIDDQDSYEHLHHFVDTVAATGCETFIIHGRKAILDGLSPKENREIPPLRYEV 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           V +IK++ P L + LNGG++   +A + L   DGVM+GR AY N ++L  VD  +     
Sbjct: 198 VQQIKQDLPQLEVILNGGIKTHKEATEHLKWADGVMLGREAYHNPSVLMDVDALYYGHE- 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                +T+  KD  R +      +   HL  G KL  +TRH++GLF+G P SR  R  L+
Sbjct: 257 ----PQTKDKKDCIRAL----YPHIEDHLSKGFKLSYVTRHILGLFNGQPGSRLFRRHLS 308

Query: 299 VEAGASTATHHIIETAFNLMIE 320
            +A    A+   IE A   M +
Sbjct: 309 EQAFKKDASIQTIEDALAYMPD 330


>gi|237797725|ref|ZP_04586186.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|237806004|ref|ZP_04592708.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331020575|gb|EGI00632.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331027114|gb|EGI07169.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 339

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL+ +ALLYTEM+   A+L GD+   L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSRHALLYTEMVTTGALLHGDRDRFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVVIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V +++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L   DGVM+GR AY N  +L  VD+     +   
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQVFDGVMLGREAYHNPYLLAQVDKQLFGSM--- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R           +M  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISR------HAALEAMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKADDPMLLLDKAAEFL 336


>gi|259418773|ref|ZP_05742690.1| tRNA-dihydrouridine synthase A [Silicibacter sp. TrichCH4B]
 gi|259344995|gb|EEW56849.1| tRNA-dihydrouridine synthase A [Silicibacter sp. TrichCH4B]
          Length = 336

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 145/321 (45%), Positives = 200/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R  R+  RLL+   LLYTEM+ A A++RG   ++L     E P+ALQ+GG+D  
Sbjct: 22  MMDWTTRECRYLHRLLSKETLLYTEMVTAPALVRGRALHLLDHDVSEHPVALQLGGSDPD 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAK+  + GY+EINLN GCPS RV  G+FGA LM +P++V DC+AAM +A+ + VT
Sbjct: 82  ELAEAAKLGAEAGYDEINLNCGCPSDRVQSGAFGAILMQSPELVADCMAAMAQAVDVEVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I+ +GV+ + IHARKA LKGLSPK+NR IP LDY++V+
Sbjct: 142 VKCRIGVDDQNPQDVLPEFLEKIRAAGVDRVTIHARKAWLKGLSPKENRDIPPLDYELVH 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K   PD+ I +NGG+  +  A   L   +DGVMIGRAAY   A +L   D        
Sbjct: 202 QMKASFPDMHISINGGIATLEDAQAQLARGLDGVMIGRAAYHQPADVLCAADPRIFGTGE 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y  R +  G +L QI+RHM+GLF G P +R+ R  L+
Sbjct: 262 VTDPVS----------VVQDMLPYIEREMQQGARLHQISRHMLGLFAGRPGARQWRRHLS 311

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   ++E A +L+I
Sbjct: 312 EGASRKGAGPELVEEALDLVI 332


>gi|161524837|ref|YP_001579849.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans ATCC
           17616]
 gi|160342266|gb|ABX15352.1| TIM-barrel protein, yjbN family [Burkholderia multivorans ATCC
           17616]
          Length = 357

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 191/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 30  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 90  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 210 RLKREFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 269 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLSDN 320

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     + + A   + +
Sbjct: 321 KKLARGDLAVFDEARAHLND 340


>gi|307310192|ref|ZP_07589841.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
 gi|306899744|gb|EFN30369.1| dihydrouridine synthase DuS [Sinorhizobium meliloti BL225C]
          Length = 353

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 185/327 (56%), Positives = 233/327 (71%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR L+++ALLYTEMIVADAILRGD++ +LG  T E P+ALQ+GG+D +
Sbjct: 27  MIDWTDRHYRFFARQLSSHALLYTEMIVADAILRGDREKLLGHDTSEHPVALQLGGSDPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K+ EAA+I E FGY+EIN+NVGCPS RV  G+FGACLM  P +V DCIAAM  A+ IPVT
Sbjct: 87  KMAEAARIAEGFGYDEINMNVGCPSDRVQSGTFGACLMQEPALVADCIAAMKAAVKIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P VALR+LV+ +K +G + +W+HARKA LKGLSP++NR+IP LDY +V+
Sbjct: 147 VKCRIGVDDQDPEVALRDLVQRVKDAGTDAVWVHARKAWLKGLSPRENREIPPLDYGLVH 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL----------PSV----------DGVMIGRAAY 220
            +K EN +LFIGLNGGL+ + QAL  L                       DGVM+GRAAY
Sbjct: 207 RLKAENANLFIGLNGGLQRLDQALSHLDPLSLPTGGTTGTAAEPACGAPLDGVMLGRAAY 266

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD----------KDFWRKISASMTDYAARHLHSG 270
            +S +LT  D YF +PLTG+ P+    D           DFW  I  +M DYAA H+ +G
Sbjct: 267 HDSGLLTAADGYFVHPLTGAEPMPVDRDGFSDHDHKLSLDFWSGIRDAMADYAAAHIENG 326

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHIL 297
           G+L  +TRHM+GLF G+P +RR R IL
Sbjct: 327 GRLIHVTRHMVGLFQGWPGARRYRQIL 353


>gi|146341642|ref|YP_001206690.1| tRNA-dihydrouridine synthase A [Bradyrhizobium sp. ORS278]
 gi|146194448|emb|CAL78473.1| tRNA-dihydrouridine synthase A [Bradyrhizobium sp. ORS278]
          Length = 339

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 194/320 (60%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+  ALLYTEM+   A++ GD+  +LGF   E P+ALQ+GG+D +
Sbjct: 21  MMDWTDRHCRVFHRLLSRRALLYTEMVTTGAVIHGDRTRLLGFDRSEHPVALQLGGSDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A+I EDFGY+EINLNVGCPS RV +G FGACLM  P +V  C+AAM + ++IPVT
Sbjct: 81  DLATSARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPALVAACVAAMKRVVTIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L  ++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 141 VKCRIGIDDQDPEVALDALADAVVDAGADALIVHARKAWLNGLSPKENRDIPPLDYDRVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + + +NGG+  +  A   L  VDGVM+GRAAY+    L  VD          
Sbjct: 201 RLKARLPRVPVIINGGITSIEAAQDHLAHVDGVMLGRAAYQEPWRLLDVDPVLFGEAGP- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   +   +   A++  Y  R +  G +L  ITRH++G +H  P +R  R  L   
Sbjct: 260 --------QRSMKDALAALEPYIERQVAQGMRLHAITRHLVGAYHAVPGARAFRRHLAER 311

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A  ++ E
Sbjct: 312 GVKPDAGIEVLREAVAMIEE 331


>gi|78066180|ref|YP_368949.1| tRNA-dihydrouridine synthase A [Burkholderia sp. 383]
 gi|77966925|gb|ABB08305.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia sp. 383]
          Length = 344

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 192/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPSLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 197 QLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYGS-TEA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 256 VPTREEAE--------AKLIEYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMIES 321
              + A   + + A   + E+
Sbjct: 308 KKLARADLAVFDEARAHLNEA 328


>gi|49474253|ref|YP_032295.1| tRNA-dihydrouridine synthase A [Bartonella quintana str. Toulouse]
 gi|49239757|emb|CAF26141.1| hypothetical protein BQ06500 [Bartonella quintana str. Toulouse]
          Length = 326

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 154/319 (48%), Positives = 214/319 (67%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTD+H RFF RLLT  ALLYTEMIVADA++ G ++ +L  + +E P+ALQ+GG+D  
Sbjct: 17  MLGWTDQHCRFFHRLLTKKALLYTEMIVADAVIHGVRERVLALNHKEHPIALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G+FGACLML PDIV + + A+ + +++ VT
Sbjct: 77  KLAEAARIAEDFGYDEINLNVGCPSNRVQSGAFGACLMLQPDIVANAVEAIKQVVTLSVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIGVD+Q   +AL  L + +  +G + +W+HARKA LKGLSPK+NR IP ++Y+ VY
Sbjct: 137 IKCRIGVDEQDEELALDFLAEKVWNAGCDALWVHARKAWLKGLSPKENRDIPPINYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++  + FIG+NG ++ + +  + L   D  M+GR  Y N  +L  +D          
Sbjct: 197 KLKRKYYNKFIGINGEIKSLDEIKEHLTLCDAAMVGRQVYHNPTLLKHIDSEIYG----- 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P     D D    +  SM DYAA+H+ SGG L  +TRHMIGLF+G   +RR R IL+  
Sbjct: 252 EPQSNLNDVD----LIESMCDYAAQHIASGGLLSHVTRHMIGLFNGRNGARRWRQILSNN 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A  H+I+ AF+ +I
Sbjct: 308 ASRRDADVHVIKEAFSALI 326


>gi|226945328|ref|YP_002800401.1| tRNA-dihydrouridine synthase A [Azotobacter vinelandii DJ]
 gi|226720255|gb|ACO79426.1| Dihydrouridine synthase yjbN family protein [Azotobacter vinelandii
           DJ]
          Length = 336

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 194/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L GD +  L     E PLALQ+GG+   
Sbjct: 25  MLDWTDRHCRFFLRQLSYHALLYTEMVTTGALLHGDARRFLRHERMEHPLALQLGGSVPG 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+EINLNVGCPS RV     GACLM +P  V DC+ AM  A++IPVT
Sbjct: 85  ELAACARLAEEAGYDEINLNVGCPSDRVQNNLIGACLMGDPARVADCVKAMRDAVTIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     LR+ V  + ++G     +HAR AIL GLSPK+NR+IP L Y+IV 
Sbjct: 145 VKHRIGIDGRDSYGELRDFVGQVCEAGCRSFIVHARIAILAGLSPKENREIPPLRYEIVA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +    L S DGVMIGR AY N  +L  VD    +     
Sbjct: 205 QLKQDFPDLEIVLNGGIKTLEECRLHLRSFDGVMIGREAYHNPYLLAQVDRELFDS---P 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  +R       +    +  Y  ++L+ GG L  ITRH++GL  GFP +RR R +L+V+
Sbjct: 262 LPALSR------HEALKRLRPYIQQYLNEGGALHHITRHVLGLGQGFPGARRFRQLLSVD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKADDPLALFDRAVTLL 333


>gi|332531883|ref|ZP_08407767.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038510|gb|EGI74953.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 313

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 190/320 (59%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G   + L F+  E P+ALQ+GG+D  
Sbjct: 4   MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFGRG-DYLHFNKHEGPVALQLGGSDPK 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM   ++IPVT
Sbjct: 63  ALAQCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVAECVAAMKNEVNIPVT 122

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++  K G +   IHARKA L GLSPK+NR++P LDY  VY
Sbjct: 123 VKTRIGIDEQDSYEFLCALIEASHKVGCDDFIIHARKAWLNGLSPKENREVPPLDYPRVY 182

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + LNGG++ + Q+L+ L  +DGVMIGR AY N  ML  VDE        +
Sbjct: 183 QLKKDYPQLDLSLNGGVKTIEQSLEHLQHIDGVMIGREAYSNPFMLNDVDEKIYGDSANT 242

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  SM DY    +  G     I RHM+G+F G P +R  R  L+  
Sbjct: 243 Q---------SRHDVVRSMYDYIEEEMRLGANFWHIARHMLGIFQGQPGARGFRRHLSES 293

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 294 GHGKQADLSVMDKALSFVPE 313


>gi|71736634|ref|YP_274126.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557187|gb|AAZ36398.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 339

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V +++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGNVQEAGCGSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +     
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDSTAL- 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 267 --VISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|126461351|ref|YP_001042465.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides ATCC 17029]
 gi|126103015|gb|ABN75693.1| TIM-barrel protein, yjbN family [Rhodobacter sphaeroides ATCC
           17029]
          Length = 331

 Score =  346 bits (888), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 149/319 (46%), Positives = 203/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 19  MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRDRLLGFSEAEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 79  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPSLVADCVAAMIAESPVPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 139 VKCRIGVDEQEPSEVLPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D  +     G
Sbjct: 199 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADRLW-----G 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 254 EEPPRD------LAAVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 307

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   + + A   +
Sbjct: 308 GASRPGAGLALFDEALEAV 326


>gi|116050795|ref|YP_790384.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa UCBPP-PA14]
 gi|254235779|ref|ZP_04929102.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|115586016|gb|ABJ12031.1| putative TIM-barrel protein [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126167710|gb|EAZ53221.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
          Length = 332

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVDSQLFGS---E 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 258 APPLSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|134295639|ref|YP_001119374.1| tRNA-dihydrouridine synthase A [Burkholderia vietnamiensis G4]
 gi|134138796|gb|ABO54539.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia vietnamiensis
           G4]
          Length = 344

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 138/322 (42%), Positives = 193/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAQAGCDTFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPALEIVINGGIKTLDEVAEHLEHVDGVMLGREAYHNPYVLAGVDARFYGS---T 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       +  A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEAEAKLIEYCAAELKRGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     + + A   + +++
Sbjct: 308 KKLARGDLSVFDEARTHLNDAI 329


>gi|262195064|ref|YP_003266273.1| hypothetical protein Hoch_1832 [Haliangium ochraceum DSM 14365]
 gi|262078411|gb|ACY14380.1| TIM-barrel protein, yjbN family [Haliangium ochraceum DSM 14365]
          Length = 376

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 190/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+R+F R ++ + LLYTEMIV   I+ GD+   L FS  E P+ALQ+GG D  
Sbjct: 47  MMECTDRHFRYFLRQISRHTLLYTEMIVTGTIIHGDRPRYLDFSEAEHPIALQLGGDDAE 106

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A+I ED+GY+E+NLNVGCPS+RV  GSFGACLM  P++V   + AM  A++IPVT
Sbjct: 107 ALATCARIAEDWGYDEVNLNVGCPSSRVSSGSFGACLMARPEVVARAVEAMRAAVAIPVT 166

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     +R  V+ + ++G +   +HARKA L GLSPK+NR++P L Y  V+
Sbjct: 167 VKHRIGIDDRDRYEDMREFVRVVAEAGADRFSVHARKAWLSGLSPKENREVPPLRYADVH 226

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG+ D+  A + L  VD VMIGRAAY    +    D  F   +   
Sbjct: 227 RLKREFPHLPIEINGGIVDLDSAQEQLAHVDAVMIGRAAYNTPWIFAEADARFFGSV-AP 285

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +T         +  +M DY       G  L +ITRHM  LF G   +R  R  LT +
Sbjct: 286 TPTQT--------AVVEAMIDYVEAQRGRGVPLHRITRHMFQLFAGQRGARGWRRYLTEQ 337

Query: 301 AGASTATHHIIETAFNLM 318
           A +  A   ++  A +  
Sbjct: 338 AKSRDAGPEVLRVALDRF 355


>gi|226940607|ref|YP_002795681.1| tRNA-dihydrouridine synthase A [Laribacter hongkongensis HLHK9]
 gi|226715534|gb|ACO74672.1| Dihydrouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 339

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 141/315 (44%), Positives = 196/315 (62%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FARLL+ +  LYTEM+   A++ GD    L F   E P+ALQ+GG++ +
Sbjct: 26  MLDWTDRHYRYFARLLSRHTWLYTEMVTTGALIHGDVPRHLTFHETEHPIALQLGGSEPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A++ E +GY+E+NLNVGCPS RV +G+FGACLM  P +V DC+ AM    ++PVT
Sbjct: 86  ELAQCARLAESWGYDEVNLNVGCPSERVQKGAFGACLMKEPGLVADCVRAMRDVTTLPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVDD      + + V  +  +G +   +HAR AILKGLSPK+NR+IP L YD  +
Sbjct: 146 VKHRIGVDDVEAFGFVSDFVGEVAAAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAW 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E PDL I +NGG+  + +A + L  VDGVMIGR AY N  +L  VD  F       
Sbjct: 206 RLKAEFPDLEILVNGGIRTLDEAAEQLGHVDGVMIGREAYHNPYLLAGVDARFYGD---E 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ TR       ++   +  Y   HL +GGK++ I RH++GL +G P +RR R +L+  
Sbjct: 263 HPVPTRA------EVIERLIPYVDAHLAAGGKVRDIARHVLGLVNGVPGARRFRQMLSDS 316

Query: 301 AGASTATHHIIETAF 315
                A   +  TA 
Sbjct: 317 RLLKDADSRLFLTAL 331


>gi|156972389|ref|YP_001443296.1| tRNA-dihydrouridine synthase A [Vibrio harveyi ATCC BAA-1116]
 gi|156523983|gb|ABU69069.1| hypothetical protein VIBHAR_00009 [Vibrio harveyi ATCC BAA-1116]
          Length = 300

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 130/308 (42%), Positives = 183/308 (59%), Gaps = 11/308 (3%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           +T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++ + L   AK+ ++ GY+
Sbjct: 1   MTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPADLATCAKLAQERGYD 59

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           EINLNVGCPS RV  G FGACLM  P +V DC+AAM   + +PVTVK RIG+DDQ     
Sbjct: 60  EINLNVGCPSDRVQNGRFGACLMAEPQLVADCVAAMKDVVDVPVTVKTRIGIDDQDSYEF 119

Query: 136 LRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   Y++KK+   L I +N
Sbjct: 120 LTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRAYQLKKDFSHLTIAIN 179

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           GG++ + +A + L  +DGVMIGR AY++  +L +VD+      T   P+K R       +
Sbjct: 180 GGVKLLEEAKEHLQYLDGVMIGREAYQSPYLLASVDQELFGSNT---PVKKR------SE 230

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
           I   M  Y    L  G  L  ITRHM+GLF   P +R+ R  ++  A    +   +++ A
Sbjct: 231 IVEEMYPYIEAQLAKGAYLGHITRHMLGLFQSMPGARQWRRHISENAHKPGSGLEVLQDA 290

Query: 315 FNLMIESL 322
              + + L
Sbjct: 291 LAKIPKEL 298


>gi|331013200|gb|EGH93256.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 339

 Score =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 197/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM  P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAYPQLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLDQCGEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPMLLLDQAAAFL 336


>gi|315125488|ref|YP_004067491.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas sp. SM9913]
 gi|315014001|gb|ADT67339.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas sp. SM9913]
          Length = 310

 Score =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 192/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T + +LYTEMI   AIL G   + L F+  E P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHCRTFHRKMTKHTVLYTEMITTGAILFGRG-DYLHFNQHEGPVALQLGGSDPQ 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + AK+  + GY+EINLNVGCPS RV  G FGACLM  P++V +C+AAM   +SIPVT
Sbjct: 60  ALAQCAKLAGERGYDEINLNVGCPSDRVQNGRFGACLMAEPELVAECVAAMKSEVSIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     L  L+++  K G +   IHARKA LKGLSPK+NR++P L+Y  VY
Sbjct: 120 VKTRIGIDEQDSYEFLCALIEASHKVGCDDFIIHARKAWLKGLSPKENREVPELNYPRVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L + +NGG++ + Q+L+ L  +DGVM+GR AY N  ML  VDE        +
Sbjct: 180 QLKKDYPQLDLSINGGVKTIEQSLEHLQYIDGVMVGREAYSNPFMLNEVDEKIYGDAANT 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  SM DY    +  G     + RHM+G+F G P +R  R  L+  
Sbjct: 240 Q---------TRHDVVRSMYDYIEEEMRLGANFWHVARHMLGIFQGQPGARGFRRHLSEN 290

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A + + E
Sbjct: 291 GHGKQADLSVMDKALSYVPE 310


>gi|34496379|ref|NP_900594.1| tRNA-dihydrouridine synthase A [Chromobacterium violaceum ATCC
           12472]
 gi|34102232|gb|AAQ58598.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 347

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 137/317 (43%), Positives = 190/317 (59%), Gaps = 9/317 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+FAR +T +  LYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 33  MLDWTDRHYRYFARQITRHTWLYTEMVTTGALLNGDVARHLRFDEAEHPVALQLGGSEPA 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ + +GY+E+NLNVGCPS RV +G+FGACLM  P +V DC+ AM  A+ I VT
Sbjct: 93  ELATCAKLAQQWGYDEVNLNVGCPSERVQKGAFGACLMAEPQLVSDCVKAMRDAVDIDVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       LR  V ++ ++G     +HAR AILKGLSPK+NR+IP L YD VY
Sbjct: 153 VKHRIGIDQIEHYDYLREFVDTVAEAGCRTFIVHARNAILKGLSPKENREIPPLKYDYVY 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++  ++  + L  VDGVM+GR AY N  ++   D  F    T  
Sbjct: 213 RLKRERPDLEILINGGVKTNAEIAEHLKHVDGVMVGREAYHNPWLMADWDALFYGDETAR 272

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                RV       +  +M  Y    L  G  ++ I RH++GLF G P +R  R +L+  
Sbjct: 273 ---PERV------AVVEAMMPYVTARLGDGSNVRHIARHILGLFQGLPGARNWRRMLSDA 323

Query: 301 AGASTATHHIIETAFNL 317
                A   ++  A+  
Sbjct: 324 KLLDGADAGLLRQAYEA 340


>gi|167646006|ref|YP_001683669.1| tRNA-dihydrouridine synthase A [Caulobacter sp. K31]
 gi|167348436|gb|ABZ71171.1| TIM-barrel protein, yjbN family [Caulobacter sp. K31]
          Length = 325

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 153/322 (47%), Positives = 205/322 (63%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R   R+L+  ALLY+EM+ + A+L GD + +LGF   + P+ALQ+GG++ +
Sbjct: 1   MMDWSDRHCRSLHRVLSRRALLYSEMVTSGAVLHGDCEKLLGFDAGQHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I EDFGY+EINLNVGCPS RV  G FGACLM  P +V DC+AAM  A+S+PVT
Sbjct: 61  DLAAAARIGEDFGYDEINLNVGCPSDRVQSGRFGACLMREPKLVADCMAAMTAAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  +L  LV    ++GV    +HARKA LKGLSPK+NR +P LDY +V+
Sbjct: 121 VKCRIGVDDQDPEQSLFELVDLSAQAGVTHFVVHARKAWLKGLSPKENRDVPPLDYPLVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG+ D+  +L  L  VDGVM+GRAAY    +L  VD          
Sbjct: 181 RLKAERPALTIVINGGIPDLDASLVQLAHVDGVMLGRAAYHEPGLLGQVDRRVFGEG--- 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D D +  +      Y A  L +G  L  ++RHM+GLFHG P +R  R ILTVE
Sbjct: 238 ------RDVDAFEAV-ELYKSYMASQLAAGVHLTAMSRHMLGLFHGMPGARAWRRILTVE 290

Query: 301 AGASTATHHIIETAFNLMIESL 322
             A+ A   +++ A   + +++
Sbjct: 291 GVAAGAGLEVVDRALAAVRQAV 312


>gi|78485554|ref|YP_391479.1| tRNA-dihydrouridine synthase A [Thiomicrospira crunogena XCL-2]
 gi|78363840|gb|ABB41805.1| tRNA-dihydrouridine synthase A [Thiomicrospira crunogena XCL-2]
          Length = 357

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 206/334 (61%), Gaps = 21/334 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R F R LT +A LY+EM+   AI+ G+  +  LG S  + P+ LQ+GG++ 
Sbjct: 25  MLDWTDRHCRVFHRQLTKHAWLYSEMVTTGAIIYGNNLERFLGHSEMDSPVVLQLGGSNP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IP 118
            +L   AK+ E++GY+EINLNVGCPS RV     GACLM +P+IV D ++AM  A+  IP
Sbjct: 85  EELAHCAKLGEEWGYSEINLNVGCPSDRVQNNMIGACLMAHPNIVADAVSAMKTAVKEIP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG+D+Q     L   V +I+ +GV+G+ IHARKA L+GLSPK+NR +P L YD 
Sbjct: 145 VTVKSRIGIDEQEDFDTLVEFVSAIQTAGVDGVIIHARKAWLQGLSPKENRDVPPLKYDW 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQAL----------KILPSVDGVMIGRAAYKNSAMLTT 228
           V +IK   P+L I +NGG++     L          + LP+VDGVM+GRA Y+   +LT 
Sbjct: 205 VRQIKALFPELEIAINGGIQTPQAGLNFLEILKDDEQSLPAVDGVMLGRAVYEKPYLLTE 264

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           VD  + +    +SP+K+R        +  +M  Y   HL  GGKL Q++RHM+GLF G P
Sbjct: 265 VDALYYDD---ASPVKSR------EAVLEAMYPYIENHLTQGGKLNQVSRHMLGLFAGLP 315

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
             R  R  ++  A  S A   +++ A+  ++  +
Sbjct: 316 GGRMWRRYISENAFKSGAGIDVLQEAYRRVVNEI 349


>gi|56461028|ref|YP_156309.1| tRNA-dihydrouridine synthase A [Idiomarina loihiensis L2TR]
 gi|56180038|gb|AAV82760.1| Predicted tRNA-dihydrouridine synthase [Idiomarina loihiensis L2TR]
          Length = 332

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 131/317 (41%), Positives = 196/317 (61%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT + LLYTEM+   AI+ G  ++ L F+ +E P+ALQ+GG++ +
Sbjct: 14  MLDWTDRHCRYFHRLLTRSTLLYTEMVTTGAIIFGQ-QDFLAFNAEEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + E A++ ++ GY+E+N+NVGCPS RV  GSFGACLM  P+ V +C+ AM     IPVT
Sbjct: 73  AMAECARLAQERGYDEVNINVGCPSDRVQNGSFGACLMAQPEKVAECVKAMKAVTDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+Q     L  L  ++  +GV+ + +HARKA L+GLSPK+NR IP L Y+ VY
Sbjct: 133 VKTRLGIDEQDSDDFLYELTDAVVAAGVDQLTLHARKAWLQGLSPKENRDIPELQYERVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             +K  PD+ + +NGG+ ++ +  + L  V GVMIGRAAY+N  +LT +D          
Sbjct: 193 RAQKRYPDVPVAINGGIVELHEVKQHLNQVHGVMIGRAAYQNPWLLTQLDSL-------- 244

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              +T+  +     +  +M  Y   H+  GG+   + RHM+GLF G    +R R  L+V+
Sbjct: 245 --SETKPAELTREAVVTAMIPYIDNHIRQGGRAWHVARHMLGLFQGMTGGKRWRQYLSVK 302

Query: 301 AGASTATHHIIETAFNL 317
              +T+   ++  A   
Sbjct: 303 GPRATSAEQLLYGALAF 319


>gi|107022641|ref|YP_620968.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia AU 1054]
 gi|116689590|ref|YP_835213.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia HI2424]
 gi|105892830|gb|ABF75995.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia cenocepacia AU
           1054]
 gi|116647679|gb|ABK08320.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia cenocepacia
           HI2424]
          Length = 365

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 191/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 38  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 97

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 98  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVRAMRDAVSVPVT 157

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 158 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 217

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 218 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYGS-TAA 276

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P++   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 277 VPMREEAE--------AQLIEYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLSDN 328

Query: 301 AGASTATHHIIETAFNLMIES 321
              +     + + A   + E+
Sbjct: 329 KKLARGDLAVFDEARAHLNEA 349


>gi|254475974|ref|ZP_05089360.1| tRNA-dihydrouridine synthase A [Ruegeria sp. R11]
 gi|214030217|gb|EEB71052.1| tRNA-dihydrouridine synthase A [Ruegeria sp. R11]
          Length = 320

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 149/321 (46%), Positives = 202/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ A A++RG   ++L  S +E P+ALQ+GG+D +
Sbjct: 6   MMDWTDRHCRYLHRLLSREALLYTEMVTAPALVRGGALHLLDHSVEEHPVALQLGGSDPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLN GCPS RV  G+FGA LM +PD+V +C+AAM   + + VT
Sbjct: 66  ELAEAARLGGQAGYDEINLNCGCPSDRVQSGAFGAVLMKSPDLVAECVAAMQAKVDVEVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   + +I  +G   + IHARKA LKGLSPK+NR IP LDYDIV+
Sbjct: 126 VKCRIGVDDQDPQEVLPGFIAAIAAAGCKRVTIHARKAWLKGLSPKENRDIPPLDYDIVH 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K E P L I +NGG+  + QA++ L   +DGVM+GRAAY   + +L   D        
Sbjct: 186 QMKAEFPALHISINGGITSLDQAVEHLDRGLDGVMVGRAAYHQPSDILCAADPRIFGTGE 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P+          ++ A M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 246 VSDPV----------EVVAQMLGYIDDEMAKGARLHQITRHMLGLFAGRPGARNWRRVLS 295

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A  S A   ++E A   + 
Sbjct: 296 EGASRSGAGTELVEAALQQVT 316


>gi|296388726|ref|ZP_06878201.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PAb1]
          Length = 332

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVDSQLFGS---E 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 258 APPLSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|146276373|ref|YP_001166532.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides ATCC 17025]
 gi|145554614|gb|ABP69227.1| TIM-barrel protein, yjbN family [Rhodobacter sphaeroides ATCC
           17025]
          Length = 335

 Score =  345 bits (885), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 150/319 (47%), Positives = 205/319 (64%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G ++ +LGFS  E P+ALQ+GG+D +
Sbjct: 23  MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRERLLGFSPAEHPVALQLGGSDPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++    G++EINLNVGCPS RV  G FGA LM  P ++ DC+AAM     +PVT
Sbjct: 83  ELAQAVRVAAPHGHDEINLNVGCPSDRVQSGCFGAVLMERPALLADCVAAMIAESPVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q PA  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 143 VKCRIGVDEQEPAEILPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  +SQA ++L   +DGVMIGRAAY    +L   D  +     G
Sbjct: 203 AMKRRFPELTICLNGGVATLSQAEELLAQGLDGVMIGRAAYNEPELLLGADRLW-----G 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +         ++ A M  Y A HL +GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 258 CEPPRD------LDRVLADMRPYIAEHLAAGGRLHQITRHMLGLFSGRPGARHWRRILSE 311

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   + + A   +
Sbjct: 312 GASRPGAGLDLFDEALEAV 330


>gi|49088070|gb|AAT51528.1| PA2795 [synthetic construct]
          Length = 333

 Score =  344 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVDSQLFGS---E 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 258 APPLSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|107102337|ref|ZP_01366255.1| hypothetical protein PaerPA_01003399 [Pseudomonas aeruginosa PACS2]
 gi|313107930|ref|ZP_07794099.1| hypothetical protein PA39016_001190015 [Pseudomonas aeruginosa
           39016]
 gi|310880601|gb|EFQ39195.1| hypothetical protein PA39016_001190015 [Pseudomonas aeruginosa
           39016]
          Length = 312

 Score =  344 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 1   MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 61  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 121 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 181 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVDSQLFGS---E 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 238 APPLSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 291

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 292 VHKAADPLRVFDQALELL 309


>gi|15597991|ref|NP_251485.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa PAO1]
 gi|218891014|ref|YP_002439880.1| tRNA-dihydrouridine synthase A [Pseudomonas aeruginosa LESB58]
 gi|38605052|sp|Q9I048|DUSA_PSEAE RecName: Full=tRNA-dihydrouridine synthase A
 gi|9948878|gb|AAG06183.1|AE004707_2 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|218771239|emb|CAW27004.1| putative TIM-barrel protein [Pseudomonas aeruginosa LESB58]
          Length = 332

 Score =  344 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGHPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVDSQLFGS---E 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 258 APPLSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|89054629|ref|YP_510080.1| tRNA-dihydrouridine synthase A [Jannaschia sp. CCS1]
 gi|88864178|gb|ABD55055.1| tRNA-U16,U17-dihydrouridine synthase [Jannaschia sp. CCS1]
          Length = 329

 Score =  344 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 146/321 (45%), Positives = 201/321 (62%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +ALLYTEM+ + A++ GD+  +L F   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRYFHRLMSRDALLYTEMVTSAAVINGDRNRLLRFDPAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  A +IV D+GY+E+NLNVGCPS RV  G FGA LM  PD+V +C+ AM     + VT
Sbjct: 74  ELAHAVRIVRDWGYDEVNLNVGCPSDRVQSGCFGAVLMRQPDLVAECVRAMRDECPVDVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL   ++++  +GV  + IHARKA L+GLSPK NR +P LDY +V+
Sbjct: 134 VKCRIGVDDQDPEDALPRFLEAMVTAGVTRVTIHARKAWLQGLSPKQNRDVPPLDYPLVF 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K+  P L I LNGG+  + +A   L   +DGVMIGRAAY   A +L   D+      T
Sbjct: 194 RMKQMFPQLHISLNGGIATLEEAGAHLEDGLDGVMIGRAAYHTPAEVLLQADQRIFGHAT 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            +             +++  M  Y   HL  GG+L QITRH++GLF G P +R  + IL+
Sbjct: 254 PARSA---------EEVALLMLPYIDAHLTDGGRLNQITRHILGLFAGRPGARGWKRILS 304

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   ++E A   +I
Sbjct: 305 EGAHQDGAGPELVERALQEVI 325


>gi|221638336|ref|YP_002524598.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides KD131]
 gi|221159117|gb|ACM00097.1| TIM-barrel protein, yjbN family [Rhodobacter sphaeroides KD131]
          Length = 313

 Score =  344 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 149/319 (46%), Positives = 203/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGQRDRLLGFSEAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 61  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPSLVADCVAAMIAESPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 121 VKCRIGVDEQEPSEVLPAFLETLAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D  +     G
Sbjct: 181 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADRLW-----G 235

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 236 EEPPRD------LAAVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 289

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   + + A   +
Sbjct: 290 GASRPGAGLALFDEALEAV 308


>gi|110834374|ref|YP_693233.1| tRNA-dihydrouridine synthase A [Alcanivorax borkumensis SK2]
 gi|110647485|emb|CAL16961.1| TIM-barrel protein, yjbN family [Alcanivorax borkumensis SK2]
          Length = 348

 Score =  344 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 136/319 (42%), Positives = 183/319 (57%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRF ARL+T + LLYTEM+VA AIL GD+   L F+ +E P+ALQ+GG+D  
Sbjct: 39  MMDWTTRDYRFLARLITRHTLLYTEMVVAQAILHGDRDRFLDFNDEEHPVALQLGGSDPQ 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A +I  D+GY+EINLNVGCPS RV +G  GA LM  P++V  C+ AM   +++PVT
Sbjct: 99  QLAQATRIAGDYGYDEINLNVGCPSDRVQQGKIGAILMAEPELVARCVEAMQAEVTVPVT 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V  ++ SG   + IHARKAIL GLSPK+NR IP L Y   Y
Sbjct: 159 VKTRIGIDDQDDYDFLYRFVDRMEASGCTSLTIHARKAILSGLSPKENRDIPPLIYQRAY 218

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK   P + I LNGG++ +++  + +  VDGVMIGR AY+N   L   D          
Sbjct: 219 AIKHAFPHIEIILNGGVKTLNEVHEHMGEVDGVMIGREAYQNPYFLAEADRVVFGDDHAI 278

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              +T         I+     Y  R    G   +   RH++ LF G P +RR R  L+  
Sbjct: 279 PSRQT---------IAEQFLPYVERRYALGHAPKHSLRHILNLFQGQPGARRFRRHLSEN 329

Query: 301 AGASTATHHIIETAFNLMI 319
                 T  ++  A + + 
Sbjct: 330 MHKPGTTPQVLMDALSQLP 348


>gi|88858983|ref|ZP_01133624.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas tunicata D2]
 gi|88819209|gb|EAR29023.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas tunicata D2]
          Length = 337

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 141/320 (44%), Positives = 188/320 (58%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +A+LYTEMI   AI+ G   + L F   E+P+ALQ+GG+D +
Sbjct: 27  MLDWTDRHCRTFHRKLTQHAVLYTEMITTGAIIYGRG-DYLHFGQHEQPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK  ++ GY EINLNVGCPS RV  G FGACLM  P++V  C+AAM +  ++PVT
Sbjct: 86  ALALCAKQADERGYQEINLNVGCPSDRVQNGRFGACLMAEPNLVAQCVAAMKEQTNMPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L  L+ +      N   IHARKA L GLSPK+NR IP LDY+ VY
Sbjct: 146 VKTRIGIDDQDSYEFLCALIDACIAVDCNDFIIHARKAWLSGLSPKENRDIPPLDYERVY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P   I +NGG++ + Q+L  L  +DGVM+GR AY N  +LT VD         S
Sbjct: 206 QLKKDYPQTHISINGGVKTIEQSLAHLQFIDGVMMGREAYANPYLLTQVDSAIYGD--AS 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   +M DY    +  G     + RHM+G+F G P  R  R  L+  
Sbjct: 264 TPVLSR------HQAVRAMYDYFEAEMTGGASFWHVARHMLGIFQGVPGGRAFRRHLSEN 317

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++E A   + E
Sbjct: 318 GHKKDADISVMEQALGFVAE 337


>gi|118497197|ref|YP_898247.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           novicida U112]
 gi|194323496|ref|ZP_03057273.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
 gi|118423103|gb|ABK89493.1| tRNA-dihydrouridine synthase [Francisella novicida U112]
 gi|194322351|gb|EDX19832.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           novicida FTE]
          Length = 327

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 190/324 (58%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N  T +
Sbjct: 193 SIKKDFPNLELGINGGITTIQETQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILT 298
                        +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+
Sbjct: 253 ISAL---------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A      TA  +    L
Sbjct: 304 ENATKKEANVDTFLTALEVFENKL 327


>gi|208778989|ref|ZP_03246335.1| RNA dihydrouridine synthase A [Francisella novicida FTG]
 gi|254372562|ref|ZP_04988051.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|254374021|ref|ZP_04989503.1| RNA dihydrouridine synthase A [Francisella novicida GA99-3548]
 gi|151570289|gb|EDN35943.1| RNA dihydrouridine synthase A [Francisella novicida GA99-3549]
 gi|151571741|gb|EDN37395.1| RNA dihydrouridine synthase A [Francisella novicida GA99-3548]
 gi|208744789|gb|EDZ91087.1| RNA dihydrouridine synthase A [Francisella novicida FTG]
          Length = 327

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 190/324 (58%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N  T +
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILT 298
                        +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+
Sbjct: 253 ISAL---------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A      TA  +    L
Sbjct: 304 ENATKKEANVDTFLTALEVFENKL 327


>gi|83952336|ref|ZP_00961067.1| tRNA-dihydrouridine synthase A [Roseovarius nubinhibens ISM]
 gi|83836009|gb|EAP75307.1| tRNA-dihydrouridine synthase A [Roseovarius nubinhibens ISM]
          Length = 343

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 146/324 (45%), Positives = 193/324 (59%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ A A++RG   ++L  + +E P+ALQ+GG+D  
Sbjct: 27  MMDWTDRHCRYLHRLLSREALLYTEMVTAPALVRGGAMHLLDHAPEEHPVALQLGGSDPE 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++  + GY+EINLN GCPS RV  G+FGA LM +P  V DC AAM  A  + VT
Sbjct: 87  ELAEAARLGAEAGYDEINLNCGCPSDRVQSGTFGAVLMTDPGRVADCCAAMIAATDVEVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  +  +GV    IHARKA LKGLSPK+NR IP LDYD+  
Sbjct: 147 VKCRIGVDDQDPEEVLPEFLARVGAAGVGRFTIHARKAWLKGLSPKENRDIPPLDYDLAR 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +    P L + +NGG+  +  A+++L    DGVM+GRAAY   A +L   D        
Sbjct: 207 RMIGLFPSLHLSINGGIATLDHAVELLDQGFDGVMLGRAAYHQPADILCAADRRIFGHDG 266

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             S  +  V          +M  Y   HL +GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 267 PDSTAEDAV---------QAMLPYIEAHLAAGGRLNQITRHMLGLFAGRPGARAWRRMLS 317

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A   ++E A   +   L
Sbjct: 318 EGASRPGAGPELVEEALTQIAPDL 341


>gi|302382184|ref|YP_003818007.1| hypothetical protein Bresu_1072 [Brevundimonas subvibrioides ATCC
           15264]
 gi|302192812|gb|ADL00384.1| TIM-barrel protein, yjbN family [Brevundimonas subvibrioides ATCC
           15264]
          Length = 341

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 155/326 (47%), Positives = 200/326 (61%), Gaps = 14/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  ALLYTEM+ A A+L GD++ +LGF   E P+ALQ+GG+D  
Sbjct: 14  MMDWTDRHCRAFHRALSTRALLYTEMVTAPAVLHGDRERLLGFDPVEHPVALQLGGSDPE 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I    GY+EINLNVGCPS RV  G FGACLM  P++V DC+AA+  A+ IP T
Sbjct: 74  QLAQAARIGAAMGYDEINLNVGCPSDRVQSGRFGACLMKEPELVADCMAAIKGAVDIPAT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PAV+L   V +    GV    +HARKA L GLSPK+NR +P LDY +V 
Sbjct: 134 VKCRIGVDDQDPAVSLFATVDASAAVGVTTFIVHARKAWLSGLSPKENRDVPPLDYGLVR 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +K+E P L I +NGG+  +  A   L      ++DGVM+GRAAY   A+L  VD     
Sbjct: 194 RLKRERPHLTICINGGIASLDAAEAHLDDTDGVALDGVMLGRAAYHEPALLGQVDRRLFG 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG       V++            Y A  L  G  L  +TRHM+GL HG P +R  R 
Sbjct: 254 EGTGDVDPFAAVER---------YKPYLAARLSEGWGLHAMTRHMLGLMHGRPGARAFRR 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ILTVEA    A   +++ A + + E+
Sbjct: 305 ILTVEAIRPGAGLEVVDRALDAVREA 330


>gi|84515494|ref|ZP_01002856.1| tRNA-dihydrouridine synthase A [Loktanella vestfoldensis SKA53]
 gi|84510777|gb|EAQ07232.1| tRNA-dihydrouridine synthase A [Loktanella vestfoldensis SKA53]
          Length = 315

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 141/323 (43%), Positives = 197/323 (60%), Gaps = 12/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL++ + L+Y+EM+ A A++ GD+  ++G+   E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLMSRHVLVYSEMVTAPAVIHGDRDRLIGYGPAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D GY+E+NLN GCPS RV  G FGA LM N  +V +C+AAM  A+ IPVT
Sbjct: 61  LLAQAARIAADMGYDEVNLNCGCPSDRVQSGFFGAVLMENAALVAECVAAMIAAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P+  L + +  +  +GV+   IHARKA L+GLSPK+NR IP LD+D+V 
Sbjct: 121 VKCRIGVDDQTPSDVLPDFIARVSAAGVDRFSIHARKAWLQGLSPKENRDIPPLDHDLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   P L + +NGG+  + QA   L   +DGVMIGRAAY     +L   D       +
Sbjct: 181 AMKALFPHLHLSVNGGITSLDQAQDFLDRGLDGVMIGRAAYHTPCDILLDADARIYADPS 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G S             +   M  Y A HL +GG+L QITRHM+G+F G P ++  R  L+
Sbjct: 241 GRS----------AEDVVHLMLPYIAEHLQNGGRLGQITRHMLGMFQGRPGAKAWRRHLS 290

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A    +  A   + ++
Sbjct: 291 EHAHQDGAGPQTVLAALAHVTQA 313


>gi|221213021|ref|ZP_03585997.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD1]
 gi|221167234|gb|EED99704.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD1]
          Length = 357

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 138/320 (43%), Positives = 189/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 30  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 90  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVAVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 210 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 269 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLSDN 320

Query: 301 AGASTATHHIIETAFNLMIE 320
                    + + A   + +
Sbjct: 321 KKLGRGDLAVFDEARAHLND 340


>gi|56707647|ref|YP_169543.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670118|ref|YP_666675.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134302420|ref|YP_001122390.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|224456717|ref|ZP_03665190.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370162|ref|ZP_04986168.1| tRNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254874464|ref|ZP_05247174.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604139|emb|CAG45141.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320451|emb|CAL08524.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134050197|gb|ABO47268.1| dihydrouridine synthase [Francisella tularensis subsp. tularensis
           WY96-3418]
 gi|151568406|gb|EDN34060.1| tRNA dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254840463|gb|EET18899.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282158805|gb|ADA78196.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 327

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 190/324 (58%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N  T +
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILT 298
                        +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+
Sbjct: 253 ISAL---------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A      TA  +    L
Sbjct: 304 ENATKKEANVDTFLTALEVFENKL 327


>gi|332560358|ref|ZP_08414680.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides WS8N]
 gi|332278070|gb|EGJ23385.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides WS8N]
          Length = 313

 Score =  344 bits (882), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 149/319 (46%), Positives = 203/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRDRLLGFSEAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 61  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPALVADCVAAMIAESPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 121 VKCRIGVDEQEPSEVLPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D  +     G
Sbjct: 181 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADRLW-----G 235

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 236 EEPPRD------LAAVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 289

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   + + A   +
Sbjct: 290 GASRPGAGLALFDEALEAV 308


>gi|289208454|ref|YP_003460520.1| TIM-barrel protein, yjbN family [Thioalkalivibrio sp. K90mix]
 gi|288944085|gb|ADC71784.1| TIM-barrel protein, yjbN family [Thioalkalivibrio sp. K90mix]
          Length = 329

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 146/316 (46%), Positives = 193/316 (61%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   R F RLLT  ALLYTEM+ A+A++ GD+  +LG    E PLALQ+GG+D  
Sbjct: 17  MMDWTDSWCRRFHRLLTRRALLYTEMVHANAVIHGDRDRLLGHVAAEHPLALQLGGSDPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  + G++EINLNVGCPS RV  G+FGACLM  P+ V   + AM  A+ +PVT
Sbjct: 77  TLAQAARIAAERGFDEINLNVGCPSDRVQSGTFGACLMAQPEQVARMVRAMQDAVDVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+Q     LRN V+++ + G     +HARKA L+GLSPKDNR +P LDY+ V+
Sbjct: 137 VKHRIGIDEQDSEADLRNFVETVARGGCRHFIVHARKAWLQGLSPKDNRDVPPLDYERVF 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L I LNGGL+D+  A   L  VDGVM GR AY    +L  VD  F +   G 
Sbjct: 197 RLKAEFPELTIVLNGGLDDVRVAHGYLERVDGVMFGRLAYHQPWVLAEVDRLFFDETGGV 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +             +   + D A      G  L ++TRH++GLFHG P +R+ R ILT  
Sbjct: 257 T----------REAVLQGLIDMAREMRAKGVPLARLTRHVLGLFHGEPGARQWRRILTEG 306

Query: 301 AGASTATHHIIETAFN 316
           A  + A   +IE A  
Sbjct: 307 AHRADAGPELIERAAE 322


>gi|77462473|ref|YP_351977.1| tRNA-dihydrouridine synthase A [Rhodobacter sphaeroides 2.4.1]
 gi|77386891|gb|ABA78076.1| tRNA-Dihydrouridine synthase [Rhodobacter sphaeroides 2.4.1]
          Length = 313

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 149/319 (46%), Positives = 203/319 (63%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+T  A+LYTEM+ A A++ G +  +LGFS  E P+ALQ+GG+D +
Sbjct: 1   MLDWTDRHCRFFHRLMTRRAMLYTEMVTAPAVIHGPRDRLLGFSEAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++ E +GY+EINLNVGCPS RV  G FGA LM  P +V DC+AAM     +PVT
Sbjct: 61  ELAQAVRLAEPYGYDEINLNVGCPSDRVQSGCFGAVLMERPSLVADCVAAMIAESPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P+  L   ++++  +GV    IHARKA L+GLSP++NR+IP LDY +V 
Sbjct: 121 VKCRIGVDEQEPSEVLPAFLETVAAAGVRHFVIHARKAWLQGLSPRENREIPPLDYPLVI 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K+  P+L I LNGG+  ++QA  +L   +DG+MIGRAAY    +L   D  +     G
Sbjct: 181 AMKRRFPELTICLNGGVGSLTQAEALLAQGLDGIMIGRAAYNEPELLLEADRLW-----G 235

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +          + A M  Y + HL  GG+L QITRHM+GLF G P +R  R IL+ 
Sbjct: 236 EEPPRD------LAAVLADMRPYISAHLEGGGRLHQITRHMLGLFAGRPGARHWRRILSE 289

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A   + + A   +
Sbjct: 290 GAARPGAGLALFDEALEAV 308


>gi|87122404|ref|ZP_01078285.1| hypothetical protein MED121_00605 [Marinomonas sp. MED121]
 gi|86162379|gb|EAQ63663.1| hypothetical protein MED121_00605 [Marinomonas sp. MED121]
          Length = 349

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 131/323 (40%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWT   YR FAR LT   LLYTEM+   A+L+GD  +  L F   E P+ALQ+GG+D 
Sbjct: 26  MLDWTTSDYRVFARALTTETLLYTEMVTTGALLKGDNPERFLRFEDIEHPIALQLGGSDA 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L + AK+ E FGY+E+NLN GCPS +V     GA LM +P+ V D + AM  A SIPV
Sbjct: 86  NALAQCAKLAEKFGYDEVNLNAGCPSYKVQHSLIGAILMAHPEKVKDAMKAMQDACSIPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+DDQ     +R+ +  +  +G     +HAR AIL GLSPK NR+IP L YD V
Sbjct: 146 TLKHRIGLDDQQDYSIVRDFIGDVATTGTQTFIVHARNAILAGLSPKQNREIPPLKYDFV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y++KK+ PDL I +NGG++ + +    L  +DGVM+GR AY N  +L+ VD    +    
Sbjct: 206 YQLKKDFPDLEIIINGGIKTLDECEHHLKHLDGVMVGREAYNNPWILSQVDSRLFD---K 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              ++ R+      +   +   +    L++G +L  +TRH++G+F G P  ++ R  L+ 
Sbjct: 263 EDQVQDRI------QALRNFVPFVEHRLNNGERLSHLTRHIMGIFLGQPGGKQFRRYLSE 316

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           +     A+  +++ A +L+ E L
Sbjct: 317 QGHKKDASIDVLKQAIDLVTEQL 339


>gi|163746890|ref|ZP_02154247.1| tRNA-dihydrouridine synthase A [Oceanibulbus indolifex HEL-45]
 gi|161380004|gb|EDQ04416.1| tRNA-dihydrouridine synthase A [Oceanibulbus indolifex HEL-45]
          Length = 335

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 143/310 (46%), Positives = 187/310 (60%), Gaps = 12/310 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+   LLYTEM+ A A++RG   ++L     E P+ALQ+GG+D +
Sbjct: 16  MMDWTDRHCRYLHRLLSRETLLYTEMVTAPALVRGGALHLLDHDPSEHPVALQLGGSDPT 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA++  + GY+EINLN GCPS RV  G+FGA LM  P +V DC+ AM  A  + VT
Sbjct: 76  ELAQAARLGAEAGYDEINLNCGCPSDRVQSGAFGAVLMQQPGLVADCVDAMRAACDVEVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 136 VKCRIGVDDQAPEEILPEFLARIVAAGCTRVTIHARKAWLQGLSPKENRDIPPLDYDLVH 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
           ++K   P+L I +NGG+  + QA   L   +DGVM+GR+AY     +L   D        
Sbjct: 196 QMKGLFPNLHISVNGGITSLDQAEAFLDAGLDGVMVGRSAYHAPTDILAGADRRIYGQGA 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            SS                 M  Y   HL SGG+L QITRHM+GLF G P +R+ R IL+
Sbjct: 256 DSS----------AEAAVQGMLPYIETHLASGGRLGQITRHMLGLFAGRPGARQWRRILS 305

Query: 299 VEAGASTATH 308
             A    A  
Sbjct: 306 EGAHKPGAGP 315


>gi|254427220|ref|ZP_05040927.1| TIM-barrel protein, yjbN family [Alcanivorax sp. DG881]
 gi|196193389|gb|EDX88348.1| TIM-barrel protein, yjbN family [Alcanivorax sp. DG881]
          Length = 350

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 139/319 (43%), Positives = 185/319 (57%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRF ARL+T + LLYTEM+VA AIL GD+   L F+ +E P+ALQ+GG+D  
Sbjct: 41  MMDWTTRDYRFLARLITRHTLLYTEMVVAQAILHGDRDRFLSFNNEEHPVALQLGGSDPQ 100

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EA++I  D+GY+EINLNVGCPS RV +G  GA LM  P++V  C+ AM  A+ +PVT
Sbjct: 101 QLAEASRIAGDYGYDEINLNVGCPSDRVQQGKIGAILMAEPELVARCVEAMQAAVRVPVT 160

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V  ++ +G   + IHARKAIL GLSPK+NR IP L Y   Y
Sbjct: 161 VKTRIGIDDQDDYDFLYRFVGRMEAAGCTSLTIHARKAILSGLSPKENRDIPPLIYQRAY 220

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IK+  P + I LNGG++ + Q  + +  VDGVMIGR AY+N   L   D          
Sbjct: 221 AIKQAFPHIEIILNGGVKTLDQVHEHMGEVDGVMIGREAYQNPYFLAEADRVVFGDDHA- 279

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I +R+       I+     Y  R    G   +   RH++ LF G P +RR R  L+  
Sbjct: 280 --IPSRL------AIAEQFLPYVERRYALGHAPKHSLRHILNLFQGQPGARRFRRHLSEN 331

Query: 301 AGASTATHHIIETAFNLMI 319
                 T  ++  A   + 
Sbjct: 332 MHKPETTPQVLMDALAQLP 350


>gi|206559989|ref|YP_002230753.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia J2315]
 gi|198036030|emb|CAR51923.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia J2315]
          Length = 353

 Score =  343 bits (880), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 189/321 (58%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 26  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPIALQLGGSERD 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 86  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVAVPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 146 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 206 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYGS-TAA 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A +  Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 265 VPTREEAE--------AQLIAYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLSDN 316

Query: 301 AGASTATHHIIETAFNLMIES 321
              +     + + A   + E+
Sbjct: 317 KKLARGDLAVFDEARAHLNEA 337


>gi|114771777|ref|ZP_01449170.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HTCC2255]
 gi|114547593|gb|EAU50484.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HTCC2255]
          Length = 318

 Score =  342 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 198/323 (61%), Gaps = 13/323 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+  RL++ N LLYTEM+ A A++ GD   +L F+  E P+ALQIGG+  ++
Sbjct: 1   MDWTDRHCRYLHRLISKNVLLYTEMVTAPALIHGDADRLLEFNQSEHPIALQIGGSHPNQ 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSIPVT 120
           L +A ++  + GY+EIN+N+GCPS RV  G FGACLM  P++V +C+ AM +A     +T
Sbjct: 61  LAQATRLGCEAGYDEININIGCPSDRVQFGRFGACLMKEPELVSECVTAMKEASTGAEIT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L + +  + ++GV+   IHARKA L GLSPK NR +P LDY++V+
Sbjct: 121 VKCRIGVDDQEPKRILPDFIDKVSQNGVSSFTIHARKAWLSGLSPKQNRDVPPLDYELVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           EIKKE P+L I LNGGL+   QA  +I   +DG MIGR AY N   +L   D  F     
Sbjct: 181 EIKKERPELEIILNGGLQTFDQAVHEINKGLDGAMIGRTAYHNPMEILANADSLFETNTN 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             S            KI   M  Y   HL +GG+L QITRHM+GLF G   ++  +  L+
Sbjct: 241 KKS----------VNKIIDEMLPYIQNHLDTGGRLNQITRHMLGLFSGQSGAKIWKRTLS 290

Query: 299 VEAGASTATHHIIETAFNLMIES 321
            EA    A   +++ A   ++E 
Sbjct: 291 DEAHKKDAGVEVVQNALRNVLEK 313


>gi|304391898|ref|ZP_07373840.1| tRNA-dihydrouridine synthase A [Ahrensia sp. R2A130]
 gi|303296127|gb|EFL90485.1| tRNA-dihydrouridine synthase A [Ahrensia sp. R2A130]
          Length = 349

 Score =  342 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 162/321 (50%), Positives = 214/321 (66%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R LT +ALLYTEM+VADA++ GD +  L F   E PLALQ+GG++  
Sbjct: 34  MMDWTDRHCRYFHRQLTRHALLYTEMVVADALIHGDIERHLRFHADEHPLALQLGGSEPE 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL+ AAK+ +D+GY+E+NLNVGCPS RV  G+FGACLM  P++V  C+ AM   +  PVT
Sbjct: 94  KLIFAAKLAQDWGYDEVNLNVGCPSDRVQSGTFGACLMREPELVARCVEAMKSVVDSPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L   +  +G +G+W+HARKA LKGLSPK+NR IP LDY+IV 
Sbjct: 154 VKCRIGVDDQEPRDALFKLAADVFAAGADGLWVHARKAWLKGLSPKENRDIPPLDYEIVR 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+   D FIGLNGGL  + QA      +DGVM+GRAAY +S  L  VD+ F       
Sbjct: 214 ELKRSYSDRFIGLNGGLATLEQAQHEGQGLDGVMLGRAAYHDSDQLRAVDKLFYGDDA-- 271

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                  D      +  +M ++AA H+ +GG+L  +TRHM+GLF G P +RR R++L+V 
Sbjct: 272 -------DSIDDTALCEAMMEHAAAHIAAGGRLHHVTRHMLGLFSGRPGARRYRNVLSVG 324

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   +I  AF++M + 
Sbjct: 325 AVPRDAGPEVIADAFSVMRQQ 345


>gi|152996532|ref|YP_001341367.1| tRNA-dihydrouridine synthase A [Marinomonas sp. MWYL1]
 gi|150837456|gb|ABR71432.1| TIM-barrel protein, yjbN family [Marinomonas sp. MWYL1]
          Length = 341

 Score =  342 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 128/319 (40%), Positives = 188/319 (58%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+DWT   YR FAR L+ N LLYTEM+   A+L+G+  +  L +   E P+ALQ+GG+D 
Sbjct: 25  MMDWTTSDYRVFARTLSKNTLLYTEMVTTGALLQGNHPERFLRYDECEHPIALQLGGSDA 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L + AK+ E  G++E+NLNVGCPS RV     GACLM +PD V + + AM    SIPV
Sbjct: 85  VALGKCAKMAEQAGFDEVNLNVGCPSDRVQNSLIGACLMAHPDKVKEAMRAMQDNCSIPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+DDQ     +R+ V  +  +GV    +HAR AIL+GLSPK+NR++P L Y  V
Sbjct: 145 TIKHRIGLDDQEDYSVVRDFVGDVATTGVTTFIVHARNAILEGLSPKENREVPPLKYHYV 204

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++KK+ PDL I +NGG++ + +  + L  VDGVM+GR AY N  +L+ VDE        
Sbjct: 205 HQLKKDFPDLEIIINGGIKTLDECKEQLAHVDGVMVGREAYHNPWILSQVDEVLFGG--- 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 +   +   +   +   Y  R L  G +L  +TRH++G+F G    ++ R  L+ 
Sbjct: 262 ------QPLVNDRYEALEAFVPYVERKLQEGERLMHLTRHILGIFQGEAGGKQFRRYLSE 315

Query: 300 EAGASTATHHIIETAFNLM 318
               + A  +++  A  L+
Sbjct: 316 NGHKADAQVNVLLEAIELV 334


>gi|254241250|ref|ZP_04934572.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|126194628|gb|EAZ58691.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
          Length = 332

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 133/318 (41%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ + LLYTEM+   A+L GD++  L +   E PLALQ+GG+  +
Sbjct: 21  MMDWTDRHCRFFLRQLSRHTLLYTEMVTTGALLHGDRQRFLRYDECEHPLALQLGGSVPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E+ GY+E+NLNVGCPS RV     GACLM NP +V DC+ AM  A+ I VT
Sbjct: 81  ELAACARLAEEAGYDEVNLNVGCPSDRVQHNMIGACLMGNPALVADCVKAMLDAVEIAVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR++P L Y++  
Sbjct: 141 VKHRIGINGRDSYAELCDFVGQVREAGCRSFMVHARIAILEGLSPKENREVPPLRYEVAA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ PDL I LNGG++ +    + L + DGVM+GR AY N  +L  VD          
Sbjct: 201 QLKKDFPDLEIVLNGGIKTLEACREHLQTFDGVMLGREAYHNPYLLAAVDSQLFGS---E 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  +R       +    +  Y  RH   GG +  +TRH++GL  GFP SRR R +L+V+
Sbjct: 258 APPLSR------SEALLRLRPYIERHQAEGGAMHHVTRHILGLAQGFPGSRRFRQLLSVD 311

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 312 VHKAADPLRVFDQALELL 329


>gi|90021133|ref|YP_526960.1| tRNA-dihydrouridine synthase A [Saccharophagus degradans 2-40]
 gi|89950733|gb|ABD80748.1| TIM-barrel protein, yjbN family [Saccharophagus degradans 2-40]
          Length = 331

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 195/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+D+H R+F R LT  + LYTEM+V  AI+ GD++  L F+  E P+ALQ+GG+D +
Sbjct: 20  MMDWSDKHCRYFWRQLTKKSRLYTEMVVTGAIIHGDRERFLQFNNAEHPIALQVGGSDPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+I +D+GY+EINLN GCPS RV  G  GA LM  P++V +CI AM KA  IPVT
Sbjct: 80  ALAQCARIAQDWGYDEINLNCGCPSDRVQNGMIGAILMSKPELVAECIDAMQKACDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD     AL N V ++ ++G N   +HARKA LKGLSPK+NR+IP L YD+V 
Sbjct: 140 VKHRIGIDDMEDYEALSNFVTTVAQTGCNTFIVHARKAWLKGLSPKENREIPPLRYDLVV 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK  P L I +NGG+  + QA  +L  +DGVMIGR AY N   L  VD+        S
Sbjct: 200 QLKKAFPHLNIVINGGINCLEQAKTLLNDLDGVMIGREAYHNPFFLADVDQKLFGTPNPS 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            ++      YA +   +G +L  ++RH++GL+ G   +R  R  +T+ 
Sbjct: 260 A---------NRHEVLDKFIHYAEQQNAAGTRLHHMSRHILGLYLGQKGARAFRRHITIH 310

Query: 301 AGASTATHHIIETAFNLM 318
           A    A+  ++  A  L+
Sbjct: 311 AANREASAVVLREAKQLV 328


>gi|49475574|ref|YP_033615.1| tRNA-dihydrouridine synthase A [Bartonella henselae str. Houston-1]
 gi|49238381|emb|CAF27608.1| hypothetical protein BH08090 [Bartonella henselae str. Houston-1]
          Length = 326

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 154/319 (48%), Positives = 212/319 (66%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEMIVADA++ G ++ +L  + +E P+ALQ+GG+D  
Sbjct: 17  MLGWTDRHCRFFYRLLTKKALLYTEMIVADAVIHGVREQLLALNHKEHPIALQLGGSDPQ 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G+FGACLML PDIV   + A+ K +++ VT
Sbjct: 77  KLAEAARIAEDFGYDEINLNVGCPSNRVQSGAFGACLMLYPDIVASAVEAIKKVVTLSVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y+ VY
Sbjct: 137 VKCRVGVDDQDEELALDLLADKVWNAGCDALWVHARKAWLKGLSPKENRDIPPLNYNRVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++  + FIG+NGG++ + +  + L   D  M+GR  Y +  +L  +D          
Sbjct: 197 KLKRKYHNKFIGINGGIKSIYEIKEHLILCDAAMVGRQVYHDPTLLKYIDSEIYGE---- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                + +      +  +M DYAA+H+ SGG L  +TRHMIGLFHG   +RR R IL+  
Sbjct: 253 -----QQNNLSDSDLIEAMCDYAAQHIASGGLLSHVTRHMIGLFHGRNGARRWRQILSNN 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A    A  H+++ AF+ +I
Sbjct: 308 ARGRDAGIHVLKEAFSALI 326


>gi|109900349|ref|YP_663604.1| tRNA-dihydrouridine synthase A [Pseudoalteromonas atlantica T6c]
 gi|109702630|gb|ABG42550.1| tRNA-U16,U17-dihydrouridine synthase [Pseudoalteromonas atlantica
           T6c]
          Length = 345

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 133/326 (40%), Positives = 188/326 (57%), Gaps = 15/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F R ++ ++LLYTEM+   AI+ G   + L F+  E P+ALQ+GG+D  
Sbjct: 17  MLDWTDKHCRYFLRQISKHSLLYTEMVTTGAIIFGKG-DYLAFNDTEHPVALQLGGSDPV 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A + ++ GY+E+N+NVGCPS RV  G FGACLM  P+ V  CI AM K + IPVT
Sbjct: 76  DMARCAVLAQEQGYDEVNINVGCPSDRVQNGRFGACLMAEPETVAACIQAMQKEVDIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ +  +G +   +HARKA LKGLSPK+NR IP L YD VY
Sbjct: 136 VKSRIGIDDMDEYKDLTDFIQIVADAGCDIFTVHARKAWLKGLSPKENRDIPPLMYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGG++ +  A   L  +DGVMIGR  Y N  +L  VD+ F       
Sbjct: 196 ALKEEFPQLNLSINGGVKTLDDATMHLEKLDGVMIGREVYSNPYILADVDKLFYQDD--- 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           SP+ +R       +I  +M  Y    + SG +   I RHM+GLF G P  R  R  L+  
Sbjct: 253 SPVPSR------EEIVHAMLPYVEAQMASGARAWNIARHMLGLFQGQPGGRIWRRYLSQH 306

Query: 301 AGAST-----ATHHIIETAFNLMIES 321
               +         ++  A   + E+
Sbjct: 307 GTGQSKNGLQVGPELLINALAAVEEA 332


>gi|325277336|ref|ZP_08142961.1| tRNA-dihydrouridine synthase A [Pseudomonas sp. TJI-51]
 gi|324097526|gb|EGB95747.1| tRNA-dihydrouridine synthase A [Pseudomonas sp. TJI-51]
          Length = 336

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 129/318 (40%), Positives = 185/318 (58%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+   LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKQTLLYTEMVTTGALLHNDADRFLRHDVSEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A++ PVT
Sbjct: 85  DLAACARLAEQAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVATPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAELCDFVGQVREAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + +    L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKADFPDLEIVLNGGIKTLGECQAHLQTFDGVMLGREAYHNPYLLAEVDQQLFG----- 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               +        +  A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 260 ----SEAAVISRSEALAQLRPYIVAHMESGGAMHHVTRHILGLAQGFKGARRFRQLLSAD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 316 IHKAAQPLAVFDQAVELL 333


>gi|149926267|ref|ZP_01914529.1| tRNA-dihydrouridine synthase A [Limnobacter sp. MED105]
 gi|149825085|gb|EDM84297.1| tRNA-dihydrouridine synthase A [Limnobacter sp. MED105]
          Length = 314

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 135/321 (42%), Positives = 186/321 (57%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +  LYTEMI   A++ GD+   L F+ +E P+A Q+GG+D  
Sbjct: 1   MIDWTDRHCRRFHRAISQHTWLYTEMITTGALVYGDRNRFLAFNDEEHPVAFQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   AK +E  GY+E+N+NVGCPS RV +G+FGACLM  P +V DC+ AM  A SI VT
Sbjct: 61  HMARCAKWIEQAGYDELNMNVGCPSERVQKGAFGACLMAEPGLVADCVKAMRDACSIDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L + V  + ++G N   +HAR A+LKGLSPK+NR IP L Y++V 
Sbjct: 121 VKHRIGLDYDESETMLFDFVGKVSEAGCNTFIVHARNAVLKGLSPKENRDIPPLRYEVVK 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P L I LNGG+  +      L   DG MIGR AY N  +L   DE    P T  
Sbjct: 181 RLKQHFPHLQIILNGGITTLEAIESHLQWADGCMIGREAYSNPWLLAGFDEVIGKPTT-- 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              KTR+D      +   +  YA + L  G  ++ IT+  +GLFHG P  R  R +L+  
Sbjct: 239 --QKTRLD------VIDELRAYAEQELSRGESIRSITKSWLGLFHGQPGGRLYRQVLSDS 290

Query: 301 AGASTATHHIIETAFNLMIES 321
                    ++E A  +M++S
Sbjct: 291 TRLKANNWQVVEDALAMMVKS 311


>gi|57339642|gb|AAW49808.1| hypothetical protein FTT0508 [synthetic construct]
          Length = 362

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 190/324 (58%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 39  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 98

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 99  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 158

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 159 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 218

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N  T +
Sbjct: 219 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 278

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILT 298
                        +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+
Sbjct: 279 ISAL---------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLS 329

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A      TA  +    L
Sbjct: 330 ENATKKEANVDTFLTALEVFENKL 353


>gi|89256833|ref|YP_514195.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115315219|ref|YP_763942.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|167009275|ref|ZP_02274206.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica FSC200]
 gi|169656701|ref|YP_001429066.2| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|254369716|ref|ZP_04985726.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|290954380|ref|ZP_06559001.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312201|ref|ZP_06803003.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144664|emb|CAJ79988.1| RNA dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115130118|gb|ABI83305.1| tRNA dihydrouridine synthase A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|157122675|gb|EDO66804.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|164551769|gb|ABU62110.2| tRNA dihydrouridine synthase [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 327

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 134/324 (41%), Positives = 189/324 (58%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+  YNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELDYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IKK+ P+L +G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N  T +
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILT 298
                        +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+
Sbjct: 253 ISAL---------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A      TA  +    L
Sbjct: 304 ENATKKEANVDTFLTALEVFENKL 327


>gi|221197852|ref|ZP_03570898.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2M]
 gi|221204590|ref|ZP_03577607.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2]
 gi|221175447|gb|EEE07877.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2]
 gi|221181784|gb|EEE14185.1| tRNA-dihydrouridine synthase A [Burkholderia multivorans CGD2M]
          Length = 357

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 138/320 (43%), Positives = 189/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 30  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVARHLAFTPNESPVALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+++PVT
Sbjct: 90  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVAVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAVEDYAFVRDFVGTVAEAGCSTFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 210 RLKHDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLADVDARFYGS-TDA 268

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 269 APTREEAE--------ARLIEYCAAELKRGTYLGAIVRHALGLYRGVPGARGWRRVLSDN 320

Query: 301 AGASTATHHIIETAFNLMIE 320
                    + + A   + +
Sbjct: 321 KKLGRGDLAVFDEARAHLND 340


>gi|254488703|ref|ZP_05101908.1| tRNA-dihydrouridine synthase A [Roseobacter sp. GAI101]
 gi|214045572|gb|EEB86210.1| tRNA-dihydrouridine synthase A [Roseobacter sp. GAI101]
          Length = 345

 Score =  342 bits (877), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 195/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RL++   LLYTEM+ + A++RG   ++L  S +E P+ALQ+GG+D +
Sbjct: 26  MMDWTDRHCRYLHRLMSKQTLLYTEMVTSPALVRGGALHLLDHSPEEHPVALQLGGSDPA 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLNVGCPS RV  GSFGA LM  P +V  C+AAM +A+ + VT
Sbjct: 86  ELAEAARLGAQAGYDEINLNVGCPSDRVQSGSFGAILMEQPALVAKCVAAMSRAVDVEVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA LKGLSPK+NR IP LDYD+V+
Sbjct: 146 VKCRIGVDDQAPETVLPEFLAHIVGAGCERVTIHARKAWLKGLSPKENRDIPPLDYDLVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K    +L I +NGG+  + QA + L   +DGVMIGR+AY + A +L   D       +
Sbjct: 206 RMKGLFSNLHISVNGGITSLDQAERFLDGGLDGVMIGRSAYHSPADILCQADRRIYGTGS 265

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++                 M  Y   H+  GG+L QITRHM+GLF G P +R  R  L+
Sbjct: 266 DTT----------AEDAVQQMLPYIDAHIDGGGRLNQITRHMMGLFAGRPGARIWRRHLS 315

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++  A + M
Sbjct: 316 ENASGPAANRQVLLDALDAM 335


>gi|86750510|ref|YP_487006.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris HaA2]
 gi|86573538|gb|ABD08095.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris HaA2]
          Length = 332

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 147/320 (45%), Positives = 196/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD   R F RLLT  A LYTEM+   A++ GD++ +LGF   E P+ALQ+GG+D +
Sbjct: 16  MMEWTDSRCRVFHRLLTKRARLYTEMVTTGAVIHGDRQRLLGFDASEHPVALQLGGSDPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAKI EDFGY+EINLNVGCPS RV EG FGACLM  P++V D +AAM +A+ IPVT
Sbjct: 76  ALATAAKIGEDFGYDEINLNVGCPSDRVKEGRFGACLMAEPELVADGVAAMKRAVEIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL  L + +  +GV+ + +HARKA L GLSPK+NR +P LDYD VY
Sbjct: 136 VKCRIGIDDQDPEAALDTLARGVVAAGVDALIVHARKAWLNGLSPKENRHVPPLDYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PDL I +NGG+  +++A   L  VDGVM+GRAAY+    L  VD          
Sbjct: 196 RLKRALPDLPIVINGGIGSIAEAKLHLAHVDGVMLGRAAYQEPWRLLEVDPELFGEAAPY 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +K             ++  Y    L  G +L  ITRH+IG + G P +R  R  L+  
Sbjct: 256 ATMK---------DALEALMPYIEDQLAQGVRLHAITRHLIGAYQGVPGARAFRRYLSEF 306

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A   + +
Sbjct: 307 GVKPDADASVLRKAMVAVEQ 326


>gi|325525397|gb|EGD03227.1| tRNA-dihydrouridine synthase A [Burkholderia sp. TJI49]
          Length = 328

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 139/321 (43%), Positives = 192/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L FS  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFSPNESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMNDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAEAGCATFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 RLKRDFPELEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TDA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 240 APTREEAE--------AKLIEYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLSDN 291

Query: 301 AGASTATHHIIETAFNLMIES 321
              +     + + A   + ++
Sbjct: 292 KKLARGDLAVFDEARAHLNDA 312


>gi|15806701|ref|NP_295421.1| tRNA-dihydrouridine synthase A [Deinococcus radiodurans R1]
 gi|6459466|gb|AAF11254.1|AE002011_5 conserved hypothetical protein [Deinococcus radiodurans R1]
          Length = 333

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 186/322 (57%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT   LLYTEM+   AIL GD+   L FS  E PLALQ+GG+D +
Sbjct: 16  MMDWTDRHCRMFHRTLTRRTLLYTEMVTTGAILHGDQGRHLDFSAPEHPLALQLGGSDAA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A++ ED+GY+E+NLN GCPS RV  GSFGACLM  PD+V   + AM  A  +PVT
Sbjct: 76  ALAECARLAEDWGYDEVNLNCGCPSDRVSSGSFGACLMGTPDVVARAVEAMRAATRLPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+++  +G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 136 VKHRIGIDDLDSYEHLTGFVRTVAAAGCEQFIVHARKAWLSGLSPKENREIPPLRYEVVQ 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L + LNGG++ +++A + L   DGVMIGRAAY+   +L   D          
Sbjct: 196 QLKADFPQLTVVLNGGVKSLTEAQQALAWADGVMIGRAAYQEPYLLAAADRDVFGEDA-- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R+   +   Y A  + +G  L ++ +H +GLF G P +R  +  L+ +
Sbjct: 254 -------QAVSRREAIEAYLPYVAAQVEAGQPLNRMMKHTLGLFAGQPGARHWKRTLSEQ 306

Query: 301 AGASTATHHIIETAFNLMIESL 322
                A   ++  A   + + +
Sbjct: 307 GHKPGAGLDVVRAALAGVPDDV 328


>gi|319898967|ref|YP_004159060.1| tRNA-dihydrouridine synthase A [Bartonella clarridgeiae 73]
 gi|319402931|emb|CBI76482.1| tRNA-dihydrouridine synthase A [Bartonella clarridgeiae 73]
          Length = 331

 Score =  341 bits (876), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 160/318 (50%), Positives = 208/318 (65%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEM +AD ++ G ++ +L FS +E P+ALQ+GG+D  
Sbjct: 22  MLGWTDRHCRFFYRLLTKKALLYTEMFIADTVIHGVRERLLAFSNEEHPIALQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML PDIV   + AM +A++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGACLMLYPDIVAQAVEAMKRAVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   +  +G +G+W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEELALDFLADRVWNAGCDGLWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K +  + FIGLNGG+  +S+  + L S D VM+GR  Y N  +L  +D         +
Sbjct: 202 NLKHKYENNFIGLNGGIRSISEIKEHLRSCDAVMVGRQVYNNPVLLCLIDSEIYGESGYN 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +  +M DY A+H+ SGG+L  +TRHMIGLF G   +RR R IL+  
Sbjct: 262 ---------LSDCDLINAMCDYTAKHIASGGRLSHVTRHMIGLFQGRDGARRWRQILSHN 312

Query: 301 AGASTATHHIIETAFNLM 318
           A    A  HI++ AF+ +
Sbjct: 313 ATRRDANVHILKEAFSAI 330


>gi|186476399|ref|YP_001857869.1| YjbN family TIM-barrel protein [Burkholderia phymatum STM815]
 gi|184192858|gb|ACC70823.1| TIM-barrel protein, yjbN family [Burkholderia phymatum STM815]
          Length = 333

 Score =  341 bits (875), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 137/320 (42%), Positives = 190/320 (59%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSFHRTLSRHAWLYTEMVTTGALIHGDVARHLAFTADEAPVALQLGGSERE 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P++V DC+ AM  A+S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMKEPELVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVDD      +R+ V +I  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDDVEDYAFVRDFVGTIADAGCDVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 197 RLKRDFPQLEIIINGGIKTLDEVETHLQHVDGVMLGREAYHNPFVLADVDARFYGS-TDA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +        A + +Y    L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 256 APTREEAE--------AQLIEYCRAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     I + A   + E
Sbjct: 308 KKLAARDLAIFDEARQHLRE 327


>gi|295676394|ref|YP_003604918.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1002]
 gi|295436237|gb|ADG15407.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1002]
          Length = 333

 Score =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDTVEEYGFVRDFVGTIAEAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    T S
Sbjct: 197 QLKRDFPQLEIIINGGIKTLDEVDTHLQHVDGVMLGREAYHNPYVLADVDARFYGS-TQS 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + +V+        A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 256 PPTRDQVE--------AKLIEYCATEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     I + A   + E L
Sbjct: 308 KRLAARDLTIFDEARQHLREPL 329


>gi|187932026|ref|YP_001892011.1| tRNA-dihydrouridine synthase A [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712935|gb|ACD31232.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 327

 Score =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 134/324 (41%), Positives = 190/324 (58%), Gaps = 11/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+  RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG    
Sbjct: 13  MLDWTDRHYRYMMRLITRHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ E+ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++
Sbjct: 73  DFISCGKLAEELGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++G++ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVDKQVQAGIDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            IKK+ P+L +G+NGG+  + +  + L  VD VM+GR AY N  +    D  F N  T +
Sbjct: 193 SIKKDFPNLELGINGGITTIQEIQQHLKYVDSVMMGREAYHNPMLFKDFDNIFYNQPTTN 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILT 298
                        +I+  M +Y    + +    KL  IT+H + LF+G PN++  R  L+
Sbjct: 253 ISAL---------EIAYKMAEYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLS 303

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
             A    A      TA  +    L
Sbjct: 304 ENATKKEAKVDTFLTALEVFKNKL 327


>gi|319407299|emb|CBI80940.1| tRNA-dihydrouridine synthase A [Bartonella sp. 1-1C]
          Length = 331

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 162/318 (50%), Positives = 208/318 (65%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTDRH RFF RLLT  ALLYTEM VAD ++ G +K +L FS +E P+A+Q+GG+D  
Sbjct: 22  MLGWTDRHCRFFYRLLTKRALLYTEMFVADTVIYGIRKKLLAFSDEEHPIAIQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGA LML+PDIV   + AM + ++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGAYLMLHPDIVARAVEAMKRTVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   I   G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEELALDFLADRIWNVGCDALWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++  + FIGLNGG++ +S+  + L S D VM+GR  Y N   L  +D          
Sbjct: 202 NLKRKYENNFIGLNGGIKSISEIKEHLRSCDAVMVGRQVYHNPIWLRLIDSEIYG----- 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P     D D    +  +M DY A+H+ SGG+L  ITRHMIGLF G   +RR R IL+ +
Sbjct: 257 EPQNNLSDYD----LINAMCDYTAKHIASGGRLSHITRHMIGLFQGRDGARRWRQILSHD 312

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A  H ++ AF  +
Sbjct: 313 ATKTDANVHTLKEAFASI 330


>gi|237746180|ref|ZP_04576660.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes HOxBLS]
 gi|229377531|gb|EEO27622.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes HOxBLS]
          Length = 328

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 193/323 (59%), Gaps = 14/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ N  LYTEM+   A+L GD    L FS +E P+ALQ+GG++ +
Sbjct: 13  MLDWTDRHCRYFHRLISRNTWLYTEMVTTGALLYGDVARHLDFSEEEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + AK+ E +GY+EINLN GCPS RV +G+FGACLM    +V DC+ AM  A+SI VT
Sbjct: 73  ELAQCAKLGEKWGYDEINLNCGCPSERVQKGAFGACLMKESKLVADCVRAMKDAVSIDVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      +R+ +  I  +G     +HAR AILKGLSPK+NR+IP L YD+VY
Sbjct: 133 VKHRIGIDDMHTYDFVRDFIGEIAGAGCQTFIVHARNAILKGLSPKENREIPPLRYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I LNGG+E   Q  + L  VDGVMIGRAAY     +   D  F    T  
Sbjct: 193 QLKKDFPGLEILLNGGVETAGQVEEHLKHVDGVMIGRAAYHYPWRMAEFDARFYGDGTVP 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL----HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                         + A+M  Y  + L      G ++  ITRHM+GL  G P +RR R I
Sbjct: 253 ENPS---------AVVAAMIPYIEKQLALYGEKGLRMHGITRHMLGLVTGMPGARRFRQI 303

Query: 297 LTVEAG-ASTATHHIIETAFNLM 318
           L+  A  AS     I+  A   +
Sbjct: 304 LSDPARLASGNPAAILMEALAAV 326


>gi|220923671|ref|YP_002498973.1| tRNA-dihydrouridine synthase A [Methylobacterium nodulans ORS 2060]
 gi|219948278|gb|ACL58670.1| TIM-barrel protein, yjbN family [Methylobacterium nodulans ORS
           2060]
          Length = 337

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 152/323 (47%), Positives = 207/323 (64%), Gaps = 11/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+  A LYTEM+   A+L G ++ ++GF   E P+A+Q+GG+D  
Sbjct: 21  MMDWTDRHCRAFHRVLSARARLYTEMVTTGAVLHGPRERLIGFDPAEHPVAIQLGGSDPG 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  +A+I E +GY E+NLNVGCPS RV +G FGACLM  P +VG+C+AAM  A++IPVT
Sbjct: 81  ELAASARIAEGYGYAEVNLNVGCPSDRVQDGRFGACLMREPALVGECVAAMKAAVAIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  S++ +GV+G+ +HARKA L+GLSPK+NR IP LDY  V+
Sbjct: 141 VKCRIGVDDQDPEAALDALTASVRAAGVDGLVVHARKAWLQGLSPKENRDIPPLDYPRVH 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
            +K  +PDL I +NGGL  ++QA   L  VDGVM+GRAAY   A+L  VD E+F  P   
Sbjct: 201 RLKAAHPDLPIAINGGLNSLAQAQAQLAHVDGVMLGRAAYAEPALLLGVDPEFFGTPAPV 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P               +   Y A  L  G +L  +TRHM+GLF+G P +R  R  L+ 
Sbjct: 261 AGPF----------AAVEAYLPYIAARLGEGIRLHAMTRHMLGLFNGRPGARAFRRHLST 310

Query: 300 EAGASTATHHIIETAFNLMIESL 322
           E   + A   ++  A + +   +
Sbjct: 311 EGLRANAGLGVLREAVSFVSREM 333


>gi|319404295|emb|CBI77888.1| tRNA-dihydrouridine synthase A [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 331

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 159/318 (50%), Positives = 207/318 (65%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+ WTD+H RFF RLLT  ALLYTEM VAD ++ G +K +L FS +E P+A+Q+GG+D  
Sbjct: 22  MLGWTDQHCRFFYRLLTKKALLYTEMFVADTVIYGIRKKLLAFSDEEHPIAIQLGGSDPK 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I EDFGY+EINLNVGCPS RV  G FGACLML+PDIV   +  M + ++I VT
Sbjct: 82  KLAEAARIAEDFGYDEINLNVGCPSDRVQAGIFGACLMLHPDIVARAVEEMKRTVTIAVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   +AL  L   +  +G + +W+HARKA LKGLSPK+NR IP L+Y  VY
Sbjct: 142 VKCRIGVDDQDEKLALDFLADRVWNAGCDALWVHARKAWLKGLSPKENRDIPPLNYKRVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++  + FIGLNGG++ +S+  + L S D  M+GR  Y N   L  +D          
Sbjct: 202 NLKRKYKNNFIGLNGGIKSISEIKEHLRSCDAAMVGRQVYHNPIWLNLIDSEIYG----- 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P     D D    +  +M DY A+H+ SGG+L  ITRHMIGLF G   +RR R IL+  
Sbjct: 257 EPQNNLSDYD----LINAMCDYTAKHIASGGRLSHITRHMIGLFQGRDGARRWRQILSHN 312

Query: 301 AGASTATHHIIETAFNLM 318
           A  + A   I++ AF  +
Sbjct: 313 ATKTDANVRILKEAFAAI 330


>gi|91976520|ref|YP_569179.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris BisB5]
 gi|91682976|gb|ABE39278.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris BisB5]
          Length = 317

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 149/320 (46%), Positives = 198/320 (61%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD   R F RLLT    LYTEM+   A++RGD++ +LGF   E P+ALQ+GG++ +
Sbjct: 1   MMEWTDTRCRVFHRLLTRRGRLYTEMLTCGAVIRGDRQRLLGFDASEHPVALQLGGSNPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA I EDFGY+EINLNVGCPS RV EG FGACLM  P +V DC+AAM +A++IPVT
Sbjct: 61  DLATAATIGEDFGYDEINLNVGCPSDRVKEGRFGACLMAEPMLVADCVAAMKRAVTIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL NL +S+  +GV+ + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 121 VKCRIGIDDQDPETALDNLAQSVVAAGVDALIVHARKAWLNGLSPKENRDIPPLDYDRVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  ++QA + L  VDGVM+GRAAY+    L  VD          
Sbjct: 181 RLKRAMPAVPIIINGGITSIAQAKQHLAYVDGVMLGRAAYQEPWRLLDVDPELFGEAAPH 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +K             ++  Y    L  G +L  ITRH+IG + G P +R  R  L+  
Sbjct: 241 ATMK---------DALEALMPYIEDQLAQGVRLHAITRHLIGAYQGVPGARAFRRYLSEF 291

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A   + E
Sbjct: 292 GVKPDADVSVLAKAMVAVGE 311


>gi|85704298|ref|ZP_01035401.1| tRNA-dihydrouridine synthase A [Roseovarius sp. 217]
 gi|85671618|gb|EAQ26476.1| tRNA-dihydrouridine synthase A [Roseovarius sp. 217]
          Length = 321

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 146/322 (45%), Positives = 193/322 (59%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  R L+ +ALLYTEM+ A A++RG   ++L  S +E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRRLSRHALLYTEMVTAPALVRGGAVHLLEHSPEEYPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++    GY EINLN GCPS RV  G FGA LM  P +V +C AAM  A  + VT
Sbjct: 61  ELARAARMGAQAGYAEINLNCGCPSDRVQSGRFGAILMTEPALVAECCAAMIDAQPVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +GV  + IHARKA L GLSPK+NR IP L+YD+V 
Sbjct: 121 VKCRIGVDDQTPEEVLPEFLAQIIAAGVQRVQIHARKAWLDGLSPKENRDIPPLNYDLVQ 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  + QA+ +L   +DGVM+GRAAY   A +L   D        
Sbjct: 181 RMKMLFPNLHISINGGITSLDQAVSLLDQGLDGVMVGRAAYHQPADILCAADRRIFGSTE 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +  +  V          +M  Y   HL SGG+L QITRHM+GLF G P +R  R  L+
Sbjct: 241 PDTTPEGAV---------QAMLPYIETHLASGGRLNQITRHMLGLFAGRPGARAWRRHLS 291

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A   + +
Sbjct: 292 EGATRPGAGPELVERALAEVTD 313


>gi|167566497|ref|ZP_02359413.1| tRNA-dihydrouridine synthase A [Burkholderia oklahomensis EO147]
 gi|167570050|ref|ZP_02362924.1| tRNA-dihydrouridine synthase A [Burkholderia oklahomensis C6786]
          Length = 339

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 136/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +  LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHTWLYTEMVTTGALVHGDVARHLAFTPGEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AMC A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMCDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKQDFPQLEIIVNGGITTLDEVERHLQHVDGVMLGREAYHNPYVLADVDARFYG---AA 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 TPAPTR------EAVEAQLVEYCATELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMI 319
              +     I + A   + 
Sbjct: 308 KRLARGDLSIFDEARAHLT 326


>gi|254245521|ref|ZP_04938842.1| tRNA-dihydrouridine synthase [Burkholderia cenocepacia PC184]
 gi|124870297|gb|EAY62013.1| tRNA-dihydrouridine synthase [Burkholderia cenocepacia PC184]
          Length = 359

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 189/321 (58%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 32  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 92  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVRAMRDAVSVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 152 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 211

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 212 RLKRDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYGA-TAA 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A +  Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 271 VPTREEAE--------AQLIAYCAAELKRGTYLGAIVRHALGLYRGMPGARGWRRVLSDN 322

Query: 301 AGASTATHHIIETAFNLMIES 321
              +     + + A   + E+
Sbjct: 323 KKLARGDLAVFDEARAHLNEA 343


>gi|170720872|ref|YP_001748560.1| tRNA-dihydrouridine synthase A [Pseudomonas putida W619]
 gi|169758875|gb|ACA72191.1| TIM-barrel protein, yjbN family [Pseudomonas putida W619]
          Length = 321

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ + LLYTEM+   A+L  D    L     E PLALQ+GG+  +
Sbjct: 10  MMDWTDRHCRFFLRLLSRHTLLYTEMVTTGALLHNDAHRFLRHDVSEHPLALQLGGSVPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+S PVT
Sbjct: 70  DLAACARLAEQAGYDEVNLNVGCPSDRVQNNMIGACLMAHPALVADCVKAMRDAVSTPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++ +G     +HAR AIL+GLSPK+NR+IP L YD+  
Sbjct: 130 VKHRIGINGRDSYAELCDFVGQVRDAGCRSFTVHARIAILEGLSPKENREIPPLRYDVAA 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + ++   L + DGVM+GR AY N  +L  VD+        +
Sbjct: 190 QLKADFPDLEIVLNGGIKTLEESKAHLETFDGVMLGREAYHNPYVLAEVDQVLFGS---N 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +        A +  Y   H+ SGG +  +TRH++GL  GF  +RR R +L+ +
Sbjct: 247 APVVSRSEAM------AKLRPYIVAHIESGGAMHHVTRHILGLGQGFKGARRFRQLLSAD 300

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A  L+
Sbjct: 301 IHKAPEPLVVFDQAAELL 318


>gi|91783334|ref|YP_558540.1| tRNA-dihydrouridine synthase A [Burkholderia xenovorans LB400]
 gi|91687288|gb|ABE30488.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia xenovorans
           LB400]
          Length = 333

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRVISRHTWLYTEMVTTGALLHGDVPRHLAFTPVEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I  +G N   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEEYGFVRDFVGTIADAGCNVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 197 QLKRDFPHLEIIINGGIKTLDEVETHLQHVDGVMLGREAYHNPYLLAGVDARFYG--SAD 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+          ++ A + DY A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 255 TPLTRE-------QVEAKLIDYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     I + A   + E +
Sbjct: 308 KRLAARDLSIFDEARQHLREPV 329


>gi|163739977|ref|ZP_02147382.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis BS107]
 gi|161386722|gb|EDQ11086.1| tRNA-dihydrouridine synthase A [Phaeobacter gallaeciensis BS107]
          Length = 315

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 148/321 (46%), Positives = 201/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+N ALLYTEM+ + A++RG   ++L  S QE P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLLSNEALLYTEMVTSPALVRGGALHLLDHSPQEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA    + GY+EINLN GCPS RV  G+FGA LM +PD+V +C+AAM   + + VT
Sbjct: 61  ELAQAAAFGAEAGYDEINLNCGCPSDRVQSGAFGAVLMKSPDLVAECVAAMRAKVDVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I  +G   + IHARKA LKGLSPK+NR IP LDY+IV+
Sbjct: 121 VKCRIGVDDQDPQEVLPVFLERIAAAGCERVTIHARKAWLKGLSPKENRDIPPLDYEIVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           ++K E P L I LNGG+  + +AL  L   +DGVMIGRAAY   + +L+  D       +
Sbjct: 181 QMKAEFPQLHISLNGGVASLDEALPHLERGLDGVMIGRAAYHQPSDILSQADPLIFGTGS 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+           +   M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 241 ATDPV----------AVVGHMLGYIDDQMAQGARLHQITRHMLGLFAGRPGARNWRRVLS 290

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   ++ETA   + 
Sbjct: 291 EGASRPGADTRLVETALEQVT 311


>gi|152980796|ref|YP_001354180.1| tRNA-dihydrouridine synthase A [Janthinobacterium sp. Marseille]
 gi|151280873|gb|ABR89283.1| tRNA-dihydrouridine synthase [Janthinobacterium sp. Marseille]
          Length = 344

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 192/318 (60%), Gaps = 1/318 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T +  LYTEM+   A+L GD    L F+ +E P+ALQ+GG++ +
Sbjct: 23  MMDWTDRHCRMFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFNEEEHPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+ E +GY+E+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+SI VT
Sbjct: 83  DLAKSAKLGEQWGYDEVNLNCGCPSERVQKGAFGACLMNETGLVADCVKAMRDAVSIDVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      +R+ V +I  +G N   +HAR AILKGLSPK+NR+IP L Y+  Y
Sbjct: 143 VKHRIGIDDITSYDFVRDFVGTIADAGCNTFIVHARNAILKGLSPKENREIPPLRYEFAY 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG + +++    L  VDGVM+GR AY N  +++T D  +      +
Sbjct: 203 QLKKDFPALEIIINGGTKTVAEIDTHLQHVDGVMLGREAYHNPFLMSTFDARYYGD-DAT 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S  +  V +     I A +  +       G K+  ITRHM+GL  G PNSR  R  L+  
Sbjct: 262 SKTRAEVVQAMIPYIHAQLQLHGKSEKGGGLKVNSITRHMLGLMAGLPNSRAFRQTLSDS 321

Query: 301 AGASTATHHIIETAFNLM 318
              +     ++  A   M
Sbjct: 322 KKLALGDPDLLLQALARM 339


>gi|332304623|ref|YP_004432474.1| TIM-barrel protein, yjbN family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332171952|gb|AEE21206.1| TIM-barrel protein, yjbN family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 345

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 136/326 (41%), Positives = 189/326 (57%), Gaps = 15/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F R ++ +ALLYTEM+   AI+ G   + L F+  E P+ALQ+GG+D +
Sbjct: 17  MLDWTDKHCRYFLRQISKHALLYTEMVTTGAIIFGKG-DYLAFNEAEHPVALQLGGSDPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A + ++ GY+E+N+NVGCPS RV  G FGACLM  P  V DCI AM K + IPVT
Sbjct: 76  DMARCAVLAQERGYDEVNINVGCPSDRVQNGRFGACLMAEPKTVADCINAMQKEVDIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L + ++ I  +G     +HARKA LKGLSPK+NR IP L YD VY
Sbjct: 136 VKSRIGIDDMDEYKDLTDFIQVIADAGCEIFTVHARKAWLKGLSPKENRDIPPLMYDRVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGG++ +  A   L  +DGVMIGR  Y N  +L  VD+ F    T  
Sbjct: 196 ALKEEFPHLNLSINGGVKTLDDAALHLDKLDGVMIGREVYSNPYILADVDKRFYQDQT-- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       +I  +M  Y  + + SG +   I RHM+GLF G P  R  R  L+  
Sbjct: 254 -PVPSR------EEIVHAMLPYVEKQMASGARAWNIARHMLGLFQGQPGGRVWRRYLSQH 306

Query: 301 AGAST-----ATHHIIETAFNLMIES 321
               +         ++  A   + E+
Sbjct: 307 GTGQSKNGLQVGPELLVNALAAVNEA 332


>gi|90423563|ref|YP_531933.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris BisB18]
 gi|90105577|gb|ABD87614.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris BisB18]
          Length = 330

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 145/322 (45%), Positives = 196/322 (60%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  A LY+EM+   A++ GD++ +LGF   E PLALQ+GG+D +
Sbjct: 14  MMDWTDRHCRVFHRRLSRRARLYSEMLTTGAVIHGDRQRLLGFDASEHPLALQLGGSDSA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAKI EDFGY+EINLNVGCPS RV +G FGACLM  P +V + IAAM +A+S+PVT
Sbjct: 74  DLATAAKIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPALVAEGIAAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P +AL +L +++  +G + + +HARKA L GLSPK+NR +P LDYD VY
Sbjct: 134 VKCRIGIDDQDPELALDSLARAVVAAGADLLVVHARKAWLNGLSPKENRDVPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + I +NGG+  +++A   L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKAALPAVPIVINGGIAGIAEAKPHLGHVDGVMLGRAAYQEPWRLLAVDPELFGEPAPY 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                            +MT Y    L  G +L  ITRH +G +HG P +R  R  L  +
Sbjct: 254 P---------SMTAALQAMTPYIEAQLAQGTRLHSITRHFVGAYHGVPGARAFRRHLAEQ 304

Query: 301 AGASTATHHIIETAFNLMIESL 322
                A   ++  A   + + +
Sbjct: 305 GVKPDAGIDVLREAIARVEDRV 326


>gi|269468879|gb|EEZ80471.1| tRNA-dihydrouridine synthase [uncultured SUP05 cluster bacterium]
          Length = 310

 Score =  339 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 131/297 (44%), Positives = 187/297 (62%), Gaps = 9/297 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+F RL++ +  LYTEMI   AIL GD+  +L +   E PL LQ+GG++  +
Sbjct: 1   MDWTDRHCRYFYRLMSKHTQLYTEMITTKAILHGDQARLLDYHQDEHPLTLQLGGSNTDE 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +   AKI +D+GY+E+N+N GCPS RV  GSFGACLM  P +V DC+ AM +  ++ +TV
Sbjct: 61  MARCAKIAQDWGYDEVNINAGCPSDRVQSGSFGACLMNTPQVVADCVDAMKQVSNLSITV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIGVDD      L N +  ++KSG +   IHARKA LKGLSPK+NR +P L+YD VY+
Sbjct: 121 KSRIGVDDMESYDELTNFISLVEKSGCDTFIIHARKAWLKGLSPKENRTVPPLNYDWVYQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           IK++ P L IG+NGG+  +  A K L  VD VM+GRA Y    +LT VDE   +  +  +
Sbjct: 181 IKQDFPSLTIGINGGINHLEDACKHLEKVDSVMLGRAVYHQPYLLTDVDEIIYHQSSSIT 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                       ++  S  DY       G  ++ +TRH++GL+HG  N+++ + +L+
Sbjct: 241 ---------SREQVLLSFIDYMKVQSQQGVPIRAMTRHILGLYHGQKNAKKFKRLLS 288


>gi|92113327|ref|YP_573255.1| tRNA-dihydrouridine synthase A [Chromohalobacter salexigens DSM
           3043]
 gi|91796417|gb|ABE58556.1| tRNA-U16,U17-dihydrouridine synthase [Chromohalobacter salexigens
           DSM 3043]
          Length = 346

 Score =  339 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 143/321 (44%), Positives = 193/321 (60%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+DWT R YR FAR LT  ALLYTEM+   AIL G  +   LG+S  E PLALQ+GG+D 
Sbjct: 29  MMDWTTRDYRAFARTLTREALLYTEMVTTGAILHGSPRERFLGYSDVEHPLALQLGGSDP 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L E A I E +GY+E+NLNVGCPS RV     GACLM  PD V   + AM  A+SIPV
Sbjct: 89  AELAECAAIAEAWGYDEVNLNVGCPSDRVQNNLIGACLMAYPDKVAAAVRAMQAAVSIPV 148

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIG+DDQ     L   + ++  +G +   IHARKA L+GLSPK+NR +P L+Y  V
Sbjct: 149 TVKCRIGIDDQDEDADLARFIGTVADAGADTFIIHARKAWLEGLSPKENRDVPPLNYARV 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + +K + P L IG+NGG++ +      L  VD VMIGR AY+N  +L  VD         
Sbjct: 209 HRLKTQYPALHIGINGGIKSLEDCQAHLEHVDSVMIGREAYQNPWLLAGVDAALYGT--- 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SP+ +R      ++ + ++  Y A  L +G KL  +TRH++GLF G P  R+ R  L+ 
Sbjct: 266 PSPVTSR------QEAARALRPYIAERLAAGAKLNHVTRHLLGLFQGCPGGRQFRRHLSE 319

Query: 300 EAGASTATHHIIETAFNLMIE 320
            A    A   + + A + + +
Sbjct: 320 NAHRPGADLAVFDEALSKVHD 340


>gi|241668892|ref|ZP_04756470.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877424|ref|ZP_05250134.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843445|gb|EET21859.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 324

 Score =  339 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 188/321 (58%), Gaps = 13/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+HYR+  RL+T   +LYTEMI  +AI+ G+K  +L ++ +E P+ LQ+GG    
Sbjct: 13  MLDWTDKHYRYMMRLITKQTMLYTEMITLNAIIHGNKDFLLKYNPEENPVTLQLGGCVPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ ++ GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L +P++
Sbjct: 73  DFITCGKLAQNLGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLDVPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D       L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDHNDSYEELYNFVNKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  +    + L  VD VMIGR AY N  +    D  F N P+  
Sbjct: 193 NIKKDFPNLELGINGGVTTIEDTQEHLKYVDSVMIGREAYHNPMLFKDFDNLFYNQPIND 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            SP+          +++  M +Y    L+S    KL  IT+H + LF+G PN++  R  L
Sbjct: 253 ISPL----------EVAYEMAEYIKIQLNSDPNMKLNNITKHTLNLFNGLPNAKVFRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +  A    A       A  + 
Sbjct: 303 SENATKKDANVDTFLKAIEVF 323


>gi|226356731|ref|YP_002786471.1| tRNA-dihydrouridine synthase A [Deinococcus deserti VCD115]
 gi|226318721|gb|ACO46717.1| putative tRNA-dihydrouridine synthase A [Deinococcus deserti
           VCD115]
          Length = 346

 Score =  339 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 134/322 (41%), Positives = 184/322 (57%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT   LLYTEM+   AIL GD++  LGF+  E P+ALQ+GG+D +
Sbjct: 21  MMDWTDRHCRVFHRTLTRRTLLYTEMVTTGAILHGDRERHLGFNRVEHPVALQLGGSDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E  ++ ED+GY+EINLN GCPS RV  GSFGACLM  PD+V   + AM     +PVT
Sbjct: 81  ALAECTRMAEDYGYDEINLNCGCPSDRVSSGSFGACLMGTPDVVARAVEAMRGVTRLPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V++++ +G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 141 VKHRIGIDDLDSYEHLTRFVRTVEAAGCQTFIVHARKAWLSGLSPKENREIPPLRYEVVE 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L + LNGG+ D+ QA   L   DGVMIGRAAY+   +L   D          
Sbjct: 201 QLKADFPHLTVVLNGGVLDLRQAQGALNWADGVMIGRAAYQTPYVLAAADHEIFGEAAVP 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R+   +   Y A  L +G  L ++ +H +GLF G P +R  +  L+ +
Sbjct: 261 ---------VTRREAIEAFLPYVAGQLAAGQPLNRMMKHTLGLFAGQPGARHWKRTLSEQ 311

Query: 301 AGASTATHHIIETAFNLMIESL 322
                A   ++  A   +   +
Sbjct: 312 GHRDGAGLEVVRAALEGVPAEV 333


>gi|332142739|ref|YP_004428477.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|332142839|ref|YP_004428577.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552761|gb|AEA99479.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552861|gb|AEA99579.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 348

 Score =  339 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 193/321 (60%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ + LLYTEM+   AI+ G   + LG++ +E P+A+Q+GG+D S
Sbjct: 25  MLDWTDRHCRYFLRLMSKHTLLYTEMVTTGAIIYGKG-DYLGYNKEEHPIAVQLGGSDPS 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + + A++ ++ GY+E+N+NVGCPS RV  GSFGACLM  P++V +C+ AM  A+ IPVT
Sbjct: 84  DMAKCAELSQERGYDEVNINVGCPSDRVKNGSFGACLMAQPEVVANCVKAMQSAVDIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DD          + ++  +G +   +HARKA L+GLSPK+NR+IP L+Y  V+
Sbjct: 144 VKCRIGIDDMDEDEDFARFIDTVADAGCDTFIVHARKAWLQGLSPKENREIPPLNYPRVH 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG++ +++  + L SVDGVM+GR  Y N  ++++VD+         
Sbjct: 204 RLKQARPELSISINGGIKTLAETQQQLESVDGVMVGREVYANPYIMSSVDKDIFGDANAQ 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S  +        R+I   M  Y  R      K     RH++GL+ G    R  R  L+  
Sbjct: 264 SLSR--------REIVLQMQQYIERQEDPYFKPWHAARHILGLYQGQAGGRIWRRYLSQN 315

Query: 301 AGASTATHHIIETAFNLMIES 321
                   +++  A + +  +
Sbjct: 316 GTGKNPDPNLLLNALDAVESA 336


>gi|297624812|ref|YP_003706246.1| TIM-barrel protein, yjbN family [Truepera radiovictrix DSM 17093]
 gi|297165992|gb|ADI15703.1| TIM-barrel protein, yjbN family [Truepera radiovictrix DSM 17093]
          Length = 354

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 144/322 (44%), Positives = 201/322 (62%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR F R +T   LLYTEM+  +A+LRGD++ +LGFS  EKPLALQ+GG D  
Sbjct: 15  MMDWTDRHYRAFMRGVTRRTLLYTEMVHVNAVLRGDRERVLGFSEFEKPLALQLGGDDPR 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL   A++ ED+GY+E+NLNVGCPS RV  G+FGACLM  P+ V  C+AAM +A ++PVT
Sbjct: 75  KLAACARVAEDWGYSELNLNVGCPSPRVQRGNFGACLMAQPERVAACVAAMREATTLPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD+     L + V+ + ++      +HARKA L GLSPK+NR +P L Y+ VY
Sbjct: 135 VKHRIGIDDRDRFDDLAHFVEVVAQAAPARFTVHARKAWLSGLSPKENRTVPPLRYEEVY 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+ +P+L I LNGG+  +  A   L  VD VMIGRAAY++   L   D  F       
Sbjct: 195 QLKRLHPELEIELNGGVRSLEAAAAHLGRVDAVMIGRAAYEDPYALARADALFYGAPHVP 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +           R++  +   YA+R L  G  L  +TRH++GLF G P +R  R +L+ +
Sbjct: 255 T----------RREVVEAFLPYASRQLERGVPLASLTRHLLGLFTGAPGARAWRRLLSEQ 304

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A    A   ++E A   + + +
Sbjct: 305 AHQPGAGVEVLERALGALPDEV 326


>gi|325914535|ref|ZP_08176879.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
 gi|325539305|gb|EGD10957.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
          Length = 334

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 139/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRMRLIGFDPVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +D+GY+EINLN GCPS RV  G FGACLM  P +V +C+AAMC A ++P+T
Sbjct: 79  LLAQAATIAQDWGYDEINLNCGCPSDRVQAGRFGACLMREPTLVAECVAAMCAATALPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYAVFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +++E P L + LNGG+  +  AL  L   DGVM+GRAAY +  +L  +D          
Sbjct: 199 RLRQERPGLPVVLNGGIAAVDTALAHLQQTDGVMLGRAAYHDPYVLHQLDAAL------- 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               T+  +     +  ++  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 252 ----TQRPEQPREALLRALRPYVESQLEQGLALKHITRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALQ 323


>gi|170732894|ref|YP_001764841.1| tRNA-dihydrouridine synthase A [Burkholderia cenocepacia MC0-3]
 gi|169816136|gb|ACA90719.1| TIM-barrel protein, yjbN family [Burkholderia cenocepacia MC0-3]
          Length = 328

 Score =  339 bits (870), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 189/321 (58%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVRAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 RLKHDFPSLEIVINGGITTLDEVAQHLEHVDGVMLGREAYHNPYVLAEVDARFYGS-TAA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A + +Y A  L  G  L  I RH +GL+ G P +R  R +L+  
Sbjct: 240 VPTREEAE--------AQLIEYCAGELKRGTCLGAIVRHALGLYRGMPGARGWRRVLSDN 291

Query: 301 AGASTATHHIIETAFNLMIES 321
              +     + + A   + E+
Sbjct: 292 KKLARGDLAVFDEARAHLNEA 312


>gi|300312882|ref|YP_003776974.1| hypothetical protein Hsero_3587 [Herbaspirillum seropedicae SmR1]
 gi|300075667|gb|ADJ65066.1| conserved hypothetical protein [Herbaspirillum seropedicae SmR1]
          Length = 357

 Score =  339 bits (869), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 188/322 (58%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T +  LYTEM+   A+L GD    L F  QE P+ALQ+GG++ +
Sbjct: 32  MMDWTDRHCRVFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFDEQEHPVALQLGGSEPA 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV +G+FGACLM  P +V DC+ AM  A+SI VT
Sbjct: 92  DLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAMRDAVSIDVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +R+ V  I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 152 VKHRIGIDEVESYDFVRDFVGQIAEAGCQTFIVHARNAILKGLSPKENREIPPLKYDYAY 211

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG++ + +  + L  VDGVM+GR AY N  ++   D  +   L G 
Sbjct: 212 QLKKDFPSLEILINGGIKTLPEIDEHLKHVDGVMLGREAYHNPYLMAGFDARYYAALEGG 271

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL------HSGGKLQQITRHMIGLFHGFPNSRRCR 294
                   +    ++  +M  Y  R L        G +L  ITRHM+GL  G P +R  R
Sbjct: 272 -------LQRSRAEVIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGLMAGMPGARAFR 324

Query: 295 HILTVEAGASTATHHIIETAFN 316
             L+     +     ++  A  
Sbjct: 325 QTLSDSKRLALGDPALLLEALQ 346


>gi|291296460|ref|YP_003507858.1| YjbN family TIM-barrel protein [Meiothermus ruber DSM 1279]
 gi|290471419|gb|ADD28838.1| TIM-barrel protein, yjbN family [Meiothermus ruber DSM 1279]
          Length = 339

 Score =  339 bits (869), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 137/321 (42%), Positives = 191/321 (59%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+  RL++    LYTEM+V  +IL G++  +L FS +E P+ALQ+GG+   
Sbjct: 16  MLDWTDRHFRYLVRLISRRVRLYTEMVVDQSILLGNRPKLLDFSPEEHPVALQLGGSVPE 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EAA+I E +GY+EINLN+GCPS RV  G FGACLML PD+V + +AAM +A+ IPVT
Sbjct: 76  KLAEAARIGEAWGYDEINLNLGCPSERVQGGGFGACLMLEPDLVAESMAAMRQAVKIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+GVD+      L   V+ +   GV    +HARKA LKGLSP +NR IP L YD VY
Sbjct: 136 AKHRLGVDEVEDYRYLARFVEKLAGVGVGVFIVHARKAYLKGLSPAENRTIPPLRYDWVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I LNGG+  + +    L  VDGVM+GRA Y++  +L   D         +
Sbjct: 196 RLKQDFPHLTIVLNGGVRTLEEVQAHLAKVDGVMLGRAVYEDPFVLEPADRRLFGEAHAT 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +          +++ +M  YA   L  G  L  + RHM+ LF G P  R  R +L+  
Sbjct: 256 TRL----------EVAQAMLRYAEAQLEQGTPLWAMARHMLNLFKGQPRGRLWRRVLSER 305

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   +++ A   +  S
Sbjct: 306 ACRRGAGVEVLQEALERVAAS 326


>gi|209885665|ref|YP_002289522.1| tRNA-dihydrouridine synthase A [Oligotropha carboxidovorans OM5]
 gi|209873861|gb|ACI93657.1| tRNA-dihydrouridine synthase A [Oligotropha carboxidovorans OM5]
          Length = 332

 Score =  339 bits (869), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 144/319 (45%), Positives = 193/319 (60%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+   A++ G ++ +LGF   E P+ALQ+GG++  
Sbjct: 14  MMDWTDRHCRVFHRALTRRALLYTEMVTTGAVIHGSRERLLGFDACEHPVALQLGGSNPR 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+AKI E FGY+EINLNVGCPS RV +G FGACLM  P +VG+C+ AM  A+ +PVT
Sbjct: 74  DLAESAKIGEGFGYDEINLNVGCPSDRVQDGRFGACLMAEPQLVGECVVAMKAAVRVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL +L +S+  +G + + +HARKA L+GLSPK+NR +P LDYD VY
Sbjct: 134 VKCRIGIDDQDPERALDDLARSVVTAGADALIVHARKAWLQGLSPKENRNVPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   PD+ I +NGG+  + +A   L  VDGVM+GRAAY+    L  VD    +     
Sbjct: 194 RLKAAMPDMTIAINGGIASIEEARGHLQHVDGVMLGRAAYQEPWRLLAVDPELFDAPPPH 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            +   ++  Y  +    G +L  ITRHM+G FHG   +R  R  L   
Sbjct: 254 A---------SMHEAIETLFPYIEKERARGTRLHSITRHMVGAFHGVAGARAFRRALAET 304

Query: 301 AGASTATHHIIETAFNLMI 319
                A    +  A  L+ 
Sbjct: 305 CVKPEAGIDELRAALRLVT 323


>gi|254439812|ref|ZP_05053306.1| Dihydrouridine synthase superfamily [Octadecabacter antarcticus
           307]
 gi|198255258|gb|EDY79572.1| Dihydrouridine synthase superfamily [Octadecabacter antarcticus
           307]
          Length = 320

 Score =  339 bits (869), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 148/322 (45%), Positives = 195/322 (60%), Gaps = 8/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ + A++RG  +++L F   E+P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLLSKRALLYTEMVTSPALVRGQARHLLRFDPAEQPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA +  D GY EINLNVGCPS RV  G FGA LM  P +V  C AAM +A    VT
Sbjct: 61  ELAKAAVMGADAGYVEINLNVGCPSDRVQSGCFGAVLMERPALVAQCCAAMIQAQPSEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P V L   +  I  +GV  + IHARKA LKGLSPK+NR IP LDYD+V 
Sbjct: 121 VKCRIGVDDQDPEVVLPEFLARIVGAGVTRVAIHARKAWLKGLSPKENRDIPPLDYDLVL 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  +  A ++L   +DGVMIGRAAY N   +L   D        
Sbjct: 181 RMKGLFPNLHISINGGIASLEHAKELLDLGLDGVMIGRAAYHNPTDILQRADAVIWGDDV 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           G  P+      D   ++   +  +       GGKL  +T+HM+GLF G P SR+ R  L+
Sbjct: 241 GPDPL------DIVMQMRNYIDAHMVDQTRGGGKLAHVTKHMMGLFAGQPGSRQWRRYLS 294

Query: 299 VEAGASTATHHIIETAFNLMIE 320
             A    A   ++E A   M +
Sbjct: 295 ENAHRDGAGWAVVEDALAAMEQ 316


>gi|158423257|ref|YP_001524549.1| tRNA-dihydrouridine synthase A [Azorhizobium caulinodans ORS 571]
 gi|158330146|dbj|BAF87631.1| dihydrouridine synthase TIM-barrel protein [Azorhizobium
           caulinodans ORS 571]
          Length = 338

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 152/318 (47%), Positives = 200/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R L+  A LYTEM+ A AI+ GD+  +LG+S  E P+ +Q+GG++ +
Sbjct: 14  MMEWTDRHCRAFHRTLSRRAWLYTEMVTAPAIIHGDRARLLGYSQAEHPVVVQLGGSNPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I  DFGY+EINLNVGCPS RV  G+FGACLM +P +V +C+AAM  A+SIPVT
Sbjct: 74  LLAEAARICADFGYDEINLNVGCPSDRVKGGNFGACLMRDPALVAECVAAMRAAVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ    AL  L  ++  +G   + +HARKA LKGLSPK+NR+IP LDYD V+
Sbjct: 134 VKCRIGVDDQDVEEALDALADAVLAAGCARLIVHARKAWLKGLSPKENREIPPLDYDRVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P + I LNGGL  +  A      +DGVM+GRAAY++  +L  VD          
Sbjct: 194 RLKARLPHVPIELNGGLVTLEDARAAGAGLDGVMLGRAAYQDPDLLLEVDAQVHGETPPH 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +        D +  I+A    Y A HL +GG+L  ITRHM+GLF G P +R  R  L  E
Sbjct: 254 A--------DAFEAIAA-FEPYIAAHLEAGGRLHDITRHMLGLFGGRPGARTYRRTLATE 304

Query: 301 AGASTATHHIIETAFNLM 318
           A    A   ++  A   +
Sbjct: 305 ALVPGAGLEVLRKAVAAI 322


>gi|170692264|ref|ZP_02883427.1| TIM-barrel protein, yjbN family [Burkholderia graminis C4D1M]
 gi|170142694|gb|EDT10859.1| TIM-barrel protein, yjbN family [Burkholderia graminis C4D1M]
          Length = 317

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 186/322 (57%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 61  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G +   +HAR AILKGLSPK+NR+IP L Y+  Y
Sbjct: 121 VKHRIGVDAVEEYGFVRDFVGTIAEAGCDVFIVHARNAILKGLSPKENREIPPLKYEYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+  + +    L  VDGVM+GR AY N  +L  VD  F       
Sbjct: 181 QLKRDFPHLEIIINGGIRTLDEVETHLQHVDGVMLGREAYHNPYLLADVDARFYGSTQAP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 241 ---------LTREQVEAQLIEYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 291

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     I + A   + E +
Sbjct: 292 KRLAARDLAIFDEARQHLREPV 313


>gi|296157694|ref|ZP_06840528.1| TIM-barrel protein, yjbN family [Burkholderia sp. Ch1-1]
 gi|295891940|gb|EFG71724.1| TIM-barrel protein, yjbN family [Burkholderia sp. Ch1-1]
          Length = 317

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 186/322 (57%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRSLHRVISRHTWLYTEMVTTGALLHGDVPRHLAFTPAEAPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I  +G N   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEEYGFVRDFVGTIADAGCNVFIVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N   L  VD  F       
Sbjct: 181 QLKRDFPHLEIIINGGIKTLDEVETHLQHVDGVMLGREAYHNPYRLADVDARFYGSTDSP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++ A + DY A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 241 ---------LTREQVEAKLIDYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 291

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     I + A   + E +
Sbjct: 292 KRLAARDLSIFDEARQHLREPV 313


>gi|115523989|ref|YP_780900.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris BisA53]
 gi|115517936|gb|ABJ05920.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris BisA53]
          Length = 332

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 147/321 (45%), Positives = 197/321 (61%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L+  ALLYTEM+   A++ GD++ +LGF   E P+ALQ+GG+   
Sbjct: 14  MMDWTDRHCRVFHRVLSRRALLYTEMVTTGAVIHGDRQRLLGFHDSEHPVALQLGGSAPR 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA I E+FGY+EINLNVGCPS RV +G FGACLM  P++V + +AAM  A+ +PVT
Sbjct: 74  DLASAAAIGEEFGYDEINLNVGCPSDRVKDGRFGACLMAEPELVAEGVAAMKHAVRVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P +AL  L +++  +GV+ + +HARKA L+GLSPK NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPELALDTLARALVDAGVDLLIVHARKAWLQGLSPKQNRDIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L I +NGG+  +++A   L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKASLPRLPIVINGGISGIAEAKPHLDHVDGVMLGRAAYQEPWRLLAVDPELFGEPAPH 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +K             +MT Y A  L  G +L  ITRH +G FH  P +R  R  L   
Sbjct: 254 ASMK---------AALEAMTPYIAEELARGTRLHAITRHFVGAFHAVPGARAFRRHLAEH 304

Query: 301 AGASTATHHIIETAFNLMIES 321
             A  A   ++  A + + + 
Sbjct: 305 GVAPDAGIAVLREAIDRIADQ 325


>gi|254449979|ref|ZP_05063416.1| tRNA-dihydrouridine synthase A [Octadecabacter antarcticus 238]
 gi|198264385|gb|EDY88655.1| tRNA-dihydrouridine synthase A [Octadecabacter antarcticus 238]
          Length = 319

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 149/319 (46%), Positives = 194/319 (60%), Gaps = 16/319 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+  ALLYTEM+ + A++RG  +++L F   E+P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYLHRLLSKRALLYTEMVTSPALVRGQARHLLRFDPVEQPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++  D GY EINLNVGCPS RV  G FGA LM  P +V  C AAM +A    VT
Sbjct: 61  ELARAAEMGADEGYPEINLNVGCPSDRVQSGCFGAVLMEQPALVAACCAAMIRAQPSEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ   + L   +  I  +GV  + IHARKA LKGLSPK+NR IP LDYD+V 
Sbjct: 121 VKCRIGVDDQDSEIVLPEFLAQIVGAGVTRVTIHARKAWLKGLSPKENRDIPPLDYDLVL 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   P+L I +NGG+  +  A ++L   +DGVMIGRAAY N A +L   D        
Sbjct: 181 RMKGLFPNLHISINGGVGSLEHAKELLDLGLDGVMIGRAAYHNPADILQRADAVIWGDDL 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL----HSGGKLQQITRHMIGLFHGFPNSRRCR 294
           G  P+           +   M  Y   H+     SGGKL  +T+HM+GLF G P SR+ R
Sbjct: 241 GPDPL----------DVVLQMRSYIEAHMSDETRSGGKLAHVTKHMMGLFAGQPGSRQWR 290

Query: 295 HILTVEAGASTATHHIIET 313
             L+  A  S A   ++E 
Sbjct: 291 RYLSENAYRSGAGWSVVED 309


>gi|331006974|ref|ZP_08330216.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC1989]
 gi|330419221|gb|EGG93645.1| tRNA-dihydrouridine synthase A [gamma proteobacterium IMCC1989]
          Length = 310

 Score =  338 bits (868), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 185/318 (58%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+  RL++ ++ LYTEM+   A+L  +    L ++ +E PLALQ+GG+D  
Sbjct: 1   MMDWSDRHCRYLWRLISQHSRLYTEMVTTGALLHREPARFLDYNPEEHPLALQLGGSDAG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A + E +GY E+NLN GCPS RV  G  GACLM +P+ V D   AM   + I VT
Sbjct: 61  DLARCAILAEQWGYYEVNLNCGCPSDRVQNGMIGACLMAHPEKVADAYQAMQDKVDIEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD      + N ++ I   G     +HARKA LKGLSPK+NR++P L+Y  V+
Sbjct: 121 IKHRIGIDDMDDYEGMVNFIRPIAARGCQTFIVHARKAWLKGLSPKENREVPPLEYAFVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++ +   L  L  VDGVM+GR AY N  +L  VD++       S
Sbjct: 181 RLKQEFPELTIVINGGIKTLDDTLMHLTKVDGVMVGREAYSNPYLLAEVDQHVFGD---S 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            PI +R        I+    DY  + +  G +L  ++RH++GL+ G P +R  R  ++  
Sbjct: 238 HPIPSRT------AIAEQYIDYCVKQMDKGSRLNHLSRHILGLYQGEPGARAFRRHISEN 291

Query: 301 AGASTATHHIIETAFNLM 318
           A    AT  ++  A   +
Sbjct: 292 AHRDNATVDVLVDALRYI 309


>gi|237748250|ref|ZP_04578730.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes OXCC13]
 gi|229379612|gb|EEO29703.1| tRNA-dihydrouridine synthase A [Oxalobacter formigenes OXCC13]
          Length = 330

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 135/323 (41%), Positives = 195/323 (60%), Gaps = 15/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +  LYTEM+   A+L GD    L FS +E P+ALQ+GG++  
Sbjct: 16  MLDWTDRHCRYFHRLISRHTWLYTEMVTTGALLFGDVARHLDFSEEEHPIALQLGGSEPG 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A++ E +GY+EINLN GCPS RV +G+FGACLM    +V +C+ AM  A+SI VT
Sbjct: 76  DLAQCARLGEKWGYDEINLNCGCPSERVQKGAFGACLMSESTLVANCVKAMQDAVSIDVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ +  + ++G     +HAR AILKGLSP++NR+IP L Y++VY
Sbjct: 136 VKHRIGIDKNESYDFVRDFIGEVAEAGCKTFIVHARNAILKGLSPRENREIPPLRYEVVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS-NPLTG 239
           ++KK+ P+L I LNGG+E   +  + +  VDGVMIGRAAY     +   D  F  +P T 
Sbjct: 196 QLKKDFPELEILLNGGIETADEVGEHIKHVDGVMIGRAAYHYPYRMAEFDARFYDDPTTA 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHL----HSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           ++P            +  +M  Y  + L      G K+  ITRHM+GL  G P +RR R 
Sbjct: 256 TTPA----------DVVKAMMPYIEKQLSLYGSKGLKMHGITRHMLGLMTGLPGARRFRQ 305

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
           IL+     ++    ++  A   +
Sbjct: 306 ILSDPTKLASGNPAVLLEALAAV 328


>gi|320335164|ref|YP_004171875.1| TIM-barrel protein, yjbN family [Deinococcus maricopensis DSM
           21211]
 gi|319756453|gb|ADV68210.1| TIM-barrel protein, yjbN family [Deinococcus maricopensis DSM
           21211]
          Length = 340

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 187/322 (58%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RL+T + LLYTEMI   AIL GD+   L FS QE P+ALQ+GG+D  
Sbjct: 17  MLDWTDRHCRAFHRLITRHTLLYTEMITTGAILHGDEARHLSFSPQEHPVALQLGGSDPV 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+  E +GY E+NLNVGCPS RV  G FGACLM  PD+V   + AM  A  +PVT
Sbjct: 77  ALAECARRAEGYGYAEVNLNVGCPSDRVQNGRFGACLMATPDVVARGVEAMRGATGLPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   V+++  +G     +HARKA L GLSPK+NR+IP L Y++V 
Sbjct: 137 VKHRIGIDDLDSYELLTAFVRTVADAGCETFIVHARKAWLSGLSPKENREIPPLRYEVVR 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P L   LNGG++ + +A   L SVDGVMIGR AY N  +L   D         +
Sbjct: 197 QLKMDFPQLTFVLNGGVKSLDEAETHLRSVDGVMIGREAYGNPYLLALADARLFGD---A 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             + TR      R++   +  YA   L     L ++T+H +GLF G   +R  +  ++  
Sbjct: 254 HVVPTR------REVVEGLIGYAEEMLARDVYLSRVTKHALGLFAGQAGARGWKRTISER 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
           A    A   ++  A   + +++
Sbjct: 308 AYLPGAGVEVLRDAMACVPDAV 329


>gi|304313001|ref|YP_003812599.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HdN1]
 gi|301798734|emb|CBL46967.1| tRNA-dihydrouridine synthase A [gamma proteobacterium HdN1]
          Length = 357

 Score =  338 bits (867), Expect = 8e-91,   Method: Composition-based stats.
 Identities = 133/315 (42%), Positives = 187/315 (59%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  R ++   LLYTEM+   A+L  +    L +   E PLALQ+GG    
Sbjct: 47  MLDWTDRHARYMLRQISQRTLLYTEMVTTGALLHTNPARWLDYHHDEHPLALQLGGNQPH 106

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +  K+   + Y+E+NLNVGCPS RV EG+FGACLM  P+IV DC+ AM  A ++P+T
Sbjct: 107 ALAQCVKLAAQWQYDEVNLNVGCPSDRVQEGAFGACLMATPNIVADCVKAMQDASNLPIT 166

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ     L++ +++++ +G     +HARKA LKGLSPK+NR+IP L+Y  V+
Sbjct: 167 VKCRIGIDDQDEEQGLQDFIETVQAAGCKTFIVHARKAWLKGLSPKENREIPPLNYPRVH 226

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ PDL + +NGG + + +  + L  +DGVMIGR AY N  +L   D+         
Sbjct: 227 RLKKDFPDLELIINGGFKTLDECAEQLAHLDGVMIGREAYHNPMVLADADQRIFGATNAP 286

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         +   M  YA R    G  ++ ITRHM+GL HG P  RR R +L+ +
Sbjct: 287 ---------ICREALIHKMHAYAERQYRDGVAVKHITRHMLGLLHGIPGGRRWRRVLSEK 337

Query: 301 AGASTATHHIIETAF 315
           A    AT  I+  A+
Sbjct: 338 APRDGATPDILLEAW 352


>gi|167919102|ref|ZP_02506193.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei BCC215]
          Length = 339

 Score =  338 bits (867), Expect = 8e-91,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EQVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLP 326


>gi|209520920|ref|ZP_03269659.1| TIM-barrel protein, yjbN family [Burkholderia sp. H160]
 gi|209498644|gb|EDZ98760.1| TIM-barrel protein, yjbN family [Burkholderia sp. H160]
          Length = 317

 Score =  337 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 187/322 (58%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+ +E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPEEAPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 61  DLARSARLGEQWGYDEINLNCGCPSERVRRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDTVEEYGFVRDFVGTIAQAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F       
Sbjct: 181 QLKRDFPQLEIIINGGIKTLDEVDTHLQHVDGVMLGREAYHNPYVLAEVDSRFYGSTQAP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 241 ---------LTREQVEAKLIEYCATEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 291

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     I + A   + E +
Sbjct: 292 KRLAARDLTIFDEARQHLREPI 313


>gi|115351522|ref|YP_773361.1| tRNA-dihydrouridine synthase A [Burkholderia ambifaria AMMD]
 gi|115281510|gb|ABI87027.1| tRNA-U16,U17-dihydrouridine synthase [Burkholderia ambifaria AMMD]
          Length = 344

 Score =  337 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGKVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 197 QLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TAA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 256 VPTREEAE--------AKLIEYCAAELKRGTYLGAIVRHALGLYRGVGGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     + + A   + +++
Sbjct: 308 KRLARGDLAVFDEARTHLNDAI 329


>gi|171317498|ref|ZP_02906688.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria MEX-5]
 gi|172060541|ref|YP_001808193.1| tRNA-dihydrouridine synthase A [Burkholderia ambifaria MC40-6]
 gi|171097327|gb|EDT42172.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria MEX-5]
 gi|171993058|gb|ACB63977.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria MC40-6]
          Length = 328

 Score =  337 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGKVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 QLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TAA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 240 VPTREEAE--------AKLIEYCAAELKRGTYLGAIVRHALGLYRGVGGARGWRRVLSDN 291

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     + + A   + +++
Sbjct: 292 KKLARGDLAVFDEARTHLNDAI 313


>gi|187923745|ref|YP_001895387.1| tRNA-dihydrouridine synthase A [Burkholderia phytofirmans PsJN]
 gi|187714939|gb|ACD16163.1| TIM-barrel protein, yjbN family [Burkholderia phytofirmans PsJN]
          Length = 333

 Score =  337 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 192/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+ +E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRVISRHTWLYTEMVTTGALLHGDVPRHLAFTPEEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G N   +HAR AILKGLSPK+NR+IP L Y+  Y
Sbjct: 137 VKHRIGVDAVEEYGFVRDFVGTIAEAGCNVFIVHARNAILKGLSPKENREIPPLKYEYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 QLKRDFPQLEIIINGGIKTLDEVEAHLEHVDGVMLGREAYHNPYVLADVDARFYG---AA 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               TR       ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 254 QTPLTR------EQVEAKLIEYCAAEMVRGTYLGAITRHALGLYRGEAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     I + A   + E +
Sbjct: 308 KRLAARDLTIFDEARQHLREPI 329


>gi|53723486|ref|YP_102906.1| tRNA-dihydrouridine synthase A [Burkholderia mallei ATCC 23344]
 gi|124383650|ref|YP_001026373.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10229]
 gi|126449152|ref|YP_001080353.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10247]
 gi|167894436|ref|ZP_02481838.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 7894]
 gi|254199845|ref|ZP_04906211.1| tRNA-dihydrouridine synthase A [Burkholderia mallei FMH]
 gi|254206173|ref|ZP_04912525.1| tRNA-dihydrouridine synthase A [Burkholderia mallei JHU]
 gi|254358573|ref|ZP_04974846.1| tRNA-dihydrouridine synthase A [Burkholderia mallei 2002721280]
 gi|52426909|gb|AAU47502.1| dihydrouridine synthase [Burkholderia mallei ATCC 23344]
 gi|124291670|gb|ABN00939.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10229]
 gi|126242022|gb|ABO05115.1| tRNA-dihydrouridine synthase A [Burkholderia mallei NCTC 10247]
 gi|147749441|gb|EDK56515.1| tRNA-dihydrouridine synthase A [Burkholderia mallei FMH]
 gi|147753616|gb|EDK60681.1| tRNA-dihydrouridine synthase A [Burkholderia mallei JHU]
 gi|148027700|gb|EDK85721.1| tRNA-dihydrouridine synthase A [Burkholderia mallei 2002721280]
          Length = 339

 Score =  337 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLP 326


>gi|307729510|ref|YP_003906734.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1003]
 gi|307584045|gb|ADN57443.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1003]
          Length = 333

 Score =  337 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 132/320 (41%), Positives = 187/320 (58%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ +PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVGVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYSFVRDFVGTIAEAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 197 RLKRDFPQLEIVINGGIKTLDEVEAHLQHVDGVMLGREAYHNPYLLADVDARFYG--SAE 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+          ++ A + +Y    +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 255 APLTRE-------QVEAKLIEYCGVEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     I + A   + E
Sbjct: 308 KRLAARDLAIFDEARQHLRE 327


>gi|167824321|ref|ZP_02455792.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 9]
          Length = 334

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 181 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 238 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 291

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 292 KRLGRGDLSIFDEARTHLT 310


>gi|254177532|ref|ZP_04884187.1| tRNA-dihydrouridine synthase A [Burkholderia mallei ATCC 10399]
 gi|160698571|gb|EDP88541.1| tRNA-dihydrouridine synthase A [Burkholderia mallei ATCC 10399]
          Length = 339

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 190/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F    + S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFY---SAS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLP 326


>gi|229589108|ref|YP_002871227.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens SBW25]
 gi|229360974|emb|CAY47834.1| tRNA-dihydrouridine synthase A [Pseudomonas fluorescens SBW25]
          Length = 336

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 138/318 (43%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ +ALLYTEM+   AIL GD    L  +  E PLALQ+GG+  +
Sbjct: 25  MMDWTDRHCRFFLRLLSKHALLYTEMVTTGAILHGDHDRFLRHNEAEHPLALQLGGSVPA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GA LM +P +V +C+ AM  A+SIPVT
Sbjct: 85  DLAACARMAEAAGYDEVNLNVGCPSDRVQNNMIGAILMAHPALVAECVKAMRDAVSIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++K +G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 145 VKHRIGINGRDSYAQLCDFVGTVKDAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+         
Sbjct: 205 QLKQDFPELEIVLNGGIKTLEQCHEHLQTFDGVMLGREAYHNPYVLAEVDQQLFGS---E 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R +          +  Y A HL SGG +  ITRH++GL  GFP +R+ R +L+V+
Sbjct: 262 APVISRAEA------LVQLRPYIAEHLASGGSMHHITRHILGLGTGFPGARKFRQLLSVD 315

Query: 301 AGASTATHHIIETAFNLM 318
              ++    +++ A  L+
Sbjct: 316 IHKASDPLALLDQAGALL 333


>gi|254258242|ref|ZP_04949296.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1710a]
 gi|254216931|gb|EET06315.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1710a]
          Length = 339

 Score =  337 bits (864), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLT 326


>gi|167902837|ref|ZP_02490042.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei NCTC
           13177]
          Length = 339

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVATAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLP 326


>gi|53719465|ref|YP_108451.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei K96243]
 gi|126438522|ref|YP_001058864.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 668]
 gi|126452196|ref|YP_001066108.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106a]
 gi|167719732|ref|ZP_02402968.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei DM98]
 gi|167738727|ref|ZP_02411501.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 14]
 gi|167815950|ref|ZP_02447630.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 91]
 gi|167911080|ref|ZP_02498171.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 112]
 gi|52209879|emb|CAH35851.1| conserved hypothetical protein [Burkholderia pseudomallei K96243]
 gi|126218015|gb|ABN81521.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 668]
 gi|126225838|gb|ABN89378.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106a]
          Length = 339

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLT 326


>gi|323526215|ref|YP_004228368.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1001]
 gi|323383217|gb|ADX55308.1| TIM-barrel protein, yjbN family [Burkholderia sp. CCGE1001]
          Length = 333

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 133/320 (41%), Positives = 188/320 (58%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R+++ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++  
Sbjct: 17  MMDWTDRHCRSLHRMISRHTWLYTEMVTTGALLHGDVPRHLAFTPDEAPVALQLGGSEPH 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 77  DLARSAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDVVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYSFVRDFVGTIAQAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +    L  VDGVM+GR AY N  +L  VD  F    +  
Sbjct: 197 RLKRDFPQLEIVINGGIKTLDEVETHLQHVDGVMLGREAYHNPYLLADVDARFYG--SSE 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+          ++ A + +Y A  +  G  L  ITRH +GL+ G   +R  R +L+  
Sbjct: 255 APLTRE-------QVEAKLVEYCAAEMARGTYLGAITRHALGLYRGEAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     I + A   + E
Sbjct: 308 KRLAARDLAIFDEARQHLRE 327


>gi|331019219|gb|EGH99275.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 339

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 196/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDEAEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACARLAEAAGYDEVNLNVGCPSDRVQNNMIGACLMAHPPLVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     +   
Sbjct: 208 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQLFGSV--- 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 265 APVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 318

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 319 IHKAENPLLLLDQAAKFL 336


>gi|312959660|ref|ZP_07774177.1| dihydrouridine synthase TIM-barrel protein YjbN [Pseudomonas
           fluorescens WH6]
 gi|311286377|gb|EFQ64941.1| dihydrouridine synthase TIM-barrel protein YjbN [Pseudomonas
           fluorescens WH6]
          Length = 328

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 198/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL+ +ALLYTEM+   AIL GD    L  +  E PLALQ+GG+  +
Sbjct: 17  MMDWTDRHCRFFLRLLSKHALLYTEMVTTGAILHGDHDRFLRHNEAEHPLALQLGGSVPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GA LM +P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAACARMAEAAGYDEVNLNVGCPSDRVQNNMIGAILMAHPALVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++K +G     +HAR AIL+GLSPK+NR IP L YD+  
Sbjct: 137 VKHRIGINGRDSYAELCDFVGTVKDAGCTSFTVHARIAILEGLSPKENRDIPPLRYDVAA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+         
Sbjct: 197 QLKRDFPELEIVLNGGIKTLEQCQEHLQTFDGVMLGREAYHNPYLLAEVDQRLFGS---E 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+  R       ++ A +  Y A HL SGG +  ITRH++GL  GFP +RR R +L+V+
Sbjct: 254 APVVGRA------QVLAQLRPYIAEHLASGGVMHHITRHVLGLGTGFPGARRFRQLLSVD 307

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 308 IHKAADPLALLDQAGALL 325


>gi|327480282|gb|AEA83592.1| tRNA-dihydrouridine synthase A [Pseudomonas stutzeri DSM 4166]
          Length = 322

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 193/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R L+ +ALLYTEM+   A+L G+    L +   E PLALQ+GG+   
Sbjct: 11  MMDWTDRHCRFFLRQLSKHALLYTEMVTTGALLHGNTARFLRYDETEHPLALQLGGSVPG 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ + VT
Sbjct: 71  DLAACAKLAEAAGYDEVNLNVGCPSDRVQNNMIGACLMGHPQLVADCVKAMRDAVGVEVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AILKGLSPK NR +P L YD+  
Sbjct: 131 VKHRIGINGRDSYSQLCDFVGQVREAGCRSFTVHARIAILKGLSPKQNRDVPPLRYDVAA 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PDL I LNGG++ + +  + L + DGVM+GR AY N  +L  VD         +
Sbjct: 191 QLKRDFPDLEIILNGGIKTLEECREHLQTFDGVMLGREAYHNPYLLAQVDSSLFGS---N 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R       +   +M  Y  RHL  GG +  +TRH++GL  GFP +RR R +L+V+
Sbjct: 248 APVISRA------QALRNMRPYIERHLAEGGAMHHVTRHVLGLGQGFPGARRFRQLLSVD 301

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A  L+
Sbjct: 302 IHKTDEPLALLDQATALL 319


>gi|226196332|ref|ZP_03791914.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei Pakistan
           9]
 gi|254297746|ref|ZP_04965199.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 406e]
 gi|157807557|gb|EDO84727.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 406e]
 gi|225931549|gb|EEH27554.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei Pakistan
           9]
          Length = 323

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 181 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 238 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 291

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 292 KRLGRGDLSIFDEARTHLT 310


>gi|167836742|ref|ZP_02463625.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis MSMB43]
          Length = 339

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 188/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHAAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDSVDDYAFVRDFVGTVAAAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPQLEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGVDARFYG---AT 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EAVEAKLVEYCATELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLM 318
              +     I + A   +
Sbjct: 308 KRLARGDLSIFDEARTHL 325


>gi|170698688|ref|ZP_02889754.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria IOP40-10]
 gi|170136392|gb|EDT04654.1| TIM-barrel protein, yjbN family [Burkholderia ambifaria IOP40-10]
          Length = 328

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 191/322 (59%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHCRSFHRTLTRDTWLYTEMITTGALLFGDAQRHLAFTPNESPVALQLGGSERD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 121 VKHRIGVDAVEDYAFVRDFVGKVAEAGCETFVVHARNAILKGLSPKENREIPPLKYDYAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F    T +
Sbjct: 181 QLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGS-TAA 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +   +        A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 240 VPTREEAE--------AKLIEYCAAELKRGAYLGAIVRHALGLYRGVGGARGWRRVLSDN 291

Query: 301 AGASTATHHIIETAFNLMIESL 322
              +     + + A   + +++
Sbjct: 292 KKLARGDLAVFDEARTHLNDAI 313


>gi|182677984|ref|YP_001832130.1| YjbN family TIM-barrel protein [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182633867|gb|ACB94641.1| TIM-barrel protein, yjbN family [Beijerinckia indica subsp. indica
           ATCC 9039]
          Length = 336

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 149/321 (46%), Positives = 202/321 (62%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F RLL+  ALLYTEMI   A+L G    +LGF   E P+A+Q+GG++  
Sbjct: 14  MMEWTDRHCRVFHRLLSRRALLYTEMITTAALLHGHVDRLLGFDDVEHPVAVQLGGSEPR 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY+EINLN+GCPS RV  G+FGACLML P++VGDC+AA+  ++S+PVT
Sbjct: 74  DLAAAARICADFGYDEINLNIGCPSERVQNGAFGACLMLEPELVGDCVAAIKASVSLPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  +I  +GV+GI +HARKA LKGLSP+ NR +P LDY +V+
Sbjct: 134 VKCRIGVDDQDPEEALGTLSAAIIAAGVDGIIVHARKAWLKGLSPRQNRDVPPLDYPLVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P++ I +NGGL       + L  VDGVM+GR AY+  AML +VD  F       
Sbjct: 194 ALKRTYPEIPIMINGGLVTHESMQEQLRHVDGVMVGRQAYQEPAMLLSVDPLFFGE---E 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+    D      +  +   Y       G  L  +TRH++GLF+G P +R  R  L  E
Sbjct: 251 APLTDATD------VVEAFIPYVEARRAEGVPLHSMTRHILGLFNGRPGARAFRRHLATE 304

Query: 301 AGASTATHHIIETAFNLMIES 321
             A  A   ++  A   ++++
Sbjct: 305 GLARDAGADVLRAAAAHVVKA 325


>gi|134095593|ref|YP_001100668.1| tRNA-dihydrouridine synthase A [Herminiimonas arsenicoxydans]
 gi|133739496|emb|CAL62547.1| tRNA-dihydrouridine synthase A [Herminiimonas arsenicoxydans]
          Length = 338

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 129/320 (40%), Positives = 191/320 (59%), Gaps = 1/320 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R +T +   YTEM+   A+L GD    L F+ +E P+ALQ+GG++ +
Sbjct: 16  MMDWTDRHCRMFHRQITRHTWFYTEMVTTGALLHGDVSRHLDFNHEEHPVALQLGGSEPA 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+ E +GY+EINLN GCPS RV +G+FGACLM    +V DC+ AM  A+ I VT
Sbjct: 76  DLAKSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMNEAALVADCVKAMRDAVQIDVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      +R+ V ++ ++G N   +HAR A+LKGLSPK+NR+IP L Y+  Y
Sbjct: 136 VKHRIGIDDIASYDFVRDFVGTVAEAGCNTFIVHARNAVLKGLSPKENREIPPLRYEFAY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +++    L  VDGVM+GR AY N  +++  D  +   +   
Sbjct: 196 QLKQDFPQLEIIINGGIKTLAEIDTHLVHVDGVMLGREAYHNPYLMSAFDARYYGDIAAP 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + +V       I A +  +       G +L  ITRHM+GL  G PN+R  R  L+  
Sbjct: 256 K-SRAQVLHAMLPYIRAQLELHGKSEKGGGLRLNSITRHMLGLMAGLPNARGFRQSLSDS 314

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     ++  A   M +
Sbjct: 315 KKLALGDPDLLLQALARMQQ 334


>gi|163735338|ref|ZP_02142772.1| tRNA-dihydrouridine synthase A [Roseobacter litoralis Och 149]
 gi|161391347|gb|EDQ15682.1| tRNA-dihydrouridine synthase A [Roseobacter litoralis Och 149]
          Length = 321

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 144/323 (44%), Positives = 191/323 (59%), Gaps = 12/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R LT   LLYTEM+ + A++RG   ++L FS  E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRMLHRQLTRQTLLYTEMVTSAALVRGGALHLLEFSPDEHPVALQLGGSDPK 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA + +  GY+EINLNVGCPS RV  G FGA LM +P +V DC+AAM  A+ +PVT
Sbjct: 61  ELAQAAVLGQTAGYDEINLNVGCPSDRVQSGCFGAVLMESPALVADCVAAMRDAVEVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY +V 
Sbjct: 121 VKCRIGVDDQNPEEVLPEFLARIVAAGCERVAIHARKAWLQGLSPKENRDIPPLDYPLVL 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K+  P+L I +NGG+  + +A   L   +DGVMIGRAAY     +L  VD        
Sbjct: 181 RMKEYFPNLHISVNGGITSLDEARAFLEAGLDGVMIGRAAYHTPTDILAAVDPVIFGTG- 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                    +         +M  Y   H+  GG+L QITRHM+GLF G P +R  R +L+
Sbjct: 240 ---------EVVAAEDAVHAMLPYIEGHVTGGGRLGQITRHMLGLFAGRPGARVWRRMLS 290

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++  A   + + 
Sbjct: 291 EGAHLPNAGSSLVLEALTQVAQQ 313


>gi|260221113|emb|CBA29353.1| tRNA-dihydrouridine synthase A [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 370

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 192/316 (60%), Gaps = 8/316 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 53  MMDWTDRHCRYFHRLLSRHALLYTEMVTTGALIHGDVPRHLRFNVEEHPVALQLGGSEPA 112

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ +D+GY+EIN+N GCPS RV  G+FGACLM    +V DC+ +M  A+ +PVT
Sbjct: 113 DLARAAKLGQDWGYDEININCGCPSERVQRGAFGACLMNEAPLVADCVKSMVDAVDVPVT 172

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     +R+ V ++  +G N    HAR A LKGLSPK+NR+IP L Y++VY
Sbjct: 173 VKHRIGIDKEESYSFVRDFVGTVADAGCNVFIAHARNAWLKGLSPKENREIPPLRYELVY 232

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P L I +NGG+   ++    L  VDGVM+GR AY N   L   D  F       
Sbjct: 233 QLKKDFPHLTIAINGGITQTAEVAGHLEHVDGVMLGREAYHNPWWLAEWDSAFYG----- 287

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +    +    ++ A M   AA+H   G     I RHM+GL HG P +RR R + T  
Sbjct: 288 APDRDITREMVEAQMVAYMEREAAQH---GTHWYSIARHMLGLRHGLPGARRWRQVWTDH 344

Query: 301 AGASTATHHIIETAFN 316
                +   ++  A +
Sbjct: 345 RLKHLSAREVMALAHD 360


>gi|254786572|ref|YP_003074001.1| tRNA-dihydrouridine synthase A [Teredinibacter turnerae T7901]
 gi|237683391|gb|ACR10655.1| tRNA-dihydrouridine synthase A [Teredinibacter turnerae T7901]
          Length = 338

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 191/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M++W+DRH R+F RLLT NALLYTEM+   A+L   D +  L F+++E PLALQ+GG++ 
Sbjct: 19  MMEWSDRHCRYFWRLLTKNALLYTEMVTTGALLNNSDVERFLKFNSEEHPLALQLGGSNP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L   A + + +GY+E+NLN GCPS RV EG  GA LM  P++V  C++AM     IPV
Sbjct: 79  DELARCAAMAQQWGYDEVNLNCGCPSDRVQEGKIGAVLMTEPELVAQCVSAMQAECDIPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIGVDDQ     L+  VK + ++G     +HARKA LKGLSPK+NR IP L+Y+ V
Sbjct: 139 TVKHRIGVDDQDEYNDLQRFVKVVSEAGCKRFIVHARKAWLKGLSPKENRDIPPLNYERV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++K+E+  L I +NGG+  +SQ   +L  +DGVMIGR AY N  +L  VD       + 
Sbjct: 199 VQLKQEHTALDIVINGGITTLSQCSALLSQLDGVMIGREAYHNPYLLAGVDAELYG--SD 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P  TR               Y    + +G KL  ++RH++GL+ G   +R  R  +T 
Sbjct: 257 NIPPVTR------DAALEQFVVYCREQIAAGQKLHHMSRHILGLYAGEYGARTFRRYITE 310

Query: 300 EAGASTATHHIIETAFNLM 318
            A    A+  ++  A + M
Sbjct: 311 RANQPGASADVLLDARDAM 329


>gi|224824837|ref|ZP_03697944.1| TIM-barrel protein, yjbN family [Lutiella nitroferrum 2002]
 gi|224603330|gb|EEG09506.1| TIM-barrel protein, yjbN family [Lutiella nitroferrum 2002]
          Length = 313

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 190/318 (59%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRFFAR +T +  LYTEM+   A+L GD    L +   E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHYRFFARQITRHTWLYTEMVTTGALLYGDVARHLRYHECEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E++GY+E+NLNVGCPS RV +G+FGACLM  P +V DC+ AM  A+ I VT
Sbjct: 61  ELARCARLAEEWGYDEVNLNVGCPSERVQKGAFGACLMAEPQLVADCVKAMRDAVGIDVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  I ++G     +HAR AILKGLSPK+NR+IP L YD VY
Sbjct: 121 VKHRIGIDAVEDYGYVRDFVGHIVEAGCATFIVHARNAILKGLSPKENREIPPLKYDYVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PD+ I LNGG++   +  + L  VDGVM+GR AY N  ++   D  F +     
Sbjct: 181 RLKRDFPDVEILLNGGVKSNDEIARHLQHVDGVMVGREAYHNPWLMADWDARFYDDAHTE 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +             +  +M  Y  + L     +L+ + RH++GL+ G P +R  R +L+ 
Sbjct: 241 A---------TRDAVVEAMLPYIEQRLAEPATQLRHVARHILGLYQGLPGARAWRRMLSD 291

Query: 300 EAGASTATHHIIETAFNL 317
            A    A   ++  A + 
Sbjct: 292 AALLKGADAGLLLAARDA 309


>gi|84687027|ref|ZP_01014910.1| tRNA-dihydrouridine synthase A [Maritimibacter alkaliphilus
           HTCC2654]
 gi|84665001|gb|EAQ11482.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2654]
          Length = 313

 Score =  336 bits (861), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 146/321 (45%), Positives = 202/321 (62%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R F R+++   LLYTEM+ A A++RG   ++L F   E P+ALQ+GG+D  
Sbjct: 1   MMDWTDSHCRVFHRMMSRETLLYTEMVTAPALVRGGVTHLLDFDPSEHPVALQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
           +L EA ++  D GY+E+NLNVGCPS RV  G+FGA L+ +PD+V  C AAM   A  + V
Sbjct: 61  ELAEATRMAVDRGYDEVNLNVGCPSDRVQSGTFGAVLLKDPDLVARCTAAMIRAAGPVEV 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIGVDDQ     L + +  +  +GV    IHARKA L+GLSPK+NR IP LDY +V
Sbjct: 121 TVKCRIGVDDQDAEAVLPDFLDRVSDAGVRRFTIHARKAWLQGLSPKENRDIPPLDYPLV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPL 237
           + +K E PDL + +NGG+  ++QA + L   +DGVMIGRAAY+  A +L T D       
Sbjct: 181 HRMKAEWPDLHLSINGGITSLTQAEEHLAAGMDGVMIGRAAYQQPADILLTADSRIFG-- 238

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             + P++         +++ +M  +  RHL +GGKL Q+TRHM+GLF G P +R  R +L
Sbjct: 239 -AADPMRDP------GEVALAMIPHIERHLSNGGKLSQVTRHMLGLFAGRPGARHWRRVL 291

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +  A    A   +IE A   +
Sbjct: 292 SENAHRPDADARLIEDAMAEL 312


>gi|254179915|ref|ZP_04886514.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1655]
 gi|184210455|gb|EDU07498.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1655]
          Length = 339

 Score =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 197 RLKRDFPQIEIVINGGVTTLDEVEQHLRYVDGVMLGREAYHNPYVLAGIDARFYG---AS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 308 KRLGRGDLSIFDEARTHLT 326


>gi|190572349|ref|YP_001970194.1| tRNA-dihydrouridine synthase A [Stenotrophomonas maltophilia K279a]
 gi|190010271|emb|CAQ43879.1| putative tRNA-dihydrouridine synthase A [Stenotrophomonas
           maltophilia K279a]
          Length = 334

 Score =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 139/317 (43%), Positives = 194/317 (61%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L   A LYTEM+ A+A++ GD++ +LGF   E+PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRVLAPGARLYTEMVHANAVIHGDRERLLGFDRSEQPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM  A+ IPVT
Sbjct: 79  LLAQAARIAAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPVLVAECVAAMVDAVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD+        + V     +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDEDNDYDVFASFVDRQVAAGAAMVVVHARNAWLKGLSPKENREVPPLKYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGGL  +         VDGVM+GRAAY +  +L  ++   +      
Sbjct: 199 RLKQERPALPVVINGGLASIEAVQAQAAHVDGVMLGRAAYHDPYLLHQLEALHTG----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++ R D      +  +M  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 254 APLQARGD------LLRAMRPYIEARLREGLALKHITRHLLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFNL 317
           A    A   +IE A  +
Sbjct: 308 AHRPGAGWSLIEQALAV 324


>gi|167626460|ref|YP_001676960.1| tRNA-dihydrouridine synthase A [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167596461|gb|ABZ86459.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 324

 Score =  335 bits (860), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 132/321 (41%), Positives = 188/321 (58%), Gaps = 13/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+HYR+  RL+T   +LYTEMI  +AI+ G+K  +L ++ +E P+ LQ+GG    
Sbjct: 13  MLDWTDKHYRYMMRLITKQTMLYTEMITLNAIIHGNKDFLLKYNPEENPVTLQLGGCVPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             +   K+ ++ GYNEIN+NVGCPS RV +G+FG  LM  P++V +C+ AM   L IP++
Sbjct: 73  DFITCGKLAQNLGYNEININVGCPSERVKKGNFGLSLMAEPELVANCVKAMKDNLDIPIS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG D+      L N V    ++GV+ + IHARK  L GLSPK+NR IP L YD+VY
Sbjct: 133 VKCRIGYDNNDSYEELYNFVNKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTG 239
            IKK+ P+L +G+NGG+  +    + L  VD VMIGR AY N  +    D  F N P+  
Sbjct: 193 NIKKDFPNLELGINGGVTTIEDTQEHLKYVDSVMIGREAYHNPMLFKNFDNLFYNQPIND 252

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHIL 297
            SP+          +++  M +Y    L+S    KL  IT+H + LF+G  N++  R  L
Sbjct: 253 ISPL----------EVAYEMAEYIKIQLNSDPNMKLNNITKHTLNLFNGLHNAKVFRRYL 302

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +  A    A       A  + 
Sbjct: 303 SENATKKDANVDTFLKAIEVF 323


>gi|323144476|ref|ZP_08079078.1| tRNA dihydrouridine synthase A [Succinatimonas hippei YIT 12066]
 gi|322415754|gb|EFY06486.1| tRNA dihydrouridine synthase A [Succinatimonas hippei YIT 12066]
          Length = 337

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 184/321 (57%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TD  +R  ARL +  ++LYTEMI ADA++ G    +L F  +E P  LQ+GG+D  
Sbjct: 18  MVDVTDSVFRRLARLFSKKSMLYTEMIAADAVIHGKNY-LLEFHDEELPCVLQLGGSDPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL  AAKI   FGY EINLN GCPS +V  G+FGA LM  PD++ DC+ AM  A+S+PVT
Sbjct: 77  KLAAAAKIGAGFGYTEINLNAGCPSDKVQSGNFGAVLMKTPDLIADCVKAMQDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+         LV++I  +G   + +HARKA L GLSPK+NR IP LDY+ VY
Sbjct: 137 VKTRIGVDEDDSVDFTLKLVETIAATGCRHVILHARKAWLNGLSPKENRTIPPLDYERVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+L I +NGG+  +      L  VDGVM+GRA   N  +L+ VD      +   
Sbjct: 197 LVKSAFPNLRITINGGITTIDAVKDQLKRVDGVMLGRAIIDNPFILSKVDSEIFGSI--- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R       ++     D AA+    G  +  + RH++GLF+  P +R  R  L+  
Sbjct: 254 EPMPSR------EELLYKAVDLAAKIKAEGIPVHHLMRHLLGLFNSCPGARLYRRYLSEH 307

Query: 301 AGASTATHHIIETAFNLMIES 321
                A   ++  A+  M ++
Sbjct: 308 MTQLGAGPDVLIKAYKSMTDA 328


>gi|296444599|ref|ZP_06886563.1| TIM-barrel protein, yjbN family [Methylosinus trichosporium OB3b]
 gi|296257867|gb|EFH04930.1| TIM-barrel protein, yjbN family [Methylosinus trichosporium OB3b]
          Length = 351

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 151/318 (47%), Positives = 199/318 (62%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL++  A LYTEM+   A++ GD++ +LGF   E+PLALQ+GG+D  
Sbjct: 30  MMDWTDRHCRFFHRLMSRRARLYTEMLTTGAVIFGDRQRLLGFDPAERPLALQLGGSDPL 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +A +I E FGY+EINLNVGCPS RV  G+FGACLML PD+V DC++AM  A+ +PVT
Sbjct: 90  DLAKATRIAEPFGYDEINLNVGCPSDRVQNGAFGACLMLRPDLVADCVSAMKDAVDLPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L + +  +G + + +HARKA L GLSPK+NR +P LDY +V+
Sbjct: 150 VKCRIGVDDQDPRTALFALCERVVAAGCDALVVHARKAWLAGLSPKENRDVPPLDYALVH 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+  P L I +NGG+E + Q    L  VDGVMIGRAAY N  +L  VD          
Sbjct: 210 ELKRAFPTLPIAINGGIETIEQMRAQLEHVDGVMIGRAAYHNPELLLAVDPQLFGE---P 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+              +   Y    L  G +L  +TRHM+GLF G P +R  R  L  E
Sbjct: 267 APLPDGF------AAVEAFIPYVEAQLRRGERLASMTRHMLGLFAGRPGARAFRRRLAAE 320

Query: 301 AGASTATHHIIETAFNLM 318
           A    A    + +A + +
Sbjct: 321 AVRPGAGVETLLSAVDEV 338


>gi|254197994|ref|ZP_04904416.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei S13]
 gi|169654735|gb|EDS87428.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei S13]
          Length = 377

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 55  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 114

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 115 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 174

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 175 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 234

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 235 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 291

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 292 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 345

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 346 KRLGRGDLSIFDEARTHLT 364


>gi|28869329|ref|NP_791948.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|38604776|sp|Q884G7|DUSA_PSESM RecName: Full=tRNA-dihydrouridine synthase A
 gi|28852570|gb|AAO55643.1| TIM-barrel protein, yjbN family [Pseudomonas syringae pv. tomato
           str. DC3000]
          Length = 336

 Score =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 137/318 (43%), Positives = 196/318 (61%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F RLL++ ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 25  MMDWTDHHCRYFMRLLSSQALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E  GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 85  GLAACARLAEAAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V ++  +G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 145 VKHRIGINGRDSYAELCDFVGTVHDAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+     +   
Sbjct: 205 QLKTDFPELEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAQVDQQLFGSV--- 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+ +R           SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+
Sbjct: 262 APVISR------HAALESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVD 315

Query: 301 AGASTATHHIIETAFNLM 318
              +     +++ A   +
Sbjct: 316 IHKAENPLLLLDQAAKFL 333


>gi|76809017|ref|YP_333391.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1710b]
 gi|76578470|gb|ABA47945.1| dihydrouridine synthase [Burkholderia pseudomallei 1710b]
          Length = 442

 Score =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 120 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 179

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 180 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 239

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 240 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 299

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 300 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 356

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 357 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 410

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 411 KRLGRGDLSIFDEARTHLT 429


>gi|255264528|ref|ZP_05343870.1| tRNA-dihydrouridine synthase A [Thalassiobium sp. R2A62]
 gi|255106863|gb|EET49537.1| tRNA-dihydrouridine synthase A [Thalassiobium sp. R2A62]
          Length = 330

 Score =  334 bits (858), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 146/323 (45%), Positives = 200/323 (61%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R  ++ ALLYTEM+ A AI+RGD +++L F   E+P+ALQ+GGAD  
Sbjct: 18  MMDWTDRHCRYFHRQFSSQALLYTEMVTAPAIVRGDARHLLAFDPAEQPVALQLGGADPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I  D GY E+NLN GCPS RV  G+FGA  M  PD+V +  +AM  A    +T
Sbjct: 78  QLAQAARIGADEGYPEVNLNCGCPSDRVQSGAFGAIHMTTPDLVAEICSAMIAASHAEIT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I+ +GV  + IHARKA L+GLSPK+NR IP LDY +V+
Sbjct: 138 VKCRIGVDDQDPHEVLPTFLTKIRAAGVRRVTIHARKAWLQGLSPKENRDIPPLDYPLVH 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
           ++K E PDL I +NGG+  + +A   L   +DGVMIGRAAY    A+LT  D+      T
Sbjct: 198 QMKAEFPDLHISINGGIASLDEAKIHLNQGLDGVMIGRAAYHTPAAILTDADQMIWGQGT 257

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             S            ++   M  Y A H+  GG++  +TRHM+GLF G P +R  R +L+
Sbjct: 258 TRSSF----------EVVDRMKPYIADHIAGGGRMHHVTRHMLGLFSGQPGARGWRQVLS 307

Query: 299 VEAGASTATHHIIETAFNLMIES 321
            + G   A   +++ A   +  +
Sbjct: 308 TQ-GQGDAPIEVLDLALARIQTA 329


>gi|114707271|ref|ZP_01440168.1| hypothetical protein FP2506_03595 [Fulvimarina pelagi HTCC2506]
 gi|114537152|gb|EAU40279.1| hypothetical protein FP2506_03595 [Fulvimarina pelagi HTCC2506]
          Length = 346

 Score =  334 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 157/321 (48%), Positives = 209/321 (65%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R LT  ALLYTEM+VADAIL G ++ +L     E P+ALQ+GG+D  
Sbjct: 26  MIDWTDRHCRFFHRQLTAKALLYTEMVVADAILHGPQEKLLDHDAAEHPVALQLGGSDPE 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
           KL  A  +  ++GY+E NLNVGCPS RV  G+FGACLM  P+ VGDC+ AM  A +  PV
Sbjct: 86  KLGAAVTVAREWGYDEFNLNVGCPSDRVQSGTFGACLMREPERVGDCLQAMRDAANETPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCR+GVDDQ    +L  L     ++GV+ IW+HARKA L+GLSPK+NR IP LDYD V
Sbjct: 146 TVKCRLGVDDQDIEESLDRLADEAIRAGVSVIWVHARKAWLEGLSPKENRDIPPLDYDRV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+  P++F+GLNGGL  ++ A + +    +DG+M GRAAY+   +L+ VD       
Sbjct: 206 GRLKRRLPNVFVGLNGGLRSVAVANETIADLELDGMMFGRAAYQTPDLLSEVDHCIYGEP 265

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +           +  + A M DYAARH+  GG+L  ITRHM+GLF+G P +RR R +L
Sbjct: 266 ERA---------IDYPALIAVMEDYAARHIALGGRLNHITRHMVGLFNGLPGARRWRQVL 316

Query: 298 TVEAGASTATHHIIETAFNLM 318
           + ++  S A   II  AF+ +
Sbjct: 317 STKSTGSEAKPAIIREAFSHI 337


>gi|134282264|ref|ZP_01768969.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 305]
 gi|134246302|gb|EBA46391.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 305]
          Length = 379

 Score =  334 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 57  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 116

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 117 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 176

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 177 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 236

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 237 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 293

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 294 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 347

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 348 KRLGRGDLSIFDEARTHLT 366


>gi|254524233|ref|ZP_05136288.1| tRNA-dihydrouridine synthase A [Stenotrophomonas sp. SKA14]
 gi|219721824|gb|EED40349.1| tRNA-dihydrouridine synthase A [Stenotrophomonas sp. SKA14]
          Length = 334

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 140/317 (44%), Positives = 192/317 (60%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L   A LYTEM+ A+A++ GD++ +LGF   E+PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRVLAPGARLYTEMVHANAVIHGDRERLLGFDRSEQPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM  A+ IPVT
Sbjct: 79  LLAQAARIAAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPVLVAECVAAMVDAVDIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD+          V     +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDEDNDYDVFAAFVDRQVAAGAAMVVVHARNAWLKGLSPKENREVPPLKYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGGL  +         VDGVM+GRAAY +  +L           TG 
Sbjct: 199 RLKQERPALPVVLNGGLASLEAVQAQAAHVDGVMLGRAAYHDPYLL----HQLETLHTG- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++ R D      +  ++  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 254 APLQARGD------LLRALRPYVEARLGEGLALKHITRHLLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFNL 317
           A    A   ++E A  +
Sbjct: 308 AHRPGADWSLVEQALAV 324


>gi|121600739|ref|YP_993040.1| tRNA-dihydrouridine synthase A [Burkholderia mallei SAVP1]
 gi|251768090|ref|ZP_04820399.1| tRNA-dihydrouridine synthase A [Burkholderia mallei PRL-20]
 gi|121229549|gb|ABM52067.1| tRNA-dihydrouridine synthase A [Burkholderia mallei SAVP1]
 gi|243060848|gb|EES43034.1| tRNA-dihydrouridine synthase A [Burkholderia mallei PRL-20]
          Length = 436

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 114 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 173

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 174 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 233

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 234 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 293

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 294 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 350

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 351 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 404

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 405 KRLGRGDLSIFDEARTHLP 423


>gi|242317073|ref|ZP_04816089.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106b]
 gi|242140312|gb|EES26714.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 1106b]
          Length = 439

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 407

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 408 KRLGRGDLSIFDEARTHLT 426


>gi|167845866|ref|ZP_02471374.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei B7210]
          Length = 333

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 188/318 (59%), Gaps = 9/318 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ + 
Sbjct: 1   MDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPAD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVTV
Sbjct: 61  LAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y 
Sbjct: 121 KHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S+
Sbjct: 181 LKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---ASA 237

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+   
Sbjct: 238 PAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDNK 291

Query: 302 GASTATHHIIETAFNLMI 319
                   I + A   + 
Sbjct: 292 RLGRGDLSIFDEARTHLT 309


>gi|237812120|ref|YP_002896571.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei MSHR346]
 gi|237505677|gb|ACQ97995.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei MSHR346]
          Length = 439

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 407

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 408 KRLGRGDLSIFDEARTHLT 426


>gi|83721523|ref|YP_443015.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis E264]
 gi|167620175|ref|ZP_02388806.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis Bt4]
 gi|257139245|ref|ZP_05587507.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis E264]
 gi|83655348|gb|ABC39411.1| dihydrouridine synthase [Burkholderia thailandensis E264]
          Length = 339

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 188/319 (58%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  +A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  ELAHSARLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAIEDYAFVRDFVGTVASAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPQLEIVINGGITTLDEVEQHLRHVDGVMLGREAYHNPYVLAGVDARFYG---AT 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 EPAPTR------EAVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMI 319
              +     I + A   + 
Sbjct: 308 KRLARGDLSIFDEARAHLT 326


>gi|217423368|ref|ZP_03454869.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 576]
 gi|217393226|gb|EEC33247.1| tRNA-dihydrouridine synthase A [Burkholderia pseudomallei 576]
          Length = 439

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 407

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 408 KRLGRGDLSIFDEARTHLP 426


>gi|85714507|ref|ZP_01045495.1| dihydrouridine synthase TIM-barrel protein yjbN [Nitrobacter sp.
           Nb-311A]
 gi|85698954|gb|EAQ36823.1| dihydrouridine synthase TIM-barrel protein yjbN [Nitrobacter sp.
           Nb-311A]
          Length = 341

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 148/321 (46%), Positives = 199/321 (61%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F RLL   A LYTEM+   A++ G++  +LGFS  E P+ALQ+GG++  
Sbjct: 8   MMEWTDRHCRVFHRLLARKARLYTEMLTTGAVIHGERDRLLGFSDVEHPVALQLGGSNPV 67

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EINLNVGCPS RV +G FGACLM  PD+V + + AM +A+S+PVT
Sbjct: 68  DLATSAKIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPDVVAETVNAMKRAVSVPVT 127

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ     L    + ++ +GV+ + +HARKA L+GLSPK+NR IP LDYD VY
Sbjct: 128 VKCRIGIDDQDTETELDIFARKVRAAGVDTLIVHARKAWLQGLSPKENRDIPPLDYDRVY 187

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L I +NGG+  +S+A + L  VDGVM+GRAAY+    L  VD          
Sbjct: 188 RLKASLPGLPIVINGGIGGISEAKQHLAHVDGVMLGRAAYQEPWRLLEVDSQLFGEAAPP 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +K         +   +M  Y    L  G +L  I+RH+IG FHG P +R  R  L   
Sbjct: 248 KTMK---------QALEAMMPYIEDQLADGARLHSISRHLIGAFHGVPGARAFRRYLAGN 298

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  + A   +++ A  L+ ES
Sbjct: 299 AVKAGAGIDVLQEAIALVDES 319


>gi|188993527|ref|YP_001905537.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           campestris str. B100]
 gi|167735287|emb|CAP53501.1| Putative dihydrouridine synthase [Xanthomonas campestris pv.
           campestris]
          Length = 366

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 193/314 (61%), Gaps = 11/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD++ ++GF   E PLALQ+GG+D +
Sbjct: 51  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRQRLIGFDAVEHPLALQLGGSDPA 110

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I + +GY+EINLN GCPS RV  G FGACLM  P +V DC+AAMC A ++PVT
Sbjct: 111 LLAQAAQIAQAWGYDEINLNCGCPSDRVQAGRFGACLMREPALVADCVAAMCAATALPVT 170

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          +  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 171 VKCRLGVDDDDDYAVFAGFIDQVVGAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 230

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  +L  L   DGVM+GRAAY +  +L  ++   S      
Sbjct: 231 RLKQERPALPVVLNGGIASVEASLAHLQHTDGVMLGRAAYHDPYVLHQLEAALSG----- 285

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R D      +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 286 RPERARAD------LLQAYQPYVQAQLDQGLALKHMTRHILGLFHGQPGGRVFRQVLSEG 339

Query: 301 AGASTATHHIIETA 314
           A    A   ++E A
Sbjct: 340 AHRPGAGWELVEQA 353


>gi|158336790|ref|YP_001517964.1| tRNA-dihydrouridine synthase A [Acaryochloris marina MBIC11017]
 gi|158307031|gb|ABW28648.1| tRNA-dihydrouridine synthase A [Acaryochloris marina MBIC11017]
          Length = 335

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 146/320 (45%), Positives = 193/320 (60%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T   LLYTEM+ + AIL GD+ ++L FS  EKPL LQ+GG +  
Sbjct: 18  MMDRTDRHFRYFMRQITQRTLLYTEMVTSAAILNGDRHHLLDFSPIEKPLVLQVGGDNPQ 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A+I  D+GY+EINLNVGCPS+RV  G FGACLM  PD V  C+ AM +A  +PV+
Sbjct: 78  DLAECARIATDWGYDEINLNVGCPSSRVQNGHFGACLMAQPDRVAACVEAMMQATHLPVS 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V+++  SG     +HARKA LKGLSPK+NR IP L Y+ VY
Sbjct: 138 VKHRIGIDDCDRYEDMAHFVQTVAASGCQIFSVHARKAWLKGLSPKENRDIPPLRYEDVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+    L+I +NGG   + Q    LP VD VMIGRAAY N  +  TVD  F +    S
Sbjct: 198 RLKQNFSHLWIEINGGFIQLFQVHNQLPKVDAVMIGRAAYDNPYLFATVDRDFYHE-DRS 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +P +         K++ +M DY       G  K   ITRHM+ LF G P SR  + +LT 
Sbjct: 257 APSR--------HKVAQAMMDYLEEWKIKGLLKPHSITRHMLQLFSGQPGSRAWKRLLTE 308

Query: 300 EAGASTATHHIIETAFNLMI 319
           +     A   II  A + ++
Sbjct: 309 QGCRPDAGPDIIHQALDKVL 328


>gi|238563470|ref|ZP_00438839.2| tRNA-dihydrouridine synthase A [Burkholderia mallei GB8 horse 4]
 gi|238520653|gb|EEP84111.1| tRNA-dihydrouridine synthase A [Burkholderia mallei GB8 horse 4]
          Length = 439

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 117 MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 176

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 177 DLAHSAKLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 236

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 237 VKHRIGVDAVEDYAFVRDFVGTVAAAGCDVFVVHARNAILKGLSPKENREIPPLKYDYAY 296

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P + I +NGG+  + +  + L  VDGVM+GR AY N  +L  +D  F      S
Sbjct: 297 RLKRDFPQIEIVINGGVTTLDEVEQHLRHVDGVMLGREAYHNPYVLAGIDARFYG---AS 353

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P  TR       ++ A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 354 APAPTR------EEVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVAGARGWRRVLSDN 407

Query: 301 AGASTATHHIIETAFNLMI 319
                    I + A   + 
Sbjct: 408 KRLGRGDLSIFDEARTHLP 426


>gi|126739044|ref|ZP_01754738.1| tRNA-dihydrouridine synthase A [Roseobacter sp. SK209-2-6]
 gi|126719661|gb|EBA16369.1| tRNA-dihydrouridine synthase A [Roseobacter sp. SK209-2-6]
          Length = 319

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 146/317 (46%), Positives = 195/317 (61%), Gaps = 12/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RLL + ALLYTEM+ A A++RG   ++L  + +E PLALQ+GGAD  
Sbjct: 1   MMDWTDRHCRFFHRLLCHEALLYTEMVTAPALVRGGALHLLDHNAEEHPLALQLGGADPV 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+   + GY+EINLN GCPS RV  G+FGA LM +PD+V DC+AAM   +++ VT
Sbjct: 61  ELAQAARHGAEAGYDEINLNCGCPSDRVQSGAFGAILMKSPDLVADCVAAMQAKVAVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   ++ I+ +G   + IHARKA L+GLSPK+NR IP LDY++V+
Sbjct: 121 VKCRIGVDDQEPREVLPRFLEKIRAAGCQRVTIHARKAWLQGLSPKENRDIPPLDYELVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           E+K+  PDL I LNGG+  + +AL  L   +DGVM+GRAAY   A +L   D        
Sbjct: 181 EMKQAFPDLHISLNGGIASLLEALPHLERGLDGVMVGRAAYHQPADILAEADPLVFGTGE 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            + P+               M  Y    +  G +L QITRHM+G F G P +R  R  L+
Sbjct: 241 VTDPV----------AAVRDMLPYIEAEMSKGARLHQITRHMLGAFAGRPGARAWRRQLS 290

Query: 299 VEAGASTATHHIIETAF 315
                  A   ++E   
Sbjct: 291 EGVSRKGAGPELVEQRL 307


>gi|260575169|ref|ZP_05843170.1| TIM-barrel protein, yjbN family [Rhodobacter sp. SW2]
 gi|259022791|gb|EEW26086.1| TIM-barrel protein, yjbN family [Rhodobacter sp. SW2]
          Length = 325

 Score =  334 bits (856), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 149/320 (46%), Positives = 205/320 (64%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R +T  A+LYTEM+ A A++ G +  +LG+   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDRHCRYFHRAMTARAMLYTEMVTALAVIHGPRDRLLGYDLAEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +A ++   +GY+EINLNVGCPS RV  G+FGA LML P +V  C+AAM  A  +PVT
Sbjct: 74  ELAQAVRLAAPWGYDEINLNVGCPSDRVQSGAFGAVLMLQPALVAACVAAMQDASPVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ+P   L   ++ ++  GV  + IHARKA L+GLSPK+NR+IP LDY +V 
Sbjct: 134 VKCRIGVDDQVPEDVLPAFLEMLRGVGVGHVIIHARKAWLQGLSPKENREIPPLDYPLVL 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K+E PDL I +NGG+  + QA  +L   +DGVMIGRAAY +  A L   D  + +P  
Sbjct: 194 RMKREFPDLTISINGGVATLDQARGLLAQGLDGVMIGRAAYHDPGATLIGADTLWGDPPG 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +             +  +M  Y A HL  GGKL QITRHM+GLF G P +R  R +L+
Sbjct: 254 RDA-----------FGVIEAMQPYIAAHLAQGGKLHQITRHMLGLFAGRPGARGWRRVLS 302

Query: 299 VEAGASTATHHIIETAFNLM 318
            +A    A   +++ A   +
Sbjct: 303 EQAVRDGAGLQVLDAALAQV 322


>gi|21233367|ref|NP_639284.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770330|ref|YP_245092.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|38604922|sp|Q8P3X4|DUSA_XANCP RecName: Full=tRNA-dihydrouridine synthase A
 gi|21115203|gb|AAM43166.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575662|gb|AAY51072.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. 8004]
          Length = 335

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 193/314 (61%), Gaps = 11/314 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD++ ++GF   E PLALQ+GG+D +
Sbjct: 20  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRQRLIGFDAVEHPLALQLGGSDPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I + +GY+EINLN GCPS RV  G FGACLM  P +V DC+AAMC A ++PVT
Sbjct: 80  LLAQAAQIAQAWGYDEINLNCGCPSDRVQAGRFGACLMREPALVADCVAAMCAATALPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          +  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 140 VKCRLGVDDDDDYAVFAGFIDQVVGAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  +L  L   DGVM+GRAAY +  +L  ++   S      
Sbjct: 200 RLKQERPALPVVLNGGIASVEASLAHLQHTDGVMLGRAAYHDPYVLHQLEAALSG----- 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R D      +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 255 RPERARAD------LLQAYQPYVQAQLDQGLALKHMTRHILGLFHGQPGGRVFRQVLSEG 308

Query: 301 AGASTATHHIIETA 314
           A    A   ++E A
Sbjct: 309 AHRPGAGWELVEQA 322


>gi|212212648|ref|YP_002303584.1| tRNA-dihydrouridine synthase A [Coxiella burnetii CbuG_Q212]
 gi|212011058|gb|ACJ18439.1| NIFR3-like protein [Coxiella burnetii CbuG_Q212]
          Length = 353

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 185/317 (58%), Gaps = 2/317 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 36  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 96  SLALCARLAEEKGFDEINLNVGCPSGRVTAGRFGACLLKEAELVADCVAAMSAEVNIPVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 156 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N  +     +  S P+   
Sbjct: 216 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANP-LFCAAFDDLSKPVFSL 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L   
Sbjct: 275 GVTDKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFLHEN 334

Query: 301 AGASTATHHIIETAFNL 317
                     IE A  L
Sbjct: 335 TRREG-PIAAIEEALRL 350


>gi|167582008|ref|ZP_02374882.1| tRNA-dihydrouridine synthase A [Burkholderia thailandensis TXDOH]
          Length = 339

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 188/319 (58%), Gaps = 9/319 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +A LYTEM+   A++ GD    L F+  E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRSFHRTISRHAWLYTEMVTTGALIHGDVARHLAFTPDEAPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  +A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 77  ELAHSARLGERWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAIEDYAFVRDFVGTVASAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+  + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPQLEIVINGGITTLDEVEQHLRHVDGVMLGREAYHNPYVLAGVDARFYG---AT 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  TR        + A + +Y A  L  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 254 EPAPTR------EAVEAKLVEYCAAELARGTYLGAIVRHALGLYRGVTGARGWRRVLSDS 307

Query: 301 AGASTATHHIIETAFNLMI 319
              +     I + A   + 
Sbjct: 308 KRLARGDLSIFDEARAHLT 326


>gi|50086096|ref|YP_047606.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ADP1]
 gi|49532072|emb|CAG69784.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ADP1]
          Length = 341

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 138/322 (42%), Positives = 193/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L +S  E P+ LQ+GG++  
Sbjct: 23  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDTKRHLDYSHGEHPIVLQLGGSNPK 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E  K+ +D+GY+E+NLNVGCPS RV     GACLM  PD+V +CIA M + + IPV 
Sbjct: 83  DLAECTKMAQDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIAKMQQVVDIPVH 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + N V ++ K+G +   +HAR A+LKGLSPK+NR+IP L Y+ VY
Sbjct: 143 VKHRIGIDDMQSYDEMLNFVDTVAKTGCHHFVVHARIALLKGLSPKENREIPPLRYEDVY 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+LFI +NGG++ +++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 203 RLKQDRPELFIEINGGIKTVAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 257 ------LDLPDRFNIMQQMMPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 308

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   IE A   + E++
Sbjct: 309 -GGNAKTRSDIEHALCNIHEAI 329


>gi|299133589|ref|ZP_07026783.1| TIM-barrel protein, yjbN family [Afipia sp. 1NLS2]
 gi|298591425|gb|EFI51626.1| TIM-barrel protein, yjbN family [Afipia sp. 1NLS2]
          Length = 316

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 149/320 (46%), Positives = 194/320 (60%), Gaps = 9/320 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R F R LT  A LYTEM+   A++RGD++ +LGF   E P+ALQ+GG++   
Sbjct: 1   MDWTDRHCRVFHRALTRRAWLYTEMLTTGAVIRGDRERLLGFDACEHPVALQLGGSNPHD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L E+AKI E FGY+EINLNVGCPS RV +G FGACLM  P +VGDC+AAM  A+ +PVTV
Sbjct: 61  LAESAKIGEGFGYDEINLNVGCPSDRVQDGRFGACLMTVPQLVGDCVAAMKAAVRVPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIGVD Q P  AL  L +++  +G + + +HARKA L+GLSPK+NR IP LDYD VY 
Sbjct: 121 KCRIGVDKQDPEQALDALAQNVVTAGADALIVHARKAWLEGLSPKENRDIPPLDYDRVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K   PD+ I +NGG+  + QA   L  VDGVM+GRAAY     L  VD       +  +
Sbjct: 181 LKAAMPDVTISINGGVTSIEQAKAHLQHVDGVMLGRAAYHEPWRLLAVDPELFGASSPHA 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
                       +   S+  Y  R    G +L  ITRHM+G FHG   +R  R  L    
Sbjct: 241 ---------SMHEAIESLFPYIERQRARGMRLHSITRHMVGAFHGVAGARAFRRALAENC 291

Query: 302 GASTATHHIIETAFNLMIES 321
             + A    +  A  L++ +
Sbjct: 292 VKADAGVEQLRDALRLVVPA 311


>gi|262377397|ref|ZP_06070620.1| tRNA-dihydrouridine synthase A [Acinetobacter lwoffii SH145]
 gi|262307627|gb|EEY88767.1| tRNA-dihydrouridine synthase A [Acinetobacter lwoffii SH145]
          Length = 341

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 140/322 (43%), Positives = 198/322 (61%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N ++YTEM+   AI+ GD K  L F+ +E+P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVIMYTEMVTTGAIIYGDAKRHLDFNAEEQPIVLQLGGSNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ +D+GYNE+NLNVGCPS RV     GACLM  PD+V +CIA M  A+ IPVT
Sbjct: 80  DLAICTKMAQDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIAEMRHAVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G N   +HAR A+LKGLSPK+NR +P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAKTGCNNFIVHARIALLKGLSPKENRDVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++  ++ LK L  VDGVMIGR AY N  +L  + + ++     +
Sbjct: 200 RLKQERPDLLIEINGGIKTYAETLKHLKHVDGVMIGREAYHNPYLLAELGQLWN----LN 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +          I   M  Y A+ +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 256 APDRF--------DIMQQMLPYIAQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +ETA   + E++
Sbjct: 306 -GGNAKTLKDVETALFNIQEAM 326


>gi|167586199|ref|ZP_02378587.1| tRNA-dihydrouridine synthase A [Burkholderia ubonensis Bu]
          Length = 339

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 187/318 (58%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +  LYTEMI   A+L GD +  L F+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRHTWLYTEMITTGALLFGDAQRHLAFTPSESPVALQLGGSERD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAVEEYAFVRDFVGTVAEAGCEVFVVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG++ + +  + L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 197 RLKRDFPSLEIVINGGIKTLDEVAQHLEHVDGVMLGREAYHNPYVLAGVDARFYGA-NDA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +   +          + +Y A  L  G  L  + RH +GL+ G   +R  R +L+  
Sbjct: 256 APTREEAE--------ERLIEYCAAELKRGTYLGAVVRHALGLYRGVAGARGWRRVLSDN 307

Query: 301 AGASTATHHIIETAFNLM 318
              +     + + A   +
Sbjct: 308 KKLAHGDLAVFDEARAHL 325


>gi|39935038|ref|NP_947314.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris CGA009]
 gi|39648889|emb|CAE27410.1| NifR3/Smm1 family protein [Rhodopseudomonas palustris CGA009]
          Length = 331

 Score =  332 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 146/320 (45%), Positives = 200/320 (62%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R F RLLT   LLYTEM+   A++ GD++ +LGF   E P+ALQ+GG++ +
Sbjct: 14  MMDWTDSHCRVFHRLLTRRGLLYTEMVTTGAVIHGDRQRLLGFDASEHPVALQLGGSNPN 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EIN+NVGCPS RV EG FGACLM  P++V + +AAM +A+S+PVT
Sbjct: 74  DLATSAKIGEDFGYDEININVGCPSDRVKEGRFGACLMAEPELVAEGVAAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPEVALDALARAVVAAGADALIVHARKAWLNGLSPKENRHIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  +++A + L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKQAMPQVPIIINGGIGSIAEAKRHLEHVDGVMLGRAAYQEPWRLLEVDPELYGETAPY 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +K         +   ++  Y  R L  G +L  ITRH+IG + G P +R  R  L+  
Sbjct: 254 PSMK---------EALEALIPYIERQLAQGLRLHAITRHVIGAYQGVPGARAFRRYLSEF 304

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A   + E
Sbjct: 305 GVKPDADASVLLKAMVAVTE 324


>gi|33239466|ref|NP_874408.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33236991|gb|AAP99060.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
          Length = 333

 Score =  332 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 135/321 (42%), Positives = 190/321 (59%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   R +T  AL+YTEMIVA A+   ++K++L F   E P+ALQ+GG D  
Sbjct: 20  MLDCTDRHFRVLMRQITGRALVYTEMIVAKALKYKNRKSLLDFDEIEHPIALQVGGDDPI 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E++GY+EINLN+GCPS +V  G+FGACLM  PD V  CI AM K  +IPVT
Sbjct: 80  VLSEAAQIAEEWGYDEINLNLGCPSPKVQSGNFGACLMGQPDQVFKCIEAMKKKTNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G+D+      L + V  +  +G +   IHARKA+L G + K+NR IP L+Y+ V 
Sbjct: 140 IKHRTGIDNLDSEQLLLDFVDKMASAGADRFSIHARKALLNGFNAKENRSIPPLEYEKVA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IKK  P+L I LNGGL++    +K L + DGVM+GRA Y N  M   +D+ F       
Sbjct: 200 KIKKCRPNLKIELNGGLQNQYDCIKALKTFDGVMVGRAIYSNPLMWKEIDDIFFGE---- 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                +  K     I   +  YA +HL   G+L  I +H + L  G   +R+ R+ L+ +
Sbjct: 256 -----KKVKINASIILRGLIPYAEKHLSKNGRLWDICKHTLHLVQGVKGARKWRNELSQK 310

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    A   I+E A   + ++
Sbjct: 311 AQNPKAELIILEKAARQLEDA 331


>gi|71279069|ref|YP_267111.1| tRNA-dihydrouridine synthase A [Colwellia psychrerythraea 34H]
 gi|71144809|gb|AAZ25282.1| TIM-barrel protein, yjbN family [Colwellia psychrerythraea 34H]
          Length = 335

 Score =  332 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 135/319 (42%), Positives = 186/319 (58%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RL+T + +LYTEM+   AILRG   + L ++  E PL LQ+GG+D+ 
Sbjct: 25  MLDWTDKHSRYFYRLMTQHTVLYTEMVTTGAILRGKG-DYLSYNDAEHPLVLQLGGSDVK 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + E AKI E +GY+E+N+NVGCPS RV  G FGACLM  P +V  C+  M  A +IPVT
Sbjct: 84  AMTECAKIAEQYGYDEVNINVGCPSDRVQNGRFGACLMAEPALVAQCVNQMQSATNIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      L   ++ + K+      IHARKA L GLSPK NR +P LDYD VY
Sbjct: 144 VKSRIGIDDLDSYEFLHTFIEEVSKADCRHFIIHARKAWLTGLSPKQNRDVPPLDYDRVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK +  DL + +NGG++  S+A + L  +DGVMIGR  Y +  ML   D       T  
Sbjct: 204 QIKNDFKDLEVSINGGIKTFSEANEHLQHIDGVMIGREIYNSPYMLADADNEIYQSDT-- 261

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                   K    ++   M  Y    + +GG+   + RHM+GL +G   +R+ R  L+  
Sbjct: 262 -------IKLSRSEVIDLMVPYIDETIANGGRAWHVLRHMLGLCNGLSGARKFRQHLSEC 314

Query: 301 AGASTATHHIIETAFNLMI 319
           AG   A   ++  AFN + 
Sbjct: 315 AGKDGAGGQVLLDAFNKVT 333


>gi|262380225|ref|ZP_06073380.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SH164]
 gi|262298419|gb|EEY86333.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SH164]
          Length = 335

 Score =  332 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 139/322 (43%), Positives = 198/322 (61%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRFFARL   N +LYTEM+   AIL GD    L ++ +E P+ LQ+GG+   
Sbjct: 16  MMDWTTRDYRFFARLFNPNMILYTEMVTTGAILFGDAGRHLNYNQEEHPVVLQLGGSSPK 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ ED+GYNE+NLNVGCPS RV     GACLM  P++V +CI+AM +A++IPVT
Sbjct: 76  DLATCTKMAEDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPELVAECISAMRQAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G N   +HAR A+L+GLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAKTGCNNFIVHARIALLQGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++ +++  + L  VDGVMIGR AY N  +L  + E ++      
Sbjct: 196 RLKQERPDLTIEINGGVKTLAETQEHLKHVDGVMIGREAYHNPYLLAELGELWN------ 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+  R       +I   M  Y A+ L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 250 LPMPDRF------EIMEQMLPYIAKRLEEGAPLSVITRHILGLFQYLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T+  +E A   +  ++
Sbjct: 302 -GGNAKTYADVENAIQNIKAAM 322


>gi|209363933|ref|YP_001424351.2| tRNA-dihydrouridine synthase A [Coxiella burnetii Dugway 5J108-111]
 gi|212218379|ref|YP_002305166.1| tRNA-dihydrouridine synthase A [Coxiella burnetii CbuK_Q154]
 gi|207081866|gb|ABS78105.2| NIFR3-like protein [Coxiella burnetii Dugway 5J108-111]
 gi|212012641|gb|ACJ20021.1| NIFR3-like protein [Coxiella burnetii CbuK_Q154]
          Length = 353

 Score =  332 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 185/317 (58%), Gaps = 2/317 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 36  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 96  SLALCARLAEEKGFDEINLNVGCPSGRVTAGRFGACLLKEAELVADCVAAMSAEVNIPVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 156 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N  +     +  S P+   
Sbjct: 216 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANP-LFCAAFDDLSKPVFSL 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L   
Sbjct: 275 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFLHEN 334

Query: 301 AGASTATHHIIETAFNL 317
                     IE A  L
Sbjct: 335 TRREG-PIAAIEEALRL 350


>gi|329888317|ref|ZP_08266915.1| tRNA-dihydrouridine synthase A [Brevundimonas diminuta ATCC 11568]
 gi|328846873|gb|EGF96435.1| tRNA-dihydrouridine synthase A [Brevundimonas diminuta ATCC 11568]
          Length = 323

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 152/326 (46%), Positives = 201/326 (61%), Gaps = 14/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR+ R F R L+  ALLYTEM+ A A++ GD+  +LGF   E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRNCRAFHRALSTRALLYTEMVTAPAVIHGDRDRLLGFDVVEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAKI E +GY+EINLNVGCPS RV  G FGACLM  P++V DC+AA+ +A+S+P T
Sbjct: 61  QLAEAAKIGEAYGYDEINLNVGCPSDRVQSGKFGACLMREPELVADCMAAIKEAVSVPAT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P ++L   V +    G++   IHARKA LKGLSPK+NR +P LDY +V 
Sbjct: 121 VKCRIGVDDQDPEISLFATVDASAAVGIDSFIIHARKAWLKGLSPKENRDVPPLDYALVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +K+E P L I +NGG+ D+ QA   L       +DGVM+GRAAY   A++  VD     
Sbjct: 181 RLKRERPHLSISINGGIGDLDQAEAHLRADDGVQLDGVMLGRAAYHEPALMGQVDRRIFG 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T    +          +       Y A  L  G  L  +TRHM+GL HG   +R  R 
Sbjct: 241 ETTPDVDVF---------EALERYRPYMAARLEEGANLAGMTRHMLGLMHGRAGARAFRR 291

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ILTVE     A   +++ A   + E+
Sbjct: 292 ILTVEGVKPGAGLEVVDRAVEAVREA 317


>gi|255320921|ref|ZP_05362095.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SK82]
 gi|255302090|gb|EET81333.1| tRNA-dihydrouridine synthase A [Acinetobacter radioresistens SK82]
          Length = 340

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 139/322 (43%), Positives = 198/322 (61%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRFFARL   N +LYTEM+   AIL GD    L ++ +E P+ LQ+GG+   
Sbjct: 21  MMDWTTRDYRFFARLFNPNMILYTEMVTTGAILFGDAGRHLNYNQEEHPVVLQLGGSSPK 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ ED+GYNE+NLNVGCPS RV     GACLM  P++V +CI+AM +A++IPVT
Sbjct: 81  DLATCTKMAEDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPELVAECISAMRQAVNIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G N   +HAR A+L+GLSPK+NR++P L Y+ VY
Sbjct: 141 VKHRIGIDDMQSYEEMLHFVDTVAKTGCNNFIVHARIALLQGLSPKENREVPPLRYEDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E PDL I +NGG++ +++  + L  VDGVMIGR AY N  +L  + E ++      
Sbjct: 201 RLKQERPDLTIEINGGVKTLAETQEHLKHVDGVMIGREAYHNPYLLAELGELWN------ 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+  R       +I   M  Y A+ L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 255 LPMPDRF------EIMEQMLPYIAKRLEEGAPLSVITRHILGLFQYLPGARKWRQALS-- 306

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T+  +E A   +  ++
Sbjct: 307 -GGNAKTYADVENAIQNIKAAM 327


>gi|308451158|ref|XP_003088566.1| hypothetical protein CRE_10759 [Caenorhabditis remanei]
 gi|308246538|gb|EFO90490.1| hypothetical protein CRE_10759 [Caenorhabditis remanei]
          Length = 338

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 132/322 (40%), Positives = 190/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT R YRFFARL   N +LYTEM+   AI+ G     L ++ +E P+ LQ+GG++  
Sbjct: 20  MMDWTTRDYRFFARLFNPNIILYTEMVTTGAIIYGGANRHLDYNHEEHPIVLQLGGSNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +K+ +D+GY+EINLNVGCPS RV     GACLM  PD+V +CIA M  A+ IPVT
Sbjct: 80  DLATCSKMAQDWGYDEINLNVGCPSDRVQNNKIGACLMAEPDLVAECIAEMRNAVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G +   +HAR A+L+GLSPK+NR +P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAKTGCDNFIVHARIALLQGLSPKENRDVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPELLIEINGGVKTFAETQAHLKHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D      I   M  Y A+ +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LDLPDRFDIIDQMLPYIAKRMQEGAPLSIITRHILGLFQNLPGARKWRQALSGG 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              + A    +E A   + E++
Sbjct: 308 NAKTFAD---VENAIINIKEAM 326


>gi|164685730|ref|ZP_01945619.2| tRNA dihydrouridine synthase A [Coxiella burnetii 'MSU Goat Q177']
 gi|165918518|ref|ZP_02218604.1| tRNA dihydrouridine synthase A [Coxiella burnetii RSA 334]
 gi|164601240|gb|EAX33765.2| tRNA dihydrouridine synthase A [Coxiella burnetii 'MSU Goat Q177']
 gi|165917764|gb|EDR36368.1| tRNA dihydrouridine synthase A [Coxiella burnetii RSA 334]
          Length = 328

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 185/317 (58%), Gaps = 2/317 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 11  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 71  SLALCARLAEEKGFDEINLNVGCPSGRVTAGRFGACLLKEAELVADCVAAMSAEVNIPVS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 131 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N  +     +  S P+   
Sbjct: 191 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANP-LFCAAFDDLSKPVFSL 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L   
Sbjct: 250 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFLHEN 309

Query: 301 AGASTATHHIIETAFNL 317
                     IE A  L
Sbjct: 310 TRREG-PIAAIEEALRL 325


>gi|92119109|ref|YP_578838.1| tRNA-dihydrouridine synthase A [Nitrobacter hamburgensis X14]
 gi|91802003|gb|ABE64378.1| tRNA-U16,U17-dihydrouridine synthase [Nitrobacter hamburgensis X14]
          Length = 336

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 151/320 (47%), Positives = 195/320 (60%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT  A LYTEM+   AI+ G +  +LGFS  E P+ALQ+GG+   
Sbjct: 18  MMDWTDRHCRLFHRLLTRKARLYTEMLTTGAIIHGARDRLLGFSDIEHPVALQLGGSHPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I EDFGY+EINLNVGCPS RV +G FGACLM  PDIV + + AM +A+S+PVT
Sbjct: 78  DLAAAARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPDIVAEGVHAMKRAVSVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P   L +  + +  +GV+ + +HARKA L+GLSPKDNR IP LDYD VY
Sbjct: 138 VKCRIGIDDQDPEAGLDSFARKVVAAGVDALIVHARKAWLQGLSPKDNRNIPPLDYDRVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L + +NGG+  +S+A   L  VDGVM+GRAAY++   L  VD          
Sbjct: 198 RLKALLPALPVIINGGIGGISEAKNHLAHVDGVMLGRAAYQDPWRLLKVDSELFGEAAPH 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + +K             +M  Y    L  G +L  ITRH++G FHG P +R  R  L   
Sbjct: 258 ATMKC---------ALEAMIPYIEDQLAGGARLHSITRHLVGAFHGVPGARAFRRYLAEN 308

Query: 301 AGASTATHHIIETAFNLMIE 320
              +     I+  A  L+ E
Sbjct: 309 GVKAGVGADILREAIALVEE 328


>gi|284929214|ref|YP_003421736.1| tRNA-U16,U17-dihydrouridine synthase [cyanobacterium UCYN-A]
 gi|284809658|gb|ADB95355.1| tRNA-U16,U17-dihydrouridine synthase [cyanobacterium UCYN-A]
          Length = 324

 Score =  331 bits (850), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 134/318 (42%), Positives = 189/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F R +T + LLYTEMI A A+  G+K  +L FS+ EKPL+LQ+GG D  
Sbjct: 14  MMDRTDRHFRYFIRQITKHTLLYTEMISATAVQNGNKSKLLDFSSDEKPLSLQLGGNDPY 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A I ED+GY+E+NLN+GCPS RV  G FGACLM  P++V   +  M +++ IP+T
Sbjct: 74  TLAECAIIAEDWGYDEVNLNIGCPSDRVQNGRFGACLMAEPELVAKSVEKMQESVDIPIT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+     +L+  V+ + +SG     +HARKA L+GLSPK+NR IP L Y  VY
Sbjct: 134 VKHRIGIDECDDYESLKYFVRIVSESGCKKFIVHARKAWLQGLSPKENRNIPPLRYQDVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P L I +NGG+ ++ Q    L  +D VM+GR AY N  +L TVD+ F      S
Sbjct: 194 SLKKDFPHLTIEINGGITNLEQISHHLQFIDSVMLGRIAYNNPYLLATVDKDFYKS---S 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +   TR       +I  ++  Y       G KL  ITRH++ LF G   ++  +  +T  
Sbjct: 251 TTPLTRY------QIIENILPYVEYWASHGLKLHSITRHLLSLFIGISGTKEWKRYITEN 304

Query: 301 AGASTATHHIIETAFNLM 318
           +         I  A + +
Sbjct: 305 SHFIGQDSKAIINALSKI 322


>gi|29654227|ref|NP_819919.1| tRNA-dihydrouridine synthase A [Coxiella burnetii RSA 493]
 gi|29541493|gb|AAO90433.1| NifR3-like protein [Coxiella burnetii RSA 493]
          Length = 353

 Score =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 185/317 (58%), Gaps = 2/317 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 36  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 96  SLALCARLAEEKGFDEINLNVGCPSGRVIAGRFGACLLKEAELVADCVAAMSAEVNIPVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 156 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 215

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N  +     +  S P+   
Sbjct: 216 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANP-LFCAAFDDLSKPVFSL 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L   
Sbjct: 275 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFLHEN 334

Query: 301 AGASTATHHIIETAFNL 317
                     IE A  L
Sbjct: 335 TRREG-PIAAIEEALRL 350


>gi|299771563|ref|YP_003733589.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. DR1]
 gi|298701651|gb|ADI92216.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. DR1]
          Length = 334

 Score =  331 bits (849), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 190/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L +S QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYSAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI  M KA+ IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHTMQKAVKIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTYFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAEMGQLWN------ 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 250 ------LEAPDRFDIMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  +L
Sbjct: 302 -GGNAKTLGDVEQAISNMQAAL 322


>gi|254418914|ref|ZP_05032638.1| TIM-barrel protein, yjbN family [Brevundimonas sp. BAL3]
 gi|196185091|gb|EDX80067.1| TIM-barrel protein, yjbN family [Brevundimonas sp. BAL3]
          Length = 338

 Score =  331 bits (849), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 153/317 (48%), Positives = 199/317 (62%), Gaps = 14/317 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+LT  ALLYTEM+ A A+L GD+  +LGF   E P+ALQ+GG++  
Sbjct: 14  MMDWTDRHCRAFHRVLTARALLYTEMVTAPAVLHGDRDYLLGFDAVEHPVALQLGGSNPM 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAAK+ E +GY+EINLNVGCPS RV  G FGACLM  P++V DC+AA+  A+SIP T
Sbjct: 74  ELAEAAKVGEAYGYDEINLNVGCPSDRVQSGKFGACLMREPELVADCMAAIRSAVSIPAT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ PA +L   V +    G+    +HARKA L+GLSPK+NR +P LDYD+V 
Sbjct: 134 VKCRIGVDDQEPATSLFATVDACAAVGIEVFIVHARKAWLQGLSPKENRDVPPLDYDLVR 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV-----DGVMIGRAAYKNSAMLTTVDEYFSN 235
            +K+E P L I +NGG+ ++ +A   L        DGVM+GRAAY   A+L   D     
Sbjct: 194 RLKRERPHLNISINGGIANLDEAEAHLAETDGVRLDGVMMGRAAYHEPAILGQADRRLYG 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T        +D+            Y A  L  G +L  ITRHM+GL HG P +R  R 
Sbjct: 254 ADTADVDAFAALDR---------YRPYIAARLEEGVRLPAITRHMLGLMHGRPGARAFRR 304

Query: 296 ILTVEAGASTATHHIIE 312
           ILTVE+  + A   +++
Sbjct: 305 ILTVESIRADAGLEVLD 321


>gi|293610334|ref|ZP_06692635.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827566|gb|EFF85930.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 338

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 134/322 (41%), Positives = 189/322 (58%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI  M KA++IPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHTMQKAVNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTYFVVHARIAILKGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LEAPDRFDIMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALSGG 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              + A    +E A   M  ++
Sbjct: 308 NAKTLAD---VENAIQNMRAAM 326


>gi|161831190|ref|YP_001596802.1| tRNA-dihydrouridine synthase A [Coxiella burnetii RSA 331]
 gi|161763057|gb|ABX78699.1| tRNA dihydrouridine synthase A [Coxiella burnetii RSA 331]
          Length = 328

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 186/317 (58%), Gaps = 2/317 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  TDRH+R F R ++ + LLYTEM+   A+L+G +   L +S +E PLALQ+GG+D  
Sbjct: 11  MMGCTDRHFRMFMRQISRHVLLYTEMVTTGALLKGKQWRCLDYSPEEHPLALQVGGSDPQ 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E+ G++EINLNVGCPS RV  G FGACL+   ++V DC+AAM   ++IPV+
Sbjct: 71  SLALCARLAEEKGFDEINLNVGCPSGRVIAGRFGACLLKEAELVADCVAAMSAEVNIPVS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R GVDDQ     L + VK++ ++G     IHARKA LKGLSP +NR +P L Y +VY
Sbjct: 131 VKTRTGVDDQDSYEHLYHFVKTVAEAGCRIFIIHARKAWLKGLSPAENRTVPPLAYPMVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++ +      L  VDGVMIGR AY N  +     +  S P+   
Sbjct: 191 QLKQDFPGLEIIINGGIKTIEAINDHLREVDGVMIGREAYANP-LFCAAFDDLSKPVFSL 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                +      +++      Y A+ L +G  L  +TRH+ GLF G P +++ R  L   
Sbjct: 250 GVADKKQTPLTPKRVLLRYLPYMAKQLANGVPLYAMTRHLNGLFQGQPGAKKWRRFLHEN 309

Query: 301 AGASTATHHIIETAFNL 317
                +    IE A  L
Sbjct: 310 -TRRESPIAAIEEALRL 325


>gi|307545712|ref|YP_003898191.1| tRNA-dihydrouridine synthase A [Halomonas elongata DSM 2581]
 gi|307217736|emb|CBV43006.1| tRNA-dihydrouridine synthase A [Halomonas elongata DSM 2581]
          Length = 336

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 142/322 (44%), Positives = 191/322 (59%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+DWT R YR FAR LT +ALLYTEM+   AIL G  +   LG+   E PLALQ+GG+D 
Sbjct: 18  MMDWTTRDYRAFARTLTRHALLYTEMVTTGAILYGSPRERFLGYDAIEHPLALQLGGSDA 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L E A I E +GY+E+NLNVGCPS RV     GACLM  PD V   + AM  A+SIPV
Sbjct: 78  GELAECAAIAEAWGYDEVNLNVGCPSDRVQNNLIGACLMAYPDKVAAAVKAMQAAVSIPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIG+DDQ     L + ++ +  +G +   +HARKA L+GLSPK NR +P L+Y  +
Sbjct: 138 TVKCRIGIDDQDEDADLAHFIQRVADAGCSTFIVHARKAWLEGLSPKQNRDVPPLNYPRI 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + +K ++P+L IGLNGGL+ +      L  VD VM+GR AY+N  +L +VD         
Sbjct: 198 HRLKAQHPELHIGLNGGLKTLENCQAQLAHVDSVMVGREAYQNPWLLASVDSRLYGE--- 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P + R         + ++  Y A+ L  G +L  +TRH++GLF G P  RR R  L+ 
Sbjct: 255 PDPAEDR------HSAARALRPYIAQRLEEGARLNHLTRHLLGLFQGCPGGRRFRRHLSE 308

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   + + A  L+ E 
Sbjct: 309 NAHRDGAGLAVFDDALGLVAED 330


>gi|325124532|gb|ADY84055.1| tRNA-dihydrouridine synthase A [Acinetobacter calcoaceticus PHEA-2]
          Length = 334

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 191/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTYFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LK 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +          I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 APDRF--------DIMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALSGG 303

Query: 301 AGASTATHHIIETAFNLMIESL 322
              + A    +E A   M  ++
Sbjct: 304 NAKTLAD---VENAIQNMRAAM 322


>gi|169634371|ref|YP_001708107.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii SDF]
 gi|169153163|emb|CAP02248.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii]
          Length = 339

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 193/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 21  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 81  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 141 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 201 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +          I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 257 APDRF--------DIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 306

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 307 -GGNAKTLTDVENAIHNMQAAI 327


>gi|239500729|ref|ZP_04660039.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB900]
          Length = 334

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 193/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +          I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 APDRF--------DIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 302 -GGNAKTLTDVENAIHNMQAAI 322


>gi|300980481|ref|ZP_07175028.1| tRNA dihydrouridine synthase A [Escherichia coli MS 200-1]
 gi|300992960|ref|ZP_07180115.1| tRNA dihydrouridine synthase A [Escherichia coli MS 45-1]
 gi|300307783|gb|EFJ62303.1| tRNA dihydrouridine synthase A [Escherichia coli MS 200-1]
 gi|300406734|gb|EFJ90272.1| tRNA dihydrouridine synthase A [Escherichia coli MS 45-1]
 gi|315287860|gb|EFU47262.1| tRNA dihydrouridine synthase A [Escherichia coli MS 110-3]
 gi|315291520|gb|EFU50880.1| tRNA dihydrouridine synthase A [Escherichia coli MS 153-1]
 gi|315297520|gb|EFU56799.1| tRNA dihydrouridine synthase A [Escherichia coli MS 16-3]
 gi|324007804|gb|EGB77023.1| tRNA dihydrouridine synthase A [Escherichia coli MS 57-2]
          Length = 288

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 129/298 (43%), Positives = 180/298 (60%), Gaps = 13/298 (4%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G   + L +S +E P+ALQ+GG+D + L + AK+ E  GY+EINLNVGCPS
Sbjct: 1   MVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPAALAQCAKLAEARGYDEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM N  +V DC+ AM   +SIPVTVK RIG+DDQ     L + + ++  
Sbjct: 60  DRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTVKTRIGIDDQDSYEFLCDFINTVSG 119

Query: 146 SG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            G      IHARKA L GLSPK+NR+IP LDY  VY++K++ P L + +NGG++ + +A 
Sbjct: 120 KGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAK 179

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
             L  +DGVM+GR AY+N  +L  VD E F +  T + P+           +  +M  Y 
Sbjct: 180 AHLQHMDGVMVGREAYQNPGILAAVDREIFGSSDTDADPV----------AVVRAMYPYI 229

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            R L  G  L  ITRHM+GLF G P +R+ R  L+  A  + A  +++E A  L+ + 
Sbjct: 230 ERELSQGTYLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADINVLEHALKLVADK 287


>gi|194364005|ref|YP_002026615.1| tRNA-dihydrouridine synthase A [Stenotrophomonas maltophilia
           R551-3]
 gi|194346809|gb|ACF49932.1| dihydrouridine synthase DuS [Stenotrophomonas maltophilia R551-3]
          Length = 343

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 138/317 (43%), Positives = 192/317 (60%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+L   A LYTEM+ A+A++ GD++ +LGF   E+PLALQ+GG+D +
Sbjct: 28  MMDWTDRHCRVFHRVLAPGARLYTEMVHANAVIHGDRERLLGFDRSEQPLALQLGGSDPA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM  A+ IPVT
Sbjct: 88  LLAQAARIAAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPALVAECVAAMVNAVDIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD+          V     +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 148 VKCRLGVDEDNDYDVFAAFVDRQVAAGAAMVVVHARNAWLKGLSPKENREVPPLKYDWAY 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGGL  +         VDGVM+GRAAY +  +L  ++   +      
Sbjct: 208 RLKQERPALPVVLNGGLASLEAVQAQAVHVDGVMLGRAAYHDPYLLHQLEALHTG----- 262

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++ R D      +  ++  Y    L  G  L+ ITRH++GLFHG    R  R +L+  
Sbjct: 263 APLQARGD------LLRALRPYVEARLGEGLALKHITRHVLGLFHGQAGGRAFRQVLSEG 316

Query: 301 AGASTATHHIIETAFNL 317
           A    A   +IE A  +
Sbjct: 317 AHRPGADWRLIEQALAV 333


>gi|310816167|ref|YP_003964131.1| tRNA-dihydrouridine synthase A [Ketogulonicigenium vulgare Y25]
 gi|308754902|gb|ADO42831.1| tRNA-dihydrouridine synthase A [Ketogulonicigenium vulgare Y25]
          Length = 329

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 147/322 (45%), Positives = 198/322 (61%), Gaps = 12/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD + R F R  + NALLYTEM+ A A++ G +  +LG+   E P+ALQ+GGAD +
Sbjct: 15  MIDWTDSNCRIFHRQFSRNALLYTEMVTAPAVIHGPRARLLGYRDAEHPVALQLGGADPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EA +I  D+ Y+EINLN GCPS RV  G+FGA LM  PD+V + ++ M  A  + VT
Sbjct: 75  QLREAVRIAADWNYDEINLNCGCPSDRVQSGAFGAVLMRQPDLVAEILSEMIAASPVEVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIGVDDQ P+  L   ++ +  SGV  + IHARKA L+GLSPK+NR IP LDYD+V+
Sbjct: 135 LKCRIGVDDQEPSDILPAFLEKVAASGVRRVIIHARKAWLQGLSPKENRDIPPLDYDLVF 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K   PDL I LNGG++ +++A  +L   +DGVMIGRAAY   A +L   D        
Sbjct: 195 AMKAAFPDLHISLNGGVKSLAEAQALLDRGLDGVMIGRAAYHEPADILGQADPLIWGEGH 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             S            +   +M      HL +GG+L QITRHM+G F G P +R+ R IL+
Sbjct: 255 AIS----------AEEAVHAMFPVIEDHLRAGGRLHQITRHMLGAFAGRPGARQWRRILS 304

Query: 299 VEAGASTATHHIIETAFNLMIE 320
            EA    A  H +E A   M +
Sbjct: 305 EEANRDGAGLHTVEKALAAMDQ 326


>gi|215484648|ref|YP_002326883.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB307-0294]
 gi|213987851|gb|ACJ58150.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB307-0294]
          Length = 334

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 193/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLN+GCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNIGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN----LE 251

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +          I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 252 APDRF--------DIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 302 -GGNAKTLTDVENAIHNMQAAI 322


>gi|328950080|ref|YP_004367415.1| TIM-barrel protein, yjbN family [Marinithermus hydrothermalis DSM
           14884]
 gi|328450404|gb|AEB11305.1| TIM-barrel protein, yjbN family [Marinithermus hydrothermalis DSM
           14884]
          Length = 339

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 132/322 (40%), Positives = 187/322 (58%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+  R ++    LYTEM+V  A++ GD+  +L F  +E PLALQIG +D  
Sbjct: 17  MMDWTDRHFRYLMRQVSRKVRLYTEMVVDRALIHGDRARLLAFHPEEHPLALQIGSSDPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              EAA+I   +GY+EINLNVGCPS RV EG FGACLM +P+ V +   AM +A  + VT
Sbjct: 77  LAFEAARIGVAWGYDEINLNVGCPSNRVQEGGFGACLMADPERVREITRAMREAAPV-VT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       L   V+++ ++GV    +HARKA L+GLSPK+NR +P L Y  VY
Sbjct: 136 VKHRIGIDHLDEYRHLARFVETVAETGVTVFIVHARKAWLQGLSPKENRAVPPLRYGEVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I LNGG+  +  A+  L   DGVMIGRAAY+        D+         
Sbjct: 196 RLKQDFPELTIVLNGGVRTLDAAMAHLEHTDGVMIGRAAYETPWAWAGADQQVFGLDRAP 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S           R++  +M  Y    L  G  L++I RH++ LF G P  RR R +L+  
Sbjct: 256 S----------RREVVMAMLPYIEARLMEGVPLRRIARHLLNLFKGAPGGRRFRRVLSEG 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
               TA   +++ A   + +++
Sbjct: 306 LLDPTAGPELVQRALEAIPDAV 327


>gi|294649316|ref|ZP_06726749.1| tRNA-dihydrouridine synthase A [Acinetobacter haemolyticus ATCC
           19194]
 gi|292824795|gb|EFF83565.1| tRNA-dihydrouridine synthase A [Acinetobacter haemolyticus ATCC
           19194]
          Length = 339

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 192/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AI+ G     L F+ +E P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAIIYGGANRHLDFNKEEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  P++V +CI +M KA+SIPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPNLVAECIHSMQKAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AIL+GLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFIVHARIAILQGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++ + +  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTLEETQQHLQHVDGVMIGREAYHNPYLLAEMGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++     +I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LEAPDRFEIMQQMMPYIHQRVAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T + IE A   +  ++
Sbjct: 306 -GGNAKTINDIENAIQNIQAAM 326


>gi|71083884|ref|YP_266604.1| tRNA-dihydrouridine synthase A [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71062997|gb|AAZ22000.1| conserved hypothetical protein [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 330

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 136/318 (42%), Positives = 183/318 (57%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RL++ N LLY+EM+V++AI RGDKK +L F+  EKP+ALQIGG+  +
Sbjct: 10  MMDCTDRHERFFLRLISKNTLLYSEMVVSEAIHRGDKKKLLEFNINEKPIALQIGGSSPT 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EA K+ EDFGY+EINLN+GCPS +V +  FGACLM  P++V DC++ M     +PVT
Sbjct: 70  LLAEATKVGEDFGYDEINLNLGCPSKKVEKNKFGACLMKEPNLVADCLSKMQSVTKLPVT 129

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG DD      L   + ++K +GV    IHARKAIL   +PK N  IP L YD VY
Sbjct: 130 IKTRIGYDDTEDYENLHRFISTLKSTGVKTFIIHARKAILGKFTPKQNLNIPPLKYDFVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KK+ P+  I +NGG+    Q    L  VDGVMIGRAAY    +L  ++    N     
Sbjct: 190 RLKKDFPNEEIIINGGITTTDQMKDHLDKVDGVMIGRAAYHTPYLLADIERDIFNNENVP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S           + +   +  Y    +  G +L QI RH +GLFHG   S   +  L+  
Sbjct: 250 S----------RQDVIEQLLPYVREEIKKGTRLNQIMRHTLGLFHGQTGSSFWKRYLSEN 299

Query: 301 AGASTATHHIIETAFNLM 318
                A    I+   + +
Sbjct: 300 MCVRDADVKKIDHIMDKI 317


>gi|110679742|ref|YP_682749.1| tRNA-dihydrouridine synthase A [Roseobacter denitrificans OCh 114]
 gi|109455858|gb|ABG32063.1| tRNA-dihydrouridine synthase A [Roseobacter denitrificans OCh 114]
          Length = 334

 Score =  329 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 145/320 (45%), Positives = 192/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R LT+ +LLYTEM+ + A++RG   ++L FS  E P+ALQ+GG+D  
Sbjct: 14  MMDWTDRHCRMVHRQLTHQSLLYTEMVTSAALVRGGALHLLAFSPDEHPVALQLGGSDPK 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA + +  GY EINLNVGCPS RV  G FGA LM NP +V DC++AM +A+ IPVT
Sbjct: 74  ELAQAAMLGQTAGYREINLNVGCPSDRVQSGCFGAVLMENPGLVADCVSAMREAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  I  +G   + IHARKA L+GLSPK+NR IP LDY +V 
Sbjct: 134 VKCRIGVDDQNPDEVLPEFLARIVAAGCERVSIHARKAWLQGLSPKENRDIPPLDYPLVL 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K+  P+L I +NGG+  + QA+  L   +DGVMIGRAAY     +L  VD        
Sbjct: 194 RMKEYFPNLHISINGGITSLEQAVGFLEAGLDGVMIGRAAYHTPTDVLGAVDPVIFGTG- 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                          +   +M  Y   H+  GG+L QITRHM+GLF   P +R  R +L+
Sbjct: 253 ---------KVVTGEEAVHAMLPYIEAHVTGGGRLAQITRHMLGLFANRPGARVWRRMLS 303

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    A   ++  A   +
Sbjct: 304 EGAHLPNAGPALVLDALAQV 323


>gi|226952909|ref|ZP_03823373.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ATCC 27244]
 gi|226836354|gb|EEH68737.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. ATCC 27244]
          Length = 343

 Score =  329 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 132/322 (40%), Positives = 191/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AI+ G     L F+ +E P+ LQ+GG++  
Sbjct: 24  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAIIYGGANRHLDFNKEEHPIVLQLGGSNPQ 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  P++V +CI +M KA+SIPVT
Sbjct: 84  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPNLVAECIHSMQKAVSIPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AIL+GLSPK+NR++P L YD VY
Sbjct: 144 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFIVHARIAILQGLSPKENREVPPLRYDDVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++   +  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 204 RLKQERPHLTIEINGGIKTFDETQQHLQHVDGVMIGREAYHNPYLLAEMGQLWN------ 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++     +I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 258 ------LEAPDRFEIMQQMMPYIHQRVAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 309

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T + IE A   +  ++
Sbjct: 310 -GGNAKTINDIENAIQNIQAAM 330


>gi|114320734|ref|YP_742417.1| tRNA-dihydrouridine synthase A [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227128|gb|ABI56927.1| tRNA-U16,U17-dihydrouridine synthase [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 343

 Score =  329 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 185/322 (57%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RLL    LL+TEM+ A A+   D +  L +S  E+PLA+Q GG+D  
Sbjct: 26  MMEWTDRHARYFLRLLAPRTLLFTEMVPALAVWHNDPERFLAYSAAERPLAVQFGGSDPE 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   A++ E + Y+E+NLNVGCPS RV  G+FGACLM +P  V DC+AAM ++  +PVT
Sbjct: 86  QLAHCARLAEAWSYDEVNLNVGCPSDRVQAGAFGACLMADPGRVADCVAAMAESTRLPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       L   V  +  +G    ++HARKA L+GLSPK+NR++P LDY  VY
Sbjct: 146 VKHRIGVDHLDSYDHLTGFVDQVAAAGCRTFYVHARKAWLQGLSPKENREVPPLDYGRVY 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K++ P L + LNGG+      L+ L   +DG M+GR AY N   L   D         
Sbjct: 206 RLKRDFPALEVILNGGITRTETLLETLDRGLDGAMVGREAYTNPWALAGWDRALFGAAGA 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +             +   Y    L  G +LQ + RH++GLF+G P  RR R  ++ 
Sbjct: 266 GVPDR--------HAAVRAFLPYVETELAGGARLQHLARHILGLFNGCPGGRRWRRHISE 317

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A  S A   +IE A  L+ E+
Sbjct: 318 QAHRSGAGPEVIEQALALVPEA 339


>gi|260556088|ref|ZP_05828307.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 19606]
 gi|260410143|gb|EEX03442.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 19606]
          Length = 339

 Score =  329 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 192/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 21  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 81  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 141 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 201 RLKQERPHLTIEINGGIKTFTETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 254

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 255 ------LEAPDRFDIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 306

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 307 -GGNAKTLTDVENAIHNMQAAI 327


>gi|86138502|ref|ZP_01057076.1| tRNA-dihydrouridine synthase A [Roseobacter sp. MED193]
 gi|85825027|gb|EAQ45228.1| tRNA-dihydrouridine synthase A [Roseobacter sp. MED193]
          Length = 349

 Score =  329 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 140/320 (43%), Positives = 197/320 (61%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R+F RLL+  ALLYTEM+ A A++RG   ++L ++ +E P+ALQ+GG+D  
Sbjct: 33  MMEWTDRHCRYFHRLLSQEALLYTEMVTAPALVRGQALHLLEYNAEEHPVALQLGGSDPQ 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++  + GY+EINLN GCPS RV  G+FGA LM +PD+V DCIA M   +++ VT
Sbjct: 93  ELGLAAQLGGEAGYDEINLNCGCPSDRVQSGAFGAVLMQSPDLVADCIAEMRAKVAVEVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L   ++ I+ +G   + IHARKA LKGLSPK+NR IP LDYD+V+
Sbjct: 153 VKCRIGVDEQEPREILPVFLEKIRAAGCQRVTIHARKAWLKGLSPKENRDIPPLDYDLVH 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
           E+K+   D+ I +NGGL+ +  A+  L   +DGVM+GRAAY     +L   D        
Sbjct: 213 EMKRAFCDMHISINGGLDTLDAAIAHLEQGLDGVMVGRAAYHQPTDILAAADVRVFGTGA 272

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P           ++   M  Y    +  G +L QITRHM+GLF G P +R  R +L+
Sbjct: 273 LRDP----------CEVVLQMLPYIEAQMGQGARLHQITRHMLGLFAGRPGARAWRRMLS 322

Query: 299 VEAGASTATHHIIETAFNLM 318
             A    +   ++  A   +
Sbjct: 323 EGASRPGSGPELVLEAMQQV 342


>gi|121605287|ref|YP_982616.1| tRNA-dihydrouridine synthase A [Polaromonas naphthalenivorans CJ2]
 gi|120594256|gb|ABM37695.1| tRNA-U16,U17-dihydrouridine synthase [Polaromonas naphthalenivorans
           CJ2]
          Length = 337

 Score =  329 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 190/322 (59%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+DRH R+F RLL+ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 24  MMDWSDRHCRYFHRLLSRHALLYTEMVTTGALIHGDVGRHLRFNAEEHPVALQLGGSEPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EIN+N GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 84  DLAHCARLGEQWGYSEININCGCPSERVQRGAFGACLMAEPKLVADCVKAMVDAVSVPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     +R+ V ++ ++G +   +HAR A LKGLSPK+NR++P L Y++V+
Sbjct: 144 VKHRIGIDREERYEFVRDFVGTVSEAGCDTFIVHARNAWLKGLSPKENREVPPLRYELVH 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE   L I +NGG+    Q    L  +DGVMIGR AY N   L + D  F      S
Sbjct: 204 RLKKEFAHLTICVNGGITTGEQVQGQLLELDGVMIGREAYHNPWWLASWDADFFGAGGES 263

Query: 241 SPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                        ++ A M DY  R     G     I RHM+GL HG P SRR R + + 
Sbjct: 264 ---------ITREQVEAQMCDYMVREAAGHGTPFSAIARHMLGLRHGLPGSRRWRQVWSD 314

Query: 300 EAGASTATHHIIETAFNLMIES 321
               +     ++  A   + ++
Sbjct: 315 HKLKTMDPRDVMMLAHADVQKA 336


>gi|169797208|ref|YP_001715001.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AYE]
 gi|213155999|ref|YP_002318044.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB0057]
 gi|301346115|ref|ZP_07226856.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB056]
 gi|301511827|ref|ZP_07237064.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB058]
 gi|301594892|ref|ZP_07239900.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB059]
 gi|332850773|ref|ZP_08433005.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332866157|ref|ZP_08436872.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013113]
 gi|169150135|emb|CAM88029.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AYE]
 gi|213055159|gb|ACJ40061.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii AB0057]
 gi|332730432|gb|EGJ61749.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332734798|gb|EGJ65892.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6013113]
          Length = 338

 Score =  329 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 192/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLN+GCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNIGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LEAPDRFDIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 306 -GGNAKTLTDVENAIHNMQAAI 326


>gi|291326742|ref|ZP_06125653.2| tRNA dihydrouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291313086|gb|EFE53539.1| tRNA dihydrouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 288

 Score =  329 bits (844), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 123/295 (41%), Positives = 177/295 (60%), Gaps = 11/295 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G   + L FS +E P+ALQ+GG+D + L + AK+ ++ GY+EINLNVGCPS
Sbjct: 1   MVTTGAIIYGKG-DYLAFSEEEHPVALQLGGSDPAALAQCAKLAQERGYDEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM +  +V DC+ AM   +SIPVTVK RIG+D+Q     L + ++++  
Sbjct: 60  DRVQNGRFGACLMGDAQLVADCVKAMQDVVSIPVTVKTRIGIDEQDSYAFLCDFIETVSD 119

Query: 146 -SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
             G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L + +NGG++ + +A 
Sbjct: 120 KGGCEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMAINGGVKTLEEAK 179

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           + L  +DGVM+GR AY+N ++LT VD           P+   VD         +M  Y  
Sbjct: 180 EHLQHLDGVMVGREAYQNPSILTVVDNQLFGE---HFPVTNGVDA------VRAMYPYIE 230

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMI 319
           + L  G  L  +TRHM+G+F G P +R+ R  L+  A    A   ++E A   + 
Sbjct: 231 KELSKGAYLGHMTRHMLGIFQGIPGARQWRRHLSENAHKKGADLAVVEQALEFVT 285


>gi|159045052|ref|YP_001533846.1| tRNA-dihydrouridine synthase A [Dinoroseobacter shibae DFL 12]
 gi|157912812|gb|ABV94245.1| tRNA-dihydrouridine synthase A [Dinoroseobacter shibae DFL 12]
          Length = 338

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 148/321 (46%), Positives = 190/321 (59%), Gaps = 13/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R  T +ALLYTEM+ A A++RGD   +L  +  E PLALQ+GG+D  
Sbjct: 20  MMDWTDRHCRMFHRQFTQHALLYTEMVTAPAVVRGDAGRLLEHAEAEHPLALQLGGSDPV 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-V 119
           +L EA +I    G++EINLNVGCPS RV  G FGA LM  P +V  C+AAM  A   P +
Sbjct: 80  ELAEAVRIACGHGFDEINLNVGCPSDRVQSGCFGAVLMEQPALVARCVAAMIAASDGPEI 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVKCRIGVDDQ P   L   ++++ ++GV    IHARKA L+GLSPK+NR IP LDY +V
Sbjct: 140 TVKCRIGVDDQQPEEMLPGFLRTVSEAGVRRFTIHARKAWLQGLSPKENRDIPPLDYPLV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPL 237
             +K+  P L + +NGG+ D+ QA   L   +DGVMIGRAAY   A +L   D  F    
Sbjct: 200 VRMKQAFPGLHLSINGGITDLDQAAAHLASGLDGVMIGRAAYHEPARVLGDADRRFFGG- 258

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                     +         +M  Y A HL  GGKL QITRHM+G F G P +R  R +L
Sbjct: 259 ---------AETVSAETAVEAMRPYIADHLARGGKLAQITRHMLGAFAGRPGARGWRRVL 309

Query: 298 TVEAGASTATHHIIETAFNLM 318
           + E     A    ++ A   +
Sbjct: 310 SEEGHRPEAGLGTLDRALAHI 330


>gi|184156887|ref|YP_001845226.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ACICU]
 gi|332874036|ref|ZP_08441971.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6014059]
 gi|183208481|gb|ACC55879.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|322506783|gb|ADX02237.1| dusA [Acinetobacter baumannii 1656-2]
 gi|323516652|gb|ADX91033.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332737777|gb|EGJ68669.1| tRNA dihydrouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 334

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 192/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  LG++ QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLGYNAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M K ++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKVVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 250 ------LEAPDRFDIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 302 -GGNAKTLTDVENAIHNMQAAI 322


>gi|262369896|ref|ZP_06063223.1| tRNA-dihydrouridine synthase A [Acinetobacter johnsonii SH046]
 gi|262314935|gb|EEY95975.1| tRNA-dihydrouridine synthase A [Acinetobacter johnsonii SH046]
          Length = 340

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 130/322 (40%), Positives = 190/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL G     L ++ +E P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVILYTEMVTTGAILFGGANRHLDYNNEEHPIVLQLGGSNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L    K+ +D+GY+E+NLNVGCPS RV     GACLM  PD+V +CIA M  A+ IPVT
Sbjct: 80  DLATCTKMAQDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIAEMQNAVEIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++ K+G +   +HAR A+L+GLSPK+NR IP L Y+ VY
Sbjct: 140 VKHRIGIDDMHSYEEMLHFVDTVTKTGCDNFIVHARIALLQGLSPKENRDIPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++  ++  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPNLLIEINGGIKTFAETQEHLKHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D     +I   M  Y A+ +     L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LDLPDRFEIIDQMLPYIAKRMAEDAPLSIITRHILGLFQNLPGARKWRQALSGG 307

Query: 301 AGASTATHHIIETAFNLMIESL 322
              + A    +E A   + +++
Sbjct: 308 NAKTFAD---VENAILNIKDAM 326


>gi|262280981|ref|ZP_06058764.1| tRNA-dihydrouridine synthase A [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257881|gb|EEY76616.1| tRNA-dihydrouridine synthase A [Acinetobacter calcoaceticus
           RUH2202]
          Length = 330

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 191/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L +S QE P+ LQ+GG++  
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYSAQEHPIVLQLGGSNPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY E+NLNVGCPS RV     GACLM  PD+V +CI  M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYGEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHTMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMHSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQTHLQHVDGVMIGREAYHNPYLLAEMGQLWN------ 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++     +I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 250 ------LEAPDRFEIMEQMLPYIEQRMAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  +L
Sbjct: 302 -GGNAKTLGDVEQAISNMQAAL 322


>gi|87301565|ref|ZP_01084405.1| hypothetical protein WH5701_02784 [Synechococcus sp. WH 5701]
 gi|87283782|gb|EAQ75736.1| hypothetical protein WH5701_02784 [Synechococcus sp. WH 5701]
          Length = 315

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 187/321 (58%), Gaps = 8/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   R ++  ALLYTEM+VA A+  G +  +L F  QE PLALQ+GG D +
Sbjct: 1   MMDCTDRHFRVLMRQISRRALLYTEMVVAQALHHGRRDTLLDFDPQEHPLALQLGGDDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+A++   +GY+EINLNVGCPS +V +G FGACLM +PD V  C+ AM  A S+PVT
Sbjct: 61  LLAESAQLAAAWGYDEINLNVGCPSPKVQQGRFGACLMADPDRVARCVEAMANASSLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ     L   V  +  +G +   +HARKA L GL PK NR IP L +D+V+
Sbjct: 121 VKHRIGIDDQDSYELLLAFVDKVAGAGASRFSVHARKAWLHGLDPKQNRTIPPLRHDLVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P   I LNGGL  +    + L  VDGVM+GRAAY +     +VD+     L  +
Sbjct: 181 QLKRDRPQFTIELNGGLLSLENCQEHLGQVDGVMVGRAAYDHPLRWASVDQELFGCLERA 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
               +         +   +  +A+R   +G +L  I RH++ L  G P +R  R  L   
Sbjct: 241 PASAST--------VVRGLIPHASRWCGAGRRLWPIARHLVHLVEGVPGARHWRRRLGER 292

Query: 301 AGASTATHHIIETAFNLMIES 321
           AG  +A   ++E A   + + 
Sbjct: 293 AGERSAGPEVLEAAAQDLEQQ 313


>gi|260549038|ref|ZP_05823259.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. RUH2624]
 gi|260407766|gb|EEX01238.1| tRNA-dihydrouridine synthase A [Acinetobacter sp. RUH2624]
          Length = 338

 Score =  329 bits (843), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 191/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 80  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LEAPDRFDIMEQMLPYIEQRMAQGAPLSIITRHILGLFQNLPGARKWRQALS-- 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A   M  ++
Sbjct: 306 -GGNAKTLTDVENAIRNMQAAI 326


>gi|193076358|gb|ABO11015.2| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 17978]
          Length = 334

 Score =  328 bits (842), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 136/322 (42%), Positives = 191/322 (59%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG+   
Sbjct: 16  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSTPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVT
Sbjct: 76  ELATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY
Sbjct: 136 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 196 RLKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 ++      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 250 ------LEAPDRFDIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS-- 301

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   +E A + M  ++
Sbjct: 302 -GGNAKTLTDVENAIHNMQAAI 322


>gi|257454432|ref|ZP_05619694.1| tRNA-dihydrouridine synthase A [Enhydrobacter aerosaccus SK60]
 gi|257448198|gb|EEV23179.1| tRNA-dihydrouridine synthase A [Enhydrobacter aerosaccus SK60]
          Length = 330

 Score =  328 bits (842), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 134/321 (41%), Positives = 182/321 (56%), Gaps = 19/321 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DW+ R Y +FARL      LYTEMI   AIL+GD    L F   E PL LQ+GG+D +
Sbjct: 22  MIDWSTRDYCYFARLFNPYTYLYTEMISTSAILQGDTDYQLRFYPNEHPLVLQLGGSDPN 81

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AKI +D+GY+EINLNVGCPS RV     GACLM  P +V D ++AM  A+ IPVT
Sbjct: 82  ELARCAKIGQDYGYDEINLNVGCPSDRVQHYKIGACLMAEPKLVADIVSAMRDAVDIPVT 141

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      + + V  + K+G   + +HAR A L+GLSPK NR+IP L Y+ VY
Sbjct: 142 VKHRIGIDNFDSYEFMADFVDHVVKAGCQHVIVHARTAWLQGLSPKQNREIPPLRYEDVY 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PD+F+ +NGG+  + +    L  VDGVMIGR AY N  +L    + +       
Sbjct: 202 RLKQDFPDVFVEINGGITTIDEIKTHLTKVDGVMIGREAYHNPYILAEAMQLWG------ 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P+ +R D      I   + D+ A     G  L  I RH +GLF G   SR+ R  L+ +
Sbjct: 256 EPVPSRAD------IFYQLLDFLAASDARGTPLTVIMRHYLGLFQGLTGSRKWRQALSGQ 309

Query: 301 -----AGASTATHHIIETAFN 316
                A    A   ++  A N
Sbjct: 310 KSLSVAQVREAGESVL--ALN 328


>gi|238027482|ref|YP_002911713.1| dihydrouridine synthase [Burkholderia glumae BGR1]
 gi|237876676|gb|ACR29009.1| Dihydrouridine synthase [Burkholderia glumae BGR1]
          Length = 336

 Score =  328 bits (841), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 127/298 (42%), Positives = 181/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R ++ +  LYTEM+   A++ GD    L F+  E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRSLHRTISRHTWLYTEMVTTGALMHGDVARHLAFTPDEAPVALQLGGSEPD 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 80  DLAKSARLGENWGYDEINLNCGCPSERVQRGAFGACLMNEPGLVADCVKAMRDAVSVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G +   +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 140 VKHRIGVDAVEEYAFVRDFVGTVAQAGCDVFIVHARNAILKGLSPKENREIPPLKYDYAY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG+  + +    L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 200 RLKQDFPDLEIIINGGITTLDEVEAHLQHVDGVMLGREAYHNPFVLAEVDRRFYGA-AAA 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +         +I   +  Y    +  G  L  I RH +GL+ G   +R  R +L+
Sbjct: 259 APTR--------EEIEERLIAYCVAEIARGTYLGAIVRHALGLYRGVHGARGWRRVLS 308


>gi|316934857|ref|YP_004109839.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris DX-1]
 gi|315602571|gb|ADU45106.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris DX-1]
          Length = 331

 Score =  327 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 146/320 (45%), Positives = 200/320 (62%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD   R F RLLT  ALLYTEM+   A++ GD++ +LGF   E PLALQ+GG++ +
Sbjct: 14  MMEWTDSPCRVFHRLLTKRALLYTEMVTTGAVIHGDRQRLLGFDASEHPLALQLGGSNPN 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EIN+NVGCPS RV EG FGACLM  P++V + +AAM +A+S+PVT
Sbjct: 74  DLATSAKIGEDFGYDEININVGCPSDRVKEGRFGACLMAEPELVAEGVAAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPEVALDALARAVVAAGADALIVHARKAWLNGLSPKENRDIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  +++A + L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKQAMPQVPIIINGGIGSIAEAKRHLDHVDGVMLGRAAYQEPWRLLEVDPELFGEPAPY 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +K         +   ++  Y  R L  G +L  ITRH+IG + G P +R  R  L+  
Sbjct: 254 PSMK---------EALEALIPYIERQLAQGLRLHAITRHVIGAYQGVPGARAFRRYLSEF 304

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A   + E
Sbjct: 305 GVKPDADASVLLKAMVAVTE 324


>gi|294677314|ref|YP_003577929.1| tRNA-dihydrouridine synthase A [Rhodobacter capsulatus SB 1003]
 gi|294476134|gb|ADE85522.1| tRNA-dihydrouridine synthase A [Rhodobacter capsulatus SB 1003]
          Length = 346

 Score =  327 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 148/321 (46%), Positives = 204/321 (63%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R+++  ALLYTEM+ A A++ G +  +L FS  E P+ALQ+GG+D +
Sbjct: 33  MLDWTDRHCRVFHRMMSRQALLYTEMVTAPAVIHGKRAQLLDFSPVEHPVALQLGGSDPA 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EA +I  D+GY+EINLNVGCPS RV  G+FGA LM  PD+V  C+AAM  A ++ VT
Sbjct: 93  ELAEATRIARDWGYDEINLNVGCPSDRVQSGAFGAVLMKTPDLVARCVAAMQAAAAVEVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +K++ ++GV    +HARKA L+GLSPK+NR+IP LDY +V+
Sbjct: 153 VKCRIGVDDQSPEEVLPAFLKTVSEAGVTRFILHARKAWLQGLSPKENREIPPLDYPLVH 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            +K+E P L + LNGG+  + Q    L   +DGVM+GRAAY+    +L   D        
Sbjct: 213 AMKREFPHLHLSLNGGVATLDQVETHLAAGMDGVMVGRAAYQEPMQVLAGADVALWG--- 269

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R +     +++ +M  Y A HL +GG+L QITRHM+GLFHG P +R  R +L+
Sbjct: 270 -------RGEVLSAVEVAEAMKPYIADHLAAGGRLHQITRHMLGLFHGRPGARGWRRVLS 322

Query: 299 VEAGASTATHHIIETAFNLMI 319
             A    A   + + A   + 
Sbjct: 323 EGATRPGAGLALYDQALAEVT 343


>gi|254424029|ref|ZP_05037747.1| TIM-barrel protein, yjbN family [Synechococcus sp. PCC 7335]
 gi|196191518|gb|EDX86482.1| TIM-barrel protein, yjbN family [Synechococcus sp. PCC 7335]
          Length = 355

 Score =  327 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 185/321 (57%), Gaps = 10/321 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +D TDRHYRFF R +T   LLYTEM+ A AI  GD   ++GF+  E PL LQ+GG D   
Sbjct: 1   MDRTDRHYRFFMRQITRRTLLYTEMVNAQAIYYGDLDRLIGFTPDENPLVLQVGGDDPKL 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  +A+   +FGY+EINLNVGCPS RV  G+FGACLM  P+ V DC++AM  A ++PV+V
Sbjct: 61  LANSARRAAEFGYSEINLNVGCPSDRVQSGNFGACLMAQPERVADCVSAMIAASALPVSV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+DDQ     + N V  +  +G     +HARKA L+GLSPKDNR IP L Y  V+ 
Sbjct: 121 KHRIGIDDQDSYEDMANFVTIVSATGCQRFSVHARKAWLQGLSPKDNRNIPPLRYADVHR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K+E P L I +NGG + ++Q    L +VD VMIGRAAY    +    D+      T   
Sbjct: 181 LKQEFPHLQIEINGGFKTLAQVKNQLRAVDAVMIGRAAYDIPFLFEKADQEIFGETTEPQ 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       ++  SM  Y   H    G +L  ITRHM+ LFHG P SR  +  LT E
Sbjct: 241 ---------TRYQVVESMLPYIDYHTQKLGTRLHSITRHMLHLFHGQPGSRIWKQTLTEE 291

Query: 301 AGASTATHHIIETAFNLMIES 321
           A    +   ++  A   + ++
Sbjct: 292 ARQLNSGVEVVADALEKVRDA 312


>gi|330897594|gb|EGH29013.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 300

 Score =  327 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 128/306 (41%), Positives = 189/306 (61%), Gaps = 9/306 (2%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
            R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  + L   +++ ++ 
Sbjct: 1   MRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAADLAACSRLAQEA 60

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVTVK RIG++ +  
Sbjct: 61  GYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVTVKHRIGINGRDS 120

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
              L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + PDL I 
Sbjct: 121 YAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKSDFPDLEIV 180

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        ++P+ +R D    
Sbjct: 181 LNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFGS---TAPVISRYDA--- 234

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312
                SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+   +     +++
Sbjct: 235 ---LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVDIHKAENPMLLLD 291

Query: 313 TAFNLM 318
            A   +
Sbjct: 292 QAAAFL 297


>gi|330816761|ref|YP_004360466.1| Dihydrouridine synthase [Burkholderia gladioli BSR3]
 gi|327369154|gb|AEA60510.1| Dihydrouridine synthase [Burkholderia gladioli BSR3]
          Length = 345

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 134/319 (42%), Positives = 184/319 (57%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   R ++ +  LYTEM+   A+L GD    L F  +E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRSLHRSISRHTWLYTEMVTTGALLHGDVARHLAFMPEEAPVALQLGGSEPE 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 80  DLAKSARLGENWGYDEINLNCGCPSERVQRGAFGACLMNEPALVADCVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 140 VKHRIGVDAVEDYAFVRDFVGTVAEAGCEVFIVHARNAILKGLSPKENREIPPLKYDYAY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ PDL I +NGG+  + +    L  VDGVM+GR AY N  +L  VD  F      +
Sbjct: 200 RLKQDFPDLEILINGGITTLDEVETHLQHVDGVMLGREAYHNPFVLAEVDARFYG---AA 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  TR       +I   +  Y    +  G  L  I RH +GL+ G   +R  R +L+  
Sbjct: 257 RPAPTR------EEIEDRLIAYCIDEVARGNYLGAIVRHALGLYRGVHGARGWRRVLSDS 310

Query: 301 AG-ASTATHHIIETAFNLM 318
              A      I   A   +
Sbjct: 311 KRLARGDVAAIFAEARAHL 329


>gi|262374231|ref|ZP_06067507.1| tRNA-dihydrouridine synthase A [Acinetobacter junii SH205]
 gi|262310789|gb|EEY91877.1| tRNA-dihydrouridine synthase A [Acinetobacter junii SH205]
          Length = 338

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 134/322 (41%), Positives = 188/322 (58%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT + YRFFARL   N +LYTEM+   AI+ G     L F+ QE P+ LQ+GG++  
Sbjct: 20  MMDWTTKDYRFFARLFNPNVVLYTEMVTTGAIIYGGANRHLDFNQQEHPIVLQLGGSNPQ 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ ED+GYNE+NLNVGCPS RV     GACLM  P++V +CI +M KA+SIPVT
Sbjct: 80  ELATCTKMAEDWGYNEVNLNVGCPSDRVQNNKIGACLMAEPNLVAECIHSMQKAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V ++  +G     +HAR AIL+GLSPK+NR++P L Y+ VY
Sbjct: 140 VKHRIGIDDMQSYEEMLHFVDTVAATGCTHFIVHARIAILQGLSPKENREVPPLRYEDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG++   +  + L  VDGVMIGR AY N  +L  + + ++      
Sbjct: 200 RLKLERPHLTIEINGGIKTFEETKQHLQHVDGVMIGREAYHNPYLLAELGQLWN------ 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 +D      I   M  Y  + +  G  L  ITRH++GLF   P +R+ R  L+  
Sbjct: 254 ------LDAPDRFDIMQQMMPYIHQRVAEGAPLSIITRHILGLFQNLPGARKWRQSLS-- 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G +  T   IE A   +  ++
Sbjct: 306 -GGNAKTITDIENAIQNIQAAM 326


>gi|84499208|ref|ZP_00997496.1| tRNA-dihydrouridine synthase A [Oceanicola batsensis HTCC2597]
 gi|84392352|gb|EAQ04563.1| tRNA-dihydrouridine synthase A [Oceanicola batsensis HTCC2597]
          Length = 314

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 199/323 (61%), Gaps = 12/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ +ALLYTEM+ A A++RG   ++L FS +E P+ALQ+GG+D  
Sbjct: 1   MMDWTDRHCRYLHRLLSRHALLYTEMVTAPALVRGGAVHLLDFSPREHPVALQLGGSDPE 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++ +  GY+EINLN GCPS RV  G FGA LM +P  V DC+AAM +A+ + VT
Sbjct: 61  ELAAAARLGQAAGYDEINLNCGCPSDRVQSGVFGAVLMRDPGRVADCVAAMREAVEVEVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P   L   +  +  +G     IHARKA L+GLSPK+NR IP LDYD+V 
Sbjct: 121 VKCRIGVDDQNPEEVLPEFLSRVGAAGCGRFIIHARKAWLQGLSPKENRDIPPLDYDLVQ 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
            ++     L + +NGG+  + QA + L   +DGVM+GRAAY + A ML   D        
Sbjct: 181 RMRGMFSGLHLSVNGGIVSLDQAERFLEAGLDGVMVGRAAYHDPASMLAQADRRIFGAG- 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                    +      ++ +M  Y   HL +GGKL Q+TRHM+GLF G P +R  R IL+
Sbjct: 240 ---------EDADAVAVARAMLPYIEAHLAAGGKLGQVTRHMLGLFAGRPGARHWRRILS 290

Query: 299 VEAGASTATHHIIETAFNLMIES 321
             A    A   ++E A   ++++
Sbjct: 291 EGAHRPGAGPELVEQALEPVLQA 313


>gi|330962294|gb|EGH62554.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 300

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 130/306 (42%), Positives = 190/306 (62%), Gaps = 9/306 (2%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
            RLL+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  + L   A++ E+ 
Sbjct: 1   MRLLSKHALLYTEMVATGALLHGDRERFLRHDDTEHPLALQLGGSTAADLAACARLAEEA 60

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVTVK RIG++ +  
Sbjct: 61  GYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVTVKHRIGINGRDS 120

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
              L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + P+L I 
Sbjct: 121 YAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKTDFPELEIV 180

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        ++P+ +R D    
Sbjct: 181 LNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFGS---TAPVISRYDA--- 234

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312
                SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+   +     +++
Sbjct: 235 ---LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVDIHKAENPMLLLD 291

Query: 313 TAFNLM 318
            A   +
Sbjct: 292 QAAAFL 297


>gi|118602457|ref|YP_903672.1| tRNA-dihydrouridine synthase A [Candidatus Ruthia magnifica str. Cm
           (Calyptogena magnifica)]
 gi|118567396|gb|ABL02201.1| tRNA-U16,U17-dihydrouridine synthase [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 322

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 131/298 (43%), Positives = 192/298 (64%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ N  L+TEM+ A AIL G+K  +L F+  E PL LQ+GG++  
Sbjct: 12  MMDWTDRHCRYFYRLISKNVQLWTEMVTARAILYGNKNRLLDFNVCEHPLVLQLGGSEPK 71

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ +AAKI +D+GYNEIN+NVGCPS RV   +FG CLM  P +V  C+ AM + + +P+T
Sbjct: 72  EMAQAAKIAQDWGYNEININVGCPSNRVQSSNFGVCLMQTPQVVAQCVDAMRQMVDVPIT 131

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      L N V +++ SG + + IHARKA LKGLSPK+NR +P L+Y+ VY
Sbjct: 132 VKSRIGVDNMDSYDELVNFVATVESSGCDNLVIHARKAWLKGLSPKENRSVPKLNYERVY 191

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +IK++ P L IG+NGG+ DM  +L+ L  VD VM+GRA Y    +L  VD          
Sbjct: 192 QIKRDFPHLAIGINGGIMDMESSLQHLEHVDSVMLGRAVYHQPYLLRKVDGLIYQ---KK 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           S I +R       ++  +  +Y      +   ++ +TRH+ GL+HG  N+++ + +L+
Sbjct: 249 SSILSR------EQVLLAFIEYMKVQHANSVLIRSMTRHIFGLYHGQKNAKKFKRLLS 300


>gi|113868264|ref|YP_726753.1| tRNA-dihydrouridine synthase A [Ralstonia eutropha H16]
 gi|113527040|emb|CAJ93385.1| transfer RNA-dihydrouridine synthase [Ralstonia eutropha H16]
          Length = 345

 Score =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 132/323 (40%), Positives = 185/323 (57%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 21  MMDWTDRHCRMFHRQLSRHTWLYTEMVTTGALLHGDVPRHLDFDAAEHPVALQLGGSEPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ + +GY E+NLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 81  DLAMAAKLGQQWGYAEVNLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMRDAVDIPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 141 VKHRIGIDKIEHYDFVRDFVGRVAEAGCGTFIVHARNAILKGLSPKENREIPPLRYEVAY 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E P+L I +NGG+    +    L  VDGVMIGR AY    +L  +D  F    +  
Sbjct: 201 QLKQEFPELEILINGGIVSYDEVAAHLEHVDGVMIGREAYHQPYVLAEMDARFYGDASAP 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
           +P +          +  +M  Y    +  GG +  +TRHM+GL  G    R  R +L+  
Sbjct: 261 APSR--------LDVELAMQRYIGDLVERGGYMGAVTRHMLGLHRGIAGGRGWRRVLSDA 312

Query: 299 --VEAGASTATHH-IIETAFNLM 318
             + A  + A    + E A   +
Sbjct: 313 KRMNAARTRADVDALFEEARAHL 335


>gi|93005625|ref|YP_580062.1| tRNA-dihydrouridine synthase A [Psychrobacter cryohalolentis K5]
 gi|92393303|gb|ABE74578.1| TIM-barrel protein, yjbN family [Psychrobacter cryohalolentis K5]
          Length = 321

 Score =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 126/319 (39%), Positives = 177/319 (55%), Gaps = 15/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YR+FARL   +  LYTEMI   A++ G++   L F T E PL LQ+GGADI+
Sbjct: 14  MIDWTTTDYRYFARLFNPHVYLYTEMISTGALIHGNRARHLRFDTLEHPLVLQLGGADIT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ + A+  +  GY+E+N+NVGCPS RV     GACLM  P+ V D +  M  A+ IPVT
Sbjct: 74  EMTQCAEFAQQHGYDEVNINVGCPSDRVQHNKIGACLMAEPNTVADLVKHMQAAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V+ +   G     +HAR A L+GLSPK NR+IP L Y+ VY
Sbjct: 134 VKHRIGIDDFDSYEFMADFVQKVAAGGCTRFIVHARTAWLQGLSPKQNREIPPLRYEDVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+E ++     L  +DGVMIGRA Y N  +L   +  +  P+   
Sbjct: 194 RLKQDFPTLDIEINGGIETVADIEAHLEHIDGVMIGRAFYHNPYLLAEANSLWDTPVPKR 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S             I A +  Y    +  G  L  +TRH +GLF G   +R+ R  L+  
Sbjct: 254 SV------------ILAQLYPYLEEQIAKGEALPTMTRHYLGLFQGLVGARKWRQALS-- 299

Query: 301 AGASTATHHIIETAFNLMI 319
            G    T   I+ A   ++
Sbjct: 300 -GKPQLTIDDIKHAATEVL 317


>gi|192290571|ref|YP_001991176.1| tRNA-dihydrouridine synthase A [Rhodopseudomonas palustris TIE-1]
 gi|192284320|gb|ACF00701.1| TIM-barrel protein, yjbN family [Rhodopseudomonas palustris TIE-1]
          Length = 330

 Score =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 144/320 (45%), Positives = 200/320 (62%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTD H R F RLLT   LLYTEM+   A++ GD++ +LGF   E P+ALQ+GG++ +
Sbjct: 14  MMEWTDSHCRVFHRLLTRRGLLYTEMVTTGAVIHGDRQRLLGFDASEHPVALQLGGSNPN 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +AKI EDFGY+EIN+NVGCPS RV EG FGACLM  P++V + +AAM +A+++PVT
Sbjct: 74  DLATSAKIGEDFGYDEININVGCPSDRVKEGRFGACLMAEPELVAEGVAAMERAVAVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P VAL  L +++  +G + + +HARKA L GLSPK+NR IP LDYD VY
Sbjct: 134 VKCRIGIDDQDPEVALDALARAVVAAGADALIVHARKAWLNGLSPKENRHIPPLDYDRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  +++A + L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKQAMPQVPIIINGGIGSIAEAKRHLEHVDGVMLGRAAYQEPWRLLEVDPELYGEPAPY 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +K         +   ++  Y  R L  G +L  ITRH+IG + G P +R  R  L+  
Sbjct: 254 PSMK---------EALEALIPYIERQLAQGLRLHAITRHVIGAYQGVPGARAFRRYLSEF 304

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   ++  A   + E
Sbjct: 305 GVKPDADASVLLKAMVAVTE 324


>gi|83592956|ref|YP_426708.1| tRNA-dihydrouridine synthase A [Rhodospirillum rubrum ATCC 11170]
 gi|83575870|gb|ABC22421.1| Dihydrouridine synthase TIM-barrel protein yjbN [Rhodospirillum
           rubrum ATCC 11170]
          Length = 349

 Score =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 141/326 (43%), Positives = 192/326 (58%), Gaps = 16/326 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R +T   LLYTEMI A A+L  D    L     E PLALQ+GG+D  
Sbjct: 26  MMDWTDRHDRWFLRQITKRTLLYTEMITAQALLHADPGRFLDHHPDEHPLALQLGGSDPR 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EA ++   FG+ EINLNVGCPS RV  G FGACLM +P +V +C++AM +A + PVT
Sbjct: 86  ALAEATRLAAPFGFAEINLNVGCPSDRVSSGRFGACLMADPALVAECLSAMAEASNAPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD      L   V  + +SG+  I +HARKA LKGLSPK+NR+IP L +D+V+
Sbjct: 146 IKHRIGIDDLDSYDQLVGFVDQVARSGIATIIVHARKAWLKGLSPKENREIPPLRHDVVH 205

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-------PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            +K + P L + LNGG+  ++QAL  L       P+VDGVMIGRAAY+   ML   D   
Sbjct: 206 RLKADFPGLEVILNGGITTLTQALDHLGSGDPAAPAVDGVMIGRAAYETPYMLAQADGLI 265

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               T   P  +R       +++ ++  Y       G  ++++TRH++GLFHG P +R  
Sbjct: 266 FGEAT---PAPSR------HEVALALLPYLDAMTARGEPVKRLTRHILGLFHGQPGARAY 316

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
           R  L        AT  ++  A   + 
Sbjct: 317 RRHLGEAGVRPDATAQVLIDALAHIP 342


>gi|91763046|ref|ZP_01265010.1| hypothetical protein PU1002_00270 [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91717459|gb|EAS84110.1| hypothetical protein PU1002_00270 [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 320

 Score =  325 bits (833), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 135/317 (42%), Positives = 182/317 (57%), Gaps = 10/317 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +D TDRH RFF RL++ N LLY+EM+V++AI RGDKK +L F+  EKP+ALQIGG+  + 
Sbjct: 1   MDCTDRHERFFLRLISKNTLLYSEMVVSEAIHRGDKKKLLEFNINEKPIALQIGGSSPTL 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EA K  EDFGY+EINLN+GCPS +V +  FGACLM  P++V DC++ M     +PVT+
Sbjct: 61  LAEATKAGEDFGYDEINLNLGCPSKKVEKNKFGACLMKEPNLVADCLSKMQSVTKLPVTI 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DD      L + + ++K +GV    IHARKAIL   +PK N  IP L YD VY 
Sbjct: 121 KTRIGYDDTEDYENLHHFISTLKSTGVKTFIIHARKAILGKFTPKQNLNIPPLKYDFVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +KK+ P+  I +NGG+    Q    L  VDGVMIGRAAY    +L  ++    N     S
Sbjct: 181 LKKDFPNEEIIINGGITTTDQMKDHLDKVDGVMIGRAAYHTPYLLADIERDIFNNENVPS 240

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
                      + +   +  Y    +  G +L QI RH +GLFHG   S   +  L+   
Sbjct: 241 ----------RQDVIEQLLPYVREEIKKGTRLNQIMRHTLGLFHGQTGSSFWKRYLSENM 290

Query: 302 GASTATHHIIETAFNLM 318
               A    I+   + +
Sbjct: 291 CVRDADVKKIDHIMDKI 307


>gi|88800086|ref|ZP_01115656.1| hypothetical protein MED297_16794 [Reinekea sp. MED297]
 gi|88777212|gb|EAR08417.1| hypothetical protein MED297_16794 [Reinekea sp. MED297]
          Length = 338

 Score =  325 bits (833), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 126/319 (39%), Positives = 190/319 (59%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT    R F RLLT  ALLYTEM+   A++ G+    L + T+E P+ALQ+GG D  
Sbjct: 14  MMDWTTSECRQFHRLLTRQALLYTEMVTTGALIHGNAGRFLRYDTEEHPIALQLGGHDAD 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L    K+ E+ GY+++NLN GCPS RV  G  GA LM + D V D + AM   ++IPVT
Sbjct: 74  ELAHCTKMAEEHGYDQVNLNAGCPSDRVQNGMIGAILMAHADKVTDALKAMQDRVNIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG+DD      LR+ V  +  SG +   +HARKAIL GLSPK+NR+IP LDYD V 
Sbjct: 134 LKHRIGIDDYDSYEFLRDFVGQVSLSGCDTFIVHARKAILSGLSPKENREIPPLDYDRVI 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K++ P+L I +NGG++   +A  ++   +DGVM+GR AY+N  +L+ VD  +      
Sbjct: 194 RLKQDFPNLNIVINGGIKSHQEAQALINRGLDGVMLGREAYQNPLILSEVDHIYYGHENP 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++ I+T         ++A +TD+  + + +G  L+ + +H +GL+ G P S++ R +L+ 
Sbjct: 254 NADIET---------LNARITDWVEQKVETGVPLKFLAKHTLGLYAGHPGSKQFRRMLSE 304

Query: 300 EAGASTATHHIIETAFNLM 318
                 A   +   A   +
Sbjct: 305 NMTKPDANAQLYRDALAKI 323


>gi|73541705|ref|YP_296225.1| tRNA-dihydrouridine synthase A [Ralstonia eutropha JMP134]
 gi|72119118|gb|AAZ61381.1| Dihydrouridine synthase TIM-barrel protein yjbN [Ralstonia eutropha
           JMP134]
          Length = 341

 Score =  325 bits (833), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 134/323 (41%), Positives = 193/323 (59%), Gaps = 13/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L F+  E P+ALQ+GG++ +
Sbjct: 13  MMDWTDRHCRTFHRQLSRHTWLYTEMVTTGALLHGDVPRHLDFNAAEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++ + +GY E+NLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 73  DLAVAARLGQQWGYAEVNLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMRDAVSIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++ ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 133 VKHRIGIDKVEHYGFVRDFVGTVAQAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+    +    L +VDGVMIGR AY    +L  +D  F       
Sbjct: 193 QLKQDFPQLEILINGGIVSYDEMASHLENVDGVMIGREAYHQPYVLAEMDGRFYGD--AE 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+++R+D      +  +M  Y    +  GG +  +TRHM+GL+ G    R  R +L+  
Sbjct: 251 APVRSRLD------VELAMQRYIGELVERGGYMGAVTRHMLGLYRGVAGGRGWRRVLSDA 304

Query: 301 AGASTATHH-----IIETAFNLM 318
              S A  H     + E A + +
Sbjct: 305 KRMSAARTHANVDALFEEARSHL 327


>gi|301169351|emb|CBW28951.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae 10810]
          Length = 285

 Score =  324 bits (832), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 123/293 (41%), Positives = 174/293 (59%), Gaps = 10/293 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+     + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPEQLKYCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++ + +  +
Sbjct: 120 KGCQEFIIHARKAWLSGLSPKENREIPPLDYARVYQLKRDFPHLTIAINGGIKTIEEMKQ 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY+N ++L  +D+   +P   ++PI T        +   SM  Y  +
Sbjct: 180 HLQYVDGVMVGREAYQNPSLLGQIDQALFDP---NAPIVTA------HEAVQSMLPYIEQ 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            L  G  L  I RHM+G F     +R+ R  L+  A    A   ++ETA + +
Sbjct: 231 QLSQGVHLNHIVRHMLGAFQNCKGARQWRRYLSENAFKQGAGVEVVETALSFV 283


>gi|269103588|ref|ZP_06156285.1| putative NifR3/Smm1 family protein [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163486|gb|EEZ41982.1| putative NifR3/Smm1 family protein [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 290

 Score =  324 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 116/295 (39%), Positives = 179/295 (60%), Gaps = 11/295 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G   + L ++ +E PL LQ+GG++ + L   AK+ ++ GY+EINLNVGCPS
Sbjct: 1   MVTTGAIIHGKG-DFLAYNEEEHPLVLQLGGSNPADLARCAKLAQERGYDEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI-K 144
            RV  G FGACLM   ++V  C+AAM + + IPVTVK RIG+D+Q     L + + ++ +
Sbjct: 60  DRVQNGMFGACLMGEAELVAHCVAAMREVVDIPVTVKTRIGIDEQDSYEFLTDFIGTVAE 119

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K G +   IHARKA LKGLSPK+NR+IP LDY  VY++K++ P+L +G+NGG++   +  
Sbjct: 120 KGGCDNFTIHARKAWLKGLSPKENREIPPLDYPRVYQLKRDFPELTMGINGGIKTFEEME 179

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           + L  +DGVM+GR AY++  ++  VD+        + P+  R      R++  +M  Y  
Sbjct: 180 EHLQHMDGVMVGREAYQSPYLMAEVDQRLFGS---TKPVMKR------REVVEAMYPYIE 230

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMI 319
           + L  G  L  ITRHM+GLF   P +R+ R  ++  A    +   +++ A   + 
Sbjct: 231 QQLAQGSYLGHITRHMLGLFQNMPGARQWRRHISENAHKPGSGIEVLQQALAKIP 285


>gi|45656544|ref|YP_000630.1| tRNA-dihydrouridine synthase A [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|294828345|ref|NP_713734.2| tRNA-dihydrouridine synthase A [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45599779|gb|AAS69267.1| conserved hypothetical protein [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|293386197|gb|AAN50752.2| tRNA-dihydrouridine synthase A [Leptospira interrogans serovar Lai
           str. 56601]
          Length = 347

 Score =  324 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 194/320 (60%), Gaps = 12/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+F RL++ +  LYTEM+   A+L GD++ +L +S +E PLA+Q+GG+D  
Sbjct: 19  MMDWTDRHFRYFLRLISKHTFLYTEMVHTGAVLHGDRRKLLSYSPEELPLAIQLGGSDPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+ KI ED+GY EINLNVGCPS RV EG+FGACLM  P+ V +   AM  ++SIP+T
Sbjct: 79  ALAESCKIGEDYGYTEINLNVGCPSDRVREGNFGACLMETPEKVAELTFAMDTSVSIPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+  +     L   ++ ++++GV    +HAR AIL GL+P  NR++P L Y  V 
Sbjct: 139 VKCRIGIPGKETFEDLCKFIECVRQTGVQRFIVHARIAILGGLTPAQNRQVPPLHYTYVE 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PDL I +NGG+  ++   + L   DGVMIGRAAY+   + + VD  F      +
Sbjct: 199 SLKKEFPDLLIEINGGIRTITSIRERLEKNDGVMIGRAAYETPYLFSEVDSLFFGE---N 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            P  +R      R+I   M DY    +     GK     RHM+GLFHG   +R  R ILT
Sbjct: 256 LPPLSR------REILLRMKDYIEEVILKEKNGKPHHALRHMLGLFHGEKGARSFRKILT 309

Query: 299 VEAGASTATHHIIETAFNLM 318
            E   S  +  ++  A   +
Sbjct: 310 -EGMYSGYSKDLLSKAIQEI 328


>gi|319897830|ref|YP_004136027.1| tRNA-dihydrouridine synthase a [Haemophilus influenzae F3031]
 gi|317433336|emb|CBY81713.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae F3031]
          Length = 285

 Score =  324 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 124/293 (42%), Positives = 174/293 (59%), Gaps = 10/293 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+     + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPEQLKYCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++ + +  +
Sbjct: 120 KGCQEFIIHARKAWLSGLSPKENREIPPLDYARVYQLKRDFPHLTIAINGGIKTIEKMKQ 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY+N ++L  +D+   +P   ++PI T        +   SM  Y  +
Sbjct: 180 HLQYVDGVMVGREAYQNPSLLGQIDQALFDP---NAPIVTA------HEAVQSMLPYIEQ 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            L  G  L  I RHM+G F     +R+ R  L+  A    A   +IETA + +
Sbjct: 231 QLSQGIHLNHIVRHMLGAFQNCKGARQWRRYLSENAFKQGAGVEVIETALSFV 283


>gi|126640633|ref|YP_001083617.1| tRNA-dihydrouridine synthase A [Acinetobacter baumannii ATCC 17978]
          Length = 318

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 135/321 (42%), Positives = 190/321 (59%), Gaps = 15/321 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWT + YRFFARL   N +LYTEM+   AIL GD K  L ++ QE P+ LQ+GG+   +
Sbjct: 1   MDWTTKDYRFFARLFNPNVVLYTEMVTTGAILFGDAKRHLDYNAQEHPIVLQLGGSTPQE 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L    K+ ED+GY+E+NLNVGCPS RV     GACLM  PD+V +CI +M KA++IPVTV
Sbjct: 61  LATCTKMAEDWGYDEVNLNVGCPSDRVQNNKIGACLMAEPDLVAECIHSMQKAVNIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+DD      + + V ++  +G     +HAR AILKGLSPK+NR++P L Y+ VY 
Sbjct: 121 KHRIGIDDMQSYEEMLHFVDTVAATGCTHFVVHARIAILKGLSPKENREVPPLRYEDVYR 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K+E P L I +NGG++  ++    L  VDGVMIGR AY N  +L  + + ++       
Sbjct: 181 LKQERPHLTIEINGGIKTFAETQAHLQHVDGVMIGREAYHNPYLLAELGQLWN------- 233

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
                ++      I   M  Y  + L  G  L  ITRH++GLF   P +R+ R  L+   
Sbjct: 234 -----LEAPDRFDIMEQMLPYIEQRLAEGAPLSIITRHILGLFQNLPGARKWRQALS--- 285

Query: 302 GASTATHHIIETAFNLMIESL 322
           G +  T   +E A + M  ++
Sbjct: 286 GGNAKTLTDVENAIHNMQAAI 306


>gi|325282314|ref|YP_004254855.1| TIM-barrel protein, yjbN family [Deinococcus proteolyticus MRP]
 gi|324314123|gb|ADY25238.1| TIM-barrel protein, yjbN family [Deinococcus proteolyticus MRP]
          Length = 346

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 139/322 (43%), Positives = 196/322 (60%), Gaps = 9/322 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT+ ALLYTEM+   A+L GD+   L F   E PLALQ+GG+D +
Sbjct: 29  MLDWTDRHCRAFHRCLTSRALLYTEMVTTGAVLHGDRARHLDFGAAEHPLALQLGGSDPA 88

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E A + E +GY+E+NLN GCPS RV  G+FGACLM  PD+V  C+AAM +A  +PVT
Sbjct: 89  ALAECAALAEHWGYDEVNLNCGCPSDRVQSGAFGACLMATPDVVAACVAAMQEATRLPVT 148

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DDQ   + LR  V+++  +G     +HARKA LKGLSPK+NR+IP L Y++V 
Sbjct: 149 VKHRIGIDDQEDYMDLRRFVETVAGAGCRTFIVHARKAWLKGLSPKENREIPPLRYELVE 208

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K E P+L I LNGG++ ++QA + L   DGVM+GRAAY+   +L  VD+        S
Sbjct: 209 QLKAEFPELTISLNGGVQTLAQAQEHLTWADGVMVGRAAYQTPYLLARVDQDIFGE-DAS 267

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P +        R++ A    Y  + L  G     +T+  +GLF G   +R  +  L+  
Sbjct: 268 PPTR--------REVLARFRPYVVQGLAEGQSFHHLTKSTLGLFAGQHGARHYKRTLSEL 319

Query: 301 AGASTATHHIIETAFNLMIESL 322
              + A   +++ A   + + +
Sbjct: 320 GHRAGAGIEVLDQAVAGVPDDV 341


>gi|241758541|ref|ZP_04756659.1| tRNA-dihydrouridine synthase A [Neisseria flavescens SK114]
 gi|241321314|gb|EER57468.1| tRNA-dihydrouridine synthase A [Neisseria flavescens SK114]
          Length = 334

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 191/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T NA LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 16  MLDWTDRHYRFMARQITRNAWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM   + IPVT
Sbjct: 76  DLAIAAKAAETYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDVVEIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V ++ +K+      +HAR A L GLSPK+NR++P L Y+ V
Sbjct: 136 VKHRIGVDRQTEYQVVADFVGTLREKTACRTFIVHARNAWLDGLSPKENREVPPLKYEYV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 196 YRLKQEFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDALFYNNTHA 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  ++A +  Y+   + SG    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 P---------IQYADLAAWLYAYSREQIASGRGTILRHIVRHALGLMHGLKNARTWRRML 306

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 307 SDATLLKDNDGSLILDAWKEVERA 330


>gi|241766211|ref|ZP_04764111.1| TIM-barrel protein, yjbN family [Acidovorax delafieldii 2AN]
 gi|241363710|gb|EER59087.1| TIM-barrel protein, yjbN family [Acidovorax delafieldii 2AN]
          Length = 313

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 128/317 (40%), Positives = 185/317 (58%), Gaps = 10/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ + LLYTEM+   A++ GD +  L ++ +E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRYLHRLLSRHTLLYTEMVTTGALIHGDVERHLRYNAEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + IPVT
Sbjct: 61  DLAHCARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVQIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ + ++  +G     +HAR A LKGLSPK+NR++P L Y +V+
Sbjct: 121 VKHRIGIDKDESYGFVRDFIGTVAAAGCEVFIVHARNAWLKGLSPKENREVPPLRYAVVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  +DGVM+GR AY N   L   D  +       
Sbjct: 181 QLKRDFPHLTIAINGGIQTDDVVHEQLGHLDGVMVGREAYHNPWWLARWDALYYG---AP 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
               TR D      + A+M +Y AR   + G     I RHM+GL HG   SRR R + + 
Sbjct: 238 ESSLTRDD------VEATMVEYMAREAAAHGTPWASIARHMLGLRHGLAGSRRWRQVWSD 291

Query: 300 EAGASTATHHIIETAFN 316
                   H ++  A  
Sbjct: 292 HRLKGLPPHEVMALAHA 308


>gi|71065349|ref|YP_264076.1| tRNA-dihydrouridine synthase A [Psychrobacter arcticus 273-4]
 gi|71038334|gb|AAZ18642.1| possible dihydrouridine synthase, TIM-barrel protein family
           [Psychrobacter arcticus 273-4]
          Length = 323

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 124/319 (38%), Positives = 176/319 (55%), Gaps = 15/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YR+FARL   +  LYTEMI   A++ G++   L F   E PL LQ+GGAD++
Sbjct: 14  MIDWTTTDYRYFARLFNPHVYLYTEMISTGALIHGNRARHLRFDALEHPLVLQLGGADMT 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ + A+  +  GY+E+N+NVGCPS RV     GACLM  P+ V D +  M  A+ IPVT
Sbjct: 74  EMTQCAEFAQQHGYDEVNINVGCPSDRVQHNKIGACLMAEPNTVADLVKHMQAAVDIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+DD      + + V+ +   G     +HAR A L+GLSPK NR+IP L Y+ VY
Sbjct: 134 VKHRIGIDDFDSYEFMADFVQKVAAGGCTRFIVHARTAWLQGLSPKQNREIPPLRYEDVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I +NGG+E ++     L  +DGVMIGRA Y N  +L   +  +  P+   
Sbjct: 194 RLKQDFPALDIEINGGIETVADIEAHLEHIDGVMIGRAFYHNPYLLAEANSLWGTPVPKR 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S             I A +  Y    +  G  L  +TRH +GLF G   +R+ R  L+  
Sbjct: 254 S------------DILAQLYPYLEEQIAKGEALPTMTRHYLGLFQGLVGARKWRQALS-- 299

Query: 301 AGASTATHHIIETAFNLMI 319
            G    T   I+ A   ++
Sbjct: 300 -GKPHLTIDDIKYAATEVL 317


>gi|94310927|ref|YP_584137.1| tRNA-dihydrouridine synthase A [Cupriavidus metallidurans CH34]
 gi|93354779|gb|ABF08868.1| tRNA-dihydrouridine synthase A [Cupriavidus metallidurans CH34]
          Length = 351

 Score =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 141/323 (43%), Positives = 192/323 (59%), Gaps = 14/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L FS  E+P+ALQ+GG++  
Sbjct: 30  MMDWTDRHCRTFHRALSQHTWLYTEMVTTGALLHGDVARHLDFSAAEQPVALQLGGSEPV 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK+ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 90  DLAQAAKLGEQWGYKEINLNCGCPSERVQRGAFGACLMAEPQLVADCVRAMRDVVSVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G +   +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 150 VKHRIGIDTIEHYGFVRDFVGTIAEAGCDIFIVHARNAILKGLSPKENREIPPLRYEVAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+K+E P L I +NGG+    +  + L  VDGVMIGR AY +   L+ +D  F     G+
Sbjct: 210 ELKREFPHLEILINGGVVSYGEIDEHLRHVDGVMIGRQAYHDPYFLSEMDARFYG---GT 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
           +PI TR           +M  Y    +  GG +   TRHM+GL  G    R  R +L+  
Sbjct: 267 APIVTR------EMAELTMQAYIGDLVEKGGYMGAATRHMLGLHRGIYGGRGWRRVLSDA 320

Query: 299 --VEAGASTATHH-IIETAFNLM 318
             + A  S A    + E A + +
Sbjct: 321 RRMNAARSRADVDALFEEARSHL 343


>gi|126729455|ref|ZP_01745269.1| tRNA-dihydrouridine synthase A [Sagittula stellata E-37]
 gi|126710445|gb|EBA09497.1| tRNA-dihydrouridine synthase A [Sagittula stellata E-37]
          Length = 339

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 146/320 (45%), Positives = 199/320 (62%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R ++ +ALLYTEM+ A A++RG   ++L     E P+ALQ+GG+D S
Sbjct: 24  MMDWTDRHCRVFHRFMSRHALLYTEMVTAPALVRGGALHLLDHDPGEHPVALQLGGSDPS 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLN GCPS RV  G+FGA LM NPD V  C+ AM  A+ + VT
Sbjct: 84  ELAEAARLGAAAGYDEINLNCGCPSDRVQSGTFGAVLMKNPDTVIRCVEAMQDAVDVDVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P V L   +  +  +G + I IHARKA L+GLSPK+NR IP LDYD+V 
Sbjct: 144 VKCRIGVDDQDPCVVLPEFLARLGAAGCSRISIHARKAWLQGLSPKENRDIPPLDYDLVM 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLT 238
           +++   P L + +NGG+  + QA+  L   +DGVM+GRAAY     +L   D        
Sbjct: 204 QMRGLFPHLHLSVNGGIGSLDQAVGFLDAGLDGVMVGRAAYHQPWDILGEADARIWGD-- 261

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                +TR  ++    +   M  Y  RHL  GG+L Q+TRHM+GLF G P +RR R +L+
Sbjct: 262 ----PQTRRGRE---DVVRDMLPYIERHLTRGGRLHQVTRHMLGLFAGCPGARRWRQVLS 314

Query: 299 VEAGASTATHHIIETAFNLM 318
            +     A   ++E A + +
Sbjct: 315 TDTTRDGAGPAVVERALSEV 334


>gi|319775424|ref|YP_004137912.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae F3047]
 gi|329122550|ref|ZP_08251132.1| tRNA-dihydrouridine synthase A [Haemophilus aegyptius ATCC 11116]
 gi|317450015|emb|CBY86228.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae F3047]
 gi|327473133|gb|EGF18558.1| tRNA-dihydrouridine synthase A [Haemophilus aegyptius ATCC 11116]
          Length = 287

 Score =  322 bits (826), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 120/296 (40%), Positives = 169/296 (57%), Gaps = 10/296 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+     + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPEQLKHCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++ + +  +
Sbjct: 120 KGCQEFIIHARKAWLSGLSPKENREIPPLDYARVYQLKRDFPHLTIAINGGIKTIEEMKQ 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY+N ++L  +D+    P                 +   SM  Y  +
Sbjct: 180 HLQYVDGVMVGREAYQNPSLLGQIDQALFYPNAA---------IVTAHEAVQSMLPYIEQ 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            L+ G  L  I RHM+G F     +R+ R  L+  A    A   ++ETA + +   
Sbjct: 231 QLNQGIHLNHIVRHMLGAFQNCKGARQWRRYLSENAFKQGAGVEVVETALSFVENE 286


>gi|21244742|ref|NP_644324.1| tRNA-dihydrouridine synthase A [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|38604924|sp|Q8PFF8|DUSA_XANAC RecName: Full=tRNA-dihydrouridine synthase A
 gi|21110436|gb|AAM38860.1| conserved hypothetical protein [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 334

 Score =  322 bits (826), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 190/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDPVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVEPAIAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRAYQPYVESQLAQGLGLKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|239815113|ref|YP_002944023.1| tRNA-dihydrouridine synthase A [Variovorax paradoxus S110]
 gi|239801690|gb|ACS18757.1| TIM-barrel protein, yjbN family [Variovorax paradoxus S110]
          Length = 333

 Score =  321 bits (824), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 188/317 (59%), Gaps = 10/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 20  MMDWTDRHCRYFHRLMSRHALLYTEMVTTGALVHGDVPRHLRFNEEEHPVALQLGGSEPA 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A  +PVT
Sbjct: 80  DLAHCARLGEEWGYDEINLNCGCPSERVQRGAFGACLMAEPALVADCVKAMVDATRLPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++ ++G  G  +HAR A L+GLSPK NR+IP L Y++V+
Sbjct: 140 VKHRIGIDKIESYEFVRDFVGAVSEAGCRGFIVHARNAWLQGLSPKQNREIPPLRYELVH 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P+L   +NGG+   +Q  + L  +DGVM+GR AY N   L   D  F   +   
Sbjct: 200 RLKHEFPELDFSINGGISASAQVHEHLRLLDGVMVGREAYHNPWWLAEWDAEFYGAV--P 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            P+           + + M DY  R     G +   I RHM+GL +G P +RR R + + 
Sbjct: 258 QPLTRE-------DVESLMCDYMVREAAEHGTQWSSIARHMLGLRNGLPGARRWRQVWSD 310

Query: 300 EAGASTATHHIIETAFN 316
               +   H ++  A  
Sbjct: 311 HRLKTRPPHEVMALAHE 327


>gi|332971008|gb|EGK09980.1| tRNA dihydrouridine synthase A [Psychrobacter sp. 1501(2011)]
          Length = 340

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 127/322 (39%), Positives = 179/322 (55%), Gaps = 15/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YRFFARL   +  LYTEMI   AI+ G+   +L F   E PL LQ+GGADI 
Sbjct: 20  MIDWTTTDYRFFARLFNPHTYLYTEMISTGAIINGNTDRLLRFDNTEHPLVLQLGGADIG 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++   A   +  G++E+N+NVGCPS RV     GACLM  P+ V   +  M   + IPVT
Sbjct: 80  EMTHGAVEAQKRGFDEVNINVGCPSDRVQHNKIGACLMAEPETVASLVRHMQAEVDIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +++ V++  ++G     +HAR A LKGLSPK+NR+IP L YD VY
Sbjct: 140 VKHRIGIDEHDSYQFMKDFVQASAEAGCQRFIVHARIAWLKGLSPKENREIPPLRYDDVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L I +NGG++ + Q    L  VDGVMIGRAAY N  +L    + +       
Sbjct: 200 RLKQEFPELQIEINGGIDSLEQIKSHLQHVDGVMIGRAAYHNPYLLAEAMQLWGEEAPSR 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                         I + +  Y  + +  G  L  I+RH++GLF G P +RR R  L+  
Sbjct: 260 E------------YILSQLYPYLEKQVAKGEPLTSISRHLLGLFQGLPGARRWRQSLS-- 305

Query: 301 AGASTATHHIIETAFNLMIESL 322
            G    T   ++ A +  + S+
Sbjct: 306 -GKQQLTVDDLKAAGDATLASI 326


>gi|318042981|ref|ZP_07974937.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CB0101]
          Length = 364

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 136/321 (42%), Positives = 187/321 (58%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADI 59
           M+D+TDRH+R   R +T  +LLYTEM+VA A+   +++  L  F   E P+ALQ+GG D 
Sbjct: 49  MMDYTDRHFRVLMRQITRRSLLYTEMVVAQALHYSERRERLIDFDPIEHPIALQVGGDDP 108

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA+I  D GY+EINLNVGCPS +V +G FGACLM  PD V  CI+AM  A  +PV
Sbjct: 109 QLLAEAARIAADRGYDEINLNVGCPSEKVQKGRFGACLMAEPDHVARCISAMAAASPLPV 168

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+D++     L   V ++  +G     +HARKA L+GL PK NR IP L Y++V
Sbjct: 169 TVKHRIGIDERDSYAELLAFVDAVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLRYELV 228

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K++ P+L I LNGGL D++   + L  VDGVM+GRAAY +     TVD    N  + 
Sbjct: 229 HQLKQDRPELTIELNGGLLDLASCSEQLQQVDGVMVGRAAYDHPLRWATVDRDLFNDSSQ 288

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                +         +   +  YA R  + GG+L  I RH++ +  G   +R  R  L  
Sbjct: 289 PMASAST--------VVRGLIPYAERWCNGGGRLWAIARHLVQVVEGVSGARHWRRDLGQ 340

Query: 300 EAGASTATHHIIETAFNLMIE 320
            AGA  A   + E A   + E
Sbjct: 341 AAGARDAGPEVFERAAAQLEE 361


>gi|260436656|ref|ZP_05790626.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 8109]
 gi|260414530|gb|EEX07826.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 8109]
          Length = 331

 Score =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 183/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+    ++N +L F   E P+ALQ+GG D 
Sbjct: 17  MLDCTDRHFRVLMRQISRRALLYSEMVVAQALHHNKRRNKLLDFDLVEHPIALQVGGDDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EINLNVGCPS +V  G+FGACLM  PD+V  C+ AM  A  +PV
Sbjct: 77  VLLAEAARLAQDWGYDEINLNVGCPSQKVQAGNFGACLMAEPDLVARCVEAMVDAGGLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L N V  +  +G +   +HARKA L+GL PK NR IP L ++ V
Sbjct: 137 TVKHRIGIDDLDSDALLTNFVDRVALAGASRFAVHARKAWLEGLDPKQNRTIPPLQHERV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L+ L   DG M+GRAAY +    T+VD       + 
Sbjct: 197 VALKQRRPDLVIELNGGLESPEDCLQALEGCDGAMVGRAAYSHPLRWTSVDALIFGEESR 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                    +     +   +  +AA HL  GG++  + RH++ L  G   +R  R  L  
Sbjct: 257 ---------QILASDVVNGLLPHAAAHLERGGRIWDLCRHLVQLVEGVRGARHWRRELGE 307

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A    A   ++  A   + E+
Sbjct: 308 KAQRPGADLDVLLNAGQQLKEA 329


>gi|319788129|ref|YP_004147604.1| TIM-barrel protein, yjbN family [Pseudoxanthomonas suwonensis 11-1]
 gi|317466641|gb|ADV28373.1| TIM-barrel protein, yjbN family [Pseudoxanthomonas suwonensis 11-1]
          Length = 337

 Score =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 133/327 (40%), Positives = 188/327 (57%), Gaps = 16/327 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +LGF   E P+ALQ+GG++  
Sbjct: 19  MMDWTDRHCRVFHRLLAPHARLYTEMVHANAVVLGDRGRLLGFDPVEHPVALQLGGSEPG 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----- 115
            L  A +I  ++GY+E+NLN GCPS RV  G FGACLM  P +V +C+AAM +       
Sbjct: 79  ALANATRIGAEWGYDEVNLNCGCPSDRVQAGRFGACLMREPSLVAECVAAMIEGAAASGR 138

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVTVKCR+GVD+          + ++  +G     +HAR A L+GLSPK+NR++P L 
Sbjct: 139 NVPVTVKCRLGVDEDHEYERFAAFIDAVAAAGCRTFVVHARNAWLQGLSPKENREVPPLR 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           YD  + +K+E P L I +NGG+   +Q  + L  VDGVM+GRAAY +  +L  +D     
Sbjct: 199 YDWAWRLKRERPGLEILVNGGIASEAQVHEQLAHVDGVMLGRAAYHDPYLLHRLDVALYG 258

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     R  +            Y    L SG  L+ ITRH++GLFHG P  R  R 
Sbjct: 259 GELADRASLLRRLR-----------PYVEAQLASGLALKHITRHVLGLFHGQPGGRLFRQ 307

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
           +L+  A    A   ++E A +    +L
Sbjct: 308 VLSEGAHRPGAGWDLVEQALDATAGAL 334


>gi|166713916|ref|ZP_02245123.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 334

 Score =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +LGF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLLGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  WLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCTATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDAAMAHLQHTDGVMLGRAAYHDPYVLHCLDAVLNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  ++  Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRALQPYVEAQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALQ 323


>gi|194289932|ref|YP_002005839.1| tRNA-dihydrouridine synthase a [Cupriavidus taiwanensis LMG 19424]
 gi|193223767|emb|CAQ69774.1| tRNA-dihydrouridine synthase A [Cupriavidus taiwanensis LMG 19424]
          Length = 337

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 133/319 (41%), Positives = 184/319 (57%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 13  MMDWTDRHCRMFHRQLSRHTWLYTEMVTTGALLHGDVPRHLDFDAAEHPVALQLGGSEPA 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ + +GY EINLN GCPS RV  G+FGACLM  P++V DC+ AM  A+ IPVT
Sbjct: 73  DLAMAAKLGQQWGYAEINLNCGCPSERVQRGAFGACLMAEPELVADCVKAMRDAVEIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  + ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 133 VKHRIGIDKIEHYDFVRDFVGKVAQAGCGTFIVHARNAILKGLSPKENREIPPLRYEVAY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K+E P+L I +NGG+    +  + L  VDGVMIGR AY    +L  +D  F    +  
Sbjct: 193 QLKREFPELEILINGGILSHDEIARHLEHVDGVMIGREAYHQPYILAEMDARFYGDASAP 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
            P +          +  +M  Y    +  GG +   TRHM+GL  G    R  R +L+  
Sbjct: 253 VPSR--------LAVELAMQRYIGDFVEQGGYMGAATRHMLGLHRGIAGGRGWRRVLSDA 304

Query: 299 --VEAGASTATHH-IIETA 314
             + A  + A    + E A
Sbjct: 305 KRMHAARTRADVDALFEEA 323


>gi|309378640|emb|CBX22711.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 336

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 140/324 (43%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK VE +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAVEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPDLEIIINGGITANEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YADLVQLLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +  A        +I  A+  +  +
Sbjct: 309 SDAALLKGNDGGLILEAWKEVERA 332


>gi|325928271|ref|ZP_08189474.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas perforans 91-118]
 gi|325541361|gb|EGD12900.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas perforans 91-118]
          Length = 334

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYTLFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDTAMAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P ++R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQSR------ESLLRAYQPYVESQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|294626706|ref|ZP_06705301.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292598954|gb|EFF43096.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 334

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 190/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPGLVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYTLFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDPAIAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRAYQPYVESRLAQGVGLKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|241662836|ref|YP_002981196.1| tRNA-dihydrouridine synthase A [Ralstonia pickettii 12D]
 gi|240864863|gb|ACS62524.1| TIM-barrel protein, yjbN family [Ralstonia pickettii 12D]
          Length = 346

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 187/321 (58%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEFEHPVALQLGGSEPD 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++ + +GY EINLN GCPS RV  G+FGACLM  P +V   + AM  A+SIPVT
Sbjct: 80  DLAQAARLGQQWGYKEINLNCGCPSERVQRGAFGACLMAEPKLVAQGVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 140 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 200 QLKRDFPHLEILLNGGVQTLEQIDAHLAHVDGVMIGREAYHHPHLMAAFDARYYGAGT-E 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+  
Sbjct: 259 APTRAEVEDA--------MIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLSD- 309

Query: 301 AGASTATHHIIETAFNLMIES 321
              + +    +  A  L  E+
Sbjct: 310 -SKALSRVKTLADAHALFDEA 329


>gi|325134929|gb|EGC57561.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M13399]
          Length = 336

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 186/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEVYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|119384161|ref|YP_915217.1| tRNA-dihydrouridine synthase A [Paracoccus denitrificans PD1222]
 gi|119373928|gb|ABL69521.1| tRNA-U16,U17-dihydrouridine synthase [Paracoccus denitrificans
           PD1222]
          Length = 329

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 139/323 (43%), Positives = 200/323 (61%), Gaps = 14/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD   R   RLL+  ALLYTEM+ A A++ GD+  +L F   E P+ALQ+GG+D +
Sbjct: 14  MMDWTDSLCRRIHRLLSRRALLYTEMVTAPALVYGDRAKLLDFDAGEHPVALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I  D+GY+EINLNVGCPS RV  G FGA LM  P++V +C+AAM  A  + VT
Sbjct: 74  QLAEAARIGADWGYDEINLNVGCPSDRVQSGCFGAVLMTRPELVAECVAAMIAASPVEVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P   L + +  ++++GV  + +HARKA L+GLSP++NR++P LDY +V+
Sbjct: 134 VKCRIGVDEQDPEAVLPDFIARMREAGVRRMTVHARKAWLQGLSPRENREVPPLDYPLVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTG 239
            +K+  PDL + +NGG+  +      L ++DGVMIGRAAY     ML   D  +      
Sbjct: 194 RMKQAFPDLHLSINGGIASLDAVRDHLAAMDGVMIGRAAYHQPWDMLGQADRLWGEEPRF 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P+          + + ++ D    HL +GG+L Q TRHM+GLFHG P +R  R  L+ 
Sbjct: 254 ADPL----------EAARALRDLVEAHLATGGRLHQATRHMLGLFHGRPGARGWRRQLSE 303

Query: 300 EAGAS---TATHHIIETAFNLMI 319
            A  +        + + A   ++
Sbjct: 304 GASRARDRAEALAVYDAALAEVM 326


>gi|225075955|ref|ZP_03719154.1| hypothetical protein NEIFLAOT_00980 [Neisseria flavescens
           NRL30031/H210]
 gi|224952670|gb|EEG33879.1| hypothetical protein NEIFLAOT_00980 [Neisseria flavescens
           NRL30031/H210]
          Length = 319

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T N  LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHYRFMARQITRNTWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM  A+ IPVT
Sbjct: 61  DLAIAAKAAETYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDAVEIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V  + +K+      +HAR A L GLSPK+NR++P L Y+ V
Sbjct: 121 VKHRIGVDRQTEYQVVADFVGMLREKTACRTYIVHARNAWLDGLSPKENREVPPLKYEYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 181 YRLKQEFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDARFYNDTHA 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  ++A +  Y+   + SG    L+ I RH +GL H   N+R  R +L
Sbjct: 241 P---------IQYADLAAWLYAYSREQIASGRGTILRHIVRHALGLMHSLKNARTWRRML 291

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +  A        +I  A+  +  +
Sbjct: 292 SDAALLKDNDGSLILDAWKEVERA 315


>gi|294666631|ref|ZP_06731869.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292603598|gb|EFF47011.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 334

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPGLVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYTLFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDPAIAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRAYQPYVESRLAQGVGLKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A  S A   ++E A  
Sbjct: 308 AHRSGAGWELVEQALE 323


>gi|309782238|ref|ZP_07676967.1| tRNA-dihydrouridine synthase A [Ralstonia sp. 5_7_47FAA]
 gi|308919009|gb|EFP64677.1| tRNA-dihydrouridine synthase A [Ralstonia sp. 5_7_47FAA]
          Length = 346

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 188/321 (58%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 20  MMDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEFEHPVALQLGGSEPD 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++ + +GY EINLN GCPS RV  G+FGACLM  P +V   + AM  A+SIPVT
Sbjct: 80  DLAQAARLGQQWGYKEINLNCGCPSERVQRGAFGACLMAEPKLVAQGVKAMRDAVSIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 140 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 200 QLKRDFPHLEILLNGGVQTLEQIDAHLAHVDGVMIGREAYHHPHLMAAFDARYYGAGT-E 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+  
Sbjct: 259 APTRAEVEDA--------MIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLSD- 309

Query: 301 AGASTATHHIIETAFNLMIES 321
              + +   ++  A  L  E+
Sbjct: 310 -SKALSRVKMLADAHALFDEA 329


>gi|78049674|ref|YP_365849.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78038104|emb|CAJ25849.1| putative dihydrouridine synthase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
          Length = 334

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGIVAVDTAMAHLQHADGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P ++R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQSR------ESLLRAYQPYVESQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALE 323


>gi|325923106|ref|ZP_08184799.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas gardneri ATCC
           19865]
 gi|325546421|gb|EGD17582.1| tRNA-U16,U17-dihydrouridine synthase [Xanthomonas gardneri ATCC
           19865]
          Length = 334

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 139/316 (43%), Positives = 196/316 (62%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG++ +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRTRLIGFDPVEHPLALQLGGSEPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++GY+EINLN GCPS RV  G FGACLM  P +VG+C+AAMC A ++PVT
Sbjct: 79  LLAQAAAIAQEWGYDEINLNCGCPSDRVQAGRFGACLMREPALVGECVAAMCAATTLPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCR+GVDD    +   + V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 IKCRLGVDDDGDYLVFASFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + +NGG+  +  AL+ L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPQLPVVINGGIAAVDTALEHLQHTDGVMLGRAAYHDPYVLHCLDAALN------ 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                R  +     +  ++  Y    L  G  L+ ITRH++GLFHG P  R  R +L+  
Sbjct: 253 -----RRPEQSREALLRALQPYVESQLEQGLALKHITRHVLGLFHGKPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A  S A   ++E A  
Sbjct: 308 AHRSGAGWDLVEQALQ 323


>gi|124267105|ref|YP_001021109.1| tRNA-dihydrouridine synthase A [Methylibium petroleiphilum PM1]
 gi|124259880|gb|ABM94874.1| tRNA-dihydrouridine synthase A [Methylibium petroleiphilum PM1]
          Length = 352

 Score =  319 bits (818), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 125/311 (40%), Positives = 180/311 (57%), Gaps = 10/311 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+ +  LYTEM+   A+L GD    L F  +E P+ALQ+GG++  
Sbjct: 35  MMDWTDRHCRHFHRLLSRHTRLYTEMVTTGALLHGDVPRHLDFGPEEHPVALQLGGSEPE 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E +GY+EINLN GCPS RV  G+FGACLM  PD+V D + AM  A+ IPVT
Sbjct: 95  DLAACAKLGERWGYDEINLNCGCPSERVQRGAFGACLMAEPDLVADGVKAMRDAVGIPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ + ++  +G     +HAR A LKGLSPK+NR++P L ++ VY
Sbjct: 155 VKHRIGIDRTESYGFVRDFIGTVAAAGCEVFIVHARNAWLKGLSPKENRELPPLRHEWVY 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L I LNGG++   +    L  VDGVM+GR AY +  ++   D  F       
Sbjct: 215 RLKRDFPALTIVLNGGVKTHDEIATHLAQVDGVMLGREAYHHPWLMADWDVRFFGD---- 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P++          I A+M  Y       G    +++RHM+GL+ G   +RR R + + +
Sbjct: 271 APLERDRA-----DIEAAMVRYMELQRLQGEPWSRVSRHMLGLWSGMSGARRWRQVWS-D 324

Query: 301 AGASTATHHII 311
                    ++
Sbjct: 325 HRLKNEPPEVV 335


>gi|330942603|gb|EGH45179.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 299

 Score =  319 bits (818), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 125/281 (44%), Positives = 179/281 (63%), Gaps = 9/281 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+  R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDQPCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P++V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPELVADCVKAMRDAVGIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG++ +     L + V  ++++G     +HAR AIL+GLSPK+NR IP L YD+V 
Sbjct: 148 VKHRIGINGRDSYAELCDFVGKVQEAGCQSFTVHARIAILEGLSPKENRDIPPLRYDVVA 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+        +
Sbjct: 208 QLKSDFPDLEIVLNGGIKTLEQCSEHLQTFDGVMLGREAYHNPYLLAHVDQQLFGS---T 264

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           +P+ +R D         SM  Y A H+ SGG +  +TRHM+
Sbjct: 265 APVISRYDA------LESMRPYIAAHIASGGNMHHVTRHML 299


>gi|119505356|ref|ZP_01627430.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2080]
 gi|119458811|gb|EAW39912.1| NifR3/Smm1 family protein [marine gamma proteobacterium HTCC2080]
          Length = 295

 Score =  318 bits (816), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 125/295 (42%), Positives = 173/295 (58%), Gaps = 9/295 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A+L GD    L + +QE PLALQ+GG++   L   AK+ E   Y+E+NLN GCPS
Sbjct: 1   MVTTGALLHGDIDRHLNYGSQEHPLALQLGGSNPQDLARCAKLAEARHYDEVNLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM  P++V DCI AM +A+ IPVTVK RIG+D Q     LR+ V  + +
Sbjct: 61  DRVQNGRFGACLMAEPELVRDCITAMREAVDIPVTVKQRIGIDHQESFDELRDFVGIVAE 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G N   +HARKA L+GLSPK NR+IP L+Y  VY +K++ P L I LNGG++ + +   
Sbjct: 121 GGCNVFIVHARKAWLEGLSPKQNREIPPLNYTWVYALKEQFPQLTIVLNGGIQSLEECEH 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GRAAY+   +L++VD           P  +R        +   ++DY   
Sbjct: 181 HLTKVDGVMLGRAAYQTPWLLSSVDSRIFG---AEDPAYSR------ESVIYKLSDYVET 231

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           +L  GG+L  +TRH++GLFH  P  R  R  L+  A  S A   ++  A   + +
Sbjct: 232 YLAQGGRLNHVTRHILGLFHQQPGGRLFRRALSEGAHLSGADATVLLAALAKVTQ 286


>gi|284800241|ref|ZP_05985987.2| tRNA dihydrouridine synthase A [Neisseria subflava NJ9703]
 gi|284795603|gb|EFC50950.1| tRNA dihydrouridine synthase A [Neisseria subflava NJ9703]
          Length = 317

 Score =  318 bits (816), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 194/324 (59%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T NA LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 1   MLDWTDRHYRFMARQITRNAWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  A K  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM  A+ IPVT
Sbjct: 61  DLAIATKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDAVEIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V ++ +K+      +HAR A L GLSPK+NR++P L Y+ V
Sbjct: 121 VKHRIGVDRQTEYQVVADFVGTLREKTACRTFIVHARNAWLDGLSPKENREVPPLKYEYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 181 YRLKQDFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDTMFYND--A 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  ++A +  Y+   +  G    L+ I RH +GL HG  N+R  R +L
Sbjct: 239 HAPIQ-------YADLAAWLYAYSREQIALGRGTILRHIVRHALGLMHGLKNARTWRRML 291

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 292 SDATLLKDNDGSLILDAWKEVERA 315


>gi|148653531|ref|YP_001280624.1| tRNA-dihydrouridine synthase A [Psychrobacter sp. PRwf-1]
 gi|148572615|gb|ABQ94674.1| TIM-barrel protein, yjbN family [Psychrobacter sp. PRwf-1]
          Length = 348

 Score =  318 bits (815), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 178/322 (55%), Gaps = 20/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT   YRFFARL   +  LYTEMI   AIL+G    +L + T E PL LQ+GGADIS
Sbjct: 28  MIDWTTTDYRFFARLFNPHTYLYTEMISTSAILQGKTDRLLRYDTLEHPLVLQLGGADIS 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ + A   +  G+NE+N+NVGCPS RV     GACLM  PD V   +  M   + IPVT
Sbjct: 88  EMTQCAVEAQKRGFNEVNINVGCPSDRVQHNKIGACLMAEPDTVAALVRNMQAHVDIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D+      +++ V +  ++G     +HAR A L GLSPK+NR+IP L Y+ VY
Sbjct: 148 VKHRIGIDEHDSYEFMQDFVSASAEAGCQRFIVHARIAWLNGLSPKENREIPPLRYEDVY 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P+L I +NGG++ + Q    L  VDGVMIGRAAY N  +L     ++       
Sbjct: 208 RLKQAFPELHIEINGGIDSIEQIKAHLQQVDGVMIGRAAYHNPYILAEAMSFWGEAAPSR 267

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            +I   +  Y  + +  G  L  + RH +GLF G P +R+ R  L+ +
Sbjct: 268 A------------QILTKLYPYLEQQVAKGEPLPSLARHFLGLFQGLPGARKWRQALSGK 315

Query: 301 AG--------ASTATHHIIETA 314
                     A+ AT  IIE A
Sbjct: 316 QQMSVDDIRRAADATLAIIERA 337


>gi|75677001|ref|YP_319422.1| tRNA-dihydrouridine synthase A [Nitrobacter winogradskyi Nb-255]
 gi|74421871|gb|ABA06070.1| tRNA-U16,U17-dihydrouridine synthase [Nitrobacter winogradskyi
           Nb-255]
          Length = 340

 Score =  317 bits (814), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 143/320 (44%), Positives = 195/320 (60%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F RLLT  A LY+EM+   A++ G +  +LGFS  E P+ALQ+GG++ +
Sbjct: 14  MMEWTDRHCRVFHRLLTRRAWLYSEMLTTGAVIHGARDRLLGFSDIEHPVALQLGGSNPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I EDFGY+EINLNVGCPS RV +G FGACLM  PDIV + + AM +A+S+PVT
Sbjct: 74  DLAIAARIGEDFGYDEINLNVGCPSDRVKDGRFGACLMAEPDIVAESVNAMKRAVSVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ    AL   V+ +  +GV+ + +HARKA L+GLSPK+NR +P LD+  VY
Sbjct: 134 VKCRIGIDDQDMESALDIFVRKVVAAGVDALIVHARKAWLQGLSPKENRNVPPLDHGRVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P L I +NGG+  + +A + L  VDGVM+GRAAY+    L  VD          
Sbjct: 194 RLKASFPGLPIIINGGIGGIPEAKQHLAHVDGVMLGRAAYQEPWRLLEVDSELFGEAPPH 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +K         +   +M  Y    L  G +L  I+RH++G FHG P +R  R  L   
Sbjct: 254 PTMK---------QALEAMVPYIEEQLAGGARLHSISRHLVGAFHGVPGARGFRRYLAEN 304

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++ A   + E
Sbjct: 305 GVKPDAGVEVLQEAIARVDE 324


>gi|58580044|ref|YP_199060.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84622040|ref|YP_449412.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188578985|ref|YP_001915914.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|58424638|gb|AAW73675.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84365980|dbj|BAE67138.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188523437|gb|ACD61382.1| tRNA-dihydrouridine synthase A [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 334

 Score =  317 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +LGF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLLGFDAVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCTATHVPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSPK+NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDYALFARFVDQVVAAGAAMVVVHARNAWLKGLSPKENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            + +E P L + LNGG+  +  A+  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLNQERPGLPVVLNGGIVAVDAAMAHLQHTDGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  ++  Y A  L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 RPEQPR------ESLLRALQPYVASQLAQGLALKHMTRHVLGLFHGQPGGRSFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A    A   ++E A  
Sbjct: 308 AHRPGAGWELVEQALQ 323


>gi|317403413|gb|EFV83926.1| hypothetical protein HMPREF0005_02052 [Achromobacter xylosoxidans
           C54]
          Length = 327

 Score =  317 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 191/316 (60%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L G+    L F   E P+ALQ+GG++  
Sbjct: 1   MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLYGNVARHLDFDEAEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ + +GY+EINLN GCPS RV +G+FGACLM  PD+V DCI AM  A+ IPVT
Sbjct: 61  ALAQSARLGQQWGYDEINLNCGCPSERVQKGAFGACLMAEPDLVADCIKAMQDAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G      HAR A+LKGLSPKDNR+IP L YD+V 
Sbjct: 121 VKHRLGLDYDESYAFVRDFVGKIYDTGCRVFIAHARNAVLKGLSPKDNREIPPLRYDVVS 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD    LNGGL D +Q+++     DGVM+GRAA+    +L+ V          S
Sbjct: 181 QLKRDFPDCVFVLNGGLADAAQSVRAAADFDGVMLGRAAWHTPRVLSEV----------S 230

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +   V      ++  +M +YAAR +  G  L+ +TR M+GL +G   +RR R +L+  
Sbjct: 231 LQLWPSVRLPGDAQVVDAMMEYAARQVAQGVPLRVMTRPMLGLVNGQSGARRWRRMLSDP 290

Query: 301 AGASTATHHIIETAFN 316
           A  +     +I  A+ 
Sbjct: 291 ALLAANDPALIYDAWR 306


>gi|317968407|ref|ZP_07969797.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CB0205]
          Length = 332

 Score =  317 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 136/321 (42%), Positives = 188/321 (58%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADI 59
           M+D+TDRH+R   R ++  +LLYTEM+VA A+   ++++ L  F   E P+ALQ+GG D 
Sbjct: 17  MMDYTDRHFRVLMRQISRRSLLYTEMVVAQALHHSERRDRLIDFDPIEHPIALQVGGDDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA+I  D GY+EINLNVGCPS +V +G FGACLM  P+ V  CI+AM +A  +PV
Sbjct: 77  VLLAEAARIAADRGYDEINLNVGCPSEKVQKGRFGACLMAEPEQVARCISAMAQASPLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+D++     L   V ++  +G     +HARKA L+GL PK NR IP L Y++V
Sbjct: 137 TVKHRIGIDERDSYGELLAFVDTVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLRYELV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K + P L I LNGGL ++S  L+ L +VDGVM+GRAAY +     TVD         
Sbjct: 197 HQLKADRPQLTIELNGGLLELSSCLEQLEAVDGVMVGRAAYDHPLRWATVDRDLFGD--S 254

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S P+           +   +  YA R   SGG+L  I RH++ +  G   +R  R  L  
Sbjct: 255 SQPVAKAST------VVRGLIPYAERWCGSGGRLWSIARHLVQVVEGVSGARHWRRDLGQ 308

Query: 300 EAGASTATHHIIETAFNLMIE 320
            AG   A   + E A   + E
Sbjct: 309 AAGQRDAGPEVFERAARQLEE 329


>gi|313667754|ref|YP_004048038.1| dihydrouridine synthase [Neisseria lactamica ST-640]
 gi|313005216|emb|CBN86649.1| Putative dihydrouridine synthase [Neisseria lactamica 020-06]
          Length = 336

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 138/324 (42%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK VE +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAVEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVHIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACRTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGITANEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +  A        +I  A+  +  +
Sbjct: 309 SDAALLKGNDGSLILEAWKEVERA 332


>gi|123967550|ref|YP_001008408.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str.
           AS9601]
 gi|123197660|gb|ABM69301.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. AS9601]
          Length = 334

 Score =  317 bits (813), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 187/310 (60%), Gaps = 10/310 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  +KK N L F+ +E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKISSEALLYTEMIVAQSLVHTNKKENFLDFNGEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS RV  G+FGA LM +P+ V  CI ++     +PV
Sbjct: 80  KILKEAARMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKDPEKVAKCIESLKLNCDLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD+    V L N V+ +  +G +   +HARKAIL GL+PK NR IP L+YD+V
Sbjct: 140 TIKHRIGVDNDDSFVKLNNFVRIVANAGADRFTVHARKAILTGLNPKQNRTIPPLNYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++K  NP L I +NGGL ++ ++LK L   DGVMIGR+ YK+    + +D+      T 
Sbjct: 200 KKLKNLNPSLLIEINGGLTNIDESLKALNDFDGVMIGRSIYKHPLRWSEIDQKIYGINTK 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          I  S+  Y  +HL +GGK   I +H+I L  G P ++  R+ ++ 
Sbjct: 260 PKSASN---------IIFSLIPYIEKHLSNGGKSWDICKHLINLVEGIPKAKIWRNQISN 310

Query: 300 EAGASTATHH 309
           ++        
Sbjct: 311 KSIKKELNIE 320


>gi|262277019|ref|ZP_06054812.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HIMB114]
 gi|262224122|gb|EEY74581.1| tRNA-dihydrouridine synthase A [alpha proteobacterium HIMB114]
          Length = 330

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 145/318 (45%), Positives = 202/318 (63%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RL++ N  LY+EMI   AIL GDKK IL FS  EKP+ALQ+GG++  
Sbjct: 13  MMDCTDRHDRYFLRLISKNIFLYSEMIATGAILNGDKKKILEFSEFEKPVALQLGGSNKK 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +LVE  KIVEDFGY+EINLN+GCPS +V +  FGACL+  PD+V DC++AM ++  +PVT
Sbjct: 73  ELVECCKIVEDFGYDEINLNLGCPSKKVQKNKFGACLIKEPDLVADCLSAMAQSTKLPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG DD      L + V+ IK +GV  I +HARKAILKGLSPK+N +IP L+Y++VY
Sbjct: 133 AKTRIGYDDVEDFDYLNSFVEKIKNTGVKTIILHARKAILKGLSPKENLRIPKLNYNMVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKK NP++ I +NG + D +Q    L  VDGVMIGRA Y++   L  +       +  +
Sbjct: 193 EIKKSNPEIEIIINGAVTDTNQIKSHLEKVDGVMIGRAIYQSPYFLADI----EKDVFKN 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             I TR       +I   + +Y    ++ G ++ QI RH +GL+HG   + R +  L+  
Sbjct: 249 DDILTR------EQIVEKLVEYVDTEVNKGTRVNQIMRHTVGLYHGQRGAGRWKRYLSDN 302

Query: 301 AGASTATHHIIETAFNLM 318
             A  +    ++   N++
Sbjct: 303 MMARDSDFQKVKHILNVV 320


>gi|187928263|ref|YP_001898750.1| tRNA-dihydrouridine synthase A [Ralstonia pickettii 12J]
 gi|187725153|gb|ACD26318.1| TIM-barrel protein, yjbN family [Ralstonia pickettii 12J]
          Length = 327

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 186/321 (57%), Gaps = 11/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEFEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++ + +GY EINLN GCPS RV  G+FGACLM  P +V   + AM  A+SIPVT
Sbjct: 61  DLAQAARLGQQWGYKEINLNCGCPSERVQRGAFGACLMAEPKLVAQGVTAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 121 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 181 QLKRDFPHLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMAAFDARYYGAGT-E 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+  
Sbjct: 240 APTRAEVEDA--------MIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLSD- 290

Query: 301 AGASTATHHIIETAFNLMIES 321
              +      +  A  L  E+
Sbjct: 291 -SKALGRVKTLADAHALFDEA 310


>gi|170748394|ref|YP_001754654.1| tRNA-dihydrouridine synthase A [Methylobacterium radiotolerans JCM
           2831]
 gi|170654916|gb|ACB23971.1| dihydrouridine synthase DuS [Methylobacterium radiotolerans JCM
           2831]
          Length = 319

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 149/321 (46%), Positives = 196/321 (61%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R L+  A LYTEM+   A+L G ++ +LGF+  E P+A+Q+GG+D  
Sbjct: 1   MMDWTDRHCRAFHRSLSARARLYTEMVTTGAVLHGPRERLLGFAAVEHPVAVQLGGSDPG 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AA+I  D GY+E+NLNVGCPS RV EG FGACLM  P +VGDC+AAM  A+ +PVT
Sbjct: 61  ELAQAARIAADLGYDEVNLNVGCPSDRVQEGRFGACLMREPALVGDCVAAMKAAVPVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  ++  +GV+G+ +HARKA L+GLSPK+NR +P LDY    
Sbjct: 121 VKCRIGVDDQDPEAALDALADAVVAAGVDGLIVHARKAWLQGLSPKENRDVPPLDYGRAA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P L I +NGGL D+  A   L  VDGVM+GRAAY   A+L  VD         +
Sbjct: 181 RLKRRLPGLPIAVNGGLRDLDSARARLAEVDGVMVGRAAYTEPALLLGVDPDLFGVPAPA 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
             +   V         A    Y A  L  G +L  +TRHM+GLF+G P +R  R  L+  
Sbjct: 241 PDVFAAV---------AMFEPYIAACLARGERLHAVTRHMLGLFNGRPGARAFRRHLSTH 291

Query: 301 AGASTATHHIIETAFNLMIES 321
                A    +  A  L+  +
Sbjct: 292 GMRPEADLATLREAVALVSRA 312


>gi|328675719|gb|AEB28394.1| tRNA-dihydrouridine synthase A [Francisella cf. novicida 3523]
          Length = 301

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/308 (41%), Positives = 178/308 (57%), Gaps = 9/308 (2%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             RL+T + +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG      +   K+ E+
Sbjct: 1   MMRLITKHTMLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPKDFISCGKLAEE 60

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            GYNEIN+NVGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++VKCRIG D   
Sbjct: 61  LGYNEININVGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPISVKCRIGYDHND 120

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
               L N V    ++GV+ + IHARK  L GLSPK+NR IP L YDIVY IKK+ P+L +
Sbjct: 121 SYEELYNFVDKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDIVYSIKKDFPNLEL 180

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKD 250
           G+NGG+  + +  + L  VD VMIGR AY N  +    D  F N P TG S ++      
Sbjct: 181 GINGGITTIEETQQHLKCVDSVMIGREAYHNPMLFKDFDNIFYNQPTTGISALEIAYKMA 240

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
            + K+      Y         KL  IT+H + LF+G PN++  R  L+  A    A    
Sbjct: 241 EYIKVQMDNDPYI--------KLNNITKHTLNLFNGLPNAKVYRRYLSENATKKEANVDT 292

Query: 311 IETAFNLM 318
             TA  + 
Sbjct: 293 FLTALEVF 300


>gi|126695351|ref|YP_001090237.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9301]
 gi|126542394|gb|ABO16636.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9301]
          Length = 334

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 190/310 (61%), Gaps = 10/310 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  DKK   L F+++E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKISSEALLYTEMIVAQSLVYTDKKEYFLDFNSEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS RV  G+FGA LM +P+ V  CI ++    ++PV
Sbjct: 80  KILKEAAQMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKDPEKVAKCIESLKNNCNLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L+YD+V
Sbjct: 140 TIKHRIGVDNDDSFVNLNNFVRIIANAGADRFTVHARKAILKGLNPKQNRTIPPLNYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++KK NP+L I +NGGL ++ Q+LK L   DGVMIGR+ YK+    + +D+        
Sbjct: 200 KKLKKSNPELLIEINGGLTNIDQSLKALNDFDGVMIGRSIYKHPLRWSEIDQKIYGINKK 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +              I  S+  Y   H+ +GGK   I +H+I L  G P ++  R+ ++ 
Sbjct: 260 NKSASN---------IIFSLIPYIEAHISNGGKSWDICKHLINLVEGIPKAKIWRNQISK 310

Query: 300 EAGASTATHH 309
           ++        
Sbjct: 311 KSIKKELDIE 320


>gi|33860574|ref|NP_892135.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|33633516|emb|CAE18473.1| conserved hypothetical protein [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
          Length = 334

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 189/310 (60%), Gaps = 10/310 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  DKK   L F+++E PL++Q GG + 
Sbjct: 20  MMDCTDKHFRMIIRKISSKALLYTEMIVAQSLIYTDKKERFLDFNSEEHPLSIQFGGDNP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAAK+ +D+GY+EIN NVGCPS RV  G+FGA LM  P  V  CI ++    S+PV
Sbjct: 80  KMLEEAAKMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKEPIKVAKCIESLKNNCSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD++     L + VK I  +G +   +HARKAILKGL+PK NR IP L YD+V
Sbjct: 140 TIKHRIGVDEEDSFDKLDSFVKEIANAGADRFTVHARKAILKGLNPKQNRTIPPLKYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++KK NP L I +NGG  ++ Q ++ L  +DGVMIGR+AYK     + +D+      T 
Sbjct: 200 RKLKKNNPKLIIEINGGFTNIDQCIEALNDLDGVMIGRSAYKYPLRWSEIDQKIYGESTK 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S             +I  S+  Y  +HL + GK   I +H+I L  G PN++  R+ ++ 
Sbjct: 260 SKKAS---------EIIFSLVPYIEKHLKNEGKTWDICKHLINLVEGIPNAKVWRNEIST 310

Query: 300 EAGASTATHH 309
           ++     +  
Sbjct: 311 KSIRQELSID 320


>gi|159902555|ref|YP_001549899.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9211]
 gi|159887731|gb|ABX07945.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9211]
          Length = 333

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 130/320 (40%), Positives = 186/320 (58%), Gaps = 9/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   R ++  +LLYTEMIVA A+     + +L F   E P++LQ+GG +  
Sbjct: 20  MLDCTDRHFRVIFRQVSRRSLLYTEMIVAKALQHQKGRRLLDFDEIEHPISLQVGGDNPK 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L +AAK+ ED+GY+EINLN+GCPS RV  G+FGACLM  P+ V  CI AM  A  IPVT
Sbjct: 80  ELADAAKLAEDWGYDEINLNLGCPSPRVQSGNFGACLMATPNQVAKCIEAMKNATQIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G+D+      L + V  I K+G +   IHARKA L+GL+PK NR IP L+Y  V 
Sbjct: 140 IKHRTGIDNFDSEEFLFSFVDQIAKAGADRFAIHARKAWLEGLNPKQNRTIPPLEYLKVK 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+L I  NGGL    + +K L   DG M+GR+AY N  +   +D          
Sbjct: 200 KLKLKRPELKIEFNGGLHTPEECVKTLKIFDGAMVGRSAYSNPMLWQEMDSLIYGEDYFP 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++  ++  YA +HL + G+L  I++H++ L    P +R  RH L+ +
Sbjct: 260 VKAS---------QVIQNLIPYAQKHLDNEGRLWDISKHLLQLVQAVPGARAWRHNLSTK 310

Query: 301 AGASTATHHIIETAFNLMIE 320
           A  S+A   I+E A   + E
Sbjct: 311 AQKSSAKLIILEKAAQQLEE 330


>gi|332525913|ref|ZP_08402054.1| tRNA-dihydrouridine synthase A [Rubrivivax benzoatilyticus JA2]
 gi|332109464|gb|EGJ10387.1| tRNA-dihydrouridine synthase A [Rubrivivax benzoatilyticus JA2]
          Length = 320

 Score =  315 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 132/317 (41%), Positives = 182/317 (57%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT +A LYTEM+   A+L GD+   L F  +E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHCRHFHRLLTQHARLYTEMVTTGALLHGDQPRHLDFGDEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E +GY+E+NLN GCPS RV  G+FGACLM  P +V D + AM  A+S+PVT
Sbjct: 61  DLAACAKLAERWGYDEVNLNCGCPSPRVQRGAFGACLMNEPALVADAVKAMRDAVSLPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+        +R+ V S+ ++G     +HAR A L+GLSPK+NR IP L Y++ +
Sbjct: 121 VKHRIGLGKDESYAFVRDFVGSVAEAGCEVFIVHARNAWLEGLSPKENRDIPPLRYEVAH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG+         L  VDGVM+GRAAY     L+T DE F       
Sbjct: 181 RLKTEFPQLTIVVNGGIAGDEAIAAQLAHVDGVMVGRAAYHEPWTLSTWDERFFGE---P 237

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P + R        +  +M  Y  R   +G     + RHM+GL++G P +RR R + +  
Sbjct: 238 APAQDRA------AVELAMVRYMERQAAAGVPWAHVARHMLGLWNGEPGARRWRQVWSD- 290

Query: 301 AGASTATHHIIETAFNL 317
                A    +  A   
Sbjct: 291 -HRLKAEPAAVVHALAQ 306


>gi|254526125|ref|ZP_05138177.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
 gi|221537549|gb|EEE40002.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9202]
          Length = 334

 Score =  315 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 189/310 (60%), Gaps = 10/310 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +T+ ALLYTEMIVA +++   KK   L F+++E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKITSKALLYTEMIVAQSLVYTKKKEKFLDFNSEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS +V  G+FGA LM +P+ V  C+ ++    S+PV
Sbjct: 80  KILKEAARMAQDWGYDEINFNVGCPSPKVCSGNFGASLMKDPEKVAKCMESLKNNCSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+D+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L+YDIV
Sbjct: 140 TIKHRIGLDNNDSFVTLNNFVRVIANAGADRFTVHARKAILKGLNPKQNRTIPPLNYDIV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++KK NP+L I +NGGL +++++LK L   DGVMIGR+ Y++    + +D+      T 
Sbjct: 200 KKLKKSNPELLIEINGGLANINESLKALNDFDGVMIGRSVYQHPLRWSEIDQKIYGINTK 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          I  S+  Y   HL  GGK   I +H+I L  G P ++  R+ ++ 
Sbjct: 260 PKSAS---------DIIFSLIPYIEAHLSKGGKSWDICKHLINLVEGIPKAKIWRNQISN 310

Query: 300 EAGASTATHH 309
           ++        
Sbjct: 311 KSIKKELNIE 320


>gi|289666419|ref|ZP_06488000.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           vasculorum NCPPB702]
 gi|289669253|ref|ZP_06490328.1| tRNA-dihydrouridine synthase A [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 334

 Score =  315 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 189/316 (59%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  ++GF   E PLALQ+GG+D +
Sbjct: 19  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVIHGDRARLIGFDVVEHPLALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I +++G++EINLN GCPS RV  G FGACLM  P +V +C+AAMC A  +P+T
Sbjct: 79  LLAQAAAIAQEWGFDEINLNCGCPSDRVQAGRFGACLMREPALVAECVAAMCAATHLPIT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDD          V  +  +G   + +HAR A LKGLSP++NR++P L YD  Y
Sbjct: 139 VKCRLGVDDDDDHAVFAGFVDQVVAAGAAMVVVHARNAWLKGLSPRENREVPPLRYDWAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGG+  +  AL  L   DGVM+GRAAY +  +L  +D   +      
Sbjct: 199 RLKQERPGLPVVLNGGITAVDTALAHLQHTDGVMLGRAAYHDPYVLHCLDAALNQ----- 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P + R        +  +   Y    L  G  L+ +TRH++GLFHG P  R  R +L+  
Sbjct: 254 QPEQPR------ESLLRAFRPYVESQLAQGLALKHMTRHVLGLFHGQPGGRAFRQVLSEG 307

Query: 301 AGASTATHHIIETAFN 316
           A        ++E A  
Sbjct: 308 AHRPGVGWQLVEQALQ 323


>gi|72383178|ref|YP_292533.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str.
           NATL2A]
 gi|72003028|gb|AAZ58830.1| tRNA-U16,U17-dihydrouridine synthase [Prochlorococcus marinus str.
           NATL2A]
          Length = 335

 Score =  315 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 187/322 (58%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R +T  +LLYTEMIVA A+     +N +L F   E P+++Q+GG + 
Sbjct: 21  MMDCTDRHFRVLMRQITKKSLLYTEMIVAQALHYSKNRNKLLDFDEIEHPISIQLGGDNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ ED+GY+EINLN+GCPS +V  G+FGACLM  P+IV  CI  M K  +IP+
Sbjct: 81  KLLAEAAQMAEDWGYDEINLNIGCPSPKVKSGNFGACLMGKPNIVASCIEKMKKTCNIPI 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D+      L   V +   +G +   +HARKA L GL+PK+NR IP L Y+ V
Sbjct: 141 TVKHRLGIDNLDSDDYLLKFVDTCSLAGADRFIVHARKAWLNGLNPKENRSIPPLQYERV 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K   P+L I LNGG+  ++ +++ L   DG M+GRAAY +  + T +D         
Sbjct: 201 QNLKNNRPELIIELNGGINTINDSIEALKVFDGAMVGRAAYSHPFLWTKIDSLIFG---- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 +       KI   +  +A +HL +GG+L QI+RH++ L    PN++  R  L+ 
Sbjct: 257 -----QKEKYLSRSKIIKKLIPFAQKHLENGGRLWQISRHILNLIENIPNAKILRQELSE 311

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +     A   I++     + ++
Sbjct: 312 KCQTQKADISILKKIAQQLEDA 333


>gi|116074290|ref|ZP_01471552.1| hypothetical protein RS9916_37607 [Synechococcus sp. RS9916]
 gi|116069595|gb|EAU75347.1| hypothetical protein RS9916_37607 [Synechococcus sp. RS9916]
          Length = 334

 Score =  315 bits (807), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 181/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+     ++ +L F   E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISTRALLYSEMVVAQALHHTNRRERLLDFDPVEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++  D+GY+EINLNVGCPS RV  G+FGACLM  PD V  C+ AM +A  +PV
Sbjct: 80  VLLAEAAQMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPDRVARCVEAMGQASRLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D       L+  V  +  +G     +HARKA L+GL PK NR IP L YD V
Sbjct: 140 TVKHRVGIDHLDSDALLQAFVDRVAAAGATRFAVHARKAWLEGLDPKQNRTIPPLQYDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P+L I LNGGL+   Q L+ L S DG M+GRAAY +      +DE        
Sbjct: 200 IALKQRRPELTIELNGGLDTPDQCLEALESCDGAMVGRAAYAHPLRWGCIDERIYGEAAR 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +              +   +  YA  HL  GG+L  + RH++ L  G P +R  R  L +
Sbjct: 260 TVTAS---------DVVLGLIPYAQAHLARGGRLWDLCRHLVQLVEGVPGARHWRRNLGL 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   ++++
Sbjct: 311 NAQRQGADIPVLEDAARQLLDA 332


>gi|17546018|ref|NP_519420.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum GMI1000]
 gi|17428313|emb|CAD15001.1| putative trna-dihydrouridine synthase protein [Ralstonia
           solanacearum GMI1000]
          Length = 344

 Score =  315 bits (807), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 133/323 (41%), Positives = 186/323 (57%), Gaps = 14/323 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 18  MMDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDEAEHPVALQLGGSEPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V D + AM  A+SIPVT
Sbjct: 78  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADGVKAMRDAVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY
Sbjct: 138 VKHRIGIDAIETYDFVRDFVGAIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +       
Sbjct: 198 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMAGFDARYYGA-DAV 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV- 299
           +P +  V+          M DY  R +  GG      RHM+GL+ G   +R  R +L+  
Sbjct: 257 APTRAEVEDA--------MIDYIGRWVARGGYAGAAVRHMLGLYRGVAGARGWRRVLSDA 308

Query: 300 ----EAGASTATHHIIETAFNLM 318
                         + ETA   +
Sbjct: 309 KALGRVKTPDDARALFETARAHL 331


>gi|293604638|ref|ZP_06687040.1| tRNA dihydrouridine synthase A [Achromobacter piechaudii ATCC
           43553]
 gi|292816969|gb|EFF76048.1| tRNA dihydrouridine synthase A [Achromobacter piechaudii ATCC
           43553]
          Length = 326

 Score =  315 bits (807), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 135/321 (42%), Positives = 189/321 (58%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RLL   A LYTEMI   A+  G+    L F   E P+ALQ+GG++  
Sbjct: 1   MIDVTDRHCRFFHRLLAPRARLYTEMITTGALQHGNIPRHLDFDEAEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++AK+   +GY+EINLN GCPS RV +G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 61  ALAQSAKLGRQWGYDEINLNCGCPSERVQKGAFGACLMAEPALVADCMKAMQDAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D +     +R+ V  I  +G      HAR A+LKGLSPKDNR+IP L YD+V 
Sbjct: 121 VKHRLGLDYENSYSFVRDFVGKIYDTGCRVFIAHARNAVLKGLSPKDNREIPPLRYDVVK 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD    LNGGL D  Q++      DGVM+GRAA+    +L+ V       +   
Sbjct: 181 QLKQDFPDCTFVLNGGLADADQSVSAADEFDGVMLGRAAWHTPRVLSEVSLRLWPSVRLP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            ++  +MT+YAAR +  G  L+ +TR M+GL +G   +RR R +L+  
Sbjct: 241 SDA----------QVVDAMTEYAARQVAKGVPLRVMTRPMLGLVNGQSGARRWRRMLSDP 290

Query: 301 AGASTATHHIIETAFNLMIES 321
           A  +     +I  A+    ++
Sbjct: 291 ALLAANNPELIYDAWRSQRQA 311


>gi|157412352|ref|YP_001483218.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9215]
 gi|157386927|gb|ABV49632.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9215]
          Length = 334

 Score =  315 bits (807), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 190/310 (61%), Gaps = 10/310 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +T+ ALLYTEMIVA +++   KK   L F+++E P+++Q GG D 
Sbjct: 20  MMDCTDKHFRMIMRKITSKALLYTEMIVAQSLVYTKKKEKFLDFNSEEHPISIQFGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ +D+GY+EIN NVGCPS +V  G+FGA LM +P+ V  C+ ++    S+PV
Sbjct: 80  KILKEAARMAQDWGYDEINFNVGCPSPKVCSGNFGASLMKDPEKVAKCMESLKNNSSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIG+D+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L+YDIV
Sbjct: 140 TIKHRIGLDNDDSFVTLNNFVRVIANAGADRFTVHARKAILKGLNPKQNRTIPPLNYDIV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++KK NP+L I +NGGL +++++LK L   DGVMIGR+ Y++    + +D+      T 
Sbjct: 200 KKLKKSNPELLIEINGGLANINESLKALNDFDGVMIGRSVYQHPLRWSEIDQKIYGINTR 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          I  S+  Y   HL  GGK   I +H+I L  G P ++  R+ ++ 
Sbjct: 260 PKSAS---------DIIFSLIPYIEAHLSKGGKSWDICKHLINLVEGIPKAKIWRNQISK 310

Query: 300 EAGASTATHH 309
           ++     +  
Sbjct: 311 KSIKKELSIE 320


>gi|296136585|ref|YP_003643827.1| TIM-barrel protein, yjbN family [Thiomonas intermedia K12]
 gi|295796707|gb|ADG31497.1| TIM-barrel protein, yjbN family [Thiomonas intermedia K12]
          Length = 349

 Score =  314 bits (806), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 132/298 (44%), Positives = 180/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T  ALLYTEM+   A+L GD    L +S+ E P+ALQ+GG++  
Sbjct: 10  MLDWTDRHCRYFHRLITQRALLYTEMVTTGALLYGDVARHLDYSSHEHPVALQLGGSEPV 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
            L   AK+  ++GY+EINLN GCPS RV  G+FGACLM  P  V D +AAM +A+S  IP
Sbjct: 70  DLARCAKLALEWGYDEINLNCGCPSPRVQRGAFGACLMAEPSRVRDSVAAMVEAVSGTIP 129

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIGVD +     +R+ V ++ + G     +HAR A L GLSPK+NR IP L  + 
Sbjct: 130 VTVKHRIGVDHEDSYGFVRDFVGTVSQGGCETFIVHARSAWLDGLSPKENRDIPPLRPEF 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           + +++++ P L   LNGG++   Q  + LP V GVM+GRAAY++   L+T D  F     
Sbjct: 190 ILQLRRDFPALAFVLNGGIKTEQQIREWLPQVSGVMVGRAAYQDPWSLSTWDREFLGSAD 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            ++P +  V+          M  Y A     G   Q ITRHM+ L+ G P  RR R +
Sbjct: 250 SAAPEREIVE--------EQMGAYIAAWKVKGLHPQAITRHMLNLWKGQPGGRRWRQV 299


>gi|83749666|ref|ZP_00946647.1| NIFR3-like protein [Ralstonia solanacearum UW551]
 gi|83723668|gb|EAP70865.1| NIFR3-like protein [Ralstonia solanacearum UW551]
          Length = 344

 Score =  314 bits (806), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 18  MMDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPD 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 78  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 138 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 198 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-V 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 257 APTRAEVEDA--------MIGYIGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 306


>gi|89900729|ref|YP_523200.1| tRNA-dihydrouridine synthase A [Rhodoferax ferrireducens T118]
 gi|89345466|gb|ABD69669.1| TIM-barrel protein, yjbN family [Rhodoferax ferrireducens T118]
          Length = 331

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 130/320 (40%), Positives = 185/320 (57%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT +ALLYTEM+   A++ GD    L ++ QE P+ALQ+GG++ +
Sbjct: 19  MLDWTDRHCRYFHRLLTQHALLYTEMVTTGALIYGDVSRHLRYNEQEHPVALQLGGSEPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E++GY+E+NLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 79  DLARCAKLGEEWGYDEVNLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMVDVVSVPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V S+ ++G     +HAR A LKGLSPK+NR +P L Y++ Y
Sbjct: 139 VKHRIGIDKTESYEFVRDFVGSVSEAGCRTFIVHARNAWLKGLSPKENRDVPPLRYELAY 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+   +Q    L  +DGVM+GR AY N   L + D  F       
Sbjct: 199 QLKRDFPSLVIVINGGITSSAQIAGHLLHLDGVMLGREAYHNPWWLASWDATFFGADATE 258

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +            ++   M DY  R     G     + RHM+GL HG P +R  R + + 
Sbjct: 259 T---------TREQVEQQMCDYMTREAAEHGTPWPTMARHMLGLRHGLPGARHWRQVWSD 309

Query: 300 EAGASTATHHIIETAFNLMI 319
                   H ++  A   + 
Sbjct: 310 HKLKGLPAHDVMALAHTPVP 329


>gi|207723253|ref|YP_002253652.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum MolK2]
 gi|206588451|emb|CAQ35414.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum MolK2]
          Length = 327

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 130/298 (43%), Positives = 182/298 (61%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++++  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRYFHRQISSHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 121 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 181 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-V 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 APTRAEVEDA--------MIGYIGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 289


>gi|261415030|ref|YP_003248713.1| TIM-barrel protein, yjbN family [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371486|gb|ACX74231.1| TIM-barrel protein, yjbN family [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302326032|gb|ADL25233.1| tRNA-dihydrouridine synthase A [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 345

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 126/330 (38%), Positives = 190/330 (57%), Gaps = 9/330 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M+D TDRH R+F RLL+ + LLY+EM+V+  +L  + K++ LG    E P  LQ+GG++ 
Sbjct: 14  MLDCTDRHERYFLRLLSKHILLYSEMVVSTGLLHCENKDLFLGHEPFEHPAVLQLGGSNP 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L  A+K+VE  G++E+NLN GCPS RV  G+FGACLM   ++V DC  AM  A+SIPV
Sbjct: 74  ADLASASKLVEAAGFSEVNLNCGCPSDRVQNGNFGACLMKEKNVVADCFKAMQDAVSIPV 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++KCRIGVDD        + +++++ +G     +HARKA LKGLSPK+NR++P L Y+ V
Sbjct: 134 SIKCRIGVDDLDSWEFFTDFIQTVRDAGCKIFIVHARKAWLKGLSPKENREVPPLHYEFV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + +K E P+L + +NGG++ + Q  + L  +DGVM+GR AY+N   L   D      +  
Sbjct: 194 HRLKAEMPELNLSINGGIKTLDQIEEQLKDLDGVMVGREAYENPWFLHDADARIFGDVRP 253

Query: 240 SSPIKTRVDKDFWR-----KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            S     +     R      +  +   Y  +    G     + +H+ GLF G P +R+ R
Sbjct: 254 ESNDPAEIIAGNARPATRKALLEAYLPYVEKQTAEGCPATILVKHLYGLFAGLPGARKFR 313

Query: 295 HILTVE---AGASTATHHIIETAFNLMIES 321
             L+ E   A        +I  A  L+ E+
Sbjct: 314 ATLSNESPRAHLYGGAAALIRKAMELVGET 343


>gi|238021360|ref|ZP_04601786.1| hypothetical protein GCWU000324_01259 [Kingella oralis ATCC 51147]
 gi|237868340|gb|EEP69346.1| hypothetical protein GCWU000324_01259 [Kingella oralis ATCC 51147]
          Length = 367

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 131/326 (40%), Positives = 194/326 (59%), Gaps = 13/326 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+ AR ++ +  LYTEMI A AI+ GD    L ++  E P+ALQ+GG+D +
Sbjct: 51  MLDWTDRHFRYLARQISRHTWLYTEMINAGAIIHGDPARFLAYNESEHPIALQLGGSDPA 110

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
           +L +AAK V  + Y+EINLN GCPS RV +G+FGACLM +  +V DC+ AM +A     +
Sbjct: 111 QLAQAAKKVAQYQYDEINLNCGCPSPRVQKGAFGACLMNDVGLVADCLNAMQQAAPDCEI 170

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIGVD Q     +R+ V ++ +K+ V    +HAR A L GLSPK+NR IP L Y  
Sbjct: 171 TVKHRIGVDKQTEYRIVRDFVGTLREKTPVRTYIVHARNAWLDGLSPKENRDIPPLKYHY 230

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY++K++ PDL I +NGG++  ++  + L  VDGVMIGR AY N+ ++   D  F +   
Sbjct: 231 VYQLKQDFPDLEIIINGGIKTNAEIAEHLRHVDGVMIGREAYHNTMIMRDWDRLFYD--- 287

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHI 296
                 +R  +  + ++   +  YA   L +G    L+ + RH +GL HG   +R  R +
Sbjct: 288 ------SRQPEISYPELIQRLYAYAQTQLAAGRGTILRHMARHYLGLMHGLHGARAWRQM 341

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           L+           +I  A+  + + L
Sbjct: 342 LSDAELLKANRAELILEAWAEVEKGL 367


>gi|91788026|ref|YP_548978.1| tRNA-dihydrouridine synthase A [Polaromonas sp. JS666]
 gi|91697251|gb|ABE44080.1| tRNA-U16,U17-dihydrouridine synthase [Polaromonas sp. JS666]
          Length = 344

 Score =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 135/322 (41%), Positives = 191/322 (59%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+ +ALLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 31  MMDWTDRHCRHFHRLLSGHALLYTEMVTTGALIHGDVARHLRFGVEEHPVALQLGGSEPA 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L + A + E +GY+EINLN GCPS RV  GSFGACLM  P +V DC+ AM   +S+PVT
Sbjct: 91  ELAQCATLGEQWGYDEINLNCGCPSERVQRGSFGACLMAEPQLVADCVKAMVDVVSVPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++ ++G +   +HAR A LKGLSPK+NR++P L Y++V+
Sbjct: 151 VKHRIGIDKGESYGFVRDFVGAVSEAGCSTFIVHARNAWLKGLSPKENREVPPLRYELVH 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K E P L I +NGG+   +Q  + L  +DGVMIGR AY N   L+  D  F       
Sbjct: 211 RLKAEFPQLTIAINGGITTSTQVAEQLQQLDGVMIGREAYHNPWWLSVWDAAFYGVADAG 270

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              ++         + A M DY AR     G     I RHM+GL HG P +RR R + + 
Sbjct: 271 RTRES---------VEAQMVDYMAREAAEHGTPWSSIARHMLGLRHGLPGARRWRQVWSN 321

Query: 300 EAGASTATHHIIETAFNLMIES 321
               +     ++  A   ++E+
Sbjct: 322 HKLKALHPRDVMALAHEAVLEA 343


>gi|78778399|ref|YP_396511.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9312]
 gi|78711898|gb|ABB49075.1| tRNA-U16,U17-dihydrouridine synthase [Prochlorococcus marinus str.
           MIT 9312]
          Length = 334

 Score =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 127/321 (39%), Positives = 193/321 (60%), Gaps = 10/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  ++K   L F+ +E P+++Q GG + 
Sbjct: 20  MMDCTDKHFRMIMRKISSKALLYTEMIVAQSLIYTNEKEKFLDFNNEEHPISIQFGGDNP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L E AK+ +D+GY+EIN NVGCPS RV  G+FGA LM +P+ V  CI ++  + S+PV
Sbjct: 80  KILKEGAKMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKDPEKVAKCIESLKNSCSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD+    V L N V+ I  +G +   +HARKAILKGL+PK NR IP L YD+V
Sbjct: 140 TIKHRIGVDEDDSFVNLNNFVRYIANAGADRFTVHARKAILKGLNPKQNRTIPPLKYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++KK NP+L I +NGG  +++++L+ L + DGVMIGR+ YK+    + +D+      T 
Sbjct: 200 KKLKKLNPELLIEINGGFTNINESLEALSNFDGVMIGRSVYKHPLRWSEIDQKVYGINTK 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          I  S+  Y   HL +GGK   I +H+I L  G P ++  R+ ++ 
Sbjct: 260 PKSAS---------DIIFSLIPYIEEHLSNGGKSWDICKHLINLVEGIPKAKVWRNQIST 310

Query: 300 EAGASTATHHIIETAFNLMIE 320
           ++         +    + + E
Sbjct: 311 KSIKKELDIDYLLKLTSRLEE 331


>gi|207743351|ref|YP_002259743.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
 gi|206594748|emb|CAQ61675.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
          Length = 327

 Score =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 130/298 (43%), Positives = 181/298 (60%), Gaps = 9/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 1   MMDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVT
Sbjct: 61  DLAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y
Sbjct: 121 VKHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  
Sbjct: 181 QLKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-V 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 APTRAEVEDA--------MIGYIGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 289


>gi|254456205|ref|ZP_05069634.1| tRNA-dihydrouridine synthase A [Candidatus Pelagibacter sp.
           HTCC7211]
 gi|207083207|gb|EDZ60633.1| tRNA-dihydrouridine synthase A [Candidatus Pelagibacter sp.
           HTCC7211]
          Length = 334

 Score =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 131/309 (42%), Positives = 191/309 (61%), Gaps = 10/309 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RL++ N +LY+EM+   + + GD+K IL +S +EKPLALQ+GG++  
Sbjct: 16  MMDCTDRHDRFFLRLMSKNVMLYSEMVATKSAIHGDRKKILSYSPEEKPLALQVGGSNKD 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L E AKI ED GY+EIN+N+GCPS +V +  FGACLM  PD+V +CI +M  + +IPVT
Sbjct: 76  ELAEVAKIAEDMGYDEININLGCPSKKVQKNMFGACLMKEPDLVAECINSMVNSCNIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG D       L N +  ++ +G     +HARKA+L GLSPK N  IP L+Y++VY
Sbjct: 136 AKTRIGFDQTEDFDYLNNFIHKMRDAGTKTFILHARKAMLTGLSPKQNLNIPKLNYNMVY 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           EIKK+NP+L I +NGG+  +S+    L   DGVMIGR+ Y+N   L  ++    N  T +
Sbjct: 196 EIKKKNPELEIIINGGISKVSEIDNHLKFCDGVMIGRSIYQNPYSLIEIERDIFN--THN 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P +         ++   + +YA + +  G K+  I RH +GL+HG   S+  +  L+  
Sbjct: 254 NPTR--------EQVVEKLLEYADKEVKLGTKINHIMRHTVGLYHGQTGSKDWKRYLSDN 305

Query: 301 AGASTATHH 309
             A  +   
Sbjct: 306 LMARESDFQ 314


>gi|294340713|emb|CAZ89105.1| tRNA-dihydrouridine synthase A [Thiomonas sp. 3As]
          Length = 352

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 131/298 (43%), Positives = 179/298 (60%), Gaps = 10/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T  ALLYTEM+   A+L GD    L +S+ E P+ALQ+GG++  
Sbjct: 10  MLDWTDRHCRYFHRLITRQALLYTEMVTTGALLYGDVARHLDYSSHEHPVALQLGGSEPV 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
            L   A++  ++GY+EINLN GCPS RV  G+FGACLM  P  V D +AAM +A+S  IP
Sbjct: 70  DLACCARLALEWGYDEINLNCGCPSPRVQRGAFGACLMAEPSRVRDSVAAMVEAVSGTIP 129

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIGVD +     +R+ V ++ + G     +HAR A L GLSPK+NR IP L  + 
Sbjct: 130 VTVKHRIGVDHEDSYGFVRDFVGTVSQGGCETFIVHARSAWLDGLSPKENRDIPPLRPEF 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           + +++++ P L   LNGG++   Q  + LP V GVM+GRAAY++   L T D  F     
Sbjct: 190 ILQLRRDFPALAFVLNGGIKTGQQIGEWLPQVSGVMVGRAAYQDPWSLATWDREFLGSAD 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            ++P +  V+          M  Y A     G   Q ITRHM+ L+ G P  RR R +
Sbjct: 250 SAAPEREIVE--------EQMGAYIAAWKAKGLHPQAITRHMLNLWKGQPGGRRWRQV 299


>gi|148238351|ref|YP_001223738.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 7803]
 gi|147846890|emb|CAK22441.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 7803]
          Length = 334

 Score =  312 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 181/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  +LLY+EM+VA A+   +++  +LGF  +E P+ LQ+GG D 
Sbjct: 20  MLDCTDRHFRQLMRQISRRSLLYSEMVVAQALHHSNRRERLLGFDPEEHPIVLQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EA ++  D+GY+EINLNVGCPS RV  G+FGACLM  P+ V  C+ AM  A   PV
Sbjct: 80  QLLAEATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPERVAQCVEAMVSASDRPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L   V  +  +G +   +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRVGIDDLDSDDLLTAFVDRVADAGASRFSVHARKAWLEGLDPKQNRTIPPLQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K   P L I LNGGL+   Q L  L   DG M+GRAAY +     +VD         
Sbjct: 200 IALKARRPQLTIELNGGLDTPEQCLDALQHCDGAMVGRAAYAHPLRWASVDTLIYGD--- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P   R        +   +  +A RHL  GG+L  I RH++ L  G P +R  R  L  
Sbjct: 257 -APQTVRA-----SDVLIGLIPHAERHLQRGGRLWDIGRHLVQLVEGVPGARHWRRDLGQ 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A  S A   ++E +   +I++
Sbjct: 311 KAQRSGADLTVLEASARQLIDA 332


>gi|148241114|ref|YP_001226271.1| tRNA-dihydrouridine synthase A [Synechococcus sp. RCC307]
 gi|147849424|emb|CAK26918.1| tRNA-dihydrouridine synthase A [Synechococcus sp. RCC307]
          Length = 335

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 137/320 (42%), Positives = 196/320 (61%), Gaps = 8/320 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+TDRH+R   R ++ +ALLYTEM+VA A+  G +  +LGF   EKP+ALQ+GG D +
Sbjct: 21  MMDYTDRHFRVVMRQVSRHALLYTEMVVAQALHHGRQDTLLGFDPLEKPIALQLGGDDPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA++ E +GY+EINLNVGCPS +V +G FGACLM  P  V  C+ AM  A  +PVT
Sbjct: 81  LLAEAAELAERWGYDEINLNVGCPSPKVKKGRFGACLMAEPQQVARCVEAMGAACRLPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D++     L + V ++  +G     +HARKA L+GL PK NR +P L YD+V+
Sbjct: 141 VKHRIGIDERDSYDELLDFVDTVAAAGCQRFAVHARKAWLEGLDPKQNRTVPPLRYDLVH 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L + LNGGLE +S   + L +VDGVM+GRAAY +      VD+      + +
Sbjct: 201 ALKRDRPALIVELNGGLESLSACQEQLHAVDGVMVGRAAYAHPLQWNRVDQEIFGD-SNA 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +PIK         ++   +  +A     SGG+L  I RH++ L  G   +R  R  L+VE
Sbjct: 260 TPIKA-------SEVLQGVLPHAEHWCSSGGRLWPIARHLVHLVEGVSGARYWRRQLSVE 312

Query: 301 AGASTATHHIIETAFNLMIE 320
           A   +A   ++E A   + E
Sbjct: 313 ASDRSARPDVLERAMRQLQE 332


>gi|116329329|ref|YP_799049.1| tRNA-dihydrouridine synthase A [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116330067|ref|YP_799785.1| tRNA-dihydrouridine synthase A [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116122073|gb|ABJ80116.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116123756|gb|ABJ75027.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 339

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 138/323 (42%), Positives = 194/323 (60%), Gaps = 12/323 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R+F RL++ +  LYTEMI   AIL GD++  L +S +E PLA+Q+GG +  
Sbjct: 19  MMDRTDRHFRYFLRLISKHTFLYTEMIHTGAILHGDRRRFLSYSPEELPLAIQLGGDNPK 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E++KI ED+GY+EINLNVGCPS RV EG+FGACLM  P+ V + + AM   +SIPVT
Sbjct: 79  ALAESSKIGEDYGYSEINLNVGCPSDRVREGNFGACLMETPERVAELVCAMDGNVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+  +     L   ++ ++++GV    +HAR AIL GLSP  NR+IP L Y  V 
Sbjct: 139 VKCRIGISGKETLEDLCRFIECVRQAGVRRFIVHARIAILGGLSPAQNRQIPPLRYAHVE 198

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PDL I +NGG+  +++    L + DGVMIGRAAY+   + + VD  F +    +
Sbjct: 199 SLKKEFPDLLIEINGGIRTLAEMQDRLKTNDGVMIGRAAYETPYLFSEVDSLFFHD---N 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           SP  +R      R++   M DY    +     GK     RHM+GLFHG   +R  R ++T
Sbjct: 256 SPSLSR------REVLLRMRDYIEEVVLKEKNGKPHHALRHMLGLFHGEKGARSFRRVVT 309

Query: 299 VEAGASTATHHIIETAFNLMIES 321
                   +  ++  A   +   
Sbjct: 310 ER-MYYDYSSDLLLDAIQEIPND 331


>gi|306840355|ref|ZP_07473124.1| tRNA-dihydrouridine synthase A [Brucella sp. BO2]
 gi|306289676|gb|EFM60872.1| tRNA-dihydrouridine synthase A [Brucella sp. BO2]
          Length = 278

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 137/282 (48%), Positives = 185/282 (65%), Gaps = 9/282 (3%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           +LGF   E P+ALQ+GG+D +KL +AA+I  DFGY+EINLNVGCPS RV  G+FGACLML
Sbjct: 1   MLGFDPAENPVALQLGGSDPAKLRQAAQIGADFGYDEINLNVGCPSDRVQSGTFGACLML 60

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            PD+V  C+AAM + +SIPVTVKCRIGVDDQ    AL  L   + ++G + +W+HARKA 
Sbjct: 61  TPDVVARCVAAMKETVSIPVTVKCRIGVDDQDTETALDALADQVLEAGADALWVHARKAW 120

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
           LKGLSPK+NR+IP LDY+ VY +K+   + F+G+NGG+  + +A   L  VD VM+GRAA
Sbjct: 121 LKGLSPKENREIPPLDYERVYRLKQRLGETFVGINGGIATLEEAEVHLQKVDAVMLGRAA 180

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
           Y N A+L  VD            +   +D          M  Y  RH+ SGG+L  ++RH
Sbjct: 181 YHNPALLADVDARLYGDGQEPPAMPEIIDA---------MCAYIDRHIASGGRLSHVSRH 231

Query: 280 MIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           M+GLF G P +RR R IL+ +A    AT  ++  A+  ++E+
Sbjct: 232 MVGLFTGQPGARRWRQILSTDATKPGATSDVVRQAYATVVEA 273


>gi|88809349|ref|ZP_01124857.1| hypothetical protein WH7805_09364 [Synechococcus sp. WH 7805]
 gi|88786568|gb|EAR17727.1| hypothetical protein WH7805_09364 [Synechococcus sp. WH 7805]
          Length = 334

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 184/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   RL++ ++LLY+EM+VA A+   +++  +LGF  +E P+ LQ+GG + 
Sbjct: 20  MLDCTDRHFRQLMRLISRHSLLYSEMVVAQALHHSNRRERLLGFDPEEHPIVLQVGGDEP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EA ++  D+GY+EINLNVGCPS RV  G+FGACLM  P+ V  C+ AM  A   P+
Sbjct: 80  RLLAEATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPERVAQCVEAMVSASDRPI 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L   V  +  +G +   +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRVGIDDLDSDDLLTAFVDRVADAGASRFSVHARKAWLEGLDPKQNRTIPPLQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +KK  P L I LNGGL+   Q L  L   DG M+GRAAY +     +VDE     +  
Sbjct: 200 IALKKRRPQLTIELNGGLDTPEQCLDALQHCDGAMVGRAAYAHPLRWASVDELIYGDVCR 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +              +   +  +A RHL  GG+L  I RH++ L  G P +R  R  L  
Sbjct: 260 TVRAS---------DVLIGLIPHAERHLQRGGRLWDIGRHLVQLVEGVPGARHWRRDLGQ 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A  + A   ++E++   +I++
Sbjct: 311 NAQRAGADLTVLESSARQLIDA 332


>gi|124024726|ref|YP_001013842.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str.
           NATL1A]
 gi|123959794|gb|ABM74577.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. NATL1A]
          Length = 335

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 188/322 (58%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R +T  +LLYTEMIVA A+     +N +L F   E P+++Q+GG + 
Sbjct: 21  MMDCTDRHFRVLMRQITKKSLLYTEMIVAQALHYSKNRNKLLDFDEIEHPISIQLGGDNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ ED+GY+EINLN+GCPS RV  G+FGACLM  P IV +CI  M ++ +IP+
Sbjct: 81  KLLAEAAQMAEDWGYDEINLNIGCPSPRVKSGNFGACLMGKPKIVANCIEKMKESCNIPI 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D+      L   V +   +G +   IHARKA L GL+PK+NR IP L Y+ V
Sbjct: 141 TVKHRLGIDNLDSDDYLLTFVDTCSLAGADRFIIHARKAWLNGLNPKENRTIPPLQYERV 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++K   P+L I LNGG+  ++ +++ L   DG M+GRAAY +  + T +D         
Sbjct: 201 QKLKNHRPELIIELNGGINTINDSIEALKVFDGAMVGRAAYSHPFLWTKIDSLIFG---- 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 +       KI   +  +A +HL + G+L QI+RH++ L    PN++  R  L+ 
Sbjct: 257 -----QKEKYLSRSKIIKRLIPFAEKHLENDGRLWQISRHILNLIENIPNAKILRQELSE 311

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +     A   I++     + ++
Sbjct: 312 KCQTQKADISILKKIAQQLEDA 333


>gi|325267704|ref|ZP_08134355.1| tRNA dihydrouridine synthase A [Kingella denitrificans ATCC 33394]
 gi|324980828|gb|EGC16489.1| tRNA dihydrouridine synthase A [Kingella denitrificans ATCC 33394]
          Length = 383

 Score =  312 bits (800), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 130/321 (40%), Positives = 183/321 (57%), Gaps = 13/321 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T +  LYTEM+ A AI+ GD    L  +  E P+ALQ+GG++ +
Sbjct: 63  MLDWTDRHYRYMARQITRHTWLYTEMVNAGAIVFGDPDRFLARNECENPVALQLGGSEPN 122

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA+   ++GY+EINLN GCPS RV +G+FGACLML+  +V DC+ AM  A     V
Sbjct: 123 LLAQAARKAAEYGYDEINLNCGCPSPRVQKGAFGACLMLDAPLVADCLNAMQDAAPDTAV 182

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D Q     L + V   ++ +      +HAR A L GLSPK+NR++P L Y++
Sbjct: 183 TVKHRIGIDRQTEYAPLADFVGHLVRHTPCRTFVVHARNAWLDGLSPKENREVPPLRYEL 242

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F     
Sbjct: 243 VYRLKQEFPDLEIIINGGIRTNEDIALHLQHVDGVMVGREAYHNPFVMHDWDRLFYRE-- 300

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              P   R       +I   + +YA + L  + G  L+ + RH +GL HG P +R  R +
Sbjct: 301 -KQPAPER------DEIVQRLYEYAQQQLSKNQGTILRHMARHYLGLLHGLPKARVWRRM 353

Query: 297 LTVEAGASTATHHIIETAFNL 317
           L+           +I  A+  
Sbjct: 354 LSDADLLRPNRPELILQAWQA 374


>gi|120611162|ref|YP_970840.1| tRNA-dihydrouridine synthase A [Acidovorax citrulli AAC00-1]
 gi|120589626|gb|ABM33066.1| tRNA-U16,U17-dihydrouridine synthase [Acidovorax citrulli AAC00-1]
          Length = 347

 Score =  312 bits (800), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 131/316 (41%), Positives = 182/316 (57%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A++ GD +  L F+ +E P+ALQ+GG++  
Sbjct: 28  MMDWTDRHCRYFHRLLSRHALLYTEMVTTGALVHGDVERHLRFNAEEHPVALQLGGSEPG 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 88  DLAHSARLGERWGYGEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDAVSVPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+        +R+ V ++ ++G     +HAR A L+GLSPK+NR+IP L YD+V+
Sbjct: 148 VKHRIGIGRSEEYAFVRDFVGTVAEAGCRVFIVHARNAWLEGLSPKENREIPPLRYDVVH 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K E PDL I +NGGL   +   + L   +DG MIGR AY N   L   D  +      
Sbjct: 208 RLKAEFPDLVIAINGGLATDAAVQEALGGGLDGAMIGREAYHNPWWLARWDALYFGDAAS 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                             +M DY AR     G     + RHM+GL +G P +RR R + +
Sbjct: 268 G---------LTREAAEEAMVDYMAREAAQHGTSWYSVARHMLGLRNGLPGARRWRQVWS 318

Query: 299 VEAGASTATHHIIETA 314
                    H ++  A
Sbjct: 319 DHRLKHLPAHEVMAIA 334


>gi|319639148|ref|ZP_07993902.1| hypothetical protein HMPREF0604_01526 [Neisseria mucosa C102]
 gi|317399587|gb|EFV80254.1| hypothetical protein HMPREF0604_01526 [Neisseria mucosa C102]
          Length = 334

 Score =  312 bits (799), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 138/324 (42%), Positives = 196/324 (60%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYRF AR +T NA LY+EM+ + A++ GDK   L F+  E+P+ALQ+GG+D  
Sbjct: 16  MLDWTDRHYRFMARQITRNAWLYSEMVNSGAVVYGDKDRFLSFNEGEQPVALQLGGSDPH 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK  E +GYNE+NLN GCPS RV +G+FGACLM + D+V DC+ AM  A+ IPVT
Sbjct: 76  DLAIAAKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNDVDLVADCLNAMQDAVEIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V ++ +K+      +HAR A L GLSPK+NR++P L Y+ +
Sbjct: 136 VKHRIGVDRQTEYQVVADFVGALREKTACRTFIVHARNAWLDGLSPKENREVPPLKYEYI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ PDL I +NGG+    +  + L  VDGVMIGR AY N  ++   D  F N    
Sbjct: 196 YRLKQDFPDLEILINGGITTNEEIAEHLKFVDGVMIGREAYHNPMLMRDWDALFYND--A 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  ++A +  Y+   + SG    L+ I RH +GL HG  N+R  R +L
Sbjct: 254 HAPIQ-------YADLAAWLYAYSREQIASGRGTILRHIVRHALGLMHGLKNARTWRRML 306

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 307 SDATLLKDNDGSLILDAWKEVERA 330


>gi|330825043|ref|YP_004388346.1| TIM-barrel protein, yjbN family [Alicycliphilus denitrificans K601]
 gi|329310415|gb|AEB84830.1| TIM-barrel protein, yjbN family [Alicycliphilus denitrificans K601]
          Length = 316

 Score =  312 bits (799), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 128/315 (40%), Positives = 178/315 (56%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   RLL+ +ALLYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 6   MMDWTDRHCRHLHRLLSRHALLYTEMVTTGALLHGDVPRHLRFGEAEHPVALQLGGSEPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 66  DLAHSARLGAQWGYDEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDVVDMPVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++  
Sbjct: 126 VKHRIGIDQTEDYGFVRDFVGTVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYEVAA 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NG L+  +  L+ L  VDGVM+GR AY N   LT  DE F     G+
Sbjct: 186 RLKSDFPQLTIAINGSLQTDAAVLEQLALVDGVMVGREAYHNPWWLTRWDELFFGAKPGT 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                        ++   M  Y  R   + G     + RHM+GL +G P +RR R + + 
Sbjct: 246 ---------LTREQVEEEMVAYMEREAAAHGTHWYAVARHMLGLRNGLPGARRWRQVWSD 296

Query: 300 EAGASTATHHIIETA 314
                     ++  A
Sbjct: 297 HRLKHLPAREVMALA 311


>gi|319762963|ref|YP_004126900.1| tim-barrel protein, yjbn family [Alicycliphilus denitrificans BC]
 gi|317117524|gb|ADV00013.1| TIM-barrel protein, yjbN family [Alicycliphilus denitrificans BC]
          Length = 316

 Score =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 128/315 (40%), Positives = 178/315 (56%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R   RLL+ +ALLYTEM+   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 6   MMDWTDRHCRHLHRLLSRHALLYTEMVTTGALLHGDVPRHLRFGEAEHPVALQLGGSEPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 66  DLAHSARLGAQWGYDEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDVVDMPVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++  
Sbjct: 126 VKHRIGIDQTEGYGFVRDFVGTVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYEVAA 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NG L+  +  L+ L  VDGVM+GR AY N   LT  DE F     G+
Sbjct: 186 RLKSDFPQLTIAINGSLQTDAAVLEQLALVDGVMVGREAYHNPWWLTRWDELFFGAKPGT 245

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                        ++   M  Y  R   + G     + RHM+GL +G P +RR R + + 
Sbjct: 246 ---------LTREQVEEEMVAYMEREAAAHGTHWYAVARHMLGLRNGLPGARRWRQVWSD 296

Query: 300 EAGASTATHHIIETA 314
                     ++  A
Sbjct: 297 HRLKHLPAREVMALA 311


>gi|121996919|ref|YP_001001706.1| tRNA-dihydrouridine synthase A [Halorhodospira halophila SL1]
 gi|121588324|gb|ABM60904.1| tRNA-U16,U17-dihydrouridine synthase [Halorhodospira halophila SL1]
          Length = 328

 Score =  311 bits (797), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 124/319 (38%), Positives = 173/319 (54%), Gaps = 11/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WT    R+F RLL  +  LYTEM+ A A+  G  +  L F   E P+A+Q GG+D  
Sbjct: 16  MMEWTTPAARYFLRLLAPHVRLYTEMVPAVALWHGAAERFLPFHPAEHPVAVQFGGSDPQ 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AA++ E +GY+E+NLNVGCPS RV  G FGACLML P  V DC+AAM    ++PVT
Sbjct: 76  ELAYAARLAEQWGYDEVNLNVGCPSDRVQSGRFGACLMLEPSRVADCVAAMRAETNLPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      L   V+++  +G     +HARKA L GLSPK+NR++P LDY  V+
Sbjct: 136 VKSRIGVDEHDSESFLDAFVETVAAAGCRTFIVHARKAWLAGLSPKENREVPPLDYQRVH 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K   P+L + +NGG+ D     + L  VDGVM+GR A+ N   L   D          
Sbjct: 196 RLKARRPELEVAINGGIADTVTLQEQLQWVDGVMVGREAFSNPYALAHWDRLLFGGELPE 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R +  +   Y       G  + Q+ + ++GLF+G P +R  R  LT  
Sbjct: 256 R-----------RGVVVAYLPYVEARRREGVPMSQLVKVLMGLFNGLPGARAWRRTLTEG 304

Query: 301 AGASTATHHIIETAFNLMI 319
           +    A   +IE A   + 
Sbjct: 305 SQQPGAGPEVIERALTCVT 323


>gi|299067351|emb|CBJ38550.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum CMR15]
          Length = 326

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 131/297 (44%), Positives = 182/297 (61%), Gaps = 9/297 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH RFF R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++   
Sbjct: 1   MDWTDRHCRFFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPDD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V D + AM  A+SIPVTV
Sbjct: 61  LAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPRLVADGVKAMRDAVSIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++VY+
Sbjct: 121 KHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVVYQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P L I LNGG++ + Q    L  +DGVMIGR AY +  ++   D  +    T  +
Sbjct: 181 LKRDFPRLEILLNGGVQTLEQIDTHLAHIDGVMIGREAYHHPHLMAGFDARYYGADT-VA 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           P +T V+          M DY  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 PTRTEVEDA--------MIDYIGRWVARGGYAGAAVRHMLGLYRGVAGARGWRRVLS 288


>gi|326317525|ref|YP_004235197.1| TIM-barrel protein, yjbN family [Acidovorax avenae subsp. avenae
           ATCC 19860]
 gi|323374361|gb|ADX46630.1| TIM-barrel protein, yjbN family [Acidovorax avenae subsp. avenae
           ATCC 19860]
          Length = 320

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 130/316 (41%), Positives = 182/316 (57%), Gaps = 11/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+ +ALLYTEM+   A++ G+ +  L F+ +E P+ALQ+GG++ +
Sbjct: 1   MMDWTDRHCRYFHRLLSRHALLYTEMVTTGALVHGNVERHLRFNAEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 61  DLAHSARLGERWGYGEINLNCGCPSERVQRGAFGACLMNEPRLVADCVKAMVDAVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+        +R+ V ++ ++G     +HAR A L+GLSPK+NR+IP L YD+V+
Sbjct: 121 VKHRIGIGRSEEYAFVRDFVGTVAEAGCRVFIVHARNAWLEGLSPKENREIPPLRYDVVH 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K E PDL I +NGGL       + L   +DG MIGR AY N   L   D  +      
Sbjct: 181 RLKAEFPDLVIAINGGLATDDAVQEALGGGLDGAMIGREAYHNPWWLARWDALYFGDAAS 240

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                             +M DY AR     G     + RHM+GL +G P +RR R + +
Sbjct: 241 G---------LTREAAEEAMVDYMAREAAQHGTSWYSVARHMLGLRNGLPGARRWRQVWS 291

Query: 299 VEAGASTATHHIIETA 314
                    H ++  A
Sbjct: 292 DHRLKHLPAHEVMAIA 307


>gi|300704326|ref|YP_003745929.1| tRNA-dihydrouridine synthase a [Ralstonia solanacearum CFBP2957]
 gi|299071990|emb|CBJ43320.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum CFBP2957]
          Length = 326

 Score =  310 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 129/297 (43%), Positives = 180/297 (60%), Gaps = 9/297 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           +DWTDRH R+F R ++ +  LYTEM+   A+L GD    L F   E P+ALQ+GG++   
Sbjct: 1   MDWTDRHCRYFHRQISRHTWLYTEMVTTGALLHGDVPRHLDFDETEHPVALQLGGSEPDD 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L ++A++ E +GY EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+SIPVTV
Sbjct: 61  LAQSARLGERWGYREINLNCGCPSERVQRGAFGACLMAEPKLVADCVRAMRDAVSIPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D       +R+ V +I ++G     +HAR AILKGLSPK+NR+IP L Y++ Y+
Sbjct: 121 KHRIGIDAIETYDFVRDFVGTIAEAGCETFIVHARNAILKGLSPKENREIPPLRYEVAYQ 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +K++ P L I LNGG++ + Q    L  VDGVMIGR AY +  ++   D  +    T  +
Sbjct: 181 LKRDFPRLEILLNGGVQTLEQIDTHLAHVDGVMIGREAYHHPHLMANFDARYYGADT-VA 239

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           P +  V+          M  Y  R +  GG      RHM+GL+ G   +R  R +L+
Sbjct: 240 PTRAEVEDA--------MIGYVGRWVERGGYAGAAVRHMLGLYRGVAGARGWRRVLS 288


>gi|328676669|gb|AEB27539.1| tRNA-dihydrouridine synthase A [Francisella cf. novicida Fx1]
          Length = 295

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 123/304 (40%), Positives = 173/304 (56%), Gaps = 11/304 (3%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           +LYTEM+  +AIL G+K+ +L ++ QE P+ LQ+GG      +   K+ E+ GYNEIN+N
Sbjct: 1   MLYTEMVTLNAILHGNKEFLLKYNPQENPVTLQLGGCVPKDFISCGKLAEELGYNEININ 60

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           VGCPS RV +G+FG  LM  P++V DC+ AM   L+IP++VKCRIG D       L + V
Sbjct: 61  VGCPSERVKKGNFGLSLMAEPELVADCVKAMKDNLNIPISVKCRIGYDHNDSYEELYDFV 120

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
               ++GV+ + IHARK  L GLSPK+NR IP L YD+VY IKK+ P+L +G+NGG+  +
Sbjct: 121 DKQVQAGVDYLCIHARKGWLSGLSPKENRTIPELKYDVVYSIKKDFPNLELGINGGITTI 180

Query: 201 SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMT 260
            +  + L  VD VMIGR AY N  +    D  F N  T               +I+  M 
Sbjct: 181 QETQQHLKYVDSVMIGREAYHNPMLFKDFDNIFYNQPT---------TDISALEIAYKMA 231

Query: 261 DYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           +Y    + +    KL  IT+H + LF+G PN++  R  L+  A    A      TA  + 
Sbjct: 232 EYIKDQMDNDPYIKLNNITKHTLNLFNGLPNAKVYRRYLSENATKKEANVDTFLTALEVF 291

Query: 319 IESL 322
              L
Sbjct: 292 ENKL 295


>gi|332284552|ref|YP_004416463.1| tRNA-dihydrouridine synthase A [Pusillimonas sp. T7-7]
 gi|330428505|gb|AEC19839.1| tRNA-dihydrouridine synthase A [Pusillimonas sp. T7-7]
          Length = 334

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 131/319 (41%), Positives = 184/319 (57%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TD+H R+F RLL   A LYTEMI   A++ G     L F   E+P+ALQ+GG++  
Sbjct: 18  MIDVTDKHCRYFHRLLAPQARLYTEMITTGALMHGKVARHLDFDPAEEPVALQLGGSEPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L E+AK+ + +GY+EINLN GCPS RV  G+FGACLM  P +V DCI AM  A+++PVT
Sbjct: 78  ALAESAKLGQQWGYDEINLNCGCPSERVQRGAFGACLMAEPQLVADCIKAMQDAVTVPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD   
Sbjct: 138 VKHRLGLDYDDSYGFVRDFVGVIHNTGCRVFIVHARNAVLKGLSPKDNREIPPLRYDAAA 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + PD    LNGG+   SQAL+++   DGVM+GRAA+    +L+ +    +  +   
Sbjct: 198 RLKADFPDSVFVLNGGIAQASQALELMRQFDGVMLGRAAWHQPGVLSEISRAMAPDVAPL 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P           +I  +M  YAA  +  G  L+ I R M+G   G   SR  R  L+  
Sbjct: 258 EPA----------QIIQAMQTYAAGQVEQGVPLRMIVRPMLGWMSGRAGSRHWRRTLSDA 307

Query: 301 AGASTATHHIIETAFNLMI 319
           A  +     ++E A+  ++
Sbjct: 308 ALLNQNDAGLLEKAWADLV 326


>gi|299531032|ref|ZP_07044445.1| tRNA-dihydrouridine synthase A [Comamonas testosteroni S44]
 gi|298720989|gb|EFI61933.1| tRNA-dihydrouridine synthase A [Comamonas testosteroni S44]
          Length = 327

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 124/314 (39%), Positives = 185/314 (58%), Gaps = 8/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RLL+ + LLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 6   MMDWTDKHCRYFHRLLSQHTLLYTEMVTTGALVHGDVARHLRFEAEEHPVALQLGGSEPA 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   +S+PVT
Sbjct: 66  DLAHSARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEAALVADCVKAMADVVSVPVT 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++V 
Sbjct: 126 VKHRIGIDKIESYDFVRDFVGTVADAGCQVFVVHARNAWLKGLSPKENREIPPLRYEVVA 185

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  VDGVM+GR AY N   + + D  +    +  
Sbjct: 186 QLKRDFPGLTIAVNGGIKTDDVVQQQLQQVDGVMVGREAYHNPWWMASWDALYYQDES-- 243

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + R  +    ++   M   A  H   G     I RHM+GL +G   +RR R + +  
Sbjct: 244 ---RERTREQIEEQMVLYMEREAREH---GTHWYSIARHMLGLRNGLAGARRWRQVWSDH 297

Query: 301 AGASTATHHIIETA 314
              +   H +++ A
Sbjct: 298 RLKTLPAHEVMKLA 311


>gi|298369820|ref|ZP_06981136.1| tRNA dihydrouridine synthase A [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298281280|gb|EFI22769.1| tRNA dihydrouridine synthase A [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 345

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 192/324 (59%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+R+ AR +T NA LY+EMI A AI+ GDK   L F+  E+P+ALQ+GG++ +
Sbjct: 27  MLDWTDRHFRYMARQITENAWLYSEMINAGAIIYGDKDRFLMFNEGEQPVALQLGGSEPA 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNEINLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 87  DLAKAAKAAEEYGYNEINLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVDIPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q         V ++ +K+      +HAR A L GLSPK+NR++P L YD V
Sbjct: 147 VKHRIGVDRQTEYGVAAEFVGTLYEKTACRTFIVHARNAWLDGLSPKENREVPPLKYDYV 206

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K++ P+L I +NGG+    Q  + L  VDGVM+GR AY N  ++   D  F    + 
Sbjct: 207 YRLKQDFPELEIIINGGITTNEQISEHLKHVDGVMVGREAYHNPMIMRDWDRLFYGESSP 266

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  +   + +Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 267 P---------VEYADLVLKLYEYSRAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 317

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +  A        +I  A+  + ++
Sbjct: 318 SDAALLKNNDGSLILDAWREVEKA 341


>gi|123965248|ref|YP_001010329.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9515]
 gi|123199614|gb|ABM71222.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9515]
          Length = 334

 Score =  309 bits (792), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 127/312 (40%), Positives = 183/312 (58%), Gaps = 10/312 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TD+H+R   R +++ ALLYTEMIVA +++  DKK   L F+ +E PL++Q GG + 
Sbjct: 20  MMDCTDKHFRMIIRQISSKALLYTEMIVAQSLVYTDKKEKFLNFNKEEHPLSIQFGGDNP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAAK+ +D+GY+EIN NVGCPS RV  G+FGA LM  P  V  CI ++    ++P+
Sbjct: 80  QMLKEAAKMAQDWGYDEINFNVGCPSPRVCSGNFGASLMKEPAKVAKCIESLKNNCNLPI 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RIGVD++     L   VK +  +G     +HARKAILKGL+PK NR IP L YD+V
Sbjct: 140 TIKHRIGVDEEDSFDQLNTFVKEVANAGAERFTVHARKAILKGLNPKQNRTIPPLRYDVV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++K+ NP L I +NGG  ++ Q +K L  +DGVMIGR+ YK     + +D         
Sbjct: 200 QKLKENNPQLLIEINGGFTNIDQCIKALERLDGVMIGRSVYKYPLRWSQIDNKIYGKNIT 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S             +I  S+  Y   HL +GGK   I +H+I L  G PN++  R+ ++ 
Sbjct: 260 SKSAS---------EIIFSLIPYIENHLQNGGKTWDICKHLINLVEGIPNAKIWRNQISS 310

Query: 300 EAGASTATHHII 311
            +     +   +
Sbjct: 311 RSIKQELSIDAL 322


>gi|221066936|ref|ZP_03543041.1| TIM-barrel protein, yjbN family [Comamonas testosteroni KF-1]
 gi|220711959|gb|EED67327.1| TIM-barrel protein, yjbN family [Comamonas testosteroni KF-1]
          Length = 322

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 123/314 (39%), Positives = 184/314 (58%), Gaps = 8/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RLL+ + LLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 1   MMDWTDKHCRYFHRLLSQHTLLYTEMVTTGALVHGDVARHLRFEAEEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++   +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   +S+PVT
Sbjct: 61  DLAHSARLGVQWGYDEINLNCGCPSERVQRGAFGACLMNEAALVADCVKAMADVVSVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G +   +HAR A LKGLSPK+NR+IP L Y++V 
Sbjct: 121 VKHRIGIDKIESYDFVRDFVGTVADAGCHVFVVHARNAWLKGLSPKENREIPPLRYEVVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  VDGVM+GR AY N   + + D  +    +  
Sbjct: 181 QLKRDFPGLTIAVNGGIKTDDVVQQQLQQVDGVMVGREAYHNPWWMASWDALYYQDES-- 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + R  +    ++   M   A  H   G     I RHM+GL +G   +RR R + +  
Sbjct: 239 ---RERTREGIEEQMVLYMEREAREH---GTHWYSIARHMLGLRNGLAGARRWRQVWSDH 292

Query: 301 AGASTATHHIIETA 314
                  H +++ A
Sbjct: 293 RLKPLPPHEVMKLA 306


>gi|264678472|ref|YP_003278379.1| TIM-barrel protein, yjbN family [Comamonas testosteroni CNB-2]
 gi|262208985|gb|ACY33083.1| TIM-barrel protein, yjbN family [Comamonas testosteroni CNB-2]
          Length = 344

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 124/314 (39%), Positives = 185/314 (58%), Gaps = 8/314 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+F RLL+ + LLYTEM+   A++ GD    L F  +E P+ALQ+GG++ +
Sbjct: 23  MMDWTDKHCRYFHRLLSQHTLLYTEMVTTGALVHGDVARHLRFEAEEHPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ E +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   +S+PVT
Sbjct: 83  DLAHSARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEAALVADCVKAMADVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y++V 
Sbjct: 143 VKHRIGIDKIESYDFVRDFVGTVADAGCQVFVVHARNAWLKGLSPKENREIPPLRYEVVA 202

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG++      + L  VDGVM+GR AY N   + + D  +    +  
Sbjct: 203 QLKRDFPGLTIAVNGGIKTDDVVQQQLQQVDGVMVGREAYHNPWWMASWDVLYYQDES-- 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
              + R  +    ++   M   A  H   G     I RHM+GL +G   +RR R + +  
Sbjct: 261 ---RERTREQIEEQMVLYMEREAREH---GTHWYSIARHMLGLRNGLAGARRWRQVWSDH 314

Query: 301 AGASTATHHIIETA 314
              +   H +++ A
Sbjct: 315 RLKTLPAHEVMKLA 328


>gi|87123334|ref|ZP_01079185.1| uncharacterized protein family protein [Synechococcus sp. RS9917]
 gi|86169054|gb|EAQ70310.1| uncharacterized protein family protein [Synechococcus sp. RS9917]
          Length = 334

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 128/322 (39%), Positives = 177/322 (54%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+V  A+   +++  +L F   E PLALQ+GG D 
Sbjct: 20  MLDCTDRHFRMLMRQISRRALLYSEMVVVQALHHSERRERLLDFDPMEHPLALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L EA ++  D+GY+EINLNVGCPS RV  G+FGACLM  PD V  C+ AM +A  +PV
Sbjct: 80  ALLAEATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPDTVARCVEAMVRASPLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L+  V  +  +G +   +HARKA L GL PK NR IP L YD V
Sbjct: 140 TVKHRVGIDDLDSDALLQAFVDRLADAGASRFAVHARKAWLDGLDPKQNRTIPPLQYDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P+L I LNGGL+     L+ L   DG M+GRA Y +    T +D         
Sbjct: 200 IALKRRRPELLIELNGGLDTPDDCLEALQHCDGAMVGRAVYAHPLRWTAIDALIYGDPAR 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S              +   +  +A RHL  GG+L  + RH++ L  G P +R  R  L  
Sbjct: 260 SISAAG---------VVRGLLPHAERHLQRGGRLWDLGRHLVHLVEGVPGARHWRRDLGQ 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   +++ A   +  +
Sbjct: 311 NAQRKGADLSVLDDAARQLEAA 332


>gi|171058412|ref|YP_001790761.1| tRNA-dihydrouridine synthase A [Leptothrix cholodnii SP-6]
 gi|170775857|gb|ACB33996.1| TIM-barrel protein, yjbN family [Leptothrix cholodnii SP-6]
          Length = 342

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 122/303 (40%), Positives = 171/303 (56%), Gaps = 9/303 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLLT    LYTEM+   A+L GD+   L F   E P+ALQ+GG+D +
Sbjct: 24  MLDWTDRHCRHFHRLLTRRTRLYTEMVTTGALLHGDQARHLDFDAIEHPVALQLGGSDPA 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ + +GY+E+NLN GCPS RV +G+FGACLM  P +V D + AM  A+ +PVT
Sbjct: 84  DLAACARLAQRWGYDEVNLNCGCPSERVQKGAFGACLMAEPALVADGVKAMRDAVDVPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A L+GLSPK+NR IP L Y+ VY
Sbjct: 144 VKHRIGIDRGESYDFVRDFVGTLADAGCEVFIVHARNAWLQGLSPKENRDIPPLRYEQVY 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ P L I +NGG+    +    L  VDGVM+GR AY     +   D  F      +
Sbjct: 204 QLKRDFPQLTIVINGGIRTDDEIAAHLAHVDGVMVGRQAYHEPWQMAGWDLRFFGE---A 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P   R       ++ A+  DY       G    Q  RH +GL++G   +R  R   +  
Sbjct: 261 APAGERA------QVEAAWMDYLQAQHLGGRPWPQAMRHALGLWNGVAGARSWRQFWSDH 314

Query: 301 AGA 303
              
Sbjct: 315 HHK 317


>gi|285017064|ref|YP_003374775.1| tRNA-dihydrouridine synthase a protein [Xanthomonas albilineans GPE
           PC73]
 gi|283472282|emb|CBA14788.1| probable trna-dihydrouridine synthase a protein [Xanthomonas
           albilineans]
          Length = 328

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 138/317 (43%), Positives = 190/317 (59%), Gaps = 11/317 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL  +A LYTEM+ A+A++ GD+  +L +   E PLALQ+GG+D +
Sbjct: 14  MMDWTDRHCRVFHRLLAPSARLYTEMVHANAVVLGDRARLLDYDAAEHPLALQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I +D+GY+EINLN GCPS RV  G FGACLM  P +V +C+AAM  A+ +PVT
Sbjct: 74  LLAQAARIGQDWGYDEINLNCGCPSDRVQAGRFGACLMREPGLVAECVAAMAAAVDVPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVD      A    V  +  +G     +HAR A L+GLSPK+NR++P L YD VY
Sbjct: 134 VKCRLGVDQDNDEAAFLAFVDHVAAAGCRQFVVHARNAWLQGLSPKENREVPPLRYDWVY 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P L + LNGGL ++  A      VDGVM+GRAAY +  +L  +D   +      
Sbjct: 194 RLKRERPQLQVVLNGGLANVETAQAQFVVVDGVMLGRAAYHDPYVLHRLDAALTGAALRP 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++  ++  Y    L  G  L+ I RH++GLFHG P  R  R +L+  
Sbjct: 254 R-----------AELLRALRPYVEVRLAEGLALKHIARHLLGLFHGQPGGRAFRQVLSEG 302

Query: 301 AGASTATHHIIETAFNL 317
           A  S A   ++E A  +
Sbjct: 303 AHRSGADWALLEQALQV 319


>gi|254805616|ref|YP_003083837.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha14]
 gi|254669158|emb|CBA07852.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha14]
          Length = 336

 Score =  308 bits (789), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 186/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|332974563|gb|EGK11483.1| tRNA dihydrouridine synthase A [Kingella kingae ATCC 23330]
          Length = 357

 Score =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 134/324 (41%), Positives = 191/324 (58%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR  AR +T +  LYTEMI A AI+ GD    L  +  E P+ALQ+GG++ +
Sbjct: 34  MLDWTDRHYRHMARQITRHTWLYTEMINAGAIVYGDPDRFLQRNECENPVALQLGGSEPT 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
            L +AA+    + Y+EINLN GCPS RV +G+FGACLML+ ++V DC+ AM  A+  IP+
Sbjct: 94  LLAQAAQKAAQYSYDEINLNCGCPSPRVQKGAFGACLMLDVNLVADCLNAMQDAVPAIPI 153

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K RIG+D Q     L + V S+  K+      +HAR A L GLSPK+NR+IP L YD 
Sbjct: 154 TIKHRIGIDKQTEYQPLADFVGSLHDKTACRTFIVHARNAWLDGLSPKENREIPPLRYDF 213

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E PDL I +NGG++  +Q  + L  VDGVM+GR AY N  ++   D  F     
Sbjct: 214 VYRLKQEFPDLEIIINGGVQTNTQIAEHLQHVDGVMMGREAYHNPYIMHDWDTLFYGE-- 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            + P  TR       +I+  + +YA + L    G  L+ + RH +GL HG   ++  R +
Sbjct: 272 -TQPAPTR------EQITQQLYNYATQQLSRQQGTILRHMVRHYLGLTHGLNGAKIWRRM 324

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           L+           +I  A+  + +
Sbjct: 325 LSDADLLRDNRPELILEAWQQVEK 348


>gi|332528538|ref|ZP_08404526.1| tRNA-dihydrouridine synthase A [Hylemonella gracilis ATCC 19624]
 gi|332042049|gb|EGI78387.1| tRNA-dihydrouridine synthase A [Hylemonella gracilis ATCC 19624]
          Length = 339

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 131/343 (38%), Positives = 181/343 (52%), Gaps = 31/343 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  A LYTEMI   A+L GD    L F   E P+ALQ+GG++ +
Sbjct: 1   MIDWTDRHCRYFHRLLSRRARLYTEMITTGALLHGDVARHLRFDDAEHPVALQLGGSEPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----S 116
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  AL     
Sbjct: 61  DLAACARLGEQWGYDEINLNCGCPSERVQRGAFGACLMAEPQLVADCVKAMRDALQNPER 120

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVTVK R+G+D       +R+ V ++ ++G     +HAR A L+GLSPK+NR+IP L Y
Sbjct: 121 VPVTVKHRVGIDRVERYDFVRDFVGTVAEAGCTTFIVHARNAWLQGLSPKENREIPPLRY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV-----------------DGVMIGRAA 219
           + V+ +K++ P L + +NGGL   +Q L+ L                    DG MIGR A
Sbjct: 181 EFVHRLKRDFPSLKVVINGGLTSDAQVLEQLQGADSPQAAADQAGGGPVPLDGAMIGREA 240

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR-HLHSGGKLQQITR 278
           Y N   L + D  +      ++             I   M DY  R     G     I R
Sbjct: 241 YHNPWWLASWDRLYFGEPGSAA---------TREDIEERMVDYMLRMQAEEGLGWYGIAR 291

Query: 279 HMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           HM+GL HG P +RR R + +           ++  A   +  +
Sbjct: 292 HMLGLRHGLPGARRWRQVWSDHRLKGEDPRQVMALAHQGVERA 334


>gi|311105398|ref|YP_003978251.1| tRNA-dihydrouridine synthase A [Achromobacter xylosoxidans A8]
 gi|310760087|gb|ADP15536.1| tRNA-dihydrouridine synthase A [Achromobacter xylosoxidans A8]
          Length = 326

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 132/316 (41%), Positives = 188/316 (59%), Gaps = 10/316 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH RFF RLL   A LYTEMI   A+L G+ +  L F   E P+ALQ+GG++  
Sbjct: 1   MIDVTDRHCRFFHRLLAPRARLYTEMITTGALLHGNVERHLDFDEAEHPVALQLGGSEPD 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ + +GY+EINLN GCPS RV +G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 61  ALAHSARLGKKWGYDEINLNCGCPSERVQKGAFGACLMAEPALVADCMKAMQDAVDIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  +  +G      HAR A+LKGL+PKDNR+IP L Y++V 
Sbjct: 121 VKHRLGLDYDESYEFVRDFVGKVYDTGCRVFIAHARNAVLKGLTPKDNREIPPLRYEVVR 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD    LNGGL D  Q+++     DGVM+GRAA+    +L+ V       L   
Sbjct: 181 QLKRDFPDCTFVLNGGLADAGQSVRAAGDFDGVMLGRAAWHTPRVLSEVSLQLWPSLRLP 240

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            ++  +M +YAAR +  G  L+ +TR M+GL +G   +RR R +L+  
Sbjct: 241 SDA----------QVVDAMMEYAARQVAVGVPLRVMTRPMLGLVNGQSGARRWRRMLSDP 290

Query: 301 AGASTATHHIIETAFN 316
           A  +     +I  A+ 
Sbjct: 291 ALLAANNPELIYDAWR 306


>gi|302390600|ref|YP_003826421.1| tRNA-U20-dihydrouridine synthase [Thermosediminibacter oceani DSM
           16646]
 gi|302201228|gb|ADL08798.1| tRNA-U20-dihydrouridine synthase [Thermosediminibacter oceani DSM
           16646]
          Length = 340

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 134/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L    ++ TEM+    I   D K   +L     E P+ +Q+ G D
Sbjct: 28  MAGITDLPFRTICKEL-GADVVITEMVSTRGIYYNDSKTAALLTIDPCEHPIGVQLFGND 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                 A K +ED  ++ IN+N+GCP+ ++ +   G  LM +P++ G  I A  KA   P
Sbjct: 87  PEFFAHAVKKIEDIPFDFININMGCPTPKIVKNGDGCALMKDPELAGKIIEATAKASDRP 146

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+           +  ++SG   + IH R         ++       D+DI
Sbjct: 147 VTVKIRKGWDEDSANAV--EFSRMAQESGAAMVIIHGRT--------REQFYSGKADWDI 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     A K+L     DGVM+GR A  N  +   +  +    
Sbjct: 197 IRRVK-EAVSIPVIGNGDVFSAQDAAKMLEYTGCDGVMVGRGALGNPFIFREIKHFLKTG 255

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +  ++ +  ++  +  R       + ++ +H+     G P+S   +  
Sbjct: 256 EKLPPPALEEKKEVIFKHLDMALEFHGER-----VGILEMRKHIAWYLKGLPHSSAVKQK 310

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A    + +++  F  +
Sbjct: 311 IQQSKHADEIKY-LLDEYFRKL 331


>gi|113955552|ref|YP_729254.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9311]
 gi|113882903|gb|ABI47861.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9311]
          Length = 334

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 126/322 (39%), Positives = 181/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  +LLY+EM+VA A+    ++  +L F  +E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRMLMRQISKQSLLYSEMVVAQALHHSKRRERLLDFDAEEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +A ++  D+GY+EINLNVGCPS RV  G+FGACLM  P  V  C+ AM  A S+PV
Sbjct: 80  ALLADATRMAADWGYDEINLNVGCPSPRVQAGNFGACLMAEPQTVARCVEAMVAASSLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      LR  V  + ++G     +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRVGIDDLDSDDLLRQFVDQVAEAGALRFSVHARKAWLEGLDPKQNRTIPALQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P L I LNGGL+     L  L   DG M+GRAAY +      +D         
Sbjct: 200 IALKESRPALTIELNGGLDTPEDCLNALKHCDGAMVGRAAYAHPLRWREIDSLIYGAAPR 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                    +     +   +  +A RHL  GG+L  + RH++ +    P +R  R+ L+ 
Sbjct: 260 ---------QVLASDVVLGLIPHAERHLQRGGRLWDLCRHLVQVVEAVPGARYWRNNLST 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A  + A   IIE A   ++++
Sbjct: 311 KAQRAGAGIEIIEEAAQQLLDA 332


>gi|319411177|emb|CBY91582.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis WUE 2594]
          Length = 336

 Score =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 186/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQTQIQAGCGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|121635516|ref|YP_975761.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis FAM18]
 gi|120867222|emb|CAM10991.1| conserved hypothetical protein [Neisseria meningitidis FAM18]
 gi|325132903|gb|EGC55580.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M6190]
 gi|325143034|gb|EGC65386.1| tRNA dihydrouridine synthase A [Neisseria meningitidis 961-5945]
 gi|325145143|gb|EGC67425.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M01-240013]
 gi|325198962|gb|ADY94418.1| tRNA dihydrouridine synthase A [Neisseria meningitidis G2136]
          Length = 336

 Score =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 186/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|269213818|ref|ZP_05982915.2| tRNA dihydrouridine synthase A [Neisseria cinerea ATCC 14685]
 gi|269145448|gb|EEZ71866.1| tRNA dihydrouridine synthase A [Neisseria cinerea ATCC 14685]
          Length = 319

 Score =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 188/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ + AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 1   MLDWTDRHYRYLARQITRNTWLYSEMVNSGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 61  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVMLVADCLNAMQDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 121 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 181 YRLKQEFPDLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 239 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 291

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 292 SDATLLKDNDGSLILEAWKEVERA 315


>gi|254670181|emb|CBA05275.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha153]
 gi|325138888|gb|EGC61438.1| tRNA dihydrouridine synthase A [Neisseria meningitidis ES14902]
          Length = 336

 Score =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 187/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|261391873|emb|CAX49332.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis 8013]
          Length = 336

 Score =  305 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 186/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQCLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDAMLLKDNDGGLILEAWEEVERA 332


>gi|15676263|ref|NP_273397.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis MC58]
 gi|7225569|gb|AAF40791.1| conserved hypothetical protein [Neisseria meningitidis MC58]
 gi|316984353|gb|EFV63327.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis H44/76]
 gi|325140997|gb|EGC63503.1| tRNA dihydrouridine synthase A [Neisseria meningitidis CU385]
 gi|325199542|gb|ADY94997.1| tRNA dihydrouridine synthase A [Neisseria meningitidis H44/76]
          Length = 336

 Score =  305 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 186/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYLARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|121607273|ref|YP_995080.1| tRNA-dihydrouridine synthase A [Verminephrobacter eiseniae EF01-2]
 gi|121551913|gb|ABM56062.1| TIM-barrel protein, yjbN family [Verminephrobacter eiseniae EF01-2]
          Length = 360

 Score =  305 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 126/320 (39%), Positives = 176/320 (55%), Gaps = 10/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLLT    LYTEM+ A A+L G  +  L  + +E P+ALQ+GG + +
Sbjct: 37  MMDWTDRHCRYFHRLLTRQTRLYTEMVNAGAVLHGGTERHLRLNAEEHPVALQLGGNEPA 96

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++   +GY+EINLN GCPS RV  G+FGA LM  P  V DC+ AM   +  PVT
Sbjct: 97  DLARAARLGAQWGYDEINLNCGCPSDRVQRGAFGARLMQTPQRVADCVKAMRDMVDRPVT 156

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  +  +G +   +HAR A L+GLSPK+NR+IP L Y +V+
Sbjct: 157 VKHRIGIDQGQSYGFVRDFVGVVADAGCSVFIVHARNAWLQGLSPKENREIPPLRYALVH 216

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS----NP 236
           ++K + P L + +NGG+   +   + L  +DGVM+GR AY     L   D  +      P
Sbjct: 217 QLKADFPRLTVVINGGIATDAVVQQQLHLLDGVMVGRQAYHQPWWLARWDALYYANRSGP 276

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             G+SP+     +   R + A M   AA H   G     I RHM+GL H  P +R  R +
Sbjct: 277 CAGASPLTREAVE---RAMVAYMEREAALH---GTPWPHIARHMLGLRHSLPGARLWRQL 330

Query: 297 LTVEAGASTATHHIIETAFN 316
            +           +   A  
Sbjct: 331 WSDHRLKDRPAREVHALALR 350


>gi|325205425|gb|ADZ00878.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M04-240196]
          Length = 336

 Score =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 133/324 (41%), Positives = 182/324 (56%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 258 P---------IGYADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|325130878|gb|EGC53608.1| tRNA dihydrouridine synthase A [Neisseria meningitidis OX99.30304]
          Length = 336

 Score =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E PDL I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPDLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YSDLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|221134737|ref|ZP_03561040.1| tRNA-dihydrouridine synthase A [Glaciecola sp. HTCC2999]
          Length = 305

 Score =  305 bits (781), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 114/296 (38%), Positives = 170/296 (57%), Gaps = 4/296 (1%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G   + LGF+  E+P+ALQ+GG+    +   A   +++GY+E+N+NVGCPS
Sbjct: 1   MVTTGAIIFGKG-DYLGFNAAEQPVALQLGGSVPEDMTHCAIKAQEYGYDEVNINVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM  P  V DC++AM   + IPVTVK RIG+DD      L   ++ + +
Sbjct: 60  DRVQNGRFGACLMAEPQTVADCVSAMQAQVDIPVTVKSRIGIDDMDEYEDLSAFIEQVAE 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G +   +HARKA L+GLSPK NR++P L Y+ VY++K+E P L + +NGG++ +++A  
Sbjct: 120 AGCDTFIVHARKAWLQGLSPKQNREVPPLMYERVYQLKEEFPHLHVSINGGVKTLAEAQH 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVMIGR AY N  +L+ VD         +   +  + K     I   +   A  
Sbjct: 180 HLSYVDGVMIGREAYSNPYILSEVDHLIYGD-NQAVLSRIEIVKRMHSYIVEQLA--APN 236

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
               G K+  I RHM+GLF G P  R  R  L+  A     +  ++  A + ++E+
Sbjct: 237 QFGQGTKVWHIVRHMLGLFQGQPGGRVWRRYLSENAVGRNTSPDVLFAALDALLET 292


>gi|254671973|emb|CBA04409.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis alpha275]
 gi|325202832|gb|ADY98286.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M01-240149]
 gi|325208825|gb|ADZ04277.1| tRNA dihydrouridine synthase A [Neisseria meningitidis NZ-05/33]
          Length = 336

 Score =  304 bits (780), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+    +  + L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEEIAQHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGGLILEAWKEVERA 332


>gi|270160148|ref|ZP_06188804.1| tRNA-dihydrouridine synthase A [Legionella longbeachae D-4968]
 gi|269988487|gb|EEZ94742.1| tRNA-dihydrouridine synthase A [Legionella longbeachae D-4968]
          Length = 316

 Score =  304 bits (780), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 124/320 (38%), Positives = 179/320 (55%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  H+R F R+L  NALLYTEM    A+     ++ L F+ +E PLALQ+GG++ +
Sbjct: 1   MIDWTYSHFRVFMRILAPNALLYTEMQTTGAVCNNPIRS-LQFNRKEHPLALQLGGSEPN 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+  E  GY+EIN+N+GCPS +V  G+FGACLM  P+ VGDCI AM +A++IPVT
Sbjct: 60  LLAQCARRAEQEGYDEININLGCPSDKVQAGNFGACLMKEPEKVGDCIRAMREAVNIPVT 119

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIGVD Q       N V  + ++G   I +HARKA L+GL+PK NR IP + YD VY
Sbjct: 120 AKTRIGVDHQDSYEFFSNFVHQLVEAGAQKIIVHARKAWLQGLNPKQNRTIPPVHYDYVY 179

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PD+ I +NG + ++++  + L  VDGVM+GR A  N   + TV       +T  
Sbjct: 180 RLKKEIPDIPIVINGNILNLNEINEHLNYVDGVMLGRLACDNPFQIATVHHGLYPEITKR 239

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            +I     +Y     + G  L  + + +  L  G P + + +  L   
Sbjct: 240 S----------RSQIFNDYLEYLLDEFYKGVSLSLLIKPIFNLGFGLPGASQWKRKLME- 288

Query: 301 AGASTATHHIIETAFNLMIE 320
               T   ++ E     ++E
Sbjct: 289 -ILQTKNIYLFEQLSQYLLE 307


>gi|161870721|ref|YP_001599894.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis 053442]
 gi|161596274|gb|ABX73934.1| conserved hypothetical protein [Neisseria meningitidis 053442]
          Length = 336

 Score =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 135/321 (42%), Positives = 186/321 (57%), Gaps = 12/321 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGVTTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLM 318
           +           +I  A+  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEV 329


>gi|218768876|ref|YP_002343388.1| tRNA-dihydrouridine synthase A [Neisseria meningitidis Z2491]
 gi|121052884|emb|CAM09236.1| conserved hypothetical protein [Neisseria meningitidis Z2491]
          Length = 336

 Score =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 132/324 (40%), Positives = 183/324 (56%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 258 P---------IGYADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|89068926|ref|ZP_01156308.1| tRNA-dihydrouridine synthase A [Oceanicola granulosus HTCC2516]
 gi|89045507|gb|EAR51571.1| tRNA-dihydrouridine synthase A [Oceanicola granulosus HTCC2516]
          Length = 319

 Score =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 143/324 (44%), Positives = 195/324 (60%), Gaps = 13/324 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+  ALLYTEM+ A A++RG   ++L     E P+ALQ+GG+D +
Sbjct: 1   MMDWTDRHCRYFHRLLSREALLYTEMVTAPALVRGGAVHLLEHDPAEHPVALQLGGSDPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA++    GY+EINLN GCPS RV  G+FGA LM  P+ V +C AAM  A    VT
Sbjct: 61  ELAEAARLGAAAGYDEINLNCGCPSDRVQSGTFGAVLMNAPERVAECCAAMIGAQPREVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q+P   L   ++++  +GV  + IHARKA L+GLSPK+NR +P LDYD+V 
Sbjct: 121 VKCRIGVDEQVPEEVLPRFLEAVAAAGVRRVAIHARKAWLQGLSPKENRDVPPLDYDLVV 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +K   P L I +NGG+  +  A  +L   +DG M+GRAAY    A+L   D        
Sbjct: 181 AMKAAFPGLHISINGGIATLDAARALLARGLDGAMVGRAAYHEPAAILLPADAAIFG--- 237

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHL-HSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                  R  +      + +M  Y  RHL   GG+L Q+TRHM+GLF G P +R  R  L
Sbjct: 238 -------RASEMTAEDAALAMLPYIERHLAGEGGRLIQVTRHMLGLFAGRPGARAWRRHL 290

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +       A   ++E A  L+ ++
Sbjct: 291 SENGTRPGAGPEVVEAALALVRQA 314


>gi|289165076|ref|YP_003455214.1| tRNA-dihydrouridine synthase A [Legionella longbeachae NSW150]
 gi|288858249|emb|CBJ12117.1| tRNA-dihydrouridine synthase A [Legionella longbeachae NSW150]
          Length = 329

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 124/320 (38%), Positives = 179/320 (55%), Gaps = 13/320 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT  H+R F R+L  NALLYTEM    A+     ++ L F+ +E PLALQ+GG++ +
Sbjct: 14  MIDWTYSHFRVFMRILAPNALLYTEMQTTGAVCNNPIRS-LQFNRKEHPLALQLGGSEPN 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L + A+  E  GY+EIN+N+GCPS +V  G+FGACLM  P+ VGDCI AM +A++IPVT
Sbjct: 73  LLAQCARRAEQEGYDEININLGCPSDKVQAGNFGACLMKEPEKVGDCIRAMREAVNIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIGVD Q       N V  + ++G   I +HARKA L+GL+PK NR IP + YD VY
Sbjct: 133 AKTRIGVDHQDSYEFFSNFVHQLVEAGAQKIIVHARKAWLQGLNPKQNRTIPPVHYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +KKE PD+ I +NG + ++++  + L  VDGVM+GR A  N   + TV       +T  
Sbjct: 193 RLKKEIPDIPIVINGNILNLNEINEHLNYVDGVMLGRLACDNPFQIATVHHGLYPEITKR 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            +I     +Y     + G  L  + + +  L  G P + + +  L   
Sbjct: 253 S----------RSQIFNDYLEYLLDEFYKGVSLSLLIKPIFNLGFGLPGASQWKRKLME- 301

Query: 301 AGASTATHHIIETAFNLMIE 320
               T   ++ E     ++E
Sbjct: 302 -ILQTKNIYLFEQLSQYLLE 320


>gi|326577440|gb|EGE27324.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis O35E]
          Length = 321

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 120/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 11  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 70

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 71  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 130

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 131 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 191 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 250 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 298


>gi|326572785|gb|EGE22771.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis BC7]
          Length = 322

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 120/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRMTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 250

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 251 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|261401825|ref|ZP_05987950.1| tRNA dihydrouridine synthase A [Neisseria lactamica ATCC 23970]
 gi|269208032|gb|EEZ74487.1| tRNA dihydrouridine synthase A [Neisseria lactamica ATCC 23970]
          Length = 336

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 136/324 (41%), Positives = 188/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM +A+ IPVT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQEAVGIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDAMLLKDNDGSLILEAWKEVERA 332


>gi|126701180|ref|YP_001090077.1| tRNA-dihydrouridine synthase [Clostridium difficile 630]
 gi|254977180|ref|ZP_05273652.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-66c26]
 gi|255094510|ref|ZP_05323988.1| tRNA-dihydrouridine synthase [Clostridium difficile CIP 107932]
 gi|255102766|ref|ZP_05331743.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-63q42]
 gi|255308587|ref|ZP_05352758.1| tRNA-dihydrouridine synthase [Clostridium difficile ATCC 43255]
 gi|255316261|ref|ZP_05357844.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-76w55]
 gi|255518922|ref|ZP_05386598.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-97b34]
 gi|255652101|ref|ZP_05399003.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-37x79]
 gi|260685074|ref|YP_003216359.1| tRNA-dihydrouridine synthase [Clostridium difficile CD196]
 gi|260688732|ref|YP_003219866.1| tRNA-dihydrouridine synthase [Clostridium difficile R20291]
 gi|306521835|ref|ZP_07408182.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-32g58]
 gi|115252617|emb|CAJ70460.1| transfer RNA-dihydrouridine synthase [Clostridium difficile]
 gi|260211237|emb|CBA66759.1| tRNA-dihydrouridine synthase [Clostridium difficile CD196]
 gi|260214749|emb|CBE07441.1| tRNA-dihydrouridine synthase [Clostridium difficile R20291]
          Length = 322

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 141/326 (43%), Gaps = 25/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LLYTEMI   A+   D   K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKE-QGCGLLYTEMINGKALCYDDENTKKMLKIEEEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I+ D+    +++N+GCP+ +V +   G+ LM NP +  + + A+ K    P
Sbjct: 76  PEFMGRAAEIMNDYSNEILDINMGCPAPKVVKNGDGSALMKNPKLAEEVLRAVVKNSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G++ + IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDD--NSVNAVEIAKIAEDCGISALAIHGRT--------REQFYTGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK N  + +  NG +  +  ++ +L     D +MIGR A  N  +   ++ Y +  
Sbjct: 186 IAEIKK-NLSIPVIGNGDVFTIEDSINMLDKTGCDAIMIGRGAQGNPWIFKRINHYMNTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          + +       A         ++++ +H+     G  NS + R  
Sbjct: 245 EILPEPTLNEKISTAIKHLKL-----AVEEHGEYVAVREMRKHIAWYLKGLRNSAKLR-- 297

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
              E         ++      M +SL
Sbjct: 298 --DEINKIEDYQEVVSKLEYYMEDSL 321


>gi|261365796|ref|ZP_05978679.1| tRNA dihydrouridine synthase A [Neisseria mucosa ATCC 25996]
 gi|288565649|gb|EFC87209.1| tRNA dihydrouridine synthase A [Neisseria mucosa ATCC 25996]
          Length = 334

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ + AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 16  MLDWTDRHYRYLARQITRNTWLYSEMVNSGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 76  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVMLVADCLNAMQDAVQIPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD QI    + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 136 VKHRIGVDRQIEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 196 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 253

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 254 RSPIE-------YADLVQRLYTYSQTQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 306

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 307 SDATLLKDNDGSLILEAWKEVERA 330


>gi|326559961|gb|EGE10359.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 46P47B1]
          Length = 322

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 121/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P IV D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQIVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 250

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 251 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|255657504|ref|ZP_05402913.1| tRNA-dihydrouridine synthase [Clostridium difficile QCD-23m63]
 gi|296452824|ref|ZP_06894511.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP08]
 gi|296879924|ref|ZP_06903896.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP07]
 gi|296258372|gb|EFH05280.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP08]
 gi|296429038|gb|EFH14913.1| tRNA-dihydrouridine synthase [Clostridium difficile NAP07]
          Length = 322

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 141/326 (43%), Gaps = 25/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LLYTEMI   A+   D   K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKE-QGCGLLYTEMINGKALCYDDENTKKMLKIEDEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I+ D+    +++N+GCP+ +V +   G+ LM NP +  + + A+ K    P
Sbjct: 76  PEFMGRAAEIMNDYSNEILDINMGCPAPKVVKNGDGSALMKNPKLAEEVLRAVVKNSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G++ + IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDD--NSVNAVEIAKIAEDCGISALAIHGRT--------REQFYTGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK N  + +  NG +  +  ++ +L     D +MIGR A  N  +   ++ Y +  
Sbjct: 186 IAEIKK-NLSIPVIGNGDVFTIEDSINMLDKTGCDAIMIGRGAQGNPWIFKRINHYMNTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          + +       A         ++++ +H+     G  NS + R  
Sbjct: 245 EILPEPTLNEKISTAIKHLKL-----AVEEHGEYVAVREMRKHIAWYLKGLRNSAKLR-- 297

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
              E         ++      M +SL
Sbjct: 298 --DEINKIEDYQEVVSKLEYYMEDSL 321


>gi|326566665|gb|EGE16806.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 12P80B1]
 gi|326569455|gb|EGE19515.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis BC8]
          Length = 322

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 120/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 250

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 251 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|239626632|ref|ZP_04669663.1| TIM-barrel protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516778|gb|EEQ56644.1| TIM-barrel protein [Clostridiales bacterium 1_7_47FAA]
          Length = 328

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 76/309 (24%), Positives = 132/309 (42%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R       + TEM+ A AIL  ++  K ++    QE+P A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGAGCVVTEMVSAKAILYNNRNTKELMQIHPQERPAAIQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +ED  Y+ I++N+GCP  ++     G+ LM NP++    ++AM KA+  P
Sbjct: 78  PDIMAQIAARIEDGPYDFIDVNMGCPVPKIVNNGEGSALMKNPELAEKILSAMVKAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D    V      K  + SGV  + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFNDT--CVNAVEFAKMAEASGVAAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A +++     DG+M+ R A  N  +   +  Y    
Sbjct: 188 IRQVK-EAVKIPVIGNGDIFTPQDAGRMMEETGCDGIMVARGAKGNPWIFRRISHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R          A +      ++++  H+     G P+S   R+ 
Sbjct: 247 EILPGPSIEEIQAMILRH-----GHMLAEYKGEQTAMREMRGHVAWYTKGMPHSAALRNE 301

Query: 297 LTVEAGAST 305
           +        
Sbjct: 302 INQVETLKG 310


>gi|326561145|gb|EGE11510.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 7169]
          Length = 322

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 124/300 (41%), Positives = 169/300 (56%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++     Y    L 
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC--YL---LW 246

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           GS P          R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 247 GSQPPS-------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|33596533|ref|NP_884176.1| tRNA-dihydrouridine synthase A [Bordetella parapertussis 12822]
 gi|33566302|emb|CAE37215.1| conserved hypothetical protein [Bordetella parapertussis]
          Length = 337

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 131/318 (41%), Positives = 184/318 (57%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGDVARHLDFDAAEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 73  ALAQAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPGLVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYDESYGFVRDFVGQIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAR 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD  I LNGGL D   A  +    DGVM+GRAA+    +L+ V   +   +   
Sbjct: 193 QLKRDFPDCVIVLNGGLADAQAARAVAGEFDGVMLGRAAWHTPRVLSEVSLQWWPAIRLP 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            ++  +M  YAA  +  G  L+ +TR ++GL +G   +RR R +L+  
Sbjct: 253 SDA----------QVVDAMMQYAATQIARGVPLRVMTRPLLGLVNGQAGARRWRRLLSDP 302

Query: 301 AGASTATHHIIETAFNLM 318
              +     ++  A+  +
Sbjct: 303 VRLAANDPSLLYEAWRSL 320


>gi|33601086|ref|NP_888646.1| tRNA-dihydrouridine synthase A [Bordetella bronchiseptica RB50]
 gi|33575521|emb|CAE32599.1| conserved hypothetical protein [Bordetella bronchiseptica RB50]
          Length = 337

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 131/318 (41%), Positives = 184/318 (57%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGDVARHLDFDAAEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 73  ALAQAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPGLVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYDESYGFVRDFVGQIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAR 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD  I LNGGL D   A  +    DGVM+GRAA+    +L+ V   +   +   
Sbjct: 193 QLKRDFPDCVIVLNGGLADAQAARAVAGEFDGVMLGRAAWHTPRVLSEVSLQWWPAIRLP 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            ++  +M  YAA  +  G  L+ +TR ++GL +G   +RR R +L+  
Sbjct: 253 SDA----------QVVDAMMQYAATQIARGVPLRVMTRPLLGLVNGQAGARRWRRLLSDP 302

Query: 301 AGASTATHHIIETAFNLM 318
              +     ++  A+  +
Sbjct: 303 VRLAANDPSLLYEAWRSL 320


>gi|296112920|ref|YP_003626858.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis RH4]
 gi|295920614|gb|ADG60965.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis RH4]
 gi|326567964|gb|EGE18061.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis BC1]
          Length = 322

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 120/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIKTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 250

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 251 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|303256981|ref|ZP_07342995.1| tRNA-dihydrouridine synthase A [Burkholderiales bacterium 1_1_47]
 gi|330999169|ref|ZP_08322888.1| tRNA dihydrouridine synthase A [Parasutterella excrementihominis
           YIT 11859]
 gi|302860472|gb|EFL83549.1| tRNA-dihydrouridine synthase A [Burkholderiales bacterium 1_1_47]
 gi|329575369|gb|EGG56913.1| tRNA dihydrouridine synthase A [Parasutterella excrementihominis
           YIT 11859]
          Length = 343

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 127/315 (40%), Positives = 179/315 (56%), Gaps = 9/315 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL++ A LYTEM+   A++ GD  + L FS  E  +ALQ+GG+D  
Sbjct: 18  MLDLTDRHCRYFHRLLSHRARLYTEMVTTGALVHGDVPHHLDFSEAEHRVALQLGGSDPK 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ + +GY+E+NLN GCPS RV +GSFGACLM  P +V DC+ AM  A  +PVT
Sbjct: 78  DLAHGAKLAQQWGYDEVNLNCGCPSERVQKGSFGACLMAEPGLVADCVKAMQDATHLPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G+D       +R+ V ++  +GV    +HAR A LKGLSPK+NR+IP L  ++VY
Sbjct: 138 IKHRVGIDANNDYGFVRDFVGTLFNAGVRVFIVHARNAWLKGLSPKENREIPPLRREVVY 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++KK+ P+  I +NG L+D+ +    L  VDGVM+GRAAY    +LT VD    N     
Sbjct: 198 QLKKDFPEAIIVINGALQDLGECEAELKHVDGVMLGRAAYYTPWLLTDVDARLYNDEHAP 257

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                        ++  +M +Y          L+   RHM GL  G   ++  R  L+  
Sbjct: 258 ---------VTRDRVIDAMEEYVRFIKPDDHSLRACCRHMHGLLTGLAGAKVWRRTLSDT 308

Query: 301 AGASTATHHIIETAF 315
           A        I   A+
Sbjct: 309 ALIREQGADIFRYAY 323


>gi|160899058|ref|YP_001564640.1| tRNA-dihydrouridine synthase A [Delftia acidovorans SPH-1]
 gi|160364642|gb|ABX36255.1| TIM-barrel protein, yjbN family [Delftia acidovorans SPH-1]
          Length = 336

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 126/322 (39%), Positives = 181/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD+H R+  RLL+ + LLYTEM+   A+L GD    L F  +E P+ALQ+GG++ S
Sbjct: 20  MMDWTDKHCRYLHRLLSRHTLLYTEMVTTGALLHGDVPRHLRFEAEEHPVALQLGGSEPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM    +V DC+ AM   + +PVT
Sbjct: 80  DLAQAARLGAQWGYDEINLNCGCPSERVQRGAFGACLMNEAPLVADCVKAMVDVVDVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V ++  +G     +HAR A LKGLSPK+NR+IP L Y+IV 
Sbjct: 140 VKHRIGIDKDESYEFVRDFVGTVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYEIVA 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I +NGG++  +    +L  VDGVM+GR AY N   L + D  +    +  
Sbjct: 200 RLKQDFPELTIAINGGIKADATVQDLLQQVDGVMVGREAYHNPWWLASWDALYYGDASVE 259

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLH-SGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              ++         I   M  Y  R     G     I RHM+GL +G   +RR R + + 
Sbjct: 260 HTRES---------IEEQMVAYMEREARTHGTHWYSIARHMLGLRNGLAGARRWRQVWSN 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
                     ++  A     E+
Sbjct: 311 HQLKQLPPSEVMRLARTKPAEA 332


>gi|319411116|emb|CBY91521.1| K05539 tRNA-dihydrouridine synthase A [Neisseria meningitidis WUE
           2594]
          Length = 338

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 132/324 (40%), Positives = 183/324 (56%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 20  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 80  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 140 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 200 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 260 P---------IGYADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 310

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 311 SDATLLKDNDGSLILEAWKEVERA 334


>gi|33592223|ref|NP_879867.1| tRNA-dihydrouridine synthase A [Bordetella pertussis Tohama I]
 gi|33571868|emb|CAE41383.1| conserved hypothetical protein [Bordetella pertussis Tohama I]
 gi|332381640|gb|AEE66487.1| tRNA-dihydrouridine synthase A [Bordetella pertussis CS]
          Length = 337

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 131/318 (41%), Positives = 184/318 (57%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L GD    L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGDVARHLDFDAAEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IPVT
Sbjct: 73  ALAQAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPALVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYDESYGFVRDFVGQIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAR 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K++ PD  I LNGGL D   A  +    DGVM+GRAA+    +L+ V   +   +   
Sbjct: 193 QLKRDFPDCVIVLNGGLADAQAAQAVAGEFDGVMLGRAAWHTPRVLSEVSLQWWPAIRLP 252

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S            ++  +M  YAA  +  G  L+ +TR ++GL +G   +RR R +L+  
Sbjct: 253 SDA----------QVVDAMMQYAATQIARGVPLRVMTRPLLGLVNGQAGARRWRRLLSDP 302

Query: 301 AGASTATHHIIETAFNLM 318
              +     ++  A+  +
Sbjct: 303 VRLAANDPSLLYEAWRSL 320


>gi|297520781|ref|ZP_06939167.1| tRNA-dihydrouridine synthase A [Escherichia coli OP50]
          Length = 261

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 117/270 (43%), Positives = 162/270 (60%), Gaps = 12/270 (4%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG+D + L + AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM  
Sbjct: 1   LGGSDPAALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRD 60

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIP 172
            +SIPVTVK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP
Sbjct: 61  VVSIPVTVKTRIGIDDQDSYEFLCDFINTVSGKGECEMFIIHARKAWLSGLSPKENREIP 120

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-E 231
            LDY  VY++K++ P L + +NGG++ + +A   L  +DGVM+GR AY+N  +L  VD E
Sbjct: 121 PLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKAHLQHMDGVMVGREAYQNPGILAAVDRE 180

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
            F +    + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R
Sbjct: 181 IFGSSDIDADPV----------AVVRAMYPYIERELSQGTYLGHITRHMLGLFQGIPGAR 230

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMIES 321
           + R  L+  A  + A  +++E A  L+ + 
Sbjct: 231 QWRRYLSENAHKAGADINVLEHALKLVADK 260


>gi|239994762|ref|ZP_04715286.1| tRNA-dihydrouridine synthase A [Alteromonas macleodii ATCC 27126]
          Length = 309

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 112/306 (36%), Positives = 174/306 (56%), Gaps = 9/306 (2%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           ++ + LLYTEM+   AI+ G   + LG++ +E P+A+Q+GG++ S + + A++ +  GY+
Sbjct: 1   MSKHTLLYTEMVTTGAIIYGKG-DYLGYNQEEHPVAVQLGGSEPSDMAKCAELSQARGYD 59

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           E+N+NVGCPS RV  GSFGACLM  P++V  C+ AM  A+ IPVTVKCRIG+DD      
Sbjct: 60  EVNINVGCPSDRVKNGSFGACLMAQPEVVASCVKAMQAAVDIPVTVKCRIGIDDMDEDED 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
               + ++  +G +   +HARKA L+GLSPK+NR+IP L+Y  V+ +K+  P+L I +NG
Sbjct: 120 FARFIDTVADAGCDTFIVHARKAWLQGLSPKENREIPPLNYPRVHRLKQARPELSISING 179

Query: 196 GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
           G++ + +  + L  VDGVM+GR  Y N  ++ TVD+             T       R+I
Sbjct: 180 GVKTLGETQQQLELVDGVMVGREVYANPYIMATVDKEIFGD--------TEAQSMSRREI 231

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
              M  Y  R      K     RH++GL+ G    R  R  L+          +++  A 
Sbjct: 232 VLKMQQYIERQDDPYFKPWHAARHILGLYQGQAGGRIWRRYLSQNGTGKNPDPNLLLNAL 291

Query: 316 NLMIES 321
           + +  +
Sbjct: 292 DAVESA 297


>gi|326577039|gb|EGE26934.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 101P30B1]
          Length = 321

 Score =  302 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 120/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 11  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 70

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 71  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 130

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 131 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 191 VYRLKQDFPDLTIEINGGISHLDDIHTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 249

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 250 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 298


>gi|325128934|gb|EGC51788.1| tRNA dihydrouridine synthase A [Neisseria meningitidis N1568]
          Length = 336

 Score =  302 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 190/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  L++EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLHSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVKIPVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+    +  + L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEEIAQHLQHVDGVMVGREAYHNPMVMREWDRLFYGDT-- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG  N+R  R +L
Sbjct: 256 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKNARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGGLILEAWKEVERA 332


>gi|325261220|ref|ZP_08127958.1| TIM-barrel protein, NifR3 family [Clostridium sp. D5]
 gi|324032674|gb|EGB93951.1| TIM-barrel protein, NifR3 family [Clostridium sp. D5]
          Length = 319

 Score =  302 bits (774), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 139/302 (46%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+  EM+ A  IL  +K  +++L     E P +LQ+ G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLVCMEMVSAKGILYNNKNTESLLEIHPDEMPASLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V     G+ LM NP +V + ++A+ KA+  P
Sbjct: 79  PKIVSEMAKKIEERPFAILDINMGCPVPKVVRNGEGSALMKNPKLVYELVSAVVKAIKKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+    V    + K I+++G   + +H R         ++       D++I
Sbjct: 139 VTVKIRKGFDED--HVNAVEIAKIIEEAGAAAVGVHGRT--------REQYYSGKADWEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A+ +      DGVMI R A  N  + + +  Y  + 
Sbjct: 189 IRKVK-EAVSIPVIGNGDVTSGEKAIAMREQTGCDGVMIARGAQGNPWIFSELTVYEQSG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V K   R  +  + +Y   +L     ++++ +H+     G   + R R  
Sbjct: 248 TLPPRPSLEEVKKTMLRHAALQL-EYKGEYLG----IREMRKHVAWYVKGLHGAARLRDA 302

Query: 297 LT 298
           + 
Sbjct: 303 IN 304


>gi|254430822|ref|ZP_05044525.1| tRNA-dihydrouridine synthase A [Cyanobium sp. PCC 7001]
 gi|197625275|gb|EDY37834.1| tRNA-dihydrouridine synthase A [Cyanobium sp. PCC 7001]
          Length = 345

 Score =  302 bits (774), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 134/332 (40%), Positives = 185/332 (55%), Gaps = 19/332 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------GDKKNILGFSTQEKP 49
           M+D TDRH+R   R +T ++LLYTEM+VA A+             G  + +LGF   EKP
Sbjct: 20  MMDCTDRHFRVLMRQITRHSLLYTEMVVALALHHARQAPGAEAPGGRLERLLGFDRIEKP 79

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +ALQ+GG D + L EA ++ E +GY+E+NLNVGCPS RV +G FGACLM +P+ V  C+A
Sbjct: 80  IALQLGGDDPALLAEACRLAEAWGYDEVNLNVGCPSDRVRKGRFGACLMAHPEQVAACVA 139

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           AM  A S+PVTVK RIG+D       L   V ++  +G     +HARKA L+GL PK NR
Sbjct: 140 AMAAACSLPVTVKHRIGIDHHDSYPELLGFVDTVAAAGACRFSVHARKAWLEGLDPKQNR 199

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
            IP L YD V+ +K++ P L + LNGGLE      + L  VDG M+GRAAY +      V
Sbjct: 200 TIPPLRYDWVHRLKRDRPQLIVELNGGLETPEACRQQLDHVDGAMVGRAAYAHPLRWAGV 259

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           D       +   P  +         +   +  +A R    GG+L  I RH++ +  G P 
Sbjct: 260 DRSLHGDPSRGEPQAS--------DVVRGLVPHAERWCGRGGRLWPIARHLVHVVEGVPG 311

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           +RR R  LT  A    A   ++E A   + ++
Sbjct: 312 ARRWRQALTEAASRPGAGPEVLELAARQLEDA 343


>gi|78211573|ref|YP_380352.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9605]
 gi|78196032|gb|ABB33797.1| uncharacterized protein family UPF0034 [Synechococcus sp. CC9605]
          Length = 331

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 134/322 (41%), Positives = 185/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+    ++N +L F   E P+ALQ+GG D 
Sbjct: 17  MLDCTDRHFRVLMRQISRRALLYSEMVVAQALHHSKRRNKLLDFDPVEHPIALQVGGDDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L EAA++ +D+GY+EINLNVGCPS +V  G+FGACLM  PD+V  C+ AM  A  +PV
Sbjct: 77  ALLAEAARLAQDWGYDEINLNVGCPSQKVQAGNFGACLMAEPDLVARCVEAMVGAGGLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD    V L N V  +  +G +   IHARKA L+GL PK NR IP L ++ V
Sbjct: 137 TVKHRIGIDDLDSDVLLMNFVDRVALAGASRFAIHARKAWLEGLDPKQNRTIPPLQHERV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L+ L   DG M+GRAAY +    T+VD       + 
Sbjct: 197 VALKQRRPDLVIELNGGLECPEDCLQALEGCDGAMVGRAAYSHPLRWTSVDALIFGEESR 256

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                    +     I   +  +AA HL  GG+L  + RH++ L  G   +R  R  L  
Sbjct: 257 ---------QILASDIVDGLLPHAAAHLEQGGRLWDLCRHLVQLVEGVRGARHWRRELGE 307

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A    A   ++  A   + ++
Sbjct: 308 KAQRPGADLKVLVQAGQQLKDA 329


>gi|326565214|gb|EGE15400.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis 103P14B1]
 gi|326573992|gb|EGE23941.1| tRNA-dihydrouridine synthase A [Moraxella catarrhalis CO72]
          Length = 322

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 120/300 (40%), Positives = 165/300 (55%), Gaps = 14/300 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D+T   +R FARL   N  LYTEMI   AIL+GD K+ L     E P+ LQ+GG++  
Sbjct: 12  MIDYTTMDFRAFARLFNPNIHLYTEMISTSAILKGDAKHHLRCHPTESPVVLQLGGSNPD 71

Query: 61  KLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +A ++ E   FGY E N+NVGCPS RV     GACLM  P +V D + AM      P
Sbjct: 72  EMAKAVRVTEALGFGYCEYNINVGCPSDRVQHNKIGACLMAEPQVVADMVRAMKNETDKP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG+DD      +R+ V+++ ++G      HAR A L+GLSPK NR+IP L Y+ 
Sbjct: 132 ITVKHRIGIDDCDSYEFMRDFVQTVAEAGCTHFITHARIAWLQGLSPKQNREIPPLRYEE 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ PDL I +NGG+  +      L  VDGVMIGRA Y N  ++            
Sbjct: 192 VYRLKQDFPDLTIEINGGISHLDDIHTQLAKVDGVMIGRAFYHNPYLMAEC-HLLWGSQP 250

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S            R+I  ++  Y  +    G  L  +TRH +GLF G   +RR R  L+
Sbjct: 251 PS-----------HRQIFENLISYLKKRADEGVNLAVLTRHYLGLFQGMAGARRWRQDLS 299


>gi|298290876|ref|YP_003692815.1| TIM-barrel protein, yjbN family [Starkeya novella DSM 506]
 gi|296927387|gb|ADH88196.1| TIM-barrel protein, yjbN family [Starkeya novella DSM 506]
          Length = 337

 Score =  302 bits (773), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 143/321 (44%), Positives = 202/321 (62%), Gaps = 9/321 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L+  A LYTEM+ A+A++ GD++ ++GFS  E P+A+Q+GG+D +
Sbjct: 14  MMEWTDRNCRAFHRVLSRRARLYTEMVTANAVIFGDRERLIGFSDAEHPVAVQLGGSDPA 73

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I  D+GY E+NLNVGCPS RV  G+FGACLM +P +V DC+AAM   +SIPVT
Sbjct: 74  ALAKAAAICADWGYAEVNLNVGCPSDRVQGGNFGACLMRSPALVADCVAAMKAEVSIPVT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L  ++  +G + + +HARKA L+GLSPK+NR IP LDY  V+
Sbjct: 134 VKCRIGVDEQDPEAALDALADAVLAAGADALIVHARKAWLEGLSPKENRDIPPLDYGRVH 193

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  P + I +NGG+  + +A   L  VDGVM+GRAAY    +L  VD  F       
Sbjct: 194 RLKQRLPHVPISINGGIASLEEAQAQLAHVDGVMLGRAAYHQPELLLRVDSLFFGEADPH 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                 V+             + A HL +GG+L  ITRHM+GLF G P +R  R  L ++
Sbjct: 254 EDAFAAVEA---------FEPHIAAHLATGGRLHDITRHMLGLFTGRPGARAFRRRLAID 304

Query: 301 AGASTATHHIIETAFNLMIES 321
              + A   ++  A + +  +
Sbjct: 305 GVKADAGLDVLRAAVDEVRRA 325


>gi|163796265|ref|ZP_02190226.1| tRNA-dihydrouridine synthase A [alpha proteobacterium BAL199]
 gi|159178407|gb|EDP62949.1| tRNA-dihydrouridine synthase A [alpha proteobacterium BAL199]
          Length = 386

 Score =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 148/320 (46%), Positives = 197/320 (61%), Gaps = 11/320 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT  ALLYTEM+ ADA+  GD+  ++GFST E P+ALQ+GG++ +
Sbjct: 68  MMDWTDRHCRMFHRHLTRRALLYTEMVTADAVRFGDRGRLIGFSTDEHPVALQLGGSEPA 127

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+I EDFGY+E+N+NVGCPS RV  G FGACLM  P +VG  + AM  A+SIPVT
Sbjct: 128 AMAEAARIAEDFGYDEVNINVGCPSDRVQSGRFGACLMREPVLVGRMVEAMRAAVSIPVT 187

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L  ++  +G   + +HARKA L+GLSPK+NR +P LDYD V 
Sbjct: 188 VKCRIGVDDQDPGPALDALTAAVAAAGCRTLIVHARKAWLQGLSPKENRDVPPLDYDRVD 247

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +K  NPD+ + LNGGL D+      L   +DG M+GRAAY+   +L   D       + 
Sbjct: 248 ALKATNPDMVVVLNGGLLDLDAVEAALARGLDGGMVGRAAYQTPWVLADADRRIFGAPS- 306

Query: 240 SSPIKTRVDKDFWRKISASMTDYAAR-HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                T +D+     +  +M +YA R     G  ++ + RHM+GLF G P +R  R  L+
Sbjct: 307 -----TDIDR---HAVVEAMAEYAGRARRDLGTPVKSVVRHMLGLFQGLPGARAWRRYLS 358

Query: 299 VEAGASTATHHIIETAFNLM 318
                  A   I+  A   +
Sbjct: 359 ETMPNPDAGPEILIEAAKRV 378


>gi|153853506|ref|ZP_01994886.1| hypothetical protein DORLON_00875 [Dorea longicatena DSM 13814]
 gi|149753661|gb|EDM63592.1| hypothetical protein DORLON_00875 [Dorea longicatena DSM 13814]
          Length = 318

 Score =  302 bits (773), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 141/319 (44%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K    +L    +E P++LQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGAGLLCMEMISAKALQYKNKNTKALLAIHPEEYPVSLQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK++E+  +  +++N+GCP  +V     G+ LM NP +V + ++A+ KA+  P
Sbjct: 76  PKIMSEMAKMIEELPFQILDINMGCPVPKVVRNGEGSALMKNPKLVHEIVSAVSKAIEKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K I+ +G   + +H R         ++       D+DI
Sbjct: 136 VTVKIRKGFDDD--HINAVEIAKIIEDAGGAAVAVHGRT--------REQYYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +AL++      DGVMIGR A  N  +   + EY    
Sbjct: 186 IRQVK-EAVSIPVIGNGDVISGEKALQMRRETGCDGVMIGRGAQGNPWIFHELQEYERTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P   ++ +   R     +             ++++ +H+     G   S + R  
Sbjct: 245 VVPPRPTPEKIKETMLRHARLQI-----EFKGDFIGIREMRKHVAWYTKGMKGSAKLRDA 299

Query: 297 LTVEAGASTATHHIIETAF 315
           +            +++ A 
Sbjct: 300 INQVESYEEL-VELLDKAI 317


>gi|319794422|ref|YP_004156062.1| tim-barrel protein, yjbn family [Variovorax paradoxus EPS]
 gi|315596885|gb|ADU37951.1| TIM-barrel protein, yjbN family [Variovorax paradoxus EPS]
          Length = 324

 Score =  301 bits (772), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 188/322 (58%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL++ +ALLYTEM+   A++ GD    L F+ +E P+ALQ+GG++ +
Sbjct: 11  MMDWTDRHCRYFHRLMSRHALLYTEMVTTGALVHGDVPRHLRFNAEEHPVALQLGGSEPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ E++GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   +S+PVT
Sbjct: 71  DLAHCAKLGEEWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVSVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  + ++G +   +HAR A L+GLSPK NR+IP L Y +V+
Sbjct: 131 VKHRIGIDKIERYEFVRDFVGQVSEAGCDTFIVHARNAWLQGLSPKQNREIPPLRYALVH 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L   +NGG+    Q  + L  +DGVM+GR AY N   L   D  F       
Sbjct: 191 RLKHDFPGLKFSINGGISVNEQVHEHLRLLDGVMVGREAYHNPWWLAEWDAEFFG--AAP 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            P+          ++ + M DY  R     G +   I RHM+GL +G P +RR R + + 
Sbjct: 249 QPLTRE-------EVESLMCDYMVREAAEHGTQWSSIARHMLGLRNGLPGARRWRQVWSD 301

Query: 300 EAGASTATHHIIETAFNLMIES 321
               +   H ++  A   + ++
Sbjct: 302 HRMKTRPPHEVMALAHEPVAQA 323


>gi|307243172|ref|ZP_07525345.1| TIM-barrel protein, nifR3 family [Peptostreptococcus stomatis DSM
           17678]
 gi|306493433|gb|EFM65413.1| TIM-barrel protein, nifR3 family [Peptostreptococcus stomatis DSM
           17678]
          Length = 319

 Score =  301 bits (772), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 83/302 (27%), Positives = 138/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L    LLYTEMI A A+   DK  K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKEL-GCGLLYTEMINAKALCYDDKNTKKMLNILDEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+I+ D+    +++N+GCP+ +V +   G+ LM NP + G  +  + K    P
Sbjct: 76  PEFMGKAAQILNDYPNEILDINMGCPAPKVVKNGDGSALMRNPKLAGQVLDQVVKNSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G+  I IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDD--NSVNALEIAKIAEDCGICAITIHGRT--------REQYYSGQADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K +   + +  NG +  +  A++I      D +MIGR A  N  +   +D Y    
Sbjct: 186 IGEVKSQI-SIPVIGNGDVTSVEDAIRIKDHTGCDAIMIGRGAQGNPWIFKRIDHYMKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P K          I+    D A +       ++++ +H+     G  +S R R  
Sbjct: 245 QLLDPPSKDEKI-----DIAIKHMDLAIKEHGEYVAVREMRKHIGWYLKGMKHSARLRDQ 299

Query: 297 LT 298
           + 
Sbjct: 300 IN 301


>gi|283795849|ref|ZP_06345002.1| tRNA-dihydrouridine synthase [Clostridium sp. M62/1]
 gi|291076480|gb|EFE13844.1| tRNA-dihydrouridine synthase [Clostridium sp. M62/1]
 gi|295091061|emb|CBK77168.1| tRNA-U20-dihydrouridine synthase [Clostridium cf. saccharolyticum
           K10]
          Length = 319

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 77/317 (24%), Positives = 144/317 (45%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+ TEM+ A A+L  ++    +L    +E+P+A+Q+ G+D
Sbjct: 19  MAGVTDLPFRILCRE-QGCGLMCTEMVSAKALLYKNRNTKPLLETKPEERPVAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A ++E+  Y+ I++N+GCP  ++     G+ LM NP + G+ ++AM + L  P
Sbjct: 78  PEIMSEMALMLEEGPYDIIDVNMGCPVPKIVNNGEGSALMKNPKLAGEILSAMTRKLKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D+  +V      K  ++SG   + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFNDE--SVNAVEFAKMAEQSGAAAVAVHGRT--------REQFYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A +++     DGVM+ R A  N  + + +D Y    
Sbjct: 188 IRQVK-EAVSIPVIGNGDIFTPQDAGRMMEETGCDGVMVARGAKGNPWIFSRIDHYLKTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +   R       +           ++++ +H+     G+P+S   R+ 
Sbjct: 247 EVLPKQGPEEVKQMILRHA-----ELLVAFKGEYTAMREMRKHVSWYTAGYPHSAALRNE 301

Query: 297 LTVEAGASTATHHIIET 313
           + +       T  ++E 
Sbjct: 302 INLVETMEELTELVLER 318


>gi|289422453|ref|ZP_06424296.1| tRNA-dihydrouridine synthase B [Peptostreptococcus anaerobius
           653-L]
 gi|289157025|gb|EFD05647.1| tRNA-dihydrouridine synthase B [Peptostreptococcus anaerobius
           653-L]
          Length = 319

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 82/325 (25%), Positives = 147/325 (45%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L    LLYTEMI A A+   D+  K +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKEL-GCGLLYTEMINAKALCYDDQNTKKMLNILDEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI+ D+    +++N+GCP+ +V +   G+ LM NP +  D +  + K  + P
Sbjct: 76  PEYMGRAAKILNDYPNEILDINMGCPAPKVIKNGDGSALMKNPKLAADVLTNVVKNSNKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +  G++ I +H R         ++       D+DI
Sbjct: 136 VTLKIRKGWDDD--SVNAVEIAKIAEDCGIDAIAVHGRT--------REQFYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +  +     ++ + + D VMIGR A  N  +   +D Y    
Sbjct: 186 IGQVKNAV-SIPVIGNGDIVSVEDVVKIREMTNCDAVMIGRGAQGNPWIFKRIDHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P K          I+      A +       ++++ +H+     G  NS R R +
Sbjct: 245 EILPGPTKEDKIN-----IAIKHMGLAVKEHGEYVAVREMRKHIGWYLKGMKNSARFRDM 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +        +   +++T  N+++  
Sbjct: 300 IN----KMESAQEVVDT-LNMLLND 319


>gi|59801940|ref|YP_208652.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA 1090]
 gi|194099440|ref|YP_002002542.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae NCCP11945]
 gi|239999677|ref|ZP_04719601.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|240014854|ref|ZP_04721767.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI18]
 gi|240017300|ref|ZP_04723840.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA6140]
 gi|240113270|ref|ZP_04727760.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|240116376|ref|ZP_04730438.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|240118665|ref|ZP_04732727.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|240121373|ref|ZP_04734335.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID24-1]
 gi|240126411|ref|ZP_04739297.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|240128876|ref|ZP_04741537.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
 gi|260439804|ref|ZP_05793620.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|291043074|ref|ZP_06568797.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|293398413|ref|ZP_06642591.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae F62]
 gi|59718835|gb|AAW90240.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193934730|gb|ACF30554.1| Conserved hypothetical protein [Neisseria gonorrhoeae NCCP11945]
 gi|291012680|gb|EFE04663.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae DGI2]
 gi|291610884|gb|EFF39981.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae F62]
 gi|317164939|gb|ADV08480.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 348

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 30  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 90  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 150 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 210 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGD--N 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 268 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 320

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 321 SDATLLKDNDGGLIFEAWKEVERA 344


>gi|254494393|ref|ZP_05107564.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 1291]
 gi|268595490|ref|ZP_06129657.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|268599350|ref|ZP_06133517.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|268602043|ref|ZP_06136210.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|268604377|ref|ZP_06138544.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|268684995|ref|ZP_06151857.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|268687257|ref|ZP_06154119.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
 gi|226513433|gb|EEH62778.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 1291]
 gi|268548879|gb|EEZ44297.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae 35/02]
 gi|268583481|gb|EEZ48157.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae MS11]
 gi|268586174|gb|EEZ50850.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID18]
 gi|268588508|gb|EEZ53184.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID1]
 gi|268625279|gb|EEZ57679.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-92-679]
 gi|268627541|gb|EEZ59941.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae SK-93-1035]
          Length = 338

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 135/324 (41%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 20  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 80  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 140 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 200 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGD--N 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 258 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 310

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 311 SDATLLKDNDGGLIFEAWKEVERA 334


>gi|124021729|ref|YP_001016036.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9303]
 gi|123962015|gb|ABM76771.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. MIT
           9303]
          Length = 334

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 182/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLYTEM+VA A+   ++  ++L F   E PL+LQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISRRALLYTEMLVAQALHHSNRLDHLLDFDIIEHPLSLQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ + +GY+EINLNVGCPS+R   G+FGACLM  PD V  C+ AM  A  +PV
Sbjct: 80  KMLAEAARLADAWGYDEINLNVGCPSSRAKAGNFGACLMAKPDQVARCVEAMAMASPLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+DD      L   V  +  +G     +HARKA L+GL PK NR IP L +  V
Sbjct: 140 TVKHRLGIDDFDSDALLMTFVDRVSLAGATRFTVHARKAWLEGLDPKQNRTIPPLQHQRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K++ P L I +NGGLE  +  L  L + DG M+GRAAY +     ++DE        
Sbjct: 200 THLKQQRPQLTIEINGGLEHPADCLTALQTCDGAMVGRAAYAHPLRWKSMDELVYGEEPR 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S             ++   +  +A  HL  GG+L  + RH++ L  G P ++  R  L +
Sbjct: 260 S---------INASQVIGGLLPHAETHLSRGGRLWDLCRHLLQLVEGVPGAKSWRRDLGI 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A  + A   +++ A   + ++
Sbjct: 311 KAQKADADLTVLQKAAQQLEDA 332


>gi|296840825|ref|ZP_06863533.2| tRNA dihydrouridine synthase A [Neisseria polysaccharea ATCC 43768]
 gi|296839826|gb|EFH23764.1| tRNA dihydrouridine synthase A [Neisseria polysaccharea ATCC 43768]
          Length = 319

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 1   MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDSS 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 61  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMQDAVGIPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 121 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 181 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMHEWDRLFYGDT-- 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 239 RSPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 291

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +  A        +I  A+  +  +
Sbjct: 292 SDAALLKGNDGGLILEAWKEVERA 315


>gi|78183599|ref|YP_376033.1| tRNA-dihydrouridine synthase A [Synechococcus sp. CC9902]
 gi|78167893|gb|ABB24990.1| uncharacterized protein family UPF0034 [Synechococcus sp. CC9902]
          Length = 334

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 132/322 (40%), Positives = 186/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLY+EM+VA A+   +++  +L F   E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISRRALLYSEMVVAQALHYTNRRDRLLDFDPIEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +AA++  D+GY+EINLNVGCPS RV  G+FGACLM +PD+V  C+ AM +A ++PV
Sbjct: 80  NLLADAARLALDWGYDEINLNVGCPSQRVQAGNFGACLMADPDLVARCVEAMGQATALPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L   V  +  +G     +HARKA L+GL PK NR IP L ++ V
Sbjct: 140 TVKHRIGIDDLDNDELLTAFVDRVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLQHERV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L  L   DG M+GRAAY +      +D         
Sbjct: 200 VALKQRRPDLLIELNGGLETPEDCLAALHECDGAMVGRAAYAHPLRWADIDHLIYG---- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  +  D    +   +  +AA HLH GG+L  + RH++ L  G P +R  R  L  
Sbjct: 256 -EPPRQLLASD----VVEGLIPHAALHLHRGGRLWDLCRHLVQLVEGVPGARHWRRELGE 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
            +    A  +I+E A   + ++
Sbjct: 311 RSQRKGADLNILEEAGRQLKDA 332


>gi|266624024|ref|ZP_06116959.1| tRNA-dihydrouridine synthase B [Clostridium hathewayi DSM 13479]
 gi|288864155|gb|EFC96453.1| tRNA-dihydrouridine synthase B [Clostridium hathewayi DSM 13479]
          Length = 328

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 141/325 (43%), Gaps = 21/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      ++ TEM+ A AIL  ++    +L    +E+P+++Q+ G+D
Sbjct: 19  MAGVTDLPFRVLCKE-QGCGMVVTEMVSAKAILYKNRNTKALLEVEERERPVSVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK++E   ++ I++N+GCP  ++     G+ +M NP +    + AM KA+  P
Sbjct: 78  PEIMADIAKLIEPGPFDIIDVNMGCPVPKIVNNGEGSAMMKNPRLAEAVLGAMVKAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  D    V      K  +  GV  + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFTDSD--VNAVEFAKMAESCGVAAVAVHGRT--------REQYYSGTADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     A  +L     DG+MI R A  N  + +    Y    
Sbjct: 188 IRRVK-EAVKIPVIGNGDVFAPEDAKALLDETGCDGIMIARGAKGNPWIFSRTIHYLETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R  +    +Y   +L     ++++ +HM     G P+S + R+ 
Sbjct: 247 ELLPPPSMEELQNMVLRH-AEMSVEYKGEYLG----IREMRKHMAWYTAGLPHSAKLRND 301

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +      +     + E   +++ ES
Sbjct: 302 INAVETLADLKTLVKERFSDIICES 326


>gi|304386595|ref|ZP_07368883.1| tRNA dihydrouridine synthase A [Neisseria meningitidis ATCC 13091]
 gi|304339424|gb|EFM05496.1| tRNA dihydrouridine synthase A [Neisseria meningitidis ATCC 13091]
          Length = 348

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 137/324 (42%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 30  MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ IPVT
Sbjct: 90  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 150 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 210 YRLKQEFPELEIIINGGITANEAIAGHLQHVDGVMVGREAYHNPIVMREWDRLFYGDT-- 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            SPI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 268 RSPIE-------YTDLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 320

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 321 SDATLLKDNDGSLILEAWKEVERA 344


>gi|218134816|ref|ZP_03463620.1| hypothetical protein BACPEC_02719 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990201|gb|EEC56212.1| hypothetical protein BACPEC_02719 [Bacteroides pectinophilus ATCC
           43243]
          Length = 319

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 83/302 (27%), Positives = 139/302 (46%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      +LY+EM+ A AI+  ++    +L    +E P+A+Q+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGCGMLYSEMVSAKAIMYNNRNTDELLKVRPEENPVAVQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ I++N+GCP  +V     G+ LM NP +VG  ++AM KA+  P
Sbjct: 76  PQIMADMAKRIEELPFDTIDVNMGCPVPKVVNNGEGSALMKNPLLVGQIVSAMAKAVKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D +  +    +   I++SG   + +H R         ++       D+DI
Sbjct: 136 VTVKIRKGFNDDM--INAPEIAHIIEESGGACVAVHGRT--------REQYYTGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG + D   A  +L     D VMIGRAA  N  +   V EY  N 
Sbjct: 186 IRQVKQRV-HIPVIGNGDITDALSARAMLDETGCDAVMIGRAARGNPWIFREVSEYLQNG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V     R                   ++++ +H      GFPNS   R+ 
Sbjct: 245 TIPQRPSDEDVRNMILRHA-----RLLVECKGEFTGIREMRKHFAWYTAGFPNSSMLRNQ 299

Query: 297 LT 298
           + 
Sbjct: 300 VN 301


>gi|213859447|ref|ZP_03385151.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 284

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 128/276 (46%), Positives = 172/276 (62%), Gaps = 13/276 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  V
Sbjct: 139 VKTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRV 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLT 238
           Y++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T
Sbjct: 199 YQLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTT 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            + P+           +  +M  Y  R L  G  L 
Sbjct: 259 DTDPV----------AVVRAMYPYIERELSQGAYLG 284


>gi|222111076|ref|YP_002553340.1| tRNA-dihydrouridine synthase a [Acidovorax ebreus TPSY]
 gi|221730520|gb|ACM33340.1| TIM-barrel protein, yjbN family [Acidovorax ebreus TPSY]
          Length = 351

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 129/315 (40%), Positives = 180/315 (57%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ + LLYTEM+   A+  GD +  L F   E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRYLHRLLSRHTLLYTEMVTTGALAHGDVQRHLRFDAAEHPVALQLGGSEPA 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 77  DLAHCARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVQVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  +  +G     +HAR A LKGLSPK+NR+IP L YD+  
Sbjct: 137 VKHRIGIDQNEDYGFVRDFVGVVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYDVAA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG +  +  L+ L  VDGVM+GR AY N   L   DE F      +
Sbjct: 197 RLKADFPQLTIAINGGFQTDAAVLEELARVDGVMVGREAYHNPWWLARWDEQFFGA-APA 255

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL-HSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           +P + +V++D        M  Y  R     G     + RHM+GL +G P +RR R + + 
Sbjct: 256 APTREQVEED--------MVAYMEREATAHGTHWYAVARHMLGLRNGLPGARRWRQVWSD 307

Query: 300 EAGASTATHHIIETA 314
                     ++  A
Sbjct: 308 HRLKHLPAREVMALA 322


>gi|254462050|ref|ZP_05075466.1| tRNA-dihydrouridine synthase A [Rhodobacterales bacterium HTCC2083]
 gi|206678639|gb|EDZ43126.1| tRNA-dihydrouridine synthase A [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 305

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 139/305 (45%), Positives = 190/305 (62%), Gaps = 11/305 (3%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           +++ ALLYTEM+ + A++RG   ++L +ST E P+ALQ+GG+D ++L EAA+I  + GY 
Sbjct: 1   MSSRALLYTEMVTSPALVRGGALHLLKYSTVEHPVALQLGGSDPAELAEAARIGAEHGYA 60

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
           EINLNVGCPS RV  G+FGA LM +P +V +C AAM KA ++ VTVKCRIGVDDQ P+  
Sbjct: 61  EINLNVGCPSDRVQNGAFGAILMRDPKLVAECCAAMIKASAVEVTVKCRIGVDDQTPSDV 120

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           L   +  +  +GV    IHARKA L+GLSPK+NR IP LDY +V ++K   P L + LNG
Sbjct: 121 LPEFLARVAGAGVGRFTIHARKAWLQGLSPKENRDIPPLDYGLVQQMKGLFPALHLSLNG 180

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           G+  ++QA   L   +DGVMIGRAAY   A +L   D          +P   R  +D   
Sbjct: 181 GITTLAQAQDALERGMDGVMIGRAAYHQPADILMEADHMIYG-----APKVERTRED--- 232

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            I   M  Y   H+  GGKL Q+TRHM+G+F G P +R  +  L+  A   ++  H +  
Sbjct: 233 -IVMEMLPYIDAHIAEGGKLGQVTRHMLGIFAGQPGARYWKRHLSENAHKHSSGSHTVVD 291

Query: 314 AFNLM 318
           A  +M
Sbjct: 292 AIEMM 296


>gi|116071792|ref|ZP_01469060.1| hypothetical protein BL107_06569 [Synechococcus sp. BL107]
 gi|116065415|gb|EAU71173.1| hypothetical protein BL107_06569 [Synechococcus sp. BL107]
          Length = 334

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 184/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLYTEM+VA A+   +++  +L F   E P+ALQ+GG D 
Sbjct: 20  MLDCTDRHFRVLMRQISRRALLYTEMVVAQALHYTNRRDRLLDFDPIEHPIALQVGGDDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +AA++  D+GY+EINLNVGCPS RV  G+FGACLM +PD+V  C+ AM +A  +PV
Sbjct: 80  NLLADAARLALDWGYDEINLNVGCPSQRVQAGNFGACLMADPDLVARCVEAMGRASGLPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L   V  +  +G     +HARKA L+GL PK NR IP L +D V
Sbjct: 140 TVKHRIGIDDLDNDELLTAFVDRVAAAGAQRFSVHARKAWLEGLDPKQNRTIPPLQHDRV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  PDL I LNGGLE     L  L   DG M+GRAAY +      +D         
Sbjct: 200 VALKQRRPDLLIELNGGLETPEDCLVALHECDGAMVGRAAYAHPLRWADIDHLIYG---- 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  +  D    +   +  +AA HL  GG+L  + RH++ L  G P +R  R  L  
Sbjct: 256 -EPPRQLLASD----VVEGLMPHAALHLQRGGRLWDLCRHLVQLVEGVPGARHWRRELGE 310

Query: 300 EAGASTATHHIIETAFNLMIES 321
            +    A  +I+E A   + ++
Sbjct: 311 RSQRKGADLNILEEAGRQLKDA 332


>gi|308388557|gb|ADO30877.1| yjbN; tRNA-dihydrouridine synthase A [Neisseria meningitidis
           alpha710]
 gi|325136923|gb|EGC59520.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M0579]
          Length = 336

 Score =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 133/324 (41%), Positives = 182/324 (56%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E +GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ I VT
Sbjct: 78  DLAKAAKAAEAYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGITVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPGLEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGDTAN 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
                       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 258 P---------IGYADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SDATLLKDNDGSLILEAWKEVERA 332


>gi|154484004|ref|ZP_02026452.1| hypothetical protein EUBVEN_01712 [Eubacterium ventriosum ATCC
           27560]
 gi|149735046|gb|EDM50932.1| hypothetical protein EUBVEN_01712 [Eubacterium ventriosum ATCC
           27560]
          Length = 317

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 78/299 (26%), Positives = 134/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      +LYTEM+ A AIL  +K    +L     E P+A+Q+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGCGMLYTEMVSAKAILYKNKNTNILLNIDKAEHPIAVQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E    V +   + I++N+GCP  ++     G+ L+  P +V   +  M KA+  P
Sbjct: 76  PDIMAEIGAKVAEGPCDFIDINMGCPVPKIVNNHEGSYLLTQPKLVEQILTKMVKAIKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  D    +    + +  +  GV+ I +H R         ++       D+D+
Sbjct: 136 VTIKVRKGFKDGE--IQAPEIARIAESCGVSAIAVHGRT--------REQYYSGKADWDV 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K E   + +  NG +     A  +      DG+M+GRAA  N  +   + EY  N 
Sbjct: 186 IKEVK-EAVKIPVIGNGDIFSAKDAKAMKEYTGCDGLMVGRAARGNPWIFKQIKEYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           +    P  T V +D   K +  + DY   +      ++++ +H+     G P+S   R 
Sbjct: 245 IIVDEPSSTEV-RDMVLKHARMLIDYKGEY----TAVREMRKHIAWYTQGLPHSAELRR 298


>gi|88811969|ref|ZP_01127222.1| Dihydrouridine synthase TIM-barrel protein yjbN [Nitrococcus
           mobilis Nb-231]
 gi|88790853|gb|EAR21967.1| Dihydrouridine synthase TIM-barrel protein yjbN [Nitrococcus
           mobilis Nb-231]
          Length = 295

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 121/297 (40%), Positives = 176/297 (59%), Gaps = 9/297 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A A+  G  + +L ++++E P+A+Q GG+D  +L   A++ E +GY+E+NLNVGCPS
Sbjct: 1   MVPAQAVWHGRGERLLAYNSEEHPVAVQFGGSDPRQLAYCARMAEAYGYDEVNLNVGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM  P++V + +AAM +A ++PVTVK RIG+D Q     L   V+ +  
Sbjct: 61  ERVQAGRFGACLMAEPNLVAELVAAMRQATTLPVTVKTRIGIDQQDDYAVLAEFVEYVAN 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G     +HARKA LKGLSPK+NR  P L YD V+ +K++ P+L I LNGG+  + QA  
Sbjct: 121 AGCRTFIVHARKAWLKGLSPKENRARPPLRYDRVWRLKRDFPELEIVLNGGMRTLEQAEG 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L SVDGVM GR AY+N  +L   D +       + P+ TR       ++  +   Y  R
Sbjct: 181 QLASVDGVMFGREAYRNPYLLAKADVWLFGD---TRPVPTR------HELVHAYLPYIER 231

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            L +G +L  +TRH++GL+ G P +R  R  L+     S A   +I  A  L+   L
Sbjct: 232 QLAAGARLSCMTRHLLGLYQGMPGARAWRSHLSARGPRSGAGVEVIMQALRLLPREL 288


>gi|325203461|gb|ADY98914.1| tRNA dihydrouridine synthase A [Neisseria meningitidis M01-240355]
          Length = 336

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 134/324 (41%), Positives = 187/324 (57%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 18  MLDWTDRHYRYMARQITRNTWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +GSFGACLM    +V DC+ AM  A+ I VT
Sbjct: 78  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGSFGACLMNEVGLVADCLNAMQDAVGITVT 137

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 138 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 198 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGD--N 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   +R  R +L
Sbjct: 256 HAPIE-------YADLVQRLYTYSQAQIQAGRGTILRHIVRHSLGLMHGLKGARTWRRML 308

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 309 SNATLLKDNDGGLILEAWEEVERA 332


>gi|160872814|ref|ZP_02062946.1| tRNA-dihydrouridine synthase A [Rickettsiella grylli]
 gi|159121613|gb|EDP46951.1| tRNA-dihydrouridine synthase A [Rickettsiella grylli]
          Length = 330

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 127/300 (42%), Positives = 174/300 (58%), Gaps = 9/300 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M+ WT RHY +F RL+   A LYTEM  A AIL+   +  +L     EK LA+Q+GG   
Sbjct: 17  MLGWTTRHYHYFFRLICKKAQLYTEMFTAQAILKSPARERLLTVDANEKALAIQLGGGIA 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S L +AAKIVE +GY+EINLNVGCPS +V  G FG  L+  P+ V D IAAM   + +PV
Sbjct: 77  SDLSKAAKIVESYGYSEINLNVGCPSEKVQSGGFGVVLLKEPNRVADAIAAMKAVVRLPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIGVD+      L + ++ +  +G +   IHARKA L G+SPK+NR+IP L+Y  V
Sbjct: 137 TVKTRIGVDNDESYDYLASFIRQVSLAGCDTFIIHARKAWLHGVSPKENREIPPLNYPWV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P L I LNGG+  + +A + L  VD VMIGRAA+ N  +   +D   S     
Sbjct: 197 YQIKRDFPHLTIVLNGGITCLKRAYQQLQHVDAVMIGRAAWYNPYLFAQLDALIS----- 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
               + R        I      Y  + L SG  L  + + ++GLFHG   +++ R  L+ 
Sbjct: 252 ---PQDRFIVPHRFSIILQYLPYLEKALKSGENLAHLIQPLLGLFHGVVGTKQWRQTLSE 308


>gi|325662824|ref|ZP_08151393.1| hypothetical protein HMPREF0490_02133 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325470876|gb|EGC74105.1| hypothetical protein HMPREF0490_02133 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 325

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 73/298 (24%), Positives = 137/298 (45%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K    +L    +E+P++LQ+ G++
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYKNKNTQDLLRIHEEERPVSLQLFGSE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  ++ +   G+ LM  P +V + ++   KA+  P
Sbjct: 82  PDTISEIAKQIEELPFAILDINMGCPVPKIVKNGEGSALMKQPKLVYEIVSKTVKAIQKP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K I+++G   + +H R         ++       D++I
Sbjct: 142 VTVKIRKGFDD--SCINAVEIAKVIEEAGGAAVAVHGRT--------REQYYSGKADWEI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A+++  L   DGVM+GR A  N  +   + EY    
Sbjct: 192 IRKVK-EAVSIPVIGNGDVTSAEDAVRMQKLTGCDGVMVGRGAQGNPWIFRELVEYDRTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              S P    + +   R  +    +Y   +L     ++++ +H+     G   +   R
Sbjct: 251 KIPSRPSLEELKETMLRH-ARLQIEYKGDYLG----IREMRKHVGWYTTGLKGAAALR 303


>gi|121594416|ref|YP_986312.1| tRNA-dihydrouridine synthase A [Acidovorax sp. JS42]
 gi|120606496|gb|ABM42236.1| tRNA-U16,U17-dihydrouridine synthase [Acidovorax sp. JS42]
          Length = 351

 Score =  299 bits (765), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 126/315 (40%), Positives = 174/315 (55%), Gaps = 10/315 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+  RLL+ + LLYTEM+   A+  GD +  L F   E P+ALQ+GG++ +
Sbjct: 17  MMDWTDRHCRYLHRLLSRHTLLYTEMVTTGALAHGDVQRHLRFDAAEHPVALQLGGSEPT 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A++ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM   + +PVT
Sbjct: 77  DLAHCARLGEQWGYDEINLNCGCPSERVQRGAFGACLMNEPQLVADCVKAMVDVVQVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D       +R+ V  +  +G     +HAR A LKGLSPK+NR+IP L YD+  
Sbjct: 137 VKHRIGIDQNEDYGFVRDFVGVVADAGCRVFIVHARNAWLKGLSPKENREIPPLRYDVAA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L I +NGG +  +  L+ L  VDGVM+GR AY N   L   DE F      +
Sbjct: 197 RLKADFPQLTIAINGGFQTDAAVLQELARVDGVMVGREAYHNPWWLARWDEQFFGAAPAA 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHL-HSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                        ++   M  Y  R     G     + RHM+GL +G P +RR R + + 
Sbjct: 257 ---------LTREQVEEDMVAYMEREATAHGTHWYAVARHMLGLRNGLPGARRWRQVWSD 307

Query: 300 EAGASTATHHIIETA 314
                     ++  A
Sbjct: 308 HRLKHLPAREVMALA 322


>gi|166030713|ref|ZP_02233542.1| hypothetical protein DORFOR_00387 [Dorea formicigenerans ATCC
           27755]
 gi|166029505|gb|EDR48262.1| hypothetical protein DORFOR_00387 [Dorea formicigenerans ATCC
           27755]
          Length = 318

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 138/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K    +L    QE P++LQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGAGLLCMEMISAKALQYKNKNTKVLLAIHPQEYPVSLQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  +  +++N+GCP  +V +   G+ LM NP +V + ++ + KA+  P
Sbjct: 76  PKIISEQAKRIEDLPFQILDINMGCPVPKVVKNGEGSALMKNPKLVFEIVSQLVKAIEKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K  +++G + + +H R         ++       D+DI
Sbjct: 136 VTVKIRKGFDDD--HINAVEIAKIAEEAGASAVAVHGRT--------REQYYSGEADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A ++  +   DGVMIGR    N  +   + EY    
Sbjct: 186 IRQVK-EAVHIPVIGNGDVTSAEKAAEMRKITGCDGVMIGRGVQGNPWIFRELAEYDRTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +  +     R  +    ++   +L     ++++ +H+     G   + + R  
Sbjct: 245 TIPPRPTQEEIRNMMLRH-ARMQLEFKGEYLG----IREMRKHVAWYVKGMKGAAKFRAQ 299

Query: 297 LT 298
           + 
Sbjct: 300 IN 301


>gi|313906481|ref|ZP_07839815.1| TIM-barrel protein, nifR3 family [Eubacterium cellulosolvens 6]
 gi|313468671|gb|EFR64039.1| TIM-barrel protein, nifR3 family [Eubacterium cellulosolvens 6]
          Length = 322

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 87/326 (26%), Positives = 148/326 (45%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+YTEM+ A AIL  ++    ++     E+P++LQ+ G++
Sbjct: 20  MAGVTDLPFRLLCRE-QGAGLVYTEMVSAKAILYKNRNTEALMQIDPGERPVSLQLFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA  +E+  ++  + N+GCP  +V     G+ LM +P + G+ IAA+ K +  P
Sbjct: 79  PEIVAEAAAQIEERPFDIFDFNMGCPVPKVVNNHEGSALMKDPKLAGEIIAAVVKRVHKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D Q  +V    + K ++ +G   I +H R         +        D+D+
Sbjct: 139 VTVKIRKGWDCQ--SVNAVEVAKVLEDAGAAAIAVHGRT--------RSQYYAGEADWDV 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG ++   +A  ++    VDG+MI R A  N  +   V  Y    
Sbjct: 189 IRQVK-EAVSIPVFGNGDVDSPEKAAALVEQTGVDGIMIARGARGNPWLFGRVRRYLEEG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P    V +   R +   +T+Y   +      L+++ +H+     GFPNS   R  
Sbjct: 248 VIPEKPSPKEVYEMIMRHM-KMLTEYKGDY----TGLREMRKHVAWYTTGFPNSAMLRKK 302

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           +              E A  L+ E L
Sbjct: 303 INE--------TETFEAAQELLYEVL 320


>gi|240081060|ref|ZP_04725603.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|240124208|ref|ZP_04737164.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID332]
          Length = 348

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 134/324 (41%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 30  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 90  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 150 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 210 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGD--N 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   ++  R +L
Sbjct: 268 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGAQTWRRML 320

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 321 SDATLLKDNDGGLIFEAWKEVERA 344


>gi|268597171|ref|ZP_06131338.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|268682834|ref|ZP_06149696.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID332]
 gi|268550959|gb|EEZ45978.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae FA19]
 gi|268623118|gb|EEZ55518.1| tRNA-dihydrouridine synthase A [Neisseria gonorrhoeae PID332]
          Length = 338

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 134/324 (41%), Positives = 189/324 (58%), Gaps = 12/324 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T NA LY+EM+ A AI+ GDK   L F+  E+P+ALQ+GG+D S
Sbjct: 20  MLDWTDRHYRYLARQITRNAWLYSEMVNAGAIVYGDKDRFLMFNEGEQPVALQLGGSDPS 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AAK  E++GYNE+NLN GCPS RV +G+FGACLM    +V DC+ AM  A+ IPVT
Sbjct: 80  DLAKAAKAAEEYGYNEVNLNCGCPSPRVQKGAFGACLMNEVGLVADCLNAMHDAVGIPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIGVD Q     + + V +++  +      +HAR A L GLSPK+NR +P L YD V
Sbjct: 140 VKHRIGVDRQTEYQTVADFVGTLRDKTACKTFIVHARNAWLDGLSPKENRDVPPLKYDYV 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L I +NGG+         L  VDGVM+GR AY N  ++   D  F      
Sbjct: 200 YRLKQEFPELEIIINGGITTNEAIAGHLQHVDGVMVGREAYHNPMVMREWDRLFYGD--N 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHIL 297
            +PI+       +  +   +  Y+   + +G    L+ I RH +GL HG   ++  R +L
Sbjct: 258 RAPIE-------YADLVQRLYTYSQVQIQAGRGTILRHIVRHSLGLMHGLKGAQTWRRML 310

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           +           +I  A+  +  +
Sbjct: 311 SDATLLKDNDGGLIFEAWKEVERA 334


>gi|331086547|ref|ZP_08335625.1| hypothetical protein HMPREF0987_01928 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330410380|gb|EGG89812.1| hypothetical protein HMPREF0987_01928 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 325

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 72/298 (24%), Positives = 136/298 (45%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K    +L    +E+P++LQ+ G++
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYKNKNTQDLLRIHEEERPVSLQLFGSE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  ++ +   G+ LM  P +V + ++   KA+  P
Sbjct: 82  PDTISEIAKQIEELPFAILDINMGCPVPKIVKNGEGSALMKQPKLVYEIVSKTVKAIQKP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K I+++G   + +H R         ++       D++I
Sbjct: 142 VTVKIRKGFDD--SCINAVEIAKVIEEAGGAAVAVHGRT--------REQYYSGKADWEI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A+++  L   DGVM+GR A  N  +   + EY    
Sbjct: 192 IRKVK-EAVSIPVIGNGDVTSAEDAVRMQKLTGCDGVMVGRGAQGNPWIFRELVEYDRTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    + +   R  +    +Y   +L     ++++ +H+     G   +   R
Sbjct: 251 KIPPRPSLEELKETMLRH-ARLQIEYKGDYLG----IREMRKHVGWYTTGLKGAAALR 303


>gi|240137455|ref|YP_002961926.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens AM1]
 gi|240007423|gb|ACS38649.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens AM1]
          Length = 340

 Score =  298 bits (763), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 144/318 (45%), Positives = 190/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 21  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DF Y EINLNVGCPS RV +G FGACLM  P +VG C+AAM  A+ +PVT
Sbjct: 81  DLAAAARIAADFSYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAAMKAAVPVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDYD V 
Sbjct: 141 VKCRLGVDDQDIEEALDAVADAVVAAGVDGLVVHARKAWLKGLSPRENRDVPPLDYDRVA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD          
Sbjct: 201 RLKRAHPDLPIAVNGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEPAPV 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     ++               A  L  G +L   TRHM+GLF+G P +R  R  L   
Sbjct: 261 ADAFAAIEA---------FEPIVAAGLERGLRLHAYTRHMLGLFNGRPGARAYRRHLATA 311

Query: 301 AGASTATHHIIETAFNLM 318
                A    +  A   +
Sbjct: 312 GMGPEAGLATLREAVAKV 329


>gi|218528939|ref|YP_002419755.1| tRNA-dihydrouridine synthase A [Methylobacterium chloromethanicum
           CM4]
 gi|218521242|gb|ACK81827.1| dihydrouridine synthase DuS [Methylobacterium chloromethanicum CM4]
          Length = 340

 Score =  298 bits (763), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 144/318 (45%), Positives = 190/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 21  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY EINLNVGCPS RV +G FGACLM  P +VG C+AAM  A+ +PVT
Sbjct: 81  DLAAAARIAADFGYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAAMKAAVPVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 141 VKCRLGVDDQDIEEALDAVADAVVAAGVDGLVVHARKAWLKGLSPRENRDVPPLDYGRVA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD          
Sbjct: 201 RLKRAHPDLPIAINGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEPAPV 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     ++               A  L  G +L   TRHM+GLF+G P +R  R  L   
Sbjct: 261 ADAFAAIEA---------FEPIVAAGLERGLRLHAYTRHMLGLFNGRPGARAYRRHLATA 311

Query: 301 AGASTATHHIIETAFNLM 318
                A    +  A   +
Sbjct: 312 GMGPEAGLATLREAVAKV 329


>gi|254559633|ref|YP_003066728.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens DM4]
 gi|254266911|emb|CAX22710.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens DM4]
          Length = 340

 Score =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 144/318 (45%), Positives = 190/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 21  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY EINLNVGCPS RV +G FGACLM  P +VG C+AAM  A+ +PVT
Sbjct: 81  DLAAAARIAADFGYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAAMKAAVPVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 141 VKCRLGVDDQDIEEALDAVADAVVAAGVDGLVVHARKAWLKGLSPRENRDVPPLDYGRVA 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD          
Sbjct: 201 RLKRAHPDLPIAVNGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEPAPV 260

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     ++               A  L  G +L   TRHM+GLF+G P +R  R  L   
Sbjct: 261 ADAFAAIEA---------FEPIVAAGLERGLRLHAYTRHMLGLFNGRPGARAYRRHLATA 311

Query: 301 AGASTATHHIIETAFNLM 318
                A    +  A   +
Sbjct: 312 GMGPEAGLATLREAVAKV 329


>gi|33862288|ref|NP_893848.1| tRNA-dihydrouridine synthase A [Prochlorococcus marinus str. MIT
           9313]
 gi|33640401|emb|CAE20190.1| conserved hypothetical protein [Prochlorococcus marinus str. MIT
           9313]
          Length = 339

 Score =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 124/322 (38%), Positives = 181/322 (56%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++  ALLYTEM+VA A+   ++  ++L F   E PL+LQ+GG D 
Sbjct: 25  MLDCTDRHFRVLMRQISRRALLYTEMLVAQALHHSNRLDHLLDFDIIEHPLSLQVGGDDP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA++ + +GY+EINLNVGCPS+R   G+FGACLM  PD V  C+ AM  A  +PV
Sbjct: 85  KILAEAARLADAWGYDEINLNVGCPSSRAKAGNFGACLMAKPDQVARCVEAMAMASPLPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+D+      L   V  +  +G     +HARKA L+GL PK NR IP L +  V
Sbjct: 145 TVKHRLGIDNFDSDALLMTFVDRVSIAGATRFTVHARKAWLEGLDPKQNRTIPPLQHQRV 204

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K++ P L I +NGGLE  +  L  L + DG M+GRAAY +     ++DE        
Sbjct: 205 THLKQQRPQLTIEINGGLEHPADCLTALQTCDGAMVGRAAYAHPLRWQSMDELVYGEQPR 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           S             ++   +  +A  HL  GG+L  + RH++ L  G P ++  R  L +
Sbjct: 265 S---------INASQVIGGLLPHAETHLSRGGRLWDLCRHLLQLVEGVPGAKAWRRDLGI 315

Query: 300 EAGASTATHHIIETAFNLMIES 321
           +A    A   +++ A   + ++
Sbjct: 316 KAQKVDADLRVLQKAAQQLEDA 337


>gi|329905074|ref|ZP_08274002.1| tRNA-dihydrouridine synthase A [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327547746|gb|EGF32522.1| tRNA-dihydrouridine synthase A [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 295

 Score =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 117/293 (39%), Positives = 174/293 (59%), Gaps = 1/293 (0%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A++ GD    L F+ +E P+ALQ+GG+D + L  +A++ + +GY+EINLN GCPS
Sbjct: 1   MVTTGALVHGDVARHLDFNDEEHPVALQLGGSDPADLAHSARLGQQWGYDEINLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV +G+FGACLM  P +V DC+ AM  A+SI VTVK RIG+D       +R+ V ++ +
Sbjct: 61  ERVQKGAFGACLMAEPQLVADCVKAMRDAVSIDVTVKHRIGIDKNESYAFMRDFVGTVAE 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G     +HAR AILKGLSPK+NR++P L YD VY++K+E PDL I +NGG++  ++   
Sbjct: 121 AGCTTFIVHARNAILKGLSPKENREVPPLRYDAVYQLKREFPDLEIIINGGIKTEAEIDL 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVM+GR AY N  ++   D  + +        +T V +     I + +    + 
Sbjct: 181 HLQHVDGVMLGREAYHNPYLMAGFDARYYDDPATPR-TRTEVLEAMLPYIRSQLGPTPSI 239

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            L +G +L  ITRHM+GL  G P +R  R  L+     +     ++  A   M
Sbjct: 240 PLKAGPRLNSITRHMLGLMAGLPGARHFRQTLSESKRLAIGDAGLLMEAMESM 292


>gi|323485860|ref|ZP_08091195.1| hypothetical protein HMPREF9474_02946 [Clostridium symbiosum
           WAL-14163]
 gi|323400848|gb|EGA93211.1| hypothetical protein HMPREF9474_02946 [Clostridium symbiosum
           WAL-14163]
          Length = 319

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 142/319 (44%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+ TEM+ A A+L  ++    IL    QE+P+A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGCGLMCTEMVSAKALLYNNRNTKPILAVREQERPVAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E+  Y+ I++N+GCP  ++     G+ LM NP++    + +M K L  P
Sbjct: 78  PDIMSDMALRLEEGPYDIIDVNMGCPVPKIVNNGEGSALMKNPELAEAILTSMVKKLHKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V      +  +  GV+ + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFDD--SCVNAVEFARMAESCGVSAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A ++  L   DGVM+ R A  N  +   ++ Y    
Sbjct: 188 IRQVK-EAVKIPVIGNGDIFTPQDAKRMIDLTGCDGVMVARGAKGNPWLFGRINHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P +  +     R      T++   H+     ++++  H+     G+PNS   R+ 
Sbjct: 247 ILLPPPDREELKATIIRH-GRLQTEFKGEHIA----MREMRGHVAWYTAGYPNSSSLRND 301

Query: 297 LTVEAGASTATHHIIETAF 315
           +   A        +IE   
Sbjct: 302 INKVASMEEL-ITLIEERL 319


>gi|294084658|ref|YP_003551416.1| tRNA-dihydrouridine synthase A [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292664231|gb|ADE39332.1| tRNA-dihydrouridine synthase A [Candidatus Puniceispirillum marinum
           IMCC1322]
          Length = 337

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 185/310 (59%), Gaps = 14/310 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH RFF RL+  +ALL+TEM+ ADAI+ GD + +LG    E PLALQ+GG+D  
Sbjct: 18  MMDWTDRHCRFFLRLVAPDALLFTEMVTADAIIHGDCERLLGHDLAEHPLALQLGGSDPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSI 117
           KL +A++I  D+G+ EINLNVGCPS RV  G FGACLM  P +V +C +AM     A  +
Sbjct: 78  KLAKASRIAMDYGFAEINLNVGCPSDRVQSGRFGACLMAEPALVAECCSAMASVTTAFDV 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VKCRIG+DD      L     ++  +GV  +++HARKA LKGLSPK+NR IP LDY 
Sbjct: 138 PVSVKCRIGIDDMDSETGLDAFTHAVADAGVTLLYVHARKAWLKGLSPKENRDIPPLDYA 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            V  +    P + I +NGG+  +  A ++ P   G+M+GRAAYK   +L  +        
Sbjct: 198 RVKRLVGAFPAIDIHINGGIVALDTARELAPDFAGMMLGRAAYKTPMILPQIAYELYGTK 257

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             S              I+ASM DYA     +   L  ITRHM+GL++G   ++  R  L
Sbjct: 258 PPSR-----------ADIAASMADYADIKTAADVPLHAITRHMLGLYNGQRGAKLWRRSL 306

Query: 298 TVEAGASTAT 307
             +A + +A 
Sbjct: 307 GEDARSRSAD 316


>gi|238922487|ref|YP_002936000.1| tRNA-dihydrouridine synthase [Eubacterium rectale ATCC 33656]
 gi|238874159|gb|ACR73866.1| tRNA-dihydrouridine synthase [Eubacterium rectale ATCC 33656]
          Length = 323

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 80/303 (26%), Positives = 140/303 (46%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L    +EKP++LQ+ G+D
Sbjct: 25  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTESLLSIDEREKPVSLQMFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ +++N+GCP  ++     G+ LM NP + G  I ++ KA+  P
Sbjct: 84  PQIMAQIAKQIEERPFDILDINMGCPVPKIVNNGEGSALMKNPLLAGQIIESIVKAIDKP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    L    ++SG + + +H R         ++       D+DI
Sbjct: 144 VTVKIRKGFDDE--HVNAVELAHVAEESGASAVAVHGRT--------REQYYSGKADWDI 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG L      +K+      DG MI R A  N  + + +  YF   
Sbjct: 194 IRQVK-EAVSIPVIGNGDLLSAEDVIKMQEQTGCDGFMIARGAQGNPWIFSQILHYFETG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +   R  +  M ++   +      + ++ +H      G+P+S R R  
Sbjct: 253 EHQEKPSFEEVRRMILRH-ARMMIEFKGEY----TGIHEMRKHTAWYTAGYPHSSRLRAA 307

Query: 297 LTV 299
           +  
Sbjct: 308 VNT 310


>gi|254468654|ref|ZP_05082060.1| tRNA-dihydrouridine synthase B [beta proteobacterium KB13]
 gi|207087464|gb|EDZ64747.1| tRNA-dihydrouridine synthase B [beta proteobacterium KB13]
          Length = 336

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 133/303 (43%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +      +  +EM+ ++++L G  K I       + +P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKY-GAGMAVSEMVTSNSLLYGSSKTIRRANHDGEVEPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G   I++N+GCP+ ++     G+ L+ + D+V   + A+ KA  IP
Sbjct: 76  PQMMAEAAQYNADKGAQIIDINMGCPAKKICNVMAGSALLQHEDLVKRILEAVVKASPIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + K  + SG+  + IH R         +      + +Y+ 
Sbjct: 136 VTLKIRTGWDKQNKNAIT--IAKIAENSGIQALAIHGRT--------RACHYTGDAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +    +AL +L   S DGVMIGRAA     +   +D Y    
Sbjct: 186 IAAVKDQI-KIPVIANGDITSPEKALHVLKKTSADGVMIGRAAQGRPWIFREIDHYIKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V+K     ++     Y          L+   +H+     G  NS   R  
Sbjct: 245 EHLPPPSIDEVEKTTIEHVTDLYDFY-----GEDSGLKIARKHISWYTKGLKNSAMFRAK 299

Query: 297 LTV 299
           + +
Sbjct: 300 MNL 302


>gi|163850379|ref|YP_001638422.1| tRNA-dihydrouridine synthase A [Methylobacterium extorquens PA1]
 gi|163661984|gb|ABY29351.1| dihydrouridine synthase DuS [Methylobacterium extorquens PA1]
          Length = 354

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 142/318 (44%), Positives = 189/318 (59%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+PLA+Q+GG++  
Sbjct: 35  MMDWTDRQCRAFHRTLSRRARLYTEMVTTGAVLHGDRERLLGFDAYEQPLAVQLGGSNPD 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  DFGY EINLNVGCPS RV +G FGACLM  P +VG C+AA+  A+ +PVT
Sbjct: 95  DLAAAARIAADFGYAEINLNVGCPSDRVQDGRFGACLMREPGLVGACVAALKAAVPVPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +G +G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 155 VKCRLGVDDQDIEEALDAVADAVVAAGGDGLVVHARKAWLKGLSPRENRDVPPLDYGRVA 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+ +PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD          
Sbjct: 215 RLKRAHPDLPIAVNGGIADIAAAKARLGEVDGVMIGRAAYTEPALLLDVDAELFGEPAPV 274

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     ++               A  L  G +L   TRHM+GLF+G P +R  R  L   
Sbjct: 275 ADAFAAIEA---------FEPIVAAGLERGLRLHAYTRHMLGLFNGRPGARAYRRHLATA 325

Query: 301 AGASTATHHIIETAFNLM 318
                A    +  A   +
Sbjct: 326 GMGPEAGLATLREAVAKV 343


>gi|302390915|ref|YP_003826735.1| tRNA-U20-dihydrouridine synthase [Acetohalobium arabaticum DSM
           5501]
 gi|302202992|gb|ADL11670.1| tRNA-U20-dihydrouridine synthase [Acetohalobium arabaticum DSM
           5501]
          Length = 322

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 150/324 (46%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A  ++ G  +   +L  S QE+P++LQI G++
Sbjct: 17  MAGVTDLPFRRIVKEF-GCGLVCTEMVSAKGLVYGSSRTEELLTISDQERPVSLQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA + +E++  + I++N+GCP+ ++ +G  G+ LM  PD+VG  + A+ +A  IP
Sbjct: 76  PEIMAEAVEKIEEYRPDIIDVNLGCPTPKIVKGGAGSVLMKEPDLVGRIVDALVRATEIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G D+    V    + ++ ++SGV  + +H R         ++       D++I
Sbjct: 136 ITVKMRKGWDED--HVNAVEIAQTAEESGVQAVAVHGRT--------REQFYKGEADWNI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K E  ++ +  NG +     A +++     DGVMI R A  N  +      Y    
Sbjct: 186 IKEVK-EAVEVPVIGNGDIFSPQDAEEMIDTTGCDGVMIARGAQGNPWIFKRTLHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R + A + DY   ++     ++++ RH +    G  N    +  
Sbjct: 245 ELLPPPTIQERIEMVVRHLEA-LVDYKGEYIA----VREMRRHTVQYIKGLYNCTEVKQK 299

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +  +A        I+      +++
Sbjct: 300 VN-QAETEEELKEILHNYKRELMD 322


>gi|323693199|ref|ZP_08107417.1| TIM-barrel protein [Clostridium symbiosum WAL-14673]
 gi|323502682|gb|EGB18526.1| TIM-barrel protein [Clostridium symbiosum WAL-14673]
          Length = 319

 Score =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 141/319 (44%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L+ TEM+ A A+L  ++    IL    +E+P+A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGCGLMCTEMVSAKALLYNNRNTKPILAVREEERPVAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E+  Y+ I++N+GCP  ++     G+ LM NP +    + +M K L  P
Sbjct: 78  PDIMSDMALRLEEGPYDIIDVNMGCPVPKIVNNGEGSALMKNPKLAEAILTSMVKKLHKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V      +  +  GV+ + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFDD--SCVNAVEFARMAESCGVSAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A ++  L   DGVM+ R A  N  +   ++ Y    
Sbjct: 188 IRQVK-EAVKIPVIGNGDIFTPQDAKRMIDLTGCDGVMVARGAKGNPWLFGRINHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P +  +     R      T++   H+     ++++  H+     G+PNS   R+ 
Sbjct: 247 ILLPPPDREELKATIIRH-GRLQTEFKGEHIA----MREMRGHVAWYTAGYPNSSSLRND 301

Query: 297 LTVEAGASTATHHIIETAF 315
           +   A        +IE   
Sbjct: 302 INKVASMEEL-ITLIEERL 319


>gi|294789628|ref|ZP_06754862.1| tRNA dihydrouridine synthase A [Simonsiella muelleri ATCC 29453]
 gi|294482429|gb|EFG30122.1| tRNA dihydrouridine synthase A [Simonsiella muelleri ATCC 29453]
          Length = 352

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 128/325 (39%), Positives = 182/325 (56%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR +T N  LYTEMI A AI+ GD    L  +  E P+ALQ+GG+D +
Sbjct: 35  MLDWTDRHYRYMARQITKNTWLYTEMINAGAIIHGDPNRFLLKNECENPIALQLGGSDSA 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA     +GY+EINLN GCPS RV +G+FGACLM   ++V  C+ A+  A  +  +
Sbjct: 95  DLAKAAAKAAQYGYDEINLNCGCPSPRVQKGAFGACLMNEVNLVSGCLNAIQDAAPNCDI 154

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T+K RIG+D Q     L + V  + +S       +HAR A L GLSPK+NR +P L YD 
Sbjct: 155 TIKHRIGLDKQTEYQPLADFVGELARSTNCRTFIVHARNAWLDGLSPKENRDVPPLRYDY 214

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY++K+E  DL I +NGG+    Q  + L  VDGVM+GR AY N  ++ + D  F    T
Sbjct: 215 VYQLKQEFVDLEIIINGGITTNEQIHQHLQYVDGVMVGREAYHNPMLMKSWDAQFYGDTT 274

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHS--GGKLQQITRHMIGLFHGFPNSRRCRHI 296
                        + ++   + DYA   L +  G  L+ + RH +GL HG   +R  R +
Sbjct: 275 PE---------ITYDELINRLYDYAKIQLAANRGTILRHMARHYLGLMHGLHGARTWRRM 325

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L+      +    ++  A  ++ E 
Sbjct: 326 LSDADLLKSNRAELLLEALAMVRED 350


>gi|294669488|ref|ZP_06734555.1| hypothetical protein NEIELOOT_01386 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308401|gb|EFE49644.1| hypothetical protein NEIELOOT_01386 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 328

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 127/325 (39%), Positives = 180/325 (55%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR  AR +T +  LYTEMI A A++ GD    L  +  E P+ALQ+GG++  
Sbjct: 1   MLDWTDRHYRHMARQITRHTWLYTEMINAGAVIYGDPDRFLLKNDGENPVALQLGGSEPQ 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA     +GY+EINLN GCPS RV +G+FGACLM   D+V DC+ AM +A     V
Sbjct: 61  DLAKAAAKAAAYGYDEINLNCGCPSPRVQKGAFGACLMKEADLVADCLNAMQEAAPDCAV 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D +     L + V ++ +K+      +HAR A L+GLSPK+NR +P L YD 
Sbjct: 121 TVKHRIGLDCETDYQPLADFVGTLAEKTDCTTFIVHARNAWLEGLSPKENRDVPPLRYDY 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E P L I +NGG++   +    L  VDGVM+GR  Y N  ++   D  F     
Sbjct: 181 VYRLKREFPALEIIINGGIKTNDEIAAHLQHVDGVMVGRECYHNPMLMRDWDRLFYGDDH 240

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHI 296
                        + ++   + DYAA  L +G    L+ + RH +GL HG   +R  R +
Sbjct: 241 AP---------VSYAELVGRLKDYAAAQLAAGRGTILRHMARHYLGLMHGLNGARHWRRM 291

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L+           +I  A+  +  +
Sbjct: 292 LSDAELLKPNDPDLILRAWEQVERA 316


>gi|71274660|ref|ZP_00650948.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Dixon]
 gi|71899628|ref|ZP_00681782.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
 gi|170730927|ref|YP_001776360.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa M12]
 gi|71164392|gb|EAO14106.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Dixon]
 gi|71730580|gb|EAO32657.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
 gi|167965720|gb|ACA12730.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa M12]
          Length = 340

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 137/319 (42%), Positives = 197/319 (61%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAARIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVN-GIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V  + ++  +  I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVSRASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN    
Sbjct: 203 YRLKRERPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSN---- 258

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT 
Sbjct: 259 -------APLLPRTLLLRALRPYVEAWLEQGLALRHIVRHLLGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|218294737|ref|ZP_03495591.1| dihydrouridine synthase DuS [Thermus aquaticus Y51MC23]
 gi|218244645|gb|EED11169.1| dihydrouridine synthase DuS [Thermus aquaticus Y51MC23]
          Length = 342

 Score =  295 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 122/322 (37%), Positives = 183/322 (56%), Gaps = 16/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+R+  R ++    LYTEM V  A+L+G+++ +LGF  +E+PLALQ+ G D  
Sbjct: 11  MVDRTDRHFRYLVRQVSRGVRLYTEMTVDQAVLKGNRERLLGFRPEERPLALQLAGHDPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E FGY+E+NLN+GCPS R  EG +GACL+ +P  V + + AM +A+ +PV+
Sbjct: 71  SLAEAARIGEAFGYDEVNLNLGCPSERAQEGGYGACLLRDPGRVAEILRAMVQAVRVPVS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D      AL  LV+   +SGV    +HAR A+L  LS + NR+IP L ++ VY
Sbjct: 131 VKMRLGLDGGESYPALARLVERFAQSGVEVFIVHARSALLA-LSTRANREIPPLRHEWVY 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L    NGG+  + +AL  L  VDG M+GRA Y++  +L   D+         
Sbjct: 190 RLKEDFPHLTFVTNGGIRSLEEALAHLKRVDGAMLGRAVYEDPFVLEEADQKVFGLPHRP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +          +++ +M  Y    +  G     + RHM+ LF G P  R  R +L+  
Sbjct: 250 SRL----------QVARAMRAYLEEEVALGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEG 299

Query: 301 AGASTATHHIIETAFNLMIESL 322
                     ++ A  L+ E +
Sbjct: 300 RSLKA-----LDEALRLVEEEV 316


>gi|197301311|ref|ZP_03166396.1| hypothetical protein RUMLAC_00042 [Ruminococcus lactaris ATCC
           29176]
 gi|197299629|gb|EDY34144.1| hypothetical protein RUMLAC_00042 [Ruminococcus lactaris ATCC
           29176]
          Length = 320

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 81/302 (26%), Positives = 139/302 (46%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  + +L     E+P++LQ  G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYNNKNTETLLEIHPDEQPVSLQFFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK VE+  ++ +++N+GCP  +V +   G+ LM NP +  + I+AM KA+  P
Sbjct: 79  PQIMSEMAKRVEERPFDIMDINMGCPVPKVVKNGEGSALMKNPKLAHEIISAMVKAIRKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K  + +G   I +H R         ++       D++I
Sbjct: 139 VTVKIRKGFDD--NCINAVEMAKIAEDAGAAAIAVHGRT--------REQYYSGKADWEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A  ++     DGVMI R A  N  + + + E+    
Sbjct: 189 IRQVK-EAVSIPVIGNGDVTSPERADAMVKETGCDGVMIARGAQGNPWIFSEMIEHERTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P    + K   R     +  Y   +L     ++++ +H+     G P S + R  
Sbjct: 248 KIPSRPTNEEIRKMMLRHAKLQL-QYKGEYLG----IREMRKHVAWYTKGLPGSAKLREE 302

Query: 297 LT 298
           + 
Sbjct: 303 IN 304


>gi|170742500|ref|YP_001771155.1| tRNA-dihydrouridine synthase A [Methylobacterium sp. 4-46]
 gi|168196774|gb|ACA18721.1| TIM-barrel protein, yjbN family [Methylobacterium sp. 4-46]
          Length = 327

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 147/318 (46%), Positives = 202/318 (63%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT +A LYTEM+   A+L G ++ ++GF   E+P+A+Q+GG+D +
Sbjct: 11  MMDWTDRHCRAFHRTLTRHARLYTEMVTTGAVLHGPRERLIGFDPAEQPVAIQLGGSDPA 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I E  GY E+NLNVGCPS RV +G FGACLM  PD+VG+C+AAM  A+++PVT
Sbjct: 71  DLAAAARIAEAEGYAEVNLNVGCPSDRVQDGRFGACLMREPDLVGECVAAMKAAVAVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVDDQ P  AL  L +S+ ++GV+G+ +HARKA L+GLSPK+NR +P LDY  V+
Sbjct: 131 VKCRIGVDDQDPEAALDALARSVARAGVDGLVVHARKAWLQGLSPKENRDVPPLDYGRVH 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K  +PDL + +NGGL  + +A   L  VDG M+GRAAY   A+L  VD          
Sbjct: 191 RLKAAHPDLPVAINGGLRSLDEARAQLAHVDGAMLGRAAYAEPALLLAVDPVLFGAPAPV 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +     V+             Y +  L  G +L  ITRHM+GLF+G P +R  R  L+ E
Sbjct: 251 ADPFEAVEA---------FLPYLSARLAEGVRLHAITRHMLGLFNGRPGARAFRRHLSTE 301

Query: 301 AGASTATHHIIETAFNLM 318
              ++A   ++  A   +
Sbjct: 302 GMRASAGTDVLRDAVARV 319


>gi|319779632|ref|YP_004130545.1| tRNA dihydrouridine synthase A [Taylorella equigenitalis MCE9]
 gi|317109656|gb|ADU92402.1| tRNA dihydrouridine synthase A [Taylorella equigenitalis MCE9]
          Length = 325

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 123/319 (38%), Positives = 181/319 (56%), Gaps = 10/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TD+H RFF RLL+  ALL+TEM+   A++ GD    L F+ +E P+ALQ+GGA+  
Sbjct: 17  MLDVTDKHCRFFHRLLSPEALLFTEMVTTGALIFGDVPRHLDFNVEEHPVALQLGGAEPK 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +K+ E++GY+EINLN GCPS RV +GSFGACLML PD+V DC  AM +  ++P++
Sbjct: 77  DLAYCSKLGEEWGYDEINLNCGCPSDRVQKGSFGACLMLEPDLVADCWVAMNECTTVPIS 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+GVDD      + + V  +   G      HAR A LKGLSPKDNR IP L YD V 
Sbjct: 137 IKHRLGVDDHNDYEFVYHFVSKLYDVGCRLFITHARNAFLKGLSPKDNRSIPPLKYDYVS 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + PD    +NGG+ +   A+++L   DG+M+GR A+        +    +     S
Sbjct: 197 RLKADFPDANFVINGGISNYELAMQLLEEFDGIMLGRLAWHEPRAFMNIA---TTEFERS 253

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P      +D        +  YA +++ +GG L+++   ++G  +G   +R+ R IL+  
Sbjct: 254 EPPNFTFIRDA-------LIGYAKKNIENGGSLREVVNPVLGFMNGLKGARKFRQILSNP 306

Query: 301 AGASTATHHIIETAFNLMI 319
                    II  AF   +
Sbjct: 307 DLLKRNDISIIGEAFAPFL 325


>gi|15836989|ref|NP_297677.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa 9a5c]
 gi|38605069|sp|Q9PGB5|DUSA_XYLFA RecName: Full=tRNA-dihydrouridine synthase A
 gi|9105221|gb|AAF83197.1|AE003890_6 conserved hypothetical protein [Xylella fastidiosa 9a5c]
          Length = 340

 Score =  294 bits (754), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 137/322 (42%), Positives = 197/322 (61%), Gaps = 12/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D+GY+EINLN GCPS RV  GSFGA LM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAARIAVDWGYSEINLNCGCPSDRVQAGSFGARLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVN-GIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V  + ++  +  I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVSRASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L   D   SN    
Sbjct: 203 YRLKRERPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFDCALSN---- 258

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y    L  G  L+ I RH+ GLFHG P  R  R +LT 
Sbjct: 259 -------APLLPRALLLRALRPYVEVWLEQGLTLRHIVRHLFGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLMIES 321
               S A   ++E A +++ + 
Sbjct: 312 GGQRSDADWSLVEQALSIIEDQ 333


>gi|163857356|ref|YP_001631654.1| tRNA-dihydrouridine synthase A [Bordetella petrii DSM 12804]
 gi|163261084|emb|CAP43386.1| putative dihydrouridine synthase [Bordetella petrii]
          Length = 358

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 130/318 (40%), Positives = 184/318 (57%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL   A LYTEMI   A+L G+    L F   E P+ALQ+GG++  
Sbjct: 34  MIDVTDRHCRYFHRLLAPRARLYTEMITTGALLHGNVGRHLDFDAAEHPVALQLGGSEPD 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++   +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+ +PVT
Sbjct: 94  ALAHAARLGRQWGYDEINLNCGCPSERVQRGAFGACLMAEPALVADCMKAMQDAVDLPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G+D       +R+ V +I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 154 IKHRLGLDYDESYSFVRDFVGAIHATGCRVFIVHARNAVLKGLSPKDNREIPPLRYDVAR 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + PD  I LNGGL D +QA+      DGVM+GRAA+    +L+ V       +   
Sbjct: 214 QLKADFPDSVIVLNGGLADAAQAVGAAGEFDGVMLGRAAWHTPRVLSEVSMQLWPSVRLP 273

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +            ++  +M  YAA  +  G  L+ I R ++GL +G   +RR R +L+  
Sbjct: 274 TDA----------QVVDAMVRYAAGQVAQGVPLRVIVRPLLGLVNGQSGARRWRRMLSDP 323

Query: 301 AGASTATHHIIETAFNLM 318
           A  +     +I  A+  +
Sbjct: 324 ARLAANDAGLIYEAWRSL 341


>gi|329119729|ref|ZP_08248409.1| tRNA dihydrouridine synthase A [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327464178|gb|EGF10483.1| tRNA dihydrouridine synthase A [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 346

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 130/325 (40%), Positives = 186/325 (57%), Gaps = 13/325 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH+RF AR ++ +ALLYTEM+ A A++ GD    L  +  E P+ALQ+GG++ +
Sbjct: 21  MLDWTDRHFRFLARQISRHALLYTEMVNAGAVVHGDAARFLLKNDCENPVALQLGGSEPA 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA     +GY+EINLN GCPS RV +G+FGACLM    +V DC+ AM  A     V
Sbjct: 81  LLAKAAAEAAAWGYDEINLNCGCPSPRVQKGAFGACLMNEVALVADCLNAMQDAAPDCAV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D Q     L + V ++ +K+      +HAR A L GLSPK+NR +P L YD 
Sbjct: 141 TVKHRIGIDRQTDYQPLADFVGTLSEKTACTVFIVHARNAWLDGLSPKENRDVPPLKYDY 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K+E P L I LNGG++  ++A   L   DGVM+GR  Y N  ++   D  F     
Sbjct: 201 VYRLKREFPALQIVLNGGIKTNAEAALHLQHTDGVMVGRECYHNPMLMRDWDRLFYGDTR 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRCRHI 296
             +          + +++  + DYAA  L  G    L+ ITRH +GL HG   +R+ R +
Sbjct: 261 EPA---------VYAELAERLRDYAAERLADGRGSILRHITRHCLGLMHGLNGARQWRRM 311

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L+           +I  A+  + ++
Sbjct: 312 LSDAELLKDNDPELIMRAWREVEKA 336


>gi|172037594|ref|YP_001804095.1| putative dihydrouridine synthase TIM-barrel protein nifR3
           [Cyanothece sp. ATCC 51142]
 gi|171699048|gb|ACB52029.1| putative dihydrouridine synthase TIM-barrel protein nifR3
           [Cyanothece sp. ATCC 51142]
          Length = 335

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 135/320 (42%), Gaps = 21/320 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R  + N+++YTEM+ A  I        ++     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYSPNSMMYTEMVSATEIHHLKQLPRLMEIDPHEQPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  + KA+ +PVTV
Sbjct: 94  MAEAAQKAVGEGAKTIDINMGCPVNKITKKGGGSSLLRQPEIAEKLVKEVVKAVDVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DD    + +    + ++ SG + + +H R         +         ++ + +
Sbjct: 154 KTRIGWDDNE--INILEFAQKMQDSGASMLTLHGRT--------RAQGYTGKARWEWIKK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + I  NG +  +  A+  L     DGVM  R       ++  +D +F      
Sbjct: 204 VK-EILTIPIIANGDIFSVEAAINCLEITGADGVMCSRGTLGYPFLVGEIDHFFQTGKLQ 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P       +  ++    + DY  +       + Q  +H+     GFP +   R  ++ 
Sbjct: 263 NQPTPID-RLECAKEHLKGLWDYKGKR-----GIYQARKHLSWYCKGFPGASELRDKVSR 316

Query: 300 EAGASTATHHIIETAFNLMI 319
                   + +++    L+I
Sbjct: 317 IETV-EEGYQLLDQGIELII 335


>gi|210610329|ref|ZP_03288358.1| hypothetical protein CLONEX_00548 [Clostridium nexile DSM 1787]
 gi|210152559|gb|EEA83565.1| hypothetical protein CLONEX_00548 [Clostridium nexile DSM 1787]
          Length = 324

 Score =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 80/302 (26%), Positives = 137/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K    +L    +E P++LQ+ G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYNNKNTKALLEIHPEELPVSLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  ++ +   G+ LM NP +V + +    +A+  P
Sbjct: 79  PDVISEIAKRIEELPFSILDINMGCPVPKIVKNGEGSALMKNPKLVYEIVRKTARAIQKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K I+ +G   + +H R         ++       D+DI
Sbjct: 139 VTVKIRKGFDDT--CINAVEIAKIIEDAGGKAVAVHGRT--------REQYYSGKADWDI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A+ I      DGVMIGR A  N  + + + EY    
Sbjct: 189 IRQVK-EAVSIPVIGNGDVVSGESAIAIQKETGCDGVMIGRGAQGNPWIFSELLEYERTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + K   R     M  Y   +L     ++++ +H+     G PNS + R  
Sbjct: 248 KMPLRPSVEAIKKMMIRHAQLQM-QYKGEYLG----IREMRKHVSWYTSGLPNSAKLRDE 302

Query: 297 LT 298
           + 
Sbjct: 303 IN 304


>gi|291526252|emb|CBK91839.1| tRNA-U20-dihydrouridine synthase [Eubacterium rectale DSM 17629]
          Length = 328

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 80/303 (26%), Positives = 140/303 (46%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L    +EKP++LQ+ G+D
Sbjct: 25  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTESLLSIDEREKPVSLQMFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ +++N+GCP  ++     G+ LM NP + G  I ++ KA+  P
Sbjct: 84  PQIMAQIAKQIEERPFDILDINMGCPVPKIVNNGEGSALMKNPILAGRIIESIVKAIDKP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    L    ++SG + + +H R         ++       D+DI
Sbjct: 144 VTVKIRKGFDDE--HVNAVELAHVAEESGASAVAVHGRT--------REQYYSGKADWDI 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG L      +K+      DG MI R A  N  + + +  YF   
Sbjct: 194 IRQVK-EAVSIPVIGNGDLLCAEDVIKMQEQTGCDGFMIARGAQGNPWIFSQILHYFETG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +   R  +  M ++   +      + ++ +H      G+P+S R R  
Sbjct: 253 EHQEKPSFEEVRRMILRH-ARMMIEFKGEY----TGIHEMRKHTAWYTAGYPHSSRLRAA 307

Query: 297 LTV 299
           +  
Sbjct: 308 VNT 310


>gi|149201731|ref|ZP_01878705.1| tRNA-dihydrouridine synthase A [Roseovarius sp. TM1035]
 gi|149144779|gb|EDM32808.1| tRNA-dihydrouridine synthase A [Roseovarius sp. TM1035]
          Length = 296

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 129/297 (43%), Positives = 171/297 (57%), Gaps = 11/297 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A A++RG    +L  S +E P+ALQ+GG+D ++L +AA++    GY EINLN GCPS
Sbjct: 1   MVTAPALVRGGAVYLLEHSPEEYPVALQLGGSDPAELAQAARMGAQAGYAEINLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGA LM  P +V  C  AM +A  + VTVKCRIGVDDQ P   L   +  +  
Sbjct: 61  DRVQSGRFGAILMTEPALVAACCVAMREAQPVEVTVKCRIGVDDQNPEEVLPEFLAHVVA 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +GV  + IHARKA L GLSPK+NR IP LDYD+V  +K   P+L I +NGG+  + QA+ 
Sbjct: 121 AGVQRVQIHARKAWLDGLSPKENRDIPPLDYDLVQRMKMLFPNLHISINGGITSLDQAVS 180

Query: 206 IL-PSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
           +L   +DGVM+GRAAY   A +L   D          +  +  V           M  Y 
Sbjct: 181 LLDQGLDGVMVGRAAYHQPADILCAADRRIFGTSGPDTTPEGAVHA---------MLPYI 231

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
             HL SGG+L QITRHM+GLF G P +R  R  L+  A    A   ++E A   + +
Sbjct: 232 EAHLASGGRLNQITRHMLGLFAGKPGARAWRRHLSEGASRPGAGPELVERALAEITD 288


>gi|71901816|ref|ZP_00683882.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
 gi|71728415|gb|EAO30580.1| Dihydrouridine synthase, DuS [Xylella fastidiosa Ann-1]
          Length = 332

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 139/319 (43%), Positives = 195/319 (61%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA+I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAARIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVK-SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V   I  S    I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVIGASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN    
Sbjct: 203 YRLKRECPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSN---- 258

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                          +  ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT 
Sbjct: 259 -------APLLPRALLLRALRPYVEAWLEQGLTLRHIVRHLLGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|291526763|emb|CBK92349.1| tRNA-U20-dihydrouridine synthase [Eubacterium rectale M104/1]
          Length = 323

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 80/303 (26%), Positives = 140/303 (46%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L    +EKP++LQ+ G+D
Sbjct: 25  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTESLLSIDEREKPVSLQMFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E+  ++ +++N+GCP  ++     G+ LM NP + G  I ++ KA+  P
Sbjct: 84  PQIMAQIAKQIEERPFDILDINMGCPVPKIVNNGEGSALMKNPILAGQIIESIVKAIDKP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    L    ++SG + + +H R         ++       D+DI
Sbjct: 144 VTVKIRKGFDDE--HVNAVELAHVAEESGASAVAVHGRT--------REQYYSGKADWDI 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG L      +K+      DG MI R A  N  + + +  YF   
Sbjct: 194 IRQVK-EAVSIPVIGNGDLLCAEDVIKMQEQTGCDGFMIARGAQGNPWIFSQILHYFETG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +   R  +  M ++   +      + ++ +H      G+P+S R R  
Sbjct: 253 EHQEKPSFEEVRRMILRH-ARMMIEFKGEY----TGIHEMRKHTAWYTAGYPHSSRLRAA 307

Query: 297 LTV 299
           +  
Sbjct: 308 VNT 310


>gi|332991645|gb|AEF01700.1| tRNA-dihydrouridine synthase A [Alteromonas sp. SN2]
          Length = 308

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 111/296 (37%), Positives = 165/296 (55%), Gaps = 5/296 (1%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   AI+ G   + LGF+ QE P+ALQ+GG++   + + A + ++ GY+E+N+NVGCPS
Sbjct: 1   MVTTGAIIYGKG-DYLGFNEQEHPVALQLGGSNPEHMAKCAALAQERGYDEVNINVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  GSFGACLM  P++V D + AM   + IPVTVKCRIG+DD          +  +  
Sbjct: 60  DRVKNGSFGACLMAQPEVVADNVKAMQAEVDIPVTVKCRIGIDDMDEYKDFARFIDIVAT 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G +   +HARKA L+GLSPK+NR IP L+Y  V+ +K+ +P+L I +NGG++ ++ A +
Sbjct: 120 AGCDTFIVHARKAWLQGLSPKENRDIPPLNYPRVHMLKESHPELSISINGGIKSLADAQE 179

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVMIGR  Y N  +L+TVD       +     +  V     + I        AR
Sbjct: 180 QLKYVDGVMIGREVYANPYILSTVDAEIFGDNSVQPISRRDVVLKMQQYIEKC----IAR 235

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
                 K   + RHM+GL+ G    R  R  L+      +   H++  A   +  +
Sbjct: 236 QDDPYFKPWHVARHMLGLYQGQAGGRIWRRYLSQNGTGKSPDPHLLMNALEAVESA 291


>gi|160939910|ref|ZP_02087257.1| hypothetical protein CLOBOL_04801 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437344|gb|EDP15109.1| hypothetical protein CLOBOL_04801 [Clostridium bolteae ATCC
           BAA-613]
          Length = 321

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 134/317 (42%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R       + TEM+ A A+L  +K  + +L     E+P A+Q+ G++
Sbjct: 19  MAGVTDLPFRVLCRE-QGAGCVVTEMVSAKAVLYNNKNTRELLQIDPAERPAAVQLFGSE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +E+  Y+ I++N+GCP  ++     G+ LM NP+   + + AM KA+  P
Sbjct: 78  PDIMAEIAARLEEGPYDYIDVNMGCPVPKIVNNGEGSALMKNPERAKEVLTAMVKAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D   +V      K  +  GV  + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFND--LSVNAVEFAKMAESCGVAAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A ++L     DG+M+ R A  N  +   ++ Y    
Sbjct: 188 IRQVK-EAVRIPVIGNGDIFTPEDAGRMLKETGCDGIMVARGAKGNPWLFGRINHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R           +    G  ++++  HM     G P+S   R+ 
Sbjct: 247 EVLPGPSMAEIKAMILRH-----GRMLVQFKGEGVAMREMRGHMAWYTKGMPHSATLRNE 301

Query: 297 LTVEAGASTATHHIIET 313
           +            +++ 
Sbjct: 302 INQVETLEG-FVELLDR 317


>gi|153815945|ref|ZP_01968613.1| hypothetical protein RUMTOR_02190 [Ruminococcus torques ATCC 27756]
 gi|317500709|ref|ZP_07958927.1| tRNA-dihydrouridine synthase B [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331089816|ref|ZP_08338709.1| hypothetical protein HMPREF1025_02292 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145846764|gb|EDK23682.1| hypothetical protein RUMTOR_02190 [Ruminococcus torques ATCC 27756]
 gi|316897903|gb|EFV19956.1| tRNA-dihydrouridine synthase B [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330403513|gb|EGG83071.1| hypothetical protein HMPREF1025_02292 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 319

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 140/303 (46%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K    ++    +E+P++LQ+ G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLGMEMVSAKAILYQNKNTEKLMEIHPEEQPVSLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V +   G+ LM NP +V + + A+ KA+  P
Sbjct: 79  PKIMSEMAKRIEERPFAILDINMGCPVPKVVKNGEGSALMKNPSLVYEIVNAIVKAIEKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    + ++ +++G + + +H R         ++       D+DI
Sbjct: 139 VTVKIRKGFDD--AHVNAVEVARAAEEAGASAVAVHGRT--------REQYYSGEADWDI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A +++     DG+MI R A  N  + + +     N 
Sbjct: 189 IRQVK-EAVSIPVIGNGDVTTPEKAEELVQTTGCDGIMIARGAQGNPWIFSEMIGKEKNG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +T   P K  +     R     +     ++      ++++ +H+     G   +   R  
Sbjct: 248 VTPPRPDKEAIRNMILRHSKLQI-----QYRGEFAGMREMRKHVAWYTKGLTGAADLRRR 302

Query: 297 LTV 299
           +  
Sbjct: 303 VNE 305


>gi|167745535|ref|ZP_02417662.1| hypothetical protein ANACAC_00226 [Anaerostipes caccae DSM 14662]
 gi|167655256|gb|EDR99385.1| hypothetical protein ANACAC_00226 [Anaerostipes caccae DSM 14662]
          Length = 332

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 139/317 (43%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    LLYTEM+ A  +         +L     E+P+A QI G++
Sbjct: 26  MAGVTDLPYRLLCKEM-GAGLLYTEMVSAKGMYYNSPNTGPLLAKEEWERPIAAQIFGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  V++ G++ I++N+GCP  ++     G+ LM +P + G  I AM   LS+P
Sbjct: 85  PELMADMAVRVQEMGFDLIDINMGCPVPKIVNNGDGSALMKDPVLAGKIIKAMADRLSVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    + K  ++SG   + +H R         ++       D+DI
Sbjct: 145 VTVKIRKGFDDE--HVNAVEMAKIAEQSGAAAVAVHGRT--------REQYYSGKADWDI 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A  +L     DG MI R A  N  +   +  YF   
Sbjct: 195 IRQVK-EAVSIPVIGNGDINSPLDAEAMLRETGCDGFMIARGAKGNPWIFKELCHYFDTG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +   R  +  M +Y   ++     ++++ +H+    HG   + + R  
Sbjct: 254 ELMPRPEIEEIIQMILRH-ARMMIEYKGEYIG----IREMRKHVSWYTHGLAGAAKLRDQ 308

Query: 297 LTVEAGASTATHHIIET 313
           +   A +      II  
Sbjct: 309 VN-HAESIGELEAIIRN 324


>gi|291551191|emb|CBL27453.1| tRNA-U20-dihydrouridine synthase [Ruminococcus torques L2-14]
          Length = 321

 Score =  292 bits (749), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 79/302 (26%), Positives = 139/302 (46%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K  +++L     E+P++LQ  G+D
Sbjct: 21  MAGVTDLPFRVLCKE-QGAGLLCMEMVSAKAILYNNKNTESLLEIHPDEQPVSLQFFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK VE+  ++ +++N+GCP  +V     G+ LM NP +V + ++AM KA+  P
Sbjct: 80  PKIMSEMAKRVEERPFDIMDINMGCPVPKVVRNGEGSALMKNPKLVYEIVSAMVKAIDKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    + K I+++G   + +H R         ++       D+DI
Sbjct: 140 VTVKIRKGFDD--SCVNAVEIAKIIEEAGAAAVAVHGRT--------REQYYSGQADWDI 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A +++     DG+MI R A  N  + + +  Y    
Sbjct: 190 IRQVK-EAVSIPVIGNGDVTSPQKAEELVKQTGCDGIMIARGAQGNPWIFSEMITYEETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P K  V     R     +     ++      ++++ +H+     G   S + R  
Sbjct: 249 TLPERPGKEEVRDMMLRHARLQL-----KYKGEFIGIREMRKHVAWYTKGLKGSAKLREE 303

Query: 297 LT 298
           + 
Sbjct: 304 IN 305


>gi|258545773|ref|ZP_05706007.1| tRNA dihydrouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258519018|gb|EEV87877.1| tRNA dihydrouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 309

 Score =  292 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 123/319 (38%), Positives = 169/319 (52%), Gaps = 14/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT    R   RL T  ALLYTEM+   A++ GD +  L     + P ALQ+GG +  
Sbjct: 1   MLDWTTPECRALHRLFTRRALLYTEMVTTGALIYGDAERHLQHHG-DAPCALQLGGGEPE 59

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
            L  A  I   +GY EINLNVGCPS RV     GACLM +  +V +C++AM  A   +PV
Sbjct: 60  ALAHACAIALPYGYQEINLNVGCPSDRVQNNRIGACLMDDAALVAECVSAMQAAAGAVPV 119

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+ +D+Q        +     +S      IHARKA L+GLSPK NR +P L+Y +V
Sbjct: 120 TVKHRLAIDEQDEREVFHFVETVASRSPCRVFIIHARKAWLQGLSPKANRDVPPLNYPLV 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           YE+K+  P+L I +NGG+ D++Q    L  VDGVM+GRAAY+N  +L   D  +      
Sbjct: 180 YEVKRRFPELTIVINGGIGDLAQCQAHLQHVDGVMLGRAAYQNPELLLLADTLYGEAAQT 239

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
              +  R+                A  L  G  L   TRH++GLF G   ++  R IL+ 
Sbjct: 240 LDAVLPRIRA------------LIAERLARGEVLSHYTRHLLGLFPGVRGAKIYRRILSE 287

Query: 300 EAGASTATHHIIETAFNLM 318
           +A +  A   + E A   +
Sbjct: 288 DARSPDAGIAVFERALAAV 306


>gi|317472901|ref|ZP_07932207.1| dihydrouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316899621|gb|EFV21629.1| dihydrouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 332

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 139/317 (43%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    LLYTEM+ A  +         +L     E+P+A QI G++
Sbjct: 26  MAGVTDLPYRLLCKEM-GAGLLYTEMVSAKGMYYNSPNTGPLLAKEEWERPIAAQIFGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  V++ G++ I++N+GCP  ++     G+ LM +P + G  I AM   LS+P
Sbjct: 85  PELMADMAVRVQEMGFDLIDINMGCPVPKIVNNGDGSALMKDPVLAGKIIKAMADRLSVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   V    + +  ++SG   + +H R         ++       D+DI
Sbjct: 145 VTVKIRKGFDDE--HVNAVEMARIAEQSGAAAVAVHGRT--------REQYYSGKADWDI 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A  +L     DG MI R A  N  +   +  YF   
Sbjct: 195 IRQVK-EAVSIPVIGNGDINSPLDAEAMLRETGCDGFMIARGAKGNPWIFKELCHYFDTG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +   R  +  M +Y   ++     ++++ +H+    HG   + + R  
Sbjct: 254 ELMPRPEIEEIIQMILRH-ARMMIEYKGEYIG----IREMRKHVSWYTHGLAGAAKLRDQ 308

Query: 297 LTVEAGASTATHHIIET 313
           +   A +      II  
Sbjct: 309 VN-HAESIGELEAIIRN 324


>gi|291561472|emb|CBL40271.1| tRNA-U20-dihydrouridine synthase [butyrate-producing bacterium
           SS3/4]
          Length = 319

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 76/306 (24%), Positives = 134/306 (43%), Gaps = 21/306 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R      L+  EM+ A AIL  +K    +L    +E+P++LQ+ G+D
Sbjct: 19  MAGVTDMPYRILCRE-QGAGLVCMEMVSAKAILYKNKNTQELLKVDERERPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +ED  Y+  ++N+GCP  ++ +   G+ LM NP +V + +  + KA+  P
Sbjct: 78  PDIVADIAASLEDGPYDIFDINMGCPVPKIVKNGEGSALMRNPKLVEEILTKLVKAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K  + +GV  + +H R         ++       D++I
Sbjct: 138 VTVKFRKGFDDT--CINAVEIAKIAESAGVAAVAVHGRT--------REQYYSGKADWNI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+KK    + +  NG +     A +++     DG+M+ R A  N  +   +  Y    
Sbjct: 188 IREVKKAV-KIPVIGNGDVFTPQDAKRLVEETGCDGIMVARGAKGNPWIFKQITHYLETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R     M             ++++ +H+     G+PNS   R+ 
Sbjct: 247 ELLPRPSVEELKAMILRHGQMMM-----EFKGELAGMREMRKHVAWYTAGYPNSAALRNE 301

Query: 297 LTVEAG 302
           +   A 
Sbjct: 302 INSVAT 307


>gi|28199556|ref|NP_779870.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa Temecula1]
 gi|182682292|ref|YP_001830452.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa M23]
 gi|38604766|sp|Q87AY2|DUSA_XYLFT RecName: Full=tRNA-dihydrouridine synthase A
 gi|28057671|gb|AAO29519.1| conserved hypothetical protein [Xylella fastidiosa Temecula1]
 gi|182632402|gb|ACB93178.1| dihydrouridine synthase DuS [Xylella fastidiosa M23]
          Length = 332

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 197/319 (61%), Gaps = 12/319 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ +
Sbjct: 23  MMNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPA 82

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L +AA I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVT
Sbjct: 83  LLAKAASIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVT 142

Query: 121 VKCRIGVDDQIPAVALRNLVK-SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VKCR+GV++          V   I  S    I +HAR A L+GLSPK+NR+IP L YD V
Sbjct: 143 VKCRLGVNEDDDYGRFAKFVDWVIGASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN    
Sbjct: 203 YRLKRECPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSN---- 258

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P+  R           ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT 
Sbjct: 259 -APVLPRALL------LRALRPYVEAWLEQGVTLRHIVRHLLGLFHGQPGGRVFRQVLTQ 311

Query: 300 EAGASTATHHIIETAFNLM 318
               S A   ++E A +++
Sbjct: 312 GGQRSDADWSLVEQALSII 330


>gi|150392209|ref|YP_001322258.1| nifR3 family TIM-barrel protein [Alkaliphilus metalliredigens QYMF]
 gi|149952071|gb|ABR50599.1| putative TIM-barrel protein, nifR3 family [Alkaliphilus
           metalliredigens QYMF]
          Length = 321

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 138/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +  + ++Y EM+ A  +  GDKK   +L    +EKP ALQI G++
Sbjct: 17  MAGVTDLPFRLICKKM-GSGMVYMEMVSAKGLYYGDKKTERLLQIHPEEKPAALQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++ D     +++N+GCP+ ++ +   G+ LML+P      + A+ +    P
Sbjct: 76  PDIMAKAAYMLNDRENIILDINMGCPTPKIVKNGDGSALMLDPPRAARVVKAVVRESIKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   +    + K ++ SG   I +H R         ++       D+DI
Sbjct: 136 VTVKIRKGWDDKQ--INAVEMAKILEDSGAQAIAVHGRT--------REQFYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG +  +  A  +L     DG+MIGR A  N  +   VD Y  N 
Sbjct: 186 IKQVKEAVT-IPVIGNGDVFSVEDARDMLEQTQCDGIMIGRGAQGNPWIFKRVDAYMKNG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P      +           D   ++      ++++ +H+     G  NS   R++
Sbjct: 245 EVLAEPGLEERVEMILEH-----MDLVIKYKGEYIGIREMRKHVGWYLKGLKNSASIRNL 299

Query: 297 LT 298
           + 
Sbjct: 300 IN 301


>gi|225025575|ref|ZP_03714767.1| hypothetical protein EIKCOROL_02477 [Eikenella corrodens ATCC
           23834]
 gi|224941613|gb|EEG22822.1| hypothetical protein EIKCOROL_02477 [Eikenella corrodens ATCC
           23834]
          Length = 317

 Score =  292 bits (747), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 127/322 (39%), Positives = 187/322 (58%), Gaps = 13/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRHYR+ AR ++ +A LYTEMI A AI+ G  +  LG    E P+ALQ+GG++ +
Sbjct: 1   MLDWTDRHYRYMARQISRHAWLYTEMIHAGAIIHGQAERFLGKDESENPVALQLGGSNPA 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            L +AA I   +GY+EINLN GCPS RV +G+FGACLM   D+V DC+ AM +A     V
Sbjct: 61  DLAKAAAIAAGWGYDEINLNCGCPSPRVQKGAFGACLMNEVDLVADCLNAMQEAAPDCAV 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK RIG+D Q     + + V ++   +      +HAR A L+GLSPK+NR +P L YD 
Sbjct: 121 TVKHRIGIDRQTEYQTVCDFVGTLSDKTACRTYIVHARNAWLEGLSPKENRDVPPLKYDY 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           VY +K++ P L I +NGG++  ++  + L  VDGVMIGR AY N  ++ + D  F     
Sbjct: 181 VYRLKQDFPHLEIIINGGIKTNTEIAEHLQHVDGVMIGREAYHNPMLMQSWDRLFYGE-- 238

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL--QQITRHMIGLFHGFPNSRRCRHI 296
                  R+ +  +  +  ++  Y  R L +   L  + + RH +GL HG  ++R  R +
Sbjct: 239 -------RLPETDFNTLIHTLYRYMQRSLAADPGLTIRHMLRHYLGLLHGRNHARVWRQM 291

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L+      +    +I  A+  +
Sbjct: 292 LSDATLLQSNRPELILEAWEKV 313


>gi|52841692|ref|YP_095491.1| tRNA-dihydrouridine synthase A [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52628803|gb|AAU27544.1| zinc binding TIM barrel protein, YjbN family [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
          Length = 334

 Score =  291 bits (746), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 120/319 (37%), Positives = 175/319 (54%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A ++ +    L F++ E PLA+Q+GGAD S
Sbjct: 18  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGA-VQNNPDRALYFNSVEHPLAIQLGGADKS 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 77  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPEHVADCIRAIKQVVGIPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 137 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +         
Sbjct: 197 ELKKEIPHIFITINGNILTVEEINNHLKHVDGVMLGRLACDNPYQIAEIHQALY------ 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
                   K    ++  +  DY      +   L  + + +  L  G P ++  +  L   
Sbjct: 251 ----PEFIKIKRSQLLMNYLDYWFDQSRANLSLSILVKPLFNLAFGLPGAKHWKKKLMNI 306

Query: 299 VEAGASTATHHIIETAFNL 317
           ++   ++    +I+   NL
Sbjct: 307 IQEKNTSGFSELIQYLLNL 325


>gi|225389821|ref|ZP_03759545.1| hypothetical protein CLOSTASPAR_03569 [Clostridium asparagiforme
           DSM 15981]
 gi|225044131|gb|EEG54377.1| hypothetical protein CLOSTASPAR_03569 [Clostridium asparagiforme
           DSM 15981]
          Length = 319

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 78/302 (25%), Positives = 136/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      ++ TEM+ A AIL  +K  K +L   ++E+P A+Q+ G+D
Sbjct: 19  MAGVTDLPFRLLCRE-QGCGMVVTEMVSAKAILYKNKNTKELLTVRSEERPAAVQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +ED  Y+ I++N+GCP  ++     G+ LM +P      ++AM +A+  P
Sbjct: 78  PEIMAEIAAQIEDGPYDVIDVNMGCPVPKIVNNGEGSALMKDPKRAEAVLSAMVRAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D+  +V      K  +  GV  + +H R         ++       D+DI
Sbjct: 138 VTVKFRKGFNDE--SVNAVEFAKMAESCGVAAVAVHGRT--------REQYYSGTADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     A ++L     DG+M+ R A  N  +   ++ Y    
Sbjct: 188 IRRVK-EAVKIPVIGNGDVFTPEDAGRLLEQTGCDGIMVARGAKGNPWIFHRINHYLETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            +   P    + +   R  S  + DY    +     ++++  HM     G  +S   R  
Sbjct: 247 ESLPGPSVQEIREMILRH-SRMLADYKGERVA----MREMRSHMAWYTSGLAHSASIRRE 301

Query: 297 LT 298
           + 
Sbjct: 302 IN 303


>gi|167768161|ref|ZP_02440214.1| hypothetical protein CLOSS21_02717 [Clostridium sp. SS2/1]
 gi|317499618|ref|ZP_07957880.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167709685|gb|EDS20264.1| hypothetical protein CLOSS21_02717 [Clostridium sp. SS2/1]
 gi|291560187|emb|CBL38987.1| tRNA-U20-dihydrouridine synthase [butyrate-producing bacterium
           SSC/2]
 gi|316893093|gb|EFV15313.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 332

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 141/321 (43%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   +      ++ TEM+ A  +  G++K+  ++    +E P+A+QI G+D
Sbjct: 25  MAGVTDLPYRLLCKE-QGAGMMCTEMVSAKGLYYGNRKSEPLMATDPKEIPIAIQIFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  V D  +  I++N+GCP  ++     G+ LM NP++ G  I A+  A+ IP
Sbjct: 84  PEIMGQMAAKVNDGRFQMIDINMGCPVPKIVNNGDGSALMKNPELAGKVIKAVVDAVDIP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D++  +    + +  +++G   I +H R         ++       D+ I
Sbjct: 144 VTVKIRKGFNDEL--INAPEMAQVAQENGAAAIAVHGRT--------REQYYSGTADWSI 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E  D+ +  NG +      L++      DG MIGR A  N  +   +  +F   
Sbjct: 194 IRKVK-EAVDIPVIGNGDITCAKDVLRMQEETGCDGFMIGRRAKGNPWIFKEILHFFETG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V     R     M D+   ++     ++++ +H+     GFP + + R  
Sbjct: 253 EEMPRPSLEEVVAMMLRH-GQMMIDFKGEYIG----VREMRKHVAWYTFGFPGAAKLREK 307

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +            +++     
Sbjct: 308 VNHTETYEDL-EELLQNYLKA 327


>gi|54294497|ref|YP_126912.1| tRNA-dihydrouridine synthase A [Legionella pneumophila str. Lens]
 gi|53754329|emb|CAH15806.1| hypothetical protein lpl1566 [Legionella pneumophila str. Lens]
          Length = 330

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 119/319 (37%), Positives = 175/319 (54%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A ++ +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGA-VQNNPDRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPEHVADCIRAIKQVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +         
Sbjct: 193 ELKKEIPHIFITINGNILTVEEINSHLKHVDGVMLGRLACDNPYQIAEIHQALY------ 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
                   K    ++  +  DY      +   L  + + +  L  G P ++  +  L   
Sbjct: 247 ----PEFIKIKRSQLLINYLDYWFDQSRANLSLSILVKPLFNLAFGLPGAKHWKKKLMNI 302

Query: 299 VEAGASTATHHIIETAFNL 317
           ++   ++    +I+   NL
Sbjct: 303 IQEKNTSGFSELIQYLLNL 321


>gi|148358992|ref|YP_001250199.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|296107041|ref|YP_003618741.1| tRNA-dihydrouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
 gi|148280765|gb|ABQ54853.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|295648942|gb|ADG24789.1| tRNA-dihydrouridine synthase A [Legionella pneumophila 2300/99
           Alcoy]
          Length = 330

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 119/319 (37%), Positives = 175/319 (54%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A ++ +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGA-VQNNPDRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPEHVADCIRAIKQVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +         
Sbjct: 193 ELKKEIPHIFITINGNILTVEEINSHLKHVDGVMLGRLACDNPYQIAEIHQALY------ 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
                   K    ++  +  DY      +   L  + + +  L  G P ++  +  L   
Sbjct: 247 ----PEFIKIKRSQLLMNYLDYWFDQSRANLSLSILVKPLFNLAFGLPGAKHWKKKLMNI 302

Query: 299 VEAGASTATHHIIETAFNL 317
           ++   ++    +I+   NL
Sbjct: 303 IQEKDTSGFSELIQYLLNL 321


>gi|164686644|ref|ZP_02210672.1| hypothetical protein CLOBAR_00237 [Clostridium bartlettii DSM
           16795]
 gi|164604373|gb|EDQ97838.1| hypothetical protein CLOBAR_00237 [Clostridium bartlettii DSM
           16795]
          Length = 322

 Score =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 139/302 (46%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      +LYTEMI A A+   D   K +     +E P+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKQ-KGCGMLYTEMINAKALCYNDENTKKMTKIEDEEHPIAIQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I+       +++N+GCP+ +V +   G+ LM NP +    + A+ +  + P
Sbjct: 76  PEYMGRAAEILNSHSNEILDINMGCPAPKVIKNGDGSALMKNPKLAEQVMRAVVEHSTKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   +V    + K  +++G++ + IH R         ++       D+DI
Sbjct: 136 VTLKIRKGWDD--NSVNAVEIAKIAEQAGISALAIHGRT--------REQYYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK ++  + +  NG + ++  A+ +L   + D +MIGR A  N  +   ++ Y    
Sbjct: 186 IKEIK-DSISIPVIGNGDVFEIEDAINMLEKTNCDAIMIGRGAQGNPWIFNRINHYMQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P            +  ++ ++          ++++ +H+     G  NS R R  
Sbjct: 245 EILAKPTAEEKISTAIEHMKLAVAEH-----GEYVAVREMRKHIGWYIKGLKNSARYRDE 299

Query: 297 LT 298
           + 
Sbjct: 300 IN 301


>gi|289807774|ref|ZP_06538403.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 258

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 115/262 (43%), Positives = 155/262 (59%), Gaps = 12/262 (4%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVTV
Sbjct: 6   LSHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVTV 65

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K RIG+DDQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  VY
Sbjct: 66  KTRIGIDDQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVY 125

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTG 239
           ++K++ P L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T 
Sbjct: 126 QLKRDFPHLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTTD 185

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P+           +  +M  Y  R L  G  L  ITRHM+GLF G P +R+ R  L+ 
Sbjct: 186 TDPV----------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQGIPGARQWRRYLSE 235

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A  + A   ++E A  L+ + 
Sbjct: 236 NAHKAGADAAVLEQALKLIADK 257


>gi|320449546|ref|YP_004201642.1| tRNA-dihydrouridine synthase A [Thermus scotoductus SA-01]
 gi|320149715|gb|ADW21093.1| tRNA-dihydrouridine synthase A [Thermus scotoductus SA-01]
          Length = 344

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 121/318 (38%), Positives = 179/318 (56%), Gaps = 17/318 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+R+  R ++    LYTEM V  A+LRG  + +L F  +E P+ALQ+ G+D  
Sbjct: 11  MVDRTDRHFRYLVRQISRKVRLYTEMTVDQAVLRGKAERLLAFHPEEHPIALQLAGSDPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I + +GY+E+NLN+GCPS +  EG FGACL+L+P  V + + AM +A+ IPVT
Sbjct: 71  SLAEAARIGQAWGYDEVNLNLGCPSEKAQEGGFGACLLLDPIRVREILKAMVEAVEIPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+GV+ +     L   V++  ++GV    +HAR A+L  LS + NR++P L +D V+
Sbjct: 131 VKLRLGVEGE-SYPLLARWVEAYGETGVRVFIVHARSALLN-LSTRKNREVPPLRHDWVH 188

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L   LNGG+  + +AL  L  VDGVM+GRA Y++  +L   D          
Sbjct: 189 RLKADFPHLTFILNGGVRTLEEALPHLKKVDGVMMGRAVYEDPFVLEEADRRVFGLAHRP 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +           ++  M  Y       G     + RHM+ LF G P  R  R +L+ E
Sbjct: 249 SRL----------DVARRMRLYLEAEAQKGTPPWAVLRHMLNLFRGQPGGRLWRRLLS-E 297

Query: 301 AGASTATHHIIETAFNLM 318
             +  A    ++ A  L+
Sbjct: 298 GRSLGA----LDQALGLL 311


>gi|146329044|ref|YP_001209939.1| tRNA-dihydrouridine synthase A [Dichelobacter nodosus VCS1703A]
 gi|146232514|gb|ABQ13492.1| tRNA-dihydrouridine synthase A [Dichelobacter nodosus VCS1703A]
          Length = 335

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 121/319 (37%), Positives = 177/319 (55%), Gaps = 15/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT    R   R+L   A LY+EMI   AIL GD +  L     E P ALQ+GG++  
Sbjct: 14  MMDWTTPACRQIHRILLPKARLYSEMITTGAILFGDAQRYLTHQNDE-PCALQLGGSNPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  A  I + + Y E+NLNVGCPS RV     GACLM +P +V  C+ AM K   +PV+
Sbjct: 73  ELARATAIAQSYHYAEMNLNVGCPSDRVQNNQIGACLMKSPRLVAQCLTAMQKESDVPVS 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G+D+Q   +   + V  I ++S      +HARKA L GLSPK+NR  P L Y+IV
Sbjct: 133 IKHRLGIDEQDEHLVF-DFVDQISQESPCRIFIVHARKAWLSGLSPKENRTAPPLHYEIV 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IK++ P+L I +NGG++ ++     L  VDGVM+GRAAY+   +L      F + +  
Sbjct: 192 YKIKEQFPELTIIINGGIDFIAACQNHLHYVDGVMLGRAAYQQPQLLLAARALFGDAVMS 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + I  ++ +                 L  G +L   TRH++GLFHG   ++R R IL+ 
Sbjct: 252 ETEIVPQITQLLMNA------------LDRGERLHDYTRHLLGLFHGKNGAKRFRQILSE 299

Query: 300 EAGASTATHHIIETAFNLM 318
            A  + +  ++ + A   M
Sbjct: 300 CAPRAGSDINVWQQALAAM 318


>gi|229594322|ref|XP_001029812.3| TIM-barrel protein, yjbN family [Tetrahymena thermophila]
 gi|225566933|gb|EAR82149.3| TIM-barrel protein, yjbN family [Tetrahymena thermophila SB210]
          Length = 466

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 119/309 (38%), Positives = 170/309 (55%), Gaps = 17/309 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M+D TD H+R F RLLT  ++LYTEMI   A+       +  L F   + P+ +Q+GG D
Sbjct: 95  MIDITDVHFRNFIRLLTRYSILYTEMIHEQAVHHNIRGPQEFLRFDPVQHPVVIQLGGND 154

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AAKI E+ GY+E+NLNVGCPS RV  G FGACLM  P++V + +  M +A SIP
Sbjct: 155 PDNLAKAAKICEEIGYDEVNLNVGCPSDRVQSGKFGACLMKEPELVAEIMRKMKEACSIP 214

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VTVKCR+GVD+       R+ +K++ + G V    +HARKA LKGL+P  NR +P L YD
Sbjct: 215 VTVKCRLGVDNFDSYEFARDFIKTVSEKGQVQHFVVHARKAFLKGLNPAQNRNVPPLKYD 274

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            V  +K+E P L   +NGG +   Q   IL     + G M+GRAAY+   + + +D  + 
Sbjct: 275 YVLRLKQEFPHLHFSINGGFKTYDQISDILKQENGLHGCMLGRAAYETPWLFSDMDRRYF 334

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ--ITRHMIGLFHGFPNSRR 292
                  P  +R      R+I      Y    +     +    + + +I LF G  +S +
Sbjct: 335 GKQN---PGFSR------REILQIWGQYGKLVIQQQPAISIPTLNKPIINLFAGEKHSAK 385

Query: 293 CRHILTVEA 301
            RH ++  A
Sbjct: 386 YRHFISDRA 394


>gi|33864554|ref|NP_896113.1| tRNA-dihydrouridine synthase A [Synechococcus sp. WH 8102]
 gi|33632077|emb|CAE06530.1| Uncharacterized protein family UPF0034 [Synechococcus sp. WH 8102]
          Length = 330

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 184/322 (57%), Gaps = 10/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M+D TDRH+R   R ++ +ALLY+EM+VA A+   ++++ +L F   E P+ALQ+GG D 
Sbjct: 16  MLDCTDRHFRVLMRQISRHALLYSEMVVAQALHHSNRRDKLLDFDAVEHPIALQVGGDDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + L +AA++  D+ Y+EINLN+GCPS +V  G+FGACLM  PD+V  C+ AM  A S+PV
Sbjct: 76  ALLADAARLASDWNYDEINLNIGCPSQKVQAGNFGACLMAEPDLVARCVEAMSNATSLPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+DD      L   V  +  +G +   +HARKA L GL PK NR IP L +D V
Sbjct: 136 TVKHRIGIDDLDSDDLLTAFVDRVASAGASRFSVHARKAWLDGLDPKQNRTIPPLQHDRV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K+  P L I LNGGLE     ++ L + DG M+GRAAY +      +D         
Sbjct: 196 QALKQRRPHLTIELNGGLESPEDCIEALRTCDGAMVGRAAYSHPLRWAAMDHLVFG---- 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P +  +  D    +   +  +AA HL SGG+L  + RH++ L  G   +R  R  L  
Sbjct: 252 -KPPRDLLASD----VVTGLLPHAAAHLSSGGRLWDLCRHLVQLVEGVRGARHWRRELGD 306

Query: 300 EAGASTATHHIIETAFNLMIES 321
            A    A   ++E A   + E+
Sbjct: 307 RAQRPGADLTVLEEAGRQLREA 328


>gi|210623235|ref|ZP_03293674.1| hypothetical protein CLOHIR_01624 [Clostridium hiranonis DSM 13275]
 gi|210153772|gb|EEA84778.1| hypothetical protein CLOHIR_01624 [Clostridium hiranonis DSM 13275]
          Length = 322

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 135/326 (41%), Gaps = 25/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +    + LLYTEMI A A+   D+K   +L    +E P+A+QI G++
Sbjct: 17  MAGVTDLAFRLICKEY-GSGLLYTEMINAKALCYDDEKTKGMLKIEEEEHPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  A +I+ +     +++N+GCP+ +V +   G+ LM  P++    I A  K    P
Sbjct: 76  PEFIAGATEILNEHSNEILDINMGCPAPKVVKNGDGSALMKTPELAAKVIEAAAKKSKKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   ++      K  + SG   I IH R         +        D+DI
Sbjct: 136 VTVKFRKGWDED--SINAVEFAKMAEASGAQAITIHGRT--------RAQYYSGTADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG +  +  A+ I      D +MIGR A  N  +   ++ Y    
Sbjct: 186 IEEIKNAV-KIPVIGNGDIVTIEDAINIRKKTGCDAIMIGRGAQGNPWIFNRINHYMKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   +       + A +       ++++ +H+     G   S R R  
Sbjct: 245 EILPEPTAEEKIRTAIKH-----FNLAIKEDGEYVAVREMRKHLGWYLKGMKKSARLR-- 297

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
              E     +   ++      + ESL
Sbjct: 298 --DEINKLESADEVVGRLEAYIAESL 321


>gi|307610165|emb|CBW99713.1| hypothetical protein LPW_14811 [Legionella pneumophila 130b]
          Length = 330

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 119/319 (37%), Positives = 174/319 (54%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A ++ +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGA-VQNNPDRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P  V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMKEPGHVADCIRAIKQVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + IHARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIIHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +         
Sbjct: 193 ELKKEIPHIFITINGNILTVEEINSHLKHVDGVMLGRLACDNPYQIAEIHQALY------ 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
                   K    ++  +  DY      +   L  + + +  L  G P ++  +  L   
Sbjct: 247 ----PEFIKIKRSQLLINYLDYWFDQSRANLSLSILVKPLFNLAFGLPGAKHWKKKLMNI 302

Query: 299 VEAGASTATHHIIETAFNL 317
           ++   ++    +I+   NL
Sbjct: 303 IQEKNTSGFSELIQYLLNL 321


>gi|78044326|ref|YP_361166.1| nifR3 family TIM-barrel protein [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996441|gb|ABB15340.1| putative TIM-barrel protein, NifR3 family [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 321

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 149/325 (45%), Gaps = 27/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   +      L  TEMI   A+L G+ K   ++    +  P+A+QI G+ 
Sbjct: 19  MAGVTDKAFRLICQSF-GAGLTVTEMINDLALLHGNSKTRQMIDLQGEAMPVAVQIFGSS 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             K+ EAA+IVE+ G + I++N+GCP+ ++ +   GA LML P++    + A+  A+S+P
Sbjct: 78  PEKMAEAARIVEEAGASMIDINMGCPAPKIVKNGEGAALMLKPELAEKIVMAVKNAVSVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R G DD    V      + ++ +G + I +H R         ++       D++I
Sbjct: 138 VSVKIRKGFDD--NTVNAIEFAQRMEAAGADLITVHGRT--------REQFYSGKADWEI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A ++  L  VD VMIGRA   N  ++  +  Y    
Sbjct: 188 IRRVKQAV-KVKVAGNGDVDSPQKAKEMLELTGVDFVMIGRAVMGNPWLIQQIVFYLERG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R       +Y  +       ++++ +H    F G P + R R I
Sbjct: 247 EILPKPSPQEKAEVALRH-----FEYLLKFKGEYIAVREMRKHGGWYFKGLPGASRLREI 301

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L         T   +  A  LM+E 
Sbjct: 302 LN-----RAKTPEEVREAL-LMMEK 320


>gi|225572777|ref|ZP_03781532.1| hypothetical protein RUMHYD_00968 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039834|gb|EEG50080.1| hypothetical protein RUMHYD_00968 [Blautia hydrogenotrophica DSM
           10507]
          Length = 320

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 70/299 (23%), Positives = 140/299 (46%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    LL  EM+ A AI   +K  ++++     E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRLLCKEM-GAGLLCMEMVSAKAIYYKNKNTESLMEIHPAEHPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E+  +  +++N+GCP  +V     G+ L+ NP ++ + +  +  A+  P
Sbjct: 78  ADLMAQIATQIEERPFEILDINMGCPVPKVVNNGEGSALLKNPKLIREIVTKVSGAIRKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG   +   V +  + K I+ SG   I +H R         ++     + D+D 
Sbjct: 138 LTVKVRIGF--EGYPVDVVEIAKIIEDSGAAAIAVHGRT--------REQYYSGHADWDA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A+++L     DG+MIGRAA  N  +   ++ +    
Sbjct: 188 IRRVK-EAVQIPVIGNGDVDSPQKAVQLLEETGCDGIMIGRAAQGNPWIFREINHWMKTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P ++++ +   R     +      +      ++++ +H+     G P+S R R 
Sbjct: 247 EFLPRPGRSQIVEMILRHARLQI-----EYKGEYTGIREMRKHVAWYTQGLPHSARLRR 300


>gi|167758614|ref|ZP_02430741.1| hypothetical protein CLOSCI_00954 [Clostridium scindens ATCC 35704]
 gi|167663810|gb|EDS07940.1| hypothetical protein CLOSCI_00954 [Clostridium scindens ATCC 35704]
          Length = 318

 Score =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 79/316 (25%), Positives = 142/316 (44%), Gaps = 25/316 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K  K +L    +E P++LQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCQE-QGAGLLCMEMISAKALQYKNKNTKTLLSIHPKEHPVSLQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V +   G+ LM NP ++ D ++   KA+  P
Sbjct: 76  PYIISEMAKRIEELPFQILDINMGCPVPKVVKNGEGSALMKNPRLIYDIVSRTAKAIRKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G DD    +    + + I+++G   + +H R         ++       D+ I
Sbjct: 136 VTAKIRKGFDD--ACINAVEIARVIEEAGGAAVAVHGRT--------REEYYSGKADWKI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +AL +      DGVMIGR A  N  +   + EY    
Sbjct: 186 IRQVK-EAVSIPVIGNGDVTSGEKALAMREQTGCDGVMIGRGAQGNPWIFRELVEYERTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P K  + KD   + +    ++   +L     ++++ +H+     G   S + R  
Sbjct: 245 ALPPRPSKQEI-KDTMLRHARLQIEFKGDYLG----IREMRKHVAWYTKGMEGSAKLR-- 297

Query: 297 LTVEAGASTATHHIIE 312
              E     +   ++E
Sbjct: 298 --DEINKVESYEELVE 311


>gi|304317751|ref|YP_003852896.1| hypothetical protein Tthe_2344 [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302779253|gb|ADL69812.1| TIM-barrel protein, nifR3 family [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 333

 Score =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 73/299 (24%), Positives = 128/299 (42%), Gaps = 20/299 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M   TD+ YR   + +      YTEM+ A  +  G +    L     E+ +ALQI G+D 
Sbjct: 31  MAGVTDKPYRLICKDM-GCGFAYTEMVSAKGLYYGSENTEFLTDIDDEENVALQIFGSDP 89

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK +       I++N+GCP+ ++ +   G+ LML PD+    I A+ K    PV
Sbjct: 90  YIMGEIAKRLNTSNAKTIDINMGCPTPKIVKNGDGSALMLKPDLAESIIKAVVKNSIKPV 149

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G DD    +    + K  +  GV  + IH R         ++       D+DI+
Sbjct: 150 TIKIRKGWDDD--HINAVEIAKMAESCGVKAVAIHGRT--------REQFYSGRADWDII 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K +N  + +  NG +     A +++     D VM+GR A  N  +   +  Y +   
Sbjct: 200 KKVK-DNLKIPVIGNGDIFTPEDAKRMIDETGCDAVMVGRGAEGNPWIFKRILHYLNTGE 258

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               P  +       + +   M DY   H      + ++ +H+     G   + + + +
Sbjct: 259 ILPEPTVSEKIDMILKHL-DMMIDYKGEH----VGILEMRKHIAWYLKGIRGASKIKQM 312


>gi|20806861|ref|NP_622032.1| hypothetical protein TTE0344 [Thermoanaerobacter tengcongensis MB4]
 gi|20515331|gb|AAM23636.1| predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Thermoanaerobacter tengcongensis MB4]
          Length = 322

 Score =  288 bits (738), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 139/324 (42%), Gaps = 27/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + +    L YTEM+ A  +  G  + K +L     EK +A+QI G+D
Sbjct: 17  MAGVTDKPFRLICQEM-GAGLTYTEMVSAKGLYYGSENTKALLDIDDGEK-VAIQIFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ + +     I++N+GCP+ ++ +   GA LML PD+    + A+ KA   P
Sbjct: 75  PEIMGEIARRLNESKALIIDINMGCPTPKIVKNGDGAALMLKPDLAEKVMEAVVKASYKP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D    V    + +  ++ G+  + +H R         ++       D++I
Sbjct: 135 VTVKIRKGWND--NNVNAVEIAQIAERVGIKAVAVHGRT--------REQFYSGKADWEI 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E+  + +  NG +     A ++L     D VMIGR A  N  +      Y    
Sbjct: 185 IKKVK-ESVKIPVIGNGDIFTPEDAKRMLDETGCDAVMIGRGAQGNPWIFKRTVHYLKTG 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R ++  M +Y          + ++ +H+     G P S R R  
Sbjct: 244 ELLPEPTIKEKVDLMIRHLT-MMVEYKGER----TGVVEMRKHIAWYLKGLPGSARMR-- 296

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
              EA     ++  I+     + +
Sbjct: 297 ---EAVFKMESYKEIKEFLEGIPK 317


>gi|194476882|ref|YP_002049061.1| hypothetical protein PCC_0411 [Paulinella chromatophora]
 gi|171191889|gb|ACB42851.1| hypothetical protein PCC_0411 [Paulinella chromatophora]
          Length = 325

 Score =  288 bits (738), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 125/330 (37%), Positives = 179/330 (54%), Gaps = 18/330 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----------DKKNILGFSTQEKPL 50
           M+ +TDRH+R   R ++ + L+YTEM+ A A+             + + ++GF   EKP+
Sbjct: 1   MMGYTDRHFRVMIRQISKHCLVYTEMVAAQALQECRDQENQTATQNIERLIGFDNCEKPI 60

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           ALQ+GG     L EAAK+   + Y+EINLNVGCPS  V +G FGACLM  P  V  C+ A
Sbjct: 61  ALQVGGDSPKLLAEAAKLATHWNYDEINLNVGCPSENVQKGRFGACLMAEPAHVARCVNA 120

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           M K   IP+TVK RIG+D+Q     L N +  + ++G N   IHARKA L GL PK NR 
Sbjct: 121 MAKVSKIPITVKHRIGIDNQDSYEQLLNFIDQVAEAGANRFCIHARKAWLTGLDPKQNRT 180

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           IP L Y++V ++K + P +FI +NGG E++  + K L   DGVM+GR  Y +      +D
Sbjct: 181 IPLLKYELVKQLKIDRPFIFIDINGGFENLMDSKKQLNWADGVMVGRQVYDHPLRWGELD 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               +    S+   +R        I AS+  YA +    GG+L  I RH++    G   +
Sbjct: 241 RIIFDDYGISANKPSR--------IIASLFPYAEKWYAIGGRLWPIARHLVHTVEGIKGA 292

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
           R  R   T  A   TA+  ++  A   + +
Sbjct: 293 RHWRRWFTEAANELTASPSLLLNAAKQLED 322


>gi|291520867|emb|CBK79160.1| tRNA-U20-dihydrouridine synthase [Coprococcus catus GD/7]
          Length = 338

 Score =  288 bits (738), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 132/303 (43%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      ++ TEM+ A AI   +K    ++    QE+P++LQ+ G+D
Sbjct: 22  MAGVTDLPFRVLCRE-QGCGMVCTEMVSAKAITYKNKNTFFLMETVPQERPVSLQLFGSD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+++ D  ++ +++N+GCP  +V     G+ LM  P++ G  + ++ + +  P
Sbjct: 81  PDIMAEAARMIADRDFDVLDVNMGCPVPKVVNNGEGSALMKQPELAGRIVRSLVETIDKP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + K ++ +G   + +H R         ++       D+ I
Sbjct: 141 VTVKIRKGFDDD--HINAVEMAKIVEANGAAAVAVHGRT--------REQYYSGKADWQI 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     A +++     D +M  R A  N  +   + +Y    
Sbjct: 191 IRRVK-EAVKIPVIGNGDVFTPQDAKRMIEETGCDAIMAARGARGNPWLFRDIIDYLEKG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P    +     R     +     R+      ++++ +H+     G+  S R R  
Sbjct: 250 ILHEKPSLKEMTDMMLRHAEMHI-----RYKGEYQGIREMRKHVAWYTAGYHGSARMRQA 304

Query: 297 LTV 299
           +  
Sbjct: 305 VNE 307


>gi|225375159|ref|ZP_03752380.1| hypothetical protein ROSEINA2194_00783 [Roseburia inulinivorans DSM
           16841]
 gi|225213033|gb|EEG95387.1| hypothetical protein ROSEINA2194_00783 [Roseburia inulinivorans DSM
           16841]
          Length = 327

 Score =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 130/303 (42%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  +K    +L    +EKP++LQ+ G+D
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNKNTEELLTIDPREKPVSLQLFGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ LM NP + G  I    KA+  P
Sbjct: 82  PDIMSEIAKQIEERPFDILDINMGCPVPKVVNNGDGSALMKNPLLAGKIIEKTAKAIKKP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    +    ++SG   I +H R         ++       D+DI
Sbjct: 142 VTVKIRKGFDDD--HINAVEMAHIAEESGAAAIAVHGRT--------REQFYSGKADWDI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +      +++    + DG MI R A  N  +   +  YF+  
Sbjct: 192 IRQVK-EAVSIPVIGNGDILTADDVIRMQDETNCDGFMIARGAEGNPWIFKQILHYFATG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V     R     +             ++++ +H      G+ NS R R  
Sbjct: 251 EKLEKPSFAEVTDMILRHAQMQIGF-----KGEYTGIREMRKHAAWYTAGYKNSSRLRAK 305

Query: 297 LTV 299
           +  
Sbjct: 306 ICE 308


>gi|303242623|ref|ZP_07329098.1| TIM-barrel protein, nifR3 family [Acetivibrio cellulolyticus CD2]
 gi|302589831|gb|EFL59604.1| TIM-barrel protein, nifR3 family [Acetivibrio cellulolyticus CD2]
          Length = 325

 Score =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 141/322 (43%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LLYTEMI A  I   D K+  +      E+P A+QI G++
Sbjct: 17  MAGVTDMPFRILCKE-QGCGLLYTEMISAKGIYYNDVKSFKLTEIDPLEEPTAIQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A+ +       I++N+GCP+ ++ +   G+ LM NP +V   I+ + +A S P
Sbjct: 76  PDIMAKVAERLSQLNTAIIDINMGCPTPKITKNGEGSALMRNPLLVRKIISEVSRASSKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   +V    + K  + SG   I +H R         ++       D+DI
Sbjct: 136 VTVKIRKGWDE--NSVNAVEIAKIAEDSGAAAIAVHGRT--------REQFYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A K+L     D +M+GR A  N  +   + EY    
Sbjct: 186 IKKVK-EAVSIPVIGNGDIFTEEDARKMLEETGCDAIMVGRGAQGNPWIFKNILEYLK-- 242

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +  +    D+D    I   M +   +       ++++ +H+     G  NS   R  
Sbjct: 243 --FNPKLSDIYDEDKIDMIKRHM-EMLVKLKGESSGIKEMRKHIAWYVKGMKNSAILREK 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +   + +     ++++   + M
Sbjct: 300 V-FHSNSQDEVINLLDEYLHSM 320


>gi|323141551|ref|ZP_08076436.1| TIM-barrel protein, nifR3 family [Phascolarctobacterium sp. YIT
           12067]
 gi|322413963|gb|EFY04797.1| TIM-barrel protein, nifR3 family [Phascolarctobacterium sp. YIT
           12067]
          Length = 360

 Score =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 137/298 (45%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    +  +EM+ A  +L  + K   +L     E+P A+Q+ G+ 
Sbjct: 42  MAGITDLPFRLICRRL-GCGMTVSEMVSAKGLLYKNVKTTEMLRIDDGERPTAIQLFGSV 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++L EAA++VE  G + I+ N+GCP  ++     G+ LM NP +  D +AAM KA+ IP
Sbjct: 101 PAELAEAARMVEASGADMIDFNMGCPVPKIVNNGEGSALMKNPQLAHDILAAMVKAVKIP 160

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD         + ++++ +GV+ + +H R         +        D+ I
Sbjct: 161 VTVKFRAGWDDANRNAV--EVARAVEAAGVSAVAVHGRT--------RQQFYEGKADWSI 210

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG +  ++  L++L     DG+MIGR A  N  + T +       
Sbjct: 211 IADVKQAV-KVPVFGNGDIFTVADGLRMLEQTGCDGLMIGRGADGNPWLFTALAAALRGE 269

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P            +     +  + + +    ++++ RH+     G P++   R
Sbjct: 270 PLPQPPSLKERLAQAAEHL-----EMLSAYKNEVVAVKEMRRHISAYLKGMPHAAEFR 322


>gi|147676594|ref|YP_001210809.1| tRNA-dihydrouridine synthase [Pelotomaculum thermopropionicum SI]
 gi|146272691|dbj|BAF58440.1| tRNA-dihydrouridine synthase [Pelotomaculum thermopropionicum SI]
          Length = 324

 Score =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 79/315 (25%), Positives = 134/315 (42%), Gaps = 22/315 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD+ +R  AR      L+ TEM+   A+L G+ K   +L  + +  P+++QI G++
Sbjct: 17  MAGITDKAFRILAREF-GCGLVCTEMVSDQALLHGNPKTCSLLDVAGEAGPVSVQIFGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA I E  G   I++N+GCP+ ++ +   GA LM  P+     + A+ + + +P
Sbjct: 76  AACMAEAAGIAESRGAGIIDINMGCPTPKIVKNGEGAALMREPEKAARIVRAVVERVKVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD  P      L +   ++G   + +H R         +        D++I
Sbjct: 136 VTVKMRKGWDDNSPNAV--ELARLAAEAGAAAVTVHGRT--------RSQLYAGKADWEI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+   D+ +  NG +     AL +L     DGVMIGRAA  N  +      +    
Sbjct: 186 IAAVKRAV-DVPVIGNGDVWTPQDALAMLEQTGCDGVMIGRAALGNPWIFRRTVHFLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R +     D           + ++ +H      G   + R R  
Sbjct: 245 ELLPGPTPAEKAAMALRHL-----DLLVEFKGEKVAVWEMRKHAAWYMKGLRGAARLREQ 299

Query: 297 LTVEAGASTATHHII 311
           +   AG+      I+
Sbjct: 300 VN-RAGSPGEIREIL 313


>gi|307578569|gb|ADN62538.1| tRNA-dihydrouridine synthase A [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 309

 Score =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 140/318 (44%), Positives = 196/318 (61%), Gaps = 12/318 (3%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           ++WTDR+ R F R+L  +A LYTEM+ A A++ GD++ +LGF++ E+P+ALQ+GG++ + 
Sbjct: 1   MNWTDRYCRVFHRVLAPSARLYTEMVHAKAVIYGDRERLLGFASVEQPVALQLGGSEPAL 60

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L +AA I  D+GY+EINLN GCPS RV  GSFGACLM  P +V DC+AAM   +S+PVTV
Sbjct: 61  LAKAASIAVDWGYSEINLNCGCPSDRVQAGSFGACLMREPALVADCVAAMAAVVSVPVTV 120

Query: 122 KCRIGVDDQIPAVALRNLVK-SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           KCR+GV++          V   I  S    I +HAR A L+GLSPK+NR+IP L YD VY
Sbjct: 121 KCRLGVNEDDDYGRFAKFVDWVIGASSSRMIVVHARNAWLQGLSPKENREIPPLRYDWVY 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+E P+L + LNGG+  +   L  L  VDGVM+GRAAY++  +L       SN     
Sbjct: 181 RLKRECPELAVVLNGGITSVEAGLDHLLMVDGVMLGRAAYQDPYILHQFYCALSN----- 235

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           +P+  R           ++  Y    L  G  L+ I RH++GLFHG P  R  R +LT  
Sbjct: 236 APVLPRALL------LRALRPYVEAWLEQGVTLRHIVRHLLGLFHGQPGGRVFRQVLTQG 289

Query: 301 AGASTATHHIIETAFNLM 318
              S A   ++E A +++
Sbjct: 290 GQRSDADWSLVEQALSII 307


>gi|187478770|ref|YP_786794.1| tRNA-dihydrouridine synthase A [Bordetella avium 197N]
 gi|115423356|emb|CAJ49890.1| tRNA-dihydrouridine synthase A [Bordetella avium 197N]
          Length = 327

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 129/318 (40%), Positives = 186/318 (58%), Gaps = 10/318 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH R+F RLL  +A LYTEMI   A++ G+ +  L F   E P+ALQ+GG++  
Sbjct: 13  MIDVTDRHCRYFHRLLAPHARLYTEMITTGALMHGNVERHLDFDETEHPVALQLGGSEPD 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA++   +GY+E+NLN GCPS RV  G+FGACLM  PD+V DC+ AM  A+ IPVT
Sbjct: 73  ALAAAARLGRQWGYDEVNLNCGCPSERVQRGAFGACLMAEPDLVADCMKAMQDAVDIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D       +R+ V  I  +G     +HAR A+LKGLSPKDNR+IP L YD+  
Sbjct: 133 VKHRLGLDYNESYAFVRDFVGKIYDTGCRVFVVHARNAVLKGLSPKDNREIPPLRYDVAA 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++K + P+  I LNGGL D +QAL      DGVM+GRAA+    +L+      S  L  S
Sbjct: 193 QLKHDFPEATIVLNGGLADATQALDAASRFDGVMLGRAAWHTPRVLSE----LSLRLWPS 248

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           + + T        ++  +M +Y  R +  G  L+ + R ++GL +    +R  R +L+  
Sbjct: 249 TRLPTDA------QVVDAMVEYTTRQVARGVPLRVMLRPLLGLVNNQSGARGWRRLLSDH 302

Query: 301 AGASTATHHIIETAFNLM 318
              +     +I  A+  +
Sbjct: 303 HRLAENDPALIYEAWRSL 320


>gi|331091971|ref|ZP_08340803.1| hypothetical protein HMPREF9477_01446 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330402870|gb|EGG82437.1| hypothetical protein HMPREF9477_01446 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 321

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 79/298 (26%), Positives = 137/298 (45%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AI   +K    +L    +E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAIQYKNKNTQALLKIHPEECPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  ++ +   G+ LM NP +V   +  +  A+  P
Sbjct: 78  PDVMSEVAKSIEELPFAILDINMGCPVPKIVKNGEGSALMQNPKLVEQIVKKVSGAIQKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G +D+  +V    + K I+ SG   + +H R         ++       D+DI
Sbjct: 138 VTVKIRKGFNDE--SVNAVEIAKIIEASGGAAVAVHGRT--------REQYYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A++I    + DG+MIGR A  N  + + +  Y  + 
Sbjct: 188 IRQVK-EAVSIPVIANGDVTCGQDAIEIQKQTNCDGIMIGRGAQGNPWIFSELLYYEKHG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    V K   R     M  Y   +L     ++++ +H+     G  NS + R
Sbjct: 247 EMPERPDVHEVKKTMLRHAKLQM-QYKGDYLG----IREMRKHIAWYTTGMKNSAKLR 299


>gi|168335421|ref|ZP_02693512.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Epulopiscium sp. 'N.t. morphotype B']
          Length = 315

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 78/314 (24%), Positives = 143/314 (45%), Gaps = 23/314 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  YR   +      L+YTEM+ A A+L  + K   +L  +  E P+A Q+ G+D
Sbjct: 17  MAGFTDLPYRNICKEF-GAGLVYTEMVSAKALLYENDKTCVLLQVADTEHPVAAQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S L   A+ V +   + I+LN+GCP+ ++ +   G+ L+ NP +V   ++A+ KA   P
Sbjct: 76  PSILSAMAQQVSESSVDFIDLNMGCPAPKITKNGEGSALLANPKLVYTIVSAVAKASPKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  +    V    + ++I+ +G + I +H R         +D       D+DI
Sbjct: 136 VTVKIRKGYTE----VNAIEVAQAIEAAGASAITLHGRT--------RDQFYSGVADWDI 183

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K +   + +  NG ++    A  +L   + D +MIGRAA  N  +      Y +  
Sbjct: 184 IKKVKSKI-AIPLIGNGDIKSPEDAKAMLDYTNCDAIMIGRAALGNPWIFQRTLHYLNTG 242

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   +  + S+  +   ++     ++++  H+     GFP + + R  
Sbjct: 243 ELLPDPTLPEKIEIILKH-TQSLIAFKGEYIG----IREMRAHLSCYIKGFPQAAKLRSD 297

Query: 297 LTVEAGASTATHHI 310
           L          + +
Sbjct: 298 LNKATSLDDIKYEL 311


>gi|326792443|ref|YP_004310264.1| hypothetical protein Clole_3376 [Clostridium lentocellum DSM 5427]
 gi|326543207|gb|ADZ85066.1| TIM-barrel protein, nifR3 family [Clostridium lentocellum DSM 5427]
          Length = 324

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 139/318 (43%), Gaps = 23/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      ++ TEM+ A  +L  + K   +L    +E P+  Q+ G+D
Sbjct: 17  MAGITDLPFRLICKEF-GVGMMTTEMVSAKGLLYENGKTNDLLYIDPKEHPIGAQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK VE    + I++N+GCP+ ++ +   G+ L+ NP+++G+ + A+ KAL+ P
Sbjct: 76  PKILSEMAKQVEQSDVDFIDINMGCPAPKITKNGEGSALLKNPELIGEIVYAVAKALTKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G +D++  V    + K I+++G + I +H R         ++     + D+DI
Sbjct: 136 LTVKIRKGFNDEM--VNAVEVAKIIEEAGASAIALHGRT--------REQFYSGSADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+    + +  NG +     A ++L     D V+I RAA  N  +      Y    
Sbjct: 186 IKEVKQHI-HIPLIGNGDIRTPQDAKRMLDYTGCDAVLIARAAQGNPWIFKRTVHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          +            +      ++++  H+     G   +   R  
Sbjct: 245 ELLPEPTFEECVPVILKHAKL-----LEAYKGEYVGMREMRSHLTSYVRGVHGAADLRRT 299

Query: 297 LTVEAGASTATHHIIETA 314
           LT  A  + A    +  A
Sbjct: 300 LT--AIETYADIERLLEA 315


>gi|46200284|ref|YP_005951.1| tRNA-dihydrouridine synthase A [Thermus thermophilus HB27]
 gi|46197912|gb|AAS82324.1| nifR3-like protein [Thermus thermophilus HB27]
          Length = 342

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 121/318 (38%), Positives = 181/318 (56%), Gaps = 16/318 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+RF  R ++    LYTEM V  A+LRG+++ +L F  +E P+ALQ+ G+D  
Sbjct: 11  MVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E FGY+EINLN+GCPS +  EG +GACL+L+   V + + AM +A+ +PVT
Sbjct: 71  SLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVQEILKAMGEAVRVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G++ +     L   V+++ ++GV    +HAR A+L  LS K NR+IP L +D V+
Sbjct: 131 VKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLA-LSTKANREIPPLRHDWVH 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P L    NGG+  + +AL  L  VDGVM+GRA Y++  +L   D          
Sbjct: 190 RLKRDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +          +++  M  Y    +  G     + RHM+ LF G P  R  R +L+  
Sbjct: 250 SRL----------EVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSE- 298

Query: 301 AGASTATHHIIETAFNLM 318
                 +   ++ A  LM
Sbjct: 299 ----GRSLQALDQALRLM 312


>gi|291534721|emb|CBL07833.1| tRNA-U20-dihydrouridine synthase [Roseburia intestinalis M50/1]
          Length = 330

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 135/322 (41%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  ++    +L    +E P++LQ+ G+D
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNRNTEELLTIDKRENPVSLQLFGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  ++ +++N+GCP  +V     G+ LM NP + G+ I    +A+  P
Sbjct: 82  PDIMSEIAKQIEDRPFDILDINMGCPVPKVVNNGDGSALMKNPKLAGEIIEKTARAIKKP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++   V    +    ++SG   + +H R         +        D+DI
Sbjct: 142 VTVKIRKGFDEE--HVNAVEMAHIAQESGAAAVAVHGRT--------RSQFYSGKADWDI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +   +   A++     DG MI R A  N  +   +  YF   
Sbjct: 192 IRQVK-EAVSIPVIGNGDILTAADVIAMQKQTGCDGFMIARGAEGNPWIFAQILHYFKTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +   R     +             +++I +H      G+ NS + R  
Sbjct: 251 EELPKPTFEEVTQMLLRHARMQL-----EFKGEYTGIREIRKHAAWYTSGYRNSSKLRGR 305

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +          +  +E  F  +
Sbjct: 306 INEVET-----YEQLEALFQEV 322


>gi|119899182|ref|YP_934395.1| putative tRNA-dihydrouridine synthase [Azoarcus sp. BH72]
 gi|119671595|emb|CAL95508.1| conserved hypothetical tRNA-dihydrouridine synthase [Azoarcus sp.
           BH72]
          Length = 357

 Score =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 142/326 (43%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L  +EM+ ++++L G  K         +  P+++QI GAD
Sbjct: 27  MAGVTDRPFRQLCKKL-GAGLAVSEMVTSNSLLYGSAKTQRRANHDGEVDPISVQIAGAD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA+   
Sbjct: 86  PAMMAEAARHNADRGAQIIDINMGCPAKKVCNVMAGSALMQDEPLVARILEAVVKAVPDT 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G + Q     +  + +  ++SG+ GI IH R         + ++ + + +YD
Sbjct: 146 PVTLKFRTGWNRQNKNAPI--IARIAEESGIQGIAIHGRT--------RADQYMGDAEYD 195

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG +    +A  +L     DGVMIGRAA     +   ++ + + 
Sbjct: 196 TIALVKT-LVKIPVIANGDITTPQKARHVLDYTGADGVMIGRAAQGRPWIFREIEHFLAT 254

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+ + + +     ++     Y          ++   +H+     G   S   R 
Sbjct: 255 GEELPPPLVSDIHQVCREHLADLYAFY-----GEDTGVKVARKHISWYTKGLVGSAAFRR 309

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +        A    ++  F  + E+
Sbjct: 310 TMNQLPDIP-AQLAAVDEFFGQLAEA 334


>gi|323705755|ref|ZP_08117328.1| TIM-barrel protein, nifR3 family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323534973|gb|EGB24751.1| TIM-barrel protein, nifR3 family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 323

 Score =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 73/299 (24%), Positives = 130/299 (43%), Gaps = 20/299 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M   TD+ YR     +      YTEM+ A  +    +    L     ++ +ALQI G+D 
Sbjct: 21  MAGVTDKPYRCICSEM-GCGFTYTEMVSAKGLYYESENTEFLTDIDDDENVALQIFGSDP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK +       I++N+GCP+ ++ +   G+ LML P++    I A+ K  S PV
Sbjct: 80  YIMGEIAKRLNTSNAKVIDINMGCPTPKIVKNGDGSALMLKPELAESVIKAVVKNSSKPV 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G DD    V    + K  +  GV  + +H R         ++     N D+DI+
Sbjct: 140 TIKIRKGWDD--AHVNAVEIAKMAENCGVKAVAVHGRT--------REQFYSGNADWDII 189

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K +N  + +  NG +     A +++     D VM+GR A  N  +   +  Y +   
Sbjct: 190 KKVK-DNLKIPVIGNGDVFSPEDAKRMIDETGCDAVMVGRGAEGNPWIFKRILHYLNTGE 248

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               PI +       R +   M +Y   H+     + ++ +H+     G   + + + +
Sbjct: 249 LLPEPIVSEKIDMILRHL-DVMIEYKGEHIG----ILEMRKHIAWYLKGIRGASKIKQM 302


>gi|254252479|ref|ZP_04945797.1| TIM-barrel protein, yjbN family [Burkholderia dolosa AUO158]
 gi|124895088|gb|EAY68968.1| TIM-barrel protein, yjbN family [Burkholderia dolosa AUO158]
          Length = 242

 Score =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 118/226 (52%), Positives = 151/226 (66%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F R LT N  LYTEMI   A+L GD +  LGF+  E P+ALQ+GG++  
Sbjct: 17  MLDWTDRHCRSFHRTLTRNTWLYTEMITTGALLFGDVQRHLGFTPSESPVALQLGGSEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAK+ E +GY+EINLN GCPS RV  G+FGACLM  P +V DC+ AM  A+S+PVT
Sbjct: 77  DLARAAKLGEQWGYDEINLNCGCPSERVQRGAFGACLMKEPQLVADCVKAMRDAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V +I  +G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 137 VKHRIGVDAIEDYAFVRDFVGTIADAGCRTFIVHARNAILKGLSPKENREIPPLKYDYAY 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            +K++ P L I +NGG++ + +    L  VDG M+GR AY N  +L
Sbjct: 197 RLKRDFPSLEIVINGGIKTLDEVALHLEHVDGAMLGREAYHNPYVL 242


>gi|240143461|ref|ZP_04742062.1| tRNA-dihydrouridine synthase [Roseburia intestinalis L1-82]
 gi|257204494|gb|EEV02779.1| tRNA-dihydrouridine synthase [Roseburia intestinalis L1-82]
          Length = 330

 Score =  285 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 135/322 (41%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A AIL  ++    +L    +E P++LQ+ G+D
Sbjct: 23  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKAILYKNRNTEELLTIDKRENPVSLQLFGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  ++ +++N+GCP  +V     G+ LM NP + G+ I    +A+  P
Sbjct: 82  PDIMSEIAKQIEDRPFDILDINMGCPVPKVVNNGDGSALMKNPKLAGEIIEKTARAIKKP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++   V    +    ++SG   + +H R         +        D+DI
Sbjct: 142 VTVKIRKGFDEE--HVNAVEMAHIAQESGAAAVAVHGRT--------RSQFYSGKADWDI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +   +   A++     DG MI R A  N  +   +  YF   
Sbjct: 192 IRQVK-EAVSIPVIGNGDILTAADVIAMQKQTGCDGFMIARGAEGNPWIFAQILHYFKTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +   R     +             +++I +H      G+ NS + R  
Sbjct: 251 EELPKPTFEEVTQMLLRHARMQL-----EFKGEYTGIREIRKHAAWYTSGYRNSSKLRGR 305

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +          +  +E  F  +
Sbjct: 306 INEVET-----YEQLEALFQEV 322


>gi|302385513|ref|YP_003821335.1| TIM-barrel protein, nifR3 family [Clostridium saccharolyticum WM1]
 gi|302196141|gb|ADL03712.1| TIM-barrel protein, nifR3 family [Clostridium saccharolyticum WM1]
          Length = 326

 Score =  285 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 127/302 (42%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +RF  R      +  TEM+ A AIL  ++    +L  +  E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRFLCRE-QGCGMAVTEMVSAKAILYKNRNTNELLKVAPGEGPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  VE+  Y  I++N+GCP  ++     G+ LM +  +    + +M KA+  P
Sbjct: 78  PEIMADIAAQVEEGPYAFIDVNMGCPMPKIVNNGEGSALMKDIGLAERILTSMVKAVKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  ++          K  +  GV  + +H R         ++       D+ I
Sbjct: 138 VTVKFRKGFTEEDCNAV--EFAKMAESCGVAAVAVHGRT--------REQYYSGTADWTI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A  ++     DGVMI R A  N  +      Y    
Sbjct: 188 IRKVK-EAVAIPVIGNGDVFKPEDAKALMEETGCDGVMIARGAKGNPWIFKRTLHYLETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P +  + K   R  +         H      ++++  HM     G P+S + R+ 
Sbjct: 247 ELLSGPDREEISKMIIRHGALET-----EHKGEAVAMREMRGHMAWYTAGLPHSAKLRND 301

Query: 297 LT 298
           + 
Sbjct: 302 IN 303


>gi|118595290|ref|ZP_01552637.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Methylophilales
           bacterium HTCC2181]
 gi|118441068|gb|EAV47695.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Methylophilales
           bacterium HTCC2181]
          Length = 341

 Score =  285 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 138/324 (42%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +      +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKSF-GAGVAVSEMVTSNSLLYGSEKTKRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAK   D G   I++N+GCP+ ++     G+ L+ +  +V D + A+  ++ IP
Sbjct: 76  PKMMADAAKYNRDRGAQIIDINMGCPAKKICNVMAGSALLKHEQLVDDILQAVVGSVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  +++G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWDRENRNAI--KIAQIAEEAGIKALAIHGRT--------RACLYRGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+ N ++ +  NG +    +A  +L     D VMIGRAA     +   ++ +    
Sbjct: 186 IAEVKQ-NINIPVIANGDIVSPEKAQYVLNYTKADAVMIGRAAQGRPWIFREIEHFLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + K   + +      Y          L+   +H+     G   S + R  
Sbjct: 245 SHHPLPTINEIQKTTIKHVLDLYDFYGEE-----TGLRVARKHISWYTKGLKKSAQFRSD 299

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +      +    + I   F+ + E
Sbjct: 300 MNSLENCND-QINAINNYFDSLKE 322


>gi|54297373|ref|YP_123742.1| tRNA-dihydrouridine synthase A [Legionella pneumophila str. Paris]
 gi|53751158|emb|CAH12569.1| hypothetical protein lpp1418 [Legionella pneumophila str. Paris]
          Length = 330

 Score =  285 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 118/319 (36%), Positives = 175/319 (54%), Gaps = 13/319 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWT+  +R   RLL  NALLYTEM    A ++ +    L F++ E P+A+Q+GGAD S
Sbjct: 14  MIDWTNSPFRTLMRLLAPNALLYTEMQTTGA-VQNNPGRALYFNSVEHPIAIQLGGADKS 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            LV+ A I E  G+NEINLN+GCPS +V  G FGACLM  P+ V DCI A+ + + IPVT
Sbjct: 73  ALVKCAIIAEQKGFNEINLNLGCPSDKVQAGRFGACLMREPEHVADCIRAIKEVVGIPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RIG+D+Q      R+    + ++G + + +HARKA L GL+PK NR IP ++YD VY
Sbjct: 133 AKTRIGIDNQDSYEFFRSFSLHLVEAGCDKLIVHARKAWLNGLNPKQNRTIPPVNYDYVY 192

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           E+KKE P +FI +NG +  + +    L  VDGVM+GR A  N   +  + +         
Sbjct: 193 ELKKEIPHIFITINGNILTIEEINSHLMYVDGVMLGRLACDNPYQIAEIHQALY------ 246

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-- 298
                   K    ++  +  DY      +   L  + + +  L  G P ++  +  L   
Sbjct: 247 ----PEFIKIKRSQLLMNYLDYWFDQSPANLSLSILVKPLFNLAFGLPGAKHWKKKLMNI 302

Query: 299 VEAGASTATHHIIETAFNL 317
           ++   ++    +I+   NL
Sbjct: 303 IQEKNTSGFSELIQYLLNL 321


>gi|225569858|ref|ZP_03778883.1| hypothetical protein CLOHYLEM_05952 [Clostridium hylemonae DSM
           15053]
 gi|225161328|gb|EEG73947.1| hypothetical protein CLOHYLEM_05952 [Clostridium hylemonae DSM
           15053]
          Length = 320

 Score =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 77/317 (24%), Positives = 139/317 (43%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A A+   +K    +L    +E P++LQ+ G+D
Sbjct: 18  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKALQYNNKNTKLLLAIHPEEYPVSLQLFGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK +E+  +  +++N+GCP  +V     G+ LM +P ++ D +    KA+  P
Sbjct: 77  PRIMSEAAKRIEELPFQILDINMGCPVPKVVRNGEGSALMKDPGLIYDIVHETVKAIDKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+         V +++ + V  I      A+      ++       D+DI
Sbjct: 137 VTVKIRKGFDDEH--------VNAVEAARV--IEEAGAAAVAVHGRTREQYYAGKADWDI 186

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     S A++     D VMIGRAA  N  +   +  Y ++ 
Sbjct: 187 IRKVK-EAVSIPVIGNGDVVSGPSSAAMQEQTGCDMVMIGRAAQGNPWIFRELRAYAADG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +  V +   +     M +Y   +L     ++++ +H+     G   + + R  
Sbjct: 246 TVLPRPAEAEVRQTMLKHAKMQM-EYKGEYLG----IREMRKHVAWYTKGLKGASKLRAQ 300

Query: 297 LTVEAGASTATHHIIET 313
           +          H + E 
Sbjct: 301 INSVESYEELKHLLFER 317


>gi|149923826|ref|ZP_01912217.1| hypothetical protein PPSIR1_20159 [Plesiocystis pacifica SIR-1]
 gi|149815338|gb|EDM74882.1| hypothetical protein PPSIR1_20159 [Plesiocystis pacifica SIR-1]
          Length = 362

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 182/325 (56%), Gaps = 5/325 (1%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+D TDRH+R   RL+T + LLYTEM+   A+L GD+++ILG+   E PLALQ+GG D  
Sbjct: 28  MMDRTDRHFRRLMRLITRHTLLYTEMVTCPAVLHGDREHILGYHPSEHPLALQLGGDDPE 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   A+I  + GY+E+N+NVGCPS RV  G+FG CLM +P  V DC+ AM +A+ +PVT
Sbjct: 88  ALAACARIAAELGYDEVNINVGCPSDRVQSGNFGVCLMKDPARVRDCVVAMREAVELPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD+      + + V  +  +  +   +HARKA L+GLSPK NR +P L Y  V+
Sbjct: 148 VKHRIGVDELDRYEDMLHFVDVVAAAEPDLFTVHARKAWLQGLSPKQNRNVPPLRYAEVH 207

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            + +E P +F+ +NGG +      + L  VD VM+GRAA+ +  +   VD+ F       
Sbjct: 208 RLARERPGVFVEINGGFKTADAIAEQLERVDAVMLGRAAWDDPWLFAAVDQRFFASE-AP 266

Query: 241 SPIKTRVDKDFWRKISASMTDYAAR----HLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +P +  V + +   +   +    AR      + G     + R ++ LF G P ++R +  
Sbjct: 267 APTRPAVVEAYLEHVHEQLAMARARVEAGSRYKGPSATILLRPIMNLFTGRPGAKRWKRT 326

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L       T        AF + +E+
Sbjct: 327 LNELCQRPTREGLDALPAFAVELEA 351


>gi|226951473|ref|ZP_03821937.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. ATCC 27244]
 gi|226837766|gb|EEH70149.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. ATCC 27244]
          Length = 341

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 145/325 (44%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDTVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  + +  Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNHARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKQVKQLIG-IPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P  + V       +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLATPDISEVKAVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
           +  VE+ A  A   ++E  F+ +++
Sbjct: 300 MYKVESTADQAK--VVEAYFDQLLD 322


>gi|253995778|ref|YP_003047842.1| TIM-barrel protein, nifR3 family [Methylotenera mobilis JLW8]
 gi|253982457|gb|ACT47315.1| TIM-barrel protein, nifR3 family [Methylotenera mobilis JLW8]
          Length = 347

 Score =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 129/303 (42%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G +K     + + +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSEKTKRRANHEGEVNPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVAQILRAVVGAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + K  +  GV  + +H R         +    + + +YD 
Sbjct: 136 VTLKIRTGWDKQNRNAI--QIAKMAEDLGVQALAMHGRT--------RACAYMGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A  +L     D VMIGRAA     +   ++ Y +  
Sbjct: 186 IAAVKQAI-KIPLIANGDITTPEKAKFVLDYTGADAVMIGRAAQGRPWIFREIEHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +       +      Y          ++   +H+     G   S + RH 
Sbjct: 245 THLLPPTVDEIHAVMLEHLHDLYEFY-----GDLTGMRMARKHISWYTKGLAGSAQFRHT 299

Query: 297 LTV 299
           +  
Sbjct: 300 MNT 302


>gi|67924974|ref|ZP_00518361.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Crocosphaera
           watsonii WH 8501]
 gi|67853187|gb|EAM48559.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Crocosphaera
           watsonii WH 8501]
          Length = 341

 Score =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 137/322 (42%), Gaps = 28/322 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R  + N+++YTEM+ A  I        ++     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYSPNSMMYTEMVSATEIHHLKQLPRLMEIDENEQPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+     G   I++N+GCP  ++ +   G+ L+  P +    +A + K++ +PVTV
Sbjct: 94  MAEAAQKAVAEGAKTIDINMGCPVNKITKKGGGSSLLRQPHLAQTLVAEVVKSVEVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DD+   + +    + ++ +G   + +H R         +      N  ++ + +
Sbjct: 154 KTRIGWDDKE--INILEFAQKMEDAGAAMLTLHGRT--------RAQGYKGNARWEWIKK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+  L     DGVM  R       ++  +D +F   +  
Sbjct: 204 VK-EILTIPVIANGDIFSVEAAINCLEITGADGVMCSRGTLGYPFLVGEIDHFFCTGIKQ 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P   R   +  ++    + +Y  +       + Q  +H+      FP +   R  ++ 
Sbjct: 263 NKPTP-REKLECAKEHLQGLWEYKGKR-----GIYQARKHLSWYCKEFPGASELRDKVS- 315

Query: 300 EAGASTATHHIIETAFNLMIES 321
                      +E  + L+ E+
Sbjct: 316 -------RIETVEEGYKLLNEA 330


>gi|297537586|ref|YP_003673355.1| TIM-barrel protein, nifR3 family [Methylotenera sp. 301]
 gi|297256933|gb|ADI28778.1| TIM-barrel protein, nifR3 family [Methylotenera sp. 301]
          Length = 346

 Score =  284 bits (728), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 126/303 (41%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G +K +       +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSEKTLRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PQMMAEAARHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVAQILRAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  GV  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWDKNNRNAV--QIARIAEDLGVQALAMHGRT--------RACLYTGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A  +L     D VMIGRAA     +   ++ +    
Sbjct: 186 IAAVKQAI-KIPLIANGDITTPEKAKFVLDYTGADAVMIGRAAQGRPWIFREIEHFIKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  T +       +      Y          ++   +H+     G  +S   RH 
Sbjct: 245 EHLPPPEVTEIRTVMLAHLHDLYDFY-----GELTGMRMARKHISWYTKGLKDSANFRHN 299

Query: 297 LTV 299
           +  
Sbjct: 300 MNT 302


>gi|154505277|ref|ZP_02042015.1| hypothetical protein RUMGNA_02791 [Ruminococcus gnavus ATCC 29149]
 gi|153794475|gb|EDN76895.1| hypothetical protein RUMGNA_02791 [Ruminococcus gnavus ATCC 29149]
          Length = 319

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 136/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EM+ A  I   +K  +++L    +E P++LQ  G+D
Sbjct: 20  MAGVTDLPFRLLCKE-QGAGLLCMEMVSAKGIFYNNKNTESLLQIHPEEVPVSLQFFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK VE+  ++ +++N+GCP  +V     G+ LM NP +V + ++A  KA+  P
Sbjct: 79  PKIVSEMAKRVEERPFSILDINMGCPVPKVVRNGEGSALMKNPKLVYELVSATVKAIKKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD+   +    + K I+++G   + +H R         ++       D++I
Sbjct: 139 VTVKIRKGFDDE--HINAVEIAKIIEEAGAAAVAVHGRT--------REQYYSGKADWEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A+ +      DGVMI R A  N  + + + EY    
Sbjct: 189 IRQVK-EAVSIPVIGNGDVTSGEKAIAMREQTGCDGVMIARGAQGNPWIFSELLEYERTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +   R     +      +      ++++ +H+     G   + R R  
Sbjct: 248 RLPDRPDVEEIKQTMLRHARLQI-----EYKGDFTGIREMRKHVAWYTKGLHGAARLRDQ 302

Query: 297 LT 298
           + 
Sbjct: 303 IN 304


>gi|225026968|ref|ZP_03716160.1| hypothetical protein EUBHAL_01224 [Eubacterium hallii DSM 3353]
 gi|224955704|gb|EEG36913.1| hypothetical protein EUBHAL_01224 [Eubacterium hallii DSM 3353]
          Length = 316

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 133/302 (44%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      ++ TEMI A A+  G+K  +  +    +EKP+ +QI G++
Sbjct: 18  MAGITDLPFRILCKE-QGADVMVTEMISAKALFYGNKNTLPLMQTEEEEKPIGVQIFGSE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +ED G++ I++N+GCP  ++     G+ LMLNP++ G  +  + KA+S+P
Sbjct: 77  PELMGEMAHKIEDKGFSYIDINMGCPVPKIVNNKEGSALMLNPELAGRIVKEVSKAVSLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     +      + ++++G   + +H R  +               D+DI
Sbjct: 137 VTVKFRKGFD--ADHINAPEFAQIMEENGAAAVAVHGRTRV--------QYYTGQADWDI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +     A+K+      DG+M+ R A  N  +   V    S  
Sbjct: 187 IRDVKNAV-SIPVIGNGDIFKGEDAVKMRDYTGCDGIMVARGAKGNPWIFREVKAALSGK 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +  V     R         + ++      ++++ +H      G   S   R+ 
Sbjct: 246 PIPERPTEEEVISMLLRHA-----QLSVQYKGEKMGIREMRKHTAWYTTGMHGSSTLRNK 300

Query: 297 LT 298
           + 
Sbjct: 301 VN 302


>gi|17228722|ref|NP_485270.1| hypothetical protein all1227 [Nostoc sp. PCC 7120]
 gi|17130574|dbj|BAB73184.1| all1227 [Nostoc sp. PCC 7120]
          Length = 350

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 137/320 (42%), Gaps = 21/320 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        I+    +E+P+++Q+       
Sbjct: 34  GVTDMVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPKERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + I++N+GCP  ++ +   G+ L+  P++    +  + KA+++PVTV
Sbjct: 94  LAEAAIKAVAEGADTIDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVNVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D+   + + +  K ++ +G   I +H R         +      N  ++ +  
Sbjct: 154 KTRIGWNDRE--ITILDFAKRMEDAGAQMITVHGRT--------RAQGYNGNARWEWIAR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+K L     DGVM  R       ++  +D +F      
Sbjct: 204 VK-EILSIPVIGNGDIFSVESAVKCLEETGADGVMCSRGTLGYPFLVGEIDHFFKTGELL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P   +   +  R    ++ +Y          ++Q  +HM     GF  +   R  L++
Sbjct: 263 PAPTPIQ-RLECARDHLQALWEYKG-----DRGVRQARKHMTWYAKGFVGAAELRGQLSL 316

Query: 300 EAGASTATHHIIETAFNLMI 319
                     +I+ A   + 
Sbjct: 317 VETVQQ-GLDLIDQATEKLT 335


>gi|297543866|ref|YP_003676168.1| NifR3 family TIM-barrel domain-containing protein
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296841641|gb|ADH60157.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter mathranii
           subsp. mathranii str. A3]
          Length = 321

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 137/318 (43%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQ+ G+D 
Sbjct: 17  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKMLTDIDEEEKVALQVFGSDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 76  DIMGEIARKLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD    V    + +  +K+G+  + +H R         ++       D+ I+
Sbjct: 136 TVKIRKGWDD--NHVNAVEIAQIAEKAGIKAVAVHGRT--------REQFYSGKADWSII 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K E+  + +  NG +     A ++L     D ++IGR A  N  +      + +   
Sbjct: 186 KKVK-ESVKIPVIGNGDIFTPQDAKRMLEETGCDAILIGRGAQGNPWIFKRTVHFLNTGE 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +   R +   M +Y          + ++ +H+     G   S + R   
Sbjct: 245 LLPEPTIQEKIEVIIRHL-EMMIEYKGER----TGILEMRKHIAWYLKGLYGSAKLR--- 296

Query: 298 TVEAGASTATHHIIETAF 315
             EA      +  I+   
Sbjct: 297 --EAVFKMEKYEEIKEFL 312


>gi|294650996|ref|ZP_06728336.1| tRNA-dihydrouridine synthase B [Acinetobacter haemolyticus ATCC
           19194]
 gi|292823097|gb|EFF81960.1| tRNA-dihydrouridine synthase B [Acinetobacter haemolyticus ATCC
           19194]
          Length = 341

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 144/325 (44%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDTVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  + +  Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNHARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKQVKQLI-SIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIGHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V       +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLATPDIAEVKTVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
           +  VE+ A  A   ++E  F+ +++
Sbjct: 300 MYKVESTADQAK--VVEAYFDQLLD 322


>gi|295110733|emb|CBL24686.1| tRNA-U20-dihydrouridine synthase [Ruminococcus obeum A2-162]
          Length = 321

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 73/299 (24%), Positives = 132/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL TEM+ A AI   +K    ++     E P+++QI G++
Sbjct: 21  MAGVTDLPFRMLCKE-QGAGLLCTEMVSAKAISFHNKNTISLMQIDPSEHPVSMQIFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ L+ NP+++ + +  +  A+  P
Sbjct: 80  PDLMAEVAKSIEEQPFDILDINMGCPVPKVVNNGEGSALLKNPELIREIVTQVSHAVKKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG +D    V    + K I+ SG   + +H R         +        D+D 
Sbjct: 140 VTAKIRIGFED--YPVDPVEIAKIIEDSGAAAVAVHGRT--------RQQYYAGEADWDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK E   + +  NG ++   +A K++     DGVMIGRA   N  +   ++ YF+  
Sbjct: 190 IRRIK-EAVSIPVIGNGDVDSPKKAEKLVRETGCDGVMIGRAVRGNPWIFREMNHYFTTG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P    + +   R     +             ++++ +H+     G  +S   R 
Sbjct: 249 ELLPRPSWEEIKEMILRHTRMQI-----ELKGEFTGIREMRKHIAWYTAGMKHSAGLRR 302


>gi|126658167|ref|ZP_01729318.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Cyanothece sp.
           CCY0110]
 gi|126620538|gb|EAZ91256.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Cyanothece sp.
           CCY0110]
          Length = 337

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 65/319 (20%), Positives = 134/319 (42%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R  + N+++YTEM+ A  I        ++     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYSPNSMMYTEMVSATEIHHLKQLPRLMEIDPNEQPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+     G   I++N+GCP  ++ +   G+ L+  P+I  + +  + K + IPVTV
Sbjct: 94  MAEAAQKAVGEGAKTIDINMGCPVNKITKKGGGSSLLRQPEIAENLVKEVVKTVDIPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DD    + +    + ++ +G + + +H R         +      N  ++ + +
Sbjct: 154 KTRIGWDDNE--INILEFAQKMEDAGASMLTLHGRT--------RAQGYTGNARWEWIKK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +KK    + +  NG +  +  A+  L     DGVM  R       ++  +D +F      
Sbjct: 204 VKK-ILTIPVIANGDIFSVEAAINCLEITGADGVMCSRGTLGYPFLVGEIDYFFQTGKEL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P       +  ++    + +Y  +       + Q  +H+     GF  +   R  ++ 
Sbjct: 263 IKPTSIE-RLECAKEHLKGLWEYKGKR-----GIYQARKHLSWYCKGFIGASELRDKVSR 316

Query: 300 EAGASTATHHIIETAFNLM 318
                   + +++ A  L+
Sbjct: 317 IETV-EEGYFLLDKAMKLI 334


>gi|167038941|ref|YP_001661926.1| nifR3 family TIM-barrel protein [Thermoanaerobacter sp. X514]
 gi|300913469|ref|ZP_07130786.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter sp. X561]
 gi|307723516|ref|YP_003903267.1| NifR3 family TIM-barrel domain-containing protein
           [Thermoanaerobacter sp. X513]
 gi|166853181|gb|ABY91590.1| putative TIM-barrel protein, nifR3 family [Thermoanaerobacter sp.
           X514]
 gi|300890154|gb|EFK85299.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter sp. X561]
 gi|307580577|gb|ADN53976.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter sp. X513]
          Length = 347

 Score =  284 bits (726), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 134/318 (42%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   L     + + +ALQI G+D 
Sbjct: 40  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKLLTDIDEGESVALQIFGSDP 98

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 99  DIMGEIAKRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 158

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD    V    + +  +K GV  + +H R         ++       D+ I+
Sbjct: 159 TVKIRKGWDD--NHVNAVEIAQIAEKVGVKAVAVHGRT--------REQFYSGKADWSII 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K E+  + +  NG +     A ++L     D ++IGR A  N  +      + +   
Sbjct: 209 KKVK-ESVKIPVIGNGDIFTPEDAKRMLEETGCDAILIGRGAQGNPWIFKRTVHFLNTGE 267

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +   R +   M +Y          + ++ +H+     G   S + R   
Sbjct: 268 LLPEPTIQEKIEVIIRHL-EMMIEYKGER----TGILEMRKHIAWYLKGLYGSAKLR--- 319

Query: 298 TVEAGASTATHHIIETAF 315
             EA      +  I+   
Sbjct: 320 --EAVFKMEKYEQIKEFL 335


>gi|125975167|ref|YP_001039077.1| nifR3 family TIM-barrel protein [Clostridium thermocellum ATCC
           27405]
 gi|256003170|ref|ZP_05428162.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum DSM
           2360]
 gi|281418412|ref|ZP_06249431.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum JW20]
 gi|125715392|gb|ABN53884.1| tRNA-U20-dihydrouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|255992861|gb|EEU02951.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum DSM
           2360]
 gi|281407496|gb|EFB37755.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum JW20]
 gi|316939332|gb|ADU73366.1| TIM-barrel protein, nifR3 family [Clostridium thermocellum DSM
           1313]
          Length = 322

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 132/321 (41%), Gaps = 21/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L YTEM+ A  I   D+K   +      E  +ALQI G+D
Sbjct: 17  MAGITDIPFRLLCKE-QGCGLTYTEMVSAKGIYYNDEKTKKLTAVDAAEGKVALQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +  + + D     I++N+GCP+ ++ +   G  LM  P++VG  +  + KA   P
Sbjct: 76  PVIMAKVTEQLNDSDACIIDINMGCPTPKITKNGDGCALMRQPELVGKIVREVSKASVKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+    +    + +  +++G   I +H R         ++       D+ I
Sbjct: 136 VTVKIRKGWDENR--INAVEIARIAEENGAAAITVHGRT--------REQFYSGKADWSI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+ +  + +  NG +     A ++    + D +MIGR A  N  +   + +Y    
Sbjct: 186 IREVKQ-SVSIPVIGNGDVFTPEDARRMFEETNCDAIMIGRGAQGNPWIFRKIIKYLEGS 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 I      +  ++    + +           ++++ +H+     G  N+ R +  
Sbjct: 245 EDFDLDISLETKINIIKRHMQMLVELKGEQ----CGVREMRKHIAWYIKGMRNASRIKEK 300

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +  +A        +++     
Sbjct: 301 V-FKATTQQEVFSLLDELLEF 320


>gi|55979985|ref|YP_143282.1| tRNA-dihydrouridine synthase A [Thermus thermophilus HB8]
 gi|55771398|dbj|BAD69839.1| tRNA-dihydrouridine synthase [Thermus thermophilus HB8]
          Length = 342

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 121/318 (38%), Positives = 180/318 (56%), Gaps = 16/318 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDRH+RF  R ++    LYTEM V  A+LRG+++ +L F  +E P+ALQ+ G+D  
Sbjct: 11  MVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPK 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA+I E FGY+EINLN+GCPS +  EG +GACL+L+   V + + AM +A+ +PVT
Sbjct: 71  SLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G++ +     L   V+++ ++GV    +HAR A+L  LS K NR+IP L +D V+
Sbjct: 131 VKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLA-LSTKANREIPPLRHDWVH 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K + P L    NGG+  + +AL  L  VDGVM+GRA Y++  +L   D          
Sbjct: 190 RLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRP 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
           S +          +++  M  Y    +  G     + RHM+ LF G P  R  R +L+  
Sbjct: 250 SRL----------EVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSE- 298

Query: 301 AGASTATHHIIETAFNLM 318
                 +   ++ A  LM
Sbjct: 299 ----GRSLQALDRALRLM 312


>gi|254518234|ref|ZP_05130290.1| tRNA-dihydrouridine synthase A [Clostridium sp. 7_2_43FAA]
 gi|226911983|gb|EEH97184.1| tRNA-dihydrouridine synthase A [Clostridium sp. 7_2_43FAA]
          Length = 348

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 119/334 (35%), Positives = 178/334 (53%), Gaps = 20/334 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD + RH+R+F+RLLT +ALLYTEM+ A AI+ GD+  IL F  +E P+ALQI  ++  
Sbjct: 18  MVDKSHRHFRYFSRLLTKDALLYTEMVTAQAIINGDRDKILYFREEEGPVALQIAASNPE 77

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              +A K+   + Y E+NLN GCPS RV     GA LM + ++V + + AM +A + P+T
Sbjct: 78  DAYKAVKLANYYNYTEVNLNCGCPSDRVSGNLMGAALMSSKELVYEILCAMKEATTKPIT 137

Query: 121 VKCRIGVDDQI------------PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +K RIG+D                   L   +  + K+  +   IHAR AILKGLSPKDN
Sbjct: 138 IKHRIGIDGTDVIENEKSKIIMSGYEDLLEFLDIVSKAKPDRYTIHARSAILKGLSPKDN 197

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R+IP LDYD+VY +K++   L I +NGG + +      L  VDGVMIGRA+Y+N  +L  
Sbjct: 198 REIPPLDYDMVYRLKRDFNHLNIEINGGFKTLDSIRDALTKVDGVMIGRASYENCYLLAN 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             + + N     +  +         +I  S T Y    +  G  +  +   +  LF G  
Sbjct: 258 FHKLYENNQNTKAISRG--------EIIKSYTPYVIEEIKKGNSIHSLIAPLQSLFQGQR 309

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            S++ + +L+           I+ T   +M + +
Sbjct: 310 GSKKYKQLLSSSNVKKENIIEILNTILEVMPQDV 343


>gi|289577559|ref|YP_003476186.1| hypothetical protein Thit_0307 [Thermoanaerobacter italicus Ab9]
 gi|289527272|gb|ADD01624.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter italicus Ab9]
          Length = 321

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 136/318 (42%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   +L    +E+ +ALQI G+D 
Sbjct: 17  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKMLTDIGEEEKVALQIFGSDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + A+ KA + PV
Sbjct: 76  DIMGEIARKLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMEAVVKASNKPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD    V    + +  +K+GV  + +H R         ++       D+ I+
Sbjct: 136 TVKIRKGWDD--NHVNAVEIAQIAEKAGVKAVAVHGRT--------REQFYSGKADWSII 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K E+  + +  NG +     A ++      D ++IGR A  N  +      Y  N  
Sbjct: 186 KKVK-ESVKIPVMGNGDIFTPQDAKRMFEETGCDAILIGRGAQGNPWIFKRTLHYLENGE 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +   R +   M +Y          + ++ +H+     G   S + R   
Sbjct: 245 LLPEPTIQEKIEVIIRHL-EMMIEYKGER----TGILEMRKHIAWYLKGLYGSAKLR--- 296

Query: 298 TVEAGASTATHHIIETAF 315
             EA      +  I+   
Sbjct: 297 --EAVFKMEKYEQIKEFL 312


>gi|291547778|emb|CBL20886.1| tRNA-U20-dihydrouridine synthase [Ruminococcus sp. SR1/5]
          Length = 324

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 128/299 (42%), Gaps = 20/299 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+  EM+ A AI   +K    ++     E P+++Q+ G++
Sbjct: 21  MAGVTDLAFRRLCKE-QGAGLICMEMVSAKAISFHNKNTEALMEIDPGEHPVSMQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ L+ +P ++ + + ++  A+S P
Sbjct: 80  PDLMAEVAKSIEERPFDILDINMGCPVPKVVNNGEGSALLKDPQLIEEIVRSVSGAVSKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D+  P   +  + K ++ +G   I +H R         +        D+D 
Sbjct: 140 VTVKVRIGFDENTPVDVV-EIAKRVEDAGAAAIAVHGRT--------RQQYYSGQADWDA 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +     A  +      D VMIGRA   N  +   ++ YF   
Sbjct: 191 IRRVKEAVT-IPVIGNGDIVSPETAEAMFKETGCDAVMIGRAVRGNPWIFRELNHYFRTG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P    V +   R     +             ++++ +H+     G  +S   R 
Sbjct: 250 EKLPRPTAEEVCEMILRHAEDQIA-----IKGEYIGIREMRKHVAWYTAGMRHSAGIRR 303


>gi|218440381|ref|YP_002378710.1| hypothetical protein PCC7424_3447 [Cyanothece sp. PCC 7424]
 gi|218173109|gb|ACK71842.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7424]
          Length = 337

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 138/322 (42%), Gaps = 21/322 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  I        I+   +QE P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYAPISMMYTEMVSATEIHHLKQLPKIMEIDSQEHPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA      G   +++N+GCP  ++ +   G+ L+  P+I  + +  + KA+ +PVTV
Sbjct: 94  MAEAAMKAVAQGAKTVDINMGCPVNKITKKGGGSSLLRQPEIAQNIVKTVVKAVDVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D    + + +  K ++ +G   + +HAR         +         ++ + +
Sbjct: 154 KTRIGWNDDE--INILDFAKKMEDAGAAMLTLHART--------RAQGYNGTARWEWIKK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A++ L     DGVM  R       ++  +D +       
Sbjct: 204 VK-EVLSIPVIANGDIFSVDAAIRCLEETGADGVMCSRGTLGYPFLVGEIDYFLKTGTLL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P   +   +  ++    + DY  +       + Q  +H+     GF  +   R  ++ 
Sbjct: 263 TPPTSLQ-RLECAKEHLQGLWDYKGQR-----GIYQSRKHLTWYCKGFAGASVLRDQVS- 315

Query: 300 EAGASTATHHIIETAFNLMIES 321
              +    +H+I+ A   ++ S
Sbjct: 316 NINSLEEGYHLIDQAIASLVNS 337


>gi|85858573|ref|YP_460775.1| tRNA-dihydrouridine synthase [Syntrophus aciditrophicus SB]
 gi|85721664|gb|ABC76607.1| tRNA-dihydrouridine synthase [Syntrophus aciditrophicus SB]
          Length = 326

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/321 (25%), Positives = 151/321 (47%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  AR     AL +TEMI A+ ++RG +K+   +     +KPL +QI G D
Sbjct: 18  MAGISNLPFRMMARE-AGCALAFTEMISANGLVRGIEKSQQYMKSCIDDKPLGVQIFGND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + +A +IV+D+G + I+LN+GCP  +V +   GA L+ +P +V   + ++ KA   P
Sbjct: 77  PTTMADAVRIVDDYGADLIDLNMGCPVKKVVKNGAGAALLKDPGLVSQILESVRKATRKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G + Q  ++    + +  ++ G++ +++HAR A+             + D+ I
Sbjct: 137 LTVKIRSGWNLQ--SINAVQIARIAEQQGIDAVFVHARTAVQG--------FAGSADWRI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG ++  + A ++  +   DGVMIGR A  N  +      Y S  
Sbjct: 187 IEEIKNSVG-IKVIGNGDVKSGADAWRMIKMTGCDGVMIGRGALGNPWIFNEALNYQSTV 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T S P+     +   R +           L     +++  +H++    G       R  
Sbjct: 246 QTHSEPVLNERKEMILRHLERETIF-----LGQKEAVKRFRKHLLWYTKGIRGGASFRSR 300

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +T  +  +      IE  F+ 
Sbjct: 301 VTTISDQNLLLRE-IEAFFDQ 320


>gi|326390246|ref|ZP_08211806.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus JW
           200]
 gi|325993691|gb|EGD52123.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus JW
           200]
          Length = 336

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 136/319 (42%), Gaps = 27/319 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + +    L YTEM+ A  +  G  + K +     +EK +ALQI G+D
Sbjct: 32  MAGVTDKPFRVICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEK-VALQIFGSD 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + P
Sbjct: 90  PDIMGEIARRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    + +  +K GV  + +H R         ++       D+ I
Sbjct: 150 VTVKIRKGWDD--NHVNAVEIAQIAEKVGVKAVAVHGRT--------REQFYSGKADWSI 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E+  + +  NG +     A ++L     D ++IGR A  N  +      + +  
Sbjct: 200 IKKVK-ESVKIPVIGNGDIFTPEDAKRMLEETGCDAILIGRGAQGNPWIFKRTVHFLNTG 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R +   M +Y          + ++ +H+     G   S + R  
Sbjct: 259 ELLPEPTIQEKIEVIIRHL-EMMIEYKGER----TGILEMRKHIAWYLKGLYGSAKLR-- 311

Query: 297 LTVEAGASTATHHIIETAF 315
              EA      +  I+   
Sbjct: 312 ---EAVFKMEKYEQIKEFL 327


>gi|145548359|ref|XP_001459860.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124427687|emb|CAK92463.1| unnamed protein product [Paramecium tetraurelia]
          Length = 346

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 128/327 (39%), Positives = 187/327 (57%), Gaps = 16/327 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI----LRGDKKNILGFSTQEKPLALQIGG 56
           M+D T  H+R F RLLT N +LYTEMI  +AI    +      +L +S  E P+  Q+GG
Sbjct: 14  MIDITYEHFRVFFRLLTKNCVLYTEMIHENAINLSRVLKPFPLVLDYSQVEHPVVCQLGG 73

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  KL +AA+I E  G++EINLNVGCPS RV +G+FGACLM  P +V  C+  M +A+ 
Sbjct: 74  NDPEKLAKAAQIAEQAGFDEINLNVGCPSERVQDGAFGACLMKEPHLVAQCMKKMKEAVK 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLD 175
           IP T+KCR+GVD+      +RN V+ + K G VN   +HARKA LKGL+P +NR +P L 
Sbjct: 134 IPCTLKCRLGVDNLDSYEFVRNFVEIVYKEGEVNHFIMHARKAFLKGLNPHENRTVPPLK 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           YD VY++KKE P++   LNGG++      ++LP+VDG+MIGR+A++N  M +  D  +  
Sbjct: 194 YDWVYQLKKEFPEIKFTLNGGIKCTEHIDQVLPNVDGIMIGRSAHENPWMFSDFDRLYYG 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QI-TRHMIGLFHGFPNSRRC 293
               +            ++I     ++      +G K+  Q+  + +I LF+G  N++R 
Sbjct: 254 GENQNY---------NRKEILEQYAEFVEEKRATGCKVSTQMCVKPIINLFNGESNNKRY 304

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R  L+           +I      M E
Sbjct: 305 RQFLSNTDNHKLGFRGMINQVIEHMHE 331


>gi|238917594|ref|YP_002931111.1| hypothetical protein EUBELI_01673 [Eubacterium eligens ATCC 27750]
 gi|238872954|gb|ACR72664.1| Hypothetical protein EUBELI_01673 [Eubacterium eligens ATCC 27750]
          Length = 321

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 136/299 (45%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A A+L  +K    ++     E+PLALQ+ G+D
Sbjct: 17  MAGVTDLPFRLLCKE-QGCGLMCTEMVSAKAVLYNNKNTEDLMKTVPGERPLALQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK + +  ++ I++N+GCP  +V     G+ LM +P +VG  +  M  AL  P
Sbjct: 76  PDIMADIAKRLSEREFDIIDVNMGCPVPKVVNNGEGSALMKDPVLVGRIVEKMADALDKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G D+   ++    +   I++SG   + +HAR         +      + D+DI
Sbjct: 136 LTIKIRAGFDE--NSINAPEIAHVIEESGGAAVAVHART--------RQQYYSGHADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG ++    A+ ++     DG+MIGRAA  N  +   V EY +N 
Sbjct: 186 IRQVK-EAVSIPVIGNGDIKSGEDAVNMMKQTGCDGIMIGRAARGNPWIFRQVSEYMNNG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P    + +   R                   ++++ +H      G  ++   R+
Sbjct: 245 TIIEPPSVEEICQMIKRHAKG-----LCEIKGEFTGIREMRKHFAWYTAGIKHAAALRN 298


>gi|90415235|ref|ZP_01223169.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2207]
 gi|90332558|gb|EAS47728.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2207]
          Length = 348

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 143/322 (44%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R +    ++ +EM+ AD      +K+ L   F+ +  P ++QI G D
Sbjct: 37  MAGVTDLPFRQLCREM-GAGMVVSEMVAADPSTWSSRKSKLRIQFADEPAPRSVQIAGYD 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+     G   I++N+GCP+ +V + + G+ L+ +PD+V D + A+  ++ +P
Sbjct: 96  PLMMAEAARFNVQQGAEIIDINMGCPAKKVLKKAAGSALLQHPDLVQDILRAVVDSVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q       ++ K  + +G+  + IH R         +  R +  ++YD 
Sbjct: 156 VTLKIRTGWDRQNRNAV--SIAKIAEDAGIAALAIHGRT--------RACRFVKEVEYDT 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  E   + +  NG +    +AL +L       VMIGR A  N  +   ++ +  + 
Sbjct: 206 IANVV-EALSIPVIANGDITTPEKALAVLEQTGAAAVMIGRGAQGNPWIFNQINHFLEHG 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-RH 295
                P    ++    R + A    Y     H+G K+    +H+   F   P  ++  RH
Sbjct: 265 EAAEKPSIEDIELVVCRHLQALHAFYGP---HAGVKI--ARKHIGWYFSALPGGKQFARH 319

Query: 296 ILTVEAGASTATHHIIETAFNL 317
              +E        +++   F  
Sbjct: 320 FNRIEDHLEQ--QNLLLQFFQQ 339


>gi|167038326|ref|YP_001665904.1| nifR3 family TIM-barrel protein [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320116727|ref|YP_004186886.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166857160|gb|ABY95568.1| putative TIM-barrel protein, nifR3 family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319929818|gb|ADV80503.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 336

 Score =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 137/319 (42%), Gaps = 27/319 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + +    L YTEM+ A  +  G  + K +     +EK +ALQI G+D
Sbjct: 32  MAGVTDKSFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEK-VALQIFGSD 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + P
Sbjct: 90  PDIMGEIARRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    + +  +K+G+  + +H R         ++       D+ I
Sbjct: 150 VTVKIRKGWDD--NHVNAVEIAQIAEKAGIKAVAVHGRT--------REQFYSGKADWSI 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E+  + +  NG +     A ++L     D ++IGR A  N  +      + +  
Sbjct: 200 IKKVK-ESVKIPVIGNGDIFTPEDAKRMLEETGCDAILIGRGAQGNPWIFKRTVHFLNTG 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R +   M +Y          + ++ +H+     G   S + R  
Sbjct: 259 ELLPEPTIQEKIEVIIRHL-EMMIEYKGER----TGILEMRKHIAWYLKGLYGSAKLR-- 311

Query: 297 LTVEAGASTATHHIIETAF 315
              EA      +  I+   
Sbjct: 312 ---EAVFKMEKYEQIKEFL 327


>gi|238019651|ref|ZP_04600077.1| hypothetical protein VEIDISOL_01525 [Veillonella dispar ATCC 17748]
 gi|237863692|gb|EEP64982.1| hypothetical protein VEIDISOL_01525 [Veillonella dispar ATCC 17748]
          Length = 328

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 145/324 (44%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++
Sbjct: 22  MAGVSDIAYRLLAKE-HGAALVCTEMVSAMGIKYKNERTHELLRIEEVERPVSMQIFGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  KA+ +P
Sbjct: 81  PEAIALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVKAVDVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  
Sbjct: 141 VTVKMRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   A ++L     D VM+GR A  N  +   +  Y +  
Sbjct: 191 IKAVK-EAVSVPVIGNGDIVEPEDAKQMLDETGCDAVMVGRGAQGNPWIFNRIHHYLATG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P          +       D   ++      +++I  H      G P S   R+ 
Sbjct: 250 EVLAAPSDIERLDMLLKH-----FDLLCQYKGESMAVKEIRTHAGWYMKGLPESAYWRNR 304

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +       T+ H+ +E+   ++ E
Sbjct: 305 VNT-IHTVTSFHNELESYRKILSE 327


>gi|218665650|ref|YP_002426431.1| tRNA-dihydrouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|218517863|gb|ACK78449.1| tRNA-dihydrouridine synthase A [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 330

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 119/307 (38%), Positives = 174/307 (56%), Gaps = 13/307 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R+F RL+  + +LYTEM+   A+L G D +  L FS  E PL LQ+GG D 
Sbjct: 24  MLDWTDRHCRYFLRLVCPSCVLYTEMVTTSALLLGRDPERFLEFSGAEHPLILQLGGDDP 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  A ++   +GY+ +NLNVGCPS RV +GSFGACLM  PD+V + +AAM +   +PV
Sbjct: 84  HAMHAAGRMARAYGYDGLNLNVGCPSPRVQKGSFGACLMTTPDLVAELVAAMGE-SGLPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G+D +    ALR  V+++  +G     +HAR A LKGLSP +NR +P L +D V
Sbjct: 143 SVKHRLGLDREEDYAALRAFVETVATAGCRHFIVHARNAWLKGLSPAENRDVPPLRWDWV 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K++ P L I +NGG  D++       +VDGVM+GRAAY +  +L  ++       T 
Sbjct: 203 HQLKRDLPHLTIEINGGFNDLAAVTAQFSAVDGVMLGRAAYHHPLLLAEIERALGRRETL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P            I + +  YA R        + ++RH+ GL  G   +   R  L  
Sbjct: 263 PEP----------EVILSGLIAYAERWGEWLPAPR-LSRHLHGLRFGQRGAGAWRRFLGT 311

Query: 300 EAGASTA 306
                +A
Sbjct: 312 AEPGESA 318


>gi|182420030|ref|ZP_02951264.1| tRNA-dihydrouridine synthase B [Clostridium butyricum 5521]
 gi|237669513|ref|ZP_04529493.1| tRNA-dihydrouridine synthase B [Clostridium butyricum E4 str. BoNT
           E BL5262]
 gi|182376067|gb|EDT73654.1| tRNA-dihydrouridine synthase B [Clostridium butyricum 5521]
 gi|237654957|gb|EEP52517.1| tRNA-dihydrouridine synthase B [Clostridium butyricum E4 str. BoNT
           E BL5262]
          Length = 321

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 146/327 (44%), Gaps = 31/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G  + K +L  + +EKP+A+QI G +
Sbjct: 17  MAGVTDISFRGLCKEM-GCGLVYTEMVSAKALYYGSENTKELLRIAEEEKPVAVQIFGRE 75

Query: 59  ISKLVEAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              +   AK+VE+          I++N+GCP+ ++ +   G+ LM  P++    +  + +
Sbjct: 76  PEIM---AKMVEEHFNHRDDICIIDINMGCPATKIVKNGEGSALMKEPELAYKIVRKIKE 132

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             + PVTVK R G D++   +      K ++++G + + IH R         +       
Sbjct: 133 VSTKPVTVKFRKGFDEE--NINAVEFAKGMEQAGADAVAIHGRT--------RKQMYQGK 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
            D+DI+  +K EN  + +  NG +     AL++  L + DG+MI R +  N  +   + +
Sbjct: 183 ADWDIIKSVK-ENVSIPVIGNGDVFSPEDALRMKELTNCDGIMIARGSQGNPWLFRQIKD 241

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                +      K RV      ++     + A ++      ++++ +H      G P   
Sbjct: 242 VLEGKIPQEVTNKERV------EMCLRHYELAIKYDGEYKAIREMRKHASWYIKGLPKCT 295

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
             R+ + V    S+    I++     +
Sbjct: 296 DIRNEINVL-DDSSKVIDILKEYKEHL 321


>gi|220908982|ref|YP_002484293.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7425]
 gi|219865593|gb|ACL45932.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7425]
          Length = 357

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 62/323 (19%), Positives = 136/323 (42%), Gaps = 28/323 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYAPDSMMYTEMVNATGLHYVRQLPKIMEVDPNERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA++    G + +++N+GCP  ++ +   G+ L+ +P+     + ++ +A+++PVTV
Sbjct: 94  LAEAAQMAVAEGADTVDINMGCPVNKITKNGGGSSLLRDPETAEAIVRSVVQAVNVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  ++   + +    + ++ +G   I +H R         +         ++ +  
Sbjct: 154 KTRIGWTEKE--INIIEFAQRMQDAGAQMITVHGRT--------RAQGYNGPAKWEWIRR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  +  A+  L     DGVM  R       ++  VD +       
Sbjct: 204 VKEALT-IPVIANGDIFSVEAAVNCLEQTGADGVMCSRGTMGYPFLVGEVDHFLKTGEHK 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P      +   R+   ++ +Y          ++Q  +HM     GFP +   R  L  
Sbjct: 263 PAPTVIERLQ-CAREHLQALWEYKG-----DRGVRQARKHMTWYAKGFPGAAELRGALC- 315

Query: 300 EAGASTATHHIIETAFNLMIESL 322
                      ++   +L+ +++
Sbjct: 316 -------QLENVQQGLDLITDTI 331


>gi|119509215|ref|ZP_01628365.1| Dihydrouridine synthase TIM-barrel protein [Nodularia spumigena
           CCY9414]
 gi|119466057|gb|EAW46944.1| Dihydrouridine synthase TIM-barrel protein [Nodularia spumigena
           CCY9414]
          Length = 363

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 136/322 (42%), Gaps = 21/322 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    +++LYTEM+ A  +    +   I+    +E+P+++Q+       
Sbjct: 47  GVTDMVFRRLVRRYAPDSMLYTEMVNATGLHYVKELPKIMEVDPRERPISIQLFDCRPDF 106

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + I++N+GCP  ++ +   G+ L+  P++    +  + KA+ +PVTV
Sbjct: 107 LAEAAIKAVAEGADTIDINMGCPVNKITKNGGGSSLLRQPEVAEAIVQEVVKAVKVPVTV 166

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D+   + + +  K ++ +G   I +H R         +      N  ++ +  
Sbjct: 167 KTRIGWNDKE--ITILDFAKRMEDAGAQMITVHGRT--------RAQGYNGNARWEWITR 216

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A++ L     DGVM  R       ++  +D +       
Sbjct: 217 VK-EVLSIPVIGNGDIFSVEAAVRCLEQTGADGVMCSRGTLGYPFLVGEIDHFLKTGEML 275

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P   +   +  R    ++ +Y          ++Q  +HM     GF  +   R  L++
Sbjct: 276 APPSPIQ-RLECARDHLQALWEYKG-----DRGVRQARKHMTWYAKGFVGAAELRGKLSL 329

Query: 300 EAGASTATHHIIETAFNLMIES 321
                     +I+     +  S
Sbjct: 330 IETVQQ-GLDLIDLGIEQLNHS 350


>gi|28209975|ref|NP_780919.1| nitrogen regulation protein nifR3 [Clostridium tetani E88]
 gi|28202410|gb|AAO34856.1| nitrogen regulation protein nifR3 [Clostridium tetani E88]
          Length = 322

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 136/324 (41%), Gaps = 25/324 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R   + +    L+YTEM+ A A+     K   +L FS +E P+A+QI G + 
Sbjct: 18  AGVTDLAFRGLCKRM-GCTLVYTEMVSAKALFYDSDKTKDMLRFSKEELPIAVQIFGKEP 76

Query: 60  SKLVEAAK--IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             +    +     +     I++N+GCP+ ++ +   G+ LM NP +  D + ++ K  + 
Sbjct: 77  DIMANVVEKYFNSNDNVCLIDINMGCPAPKIVKNGEGSALMKNPKLASDIVESIKKVSTK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      K ++ SG + + IH R         ++       D++
Sbjct: 137 PVTVKFRKGFDND--NINALEFAKIMENSGADALTIHGRT--------REQMYQGKADWE 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E+  + +  NG +     A+ ++   + DGVM+ R A  N  +   + E    
Sbjct: 187 IIKKVK-ESVKIPVIGNGDVFTGEDAINMIESTNCDGVMVARGALGNPWIFNQISEALKG 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    + +        ++  Y          ++++ +H+     G  N  + + 
Sbjct: 246 QQIL-EPSPDEILEVCIEHFKRALYYY-----DEKKAVREMRKHIGWYIKGLKNCSKVKD 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
            +  E        +I+E      +
Sbjct: 300 TINKEVDK-DKVLNILEEYRKEFV 322


>gi|319941968|ref|ZP_08016289.1| TRNA-dihydrouridine synthase A [Sutterella wadsworthensis 3_1_45B]
 gi|319804621|gb|EFW01491.1| TRNA-dihydrouridine synthase A [Sutterella wadsworthensis 3_1_45B]
          Length = 347

 Score =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 123/322 (38%), Positives = 172/322 (53%), Gaps = 14/322 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  RFF RLLT    LYTEM+   AI  G +  +LG S    P ALQ+GG+D  
Sbjct: 27  MLDWTDRPCRFFERLLTRRGRLYTEMVTTGAIRFGSRDALLGNSRVAGPTALQLGGSDPK 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  A +    +GY+E NLN GCPS RV +GSFGACLML+  +V +C+ AM  A   PVT
Sbjct: 87  ELAFAVEAAAPYGYDEFNLNCGCPSPRVQKGSFGACLMLDAKLVAECVRAMRDATDKPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD++     +R+ V  +  +G     +HAR A L+GLSPK+NR++P L     +
Sbjct: 147 VKHRIGVDERSDYGFVRDFVGEVYDAGCRTFIVHARAAWLQGLSPKENREVPPLMRSRAW 206

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV------DGVMIGRAAYKNSAMLTTVDEYFS 234
           E+K++ PD  I LNG ++  ++   +L  V      DGVM+GRAAY+   ML+ VD    
Sbjct: 207 ELKRDFPDAVIVLNGAVKTTAECRALLDEVHDGVRIDGVMVGRAAYQTPWMLSEVDSVLY 266

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                    +T   +     + A +  Y A   H    ++   RH+ GL  G   +R  R
Sbjct: 267 GES-----CRTLTREAVIAAVEAEVEQYYAADEHV---IRAFARHLNGLCQGLSGARVWR 318

Query: 295 HILTVEAGASTATHHIIETAFN 316
             L           ++   A+ 
Sbjct: 319 RTLADPKIIKAEGPNLYRRAWR 340


>gi|75906868|ref|YP_321164.1| dihydrouridine synthase TIM-barrel protein nifR3 [Anabaena
           variabilis ATCC 29413]
 gi|75700593|gb|ABA20269.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Anabaena
           variabilis ATCC 29413]
          Length = 350

 Score =  281 bits (720), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 136/320 (42%), Gaps = 21/320 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 34  GVTDMVFRRLVRRYAPDSMMYTEMVNATGLHYVQQLPKIMEVDPNERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + I++N+GCP  ++ +   G+ L+  P++    +  + KA+++PVTV
Sbjct: 94  LAEAAIKAVAEGADTIDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVNVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D+   + + +  K ++ +G   I +H R         +      N  ++ +  
Sbjct: 154 KTRIGWNDRE--ITILDFAKRMEDAGAQMITVHGRT--------RAQGYNGNARWEWIAR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+K L     DGVM  R       ++  +D +       
Sbjct: 204 VK-EILSIPVIGNGDIFSVESAVKCLEETGADGVMCSRGTLGYPFLVGEIDHFLKTGELL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P   +   +  R    ++ +Y          ++Q  +HM     GF  +   R  L+V
Sbjct: 263 TAPTPIQ-RLECARDHLQALWEYKG-----DRGVRQARKHMTWYAKGFVGAAELRGQLSV 316

Query: 300 EAGASTATHHIIETAFNLMI 319
                     +I+ A   + 
Sbjct: 317 IETVQQ-GLDLIDKATEKLT 335


>gi|269121360|ref|YP_003309537.1| dihydrouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615238|gb|ACZ09606.1| dihydrouridine synthase DuS [Sebaldella termitidis ATCC 33386]
          Length = 337

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 116/328 (35%), Positives = 171/328 (52%), Gaps = 22/328 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDR++R F R++  + LLYTEM+ A AI+ GD + ILGF   E P+ALQI      
Sbjct: 13  MVDKTDRYFRNFVRMINKDVLLYTEMVTAQAIIHGDLERILGFDEAEHPIALQIAATTPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              +A K  E++ Y+EINLNVGCPS RV     GACLM  P++V D + A+ +A    VT
Sbjct: 73  DAYKAVKTAENYAYDEINLNVGCPSDRVSGNMMGACLMAYPELVLDILKAIKEATGKAVT 132

Query: 121 VKCRIGVDDQ------------IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +K RIG+D +                 + N +  I+K+G +   +HAR A+L GL PK N
Sbjct: 133 IKHRIGIDGKGILPDNAEKTLFDKYEDMLNFINIIEKAGADRYTVHARIAVLAGLDPKQN 192

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R++P L YD VY +K E P + I +NGG++      + L  VDGVMIGR  Y N  +L  
Sbjct: 193 REVPPLRYDEVYRLKAEKPYMQIEINGGIKTKEDITEHLKYVDGVMIGREFYDNPMLLAE 252

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V+ +++N            +     ++   M  Y  +   +  +     RH +GLFH   
Sbjct: 253 VNSFYNNGE----------ENISRYQVLEKMIPYLEKMEMNNERTHLFLRHTLGLFHNVK 302

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFN 316
            S+  ++ ++ +   +     II     
Sbjct: 303 GSKYWKNSISSQNLKNNKGSLIIREILK 330


>gi|114331206|ref|YP_747428.1| putative TIM-barrel protein, nifR3 family protein [Nitrosomonas
           eutropha C91]
 gi|114308220|gb|ABI59463.1| tRNA-U20-dihydrouridine synthase [Nitrosomonas eutropha C91]
          Length = 337

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 135/306 (44%), Gaps = 21/306 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +   A+  +EMI ++++L G +K +       + KP+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAAMAVSEMISSNSLLYGSEKTLRRARHEGEVKPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + +AA+   D G   I++N+GCP+ ++     G+ L+ + D+V   + A+ +A+ IP
Sbjct: 76  PAMMAQAARHNADHGAEIIDINMGCPAKKICNVMAGSALLKDEDLVSKILGAVVQAVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + +  + +G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDTQHKNAVA--VARIAESAGIQALAIHGRT--------RACAYRGQAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K    ++ +  NG +    +A ++L    VD VMIGRAA     +   ++ Y +  
Sbjct: 186 IATVKAAI-NIPVIANGDINTPEKAREVLEYTGVDAVMIGRAAQGRPWIFREINHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +     +      Y          ++   +H+     G   S   RH 
Sbjct: 245 NFLPLPEVAEIHRVLIDHLQELYQFY-----GEYSGVRIARKHISWYTRGLAGSAVFRHA 299

Query: 297 LTVEAG 302
           +   A 
Sbjct: 300 MNRLAS 305


>gi|30248878|ref|NP_840948.1| hypothetical protein NE0874 [Nitrosomonas europaea ATCC 19718]
 gi|30138495|emb|CAD84785.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Nitrosomonas europaea ATCC 19718]
          Length = 337

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 71/306 (23%), Positives = 129/306 (42%), Gaps = 21/306 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +   A+  +EM+ ++++L G +K         + KP+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAAMAVSEMVSSNSLLYGSEKTRRRACHDGEVKPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   I++N+GCP+ ++     G+ L+ + ++V   + A+ +A+ IP
Sbjct: 76  PVMMAQAARHNADQGAEIIDINMGCPAKKICNVMAGSALLKDENLVSRILDAVVQAVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + +  + +G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDTQHKNAIT--VARIAESAGIQALAIHGRT--------RACAYRGQAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + I  NG +    +A  +L     D VMIGRAA     +    D Y +  
Sbjct: 186 IAAVKTSI-RIPIIANGDITTPEKAWAVLEYTGADAVMIGRAAQGKPWIFRETDHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +     +      Y          ++   +H+     G   S   RH 
Sbjct: 245 SFLPPPEVAEIQRVLIDHLYELYHFY-----GEYSGVRIARKHISWYTRGLAGSAAFRHA 299

Query: 297 LTVEAG 302
           +   A 
Sbjct: 300 MNRLAT 305


>gi|312130655|ref|YP_003997995.1| tRNA-u20-dihydrouridine synthase [Leadbetterella byssophila DSM
           17132]
 gi|311907201|gb|ADQ17642.1| tRNA-U20-dihydrouridine synthase [Leadbetterella byssophila DSM
           17132]
          Length = 348

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 137/318 (43%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE + ++ ++R   K++  L     E+P+ +Q+ G+D
Sbjct: 25  MEDVSDPPFRQVCKE-NGADMMYTEFVSSEGLIRNAVKSVRKLDIFPYERPIGIQLFGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + E  KI  +   + I++N GCP  +V     GA L+ +  ++     A+ KA  +P
Sbjct: 84  VETMAECTKISTEVNPDLIDINYGCPVKKVACRGAGAALLQDIPLMARMTEAVVKATHLP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    + + ++  G+  + IH R         +        D+ +
Sbjct: 144 VTVKTRLGWDDSTKNIE--EVAERLQDVGIQALTIHGRT--------RAQLYKGEADWSL 193

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL+      VDG+MIGRAA     +   +  YF  
Sbjct: 194 IAKVKNNPRIKIPIFGNGDIDSPEKALEYKNRFGVDGIMIGRAAIGYPWIFNEIKHYFQT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P   +      + +      ++         + ++ RH    F G PN +  R 
Sbjct: 254 GEYLPAPNMEQRVNAATQHLK-----FSVEWKGETLGILEMRRHYSNYFKGLPNFKEHRM 308

Query: 296 ILTVEAGASTATHHIIET 313
            L      S     I+ET
Sbjct: 309 KL----VQSMNLEEILET 322


>gi|198283800|ref|YP_002220121.1| dihydrouridine synthase DuS [Acidithiobacillus ferrooxidans ATCC
           53993]
 gi|198248321|gb|ACH83914.1| dihydrouridine synthase DuS [Acidithiobacillus ferrooxidans ATCC
           53993]
          Length = 325

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 119/307 (38%), Positives = 174/307 (56%), Gaps = 13/307 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R+F RL+  + +LYTEM+   A+L G D +  L FS  E PL LQ+GG D 
Sbjct: 19  MLDWTDRHCRYFLRLVCPSCVLYTEMVTTSALLLGRDPERFLEFSGAEHPLILQLGGDDP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  A ++   +GY+ +NLNVGCPS RV +GSFGACLM  PD+V + +AAM +   +PV
Sbjct: 79  HAMHAAGRMARAYGYDGLNLNVGCPSPRVQKGSFGACLMTTPDLVAELVAAMGE-SGLPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G+D +    ALR  V+++  +G     +HAR A LKGLSP +NR +P L +D V
Sbjct: 138 SVKHRLGLDREEDYAALRAFVETVATAGCRHFIVHARNAWLKGLSPAENRDVPPLRWDWV 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +++K++ P L I +NGG  D++       +VDGVM+GRAAY +  +L  ++       T 
Sbjct: 198 HQLKRDLPHLTIEINGGFNDLAAVTAQFSAVDGVMLGRAAYHHPLLLAEIERALGRRETL 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P            I + +  YA R        + ++RH+ GL  G   +   R  L  
Sbjct: 258 PEP----------EVILSGLIAYAERWGEWLPAPR-LSRHLHGLRFGQRGAGAWRRFLGT 306

Query: 300 EAGASTA 306
                +A
Sbjct: 307 AEPGESA 313


>gi|291542003|emb|CBL15113.1| tRNA-U20-dihydrouridine synthase [Ruminococcus bromii L2-63]
          Length = 328

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 77/299 (25%), Positives = 135/299 (45%), Gaps = 20/299 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +DR YR         A   +EM+ + A+    KK+  ++  S  E+P  +QI G D
Sbjct: 24  MAGVSDRAYRELCVRF-GAAYCVSEMVSSKALSFNSKKSEELMEISDLERPCGIQIFGDD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAK   +   + I++N+GCP+ ++     G+ LM NP + G+ + A+     IP
Sbjct: 83  PKCMADAAKHALENKPDIIDINMGCPAPKISSNGSGSALMKNPRLCGEIVKAVTAVTDIP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD   +V    + K  + +G   I +H R         +     P +DYDI
Sbjct: 143 VTVKIRKGWDDD--SVNAVEVAKICESAGAAAITVHGRT--------RQQYYKPPVDYDI 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +E+  + +  NG ++   +A +++     D VMIGRA   N  + + ++ Y  NP
Sbjct: 193 IRAV-RESVSVPVIANGDIDSAERAKEVMDITGCDLVMIGRATLGNPWIFSQINAYLENP 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                            +  + M +Y   H+     + Q  + ++G F G   +   R+
Sbjct: 252 NVKIHTPDLEERLGVMIEHISKMVEYKGEHMA----MLQARKLVVGYFKGMKGAAALRN 306


>gi|302672113|ref|YP_003832073.1| tRNA dihydrouridine synthase A DusA2 [Butyrivibrio proteoclasticus
           B316]
 gi|302396586|gb|ADL35491.1| tRNA dihydrouridine synthase A DusA2 [Butyrivibrio proteoclasticus
           B316]
          Length = 325

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 130/302 (43%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R +    L+  EM+ A AI   +K    ++     E P++LQ+ G++
Sbjct: 23  MAGVSDLPFRLLCREM-GAGLVCMEMVSAKAITYKNKNTNMLMEIHEDEHPVSLQLFGSE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +A ++++D  Y+ +++N+GCP  +V     G+ LM NP+++   + A+ +    P
Sbjct: 82  PEIMQQAVEMIKDRPYDILDVNMGCPVPKVVGNGEGSALMKNPELIEKIVKALTEVSDRP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G      +V       + ++ G   + +H R         ++       D+ I
Sbjct: 142 VTVKIRRGF--TEASVNAVECALAAQEGGAAAVAVHGRT--------REQYYSGRADWTI 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG + D     ++      DGVM+ RAA  N  +   +  YF   
Sbjct: 192 IRQVK-EALKIPVIGNGDVVDGPSTKRMFEETGCDGVMVARAAQGNPFLFREIKSYFETG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R       D   ++      ++++ +H+     G P S R R+ 
Sbjct: 251 EACERPTAQEIYDTVIRHA-----DLQLKYKGEFIGIREMRKHVSWYTVGMPGSARFRNE 305

Query: 297 LT 298
           + 
Sbjct: 306 IN 307


>gi|313678961|ref|YP_004056700.1| tRNA-u16,u17-dihydrouridine synthase [Oceanithermus profundus DSM
           14977]
 gi|313151676|gb|ADR35527.1| tRNA-U16,U17-dihydrouridine synthase [Oceanithermus profundus DSM
           14977]
          Length = 321

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 109/309 (35%), Positives = 156/309 (50%), Gaps = 12/309 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TDRH+RF  RL++    LY+EM+V   ++ GD    L F   E P+ALQ+G AD  
Sbjct: 11  MMERTDRHFRFLMRLVSRRTRLYSEMVVDRTLIHGDPPRHLDFHPAEHPVALQLGSADPR 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
               A  +   +GY+E+NLNVGCPS RV  G FG  LM  P+ V + + A+ +   + +T
Sbjct: 71  LAARAVAVTRPWGYDEVNLNVGCPSPRVQAGGFGVVLMRRPERVAEIVRAVHQETGVRMT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D+      L   V+ +  +GV    +HARKA  +GL PK NR +P L++  VY
Sbjct: 131 VKHRVGLDEDDDYAFLARFVEVVAAAGVQVFVVHARKAWTEGLDPKANRTVPPLEHAKVY 190

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K++ P+L I  NGG+ D  +A   L  VDGVM+GRA +       + D          
Sbjct: 191 RLKRDFPELTIVTNGGVADPEEARAHLEHVDGVMVGRAMWDRPWRWASADRVLWGDARVP 250

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL--T 298
                       R +      Y    L  G  L+ + R +  LF G P  RR R  L   
Sbjct: 251 D----------RRTVLERYEAYLHERLAEGVPLRALVRPLFNLFKGEPGGRRWRRTLDAA 300

Query: 299 VEAGASTAT 307
           + AG   A 
Sbjct: 301 LRAGRPPAG 309


>gi|188992985|ref|YP_001904995.1| Putative TIM-barrel protein; NifR3 family [Xanthomonas campestris
           pv. campestris str. B100]
 gi|167734745|emb|CAP52955.1| Putative TIM-barrel protein; NifR3 family [Xanthomonas campestris
           pv. campestris]
          Length = 468

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 153 MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 211

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   ++A+ +A+ +P
Sbjct: 212 PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILSAVVRAVDVP 271

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D       +Y  
Sbjct: 272 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGTAEYAT 321

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L    VD VMIGRAA     +   V  Y +  
Sbjct: 322 IAQIKAAL-QIPVIANGDIDSPQKAAQVLRDTGVDAVMIGRAAQGRPWIFGEVAHYLATG 380

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 381 ALLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 435

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 436 VN-RAETPEAQLALTRDYFDALI 457


>gi|254520540|ref|ZP_05132596.1| nifR3 family TIM-barrel protein [Clostridium sp. 7_2_43FAA]
 gi|226914289|gb|EEH99490.1| nifR3 family TIM-barrel protein [Clostridium sp. 7_2_43FAA]
          Length = 328

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 144/325 (44%), Gaps = 25/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G+   K++L  + +E P+A QI G D
Sbjct: 17  MAGVTDISFRGLCKEM-GCGLVYTEMVSAKALYYGNENTKSLLRIADEETPVAAQIFGND 75

Query: 59  ISKLVEAAKI--VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              + E  +    E      +++N+GCP  ++ +   G+ L+ +P++  + +  + K  +
Sbjct: 76  PRIMAEVVQRYFNEREDICLVDINMGCPVNKITKNGEGSALLKHPELAANIVREIKKVST 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R G D+    +      K ++++GV+ + +H R         K+       D+
Sbjct: 136 KPVTVKFRKGWDEG--NINAVEFAKRLEEAGVDAVTVHGRT--------KEQMYEGKADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ ++K ++  + +  NG +     A+++    + DG+MI R +  N  +   ++    
Sbjct: 186 DIIGKVK-DSVSIPVLGNGDVFTSEDAIELKNKTNCDGIMIARGSMGNPWIFKQIEYALK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +        R++      +     + A ++      ++++ +H      G P S   R
Sbjct: 245 GKVPLEITYLDRIN------MCLRHYELALKYDGERKAVREMRKHASWYIKGLPKSADIR 298

Query: 295 HILTVEAGASTATHHIIETAFNLMI 319
            ++      S+A   ++    N + 
Sbjct: 299 GVMNTLED-SSAVIELLNNYKNELT 322


>gi|209963474|ref|YP_002296389.1| tRNA-dihydrouridine synthase B, putative [Rhodospirillum centenum
           SW]
 gi|209956940|gb|ACI97576.1| tRNA-dihydrouridine synthase B, putative [Rhodospirillum centenum
           SW]
          Length = 338

 Score =  280 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 137/322 (42%), Gaps = 21/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   +D  +R   +  T   L+ +EMI + A++R  ++++L   +S +E P+++Q+ G D
Sbjct: 24  MSGVSDMPFRRLVKR-TGAGLVVSEMIASQAMIRASRESMLKTEWSPEEAPISMQLAGCD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++ ED G + I++N GCP  +V  G  G+ LM +  + G  +    KA+S+P
Sbjct: 83  PEAMAEAARLNEDRGAHIIDINFGCPVKKVVNGYAGSALMKDEPLAGRIMEQTVKAVSVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D     +    L +  ++ G+  + +H R         +        D+  
Sbjct: 143 VTMKMRKGWD--AGNLNAPRLARIAEECGIRMVTVHGRT--------RCQMYNGTADWKF 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +  ++  ++ L     DGVMIGR  Y     L  V  Y    
Sbjct: 193 IRTVK-EAVSIPVIANGDINTLADVVRCLEESGADGVMIGRGTYGRPWFLAQVMHYLRTG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P              A +  Y A        L+   +H+     G P S   R+ 
Sbjct: 252 EARPDPSLAEQLTIVLEHYEAILEHYGAE-----AGLRIARKHVAWYSKGLPGSADYRNA 306

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +      +     I++    LM
Sbjct: 307 IMTMDQPARVKQAIVDFYRALM 328


>gi|82701266|ref|YP_410832.1| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrosospira
           multiformis ATCC 25196]
 gi|82409331|gb|ABB73440.1| tRNA-U20-dihydrouridine synthase [Nitrosospira multiformis ATCC
           25196]
          Length = 337

 Score =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 131/302 (43%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKSM-GAGMAVSEMVSSNSLLWGSEKTRRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+     G   I++N+GCP+ ++     G+ L+ +P +VG  + A+  A+ +P
Sbjct: 76  PAMMAEAARYNVAQGAQIIDINMGCPAKKICNVMAGSALLQDPPLVGRILDAVIGAVRVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q       ++ +  + +G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWDTQHKNA--LSIARIAENAGIQALAIHGRT--------RACAYTGHAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +    +A  +L     D VMIGRAA     +   +D Y +  
Sbjct: 186 IAAVKAEV-RIPVVANGDITTPEKAKHVLDYTGADAVMIGRAAQGRPWIFREIDHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +     +    + Y          ++   +H+     G   S   RH 
Sbjct: 245 SHLPLPEVAEIHRVLVAHLHDLYSFY-----GEYSGVRIARKHISWYTKGLVGSAGFRHA 299

Query: 297 LT 298
           + 
Sbjct: 300 MN 301


>gi|134298050|ref|YP_001111546.1| nifR3 family TIM-barrel protein [Desulfotomaculum reducens MI-1]
 gi|134050750|gb|ABO48721.1| tRNA-U20-dihydrouridine synthase [Desulfotomaculum reducens MI-1]
          Length = 319

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 138/325 (42%), Gaps = 27/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR      L  TEMI   A+L  + +   +L F  +  PL++QI G++
Sbjct: 17  MAGVTDRAYRILARE-QGCGLAVTEMISDLALLYANPRTYRMLDFRGETVPLSVQIFGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              + +AA IV + G   +++N+GCP+ ++ + + G+ LM  P +    + A+ K++  +
Sbjct: 76  PESMGKAAAIVVERGATIVDINMGCPTPKIVKNNEGSALMKTPQLAAKIVEAVVKSVPAV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+Q  +V      + ++ +G + + +H R         +        D++
Sbjct: 136 PVTVKIRKGWDEQ--SVNAVEFARLVEAAGASAVAVHGRT--------RSQFYSGKADWE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E   + +  NG +     A K+  L   DGVM+GR A  N  +   +  Y   
Sbjct: 186 SIRKVK-EALKIPVIGNGDIWCARDAAKMLELTGCDGVMVGRGAMGNPWIFREIVYYLKT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P      +   R +   +             + ++ +H      G   + R R 
Sbjct: 245 GMELPCPSAQERVETAIRHLQLMVESKGEE-----VAVFEMRKHAAWYTKGMRGAARIRE 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +             IE     +++
Sbjct: 300 TINKSQSKKE-----IEDILRSLLD 319


>gi|160878583|ref|YP_001557551.1| NifR3 family TIM-barrel protein [Clostridium phytofermentans ISDg]
 gi|160427249|gb|ABX40812.1| TIM-barrel protein, nifR3 family [Clostridium phytofermentans ISDg]
          Length = 324

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 131/303 (43%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD  +R   +      L+YTEM+ A  I   +K   +    +E  +P+ALQ+ G D
Sbjct: 19  MAGVTDLPFRLLCKE-QGADLIYTEMVSAKGIYYNNKNTEVLLEVEEKERPVALQLFGED 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E   ++ +++N+GCP  +V     G+ LML P+ +G+ ++A+ KA+  P
Sbjct: 78  PYIMSEMAKRIEHRNFDFLDINMGCPVPKVVNNGEGSALMLKPERIGEIVSAISKAIKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G       +    + K I++SG   I +H R         ++       D+DI
Sbjct: 138 VTVKIRKGF--TKDNINAVEVAKVIEQSGGAAIAVHGRT--------REQYYSGEADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++      +++     D VMI R    N    +    Y +  
Sbjct: 188 IKAVK-EAVSIPVIGNGDVQTPEDVKRMMSYTGCDAVMIARGVRGNPWFFSQAKHYLNTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    V +   R         A         + ++ +H+     G+P S + R+ 
Sbjct: 247 EILAKPSVPEVIEMILRH-----GRLAIEVKGEFTAMHEMRKHVAWYTMGYPKSAKLRNQ 301

Query: 297 LTV 299
           +  
Sbjct: 302 VNE 304


>gi|315650052|ref|ZP_07903131.1| tRNA-dihydrouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315487681|gb|EFU77985.1| tRNA-dihydrouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 334

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 139/298 (46%), Gaps = 22/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   +D  +R   + +   +LL TEM+ A AI     + ++++     E P++LQ+ G+D
Sbjct: 35  MAGVSDLPFRHLCKEM-GASLLVTEMVSAKAIYFKNKNTRSLMKTDKYEHPISLQLFGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +ED  ++  + N+GCP  ++     G  LM NP +V + ++ + K++  P
Sbjct: 94  PDIIADMAASIEDGDFDIFDFNMGCPVPKIVNNGEGCALMKNPKLVEEILSKLVKSVKKP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +  ++   ++ K  + +GV+ + +H R         ++   +   D+DI
Sbjct: 154 VTLKIRRGFDSE--SINAVDIAKIAENAGVSAVTVHGRT--------REQYYLGKADWDI 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K    ++ +  NG + D   A ++      DG+M+ RAA  N  +   + EY    
Sbjct: 204 IKDVKSAV-NIPVIGNGDVADGESAKRMYEYTGCDGIMVARAARGNPWIFREIREYL-TG 261

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T   P K  + +   R     M      +      ++++ +H+    HG  NS   R
Sbjct: 262 YTVKKPSKEEIIEMILRHCRLQM-----EYDDEVMAVRKMRKHVAWYTHGMKNSSVLR 314


>gi|251794118|ref|YP_003008849.1| hypothetical protein Pjdr2_0082 [Paenibacillus sp. JDR-2]
 gi|247541744|gb|ACS98762.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. JDR-2]
          Length = 338

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 152/326 (46%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL G+K+ +  L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAILHGNKRTMEMLFVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK+V +    + I++N+GCP  +V +   GA  +L+P+ + + ++A+  A+S 
Sbjct: 77  RESLVEAAKVVDQQTNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVTAAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD+       +  K+++ +G   + +H R         ++ +     ++D
Sbjct: 137 PVTVKMRIGWDDEHIYAV--DNAKAVESAGGKAVSVHGRT--------REQQYTGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+    + +  NG +     A ++L     DGVMIGR A  N  ML    +Y  +
Sbjct: 187 IIRDVKQAV-SIPVIGNGDVFSPEDARRMLDHTGCDGVMIGRGALGNPWMLYRTIQYLES 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+          +++    D           ++++ +HM     G P + R + 
Sbjct: 246 GELLPDPLPRE-----KLEVAILHMDRLVALRGEAAAVREMRKHMAWYLKGLPGAARVKD 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ++  E G       ++E     + E 
Sbjct: 301 VIMEETGRDKL-VEVMENYIASLDEE 325


>gi|220930307|ref|YP_002507216.1| hypothetical protein Ccel_2942 [Clostridium cellulolyticum H10]
 gi|220000635|gb|ACL77236.1| TIM-barrel protein, nifR3 family [Clostridium cellulolyticum H10]
          Length = 320

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 70/301 (23%), Positives = 130/301 (43%), Gaps = 21/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+YTEM+ A  +   D K+  +     +E+P A+QI G+D
Sbjct: 17  MAGVTDMPFRILCKE-QECGLVYTEMVSAKGMHYDDDKSNKLTLMHEKERPGAVQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ +       I++N+GCP+ ++ +   G+ LM NP++V + I ++  A   P
Sbjct: 76  PKIMAEVAEKLNKSDAAIIDINMGCPAPKITKNGEGSALMKNPELVAEIIKSVVSASQKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    +    + +  +K+G   I +H R         ++       D+DI
Sbjct: 136 VTVKIRKGWDD--STINAIEIARIAEKNGARAIAVHGRT--------REQYYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A K+L     D +M+GR A  N  +   + ++  + 
Sbjct: 186 IRQVK-EAVSIPVIGNGDVTGPKEAQKLLEETRCDAIMVGRGAQGNPWIFKKIVKFLEDG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P      +   R       D           + ++  H+     G  ++   +  
Sbjct: 245 TIISDPSPKEKIETIIRH-----MDMLIDLKGEKTGILEMRSHIAWYIKGMRDAAYTKQK 299

Query: 297 L 297
           +
Sbjct: 300 I 300


>gi|315224769|ref|ZP_07866591.1| tRNA-dihydrouridine synthase B [Capnocytophaga ochracea F0287]
 gi|314945262|gb|EFS97289.1| tRNA-dihydrouridine synthase B [Capnocytophaga ochracea F0287]
          Length = 327

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 145/325 (44%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    +LY+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MHGADMLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMALSAKIVATVNPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVNSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+Q  ++ +  + + ++  G++ + IHAR         +      + D+  
Sbjct: 138 VTVKTRLGWDEQ--SINIEEVAERLQDVGISALTIHART--------RSQMYKGHSDWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL+      VDG+MIGRAA     +   +  YF+ 
Sbjct: 188 IAKVKNNPRIHIPIFGNGDIDSPEKALEYRNTYGVDGIMIGRAAIGYPWIFNEIKHYFAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                SP  +   +     +      ++         + ++ RH    F G PN +  R 
Sbjct: 248 GELLPSPTISDRVEAAKNHLL-----WSVEWKGERQGVLEMRRHYANYFKGIPNFKEHRQ 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L        ++  II+    ++ E
Sbjct: 303 RLVTL----DSSEEIIKE-LEVVRE 322


>gi|163815371|ref|ZP_02206746.1| hypothetical protein COPEUT_01536 [Coprococcus eutactus ATCC 27759]
 gi|158449345|gb|EDP26340.1| hypothetical protein COPEUT_01536 [Coprococcus eutactus ATCC 27759]
          Length = 324

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 143/326 (43%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D+ +R   +      +LY+EM+ A AI   +K    +L    +EKP  LQ+ G+D
Sbjct: 16  MAGVCDQPFRLLCKE-QGCDILYSEMVSAKAIYYNNKNTKPLLAMDEREKPFGLQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E  GY+ I++N+GCP  +V     G+ LM +P +VG  +  +  A+SIP
Sbjct: 75  PVIMAEMAKKIEGNGYSFIDINMGCPVPKVVNNGEGSALMKDPLLVGRIVETVANAISIP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G D +   +    +    ++SG   + +H R         +      + D+D+
Sbjct: 135 LTIKIRSGFDPE--HINAPEIAHIAQESGAAAVAVHGRT--------RQQYYQGHADWDV 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+   ++ +  NG +      + +      DG MIGR A  N  +   +  Y+ + 
Sbjct: 185 IARVKQ-VCNIPVIGNGDINTPKDIIDMRNQTDCDGFMIGRGARGNPWIFRDMKYYYEHG 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V     R  +  MT++   ++     + ++ +H+     G  +S R R  
Sbjct: 244 DLPPRPDAHEVRGMILRH-ARLMTEFKGEYIG----IHEMRKHVAWYSAGMYDSARLRG- 297

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           L  E         +++     + E +
Sbjct: 298 LVNEVETYDELVELLDRWEESIPEKV 323


>gi|213962326|ref|ZP_03390589.1| tRNA-dihydrouridine synthase B [Capnocytophaga sputigena Capno]
 gi|213954992|gb|EEB66311.1| tRNA-dihydrouridine synthase B [Capnocytophaga sputigena Capno]
          Length = 326

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 76/327 (23%), Positives = 149/327 (45%), Gaps = 26/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    +LY+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MHGADMLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+  + ++P
Sbjct: 78  EEAMALSAKIVATVNPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVNSTTLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+Q  ++ +  + + ++  G++ + IHAR         +      + D+  
Sbjct: 138 VTVKTRLGWDEQ--SINIEEVAERLQDVGISALTIHART--------RSQMYKGHSDWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL+      +DG+MIGRAA     +   +  YF+ 
Sbjct: 188 IAKVKNNPRMHIPIFGNGDIDSPEKALEYRNTYGIDGIMIGRAAIGYPWIFNEIKHYFAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                SP      +     +      ++         + ++ RH    F G PN +  RH
Sbjct: 248 GELLPSPTIADRVEAAKNHLL-----WSVEWKGERQGVVEMRRHYANYFKGIPNFKEHRH 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L        A+  +++ A + ++E L
Sbjct: 303 KLVTL----DASQEVVK-ALDNVLEVL 324


>gi|160893102|ref|ZP_02073890.1| hypothetical protein CLOL250_00648 [Clostridium sp. L2-50]
 gi|156865185|gb|EDO58616.1| hypothetical protein CLOL250_00648 [Clostridium sp. L2-50]
          Length = 317

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 141/302 (46%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D+ +R  A+      +LYTEMI A  +   +K    +L  S +E P+ +Q+ G+D
Sbjct: 12  MAGVCDQPFRLLAKE-QGCDILYTEMISAKGLYYDNKNTVPLLAVSPEEDPIGVQLFGSD 70

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK +ED G+  +++N+GCP  ++     G+ LM NP ++G  ++AM KA  +P
Sbjct: 71  PELLAEMAKKIEDRGFAFVDVNMGCPVPKIVNNGEGSALMKNPLLIGKIVSAMTKACKLP 130

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +   +    +    ++SGV  + +H R         ++     + D+ +
Sbjct: 131 VTIKIRSGFDSE--HINAPEVAHIAEESGVAAVAVHGRT--------REQYYHGHADWGV 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K    ++ +  NG +      +++    + D  MIGR A  N  +   +  YF   
Sbjct: 181 IADVK-AAVNIPVIGNGDILTPEDVIRMKEQTNCDAFMIGRGARGNPWIFHELKTYFETG 239

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P K +V +   R  +  M D+          + ++ +H+     G  +S R R++
Sbjct: 240 EIPPRPDKQQVKETMLRH-ARLMIDFKGEF----TGIHEMRKHVAWYSAGMYDSSRLRNL 294

Query: 297 LT 298
           + 
Sbjct: 295 IN 296


>gi|254490327|ref|ZP_05103516.1| putative TIM-barrel protein, nifR3 family [Methylophaga thiooxidans
           DMS010]
 gi|224464460|gb|EEF80720.1| putative TIM-barrel protein, nifR3 family [Methylophaga thiooxydans
           DMS010]
          Length = 334

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 73/306 (23%), Positives = 135/306 (44%), Gaps = 21/306 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EMI A+  L   KK++L      + +P ++QI GAD
Sbjct: 22  MAGVTDRPFRQLCRRL-GAGMAVSEMITANKALWASKKSLLRANHEGEPEPRSVQIAGAD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G + I++N+GCP+ +V     G+ L+ +  +V D + ++ KA+ +P
Sbjct: 81  PVMMAEAARHNVDQGAHIIDINMGCPAKKVCNVMAGSALLQHETLVADILESVVKAVDVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +++G+  + +H R         + +    + +YD 
Sbjct: 141 VTLKIRTGWDRDNRNGVT--IARIAEEAGIQLLSVHGRT--------RADAYKGDAEYDT 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG ++   +A  +L     DG+MIGRAA  N  +   +  Y ++ 
Sbjct: 191 IAEIKSRI-SIPLIANGDIDSPQKAQLVLEKTGADGLMIGRAAQGNPWIFKQILHYLNHG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    + K     +      Y          ++   +H+     G  +    R  
Sbjct: 250 QLLATPAVNEICKVLLEHLENLYDFY-----GDYTGVRMARKHIAWYSKGLRDGNAFRQH 304

Query: 297 LTVEAG 302
           +     
Sbjct: 305 MNQLEH 310


>gi|193214513|ref|YP_001995712.1| TIM-barrel protein, nifR3 family [Chloroherpeton thalassium ATCC
           35110]
 gi|193087990|gb|ACF13265.1| TIM-barrel protein, nifR3 family [Chloroherpeton thalassium ATCC
           35110]
          Length = 402

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 80/322 (24%), Positives = 134/322 (41%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      +++TE I +D ++R     K  L     E+P+A+QI G  
Sbjct: 61  MEDVTDPSFRRLCKHY-GADIVFTEFISSDGLIRHAVKSKRKLDVFDDERPVAIQIFGNQ 119

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAA++ E  G + I++N GCP+ +V     G+ L+  PD++     A+ KA+ +P
Sbjct: 120 IEPMVEAAQMAEAAGPDFIDINYGCPAKKVAGKGAGSGLLCQPDLMEKITDAVVKAVRLP 179

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D++  ++++ + V+ ++  G+  + IH R         +        D+  
Sbjct: 180 VTAKTRIGWDER--SISILDTVRRLEGCGIQALSIHGRT--------RAQMYKGRADWSW 229

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +    KE   + I  NG +     A ++     VDGVMIGR A  N  +           
Sbjct: 230 IAR-AKEVATIPIIGNGDIWTAEDAKRMFDETGVDGVMIGRGAIGNPFLFREAKHLIQTG 288

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                           R +  S+             + ++ RH      G PN  + R  
Sbjct: 289 EHLPQATHRERVAVAIRHLEMSL-----ERKGEKYGVLEMRRHYSTYLKGLPNVSKVRDY 343

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L  E        ++I  A    
Sbjct: 344 LVRE-----NDPNLIVEALRRF 360


>gi|325982360|ref|YP_004294762.1| TIM-barrel protein, nifR3 family [Nitrosomonas sp. AL212]
 gi|325531879|gb|ADZ26600.1| TIM-barrel protein, nifR3 family [Nitrosomonas sp. AL212]
          Length = 335

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 125/302 (41%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G KK         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKSM-GAGMAVSEMVSSNSLLWGSKKTQRRANHEGEVSPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+   + G   I++N+GCP+ ++     G+ L+ +  +V   + A+ +A+ IP
Sbjct: 76  PQMLAAAAQYNAENGAQIIDINMGCPAKKICNVMAGSALLQDEKLVEKILIAVVRAVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        +    + SG+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDKQHKNA--LAIAHIAENSGIQALAIHGRT--------RACAYTGTAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A +IL     D +MIGRAA     +   +D + +  
Sbjct: 186 IAAVK-AAVRIPVIANGDITTPEKAKQILVYTKADAIMIGRAAQGRPWIFREIDHFLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP  + +       +      Y          ++   +H+     G   S   R  
Sbjct: 245 QHLQSPEVSDIHSVLIDHLHDLYHFY-----GEYSGVRIARKHISWYTKGLMGSAGFRQA 299

Query: 297 LT 298
           + 
Sbjct: 300 MN 301


>gi|254409857|ref|ZP_05023638.1| putative TIM-barrel protein, nifR3 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196183854|gb|EDX78837.1| putative TIM-barrel protein, nifR3 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 334

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 132/319 (41%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  +        I+     EKP+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYAPESMMYTEMVHAAGLHHVQGLSKIMDVDPNEKPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA+     G + +++N+GCP  ++ +   G+ L+  P+     + A+ +A+S+PVTV
Sbjct: 94  LGEAAQKAVAEGADTVDINMGCPVNKITKKGGGSSLLREPETAVAIVRAVVEAVSVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  D    + + N  + ++++G   + +HAR         +         ++ + +
Sbjct: 154 KTRIGWSDDE--INILNFAQRMEEAGAQMLTLHART--------RAQGYKGEAKWEWIGK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  +  A++ L     DGVM  R       ++  +D +       
Sbjct: 204 VKQ-ILSIPVIANGDIFSVESAVRCLEQTGADGVMCSRGTLGYPFLVGEIDHFLKTGKQL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P          R I A     A         +QQ  +H+     GF  +   R  L+ 
Sbjct: 263 APPTPVE------RLICAKEHLQALWEYKGDRGVQQARKHLAWYTKGFVGASDLRDQLSR 316

Query: 300 EAGASTATHHIIETAFNLM 318
                     +I+TA   +
Sbjct: 317 IETVEQ-GVTLIDTAIAKL 334


>gi|293609802|ref|ZP_06692104.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828254|gb|EFF86617.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 341

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVTAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V       ++     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKDVLLGHLTELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYKVESTAEQAI--VVENYFNQLL 321


>gi|319943752|ref|ZP_08018033.1| tRNA-dihydrouridine synthase A [Lautropia mirabilis ATCC 51599]
 gi|319742985|gb|EFV95391.1| tRNA-dihydrouridine synthase A [Lautropia mirabilis ATCC 51599]
          Length = 382

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 121/346 (34%), Positives = 178/346 (51%), Gaps = 33/346 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R F RLL+    LYTEM+ A AI  GD  ++LG   +   + LQ+GG D  
Sbjct: 21  MMDWTDRHCRSFHRLLSRRTWLYTEMVTAQAIAHGDLDHLLGRGEEGDRVVLQLGGNDPQ 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+  + +GY+EINLN GCPS RV EG+FGACLM  P+ V DC+AAM   + +PVT
Sbjct: 81  LLARAAREGQAYGYDEINLNCGCPSDRVREGAFGACLMAEPERVADCVAAMQAVVQVPVT 140

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG+D +     + + V  +  +G     +HAR A L GL PK NR+IP L Y++V+
Sbjct: 141 VKHRIGIDRREDYEFVHHFVDVVAAAGCRRFVVHARNAWLDGLDPKQNREIPPLRYEVVH 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-------------------------PSVD---- 211
            + ++ P     LNGGL+D++  L  +                            D    
Sbjct: 201 RLAQDFPHCAFELNGGLQDLAHGLAAVCPTEASGPDSETASEGPAVVDAMAGAEADSPAT 260

Query: 212 ---GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
              G M GR AY +  +L  VD++ +      +P+           + A++  Y  R   
Sbjct: 261 RLVGAMYGRRAYHDPWLLAGVDDWLAR-HAAEAPVTDAAQPLTRAAVVAALVGYLERGAA 319

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
            G +++ + RH++GL+ G P +R  R +L+     S     ++  A
Sbjct: 320 HGVEVRHLARHVLGLYLGHPAARLWRRMLSESRALSRNDPGLLREA 365


>gi|93005906|ref|YP_580343.1| dihydrouridine synthase TIM-barrel protein nifR3 [Psychrobacter
           cryohalolentis K5]
 gi|92393584|gb|ABE74859.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Psychrobacter
           cryohalolentis K5]
          Length = 343

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 78/321 (24%), Positives = 140/321 (43%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 39  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDNEIAPISAQIAGAE 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL EAA+   D G   I++N+GCP+ +V     G+ L+ + D+V   + A   A+  P
Sbjct: 98  PDKLAEAARYQIDNGAQIIDINMGCPAKKVCRKLAGSALLQDEDLVARLLDAAVNAVDAP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G ++      +  + K  +++G+  I IH R         +++       Y++
Sbjct: 158 VTLKTRLGYENGR--ENILRVAKRAEQAGIAAIAIHGRT--------REDMYTGEARYEL 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K E+  + +  NG ++   +A ++  L   D VMIGRAA     +   ++ +    
Sbjct: 208 IREVK-ESISIPVIANGDIDSAQKAQRVYELTGCDAVMIGRAAQGQPWIFRDIEHFLRTG 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T +SP  + +       +      Y           +   +H+     G PNS   R  
Sbjct: 267 ETLASPSVSEIKGIVLTHLEELYGFY-----GEYSGCRIARKHIAWYTTGIPNSNAFRQA 321

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +  E   +     ++E   N 
Sbjct: 322 MYGEESTAG-QFRVVEDFLNA 341


>gi|256819324|ref|YP_003140603.1| TIM-barrel protein, nifR3 family [Capnocytophaga ochracea DSM 7271]
 gi|256580907|gb|ACU92042.1| TIM-barrel protein, nifR3 family [Capnocytophaga ochracea DSM 7271]
          Length = 327

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 144/325 (44%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    +LY+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MHGADMLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMALSAKIVATVNPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVNSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+Q  ++ +  + + ++  G++ + IHAR         +      + D+  
Sbjct: 138 VTVKTRLGWDEQ--SINIEEVAERLQDVGISALTIHART--------RSQMYKGHSDWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL+      VDG+MIGRAA     +   +  YF+ 
Sbjct: 188 IAKVKNNPRIHIPIFGNGDIDSPEKALEYRNTYGVDGIMIGRAAIGYPWIFNEIKHYFAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                SP  +   +     +      ++         + ++ RH    F G PN +  R 
Sbjct: 248 GKLLPSPTISDRVEAAKNHLL-----WSVEWKGERQGVLEMRRHYANYFKGIPNFKEHRQ 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L        ++  II     ++ E
Sbjct: 303 RLVTL----DSSEEIIRE-LEVVRE 322


>gi|291520200|emb|CBK75421.1| tRNA-U20-dihydrouridine synthase [Butyrivibrio fibrisolvens 16/4]
          Length = 327

 Score =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 133/302 (44%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +     AL   EM+ A  I+  +K  +++L    +E+P++LQ+ G+D
Sbjct: 21  MAGVTDLPFRLLCKE-QGAALCCMEMVSAKGIMYNNKNTESLLTVDERERPVSLQLFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  +E   ++ +++N+GCP  +V     G+ LM NP + G  I +M KA+  P
Sbjct: 80  PEIMGAMAAKIEHRNFDILDINMGCPVPKVVNNGDGSALMKNPVLAGKIIESMVKAIEKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++   V    +    ++SG   + +H R         ++       D+ I
Sbjct: 140 VTVKIRKGFDEE--HVNAVEMAHVAQESGAAAVAVHGRT--------REQFYSGKADWSI 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG + D     ALK   + DG MIGR A  N  +   +  YF   
Sbjct: 190 IADVKNAV-SIPVIGNGDILDAKDVIALKEQTNCDGFMIGRGAQGNPWIFHQILHYFETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + K   R       ++   +L     ++++ +H      G+  + + R  
Sbjct: 249 ELIGKPPMEEMVKTMLRHAKLQ-IEFKGDYLG----IREMRKHAAWYTAGYKGASKLRGR 303

Query: 297 LT 298
           + 
Sbjct: 304 IN 305


>gi|110834874|ref|YP_693733.1| NifR3 family TIM-barrel protein [Alcanivorax borkumensis SK2]
 gi|110647985|emb|CAL17461.1| TIM-barrel protein, putative, NifR3 family, putative [Alcanivorax
           borkumensis SK2]
          Length = 346

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 146/322 (45%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    LL +EM+ +D  L   +K+   L  S +  P+++QI G +
Sbjct: 17  MAGVTDRPFRRLCRDL-GAGLLVSEMVTSDTRLWNSRKSRQRLDHSGEPGPISVQIAGGE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V + + G+ L+ +PD+V   + A+ +A+++P
Sbjct: 76  PAMLAEAARANVEHGAQIIDINMGCPAKKVCKRAAGSALLADPDLVARILDAVTQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  + +G+  + IH R         + ++   + +Y  
Sbjct: 136 VTLKIRTGPDRDQRNAI--DIARIAETAGIQALAIHGRT--------RADKFNGDAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  +  ++ I  NG ++   +A ++L     DG+MIGRAA  N  +      Y  + 
Sbjct: 186 IKQVV-DAVNIPIMANGDVDSPEKAKRVLESTGADGIMIGRAAQGNPWIFRDTLYYLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P+ T V     + +      Y          ++   +H+       PN    R  
Sbjct: 245 SLPAAPLVTEVHDCVQQHLYELHDFYGEFM-----GVRIARKHLGWYTQNLPNGEDFRRG 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      IE  F  +
Sbjct: 300 FNTLENATDQRVA-IEQFFQQI 320


>gi|16331567|ref|NP_442295.1| hypothetical protein slr0644 [Synechocystis sp. PCC 6803]
 gi|2833467|sp|Q55724|DUS1_SYNY3 RecName: Full=Probable tRNA-dihydrouridine synthase 1
 gi|1001634|dbj|BAA10365.1| slr0644 [Synechocystis sp. PCC 6803]
          Length = 355

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 60/317 (18%), Positives = 127/317 (40%), Gaps = 21/317 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     A+LYTEM+ A  I        ++    +E P+++Q+       
Sbjct: 51  GVTDLVFRRLVRRYAPQAMLYTEMVSATEIHHLRTLPQVMEIDPRENPISIQLFDCRPDF 110

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+     G   +++N+GCP  ++ +   G+ L+  P +    +  +  A+ +PVTV
Sbjct: 111 MAEAAQKAVAQGAQSVDINMGCPVNKITKKGGGSSLLRQPAVAEAIVKTVVAAVDVPVTV 170

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD    + +    + ++ +G   + +H R         +         +  + +
Sbjct: 171 KTRLGWDDGE--INIVEFAQRLQDAGAQMLTLHGRT--------RAQGYNGRARWQWIAK 220

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  +  A+  L     DGVM  R +     ++  ++ +F      
Sbjct: 221 VKQALT-IPVIANGDIFSVEAAIACLEETGADGVMCSRGSLGYPFLVGEIEHFFKTGEKR 279

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P          ++    + +Y  +       L Q  +H+      FP +   R  L  
Sbjct: 280 KAPTVAE-KLTCAQEHLQMLWEYKGQR-----GLFQARKHLAWYCKDFPGAAALREQL-F 332

Query: 300 EAGASTATHHIIETAFN 316
           +  +      +++ A +
Sbjct: 333 QINSVQEGKDLLDQAIS 349


>gi|256751234|ref|ZP_05492115.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus
           CCSD1]
 gi|256749959|gb|EEU62982.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter ethanolicus
           CCSD1]
          Length = 344

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 134/318 (42%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLALQIGGADI 59
           M   TD+ +R   + +    L YTEM+ A  +  G +   L     + + +ALQI G+D 
Sbjct: 40  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKLLTDIDEGESVALQIFGSDP 98

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + PV
Sbjct: 99  DIMGEIAKRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKPV 158

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD    V    + +  +K GV  + +H R         ++       D+ I+
Sbjct: 159 TVKIRKGWDD--NHVNAVEIAQIAEKVGVKAVAVHGRT--------REQFYSGKADWSII 208

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K E+  + +  NG +     A ++L     D ++IGR A  N  +      + +   
Sbjct: 209 KKVK-ESVKIPVMGNGDVFTPEDAKRMLEETGCDAILIGRGAQGNPWIFKRTVHFLNTGE 267

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +   R +   M +Y          + ++ +H+     G   S + R   
Sbjct: 268 LLPEPTIQEKIEVIIRHL-EMMIEY----RGERTGILEMRKHIAWYLKGLYGSAKLR--- 319

Query: 298 TVEAGASTATHHIIETAF 315
             EA      +  I+   
Sbjct: 320 --EAVFKMEKYEQIKEFL 335


>gi|307267135|ref|ZP_07548645.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|306917855|gb|EFN48119.1| TIM-barrel protein, nifR3 family [Thermoanaerobacter wiegelii
           Rt8.B1]
          Length = 321

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 136/319 (42%), Gaps = 27/319 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + +    L YTEM+ A  +  G  + K +     +EK +ALQI G+D
Sbjct: 17  MAGVTDKPFRLICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEK-VALQIFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ + D     +++N+GCP+ ++ +   GA LML P++    + ++ KA + P
Sbjct: 75  PDIMGEIARRLNDSKALILDINMGCPTPKIVKNGDGAALMLKPELAEKVMESVVKASNKP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    + +  +K GV  + +H R         ++       D+ I
Sbjct: 135 VTVKIRKGWDD--NHVNAVEIAQIAEKVGVKAVAVHGRT--------REQFYSGKADWSI 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E+  + +  NG +     A ++L     D ++IGR A  N  +      + +  
Sbjct: 185 IKKVK-ESVKIPVMGNGDVFTPEDAKRMLEETGCDAILIGRGAQGNPWIFKRTVHFLNTG 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R +   M +Y          + ++ +H+     G   S + R  
Sbjct: 244 ELLPEPTIQEKIEVIIRHL-EMMIEYKGER----TGILEMRKHIAWYLKGLYGSAKLR-- 296

Query: 297 LTVEAGASTATHHIIETAF 315
              EA      +  I+   
Sbjct: 297 ---EAVFKMEKYEQIKEFL 312


>gi|303230948|ref|ZP_07317691.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514330|gb|EFL56329.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 330

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 133/303 (43%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     +++ TEM+ A  I   +++   +L     E P+++QI G+D
Sbjct: 21  MAGVSDIAYRLLAKE-HGASMVCTEMVSAMGIKYKNERTHELLRMEAVEHPVSMQIFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V D G + +++N+GCP  +V     G+ LM  PD+      A  KA+ +P
Sbjct: 80  PEAIALGAKVVADAGADIVDINMGCPVKKVVSSGDGSALMKTPDLAARVAEAAVKAVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG DD    + + +  K I+ +GV  + +H R         ++   +   ++  
Sbjct: 140 VTVKMRIGWDDD--HINVVDFAKRIESTGVAAVAVHGRT--------REQMYMGRANWSY 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K ++  + +  NG +     AL+++     D VMIGR A  N  +    + Y +  
Sbjct: 190 IKAVK-DSLSIPVIGNGDVWTPEDALRMMQETGCDAVMIGRGAQGNPWIFERTNHYLTTG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P       D   K    +  Y    L     +++I  H      G P +   R+ 
Sbjct: 249 ELSPEPTYLE-RLDMLLKHFELLCQYKGDSLG----VREIRTHAGWYMKGMPEAAYWRNR 303

Query: 297 LTV 299
           +  
Sbjct: 304 VNT 306


>gi|121535055|ref|ZP_01666872.1| putative TIM-barrel protein, nifR3 family [Thermosinus
           carboxydivorans Nor1]
 gi|121306305|gb|EAX47230.1| putative TIM-barrel protein, nifR3 family [Thermosinus
           carboxydivorans Nor1]
          Length = 317

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 72/309 (23%), Positives = 137/309 (44%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R  A+ +    L+Y+EM+    +L  +   +  +    +E+P+A+QI G++
Sbjct: 17  MAGVTDLPFRLLAKEM-GCGLVYSEMVSDKGLLYNNANTLSLIRIDERERPVAIQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+IV   G + I++N+GCP+ ++ +   GA LM  P++    IA++ +A  +P
Sbjct: 76  PESMAAAARIVARAGADIIDINMGCPTPKIVKNGEGAALMRRPELAYRIIASVVEAAEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   ++    + +  +++G + + +H R         ++       D+ I
Sbjct: 136 VTVKMRKGWDE--SSINAVEIARLAERAGASAVSVHGRT--------REQFYAGQADWSI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+       G NG +     A ++L     DG+MIGR A  N  +L  V  Y +  
Sbjct: 186 IRAVKEAVTIPVNG-NGDVRTPQDAARMLTETGCDGIMIGRGAQGNPWLLRQVAHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R +   + +Y   ++     ++++  H      G PN+   R  
Sbjct: 245 EILPGPTLQERFNMLLRHL-DMLIEYKGEYIG----IREMRSHAAWYTKGLPNAADLRRR 299

Query: 297 LTVEAGAST 305
                    
Sbjct: 300 FNRAETRQD 308


>gi|296131768|ref|YP_003639015.1| TIM-barrel protein, nifR3 family [Thermincola sp. JR]
 gi|296030346|gb|ADG81114.1| TIM-barrel protein, nifR3 family [Thermincola potens JR]
          Length = 340

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 139/318 (43%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD+ YR  A  L  + L+ TEM+ A A+       K +L  S ++ P+++QI G  
Sbjct: 30  MAGVTDKAYRLIA-ELAGSGLVCTEMVSATALRYNSERTKTMLDLSGEKGPISVQIFGNQ 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK  E  G   I++N+GCP+ +V +   G  LM +  +  + ++A+ KA+ IP
Sbjct: 89  PELMSRAAKFAETQGAAIIDINMGCPAPKVVKNFEGCALMRDLPLAREIMSAVVKAVQIP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++  +V    L K  +++G+  + +H R         +        D+DI
Sbjct: 149 VTVKMRKGWDEE--SVNAVELAKMAQETGIAAVTVHGRT--------RGQFYSGKADWDI 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   AL ++     D VMIGR A  N  + +   +     
Sbjct: 199 IARVK-EAVQIPVIGNGDIFEPVHALAMMKQTGCDAVMIGRGALGNPWLFSRTVKLLETG 257

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   + +       A         ++++ +H+     G   + R R  
Sbjct: 258 EIPPEPSIDERLEMAKKHL-----QLAVAFKGEYRAVREMRKHIAWYIKGLREAARVREK 312

Query: 297 LTVEAGASTATHHIIETA 314
           +  +A +      +++  
Sbjct: 313 VN-QAVSVEELVRLLDQY 329


>gi|302879858|ref|YP_003848422.1| TIM-barrel protein, nifR3 family [Gallionella capsiferriformans
           ES-2]
 gi|302582647|gb|ADL56658.1| TIM-barrel protein, nifR3 family [Gallionella capsiferriformans
           ES-2]
          Length = 340

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 130/321 (40%), Gaps = 21/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKRM-GAGMAVSEMVASNSLLYGSEKTKRRANHEGEVDPISVQIVGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAAK   D G   I++N+GCP+ ++     G+ L+ N  +V   + A+  A++ P
Sbjct: 76  PKMLAEAAKYNVDHGAQIIDINMGCPAKKICNVMAGSALLQNEPLVAKLLEAVVGAVNAP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  + SG+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWDTHNRNAV--RIAQIAEASGIQALAIHGRT--------RACAYTGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K  +  + I  NG +    +A  +L     D VMIGRAA     +   ++ +    
Sbjct: 186 IRAVK-ASVTIPIIANGDITTPEKARYVLQYSGADAVMIGRAAQGRPWLFREIEHFLQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP  + + +     +      Y          L+   +H+     G   S   RH 
Sbjct: 245 EHMPSPEVSEIHRVLLAHVVELYDFYGEH-----TGLRIARKHISWYTKGLAGSAHFRHQ 299

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +      +     + E     
Sbjct: 300 MNQLESVAEQHAAVDEFFAEQ 320


>gi|260556608|ref|ZP_05828826.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii ATCC 19606]
 gi|260409867|gb|EEX03167.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii ATCC 19606]
          Length = 341

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVIAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 300 MYKVETTAEQAL--VVESYFNQLL 321


>gi|260588921|ref|ZP_05854834.1| tRNA-dihydrouridine synthase B [Blautia hansenii DSM 20583]
 gi|260540700|gb|EEX21269.1| tRNA-dihydrouridine synthase B [Blautia hansenii DSM 20583]
          Length = 318

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 139/303 (45%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A AI     + ++++    +E+P++LQ+ G++
Sbjct: 19  MAGVTDLPFRLLCKE-QGAGLICTEMVSAKAIHFKNKNTESLMEIDERERPVSLQLFGSE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + AK +E   ++ +++N+GCP  +V     G+ LM NP +V + +  + +A+  P
Sbjct: 78  PDLMADIAKQIEYRNFDILDINMGCPVPKVVNNGEGSALMKNPKLVHEIVYKVSRAIKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G  +   +V    + K ++ +G   + +H R         ++       D+DI
Sbjct: 138 LTVKIRKGFTED--SVNAVEIAKILEDAGAAAVAVHGRT--------REQYYSGQADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +A K++     DG+MIGRA   N  + + +  Y    
Sbjct: 188 IRQVK-EAVSIPVIGNGDVTSPEKAEKLVKETGCDGIMIGRAVQGNPWLFSEILYYQETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +   R     +      +  +   ++++ +H+     G P+S   R +
Sbjct: 247 KIKPKPSMEEIKEMMLRHARLQL-----EYKGTYTGMREMRKHVAWYTSGMPHSASVRRM 301

Query: 297 LTV 299
           +  
Sbjct: 302 VNE 304


>gi|332800061|ref|YP_004461560.1| TIM-barrel protein, nifR3 family [Tepidanaerobacter sp. Re1]
 gi|332697796|gb|AEE92253.1| TIM-barrel protein, nifR3 family [Tepidanaerobacter sp. Re1]
          Length = 323

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 140/325 (43%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    +L TEMI    ++  D K   +L  +  E P+ +Q+ G  
Sbjct: 15  MAGITDMPFRTICKQM-GADVLMTEMISTRGLVYNDNKTAKLLQVNPDENPIGVQLFGNA 73

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                E+ K ++D  ++ IN+N+GCP+ ++ +   G  LM +  +    I    +A   P
Sbjct: 74  PKDFEESVKKIDDLPFDFININMGCPTPKIVKNGDGCALMKDVKLASSIIKVTARASRKP 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R G D    ++       + + SG + I IH R         ++       D+DI
Sbjct: 134 VSVKIRKGWDKD--SINAVEFSSAAEDSGASMIIIHGRT--------REMFYSGKADWDI 183

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +  D+ +  NG +     A+++L     DG+MIGR A  N  +   V  +    
Sbjct: 184 IKSVK-DAVDIAVVGNGDVFTSEDAVEMLKKTGCDGIMIGRGALGNPWIFREVKYFLKTG 242

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P      +     ++ +++ Y   HL     + ++ +H+     G P+S   ++ 
Sbjct: 243 KKTAAPTLKERLEIMLLHLNNAIS-YHGEHLG----VLEMRKHLAWYIKGLPHSAPVKNA 297

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L  +     +   I+   F  + ++
Sbjct: 298 L-QQCRDVGSIEEILNNYFYRLKQT 321


>gi|331083389|ref|ZP_08332501.1| hypothetical protein HMPREF0992_01425 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330404082|gb|EGG83630.1| hypothetical protein HMPREF0992_01425 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 318

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 138/303 (45%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEM+ A AI     + ++++    +E+P++LQ+ G++
Sbjct: 19  MAGVTDLPFRLLCKE-QGAGLICTEMVSAKAIHFKNKNTESLMEIDERERPVSLQLFGSE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E   ++ +++N+GCP  +V     G+ LM NP +V + +  + +A+  P
Sbjct: 78  PDLMAEIAKQIEHRNFDILDINMGCPVPKVVNNGEGSALMKNPKLVHEIVYKVSRAIKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G  +   +V    + K ++ +G   + +H R         ++       D+DI
Sbjct: 138 LTVKIRKGFTED--SVNAVEIAKILEDAGAAAVAVHGRT--------REQYYSGQADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + I  NG +    +A K++     DG+M+GRA   N  + + +  Y    
Sbjct: 188 IRQVK-EAVSIPIIGNGDVTSPEKAEKLVKETGCDGIMLGRAVQGNPWLFSEILYYQETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + K   R     +      +      ++++ +H+     G P+S   R +
Sbjct: 247 KMKPKPSMEEIKKMMLRHAKLQL-----EYKGVYTGMREMRKHVAWYTSGMPHSASVRRM 301

Query: 297 LTV 299
           +  
Sbjct: 302 VNE 304


>gi|262278220|ref|ZP_06056005.1| tRNA-dihydrouridine synthase B [Acinetobacter calcoaceticus
           RUH2202]
 gi|262258571|gb|EEY77304.1| tRNA-dihydrouridine synthase B [Acinetobacter calcoaceticus
           RUH2202]
          Length = 341

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  L+  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLQMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PEQLAEAARHQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDTVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKQVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYKVESTAEQAI--VVENYFNQLL 321


>gi|148284888|ref|YP_001248978.1| putative tRNA-dihydrouridine synthase [Orientia tsutsugamushi str.
           Boryong]
 gi|146740327|emb|CAM80734.1| putative tRNA-dihydrouridine synthase [Orientia tsutsugamushi str.
           Boryong]
          Length = 322

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 139/322 (43%), Gaps = 23/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A+++  +++++  +  E  +    +Q+ G 
Sbjct: 19  MSGVTDLPFRKLVKQF-GAGLVVSEMVASRAMIQETRRSMMKSAIIENDITGSCVQLAGC 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AAK+ +D G   I++N GCP+ +V  G  G+ LM +  +    +A   K++SI
Sbjct: 78  EPDVVADAAKMNQDMGAQIIDINFGCPAKKVVGGYAGSALMKDESLAAKILAETVKSVSI 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D+      +  + K  +  G+  I +H R         +        D+ 
Sbjct: 138 PVTLKMRTGWDESCRNAHI--IAKIAEDCGIQMITVHGRT--------RCQFYSGKSDWA 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E+  + +  NG +  +  A+  L     DGVM+GR AY    +L+ +  Y + 
Sbjct: 188 FIRKVK-ESIKIPVVANGDITSVDDAIDCLRISGADGVMVGRGAYGKPWLLSQISHYLAF 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                SP      K       + ++ Y   H      ++   +H+     G PNS   R 
Sbjct: 247 QDYLPSPSLIEQKKIILNHYESMLSYYGTEH-----GIKIARKHLGWYSKGLPNSTEFRS 301

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +T           II   F L
Sbjct: 302 KVTTITSVEQV-QEIINQFFQL 322


>gi|332884058|gb|EGK04338.1| hypothetical protein HMPREF9456_01366 [Dysgonomonas mossii DSM
           22836]
          Length = 331

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 140/301 (46%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G +
Sbjct: 18  MEDVTDMGFRLMCKQF-GADMVYTEFVSSDALIRHVNKTQAKLTISEEERPVAIQIYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKI E+   N +++N GCP  +V     G+ +M  P+++ +  AA+ KA+ IP
Sbjct: 77  VDAMVEAAKICEEANPNILDINFGCPVKKVAGKGAGSGMMKTPELMVEITAAVVKAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +      + D+++
Sbjct: 137 VTVKTRLGWDHESKIIV--ELAEQLQDVGIQALTIHGRT--------RSQMYTGDADWEL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG +       +      VD VMIGR +  +  +   V  Y   
Sbjct: 187 IGDVKNNPRIHIPIVGNGDVTSPEICKRRFDETGVDAVMIGRGSIGSPWIFEEVKHYLRT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             T       + + +++  +   M      H    G +    RH+    LF G P+ ++ 
Sbjct: 247 GET-----LPKKEFEWYLDVLKEMIRKNVVHSGERGGIIHSRRHLAASSLFKGLPDFKKV 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|217969866|ref|YP_002355100.1| hypothetical protein Tmz1t_1445 [Thauera sp. MZ1T]
 gi|217507193|gb|ACK54204.1| TIM-barrel protein, nifR3 family [Thauera sp. MZ1T]
          Length = 346

 Score =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 141/326 (43%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EM+ ++++L G +K       + +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGVAVSEMVTSNSLLYGSEKTRRRADHTGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + EAAK   D G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA+   
Sbjct: 76  PAMMAEAAKFNADNGAQIIDINMGCPAKKVCNVMAGSALMQDEPLVARILEAVVKAVPDT 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G +          + +  ++SG+  I IH R         + ++ +   +YD
Sbjct: 136 PVTLKFRTGWNRANKNA--PTIARIAEESGIRAIAIHGRT--------RADQYMGEAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K    ++ +  NG +    +A  +L     DGVMIGRAA     +   ++ + + 
Sbjct: 186 TIAHVKT-LVNIPVIANGDIGSPQKAKHVLDYTGADGVMIGRAAQGRPWIFREIEHFLAT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+ + + +     ++     Y          ++   +H+     G   S   R 
Sbjct: 245 GELLPPPLVSEIHQVCREHLADLYAFY-----GDDRGVKIARKHISWYTKGLVGSAAFRR 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +        A    ++  F  + E+
Sbjct: 300 AMNQIPDIP-AQLAAVDDFFGQLAEA 324


>gi|158319498|ref|YP_001512005.1| nifR3 family TIM-barrel protein [Alkaliphilus oremlandii OhILAs]
 gi|158139697|gb|ABW18009.1| putative TIM-barrel protein, nifR3 family [Alkaliphilus oremlandii
           OhILAs]
          Length = 324

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 136/320 (42%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    ++Y EM+ A  +   DKK   +L     EKP+ALQI G++
Sbjct: 17  MAGVTDLSFRLICKAMD-CGMVYMEMVSAKGLYYKDKKTEELLKIHDHEKPVALQIFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA ++ D     +++N+GCP+ ++ +   G+ LM +  + G+ I A+ K    P
Sbjct: 76  PDIMARAAYMLNDRANAILDINMGCPTPKIVKNGDGSALMKDIKLAGEVIKAVVKESIKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   +V    L K I+ SG   + +H R         ++       D+ I
Sbjct: 136 VTVKIRKGWDEH--SVNAVELAKVIEDSGAKAVAVHGRT--------REQFYAGKADWSI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+    + +  NG +  +   +++L   + DG+MIGR +  N  +   +  Y    
Sbjct: 186 IKEVKEAVT-IPVIGNGDVFTIEDGIRLLEYTNCDGIMIGRGSQGNPWLFKRLVHYMKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          + +     D   R+      ++++ +H+     G   +   R+ 
Sbjct: 245 EVLPEPRAEEKVLMALKHL-----DLVIRNKGEYIGVKEMRKHIAWYLKGLRGTASLRNQ 299

Query: 297 LTVEAGASTATHHIIETAFN 316
           +      +     ++     
Sbjct: 300 INTTGTKAD-IEELLMNYLE 318


>gi|299769181|ref|YP_003731207.1| TIM-barrel protein, nifR3 family protein [Acinetobacter sp. DR1]
 gi|298699269|gb|ADI89834.1| TIM-barrel protein, nifR3 family protein [Acinetobacter sp. DR1]
          Length = 341

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 142/324 (43%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVTAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  ++ G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEVGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V       +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKHVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYKVESTAEQAL--VVENYFNQLL 321


>gi|260549656|ref|ZP_05823873.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. RUH2624]
 gi|260407173|gb|EEX00649.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. RUH2624]
          Length = 341

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVIAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELINIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V       +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKDVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 300 MYKVETTAEQAL--VVESYFNQLL 321


>gi|253681232|ref|ZP_04862030.1| tRNA-dihydrouridine synthase B [Clostridium botulinum D str. 1873]
 gi|253562470|gb|EES91921.1| tRNA-dihydrouridine synthase B [Clostridium botulinum D str. 1873]
          Length = 320

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 79/305 (25%), Positives = 138/305 (45%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    L+YTEMI A  +   +   K +L  S +EKP+A QI G+D
Sbjct: 17  MAGVTDIAYRGLCKEM-GCGLVYTEMISAKGMYYNNENTKKLLMLSKEEKPVAAQIFGSD 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I+ ED G   I++N+GCP+ ++ +   G+ LM  P++    +  M K    
Sbjct: 76  PLVMARACEILNEDNGVCIIDINMGCPAPKIVKNGEGSALMKTPELAAKIVMEMKKISKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      K ++++GV+ + IH R         +        D+D
Sbjct: 136 PVTVKFRKGFDND--NINAVEFAKRMEQAGVDAVAIHGRT--------RAQMYEGKADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K E  D+ +  NG +    +A  LK   + DG+MI R A  N  +   +    +N
Sbjct: 186 IIRRVK-EAVDIPVIGNGDVFSAEKAFQLKEETNCDGIMIARGAMGNPWIFKQIQLALNN 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + ++D      +       A ++      ++++ +H+     G  N    ++
Sbjct: 245 EKVIYPTPEEKID------MCIRHLKLAIQYHGELKAVREMRKHIAWYIKGIKNCTDIKN 298

Query: 296 ILTVE 300
            + VE
Sbjct: 299 KINVE 303


>gi|160934849|ref|ZP_02082235.1| hypothetical protein CLOLEP_03724 [Clostridium leptum DSM 753]
 gi|156866302|gb|EDO59674.1| hypothetical protein CLOLEP_03724 [Clostridium leptum DSM 753]
          Length = 330

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 137/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR +R         A + +EM+ A A+  GDKK+  ++  S+QE+P A+Q+ G D
Sbjct: 18  MAGTADRAFREICASF-GAAYVISEMVSAKALTYGDKKSRELMELSSQERPAAIQLFGDD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA +  ++    I+LN+GCP+ ++     G+ LM  P + G  + A+ KA+ +P
Sbjct: 77  PQTMAEAAVLALEYQPEIIDLNMGCPAPKITSNGCGSALMKKPALCGRIVEAVKKAVPVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     V    + K  + +G + I +H R         ++    P+ D++ 
Sbjct: 137 VTVKIRKGWD--TRTVNAVEVAKICENAGADAIAVHGRT--------REQMYAPSADWES 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A  +L     D VMIGR A  N  +   V+ +  + 
Sbjct: 187 IRQVK-EAVSIPVIGNGDVFTAEDAAAMLEQTGCDLVMIGRGALGNPWIFQQVNAWLGSQ 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +P          R I          H      +++  +H      G   +   R  
Sbjct: 246 VQLPAPGPAEKMYGMLRHIRLLCDYKGEEH-----GMREARKHAGWYLKGLKGAAGFRRE 300

Query: 297 ---LTVEAGASTATHHIIET 313
              L   +   +    ++E 
Sbjct: 301 AGSLKAYSDLESLCRKVLEE 320


>gi|89094591|ref|ZP_01167529.1| hypothetical protein MED92_01129 [Oceanospirillum sp. MED92]
 gi|89081190|gb|EAR60424.1| hypothetical protein MED92_01129 [Oceanospirillum sp. MED92]
          Length = 328

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 134/322 (41%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ +D  L   +K+   L  + + +P ++QI G D
Sbjct: 18  MAGVTDRPFRQLCKRM-GAGLVVSEMVTSDTRLWKSRKSTYRLNHTGEAEPRSVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA +  + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 77  PIMMAEAAAMNVERGAQIIDINMGCPAKKVCNKAAGSALLKDEALVSDILHAVVNAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + +  + +G+  + +H R         +        +Y+ 
Sbjct: 137 VTLKIRTGWDQQNRNGIT--IAQIAEDAGIQALAVHGRT--------RSCGYKGEAEYNT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +I        +  NG +    +A ++L       VMIGRAA  +  +   +D Y    
Sbjct: 187 IADIVNAV-SFPVFANGDISSPEKAKQVLEHTGCAAVMIGRAAQGSPWLFREIDHYLRTG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
                P    V +     +    + Y          ++   +H+       PN    R  
Sbjct: 246 RILPPPTLKEVREILLAHLQELHSFY-----GDYMGVRIARKHVGWYLQNRPNGSSFRKQ 300

Query: 295 -HILTVEAGASTATHHIIETAF 315
            +IL   A  + A     E AF
Sbjct: 301 FNILETAADQAAAIEAFFEEAF 322


>gi|304319794|ref|YP_003853437.1| NifR3/Smm1 family protein [Parvularcula bermudensis HTCC2503]
 gi|303298697|gb|ADM08296.1| NifR3/Smm1 family protein [Parvularcula bermudensis HTCC2503]
          Length = 335

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 136/308 (44%), Positives = 183/308 (59%), Gaps = 12/308 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR+ R+  RLL+  A LYTEM+V +AIL GD+  +LGF + E P+ALQIGG+D  
Sbjct: 17  MIDWTDRYCRWVHRLLSAKARLYTEMVVDEAILHGDRDRLLGFDSAEHPVALQIGGSDPR 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL E A I    GY+EINLNVGCPS RV  G FGACLM  P+ V + + AM  A+   VT
Sbjct: 77  KLAEVAAIGAQAGYDEINLNVGCPSDRVQSGRFGACLMAEPETVAEGVRAMAAAVPCEVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIG+DDQ P  AL   + +++ +GV  + +HARKA L+GLSPK+NR IP LDYD+V 
Sbjct: 137 VKCRIGIDDQSPEEALPRFLDAVEAAGVRTVIVHARKAWLEGLSPKENRTIPPLDYDLVV 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
              +  P L   LNGGL   + A + L +  GVM+GRAAY+   +L+ VD+        +
Sbjct: 197 REAQRRPALSFILNGGLAGGAAAERWLTTFPGVMLGRAAYEQPFLLSEVDQRLFGAPPAA 256

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                       R     +   A R       + +  RHM+GL+HG P ++  R  L+ E
Sbjct: 257 ------------RSRLEIVEAVADRAAAEAVPIWRYARHMLGLYHGQPGAKTWRRQLSEE 304

Query: 301 AGASTATH 308
             ++ A  
Sbjct: 305 GRSAKACP 312


>gi|313894573|ref|ZP_07828136.1| TIM-barrel protein, nifR3 family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313440763|gb|EFR59192.1| TIM-barrel protein, nifR3 family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 328

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 142/322 (44%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++
Sbjct: 22  MAGVSDIAYRLLAKE-HGAALVCTEMVSAMGIKYKNERTHELLRLEEVERPVSMQIFGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A++V D G + +++N+GCP  +V     G+ LM NPD+      A  KA+++P
Sbjct: 81  PEAIALGAQVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVKAVNVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    ++ + +  K ++ +GV  I +H R         K+     + D+  
Sbjct: 141 VTVKMRIGWDSD--SINVVDFAKRVESTGVAAIAVHGRT--------KEQMYSGHADWSY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   A ++L     D VM+GR A  N  +   +  Y +  
Sbjct: 191 IKAVK-EAVSVPVIGNGDIVEPEDAKRMLDETGCDAVMVGRGAQGNPWIFGRIHHYLATG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          +       D   ++      +++I  H      G P S   R+ 
Sbjct: 250 EILPAPTDIERLDMLLKH-----FDLLCQYKGESMAVKEIRTHAGWYMKGLPESSYWRNR 304

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +          H+ +E+   ++
Sbjct: 305 VNT-IHTVANFHNELESYRKIL 325


>gi|118442953|ref|YP_877134.1| NifR3 family protein [Clostridium novyi NT]
 gi|118133409|gb|ABK60453.1| nifR3 family enzyme [Clostridium novyi NT]
          Length = 321

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 74/305 (24%), Positives = 139/305 (45%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    L+YTEMI A  +   +   K +L  S +EKP+A QI G+D
Sbjct: 17  MAGVTDIAYRGLCKEM-GCGLVYTEMISAKGMYYDNENTKKLLKLSEEEKPVAAQIFGSD 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I+ ED G   +++N+GCP+ ++ +   G+ LM NP + G+ +  M K  + 
Sbjct: 76  PKVMARACEILNEDDGVGIVDINMGCPAPKIVKNGEGSALMKNPKLAGEIVREMKKVSNK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +   +   +++++G + + IH R         +        D+D
Sbjct: 136 PVTVKFRKGFDND--NINAVDFAMAMEQAGADAVAIHGRT--------RAQMYEGKADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E+  + +  NG +       ALK   + DG+M+ R A  N  +   + +  + 
Sbjct: 186 IIRKVK-ESVSIPVIGNGDVFSAEDAFALKNSTNCDGIMVARGAMGNPWIFKQIQQAINE 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     ++D      +     + A  +      ++++ +H+     G       ++
Sbjct: 245 EEVIYPTPIEKID------LCIRHLNLAVHYHGELKGVREMRKHIAWYIKGIKKCTEIKN 298

Query: 296 ILTVE 300
            + VE
Sbjct: 299 KINVE 303


>gi|331268356|ref|YP_004394848.1| putative TIM-barrel protein, nifR3 family [Clostridium botulinum
           BKT015925]
 gi|329124906|gb|AEB74851.1| putative TIM-barrel protein, nifR3 family [Clostridium botulinum
           BKT015925]
          Length = 320

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 77/305 (25%), Positives = 140/305 (45%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +    L+YTEMI A  +   +   K +L  S +EKP+A QI G+D
Sbjct: 17  MAGVTDIAYRGLCKEM-GCGLVYTEMISAKGMYYNNENTKKLLMLSKEEKPVAAQIFGSD 75

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I+ ED G   I++N+GCP+ ++ +   G+ LM  P++  + +  M K    
Sbjct: 76  PLVMARACEILNEDNGVCIIDINMGCPAPKIVKNGEGSALMKTPELAAEIVLEMKKISKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      K ++++G + I IH R         +        D+D
Sbjct: 136 PVTVKFRKGFDND--NINAIEFAKRMEQAGADAIAIHGRT--------RAQMYEGKADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K E+ ++ +  NG +    +A  L+   + DG+MI R A  N  +   +    +N
Sbjct: 186 IIRRVK-ESVNIPVIGNGDVFSAEKAFQLREETNCDGIMIARGAMGNPWIFKQIQLALNN 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + ++D      +     + A ++      ++++ +H+     G  N    ++
Sbjct: 245 EEVIYPTSEEKID------MCIRHLNLAIQYHGELKAVREMRKHIAWYIKGIKNCTDIKN 298

Query: 296 ILTVE 300
            + VE
Sbjct: 299 KINVE 303


>gi|304405776|ref|ZP_07387434.1| TIM-barrel protein, nifR3 family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345019|gb|EFM10855.1| TIM-barrel protein, nifR3 family [Paenibacillus curdlanolyticus
           YK9]
          Length = 342

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 88/326 (26%), Positives = 150/326 (46%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL G+K+   +L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAILHGNKRTLEMLYVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAKIV+     + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +A+  
Sbjct: 77  RESLVEAAKIVDKQTNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVTEAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD+   +      ++++++G + + +H R         ++       ++D
Sbjct: 137 PVTVKMRIGWDDE--HIFAVENARAVERAGGSAVSVHGRT--------REQLYTGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K E   + +  NG +     A ++L    VDGVMIGR A  N  ML    +Y +N
Sbjct: 187 IIKEVK-EAVSIPVIGNGDVFTPEDAKRMLDHTGVDGVMIGRGALGNPWMLYRTIQYLTN 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           +I+    D           ++++ +HM     G   S R + 
Sbjct: 246 GELLPDPTPKEKM-----EIAILHMDRLVSLKGESTAVREMRKHMAWYMKGLQGSARIKD 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +  E         I+      + E 
Sbjct: 301 TIMEETSRDKM-VAILNQYIESLPED 325


>gi|153813030|ref|ZP_01965698.1| hypothetical protein RUMOBE_03438 [Ruminococcus obeum ATCC 29174]
 gi|149830832|gb|EDM85922.1| hypothetical protein RUMOBE_03438 [Ruminococcus obeum ATCC 29174]
          Length = 327

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 135/302 (44%), Gaps = 27/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL TEM+ A AI   +K    ++     E P+++QI G++
Sbjct: 25  MAGVTDLPFRILCKE-QGAGLLCTEMVSAKAISFHNKNTISLMQIDPVEHPVSMQIFGSE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  ++ +++N+GCP  +V     G+ L+ NP+++ + +  + +A+  P
Sbjct: 84  PDLMAEVAKSIEEQPFDILDINMGCPVPKVVNNGEGSALLKNPELIREIVTKVSRAVKKP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG   +   V    + K I+ SG   + +H R         +        D+D 
Sbjct: 144 VTAKIRIGF--EGYPVDPVEIAKIIEDSGAAAVAVHGRT--------RQQYYAGEADWDT 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK E   + +  NG ++   +A  ++     DG+MIGRA   N  +   ++ YF+  
Sbjct: 194 IRRIK-EAVSIPVIGNGDVDSPKKAEALVRETGCDGIMIGRAVRGNPWIFREMNHYFTTG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG---KLQQITRHMIGLFHGFPNSRRC 293
                P         W +I   +  +A   +   G    ++++ +H+     G  +S   
Sbjct: 253 ELLPRPS--------WEEIREMILRHARMQIELKGEFTGIREMRKHIAWYTSGMRHSAGL 304

Query: 294 RH 295
           R 
Sbjct: 305 RR 306


>gi|255320752|ref|ZP_05361927.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SK82]
 gi|262379471|ref|ZP_06072627.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SH164]
 gi|255302129|gb|EET81371.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SK82]
 gi|262298928|gb|EEY86841.1| tRNA-dihydrouridine synthase B [Acinetobacter radioresistens SH164]
          Length = 347

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 141/324 (43%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 24  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   I++N+GCP+ +V     G+ L+ + ++V   +  +  A+ +P
Sbjct: 83  PEQLAEAARYQIANGAQIIDINMGCPAKKVCNKLAGSALLQDEELVARILDTVVAAVDVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  + +  YD+
Sbjct: 143 VTLKTRLGYLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNHARYDL 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+KK    + +  NG ++   +A  +L     D +MIGRAA     +   +  Y +  
Sbjct: 193 IREVKK-IIHIPVIANGDIDSPEKAKFVLEHTGADAIMIGRAAQGRPWIFREIAHYLNTG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V       ++     Y           +   +H+     G   S   R  
Sbjct: 252 EYLKAPDIEEVKHVLLGHLNELYEFY-----GEYSGCRIARKHIAWYTKGLYASNEFRQK 306

Query: 297 L-TVEAGASTATHHIIETAFNLMI 319
           +  VE+    A   ++E  FN ++
Sbjct: 307 MYQVESTLEQAK--VVEAYFNQLL 328


>gi|71065857|ref|YP_264584.1| NifR3 family TIM-barrel protein [Psychrobacter arcticus 273-4]
 gi|71038842|gb|AAZ19150.1| probable TIM-barrel protein, nifR3 family [Psychrobacter arcticus
           273-4]
          Length = 343

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 140/319 (43%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 39  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDNEIAPISAQIAGAE 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL EAA+   D G   I++N+GCP+ +V     G+ L+ + D+V   + A   A+  P
Sbjct: 98  PDKLAEAARYQIDNGAQIIDINMGCPAKKVCRKLAGSALLQDEDLVARLLDAAVNAVDAP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G ++      +  + K  +++G+  I IH R         +++       YD+
Sbjct: 158 VTLKTRLGYENGR--ENILRVAKRAEQAGIAAIAIHGRT--------REDMYTGEARYDL 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K E+  + +  NG ++   +A ++  L   D VMIGRAA     +   ++ +  + 
Sbjct: 208 IREVK-ESISIPVIANGDIDSAQKAQRVYELTGCDAVMIGRAAQGQPWIFRDIEHFLRSG 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T + P  + + K     +      Y           +   +H+     G PNS   R  
Sbjct: 267 ETLAPPSVSEIKKIVLTHLEELYGFY-----GEYSGCRIARKHIAWYTTGIPNSNAFRQA 321

Query: 297 LTVEAGASTATHHIIETAF 315
           +  E   +     ++E   
Sbjct: 322 MYGEESTAG-QFRVVEDFL 339


>gi|258593836|emb|CBE70177.1| putative tRNA-dihydrouridine synthase (Nitrogen regulation protein
           nifR3) [NC10 bacterium 'Dutch sediment']
          Length = 336

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 125/299 (41%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R +    +  +EM+ ++++L G +K         +  P+++Q+ GAD
Sbjct: 17  MAGVTDRPFRMLCRSM-GAGMAVSEMVASNSLLYGSEKTKRRANHEGETDPISVQLLGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   D G   I++N+GCP+ ++     G+ L+ N  +V   +  +  A+S+P
Sbjct: 76  PKMLAQAARYNVDAGAQIIDINMGCPAKKICNVMAGSALLQNEALVAQILETVVAAVSVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + +  + SG+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDTQNRNAV--RIAQIAEISGIQALAIHGRT--------RACAYTGEAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K  +  + I  NG +    +A  ++     D VMIGRAA     +   +  +    
Sbjct: 186 IAAVK-ASVKIPIIANGDITTPEKAHYVVQHTGADAVMIGRAAQGRPWLFREIAHFLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           L   +P    + +     +      Y          L+   +H+     G   S + R 
Sbjct: 245 LHLPAPQVVEIQRVLLNHLHGLYDLYGEH-----TGLRVARKHISWYTKGLAGSAQFRR 298


>gi|284048925|ref|YP_003399264.1| TIM-barrel protein, nifR3 family [Acidaminococcus fermentans DSM
           20731]
 gi|283953146|gb|ADB47949.1| TIM-barrel protein, nifR3 family [Acidaminococcus fermentans DSM
           20731]
          Length = 331

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 79/302 (26%), Positives = 134/302 (44%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L       +EM+ A A+L  + K   +L    +E P+A+Q+ G+ 
Sbjct: 24  MAGVTDLPFRVICREL-GADYTVSEMVSAKALLFKNPKTFAMLEVDPREHPVAIQLFGSV 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +LV+ AKIV + G + I+ N+GCP  ++     G+ LM +P+    C+AA+  A+  P
Sbjct: 83  PEELVKGAKIVAEHGADIIDFNMGCPVHKIVANGEGSALMKDPERAYACLAALVDAVDRP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+         + +  +K+GV  + +H R         +        D+DI
Sbjct: 143 VTVKFRAGWDEDHRNAV--EIARLAEKAGVAAVAVHGRT--------RGQFYSGKADWDI 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     AL +L     DGVMI R A  N  +   V    +  
Sbjct: 193 IRQVK-EAVSIPVLGNGDVFTAQDALDLLAATHCDGVMIARGAQGNPWIFREVQAVLAGK 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 ++ R      R+    +T +          ++++  H    F G P+S   R+ 
Sbjct: 252 TIPPVTLEERFA--MVRRHLRDLTAFKGE----KVAIREMRHHGACYFTGLPHSAHYRNA 305

Query: 297 LT 298
           + 
Sbjct: 306 IN 307


>gi|307150162|ref|YP_003885546.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7822]
 gi|306980390|gb|ADN12271.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 7822]
          Length = 337

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 64/319 (20%), Positives = 133/319 (41%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  I        I+    QE P+++Q+       
Sbjct: 34  GVTDLIFRRLVRRYAPTSMMYTEMVSATEIHHLQQLPKIMEIDPQEHPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA      G   +++N+GCP  ++ +   G+ L+  P+I  + +  +  A+ +PVTV
Sbjct: 94  MAEAATKAVAEGAKTVDINMGCPVNKITKKGGGSSLLRQPEIAQEIVKTVVSAVEVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D+   + + +  K ++ +G   + +HAR         +         ++ +  
Sbjct: 154 KTRIGWNDEE--ITILDFAKRMEDAGAAMLTLHART--------RAQGYNGTARWEWIRR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  AL+ L     DGVM  R       ++  +D +       
Sbjct: 204 VK-EILSIPVIANGDIFSVEAALRCLEETGADGVMCSRGTLGYPFLVGEIDYFLKTGKEL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P   +   +  ++    + +Y  +       + Q  +H+     GF  +   R  ++ 
Sbjct: 263 ATPTPLQ-RLECAKEHLKGLWEYKGQR-----GIYQSRKHLTWYCKGFAGASLLRDEVS- 315

Query: 300 EAGASTATHHIIETAFNLM 318
              +    + +I  A   +
Sbjct: 316 RINSLQEGYELINKAIKQL 334


>gi|229825760|ref|ZP_04451829.1| hypothetical protein GCWU000182_01123 [Abiotrophia defectiva ATCC
           49176]
 gi|229790323|gb|EEP26437.1| hypothetical protein GCWU000182_01123 [Abiotrophia defectiva ATCC
           49176]
          Length = 331

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 137/325 (42%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +     AL YTEM+ A      +K    ++    +E+P +LQI G+D
Sbjct: 20  MAGVTDLPFRVLCKE-NGVALTYTEMVSAKGFKYKNKNTEELITVDERERPTSLQIFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  V D  ++ +++N+GCP  +V     G+ LM  P+ + + + ++ K    P
Sbjct: 79  ADIMGEMAAAVNDRNFDILDVNMGCPVPKVVNNGEGSALMEQPEKIAEIVKSLKKNSKKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G    +       + K  + +GV+ I +H R         +        D++I
Sbjct: 139 VTIKIRAGF--TVANKNAVEVAKIAEAAGVDAIAVHGRT--------RSQYYSGQADWNI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + I  NG +     A K+L     DG+MI R A  N  +   ++ Y    
Sbjct: 189 IKAVK-EAVSIPIIGNGDVVTELDAKKMLEETSCDGIMIARGARGNPWIFNRINTYLEKG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R+ +  M +Y   +      ++++ +H+     G+PNS + R  
Sbjct: 248 EILPPPTADEFLNMILRQAT-WMIEYKGLY----TGVREMRKHIAWFTAGYPNSTKLRGE 302

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +            ++E   + + +S
Sbjct: 303 VNKLETYEDLKK-LMENYVDSIRDS 326


>gi|88799449|ref|ZP_01115026.1| tRNA-dihydrouridine synthase B [Reinekea sp. MED297]
 gi|88777759|gb|EAR08957.1| tRNA-dihydrouridine synthase B [Reinekea sp. MED297]
          Length = 329

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 148/320 (46%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L    K+   L  S + +P+++QI G D
Sbjct: 18  MAGVTDQPFRKLCRSL-GAGLVVSEMVTSDKRLWKTNKSRWRLDHSGEAEPISVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAAK   +FG   I++N+GCP+ +V   + G+ LM +  +V + + A+  A+S+P
Sbjct: 77  AQMLAEAAKTNAEFGAQVIDINMGCPAKKVCNKAAGSALMKDERLVHEILTAVTAAVSVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + +  + +G+  + +H R         + +    + +YD 
Sbjct: 137 VTLKIRTGWDRQSKNAIA--IARMAEDAGIALLSVHGRT--------RADAYRGDAEYDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A ++L     DGVMIGRAA  N  +   ++ Y    
Sbjct: 187 IARVK-EAVSIPVLANGDIDHPEKAAQVLRDTGADGVMIGRAAQGNPWIFREINHYLKTG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR-RCRH 295
              + P    V       +SA    Y          L+   +H+   F     ++   RH
Sbjct: 246 ECLAPPAFEEVQTTLLNHLSALYQFY-----GDYMGLRIARKHLGWYFTAQGVAKTEYRH 300

Query: 296 ILTVEAGAS--TATHHIIET 313
           I  +++  +  +A   +++T
Sbjct: 301 IHQLDSSQAQLSAVQQLLDT 320


>gi|325299590|ref|YP_004259507.1| TIM-barrel protein, nifR3 family [Bacteroides salanitronis DSM
           18170]
 gi|324319143|gb|ADY37034.1| TIM-barrel protein, nifR3 family [Bacteroides salanitronis DSM
           18170]
          Length = 338

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 145/328 (44%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K +  L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLLCKEF-GADMVYTEFVSSDALIRSVDKTMMKLNISAAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQARPDILDLNFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVNAVQIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDENHKVIV--ELAEQLQDCGIEALTIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMRIPIIGNGDITTPQRAKECFDRYGVDSIMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+  R   D  R+      +     L+    +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFRWKLDVLRREIQDSINL----LNERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A      + I++    ++ E 
Sbjct: 302 R-IAMLRAETQEELYAILDRIGTILEEQ 328


>gi|91774707|ref|YP_544463.1| dihydrouridine synthase TIM-barrel protein nifR3 [Methylobacillus
           flagellatus KT]
 gi|91708694|gb|ABE48622.1| tRNA-U20-dihydrouridine synthase [Methylobacillus flagellatus KT]
          Length = 343

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 125/302 (41%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G  K +       +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRVLCKKM-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVAQILKAVVNAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  GV  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWDKHNRNAVA--VARMAEDIGVQALAIHGRT--------RACLYTGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A  +L     D VMIGRAA     +    + + +  
Sbjct: 186 IAAVKQAI-RIPLIANGDITTPEKAKFVLDYTKADAVMIGRAAQGRPWIFRETEHFLNTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    + +     I      Y          ++   +H+     G   S   RH 
Sbjct: 245 EHLPAPEVEEIHQVMLEHIHDLYHFY-----GELTGMRVARKHISWYTKGLVGSANFRHH 299

Query: 297 LT 298
           + 
Sbjct: 300 MN 301


>gi|145589360|ref|YP_001155957.1| tRNA-dihydrouridine synthase A [Polynucleobacter necessarius subsp.
           asymbioticus QLW-P1DMWA-1]
 gi|145047766|gb|ABP34393.1| tRNA-U16,U17-dihydrouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
          Length = 347

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 118/336 (35%), Positives = 182/336 (54%), Gaps = 19/336 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R LT  A+LYTEM+   A++ GD    L +S  + P+ LQ+GG++ +
Sbjct: 1   MMEWTDRHCRSFHRALTTEAVLYTEMVTTGALMHGDVPRHLDYSQDQHPVVLQLGGSEPN 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  +A++ + +GY+EI+LN GCPS RV  G+FGACLM  P +V DC+ AM  A+ IP++
Sbjct: 61  DLARSAELAQQWGYDEIDLNCGCPSERVQRGAFGACLMAEPKLVADCVKAMQNAVDIPIS 120

Query: 121 VKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           VK R+G+D       +       + + ++  +G + + IHAR A+LKGLSPK+NR  P L
Sbjct: 121 VKHRLGLDSMDAANSEKDYQFALDFIMAVADAGASQVTIHARNAVLKGLSPKENRSKPPL 180

Query: 175 DYDIVYEIK----KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            Y++  +++    K+ P+L + LNGGLE   Q        DG M+GRAAY   AML   D
Sbjct: 181 RYEVAAKLRLDAQKQFPNLKVLLNGGLESNDQIAGHWHDFDGFMVGRAAYHFPAMLLGWD 240

Query: 231 EYFSN-----PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           +  +          S     R+     +++ +   +  A+       +   TRH++GL H
Sbjct: 241 DMINTNGDAAGYLFSETEWHRIQIALVKQVQSWFDECQAK--GKPFYIGAFTRHILGLAH 298

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           G   SR  R  L+     + A         +  I++
Sbjct: 299 GRAGSRYWRQRLSD--HHALAKVQSKAAILDFFIDA 332


>gi|291612763|ref|YP_003522920.1| TIM-barrel protein, nifR3 family [Sideroxydans lithotrophicus ES-1]
 gi|291582875|gb|ADE10533.1| TIM-barrel protein, nifR3 family [Sideroxydans lithotrophicus ES-1]
          Length = 335

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 131/302 (43%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +    +  +EM+ ++++L G +K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKRM-GAGMAVSEMVASNSLLYGSEKTKRRANHEGEVDPISVQIVGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   D G   I++N+GCP+ ++     G+ LM N  +V + +  +  A+ +P
Sbjct: 76  PKMLAQAARYNVDNGAQIIDINMGCPAKKICNVMAGSALMQNEKLVAEILEEVVGAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ +  + SG+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWDKNNRNAV--NIARIAEASGIQALAIHGRT--------RACAYTGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG +    +A  +L     D VMIGRAA     +   ++ +    
Sbjct: 186 IRAVKAEV-NIPVIANGDITTPEKARFVLQHTGADAVMIGRAAQGRPWLFREIEHFLQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    + +D        + D+   H      L+   +H+     G   S   RH 
Sbjct: 245 THLLAPHVGEI-QDVLIAHMHDLYDFYGEH----TGLRVARKHISWYTKGLTGSAVFRHR 299

Query: 297 LT 298
           + 
Sbjct: 300 MN 301


>gi|198274476|ref|ZP_03207008.1| hypothetical protein BACPLE_00624 [Bacteroides plebeius DSM 17135]
 gi|198272678|gb|EDY96947.1| hypothetical protein BACPLE_00624 [Bacteroides plebeius DSM 17135]
          Length = 328

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 136/301 (45%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K +L    S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKQF-GADMVYTEFVSSDALIRSVGKTMLKLNISEKERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     G+ ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQAKPDILDLNFGCPVKRVAGKGAGSGMLQNVPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAEHKIIV--ELAEQLQDCGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMRIPIIGNGDITTPQRAKECFEQYGVDAIMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+  +   D  R+      +     L     +  + RH+    LF G PN +  
Sbjct: 247 GEELP-PLSFKWRMDVLRQEVLDSVNL----LDERRGILHVRRHLAASPLFKGIPNFKDT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|322807847|emb|CBZ05422.1| tRNA dihydrouridine synthase B [Clostridium botulinum H04402 065]
          Length = 323

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 140/317 (44%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +   D     I ++N+GCP+ ++ +   G+ LM +P +  + I AM K    
Sbjct: 76  PEIMANAVEFFNDNNDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKVAKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G D     +      K +++SG + I IH R         ++       D+ 
Sbjct: 136 PITVKFRKGFDK--NNINAVEFAKVMEQSGADAITIHGRT--------REQMYEGKADWT 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K     + +  NG +     A++++   + DGVM+GR A  N  +   ++E    
Sbjct: 186 IISKVKNAV-SIPVIGNGDVFSAEDAIEMINKTNCDGVMVGRGAQGNPWIFKQINEKIKG 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R+D      I  +    A  +      ++++ +H+     G  N    + 
Sbjct: 245 EHVYYPTSQERID------ICINHYKRALEYFEEHKAVREMRKHVAVYVKGLKNCTDIKD 298

Query: 296 ILTVEAGASTATHHIIE 312
            + +E G+      +I+
Sbjct: 299 KVNMEKGSDKVLEELIK 315


>gi|228473706|ref|ZP_04058454.1| tRNA-dihydrouridine synthase B [Capnocytophaga gingivalis ATCC
           33624]
 gi|228274853|gb|EEK13670.1| tRNA-dihydrouridine synthase B [Capnocytophaga gingivalis ATCC
           33624]
          Length = 324

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 69/304 (22%), Positives = 133/304 (43%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      +LY+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKKY-GADMLYSEFISSEGLIRDAIKSRKKLDIFDDERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +A+IVE    + +++N GCP  +V     GA ++ + D++     A+ K+  +P
Sbjct: 78  EEAMALSARIVETVSPDVVDINFGCPVKKVVAKGAGAAVLKDIDLMVRLTQAVVKSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + +  + + ++  G+  + IHAR  +             + D+  
Sbjct: 138 VTVKTRLGWDSET--INIEEVAERLQDVGIQALSIHARTRV--------QMYKGHSDWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL+      VDG+MIGRAA     +   +  Y + 
Sbjct: 188 IAKVKNNPRIHIPIFGNGDIDSPEKALEYKERYGVDGIMIGRAAIGYPWIFQEIKHYMAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  +   +   + +      +A         + +  RH    F G P+ +  + 
Sbjct: 248 RELLPPPTLSERAEAALQHLL-----WAVEWKGERLGILETRRHYSNYFKGIPHFKEYKQ 302

Query: 296 ILTV 299
            L  
Sbjct: 303 QLVT 306


>gi|326335679|ref|ZP_08201865.1| tRNA-dihydrouridine synthase B [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325692108|gb|EGD34061.1| tRNA-dihydrouridine synthase B [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 326

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 142/317 (44%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L     +LY+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKL-HGADMLYSEFISSEGLIRDAIKSRKKLDIFEDERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +A+IVE    + +++N GCP  +V     GA ++ + D++     A+ ++ ++P
Sbjct: 78  EEAMSLSARIVETVSPDVVDINFGCPVKKVVAKGAGAAVLKDIDLMVRLAKAVVRSTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G+  + IHAR  +             + D+  
Sbjct: 138 VTVKTRLGWD--TDSINIEEVAERLQDVGIQALSIHARTRV--------QMYKGHSDWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL  K    VDG+MIGRAA     +   + +Y + 
Sbjct: 188 IAKVKNNPRIHIPIFGNGDIDSPEKALVYKNKYGVDGIMIGRAAIGYPWIFHEIKQYLAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P  ++      + +      +A         + +  RH    F G P+ +  + 
Sbjct: 248 GEKVAPPTLSQRADVALQHLL-----WAVEWKGERLGILETRRHYANYFKGIPHFKEYKQ 302

Query: 296 ILTVEAGASTATHHIIE 312
            L      S   + ++E
Sbjct: 303 QLVTLDDLSALKNLLLE 319


>gi|160891700|ref|ZP_02072703.1| hypothetical protein BACUNI_04155 [Bacteroides uniformis ATCC 8492]
 gi|270295204|ref|ZP_06201405.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|156859107|gb|EDO52538.1| hypothetical protein BACUNI_04155 [Bacteroides uniformis ATCC 8492]
 gi|270274451|gb|EFA20312.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 326

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 88/326 (26%), Positives = 144/326 (44%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKHF-GADMVYTEFVSADALIRSVGKTQQKLNISDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TATMVEAARIVEQAHPDTLDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +   L  VD +MIGRA++        V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWFFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P       ++   +     + +   L     +  + RH+    LF G PN R  
Sbjct: 247 GEELPPPSS-----EWRLNVLRQEVEDSVNLLDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
           R I  + A      + I E    L+ 
Sbjct: 302 R-IAMLRAETKEELYRIFEEIEPLLP 326


>gi|34495999|ref|NP_900214.1| regulatory gene required to sense and relay the nitrogen status
           [Chromobacterium violaceum ATCC 12472]
 gi|34101852|gb|AAQ58220.1| Regulatory gene required to sense and relay the nitrogen status
           [Chromobacterium violaceum ATCC 12472]
          Length = 352

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 126/299 (42%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EMI A+  L    K +       + +P+ +QI G +
Sbjct: 17  MAGVTDRPFRMLCKRL-GAGMAVSEMITANKALWTTPKTLRRANHEGEVEPIVVQIAGGE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA++  + G   I++N+GCP+ +V   + G+ L+ + D VG  + A+ KA+ +P
Sbjct: 76  PQMLADAARLNVEHGAQIIDINMGCPAKKVCNVAAGSALLRDLDNVGRILEAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   ++       + K  + +G+  + +H R         +++    + +YD 
Sbjct: 136 VTLKTRTGWSREVKTA--LAVAKMAEDAGIAALALHGRT--------REDMYRGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPVVANGDIDSPQKARHVLDYTGADAIMIGRAAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           +    P+   + +     +      Y           +   +H+     G       R 
Sbjct: 245 IELPPPMVGEIRELMLGHLDELYGFY-----GEYSGCRIARKHIAWYTKGLAGGNAFRQ 298


>gi|258513601|ref|YP_003189823.1| TIM-barrel protein, nifR3 family [Desulfotomaculum acetoxidans DSM
           771]
 gi|257777306|gb|ACV61200.1| TIM-barrel protein, nifR3 family [Desulfotomaculum acetoxidans DSM
           771]
          Length = 322

 Score =  275 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 135/302 (44%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR YR  A+      L+ TEMI   A+L G+ K   +L  + +  P+++QI G+ 
Sbjct: 18  MAGITDRAYRILAKE-AGCGLVCTEMISDQALLYGNPKTNILLDCTGETPPISMQIFGSS 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA I E  G + I++N+GCP+ ++ +   GA LM  P++    I+ + +++ +P
Sbjct: 77  PEYMARAASITEARGASIIDINMGCPTPKIVKNGEGAALMRKPELAQKIISDVVQSVRVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+  P      L+   +++G   + +H R         +        D+DI
Sbjct: 137 VTVKIRKGWDESFPNAVEMALL--AEEAGAKAVTVHGRT--------RSQFYSGKADWDI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +KK    + +  NG + +   A+++L     D VMIGRA+  N  + ++   +    
Sbjct: 187 IKSVKKAVT-IPVIGNGDIREPRDAVRMLMHTGCDAVMIGRASLGNPWIFSSTVHFLDCG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P   +      R +     +           ++++ +H      G   + R R  
Sbjct: 246 ENLPAPSPRQRLSVALRHL-----ELLIELKGEYIAIREMRKHAAWYTRGLREANRIREK 300

Query: 297 LT 298
           + 
Sbjct: 301 IN 302


>gi|170717873|ref|YP_001784929.1| nifR3 family TIM-barrel protein [Haemophilus somnus 2336]
 gi|168826002|gb|ACA31373.1| putative TIM-barrel protein, nifR3 family [Haemophilus somnus 2336]
          Length = 327

 Score =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 71/323 (21%), Positives = 140/323 (43%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L  +EM+ A+  +   +K+ L           A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSFY-GAGLTCSEMMSANPQVWHTEKSRLRLAHHQDAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + ++ KA+++P
Sbjct: 76  PVEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKKILYSVVKAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +       ++ K  +++G+  + IH R         ++     N +YD 
Sbjct: 136 VTLKIRTGWNQEHRN--CIDIAKIAEQAGIQALSIHGRT--------RECLFNGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K++   + +  NG +    QA ++L     DG+MIGR A     +  ++       
Sbjct: 186 IKKVKEQI-SIPVIANGDITTAKQAQEVLSYTGTDGIMIGRGALGKPWLFQSIVSLIETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +T   P          + I      Y       G ++    +H+     G   +   R  
Sbjct: 245 ITIPEPSLDEKCSVILQHIRDLHQFYGE---DKGYRI--ARKHVSWYLEGIQPNSDFRQT 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
                 A  A    +E  FN ++
Sbjct: 300 FNAITNAK-AQLIALEDFFNFIL 321


>gi|255281436|ref|ZP_05345991.1| tRNA-dihydrouridine synthase B [Bryantella formatexigens DSM 14469]
 gi|255267924|gb|EET61129.1| tRNA-dihydrouridine synthase B [Bryantella formatexigens DSM 14469]
          Length = 333

 Score =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 131/303 (43%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    LL TEM+ A AI     + + ++     E P++LQ+ G+D
Sbjct: 19  MAGVTDLPFRLLCKEM-GAGLLCTEMVSAKAISFHNKNTERLMETGDGEHPVSLQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ +E+  ++ ++ N+GCP  +V     G+ LM NP +  + +     A+  P
Sbjct: 78  ADLICEVARQIEERPFDILDFNMGCPVPKVVNNGEGSALMKNPALAEEIVRKTAAAIKKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V      K ++ +G   I +H R         +        D+DI
Sbjct: 138 VTVKFRKGFDDD--HVNAVEFAKRMEAAGAAAIAVHGRT--------RAQYYAGRADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG ++    A K+      DG+MIGRAA  N  +   +  Y    
Sbjct: 188 IRQVK-EAVKIPVIGNGDVDGPESARKMFAETGCDGIMIGRAARGNPWIFQELAAYDKGG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V     R  +  +     ++      ++++ +H+     G+P+S   R  
Sbjct: 247 SIPERPQPAEVKNMILRHAALQI-----QYKGEYTGIREMRKHVAWYTAGYPHSAALRRR 301

Query: 297 LTV 299
           +  
Sbjct: 302 VNE 304


>gi|21230237|ref|NP_636154.1| hypothetical protein XCC0763 [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66769771|ref|YP_244533.1| hypothetical protein XC_3469 [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|38604923|sp|Q8PCH1|DUSB_XANCP RecName: Full=tRNA-dihydrouridine synthase B
 gi|21111780|gb|AAM40078.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575103|gb|AAY50513.1| conserved hypothetical protein [Xanthomonas campestris pv.
           campestris str. 8004]
          Length = 332

 Score =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   ++A+ +A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILSAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D       +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGTAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L    VD VMIGRAA     +   V  Y +  
Sbjct: 186 IAQIKAAL-QIPVIANGDIDSPQKAAQVLRDTGVDAVMIGRAAQGRPWIFGEVAHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 ALLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPEAQLALTRDYFDALI 321


>gi|310658259|ref|YP_003935980.1| tim-barrel protein [Clostridium sticklandii DSM 519]
 gi|308825037|emb|CBH21075.1| putative TIM-barrel protein, , NifR3 family [Clostridium
           sticklandii]
          Length = 322

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 144/303 (47%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +     +LLYTEMI A A+   DK    +L    QEKP+A+QI G++
Sbjct: 17  MAGVTDLPFRLICKQF-EASLLYTEMINAKAVCYEDKNTFDMLLVEDQEKPVAVQIFGSE 75

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA+ + +   +  I++N+GCP+ +V +   G+ LM NP +  D +  +  A ++
Sbjct: 76  PGFMAEAARTLTELNRFEIIDINMGCPAPKVVKAGDGSALMKNPKLAYDIVNKVKAATNL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D++  ++      K ++++G + + +H R         ++       D++
Sbjct: 136 PVTVKFRKGWDEK--SINALEFGKLMQEAGADAVTLHGRT--------REQYYSGTADWE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K++   + +  NG +     A +IL     D +MIGR A  N  +   V++Y   
Sbjct: 186 IIKELKEKLT-IPVIANGDITSFDAAERILDITKADALMIGRGAQGNPFIFKEVNDYME- 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+ +   +        + S    A ++      + ++ +H+     G  NS R + 
Sbjct: 244 ----SAILPKEICPKLKIDTAISHYKLALKYKTQHKAVTEMRKHLGWYLKGLKNSARIKD 299

Query: 296 ILT 298
            + 
Sbjct: 300 HIN 302


>gi|189459730|ref|ZP_03008515.1| hypothetical protein BACCOP_00358 [Bacteroides coprocola DSM 17136]
 gi|189433577|gb|EDV02562.1| hypothetical protein BACCOP_00358 [Bacteroides coprocola DSM 17136]
          Length = 328

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 81/301 (26%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K +L    S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLLCKEF-GADMVYTEFVSSDALIRSVGKTMLKLNISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     G+ ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQANPDILDLNFGCPVKRVAGKGAGSGMLQNVPKMLEITKAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAEHKIIV--ELAEQLQDCGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPQRAQECFDRYGVDAIMIGRASFGRPWIFKEVKHYLKT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+  +   D  R+      +     L     +  + RH+    LF G PN +  
Sbjct: 247 GEELP-PLSFKWKMDVLRREVQDSVNL----LDERRGILHVRRHLAASPLFKGIPNFKDT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|295093088|emb|CBK82179.1| tRNA-U20-dihydrouridine synthase [Coprococcus sp. ART55/1]
          Length = 322

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 136/298 (45%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D+ +R   +      +LY+EM+ A AI   +K    +L    +EKP  LQ+ G+D
Sbjct: 12  MAGVCDQPFRLLCKE-QGCDILYSEMVSAKAIYYKNKNTKPLLAMDEREKPFGLQLFGSD 70

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E  GY+ I++N+GCP  +V     G+ LM +P +VG  + AM KA+SIP
Sbjct: 71  PEIMAEMAKRIESNGYSFIDVNMGCPVPKVVNNGEGSALMKDPVLVGRIVEAMAKAISIP 130

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G D +   +    +    ++SG   + +H R         +      + D+ +
Sbjct: 131 LTIKIRSGFDSE--HINAPEIAHIAQESGAAAVAVHGRT--------RQQYYQGHADWSV 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +      + +    + DG MIGR A  N  +   +  Y+ + 
Sbjct: 181 IARVKEAC-IIPIIGNGDINTPQDIIDMRAQTNCDGFMIGRGARGNPWIFRDMKYYYEHG 239

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    V KD   + +  M ++   +      + ++ +H+     G  +S R R
Sbjct: 240 ELPDKPDIYEV-KDMMLRHARLMVEFKGEY----TGIHEMRKHVAWYSVGMYDSARLR 292


>gi|157826622|ref|YP_001495686.1| putative dihydrouridine synthase Dus [Rickettsia bellii OSU 85-389]
 gi|157801926|gb|ABV78649.1| Putative dihydrouridine synthase Dus [Rickettsia bellii OSU 85-389]
          Length = 406

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EMI + A++   ++++   S          +Q+ G 
Sbjct: 98  MSGVTDLEFRRLVKRF-GAGLVVSEMIASRAMIVESRQSLQKCSIMQDDATSACVQLAGC 156

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 157 EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVNGYSGSALMRDEGLAAKIFEAAVKAVKI 216

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DDQ        L K  ++SG+  + +H R         +      N D++
Sbjct: 217 PVTVKMRMGWDDQTKNA--PTLAKIAERSGIQMVTVHGRT--------RCQFYSGNADWE 266

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L     DGVM+GR AY    +++ +D Y   
Sbjct: 267 FIKNVK-EAVKIPVIANGDITNFAKAKEALEKSSADGVMVGRGAYGKPWLISQIDHYLKT 325

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P              A +  Y          +    +HM     G PNS   R 
Sbjct: 326 GEEKPAPSIESQLDIVLEHYQAIVDYY-----GESAGVPIARKHMGWYSSGLPNSAEFRG 380

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            + +          I+E   +++
Sbjct: 381 AVNLMNDPIAVKDKIVEFYTSVI 403


>gi|325281330|ref|YP_004253872.1| TIM-barrel protein, nifR3 family [Odoribacter splanchnicus DSM
           20712]
 gi|324313139|gb|ADY33692.1| TIM-barrel protein, nifR3 family [Odoribacter splanchnicus DSM
           20712]
          Length = 333

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 79/318 (24%), Positives = 140/318 (44%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D T+  +R F +       LY+E + ADA++R   K++  L     E+P+ +QI G  
Sbjct: 18  MEDVTNPPFRKFCKKY-GADWLYSEFVSADALVRSVNKSLKKLTIDETERPVTIQIYGRF 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAAKIVE+   + I++N GCP  RV +   GA ++ +  ++ +    + +A+ IP
Sbjct: 77  IDSMVEAAKIVEEVRPDFIDINFGCPVKRVAQKGAGAGMLKDIPLMVEMTRQIVQAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D +   + + ++ + ++  G+  + IH R         +        D++ 
Sbjct: 137 VTAKTRLGWDCE--HIIIEDIAERLQDVGIQALAIHGRT--------RSQMYSGEADWEP 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +    +A +      VDGVMIGRA   +  +   +  YF  
Sbjct: 187 IARVKNNPRIKIPILGNGDITSPEKAKEAFERYGVDGVMIGRATIGHPWIFKQIRHYFET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    +I       +   +     L  + RHM  +F G P+ R  R 
Sbjct: 247 GELLPDLSVKEQIEVIKEQILL-----SVEWIDEVRGLLHMRRHMASMFKGLPHFRDLR- 300

Query: 296 ILTVEAGASTATHHIIET 313
           I  ++A        + + 
Sbjct: 301 IRMLQAPTIDVLWEVFDE 318


>gi|256419707|ref|YP_003120360.1| hypothetical protein Cpin_0661 [Chitinophaga pinensis DSM 2588]
 gi|256034615|gb|ACU58159.1| TIM-barrel protein, nifR3 family [Chitinophaga pinensis DSM 2588]
          Length = 354

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 133/318 (41%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRAVCKE-KGADLMYTEFISSEGLIRDAIKSRRKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+IVE    + +++N GCP  +V     G+ ++ +   +    AA+ KA  +P
Sbjct: 78  EEPMAMAAQIVEATNPDLLDINYGCPVKKVVCKGAGSGILKDIPKMVKLTAAVVKATKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    + + ++  G+  + IH R         +      + D+ +
Sbjct: 138 VTVKTRLGWDDDTKNIE--EVAERLQDVGIQALTIHGRT--------RTQMYKGHADWTL 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG +    QA+       VDGVMIGRAA     +   +  +   
Sbjct: 188 IGKVKNNPRIHIPIFGNGDICTPEQAIAAREKYGVDGVMIGRAAIGYPWIFNEIKHFMQT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++      ++ +       + ++ RH      G P+ +  R 
Sbjct: 248 GEHLPPPSVLERV-----EVCKKHLQHSVQWKGDVVGILEMRRHYTNYLKGLPHIKEFRQ 302

Query: 296 ILTVEAGASTATHHIIET 313
            L   +  + A   +++ 
Sbjct: 303 QLVTCSTLA-AVEDVLDA 319


>gi|212692328|ref|ZP_03300456.1| hypothetical protein BACDOR_01824 [Bacteroides dorei DSM 17855]
 gi|237711412|ref|ZP_04541893.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|237726127|ref|ZP_04556608.1| dehydrogenase [Bacteroides sp. D4]
 gi|265752818|ref|ZP_06088387.1| dehydrogenase [Bacteroides sp. 3_1_33FAA]
 gi|212665205|gb|EEB25777.1| hypothetical protein BACDOR_01824 [Bacteroides dorei DSM 17855]
 gi|229435935|gb|EEO46012.1| dehydrogenase [Bacteroides dorei 5_1_36/D4]
 gi|229454107|gb|EEO59828.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|263236004|gb|EEZ21499.1| dehydrogenase [Bacteroides sp. 3_1_33FAA]
          Length = 329

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 80/301 (26%), Positives = 139/301 (46%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K +  L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSADALIRSVGKTMQKLNINDEERPVAVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEEAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNEHKIIV--DLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +   L  VD +MIGRA++    +   +  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWIFKEIKHYIET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                +           +++       +   L     +  + RH+    LF G PN +  
Sbjct: 247 GKELPALSFEWRLNVLRQEVLD-----SVNLLDERRGILHVRRHLAASPLFKGIPNFKET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|170760677|ref|YP_001788862.1| dihydrouridine synthase [Clostridium botulinum A3 str. Loch Maree]
 gi|169407666|gb|ACA56077.1| dihydrouridine synthase [Clostridium botulinum A3 str. Loch Maree]
          Length = 323

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 139/317 (43%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +    +     +++N+GCP+ ++ +   G+ LM +P +  + I AM K    
Sbjct: 76  PEIMANAVEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKVAKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G D     +      K +++SGV+ I IH R         ++       D+ 
Sbjct: 136 PITVKFRKGFDK--NNINAVEFAKIMEQSGVDAITIHGRT--------REQMYEGKADWA 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K  +  + +  NG +     AL+++     DG+MIGR A  N  +   ++E    
Sbjct: 186 IISKVKN-SVSIPVIGNGDVFSSEDALEMINKTDCDGIMIGRGAQGNPWIFKQINEKIKG 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R+D      I  +    +  +      ++++ +H+     G  N    + 
Sbjct: 245 KHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAAYVKGLKNCTDIKD 298

Query: 296 ILTVEAGASTATHHIIE 312
            + +E         +I+
Sbjct: 299 KVNMEKDPDKVLEELIK 315


>gi|331003606|ref|ZP_08327102.1| hypothetical protein HMPREF0491_01964 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412326|gb|EGG91718.1| hypothetical protein HMPREF0491_01964 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 320

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 73/298 (24%), Positives = 135/298 (45%), Gaps = 22/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  +R   + +   +LL TEM+ A AI   +K    ++     E P+ALQ+ G+D
Sbjct: 22  MAGVSDLPFRRLCKEM-GASLLVTEMVSAKAIYFKNKNTEPLMKIDKDEHPVALQLFGSD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  +E+  ++  + N+GCP  ++     G+ LM NP +V + ++ + K++  P
Sbjct: 81  PDIIALMAAQIENRDFDIFDFNMGCPVPKIVNNGEGSALMKNPKLVEEILSKLVKSVKKP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G ++    +    + K  + SGV+ I +HAR         ++       D+ I
Sbjct: 141 VTLKIRKGFNED--NINAVEIAKIAEASGVSAIAVHART--------REQYYSGKADWSI 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K    ++ +  NG ++D   A ++      DG+MI RAA  N  +   + +YF + 
Sbjct: 191 IKAVKSAV-NIPVIGNGDVKDGKSAEEMYEYTGCDGIMIARAARGNPWIFREIRDYFCSK 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T   P K  V     +     M      +      ++++ +H+    HG   S   R
Sbjct: 250 -TVEKPAKDEVIDMILKHCRLQM-----EYDDEIMAVRKMRKHVAWYTHGMKGSSTLR 301


>gi|317478240|ref|ZP_07937405.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
 gi|316905547|gb|EFV27336.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
          Length = 326

 Score =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 89/326 (27%), Positives = 145/326 (44%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKHF-GADMVYTEFVSADALIRSVGKTQQKLNISDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TATMVEAARIVEQAHPDTLDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +   L  VD +MIGRA++        V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWFFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+ +    +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSSEWRLNVLRQEVEDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
           R I  + A      + I E    L+ 
Sbjct: 302 R-IAMLRAETKEELYRIFEEIEPLLP 326


>gi|333029581|ref|ZP_08457642.1| TIM-barrel protein, nifR3 family [Bacteroides coprosuis DSM 18011]
 gi|332740178|gb|EGJ70660.1| TIM-barrel protein, nifR3 family [Bacteroides coprosuis DSM 18011]
          Length = 329

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 129/301 (42%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L    +E+P+A+QI G +
Sbjct: 18  MEDVTDPAFRLMCKRF-GADMVYTEFVSSDALIRYVNKTTEKLKIYDEERPVAIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  +V     G+ +M  P+ +     A+  A+ IP
Sbjct: 77  TDAMVEAAKIVEEAKPDILDINFGCPVRKVAGKGAGSGMMKTPEKMIAITKAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDDDNKIIV--ELAEQLQDFGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +     A        VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDITSAESAKDHFEKYGVDAIMIGRASFGRPWIFEEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                             +++ S+       L     +    RH+    LF G PN +  
Sbjct: 247 GEKLEPRPFKWYLSILKEQVANSI-----ERLDERRGILHTRRHLASTPLFKGIPNFKET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|319900676|ref|YP_004160404.1| tRNA-U20-dihydrouridine synthase [Bacteroides helcogenes P 36-108]
 gi|319415707|gb|ADV42818.1| tRNA-U20-dihydrouridine synthase [Bacteroides helcogenes P 36-108]
          Length = 332

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 87/320 (27%), Positives = 142/320 (44%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  ST+E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKQF-GADMVYTEFVSADALIRSVSKTEQKLNISTEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADHKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + +  NG +    +A +   L  VD +MIGRA++        V  Y   
Sbjct: 187 IGEVKKNPRMHIPVIGNGDITTPERAKECFDLYGVDAIMIGRASFGRPWFFKEVRHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSPEWKLNVLRREVEDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIET 313
           R I  + A      + I + 
Sbjct: 302 R-IAMLRAETKEELYRIFDA 320


>gi|120556355|ref|YP_960706.1| nifR3 family TIM-barrel protein [Marinobacter aquaeolei VT8]
 gi|120326204|gb|ABM20519.1| tRNA-U20-dihydrouridine synthase [Marinobacter aquaeolei VT8]
          Length = 332

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 133/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    L  +EM++AD+ L   +K    L    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRM-GAGLAVSEMVIADSKLWHTRKSRTRLNHEGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   +FG   I++N+GCP+ +V   + G+ LM +  +V + + A+ KA+ +P
Sbjct: 80  PEMLADAARQNAEFGAQIIDINMGCPAKKVCNKAAGSALMKDEKLVREILEAVVKAVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D       +  + +  + +G+  + +H R         + ++   + +YD 
Sbjct: 140 VTLKMRTGWDRDNRNAPV--IARMAEDAGIQALAVHGRT--------RADKYNGDAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K  +  + +  NG +    +A ++L     DG++IGR A     +   +  Y    
Sbjct: 190 IAEVK-ASVGIPVFANGDITTPEKARQVLSHTGADGLLIGRGAQGRPWIFREILHYLETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P    V++     +      Y          ++   +H+        +S++ R 
Sbjct: 249 EHLPQPPMDEVERILAGHLEELHRFY-----GELMGVRIARKHVGWYLQSHDDSKQFRQ 302


>gi|294664625|ref|ZP_06729963.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292605605|gb|EFF48918.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 332

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     N +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGNAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + +  
Sbjct: 186 IAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EGLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPDAQLALTRDYFDALI 321


>gi|294626097|ref|ZP_06704705.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292599633|gb|EFF43762.1| conserved hypothetical protein [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 332

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLYRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + +  
Sbjct: 186 IAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EGLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGMRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPDAQLALTRDYFDALI 321


>gi|227824807|ref|ZP_03989639.1| conserved hypothetical protein [Acidaminococcus sp. D21]
 gi|226905306|gb|EEH91224.1| conserved hypothetical protein [Acidaminococcus sp. D21]
          Length = 321

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 145/325 (44%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R         +EM+ A A+L  ++K   +L    +E P A+Q+ G+ 
Sbjct: 16  MAGVTDLPFRVICRE-NGADYTVSEMVSAKALLYKNQKTFAMLTIDPKEHPTAIQLFGSV 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S+L  A KIVE  G + I++N+GCP  ++     G+ LM +PD V   +AA+  A+SIP
Sbjct: 75  PSELAAAGKIVESRGADMIDVNMGCPVHKIVSNGEGSALMKDPDKVYAILAALVDAVSIP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+     A+  + +  +K+GV+ + +H R         +        D+DI
Sbjct: 135 VTVKFRAGWDEAHKNAAV--IAQMAEKAGVSAVCVHGRT--------RAQFYQGKADWDI 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E+  + +  NG +     AL++      DGVMI R A  N  +   V       
Sbjct: 185 IRAVK-ESVGIPVLGNGDIFHAEDALRMKEETGCDGVMIARGAEGNPWIFRDVKALLHGK 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP+  +      R+    +  +          ++++  H      G P+S   R+ 
Sbjct: 244 AI--SPVSVQERFAMIRRHLHDLILFKGER----VGVREMRHHGAMYLTGLPHSAYYRNT 297

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +  +A    A   ++      ++++
Sbjct: 298 IN-QAQTEEALLAVLGEYEEKLLQA 321


>gi|261855785|ref|YP_003263068.1| dihydrouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836254|gb|ACX96021.1| dihydrouridine synthase DuS [Halothiobacillus neapolitanus c2]
          Length = 357

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 185/322 (57%), Gaps = 11/322 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD HYR  ARL+T NA LYTEM+   A+L GD    L F+  E P+ALQ+GG+D S
Sbjct: 16  MLDWTDTHYRVLARLMTRNARLYTEMVTTGALLHGDVSRHLSFNAAEHPVALQLGGSDPS 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA +  ++GY+EINLNVGCPS RV  GSFGACLM  P++V   + AM  ++ +PVT
Sbjct: 76  DLAAAAVLGAEWGYDEINLNVGCPSDRVQNGSFGACLMATPEVVAKGVRAMQASVDVPVT 135

Query: 121 VKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G+D      A    +  +  + G     IHARKA L GLSPK+NR+IP L  D V
Sbjct: 136 LKTRVGIDRSDSFEAFARFIDIVAGQGGCEVFIIHARKAWLDGLSPKENREIPPLRRDFV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           Y I+   P+L   LNG LE + +    L  V  G+M+GRAAY++   L  VD+   +   
Sbjct: 196 YRIQDAYPELTFVLNGKLETIPEMQAELARVPGGIMVGRAAYQHVDWLRFVDQMLFD--- 252

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S+PI TR        +      Y  + L SG  +  + + ++ LF+G P +R  R  L+
Sbjct: 253 HSAPIPTR------SAVVQGYRAYMLQALESGTPMPPLLKPLLTLFNGLPGARAFRRHLS 306

Query: 299 VEAGASTATHHIIETAFNLMIE 320
            +        H+++ A +L+ +
Sbjct: 307 EQGPRRKTDIHVLDEALDLIPD 328


>gi|158334547|ref|YP_001515719.1| dihydrouridine synthase [Acaryochloris marina MBIC11017]
 gi|158304788|gb|ABW26405.1| dihydrouridine synthase (Dus) [Acaryochloris marina MBIC11017]
          Length = 342

 Score =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 128/315 (40%), Gaps = 24/315 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     ++LYTEM+ A  +    +   ++     E+P+++Q+       
Sbjct: 37  GVTDLVFRRLVRRYAPESMLYTEMVHASQVCHARELSKVMDVDLDEQPISVQLFDCRPHF 96

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA++    G + I+LN+GCP  ++ +   G+ L+ +P+     + A+  A+ +PVTV
Sbjct: 97  LAEAAQMAVQEGADTIDLNMGCPVNKITKKGGGSSLLRDPETAEAIVRAVVSAVKVPVTV 156

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG   +   + +    + ++ +G   I +H R         +         +  + +
Sbjct: 157 KTRIGW--KEDEINILEFAQRMQDAGAKMITVHGRT--------RAQGYNGPAQWHWIKQ 206

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K++   + +  NG +  +  A+  L     DGVM  R       ++  +D +       
Sbjct: 207 VKEKL-SIPVIANGDIVSVESAMACLEMTGADGVMCSRGTLGYPYLVGEIDYFLKTGQQK 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR----H 295
           + P      +   R+    + +Y          + Q  +HM     GF  +   R     
Sbjct: 266 APPTIIERLQ-CAREHLQGLWEYKGI-----KGIHQARKHMTWYVKGFVGAAELRDRLCR 319

Query: 296 ILTVEAGASTATHHI 310
           I +VE G       I
Sbjct: 320 INSVEEGLDLLDQTI 334


>gi|329962719|ref|ZP_08300642.1| putative tRNA-dihydrouridine synthase B [Bacteroides fluxus YIT
           12057]
 gi|328529553|gb|EGF56456.1| putative tRNA-dihydrouridine synthase B [Bacteroides fluxus YIT
           12057]
          Length = 325

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/325 (27%), Positives = 144/325 (44%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  S  E+P+ +QI G D
Sbjct: 18  MEDVTDPAFRLMCKQF-GADMVYTEFVSADALIRSVGKTRQKLNISDAERPVTIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N  ++ +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNVPLMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +   L  VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMRIPIIGNGDITTPQRAKECFDLYGVDAIMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+ +    +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSSEWRMEVLRREVEDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A      + I +T   L+
Sbjct: 302 R-IAMLRAETKEELYRIFDTIAPLL 325


>gi|254427671|ref|ZP_05041378.1| putative TIM-barrel protein, nifR3 family [Alcanivorax sp. DG881]
 gi|196193840|gb|EDX88799.1| putative TIM-barrel protein, nifR3 family [Alcanivorax sp. DG881]
          Length = 346

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 143/322 (44%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    LL +EM+ +D  L   +K+   L  S +  P+++QI G +
Sbjct: 17  MAGVTDRPFRRLCRDL-GAGLLVSEMVTSDTRLWNSRKSRQRLDHSGEPGPISVQIAGGE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   D G   I++N+GCP+ +V + + G+ L+ +PD+V   + A+  A+ +P
Sbjct: 76  PTMLAEAARANVDHGAQIIDINMGCPAKKVCKRAAGSALLADPDLVSRILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  + +G+  + IH R         + ++   + +Y  
Sbjct: 136 VTLKIRTGPDRDQRNA--LAIARIAEAAGIQALAIHGRT--------RADKFNGDAEYTT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  +  ++ +  NG ++   +A ++L      G+MIGRAA  N  +      Y  + 
Sbjct: 186 IKQVV-DAVNIPVMANGDVDSPEKAKRVLESTGAGGIMIGRAAQGNPWIFRDTLYYLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P+ T V     + +S     Y          ++   +H+       P+    R  
Sbjct: 245 SLPAAPLVTEVHDCVQQHLSELHHFYGEFM-----GVRIARKHLGWYTQNLPDGEDFRRG 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      IE  F  +
Sbjct: 300 FNTLENATDQCVA-IEQFFQQI 320


>gi|113460710|ref|YP_718776.1| tRNA-dihydrouridine synthase B [Haemophilus somnus 129PT]
 gi|112822753|gb|ABI24842.1| tRNA-U20-dihydrouridine synthase [Haemophilus somnus 129PT]
          Length = 327

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 140/323 (43%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L  +EM+ A+  +   +K+ L           A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSFY-GAGLTCSEMMSANPQVWHTEKSRLRLAHHQDAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + ++ +A+++P
Sbjct: 76  PIEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKKILYSVVRAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +       ++ K  +++G+  + IH R         ++     N +YD 
Sbjct: 136 VTLKIRTGWNQEHRN--CIDIAKIAEQAGIQALSIHGRT--------RECLFNGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K++   + +  NG +    QA ++L     DG+MIGR A     +  ++       
Sbjct: 186 IKKVKEQI-SIPVIANGDITTAKQAQEVLNYTGTDGIMIGRGALGKPWLFQSIVSLIETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +T   P          + I      Y       G ++    +H+     G   +   R  
Sbjct: 245 ITIPEPSLDEKCSVILQHIRDLHQFYGE---DKGYRI--ARKHVSWYLEGIQPNSDFRQT 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
                 A  A    +E  FN ++
Sbjct: 300 FNAITNAK-AQLIALEDFFNFIL 321


>gi|209526027|ref|ZP_03274560.1| TIM-barrel protein, nifR3 family [Arthrospira maxima CS-328]
 gi|209493553|gb|EDZ93875.1| TIM-barrel protein, nifR3 family [Arthrospira maxima CS-328]
          Length = 335

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 138/319 (43%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    N+++YTEM+ A  I+   +   ++     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYAPNSMMYTEMVHASQIIHVRELPILMEIDPGERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           LVEAA+   + G + I++N+GCP  ++ +   G+ L+  P+I    + ++ +A+S+P+TV
Sbjct: 94  LVEAARKAVEEGADTIDVNMGCPVNKITKNGGGSSLLRQPEIAEKIVRSLNEAVSVPITV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D+    + + +  K ++ +G   + IH R         +        +++ +  
Sbjct: 154 KTRLGWDEDE--INILDFSKRMENAGAQMLTIHGRT--------RAQGYTGKANWEWIAR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+ N  + +  NG +  +S A++ L     DGVM  R       ++  +D +       
Sbjct: 204 VKQ-NVSIPVIANGDIVSVSSAVQCLQETGADGVMCSRGTLGYPFLVGEIDYFLKTGQMK 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P      +     + A       R       + Q  +HM     GFP +   R  L  
Sbjct: 263 TAPTVVERLECAKEHLQALWVYKGQR------GIYQSRKHMTWYAKGFPGANELREQLAK 316

Query: 300 EAGASTATHHIIETAFNLM 318
                     +++ A  + 
Sbjct: 317 VETVQQ-GCDLLDGAIAIF 334


>gi|294011661|ref|YP_003545121.1| tRNA-dihydrouridine synthase [Sphingobium japonicum UT26S]
 gi|292674991|dbj|BAI96509.1| tRNA-dihydrouridine synthase [Sphingobium japonicum UT26S]
          Length = 339

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 78/304 (25%), Positives = 131/304 (43%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI   A++R  ++++    +   E+P+++Q+ G  
Sbjct: 23  MTGVTDMPFRTLVRRY-GSGLNVTEMIATAAMIRETRQSLQKAAWHPLEEPVSMQLAGCS 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ EAAK+  D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+ +P
Sbjct: 82  PSEMAEAAKLNADRGAAIIDINMGCPVKKVVNGDAGSALMRDLPLAASLIEATVKAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++    L +  +  G   I +H R         +      + D+  
Sbjct: 142 VTVKMRMGWD--HASLNAPELARIAEDLGAKLITVHGRT--------RCQMYKGSADWAF 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K +   L + +NG +  +  A   L     DGVMIGR AY    ++  V  +F   
Sbjct: 192 VRSVK-DAVSLPVIVNGDICSIDDAETALEQSGADGVMIGRGAYGRPWLIGQVMHWFRTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P      +       A +      H  +   +    +H+     G P S   R+ 
Sbjct: 251 QRLADPSLEEQYRVITEHYRAML-----EHYDNHTGVNMARKHIGWYTKGLPGSAEFRNA 305

Query: 297 LTVE 300
           +  E
Sbjct: 306 VNQE 309


>gi|114565683|ref|YP_752837.1| nifR3 family TIM-barrel protein [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114336618|gb|ABI67466.1| putative TIM-barrel protein, NifR3 family [Syntrophomonas wolfei
           subsp. wolfei str. Goettingen]
          Length = 318

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 139/309 (44%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D+ YR  AR      L+ +EM+    ++ G  +   I   S +++P+A+QI G++
Sbjct: 18  MAGVSDKAYRVLARDF-GCGLVCSEMVSDKGLVYGQGRTSKIADSSGEKRPVAVQIFGSE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+IVE+ G + I++N+GCP+ ++ +   GA LML+       +  + + + +P
Sbjct: 77  AESMATAARIVEEMGADIIDINMGCPTPKIVKNGEGAALMLDITKSRGIVREVLRVVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   ++    L + +++ GV  I +H R         +      + D+++
Sbjct: 137 VTVKMRKGWDE--NSINCLELAQKLEEEGVAAICLHPRS--------RQQFFSGSADWNL 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+KKE   + +  NG +     A ++      D VMIGRAA  N  +     E   N 
Sbjct: 187 IKEMKKEL-KIPVIGNGDIWSADDAQRMIDFTGCDAVMIGRAALGNPFIFRETFELLENN 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +    +   R ++      +         ++++ +H      G P + R R  
Sbjct: 246 RRIPPPSREERLQTATRHLNLVCQFKSEA-----VAVREMRKHFAWYIKGLPGATRVRQE 300

Query: 297 LTVEAGAST 305
           +   A    
Sbjct: 301 INRAASRDE 309


>gi|78046424|ref|YP_362599.1| nifR3 family TIM-barrel protein [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78034854|emb|CAJ22499.1| putative TIM-barrel protein; NifR3 family [Xanthomonas campestris
           pv. vesicatoria str. 85-10]
          Length = 332

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + S  
Sbjct: 186 IAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLSTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EVLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPEAQLALTRDYFDALI 321


>gi|300864213|ref|ZP_07109097.1| nifR3 family TIM-barrel protein [Oscillatoria sp. PCC 6506]
 gi|300337787|emb|CBN54243.1| nifR3 family TIM-barrel protein [Oscillatoria sp. PCC 6506]
          Length = 334

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 130/319 (40%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYAPESMMYTEMVNATGLHYVKQLPRIMEVDPNERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  AA + E  G + I++N+GCP  ++ +   G+ L+ +P+     + ++ KA+++PVTV
Sbjct: 94  LAAAAVMAEKEGADTIDINMGCPVNKITKNGGGSSLLRDPENAEAIVRSVVKAVNVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  D+   + +    K ++ +G   I +H R         +         ++ +  
Sbjct: 154 KTRIGWSDKE--ITILEFAKRMQDAGAQMITVHGRT--------RAQGYNGPAKWEWIRR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+  L     DGVM  R       ++  +D +    +  
Sbjct: 204 VK-EILSIPVIANGDIFSVEAAVNCLAETGADGVMCSRGTLGYPFLVGEIDYFLKTGMEK 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P      +     + A + +Y          ++Q  +H+     GF N+   R  L +
Sbjct: 263 ILPTPIERLECAKEHLRA-LWEYKGE-----SGIRQARKHLTWYAKGFANAGELRGQLAI 316

Query: 300 EAGASTATHHIIETAFNLM 318
                      I+ A   +
Sbjct: 317 VETV-EEGCEKIDRAIQQL 334


>gi|113475058|ref|YP_721119.1| nifR3 family TIM-barrel protein [Trichodesmium erythraeum IMS101]
 gi|110166106|gb|ABG50646.1| putative TIM-barrel protein, nifR3 family [Trichodesmium erythraeum
           IMS101]
          Length = 334

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 133/299 (44%), Gaps = 20/299 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  +    +   I+     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRHAPESMMYTEMVNATGLHYVKELPQIMEVDNNERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA++    G + +++N+GCP  ++ +   G+ L+  P++ G+ ++ + KA+ IPVTV
Sbjct: 94  LAEAAEMAVKEGADTVDINMGCPVNKITKNGGGSSLLRQPELAGEIVSKVVKAVPIPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  +Q   + +    + ++ +G   + +H R         +         ++ + +
Sbjct: 154 KTRIGWSNQE--INILEFAQRMEDAGAQMLTLHGRT--------RAQGYNGPARWEWITK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A++ L     DGVM  R       ++  +D +  N +  
Sbjct: 204 VK-EILSIPVIANGDIFSVDAAIRCLEETRADGVMCSRGTLGYPFLVGEIDYFLKNGVKK 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            SP       +  ++   ++ +Y          ++Q  +H+     GFP +   R  L 
Sbjct: 263 VSPTAAE-KLECAKEHLRALWEYKG-----DRGIRQARKHLTWYSKGFPGAGELRGQLA 315


>gi|189183831|ref|YP_001937616.1| NifR3 protein [Orientia tsutsugamushi str. Ikeda]
 gi|189180602|dbj|BAG40382.1| NifR3 protein [Orientia tsutsugamushi str. Ikeda]
          Length = 320

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 137/320 (42%), Gaps = 23/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A+++  +K+++  +  E  +    +Q+ G 
Sbjct: 19  MSGVTDLPFRKLVKQF-GAGLVVSEMVASRAMIQETRKSMMKSAIIENDITGSCVQLAGC 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AAK+ +D G   I++N GCP+ +V  G  G+ LM +  +    +A   K++SI
Sbjct: 78  EPDVIADAAKMNQDMGAQIIDINFGCPAKKVVGGYAGSALMRDEILAAKILAETVKSVSI 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D       +  + K  ++ G+  I +H R         +        D+ 
Sbjct: 138 PVTLKMRTGWDVSCRNANI--IAKIAEECGIQMITVHGRT--------RCQFYSGKSDWA 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E+  + +  NG +  +  A+  L     DGVMIGR AY    +L+ +  Y + 
Sbjct: 188 FIRKVK-ESIKIPVVANGDITSVDDAIDCLKASGADGVMIGRGAYGKPWLLSQISHYLAF 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                SP      +       + ++ Y          ++   +H+     G PN+   R 
Sbjct: 247 QDYLPSPSLIEQKQIILNHYESILSYYGTE-----AGMKIARKHLGWYSKGLPNATEFRS 301

Query: 296 ILTVEAGASTATHHIIETAF 315
            +T           II   F
Sbjct: 302 KVTTITSVEQVK-EIINQFF 320


>gi|325926552|ref|ZP_08187868.1| tRNA-U20-dihydrouridine synthase [Xanthomonas perforans 91-118]
 gi|325543060|gb|EGD14507.1| tRNA-U20-dihydrouridine synthase [Xanthomonas perforans 91-118]
          Length = 332

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + S  
Sbjct: 186 IAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLSTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EVLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPEAQLALTRDYFDALI 321


>gi|332826846|gb|EGJ99646.1| hypothetical protein HMPREF9455_03909 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 330

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 139/301 (46%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G +
Sbjct: 18  MEDVTDMGFRLMCKRF-GADMVYTEFVSSDALIRHVNKTQAKLTISEEERPVAIQIYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKI E+   + +++N GCP  +V     G+ +M  P+++ +  AA+ KA++IP
Sbjct: 77  VDAMVEAAKICEEASPDILDINFGCPVKKVAGKGAGSGMMRTPELMVEITAAVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    L + ++ +G+  + +H R         +        D+ +
Sbjct: 137 VTVKTRLGWDNDSKIIV--ELAEQLQDTGIQALTLHGRT--------RAQMYSGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +       +      VD VMIGR +     +   V  Y + 
Sbjct: 187 IGAVKNNPRMHIPIIGNGDVTTPEICKRRFDETGVDAVMIGRGSIGGPWIFEEVKHYLAT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  + +  ++  +   +      H    G +    RH+ G  +F G P+ ++ 
Sbjct: 247 GE-----LMPKKEFTWYLDVLKDLVSRNIAHSGERGGIIHSRRHLAGSPVFKGIPDFKKV 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|332879824|ref|ZP_08447513.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332682201|gb|EGJ55109.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 324

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 142/322 (44%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L     +LY+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKL-HGADMLYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV     + +++N GCP  +V     GA ++ + D++     A+ ++  +P
Sbjct: 78  EEAMALSAKIVATVRPDLVDINFGCPVKKVVSKGAGAGVLKDIDLMVRLTKAVVRSTDLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ +  + + ++  G++ + IHAR         +      + D+  
Sbjct: 138 VTVKTRLGWDE--SSINIEEVAERLQDVGISALTIHART--------RSQMYKGHSDWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG +++  +AL+      VDG+MIGRAA     +   +  YF+ 
Sbjct: 188 IAKVKNNPRIHIPIFGNGDIDNPEKALEYRNKYGVDGIMIGRAAIGYPWIFREIKHYFAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P            +      ++         + ++ RH    F G PN +  R 
Sbjct: 248 GELLAPPTIADRVAAARNHLI-----WSVEWKGERQGVLEMRRHYANYFKGLPNFKEHRQ 302

Query: 296 ILTVEAGAS---TATHHIIETA 314
            L     A+   TA   I+   
Sbjct: 303 RLVTLDSAAEIVTALEEIVAKY 324


>gi|187777496|ref|ZP_02993969.1| hypothetical protein CLOSPO_01071 [Clostridium sporogenes ATCC
           15579]
 gi|187774424|gb|EDU38226.1| hypothetical protein CLOSPO_01071 [Clostridium sporogenes ATCC
           15579]
          Length = 323

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 138/317 (43%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+  G      +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYGSNNTTELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +I  D     I ++N+GCP+ ++ +   G+ LM +P +    I AM K    
Sbjct: 76  PDIMANAVEIFNDNNDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASQIIKAMKKVAKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G D     +      K +++SG + I IH R         ++       D+ 
Sbjct: 136 PITVKFRKGFDK--NNINAVEFAKIMEQSGADAITIHGRT--------REQMYEGKADWT 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K     + +  NG +     A++++   + DGVM+GR A  N  +   ++E    
Sbjct: 186 IISKVKNAV-SIPVIGNGDVFSAEDAIEMINKTNCDGVMVGRGAQGNPWIFKQINEKIKG 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R+D      I  +    A  +      ++++ +H+     G  N    + 
Sbjct: 245 EHVYYPTSQERID------ICINHYKRALEYFEEHKAVREMRKHVAVYVKGLKNCTDIKD 298

Query: 296 ILTVEAGASTATHHIIE 312
            + +E  +      +I+
Sbjct: 299 KVNMEKDSHKVLEELIK 315


>gi|29348482|ref|NP_811985.1| dehydrogenase [Bacteroides thetaiotaomicron VPI-5482]
 gi|29340386|gb|AAO78179.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Bacteroides thetaiotaomicron VPI-5482]
          Length = 330

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 85/329 (25%), Positives = 140/329 (42%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNQRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN +  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVIDSVNL----LDERRGILHVRRHLAASPLFKGIPNFKET 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R      A     T   +   F  + E +
Sbjct: 302 R-----IAMLRAETKEELFRIFETIPEKV 325


>gi|284053044|ref|ZP_06383254.1| dihydrouridine synthase TIM-barrel protein nifR3 [Arthrospira
           platensis str. Paraca]
 gi|291568799|dbj|BAI91071.1| hypothetical protein [Arthrospira platensis NIES-39]
          Length = 338

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 136/319 (42%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    N+++YTEM+ A  I+       ++     E+P+++Q+       
Sbjct: 37  GVTDLVFRRLVRRYAPNSMMYTEMVHASQIIHVRKLPILMEIDPGERPISIQLFDCRPDF 96

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           LVEAA+   + G + I++N+GCP  ++ +   G+ L+  P+I    + ++ +A+S+P+TV
Sbjct: 97  LVEAARKAVEEGADTIDVNMGCPVNKITKNGGGSSLLRQPEIAEKIVRSLNEAVSVPITV 156

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD    + + +  K ++ +G   + IH R         +        +++ +  
Sbjct: 157 KTRLGWDDDE--INILDFSKRMEDAGAQMLTIHGRT--------RAQGYTGKANWEWIAR 206

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  +S A++ L     DGVM  R       ++  +D +       
Sbjct: 207 VKQSL-SIPVIANGDIVSVSSAVQCLQETGADGVMCSRGTLGYPFLVGEIDYFLKTGQMK 265

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           ++P      +     + A       R       + Q  +HM     GFP +   R  L  
Sbjct: 266 TAPTVVERLECAKEHLQALWVYKGQR------GIYQSRKHMTWYAKGFPGANELREQLAK 319

Query: 300 EAGASTATHHIIETAFNLM 318
                     +++ A  + 
Sbjct: 320 VETVEQ-GCDLLDGAIAIF 337


>gi|239946645|ref|ZP_04698398.1| tRNA-dihydrouridine synthase [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239920921|gb|EER20945.1| tRNA-dihydrouridine synthase [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 325

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 137/325 (42%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   ++++              +Q+ G 
Sbjct: 18  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLQKSAIMRDDATSACIQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ +
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVKAVKL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  + SGV  + +H R         +      N D+D
Sbjct: 137 PVTVKMRMGWDDNTKNA--PTLAKIAESSGVQMVTVHGRT--------RCQFYSGNADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L    VDG+M+GR AY    +++ +D Y   
Sbjct: 187 FIRSVK-EAVKIPVIANGDITNFAKAKEALQKSGVDGIMVGRGAYGKPWLISQIDHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P              A +  Y          +    +H+     G PNS   R 
Sbjct: 246 GKEKSAPSIAEQLDIVTEHYDAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            + +    +     I E   N+M E
Sbjct: 301 AVNLMNDPAAVKEKIAEFYNNVMKE 325


>gi|255527649|ref|ZP_05394509.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
 gi|296186914|ref|ZP_06855315.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
 gi|255508662|gb|EET85042.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
 gi|296048628|gb|EFG88061.1| TIM-barrel protein, nifR3 family [Clostridium carboxidivorans P7]
          Length = 326

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 141/321 (43%), Gaps = 28/321 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEMI A A+  G  + K++L  S QE P A+QI G D
Sbjct: 17  MAGVTDIAFRELCKEMGCE-LVYTEMISAKALFYGSKNTKDMLVISKQEAPAAVQIFGND 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +A     D      +++N+GCP+ ++ +   G+ LM +P +    +  + KA S 
Sbjct: 76  PLVMAKACDFFNDNEDICLVDINMGCPAPKIVKNGEGSALMKDPKLAAQIVKEVKKASSK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R G D     +      K ++++GV+ + +H R         ++       D++
Sbjct: 136 PVTAKFRKGFDSD--NINAVEFAKELEQAGVDAVTVHGRT--------REQMYEGKADWN 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+    + +  NG +     A+ I    + D +MIGR A  N  +   +DE   N
Sbjct: 186 MIEKVKQAV-SIPVIGNGDVVTPEDAVSIFKTTNCDAIMIGRGAMGNPWIFNQIDEKIKN 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   + R+D          M  Y  A  +      ++++ +H+     G  N++  
Sbjct: 245 INVTYPSEEDRID--------MCMEHYRRAISYEGEAKAVREMRKHVGWYLKGLSNNKEI 296

Query: 294 RHILTVEAGASTATHHIIETA 314
           +  +  E  +S     I++  
Sbjct: 297 KDAVNYE-KSSEKVISILKEY 316


>gi|239995215|ref|ZP_04715739.1| tRNA-dihydrouridine synthase B [Alteromonas macleodii ATCC 27126]
          Length = 320

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 133/326 (40%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L+ +EM+ ++  +    K+   +    +E   ++QI GAD
Sbjct: 5   MAGVTDRPFRQLCKRL-GAGLVVSEMLSSNPKVWNTAKSQARMNHEGEEGIRSVQIAGAD 63

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PD V   I A+  A+ +P
Sbjct: 64  PELMAQAAQFNVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDTVEAIIKAVVNAVDVP 123

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +++G+  + +H R         +        +Y  
Sbjct: 124 VTLKIRTGWNPENRNGV--EIARIAEQNGIQSLAVHGRT--------RACMYKGEAEYST 173

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG +    +A ++L     DGVMIGR A     +   +  Y    
Sbjct: 174 IRQIKAAI-SIPVIANGDITSPEKAQEVLNYTGADGVMIGRGAQGKPWIFKQIQHYLETG 232

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P  + + +     ++     Y          ++   +H+          R+ R  
Sbjct: 233 ENLPAPPLSELYELLHEHVANVQDFY-----GDIAGVRIARKHVGWYLAEHDTDRQFRKT 287

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
                    A   +   A N   ++L
Sbjct: 288 FNA---IDDANEQL--DALNAYFQAL 308


>gi|150014995|ref|YP_001307249.1| nifR3 family TIM-barrel protein [Clostridium beijerinckii NCIMB
           8052]
 gi|149901460|gb|ABR32293.1| putative TIM-barrel protein, nifR3 family [Clostridium beijerinckii
           NCIMB 8052]
          Length = 321

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 137/308 (44%), Gaps = 30/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G  + + +L  + +EKP+A QI G +
Sbjct: 17  MAGVTDISFRGLCKEM-GCGLVYTEMVSAKALYYGSENTQTLLRIADEEKPVAAQIFGRE 75

Query: 59  ISKLVEAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              +   A+I E++         I++N+GCP+ ++ +   G+ LM  P++  D +  + K
Sbjct: 76  PDVM---ARICEEYLNNRKDICIIDINMGCPAPKIVKNGEGSALMKEPELAYDIVRTIKK 132

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             + PVTVK R G D+    +      K ++++G + I +H R         +       
Sbjct: 133 VSTKPVTVKFRKGFDED--NINAVEFAKGMEQAGADAIAVHGRT--------RKQMYQGK 182

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
            D+DI+  +K ++  + +  NG +     A+++    + DG+MI R +  N  +   ++ 
Sbjct: 183 ADWDIIKRVK-DSVSIPVIGNGDVFSPEDAIRMKRTTNCDGIMIARGSQGNPWIFRQINN 241

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +  +        ++      ++     + A ++      ++++ +H      G P   
Sbjct: 242 LLNGEVIQEVSDNEKI------EMCIRHYELAIKYDGEFKAIREMRKHASWYIKGLPRCT 295

Query: 292 RCRHILTV 299
             ++ +  
Sbjct: 296 ELKNKINT 303


>gi|262368472|ref|ZP_06061801.1| tRNA-dihydrouridine synthase B [Acinetobacter johnsonii SH046]
 gi|262316150|gb|EEY97188.1| tRNA-dihydrouridine synthase B [Acinetobacter johnsonii SH046]
          Length = 341

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 67/323 (20%), Positives = 140/323 (43%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ +D  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRSLCKYF-GAGHAVSEMMTSDQTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   +  +  A+ +P
Sbjct: 76  PKELAEAARYQVSNGAQIVDINMGCPAKKVCNKLAGSALLKDEDLVARILDEVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  + +G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNG--HENILRVAKRAEDAGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKDVKQLI-RIPVVANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    V +     ++     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPSIQEVKEVLLGHLAELYAFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +  +  ++T    ++   F+ ++
Sbjct: 300 M-YKVESTTEQFKVVADYFDQLL 321


>gi|330501709|ref|YP_004378578.1| nifR3 family TIM-barrel protein [Pseudomonas mendocina NK-01]
 gi|328915995|gb|AEB56826.1| nifR3 family TIM-barrel protein [Pseudomonas mendocina NK-01]
          Length = 313

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 1   MAGVTDRPFRQLCRRL-GAGLVVSEMVTSDVRLWNSRKSSLRLLHAGDPEPRSVQIAGGD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 60  PQMMADAARKNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEPLVREILDAVVGAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q     +  + K  + +G++ + +H R         + +      +Y+ 
Sbjct: 120 VTLKIRTGWDRQNKNGII--VAKIAEDAGISALAVHGRT--------RADLYTGEAEYET 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     D ++IGRAA     +   ++ Y    
Sbjct: 170 IAAIKQAV-SIPVFANGDIDSPEKAKAVLDATGADALLIGRAAQGRPWIFREIEHYLRTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 229 EILPAPSLLEVERILLEHLAALHAFY-----GELMGVRIARKHVGWYLATLPGAREFR 281


>gi|254881117|ref|ZP_05253827.1| dehydrogenase [Bacteroides sp. 4_3_47FAA]
 gi|294777525|ref|ZP_06742976.1| TIM-barrel protein, nifR3 family [Bacteroides vulgatus PC510]
 gi|319640124|ref|ZP_07994851.1| hypothetical protein HMPREF9011_00448 [Bacteroides sp. 3_1_40A]
 gi|254833910|gb|EET14219.1| dehydrogenase [Bacteroides sp. 4_3_47FAA]
 gi|294448593|gb|EFG17142.1| TIM-barrel protein, nifR3 family [Bacteroides vulgatus PC510]
 gi|317388402|gb|EFV69254.1| hypothetical protein HMPREF9011_00448 [Bacteroides sp. 3_1_40A]
          Length = 329

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 137/301 (45%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K +  L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSADALIRSVGKTMQKLNINDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  RV     GA ++ N  ++ +   A+   + IP
Sbjct: 77  TETMVEAAKIVEEAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDTVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNEHKIIV--DLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDITTPQRAKECFDQYGVDAIMIGRASFGRPWIFKEVKHYIET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                +           +++       +   L     +  + RH+    LF G PN +  
Sbjct: 247 GKELPALSFEWRLNVLRQEVLD-----SVNLLDERRGILHVRRHLAASPLFKGIPNFKET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|253580949|ref|ZP_04858211.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847791|gb|EES75759.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 321

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 132/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+  EMI A AI   +K    ++     E P+++Q+ G++
Sbjct: 21  MAGVTDLPFRTLCKE-QGAGLICMEMISAKAISFHNKNTIALMEIDPCEHPVSMQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +ED  ++ +++N+GCP  +V     G+ L+ NP+++ + +  +  A+S P
Sbjct: 80  PDLMAEVAKSIEDRDFDILDINMGCPVPKVVNNGEGSALLKNPNLIEEIVRKVSSAISKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG +++   V +  + K I+ +G   + +H R         +        D+D 
Sbjct: 140 LTVKVRIGFENE--PVDIVEIAKRIEDAGAAALAVHGRT--------RQQYYSGTADWDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++    ++AL      D VM+GRA   N  +   ++ YF   
Sbjct: 190 IRRVKEAIT-IPVIGNGDVDSPLKAEALVKQTGCDAVMVGRAVRGNPWLFRELNHYFRTG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P    + +   R     +             ++++ +H+     G  +S   R 
Sbjct: 249 ELLERPSVEEIREMILRHARKQI-----ELKGEFVGIREMRKHVAWYTAGMRHSAGLRR 302


>gi|298385818|ref|ZP_06995375.1| hypothetical protein HMPREF9007_02527 [Bacteroides sp. 1_1_14]
 gi|298261046|gb|EFI03913.1| hypothetical protein HMPREF9007_02527 [Bacteroides sp. 1_1_14]
          Length = 330

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 85/329 (25%), Positives = 140/329 (42%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNQRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN +  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVIDSVNL----LDERRGILHVRRHLAASPLFKGIPNFKET 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R      A     T   +   F  + E +
Sbjct: 302 R-----IAMLRAETKEELFRIFETIPEKV 325


>gi|332143328|ref|YP_004429066.1| tRNA-dihydrouridine synthase B [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327553350|gb|AEB00069.1| tRNA-dihydrouridine synthase B [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 332

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 131/326 (40%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L+ +EM+ ++  +    K+   +    +E   ++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGLVVSEMLSSNPKVWNTAKSQARMNHEGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   I++N+GCP+ +V++   G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PELMAQAAQFNVDNGAQIIDINMGCPAKKVNKKLAGSALLQYPDTVEAIVKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +++G+  + +H R         +        +Y  
Sbjct: 136 VTLKIRTGWNPENRNGV--EIARIAEQNGIQSLAVHGRT--------RACMYKGEAEYST 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK     + +  NG +    +A ++L     DGVMIGR A     +   +  Y    
Sbjct: 186 IRRIKAAI-SIPVIANGDITSPQKAQEVLNYTGADGVMIGRGAQGKPWIFNQIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P  +   +     ++     Y          ++   +H+          R+ R  
Sbjct: 245 ENLAPPPLSEQYEILHEHVANVQDFY-----GDIAGVRIARKHVGWYLSEHDTDRQFRKT 299

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
                    A   +   A N   ++L
Sbjct: 300 FNA---IDDANEQL--DALNAYFQAL 320


>gi|166710692|ref|ZP_02241899.1| hypothetical protein Xoryp_04310 [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 328

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 138/326 (42%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + ++V   + A+ +A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEELVARILTAVVQAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARLAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + +  
Sbjct: 186 IAQIKAAL-RIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EVLPPPSLAFVRDTLLSHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           +   A    A   +    F+ +I S+
Sbjct: 300 VN-RAETPEAQLALTRDYFDALIASV 324


>gi|148381462|ref|YP_001256003.1| dihydrouridine synthase [Clostridium botulinum A str. ATCC 3502]
 gi|153932994|ref|YP_001385837.1| dihydrouridine synthase [Clostridium botulinum A str. ATCC 19397]
 gi|153935504|ref|YP_001389244.1| dihydrouridine synthase [Clostridium botulinum A str. Hall]
 gi|148290946|emb|CAL85082.1| putative dihydrouridine synthase [Clostridium botulinum A str. ATCC
           3502]
 gi|152929038|gb|ABS34538.1| dihydrouridine synthase [Clostridium botulinum A str. ATCC 19397]
 gi|152931418|gb|ABS36917.1| dihydrouridine synthase [Clostridium botulinum A str. Hall]
          Length = 323

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 139/317 (43%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +    +     +++N+GCP+ ++ +   G+ LM +P +  + I AM K    
Sbjct: 76  PEIMANAVEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKVAKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G D     +      K +++SGV+ I IH R         ++       D+ 
Sbjct: 136 PITVKFRKGFDK--NNINAVEFAKIMEQSGVDAITIHGRT--------REQMYEGKADWA 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K  +  + +  NG +     AL+++     DG+MIGR A  N  +   ++E    
Sbjct: 186 IISKVKN-SVSIPVIGNGDVFSSEDALEMINKTYCDGIMIGRGAQGNPWIFKQINEKIKG 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R+D      I  +    +  +      ++++ +H+     G  N    + 
Sbjct: 245 EHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAVYVKGLKNCTDIKD 298

Query: 296 ILTVEAGASTATHHIIE 312
            + +E         +I+
Sbjct: 299 KVNMEKDPDKVLEELIK 315


>gi|260889590|ref|ZP_05900853.1| tRNA dihydrouridine synthase A [Leptotrichia hofstadii F0254]
 gi|260861001|gb|EEX75501.1| tRNA dihydrouridine synthase A [Leptotrichia hofstadii F0254]
          Length = 332

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 119/329 (36%), Positives = 166/329 (50%), Gaps = 23/329 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDR++R F R++  + LLYTEMI A A+L GD   ILGF   E P+ LQI   +  
Sbjct: 15  MVDRTDRNFRNFVRMINKDVLLYTEMITAQAVLNGDLDYILGFDEVEHPIVLQIAATNPK 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +  +A KI E + Y+EINLNVGCPS RV     GA LM  P+ V + + +M  A   PV+
Sbjct: 75  EAYQAVKIAEKYNYDEINLNVGCPSDRVSGNMMGAYLMAFPEEVANIVKSMKDATGKPVS 134

Query: 121 VKCRIGVDDQ------------IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           VK RIG+D +                 + N +   K++GV+   IHAR AIL GL PK N
Sbjct: 135 VKHRIGIDGKNVLPNSFKRTLLDKYEDMENFISITKQAGVSKYIIHARIAILAGLDPKQN 194

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R IP L YD VY +KK+NPDL I +NGG++ + +  + L  VD  M+GR  Y N  +LT 
Sbjct: 195 RSIPPLRYDEVYRVKKDNPDLHIEINGGIKTVEEIDEHLKYVDSAMLGREIYDNPMILTE 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             +Y+   +  +            ++I   M  Y         +      H  GLFH   
Sbjct: 255 FGKYYGKEINITR-----------KEIIEKMIYYVENMEKQQLRPHLFLMHAHGLFHNVR 303

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNL 317
            S+  +  +      S     +++   N 
Sbjct: 304 GSKAWKRAINEPKANSGTLRELLKKIENF 332


>gi|300727518|ref|ZP_07060909.1| TIM-barrel protein, NifR3 family [Prevotella bryantii B14]
 gi|299775221|gb|EFI71822.1| TIM-barrel protein, NifR3 family [Prevotella bryantii B14]
          Length = 333

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/328 (25%), Positives = 145/328 (44%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +     E+P+ +QI G +
Sbjct: 18  MEDVTDIGFRKLCKRY-GAAMMYTEFVSADAIIRSIKSTLNKMIIDDDERPVGIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE F  + I++N GCP  +V     GA L+ N  ++ D    + +A+++P
Sbjct: 77  VESMVEAAKIVEQFHPDVIDINFGCPVKKVAGKGAGAGLLRNIPLMLDIAKHVVEAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D     + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTAKTRLGWDQD--NLVITDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +  +      VD VM+GRA +    +   + +Y   
Sbjct: 187 IGEVKKNPRIHIPIIGNGDITTPEECKRAFDDFGVDAVMVGRATFGRPWIFKEIRDYLDG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P    +D +    I           +     +    RH+    +F G P+ ++ 
Sbjct: 247 -----KPDDKLLDINKKIDILEEQLKINVERIDEYRGILHTRRHLAASPIFKGIPDFKQT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A  +     I+E    L+  S
Sbjct: 302 R-IAMLRATKTDDLIEILENCRILLANS 328


>gi|167749581|ref|ZP_02421708.1| hypothetical protein EUBSIR_00539 [Eubacterium siraeum DSM 15702]
 gi|167657435|gb|EDS01565.1| hypothetical protein EUBSIR_00539 [Eubacterium siraeum DSM 15702]
          Length = 327

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 129/300 (43%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D+  R   +     ALL  EM  A  +   D+K   +L  +  E+P+A+Q+ G++
Sbjct: 20  MASVADKAMRTMCKKY-GAALLTGEMASAKGLCYSDRKTAALLTVTDYERPMAIQLFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA I   +  + I++N GCP  +V     G+ LM +P ++G  + A+ KA  IP
Sbjct: 79  PEFMAKAAVIAAQYKPDFIDINCGCPVPKVAGNGAGSALMNDPVLLGHIVEAVVKATDIP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++   V    + +  ++SG + + +H R         K+       D +I
Sbjct: 139 VTVKIRKGWDEK--NVNAVEVARVAQESGASAVAVHGRT--------KNQMYSGKADLEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+    + +  NG ++      ++      D VM+GRAA     + + +  Y    
Sbjct: 189 IAEVKQAL-SIAVIGNGDVDSGESCKRMYDYTGCDLVMVGRAACGRPWIFSEIKHYLETG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T   P      +     I     D           +++  +H      G P + + R++
Sbjct: 248 ETLPPPSPDEQLEIMNEHIRLLCAD-----KGEYIGMKEARKHTAWYLKGRPGAAKLRNM 302


>gi|153941130|ref|YP_001392876.1| dihydrouridine synthase [Clostridium botulinum F str. Langeland]
 gi|170756229|ref|YP_001783162.1| dihydrouridine synthase [Clostridium botulinum B1 str. Okra]
 gi|152937026|gb|ABS42524.1| dihydrouridine synthase [Clostridium botulinum F str. Langeland]
 gi|169121441|gb|ACA45277.1| dihydrouridine synthase [Clostridium botulinum B1 str. Okra]
 gi|295320853|gb|ADG01231.1| dihydrouridine synthase [Clostridium botulinum F str. 230613]
          Length = 323

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 139/317 (43%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +    +     +++N+GCP+ ++ +   G+ LM +P +  + I AM K    
Sbjct: 76  PEIMANAVEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKVAKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G D     +      K +++SGV+ I IH R         ++       D+ 
Sbjct: 136 PITVKFRKGFDK--NNINAVEFAKIMEQSGVDAITIHGRT--------REQMYEGKADWA 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K  +  + +  NG +     AL+++     DG+MIGR A  N  +   ++E    
Sbjct: 186 IISKVK-SSVSIPVIGNGDVFSSEDALEMINKTDCDGIMIGRGAQGNPWIFKQINEKIKG 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R+D      I  +    +  +      ++++ +H+     G  N    + 
Sbjct: 245 EHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAVYVKGLKNCTDIKD 298

Query: 296 ILTVEAGASTATHHIIE 312
            + +E         +I+
Sbjct: 299 KVNMEKDPDKVLEELIK 315


>gi|86609094|ref|YP_477856.1| dihydrouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557636|gb|ABD02593.1| dihydrouridine synthase family protein [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 361

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 133/322 (41%), Gaps = 21/322 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISK 61
             TD+ +R   R    ++L+YTEM+ A  +    +   I+     E+P+ +Q+       
Sbjct: 35  GVTDQVFRGLVRRFAPHSLVYTEMVSATGLHYARQLPRIMEVGEGEQPIGIQLFDCRPDF 94

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA++  D G   +++N+GCP  ++ +   G+ L+ +PD     + A+  A+ +PVTV
Sbjct: 95  LAEAARMAVDEGATLVDINMGCPVNKITKNGGGSSLLRDPDTAARIVEAVANAVEVPVTV 154

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G  DQ   + + +    ++++G   + +HAR         +         +D +  
Sbjct: 155 KTRLGWSDQE--INILDFAHRLQEAGAQLLTLHART--------RAQGFNGKARWDWIRR 204

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +   + A+K L     DGVM  R       ++  +D +       
Sbjct: 205 VKQHL-RIPVIANGDIFSTAAAVKCLEETGADGVMCSRGTMGYPFLVGEIDHFLKTGQER 263

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P      +     +   + +Y          ++Q  +HM      F  + + R +L  
Sbjct: 264 PAPTPLERIQMALEHL-RGLWEYKGER-----GIRQARKHMTWYIKDFAGASQFRALLCR 317

Query: 300 EAGASTATHHIIETAFNLMIES 321
                     ++  A     E+
Sbjct: 318 IETVQE-GEALLLQAMERCQEA 338


>gi|325915592|ref|ZP_08177900.1| tRNA-U20-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
 gi|325538152|gb|EGD09840.1| tRNA-U20-dihydrouridine synthase [Xanthomonas vesicatoria ATCC
           35937]
          Length = 354

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 136/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 39  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+ +A+ +P
Sbjct: 98  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEALVARILRAVVQAVDVP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D       +Y  
Sbjct: 158 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGTAEYAT 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG ++   +A ++L    VD VMIGRAA     +   V  Y +  
Sbjct: 208 IGEIKAAL-QIPVIANGDIDSPQKAAQVLRDTGVDAVMIGRAAQGRPWIFGEVAHYLATG 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 267 ALLPAPTLAFVRDTLLDHLQALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 321

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 322 VN-RAETPEAQLALTSDYFDALI 343


>gi|189464643|ref|ZP_03013428.1| hypothetical protein BACINT_00986 [Bacteroides intestinalis DSM
           17393]
 gi|189436917|gb|EDV05902.1| hypothetical protein BACINT_00986 [Bacteroides intestinalis DSM
           17393]
          Length = 329

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 88/329 (26%), Positives = 144/329 (43%), Gaps = 24/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +    N ++YTE + ADA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKFGAN-MVYTEFVSADALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE+   + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEEARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDVTTPQRAKECFELYGVDAIMIGRASFGRPWIFKEVRHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+         R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSAEWKLGVLRQEVIDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R I  + A        I +   + +  +L
Sbjct: 302 R-IAMLRAETKEELFRIFDDIESSLFSAL 329


>gi|168180991|ref|ZP_02615655.1| dihydrouridine synthase [Clostridium botulinum NCTC 2916]
 gi|168183602|ref|ZP_02618266.1| dihydrouridine synthase [Clostridium botulinum Bf]
 gi|226950978|ref|YP_002806069.1| dihydrouridine synthase [Clostridium botulinum A2 str. Kyoto]
 gi|237796983|ref|YP_002864535.1| dihydrouridine synthase [Clostridium botulinum Ba4 str. 657]
 gi|182668088|gb|EDT80067.1| dihydrouridine synthase [Clostridium botulinum NCTC 2916]
 gi|182673187|gb|EDT85148.1| dihydrouridine synthase [Clostridium botulinum Bf]
 gi|226844028|gb|ACO86694.1| dihydrouridine synthase [Clostridium botulinum A2 str. Kyoto]
 gi|229261947|gb|ACQ52980.1| dihydrouridine synthase [Clostridium botulinum Ba4 str. 657]
          Length = 323

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 139/317 (43%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   + L    L+YTEM+ A A+     + K +   S +EKP+ALQ+ G +
Sbjct: 17  MAGFTDIAFREICKEL-GCGLVYTEMVSAKALYYESNNTKELCVISNKEKPVALQLFGHE 75

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  A +    +     +++N+GCP+ ++ +   G+ LM +P +  + I AM K    
Sbjct: 76  PEIMANAVEFFNNNDDVCILDVNMGCPAPKIVKNGDGSALMKDPKLASEIIKAMKKVAKK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G D     +      K +++SGV+ I IH R         ++       D+ 
Sbjct: 136 PITVKFRKGFDK--NNINAVEFAKIMEQSGVDAITIHGRT--------REQMYEGKADWA 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K  +  + +  NG +     AL+++     DG+MIGR A  N  +   ++E    
Sbjct: 186 IISKVKN-SVSIPVIGNGDVFSSEDALEMINKTDCDGIMIGRGAQGNPWIFKQINEKIKG 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R+D      I  +    +  +      ++++ +H+     G  N    + 
Sbjct: 245 EHVYYPTPQERID------ICINHYKKSLEYFEEHKAVREMRKHVAVYVKGLKNCTDIKD 298

Query: 296 ILTVEAGASTATHHIIE 312
            + +E         +I+
Sbjct: 299 KVNMEKDPDKVLEELIK 315


>gi|226942119|ref|YP_002797193.1| NifR3 [Laribacter hongkongensis HLHK9]
 gi|226717046|gb|ACO76184.1| NifR3 [Laribacter hongkongensis HLHK9]
          Length = 341

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 139/322 (43%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L  +EMI ++  L   +K +     + +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCRRF-GAGLAVSEMIASNTALATSRKTLKRADHTGEPGPVSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+   D+G   I++N+GCP+ +V   + G+ L+ +  +V   + A+ +A+ +P
Sbjct: 76  PQEMADAARRNVDYGAQIIDINMGCPAKKVCNVAAGSALLKDEPLVARILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  ++SG+  + +H R         ++++ +   +YD 
Sbjct: 136 VTLKTRTGWSREHRNA--LAVARLAEESGIAALALHGRT--------REDKYLGEAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGRAA     +   +  + +  
Sbjct: 186 IRAVK-AAVRIPVIANGDIDSPEKARHVLDYTGADAIMIGRAAQGRPWLFRDIQHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  + +       +      Y           +   +H+    HG  ++   R  
Sbjct: 245 ERLPPPRVSEISAVLLEHLDDLYGFY-----GEYLGCRVARKHIAWYTHGLFDANAFRQA 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +  +  ++ A    +   F+ +
Sbjct: 300 M-YQLDSTAAQRAAVARYFDQL 320


>gi|332995671|gb|AEF05726.1| tRNA-dihydrouridine synthase B [Alteromonas sp. SN2]
          Length = 332

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 135/326 (41%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  +    K+   +    +E   ++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAGLVVSEMLSSNPKVWNTAKSQARMNHEGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P  V   I A+  A+ +P
Sbjct: 76  PELMAQAAQFNVENGAQIIDINMGCPAKKVNKKLAGSALLQYPSTVESIIKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +          + +  +++G+  + +H R         +        ++D 
Sbjct: 136 VTLKIRTGWNTDNRNGV--EIARIAEQNGIQSLAVHGRT--------RACMYKGEAEFDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A ++L     DGVMIGR A  N  +   +  Y    
Sbjct: 186 IRRIKEAI-SIPVIANGDITSPEKAQQVLNCTGADGVMIGRGAQGNPWIFKEILHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  +   +     ++   + Y          ++   +H+          R+ R  
Sbjct: 245 ENLKPPPLSEQYEILHEHVANVQSFY-----GEVAGVRIARKHVGWYLSEHDTDRQFRK- 298

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
            +  A    A+  +   A N   E+L
Sbjct: 299 -SFNAI-EDASAQL--EALNAYFEAL 320


>gi|307292784|ref|ZP_07572630.1| TIM-barrel protein, nifR3 family [Sphingobium chlorophenolicum L-1]
 gi|306880850|gb|EFN12066.1| TIM-barrel protein, nifR3 family [Sphingobium chlorophenolicum L-1]
          Length = 339

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 78/304 (25%), Positives = 130/304 (42%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI   A++R  ++++    +   E+P+++Q+ G  
Sbjct: 23  MTGVTDMPFRTLVRRY-GSGLNVTEMIATAAMIRETRQSLQKAAWHPLEEPVSMQLAGCS 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAK+  D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+ +P
Sbjct: 82  PTEMAEAAKLNADRGAAIIDINMGCPVKKVVNGDAGSALMRDLPLAASLIEATVKAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++    L +  +  G   I +H R         +      + D+  
Sbjct: 142 VTVKMRMGWD--HASLNAPELARIAEDLGAKLITVHGRT--------RCQMYKGSADWAF 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K E   L + +NG +  +  A   L     DGVMIGR AY    ++  V  +F   
Sbjct: 192 VRSVK-EAVSLPVIVNGDICSIDDAETALEQSGADGVMIGRGAYGRPWLIGQVMHWFRTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P              A +  Y      +   +    +H+     G P S   R+ 
Sbjct: 251 ERLADPSLEEQYGLITEHYRAMLDHY-----DNHTGVNMARKHIGWYTKGLPGSAEFRNA 305

Query: 297 LTVE 300
           +  E
Sbjct: 306 VNQE 309


>gi|21241586|ref|NP_641168.1| hypothetical protein XAC0816 [Xanthomonas axonopodis pv. citri str.
           306]
 gi|38604925|sp|Q8PP72|DUSB_XANAC RecName: Full=tRNA-dihydrouridine synthase B
 gi|21106942|gb|AAM35704.1| conserved hypothetical protein [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 332

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + ++V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEELVARILTAVVQAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARIAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + +  
Sbjct: 186 IAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EVLPPPSLAFVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPDAQLALTRDYFDALI 321


>gi|238026250|ref|YP_002910481.1| putative TIM-barrel protein, nifR3 family protein [Burkholderia
           glumae BGR1]
 gi|237875444|gb|ACR27777.1| Putative TIM-barrel protein, nifR3 family protein [Burkholderia
           glumae BGR1]
          Length = 347

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 131/308 (42%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   ++A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVSAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G+  + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHRNA--LTIARLAEDAGIAMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYETIAAVK-AAVKIPVVANGDITSPAKAKAVLDFTGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +     T  +P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGTTLPAPSVDEIQQLLNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 AFRHRMNT 308


>gi|217075895|gb|ACJ86307.1| unknown [Medicago truncatula]
          Length = 432

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 113/331 (34%), Positives = 171/331 (51%), Gaps = 18/331 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+ A+ I+    +    L +S ++ P+ LQIGG++
Sbjct: 74  MMDWTDNHYRTLARLISKHAWLYTEMLAAETIVHQKDNLDRFLAYSPEQHPIVLQIGGSN 133

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           I  L +A ++   + Y+EINLN GCPS RV     FG  LML+P  V + ++A+    ++
Sbjct: 134 IESLAKATELANAYCYDEINLNCGCPSPRVAGHGSFGVSLMLDPKFVAEAMSAIAANTNV 193

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V ++   S      IH+RKA+L G+SP +NR IP L Y
Sbjct: 194 PVSVKCRIGVDDRDSYDELCEFVSTVSSLSPTKHFIIHSRKALLNGISPAENRSIPPLKY 253

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  Y + ++ PDL   +NGG+  + +          GVMIGRAA+ N   +L  VD    
Sbjct: 254 EYFYGLLRDFPDLTFTINGGITSVDEVNAARDAGAHGVMIGRAAFYNPWHILGHVDTAIY 313

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK---LQQITRHMIGLFHGFPNSR 291
                 S   TR      R++      Y    L   G    ++ I + ++ LFH  P + 
Sbjct: 314 G---APSCGLTR------RQVLEKYIVYGDSELGKYGHRPTVRDIVKPLLNLFHSAPGNG 364

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMIESL 322
           + +          T      E   + + +S+
Sbjct: 365 QWKRNADAAFRNCTTIKSFFEETIDAIPDSV 395


>gi|145339824|ref|NP_567149.2| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|24030197|gb|AAN41279.1| unknown protein [Arabidopsis thaliana]
 gi|332646975|gb|AEE80496.1| FMN-linked oxidoreductase-like protein protein [Arabidopsis
           thaliana]
          Length = 419

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 109/328 (33%), Positives = 170/328 (51%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL+T +A LYTEMI A+ ++         L FS Q+ P+ LQ+GG++
Sbjct: 59  MMDWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSN 118

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +AAK+ + +GY+EINLN GCPS +V     FG  LML P +VG+ ++A+    ++
Sbjct: 119 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKLVGEAMSAIAANTNV 178

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVD+      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y
Sbjct: 179 PVTVKCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKY 238

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  Y + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N    L  VD    
Sbjct: 239 EYYYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNNPWQTLGQVDTAVY 298

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +    +           H +    ++ + + ++ LFH    +   +
Sbjct: 299 G-----VPSSGLTRRQVLEQYQVYGDSVLGTHGNGRPNVRDLVKPLLNLFHSENGNSLWK 353

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                      +   ++E +   + + +
Sbjct: 354 RRADAAFKECRSVGSLLEESLRAIPDCV 381


>gi|85711853|ref|ZP_01042908.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
 gi|85694250|gb|EAQ32193.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
          Length = 320

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 125/300 (41%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R     L    +  +EM+ ++  +    K++  +  S +    ++QI G++
Sbjct: 17  MAGVTDQPFRQLCYKL-GAGMTVSEMLSSNPKVWQTDKSMQRMDHSGELGIRSVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAKI    G   I++N+GCP+ +V++   G+ LM +P +V   + A+ +A+ +P
Sbjct: 76  PELMAQAAKINVSQGAQIIDINMGCPAKKVNKKLAGSALMQHPALVESILTAVVEAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +          + +  ++ G+  + +H R         +        +Y+ 
Sbjct: 136 VTLKTRTGWNLDHKNGI--EIAQIAERCGIQALAVHGRT--------RACMYKGEAEYNT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK E   + +  NG +    QA  +L     D +MIGR A  N  +   +  +    
Sbjct: 186 IRAIK-ETISIPVIANGDITSPEQAAHVLRYTGADAIMIGRGAQGNPWIFKQIQYFLEYG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V       + A    Y          ++   +H+    +  PN R  R  
Sbjct: 245 EHLQAPPLDEVAHTVVEHVKALHQFY-----GEYKGVRIARKHVGWYLNERPNGREFRQA 299


>gi|224537320|ref|ZP_03677859.1| hypothetical protein BACCELL_02198 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521051|gb|EEF90156.1| hypothetical protein BACCELL_02198 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 329

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSADALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE+   + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEEARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +   L  VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDITSPQRAKECFDLYGVDAIMIGRASFGRPWIFKEVRHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+         R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSAEWKLSVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|253569151|ref|ZP_04846561.1| dehydrogenase [Bacteroides sp. 1_1_6]
 gi|251841170|gb|EES69251.1| dehydrogenase [Bacteroides sp. 1_1_6]
          Length = 330

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 85/329 (25%), Positives = 140/329 (42%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAIVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IEEVKNNQRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN +  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVIDSVNL----LDERRGILHVRRHLAASPLFKGIPNFKET 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R      A     T   +   F  + E +
Sbjct: 302 R-----IAMLRAETKEELFRIFETIPEKV 325


>gi|5834292|gb|AAD53896.1|AF176314_6 NifR3-like protein [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 344

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 138/305 (45%), Gaps = 21/305 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 32  MTGVTDLPFRRIVRRY-GSGLNVTEMIASQAMIRETRQSLQKSTWDPYEEPISVQLVGCT 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E+AK+ +D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 91  PDDMAESAKLNQDRGAAIIDINMGCPVRKVVSGDAGSALMRDLKLAASIIEATVKAVSLP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D  + ++    L +  +  GV  + +H R         ++     + D+  
Sbjct: 151 VTLKMRMGWD--LNSLNAPELARIAQDIGVQMVTVHGRT--------RNQLYKGHADWAF 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K +   + + +NG +  +  A   L     DG+M+GR +Y    +L+ + +  ++ 
Sbjct: 201 VRQVK-DAVSIPVIVNGDINSLDDAKTALQQSGADGIMVGRGSYGKPWLLSQLMQGLTDG 259

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P      +           D+   +  +   +    +H+     G P S   R+ 
Sbjct: 260 EMEKAPSIDEQYRTITEHY-----DHMLSYYGTITGVNIARKHIGWYTKGLPASAEFRNK 314

Query: 297 LTVEA 301
           +  E 
Sbjct: 315 INREE 319


>gi|298491317|ref|YP_003721494.1| TIM-barrel protein ['Nostoc azollae' 0708]
 gi|298233235|gb|ADI64371.1| TIM-barrel protein, nifR3 family ['Nostoc azollae' 0708]
          Length = 351

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 70/319 (21%), Positives = 131/319 (41%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 34  GVTDMVFRRLVRRYAPESMMYTEMVNATGLHYVKHLPKIMEVDPNERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + +++N+GCP  ++ +   G+ L+  PD+    +  + KA+ +PVTV
Sbjct: 94  LAEAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPDVAEAIVREVVKAVDVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +DQ   + + +  K ++ +G   I +H R         +      N  ++ + +
Sbjct: 154 KTRIGWNDQE--ITILDFAKRMEDAGAQMITVHGRT--------RAQGYNGNARWEWIGQ 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+K L     DGVM  R       ++  VD +       
Sbjct: 204 VK-EVLSIPVIGNGDIFSVEAAVKCLEETGADGVMCSRGTLGYPFLVGEVDHFLKTGELL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P   +  +     +      YA         ++Q  +HM     GF  +   R  L++
Sbjct: 263 PPPNPIQRMECAREHL------YALWEYKGDRGVRQARKHMTWYAKGFVGAAELRGYLSL 316

Query: 300 EAGASTATHHIIETAFNLM 318
                     +I+ A   +
Sbjct: 317 VETVQQ-GLDLIDRAIEKL 334


>gi|254423948|ref|ZP_05037666.1| putative TIM-barrel protein, nifR3 family [Synechococcus sp. PCC
           7335]
 gi|196191437|gb|EDX86401.1| putative TIM-barrel protein, nifR3 family [Synechococcus sp. PCC
           7335]
          Length = 362

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 131/317 (41%), Gaps = 24/317 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD+ +R   R     +++YTEM+ A  +        ++     E+P+++Q+       
Sbjct: 61  GVTDKVFRRLVRRYAPQSMMYTEMVSAAELHHLQRLPILMDIDPDERPISIQLFDRRPDF 120

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  AA    D G + I++N+GCP  ++ +   G+ L+ +PD     + A+CKA+ +PVTV
Sbjct: 121 LATAACKAVDQGADTIDINMGCPVNKITKNGGGSSLLRDPDTAVRIVDAVCKAVDVPVTV 180

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  D+   +   +  + ++ +G   + +H R         +         ++ +  
Sbjct: 181 KTRIGWSDEE--INAVDFARRMESAGAQMLTLHGRT--------RAQGYTGTARWEWIAR 230

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K     + +  NG +  +  AL+ L     DG+M  R       ++  +D +       
Sbjct: 231 VKAALT-IPVIANGDIFSIESALRCLVETKADGIMCSRGTLGYPFLVGEIDHFIKTGGIR 289

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL-- 297
            +P            ++  + +Y          ++Q  +HM      FP +   R  L  
Sbjct: 290 PAPSVVERLTCAKEHLT-MLWEYKGIR-----GIRQARKHMAWYAKDFPGAAELRDRLCR 343

Query: 298 --TVEAGASTATHHIIE 312
             +VEAG       I++
Sbjct: 344 IDSVEAGCDLLDQTILQ 360


>gi|241761902|ref|ZP_04759987.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ATCC 10988]
 gi|260752443|ref|YP_003225336.1| hypothetical protein Za10_0199 [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|241373582|gb|EER63154.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ATCC 10988]
 gi|258551806|gb|ACV74752.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
          Length = 341

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 142/324 (43%), Gaps = 21/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 32  MTGVTDLPFRRIVRRY-GSGLNVTEMIASQAMIRETRQSLQKSTWDPSEEPISVQLVGCT 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E+AK+ +D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 91  PDDMAESAKLNQDRGAAIIDINMGCPVRKVVSGDAGSALMRDLKLAASIIEATVKAVSLP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D  + ++    L +  +  GV  + +H R         ++     + D+  
Sbjct: 151 VTLKMRMGWD--LNSLNAPELARIAQDIGVQMVTVHGRT--------RNQLYKGHADWAF 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K +   + + +NG +  +  A   L     DG+M+GR +Y    +L+ + +  ++ 
Sbjct: 201 VRQVK-DAVSIPVIVNGDINSLDDAKTALQQSGADGIMVGRGSYGKPWLLSQLMQGLTDG 259

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P      +           D+   +  +   +    +H+     G P S   R+ 
Sbjct: 260 EMEKAPSIDEQYRTITEHY-----DHMLSYYGTITGVNIARKHIGWYTKGLPASAEFRNK 314

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +  E         + E     + +
Sbjct: 315 INREEDPDRVKEMLAEFYRPWLSQ 338


>gi|295677642|ref|YP_003606166.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1002]
 gi|295437485|gb|ADG16655.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1002]
          Length = 358

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PDMMAEAARYNVGNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVNAVGVG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWNRENKNA--LNVARLAQAAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K    D+ +  NG +    +A ++L     D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVK-AAVDIPVVANGDITSPQKAREVLAATGADAIMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 LFRHRMNT 308


>gi|86606306|ref|YP_475069.1| dihydrouridine synthase family protein [Synechococcus sp. JA-3-3Ab]
 gi|86554848|gb|ABC99806.1| dihydrouridine synthase family protein [Synechococcus sp. JA-3-3Ab]
          Length = 346

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 133/322 (41%), Gaps = 21/322 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADISK 61
             TD+ +R   R     +L+YTEM+ A  +    +   I+     E+P+ +Q+       
Sbjct: 23  GVTDKVFRGLVRRFGPQSLVYTEMVNATGLHYARELPRIMEVGEGEQPIGIQLFDCRPHF 82

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA++  D G   +++N+GCP  ++     G+ L+  PD     + A+ KA+ +PVTV
Sbjct: 83  LAEAARMAVDEGATLVDINMGCPVNKITRNGGGSALLREPDTAARIVEAVAKAVPVPVTV 142

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G  DQ   + + +    ++++G   + +H R    +G S K         +D +  
Sbjct: 143 KTRLGWSDQE--INILDFAHRLQEAGAQLLTLHGRTRA-QGFSGK-------ARWDWIRR 192

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E+  + +  NG +     A+K L     DGVM  R       ++  +D +       
Sbjct: 193 VK-EHLRIPVIANGDIFSTDAAVKCLEETGADGVMCSRGTMGYPFLVGQIDHFLKTGQER 251

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P      +     +   + +Y          ++Q  +HM      F  + + R +L  
Sbjct: 252 PAPTPLDRIQMALEHL-RGLWEYKGER-----GIRQARKHMTWYIKDFAGASQFRALLCR 305

Query: 300 EAGASTATHHIIETAFNLMIES 321
                     ++  A     E+
Sbjct: 306 IETLQE-GEALLLQAMERCQEA 326


>gi|167752089|ref|ZP_02424216.1| hypothetical protein ALIPUT_00331 [Alistipes putredinis DSM 17216]
 gi|167660330|gb|EDS04460.1| hypothetical protein ALIPUT_00331 [Alistipes putredinis DSM 17216]
          Length = 340

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 133/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R+  +      ++YTE I +D ++R   K++  L  +  E+P+ +Q+ G  
Sbjct: 18  MEDVTDPSFRYMCKRF-GADVVYTEFISSDGLIRDAGKSLAKLRIAESERPVGIQLYGHL 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+I E    + I++N GCP  ++     G+ +M +  ++ +    + +A+  P
Sbjct: 77  VEPMVEAARIAEAADPDIIDINFGCPVKKIAGRGAGSGMMRDVPLMVEMTRRIVEAVKKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +    +   ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDEESKNIE--EIALRLQDVGIAALTIHGRT--------RAQMYRGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +A ++     VDGVMIGRA Y    +   V  +   
Sbjct: 187 IGKVKNNPAIRIPIIGNGDIDSGPKAREMFDRYGVDGVMIGRATYGRPWIFREVKHFLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P      +     ++ S+             + ++ RH+   F G PN +  R
Sbjct: 247 GEVMPQPSVAERVEIAKEHLAKSL-----EIKGDRVGILEMRRHLSNYFKGLPNFKETR 300


>gi|58583410|ref|YP_202426.1| hypothetical protein XOO3787 [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84625224|ref|YP_452596.1| hypothetical protein XOO_3567 [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188575339|ref|YP_001912268.1| tRNA-dihydrouridine synthase B [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|58428004|gb|AAW77041.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84369164|dbj|BAE70322.1| conserved hypothetical protein [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|188519791|gb|ACD57736.1| tRNA-dihydrouridine synthase B [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 332

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 136/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDPRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + ++V   + A+ +A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEELVARILTAVVQAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNG--PTIARLAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + +  
Sbjct: 186 IAQIKAAL-RIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EVLPPPSLAFVRDTLLSHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPEAQLALTRDYFDALI 321


>gi|330813858|ref|YP_004358097.1| hypothetical protein SAR11G3_00883 [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486953|gb|AEA81358.1| hypothetical protein SAR11G3_00883 [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 294

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 120/293 (40%), Positives = 173/293 (59%), Gaps = 10/293 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A L GD++ +LGF+  EKPLALQ+GG++ + L E AKI ED GY+EIN+N+GCPS
Sbjct: 1   MVSTGAALNGDREKVLGFNNFEKPLALQVGGSNKNDLAEVAKIAEDMGYDEININLGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            +V +  FGACL+  PD+V DCI +M  A  IPVT K RIG DD      L + V  +  
Sbjct: 61  KKVQKNQFGACLIKEPDLVADCIDSMVNACKIPVTAKTRIGYDDVEEFNYLNSFVNKMSN 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G   + +HAR+AILKGLSPK+N  IP L+Y +V +IK+ENP+L I +NGG+ + S+  +
Sbjct: 121 AGCKTVILHARRAILKGLSPKENLNIPKLNYPMVNQIKQENPNLEIIINGGITECSEIKE 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVMIGR  Y++   L  ++    N    +S I TR       +I   +  Y + 
Sbjct: 181 HLLHVDGVMIGRKIYQSPYFLADIEREIFN----NSEILTRA------QIVEEIVKYVSY 230

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            +  G ++ QI RH +GL+HG   S   +  L+    A  +    +     ++
Sbjct: 231 EVQKGTRVNQIMRHTVGLYHGQKGSTEWKRYLSNNMMARDSDFQKVNHILEIV 283


>gi|134047750|sp|Q92JQ6|DUS_RICCN RecName: Full=Probable tRNA-dihydrouridine synthase
          Length = 331

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 134/326 (41%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G 
Sbjct: 18  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +
Sbjct: 77  EPNVIAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMKDEQLAAKIFEATVEAVKL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  + SGV  I +H R         +      N D+D
Sbjct: 137 PVTVKMRMGWDDNTKNA--PTLAKIAESSGVQMITVHGRT--------RCQFYSGNADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y   
Sbjct: 187 FIRSVK-ESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P              A +  Y          +    +H+     G PNS   R 
Sbjct: 246 GEEKSAPSIAEQLDIVTEHYEAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +      A    I   +  ++E+
Sbjct: 301 AVNL-MNDPLAVKEKIAEFYTSVMET 325


>gi|167856275|ref|ZP_02479007.1| DNA-binding protein Fis [Haemophilus parasuis 29755]
 gi|219871522|ref|YP_002475897.1| tRNA-dihydrouridine synthase B [Haemophilus parasuis SH0165]
 gi|167852599|gb|EDS23881.1| DNA-binding protein Fis [Haemophilus parasuis 29755]
 gi|219691726|gb|ACL32949.1| tRNA-dihydrouridine synthase B [Haemophilus parasuis SH0165]
          Length = 325

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 130/300 (43%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSKLRLSHHHEIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAKI   +G   I++N+GCP+ +V++   G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PTEMAEAAKINVAYGAEIIDINMGCPAKKVNKKMAGSALLREPDLVARILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        +    +++G++ + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPENRN--CLEIANIAEQAGISALTIHGRT--------RSCLFEGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A ++L     D VMIGR +     + + + ++F   
Sbjct: 186 IKAVKQAV-SIPIIANGDITSAEKAKQVLDYTQADAVMIGRGSLGRPWLFSEIGKFFEKG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S+       +   + I      Y       G ++  + +H+         +   R  
Sbjct: 245 DLVSTLPLNDKCQLMLQHIENLHQFYGEE---KGYRI--VRKHVGWYVEQLKPNANFRRT 299


>gi|330815564|ref|YP_004359269.1| Putative TIM-barrel protein, nifR3 family protein [Burkholderia
           gladioli BSR3]
 gi|327367957|gb|AEA59313.1| Putative TIM-barrel protein, nifR3 family protein [Burkholderia
           gladioli BSR3]
          Length = 347

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 131/308 (42%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   ++A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVSAVVAAVGSG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D          + +  +++G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWDRDHKNA--LTIARLAEEAGISMLTVHGRT--------RADLYRGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  +  + +  NG +    +A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYETIAAVK-ASVKIPVVANGDITSPRKARAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +     T  +P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGETLPAPSVDEIQQLLNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 AFRHRMNT 308


>gi|91206014|ref|YP_538369.1| putative dihydrouridine synthase Dus [Rickettsia bellii RML369-C]
 gi|122425270|sp|Q1RH84|DUS_RICBR RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|91069558|gb|ABE05280.1| Putative dihydrouridine synthase Dus [Rickettsia bellii RML369-C]
          Length = 326

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 137/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EMI + A++   ++++   S          +Q+ G 
Sbjct: 18  MSGVTDLEFRRLVKRF-GAGLVVSEMIASRAMIVESRQSLQKCSIMQDDATSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVNGYSGSALMRDEGLAAKIFEAAVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DDQ        L K  ++SG+  + +H R         +      N D++
Sbjct: 137 PVTVKMRMGWDDQTKNA--PTLAKIAERSGIQMVTVHGRT--------RCQFYSGNADWE 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L     DGVM+GR AY    +++ +D Y   
Sbjct: 187 FIKNVK-EAVKIPVIANGDITNFAKAKEALEKSSADGVMVGRGAYGKPWLISQIDHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P              A +  Y          +    +HM     G PNS   R 
Sbjct: 246 GEEKPAPSIESQLDIVLEHYQAIVDYY-----GESAGVPIARKHMGWYSSGLPNSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            + +          I+E   +++
Sbjct: 301 AVNLMNDPIAVKDKIVEFYTSVI 323


>gi|295085714|emb|CBK67237.1| tRNA-U20-dihydrouridine synthase [Bacteroides xylanisolvens XB1A]
          Length = 331

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 86/328 (26%), Positives = 138/328 (42%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLICKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I +   +   E+
Sbjct: 302 R-IAMLRAETKEELFQIFDEITSQRKEN 328


>gi|152986975|ref|YP_001350893.1| hypothetical protein PSPA7_5572 [Pseudomonas aeruginosa PA7]
 gi|150962133|gb|ABR84158.1| conserved hypothetical protein [Pseudomonas aeruginosa PA7]
          Length = 332

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +++G+  + +H R         + +      +Y+ 
Sbjct: 139 VTLKIRTGWDRDNRNGVT--VARLAEQAGIQALAVHGRT--------RADLYTGEAEYET 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A K++    VD ++IGRAA     +   +D Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +     V+      ++     Y          ++   +H+       P +R  R
Sbjct: 248 EHLPAAPLPEVESILLEHLAELHLFYGEEM-----GVRIARKHVGWYLATLPGAREFR 300


>gi|150003654|ref|YP_001298398.1| dehydrogenase [Bacteroides vulgatus ATCC 8482]
 gi|149932078|gb|ABR38776.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Bacteroides vulgatus ATCC 8482]
          Length = 329

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 136/301 (45%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K +  L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSADALIRSVGKTMQKLNINDEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AAKIVE+   + +++N GCP  RV     GA ++ N  ++ +   A+   + IP
Sbjct: 77  TETMVAAAKIVEEAHPDILDINFGCPVKRVAGKGAGAGMLQNIPLMLEITRAVVDTVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNEHKIIV--DLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDITTPQRAKECFDQYGVDAIMIGRASFGRPWIFKEVKHYIET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                +           +++       +   L     +  + RH+    LF G PN +  
Sbjct: 247 GKELPALSFEWRLNVLRQEVLD-----SVNLLDERRGILHVRRHLAASPLFKGIPNFKET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|15891934|ref|NP_359648.1| nifR3-like protein [Rickettsia conorii str. Malish 7]
 gi|15619043|gb|AAL02549.1| nifR3-like protein [Rickettsia conorii str. Malish 7]
          Length = 339

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 134/326 (41%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G 
Sbjct: 26  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGC 84

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +
Sbjct: 85  EPNVIAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMKDEQLAAKIFEATVEAVKL 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  + SGV  I +H R         +      N D+D
Sbjct: 145 PVTVKMRMGWDDNTKNA--PTLAKIAESSGVQMITVHGRT--------RCQFYSGNADWD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y   
Sbjct: 195 FIRSVK-ESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P              A +  Y          +    +H+     G PNS   R 
Sbjct: 254 GEEKSAPSIAEQLDIVTEHYEAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 308

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +      A    I   +  ++E+
Sbjct: 309 AVNL-MNDPLAVKEKIAEFYTSVMET 333


>gi|167586152|ref|ZP_02378540.1| putative TIM-barrel protein, nifR3 family [Burkholderia ubonensis
           Bu]
          Length = 354

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVKQIVEAVVGAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYETIAAVKAAVG-IPVVANGDITSPQKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P+   + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPLIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|15600045|ref|NP_253539.1| hypothetical protein PA4852 [Pseudomonas aeruginosa PAO1]
 gi|107103951|ref|ZP_01367869.1| hypothetical protein PaerPA_01005022 [Pseudomonas aeruginosa PACS2]
 gi|218893946|ref|YP_002442815.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
 gi|254238426|ref|ZP_04931749.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|254244250|ref|ZP_04937572.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|313109844|ref|ZP_07795778.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
 gi|38605049|sp|Q9HUW1|DUSB_PSEAE RecName: Full=tRNA-dihydrouridine synthase B
 gi|9951123|gb|AAG08237.1|AE004898_8 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|126170357|gb|EAZ55868.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|126197628|gb|EAZ61691.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|218774174|emb|CAW29991.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
 gi|310882280|gb|EFQ40874.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
          Length = 332

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 132/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +Y+ 
Sbjct: 139 VTLKIRTGWDRDNRNGVT--VAKLAEQAGIQALAVHGRT--------RADLYTGEAEYET 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A K++    VD ++IGRAA     +   +D Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +     V       ++     Y          ++   +H+       P +R  R
Sbjct: 248 EHLPAAPLPEVQSILLEHLAELHLFYGEEM-----GVRIARKHVGWYLATLPGAREFR 300


>gi|226324186|ref|ZP_03799704.1| hypothetical protein COPCOM_01965 [Coprococcus comes ATCC 27758]
 gi|225207735|gb|EEG90089.1| hypothetical protein COPCOM_01965 [Coprococcus comes ATCC 27758]
          Length = 322

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 135/326 (41%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      LL  EMI A A+   +K    +L    +E P++LQ+ G D
Sbjct: 21  MAGVTDLPFRLLCKE-QGAGLLCMEMISAKALRYKNKNTKALLAIDPREYPVSLQLFGED 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E AK +E+  +  +++N+GCP  +V     G+ LM +P  + D +    +A+  P
Sbjct: 80  PDIISEQAKRIEELPFQILDINMGCPVPKVVRNGEGSALMKDPKRIYDIVYKTARAIKKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD    +    + K  +++G   I +H R         ++     N D++I
Sbjct: 140 VTIKIRKGFDDT--CINAPEIAKVAEEAGAAAIAVHGRT--------REQYYSGNADWEI 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +    +AL +      DGVMIGR    N  +   +  Y    
Sbjct: 190 IRKVK-EAVKIPVIGNGDVTSGQKALDMFEQTGCDGVMIGRGCQGNPWIFRELLAYEETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P   ++ +   R     +             ++++ +H+     G   S + R  
Sbjct: 249 SIPERPGTDQIRETMLRHARLQI-----EFKGDYIGIREMRKHVAWYTKGMQGSAKLRDE 303

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           +              E   NL++E +
Sbjct: 304 IN--------QVESYEELENLLMEKI 321


>gi|308048175|ref|YP_003911741.1| tRNA-U20-dihydrouridine synthase [Ferrimonas balearica DSM 9799]
 gi|307630365|gb|ADN74667.1| tRNA-U20-dihydrouridine synthase [Ferrimonas balearica DSM 9799]
          Length = 321

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 133/319 (41%), Gaps = 23/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    L  +EM+ ++ ++   +K++  +  S++    ++QI G +
Sbjct: 19  MAGVTDLPFRQLCRRL-GAGLAVSEMLSSNPLVWATEKSMARMDHSSESGIRSVQIAGCE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+ +PD+V   + A+  A+ +P
Sbjct: 78  PELMAQAAQFNVERGAQIIDINMGCPAKKVNKKLAGSALLRHPDLVRQILHAVVNAVEVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++SG+  + +H R         +        +YD 
Sbjct: 138 VTLKIRTGWDPDNRNGV--EIAQIAEQSGIAALAVHGRT--------RQCMYKGEAEYDT 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ +  + +  NG ++   +A  +L    VDG+MIGR A     +   +  Y +  
Sbjct: 188 IAAIKR-SVSIPVIANGDIDSPEKAKFVLDHTGVDGLMIGRPAQGRPWIFREIQHYLATG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
              + P      +     +      Y          ++   +H+         P  RR  
Sbjct: 247 EHLAPPSLEERKELMTGHLEHLHAFYGDER-----GMRIARKHVGWYLDNQQQPELRRQF 301

Query: 295 HILTVEAGASTATHHIIET 313
           + L        A     E 
Sbjct: 302 NALDSACAQRDALAGFFEQ 320


>gi|88858409|ref|ZP_01133051.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas tunicata D2]
 gi|88820026|gb|EAR29839.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas tunicata D2]
          Length = 323

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 133/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K++  +  S +    A+QI GAD
Sbjct: 17  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPDVWKTEKSMNRMDHSGESGIRAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   +++N+GCP+ +V++   G+ L+  PD+V + I A+  A+ +P
Sbjct: 76  PELMAQAAQFNVANGAQIVDINMGCPAKKVNKKLAGSALLQYPDLVEEIIKAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         K        +Y  
Sbjct: 136 VTLKIRTGWDTDNRNGV--EIAKIAERNGIASLAVHGRT--------KACMYKGEAEYQT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ +  + I  NG +    +A ++L     D +MIGRAA     +      Y    
Sbjct: 186 IRDIKR-SVSIPIVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFRETAHYLQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V       I+     Y      S   ++   +H+        N  + R +
Sbjct: 245 ELLPTPDIAEVRSILMEHINHLFEFY-----GSVMGVRIARKHVSWYLQAHDNEGQFRRV 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                  +      +E  F  +
Sbjct: 300 FNALETNNQ-QVSALEKYFETL 320


>gi|226493267|ref|NP_001141027.1| hypothetical protein LOC100273106 [Zea mays]
 gi|194702264|gb|ACF85216.1| unknown [Zea mays]
 gi|195645254|gb|ACG42095.1| tRNA-dihydrouridine synthase A [Zea mays]
          Length = 425

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 114/332 (34%), Positives = 174/332 (52%), Gaps = 19/332 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 63  MMDWTDNHYRTLARLISRHAWLYTEMVVAETIVHQKDNLDRFLAFPEEQHPIVLQIGGSN 122

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++  D+ Y+EINLN GCPS +V     FGA LM +P+ VGD ++ +     +
Sbjct: 123 LENLAKATELANDYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSTIAANCDV 182

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V  +  KS      IHARKA+L GLSP +NRKIP L Y
Sbjct: 183 PVSVKCRIGVDDRDSYEELCEFVDKVISKSPTRHFIIHARKALLSGLSPAENRKIPPLKY 242

Query: 177 DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ P++   LNGG+ ++   +  +     GVM+GRAAY N   ML  VD    
Sbjct: 243 EYYFALLRDFPEIKFTLNGGITNVSQVSASMRQGAHGVMVGRAAYNNPWNMLGHVDGEIY 302

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFHGFPNS 290
              T              R+I  +   Y    +   G     ++Q+ + ++ LFH  P +
Sbjct: 303 GKQTRY---------ISRRQILENYQAYGDSIIDQYGPSRPNVRQLVKPLLNLFHSEPGN 353

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              +                +E   + + +S+
Sbjct: 354 SLWKRKADSALRHCKTVKTFLEETLDAISDSV 385


>gi|157827878|ref|YP_001494120.1| nifR3-like protein [Rickettsia rickettsii str. 'Sheila Smith']
 gi|157800359|gb|ABV75612.1| nifR3-like protein [Rickettsia rickettsii str. 'Sheila Smith']
          Length = 331

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 135/326 (41%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G 
Sbjct: 18  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +
Sbjct: 77  EPNVIAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVEAVKL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  + SGV  I +H R         +      N D+D
Sbjct: 137 PVTVKMRMGWDDNTKNA--PTLAKIAESSGVQMITVHGRT--------RCQFYSGNADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y   
Sbjct: 187 FIRSVK-ESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P          +   A +  Y          +    +H+     G PNS   R 
Sbjct: 246 GEEKSAPSIAEQLDIVTKHYEAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +      A    I   +  ++E+
Sbjct: 301 AVNL-MNDPLAVKEKIAEFYTSVMET 325


>gi|188580153|ref|YP_001923598.1| tRNA-dihydrouridine synthase A [Methylobacterium populi BJ001]
 gi|179343651|gb|ACB79063.1| dihydrouridine synthase DuS [Methylobacterium populi BJ001]
          Length = 324

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 144/318 (45%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDR  R F R L+  A LYTEM+   A+L GD++ +LGF   E+P+A+Q+GG++  
Sbjct: 1   MMDWTDRQCRAFHRALSRRARLYTEMVTTGAVLHGDRERLLGFDAGEQPVAVQLGGSNPH 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AA+I  D+GY EINLNVGCPS RV EG FGACLM  P +VG+C+AAM  A+++PVT
Sbjct: 61  DLAAAARIAADYGYAEINLNVGCPSDRVQEGRFGACLMREPGLVGECVAAMKAAVAVPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCR+GVDDQ    AL  +  ++  +GV+G+ +HARKA LKGLSP++NR +P LDY  V 
Sbjct: 121 VKCRLGVDDQDIEEALDAVAGAVVAAGVDGLIVHARKAWLKGLSPRENRDVPPLDYGRVA 180

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +K+  PDL I +NGG+ D++ A   L  VDGVMIGRAAY   A+L  VD          
Sbjct: 181 RLKQVRPDLPIAVNGGIADIAAAKARLTEVDGVMIGRAAYTEPALLLDVDPELFGEAA-- 238

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                            +     A  L  G +L   TRHM+GLF+G P +R  R  L   
Sbjct: 239 -------PAADAFAAVEAFEPVVAAGLERGLRLHAYTRHMLGLFNGRPGARAYRRHLATA 291

Query: 301 AGASTATHHIIETAFNLM 318
             A+ A    +  A   +
Sbjct: 292 GMAAEADLATLREAVAKV 309


>gi|294795205|ref|ZP_06760339.1| tRNA-dihydrouridine synthase [Veillonella sp. 3_1_44]
 gi|294453997|gb|EFG22372.1| tRNA-dihydrouridine synthase [Veillonella sp. 3_1_44]
          Length = 328

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 144/324 (44%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++
Sbjct: 22  MAGVSDIAYRLLAKK-HGAALVCTEMVSAMGIKYKNERTHELLRIEEAERPVSMQIFGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +P
Sbjct: 81  PEAIALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAIDVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  
Sbjct: 141 VTVKMRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   A ++L     D VM+GR A  N  +   +  Y +  
Sbjct: 191 IKAVK-EAVSVPVLGNGDIVNPEDAKQMLDETGCDAVMVGRGAQGNPWIFGRIHHYLATG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          +       D   ++      +++I  H      G P S   R+ 
Sbjct: 250 EVLPAPTDIERLDMLLKH-----FDLLCQYKGESMAVKEIRTHAGWYMKGLPESAYWRNR 304

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +       T+ H+ +E+   ++ E
Sbjct: 305 VNT-IHTVTSFHNELESYRKILSE 327


>gi|255536036|ref|YP_003096407.1| tRNA dihydrouridine synthase B [Flavobacteriaceae bacterium
           3519-10]
 gi|255342232|gb|ACU08345.1| tRNA dihydrouridine synthase B [Flavobacteriaceae bacterium
           3519-10]
          Length = 332

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 143/325 (44%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    L+Y+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MHGADLMYSEFISSEGLIRDAMKSRKKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIVE    + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMALSAKIVEAVEPDIVDINFGCPVKKVVCKGAGAGVLKDIDLMIRLTKAVVSSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + +  + + +++ GV  + IHAR         +        D++ 
Sbjct: 138 VTVKTRLGWDTEG--INIMEVAERLQEVGVKALTIHART--------RAQMYKGEADWNY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ +K   N ++ I  NG ++   +AL+       DG+MIGR A     +   V  +F+ 
Sbjct: 188 IHAVKNNPNIEIPIFGNGDVDSPEKALEYKQKYDCDGIMIGRGAIGYPWIFNEVKHFFAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  ++  +   R+ +    ++    L     L ++ +H    F G P+ +  R 
Sbjct: 248 GEKLPEPTISQRLEAV-RQHAEWSMEWKGERLG----LIEMRQHYSNYFRGIPHFKDFRR 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
                         +I  A +   E
Sbjct: 303 KFLEVFTLDEMD-EVIAEADDFYKE 326


>gi|168830124|gb|ACA34352.1| tRNA-dihydrouridine synthase [Paenibacillus polymyxa]
          Length = 342

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 83/323 (25%), Positives = 151/323 (46%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAIIHGNKRTREMLFVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK+V ++   + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +++S 
Sbjct: 77  RKSLVEAAKVVNQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVVESVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +          ++++++G   + +H R         ++     + ++D
Sbjct: 137 PVTVKMRIGWDSEHIYAV--ENARAVERAGGQAVSVHGRT--------REQLYTGHANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K E   + +  NG +     A ++  L + DGVMIGR A  N  ML    EY   
Sbjct: 187 IIKEVK-EAVSIPVIGNGDVASPEDARRMLDLTNCDGVMIGRGALGNPWMLYRTIEYLQT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     I+    D           ++++ +H+     GF  S R + 
Sbjct: 246 GELLPDPSPEEKIR-----IAILHMDRLVALKGEAVAVREMRKHLAWYLKGFKGSARIKD 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
           ++  E         I++   + +
Sbjct: 301 VIMEETKRDDM-VRILDQFVSQL 322


>gi|260439202|ref|ZP_05793018.1| tRNA-dihydrouridine synthase B [Butyrivibrio crossotus DSM 2876]
 gi|292808217|gb|EFF67422.1| tRNA-dihydrouridine synthase B [Butyrivibrio crossotus DSM 2876]
          Length = 320

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 134/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +     + TEM+ A A+L  +K    +L    +E P ALQ+ G+D
Sbjct: 17  MAGVTDLPYRLICKEM-GCDYMVTEMVSAKAVLYNNKNTDILLQTLPEEAPSALQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A  +E  G+   ++N+GCP  ++     G+ LM NP + G  +  M K ++ P
Sbjct: 76  PEIMADIALRLEPLGFAAFDINMGCPVPKIVNNGEGSSLMKNPSLAGKIVDTMVKKITKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++   V        +++SG   + +H R         ++       D+DI
Sbjct: 136 VTVKFRKGFDEE--HVNAVEFAHIMEESGAAAVTVHGRT--------REQFYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +     ALK+      DG+ +GR A  N  +   +       
Sbjct: 186 IAAVK-DKVKIPVFGNGDIFSSEDALKMFHYTGCDGIAVGRGAKGNPWLFREIKAAIHGD 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +  + P  T + KD  +K +  MT+Y   ++     ++++ +H+     G  N    R
Sbjct: 245 VIPARPSLTEI-KDMIKKHATLMTEYKPEYM----VVREMRKHVSWYTTGLHNCAALR 297


>gi|325529035|gb|EGD06045.1| tRNA-dihydrouridine synthase B [Burkholderia sp. TJI49]
          Length = 355

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKKL-GAGYAVSEMVASNAQLWKSAKTMRRANHTGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--IARLAEAAGISMLTVHGRT--------RADLYRGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|300691712|ref|YP_003752707.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum PSI07]
 gi|299078772|emb|CBJ51432.1| tRNA-dihydrouridine synthase A [Ralstonia solanacearum PSI07]
          Length = 302

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 119/296 (40%), Positives = 170/296 (57%), Gaps = 11/296 (3%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+   A+L GD    L F   E P+ALQ+GG++   L ++A++ E +GY EINLN GCPS
Sbjct: 1   MVTTGALLHGDVPRHLDFDEMEHPVALQLGGSEPGDLAQSARLGERWGYREINLNCGCPS 60

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G+FGACLM  P +V DC+ AM   +SIPVTVK RIG+D       +R+ V +I +
Sbjct: 61  ERVQRGAFGACLMAEPKLVADCVKAMRDTVSIPVTVKHRIGIDAIETYDFVRDFVGTIAE 120

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G     +HAR AILKGLSPK+NR+IP L Y++VY++K++ P L I LNGG++ + Q   
Sbjct: 121 AGCETFIVHARNAILKGLSPKENREIPPLRYEVVYQLKRDFPQLEILLNGGVQALEQIDA 180

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L  VDGVMIGR AY +  ++ + D  +    T  +P +  V+          M DY  R
Sbjct: 181 HLAHVDGVMIGREAYHHPHLMASFDARYYGADT-VAPTRAEVEDA--------MVDYIGR 231

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            +  GG      RHM+GL+ G   +R  R +L+     +      ++ A  L   +
Sbjct: 232 WVERGGYAGAAVRHMLGLYRGVAGARGWRRVLSD--AKALGRVKTLDDARALFETA 285


>gi|224025557|ref|ZP_03643923.1| hypothetical protein BACCOPRO_02297 [Bacteroides coprophilus DSM
           18228]
 gi|224018793|gb|EEF76791.1| hypothetical protein BACCOPRO_02297 [Bacteroides coprophilus DSM
           18228]
          Length = 327

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 142/328 (43%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K +L    S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSADALIRSVSKTLLKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + ++LN GCP  RV     G+ L+ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAARIVEQAKPDILDLNFGCPVKRVAGKGAGSGLLQNIPKMLEITRAVVNAVRIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAEHKIIV--PLAEQLQDCGIEALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD +M+GRA++    +   +  +   
Sbjct: 187 IGEVKNNPRMRIPIIGNGDVTTPQRAQECFDRYGVDAIMVGRASFGRPWIFKEIKHFLQT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+  +   D  R+        +   L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFQWRMDVLRQEVKD----SVALLDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R      A     T   +    N + E+
Sbjct: 302 R-----IAMLRAETLEELNAILNHIEEN 324


>gi|56552023|ref|YP_162862.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|56543597|gb|AAV89751.1| TIM-barrel protein, nifR3 family [Zymomonas mobilis subsp. mobilis
           ZM4]
          Length = 341

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 142/324 (43%), Gaps = 21/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 32  MTGVTDLPFRRIVRRY-GSGLNVTEMIASQAMIRETRQSLQKSTWDPYEEPISVQLVGCT 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E+AK+ +D G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 91  PDDMAESAKLNQDRGAAIIDINMGCPVRKVVSGDAGSALMRDLKLAASIIEATVKAVSLP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D  + ++    L +  +  GV  + +H R         ++     + D+  
Sbjct: 151 VTLKMRMGWD--LNSLNAPELARIAQDIGVQMVTVHGRT--------RNQLYKGHADWAF 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K +   + + +NG +  +  A   L     DG+M+GR +Y    +L+ + +  ++ 
Sbjct: 201 VRQVK-DAVSIPVIVNGDINSLDDAKTALQQSGADGIMVGRGSYGKPWLLSQLMQGLTDG 259

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P      +           D+   +  +   +    +H+     G P S   R+ 
Sbjct: 260 EMEKAPSIDEQYRTITEHY-----DHMLSYYGTITGVNIARKHIGWYTKGLPASAEFRNK 314

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +  E         + E     + +
Sbjct: 315 INREEDPDRVKEMLAEFYRPWLSQ 338


>gi|302876583|ref|YP_003845216.1| TIM-barrel protein, nifR3 family [Clostridium cellulovorans 743B]
 gi|307687258|ref|ZP_07629704.1| TIM-barrel protein, nifR3 family [Clostridium cellulovorans 743B]
 gi|302579440|gb|ADL53452.1| TIM-barrel protein, nifR3 family [Clostridium cellulovorans 743B]
          Length = 321

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 67/323 (20%), Positives = 137/323 (42%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R    L     L+YTEM+ A  +  G +    +L    +E+P+A+QI G D
Sbjct: 17  MAGVTDSPFRTLC-LEQGCGLVYTEMVSAKGLFYGSENTEALLKVIDEERPVAVQIFGRD 75

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +A +  +    +  I++N+GCP+ ++ +   G+ LM  P++  + +  +    S 
Sbjct: 76  PYIMAKACEYFDKKDEFCIIDVNMGCPAPKIVKNGEGSALMKEPELAYEIVKTLKNTTSK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      K I+++G + I +H R         +        D++
Sbjct: 136 PVTVKFRKGFDED--NINAVEFAKVIEEAGADAIAVHGRT--------RAQMYQGKADWN 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++KK    + +  NG +     A     + + DG+M+ R +  N  +   + +  SN
Sbjct: 186 IIAQVKKAVT-IPVIGNGDVFSHEDAQNLIHISNCDGIMVARGSQGNPWLFNQIKQKLSN 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     ++D          M++           ++++ +H+     G  +    R+
Sbjct: 245 EEIKYPTGAEKIDMCIRHYQLELMSN------EEVKAVREMRKHIAFYVKGLKDCTVIRN 298

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            +  E  A      +++   N++
Sbjct: 299 AVNYETDAKKVIDLLLKYKENII 321


>gi|78186164|ref|YP_374207.1| dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           luteolum DSM 273]
 gi|78166066|gb|ABB23164.1| tRNA-U20-dihydrouridine synthase [Chlorobium luteolum DSM 273]
          Length = 354

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 82/318 (25%), Positives = 144/318 (45%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE + A+A+ RG +K +  L     E+PLA+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKR-HGADIVYTEFVSAEALRRGIEKTVRKLKADPVERPLAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I E+F  + +++N GCP+ +V     GA L+  P+ +     A+ KA+ +P
Sbjct: 76  VESMVEAAVIAEEFQPDYLDINFGCPTKKVAGKGAGAALLKEPEKMAAIAEAVVKAVRLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D +  ++ + ++++ ++ +G+  + +H R         + +      D+  
Sbjct: 136 VTAKTRIGWDHE--SINILDVLRRLEDAGIQALALHGRT--------RSDMYKGKADWGW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K+    + +  NG +     AL++      DGVMIGR +  N  + +         
Sbjct: 186 IAEAKRHA-RIPLIANGDVWSPEDALRMFLETGADGVMIGRGSIGNPFIFSGTKHLLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRRCR 294
                P       DF  +I A++          G K    ++ RH      G P     R
Sbjct: 245 TPPPPP-------DFRLRIKAAIEHLQLSVEFKGEKYGTLEMRRHYATYLKGLPKVSVVR 297

Query: 295 HILTVEAGASTATHHIIE 312
           + L  E         ++E
Sbjct: 298 NKLVREEDWRAVESILLE 315


>gi|192361714|ref|YP_001983204.1| tRNA-dihydrouridine synthase [Cellvibrio japonicus Ueda107]
 gi|190687879|gb|ACE85557.1| tRNA-dihydrouridine synthase [Cellvibrio japonicus Ueda107]
          Length = 329

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 135/322 (41%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ AD+ L   +K+ L    + + +P+A+QI G D
Sbjct: 18  MAGVTDRPFRQLCREL-GAGMVVSEMLTADSTLWSSRKSSLRMDHTGEAEPIAVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++    G   I++N+GCP+ +V + + G+ L+ +  +V   + A+ KA+ +P
Sbjct: 77  PEMLAEAARLNAANGAQIIDINMGCPAKKVCKKAAGSALLQDEPLVASILEAVVKAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   ++       + +  + SG+  + +H R         + +    + +YD 
Sbjct: 137 VTLKFRTGWSSEVRNA--LRIARIAEDSGIQALALHGRT--------RADGFAGSAEYDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +    + +  NG +    +A  +L       VMIGRAA     +   ++ Y    
Sbjct: 187 IASVVQAV-KIPVFANGDIASPEKAKAVLQHTGAAAVMIGRAAQGRPWIFREIEHYLRTG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
                P  T+V       +      Y           +   +H+       P+S   R  
Sbjct: 246 EQLPEPPLTQVRDILSTHLRELYAFY-----GEVMGPRIARKHVGWYLQTVPDSESFRKA 300

Query: 295 -HILTVEAGASTATHHIIETAF 315
            + +       T+  H  E   
Sbjct: 301 FNAIEHAEVQQTSVQHFFEQLL 322


>gi|165932567|ref|YP_001649356.1| tRNA-dihydrouridine synthase [Rickettsia rickettsii str. Iowa]
 gi|165907654|gb|ABY71950.1| tRNA-dihydrouridine synthase [Rickettsia rickettsii str. Iowa]
          Length = 339

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 135/326 (41%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G 
Sbjct: 26  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGC 84

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +
Sbjct: 85  EPNVIAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVEAVKL 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  + SGV  I +H R         +      N D+D
Sbjct: 145 PVTVKMRMGWDDNTKNA--PTLAKIAESSGVQMITVHGRT--------RCQFYSGNADWD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y   
Sbjct: 195 FIRSVK-ESVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P          +   A +  Y          +    +H+     G PNS   R 
Sbjct: 254 GEEKSAPSIAEQLDIVTKHYEAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 308

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +      A    I   +  ++E+
Sbjct: 309 AVNL-MNDPLAVKEKIAEFYTSVMET 333


>gi|313676850|ref|YP_004054846.1| tRNA-u20-dihydrouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312943548|gb|ADR22738.1| tRNA-U20-dihydrouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 332

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 134/325 (41%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE I ++ ++R   K+   L     EKP+ +QI G D
Sbjct: 19  MEDVSDPPFRAVCKE-NGADLMYTEFISSEGLIRDAIKSRQKLDIFDYEKPIGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  A  IV     + +++N GCP  +V     GA ++ + D++     A+ K+  +P
Sbjct: 78  EEAMSMATSIVNVTQPDLVDINFGCPVKKVVTKGAGAGVLKDVDLMVRLTEAVVKSTDLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    + + ++  G+  + IH R         +        D+ +
Sbjct: 138 VTVKTRLGWDESSKNIE--EVAERLQDVGIKALSIHGRT--------RQQMYKGEADWSL 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K     ++ I  NG ++   +AL+      VDG+MIGRAA     +   +  YF  
Sbjct: 188 IAKVKNNPRINIPIFGNGDIDSPQKALEYRNRYGVDGLMIGRAAIGYPWIFNEIKHYFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +   + +      ++         + ++ RH    F G P+ +  R 
Sbjct: 248 GEVLPPPNLEDRIETAKKHLK-----FSVEWKGEKLGIFEMRRHYTNYFKGIPHFKPYRT 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L          +  +    + + E
Sbjct: 303 RLVE-----GENYQAVLDTLDEVQE 322


>gi|160884735|ref|ZP_02065738.1| hypothetical protein BACOVA_02724 [Bacteroides ovatus ATCC 8483]
 gi|156109770|gb|EDO11515.1| hypothetical protein BACOVA_02724 [Bacteroides ovatus ATCC 8483]
          Length = 331

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 138/328 (42%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   +  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEIKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I +   +   E+
Sbjct: 302 R-IAMLRAETKEELFRIFDEITSQRKEN 328


>gi|237748976|ref|ZP_04579456.1| tRNA-dihydrouridine synthase [Oxalobacter formigenes OXCC13]
 gi|229380338|gb|EEO30429.1| tRNA-dihydrouridine synthase [Oxalobacter formigenes OXCC13]
          Length = 324

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 136/326 (41%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  A+ +LR   K+        + +P A+QI G+D
Sbjct: 17  MAGITDRPFRQLCKKL-GAGYAVSEMAAANPLLRNTPKSRRRIIHEGEVEPRAVQIVGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + ++A+   D G   I++N+GCP+ +V     G+ L+ N  +VG  + A+  A+S+P
Sbjct: 76  PATMADSARYNVDQGAQIIDINMGCPAKKVCNNWCGSALLQNEPLVGQILEAVTDAVSVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D     +    + K  + +G+  + +H R         +++      +YD 
Sbjct: 136 VTLKFRTGWDR--SHINAPEIAKIAESAGIAALTLHGRT--------REDAYRGMAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  NG ++   +A  +L     D +MIGR A     +   +D +  N 
Sbjct: 186 IAEVK-SLVSIPVVANGDIDSPEKAKAVLEKTGADAIMIGRGAQGKPWIFREIDYFLKND 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +     +      Y          ++   +H+       P+  + R  
Sbjct: 245 AFLPPPDFNEIRQIMHEHLQEHYAFYGEA-----VGVRTARKHIGWYAKNLPDGEKLRSA 299

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
               A       + ++  F  +++ L
Sbjct: 300 -ANHAQTCEEQINEVDRFFMTLLQGL 324


>gi|153807028|ref|ZP_01959696.1| hypothetical protein BACCAC_01305 [Bacteroides caccae ATCC 43185]
 gi|149130148|gb|EDM21358.1| hypothetical protein BACCAC_01305 [Bacteroides caccae ATCC 43185]
          Length = 331

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 84/322 (26%), Positives = 135/322 (41%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPQMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   +  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEMKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVIDSVNL----LDERKGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAF 315
           R I  + A        I     
Sbjct: 302 R-IAMLRAETKEELFQIFNEIL 322


>gi|167763922|ref|ZP_02436049.1| hypothetical protein BACSTE_02304 [Bacteroides stercoris ATCC
           43183]
 gi|167698038|gb|EDS14617.1| hypothetical protein BACSTE_02304 [Bacteroides stercoris ATCC
           43183]
          Length = 325

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 142/325 (43%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKGF-GADMVYTEFVSSDALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVADAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAGSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPQRAKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+ +    +  R+        + + L     +  + RH+    LF G PN R  
Sbjct: 247 GE-EIPPLSSEWKLNVLRQEVED----SVKLLDERRGILHVRRHLAASPLFKGIPNFRET 301

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A      + I      L+
Sbjct: 302 R-IAMLRAETKEELYRIFNEIEKLI 325


>gi|332970947|gb|EGK09921.1| tRNA-dihydrouridine synthase [Desmospora sp. 8437]
          Length = 335

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/310 (25%), Positives = 138/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  AR      L+  EM+   AIL G+ +   +L    +EKPL+LQI G D
Sbjct: 22  MAGVCNPAFRLIAREF-GTGLVCAEMVSDKAILHGNARTKKMLLVDEREKPLSLQIFGGD 80

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA++V+     + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +A+  
Sbjct: 81  KETLVEAARVVDKQTNADIIDINMGCPVPKVIKCDAGARWLLDPNKIEEMVSAVVEAVDK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+           K+++++G   + +H R         +        D+D
Sbjct: 141 PVTVKMRTGWDENHIYAV--ENAKALERAGAQAVSLHGRT--------RQQMYTGKADWD 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG ++    A ++L     DGVMIGRAA  N  ML     Y S 
Sbjct: 191 IIRQVK-EAVKIPVIGNGDVQTPQDAKRMLDTTGCDGVMIGRAALGNPWMLYRTIHYLST 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           +I+    D           ++++ +H      G   + R + 
Sbjct: 250 GELLPEPTPKEKV-----EIALLHMDRLIALRGEEVAVREMRKHASWYLRGMRGAARIKD 304

Query: 296 ILTVEAGAST 305
            +  +     
Sbjct: 305 QVNEQTTREG 314


>gi|83720266|ref|YP_441799.1| dihydrouridine synthase [Burkholderia thailandensis E264]
 gi|167580621|ref|ZP_02373495.1| dihydrouridine synthase [Burkholderia thailandensis TXDOH]
 gi|167618727|ref|ZP_02387358.1| dihydrouridine synthase [Burkholderia thailandensis Bt4]
 gi|257137966|ref|ZP_05586228.1| dihydrouridine synthase [Burkholderia thailandensis E264]
 gi|83654091|gb|ABC38154.1| dihydrouridine synthase [Burkholderia thailandensis E264]
          Length = 355

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVDAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + K  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAV--KIAKLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPQKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQGGELLPPPRIDEIRQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|154489885|ref|ZP_02030146.1| hypothetical protein PARMER_00114 [Parabacteroides merdae ATCC
           43184]
 gi|154089327|gb|EDN88371.1| hypothetical protein PARMER_00114 [Parabacteroides merdae ATCC
           43184]
          Length = 343

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 140/319 (43%), Gaps = 24/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRF-GADMVYTEFVSADALIRSVNKTQQKLNVADEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+I E    + +++N GCP  RV     GA ++ N  ++ D    + KA++IP
Sbjct: 77  VPTMVEAAQICEAAHPDILDINFGCPVKRVAGKGAGAGMLRNIPLMLDITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRIIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +       +      VD VMIGR +     +   V  Y   
Sbjct: 187 IGEVKNNPRIQIPIIGNGDVTSAEICKQRFEQYGVDAVMIGRGSIGRPWIFREVRHYLDT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             T  +   +     ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GETLPAESFS-----WYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGIADFKQT 301

Query: 294 RHILTVEAGASTATHHIIE 312
           R +  + A    A   I++
Sbjct: 302 R-VAMLRAETVEALFDILD 319


>gi|289663593|ref|ZP_06485174.1| hypothetical protein XcampvN_11094 [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 332

 Score =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 138/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D    G +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTISDRRFWGTRKSLHRMDHAGEPDPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++P
Sbjct: 76  PQQLAEAARYNVDHGAQLIDINMGCPAKKVCNAWAGSALMRDEDLVARILTAVVRAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D       +  + +  +  G+  + +H R         +D     + +Y  
Sbjct: 136 VTLKIRTGWDCDHRNGPV--IARIAQDCGIAALAVHGRT--------RDQHYTGSAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   V  + +  
Sbjct: 186 IAQIKAAL-QIPVVANGDIDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P S   R +
Sbjct: 245 EVLPPPSLAFVRDTLLSHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    A   +    F+ +I
Sbjct: 300 VN-RAETPEAQLALTRDYFDALI 321


>gi|268315976|ref|YP_003289695.1| TIM-barrel protein, nifR3 family [Rhodothermus marinus DSM 4252]
 gi|262333510|gb|ACY47307.1| TIM-barrel protein, nifR3 family [Rhodothermus marinus DSM 4252]
          Length = 358

 Score =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 141/325 (43%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      +++TE I +  ++   +  +  L    +E+P+ +QI G +
Sbjct: 18  MEDVSDPPFRLLCKRY-GADMVFTEFISSGGLVHESEDAVKKLDIYDEERPVGIQIFGGE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + ++ EAA+IV+  G + I++N GCP  +V     GA ++ + + +     A+ +  + P
Sbjct: 77  LEQVREAARIVDQIGPDVIDINFGCPVRKVVCKDAGAGVLRDLNKMRALTEAVIEVATRP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD+  ++ +  + + ++  GV  + +HAR         +      +  ++ 
Sbjct: 137 VTVKTRLGWDDR--SIRILEVARMLEDCGVQALTVHART--------RAQMYKGSARWEW 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG      +  ++     VDGVMIGR A  N  +      Y    
Sbjct: 187 LRRLKELGLSIPIIGNGDALTPEKVKQMFDETGVDGVMIGRGAIGNPWIFRDAKIYMETG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +     + A   +   + L     + ++ R   G F GFP + R R +
Sbjct: 247 ELPPPPSWEERVR-----VVAEHLELKCQWLGERKGVLEMRRMYGGYFKGFPGASRLRQL 301

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           L  +   +     ++E   N   + 
Sbjct: 302 LMDKETKA----EVLEILLNFRPDD 322


>gi|218131619|ref|ZP_03460423.1| hypothetical protein BACEGG_03239 [Bacteroides eggerthii DSM 20697]
 gi|217985922|gb|EEC52261.1| hypothetical protein BACEGG_03239 [Bacteroides eggerthii DSM 20697]
          Length = 327

 Score =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 135/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKNF-GADMVYTEFVSSDALIRSVSKTEQKLKISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   ++  A+ IP
Sbjct: 77  TDTMVEAARIVEQAHPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRSVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDASNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E++      + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVRNNPRMHIPIIGNGDITTPQRAKECFDRYGVDAIMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+ +    +  R+        + + L     +  + RH+    LF G PN R  
Sbjct: 247 GEEMP-PLSSEWKLNVLRQEVED----SVKLLDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|116053000|ref|YP_793318.1| hypothetical protein PA14_64180 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|296391685|ref|ZP_06881160.1| hypothetical protein PaerPAb_26189 [Pseudomonas aeruginosa PAb1]
 gi|115588221|gb|ABJ14236.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 332

 Score =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +++G+  + +H R         + +      +Y+ 
Sbjct: 139 VTLKIRTGWDRDNRNGV--SVARLAEQAGIQALAVHGRT--------RADLYTGEAEYET 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A K++    VD ++IGRAA     +   +D Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +     V       ++     Y          ++   +H+       P +R  R
Sbjct: 248 EHLPAAPLPEVQSILLEHLAELHLFYGEEM-----GVRIARKHVGWYLATLPGAREFR 300


>gi|46202328|ref|ZP_00053405.2| COG0042: tRNA-dihydrouridine synthase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 335

 Score =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 74/326 (22%), Positives = 147/326 (45%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD   R   + L    L+ +EMI + A++R +++ +     + +E P+++Q+ G +
Sbjct: 25  MAGVTDMPNRRLVKRL-GAGLVVSEMIASQAMIRQNRQTMQMAQHTAEEFPMSVQLAGCE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAAK+ +D G   I++N+GCP  +V  +G  G+ LM N ++    ++A+ KA+ I
Sbjct: 84  PKVMAEAAKLNQDLGVAIIDINMGCPVKKVALKGEAGSALMRNENLAARIMSAVVKAVDI 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D         +L +  ++ G+  + +H R         ++       D+ 
Sbjct: 144 PVTLKMRTGWDMNSRNA--PSLARVAEECGIRMVTVHGRT--------RNQMYTGQADWA 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K+    + +  NG +E +  A+++L     DGVMIGR  Y    +   V  + + 
Sbjct: 194 FIGEVKRAV-SIPVIGNGDVESIDDAVRMLELSDADGVMIGRGTYGRPWLPGQVAHFLAT 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P +    +     + A ++ Y +        ++   +H+     G P S   R 
Sbjct: 253 GERLPDPSRAEQLEIMLGHLDAMLSHYGSE-----PGVRIARKHVAWYSKGLPGSAEFRA 307

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +      +     II+    ++ ++
Sbjct: 308 EINRTNDPAIMRQSIIDFYAPILEKA 333


>gi|161525860|ref|YP_001580872.1| NifR3 family TIM-barrel protein [Burkholderia multivorans ATCC
           17616]
 gi|189349419|ref|YP_001945047.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans ATCC
           17616]
 gi|221202292|ref|ZP_03575326.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2M]
 gi|221209106|ref|ZP_03582100.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2]
 gi|221214496|ref|ZP_03587467.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD1]
 gi|160343289|gb|ABX16375.1| TIM-barrel protein, nifR3 family [Burkholderia multivorans ATCC
           17616]
 gi|189333441|dbj|BAG42511.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans ATCC
           17616]
 gi|221165753|gb|EED98228.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD1]
 gi|221171010|gb|EEE03463.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2]
 gi|221177866|gb|EEE10279.1| tRNA-dihydrouridine synthase B [Burkholderia multivorans CGD2M]
          Length = 354

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKKL-GAGYAVSEMVASNAQLWKSAKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--IARLAEAAGISMLTVHGRT--------RADLYRGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYETIAAVK-AAVRIPVVANGDITSPAKAKAVLEATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 AFRHRMNT 308


>gi|237721929|ref|ZP_04552410.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|229448798|gb|EEO54589.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
          Length = 331

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 87/328 (26%), Positives = 137/328 (41%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      + YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRF-GADMAYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPERCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFDWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I E   +   E+
Sbjct: 302 R-IAMLRAETKEELFRIFEEITSQRKEN 328


>gi|299144973|ref|ZP_07038041.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 3_1_23]
 gi|298515464|gb|EFI39345.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 3_1_23]
          Length = 331

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 86/320 (26%), Positives = 135/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRF-GADMVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPQRCKECFDHYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFDWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIET 313
           R I  + A        I E 
Sbjct: 302 R-IAMLRAETKEELFRIFEE 320


>gi|206561672|ref|YP_002232437.1| putative nitrogen regulation-related protein [Burkholderia
           cenocepacia J2315]
 gi|198037714|emb|CAR53657.1| putative nitrogen regulation-related protein [Burkholderia
           cenocepacia J2315]
          Length = 355

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 126/308 (40%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PEMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|238650328|ref|YP_002916180.1| nifR3-like protein [Rickettsia peacockii str. Rustic]
 gi|238624426|gb|ACR47132.1| nifR3-like protein [Rickettsia peacockii str. Rustic]
          Length = 339

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/326 (24%), Positives = 133/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G 
Sbjct: 26  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGC 84

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ E  G   I+LN GCP+ +V  G  G+ LM +  +      A  +A+ +
Sbjct: 85  EPNVIAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGSALMRDEQLAAKIFEATVEAVKL 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  + SGV  I +H R         +      N D+D
Sbjct: 145 PVTVKMRMGWDDNTKNA--PTLAKIAESSGVQMITVHGRT--------RCQFYSGNADWD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E+  + +  NG + + ++A   L     DG+M+GR AY    +++ +D Y   
Sbjct: 195 FIRSVK-ESVKIPVIANGDITNFAKAKAALQKSGADGIMVGRGAYGKPWLISQIDHYLKT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P              A +  Y          +    +H+     G PNS   R 
Sbjct: 254 GEEKSAPSIAEQLDIVTEHYEAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 308

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +      A    I   +  ++E+
Sbjct: 309 AVNL-MNDPLAVKEKIAEFYTSVMET 333


>gi|157803198|ref|YP_001491747.1| nifR3-like protein [Rickettsia canadensis str. McKiel]
 gi|157784461|gb|ABV72962.1| nifR3-like protein [Rickettsia canadensis str. McKiel]
          Length = 326

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 139/326 (42%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   ++++              +Q+ G 
Sbjct: 18  MSGVTDLEFRRLVKRF-GVGLVVSEMVASRAMIVESRQSLQKSAIMRDDATSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V EG  G+ LM +  +      A  KA+ I
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVEGYSGSALMRDEQLAAKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DDQ        L    + SG+  + +H R         +      N D+D
Sbjct: 137 PVTVKMRMGWDDQTKNA--PTLANIAENSGIQMVTVHGRT--------RCQFYSGNADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E  ++ +  NG + + ++A + L     DG+MIGR AY    +++ +D Y   
Sbjct: 187 FIRSVK-EVVNIPVIANGDITNFTKAKEALQKSGADGIMIGRGAYGKPWLISQIDHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P              A +  Y          +    +H+     G PNS   R 
Sbjct: 246 GEAKPAPSIAEQLDIVTEHYEAIIDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +    S A    I+  +  +I++
Sbjct: 301 AVNL-MNDSVAVKEKIKEFYTSIIDT 325


>gi|317474747|ref|ZP_07934021.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|316909428|gb|EFV31108.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 327

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 135/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKNF-GADMVYTEFVSSDALIRSVSKTEQKLKISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   ++  A+ IP
Sbjct: 77  TDTMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRSVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDASNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E++      + I  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVRNNPRMHIPIIGNGDITTPQRAKECFDRYGVDAIMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+ +    +  R+        + + L     +  + RH+    LF G PN R  
Sbjct: 247 GEEMP-PLSSEWKLNVLRQEVED----SVKLLDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|78065255|ref|YP_368024.1| dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia sp.
           383]
 gi|77966000|gb|ABB07380.1| tRNA-U20-dihydrouridine synthase [Burkholderia sp. 383]
          Length = 355

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P+   +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPLIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|297817686|ref|XP_002876726.1| hypothetical protein ARALYDRAFT_486864 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297322564|gb|EFH52985.1| hypothetical protein ARALYDRAFT_486864 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 405

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 110/328 (33%), Positives = 173/328 (52%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD HYR  ARL+T +A LYTEMI A+ ++    +    L FS Q+ P+ LQ+GG++
Sbjct: 44  MMEWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQANLDRFLAFSPQQHPIVLQLGGSN 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +AAK+ + +GY+EINLN GCPS +V     FG  LML P +VG+ ++A+    ++
Sbjct: 104 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVRLMLKPKLVGEAMSAIAANTNV 163

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVDD      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y
Sbjct: 164 PVTVKCRIGVDDHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKY 223

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  Y + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N   ML  VD    
Sbjct: 224 EYFYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNNPWQMLGHVDTAVY 283

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P +    +    +           H +    ++ + + ++ LFH    +   +
Sbjct: 284 G-----VPSRGLTRRQVLEQYQVYGDSVLGTHGNGRPNVRDLVKPLLNLFHSENGNSLWK 338

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                      +   ++E +   + + +
Sbjct: 339 RRADAAFKECRSVGSLLEESLRAIPDCV 366


>gi|298482601|ref|ZP_07000786.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. D22]
 gi|298271308|gb|EFI12884.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. D22]
          Length = 331

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 138/328 (42%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   +  Y   
Sbjct: 187 IGEVKNNPRIHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEIKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I +   +   E+
Sbjct: 302 R-IAMLRAETKEELFRIFDEITSQRKEN 328


>gi|291515732|emb|CBK64942.1| tRNA-U20-dihydrouridine synthase [Alistipes shahii WAL 8301]
          Length = 340

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 136/319 (42%), Gaps = 21/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R+  +      ++YTE I +D ++R   K++  L     E+P+ +QI G  
Sbjct: 18  MEDVTDPSFRYMCKRF-GADMVYTEFISSDGLIRDAAKSLKKLEIDDAERPVGIQIYGHL 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAA++ E  G + I++N GCP  ++     G+ +M +  ++ +    +  A+  P
Sbjct: 77  IDPMVEAARMAEAAGPDVIDINFGCPVKKIAGRGAGSGMMRDVPLMVEMTRRIVAAVKKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +    +   ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDEESKNIE--EIALRLQDVGIAALTIHGRT--------RAQMYRGEADWTL 186

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +A ++     VDGVMIGRA Y    +   V  Y S 
Sbjct: 187 IGKVKNNPQIRIPIIGNGDVDSGPKAREMFDRYGVDGVMIGRATYGRPWIFREVKHYLST 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +  S+             + ++ RHM   F G P+ +  R 
Sbjct: 247 GEALPQPSVAERVAIAKEHLQKSL-----EIKGDHVGILEMRRHMTNYFKGLPDFKSTRL 301

Query: 296 ILTVEAGASTATHHIIETA 314
            L      +     + E A
Sbjct: 302 KLVTSLDTAELFATLDEIA 320


>gi|209517509|ref|ZP_03266349.1| TIM-barrel protein, nifR3 family [Burkholderia sp. H160]
 gi|209502042|gb|EEA02058.1| TIM-barrel protein, nifR3 family [Burkholderia sp. H160]
          Length = 353

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PDMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVNAVGVG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWNRENKNA--LNVARLAQAAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A ++L     D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVK-AAVRIPVVANGDITSPQKAREVLAATGADAIMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 LFRHRMNT 308


>gi|313206097|ref|YP_004045274.1| tRNA-u20-dihydrouridine synthase [Riemerella anatipestifer DSM
           15868]
 gi|312445413|gb|ADQ81768.1| tRNA-U20-dihydrouridine synthase [Riemerella anatipestifer DSM
           15868]
 gi|315023721|gb|EFT36724.1| tRNA dihydrouridine synthase B [Riemerella anatipestifer RA-YM]
 gi|325336459|gb|ADZ12733.1| tRNA-dihydrouridine synthase [Riemerella anatipestifer RA-GD]
          Length = 325

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 142/322 (44%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    L+Y+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MHGADLMYSEFISSEGLIRDAIKSKKKLDIFDYERPIGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIVE    + +++N GCP  +V     GA ++ + D++     A+  +  +P
Sbjct: 78  EEAMAMSAKIVETVQPDLVDINFGCPVKKVVCKGAGAGVLKDIDLMVRLTKAVVNSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++++G+  + IHAR         +        D++ 
Sbjct: 138 VTVKTRLGWD--TNSINIDEVAERLQEAGIKALTIHART--------RAQMYKGEADWEH 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+  N ++ I  NG ++   +AL        DGVMIGRAA     +   V  +F  
Sbjct: 188 ISRIKQNPNIEIPIFGNGDIDSPQKALDYKNKYACDGVMIGRAAIGYPWIFNEVKHFFQT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR- 294
                 P                  +++A        L ++ +H    F G P+ +  R 
Sbjct: 248 GKLLPEPTLQDRLT-----AVRQHAEWSAEWKGERLGLIEMRQHYSNYFRGVPHFKEYRK 302

Query: 295 ---HILTVEAGASTATHHIIET 313
               ILT+E    +    IIE 
Sbjct: 303 RFLEILTLEE-MDSLISQIIEA 323


>gi|229829710|ref|ZP_04455779.1| hypothetical protein GCWU000342_01807 [Shuttleworthia satelles DSM
           14600]
 gi|229791699|gb|EEP27813.1| hypothetical protein GCWU000342_01807 [Shuttleworthia satelles DSM
           14600]
          Length = 341

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 140/321 (43%), Gaps = 26/321 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   +D  +R          L+ TEM+ A AI   ++  K +L  S +E+P++LQI G+D
Sbjct: 38  MAGVSDLPFRLLCHE-QGAGLVCTEMVSAKAIAYKNRNTKELLKVSDEERPVSLQIFGSD 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ +ED  ++ +++N+GCP  +V     G+ L+ NP + G  I A+  A+  P
Sbjct: 97  PVIMAEQARQIEDLHWDILDINMGCPVPKVFNNGDGSALLRNPLLAGQIIEAVAGAIHKP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+GV      +    +    ++SG   + +H R         +D   +   D++ 
Sbjct: 157 LTVKIRLGVSPDT--INAVEMAHIAQESGAAAVAVHGRT--------RDQFYMGAADWEQ 206

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++  +    +     VD  MI RAA  N  +   +  ++   
Sbjct: 207 IARVKQAV-SIPVIGNGDIKSPADVQAMYEQTGVDAYMIARAAQGNPWIFRQILHFYQEG 265

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R+ +  M D    +L     ++++ +       G+P S R R +
Sbjct: 266 EEPVKPGPQEMCDTMLRQ-ARMMCDLKGEYLG----IREMRKQAAWYTAGYPRSARLRGM 320

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +         T+  +E  F  
Sbjct: 321 VN-----DVETYEDLEQLFRA 336


>gi|67458404|ref|YP_246028.1| nifR3 family TIM-barrel protein [Rickettsia felis URRWXCal2]
 gi|75537122|sp|Q4UNJ4|DUS_RICFE RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|67003937|gb|AAY60863.1| Putative TIM-barrel protein, nifR3 family [Rickettsia felis
           URRWXCal2]
          Length = 325

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 137/325 (42%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF---STQEKPLALQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++              +Q+ G 
Sbjct: 18  MSDITDLEFRKLVKRF-GAGLVVSEMIASRAMVVKSRQSMQKCAIVHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDEQLAAKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G DD        +L K  + SGV  + +H R         +      N D+D
Sbjct: 137 PITVKMRMGWDDNTKNA--PDLAKIAESSGVQMVTVHGRT--------RCQFYSGNADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L     DG+M+GR AY    +++ +  Y   
Sbjct: 187 FIRSVK-EAVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLVSQIAHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P             +A +  Y          +    +H+     G P+S   R 
Sbjct: 246 GEEKPAPSIAEQLDIVTEHYNAILDYY-----GESVGVPIARKHIGWYSSGLPSSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            + +    +     I E   ++M E
Sbjct: 301 AVNLMNDPAEVKEKIAEFYTSVMKE 325


>gi|94309374|ref|YP_582584.1| dihydrouridine synthase TIM-barrel protein nifR3 [Cupriavidus
           metallidurans CH34]
 gi|93353226|gb|ABF07315.1| tRNA-dihydrouridine synthase B [Cupriavidus metallidurans CH34]
          Length = 381

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 136/324 (41%), Gaps = 27/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+++QI GA+
Sbjct: 44  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPISVQIAGAE 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            S + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 103 PSMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVEAVVAAVGDR 162

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + + ++ +G++ + IH R         + +      +Y
Sbjct: 163 VPVTLKIRTGWDREHKNA--LRVARMVEDAGISMLTIHGRT--------RADLYHGEAEY 212

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ Y  
Sbjct: 213 ETIAAVKSSI-RIPVVANGDITTPQKARHVLAVTGADAIMIGRAAQGRPWLFREIEHYLK 271

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 SP    +       ++     Y          ++   +H+     G   +   R
Sbjct: 272 TGELLPSPEVAEIRAIMNHHLADHYAFYGEF-----TGVRTARKHIAWYTRGLKGANLFR 326

Query: 295 HIL----TVEAGASTATHHIIETA 314
           H +    + +A  +       E A
Sbjct: 327 HRMNTLESTDAQLAAVNAFFDEQA 350


>gi|83749328|ref|ZP_00946325.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
 gi|83724006|gb|EAP71187.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
          Length = 382

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 131/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 43  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 101

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 102 PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 161

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + +  +++G++ + +H R         + +      +Y
Sbjct: 162 VPVTLKIRTGWDRKHRNA--LTVARIAQEAGISMLTVHGRT--------RADLYHGEAEY 211

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG +   ++A ++L     D +MIGRAA     +   ++ +  
Sbjct: 212 ETIAAVK-ASVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAAQGRPWLFREIEHFLQ 270

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 271 TGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 325

Query: 295 HILTV 299
           H +  
Sbjct: 326 HRMNT 330


>gi|171463466|ref|YP_001797579.1| dihydrouridine synthase DuS [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|171193004|gb|ACB43965.1| dihydrouridine synthase DuS [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 362

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 111/313 (35%), Positives = 175/313 (55%), Gaps = 17/313 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++WTDRH R F R LT  A+LYTEM+   A++ GD    L +S  + P+ LQ+GG++ +
Sbjct: 16  MMEWTDRHCRSFHRALTKKAVLYTEMVTTGALMHGDVPRHLDYSQDQHPVILQLGGSEPN 75

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L ++A++ + +GY+EI+LN GCPS R+  G+FGACLM  P++V +C+ +M  A+ +P++
Sbjct: 76  DLAKSAELAQQWGYDEIDLNCGCPSERMQRGAFGACLMAEPNLVAECVKSMKSAVDVPIS 135

Query: 121 VKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           VK R+G+D       +       N + ++  +G + + IHAR A+LKGLSPK+NR  P L
Sbjct: 136 VKHRLGLDSMDAAHSEADYQFALNFILAVADAGASQVTIHARNAVLKGLSPKENRSRPPL 195

Query: 175 DYDIVYEIKKE----NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
            Y++  +++ +     P L + LNGGLE   Q        DG M+GRAAY   A+L   D
Sbjct: 196 RYEVAAKLRLDAQIHFPKLKVLLNGGLETNEQIAGHWNGFDGFMVGRAAYHFPALLLGWD 255

Query: 231 EYFSNPLTG-----SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           +  +          S     R+     +++ A   +   +       +   TRH++GL H
Sbjct: 256 DMITTDGDAAGYLFSESEWHRIQIALVKQVHAWFDE--CQSKGKPFYIGVFTRHILGLAH 313

Query: 286 GFPNSRRCRHILT 298
           G   SR  R  L+
Sbjct: 314 GRAGSRYWRQRLS 326


>gi|257453865|ref|ZP_05619143.1| tRNA-dihydrouridine synthase B [Enhydrobacter aerosaccus SK60]
 gi|257448792|gb|EEV23757.1| tRNA-dihydrouridine synthase B [Enhydrobacter aerosaccus SK60]
          Length = 332

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 133/309 (43%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R  A+         +EM+ +DA L    K +    F  +  P++ QI G++
Sbjct: 26  MAGVTDKPFRMLAKSF-GAGHAVSEMMTSDATLFAHHKTLYRANFEGEIAPISAQIAGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             K+ EAA+     G   +++N+GCP+ +V +   G+ L+ + D+V   + A   A+ +P
Sbjct: 85  PEKIAEAARYQVANGAQIVDINMGCPAKKVCKKLAGSALLKDEDLVKRLLDATVNAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++G+  I IH R         ++++ + +  Y++
Sbjct: 145 VTLKTRLGYANGE--ENILRVAQMAEEAGIAMIVIHGRT--------REDKYLGSARYEL 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + + +NG ++   +A ++      DG+MIGRA      +   +  Y    
Sbjct: 195 IKEVKNLLT-IPVIVNGDIDSPQKAKQVYEQTGADGIMIGRAGQGQPWIFRDIAHYLETG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP    + +     +      Y           +   +H+     G  NS   R  
Sbjct: 254 EILPSPTMDELKEIVLSHLQEIYAFY-----GEYSGCRIARKHIAWYTSGIANSNAFRQA 308

Query: 297 LTVEAGAST 305
           +  E   + 
Sbjct: 309 MYEEDTTAG 317


>gi|310639544|ref|YP_003944302.1| tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa SC2]
 gi|309244494|gb|ADO54061.1| tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa SC2]
          Length = 342

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/323 (25%), Positives = 150/323 (46%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAIIHGNKRTREMLFVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK+V ++   + I++N+GCP  +V +   GA  +L+P+ + + ++A+ +++S 
Sbjct: 77  RESLVKAAKVVDQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSAVVESVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +          ++++++G   + +H R         ++     + ++D
Sbjct: 137 PVTVKMRIGWDSEHIYAV--ENARAVERAGGQAVSVHGRT--------REQLYTGHANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K E   + +  NG +     A ++  L   DGVMIGR A  N  ML    EY   
Sbjct: 187 IIKEVK-EAVSIPVIGNGDVVTPEDARRMLDLTHCDGVMIGRGALGNPWMLYRTIEYLQT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     I+    D           ++++ +H+     G  +S R + 
Sbjct: 246 GKLLPDPSPEEKIR-----IAILHMDRLVALKGEAVAVREMRKHLAWYLKGLKDSARIKD 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
           ++  E         I++   + +
Sbjct: 301 LIMEETKRDDM-VRILDQFVSQL 322


>gi|242072588|ref|XP_002446230.1| hypothetical protein SORBIDRAFT_06g006720 [Sorghum bicolor]
 gi|241937413|gb|EES10558.1| hypothetical protein SORBIDRAFT_06g006720 [Sorghum bicolor]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 114/332 (34%), Positives = 172/332 (51%), Gaps = 19/332 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 1   MMDWTDNHYRTLARLISRHAWLYTEMVVAETIVHQKDNLDRFLAFPEEQHPIVLQIGGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++  D+ Y+EINLN GCPS +V     FGA LM  P+ VGD ++ +     +
Sbjct: 61  LENLAKATELANDYSYDEINLNCGCPSGKVAGHGCFGARLMFEPEFVGDAMSTIAANCDV 120

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V   + KS      IHARKA+L GLSP +NRK+P L Y
Sbjct: 121 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRKVPPLKY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ P +   +NGG+ ++   +  I     GVM+GRAAY N   ML  VD    
Sbjct: 181 EYYFALLRDFPGIKFTVNGGITNVGQVSASIRQGAHGVMVGRAAYNNPWNMLGHVDGEIY 240

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFHGFPNS 290
              T              R+I  S   Y    +   G     ++Q+ + ++ LFH  P +
Sbjct: 241 GKQTR---------CISRRQILESYQAYGDSIIDQYGPSRPNVRQLVKPLLNLFHSEPGN 291

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              +                +E   + + +S+
Sbjct: 292 SLWKRKADSALRHCKTVKTFLEETLDAIPDSV 323


>gi|326204271|ref|ZP_08194130.1| TIM-barrel protein, nifR3 family [Clostridium papyrosolvens DSM
           2782]
 gi|325985546|gb|EGD46383.1| TIM-barrel protein, nifR3 family [Clostridium papyrosolvens DSM
           2782]
          Length = 320

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 66/301 (21%), Positives = 128/301 (42%), Gaps = 21/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+YTEM+ A  +   D K+  +      EKP A+QI G+D
Sbjct: 17  MAGVTDMPFRILCKE-QECGLVYTEMVSAKGMHYDDDKSNKLTLMHEIEKPGAVQIFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + E  + +       I++N+GCP+ ++ +   G+ LM NP ++ + I A+  A   P
Sbjct: 76  PTIMAEVTEKLNASDAAIIDINMGCPAPKITKNGEGSALMKNPQLIAEIIRAVAAASQKP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+ +  +    + +  +++G + + +H R         ++       D+DI
Sbjct: 136 VTVKIRKGWDESL--INAVEIARIAEENGASAVAVHGRT--------REQYYSGKADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +    +A K+L     D +M+GR A  N  +   +  +  + 
Sbjct: 186 IRRVK-EAVSIPVIGNGDVTGPKEARKLLEETKCDAIMVGRGAQGNPWIFKKIVRFLEDG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R +   + D           + ++  H+     G  ++   +  
Sbjct: 245 TIVPDPSPEEKIDTIIRHM-NMLIDLKGER----TGILEMRSHIAWYIKGMRDAAYTKQK 299

Query: 297 L 297
           +
Sbjct: 300 I 300


>gi|22298534|ref|NP_681781.1| nitrogen regulation protein NifR3-like protein [Thermosynechococcus
           elongatus BP-1]
 gi|22294714|dbj|BAC08543.1| tll0991 [Thermosynechococcus elongatus BP-1]
          Length = 347

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 63/320 (19%), Positives = 128/320 (40%), Gaps = 21/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADIS 60
              TD  +R   R     +++YTEM+ A  +        I+     E P+++Q+      
Sbjct: 35  AGVTDLVFRRLVRRYAPESMMYTEMVSASGLHYLKTLPRIMEVDANEHPISIQLFDCRPD 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA      G + +++N+GCP  ++ +   G+ L+ +       +  + KA+ +PVT
Sbjct: 95  FLAEAAIKAVAEGADTVDINMGCPVNKITKNGGGSSLLRDVQTAVAIVRTVSKAVPVPVT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG  D+   + + +  K+++ +G   I +H R         +         ++ + 
Sbjct: 155 VKTRIGWSDEE--INILDFAKAMEDAGAAMITVHGRT--------RAQGFNGPARWEWIA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K E   + +  NG +  +  A++ L     DGVM  R       ++  +D +      
Sbjct: 205 RVK-ERVSIPVIANGDIFSVEAAVRCLEQTGADGVMCSRGTMGYPFLVGEIDHFLKTGEL 263

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +P      +     + A + +Y          ++Q  +H+     GF ++   R  L 
Sbjct: 264 RPAPTVVERLQCARDHLIA-LWEYKGER-----GIRQARKHLTWYAKGFADAAELRSELC 317

Query: 299 VEAGASTATHHIIETAFNLM 318
                  A   +++ A   +
Sbjct: 318 RIETL-EAGLALLDRAIERL 336


>gi|171319643|ref|ZP_02908737.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria MEX-5]
 gi|171095134|gb|EDT40140.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria MEX-5]
          Length = 355

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PNAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVKSAV-RIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|251780604|ref|ZP_04823524.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243084919|gb|EES50809.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 321

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 147/324 (45%), Gaps = 25/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+ TEM+ A A+  G  + + +L  S +E P+A+QI G +
Sbjct: 17  MAGVTDLSFRGLCKEM-GCGLVCTEMVSAKALYYGSENTQTLLRVSDKEAPVAVQIFGRE 75

Query: 59  ISKLVE-AAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              + E   K +        I++N+GCP+ ++ +   G+ LML PD+  D + A+ K   
Sbjct: 76  PEIMAEICEKYLNPREDVCIIDINMGCPAPKIVKNKEGSALMLEPDLAYDIVKAIKKVSK 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R G DD+   +      K+++++G + I +H R         +      + D+
Sbjct: 136 KPVTVKFRKGYDDE--HINAVEFGKALEEAGADAIAVHGRT--------RKQMYEGHSDW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+ ++K E   + +  NG +     A+K+  L + DG++I R +  N  +   + +  +
Sbjct: 186 EIIKKVK-EAVSIPVLGNGDVFSPEDAIKMKELTNCDGILIARGSMGNPWIFKQIQDALN 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +      + +++      +     + A ++      ++++ +H      G P S   +
Sbjct: 245 GKIVKEISYQDKIN------MCIRHYELAIKNDGEYKAIREMRKHASWYIKGIPRSTEIK 298

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
           + + +    S     I+E   N +
Sbjct: 299 NQINIL-NDSNEVISILEQYKNTL 321


>gi|241662015|ref|YP_002980375.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12D]
 gi|240864042|gb|ACS61703.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12D]
          Length = 355

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 130/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +       ++ +  + +G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDREHRNA--LSVARIAQDAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ +  
Sbjct: 186 DTIAAVK-ASVRIPVVANGDITTPAKAKHVLAVTGADAIMIGRAAQGRPWLFREIEHFLQ 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNAHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|49088166|gb|AAT51539.1| PA4852 [synthetic construct]
          Length = 333

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 132/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    ++ +EM+ +D  L   +K+ L      +++P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGMVVSEMVTSDVRLWNSRKSRLRLIHDGEDEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 79  PAMLAEAAQRNVELGAQIIHINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVRAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +Y+ 
Sbjct: 139 VTLKIRTGWDRDNRNGVT--VAKLAEQAGIQALAVHGRT--------RADLYTGEAEYET 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A K++    VD ++IGRAA     +   +D Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPEKARKVIEQTGVDALLIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +     V       ++     Y          ++   +H+       P +R  R
Sbjct: 248 EHLPAAPLPEVQSILLEHLAELHLFYGEEM-----GVRIARKHVGWYLATLPGAREFR 300


>gi|237717083|ref|ZP_04547564.1| dehydrogenase [Bacteroides sp. D1]
 gi|262405851|ref|ZP_06082401.1| dehydrogenase [Bacteroides sp. 2_1_22]
 gi|294647812|ref|ZP_06725364.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CC 2a]
 gi|294806206|ref|ZP_06765053.1| TIM-barrel protein, nifR3 family [Bacteroides xylanisolvens SD CC
           1b]
 gi|229443066|gb|EEO48857.1| dehydrogenase [Bacteroides sp. D1]
 gi|262356726|gb|EEZ05816.1| dehydrogenase [Bacteroides sp. 2_1_22]
 gi|292636720|gb|EFF55186.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CC 2a]
 gi|294446462|gb|EFG15082.1| TIM-barrel protein, nifR3 family [Bacteroides xylanisolvens SD CC
           1b]
          Length = 331

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 86/328 (26%), Positives = 138/328 (42%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTSPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFEWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I +   +   E+
Sbjct: 302 R-IAMLRAETKEELFRIFDEITSQRKEN 328


>gi|254253220|ref|ZP_04946538.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           dolosa AUO158]
 gi|124895829|gb|EAY69709.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           dolosa AUO158]
          Length = 355

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 126/308 (40%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYETIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQLVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 AFRHRMNT 308


>gi|326798717|ref|YP_004316536.1| hypothetical protein Sph21_1303 [Sphingobacterium sp. 21]
 gi|326549481|gb|ADZ77866.1| TIM-barrel protein, nifR3 family [Sphingobacterium sp. 21]
          Length = 333

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 139/323 (43%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R   K+   L     E+P+ +QI G+D
Sbjct: 21  MEDVSDPPFRYVCKQ-NGVDMMYTEFISSEGLIRHAAKSKQKLDIFEYERPIGIQIFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I      + I++N GCP   V     GA L+ + D +     A+  A  +P
Sbjct: 80  IKSMEEATEIATLAKPDLIDINYGCPVKNVACRGAGASLLQDIDKMVAMTKAVVNATHLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    + + ++  G+  + IH R         +      + D+ +
Sbjct: 140 VTVKTRLGWDDHTKNI--YEVAERLQDIGIQALSIHGRT--------RSQMYKGSADWSL 189

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++KK     + I  NG ++ + +  A ++   VDG+MIGRA+     +   +  +F  
Sbjct: 190 IKKVKKNPRIHIPIFGNGDVDSVEKAAAWRLEYEVDGIMIGRASIGYPWIFREIKHFFET 249

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P IK RVD      +  +    +         + ++ RH    F G PN +  R
Sbjct: 250 GTYLDGPTIKERVD------VCKTHFVKSIEWKGEKTGIFEMRRHYANYFKGIPNFKEYR 303

Query: 295 HILTVEAGASTATHHIIETAFNL 317
             L            + E AF  
Sbjct: 304 MKLVSLDKVPEINEVLDEIAFQF 326


>gi|253576834|ref|ZP_04854159.1| tRNA-dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251843701|gb|EES71724.1| tRNA-dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 333

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 87/321 (27%), Positives = 150/321 (46%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL G+K+   +L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAILHGNKRTREMLFVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + LVEAAK+V ++   + I++N+GCP  +V +   GA  +L+P+ + + +AA+  A+S 
Sbjct: 77  RASLVEAAKVVDQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVAAVVDAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +   V   +  K+++++G   + +H R         ++       D+ 
Sbjct: 137 PVTVKMRIGWDAEHIYVV--DNAKAVERAGGKAVSVHGRT--------REQLYTGKADWS 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E   + +  NG +     A ++L     DGVMIGR A  N  ML    EY   
Sbjct: 187 YIRQVK-EAVSIPVIGNGDVATPEDAKRMLDETGCDGVMIGRGALGNPWMLYRTVEYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P     D +   +I+    D  A        ++++ +H+     G   + R + 
Sbjct: 246 GVLLPEP-----DAEEKIRIAILHMDRLAALKGELVAVREMRKHLAWYLKGLKGAARIKD 300

Query: 296 ILTVEAGASTATHHIIETAFN 316
           ++  E         I+E    
Sbjct: 301 LIMEENHRDEM-VRILENFVA 320


>gi|293373770|ref|ZP_06620116.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CMC 3f]
 gi|292631260|gb|EFF49892.1| TIM-barrel protein, nifR3 family [Bacteroides ovatus SD CMC 3f]
          Length = 331

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 86/328 (26%), Positives = 137/328 (41%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      + YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRF-GADMAYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      +D VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPQRCKECFDHYGIDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFDWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I E   +   E+
Sbjct: 302 R-ISMLRAETKEELFRIFEEITSQRKEN 328


>gi|300705135|ref|YP_003746738.1| tRNA-dihydrouridine synthase b [Ralstonia solanacearum CFBP2957]
 gi|299072799|emb|CBJ44154.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum CFBP2957]
          Length = 357

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 131/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + +  +++G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDREHRNA--LTVARIAQEAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG +   ++A ++L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVK-ASVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAAQGRPWLFREIEHFLQ 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|281422351|ref|ZP_06253350.1| tRNA-dihydrouridine synthase B [Prevotella copri DSM 18205]
 gi|281403582|gb|EFB34262.1| tRNA-dihydrouridine synthase B [Prevotella copri DSM 18205]
          Length = 328

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 136/301 (45%), Gaps = 24/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G  
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRSIKSTVSKLTISDEERPVGIQIYGRT 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + I++N GCP  +V     GA ++ N  ++ D    + KA+++P
Sbjct: 77  TEDMVEAAKIVEQAKPDVIDINFGCPVKKVAGKGAGAGMLRNIPLMLDITREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDCE--NLIITDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A        VD VMIGRA +    +   + +Y  N
Sbjct: 187 IGEVKNNPRIHIPIIGNGDITTPEEAKLAFERYGVDAVMIGRATFGRPWIFKEIRDYLDN 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  ++D      +           +     +    RH+    +F G P+ R+ 
Sbjct: 247 TGAAPLTVDEKID------LLEEQLRINVERIDEYRGILHTRRHLAASPIFKGIPDFRQT 300

Query: 294 R 294
           R
Sbjct: 301 R 301


>gi|326387744|ref|ZP_08209350.1| dihydrouridine synthase TIM-barrel protein nifR3 [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326207790|gb|EGD58601.1| dihydrouridine synthase TIM-barrel protein nifR3 [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 342

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 136/302 (45%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G +
Sbjct: 29  MTGVSDLPFRRMVRRF-GSGLNVTEMIASPAAIRETRQSIQKAAWDPAEEPVSMQLVGCE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ ED G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 88  PEQMGEAAKLSEDRGAAIIDINMGCPVRKVVNGDAGSALMRDIPLAARLIEATVKAVSVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G      ++    L +  +  G   I +H R         ++     + D+  
Sbjct: 148 VTVKMRMGWC--HDSLNAPELARIAQDLGAKMITVHGRT--------RNQMYKGSADWGF 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K +   + + +NG +  ++     L     DGVMIGR AY    +L  +  +    
Sbjct: 198 VRKVK-DAVSIPVIVNGDICSIADVATALEQSGADGVMIGRGAYGRPWLLGQIMHWLRTG 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P   +  +         ++ Y A    +GG +    +H+     G P S   R+ 
Sbjct: 257 EELADPALDQQYEVIIEHYQDMLSHYGA---MTGGNM--ARKHLGWYTKGLPGSAEFRNR 311

Query: 297 LT 298
           + 
Sbjct: 312 VN 313


>gi|260172925|ref|ZP_05759337.1| dehydrogenase [Bacteroides sp. D2]
 gi|315921208|ref|ZP_07917448.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313695083|gb|EFS31918.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 331

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 87/328 (26%), Positives = 138/328 (42%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKRF-GADMVYTEFVSSDALIRAVSKTAQKLSISDAERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEQAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVRIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKVIV--ELAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTPKRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+      +     L     +  + RH+    LF G PN R  
Sbjct: 247 GEELP-PLSFDWCMEVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGIPNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I E   +   E+
Sbjct: 302 R-IAMLRAETKEELFRIFEEITSQRKEN 328


>gi|317494239|ref|ZP_07952655.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316918012|gb|EFV39355.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 334

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGMAVSEMLSSNPEVWQTDKSRLRMVHLDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  D G   I++N+GCP+ +V+    G+ L+  PD+VG  ++A+  A+ +P
Sbjct: 76  PDDMAAAAKINADSGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVGKILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       +      Y      SG   +   +H+           + R  
Sbjct: 245 ELLPPMPLEEVKHLLLGHVQELHNFY-----GSGKGFRIARKHVSWYLQEHAPCDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|255021033|ref|ZP_05293086.1| tRNA-dihydrouridine synthase A [Acidithiobacillus caldus ATCC
           51756]
 gi|254969447|gb|EET26956.1| tRNA-dihydrouridine synthase A [Acidithiobacillus caldus ATCC
           51756]
          Length = 335

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 114/298 (38%), Positives = 160/298 (53%), Gaps = 13/298 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-DKKNILGFSTQEKPLALQIGGADI 59
           M+DWTDRH R+F RL+  + +LYTEMI   A++ G   +  L F+  E+PL LQ+GG D 
Sbjct: 22  MLDWTDRHCRYFLRLICPSCVLYTEMIHTSALVLGKSPERYLAFTAAEQPLVLQLGGDDP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  AA +  D+GY  +NLNVGCPS RV  G+FGACLML P +V + I A+     +PV
Sbjct: 82  EAMARAAILARDYGYTGVNLNVGCPSTRVQRGNFGACLMLTPALVREIIDAL-AGSGLPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G+D Q     L + V  +         +HAR A L+GLSP  NR IP L +D V
Sbjct: 141 SVKHRLGLDRQEDYGQLADFVAQVAAGSCRHFVVHARNAWLRGLSPAANRTIPPLRWDWV 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +K++ P L   LNGGL+ + +       VDGVMIGRAAY     LT ++         
Sbjct: 201 ARLKEDFPGLRFELNGGLDTVPKVEAQWSRVDGVMIGRAAYHRPLFLTELELALGRRQAP 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           +             ++ A++  Y      +    + +TRH+ G F G P +   R  L
Sbjct: 261 AR----------RAEVFAALLAYTEDWGAALPAPR-LTRHLHGFFFGEPGANAWRQFL 307


>gi|15896446|ref|NP_349795.1| NifR3 family protein [Clostridium acetobutylicum ATCC 824]
 gi|15026269|gb|AAK81135.1|AE007815_5 NifR3 family enzyme [Clostridium acetobutylicum ATCC 824]
 gi|325510604|gb|ADZ22240.1| NifR3 family enzyme [Clostridium acetobutylicum EA 2018]
          Length = 321

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 142/320 (44%), Gaps = 26/320 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L YTEM+ A A+  G  + + ++  S +E+  A+Q+ G++
Sbjct: 17  MAGVTDIVFRKICKGM-GADLTYTEMVSAKALYYGSENTEELMKISDEEEYAAVQMFGSE 75

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +A  K  ED     I++N+GCP+ ++ +   G+ LM +P +  + + A+ KA + 
Sbjct: 76  PDIMAKACEKFNEDDKICIIDINMGCPAHKIVKNGEGSALMKSPKLAYEIVKAVKKASNK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      K I+ +G + I +H R         +        D+D
Sbjct: 136 PVTVKFRKGFDED--NINAVEFAKVIEDAGADMITVHGRT--------RAQMYEGKADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF-S 234
           I+  +KK +  + +  NG +     A+++L   + DGVM+ RAA  N  +   +     S
Sbjct: 186 IIKAVKK-SVSIPVIGNGDIVSGEDAVRMLEYTNCDGVMVARAAMGNPWIFREIKAAINS 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +   +P++          +       A ++      ++++ +++        N    +
Sbjct: 245 TQIIKPTPVEK-------LDMCIFHYKEAVKYYGEKKAVREMRKNIAWYIKSLKNCTDIK 297

Query: 295 HILTVEAGASTATHHIIETA 314
            ++  E   S     I+E  
Sbjct: 298 CLINSEES-SDEVIGILEQY 316


>gi|218288833|ref|ZP_03493084.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           LAA1]
 gi|218240922|gb|EED08099.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           LAA1]
          Length = 328

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 140/323 (43%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+ L    ++  EM+    ++ G++K+  +      E P++LQ+ G D
Sbjct: 19  MAGVCNPPFRRLAKEL-GAGMVCAEMVSDKGLVSGNEKSKKMTTILPDEHPVSLQLVGYD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ + +AA++V +   + I++N+GCP  ++ +   GA L  +P+     + A+   ++ P
Sbjct: 78  LASMEQAAEMVGETNADLIDINMGCPVLKICKTGSGAALARDPNYAAKIVRAVVSRVNKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    +  +++++G   + +H R A                D+DI
Sbjct: 138 VTVKFRKGWDDD--HVNAVEVALAVQEAGAQAVAVHGRTAK--------QMYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + D   A +++     D VM+GRAA  N  +   +  Y    
Sbjct: 188 IRRVK-EAVRIPVIGNGDVVDPISAKRLMEETGCDAVMVGRAALGNPWIFREIAHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R +   + ++    +     ++++ +H      G P +   R +
Sbjct: 247 ELLPPPSVEERLEVTLRHM-RMLVEFKGEDIG----VREMRKHAAWYVKGLPGAAEVRTL 301

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           L  +   +     ++      ++
Sbjct: 302 LNQQTTMAGM-EAVLRDYCEWVL 323


>gi|295694791|ref|YP_003588029.1| TIM-barrel protein, nifR3 family [Bacillus tusciae DSM 2912]
 gi|295410393|gb|ADG04885.1| TIM-barrel protein, nifR3 family [Bacillus tusciae DSM 2912]
          Length = 331

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 136/327 (41%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   ++  +R  A+ +    ++  EM+    I+  + K   +L     E P++LQ+ G+D
Sbjct: 22  MAGVSNPAFRILAKEM-GAGMVCAEMVATKGIVNANAKTLRMLHILPDEHPVSLQLVGSD 80

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V AA+ V      + I++N+GCP  ++++   GA L  +PD     + A+ + +  
Sbjct: 81  LDSMVRAAETVGTATNADVIDINMGCPVLKIYKNGSGAALARDPDYAARIVRAVVQTVDK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD    V    +  +++++G   + +H R A              + D+ 
Sbjct: 141 PVTVKFRKGWDDD--HVNAVEVALAVEEAGAKAVTVHGRTAK--------QMYSGHADWS 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG +     A+++L     DGVMIGR A  N  +      Y   
Sbjct: 191 IIRQVK-EAVRIPVIGNGDVSTPEAAVQMLQETGCDGVMIGRGALGNPWIFRETVHYLKK 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +   R +     +           ++++ +H      G P++   R 
Sbjct: 250 GQKLPPPGVDERIRVCLRHL-----ELLVAEKGPWIGVREMRKHAGWYIKGLPDAALMRQ 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L  EA        ++E     +   +
Sbjct: 305 QLN-EAETEEQMRSLLEGYAERLTRRV 330


>gi|115350640|ref|YP_772479.1| nifR3 family TIM-barrel protein [Burkholderia ambifaria AMMD]
 gi|170699610|ref|ZP_02890649.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria IOP40-10]
 gi|115280628|gb|ABI86145.1| tRNA-U20-dihydrouridine synthase [Burkholderia ambifaria AMMD]
 gi|170135492|gb|EDT03781.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria IOP40-10]
          Length = 355

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|77359313|ref|YP_338888.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874224|emb|CAI85445.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 326

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K++  +  S +    A+QI GAD
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGLAVSEMLSSNPDVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + +H R         +        +Y  
Sbjct: 139 VTLKIRTGWDLDNRNGV--EIARIAERYGIASLAVHGRT--------RACMYKGEAEYAT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y    
Sbjct: 189 IRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       ++   T Y           +   +H+           + R +
Sbjct: 248 EHLQPPAIAEVRSILMEHLTNLHTFY-----GEPMGARIARKHVSWYLQTHDRDGQFRRV 302

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                        ++E  F  +
Sbjct: 303 FNT-IDNPLTQVDVLEQYFKTL 323


>gi|299142013|ref|ZP_07035147.1| dehydrogenase [Prevotella oris C735]
 gi|298576475|gb|EFI48347.1| dehydrogenase [Prevotella oris C735]
          Length = 336

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 81/320 (25%), Positives = 145/320 (45%), Gaps = 25/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +  +  E+P+ +QI G +
Sbjct: 18  MEDVTDIGFRMLCKRY-GAAMVYTEFVSADAIIRSIKSTLDKMTINDAERPVGIQIYGRN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I+LN GCP  +V     G+ ++ N  ++ D    + KA+S P
Sbjct: 77  VESMVEAAKIVEQVKPDLIDLNFGCPVKKVAGKGAGSGMLRNIPLLLDITRNVVKAVSTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--SLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG +    +A +      VD VM+GRA +    +   + ++  N
Sbjct: 187 IGKVKSNPRIHIPIIGNGDITTPEEAKRAFDDYGVDAVMVGRATFGRPWVFKEMRDFIDN 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             +    I  ++D      I           +     +    RH+    +F G P+ ++ 
Sbjct: 247 TTSSPLTIDDKID------ILEEQLRINVERIDEYRGIIHTRRHLASSPIFKGIPDFKQT 300

Query: 294 RHILTVEAGASTATHHIIET 313
           R I  + A        I+E 
Sbjct: 301 R-IAMLRATKVDELIAILEE 319


>gi|107021769|ref|YP_620096.1| dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           cenocepacia AU 1054]
 gi|116688716|ref|YP_834339.1| nifR3 family TIM-barrel protein [Burkholderia cenocepacia HI2424]
 gi|170732013|ref|YP_001763960.1| NifR3 family TIM-barrel protein [Burkholderia cenocepacia MC0-3]
 gi|254246304|ref|ZP_04939625.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           cenocepacia PC184]
 gi|105891958|gb|ABF75123.1| tRNA-U20-dihydrouridine synthase [Burkholderia cenocepacia AU 1054]
 gi|116646805|gb|ABK07446.1| tRNA-U20-dihydrouridine synthase [Burkholderia cenocepacia HI2424]
 gi|124871080|gb|EAY62796.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           cenocepacia PC184]
 gi|169815255|gb|ACA89838.1| TIM-barrel protein, nifR3 family [Burkholderia cenocepacia MC0-3]
          Length = 355

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|284037281|ref|YP_003387211.1| hypothetical protein Slin_2392 [Spirosoma linguale DSM 74]
 gi|283816574|gb|ADB38412.1| TIM-barrel protein, nifR3 family [Spirosoma linguale DSM 74]
          Length = 329

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 138/326 (42%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE I ++ ++R   K++  L     E+P+ +Q+ G+D
Sbjct: 19  MEDVSDPPFRAVCK-ANGADLMYTEFISSEGLIRDAAKSVQKLDIFEYERPIGIQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + E A+I      + I++N GCP   V     GA L+ +   +     A+ KA  +P
Sbjct: 78  VETMGECARIASRANPDLIDINYGCPVKNVACRGAGAALLQDIPKMVRMTDAVVKATHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    V    + + ++  G+  + +H R  +               D+ +
Sbjct: 138 VTVKTRLGWDESTKNV--GEVAERLQDIGIKALTVHGRTRV--------QMYKGEADWTL 187

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  IK +NP   + I  NG ++   +A++      VDGVMIGRA+  +  +   +  +  
Sbjct: 188 IGRIK-DNPRIQIPIFGNGDIDSPEKAVEYKNRFGVDGVMIGRASIGHPWVFNEIKHFVQ 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +     D++ R       L ++ RH    F G P+ +  R
Sbjct: 247 TGQHLPPPTVADRV-----AVCRQHLDFSIRWKGEIVGLFEMRRHYANYFKGLPDFKPYR 301

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
             L      S  +  + E   N + E
Sbjct: 302 MRLVTTDSYSGVSDILAEIQENYITE 327


>gi|300857284|ref|YP_003782268.1| putative tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
 gi|300437399|gb|ADK17166.1| predicted tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
          Length = 320

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 146/326 (44%), Gaps = 30/326 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R     +      YTEMI A A+     +   +L  S+ EKPL +QI G+D
Sbjct: 17  MAGVTDRAFRELCIEM-KCGFTYTEMISAKALFYDSDRTKQMLKVSSIEKPLGVQIFGSD 75

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +       +     I++N+GCP+ ++ +   G+ LM N  +    +  + KA + 
Sbjct: 76  PLIMAKVCDFFNCNEDIAIIDINMGCPAPKIVKNGEGSALMKNSSLASQIVKEVKKASAK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D     + + +  + +++SG + + +H R +              + ++D
Sbjct: 136 PVTVKMRIGFD--FDNINVVDFAQIMEQSGADAVTVHGRTST--------QMYNGSANWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF-S 234
           I+ ++KK+  ++ +  NG +     A+++      DGVM+GR +  N  +   + E    
Sbjct: 186 IISQVKKKV-NIPVIGNGDVFTAEDAIRLFNNTGCDGVMVGRGSMGNPWIFKQICEIRNH 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG--GKLQQITRHMIGLFHGFPNSRR 292
            P+   SP+          KI+  M  Y     ++G    ++++ +H+     G  NS+ 
Sbjct: 245 QPVIFPSPL---------EKINLCMEHYRRAIYYNGEDRAVREMRKHIAWYIKGLKNSKE 295

Query: 293 CRHILTVEAGASTATHHIIETAFNLM 318
            +  +  E   S     I+    +L+
Sbjct: 296 IKDKINCE-KKSENVFKILNEYKSLL 320


>gi|189347606|ref|YP_001944135.1| TIM-barrel protein, nifR3 family [Chlorobium limicola DSM 245]
 gi|189341753|gb|ACD91156.1| TIM-barrel protein, nifR3 family [Chlorobium limicola DSM 245]
          Length = 347

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 145/326 (44%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE I A+A+ RG +K +  L     E+P+A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKR-CGADIVYTEFISAEALRRGVEKTMRKLAVDEIERPVAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++EAA + E +  + +++N GCP+ +V     GA L+  P+ +     A+ K++ IP
Sbjct: 76  VESMIEAAAVAETYNPDFLDINFGCPTKKVAGKGAGAALLREPEKMQAIAEAVVKSVGIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D    ++ +  ++  ++ +G+  + IH R         + +      D + 
Sbjct: 136 VTAKTRIGWD--HDSINIIEVLHRLEDAGIRALAIHGRT--------RSDMYKGRADRER 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K+E   + +  NG +     AL +      DGVMIGR +  N  + +         
Sbjct: 186 IAEAKREA-SIPVIANGDIWSAEDALAMFDQTGADGVMIGRGSIGNPFIFSQAKHLIRTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRRCR 294
                P        F  +I A++        + G K    ++ RH      G P   + R
Sbjct: 245 TPAPPP-------GFRERIHAAIEHLKLSVQYKGEKYGNLEMRRHYATYLKGLPKVSQVR 297

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
           + L  E G      HI+E      +E
Sbjct: 298 NKLVREDGW----EHIVEILLAYEVE 319


>gi|207742357|ref|YP_002258749.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
 gi|206593747|emb|CAQ60674.1| trna-dihydrouridine synthase protein [Ralstonia solanacearum
           IPO1609]
          Length = 356

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 131/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + +  +++G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDRKHRNA--LTVARIAQEAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG +   ++A ++L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVK-ASVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAAQGRPWLFREIEHFLQ 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|1171716|sp|P45672|DUS_AZOBR RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|599600|emb|CAA86063.1| nifR3-like protein [Azospirillum brasilense]
          Length = 328

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 73/298 (24%), Positives = 128/298 (42%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +  +   L+ +EM+ + A++R +++   ++    ++ P+A+Q+ G +
Sbjct: 19  MSGVTDLPFRRLVKQ-SGCGLVVSEMVASQAMIRENRQTLRMVECEPEQFPMAVQLAGCE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK+ ED G   I++N GCP  +V  G  G+ LM +  +    + A  KA++IP
Sbjct: 78  PDVMAEAAKLNEDRGAAIIDINFGCPVKKVVNGHAGSSLMRDEALAARILEATAKAVTIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD   ++    L +  ++ G+  + +H R         ++       D+  
Sbjct: 138 VTLKMRKGWDD--SSLNAPRLARIAEECGIKLVTVHGRT--------REQFYNGTADWSF 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + + +NG +       + L     DGVMIGR AY        V  Y    
Sbjct: 188 IRSVK-EAVSIPVVVNGDITSFDAVDRALAESGADGVMIGRGAYGRPWFPAQVMHYIRTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P              A +T Y        G L+   +H+     G  +S   R
Sbjct: 247 ERLPDPPLHEQLDTLLEHYDAMLTHYGVE-----GGLRVARKHISWYSTGLRDSAEFR 299


>gi|186684114|ref|YP_001867310.1| nifR3 family TIM-barrel protein [Nostoc punctiforme PCC 73102]
 gi|186466566|gb|ACC82367.1| putative TIM-barrel protein, nifR3 family [Nostoc punctiforme PCC
           73102]
          Length = 351

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 133/321 (41%), Gaps = 21/321 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 34  GVTDMVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPNERPISVQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + +++N+GCP  ++ +   G+ L+  P++    +  + KA+ +PVTV
Sbjct: 94  LAEAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVDVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D    + + +  K ++ +G   I +H R         +      N  ++ +  
Sbjct: 154 KTRIGWNDNE--ITILDFAKRMEDAGAQMITVHGRT--------RAQGYNGNARWEWITR 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+K L     DGVM  R       ++  +D +       
Sbjct: 204 VK-EVLSIPVIGNGDIFSVEAAVKCLEQTGADGVMCSRGTLGYPFLVGEIDHFLKTGEIL 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +P   +   +  R    ++ +Y          ++Q  +HM     GF  +   R  L++
Sbjct: 263 PTPTPIQ-RLECARDHLQALWEYKG-----DRGVRQARKHMTWYAKGFVGAAELRGQLSL 316

Query: 300 EAGASTATHHIIETAFNLMIE 320
                     +I+ A   +  
Sbjct: 317 VE-KVDQGLAMIDQAIEKLTN 336


>gi|172059673|ref|YP_001807325.1| NifR3 family TIM-barrel protein [Burkholderia ambifaria MC40-6]
 gi|171992190|gb|ACB63109.1| TIM-barrel protein, nifR3 family [Burkholderia ambifaria MC40-6]
          Length = 355

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAIT--VARLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    +       +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQHVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|332982222|ref|YP_004463663.1| tRNA-U20-dihydrouridine synthase [Mahella australiensis 50-1 BON]
 gi|332699900|gb|AEE96841.1| tRNA-U20-dihydrouridine synthase [Mahella australiensis 50-1 BON]
          Length = 326

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 76/301 (25%), Positives = 131/301 (43%), Gaps = 20/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R          L+ TEM+ A  +L   K +I   S++E+P+A+Q+ G +  
Sbjct: 20  MAGVTDMAFRILCHR-EGCGLVATEMVSAKGVLYNSKDDIWHVSSEERPVAIQLFGHEPD 78

Query: 61  KLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            + EAAKI+    + + I++N+GCP A+V   S G  LM +  +    + A+  A+  PV
Sbjct: 79  VMAEAAKIICHNVFPDIIDINMGCPVAKVVNKSEGCALMRDIPLAFSIMKAVVNAVRQPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D+Q   V    L  + + +G++ + +H R         ++       D+DI+
Sbjct: 139 TVKIRKGWDEQ--HVNAAELAVAAEHAGISAVTVHGRT--------REQFYTGIADWDII 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+ +  + +  NG ++    A ++L     DGVMIGRAA  N  +      Y     
Sbjct: 189 GAVKQ-SVSIPVIGNGDVKSPHDAKQMLEYTGCDGVMIGRAACGNPWVFKRTIHYLRTGE 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P            +     D           ++Q+ +H+     G  ++   R  L
Sbjct: 248 LLPLPTAEDRINKAIEHL-----DMEIALKGEYLAVRQMRKHIAWYIKGLRDASLVRDKL 302

Query: 298 T 298
            
Sbjct: 303 N 303


>gi|187927485|ref|YP_001897972.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12J]
 gi|309779813|ref|ZP_07674568.1| tRNA-dihydrouridine synthase B [Ralstonia sp. 5_7_47FAA]
 gi|187724375|gb|ACD25540.1| TIM-barrel protein, nifR3 family [Ralstonia pickettii 12J]
 gi|308921390|gb|EFP67032.1| tRNA-dihydrouridine synthase B [Ralstonia sp. 5_7_47FAA]
          Length = 355

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 130/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +       ++ +  + +G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDREHRNA--LSVARIAQDAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ +  
Sbjct: 186 DTIAAVK-ASVRIPVVANGDITTPAKAKHVLAVTGADAIMIGRAAQGRPWLFREIEHFLQ 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNAHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|21536881|gb|AAM61213.1| unknown [Arabidopsis thaliana]
          Length = 404

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 109/328 (33%), Positives = 170/328 (51%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL+T +A LYTEMI A+ ++         L FS Q+ P+ LQ+GG++
Sbjct: 44  MMDWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSN 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +AAK+ + +GY+EINLN GCPS +V     FG  LML P +VG+ ++A+    ++
Sbjct: 104 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKLVGEAMSAIAANTNV 163

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVD+      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y
Sbjct: 164 PVTVKCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKY 223

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  Y + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N    L  VD    
Sbjct: 224 EYYYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNNPWQTLGHVDTAVY 283

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +    +           H +    ++ + + ++ LFH    +   +
Sbjct: 284 G-----VPSSGLTRRQVLEQYQVYGDSVLGTHGNGRPNVRDLVKPLLNLFHSENANSLWK 338

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                      +   ++E +   + + +
Sbjct: 339 RRADAAFKECRSVGSLLEESLRAIPDCV 366


>gi|326565385|gb|EGE15562.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 103P14B1]
 gi|326573374|gb|EGE23342.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 101P30B1]
          Length = 341

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 138/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 37  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL +AA+     G   +++N+GCP+ +V     G+ L+ + D+V   + +   A+ +P
Sbjct: 96  PDKLAQAAQFQVANGAQIVDINMGCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++GV  I IH R         +++       Y++
Sbjct: 156 VTLKTRLGFANGQ--ENILKIAQIAEQAGVAAITIHGRT--------REDFYTGQARYEL 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++KK    + I +NG ++   +AL I      D VMIGRAA     +   +  + +  
Sbjct: 206 ITQVKKAA-KIPIIVNGDIDSPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTG 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +SP    + +   R +      Y           +   +H+     G PNS   R  
Sbjct: 265 ELLASPTVGEIHEVVLRHLDELYRFY-----GEYSGCRIARKHIAWYTGGLPNSNAFRDA 319

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +        A   +++  F  +
Sbjct: 320 MYACETTK-AQFEVVDKFFKTI 340


>gi|300692483|ref|YP_003753478.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum PSI07]
 gi|299079543|emb|CBJ52221.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum PSI07]
          Length = 356

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 130/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + +  +++G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDREHRNA--LTVARIAQEAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ +  
Sbjct: 186 DTIAAVKG-SVRIPVVANGDITTPAKARHVLDVTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|188588843|ref|YP_001919615.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188499124|gb|ACD52260.1| tRNA-dihydrouridine synthase B [Clostridium botulinum E3 str.
           Alaska E43]
          Length = 321

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 147/324 (45%), Gaps = 25/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+ TEM+ A A+  G  + + +L  S +E P+A+QI G +
Sbjct: 17  MAGVTDLSFRGLCKEM-GCGLVCTEMVSAKALYYGSENTQTLLRVSDKEAPVAVQIFGRE 75

Query: 59  ISKLVE-AAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              + E   K +        I++N+GCP+ ++ +   G+ LML PD+  D + A+ K   
Sbjct: 76  PEIMAEICEKYLNPREDVCIIDINMGCPAPKIVKNKEGSALMLEPDLAHDIVKAIKKVSK 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R G DD+   +      K+++++G + I +H R         +      + D+
Sbjct: 136 KPVTVKFRKGYDDE--HINAVEFGKALEEAGADAIAVHGRT--------RKQMYEGHSDW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+ ++K E   + +  NG +     A+K+  L + DG++I R +  N  +   + +  +
Sbjct: 186 EIIKKVK-EAVSIPVLGNGDVFSPEDAIKMKELTNCDGILIARGSMGNPWIFKQIQDALN 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +      + +++      +     + A ++      ++++ +H      G P S   +
Sbjct: 245 GKIVEEISYQDKIN------MCIRHYELAIKNDGEYKAIREMRKHASWYIKGIPRSTEIK 298

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
           + + +    S     I+E   N +
Sbjct: 299 NQINIL-NDSNEVISILEQYKNTL 321


>gi|144899194|emb|CAM76058.1| Dihydrouridine synthase, DuS [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 335

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 142/323 (43%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TD   R   + +    L+ +EMI + A++R +++ +   S   +E P+++Q+ G +
Sbjct: 25  MSGVTDMPCRRLVKRM-GAGLVVSEMIASQAMIRANRQTMKMASNCAEEHPMSVQLAGCE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA++  D G   I++N+GCP  +V  +G  G+ LM +  + G  + A  +A+ +
Sbjct: 84  PEVMAEAARMNADRGAAIIDINMGCPVKKVAVKGEAGSALMKDEILAGQLMEATVRAVDV 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+KCR+G D     +    L +  ++SG+  + IH R         +        D+ 
Sbjct: 144 PVTLKCRMGWD--HNRLNAPRLARIAQESGIKMVTIHGRT--------RQQFYTGTADWK 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V ++K +  D+ + +NG +E +  A++ L     DGVMIGR +Y        V  Y + 
Sbjct: 194 FVRQVK-DAVDIPVIVNGDIETIDDAIRALAESGADGVMIGRGSYGRPWFPGQVAHYLAT 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P   +            ++ Y      +   ++   +H+     G   S   R 
Sbjct: 253 GERPADPALDQQLAILLEHFDDMLSHY-----GTDTGVRMARKHIAWYSKGLHGSAEFRS 307

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            +   + A      I +    L+
Sbjct: 308 HVNKMSDAQAVRAAIHDFYLPLL 330


>gi|149278184|ref|ZP_01884322.1| probable TIM-barrel protein, NifR3 family [Pedobacter sp. BAL39]
 gi|149230950|gb|EDM36331.1| probable TIM-barrel protein, NifR3 family [Pedobacter sp. BAL39]
          Length = 335

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 145/325 (44%), Gaps = 29/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +RF  +  +   ++YTE I ++ ++R   K+   L     E+P+ +QI G++
Sbjct: 20  MEDVSDPPFRFVCKQ-SGVDMMYTEFISSEGLIRDAAKSRAKLDIFEYERPIGIQIFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I    G + +++N GCP  +V     G+ L+ + D + +   A+  A  +P
Sbjct: 79  IDHMREATEIASMAGPDLMDINYGCPVKQVACRGAGSALLQDIDKMVEMTKAVVNATHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    V    + + ++  G+ G+ IH R         +        D+ +
Sbjct: 139 VTVKTRLGWDDNTKNVE--EVAERLQDIGIQGLTIHGRT--------RAQMYKGEADWTL 188

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + EIK+     + I  NG ++ + +A   ++   VDG+MIGRAA     +   +  +F  
Sbjct: 189 IREIKRNPRIKIPIFGNGDVDSIQKAADWRLEYEVDGIMIGRAAIGYPWIFREIKHFFKT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T   P            +  +  + +         + ++ RH    F G P+ +  R 
Sbjct: 249 GQTLPGPTIEERV-----AVCRTHLEKSIAWKGPKVGVFEMRRHYSNYFKGLPDFKSYRM 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L  E          IET +N++ E
Sbjct: 304 SLVKEDN--------IETIYNILDE 320


>gi|255693550|ref|ZP_05417225.1| zinc-binding TIM-barrel protein, nifR3 family [Bacteroides
           finegoldii DSM 17565]
 gi|260620615|gb|EEX43486.1| zinc-binding TIM-barrel protein, nifR3 family [Bacteroides
           finegoldii DSM 17565]
          Length = 325

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 86/325 (26%), Positives = 139/325 (42%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRAVSKAAQKLSISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAKIVE+   + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TETMVEAAKIVEEAQPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDANNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +  +      VD VMIGRA++    +   V  Y   
Sbjct: 187 IGEVKKNPRMHIPIIGNGDVTTPQRCKECFDRYGVDAVMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      D  R+      +     L     +  + RH+    LF G  N R  
Sbjct: 247 GEELP-PLSFGWCMDVLRQEVVDSVNL----LDERRGILHVRRHLAASPLFKGISNFRNT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A        I +     +
Sbjct: 302 R-IAMLRAETKEELFRIFDEILATI 325


>gi|110597836|ref|ZP_01386119.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           ferrooxidans DSM 13031]
 gi|110340561|gb|EAT59044.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           ferrooxidans DSM 13031]
          Length = 347

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 78/304 (25%), Positives = 141/304 (46%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE I A+A+ RG +K +  L   T E+PLA+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKQ-HGADIVYTEFISAEALRRGAEKTVRKLRADTVERPLAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++EAA I E+F  + +++N GCP+ +V     GA L+  P+ +     A+ KA+SIP
Sbjct: 76  VESMIEAAVIAEEFRPDYLDINFGCPTKKVAGKGAGAALLREPEKMTLIAEAVVKAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D +  ++ + +++  ++ +G+  + +H R         +        D++ 
Sbjct: 136 VTAKTRIGWDRE--SINIIDVLHRLEGAGIQALAVHGRT--------RSEMYKGRADWNW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K++   + I  NG +     A+++      DGVMIGR +  N  +     +     
Sbjct: 186 IREVKEQA-SIPIIANGDIWSAEDAVRMFAETGADGVMIGRGSIGNPFIFAAAKQLLHTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P   +        +       +         + ++ RH      G P   + R+ 
Sbjct: 245 IPLPPPDFRQRIDAAVEHLKL-----SVEFKGDKYGVLEMRRHYSTYLKGLPMVSQVRNK 299

Query: 297 LTVE 300
           L  E
Sbjct: 300 LVRE 303


>gi|188591247|ref|YP_001795847.1| tRNA-dihydrouridine synthase b [Cupriavidus taiwanensis LMG 19424]
 gi|170938141|emb|CAP63127.1| tRNA-dihydrouridine synthase B [Cupriavidus taiwanensis LMG 19424]
          Length = 353

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 65/305 (21%), Positives = 131/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            S + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PSMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVEAVVAAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G + +        + + ++ +G++ + IH R         + +    + +Y
Sbjct: 136 VPVTLKIRTGWNRENRNA--LRVAQMVQDAGISMLTIHGRT--------RADLYHGDAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K     + +  NG +    +A ++  L   D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVK-AAVSIPVVANGDITTPQKAKQVLALTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 SP    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGEMLPSPEVAEIRAIMNAHLEDHYAFYGEF-----TGVRTARKHIAWYTRGLRGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|52424587|ref|YP_087724.1| hypothetical protein MS0532 [Mannheimia succiniciproducens MBEL55E]
 gi|52306639|gb|AAU37139.1| unknown [Mannheimia succiniciproducens MBEL55E]
          Length = 341

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 138/325 (42%), Gaps = 28/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  +     A+QI G+D
Sbjct: 35  MAGITDQPFRKLCAAY-GAGLTFSEMMSTNPQVWHTEKSRLRLAHHQAAGINAVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  D+G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+S+P
Sbjct: 94  PKEIAKAAQINVDYGAEIIDINMGCPAKKVNRKMAGSALLQYPDLVRQILEHVVNAVSVP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + K  ++SG+  + IH R         ++     N +YD 
Sbjct: 154 VTLKIRTGWNKEHRN--CVEIAKIAEQSGIQALTIHGRT--------RECLFEGNAEYDN 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG +    +A  +L     D VMIGR A  N  +  +V+      
Sbjct: 204 IKAVKRQV-SIPVIANGDITSAEKAKSVLEYTGADAVMIGRGALGNPWLFKSVESLVETG 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF---PNSRRC 293
                P          + I +    Y       G ++    +H+     G     N ++ 
Sbjct: 263 SIVFEPSLDEKCGVILQHIQSLHQFYGEE---KGYRI--ARKHVAWYLQGIQPSSNFKQT 317

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
            + +T            +E  FN +
Sbjct: 318 FNAITE----PQEQLIALEEFFNSI 338


>gi|261403946|ref|YP_003240187.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. Y412MC10]
 gi|261280409|gb|ACX62380.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. Y412MC10]
          Length = 343

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 146/325 (44%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D
Sbjct: 20  MAGVCNPAFRLIAKEF-GTGLVCAEMVSGKAIVHGNKRTQEMLFVDEREKPLSLQIFGGD 78

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK+V +    + I++N+GCP+ +V +   GA  +L+ + + + +AA+  A++ 
Sbjct: 79  RVSLVEAAKVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLDSNKIYEMVAAVVDAVNK 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D            ++++++G   + +H R         +D     + D+D
Sbjct: 139 PVTVKMRTGWDSDHIYAV--ENAQAVERAGGQAVSVHGRT--------RDQLYTGHADWD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG +     A ++L     DGVMIGR A  N  ML    EY   
Sbjct: 189 IIRQVK-EAVSIPVIGNGDVVTPEDARRMLDTTGCDGVMIGRGALGNPWMLYRTVEYLKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S P      +     I+    D           ++++ +H+     G   S R + 
Sbjct: 248 GQLLSDPSPQEKIR-----IAILHMDRLIALRGEAVAVREMRKHLSWYLKGLKGSARIKD 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
           I+  E         ++    N + +
Sbjct: 303 IIMEE-TKRDELVSLLNNFVNNLED 326


>gi|145219156|ref|YP_001129865.1| nifR3 family TIM-barrel protein [Prosthecochloris vibrioformis DSM
           265]
 gi|145205320|gb|ABP36363.1| tRNA-U20-dihydrouridine synthase [Chlorobium phaeovibrioides DSM
           265]
          Length = 354

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 139/316 (43%), Gaps = 21/316 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE + A+A+ RG +K    L     E+P+A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKR-HGADIVYTEFVSAEALRRGVEKTTRKLIADPVERPIAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I E F  + +++N GCP+ +V     GA L+  P+ +     A+ +A++IP
Sbjct: 76  VESMTEAARIAESFEPDYLDINFGCPTKKVAGKGAGAALLREPEKMAAITEAVVRAVNIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D    ++ + ++++ ++ +G+  + +H R         +        D+D 
Sbjct: 136 VTAKTRLGWDRD--SINIIDVLRRLEDAGIQALALHGRT--------RSEMYKGRADWDW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E  +    + +  NG +     AL++      +G+MIGR A  N  + +         
Sbjct: 186 IAETVRHA-SIPVIANGDVWSPEDALQMFNHTGAEGIMIGRGAIGNPFIFSGTRHLLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P      +     +  S+     R+        ++ RH      G P     R+ 
Sbjct: 245 NLPSPPDFRDRIEAALEHLELSVQFKGERY-----GTLEMRRHYSTYLKGLPKVSVVRNK 299

Query: 297 LTVEAGASTATHHIIE 312
           L  E         +++
Sbjct: 300 LVREESPEQVASILLD 315


>gi|226329369|ref|ZP_03804887.1| hypothetical protein PROPEN_03274 [Proteus penneri ATCC 35198]
 gi|225202555|gb|EEG84909.1| hypothetical protein PROPEN_03274 [Proteus penneri ATCC 35198]
          Length = 307

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 130/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    S +    ++QI G+D
Sbjct: 1   MAGVTDRPFRSLCYDM-GAGMTVSEMLSSNPQVWQTDKSRLRMVHSDELGIRSVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  D G   I++N+GCP+ +V++   G+ L+ +PD+V + ++A+  A+ +P
Sbjct: 60  PVDMAAAAKINADSGAQIIDINMGCPAKKVNKKLAGSALLRHPDLVAEILSAVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            + K  ++ G+  + IH R         ++       +YD 
Sbjct: 120 VTLKIRTGWSPDERN--CVEIAKLAERCGIQALTIHGRT--------RECLFKGEAEYDS 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IRTVKQ-NVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +   + +      Y       G   +   +H+           + R  
Sbjct: 229 ELLPPLPIAEVQQIMQKHVRELHDFY-----GQGKGTRIARKHVSWYLKEHAPDDQFRRS 283

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 AS      +E  F   +  
Sbjct: 284 FNAIEDASE-QLEALEAYFENFLRK 307


>gi|53715845|ref|YP_101837.1| putative TIM-barrel enzyme [Bacteroides fragilis YCH46]
 gi|60683764|ref|YP_213908.1| putative TIM-barrel protein, dihydrouridine synthase [Bacteroides
           fragilis NCTC 9343]
 gi|253564624|ref|ZP_04842081.1| conserved hypothetical protein [Bacteroides sp. 3_2_5]
 gi|265764712|ref|ZP_06092987.1| conserved hypothetical protein [Bacteroides sp. 2_1_16]
 gi|52218710|dbj|BAD51303.1| putative TIM-barrel enzyme [Bacteroides fragilis YCH46]
 gi|60495198|emb|CAH10019.1| putative TIM-barrel protein, possible dihydrouridine synthase
           [Bacteroides fragilis NCTC 9343]
 gi|251948400|gb|EES88682.1| conserved hypothetical protein [Bacteroides sp. 3_2_5]
 gi|263254096|gb|EEZ25530.1| conserved hypothetical protein [Bacteroides sp. 2_1_16]
 gi|301165349|emb|CBW24921.1| putative TIM-barrel protein, possible dihydrouridine synthase
           [Bacteroides fragilis 638R]
          Length = 324

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 77/301 (25%), Positives = 130/301 (43%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L    +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKKF-GADMVYTEFVSSDALIRSVNKTTQKLTICDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AA+IVE+   + +++N GCP  +V     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TEAMVGAARIVEEAQPDILDINFGCPVKKVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADHKIIV--DLAEQLQDCGIAALAIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +   + A +      VD +MIGR +     +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTAAGAKECFERYGVDAIMIGRGSIGRPWIFREVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                     R   +++  +       +   L     +  I RH+    LF G PN R  
Sbjct: 247 GEE-----LPRESFEWYLDVLREEVLNSVARLDERRGIIHIRRHLAATPLFKGIPNFRET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|256380793|ref|YP_003104453.1| TIM-barrel protein, nifR3 family [Actinosynnema mirum DSM 43827]
 gi|255925096|gb|ACU40607.1| TIM-barrel protein, nifR3 family [Actinosynnema mirum DSM 43827]
          Length = 393

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 74/308 (24%), Positives = 124/308 (40%), Gaps = 24/308 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R   +   L   EMI A A++  D K +  L F   E P ++Q+   
Sbjct: 39  MAGITNIAFRQLCREFGSPGSLYVCEMITARAVVERDSKTMEMLAFGPDEHPRSMQLYSV 98

Query: 58  DISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-- 114
           D   + EA K++  +   + I++N GCP  +V     GA L     +  + + A  +A  
Sbjct: 99  DPVSMSEAVKLITGEDRADHIDMNFGCPVPKVTRKGGGAALPYKRKLFREIVRAAVRAAE 158

Query: 115 -LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVTVK RIG+DD+   +   +  +  +  G   + +HAR A          R    
Sbjct: 159 PAGVPVTVKFRIGIDDE--HLTYLDAGRIAEDEGAQAVALHARTA--------AQRYSGT 208

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            D+  +  +K+    + +  NG +     AL ++     DGV++GR       +   +  
Sbjct: 209 ADWSAITRLKEAVTSIPVLGNGDIFSARDALDMVARTGCDGVVVGRGCLGRPWLFGELQA 268

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
            F      + P   +V    WR          A HL     ++ + +HM     GFP   
Sbjct: 269 AFRGEPLPAPPTLGKVADILWRH-----GALLADHLGEEKGVRDLRKHMAWYLKGFPVGG 323

Query: 292 RCRHILTV 299
             R  L +
Sbjct: 324 DLRRSLAM 331


>gi|329956495|ref|ZP_08297092.1| TIM-barrel protein, nifR3 family [Bacteroides clarus YIT 12056]
 gi|328524392|gb|EGF51462.1| TIM-barrel protein, nifR3 family [Bacteroides clarus YIT 12056]
          Length = 325

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 142/325 (43%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLMCKGF-GADMVYTEFVSSDALIRSVSKTEQKLNISDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + +++N GCP  RV     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TDTMVEAARIVEQARPDILDINFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVADAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDAGNKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG +    +A +      VD +MIGRA++    +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPVIGNGDVTTPQRAKECFDRYGVDAIMIGRASFGRPWIFKEVKHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P+      +  R+        + + L     +  + RH+    LF G PN R  
Sbjct: 247 GEEMP-PLSAEWKLNVLRREVED----SVKLLDERRGILHVRRHLAASPLFKGIPNFRDT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A      + I +    L+
Sbjct: 302 R-IAMLRAETKEELYRIFKEIEKLI 325


>gi|330444963|ref|ZP_08308617.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328493081|dbj|GAA03114.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 321

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 123/300 (41%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K++  +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPDLWKTSKSLNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD+V D +  +  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQYPDLVEDILRTVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +       ++ K  ++ G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWDLENRN--CVDIAKLAEQCGIQALALHGRT--------KACMYKGEAEYDY 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y +  
Sbjct: 186 IRAVKQAI-SIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGKPWIFREIHHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    V +     +      Y          L+   +H+         +   R  
Sbjct: 245 EHLAAPSIDEVSEIMLGHVQELHQFY-----GEYLGLRIARKHVSWYLKEHAPAGDFRQT 299


>gi|38604693|sp|O52533|DUSB_PROVU RecName: Full=tRNA-dihydrouridine synthase B
 gi|3885442|gb|AAC77884.1| yhdG homolog [Proteus vulgaris]
          Length = 323

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 130/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    S +    ++QI G+D
Sbjct: 17  MAGVTDRPFRSLCYDM-GAGMTVSEMLSSNPQVWQTDKSRLRMVHSDELGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  D G   I++N+GCP+ +V++   G+ L+ +PD+V + ++A+  A+ +P
Sbjct: 76  PVDMAAAAKINADSGAQIIDINMGCPAKKVNKKLAGSALLRHPDLVAEILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            + K  ++ G+  + IH R         ++       +YD 
Sbjct: 136 VTLKIRTGWSPDERN--CVEIAKLAERCGIQALTIHGRT--------RECLFKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-NVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +   + +      Y       G   +   +H+           + R  
Sbjct: 245 ELLPPLPIAEVQQIMQKHVRELHDFY-----GQGKGTRIARKHVSWYLKEHAPDDQFRRS 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 AS      +E  F   +  
Sbjct: 300 FNAIEDASE-QLEALEAYFENFLRK 323


>gi|134294770|ref|YP_001118505.1| nifR3 family TIM-barrel protein [Burkholderia vietnamiensis G4]
 gi|134137927|gb|ABO53670.1| tRNA-U20-dihydrouridine synthase [Burkholderia vietnamiensis G4]
          Length = 355

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L    K +       + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSAKTMRRANHEGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVDNGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDREHKNAVT--VARLAEAAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +   ++A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYETIAAVKAAVG-IPVVANGDIASPAKAKAVLDATGADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIRQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|113866532|ref|YP_725021.1| transfer RNA-dihydrouridine synthase [Ralstonia eutropha H16]
 gi|113525308|emb|CAJ91653.1| transfer RNA-dihydrouridine synthase [Ralstonia eutropha H16]
          Length = 353

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 130/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            S + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PSMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVQAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G + +        +   ++ +G++ + IH R         + +    N +Y
Sbjct: 136 VPVTLKIRTGWNRENRNA--LRIAHMVEDAGISMLTIHGRT--------RADLYHGNAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K     + +  NG +    +A ++  L   D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVK-AAVSIPVVANGDITTPQKAKQVLALTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 SP    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGEMLPSPEVAEIRAIMNAHLEDHYAFYGEF-----TGVRTARKHIAWYTRGLRGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|329925512|ref|ZP_08280386.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. HGF5]
 gi|328939795|gb|EGG36135.1| TIM-barrel protein, nifR3 family [Paenibacillus sp. HGF5]
          Length = 343

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 82/310 (26%), Positives = 141/310 (45%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D
Sbjct: 20  MAGVCNPAFRLIAKEF-GTGLVCAEMVSGKAIVHGNKRTQEMLFVDEREKPLSLQIFGGD 78

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK+V +    + I++N+GCP+ +V +   GA  +L+ + + + +AA+  A++ 
Sbjct: 79  RVSLVEAAKVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLDSNKIYEMVAAVVDAVNK 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D            ++++++G   + +H R         ++     + D+D
Sbjct: 139 PVTVKMRTGWDSDHIYAV--ENAQAVERAGGQAVSVHGRT--------REQLYTGHADWD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG +     A ++L     DGVMIGR A  N  ML    EY   
Sbjct: 189 IIRQVK-EAVSIPVIGNGDVVTPEDARRMLDTTGCDGVMIGRGALGNPWMLYRTVEYLKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S P      +     I+    D           ++++ +H+     G   S R + 
Sbjct: 248 GQLLSDPSPQEKIR-----IAILHMDRLIALRGEAVAVREMRKHLSWYLKGLKGSARIKD 302

Query: 296 ILTVEAGAST 305
           I+  E     
Sbjct: 303 IIMEETKRDE 312


>gi|258512048|ref|YP_003185482.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257478774|gb|ACV59093.1| TIM-barrel protein, nifR3 family [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
          Length = 328

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 140/323 (43%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+ L    ++  EM+    ++ G++K+  +      E P++LQ+ G D
Sbjct: 19  MAGVCNPPFRRLAKEL-GAGMVCAEMVSDKGLVSGNEKSKKMTTILPDEHPVSLQLVGYD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ + +AA++V +   + I++N+GCP  ++ +   GA L  +P+     + A+   ++ P
Sbjct: 78  LASMEQAAEMVGETNADLIDINMGCPVLKICKTGSGAALARDPNYAAKIVRAVVSRVNKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V    +  +++++G   + +H R A                D+DI
Sbjct: 138 VTVKFRKGWDDD--HVNAVEVALAVQEAGAQAVAVHGRTAK--------QMYSGKADWDI 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + D   A +++     D VM+GRAA  N  +   +  Y    
Sbjct: 188 IRRVK-EAVRIPVIGNGDVVDPISAKRLMEETGCDAVMVGRAALGNPWIFREIAHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   R +   + ++    +     ++++ +H      G P +   R +
Sbjct: 247 ELLPPPSVEERLEVTLRHM-RMLVEFKGEDIG----VREMRKHAAWYVKGLPGAAEVRTL 301

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +  +   +     ++      ++
Sbjct: 302 INQQTTMAGM-EAVLRDYCEWVL 323


>gi|157372656|ref|YP_001480645.1| tRNA-dihydrouridine synthase B [Serratia proteamaculans 568]
 gi|157324420|gb|ABV43517.1| putative TIM-barrel protein, nifR3 family [Serratia proteamaculans
           568]
          Length = 321

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 17  MAGITDRPFRALCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAARINVAGGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILHAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +  G+  + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWEPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPPPLGEVKRLLIGHIRELHGFY-----GQGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|326560525|gb|EGE10907.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 7169]
          Length = 341

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 138/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 37  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL +AA+     G   +++N+GCP+ +V     G+ L+ + D+V   + +   A+ +P
Sbjct: 96  PDKLAQAAQFQVANGAQIVDINMGCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++GV  I IH R         +++       Y++
Sbjct: 156 VTLKTRLGFANGQ--ENILKIAQIAEQAGVAAITIHGRT--------REDFYTGQARYEL 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++KK    + I +NG ++   +AL I      D VMIGRAA     +   +  + +  
Sbjct: 206 ITQVKKAA-KIPIIVNGDIDSPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTG 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +SP    + +   R +      Y           +   +H+     G PNS   R  
Sbjct: 265 ELLASPTVGEIHEVVLRHLDELYRFY-----GEYSGCRIARKHIAWYTGGLPNSNAFRDA 319

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +            +++  FN +
Sbjct: 320 MYACETTKE-QFEVVDKFFNTI 340


>gi|326564876|gb|EGE15080.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 12P80B1]
          Length = 340

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 137/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 36  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAE 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL +AA+     G   +++N+GCP+ +V     G+ L+ + D+V   + +   A+ +P
Sbjct: 95  PDKLAQAAQFQVANGAQIVDINMGCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++GV  I IH R         +++       Y++
Sbjct: 155 VTLKTRLGFANGQ--ENILKIAQIAEQAGVAAITIHGRT--------REDFYTGQARYEL 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++KK    + I +NG ++   +AL I      D VMIGRAA     +   +  + +  
Sbjct: 205 ITQVKKAA-KIPIIVNGDIDSPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTG 263

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +SP    + +   R +      Y           +   +H+     G PNS   R  
Sbjct: 264 ELLASPTVGEIHEVVLRHLDELYRFY-----GEYSGCRIARKHIAWYTGGLPNSNAFRDA 318

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +            +++  F  +
Sbjct: 319 MYACETTKE-QFEVVDKFFKTI 339


>gi|313158033|gb|EFR57439.1| TIM-barrel protein, nifR3 family [Alistipes sp. HGB5]
          Length = 340

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 135/300 (45%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R+  +      ++YTE I +D ++R   K++  L     E+P+ +Q+ G  
Sbjct: 18  MEDVTDPSFRYMCKRF-GADVVYTEFISSDGLIRDAAKSLKKLEIDAAERPVGIQLYGHL 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +VEAA++ E  G + I++N GCP  ++     G+ +M +  ++ +    + +A+  P
Sbjct: 77  IEPMVEAARMAEAAGPDIIDINFGCPVKKIAGRGAGSGMMRDVPLMVEMTRRIVQAVRKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++   +    +   ++  G+  + +H R         +        D+ +
Sbjct: 137 VTVKTRLGWDEESKNIE--EIALRLQDVGIAALTVHGRT--------RAQMYRGEADWTL 186

Query: 179 VYEIKKENP--DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++K  NP   + I  NG ++   +A ++     VDGVMIGRA Y    +   V  Y +
Sbjct: 187 IGKVKN-NPQIHIPIIGNGDVDSGPKAAEMFDRYGVDGVMIGRATYGRPWIFREVKHYLA 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +     +  S+             + ++ RH+   F G P+ +  R
Sbjct: 246 TGEVLPQPSVCERVEIAKEHLRKSL-----EVKGEFVGILEMRRHLSNYFKGLPDFKPTR 300


>gi|312797262|ref|YP_004030184.1| tRNA-dihydrouridine synthase [Burkholderia rhizoxinica HKI 454]
 gi|312169037|emb|CBW76040.1| tRNA-dihydrouridine synthase [Burkholderia rhizoxinica HKI 454]
          Length = 392

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 132/308 (42%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +   +   +EM+ ++A L   +K +       + +P+A+QI GAD
Sbjct: 56  MAGVTDRPFRQLCKRM-GASYAVSEMVASNAQLWKSEKTMRRANHDGEVEPIAVQIAGAD 114

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + L +AA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+ +A+S  
Sbjct: 115 PAMLAQAAQYNVAHGAQIIDINMGCPAKKVCNVAAGSALLQNEALVARILEAVVRAVSTG 174

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  +++G++ + +H R         + +     
Sbjct: 175 PDAVPVTLKIRTGWDREHRNA--LTIARLAEQAGISMLTVHGRT--------RADLYHGQ 224

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K  +  + +  NG +    +A ++L     D +MIGRAA     +   +  
Sbjct: 225 AEYDTIAAVK-ASVHIPVVANGDITTPHKAREVLSITGADAIMIGRAAQGRPWLFREIGH 283

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           + +       P    + +     +      Y          ++   +H+     G   + 
Sbjct: 284 FLATGEVLPPPRIDEIQQWMNEHLQDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 338

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 339 AFRHRMNT 346


>gi|300776181|ref|ZP_07086040.1| tRNA-dihydrouridine synthase B [Chryseobacterium gleum ATCC 35910]
 gi|300505314|gb|EFK36453.1| tRNA-dihydrouridine synthase B [Chryseobacterium gleum ATCC 35910]
          Length = 331

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 134/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    L+Y+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MHGADLMYSEFISSEGLIRDAIKSRKKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +A+IVE    + +++N GCP  +V     GA ++ + D++     A+  +  + 
Sbjct: 78  EEAMAMSARIVETVNPDLVDINFGCPVKKVVCKGAGAGVLKDIDLMVRLTKAVVSSTHLS 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++++G+  + IHAR         +        D++ 
Sbjct: 138 VTVKTRLGWD--STSINIDEVAERLQETGIKALTIHART--------RAQMYKGEADWEH 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+  N ++ I  NG ++   +AL+       DG+MIGRAA     +   +  +F  
Sbjct: 188 ISRIKQNPNIEIPIFGNGDIDSAEKALEYKQKYACDGIMIGRAAIGYPWIFNEIKHFFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P  +               +++A        L ++ +H    F G P+ +  R
Sbjct: 248 GEHLPEPTISDRLL-----AVRQHAEWSAEWKGERLGLVEMRQHYSNYFRGIPHFKEFR 301


>gi|255012934|ref|ZP_05285060.1| putative TIM-barrel enzyme [Bacteroides sp. 2_1_7]
          Length = 329

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRF-GADMVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITKEVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +       +      VD VMIGRA+     +   V  Y + 
Sbjct: 187 IGAVKNNPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLTT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  +    ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GE-----LLPQEPFSWYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFKQT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|71909277|ref|YP_286864.1| dihydrouridine synthase TIM-barrel protein nifR3 [Dechloromonas
           aromatica RCB]
 gi|71848898|gb|AAZ48394.1| tRNA-U20-dihydrouridine synthase [Dechloromonas aromatica RCB]
          Length = 337

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 121/299 (40%), Gaps = 22/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G  K +   + + +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
              + EAAK   D G   I++N+GCP+ +V     G+ LM +   VG  + A+  A+ + 
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKVCNVMAGSALMQDEQQVGRILDAVVAAIPNT 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G    +       + +  + +G+  + IH R    +             +YD
Sbjct: 136 PVTLKFRTGW--NLANKNAPTIARIAESAGIRAVAIHGRTRCQQ--------YTGEAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG +    +A  +L     DGVMIGRAA     +   ++ Y   
Sbjct: 186 TIAMVKTLI-SIPVIANGDITTPEKAKHVLDVTGADGVMIGRAAQGRPWLFREIEHYLKT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                      +       +      Y           +   +H+     G   S   R
Sbjct: 245 GEHLPPAEVMEIHSILLEHLEDLYAFYGPE-----TGFKVARKHISWYTKGLVGSAAFR 298


>gi|319936962|ref|ZP_08011372.1| transcriptional regulator [Coprobacillus sp. 29_1]
 gi|319807898|gb|EFW04477.1| transcriptional regulator [Coprobacillus sp. 29_1]
          Length = 335

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 144/323 (44%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+ +EM+   A+  G++K   +L     E P+++Q+ G D
Sbjct: 17  MAGITNVAFRKIIKEF-GAGLVVSEMVSDKALCYGNQKTIEMLKVDENEHPMSIQVFGGD 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V AAK V++    + I++N+GCP  +V +   G+ L+  PD+V D + ++ +A+S 
Sbjct: 76  VESMVTAAKFVDENSNCDIIDINMGCPVNKVLKAHAGSYLLQFPDLVYDIVKSVVEAVSK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D    ++    + + I+++G + I +H R         +      + D+ 
Sbjct: 136 PVTVKIRIGYD--FDSINCVEIAQLIERAGASAIAVHGRT--------RSQMYEGHADWS 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E   + +  NG ++    A ++L     D VM+GRAA  N  ++  + EY  +
Sbjct: 186 WIKKVK-EAVSIPVIGNGDVKTAKDAKRMLEETGCDAVMVGRAALGNPWVIKQMVEYVEH 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P          +     +             ++Q+  H      G  ++   ++
Sbjct: 245 DILLGDPTADERIDQCLKHAQRLIP-----VEGEKNAIRQMRGHAPWYIKGLKSASVIKN 299

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            L+           I+E   + +
Sbjct: 300 YLSKVDTYQQM-QEILEAYRHYL 321


>gi|119486469|ref|ZP_01620527.1| Dihydrouridine synthase TIM-barrel protein [Lyngbya sp. PCC 8106]
 gi|119456371|gb|EAW37502.1| Dihydrouridine synthase TIM-barrel protein [Lyngbya sp. PCC 8106]
          Length = 344

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 134/320 (41%), Gaps = 23/320 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  +    +   ++     E+P+++Q+       
Sbjct: 34  GVTDLVFRRLVRRYAPESMMYTEMVHASQVRHLEELPQMMEVDPNERPISIQLFDCRPDF 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA+     G N +++N+GCP  ++ +   G+ L+  P +    + ++ +A+++PVTV
Sbjct: 94  LAEAAQRAVTEGANTVDINMGCPVNKITKKGGGSSLLRQPKVAEAIVQSVVEAVNVPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DD    + + +  K ++ SG   I IHAR         +        +++ + +
Sbjct: 154 KTRIGWDDNE--INILDFAKRMEDSGAAMITIHART--------RAAGYNGKANWEWIAK 203

Query: 182 IKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  +  A+    L   DGVM  R       ++  +D +       
Sbjct: 204 VKQ-ILSIPVIANGDIISVESAIDCLQLTGADGVMCSRGTLGYPFLVGEIDAFLKTGEVK 262

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILT 298
                     +   ++  +     A   + G + + Q  +HM     GF  +   R+ L 
Sbjct: 263 P-------GANIMERLLCAKEHLKALGEYKGERGIYQSRKHMTWYAKGFAGANELRNQLA 315

Query: 299 VEAGASTATHHIIETAFNLM 318
                      +I+ A  ++
Sbjct: 316 KIESVEQ-GCDLIDRAIAIL 334


>gi|281424760|ref|ZP_06255673.1| tRNA-dihydrouridine synthase [Prevotella oris F0302]
 gi|281401130|gb|EFB31961.1| tRNA-dihydrouridine synthase [Prevotella oris F0302]
          Length = 334

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/328 (25%), Positives = 145/328 (44%), Gaps = 25/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +  +  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRMLCKRY-GAAMVYTEFVSADAIIRSIKSTLDKMAINDAERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I+LN GCP  +V     G+ ++ N  ++ D    + KA+S P
Sbjct: 77  VESMVEAAKIVEQVKPDLIDLNFGCPVKKVAGKGAGSGMLRNIPLLLDITRNVVKAVSTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--SLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +    +A        VD VM+GRA +    +   + ++  N
Sbjct: 187 IGNVKSNPRIHIPIIGNGDITTPEEAKHAFDDYGVDAVMVGRATFGRPWVFKEMRDFIDN 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             +    I  ++D      I           +     +    RH+    +F G P+ ++ 
Sbjct: 247 TTSSPLTIDDKID------ILEEQLRINVERIDEYRGIIHTRRHLASSPIFKGIPDFKQT 300

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I+E     +  S
Sbjct: 301 R-IAMLRATKVDELIAILEECREKLRPS 327


>gi|260914496|ref|ZP_05920965.1| tRNA-dihydrouridine synthase B [Pasteurella dagmatis ATCC 43325]
 gi|260631597|gb|EEX49779.1| tRNA-dihydrouridine synthase B [Pasteurella dagmatis ATCC 43325]
          Length = 316

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 133/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R         AL ++EM+  +  +   +K+ L           A+QI G+D
Sbjct: 1   MAGITDQPFRKICSHY-GAALTFSEMMSTNPRVWHTEKSKLRLAHHQDAGINAVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 60  PIEMAAAAQVNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILEAVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  +++G+  + IH R         K      + +YD 
Sbjct: 120 VTLKIRTGWDKENRN--CLEIAQIAEQAGIQALTIHGRT--------KTCMFEGDAEYDS 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A  +L   + D VMIGR A  +  +   V+      
Sbjct: 170 IRAVKQHI-SIPVIANGDITSAEKAKFVLDYTNADAVMIGRGALGSPWIFNQVNSLIEKK 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          + I      Y       G ++    +H+     G   +   R  
Sbjct: 229 SITLAPSLDEKCAVILQHIRDLHQFYGVE---KGYRI--ARKHVTWYLQGIQPNSVFRQA 283

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
                 +       +E  FNL++
Sbjct: 284 FNA-ITSPEEQLIALEDFFNLIL 305


>gi|256838548|ref|ZP_05544058.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|298374169|ref|ZP_06984127.1| hypothetical protein HMPREF0104_00320 [Bacteroides sp. 3_1_19]
 gi|256739467|gb|EEU52791.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|298268537|gb|EFI10192.1| hypothetical protein HMPREF0104_00320 [Bacteroides sp. 3_1_19]
          Length = 329

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRF-GADMVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEAHPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +       +      VD VMIGRA+     +   +  Y + 
Sbjct: 187 IGAVKNNPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREIKHYLTT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  +    ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GK-----LLPQEPFSWYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFKQT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|218258330|ref|ZP_03474732.1| hypothetical protein PRABACTJOHN_00387 [Parabacteroides johnsonii
           DSM 18315]
 gi|218225570|gb|EEC98220.1| hypothetical protein PRABACTJOHN_00387 [Parabacteroides johnsonii
           DSM 18315]
          Length = 343

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 141/319 (44%), Gaps = 24/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + ADA++R   K    L  + +E+P+A+QI G D
Sbjct: 18  MEDVTDVSFRLMCKRF-GADMVYTEFVSADALIRSVNKTQQKLNVANEERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+I E    + +++N GCP  RV     GA ++ N  ++ D    + KA++IP
Sbjct: 77  VPTMVEAAQICEAAHPDILDINFGCPVKRVAGKGAGAGMLRNISLMLDITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRIIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +       +      VD VMIGR +     +   V  + + 
Sbjct: 187 IGEVKKNPRMQIPIIGNGDVTSAEICKQRFEQYGVDAVMIGRGSIGRPWIFREVKHFLNT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                +   +     ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GELLPAESFS-----WYLDILKKQVEQSVARLDERRGILHIRRHLAATPLFKGIADFKQT 301

Query: 294 RHILTVEAGASTATHHIIE 312
           R +  + A    A   I++
Sbjct: 302 R-VAMLRAETVEALFDILD 319


>gi|282879049|ref|ZP_06287809.1| TIM-barrel protein, nifR3 family [Prevotella buccalis ATCC 35310]
 gi|281298783|gb|EFA91192.1| TIM-barrel protein, nifR3 family [Prevotella buccalis ATCC 35310]
          Length = 329

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 147/329 (44%), Gaps = 24/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     +++YTE + A+A++R  + ++  L  S  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRQLCKRF-GVSMVYTEFVSAEALVRSIQASLNKLTISDAERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I++N GCP  +V     GA ++ N  ++ +    + KA+  P
Sbjct: 77  VESMVEAAKIVEQAHPDVIDINFGCPVKKVAGKGAGAGMLRNIPLLLEITREVVKAVHTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + +  L + ++  G+  + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDE--NNLIITELAEQLQDCGIQALTIHGRT--------RSQMYTGNADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD +M+GRAA+    +   + +Y   
Sbjct: 187 IGEVKNNPRIHIPIIGNGDITSPQEAKQAFERFGVDAIMVGRAAFGQPWIFKEMRDYLDG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P    +  +    I           +     +    RH+    +F G P+ R+ 
Sbjct: 247 -----KPYDASLGINKKIDILKEQLHINVSRIDEYRGILHTRRHLAASPIFKGIPDFRQT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R I  + A       +I+E     +++ L
Sbjct: 302 R-IAMLRASTVVELENILEACRKRLVDEL 329


>gi|150009773|ref|YP_001304516.1| putative TIM-barrel enzyme [Parabacteroides distasonis ATCC 8503]
 gi|149938197|gb|ABR44894.1| putative TIM-barrel enzyme [Parabacteroides distasonis ATCC 8503]
          Length = 329

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRF-GADMVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +       +      VD VMIGRA+     +   V  Y + 
Sbjct: 187 IRAVKNNPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLTT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  +    ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GE-----LLPQEPFSWYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFKQT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|254523878|ref|ZP_05135933.1| tRNA-dihydrouridine synthase B [Stenotrophomonas sp. SKA14]
 gi|219721469|gb|EED39994.1| tRNA-dihydrouridine synthase B [Stenotrophomonas sp. SKA14]
          Length = 357

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 133/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K+I  +    +  P+++QI G +
Sbjct: 43  MAGVTDKPFRLLCKRL-GAGLAASEMTISDPRFWNTRKSIHRMDHDGEPAPISVQIAGTE 101

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 102 PQQLAEAARYNVDHGAQIIDINMGCPAKKVCNAWAGSALMRDEQLVARILEAVVNAVDVP 161

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D       L  + +  + SG+  + +H R         +D       +Y  
Sbjct: 162 VTLKIRTGWDCDHRNGPL--IARIAEDSGIAALAVHGRT--------RDQHYTGQAEYGT 211

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG ++   +A  +L    VD VMIGR+A     +   V  Y +  
Sbjct: 212 IGEIKAAL-RIPVIANGDIDSPQKAALVLKQTGVDAVMIGRSAQGRPWIFREVAHYLATG 270

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P +   R +
Sbjct: 271 EELPPPSLAEVRDILLGHLHALHAFYGEPQ-----GVRIARKHLGWYAKDRPENAAFRAV 325

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    +   +    F+ +I
Sbjct: 326 VN-RAQDPQSQIALTTEYFDRLI 347


>gi|282880523|ref|ZP_06289230.1| TIM-barrel protein, nifR3 family [Prevotella timonensis CRIS 5C-B1]
 gi|281305626|gb|EFA97679.1| TIM-barrel protein, nifR3 family [Prevotella timonensis CRIS 5C-B1]
          Length = 327

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 144/327 (44%), Gaps = 24/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     +++YTE + A+A++R  K  +  L    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GVSMVYTEFVSAEALVRSIKSTVNKLTICEEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IV     + I+LN GCP  +V     GA ++ N  ++ +    + KA+ IP
Sbjct: 77  VASMVEAAQIVAQSKPDVIDLNFGCPVKKVAGKGAGAGMLQNIPLMLEITREVVKAVHIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWD--ASHLIITELAEQLQDCGIQALTIHGRT--------RSQMYTGKADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +    +A        VDGVM+GRA++    +   +  Y   
Sbjct: 187 IGEVKKNPRIHIPIIGNGDITSAEEAKHAFETYGVDGVMVGRASFGCPWIFKEMRNYLDG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P     D +    I           +     +    RH+    +F G P+ R+ 
Sbjct: 247 -----KPSDESFDLNKKLDILLEQLHINVARIDEYRGILHTRRHLAASPIFKGIPDFRQT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R I  + A        I+E    ++++
Sbjct: 302 R-IAMLRATTVKELEDILEKCREIIVK 327


>gi|167837831|ref|ZP_02464714.1| dihydrouridine synthase [Burkholderia thailandensis MSMB43]
          Length = 354

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVDAVGTG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + K  + +G++ + +H R         + +    +
Sbjct: 137 PGAVPVTLKIRTGWDREHRNAV--EIAKLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +  
Sbjct: 187 AEYDTITAVK-AAVRIPVVANGDITSPQKAKAVLDATGADALMIGRAAQGRPWLFREIGH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +  +      P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQSGELLPPPRIDEIRQVMHEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|298372677|ref|ZP_06982667.1| hypothetical protein HMPREF0156_00722 [Bacteroidetes oral taxon 274
           str. F0058]
 gi|298275581|gb|EFI17132.1| hypothetical protein HMPREF0156_00722 [Bacteroidetes oral taxon 274
           str. F0058]
          Length = 325

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 131/301 (43%), Gaps = 22/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      L+YTE + ADA++R   + +  L    +E+P+A+QI G D
Sbjct: 18  MEDVTDPAFRLVCKEF-GADLVYTEFVSADALVRFVNRTMQKLTIVDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V+AAKIV +   + I++N GCP  ++     GA L+ +   + D   ++ KA+++P
Sbjct: 77  PQTMVDAAKIVAESNPDIIDINFGCPVKKIASKGAGAGLLRDIPRLLDITQSVVKAVNLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD      +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDDNSK--IICTLARQLQDCGIAALAIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K +    + I  NG +     A        VD +M+GR A  N+ +   +      
Sbjct: 187 IGEVKNDPKIKIPIIGNGDITTPEVAEDKFHRYGVDAIMVGRGAIGNAWIFAEIKNRLLG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
               S P      +   R I  S              +    RH+    +F G PN +  
Sbjct: 247 ENRYSVPNFESRKEILKRHIINS----IEWLKDERKGIIHSRRHIAATPIFKGIPNFKPT 302

Query: 294 R 294
           R
Sbjct: 303 R 303


>gi|18311449|ref|NP_563383.1| putative dihydrouridine synthase [Clostridium perfringens str. 13]
 gi|110799132|ref|YP_697155.1| putative dihydrouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|110803269|ref|YP_699723.1| putative dihydrouridine synthase [Clostridium perfringens SM101]
 gi|168206862|ref|ZP_02632867.1| putative dihydrouridine synthase [Clostridium perfringens E str.
           JGS1987]
 gi|168211211|ref|ZP_02636836.1| putative dihydrouridine synthase [Clostridium perfringens B str.
           ATCC 3626]
 gi|168215145|ref|ZP_02640770.1| putative dihydrouridine synthase [Clostridium perfringens CPE str.
           F4969]
 gi|168218227|ref|ZP_02643852.1| putative dihydrouridine synthase [Clostridium perfringens NCTC
           8239]
 gi|182626021|ref|ZP_02953784.1| putative dihydrouridine synthase [Clostridium perfringens D str.
           JGS1721]
 gi|18146133|dbj|BAB82173.1| probable transcriptional regulator [Clostridium perfringens str.
           13]
 gi|110673779|gb|ABG82766.1| putative dihydrouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|110683770|gb|ABG87140.1| putative dihydrouridine synthase [Clostridium perfringens SM101]
 gi|170661755|gb|EDT14438.1| putative dihydrouridine synthase [Clostridium perfringens E str.
           JGS1987]
 gi|170710780|gb|EDT22962.1| putative dihydrouridine synthase [Clostridium perfringens B str.
           ATCC 3626]
 gi|170713442|gb|EDT25624.1| putative dihydrouridine synthase [Clostridium perfringens CPE str.
           F4969]
 gi|177908728|gb|EDT71239.1| putative dihydrouridine synthase [Clostridium perfringens D str.
           JGS1721]
 gi|182379765|gb|EDT77244.1| putative dihydrouridine synthase [Clostridium perfringens NCTC
           8239]
          Length = 326

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 63/307 (20%), Positives = 140/307 (45%), Gaps = 24/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    ++ TEM+ A A+  G  + K ++  + +EKP++ Q+ G D
Sbjct: 17  MAGVTDISFRGLCKEM-GAGIVCTEMVSAKALYYGSENTKELMRIADEEKPVSCQMFGND 75

Query: 59  ISKLVEAAK--IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              +    +     +     I++N+GCP+ ++ +   G+ LM NP +  + ++++ K  +
Sbjct: 76  PEIMAYVTEKHFNTNDDICIIDVNMGCPAPKIVKNGEGSALMKNPKLAYEIMSSIKKVAT 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R+G D++   +      K ++++GV+ I +H R         +        ++
Sbjct: 136 KPVTVKFRMGFDEE--NINAVEFAKIMEEAGVDAIAVHGRT--------RAQMYEGKANW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ ++K E  ++ +  NG +     A  LK   + DG+M+ R +  N  +   + +  +
Sbjct: 186 DIIRQVK-EAVNIPVIGNGDVFTAEDALSLKNQTNCDGIMVARGSMGNPWIFKQIVQKLN 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                    + ++D      +     + + ++      ++++ +H      G  N    +
Sbjct: 245 GEEVYMPTPEEKID------MCIRHYNLSLKYDGEYKAVREMRKHAAWYIKGLNNCTEVK 298

Query: 295 HILTVEA 301
           + L +EA
Sbjct: 299 NRLNLEA 305


>gi|296113151|ref|YP_003627089.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis RH4]
 gi|295920845|gb|ADG61196.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis RH4]
 gi|326560349|gb|EGE10736.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis 46P47B1]
 gi|326565746|gb|EGE15908.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis BC1]
 gi|326577196|gb|EGE27090.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis O35E]
          Length = 341

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 137/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 37  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL +AA+     G   +++N+GCP+ +V     G+ L+ + D+V   + +   A+ +P
Sbjct: 96  PDKLAQAAQFQVANGAQIVDINMGCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++GV  I IH R         +++       Y++
Sbjct: 156 VTLKTRLGFANGQ--ENILKIAQIAEQAGVAAITIHGRT--------REDFYTGQARYEL 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++KK    + I +NG ++   +AL I      D VMIGRAA     +   +  + +  
Sbjct: 206 ITQVKKAA-KIPIIVNGDIDSPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTG 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +SP    + +   R +      Y           +   +H+     G PNS   R  
Sbjct: 265 ELLASPTVGEIHEVVLRHLDELYRFY-----GEYSGCRIARKHIAWYTGGLPNSNAFRDA 319

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +            +++  F  +
Sbjct: 320 MYACETTKE-QFEVVDKFFKTI 340


>gi|288958350|ref|YP_003448691.1| tRNA-dihydrouridine synthase B [Azospirillum sp. B510]
 gi|288910658|dbj|BAI72147.1| tRNA-dihydrouridine synthase B [Azospirillum sp. B510]
          Length = 340

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 138/326 (42%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D  +R   +  +   L+ +EMI + A++R +++   ++    +E P+A+Q+ G +
Sbjct: 31  MSGVSDLPFRRLVKR-SGCGLVVSEMIASQAMIRENRQTLRMVETEPEEFPMAVQLAGCE 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK+ +D G   +++N GCP  +V  G  G+ LM +  + G  + A+ KA+SIP
Sbjct: 90  PEVMAEAAKLNQDRGAAVVDINFGCPVKKVVNGHAGSSLMRDEALAGRILEAVVKAVSIP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D     +   +L +  ++ G+  + +H R  +               D+  
Sbjct: 150 VTLKMRLGWDGTR--LNAPSLARIAEQCGIRMVTVHGRTRM--------QFYTGTADWTA 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K E   + + +NG +       + L     DGVMIGR +Y      + V  Y    
Sbjct: 200 VRAVK-EAVSIPVVVNGDVTSFDAVDRALSESGADGVMIGRGSYGRPWFPSQVMRYLRTG 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P              + ++ Y      S G ++   +H+     G   S   R  
Sbjct: 259 ERLPDPPLHEQMDILLEHFDSMLSHY-----GSDGGIKVARKHVSWYSTGLRGSNEFRQE 313

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           +    G   A    I   +   IE +
Sbjct: 314 IN-RLGDPAAVRDRIRAFYEPAIERM 338


>gi|326796326|ref|YP_004314146.1| hypothetical protein Marme_3091 [Marinomonas mediterranea MMB-1]
 gi|326547090|gb|ADZ92310.1| TIM-barrel protein, nifR3 family [Marinomonas mediterranea MMB-1]
          Length = 329

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 134/319 (42%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R          L+ +EM+ +D  L    K+   L    + +P ++QI GA+
Sbjct: 19  MAGVTDLPFRRLCYQ-QGAGLVVSEMVTSDVRLWNSTKSKHRLVHDKEIQPRSVQIAGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + ++  ++ +P
Sbjct: 78  AEMMVEAAQKNVELGAQIIDINMGCPAKKVLNKAAGSALLKDESLVQDILKSVVDSVEVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + +H R         +  +     +YD 
Sbjct: 138 VTLKIRTGWSSEQRNG--LTIAKIAEDCGIQALAVHGRT--------RACKFQGEAEYDT 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK+    + +  NG + D   A +++     D VMIGRAA     +   ++ Y  + 
Sbjct: 188 IAEIKQSVG-IPVFANGDITDAQTAQRVMTYTKADAVMIGRAAQGRPWIFNEINHYLRHG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP    + +     + A    Y          ++   +H+        ++   R +
Sbjct: 247 ELPPSPDIESIKETVVEHVKALHQFYGEFM-----GIRIARKHVGWYLKTLADTSSFRSL 301

Query: 297 LTVEAGASTATHHIIETAF 315
              +   +     ++E+ F
Sbjct: 302 FN-KTDDANEQLDVLESFF 319


>gi|257092432|ref|YP_003166073.1| TIM-barrel protein, nifR3 family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257044956|gb|ACV34144.1| TIM-barrel protein, nifR3 family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 350

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 65/326 (19%), Positives = 133/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L  +EM+ ++++L G  K         +  P+++QI GA 
Sbjct: 17  MAGVTDRPFRQLCKKM-GAGLAVSEMVTSNSLLYGSAKTQRRARHDGEVAPVSVQIAGAS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + +AA+   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+   
Sbjct: 76  PAMMADAARYNVDRGAQIIDINMGCPAKKICNVMAGSALLRDESLVARILEAVVTAVPDT 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D          +++  ++SG+  + +H R         +        +Y+
Sbjct: 136 PVTLKIRTGWDKTNRNA--LRILQIAEQSGIRALAMHGRT--------RACGYSGAAEYE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K     + +  NG +    +A  +  L   D VMIGRAA     +   ++ +  +
Sbjct: 186 TIREVK-AVARIPVIANGDIGSPEKAQFVLDLTGADAVMIGRAAQGRPWLFREIEHFLES 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    + +     +      Y          ++   +H+     G   S   RH
Sbjct: 245 GTHLMPPRVGEIREILLGHLEDLYVFYGIE-----TGVRVARKHISWYTKGLLGSAAFRH 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ++  +          ++  F+ + E 
Sbjct: 300 MMN-KLPTVDLQRQAVDDFFSALAED 324


>gi|326570396|gb|EGE20436.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis BC8]
          Length = 341

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 137/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 37  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL +AA+     G   +++N+GCP+ +V     G+ L+ + D+V   + +   A+ +P
Sbjct: 96  PDKLAQAAQFQVANGAQIVDINMGCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++GV  I IH R         +++       Y++
Sbjct: 156 VTLKTRLGFANGQ--ENILKIAQIAEQAGVAAITIHGRT--------REDFYTGQARYEL 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++KK    + I +NG ++   +AL I      D VMIGRAA     +   +  + +  
Sbjct: 206 ITQVKKAA-KIPIIVNGDIDSPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTG 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +SP    + +   R +      Y           +   +H+     G PNS   R  
Sbjct: 265 ELLASPTAGEIHEVVLRHLDELYRFY-----GEYSGCRIARKHIAWYTGGLPNSNAFRDA 319

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +            +++  F  +
Sbjct: 320 MYACETTKE-QFEVVDKFFKTI 340


>gi|194364415|ref|YP_002027025.1| TIM-barrel protein, nifR3 family [Stenotrophomonas maltophilia
           R551-3]
 gi|194347219|gb|ACF50342.1| TIM-barrel protein, nifR3 family [Stenotrophomonas maltophilia
           R551-3]
          Length = 331

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 133/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K+I  +    +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAASEMTISDPRFWNTRKSIHRMDHDGEPAPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQIIDINMGCPAKKVCNAWAGSALMRDEQLVARILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D       L  + +  + SG+  + +H R         +D       +Y  
Sbjct: 136 VTLKIRTGWDCDHRNGPL--IARIAEDSGIAALAVHGRT--------RDQHYTGQAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG ++   +A  +L    VD VMIGR+A     +   V  Y +  
Sbjct: 186 IGEIKAAL-RIPVIANGDIDSPQKAAFVLKQTGVDAVMIGRSAQGRPWIFREVAHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P +   R +
Sbjct: 245 EELPPPSLAEVRDILLGHLHALHAFYGEPQ-----GVRIARKHLGWYAKDRPENAAFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    +   +    F+ +I
Sbjct: 300 VN-RAEDPASQIALTTDYFDSLI 321


>gi|299067934|emb|CBJ39148.1| tRNA-dihydrouridine synthase B [Ralstonia solanacearum CMR15]
          Length = 356

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 130/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + +  +++G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDREHRNA--LTVARIAQEAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVK-ASVRIPVVANGDIGTPAKARHVLEVTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|194337545|ref|YP_002019339.1| TIM-barrel protein, nifR3 family [Pelodictyon phaeoclathratiforme
           BU-1]
 gi|194310022|gb|ACF44722.1| TIM-barrel protein, nifR3 family [Pelodictyon phaeoclathratiforme
           BU-1]
          Length = 352

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 143/324 (44%), Gaps = 25/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE I A+A+ RG +K++  L     E+P A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKR-HGADIVYTEFISAEALRRGVEKSLRKLKTDEVERPFAIQIFGSS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +V+AA I E +  + +++N GCP+ +V     GA L+  P+ +     A+ KA+SIP
Sbjct: 76  IESMVDAAVIAEGYCPDYLDINFGCPTKKVAGKGAGAALLREPEKMTAISEAVVKAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D +  ++ + +++  ++  G+  + +H R         +        + + 
Sbjct: 136 VTVKTRIGWDLE--SINILDILPRLEDVGIQALALHGRT--------RSEMFKGRANREW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K++   + +  NG +     AL +      DGVMIGR +  N  +     E     
Sbjct: 186 IRQVKEQA-RIPVIANGDIWSAEDALAMFAETGADGVMIGRGSIGNPFIFEAAKELLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P     D      ++      + +       + ++ RH      G P   R R+ 
Sbjct: 245 KPMPPP-----DFRARIDVAIEHLKLSVQFKGEKYGVLEMRRHYSTYLKGLPMVSRVRNK 299

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           L  E G       +I+       E
Sbjct: 300 LVREDGW----EQVIDILLAYKQE 319


>gi|332531770|ref|ZP_08407655.1| tRNA dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038746|gb|EGI75188.1| tRNA dihydrouridine synthase B [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 326

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 133/327 (40%), Gaps = 32/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K++  +  S +    A+QI GAD
Sbjct: 20  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPKVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + +H R         +      + +Y  
Sbjct: 139 VTLKIRTGWDPDNRNGV--EIARIAERYGIASLAVHGRT--------RACMYKGDAEYAT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y    
Sbjct: 189 IRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-----GFPNSR 291
                P    V       ++     Y           +   +H+          G    R
Sbjct: 248 EHLQPPAIAEVRSILMEHLTNLHMFY-----GEPMGARIARKHVSWYLQTHDSDGQ--FR 300

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
           R  + L        A    +E  F  +
Sbjct: 301 RVFNAL----DNPQAQVVALEQYFKTL 323


>gi|294793386|ref|ZP_06758531.1| tRNA-dihydrouridine synthase [Veillonella sp. 6_1_27]
 gi|294455817|gb|EFG24182.1| tRNA-dihydrouridine synthase [Veillonella sp. 6_1_27]
          Length = 328

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 144/324 (44%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++
Sbjct: 22  MAGVSDIAYRLLAKK-HGAALVCTEMVSAMGIKYKNERTHELLRIEEAERPVSMQIFGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +P
Sbjct: 81  PEAIALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAVDVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  
Sbjct: 141 VTVKMRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   A ++L     D VMIGR A  N  +   +  Y +  
Sbjct: 191 IKAVK-EAVSVPVLGNGDIVEPEDAKQMLDETGCDAVMIGRGAQGNPWIFDRIHHYLATG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          +       D   ++      +++I  H      G P S   R+ 
Sbjct: 250 EVLPAPTDIERLDMLLKH-----FDLLCQYKGESMAVKEIRTHAGWYMKGLPESAYWRNR 304

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +       T+ H+ +E+   ++ E
Sbjct: 305 VNT-IHTVTSFHNELESYRKILSE 327


>gi|325954824|ref|YP_004238484.1| hypothetical protein Weevi_1197 [Weeksella virosa DSM 16922]
 gi|323437442|gb|ADX67906.1| TIM-barrel protein, nifR3 family [Weeksella virosa DSM 16922]
          Length = 332

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 140/326 (42%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + +    L+YTE I ++ ++R   K+   L    +E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCK-MNGADLMYTEFISSEGLIRDAIKSRKKLDIFDEERPIGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIVE    + +++N GCP  +V     GA ++ + D++     ++ ++  +P
Sbjct: 78  EEAMAMSAKIVETVEPDLVDINFGCPVKKVVCKGAGAGVLKDVDLMVRLTKSVVESTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++++G+  + IH R         +      + D+  
Sbjct: 138 VTVKTRLGWD--HDSINIDEVAERLQETGIKALAIHGRT--------RAQMYKGHSDWSH 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K   N ++ I  NG ++   +A++      VDG+MIGRAA  +  +   +  Y   
Sbjct: 188 IARVKANPNIEIPIFGNGDIDSPQKAIEFKEKYGVDGIMIGRAAIGHPWIFNKIKHYRET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     +      +A         + +   H    F G PN +  R 
Sbjct: 248 GEFLPEPTIQERVEAARNHLL-----WAMEWKGERTGILETRMHYTNYFKGIPNFKPYRT 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L  +          IE  F  + E 
Sbjct: 303 KLVTQDNLID-----IEATFKEIEEE 323


>gi|302811002|ref|XP_002987191.1| hypothetical protein SELMODRAFT_125523 [Selaginella moellendorffii]
 gi|300145088|gb|EFJ11767.1| hypothetical protein SELMODRAFT_125523 [Selaginella moellendorffii]
          Length = 363

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 116/329 (35%), Positives = 178/329 (54%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD H+R  AR+L+  + LYTEM+VA+ I+    D +  L F   + P+ LQ+GG++
Sbjct: 9   MMEWTDNHFRALARILSRCSWLYTEMVVAETIVHHENDLERWLEFPAAQHPIVLQLGGSN 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L +AAK+V  FGY+EIN N GCPS++V     FGA LML+P +VG+ + A+ +  S 
Sbjct: 69  LANLSKAAKLVSAFGYDEINFNCGCPSSKVAGHGCFGARLMLSPRLVGEAMQAIGEESSA 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVDD      L N V ++   S      IHARKA+L+GLSP  NR  P L Y
Sbjct: 129 PVTVKCRIGVDDSDSYDQLCNFVSTVSSLSPTQHFIIHARKALLEGLSPAQNRVAPPLKY 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM-LTTVDEYF 233
           + V  + ++ PDL   LNGG+  + Q   ++    V+GVM+GRAAY      L   D   
Sbjct: 189 EYVLALMRDFPDLQFTLNGGITTVEQVNYLISDKGVNGVMLGRAAYNTPWCTLARADSCI 248

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   P +    +   R+          ++ ++   ++ + + +  LFHG   S R 
Sbjct: 249 YG-----MPERRITRRQVLREYEEYAESVIGKYGNNKPGIRVLVKPVANLFHGEKGSSRW 303

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  +   +        ++E    ++ +S+
Sbjct: 304 RQAIDEHS-----FSELLEKTMAVLPDSV 327


>gi|326575731|gb|EGE25654.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moraxella
           catarrhalis CO72]
          Length = 341

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 137/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EMI+AD  L   KK++    F  +  P++ QI GA+
Sbjct: 37  MAGVTDNPFRRLCKSF-GAGHAVSEMIIADTALYARKKSLYRANFDGEIAPISAQIAGAE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL +AA+     G   +++N+GCP+ +V     G+ L+ + D+V   + +   A+ +P
Sbjct: 96  PDKLAQAAQFQVANGAQIVDINMGCPAKKVCRKLAGSALLQDEDLVRRLLDSAVLAVDVP 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + +  +++GV  I IH R         +++       Y++
Sbjct: 156 VTLKTRLGFANGQ--ENILKIAQIAEQAGVAAITIHGRT--------REDFYTGQARYEL 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++KK    + I +NG ++   +AL I      D VMIGRAA     +   +  + +  
Sbjct: 206 ITQVKKAA-KIPIIVNGDIDSPQKALDIQAKTGADAVMIGRAAQGKPWLFQQIAHFANTG 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +SP    + +   R +      Y           +   +H+     G PNS   R  
Sbjct: 265 ELLASPTVGEIHEVVLRHLDELYRFY-----GEYSGCRIARKHIAWYTGGLPNSNAFRDA 319

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +            +++  F  +
Sbjct: 320 MYACETTKE-QFEVVDKFFKTI 340


>gi|16272917|ref|NP_439142.1| hypothetical protein HI0979 [Haemophilus influenzae Rd KW20]
 gi|1176212|sp|P44965|DUSB_HAEIN RecName: Full=tRNA-dihydrouridine synthase B
 gi|1574007|gb|AAC22639.1| nitrogen fixation protein (nifR3) [Haemophilus influenzae Rd KW20]
          Length = 330

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLNYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|152978326|ref|YP_001343955.1| nifR3 family TIM-barrel protein [Actinobacillus succinogenes 130Z]
 gi|150840049|gb|ABR74020.1| putative TIM-barrel protein, nifR3 family [Actinobacillus
           succinogenes 130Z]
          Length = 331

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 138/325 (42%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+ A+  +   +K+ L           A+QI G+D
Sbjct: 17  MAGITDQPFRKLCAEY-GAGLTFSEMMSANPQVWHTEKSKLRLAHHEDAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  P+++ D + A+  A+ +P
Sbjct: 76  PQEMAQAARVNVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPELIRDILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +       ++ K  ++ G+  + +H R         ++       +YD 
Sbjct: 136 VTLKIRTGWDRKHRN--CLDIAKIAEQCGIRALTVHGRT--------RECLFDGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG +    +A  +L     D VMIGRAA     +  +V     N 
Sbjct: 186 IKAVKEQV-SIPVIANGDIISAEKARLVLEYTGADAVMIGRAALGRPWIFRSVAGLIENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P          R I      Y  +    G ++    +H+     G       R  
Sbjct: 245 SIISEPGIDEKCGQILRHIDELHRFYGEQ---KGYRI--ARKHIAWYLQGIQFDSDFRQ- 298

Query: 297 LTVEAGASTATHHI-IETAFNLMIE 320
            T  A        I +E  FNL+ +
Sbjct: 299 -TFNAITDAKKQLIALENFFNLVRK 322


>gi|282850019|ref|ZP_06259401.1| TIM-barrel protein, nifR3 family [Veillonella parvula ATCC 17745]
 gi|282580208|gb|EFB85609.1| TIM-barrel protein, nifR3 family [Veillonella parvula ATCC 17745]
          Length = 328

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 144/324 (44%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++
Sbjct: 22  MAGVSDIAYRLLAKK-HGAALVCTEMVSAMGIKYKNERTHELLRIEEAERPVSMQIFGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V D G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +P
Sbjct: 81  PEAIALGAKVVADAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAVDVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  
Sbjct: 141 VTVKMRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   A ++L     D VMIGR A  N  +   +  Y +  
Sbjct: 191 IKAVK-EAVSVPVLGNGDIVEPEDAKQMLDETGCDAVMIGRGAQGNPWIFDRIHHYLATG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          +       D   ++      +++I  H      G P S   R+ 
Sbjct: 250 EVLPAPTDIERLDMLLKH-----FDLLCQYKGESMAVKEIRTHAGWYMKGLPESAYWRNR 304

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +       T+ H+ +E+   ++ E
Sbjct: 305 VNT-IHTVTSFHNELESYRKILFE 327


>gi|301169704|emb|CBW29305.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae 10810]
          Length = 326

 Score =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDKSNRNSV--QIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|262382918|ref|ZP_06076055.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
 gi|262295796|gb|EEY83727.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
          Length = 329

 Score =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKRF-GADMVYTEFVSSDALIRNVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITREVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRIIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +       +      VD VMIGRA+     +   V  Y + 
Sbjct: 187 IGAVKNNPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLTT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  +    ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GE-----LLPQEPFSWYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFKQT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|301312349|ref|ZP_07218266.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 20_3]
 gi|300829771|gb|EFK60424.1| TIM-barrel protein, putative, NifR3 family [Bacteroides sp. 20_3]
          Length = 329

 Score =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L  S  E+P+A+QI G D
Sbjct: 18  MEDVTDISFRLMCKSF-GADMVYTEFVSSDALIRSVNKTQQKLNVSDDERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+I E+   + +++N GCP  +V     GA ++ N  ++ +    + KA++IP
Sbjct: 77  VASMVEAARICEEARPDILDINFGCPVKKVAGKGAGAGMLRNIPLMLEITKEVVKAVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADNRVIV--DLAEQLQDCGIAALSIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +       +      VD VMIGRA+     +   V  Y + 
Sbjct: 187 IGAVKNNPRMQIPIIGNGDVTSAEICKQRFEDYGVDAVMIGRASIGRPWIFREVKHYLTT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                  +  +    ++  I     + +   L     +  I RH+    LF G  + ++ 
Sbjct: 247 GE-----LLPQEPFSWYLDILKKQVEQSVERLDERRGILHIRRHLAATPLFKGITDFKQT 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|145637283|ref|ZP_01792944.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittHH]
 gi|145269535|gb|EDK09477.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittHH]
          Length = 326

 Score =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHD 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|332289637|ref|YP_004420489.1| tRNA-dihydrouridine synthase B [Gallibacterium anatis UMN179]
 gi|330432533|gb|AEC17592.1| tRNA-dihydrouridine synthase B [Gallibacterium anatis UMN179]
          Length = 324

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 130/318 (40%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R         AL ++EM+  +  +   +K+ L      Q    A+QI G+D
Sbjct: 17  MAGITDLPFRRICSQY-GAALTFSEMMSTNPDVWHTEKSKLRLAHHPQIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++   +G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDEMAQAAQVNVGYGAEIIDINMGCPAKKVNRKLAGSALLQYPDLVAKILNAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q     L  + K  + +G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDQQHKNCVL--IAKIAQDAGIQALSIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +KK    + +  NG ++   +A  +L     D +M+GR A  N  +   + E     
Sbjct: 186 IKAVKKAV-SIPVIANGDIDSAEKAKYVLDYTEADAIMLGRGALGNPWIFREITELLETS 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                   +       + I+A    Y A     G ++    +H+             +  
Sbjct: 245 KVVQQVPFSEKKTVILQHIAALHQFYGAE---KGYRI--ARKHVAWYLDRLSPVSDFKRS 299

Query: 296 --ILTVEAGASTATHHII 311
              LT  +   TA    +
Sbjct: 300 FNALTNPSDQLTALEEFL 317


>gi|73540195|ref|YP_294715.1| dihydrouridine synthase TIM-barrel protein nifR3 [Ralstonia
           eutropha JMP134]
 gi|72117608|gb|AAZ59871.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ralstonia
           eutropha JMP134]
          Length = 356

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 131/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+++QI GA+
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPISVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PGMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVVRIVEAVVAAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G + +        + + ++ +G++ + IH R         + +    + +Y
Sbjct: 136 VPVTLKIRTGWNRENRNA--LRIARMVEDAGISMLTIHGRT--------RADLYHGDAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K E   + +  NG +    +A ++  L   D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVKAEL-RIPVVANGDITTPQKAKQVLALTGADAIMIGRAAQGRPWLFREIEHFMK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 SP    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGELLPSPEVAEIRAIMNAHLEDHYAFYGEF-----TGVRTARKHIAWYTRGLRGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|269797571|ref|YP_003311471.1| hypothetical protein Vpar_0508 [Veillonella parvula DSM 2008]
 gi|269094200|gb|ACZ24191.1| TIM-barrel protein, nifR3 family [Veillonella parvula DSM 2008]
          Length = 328

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 144/324 (44%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     AL+ TEM+ A  I   +++   +L     E+P+++QI G++
Sbjct: 22  MAGVSDIAYRLLAKE-HGAALVCTEMVSAMGIKYKNERTHELLRIEDVERPVSMQIFGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V + G + +++N+GCP  +V     G+ LM NPD+      A  +A+ +P
Sbjct: 81  PEAIALGAKVVANAGADIVDINMGCPVKKVVTSGDGSALMKNPDLAARVAEAAVEAVDVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    ++ + +  K I+ +GV  I +H R         K+     + D+  
Sbjct: 141 VTVKMRIGWDSD--SINVVDFAKRIESTGVAAIAVHGRT--------KEQMYSGHADWSY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG + +   A ++L     D VM+GR A  N  +   +  Y +  
Sbjct: 191 IKAVK-EAVSVPVLGNGDIVEPEDAKQMLDETGCDAVMVGRGAQGNPWIFGRIHHYLATG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          +       D   ++   G  +++I  H      G P S   R+ 
Sbjct: 250 EVLPGPTDIERLDMLLKH-----FDLLCQYKGEGMAVKEIRTHAGWYMKGLPESAYWRNR 304

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +       T+ H+ +E+   ++ E
Sbjct: 305 VNT-IQTVTSFHNELESYRKILSE 327


>gi|68249564|ref|YP_248676.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae 86-028NP]
 gi|68057763|gb|AAX88016.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae 86-028NP]
          Length = 326

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L   +S      A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAYSDDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVEKILREVVAAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGKAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAIV-IPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLNEKCGQILRHIQELHQFYGEQ---KGYRIT--RKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|319775087|ref|YP_004137575.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae F3047]
 gi|329123002|ref|ZP_08251573.1| tRNA-dihydrouridine synthase B [Haemophilus aegyptius ATCC 11116]
 gi|317449678|emb|CBY85884.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae F3047]
 gi|327471933|gb|EGF17373.1| tRNA-dihydrouridine synthase B [Haemophilus aegyptius ATCC 11116]
          Length = 326

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|315644402|ref|ZP_07897542.1| TIM-barrel protein, nifR3 family [Paenibacillus vortex V453]
 gi|315280279|gb|EFU43571.1| TIM-barrel protein, nifR3 family [Paenibacillus vortex V453]
          Length = 343

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 83/326 (25%), Positives = 146/326 (44%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D
Sbjct: 20  MAGVCNPAFRLIAKEF-GTGLVCAEMVSGKAIVHGNKRTQEMLFVDEREKPLSLQIFGGD 78

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK+V +    + I++N+GCP+ +V +   GA  +LN + + + +AA+  A++ 
Sbjct: 79  RDSLVEAAKVVDQQTNADIIDINMGCPAPKVTKMDAGARWLLNSNKIYEMVAAVVDAVNK 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D            ++++++G   + +H R         ++     + D+D
Sbjct: 139 PVTVKMRTGWDSDHIYAV--ENAQAVERAGGQAVSVHGRT--------REQLYTGHADWD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG +     A ++L     DGVMIGR A  N  ML    EY  +
Sbjct: 189 IIRQVK-EAVSIPVIGNGDVVTPEDARRMLDITGCDGVMIGRGALGNPWMLYRTIEYLKS 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     I+    D           ++++ +H+     G   S R + 
Sbjct: 248 GQLLPDPAPQEKIR-----IAILHMDRLIALRGEEVAVREMRKHLSWYLKGLKGSARIKD 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           I+  E         +++   N +   
Sbjct: 303 IIMEE-TKRDEMVSLLDNFVNSLEHQ 327


>gi|187932418|ref|YP_001884422.1| NifR3 family protein [Clostridium botulinum B str. Eklund 17B]
 gi|187720571|gb|ACD21792.1| NifR3 family protein [Clostridium botulinum B str. Eklund 17B]
          Length = 321

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 141/305 (46%), Gaps = 24/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    L+YTEM+ A A+  G  + + +L  S +E P+A+QI G +
Sbjct: 17  MAGVTDLSFRGLCKEM-GCGLVYTEMVSAKALYYGSENTQTLLRVSNEEAPVAVQIFGRE 75

Query: 59  ISKLVE-AAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              + E   K +        I++N+GCP+ ++     G+ LML P++  D + A+ K   
Sbjct: 76  PEIMAEICEKYLNPREDVCIIDINMGCPAPKIVRNKEGSALMLEPNLAHDIVKAIKKVSK 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R G DD+   +      K+++++G + I +H R         +      + D+
Sbjct: 136 KPVTVKFRKGYDDE--HINAVEFGKALEEAGADAIAVHGRT--------RKQMYEGHSDW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+ ++K E   + +  NG +     A+K+  L + DG++I R +  N  +   + +  +
Sbjct: 186 EIIKKVK-EAVSIPVLGNGDVFSPEDAIKMKELTNCDGILIARGSMGNPWIFKQIQDALN 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +      + +++      +     + A ++      ++++ +H      G P S   +
Sbjct: 245 GKIVEEISYQDKIN------MCIRHYELAIKNDGEYKAIREMRKHASWYIKGLPRSTDIK 298

Query: 295 HILTV 299
           + + +
Sbjct: 299 NQINI 303


>gi|190572832|ref|YP_001970677.1| putative tRNA-dihydrouridine synthase B [Stenotrophomonas
           maltophilia K279a]
 gi|190010754|emb|CAQ44363.1| putative tRNA-dihydrouridine synthase B [Stenotrophomonas
           maltophilia K279a]
          Length = 331

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 133/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K+I  +    +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAASEMTISDPRFWNTRKSIHRMDHDGEPAPISVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 76  PQQLAEAARYNVDHGAQIIDINMGCPAKKVCNAWAGSALMRDEQLVARILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D       L  + +  + SG+  + +H R         +D       +Y  
Sbjct: 136 VTLKIRTGWDCDHRNGPL--IARIAEDSGIAALAVHGRT--------RDQHYTGQAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG ++   +A  +L    VD VMIGR+A     +   V  Y +  
Sbjct: 186 IGEIKAAL-RIPVIANGDIDSPQKAAYVLKETGVDAVMIGRSAQGRPWIFREVAHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+       P +   R +
Sbjct: 245 EELPPPSLAEVRDILLGHLHALHAFYGEPQ-----GVRIARKHLGWYAKDRPENAAFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A    +   +    F+ +I
Sbjct: 300 VN-RAEDPASQIALTTEYFDRLI 321


>gi|325105644|ref|YP_004275298.1| tRNA-U20-dihydrouridine synthase [Pedobacter saltans DSM 12145]
 gi|324974492|gb|ADY53476.1| tRNA-U20-dihydrouridine synthase [Pedobacter saltans DSM 12145]
          Length = 330

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 139/327 (42%), Gaps = 28/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      L+YTE I ++ ++R   K+   L     E+P+ +QI G+D
Sbjct: 20  MEDVSDPPFRYVCKQ-NGVDLMYTEFISSEGLIRDAAKSRQKLDVFEYERPIGIQIFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I      + I++N GCP   V     G+ L+ + D +    AA+ KA  +P
Sbjct: 79  IDHMFEATEIATQANPDLIDINYGCPVKNVACRGAGSALLQDIDKMVAMTAAVVKATHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    + + ++  G+  + IH R         +        D+ +
Sbjct: 139 VTVKTRLGWDDNTKNI--YEVAERLQDVGIQALSIHGRT--------RAQMYKGEADWTL 188

Query: 179 VYEIKKE-NPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG ++    +   ++   +DG+MIGRAA     +   V  +F  
Sbjct: 189 IKEVKKNPRIKIPIFGNGDVDSAIKAANWRLEYEIDGIMIGRAAIGYPWIFREVKHFFKT 248

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P I  RVD      +  +    +         + ++ RH    F G PN +  R
Sbjct: 249 GQHLEGPTIDERVD------VCLTHLRKSVEWKGPKTGIFEMRRHYANYFKGVPNFKEYR 302

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             L      S  +   IE   N +   
Sbjct: 303 MKLV-----SLDSIETIEDVLNDIRNK 324


>gi|309973521|gb|ADO96722.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae R2846]
          Length = 326

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|269103648|ref|ZP_06156345.1| tRNA dihydrouridine synthase B [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163546|gb|EEZ42042.1| tRNA dihydrouridine synthase B [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 348

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 121/300 (40%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K++  +    +    ++QI G+D
Sbjct: 44  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPDLWKTSKSMNRMVHEGESGIRSVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  P ++ + +  +  A+ +P
Sbjct: 103 PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQYPHLIEEILKEVVGAVDVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +       ++ K  ++ G+  + +H R         K        +YD 
Sbjct: 163 VTLKTRTGWDTENRN--CVDIAKLAEQCGIQALALHGRT--------KACMYKGEAEYDY 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y +  
Sbjct: 213 IRAVKQAVT-IPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGKPWIFREIHHYLTTG 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    V +     +      Y          L+   +H+         +   R  
Sbjct: 272 EHLAPPSFDEVSEIMLGHVRELHRFY-----GEYLGLRIARKHVSWYLKEHAPAGNFRQT 326


>gi|315186658|gb|EFU20417.1| TIM-barrel protein, nifR3 family [Spirochaeta thermophila DSM 6578]
          Length = 333

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 130/318 (40%), Gaps = 22/318 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R         ++ YTEM+ A+ I+    K   ++  S +E+   +Q+  +  
Sbjct: 27  AGVSDLPFREVCISF-GASMTYTEMVSAEGIVYNTGKTFSLVRRSPKERFWGIQLFSSRP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L  A +++        +LN GCP  +V +   GA LM +P+ V   + AM +A S+PV
Sbjct: 86  DMLARAVEMLSPLAPTLFDLNCGCPIPKVVKTGAGAALMRDPERVYAMVKAMREASSVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD   ++  R + ++  ++G   + +H R         +         ++ +
Sbjct: 146 TVKIRSGWDD--LSLTYREVAQAAFEAGAGAVCLHPRT--------RAQGYAGAARWEHI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K  +P   +  +G +     A  +L     D V++ R A     +   + +      
Sbjct: 196 ADLKARHPSHPVIASGDILSPEAARAVLEETGCDAVLVARGALGAPWIFRQIRDLLETG- 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            G +PI  R   +  R+       Y    +      +++ +HM     G P + R R  L
Sbjct: 255 -GYAPISLRERVETMREHLERAIAYKGEEIA----CREMRKHMGWYVKGLPGAARVRERL 309

Query: 298 TVEAGASTATHHIIETAF 315
            V A    A   I+E   
Sbjct: 310 -VRASTREAYLTILEELL 326


>gi|148241561|ref|YP_001226718.1| tRNA-dihydrouridine synthase [Synechococcus sp. RCC307]
 gi|147849871|emb|CAK27365.1| Probable tRNA-dihydrouridine synthase [Synechococcus sp. RCC307]
          Length = 335

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 68/313 (21%), Positives = 135/313 (43%), Gaps = 21/313 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADIS 60
              +D+ +R   R    +ALL+TEM+ A ++  G  +  +   +T+E P+ +Q+      
Sbjct: 27  AGVSDKVFRRLVRRWCPDALLFTEMVNATSLELGHGRGKVEELATEEGPIGVQLFDYRPQ 86

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK  E  G   I++N+GCP  ++ +   G+ L+  PD+    + A+ +A+ +PVT
Sbjct: 87  AMAEAAKRAEGAGAFLIDINMGCPVKKIAKKGGGSGLIREPDLAARIVEAVSQAVQVPVT 146

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G              + ++ +G   + +H R         ++     + D+  + 
Sbjct: 147 VKTRLGWCGSDADPVT--WCQQLQNAGAQLLTLHGRT--------REQGFKGHADWQAIA 196

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           ++K     + +  NG +     A + L     DGVM+GR +     ++  +D        
Sbjct: 197 QVKAALT-IPVIANGDINTPDDAQRCLAITGADGVMVGRGSMGAPWLVGQIDAALRGLPM 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +P  +   +    ++ A +++           L    +HM     GFP + + RH L 
Sbjct: 256 PLAPDASGRLQLAKEQLLALVSE------RGDHGLLIARKHMGWTCTGFPGAPQLRHQL- 308

Query: 299 VEAGASTATHHII 311
           + A    A   ++
Sbjct: 309 MRAPTPDAAVELL 321


>gi|134103510|ref|YP_001109171.1| dihydrouridine synthase TIM-barrel protein nifR3 [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291005944|ref|ZP_06563917.1| dihydrouridine synthase TIM-barrel protein nifR3 [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133916133|emb|CAM06246.1| dihydrouridine synthase TIM-barrel protein nifR3 [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 387

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 125/303 (41%), Gaps = 24/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R+  R      L   EMI + A++      +  + F   E P ++Q+ G D
Sbjct: 34  MAGITNVAFRWLCREY-GAGLYVCEMITSRALVERHPTTMQMVTFDPDEHPRSMQLYGVD 92

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA--- 114
              + +A +++ + G  + +++N GCP  +V     G+ L     + G+ + A  +A   
Sbjct: 93  PETMGQAVRMIVEEGLADHVDMNFGCPVPKVTRKGGGSALPYKRRLFGEIVRAAVRAAEP 152

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+DD+   +   +  +  + +G   + +H R A          R     
Sbjct: 153 AGVPVTVKFRIGIDDE--HITYLDAGRIAEDNGAAAVALHGRTA--------AQRYSGQA 202

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K+    + +  NG +     AL+++     DGV++GR       +   +   
Sbjct: 203 DWSAIARLKETVRTIPVLGNGDIFSADDALRMVAETGCDGVVVGRGCLGRPWLFRDLQAA 262

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +     +     +  A H+     L+ + +HM     GFP    
Sbjct: 263 FAGEPVPEGPNLGEVCR-----VLRRHGELLADHMGEEKGLRDLRKHMAQYLRGFPVGSD 317

Query: 293 CRH 295
            RH
Sbjct: 318 LRH 320


>gi|78188223|ref|YP_378561.1| dihydrouridine synthase TIM-barrel protein nifR3 [Chlorobium
           chlorochromatii CaD3]
 gi|78170422|gb|ABB27518.1| tRNA-U20-dihydrouridine synthase [Chlorobium chlorochromatii CaD3]
          Length = 348

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 137/304 (45%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE I A+A+ RG +K++  L     E+P A+QI G+ 
Sbjct: 17  MEDVTDRSFRQLCKR-HGADIVYTEFISAEALRRGAEKSLRKLKVDDMERPYAIQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I   +  + +++N GCP  +V     GA L+  P+ +    AA+ KA++IP
Sbjct: 76  VESMVEAAIIAASYQPDYLDINFGCPVKKVAGKGAGAALLREPEKMAAISAAVVKAVAIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D    ++ + +++  ++ +G+  + +H R         +        D+  
Sbjct: 136 VTAKTRIGWD--FDSINILDIIPRLEDAGIQALALHGRT--------RSQMYKGTADWQW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K++   + +  NG + +   A ++    + DGVMIGR +  N  +      + ++ 
Sbjct: 186 IRAAKEKA-HIPLIANGDIWNAEDAARMFDVTAADGVMIGRGSIGNPFIFQQAKHFLAHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P   +           S+      +      + ++ RH      G P   R R+ 
Sbjct: 245 TLLPPPDFRQRIAVAIEHFQLSLA-----YKGEKYGVLEMRRHYSTYLKGLPMVSRVRNK 299

Query: 297 LTVE 300
           L  E
Sbjct: 300 LVRE 303


>gi|317504340|ref|ZP_07962326.1| tRNA-dihydrouridine synthase [Prevotella salivae DSM 15606]
 gi|315664531|gb|EFV04212.1| tRNA-dihydrouridine synthase [Prevotella salivae DSM 15606]
          Length = 335

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 81/320 (25%), Positives = 145/320 (45%), Gaps = 25/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +  +  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRMLCKRY-GAAMVYTEFVSADAIIRSIKSTLDKMSINDAERPVGVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I+LN GCP  +V     G+ ++ N  ++ D    + +A+S P
Sbjct: 77  VESMVEAARIVERVNPDLIDLNFGCPVKKVAGKGAGSGMLRNIPLLLDITRNVVQAVSTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--SLVITELAEQLQDCGIKALTIHGRT--------RAQMYTGEADWRL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K+     + I  NG +    +A +      VD VM+GRA +    +   + +Y  N
Sbjct: 187 IGEVKRNPRIHIPIIGNGDITTPEEAKRAFDDYGVDAVMVGRATFGRPWVFKEMRDYIDN 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             + +  +  ++D      I           +     +    RH+    +F G P+ +  
Sbjct: 247 TPSTALTLDDKID------ILEEQLRINVERIDEYRGIIHTRRHLASSPIFKGIPDFKST 300

Query: 294 RHILTVEAGASTATHHIIET 313
           R I  + A        I+E 
Sbjct: 301 R-IAMLRATKVDELIEILEE 319


>gi|153952822|ref|YP_001393587.1| Dus [Clostridium kluyveri DSM 555]
 gi|146345703|gb|EDK32239.1| Dus [Clostridium kluyveri DSM 555]
          Length = 320

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R          L+YTEMI A A+  G K  +++L  S  E P+A+QI G D
Sbjct: 17  MAGITDRAFRELCIEF-KCGLVYTEMISAKALFYGSKATESMLIVSPVEAPIAVQIFGND 75

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +A     E+     +++N+GCP+ ++     G+ LM NP +  + +  + KA   
Sbjct: 76  PVIMAKACDYFNENKDICMVDINMGCPAPKIVRNGEGSALMKNPKLASEIVKEVKKASLK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +  ++   N  + +++SG + + IH R +                ++D
Sbjct: 136 PVTVKMRIGFDSE--SINAVNFARIMEQSGADAVTIHGRTST--------QMYNGKANWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY-FS 234
           I+ ++K+    + +  NG +  +  A ++      DG+MIGR +  N  + + + E   S
Sbjct: 186 IISDVKQSI-KIPVIGNGDVFTVEDASRLFEFTKCDGIMIGRGSLGNPWIFSQIYENKNS 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRR 292
             +T  +P          +KI   +  Y     ++G    ++++ + +     G  NS+ 
Sbjct: 245 RSITYPTP---------QQKIDMCIEHYNRAIYYNGEYKAVREMRKQIGWYIKGLKNSKE 295

Query: 293 CRHILTVEAGASTATHHIIETA 314
            +  +  E   S     I+   
Sbjct: 296 IKEKINCEE-RSEIVFEILNQY 316


>gi|149376839|ref|ZP_01894595.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Marinobacter
           algicola DG893]
 gi|149358846|gb|EDM47314.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Marinobacter
           algicola DG893]
          Length = 332

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 134/320 (41%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    L  +EM++AD+ L   +K    +    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRM-GAGLAVSEMVIADSKLWHTRKSKTRMNHEGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA++  +FG   I++N+GCP+ +V   + G+ LM +  +V D + A+  A+ IP
Sbjct: 80  PEMLANAARLNAEFGAQIIDINMGCPAKKVCNKAAGSALMKDEALVRDILKAVVAAVDIP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +     L  + +  + +G+  + IH R         + +      +YD 
Sbjct: 140 VTLKMRTGWDREHRNAPL--IARMAEDAGIQALAIHGRT--------RADAYKGEAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +    QA  +L     DG++IGR A     +   +  +    
Sbjct: 190 IADVK-SRVSIPVFANGDINSPEQAQHVLKFTGADGLLIGRGAQGRPWIFREILHFLETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    V++     + A    Y          ++   +H+          ++ R  
Sbjct: 249 RHLAEPPVDEVEQVLSEHLDALHRFYGETM-----GVRIARKHVGWYLQSHDEEKQFRKR 303

Query: 297 LTVEAGASTATHHIIETAFN 316
                  + A    I+  F 
Sbjct: 304 FNA-IDDAMAQKDSIQQYFA 322


>gi|312890783|ref|ZP_07750313.1| tRNA-U20-dihydrouridine synthase [Mucilaginibacter paludis DSM
           18603]
 gi|311296746|gb|EFQ73885.1| tRNA-U20-dihydrouridine synthase [Mucilaginibacter paludis DSM
           18603]
          Length = 330

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 139/323 (43%), Gaps = 29/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R   K+   L     E+P+ +QI G+D
Sbjct: 20  MEDVSDPPFRYVCKQ-NGADMMYTEFISSEGLIRDAAKSRKKLDIFGYERPIGIQIFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I      + +++N GCP  +V     GA L+ + D +     A+ ++  +P
Sbjct: 79  IESMREATRIATKAEPDLMDINYGCPVKQVACRGAGASLLQDIDKMVAMTRAVVESTHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    V    + + +++ G+  + IH R         +        D+ +
Sbjct: 139 VTVKTRLGWDDNTKNV--YEVAERLQEVGIKALTIHGRT--------RAQMYKGEADWRL 188

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + EIKK  N ++ I  NG ++   +A   ++   VDG+MIGRAA     +   +  +F  
Sbjct: 189 IAEIKKNPNIEIPIFGNGDIDSPEKAANWRLEYGVDGMMIGRAAIGYPWIFREIKHFFET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +  +  + +         + ++ RH    F G  + +  R 
Sbjct: 249 GEHRDKPTIAERV-----DVCKTHLEKSIEWKGRRTGIFEMRRHYSNYFKGLDHFKEYRM 303

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            L             +E  ++L+
Sbjct: 304 QL--------VGTEDVEEIYDLL 318


>gi|255036755|ref|YP_003087376.1| TIM-barrel protein, nifR3 family [Dyadobacter fermentans DSM 18053]
 gi|254949511|gb|ACT94211.1| TIM-barrel protein, nifR3 family [Dyadobacter fermentans DSM 18053]
          Length = 329

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 139/328 (42%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE + ++ ++R   K++  L     E+P+ +Q+ G+D
Sbjct: 19  MEDVSDPPFRAVCKE-NGADLMYTEFVSSEGLIRDAAKSVQKLDIFEYERPVGIQLFGSD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +   A+I      + I++N GCP   V     GA L+ +   +     ++ K+  +P
Sbjct: 78  VETMGSCAEIASRVNPDLIDINYGCPVKNVACRGAGAALLQDVPKMVKMTESVIKSTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +    + + ++  G+  + IH R  +               D+ +
Sbjct: 138 VTVKTRLGWDDNTKNIQ--EVAERLQDIGIKALSIHGRTRV--------QMYKGAADWSL 187

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++K ENP   + I  NG ++   +AL+      VDG+MIGRA   N  +   +  Y  
Sbjct: 188 IAKVK-ENPRITIPIFGNGDVDTPEKALEYKNTYGVDGIMIGRATIGNPWIFNEIKHYLK 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P   +        +     +++ R       + ++ RH    F G  + +  R
Sbjct: 247 TGEKLPPPTMEQRV-----DVCRRHLEFSIRWKGPVAGVFEMRRHYTNYFKGLEHFKPYR 301

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
             L VEA        I++   N   E +
Sbjct: 302 MRL-VEAPTFDELDSILKEISNDYSEMV 328


>gi|255012000|ref|ZP_05284126.1| putative TIM-barrel protein, dihydrouridine synthase [Bacteroides
           fragilis 3_1_12]
 gi|313149838|ref|ZP_07812031.1| dehydrogenase [Bacteroides fragilis 3_1_12]
 gi|313138605|gb|EFR55965.1| dehydrogenase [Bacteroides fragilis 3_1_12]
          Length = 325

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 76/301 (25%), Positives = 127/301 (42%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + +DA++R   K    L    +E+P+A+QI G D
Sbjct: 18  MEDVTDLAFRLMCKKF-GADMVYTEFVSSDALIRSVNKTTQKLTICDEERPVAIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AA+IVE+   + +++N GCP  +V     GA ++ N   + +   A+  A+ IP
Sbjct: 77  TEAMVGAARIVEEAQPDILDINFGCPVKKVAGKGAGAGMLQNIPKMLEITRAVVDAVKIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDADHKIIV--DLAEQLQDCGIAALAIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +   + A +      VD +MIGR +     +   V  Y   
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTSATGAKECFERYGVDAIMIGRGSIGRPWIFREVKYYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                             ++       +   L     +  I RH+    LF G PN R  
Sbjct: 247 GEELPQESFEWYLNVLREEVLN-----SVARLDERRGIIHIRRHLAATPLFKGIPNFRET 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|305665851|ref|YP_003862138.1| putative TIM-barrel enzyme, putative dehydrogenase [Maribacter sp.
           HTCC2170]
 gi|88710622|gb|EAR02854.1| putative TIM-barrel enzyme, possible dehydrogenase [Maribacter sp.
           HTCC2170]
          Length = 332

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 71/329 (21%), Positives = 141/329 (42%), Gaps = 24/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ + D++     AM +   +P
Sbjct: 78  LDSMLRSVEIVEASNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTKAMVEHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +  ++ +  + + ++  G   I IH R  +               ++  
Sbjct: 138 VTVKTRLGWDQE--SIKIVEVAERLQDVGCKAISIHGRTRV--------QMYKGEANWVP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + +  NG ++    A+++     +DG MIGRA+         V  YF  
Sbjct: 188 IAEVKNNQRMHIPVFGNGDVDSPEAAMRMRDEFGLDGAMIGRASIGYPWFFNEVKHYFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +   R +       A         + +  RH    F G PN +  R 
Sbjct: 248 GRHLAPPTMQERVEAARRHL-----QMAIDWKGEKLGVFETRRHYTNYFKGIPNFKEYRM 302

Query: 296 ILTVEAGAST---ATHHIIETAFNLMIES 321
            +     ++    A   ++E   N + + 
Sbjct: 303 KMVTSDESTDVFAAFDEVLEKFGNHVFDD 331


>gi|224531739|ref|ZP_03672371.1| tRNA-dihydrouridine synthase A [Borrelia valaisiana VS116]
 gi|224511204|gb|EEF81610.1| tRNA-dihydrouridine synthase A [Borrelia valaisiana VS116]
          Length = 335

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 111/329 (33%), Positives = 179/329 (54%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E +  ++E NLNVGCPS ++   ++GACLM N + VG+ +  M ++ + PV
Sbjct: 72  DALKAIQILEKYFNFDEYNLNVGCPSLKIQNANYGACLMNNANQVGEILKTMKESTNKPV 131

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N V+ I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRLLTSDYKNESYSEVKNFVRIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L +VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSAVDSVMIGRSAFENPYFIAKASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            N  T   P +        + I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 LNE-TDEIPTR--------KDILMQMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E++
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPENI 330


>gi|116071136|ref|ZP_01468405.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           BL107]
 gi|116066541|gb|EAU72298.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           BL107]
          Length = 338

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 144/322 (44%), Gaps = 21/322 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADIS 60
              TD+ +R   R  + ++LL+TEM+ A ++  G     +    +++ P+A+Q+      
Sbjct: 34  AGVTDKIFRGLVRRWSRDSLLFTEMVNATSLELGHGYGKMDDLLSEDGPIAVQLFDHRPQ 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  E  G   +++N+GCP  ++ +   G+ L+ +PD+    + A+ +A+SIPVT
Sbjct: 94  AMADAARRAEQAGAFLVDINMGCPVRKIAKKGGGSGLIRDPDLATQILEAVVEAVSIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G              + ++ +G   + +H R         ++       D++ + 
Sbjct: 154 VKTRLGWCGSNSDPIT--WCRQLQNAGAQMLTLHGRT--------REQGFKGQADWNAIA 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+    + +  NG +   + AL+ L     DGVM+GR    +  ++  ++  F N   
Sbjct: 204 AVKQALT-IPVIANGDINSPTDALQCLDVTGADGVMVGRGTMGSPWLVGQIEAAFMNRPI 262

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P     D      ++            S G L    +HM     GFP + + RH L 
Sbjct: 263 PATP-----DSGARLHLAKEQLHDLVSSRGSHG-LLIARKHMSWTCTGFPGASQLRHAL- 315

Query: 299 VEAGASTATHHIIETAFNLMIE 320
           + A      + +++ A N + +
Sbjct: 316 MRAPTPNDAYQLLDKAINDLEQ 337


>gi|89075353|ref|ZP_01161775.1| putative Dihydrouridine synthase [Photobacterium sp. SKA34]
 gi|90581290|ref|ZP_01237087.1| putative Dihydrouridine synthase [Vibrio angustum S14]
 gi|89048902|gb|EAR54471.1| putative Dihydrouridine synthase [Photobacterium sp. SKA34]
 gi|90437529|gb|EAS62723.1| putative Dihydrouridine synthase [Vibrio angustum S14]
          Length = 321

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 60/300 (20%), Positives = 124/300 (41%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K++  +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPDLWKTSKSLNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  P+++ D + ++  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQYPNLIEDILRSVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +       ++ K  ++ G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWDLENRN--CVDIAKLAEQCGIQALALHGRT--------KACMYKGEAEYDY 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y +  
Sbjct: 186 IRAVKQAI-SIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGKPWIFREIHHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    + +     +      Y          L+   +H+         +   R  
Sbjct: 245 EHLAAPSIDEISEIMLGHVQELHQFY-----GEYLGLRIARKHVSWYLKEHAPAGDFRQT 299


>gi|169343168|ref|ZP_02864189.1| putative dihydrouridine synthase [Clostridium perfringens C str.
           JGS1495]
 gi|169298720|gb|EDS80796.1| putative dihydrouridine synthase [Clostridium perfringens C str.
           JGS1495]
          Length = 326

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 63/307 (20%), Positives = 140/307 (45%), Gaps = 24/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + +    ++ TEM+ A A+  G  + K ++  + +EKP++ Q+ G D
Sbjct: 17  MAGVTDISFRGLCKEM-GVGIVCTEMVSAKALYYGSENTKELMRIADEEKPVSCQMFGND 75

Query: 59  ISKLVEAAK--IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              +    +     +     I++N+GCP+ ++ +   G+ LM NP +  + ++++ K  +
Sbjct: 76  PEIMAYVTEKHFNTNDDICIIDVNMGCPAPKIVKNGEGSALMKNPKLAYEIMSSIKKVAT 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R+G D++   +      K ++++GV+ I +H R         +        ++
Sbjct: 136 KPVTVKFRMGFDEE--NINAVEFAKIMEEAGVDAIAVHGRT--------RAQMYEGKANW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ ++K E  ++ +  NG +     A  LK   + DG+M+ R +  N  +   + +  +
Sbjct: 186 DIIRQVK-EAVNIPVIGNGDVFTAEDALSLKNQTNCDGIMVARGSMGNPWIFKQIVQKLN 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                    + ++D      +     + + ++      ++++ +H      G  N    +
Sbjct: 245 GEEVYMPTPEEKID------MCIRHYNLSLKYDGEYKAVREMRKHAAWYIKGLNNCTEVK 298

Query: 295 HILTVEA 301
           + L +EA
Sbjct: 299 NRLNLEA 305


>gi|320010920|gb|ADW05770.1| TIM-barrel protein, nifR3 family [Streptomyces flavogriseus ATCC
           33331]
          Length = 382

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 124/319 (38%), Gaps = 21/319 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDASETPRSIQLYGV 86

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+ +A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVAQAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD        +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HTTYLDAGRIAVEEGVTAVALHGRTT--------AQHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWSADDALRMMRETGCDGVVVGRGCLGRPWLFGDLVSAF 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               T  +P+  +V     R  +                +    +H+     GF      
Sbjct: 257 EGTGTRQAPVLRQVADVMLRHATL----LGEWIGDESRGVIDFRKHVAWYLKGFAVGSDM 312

Query: 294 RHILTVEAGASTATHHIIE 312
           R  L V +        + E
Sbjct: 313 RRKLAVTSSLEELGTQLQE 331


>gi|315127804|ref|YP_004069807.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas sp. SM9913]
 gi|315016318|gb|ADT69656.1| tRNA-dihydrouridine synthase B [Pseudoalteromonas sp. SM9913]
          Length = 326

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 134/327 (40%), Gaps = 32/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K++  +  S +    A+QI GAD
Sbjct: 20  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPKVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + +H R         +      + +Y  
Sbjct: 139 VTLKIRTGWDQDNRNGV--EIARIAERYGIASLAVHGRT--------RACMYKGDAEYAT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y    
Sbjct: 189 IRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-----GFPNSR 291
                P    V       ++     Y           +   +H+          G    R
Sbjct: 248 EHMQPPAIAEVRSILMEHLTNLHVFY-----GEPMGARIARKHVSWYLQTHDSDGQ--FR 300

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
           R  + L      S A    +E  F  +
Sbjct: 301 RVFNAL----DNSEAQVVALEQYFKTL 323


>gi|254360638|ref|ZP_04976787.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|261493347|ref|ZP_05989873.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. BOVINE]
 gi|261496613|ref|ZP_05992993.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|110735319|gb|ABG89230.1| putative nitrogen fixation protein [Mannheimia haemolytica]
 gi|153091178|gb|EDN73183.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|261307816|gb|EEY09139.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. OVINE]
 gi|261310991|gb|EEY12168.1| putative nitrogen fixation protein [Mannheimia haemolytica serotype
           A2 str. BOVINE]
          Length = 329

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 139/305 (45%), Gaps = 25/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSRLRLAHHDEIGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AAKI  ++G + I++N+GCP+ +V++   G+ L+ NP +V   + ++  A+ +P
Sbjct: 76  PVEMAKAAKINVEYGADIIDINMGCPAKKVNKNMAGSALLRNPKLVAQILDSVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +++G+  + IH R         +        +Y+ 
Sbjct: 136 VTLKIRTGWDQENRN--CLQIAKIAEQAGIKALTIHGRT--------RSCLFNGEAEYES 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRA++ N  +   ++++F   
Sbjct: 186 IKAVKEAI-SIPVIANGDIDSAEKAKFVLDYTKADAIMIGRASFGNPWIFKEINDFFETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF---PNSRRC 293
           L+    I  +    F + I      Y       G ++    +H+           N +R 
Sbjct: 245 LSSPLSIDKKYQLMF-KHIEDLHQFYGEE---KGYRI--ARKHVGWYTEKLNPESNFKRT 298

Query: 294 RHILT 298
            + L+
Sbjct: 299 FNTLS 303


>gi|114773260|ref|ZP_01450495.1| tRNA-dihydrouridine synthase B [alpha proteobacterium HTCC2255]
 gi|114546379|gb|EAU49288.1| tRNA-dihydrouridine synthase B [alpha proteobacterium HTCC2255]
          Length = 333

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 133/322 (41%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  +   +K+   +  + +    ++QI G+D
Sbjct: 21  MAGVTDRPFRQMCKQM-GAGLVVSEMLSSNPKVWHTEKSKMRMDHTGEHGVRSVQIAGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+   + G   I++N+GCP+ +V++   G+ L+  P+IV + + A+  ++ +P
Sbjct: 80  PNLMAEAAQFNVNNGAQIIDINMGCPAKKVNKKMAGSALLQYPEIVEEILDAVVNSVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++  +  + +H R         K      N +YD 
Sbjct: 140 VTLKIRTGWDTDNRNGV--QIAKLAQQYNIQSLAVHGRT--------KACMYKGNAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+   ++ +  NG +    +A  +L     DG+MIGR A  N  +   +  Y  + 
Sbjct: 190 IRAIKRAV-EIPVIANGDITTPEKAKYVLQHTNADGLMIGRGAQGNPWIFREILHYLEHG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  T         +S     Y          ++   +H+      +   R  R  
Sbjct: 249 ERLPEPELTEQCTVMLEHVSNVHKFYGGI-----SGVRIARKHVGWYIAKYDQGRSFREH 303

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                G   A   +   A  + 
Sbjct: 304 FN---GIDDAAEQL--DALEMF 320


>gi|197287426|ref|YP_002153298.1| tRNA-dihydrouridine synthase B [Proteus mirabilis HI4320]
 gi|227358312|ref|ZP_03842653.1| tRNA-dihydrouridine synthase B [Proteus mirabilis ATCC 29906]
 gi|194684913|emb|CAR47079.1| tRNA-dihydrouridine synthase B [Proteus mirabilis HI4320]
 gi|227161648|gb|EEI46685.1| tRNA-dihydrouridine synthase B [Proteus mirabilis ATCC 29906]
          Length = 323

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 129/325 (39%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    S +    ++QI G+D
Sbjct: 17  MAGVTDRPFRSLCYDM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHSDELGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAKI  + G   I++N+GCP+ +V++   G+ L+  PD+V + ++A+  A+ +P
Sbjct: 76  PVDMATAAKINVEGGAQIIDINMGCPAKKVNKKLAGSALLRYPDLVAEILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            + K  +  G+  + IH R         ++       +YD 
Sbjct: 136 VTLKIRTGWSPDERN--CVEIAKLAEDCGIAALTIHGRT--------RECLFKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                    +V +   + +      Y       G   +   +H+           + R  
Sbjct: 245 ELLPPLPIAKVQQIMQKHVRELHDFY-----GQGKGTRIARKHVSWYLKEHAPDDQFRRS 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 AS      +E  F   +  
Sbjct: 300 FNAIEDASE-QLEALEAYFENFLRK 323


>gi|157825185|ref|YP_001492905.1| nifR3 family TIM-barrel protein [Rickettsia akari str. Hartford]
 gi|157799143|gb|ABV74397.1| Putative TIM-barrel protein, nifR3 family [Rickettsia akari str.
           Hartford]
          Length = 327

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 134/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++              +Q+ G 
Sbjct: 18  MSDITDLEFRKLVKRF-GAGLVVSEMIASRAMVVKSRQSMQKCAIMHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ ED G   I+LN GCP+ +V  G  GA LM +  +      A  KA+ I
Sbjct: 77  EPNVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGAALMSDEQLASKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G DD         L K  + SG+  + +H R         +      N D++
Sbjct: 137 PITVKMRMGWDDNTKNA--PTLSKIAENSGIQMVTVHGRT--------RCQFYSGNADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y   
Sbjct: 187 FIRSVK-EAVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWIISQIDHYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P              A +  Y          +    +H+     G P+S   R 
Sbjct: 246 GERKPDPSIAEQLDIVTEHCEAILDYY-----GKSVGIPIARKHISWYSSGLPSSAEFRG 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            + +    +     I E   ++M
Sbjct: 301 AVNLMHDPAELKEKIAEFYTSIM 323


>gi|295136512|ref|YP_003587188.1| tRNA-dihydrouridine synthase [Zunongwangia profunda SM-A87]
 gi|294984527|gb|ADF54992.1| tRNA-dihydrouridine synthase [Zunongwangia profunda SM-A87]
          Length = 330

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 144/323 (44%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++E+ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLESVEIVEKSGPDIIDINFGCPVKKVVSKGAGAGILKDVDLMVSLTKAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +        D+  
Sbjct: 138 ITVKTRLGWD--HDSIKIMEVAERLQDVGCKAISIHGRT--------RAQMYKGVADWKP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + +  NG ++   +A+++     +DG MIGRA+  N      V  YF  
Sbjct: 188 IADVKNNPRMHIPVFGNGDVDTPEKAVEMRDQYGLDGAMIGRASIGNPWFFREVKHYFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S P      +   RK      D+    L     + +  RH    F G P+ +  R 
Sbjct: 248 GEHLSPPTLQERVEAA-RKHLQMSIDWKGEKLG----VFETRRHYTNYFKGIPHFKEYRM 302

Query: 296 IL--TVEAGASTATHHIIETAFN 316
            +  + +A    A    +E  F 
Sbjct: 303 KMVTSDDAADVFAAFDEVERDFA 325


>gi|332184999|ref|ZP_08386748.1| TIM-barrel , nifR3 family protein [Sphingomonas sp. S17]
 gi|332014723|gb|EGI56779.1| TIM-barrel , nifR3 family protein [Sphingomonas sp. S17]
          Length = 333

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/308 (25%), Positives = 130/308 (42%), Gaps = 21/308 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G  
Sbjct: 23  MTGVTDMPFRTLVRRY-GSGLNVTEMIASQAAIRATRQSIQKAAWHPLEEPVSMQLVGCT 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+  D G   I++N+GCP  +V  G  G+ LM +  +  + I A  KA+ +P
Sbjct: 82  PYEMGEAAKLNADRGAAIIDINMGCPVRKVVNGDAGSALMRDLKLASEIIRATVKAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G      ++    L +  +  GV  I +H R         ++     + D+  
Sbjct: 142 VTLKMRMGWC--HDSLNAPELSRIAEDIGVKMITVHGRT--------RNQMYKGSADWGF 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +  +  A   L     DGVMIGR AY    +L  V  +F+  
Sbjct: 192 IRNVK-EAVSIPVIANGDICSIDDADTALDQSGADGVMIGRGAYGRPWLLGQVMHWFATG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +       A +  Y          +    +H+     G   S   R+ 
Sbjct: 251 ERLDDPSLDEQYRAVAEHYDAMLDHYGTE-----TGVNMARKHIGWYTRGLHGSAEFRNK 305

Query: 297 LTVEAGAS 304
           +  E  A 
Sbjct: 306 VNQEPSAD 313


>gi|322834713|ref|YP_004214740.1| TIM-barrel protein, nifR3 family [Rahnella sp. Y9602]
 gi|321169914|gb|ADW75613.1| TIM-barrel protein, nifR3 family [Rahnella sp. Y9602]
          Length = 321

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRALCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHNDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ KA+ +P
Sbjct: 76  PEDMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVQIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V +     +      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPPPMGEVQRLLIGHVRELHDFY-----GQGKGFRIARKHVSWYLQEHAPNDQFRRS 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|169627854|ref|YP_001701503.1| tRNA-dihydrouridine synthase [Mycobacterium abscessus ATCC 19977]
 gi|169239821|emb|CAM60849.1| Probable tRNA-dihydrouridine synthase [Mycobacterium abscessus]
          Length = 391

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 131/335 (39%), Gaps = 34/335 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A+         +  FS +E P +L
Sbjct: 31  MAGVTNVAFRTLCRELELATTGTVSGLYVCEMVTARALAERHPVTLHMTTFSPEESPRSL 90

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK+V D G  + I++N GCP  +V     GA L     + G  +AA 
Sbjct: 91  QLYSVDPETTYRAAKMVVDEGLADHIDMNFGCPVPKVTRNGGGAALPYKRRLFGQIVAAA 150

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK R+G+DD        +     +  G   + +HAR A          
Sbjct: 151 VRATAGTDIPVTVKFRVGIDDDHH--THLDAGAIAESEGAAAVALHARTA--------SQ 200

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D+  +  +K     + +  NG + D + A+ ++     DGV+IGR       + 
Sbjct: 201 RYSGTADWSQIAALKNHVTTIPVLGNGDIFDAADAVAMMEQTGCDGVVIGRGCLGRPWLF 260

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P   +V     R       +    H      L+ + +H+    HG
Sbjct: 261 AELSAVFNGQTIPAPPNLGQVTVIMRRHA-----ELLVDHFGEDKALRDMRKHIAWYLHG 315

Query: 287 FPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           FP     R  L + +  +      ++T    + +S
Sbjct: 316 FPAGGDIRRALALVSTRAE-----LDTLLEQLDQS 345


>gi|229586241|ref|YP_002844742.1| Putative dihydrouridine synthase Dus [Rickettsia africae ESF-5]
 gi|228021291|gb|ACP52999.1| Putative dihydrouridine synthase Dus [Rickettsia africae ESF-5]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 133/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EM+ + A++   R   K             +Q+ G 
Sbjct: 26  MSGVTDLEFRRLVKRF-GAGLVVSEMVASRAMIVESRQSLKKSAIMRDDATSACVQLAGC 84

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAK+ E  G   I+LN GCP+ +V  G  G  LM +  +      A  +A+ +
Sbjct: 85  EPNVIAEAAKMNEGMGAKIIDLNFGCPAKKVVGGYSGLVLMRDEQLAAKIFEATVEAVKL 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L K  +  GV  I +H R         +      N+D+D
Sbjct: 145 PVTVKMRMGWDDNTKNA--PTLAKIAESLGVQMITVHGRT--------RCQFYSGNVDWD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E+  + +  NG + + ++A + L     DG+M+GR AY    +++ +D Y   
Sbjct: 195 FIRSVK-ESVKIQVIANGDITNFAKAKEALQKSGADGIMVGRGAYGKPWLISQIDHYLKT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+P              A +  Y          +    +H+     G PNS   R 
Sbjct: 254 GEEKSAPSIAEQLDIVTEHYEAILDYY-----GESVGVPIARKHIGWYSSGLPNSAEFRG 308

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            + +      A    I   +  ++E+
Sbjct: 309 AVNL-MNDPLAVKEKIAEFYTSVMET 333


>gi|87199943|ref|YP_497200.1| dihydrouridine synthase TIM-barrel protein nifR3 [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87135624|gb|ABD26366.1| tRNA-U20-dihydrouridine synthase [Novosphingobium aromaticivorans
           DSM 12444]
          Length = 351

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 130/303 (42%), Gaps = 23/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G +
Sbjct: 29  MTGVSDLPFRTIVRRF-GSGLNVTEMIASPAAIRETRQSIQKAAWHPTEEPVSMQLVGCE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ ED G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+ +P
Sbjct: 88  PEQMAEAAKLSEDKGAAIIDINMGCPVRKVVNGDAGSALMRDIPLATRLIEATVKAVKVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G      ++    L +  +  G   I +H R         ++     + D+  
Sbjct: 148 VTVKMRMGWC--HDSLNAPELARIAEDLGAKMITVHGRT--------RNQMYKGSADWAF 197

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V  +K E   + + +NG    +ED++ A++     DGVMIGR +Y    +L  +  +   
Sbjct: 198 VRSVK-EAVSIPVIVNGDICGIEDVATAIEQ-SGADGVMIGRGSYGRPWLLGQIMHWLDT 255

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P              A        H      +    +H+     G   S   R+
Sbjct: 256 GERLADPPLAEQYALIVEHYHAMQ-----EHYGEMTGVNMARKHLGWYTKGLHGSADFRN 310

Query: 296 ILT 298
            + 
Sbjct: 311 KVN 313


>gi|149184568|ref|ZP_01862886.1| tRNA-dihydrouridine synthase [Erythrobacter sp. SD-21]
 gi|148831888|gb|EDL50321.1| tRNA-dihydrouridine synthase [Erythrobacter sp. SD-21]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 134/302 (44%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI ++A +R  ++++    +   E+P+++Q+ G D
Sbjct: 30  MTGVTDLPFRKLVRKY-GSGLNVTEMIASEAAIRETRQSVQKAAWDPIEEPVSMQLVGCD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S + EAAK+ +  G + I++N GCP  +V     G+ LM    +    + A  +A+ +P
Sbjct: 89  PSSMAEAAKLQQGNGADIIDINFGCPVRKVVGQLAGSALMREVPLATRLMEATVRAVDVP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     +    L +  +  GV  + +H R         ++     + D++ 
Sbjct: 149 VTVKMRMGWDHAD--LNAPELARIAEDLGVKMVTVHGRT--------RNQMYKGSADWEF 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K +  ++ + +NG +  +  A K L     DG+MIGR AY N  +L  V  ++   
Sbjct: 199 VRKVK-DAVNIPVIVNGDICTIDDAAKALDQSGADGLMIGRGAYGNPWLLAQVMHWWHTG 257

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP      +         +  Y  +       ++   +H+     G   S   R+ 
Sbjct: 258 ERLESPSFDEQYEVVVEHYRDMLELYGEQ-----VGVKIARKHLGWYTKGMHGSAEFRNR 312

Query: 297 LT 298
           + 
Sbjct: 313 VN 314


>gi|260580070|ref|ZP_05847900.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           RdAW]
 gi|260093354|gb|EEW77287.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           RdAW]
          Length = 357

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLNYTGADAIMIGRAALGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|120437655|ref|YP_863341.1| tRNA-dihydrouridine synthase [Gramella forsetii KT0803]
 gi|117579805|emb|CAL68274.1| tRNA-dihydrouridine synthase [Gramella forsetii KT0803]
          Length = 330

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 73/299 (24%), Positives = 134/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+   L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIREAAKSTMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K  S+P
Sbjct: 78  LESMLQSVEIVEKSGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKNTSLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +        D+  
Sbjct: 138 ITVKTRLGWD--HDSIKIVEVAERLQDVGCKAISIHGRT--------RAQMYKGEADWAP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG ++   +A+++     +DG MIGRA+         V  YF  
Sbjct: 188 IAEVKNNPRMHIPVFGNGDVDSPEKAMEMRDNFGLDGAMIGRASIGYPWFFREVKHYFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               + P       D  R+      D+    L     + +  RH    F G P+ +  R
Sbjct: 248 GKHLAPPTLEERV-DAARRHLQMAIDWKGERLG----VFETRRHYTNYFKGIPHFKEYR 301


>gi|56476040|ref|YP_157629.1| tRNA-dihydrouridine synthase [Aromatoleum aromaticum EbN1]
 gi|56312083|emb|CAI06728.1| tRNA-dihydrouridine synthase [Aromatoleum aromaticum EbN1]
          Length = 350

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 135/326 (41%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EM+ ++++L G  K       + +  P+++QI GAD
Sbjct: 28  MAGVTDRPFRQLCKKL-GAGVAVSEMVTSNSLLYGSAKTRRRAEHAGEADPISVQIAGAD 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            + + +AA+   D G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+   
Sbjct: 87  PAMMADAARYNADNGAQIIDINMGCPAKKVCNVMAGSALMQDEPLVARILEAVVAAVPGT 146

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G +          + +  + SG+  + IH R         + ++   N +YD
Sbjct: 147 PVTLKFRTGWNRDNRNA--PTIARIAEASGIRAVAIHGRT--------RADQYTGNAEYD 196

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K     + +  NG +    +A  +L     DGVMIGRAA     +   ++ Y + 
Sbjct: 197 TIAEVK-SLVKIPVIANGDITTPEKARYVLDYTGADGVMIGRAAQGRPWIFREIEHYLAT 255

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+   + +     +      Y          ++   +H+     G   S   R 
Sbjct: 256 GTLLPPPLVAEILQVCREHLGDLYAFYGEE-----TGVRIARKHISWYTKGLVGSAAFRR 310

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +   +         ++  F  + E 
Sbjct: 311 TMNQLSDVRE-QLEAVDDFFGRLAEQ 335


>gi|82753060|ref|XP_727524.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23483411|gb|EAA19089.1| Uncharacterized protein family UPF0034, putative [Plasmodium yoelii
           yoelii]
          Length = 531

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 111/353 (31%), Positives = 180/353 (50%), Gaps = 40/353 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R+++    L+TEMIV + +L    + +  LGF+  E P+  Q+GG+D
Sbjct: 159 MINVTNRHFRALVRIISKKVQLWTEMIVDNTLLYNINNLEEHLGFNKNEHPIVCQLGGSD 218

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA +VE  GY+EIN+NVGCPS +V     FGA LM NP +V + +  + K + I
Sbjct: 219 PTSLSEAAILVEQAGYDEININVGCPSTKVANKGAFGAYLMKNPQLVKNIVYEIKKKVQI 278

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVD+      LR+ ++++  +G +   IH+RKA LKGL PK NR IP L+Y+
Sbjct: 279 PVTVKIRTGVDNLDSFSFLRSFIETVSSAGCDHFIIHSRKAWLKGLDPKQNRSIPPLEYN 338

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--------------VD------------ 211
            V+++ K  P +   LNGG++ + Q + +L                 D            
Sbjct: 339 KVFDLCKLYPHIKFTLNGGIKSIEQGVALLNGYAPINNMSGKHNNSTDNNYIKIEDYDIN 398

Query: 212 ---GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
              GVMIGRA  +N  +L   D+   N  + S+    R   D ++      + +     +
Sbjct: 399 PLYGVMIGRACMENITVLAKTDKLVYNYDSPSTAHSRRTVLDAYKFYLEQNSSF-----Y 453

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATH---HIIETAFNLM 318
           +     ++ + ++G+  G P  R  R+ +        +T     I++ A   +
Sbjct: 454 TLVNAFELLKPILGILKGMPGHRLFRNKIDSYIRKYASTLNCAQILDKAMEDV 506


>gi|317057657|ref|YP_004106124.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 7]
 gi|315449926|gb|ADU23490.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 7]
          Length = 326

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 62/298 (20%), Positives = 120/298 (40%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D+ YR   R     A L +EMI +  +   D+K   +     +E+P ALQ+ G D
Sbjct: 20  MASVADKSYRLLCREF-GAAYLVSEMISSKGLCYNDRKTGELCEIEDEERPYALQLFGED 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++     + I++N+GCP  ++     G+ LM +     +      K    P
Sbjct: 79  PYFMGKAAYLLGKHKPDIIDINMGCPVPKIVGNGSGSALMKDIPRAVEIAKETVKNACCP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD           K+++++G+  + +H R         +        D++I
Sbjct: 139 VTVKFRAGWDDTSKNAV--EFAKALEQTGIAAMAVHGRT--------RQQFYSGEADWEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG ++D     ++      D VM+ R +Y    +   +  +    
Sbjct: 189 IRQVKQAV-SIPVFGNGDVKDGESCKRMYEETGCDLVMLARGSYGRPWVFREIKHFLETG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P      +   R        Y  ++      +++  +++     G PNS + R
Sbjct: 248 EKLPEPDIKERMEIMLRH-----CRYLCKYKGEVRGMKEARKNVAWYVKGLPNSAKLR 300


>gi|310766173|gb|ADP11123.1| tRNA-dihydrouridine synthase B [Erwinia sp. Ejp617]
          Length = 305

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 132/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 1   MAGITDRPFRTLCYAM-GAGMTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRTVQIAGCD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 60  PQEMAEAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILSAVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +      + +YD 
Sbjct: 120 VTLKIRTGWDSDNRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGDAEYDS 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IRTVKQ-NVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y  R    G ++    +H+         + + R  
Sbjct: 229 ELLAPMPLAEVKRLLIGHIRELHGFYGQR---KGYRI--ARKHVSWYLQENAPNDQFRRT 283

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 284 FNAIEDASE-QLEALEAYFENL 304


>gi|15612660|ref|NP_240963.1| nitrogen regulation transcriptional regulator [Bacillus halodurans
           C-125]
 gi|10172709|dbj|BAB03816.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) [Bacillus halodurans C-125]
          Length = 334

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 143/329 (43%), Gaps = 25/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  ++K+  +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNPAFRLIAKEF-GAGLVCAEMVSDKAILHKNEKSLSMLYVDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + D ++A+   +  
Sbjct: 77  KETLVEAAKFVDKNTNADIIDINMGCPVPKITKCDAGARWLLDPNKIYDMVSAVVDEVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++          ++++++G   + +H R  +               D++
Sbjct: 137 PVTVKMRIGWDEEHIYAV--ENAQAVERAGGAAVAVHGRTRV--------QMYEGTADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+    + +  NG ++    A ++L    VDGVMIGRAA  N  ML     Y   
Sbjct: 187 IIREVKQAVG-IPVIGNGDVKTPQDAKRMLDEIGVDGVMIGRAALGNPWMLYRTIHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D   +       ++++ +H      G   + + R 
Sbjct: 246 GELLPDPTPREKM-----DVCMIHLDRLIKLKGENVAVREMRKHAAWYLKGLRGNGKIRD 300

Query: 296 ILTVEAGASTATHHI---IETAFNLMIES 321
            +         +  +   IE     M E 
Sbjct: 301 QINQFETREDVSSTLYAYIEELEAKMAEK 329


>gi|300770292|ref|ZP_07080171.1| tRNA-dihydrouridine synthase B [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300762768|gb|EFK59585.1| tRNA-dihydrouridine synthase B [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 331

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 139/327 (42%), Gaps = 22/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R   K+   L     E+P+ +QI G++
Sbjct: 21  MEDVSDPPFRYVCKQ-NGVDMMYTEFISSEGLIRDAAKSRQKLDIFEYERPIGIQIFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + ++++I      + I++N GCP   V     G+ L+ + D +     A+ +A  +P
Sbjct: 80  IEHMRQSSEICSLANPDLIDINYGCPVKNVVCKGAGSSLLQDVDKMVAMTKAVVEATHLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    V    + + ++  G+  + IH R         +        D+ +
Sbjct: 140 VTVKTRLGWDDNTKNV--YEVAERLQDVGIKALSIHGRT--------RAQMYKGQADWSM 189

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K+     + I  NG ++ + +A        VDG+MIGRA+     +   +  +F  
Sbjct: 190 IRDVKRNPRIKIPIFGNGDIDSVEKAAAWRQEFEVDGIMIGRASIGYPWIFREIKHFFET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++  +    +         + ++ RH    F G PN +  R 
Sbjct: 250 GQRLEGPTIVERV-----EVCRTHLTKSIEWKGEKTGIFEMRRHYANYFKGIPNFKEYRM 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L V   +    H +++   +   E +
Sbjct: 305 KL-VGLQSHHEIHEVLDEIQHQFTEEI 330


>gi|17545225|ref|NP_518627.1| NIFR3-like protein [Ralstonia solanacearum GMI1000]
 gi|17427516|emb|CAD14034.1| putative trna-dihydrouridine synthase protein [Ralstonia
           solanacearum GMI1000]
          Length = 356

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 61/305 (20%), Positives = 130/305 (42%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   ++ +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSERTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+   + G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 76  PMMMAEAARYNVERGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAVVGAVGDR 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G D +        + +  +++G++ + +H R         + +      +Y
Sbjct: 136 VPVTLKIRTGWDREHRNA--LTVARIAQEAGISMLTVHGRT--------RADLYHGEAEY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG +   ++A  +L     D +MIGRAA     +   ++ +  
Sbjct: 186 ETIAAVK-ASVRIPVVANGDIGTPAKARHVLEVTGADAIMIGRAAQGRPWLFREIEHFLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P    +       +      Y          ++   +H+     G   +   R
Sbjct: 245 TGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKHIAWYTRGLAGANLFR 299

Query: 295 HILTV 299
           H +  
Sbjct: 300 HRMNT 304


>gi|309751355|gb|ADO81339.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae R2866]
          Length = 326

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKLVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|291166185|gb|EFE28231.1| TIM-barrel protein, NifR3 family [Filifactor alocis ATCC 35896]
          Length = 319

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 136/324 (41%), Gaps = 26/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D  +R          L YTEMI A A+  GD+    ++     E  +A+QI G +
Sbjct: 17  MAGINDFPFRLMCHRY-GAVLTYTEMINAKALCYGDENTWKMMQVHPDEGDVAIQIFGNE 75

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EA + +E    +  I++N+GCP+ +V +   G+ LM  P++    +    +   +
Sbjct: 76  PEFIAEAVRKIEQLSRFVLIDINMGCPAPKVVKNGDGSALMKKPELAQKIVETAKQNTIL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D     V      K ++++G + + +H R         ++       D++
Sbjct: 136 PVTVKFRKGWDSTQ--VNALEFAKQMQEAGADAVTVHGRT--------REEFYSGVADWN 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           IV EIKK    + +  NG ++D     +   L SVD VMIGR A  N  +         N
Sbjct: 186 IVKEIKKAL-YIPVIGNGDIKDQETFEERVKLSSVDAVMIGRGAQGNPFLF--------N 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            L  + P K  V       I     +  A +      ++++ +H+     G P + + R+
Sbjct: 237 SLVRNGPKKENVPFQEIYDIVKEHYELEAEYKGIDKAVREMRKHIGWYIKGLPMAAKVRN 296

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
            +       TA   ++   F  + 
Sbjct: 297 EINQTTDIQTAQK-LLTEYFEHLT 319


>gi|90407140|ref|ZP_01215328.1| tRNA-dihydrouridine synthase [Psychromonas sp. CNPT3]
 gi|90311716|gb|EAS39813.1| tRNA-dihydrouridine synthase [Psychromonas sp. CNPT3]
          Length = 319

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 125/299 (41%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M   TD  +R   R L    L  +EM+ ++  +   KK+ L      +    ++QI GAD
Sbjct: 17  MAGVTDLPFRELCRKL-GAGLAVSEMLSSNPRVWDSKKSRLRMDQRNESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++    G   I++N+GCP+ +V++   G+ L+ +P +V   + ++  A+ +P
Sbjct: 76  PGEMAKAAQVCVQNGAQIIDINMGCPAKKVNKKKAGSALLPHPKLVQAILESVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++SG+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWDPENRNG--LQIAQIAQQSGIQALAVHGRT--------RQCLYKGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I KEN  + +  NG +  + +A  +L     D +MIGR A     +   ++ Y    
Sbjct: 186 IK-IIKENVTIPVIANGDITSVEKAKYVLDYTGADAIMIGRGAQGAPWIFNEINHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              S   K  V +     + A    Y           +   +H+             R 
Sbjct: 245 EKKSPLEKKEVAQILLGHVQALHAFY-----GEVMGPRIARKHVGWYLQAQDKFCCFRQ 298


>gi|167998448|ref|XP_001751930.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162697028|gb|EDQ83365.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 373

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 127/332 (38%), Positives = 180/332 (54%), Gaps = 19/332 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWT+ H+R  ARL++ +A LYTEM+V D I     +   IL F     P+ LQ+GG +
Sbjct: 20  MMDWTNNHFRTIARLMSKHAWLYTEMVVDDTINYQQDNLDMILKFPESHHPIVLQLGGCN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
             KL  A+++   +GY+EINLN GCPS  V   SFGA LML P++VG C+ A+ K     
Sbjct: 80  PEKLFRASQLASLYGYDEINLNCGCPSDNVTGRSFGAALMLEPELVGQCVTAIAKGSPGT 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L N ++ +   S      IHARKA+LKGLSP +NR+IP L Y
Sbjct: 140 PVSVKCRIGVDDFDSYDFLHNFIRIVSSTSPTKHFIIHARKAVLKGLSPDENRRIPPLKY 199

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           D V+ + ++ P+L   LNGG+  + Q  + L   V GVM+GR AY +   +L  VD    
Sbjct: 200 DYVFALMRDFPNLKFTLNGGVVGIHQVNEALNRGVFGVMLGRTAYNSPWSVLANVDRVVY 259

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG----KLQQITRHMIGLFHGFPNS 290
             +T   P+ TR      R+I      Y    LH  G     ++QI + + GLF+     
Sbjct: 260 GDMT---PVLTR------RQILEKYVVYGDAELHRYGYKKPGIRQIAQPLSGLFYREKGV 310

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R  L     +S   H ++     ++ +S+
Sbjct: 311 GLWRRALDEYIRSSQTLHALLRDTLRVIPDSV 342


>gi|282901225|ref|ZP_06309154.1| Dihydrouridine synthase TIM-barrel protein nifR3
           [Cylindrospermopsis raciborskii CS-505]
 gi|281193925|gb|EFA68893.1| Dihydrouridine synthase TIM-barrel protein nifR3
           [Cylindrospermopsis raciborskii CS-505]
          Length = 340

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 131/317 (41%), Gaps = 21/317 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 32  GVTDLVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPNERPISIQLFDCRPDF 91

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + +++N+GCP  ++ +   G+ L+  P++    +  + KA+++PVTV
Sbjct: 92  LAEAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVKAVNVPVTV 151

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  D+   + + +  K ++ +G   I +H R         +      N  ++ + +
Sbjct: 152 KTRIGWSDKE--ITILDFAKRMEDAGAKMITVHGRT--------RAQGYNGNARWEWIAK 201

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  ++ A+K L     DGVM  R       ++  VD +       
Sbjct: 202 VKQ-ILSIPVIANGDIFSVAAAVKCLAETGADGVMCSRGTLGYPFLVGEVDHFLKTGELL 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P  T+  +     +      YA         ++Q  +H+      F  +   R  L+ 
Sbjct: 261 PPPTPTQRLECAREHL------YALWEYKGDRGVRQARKHLTWYAKDFMGAADLRGKLST 314

Query: 300 EAGASTATHHIIETAFN 316
                     +I+ A  
Sbjct: 315 IETVQQ-GLDLIDKAIE 330


>gi|296535536|ref|ZP_06897718.1| tRNA-dihydrouridine synthase B [Roseomonas cervicalis ATCC 49957]
 gi|296264122|gb|EFH10565.1| tRNA-dihydrouridine synthase B [Roseomonas cervicalis ATCC 49957]
          Length = 374

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 132/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    ++ +EMI + A++R +++   +        P ++Q+ G D
Sbjct: 38  MSGVTDLPFRRLCRELQ-APMVVSEMIASQAMVRENRQTLKMAEVDGFGGPTSVQLAGCD 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + + EAAK+  D G   +++N GCP  +V      G+ LM +       + A+ KA+S 
Sbjct: 97  PAVMAEAAKLAVDHGAAIVDINFGCPVKKVALGQQAGSALMRDEIGAARILEAVVKAVST 156

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D    ++    L K  ++SG+  + +H R         +        D+ 
Sbjct: 157 PVTLKMRMGWD--HNSLNAPRLAKIAEESGIKLVTVHGRT--------RQMFYTGTADWA 206

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  +K+    L + +NG +     A + L     DGVMIGR  Y    +L  +  Y + 
Sbjct: 207 FVANVKQAVG-LPVIVNGDILTPQHAAEALRQSGADGVMIGRGCYGRPWLLARIATYLTT 265

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P     D      I          H      ++   +H+     G P S   R 
Sbjct: 266 GEDLPEP-----DLATQYDILRRHYHAMLEHHGPHPGVRLARKHLAWYSKGLPGSAEFRV 320

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +   A    A   ++   +  +IE 
Sbjct: 321 AVN-RAETPEAALALLHEFYAPLIEQ 345


>gi|219853487|ref|YP_002470609.1| hypothetical protein CKR_0144 [Clostridium kluyveri NBRC 12016]
 gi|219567211|dbj|BAH05195.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 322

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 145/322 (45%), Gaps = 30/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R          L+YTEMI A A+  G K  +++L  S  E P+A+QI G D
Sbjct: 19  MAGITDRAFRELCIEF-KCGLVYTEMISAKALFYGSKATESMLIVSPVEAPIAVQIFGND 77

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +A     E+     +++N+GCP+ ++     G+ LM NP +  + +  + KA   
Sbjct: 78  PVIMAKACDYFNENKDICMVDINMGCPAPKIVRNGEGSALMKNPKLASEIVKEVKKASLK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +  ++   N  + +++SG + + IH R +                ++D
Sbjct: 138 PVTVKMRIGFDSE--SINAVNFARIMEQSGADAVTIHGRTST--------QMYNGKANWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY-FS 234
           I+ ++K+    + +  NG +  +  A ++      DG+MIGR +  N  + + + E   S
Sbjct: 188 IISDVKQSI-KIPVIGNGDVFTVEDASRLFEFTKCDGIMIGRGSLGNPWIFSQIYENKNS 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRR 292
             +T  +P          +KI   +  Y     ++G    ++++ + +     G  NS+ 
Sbjct: 247 RSITYPTP---------QQKIDMCIEHYNRAIYYNGEYKAVREMRKQIGWYIKGLKNSKE 297

Query: 293 CRHILTVEAGASTATHHIIETA 314
            +  +  E   S     I+   
Sbjct: 298 IKEKINCEE-RSEIVFEILNQY 318


>gi|238782959|ref|ZP_04626987.1| tRNA-dihydrouridine synthase B [Yersinia bercovieri ATCC 43970]
 gi|238716162|gb|EEQ08146.1| tRNA-dihydrouridine synthase B [Yersinia bercovieri ATCC 43970]
          Length = 321

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRALCHSM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDDMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLNGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|145640649|ref|ZP_01796232.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           R3021]
 gi|145274575|gb|EDK14438.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           22.4-21]
          Length = 353

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHD 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|145632364|ref|ZP_01788099.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           3655]
 gi|144987271|gb|EDJ93801.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           3655]
          Length = 353

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLNYTGADAIMIGRAALGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|301155534|emb|CBW15002.1| tRNA-dihydrouridine synthase B [Haemophilus parainfluenzae T3T1]
          Length = 326

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 134/325 (41%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E+    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAHY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEELGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I   +G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PLEMAQAAAINVAYGAEIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILKEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++SG+  + IH R         K+       +YD 
Sbjct: 136 VTLKIRTGWDK--ANRNCVQIGKIAEQSGIQALTIHGRT--------KECLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++  S+A K+L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IRAVKQSI-SIPVIANGDIDSASKAKKVLEYTGADAIMIGRAALGNPWLFQAVEALVEHD 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P            I      Y  +    G ++    +H+     G       R  
Sbjct: 245 TIIQTPSLREKCGHILHHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFRQT 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                        ++E   N +++ 
Sbjct: 300 FNA-INEPKEQLIVLEDFLNSILDK 323


>gi|186477299|ref|YP_001858769.1| NifR3 family TIM-barrel protein [Burkholderia phymatum STM815]
 gi|184193758|gb|ACC71723.1| TIM-barrel protein, nifR3 family [Burkholderia phymatum STM815]
          Length = 357

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 62/308 (20%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + +       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 21  MAGVTDRPFRQLCKRM-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 80  PQMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVNAVGVG 139

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G + +       N+ +  + +G++ + +H R         + +     
Sbjct: 140 PDAVPVTLKIRTGWNRENKNA--LNVARLAESAGISMLTVHGRT--------RADLYHGE 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K    ++ +  NG +    +A  +L     D +MIGRAA     +   ++ 
Sbjct: 190 AEYETIAAVK-AAVNIPVVANGDITSPHKARAVLAATDADAIMIGRAAQGRPWLFREIEH 248

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +        +P    + +     +      Y          ++   +H+     G   + 
Sbjct: 249 FLQTGELMEAPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 303

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 304 VFRHRMNT 311


>gi|227538764|ref|ZP_03968813.1| tRNA-dihydrouridine synthase [Sphingobacterium spiritivorum ATCC
           33300]
 gi|227241273|gb|EEI91288.1| tRNA-dihydrouridine synthase [Sphingobacterium spiritivorum ATCC
           33300]
          Length = 331

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 139/327 (42%), Gaps = 22/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R+  +      ++YTE I ++ ++R   K+   L     E+P+ +QI G++
Sbjct: 21  MEDVSDPPFRYVCKQ-NGVDMMYTEFISSEGLIRDAAKSRQKLDIFEYERPIGIQIFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + ++++I      + I++N GCP   V     G+ L+ + D +     A+ +A  +P
Sbjct: 80  IEHMRQSSEICSLANPDLIDINYGCPVKNVVCKGAGSSLLQDIDKMVAMTKAVVEATHLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    V    + + ++  G+  + IH R         +        D+ +
Sbjct: 140 VTVKTRLGWDDNTKNV--YEVAERLQDVGIKALSIHGRT--------RAQMYKGQADWSM 189

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K+     + I  NG ++ + +A        VDG+MIGRA+     +   +  +F  
Sbjct: 190 IRDVKRNPRIKIPIFGNGDIDSVEKAAAWRQEFEVDGIMIGRASIGYPWIFREIKHFFET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++  +    +         + ++ RH    F G PN +  R 
Sbjct: 250 GQRLEGPTIAERV-----EVCRTHLTKSIEWKGEKTGIFEMRRHYANYFKGIPNFKEYRM 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L V   +    H +++   +   E +
Sbjct: 305 KL-VGLQSHHEIHEVLDEIQHQFAEEI 330


>gi|21674741|ref|NP_662806.1| NifR3 family TIM-barrel protein [Chlorobium tepidum TLS]
 gi|21647952|gb|AAM73148.1| TIM-barrel protein, nifR3 family [Chlorobium tepidum TLS]
          Length = 352

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 146/326 (44%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE I A+A+ RG +K+I   +    E+P+A+QI G  
Sbjct: 22  MEDVTDRAFRQLCKQ-HGADIVYTEFISAEALRRGVEKSIRKITVADHERPVAVQIFGNT 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I E +  + +++N GCP  +V     GA L+  P+ + +  +A+  A+S+P
Sbjct: 81  VESMVEAAAIAETYEPDYLDINFGCPVKKVAGRGAGAALLKEPEKLSEIASAVVNAVSLP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D    ++ + + V+ ++ +G+  + +H R         + +      D+  
Sbjct: 141 VTAKTRIGWD--HDSINITDTVRRLEDAGIRAVAVHGRT--------RSDMYKGRADWGR 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K+    + +  NG +     A+ +      DG+MIGR +  N  +           
Sbjct: 191 IAEAKQAC-SIPVIANGDVWLPEDAVAMFERTGADGIMIGRGSIGNPFIFEQAKSLVKEG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +  S+P   +  +     +  S+      +      + ++ RH      G P   + R++
Sbjct: 250 VRLSAPSYRQRIQAAVDHLRLSL-----EYKGEKYGVLEMRRHYSTYLKGLPGVSKVRNL 304

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           L  E         ++   F    E+L
Sbjct: 305 LVRE-PDPAVIVELLRE-FEAACEAL 328


>gi|325182221|emb|CCA16675.1| tRNAdihydrouridine synthase putative [Albugo laibachii Nc14]
          Length = 563

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 116/338 (34%), Positives = 177/338 (52%), Gaps = 18/338 (5%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADI 59
           +DWTDRHYR+  RL+T++  LYTEM+V   +L    +    LG    E PLA+Q+GG  I
Sbjct: 218 MDWTDRHYRYLMRLITHHTQLYTEMLVDQTLLYQKDNLHYFLGHDDDESPLAVQLGGNSI 277

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
             L  AA++  ++G +NEINLN GCPS +V +  FGA LML P+ V D  A M  A   +
Sbjct: 278 DTLAAAAQLCREYGGFNEINLNCGCPSPKVSKQCFGAQLMLQPERVRDICAGMIGANSSM 337

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +TVKCRIGVDD      L+  +  +  SGV    +HARK  L GL+P +NR IP L+
Sbjct: 338 DPEITVKCRIGVDDCDSYEELKRFISVVSASGVEHFIVHARKCWLSGLNPHENRTIPTLN 397

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD VY++K + P+L   LNGG+  + +A ++L   ++DG+MIGRAAYK        D   
Sbjct: 398 YDFVYQLKSDFPNLAFTLNGGVASIEEAHRLLQTSNMDGIMIGRAAYKYPWNFRNADRLL 457

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL--HSGGKLQQIT--RHMIGLFHGFPN 289
                  +  +  + + +          + +  +  +S   +   T  + ++ LF G   
Sbjct: 458 YGAKRNPNLSRREIIERYIDYAEDLQERWGSDKILDNSKFAMPTTTLVKPLLSLFSGEHG 517

Query: 290 SRRCRHILTV-----EAGASTATHHIIETAFNLMIESL 322
            +  +  +       +         I+E+A  L+ +S+
Sbjct: 518 GKVFKRKIGEFWCINKEDRPGL-REIVESAVRLLPDSM 554


>gi|302789157|ref|XP_002976347.1| hypothetical protein SELMODRAFT_104800 [Selaginella moellendorffii]
 gi|300155977|gb|EFJ22607.1| hypothetical protein SELMODRAFT_104800 [Selaginella moellendorffii]
          Length = 358

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 116/328 (35%), Positives = 178/328 (54%), Gaps = 12/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD H+R  AR+L+  + LYTEM+VA+ I+    D +  L F   + P+ LQ+GG++
Sbjct: 9   MMEWTDNHFRALARILSRCSWLYTEMVVAETIVHHENDLERWLEFPAAQHPIVLQLGGSN 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L +AAK+V  FGY+EIN N GCPS++V     FGA LML+P +VG+ + A+ +  S 
Sbjct: 69  LANLSKAAKLVSAFGYDEINFNCGCPSSKVAGHGCFGARLMLSPRLVGEAMQAIAEESSA 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVTVKCRIGVDD      L N V ++   S      IHARKA+L+GLSP  NR  P L Y
Sbjct: 129 PVTVKCRIGVDDSDSYDQLCNFVSTVSSLSPTRHFIIHARKALLEGLSPAQNRVAPPLKY 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM-LTTVDEYF 233
           + V  + ++ PDL   LNGG+  + Q   ++    V+GVM+GRAAY      L   D   
Sbjct: 189 EYVLALMRDFPDLQFTLNGGITTVEQVNYLITDKGVNGVMLGRAAYNTPWCTLARADSCI 248

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   P +    +   R+          ++ ++   ++ + + +  LFHG   S R 
Sbjct: 249 YG-----MPERRITRRQVLREYEEYAESVIGKYGNNKPGIRVLVKPVANLFHGEKGSSRW 303

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R  +      + A++ +   +   ++ S
Sbjct: 304 RQAIDEHVRHAKASNTLSSFSLRFVLSS 331


>gi|167564059|ref|ZP_02356975.1| dihydrouridine synthase [Burkholderia oklahomensis EO147]
 gi|167571203|ref|ZP_02364077.1| dihydrouridine synthase [Burkholderia oklahomensis C6786]
          Length = 334

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 128/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 1   MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 60  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGTG 119

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + K  + +G++ + +H R         + +    +
Sbjct: 120 PDAVPVTLKIRTGWDREHKNAIT--VAKLAEAAGISMLTVHGRT--------RADLYRGD 169

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +  
Sbjct: 170 AEYDTIAAVK-AAVRIPVVANGDITSPHKAKAVLDATGADALMIGRAAQGRPWLFREIGH 228

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +  +      P    + +     +      Y          ++   +H+     G   + 
Sbjct: 229 FLQSGELLPPPRIDEIRQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 283

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 284 GFRHRMNT 291


>gi|302872718|ref|YP_003841354.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor obsidiansis
           OB47]
 gi|302575577|gb|ADL43368.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor obsidiansis
           OB47]
          Length = 328

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 135/303 (44%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEM+ + A++ G  K   ++ FS +EK   +QI G+D
Sbjct: 13  MAGFTDKVFRRLCSRF-GADVTVTEMVSSKALVLGSTKTKELISFSQEEKIRGVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+I++D F Y+ I++N+GCP  ++ +   G  LM NP +    +  + K    
Sbjct: 72  PEVMAQAAEILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLASRIVERVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++  ++        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEE--SINAPEFAYILQESGASFVTVHGRT--------RKQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG + D   A ++      D +MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVK-ERLKIPVVANGDITDFESAKRVYEITGADSIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETEVLPHMKIRVAIEFFRQLCIEKGEKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 KIN 298


>gi|323343751|ref|ZP_08083978.1| tRNA-dihydrouridine synthase B [Prevotella oralis ATCC 33269]
 gi|323095570|gb|EFZ38144.1| tRNA-dihydrouridine synthase B [Prevotella oralis ATCC 33269]
          Length = 346

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/325 (25%), Positives = 145/325 (44%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE I A+A++R  K  +  L  S +E+P+ +QI G D
Sbjct: 38  MEDVTDIGFRLLCKRF-GAAMVYTEFISAEALVRSIKATMSKLTISDEERPVGIQIYGRD 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE+   + I+LN GCP  +V     GA ++ N  ++ +    + KA+  P
Sbjct: 97  VVSMVEAAKIVEEAHPDVIDLNFGCPVKKVASKGAGAGMLRNIPLLLEITREVVKAVHTP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G++ + IH R         +        D+ +
Sbjct: 157 VTVKTRLGWD--ANNLIIADLAEQLQDCGIHALTIHGRT--------RSQMYTGKADWTL 206

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K+     + I  NG +   S+A +       D VMIGRA +    +   + ++  N
Sbjct: 207 IGEVKRNPRIHIPIIGNGDIASPSEAKEAFDRYGTDAVMIGRATFGRPWIFREIIDFLEN 266

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             T ++             I           +     +    RH+    +F G P+ R+ 
Sbjct: 267 SDTPAALTLNDKI-----DILEEQLRINVERIDEYRGILHTRRHLAASPVFKGIPDFRQT 321

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A        I+E     +
Sbjct: 322 R-IAMLRASTFDELMAILEDCRARL 345


>gi|307106508|gb|EFN54753.1| hypothetical protein CHLNCDRAFT_23819 [Chlorella variabilis]
          Length = 374

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 116/328 (35%), Positives = 179/328 (54%), Gaps = 7/328 (2%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADIS 60
           +DWTD +YR  ARL++ +  LYTEM+V   I+        L F  ++ P+  Q+GG+D +
Sbjct: 1   MDWTDLYYRQLARLISRHTWLYTEMVVDQTIIHTPFIDKFLWFPPEQHPIVCQLGGSDPT 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSIPV 119
            L  AA IVE +GY+EINLN GCPS RV     FGA +ML P +V DC  AM +A+ +P+
Sbjct: 61  LLARAAAIVERYGYDEINLNCGCPSDRVAGAGCFGAAMMLRPQLVADCCKAMREAVLMPI 120

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVKCR+GVD       L N V+ + K SGV+   IHARK +LKGL+P  NR +P L Y+ 
Sbjct: 121 TVKCRLGVDSFDSYPQLVNFVEVVSKGSGVSHFVIHARKCLLKGLNPHQNRTVPPLRYEW 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA-MLTTVDEYFSNP 236
           V+ +K++ P L   LNGG+  + +    L   + GVM+GRAAY      L   D      
Sbjct: 181 VWALKRDFPHLEFSLNGGVLTLEEVASALALGIMGVMVGRAAYNMPWDALGDADRAIFGA 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDY-AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              ++  + +V  D+     + +  +      H    ++ + + ++G+FHG P +++ R 
Sbjct: 241 EANAATSRRQVLHDYAAWADSMIGHWRVEEDGHKSPNVRMLVKPLLGMFHGEPRAKKWRA 300

Query: 296 ILTVEAGASTATHHIIETAFNLM-IESL 322
            +      +     +++    ++  ESL
Sbjct: 301 AVDAALKTAETVGEVLDATLPVLKPESL 328


>gi|152981141|ref|YP_001351996.1| tRNA-dihydrouridine synthase [Janthinobacterium sp. Marseille]
 gi|151281218|gb|ABR89628.1| tRNA-dihydrouridine synthase [Janthinobacterium sp. Marseille]
          Length = 338

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 65/302 (21%), Positives = 121/302 (40%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K+        + +P A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMAASNPRLWASDKSTRRTNHDGEVEPKAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK   D G   I++N+GCP  +V     G+ L+ +  +V + + A+  ++++P
Sbjct: 76  PVLLAECAKFNVDRGAQIIDINMGCPVKKVCNSWCGSALLQHESLVAEILEAVVASVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ +  ++SG+  + +H R         + +    + +Y+ 
Sbjct: 136 VTLKFRTGWDRAHKNA--LNIARIAEQSGIAMLTLHGRT--------RADGYSGDAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ Y    
Sbjct: 186 ITAVK-AAVSIPVVANGDITTPEKARYVLDVTGADAIMIGRAAQGRPWIFREIEHYLRTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P+   V       + A    Y          ++   +H+             R  
Sbjct: 245 TYLPAPMIAEVRTLMDEHLRAHYAFY-----GEYLGVRTARKHIGWYVRELVGGEAFRQQ 299

Query: 297 LT 298
           + 
Sbjct: 300 MN 301


>gi|148826373|ref|YP_001291126.1| DNA-binding protein Fis [Haemophilus influenzae PittEE]
 gi|148716533|gb|ABQ98743.1| DNA-binding protein Fis [Haemophilus influenzae PittEE]
          Length = 353

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|317402229|gb|EFV82818.1| hypothetical protein HMPREF0005_00223 [Achromobacter xylosoxidans
           C54]
          Length = 341

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 69/306 (22%), Positives = 129/306 (42%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMAASNPKLWDSVKTSRRLNHDGEIAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EAA    + G   I++N+GCP  +V   + G+ L+ + D++   + A+ +A   L
Sbjct: 76  PAMMAEAAVFNANKGARIIDINMGCPVKKVCNVASGSALLRHEDLIARILDAVVEACAPL 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D     V    + +  + +G+  + +H R         + +      +
Sbjct: 136 GVPVTLKTRTGWDRDSRNV--LRVARLAENAGIAALTLHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  ++ E   + +  NG ++   +A ++L     D VMIGRAA     +   VD Y 
Sbjct: 186 YDTIRAVRAEL-KIPLIANGDIDSPEKAKRVLDYTGADAVMIGRAAQGRPWIFREVDHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               T + P    + +     +      Y          ++   +H+     G P++   
Sbjct: 245 RTGETLAPPGYGEMRELLLEHLDDHYRFYGEH-----TGVRTARKHIGWYLDGLPDADSF 299

Query: 294 RHILTV 299
           R  + +
Sbjct: 300 RDRMNL 305


>gi|226321200|ref|ZP_03796737.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 29805]
 gi|226233397|gb|EEH32141.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 29805]
          Length = 335

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANKVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|238797912|ref|ZP_04641403.1| tRNA-dihydrouridine synthase B [Yersinia mollaretii ATCC 43969]
 gi|238718217|gb|EEQ10042.1| tRNA-dihydrouridine synthase B [Yersinia mollaretii ATCC 43969]
          Length = 321

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDDMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLNGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|325288416|ref|YP_004264597.1| tRNA-U20-dihydrouridine synthase [Syntrophobotulus glycolicus DSM
           8271]
 gi|324963817|gb|ADY54596.1| tRNA-U20-dihydrouridine synthase [Syntrophobotulus glycolicus DSM
           8271]
          Length = 321

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 146/320 (45%), Gaps = 24/320 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD+ +R   R L     +YTEMI   A++  + K   +L    +E+P  +Q+ G++ 
Sbjct: 18  AGVTDKAFRQIVRQLGGK-YMYTEMISDKALIFHNPKTIKMLDLKEEEEPRIVQLFGSEP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI ++ G   I++N+GCP+ ++ +   GA L+ N     +  + + KA+ +PV
Sbjct: 77  RIMGEAAKIAQNCGATVIDINMGCPTPKIVKNGEGAALLKNIQSAVEIASNVVKAVDVPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G D     +    L + ++++GV  + +HAR         ++       D++ +
Sbjct: 137 SVKMRLGWDRG--NIVAVELGRRLEEAGVVMLTLHART--------REQYYAGEADWEWI 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K++   + +  NG +     A K++     DGVMIGR    N  ++     +  +  
Sbjct: 187 AKLKEKV-KIPVIGNGDICSPQDAAKMISNTGCDGVMIGRGVMGNPWIIERTAIFLKDHF 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-HI 296
           +   P       +  R+  A +  Y    +     + ++ +H +    G  +S R R  I
Sbjct: 246 SKQEPGNQE-RLEVLRRHFALLLKYKGERIG----VNEMRKHAVWYTKGIRHSARFRDQI 300

Query: 297 LTVEAGASTATHHIIETAFN 316
           +  E         ++E  F+
Sbjct: 301 MKSETSRDM--VQVMERIFS 318


>gi|256821476|ref|YP_003145439.1| TIM-barrel protein, nifR3 family [Kangiella koreensis DSM 16069]
 gi|256795015|gb|ACV25671.1| TIM-barrel protein, nifR3 family [Kangiella koreensis DSM 16069]
          Length = 329

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 146/327 (44%), Gaps = 24/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R   + L    L  +EMI A+  LR  +K++   + Q +P   ++QI GA+
Sbjct: 20  MAGVTDRPFRQLCKEL-GAGLTVSEMIAANPQLRNTRKSMQRSNHQGEPGIRSVQIAGAE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+     G   I++N+GCP+ +V + + G+ L+ +P +V D + A+  A+ +P
Sbjct: 79  PEMLAQAAQYNVQNGAEIIDINMGCPAKKVCKKAAGSALLQDPQLVEDILNAVVAAVEVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +          + +  +++G+  + +H R         + ++ + N +YD 
Sbjct: 139 VTLKIRTGWNHDNRNGV--QIARIAEQAGIQSLAVHGRT--------RADKYLGNAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ +  + +  NG +    +A  +L    VDG+MIGR A  N  +   V  Y    
Sbjct: 189 IATIKQ-SVSIPVVANGDITSPEKAKFVLDYTGVDGLMIGRGAQGNPWIFREVWHYLQTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    V +     I+A    Y A         +   +H+        ++   R  
Sbjct: 248 DKLAPPSWQEVRQVLLGHIAALHEFYGAVM-----GPRIARKHVSWYLQEQADANEFRR- 301

Query: 297 LTVEAGASTATHH-IIETAFNLMIESL 322
            T  A    A    +++  F    +++
Sbjct: 302 -TFNAIDDGAEQLGVLDRYFEQKQQAI 327


>gi|292900840|ref|YP_003540209.1| tRNA-dihydrouridine synthase B [Erwinia amylovora ATCC 49946]
 gi|291200688|emb|CBJ47820.1| tRNA-dihydrouridine synthase B [Erwinia amylovora ATCC 49946]
 gi|312170828|emb|CBX79088.1| putative dehydrogenase [Erwinia amylovora ATCC BAA-2158]
          Length = 321

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA--LQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMMSSNPEVWASDKSRLRMVHSDEPGVRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   + A+  A+ +P
Sbjct: 76  PQEMAEAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDSDNRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + +  NG + D  +A  +L     DG+MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-NVSIPVIANGDITDPHKARAVLDYTGADGLMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y  R    G ++    +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIGHLRELHDFYGQR---KGYRI--ARKHVSWYLQENAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|229846037|ref|ZP_04466149.1| DNA-binding protein Fis [Haemophilus influenzae 7P49H1]
 gi|229811041|gb|EEP46758.1| DNA-binding protein Fis [Haemophilus influenzae 7P49H1]
          Length = 353

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKFGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|325579238|ref|ZP_08149194.1| tRNA-dihydrouridine synthase B [Haemophilus parainfluenzae ATCC
           33392]
 gi|325159473|gb|EGC71607.1| tRNA-dihydrouridine synthase B [Haemophilus parainfluenzae ATCC
           33392]
          Length = 326

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 135/325 (41%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E+    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCAHY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHSEELGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I   +G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PLEMAQAAAINVAYGAEIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILKEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++SG+  + IH R         K+       +YD 
Sbjct: 136 VTLKIRTGWDK--VNRNCVQIGKIAEQSGIQALTIHGRT--------KECLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++  S+A K+L     D +MIGRA+  N  +   V+    + 
Sbjct: 186 IRAVKQSI-SIPVIANGDIDSASKAKKVLEYTGADAIMIGRASLGNPWLFQAVEALVEHD 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          R I      Y  +    G ++    +H+     G       R  
Sbjct: 245 TIIQTPSLREKCGHILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFRQT 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                        ++E   N +++ 
Sbjct: 300 FNA-INEPKEQLIVLEDFLNSILDK 323


>gi|254230100|ref|ZP_04923497.1| tRNA-dihydrouridine synthase B [Vibrio sp. Ex25]
 gi|151937389|gb|EDN56250.1| tRNA-dihydrouridine synthase B [Vibrio sp. Ex25]
          Length = 340

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 35  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P+I+ + + A+  A+ +P
Sbjct: 94  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 154 VTLKTRTGWD--TDNKNCVQIAKLAENCGIQALALHGRT--------KACMYKGEAEYDS 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 204 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 263 TTMEELPTEEVKTIMLGHVNALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 317

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 318 FNAIDAAP-LQIEALEGYFDNV 338


>gi|226942843|ref|YP_002797916.1| Dihydrouridine synthase [Azotobacter vinelandii DJ]
 gi|226717770|gb|ACO76941.1| Dihydrouridine synthase [Azotobacter vinelandii DJ]
          Length = 322

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 68/314 (21%), Positives = 134/314 (42%), Gaps = 21/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EM+ +D  L   +K+ L      + +P ++QI G D
Sbjct: 10  MAGVTDRPFRALCRRL-GAGMTVSEMLTSDVRLWNSRKSRLRLPHGDEPEPRSVQIAGGD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+   + G   I++N+GCP+ +V   + G+ LM +  +V + + A+  A+ +P
Sbjct: 69  PQRLAEAARRNVELGAQIIDINMGCPAKKVCNKAAGSALMRDEALVAEILRAVVTAVEVP 128

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +++G+  + +H R         + +      +YD 
Sbjct: 129 VTLKIRTGWDRANRNGV--GIARLAEQAGIAALAVHGRT--------RADLYGGAAEYDT 178

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ Y    
Sbjct: 179 IAAIKRAV-SIPVFANGDIDSPEKARQVLDATGADGLLIGRAAQGRPWIFREIEHYLRTG 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +     V+      ++A    Y          ++   +H+       P ++  R  
Sbjct: 238 ERLPAMTALEVEPVLLEHLAALYRFYGEE-----LGVRIARKHVGWYLASLPGAQEFRAQ 292

Query: 297 LTVEAGASTATHHI 310
                     + H+
Sbjct: 293 FNRLDTTDAQSAHV 306


>gi|74318474|ref|YP_316214.1| dihydrouridine synthase [Thiobacillus denitrificans ATCC 25259]
 gi|74057969|gb|AAZ98409.1| dihydrouridine synthase [Thiobacillus denitrificans ATCC 25259]
          Length = 350

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 124/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EM+ ++++L G  K         +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGMAVSEMVTSNSLLYGSAKTARRANHEGEVDPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              + EAA+   D G   I++N+GCP+ +V     G+ L+ +  +VG  + A+  A+  +
Sbjct: 76  PRMMAEAARHNADRGAQIIDINMGCPAKKVCNVMAGSALLQDEALVGRILDAVVAAVPEL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D +        ++   + +GV  + IH R         +        +YD
Sbjct: 136 PVTLKIRTGWDREHRNA--LAILGIAENAGVKALAIHGRT--------RACGYSGEAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG +    +A  +L     D VMIGRAA     +   ++ Y   
Sbjct: 186 TIRAVKAAA-RIPVIANGDITTPEKARHVLEHTGADAVMIGRAAQGRPWIFREIEHYLRT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    + +     +      Y          ++   +H+     G   S   RH
Sbjct: 245 GEHLPQPEVAEIHRVLLDHLHDLYGFY-----GEVTGVRVARKHISWYTRGLVGSSAFRH 299

Query: 296 ILT 298
            + 
Sbjct: 300 AMN 302


>gi|167754846|ref|ZP_02426973.1| hypothetical protein CLORAM_00350 [Clostridium ramosum DSM 1402]
 gi|167704896|gb|EDS19475.1| hypothetical protein CLORAM_00350 [Clostridium ramosum DSM 1402]
          Length = 326

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 137/303 (45%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+Y+EM+   A+  G+ K   +L     E P+++Q+ G +
Sbjct: 18  MAGITNMAFRKIIKDF-GAGLVYSEMVSDKALCYGNAKTIEMLQVDDGEHPVSIQLFGGE 76

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V+AAK ++     + I++N+GCP  +V +   G+ L+L PD + + +  +   ++ 
Sbjct: 77  VETMVQAAKYIDKHSNCDIIDINMGCPVNKVLKADAGSKLLLYPDKIYEIVKGVVDNVTK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +    + + I+K+G + I IH R         +      + D++
Sbjct: 137 PVTVKIRSGFDKE--HINAIEVAQLIEKAGASAIAIHGRT--------RSQMYEGHADWE 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG ++ +  A ++L    VD VMIGRAA  N  ++  V E    
Sbjct: 187 IIRQVK-EAVKIPVIGNGDIKSVEDAKRMLEETKVDAVMIGRAALGNPWLIKQVVESLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T S P                M             + Q+  H      G  +S R ++
Sbjct: 246 GETISEPTYQEKITQCLAHARRLM-----EIEPEKVAMFQMRGHAPWYIKGLKSSARVKN 300

Query: 296 ILT 298
            L+
Sbjct: 301 ELS 303


>gi|94500040|ref|ZP_01306575.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Oceanobacter sp.
           RED65]
 gi|94427898|gb|EAT12873.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Oceanobacter sp.
           RED65]
          Length = 328

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 139/321 (43%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+   L  + + +P+++QI G D
Sbjct: 18  MAGVTDRPFRQLCRQL-GAGLVVSEMVTSDVKLWNSRKSRQRLDHAGEAEPISVQIAGGD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +    G   I++N+GCP+ +V   + G+ LM +  +V D + A+  ++ IP
Sbjct: 77  PEMMAQAAIMSAAHGAQIIDINMGCPAKKVCNKAAGSALMKDEVLVRDILQAVVDSVDIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +     +  L    ++ G+  + IH R         +       ++YD 
Sbjct: 137 VTLKMRTGWAPEHKNAPV--LAGMAEEIGIAALAIHGRT--------RSCGYKGEVEYDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N ++ +  NG + +  QA  +L     DGVM+GRAA     +   ++ + +  
Sbjct: 187 IKTIKQ-NVNIPVLANGDITNAEQAKFVLDYTGADGVMLGRAAQGRPWIFREINHFLTTG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    V+      + A    Y          ++   +H+        + R  R  
Sbjct: 246 EPLAAPSIKEVEAILIGHLHALYGFY-----GDYLGVRIARKHVGWYLQAHDHDRAVRKQ 300

Query: 297 LTVEAGASTATHHIIETAFNL 317
                        +I+T FN 
Sbjct: 301 FNQLESCED-QIALIKTFFNQ 320


>gi|148553172|ref|YP_001260754.1| nifR3 family TIM-barrel protein [Sphingomonas wittichii RW1]
 gi|148498362|gb|ABQ66616.1| putative TIM-barrel protein, nifR3 family [Sphingomonas wittichii
           RW1]
          Length = 333

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 131/304 (43%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   +D  +R   R    + L  TEMI + A +R  ++++    +   E+P+++Q+ G  
Sbjct: 24  MTGVSDLPFRKVVRGY-GSGLNVTEMIASQAAIRETRQSVQKALWDPAEEPVSMQLVGCT 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ +D G   I++N+GCP  +V  G  G+ LM  P++  + + A   A+ +P
Sbjct: 83  PKEMGEAAKLSQDRGAAIIDINMGCPVRKVVNGDAGSALMRTPELAVEIVKATVAAVEVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D    ++    L +  +  GV  I +H R         +      + D+  
Sbjct: 143 VTLKMRMGWD--HDSLNAPELARIAEDVGVKMITVHGRT--------RCQMYKGSADWAF 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + + +NG +  +  A   L     DG+MIGR AY    +L+ V  Y +  
Sbjct: 193 IRRVK-EAVSIPVIVNGDICSIEDAETALDQSGADGLMIGRGAYGRPWLLSQVMHYLATG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P   +          A +  Y          +    +H+     G   S   R+ 
Sbjct: 252 ERRPDPTIEQQYHVILAHYHAMLELYGKE-----VGVNMARKHIGWYTKGLAGSAEFRNA 306

Query: 297 LTVE 300
           +  E
Sbjct: 307 VNQE 310


>gi|163754515|ref|ZP_02161637.1| probable TIM-barrel protein, NifR3 family [Kordia algicida OT-1]
 gi|161325456|gb|EDP96783.1| probable TIM-barrel protein, NifR3 family [Kordia algicida OT-1]
          Length = 330

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 138/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+   L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSTMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LDSMLKSVEIVEKSGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + +  + + ++  G   I IH R         +        ++  
Sbjct: 138 VTVKTRLGWDE--NTIKIVEVAERLQDVGCASIAIHGRT--------RAQMYKGEANWHP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + +  NG ++   +A+ +     +DG MIGRA+         V  +F  
Sbjct: 188 IAAVKNNPRMHIPVFGNGDVDSPEKAMLMRDKFGLDGAMIGRASIGYPWFFREVKHFFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +   R +     D+    L     + +  RH    F G P+ +  R 
Sbjct: 248 GEHMAKPTMEERIEAARRHL-QMSIDWKGERLG----VFETRRHYTNYFKGIPHFKEYRQ 302

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            L     ++     +++  +   
Sbjct: 303 RLVTTDDSAGV-FQVLDEVYEKF 324


>gi|293394168|ref|ZP_06638468.1| tRNA-dihydrouridine synthase B [Serratia odorifera DSM 4582]
 gi|291423146|gb|EFE96375.1| tRNA-dihydrouridine synthase B [Serratia odorifera DSM 4582]
          Length = 321

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 17  MAGITDRPFRTLCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAAQINVASGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILLAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-NVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLGEVKRLLIGHIRELHGFY-----GQGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|94496405|ref|ZP_01302982.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sphingomonas sp.
           SKA58]
 gi|94424151|gb|EAT09175.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sphingomonas sp.
           SKA58]
          Length = 343

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 134/309 (43%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A++R  ++++    +   E+P+++Q+ G  
Sbjct: 26  MTGVTDMPFRTLVRRY-GSGLNVTEMIASAAMIRETRQSLQKAAWHPLEEPVSMQLAGCS 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  D G   I++N+GCP  +V  G  G+ LM +  +    I A  +A+ +P
Sbjct: 85  PREMADAARLNADRGAAIIDINMGCPVKKVVNGDAGSALMRDLPLAASLIKATVEAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++    L    +  G   I +H R         ++     + D+  
Sbjct: 145 VTVKMRMGWD--HASLNAPELAHIAEDLGAKLITVHGRT--------RNQMYKGSADWAF 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K +   L + +NG +  +  A   L     DGVMIGR AY    ++  V  + ++ 
Sbjct: 195 VRKVK-DAVKLPVVVNGDICSIEDADTALEQSGADGVMIGRGAYGRPWLIGQVMAWLTDG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P              A M D+  RH      +    +H+     G   S   R+ 
Sbjct: 254 TRLPDPSLEEQYHVIVEHYRA-MLDHYDRH----TGVNMARKHIGWYTKGLTGSAEFRNA 308

Query: 297 LTVEAGAST 305
           +  E  A T
Sbjct: 309 VNQEPDADT 317


>gi|304383997|ref|ZP_07366453.1| tRNA-dihydrouridine synthase B [Prevotella marshii DSM 16973]
 gi|304334889|gb|EFM01163.1| tRNA-dihydrouridine synthase B [Prevotella marshii DSM 16973]
          Length = 326

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 140/318 (44%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     +++YTE + A+A++R  +  +  L    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRY-GASMVYTEFVSAEALVRSIRSTMSKLTICDEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+IVE    + I+LN GCP  +V     GA ++ N  ++ +    + KA++ P
Sbjct: 77  KDAMVEAARIVERAKPDVIDLNFGCPVKKVAGKGAGAGMLRNVPLMLEITREVVKAVNTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + + +L + ++  G+  + IH R         +        D+  
Sbjct: 137 VTVKTRLGWDAE--NIIIEDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSW 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + +  NG +    QA +      VD VMIGRA +    +   +++    
Sbjct: 187 IGKVKANPRLHIPVIGNGDIASPEQAKEAFEQYGVDAVMIGRATFGRPWIFKEINDSLQG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                S     ++      I           +     +    RH+    +F G P+ ++ 
Sbjct: 247 LQPDPS-----LNVRAKISILEEQLHINIERIDEYRGILHTRRHLAASPIFKGIPDFKQT 301

Query: 294 RHILTVEAGASTATHHII 311
           R I  + A + +    I+
Sbjct: 302 R-IAMLRATSESELLAIL 318


>gi|254478500|ref|ZP_05091876.1| putative TIM-barrel protein, nifR3 family [Carboxydibrachium
           pacificum DSM 12653]
 gi|214035589|gb|EEB76287.1| putative TIM-barrel protein, nifR3 family [Carboxydibrachium
           pacificum DSM 12653]
          Length = 291

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 75/307 (24%), Positives = 131/307 (42%), Gaps = 26/307 (8%)

Query: 18  NNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
              L YTEM+ A  +  G  + K +L     EK +A+QI G+D   + E A+ + +    
Sbjct: 2   GAGLTYTEMVSAKGLYYGSENTKALLDIDNGEK-VAIQIFGSDSEIMGEIARRLNESKAL 60

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ ++ +   GA LML PD+    + A+ KA   PVTVK R G +D    V 
Sbjct: 61  IIDINMGCPTPKIVKNGDGAALMLKPDLAEKVMEAVVKASYKPVTVKIRKGWND--NNVN 118

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  ++ G+  + +H R         ++       D++I+ ++K E+  + +  NG
Sbjct: 119 AVEIAQIAERVGIKAVAVHGRT--------REQFYSGKADWEIIKKVK-ESVKIPVIGNG 169

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            +     A ++L     D VMIGR A  N  +      Y         P          R
Sbjct: 170 DIFTPEDAKRMLDETGCDAVMIGRGAQGNPWIFKRTVHYLKTGELLPEPTIKEKVDLMIR 229

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            ++  M +Y          + ++ +H+     G P S R R     EA     ++  I+ 
Sbjct: 230 HLT-MMVEYKGE----KTGVVEMRKHIAWYLKGLPGSARMR-----EAVFKMESYKEIKE 279

Query: 314 AFNLMIE 320
               + +
Sbjct: 280 FLEGIPK 286


>gi|119946821|ref|YP_944501.1| tRNA-dihydrouridine synthase [Psychromonas ingrahamii 37]
 gi|119865425|gb|ABM04902.1| tRNA-dihydrouridine synthase [Psychromonas ingrahamii 37]
          Length = 319

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 125/299 (41%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R      L  +EM+ ++  +   +K+ L   +  +    ++QI G++
Sbjct: 17  MAGVTDRPFRELCRK-QGAGLAVSEMLSSNPRVWNSRKSKLRMDYHNESGIRSVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++    G   I++N+GCP+ +V++   G+ L+ +P++V   +  +  A+ +P
Sbjct: 76  PLAMATAAQLSVQQGAQIIDINMGCPAKKVNKKKAGSALLPHPELVRAILETVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++SG+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDPDSRNG--LEIARIAEQSGIQALAVHGRT--------RQCFYNGFAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ N  + +  NG +  + +A  +L     D +MIGR A     +   ++ Y +  
Sbjct: 186 IKKIKQ-NVTIPVIANGDITSVEKAKFVLDYTGADAIMIGRGAQGAPWIFNEINHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              SSP K  +       + A    Y           +   +H+             + 
Sbjct: 245 EQLSSPAKAEIAHILLGHVQALHGFY-----GEVMGPRIARKHVGWYLKEQDQLGHFKR 298


>gi|303228846|ref|ZP_07315659.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516466|gb|EFL58395.1| TIM-barrel protein, nifR3 family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 330

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 133/303 (43%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  A+     +++ TEM+ A  I   +++   +L     E P+++QI G++
Sbjct: 21  MAGVSDIAYRLLAKE-HGASMVCTEMVSAMGIKYKNERTHELLRMEEVEHPVSMQIFGSN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   AK+V   G + +++N+GCP  +V     G+ LM  PD+      A  KA+ +P
Sbjct: 80  PEAIALGAKVVAAAGADIVDINMGCPVKKVVSSGDGSALMKTPDLAARVAEAAVKAVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG DD+   + + +  K I+ +GV  + +H R         ++   +   D+  
Sbjct: 140 VTVKMRIGWDDE--HINVVDFAKRIESTGVAAVAVHGRT--------REQMYMGRADWSY 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K ++  + +  NG +     AL+++     D VMIGR A  N  +    + Y +  
Sbjct: 190 IKAVK-DSLSIPVIGNGDVWTPEDALRMMQETGCDAVMIGRGAQGNPWIFERTNHYLTTG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          +       +   R+  +   +++I  H      G P +   R+ 
Sbjct: 249 ELRPEPTYLERLDMLLKH-----FELLCRYKGAALGVREIRTHAGWYMRGMPEAAYWRNR 303

Query: 297 LTV 299
           +  
Sbjct: 304 VNT 306


>gi|52078576|ref|YP_077367.1| putative dihydrouridine synthase TIM-barrel protein [Bacillus
           licheniformis ATCC 14580]
 gi|52783937|ref|YP_089766.1| YacF [Bacillus licheniformis ATCC 14580]
 gi|319648605|ref|ZP_08002819.1| tRNA-dihydrouridine synthase 1 [Bacillus sp. BT1B_CT2]
 gi|52001787|gb|AAU21729.1| putative Dihydrouridine synthase TIM-barrel protein [Bacillus
           licheniformis ATCC 14580]
 gi|52346439|gb|AAU39073.1| YacF [Bacillus licheniformis ATCC 14580]
 gi|317389372|gb|EFV70185.1| tRNA-dihydrouridine synthase 1 [Bacillus sp. BT1B_CT2]
          Length = 333

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 143/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILYNNAKTMGMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+P+ + + ++A+ +A+  
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVEAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +      ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAVENARAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   + + R+
Sbjct: 246 GELKDEPKVREKIS-----VCKLHLDRLIGLKGENVAVREMRKHAAWYLKGIRGNAKVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF +  E+
Sbjct: 301 EINHCETRDELVQ--LLDAFTIEAEA 324


>gi|284008660|emb|CBA75295.1| tRNA-dihydrouridine synthase B [Arsenophonus nasoniae]
          Length = 458

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 124/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    S +    ++QI G+D
Sbjct: 46  MAGITDRPFRSLCYSM-GAGMTVSEMLSSNPQVWKTDKSRLRMIHSDELGIRSVQIAGSD 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+  P+++   + A+  A+ +P
Sbjct: 105 PDEMATAARINVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELIEKILLAVVNAVDVP 164

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  ++ G+  + IH R         +        +YD 
Sbjct: 165 VTLKVRTGWSPEERN--CIKIAQLAERCGIQAVTIHGRT--------RACLFNGAAEYDS 214

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+ N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 215 IRAAKQ-NVTIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLETG 273

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       +      Y       G  ++   +H+           + R  
Sbjct: 274 ELLPPMPIAEVQCLMQAHVKELHDFY-----GQGKGIRIARKHVSWYLREHAPDDQFRRT 328

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS     ++E  F   
Sbjct: 329 FNTIEDASE-QLEVLEAYFEKF 349


>gi|322514995|ref|ZP_08068006.1| tRNA-dihydrouridine synthase B [Actinobacillus ureae ATCC 25976]
 gi|322119011|gb|EFX91182.1| tRNA-dihydrouridine synthase B [Actinobacillus ureae ATCC 25976]
          Length = 339

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 69/304 (22%), Positives = 136/304 (44%), Gaps = 25/304 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA--LQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L  +  E+     +QI GAD
Sbjct: 36  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSRLRLAHHEEIGVNAVQIAGAD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 95  PQEMAAAAKVNVEYGAEIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVDVP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +K+G++ + IH R         +D       +Y+ 
Sbjct: 155 VTLKIRTGWDQENRN--CLEIAKIAEKAGISALTIHGRT--------RDCLFNGEAEYES 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A  +L     D VMIGR ++    +   V ++  N 
Sbjct: 205 IKAVKQAV-SIPIIANGDVTSAEKAKYVLDYTKADAVMIGRGSFGRPWLFKEVKDFLENG 263

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP---NSRRC 293
            + +S +  + +    + I      Y       G ++    +H+           N +R 
Sbjct: 264 RSSNSSLDEKCELM-LKHIEDLHQFYGEE---KGYRI--ARKHVGWYVEQLAPNSNFKRT 317

Query: 294 RHIL 297
            + L
Sbjct: 318 FNAL 321


>gi|294668302|ref|ZP_06733406.1| hypothetical protein NEIELOOT_00215 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291309756|gb|EFE50999.1| hypothetical protein NEIELOOT_00215 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 340

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 138/320 (43%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R  AR         +EM+ +D +LR  KK++    F  ++   A+QI G+D
Sbjct: 18  MAGITDKPFRRLARRF-GAGYAVSEMLASDPLLRHTKKSLSRGDFDGEDGLRAVQIAGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+   + G   I++N+GCP  +V     G+ L+ N  +V D + A+  A+ +P
Sbjct: 77  PKQMAEAARYNVENGAQIIDINMGCPVKKVCNVLAGSALLQNEKLVDDILRAVVSAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    +  R + K  +++G+  + +H R         ++        YD+
Sbjct: 137 VTLKTRLGFAENNKNI--RTVAKMAEQAGIAALAVHGRT--------REQMYKGQASYDL 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K +   + + +NG +    +A ++L     DGVMIGR A     +   +  +  + 
Sbjct: 187 IAEVKHDI-SIPLWVNGDITTPQKAAEVLRQTGADGVMIGRGAQGRPWLFADIAHFLQHG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
              +              +      Y          L+   +H+      FP+   CR  
Sbjct: 246 SLPAPVTFQTASAAMLEHLREMYDFY-----GETAGLRIARKHIGWYLAPFPDGEACRKH 300

Query: 295 -HILTVEAGASTATHHIIET 313
            +IL   A    A    +E 
Sbjct: 301 INILDFAAAQYDAVSAFLER 320


>gi|145628084|ref|ZP_01783885.1| DNA-binding protein Fis [Haemophilus influenzae 22.1-21]
 gi|145630072|ref|ZP_01785854.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           R3021]
 gi|145638199|ref|ZP_01793809.1| DNA-binding protein Fis [Haemophilus influenzae PittII]
 gi|144979859|gb|EDJ89518.1| DNA-binding protein Fis [Haemophilus influenzae 22.1-21]
 gi|144984353|gb|EDJ91776.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           R3021]
 gi|145272528|gb|EDK12435.1| DNA-binding protein Fis [Haemophilus influenzae PittII]
          Length = 353

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 140/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKLVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|312876693|ref|ZP_07736673.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796533|gb|EFR12882.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 328

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 135/303 (44%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEM+ + A++ G  K   ++ FS +EK   +QI G+D
Sbjct: 13  MAGFTDKVFRRLCSKF-GADVTVTEMVSSKALVLGSAKTKELISFSEEEKIRGIQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++ +   G  LM NP +    +  + K    
Sbjct: 72  PEVMAQSVKILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++   +        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEED--INAPEFAYILQESGASFVTVHGRT--------RAQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K++   + +  NG + D   A +       DG+MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVKEKV-KIPVVANGDITDFESAKRAYEVTRADGIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T+V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETKVLPHMKIRVAIEFFSQLCSEKGEKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 KIN 298


>gi|291619129|ref|YP_003521871.1| DusB [Pantoea ananatis LMG 20103]
 gi|291154159|gb|ADD78743.1| DusB [Pantoea ananatis LMG 20103]
          Length = 349

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 133/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 45  MAGITDRPFRTLCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+ +P
Sbjct: 104 PSEMAQAARINVDAGAQVIDINMGCPAKKVNRKMAGSALLQYPSVVESILSAVVNAVDVP 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         +      + +YD 
Sbjct: 164 VTLKIRTGWDPENRNCVA--IAQLAERCGIQALTIHGRT--------RACLFNGDAEYDS 213

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 214 IRTVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 272

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y      SG   +   +H+         + + R  
Sbjct: 273 ELLAPLPLAEVKRLLVSHIRELHDFY-----GSGKGYRIARKHVSWYLQEHAPNDQFRRT 327

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 328 FNAIEDASE-QLEALEAYFENL 348


>gi|237735422|ref|ZP_04565903.1| transcriptional regulator [Mollicutes bacterium D7]
 gi|229381167|gb|EEO31258.1| transcriptional regulator [Coprobacillus sp. D7]
          Length = 331

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 137/303 (45%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+Y+EM+   A+  G+ K   +L     E P+++Q+ G +
Sbjct: 23  MAGITNMAFRKIIKDF-GAGLVYSEMVSDKALCYGNAKTIEMLQVDDGEHPVSIQLFGGE 81

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V+AAK ++     + I++N+GCP  +V +   G+ L+L PD + + +  +   ++ 
Sbjct: 82  VETMVQAAKYIDKHSNCDIIDINMGCPVNKVLKADAGSKLLLYPDKIYEIVKGVVDNVTK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +    + + I+K+G + I IH R         +      + D++
Sbjct: 142 PVTVKIRSGFDKE--HINAIEVAQLIEKAGASAIAIHGRT--------RSQMYEGHADWE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG ++ +  A ++L    VD VMIGRAA  N  ++  V E    
Sbjct: 192 IIRQVK-EAVKIPVIGNGDIKSVEDAKRMLEETKVDAVMIGRAALGNPWLIKQVVESLKT 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T S P                M             + Q+  H      G  +S R ++
Sbjct: 251 GETISEPTYQEKITQCLAHARRLM-----EIEPEKVAMFQMRGHAPWYIKGLKSSARVKN 305

Query: 296 ILT 298
            L+
Sbjct: 306 ELS 308


>gi|216264796|ref|ZP_03436788.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 156a]
 gi|225549125|ref|ZP_03770100.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 94a]
 gi|215981269|gb|EEC22076.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 156a]
 gi|225370351|gb|EEG99789.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 94a]
 gi|312148382|gb|ADQ31041.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi JD1]
          Length = 335

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|307824225|ref|ZP_07654451.1| TIM-barrel protein, nifR3 family [Methylobacter tundripaludum SV96]
 gi|307734605|gb|EFO05456.1| TIM-barrel protein, nifR3 family [Methylobacter tundripaludum SV96]
          Length = 327

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 137/323 (42%), Gaps = 21/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   +DR +R   +      L  +EM+ ++  LR  K+ +L      +    ++QI G +
Sbjct: 17  MAGISDRPFRELCKQF-GAGLAVSEMVASNPALRQHKRTLLKADHDGETGIRSVQILGTN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AAK+    G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+ IP
Sbjct: 76  PQLMADAAKLNAQRGAQIIDINMGCPAKKVCSVAAGSALLRDEALVKRILDAVVNAVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  + +G+  + IH R         +  +     +++ 
Sbjct: 136 VTLKIRTGWDLHSRNAV--EIARIAENAGIAALTIHGRT--------RACKFEGRAEHET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG ++   QA  +L     D +MIGRAA  N  + + +  + ++ 
Sbjct: 186 LKKVKRAI-SIPVIANGDIDSPEQARFVLESTGADAIMIGRAAQGNPWLFSQISHFINHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  T +       +    + Y      +   ++   +H+   F    +  +    
Sbjct: 245 KHLEKPTVTDIHNTISSHLDKLYSFY-----GNASGVRIARKHIAWYFKHLESVAQDAQS 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
               A   +    +I +AFNL+ 
Sbjct: 300 NINRAQCPSQQIALINSAFNLLT 322


>gi|224533852|ref|ZP_03674440.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi CA-11.2a]
 gi|224513145|gb|EEF83508.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi CA-11.2a]
          Length = 333

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 69

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPI 129

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 250 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAIETLPEKI 328


>gi|148977178|ref|ZP_01813805.1| NifR3/Smm1 family protein [Vibrionales bacterium SWAT-3]
 gi|145963460|gb|EDK28723.1| NifR3/Smm1 family protein [Vibrionales bacterium SWAT-3]
          Length = 322

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 125/323 (38%), Gaps = 24/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  +    K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKVWKTSKSQQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G   I++N+GCP+ +V++   G+ L+  PD++ + + A+  A+ +P
Sbjct: 76  PQLMAEAAQFNVDNGAQIIDINMGCPAKKVNKKLAGSALLQYPDLIEEILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         +        +Y  
Sbjct: 136 VTLKTRTGWD--TDNRNCVQIAKIAEDCGIQALALHGRT--------RACMYKGEAEYKH 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAAKQAV-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFNEILHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       + A    Y           +   +H+         +   R  
Sbjct: 245 TTMDPLPVSEVKDIMLGHVHALHEFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LT-VEAGASTATHHIIETAFNLM 318
              +EAG        +E  F+ +
Sbjct: 300 FNALEAG--DLQLEALEGYFDNV 320


>gi|15594570|ref|NP_212359.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi B31]
 gi|218249426|ref|YP_002374748.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi ZS7]
 gi|226321543|ref|ZP_03797069.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi Bol26]
 gi|2688130|gb|AAC66623.1| conserved hypothetical protein [Borrelia burgdorferi B31]
 gi|218164614|gb|ACK74675.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi ZS7]
 gi|226232732|gb|EEH31485.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi Bol26]
 gi|312149107|gb|ADQ29178.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi N40]
          Length = 335

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMGNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYKLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|225550111|ref|ZP_03771071.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 118a]
 gi|225369223|gb|EEG98676.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 118a]
          Length = 333

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 69

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 129

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 250 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAIETLPEKI 328


>gi|221217675|ref|ZP_03589143.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 72a]
 gi|223888837|ref|ZP_03623428.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 64b]
 gi|224532647|ref|ZP_03673268.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi WI91-23]
 gi|221192352|gb|EEE18571.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 72a]
 gi|223885653|gb|EEF56752.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 64b]
 gi|224512427|gb|EEF82807.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi WI91-23]
          Length = 335

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|270263300|ref|ZP_06191570.1| tRNA-dihydrouridine synthase B [Serratia odorifera 4Rx13]
 gi|270042988|gb|EFA16082.1| tRNA-dihydrouridine synthase B [Serratia odorifera 4Rx13]
          Length = 321

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 17  MAGITDRPFRTLCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAARINVAGGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILHAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLGEVKRLLIGHIRELHGFY-----GQGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|253998095|ref|YP_003050158.1| TIM-barrel protein, nifR3 family [Methylovorus sp. SIP3-4]
 gi|253984774|gb|ACT49631.1| TIM-barrel protein, nifR3 family [Methylovorus sp. SIP3-4]
          Length = 350

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 126/302 (41%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L  +EM+ ++++L G  K +       + +P+++QI GAD
Sbjct: 24  MAGVTDRPFRMLCKKL-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVEPISVQIAGAD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 83  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVSQILKAVVAAVDVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  GV  + +H R         +      + +YD 
Sbjct: 143 VTLKIRTGWDKNNRNAVA--VARMAEDIGVQALAMHGRT--------RACLYNGDAEYDT 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A  +L     D VMIGRAA     +   +  +    
Sbjct: 193 IAAVKQAI-KIPLIANGDITTPEKAKFVLEYTQADAVMIGRAAQGRPWIFREIAHFLETG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  + + +     +      Y          ++   +H+     G  +S   RH 
Sbjct: 252 EHLPPPEVSEIHQVMLDHVQDLYDFY-----GELTGMRVARKHISWYTKGLKDSANFRHH 306

Query: 297 LT 298
           + 
Sbjct: 307 MN 308


>gi|332978428|gb|EGK15144.1| tRNA-dihydrouridine synthase B [Psychrobacter sp. 1501(2011)]
          Length = 346

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 142/320 (44%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EM+ ADA L   KK++    F  +  P++ QI GAD
Sbjct: 36  MAGVTDNPFRRLCKSF-GAGHAVSEMMTADATLYAHKKSLFRANFDGEIAPISAQIAGAD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + KL EAA+   + G   I++N+GCP+ +V     G+ L+ + D+V   + A   A+  P
Sbjct: 95  VDKLAEAAQYQVNNGAQIIDINMGCPAKKVCRKLAGSALLKDEDLVARLLDATVAAVDAP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G ++      +  + K  +++G+  I IH R         ++++   N  YD+
Sbjct: 155 VTLKTRLGYENGQ--ENILRVAKRAEEAGIAAIAIHGRT--------REDKYGGNARYDL 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+   ++ +  NG ++   +++++      D +MIGRAA     +   +  Y    
Sbjct: 205 IREVKQ-LVNIPVIANGDIDSPQKSIEVYNQTGCDAIMIGRAAQGQPWLFRDIAHYLQTG 263

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP   ++ +     +      Y           +   +H+     G  +S   R  
Sbjct: 264 EVLPSPNIEQLKEIVLTHLEELYDFY-----GEYSGCRIARKHIAWYTSGIEDSNAFRQA 318

Query: 297 LTVEAGASTATHHIIETAFN 316
           +  E   S   + +++T  +
Sbjct: 319 MYGEETTSG-QYKVVDTFLS 337


>gi|322381161|ref|ZP_08055164.1| tRNA-dihydrouridine synthase B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154737|gb|EFX47008.1| tRNA-dihydrouridine synthase B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 326

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 142/319 (44%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+ + +  L    +EKPL+LQI G D
Sbjct: 6   MAGVCNPAFRLIAKEF-GCGLVCAEMVSDKAIVHGNSRTMEMLYVDEREKPLSLQIFGGD 64

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+ +   + I++N+GCP  +V +   GA  +L+P  + + ++A+ + +S 
Sbjct: 65  KETLVAAAKYVDLNTNADIIDINMGCPVPKVTKCDAGARWLLDPQKIEEMVSAVVEVVSK 124

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D +          ++++++G + + +H R         ++       ++D
Sbjct: 125 PVTVKMRMGWDSEHIYAVRN--AQAVERAGGSAVSLHGRT--------REQLYTGTANWD 174

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+    + +  NG +     A ++L     DGVMIGR A  N  ML     Y + 
Sbjct: 175 IIREVKQSI-SIPLIGNGDVVTPEDAKRMLEETGCDGVMIGRGALGNPWMLYRTVHYLTE 233

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     I+    D   +       ++++ +H+     G   S R + 
Sbjct: 234 GELLPEPGVREKMR-----IAILHMDRLVKLKGEKVAVKEMRKHLAWYLKGLKGSARVKD 288

Query: 296 ILTVEAGASTATHHIIETA 314
            +  +         + + A
Sbjct: 289 QVMEKTTRDEMVRILTDFA 307


>gi|262373055|ref|ZP_06066334.1| tRNA-dihydrouridine synthase B [Acinetobacter junii SH205]
 gi|262313080|gb|EEY94165.1| tRNA-dihydrouridine synthase B [Acinetobacter junii SH205]
          Length = 341

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 145/326 (44%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  + +G+  + +H R         +++  +    Y++
Sbjct: 136 VTLKTRLGFLNGE--ENILRVAKRAEDAGIAALALHGRT--------REDMYLNTARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+KK N  + +  NG ++   +A  +L     D VMIGRAA     +   +  Y    
Sbjct: 186 IREVKK-NIHIPLIANGDIDSPEKAKYVLDYTGADAVMIGRAAQGRPWIFREIAHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     ++     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPEIVEVKQVLMGHLAELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +  VE  A  A   ++E+ F+ +++ 
Sbjct: 300 MYKVENTADQAK--VVESYFDQLLDQ 323


>gi|160897010|ref|YP_001562592.1| NifR3 family TIM-barrel protein [Delftia acidovorans SPH-1]
 gi|160362594|gb|ABX34207.1| TIM-barrel protein, nifR3 family [Delftia acidovorans SPH-1]
          Length = 356

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 65/306 (21%), Positives = 119/306 (38%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 22  MAGVTDRPFRQLCKAL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+   D G   I++N+GCP+ +V     G+ LM N  +  +   A+ +A    
Sbjct: 81  AEMMAEAARYNLDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAQAVVEACAPH 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G  D      +  L +  ++ G+  + +H R         ++       +
Sbjct: 141 GVPVTLKMRTGWCDAHRNAVV--LARRFEEVGIQMLTVHGRT--------REQGYKGFAE 190

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   +  + 
Sbjct: 191 YDTIAAVK-AAVRVPVVANGDITSPEKARDVLAYTGADAVMIGRAAQGRPWIFREIAHFM 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   + +     +    + Y       G  ++   +H+       P     
Sbjct: 250 ATGEHMAPPLVAELRRLLLDHLQDHYSLY-----GEGTGVRSARKHIAWYLRSLPGGEAF 304

Query: 294 RHILTV 299
           R  +  
Sbjct: 305 RQHINT 310


>gi|163786900|ref|ZP_02181348.1| probable TIM-barrel protein, NifR3 family [Flavobacteriales
           bacterium ALC-1]
 gi|159878760|gb|EDP72816.1| probable TIM-barrel protein, NifR3 family [Flavobacteriales
           bacterium ALC-1]
          Length = 331

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 139/325 (42%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE + ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFVSSEGLIRNAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++   IVE    + I++N GCP  +V     GA ++ +  ++    A M K  ++P
Sbjct: 78  MESMLQTIDIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDICLMEKLTAEMVKRTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G   I IH R         +      + D+  
Sbjct: 138 VTVKTRLGWD--HDSIKIVEVAERLQDVGCKSIAIHGRT--------RAQMYKGDADWKP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG +    +A ++     +DG MIGRA   N      V  YF  
Sbjct: 188 IAEVKNNPRMHIPVFGNGDINTPERAAEMRDSYGLDGAMIGRATIGNPWFFKQVKHYFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +PI      +  R+      D+    L     + ++ RH    F G P+ +  R 
Sbjct: 248 GEHL-APISLAERVEAARRHLQMSIDWKGEVLG----VFEMRRHYTNYFKGIPHFKEYRM 302

Query: 296 ILTVEAGAST---ATHHIIETAFNL 317
            +     +     A   ++E   + 
Sbjct: 303 KMVTSDDSKDVFAAFDEVLEKFSDH 327


>gi|138893752|ref|YP_001124205.1| nitrogen regulation transcriptional regulator [Geobacillus
           thermodenitrificans NG80-2]
 gi|134265265|gb|ABO65460.1| Transcriptional regulator involved in nitrogen regulation,
           NifR3/Smm1 family [Geobacillus thermodenitrificans
           NG80-2]
          Length = 333

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 75/326 (23%), Positives = 142/326 (43%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  ++K   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  +V     GA  +L+P+ + D +A++  A+  
Sbjct: 77  KETLVKAAKFVDKNTNADIIDINMGCPVPKVTNCDAGAKWLLDPNKIYDVVASIVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+           ++++++G   + +H R  +               D++
Sbjct: 137 PVTVKMRIGWDEHHIYAV--ENAQAVERAGGKAVAVHGRTRV--------QMYEGKADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 187 IIKQVK-EAVNIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  T         +     D           ++++ +H      G   + + R+
Sbjct: 246 GELIPEPTPTEKI-----DVCLLHLDRLIALKGEYIAVKEMRKHAAWYLKGIRGAAKIRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +            +++ A +   ++
Sbjct: 301 AINECETRDELAALLLKVAQDAENQA 326


>gi|146295635|ref|YP_001179406.1| nifR3 family TIM-barrel protein [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409211|gb|ABP66215.1| tRNA-U20-dihydrouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 328

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 138/327 (42%), Gaps = 27/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEM+ A AI  G +K   ++ FS  EK   +QI G+D
Sbjct: 13  MAGFTDKVFRSLCSRF-GADVTVTEMVSAKAITMGSQKTKELISFSEDEKIKGVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EA KI++D F Y+ I++N+GCP  +V +   G+ LM NP +    +  + K    
Sbjct: 72  PHVMAEAVKIIQDEFEYDFIDINMGCPVPKVVKSGEGSALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++   +        +++SG + I +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEE--NINAPEFACIMQESGASFITVHGRT--------RTQMYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K++   + +  NG + D   A K       D +MIGRAA  N  +   + E F N
Sbjct: 182 IIKMVKEKV-KIPVVANGDIVDFESAKKAYEITEADSIMIGRAALGNPWVFLQIKEGFEN 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  + TRV      K++                + +  +H+     G  N+ + R 
Sbjct: 241 GQ-----VTTRVLPHEKVKVAIEFFRQLCTEKSEKMAVLEARKHLSFFIKGIENAAKIRD 295

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +            I+ +    +   L
Sbjct: 296 KIN-----RIDNAEILISYLEQLKAEL 317


>gi|84393068|ref|ZP_00991834.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
 gi|84376320|gb|EAP93202.1| NifR3/Smm1 family protein [Vibrio splendidus 12B01]
          Length = 322

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 126/323 (39%), Gaps = 24/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  +    K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKVWKTSKSQQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   D G   I++N+GCP+ +V++   G+ L+ +P+++ D + A+  A+ +P
Sbjct: 76  PQLMAEAAQFNVDNGAQIIDINMGCPAKKVNKKLAGSALLQHPELIEDILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         +        +Y  
Sbjct: 136 VTLKTRTGWD--TDNRNCVQIAKIAEDCGIQALALHGRT--------RACMYKGEAEYKH 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAAKQAV-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFNEILHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMDPLPISEVKDIMLGHVNALHEFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LTV-EAGASTATHHIIETAFNLM 318
               EAG        +E  F+ +
Sbjct: 300 FNAFEAG--DLQLEALEGFFDNV 320


>gi|225181735|ref|ZP_03735174.1| TIM-barrel protein, nifR3 family [Dethiobacter alkaliphilus AHT 1]
 gi|225167606|gb|EEG76418.1| TIM-barrel protein, nifR3 family [Dethiobacter alkaliphilus AHT 1]
          Length = 319

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 129/316 (40%), Gaps = 22/316 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              TD  +R  AR +   AL++TEMI A   +   ++ +    F+ QE+P+ +Q+ G+D 
Sbjct: 18  AGVTDSSFRILAREM-GCALVFTEMISAKGAVCAPEQTLKIARFTAQERPIGIQLFGSDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
                A ++      + +++N+GCP  +V     G  LM +PD       A+C A ++PV
Sbjct: 77  EIFARATELCNGQAPDLLDINMGCPVKKVAGKGEGCALMRDPDKAYAITKAVCDAATMPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD    V    +  +++++G   + +H R         +        D+ ++
Sbjct: 137 TVKMRKGWDD--SEVNAVEVALAVQEAGAAAVTVHGRT--------RAQGYSGRADWSVI 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG + +   A ++L     D VM+ R    N  ++     Y     
Sbjct: 187 ARVK-EALRVPVVGNGDIWEPQDAQRMLQQTGCDAVMLARGVLGNLWLIRRTVHYLETGE 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +   R +                 ++++ +HM     G   + + R+ +
Sbjct: 246 LLPEPEMAERVRLACRHLK-----MVVDEKGEYMGVREMRKHMAWYLKGMRGAAQVRNEI 300

Query: 298 TVEAGASTATHHIIET 313
            + A        I+E 
Sbjct: 301 -MRAKTKEEMTAILEN 315


>gi|86144145|ref|ZP_01062482.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Leeuwenhoekiella blandensis MED217]
 gi|85829407|gb|EAQ47872.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Leeuwenhoekiella blandensis MED217]
          Length = 334

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 145/325 (44%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLQSVEIVEASKPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +      N D+  
Sbjct: 138 ITVKTRLGWD--HDSIKIVEVAERLQDVGCKAIAIHGRT--------RAQMYKGNADWKP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + +  NG ++   +A+++     +DG MIGRA+         V  +F+ 
Sbjct: 188 IAEVKNNQRMHIPVFGNGDVDTPERAVEMRDQYGLDGAMIGRASIGYPWFFREVKHFFNT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P       D  R+      D+    L     + +  RH    F G P  +  R 
Sbjct: 248 GEHMAPPTMQERV-DAARRHLQMSIDWKGEKLG----VFETRRHYTNYFKGIPGFKPYRM 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +      S A   +   AF+ + E
Sbjct: 303 KMVT----SDAPEDVF-AAFDEVEE 322


>gi|225551987|ref|ZP_03772927.1| tRNA-dihydrouridine synthase A [Borrelia sp. SV1]
 gi|225370985|gb|EEH00415.1| tRNA-dihydrouridine synthase A [Borrelia sp. SV1]
          Length = 335

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M++ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MINITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    IHAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIIHARIAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+++  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIEINGGIKNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAIETLPEKI 330


>gi|282897396|ref|ZP_06305398.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Raphidiopsis
           brookii D9]
 gi|281198048|gb|EFA72942.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Raphidiopsis
           brookii D9]
          Length = 339

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 131/319 (41%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        I+     E+P+++Q+       
Sbjct: 32  GVTDLVFRRLVRRYAPDSMMYTEMVNATGLHYVKQLPKIMEVDPNERPISIQLFDCRPDF 91

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L EAA      G + +++N+GCP  ++ +   G+ L+  P++    +  +  A+++PVTV
Sbjct: 92  LAEAAVKAVAEGADTVDINMGCPVNKITKNGGGSSLLRQPEVAEAIVREVVNAINVPVTV 151

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  D+   + + +  K ++ +G   I +H R         +      N  ++ + +
Sbjct: 152 KTRIGWSDKE--ITILDFAKRMEDAGAKMITVHGRT--------RAQGYNGNARWEWIAK 201

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K+    + +  NG +  ++ A+K L     DGVM  R       ++  VD +       
Sbjct: 202 VKQ-ILSIPVIANGDIFSVAAAVKCLEETGADGVMCSRGTLGYPFLVGEVDHFLKTGELL 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            SP  T+  +     +      YA         ++Q  +H+      F  +   R  L+ 
Sbjct: 261 PSPTPTQRLECAREHL------YALWEYKGDRGVRQARKHLTWYAKDFMGAADLRGKLST 314

Query: 300 EAGASTATHHIIETAFNLM 318
                     +I  A   +
Sbjct: 315 IESVQQ-GLDLINQATERL 332


>gi|83311464|ref|YP_421728.1| NifR3-like protein [Magnetospirillum magneticum AMB-1]
 gi|82946305|dbj|BAE51169.1| NifR3-like protein [Magnetospirillum magneticum AMB-1]
          Length = 305

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 141/317 (44%), Gaps = 22/317 (6%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAK 67
           R   + L    L+ +EMI + A++R +++ +     + +E P+++Q+ G +   + EAAK
Sbjct: 4   RRLVKRL-GAGLVVSEMIASQAMIRQNRQTMQMAQHTAEEFPMSVQLAGCEPKVMAEAAK 62

Query: 68  IVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + +D G   I++N+GCP  +V  +G  G+ LM N ++    + A+ KA+ IPVT+K R G
Sbjct: 63  LNQDLGAAIIDINMGCPVKKVALKGEAGSALMRNENLAARILTAVVKAVDIPVTLKMRTG 122

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            D         +L +  ++ G+  + +H R         ++       D+  + E+K+  
Sbjct: 123 WDMNSRNA--PSLARVAEECGIRMVTVHGRT--------RNQMYTGQADWAFIGEVKRAV 172

Query: 187 PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             + +  NG +E +  A+++L     DGVMIGR  Y    +   V  Y +       P +
Sbjct: 173 -SIPVIGNGDVESIDDAVRMLELSGADGVMIGRGTYGRPWLPGQVAHYLATGERLPDPSR 231

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAS 304
               +     + A ++ Y +        ++   +HM     G P S   R  +       
Sbjct: 232 AEQLQIMLEHLDAMLSHYGSE-----PGVRIARKHMAWYSKGLPGSAEFRAEVNRTNDPD 286

Query: 305 TATHHIIETAFNLMIES 321
                I E    L+ ++
Sbjct: 287 QLRLAITEFYAPLLEKA 303


>gi|126664725|ref|ZP_01735709.1| hypothetical protein MELB17_02765 [Marinobacter sp. ELB17]
 gi|126631051|gb|EBA01665.1| hypothetical protein MELB17_02765 [Marinobacter sp. ELB17]
          Length = 332

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 125/289 (43%), Gaps = 21/289 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R +    L  +EM++AD+ +   +K+   L    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRM-GAGLAVSEMVIADSKMWHTRKSRSRLNHQGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +    G   I++N+GCP+ +V   + G+ LM +  +V   + A+  A+ IP
Sbjct: 80  PEMLAQAACMNAASGAQIIDINMGCPAKKVCNKAAGSALMKDEALVLQILKAVVAAVDIP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+      +  + +  +++G+  + IH R    K           N +YD 
Sbjct: 140 VTLKMRTGWDENHRNAPI--IARMAEEAGIQALAIHGRTRTDK--------YTGNAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +    +A ++L     DG++IGRAA     +   +  +    
Sbjct: 190 IARVKSDVG-IPVFANGDITSPEKAREVLQYTGADGLLIGRAAQGQPWIFREILHFLETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
                P    V+      + A    Y          ++   +H+     
Sbjct: 249 EHMKPPPLDEVETILSEHLLALHDFYGETM-----GVRIARKHVGWYLQ 292


>gi|297616351|ref|YP_003701510.1| hypothetical protein Slip_0145 [Syntrophothermus lipocalidus DSM
           12680]
 gi|297144188|gb|ADI00945.1| TIM-barrel protein, nifR3 family [Syntrophothermus lipocalidus DSM
           12680]
          Length = 329

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 144/321 (44%), Gaps = 28/321 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD+ +R   +      L+ TEMI A A++ G +K +  L  S +E P+A+Q+ G+D
Sbjct: 18  MAGFTDKAFRIILKN-HGAGLVATEMISAQALVYGQEKTMFMLDLSGEEPPVAVQLFGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+I  D G + I++N+GCP+ R+ +   GA LM +P+     + A+ KA+S+P
Sbjct: 77  PRIIAQAARIAADRGAHIIDINMGCPTPRIVKNGEGAALMRDPNRAVRIVEAVVKAVSVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+   ++    +    +++G + + +H R         ++       D+ +
Sbjct: 137 VTVKMRSGWDE--NSINCCQIAVLAEEAGAHAVTVHPRT--------REQLFSGKADWSL 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A ++L     D VMIGR    N  +     +Y    
Sbjct: 187 IRAVKQ-VVKIPVIGNGDVTSPQKARQMLEETGCDAVMIGRGCLGNPFIFRRTLQYLETG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
                P          + +       A R       + ++ +H+     G P++   R  
Sbjct: 246 EIPPEPTAEERINVARQHLVL-----ACRFKGETKAVLEMRKHLGWYIKGLPHATAVRAR 300

Query: 295 ----HILTV-EAGASTATHHI 310
                 L+  EA     +H +
Sbjct: 301 MNQARTLSEIEAILEGLSHRL 321


>gi|110636783|ref|YP_676990.1| NifR3 family TIM-barrel protein [Cytophaga hutchinsonii ATCC 33406]
 gi|110279464|gb|ABG57650.1| tRNA-U20-dihydrouridine synthase [Cytophaga hutchinsonii ATCC
           33406]
          Length = 329

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 142/325 (43%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I A+ ++R   K++  L     E+P+ +QI G  
Sbjct: 19  MEDVSDPPFRALCKQ-QGADMMYTEFIAAEGLIRDAAKSVHKLDIFDYERPMGIQIFGDK 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + +AA I E+ G   +++N GCP  +V     G+  +L+   +      + K  ++P
Sbjct: 78  IDVMCDAAAIAEEAGPELVDINFGCPVKKVACKGAGSGALLDIPKMVKMTEEIVKRCTLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ + ++ + ++  G+  + IH R         +        D+  
Sbjct: 138 VTVKTRLGWD--HDSIHIVDIARRLQDVGIKALTIHGRT--------RQQMYKGEADWSW 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K +++  + I  NG ++   +AL+      VDG+MIGRAA     +   V  +F+ 
Sbjct: 188 IAKVKEQQDIHIPIFGNGDIDSPEKALEYKNRYGVDGIMIGRAAIGYPWIFKEVKHFFAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++      ++         + ++  H    F G  N +  R 
Sbjct: 248 GEKLGPPTIRERV-----EVCKKHLAFSVEWKGPKEGIFEMRMHYTNYFRGIQNFKPYRQ 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L VEAG+   T  I++     + E
Sbjct: 303 RL-VEAGSYEDTFAILDEVAEQLSE 326


>gi|84999912|ref|XP_954677.1| hypothetical protein [Theileria annulata]
 gi|65305672|emb|CAI73997.1| hypothetical protein, conserved [Theileria annulata]
          Length = 408

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 112/317 (35%), Positives = 173/317 (54%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D T   +R F RLLT    L+TEM VA +++   ++++   L F   E P+  Q+GG 
Sbjct: 91  MLDVTYLQFRQFMRLLTRKTQLWTEMFVASSLINASEESVSRWLKFEENEHPIVAQLGGN 150

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALS 116
               LVEA +I++ FGY+EINLNVGCPS RV     FGA LM   ++V D +  M K L 
Sbjct: 151 CPETLVEAGRILKKFGYDEINLNVGCPSPRVSGKGCFGASLMREKELVRDIVHNMIKELE 210

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R+GVD+      +++ V ++ +SG     IH+RKA LKG++PK NR +P L Y
Sbjct: 211 IPVTVKTRLGVDESDSYEFVKDFVSTVSQSGCEHFIIHSRKAWLKGINPKKNRTVPPLQY 270

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVD---------GVMIGRAAYKNSAM 225
           + V+ ++++ P L   +NGG + M   L  L   +VD         GVMIGR AY+N  +
Sbjct: 271 EKVFRLQRDFPHLKFTINGGFKTMESILDALNSENVDTDNNPHKLNGVMIGRLAYENPCI 330

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKD--FWRKIS--ASMTDYAARHLHSGGKLQQ--ITRH 279
           L+ VD+         +    R+  +  + + I+   +  +Y   ++     +    I + 
Sbjct: 331 LSNVDKIIYGVENPDTCYTRRILLEVFYLKFIANFQNYANYIDENVEETANMNISLIVKP 390

Query: 280 MIGLFHGFPNSRRCRHI 296
           ++G+FHG   ++  R  
Sbjct: 391 ILGVFHGEQGNKIFRRK 407


>gi|312794505|ref|YP_004027428.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181645|gb|ADQ41815.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 328

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 135/303 (44%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEM+ + A++ G  K   ++ FS +EK   +QI G+D
Sbjct: 13  MAGFTDKVFRRLCSKF-GADVTVTEMVSSKALVLGSAKTKELISFSEEEKIRGIQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++ +   G  LM NP +    +  + K    
Sbjct: 72  PEVMAQSVKILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++   +        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEED--INAPEFAYILQESGASFVTVHGRT--------RAQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K++   + +  NG + D   A +       DG+MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVKEKV-KIPVVANGDITDFESAKRAYEVTRADGIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T+V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETKVLPHMKIRVAIEFFSQLCSEKGEKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 KIN 298


>gi|134047751|sp|Q9ZED2|DUS_RICPR RecName: Full=Probable tRNA-dihydrouridine synthase
          Length = 327

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 133/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++              +Q+ G 
Sbjct: 18  MSDVTDLEFRKLVKRF-GAGLVVSEMIASRAMIMKSRQSMQKCAIMHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPDVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDEQLAAKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD         L K    SGV  + +H R         +      N ++D
Sbjct: 137 PVTVKMRIGWDDNTRNA--PTLAKIAANSGVQMVTVHGRT--------RCQFYSGNANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L     DG+M+GR  Y    +++ +  Y   
Sbjct: 187 FIRTVK-EAVKIPVIANGDITNFAKAKEALQRSGADGIMVGRGVYGKPWLISQIAYYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P          +   A +  Y          +    +H+I   +G P+S   R 
Sbjct: 246 GKEKPAPSIAEQLDIITKHYDAIIDYY-----GKSVGVPIARKHIIWYSNGLPSSAEFRC 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            + +          I E   ++M
Sbjct: 301 TVNLMKDPIAVKEKIAEFYMSVM 323


>gi|225075968|ref|ZP_03719167.1| hypothetical protein NEIFLAOT_00993 [Neisseria flavescens
           NRL30031/H210]
 gi|224952683|gb|EEG33892.1| hypothetical protein NEIFLAOT_00993 [Neisseria flavescens
           NRL30031/H210]
          Length = 334

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 138/325 (42%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPSLRHTKKTLRRSDFEGEGGVVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +VG+ + A+  A+ +P
Sbjct: 76  PQQMAEAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVGEILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D+     L  + K  ++SG+  + IH R         +         Y++
Sbjct: 136 VTLKTRLGWHDEHQN--LPTIAKIAEESGIAALAIHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A     +   +  Y  + 
Sbjct: 186 IAETKGRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWLFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +   T  +      I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLTEYNATILNHIRAMHEFY-----GEVAGIRIARKHIGWYIDEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++TA +  +      + E 
Sbjct: 300 INCL-DSATAQYDTLAAYLETLSEK 323


>gi|325286202|ref|YP_004261992.1| TIM-barrel protein, nifR3 family [Cellulophaga lytica DSM 7489]
 gi|324321656|gb|ADY29121.1| TIM-barrel protein, nifR3 family [Cellulophaga lytica DSM 7489]
          Length = 330

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 141/326 (43%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LDSMLRSVEIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVKLTDAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G   I IH R  +             N D+  
Sbjct: 138 VTVKTRLGWD--TDSIKIVEVAERLQDVGCAAIAIHGRTRV--------QMYKGNADWKP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K  +   + +  NG ++    A+K+     +DG MIGRA+         V  +   
Sbjct: 188 IAQVKNNQRMHIPVFGNGDVDSPEAAVKMRDEYGLDGAMIGRASIGYPWFFNEVKHFIKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +   R +       A         + +  RH    F G P+ ++ R 
Sbjct: 248 GEHKAPPTMQERVEAARRHL-----QMAIDWKGEKLGVFETRRHYTNYFKGIPDFKQYRM 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +      S  +  +   AF+ +++ 
Sbjct: 303 KMVT----SDDSVDVF-AAFDEVLDK 323


>gi|15603891|ref|NP_220406.1| NIFR3-like protein (nifR3) [Rickettsia prowazekii str. Madrid E]
 gi|3860582|emb|CAA14483.1| NIFR3-LIKE PROTEIN (nifR3) [Rickettsia prowazekii]
 gi|292571607|gb|ADE29522.1| Putative dihydrouridine synthase Dus [Rickettsia prowazekii Rp22]
          Length = 341

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 133/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGGA 57
           M D TD  +R   +      L+ +EMI + A++   ++++              +Q+ G 
Sbjct: 32  MSDVTDLEFRKLVKRF-GAGLVVSEMIASRAMIMKSRQSMQKCAIMHDDPTSACVQLAGC 90

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 91  EPDVIAEAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDEQLAAKIFEATVKAVKI 150

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD         L K    SGV  + +H R         +      N ++D
Sbjct: 151 PVTVKMRIGWDDNTRNA--PTLAKIAANSGVQMVTVHGRT--------RCQFYSGNANWD 200

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG + + ++A + L     DG+M+GR  Y    +++ +  Y   
Sbjct: 201 FIRTVK-EAVKIPVIANGDITNFAKAKEALQRSGADGIMVGRGVYGKPWLISQIAYYLKT 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P          +   A +  Y          +    +H+I   +G P+S   R 
Sbjct: 260 GKEKPAPSIAEQLDIITKHYDAIIDYY-----GKSVGVPIARKHIIWYSNGLPSSAEFRC 314

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            + +          I E   ++M
Sbjct: 315 TVNLMKDPIAVKEKIAEFYMSVM 337


>gi|103486763|ref|YP_616324.1| dihydrouridine synthase TIM-barrel protein nifR3 [Sphingopyxis
           alaskensis RB2256]
 gi|98976840|gb|ABF52991.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sphingopyxis
           alaskensis RB2256]
          Length = 332

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 124/302 (41%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI + A +R  +++I    +   E+P+++Q+ G  
Sbjct: 23  MTGVTDLPFRKLVR-YYGSGLNVTEMIASQAAIRETRQSIQKAAWDPVEEPVSMQLVGCT 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAAK+ ED G   I++N+GCP  +V  G  G+ LM +  +    I A  KA+S+P
Sbjct: 82  PYEMGEAAKLNEDRGAAIIDINMGCPVRKVTNGDAGSALMRDLRLAAALIDACVKAVSVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G      ++    L    +  G   + +H R         ++       D+  
Sbjct: 142 VTVKMRMGWC--HDSLNAPELAHIAEDLGAKLVTVHGRT--------RNQMYRGEADWGF 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K E   + + +NG +     A   L     DGVMIGR AY    +L  V       
Sbjct: 192 VRKVK-EAVSIPVIVNGDICSADDARTALAQSGADGVMIGRGAYGRPWLLGQVMAALRGE 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P              A +  Y          +    +H+     G P S   R+ 
Sbjct: 251 GERPDPGLDEQYDVITSHYRAMIDHY-----GETTGVNMARKHLGWYVKGLPGSAEFRNK 305

Query: 297 LT 298
           + 
Sbjct: 306 VN 307


>gi|319778453|ref|YP_004129366.1| tRNA dihydrouridine synthase B [Taylorella equigenitalis MCE9]
 gi|317108477|gb|ADU91223.1| tRNA dihydrouridine synthase B [Taylorella equigenitalis MCE9]
          Length = 326

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 75/329 (22%), Positives = 134/329 (40%), Gaps = 27/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM  ++  L    K    L    + +P+A+Q+ GAD
Sbjct: 17  MAGVTDRPFRKLCRKL-GAGYAVSEMAASNPQLWDSIKTARRLDHKGEVEPIAVQLLGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + +AA      G   I++N+GCP+ +V   + G+ LM +   V   + ++ K     
Sbjct: 76  PDMMAQAALFNISKGARIIDINLGCPAKKVCNVACGSALMRDLGKVESILKSVIKICNPY 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        +    +  GV+ I IH R         + +      +
Sbjct: 136 DVPVTLKTRTGWDREHKNA--LEIAMLAESLGVSAITIHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  +K EN  + +  NG ++   +A  +L     DG+MIGRAA  N  +   ++ Y 
Sbjct: 186 YETIKTVK-ENIAIPVIANGDIDSPQKAKYVLDYTGADGLMIGRAAQGNPWIFKEINHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            N      P  + +       +      Y          ++   +H+      FP ++  
Sbjct: 245 KNNKIFPQPTFSEMQTVILEHLEEHYEFY-----GEVSGVKTARKHLSWYLAPFPQAQDF 299

Query: 294 -RHILTVEAGASTATHHIIETAFNLMIES 321
            + +L +E   S   +  ++  FN  I  
Sbjct: 300 VKSLLLIETTKSQ--YRAVDQWFNQQINK 326


>gi|298207228|ref|YP_003715407.1| putative TIM-barrel enzyme, possible dehydrogenase [Croceibacter
           atlanticus HTCC2559]
 gi|83849864|gb|EAP87732.1| putative TIM-barrel enzyme, possible dehydrogenase [Croceibacter
           atlanticus HTCC2559]
          Length = 330

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 135/299 (45%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE  G + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LESMLKSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D++  ++ +  + + ++  G   I IH R         +      +  ++ 
Sbjct: 138 VTVKTRLGWDEE--SIKIVEVAERLQDVGCAAIAIHGRT--------RKQMYKGDAKWEQ 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + +  NG +    +A+++     +DG MIGRA+         V  +F  
Sbjct: 188 IADVKNNPRMHIPVFGNGDVNTPERAVEMRDKYGLDGAMIGRASIGYPWFFREVKHFFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P       D  R+      D+    L     + +  RH    F G P+ +  R
Sbjct: 248 GKHLPPPNMIE-RLDAARRHLQMSIDWKGEKLG----VFETRRHYTNYFKGIPHFKEYR 301


>gi|22124133|ref|NP_667556.1| tRNA-dihydrouridine synthase B [Yersinia pestis KIM 10]
 gi|45443621|ref|NP_995160.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Microtus
           str. 91001]
 gi|162420960|ref|YP_001605752.1| tRNA-dihydrouridine synthase B [Yersinia pestis Angola]
 gi|167401994|ref|ZP_02307477.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|21956887|gb|AAM83807.1|AE013621_7 putative dehydrogenase [Yersinia pestis KIM 10]
 gi|45438491|gb|AAS64037.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Yersinia pestis biovar Microtus str. 91001]
 gi|162353775|gb|ABX87723.1| dihydrouridine synthase [Yersinia pestis Angola]
 gi|167048580|gb|EDR59988.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
          Length = 355

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 51  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 110 PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 169

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 170 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 219

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 220 IRAVKQ-TVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 278

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 279 ELLPPMPLGEVQRLLDGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 333

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 334 FNAIEDASE-QLEALEAYFENL 354


>gi|116309197|emb|CAH66291.1| OSIGBa0113C11.1 [Oryza sativa Indica Group]
          Length = 368

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 115/328 (35%), Positives = 175/328 (53%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 1   MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V     FGA LM +P+ VGD ++A+    ++
Sbjct: 61  LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 120

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V   + KS      IHARKA+L GLSP +NRK+P L Y
Sbjct: 121 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRKVPPLKY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD    
Sbjct: 181 EYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVDSEVY 240

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T  S  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P +   +
Sbjct: 241 GMPTRRS-SRRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEPGNGLWK 295

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                           +E   + +  S+
Sbjct: 296 RKADSTLRHCKTLESFLEETLDAIPNSV 323


>gi|311696116|gb|ADP98989.1| tRNA-dihydrouridine synthase B [marine bacterium HP15]
          Length = 332

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 69/298 (23%), Positives = 134/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM++AD+ L   +K    L    + +P ++QI G D
Sbjct: 21  MAGVTDRPFRLLCRRL-GAGLAVSEMVIADSKLWHTRKSQTRLNHEGEPEPRSVQIAGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   +FG   I++N+GCP+ +V   + G+ LM +  +V D + ++ +A+ +P
Sbjct: 80  PQMLADAARQNAEFGAQIIDINMGCPAKKVCNKAAGSALMKDEALVRDILESVVQAVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D       +  + +  + +G+  + IH R         + ++   N +YD 
Sbjct: 140 VTLKMRTGWDRDNRNALV--IARMAEDAGIQAVAIHGRT--------RADKYEGNAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +    +A  +L     DG++IGRAA  +  +   +  +    
Sbjct: 190 IADVKSRI-SIPVFANGDVTSPEKARDVLRHTGADGLLIGRAAQGSPWIFREIRHFLETG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              ++P    V++     + A    Y          ++   +H+          ++ R
Sbjct: 249 SHMAAPELDEVEEILTEHLQALHAFYGETM-----GVRIARKHVGWYLQSHDPGKQFR 301


>gi|312126436|ref|YP_003991310.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311776455|gb|ADQ05941.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 328

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 136/303 (44%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEM+ + A++ G  K   ++ FS +EK  ++QI G+D
Sbjct: 13  MAGFTDKVFRRLCSRF-GADVTVTEMVSSKALVLGSAKTKELISFSEEEKIRSVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + E+ KI++D F Y+ I++N+GCP  +V +   G+ LM NP +    +  + K    
Sbjct: 72  AKIMAESVKILQDEFEYDFIDINMGCPVPKVVKSGEGSALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G DD+   +        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDDE--NINAPEFAYILQESGASFVTVHGRT--------RAQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K++   + +  NG + D   A +       D +MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVKEKV-KIPVIANGDIVDFESAKRAYEVTRADSIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T+V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETKVLPHMKIRVAIEFFTQLCSEKGEKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 KIN 298


>gi|218710863|ref|YP_002418484.1| tRNA-dihydrouridine synthase B [Vibrio splendidus LGP32]
 gi|218323882|emb|CAV20243.1| tRNA-dihydrouridine synthase B [Vibrio splendidus LGP32]
          Length = 325

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 124/323 (38%), Gaps = 24/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  +    K+   +    +    ++QI GAD
Sbjct: 20  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKVWKTSKSQQRMVHEGESGIRSVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+     G   I++N+GCP+ +V++   G+ L+ +P+++ D + A+  A+ +P
Sbjct: 79  PQLMAEAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQHPELIEDILKAVVNAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         +        +Y  
Sbjct: 139 VTLKTRTGWD--TDNRNCVQIAKIAEDCGIQALALHGRT--------RACMYKGEAEYKH 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 189 IKAAKQAV-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFNEILHYLENG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       + A    Y           +   +H+         +   R  
Sbjct: 248 TTMDPLPISEVKDIMLGHVLALHEFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 302

Query: 297 LTV-EAGASTATHHIIETAFNLM 318
               EAG        +E  F+ +
Sbjct: 303 FNAFEAG--DLQLEALEGFFDNV 323


>gi|91228890|ref|ZP_01262792.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
 gi|91187555|gb|EAS73885.1| NifR3/Smm1 family protein [Vibrio alginolyticus 12G01]
          Length = 322

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P+I+ + + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCVQIAKLAENCGIQALALHGRT--------KACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMEELPTEEVKTIMLGHVNALHEFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 300 FNAIDAAP-LQIEALEGYFDNV 320


>gi|285019545|ref|YP_003377256.1| tRNA-dihydrouridine synthase b protein [Xanthomonas albilineans GPE
           PC73]
 gi|283474763|emb|CBA17262.1| probable trna-dihydrouridine synthase b protein [Xanthomonas
           albilineans]
          Length = 332

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 136/323 (42%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K++  +  + +  P+++QI G  
Sbjct: 17  MAGVTDKPFRLLCKRL-GAGLAVSEMTLSDPRFWQTRKSLQRMDHAGEPDPISVQIAGTQ 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L +AA+   D G   I++N+GCP+ +V     G+ LM +  +V   ++A+ KA  +P
Sbjct: 76  PQQLADAARYNADHGAQLIDINMGCPAKKVCNAWAGSALMRDEALVARILSAVVKASPVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +D       +Y  
Sbjct: 136 VTLKIRTGWDSDHRNG--PTIARIAEDCGIAALAVHGRT--------RDQHYSGQAEYAT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG ++   +A ++L     D VMIGRAA     +   +  Y ++ 
Sbjct: 186 IAQIK-AMLRIPVIANGDIDSPHKAAQVLAATGADAVMIGRAAQGRPWIFGEIAHYLAHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V       + A    Y          ++   +H+       P +   R +
Sbjct: 245 EVSPAPSLAFVRDTLLGHLHALYAFYGEAQ-----GVRIARKHLGWYAKDRPENAAFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
           +   A ++ A   +    F+ +I
Sbjct: 300 VN-RAESAQAQLALTADYFDALI 321


>gi|260581942|ref|ZP_05849738.1| tRNA-dihydrouridine synthase [Haemophilus influenzae NT127]
 gi|260095135|gb|EEW79027.1| tRNA-dihydrouridine synthase [Haemophilus influenzae NT127]
          Length = 353

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 139/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRA   N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRATLGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|195941421|ref|ZP_03086803.1| tRNA-dihydrouridine synthase A [Borrelia burgdorferi 80a]
          Length = 324

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 176/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 1   MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQNPLESPIAIQIATNSKN 60

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 61  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 120

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 121 SIKHRLGIRPLSSDYKNESYSEVKNFVKIISDFGIKNFIVHARIAILKGFSPKNNRNIPK 180

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI +NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 181 LRHEFVYNLKKENKNLFIEINGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 240

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 241 ---LNETDEILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGIVFSKEGAKKF 290

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 291 RQNLTAPFPKNLKKHEILLKAIETLPEKI 319


>gi|313200160|ref|YP_004038818.1| tim-barrel protein, nifr3 family [Methylovorus sp. MP688]
 gi|312439476|gb|ADQ83582.1| TIM-barrel protein, nifR3 family [Methylovorus sp. MP688]
          Length = 343

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 126/302 (41%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L    L  +EM+ ++++L G  K +       + +P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKKL-GAGLAVSEMVTSNSLLYGSAKTLRRANHEGEVEPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK   D G   I++N+GCP+ ++     G+ L+ +  +V   + A+  A+ +P
Sbjct: 76  PKMMAEAAKHNVDNGAQIIDINMGCPAKKICNVMAGSALLKDEPLVSQILKAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  GV  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWDKNNRNAVA--VARMAEDIGVQALAMHGRT--------RACLYNGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    +A  +L     D VMIGRAA     +   +  +    
Sbjct: 186 IAAVKQAI-KIPLIANGDITTPEKAKFVLEYTQADAVMIGRAAQGRPWIFREIAHFLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  + + +     +      Y          ++   +H+     G  +S   RH 
Sbjct: 245 EHLPPPEVSEIHQVMLDHVQDLYDFY-----GELTGMRVARKHISWYTKGLKDSANFRHH 299

Query: 297 LT 298
           + 
Sbjct: 300 MN 301


>gi|254506424|ref|ZP_05118566.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus 16]
 gi|219550598|gb|EED27581.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus 16]
          Length = 335

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 65/321 (20%), Positives = 124/321 (38%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI GAD
Sbjct: 32  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGAD 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A+  A+ +P
Sbjct: 91  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIEDILKAVVNAVDVP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +Y+ 
Sbjct: 151 VTLKTRTGWD--TDNKNCVQIAKLAEDCGIQALALHGRT--------KACMYKGEAEYNS 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  +  N 
Sbjct: 201 IKAVKQAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIQHFLENG 259

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 260 TTMPDLPLAEVKDILLGHVNALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 314

Query: 297 LTVEAGASTATHHIIETAFNL 317
                  +      +E  F+L
Sbjct: 315 FNA-IDVAELQLEALEGYFDL 334


>gi|51598486|ref|YP_072674.1| tRNA-dihydrouridine synthase A [Borrelia garinii PBi]
 gi|51573057|gb|AAU07082.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 333

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 111/329 (33%), Positives = 172/329 (52%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K ++  +  E P+A+QI      
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKVVKQTPLESPIAIQIATNCKF 69

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 129

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N +K I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRLLNSDYKNESYSEVKNFIKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                    I TR D      I   M +Y   +  +   +  + +H++G+      +R+ 
Sbjct: 250 LGETDK---IPTRKD------ILMKMVEYIKEY-ENYLSINILCKHLMGITFSKEGARKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAMETLPEKI 328


>gi|319897509|ref|YP_004135706.1| tRNA-dihydrouridine synthase b [Haemophilus influenzae F3031]
 gi|317433015|emb|CBY81386.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae F3031]
          Length = 326

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 139/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAINVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++  +  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCSIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|51894293|ref|YP_076984.1| putative transcriptional regulator [Symbiobacterium thermophilum
           IAM 14863]
 gi|51857982|dbj|BAD42140.1| putative transcriptional regulator [Symbiobacterium thermophilum
           IAM 14863]
          Length = 345

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 135/324 (41%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+ TE +   A+L   K+   ++     E+P  +Q+ GAD
Sbjct: 28  MAGVTNWPFRRLCKE-HGCGLVVTEFVSDKALLYDSKRTREMIRLLPDERPAGVQLFGAD 86

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
              +  AA  V +    + I++N+GCP+ +V +G  G+ L+  P++  + +  + +A+  
Sbjct: 87  PDTMARAAARVVELEQPDLIDINMGCPAPKVTKGRGGSSLLKEPELAQEIVRRVVQAVAP 146

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D +  ++    + K ++++G   I +H R         K+       D+
Sbjct: 147 TPVTVKMRIGWDSR--SINAVEVAKRVEEAGARMITVHGRT--------KEQHYSGRADW 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++  + +    + +  NG + D  +A   L    V G+ +GR A  N  + +    Y  
Sbjct: 197 GVIAAVARAV-SIPVLGNGDIADPREAEARLRTSGVAGLAVGRGALGNPWIFSRTLHYLE 255

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +   R +   M +Y    L     ++++ +H      G   S   R
Sbjct: 256 TGELLPEPGVRERVETALRHLDL-MIEYKGEFLA----VREMRKHAAWYLKGLHGSAGVR 310

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
             +  EA  +     ++    + M
Sbjct: 311 AAVN-EAERADDLRALLLGYLDRM 333


>gi|319952943|ref|YP_004164210.1| tRNA-u20-dihydrouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319421603|gb|ADV48712.1| tRNA-U20-dihydrouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 332

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 70/320 (21%), Positives = 140/320 (43%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++  IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLQSVAIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G DD   ++ +  + + ++  G   I IH R         +      + ++  
Sbjct: 138 ITVKTRLGWDDD--SIRIVEVAERLQDVGCKAIAIHGRT--------RAQMYKGDANWAP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K  +   + +  NG +     A+K+     +DG MIGRA+         V  +F  
Sbjct: 188 IADVKNNQRMHIPVFGNGDVNTPEAAMKMRDEYGLDGAMIGRASIGYPWFFNEVKHFFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +   R +     D+    L     + +  RH    F G PN +  R 
Sbjct: 248 GEHLAPPTIQERVEAAQRHL-QMAIDWKGEQLG----VFETRRHYTNYFKGIPNFKEHRM 302

Query: 296 ILTVEAGAST---ATHHIIE 312
            +     +     A   +++
Sbjct: 303 KMVTSDHSEDVFKAFEEVLK 322


>gi|262037496|ref|ZP_06010955.1| tRNA-dihydrouridine synthase A [Leptotrichia goodfellowii F0264]
 gi|261748426|gb|EEY35806.1| tRNA-dihydrouridine synthase A [Leptotrichia goodfellowii F0264]
          Length = 329

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 116/332 (34%), Positives = 166/332 (50%), Gaps = 27/332 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TDR++R F R++  + LLYTEMI A A++ GD   IL F   E P+ LQ+   +  
Sbjct: 10  MVDRTDRNFRNFVRMINKDVLLYTEMITAQAVINGDSDYILEFDDTEHPIVLQLAVTNKK 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +  EA KI E + Y+EINLNVGCPS RV     GA LM  P+ V + +A + KA   PV+
Sbjct: 70  EAYEAIKIAEKYDYDEINLNVGCPSDRVSGNMMGAYLMAFPETVAEIVAGIKKATDKPVS 129

Query: 121 VKCRIGVDDQ------------IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +K RIG+D +                 + N V   +K+GV    +HAR A+L+GL PK N
Sbjct: 130 IKHRIGIDGKNILPETFKRTLLDKYEDMLNFVNITQKAGVKKYVVHARIAVLEGLDPKQN 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           R+IP L Y+ VY +KKE P+L I +NGG++   Q  + L   D VM+GR  Y N  +L+ 
Sbjct: 190 REIPPLRYEEVYRLKKERPELHIEINGGIKTTEQIDEHLKYADSVMLGREIYDNPMILSK 249

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             +Y+            +  +    +I   M  Y  +      +      H  GLFHG  
Sbjct: 250 FGKYYG-----------KNIEIAREEIIEKMILYVEKMERENKRPHLFLMHTHGLFHGVK 298

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
            S+  +     E  A  A    +      + +
Sbjct: 299 GSKYWKR----EINAPQADSKTLRRLLKEVKD 326


>gi|311104203|ref|YP_003977056.1| tRNA-dihydrouridine synthase B [Achromobacter xylosoxidans A8]
 gi|310758892|gb|ADP14341.1| tRNA-dihydrouridine synthase B [Achromobacter xylosoxidans A8]
          Length = 341

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 68/297 (22%), Positives = 120/297 (40%), Gaps = 24/297 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMAASNPKLWDSVKTSRRLNHDGEIAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EAA      G   I++N+GCP  +V   + G+ L+ + D +   + A+  A   L
Sbjct: 76  PAMMAEAAVFNASKGARIIDINMGCPVKKVCNVASGSALLRHEDQIARILDAVVGACAPL 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        + K  + +G+  + +H R         + +      +
Sbjct: 136 DVPVTLKTRTGWDRESRNA--LRVAKMAENAGIAALTLHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K E   + +  NG +    +A  +L     D VMIGRAA     +   +D Y 
Sbjct: 186 YDTIRAVKAEL-KIPVVANGDITTPEKAKHVLDYTGADAVMIGRAAQGRPWIFREIDHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               T + P    + +     +      Y          ++   +H+     G P +
Sbjct: 245 RTGETLAPPSYGEMRELLLEHLDDHYRFYGEH-----TGVRTARKHIGWYLDGLPGA 296


>gi|288800405|ref|ZP_06405863.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 299 str. F0039]
 gi|288332618|gb|EFC71098.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 299 str. F0039]
          Length = 333

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 87/321 (27%), Positives = 148/321 (46%), Gaps = 25/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  I  L  +  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRNIKSTINKLSIADSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE    + I+LN GCP  +V     G+ ++ N  ++ D    + KA+  P
Sbjct: 77  VESMVEAAKIVEQVSPDVIDLNFGCPVKKVASKGAGSGMLRNIPLMLDITREVVKAVKTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + +  L + ++  G+  + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDSE--NLVITTLAEQLQDCGIEALTIHGRT--------RAQMYTGNADWSL 186

Query: 179 VYEIKKENP--DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K +NP   + I  NG +    +A        VD VM+GRA +    +   ++E   
Sbjct: 187 IKEVK-DNPRIHIPIIGNGDITTAEEAKMAFEQYGVDAVMVGRATFGRPWVFKEMNELIQ 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
             + G++   T  DK     I     +     +     +    RH+    +F G P+ ++
Sbjct: 246 G-IDGTNTALTIDDKI---DILKEQLEINVEKIDEYRGILHTRRHLASSPIFKGIPDFKQ 301

Query: 293 CRHILTVEAGASTATHHIIET 313
            R I  + A      + I+E 
Sbjct: 302 TR-IAMLRANTVNELNSILED 321


>gi|125547565|gb|EAY93387.1| hypothetical protein OsI_15183 [Oryza sativa Indica Group]
          Length = 437

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 114/328 (34%), Positives = 175/328 (53%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 70  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 129

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V     FGA LM +P+ VGD ++A+    ++
Sbjct: 130 LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 189

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV++KCRIGVDD+     L   V   + KS      IHARKA+L GLSP +NRK+P L Y
Sbjct: 190 PVSIKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRKVPPLKY 249

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD    
Sbjct: 250 EYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVDSEVY 309

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T  S  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P +   +
Sbjct: 310 GMPTRRS-SRRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEPGNGLWK 364

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                           +E   + +  S+
Sbjct: 365 RKADSTLRHCKTLESFLEETLDAIPNSV 392


>gi|126653300|ref|ZP_01725411.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) protein [Bacillus sp. B14905]
 gi|126589974|gb|EAZ84103.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) protein [Bacillus sp. B14905]
          Length = 346

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/310 (25%), Positives = 144/310 (46%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+Y EMI    I++ ++K   +L    +E PL+LQI G D
Sbjct: 25  MAGICNSAFRLTVKEF-GAGLVYAEMISDKGIVQKNEKTLGMLYIDERENPLSLQIFGGD 83

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA L+L+P+ V + +AA+  A+  
Sbjct: 84  KETLVEAAKYVDQNTSADIIDINMGCPVNKIIKCEAGARLLLDPNKVYEMVAAVVDAVKK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P++VK RIG DD+   +      ++++++G + + +H R  +               ++D
Sbjct: 144 PISVKMRIGWDDE--HIFAIENAQAVERAGASAVAVHGRTRV--------QMYEGKANWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K EN  + +  NG +E    A ++L    VD VMIGRAA  N  M+    +Y   
Sbjct: 194 IIRQVK-ENVKIPVLGNGDVETPQDAKRMLETTGVDAVMIGRAALGNPWMIYRTVQYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     +   +    G  ++++ +H      G   + + R+
Sbjct: 253 GELKEEPSVCE-----KMDVCLLHFERLLQLKGEGIAVREMRKHASWYLKGIRGNGKARN 307

Query: 296 ILTVEAGAST 305
            +     A+ 
Sbjct: 308 AINQTETAAE 317


>gi|238758368|ref|ZP_04619546.1| tRNA-dihydrouridine synthase B [Yersinia aldovae ATCC 35236]
 gi|238703491|gb|EEP96030.1| tRNA-dihydrouridine synthase B [Yersinia aldovae ATCC 35236]
          Length = 321

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 76  PHEMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPELVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVTIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLNGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|238764617|ref|ZP_04625563.1| tRNA-dihydrouridine synthase B [Yersinia kristensenii ATCC 33638]
 gi|238697207|gb|EEP89978.1| tRNA-dihydrouridine synthase B [Yersinia kristensenii ATCC 33638]
          Length = 321

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 126/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 76  PDEMAAAAQINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPELVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-IVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLNGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|53720502|ref|YP_109488.1| putative nitrogen regulation-related protein [Burkholderia
           pseudomallei K96243]
 gi|53726195|ref|YP_103916.1| dihydrouridine synthase [Burkholderia mallei ATCC 23344]
 gi|76810759|ref|YP_334772.1| dihydrouridine synthase [Burkholderia pseudomallei 1710b]
 gi|121599461|ref|YP_991623.1| tRNA-dihydrouridine synthase B [Burkholderia mallei SAVP1]
 gi|124384557|ref|YP_001027118.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10229]
 gi|126442123|ref|YP_001060371.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 668]
 gi|126451189|ref|YP_001082064.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10247]
 gi|134280126|ref|ZP_01766837.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 305]
 gi|167000510|ref|ZP_02266322.1| tRNA-dihydrouridine synthase B [Burkholderia mallei PRL-20]
 gi|167721169|ref|ZP_02404405.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei DM98]
 gi|167740145|ref|ZP_02412919.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 14]
 gi|167817358|ref|ZP_02449038.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 91]
 gi|167825766|ref|ZP_02457237.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 9]
 gi|167895835|ref|ZP_02483237.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 7894]
 gi|167904226|ref|ZP_02491431.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei NCTC
           13177]
 gi|167920438|ref|ZP_02507529.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei BCC215]
 gi|217420460|ref|ZP_03451965.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 576]
 gi|226198391|ref|ZP_03793960.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pakistan
           9]
 gi|237813759|ref|YP_002898210.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei MSHR346]
 gi|238561989|ref|ZP_00441078.2| tRNA-dihydrouridine synthase B [Burkholderia mallei GB8 horse 4]
 gi|254178920|ref|ZP_04885574.1| tRNA-dihydrouridine synthase B [Burkholderia mallei ATCC 10399]
 gi|254180692|ref|ZP_04887290.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1655]
 gi|254191521|ref|ZP_04898024.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pasteur
           52237]
 gi|254194903|ref|ZP_04901333.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei S13]
 gi|254202628|ref|ZP_04908991.1| tRNA-dihydrouridine synthase B [Burkholderia mallei FMH]
 gi|254207967|ref|ZP_04914317.1| tRNA-dihydrouridine synthase B [Burkholderia mallei JHU]
 gi|254261098|ref|ZP_04952152.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1710a]
 gi|254299222|ref|ZP_04966672.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 406e]
 gi|254355893|ref|ZP_04972171.1| tRNA-dihydrouridine synthase B [Burkholderia mallei 2002721280]
 gi|52210916|emb|CAH36904.1| putative nitrogen regulation-related protein [Burkholderia
           pseudomallei K96243]
 gi|52429618|gb|AAU50211.1| dihydrouridine synthase [Burkholderia mallei ATCC 23344]
 gi|76580212|gb|ABA49687.1| dihydrouridine synthase [Burkholderia pseudomallei 1710b]
 gi|121228271|gb|ABM50789.1| tRNA-dihydrouridine synthase B [Burkholderia mallei SAVP1]
 gi|124292577|gb|ABN01846.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10229]
 gi|126221616|gb|ABN85122.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 668]
 gi|126244059|gb|ABO07152.1| tRNA-dihydrouridine synthase B [Burkholderia mallei NCTC 10247]
 gi|134248133|gb|EBA48216.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 305]
 gi|147746875|gb|EDK53952.1| tRNA-dihydrouridine synthase B [Burkholderia mallei FMH]
 gi|147751861|gb|EDK58928.1| tRNA-dihydrouridine synthase B [Burkholderia mallei JHU]
 gi|148024868|gb|EDK83046.1| tRNA-dihydrouridine synthase B [Burkholderia mallei 2002721280]
 gi|157809277|gb|EDO86447.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 406e]
 gi|157939192|gb|EDO94862.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pasteur
           52237]
 gi|160694834|gb|EDP84842.1| tRNA-dihydrouridine synthase B [Burkholderia mallei ATCC 10399]
 gi|169651652|gb|EDS84345.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei S13]
 gi|184211231|gb|EDU08274.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1655]
 gi|217395872|gb|EEC35889.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 576]
 gi|225929574|gb|EEH25592.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei Pakistan
           9]
 gi|237502697|gb|ACQ95015.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei MSHR346]
 gi|238523449|gb|EEP86887.1| tRNA-dihydrouridine synthase B [Burkholderia mallei GB8 horse 4]
 gi|243063564|gb|EES45750.1| tRNA-dihydrouridine synthase B [Burkholderia mallei PRL-20]
 gi|254219787|gb|EET09171.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1710a]
          Length = 354

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 127/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGAG 136

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D          +    + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWDRDHKNA--LRIATLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPRKAKAVLDATRADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +  +      P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQSGELLPPPRIDEIRQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|297602354|ref|NP_001052360.2| Os04g0278900 [Oryza sativa Japonica Group]
 gi|255675275|dbj|BAF14274.2| Os04g0278900 [Oryza sativa Japonica Group]
          Length = 368

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 114/328 (34%), Positives = 174/328 (53%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 1   MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V     FGA LM +P+ VGD ++A+    ++
Sbjct: 61  LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 120

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V   + KS      IHARKA+L GLSP +NR +P L Y
Sbjct: 121 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRNVPPLKY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   ML  VD    
Sbjct: 181 EYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNMLGHVDSEVY 240

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T  S  + ++ + +     + M  Y      S   ++Q+ + ++ LFH  P +   +
Sbjct: 241 GMPTRRS-SRRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFHSEPGNGLWK 295

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                           +E   + +  S+
Sbjct: 296 RKADSTLRHCKTLESFLEETLDAIPNSV 323


>gi|85374084|ref|YP_458146.1| tRNA-dihydrouridine synthase [Erythrobacter litoralis HTCC2594]
 gi|84787167|gb|ABC63349.1| tRNA-dihydrouridine synthase [Erythrobacter litoralis HTCC2594]
          Length = 338

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 76/300 (25%), Positives = 130/300 (43%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI ++A +R  ++++   +    E P+++Q+ G D
Sbjct: 29  MTGVTDLPFRTLVRRF-GSGLNVTEMIASEAAIRETRQSVQKAAWDKTEDPVSMQLVGCD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK+ ED G   I++N GCP  +V     G+ LM    +    + A   A+ +P
Sbjct: 88  PVSMGEAAKLQEDNGAAIIDINFGCPVRKVVGQLAGSALMREVPLATRLMEATVNAVDVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++    L +  +  GV  I +H R         ++     + D+  
Sbjct: 148 VTVKMRMGWD--HASLNAPELARIAEDLGVQMITVHGRT--------RNQMYKGSADWSF 197

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K +   + + +NG    +ED + AL+     DG+MIGR AY    +L  V  ++  
Sbjct: 198 IRKVK-DAVSIPVIVNGDICGIEDAANALEQ-SGADGLMIGRGAYGKPWLLAQVMHWWKT 255

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                SP      +         +  Y       G K+    +H+     G   S   R+
Sbjct: 256 GDRLESPDFDLQYETLVEHYGRMLDHYGRE---VGTKI--ARKHLGWYTKGMHGSAEFRN 310


>gi|90413381|ref|ZP_01221374.1| putative Dihydrouridine synthase [Photobacterium profundum 3TCK]
 gi|90325623|gb|EAS42092.1| putative Dihydrouridine synthase [Photobacterium profundum 3TCK]
          Length = 321

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 60/299 (20%), Positives = 120/299 (40%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPDLWKTAKSQNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +P ++ + + ++  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQHPALIEEILRSVVGAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D  +      ++ K  ++ G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWD--LDNRNCVDIAKIAEQCGIQALALHGRT--------KSCMYKGEAEYDY 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y +  
Sbjct: 186 IRAAKQAV-SIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFREIQHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +P    V       +      Y          L+   +H+         +   R 
Sbjct: 245 EYLPAPSMDEVSGIMLGHVQELHRFY-----GEYLGLRIARKHVSWYLKEHAPAGDFRR 298


>gi|327395459|dbj|BAK12881.1| tRNA-dihydrouridine synthase B DusB [Pantoea ananatis AJ13355]
          Length = 337

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 132/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    S +    A+QI G D
Sbjct: 33  MAGITDRPFRTLCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDESGIRAVQIAGCD 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+ +P
Sbjct: 92  PSEMAQAARINVDAGAQVIDINMGCPAKKVNRKMAGSALLQYPSVVESILSAVVNAVDVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         +      + +YD 
Sbjct: 152 VTLKIRTGWDPENRNCVA--IAQLAERCGIQALTIHGRT--------RACLFNGDAEYDS 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 202 IRTVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 260

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y      SG   +   +H+         + + R  
Sbjct: 261 ELLAPLPLAEVKRLLVSHIRELHDFY-----GSGKGYRIARKHVSWYLQEHAPNDQFRRT 315

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 316 FNAIEDASE-QLEALEAYFENL 336


>gi|269966802|ref|ZP_06180875.1| tRNA-dihydrouridine synthase B [Vibrio alginolyticus 40B]
 gi|269828469|gb|EEZ82730.1| tRNA-dihydrouridine synthase B [Vibrio alginolyticus 40B]
          Length = 340

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 124/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 35  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP  +V++   G+ L+  P+I+ + + A+  A+ +P
Sbjct: 94  PQLMADAAQFSVENGAQIIDINMGCPDKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 154 VTLKTRTGWD--TDNKNCVQIAKLAENCGIQALALHGRT--------KACMYKGEAEYDS 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 204 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 263 TTMEELPTEEVKTIMLGHVNALHEFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 317

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 318 FNAIDAAP-LQIEALEGYFDNV 338


>gi|148828154|ref|YP_001292907.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittGG]
 gi|148719396|gb|ABR00524.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittGG]
          Length = 326

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 139/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 17  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  P +V   +  +  A+++P
Sbjct: 76  PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPYLVEKILREVVSAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 186 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 245 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 300 FNAISD----PKEQLIVLEDFFNLILDK 323


>gi|124002638|ref|ZP_01687490.1| NifR [Microscilla marina ATCC 23134]
 gi|123991866|gb|EAY31253.1| NifR [Microscilla marina ATCC 23134]
          Length = 330

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 141/317 (44%), Gaps = 24/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I A+ ++R   K++  L     E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRAACKQ-NGADVMYTEFIAAEGLIRDAHKSVQKLDIYDYERPIGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  +  AA IVE      +++N GCP  +V     GA ++ +   +      + K + +P
Sbjct: 78  IESMRLAADIVERTQPEILDINYGCPVKKVACKGAGAGILQDLPKMQKMTEEIVKRVKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD   ++ +  + K ++  G+  + IH R         +        +++ 
Sbjct: 138 VTVKTRLGWDD--SSIKIMEVAKRLQDVGIKALSIHGRT--------RKQMYKGEANWEP 187

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+K  NPD  + I  NG ++   +AL+      +DG+MIGRAA     +   +  Y +
Sbjct: 188 IAEVKN-NPDIHIPIFGNGDIDTPEKALEYKNRYGIDGIMIGRAAIGYPWIFNEIKHYMA 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                + P   +      + +      ++         + ++ RH    F GF   +  R
Sbjct: 247 TGKKLAPPTLEQRVAVCHQHLV-----HSVEWKGEKQGVFEMRRHYTNYFRGFHGFKPFR 301

Query: 295 HILTVEAGASTATHHII 311
             L VEAG+      I+
Sbjct: 302 TRL-VEAGSPQEVIDIL 317


>gi|169825710|ref|YP_001695868.1| tRNA-dihydrouridine synthase 1 [Lysinibacillus sphaericus C3-41]
 gi|168990198|gb|ACA37738.1| Probable tRNA-dihydrouridine synthase 1 [Lysinibacillus sphaericus
           C3-41]
          Length = 346

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/310 (25%), Positives = 144/310 (46%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+Y EMI    I++ ++K   +L    +E PL+LQI G D
Sbjct: 25  MAGICNSAFRLTVKEF-GAGLVYAEMISDKGIVQKNEKTLGMLYIDERENPLSLQIFGGD 83

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA L+L+P+ V + +AA+  A+  
Sbjct: 84  KETLVEAAKYVDQNTTADIIDINMGCPVNKIIKCEAGARLLLDPNKVYEMVAAVVDAVKK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P++VK RIG DD+   +      ++++++G + + +H R  +               ++D
Sbjct: 144 PISVKMRIGWDDE--HIFAIENAQAVERAGASAVAVHGRTRV--------QMYEGKANWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K EN  + +  NG +E    A ++L    VD VMIGRAA  N  M+    +Y   
Sbjct: 194 IIRQVK-ENVKIPVLGNGDVETPQDAKRMLETTGVDAVMIGRAALGNPWMIYRTVQYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     +   +    G  ++++ +H      G   + + R+
Sbjct: 253 GELKEEPSVRE-----KMDVCLLHFERLLQLKGEGIAVREMRKHASWYLKGIRGNGKARN 307

Query: 296 ILTVEAGAST 305
            +     A+ 
Sbjct: 308 AINQTETAAE 317


>gi|293603643|ref|ZP_06686064.1| tRNA-dihydrouridine synthase B [Achromobacter piechaudii ATCC
           43553]
 gi|292818079|gb|EFF77139.1| tRNA-dihydrouridine synthase B [Achromobacter piechaudii ATCC
           43553]
          Length = 341

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 123/297 (41%), Gaps = 24/297 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMAASNPKLWDSVKTSRRLNHDGEIAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EAA    + G   I++N+GCP  +V   + G+ L+ + D++   + A+  A   L
Sbjct: 76  PAMMAEAAVFNANKGARIIDINMGCPVKKVCNVASGSALLRHEDLIVRILDAVVSACAPL 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        + K  + +G+  + +H R         + +      +
Sbjct: 136 GVPVTLKTRTGWDRESRNA--LRVAKLAENAGIAALTLHGRT--------RADLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K E   + +  NG ++   +A  +L     D VMIGRAA     +   +D Y 
Sbjct: 186 YDTIRAVKAELT-IPVIANGDIDSPEKAKHVLDYTGADAVMIGRAAQGRPWIFREIDHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               + + P    + +     +      Y          ++   +H+     G P +
Sbjct: 245 RTGESLAPPSHGEMRELLLEHLDDHYRFYGEH-----TGVRTARKHIGWYLDGLPGA 296


>gi|54310476|ref|YP_131496.1| putative dihydrouridine synthase [Photobacterium profundum SS9]
 gi|46914919|emb|CAG21694.1| putative Dihydrouridine synthase [Photobacterium profundum SS9]
          Length = 321

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 60/299 (20%), Positives = 120/299 (40%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPDLWKTAKSQNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +P ++ + + ++  A+ +P
Sbjct: 76  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKRLAGSALLQHPALIEEILRSVVGAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D  +      ++ K  ++ G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWD--LDNRNCVDIAKIAEQCGIQALALHGRT--------KSCMYKGEAEYDY 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y +  
Sbjct: 186 IRAAKQAV-SIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFREIQHYLTTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +P    V       +      Y          L+   +H+         +   R 
Sbjct: 245 EYLPAPSMDEVSGIMLGHVQELHRFY-----GEYLGLRIARKHVSWYLKEHAPAGDFRR 298


>gi|283458530|ref|YP_003363158.1| tRNA -dihydrouridine synthase [Rothia mucilaginosa DY-18]
 gi|283134573|dbj|BAI65338.1| tRNA-dihydrouridine synthase [Rothia mucilaginosa DY-18]
          Length = 442

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 124/302 (41%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T++ +R          L  TEM+ A A++    +++  +     EK  ++QI G D
Sbjct: 83  MAGVTNKAFRRLCSEYGG-GLYVTEMVTARALVERKPESMRIIEHDPDEKIRSIQIYGVD 141

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A ++V +    + I+LN GCP+ +V     GA L    D+    +    K    
Sbjct: 142 AVNVGKAVRMVVEEDRADHIDLNFGCPAPKVTRRGGGAALPWKTDLFTAIVQTAVKEASR 201

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + +GV  I +H R A                
Sbjct: 202 NDIPLTIKMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTA--------AQHYSGKA 251

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + ++++  PD+ I  NG +     A++++    VDGV+IGR       +   +   
Sbjct: 252 DWDSIAQLRELIPDVPILGNGDIFSAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNA 311

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P  T V    +R     +  +          L++I +H+   F G+P    
Sbjct: 312 FEGSSERIRPTLTEVSDMIYRHAELLVETFG----DETRGLREIRKHVAWYFKGYPVGGE 367

Query: 293 CR 294
            R
Sbjct: 368 LR 369


>gi|153839624|ref|ZP_01992291.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus AQ3810]
 gi|308094610|ref|ZP_05890528.2| NifR3 family protein [Vibrio parahaemolyticus AN-5034]
 gi|308095202|ref|ZP_05903963.2| NifR3 family protein [Vibrio parahaemolyticus Peru-466]
 gi|308126676|ref|ZP_05911720.2| NifR3 family protein [Vibrio parahaemolyticus AQ4037]
 gi|149746863|gb|EDM57851.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus AQ3810]
 gi|308088061|gb|EFO37756.1| NifR3 family protein [Vibrio parahaemolyticus Peru-466]
 gi|308094109|gb|EFO43804.1| NifR3 family protein [Vibrio parahaemolyticus AN-5034]
 gi|308109548|gb|EFO47088.1| NifR3 family protein [Vibrio parahaemolyticus AQ4037]
          Length = 340

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 123/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L    K+   +    +    ++QI G+D
Sbjct: 35  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P I+ + + A+  A+ +P
Sbjct: 94  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPTIIEEILKAVVNAVDVP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 154 VTLKTRTGWD--TDNKNCVQIAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 204 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 263 TTMDELPTQEVKAIMLGHVNALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 317

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 318 FNAIDAAP-LQIEALEGYFDNV 338


>gi|86147886|ref|ZP_01066191.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
 gi|85834313|gb|EAQ52466.1| NifR3/Smm1 family protein [Vibrio sp. MED222]
          Length = 322

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 124/323 (38%), Gaps = 24/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  +    K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKVWKTSKSQQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+     G   I++N+GCP+ +V++   G+ L+ +P+++ D + A+  A+ +P
Sbjct: 76  PQLMAEAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQHPELIEDILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         +        +Y  
Sbjct: 136 VTLKTRTGWD--TDNRNCVQIAKIAEDCGIQALALHGRT--------RACMYKGEAEYKH 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +   K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAAKQAV-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFNEILHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       + A    Y           +   +H+         +   R  
Sbjct: 245 TTMDPLPISEVKDIMLGHVLALHEFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LTV-EAGASTATHHIIETAFNLM 318
               EAG        +E  F+ +
Sbjct: 300 FNAFEAG--DLQLEALEGFFDNV 320


>gi|257126021|ref|YP_003164135.1| dihydrouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257049960|gb|ACV39144.1| dihydrouridine synthase DuS [Leptotrichia buccalis C-1013-b]
          Length = 331

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 118/331 (35%), Positives = 164/331 (49%), Gaps = 28/331 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           MVD TDR++R F R++  + LLYTEMI A AI+   D   +LGF   E P+ LQI   + 
Sbjct: 13  MVDRTDRNFRNFVRMINKDVLLYTEMITAQAIINTKDLNYLLGFDKIENPIVLQIAATNP 72

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +  EA KI E + Y+EINLN+GCPS RV     GA LM  P++V D I AM  A + P+
Sbjct: 73  KEAYEAVKIAEKYDYDEINLNIGCPSDRVSGNMMGAYLMAFPEVVADIIKAMKDATNKPI 132

Query: 120 TVKCRIGVDDQ------------IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           ++K RIG+D +                 + N +   KK+GVN   IHAR A+L GL PK 
Sbjct: 133 SIKHRIGIDGKNILPDYFERTLLDKYEDMMNFINITKKTGVNKYIIHARIAVLAGLDPKQ 192

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           NR IP L YD VY +KKENPDL I +NG ++ + +  + L   D VM+GR  Y N  +LT
Sbjct: 193 NRSIPPLRYDEVYRVKKENPDLHIEINGEIKSVDEIDEHLKYTDSVMMGREIYDNPMILT 252

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
              +Y+   +  +             +I   M  Y         +      H  GLFH  
Sbjct: 253 EFGKYYGKDINITR-----------EEIIEKMIYYVENMERQNIRPHLFLMHTHGLFHNV 301

Query: 288 PNSRRCRHILTVEAGASTATHHIIETAFNLM 318
             S+  +  +        A    +    + +
Sbjct: 302 RGSKFWKRAINN----PKANSETLRKLLSEI 328


>gi|262367311|gb|ACY63868.1| hypothetical protein YPD8_3198 [Yersinia pestis D182038]
          Length = 305

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 1   MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 60  PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 120 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IRAVKQ-TVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 229 ELLPPMPLGEVQRLLDGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 283

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 284 FNAIEDASE-QLEALEAYFENL 304


>gi|88608299|ref|YP_506262.1| putative tRNA-dihydrouridine synthase [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600468|gb|ABD45936.1| putative tRNA-dihydrouridine synthase [Neorickettsia sennetsu str.
           Miyayama]
          Length = 331

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 124/324 (38%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  YR   +      L+ +EMI + A++   K  +     S +E   A+Q+ G +
Sbjct: 19  MSGVTDMPYRDLVKSF-GAGLVVSEMIASRAMILKTKDTMKKVSLSPREDITAIQLAGFE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAKI ED G   I++N GCP  +V  G  G+ LM +       + A  KA+ IP
Sbjct: 78  PDVMAEAAKINEDMGAKIIDINFGCPVKKVVNGYAGSYLMKDECHAAKILEATVKAVKIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+         L K  +  G+  I IH R         +        D+  
Sbjct: 138 VTLKMRTGWDENHRNA--PKLAKIAEDLGIKMITIHGRT--------RAQMYKGKSDWQF 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++    A + L     DG+MIGR AY     +  +  +    
Sbjct: 188 IRTVKN-TVKIPVIANGDIKTYEDAERALVESGADGIMIGRGAYGKPWSIRNMLHFLRTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          + IS+  + Y          +    +H++     + NS   R  
Sbjct: 247 KKLQEPTPQEKLPIILQHISSIFSHYGTEM-----GIGIARKHILWYSANYKNSAEFRQQ 301

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +  E          +E     + E
Sbjct: 302 ICQETC--------VEKLLERVEE 317


>gi|323498782|ref|ZP_08103768.1| NifR3/Smm1 family protein [Vibrio sinaloensis DSM 21326]
 gi|323316144|gb|EGA69169.1| NifR3/Smm1 family protein [Vibrio sinaloensis DSM 21326]
          Length = 320

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 64/320 (20%), Positives = 124/320 (38%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K++  +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKLWNTSKSMQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P+I+ D + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQFPEIIEDILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCVQIAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  +  N 
Sbjct: 186 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIQHFLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TKMADLPLEEVKDILLGHVNALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 A       +E  F+
Sbjct: 300 FNAIDAAP-LQLDALEEYFD 318


>gi|225016372|ref|ZP_03705564.1| hypothetical protein CLOSTMETH_00275 [Clostridium methylpentosum
           DSM 5476]
 gi|224950868|gb|EEG32077.1| hypothetical protein CLOSTMETH_00275 [Clostridium methylpentosum
           DSM 5476]
          Length = 328

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 122/298 (40%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +DR YR   +     A +  EM+ A  +   D+K+  +L  S QE+P+A+Q+ G D
Sbjct: 20  MASVSDRAYRETCKQF-EAAYVVGEMVSAKGLHYSDRKSEELLSVSAQERPMAVQLFGDD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA      +  + I++N+GCP  +V     G+ LM NP + G+ + A   A  +P
Sbjct: 79  PGYMAEAVHKALRYEPDLIDINMGCPVPKVAGNGCGSALMKNPVLAGEIVRAAADASRVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD   +V      K +++SG   + +H R         +        D+ I
Sbjct: 139 VTVKFRKGWDD--SSVNAVEFAKRMEQSGAAAVTVHGRT--------RRQMYQGEADWQI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +     A  +     VD VM+ R +Y    +   + +Y    
Sbjct: 189 IRQVK-EAVSIPVIGNGDVVSPESAKAMYDQTGVDLVMVARGSYGRPWLFGQIRDYLETG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P   R  +                +      +++  +H      G   + R R
Sbjct: 248 RYEPDPPFARQMEIMLEHA-----RLICAYKGEFIGMKEARKHAAWYLKGIHGAARFR 300


>gi|123443997|ref|YP_001007967.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090958|emb|CAL13840.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 321

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDEMAAAARINVANGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSAEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRSVKQ-IVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLNGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|312109228|ref|YP_003987544.1| hypothetical protein GY4MC1_0077 [Geobacillus sp. Y4.1MC1]
 gi|311214329|gb|ADP72933.1| TIM-barrel protein, nifR3 family [Geobacillus sp. Y4.1MC1]
          Length = 333

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 141/322 (43%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  ++K   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  +V +   GA  +L+P+ + D +AA+  A+  
Sbjct: 77  KETLVEAAKFVDKHTNADIIDINMGCPVPKVTKCDAGAKWLLDPNKIYDVVAAIVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+           ++++++G   + +H R  +               D++
Sbjct: 137 PVTVKMRIGWDENHIYAV--ENAQAVERAGGKAVAVHGRTRV--------QMYEGKADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 187 IIKQVK-EAVNIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVRYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     +   +      H+     ++++ +H      G   + + R+
Sbjct: 246 GELIPEPTVREKIEVCLLHLDR-LIALKGEHIA----VKEMRKHAAWYLKGVRGNAKIRN 300

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +            ++  A  +
Sbjct: 301 AINECETREQLAALLLNFAEEV 322


>gi|332304569|ref|YP_004432420.1| TIM-barrel protein, nifR3 family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332171898|gb|AEE21152.1| TIM-barrel protein, nifR3 family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 333

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 126/298 (42%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  +    K+   +    ++   A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAGLVVSEMLSSNPDVWRSNKSKQRMDHVGEKGIRAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   +++N+GCP+ +V++   G+ L+ +P +V   + ++ +A+ +P
Sbjct: 76  PLLMAQAAQFNVDNGAQIVDINMGCPAKKVNKKLAGSALLQDPQLVEQIVQSVVEAVQVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +          + K  +++G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWNTDNRNGV--QIAKIAEQNGIQSLAVHGRT--------RACMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +  +  A  +L     D +MIGR A  N  +   +  +    
Sbjct: 186 IKAIKQAV-SIPVVANGDITCVHSAKHVLEYTKADALMIGRGAQGNPWIFRQIQHFLQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               SP  + V       ++     Y           +   +H+          RR R
Sbjct: 245 EILPSPPLSEVRDVLLSHVANVHQFY-----GELKGARIARKHVGWYLAEHDRERRFR 297


>gi|219685843|ref|ZP_03540651.1| tRNA-dihydrouridine synthase A [Borrelia garinii Far04]
 gi|219672617|gb|EED29648.1| tRNA-dihydrouridine synthase A [Borrelia garinii Far04]
          Length = 333

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 175/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K ++  +  E P+A+QI      
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKVVKQTPLESPIAIQIATNCKF 69

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMRENTNKPI 129

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRLLNSDYKNESYSEVKNFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L+ +  I TR D      I   M +Y   +  +   +  + +H++G+      +R+ 
Sbjct: 250 ---LSETDKIPTRKD------ILMQMVEYVKEY-ENYLSINILFKHLMGIIFSKEGARKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLKKHEILLKAMETLPEKI 328


>gi|154684599|ref|YP_001419760.1| YacF [Bacillus amyloliquefaciens FZB42]
 gi|154350450|gb|ABS72529.1| YacF [Bacillus amyloliquefaciens FZB42]
          Length = 333

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 140/326 (42%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + + +  L    +EKPL+LQI G  
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGK 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+PD + + ++A+  A+  
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D++          ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDEEHIYAVKN--AQAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D   +       ++++ +H      G   +   R+
Sbjct: 246 GELKDEPKVREKMS-----VCKLHLDRLIKLKGENVAVREMRKHAAWYLKGVRGNANVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF    E+
Sbjct: 301 EINQCETREEVVQ--LLDAFTAEAEA 324


>gi|255327241|ref|ZP_05368315.1| putative tRNA-dihydrouridine synthase [Rothia mucilaginosa ATCC
           25296]
 gi|255295521|gb|EET74864.1| putative tRNA-dihydrouridine synthase [Rothia mucilaginosa ATCC
           25296]
          Length = 430

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 124/302 (41%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T++ +R          L  TEM+ A A++    +++  +     EK  ++QI G D
Sbjct: 71  MAGVTNKAFRRLCSEYGG-GLYVTEMVTARALVERKPESMRIIEHDPDEKIRSIQIYGVD 129

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A ++V +    + I+LN GCP+ +V     GA L    D+    +    K    
Sbjct: 130 AVNVGKAVRMVVEEDRADHIDLNFGCPAPKVTRRGGGAALPWKTDLFTAIVQTAVKEASR 189

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + +GV  I +H R A                
Sbjct: 190 NDIPLTIKMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTA--------AQHYSGKA 239

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + ++++  PD+ I  NG +     A++++    VDGV+IGR       +   +   
Sbjct: 240 DWDSIAQLRELIPDVPILGNGDIFSAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNA 299

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P  T V    +R     +  +          L++I +H+   F G+P    
Sbjct: 300 FEGSSERIRPTLTEVSDMIYRHAELLVETFG----DETRGLREIRKHVAWYFKGYPVGGE 355

Query: 293 CR 294
            R
Sbjct: 356 LR 357


>gi|292486759|ref|YP_003529629.1| putative dehydrogenase [Erwinia amylovora CFBP1430]
 gi|291552176|emb|CBA19213.1| putative dehydrogenase [Erwinia amylovora CFBP1430]
          Length = 321

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA--LQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMMSSNPEVWASDKSRLRMVHSDEPGVRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   + A   A+ +P
Sbjct: 76  PQEMAEAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILTAEVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDSDNRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + +  NG + D  +A  +L     DG+MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-NVSIPVIANGDITDPHKARAVLDYTGADGLMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y  R    G ++    +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIGHLRELHDFYGQR---KGYRI--ARKHVSWYLQENAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|149369324|ref|ZP_01889176.1| probable TIM-barrel protein, NifR3 family [unidentified eubacterium
           SCB49]
 gi|149356751|gb|EDM45306.1| probable TIM-barrel protein, NifR3 family [unidentified eubacterium
           SCB49]
          Length = 332

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 71/325 (21%), Positives = 140/325 (43%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA 
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE  G + I++N GCP  +V     GA ++ + D++     AM K   +P
Sbjct: 78  LESMLRSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G   I IH R         +      + D+  
Sbjct: 138 VTVKTRLGWD--HDSIKIVEVAERLQDVGCKAISIHGRT--------RAQMYKGDADWAP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + +  NG ++   +A+ +     +DG MIGRA+         V  + + 
Sbjct: 188 IAEVKNNQRMHIPVFGNGDVDTPEKAILMRDKYGLDGAMIGRASIGYPWFFKEVKHFMAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P  T   +   R +       A         + +  RH    F G P+ +  R 
Sbjct: 248 GTHAAPPTMTERVEAARRHL-----QMAIDWKGETLGVFETRRHYTNYFKGIPHFKEYRM 302

Query: 296 ILTVEAGAST---ATHHIIETAFNL 317
            +     ++    A   ++E   + 
Sbjct: 303 KMVTSDQSADVFAAFDEVLEKFSDF 327


>gi|309810988|ref|ZP_07704786.1| TIM-barrel protein, nifR3 family [Dermacoccus sp. Ellin185]
 gi|308434952|gb|EFP58786.1| TIM-barrel protein, nifR3 family [Dermacoccus sp. Ellin185]
          Length = 410

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 127/318 (39%), Gaps = 33/318 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----------LLYTEMIVADAILRGDKKNI--LGFSTQE 47
           M   T+R +R   R   ++            L  +EMI + A++      +  +     E
Sbjct: 39  MAGITNRAFRRLCRQYGDDGSVAAGASGATSLYVSEMITSRALVERVPLTMKLIETDPDE 98

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P ++Q+   D     +AA+I+   G  + I+LN GCP  +V     G+ L    ++   
Sbjct: 99  NPRSIQLYCTDPLNAGKAARILASEGRADHIDLNFGCPVPKVTRKGGGSALPWKTELFRG 158

Query: 107 CIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            ++A+ +      IPVTVK R G+D     +      +  +  GV  + +HAR A     
Sbjct: 159 IVSAVVREASPYDIPVTVKMRKGID--TDHLTYLEAARIAEGEGVAAVALHARTA----- 211

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                    + D+  +  +K+    + +  NG +     A++++     DGV++GR    
Sbjct: 212 ---AQAYSGHADWSAIRTLKETVTSIPVLGNGDIWSAEDAMRMVAETGCDGVVVGRGCLG 268

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T +   F+       P    V     R+ +  + ++    L      + I +H+ 
Sbjct: 269 RPWLFTDLAAAFAGSDARVDPTLGEVCAT-LRRHAEYLVEFYDDEL---KGCRDIRKHIA 324

Query: 282 GLFHGFPNSRRCRHILTV 299
             F GFP   + RH L +
Sbjct: 325 WYFKGFPVGSQLRHQLAL 342


>gi|68071985|ref|XP_677906.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56498194|emb|CAH96102.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 441

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 108/353 (30%), Positives = 178/353 (50%), Gaps = 40/353 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R+++    L+TEMIV + +L    + +  LGF+  E P+  Q+GG+D
Sbjct: 69  MINVTNRHFRALVRIISKKVQLWTEMIVDNTLLYNINNLEEHLGFNKNEHPIVCQLGGSD 128

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
              L EAA +VE  GY+E+N+NVGCPS +V     FGA LM  P +V + +  + K + I
Sbjct: 129 PISLSEAAILVEQAGYDELNINVGCPSTKVANKGAFGAYLMKKPQLVKNIVYEIKKKVQI 188

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVDD      LR+ ++++  +G +   IH+RKA LKGL PK NR IP L+Y+
Sbjct: 189 PVTVKIRTGVDDLDSFSFLRSFIETVSSAGCDHFIIHSRKAWLKGLDPKQNRSIPPLEYN 248

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--------------VD------------ 211
            V+++ K  P++   LNGG++ + Q + +L                 D            
Sbjct: 249 KVFDLCKLYPNIKFTLNGGIKSIEQGVALLNGYAPINNMSGKHNNCTDNNYIKIKDYDIN 308

Query: 212 ---GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
              GVMIGR+  +N  +L   D+   N    ++    R   D ++      + +     +
Sbjct: 309 PLYGVMIGRSCMENITVLAKTDKLVYNYDIPTTAYNRRTVLDAYKSYLEQNSSF-----Y 363

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTA---THHIIETAFNLM 318
           S     ++ + ++G+  G P  R  R+ +        +      I++ A + +
Sbjct: 364 SLVNAFELLKPILGILKGMPGHRLFRNKIDSYIRKYASILNCAQILDKAMSDV 416


>gi|313885908|ref|ZP_07819648.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|312924663|gb|EFR35432.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica
           PR426713P-I]
          Length = 329

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/302 (25%), Positives = 133/302 (44%), Gaps = 25/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +     +L+YTE I ADA++R     +  +     E+P+A+QI G D
Sbjct: 18  MEDVSDAPFRLLCKQF-GASLVYTEFISADALVRYVPSTMRKMRIDPAERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I      + ++LN GCP  RV     G+ ++ +P+++ +  AA+  A S P
Sbjct: 77  VETMCEAARIACQLEPDLLDLNFGCPVKRVAGKGAGSGMLRDPELLLEITAAVVAAASCP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  L   ++  G+  + IH R         + +    + D+ +
Sbjct: 137 VTVKTRLGWD--HDSLIITELAPRLQACGIAALTIHGRT--------RSDMYKGSADWTL 186

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+ + NP+  + I  NG +    +         VDGVM+GRAA     +   +     
Sbjct: 187 IGEV-RSNPEIQIPIIGNGDITTGEEVRHAFDTYGVDGVMVGRAAIGQPWIFGEMRAAVD 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              T       +       +I   +       L     +    RH+    LF G PN R 
Sbjct: 246 PTFTAPQLTSQQQL-----EILKEIVHKNIEKLDERRGILHSRRHLAATPLFKGIPNFRA 300

Query: 293 CR 294
            R
Sbjct: 301 LR 302


>gi|28899658|ref|NP_799263.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|308125328|ref|ZP_05774543.2| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus K5030]
 gi|28807910|dbj|BAC61147.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|308112839|gb|EFO50379.1| tRNA-dihydrouridine synthase B [Vibrio parahaemolyticus K5030]
          Length = 331

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 123/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P I+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPTIIEEILKAVVNAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCVQIAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 195 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMDELPTQEVKAIMLGHVNALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIDAAP-LQIEALEGYFDNV 329


>gi|126662469|ref|ZP_01733468.1| probable TIM-barrel protein, NifR3 family [Flavobacteria bacterium
           BAL38]
 gi|126625848|gb|EAZ96537.1| probable TIM-barrel protein, NifR3 family [Flavobacteria bacterium
           BAL38]
          Length = 316

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 136/305 (44%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L     L+Y+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 1   MEDVSDPPFRRLCKL-HGADLMYSEFISSEGLIRDAMKSKQKLDIFDYERPVGIQIFGGD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +++IV+    + +++N GCP  +V     GA ++ + D++     A+ K  S+P
Sbjct: 60  EEAMEMSSRIVDAVQPDLVDINFGCPVKKVVCKGAGAGVLKDVDLMVRLTKAVIKGTSLP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ +  + + ++  GV  + +HAR         +      + D+  
Sbjct: 120 VTVKTRLGWDE--SSINIDEVAERLQDIGVQALTVHART--------RAQMYKGHSDWSH 169

Query: 179 VYEIKKENPDL--FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  IK ENP +   I  NG ++   +AL+      +DG+MIGRAA     +   +  YF+
Sbjct: 170 IQRIK-ENPRITMPIFGNGDIDSPEKALEYKNKFGLDGMMIGRAAIGYPWIFNEIKHYFA 228

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                + P      +     +      ++         + ++ RH    F G    +  +
Sbjct: 229 TGEKLAPPSMNGRIEAARNHLI-----WSIEWKGERLGINEMRRHYTNYFKGIHGFKEYK 283

Query: 295 HILTV 299
             L  
Sbjct: 284 QKLVT 288


>gi|51597867|ref|YP_072058.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis IP
           32953]
 gi|108809658|ref|YP_653574.1| tRNA-dihydrouridine synthase B [Yersinia pestis Antiqua]
 gi|108813677|ref|YP_649444.1| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516]
 gi|145597577|ref|YP_001161653.1| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides F]
 gi|153948925|ref|YP_001399379.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis IP
           31758]
 gi|153997407|ref|ZP_02022507.1| tRNA-dihydrouridine synthase B [Yersinia pestis CA88-4125]
 gi|165937393|ref|ZP_02225956.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|166011363|ref|ZP_02232261.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166214187|ref|ZP_02240222.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167420730|ref|ZP_02312483.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167425544|ref|ZP_02317297.1| dihydrouridine synthase [Yersinia pestis biovar Mediaevalis str.
           K1973002]
 gi|170022704|ref|YP_001719209.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis YPIII]
 gi|186897062|ref|YP_001874174.1| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis PB1/+]
 gi|218930665|ref|YP_002348540.1| tRNA-dihydrouridine synthase B [Yersinia pestis CO92]
 gi|229836798|ref|ZP_04456963.1| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides A]
 gi|229839302|ref|ZP_04459461.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229899866|ref|ZP_04515007.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229904177|ref|ZP_04519288.1| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516]
 gi|270488618|ref|ZP_06205692.1| TIM-barrel protein, nifR3 family [Yersinia pestis KIM D27]
 gi|294505248|ref|YP_003569310.1| hypothetical protein YPZ3_3139 [Yersinia pestis Z176003]
 gi|38604949|sp|Q8ZAX7|DUSB_YERPE RecName: Full=tRNA-dihydrouridine synthase B
 gi|51591149|emb|CAH22814.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108777325|gb|ABG19844.1| hypothetical protein YPN_3517 [Yersinia pestis Nepal516]
 gi|108781571|gb|ABG15629.1| hypothetical protein YPA_3667 [Yersinia pestis Antiqua]
 gi|115349276|emb|CAL22243.1| conserved hypothetical protein [Yersinia pestis CO92]
 gi|145209273|gb|ABP38680.1| hypothetical protein YPDSF_0261 [Yersinia pestis Pestoides F]
 gi|149289044|gb|EDM39124.1| tRNA-dihydrouridine synthase B [Yersinia pestis CA88-4125]
 gi|152960420|gb|ABS47881.1| dihydrouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|165914498|gb|EDR33112.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|165989747|gb|EDR42048.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166204674|gb|EDR49154.1| dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166961536|gb|EDR57557.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167055558|gb|EDR65351.1| dihydrouridine synthase [Yersinia pestis biovar Mediaevalis str.
           K1973002]
 gi|169749238|gb|ACA66756.1| TIM-barrel protein, nifR3 family [Yersinia pseudotuberculosis
           YPIII]
 gi|186700088|gb|ACC90717.1| TIM-barrel protein, nifR3 family [Yersinia pseudotuberculosis
           PB1/+]
 gi|229678295|gb|EEO74400.1| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516]
 gi|229687358|gb|EEO79433.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229695668|gb|EEO85715.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229705741|gb|EEO91750.1| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides A]
 gi|262363311|gb|ACY60032.1| hypothetical protein YPD4_3128 [Yersinia pestis D106004]
 gi|270337122|gb|EFA47899.1| TIM-barrel protein, nifR3 family [Yersinia pestis KIM D27]
 gi|294355707|gb|ADE66048.1| hypothetical protein YPZ3_3139 [Yersinia pestis Z176003]
 gi|320017182|gb|ADW00754.1| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 321

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 76  PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLDGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|54022573|ref|YP_116815.1| putative dihydrouridine synthase [Nocardia farcinica IFM 10152]
 gi|54014081|dbj|BAD55451.1| putative dihydrouridine synthase [Nocardia farcinica IFM 10152]
          Length = 382

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 122/304 (40%), Gaps = 24/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGA 57
           M   T+  +R   R   +   +   EMI A A++  ++K   ++ F   E P ++Q+ G 
Sbjct: 27  MAGITNLAFRKLCREFGSATSIYVCEMITARAVVERNEKTLHMMSFDADEHPRSMQLYGV 86

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-- 114
           D   L EA +I+   G  + I++N+GCP  +V     GA L     +    + AM  A  
Sbjct: 87  DPQTLGEAVRIIVGEGWADHIDMNLGCPVPKVTRLGGGAALPYKRALFARIVRAMVAAAE 146

Query: 115 -LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVTVK RIG+DD        +  +  +  G   + +HAR A          R    
Sbjct: 147 PAGVPVTVKFRIGIDDDHH--TYLDTGRIAEAEGARAVSLHARTA--------AQRYSGQ 196

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            D+  +  +K+    + +  NG +     A++++     DGV++GR       +   +  
Sbjct: 197 ADWSAIARLKEAVTTIPVLGNGDIFAAEDAVRMMAETGCDGVVVGRGCLGRPWLFAELQA 256

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                     P   RV +  +R          + HL     ++ + +HM     GFP   
Sbjct: 257 ALRGQPLPEPPNLGRVGEVLYRH-----GALLSEHLGEDKAMRDLRKHMAWYLMGFPVGA 311

Query: 292 RCRH 295
             R 
Sbjct: 312 DLRR 315


>gi|255529934|ref|YP_003090306.1| TIM-barrel protein, nifR3 family [Pedobacter heparinus DSM 2366]
 gi|255342918|gb|ACU02244.1| TIM-barrel protein, nifR3 family [Pedobacter heparinus DSM 2366]
          Length = 335

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 142/326 (43%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +RF  +  +   ++YTE I ++ ++R   K+   L     E+P+ +QI G++
Sbjct: 20  MEDVSDPPFRFVCKQ-SGVDMMYTEFISSEGLIRDAAKSRAKLDIFEYERPIGIQIFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EA +I    G + +++N GCP   V     GA L+ + D +     A+ KA  +P
Sbjct: 79  IDHMREATEIATLAGPDLMDINYGCPVKNVACRGAGASLLQDIDKMVRMTEAVVKATHLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    V    + + ++  G+  + IH R         +        D+ +
Sbjct: 139 VTVKTRLGWDDNTKNVE--EVAERLQDIGIQALTIHGRT--------RAQLYKGEADWTL 188

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + +IK+     + I  NG ++ + +A   ++   VDG+MIGRAA     +   +  +F+ 
Sbjct: 189 IRQIKRNPRIKIPIFGNGDVDSIRKAADWRLEYEVDGIMIGRAAIGYPWIFREIRHFFNT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T + P            +  +  + +         + ++ RH    F G P+ +  R 
Sbjct: 249 GKTLAGPSIEERVS-----VCRTHFEKSIAWKGPRVGIFEMRRHYANYFKGIPDFKSYRM 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L  E          I +  + + E 
Sbjct: 304 QLVKE-----ENIDTIHSILDEIAEK 324


>gi|256424776|ref|YP_003125429.1| hypothetical protein Cpin_5809 [Chitinophaga pinensis DSM 2588]
 gi|256039684|gb|ACU63228.1| TIM-barrel protein, nifR3 family [Chitinophaga pinensis DSM 2588]
          Length = 345

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 135/317 (42%), Gaps = 25/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M D +D  +R   R      LLYTE I ++ +++     +  L    +E+P  +QI G D
Sbjct: 19  MEDVSDPPFRVVCRE-NGADLLYTEFISSEGLVKDTEKCRRKLAIFDEERPAGVQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             KL  AA+IV+    + +++N GCP   +     G+ ++ + D++    AA  K+  +P
Sbjct: 78  EGKLSMAARIVDMTQPDLLDINFGCPIKGIVSKGAGSGVLKDIDLMVRLTAACVKSTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    + + ++  G+  + IH R         +         +++
Sbjct: 138 VTVKTRLGWDEDTQNIE--EVAERLQDVGIKALAIHGRT--------RTQMYKGEASWEL 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL+      VDG+MIGRAA     +   V  Y   
Sbjct: 188 IAKVKNNPRIHIPIFGNGDIDSPQKALEYKNRYGVDGIMIGRAAIGYPWIFREVKHYLQT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P          R++     + + +    G  +  + +H      G P+ +  R 
Sbjct: 248 GEMLPAPTLEDRIAVCKRQL-----EKSVQWRGEGHGIFAMRKHYFNYLKGLPDFKAFRS 302

Query: 296 ILTVEAGASTATHHIIE 312
            L        A+  I++
Sbjct: 303 RLVT----PEASAEIMD 315


>gi|321313751|ref|YP_004206038.1| tRNA-dihydrouridine synthase B [Bacillus subtilis BSn5]
 gi|320020025|gb|ADV95011.1| tRNA-dihydrouridine synthase B [Bacillus subtilis BSn5]
          Length = 333

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 143/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + + +  L    +EKPL+LQI G  
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGK 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+PD + + ++A+  A++ 
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +      ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAVKNAQAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   +   R+
Sbjct: 246 GELKEEPQVRE-----KMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF + +E+
Sbjct: 301 EINHCETREEFVQ--LLDAFTVEVEA 324


>gi|251791404|ref|YP_003006125.1| tRNA-dihydrouridine synthase B [Dickeya zeae Ech1591]
 gi|247540025|gb|ACT08646.1| TIM-barrel protein, nifR3 family [Dickeya zeae Ech1591]
          Length = 321

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 128/326 (39%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGVSDRPFRALCYAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  + G   I++N+GCP+ +V+    G+ L+  P++V   + A+ KA+ +P
Sbjct: 76  PDEMAEAARINAENGAQVIDINMGCPAKKVNRKMAGSALLQYPELVKQILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTVHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPVIANGDITDPRKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLIGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
                    A   +   A     E+L
Sbjct: 300 FNA---IEDAGEQL--EALKAYFENL 320


>gi|222112079|ref|YP_002554343.1| tim-barrel protein, nifr3 family [Acidovorax ebreus TPSY]
 gi|221731523|gb|ACM34343.1| TIM-barrel protein, nifR3 family [Acidovorax ebreus TPSY]
          Length = 353

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 115/306 (37%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +  +   A+  A    
Sbjct: 76  AAMMAEAALYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAEAVVAACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   Q     +  L +  +  G+  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQQHKNAVV--LARRFEDVGIQMLTVHGRT--------REQGYKGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   +  Y 
Sbjct: 186 YDTIAAVK-AAVRVPVVANGDITSPEKARAVLAATGADAVMIGRAAQGRPWIFREIGHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLEHLQDHYGLYGEA-----SGVRSARKHIAWYVRALPGGEAL 299

Query: 294 RHILTV 299
           R  +  
Sbjct: 300 RQHINT 305


>gi|123430787|ref|XP_001307959.1| TIM-barrel protein, nifR3 family protein [Trichomonas vaginalis G3]
 gi|121889614|gb|EAX95029.1| TIM-barrel protein, nifR3 family protein [Trichomonas vaginalis G3]
          Length = 301

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 143/302 (47%), Gaps = 24/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  +R  A       +  TEM+ A A++  +KK   +L  S +EK +A+QI G+D
Sbjct: 1   MAGYTDIAFREVATE-KGADITVTEMVSAMALVYENKKTIDLLDISPKEKKVAVQIFGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I+ D+ ++ +++N+GCP+ ++ + + G+ L+ NP +V D + ++ K  + P
Sbjct: 60  PDVMGEAARILNDYDFSYVDINMGCPAPKIVKNNSGSHLLSNPSLVYDIVKSVVKNSNKP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G+      V+    +K+I+ +G + + +H R         ++       D+D 
Sbjct: 120 VTAKVRKGI----GGVSSMKAIKNIEAAGASFVTVHGRT--------REEYYTGKADWDF 167

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K EN  + +  NG ++    A++      VDG+ IGR A  N  +   ++E     
Sbjct: 168 IKEVK-ENVKIPVIGNGDVDSPEDAIEKINYSKVDGLAIGRGAIGNPYIFNQIEELIKTG 226

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P           ++   ++    +H      + ++ +     F G   S+  R+ 
Sbjct: 227 DYYK-PSDKEKLLLMIDELERKISYKGEKH-----GILEMRKVYAEYFKGMKGSKEVRNK 280

Query: 297 LT 298
           L 
Sbjct: 281 LN 282


>gi|165927556|ref|ZP_02223388.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165920450|gb|EDR37727.1| dihydrouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
          Length = 323

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 19  MAGITDRPFRALCHGM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHVDEPGIRNVQIAGND 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +P
Sbjct: 78  PDEMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 138 VTLKIRTGWSPEHRN--CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDS 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 188 IRAVKQ-TVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 247 ELLPPMPLGEVQRLLDGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 301

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 302 FNAIEDASE-QLEALEAYFENL 322


>gi|317495837|ref|ZP_07954200.1| dihydrouridine synthase [Gemella moribillum M424]
 gi|316914014|gb|EFV35497.1| dihydrouridine synthase [Gemella moribillum M424]
          Length = 335

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 82/303 (27%), Positives = 137/303 (45%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  ++K +  L    +E+PL+LQI G +
Sbjct: 18  MAGVCNAAFRLTAKEF-GAGLVCAEMVSDKAILFNNQKTMNMLYIDPRERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  LVEAAK V+     + I+LN+GCP  ++ +   G+ L+L+PD V + IA +  A+S 
Sbjct: 77  IDTLVEAAKYVDKNTEADIIDLNMGCPVPKITKVDAGSKLLLDPDKVYEVIARLVDAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD+   +   +  ++ +++G + I IH R  +               ++D
Sbjct: 137 PVTVKMRMGWDDEHIYI--MDNARNAERAGASAIAIHGRTKV--------QMYSGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++KKE   + +  NG +     A K+L   + D VMIGRAA  N  ML    +Y   
Sbjct: 187 VIRDVKKEL-KIPVIGNGDVTTPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   M             + ++ +H      G     + + 
Sbjct: 246 GELSDEPSPREKIDVCLLHLRRLM-----EIKPEKVAVHEMRKHAAYYMKGIKGGSKVKK 300

Query: 296 ILT 298
            L 
Sbjct: 301 ELN 303


>gi|167771298|ref|ZP_02443351.1| hypothetical protein ANACOL_02656 [Anaerotruncus colihominis DSM
           17241]
 gi|167666549|gb|EDS10679.1| hypothetical protein ANACOL_02656 [Anaerotruncus colihominis DSM
           17241]
          Length = 324

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 125/298 (41%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M    D  +R   +     A +  EM  A  +   D+K   +LG +  E+P+A+Q+ G +
Sbjct: 17  MAGVADSAFRQICKQF-GAAYMVGEMASAKGMHYSDRKTARLLGVNDVERPVAVQLFGDE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK    F  + I++N+GCP+ +V     GA LM N  +      A  KA+ +P
Sbjct: 76  PEIVAEAAKKALAFCPDVIDINMGCPAPKVAGNGGGAALMKNVALAARITEATVKAVDLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD    V      +++++SG   + +H R  +            P +D DI
Sbjct: 136 VTVKFRKGWDD--AHVNAVEFARAMEQSGAAALTVHGRTRM--------QYYAPPVDLDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG   D+   + +      D VMIGR A  +  + + V  Y  + 
Sbjct: 186 IAAVK-AAVSIPVIGNGDCIDIQSVVNMYDYTKCDLVMIGRGALGSPWIFSQVARYLKDG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +T  +P          R IS    +   R       +++  +H      G   +   R
Sbjct: 245 VTLPTPNLQTRMDVMLRHISLICENKGERQ-----AMREARKHAAWYMKGMRGAAAFR 297


>gi|288929784|ref|ZP_06423627.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 317 str. F0108]
 gi|288328885|gb|EFC67473.1| TIM-barrel protein, putative, NifR3 family [Prevotella sp. oral
           taxon 317 str. F0108]
          Length = 329

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 142/325 (43%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYTEFVSAEALVRSVKSTVSKLTISDEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  +V     GA ++ N  ++ +    + +A+  P
Sbjct: 77  VESMVEAARIVEQSRPDVIDINFGCPVKKVAGKGAGAGMLRNVPLMLEITREVVRAVRTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +   + +  L + ++  G+  + IH R         +        D+  
Sbjct: 137 VTVKTRLGWDCEE--IIIPTLAEQLQDCGIAALTIHGRT--------RSQMYTGEADWRY 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    QA ++     VD VM+GRA +    +   + ++   
Sbjct: 187 IGEVKANPRIHIPIIGNGDICTPQQAKEVFSRYGVDAVMVGRATFGRPWVFKEMKDHLEG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P    +  D    +           +     +    RH+    +F G P+ ++ 
Sbjct: 247 -----LPQDPSLTIDRKIDLLEEQLRINIERIDEYRGILHTRRHLAASPIFKGIPDFKQT 301

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A        I+E+    +
Sbjct: 302 R-IAMLRADKQEELIAILESCRERL 325


>gi|219684515|ref|ZP_03539458.1| tRNA-dihydrouridine synthase A [Borrelia garinii PBr]
 gi|219671877|gb|EED28931.1| tRNA-dihydrouridine synthase A [Borrelia garinii PBr]
          Length = 335

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 113/329 (34%), Positives = 175/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K ++  +  E P+A+QI      
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKVVKQTPLESPIAIQIATNCKF 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   + GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANCGACLMSNANQVGEILKTMKENTNKPI 131

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              ++N VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRLLNSDYKNESYSEVKNFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY +KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYNLKKENKNLFIETNGGINNSEQIKKHLSFVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L+ +  I TR D      I   M +Y   +  +   +  + +H++G+      +R+ 
Sbjct: 252 ---LSETDKIPTRKD------ILMQMVEYVKEY-ENYLSINILFKHLMGIIFSKEGARKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLKKHEILLKAMETLPEKI 330


>gi|38604767|sp|Q87KU1|DUSB_VIBPA RecName: Full=tRNA-dihydrouridine synthase B
 gi|328472220|gb|EGF43090.1| NifR3/Smm1 family protein [Vibrio parahaemolyticus 10329]
          Length = 322

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 123/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L    K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  P I+ + + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPTIIEEILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCVQIAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAVKEAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMDELPTQEVKAIMLGHVNALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 300 FNAIDAAP-LQIEALEGYFDNV 320


>gi|261878855|ref|ZP_06005282.1| tRNA-dihydrouridine synthase [Prevotella bergensis DSM 17361]
 gi|270334534|gb|EFA45320.1| tRNA-dihydrouridine synthase [Prevotella bergensis DSM 17361]
          Length = 336

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 145/327 (44%), Gaps = 19/327 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE + A+AI+R  K  +  +     E+P+ +QI G D
Sbjct: 19  MEDVTDIGFRKLCKRY-GADMMYTEFVSAEAIIRNIKSTLDKMQIDDDERPVGIQIYGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAK+VE    + I++N GCP  +V     GA ++ N  ++ D   A+  A+ +P
Sbjct: 78  VESMVEAAKMVETVEPDVIDINFGCPVKKVAGKGAGAGMLKNIPLMLDITRAVVDAVRVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D  +  + + +L + ++  G+  + IH R         +      + D+ +
Sbjct: 138 VTAKTRLGWD--LDNLIITDLAEQLQDCGIRALTIHGRT--------RSQMYTGDADWSL 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K+     + I  NG +    QA +      VD VMIGRA +    +   + +Y ++
Sbjct: 188 IGEVKRNPRIHIPIIGNGDITTPEQAKQAFERYGVDAVMIGRATFGCPWIFKEMRDYLNS 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
              G       +  D    I           +     +    RH+    +F   PN R+ 
Sbjct: 248 TSGGGLEPAAPLTVDDKIDILEEQLRINVERIDEYRGILHTRRHLASSPIFKNIPNFRQT 307

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R I  ++A        I+E    ++ E
Sbjct: 308 R-IAMLQANTMEELTGILEECRLVLRE 333


>gi|16077149|ref|NP_387962.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221307891|ref|ZP_03589738.1| hypothetical protein Bsubs1_00410 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312213|ref|ZP_03594018.1| hypothetical protein BsubsN3_00410 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317146|ref|ZP_03598440.1| hypothetical protein BsubsJ_00410 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221321409|ref|ZP_03602703.1| hypothetical protein BsubsS_00410 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|586896|sp|P37567|DUS1_BACSU RecName: Full=Probable tRNA-dihydrouridine synthase 1
 gi|467469|dbj|BAA05315.1| unknown [Bacillus subtilis]
 gi|2632348|emb|CAB11857.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|291482453|dbj|BAI83528.1| hypothetical protein BSNT_00139 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 333

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 143/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + + +  L    +EKPL+LQI G  
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGK 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+PD + + ++A+  A++ 
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVNK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +      ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAVKNAQAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   +   R+
Sbjct: 246 GKLKEEPQVRE-----KMAVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVKGNANVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF + +E+
Sbjct: 301 EINHCETREEFVQ--LLDAFTVEVEA 324


>gi|225012555|ref|ZP_03702991.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-2A]
 gi|225003532|gb|EEG41506.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-2A]
          Length = 312

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/321 (24%), Positives = 146/321 (45%), Gaps = 26/321 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   + L    ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 1   MEDVSDPPFRALCKEL-GADVVYTEFISSEGLIRDAAKSVQKLDIYEKERPVGIQIFGAN 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ +  ++     AM K   +P
Sbjct: 60  LDSMLRSVEIVEASNPDIIDINFGCPVKKVVSKGAGAGILKDIPLMVKLTEAMAKHTHLP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G DD   ++ +  + + ++ +G   I IH R         +      + ++  
Sbjct: 120 ITVKTRLGWDD--ASIKIVEVAERLQDAGAKAISIHGRT--------RAQMYKGDANWHP 169

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K  +   + I  NG ++   +A  +     +DG MIGRA+  N      V  +F  
Sbjct: 170 IAEVKNNQRMQIPIFGNGDVDSPEKAKLMRDEFGLDGAMIGRASIGNPWFFNEVKHFFET 229

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               ++P I+ RV       ++    + A         + +  RH    F G PN +  R
Sbjct: 230 GTYAAAPSIEDRV------AVARRHLEMAIDWKGEIQGVLETRRHYTNYFKGIPNFKPLR 283

Query: 295 -HILTVE--AGASTATHHIIE 312
             ++T    AG       IIE
Sbjct: 284 TRMVTSNDSAGVFEVFDEIIE 304


>gi|296166415|ref|ZP_06848847.1| dihydrouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295898176|gb|EFG77750.1| dihydrouridine synthase [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 377

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 130/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERSKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIVDEGLADHIDMNFGCPVPKVTKRGGGAALPYKRRLFGQIVAAA 136

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK R+G+DD+       +  +  +  G   + +HAR A          
Sbjct: 137 VRATEGARIPVTVKFRVGIDDEHH--THLDAGRIAESEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQHVRTIPVLGNGDIYDASDALTMMATTGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F++    + P    V       I        A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTDSPAPTPPTLGEVA-----DIVRRHGKLLAAHFGEDKGMRDIRKHIGWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAM 314


>gi|145332939|ref|NP_001078335.1| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|332646976|gb|AEE80497.1| FMN-linked oxidoreductase-like protein protein [Arabidopsis
           thaliana]
          Length = 386

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 105/324 (32%), Positives = 166/324 (51%), Gaps = 11/324 (3%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           +D HYR  ARL+T +A LYTEMI A+ ++         L FS Q+ P+ LQ+GG+++  L
Sbjct: 30  SDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSNVENL 89

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +AAK+ + +GY+EINLN GCPS +V     FG  LML P +VG+ ++A+    ++PVTV
Sbjct: 90  AKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKLVGEAMSAIAANTNVPVTV 149

Query: 122 KCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           KCRIGVD+      L + +  +   S      +H+RKA+L G+SP DNR+IP L Y+  Y
Sbjct: 150 KCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKYEYYY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFSNPLT 238
            + ++ PDL   +NGG+  +S+    L     GVM+GRAAY N    L  VD        
Sbjct: 210 ALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNNPWQTLGQVDTAVYG--- 266

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P      +    +           H +    ++ + + ++ LFH    +   +    
Sbjct: 267 --VPSSGLTRRQVLEQYQVYGDSVLGTHGNGRPNVRDLVKPLLNLFHSENGNSLWKRRAD 324

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
                  +   ++E +   + + +
Sbjct: 325 AAFKECRSVGSLLEESLRAIPDCV 348


>gi|223041958|ref|ZP_03612142.1| tRNA-dihydrouridine synthase B [Actinobacillus minor 202]
 gi|240950369|ref|ZP_04754638.1| tRNA-dihydrouridine synthase B [Actinobacillus minor NM305]
 gi|223017215|gb|EEF15643.1| tRNA-dihydrouridine synthase B [Actinobacillus minor 202]
 gi|240295126|gb|EER45948.1| tRNA-dihydrouridine synthase B [Actinobacillus minor NM305]
          Length = 322

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 138/322 (42%), Gaps = 25/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L           A+QI GAD
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSKLRLAHHRDIGVNAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAK+   +G   I++N+GCP+ +V++   G+ L+  P +V + + A+  A+ +P
Sbjct: 76  PTEMAEAAKVNVAYGAEIIDINMGCPAKKVNKKMAGSALLREPKLVENILKAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        +    ++SGV+ + IH R         +        +Y+ 
Sbjct: 136 VTLKIRTGWDLENRN--CLEIAHIAEQSGVSALTIHGRT--------RSCLFEGVAEYES 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A ++L     D VMIGR AY    +   V+++  + 
Sbjct: 186 IKAVKQAV-SIPIIANGDITSAEKAKEVLDYTGADAVMIGRGAYGRPWLFKEVNDFLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG-FPNS--RRC 293
              S  +  +      R ++     Y       G ++    +H+        P S  +R 
Sbjct: 245 AYSSLSLDNKCHLM-LRHVADLHQFYGEE---KGYRI--ARKHVGWYSENLLPGSNFKRT 298

Query: 294 RHILTVEAGASTATHHIIETAF 315
            + L        A    +E+  
Sbjct: 299 FNALDTTKAQIKALEDFVESLL 320


>gi|295401955|ref|ZP_06811917.1| TIM-barrel protein, nifR3 family [Geobacillus thermoglucosidasius
           C56-YS93]
 gi|294975957|gb|EFG51573.1| TIM-barrel protein, nifR3 family [Geobacillus thermoglucosidasius
           C56-YS93]
          Length = 333

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 140/322 (43%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  ++K   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  +V +   GA  +L+P+ + D +AA+  A+  
Sbjct: 77  KETLVEAAKFVDKHTNADIIDINMGCPVPKVTKCDAGAKWLLDPNKIYDVVAAIVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+           ++++++G   + +H R  +               D++
Sbjct: 137 PVTVKMRIGWDENHIYAV--ENAQAVERAGGKAVAVHGRTRV--------QMYEGKADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 187 IIKQVK-EAVNIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVRYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   +      H+     ++++ +H      G   + + R+
Sbjct: 246 GELIPEPTVREKIGVCLLHLDR-LIALKGEHIA----VKEMRKHAAWYLKGVRGNAKIRN 300

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +            ++  A  +
Sbjct: 301 AINECETREQLAALLLNFAEEV 322


>gi|241759199|ref|ZP_04757306.1| NifR3 family protein [Neisseria flavescens SK114]
 gi|241320520|gb|EER56809.1| NifR3 family protein [Neisseria flavescens SK114]
          Length = 334

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 136/325 (41%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   + +QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPSLRHTKKTLRRSDFEGEGGVVVVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +VG+ + A+  A+ +P
Sbjct: 76  PQQMAEAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVGEILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D+     L  + K  ++SG+  + IH R         +         Y++
Sbjct: 136 VTLKTRLGWHDEHQN--LPTIAKIAEESGIAALAIHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A+ +L   + DG+MIGR A     +   +  Y  + 
Sbjct: 186 IAETKGRL-NIPVWVNGDITSPQKAVAVLKQTAADGIMIGRGAQGRPWLFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +      +      I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECNATILNHIRAMHEFY-----GEVAGVRIARKHIGWYIDEMPDGEQTRRD 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           + +    + A +  +      + E 
Sbjct: 300 INLLDSVA-AQYDTLAAYLETLSEK 323


>gi|156935780|ref|YP_001439696.1| tRNA-dihydrouridine synthase B [Cronobacter sakazakii ATCC BAA-894]
 gi|156534034|gb|ABU78860.1| hypothetical protein ESA_03650 [Cronobacter sakazakii ATCC BAA-894]
          Length = 327

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 23  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPEVWASDKSRLRMVHVDEPGIRTVQIAGSV 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 82  PEEMAEAARINVDNGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTAVVNAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +      N +YD 
Sbjct: 142 VTLKIRTGWDP--ANRNCVEIAQLAEECGIQALTIHGRT--------RACLFQGNAEYDS 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG +    +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 192 IRTVKQKV-SIPVIANGDITSPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 251 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVAWYLQEHAPDDQFRRT 305

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 306 FNAIEDASE-QLEALEAYFE 324


>gi|261819596|ref|YP_003257702.1| tRNA-dihydrouridine synthase B [Pectobacterium wasabiae WPP163]
 gi|261603609|gb|ACX86095.1| TIM-barrel protein, nifR3 family [Pectobacterium wasabiae WPP163]
          Length = 321

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTIHGRT--------RACLFNGFAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLAPLPLVEVKRLLIEHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|56418608|ref|YP_145926.1| nitrogen regulation transcriptional regulator [Geobacillus
           kaustophilus HTA426]
 gi|261417574|ref|YP_003251256.1| hypothetical protein GYMC61_0074 [Geobacillus sp. Y412MC61]
 gi|297528448|ref|YP_003669723.1| hypothetical protein GC56T3_0072 [Geobacillus sp. C56-T3]
 gi|319765232|ref|YP_004130733.1| hypothetical protein GYMC52_0075 [Geobacillus sp. Y412MC52]
 gi|56378450|dbj|BAD74358.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) [Geobacillus kaustophilus HTA426]
 gi|261374031|gb|ACX76774.1| TIM-barrel protein, nifR3 family [Geobacillus sp. Y412MC61]
 gi|297251700|gb|ADI25146.1| TIM-barrel protein, nifR3 family [Geobacillus sp. C56-T3]
 gi|317110098|gb|ADU92590.1| TIM-barrel protein, nifR3 family [Geobacillus sp. Y412MC52]
          Length = 333

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 137/317 (43%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  ++K   +L    +EKP++LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVYNNEKTLNMLYIDEREKPISLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++     GA  +L+P+ + D +AA+  A+  
Sbjct: 77  KETLVKAAKFVDKNTNADIIDINMGCPVPKITNCDAGAKWLLDPNKIYDVVAAIVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++          ++++++G   + +H R  +               D++
Sbjct: 137 PVTVKMRIGWDEKHIYAV--ENAQAVERAGGKAVAVHGRTRV--------QMYEGKADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 187 IIKQVK-EAVNIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVRYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   + + R+
Sbjct: 246 GELIPEPTPREKI-----DVCLLHLDRLIALKGEYIAVKEMRKHAAWYLKGIRGAAKIRN 300

Query: 296 ILTVEAGASTATHHIIE 312
            +            ++ 
Sbjct: 301 AINECETRDELAALLLR 317


>gi|296284138|ref|ZP_06862136.1| tRNA-dihydrouridine synthase [Citromicrobium bathyomarinum JL354]
          Length = 339

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 129/302 (42%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI ++A +R  ++++   +    E+P+++Q+ G D
Sbjct: 30  MTGVTDMPFRTLVRRY-GSGLNVTEMIASEAAIRETRQSVQKAAWDRIEEPVSMQLVGCD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAAK+ E  G   I++N GCP  +V     G+ LM    +    + A  KA+ +P
Sbjct: 89  PASMAEAAKLQEGNGAAIIDINFGCPVRKVVGQLAGSALMREVPLATKLMEATVKAVDVP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++    L +  +  GV  I +H R         ++     + D+  
Sbjct: 149 VTVKMRMGWD--HDSLNAPELARIAEDLGVKMITVHGRT--------RNQMYKGSADWSF 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K +  ++ + +NG +  +  A + L     DG+MIGR AY    +L  V  ++   
Sbjct: 199 IAKVK-DAVNIPVIVNGDICSIDDAARALEQSGADGLMIGRGAYGRPWLLGQVMHWWQTG 257

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P                +  Y          ++   +H+     G   S   R  
Sbjct: 258 EKRADPPLNEQYAVVVEHFRRMLDHYTPE-----VGVKIARKHLGWYVKGLYGSSEFRKA 312

Query: 297 LT 298
           + 
Sbjct: 313 VN 314


>gi|295394807|ref|ZP_06805022.1| dihydrouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
 gi|294972403|gb|EFG48263.1| dihydrouridine synthase [Brevibacterium mcbrellneri ATCC 49030]
          Length = 382

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 129/327 (39%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   T+  +R   R      L  TEM+   A++    K++     +  E P ++Q+ G D
Sbjct: 24  MAGITNTAFRRLCREY-GAGLYVTEMVTTRALVERSPKSMRIIHHEPYETPRSVQLYGVD 82

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALS 116
              + +A ++ VE+   + I+LN GCP  +V     G+ L    D+    +  A+ +A  
Sbjct: 83  PVTVGQAVRMLVEEDRADHIDLNFGCPVPKVTRKGGGSALPWKIDLFTAIVTTAVREAGD 142

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R G+D     +   +  +   ++GV  + +H R           +      D+
Sbjct: 143 IPVTVKMRKGID--ADHLTYLDAGQIAARAGVAAMTLHGRTT--------ADLYSGTADW 192

Query: 177 DIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +  +K    D + +  NG +     A  ++     DGV+IGR       +   +    
Sbjct: 193 DAIARLKDTIGDAIPVLGNGDIFSAEDAQAMMAKTGCDGVVIGRGCQGRPWLFGDLQAAL 252

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +       P    V +  +      + +Y     +    ++ + +H+   F G+P     
Sbjct: 253 NGSDERIRPNLGEVAQTVYTHGV-YLAEYYDDEFY---GVRDLRKHIAWYFKGYPVGGDL 308

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R  L   A  S+     +E    L+ E
Sbjct: 309 RKRL---AHVSS-----LEELRALLDE 327


>gi|167629403|ref|YP_001679902.1| dihydrouridine synthase tim-barrel nifr3 family protein
           [Heliobacterium modesticaldum Ice1]
 gi|167592143|gb|ABZ83891.1| dihydrouridine synthase tim-barrel nifr3 family protein
           [Heliobacterium modesticaldum Ice1]
          Length = 331

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 138/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   +      L+YTEMI   A+   ++  +  L  + + +P+A+QI G++
Sbjct: 25  MAGVTDKPFRTVLKE-HRCPLVYTEMISDKALTYANRNTMEILDITGEARPIAVQIFGSE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+IVE  G + I++N+GCP+ ++     GACL+  PD+  D   A+ +A+ +P
Sbjct: 84  PAVMAEAARIVEAAGASIIDINMGCPAPKIVRNGEGACLLKTPDLAVDIAEAVVRAVQVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG       +    L   ++  GV  + +H R         ++       D+ +
Sbjct: 144 VTVKMRIGWSSGR--IVAPELAPRLEAVGVQALTVHGRT--------REMFYSGQADWSV 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E  ++   + +  NG + +   AL++L       VMIGR    N  + + +  +    
Sbjct: 194 IAETVRQV-SIPVIGNGDVWEPDDALRMLVETGCAAVMIGRGCMGNPWIFSRLVHWAETG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P            +     ++          ++++  H+     G   + R R  
Sbjct: 253 EMPPPPSPEERINQALLHL-----EHIVALKGEERGVREMRGHLSWYLKGIRGASRLRAE 307

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +  +A    +   ++      +
Sbjct: 308 IN-QAPDRESVVRLLTEHREQV 328


>gi|117619221|ref|YP_857984.1| tRNA-dihydrouridine synthase B [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560628|gb|ABK37576.1| tRNA-dihydrouridine synthase B [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 321

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 127/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     L    +  +EM++A+  +   +K  +    S +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRL-GAGMAVSEMLLANPDVWDTQKTRMRMDHSAEGGLRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   +++N+GCP+ +V++   G+ L+  PD+V     A+  A+ +P
Sbjct: 76  PEMMAFAARYNVEQGAQIVDINMGCPAKKVNKKLAGSALLRQPDLVRTICRAVVDAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         + +      +YD 
Sbjct: 136 VTLKIRTGWDPDNRNGE--EIARIAEDCGIAALAVHGRT--------RTDLYRGEAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L    VD VMIGRAA     +   +  +    
Sbjct: 186 IRAIKQAV-SIPVVANGDIDSPEKARYVLDYTGVDAVMIGRAAQGRPWIFREIRHFLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +  V       ++     Y A         +   +H+          R  R  
Sbjct: 245 TKLPPPEREEVRTLMNEHVTNLHQFYGA-----YLGARIARKHVGWYLDEEETGREFRKH 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                  + A    +E  F+
Sbjct: 300 FNAL-DCADAQLEALEAYFD 318


>gi|253686643|ref|YP_003015833.1| TIM-barrel protein, nifR3 family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251753221|gb|ACT11297.1| TIM-barrel protein, nifR3 family [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 321

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 129/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++++ KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSSVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTIHGRT--------RACLFNGSAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIEHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|15602952|ref|NP_246024.1| hypothetical protein PM1087 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|12721426|gb|AAK03171.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 334

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 132/326 (40%), Gaps = 28/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L      +    A+QI G D
Sbjct: 19  MAGITDQPFRRICTHY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHHQEAGINAVQIAGCD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  + K++++P
Sbjct: 78  PDEMAKAAQINVEYGAEIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILNKVVKSVTVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + IH R         +        +YD 
Sbjct: 138 VTLKIRTGWDKDNRN--CLEIAKIAEQCGIQALTIHGRT--------RSCMFEGEAEYDN 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG +    +A  +L   + D +MIGR +  N  +   ++      
Sbjct: 188 IKAVKEQL-SIPIIANGDITSAEKAKYVLDYTNADAIMIGRGSLGNPWLFRVMESLIEKD 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF---PNSRRC 293
                P          + I      Y           +   +H+     G    P  R+ 
Sbjct: 247 SIVLEPSLNEKCNVILQHIQELHQFYGVE-----KGCRIARKHVAWYLQGIQPNPVFRQA 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
            + +T            +E  FNL++
Sbjct: 302 FNAITD----PKEQLIALEGFFNLIL 323


>gi|317126821|ref|YP_004093103.1| hypothetical protein Bcell_0081 [Bacillus cellulosilyticus DSM
           2522]
 gi|315471769|gb|ADU28372.1| TIM-barrel protein, nifR3 family [Bacillus cellulosilyticus DSM
           2522]
          Length = 331

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/310 (24%), Positives = 136/310 (43%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  ++++  +L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAILHKNQRSLKMLYVDDREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK+V+     + I++N+GCP  ++     GA  +LNPD + + ++ +  A+  
Sbjct: 77  KDTLVEAAKVVDKQTNADIIDINMGCPVPKITSCDAGARWLLNPDKIYEMVSYVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENAEAVERAGGKAVAVHGRTRV--------QMYEGEANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K    ++ +  NG ++    A +++    VDGVMIGRAA  N  ML     Y   
Sbjct: 187 IIRDVKNAV-NIPVIGNGDIKTPEDAKRMIDTTGVDGVMIGRAALGNPWMLYRTIHYLQT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   S   R+
Sbjct: 246 GENKPEPSDKEKM-----DVCILHMDRLVSLKGEVVAVREMRKHAAWYIKGMKGSSTLRN 300

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 301 AINSVTKRDD 310


>gi|282861786|ref|ZP_06270850.1| TIM-barrel protein, nifR3 family [Streptomyces sp. ACTE]
 gi|282563602|gb|EFB69140.1| TIM-barrel protein, nifR3 family [Streptomyces sp. ACTE]
          Length = 383

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 63/319 (19%), Positives = 122/319 (38%), Gaps = 21/319 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 28  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDASETPRSIQLYGV 87

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKAL 115
           D   + +A +++ +    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 88  DPVTVGKAVRMIVEEDLADHIDLNFGCPVPKVTRKGGGSALPFKRPLLRAILKEAVAGAG 147

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 148 DLPVTIKMRKGIDDD--HLTYLDAGRIAVEEGVTAVALHGRTT--------AQHYGGTAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 198 WEAIARLKEHVPEIPVLGNGDIWSADDALRMMRETGCDGVVVGRGCLGRPWLFGDLVAAF 257

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P   +V     R  +                +    +H+     GF      
Sbjct: 258 EGTGARQTPTLRQVADVMLRHATL----LGEWIGDESRGVIDFRKHVAWYLKGFAVGSEM 313

Query: 294 RHILTVEAGASTATHHIIE 312
           R  L V +        + E
Sbjct: 314 RRKLAVTSSLEELDAQLRE 332


>gi|216263891|ref|ZP_03435885.1| tRNA-dihydrouridine synthase A [Borrelia afzelii ACA-1]
 gi|215979935|gb|EEC20757.1| tRNA-dihydrouridine synthase A [Borrelia afzelii ACA-1]
          Length = 335

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 112/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNSKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   ++GACLM N + VG+ +  M +  + P+
Sbjct: 72  DALKAVQILEKHFNFDEYNLNVGCPSLKIQNANYGACLMSNANQVGEILKTMKETTNKPI 131

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              +++ VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRLLPSDYKNESYSEVKSFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LRHEFVYKLKKENKNLFIETNGGISNSEQIKKHLSVVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDKILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 302 RQNLTAPFPKNLRKHEILLKAMETLPEKI 330


>gi|111115049|ref|YP_709667.1| tRNA-dihydrouridine synthase A [Borrelia afzelii PKo]
 gi|110890323|gb|ABH01491.1| conserved hypothetical protein [Borrelia afzelii PKo]
          Length = 333

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 112/329 (34%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 10  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNSKN 69

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   ++GACLM N + VG+ +  M +  + P+
Sbjct: 70  DALKAVQILEKHFNFDEYNLNVGCPSLKIQNANYGACLMSNANQVGEILKTMKETTNKPI 129

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              +++ VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 130 SIKHRLGIRLLPSDYKNESYSEVKSFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++KKEN +LFI  NGG+ +  Q  K L  VD VMIGR+A++N   +      F
Sbjct: 190 LRHEFVYKLKKENKNLFIETNGGISNSEQIKKHLSVVDSVMIGRSAFENPYFIANASREF 249

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 250 ---LNETDKILTRKD------ILMQMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKKF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E +
Sbjct: 300 RQNLTAPFPKNLRKHEILLKAMETLPEKI 328


>gi|145634155|ref|ZP_01789866.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittAA]
 gi|229843962|ref|ZP_04464103.1| DNA-binding protein Fis [Haemophilus influenzae 6P18H1]
 gi|145268599|gb|EDK08592.1| ribosomal protein L11 methyltransferase [Haemophilus influenzae
           PittAA]
 gi|229812956|gb|EEP48644.1| DNA-binding protein Fis [Haemophilus influenzae 6P18H1]
          Length = 353

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 139/328 (42%), Gaps = 28/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L  +  E     A+QI G+D
Sbjct: 44  MAGITDQPFRRLC-AYYGAGLTFSEMMSTNPQVWHTEKSKLRLAHSEDLGLNAVQIAGSD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA I  ++G   I++N+GCP+ +V+    G+ L+  P +V   +  +  A+++P
Sbjct: 103 PLEMAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPYLVEKILREVVSAVNVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGRAA  N  +   V+    + 
Sbjct: 213 IKAVKQAI-AIPVIANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHN 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                P          R I      Y  +    G ++    +H+     G  P+S  ++ 
Sbjct: 272 SISQMPSLKEKCGQILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGIQPDSVFKQT 326

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
            + ++           ++E  FNL+++ 
Sbjct: 327 FNAISD----PKEQLIVLEDFFNLILDK 350


>gi|325123027|gb|ADY82550.1| tRNA-dihydrouridine synthase B [Acinetobacter calcoaceticus PHEA-2]
          Length = 341

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  + +G+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEDAGIAALALHGRT--------REDMYLNTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELINIPLIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKQVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYKVESTAEQAI--VVENYFNQLL 321


>gi|150026283|ref|YP_001297109.1| tRNA-dihydrouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772824|emb|CAL44308.1| Probable tRNA-dihydrouridine synthase [Flavobacterium psychrophilum
           JIP02/86]
          Length = 330

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 138/305 (45%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +L     L+Y+E I ++ ++R   K+   L     E+P+ +QI G D
Sbjct: 19  MEDVSDPPFRRLCKL-HGADLMYSEFISSEGLIRDAIKSRQKLDIFDYERPVGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV+    + +++N GCP  +V     GA ++ + D++     A+ ++ ++P
Sbjct: 78  EEAMAMSAKIVDAVHPDLVDINYGCPVKKVVCKGAGAGVLKDVDLMVRLTKAVIRSTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD   ++ +  + + ++  GV  + +HAR         +      + D+  
Sbjct: 138 VTVKTRLGWDD--NSINIDEVAERLQDIGVQALTVHART--------RAQMYKGHSDWTH 187

Query: 179 VYEIKKENPDL--FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP +   I  NG ++   +AL+      +DG+MIGRAA     +   +  YF+
Sbjct: 188 IERVKN-NPRITMPIFGNGDIDSPEKALEYKNKFGLDGMMIGRAAIGYPWIFNEIKHYFA 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P      +     ++ SM             + ++ RH    F G  + +  +
Sbjct: 247 TGEHLPAPTVIDRVEAARNHLTWSM-----DWKGERVGIVEMRRHYTNYFKGIHSFKEYK 301

Query: 295 HILTV 299
             L  
Sbjct: 302 QRLVT 306


>gi|228470160|ref|ZP_04055069.1| NifR3 family protein [Porphyromonas uenonis 60-3]
 gi|228308298|gb|EEK17153.1| NifR3 family protein [Porphyromonas uenonis 60-3]
          Length = 330

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 143/329 (43%), Gaps = 26/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +     +L+YTE I ADA++R     +  +     E+P+A+QI G D
Sbjct: 18  MEDVSDAPFRLLCKQF-GASLVYTEFISADALVRYVPSTMRKMRIDPAERPVAIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I      + ++LN GCP  RV     G+ ++  P+++ +  AA+  A + P
Sbjct: 77  VETMCEAARIACQLEPDLLDLNFGCPVKRVAGKGAGSGMLREPELLLEITAAVVAAANCP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  L   ++  G+  + IH R         + +    + D+ +
Sbjct: 137 VTVKTRLGWD--HNSLIITELAPRLQACGIAALTIHGRT--------RSDMYKGSADWTL 186

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+ + NP+  + I  NG +    +         VDGVM+GRAA     +   +     
Sbjct: 187 IGEV-RSNPEIQIPIIGNGDITTGEEVRHAFDTYGVDGVMVGRAAIGQPWIFGEMRAAVD 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              T       ++      +I   +       L     +    RH+    LF G PN R 
Sbjct: 246 PTFTAP-----KLSSQQQLEILKEIVHKNIEKLDERRGILHSRRHLAATPLFKGIPNFRA 300

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R I  ++A        ++     L+ ++
Sbjct: 301 LR-IAMLQAPTLADLDDVLAQVEPLLPQT 328


>gi|38605042|sp|Q9CLW3|DUSB_PASMU RecName: Full=tRNA-dihydrouridine synthase B
          Length = 332

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 132/326 (40%), Gaps = 28/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L      +    A+QI G D
Sbjct: 17  MAGITDQPFRRICTHY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHHQEAGINAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  + K++++P
Sbjct: 76  PDEMAKAAQINVEYGAEIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILNKVVKSVTVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDKDNRN--CLEIAKIAEQCGIQALTIHGRT--------RSCMFEGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG +    +A  +L   + D +MIGR +  N  +   ++      
Sbjct: 186 IKAVKEQL-SIPIIANGDITSAEKAKYVLDYTNADAIMIGRGSLGNPWLFRVMESLIEKD 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF---PNSRRC 293
                P          + I      Y           +   +H+     G    P  R+ 
Sbjct: 245 SIVLEPSLNEKCNVILQHIQELHQFYGVE-----KGCRIARKHVAWYLQGIQPNPVFRQA 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
            + +T            +E  FNL++
Sbjct: 300 FNAITD----PKEQLIALEGFFNLIL 321


>gi|224534214|ref|ZP_03674792.1| tRNA-dihydrouridine synthase A [Borrelia spielmanii A14S]
 gi|224514316|gb|EEF84632.1| tRNA-dihydrouridine synthase A [Borrelia spielmanii A14S]
          Length = 335

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 111/329 (33%), Positives = 177/329 (53%), Gaps = 17/329 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ GD K I+  +  E P+A+QI     +
Sbjct: 12  MVNITDEHFRYLIRLLSKKVTLYTPMISAKSIIMGDVKKIVKQTPLESPIAIQIATNCKN 71

Query: 61  KLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             ++A +I+E    ++E NLNVGCPS ++   ++GACLM   D VG  +  M +  + P+
Sbjct: 72  DALKAIQILEKHFNFDEYNLNVGCPSLKIQNANYGACLMSKADQVGKILKTMKENTNKPI 131

Query: 120 TVKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K R+G+              +++ VK I   G+    +HAR AILKG SPK+NR IP 
Sbjct: 132 SIKHRLGIRLLPSDYKNESYSEVKSFVKIISDFGIKNFIVHARVAILKGFSPKNNRNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L ++ VY++K EN +LFI +NGG+ ++ Q  K L  VD VMIGR+A++N   +      F
Sbjct: 192 LKHEFVYKLKNENKNLFIEINGGINNLEQIKKHLSVVDSVMIGRSAFENPYFIANASREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  +  I TR D      I   M +Y   +  +   +  + +H++G+      +++ 
Sbjct: 252 ---LNETDKILTRKD------ILMKMVEYIKEY-ENYLSINILFKHLMGITFSKEGAKKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  LT     +   H I+  A   + E++
Sbjct: 302 RQNLTAPFPKNLRKHEILLKAIETLPETI 330


>gi|312136045|ref|YP_004003383.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor owensensis
           OL]
 gi|311776096|gb|ADQ05583.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor owensensis
           OL]
          Length = 328

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 138/303 (45%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R        N +  TEM+ + A++ G  K   ++ FS +EK   +QI G+D
Sbjct: 13  MAGFTDKVFRRLCSRFGAN-VTVTEMVSSKALVLGSTKTKELISFSQEEKIRGVQIFGSD 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++ +   G  LM NP +    + ++ K    
Sbjct: 72  PKVMAQSVKILQDEFEYDFIDINMGCPVPKLVKSGEGCALMKNPSLASRIVESIAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D++  ++        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDEE--SINAPEFAYILQESGASFVTVHGRT--------RTQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K++   + +  NG + D   A ++      D +MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVKEKV-KIPVVANGDITDFESAKRVYEVTGADSIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T+V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETKVLPHMKIRVAIEFFRQLCSEKGEKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 RIN 298


>gi|312884763|ref|ZP_07744464.1| NifR3/Smm1 family protein [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367676|gb|EFP95227.1| NifR3/Smm1 family protein [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 322

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 123/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDIIEDILRAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +  G+    +H R         K        +YD 
Sbjct: 136 VTLKTRTGWDTENKNCVH--IAKLAEDCGIQAFALHGRT--------KACMYKGLAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  +  N 
Sbjct: 186 IKAVKQAI-SIPVIANGDIDSPERAKHVLDYTGADALMIGRPAQGRPWIFQEIQHFLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       + A    Y           +   +H+         +   R  
Sbjct: 245 TTMPPLPYQEVKSILLGHVIALHEFY-----GEYLGPRIARKHVGWYLKEHEQACEFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                  +      +E  F+ +
Sbjct: 300 FNA-IDVAELQLEALEGYFDNV 320


>gi|227327926|ref|ZP_03831950.1| tRNA-dihydrouridine synthase B [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 321

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTIHGRT--------RACLFNGFAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIEHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|251793182|ref|YP_003007910.1| tRNA-dihydrouridine synthase B [Aggregatibacter aphrophilus NJ8700]
 gi|247534577|gb|ACS97823.1| tRNA-dihydrouridine synthase B [Aggregatibacter aphrophilus NJ8700]
          Length = 320

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 134/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRICATY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHHQEAGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  P +V   +  + K++ +P
Sbjct: 76  PDEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPQLVRQILETVVKSVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  ++SG+  + IH R         +  +     +Y+ 
Sbjct: 136 VTLKIRTGWDLENRN--CVEIAKIAEQSGIQALTIHGRT--------RACKFEGEAEYEH 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG +    +A  +L     DG+MIGR A     +  +V     + 
Sbjct: 186 IRLVKQQV-SIPVIANGDITSAQKAKAVLDYTGADGIMIGRGALGRPWLFQSVVGLVEHD 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +   + I      Y       G ++    +H+             +  
Sbjct: 245 SIIQEPSSEEKCRVILQHICELHRFYGEE---KGYRI--ARKHIAWYLQDIQPDSVFKQD 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 +++A    +E  F+L+
Sbjct: 300 FNA-ITSASAQLAALERFFSLI 320


>gi|332874803|ref|ZP_08442673.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6014059]
 gi|332737064|gb|EGJ68021.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6014059]
          Length = 348

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 24  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 83  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 143 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 193 IKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 252 EHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 306

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 307 MYKVETTAEQAL--VVESYFNQLL 328


>gi|261379246|ref|ZP_05983819.1| tRNA-dihydrouridine synthase B [Neisseria subflava NJ9703]
 gi|284797670|gb|EFC53017.1| tRNA-dihydrouridine synthase B [Neisseria subflava NJ9703]
          Length = 334

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 136/325 (41%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPSLRHTKKTLRRSDFEGEGGVVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +V + + A+  A+ +P
Sbjct: 76  PQQMAEAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAEILEAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  ++     L  + K  ++SG+  + IH R         +         Y++
Sbjct: 136 VTLKTRLGWHNEHQN--LPTIAKIAEESGIAALAIHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A  +  +   +  Y  + 
Sbjct: 186 IAETKGRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGSPWLFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +      +      I A    Y          ++   +H+       PN  + R  
Sbjct: 245 VLPPALSLAECNATILNHIRAMYEFY-----GEVAGVRIARKHIGWYIDEMPNGEQTRRD 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A +  +      + E 
Sbjct: 300 IN-RLDSAAAQYDTLAAYLETLSEK 323


>gi|332300620|ref|YP_004442541.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica DSM
           20707]
 gi|332177683|gb|AEE13373.1| TIM-barrel protein, nifR3 family [Porphyromonas asaccharolytica DSM
           20707]
          Length = 331

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 133/302 (44%), Gaps = 25/302 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +     +L+YTE I ADA++R     +  +     E+P+A+QI G +
Sbjct: 18  MEDVSDAPFRLLCKQF-GASLVYTEFISADALVRYVPSTMRKMRIDPAERPVAIQIYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I      + ++LN GCP  RV     G+ ++ +P+++ +  AA+  A S P
Sbjct: 77  VETMCEAARIACQLEPDLLDLNFGCPVKRVAGKGAGSGMLRDPELLLEITAAVVAAASCP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  L   ++  G+  + IH R         + +    + D+ +
Sbjct: 137 VTVKTRLGWD--HNSLIITELAPRLQACGIAALTIHGRT--------RSDMYKGSADWTL 186

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + E+ + NP+  + I  NG +    +         VDGVM+GRAA     +   +     
Sbjct: 187 IGEV-RSNPEIQIPIIGNGDITTGEEVRHAFDTYGVDGVMVGRAAIGQPWIFGEMRAAVD 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
              T       +       +I   +       L     +    RH+    LF G PN R 
Sbjct: 246 PTFTAPQLTSQQQL-----EILKEIVHKNIEKLDERRGILHSRRHLAATPLFKGIPNFRA 300

Query: 293 CR 294
            R
Sbjct: 301 LR 302


>gi|329770278|ref|ZP_08261666.1| tRNA-dihydrouridine synthase 1 [Gemella sanguinis M325]
 gi|328836836|gb|EGF86484.1| tRNA-dihydrouridine synthase 1 [Gemella sanguinis M325]
          Length = 335

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/303 (26%), Positives = 138/303 (45%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  +KK +  L    +E+PL+LQI G +
Sbjct: 18  MAGVCNAAFRLTAKEF-GAGLVCAEMVSDKAILFNNKKTMNMLYIDPRERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  LVEAAK V+     + I+LN+GCP  ++ +   G+ L+L+PD V + I+ +  ++S 
Sbjct: 77  IDTLVEAAKYVDKNTEADIIDLNMGCPVPKITKVDAGSKLLLDPDKVYEVISRIVDSVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD+   + + +  ++ +++G + + IH R  +               ++D
Sbjct: 137 PVTVKMRMGWDDE--HIFVMDNARNAERAGASAVAIHGRTKV--------QMYSGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++KKE   + +  NG +     A K+L   + D VMIGRAA  N  ML    +Y   
Sbjct: 187 VIRDVKKEL-KIPVIGNGDVTTPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   M             + ++ +H      G     + + 
Sbjct: 246 GELTPEPTPREKIDVCLLHLRRLM-----EIKPEKVAVHEMRKHAAYYMKGIKGGAKVKK 300

Query: 296 ILT 298
            L 
Sbjct: 301 ELN 303


>gi|172087771|ref|YP_205772.2| tRNA-dihydrouridine synthase B [Vibrio fischeri ES114]
 gi|171902358|gb|AAW86884.2| tRNA-dihydrouridine synthase B [Vibrio fischeri ES114]
          Length = 349

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 64/324 (19%), Positives = 127/324 (39%), Gaps = 26/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI GAD
Sbjct: 44  MAGVTDRPFRELCMRY-GAGMAVSEMMSSNPKLWKTSKSQNRMVHEGESGIRSVQIAGAD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ + + A+  A+ +P
Sbjct: 103 PKLMAEAAQHCVETGAQIIDINMGCPAKKVNKKLAGSALLQRPDLIEEILLAVVNAVDVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +        +YD 
Sbjct: 163 VTLKTRTGWDPDNRN--CVQVAKMAEQCGIQALALHGRT--------RACMYKGEAEYDN 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y    
Sbjct: 213 IKAVKEAI-SIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFKEIQHYLETG 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       + A    Y           +   +H+         +   R  
Sbjct: 272 ELMPPLPIEEVKATLLGHVHALHQFYGEF-----LGPRIARKHVGWYLKEHEQANDFRR- 325

Query: 297 LTVEAGASTATHHI--IETAFNLM 318
            +  A    A+  +  +E+ F+ +
Sbjct: 326 -SFNAI-EDASLQLSQLESYFDHV 347


>gi|254496444|ref|ZP_05109322.1| tRNA-dihydrouridine synthase A [Legionella drancourtii LLAP12]
 gi|254354340|gb|EET12997.1| tRNA-dihydrouridine synthase A [Legionella drancourtii LLAP12]
          Length = 305

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 110/311 (35%), Positives = 156/311 (50%), Gaps = 12/311 (3%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
            R+L  +ALLYTEM    AI + + +  L F+ QE PLALQ+GG+D   L   AK+ E  
Sbjct: 1   MRILAPHALLYTEMQTTGAI-QNNPRRSLPFNHQEHPLALQLGGSDPGALGRCAKLAEQE 59

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY+E+N+N+GCPS +V  G FGACLM  P  V  CI AM +  SIPVT K RIG+D Q  
Sbjct: 60  GYDEVNINLGCPSDKVKAGHFGACLMNEPAQVMACIKAMREETSIPVTAKVRIGIDHQDS 119

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                  V+ +  +G   I +HARKA L GLSPK NR +P ++YD VY IKKE P + + 
Sbjct: 120 YEFFSAFVQQLIAAGSQKIIVHARKAWLNGLSPKQNRTVPPVNYDYVYRIKKEIPHIPVV 179

Query: 193 LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           +NG + +  +  + L  VDGVM+GR A  N   +  + E               + K   
Sbjct: 180 INGNILNSQEINEHLHYVDGVMLGRLACDNPYQIAEIHEILY----------PSMQKLTR 229

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT-VEAGASTATHHII 311
            +      DY       G  L  + + +  L  G   + + +  L  +      +    +
Sbjct: 230 SEAFIRYLDYLFDEHSKGVSLSLLIKPVFNLAFGLSGASQWKKKLMLILQTKDLSLFDSL 289

Query: 312 ETAFNLMIESL 322
                 + ES+
Sbjct: 290 TQYLVEIEESM 300


>gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or NifR3-like protein [Herbaspirillum
           seropedicae SmR1]
 gi|300072539|gb|ADJ61938.1| tRNA-dihydrouridine synthase protein or NifR3-like protein
           [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 63/299 (21%), Positives = 121/299 (40%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  +D  L   +K    +    + +P A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMAASDPRLWQSEKTSRRINHDGEMEPKAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L + AK   + G   I++N+GCP  +V     G+ L+ + ++V   + A+  A+ +P
Sbjct: 76  PVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +          +    + +G+  + +H R         + +      +Y+ 
Sbjct: 136 VTLKFRTGWNRANKNA--LKIAARAEAAGIAMLTLHGRT--------RADGYSGEAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +  L   D VM+GRAA     +   +D +    
Sbjct: 186 IAAVK-AAVKIPVVANGDITTPEKARDVLLLTKADAVMVGRAAQGRPWIFREIDHFLRTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +P+ + V++     + A    Y          ++   +H+       P   + R 
Sbjct: 245 EHLPAPLVSEVEQLMDEHLQAHYAFY-----GDYLGVRTARKHIGWYVRDLPGGEQFRR 298


>gi|222530304|ref|YP_002574186.1| NifR3 family protein [Caldicellulosiruptor bescii DSM 6725]
 gi|222457151|gb|ACM61413.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor bescii DSM
           6725]
          Length = 328

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 132/303 (43%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEMI + A++ G  K   ++ FS +EK   +QI G D
Sbjct: 13  MAGFTDKVFRRLCSRF-GADVTVTEMISSKALVLGSAKTKDLISFSEEEKIRGVQIFGND 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++     G  LM NP +    +  + K    
Sbjct: 72  PEVMAQSVKILQDEFEYHFIDINMGCPVPKLVRSGEGCALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G DD+   +        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDDE--NINAPEFAYILQESGASFVTVHGRT--------RAQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K++   + +  NG + D   A K       D +MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVKEKL-KIPVIANGDIVDFESAKKAYEVTRADSIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T+V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETKVLPHMKIRVAIEFFTQLCSEKGDKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 KIN 298


>gi|50364844|ref|YP_053269.1| tRNA dihydrouridine synthetase [Mesoplasma florum L1]
 gi|50363400|gb|AAT75385.1| tRNA dihydrouridine synthetase [Mesoplasma florum L1]
          Length = 325

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 138/309 (44%), Gaps = 23/309 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  ++      L+  EM+  + +   +KK   +L    +E P+++QI G D
Sbjct: 17  MAGVSNPPFRLISKE-KGADLVCAEMVSVEGMTHNNKKTFSMLAVEKKEHPMSMQIFGND 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   + A K +++    + I+LN+GCP+ +V    + G+ L+  P+++ D + A+ +  S
Sbjct: 76  VESFIVATKWIDENVDCDIIDLNIGCPAPKVAVRSASGSSLLKTPELIYDIVKAVVENTS 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R+G D +  +V    + K I+K+G +GI +H R         +      + D+
Sbjct: 136 KPVTAKIRLGWDKE--SVNAVEVSKLIEKAGASGITVHGRT--------RSEFYSGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+K E  ++ +  NG + D   A  +L     DGVMI R    N  +   +  +  
Sbjct: 186 EKIKEVK-EAVNIPVIGNGDVIDGPSAKAMLELTGCDGVMISRGCQGNPWIFREIAHFLE 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +   +  +  + DY       G  +++  +H+   F   P +    
Sbjct: 245 TGEELDKPSFAEWKETVLKH-AKMLIDYKQ---DEGSAIREFRKHLTWYFAALPKTEIL- 299

Query: 295 HILTVEAGA 303
           + L  EA  
Sbjct: 300 NQLKEEANK 308


>gi|260596118|ref|YP_003208689.1| tRNA-dihydrouridine synthase B [Cronobacter turicensis z3032]
 gi|260215295|emb|CBA27235.1| tRNA-dihydrouridine synthase B [Cronobacter turicensis z3032]
          Length = 327

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 23  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPEVWASDKSRLRMVHVDEPGIRTVQIAGSV 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  D G   I++N+GCP+ +V+    G+ L+  P++V   + A+  A+ +P
Sbjct: 82  PEEMAEAARINVDNGAQIIDINMGCPAKKVNRKLAGSALLQYPELVKSILTAVVNAVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +      N +YD 
Sbjct: 142 VTLKIRTGWDP--ANRNCVEIAQLAEECGIQALTIHGRT--------RACLFQGNAEYDS 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG +    +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 192 IRTVKQKV-SIPVIANGDITSPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 251 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVAWYLQEHAPDDQFRRT 305

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 306 FNAIEDASE-QLEALEAYFE 324


>gi|227114010|ref|ZP_03827666.1| tRNA-dihydrouridine synthase B [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 321

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++++ KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSSVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTIHGRT--------RACLFNGFAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIEHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|197119180|ref|YP_002139607.1| TIM barrel oxidoreductase NifR3 [Geobacter bemidjiensis Bem]
 gi|197088540|gb|ACH39811.1| TIM barrel oxidoreductase NifR3 [Geobacter bemidjiensis Bem]
          Length = 321

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 134/325 (41%), Gaps = 28/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+   R  +R     +  +TEM+  + + R  +K+  +L  S +++P+ +Q+ G D
Sbjct: 21  MAGITNLPMRIISRE-GGASFAFTEMVSVNGLTREGQKSFDLLKSSPEDRPIGMQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++VE++G   I++N+GCP  +V     G+ LM +P  VG  + ++  A  +P
Sbjct: 80  PEMLAEAARLVEEYG-ELIDINMGCPVRKVVGTGAGSALMKDPQKVGRIVRSVRAATKLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G            + +  ++ G + + +H R         +        D+  
Sbjct: 139 LTIKIRTGWVCGDD--TFLEVGRIAQEEGCDAVTLHPRS--------RAQMFEGKADWSR 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  +G L   + A+ +L     D VM+ R A  N  +        +  
Sbjct: 189 IGELKSAL-SIPVIGSGDLFSAADAVGMLAETGCDSVMVARGAMGNPWIFREALSLLAGE 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 ++ R+       +S    +  A        L ++ +H+     G P + + R  
Sbjct: 248 EPAPPTVQERL------AVSRRHLELFAEFAGGRVALMEMRKHLSWYSKGLPGAAQFRAA 301

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +        +   +I  A     ++
Sbjct: 302 VN----RIESAPELI-RAMEEFFDA 321


>gi|306821056|ref|ZP_07454674.1| tRNA-dihydrouridine synthase [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550892|gb|EFM38865.1| tRNA-dihydrouridine synthase [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 329

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 146/324 (45%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  +R        N   +TEMI A A+   D+K   +L  S Q+K + +QI G++
Sbjct: 25  MAGFTDLPFRLICEEYGCN-FTFTEMINAKALCYHDEKTTQMLDVSGQKKYVGVQIFGSE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  + +A KI+ D   ++ I++N+GCP+ ++ +   G+ LM NP +    +    K  SI
Sbjct: 84  IEYIGKAVKIINDLERFSHIDINMGCPAPKIVKNGDGSALMKNPSLASKIVEEAKKNSSI 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      K +++SG + I +H R                  D+D
Sbjct: 144 PVTVKIRKGFDEH--NINAVEFAKMLEQSGADAITVHGRTT--------RQYYSGVADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+    + +  NG ++    A +++   S D V+I RAA  N  +   +++YF N
Sbjct: 194 IIAEVKQAV-KVPVIGNGDVKSPEDAKRMMEYTSCDSVLIARAAQGNPFLFAQINDYFEN 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     RV      +I+      +     +   ++++ + +     G  NS   ++
Sbjct: 253 GSYDDIQDSQRV------EIALKHYKLSMEKFETSIAVREMRKQINCYLKGIKNSCVVKN 306

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
            + ++         ++E     +I
Sbjct: 307 QINMQ-NDYEKVIEMLENFAKSLI 329


>gi|332519407|ref|ZP_08395874.1| TIM-barrel protein, nifR3 family [Lacinutrix algicola 5H-3-7-4]
 gi|332045255|gb|EGI81448.1| TIM-barrel protein, nifR3 family [Lacinutrix algicola 5H-3-7-4]
          Length = 331

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 136/321 (42%), Gaps = 24/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE + ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFVSSEGLIRNAAKSVMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++E   IV     + I++N GCP  +V     GA ++ +  ++    A M K  +IP
Sbjct: 78  MDSMLETIDIVSASNPDIIDINFGCPVKKVVSKGAGAGILKDICLMEQLTAEMVKRTNIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +        D+  
Sbjct: 138 ITVKTRLGWD--HDSIKIVEVAERLQDVGCKAIAIHGRT--------RAQMYKGEADWKP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + +  NG +    +A+++     +DG MIGRA   N      V  +F  
Sbjct: 188 IAQVKNNPRMHIPVFGNGDVTSPERAMEMRDDYGLDGCMIGRATIGNPWFFKQVKHFFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 PI  +   +  R+      D+    L     + +  RH    F G P+ +  R 
Sbjct: 248 GEHY-RPITMQERVEAARRHLQMSIDWKGEVLG----VFETRRHYTNYFKGIPHFKEYRM 302

Query: 296 ILTVEAGAST---ATHHIIET 313
            +     +     A   ++E 
Sbjct: 303 KMVTSDDSKDVFAAFDEVLEK 323


>gi|328882334|emb|CCA55573.1| tRNA dihydrouridine synthase B [Streptomyces venezuelae ATCC 10712]
          Length = 389

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 128/319 (40%), Gaps = 20/319 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E+P ++Q+ G 
Sbjct: 33  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDATEQPRSIQLYGV 92

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 93  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILHEAVTNAG 152

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 153 DLPVTMKMRKGIDDD--HITFLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 202

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 203 WDAIARLKEHVPEIPVLGNGDIWSADDALRMMRETGCDGVVVGRGCLGRPWLFADLVAAF 262

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                G +    R   D   + +  + ++          +    +H+     GF      
Sbjct: 263 EGTGGGYAQPGLREVADAMVRHARLLGEWLG---DEARGVIDFRKHVAWYLKGFSVGSEM 319

Query: 294 RHILTVEAGASTATHHIIE 312
           R  L + +     +  + E
Sbjct: 320 RKKLAITSSLDELSAQLSE 338


>gi|238754658|ref|ZP_04616011.1| tRNA-dihydrouridine synthase B [Yersinia ruckeri ATCC 29473]
 gi|238707117|gb|EEP99481.1| tRNA-dihydrouridine synthase B [Yersinia ruckeri ATCC 29473]
          Length = 321

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 123/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRALCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   ++A+  A+ +P
Sbjct: 76  PDDMAAAARINVAGGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CIEIAQLAESCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQHV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPMPLGEVQRLLNGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|296329583|ref|ZP_06872069.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305672780|ref|YP_003864451.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|296153326|gb|EFG94189.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305411023|gb|ADM36141.1| tRNA-dihydrouridine synthase B [Bacillus subtilis subsp. spizizenii
           str. W23]
          Length = 333

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 142/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + + +  L    +EKPL+LQI G  
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILYNNARTMGMLYIDEREKPLSLQIFGGK 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+PD + + ++A+  A+  
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +      K+++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAVENAKAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ +  + +  NG ++    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKDVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   +   R+
Sbjct: 246 GELKEEPQVREKM-----AVCKLHLDRLINLKGENVAVREMRKHAAWYLKGVRGNANVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF + +E+
Sbjct: 301 EINHCETREEFVQ--LLDAFTVEVEA 324


>gi|293374618|ref|ZP_06620934.1| TIM-barrel protein, nifR3 family [Turicibacter sanguinis PC909]
 gi|325841874|ref|ZP_08167505.1| TIM-barrel protein, nifR3 family [Turicibacter sp. HGF1]
 gi|292646768|gb|EFF64762.1| TIM-barrel protein, nifR3 family [Turicibacter sanguinis PC909]
 gi|325489829|gb|EGC92182.1| TIM-barrel protein, nifR3 family [Turicibacter sp. HGF1]
          Length = 336

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 76/304 (25%), Positives = 132/304 (43%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   + +    L+Y EM+   A++  +KK   +L     E+PL++QI G+D
Sbjct: 19  MAGVCNAAFRTIIKEM-GTGLIYAEMVSDKAVVYQNKKTLDMLYVDPAERPLSMQIFGSD 77

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
               VEAAK V+     + I++N+GCP  +V +   GA L+L PD + D +A +   +  
Sbjct: 78  KETFVEAAKYVDANCDCDIIDINMGCPVPKVTKNEAGARLLLEPDKIYDIVANVVDVVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +        L   I+++G + I +H R         +        D+ 
Sbjct: 138 PVTVKMRTGWDKEHIYAIENAL--KIEQAGASAIAVHGRT--------RSQMYEGKADWG 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K     + +  NG +     A ++L    VDG+MIGRAA  N  ++  +  Y + 
Sbjct: 188 IIKDVKDAIKTIPVIGNGDINSPEMAKRVLEESGVDGIMIGRAALGNPWLMKKIVHYLAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++    D           L ++  HM     G   +   + 
Sbjct: 248 DELIEEPSAHEKLR-----LAVDHMDRLIDLKCEKVALLEMRSHMAWYIKGLEGATHVKR 302

Query: 296 ILTV 299
           ++T 
Sbjct: 303 MITT 306


>gi|291458632|ref|ZP_06598022.1| tRNA-dihydrouridine synthase B [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291419165|gb|EFE92884.1| tRNA-dihydrouridine synthase B [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 316

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 128/309 (41%), Gaps = 22/309 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R         AL  TEM+ A A+L   +    IL     E PLA+Q+ G+D
Sbjct: 17  MAGVTDLPFRILCEE-QGIALSCTEMVSAKAVLYESRNTEAILERGKGESPLAVQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A  +E+  ++ +++N+GCP  ++     G+ LM  P++ G  I AM   +  P
Sbjct: 76  PEIMGEIAVRLEER-FDVLDVNMGCPVPKIVRNGEGSALMRKPELAGRIIKAMVSRVHKP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G              K ++ +G   + +H R         ++       D+++
Sbjct: 135 VTVKFRKGFSAGESTA--PEFAKRMEDAGAAAVTVHGRT--------REQYYSGKADWEV 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     A ++L    VDG+ + RA   N  ++     +  + 
Sbjct: 185 LRSVK-EAVSIPVIGNGDVFSPEDAKRMLKSTGVDGIALARAVRGNPWLIRRTVLFLESG 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P      +   R I A M +Y    +     ++++ +H+     G P S   R  
Sbjct: 244 VLPEEPGLEERLRLMERHI-ALMVEYKGERVA----VREMRKHLSWYTAGLPRSSDFRRR 298

Query: 297 LTVEAGAST 305
           +     +  
Sbjct: 299 VNAAETSEE 307


>gi|209696242|ref|YP_002264172.1| tRNA-dihydrouridine synthase B [Aliivibrio salmonicida LFI1238]
 gi|208010195|emb|CAQ80522.1| tRNA-dihydrouridine synthase B [Aliivibrio salmonicida LFI1238]
          Length = 322

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 63/324 (19%), Positives = 126/324 (38%), Gaps = 26/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD+ +R          +  +EM+ ++  L    K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDKPFRELCMRY-GAGMAVSEMMSSNPKLWKTSKSQNRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ + + A+ KA+ +P
Sbjct: 76  PKLMAEAARYCVETGAQIIDINMGCPAKKVNKKLAGSALLQRPDLIEEILLAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  ++ G+  + +H R         +      + +YD 
Sbjct: 136 VTLKTRTGWDPDNRN--CVQVAKMAEQCGIQALALHGRT--------RACMYKGDAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y    
Sbjct: 186 IKAVKEAI-SIPVIANGDIDSPEKARFVLDYTGADALMIGRPAQGRPWIFQEIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       + A    Y           +   +H+         +   R  
Sbjct: 245 EFMPPLPIEEVKATLLGHVQALHLFYGEF-----LGPRIARKHVGWYLKEHEQANEFRRG 299

Query: 297 LT--VEAGASTATHHIIETAFNLM 318
                +A         +E+ F+ +
Sbjct: 300 FNAIEDAHQQ---LQQLESYFDHV 320


>gi|239501090|ref|ZP_04660400.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB900]
 gi|193077993|gb|ABO12912.2| putative protein NifR3 family [Acinetobacter baumannii ATCC 17978]
 gi|322509004|gb|ADX04458.1| dusB [Acinetobacter baumannii 1656-2]
 gi|323518988|gb|ADX93369.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 341

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 300 MYKVETTAEQAL--VVESYFNQLL 321


>gi|307544768|ref|YP_003897247.1| hypothetical protein HELO_2178 [Halomonas elongata DSM 2581]
 gi|307216792|emb|CBV42062.1| putative TIM-barrel protein, nifR3 family [Halomonas elongata DSM
           2581]
          Length = 363

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 73/290 (25%), Positives = 131/290 (45%), Gaps = 21/290 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TDR +R  AR L    L+  EM+ +D  L   +K+ L      +  P A+QI G D
Sbjct: 35  MAGVTDRPFRALARRL-GAGLVVGEMVTSDPNLWHTRKSRLRMDHRGEPGPRAVQIAGGD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA++  + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ IP
Sbjct: 94  AAMLAEAARLNAEMGAEVIDINMGCPAKKVCNKAAGSALLRDEALVAEILDAVVAAVDIP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  + +G+  + +H R         +  R     +YD 
Sbjct: 154 VTLKIRTGWCAESNNGV--RVARLAESAGIQALAVHGRH--------RQQRYGGEAEYDT 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK     + +  NG ++   +A ++L     D VMIGR A  N  +   +D Y  + 
Sbjct: 204 IAAIKAAVG-IPVFANGDIDSPEKARRVLDYTGADAVMIGRGAQGNPWIFREIDHYLRHG 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
              + P  T       R   +++ D+   H+     ++   +H+     G
Sbjct: 263 RRMAPPDDTERAA-VLRDHLSALHDFYGEHMG----VRIARKHIGWYLAG 307


>gi|212637921|ref|YP_002314441.1| tRNA-dihydrouridine synthase [Anoxybacillus flavithermus WK1]
 gi|212559401|gb|ACJ32456.1| tRNA-dihydrouridine synthase [Anoxybacillus flavithermus WK1]
          Length = 351

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 139/313 (44%), Gaps = 28/313 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L    +EKPL+LQI G +
Sbjct: 36  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILFNNPKTMGMLYIDEREKPLSLQIFGGE 94

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+     + I++N+GCP  ++ +   GA  +L+P+ + D +AA+  A+  
Sbjct: 95  KETLVQAAKYVDQHTNADIIDINMGCPVPKITKCDAGAKWLLDPNKIYDMVAAVVDAVEK 154

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+           ++++++G   + +H R  +               D++
Sbjct: 155 PVTVKMRIGWDENHIYAV--ENAQAVERAGGQAVAVHGRTRV--------QMYEGKADWN 204

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K E   + +  NG ++    A ++L    VDGVMIGRAA  N  M+     Y   
Sbjct: 205 VIKQVK-EAVRIPVIGNGDVQTPQDAKRMLEQTGVDGVMIGRAALGNPWMIYRTVRYLET 263

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                 P    K  V      ++ A   +Y A        ++++ +H      G   + +
Sbjct: 264 GELIPEPSVREKIEVCILHLDRLIALKNEYIA--------VKEMRKHAAWYLKGIRGNAK 315

Query: 293 CRHILTVEAGAST 305
            R+ +        
Sbjct: 316 VRNAINECQTRDE 328


>gi|85708679|ref|ZP_01039745.1| tRNA-dihydrouridine synthase [Erythrobacter sp. NAP1]
 gi|85690213|gb|EAQ30216.1| tRNA-dihydrouridine synthase [Erythrobacter sp. NAP1]
          Length = 340

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 132/299 (44%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   R    + L  TEMI ++A +R  ++++    +   E+P+++Q+ G D
Sbjct: 29  MTGVTDMPFRTLVRRY-GSGLNVTEMIASEAAIRETRQSVQKAEWDKTEEPVSMQLVGCD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S + EAAK+ E  G   I++N GCP  +V     G+ LM    +    + A  KA+ +P
Sbjct: 88  PSSMGEAAKLQEGNGAAIIDINFGCPVRKVVGQFAGSALMREVPLATKLMEATVKAVDVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D Q  ++    + +  +  GV  I +H R         ++     + D+  
Sbjct: 148 VTVKMRMGWDHQ--SLNAPEMARIAEDLGVKMITVHGRT--------RNQMYKGSADWSF 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E  ++ + +NG +  +  A   L     DG+MIGR AY    +L  V  ++   
Sbjct: 198 IRKVK-EAVNIPVIVNGDICTIQDAATALEQSGADGLMIGRGAYGKPWLLGQVMHWWRTG 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +  +P                +  Y     + G K+    +H+     G   S   R+
Sbjct: 257 ESIPTPSFDEQYSVLVEHYHRMLDHYGR---NVGTKI--ARKHLGWYTKGMHGSAEFRN 310


>gi|50119216|ref|YP_048383.1| tRNA-dihydrouridine synthase B [Pectobacterium atrosepticum
           SCRI1043]
 gi|49609742|emb|CAG73176.1| putative dihydrourdine synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 321

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAAARINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTIHGRT--------RACLFNGFAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLAPLPLVEVKRLLIEHIRELHDFY-----GPGKGFRIARKHVSWYIQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|254796745|ref|YP_003081581.1| NifR3 family protein [Neorickettsia risticii str. Illinois]
 gi|254589992|gb|ACT69354.1| NifR3 family protein [Neorickettsia risticii str. Illinois]
          Length = 313

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 119/304 (39%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  YR   +      L+ +EMI + A++   K  +     S +E   A+Q+ G +
Sbjct: 1   MSGVTDMPYRDLVKSF-GAGLVVSEMIASRAMILKTKDTMKKVSLSPREDITAIQLAGFE 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAKI ED G   I++N GCP  +V  G  G+ LM +       +    KA+ IP
Sbjct: 60  PDVMAEAAKINEDMGAKIIDINFGCPVKKVVNGYAGSYLMKDECHAAKILETTVKAVKIP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+         L K  +  G+  I IH R         +        D+  
Sbjct: 120 VTLKMRTGWDENHRNA--PKLAKIAEDLGIKMITIHGRT--------RAQMYKGKSDWQF 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++    A + L     DG+M+GR AY     +  +  +    
Sbjct: 170 IRMVKN-TVKIPVIANGDIKTYEDAERALAESGADGIMVGRGAYGKPWSIRNMLHFLRTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          + IS+  + Y          +    +H++     + NS   R  
Sbjct: 229 EKLQEPTPQEKLPIILQHISSIFSHYGTE-----TGIGIARKHILWYSANYKNSAEFRQQ 283

Query: 297 LTVE 300
           +  E
Sbjct: 284 ICQE 287


>gi|169351459|ref|ZP_02868397.1| hypothetical protein CLOSPI_02239 [Clostridium spiroforme DSM 1552]
 gi|169291681|gb|EDS73814.1| hypothetical protein CLOSPI_02239 [Clostridium spiroforme DSM 1552]
          Length = 326

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 132/303 (43%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+Y+EM+   A+  G+ K   +L     E P+++Q+ G +
Sbjct: 18  MAGITNMAFRKIIKDF-GAGLVYSEMVSDKALCYGNTKTIDMLQVDDGEHPVSIQLFGGE 76

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V+AAK ++     + I++N+GCP  +V +   G+ L+L PD + + +  +   +S 
Sbjct: 77  VGTMVKAAKFIDQHSNCDIIDINMGCPVNKVLKADAGSKLLLYPDKIYEIVKGIVDNVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +    + K I+K+G + I IH R         +        D+ 
Sbjct: 137 PVTVKIRSGFDSK--HINAVEVAKLIEKAGASAIAIHGRT--------RSQMYEGKADWK 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K     + +  NG +  +  A ++L    VD VMIGRAA  N  ++  V +    
Sbjct: 187 IIADVK-AAVKIPVIGNGDVRSVEDARRMLEETGVDAVMIGRAALGNPWLIKQVVQSLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P                M             + Q+  H      G  +S R ++
Sbjct: 246 GVIIEEPTYQEKIAQCLSHAKKLM-----EIEPEKVAMFQMRGHAPWYIKGLKSSARVKN 300

Query: 296 ILT 298
            L+
Sbjct: 301 ELS 303


>gi|224823445|ref|ZP_03696554.1| TIM-barrel protein, nifR3 family [Lutiella nitroferrum 2002]
 gi|224603900|gb|EEG10074.1| TIM-barrel protein, nifR3 family [Lutiella nitroferrum 2002]
          Length = 342

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 133/320 (41%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L    +  +EMI ++  L    K +       + +P+++QI GAD
Sbjct: 17  MAGVTDRPFRMLCKRL-GAGMAVSEMITSNKALWTTAKTLRRANHDGEVEPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AA++  + G   I++N+GCP+ +V   + G+ L+ +  +VG  + A+ +A+ +P
Sbjct: 76  PAQMAAAARLNVEQGAQIIDINMGCPAKKVCNVAAGSALLRDEALVGRILEAVVQAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +++      +YD 
Sbjct: 136 VTLKTRTGWSREHKTA--LRVARLAEDCGIAALALHGRT--------REDMYHGAAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A ++L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAI-SIPLIANGDIDSPQRARQVLDYTGADAIMIGRAAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P    + +     +      Y           +   +H+     G   S   R  
Sbjct: 245 ETLPAPTVAEIRQLLLEHLDELYGFY-----GEYSGCRIARKHIAWYTRGLRGSNEFRQA 299

Query: 297 ---LTVEAGASTATHHIIET 313
              L   AG   A     + 
Sbjct: 300 MYRLEDTAGQRAAVADYFDR 319


>gi|169795120|ref|YP_001712913.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AYE]
 gi|213158218|ref|YP_002320269.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AB0057]
 gi|215482668|ref|YP_002324864.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB307-0294]
 gi|301345210|ref|ZP_07225951.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB056]
 gi|301594626|ref|ZP_07239634.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB059]
 gi|332854000|ref|ZP_08435116.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013150]
 gi|332869720|ref|ZP_08438908.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013113]
 gi|169148047|emb|CAM85910.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AYE]
 gi|213057378|gb|ACJ42280.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii AB0057]
 gi|213987896|gb|ACJ58195.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB307-0294]
 gi|332728282|gb|EGJ59664.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013150]
 gi|332732622|gb|EGJ63855.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii 6013113]
          Length = 341

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 300 MYKVETTAEQAL--VVESYFNQLL 321


>gi|311029014|ref|ZP_07707104.1| YacF [Bacillus sp. m3-13]
 gi|311032310|ref|ZP_07710400.1| YacF [Bacillus sp. m3-13]
          Length = 333

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 138/304 (45%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L    +EKPL+LQI G +
Sbjct: 18  MAGVCNAAFRLTVKEF-GAGLVCAEMVSDKAILYKNAKTMGMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KDTLVEAAKFVDKNTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+    +      ++++++G   + +H R  +             + D+D
Sbjct: 137 PVTVKMRTGWDED--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGHADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E+ ++ +  NG ++    A ++L    VDGVMIGRAA  N  M+ +  +Y   
Sbjct: 187 IIKQVK-ESVNIPVIGNGDVQTPQDAKRMLEETGVDGVMIGRAALGNPWMIYSTVQYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   +   R+
Sbjct: 246 GKLVGEPSVREKM-----DVCKLHLDRLIDLKGENTAVREMRKHTAWYLKGIRGNALVRN 300

Query: 296 ILTV 299
            +  
Sbjct: 301 SINE 304


>gi|203284144|ref|YP_002221884.1| tRNA-dihydrouridine synthase A [Borrelia duttonii Ly]
 gi|201083587|gb|ACH93178.1| tRNA-dihydrouridine synthase A [Borrelia duttonii Ly]
          Length = 335

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 115/328 (35%), Positives = 175/328 (53%), Gaps = 17/328 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ G+   I+  +  + P+A+QI     +
Sbjct: 12  MVEITDEHFRYIIRLLSKKITLYTPMISAKSIIMGELNTIVKQNPNDSPIAIQIATNCEN 71

Query: 61  KLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E +F ++E NLNVGCPS+R+ + ++GACLM NP  VG  + AM K  + P+
Sbjct: 72  DAAKAIEILEKNFNFDEYNLNVGCPSSRIQKANYGACLMQNPIQVGKILKAMQKNTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+        +     L+  V  I + G+    +HAR AIL G SPKDN  IP 
Sbjct: 132 SIKHRIGIRHNKKEYQEETYTELKQFVDKIIEYGIKNFIVHARIAILNGYSPKDNHNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L YD VY++KKE  + FI +NGG+ + +     L  VD VMIGRAA +N   +  +   F
Sbjct: 192 LKYDFVYQLKKEYKNTFIEINGGIINSNHIETHLSYVDSVMIGRAAAQNPYFVAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR      ++I   M +Y   + +    +  I RH++ + +   N+R+ 
Sbjct: 252 ---LGEKEQIPTR------KEILFQMVEYIKEY-NEHPTINTILRHIMRVIYSQKNARKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R  LT     +   H I+  A   + E 
Sbjct: 302 RQALTAPFNQNLKNHEILLNAIEHLKED 329


>gi|311070728|ref|YP_003975651.1| tRNA-dihydrouridine synthase B [Bacillus atrophaeus 1942]
 gi|310871245|gb|ADP34720.1| tRNA-dihydrouridine synthase B [Bacillus atrophaeus 1942]
          Length = 333

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 144/326 (44%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L    +EKPL+LQI G  
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILYNNAKTMGMLYIDEREKPLSLQIFGGK 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+PD + + ++A+ +++  
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVVESVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +      ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAVKNAQAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGVDGVMIGRAALGNPWMIYRTVQYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   + + R+
Sbjct: 246 GELKDEPQVREKM-----AVCKLHLDRLIDLKGENVAVREMRKHAAWYLKGVRANAKVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF + +E+
Sbjct: 301 EINHCETREELVQ--LLDAFTVEVEA 324


>gi|33151668|ref|NP_873021.1| putative dehydrogenase [Haemophilus ducreyi 35000HP]
 gi|38604734|sp|Q7VNP2|DUSB_HAEDU RecName: Full=tRNA-dihydrouridine synthase B
 gi|33147889|gb|AAP95410.1| putative dehydrogenase [Haemophilus ducreyi 35000HP]
          Length = 320

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 137/319 (42%), Gaps = 25/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L    L ++EM+  +  +   +K+ L      +    A+QI G++
Sbjct: 17  MAGITDQPFRRLCSQL-GAGLTFSEMMSTNPDVWHTEKSRLRLAHHAEIGINAVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAAKI   +G   I++N+GCP+ +V++   G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PTEIAEAAKINVAYGAQIIDINMGCPAKKVNKKMAGSALLREPQLVARILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +K+G++ + IH R         +D       +Y+ 
Sbjct: 136 VTLKIRTGWDKTHKN--FLQIAKIAEKAGISALTIHGRT--------RDCLFNGQAEYES 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A  +L     D VMIGR ++    +   + ++    
Sbjct: 186 IKAVKQAVF-MPIIANGDITSPQKAKDVLDYTGADAVMIGRGSFGRPWLFQELKQFLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNS--RRC 293
                 I  +  +   + I      Y  +    G ++    +H+        P S  +R 
Sbjct: 245 DIIDLSIDEK-CQLMLKHIEDLHHFYGEQ---KGYRI--ARKHVGWYLDQLTPGSNFKRT 298

Query: 294 RHILTVEAGASTATHHIIE 312
            + L+       A   +++
Sbjct: 299 FNALSSTTEQLIALKDLVK 317


>gi|88802043|ref|ZP_01117571.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Polaribacter irgensii 23-P]
 gi|88782701|gb|EAR13878.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Polaribacter irgensii 23-P]
          Length = 333

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 129/299 (43%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-NGADVVYTEFISSEGLIRDAAKSLMKLDIYEKERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++   +IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 78  LESMLRTIEIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +        D+  
Sbjct: 138 ITVKTRLGWD--HDSIRIVEVAERLQDVGCAAISIHGRT--------RAQMYKGEADWKP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K  +   + +  NG +    +A+++     +DG MIGRAA         V  YF  
Sbjct: 188 IAAVKNNQRMHIPVFGNGDVTTPEKAMEMRDSYGLDGAMIGRAAIGYPWFFNEVKHYFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P   +  +   R +       A         + +  RH    F G P+ +  R
Sbjct: 248 GEHLGQPTIAQRVEMARRHL-----QMAIDWKGPLLGVFETRRHYTNYFKGIPHFKEHR 301


>gi|224541983|ref|ZP_03682522.1| hypothetical protein CATMIT_01156 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525040|gb|EEF94145.1| hypothetical protein CATMIT_01156 [Catenibacterium mitsuokai DSM
           15897]
          Length = 325

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 138/303 (45%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  YR   +      L+ +EM+   A+  G++K   +L     E P+++QI G +
Sbjct: 18  MAGITNVAYRRLVKEF-GAGLVVSEMVSDKALCYGNQKTIDMLAVGEDEHPMSMQIFGGE 76

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +V+AAK VE+    + I++N+GCP  +V +   G+ LM  P++  D + A+ +A+++
Sbjct: 77  VETMVKAAKFVEEHSDCDIIDINMGCPVNKVLKAHAGSYLMQYPELAYDIVKAVVEAVNV 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D  +  +    + + ++K+G + + IH R         +      + D+ 
Sbjct: 137 PVTVKMRIGYD--MKHINCVEMAQLMEKAGASAVAIHGRT--------RSQMYEGHADWS 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E   + +  NG +     A +++     D VM+GR A  N  ++  + +Y   
Sbjct: 187 WIKKVK-EAVSIPVIGNGDVRTPEDAKRMMEETGCDAVMVGRGALGNPFVIRRMVKYLEE 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P     D     ++         +       ++Q+         G   S + ++
Sbjct: 246 GILEEEP-----DYHARIQLCIDHAHRLVKTEGEKNAIRQMRGQAPWYVKGLRGSAKIKN 300

Query: 296 ILT 298
            LT
Sbjct: 301 HLT 303


>gi|312621326|ref|YP_004022939.1| tim-barrel protein, nifr3 family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312201793|gb|ADQ45120.1| TIM-barrel protein, nifR3 family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 328

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 132/303 (43%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD+ +R          +  TEM+ + A++ G  K   ++ FS +EK   +QI G D
Sbjct: 13  MAGFTDKVFRRLCSRF-GADVTVTEMVSSKALVLGSAKTKELISFSDEEKIRGVQIFGND 71

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + ++ KI++D F Y+ I++N+GCP  ++     G  LM NP +    +  + K    
Sbjct: 72  PEVMAQSVKILQDEFEYHFIDINMGCPVPKLVRSGEGCALMKNPSLAAKIVEEVAKVSRK 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G DD+   +        +++SG + + +H R         +        D++
Sbjct: 132 PVSVKIRKGFDDE--NINAPEFAYILQESGASFVTVHGRT--------RAQLYSGKADWE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K++   + +  NG + D   A K       D +MIGRAA  N  +   + E F  
Sbjct: 182 IIRKVKEKL-KIPVIANGDIVDFESAKKAYEVTRADSIMIGRAALGNPWVFLQIKEGFEK 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  ++T+V      +++                + +  +H+     G  N+ + R 
Sbjct: 241 GY-----VETKVLPHMKIRVAIEFFTQLCSEKGDKMAVLEARKHLSFFVKGIENAAKIRD 295

Query: 296 ILT 298
            + 
Sbjct: 296 KIN 298


>gi|194017978|ref|ZP_03056585.1| tRNA-dihydrouridine synthase B [Bacillus pumilus ATCC 7061]
 gi|194010315|gb|EDW19890.1| tRNA-dihydrouridine synthase B [Bacillus pumilus ATCC 7061]
          Length = 333

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 142/318 (44%), Gaps = 23/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EMI   AIL  + + +  L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMISDKAILINNARTMGMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  
Sbjct: 77  KDTLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +   +  ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAIDNARAVERAGGQAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L    VD VMIGRAA  N  M+     Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGVDAVMIGRAALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   + D    H+     ++++ +H      G   +   R+
Sbjct: 246 GELKEEPNVREKMSVCKLHLDR-LIDLKGEHVA----VREMRKHAAWYLKGVRGNADVRN 300

Query: 296 ILTVEAGASTATHHIIET 313
            +      +     +++ 
Sbjct: 301 QINQSETRAEL-VQVLDD 317


>gi|303237786|ref|ZP_07324344.1| TIM-barrel protein, nifR3 family [Prevotella disiens FB035-09AN]
 gi|302482011|gb|EFL45048.1| TIM-barrel protein, nifR3 family [Prevotella disiens FB035-09AN]
          Length = 321

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 146/325 (44%), Gaps = 31/325 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADA++R  K  +       +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAVIRSIKSTLNKIVIDDEERPVGIQIYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE+   + I++N GCP  +V     G+ ++ N  ++ +    + KA+  P
Sbjct: 77  VASMVEAAKIVEEVHPDVIDINFGCPVKKVANKGAGSGMLRNIPLLLEITREVVKAVKTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    + + +L + ++  G+  + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDD--NNLIITDLAEQLQNCGIQALTIHGRT--------RAQMYTGNADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +E+++ A K      VD VMIGRA +    + +  D+    
Sbjct: 187 IGEVKNNPRIHIPIIGNGDIENIADAHKHFDKYGVDAVMIGRATFGCPWLFSETDDA--- 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                     ++  D    I   M       +     +    RH+    +F G P+ ++ 
Sbjct: 244 ---------PKLTIDDKIDILEEMLRINVERIDEYRGILHTRRHLAASPIFKGIPDFKQT 294

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A        I+      +
Sbjct: 295 R-IAMLRASKVDEIIAILNECRERL 318


>gi|169632777|ref|YP_001706513.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii SDF]
 gi|169151569|emb|CAP00342.1| tRNA-dihydrouridine synthase B [Acinetobacter baumannii]
          Length = 341

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQAANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 300 MYKVETTAEQAL--VVESYFNQLL 321


>gi|126207677|ref|YP_001052902.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           L20]
 gi|126096469|gb|ABN73297.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 320

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 132/287 (45%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L   +L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCTKL-GASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 76  PAEMAMAAKVNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +K+G++ + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWDQENRN--CLEIAKIAEKAGISALTIHGRT--------RHCLFEGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A  +L     D VMIGR ++    +   V+++  N 
Sbjct: 186 IKAVKQAV-SIPIIANGDITSAEKAKYVLDYTQADAVMIGRGSFGRPWLFKEVEQFLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                P+  +    F + I      Y  +    G ++    +H+   
Sbjct: 245 RLLDLPLDEKCRLMF-KHIEDLHRFYGEQ---KGYRI--ARKHVGWY 285


>gi|260893702|ref|YP_003239799.1| TIM-barrel protein, nifR3 family [Ammonifex degensii KC4]
 gi|260865843|gb|ACX52949.1| TIM-barrel protein, nifR3 family [Ammonifex degensii KC4]
          Length = 326

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 80/322 (24%), Positives = 141/322 (43%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M   TDR +R  AR      L +TEM+ A A+ R    +K++L F  +E  +  Q+ G+D
Sbjct: 22  MAGITDRAFRLVARE-GGARLCWTEMLPAPALARSSEARKHLLDFLGEEG-VVAQLFGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA +VE+ G   ++LN+GCP  +V +   GA L+ +P      + A+C+ + +P
Sbjct: 80  PEEMAEAALVVEEAGAVAVDLNMGCPVEKVVKIGAGAALLRDPRQAAAIVEAVCRRVKVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D++ P      + + ++++G   + +H R         +        D++ 
Sbjct: 140 VTVKLRKGWDEKSPPAW--EMARLLEEAGAKALIVHGR--------YRHEFFGGRADWEA 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     AL++L     DGVM+GRAA  N  + T    Y  + 
Sbjct: 190 IRRVK-EAVKIPVIGNGDVRTPEDALRMLASTGCDGVMVGRAARGNPWIFTRCQLYSLSG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          + ++     Y  + L+ G  +            G P +   R  
Sbjct: 249 EIPPPPSPAERVAQGLKHLALLEALYGDKALNRGRMVVD------WYTRGLPGASALRGQ 302

Query: 297 LTVEAGASTATHHIIETAFNLM 318
              +A    A   ++E     +
Sbjct: 303 -AYQARDFAALRSLLERYLYQV 323


>gi|109896601|ref|YP_659856.1| nifR3 family TIM-barrel protein [Pseudoalteromonas atlantica T6c]
 gi|109698882|gb|ABG38802.1| tRNA-U20-dihydrouridine synthase [Pseudoalteromonas atlantica T6c]
          Length = 333

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 128/298 (42%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + +    L+ +EM+ ++  +    K+   +    ++   A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRM-GAGLVVSEMLSSNPDVWRSSKSKQRMDHVGEKGIRAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   +++N+GCP+ +V++   G+ L+ +P +V   + ++ +A+ +P
Sbjct: 76  PLLMAQAAQFNVDNGAQIVDINMGCPAKKVNKKLAGSALLQDPQLVERIVQSVVEAVQVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +          + K  +++G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWNTDNRNGV--QIAKIAEQNGIQSLAVHGRT--------RACMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +  +  A  +L   + D +MIGR A  N  +   +  +    
Sbjct: 186 IKAIKQAV-SIPVVANGDITCVHSAKHVLEYTNADALMIGRGAQGNPWIFRQIQHFLQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               SP    V       ++     Y       G ++    +H+          R+ R
Sbjct: 245 EILPSPPLGEVRDVLLAHVANVHQFYGEF---KGARI--ARKHVGWYLAEHDRERQFR 297


>gi|187479247|ref|YP_787272.1| tRNA-dihydrouridine synthase B [Bordetella avium 197N]
 gi|115423834|emb|CAJ50385.1| tRNA-dihydrouridine synthase B [Bordetella avium 197N]
          Length = 341

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 67/301 (22%), Positives = 123/301 (40%), Gaps = 24/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    +  P+++QI GAD
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMAASNPRLWDSVKTSRRLNHDGEIAPISVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EAA    + G   I++N+GCP  +V   + G+ L+ + D++   + A+  A   L
Sbjct: 76  PAMMAEAAVFNVNKGARIIDINMGCPVKKVCNMASGSALLRHEDLIARILDAVVGACAPL 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        + +  ++SG+  + +H R         + +      +
Sbjct: 136 GVPVTLKTRTGWDRESRNA--LRVARMAEQSGIALLTLHGRT--------RCDLYTGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K E   + +  NG ++   +A  +L     D VMIGRAA     +   +D + 
Sbjct: 186 YDTLRAVKAEIG-IPVVANGDIDSPEKARDVLRYTGADAVMIGRAAQGRPWIFREIDHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               T + P    +       +      Y          ++   +H+       P +   
Sbjct: 245 RTGETLAPPSHAEMRDLLLEHLDDHYRFYGEH-----TGVRTARKHIGWYIDSLPGAEPF 299

Query: 294 R 294
           R
Sbjct: 300 R 300


>gi|86131460|ref|ZP_01050058.1| dihydrouridine synthase (Dus) [Dokdonia donghaensis MED134]
 gi|85817905|gb|EAQ39073.1| dihydrouridine synthase (Dus) [Dokdonia donghaensis MED134]
          Length = 330

 Score =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 138/326 (42%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA 
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ + +IVE  G + I++N GCP  +V     GA ++ + D++     +M +   +P
Sbjct: 78  EESMLRSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVKLTKSMVEHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D +  ++ +  + + ++  G   I IH R         +      + D+  
Sbjct: 138 VTVKTRLGWDHE--SIKIVEVAERLQDVGCAAISIHGRT--------RAQMYKGDADWKP 187

Query: 179 VYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K  +   + +  NG +    +A+++     +DG MIGRA+         V  +   
Sbjct: 188 IAAVKNNQRMHIPVFGNGDVNSPERAVEMRDEYGLDGAMIGRASIGYPWFFNEVKHFMKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +   R +     + +         + +  RH    F G P+ +  R 
Sbjct: 248 GEHKKPPTLVERVEAARRHL-----EMSIAWKGEILGVFETRRHYTNYFRGIPHFKEYRM 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L      S  +  +   A NL+ E 
Sbjct: 303 KLVT----SDKSEDVF-AALNLIEEK 323


>gi|262376252|ref|ZP_06069482.1| tRNA-dihydrouridine synthase B [Acinetobacter lwoffii SH145]
 gi|262308853|gb|EEY89986.1| tRNA-dihydrouridine synthase B [Acinetobacter lwoffii SH145]
          Length = 341

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 73/324 (22%), Positives = 143/324 (44%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ +D  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTSDKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PHDLAEAARYQVANGAQIVDINMGCPAKKVCNRLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y +
Sbjct: 136 VTLKTRLGYLNGQ--ENIIRVAKRAEQAGIAALALHGRT--------REDMYLNTARYSL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKDVK-EMLKIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P  T V       ++     Y     +SG ++    +H+     G  +S   R  
Sbjct: 245 QHLDAPSITEVKDVLLGHLTELYEFYGE---YSGCRIS--RKHIAWYTKGLRSSNEFRQN 299

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +      +   + ++E  FN ++E
Sbjct: 300 MYQVENTAD-QYRVVEDYFNALLE 322


>gi|262273282|ref|ZP_06051097.1| tRNA dihydrouridine synthase B [Grimontia hollisae CIP 101886]
 gi|262222655|gb|EEY73965.1| tRNA dihydrouridine synthase B [Grimontia hollisae CIP 101886]
          Length = 335

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 122/322 (37%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  +    K+   +    ++   ++QI GA+
Sbjct: 31  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPAMWHTAKSKNRMVHLDEKGIRSVQIAGAE 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+   D G   +++N+GCP  +V++   G+ L+  PDI+   + A+  A+ +P
Sbjct: 90  PALMAEAARFCVDNGAQIVDINMGCPVKKVNKKLAGSALLTRPDIIEQILKAVVSAVDVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         +        +YD 
Sbjct: 150 VTLKTRTGWDPDNKN--CIQIAKMAEDCGIQALALHGRT--------RACMYKGEAEYDS 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGR A     +   +  Y +  
Sbjct: 200 IKAVK-EAVSIPVIANGDIDSPQKAKFVLDYTGADALMIGRPAQGRPWIFREIQHYLTTG 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V       +      Y          L+   +H+             R  
Sbjct: 259 EALDAPPLEEVKTILLGHVQELHQFY-----GDLKGLRIARKHVGWYLKEHDQIGDFRQT 313

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       ++  F  +
Sbjct: 314 FNAIEDAQG-QIDALQDYFENV 334


>gi|297194493|ref|ZP_06911891.1| dihydrouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
 gi|197718697|gb|EDY62605.1| dihydrouridine synthase [Streptomyces pristinaespiralis ATCC 25486]
          Length = 389

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 125/319 (39%), Gaps = 21/319 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDETETPRSIQLYGV 93

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 94  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPFKRPLLRAILHEAVTNAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 154 ALPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +   + AL+++     DGV++GR       +   +   F
Sbjct: 204 WDAIARLKEHVPEIPVLGNGDIWSAADALRMMRETGCDGVVVGRGCLGRPWLFADLVAAF 263

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 + P   +V     R  +                +    +H+     GF      
Sbjct: 264 EGREDYARPTLRQVADVMLRHATL----LGEWIGDESRGVVDFRKHVAWYLKGFAVGSEM 319

Query: 294 RHILTVEAGASTATHHIIE 312
           R  L + +        + E
Sbjct: 320 RKKLAITSSLDELGAQLSE 338


>gi|159027862|emb|CAO87075.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 350

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 62/320 (19%), Positives = 129/320 (40%), Gaps = 23/320 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    +++LY  M+ A  I +  +   ++    +E+P+++Q+       
Sbjct: 41  GVTDLVFRRLVRRFAPDSMLYRSMVNATEISQLQELPQLMVIGDKEQPISMQLFDCRPDF 100

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +  AA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  + +A+S+PVTV
Sbjct: 101 MAVAAEKAVKEGAMTIDINMGCPVNKITKKGGGSSLLRQPEIAEQIVREVVRAVSVPVTV 160

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G + Q   + + +  + ++ +GV  + +HAR         ++       D+  +  
Sbjct: 161 KTRLGWNAQE--INIIDFARRLEDAGVQMLTLHART--------REQGYHGPADWQWIKR 210

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+  L     DGVM  R       ++  +D Y       
Sbjct: 211 VK-EVLSIPVIANGDIVSVETAINCLEFTEADGVMCSRGTLGYPYLVGEIDYYLKTGKKL 269

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCRHILT 298
             P    +       +           L+ G + + Q  +H+      F  +   R   +
Sbjct: 270 PKPTSIDLLSLAKEHLQ-------GLWLYKGQRGIWQARKHLAWYCQDFTGAAVWRDRFS 322

Query: 299 VEAGASTATHHIIETAFNLM 318
                      +I+ A   +
Sbjct: 323 RIESL-GEGCDLIDGAIAQL 341


>gi|53728909|ref|ZP_00134632.2| COG0042: tRNA-dihydrouridine synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|165975645|ref|YP_001651238.1| putative dehydrogenase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|190149460|ref|YP_001967985.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|303250745|ref|ZP_07336941.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307245001|ref|ZP_07527098.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307249401|ref|ZP_07531393.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307251720|ref|ZP_07533624.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253954|ref|ZP_07535806.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307258409|ref|ZP_07540150.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|307260647|ref|ZP_07542339.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307262779|ref|ZP_07544406.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|165875746|gb|ABY68794.1| putative dehydrogenase [Actinobacillus pleuropneumoniae serovar 3
           str. JL03]
 gi|189914591|gb|ACE60843.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|302650415|gb|EFL80575.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306854166|gb|EFM86374.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306858587|gb|EFM90651.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306860806|gb|EFM92815.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306863158|gb|EFM95100.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306867593|gb|EFM99440.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306869724|gb|EFN01509.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306871924|gb|EFN03641.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 320

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 132/287 (45%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L   +L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCTKL-GASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 76  PAEMAMAAKVNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +K+G++ + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWDQENRN--CLEIAKIAEKAGISALTIHGRT--------RHCLFEGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A  +L     D VMIGR ++    +   V+++  N 
Sbjct: 186 IKAVKQAV-SIPIIANGDITSAEKAKYVLDYTQADAVMIGRGSFGRPWLFKEVEQFLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                P+  +    F + I      Y  +    G ++    +H+   
Sbjct: 245 RLLDLPLDEKCRLMF-KHIEDLHRFYGEQ---KGYRI--ARKHVGWY 285


>gi|319639135|ref|ZP_07993891.1| tRNA-dihydrouridine synthase B [Neisseria mucosa C102]
 gi|317399612|gb|EFV80277.1| tRNA-dihydrouridine synthase B [Neisseria mucosa C102]
          Length = 334

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 135/325 (41%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRICREF-GAGWAVCEMLTSDPTLRNTKKTLRRSDFEGEGGVVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+     G   I++N+GCP+ +V     G+ LM N  +V + +AA+  A+ +P
Sbjct: 76  PQQMAEAAQYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAEILAAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D+     L  + K  ++SG+  + IH R         +         Y++
Sbjct: 136 VTLKTRLGWHDEHQN--LPTIAKIAEESGIAALAIHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A     +   +  Y  + 
Sbjct: 186 IAETKGRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWLFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +      +      I A    Y          ++   +H+       P+    R  
Sbjct: 245 VLPPALSLAECNATILNHIRAMHAFY-----GEVAGVRIARKHIGWYIDEMPDGEHTRRD 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A +  +      + E 
Sbjct: 300 IN-RLDSAAAQYDTLAAYLETLSEK 323


>gi|301092884|ref|XP_002997293.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262111428|gb|EEY69480.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 379

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 119/345 (34%), Positives = 178/345 (51%), Gaps = 23/345 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTDRHYRF  R++T   LL+TEM+V   +L  R +    LG    E PLALQ+GG  
Sbjct: 15  MMDWTDRHYRFMMRMITKKTLLFTEMVVDQTLLYQRKNLDYFLGHDPAEAPLALQLGGNS 74

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L  AA + + +G + EINLN GCPSA V    FGA LML P+ V D   +M  ++++
Sbjct: 75  VEDLGAAAHLSQSYGGFCEINLNTGCPSALVSSRCFGARLMLEPERVRDICDSMRHSVAL 134

Query: 118 -----------PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                       VTVKCRIGVDD      L + V ++  +GV  I +HARK +LKGLS K
Sbjct: 135 ASEGNPDHPTAEVTVKCRIGVDDCDSYDELHHYVAAVASAGVRHIIVHARKCLLKGLSTK 194

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           DNR IP L Y++VY +K++ P+L   LNGG++ +  A ++L   +VDG+MIGRAAY    
Sbjct: 195 DNRTIPPLRYEVVYRLKQDFPELSFTLNGGVKSIQHARELLNTTNVDGIMIGRAAYNTPW 254

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT----RHM 280
                D    N     +  +  + + +          + +    S       T    + +
Sbjct: 255 NFRDADRLIFNAERNPNLSRREIIERYLEYAEDLQAKWGSTEPLSDSPYTMATSALMKPL 314

Query: 281 IGLFHGFPNSRRCRHILTVEAGASTATHHI---IETAFNLMIESL 322
           + LF+G    +  +  ++ +         +   IE+A  ++   +
Sbjct: 315 LSLFNGEFGGKAFKREISAQWSKKGPRPELREMIESAMKVLPSEV 359


>gi|188532430|ref|YP_001906227.1| tRNA-dihydrouridine synthase B [Erwinia tasmaniensis Et1/99]
 gi|188027472|emb|CAO95319.1| tRNA-dihydrouridine synthase B [Erwinia tasmaniensis Et1/99]
          Length = 321

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +P
Sbjct: 76  PTEMAGAARINAASGAQVIDINMGCPAKKVNRKMAGSALLQHPELVKSILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDSDNRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-NVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y  R    G ++    +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIGHLRELHDFYGQR---KGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|157148839|ref|YP_001456158.1| tRNA-dihydrouridine synthase B [Citrobacter koseri ATCC BAA-895]
 gi|157086044|gb|ABV15722.1| hypothetical protein CKO_04672 [Citrobacter koseri ATCC BAA-895]
          Length = 321

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 127/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA--LQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGVRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPHKARAVLNYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      ++  F 
Sbjct: 300 FNAIEDASE-QLEALKAYFE 318


>gi|317049793|ref|YP_004117441.1| TIM-barrel protein, nifR3 family [Pantoea sp. At-9b]
 gi|316951410|gb|ADU70885.1| TIM-barrel protein, nifR3 family [Pantoea sp. At-9b]
          Length = 321

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TD+ +R          +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGVTDKPFRTLCYE-NGAGMTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P +V   + A+  A+ +P
Sbjct: 76  PDEMAAAARINVASGAQVIDINMGCPAKKVNRKMAGSALLQHPQLVESILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDKENRN--CVEIAQLAERCGIQALTIHGRT--------RACLFEGQAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V       I      Y  R    G ++    +H+           + R  
Sbjct: 245 ELLAPKPLAEVKHMLIGHIRELHDFYGQR---KGYRI--ARKHVSWYLQENAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|189501100|ref|YP_001960570.1| TIM-barrel protein, nifR3 family [Chlorobium phaeobacteroides BS1]
 gi|189496541|gb|ACE05089.1| TIM-barrel protein, nifR3 family [Chlorobium phaeobacteroides BS1]
          Length = 346

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 133/318 (41%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE + A+A+ RG  K+I  + F   E+P  +QI G  
Sbjct: 17  MEDVTDRSFRKICKRF-GADIVYTEFVSAEALRRGVGKSIQKMLFEESERPAVIQIFGNS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA I      + +++N GCP+ +V     GA L+  P+ +    AA+ KA+SIP
Sbjct: 76  GEAMAEAAVIAASAKPDYLDINFGCPAKKVAGKGAGAALLREPEKMAAITAAVVKAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D    +V + +++  ++ +G+  I +H R         +        D+D 
Sbjct: 136 VTVKTRIGWDRD--SVNILDIIPRLEDAGIAAIAVHGRT--------RSEMYKGRADWDW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +     AL +      DG+MIGR A  N  +   V E     
Sbjct: 186 IARVKEHA-KIPVIANGDIWSPQDALAMFSHTGADGIMIGRGAIGNPFIFRQVKELLQGG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P            +S      +  H        ++ RH      G P   R R  
Sbjct: 245 AVTTLPDFRDRISVAIEHLSL-----SVEHKGEKYGTLEMRRHYSTYLKGLPRVSRVRDK 299

Query: 297 LTVEAGASTATHHIIETA 314
           L  E         I+   
Sbjct: 300 LVREEKWQQV-IEILRAY 316


>gi|300743944|ref|ZP_07072964.1| putative tRNA-dihydrouridine synthase [Rothia dentocariosa M567]
 gi|300380305|gb|EFJ76868.1| putative tRNA-dihydrouridine synthase [Rothia dentocariosa M567]
          Length = 402

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 128/302 (42%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T++ +R   R      L  TEM+ A A++    +++  +     E+  ++QI G D
Sbjct: 43  MAGVTNKAFRRLCREYGG-GLYVTEMVTARALVERKPESMRIIEHDADEQIRSIQIYGVD 101

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A ++V +    + I+LN GCP+ +V +   GA L    D+    +    K    
Sbjct: 102 AVNVGKAIRLVVEEDRADHIDLNFGCPAPKVTKRGGGAALPWKTDLFTAIVHTAVKEASR 161

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + +GV  I +H R A                
Sbjct: 162 NDIPLTIKMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTA--------AQHYSGTA 211

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + ++++  PD+ I  NG +     A++++    VDGV+IGR       +   +   
Sbjct: 212 DWDSIAQLREAIPDVPILGNGDIFAAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNA 271

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P  + V    +R     +  +A  +      L++I +H+   F G+P    
Sbjct: 272 FEGSTERIRPTLSEVAAMIYRHAELLVETFADEY----KGLREIRKHVAWYFKGYPVGGE 327

Query: 293 CR 294
            R
Sbjct: 328 LR 329


>gi|241888813|ref|ZP_04776119.1| tRNA-dihydrouridine synthase B [Gemella haemolysans ATCC 10379]
 gi|241864489|gb|EER68865.1| tRNA-dihydrouridine synthase B [Gemella haemolysans ATCC 10379]
          Length = 335

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/304 (26%), Positives = 137/304 (45%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  +KK +  L    +E+PL+LQI G +
Sbjct: 18  MAGVCNAAFRLTAKEF-GAGLVCAEMVSDKAILFNNKKTMNMLYIDPRERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  LVEAAK V+     + I+LN+GCP  ++ +   G+ L+L+PD V + IA +  ++S 
Sbjct: 77  IETLVEAAKYVDKNTEADIIDLNMGCPVPKITKVDAGSKLLLDPDKVYEVIARLVDSVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD+   +   +  ++ +++G + I IH R  +               ++D
Sbjct: 137 PVTVKMRMGWDDEHIYI--MDNARNAERAGASAIAIHGRTKV--------QMYSGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++KKE   + +  NG +     A K+L   + D VMIGRAA  N  ML    +Y   
Sbjct: 187 VIRDVKKEL-KIPVIGNGDVTSPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   M             + ++ +H      G     + + 
Sbjct: 246 GELTEEPSPREKIDVCLLHLRRLM-----EIKPERVAVHEMRKHAAYYMKGIKGGAKVKK 300

Query: 296 ILTV 299
            L  
Sbjct: 301 ELNT 304


>gi|184159024|ref|YP_001847363.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|183210618|gb|ACC58016.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
          Length = 325

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 1   MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 60  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  +++G+  + +H R         +++  +    Y++
Sbjct: 120 VTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT--------REDMYLNTARYEL 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 229 EHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIAWYTKGLRSSNEFRQN 283

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE  A  A   ++E+ FN ++
Sbjct: 284 MYKVETTAEQAL--VVESYFNQLL 305


>gi|307256215|ref|ZP_07538002.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865396|gb|EFM97292.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
          Length = 320

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 131/287 (45%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L   +L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCTKL-GASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AAK   ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 76  PAEMAMAAKFNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +K+G++ + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWDQENRN--CLKIAKIAEKAGISALTIHGRT--------RHCLFEGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A  +L     D VMIGR ++    +   V+++  N 
Sbjct: 186 IKAVKQAV-SIPIIANGDITSAEKAKYVLDYTQADAVMIGRGSFGRPWLFKEVEQFLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                P+  +    F + I      Y  +    G ++    +H+   
Sbjct: 245 RLLDLPLDEKCRLMF-KHIEDLHRFYGEQ---KGYRI--ARKHVGWY 285


>gi|313889105|ref|ZP_07822761.1| TIM-barrel protein, nifR3 family [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844845|gb|EFR32250.1| TIM-barrel protein, nifR3 family [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 308

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 139/302 (46%), Gaps = 24/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  +R  A       +  TEM+ A A++  +KK   +L  S +EK +A+QI G+D
Sbjct: 8   MAGYTDIAFREVATE-KGADITVTEMVSAMALVYENKKTIDLLDISPKEKKVAVQIFGSD 66

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+I+ D+ ++ +++N+GCP+ ++ + + G+ L+ +P +V D + ++ K  + P
Sbjct: 67  PDVMGQAARILNDYDFSYVDINMGCPAPKIVKNNSGSHLLSDPSLVYDIVKSVVKNSNKP 126

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G+       A++N    I+ +G   + +H R         ++       D+D 
Sbjct: 127 VTAKVRKGIGGLSSMKAIKN----IEAAGATFVTVHGRT--------REEYYTGKADWDF 174

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K  N  + +  NG ++    A++      VDG+ IGR A  N  +   ++E     
Sbjct: 175 IKEVK-ANVKIPVIGNGDVDSPEDAIEKINYSKVDGLAIGRGAIGNPYIFNQIEELIETG 233

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                  K ++              Y    L     + ++ +     F G  +S+  R+ 
Sbjct: 234 DYYKPSDKEKLLLMIDE--LERKISYKGEKLG----ILEMRKVYAEYFKGMKDSKEVRNK 287

Query: 297 LT 298
           L 
Sbjct: 288 LN 289


>gi|222152139|ref|YP_002561299.1| hypothetical protein MCCL_1896 [Macrococcus caseolyticus JCSC5402]
 gi|222121268|dbj|BAH18603.1| conserved hypothetical protein [Macrococcus caseolyticus JCSC5402]
          Length = 334

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 146/326 (44%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  ++K +  L     E+PL+LQI G +
Sbjct: 18  MAGVCNAAFRLTVKEF-GAGLVCAEMVSDKAILFNNEKTMKMLYIDENERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP +++ +   GA  +L+P  + + ++A+ +A++ 
Sbjct: 77  KETLVEAAKYVDQNTTADIIDINMGCPVSKIIKCEAGARWLLDPPKIYEMVSAVVEAVNK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD+          K I+K+G + I +H R  +             + D+D
Sbjct: 137 PVTVKMRIGWDDEHIYAV--ENAKMIEKAGASAIAVHGRTRV--------QMYEGHADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K E   + +  NG +     A K+L    VD VMIGR A  N  M+     Y   
Sbjct: 187 VIRQVK-EAVSIPVIGNGDVTSPELAKKMLDETGVDAVMIGREALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+ +         ++    D           + ++ +H      G   + + R 
Sbjct: 246 GELMPEPLISEKM-----DVAVLHLDRLINLKGEKVAVMEMRKHASWYLKGIRGNGKARK 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           ++  +A        I+ T F   +E+
Sbjct: 301 LIN-QAETRDELVDILRT-FEQEVEA 324


>gi|225631215|ref|ZP_03787910.1| NifR3 family protein [Wolbachia endosymbiont of Muscidifurax
           uniraptor]
 gi|225591088|gb|EEH12275.1| NifR3 family protein [Wolbachia endosymbiont of Muscidifurax
           uniraptor]
          Length = 310

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 133/313 (42%), Gaps = 21/313 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++    +++   +  +   A+Q+ G +  
Sbjct: 9   MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTHQSLQK-AKVDALTAVQLAGCEPY 66

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVT
Sbjct: 67  VMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNVPVT 126

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +D+        L K  +  G   I +H R         +        D+  V 
Sbjct: 127 VKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFVR 176

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG +++++     L     DGVMIGR AY    ++     + S   T
Sbjct: 177 NVKEQV-KIPVIVNGDIKNLNDIQNALKESGADGVMIGRGAYGKPWLINQAMNFLSGSET 235

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R+       I     D    +  +   ++   +H+     G   S   R  + 
Sbjct: 236 SEPTASERLS------IILEHYDNILEYYGNDTGIKMARKHIGWYSSGLQGSSEFRVRVN 289

Query: 299 VEAGASTATHHII 311
               ++    +II
Sbjct: 290 NMTDSTEVKENII 302


>gi|225010313|ref|ZP_03700785.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-3C]
 gi|225005792|gb|EEG43742.1| TIM-barrel protein, nifR3 family [Flavobacteria bacterium MS024-3C]
          Length = 330

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 141/320 (44%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+   L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSTMKLDIYEKERPVGIQIFGAE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++A +IVE    + I++N GCP  +V   + GA ++ +  ++     AM K   +P
Sbjct: 78  MDSMLQAIEIVEASKPDIIDINFGCPVKKVVCKNAGAGILRDIPLMVKLTEAMVKHTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D  + ++ +  + + ++  G+  I IH R  +             N D+  
Sbjct: 138 VTVKTRLGWD--LDSIKIVEVAERLQDVGIAAISIHGRTRV--------QMYKGNADWGP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG ++    A+K+     +DG MIGRA+         V  +F  
Sbjct: 188 IAEVKNNPRMHIPVFGNGDVDTPEMAVKMRDEYGLDGAMIGRASIGYPWFFNEVKHFFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +   R +  S+             + +  RH    F G PN +  R 
Sbjct: 248 GTHKAPPTLEERVEAARRHLQMSI-----DWKGEKLGVFETRRHYTNYFKGIPNFKEYRM 302

Query: 296 -ILTVEAGAS--TATHHIIE 312
            ++T +       A   +++
Sbjct: 303 KMVTSDESKDVFDAFDEVLD 322


>gi|329767828|ref|ZP_08259344.1| tRNA-dihydrouridine synthase 1 [Gemella haemolysans M341]
 gi|328838929|gb|EGF88523.1| tRNA-dihydrouridine synthase 1 [Gemella haemolysans M341]
          Length = 335

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/304 (26%), Positives = 137/304 (45%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  +KK +  L    +E+PL+LQI G +
Sbjct: 18  MAGVCNAAFRLTAKEF-GAGLVCAEMVSDKAILFNNKKTMNMLYIDPRERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  LVEAAK V+     + I+LN+GCP  ++ +   G+ L+L+PD V + IA +  ++S 
Sbjct: 77  IDTLVEAAKYVDKNTEADIIDLNMGCPVPKITKVDAGSKLLLDPDKVYEVIARLVDSVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD+   +   +  ++ +++G + I IH R  +               ++D
Sbjct: 137 PVTVKMRMGWDDEHIYI--MDNARNAERAGASAIAIHGRTKV--------QMYSGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++KKE   + +  NG +     A K+L   + D VMIGRAA  N  ML    +Y   
Sbjct: 187 VIRDVKKEL-KIPVIGNGDVTTPELAKKMLDDTNCDAVMIGRAALGNPWMLYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   M             + ++ +H      G     + + 
Sbjct: 246 GELTEEPTPREKIDVCLLHLRRLM-----EIKPEKVAVHEMRKHAAYYMKGIKGGAKVKK 300

Query: 296 ILTV 299
            L  
Sbjct: 301 ELNT 304


>gi|225629894|ref|YP_002726685.1| NifR3 family protein [Wolbachia sp. wRi]
 gi|225591875|gb|ACN94894.1| NifR3 family protein [Wolbachia sp. wRi]
          Length = 320

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 134/313 (42%), Gaps = 21/313 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++   ++++   +  +   A+Q+ G +  
Sbjct: 19  MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSLQK-AKVDALTAVQLAGCEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVT
Sbjct: 77  VMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNMPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +D+        L K  +  G   I +H R         +        D+  V 
Sbjct: 137 VKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFVR 186

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG +++++     L     DGVMIGR AY    ++     + S   T
Sbjct: 187 NVKEQV-KIPVIVNGDIKNLNDIQNALKESGADGVMIGRGAYGKPWLINQAMNFLSGSET 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R+       I     D    +  +   ++   +H+     G   S   R  + 
Sbjct: 246 SEPTASERLS------IILEHYDNILEYYGNDTGIKMARKHIGWYSSGLQGSSEFRVRVN 299

Query: 299 VEAGASTATHHII 311
               ++    +II
Sbjct: 300 NMTDSTEVKENII 312


>gi|311113192|ref|YP_003984414.1| tRNA-dihydrouridine synthase B [Rothia dentocariosa ATCC 17931]
 gi|310944686|gb|ADP40980.1| tRNA-dihydrouridine synthase B [Rothia dentocariosa ATCC 17931]
          Length = 388

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 70/302 (23%), Positives = 127/302 (42%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T++ +R   R      L  TEM+ A A++    +++  +     E+  ++QI G D
Sbjct: 29  MAGVTNKAFRRLCREYGG-GLYVTEMVTARALVERKPESMRIIEHDADEQIRSIQIYGVD 87

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A ++V +    + I+LN GCP+ +V +   GA L    D+    +    K    
Sbjct: 88  AVNVGKAIRLVVEEDRADHIDLNFGCPAPKVTKRGGGAALPWKTDLFTAIVHTAVKEASR 147

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + +GV  I +H R A                
Sbjct: 148 NDIPLTIKMRKGIDDD--HITFLESAKIARDAGVAAIALHGRTA--------AQHYSGTA 197

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + ++++   D+ I  NG +     A++++    VDGV+IGR       +   +   
Sbjct: 198 DWDSIAQLREAISDVPILGNGDIFAAEDAVRMVEQTGVDGVVIGRGCQGRPWLFGDLQNA 257

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P  + V    +R     +  +A  +      L++I +H+   F G+P    
Sbjct: 258 FEGSTERIRPTLSEVAAMIYRHAELLVETFADEY----KGLREIRKHVAWYFKGYPVGGE 313

Query: 293 CR 294
            R
Sbjct: 314 LR 315


>gi|56961898|ref|YP_173620.1| tRNA-dihydrouridine synthase [Bacillus clausii KSM-K16]
 gi|56908132|dbj|BAD62659.1| tRNA-dihydrouridine synthase [Bacillus clausii KSM-K16]
          Length = 333

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 140/317 (44%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  ++K+  +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNPAFRLIAKEF-GAGLVCAEMVSDKAILHKNEKSLQMLYVDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V ++   + I++N+GCP  ++ +   GA  +L+P  + + +AA+  A+  
Sbjct: 77  KDTLVEAARFVDQNTNADIIDINMGCPVPKITKCDAGARWLLDPKKIYEMVAAVVDAVKK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+           ++++++G + + +H R  +               D++
Sbjct: 137 PVTVKMRIGWDEDHIYAI--ENARAVERAGGSAVAVHGRTRV--------QMYEGVADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++KK   ++ +  NG +     A ++L    VDGVMIGRAA  N  ML    +Y  N
Sbjct: 187 IIGDVKKAV-NIPVIGNGDVATPQDAKRMLDEYGVDGVMIGRAALGNPWMLYRTIQYLEN 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++     D           ++++ +H      G     + R 
Sbjct: 246 GTLPPEPTPREKI-----EVCLIHLDRLVALKGERVAVREMRKHTAWYIKGLRGKAKIRD 300

Query: 296 ILTVEAGASTATHHIIE 312
            +            + E
Sbjct: 301 KVNQFETRDDVVKALYE 317


>gi|203287682|ref|YP_002222697.1| tRNA-dihydrouridine synthase A [Borrelia recurrentis A1]
 gi|201084902|gb|ACH94476.1| tRNA-dihydrouridine synthase A [Borrelia recurrentis A1]
          Length = 335

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 115/328 (35%), Positives = 174/328 (53%), Gaps = 17/328 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV+ TD H+R+  RLL+    LYT MI A +I+ G+   I+  +  + P+A+QI     +
Sbjct: 12  MVEITDEHFRYIIRLLSKKITLYTPMISAKSIIIGELNTIVKQNPNDSPIAIQIATNCEN 71

Query: 61  KLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E +F ++E NLNVGCPS+R+ + ++GACLM NP  VG  + AM K  + P+
Sbjct: 72  DAAKAIEILEKNFNFDEYNLNVGCPSSRIQKANYGACLMQNPIQVGKILKAMQKNTNKPI 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+        +     L+  V  I + G+    +HAR AIL G SPKDN  IP 
Sbjct: 132 SIKHRIGIRHNKKEYQEETYTELKQFVDKIIEYGIKNFIVHARIAILNGYSPKDNHNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L YD VY++KKE  + FI +NGG+ + +     L  VD VMIGRAA +N   +  +   F
Sbjct: 192 LKYDFVYQLKKEYKNTFIEINGGIINSNHIETHLSYVDSVMIGRAAAQNPYFVAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR      ++I   M +Y   + +    +  I RH++ + H   N+ + 
Sbjct: 252 ---LGEKEQIPTR------KEILFQMVEYIKEY-NEHPTINTILRHIMRVIHSQKNACKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R  LT     +   H I+  A   + E 
Sbjct: 302 RQALTAPFNQNLKNHEILLNAIEHLKED 329


>gi|121595878|ref|YP_987774.1| nifR3 family TIM-barrel protein [Acidovorax sp. JS42]
 gi|120607958|gb|ABM43698.1| tRNA-U20-dihydrouridine synthase [Acidovorax sp. JS42]
          Length = 353

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 65/306 (21%), Positives = 114/306 (37%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + +  AA    D G   I++N+GCP+ +V     G+ LM N  +  +   A+  A    
Sbjct: 76  AAMMAVAALYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAEAVVAACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   Q     +  L +  +  G+  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQQHKNAVV--LARRFEDVGIQMLTVHGRT--------REQGYKGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   +  Y 
Sbjct: 186 YDTIAAVK-AAVRVPVVANGDITSPEKARAVLAATGADAVMIGRAAQGRPWIFREIGHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLEHLQDHYGLYGEA-----SGVRSARKHIAWYVRALPGGEAL 299

Query: 294 RHILTV 299
           R  +  
Sbjct: 300 RQHINT 305


>gi|157690863|ref|YP_001485325.1| dihydrouridine synthase [Bacillus pumilus SAFR-032]
 gi|157679621|gb|ABV60765.1| dihydrouridine synthase [Bacillus pumilus SAFR-032]
          Length = 333

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 141/318 (44%), Gaps = 23/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + + +  L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILINNARTMGMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  
Sbjct: 77  KDTLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +   +  ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDED--HIFAIDNARAVERAGGQAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ +  + +  NG ++    A ++L     D VMIGRAA  N  M+     Y   
Sbjct: 187 IIKEVKQ-SVSIPVIGNGDVKTPQDAKRMLDETGADAVMIGRAALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   + D    H+     ++++ +H      G   +   R+
Sbjct: 246 GELKEEPNVREKMSVCKLHLDR-LIDLKGEHVA----VREMRKHAAWYLKGVRGNADVRN 300

Query: 296 ILTVEAGASTATHHIIET 313
            +      +     +++ 
Sbjct: 301 QINQSETRAEL-VQVLDD 317


>gi|50085634|ref|YP_047144.1| hypothetical protein ACIAD2557 [Acinetobacter sp. ADP1]
 gi|49531610|emb|CAG69322.1| tRNA-dihydrouridine synthase B [Acinetobacter sp. ADP1]
          Length = 341

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 143/324 (44%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMSKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D+V   + A+  A+ +P
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +      +  + K  ++SG+  + +H R         +++  +    YD+
Sbjct: 136 VTLKTRLGFLNGQ--ENILRVAKQAEQSGIAALALHGRT--------REDMYLSTARYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG ++   +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IKQVK-SILTIPVIANGDIDSPQKAKYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
              ++P    V +     +S     Y           +   +H+     G  +S   R  
Sbjct: 245 EHLAAPDIAEVKEVLLGHLSELYRFY-----GEYSGCRIARKHIAWYTKGLHSSNEFRQN 299

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
           +  VE+ A  A   ++E  FN ++
Sbjct: 300 MYQVESTAEQA--RLVEAYFNHLL 321


>gi|282858670|ref|ZP_06267828.1| TIM-barrel protein, nifR3 family [Prevotella bivia JCVIHMP010]
 gi|282588588|gb|EFB93735.1| TIM-barrel protein, nifR3 family [Prevotella bivia JCVIHMP010]
          Length = 325

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 142/328 (43%), Gaps = 33/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +    +E+P  +QI G +
Sbjct: 18  MEDVTDIGFRKMCKRY-GAAMVYTEFVSADAIIRSIKSTLSKMVIDDEERPTGIQIYGNN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE+   + I++N GCP  +V     G+ ++ N  ++ D    + KA+++P
Sbjct: 77  VESMVEAAKIVEEAKPDVIDINFGCPVKKVAGKGAGSGMLKNIPLLLDITREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + +  L + I+  G   + IH R         +      N D+ +
Sbjct: 137 VTVKTRLGWDE--NNLVITELAEQIQDCGAKALTIHGRT--------RAQMYTGNADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +  +  A +      VD VMIGRA +    + +   +  + 
Sbjct: 187 IGEVKKNPRIHIPIIGNGDITSVKDAYEHFDKYGVDAVMIGRATFGCPWLFSKEQDALT- 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                         D    +   M       +     +    RH+    +F G P+ ++ 
Sbjct: 246 -------------LDDKVDVLEEMLRINVERIDEYRGILHTRRHLASSPIFKGVPDFKQM 292

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  +          ++E     + E 
Sbjct: 293 R-IAMLRCTKMNELLTMLEEIRGFLKEK 319


>gi|327312701|ref|YP_004328138.1| TIM-barrel protein, nifR3 family [Prevotella denticola F0289]
 gi|326945572|gb|AEA21457.1| TIM-barrel protein, nifR3 family [Prevotella denticola F0289]
          Length = 355

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 144/329 (43%), Gaps = 33/329 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  +  +  +     E+P+ +QI G D
Sbjct: 47  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAIIRSIRSTLSKMVIDDSERPVGIQIYGRD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IVE    + I++N GCP  +V     G+ ++ N  ++ +    + KA+SIP
Sbjct: 106 VASMVEAARIVEQAKPDVIDINFGCPVKKVAGKGAGSGMLKNIPLLLEITREVVKAVSIP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 166 VTVKTRLGWDKD--NLVITDLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWTL 215

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +  + +A +      VD VMIGRA +    +          
Sbjct: 216 IGEVKKNPRIHIPIIGNGDVTSVREAGEKFDRYGVDAVMIGRATFGCPWIFRQ------- 268

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                   +  +  D    +   M       +     +    RH+    +F G P+ R+ 
Sbjct: 269 -------GEGELTLDEKIDVLEEMLRINVERIDEYRGIIHTRRHLAATPIFKGIPDFRQT 321

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R I  + A        I+E     +  +L
Sbjct: 322 R-ISMLRATKMEELMTILENCRERLRGNL 349


>gi|120609588|ref|YP_969266.1| nifR3 family TIM-barrel protein [Acidovorax citrulli AAC00-1]
 gi|120588052|gb|ABM31492.1| tRNA-U20-dihydrouridine synthase [Acidovorax citrulli AAC00-1]
          Length = 353

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 65/306 (21%), Positives = 118/306 (38%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKAL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +  +   A+  A    
Sbjct: 76  AAMMSEAALYNIDRGAEIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAQAVVDACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G   Q        L ++ +  G+  + +H R         ++     + +
Sbjct: 136 NVPVTLKMRTGWCQQHRNAV--QLARAFEGVGIQMLTVHGRT--------REQGYKGHAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 186 YDTIAAVK-AAVRVPVVANGDIDSPEKAKAVLAATGADAIMIGRAAQGRPWIFREIGHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLDHLQDHYALYGEA-----TGVRSARKHIAWYVRALPGGEAF 299

Query: 294 RHILTV 299
           R  +  
Sbjct: 300 RQHINT 305


>gi|308171971|ref|YP_003918676.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens DSM 7]
 gi|307604835|emb|CBI41206.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens DSM 7]
 gi|328551782|gb|AEB22274.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens TA208]
 gi|328910042|gb|AEB61638.1| tRNA-dihydrouridine synthase B [Bacillus amyloliquefaciens LL3]
          Length = 333

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 141/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L    +EKPL+LQI G +
Sbjct: 18  MAGVCNAAFRLTVKEF-GAGLVCAEMVSDKAILYNNAKTMGMLFIEEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  
Sbjct: 77  KETLVEAAKFVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVSAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+           ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDEDHIYAV--KNAQAVERAGGKAVALHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+    + +  NG ++    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKEVKQSL-SIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVQYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D   +       ++++ +H      G   +   R+
Sbjct: 246 GELKDEPKVREKMS-----VCKLHLDRLIKLKGEKVAVREMRKHAAWYLKGVRGNAEVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +             +  AF   +E+
Sbjct: 301 GINHCEAREEFVQ--LLDAFTAEVEA 324


>gi|288554691|ref|YP_003426626.1| nitrogen regulation transcriptional regulator [Bacillus
           pseudofirmus OF4]
 gi|288545851|gb|ADC49734.1| nitrogen regulation transcriptional regulator [Bacillus
           pseudofirmus OF4]
          Length = 333

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 146/327 (44%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  ++++  +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNPAFRLIAKEF-GAGLVCAEMVSDKAILHKNERSLSMLYVDDREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA   A+  
Sbjct: 77  KETLVEAAKFVDKNTNADIIDINMGCPVPKITKCDAGARWLLDPNKIYEMVAATVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      ++++++G + + +H R  +             + D++
Sbjct: 137 PVTVKMRIGWDED--HIFAVENARAVERAGGSAVAVHGRTRV--------QMYEGHADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K +  ++ +  NG ++    A +++    VDGVMIGRAA  N  ML    +Y  N
Sbjct: 187 IIKEVK-DAVNIPVIGNGDVQSPQDARRMIDEIGVDGVMIGRAALGNPWMLYRTVKYLEN 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G     R R 
Sbjct: 246 GELMPDPTPREKI-----DVCMIHLDRLIALRGESVAVREMRKHAAWYLKGLRGGGRIRD 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            + +           +    + + E +
Sbjct: 301 QINMFESRDDVAKT-LYDYIDQLEEEM 326


>gi|42519943|ref|NP_965858.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|42409680|gb|AAS13792.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 320

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 134/313 (42%), Gaps = 21/313 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++   ++++   +  +   A+Q+ G +  
Sbjct: 19  MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSLQK-AKVDALTAVQLAGCEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVT
Sbjct: 77  VMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNMPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +D+        L K  +  G   I +H R         +        D+  V 
Sbjct: 137 VKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFVR 186

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG +++++     L     DGVMIGR AY    ++     + S   T
Sbjct: 187 NVKEQV-KIPVIVNGDIKNLNDIQNALKESGADGVMIGRGAYGKPWLINQAMNFLSGSET 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R+       I     D    +  +   ++   +H+     G   S   R  + 
Sbjct: 246 SEPTASERLS------IILEHYDNILEYYGNDTGIKMARKHIGWYSSGLQGSSEFRVRVN 299

Query: 299 VEAGASTATHHII 311
               ++    +II
Sbjct: 300 NMTDSTEVKENII 312


>gi|260910934|ref|ZP_05917575.1| dihydrouridine synthase [Prevotella sp. oral taxon 472 str. F0295]
 gi|260634925|gb|EEX52974.1| dihydrouridine synthase [Prevotella sp. oral taxon 472 str. F0295]
          Length = 333

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 139/319 (43%), Gaps = 24/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYTEFVSAEALVRSVKSTVSKLTISDEERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  RV     GA ++ N  ++ +    + +A+  P
Sbjct: 77  VESMVEAARIVEQSHPDVIDINFGCPVKRVAGKGAGAGMLRNVPLMLEITREVVRAVRTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G + +   + +  L + ++  G+  + IH R         +        D+  
Sbjct: 137 VTVKTRLGWNCEE--IIIPTLAEQLQDCGIAALTIHGRT--------RSQMYTGEADWRY 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    QA +      VD VM+GRA +    +   + ++   
Sbjct: 187 IGEVKANPRIHIPIIGNGDICTPQQAKEAFDRYGVDAVMVGRATFGRPWVFKEMKDHLEG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P    +  D    +           +     +    RH+    +F G P+ ++ 
Sbjct: 247 -----LPQDPSLTLDRKIDLLEEQLRINIERIDEYRGILHTRRHLAASPIFKGIPDFKQT 301

Query: 294 RHILTVEAGASTATHHIIE 312
           R I  + A        I+E
Sbjct: 302 R-IAMLRADKQEELIAILE 319


>gi|302560757|ref|ZP_07313099.1| tRNA-dihydrouridine synthase [Streptomyces griseoflavus Tu4000]
 gi|302478375|gb|EFL41468.1| tRNA-dihydrouridine synthase [Streptomyces griseoflavus Tu4000]
          Length = 390

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 63/324 (19%), Positives = 129/324 (39%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E+P ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDESERPRSIQLYGV 93

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ + G  + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 94  DPVTVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRSILREAVGGAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 154 DLPVTIKMRKGIDDD--HLTYLDAGRIAVEEGVTAVALHGRTT--------AQHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 204 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 263

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +    R   D   + +  + ++          +    +H+     GF      
Sbjct: 264 EGRPQDLTRPALREVADVMVRHATLLGEWIG---DESRGVIDFRKHVAWYLKGFAVGSEM 320

Query: 294 RHIL----TVEAGASTATHHIIET 313
           R  L    ++E   +      ++ 
Sbjct: 321 RKRLAVTSSLEELRAGLDELDLDQ 344


>gi|188025691|ref|ZP_02959486.2| hypothetical protein PROSTU_01344 [Providencia stuartii ATCC 25827]
 gi|188022767|gb|EDU60807.1| hypothetical protein PROSTU_01344 [Providencia stuartii ATCC 25827]
          Length = 337

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L    +++P   ++QI G D
Sbjct: 33  MAGITDRPFRSLCYDM-GAGMTVSEMLSSNPQVWKTDKSRLRMIHRDEPGVRSVQIAGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   ++A+ KA+ +P
Sbjct: 92  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPDLVKSILSAVVKAVDVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 152 VTLKIRTGWSPEERN--CIEIAKLAEDCGIQALTIHGRT--------RACLFNGEAEYDN 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +M+GRAA     +   +  Y    
Sbjct: 202 IRAVKQ-TVAIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQHYLDTG 260

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G   +   +H+           + R  
Sbjct: 261 EMLPPMPMAEVKRIMIAHVQELHDFY-----GQGKGARIARKHVSWYLKEHAPDDQFRRS 315

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS     ++E  F   
Sbjct: 316 FNAIEDASE-QLEVLEAFFEYF 336


>gi|148652760|ref|YP_001279853.1| nifR3 family TIM-barrel protein [Psychrobacter sp. PRwf-1]
 gi|148571844|gb|ABQ93903.1| putative TIM-barrel protein, nifR3 family [Psychrobacter sp.
           PRwf-1]
          Length = 344

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 70/320 (21%), Positives = 140/320 (43%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   +         +EM+ ADA L   KK++    F  +  P++ QI GAD
Sbjct: 36  MAGVTDNPFRRLCKSF-GAGHAVSEMMTADATLYAHKKSLFRANFEGEIAPISAQIAGAD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + K+ EAA+   + G   I++N+GCP+ +V     G+ L+ + D+V   + A   A+  P
Sbjct: 95  VDKIAEAAQYQVNNGAQIIDINMGCPAKKVCRKLAGSALLKDEDLVARLLDATVAAVDAP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G ++      +  + K  +++G+  I IH R         ++++      YD+
Sbjct: 155 VTLKTRLGYENGQ--ENILRVAKRAEEAGIAAIAIHGRT--------REDKYGGQARYDL 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+   ++ +  NG ++   +A+++      D +MIGRAA     +   +  Y    
Sbjct: 205 IREVKQ-LVNIPVIANGDIDSPQKAIEVYEQTGCDAIMIGRAAQGQPWLFRDIAHYLQTG 263

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P   ++ +     +      Y           +   +H+     G  +S   R  
Sbjct: 264 EILPAPSIEQLRQIVLTHLQELYDFY-----GEYSGCRIARKHIAWYTSGIEDSNAFRQA 318

Query: 297 LTVEAGASTATHHIIETAFN 316
           +  E   +   + +++   +
Sbjct: 319 MYGEESTAG-QYKVVDKFLS 337


>gi|325677940|ref|ZP_08157582.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 8]
 gi|324110494|gb|EGC04668.1| TIM-barrel protein, nifR3 family [Ruminococcus albus 8]
          Length = 325

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 131/318 (41%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D+ YR   R     A + +EMI +  +  GD+K   +     QE+P ALQI G D
Sbjct: 20  MASVADKSYRLLCREF-GAAYMVSEMISSKGLCYGDRKTGELCEIEPQERPYALQIFGED 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++ ++  + I++N+GCP  ++     G+ LM +     +      K    P
Sbjct: 79  PYYMGKAAYLLGEYKPDIIDINMGCPVPKIVGNGSGSALMKDIPRAVEIARETVKNAGCP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD   ++      K+++++GV  + +H R         +        D +I
Sbjct: 139 VTVKFRAGWDDT--SINAVEFAKALEQTGVAAMAVHGRT--------RAQFYSGEADREI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  NG + D     ++      D VM+ R +Y    +   +  Y    
Sbjct: 189 IRQVKQAV-SVPVFGNGDVTDGESCKQMYEQTGCDLVMLARGSYGRPWVFREIRHYLETG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                P  T  ++    +I      Y  ++      +++  +++     G PNS + R  
Sbjct: 248 EVL--PPLTVKERM---EIMLKHCGYLCKYKGEERGMKEARKNVAWYVKGLPNSAKLRAE 302

Query: 296 --ILTVEAGASTATHHII 311
              L+    A      +I
Sbjct: 303 CGELSTYEQAEEMAARVI 320


>gi|307129031|ref|YP_003881047.1| tRNA-dihydrouridine synthase B [Dickeya dadantii 3937]
 gi|306526560|gb|ADM96490.1| tRNA-dihydrouridine synthase B [Dickeya dadantii 3937]
          Length = 321

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGVSDRPFRALCYAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P++V   + A+ KA+ +P
Sbjct: 76  PDEMAAAARINAENGAQVIDINMGCPAKKVNRKMAGSALLQYPELVKQILIAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +    A   + K  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRNCA--EIAKLAEDCGIQALTVHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPIIANGDITDPRKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLIGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|283788098|ref|YP_003367963.1| tRNA-dihydrouridine synthase B [Citrobacter rodentium ICC168]
 gi|282951552|emb|CBG91251.1| tRNA-dihydrouridine synthase B [Citrobacter rodentium ICC168]
          Length = 321

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 127/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA--LQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGVRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYG---HAKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|119776357|ref|YP_929097.1| tRNA-dihydrouridine synthase B [Shewanella amazonensis SB2B]
 gi|119768857|gb|ABM01428.1| tRNA-dihydrouridine synthase B [Shewanella amazonensis SB2B]
          Length = 323

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 133/326 (40%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         A+  +EM+ A+  L    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAAMAVSEMLSANPELWDTDKSRQRMAHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+   + G   I++N+GCP+ +V++   G+ LM  PD+V   + A+  A+ +P
Sbjct: 76  PEQMAWAARFNVEQGAQIIDINMGCPAKKVNKKQAGSALMQYPDLVEQILRAVVGAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +  G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWEPEHRNGV--QIARIAEDCGIASLAVHGRT--------RQCMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ +  + +  NG +    +A  +L     D +MIGR A     +   +  +    
Sbjct: 186 IRAIKQ-SVSIPVVANGDIVSPEKARFVLDYTGADALMIGRGAQGRPWIFREIQHFLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
              +        +     +S     Y          ++   +HM          + R   
Sbjct: 245 EQLAPVGDEEKRRVMLEHLSKLYDLYGEF-----KGIRFARKHMGWYLDQDEQRDFRSQF 299

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
           + L   A   +A    +E  F+ +++
Sbjct: 300 NALETAAEQRSA----VERYFDELVQ 321


>gi|332291315|ref|YP_004429924.1| TIM-barrel protein, nifR3 family [Krokinobacter diaphorus 4H-3-7-5]
 gi|332169401|gb|AEE18656.1| TIM-barrel protein, nifR3 family [Krokinobacter diaphorus 4H-3-7-5]
          Length = 330

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 136/322 (42%), Gaps = 23/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+++      +E+P+ +QI GA 
Sbjct: 19  MEDVSDPPFRALCKE-QGADVVYTEFISSEGLIRDAAKSVMKLDIYEKERPVGIQIFGAV 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ + +IVE  G + I++N GCP  +V     GA ++ + D++     AM     +P
Sbjct: 78  EESMLRSVEIVEASGPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTKAMVNHTKLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G   I IH R         +      + D+  
Sbjct: 138 VTVKTRLGWD--HDSIKIVEVAERLQDVGCAAISIHGRT--------RAQMYKGDADWGP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG +    +A+++     +DG MIGRA+         V  +   
Sbjct: 188 IAEVKNNPRMQIPVFGNGDVNTPERAVEMRDKYGLDGAMIGRASIGYPWFFNEVKHFMET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +   R +     D+    L     + +  RH    F G P+ +  R 
Sbjct: 248 GTHKAPPTMKERIEAARRHL-QMSIDWKGEVLG----VFETRRHYTNYFRGIPHFKEYRM 302

Query: 296 ILTVEAGAST--ATHHIIETAF 315
            L     +    +   +IE  F
Sbjct: 303 KLVTSDQSEDVFSALDLIEKEF 324


>gi|160916172|ref|ZP_02078379.1| hypothetical protein EUBDOL_02199 [Eubacterium dolichum DSM 3991]
 gi|158431896|gb|EDP10185.1| hypothetical protein EUBDOL_02199 [Eubacterium dolichum DSM 3991]
          Length = 335

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 136/326 (41%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+YTEM+   A+   ++K   +      E PLALQ+ G D
Sbjct: 22  MAGISNPAFRVICKQF-GAGLIYTEMVSDKALYYDNEKTIGMTAVEENEHPLALQLFGHD 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  +V AAK++++    + I++N+GCP  ++ + + G+ LM +P+     + A+ + +  
Sbjct: 81  IETMVYAAKLMDEKTNCDIIDINMGCPVTKIVKSNAGSALMKDPEHAIAMVKAVVENVKK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +   +    L K ++  GV  I +H R         K      + D+ 
Sbjct: 141 PVTVKMRIGWDLE--HINCVELAKGLEAVGVAAIAVHGRT--------KKQMYEGHADWS 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K +   + +  NG +     A ++L     D VM+GR    +  ++  +  Y   
Sbjct: 191 YIKMVK-DAVSIPVIGNGDIHCGEDAKRMLEETGCDAVMVGRGVLGDPWLIKDIVAYLEC 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +                 M D    H+     ++++  H      G P S R + 
Sbjct: 250 GEHLEAVSLQEKFAMARLHAKRLM-DLKGEHIG----IREMRGHAAWYVKGLPKSHRLKD 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            LT       A++  +E   +   + 
Sbjct: 305 ALT-----KIASYQDLEDILSAYEKE 325


>gi|149190656|ref|ZP_01868924.1| tRNA-dihydrouridine synthase [Vibrio shilonii AK1]
 gi|148835539|gb|EDL52508.1| tRNA-dihydrouridine synthase [Vibrio shilonii AK1]
          Length = 309

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 62/300 (20%), Positives = 114/300 (38%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI GAD
Sbjct: 4   MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKLWKTAKSQQRMVHEGESGIRSVQIAGAD 62

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ D +  +  A+ +P
Sbjct: 63  PKLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLKYPDIIEDILRTVVDAVDVP 122

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +  G+  + +H R         +        +YD 
Sbjct: 123 VTLKTRTGWD--TDNKNCVQIAKLAEDCGIQALALHGRT--------RTCMYKGEAEYDS 172

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 173 IKAVKNAI-SIPVIANGDIDSPEKAKFVLDYTGADALMIGRPAQGRPWIFEEIQHYLENG 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       + A    Y           +   +H+         +   R  
Sbjct: 232 TLMPERPTEDVQGILLGHVQALHQFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRA 286


>gi|320539409|ref|ZP_08039078.1| putative tRNA-dihydrouridine synthase B [Serratia symbiotica str.
           Tucson]
 gi|320030534|gb|EFW12544.1| putative tRNA-dihydrouridine synthase B [Serratia symbiotica str.
           Tucson]
          Length = 335

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 124/323 (38%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 17  MAGITDRPFRALCHTM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGLRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ + 
Sbjct: 76  PDDMAAAARINVASGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKQILHAVVNAVDVT 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILKGLSPKDNRKIPNLDYD 177
           VT+K R G   +        + +  +  G+  +  IH R         +      N +YD
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTTIHGRT--------RACLFNGNAEYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +   K+ N  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y   
Sbjct: 186 SIRAAKQ-NVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGKPWIFREIQHYLDT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                      V +   + I      Y       G   +   +H+         + + R 
Sbjct: 245 GELLPPMPLGEVKRLLIKHIRELHGFY-----GQGKGARIARKHVSWYLQEHAPNDQFRR 299

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
                  AS      +E  F  +
Sbjct: 300 TFNAIEDASE-QLEALEAYFENL 321


>gi|310829340|ref|YP_003961697.1| tRNA-dihydrouridine synthase [Eubacterium limosum KIST612]
 gi|308741074|gb|ADO38734.1| tRNA-dihydrouridine synthase [Eubacterium limosum KIST612]
          Length = 324

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 135/302 (44%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +T+  +R  A+       +++EMI    +   DKK   ++    +E P  +Q+ G++
Sbjct: 18  MAGYTNLPFRLIAKRY-GAGAVFSEMISGKGLYYKDKKTAELMLTCDEEAPAGIQLFGSE 76

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L E   K +    +  ++ N GCP+ ++ +   G+ LM NP+ +G  I A+ K    
Sbjct: 77  PEILSEVVEKYINATAFAFLDFNAGCPAPKIVKNGEGSALMRNPERLGAVIRAIKKVSEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV +K RIG D Q  +V +R + + ++++G +   IH R         +D       D+ 
Sbjct: 137 PVIIKTRIGWDAQ--SVNVREVAEILEEAGADAHTIHGRT--------RDAFYSGKADWK 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK N  + I LNG ++   +A++       D VMIGRA+  N  +   ++   S 
Sbjct: 187 IIEEVKK-NSRIPIILNGDIDSGEKAVQAFETTGCDAVMIGRASVGNPFIFREINHRLST 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T   P      +   + +     +           ++++ +H+     G  N+   R+
Sbjct: 246 GETLPVPSPEERIQTAIKHV-----ELVGMMKRPEAAIKEMRKHLAAYTKGLKNATNLRN 300

Query: 296 IL 297
            +
Sbjct: 301 EI 302


>gi|89889708|ref|ZP_01201219.1| tRNA-dihydrouridine synthase [Flavobacteria bacterium BBFL7]
 gi|89517981|gb|EAS20637.1| tRNA-dihydrouridine synthase [Flavobacteria bacterium BBFL7]
          Length = 330

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 69/310 (22%), Positives = 135/310 (43%), Gaps = 21/310 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K+   L     E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKE-NGADVVYTEFISSEGLIRDAAKSTMKLDIYEAERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++++ +IVE    + I++N GCP  +V     GA ++ + D++    AAM K   +P
Sbjct: 78  LDSMLQSVEIVERTKPDIIDINFGCPVKKVVSRGAGAGILKDIDLMVSLTAAMVKHTDLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G DD   ++ +  + + ++  G+  I IH R         +      N D+  
Sbjct: 138 ITVKTRLGWDDD--SIKIVEVAERLQDVGIKAISIHGRT--------RAQMYKGNADWKP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + +  NG +    +A+++     +DG MIGRA+         V  +F  
Sbjct: 188 IADVKNNPRMHIPVFGNGDVNTPERAVEMRDEYGLDGAMIGRASIGYPWFFREVKHFFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P           +++    + +         + +  RH    F G PN +  R 
Sbjct: 248 GTHMAKPTMQERV-----EVARRHLEMSIAWKGETLGVIETRRHYTNYFKGIPNFKEYRM 302

Query: 296 ILTVEAGAST 305
            +     +  
Sbjct: 303 KMVTSDDSQG 312


>gi|220930917|ref|YP_002507825.1| putative TIM-barrel protein, nifR3 family [Halothermothrix orenii H
           168]
 gi|219992227|gb|ACL68830.1| putative TIM-barrel protein, nifR3 family [Halothermothrix orenii H
           168]
          Length = 333

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 137/318 (43%), Gaps = 23/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLA-LQIGGA 57
           M   TD  +R  +R + N  L+YTEM+ +  ++ G++K   ++ F   +K L  +QI G 
Sbjct: 17  MAGVTDYPFRQISREM-NCQLIYTEMVSSKGLIYGNRKTRDLMDFDRGKKGLIGIQIFGG 75

Query: 58  DISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D   +  AA +I   +  + I++N+GCP+ ++ +   GA LM  P+     + A+  A+ 
Sbjct: 76  DPETMARAAVQIKNHYRPDLIDINMGCPTPKIVKNGSGAALMKVPERAKRVMEAVASAVD 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R+G D     V   ++ K  ++ G+  + IH R         +++      ++
Sbjct: 136 IPVTVKIRMGWD--HSHVNAVDIAKIAEEVGLKAVAIHGRT--------REDFYRGEANW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ E+K+E   + +  NG +     A K++     DGVM+ R    N  +L        
Sbjct: 186 DIIREVKREVT-IPVIGNGDVFTPEDAKKMMEETGCDGVMVARGVRGNPWLLKRAYYLVK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P          + +     D A  +      + ++ +H+     G P +   +
Sbjct: 245 KGEHLPGPTWEERINMAIKHL-----DMAVAYYGEKVAIPRMRKHIGWYLKGLPGNSDIK 299

Query: 295 HILTVEAGASTATHHIIE 312
             +            +I+
Sbjct: 300 DRVNKMNCYQGVKEVLIK 317


>gi|331006292|ref|ZP_08329609.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC1989]
 gi|330419913|gb|EGG94262.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC1989]
          Length = 334

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 64/296 (21%), Positives = 122/296 (41%), Gaps = 28/296 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---------ILGFSTQEKPLA 51
           M   TD  +R     L    +  +EM+ +D  L   +K+         I   + ++   +
Sbjct: 1   MAGVTDEPFRRLCSEL-GAGMTVSEMVTSDERLWSSRKSQQRLSSLTSIKDRANRKDIRS 59

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G D   +  AAK     G + I++N+GCP+ +V + + G+ L+ +  +V + + A+
Sbjct: 60  VQLAGNDPEMMAAAAKTNAKMGADVIDINMGCPAKKVCKKAAGSALLKDEKLVSEILNAV 119

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A+ IPVT+K R G   ++       + +  + SG+  + +H R         +     
Sbjct: 120 VGAVDIPVTLKIRTGWSPELRNGVT--IAQIAEDSGIQALAVHGRT--------RACAFK 169

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTV 229
            + +YD + EI ++   + +  NG +    +A  +L   D   VMIGRAA  N  +   +
Sbjct: 170 GHAEYDTIAEIVQQI-SIPVFANGDIYSAEKAKMVLQHTDAAAVMIGRAAQGNPWIFREI 228

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           + Y +       P    V     + I      Y          L+   +H+     
Sbjct: 229 NHYLATGQHLKKPSAEEVCLTLSQHIKELHYFY-----GELMGLRIARKHVGWYLK 279


>gi|260903895|ref|ZP_05912217.1| putative TIM-barrel protein, nifR3 family [Brevibacterium linens
           BL2]
          Length = 396

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 123/308 (39%), Gaps = 24/308 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  TEM+ + A++    K++  +     E P ++Q+ G D
Sbjct: 36  MAGITNTAFRRLCREY-GAGLYVTEMVTSRALVERSPKSMRIIRHEPYETPRSVQLYGVD 94

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A ++ VE+   + I+LN GCP  +V     G+ L    D+    +         
Sbjct: 95  PVTIGQAVRMLVEEDRADHIDLNFGCPVPKVTRKGGGSALPWKKDLFESIVTTAVTEADR 154

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+TVK R G+D         +  ++ + +GV  + +H R A         +      
Sbjct: 155 GGIPLTVKMRKGIDKDHQ--TFLDAGETARNAGVAAVALHGRSA--------ADLYSGQA 204

Query: 175 DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           D+D +  +K    D + +  NG +     AL+++     DGV+IGR       +   +  
Sbjct: 205 DWDAIARLKDHLGDTVPVLGNGDIFAAEDALEMMRRTGCDGVVIGRGCQGRPWLFGDLAN 264

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +       P    V +  ++     + +Y     +    ++ + +H+   F G+P   
Sbjct: 265 ALNGSDERFRPGLAEVARAVYKH-GEYLAEYYEDEFY---GVRDLRKHIAWYFKGYPVGG 320

Query: 292 RCRHILTV 299
             R  L +
Sbjct: 321 DLRRQLAM 328


>gi|330826412|ref|YP_004389715.1| TIM-barrel protein, nifR3 family [Alicycliphilus denitrificans
           K601]
 gi|329311784|gb|AEB86199.1| TIM-barrel protein, nifR3 family [Alicycliphilus denitrificans
           K601]
          Length = 352

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/329 (20%), Positives = 123/329 (37%), Gaps = 25/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKDLWASLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +      A+  A    
Sbjct: 76  AAMMAEAAVYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVQIAEAVVAACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   +        L ++ +  GV  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQRHKNAV--QLARAFEGVGVQMLTVHGRT--------REQGYKGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K +   + +  NG +    +A  +L     D VMIGRAA     +   +  Y 
Sbjct: 186 YDTIAAVKAQV-AVPVVANGDITSPEKARAVLAHTGADAVMIGRAAQGRPWIFREIGHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLEHLQDHYGLY-----GQASGVRSARKHIAWYVRDLPGGEAF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  +      + A    +   F+ + E +
Sbjct: 300 RQHINTIEDCA-AQWQAVAGFFDALGERM 327


>gi|237730178|ref|ZP_04560659.1| tRNA-dihydrouridine synthase B [Citrobacter sp. 30_2]
 gi|226908784|gb|EEH94702.1| tRNA-dihydrouridine synthase B [Citrobacter sp. 30_2]
          Length = 321

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHIRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                  S+     +E  F 
Sbjct: 300 FNAIED-SSEQLAALEAYFE 318


>gi|308066907|ref|YP_003868512.1| tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa E681]
 gi|305856186|gb|ADM67974.1| Probable tRNA-dihydrouridine synthase 1 [Paenibacillus polymyxa
           E681]
          Length = 342

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 150/323 (46%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+K+   +L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAIIHGNKRTREMLFVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK+V ++   + I++N+GCP  +V +   GA  +L+P+ + + ++++ +++S 
Sbjct: 77  RESLVKAAKVVDQETNADIIDINMGCPVPKVTKCDAGARWLLDPNKIYEMVSSVVESVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +          ++++++G   + +H R         ++     + ++D
Sbjct: 137 PVTVKMRIGWDSEHIYAV--ENARAVERAGGQAVSVHGRT--------REQLYTGHANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K E   + +  NG +     A ++  L   DGVMIGR A  N  ML    EY  +
Sbjct: 187 IIKEVK-EAVSIPVIGNGDVASPEDARRMLDLTHCDGVMIGRGALGNPWMLYRTIEYLQS 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     I+    D           ++++ +H+     G   S R + 
Sbjct: 246 GELLPDPSPEEKIR-----IAILHMDRLVALKGEAVAVREMRKHLAWYLKGLKGSARIKD 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
           ++  E         I++   + +
Sbjct: 301 VIMEETKRDDM-VRILDQFVSQL 322


>gi|58698977|ref|ZP_00373831.1| dihydrouridine synthase [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534506|gb|EAL58651.1| dihydrouridine synthase [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 302

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 134/313 (42%), Gaps = 21/313 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++   ++++   +  +   A+Q+ G +  
Sbjct: 1   MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSLQK-AKVDALTAVQLAGCEPD 58

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A+ KA+++PVT
Sbjct: 59  VMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVNMPVT 118

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +D+        L K  +  G   I +H R         +        D+  V 
Sbjct: 119 VKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFVR 168

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG +++++     L     DGVMIGR AY    ++     + S   T
Sbjct: 169 NVKEQV-KIPVIVNGDIKNLNDIQNALKESGADGVMIGRGAYGKPWLINQAMNFLSGSET 227

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R+       I     D    +  +   ++   +H+     G   S   R  + 
Sbjct: 228 SEPTASERLS------IILEHYDNILEYYGNDTGIKMARKHIGWYSSGLQGSSEFRVRVN 281

Query: 299 VEAGASTATHHII 311
               ++    +II
Sbjct: 282 NMTDSTEVKENII 294


>gi|332098832|gb|EGJ03789.1| TIM-barrel protein, nifR3 family protein [Shigella boydii 3594-74]
          Length = 305

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 1   MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 60  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 120 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 229 ELLPPLPLAEVKRLLCAHVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 283

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 284 FNAIEDASE-QLEALEAYFE 302


>gi|218247166|ref|YP_002372537.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 8801]
 gi|257060238|ref|YP_003138126.1| hypothetical protein Cyan8802_2418 [Cyanothece sp. PCC 8802]
 gi|218167644|gb|ACK66381.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 8801]
 gi|256590404|gb|ACV01291.1| TIM-barrel protein, nifR3 family [Cyanothece sp. PCC 8802]
          Length = 336

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 66/318 (20%), Positives = 133/318 (41%), Gaps = 21/318 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R     +++YTEM+ A  I        ++  +  E P+++Q+       
Sbjct: 30  GVTDLVFRRLVRRYAPQSMMYTEMVSATEIHHLKAIPRLMEIAPDEDPISIQLFDCRPDF 89

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  + K + IPVTV
Sbjct: 90  MAEAAEKAVAEGAKTIDINMGCPVNKITKKGGGSSLLRQPEIAQAIVKEVVKTVDIPVTV 149

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG DDQ   + + +  K ++ +G   + IH R         +         ++ + +
Sbjct: 150 KTRIGWDDQE--ITILDFAKKMEDAGAQMLTIHGRT--------RAQGYNGKARWEWIAK 199

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+K L   + DGVM  R       ++  +D +     T 
Sbjct: 200 VK-EIVSIPVIANGDIFSVDAAIKCLEETNADGVMCSRGTLGYPFLVGEIDYFLQTG-TR 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            + +      +  ++   ++ +Y          + Q  +H+     GF  +   R  ++ 
Sbjct: 258 RAIVTPSQRLECAKEHFNNLWEYKGI-----KGIYQSRKHLSWYCKGFSGASELRDRVSR 312

Query: 300 EAGASTATHHIIETAFNL 317
                   + +++ A  L
Sbjct: 313 IETL-EEGNQLLDHAIEL 329


>gi|319764305|ref|YP_004128242.1| tim-barrel protein, nifr3 family [Alicycliphilus denitrificans BC]
 gi|317118866|gb|ADV01355.1| TIM-barrel protein, nifR3 family [Alicycliphilus denitrificans BC]
          Length = 352

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/329 (20%), Positives = 123/329 (37%), Gaps = 25/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKDLWASLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +      A+  A    
Sbjct: 76  AAMMAEAAVYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQNEALAVQIAEAVVAACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   +        L ++ +  GV  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQRHRNAV--QLARAFEGVGVQMLTVHGRT--------REQGYKGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K +   + +  NG +    +A  +L     D VMIGRAA     +   +  Y 
Sbjct: 186 YDTIAAVKAQV-AVPVVANGDITSPEKACAVLAHTGADAVMIGRAAQGRPWIFREIGHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLEHLQDHYGLY-----GQASGVRSARKHIAWYVRDLPGGEAF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  +      + A    +   F+ + E +
Sbjct: 300 RQHINTIEDCA-AQWQAVAGFFDALGERM 327


>gi|219666230|ref|YP_002456665.1| hypothetical protein Dhaf_0161 [Desulfitobacterium hafniense DCB-2]
 gi|219536490|gb|ACL18229.1| TIM-barrel protein, nifR3 family [Desulfitobacterium hafniense
           DCB-2]
          Length = 321

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 131/301 (43%), Gaps = 21/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R +     ++TEMI   A+   + +   +L  S +  P  +Q+ G++
Sbjct: 17  MAGVTDKAFRETVRSVGG-LHVWTEMISDKALTYMNSRTLEMLDLSGEASPRIVQLFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +  +     I++N+GCP+ ++ +   G+ L+ +  +      A+ KA+ +P
Sbjct: 76  PEVMAKAAALAVERDAEIIDINMGCPTPKIVKNGEGSALLQDLPLAQRIAEAVVKAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G   +   +    L K ++  GV  + +H R         ++       + D 
Sbjct: 136 VTVKMRLGWTAER--IVAPELAKRVEAVGVQMVSVHGRT--------REQFYAGTANRDG 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +    +A  +L     DGVM+GR +  N  ++  ++ + +  
Sbjct: 186 IKKVKG-GVSIPVIANGDIFSPQEAKTVLEATGCDGVMVGRGSLGNPWLIPQINVFLNKG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P   +  K         + +Y    +     L ++ +H +    G  N+ + R  
Sbjct: 245 VLLEEPSLEQKLKVATEHFERVL-NYKGERIG----LNEMRKHAVWYIKGIRNAAQMRDY 299

Query: 297 L 297
           +
Sbjct: 300 I 300


>gi|239817593|ref|YP_002946503.1| hypothetical protein Vapar_4632 [Variovorax paradoxus S110]
 gi|239804170|gb|ACS21237.1| TIM-barrel protein, nifR3 family [Variovorax paradoxus S110]
          Length = 352

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/330 (20%), Positives = 132/330 (40%), Gaps = 27/330 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 19  MAGVTDRPFRMLCREL-GAGYAVSEMVTSRKELWNTLKTSRRANHDGEPGPIAVQIAGTD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    + G   I++N+GCP+ +V     G+ LM +  +  + + A+  A    
Sbjct: 78  AAMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMRDEPLALEIVQAVVDAAQPH 137

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G  ++        L +  + +GV  + +H R         ++     + +
Sbjct: 138 NVPVTLKMRTGWSEEHRNAV--KLARDFESAGVQMLTVHGRT--------REQGYKGSAE 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A ++L     D VMIGRAA     +   +  + 
Sbjct: 188 YDTIAAVK-AAVRVPVVANGDIRSPEKAREVLAATGADAVMIGRAAQGRPWIFREIAHFL 246

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P+    
Sbjct: 247 ATGTHLAPPLVAEVRRLLLDHLVEHYALYGEF-----SGVRTARKHIGWYVRTLPDGEAF 301

Query: 294 R-HILTVEAGASTATHHIIETAFNLMIESL 322
           R  + T+E   S A    +   F+ + + +
Sbjct: 302 RARMNTIE--DSAAQLRAVGDYFDGLADRM 329


>gi|258624522|ref|ZP_05719466.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM603]
 gi|258583219|gb|EEW08024.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM603]
          Length = 331

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 122/322 (37%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++   +  +  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIESILKTVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCVSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       + A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPILEVKDIMLGHVKALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIETADQ-QLDELEGYFDNV 329


>gi|309389966|gb|ADO77846.1| tRNA-U20-dihydrouridine synthase [Halanaerobium praevalens DSM
           2228]
          Length = 324

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 136/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP---LALQIGGA 57
           M   +D  YR   R +    LLYTEM+ A     G+++     +  EKP   +A+QI G 
Sbjct: 17  MAGVSDYPYRQLIREMGVE-LLYTEMVSAKGYEYGNRRTSELITFSEKPQAKIAVQIFGE 75

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D   + +AA  IVE++G + I++N+GCP+ ++ +   G+ LM N ++  + I A+  +  
Sbjct: 76  DPKFMAQAAAGIVEEYGADLIDINMGCPARKIVKNGAGSALMKNLNLAAEVIEAVVDSAK 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVTVK R G D +         V +   +    +    R    KG            D+
Sbjct: 136 VPVTVKMRSGWDQKNINAVELAKVAAEAGAAAVAVHGRTRNQFYKG----------EADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+  +     ++ +  NG +   + A  I       G+MIGRAA     +   V +Y  
Sbjct: 186 EIIKAVV-AAVEIPVIGNGDIFSAAAAKAIFEQTKCQGIMIGRAAQGYPWIFKEVIQYLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 SP   +  +   R +  ++  Y  RH      +  + +H+     G  N+   +
Sbjct: 245 TGKIIDSPAAYQKIEMAIRHLKLAVNYYGERH-----GVPIMRKHISWYLKGLANASEMK 299

Query: 295 HILTVEAGASTATHHIIETA 314
           + +  +   +     +++  
Sbjct: 300 NKVN-QLTKADELIELLQKY 318


>gi|323527305|ref|YP_004229458.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1001]
 gi|323384307|gb|ADX56398.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1001]
          Length = 357

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G+  + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENKNA--LNVARLAEAAGIAMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   ++ 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPEKARHVLAVTGADAVMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +       S P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLSPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 VFRHRMNT 308


>gi|326315661|ref|YP_004233333.1| TIM-barrel protein, nifR3 family [Acidovorax avenae subsp. avenae
           ATCC 19860]
 gi|323372497|gb|ADX44766.1| TIM-barrel protein, nifR3 family [Acidovorax avenae subsp. avenae
           ATCC 19860]
          Length = 353

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 119/306 (38%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKAL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM N  +  +   A+ +A    
Sbjct: 76  AAMMSEAALYNIDRGAEIIDINMGCPAKKVCNKWAGSALMQNEALAVEIAQAVVEACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G   Q        L ++ +  G+  + +H R         ++     + +
Sbjct: 136 NVPVTLKMRTGWCQQHRNAV--QLARAFEDVGIRMLTVHGRT--------REQGYKGHAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  +K     + +  NG ++   +A  +L     D +MIGRAA     +   +  Y 
Sbjct: 186 YETIAAVK-AAVRVPVVANGDIDSPEKAKAVLAATGADAIMIGRAAQGRPWIFREIGHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLDHLHDHYALYGEA-----TGVRSARKHIAWYVRALPGGEAF 299

Query: 294 RHILTV 299
           R  +  
Sbjct: 300 RQHINT 305


>gi|255082067|ref|XP_002508252.1| predicted protein [Micromonas sp. RCC299]
 gi|226523528|gb|ACO69510.1| predicted protein [Micromonas sp. RCC299]
          Length = 401

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 108/349 (30%), Positives = 171/349 (48%), Gaps = 28/349 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D+T  H+R   RLL+ +  LYTEM V   ++  D   +   L F T   P  LQ+GG+
Sbjct: 12  MMDYTTAHFRHLCRLLSRHTWLYTEMEVDQTLVHTDHPRLDRYLDFPTATHPSVLQLGGS 71

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKAL- 115
           D   +  A  +   +GY+EINLN GCPS +V     FGA LML P++V D +AAM +   
Sbjct: 72  DPETMARATAVAAPYGYDEINLNCGCPSPKVAGKGAFGAALMLEPELVRDVVAAMRENSG 131

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKS-------GVNGIWIHARKAILKGLSPKDN 168
             PVTVKCRIGVDD      L   V+++  +       G     IHARKA+L GLSP +N
Sbjct: 132 GAPVTVKCRIGVDDHDSYDDLCRFVETVACAMVPTRTDGRPLFAIHARKALLAGLSPAEN 191

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---------GVMIGRAA 219
           R +P L Y+  Y + ++ P++   +NGG++ + +A ++   V          G MIGRA 
Sbjct: 192 RTVPPLRYEWAYALARDFPEVAFVVNGGIDTLEEAAEVARGVGVPTGGGRLVGTMIGRAV 251

Query: 220 YKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGGKLQQIT 277
           + +   +L+  D       +     +  +  ++ +   A+   +   +  +S    + + 
Sbjct: 252 HADPWGVLSDADVRVFGAESNPRTSRRDLLNEYVKYCDATRGRFGTTKDGYSVPSTRHLM 311

Query: 278 RHMIGLFHGFPNSRRCRH----ILTVEAGASTATH-HIIETAFNLMIES 321
             +  LF G PN++  R      L  +A     T   I+E    ++ + 
Sbjct: 312 HPLQNLFLGEPNAKVWRRRVDEALKEDARNPDVTVGDILERTLGVLSDE 360


>gi|146313333|ref|YP_001178407.1| tRNA-dihydrouridine synthase B [Enterobacter sp. 638]
 gi|145320209|gb|ABP62356.1| tRNA-U20-dihydrouridine synthase [Enterobacter sp. 638]
          Length = 321

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   +  +  A+ +P
Sbjct: 76  PEEMAQAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILLGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G ++    +H+         + + R  
Sbjct: 245 ELLDPLPLAEVKRLLCAHIRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDAS-VQLEALEAYFE 318


>gi|124506924|ref|XP_001352059.1| dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|23505088|emb|CAD51870.1| dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 577

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 116/353 (32%), Positives = 181/353 (51%), Gaps = 40/353 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R++T  A L+TEMIV + +L      +  LGF   E P+  Q+GG D
Sbjct: 205 MINVTNRHFRAMVRIITKRAQLWTEMIVDNTLLYNLNNLEEHLGFDNNEHPIVCQLGGCD 264

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           ++ + EAA +VE  GY+EIN+NVGCPS +V     FGA LM NP+ V + +  + K + I
Sbjct: 265 MNSMSEAAILVEQAGYDEININVGCPSTKVANKGAFGASLMKNPEQVRNIVYEIKKKVQI 324

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVD+      L+  ++++   G N   +HARKA LKGL PK NRKIP L+Y 
Sbjct: 325 PVTVKIRTGVDNYDSFDFLKTFIETVSSVGCNHFIVHARKAWLKGLDPKQNRKIPPLEYY 384

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS---------------------------- 209
            VY++ K  P L   LNGG++ + +A+ +L                              
Sbjct: 385 KVYDLCKLYPHLKFTLNGGIQTIQEAIALLNGYMPENYNNNNNNNNDTSNFIQIDNYNIN 444

Query: 210 -VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            ++G+MIGRA  +N  +L+  D+   N    S+    R   + ++K     + +     +
Sbjct: 445 PLNGIMIGRACMENITVLSQTDKLVYNQDIPSTAYSRRTILEAYKKYLEKNSLF-----Y 499

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATH---HIIETAFNLM 318
           +     ++ + ++G+  G P  R  R+ L       T+T     I+E A   +
Sbjct: 500 NLSSSFELLKPVLGILKGMPGHRIFRNKLDTYIRNYTSTLPCSEILEKAIADV 552


>gi|254495051|ref|ZP_01053788.2| dihydrouridine synthase (Dus) [Polaribacter sp. MED152]
 gi|213690633|gb|EAQ43216.2| dihydrouridine synthase (Dus) [Polaribacter sp. MED152]
          Length = 315

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 130/299 (43%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 1   MEDVSDPPFRALCKE-NGADVVYTEFISSEGLIRDAAKSVIKLDIYEKERPVGIQIFGAN 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++  +IVE    + I++N GCP  +V     GA ++ + D++     AM K  ++P
Sbjct: 60  LDSMLKTIEIVEKSNPDIIDINFGCPVKKVVSKGAGAGILKDIDLMVSLTEAMVKHTNLP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +      N D+  
Sbjct: 120 ITVKTRLGWD--HDSIRIVEVAERLQDVGCKAISIHGRT--------RAQMYKGNADWVP 169

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + +  NG +    +A+++     +DG MIGRA+         V  +F  
Sbjct: 170 IAAVKNNPRMHIPVFGNGDVTTPERAMEMRDKYGLDGAMIGRASIGYPWFFNEVKHFFKT 229

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               + P      K   R +       A         + +  RH    F G P+ +  R
Sbjct: 230 GEHLAKPSIAERTKVARRHL-----QMAIDWKGERLGVVETRRHYTNYFKGIPHFKDYR 283


>gi|262163830|ref|ZP_06031570.1| tRNA dihydrouridine synthase B [Vibrio mimicus VM223]
 gi|262027810|gb|EEY46475.1| tRNA dihydrouridine synthase B [Vibrio mimicus VM223]
          Length = 331

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 124/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++ + +  +  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIENILKTVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCVSIAQLAENCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEHTGADALMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       + A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPISEVKDIMLGHVKALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIETADQ-QLDELEGYFDNV 329


>gi|296104976|ref|YP_003615122.1| tRNA-dihydrouridine synthase B [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059435|gb|ADF64173.1| tRNA-dihydrouridine synthase B [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 321

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLAPLPLAEVKRLLCSHVRELHDHYGQ---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|293399909|ref|ZP_06644055.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291306309|gb|EFE47552.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 338

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 136/326 (41%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+YTEM+   A+   ++K   +     +E PL +QI G D
Sbjct: 22  MAGISNPAFRVICKQF-GAGLIYTEMVSDKALYYENEKTLHMTAVEKEEHPLTMQIFGHD 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  +V AAK++++    + I++N+GCP  ++ + + G+ LM + D       A+  ++  
Sbjct: 81  IETMVYAAKLLDEKSDCDIIDINMGCPVNKIIKSNAGSALMKDIDHAVTMTKAVVDSVKK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D  + ++    L K +   GV+ + +H R         +        D+ 
Sbjct: 141 PVTVKMRIGWD--MDSINCVELAKGLASVGVSALAVHGRT--------RKQMYEGKADWQ 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+    + +  NG +     A ++L     D +M+GR    +  ++  +  Y + 
Sbjct: 191 YIKAVKQAV-SIPVMGNGDIRSSEDAKRMLDTTGCDAIMVGRGVLGDPWLIKEIATYLAT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+         R  +  + D    H      ++++  H      G P S + + 
Sbjct: 250 GEKLP-PVSVNEKFTMARLHAKRLCDLKGEH----VGMREMRGHAAWYVKGLPKSHQLKD 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            LT       A    I  A+  + + 
Sbjct: 305 SLTKMDTY--AQMEEILCAYEKVYQE 328


>gi|290960587|ref|YP_003491769.1| dihydrouridine synthase [Streptomyces scabiei 87.22]
 gi|260650113|emb|CBG73229.1| putative dihydrouridine synthase [Streptomyces scabiei 87.22]
          Length = 384

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 131/321 (40%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 28  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDATETPRSIQLYGV 87

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ + G  + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 88  DPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGAG 147

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 148 DLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 198 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 257

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +    R   D   + +  + +++         +    +H+     GF      
Sbjct: 258 EGRTEDLARPALREVADVMVRHATLLGEWSG---DEAKGVVDFRKHVAWYLKGFAVGSEM 314

Query: 294 RHILTVEAGAST--ATHHIIE 312
           R  L V +  +   A    ++
Sbjct: 315 RKRLAVTSSLAELRAGLDELD 335


>gi|38604694|sp|O52539|DUSB_ERWCA RecName: Full=tRNA-dihydrouridine synthase B
 gi|3885444|gb|AAC77892.1| yhdG homolog [Pectobacterium carotovorum]
          Length = 321

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 126/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGISDRPFRALCHAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  A +I  D G   I++N+GCP+ +V+    G+ L+  PD+V   ++ + KA+ +P
Sbjct: 76  PDEMAAARRINADSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKQILSTVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTIHGRT--------RACLFNGFAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLAPLPLVEVKRLLIEHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|329934687|ref|ZP_08284728.1| tRNA dihydrouridine synthase B [Streptomyces griseoaurantiacus
           M045]
 gi|329305509|gb|EGG49365.1| tRNA dihydrouridine synthase B [Streptomyces griseoaurantiacus
           M045]
          Length = 380

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 66/313 (21%), Positives = 126/313 (40%), Gaps = 22/313 (7%)

Query: 1   MVDWTDRHYRFFARLLT-NNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R  +    L  +EMI   A++  + K +  + F   EKP ++Q+ G 
Sbjct: 24  MAGITNAPFRTLCREFSAGKGLYVSEMITTRALVERNDKTMQLIRFDASEKPRSIQLYGV 83

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ + G  + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 84  DPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRSILREAVSGAG 143

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+D+    +   +  +   + GV  I +H R A                D
Sbjct: 144 DLPVTMKMRKGIDED--HLTYLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 194 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 253

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P     P   +V     R  +                +    +H+     GF     
Sbjct: 254 EGRPDDLVRPTLRQVADVMVRHATL----LGEWLGDEARGVVDFRKHVAWYLKGFAVGSE 309

Query: 293 CRHILTVEAGAST 305
            R  L + +  + 
Sbjct: 310 MRKRLAITSSLAE 322


>gi|163841639|ref|YP_001626044.1| tRNA-dihydrouridine synthase [Renibacterium salmoninarum ATCC
           33209]
 gi|162955115|gb|ABY24630.1| tRNA-dihydrouridine synthase [Renibacterium salmoninarum ATCC
           33209]
          Length = 393

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 130/321 (40%), Gaps = 24/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EM+ + A++    +++  +     EK  ++Q+ G D
Sbjct: 34  MAGITNTAFRRLCREYGG-GLYVAEMVTSRALVERTPESLRIISHDEDEKVRSVQLYGVD 92

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKAL- 115
              + +A ++ VE+   + I+LN GCP A+V     GA L    ++    +  A+ +A  
Sbjct: 93  PITVGKAVRMLVEEDHADHIDLNFGCPVAKVTRRGGGAALPWKTELFASIVRTAVREASK 152

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+DD    +      K  + SGV  + +H R A                
Sbjct: 153 GDIPLTIKMRKGIDDD--HLTYLEAGKIARDSGVAAVALHGRTA--------SQFYSGTA 202

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +++   D+ +  NG +     A++++    +DGV+IGR       +   +   
Sbjct: 203 DWSAIARLREAVTDIPVLGNGDIWSAEDAIRMVRETGIDGVVIGRGCQGRPWLFGDLMAA 262

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P   +V    +R     +  +       G  L+ I +HM   F G+     
Sbjct: 263 FDGDSRRFRPGLKQVADTVYRHAQLLIETFGEE----GKALRDIRKHMAWYFKGYVVGSE 318

Query: 293 CRHILTVEAGASTATHHIIET 313
            R  L + +    A   +++ 
Sbjct: 319 LRTKLAMVSTL-EALRELLDQ 338


>gi|194430249|ref|ZP_03062746.1| tRNA-dihydrouridine synthase B [Escherichia coli B171]
 gi|194411720|gb|EDX28045.1| tRNA-dihydrouridine synthase B [Escherichia coli B171]
          Length = 321

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 127/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      YA      G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYAP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|229917391|ref|YP_002886037.1| TIM-barrel protein, nifR3 family [Exiguobacterium sp. AT1b]
 gi|229468820|gb|ACQ70592.1| TIM-barrel protein, nifR3 family [Exiguobacterium sp. AT1b]
          Length = 331

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 135/327 (41%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EM+    IL  + +   +L    +EKPL+LQI G  
Sbjct: 20  MAGVTNPAFRLIAKEF-GAGLVCAEMVSDKGILLENARTMRMLYVDEREKPLSLQIFGGS 78

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AA+ V ++   + I++N+GCP  +V +   GA  +L+PD V + + A+   +  
Sbjct: 79  KDTLVRAAQYVDQNTNADIIDINMGCPVPKVTKCDAGAKWLLDPDKVYEMVNAVTNVVEK 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD    + + + VK+ +  G   I IH R         +  +     ++D
Sbjct: 139 PVTVKMRLGWDDD--HIFILDNVKAAQTGGAAAIAIHGRT--------RAQQYEGTANWD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E KK    + I  NG +     A +++    VD VMIGRAA  N  ML    +Y   
Sbjct: 189 WIGEAKK-VATVPIIGNGDIATPQDAKRVIDQYGVDAVMIGRAALGNPWMLYQTVQYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I     D  +        ++++ +H      G   S   R 
Sbjct: 248 GELPPEPAAREKI-----DICMLHLDRLSAIKGELTAVREMRQHAAWYLKGLKGSGPIRK 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +        A   ++    + +   L
Sbjct: 303 QINETESR-EAFAAVLYGFVDQLERQL 328


>gi|77919588|ref|YP_357403.1| dihydrouridine synthase [Pelobacter carbinolicus DSM 2380]
 gi|77545671|gb|ABA89233.1| tRNA-U20-dihydrouridine synthase [Pelobacter carbinolicus DSM 2380]
          Length = 342

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 137/322 (42%), Gaps = 28/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD   R   R      L +TEMI A+ ++ G    +++L  +  ++PL +Q+ G +
Sbjct: 36  MAGITDLACRLLMRPY-GIGLAFTEMISANGLVLGGDATRDLLASTPSDRPLGIQLFGEN 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +A K VE  G + I+LN+GCP  +V     G+ LM  P  V   IAAM +A  +P
Sbjct: 95  PKYLSQACKQVESHG-DLIDLNIGCPVKKVVRSGAGSALMQTPARVAQIIAAMRRATHLP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G D     +    +    ++ GV+ I +H R         +      + ++D+
Sbjct: 154 LTVKIRAGWD--ASHINFLEIAHIAEQEGVDAITLHPRT--------RSQGFSGSANWDL 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+ +  + +  +G + +   A ++L     D VMIGR  Y N  +   +       
Sbjct: 204 IAELKRRST-IPVIGSGDIFEAQYAQRMLQQTGCDAVMIGRGCYGNPWLARDILAMRQGQ 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
                  + R D      ++    +   R       +  + +H+     G P + + R  
Sbjct: 263 TPAPVTPEERCD------VALRHMELFLRFNDERKAVFDLRKHLCWYAKGLPGAAQFRSS 316

Query: 295 --HILTVEAGASTATHHIIETA 314
               +++E    T   H  E A
Sbjct: 317 INRAMSIEEMR-TLVMHFFEHA 337


>gi|152973924|ref|YP_001373441.1| nifR3 family TIM-barrel protein [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152022676|gb|ABS20446.1| putative TIM-barrel protein, nifR3 family [Bacillus cytotoxicus NVH
           391-98]
          Length = 332

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 78/300 (26%), Positives = 140/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILFNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVEAAKYVDQNTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGNPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   + D    H+     ++++ +H      G   + R R+
Sbjct: 246 GELMPEPTAREKVDVCMLHLDR-LIDLKNEHIA----VREMRKHAAWYLKGVRGNARVRN 300


>gi|162148051|ref|YP_001602512.1| tRNA-dihydrouridine synthase [Gluconacetobacter diazotrophicus PAl
           5]
 gi|161786628|emb|CAP56210.1| tRNA-dihydrouridine synthase [Gluconacetobacter diazotrophicus PAl
           5]
          Length = 356

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 135/311 (43%), Gaps = 22/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R  AR L    L+ +EMI + A++R ++    +   +  + P A+Q+ G +
Sbjct: 29  MSGVTDLPFRRLARRL-GAGLVISEMIASWAMVRENQATLRMAEVADDDGPNAVQLAGCE 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+I  D G + +++N GCP  +V      G+ LM +  +    + A+ +A+ +
Sbjct: 88  PEAMAQAARIAVDRGADMVDINFGCPVKKVAVGQQAGSALMRDEALAARLLDAVVRAVDV 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D    ++    L +  +++G+  + +H R         +        D+ 
Sbjct: 148 PVTLKMRMGWD--HASLNAPALARIAEQTGIRMVTVHGRT--------RQQFYNGTADWS 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V ++K +   L + +NG ++ +  A +   L   DGVMIGR  Y     L  V +  + 
Sbjct: 198 FVRQVK-DAVSLPVIVNGDIQTVDDARQALALSGADGVMIGRGCYGRPWFLAQVAQALTT 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P     D    + I     D    H  +   L+   +H+     G P+S   R 
Sbjct: 257 GDIVPDP-----DLATEKAIVLDHYDMMLSHFGAHPGLRLARKHVAWYSAGLPDSAGFRA 311

Query: 296 ILTVEAGASTA 306
            +     A  A
Sbjct: 312 AINRVDQAQEA 322


>gi|268590774|ref|ZP_06124995.1| tRNA-dihydrouridine synthase B [Providencia rettgeri DSM 1131]
 gi|291313551|gb|EFE54004.1| tRNA-dihydrouridine synthase B [Providencia rettgeri DSM 1131]
          Length = 327

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 122/320 (38%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     +    +  +EM+ ++  +    K+ L      +    ++QI G D
Sbjct: 17  MAGITDKPFRSLCYDM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHRDELGVRSVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PDIV   +  + KA+ +P
Sbjct: 76  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPDIVKSILEGVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEERN--CIEIAKLAEDCGIQALTIHGRT--------RACLFNGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +M+GRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVTIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G   +   +H+           + R  
Sbjct: 245 EILPPMPMAEVKRIMLAHVQELHDFY-----GQGKGARIARKHVSWYLKEHAPDDQFRRS 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS     ++E  F 
Sbjct: 300 FNTIEDASE-QLEVLEAFFE 318


>gi|146298835|ref|YP_001193426.1| nifR3 family TIM-barrel protein [Flavobacterium johnsoniae UW101]
 gi|146153253|gb|ABQ04107.1| tRNA-dihydrouridine synthase B-like protein [Flavobacterium
           johnsoniae UW101]
          Length = 332

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 132/305 (43%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M D +D  +R   +      ++Y+E I ++ ++R   K+ +       E+P+ +QI G D
Sbjct: 21  MEDVSDPPFRRLCKT-HGADMMYSEFISSEGLIRDAIKSRMKLDIFDYERPVGIQIFGGD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  ++KIV     + +++N GCP  +V     GA ++ + D++     A+ K   +P
Sbjct: 80  EEAMEMSSKIVSTVKPDLVDINFGCPVKKVVCRGAGAGVLKDVDLMVRLTKAVIKGTDLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+   ++ +  + + ++  GV  + IHAR         +      + D+  
Sbjct: 140 VTVKTRLGWDE--SSINIDEVAERLQDIGVQALTIHART--------RAQMYKGHSDWSH 189

Query: 179 VYEIKKENPDL--FIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP +   I  NG ++   +AL+      +DG+MIGRAA     +   +  YF 
Sbjct: 190 IARVKN-NPRITMPIFGNGDIDSPEKALQYKNEYGIDGIMIGRAAIGYPWIFNEIKHYFK 248

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P      +     +  SM             + ++ RH    F G  + +  +
Sbjct: 249 TGEHLPAPTVIDRVEAARNHLKWSM-----EWKGERLGIVEMRRHYTNYFKGIHSFKEFK 303

Query: 295 HILTV 299
             L  
Sbjct: 304 QKLVT 308


>gi|258620655|ref|ZP_05715692.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM573]
 gi|258587170|gb|EEW11882.1| tRNA-dihydrouridine synthase B [Vibrio mimicus VM573]
          Length = 331

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 122/322 (37%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+ +PD++   +  +  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRHPDVIESILKTVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNRNCVSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       + A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPILEVKDIMLGHVKALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIETADQ-QLDELEGYFDNV 329


>gi|303252012|ref|ZP_07338183.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307247175|ref|ZP_07529226.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|302649442|gb|EFL79627.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306856313|gb|EFM88465.1| tRNA-dihydrouridine synthase B [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
          Length = 320

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 132/287 (45%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L   +L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 17  MAGITDQPFRRLCTKL-GASLTFSEMMSTNPEVWHTEKSRLRLAHHEEIGINAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AAK+  ++G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 76  PAEMAMAAKVNVEYGAQIIDINMGCPAKKVNKKMAGSALLREPELVAQILDAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +K+G++ + IH R         +      N +YD 
Sbjct: 136 VTLKIRTGWDQENRN--CLEIAKIAEKAGISALTIHGRT--------RHCLFEGNAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG +    +A  +L     D VMIGR ++    +   V+++  N 
Sbjct: 186 IKAVKQAV-SIPIIANGDITSAGKAKYVLDYTQADAVMIGRGSFGRPWLFKEVEQFLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                P+  +    F + I      Y  +    G ++    +H+   
Sbjct: 245 RLLDLPLDEKCRLMF-KHIEDLHRFYGEQ---KGYRI--ARKHVGWY 285


>gi|239979346|ref|ZP_04701870.1| putative dihydrouridine synthase [Streptomyces albus J1074]
          Length = 389

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 61/317 (19%), Positives = 124/317 (39%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E+P ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIQFGETERPRSIQLYGV 93

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ D    + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 94  DPATVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD        +  +   + GV  + +H R A                D
Sbjct: 154 DLPVTIKMRKGIDDD--HTTYLDAGRIAVEEGVTAVALHGRTA--------AQHYSGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+   ++ +  NG +   + A++++     DGV++GR       +   +   F
Sbjct: 204 WEAIARLKEHVTEIPVLGNGDIWSAADAVRMMAETGCDGVVVGRGCLGRPWLFGDLVAAF 263

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V     R                   +    +H+     GF      
Sbjct: 264 EGTGAPAAPTLREVADVMVRHAQL----LGEWIGDEARGVIDFRKHVAWYLKGFSVGSDL 319

Query: 294 RHILTVEAGASTATHHI 310
           R  L + +  +     +
Sbjct: 320 RRSLAITSSLAELREQL 336


>gi|161616409|ref|YP_001590374.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|161365773|gb|ABX69541.1| hypothetical protein SPAB_04218 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 305

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 1   MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 60  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 120 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IRAVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 229 ELLPPLPLAEVKRLLCTHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 283

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 284 FNAIEDASE-QLEALEAYFE 302


>gi|320530154|ref|ZP_08031224.1| TIM-barrel protein, nifR3 family [Selenomonas artemidis F0399]
 gi|320137587|gb|EFW29499.1| TIM-barrel protein, nifR3 family [Selenomonas artemidis F0399]
          Length = 323

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 133/319 (41%), Gaps = 23/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR  AR +    L + EM+ +  I   ++    +L     E+PLA+QI    
Sbjct: 20  MAGVTDTAYRIIAREM-GCPLAFAEMVSSQGIHYRNEYTLLMLRSEPAERPLAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  + ++ N+GCP+ +V +   G+ LM +P    + + A+ +A ++
Sbjct: 79  AAMAAEAAAYIEELGTADILDFNMGCPAPKVVKNGEGSALMRDPKKAEEILKAIRRATTL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R+G DD         + +  + +GV+ + +H R         +      + DY+
Sbjct: 139 PFTVKMRLGWDDDSRNAV--EIARIAEGAGVDAVAVHGRT--------RAQFYSGSADYE 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K+    + + ++G +   +   + L     DGVMIGR A  N  +   +  +   
Sbjct: 189 AIAEVKRAVG-IPVIVSGDIRRPADLKRALDITGADGVMIGRGAQGNPWVFPQLIHWLRT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          R I     D    +      ++++ +H      G P S + R 
Sbjct: 248 GEELPPPTPAERAAVVLRHI-----DLLISYKGDYIGIREMRKHAAWYTRGLPGSAQLRE 302

Query: 296 ILTVEAGASTATHHIIETA 314
                A    A   I+  A
Sbjct: 303 QFN-RADTRDAFVEILHEA 320


>gi|242241086|ref|YP_002989267.1| tRNA-dihydrouridine synthase B [Dickeya dadantii Ech703]
 gi|242133143|gb|ACS87445.1| TIM-barrel protein, nifR3 family [Dickeya dadantii Ech703]
          Length = 321

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R    L     +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGVSDRPFRVLC-LTMGAGMAVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  AA I  D G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ K++S+P
Sbjct: 76  PAEMAAAASINMDSGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVKRILTAVVKSVSVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIARLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQAV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLIGHIRELHDFY-----GPGKGFRIARKHVSWYLQAHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|209542669|ref|YP_002274898.1| TIM-barrel protein, nifR3 family [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209530346|gb|ACI50283.1| TIM-barrel protein, nifR3 family [Gluconacetobacter diazotrophicus
           PAl 5]
          Length = 353

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 135/311 (43%), Gaps = 22/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R  AR L    L+ +EMI + A++R ++    +   +  + P A+Q+ G +
Sbjct: 26  MSGVTDLPFRRLARRL-GAGLVISEMIASWAMVRENQATLRMAEVADDDGPNAVQLAGCE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+I  D G + +++N GCP  +V      G+ LM +  +    + A+ +A+ +
Sbjct: 85  PEAMAQAARIAVDRGADMVDINFGCPVKKVAVGQQAGSALMRDEALAARLLDAVVRAVDV 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D    ++    L +  +++G+  + +H R         +        D+ 
Sbjct: 145 PVTLKMRMGWD--HASLNAPALARIAEQTGIRMVTVHGRT--------RQQFYNGTADWS 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V ++K +   L + +NG ++ +  A +   L   DGVMIGR  Y     L  V +  + 
Sbjct: 195 FVRQVK-DAVSLPVIVNGDIQTVDDARQALALSGADGVMIGRGCYGRPWFLAQVAQALTT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P     D    + I     D    H  +   L+   +H+     G P+S   R 
Sbjct: 254 GDIVPDP-----DLATEKAIVLDHYDMMLSHFGAHPGLRLARKHVAWYSAGLPDSAGFRA 308

Query: 296 ILTVEAGASTA 306
            +     A  A
Sbjct: 309 AINRVDQAQEA 319


>gi|291451221|ref|ZP_06590611.1| dihydrouridine synthase [Streptomyces albus J1074]
 gi|291354170|gb|EFE81072.1| dihydrouridine synthase [Streptomyces albus J1074]
          Length = 396

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 61/317 (19%), Positives = 124/317 (39%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E+P ++Q+ G 
Sbjct: 41  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIQFGETERPRSIQLYGV 100

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ D    + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 101 DPATVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVSGAG 160

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD        +  +   + GV  + +H R A                D
Sbjct: 161 DLPVTIKMRKGIDDD--HTTYLDAGRIAVEEGVTAVALHGRTA--------AQHYSGTAD 210

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+   ++ +  NG +   + A++++     DGV++GR       +   +   F
Sbjct: 211 WEAIARLKEHVTEIPVLGNGDIWSAADAVRMMAETGCDGVVVGRGCLGRPWLFGDLVAAF 270

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 ++P    V     R                   +    +H+     GF      
Sbjct: 271 EGTGAPAAPTLREVADVMVRHAQL----LGEWIGDEARGVIDFRKHVAWYLKGFSVGSDL 326

Query: 294 RHILTVEAGASTATHHI 310
           R  L + +  +     +
Sbjct: 327 RRSLAITSSLAELREQL 343


>gi|91217813|ref|ZP_01254768.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Psychroflexus torquis ATCC 700755]
 gi|91184014|gb|EAS70402.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Psychroflexus torquis ATCC 700755]
          Length = 330

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 133/323 (41%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE + ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRALCKEY-GADMVYTEFVSSEGLIRDAAKSMQKLDIYERERPVGIQIFGAN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ + +IVE    + I++N GCP  +V     GA ++ + D++      M K   +P
Sbjct: 78  LDSMLRSVEIVEKTKPDVIDINFGCPVKKVVSKGAGAGILKDIDLMVKLTGEMVKHTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D    ++ +  + + ++  G   I IH R         +        D+  
Sbjct: 138 ITVKTRLGWD--HDSIKIYEVAERLQDVGCKAISIHGRT--------RAQMYKGEADWKP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG +    +A  ++    +DG MIGR++  +      V  YF  
Sbjct: 188 IAEVKNNPRMHIPVFGNGDVNSPEKAALMRDEYGLDGAMIGRSSIGSPWFFKAVKHYFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+      A         + +  RH    F G P+ +  R 
Sbjct: 248 GTHCEPPSLVERV-----DIARRHLQMAIDWKGEKLGVFETRRHYTNYFKGIPHFKDYRM 302

Query: 296 ILTVEAGAST--ATHHIIETAFN 316
            +     +    A    +E  F+
Sbjct: 303 KMVTSDHSEDVFAVFDEVEDKFS 325


>gi|297199529|ref|ZP_06916926.1| dihydrouridine synthase [Streptomyces sviceus ATCC 29083]
 gi|297147421|gb|EDY56956.2| dihydrouridine synthase [Streptomyces sviceus ATCC 29083]
          Length = 395

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 124/312 (39%), Gaps = 21/312 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   EKP ++Q+ G 
Sbjct: 40  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLVHFDESEKPRSIQLYGV 99

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ + G  + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 100 DPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSGAG 159

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 160 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVTAIALHGRTA--------SQHYGGTAD 209

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       + + +   F
Sbjct: 210 WDAIARLKEHVPEIPVLGNGDIWSARDALRMVRETGCDGVVVGRGCLGRPWLFSDLVAAF 269

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   P    V     R  +                +    +H+     GF      
Sbjct: 270 EGREEFCRPDLREVADVMVRHATL----LGEWIGDEARGVIDFRKHVAWYLKGFAVGSEM 325

Query: 294 RHILTVEAGAST 305
           R  L + +  S 
Sbjct: 326 RKRLAITSSLSE 337


>gi|268610842|ref|ZP_06144569.1| tRNA-dihydrouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 330

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 125/299 (41%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR YR   +     A + +EM+ A  I   D+K   +   + +E+P+A+Q+ G++
Sbjct: 21  MAGVADRAYRLMCKKY-GAAYVVSEMVSAKGICYSDRKTASLCTVTAEERPMAVQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
              + EA KIV ++  + I++N+GCP  +V     G+ LM +  +      A  KA   +
Sbjct: 80  PEFMAEAVKIVLEYEPDIIDINMGCPVPKVVNTGAGSALMKDVPLAAKITEAAVKAAGDV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G     P      + K+++ SG   + +H R         +D         D
Sbjct: 140 PVTVKHRAGWHYGEPNAV--EMAKALEASGAAAVAVHGRS--------RDQYYSGQSHND 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+    + +  NG + D    +++      D VMIGR +Y N  +   ++     
Sbjct: 190 IIRDVKQAV-SIPVIGNGDITDADSCMRMYEETGCDLVMIGRGSYGNPFIFREIEARL-G 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               + P      +     I   +        +    + +  +H     +G+  S + R
Sbjct: 248 GEDYTPPSLEEKMRVMLEHIRLILQ---LSEKNEELAIHEARKHAAWYMNGYYGSAKFR 303


>gi|295097749|emb|CBK86839.1| tRNA-U20-dihydrouridine synthase [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 321

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLAPLPLAEVKRLLCSHVRELHDHYGQ---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|322420178|ref|YP_004199401.1| TIM-barrel protein, nifR3 family [Geobacter sp. M18]
 gi|320126565|gb|ADW14125.1| TIM-barrel protein, nifR3 family [Geobacter sp. M18]
          Length = 321

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 132/322 (40%), Gaps = 34/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+   R  AR     +L +TEM+  + + R  +K+  +L  ++ ++P+ +Q+ G +
Sbjct: 21  MAGITNLPMRLIARE-GGASLTFTEMVSVNGLTREGRKSFDLLKTTSGDRPIGMQLFGDE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++VE++G   +++N+GCP  +V     G+ LM +P  VG  + ++ KA  +P
Sbjct: 80  PEMLAEAARLVEEYG-ELLDINMGCPVKKVVGTGAGSALMKDPLKVGRIVRSVRKATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TVK R G            + +  ++ G + I +H R         +        D+  
Sbjct: 139 FTVKIRTGWVCGDD--TFPEVGRIAQEEGCDAITLHPRS--------RAQMFEGKADWAK 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  +G L      +++L     D VM+ R A  N  +        +  
Sbjct: 189 IGELK-STLKIPVIGSGDLFSADDVVRMLSETGCDAVMVARGAMGNPWLFREALALLAGE 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 +  R+       ++    +           L ++ +H+     G P + + R  
Sbjct: 248 TPVPPTVAERL------AVARRHLELFTEFEGGRVALMEMRKHLSWYSKGLPGAAQFR-- 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                    A  + IE A  L+
Sbjct: 300 ---------AAVNRIEDAAELV 312


>gi|146305745|ref|YP_001186210.1| nifR3 family TIM-barrel protein [Pseudomonas mendocina ymp]
 gi|145573946|gb|ABP83478.1| tRNA-U20-dihydrouridine synthase [Pseudomonas mendocina ymp]
          Length = 332

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 70/298 (23%), Positives = 131/298 (43%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDRPFRQLCRRL-GAGLVVSEMVTSDVRLWNSRKSSLRLLHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  PQMLAEAARKNVELGAQIIDINMGCPAKKVCNKAAGSALLRDEPLVREILEAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q        + K  + +G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRQNKNGIT--VAKIAEDAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     D ++IGRAA     +   ++ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPQKAKAVLDATGADALLIGRAAQGRPWIFREIEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 EILPAPSLLEVERILLEHLAALHAFY-----GDLMGVRIARKHVGWYLATLPGAREFR 300


>gi|15803794|ref|NP_289828.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 EDL933]
 gi|15833386|ref|NP_312159.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           Sakai]
 gi|16131148|ref|NP_417726.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           MG1655]
 gi|26249852|ref|NP_755892.1| tRNA-dihydrouridine synthase B [Escherichia coli CFT073]
 gi|74313789|ref|YP_312208.1| tRNA-dihydrouridine synthase B [Shigella sonnei Ss046]
 gi|82545631|ref|YP_409578.1| tRNA-dihydrouridine synthase B [Shigella boydii Sb227]
 gi|82778569|ref|YP_404918.1| tRNA-dihydrouridine synthase B [Shigella dysenteriae Sd197]
 gi|89110020|ref|AP_003800.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           W3110]
 gi|91212691|ref|YP_542677.1| tRNA-dihydrouridine synthase B [Escherichia coli UTI89]
 gi|110643504|ref|YP_671234.1| tRNA-dihydrouridine synthase B [Escherichia coli 536]
 gi|117625551|ref|YP_858874.1| tRNA-dihydrouridine synthase B [Escherichia coli APEC O1]
 gi|157156175|ref|YP_001464734.1| tRNA-dihydrouridine synthase B [Escherichia coli E24377A]
 gi|157162741|ref|YP_001460059.1| tRNA-dihydrouridine synthase B [Escherichia coli HS]
 gi|168752560|ref|ZP_02777582.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4113]
 gi|168758937|ref|ZP_02783944.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764879|ref|ZP_02789886.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4501]
 gi|168769123|ref|ZP_02794130.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4486]
 gi|168777676|ref|ZP_02802683.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4196]
 gi|168783829|ref|ZP_02808836.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4076]
 gi|168786153|ref|ZP_02811160.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC869]
 gi|168802602|ref|ZP_02827609.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC508]
 gi|170018497|ref|YP_001723451.1| tRNA-dihydrouridine synthase B [Escherichia coli ATCC 8739]
 gi|170082788|ref|YP_001732108.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170680881|ref|YP_001745531.1| tRNA-dihydrouridine synthase B [Escherichia coli SMS-3-5]
 gi|170765665|ref|ZP_02900476.1| tRNA-dihydrouridine synthase B [Escherichia albertii TW07627]
 gi|187734046|ref|YP_001881952.1| tRNA-dihydrouridine synthase B [Shigella boydii CDC 3083-94]
 gi|188491759|ref|ZP_02999029.1| tRNA-dihydrouridine synthase B [Escherichia coli 53638]
 gi|191169157|ref|ZP_03030915.1| tRNA-dihydrouridine synthase B [Escherichia coli B7A]
 gi|191173814|ref|ZP_03035335.1| tRNA-dihydrouridine synthase B [Escherichia coli F11]
 gi|193066463|ref|ZP_03047508.1| tRNA-dihydrouridine synthase B [Escherichia coli E22]
 gi|193071520|ref|ZP_03052430.1| tRNA-dihydrouridine synthase B [Escherichia coli E110019]
 gi|194435099|ref|ZP_03067336.1| tRNA-dihydrouridine synthase B [Shigella dysenteriae 1012]
 gi|194440027|ref|ZP_03072084.1| tRNA-dihydrouridine synthase B [Escherichia coli 101-1]
 gi|195940004|ref|ZP_03085386.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4024]
 gi|208806407|ref|ZP_03248744.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814013|ref|ZP_03255342.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821905|ref|ZP_03262225.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4042]
 gi|209396246|ref|YP_002272722.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920732|ref|YP_002294816.1| tRNA-dihydrouridine synthase B [Escherichia coli SE11]
 gi|215488567|ref|YP_002330998.1| tRNA-dihydrouridine synthase B [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217327776|ref|ZP_03443859.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14588]
 gi|218550544|ref|YP_002384335.1| tRNA-dihydrouridine synthase B [Escherichia fergusonii ATCC 35469]
 gi|218555824|ref|YP_002388737.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI1]
 gi|218560329|ref|YP_002393242.1| tRNA-dihydrouridine synthase B [Escherichia coli S88]
 gi|218691551|ref|YP_002399763.1| tRNA-dihydrouridine synthase B [Escherichia coli ED1a]
 gi|218696959|ref|YP_002404626.1| tRNA-dihydrouridine synthase B [Escherichia coli 55989]
 gi|218702033|ref|YP_002409662.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI39]
 gi|218706874|ref|YP_002414393.1| tRNA -dihydrouridine synthase B [Escherichia coli UMN026]
 gi|227887986|ref|ZP_04005791.1| tRNA-dihydrouridine synthase B [Escherichia coli 83972]
 gi|237705982|ref|ZP_04536463.1| tRNA-dihydrouridine synthase B [Escherichia sp. 3_2_53FAA]
 gi|238902359|ref|YP_002928155.1| tRNA-dihydrouridine synthase B [Escherichia coli BW2952]
 gi|253771910|ref|YP_003034741.1| tRNA-dihydrouridine synthase B [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038424|ref|ZP_04872482.1| tRNA-dihydrouridine synthase B [Escherichia sp. 1_1_43]
 gi|254163195|ref|YP_003046303.1| tRNA-dihydrouridine synthase B [Escherichia coli B str. REL606]
 gi|254795203|ref|YP_003080040.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14359]
 gi|256018826|ref|ZP_05432691.1| tRNA-dihydrouridine synthase B [Shigella sp. D9]
 gi|256024166|ref|ZP_05438031.1| tRNA-dihydrouridine synthase B [Escherichia sp. 4_1_40B]
 gi|260846065|ref|YP_003223843.1| tRNA-dihydrouridine synthase B [Escherichia coli O103:H2 str.
           12009]
 gi|260857387|ref|YP_003231278.1| tRNA-dihydrouridine synthase B [Escherichia coli O26:H11 str.
           11368]
 gi|260870011|ref|YP_003236413.1| tRNA-dihydrouridine synthase B [Escherichia coli O111:H- str.
           11128]
 gi|261255121|ref|ZP_05947654.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284627|ref|YP_003501445.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str.
           CB9615]
 gi|293406862|ref|ZP_06650788.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1412]
 gi|293412628|ref|ZP_06655351.1| tRNA-dihydrouridine synthase B [Escherichia coli B354]
 gi|293416685|ref|ZP_06659324.1| tRNA-dihydrouridine synthase B [Escherichia coli B185]
 gi|293449583|ref|ZP_06664004.1| tRNA-dihydrouridine synthase B [Escherichia coli B088]
 gi|297519369|ref|ZP_06937755.1| tRNA-dihydrouridine synthase B [Escherichia coli OP50]
 gi|298382603|ref|ZP_06992200.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1302]
 gi|300824972|ref|ZP_07105071.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 119-7]
 gi|300898032|ref|ZP_07116403.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 198-1]
 gi|300904454|ref|ZP_07122300.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 84-1]
 gi|300917419|ref|ZP_07134084.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 115-1]
 gi|300925995|ref|ZP_07141818.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 182-1]
 gi|300928705|ref|ZP_07144223.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 187-1]
 gi|300937387|ref|ZP_07152222.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 21-1]
 gi|300948346|ref|ZP_07162454.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 116-1]
 gi|300958258|ref|ZP_07170405.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 175-1]
 gi|300979714|ref|ZP_07174664.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 200-1]
 gi|300991058|ref|ZP_07179479.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 45-1]
 gi|301022203|ref|ZP_07186118.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 69-1]
 gi|301047884|ref|ZP_07194931.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 185-1]
 gi|301304273|ref|ZP_07210387.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 124-1]
 gi|301647036|ref|ZP_07246868.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 146-1]
 gi|306816397|ref|ZP_07450529.1| tRNA-dihydrouridine synthase B [Escherichia coli NC101]
 gi|307314983|ref|ZP_07594571.1| TIM-barrel protein, nifR3 family [Escherichia coli W]
 gi|309785585|ref|ZP_07680216.1| TIM-barrel , nifR3 family protein [Shigella dysenteriae 1617]
 gi|309793839|ref|ZP_07688265.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 145-7]
 gi|331643960|ref|ZP_08345091.1| tRNA-dihydrouridine synthase B [Escherichia coli H736]
 gi|331649061|ref|ZP_08350149.1| tRNA-dihydrouridine synthase B [Escherichia coli M605]
 gi|331654858|ref|ZP_08355858.1| tRNA-dihydrouridine synthase B [Escherichia coli M718]
 gi|331659549|ref|ZP_08360491.1| tRNA-dihydrouridine synthase B [Escherichia coli TA206]
 gi|331664869|ref|ZP_08365774.1| tRNA-dihydrouridine synthase B [Escherichia coli TA143]
 gi|331670084|ref|ZP_08370929.1| tRNA-dihydrouridine synthase B [Escherichia coli TA271]
 gi|331679333|ref|ZP_08380005.1| tRNA-dihydrouridine synthase B [Escherichia coli H591]
 gi|331684900|ref|ZP_08385492.1| tRNA-dihydrouridine synthase B [Escherichia coli H299]
 gi|332279908|ref|ZP_08392321.1| tRNA-dihydrouridine synthase B [Shigella sp. D9]
 gi|78100049|sp|P0ABT7|DUSB_ECO57 RecName: Full=tRNA-dihydrouridine synthase B
 gi|78100050|sp|P0ABT6|DUSB_ECOL6 RecName: Full=tRNA-dihydrouridine synthase B
 gi|78100051|sp|P0ABT5|DUSB_ECOLI RecName: Full=tRNA-dihydrouridine synthase B
 gi|12517887|gb|AAG58388.1|AE005553_10 putative dehydrogenase [Escherichia coli O157:H7 str. EDL933]
 gi|26110280|gb|AAN82466.1|AE016767_226 Hypothetical protein yhdG [Escherichia coli CFT073]
 gi|145976|gb|AAA23782.1| 'ORF1' [Escherichia coli]
 gi|606201|gb|AAA58064.1| ORF_o321 [Escherichia coli str. K-12 substr. MG1655]
 gi|1789660|gb|AAC76292.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           MG1655]
 gi|13363605|dbj|BAB37555.1| putative dehydrogenase [Escherichia coli O157:H7 str. Sakai]
 gi|73857266|gb|AAZ89973.1| putative dehydrogenase [Shigella sonnei Ss046]
 gi|81242717|gb|ABB63427.1| putative dehydrogenase [Shigella dysenteriae Sd197]
 gi|81247042|gb|ABB67750.1| putative dehydrogenase [Shigella boydii Sb227]
 gi|85676051|dbj|BAE77301.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K12 substr.
           W3110]
 gi|91074265|gb|ABE09146.1| putative dehydrogenase [Escherichia coli UTI89]
 gi|110345096|gb|ABG71333.1| tRNA-dihydrouridine synthase B [Escherichia coli 536]
 gi|115514675|gb|ABJ02750.1| tRNA-dihydrouridine synthase B [Escherichia coli APEC O1]
 gi|157068421|gb|ABV07676.1| tRNA-dihydrouridine synthase B [Escherichia coli HS]
 gi|157078205|gb|ABV17913.1| tRNA-dihydrouridine synthase B [Escherichia coli E24377A]
 gi|169753425|gb|ACA76124.1| TIM-barrel protein, nifR3 family [Escherichia coli ATCC 8739]
 gi|169890623|gb|ACB04330.1| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170124811|gb|EDS93742.1| tRNA-dihydrouridine synthase B [Escherichia albertii TW07627]
 gi|170518599|gb|ACB16777.1| tRNA-dihydrouridine synthase B [Escherichia coli SMS-3-5]
 gi|187431038|gb|ACD10312.1| tRNA-dihydrouridine synthase B [Shigella boydii CDC 3083-94]
 gi|187767124|gb|EDU30968.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4196]
 gi|188013631|gb|EDU51753.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4113]
 gi|188486958|gb|EDU62061.1| tRNA-dihydrouridine synthase B [Escherichia coli 53638]
 gi|188998885|gb|EDU67871.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4076]
 gi|189354344|gb|EDU72763.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4401]
 gi|189361809|gb|EDU80228.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365202|gb|EDU83618.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4501]
 gi|189373964|gb|EDU92380.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC869]
 gi|189375438|gb|EDU93854.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC508]
 gi|190900799|gb|EDV60590.1| tRNA-dihydrouridine synthase B [Escherichia coli B7A]
 gi|190905864|gb|EDV65482.1| tRNA-dihydrouridine synthase B [Escherichia coli F11]
 gi|192925892|gb|EDV80541.1| tRNA-dihydrouridine synthase B [Escherichia coli E22]
 gi|192955157|gb|EDV85650.1| tRNA-dihydrouridine synthase B [Escherichia coli E110019]
 gi|194416661|gb|EDX32793.1| tRNA-dihydrouridine synthase B [Shigella dysenteriae 1012]
 gi|194421031|gb|EDX37061.1| tRNA-dihydrouridine synthase B [Escherichia coli 101-1]
 gi|208726208|gb|EDZ75809.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735290|gb|EDZ83977.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4045]
 gi|208742028|gb|EDZ89710.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4042]
 gi|209157646|gb|ACI35079.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC4115]
 gi|209757538|gb|ACI77081.1| putative dehydrogenase [Escherichia coli]
 gi|209757540|gb|ACI77082.1| putative dehydrogenase [Escherichia coli]
 gi|209757542|gb|ACI77083.1| putative dehydrogenase [Escherichia coli]
 gi|209757544|gb|ACI77084.1| putative dehydrogenase [Escherichia coli]
 gi|209757546|gb|ACI77085.1| putative dehydrogenase [Escherichia coli]
 gi|209913991|dbj|BAG79065.1| putative tRNA-dihydrouridine synthase B [Escherichia coli SE11]
 gi|215266639|emb|CAS11078.1| tRNA-dihydrouridine synthase B [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217320143|gb|EEC28568.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353691|emb|CAU99946.1| tRNA-dihydrouridine synthase B [Escherichia coli 55989]
 gi|218358085|emb|CAQ90731.1| tRNA-dihydrouridine synthase B [Escherichia fergusonii ATCC 35469]
 gi|218362592|emb|CAR00217.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI1]
 gi|218367098|emb|CAR04871.1| tRNA-dihydrouridine synthase B [Escherichia coli S88]
 gi|218372019|emb|CAR19875.1| tRNA-dihydrouridine synthase B [Escherichia coli IAI39]
 gi|218429115|emb|CAR09922.1| tRNA-dihydrouridine synthase B [Escherichia coli ED1a]
 gi|218433971|emb|CAR14888.1| tRNA-dihydrouridine synthase B [Escherichia coli UMN026]
 gi|222034976|emb|CAP77719.1| tRNA-dihydrouridine synthase B [Escherichia coli LF82]
 gi|226840048|gb|EEH72069.1| tRNA-dihydrouridine synthase B [Escherichia sp. 1_1_43]
 gi|226899022|gb|EEH85281.1| tRNA-dihydrouridine synthase B [Escherichia sp. 3_2_53FAA]
 gi|227835382|gb|EEJ45848.1| tRNA-dihydrouridine synthase B [Escherichia coli 83972]
 gi|238863714|gb|ACR65712.1| tRNA-dihydrouridine synthase B [Escherichia coli BW2952]
 gi|242378794|emb|CAQ33586.1| tRNA dihydrouridine synthase [Escherichia coli BL21(DE3)]
 gi|253322954|gb|ACT27556.1| TIM-barrel protein, nifR3 family [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975096|gb|ACT40767.1| tRNA-dihydrouridine synthase B [Escherichia coli B str. REL606]
 gi|253979252|gb|ACT44922.1| tRNA-dihydrouridine synthase B [Escherichia coli BL21(DE3)]
 gi|254594603|gb|ACT73964.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           TW14359]
 gi|257756036|dbj|BAI27538.1| tRNA-dihydrouridine synthase B [Escherichia coli O26:H11 str.
           11368]
 gi|257761212|dbj|BAI32709.1| tRNA-dihydrouridine synthase B [Escherichia coli O103:H2 str.
           12009]
 gi|257766367|dbj|BAI37862.1| tRNA-dihydrouridine synthase B [Escherichia coli O111:H- str.
           11128]
 gi|260447713|gb|ACX38135.1| TIM-barrel protein, nifR3 family [Escherichia coli DH1]
 gi|281180302|dbj|BAI56632.1| putative tRNA-dihydrouridine synthase B [Escherichia coli SE15]
 gi|284923274|emb|CBG36368.1| tRNA-dihydrouridine synthase B [Escherichia coli 042]
 gi|290764500|gb|ADD58461.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str.
           CB9615]
 gi|291322673|gb|EFE62102.1| tRNA-dihydrouridine synthase B [Escherichia coli B088]
 gi|291426868|gb|EFE99900.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1412]
 gi|291432041|gb|EFF05024.1| tRNA-dihydrouridine synthase B [Escherichia coli B185]
 gi|291469399|gb|EFF11890.1| tRNA-dihydrouridine synthase B [Escherichia coli B354]
 gi|294493598|gb|ADE92354.1| tRNA-dihydrouridine synthase B [Escherichia coli IHE3034]
 gi|298277743|gb|EFI19259.1| tRNA-dihydrouridine synthase B [Escherichia coli FVEC1302]
 gi|300300227|gb|EFJ56612.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 185-1]
 gi|300307932|gb|EFJ62452.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 200-1]
 gi|300315076|gb|EFJ64860.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 175-1]
 gi|300358251|gb|EFJ74121.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 198-1]
 gi|300397616|gb|EFJ81154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 69-1]
 gi|300403616|gb|EFJ87154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 84-1]
 gi|300406979|gb|EFJ90517.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 45-1]
 gi|300415329|gb|EFJ98639.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 115-1]
 gi|300417939|gb|EFK01250.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 182-1]
 gi|300452135|gb|EFK15755.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 116-1]
 gi|300457561|gb|EFK21054.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 21-1]
 gi|300463294|gb|EFK26787.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 187-1]
 gi|300522538|gb|EFK43607.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 119-7]
 gi|300840399|gb|EFK68159.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 124-1]
 gi|301074786|gb|EFK89592.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 146-1]
 gi|305849962|gb|EFM50421.1| tRNA-dihydrouridine synthase B [Escherichia coli NC101]
 gi|306905566|gb|EFN36098.1| TIM-barrel protein, nifR3 family [Escherichia coli W]
 gi|307555354|gb|ADN48129.1| tRNA-dihydrouridine synthase B [Escherichia coli ABU 83972]
 gi|308122796|gb|EFO60058.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 145-7]
 gi|308926705|gb|EFP72181.1| TIM-barrel , nifR3 family protein [Shigella dysenteriae 1617]
 gi|309703679|emb|CBJ03020.1| tRNA-dihydrouridine synthase B [Escherichia coli ETEC H10407]
 gi|312947817|gb|ADR28644.1| tRNA-dihydrouridine synthase B [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315137843|dbj|BAJ45002.1| tRNA-dihydrouridine synthase B [Escherichia coli DH1]
 gi|315257186|gb|EFU37154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 85-1]
 gi|315289033|gb|EFU48431.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 110-3]
 gi|315294811|gb|EFU54154.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 153-1]
 gi|315300924|gb|EFU60144.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 16-3]
 gi|320177099|gb|EFW52115.1| tRNA dihydrouridine synthase B [Shigella dysenteriae CDC 74-1112]
 gi|320640052|gb|EFX09633.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           G5101]
 gi|320645622|gb|EFX14631.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H- str.
           493-89]
 gi|320662003|gb|EFX29411.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str. USDA
           5905]
 gi|323376854|gb|ADX49122.1| TIM-barrel protein, nifR3 family [Escherichia coli KO11]
 gi|323936257|gb|EGB32549.1| dihydrouridine synthase [Escherichia coli E1520]
 gi|323941647|gb|EGB37826.1| dihydrouridine synthase [Escherichia coli E482]
 gi|323946893|gb|EGB42909.1| dihydrouridine synthase [Escherichia coli H120]
 gi|323951220|gb|EGB47095.1| dihydrouridine synthase [Escherichia coli H252]
 gi|323957592|gb|EGB53306.1| dihydrouridine synthase [Escherichia coli H263]
 gi|323961092|gb|EGB56706.1| dihydrouridine synthase [Escherichia coli H489]
 gi|323966438|gb|EGB61872.1| dihydrouridine synthase [Escherichia coli M863]
 gi|323970325|gb|EGB65595.1| dihydrouridine synthase [Escherichia coli TA007]
 gi|323979021|gb|EGB74099.1| dihydrouridine synthase [Escherichia coli TW10509]
 gi|324009089|gb|EGB78308.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 57-2]
 gi|324015869|gb|EGB85088.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 60-1]
 gi|324020742|gb|EGB89961.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 117-3]
 gi|324115136|gb|EGC09100.1| dihydrouridine synthase [Escherichia fergusonii B253]
 gi|324119440|gb|EGC13323.1| dihydrouridine synthase [Escherichia coli E1167]
 gi|331037431|gb|EGI09655.1| tRNA-dihydrouridine synthase B [Escherichia coli H736]
 gi|331042808|gb|EGI14950.1| tRNA-dihydrouridine synthase B [Escherichia coli M605]
 gi|331048240|gb|EGI20317.1| tRNA-dihydrouridine synthase B [Escherichia coli M718]
 gi|331054131|gb|EGI26160.1| tRNA-dihydrouridine synthase B [Escherichia coli TA206]
 gi|331058117|gb|EGI30099.1| tRNA-dihydrouridine synthase B [Escherichia coli TA143]
 gi|331062997|gb|EGI34911.1| tRNA-dihydrouridine synthase B [Escherichia coli TA271]
 gi|331073398|gb|EGI44721.1| tRNA-dihydrouridine synthase B [Escherichia coli H591]
 gi|331078515|gb|EGI49721.1| tRNA-dihydrouridine synthase B [Escherichia coli H299]
 gi|332102260|gb|EGJ05606.1| tRNA-dihydrouridine synthase B [Shigella sp. D9]
          Length = 321

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|302530992|ref|ZP_07283334.1| dihydrouridine synthase TIM-barrel protein nifR3 [Streptomyces sp.
           AA4]
 gi|302439887|gb|EFL11703.1| dihydrouridine synthase TIM-barrel protein nifR3 [Streptomyces sp.
           AA4]
          Length = 381

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 118/303 (38%), Gaps = 24/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      +   EMI A A++       +++ F   EKP ++Q+ G D
Sbjct: 29  MAGITNVAFRQLCQEY-GAGIYVCEMITARAVVERHPGTMHMMTFGENEKPRSMQLYGVD 87

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + EA +I+   G  + ++ N GCP A+V     GA L     +  D +    KA   
Sbjct: 88  PKTMAEAVRIIVGEGLADHVDSNFGCPVAKVTRKGGGAALPFKRRLFADIVRESAKAAAE 147

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P TVK R+G+DD        +  +  +  G   + +HAR A          R     
Sbjct: 148 GGVPFTVKFRVGIDDDHH--TFLDAGRIAEAEGAAAVSLHARTA--------AQRYSGQA 197

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K+    + +  NG +     AL+++     DGV++GR       +   ++  
Sbjct: 198 DWSKIAALKEAVTSIPVLGNGDIFSADDALRMVAETGCDGVVVGRGCLGRPWLFGELEAA 257

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P    V +     +    T+    H      ++ I +HM     GFP    
Sbjct: 258 FQGREIPEGPNLGEVAR-----VLRRHTELLIEHDGPDKAMRDIRKHMAWYLMGFPVGSE 312

Query: 293 CRH 295
            R 
Sbjct: 313 LRR 315


>gi|294812524|ref|ZP_06771167.1| Putative dihydrouridine synthase [Streptomyces clavuligerus ATCC
           27064]
 gi|326441023|ref|ZP_08215757.1| dihydrouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|294325123|gb|EFG06766.1| Putative dihydrouridine synthase [Streptomyces clavuligerus ATCC
           27064]
          Length = 417

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 65/333 (19%), Positives = 128/333 (38%), Gaps = 37/333 (11%)

Query: 1   MVDWTDRHYRFFARLL-----------------TNNALLYTEMIVADAILRGDKKNI--L 41
           M   T+  +R   R                       L  +EMI   A++  ++K +  +
Sbjct: 46  MAGITNAPFRTLCREFAEGSRAFGGRPPVRGASGGKGLFVSEMITTRALVERNEKTMQLI 105

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
            F   E P ++Q+ G D   + +A +++ D G  + I+LN GCP  +V     G+ L   
Sbjct: 106 HFDASETPRSIQLYGVDPVTVGKAVRMIVDEGLADHIDLNFGCPVPKVTRKGGGSALPYK 165

Query: 101 PDIVGDCI-AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             ++   +  A+  A  +PVT+K R G+DD    +   +  +     GV  I +H R A 
Sbjct: 166 RPLLRAILREAVSNAGQLPVTMKMRKGIDDD--HLTFLDAGRIAVDEGVTAIALHGRTA- 222

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
                          D++ +  +K+  P++ +  NG +     AL+++     DGV++GR
Sbjct: 223 -------AQHYGGTADWEAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGR 275

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  +   +   F    + ++P    V     R+ +  + ++          +    
Sbjct: 276 GCLGRPWLFGDLVSAFEGDGSAAAPTLREVAA-VMRRHAELLGEWIG---DEARGVIDFR 331

Query: 278 RHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           +H+     GF      R  L + +  +     +
Sbjct: 332 KHVAWYLKGFSVGSEMRKRLAITSSLAELDEQL 364


>gi|168068461|ref|XP_001786082.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162662169|gb|EDQ49105.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 402

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 121/331 (36%), Positives = 175/331 (52%), Gaps = 20/331 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VAD I+    +    L F+  + P+ LQ+GG+D
Sbjct: 31  MMDWTDNHYRTLARLMSKHAWLYTEMVVADTIIHQQDNLDKFLKFNEVQHPIVLQLGGSD 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKAL-S 116
             KL++A+ +   + Y+EINLN GCPS +V     FGA LML   +V +C+AA+ +    
Sbjct: 91  PEKLLKASLLASVYEYDEINLNCGCPSEKVAGHGCFGASLMLESGLVAECMAAIAEGSPG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            PVTVKCRIGVDD      L   V ++   S      +HARKAILKGLSP  NR IP L 
Sbjct: 151 TPVTVKCRIGVDDFDSYDLLHKFVTTVSSSSPTQHFVVHARKAILKGLSPAANRTIPPLK 210

Query: 176 YDIVYEIKKENPDLFIGLNGG-LEDMSQALKILPSVDGVMIGRAAYKNSA-MLTTVDEYF 233
           Y+ VY + ++ P+L   LNGG +        +   V GVM+GRAAY      L  VD   
Sbjct: 211 YEYVYALIRDFPNLKFTLNGGVVNTHQVNEALQEGVFGVMLGRAAYNYPWATLGNVDNSV 270

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFHGFPN 289
                 S+P  TR      R+I     +YA   LH  G     ++ + + ++G+FH    
Sbjct: 271 YGD---STPRLTR------RQILEKYVEYADAELHKYGPKKPSVRHLVKPLLGIFHAESG 321

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           +   R  +      +     +++    ++ +
Sbjct: 322 AGVWRRAVDNSLRNAETVGALLKETLCVLPD 352


>gi|68171250|ref|ZP_00544653.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ehrlichia
           chaffeensis str. Sapulpa]
 gi|88657985|ref|YP_507556.1| putative tRNA-dihydrouridine synthase [Ehrlichia chaffeensis str.
           Arkansas]
 gi|67999332|gb|EAM85978.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ehrlichia
           chaffeensis str. Sapulpa]
 gi|88599442|gb|ABD44911.1| putative tRNA-dihydrouridine synthase [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 317

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 73/296 (24%), Positives = 126/296 (42%), Gaps = 20/296 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R+  + L    LL +EMI + A++    K  L  S  +   A+Q+ G D +
Sbjct: 17  MSGVTDFPFRYLVKSL-GAGLLVSEMIASRAMI-IQTKQSLQKSQIQINTAVQLAGCDPT 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AAK+ ED G   I++N GCP  +V     G+ LM +       + ++ KA+ IPVT
Sbjct: 75  IMADAAKLNEDMGAQIIDINFGCPVKKVVNSYAGSALMKDETTAAKILESVVKAVKIPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G D+    +    L K  +++G+  I IH R         +        D+  + 
Sbjct: 135 LKMRTGWDN--NNLNSPKLAKIAEETGIKMITIHGRT--------RTQMFTGKADWKFIR 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            IKK    + + +NG +++++     L     DG+MIGR AY     +     +  +   
Sbjct: 185 NIKK-CVKIPVIVNGDIKNLNDIKTSLEESQADGIMIGRGAYGKPWFINQALHFIKSGTI 243

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              P  +   K     I  +  D+   +      ++   +H+        NS   R
Sbjct: 244 LPDPSPSEKLK-----IITNHYDHMIEYYGKDTGVKISKKHIGWYSSSLENSSEFR 294


>gi|317131177|ref|YP_004090491.1| TIM-barrel protein, nifR3 family [Ethanoligenens harbinense YUAN-3]
 gi|315469156|gb|ADU25760.1| TIM-barrel protein, nifR3 family [Ethanoligenens harbinense YUAN-3]
          Length = 319

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 124/298 (41%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D  +R   +     A +  EM  A   +    K   +LG +  E+P+A+Q+ G++
Sbjct: 17  MAGVADTAFRTVCK-AHGAAYVVGEMASAKGFVMQATKTAELLGVTDAERPMAIQLFGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+    F  + I++N+GCP+ +V     G+ L+ +P + G  + A+  A+ +P
Sbjct: 76  PDVMAEAARRALAFSPDIIDINMGCPAPKVAGNGGGSALLKDPALAGRIVRAVANAVPVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     V    + +  +++G   + +H R         +  +  P  D+DI
Sbjct: 136 VTVKIRKGWD--AAHVNAVEIARIAEENGAAAVAVHGRT--------RAQQYAPPADWDI 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +++    + +  NG ++    A  +L     D VMIGRAA     +   V+ Y    
Sbjct: 186 IAAVRRAV-RIPVIGNGDVDSPQAAAHMLAQTGCDLVMIGRAALGRPWLFGQVETYLRTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P   R        +   +      H+     +++  +H      G   +   R
Sbjct: 245 ELLPEPNPARRMAVLLDHV-RLLCALKGEHIG----MREARKHAAWYMKGLHGAALLR 297


>gi|332662824|ref|YP_004445612.1| TIM-barrel protein, nifR3 family [Haliscomenobacter hydrossis DSM
           1100]
 gi|332331638|gb|AEE48739.1| TIM-barrel protein, nifR3 family [Haliscomenobacter hydrossis DSM
           1100]
          Length = 352

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 141/319 (44%), Gaps = 24/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I  + ++R   K++  L    +E+P+ +QI GA+
Sbjct: 38  MEDVSDPPFRALCKK-QGADMMYTEFISVEGLIRDATKSLQKLDIYDEERPIGVQIFGAE 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  ++ AA+IVE      +++N GCP  +V     GA ++ +   + +   A+ K+ ++P
Sbjct: 97  LDSMMRAAEIVEAANPEVLDINYGCPVQKVVCKMAGAGILRDVKKMVELTQAVVKSTNLP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  + + ++  G+  + IHAR  +               D+  
Sbjct: 157 VTVKTRLGWD--HNTIFIEEVAERLQDIGIKALSIHARTRV--------QMYKGESDWSW 206

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +A++     +VDG+MIGRA+     +   +  Y + 
Sbjct: 207 ISKVKNNPRIHIPIFGNGDIDTPQKAVEYRERYAVDGIMIGRASIGYPWIFREIKHYMAT 266

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P I  RVD             ++     +   + ++ RH    F GFP  +  R
Sbjct: 267 GELLPPPDIHERVDA------VRQHLQHSIDWKGAKLGVVEMRRHYTNYFRGFPGIKEFR 320

Query: 295 HILTVEAGASTATHHIIET 313
             L  E         I++ 
Sbjct: 321 SQLVTEEN-PAILFEILDR 338


>gi|213420756|ref|ZP_03353822.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 311

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 7   MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 65

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ IP
Sbjct: 66  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDIP 125

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 126 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 175

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 176 IRAVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 235 ELLPPLPLAEVKRLLCTHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 289

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 290 FNAIEDASE-QLEALEAYFE 308


>gi|228989283|ref|ZP_04149276.1| tRNA-dihydrouridine synthase 1 [Bacillus pseudomycoides DSM 12442]
 gi|228995466|ref|ZP_04155136.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock3-17]
 gi|229003089|ref|ZP_04160941.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock1-4]
 gi|228758172|gb|EEM07365.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock1-4]
 gi|228764327|gb|EEM13204.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides Rock3-17]
 gi|228770493|gb|EEM19064.1| tRNA-dihydrouridine synthase 1 [Bacillus pseudomycoides DSM 12442]
          Length = 332

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 77/310 (24%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  ++K   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILFNNQKTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+ +   + I++N+GCP  ++ +   GA  +L+PD V + +AA+  A+  
Sbjct: 77  KETLVGAAKYVDKNTTADIIDINMGCPVPKITKCDAGAKWLLDPDKVYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDIETPQDAKRMLDEVGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   + R R+
Sbjct: 246 GELMPEPTVREKM-----DVCMLHLDRLIDLKNEDIAVREMRKHAAWYLKGVRGNARVRN 300

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 301 AINTCDTRED 310


>gi|330953066|gb|EGH53326.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae Cit 7]
          Length = 337

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 134/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAQIKQAV-SIPVFANGDIDSPEKARHVLKATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 ETLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|327481992|gb|AEA85302.1| NifR3 family TIM-barrel protein [Pseudomonas stutzeri DSM 4166]
          Length = 337

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 136/314 (43%), Gaps = 21/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R     A++ +EM+ +D  L   +K+ L    + + +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRF-GAAMVVSEMLTSDVRLWNSRKSRLRMPHADEPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ LM +  +V D + A+  A+ +P
Sbjct: 79  PQMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALMRDERLVADILEAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q    A   + +  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRQNKNGAA--IARIAEQAGIAALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   V+ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPHKAARVLQVTGADGLLIGRAAQGRPWIFREVEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    V+      + A    Y          ++   +H+       P +R  R  
Sbjct: 248 ELLAAPTLGEVESTLLEHVQALHEFY-----GEVMGVRIARKHVGWYLATLPGARDFRAR 302

Query: 297 LTVEAGASTATHHI 310
                        I
Sbjct: 303 FNHLEDRDAQGSSI 316


>gi|330895634|gb|EGH27940.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330976782|gb|EGH76819.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 337

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 134/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAQIKQAV-SIPVFANGDIDSPQKARHVLKATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 ETLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|117926944|ref|YP_867561.1| nifR3 family TIM-barrel protein [Magnetococcus sp. MC-1]
 gi|117610700|gb|ABK46155.1| tRNA-U20-dihydrouridine synthase [Magnetococcus sp. MC-1]
          Length = 336

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 81/322 (25%), Positives = 142/322 (44%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TD  +R  AR      L  +EMI + A++R   K++L      +E PL++QI G+D
Sbjct: 27  MAGVTDAPFRLIARRY-GADLTVSEMIASQAMIRNTSKSLLIGTAHEEEHPLSVQIAGSD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++  D G   I++N+GCP  +V +G  GA LM +  +V   +AA+  A+ +P
Sbjct: 86  PQVMAEAARMNVDRGAEIIDINMGCPVKKVVKGQAGAALMRDEALVARILAAVVAAVPVP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D     +    + +  ++ GV  + +H R  +             + D+  
Sbjct: 146 VTLKIRLGWDK--SNLNGARIGQIAEQQGVRMLTVHGRTRM--------QMYRGHADWQC 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG L    +A +  +L  VDG+MIGRAA     +   +  Y  + 
Sbjct: 196 IASIKQAVT-IPVVGNGDLHTPQEAKEKWLLSGVDGLMIGRAAMGCPWLFGQIAHYLRSG 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P                + D+   H+ +    +   +H+     G PNS   R  
Sbjct: 255 QEKPPPDLAEQHALVLEHFDR-LIDFYGPHIGN----RMARKHLAWYAKGLPNSAHYRSA 309

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +         T H+++  +  +
Sbjct: 310 IN-HCPTPEETRHLVDDFYRGV 330


>gi|310824089|ref|YP_003956447.1| tRNA-dihydrouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309397161|gb|ADO74620.1| tRNA-dihydrouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 354

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 131/322 (40%), Gaps = 30/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQ-EKPLALQIGGA 57
           M   ++R +R  A      AL  TE++ A  ++R +++ +  L FS + E+P +LQI G 
Sbjct: 35  MAGVSERPFRVIAFKW-GAALCPTELVSAQGLMRANQRTLKYLRFSPEVERPYSLQIFGG 93

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AA + +  G   I++N+GCP  +V +   G+ LM  P      + A+ +A  +
Sbjct: 94  EPEAMAQAALVGKAHGAQIIDINMGCPVKKVTKNGAGSALMCEPLRAARIVQAIAEATGL 153

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R G D          +   +  +G   + IH R         +D       D+ 
Sbjct: 154 PVTCKIRSGWDAHHRN--YLQMAGELFSAGCAALAIHPRT--------RDQGYSGFADWS 203

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+  PD  +  NG ++  + A ++      D VMIGR A  N  +   +      
Sbjct: 204 VIADLKRHFPDRTLIGNGDVKTPADARRMRETTGCDFVMIGRGALGNPWIFREL------ 257

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR- 294
              G  P              A   ++    L   G ++   RHM    HG   +   R 
Sbjct: 258 -AGGPPPTPEERCAGVLEHFRA-HVEFVGEPL---GAVRSFRRHMAWYAHGLHGAAAFRA 312

Query: 295 --HILTVEAGASTATHHIIETA 314
             + L   A    A      +A
Sbjct: 313 EVNTLETPASVEDAVVRFFASA 334


>gi|311277777|ref|YP_003940008.1| TIM-barrel protein, nifR3 family [Enterobacter cloacae SCF1]
 gi|308746972|gb|ADO46724.1| TIM-barrel protein, nifR3 family [Enterobacter cloacae SCF1]
          Length = 321

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I  + G   I++N+GCP+ +V+    G+ L+ +P +V   + A+ KA+ +P
Sbjct: 76  PEEMAEAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQHPSLVESILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEGCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVSIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|261363918|ref|ZP_05976801.1| tRNA-dihydrouridine synthase B [Neisseria mucosa ATCC 25996]
 gi|288567925|gb|EFC89485.1| tRNA-dihydrouridine synthase B [Neisseria mucosa ATCC 25996]
          Length = 334

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 133/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLRRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 136 VTLKTRLGWHDDHKN--LPAIARIAEDCGIAALAVHGRT--------RTQMYKGEAAYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K     + + +NG +    +A  +L   + DG+MIGR A     +   +  Y  + 
Sbjct: 186 IAETKGRL-KIPVWVNGDITSPQKAATVLKQTAADGIMIGRGAQGRPWLFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +      +      + A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECNATILNHVRAMHAFY-----GEVAGVRIARKHIGWYIDAMPDGEQTRRD 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A +  +     ++ E 
Sbjct: 300 IN-RLDSAAAQYDTLAAYLEMLSEK 323


>gi|297160659|gb|ADI10371.1| putative dihydrouridine synthase [Streptomyces bingchenggensis
           BCW-1]
          Length = 377

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 124/319 (38%), Gaps = 21/319 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  D K +  + F   EKP ++Q+ G 
Sbjct: 22  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERDAKTMRLIHFDGTEKPRSIQLYGV 81

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 82  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRSILREAVTGAG 141

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 142 PLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     A++++     DGV++GR       +   +   F
Sbjct: 192 WDAIARLKEAVPEIPVLGNGDIWSADDAVRMMRRTGCDGVVVGRGCLGRPWLFGDLVAAF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 + P    V     R         A    +    +    +H+     GF      
Sbjct: 252 EGGGAPARPTLKEVAAVMRRHAEL----LAQWLENEERGVIDFRKHVAWYTKGFSVGSEM 307

Query: 294 RHILTVEAGASTATHHIIE 312
           R  L + +  +     + E
Sbjct: 308 RKRLAITSSLAELDALLGE 326


>gi|333027267|ref|ZP_08455331.1| putative dihydrouridine synthase [Streptomyces sp. Tu6071]
 gi|332747119|gb|EGJ77560.1| putative dihydrouridine synthase [Streptomyces sp. Tu6071]
          Length = 401

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 120/312 (38%), Gaps = 21/312 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 46  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMRLVQFGPAETPRSIQLYGV 105

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +AA+++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 106 DPVTVGKAARMIRDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVAGAD 165

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +     G+  I +H R                  D
Sbjct: 166 GLPVTMKMRKGIDDD--HLTALDAGRIAVDEGITAIALHGRTT--------AQHYGGTAD 215

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P+L +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 216 WDAIARLKEHVPELPVLGNGDIWTAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 275

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L  + P    V     R  +                +    +H+     GF      
Sbjct: 276 EGALRPTPPGLREVAAVMLRHAAL----LGEWLEDEERGVIDFRKHVAWYLKGFSVGSEK 331

Query: 294 RHILTVEAGAST 305
           R  L   +  + 
Sbjct: 332 RRALATTSTLAA 343


>gi|119358060|ref|YP_912704.1| nifR3 family TIM-barrel protein [Chlorobium phaeobacteroides DSM
           266]
 gi|119355409|gb|ABL66280.1| tRNA-U20-dihydrouridine synthase [Chlorobium phaeobacteroides DSM
           266]
          Length = 347

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 131/304 (43%), Gaps = 21/304 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE + A+A+ RG +K +  L     E+P+A+QI G+ 
Sbjct: 17  MEDVTDRAFRQLCKRF-GADIVYTEFVSAEALRRGAEKTLRKLVLEAGERPVAVQIFGST 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEA  + E++  + I++N GCP+ +V     GA L+  P  +     A+ +  S+P
Sbjct: 76  VESMVEATAVAEEYAPDFIDINFGCPTKKVAGKGAGAALLREPGKMAAIAEAVVRRSSLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D    ++ + ++++ ++ +G+  + IH R         + +      D++ 
Sbjct: 136 VTAKTRIGWD--HDSINIIDVLRRLEDAGIQALAIHGRT--------RSDMYKGRADWNW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K     + +  NG +     AL +      DG+MIGR A  N  +           
Sbjct: 186 IAEAKNHA-RIPVIANGDIWSAEDALAMFRHTGADGIMIGRGAIGNPFIFGQAKHLLQTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P  +          +    + +           ++ RH      G P     R+ 
Sbjct: 245 VVLPMPGFS-----LRIHAAIDHLELSVACKGEKYGTIEMRRHYSTYLKGLPKVSVVRNA 299

Query: 297 LTVE 300
           +  E
Sbjct: 300 IVRE 303


>gi|115375744|ref|ZP_01462997.1| tRNA-dihydrouridine synthase B [Stigmatella aurantiaca DW4/3-1]
 gi|115367218|gb|EAU66200.1| tRNA-dihydrouridine synthase B [Stigmatella aurantiaca DW4/3-1]
          Length = 369

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 131/322 (40%), Gaps = 30/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQ-EKPLALQIGGA 57
           M   ++R +R  A      AL  TE++ A  ++R +++ +  L FS + E+P +LQI G 
Sbjct: 50  MAGVSERPFRVIAFKW-GAALCPTELVSAQGLMRANQRTLKYLRFSPEVERPYSLQIFGG 108

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AA + +  G   I++N+GCP  +V +   G+ LM  P      + A+ +A  +
Sbjct: 109 EPEAMAQAALVGKAHGAQIIDINMGCPVKKVTKNGAGSALMCEPLRAARIVQAIAEATGL 168

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R G D          +   +  +G   + IH R         +D       D+ 
Sbjct: 169 PVTCKIRSGWDAHHRN--YLQMAGELFSAGCAALAIHPRT--------RDQGYSGFADWS 218

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+  PD  +  NG ++  + A ++      D VMIGR A  N  +   +      
Sbjct: 219 VIADLKRHFPDRTLIGNGDVKTPADARRMRETTGCDFVMIGRGALGNPWIFREL------ 272

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR- 294
              G  P              A   ++    L   G ++   RHM    HG   +   R 
Sbjct: 273 -AGGPPPTPEERCAGVLEHFRA-HVEFVGEPL---GAVRSFRRHMAWYAHGLHGAAAFRA 327

Query: 295 --HILTVEAGASTATHHIIETA 314
             + L   A    A      +A
Sbjct: 328 EVNTLETPASVEDAVVRFFASA 349


>gi|301060119|ref|ZP_07200986.1| putative tRNA-dihydrouridine synthase B [delta proteobacterium
           NaphS2]
 gi|300445631|gb|EFK09529.1| putative tRNA-dihydrouridine synthase B [delta proteobacterium
           NaphS2]
          Length = 331

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 78/302 (25%), Positives = 132/302 (43%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R L    L  TEM+ A  + RG +K    L    +EKP+A+QI GAD
Sbjct: 18  MAGITNPPFRQIVREL-GAGLTVTEMVSAVGLSRGHQKTFHYLESVAREKPVAVQIFGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+     G + +++N+GCP+ +V +   G  L+ +P  +   + A+ KA +IP
Sbjct: 77  PVIMAAAAEKAVSKGADLVDINMGCPARKVIKNGSGGALLRSPSAIERMVTAVRKACTIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G   +        +   ++  GV+ + +H R  + +G S          D+ I
Sbjct: 137 LTVKIRAGWSPEE--ANFLEITDILEDCGVDAVTVHPRF-VKQGFS-------GRADWRI 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK    + +  NG +     AL++      DGVMIGR A  N  +   + +     
Sbjct: 187 IREIKKRLT-IPVIGNGDVSRPEMALEMRKETGCDGVMIGRGALGNPWIFRQILDLEKGI 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 +  R      ++I        +R +      + +   ++    G P+S R R  
Sbjct: 246 GAQPPDLFER------KRIIRLHFSLLSRMMGEYVAAKMMRAQLLWYTKGLPHSSRFRGA 299

Query: 297 LT 298
            T
Sbjct: 300 FT 301


>gi|148262987|ref|YP_001229693.1| nifR3 family TIM-barrel protein [Geobacter uraniireducens Rf4]
 gi|146396487|gb|ABQ25120.1| tRNA-U20-dihydrouridine synthase [Geobacter uraniireducens Rf4]
          Length = 347

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 127/302 (42%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+   R  AR     AL +TEM+  + ++R  KK   +L    +++PL +QI G D
Sbjct: 42  MAGLTNLPMRVLARE-CGAALTFTEMVSVNGLVREGKKTFDLLRRDQEDRPLGIQIFGDD 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E A++VE +G   I++N+GCP  +V     G+ L+  P  V   + A+ KA S+P
Sbjct: 101 PDLLAEGARLVEPYG-ELIDINMGCPVRKVVGSGAGSALLREPAKVALILKAVRKATSLP 159

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G   +  +     + +  +  GV+ + +H R         +      + D+  
Sbjct: 160 LTIKIRTGWVVEEQS--FLEIGRIAEAEGVDAVTLHPRS--------RAQMFEGHADWSR 209

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  +G +   +    +L     DGVMI R    N  +           
Sbjct: 210 ITELKGAL-SIPVIGSGDIFSAADVTAMLAQTGCDGVMIARGGLGNPWIFREALALLR-- 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             G  PI   V +      +    D           L+++ +H+     G P   + R++
Sbjct: 267 --GEEPIPPAVGEKL--AAAMRHLDLFIETFGEHTALREMRKHLSWYAKGVPGVAQFRNM 322

Query: 297 LT 298
           + 
Sbjct: 323 IN 324


>gi|220933549|ref|YP_002512448.1| nifR3 family TIM-barrel protein [Thioalkalivibrio sp. HL-EbGR7]
 gi|219994859|gb|ACL71461.1| nifR3 family TIM-barrel protein [Thioalkalivibrio sp. HL-EbGR7]
          Length = 327

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 69/297 (23%), Positives = 132/297 (44%), Gaps = 21/297 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EM++AD  L    K+   L  + +  P+++QI GA+
Sbjct: 17  MAGVTDRPFRLLCRRL-GADMAVSEMVIADTRLWHTPKSRQRLDHAGEPDPISVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA+   D G   I++N+GCP+ +V   + G+ L+ +  +V + +  + KA+ +P
Sbjct: 76  PAMLAEAARRNADNGAQIIDINMGCPAKKVCNRAAGSALLGDERLVSEILETVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G+D     +    + +  + SG+  + +H R         +       +DYD 
Sbjct: 136 VTLKIRLGLDRD--HLNALTIARIAEHSGIQALAVHGRT--------RACAYKGTVDYDA 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + +  NG +    QA  +L     D +MIGRAA     +   +  + +  
Sbjct: 186 IAAVKQ-SVRIPVIANGDINTPEQARAVLARTGADALMIGRAAQGRPWIFREMAHFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               +P    +       + A    Y  +       ++   +H+       P + R 
Sbjct: 245 QHLPAPTADEIAALLREHLEALYGFYGEQ-----SGVRIARKHIGWYLRAHPAAARF 296


>gi|297582412|ref|YP_003698192.1| TIM-barrel protein, nifR3 family [Bacillus selenitireducens MLS10]
 gi|297140869|gb|ADH97626.1| TIM-barrel protein, nifR3 family [Bacillus selenitireducens MLS10]
          Length = 332

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 81/314 (25%), Positives = 137/314 (43%), Gaps = 23/314 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AIL  +K++  +L  + +EKPL+LQI G  
Sbjct: 19  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKAILHQNKRSINMLYVAEREKPLSLQIFGGT 77

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAKIV+     + I++N+GCP  +V     GA  +LNPD + + + A+ +A+  
Sbjct: 78  KETLVEAAKIVDTQTNADIIDINMGCPVPKVTSCDAGARWLLNPDRIYEMVDAVVQAVDK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD        +  K+++ +G   I +H R  +               D+ 
Sbjct: 138 PVTVKMRKGWDDDTVYAV--DNAKAVEAAGGKAIALHGRTRV--------QMYEGEADWS 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+    + I  NG ++    A +++     DGVMIGRAA  N  ML     +   
Sbjct: 188 IIKTVKEAVG-IPIIGNGDVQTPEDAKRMMTETGADGVMIGRAALGNPWMLYRTIHFLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR- 294
               + P      +     ++    D           ++++ +H      G   + + R 
Sbjct: 247 GENIAEPSPEEKMR-----VAILHMDRLIDWKGERVAVKEMRKHASYYMRGIRGAAKLRD 301

Query: 295 HILTVEAGASTATH 308
            +  +E     A  
Sbjct: 302 QVNQMETREEMAGV 315


>gi|89892963|ref|YP_516450.1| hypothetical protein DSY0217 [Desulfitobacterium hafniense Y51]
 gi|89332411|dbj|BAE82006.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 326

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 131/301 (43%), Gaps = 21/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD+ +R   R +     ++TEMI   A+   + +   +L  S +  P  +Q+ G++
Sbjct: 22  MAGVTDKAFRETVRSVGG-LHVWTEMISDKALTYMNSRTLEMLDLSGEASPRIVQLFGSE 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +  +     I++N+GCP+ ++ +   G+ L+ +  +      A+ KA+ +P
Sbjct: 81  PEVMAKAAALAVERDAEIIDINMGCPTPKIVKNGEGSALLQDLPLAQRIAEAVVKAVEVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G   +   +    L K ++  GV  + +H R         ++       + D 
Sbjct: 141 VTVKMRLGWTAER--IVAPELAKRVEAVGVQMVSVHGRT--------REQFYAGTANRDG 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +    +A  +L     DGVM+GR +  N  ++  ++ + +  
Sbjct: 191 IKKVKG-GVSIPVIANGDIFSPQEAKTVLEATGCDGVMVGRGSLGNPWLIPQINVFLNKG 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P   +  K         + +Y    +     L ++ +H +    G  N+ + R  
Sbjct: 250 VLLEEPSLEQKLKVATEHFERVL-NYKGERIG----LNEMRKHAVWYIKGIRNAAQMRDY 304

Query: 297 L 297
           +
Sbjct: 305 I 305


>gi|294790522|ref|ZP_06755680.1| putative tRNA-dihydrouridine synthase [Scardovia inopinata F0304]
 gi|294458419|gb|EFG26772.1| putative tRNA-dihydrouridine synthase [Scardovia inopinata F0304]
          Length = 398

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 70/302 (23%), Positives = 123/302 (40%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++ G+ K   +  F+  EK  +LQ+ G +
Sbjct: 38  MAGVTNWPFRVLCEDYGPDGLYVAEMITARALVAGNPKAFRLTRFAPSEKFRSLQLYGVN 97

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            + + +AA ++ D    + ++LN GCP  +V     G+ L    D++ D    + A+C+ 
Sbjct: 98  PAIVQQAAAMIVDGNLADHLDLNFGCPVPKVTRRGGGSALPWKTDLLQDIIHRVVAVCQP 157

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R G+DD      +R     I+  G   + +HAR                + 
Sbjct: 158 AGIPVTAKIRTGIDDDHS--TMREAATIIEGEGCACVTLHARTT--------AQYYGGHS 207

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K+    + +  NG +     AL ++     DGV +GR       +   +   
Sbjct: 208 DWSKIAELKQ-LVSIPVIGNGDIWSAEDALAMVEQTGCDGVAVGRGCQGRPWLFADLKNA 266

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+      SP   +V +   R     +  Y      +   +  + +H+     GFP    
Sbjct: 267 FAGSCQRVSPSLGQVCQVIMRHARLLVDFYDGDETMA---VHDLRKHIAWYLKGFPVGGH 323

Query: 293 CR 294
            R
Sbjct: 324 TR 325


>gi|330831061|ref|YP_004394013.1| tRNA-dihydrouridine synthase B [Aeromonas veronii B565]
 gi|328806197|gb|AEB51396.1| tRNA-dihydrouridine synthase B [Aeromonas veronii B565]
          Length = 305

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 124/320 (38%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     L    +  +EM++A+  +   +K  +    S +    ++QI GAD
Sbjct: 1   MAGVTDRPFRELCLRL-GAGMAVSEMLLANPDVWDTQKTRMRMDHSAEGGLRSVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   +++N+GCP+ +V++   G+ L+  PD V     A+  A+ +P
Sbjct: 60  PEMMAFAARYNVEQGAQIVDINMGCPAKKVNKKLAGSALLRAPDQVKAICRAVVDAVEVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +        +YD 
Sbjct: 120 VTLKIRTGWDPDNRNGV--EIARIAEDCGIAALAVHGRT--------RACLYKGEAEYDT 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L    VD VMIGRAA     +   +  +    
Sbjct: 170 IRAIKQAV-SIPVVANGDINSPEKARYVLDYTGVDAVMIGRAAQGRPWIFREIRHFLETG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +  V       ++     Y A         +   +H+          R  R  
Sbjct: 229 TKLPPPEREEVRTLMNEHVTNLHRFYGA-----YLGARIARKHVGWYLDEEETGREFRKH 283

Query: 297 LTVEAGASTATHHIIETAFN 316
                  + A    +E  F+
Sbjct: 284 FNAL-DCADAQLEALEAYFD 302


>gi|16766679|ref|NP_462294.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|62181892|ref|YP_218309.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|167552906|ref|ZP_02346657.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167993972|ref|ZP_02575065.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168233971|ref|ZP_02659029.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168239413|ref|ZP_02664471.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|168245212|ref|ZP_02670144.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168463378|ref|ZP_02697295.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168822715|ref|ZP_02834715.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443531|ref|YP_002042640.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194450924|ref|YP_002047412.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194468944|ref|ZP_03074928.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194737360|ref|YP_002116332.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197247823|ref|YP_002148308.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197262350|ref|ZP_03162424.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198242306|ref|YP_002217354.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387464|ref|ZP_03214076.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204931223|ref|ZP_03222017.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205354285|ref|YP_002228086.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858632|ref|YP_002245283.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213051972|ref|ZP_03344850.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213428299|ref|ZP_03361049.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213580280|ref|ZP_03362106.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
 gi|213619017|ref|ZP_03372843.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213853023|ref|ZP_03382555.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|238913536|ref|ZP_04657373.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|60392220|sp|P0A2R6|DUSB_SALTY RecName: Full=tRNA-dihydrouridine synthase B
 gi|60392221|sp|P0A2R7|DUSB_SALTI RecName: Full=tRNA-dihydrouridine synthase B
 gi|16421945|gb|AAL22253.1| putative TIM-barrel enzyme [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|62129525|gb|AAX67228.1| putative TIM-barrel enzyme, possibly dehydrogenase [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|194402194|gb|ACF62416.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194409228|gb|ACF69447.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194455308|gb|EDX44147.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194712862|gb|ACF92083.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|195633240|gb|EDX51654.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197211526|gb|ACH48923.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197240605|gb|EDY23225.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197287911|gb|EDY27299.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|197936822|gb|ACH74155.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199604562|gb|EDZ03107.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204319990|gb|EDZ05196.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205274066|emb|CAR39072.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205322522|gb|EDZ10361.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205328090|gb|EDZ14854.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205332030|gb|EDZ18794.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205336039|gb|EDZ22803.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205340899|gb|EDZ27663.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|206710435|emb|CAR34793.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|261248547|emb|CBG26385.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995593|gb|ACY90478.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159933|emb|CBW19452.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|320087832|emb|CBY97596.1| putative dehydrogenase [Salmonella enterica subsp. enterica serovar
           Weltevreden str. 2007-60-3289-1]
 gi|322643429|gb|EFY39993.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322684757|gb|EFY80758.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716382|gb|EFZ07953.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131746|gb|ADX19176.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323209994|gb|EFZ94899.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323219032|gb|EGA03538.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323247308|gb|EGA31273.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323263870|gb|EGA47389.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|326625133|gb|EGE31478.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629408|gb|EGE35751.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990242|gb|AEF09225.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 321

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCTHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|114327892|ref|YP_745049.1| tRNA-dihydrouridine synthase [Granulibacter bethesdensis CGDNIH1]
 gi|114316066|gb|ABI62126.1| tRNA-dihydrouridine synthase [Granulibacter bethesdensis CGDNIH1]
          Length = 370

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 85/330 (25%), Positives = 143/330 (43%), Gaps = 28/330 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL------ALQI 54
           M   TD  +R  AR +    ++ +EMI + A++R + K  L  +    P       ALQ+
Sbjct: 48  MSGVTDLPFRMLAREM-GTGMVVSEMIASWAMVREN-KTTLRMAEPAGPPSPGSPNALQL 105

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCK 113
            G D   + EAA+I  D G   I++N GCP  +V    S G+ LM +       + A  K
Sbjct: 106 AGCDPEAMAEAARIAIDKGAELIDINFGCPVKKVAVGQSAGSALMRDEVTAAKILEATVK 165

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           A+S+PVT+K R+G D Q  ++    L K  + SG+  I +H R         +       
Sbjct: 166 AVSVPVTLKMRMGWDHQ--SLNAPALAKIAEASGIRMITVHGRT--------RQQFYEGK 215

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDE 231
            D+  V  +K+    L + +NG ++ + QA +   +   DGVM+GR  Y        V  
Sbjct: 216 ADWAFVARVKQAT-SLPVIVNGDIQTVEQAAEARAISGADGVMVGRGCYGRPWFPRQVAA 274

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           Y  + +    P  +       ++I  +  D   R   +   ++   +H+     G   S 
Sbjct: 275 YLRDGVHIPEPPLSE-----RKQILLNHYDAMLRCFGTDAGMRLARKHVSWYTTGLHGSA 329

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMIES 321
             R  +   A   +    +I+T F+ +IE+
Sbjct: 330 AFRATVNRLAD-PSQVLALIDTFFDPLIEA 358


>gi|33594297|ref|NP_881941.1| hypothetical protein BP3414 [Bordetella pertussis Tohama I]
 gi|33598080|ref|NP_885723.1| hypothetical protein BPP3564 [Bordetella parapertussis 12822]
 gi|33602973|ref|NP_890533.1| hypothetical protein BB3999 [Bordetella bronchiseptica RB50]
 gi|33564372|emb|CAE43677.1| conserved hypothetical protein [Bordetella pertussis Tohama I]
 gi|33566638|emb|CAE38848.1| conserved hypothetical protein [Bordetella parapertussis]
 gi|33568604|emb|CAE34362.1| conserved hypothetical protein [Bordetella bronchiseptica RB50]
 gi|332383708|gb|AEE68555.1| hypothetical protein BPTD_3366 [Bordetella pertussis CS]
          Length = 343

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 121/300 (40%), Gaps = 24/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR   + L       +EM  ++  L    K    L    +  P+++QI GAD
Sbjct: 19  MAGVTDRPYRQLCKRL-GAGYAVSEMAASNPRLWDSVKTSRRLNHEGEIDPISVQIAGAD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EAA      G   I++N+GCP  +V   + G+ L+ + D++   + A+  A   L
Sbjct: 78  PTMMAEAAAFNVAKGARIIDINMGCPVKKVCNVASGSALLRHEDLIVRILEAVVAACAPL 137

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        + +  +++G+  + +H R         + +      +
Sbjct: 138 GVPVTLKTRTGWDREHRNA--LRVGRLAEQAGIAALTLHGRT--------RADLYTGQAE 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K E   + +  NG ++   +A ++L     D VMIGRAA     +   +D Y 
Sbjct: 188 YDTIRAVKAEL-KIPVIANGDIDSPEKARQVLDYTGADAVMIGRAAQGRPWIFREIDHYL 246

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 + P    +       +      Y          ++   +H+       P +   
Sbjct: 247 RTGARLAPPSYGEMRDLLLEHLDDHYRFYGEH-----TGVRTARKHIGWYLDDLPGAAAF 301


>gi|300817485|ref|ZP_07097701.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 107-1]
 gi|300529783|gb|EFK50845.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 107-1]
          Length = 321

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 EMLPPLPLAEVKRLLCAHVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|161506059|ref|YP_001573171.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867406|gb|ABX24029.1| hypothetical protein SARI_04246 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 321

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G  
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGGS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILVGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+E   + I  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQEV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|78223758|ref|YP_385505.1| dihydrouridine synthase TIM-barrel protein nifR3 [Geobacter
           metallireducens GS-15]
 gi|78195013|gb|ABB32780.1| tRNA-U20-dihydrouridine synthase [Geobacter metallireducens GS-15]
          Length = 324

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 129/320 (40%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  AR     +L +TEM+  + ++R  +K   +L    +++PL +Q+ G D
Sbjct: 21  MAGITNLPFRLLARE-EGASLCFTEMVSVNGLVREGRKTFELLRSVPEDRPLGIQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E A++VE  G + I++N+GCP  +V     G+ L+  P  V   I    +A  +P
Sbjct: 80  PQLLAEGARMVEGHG-DLIDINMGCPVKKVVGTGAGSALLREPAKVRAIIRETRRATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G           ++ +  ++ G + I +H R         +      + D+  
Sbjct: 139 LTVKIRSGWACGE--ANFLDIAQIAEEEGCDAITLHPRS--------RSQMFEGHADWQQ 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+ +  + +  +G L   +    +L     DGVM+ R A  N  +           
Sbjct: 189 IAEMKQ-SVKIPVIGSGDLFTAADVTAMLAETGCDGVMVARGALGNPWIFRQALALLDGR 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +     R+      + +    +           L+++ +H     HG   + + R  
Sbjct: 248 EPDAPSTGERL------RAALRHLELFTELAGERVALREMRKHFSWYSHGLSGAAQFRKA 301

Query: 297 LTVEAGASTATHHIIETAFN 316
           + +  G   A    +   F 
Sbjct: 302 VNIIEGK-EALLEALHRFFA 320


>gi|229817348|ref|ZP_04447630.1| hypothetical protein BIFANG_02610 [Bifidobacterium angulatum DSM
           20098]
 gi|229785137|gb|EEP21251.1| hypothetical protein BIFANG_02610 [Bifidobacterium angulatum DSM
           20098]
          Length = 377

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 121/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F   E+  +LQ+ G +
Sbjct: 17  MAGVTNWPFRVLCEQYGPSGLYVAEMITARALVARNPKALRLCRFDPSERVRSLQLYGVN 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D++ + I+ + K   A
Sbjct: 77  PAIVEQAAKIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEIISRVVKVCSA 136

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +IPVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 137 ANIPVTAKFRVGIDHE--HETFLQAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 186

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K+E  D+ +  NG +     AL ++     DGV IGR       +   +   
Sbjct: 187 DWTRIAELKQEL-DIPVFGNGDIWGADDALAMIDQTGCDGVAIGRGCQGRPWLFADIKHA 245

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V     R        Y      +   +  + +H+     GFP    
Sbjct: 246 FEGSTQRINPTLGEVCAVIERHAELLTRFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 302

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 303 TRKAFMECESLDDVRREI 320


>gi|302185202|ref|ZP_07261875.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae 642]
          Length = 337

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 134/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAQIKQAV-SIPVFANGDIDSPEKARHVLKATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 ETLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|239931403|ref|ZP_04688356.1| dihydrouridine synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 392

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 127/311 (40%), Gaps = 22/311 (7%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  + K +  + F   E+P +LQ+ G 
Sbjct: 28  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNDKTMQLITFDASERPRSLQLYGV 87

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ +    + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 88  DPATVGKAVRMIVEEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 147

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 148 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVRAIALHGRTT--------AQHYGGTAD 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 198 WEAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 257

Query: 234 SNPL-TGSSPIKTRVDKDFWRKISASMTDYA----ARHLHSGGKLQQITRHMIGLFHGFP 288
                 G+  +  R  +   R+++  M  +A             +    +H+     GF 
Sbjct: 258 EGGTRAGAGDLGGRGTRPTLREVADIMVRHATLLGEWIGDESRGVIDFRKHVAWYLKGFA 317

Query: 289 NSRRCRHILTV 299
                R  L V
Sbjct: 318 VGSEMRKRLAV 328


>gi|302518906|ref|ZP_07271248.1| dihydrouridine synthase [Streptomyces sp. SPB78]
 gi|318062752|ref|ZP_07981473.1| dihydrouridine synthase [Streptomyces sp. SA3_actG]
 gi|318080557|ref|ZP_07987889.1| dihydrouridine synthase [Streptomyces sp. SA3_actF]
 gi|302427801|gb|EFK99616.1| dihydrouridine synthase [Streptomyces sp. SPB78]
          Length = 402

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/312 (20%), Positives = 119/312 (38%), Gaps = 21/312 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 47  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMRLVQFGPAETPRSIQLYGV 106

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +AA+++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 107 DPVTVGKAARMIRDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVAGAD 166

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +     G+  I +H R                  D
Sbjct: 167 GLPVTMKMRKGIDDD--HLTALDAGRIAVDEGITAIALHGRTT--------AQHYGGTAD 216

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P+L +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 217 WDAIARLKEHVPELPVLGNGDIWTAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 276

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 + P    V     R  +                +    +H+     GF      
Sbjct: 277 EGAPRPTPPGLREVAAVMLRHATL----LGEWLEDEERGVIDFRKHVAWYLKGFSVGSEK 332

Query: 294 RHILTVEAGAST 305
           R  L   +  + 
Sbjct: 333 RRALATTSTLAA 344


>gi|58584719|ref|YP_198292.1| tRNA-dihydrouridine synthase [Wolbachia endosymbiont strain TRS of
           Brugia malayi]
 gi|58419035|gb|AAW71050.1| tRNA-dihydrouridine synthase [Wolbachia endosymbiont strain TRS of
           Brugia malayi]
          Length = 310

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 72/296 (24%), Positives = 129/296 (43%), Gaps = 21/296 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++   ++++   +  ++  A+Q+ G +  
Sbjct: 11  MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSMQK-AKVDELTAVQLAGCEPD 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V  G  G+ LM N     + I A+ KA+++PVT
Sbjct: 69  IMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRNEKKAAEIIEAVVKAVNVPVT 128

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +++        L K  +  G   I +H R         +        D+  + 
Sbjct: 129 VKIRTGWNNENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFIR 178

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG ++ ++     L     DGVMIGR AY    ++     + S    
Sbjct: 179 NVKEQV-KIPVIVNGDIKSLNDIQNALKESRADGVMIGRGAYGRPWLINQAINFLSGSEV 237

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  ++       I     D    +  +   ++   +H+     GF NS   R
Sbjct: 238 SEPTASEKLS------IILEHYDNILEYYGNDAGIKIARKHIGWYSSGFKNSSEFR 287


>gi|87120520|ref|ZP_01076414.1| Dihydrouridine synthase TIM-barrel protein [Marinomonas sp. MED121]
 gi|86164163|gb|EAQ65434.1| Dihydrouridine synthase TIM-barrel protein [Marinomonas sp. MED121]
          Length = 322

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/298 (21%), Positives = 124/298 (41%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R          L+ +EM+ +D  L    K+   L    +  P ++QI G D
Sbjct: 19  MAGITDIPFRRLCHQ-QGAGLVVSEMVTSDVRLWNTNKSRNRLVHDAEVSPRSVQIAGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+ +++  P
Sbjct: 78  ADMMAQAARQNIELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVREILEAVVESVDAP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  +         + +  +  G+  + +H R         +  +   N +YD 
Sbjct: 138 VTLKIRTGWSEDQKNG--LRIARMAEDIGIQALAVHGRT--------RACKFQGNAEYDT 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK+    + +  NG + D  +A   K     DG+MIGRAA     +   V  +  + 
Sbjct: 188 IAEIKQAL-SIPVFANGDINDAHKAKFVKDYTGADGIMIGRAAQGRPWIFREVAHFLEHN 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              S+P    V +     ++A    Y          ++   +H+        +    R
Sbjct: 247 EELSAPTLDEVKQLVLSHVAALHQFY-----GDYLGVRIARKHVGWYLRTLSDLSTFR 299


>gi|291439776|ref|ZP_06579166.1| dihydrouridine synthase [Streptomyces ghanaensis ATCC 14672]
 gi|291342671|gb|EFE69627.1| dihydrouridine synthase [Streptomyces ghanaensis ATCC 14672]
          Length = 398

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 127/311 (40%), Gaps = 22/311 (7%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  + K +  + F   E+P +LQ+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNDKTMQLITFDASERPRSLQLYGV 93

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ +    + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 94  DPATVGKAVRMIVEEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 154 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVRAIALHGRTT--------AQHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 204 WEAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 263

Query: 234 SNPL-TGSSPIKTRVDKDFWRKISASMTDYA----ARHLHSGGKLQQITRHMIGLFHGFP 288
                 G+  +  R  +   R+++  M  +A             +    +H+     GF 
Sbjct: 264 EGGTRAGAGDLGGRGTRPTLREVADIMVRHATLLGEWIGDESRGVIDFRKHVAWYLKGFA 323

Query: 289 NSRRCRHILTV 299
                R  L V
Sbjct: 324 VGSEMRKRLAV 334


>gi|291534002|emb|CBL07115.1| tRNA-U20-dihydrouridine synthase [Megamonas hypermegale ART12/1]
          Length = 318

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 131/302 (43%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  Y   A+ +    L+Y+EM+    I   +++   +L    +++PLA+Q+   +
Sbjct: 17  MAGVTDTAYCILAQRM-GCGLVYSEMVSDQGINFHNERTLEMLKTVPEQRPLAIQLFSGN 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
             ++ +AA  V      + I++N+GCP+ ++   + G+ LM +P +  + + A  +A+  
Sbjct: 76  PERMYKAASFVASLNCCDMIDINMGCPAPKIVRNNEGSALMKDPVLAYEIMCATREAVKD 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVTVK R G D +   V    +    +K+G++ I +H R         ++     + D+
Sbjct: 136 MPVTVKMRKGWDSEHCNVV--EMAGLAQKAGLDAIAVHGRT--------REEFYRGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ E+K+   D+ +  NG +        I      D VMIGR A  N  +     E+  
Sbjct: 186 DIIREVKQAV-DIPVIGNGDVRTCQDLKNIFERTGCDAVMIGRGAQGNPWIFRRFKEFLF 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +    P       D  +++     D   +        +++ +H     HG   S   R
Sbjct: 245 TGVDPGEPS-----IDERKQVILEHLDMLLKWKGDYIGPREMRKHATWYTHGLYGSASLR 299

Query: 295 HI 296
             
Sbjct: 300 QK 301


>gi|254382913|ref|ZP_04998269.1| dihydrouridine synthase [Streptomyces sp. Mg1]
 gi|194341814|gb|EDX22780.1| dihydrouridine synthase [Streptomyces sp. Mg1]
          Length = 398

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 70/320 (21%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   EKP ++Q+ G 
Sbjct: 42  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATEKPRSIQLYGV 101

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A + IVE+   + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 102 DPATVGKAVRMIVEEDRADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 161

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G++D    +   +  +   + GV  I +H R                  D
Sbjct: 162 DLPVTMKMRKGINDD--HLTYLDAGRIAVEEGVTAIALHGRTT--------AQHYGGTAD 211

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 212 WEAIARLKEHVPEIPVLGNGDIWCAEDALRMVRETGCDGVVVGRGCLGRPWLFNDLVAAF 271

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P     P    V     R                   +    +H+     GF     
Sbjct: 272 EGRPEDFHKPTLREVAATMHRHAQL----LGEWIGDEARGVIDFRKHVAWYLKGFSVGSE 327

Query: 293 CRHILTVEAGASTATHHIIE 312
            R  L V +  S    H+ E
Sbjct: 328 MRKKLAVTSSLSELDAHLSE 347


>gi|289675674|ref|ZP_06496564.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae FF5]
          Length = 320

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 134/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 3   MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 61

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 62  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 121

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 122 VTLKIRTGWDRDNRNG--LTVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 171

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 172 IAQIKQAV-SIPVFANGDIDSPQKARHVLKATGADGLLIGRAAQGRPWIFREIEHFLRTG 230

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 231 ETLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 285


>gi|168262591|ref|ZP_02684564.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205348570|gb|EDZ35201.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 321

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCTHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|39996108|ref|NP_952059.1| dihydrouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39982873|gb|AAR34332.1| dihydrouridine synthase family protein [Geobacter sulfurreducens
           PCA]
          Length = 325

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 137/322 (42%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  AR      L +TEM+  + ++R  KK+  +L     ++PL +Q+ G D
Sbjct: 21  MAGITNLPFRLLARE-QGAGLCFTEMVSVNGLVREGKKSFELLRSVPGDRPLGIQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  V+ +G + I++N+GCP  +V     G+ LM  PD V   + A+ +A  +P
Sbjct: 80  PDVMGRVAATVDGYG-DLIDINMGCPVKKVVGTGAGSALMREPDKVRAIVRAVRRATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G   +        + +  ++ G N + +H R         +        D+  
Sbjct: 139 LTVKIRSGWSCED--ANFIQIARIAEEEGCNAVTLHPRS--------RAQMFEGTADWTK 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+    + +  +G L   +    +L     DGVMI R A  N  +     +  +  
Sbjct: 189 LAELKQAV-AIPVIGSGDLFSAADVAAMLDRTGCDGVMIARGALGNPWIFRQALDLMAGR 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++    R+     R+  A  T+ A   + +    +++ +H+    HG P + + R  
Sbjct: 248 EPAAASPAERLA--VARRHLALFTEMAGERVAA----REMRKHLGWYSHGLPGAAQFRKE 301

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +    G + A    +   F  +
Sbjct: 302 INEIEG-NGALMEAVSRFFTAV 322


>gi|301326298|ref|ZP_07219671.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 78-1]
 gi|300846999|gb|EFK74759.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 78-1]
          Length = 321

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +   + +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNTVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|3915489|sp|O52536|DUSB_KLEPN RecName: Full=tRNA-dihydrouridine synthase B
 gi|2773320|gb|AAC77888.1| yhdG homolog [Klebsiella pneumoniae]
          Length = 321

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 127/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+ KA+ +P
Sbjct: 76  PKEMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVKAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  ++ G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWEPEHRN--CVEIAQLAEECGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHGFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                  S+     +E  F 
Sbjct: 300 FNAIED-SSEQLEALEAYFE 318


>gi|254389020|ref|ZP_05004250.1| dihydrouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|197702737|gb|EDY48549.1| dihydrouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 391

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/333 (19%), Positives = 128/333 (38%), Gaps = 37/333 (11%)

Query: 1   MVDWTDRHYRFFARLL-----------------TNNALLYTEMIVADAILRGDKKNI--L 41
           M   T+  +R   R                       L  +EMI   A++  ++K +  +
Sbjct: 20  MAGITNAPFRTLCREFAEGSRAFGGRPPVRGASGGKGLFVSEMITTRALVERNEKTMQLI 79

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
            F   E P ++Q+ G D   + +A +++ D G  + I+LN GCP  +V     G+ L   
Sbjct: 80  HFDASETPRSIQLYGVDPVTVGKAVRMIVDEGLADHIDLNFGCPVPKVTRKGGGSALPYK 139

Query: 101 PDIVGDCI-AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             ++   +  A+  A  +PVT+K R G+DD    +   +  +     GV  I +H R A 
Sbjct: 140 RPLLRAILREAVSNAGQLPVTMKMRKGIDDD--HLTFLDAGRIAVDEGVTAIALHGRTA- 196

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
                          D++ +  +K+  P++ +  NG +     AL+++     DGV++GR
Sbjct: 197 -------AQHYGGTADWEAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGR 249

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  +   +   F    + ++P    V     R+ +  + ++          +    
Sbjct: 250 GCLGRPWLFGDLVSAFEGDGSAAAPTLREVAA-VMRRHAELLGEWIG---DEARGVIDFR 305

Query: 278 RHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           +H+     GF      R  L + +  +     +
Sbjct: 306 KHVAWYLKGFSVGSEMRKRLAITSSLAELDEQL 338


>gi|170077562|ref|YP_001734200.1| dihydrouridine synthase (Dus) [Synechococcus sp. PCC 7002]
 gi|169885231|gb|ACA98944.1| Dihydrouridine synthase (Dus) [Synechococcus sp. PCC 7002]
          Length = 353

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 60/319 (18%), Positives = 127/319 (39%), Gaps = 21/319 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISK 61
             TD  +R   R    ++++YTEM+ A  +        ++     E+P+++Q+       
Sbjct: 36  GVTDLVFRRLVRRYAPSSMMYTEMVRAQEVHHLQTLPRLMEIDPGEQPISIQLFDCRPDF 95

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAK     G   I++N+GCP  ++     G+ L+  P++    + A+ +A+ +PVTV
Sbjct: 96  MGEAAKKAVAEGAQTIDINMGCPVNKITRKGGGSSLLRQPEVAVAIVKAVVEAVDVPVTV 155

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG  D    + + +  + ++ +G   + +H R         +         +  + +
Sbjct: 156 KTRIGWAD--AEIVIVDFARRLEDAGAQMLTVHGRT--------RAQGYTGKAQWQWIKK 205

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E   + +  NG +  +  A+  L     DGVM  R       ++  +D +       
Sbjct: 206 VK-EVLSIPVIANGDIFSVDAAIACLEATGADGVMCSRGTLGYPFLVGEIDHFLKTGQRR 264

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P    + +   ++    +  Y  +       + Q  +H+      FP +   R  L  
Sbjct: 265 PQPTVVELLQ-CAKEHLDGLWAYKGQ-----KGIYQSRKHLTWYCRDFPGAADFRDRLN- 317

Query: 300 EAGASTATHHIIETAFNLM 318
           +         +++ A   +
Sbjct: 318 KINTVAEGQALLDEAIEQV 336


>gi|190570967|ref|YP_001975325.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357239|emb|CAQ54661.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 316

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 133/314 (42%), Gaps = 21/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++   ++++   +  ++  A+Q+ G +  
Sbjct: 19  MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSMQK-AKVDELTAVQLAGCEPD 76

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ E  G   I++N GCP  +V  G  G+ LM +     + I A+ KA+S+PVT
Sbjct: 77  VMAEAAKLNEGMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVSVPVT 136

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +D+        L K  +  G   I +H R         +        D+  V 
Sbjct: 137 VKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFVR 186

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG ++ ++     L     DGVMIGR  Y    ++     + S    
Sbjct: 187 NVKEQV-KIPVIVNGDIKSLNDVQSALKESGADGVMIGRGTYGKPWLINQAINFLSGNKV 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R+       I     D    +  S   ++   +H+     G  NS   R  + 
Sbjct: 246 SEPTASERLS------IILKHYDSILEYYGSDTGIKMARKHIGWYSSGLQNSSEFRVRVN 299

Query: 299 VEAGASTATHHIIE 312
               ++    +II+
Sbjct: 300 NIIDSTEVKENIID 313


>gi|171057225|ref|YP_001789574.1| NifR3 family TIM-barrel protein [Leptothrix cholodnii SP-6]
 gi|170774670|gb|ACB32809.1| TIM-barrel protein, nifR3 family [Leptothrix cholodnii SP-6]
          Length = 346

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/328 (19%), Positives = 129/328 (39%), Gaps = 25/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   LR   K    L  + +  P+A+QI G +
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRPELRDSLKTSRRLDHTGEVAPIAVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+   + G   I++N+GCP+ +V     G+ LM N  +    I A+  A    
Sbjct: 76  PEMMAEAARYNIERGAQIIDINMGCPAKKVCNVWAGSALMQNESLALRIIDAVVAASAPH 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   +        + ++ + +G+  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQEQKNA--LQIARAAQDAGIAMVTVHGRT--------REQGYKGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  +  +K     + +  NG ++   +A ++L     D VMIGRAA     +   +  + 
Sbjct: 186 YRTIAAVKAAL-QIPVVANGDIDSPEKAARVLRATGADAVMIGRAAQGRPWIFREIAHHL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +      +P   +V       +    + Y  R       ++   +H+    H  P     
Sbjct: 245 ATGQAMDAPRTLQVRDWLLEHLQDHYSLYGER-----SGVRTARKHIGWAVHALPGGAHF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R  +      +      ++   + + ++
Sbjct: 300 RAEMNRIETTAD-QWRAVDDYLSDLADA 326


>gi|162448213|ref|YP_001621345.1| tRNA-dihydrouridine synthase [Acholeplasma laidlawii PG-8A]
 gi|161986320|gb|ABX81969.1| tRNA-dihydrouridine synthase [Acholeplasma laidlawii PG-8A]
          Length = 336

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 85/325 (26%), Positives = 148/325 (45%), Gaps = 25/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  AR L    +++ EM+   AI   + K   +L  + +EKP A QI G+D
Sbjct: 19  MAGVSNHPFRLMARQL-GAGVVFAEMVSDKAIFFQNPKTLQMLYMTVEEKPAAQQIFGSD 77

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALS 116
           +  +VEAA  ++     + I++N+GCP  +V  G+  GA LM +P  + D + A+ + +S
Sbjct: 78  LETMVEAAMFIDKNSNCDFIDINMGCPVPKVAIGAQAGASLMKDPQKIYDIVKAIKEKVS 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R G D +  +V    + K I+K+G + I +HAR         +        D 
Sbjct: 138 KPVTVKIRSGWDSE--SVNAVEVAKMIEKAGASLITVHART--------RAQGYSGEPDL 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D++  +K E   + +  NG + D   A  +L     D VMIGRA+  N  +   ++ Y +
Sbjct: 188 DVIKAVK-EAVSIPVIGNGNIVDGKSAKHMLEYTGCDAVMIGRASLGNPWIFREINAYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T   P++T    +  + +     D  A+         ++  H      G P + + R
Sbjct: 247 GEET---PVRT---YEEVKTLMIRHFDDLAKLKGEHTACLEMRSHGPWYLKGLPKASQVR 300

Query: 295 HILTVEAGASTATHHIIETAFNLMI 319
             L      +      +E  F+ ++
Sbjct: 301 AKLARTTNRAE-YMENLEMYFDDVM 324


>gi|271498831|ref|YP_003331856.1| nifR3 family TIM-barrel protein [Dickeya dadantii Ech586]
 gi|270342386|gb|ACZ75151.1| TIM-barrel protein, nifR3 family [Dickeya dadantii Ech586]
          Length = 321

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +DR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGVSDRPFRALCYAM-GAGMTVSEMLSSNPEVWRSDKSRLRMVHSDEPGIRAVQIAGGD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PDEMAQAARINAESGAQIIDINMGCPAKKVNRKMAGSALLQYPALVKQILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAKLAEDCGIQALTVHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPVIANGDITDPRKARAVLDYSGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKHLLIGHIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      ++  F  +
Sbjct: 300 FNAIEDASE-QLEALKAYFENL 320


>gi|304312297|ref|YP_003811895.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HdN1]
 gi|301798030|emb|CBL46252.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HdN1]
          Length = 332

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 126/326 (38%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L       +EM+  +  L   +K+   L     E   A+QI G D
Sbjct: 21  MAGITDLPFRTLCRKL-GAGYTVSEMVAGNPKLINTRKSSLRLRHDGDESLRAVQIVGWD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I  D G   I++N+GCP+ +V   + G+ L+ +  +V   + A+ KA+ +P
Sbjct: 80  PQSMAEAARINADQGAGVIDINMGCPAKKVCSKAAGSALLKDEALVERILNAVVKAVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +++G+  + +H R         +        +YD 
Sbjct: 140 VTLKIRTGWDANQRNGVT--IARIAEQAGIQALAVHGRT--------RACAFKGLAEYDT 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK     + +  NG +    +A ++L    VDG+M+GR+A  N  +   +  Y    
Sbjct: 190 IAQIKAAI-YIPVMANGDISSPEKAKEVLEHTAVDGIMVGRSALGNPWVFRAITHYLKTG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + +    Y           +   +HM             R  
Sbjct: 249 TQLPPPALHEVKDVVLGHLQSLYDFY-----GDPLGPRIARKHMGWYVEKHKGGSTFRKA 303

Query: 297 LT--VEAGASTATHHIIETAFNLMIE 320
                 A    A+       F  +IE
Sbjct: 304 FNQLETATQQLASAQ---EFFEQLIE 326


>gi|170693384|ref|ZP_02884543.1| TIM-barrel protein, nifR3 family [Burkholderia graminis C4D1M]
 gi|170141539|gb|EDT09708.1| TIM-barrel protein, nifR3 family [Burkholderia graminis C4D1M]
          Length = 374

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 34  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 93  PDMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVAAVGVG 152

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 153 PDAVPVTLKIRTGWNRENKNA--LNVARLAEAAGISMLTVHGRT--------RADLYHGD 202

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ 
Sbjct: 203 AEYETIAAVK-AAVRIPVVANGDISSPEKARHVLAVTGADAIMIGRAAQGRPWLFREIEH 261

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 262 FLQTGELLPPPRIDEIQQVMNEHLQDHYGFYGEF-----TGVRTARKHIGWYTRGLSGAN 316

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 317 LFRHRMNT 324


>gi|327402492|ref|YP_004343330.1| tRNA-U20-dihydrouridine synthase [Fluviicola taffensis DSM 16823]
 gi|327318000|gb|AEA42492.1| tRNA-U20-dihydrouridine synthase [Fluviicola taffensis DSM 16823]
          Length = 333

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 134/305 (43%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE I ++ ++R   K+   L     EKP+ +QI G D
Sbjct: 19  MEDVSDPPFRALCKK-HGADLMYTEFISSEGLIRDAIKSRQKLDIFDYEKPIGIQIFGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  +AKIV+    + +++N GCP  +V     GA ++ + D++     A  K+ S+P
Sbjct: 78  EEAMAMSAKIVDATAPDLLDINFGCPVKKVVSKGAGAGVLKDVDLMVRLTQACIKSTSLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD +  + +  + + ++  GV  + IH R         +        D+  
Sbjct: 138 VTVKTRLGWDDSM--INIMEVAERLQDIGVEALSIHGRT--------RSQMYKGEADWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG ++   +A++      VDG+M+GRA+     +   +  + + 
Sbjct: 188 IAAVKNNPRIKIPIFGNGDIDSPEKAVEYKNRYGVDGIMVGRASIGYPWIFNEIKHFMAT 247

Query: 236 PLTGSSP-IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               + P +K RV+       +      + +       + ++ RH    F G  + +  R
Sbjct: 248 GEHLAVPGVKERVEA------ARDHLMMSVKWKGERLGVVEMKRHYTNYFKGIAHFKEYR 301

Query: 295 HILTV 299
             L  
Sbjct: 302 TKLVT 306


>gi|315633700|ref|ZP_07888990.1| tRNA-dihydrouridine synthase B [Aggregatibacter segnis ATCC 33393]
 gi|315477742|gb|EFU68484.1| tRNA-dihydrouridine synthase B [Aggregatibacter segnis ATCC 33393]
          Length = 342

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 134/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R          L ++EM+  +  +   +K+ L           A+QI G+D
Sbjct: 39  MAGITDQPFRKICAHY-GAGLTFSEMMSTNPQVWHTEKSKLRLAHHQDAGINAVQIAGSD 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ K++++P
Sbjct: 98  PDEMAQAAQVNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVQQILEAVVKSVNVP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  ++SG+  + +H R         +  +     +YD 
Sbjct: 158 VTLKIRTGWDTENRN--CVEIAKIAEQSGIQALTVHGRT--------RACKFEGVAEYDS 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    QA  +L     DGVMIGR A     +  T+     + 
Sbjct: 208 IKAVKQAV-SIPVIANGDMISPQQAKFVLDYTGADGVMIGRGALGRPWVFQTMVGLVEHN 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P          + I      Y       G ++    +H+             +  
Sbjct: 267 SIVNEPSLEEKCGVILQHIRELHQFYGDE---KGYRI--ARKHIAWYLQDIQPHSVFKQD 321

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 +++A    +E  F L+
Sbjct: 322 FNA-ITSASAQLDALEQFFRLI 342


>gi|78779403|ref|YP_397515.1| dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9312]
 gi|78712902|gb|ABB50079.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9312]
          Length = 335

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 139/324 (42%), Gaps = 25/324 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADIS 60
              TD  +R   R    N+LL+TEMI A ++ +G   + I   + +E P+ +QI      
Sbjct: 26  AGVTDNIFRRLVRKWAPNSLLFTEMINATSLKKGFGTQKINQINLEEGPVGVQIFDNRPY 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVT
Sbjct: 86  AVSEAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVKIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D +     + + +  ++ +G   I +H R    +G S K        D++++ 
Sbjct: 146 VKTRLGWDSKE--ENIEDFLFKLQDAGATMITLHGRTRK-QGFSGKS-------DWEMIG 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +KK   ++ +  NG +++   AL  L   + DGVMIGR    +   L  +D        
Sbjct: 196 RLKK-LLEIPVIANGDIKNPDDALNCLNKTNADGVMIGRGILGSPWKLGEIDYAIKENKN 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +           L    +H+      F  +   R+ L 
Sbjct: 255 FKEPNAEEKLYLIIEHLDELIKEKG------DHGLLIARKHISWTCKDFKGASNLRNNLV 308

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
                +      ++   N MI++L
Sbjct: 309 RAVDKNE-----VKNLINKMIKTL 327


>gi|298505124|gb|ADI83847.1| TIM barrel oxidoreductase NifR3 [Geobacter sulfurreducens KN400]
          Length = 325

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 137/322 (42%), Gaps = 24/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  AR      L +TEM+  + ++R  KK+  +L     ++PL +Q+ G D
Sbjct: 21  MAGITNLPFRLLARE-QGAGLCFTEMVSVNGLVREGKKSFELLRSVPGDRPLGIQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A  V+ +G + I++N+GCP  +V     G+ LM  PD V   + A+ +A  +P
Sbjct: 80  PDVMGRVAATVDGYG-DLIDINMGCPVKKVVGTGAGSALMREPDKVRAIVRAVRRATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G   +        + +  ++ G N + +H R         +        D+  
Sbjct: 139 LTVKIRSGWSCED--ANFIQIARIAEEEGCNAVTLHPRS--------RAQMFEGTADWTK 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+    + +  +G L   +    +L     DGVMI R A  N  +     +  +  
Sbjct: 189 LAELKRAV-AIPVIGSGDLFSAADVAAMLDRTGCDGVMIARGALGNPWIFRQALDLMAGR 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++    R+     R+  A  T+ A   + +    +++ +H+    HG P + + R  
Sbjct: 248 EPAAASPAERLA--VARRHLALFTEMAGERVAA----REMRKHLGWYSHGLPGAAQFRKE 301

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +    G + A    +   F  +
Sbjct: 302 INEIEG-NGALMEAVSRFFTAV 322


>gi|294787455|ref|ZP_06752708.1| putative tRNA-dihydrouridine synthase [Parascardovia denticolens
           F0305]
 gi|294484811|gb|EFG32446.1| putative tRNA-dihydrouridine synthase [Parascardovia denticolens
           F0305]
          Length = 417

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 120/302 (39%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A+   + K   +  F+  EK  +LQ+ G +
Sbjct: 55  MAGVTNWPFRLLCEGYGPDGLYVAEMITARALTARNPKAFRLCRFAPSEKFRSLQLYGVN 114

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
              + EAAK+V D    + ++LN GCP  +V     G+ L    D++ D    + A+C+ 
Sbjct: 115 PLVVEEAAKMVVDGDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQDLIHRVVAVCQP 174

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + IPVT K R+GVDD+     +    K I+  G   + +HAR                + 
Sbjct: 175 VGIPVTAKIRVGVDDE--HETMIEAAKIIEGEGCAFVTLHARTT--------AQYYGGHS 224

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + ++K E   + +  NG +     A+ +      DGV IGR       +   +   
Sbjct: 225 DWSRIAQLK-EAVSIPVIGNGDIWTAEDAMAMARQTGCDGVAIGRGCQGRPWLFGDIRNA 283

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P   +V +   +        Y          +  + +H+     GFP   +
Sbjct: 284 FEGRNERFDPSLAQVGQTIVKHAHFLTEFYEG---DENMAVHDLRKHIAWYLKGFPVGGK 340

Query: 293 CR 294
            R
Sbjct: 341 TR 342


>gi|146283597|ref|YP_001173750.1| NifR3 family TIM-barrel protein [Pseudomonas stutzeri A1501]
 gi|145571802|gb|ABP80908.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas stutzeri
           A1501]
          Length = 337

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 135/314 (42%), Gaps = 21/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R     AL  +EM+ +D  L   +K+ L    + + +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRF-GAALEVSEMLTSDVRLWNSRKSRLRMPHADEPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ LM +  +V D + A+  A+ +P
Sbjct: 79  PQMLAEAAQRNVELGAQIIDINMGCPAKKVCNKAAGSALMRDERLVADILEAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q    A   + +  ++SG+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRQNKNGAT--IARIAEQSGIAALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   V+ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPHKAARVLQVTGADGLLIGRAAQGRPWIFREVEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P    V+      + A    Y          ++   +H+       P +R  R  
Sbjct: 248 ELLAAPTLGEVESTLLEHVQALHEFY-----GEVMGVRIARKHVGWYLATLPGARDFRAR 302

Query: 297 LTVEAGASTATHHI 310
                        I
Sbjct: 303 FNHLEDRDAQGSSI 316


>gi|260886975|ref|ZP_05898238.1| tRNA-dihydrouridine synthase [Selenomonas sputigena ATCC 35185]
 gi|330839239|ref|YP_004413819.1| TIM-barrel protein, nifR3 family [Selenomonas sputigena ATCC 35185]
 gi|260863037|gb|EEX77537.1| tRNA-dihydrouridine synthase [Selenomonas sputigena ATCC 35185]
 gi|329747003|gb|AEC00360.1| TIM-barrel protein, nifR3 family [Selenomonas sputigena ATCC 35185]
          Length = 318

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR     +    L+YTEM+  + I   +++   +L    +E+PLA+Q+ G +
Sbjct: 17  MAGVTDMAYRILVHEM-GCPLVYTEMVSTNGINYRNERTLKMLQTDPRERPLAMQLFGNE 75

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +  AA  VE  G  + I+ N+GCP+ ++ +   G+ L+L+P      + A+ +A+ +
Sbjct: 76  PEAVARAAAYVESLGVADVIDFNMGCPAPKIVKNGEGSALLLDPVRAERILKALKRAVKL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D     V    +    + +GV+ I +H R         ++       D+ 
Sbjct: 136 PVTVKIRKGWD--AAHVNAVEIAVRAEAAGVDAIAVHGRT--------REQFYSGEADWA 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I++ +K E   + +  NG +  +   ++I      DGVM+GRAA  N  +   +  +   
Sbjct: 186 IIHAVK-ERVAIPVIANGDVRSVVDLVRIFEVTDADGVMVGRAAQGNPWIFREMAGFLRT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P  +       R +     D            +++ +H      G  N  R R 
Sbjct: 245 GEVAAPPTASERRALILRHL-----DMLLETKGDYVGPREMRKHATWYTRGMKNGARLRE 299

Query: 296 ILTVEAGAST 305
           +       + 
Sbjct: 300 LFNRAETRAD 309


>gi|297180133|gb|ADI16356.1| hypothetical protein [uncultured bacterium HF130_01F24]
          Length = 329

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 137/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV  +D+ +R          L   EM+ +++ L  +++N L  +      P  +QI G+D
Sbjct: 17  MVGVSDKPFREVCEQ-NGAGLTTAEMLTSNSDLWKNERNRLKRTQPILSGPNVVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA++  ++G + I++N+GCP+ +V + + G+ L+ +P +V   + ++  ++ IP
Sbjct: 76  PKMMSQAAQLNAEWGADVIDINMGCPAKKVLKKAAGSALLKDPKLVRSILESVINSVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            + K  +  GV  + +H R         ++ R    ++Y+ 
Sbjct: 136 VTLKIRTGWCPATKNGV--EVAKIAEDCGVALLTVHGRT--------RECRFKGKVEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ +  + I  NG +     A ++L     DG+MIGR+A     +   V +Y  + 
Sbjct: 186 IAKIKQ-SVRIPIIANGDINSPQTAKRVLEYTKADGLMIGRSAIGKPWIFDQVHQYLVSG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P      K     +    T Y          +    +H+        +S+     
Sbjct: 245 TEKSEPNLPSKLKIVESHLREIQTFY-----GEIKGVWYARKHIARYVESLKSSKEFLRS 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
              E     A   ++ + F  +
Sbjct: 300 FNRETEGP-AQIDLLRSYFANL 320


>gi|238896768|ref|YP_002921513.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae NTUH-K2044]
 gi|262042817|ref|ZP_06015970.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|329997541|ref|ZP_08302819.1| tRNA-dihydrouridine synthase B [Klebsiella sp. MS 92-3]
 gi|238549095|dbj|BAH65446.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259039884|gb|EEW41002.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328539024|gb|EGF65068.1| tRNA-dihydrouridine synthase B [Klebsiella sp. MS 92-3]
          Length = 321

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  ++ G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWEPEHRN--CVEIAQLAEECGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|71281750|ref|YP_267308.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
 gi|71147490|gb|AAZ27963.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
          Length = 338

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 121/291 (41%), Gaps = 21/291 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     L    L  +EM+ ++  +   +K+ L           ++QI G+ 
Sbjct: 17  MAGITDQPFRQLCCQL-GAGLAVSEMLSSNPKVWNTEKSKLRMLHGDAAGIRSVQIAGSC 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AAK+  D G   I++N+GCP+ +V++   G+ L+  P  V   + ++  A+ IP
Sbjct: 76  PDELAFAAKVNADNGAQIIDINMGCPAKKVNKKLAGSALLREPAQVERIVQSVVNAVDIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G  +         + K  + SG+  + +H R         +++    N +YD 
Sbjct: 136 VTLKIRTGWCEDTRNGI--EIAKIAENSGIASLAVHGRT--------RNDFYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK     + +  NG +    +AL++L     D +M+GR A     +   ++ + +  
Sbjct: 186 IKAIKLAI-SIPVVANGDITSPEKALQVLDHTGADAIMVGRGAQGRPWIFREINYFLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
              S+P  + V       +      Y       G  +    +H+       
Sbjct: 245 NKMSAPELSEVRSIVLAHVMELHQFYGDF---KGVMI--ARKHVSWYVQNL 290


>gi|255068432|ref|ZP_05320287.1| tRNA-dihydrouridine synthase B [Neisseria sicca ATCC 29256]
 gi|255047318|gb|EET42782.1| tRNA-dihydrouridine synthase B [Neisseria sicca ATCC 29256]
          Length = 334

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 131/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLRRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 136 VTLKTRLGWHDDHKN--LPAIARIAEDCGIAALAVHGRT--------RTQMYKGEATYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A     +   +  Y  + 
Sbjct: 186 IAETKGRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWLFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +          +      I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPVLSLAECNDTILNHIRAMHAFY-----GEVAGVRIARKHIGWYIDEMPDGEQTRRD 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A +  +      + E 
Sbjct: 300 INCL-DSAAAQYDTLAAYLEALSEK 323


>gi|187918097|ref|YP_001883660.1| tRNA-dihydrouridine synthase A [Borrelia hermsii DAH]
 gi|119860945|gb|AAX16740.1| NIFR3-like protein [Borrelia hermsii DAH]
          Length = 335

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 107/328 (32%), Positives = 172/328 (52%), Gaps = 17/328 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV  TD H+R+  RLL+    LYT MI A +I+ G+   ++  +  + P+A+QI  +  +
Sbjct: 12  MVAITDEHFRYMIRLLSKKVTLYTPMISAKSIIMGNLNKVVKQTPTDSPIAIQIATSCEN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E+ F ++E NLNVGCPS++V   ++GACLM  P  VG  + AM K  + PV
Sbjct: 72  DAAKAIEILENKFNFDEYNLNVGCPSSKVQNANYGACLMQTPTQVGKILKAMKKNTNKPV 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+ +      +     L+  V+ I +  +    +HAR AIL G SPKDN+ IP 
Sbjct: 132 SIKHRIGIRNNKREYHEENYTELQQFVEKIMEYEIKNFTVHARIAILNGYSPKDNQNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L +D VY +K+E+ ++FI +NGG++        L  VD VMIGRA  K+  ++  +   F
Sbjct: 192 LRHDFVYRLKQEHKNIFIEVNGGIKSSDHIKTHLSYVDSVMIGRAVAKDPYLIAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR       +I   M +Y   +      +  I +H++ +     N+ + 
Sbjct: 252 ---LEEKEKIPTR------EEILLKMVEYIKEY-DECLSISTILKHIMSIVFAKENACKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R  L+     +   H I+ +A   + E 
Sbjct: 302 RQTLSAPFPKNLKNHEILLSAIEHLRED 329


>gi|299534036|ref|ZP_07047388.1| putative TIM-barrel protein, nifR3 family [Comamonas testosteroni
           S44]
 gi|298717945|gb|EFI58950.1| putative TIM-barrel protein, nifR3 family [Comamonas testosteroni
           S44]
          Length = 354

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 119/306 (38%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+++QI G +
Sbjct: 20  MAGVTDRPFRQLCKAL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPISVQIAGTE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA    + G   I++N+GCP+ +V     G+ LM N  +  +   A+ +A    
Sbjct: 79  APMMAEAAIYNIERGAQIIDINMGCPAKKVCNKWAGSALMQNEPLAVEIAQAVVEAARPY 138

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G  D      L  L +  +  G+  + +H R         ++       +
Sbjct: 139 NVPVTLKMRTGWCDTHKNAVL--LARQFEDVGIQMLTVHGRT--------REQGYKGFAE 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K+    + +  NG +    +A  +L     D +M+GRAA     +   +  + 
Sbjct: 189 YDTIAAVKQAV-KVPVVANGDVNSPEKARDVLAYTGADAIMVGRAAQGRPWIFREIAHFL 247

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   + +     +    + Y       G  ++   +H+       P     
Sbjct: 248 ATGEHLAPPLVAELRRLLLEHLQDHYSLY-----GEGVGVRSARKHIAWYLRALPGGEEF 302

Query: 294 RHILTV 299
           R  +  
Sbjct: 303 RKHINT 308


>gi|51473224|ref|YP_066981.1| NifR3-like protein [Rickettsia typhi str. Wilmington]
 gi|81826343|sp|Q68XZ3|DUS_RICTY RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|51459536|gb|AAU03499.1| NifR3-like protein [Rickettsia typhi str. Wilmington]
          Length = 327

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 131/323 (40%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGGA 57
           M + TD  +R   +      L+ +EMI + A++   ++++              +Q+ G 
Sbjct: 18  MSNITDLEFRKLVKRF-GAGLVVSEMIASRAMIMKSRQSMQKCAIMHDDPTSACVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AAK+ ED G   I+LN GCP+ +V  G  G+ LM +  +      A  KA+ I
Sbjct: 77  EPDVIADAAKMNEDMGAKIIDLNFGCPAKKVVGGYAGSALMRDERLATKIFEATVKAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         L      SGV  + +H R         +      N ++D
Sbjct: 137 PVTVKMRMGWDDNTKNA--PTLAVIAASSGVQMVTVHGRT--------RCQFYSGNANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KE   + +  NG + + ++A + L     DG+M+GR  Y    +++ +  Y   
Sbjct: 187 FI-RVVKEAVKIPVIANGDITNFAKAKEALQKSGADGIMVGRGVYGKPWLISQIAYYLKT 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P          +   A +  Y          +    +H+I    G P+S   R 
Sbjct: 246 GKEKPAPSIAEQLDIIIKHYDAIIDYY-----GKSVGVPIARKHIIWYSSGLPSSAEFRC 300

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            + +          I E   ++M
Sbjct: 301 AVNLMNDPIAVKEKIAEFYMSVM 323


>gi|302345940|ref|YP_003814293.1| TIM-barrel protein, nifR3 family [Prevotella melaninogenica ATCC
           25845]
 gi|302150111|gb|ADK96373.1| TIM-barrel protein, nifR3 family [Prevotella melaninogenica ATCC
           25845]
          Length = 318

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 142/327 (43%), Gaps = 33/327 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADA++R  K  +  L     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAVIRSIKSTLSKLVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE    + I++N GCP  +V     G+ ++ N  ++ D    + KA++ P
Sbjct: 77  VASMVEAAKIVEQVKPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLDITREVVKAVNTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--NLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +  + +A +      VD VMIGRA +    +          
Sbjct: 187 IGEVKNNPRIHIPIIGNGDVTSIEEAHEKFDRYGVDAVMIGRATFGCPWLFNQ------- 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                   + ++  D    I   M       +     +    RH+    +F G P+ ++ 
Sbjct: 240 -------GEKQLTIDDKIDILEEMLRINVERIDEHRGILHTRRHLAASPIFKGIPDFKKT 292

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R I  +          I+E     + E
Sbjct: 293 R-IAMLRTTKIDELMAILEDCREKLRE 318


>gi|288925390|ref|ZP_06419324.1| TIM-barrel protein, putative, NifR3 family [Prevotella buccae D17]
 gi|288337861|gb|EFC76213.1| TIM-barrel protein, putative, NifR3 family [Prevotella buccae D17]
          Length = 321

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 134/301 (44%), Gaps = 34/301 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G  
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRSIKSTVSKLTISDEERPVGIQIYGRT 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  +V     GA ++ N  ++ D    + KA+ +P
Sbjct: 77  VEDMVEAARIVEQARPDVIDINFGCPVKKVAGKGAGAGMLKNVPLMLDITREVVKAVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWD--SNNLIISELAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +  +++A +      VD VMIGRA +    + +        
Sbjct: 187 IGEVKNNPRIHIPIIGNGDIGSIAEAHEAFDRYGVDAVMIGRATFGQPWLFSE------Q 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
           PLT    I           +           +     +    RH+    +F G PN R+ 
Sbjct: 241 PLTYEEKIG----------VLEEQLRINVERIGEYRGILHTRRHLAASPIFKGIPNFRQT 290

Query: 294 R 294
           R
Sbjct: 291 R 291


>gi|260591922|ref|ZP_05857380.1| tRNA-dihydrouridine synthase [Prevotella veroralis F0319]
 gi|260536206|gb|EEX18823.1| tRNA-dihydrouridine synthase [Prevotella veroralis F0319]
          Length = 318

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 143/327 (43%), Gaps = 33/327 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRY-GAAMVYTEFVSADAIIRSIKSTLSKMVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE    + I++N GCP  +V     G+ ++ N  ++ +    + KA+++P
Sbjct: 77  VASMVEAAKIVEQVKPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLEITREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWD--TEHLIITDLAEQLQDCGIQALTIHGRT--------RSQMYTGQADWTL 186

Query: 179 VYEI-KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+ K     + I  NG + +  +A +      VD VMIGRA +    + +        
Sbjct: 187 IGEVTKNPRIKIPIIGNGDVTNRLEASEKFDTYGVDAVMIGRATFGCPWIFS-------- 238

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                 P    +  D    +   M       +     +    RH+    +F G P+ ++ 
Sbjct: 239 ------PRAEEISLDEKIDVLEEMLKINVERIDEYRGILHTRRHLAASPIFKGIPDFKQM 292

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R I  + A        I+E     + E
Sbjct: 293 R-ISMLRATKVDELMSILEDCRERLRE 318


>gi|307719541|ref|YP_003875073.1| hypothetical protein STHERM_c18650 [Spirochaeta thermophila DSM
           6192]
 gi|306533266|gb|ADN02800.1| hypothetical protein STHERM_c18650 [Spirochaeta thermophila DSM
           6192]
          Length = 333

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 126/318 (39%), Gaps = 22/318 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R         ++ YTEM+ A+ I+    K   ++    +E+   +Q+  +  
Sbjct: 27  AGVSDLPFREVCISF-GASMTYTEMVSAEGIVYHTGKTFSLVQRGPEERFWGIQLFSSRP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L  A +++        +LN GCP  +V +   GA LM +P+ V   + AM +A  +PV
Sbjct: 86  DMLARAVEVLSPLAPTLFDLNCGCPVPKVVKTGAGAALMRDPERVYAMVKAMRQASPVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D+   ++  R + ++  ++G   + +H R         +         ++ +
Sbjct: 146 TVKIRSGWDEH--SLTYREVAQAAFEAGAGAVCLHPRT--------RAQGYAGAARWEHI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K  +P   I  +G +     A  ++     D V++ R A     +   + +      
Sbjct: 196 ADLKARHPSHPIIASGDILSPEAARAVVEETGCDAVLVARGALGAPWIFRQIRDLQEKG- 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            G +PI  R   +  R        Y       G   +++ +HM     G P + R R  L
Sbjct: 255 -GYAPISLRERVETMRAHLERAIAYKGE----GIACREMRKHMGWYVKGLPGAARVRERL 309

Query: 298 TVEAGASTATHHIIETAF 315
            V A    A   I+    
Sbjct: 310 -VRASTREAYLAILAELL 326


>gi|261342713|ref|ZP_05970571.1| tRNA-dihydrouridine synthase B [Enterobacter cancerogenus ATCC
           35316]
 gi|288315366|gb|EFC54304.1| tRNA-dihydrouridine synthase B [Enterobacter cancerogenus ATCC
           35316]
          Length = 321

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +P
Sbjct: 76  PEEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVKAILTAVVSAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGYAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLAPLPLAEVKRLLCSHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDAS-VQLEALEAYFE 318


>gi|264680133|ref|YP_003280042.1| hypothetical protein CtCNB1_4000 [Comamonas testosteroni CNB-2]
 gi|262210648|gb|ACY34746.1| putative TIM-barrel protein, nifR3 family [Comamonas testosteroni
           CNB-2]
          Length = 367

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 119/306 (38%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+++QI G +
Sbjct: 33  MAGVTDRPFRQLCKAL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPISVQIAGTE 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA    + G   I++N+GCP+ +V     G+ LM N  +  +   A+ +A    
Sbjct: 92  APMMAEAAIYNIERGAQIIDINMGCPAKKVCNKWAGSALMQNEPLAVEIAQAVVEAARPY 151

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G  D      L  L +  +  G+  + +H R         ++       +
Sbjct: 152 NVPVTLKMRTGWCDTHKNAVL--LARQFEDVGIQMLTVHGRT--------REQGYKGFAE 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K+    + +  NG +    +A  +L     D +M+GRAA     +   +  + 
Sbjct: 202 YDTIAAVKQAV-KVPVVANGDVNSPEKARDVLAYTGADAIMVGRAAQGRPWIFREIAHFL 260

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   + +     +    + Y       G  ++   +H+       P     
Sbjct: 261 ATGEHLAPPLVAELRRLLLEHLQDHYSLY-----GEGVGVRSARKHIAWYLRALPGGEEF 315

Query: 294 RHILTV 299
           R  +  
Sbjct: 316 RKHINT 321


>gi|329295746|ref|ZP_08253082.1| TIM-barrel protein, nifR3 family [Plautia stali symbiont]
          Length = 321

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +D+ +R          +  +EM+ +++ +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGVSDKPFRTLC-YDNGAGMTVSEMLSSNSEVWASDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I    G   I++N+GCP+ +V+    G+ L+ +P +V   + A+  A+ +P
Sbjct: 76  PDEMAAAARINVASGAQVIDINMGCPAKKVNRKMAGSALLQHPQLVESILRAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDKENRN--CVEIAQLAERCGIQALTIHGRT--------RACLFEGQAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +M+GRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVAIPIIANGDITDPHKARAVLDYTGADALMVGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V       I      Y  R  +     +   +H+           + R  
Sbjct: 245 ELLAPKPLAEVKHILIGHIRELHDFYGQRKEY-----RIARKHVSWYLQESAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|40063277|gb|AAR38095.1| NifR3/Smm1 family protein [uncultured marine bacterium 578]
          Length = 322

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 136/287 (47%), Gaps = 21/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA--ILRGDKKNILGFSTQEKPLALQIGGAD 58
           M   +D+ +R   R     AL  +EM+V     +     K+ L F +++ P+++QI G++
Sbjct: 17  MAGTSDKPFRMICRE-QGAALTTSEMVVMQKHLLNTNKSKHRLDFRSEQSPISIQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L E+AK   +FG + I++N+GCP+ +V   + G+ LM N  +V D I A+  A++IP
Sbjct: 76  SQELAESAKQALEFGADIIDINMGCPAKKVCNKAAGSALMKNEKLVEDIIKAVVNAVNIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +++        + K  + +G+  + IH R         +  +   + +YD 
Sbjct: 136 VTLKMRTGWNEENKNA--PTIAKIAEDNGIKMLAIHGRT--------RAQKYNGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V +IK     + +  NG +    +A K+L     D VM+GRA   N  ++  ++ Y    
Sbjct: 186 VKKIKG-IVSIPVVANGDITSAQKAKKVLDYTGADAVMLGRATQGNPWLVGQINNYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +  +P+  +      R I      Y  +    G +L    +H+   
Sbjct: 245 KSPKAPLLDKKISLILRHILQIHDFYGHKM---GTQLS--RKHIFWY 286


>gi|325860196|ref|ZP_08173321.1| TIM-barrel protein, nifR3 family [Prevotella denticola CRIS 18C-A]
 gi|325482283|gb|EGC85291.1| TIM-barrel protein, nifR3 family [Prevotella denticola CRIS 18C-A]
          Length = 319

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 83/325 (25%), Positives = 145/325 (44%), Gaps = 33/325 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  +  +  +     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAIIRSIRSTLSKMVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IVE    + I++N GCP  +V     G+ ++ N  ++ +    + KA+SIP
Sbjct: 77  VASMVEAARIVEQAKPDVIDINFGCPVKKVAGKGAGSGMLKNIPLLLEITREVVKAVSIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDKD--NLVIADLAEQLQDCGIQALTIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + I  NG +  + +A +      VD VMIGRA +    +          
Sbjct: 187 IGEVKKNPRIHIPIIGNGDVTSVREAGEKFDRYGVDAVMIGRATFGCPWIFRQ------- 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
              G  P+  ++D      +   M       +     +    RH+    +F G P+ R+ 
Sbjct: 240 -GEGELPLDEKID------VLEEMLRINVERIDEYRGIIHTRRHLAASPIFKGIPDFRQT 292

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A        I+E     +
Sbjct: 293 R-ISMLRATKMEELMTILENCRERL 316


>gi|283836191|ref|ZP_06355932.1| tRNA-dihydrouridine synthase B [Citrobacter youngae ATCC 29220]
 gi|291067542|gb|EFE05651.1| tRNA-dihydrouridine synthase B [Citrobacter youngae ATCC 29220]
          Length = 321

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA--LQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGVRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVKSGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                  S+     +E  F 
Sbjct: 300 FNAIED-SSEQLAALEAYFE 318


>gi|319795861|ref|YP_004157501.1| tim-barrel protein, nifr3 family [Variovorax paradoxus EPS]
 gi|315598324|gb|ADU39390.1| TIM-barrel protein, nifR3 family [Variovorax paradoxus EPS]
          Length = 352

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 121/308 (39%), Gaps = 25/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM+ +   L G  K         +  P+A+QI G D
Sbjct: 19  MAGVTDRPFRMLCREL-GAGYAVSEMVTSRKELWGTLKTSRRANHDGEPGPIAVQIAGTD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EA     + G   I++N+GCP+ +V     G+ LM +  +  + + A+  A    
Sbjct: 78  AAMMAEATVYNIERGAQIIDINMGCPAKKVCNKWAGSALMRDEPLALEIVQAVVDAAQPF 137

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G  +         L +  + +GV  + +H R         ++     + +
Sbjct: 138 NVPVTLKMRTGWSEDNRNAV--KLARDFESAGVQMLTVHGRT--------REQGYKGHAE 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   +  + 
Sbjct: 188 YDTIAAVK-AAVRVPVVANGDINSPEKARDVLAATGADAVMIGRAAQGRPWIFREIAHFL 246

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 + P+   V +     +      Y          ++   +H+       P+    
Sbjct: 247 ETGTHRAPPLVAEVRRLLLDHLVEHYALYGDF-----SGVRTARKHIGWYVRTLPDGEAF 301

Query: 294 R-HILTVE 300
           R  + T+E
Sbjct: 302 RGRMNTIE 309


>gi|302551272|ref|ZP_07303614.1| dihydrouridine synthase [Streptomyces viridochromogenes DSM 40736]
 gi|302468890|gb|EFL31983.1| dihydrouridine synthase [Streptomyces viridochromogenes DSM 40736]
          Length = 412

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 64/324 (19%), Positives = 130/324 (40%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E+P ++Q+ G 
Sbjct: 56  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDASERPRSVQLYGV 115

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ +    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 116 DPATVGKAVRMIAEEDLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVSGAG 175

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 176 DLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 225

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       + + +   F
Sbjct: 226 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFSDLVAAF 285

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +    R   D   + +  + ++          +    +H+     GF      
Sbjct: 286 EGRHDDVARPTLREVADVMVRHATLLGEWIG---DESKGVVDFRKHVAWYLKGFAVGSEM 342

Query: 294 RHIL----TVEAGASTATHHIIET 313
           R  L    ++E   +      ++ 
Sbjct: 343 RGRLAITSSLEQLRAGLDELDLDQ 366


>gi|315606822|ref|ZP_07881831.1| tRNA-dihydrouridine synthase B [Prevotella buccae ATCC 33574]
 gi|315251487|gb|EFU31467.1| tRNA-dihydrouridine synthase B [Prevotella buccae ATCC 33574]
          Length = 321

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 134/301 (44%), Gaps = 34/301 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  +  L  S +E+P+ +QI G  
Sbjct: 18  MEDVTDIGFRMLCKRF-GAAMVYTEFVSAEALVRSIKSTVSKLTISDEERPVGIQIYGRT 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA+IVE    + I++N GCP  +V     GA ++ N  ++ D    + KA+ +P
Sbjct: 77  VEDMVEAARIVEQARPDVIDINFGCPVKKVAGKGAGAGMLKNVPLMLDITREVVKAVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWD--SNNLIISELAEQLQDCGIQALTIHGRT--------RSQMYTGEADWSL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +  +++A +      VD VMIGRA +    + +        
Sbjct: 187 IGEVKNNPRIHIPIIGNGDIGSIAEAHEAFDRYGVDAVMIGRATFGQPWLFSE------Q 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
           PLT    I           +           +     +    RH+    +F G PN R+ 
Sbjct: 241 PLTYEEKIG----------VLEEQLRINVERIGEYRGILHTRRHLAASPIFKGIPNFRQT 290

Query: 294 R 294
           R
Sbjct: 291 R 291


>gi|254805203|ref|YP_003083424.1| putative tRNA-dihydrouridine synthase [Neisseria meningitidis
           alpha14]
 gi|254668745|emb|CBA06597.1| putative tRNA-dihydrouridine synthase [Neisseria meningitidis
           alpha14]
          Length = 374

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 70/325 (21%), Positives = 131/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 114 PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 174 VTLKTRLGWHDDHKN--LPAVARIAEDCGIAALAVHGRT--------RTQMYKGEAAYDL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECTATILNHIRAMHAFY-----GDTAGVRIARKHIGWYIDEMPDGEQARRD 337

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + ++      + E 
Sbjct: 338 INCL-DSAAAQYDMLAGYLERLAEK 361


>gi|124025154|ref|YP_001014270.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. NATL1A]
 gi|123960222|gb|ABM75005.1| tRNA-dihydrouridine synthase [Prochlorococcus marinus str. NATL1A]
          Length = 330

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 139/317 (43%), Gaps = 21/317 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADIS 60
              +D+ +R F R  +  ALL+TEM+ A ++  G  +  ++  S +  P+ +Q+      
Sbjct: 28  AGVSDQIFRNFVRRWSPKALLFTEMVNAKSLELGHGEEKVIELSEESGPIGVQLFDHRPD 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +V+AA   E  G   I++N+GCP  ++     G+ L+  P++    +  + KA+SIPVT
Sbjct: 88  SMVDAAIKAESSGAFLIDINMGCPVKKIARKGGGSALLKEPELAQLIVKKVSKAISIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G  +        +    ++++G   I +H R         +      + ++  + 
Sbjct: 148 VKIRLGWCETTSDPV--SFALGLQEAGAQLITVHGRT--------RRQGFSGHSNWKAIA 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           +IKK   D+ +  NG +++   A++ L   + DGVMIGRA+     ++  +DE   N  T
Sbjct: 198 QIKKSL-DIPVIANGDIKNSRDAIECLKITNADGVMIGRASMGAPWLVGQIDEEIKNQTT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P   ++      +    +      H      L    +HM     GF  +   RH L 
Sbjct: 257 FKPP-DAKMKVSLSLEHLKLLVSKKGSH-----GLLIARKHMNWTCRGFEGASTLRHKL- 309

Query: 299 VEAGASTATHHIIETAF 315
           V A        ++E   
Sbjct: 310 VRASTPNDAIKLLEDEL 326


>gi|193211956|ref|YP_001997909.1| TIM-barrel protein, nifR3 family [Chlorobaculum parvum NCIB 8327]
 gi|193085433|gb|ACF10709.1| TIM-barrel protein, nifR3 family [Chlorobaculum parvum NCIB 8327]
          Length = 347

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 141/326 (43%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TDR +R   +      ++YTE + A+AI RG +K+I  L     E+P+A+QI G  
Sbjct: 17  MEDVTDRAFRQLCKR-HGADIVYTEFVSAEAIRRGAEKSIRKLRMDAHERPVAVQIFGNT 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAA I E F  + +++N GCP  +V     GA L+  P+ +    AA+  A+S+P
Sbjct: 76  VESMVEAASIAESFEPDCLDINFGCPVKKVAGRGAGAALLKEPEKLSAIAAAVVGAVSLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D    ++ + + V+ ++ +G+  + +H R         + +      D+  
Sbjct: 136 VTAKTRIGWD--HDSINITDTVRRLEDAGIQAVAVHGRT--------RSDMYKGRADWGR 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K+    + +  NG +     A+ +      DG+MIGR +  N  +           
Sbjct: 186 IAEAKRAC-SIPVIANGDVWSADDAVAMFAETGADGIMIGRGSIGNPFIFAQAKSLVKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P            +  S+     +H      + ++ RH      G P   + R++
Sbjct: 245 ERLPLPSYRDRIDAAREHLRLSLEYKGEKH-----GVLEMRRHYSTYLKGLPGVSKVRNL 299

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           L  E         ++   F    E+L
Sbjct: 300 LVRE-PDPAVIVELLRE-FEAACEAL 323


>gi|325268625|ref|ZP_08135255.1| tRNA-dihydrouridine synthase B [Prevotella multiformis DSM 16608]
 gi|324989153|gb|EGC21106.1| tRNA-dihydrouridine synthase B [Prevotella multiformis DSM 16608]
          Length = 319

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 146/328 (44%), Gaps = 33/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  +  +  +    +E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAIIRSIRSTLSKMVIDDRERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA+IVE  G + I++N GCP  +V     G+ ++ N  ++ +    + KA+ +P
Sbjct: 77  VASMVEAARIVEQAGPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLEITREVVKAVKVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D     + + +L + ++  G+  + IH R         +      + D+ +
Sbjct: 137 VTVKTRLGWD--HDHLIITDLAEQLQDCGIQTLTIHGRT--------RAQMYTGSADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+KK     + +  NG ++D+  A +      VD VMIGRA +    +          
Sbjct: 187 IGEVKKNPRIHIPVIGNGDVKDVGDAREKFDRYGVDAVMIGRATFGCPWIFGK------- 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                     ++  D    +   M       +     +    RH+    +F G P+ ++ 
Sbjct: 240 -------GTEKLTLDDKIDVLEEMLRINVERIDEYRGILHTRRHLAASPIFKGIPDFKQT 292

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  + A        I+E     +  S
Sbjct: 293 R-IAMLRATKKDELLAILEDCRERLKRS 319


>gi|206580487|ref|YP_002236325.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae 342]
 gi|288933313|ref|YP_003437372.1| hypothetical protein Kvar_0430 [Klebsiella variicola At-22]
 gi|290511636|ref|ZP_06551005.1| tRNA-dihydrouridine synthase B [Klebsiella sp. 1_1_55]
 gi|206569545|gb|ACI11321.1| tRNA-dihydrouridine synthase B [Klebsiella pneumoniae 342]
 gi|288888042|gb|ADC56360.1| TIM-barrel protein, nifR3 family [Klebsiella variicola At-22]
 gi|289776629|gb|EFD84628.1| tRNA-dihydrouridine synthase B [Klebsiella sp. 1_1_55]
          Length = 321

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSV 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P+ V   + A+  A+ +P
Sbjct: 76  PEEMAAAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPEQVKSILTAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  ++ G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWEPEHRN--CVEIAQLAEECGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|303256192|ref|ZP_07342208.1| tRNA-dihydrouridine synthase B [Burkholderiales bacterium 1_1_47]
 gi|331001248|ref|ZP_08324874.1| tRNA-dihydrouridine synthase B [Parasutterella excrementihominis
           YIT 11859]
 gi|302860921|gb|EFL83996.1| tRNA-dihydrouridine synthase B [Burkholderiales bacterium 1_1_47]
 gi|329568975|gb|EGG50771.1| tRNA-dihydrouridine synthase B [Parasutterella excrementihominis
           YIT 11859]
          Length = 326

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 69/288 (23%), Positives = 136/288 (47%), Gaps = 22/288 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGADI 59
             +TD  +R   R L   A    EM+ +   LR  +K+   FS  ++  P A+Q+ G+D 
Sbjct: 23  AGFTDLPFRQICRKL-GAAYAVAEMVASQKHLRESRKSQERFSLGSESYPRAIQLLGSDP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L + A+     G   ++ N GCP+ +V     G+ L+ +  +V   + A+ +A+ +PV
Sbjct: 82  VDLADTARYAVQCGAQIVDFNCGCPAKKVCSVECGSALLKDEALVEKLLKALTEAVDVPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D +   +   N+    +++G+  + +H R         ++      +DY  +
Sbjct: 142 TLKYRLGWDAE--HINALNIAAIAQEAGIKMLVLHGRT--------REQGFKGEVDYQRI 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K  + D+ +  NG ++ + +A  +L     DG+MIGRAA  N  + + +++  S  +
Sbjct: 192 AEVK-ASVDIPVIANGDIDSVEKAEAVLAQTGADGIMIGRAAIGNPWIFSQINDKLSGRI 250

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +P K+++ +     +    + Y          L+ I +H+ G F 
Sbjct: 251 -PQAPSKSQLIETIGEHLQLHFSFY-----EKEKGLKTIRKHLSGYFK 292


>gi|317125242|ref|YP_004099354.1| hypothetical protein Intca_2117 [Intrasporangium calvum DSM 43043]
 gi|315589330|gb|ADU48627.1| TIM-barrel protein, nifR3 family [Intrasporangium calvum DSM 43043]
          Length = 419

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 125/318 (39%), Gaps = 33/318 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----------LLYTEMIVADAILRGDKKNI--LGFSTQE 47
           M   T+R +R   R   N             L  +EMI   A++  + + +  +     E
Sbjct: 48  MAGITNRAFRRLCREYGNEGAVTGGASGATSLYVSEMITTRALVERNAETMRLIEHDPDE 107

Query: 48  KPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P ++Q+   D +    AA+I V++   + I+LN GCP  +V     G+ L    D+   
Sbjct: 108 NPRSIQLYSVDPATARAAARILVQEDRADHIDLNFGCPVPKVTRKGGGSALPWKRDLFRS 167

Query: 107 CIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            + A+ +      IPVTVK R G+DD+   +       + +  G   + +H R A     
Sbjct: 168 IVGAVVEEGARRDIPVTVKMRKGIDDE--HLTYLEAGLAAEDEGAAAVALHGRTA----- 220

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                      D+  +  +K+    + +  NG +     AL+++     DGV++GR    
Sbjct: 221 ---AQAYSGTADWAAIRLLKQTVTTVPVLGNGDIWSAEDALRMVAETGCDGVVVGRGCLG 277

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T +   F+      +P    V  D  R  +  +TD+      +    + I +H+ 
Sbjct: 278 RPWLFTDLAAAFAGSSARVTPSLG-VVADTLRTHTLYLTDFYGDEERA---CRDIRKHIA 333

Query: 282 GLFHGFPNSRRCRHILTV 299
               GFP     R  L +
Sbjct: 334 WYLKGFPAGSTLRSSLAL 351


>gi|213019483|ref|ZP_03335289.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212994905|gb|EEB55547.1| NifR3 family protein [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 298

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 133/314 (42%), Gaps = 21/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L   +LL +EMI + A++   ++++   +  ++  A+Q+ G +  
Sbjct: 1   MSGVTDYPFRSIVKKL-GASLLVSEMIASRAMIMQTRQSMQK-AKVDELTAVQLAGCEPD 58

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ E  G   I++N GCP  +V  G  G+ LM +     + I A+ KA+S+PVT
Sbjct: 59  VMAEAAKLNEGMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEAVVKAVSVPVT 118

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G +D+        L K  +  G   I +H R         +        D+  V 
Sbjct: 119 VKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLYNGQADWKFVR 168

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K++   + + +NG ++ ++     L     DGVMIGR  Y    ++     + S    
Sbjct: 169 NVKEQV-KIPVIVNGDIKSLNDVQSALKESGADGVMIGRGTYGKPWLINQAINFLSGNKV 227

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
                  R+       I     D    +  S   ++   +H+     G  NS   R  + 
Sbjct: 228 SEPTASERLS------IILKHYDSILEYYGSDTGIKMARKHIGWYSSGLQNSSEFRVRVN 281

Query: 299 VEAGASTATHHIIE 312
               ++    +II+
Sbjct: 282 NIIDSTEVKENIID 295


>gi|209364495|dbj|BAG74734.1| tRNA dihydrouridine synthase [Vibrio parahaemolyticus]
          Length = 211

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 101/201 (50%), Positives = 137/201 (68%), Gaps = 2/201 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RL+T   LLYTEM+   AI+ G   + L ++ +E PLALQ+GG++  
Sbjct: 12  MLDWTDRHCRYFHRLMTKETLLYTEMVTTGAIIHGKG-DFLAYNEEEHPLALQLGGSNPE 70

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK+ ++ GY+EINLNVGCPS RV  G FGACLM  P +V +C+AAM + + +PVT
Sbjct: 71  DLATCAKLAQERGYDEINLNVGCPSDRVQNGRFGACLMAEPQLVAECVAAMKEVVDVPVT 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK RIG+DDQ     L + V  + +K G     IHARKA L GLSPK+NR+IP LDY   
Sbjct: 131 VKTRIGIDDQDSYEFLTDFVSIVSEKGGCEQFTIHARKAWLSGLSPKENREIPPLDYPRA 190

Query: 180 YEIKKENPDLFIGLNGGLEDM 200
           Y++K++   L I +NGG++ +
Sbjct: 191 YQLKQDFSHLTIAINGGVKSL 211


>gi|66047631|ref|YP_237472.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae B728a]
 gi|63258338|gb|AAY39434.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           syringae pv. syringae B728a]
 gi|330969391|gb|EGH69457.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 337

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 133/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 189 IALIKQAV-SIPVFANGDIDSPEKARHVLKATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 ETLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|332709280|ref|ZP_08429243.1| putative TIM-barrel protein, nifR3 family [Lyngbya majuscula 3L]
 gi|332351954|gb|EGJ31531.1| putative TIM-barrel protein, nifR3 family [Lyngbya majuscula 3L]
          Length = 297

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 125/304 (41%), Gaps = 21/304 (6%)

Query: 21  LLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++YTEM+ A  +    +   ++     EKP+++Q+       L +AA+     G + +++
Sbjct: 1   MMYTEMVHASQLKYLRELPKVMEVDPLEKPISIQLFDCRPEFLAQAAQRAVAEGADTVDI 60

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+GCP  ++ +   G+ L+ +P+     + ++ KA+ +PVTVK RIG  +Q   +     
Sbjct: 61  NMGCPVNKITKNGGGSALLRDPETAEAIVRSVVKAVEVPVTVKTRIGWTNQE--INAVEF 118

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + ++ +G   + +H R         +D     +  ++ +  +K +   + +  NG +  
Sbjct: 119 AQRMEDAGAQMLTLHGRT--------RDQGYNGSARWEWIKRVK-DVLSIPVIANGDILS 169

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +  A++ L     DGVM  R       ++  +D +         P       +  ++   
Sbjct: 170 VDAAVRCLEETGADGVMCSRGTLGYPFLVGEIDYFLKTGQLLP-PTTPVQLLECAKEHLQ 228

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +  Y          + Q  +HM     GFP +   R  L+           +IE A   
Sbjct: 229 GLWHYKGER-----GIYQSRKHMAWYAKGFPGAGELRKKLSRIETVDQ-GVELIENAIAK 282

Query: 318 MIES 321
           +  S
Sbjct: 283 LQPS 286


>gi|332285254|ref|YP_004417165.1| hypothetical protein PT7_2001 [Pusillimonas sp. T7-7]
 gi|330429207|gb|AEC20541.1| hypothetical protein PT7_2001 [Pusillimonas sp. T7-7]
          Length = 353

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 121/300 (40%), Gaps = 24/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR   + L       +EM  ++  L  + K    L    +  P+A+QI G+D
Sbjct: 17  MAGVTDRPYRKLCKTL-GAGYAVSEMAASNPRLWNNVKTSRRLNHEGEIDPVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA    D G   I++N+GCP  +V   + G+ L+ N  +V   + ++  A    
Sbjct: 76  PDMMAEAAIFNIDKGARIIDINMGCPVKKVCNVASGSALLRNEQLVARILRSVVDACQPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        + +  +  GV  I +H R         + +      +
Sbjct: 136 DVPVTLKTRTGWDRESRNAVH--IAQLAQDIGVAAITLHGRT--------RCDLYQGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + ++K+    + +  NG ++   +A  +L   + D VM+GRAA     +   +  Y 
Sbjct: 186 YDTIRDVKRAL-QIPVIANGDIDSPEKAKYVLEYTNADAVMVGRAAQGRPWIFREISHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            +    S P    +       +      Y          ++   +H+       P+++  
Sbjct: 245 VHGSHLSPPTYGELRDCLLDHLEDHYQFYGEF-----TGVRSARKHIGWYLADLPDAQSF 299


>gi|312113493|ref|YP_004011089.1| hypothetical protein Rvan_0714 [Rhodomicrobium vannielii ATCC
           17100]
 gi|311218622|gb|ADP69990.1| TIM-barrel protein, nifR3 family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 338

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 130/313 (41%), Gaps = 21/313 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ TEM+ + +++R  +K +      T    LA+Q+ G D
Sbjct: 34  MSGVTDRPFRRIVRKF-GADLVVTEMLASKSVIRQQRKTLRMSERETDGGLLAVQLAGRD 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + +AA++ ED G + I+LN GCP  +V +   G+ LM +         A+  A+++P
Sbjct: 93  PTIMADAARLAEDRGADIIDLNFGCPVKKVVKDMVGSALMRDEVHAAKIFEAVVNAVTVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G       +    L +  +  G+  + +H R         +      + D+  
Sbjct: 153 VTLKMRMGWSPDE--LNAPRLARIAEGCGIAMVTVHGRT--------RCQFYGGDADWGF 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K E   + + +NG +   + A++ L     DGVMIGR AY    ++  V       
Sbjct: 203 VRRVK-EAVSIPVIVNGDIVTPADAVRALAASGADGVMIGRGAYGRPWIIAQVAAALRGE 261

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P   RV  D   +   +M DY          +    +H      G P +   R  
Sbjct: 262 TVSDEPSL-RVRLDTMAEHFEAMLDYYGER----AGVPIARKHFGWYSAGLPGATAFRDA 316

Query: 297 LTVEAGASTATHH 309
           + V   A+     
Sbjct: 317 VNVAEAAADVRRQ 329


>gi|260061331|ref|YP_003194411.1| hypothetical protein RB2501_07020 [Robiginitalea biformata
           HTCC2501]
 gi|88785463|gb|EAR16632.1| putative TIM-barrel enzyme, possible dehydrogenase, contains a
           highly conserved dihydrouridine synthase domain
           [Robiginitalea biformata HTCC2501]
          Length = 330

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 135/323 (41%), Gaps = 22/323 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE I ++ ++R   K++  L    +E+P+ +QI GA+
Sbjct: 19  MEDVSDPPFRTLCKE-QGADVMYTEFISSEGLIRDAAKSVVKLDIYEKERPIGIQIFGAE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +++A  IV + G + I++N GCP  +V   + GA ++ +  ++     AM K   +P
Sbjct: 78  LDSMLQAVDIVTETGPDIIDINFGCPVKKVVCKNAGAGILRDIPLMVKLTEAMVKRTHLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ +  + + ++  G+  I IH R  +               D+  
Sbjct: 138 VTVKTRLGWD--HNSIKIVEVAERLQDVGIQSIAIHGRTRV--------QMYKGEADWRP 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + +  NG ++    A+++     +DG MIGRA+         V  YF  
Sbjct: 188 IAEVKNNPRMHIPVFGNGDVDTPEAAVRMRDEYGLDGAMIGRASIGYPWFFREVKHYFET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P     D +     +      A         + +  RH    F G PN +  R 
Sbjct: 248 GEHLPPP-----DMEARVAAARRHLQMAIDWKGEKLGVFETRRHYTNYFKGIPNFKPYRM 302

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            +     ++       + A    
Sbjct: 303 KMVTSDDSADVFAA-FDEALEAF 324


>gi|91785159|ref|YP_560365.1| dihydrouridine synthase TIM-barrel protein nifR3 [Burkholderia
           xenovorans LB400]
 gi|91689113|gb|ABE32313.1| tRNA-U20-dihydrouridine synthase [Burkholderia xenovorans LB400]
          Length = 352

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENRNA--LNVARLAESAGISMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A ++L     D +MIGRAA     +   +  
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPQKAREVLAATGADALMIGRAAQGRPWLFREIGH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 VFRHRMNT 308


>gi|289625299|ref|ZP_06458253.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|330867132|gb|EGH01841.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330871020|gb|EGH05729.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 337

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P  + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 EKLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFR 300


>gi|307564816|ref|ZP_07627344.1| TIM-barrel protein, nifR3 family [Prevotella amnii CRIS 21A-A]
 gi|307346538|gb|EFN91847.1| TIM-barrel protein, nifR3 family [Prevotella amnii CRIS 21A-A]
          Length = 325

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 144/329 (43%), Gaps = 35/329 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADAI+R  K  +  +     E+P  +QI G +
Sbjct: 18  MEDVTDIGFRSMCKRY-GAAMVYTEFVSADAIIRNIKSTLSKMVIDDNERPTGIQIYGNN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE+   + I++N GCP  +V     GA L+ N  ++ + +  + KA+++P
Sbjct: 77  VESMVEAAKIVEEAKPDVIDINFGCPVKKVAGKGAGAGLLRNIPLLLNIVREVVKAVNVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + + +L + I+  G   + IH R         ++       D+ +
Sbjct: 137 VTVKTRLGWDEH--NLIITDLAEQIQDCGAKALTIHGRT--------REQMYTGKADWTL 186

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++ K NP   + I  NG +  +  A        VD VMIGRA +    +         
Sbjct: 187 IGKVAK-NPHITIPIIGNGDIVSVKDAYDHFDKYGVDAVMIGRATFGCPWLFCK------ 239

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
                    +T +  D    +   M       +     +    RH+    +F G P+ ++
Sbjct: 240 --------DQTSLSLDDKIDVLEEMLRINVERIDEYRGILHTRRHLAASPIFKGIPDFKQ 291

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R I  +          ++E     + E+
Sbjct: 292 MR-IAMLRCSKMEELIKMLEEIRGFLKEN 319


>gi|258655080|ref|YP_003204236.1| hypothetical protein Namu_4974 [Nakamurella multipartita DSM 44233]
 gi|258558305|gb|ACV81247.1| TIM-barrel protein, nifR3 family [Nakamurella multipartita DSM
           44233]
          Length = 398

 Score =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 125/318 (39%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EMI   A++ GD K+  ++ F   E P ++Q+ G D
Sbjct: 44  MAGVTNAPFRSLCREF-GAGLYVCEMITTRALVAGDPKSRAMMRFEPDEHPRSVQLYGVD 102

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A ++V +    + I+LN GCP  +V     G+ +     +    + +       
Sbjct: 103 PVVVGQAVRLVVEQDLADHIDLNFGCPVPKVTRKGGGSAIPYKRRLFESIVRSAVDQATP 162

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D     +   +  +  + +GV  + +HAR AI               
Sbjct: 163 HGVPVTVKMRIGIDSD--HITYLDAGRIAEDAGVAAVALHARTAI--------QHYSGQA 212

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D++ +  +K+    + +  NG +   S AL ++     DGV++GR       +   +   
Sbjct: 213 DWETIGRLKQAVTSVPVLGNGDIFAASDALTMMAMTGCDGVVVGRGCQGRPWLFAELAAA 272

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F      + P    V +   R             + +   ++++ +H      GF    +
Sbjct: 273 FDGRPAPTPPDLRAVAEVMRRHAVL-----LVAEMGADRGIRELRKHTAWYLRGFAVGSQ 327

Query: 293 CRHILTVEAGASTATHHI 310
            R  L + A  +     I
Sbjct: 328 VRRELGMVASLTELDELI 345


>gi|123968631|ref|YP_001009489.1| nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. AS9601]
 gi|123198741|gb|ABM70382.1| putative nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. AS9601]
          Length = 335

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 137/324 (42%), Gaps = 25/324 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADIS 60
              TD  +R   R    N+LL+TEMI A ++ +G   + I     +E P+ +QI      
Sbjct: 26  AGVTDNIFRRLVRKWAPNSLLFTEMINATSLKKGYGTQKINQIDLEEGPIGVQIFDNRPY 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ +PVT
Sbjct: 86  AVSEAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVRVPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D +     + + +  ++ +G   I +H R    +G S K        D++++ 
Sbjct: 146 VKTRLGWDSKE--ENIEDFLFKLQDAGATMITLHGRTRK-QGFSGKS-------DWEMIG 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +KK   ++ +  NG +++   AL  L     DGVMIGR    +   +  +D        
Sbjct: 196 RLKK-LLEIPVIANGDIKNPDDALNCLKKTKADGVMIGRGILGSPWKIGEIDYALRENKN 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +           L    +H+      F  +   R+ L 
Sbjct: 255 FKEPNTEEKLYLIIEHLDELIKEKG------DHGLLIARKHISWTCKDFKGASNLRNNLV 308

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
                +      ++   N MI++L
Sbjct: 309 RAVDKNE-----VKNLINKMIQTL 327


>gi|156097374|ref|XP_001614720.1| tRNA-dihydrouridine synthase A [Plasmodium vivax SaI-1]
 gi|148803594|gb|EDL44993.1| tRNA-dihydrouridine synthase A, putative [Plasmodium vivax]
          Length = 509

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 112/324 (34%), Positives = 169/324 (52%), Gaps = 32/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R +T  A ++TEMIV + +L      +  LGF++ E P+  Q+GG+D
Sbjct: 142 MINVTNRHFRALVRTITRRAQVWTEMIVDNTLLYNLNNLEEHLGFNSNEHPIVCQLGGSD 201

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA +VE  GY+EINLNVGCPS +V     FGA LM  P+ V + +  + + + I
Sbjct: 202 ATSLAEAAVLVEQAGYDEINLNVGCPSTKVANKGAFGAYLMKKPEHVRNIVYEIKRKVHI 261

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R GVDD      LR+ V+ I   G +   +HARKA LKGL PK NR +P L+Y 
Sbjct: 262 PVSVKIRTGVDDCDSFPFLRSFVECISSVGCSHFIVHARKAWLKGLDPKQNRSVPPLEYP 321

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS-------VD-----------------GV 213
            VY + +  P L   LNGG++ + +A+ +L         VD                 GV
Sbjct: 322 KVYSLCQLYPHLKFTLNGGVKTVEEAVALLNGYLPKKGNVDSEKTYVQVKNYQVNPLHGV 381

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GRA  +N+ +L+  D+   N     +    R   D ++      +      L S    
Sbjct: 382 MLGRACMENTTVLSQTDQLVYNEKPPHTAFSRRTVLDAYKSYLEENSS-----LCSLSSA 436

Query: 274 QQITRHMIGLFHGFPNSRRCRHIL 297
            ++ + ++G+  G P  R  R+ L
Sbjct: 437 FELLKPVLGILKGMPGHRIFRNKL 460


>gi|311895936|dbj|BAJ28344.1| putative tRNA-dihydrouridine synthase [Kitasatospora setae KM-6054]
          Length = 395

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 66/307 (21%), Positives = 122/307 (39%), Gaps = 24/307 (7%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  + K +  + F   EKP ++Q+ G 
Sbjct: 39  MAGITNAPFRTLCREQSGGRGLYVSEMITTRALVERNAKTMQLIKFDPSEKPRSIQLYGV 98

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKAL 115
           D   + +AA+++   G  + I+LN GCP  +V     G+ L    +++ D +  A+  A 
Sbjct: 99  DPETVGKAARMISAEGLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRDILRQAVANAG 158

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV+ I +H R A                D
Sbjct: 159 DLPVTMKMRKGIDDD--HLTYLDAGRIGAEEGVSAIALHGRTA--------AQHYGGTAD 208

Query: 176 YDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +  +  +++  P  + +  NG +     A++++     DGV++GR       +   +   
Sbjct: 209 WSAIARLRESVPAGIPVLGNGDIWSADDAVRMMRETGCDGVVVGRGCLGRPWLFKDLVSI 268

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-SGGKLQQITRHMIGLFHGFPNSR 291
           F   +  + P    V +   R             L      +    +H+     GF    
Sbjct: 269 FEGDVDYARPTFDYVARAMVRHA-----QLLGEWLGDEARGVIDFRKHVAWYTKGFSVGS 323

Query: 292 RCRHILT 298
             R  L 
Sbjct: 324 ELRVRLA 330


>gi|254526611|ref|ZP_05138663.1| NifR3 family enzyme [Prochlorococcus marinus str. MIT 9202]
 gi|221538035|gb|EEE40488.1| NifR3 family enzyme [Prochlorococcus marinus str. MIT 9202]
          Length = 345

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 135/315 (42%), Gaps = 21/315 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADIS 60
              TD  +R   R    N+LL+TEMI A ++ +G  K  I     +E P+ +QI      
Sbjct: 30  AGVTDDIFRRLVRKWAPNSLLFTEMINATSLKKGFGKQKINQIDLEEGPVGVQIFDYRPH 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVT
Sbjct: 90  AVSEAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVKIPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D +     + + +  ++ +G   I +H R    +G S K        D++++ 
Sbjct: 150 VKTRLGWDSKE--ENIEDFLFKLQDAGATMITLHGRTRK-QGFSGKS-------DWEMIG 199

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K    ++ +  NG +++   AL  L   + DGVMIGR    +   +  +D   S    
Sbjct: 200 RLK-SLLEIPVIANGDIKNPDDALNCLKKTNADGVMIGRGILGSPWKIGEIDYAISENKN 258

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +           L    +H+      F  +   R+ L 
Sbjct: 259 FKKPNTEEKLYLIIEHLDELIKEKG------DHGLLIARKHISWTCKDFKGASNLRNKL- 311

Query: 299 VEAGASTATHHIIET 313
           V A       ++I+ 
Sbjct: 312 VRAVDKNEVKNLIKK 326


>gi|84496809|ref|ZP_00995663.1| transcriptional regulator, NifR3/Smm1 family protein [Janibacter
           sp. HTCC2649]
 gi|84383577|gb|EAP99458.1| transcriptional regulator, NifR3/Smm1 family protein [Janibacter
           sp. HTCC2649]
          Length = 407

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 66/318 (20%), Positives = 125/318 (39%), Gaps = 32/318 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----------LLYTEMIVADAILRGDKKNI--LGFSTQE 47
           M   T+R +R   R   +             L   EM+ + A++    + +  +    +E
Sbjct: 35  MAGITNRAFRRLCREYGSAGSEAGGASGATSLYVNEMVTSRALVERTPETMRLISHGPEE 94

Query: 48  KPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P ++Q+   D      AA+++  +   + I+LN GCP  +V     GA L    ++   
Sbjct: 95  HPRSVQLYSVDPVTAGLAARMLVTEDRADHIDLNFGCPVPKVTRKGGGAALPWKTELFRG 154

Query: 107 CIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            ++A+ +     ++PVTVK RIG+D     +   +  +  +  GV  + +H R A     
Sbjct: 155 IVSAVVREANPYNVPVTVKMRIGID--ADHITYLDAGRIAEGEGVAAVALHGRTA----- 207

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                      D+  +  +K+    + +  NG +     AL+++     DGV++GR    
Sbjct: 208 ---AQAYSGQADWSAIARLKEAVTTIPVLGNGDIWSAEDALEMVRQTGCDGVVVGRGCLG 264

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T +   F+   T   P    V +   R     +  Y    L +    + I +H+ 
Sbjct: 265 RPWLFTDLAAAFAGTPTRVQPGLREVTQTLSRHTRYLIDFYDGDELRA---CRDIRKHIA 321

Query: 282 GLFHGFPNSRRCRHILTV 299
               GFP     R+ L +
Sbjct: 322 WYLKGFPAGSTVRNQLAL 339


>gi|294675099|ref|YP_003575715.1| hypothetical protein PRU_2465 [Prevotella ruminicola 23]
 gi|294473955|gb|ADE83344.1| putative TIM-barrel protein, NifR3 family [Prevotella ruminicola
           23]
          Length = 315

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 144/325 (44%), Gaps = 35/325 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + A+A++R  K  I  L  S  E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYTEFVSAEALIRDVKSTISKLTISDTERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +VEAAKIVE  G + I++N GCP  +V     GA ++ N   + +  + +  A+ +P
Sbjct: 77  VEAMVEAAKIVEQAGPDLIDINFGCPVKKVAGKGAGAGMLQNIPKMLEITSKVVDAVKLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G + +   + +  L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWNHEQ--LIITELAEQLQDCGIKALTIHGRT--------RSQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K+     + I  NG +  + +A +      VD +MIGRA +    + +        
Sbjct: 187 IGEVKRNPRIHIPIIGNGDIHSLDEADEAFKTYGVDAIMIGRATFGCPWIFS-------- 238

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                   +  +D +    I   +       +     +    RH+    +F G P+ R+ 
Sbjct: 239 --------REELDFNQKLDILEELLRINVERIDEKRGILHTRRHLAATPIFKGIPDFRQT 290

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R I  + A        I+E    L+
Sbjct: 291 R-IAMLRAEKMDELLQILEDTRKLL 314


>gi|126696436|ref|YP_001091322.1| nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9301]
 gi|126543479|gb|ABO17721.1| putative nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9301]
          Length = 335

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 75/324 (23%), Positives = 138/324 (42%), Gaps = 25/324 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADIS 60
              TD  +R   R    N+LL+TEMI A ++ +G   + I     +E P+ +QI      
Sbjct: 26  AGVTDIIFRRLVRKWAPNSLLFTEMINATSLKKGYGTQKINQIDLEEGPIGVQIFDNRPY 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ +PVT
Sbjct: 86  AVSEAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAIELVKNVVKAVRVPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D +     + + +  ++ +G   I +H R    +G S K        D++++ 
Sbjct: 146 VKTRLGWDSKE--ENIEDFLFKLQDAGATMITLHGRTRK-QGFSGKS-------DWEMIG 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +KK   ++ +  NG +++   AL  L   + DGVMIGR    +   +  +D        
Sbjct: 196 RLKK-LLEIPVIANGDIKNPDDALNCLKKTNADGVMIGRGILGSPWKIGEIDYALRENKN 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +           L    +H+      F  +   R+ L 
Sbjct: 255 FKEPNIEEKLYLIIEHLDELVKEKG------DHGLLIARKHISWTCKDFKGASNLRNNLV 308

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
                +      ++   N MI++L
Sbjct: 309 RAVDKNE-----VKNLINKMIKTL 327


>gi|229083394|ref|ZP_04215744.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-44]
 gi|228699930|gb|EEL52565.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-44]
          Length = 332

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +++   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNQRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+     + I++N+GCP  ++ +   GA  +L+PD V + +AA+  A+  
Sbjct: 77  KETLVGAAKYVDKSTTADIIDINMGCPVPKITKCDAGAKWLLDPDKVYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      ++I+++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENARAIERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +E    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGNPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   + R R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENIAVREMRKHAAWYLKGVSGNARVRN 300

Query: 296 ILTVEAGAST 305
            + V      
Sbjct: 301 GINVCNTRQD 310


>gi|257483333|ref|ZP_05637374.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289647824|ref|ZP_06479167.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298488946|ref|ZP_07006969.1| tRNA dihydrouridine synthase B [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298156444|gb|EFH97541.1| tRNA dihydrouridine synthase B [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|331012552|gb|EGH92608.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 337

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 133/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 EKLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|302534306|ref|ZP_07286648.1| dihydrouridine synthase [Streptomyces sp. C]
 gi|302443201|gb|EFL15017.1| dihydrouridine synthase [Streptomyces sp. C]
          Length = 386

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   EKP ++Q+ G 
Sbjct: 30  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATEKPRSIQLYGV 89

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A + IVE+   + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 90  DPVTVGKAVRMIVEEDRADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVAGAG 149

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+ D+   +   +  +   + G+  I +H R                  D
Sbjct: 150 GLPVTMKMRKGITDE--HLTYLDAGRIAVEEGITAIALHGRTT--------AQHYGGTAD 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 200 WEAIARLKEHVPEIPVLGNGDIWCAEDALRMVRETGCDGVVVGRGCLGRPWLFNDLVAAF 259

Query: 234 SN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              P     P    V     R                   +    +H+     GF     
Sbjct: 260 EGRPEDFHKPNLREVASTMLRHAQL----LGEWIGDEARGVIDFRKHVAWYLKGFAVGSE 315

Query: 293 CRHILTVEAGASTATHHIIE 312
            R  L V +  +    H+ E
Sbjct: 316 MRGKLAVTSSLAELDAHLSE 335


>gi|239940987|ref|ZP_04692924.1| putative dihydrouridine synthase [Streptomyces roseosporus NRRL
           15998]
 gi|239987465|ref|ZP_04708129.1| putative dihydrouridine synthase [Streptomyces roseosporus NRRL
           11379]
 gi|291444424|ref|ZP_06583814.1| dihydrouridine synthase [Streptomyces roseosporus NRRL 15998]
 gi|291347371|gb|EFE74275.1| dihydrouridine synthase [Streptomyces roseosporus NRRL 15998]
          Length = 382

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 62/317 (19%), Positives = 119/317 (37%), Gaps = 21/317 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 86

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSGAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HLTFLDAGRIAVEEGVTAVALHGRTT--------AQHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +    
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWCADDALRMMRETGCDGVVVGRGCLGRPWLFADLVSAM 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P    V     R  +                +    +H+     GF      
Sbjct: 257 EGRTERHAPTLREVADVMVRHATL----LGEWIGDEARGVIDFRKHVAWYLKGFAVGSEM 312

Query: 294 RHILTVEAGASTATHHI 310
           R  L + +        +
Sbjct: 313 RKKLAITSSLEELGGQL 329


>gi|332530304|ref|ZP_08406250.1| NifR3 family TIM-barrel protein [Hylemonella gracilis ATCC 19624]
 gi|332040290|gb|EGI76670.1| NifR3 family TIM-barrel protein [Hylemonella gracilis ATCC 19624]
          Length = 375

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 69/348 (19%), Positives = 123/348 (35%), Gaps = 43/348 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K       S +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRKLCKAL-GAGYAVSEMVTSRKELWNSLKTSRRADHSGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    + G   I++N+GCP+ +V     G+ LM +  +  +   A+  A    
Sbjct: 76  AAMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMQDEALALEIAEAVVAACEPH 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G            L  + + +G+  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQANKNAVT--LACAFEGAGIRMLTVHGRT--------REQGYGGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   V  Y 
Sbjct: 186 YDTIAAVK-AAVRVPVVANGDITSPEKARAVLAHTGADAVMIGRAAQGRPWIFREVAHYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG----------------------- 270
           +     + P+   V +     +      Y       G                       
Sbjct: 245 ATGEHLAPPLVAEVKRLLLDHLQEHYALYGDDRWAEGLAARPDTLTALPSASTGVQPGTS 304

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
             ++   +H+     G P     R  +     +  A    +   F+ +
Sbjct: 305 TGVRSARKHIGWYVRGLPGGEAFRARMNALDDSR-AQWQAVADYFDEL 351


>gi|72383560|ref|YP_292915.1| dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. NATL2A]
 gi|72003410|gb|AAZ59212.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. NATL2A]
          Length = 330

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 139/317 (43%), Gaps = 21/317 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADIS 60
              +D+ +R F R  +  ALL+TEM+ A ++  G  +  ++  S +  P+ +Q+      
Sbjct: 28  AGVSDQIFRNFVRRWSPKALLFTEMVNAKSLELGHGEEKVIELSEESGPIGVQLFDHRPD 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +V+AA   E  G   I++N+GCP  ++     G+ L+  P++    +  + KA+SIPVT
Sbjct: 88  SMVDAAIKAESSGAFLIDINMGCPVKKIARKGGGSALLKEPELAQLIVKKVSKAISIPVT 147

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G  +        +    ++++G   I +H R         +      + ++  + 
Sbjct: 148 VKIRLGWCETTSDPV--SFALGLQEAGAQLITVHGRT--------RRQGFSGHANWKAIA 197

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           +IKK   D+ +  NG +++   A++ L   + DGVMIGRA+     ++  +DE   N  T
Sbjct: 198 KIKKSL-DIPVIANGDIKNSRDAIECLKITNADGVMIGRASMGAPWLVGQIDEEIKNQTT 256

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P   ++      +    +      H      L    +HM     GF  +   RH L 
Sbjct: 257 FKPP-DAKMKVSLSLEHLKLLVSKKGNH-----GLLIARKHMNWTCRGFEGASNLRHKL- 309

Query: 299 VEAGASTATHHIIETAF 315
           V A        ++E   
Sbjct: 310 VRARTPNDAIKLLEDEL 326


>gi|325128475|gb|EGC51355.1| dihydrouridine synthase [Neisseria meningitidis N1568]
          Length = 374

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 132/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 174 VTLKTRLGWHDDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECAAAILNHIRAIHAFY-----GDTAGVRIARKHIGWYIDEMPDGEQTRRE 337

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + ++      + E 
Sbjct: 338 IN-RLDSAAAQYDMLAGYLERLAEK 361


>gi|296157346|ref|ZP_06840182.1| TIM-barrel protein, nifR3 family [Burkholderia sp. Ch1-1]
 gi|295892682|gb|EFG72464.1| TIM-barrel protein, nifR3 family [Burkholderia sp. Ch1-1]
          Length = 352

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       ++ +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENRNA--LSVARLAESAGISMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A ++L     D +MIGRAA     +   +  
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPQKAREVLAATGADAIMIGRAAQGRPWLFREIGH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 VFRHRMNT 308


>gi|424091|gb|AAA69019.1| ORF1 protein [Salmonella enterica subsp. enterica serovar
           Typhimurium]
          Length = 321

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PVEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + I  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPIIANGDITNPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+           + R  
Sbjct: 245 ELLPRRASAEVKRLLCTHVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|71735544|ref|YP_276563.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71556097|gb|AAZ35308.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|320322743|gb|EFW78836.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320330472|gb|EFW86451.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 337

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 133/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 EKLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|325002690|ref|ZP_08123802.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudonocardia
           sp. P1]
          Length = 394

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 67/306 (21%), Positives = 120/306 (39%), Gaps = 23/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R          EMI A  ++  +     ++ F   E P ++Q+ G D
Sbjct: 42  MAGITNPGFRRLCRE-QGAGYYVCEMITARGLVEKNPLTFRMIAFDADEHPRSMQLYGVD 100

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
              +  AA+++ +    + I++N GCP  +V     GA L     +    ++A  + A  
Sbjct: 101 PDSMRRAAQMIVERDLADHIDMNFGCPVPKVTRRGGGAALPFKRKLFERIVSAAVEGAGD 160

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG+DD        +  +    SG   + +HAR A          R     D+
Sbjct: 161 RPVTVKMRIGIDDDHH--TYLDAARIAVDSGAVAVALHARTA--------SQRYSGQADW 210

Query: 177 DIVYEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +  +++  P  + +  NG +     AL ++     DGV++GR       +   ++  F
Sbjct: 211 DAISRLREHVPAHVPVLGNGDIFSAQDALDMVARTGCDGVVVGRGCLGRPWLFGDLEAAF 270

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P   +V     R            H+     ++ + +H+     GFP     
Sbjct: 271 AGRELPAPPDLGQVAATLRRHAVL-----LCEHMGDHKGIRDVRKHIAWYLKGFPVGPEL 325

Query: 294 RHILTV 299
           R  L +
Sbjct: 326 RRSLGM 331


>gi|170723771|ref|YP_001751459.1| NifR3 family TIM-barrel protein [Pseudomonas putida W619]
 gi|169761774|gb|ACA75090.1| TIM-barrel protein, nifR3 family [Pseudomonas putida W619]
          Length = 337

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 65/298 (21%), Positives = 131/298 (43%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCKRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAARANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVGAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ +  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRANKNG--LNVARIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L    VDG++IGRAA     +   ++ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDITSPEKARAVLDATGVDGLLIGRAAQGRPWIFREIEHYLGTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P  +  R
Sbjct: 248 QHLPAPQLDEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATRPGGKEFR 300


>gi|205371966|ref|ZP_03224784.1| YacF [Bacillus coahuilensis m4-4]
          Length = 332

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 140/325 (43%), Gaps = 25/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  + K +  L    +E PL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVLQNAKTMNMLYIDEREYPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+       I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVEAAKFVDKHSNAAIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+           + I+++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDEDHIYAV--ENARMIERAGGQAVSLHGRTRV--------QMYEGEANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+    + +  NG ++    A ++L     DGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIREVKQSVG-IPVIGNGDVQTPQDAKRMLDETGADGVMIGRAALGNPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P   R   D  +     + +    H+     ++++ +H      G   + + R+
Sbjct: 246 GQLIDEPG-AREKIDVCKLHLDRLINLKGEHVA----VREMRKHAAWYLKGIRGNGKFRN 300

Query: 296 ILTVEAGAST--ATHH-IIETAFNL 317
            +          A    ++E A  L
Sbjct: 301 AVNESNTRHDLVAVLDGLVEQAEEL 325


>gi|89100493|ref|ZP_01173354.1| YacF [Bacillus sp. NRRL B-14911]
 gi|89084759|gb|EAR63899.1| YacF [Bacillus sp. NRRL B-14911]
          Length = 338

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 148/329 (44%), Gaps = 30/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EMI    I+  ++K +  L    +EKPL+LQI G +
Sbjct: 26  MAGICNSAFRLTVKEF-GAGLVCAEMISDKGIVMKNEKTMNMLYIDEREKPLSLQIFGGE 84

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V++    + I++N+GCP  ++ +   GA  +L+PD + + ++A+  A+S 
Sbjct: 85  KDTLVEAAKFVDENTNADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSAVTAAVSK 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD           ++++++G   + +H R  +               ++D
Sbjct: 145 PVTVKMRMGWDDDHIYAVRN--AQAVERAGGKAVALHGRTRV--------QMYEGQANWD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+ N  + +  NG ++    A ++L    VDGVMIGRAA  N  M+    +Y   
Sbjct: 195 IIKEVKQ-NISIPLIGNGDVQTPQDAKRMLEETGVDGVMIGRAALGNPWMIYRTVKYLET 253

Query: 236 PLTGSSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                 P       V      ++ A  ++Y A        ++++ +H      G   + +
Sbjct: 254 GQLMDEPSVREKIDVCILHLDRLIALKSEYIA--------VREMRKHAAWYLKGIRGNGK 305

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R+ +             +  A  L  E+
Sbjct: 306 ARNAVNECNTREELVT--LLNALALDAEA 332


>gi|325134359|gb|EGC57004.1| dihydrouridine synthase [Neisseria meningitidis M13399]
 gi|325205824|gb|ADZ01277.1| dihydrouridine synthase [Neisseria meningitidis M04-240196]
          Length = 374

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 131/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 174 VTLKTRLGWHDDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECAAAILNHIRAIHAFY-----GDTAGVRIARKHIGWYIDEMPDGEQTRRE 337

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + ++      + E 
Sbjct: 338 IN-RLDSAAAQYDMLAGYLERLAEK 361


>gi|187925312|ref|YP_001896954.1| hypothetical protein Bphyt_3339 [Burkholderia phytofirmans PsJN]
 gi|187716506|gb|ACD17730.1| TIM-barrel protein, nifR3 family [Burkholderia phytofirmans PsJN]
          Length = 354

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 131/308 (42%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +    +
Sbjct: 137 PDAVPVTLKIRTGWNRENKNA--LNVARLAESAGISMLTVHGRT--------RADLYHGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A ++L     D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVK-AAVRIPVVANGDITSPHKAREVLAATGADAIMIGRAAQGRPWLFREIEY 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 VFRHRMNT 308


>gi|229113752|ref|ZP_04243188.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-3]
 gi|228669749|gb|EEL25155.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-3]
          Length = 339

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDKYTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 307

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 308 GINTCNTRQD 317


>gi|227873295|ref|ZP_03991560.1| dihydrouridine synthase [Oribacterium sinus F0268]
 gi|227840862|gb|EEJ51227.1| dihydrouridine synthase [Oribacterium sinus F0268]
          Length = 344

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 136/324 (41%), Gaps = 30/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   + +   +L +TEM+ A AI  G++    +L    +   ++ Q+ G+D
Sbjct: 46  MAGVTDLPYRILCKEM-GLSLSFTEMVSAKAIYYGNQNTDSLLVHKGEPGLVSAQLFGSD 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + E A  +E+  ++ I++N+GCP  +V     G+ LM N  +    ++ M KAL  P
Sbjct: 105 PALMAEMACRIEE-DFDGIDVNMGCPVPKVVRNQEGSALMTNLPLAEQVLSTMAKALKKP 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK RIG  D   A+ +    K  + SGV  + IH R         ++       ++  
Sbjct: 164 LTVKFRIGFTDD--AINVVEFAKMAEASGVASVTIHGRT--------REQYYRGKANWQY 213

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E  KE   + +  NG +     AL +L    VDGV + R    N  ++       S  
Sbjct: 214 IKE-AKEAVKIPVFGNGDIFQEEDALAMLLSTGVDGVALARGIQGNPFLIRACVSLLSEG 272

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                   +   +   R +   M +    HL     L ++ +H+     G  N+ R R  
Sbjct: 273 KKLPPVSLSERKEMMLRHLKL-MVEIKGEHLA----LLEMRKHLSWYMEGLENAARWRQR 327

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +  E          +E  F ++ E
Sbjct: 328 VNTEND--------LEKVFQMVRE 343


>gi|288803773|ref|ZP_06409201.1| TIM-barrel protein, putative, NifR3 family [Prevotella
           melaninogenica D18]
 gi|288333760|gb|EFC72207.1| TIM-barrel protein, putative, NifR3 family [Prevotella
           melaninogenica D18]
          Length = 319

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 142/328 (43%), Gaps = 33/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++YTE + ADA++R  K  +  L     E+P+ +QI G D
Sbjct: 18  MEDVTDIGFRKMCKRF-GAAMVYTEFVSADAVIRSIKSTLSKLVIDDSERPVGIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAAKIVE    + I++N GCP  +V     G+ ++ N  ++ D    + KA++ P
Sbjct: 77  VASMVEAAKIVEQVKPDVIDINFGCPVKKVANKGAGSGMLKNIPLLLDITREVVKAVNTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + + +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDND--NLIITDLAEQLQDCGIQALTIHGRT--------RAQMYTGEADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +  + +A +      VD VMIGRA +    +          
Sbjct: 187 IGEVKNNPRIHIPIIGNGDVTSIEEAHEKFDHYGVDAVMIGRATFGCPWLFNQ------- 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
                   + ++  D    I   M       +     +    RH+    +F G P+ ++ 
Sbjct: 240 -------GEKQLTIDDKIDILEEMLRINVDRIDEHRGILHTRRHLAASPIFKGIPDFKKT 292

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R I  +          I+E     + E 
Sbjct: 293 R-IAMLRTTKMDELMAILEDCREKLREE 319


>gi|300790789|ref|YP_003771080.1| dihydrouridine synthase [Amycolatopsis mediterranei U32]
 gi|299800303|gb|ADJ50678.1| putative dihydrouridine synthase [Amycolatopsis mediterranei U32]
          Length = 379

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 122/323 (37%), Gaps = 25/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  +R          +   EMI A A++       +++ F   EKP ++Q+ G D
Sbjct: 29  MAGITNVAFRQLCAEY-GAGIYVCEMITARAVVERHPGTMHMMTFGADEKPRSMQLYGVD 87

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALS 116
              + EA +I+   G  + ++ N GCP A+V     GA L     +    +   +  A  
Sbjct: 88  PKTIAEAVRIIVGEGLADHVDSNFGCPVAKVTRKGGGAALPFKRKLFEAIVRESVKAAGD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            P TVK RIG+DD        +  +  +  G   + +HAR A          R     D+
Sbjct: 148 TPFTVKFRIGIDDDHR--TFLDAGRIAEAEGAAAVSLHARTA--------AQRYSGQADW 197

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E+K+    + +  NG +     AL+++     DGV++GR       +   ++  F+
Sbjct: 198 TKIAELKEAVTSIPVLGNGDIFSAEDALRMVDETGCDGVVVGRGCLGRPWLFGELEAAFA 257

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                + P    V       +    T+    H      ++ I +HM     GFP     R
Sbjct: 258 GRPLPTPPNLGEVA-----AVLRRHTELLIEHDGHDKAMRDIRKHMAWYLMGFPVGSELR 312

Query: 295 H---ILTVEAGASTATHHIIETA 314
               +L+           +   A
Sbjct: 313 RGFAMLSSMDQLDDLIAQLDHDA 335


>gi|255553550|ref|XP_002517816.1| tRNA-dihydrouridine synthase A, putative [Ricinus communis]
 gi|223543088|gb|EEF44623.1| tRNA-dihydrouridine synthase A, putative [Ricinus communis]
          Length = 375

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 105/328 (32%), Positives = 171/328 (52%), Gaps = 11/328 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ ++ LYTEM+ A+ I+   G+    L FS Q+ P+ LQIGG++
Sbjct: 16  MMDWTDHHYRTLARLISKHSWLYTEMLAAETIVYQQGNLDRFLAFSPQQHPIVLQIGGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   +GY+EIN N GCPS RV     FG  LML+P  VG+ ++ +     +
Sbjct: 76  LDNLAKATELATAYGYDEINFNCGCPSPRVAGHGCFGVRLMLDPKFVGEAMSVIAANTDV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVD+      L + +  +   S      IH+RKA+L G+SP +NRKIP L Y
Sbjct: 136 PVSVKCRIGVDNHDSYNELCDFIYKVSSLSPTKHFIIHSRKALLNGISPAENRKIPPLKY 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ PDL   +NGG+  +    L +     GVM+GRAA+ N   +L  VD    
Sbjct: 196 EYYFALLRDFPDLRFTINGGINCIDEVNLALREGAHGVMVGRAAFNNPWTVLGHVDSAIY 255

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P      +    +  A        + ++   ++ + + ++GLF+  P +   +
Sbjct: 256 G-----APESGLTRRQVLEQYQAYADAILGTYGNNRPNVRDVVKPLLGLFYSEPGNGLWK 310

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
                   + T      E     + +++
Sbjct: 311 RRADAAFQSCTTIKSFFEETLVAIPDTV 338


>gi|330887987|gb|EGH20648.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. mori str.
           301020]
          Length = 337

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 132/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  +  H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAGHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 EKLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|110807120|ref|YP_690640.1| tRNA-dihydrouridine synthase B [Shigella flexneri 5 str. 8401]
 gi|38604763|sp|Q83PZ5|DUSB_SHIFL RecName: Full=tRNA-dihydrouridine synthase B
 gi|110616668|gb|ABF05335.1| putative dehydrogenase [Shigella flexneri 5 str. 8401]
 gi|281602637|gb|ADA75621.1| tRNA-dihydrouridine synthase B [Shigella flexneri 2002017]
 gi|313648498|gb|EFS12940.1| TIM-barrel , nifR3 family protein [Shigella flexneri 2a str. 2457T]
 gi|332752422|gb|EGJ82812.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri
           4343-70]
 gi|332752463|gb|EGJ82852.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-671]
 gi|332754236|gb|EGJ84602.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri
           2747-71]
 gi|332765259|gb|EGJ95486.1| tRNA dihydrouridine synthase [Shigella flexneri 2930-71]
 gi|333000253|gb|EGK19836.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-218]
 gi|333014546|gb|EGK33893.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-304]
          Length = 321

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+ 
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSA 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|212711052|ref|ZP_03319180.1| hypothetical protein PROVALCAL_02121 [Providencia alcalifaciens DSM
           30120]
 gi|212686220|gb|EEB45748.1| hypothetical protein PROVALCAL_02121 [Providencia alcalifaciens DSM
           30120]
          Length = 325

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 62/320 (19%), Positives = 120/320 (37%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     +    +  +EM+ ++  +    K+ L      +    ++QI G D
Sbjct: 17  MAGITDKPFRSLCYAM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHRDELGVRSVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P+IV   +  +  A+ +P
Sbjct: 76  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPEIVKSILETVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEERN--CIEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +M+GRAA     +   +  Y    
Sbjct: 186 IRAVKQ-TVSIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       +      Y       G   +   +H+           + R  
Sbjct: 245 EILPPMPMAEVKSIMLGHVRELHDFY-----GQGKGARIARKHVSWYLQEHAPDDQFRRS 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS     ++E  F 
Sbjct: 300 FNAIEDASE-QLEVLEAFFE 318


>gi|261378953|ref|ZP_05983526.1| tRNA-dihydrouridine synthase B [Neisseria cinerea ATCC 14685]
 gi|269144654|gb|EEZ71072.1| tRNA-dihydrouridine synthase B [Neisseria cinerea ATCC 14685]
          Length = 336

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 130/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +    A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGVAAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 136 VTLKTRLGWHDD--YKNLPAVARIAEDCGIASLAVHGRT--------RTQMYKGEAAYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+    R  
Sbjct: 245 VLPPALSLAECTATILNHIRAIHAFY-----GETAGVRIARKHIGWYIDEMPDGEHTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + ++      + E 
Sbjct: 300 INYL-DSAAAQYDMLAGYLERLAEK 323


>gi|294629227|ref|ZP_06707787.1| tRNA-dihydrouridine synthase [Streptomyces sp. e14]
 gi|292832560|gb|EFF90909.1| tRNA-dihydrouridine synthase [Streptomyces sp. e14]
          Length = 416

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 64/321 (19%), Positives = 128/321 (39%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E+P ++Q+ G 
Sbjct: 60  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIRFDATEQPRSIQLYGV 119

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D + + +A +++ +    + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 120 DPATVGKAVRMIAEEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAIVREAVSGAG 179

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV+ I +H R                  D
Sbjct: 180 DLPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVSAIALHGRTT--------AQHYGGTAD 229

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 230 WDAIARLKEHVPEIPVLGNGDIWSAGDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 289

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                       R   D   + +  + ++          +    +H+     GF      
Sbjct: 290 EGRTDDFVRPTLREVADVMVRHATLLGEWIG---DESRGVIDFRKHVAWYLKGFAVGSEM 346

Query: 294 RHILTVEAGAST--ATHHIIE 312
           R  L + A      A    ++
Sbjct: 347 RKRLAITASLDELRAGLDELD 367


>gi|330960008|gb|EGH60268.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 337

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 69/298 (23%), Positives = 132/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A ++L     DG++IGRAA     +   ++ Y    
Sbjct: 189 IATIKQAV-SIPVFANGDINSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T  +   + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 ETLPALQLSEVERILLEHLAALHVFY-----GDVMGVRIARKHVGWYLATLPGAREFR 300


>gi|118497579|ref|YP_898629.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           novicida U112]
 gi|195536275|ref|ZP_03079282.1| putative TIM-barrel protein, nifR3 family [Francisella tularensis
           subsp. novicida FTE]
 gi|118423485|gb|ABK89875.1| tRNA-dihydrouridine synthase [Francisella novicida U112]
 gi|194372752|gb|EDX27463.1| putative TIM-barrel protein, nifR3 family [Francisella tularensis
           subsp. novicida FTE]
          Length = 328

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 142/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG DD+   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDDK--NINAIEVAKACEDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D+ +  NG +     A  ++    VD VM+GRA+  N  +   + +Y +
Sbjct: 188 DIIRDVRKAV-DIVVIGNGDVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAKYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
             L            I+E   + + +
Sbjct: 302 MKLNQLEH-EQEIFKILEEYKSFLKK 326


>gi|308176716|ref|YP_003916122.1| tRNA-dihydrouridine synthase [Arthrobacter arilaitensis Re117]
 gi|307744179|emb|CBT75151.1| putative tRNA-dihydrouridine synthase [Arthrobacter arilaitensis
           Re117]
          Length = 394

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 69/326 (21%), Positives = 126/326 (38%), Gaps = 28/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+R +R   R      L  TEM+ A A++  + +++  +     E+  ++QI G D
Sbjct: 35  MAGVTNRAFRRLCREYGG-GLYVTEMVTARALVERNPESLRIISHDPDEEIRSIQIYGVD 93

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CKA 114
              +  A ++V D    + ++LN GCP  +V     G+ L    D+    I A       
Sbjct: 94  PGTVRAAVRMVVDENLADHVDLNFGCPVPKVTRKGGGSALPWKSDLYTSIIEAATSEAAK 153

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+TVK RIG+D     +      K  +  G   + +HAR A              + 
Sbjct: 154 GDIPLTVKMRIGIDKD--HLTYLESAKIARDHGAAAVTLHARTA--------GQYYAGHS 203

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +++   D+ +  NG +     A++++      GVM+GR       +   +   
Sbjct: 204 DWDAITTLREAMDDMPVLGNGDIFSAEDAIEMVEQTGAAGVMVGRGCQGRPWIFGDLQAA 263

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P   +V    +R        +       G  ++ I +H+   F G+P    
Sbjct: 264 FEGREDRFRPGVRKVADTVYRHGELLTEFF----EDEGKGMRDIRKHIAWYFKGYPVGGE 319

Query: 293 CRHILTVEAGASTATHHIIETAFNLM 318
            R  L   A   +    ++    + +
Sbjct: 320 IRSQL---AQVPS--LAVLRELLDQL 340


>gi|261344930|ref|ZP_05972574.1| tRNA-dihydrouridine synthase B [Providencia rustigianii DSM 4541]
 gi|282567071|gb|EFB72606.1| tRNA-dihydrouridine synthase B [Providencia rustigianii DSM 4541]
          Length = 331

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 63/320 (19%), Positives = 121/320 (37%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R     +    +  +EM+ ++  +    K+ L      +    ++QI G D
Sbjct: 23  MAGITDKPFRTLCYAM-GAGMTVSEMLSSNPQVWKTDKSKLRMVHRDELGVRSVQIAGND 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  + G   I++N+GCP+ +V+    G+ L+  P+IV   +  + K++ +P
Sbjct: 82  PDEMAAAAQINVESGAQIIDINMGCPAKKVNRKLAGSALLRYPEIVKSILETVVKSVDVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + K  +  G+  + IH R         +        +YD 
Sbjct: 142 VTLKIRTGWSPEERN--CIEIAKLAEDCGIQALTIHGRT--------RACLFNGEAEYDN 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +M+GRAA     +   +  Y    
Sbjct: 192 IRAVKQ-TVSIPVIANGDITDPLKARAVLDYTGADALMVGRAAQGRPWIFREIQHYLDTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       +      Y       G   +   +H+           + R  
Sbjct: 251 EILPPMPMAEVKSTMLGHVRELHDFY-----GQGKGARIARKHVSWYLQEHAPDDQFRRS 305

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS     ++E  F 
Sbjct: 306 FNAIEDASE-QLEVLEAFFE 324


>gi|37527935|ref|NP_931280.1| tRNA-dihydrouridine synthase B [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787371|emb|CAE16460.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 321

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 126/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G+D
Sbjct: 17  MAGITDRPFRSLCYKM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHSDEPGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAKI    G   I++N+GCP+ +V+    G+ L+  P++V   ++A+  A+ +P
Sbjct: 76  PDEMAAAAKINVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELVEKILSAVVNAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWSPEERN--CVKIAQLAEHCGIQALAIHGRT--------RSCLFNGEAEYDN 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y +  
Sbjct: 186 IRTVKQ-TVAIPVIANGDITDPLKARAVLEYTGADALMIGRAAQGRPWIFREIQHYLATG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S      V       I      Y       G ++    +H+           + R  
Sbjct: 245 ELLSPMPIGEVQHLMNEHIQELHDFYGP---SKGARI--ARKHVSWYLREHAPDDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS     ++   F 
Sbjct: 300 FNTIEDASE-QLEVLGAYFE 318


>gi|229074137|ref|ZP_04207184.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-18]
 gi|229100873|ref|ZP_04231680.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-28]
 gi|228682551|gb|EEL36621.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-28]
 gi|228709031|gb|EEL61157.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-18]
          Length = 339

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDKYTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 307

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 308 GINTCNTRQD 317


>gi|73666942|ref|YP_302958.1| dihydrouridine synthase TIM-barrel protein nifR3 [Ehrlichia canis
           str. Jake]
 gi|72394083|gb|AAZ68360.1| tRNA-U20-dihydrouridine synthase [Ehrlichia canis str. Jake]
          Length = 317

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 74/296 (25%), Positives = 124/296 (41%), Gaps = 20/296 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + +    LL +EMI + A++    K  L  S  +   A+Q+ G D +
Sbjct: 17  MSGVTDFPFRCLVKNI-GAGLLVSEMIASRAMI-IQTKQSLQKSQIQANTAVQLAGCDPA 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V     G+ LM +       + ++ KA+ IPVT
Sbjct: 75  IMAEAAKLNEDMGAKIIDINFGCPVKKVVNSYAGSALMKDEITAAKILESVVKAVKIPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G D+    +    L K  ++SG+  I IH R         +        D+  + 
Sbjct: 135 LKMRTGWDN--NNLNSPKLAKIAEESGIKMITIHGRT--------RTQMFNGKADWKFIS 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            IKK    + +  NG ++++      L     DGVMIGR AY     +     +  + + 
Sbjct: 185 NIKK-CVKIPVIANGDIKNLDDIKTSLEESQADGVMIGRGAYGKPWFINQALHFIKSGII 243

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              P  +        +I  +  D+   +      ++   +H+        NS   R
Sbjct: 244 LPEPSPSE-----KLQIITNHYDHMIEYYGKDIGVKISKKHISWYSASLDNSAEFR 294


>gi|182438840|ref|YP_001826559.1| putative dihydrouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178467356|dbj|BAG21876.1| putative dihydrouridine synthase [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 382

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 117/306 (38%), Gaps = 21/306 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 86

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSNAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HLTFLDAGRIAVEEGVTAVALHGRTT--------AQHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +    
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWCADDALRMMRETGCDGVVVGRGCLGRPWIFADLVNAM 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P    V     R  +                +    +H+     GF      
Sbjct: 257 EGREARHAPALREVADVMVRHATL----LGEWIGDEARGVIDFRKHVAWYLKGFAVGSEM 312

Query: 294 RHILTV 299
           R  L V
Sbjct: 313 RKKLAV 318


>gi|307730942|ref|YP_003908166.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1003]
 gi|307585477|gb|ADN58875.1| TIM-barrel protein, nifR3 family [Burkholderia sp. CCGE1003]
          Length = 358

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 129/308 (41%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V   + A+  A+   
Sbjct: 77  PAMMAEAARYNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGVG 136

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PVT+K R G + +       N+ +  + +G++ + +H R         + +     
Sbjct: 137 PDAVPVTLKIRTGWNRENRNA--LNVARLAEAAGISMLTVHGRT--------RADLYHGE 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A  +L     D +MIGRAA     +   ++ 
Sbjct: 187 AEYETIAAVK-AAVRIPVVANGDITSPEKARHVLAVTGADAIMIGRAAQGRPWLFREIEH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +         P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQTGELLPPPRIDEIQQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 VFRHRMNT 308


>gi|148549897|ref|YP_001269999.1| nifR3 family TIM-barrel protein [Pseudomonas putida F1]
 gi|148513955|gb|ABQ80815.1| putative TIM-barrel protein, nifR3 family [Pseudomonas putida F1]
 gi|313500799|gb|ADR62165.1| TRNA-dihydrouridine synthase B [Pseudomonas putida BIRD-1]
          Length = 337

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 131/298 (43%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAAKANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVSAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRANKNG--LNVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L    VDG++IGRAA     +   ++ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDITSPEKARAVLETTGVDGLLIGRAAQGRPWIFREIEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P  +  R
Sbjct: 248 EHLPAPQLDEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATRPGGKEFR 300


>gi|88855014|ref|ZP_01129679.1| transcriptional regulator, NifR3/Smm1 family protein [marine
           actinobacterium PHSC20C1]
 gi|88815542|gb|EAR25399.1| transcriptional regulator, NifR3/Smm1 family protein [marine
           actinobacterium PHSC20C1]
          Length = 388

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 116/300 (38%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +++  +     E   ++Q+ G D
Sbjct: 31  MAGITNTAFRRLCREY-GAGLYVSEMITSRALVERTPESMRLITHHESETTRSIQLYGVD 89

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + EA   +V +   + I+LN GCP  +V     GA L    D+  D +  A+  A  
Sbjct: 90  PKTVKEAVTMLVAENRADHIDLNFGCPVPKVTRKGGGAALPWKIDLFRDIVEGAVKAAGD 149

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T+K R G+D     +      +    +GV  I +HAR A                D+
Sbjct: 150 VPLTIKMRKGIDSD--HLTYLEAARVGAGAGVASIALHARTA--------AEFYSGTADW 199

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K    D  I  NG +   + AL+++     DGV++GR       +   +   F 
Sbjct: 200 SAIEKLKNTITDTPILGNGDIWSAADALRMVDETGCDGVVVGRGCLGRPWLFGDLAAAFR 259

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                + P    V   F R     +  +           + I +H+   F G+      R
Sbjct: 260 GETLKAEPSLGEVAAAFKRHAELLVEFFGEE----DRACRDIRKHVAWYFKGYAVGGELR 315


>gi|221054640|ref|XP_002258459.1| dihydrouridine synthase [Plasmodium knowlesi strain H]
 gi|193808528|emb|CAQ39231.1| dihydrouridine synthase, putative [Plasmodium knowlesi strain H]
          Length = 508

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 109/323 (33%), Positives = 164/323 (50%), Gaps = 32/323 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M++ T+RH+R F R +T  A L+TEMIV + +L          GF++ E P+  Q+GG+D
Sbjct: 141 MINVTNRHFRAFVRTITRRAQLWTEMIVDNTLLYNLNNLEEYLGFNSNEHPVVCQLGGSD 200

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA +VE  GY+EINLNVGCPS +V     FGA LM  P+ V + +  + + + I
Sbjct: 201 PTSLAEAAVLVEQAGYDEINLNVGCPSTKVANKGAFGAYLMKKPEHVRNIVYEIKRKVQI 260

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R GVDD      LR+ ++ +   G     +HARKA LKGL PK NR +P L Y 
Sbjct: 261 PVSVKIRTGVDDCDSFPFLRSFIECVSSVGCTHFIVHARKAWLKGLDPKQNRSVPPLQYS 320

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS-------VD-----------------GV 213
            VY + +  P L   LNGG++ + +A+ +L          D                 GV
Sbjct: 321 KVYTLCQLYPHLKFTLNGGIKTIEEAVALLNGYLPREDKCDGEKTYVQVQNYHVNPLNGV 380

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GRA  +N+ +L+  D+   N     +    R   D ++      +      L S    
Sbjct: 381 MLGRACMENTTVLSQTDQLVYNEKPPHTAFSRRTVLDAYKSYLEENSS-----LCSLSSA 435

Query: 274 QQITRHMIGLFHGFPNSRRCRHI 296
            ++ + ++G+  G P  R  R+ 
Sbjct: 436 FELLKPILGILKGMPGHRIFRNK 458


>gi|330989163|gb|EGH87266.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 337

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 134/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANIELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +    + +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGDAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P  + V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 EKLPAPQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVSWYLATLPGAREFRAH 302


>gi|326384894|ref|ZP_08206569.1| TIM-barrel protein, nifR3 family [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326196413|gb|EGD53612.1| TIM-barrel protein, nifR3 family [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 390

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 126/313 (40%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F   E P ++
Sbjct: 30  MAGVTNVAFRVLCRELELARTGTVSGLYVCEMVTARALVERHPVTMHMTAFDPSETPRSM 89

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V     G+ +     +  + +AA 
Sbjct: 90  QLYTVDPEYTYQAAKMIVDENLADHIDMNFGCPVPKVTRKGGGSAIPYKRRLFRNIVAAA 149

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +     G   + +HAR A          
Sbjct: 150 VRATEGTDIPVTVKFRIGIDDDHH--THLDAGRIAAAEGAQAVALHARTA--------SQ 199

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R      +D +  +K+   D+ +  NG + +   A++++     DGV+IGR       + 
Sbjct: 200 RYSGTAAWDEIARLKEHVTDVPVLGNGDIFEAEDAVRMMAQTGCDGVVIGRGCLGRPWLF 259

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +          + P    V +   R       +  A H   G  +++I +H+     G
Sbjct: 260 AELSARLRGVEAPTPPNLGEVAEIMIRH-----GELLAAHHGEGKGMREIRKHVAWYLRG 314

Query: 287 FPNSRRCRHILTV 299
           FP     R  L++
Sbjct: 315 FPAGSDLRSSLSL 327


>gi|254374394|ref|ZP_04989876.1| hypothetical protein FTDG_00561 [Francisella novicida GA99-3548]
 gi|151572114|gb|EDN37768.1| hypothetical protein FTDG_00561 [Francisella novicida GA99-3548]
          Length = 324

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 141/324 (43%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG DD+   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDDK--NINAIEVAKACEDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D+ +  NG +     A  ++    VD VM+GRA+  N  +   + +Y +
Sbjct: 188 DIIRDVRKAV-DIVVIGNGDVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAKYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
             L            I+E   N +
Sbjct: 302 MKLNQLEH-EQEIFAILEQYKNTL 324


>gi|237798366|ref|ZP_04586827.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331021218|gb|EGI01275.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 337

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/298 (23%), Positives = 132/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLANAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPEKARRVLQATGADGLLIGRAAQGRPWIFREIEHYLLTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T  +   + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 ETLPALQLSEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATLPGAREFR 300


>gi|289705787|ref|ZP_06502170.1| TIM-barrel protein, nifR3 family [Micrococcus luteus SK58]
 gi|289557503|gb|EFD50811.1| TIM-barrel protein, nifR3 family [Micrococcus luteus SK58]
          Length = 436

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 64/307 (20%), Positives = 119/307 (38%), Gaps = 22/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EM+ A A++    +++  +     E P ++Q+   D
Sbjct: 76  MAGITNTAFRRLCREYGG-GLYVNEMVTARALVERKPESMRIIQHDPDEVPRSVQLYSVD 134

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
                 A ++ VE+   + I++N GCP  +V     G+ L    ++    + A       
Sbjct: 135 PVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVTEAAK 194

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVTVK R G+D+    +   +  ++ +  GV  + +H R                  
Sbjct: 195 RDIPVTVKMRRGIDED--HLTFLDAGRTARDLGVAAVALHGRTT--------RQFYSGTA 244

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D +  +++  PD+ +  NG +     A+ ++    VDGV+IGR       +   +   
Sbjct: 245 VWDDIARLREALPDIPVLGNGDIWSAEDAIAMVEQTGVDGVVIGRGCQGRPWLFGDLQAA 304

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P    V    +R     +  +    L +   L+ I +H+   F G+P    
Sbjct: 305 FEGRQDRFQPTLGMVADTLYRHAELLVGTFGGDELKA---LRDIRKHVAWYFKGYPVGSE 361

Query: 293 CRHILTV 299
            R  L+ 
Sbjct: 362 IRTALST 368


>gi|157413462|ref|YP_001484328.1| dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9215]
 gi|157388037|gb|ABV50742.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Prochlorococcus
           marinus str. MIT 9215]
          Length = 341

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 134/315 (42%), Gaps = 21/315 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADIS 60
              TD  +R   R    N+LL+TEMI A ++ +G   + I     +E P+ +QI      
Sbjct: 26  AGVTDDIFRRLVRKWAPNSLLFTEMINATSLKKGFGTQKINQIDLEEGPVGIQIFDYRPH 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK  ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVT
Sbjct: 86  AVSEAAKQAEDSGAFLIDINMGCPVKKIAKKGGGSALIKDRKLAMELVKNVVKAVKIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D +     + + +  ++ +G   I IH R    +G S K        D++++ 
Sbjct: 146 VKTRLGWDSKE--ENIEDFLFKLQDAGATMITIHGRTRK-QGFSGKS-------DWEMIG 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K    ++ +  NG +++   AL  L   + DGVMIGR    +   +  +D   S    
Sbjct: 196 RLK-SLLEIPVIANGDIKNPDDALNCLKKTNADGVMIGRGILGSPWKIGEIDYAISENKN 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +           L    +H+      F  +   R+ L 
Sbjct: 255 FKKPNTEEKLYLIIEHLDELIKEKG------DHGLLLARKHISWTCKDFKGASNLRNKL- 307

Query: 299 VEAGASTATHHIIET 313
           V A        +I+ 
Sbjct: 308 VRAVDKNEVKSLIKK 322


>gi|313894860|ref|ZP_07828420.1| TIM-barrel protein, nifR3 family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312976541|gb|EFR41996.1| TIM-barrel protein, nifR3 family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 323

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 133/319 (41%), Gaps = 23/319 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++    +L     E+PLA+QI    
Sbjct: 20  MAGVTDTAYRIIASEM-GCPLAFAEMVSSQGIHYRNEHTLLMLRSEPAERPLAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  + ++ N+GCP+ +V +   G+ LM +P    + + A+ +A+ +
Sbjct: 79  AAMAAEAAAYIEELGTADILDFNMGCPAPKVVKNGEGSALMRDPKKAEEILKAIRRAVKL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R+G DD         + +  + +GV+ + +H R         ++     + DY+
Sbjct: 139 PFTVKMRLGWDDTSRNAV--EIARIAEAAGVDAVAVHGRT--------REQFYSGSADYE 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K+    + + ++G +   +   + L     DGVMIGR A  N  +   +  +   
Sbjct: 189 AIAEVKRAVG-IPVIVSGDIRRPADLRRALAITGADGVMIGRGAQGNPWVFPQLIHWLRT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          R +     D    +      ++++ +H      G P S + R 
Sbjct: 248 GEELPPPTPAERAAVVLRHL-----DLLISYKGDYIGIREMRKHAAWYTRGLPGSAQLRE 302

Query: 296 ILTVEAGASTATHHIIETA 314
                +    A   I+  A
Sbjct: 303 RFN-RSDTRDAFVEILHGA 320


>gi|326779495|ref|ZP_08238760.1| TIM-barrel protein, nifR3 family [Streptomyces cf. griseus
           XylebKG-1]
 gi|326659828|gb|EGE44674.1| TIM-barrel protein, nifR3 family [Streptomyces cf. griseus
           XylebKG-1]
          Length = 382

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 117/306 (38%), Gaps = 21/306 (6%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 27  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 86

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 87  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRPLLRAILREAVSNAG 146

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  + +H R                  D
Sbjct: 147 DLPVTIKMRKGIDDD--HLTFLDAGRIAVEEGVTAVALHGRTT--------AQHYGGTAD 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +    
Sbjct: 197 WDAIARLKEHVPEIPVLGNGDIWCADDALRMMRETGCDGVVVGRGCLGRPWIFADLVNTM 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P    V     R  +                +    +H+     GF      
Sbjct: 257 EGREARHAPALREVADVMVRHATL----LGEWIGDEARGVIDFRKHVAWYLKGFAVGSEM 312

Query: 294 RHILTV 299
           R  L V
Sbjct: 313 RKKLAV 318


>gi|221065205|ref|ZP_03541310.1| TIM-barrel protein, nifR3 family [Comamonas testosteroni KF-1]
 gi|220710228|gb|EED65596.1| TIM-barrel protein, nifR3 family [Comamonas testosteroni KF-1]
          Length = 354

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 62/306 (20%), Positives = 121/306 (39%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G +
Sbjct: 20  MAGVTDRPFRQLCKAL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA    + G   I++N+GCP+ +V     G+ LM N  +  +   A+ +A    
Sbjct: 79  ALMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMQNEPLAVEIAQAVVEAARPY 138

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G  D      L  L +  ++ G+  + +H R         ++       +
Sbjct: 139 NVPVTLKMRTGWCDTHKNAVL--LARQFEEVGIQMLTVHGRT--------REQGYKGFAE 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K+    + +  NG +    +A  +L     D +M+GRAA     +   +  + 
Sbjct: 189 YDTIAAVKQAV-RVPVVANGDINSPEKARDVLAYTGADAIMVGRAAQGRPWIFREIAHFL 247

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     ++P+   + +     +    + Y       G  ++   +H+       P     
Sbjct: 248 ATGEHMAAPLVAELRRLLLEHLQDHYSLY-----GEGVGVRSARKHIAWYLRALPGGEEF 302

Query: 294 RHILTV 299
           R  +  
Sbjct: 303 RKHINT 308


>gi|218768425|ref|YP_002342937.1| hypothetical protein NMA1633 [Neisseria meningitidis Z2491]
 gi|121052433|emb|CAM08769.1| conserved hypothetical protein [Neisseria meningitidis Z2491]
          Length = 336

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 131/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         YD+
Sbjct: 136 VTLKTRLGWHDDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEAAYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECTATILNHIRAMHAFY-----GDTAGVRIARKHIGWYIDEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + +       + E 
Sbjct: 300 IN-RLDSAAAQYDMFAGYLERLAEK 323


>gi|26991500|ref|NP_746925.1| NifR3 family TIM-barrel protein [Pseudomonas putida KT2440]
 gi|38604777|sp|Q88DK5|DUSB_PSEPK RecName: Full=tRNA-dihydrouridine synthase B
 gi|24986580|gb|AAN70389.1|AE016680_9 TIM-barrel protein, putative, NifR3 family [Pseudomonas putida
           KT2440]
          Length = 337

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 131/298 (43%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAAKANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVSAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRANKNG--LNVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L    VDG++IGRAA     +   ++ Y    
Sbjct: 189 IGAIKQAV-SIPVFANGDITSPEKARAVLETTGVDGLLIGRAAQGRPWIFREIEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P  +  R
Sbjct: 248 EHLPAPQLDEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATRPGGKEFR 300


>gi|326334004|ref|ZP_08200233.1| putative tRNA-dihydrouridine synthase [Nocardioidaceae bacterium
           Broad-1]
 gi|325948153|gb|EGD40264.1| putative tRNA-dihydrouridine synthase [Nocardioidaceae bacterium
           Broad-1]
          Length = 378

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/305 (22%), Positives = 125/305 (40%), Gaps = 25/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD+  K++L F   E   ++Q+ G D
Sbjct: 23  MAGVTNAAFRRLCAE-QGAGLYVCEMITSRGLVEGDQHTKDMLVFDEAETVRSVQLYGTD 81

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              + +A +I+  D+G   ++LN GCP  +V     G  L     ++G+ +    +A   
Sbjct: 82  PVYVGKATEILCADYGVAHVDLNFGCPVPKVTRKGGGGALPYKRGLLGEILEHAVRAAEP 141

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +   +  +  ++SG   I +H R                  
Sbjct: 142 YDVPVTMKTRKGIDDD--HLTYMDAGRIAQESGAAAIALHGRT--------VAQAYSGTA 191

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D + E+K  + D+ +  NG + + + A++++    VDGV+IGR       +   +   
Sbjct: 192 DWDAIAELK-ASVDIPVLGNGDIWEAADAIRMVEETGVDGVVIGRGCLGRPWLFRDLVAA 250

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V       I     +    H+      ++I +H+     GF     
Sbjct: 251 FAGETVNVLPNLGEVT-----DIMRRHAELLCEHMGEERGCKEIRKHIAWYLKGFGAGGE 305

Query: 293 CRHIL 297
            R  L
Sbjct: 306 LRRTL 310


>gi|229094797|ref|ZP_04225803.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-29]
 gi|228688665|gb|EEL42537.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-29]
          Length = 339

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 138/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDKYTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++ +G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDEE--HIFAIENARAVECAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 307

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 308 GINTCNTRQD 317


>gi|313667869|ref|YP_004048153.1| tRNA-dihydrouridine synthase [Neisseria lactamica ST-640]
 gi|313005331|emb|CBN86764.1| putative tRNA-dihydrouridine synthase [Neisseria lactamica 020-06]
          Length = 336

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHKNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIGEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A +  +      +
Sbjct: 300 IN-RLDSAAAQYDTLAGYLERV 320


>gi|229053922|ref|ZP_04195357.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH603]
 gi|228721463|gb|EEL72983.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH603]
          Length = 332

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAVENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVETPQDAKRMLDEVGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 300

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 301 GINTCDTRED 310


>gi|315226975|ref|ZP_07868763.1| tRNA-dihydrouridine synthase B [Parascardovia denticolens DSM
           10105]
 gi|315121107|gb|EFT84239.1| tRNA-dihydrouridine synthase B [Parascardovia denticolens DSM
           10105]
          Length = 386

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 120/302 (39%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A+   + K   +  F+  EK  +LQ+ G +
Sbjct: 24  MAGVTNWPFRLLCEGYGPDGLYVAEMITARALTARNPKAFRLCRFAPSEKFRSLQLYGVN 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
              + EAAK+V D    + ++LN GCP  +V     G+ L    D++ D    + A+C+ 
Sbjct: 84  PLVVEEAAKMVVDGDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQDLIHRVVAVCQP 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + IPVT K R+GVDD+     +    K I+  G   + +HAR                + 
Sbjct: 144 VGIPVTAKIRVGVDDE--HETMIEAAKIIEGEGCAFVTLHARTT--------AQYYGGHS 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + ++K E   + +  NG +     A+ +      DGV IGR       +   +   
Sbjct: 194 DWSRIAQLK-EAVSIPVIGNGDIWTAEDAMAMARQTGCDGVAIGRGCQGRPWLFGDIRNA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P   +V +   +        Y          +  + +H+     GFP   +
Sbjct: 253 FEGRNERFDPSLAQVGQTIVKHAHFLTEFYEG---DENMAVHDLRKHIAWYLKGFPVGGK 309

Query: 293 CR 294
            R
Sbjct: 310 TR 311


>gi|284928866|ref|YP_003421388.1| hypothetical protein UCYN_02850 [cyanobacterium UCYN-A]
 gi|284809325|gb|ADB95030.1| putative TIM-barrel protein, nifR3 family [cyanobacterium UCYN-A]
          Length = 322

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 130/298 (43%), Gaps = 20/298 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TDR +R   R  + N+++YTEMI A  +    K   L    ++KP+ +QI  +    
Sbjct: 22  AGVTDRIFRKLVRRYSPNSMIYTEMINATELCHLKKVQQL-VDIEQKPIGVQIFDSRYDF 80

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +VEAAK +E  G   I++N+GCP  ++ +   G+ L+  P +    I  + + + IP+TV
Sbjct: 81  IVEAAKKIESQGAQIIDINMGCPVNKITKKGGGSSLLKQPKVAQKIIYEITRIVKIPITV 140

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG +D    + + +  K ++ +G   + IHAR         +D        +  V +
Sbjct: 141 KTRIGWND--SGIDILDFAKMMEDAGAAMLTIHART--------RDQGYNGTSHWKWVKK 190

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           IK EN  + I  NG +  +  A+K L   + DGVM  R       ++  +D +F      
Sbjct: 191 IK-ENLLIPIIANGNIFSIEDAVKCLEITNADGVMCSRGTLGYPFLVGEIDYFFQTGYCS 249

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                 +  K     +         + ++ G       +H+     GFP +   R  +
Sbjct: 250 QIITPYQRLKCAKEHLKELWKYKGNQGIYQG------RKHLRWYCQGFPGASELRKKI 301


>gi|238022274|ref|ZP_04602700.1| hypothetical protein GCWU000324_02181 [Kingella oralis ATCC 51147]
 gi|237866888|gb|EEP67930.1| hypothetical protein GCWU000324_02181 [Kingella oralis ATCC 51147]
          Length = 333

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/309 (22%), Positives = 127/309 (41%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R         +EM+  +  L+   K       + +   +A+QI G+D
Sbjct: 16  MAGITDLPFRQLTRQF-GAQWAASEMVTVNPDLQHTAKTRHRQNHAGESGVIAVQIAGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++L  AA+     G   I++N+GCP  +V     G+ L+ N  +V   +  + +A+++P
Sbjct: 75  PAQLAAAAQHNVALGAQVIDINMGCPVKKVCNVLAGSALLQNEKLVAQILNTVVRAVNVP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD+   +    + +  + +G+  + IH R         +         Y++
Sbjct: 135 VTLKTRLGWDDEHQNI--PTIAQIAEDAGIAALAIHGRT--------RSQMYRGQAQYEL 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   L I  NG +    +A  +L     D +MIGR A     +   +  Y  + 
Sbjct: 185 IAAVKQQ-SRLPIWANGDITSPQKAAAVLAQTGADAIMIGRGAQGQPWLFADIQHYLQHG 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                           R ++A    Y     ++G ++    +H+       PNS+  R  
Sbjct: 244 TLPPPMPFQAASATILRHLAAMHHFYGD---NAGTRI--ARKHIGWYLARIPNSQTARQH 298

Query: 297 LTVEAGAST 305
           L     AS 
Sbjct: 299 LNQINHASE 307


>gi|41472|emb|CAA44270.1| ORF1 [Escherichia coli]
          Length = 321

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    L  +EM+ ++  +    K+ L     ++P    +QI G+D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  PD+V   +  +   + +P
Sbjct: 76  PKEMADAARINVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNRVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K++   + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQKV-SIPVIANGDITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     +      Y       G ++    +H+         + + R  
Sbjct: 245 ELLPPLPLAEVKRLLCAHVRELDDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS      +E  F 
Sbjct: 300 FNAIEDASE-QLEALEAYFE 318


>gi|145222259|ref|YP_001132937.1| nifR3 family TIM-barrel protein [Mycobacterium gilvum PYR-GCK]
 gi|145214745|gb|ABP44149.1| putative TIM-barrel protein, nifR3 family [Mycobacterium gilvum
           PYR-GCK]
          Length = 455

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 127/309 (41%), Gaps = 29/309 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+ +E P +L
Sbjct: 95  MAGVTNVAFRTLCRELELSRAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSL 154

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK++ D    + I++N GCP  +V     GA L     + G  ++A 
Sbjct: 155 QLYTVDPVNTYAAAKMIVDENLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGQIVSAA 214

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD+       +  +   + G   + +HAR A          
Sbjct: 215 VRATEGTDIPVTVKFRIGIDDEHH--THLDAGRIAAEEGAAAVALHARTA--------AQ 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R   + D+D +  +K    ++ +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 265 RYSGSADWDQIAALKAHVTNVPVLGNGDIFDARDALAMMAATGCDGVVIGRGCLGRPWLF 324

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V      +I     +  A H      ++ I +H+    HG
Sbjct: 325 AELSAAFTGATPATPPTLGEVA-----QIIRRHGELLAAHFGEDKGMRDIRKHVAWYMHG 379

Query: 287 FPNSRRCRH 295
           FP     R 
Sbjct: 380 FPAGADLRR 388


>gi|163938084|ref|YP_001642968.1| nifR3 family TIM-barrel protein [Bacillus weihenstephanensis KBAB4]
 gi|229009585|ref|ZP_04166812.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides DSM 2048]
 gi|229131083|ref|ZP_04259996.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST196]
 gi|229165064|ref|ZP_04292860.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH621]
 gi|163860281|gb|ABY41340.1| putative TIM-barrel protein, nifR3 family [Bacillus
           weihenstephanensis KBAB4]
 gi|228618449|gb|EEK75478.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH621]
 gi|228652420|gb|EEL08344.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST196]
 gi|228751729|gb|EEM01528.1| tRNA-dihydrouridine synthase 1 [Bacillus mycoides DSM 2048]
          Length = 332

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   I +H R  +               D++
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAIAVHGRTRV--------QMYEGKADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 300

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 301 GINTCDTRED 310


>gi|167035862|ref|YP_001671093.1| NifR3 family TIM-barrel protein [Pseudomonas putida GB-1]
 gi|166862350|gb|ABZ00758.1| TIM-barrel protein, nifR3 family [Pseudomonas putida GB-1]
          Length = 337

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 132/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMSLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAAKANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVGAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ K  +++G+  + +H R         + +    + +YD 
Sbjct: 139 VTLKIRTGWDRANKNG--LNVAKIAEQAGIQALAVHGRT--------RADLYTGDAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L    VDG++IGRAA     +   ++ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDITSPEKARAVLDATGVDGLLIGRAAQGRPWIFREIEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P  +  R
Sbjct: 248 EHLPAPQLDEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATRPGGKEFR 300


>gi|225450085|ref|XP_002277955.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 433

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 99/302 (32%), Positives = 158/302 (52%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWT+ HYR  ARL++ +A LYTEMI A+ I+    +    L FS  + P+ LQIGG +
Sbjct: 72  MMDWTNNHYRTLARLISKHAWLYTEMIAAETIVYQEKNLDRFLEFSPDQHPIVLQIGGNN 131

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   + Y+EINLN GCPS +V     FG  LML+P  V + ++ +     +
Sbjct: 132 LDNIAKATELANSYCYDEINLNCGCPSPKVAGHGCFGVRLMLDPKFVAEAMSVIAANSDV 191

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L + +  +  +S      IH+RKA+L G+SP DNRKIP L Y
Sbjct: 192 PVSVKCRIGVDDHDSYNELCDFIYKVSSQSPTRHFIIHSRKALLNGISPADNRKIPPLKY 251

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  + + ++ PDL   +NGG+  + +    L     GVM+GRAAY N    L  VD    
Sbjct: 252 EYYFGLLRDFPDLRFTINGGINCVDEVNAALRQGAHGVMVGRAAYHNPWYTLGHVDSAVY 311

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P+     +    +          ++      ++++ + ++  F+  P +   +
Sbjct: 312 G-----APVSDLSRRQVLEQYQVYGDSVLEKYGPHRPSIREVVKPLLHFFYSEPGNGLWK 366

Query: 295 HI 296
             
Sbjct: 367 RK 368


>gi|297736275|emb|CBI24913.3| unnamed protein product [Vitis vinifera]
          Length = 423

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 99/302 (32%), Positives = 158/302 (52%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWT+ HYR  ARL++ +A LYTEMI A+ I+    +    L FS  + P+ LQIGG +
Sbjct: 62  MMDWTNNHYRTLARLISKHAWLYTEMIAAETIVYQEKNLDRFLEFSPDQHPIVLQIGGNN 121

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   + Y+EINLN GCPS +V     FG  LML+P  V + ++ +     +
Sbjct: 122 LDNIAKATELANSYCYDEINLNCGCPSPKVAGHGCFGVRLMLDPKFVAEAMSVIAANSDV 181

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L + +  +  +S      IH+RKA+L G+SP DNRKIP L Y
Sbjct: 182 PVSVKCRIGVDDHDSYNELCDFIYKVSSQSPTRHFIIHSRKALLNGISPADNRKIPPLKY 241

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  + + ++ PDL   +NGG+  + +    L     GVM+GRAAY N    L  VD    
Sbjct: 242 EYYFGLLRDFPDLRFTINGGINCVDEVNAALRQGAHGVMVGRAAYHNPWYTLGHVDSAVY 301

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P+     +    +          ++      ++++ + ++  F+  P +   +
Sbjct: 302 G-----APVSDLSRRQVLEQYQVYGDSVLEKYGPHRPSIREVVKPLLHFFYSEPGNGLWK 356

Query: 295 HI 296
             
Sbjct: 357 RK 358


>gi|319654916|ref|ZP_08008990.1| YacF protein [Bacillus sp. 2_A_57_CT2]
 gi|317393341|gb|EFV74105.1| YacF protein [Bacillus sp. 2_A_57_CT2]
          Length = 333

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 70/310 (22%), Positives = 134/310 (43%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  ++K +  L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVTKNEKTMNMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+ +   + I++N+GCP  ++ +   GA  +L+PD + + ++ +  A+  
Sbjct: 77  KETLVEAAKFVDKNTNADIIDINMGCPVPKITKCDAGAKWLLDPDKIYEMVSVVTDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+           ++++++G   + +H R  +               ++D
Sbjct: 137 PVTVKMRMGWDEDHIYAVRN--AQAVERAGGKAVALHGRTRV--------QMYEGKANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+   ++ +  NG ++    A ++L     DGVMIGRAA  N  M+    +Y   
Sbjct: 187 IIREVKQSI-NIPLIGNGDVQTPEDAKRMLDETGCDGVMIGRAALGNPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D           ++++ +H      G   + + R+
Sbjct: 246 GELMGEPSIREKI-----DVCILHLDRLISLKGEFIAVREMRKHTAWYLKGIRGNAKVRN 300

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 301 AVNECDTRED 310


>gi|297795405|ref|XP_002865587.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297311422|gb|EFH41846.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 388

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 107/305 (35%), Positives = 156/305 (51%), Gaps = 19/305 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+ WTD HYR  ARL+T +A LYTEM+ A+ I+    +  + L +S  + P+ LQIGG +
Sbjct: 17  MMGWTDNHYRTLARLITKHAWLYTEMLAAETIVYQEDNLDSFLAYSPDQHPIVLQIGGRN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC-LMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   +GY+EIN N GCPS +V         LML+P  VG+ ++ +    + 
Sbjct: 77  LENLAKATRLANAYGYDEINFNCGCPSPKVSGRGCFGALLMLDPKFVGEAMSVIASNTNA 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            VTVKCRIGVDD      L + +  +   S      IH+RKA+L GLSP DNR+IP L Y
Sbjct: 137 AVTVKCRIGVDDHDSYNELCDFIHIVSSLSPTKHFIIHSRKALLSGLSPSDNRRIPPLKY 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  + + ++ PDL   +NGG+  + +A   L     GVM+GRA Y N    L  VD    
Sbjct: 197 EFFFALLRDFPDLKFTINGGINSVVEADAALRSGAHGVMLGRAVYYNPWHTLGHVDTVIY 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFHGFPNS 290
              +              R++      Y    L   GK    L+ I R +I LFH    +
Sbjct: 257 GSPSSG---------ITRRQVLEKYQVYGESVLGKYGKGRPNLRDIVRPLINLFHSESGN 307

Query: 291 RRCRH 295
            + + 
Sbjct: 308 GQWKR 312


>gi|325201880|gb|ADY97334.1| dihydrouridine synthase [Neisseria meningitidis M01-240149]
 gi|325208367|gb|ADZ03819.1| dihydrouridine synthase [Neisseria meningitidis NZ-05/33]
          Length = 336

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNAQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 136 VTLKTRLGWHDDHKN--LPAVARIAEDCGIAALAVHGRT--------RTQMYKGEAAYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             + A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECSAAILNHVRAMHAFY-----GETAGVRIARKHIGWYIDEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERL 320


>gi|325144658|gb|EGC66956.1| dihydrouridine synthase [Neisseria meningitidis M01-240013]
          Length = 336

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 131/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECAAAILNHIRAIHAFY-----GDTAGVRIARKHIGWYIDEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + ++      + E 
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERLAEK 323


>gi|257068855|ref|YP_003155110.1| putative TIM-barrel protein, nifR3 family [Brachybacterium faecium
           DSM 4810]
 gi|256559673|gb|ACU85520.1| putative TIM-barrel protein, nifR3 family [Brachybacterium faecium
           DSM 4810]
          Length = 415

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 127/325 (39%), Gaps = 27/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTN------NALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R            L  +EM+   A++    +   ++    QE P ++
Sbjct: 50  MAGITNMAFRLLCREFGALHSEDDGGLYVSEMVTTRALVEDHRESWRLVTMGAQETPRSV 109

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+ G D + +  A +++ +    + I+LN GCP  +V     G  L    ++    ++A 
Sbjct: 110 QLYGVDPATVRRAVEMIRERDLADHIDLNFGCPVPKVTRRGGGGVLPWKSELFTRIVSAA 169

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A    +PVTVK RIG+DD+      R+     ++ G   I +H R  +          
Sbjct: 170 VEAAGPEVPVTVKTRIGIDDEHQ--TFRDAGLIAQEVGAAAIALHGRTVV--------QH 219

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                 +D + E+K+   D+ +  NG +     A+ ++     DGV++GR       +  
Sbjct: 220 YSGTARWDAISELKELVTDIPVLGNGDIWCAEDAIDMMDRTGCDGVVVGRGCQGRPWLFA 279

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +   F+       P    V +   R     +  +       G  L+ + +H+   F G+
Sbjct: 280 DLAAGFAGRPERVRPSLGEVAQILRRHAELLIEFF----EDEGRALRDLRKHVAWYFKGY 335

Query: 288 PNSRRCRHILTVEAGASTATHHIIE 312
           P   + RH L      +     + E
Sbjct: 336 PVGGQMRHRLATMESLADLDAKLAE 360


>gi|228937378|ref|ZP_04100025.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970264|ref|ZP_04130924.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228976834|ref|ZP_04137247.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis Bt407]
 gi|228782930|gb|EEM31095.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis Bt407]
 gi|228789499|gb|EEM37418.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228822336|gb|EEM68317.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|326937868|gb|AEA13764.1| Nif3 family protein [Bacillus thuringiensis serovar chinensis
           CT-43]
          Length = 332

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 139/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 300

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 301 GINTCNTRED 310


>gi|213966461|ref|ZP_03394635.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           amycolatum SK46]
 gi|213950887|gb|EEB62295.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           amycolatum SK46]
          Length = 385

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 73/317 (23%), Positives = 124/317 (39%), Gaps = 34/317 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K +    F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCREQELQRTGTVSGLYVCEMVTARALVERNEKTMHMTTFAPDENPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAAK++ D    + I++N GCP  +V     G+ L     + G+ +AA 
Sbjct: 77  QLYTTDPKWTYEAAKMIVDENLADHIDMNFGCPVPKVTRKGGGSALPYKRRLFGNIVAAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +   + G   + +HAR A          
Sbjct: 137 VKATEGTDIPVTVKFRVGIDDEHH--THLDAGRIAAEMGAQAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKE-----NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
           R   + D+  +  +K+        D+ +  NG +   + A K+L     DGV++GR    
Sbjct: 187 RYSGHADWSQIARLKEHMVDSSFSDIPVLGNGDIFASTDARKMLDETGCDGVVVGRGCLG 246

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              +   +           +P    V     R       +    H       + + +H+ 
Sbjct: 247 RPWLFAQLSAELRGEEVPPAPTFGEVAGIIRRHA-----ELLVEHEGERKGCRDLRKHIA 301

Query: 282 GLFHGFPNSRRCRHILT 298
               G+P     R  L 
Sbjct: 302 WYLRGYPAGSEVRKSLA 318


>gi|295839031|ref|ZP_06825964.1| tRNA-dihydrouridine synthase [Streptomyces sp. SPB74]
 gi|295827295|gb|EDY44581.2| tRNA-dihydrouridine synthase [Streptomyces sp. SPB74]
          Length = 402

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 64/310 (20%), Positives = 119/310 (38%), Gaps = 21/310 (6%)

Query: 3   DWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G D 
Sbjct: 49  GITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMRLVQFGPTETPRSIQLYGVDP 108

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSI 117
           + + +AA++V E+   + I+LN GCP  +V     G+ L     ++   +  A+  A  +
Sbjct: 109 ATVGKAARMVREENLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAILREAVAGADGL 168

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G+D+    +   +  +     G+  I +H R                  D+D
Sbjct: 169 PVTMKMRKGIDED--HLTAFDAGRIAVDEGITAIALHGRTT--------AQHYGGTADWD 218

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+  P+L +  NG +     AL+++     DGV++GR       +   +   F  
Sbjct: 219 AIARLKEHVPELPVLGNGDIWTAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAFEG 278

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P    V     R                   +    +H+     GF      R 
Sbjct: 279 APRPTPPGLREVAAVMLRHARL----LGEWLEDEERGVIDFRKHVAWYLKGFSVGSEKRR 334

Query: 296 ILTVEAGAST 305
            L   +  + 
Sbjct: 335 ALATTSTLAE 344


>gi|254372943|ref|ZP_04988432.1| hypothetical protein FTCG_00514 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151570670|gb|EDN36324.1| hypothetical protein FTCG_00514 [Francisella novicida GA99-3549]
          Length = 327

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 137/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG DD+   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDDK--NINAIEVAKACEDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+  ++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRNVRKAV-DTVVIGNGDVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 302 MKLNQLEH-EQEIFKVLEEY 320


>gi|293571080|ref|ZP_06682121.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E980]
 gi|291608863|gb|EFF38144.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E980]
          Length = 334

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 134/326 (41%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 21  MAGITNSAFRVTVKEF-GAGLVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGN 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE+    + I++N+GCP  +V +   GA  +L+P+ V + + A+  A+ I
Sbjct: 80  KDSLVEAAQFVEENTAADIIDINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   V       + + +G + I +H R  +               D++
Sbjct: 140 PVTVKMRIGWDEE--HVFAVENALAAQSAGASAIAMHGRTRV--------QMYEGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+     Y   
Sbjct: 190 ILKEVKKHLTIPFMG-NGDVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +        A         ++   H      G P + + + 
Sbjct: 249 GELIPEPTPAEKIATAKLHLQR-----LADLKGEKVACREFRTHAAYYLKGIPRAAKVKV 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +       T     I    +  +E 
Sbjct: 304 AIN-----QTENQQEINDLLDQFVEK 324


>gi|325273604|ref|ZP_08139822.1| tRNA-dihydrouridine synthase B [Pseudomonas sp. TJI-51]
 gi|324101258|gb|EGB98886.1| tRNA-dihydrouridine synthase B [Pseudomonas sp. TJI-51]
          Length = 337

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 131/298 (43%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCQRL-GAGMVVSEMVSSDMNLWNSRKSSLRRIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAARANVEAGAQIIDINMGCPAKKVCNKAAGSALLKDEALVHEILHAVVGAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRANKNG--LNVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L    VDG++IGRAA     +   ++ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDITSPEKARAVLDATGVDGLLIGRAAQGRPWIFREIEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V+    + ++A    Y          ++   +H+       P  +  R
Sbjct: 248 EHLPAPQLDEVEHILLQHLAALHAFY-----GDVMGVRIARKHVGWYLATRPGGKEFR 300


>gi|302869263|ref|YP_003837900.1| TIM-barrel protein, nifR3 family [Micromonospora aurantiaca ATCC
           27029]
 gi|302572122|gb|ADL48324.1| TIM-barrel protein, nifR3 family [Micromonospora aurantiaca ATCC
           27029]
          Length = 387

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 119/311 (38%), Gaps = 24/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EMI   A++  + K   ++ F  +EKP +LQ+ G D
Sbjct: 25  MAGITNVGFRRLCREQGG-GIYVCEMITTRALVERNPKTLRMIAFGAEEKPRSLQLYGTD 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
                 A +IV +    + I+LN GCP  +V     G+ L     +    + A   A S 
Sbjct: 84  PEITAAAVRIVVERDLADHIDLNFGCPVPKVTRRGGGSALPWRRRLFARLVRAAVDAASP 143

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+DD         L    + +GV  + +H R A          R     
Sbjct: 144 AGVPVTVKMRKGIDDDHLTYVEAGLA--AQDAGVAAVALHGRTA--------AQRYSGTA 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K    D+ +  NG + +   AL+++    VDGV+IGR       +   ++  
Sbjct: 194 DWDAIATLKSAL-DVPVLGNGDIWEADDALRMVAHTGVDGVVIGRGCLGRPWLFADLEAA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR----HLHSGGKLQQITRHMIGLFHGFP 288
           F+       P    V     R     +  + A                 +H+     GFP
Sbjct: 253 FNGSAERRLPSLGEVAVTMRRHAELLVEQFVAGARNPARGERDGCTDFRKHVAWYLKGFP 312

Query: 289 NSRRCRHILTV 299
                R  L +
Sbjct: 313 IGSELRRSLAM 323


>gi|95930445|ref|ZP_01313181.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Desulfuromonas
           acetoxidans DSM 684]
 gi|95133485|gb|EAT15148.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Desulfuromonas
           acetoxidans DSM 684]
          Length = 325

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 127/302 (42%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  YR    + +  AL Y+EMI  + ++R   + +  L  +  E P A+Q+ G D
Sbjct: 22  MAGITNSPYRQIV-MESGAALTYSEMISGNGLIRDGLRTLELLKRTLVETPFAVQLFGDD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA I   +G   I+LN+GCP  +V     G+ LM  P  V   I AM +A S+P
Sbjct: 81  PEVLAEAAHIASRYG-ELIDLNMGCPVKKVVRSGAGSALMQEPQKVAKIICAMRQATSLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G         L  + +  +  G + + +H R    +G     N       +  
Sbjct: 140 LTVKIRSGWTVADINFQL--IGQICQDEGADAVILHPRTRC-QGFGGHSN-------WQH 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+    + +  +G +     A  +L     DG+MIGR +Y N  +   + +  +  
Sbjct: 190 IRQLKQHLT-IPVIGSGDIITADDAFAMLEQTGCDGIMIGRGSYGNPWLFNAIVQRAAGE 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P + +  +   R ++     Y  R       L  + +H+     G   +   R  
Sbjct: 249 EV-TPPSRQQRLETALRHLNLYAGYYGER-----KTLLDMRKHLCWYSRGLNGASEFRAA 302

Query: 297 LT 298
           + 
Sbjct: 303 IN 304


>gi|325138386|gb|EGC60954.1| dihydrouridine synthase [Neisseria meningitidis ES14902]
 gi|325142617|gb|EGC65009.1| dihydrouridine synthase [Neisseria meningitidis 961-5945]
          Length = 374

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 114 PQQMADAARYNVSLGAQVIDINMGCPAKKVCNAQAGSALMQNEPLVAAILEAVVRAVDVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 174 VTLKTRLGWHDDHKN--LPAVARIAEDCGIAALAVHGRT--------RTQMYKGEAAYDL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +    + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAAAVFKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             + A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECSAAILNHVRAMHAFY-----GETAGVRIARKHIGWYIGEMPDGEQARRE 337

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 338 IN-RLDSAAAQYDMLAGYLERL 358


>gi|189425844|ref|YP_001953021.1| hypothetical protein Glov_2788 [Geobacter lovleyi SZ]
 gi|189422103|gb|ACD96501.1| TIM-barrel protein, nifR3 family [Geobacter lovleyi SZ]
          Length = 325

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 130/316 (41%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              T+  +R   R      L +TEMI  + ++R  +K +  L  S  ++PL +Q+ G   
Sbjct: 24  AGITNHVFRLICRQ-AGACLAFTEMISVNGMVREGEKTLALLSSSPDDRPLGVQLFGNAP 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L +AA +V+D   + I++N+GCP  +V     G+ L+ +   + + + ++ +  ++P+
Sbjct: 83  ELLAQAASMVKD-NADLIDINMGCPVRKVVGTGAGSALLQDTARIAEIVRSVRRTTNLPL 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G          + + +  +  G + I +H R         +        D+  +
Sbjct: 142 TIKIRSGWQCGDD--TWQEVGRIAEAEGCDAITLHPRS--------RAQMFNGQADWQQI 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K+    + +  +G L       ++L     DG+M+ R A  N  + +   E      
Sbjct: 192 GQLKQ-LVKIPVIGSGDLFTPQDCRRMLSETGCDGLMVARGALGNPWIFSQTCELLEGR- 249

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +P+          +  A  TDYA         ++++ +H+    HG P +   R  +
Sbjct: 250 -PVTPVSCADRMAMAEQHLALFTDYAGE----SVAVREMKKHLGWYIHGVPGAAALRRTV 304

Query: 298 TVEAGASTATHHIIET 313
              A        +IE 
Sbjct: 305 NT-ARNMNELLDVIEQ 319


>gi|15677280|ref|NP_274433.1| nifR3 protein [Neisseria meningitidis MC58]
 gi|7226660|gb|AAF41782.1| nifR3 protein [Neisseria meningitidis MC58]
 gi|316985807|gb|EFV64750.1| TIM-barrel , nifR3 family protein [Neisseria meningitidis H44/76]
 gi|325140374|gb|EGC62895.1| dihydrouridine synthase [Neisseria meningitidis CU385]
 gi|325199962|gb|ADY95417.1| dihydrouridine synthase [Neisseria meningitidis H44/76]
          Length = 336

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 132/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECAAAILNHIRAIHAFY-----GDTAGVRIARKHIGWYIDEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A + ++      + E 
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERLAEK 323


>gi|312144282|ref|YP_003995728.1| TIM-barrel protein, nifR3 family [Halanaerobium sp. 'sapolanicus']
 gi|311904933|gb|ADQ15374.1| TIM-barrel protein, nifR3 family [Halanaerobium sp. 'sapolanicus']
          Length = 327

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 77/304 (25%), Positives = 137/304 (45%), Gaps = 23/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKP-LALQIGGA 57
           M   +D  YR   R +    LLYTEM+ A     G+   K ++ F  +E   +A+QI G 
Sbjct: 19  MAGVSDYPYRQIVREM-GVKLLYTEMVSAKGYEYGNNRTKELVEFEKKEDGKIAVQIFGE 77

Query: 58  DISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   +  AAK I  D+  + I++N+GCP+ ++     G+ LM N ++  + I  + +A+S
Sbjct: 78  EADFMAAAAKNIANDYDIDIIDINMGCPARKIVSNGAGSALMKNLELAENIIGRVVEAVS 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R G D+    +    L K+ +K G  G+ +H R         +        D+
Sbjct: 138 IPVTVKMRSGWDED--NINAVELAKTAEKMGAAGLAVHGRT--------RKQFYKGKADW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            I+ ++  +  ++ +  NG +     A K     +  G+MIGRAA  N  +   V EY  
Sbjct: 188 QIIKDVV-DAVEIPVIANGDIFSAEDAAKAFDFINCSGIMIGRAAQGNPWIFKEVIEYLK 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           N      P   +  +   + I+ ++  Y  +       +  + +H+     G P + + +
Sbjct: 247 NGRKIKGPSNQQKLEIAVKHINLAVDFYGEKQ-----AIPLMRKHIAWYLKGMPYASKVK 301

Query: 295 HILT 298
             + 
Sbjct: 302 SKVN 305


>gi|222093846|ref|YP_002527895.1| tim-barrel protein, putative, nifr3 family [Bacillus cereus Q1]
 gi|221237893|gb|ACM10603.1| TIM-barrel protein, putative, NifR3 family [Bacillus cereus Q1]
          Length = 324

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 10  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 68

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 69  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 129 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 178

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 179 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 238 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 292


>gi|119475082|ref|ZP_01615435.1| Dihydrouridine synthase TIM-barrel protein nifR3 [marine gamma
           proteobacterium HTCC2143]
 gi|119451285|gb|EAW32518.1| Dihydrouridine synthase TIM-barrel protein nifR3 [marine gamma
           proteobacterium HTCC2143]
          Length = 351

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 124/289 (42%), Gaps = 21/289 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L    L+ +EM+ +D  L   +K+   L  S +  P ++QI G D
Sbjct: 10  MAGVTDLPFRQLCRRL-GAGLVVSEMVTSDTRLWHTRKSQQRLNHSGETGPRSVQIAGGD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA +    G   I++N+GCP+ +V + + G+ L+ +P +V D + A+  A+ +P
Sbjct: 69  AAMMAEAASMNVARGAQIIDINMGCPAKKVCKKAAGSALLKDPGLVTDILTAVIAAVDVP 128

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            + +  + +G+  + +H R    K           + +YD 
Sbjct: 129 VTLKIRTGW--STDYRNGVEIARIAEDAGIAALAVHGRTRACKFN--------GDAEYDT 178

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK     + I  NG +    +AL ++     D VM+GRAA     +   +D +    
Sbjct: 179 IAAIKSAV-SIPIIANGDITSPQKALAVMQYTGADAVMVGRAAQGQPWICGEIDHFLRTG 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
            T + P +  +       + A    Y          ++   +H+     
Sbjct: 238 NTLAPPSRESIKCILLDHLDALHRFYGEFM-----GVKIARKHVGWYLK 281


>gi|15238854|ref|NP_199608.1| nitrogen regulation family protein [Arabidopsis thaliana]
 gi|145334771|ref|NP_001078731.1| nitrogen regulation family protein [Arabidopsis thaliana]
 gi|10177748|dbj|BAB11061.1| unnamed protein product [Arabidopsis thaliana]
 gi|18175722|gb|AAL59916.1| unknown protein [Arabidopsis thaliana]
 gi|20466015|gb|AAM20229.1| unknown protein [Arabidopsis thaliana]
 gi|332008217|gb|AED95600.1| tRNA-dihydrouridine synthase A [Arabidopsis thaliana]
 gi|332008218|gb|AED95601.1| tRNA-dihydrouridine synthase A [Arabidopsis thaliana]
          Length = 387

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 107/305 (35%), Positives = 156/305 (51%), Gaps = 19/305 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+ WTD HYR  ARL+T +A LYTEM+ A+ I+    +  + L FS  + P+ LQIGG +
Sbjct: 17  MMGWTDNHYRTLARLITKHAWLYTEMLAAETIVYQEDNLDSFLAFSPDQHPIVLQIGGRN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC-LMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EIN N GCPS +V         LML+P  VG+ ++ +    + 
Sbjct: 77  LENLAKATRLANAYAYDEINFNCGCPSPKVSGRGCFGALLMLDPKFVGEAMSVIAANTNA 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            VTVKCRIGVDD      L + +  +   S      IH+RKA+L GLSP DNR+IP L Y
Sbjct: 137 AVTVKCRIGVDDHDSYNELCDFIHIVSSLSPTKHFIIHSRKALLSGLSPSDNRRIPPLKY 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           +  + + ++ PDL   +NGG+  + +A   L     GVM+GRA Y N   +L  VD    
Sbjct: 197 EFFFALLRDFPDLKFTINGGINSVVEADAALRSGAHGVMLGRAVYYNPWHILGHVDTVVY 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLFHGFPNS 290
              +              R++      Y    L   GK    L+ I R +I LFH    +
Sbjct: 257 GSPSSG---------ITRRQVLEKYKLYGESVLGKYGKGRPNLRDIVRPLINLFHSESGN 307

Query: 291 RRCRH 295
            + + 
Sbjct: 308 GQWKR 312


>gi|299536698|ref|ZP_07050008.1| tRNA-dihydrouridine synthase 1 [Lysinibacillus fusiformis ZC1]
 gi|298727812|gb|EFI68377.1| tRNA-dihydrouridine synthase 1 [Lysinibacillus fusiformis ZC1]
          Length = 346

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 146/320 (45%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+Y EMI    I++ ++K   +L    +E PL+LQI G D
Sbjct: 25  MAGICNSAFRLTVKEF-GAGLVYAEMISDKGIVQKNEKTLGMLYIDERENPLSLQIFGGD 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V++    + I++N+GCP  ++ +   GA L+L+P+ V + +AA+  A+  
Sbjct: 84  KETLVEAAKYVDENTTADIIDINMGCPVNKIIKCEAGARLLLDPNKVYEMVAAVVDAVKK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D++   +      ++++++G   + +H R  +               ++D
Sbjct: 144 PVSVKMRIGWDEE--HIFAIENAQAVERAGAAAVAVHGRTRV--------QMYEGKANWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K EN  + +  NG +E    A ++L    VD VMIGRAA  N  M+    +Y + 
Sbjct: 194 YIRQVK-ENVSIPVLGNGDVETPQDAKRMLETTGVDAVMIGRAALGNPWMIYRTVQYLAT 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     +   +    G  ++++ +H      G   + + R+
Sbjct: 253 GELKEEPSVRE-----KMDVCLLHFERLLQLKGEGIAVREMRKHASWYLKGIRGNGKARN 307

Query: 296 ILTVEAGASTATHHIIETAF 315
            +      + A   ++  + 
Sbjct: 308 AI--NQTETAAELRVLLNSL 325


>gi|315504262|ref|YP_004083149.1| tim-barrel protein, nifr3 family [Micromonospora sp. L5]
 gi|315410881|gb|ADU08998.1| TIM-barrel protein, nifR3 family [Micromonospora sp. L5]
          Length = 387

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 119/311 (38%), Gaps = 24/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EMI   A++  + K   ++ F  +EKP +LQ+ G D
Sbjct: 25  MAGITNVGFRRLCREQGG-GIYVCEMITTRALVERNPKTLRMIAFGAEEKPRSLQLYGTD 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
                 A +IV +    + I+LN GCP  +V     G+ L     +    + A   A S 
Sbjct: 84  PEITAAAVRIVVERDLADHIDLNFGCPVPKVTRRGGGSALPWRRRLFARLVRAAVDAASP 143

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+DD         L    + +GV  + +H R A          R     
Sbjct: 144 AGVPVTVKMRKGIDDDHLTYVEAGLA--AQDAGVAAVALHGRTA--------AQRYSGTA 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K    D+ +  NG + +   AL+++    VDGV+IGR       +   ++  
Sbjct: 194 DWDAIATLKAAL-DVPVLGNGDIWEADDALRMVAHTGVDGVVIGRGCLGRPWLFADLEAA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR----HLHSGGKLQQITRHMIGLFHGFP 288
           F+       P    V     R     +  + A                 +H+     GFP
Sbjct: 253 FNGSAERRLPSLGEVAVTMRRHAELLVEQFVAGARNPARGERDGCTDFRKHVAWYLKGFP 312

Query: 289 NSRRCRHILTV 299
                R  L +
Sbjct: 313 IGSELRRSLAM 323


>gi|229194466|ref|ZP_04321270.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1293]
 gi|228589056|gb|EEK47070.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1293]
          Length = 339

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVKK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 307


>gi|227552661|ref|ZP_03982710.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257888629|ref|ZP_05668282.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897416|ref|ZP_05677069.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|293378826|ref|ZP_06624981.1| TIM-barrel protein, nifR3 family [Enterococcus faecium PC4.1]
 gi|227178190|gb|EEI59162.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257824683|gb|EEV51615.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257833981|gb|EEV60402.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|292642367|gb|EFF60522.1| TIM-barrel protein, nifR3 family [Enterococcus faecium PC4.1]
          Length = 334

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 137/329 (41%), Gaps = 25/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 21  MAGITNSAFRVTVKEF-GAGLVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGN 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE+    + I++N+GCP  +V +   GA  +L+P+ V + + A+  A+ I
Sbjct: 80  KDSLVEAAQFVEENTAADIIDINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   V       + + +G + I +H R  +               D++
Sbjct: 140 PVTVKMRIGWDEE--HVFAVENALAAQSAGASAIAMHGRTRV--------QMYEGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+     Y   
Sbjct: 190 ILKEVKKHLTIPFMG-NGDVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +        A         ++   H      G P + + + 
Sbjct: 249 GELIPEPTPAEKIATAKLHLQR-----LADLKGEKVACREFRTHAAYYLKGIPRAAKVKV 303

Query: 296 ILTVEAGA---STATHHIIETAFNLMIES 321
            +         +      +E A  ++++ 
Sbjct: 304 AINQTENQQEINGLLDQFVEKAEKVLLKQ 332


>gi|269794702|ref|YP_003314157.1| TIM-barrel protein, nifR3 family [Sanguibacter keddieii DSM 10542]
 gi|269096887|gb|ACZ21323.1| putative TIM-barrel protein, nifR3 family [Sanguibacter keddieii
           DSM 10542]
          Length = 406

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 128/325 (39%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EM+ + AI+  +++   I+ F   E P + Q+ G D
Sbjct: 46  MAGVTNTAFRKLCREHGPGGLYVAEMVTSRAIVERNEQALRIVTFEDGESPRSAQVYGVD 105

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            + +  A +I+   G  + ++LN GCP  +V     GA L    ++    + A  +A   
Sbjct: 106 PATVGAAVEIIAGEGRADHVDLNFGCPVPKVTRKGGGAVLPWKRELFTRIVDAAVEAGAR 165

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+DD    +         +++GV  + +HAR A         +      
Sbjct: 166 HDVPVTIKMRKGIDDD--HLTYLEAGLIAEQAGVAAVALHARTA--------ADYYSGTA 215

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + ++K+    + +  NG +     AL+++     DGV++GR       +   +   
Sbjct: 216 DWSAIRQLKETVTSIPVLGNGDIWSAEDALEMVRQTGCDGVVVGRGCQGRPWLFADLMAA 275

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +  +R        +      +    + + +HM     G+     
Sbjct: 276 FNGSDERVKPGLHEVAETIYRHGELMAEFFQDEDKGT----RDLRKHMAWYLKGYAVGGD 331

Query: 293 CRHILTVEAGASTATHHIIETAFNL 317
            R  L + +  +    H+   A + 
Sbjct: 332 ARRALAMVSSLAELRQHL--DALDH 354


>gi|324324066|gb|ADY19326.1| putative TIM-barrel protein, NifR3 family [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 332

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 142/327 (43%), Gaps = 27/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +             +    +  +E +
Sbjct: 301 GINACNTRED-----LANVLSTFVEEV 322


>gi|73668536|ref|YP_304551.1| hypothetical protein Mbar_A1003 [Methanosarcina barkeri str.
           Fusaro]
 gi|72395698|gb|AAZ69971.1| tRNA-U20-dihydrouridine synthase [Methanosarcina barkeri str.
           Fusaro]
          Length = 323

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 82/303 (27%), Positives = 139/303 (45%), Gaps = 26/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M D T+  +R   R      L YTEMI ADA+L  ++K++L    S +++P  +Q+ G+ 
Sbjct: 22  MADVTNLAFRLLCRQ-NGADLTYTEMISADALLNENRKSLLKGLSSPEDRPFGVQLVGSS 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             KL EAA  +ED +    I++N+GCP+ R+     G+ L+ +  ++ + I+ +   L  
Sbjct: 81  PEKLREAALFIEDEYRPELIDVNMGCPAKRITGTGCGSALLNSKKLIYEIISDLTDVLKT 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RI   D+        + + I+++G + + IH R+A        +     + D  
Sbjct: 141 PVTAKIRILKRDEKT----LEIARLIEEAGASALTIHGRRA--------EQMYSGSSDLT 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++  +K+E   + +  NG + +   A   L     DG+MIGRAA  N  +   +  Y   
Sbjct: 189 VIRAVKQEL-SIPVIANGDIRNEESAEAALDFTECDGLMIGRAAMGNPFIFKRIRHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R  +DF   I A + +Y    LH+      I  H      G   SR+ R 
Sbjct: 248 GERLEFDRQVRQLEDFENYI-ALLEEY---DLHASTN---IRMHAHWFTKGLRGSRQIRE 300

Query: 296 ILT 298
            + 
Sbjct: 301 KIN 303


>gi|56707655|ref|YP_169551.1| Nif3 family protein [Francisella tularensis subsp. tularensis SCHU
           S4]
 gi|110670126|ref|YP_666683.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC198]
 gi|134302001|ref|YP_001121970.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|224456726|ref|ZP_03665199.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370168|ref|ZP_04986174.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254874472|ref|ZP_05247182.1| nif3 family protein [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|56604147|emb|CAG45152.1| Nif3 family protein [Francisella tularensis subsp. tularensis SCHU
           S4]
 gi|110320459|emb|CAL08535.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC198]
 gi|134049778|gb|ABO46849.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151568412|gb|EDN34066.1| Nif3 family protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254840471|gb|EET18907.1| nif3 family protein [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|282158815|gb|ADA78206.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 327

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 139/320 (43%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVEHNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I+  V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  INSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 302 MKLNQLEH-EQEIFKVLEEY 320


>gi|262203780|ref|YP_003274988.1| hypothetical protein Gbro_3919 [Gordonia bronchialis DSM 43247]
 gi|262087127|gb|ACY23095.1| TIM-barrel protein, nifR3 family [Gordonia bronchialis DSM 43247]
          Length = 394

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 124/313 (39%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+ +E P ++
Sbjct: 34  MAGVTNVAFRTLCRELEIARTGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSM 93

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK++ D    + I++N GCP  +V     G+ +     +    +AA 
Sbjct: 94  QLYTVDPEYTYAAAKMIVDEDLADHIDMNFGCPVPKVTRKGGGSAIPYKRTLFRKIVAAA 153

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD+       +  +   + G   + +HAR A          
Sbjct: 154 VRATEGTDIPVTVKFRIGIDDEHR--THLDAGRIAAEEGAKAVALHARTA--------SQ 203

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D+D +  +K    D+ +  NG + +   A++++     DGV+IGR       + 
Sbjct: 204 RYSGQADWDEIARLKDHVTDVPVLGNGDIFEPVDAVEMMRRTGCDGVVIGRGCLGRPWLF 263

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +    +     + P    V     R       +    H       ++I +H+     G
Sbjct: 264 AELAAEMNGVEAPTPPTLGEVADIIVRH-----CELLVAHHGEMKGCREIRKHVAWYLRG 318

Query: 287 FPNSRRCRHILTV 299
           FP     R  + +
Sbjct: 319 FPAGSELRRQMAL 331


>gi|108761670|ref|YP_634429.1| putative tRNA-dihydrouridine synthase [Myxococcus xanthus DK 1622]
 gi|108465550|gb|ABF90735.1| putative tRNA-dihydrouridine synthase [Myxococcus xanthus DK 1622]
          Length = 337

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 134/299 (44%), Gaps = 27/299 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQ-EKPLALQIGGA 57
           M   ++  +R  A  L   AL  TE++ +  ++R +++ +  L +  + E+P +LQI G 
Sbjct: 18  MAGVSEMPFRVLAFRL-GAALCPTELVSSQGLMRANQRTLKYLRYDAEVERPYSLQIYGG 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   +  AA +  + G   I++N+GCP  +V +   G+ L+ +     D +  + +A  +
Sbjct: 77  EPEAMARAAVVGREAGAQIIDINMGCPVKKVVKNGAGSGLLCDVPRAADIVRRIREATGL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R G D    ++    +  +++++G  G+ IH R         ++       D+ 
Sbjct: 137 PVTCKIRSGWD--ARSLNYLQVAGALQEAGCAGLAIHPRT--------REQGYSGQADWS 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+  P+L I  NG ++  + A ++L     D VMIGRAA  N  +          
Sbjct: 187 VIADLKRHFPELPIIGNGDVKTPADAARMLETTGCDFVMIGRAALGNPWIFRE------- 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            L G  P   R   +   +   +  D+    L   G ++   + +    HG   +   R
Sbjct: 240 -LLGGPPATPRERCELVLEHFRAHLDFMGDPL---GAVRSFRKQLAWYAHGLYGAAAFR 294


>gi|301051814|ref|YP_003790025.1| putative TIM-barrel protein [Bacillus anthracis CI]
 gi|300373983|gb|ADK02887.1| possible TIM-barrel protein, NifR3 family [Bacillus cereus biovar
           anthracis str. CI]
          Length = 332

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 300


>gi|167628121|ref|YP_001678621.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167598122|gb|ABZ88120.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 324

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 140/324 (43%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENIEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG DD+   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDDE--NINAIEVAKACEDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ ++KK   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVKKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +     +   +    A+       +++I  H        P S+  R
Sbjct: 247 TGELIPPPTPVERVEVLGEHLRRLIKLKTAK-----VAVKEIRTHASFYLADLPGSKEFR 301

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
             L            ++E   N  
Sbjct: 302 MKLNQLEH-EQEIFRVLEEYSNSF 324


>gi|229136922|ref|ZP_04265550.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST26]
 gi|229153854|ref|ZP_04281985.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 4342]
 gi|228629658|gb|EEK86354.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 4342]
 gi|228646587|gb|EEL02793.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST26]
          Length = 339

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 307


>gi|183984825|ref|YP_001853116.1| transcriptional regulator [Mycobacterium marinum M]
 gi|183178151|gb|ACC43261.1| transcriptional regulator [Mycobacterium marinum M]
          Length = 377

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 128/313 (40%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELEQAKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++ + G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 77  QLYTVDPDTTYAAARMIAEEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 136

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            + +    IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 137 VRGVEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQHVRTVPVLGNGDIYDASDALAMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I     +  A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGNPGPTPPTLGEVT-----DIIRRHGELLAAHFGEDKGMRDIRKHVAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSDLRRALAL 314


>gi|188584754|ref|YP_001916299.1| TIM-barrel protein, nifR3 family [Natranaerobius thermophilus
           JW/NM-WN-LF]
 gi|179349441|gb|ACB83711.1| TIM-barrel protein, nifR3 family [Natranaerobius thermophilus
           JW/NM-WN-LF]
          Length = 327

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 61/294 (20%), Positives = 126/294 (42%), Gaps = 21/294 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR      +   L+  EM+ A  ++ G+KK   ++    Q    + QI G+D
Sbjct: 20  MAGVTDYPYRRILAKFS-PGLICGEMVSAKGMVYGNKKTEEMVIHHNQGVHYSQQIFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA  +E+ G + I++N+GCP+ ++ +   G+ L+  P +  + +  +  ++++P
Sbjct: 79  PKVMADAAVKLENLGVDSIDVNMGCPAPKIVKNGEGSALLKKPHLAQEIVREIVNSVNLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D +        L   +++ G+  + +H R          + +     D+++
Sbjct: 139 VTVKIRKGFDRKSSDP--LELALRLQEVGIKALAVHGRTC--------EQQYSGKADWEV 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K    D+ +  NG +     A+  L   + DG+M+GR    N  ++          
Sbjct: 189 VAKLKN-YLDIPVIGNGDIFSSEDAVSALEMTACDGIMLGRGLMGNPWLIEQTKGMLIKD 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               SP    +  +          + A ++      + ++ +H+       P S
Sbjct: 248 EKIESPEIHEIKNEMKSH-----FENAIKYYGESKGIAEMRKHISWYLKSLPGS 296


>gi|315442689|ref|YP_004075568.1| hypothetical protein Mspyr1_10440 [Mycobacterium sp. Spyr1]
 gi|315260992|gb|ADT97733.1| putative TIM-barrel protein, nifR3 family [Mycobacterium sp. Spyr1]
          Length = 361

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 127/309 (41%), Gaps = 29/309 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+ +E P +L
Sbjct: 1   MAGVTNVAFRTLCRELELSRAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSL 60

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK++ D    + I++N GCP  +V     GA L     + G  ++A 
Sbjct: 61  QLYTVDPVNTYAAAKMIVDEDLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGQIVSAA 120

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD+       +  +   + G   + +HAR A          
Sbjct: 121 VRATEGTDIPVTVKFRIGIDDEHH--THLDAGRIAAEEGAAAVALHARTA--------AQ 170

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R   + D+D +  +K    ++ +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 171 RYSGSADWDQIAALKAHVTNVPVLGNGDIFDARDALAMMAATGCDGVVIGRGCLGRPWLF 230

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V      +I     +  A H      ++ I +H+    HG
Sbjct: 231 AELSAAFTGATPATPPTLGEVA-----QIIRRHGELLAAHFGEDKGMRDIRKHVAWYMHG 285

Query: 287 FPNSRRCRH 295
           FP     R 
Sbjct: 286 FPAGADLRR 294


>gi|229015478|ref|ZP_04172477.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1273]
 gi|229021687|ref|ZP_04178270.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1272]
 gi|228739623|gb|EEL90036.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1272]
 gi|228745821|gb|EEL95824.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1273]
          Length = 339

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 138/310 (44%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDKYTTADIIDINMGCPVPKITKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      ++++++G   + +H R  +               D++
Sbjct: 144 PVTVKMRIGWDED--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWN 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVRN 307

Query: 296 ILTVEAGAST 305
            +        
Sbjct: 308 GINTCNTRED 317


>gi|332678280|gb|AEE87409.1| tRNA dihydrouridine synthase B [Francisella cf. novicida Fx1]
          Length = 325

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 140/325 (43%), Gaps = 24/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETAFNLMI 319
             L            ++E   N  +
Sbjct: 302 MKLNQLEH-EQEIFRVLEDYKNSFV 325


>gi|306836817|ref|ZP_07469775.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49726]
 gi|304567278|gb|EFM42885.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49726]
          Length = 381

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 125/310 (40%), Gaps = 31/310 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K +    F+  E P +L
Sbjct: 19  MAGVTNVAFRTLCREQELARTGTVSGLYVCEMVTARALVERNEKTMHMTTFAPDEDPRSL 78

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           QI   D     +AAKI+ D    + I++N GCP  +V     G+ L     + G+ ++A 
Sbjct: 79  QIYTVDPEYTYKAAKIIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAA 138

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA    +IPVTVK R+G+DD+       +  +    SG   + +H R A          
Sbjct: 139 VKATEGTNIPVTVKMRVGIDDEHH--THLDAGRIAVDSGAAAVTLHGRTA--------AQ 188

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   +  +D +  +K+   D  + +  NG +     A +++     DGV +GR       
Sbjct: 189 RYSGDARWDEIARLKEHLADTGVPVLGNGDIFRADDARRMMEATGCDGVQVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          + P    V +   R       +  A+H       + I +H+    
Sbjct: 249 LFAELSAALRGESIPAEPTLGEVTQVIHRHA-----ELLAQHEGEDHASRDIRKHIGWYL 303

Query: 285 HGFPNSRRCR 294
            GFP   + R
Sbjct: 304 RGFPVGGQVR 313


>gi|42779155|ref|NP_976402.1| NifR3 family TIM-barrel protein [Bacillus cereus ATCC 10987]
 gi|217957652|ref|YP_002336194.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH187]
 gi|42735070|gb|AAS39010.1| TIM-barrel protein, putative, NifR3 family [Bacillus cereus ATCC
           10987]
 gi|217063780|gb|ACJ78030.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH187]
          Length = 332

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 300


>gi|311745604|ref|ZP_07719389.1| TIM-barrel protein, putative, NifR3 family [Algoriphagus sp. PR1]
 gi|126578167|gb|EAZ82387.1| TIM-barrel protein, putative, NifR3 family [Algoriphagus sp. PR1]
          Length = 329

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 141/315 (44%), Gaps = 25/315 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE I ++ ++R   K++  L     EKP+ +QI G D
Sbjct: 19  MEDVSDPPFRAVCKQ-NGADLMYTEFISSEGLIRDAAKSVQKLDIYDYEKPIGIQIFGND 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EAA I  + G + +++N GCP  +V     GA ++L+ D +    A + KA+ IP
Sbjct: 78  IESMREAAAIAAEAGPDILDINYGCPVNKVACKGAGAGILLDIDKMVSMTAEIVKAVDIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    + +  + + ++  G+  I IHAR         +        D+  
Sbjct: 138 VTVKTRLGWDNDT--IRIVEVAERLQDVGIQAISIHART--------RKQMYKGEADWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K+     + +  NG ++   +AL+     +VDG+MIGRA+     +   +  + + 
Sbjct: 188 LNLVKENPRLHIPVFGNGDIDSPEKALEYKTKYNVDGMMIGRASIGYPWIFNEIKHFLAT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P            ++    D++         + ++ RH    F G PN +  R 
Sbjct: 248 GEKLEAPSIEERI-----AVAKQHLDFSVEWKGEKQGILEMRRHYTNYFRGMPNFKPIR- 301

Query: 296 ILTVEAGASTATHHI 310
               E   + +  H+
Sbjct: 302 ---TEMVTADSYQHV 313


>gi|222054815|ref|YP_002537177.1| TIM-barrel protein, nifR3 family [Geobacter sp. FRC-32]
 gi|221564104|gb|ACM20076.1| TIM-barrel protein, nifR3 family [Geobacter sp. FRC-32]
          Length = 326

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 136/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+   R  AR     AL +TEMI  + ++R  KK   +L     ++P+ +QI G D
Sbjct: 21  MAGLTNLPMRILARE-CGAALTFTEMISVNGLVREGKKTFDLLRRDPMDRPMGIQIFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E A++VE +G   I++N+GCP  +V     G+ L+  P  VG  I A+ KA S+P
Sbjct: 80  PQLLAEGARLVEQYG-ELIDINMGCPVRKVVGSGAGSALLREPAKVGMIIKAVRKATSLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G            + +  +  GV+G+ +H R         +      + D+  
Sbjct: 139 LTIKIRTGWGAADH--TFLEIGRIAEAEGVDGVTLHPRS--------RAQMFEGHADWSR 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K E   + +  +G +   +  + ++     DGVM+ R    N  +        S  
Sbjct: 189 IRELK-EALSIPVIGSGDIFTAADVVAMIDQTGCDGVMVARGGLGNPWLFREALALLS-- 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             G+ PI     +   R ++    D           ++++ +H+     G P +   R +
Sbjct: 246 --GNEPIPPTAAEK--RSLALRHLDLFLEATGEHVAVREMRKHLSWYAKGMPGAAHFRAM 301

Query: 297 LTVEAGASTATHHIIETAFN 316
           +       TA    +E  F+
Sbjct: 302 INHIEDR-TALIAALEDFFS 320


>gi|47570200|ref|ZP_00240854.1| NifR3/smm1 family protein [Bacillus cereus G9241]
 gi|47553144|gb|EAL11541.1| NifR3/smm1 family protein [Bacillus cereus G9241]
          Length = 324

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 10  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 68

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 69  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 129 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 178

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 179 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 238 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 292


>gi|228898829|ref|ZP_04063112.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 4222]
 gi|228860854|gb|EEN05231.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 4222]
          Length = 332

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 138/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++I+++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAIERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|187931839|ref|YP_001891824.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712748|gb|ACD31045.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 327

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 139/320 (43%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I+  V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  INSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 302 MKLNQLEH-EQEIFKVLEEY 320


>gi|257886013|ref|ZP_05665666.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
 gi|293553701|ref|ZP_06674325.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1039]
 gi|257821869|gb|EEV48999.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
 gi|291602276|gb|EFF32504.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1039]
          Length = 334

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 83/326 (25%), Positives = 134/326 (41%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 21  MAGITNSAFRVTVKEF-GAGLVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGN 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE+    + I++N+GCP  +V +   GA  +L+P+ V + + A+  A+ I
Sbjct: 80  KDSLVEAAQFVEENTAADIIDINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   V       + + +G + I +H R  +               D++
Sbjct: 140 PVTVKMRIGWDEE--HVFAVENALAAQSAGASAIAMHGRTRV--------QMYEGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+     Y   
Sbjct: 190 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +        A         ++   H      G P + + + 
Sbjct: 249 GELIPEPTPAEKIATAKLHLQR-----LADLKGEKVACREFRTHAAYYLKGIPRAAKVKV 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +       T     I    +  +E 
Sbjct: 304 AIN-----QTEKQQEINDLLDQFVEK 324


>gi|228983331|ref|ZP_04143545.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228776445|gb|EEM24797.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 339

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLGT 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 307


>gi|257899975|ref|ZP_05679628.1| dihydrouridine synthase [Enterococcus faecium Com15]
 gi|257837887|gb|EEV62961.1| dihydrouridine synthase [Enterococcus faecium Com15]
          Length = 334

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 84/326 (25%), Positives = 134/326 (41%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 21  MAGITNSAFRVTVKEF-GAGLVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGN 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE+    + I++N+GCP  +V +   GA  +L+P+ V + + A+  A+ I
Sbjct: 80  KDSLVEAAQFVEENTAADIIDINMGCPVNKVIKAEAGAKWLLDPEKVYEMVKAVSSAVDI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   V       + + +G + I +H R  +               D++
Sbjct: 140 PVTVKMRIGWDEE--HVFAVENALAAQSAGASAIAMHGRTRV--------QMYEGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+     Y   
Sbjct: 190 ILKEVKKHLTIPFMG-NGDVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +        A         ++   H      G P + + + 
Sbjct: 249 GELIPEPTPAEKIATAKLHLQR-----LADLKGEKIACREFRTHAAYYLKGIPRAAKVKV 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +       T     I    +  +E 
Sbjct: 304 AIN-----QTENQQEINDLLDQFVEK 324


>gi|291457508|ref|ZP_06596898.1| putative tRNA-dihydrouridine synthase [Bifidobacterium breve DSM
           20213]
 gi|291381343|gb|EFE88861.1| putative tRNA-dihydrouridine synthase [Bifidobacterium breve DSM
           20213]
          Length = 453

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 123/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F++ EK  +LQ+ G +
Sbjct: 93  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVARNPKALRLCHFASSEKIRSLQLYGVN 152

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  + I    A+C+ 
Sbjct: 153 PSITEQAAKIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELIQRVVAVCEP 212

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 213 AGIPVTAKIRVGID--HDHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 262

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ D+ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 263 DWSRIGELK-EHLDIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 321

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F +     +P    V +            Y    + +   +  + +H+     GFP    
Sbjct: 322 FEDNPERLNPNLGEVCRVIHHHAELLTQFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 378

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 379 TRKAFMECENLADVDREI 396


>gi|208779377|ref|ZP_03246723.1| putative TIM-barrel protein, nifR3 family [Francisella novicida
           FTG]
 gi|208745177|gb|EDZ91475.1| putative TIM-barrel protein, nifR3 family [Francisella novicida
           FTG]
          Length = 328

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 141/326 (43%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG ++Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWNEQ--NINAIEVAKACEDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
             L            ++E   + + +
Sbjct: 302 MKLNQLEH-EQEIFKVLEEYKSFLKK 326


>gi|172056107|ref|YP_001812567.1| NifR3 family TIM-barrel protein [Exiguobacterium sibiricum 255-15]
 gi|171988628|gb|ACB59550.1| TIM-barrel protein, nifR3 family [Exiguobacterium sibiricum 255-15]
          Length = 332

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 130/302 (43%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+    IL  +++ +  L    +EKPL+LQI G  
Sbjct: 21  MAGVCNPAFRLIAKEF-GAGLVCAEMVSDKGILYENERTMQMLYVDDREKPLSLQIYGGS 79

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AA+ V  +   + I++N+GCP  +V +   GA  +L+PD V + + A+ +A+  
Sbjct: 80  KETLVQAAQYVDANTNADIIDINMGCPVPKVTKCDAGAKWLLDPDKVYEMVHAVSQAVDK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D         + V++ +  G   + IH R         +  +     D++
Sbjct: 140 PVTVKMRTGWDSHHIY--CVDNVRAAEAGGAKAVAIHGRT--------RSQKYEGVADWN 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E K+    + I  NG ++    A +++    VDGVMIGRAA  N  ML    +Y  +
Sbjct: 190 IIGEAKRAVT-IPIIGNGDVQTPQDAKRMIDEIGVDGVMIGRAALGNPWMLYQTIQYLES 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I     +           ++++  H+     G   +   R 
Sbjct: 249 GTLSVEPTPREKI-----DICLLHAERLVALKGEDLAVREMRTHVAWYLKGLSGNGHVRK 303

Query: 296 IL 297
            L
Sbjct: 304 AL 305


>gi|228963176|ref|ZP_04124346.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228796561|gb|EEM43999.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 332

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 138/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++I+++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAIERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|104783798|ref|YP_610296.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           entomophila L48]
 gi|95112785|emb|CAK17513.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           entomophila L48]
          Length = 337

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 131/298 (43%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M   TD+ +R   + L    ++ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRTLCKRL-GAGMVVSEMVTSDMSLWNSRKSSLRRIHEGDAEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMMAAAARANVEAGAQIIDINMGCPAKKVCNKAAGSALLRDEALVSEILHAVVGAVEVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ K  +++G+  + +H R         + +    + +YD 
Sbjct: 139 VTLKIRTGWDRANKNG--LNVAKIAEQAGIQALAVHGRT--------RADLYTGDAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L     DG++IGRAA     +   V+ Y    
Sbjct: 189 IAAIKQAV-SIPVFANGDITSPQKARAVLDATGADGLLIGRAAQGRPWIFREVEHYLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P    V++     ++A    Y          ++   +H+       P  +  R
Sbjct: 248 EHLPAPALDEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATRPGGKEFR 300


>gi|37520616|ref|NP_923993.1| hypothetical protein gll1047 [Gloeobacter violaceus PCC 7421]
 gi|35211610|dbj|BAC88988.1| gll1047 [Gloeobacter violaceus PCC 7421]
          Length = 342

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 129/320 (40%), Gaps = 21/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADIS 60
              TD+ +R   R    ++LLYTEM+ A  +        I+  +  E P+ +Q+      
Sbjct: 32  AGVTDKAFRQLVRRYAPHSLLYTEMVSASGLHYSRSLPQIMDIAPGETPIGIQLFDCRPD 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L EAA++ E  G + I++N+GCP  ++ +   G+ L+ +P      +A +  A+S+PVT
Sbjct: 92  FLAEAARVAEAQGADVIDINMGCPVNKITKNGGGSSLLRDPATAAKIVAVVAAAVSLPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G  D    + +    + +++SG   + +HAR         +         ++ + 
Sbjct: 152 VKTRLGWSDGE--INILEFARLMQESGAQMLTVHART--------RAQSFEGTARWEWIA 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K +   + +  NG +  +  A++   L   DGVM  R       ++  +D Y      
Sbjct: 202 RVKAQL-AIPVIANGDIFSIDAAIRCLELTGADGVMCARGTMGAPHLVGQIDHYLRTGER 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P   R   +        + DY          +++  +HM      FP +   R  L 
Sbjct: 261 LPDPTP-RARLEMACVHLHLLFDYLGA-----PGVRRARKHMGWYVRDFPGAAALRAQLM 314

Query: 299 VEAGASTATHHIIETAFNLM 318
                      ++  A   +
Sbjct: 315 CIETVPE-GERLLNEAIERL 333


>gi|218895212|ref|YP_002443623.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus G9842]
 gi|218540937|gb|ACK93331.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus G9842]
          Length = 332

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 139/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++I+++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAIERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|227502147|ref|ZP_03932196.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49725]
 gi|227077131|gb|EEI15094.1| dihydrouridine synthase [Corynebacterium accolens ATCC 49725]
          Length = 381

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 125/310 (40%), Gaps = 31/310 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K +    F+  E P +L
Sbjct: 19  MAGVTNVAFRTLCREQELARTGTVSGLYVCEMVTARALVERNEKTMHMTTFAPNEDPRSL 78

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           QI   D     +AAKI+ D    + I++N GCP  +V     G+ L     + G+ ++A 
Sbjct: 79  QIYTVDPEYTYKAAKIIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAA 138

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA    +IPVTVK R+G+DD+       +  +    SG   + +H R A          
Sbjct: 139 VKATEGTNIPVTVKMRVGIDDEHH--THLDAGRIAVDSGAAAVTLHGRTA--------AQ 188

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   +  +D +  +K+   D  + +  NG +     A +++     DGV +GR       
Sbjct: 189 RYSGDARWDEIARLKEHLADTGVPVLGNGDIFRADDARRMMEATGCDGVQVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          + P    V +   R       +  A+H       + I +H+    
Sbjct: 249 LFAELGAALRGESIPAEPTLGEVTQVILRHA-----ELLAQHEGEDHASRDIRKHIGWYL 303

Query: 285 HGFPNSRRCR 294
            GFP   + R
Sbjct: 304 RGFPVGGQVR 313


>gi|62259886|gb|AAX77872.1| unknown protein [synthetic construct]
          Length = 362

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 139/320 (43%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 45  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVEHNWETMEMLYMENSEKPLGIQIFGTD 103

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I+  V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 104 INSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 163

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 164 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 213

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 214 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 272

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 273 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 327

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 328 MKLNQLEH-EQEIFKVLEEY 346


>gi|228905872|ref|ZP_04069770.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 200]
 gi|228853812|gb|EEM98571.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis IBL 200]
          Length = 332

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 137/299 (45%), Gaps = 22/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++I+++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAIERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P            +     D      +    ++++ +H      G   +   R
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNASVR 299


>gi|304387247|ref|ZP_07369443.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis ATCC 13091]
 gi|304338714|gb|EFM04828.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis ATCC 13091]
          Length = 336

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 130/325 (40%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHEDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECAAAILNHIRAMHAFY-----GETAGVRIARKHIGWYIGEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     ++ A +  +      + E 
Sbjct: 300 IN-RLDSAAAQYDTLAGYLERVAEK 323


>gi|70734170|ref|YP_257810.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens Pf-5]
 gi|68348469|gb|AAY96075.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens Pf-5]
          Length = 337

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 135/300 (45%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVNEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRENKNG--LTVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ + S  
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSPEKARRVLHATGADGLLIGRAAQGRPWIFREIEHFLSTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P    V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 ETLPAPELFEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATLPGAREFRAH 302


>gi|78484786|ref|YP_390711.1| dihydrouridine synthase TIM-barrel protein nifR3 [Thiomicrospira
           crunogena XCL-2]
 gi|78363072|gb|ABB41037.1| Dihydrouridine synthase [Thiomicrospira crunogena XCL-2]
          Length = 320

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 136/322 (42%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M   TDR YR   R  +  +   +EM+ +   LR   K+    +  T+  P  +Q+ G  
Sbjct: 17  MAGITDRVYRDICRE-SGASYAVSEMVASKKQLRESAKSSTRHADKTETSPRIVQLLGTH 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +LV+AA   +  G + I+LN+GCP+ +V + + G+ LM  P+ V D   ++ +A+ +P
Sbjct: 76  PEELVDAALWQQSQGADIIDLNMGCPAKKVCDVAAGSALMGQPERVADIFKSLTEAIDLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D  +  +    + K  ++ G+  I IH R         + ++     +YD 
Sbjct: 136 VTVKIRTGTD--VDNINAVEIAKLAQELGLKAITIHGRT--------RADKFNGQAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+   D+ +  NG +    +A  +L     DG+MIGRAA     +   +  +    
Sbjct: 186 IKAVKQAV-DIPVIANGDICSPKEAQFVLKYTGSDGIMIGRAAQGYPWIFREIAHFLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               SP      +   R  S     Y   HL      +   +H+       PN    R  
Sbjct: 245 DCLPSPSFAEFQQVMTRHFSELEILY-GEHLGH----KIARKHLGWYSQYLPNGTELRKR 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                    A  ++I   F+ +
Sbjct: 300 FNRLENT-QAQLNLINHYFDTL 320


>gi|119953021|ref|YP_945230.1| tRNA-dihydrouridine synthase A [Borrelia turicatae 91E135]
 gi|119861792|gb|AAX17560.1| NIFR3-like protein [Borrelia turicatae 91E135]
          Length = 335

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 110/328 (33%), Positives = 175/328 (53%), Gaps = 17/328 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV  TD H+R+  RLL+    LYT MI A +I+ G    I+  +  + P+A+QI     +
Sbjct: 12  MVAITDEHFRYIIRLLSKKVTLYTPMISAKSIIMGKLNTIVKQTPTDSPIAIQIATDCEN 71

Query: 61  KLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +A +I+E+ F ++E NLNVGCPS+RV + ++GACLM  P  VG  + AM K  + PV
Sbjct: 72  DAAKAIEILENKFNFDEYNLNVGCPSSRVQDANYGACLMQTPTQVGKILQAMKKNTNKPV 131

Query: 120 TVKCRIGVDD------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++K RIG+        +     L+  V+ I +  +    IHAR AIL G SPKDN+ IP 
Sbjct: 132 SIKHRIGIRHNKREYHETNYRELKQFVEKIIEYEIKNFTIHARVAILNGYSPKDNQNIPK 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L +++VY++K+++ ++FI +NGG+   +     L  VD VMIGRAA K+   +  +   F
Sbjct: 192 LRHELVYQLKQDHKNIFIEINGGIISSNHIKTHLSYVDSVMIGRAAAKDPYFIAKISREF 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L     I TR       ++   M +Y   + +    +  I +H++ +     N+R+ 
Sbjct: 252 ---LEEKEKIPTR------EEVLLKMVEYIKEY-NEHLSINTILKHIMRIVFAKDNARKF 301

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R IL+     +   H I+ +A   + E 
Sbjct: 302 RQILSAPFPKNLKNHEILLSAIEHLRED 329


>gi|118475847|ref|YP_892998.1| NifR3 family TIM-barrel protein [Bacillus thuringiensis str. Al
           Hakam]
 gi|229089207|ref|ZP_04220489.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-42]
 gi|229182470|ref|ZP_04309722.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BGSC 6E1]
 gi|118415072|gb|ABK83491.1| tRNA-U20-dihydrouridine synthase [Bacillus thuringiensis str. Al
           Hakam]
 gi|228601050|gb|EEK58618.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BGSC 6E1]
 gi|228694170|gb|EEL47851.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock3-42]
          Length = 339

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 307


>gi|269215243|ref|ZP_05987998.2| tRNA-dihydrouridine synthase B [Neisseria lactamica ATCC 23970]
 gi|269207980|gb|EEZ74435.1| tRNA-dihydrouridine synthase B [Neisseria lactamica ATCC 23970]
          Length = 366

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRDF-GAGWAVCEMLASDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ KA  +P
Sbjct: 106 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHKNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKCRL-NIPVWVNGDITSPQKAQTVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIGEMPDGEQTRRD 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A +  +      +
Sbjct: 330 IN-RLDSAAAQYDTLAGYLERV 350


>gi|118473981|ref|YP_890003.1| tRNA-dihydrouridine synthase [Mycobacterium smegmatis str. MC2 155]
 gi|118175268|gb|ABK76164.1| tRNA-dihydrouridine synthase, putative [Mycobacterium smegmatis
           str. MC2 155]
          Length = 389

 Score =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 132/327 (40%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+ +E P +L
Sbjct: 29  MAGVTNVAFRTLCRELEIARAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPENTYKAAKMIVDEDLADHIDMNFGCPVPKVTKRGGGAALPYKRRLFGQIVAAA 148

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD+       +  +   + G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDDEHH--THLDAGRIAAEEGAAAVALHARTA--------AQ 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K     + +  NG + +   + A+      DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIAALKAHVTGIPVLGNGDIFEADDALAMMAATGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+N    + P    V       I     +  +RH      ++ I +H+    HG
Sbjct: 259 AELSAAFNNRPIPTPPTLGEVA-----DIVRRHGELLSRHFGEDKGMRDIRKHVAWYLHG 313

Query: 287 FPNSRRCRHILTVEAGASTATHHIIET 313
           FP     R  L +          +++ 
Sbjct: 314 FPAGADLRRALALVKTRRELD-ELLDQ 339


>gi|240122834|ref|ZP_04735790.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID332]
          Length = 364

 Score =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 330 INRLDNAA-AQYDTLAGYLERL 350


>gi|309778095|ref|ZP_07673033.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 3_1_53]
 gi|308914154|gb|EFP59956.1| zinc-binding TIM-barrel protein, nifR3 family [Erysipelotrichaceae
           bacterium 3_1_53]
          Length = 338

 Score =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 122/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+YTEM+   A+   ++K   +     QE PL +QI G D
Sbjct: 22  MAGISNPAFRVICKEF-GAGLIYTEMVSDKALYYDNEKTVGMTDVEEQEHPLTMQIFGHD 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  +V AAK +++    + I++N+GCP  ++ +   G+ LM + D   +   A+ +++  
Sbjct: 81  IETMVYAAKFLDEKTACDIIDINMGCPVTKIVKSFAGSALMKDVDHAVEMSRAVVQSVKK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D  +  +    L K ++  GV  + +H R         K      + D+ 
Sbjct: 141 PVTVKMRIGWD--MDQITCVELAKGLEAVGVQALAVHGRT--------KKQMYEGSADWS 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG +     A ++L     D VMIGR    +  ++  +  Y   
Sbjct: 191 YIRRVK-EAVSIPVMGNGDVRSGEDAQRMLEETGCDAVMIGRGVLGDPWLIKDIVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                                                ++++  H      G P S + + 
Sbjct: 250 REHMPEVTLEEKFAMARLHAKRLCNLKGEF-----VGIREMRGHAAWYVKGLPKSHQLKD 304

Query: 296 ILT 298
            LT
Sbjct: 305 QLT 307


>gi|240127544|ref|ZP_04740205.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-93-1035]
          Length = 372

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 114 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 174 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 337

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 338 INRLDNAA-AQYDTLAGYLERL 358


>gi|92114408|ref|YP_574336.1| dihydrouridine synthase TIM-barrel protein nifR3 [Chromohalobacter
           salexigens DSM 3043]
 gi|91797498|gb|ABE59637.1| tRNA-U20-dihydrouridine synthase [Chromohalobacter salexigens DSM
           3043]
          Length = 343

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 137/317 (43%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L+ +EM+ +D  L   +K+   L  + +  P A+QI G D
Sbjct: 29  MAGVTDRPFRQLCREL-GAGLVVSEMVTSDTRLWHTRKSRQRLDHTGEPGPRAVQIAGGD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L EAA++    G   +++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 88  AAMLAEAARLNVAQGAEIVDINMGCPAKKVCNKAAGSALLRDERLVAEILEAVVAAVDVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   Q        + K  + +G+  + +H R         ++ R     +YD 
Sbjct: 148 VTLKIRTGWCPQTRNGV--RVAKLAESAGIQALAVHGRT--------REQRYRGEAEYDT 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    L +  NG ++   +A ++L     D VMIGR A  N  +   +D Y    
Sbjct: 198 IAAIKQAV-SLPVFANGDIDGAEKAARVLDYTKADAVMIGRGAQGNPWIFREIDHYLRTG 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R + A    Y     H G ++    +H+       P +   R  
Sbjct: 257 DCLPRPTPDDIATLMHRHLEALHAFYGE---HMGVRI--ARKHVGWYLATQPQAAALRAR 311

Query: 297 LTVEAGASTATHHIIET 313
             V     +A H  ++ 
Sbjct: 312 FNVLEQ-PSAQHRFVDA 327


>gi|241668651|ref|ZP_04756229.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877184|ref|ZP_05249894.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843205|gb|EET21619.1| tRNA-dihydrouridine synthase [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 324

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 140/324 (43%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENIEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + D + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVDKIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG DD+   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDDE--NINAIEVAKACEDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +     +   +    A+       +++I  H        P S+  R
Sbjct: 247 TGELIPPPTPVERVEVLGEHLRRLIKLKTAK-----VAVKEIRTHASFYLADLPGSKEFR 301

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
             L            ++E   N  
Sbjct: 302 MKLNQLEHERE-IFRVLEEYSNSF 324


>gi|52145141|ref|YP_081688.1| NifR3 family TIM-barrel protein [Bacillus cereus E33L]
 gi|196041789|ref|ZP_03109079.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           NVH0597-99]
 gi|196047389|ref|ZP_03114602.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB108]
 gi|225862129|ref|YP_002747507.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB102]
 gi|51978610|gb|AAU20160.1| possible TIM-barrel protein, NifR3 family [Bacillus cereus E33L]
 gi|196021791|gb|EDX60485.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB108]
 gi|196027409|gb|EDX66026.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           NVH0597-99]
 gi|225787877|gb|ACO28094.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus 03BB102]
          Length = 332

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 300


>gi|228912815|ref|ZP_04076463.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228925329|ref|ZP_04088426.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228931578|ref|ZP_04094485.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228943882|ref|ZP_04106268.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229119738|ref|ZP_04249000.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 95/8201]
 gi|228663763|gb|EEL19341.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 95/8201]
 gi|228815839|gb|EEM62074.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228828130|gb|EEM73857.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228834376|gb|EEM79916.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228846875|gb|EEM91879.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 339

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 307


>gi|47525329|ref|YP_016678.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49183110|ref|YP_026362.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. Sterne]
 gi|47500477|gb|AAT29153.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           'Ames Ancestor']
 gi|49177037|gb|AAT52413.1| TIM-barrel protein, putative, NifR3 family [Bacillus anthracis str.
           Sterne]
          Length = 324

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 10  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 68

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 69  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 129 PVTVKMRIGWDED--HIFAIENAKAVERAGGQVVAVHGRTRV--------QMYEGKADWD 178

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 179 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 238 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 292


>gi|237809273|ref|YP_002893713.1| TIM-barrel protein, nifR3 family [Tolumonas auensis DSM 9187]
 gi|237501534|gb|ACQ94127.1| TIM-barrel protein, nifR3 family [Tolumonas auensis DSM 9187]
          Length = 322

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 56/299 (18%), Positives = 126/299 (42%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +D+ +R     +    +  +EM+ A+       K++  +  + +    A+QI G++
Sbjct: 17  MAGVSDQPFRQLCLRM-GAGMAVSEMMSANPDTWDTDKSLKRMYLADEPGIRAVQIVGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   +++N+GCP+ +++    G+ L+ +P +V + +  +  A+ +P
Sbjct: 76  PEWMADAARRSVSEGAQIVDINMGCPAKKINRRLAGSALLQDPALVREILQTVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  +  GV  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDTEHRNG--LEIAEIAESCGVQALTVHGRT--------RACLFNGQAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     D +MIGRAA     + + +  + ++ 
Sbjct: 186 IRAIKQHI-SIPVVANGDIDTPQKAQAVLEYTGADAIMIGRAAQGQPWLFSRIRHFLTHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               SP    V       ++A    Y          ++   +H+      + +++  R 
Sbjct: 245 SDLPSPEWDAVRIIVLEHVAALHQFY-----GEYKGVRFARKHVAWYLERYGSAKHFRR 298


>gi|145590054|ref|YP_001156651.1| nifR3 family TIM-barrel protein [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048460|gb|ABP35087.1| tRNA-U20-dihydrouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
          Length = 338

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 139/327 (42%), Gaps = 27/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A+L   +K         + KP+A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVASNALLWKSEKTQRRANHIGEFKPIAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + +  AAKI  D G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+   
Sbjct: 76  PAMMAAAAKINVDHGAQIIDINMGCPAKKVCNVAAGSALLRDEPLVQQILEAVVNAVGVG 135

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVT+K R G D +        + +  +KSG++ + +H R         + +     
Sbjct: 136 PDAVPVTLKIRTGWDREHKNAI--EIARLAEKSGISMLTVHGRT--------RADLYHGE 185

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K  + ++ +  NG +    +A ++L     D +MIGRAA     +   ++ 
Sbjct: 186 AEYETITAVKN-SVNIPVVANGDIHSPEKAEQVLKITGADAIMIGRAAQGRPWIFREINH 244

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           Y        +P    +       +      Y   H+     L+   +H+     G  +S 
Sbjct: 245 YLETGGKLPTPEINEIQAIMNAHLLDHYEFY-GEHIG----LRTARKHIGWYCKGLRDSH 299

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
             R  +   A        ++   FN M
Sbjct: 300 AFRQRMNT-ADDCKTQLQMVNDYFNEM 325


>gi|298708539|emb|CBJ49172.1| FAD binding / catalytic/ tRNA dihydrouridine synthase [Ectocarpus
           siliculosus]
          Length = 469

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 111/334 (33%), Positives = 168/334 (50%), Gaps = 22/334 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQ-EKPLALQIGGA 57
           M+++TDRH R+  RLLT   +L+TEM+ +  I+    D    L ++ + E P+ LQIGG+
Sbjct: 87  MMEYTDRHMRYLLRLLTTRTVLWTEMVPSSTIIHNPDDLGRFLDYNEEVEHPVVLQIGGS 146

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKAL- 115
           D + + EA ++   + Y+ INLN GCPS +V     FGA LM +P +V D   AM     
Sbjct: 147 DTTDVREACRLARPYKYDAINLNCGCPSEKVAGKGAFGAALMRSPSLVKDLCLAMKDGAG 206

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPN 173
              P+TVKCRIGVD+      L   V+ + + +GV    +HARKAIL GLSP  NR IP 
Sbjct: 207 EDTPITVKCRIGVDNDDSYEQLAAFVEEVSRGAGVPHFIVHARKAILGGLSPAQNRNIPP 266

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           L YD VY + K+ PD+   LNGG+    +A+  L     GVM+GR+   N    +  D  
Sbjct: 267 LKYDFVYRLVKDFPDVDFTLNGGVNTYEEAVSCLEQGAHGVMVGRSWSSNPWYWSQADSM 326

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-----LQQITRHMIGLFHGF 287
                    P  TR      R++     +Y  R   + G+      +++ + +  +FHG 
Sbjct: 327 LFG---AKDPGLTR------REVLERYAEYGERQEKACGEKWLACRRRLAKPIWHMFHGE 377

Query: 288 PNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
              ++ R  L        +   I++ +   M + 
Sbjct: 378 KGGKKFRVALEGMLREDKSFGEIVQKSLLAMPQD 411


>gi|15607963|ref|NP_215338.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           H37Rv]
 gi|15840236|ref|NP_335273.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis CDC1551]
 gi|148660601|ref|YP_001282124.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis H37Ra]
 gi|148822029|ref|YP_001286783.1| transcriptional regulator [Mycobacterium tuberculosis F11]
 gi|215410393|ref|ZP_03419201.1| transcriptional regulator [Mycobacterium tuberculosis 94_M4241A]
 gi|218752486|ref|ZP_03531282.1| transcriptional regulator [Mycobacterium tuberculosis GM 1503]
 gi|219556682|ref|ZP_03535758.1| transcriptional regulator [Mycobacterium tuberculosis T17]
 gi|253797770|ref|YP_003030771.1| transcriptional regulator [Mycobacterium tuberculosis KZN 1435]
 gi|254231135|ref|ZP_04924462.1| hypothetical protein TBCG_00813 [Mycobacterium tuberculosis C]
 gi|254549795|ref|ZP_05140242.1| transcriptional regulator [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260185716|ref|ZP_05763190.1| transcriptional regulator [Mycobacterium tuberculosis CPHL_A]
 gi|260199838|ref|ZP_05767329.1| transcriptional regulator [Mycobacterium tuberculosis T46]
 gi|289442226|ref|ZP_06431970.1| transcriptional regulator [Mycobacterium tuberculosis T46]
 gi|289446387|ref|ZP_06436131.1| transcriptional regulator [Mycobacterium tuberculosis CPHL_A]
 gi|289553080|ref|ZP_06442290.1| transcriptional regulator [Mycobacterium tuberculosis KZN 605]
 gi|289568776|ref|ZP_06449003.1| transcriptional regulator [Mycobacterium tuberculosis T17]
 gi|289749339|ref|ZP_06508717.1| transcriptional regulator [Mycobacterium tuberculosis T92]
 gi|289760952|ref|ZP_06520330.1| transcriptional regulatory protein [Mycobacterium tuberculosis GM
           1503]
 gi|297633335|ref|ZP_06951115.1| transcriptional regulator [Mycobacterium tuberculosis KZN 4207]
 gi|297730319|ref|ZP_06959437.1| transcriptional regulator [Mycobacterium tuberculosis KZN R506]
 gi|298524313|ref|ZP_07011722.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|306774946|ref|ZP_07413283.1| transcriptional regulator [Mycobacterium tuberculosis SUMu001]
 gi|306783489|ref|ZP_07421811.1| transcriptional regulator [Mycobacterium tuberculosis SUMu003]
 gi|306787853|ref|ZP_07426175.1| transcriptional regulator [Mycobacterium tuberculosis SUMu004]
 gi|306796592|ref|ZP_07434894.1| transcriptional regulator [Mycobacterium tuberculosis SUMu006]
 gi|306802450|ref|ZP_07439118.1| transcriptional regulator [Mycobacterium tuberculosis SUMu008]
 gi|306966858|ref|ZP_07479519.1| transcriptional regulator [Mycobacterium tuberculosis SUMu009]
 gi|307078781|ref|ZP_07487951.1| transcriptional regulator [Mycobacterium tuberculosis SUMu011]
 gi|308370149|ref|ZP_07420479.2| transcriptional regulator [Mycobacterium tuberculosis SUMu002]
 gi|308378726|ref|ZP_07483710.2| transcriptional regulator [Mycobacterium tuberculosis SUMu010]
 gi|313657644|ref|ZP_07814524.1| transcriptional regulator [Mycobacterium tuberculosis KZN V2475]
 gi|6647988|sp|O53835|DUS_MYCTU RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|2916881|emb|CAA17629.1| POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [Mycobacterium
           tuberculosis H37Rv]
 gi|13880393|gb|AAK45087.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis CDC1551]
 gi|124600194|gb|EAY59204.1| hypothetical protein TBCG_00813 [Mycobacterium tuberculosis C]
 gi|148504753|gb|ABQ72562.1| NifR3/SMM1 family protein [Mycobacterium tuberculosis H37Ra]
 gi|148720556|gb|ABR05181.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis F11]
 gi|253319273|gb|ACT23876.1| transcriptional regulator [Mycobacterium tuberculosis KZN 1435]
 gi|289415145|gb|EFD12385.1| transcriptional regulator [Mycobacterium tuberculosis T46]
 gi|289419345|gb|EFD16546.1| transcriptional regulator [Mycobacterium tuberculosis CPHL_A]
 gi|289437712|gb|EFD20205.1| transcriptional regulator [Mycobacterium tuberculosis KZN 605]
 gi|289542530|gb|EFD46178.1| transcriptional regulator [Mycobacterium tuberculosis T17]
 gi|289689926|gb|EFD57355.1| transcriptional regulator [Mycobacterium tuberculosis T92]
 gi|289708458|gb|EFD72474.1| transcriptional regulatory protein [Mycobacterium tuberculosis GM
           1503]
 gi|298494107|gb|EFI29401.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           94_M4241A]
 gi|308216500|gb|EFO75899.1| transcriptional regulator [Mycobacterium tuberculosis SUMu001]
 gi|308325163|gb|EFP14014.1| transcriptional regulator [Mycobacterium tuberculosis SUMu002]
 gi|308331710|gb|EFP20561.1| transcriptional regulator [Mycobacterium tuberculosis SUMu003]
 gi|308335508|gb|EFP24359.1| transcriptional regulator [Mycobacterium tuberculosis SUMu004]
 gi|308342985|gb|EFP31836.1| transcriptional regulator [Mycobacterium tuberculosis SUMu006]
 gi|308350809|gb|EFP39660.1| transcriptional regulator [Mycobacterium tuberculosis SUMu008]
 gi|308355442|gb|EFP44293.1| transcriptional regulator [Mycobacterium tuberculosis SUMu009]
 gi|308359398|gb|EFP48249.1| transcriptional regulator [Mycobacterium tuberculosis SUMu010]
 gi|308363303|gb|EFP52154.1| transcriptional regulator [Mycobacterium tuberculosis SUMu011]
 gi|328457549|gb|AEB02972.1| transcriptional regulator [Mycobacterium tuberculosis KZN 4207]
          Length = 389

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 125/313 (39%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 148

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|167967511|ref|ZP_02549788.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis H37Ra]
 gi|215426084|ref|ZP_03424003.1| transcriptional regulator [Mycobacterium tuberculosis T92]
 gi|306806659|ref|ZP_07443327.1| transcriptional regulator [Mycobacterium tuberculosis SUMu007]
 gi|308397233|ref|ZP_07492455.2| transcriptional regulator [Mycobacterium tuberculosis SUMu012]
 gi|308346868|gb|EFP35719.1| transcriptional regulator [Mycobacterium tuberculosis SUMu007]
 gi|308366954|gb|EFP55805.1| transcriptional regulator [Mycobacterium tuberculosis SUMu012]
 gi|323720747|gb|EGB29819.1| transcriptional regulator [Mycobacterium tuberculosis CDC1551A]
          Length = 377

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 125/313 (39%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 17  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 77  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 137 VRATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSALRRALAM 314


>gi|261206686|ref|ZP_05921384.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium TC 6]
 gi|289565048|ref|ZP_06445502.1| tRNA-dihydrouridine synthase 1 [Enterococcus faecium D344SRF]
 gi|294614891|ref|ZP_06694782.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1636]
 gi|260079179|gb|EEW66872.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium TC 6]
 gi|289163255|gb|EFD11101.1| tRNA-dihydrouridine synthase 1 [Enterococcus faecium D344SRF]
 gi|291592177|gb|EFF23795.1| tRNA-dihydrouridine synthase B [Enterococcus faecium E1636]
          Length = 331

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 83/326 (25%), Positives = 134/326 (41%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 21  MAGITNSAFRVTVKEF-GAGLVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGN 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE+    + I++N+GCP  +V +   GA  +L+P+ V + + A+  A+ I
Sbjct: 80  KDSLVEAAQFVEENTAADIIDINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVDI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   V       + + +G + I +H R  +               D++
Sbjct: 140 PVTVKMRIGWDEE--HVFAVENALAAQSAGASAIAMHGRTRV--------QMYEGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+     Y   
Sbjct: 190 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +        A         ++   H      G P + + + 
Sbjct: 249 GELIPEPTPAEKIATAKLHLQR-----LADLKGEKVACREFRTHAAYYLKGIPRAAKVKV 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +       T     I    +  +E 
Sbjct: 304 AIN-----QTEKQQEINDLLDQFVEK 324


>gi|49481554|ref|YP_034429.1| NifR3 family TIM-barrel protein [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|167635018|ref|ZP_02393335.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0442]
 gi|170688920|ref|ZP_02880122.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0465]
 gi|196036383|ref|ZP_03103780.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus W]
 gi|254682297|ref|ZP_05146158.1| NifR3 family TIM-barrel protein [Bacillus anthracis str.
           CNEVA-9066]
 gi|254744620|ref|ZP_05202299.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. Kruger B]
 gi|300119171|ref|ZP_07056872.1| NifR3 family TIM-barrel protein [Bacillus cereus SJ1]
 gi|49333110|gb|AAT63756.1| possible TIM-barrel protein, NifR3 family [Bacillus thuringiensis
           serovar konkukian str. 97-27]
 gi|167529492|gb|EDR92242.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0442]
 gi|170667144|gb|EDT17905.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0465]
 gi|195991013|gb|EDX54984.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus W]
 gi|298723493|gb|EFI64234.1| NifR3 family TIM-barrel protein [Bacillus cereus SJ1]
          Length = 332

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 300


>gi|330807319|ref|YP_004351781.1| tRNA-dihydrouridine synthase B [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327375427|gb|AEA66777.1| tRNA-dihydrouridine synthase B [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 335

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 134/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLAEAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVTEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +     +  + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRENKNGLV--VAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAAIKQAV-SIPVFANGDVDSPEKARYVLDATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              + P  + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 EKLAPPQLSEVERILLEHLAALHAFY-----GEVMGVRIARKHVGWYLATLPGAREFR 300


>gi|228919026|ref|ZP_04082406.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840675|gb|EEM85936.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 324

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 138/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 10  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 68

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 69  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 129 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 178

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 179 IIKQVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 238 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 292


>gi|229188361|ref|ZP_04315410.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 10876]
 gi|228595160|gb|EEK52930.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus ATCC 10876]
          Length = 324

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 137/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 10  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 68

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 69  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 129 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 178

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 179 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 238 GELMPEPTVREKI-----DVCMLHLDRLINLKNESVAVREMRKHAAWYLKGVRGNASVRN 292


>gi|20257536|gb|AAM15930.1|AF494454_1 NifR3-like protein [Gluconacetobacter diazotrophicus]
          Length = 325

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 134/307 (43%), Gaps = 22/307 (7%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKL 62
           TD  +R  AR L    L+ +EMI + A++R ++    +   +  + P A+Q+ G +   +
Sbjct: 2   TDLPFRRLARRL-GAGLVISEMIASWAMVRENQATLRMAEVADDDGPNAVQLAGCEPEAM 60

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +AA+I  D G + +++N GCP  +V      G+ LM +  +    + A+ +A+ +PVT+
Sbjct: 61  AQAARIAVDRGADMVDINFGCPVKKVAVGQQAGSALMRDEALAARLLDAVVRAVDVPVTL 120

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    ++    L +  +++G+  + +H R         +        D+  V +
Sbjct: 121 KMRMGWD--HASLNAPALARIAEQTGIRMVTVHGRT--------RQQFYNGTADWSFVRQ 170

Query: 182 IKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K +   L + +NG ++ +  A +   L   DGVMIGR  Y     L  V +  +     
Sbjct: 171 VK-DAVSLPVIVNGDIQTVDDARQALALSGADGVMIGRGCYGRPWFLAQVAQALTTGDIV 229

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             P     D    + I     D    H  +   L+   +H+     G P+S   R  +  
Sbjct: 230 PDP-----DLATEKAIVLDHYDMMLSHFGAHPGLRLARKHVAWYSAGLPDSAGFRAAINR 284

Query: 300 EAGASTA 306
              A  A
Sbjct: 285 VDQAQEA 291


>gi|218901278|ref|YP_002449112.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH820]
 gi|218538152|gb|ACK90550.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH820]
          Length = 332

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 143/327 (43%), Gaps = 27/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESIAVREMRKHAAWYLKGIRGNANVRN 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +             +    ++ +E +
Sbjct: 301 GINACNTRED-----LANVLDVFVEEV 322


>gi|227541059|ref|ZP_03971108.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227183319|gb|EEI64291.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 405

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 70/312 (22%), Positives = 124/312 (39%), Gaps = 30/312 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        + + L   EM+ A A++  + K   +  FS+ E+P +L
Sbjct: 53  MAGVTNVAFRLLCREQELEKAGSVSGLYVCEMVTARALVERNVKTLHMAAFSSVEEPRSL 112

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK I E+   + +++N GCP  +V     GA L    ++    + A 
Sbjct: 113 QLYTTDPEYTYKAAKMIAEENLADHLDMNFGCPVPKVTRKGGGAALPYKRELFKRIVDAA 172

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            + +    IPVTVK RIG+D +     + +  +  ++ G   + +HAR A          
Sbjct: 173 VRGVSGTDIPVTVKFRIGIDAE--HETMLDAGRIAQEEGAAAVTLHARTA--------AE 222

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R      ++ + E+K+   D+ +  NG +   +  L +      DG+ IGR       + 
Sbjct: 223 RYSGQAHWERIAELKQAL-DVPVFGNGDVFSAADGLAMFEQTGCDGIEIGRGCLGRPWLF 281

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           + +    S       P    V       I     +  A H       + I +H+   F G
Sbjct: 282 SDLALALSGRPVPPPPTLGEVCT-----ILRRHAELLAIHQGEASACRDIRKHVGWYFRG 336

Query: 287 FPNSRRCRHILT 298
           +      R  L+
Sbjct: 337 YAVGGSFRASLS 348


>gi|294508555|ref|YP_003572614.1| tRNA-dihydrouridine synthase B [Salinibacter ruber M8]
 gi|294344884|emb|CBH25662.1| tRNA-dihydrouridine synthase B [Salinibacter ruber M8]
          Length = 492

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 142/326 (43%), Gaps = 25/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE + +  +LR  +     L    +E+P+ +Q+ G  
Sbjct: 131 MEDVSDPPFRILCKRY-GADMMYTEFVSSAGLLREQEHEHQKLEIFDEERPIGIQVWGGG 189

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I ++  A  +V+  G + I++N GCP  ++ +   GA ++ N D + +  AA+ +  + P
Sbjct: 190 IDEVRNATPMVDAAGPDVIDINFGCPVRKIVQKDGGAGVLRNLDKMRNITAAVMEEATRP 249

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD   ++ + ++ + ++  GV  + +HAR         ++ +   +  ++ 
Sbjct: 250 VTVKTRLGWDDD--SIHIVDVARMLEDMGVAALTVHART--------REQKYKGDARWEW 299

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+E   D+    NG   D      +     VDGVM+GR A  N  +     +Y   
Sbjct: 300 LRTIKEEGTRDMPFIGNGDALDPEAIEAMFEETGVDGVMLGRGALGNPWIFERAKKYMET 359

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P     D +   ++ A         L     + ++ ++    F GF N+   RH
Sbjct: 360 GELPPPP-----DWEERVQVVAEHLSLKCEWLGERTGVMEMRKNYSSYFKGFRNASTLRH 414

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L      +     ++E   N   ++
Sbjct: 415 ELMQPETKAG----VLEVMLNFKPDA 436


>gi|239998283|ref|ZP_04718207.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 35/02]
 gi|240114998|ref|ZP_04729060.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID18]
          Length = 364

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 330 INRLDNAA-AQYDTLAGYLERL 350


>gi|312871514|ref|ZP_07731607.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 3008A-a]
 gi|311092909|gb|EFQ51260.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 3008A-a]
          Length = 331

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 126/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++     E P++LQI G  
Sbjct: 21  MAGISNAAFRMVCKQF-GAGLVVCEMISDHGIIYRNKKTLEMMKIDPNEHPMSLQIFGGS 79

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+D    + IN+N+GCP  +V +   GA  +L+PD +   + A+   +  
Sbjct: 80  EETLVEAARYVDDNTHADIININMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G   + +H R         +      + D+ 
Sbjct: 140 PVTVKMRTGWDEDHIYAVENALA--AQEAGACAVAMHGRT--------RKQLYTGHADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+       F+G NG +     A K+L       VM+GRA   N  +L  +  Y   
Sbjct: 190 ILKEVSDALTIPFVG-NGDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S             ++                 + +  R       G P S R R 
Sbjct: 249 GELLSPQTVEERVITCKEQLRK-----LVELKGEKIAVPEFRRQAAYYLKGIPRSARTRA 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +  +       +++++     +   L
Sbjct: 304 KIN-DVWTQQEVYNLLDEFVENLESKL 329


>gi|226309767|ref|YP_002769661.1| tRNA-dihydrouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226092715|dbj|BAH41157.1| probable tRNA-dihydrouridine synthase [Brevibacillus brevis NBRC
           100599]
          Length = 342

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 79/303 (26%), Positives = 134/303 (44%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+    I+ G+KK   +L    +EKPL+LQI G D
Sbjct: 17  MAGVCNPAFRLIAKEF-GTGLVCAEMVSDKGIVHGNKKTIDMLFVDEREKPLSLQIFGGD 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+     + I++N+GCP  ++     GA L+L+PD + + ++++  A+  
Sbjct: 76  KETLVSAAKYVDQHTNADIIDINMGCPVPKITSCDAGARLLLDPDKIYEVVSSVVDAVDK 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    V   +  K+++++G   I +H R  +               D+D
Sbjct: 136 PVTVKMRLGWDEDHLYV--LDNAKAVERAGGKAIAVHGRTRV--------QMYKGKADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG +     A ++L     DGVMIGRAA  N  ML    +Y + 
Sbjct: 186 WIRRVK-ETVSIPVIGNGDVATPEDARRMLDTTGCDGVMIGRAALGNPWMLYRTIQYLTT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              G  P                +     R       + ++ +H      G   S   ++
Sbjct: 245 GELGPEPTAREKMNICLLHAERLIALKGPR-----VGVLEMRKHAAYYLKGLKGSTHTKN 299

Query: 296 ILT 298
           ++ 
Sbjct: 300 LVN 302


>gi|118589891|ref|ZP_01547295.1| tRNA-dihydrouridine synthase, putative [Stappia aggregata IAM
           12614]
 gi|118437388|gb|EAV44025.1| tRNA-dihydrouridine synthase, putative [Stappia aggregata IAM
           12614]
          Length = 334

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 70/287 (24%), Positives = 130/287 (45%), Gaps = 20/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD  +R  A       ++ +EM+ +++ ++GD +  +    Q+K L  +Q+ G + 
Sbjct: 20  MSGVTDLPFRRLAARY-GAGMVVSEMVASESFVKGDAETQMRAEAQDKGLHVVQLAGREA 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAK+V   G + I++N+GCP+ +V  G  G+ LM + D     I A   A+ IPV
Sbjct: 79  RWMGEAAKVVAGLGADVIDINMGCPAKKVTSGYSGSALMRDLDHALTLIEATVAAVDIPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+  ++    L +  + +G+  I +H R         +      N D+  +
Sbjct: 139 TLKMRLGWDDK--SLNAPELARRAEAAGIKLITVHGRT--------RCQFYKGNADWRAI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  NG  +    AL++L     DGVMIGR AY    +   +  + +   
Sbjct: 189 AAVKEAI-SVPLIANGDCKGFENALRMLELSGADGVMIGRGAYGRPWLPGHIGHFLATGE 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +P    + +       A ++ Y  R       ++   +H+    
Sbjct: 248 KLEAPRGAELAELVAEHYEAVLSHYGERQ-----GVRIARKHLGWYL 289


>gi|257057698|ref|YP_003135530.1| putative TIM-barrel protein, nifR3 family [Saccharomonospora
           viridis DSM 43017]
 gi|256587570|gb|ACU98703.1| putative TIM-barrel protein, nifR3 family [Saccharomonospora
           viridis DSM 43017]
          Length = 379

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 126/318 (39%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EMI A A++       +++ F   E P ++Q+ G D
Sbjct: 26  MAGITNVAFRRLCREY-GAGLYVCEMITARAVVERHPGTMHMMTFDASEYPRSMQLYGVD 84

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            + + EA KI+   G  + I+ N GCP A+V     GA L     + G+ + A  +A   
Sbjct: 85  PATMKEAVKIIVGEGLADHIDANFGCPVAKVTRKGGGAALPFKRKLFGNIVRASVEAAEP 144

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P TVK R+G+DD        +  +  +  G   + +HAR A          R     
Sbjct: 145 AGVPFTVKFRVGIDDDHH--TYLDAGRIAEAEGAAAVALHARTA--------AQRYSGKA 194

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K+    + +  NG +     AL+++     DGV+IGR       +   ++  
Sbjct: 195 DWSHIARLKEAVTSIPVLGNGDIFTAHDALRMVAETGCDGVVIGRGCLGRPWLFGELEAA 254

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+     + P    V +     +     +    H      ++ + +HM   F GFP   +
Sbjct: 255 FAGKPIPAGPNLGEVAR-----VLRRHAELLVEHDGPDKAMRDLRKHMAWYFMGFPVGSQ 309

Query: 293 CRHILTVEAGASTATHHI 310
            R    + +        I
Sbjct: 310 LRRRFAMVSSLDELDELI 327


>gi|308270351|emb|CBX26963.1| Probable tRNA-dihydrouridine synthase [uncultured Desulfobacterium
           sp.]
          Length = 351

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 128/321 (39%), Gaps = 23/321 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              T+  +R  A+      L+ +EM+ A+ I+ G KK   +L   ++E+P++ QI G+D 
Sbjct: 43  AGITNLPFRLIAKR-AGCGLVCSEMVSANGIVYGSKKTLGMLDSLSEERPVSFQIFGSDP 101

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA IVE  G + I++N GC   +V +   G  LM  P      + A+ K + IPV
Sbjct: 102 LIMAEAAVIVESSGADIIDINFGCSVKKVVKTGAGVALMKEPGRTEAILMAIKKCVKIPV 161

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G +            K  +  G++ I +H R A                D+ ++
Sbjct: 162 TIKIRTGWEKTG--EQALKTAKIAEHCGIDAIAVHPRTASQGFR--------GLADWSVI 211

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+ N  + +  NG +     A+ +      D VMIGRAA  N  +   +    S   
Sbjct: 212 SRVKQ-NVSIPVIGNGDILTAYDAVSMQSQTGCDAVMIGRAAIGNPWIFEQIRALMSKEP 270

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              + +  R D               A +         +   +     G  ++ + R  +
Sbjct: 271 IAPASLAQRFDGM------KGYLKANAEYFGEKQACFMMRSRLGWFVKGLDSNAKFRESV 324

Query: 298 TVEAGASTATHHIIETAFNLM 318
                   A   II + ++ +
Sbjct: 325 KHITSEQEA-IDIINSYYDFL 344


>gi|307329095|ref|ZP_07608262.1| TIM-barrel protein, nifR3 family [Streptomyces violaceusniger Tu
           4113]
 gi|306885290|gb|EFN16309.1| TIM-barrel protein, nifR3 family [Streptomyces violaceusniger Tu
           4113]
          Length = 406

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 121/319 (37%), Gaps = 30/319 (9%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  D K +  + F   EKP ++Q+ G 
Sbjct: 34  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERDAKTMRLIHFDGSEKPRSIQLYGV 93

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 94  DPMTVGKAVQMIVDENLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRSILREAVTAAG 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 154 PLPVTMKMRKGIDDD--HITFLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K+  P++ +  NG +     A++++     DGV++GR       +   +   F
Sbjct: 204 WEAIARLKEAVPEIPVLGNGDIWSADDAVRMMRETGCDGVVVGRGCLGRPWLFGDLVAAF 263

Query: 234 SNPLTGS------------SPIKTRVDKDFWRKISASMTDYAARHLH-SGGKLQQITRHM 280
                              +P   R        +     +  A  L      +    +H+
Sbjct: 264 EPGQEAPVDGSEVPVSGSEAPGYPRPTLKEVAAVMRRHAELLAEWLEDEERGVIDFRKHV 323

Query: 281 IGLFHGFPNSRRCRHILTV 299
                GF      R  L +
Sbjct: 324 AWYTKGFSVGSEMRKRLAI 342


>gi|213968003|ref|ZP_03396149.1| TIM-barrel protein, NifR3 family [Pseudomonas syringae pv. tomato
           T1]
 gi|301383681|ref|ZP_07232099.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato Max13]
 gi|302059950|ref|ZP_07251491.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato K40]
 gi|302131616|ref|ZP_07257606.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato NCPPB 1108]
 gi|213927346|gb|EEB60895.1| TIM-barrel protein, NifR3 family [Pseudomonas syringae pv. tomato
           T1]
 gi|330873654|gb|EGH07803.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 337

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  AQMMADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ Y    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARHVLQATGADGLLIGRAAQGRPWIFREIEHYLLTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T  +   + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 ETLPALQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVGWYLATLPGAREFR 300


>gi|311740227|ref|ZP_07714059.1| dihydrouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
 gi|311304782|gb|EFQ80853.1| dihydrouridine synthase [Corynebacterium pseudogenitalium ATCC
           33035]
          Length = 379

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 125/310 (40%), Gaps = 31/310 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K   +  F+ QE P +L
Sbjct: 17  MAGVTNVAFRTLCREQELQRTGTVSGLYVCEMVTARALVERNEKTLHMTTFAPQEDPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           QI   D     +AAK++ D    + I++N GCP  +V     G+ L     + G+ ++A 
Sbjct: 77  QIYTVDPEYTYKAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA    +IPVTVK R+G+DD+       +  +   +SG   + +H R A          
Sbjct: 137 VKATEGTNIPVTVKMRVGIDDEHH--THLDAGRIAVESGAAAVTLHGRTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R      +D +  +K+   D  + +  NG +     A +++     DGV +GR       
Sbjct: 187 RYSGEARWDEIARLKEHLADTGVPVLGNGDIFRAEDARRMMEQTGCDGVQVGRGCLGRPW 246

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          + P    V +   R       +  A H       + I +H+    
Sbjct: 247 LFAELGAALRGESIPAEPTLGEVTQVILRHA-----ELLAEHDGEDNASRDIRKHIGWYL 301

Query: 285 HGFPNSRRCR 294
            GFP   + R
Sbjct: 302 RGFPVGGQVR 311


>gi|65317537|ref|ZP_00390496.1| COG0042: tRNA-dihydrouridine synthase [Bacillus anthracis str.
           A2012]
 gi|270000590|ref|NP_842644.2| NifR3 family TIM-barrel protein [Bacillus anthracis str. Ames]
 gi|269850221|gb|AAP24130.2| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Ames]
          Length = 339

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQVVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 307


>gi|69250952|ref|ZP_00605186.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium DO]
 gi|257879863|ref|ZP_05659516.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257882589|ref|ZP_05662242.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|257891704|ref|ZP_05671357.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257894179|ref|ZP_05673832.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|258614292|ref|ZP_05712062.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecium
           DO]
 gi|260559535|ref|ZP_05831716.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium C68]
 gi|293563202|ref|ZP_06677658.1| NifR3 family protein [Enterococcus faecium E1162]
 gi|293570124|ref|ZP_06681204.1| NifR3 family protein [Enterococcus faecium E1071]
 gi|294618637|ref|ZP_06698176.1| NifR3 family protein [Enterococcus faecium E1679]
 gi|294623713|ref|ZP_06702546.1| NifR3 family protein [Enterococcus faecium U0317]
 gi|314938206|ref|ZP_07845506.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a04]
 gi|314943101|ref|ZP_07849900.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133C]
 gi|314949298|ref|ZP_07852641.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0082]
 gi|314952231|ref|ZP_07855246.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133A]
 gi|314992089|ref|ZP_07857539.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133B]
 gi|314996272|ref|ZP_07861328.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a01]
 gi|68193901|gb|EAN08482.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium DO]
 gi|257814091|gb|EEV42849.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818247|gb|EEV45575.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|257828064|gb|EEV54690.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257830558|gb|EEV57165.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|260074634|gb|EEW62955.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecium C68]
 gi|291587496|gb|EFF19380.1| NifR3 family protein [Enterococcus faecium E1071]
 gi|291595156|gb|EFF26494.1| NifR3 family protein [Enterococcus faecium E1679]
 gi|291596928|gb|EFF28146.1| NifR3 family protein [Enterococcus faecium U0317]
 gi|291604852|gb|EFF34330.1| NifR3 family protein [Enterococcus faecium E1162]
 gi|313589516|gb|EFR68361.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a01]
 gi|313593303|gb|EFR72148.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133B]
 gi|313595626|gb|EFR74471.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133A]
 gi|313598160|gb|EFR77005.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133C]
 gi|313642402|gb|EFS06982.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0133a04]
 gi|313644304|gb|EFS08884.1| TIM-barrel protein, nifR3 family [Enterococcus faecium TX0082]
          Length = 334

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/326 (25%), Positives = 134/326 (41%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 21  MAGITNSAFRVTVKEF-GAGLVVCEMISDQGIHFRNKKTLEMLHIEETEHPLSLQIFGGN 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE+    + I++N+GCP  +V +   GA  +L+P+ V + + A+  A++I
Sbjct: 80  KDSLVEAAQFVEENTAADIIDINMGCPVNKVIKAEAGAKWLLDPEKVYEMVQAVSSAVNI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K RIG D++   V       + + +G + I +H R  +               D++
Sbjct: 140 PVTIKMRIGWDEE--HVFAVENALAAQSAGASAIAMHGRTRV--------QMYEGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A  +L     DGVMIGRAA  N  M+     Y   
Sbjct: 190 VLKEVKKHLTIPFMG-NGDVKTPEDAKWMLDYVGADGVMIGRAALGNPWMIHRTQHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +        A         ++   H      G P + + + 
Sbjct: 249 GELIPEPTPAEKIATAKLHLQR-----LADLKGEKVACREFRTHAAYYLKGIPRAAKVKV 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +       T     I    +  +E 
Sbjct: 304 AIN-----QTEKQQEINDLLDQFVEK 324


>gi|30018347|ref|NP_829978.1| Nif3 family protein [Bacillus cereus ATCC 14579]
 gi|218231778|ref|YP_002364926.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus B4264]
 gi|228950624|ref|ZP_04112759.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228956517|ref|ZP_04118314.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229067840|ref|ZP_04201158.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus F65185]
 gi|229125593|ref|ZP_04254626.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-Cer4]
 gi|229142882|ref|ZP_04271324.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST24]
 gi|229148485|ref|ZP_04276742.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1550]
 gi|229176676|ref|ZP_04304081.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 172560W]
 gi|29893887|gb|AAP07179.1| Nif3 family protein [Bacillus cereus ATCC 14579]
 gi|218159735|gb|ACK59727.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus B4264]
 gi|228606843|gb|EEK64259.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus 172560W]
 gi|228635027|gb|EEK91599.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus m1550]
 gi|228640594|gb|EEK96982.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-ST24]
 gi|228657910|gb|EEL13715.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus BDRD-Cer4]
 gi|228715324|gb|EEL67182.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus F65185]
 gi|228803207|gb|EEM50028.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228809099|gb|EEM55583.1| tRNA-dihydrouridine synthase 1 [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 332

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 138/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|118616290|ref|YP_904622.1| transcriptional regulator [Mycobacterium ulcerans Agy99]
 gi|118568400|gb|ABL03151.1| transcriptional regulator [Mycobacterium ulcerans Agy99]
          Length = 377

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 128/313 (40%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELEEAKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++ + G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 77  QLYTVDPDTTYAAARMIAEEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 136

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            + +    IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 137 VRGVEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQHVRTVPVLGNGDIYDASDALAMIAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I     +  A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGNPGPTPPTLGEVT-----DIIRRHGELLAAHFGEDKGVRDIRKHVAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSDLRRALAL 314


>gi|313899890|ref|ZP_07833393.1| TIM-barrel protein, nifR3 family [Clostridium sp. HGF2]
 gi|312955505|gb|EFR37170.1| TIM-barrel protein, nifR3 family [Clostridium sp. HGF2]
          Length = 338

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 66/303 (21%), Positives = 123/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+YTEM+   A+   ++K   +     QE PLA+QI G D
Sbjct: 22  MAGISNPAFRVICKEF-GAGLIYTEMVSDKALYYDNEKTVGMTDVEEQEHPLAMQIFGHD 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  +V AAK +++    + I++N+GCP  ++ +   G+ LM + D   +   A+ +++  
Sbjct: 81  IEIMVYAAKFLDEKTDCDIIDINMGCPVTKIVKSFAGSALMKDVDHAVEMSRAVVQSVKK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D  +  +    L + ++  GV  + +H R         +        D+ 
Sbjct: 141 PVTVKMRIGWD--MDQITCLELARGLESVGVQALAVHGRT--------RKQMYEGCADWS 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E   + +  NG +     A ++L     D VMIGR    +  ++  +  Y   
Sbjct: 191 YIKKVK-EAVSIPVMGNGDVRSGEDAERMLKETGCDAVMIGRGVLGDPWLIKDIAHYLEC 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                                                ++++  H      G P S + + 
Sbjct: 250 GKHMPEVTLEETFAMARLHAKRLCNLKGEF-----VGIREMRGHAAWYVKGLPKSHQLKD 304

Query: 296 ILT 298
            L+
Sbjct: 305 QLS 307


>gi|261392320|emb|CAX49847.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis 8013]
          Length = 336

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             + A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECSAAILNHVRAMHAFY-----GETAGVRIARKHIGWYIDEMPDGEQTRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERL 320


>gi|255325926|ref|ZP_05367018.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           tuberculostearicum SK141]
 gi|255297138|gb|EET76463.1| dihydrouridine synthase TIM-barrel protein nifR3 [Corynebacterium
           tuberculostearicum SK141]
          Length = 379

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/310 (23%), Positives = 125/310 (40%), Gaps = 31/310 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K   +  F+ QE P +L
Sbjct: 17  MAGVTNVAFRTLCREQELQRTGTVSGLYVCEMVTARALVERNEKTLHMTTFAPQEDPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           QI   D     +AAK++ D    + I++N GCP  +V     G+ L     + G+ ++A 
Sbjct: 77  QIYTVDPEYTYKAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVSAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA    +IPVTVK R+G+DD+       +  +   +SG   + +H R A          
Sbjct: 137 VKATEGTNIPVTVKMRVGIDDEHH--THLDAGRIAVESGAAAVTLHGRTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R      +D +  +K+   D  + +  NG +     A +++     DGV +GR       
Sbjct: 187 RYSGEARWDEIARLKEHLADTGVPVLGNGDIFRAEDARRMMEQTGCDGVQVGRGCLGRPW 246

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          + P    V +   R       +  A H       + I +H+    
Sbjct: 247 LFAELGAALRGESIPAEPTLGEVTQVILRHA-----ELLAEHDGEDNASRDIRKHIGWYL 301

Query: 285 HGFPNSRRCR 294
            GFP   + R
Sbjct: 302 RGFPVGGQVR 311


>gi|28871979|ref|NP_794598.1| TIM-barrel protein , NifR3 family [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|38604772|sp|Q87VS1|DUSB_PSESM RecName: Full=tRNA-dihydrouridine synthase B
 gi|28855232|gb|AAO58293.1| TIM-barrel protein, putative, NifR3 family [Pseudomonas syringae
           pv. tomato str. DC3000]
 gi|331014695|gb|EGH94751.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 337

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  AQMMADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ Y    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARHVLQATGADGLLIGRAAQGRPWIFREIEHYLLTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T  +   + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 KTLPALQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVGWYLATLPGAREFR 300


>gi|254724217|ref|ZP_05186002.1| NifR3 family TIM-barrel protein [Bacillus anthracis str. A1055]
          Length = 332

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 300


>gi|165872591|ref|ZP_02217223.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0488]
 gi|167641547|ref|ZP_02399795.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0193]
 gi|170707493|ref|ZP_02897946.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0389]
 gi|177655621|ref|ZP_02936984.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0174]
 gi|190569012|ref|ZP_03021913.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis
           Tsiankovskii-I]
 gi|227812750|ref|YP_002812759.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           CDC 684]
 gi|229600702|ref|YP_002864728.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0248]
 gi|254735478|ref|ZP_05193186.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Western North America USA6153]
 gi|254756325|ref|ZP_05208354.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Vollum]
 gi|254762381|ref|ZP_05214223.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           Australia 94]
 gi|164711719|gb|EDR17264.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0488]
 gi|167510532|gb|EDR85930.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0193]
 gi|170127489|gb|EDS96363.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0389]
 gi|172080032|gb|EDT65131.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0174]
 gi|190559936|gb|EDV13920.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis
           Tsiankovskii-I]
 gi|227005785|gb|ACP15528.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           CDC 684]
 gi|229265110|gb|ACQ46747.1| putative TIM-barrel protein, NifR3 family [Bacillus anthracis str.
           A0248]
          Length = 332

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQVVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGIRGNANVRN 300


>gi|121635111|ref|YP_975356.1| hypothetical protein NMC1354 [Neisseria meningitidis FAM18]
 gi|120866817|emb|CAM10575.1| conserved hypothetical protein [Neisseria meningitidis FAM18]
 gi|325132397|gb|EGC55090.1| dihydrouridine synthase [Neisseria meningitidis M6190]
 gi|325198556|gb|ADY94012.1| dihydrouridine synthase [Neisseria meningitidis G2136]
          Length = 336

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A+ +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNAQAGSALMQNEPLVAAILEAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         YD+
Sbjct: 136 VTLKTRLGWHDDHKN--LPAVARIAEDCGIAALAVHGRT--------RTQMYKGEAAYDL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +    + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAAAVFKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             + A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECSAAILNHVRAMHAFY-----GETAGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERL 320


>gi|296314359|ref|ZP_06864300.1| tRNA-dihydrouridine synthase B [Neisseria polysaccharea ATCC 43768]
 gi|296838915|gb|EFH22853.1| tRNA-dihydrouridine synthase B [Neisseria polysaccharea ATCC 43768]
          Length = 336

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R F R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRFCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFTDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + +  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHKN--LPAVARIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             + A    Y      +   ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECSAAILNHVRAMHAFY-----GNTAGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A +  +      +
Sbjct: 300 IN-RLDSAAAQYDTLAGYLERL 320


>gi|256787882|ref|ZP_05526313.1| hypothetical protein SlivT_25631 [Streptomyces lividans TK24]
 gi|289771765|ref|ZP_06531143.1| dihydrouridine synthase [Streptomyces lividans TK24]
 gi|289701964|gb|EFD69393.1| dihydrouridine synthase [Streptomyces lividans TK24]
          Length = 406

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 68/344 (19%), Positives = 130/344 (37%), Gaps = 46/344 (13%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 32  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 91

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ + G  + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 92  DPVTVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAIVREAVTGAG 151

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 152 DLPVTMKMRKGLDDD--HLTYLDAGRIAVEEGVTAIALHGRTT--------AQHYGGTAD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 202 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 261

Query: 234 SNPL-TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----------------- 275
                +   P    V     R  +          + +GG  ++                 
Sbjct: 262 EGRTDSFVRPTLREVADVMVRHATL-----LGEWIGNGGTARRATVEGGGGRREGEARGV 316

Query: 276 --ITRHMIGLFHGFPNSRRCRHIL----TVEAGASTATHHIIET 313
               +H+     GF      R  L    ++EA  +      ++ 
Sbjct: 317 IDFRKHVAWYLKGFAVGSEMRKRLAVTSSLEALRAGLDELDLDQ 360


>gi|291516129|emb|CBK69745.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. longum F8]
          Length = 414

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  + I    A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELIQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 174 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEIMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|120406034|ref|YP_955863.1| nifR3 family TIM-barrel protein [Mycobacterium vanbaalenii PYR-1]
 gi|119958852|gb|ABM15857.1| putative TIM-barrel protein, nifR3 family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 377

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 126/313 (40%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+ +E P +L
Sbjct: 17  MAGVTNVAFRTLCRELELSRAGTVSGLYVCEMVTARALVERHPVTMHMTTFAPEESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D    + I++N GCP  +V     GA L     + G  I A 
Sbjct: 77  QLYTVDPANTYAAAKMIVDENLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGQIIRAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             A     IPVTVK RIG+DD        +  +     G   + +HAR A          
Sbjct: 137 VAATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAADEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R   + D++ +  +K    ++ +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 187 RYSGSADWEQIAALKAHVTNIPVLGNGDIFDARDALAMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V      +I     +  A H      ++ I +H+    HG
Sbjct: 247 AELSAAFNGTAPATPPTLGEVA-----QIIRRHGELLAAHFGEDKGMRDIRKHVAWYMHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGADLRRSLAL 314


>gi|254820536|ref|ZP_05225537.1| dihydrouridine synthase [Mycobacterium intracellulare ATCC 13950]
          Length = 377

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 80/313 (25%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERSKVGTVSGLYVCEMVTARALVERHPVTMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D G  + I++N GCP  +V +   G+ L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIADEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAA 136

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD+       +  +  +  G   + +HAR A          
Sbjct: 137 VRATEGTQIPVTVKFRIGIDDEHH--THLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D+D +  +K+    + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWDEIARLKQHVRTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPPPTPPTLGEVA-----DIVRRHGQLLAAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAM 314


>gi|156082854|ref|XP_001608911.1| dihydrouridine synthase (Dus) domain containing protein [Babesia
           bovis T2Bo]
 gi|154796161|gb|EDO05343.1| dihydrouridine synthase (Dus) domain containing protein [Babesia
           bovis]
          Length = 362

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 110/335 (32%), Positives = 167/335 (49%), Gaps = 21/335 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGA 57
           M+D T   +R F RL+T  A L+TEM+   +++ GD     ++L     E P+ LQ+GG 
Sbjct: 23  MLDITYYEFRQFMRLITKRAQLWTEMMADGSLIYGDSDKVGSMLHCDANEHPIVLQLGGN 82

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALS 116
           ++  L +A  I   +GY E NLNVGCPS RV     FGA LM +  +VG  +  +   L 
Sbjct: 83  NLDSLSKAGNIALGYGYTEFNLNVGCPSTRVSGKGCFGAALMNDAPLVGRIVKHLRSELG 142

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R+GVD       +R+ + ++   G     +HARKA L G++P+ NR IP LD+
Sbjct: 143 TPVTVKHRLGVDHNDSYEFVRDFISTVADQGCTDFIVHARKAWLNGINPRKNRSIPPLDH 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + VY + +E P+L I +NGG++ + +    L   V GVM+GR AY+N   L  VD     
Sbjct: 203 ERVYRLCQEFPNLNISINGGIKSLEEIKYALSRGVYGVMVGRMAYENPCGLVRVDTDIYG 262

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--QITRHMIGLFHGFPNSRRC 293
             T  +  KTR      R +  +  ++          +    + + ++G FHG   ++  
Sbjct: 263 EATNPATCKTR------RILLETYANFIDSQASRTSDMNVCMLVKPILGTFHGEVGTKIF 316

Query: 294 RHILTVEAGASTATH--------HIIETAFNLMIE 320
           R  L+      T  +        H I  A  +M E
Sbjct: 317 RQALSDMNVYETLDYPRSGTKCGHYIRRAIAIMDE 351


>gi|240080043|ref|ZP_04724586.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA19]
          Length = 364

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDESLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 330 INRLDNAA-AQYDTLAGYLERL 350


>gi|239917156|ref|YP_002956714.1| putative TIM-barrel protein, nifR3 family [Micrococcus luteus NCTC
           2665]
 gi|281414375|ref|ZP_06246117.1| putative TIM-barrel protein, nifR3 family [Micrococcus luteus NCTC
           2665]
 gi|239838363|gb|ACS30160.1| putative TIM-barrel protein, nifR3 family [Micrococcus luteus NCTC
           2665]
          Length = 436

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 63/307 (20%), Positives = 117/307 (38%), Gaps = 22/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EM+ A A++    +++  +     E P ++Q+   D
Sbjct: 76  MAGITNTAFRRLCREYGG-GLYVNEMVTARALVERKPESMRIIQHDPDEVPRSVQLYSVD 134

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
                 A ++ VE+   + I++N GCP  +V     G+ L    ++    + A       
Sbjct: 135 PVTTGAAVRMLVEEDRCDHIDMNFGCPVPKVTRRGGGSALPWKSELFASIVKAAVTEAAK 194

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVTVK R G+D+    +   +  ++ +  GV  + +H R                  
Sbjct: 195 KDIPVTVKMRRGIDED--HLTFLDAGRTARDLGVAAVALHGRTT--------RQFYSGTA 244

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D +  +++  PD+ +  NG +     A+ ++    VDGV+IGR       +   +   
Sbjct: 245 VWDDIARLREALPDIPVLGNGDIWSAEDAIAMVERTGVDGVVIGRGCQGRPWLFGDLQAA 304

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F        P    V    +R     +  +      +   L+ I +H+   F G+P    
Sbjct: 305 FEGRQDRFHPTLGMVADTLYRHAELLVDTFGGDETKA---LRDIRKHVAWYFKGYPVGSE 361

Query: 293 CRHILTV 299
            R  L  
Sbjct: 362 IRTALAT 368


>gi|229159249|ref|ZP_04287274.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus R309803]
 gi|228624264|gb|EEK81065.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus R309803]
          Length = 339

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 137/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVKK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +     A +++    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQ-SVNIPVIGNGDVATPQDAKRMIDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 307


>gi|260204013|ref|ZP_05771504.1| putative transcriptional regulatory protein [Mycobacterium
           tuberculosis K85]
 gi|289573441|ref|ZP_06453668.1| transcriptional regulator [Mycobacterium tuberculosis K85]
 gi|289537872|gb|EFD42450.1| transcriptional regulator [Mycobacterium tuberculosis K85]
          Length = 389

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 125/313 (39%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGCGAALPFKRRLFGQIVAAA 148

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|206972564|ref|ZP_03233507.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH1134]
 gi|206732466|gb|EDZ49645.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus AH1134]
          Length = 332

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 139/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +              +D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKVDWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|309804685|ref|ZP_07698750.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           09V1-c]
 gi|309807001|ref|ZP_07700983.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           03V1-b]
 gi|309809597|ref|ZP_07703454.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN
           2503V10-D]
 gi|308166077|gb|EFO68295.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           09V1-c]
 gi|308166621|gb|EFO68818.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           03V1-b]
 gi|308170078|gb|EFO72114.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN
           2503V10-D]
          Length = 331

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 125/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++     E P++LQI G  
Sbjct: 21  MAGISNAAFRMVCKQF-GAGLVVCEMISDHGIIYRNKKTLDMMKIDPNEHPMSLQIFGGS 79

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+D    + IN+N+GCP  +V +   GA  +L+PD +   + A+   +  
Sbjct: 80  EETLVEAARYVDDNTHADIININMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G   + +H R         +      + D+ 
Sbjct: 140 PVTVKMRTGWDEDHIYAVENALA--AQEAGACAVAMHGRT--------RKQLYTGHADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+       F+G NG +     A K+L       VM+GRA   N  +L  +  Y   
Sbjct: 190 ILKEVSDALTIPFVG-NGDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +             ++                 + +  R       G P S R R 
Sbjct: 249 GELLAPQTVEERVTTCKEQLRK-----LVELKGEKIAVPEFRRQAAYYLKGIPRSARTRA 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +  +       +++++         L
Sbjct: 304 KIN-DVWTQQEVYNLLDEFVEKFESKL 329


>gi|253700031|ref|YP_003021220.1| hypothetical protein GM21_1403 [Geobacter sp. M21]
 gi|251774881|gb|ACT17462.1| TIM-barrel protein, nifR3 family [Geobacter sp. M21]
          Length = 321

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 65/309 (21%), Positives = 127/309 (41%), Gaps = 23/309 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+   R  +R     +  +TEM+  + + R  +K+  +L    +++P+ +Q+ G D
Sbjct: 21  MAGITNLPMRIVSRE-GGASFAFTEMVSVNGLTREGRKSFDLLKSCAEDRPIGMQLFGDD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++VED G   I++N+GCP  +V     G+ LM +P  VG  + ++  A  +P
Sbjct: 80  PEMLAEAARLVEDHG-ELIDINMGCPVRKVVGTGAGSALMKDPRKVGRIVRSVRAATRLP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G            + +  ++ G + + +H R         +        D+  
Sbjct: 139 LTIKIRTGWVCGDD--TFLEVGRIAQEEGCDAVTLHPRS--------RAQMFEGKADWSR 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  +G L   +    +L     D VM+ R A  N  +        +  
Sbjct: 189 IAELK-STLSIPVIGSGDLFSAADVAGMLAETGCDAVMVARGAMGNPWIFREALSLLAGE 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 ++ R+     R+     T++A   +     L ++ +H+     G P +   R  
Sbjct: 248 EPAPPSVQERLALS--RRHLELFTEFAGGRVA----LMEMRKHLSWYSKGLPGAAHFRAA 301

Query: 297 LTVEAGAST 305
           +     A  
Sbjct: 302 VNRIESAPE 310


>gi|319943013|ref|ZP_08017296.1| tRNA-dihydrouridine synthase B [Lautropia mirabilis ATCC 51599]
 gi|319743555|gb|EFV95959.1| tRNA-dihydrouridine synthase B [Lautropia mirabilis ATCC 51599]
          Length = 358

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 130/327 (39%), Gaps = 29/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR   + L       +EM  ++  L    K    +  + + +P A+QI GAD
Sbjct: 32  MAGVTDRPYRQLCKRL-GAGYAVSEMAASNPRLWNSVKTSRRIDHAGEIEPKAVQIAGAD 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+   + G   I++N+GCP  +V     G+ LM N  +  + I  + KA+ +P
Sbjct: 91  PAMMAEAARFNVERGAQIIDINMGCPVKKVCNVYAGSALMGNEPLAIEIIERVVKAVPVP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G+D            ++ + +G   I +H R         +  R    +DY  
Sbjct: 151 VTVKMRTGIDPDHRNAVALA--RAAEAAGAVMITVHGRS--------RACRYHGPVDYTT 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  NG ++   +A  +L     D VMIGRAA     +   VD Y ++ 
Sbjct: 201 IAEVKAAVG-IPVVANGNIDSPEKARDVLAQTGADAVMIGRAAQGRPWIFREVDHYLAHG 259

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR---- 292
               +P    V       ++     Y          ++   +H+          R+    
Sbjct: 260 TRLPAPTWREVRDLLLEHLNDHYRFYGEF-----TGVRTARKHIGWYLQALCGDRQPDEA 314

Query: 293 ---CRHILTVEAGASTATHHIIETAFN 316
               RH +     A      ++E  F 
Sbjct: 315 TEALRHAINDCEQADG-QVRLLERYFA 340


>gi|239620834|ref|ZP_04663865.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|322691517|ref|YP_004221087.1| dihydrouridine synthase [Bifidobacterium longum subsp. longum JCM
           1217]
 gi|239516410|gb|EEQ56277.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|320456373|dbj|BAJ66995.1| putative dihydrouridine synthase [Bifidobacterium longum subsp.
           longum JCM 1217]
          Length = 414

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 123/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR A              + 
Sbjct: 174 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTA--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|161870286|ref|YP_001599456.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis 053442]
 gi|161595839|gb|ABX73499.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis 053442]
          Length = 374

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 174 VTLKTRLGWHEDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             + A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECSAAILNHVRAMHAFY-----GETAGVRIARKHIGWYIDEMPDGEQTRRE 337

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 338 IN-RLDSAAAQYDMLAGYLERL 358


>gi|31792011|ref|NP_854504.1| transcriptional regulatory protein [Mycobacterium bovis AF2122/97]
 gi|121636747|ref|YP_976970.1| putative transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|224989218|ref|YP_002643905.1| putative transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Tokyo 172]
 gi|31617598|emb|CAD93708.1| POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [Mycobacterium bovis
           AF2122/97]
 gi|121492394|emb|CAL70862.1| Possible transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Pasteur 1173P2]
 gi|224772331|dbj|BAH25137.1| putative transcriptional regulatory protein [Mycobacterium bovis
           BCG str. Tokyo 172]
          Length = 389

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 125/313 (39%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGCGAALPFKRRLFGQIVAAA 148

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|309803746|ref|ZP_07697832.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           11V1-d]
 gi|309808758|ref|ZP_07702644.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           01V1-a]
 gi|312872541|ref|ZP_07732609.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF
           2062A-h1]
 gi|312874764|ref|ZP_07734783.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2053A-b]
 gi|325912444|ref|ZP_08174839.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 143-D]
 gi|325913104|ref|ZP_08175474.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 60-B]
 gi|329920464|ref|ZP_08277196.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN 1401G]
 gi|308164155|gb|EFO66416.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           11V1-d]
 gi|308167994|gb|EFO70126.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LactinV
           01V1-a]
 gi|311089509|gb|EFQ47934.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2053A-b]
 gi|311091903|gb|EFQ50279.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF
           2062A-h1]
 gi|325475786|gb|EGC78957.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 143-D]
 gi|325477525|gb|EGC80667.1| TIM-barrel protein, nifR3 family [Lactobacillus iners UPII 60-B]
 gi|328936140|gb|EGG32593.1| TIM-barrel protein, nifR3 family [Lactobacillus iners SPIN 1401G]
          Length = 331

 Score =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 125/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++     E P++LQI G  
Sbjct: 21  MAGISNAAFRMVCKQF-GAGLVVCEMISDHGIIYRNKKTLEMMKIDPNEHPMSLQIFGGS 79

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+D    + IN+N+GCP  +V +   GA  +L+PD +   + A+   +  
Sbjct: 80  EETLVEAARYVDDNTHADIININMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G   + +H R         +      + D+ 
Sbjct: 140 PVTVKMRTGWDEDHIYAVENALA--AQEAGACAVAMHGRT--------RKQLYTGHADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+       F+G NG +     A K+L       VM+GRA   N  +L  +  Y   
Sbjct: 190 ILKEVSDALTIPFVG-NGDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +             ++                 + +  R       G P S R R 
Sbjct: 249 GELLAPQTVEERVTTCKEQLRK-----LVELKGEKIAVPEFRRQAAYYLKGIPRSARTRA 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +  +       +++++         L
Sbjct: 304 KIN-DVWTQQEVYNLLDEFVEKFESKL 329


>gi|21220959|ref|NP_626738.1| hypothetical protein SCO2497 [Streptomyces coelicolor A3(2)]
 gi|6580664|emb|CAB63312.1| conserved hypothetical protein SCC82.03c [Streptomyces coelicolor
           A3(2)]
          Length = 406

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 68/344 (19%), Positives = 130/344 (37%), Gaps = 46/344 (13%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  ++K +  + F   E P ++Q+ G 
Sbjct: 32  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERNEKTMQLIHFDATETPRSIQLYGV 91

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ + G  + I+LN GCP  +V     G+ L     ++   +  A+  A 
Sbjct: 92  DPVTVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPYKRHLLRAIVREAVTGAG 151

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R                  D
Sbjct: 152 DLPVTMKMRKGLDDD--HLTYLDAGRIAVEEGVTAIALHGRTT--------AQHYGGTAD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     AL+++     DGV++GR       +   +   F
Sbjct: 202 WDAIARLKEHVPEIPVLGNGDIWSAEDALRMVRETGCDGVVVGRGCLGRPWLFADLVAAF 261

Query: 234 SNPL-TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----------------- 275
                +   P    V     R  +          + +GG  ++                 
Sbjct: 262 EGRTDSFVRPTLREVADVMVRHATL-----LGEWIENGGTARRATVEGGGGRREGEARGV 316

Query: 276 --ITRHMIGLFHGFPNSRRCRHIL----TVEAGASTATHHIIET 313
               +H+     GF      R  L    ++EA  +      ++ 
Sbjct: 317 IDFRKHVAWYLKGFAVGSEMRKRLAVTSSLEALRAGLDELDLDQ 360


>gi|149927720|ref|ZP_01915972.1| dihydrouridine synthase [Limnobacter sp. MED105]
 gi|149823546|gb|EDM82776.1| dihydrouridine synthase [Limnobacter sp. MED105]
          Length = 333

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 114/291 (39%), Gaps = 24/291 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    + KP+A+QI GAD
Sbjct: 1   MAGVTDRPFRQLCKKL-GAGHAVSEMAASNPALWKTDKSTRRLNHYGETKPIAVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              +  AA    + G   I++N+GCP+ +V   + G+ L+ N  +V   + A+       
Sbjct: 60  PEMMAHAAAYNIERGAQIIDINMGCPAKKVCAVAAGSALLQNESLVEQILKAVHAECEQR 119

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +P+T+K R G   +        + +  +  GV+ + +H R         +      + +
Sbjct: 120 GVPLTLKYRTGWSPEHKNAIH--IAQMAESIGVSLLTLHGRT--------RACGYTGDAE 169

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K+    + +  NG +    +A  +L     DG+MIGRAA  N  +   V  Y 
Sbjct: 170 YDTIKAVKQAV-SIPVIANGDITSPEKAKHVLDYTGADGLMIGRAAQGNPWIFREVLHYL 228

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 + P      +     +      Y  +       +    +H+    
Sbjct: 229 KTGEHINPPTLEEAHEVMMHHLRDHHEFYGEK-----TGMLTARKHLQWYL 274


>gi|229107762|ref|ZP_04237399.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-15]
 gi|228675735|gb|EEL30942.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock1-15]
          Length = 332

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 138/300 (46%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGRADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|229027922|ref|ZP_04184077.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1271]
 gi|229170926|ref|ZP_04298529.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus MM3]
 gi|228612592|gb|EEK69811.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus MM3]
 gi|228733436|gb|EEL84263.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH1271]
          Length = 339

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 25  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 84  KETLVDAAKYVDKYTTADIIDINMGCPVPKIIKCDAGAKWLLDPNKIYEMVAAVVDAVEK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D     +      K+++++G   + +H R  +               D+D
Sbjct: 144 PVTVKMRIGWD--ADHIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +E    A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 194 IIKQVKQAV-NIPVIGNGDVETPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 253 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGVRGNATVRN 307


>gi|261856280|ref|YP_003263563.1| hypothetical protein Hneap_1691 [Halothiobacillus neapolitanus c2]
 gi|261836749|gb|ACX96516.1| TIM-barrel protein, nifR3 family [Halothiobacillus neapolitanus c2]
          Length = 333

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 123/287 (42%), Gaps = 21/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   +DR +R   R      L+ TEM+ A   L+   K+ L    S   +P A+Q+ G D
Sbjct: 31  MAGVSDRPFRQLCREY-GAGLVVTEMMSAKPELQSSAKSRLRQIDSNDIEPRAVQLLGND 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA+     G   I+LN+GCP+ +V + + G+ LM  PD V   + A+  A+  P
Sbjct: 90  PFELAEAARFAVSQGAQLIDLNLGCPAKKVCKRAAGSALMAEPDTVARLLEALVAAVDCP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V++K R G D +        + K  + +G++ + IH R         + +R     +YD 
Sbjct: 150 VSLKMRTGPDREWRNAVA--IAKIAENAGISMLSIHGRT--------RADRYEGEAEYDT 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+     DL +  NG +    +A +++      G+M+GR A+    + + +    +  
Sbjct: 200 IAEVV-AAVDLPVFANGDITTPQKARQVIAHTGAAGIMVGRGAFGQPWIFSALKAELTGQ 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
              S P +        ++       Y          ++   +H+   
Sbjct: 259 PLPSPPDRAERVVAIKKQFEKIYHHY-----GDSLGIRIARKHLGWY 300


>gi|332654653|ref|ZP_08420396.1| TIM-barrel protein, NifR3 family [Ruminococcaceae bacterium D16]
 gi|332516617|gb|EGJ46223.1| TIM-barrel protein, NifR3 family [Ruminococcaceae bacterium D16]
          Length = 306

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 121/302 (40%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R      L  TEM+ A A+   DKK   +L     E P A QI G+D
Sbjct: 1   MAGVTDVAFRTICRE-QGAGLTCTEMVSAKALCYQDKKTVPLLQLGEGEHPAAAQIFGSD 59

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + E A I  +  G + I++N+GCP  +V     G+ LM +PD     + A+ +    
Sbjct: 60  PVCMQEGAAIAHEVSGADLIDINMGCPVPKVANSGDGSGLMRDPDKAVKVLEAVIRGAGC 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D    ++      K+++++G   + +H R         ++       ++D
Sbjct: 120 PVTVKFRLGWDKG--SINCVEFAKAMEQAGAAAVAVHGRT--------RNQMYSGTANWD 169

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+KK    + +  NG +     A +IL     D  MIGR  + N  +          
Sbjct: 170 WIREVKKAV-KIPVIANGDVFKGEDAPRILKYTGADMAMIGRGVFGNPWLFAQCKAALEG 228

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +   R+      + +A +        +  RH      G P++   + 
Sbjct: 229 REIPPMPPLEERCRTAVRQ-----FELSAANKGEKIACLEARRHYAWYLKGVPHAGYYKE 283

Query: 296 IL 297
            +
Sbjct: 284 QI 285


>gi|229039981|ref|ZP_04189745.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH676]
 gi|228727389|gb|EEL78582.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus AH676]
          Length = 332

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 137/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+     Y   
Sbjct: 187 IIKQVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVRYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|322689556|ref|YP_004209290.1| dihydrouridine synthase [Bifidobacterium longum subsp. infantis
           157F]
 gi|320460892|dbj|BAJ71512.1| putative dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 414

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  ++Q+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSMQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 174 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|296454480|ref|YP_003661623.1| putative TIM-barrel protein [Bifidobacterium longum subsp. longum
           JDM301]
 gi|296183911|gb|ADH00793.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. longum JDM301]
          Length = 414

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVARNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  + I    A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELIQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 174 AGIPVTSKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|229077366|ref|ZP_04210033.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-2]
 gi|228705945|gb|EEL58264.1| tRNA-dihydrouridine synthase 1 [Bacillus cereus Rock4-2]
          Length = 332

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 137/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDKYTTADIIDINMGCPVPKIVKCDAGARWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   +      ++++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDEE--HIFAIENARAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKRVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKGVRGNASVRN 300


>gi|29832192|ref|NP_826826.1| dihydrouridine synthase [Streptomyces avermitilis MA-4680]
 gi|29609310|dbj|BAC73361.1| putative dihydrouridine synthase [Streptomyces avermitilis MA-4680]
          Length = 401

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 37/323 (11%)

Query: 1   MVDWTDRHYRFFARLL------------------TNNALLYTEMIVADAILRGDKKNI-- 40
           M   T+  +R   R                        L  +EMI   A++  ++K +  
Sbjct: 28  MAGITNAPFRTLCRGFAEGHGWESGGRPPKGAADGGKGLFVSEMITTRALVERNEKTMQL 87

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           + F   EKP ++Q+ G D + + +A +++ + G  + I+LN GCP  +V     G+ L  
Sbjct: 88  IHFDATEKPRSIQLYGVDPATVGKAVRMIAEEGLADHIDLNFGCPVPKVTRKGGGSALPY 147

Query: 100 NPDIVGDCI-AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             +++   +  A+  A ++PVT+K R G+DD    +   +  +   + GV  I +H R A
Sbjct: 148 KRNLLRAILREAVSGAGNLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTA 205

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
                           D+D +  +K+  P++ +  NG +     A++++     DGV++G
Sbjct: 206 --------AQHYGGTADWDAIARLKEHVPEIPVLGNGDIWSAEDAVRMVRETGCDGVVVG 257

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           R       + + +   F      S+    R   D   + +  + ++          +   
Sbjct: 258 RGCLGRPWLFSDLVAAFEGRTDDSARPTLRAVADVMVRHATLLGEWIG---DEARGVIDF 314

Query: 277 TRHMIGLFHGFPNSRRCRHILTV 299
            +H+     GF      R  L +
Sbjct: 315 RKHVAWYLKGFAVGSEMRKRLAI 337


>gi|294637763|ref|ZP_06716038.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda ATCC 23685]
 gi|291089111|gb|EFE21672.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda ATCC 23685]
          Length = 334

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 129/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHMDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAKI  DFG   I++N+GCP+ +V+    G+ L+  PD V   + A+  A+++P
Sbjct: 76  PDEMAAAAKINADFGAQIIDINMGCPAKKVNRKLAGSALLQYPDQVEQILRAVVGAVAVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPAHRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQHV-SIPIIANGDITDPHKAKAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     + +     +      Y      SG  L+   +H+         + + R  
Sbjct: 245 ELLPPMPLGEIKRLLAGHVKELHDFY-----GSGKGLRIARKHVSWYLQAHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFEKL 320


>gi|330997166|ref|ZP_08321019.1| TIM-barrel protein, nifR3 family [Paraprevotella xylaniphila YIT
           11841]
 gi|329570961|gb|EGG52668.1| TIM-barrel protein, nifR3 family [Paraprevotella xylaniphila YIT
           11841]
          Length = 346

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 80/332 (24%), Positives = 146/332 (43%), Gaps = 27/332 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++Y+E + ADA++R   +++  L     E+P+A+QI G +
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYSEFVAADALVRMVNRSLEKLAVCDDERPVAIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+IV +    + ++LN GCP  RV     GA ++ N   + +   A+  A+ I
Sbjct: 77  PGPVADAARIVVERARPDVLDLNFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ 
Sbjct: 137 PVTVKTRLGWDESSKVIV--DLAERLQDCGIRALTIHGRT--------RAQMYTGEADWT 186

Query: 178 IVYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ E+K  NP   + I  NG +    +A +      VD VM+GRA +    +   + +  
Sbjct: 187 LIGEVKN-NPRMTIPIIGNGDITSPERARECFDRYGVDAVMVGRATFGRPWIFKEITDVL 245

Query: 234 SNPLTGSSPIKTR-----VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHG 286
           +     ++    +     +  D+   +       + R +     +    RH+    +F G
Sbjct: 246 NPGSASAAHEAVKSGYPVMSADWKIDVLKEQVLTSVRRIDEYRGILHSRRHLAASPVFKG 305

Query: 287 FPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            PN R  R I  + A        I+E A   +
Sbjct: 306 IPNFRETR-IAMLRAETVDELFAILERAREAV 336


>gi|227489463|ref|ZP_03919779.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227090641|gb|EEI25953.1| possible tRNA-dihydrouridine synthase [Corynebacterium
           glucuronolyticum ATCC 51867]
          Length = 371

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 71/312 (22%), Positives = 124/312 (39%), Gaps = 30/312 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        + + L   EM+ A A++  ++K   +  FS+ E+P +L
Sbjct: 19  MAGVTNVAFRLLCREQELEKAGSVSGLYVCEMVTARALVERNEKTLHMAAFSSVEEPRSL 78

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK I E+   + ++LN GCP  +V     GA L    ++    + A 
Sbjct: 79  QLYTTDPEYTYKAAKMIAEENLADHVDLNFGCPVPKVTRKGGGAALPYKRELFKRIVDAT 138

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            + +    IPVTVK RIG+D       + +  +  ++ G   + +HAR A          
Sbjct: 139 VRGVSGTDIPVTVKFRIGID--ADHETMLDAGRIAQEEGAAAVTLHARTA--------AE 188

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R      ++ + E+K+   D+ +  NG +   +  L +      DG+ IGR       + 
Sbjct: 189 RYSGQAHWERIAELKQAL-DVPVFGNGDVFSAADGLAMFEQTGCDGIEIGRGCLGRPWLF 247

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           + +    S       P    V       I     +  A H       + I +H+   F G
Sbjct: 248 SDLALALSGRPVPPPPTLGEVCT-----ILRRHAELLAIHQGEASACRDIRKHVGWYFRG 302

Query: 287 FPNSRRCRHILT 298
           +      R  L+
Sbjct: 303 YAVGGSFRASLS 314


>gi|23464743|ref|NP_695346.1| NifR3-like protein [Bifidobacterium longum NCC2705]
 gi|189438998|ref|YP_001954079.1| tRNA-dihydrouridine synthase [Bifidobacterium longum DJO10A]
 gi|213691694|ref|YP_002322280.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|317481587|ref|ZP_07940623.1| dihydrouridine synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|23325312|gb|AAN23982.1| possible NifR3-like protein [Bifidobacterium longum NCC2705]
 gi|189427433|gb|ACD97581.1| tRNA-dihydrouridine synthase [Bifidobacterium longum DJO10A]
 gi|213523155|gb|ACJ51902.1| putative TIM-barrel protein, nifR3 family [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|316916947|gb|EFV38333.1| dihydrouridine synthase [Bifidobacterium sp. 12_1_47BFAA]
 gi|320457785|dbj|BAJ68406.1| putative dihydrouridine synthase [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 414

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 174 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|259501002|ref|ZP_05743904.1| tRNA-dihydrouridine synthase [Lactobacillus iners DSM 13335]
 gi|302190549|ref|ZP_07266803.1| tRNA-dihydrouridine synthase [Lactobacillus iners AB-1]
 gi|259167696|gb|EEW52191.1| tRNA-dihydrouridine synthase [Lactobacillus iners DSM 13335]
          Length = 331

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 125/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++     E P++LQI G  
Sbjct: 21  MAGISNAAFRMVCKQF-GAGLVVCEMISDHGIIYRNKKTLDMMKIDPNEHPMSLQIFGGS 79

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+D    + IN+N+GCP  +V +   GA  +L+PD +   + A+   +  
Sbjct: 80  EETLVEAARYVDDNTHADIININMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G   + +H R         +      + D+ 
Sbjct: 140 PVTVKMRTGWDEDHIYAVENALA--AQEAGACAVAMHGRT--------RKQLYTGHADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+       F+G NG +     A K+L       VM+GRA   N  +L  +  Y   
Sbjct: 190 ILKEVSDALTIPFVG-NGDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +             ++                 + +  R       G P S R R 
Sbjct: 249 GELLAPQTVEERVITCKEQLRK-----LVELKGEKIAVPEFRRQAAYYLKGIPRSARTRA 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +  +       +++++         L
Sbjct: 304 KIN-DVWTQQEVYNLLDEFVEKFESKL 329


>gi|328675866|gb|AEB28541.1| tRNA dihydrouridine synthase B [Francisella cf. novicida 3523]
          Length = 325

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 77/308 (25%), Positives = 134/308 (43%), Gaps = 23/308 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKE-HGAGLIYTEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG DDQ   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDDQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMIEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        P S+  R
Sbjct: 247 TGELIPPPTSVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLADLPGSKEFR 301

Query: 295 HILTVEAG 302
             L     
Sbjct: 302 MKLNQLEH 309


>gi|194097785|ref|YP_002000828.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae NCCP11945]
 gi|254493061|ref|ZP_05106232.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 1291]
 gi|268600667|ref|ZP_06134834.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID18]
 gi|268681451|ref|ZP_06148313.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID332]
 gi|268685922|ref|ZP_06152784.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-93-1035]
 gi|193933075|gb|ACF28899.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae NCCP11945]
 gi|226512101|gb|EEH61446.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 1291]
 gi|268584798|gb|EEZ49474.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID18]
 gi|268621735|gb|EEZ54135.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID332]
 gi|268626206|gb|EEZ58606.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-93-1035]
 gi|317163563|gb|ADV07104.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 334

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 300 INRLDNAA-AQYDTLAGYLERL 320


>gi|188993880|ref|YP_001928132.1| putative TIM-barrel protein [Porphyromonas gingivalis ATCC 33277]
 gi|188593560|dbj|BAG32535.1| putative TIM-barrel protein [Porphyromonas gingivalis ATCC 33277]
          Length = 333

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 77/301 (25%), Positives = 133/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      L+Y+E + ADA++R        +     E+P+A+QI G D
Sbjct: 18  MEDVTDVAFRIMCKQF-GADLVYSEFLSADALIRQVAGTFRKMAIDESERPMAVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA++ E  G + I+LN GCP  RV     G+ ++ N  ++ +    + KA+ +P
Sbjct: 77  VASMVEAARLCESAGPDLIDLNFGCPVKRVAGKGAGSGMLRNIPLMIEITREVVKAVKLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNDSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGTADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD VM+GRA+     +   +  +   
Sbjct: 187 IGEVKNNPRMQIPIIGNGDVTTPQEARRAFDVYGVDAVMVGRASIGQPWIFEDMKHFLRT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             T  S         ++  I    T    R L     +    RH+    +F G PN +  
Sbjct: 247 GETLPSRPFC-----YYMDILRRQTLNNIRKLDERRGILHTRRHIAASPIFKGIPNFKPM 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|258648271|ref|ZP_05735740.1| tRNA-dihydrouridine synthase B [Prevotella tannerae ATCC 51259]
 gi|260852187|gb|EEX72056.1| tRNA-dihydrouridine synthase B [Prevotella tannerae ATCC 51259]
          Length = 343

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/332 (24%), Positives = 145/332 (43%), Gaps = 24/332 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   R +   A+ Y+E + +DA++R  ++++  L  S  E+P+A+QI G  
Sbjct: 18  MEDVTDIGFRRLCRQM-GAAMAYSEFVASDALVRNVRRSLDKLAVSDAERPVAIQIYGRF 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAAKIVE+    + ++LN GCP  RV     GA L+ N  ++ +    + +A+ I
Sbjct: 77  PDAMAEAAKIVEETSHPDILDLNFGCPVKRVAGKGAGAGLLQNVPLMLEITRRVVEAVKI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D +     +  L + ++  G++ + IH R         +        D+ 
Sbjct: 137 PVTVKTRLGWDSE--HEIITELAEQLQDCGISALTIHGRT--------RAQMYKGEADWR 186

Query: 178 IVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT----VD 230
           ++ E+K+     + I  NG L       +      VD  M+GRA +    +       V 
Sbjct: 187 LIGEVKRNPRIHIPIIGNGDLTTGEDVRRAFEHYGVDACMVGRATFGRPWIFKEMYDAVH 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFP 288
           +    P+         +  D+   +  +    +   +     +  + RH+    LF G P
Sbjct: 247 DQHHTPVNAIESSYEPLSADWKLDVLKAQVVQSVNRIDEYRGILHVRRHIAATPLFKGIP 306

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           + R  + I  + A    A    IE    L+ +
Sbjct: 307 DFRE-KRISLLRAETVDALFEQIEAVRPLVRQ 337


>gi|71031827|ref|XP_765555.1| tRNA-dihydrouridine synthase A [Theileria parva strain Muguga]
 gi|68352512|gb|EAN33272.1| tRNA-dihydrouridine synthase A, putative [Theileria parva]
          Length = 471

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 117/370 (31%), Positives = 180/370 (48%), Gaps = 54/370 (14%)

Query: 1   MVDWTDRHYRFFA----------RLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQE 47
           M+D T  H+R+F           RLLT    L+TEM VA +++    +++   L F   E
Sbjct: 91  MLDVTYLHFRYFMDFKFDFRQFMRLLTRKTQLWTEMFVASSLINASNESVSRWLKFEENE 150

Query: 48  KPLALQIG----------GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS----- 92
            P+  Q+G          G     LVEA +I++ FGY+EINLN GCPS RV         
Sbjct: 151 HPIVAQLGIFYQHKIVPGGNCPETLVEAGRILKKFGYDEINLNAGCPSPRVSGKGIYKFM 210

Query: 93  --------FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
                   FGA LM   ++V D    M + L +PVTVK R+GVD+      +R+ V ++ 
Sbjct: 211 LKLFNLGCFGASLMKEKELVRDIAHHMLRELEMPVTVKTRLGVDEFDSYEFVRDFVSTVS 270

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           +SG +   IH+RKA LKG++PK NR IP L Y+ VY ++++ P L   +NGG + M   L
Sbjct: 271 ESGCDHFIIHSRKAWLKGINPKQNRTIPPLQYEKVYRLQRDFPHLKFTINGGFKTMESIL 330

Query: 205 KIL--PSVD---------GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD-FW 252
           + L   ++D         GVMIGR AY+N  +L+ VD+         +    R+  + + 
Sbjct: 331 EALNSENLDSNNNPHKLNGVMIGRLAYENPCLLSNVDKLIYGVENPDTCYTRRILLENYA 390

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIE 312
             I  +  D A         +  I + ++G+FHG   ++  R  L+         +H  E
Sbjct: 391 NYIDENQVDTA------NLNISLIVKPILGVFHGEQGNKIFRQSLSNVYDYDDFIYHSGE 444

Query: 313 TAFNLMIESL 322
           +  ++ I  +
Sbjct: 445 SRHSMFIHKV 454


>gi|225024157|ref|ZP_03713349.1| hypothetical protein EIKCOROL_01025 [Eikenella corrodens ATCC
           23834]
 gi|224943182|gb|EEG24391.1| hypothetical protein EIKCOROL_01025 [Eikenella corrodens ATCC
           23834]
          Length = 334

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 134/313 (42%), Gaps = 25/313 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R  AR          EMI ++  L+  +K +  +  S +   +A+QI G++
Sbjct: 17  MAGITDKPFRMLARQF-GAGWTVGEMISSNPDLQNTRKTLNRIDRSGESGVIAVQIAGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAA+     G   I++N+GCP+ +V +   G+ L+ N  +V + + A+ +A+ +P
Sbjct: 76  PAQMAEAARYNVAQGAQLIDINMGCPAKKVCQVQAGSALLQNEPLVAEILHAVVRAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D+   +    + +  + +G+  I IH R         +        +Y +
Sbjct: 136 VTLKTRLGWHDEHKNI--LTIARMAEDAGIAAIAIHGRT--------RTQMYRGQAEYGL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K+    + + +NG ++   +A ++L     DGVMIGR A     +   V  Y ++ 
Sbjct: 186 IAEAKRRL-SIPVWVNGDIDSPQKAARVLAETGADGVMIGRTAQGRPWLFRDVAHYLAHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                       +     I A    Y          ++   +H+       P     R  
Sbjct: 245 SLPQPLPFQVASEALLGHIRAMYGFYGEA-----AGMRIARKHIGWYLADLPEGEAERRR 299

Query: 297 L----TVEAGAST 305
           L    + EA  + 
Sbjct: 300 LNVLESAEAQYNG 312


>gi|312132439|ref|YP_003999778.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp. longum
           BBMN68]
 gi|311773058|gb|ADQ02546.1| tRNA-dihydrouridine synthase [Bifidobacterium longum subsp. longum
           BBMN68]
          Length = 414

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 174 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|218781043|ref|YP_002432361.1| TIM-barrel protein, nifR3 family [Desulfatibacillum alkenivorans
           AK-01]
 gi|218762427|gb|ACL04893.1| TIM-barrel protein, nifR3 family [Desulfatibacillum alkenivorans
           AK-01]
          Length = 332

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 78/323 (24%), Positives = 142/323 (43%), Gaps = 23/323 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              T+   R  A+     AL+ +EMI ++ ++R  KK +  +    +E+PL++QI G+D 
Sbjct: 19  AGVTNLPLRLMAKR-HGAALVCSEMISSNGLIRYQKKTMELMASKEEERPLSIQIFGSDP 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L ++A+IV + G + +++N GC   +V +G  G+ LM +       +  + KA+S+P 
Sbjct: 78  GVLADSARIVAEHGADIVDINFGCSVKKVLKGGAGSALMADLPRAEKILKEVRKAISLPF 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G D          L +  + +GV+ + +H R A  +G S        + D+  +
Sbjct: 138 TIKMRSGWD--ASGDEAMALGRIAQDAGVDAVALHPRTAK-QGFS-------GHSDWSQI 187

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+E   + +  NG +      L+++     DGVMIGRA      +         N  
Sbjct: 188 KRLKQELT-IPVIGNGDVTKPEHVLEMMEQTGCDGVMIGRAVLYAPWIFRQALCLLENR- 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                    +D D  +K+     D    +L      + +   +     G PN+ + R  +
Sbjct: 246 -----PMEEIDLDDRKKVLFDYLDDTMDYLGEEHGCRVMRSRLAWFVKGLPNAAKFRGEI 300

Query: 298 TVEAGASTATHHIIETAFNLMIE 320
           T  A    A   +IE  F  + +
Sbjct: 301 TRIASKEQA-RDLIEEFFRSIEK 322


>gi|78184219|ref|YP_376654.1| dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9902]
 gi|78168513|gb|ABB25610.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9902]
          Length = 356

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 141/320 (44%), Gaps = 21/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADIS 60
              TD+ +R   R  + ++LL+TEM+ A ++  G     +     +E P+A+Q+      
Sbjct: 45  AGVTDKIFRGLVRRWSRDSLLFTEMVNATSLELGHGYGKMDDLKAEEGPIAVQLFDHRPH 104

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +  AA+  E  G   I++N+GCP  ++ +   G+ L+ +P++    + A+  A+SIPVT
Sbjct: 105 AMAHAARRAEQAGAFLIDINMGCPVRKIAKKGGGSGLIRDPNLATQILEAVVDAVSIPVT 164

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G              + ++ +G   + +H R         ++       +++ + 
Sbjct: 165 VKTRLGWCGSSSDPIT--WCRQLQNAGAQMLTLHGRT--------REQGFKGQANWNAIA 214

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           E+K+    + +  NG +   + AL+ L     DGVM+GR    +  ++  ++  F N   
Sbjct: 215 EVKQALT-IPVIANGDINSPTDALRCLEITGADGVMVGRGTMGSPWLVGQIEAAFMNRPI 273

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P     D      ++            S G L    +HM     GFP + + RH L 
Sbjct: 274 PATP-----DSGARLHLAKEQLHDLVSSRGSHG-LLIARKHMSWTCTGFPGAPQLRHSL- 326

Query: 299 VEAGASTATHHIIETAFNLM 318
           + A      + +I+ A N +
Sbjct: 327 MRATTPDDAYQLIDNAINSL 346


>gi|312874301|ref|ZP_07734333.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2052A-d]
 gi|315653938|ref|ZP_07906854.1| tRNA-dihydrouridine synthase [Lactobacillus iners ATCC 55195]
 gi|311090174|gb|EFQ48586.1| TIM-barrel protein, nifR3 family [Lactobacillus iners LEAF 2052A-d]
 gi|315488634|gb|EFU78280.1| tRNA-dihydrouridine synthase [Lactobacillus iners ATCC 55195]
          Length = 331

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 125/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++     E P++LQI G  
Sbjct: 21  MAGISNAAFRMVCKQF-GAGLVVCEMISDHGIIYRNKKTLEMMKIDPNEHPMSLQIFGGS 79

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+D    + IN+N+GCP  +V +   GA  +L+PD +   + A+   +  
Sbjct: 80  EETLVEAARYVDDNTHADIININMGCPVPKVTKTDSGAKWLLDPDKIYQMVKAVVNNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G   + +H R         +      + D+ 
Sbjct: 140 PVTVKMRTGWDEDHIYAVENALA--AQEAGACAVAMHGRT--------RKQLYTGHADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+       F+G NG +     A K+L       VM+GRA   N  +L  +  Y   
Sbjct: 190 ILKEVSDALTIPFVG-NGDVTTPQLAKKMLDEVGCSAVMVGRAVLGNPWILKEITHYLDT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +             ++                 + +  R       G P S R R 
Sbjct: 249 GELLAPQTVEERVITCKEQLRK-----LVELKGEKIAVPEFRRQAAYYLKGIPRSARTRA 303

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +  +       +++++         L
Sbjct: 304 KIN-DVWTQQEVYNLLDEFVEKFESKL 329


>gi|227546857|ref|ZP_03976906.1| dihydrouridine synthase [Bifidobacterium longum subsp. infantis
           ATCC 55813]
 gi|227212819|gb|EEI80700.1| dihydrouridine synthase [Bifidobacterium longum subsp. infantis
           ATCC 55813]
          Length = 414

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 54  MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKNRSLQLYGVN 113

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 114 PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 174 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 224 DWSRIGELK-EHLNVPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 283 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 339

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 340 TRKAFMECESLADVDREI 357


>gi|313115110|ref|ZP_07800598.1| TIM-barrel protein, nifR3 family [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622587|gb|EFQ06054.1| TIM-barrel protein, nifR3 family [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 371

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 121/320 (37%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD   R             +EM+ + A++ GD K   +L       P  +QI G  
Sbjct: 52  MAGFTDAPCRRLMAQ-HGAGFTVSEMVSSRALVYGDHKTVSLLKAEPNGAPYGVQIFGEV 110

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA   +E + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  +      P
Sbjct: 111 PEIMGEATAAIEQYEFDFVDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEQVVANTKRP 170

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     +      K+ +++G   I +HAR         ++    P +D +I
Sbjct: 171 VTVKMRKGWD--ADHITAVECAKACEQAGAALIAVHART--------REQMYTPGIDPEI 220

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +     A++++     DGVMI R A  +  +   V+      
Sbjct: 221 IARVK-DAVRVPVLGNGDIHSAEDAVEMMQATGCDGVMIARGALGDPWLFERVNAAIEGL 279

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P          R++                 + Q     +    G   +   R  
Sbjct: 280 PAPKAPNLQARMNALRRQVEEM-----VEQKGEFVAMPQARSQTMHYMKGLKGAANLRRY 334

Query: 297 LTVEAGASTATHHIIETAFN 316
                        +I+  F 
Sbjct: 335 CCTLTHLEDLD-ELIDAVFE 353


>gi|268594138|ref|ZP_06128305.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 35/02]
 gi|268547527|gb|EEZ42945.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae 35/02]
          Length = 340

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 23  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 82  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 142 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 192 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 251 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 305

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 306 INRLDNAA-AQYDTLAGYLERL 326


>gi|83814729|ref|YP_446617.1| NifR3 family protein [Salinibacter ruber DSM 13855]
 gi|83756123|gb|ABC44236.1| NifR3 family enzyme [Salinibacter ruber DSM 13855]
          Length = 443

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 141/326 (43%), Gaps = 25/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      ++YTE + +  +LR  +     L    +E+P+ +Q+ G  
Sbjct: 82  MEDVSDPPFRILCKRY-GADMMYTEFVSSAGLLREQEHEHQKLEIFDEERPIGIQVWGGG 140

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I ++  A  +V+  G + I++N GCP  ++ +   GA ++ N D + +  AA+ +  + P
Sbjct: 141 IDEVRNATPMVDAAGPDVIDINFGCPVRKIVQKDGGAGVLRNLDKMRNITAAVMEEATRP 200

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD   ++ + ++ + ++  GV  + +HAR         ++ +   +  ++ 
Sbjct: 201 VTVKTRLGWDDD--SIHIVDVARMLEDMGVAALTVHART--------REQKYKGDARWEW 250

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  IK+E   D+    NG   D      +     VDGVM+GR A  N  +      Y   
Sbjct: 251 LRTIKEEGTRDMPFIGNGDALDPEAIEAMFEETGVDGVMLGRGALGNPWIFERAKTYMET 310

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P     D +   ++ A         L     + ++ ++    F GF N+   RH
Sbjct: 311 GELPPPP-----DWEERVQVVAEHLSLKCEWLGERTGVMEMRKNYSSYFKGFRNASTLRH 365

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L      +     ++E   N   ++
Sbjct: 366 ELMQPETKAG----VLEVMLNFKPDA 387


>gi|20088934|ref|NP_615009.1| hypothetical protein MA0035 [Methanosarcina acetivorans C2A]
 gi|19913780|gb|AAM03489.1| conserved hypothetical protein [Methanosarcina acetivorans C2A]
          Length = 323

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 132/303 (43%), Gaps = 26/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M D T+  +R   R      L YTEMI ADA+L   +K+ +    S +++P  +Q+ G+ 
Sbjct: 22  MADVTNLAFRLLCRQ-DGADLAYTEMINADALLNESRKSFIKGLNSPEDRPFGVQLVGSC 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             KL EAA  VE+ +    I++N+GCP+  +     G+ L+ +P++V   I+ +  AL+ 
Sbjct: 81  PKKLREAALFVEEEYEPEVIDINMGCPAKCITGAGCGSALLNSPELVRKIISELADALNT 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+   ++        +   I+K+G + + +H R A              N +  
Sbjct: 141 PVSAKIRLLGKEEKT----LEIACLIEKAGASALTVHGRTA--------AQMYSGNANLM 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG ++D   A K   L   DG+MIGRAA  N  +   +  Y   
Sbjct: 189 GIKAVKNEL-SIPVIANGDIKDEESAKKTLELTGCDGLMIGRAAMGNPFIFRRIRHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   + R  +DF + IS          ++       +  H      G   SR  R 
Sbjct: 248 GEKLEVERQARQLEDFEKYISLLEKHNLLSSIN-------LRMHAHWFTKGLHGSRHVRE 300

Query: 296 ILT 298
            + 
Sbjct: 301 KIN 303


>gi|302545533|ref|ZP_07297875.1| putative tRNA-dihydrouridine synthase [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463151|gb|EFL26244.1| putative tRNA-dihydrouridine synthase [Streptomyces himastatinicus
           ATCC 53653]
          Length = 383

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 66/318 (20%), Positives = 127/318 (39%), Gaps = 27/318 (8%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M   T+  +R   R       L  +EMI   A++  D K +  + F   EKP ++Q+ G 
Sbjct: 22  MAGITNAPFRTLCREFSGGKGLFVSEMITTRALVERDAKTMRLIHFDGTEKPRSIQLYGV 81

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL 115
           D   + +A +++ D    + I+LN GCP  +V     G+ L    +++   +  A+  A 
Sbjct: 82  DPVTVGKAVRMIVDEDLADHIDLNFGCPVPKVTRKGGGSALPYKRNLLRAILREAVTGAG 141

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G+DD    +   +  +   + GV  I +H R A                D
Sbjct: 142 PLPVTMKMRKGIDDD--HITYLDAGRIAVEEGVTAIALHGRTA--------AQHYGGTAD 191

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D +  +K+  P++ +  NG +     A++++     DGV++GR       +   +   F
Sbjct: 192 WDAIARLKETVPEIPVLGNGDIWSAEDAVRMMDRTGCDGVVVGRGCLGRPWLFGDLVAAF 251

Query: 234 S------NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +           + P    V     R+ +  + ++          +    +H+     GF
Sbjct: 252 APGGETGGGAGSARPTLKEV-AGVMRRHAELLAEWLEDEE---RGVIDFRKHVAWYTKGF 307

Query: 288 PNSRRCRHILTVEAGAST 305
                 R  L + +  + 
Sbjct: 308 SVGSEMRKRLAITSSLAE 325


>gi|254363760|ref|ZP_04979806.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis str. Haarlem]
 gi|134149274|gb|EBA41319.1| hypothetical transcriptional regulatory protein [Mycobacterium
           tuberculosis str. Haarlem]
          Length = 339

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 125/313 (39%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 148

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSALRRALAM 326


>gi|91787028|ref|YP_547980.1| dihydrouridine synthase TIM-barrel protein nifR3 [Polaromonas sp.
           JS666]
 gi|91696253|gb|ABE43082.1| tRNA-U20-dihydrouridine synthase [Polaromonas sp. JS666]
          Length = 356

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 116/306 (37%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K       + +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVTSRRDLWDSLKTSRRANHAGEAAPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA    D G   I++N+GCP+ +V     G+ LM +  +    + A+  A    
Sbjct: 76  AQMMAEAAAYNVDRGAQIIDINMGCPAKKVCNKWAGSALMQDETLALQIVEAVVAACAPH 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G            + ++ + +GV  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQAHKNA--LAIARAAESAGVQMVTVHGRT--------REQGYKGLAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D VMIGRAA     +   V  + 
Sbjct: 186 YDTIAAVKSAL-RIPVVANGDISSPEKARDVLAYTGADAVMIGRAAQGRPWIFREVAHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V     R++                 ++   +H+       P     
Sbjct: 245 ATGTHLAPPLVAEV-----RRLLLDHLLDHYDLYGQYTGVRTARKHIGWYVKTLPGGEVF 299

Query: 294 RHILTV 299
           R  + +
Sbjct: 300 RAKMNL 305


>gi|206977953|ref|ZP_03238840.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           H3081.97]
 gi|206743859|gb|EDZ55279.1| putative TIM-barrel protein, NifR3 family [Bacillus cereus
           H3081.97]
          Length = 332

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 136/300 (45%), Gaps = 22/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  +K+   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILLNNKRTLDMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  ++ +   GA  +L+P+ + + +AA+  A+  
Sbjct: 77  KETLVDAAKYVDQYTTADIIDINMGCPVPKIVKCDAGAKWLLDPNKIYEMVAAVVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+    +      K+++++G   + +H R  +               D+D
Sbjct: 137 PVTVKMRIGWDED--HIFAIENAKAVERAGGQAVAVHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K+   ++ +  NG +     A ++L    VDGVMIGRAA  +  M+    +Y   
Sbjct: 187 IIKQVKQAV-NISVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +     D      +    ++++ +H      G   +   R+
Sbjct: 246 GELMPEPTVREKI-----DVCMLHLDRLIDLKNENVAVREMRKHAAWYLKGIRGNATVRN 300


>gi|254672934|emb|CBA07315.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis alpha275]
          Length = 374

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCREF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 174 VTLKTRLGWHEDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIGEMPDGEQARRE 337

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 338 IN-RLDSAAAQYDMLAGYLERL 358


>gi|260584305|ref|ZP_05852052.1| zinc-binding TIM-barrel protein, nifR3 family [Granulicatella
           elegans ATCC 700633]
 gi|260157823|gb|EEW92892.1| zinc-binding TIM-barrel protein, nifR3 family [Granulicatella
           elegans ATCC 700633]
          Length = 339

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 135/327 (41%), Gaps = 22/327 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   ++K   +L     E PL++QI G +
Sbjct: 19  MAGISNSAFRVTVKEF-GAGLVVCEMISDKGIQFRNEKTLSMLHIEPNEYPLSVQIMGGN 77

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +      I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+  
Sbjct: 78  KDTLVEAAKYVAENTEAAIIDINMGCPVNKVIKAEAGAKWLLDPNKVYEMVAAVVDAVDK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L    +++G + + +H R  +               +++
Sbjct: 138 PVTVKMRTGWDDEHLYAVENALA--AERAGASAVAMHGRTRV--------QMYDGKANWE 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK    + +  NG +     A K++    VDGVMIGRAA  N  M+     Y   
Sbjct: 188 ILGEVKKNLTRIPLIGNGDVRSPQDAKKMIEIAGVDGVMIGRAALANPWMIKQTVHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                             +I+ +  D  A         ++  +       G P + + + 
Sbjct: 248 GELLPENTVPEKI-----EIAKTHLDRLANLKGESVATKEFRKLAAYYLKGIPRATKTKV 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +      S     I++      +E +
Sbjct: 303 AINESTTVSQVK-QILDQFVQEHLERV 328


>gi|34539899|ref|NP_904378.1| NifR3 family TIM-barrel protein [Porphyromonas gingivalis W83]
 gi|34396210|gb|AAQ65277.1| TIM-barrel protein, putative, NifR3 family [Porphyromonas
           gingivalis W83]
          Length = 333

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 134/301 (44%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      L+Y+E + ADA++R        +     E+P+A+QI G D
Sbjct: 18  MEDVTDVAFRIMCKQF-GADLVYSEFLSADALIRQVAGTFRKMAIDESERPMAVQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ +VEAA++ E  G N I+LN GCP  RV     G+ ++ N  ++ +    + KA+ +P
Sbjct: 77  VASMVEAARLCESAGPNLIDLNFGCPVKRVAGKGAGSGMLRNIPLMIEITREVVKAVKLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ +
Sbjct: 137 VTVKTRLGWDNDSKIIV--DLAEQLQDCGIAALTIHGRT--------RAQMYTGTADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD VM+GRA+     +   +  +   
Sbjct: 187 IGEVKNNPRMQIPIIGNGDVTTPQEARRAFDVYGVDAVMVGRASIGQPWIFEDMKHFLRT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRRC 293
             T  S   +     ++  I    T    R L     +    RH+    +F G PN +  
Sbjct: 247 GETLPSRPFS-----YYMDILRRQTLNNIRKLDERRGILHTRRHIAASPIFKGIPNFKPM 301

Query: 294 R 294
           R
Sbjct: 302 R 302


>gi|296114943|ref|ZP_06833589.1| TIM-barrel protein, nifR3 family [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978501|gb|EFG85233.1| TIM-barrel protein, nifR3 family [Gluconacetobacter hansenii ATCC
           23769]
          Length = 385

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 134/324 (41%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD  +R  AR L    L+ +EMI + A++R +   +         L A+Q+ G D 
Sbjct: 55  MSGVTDLPFRRLARRL-GAGLVVSEMIASWAMVRENSNTLRMAEVAGDGLNAVQLAGCDP 113

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +AA+I  D G N I++N GCP  +V      G+ LM +  +    +A + +A+ +P
Sbjct: 114 DAMAQAARIAVDRGANLIDINFGCPVKKVAVGQQAGSALMRDEALAARLLATVVRAVDVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D    ++    L +  +++G+  + +H R         +        D+  
Sbjct: 174 VTLKMRMGWD--HDSLNAPTLARIAQEAGIRMVTVHGRT--------RQQFYNGTADWRF 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K+   DL + +NG +  +  A + L     DGVMIGR  Y        V    +  
Sbjct: 224 VRRVKEAI-DLPVIVNGDILTVGDAREALAQSGADGVMIGRGCYGRPWFPAQVGAALTRG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P     D    + I          H  +   L+   +H+     G P+S   R  
Sbjct: 283 VIVDEP-----DLATEKDIVLEHYTMMVEHFGAHPGLRLARKHVSWYSAGLPDSAGFRAA 337

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +             ++ A +++ E
Sbjct: 338 VN--------RVDTVDAALSMIGE 353


>gi|25029017|ref|NP_739071.1| putative transcription regulator [Corynebacterium efficiens YS-314]
 gi|259505993|ref|ZP_05748895.1| tRNA-dihydrouridine synthase [Corynebacterium efficiens YS-314]
 gi|23494304|dbj|BAC19271.1| putative transcription regulator [Corynebacterium efficiens YS-314]
 gi|259166474|gb|EEW51028.1| tRNA-dihydrouridine synthase [Corynebacterium efficiens YS-314]
          Length = 381

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 70/324 (21%), Positives = 125/324 (38%), Gaps = 31/324 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNN--ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R      T     L   EM+ A A++  ++K   +  F+  E P +L
Sbjct: 19  MAGVTNVAFRTLCREQEMQRTGTISGLYVCEMVTARALVERNEKTLHMTTFAPDENPRSL 78

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAAK++ D    + I++N GCP  +V     G+ +     +  + ++A 
Sbjct: 79  QLYTVDPQYTYEAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSAIPYKRRLFENIVSAA 138

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK R+G+DD+       +  +    +G   + +HAR A          
Sbjct: 139 VRATEGTDIPVTVKFRVGIDDEHH--THLDAGRIAVDAGAKSVALHARTA--------AQ 188

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R     D++ +  +K+   D  + +  NG +     A +++     DGV++GR       
Sbjct: 189 RYSGQADWNEIARLKEHLADTGVPVLGNGDIFAAEDATRMMEQTGCDGVVVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +   R     M     +H      ++ + +HM    
Sbjct: 249 LFAELSAAVRGEPIPEEPTLGEVTRIILRHAELLM-----QHDGELKGIRDLRKHMGWYL 303

Query: 285 HGFPNSRRCRHILTVEAGASTATH 308
            GFP     R  L   +  +    
Sbjct: 304 RGFPVGGEFRANLARVSTYAELGE 327


>gi|332881487|ref|ZP_08449136.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332680485|gb|EGJ53433.1| TIM-barrel protein, nifR3 family [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 341

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 80/334 (23%), Positives = 146/334 (43%), Gaps = 27/334 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D TD  +R   +     A++Y+E + ADA++R   +++  L     E+P+A+QI G +
Sbjct: 18  MEDVTDIGFRLLCKRF-GAAMVYSEFVAADALVRMVNRSLEKLAVCDDERPVAIQIYGKE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA+IV +    + ++LN GCP  RV     GA ++ N   + +   A+  A+ I
Sbjct: 77  PGPVADAARIVVERARPDMLDLNFGCPVKRVAGKGAGAGMLQNIPKMLEITRAVVDAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    +   +L + ++  G+  + IH R         +        D+ 
Sbjct: 137 PVTVKTRLGWDESSKVIV--DLAERLQDCGIRALTIHGRT--------RAQMYTGEADWT 186

Query: 178 IVYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ E+K  NP   + I  NG +    +A +      VD VM+GRA +    +   + +  
Sbjct: 187 LIGEVKN-NPRMTIPIIGNGDITSPERARECFDCYGVDAVMVGRATFGRPWIFKEIMDVL 245

Query: 234 SNPLTGSSPIKTR-----VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHG 286
           +      +    +     +  D+   +       + R +     +    RH+    +F G
Sbjct: 246 NPESVSVAHEAVKSGYPVMSADWKIDVLKEQVLTSVRRIDEYRGILHSRRHLAASPVFKG 305

Query: 287 FPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
            PN R  R I  + A        I+E A   + +
Sbjct: 306 IPNFRETR-IAMLRAETVDELFAILERAREAVRQ 338


>gi|152967309|ref|YP_001363093.1| TIM-barrel protein, nifR3 family [Kineococcus radiotolerans
           SRS30216]
 gi|151361826|gb|ABS04829.1| putative TIM-barrel protein, nifR3 family [Kineococcus
           radiotolerans SRS30216]
          Length = 388

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 123/305 (40%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   T+  YR   R         +EM+ + A++    +   ++ F+  E+P +LQ+ G D
Sbjct: 28  MAGITNTAYRQLCRE-HGEGFYVSEMVTSRALVERHAETMRLVTFTASERPRSLQLYGVD 86

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKAL- 115
            + +  A ++V +    + ++LN GCP  +V     G+ L    ++    +  A+ +A  
Sbjct: 87  PTTVAAAVRMVVEDDLADHVDLNFGCPVPKVTRKGGGSALPWKAELFRSIVRGAVAEASR 146

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+TVK R G+DD    +      K+ ++ G   + +H R A                
Sbjct: 147 GGIPLTVKMRKGIDDD--HLTYLQAGKAAEQEGAAAVALHGRTA--------SQHYSGQA 196

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D++ +  +K+    + +  NG +     AL+++     DGV++GR       +   ++  
Sbjct: 197 DWEAIARLKETVTTIPVLGNGDVWSAEDALEMVRRTGCDGVVVGRGCLGRPWLFADLEAG 256

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P   +V +   R     +  Y           + I +H+     G+P    
Sbjct: 257 FAGREDRVKPGLRQVAQVLRRHAELLVEFYG----DELRGCRDIRKHVSWYLKGYPVGGD 312

Query: 293 CRHIL 297
            R  L
Sbjct: 313 VRARL 317


>gi|89256322|ref|YP_513684.1| Nif3 family protein [Francisella tularensis subsp. holarctica LVS]
 gi|156502395|ref|YP_001428460.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica FTNF002-00]
 gi|167010847|ref|ZP_02275778.1| NifR3/Smm1 family protein [Francisella tularensis subsp. holarctica
           FSC200]
 gi|254367656|ref|ZP_04983677.1| nif3 family protein [Francisella tularensis subsp. holarctica 257]
 gi|290952884|ref|ZP_06557505.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica URFT1]
 gi|295313929|ref|ZP_06804494.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica URFT1]
 gi|89144153|emb|CAJ79414.1| Nif3 family protein [Francisella tularensis subsp. holarctica LVS]
 gi|134253467|gb|EBA52561.1| nif3 family protein [Francisella tularensis subsp. holarctica 257]
 gi|156252998|gb|ABU61504.1| tRNA-dihydrouridine synthase, TIM-barrel family protein
           [Francisella tularensis subsp. holarctica FTNF002-00]
          Length = 327

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 137/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      ++Y EM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFRTICKEY-GAGMIYMEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINIGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 302 MKLNQLEH-EQEIFKVLEEY 320


>gi|126452924|ref|YP_001067633.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106a]
 gi|167847249|ref|ZP_02472757.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei B7210]
 gi|167912486|ref|ZP_02499577.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 112]
 gi|242318092|ref|ZP_04817108.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106b]
 gi|126226566|gb|ABN90106.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106a]
 gi|242141331|gb|EES27733.1| tRNA-dihydrouridine synthase B [Burkholderia pseudomallei 1106b]
          Length = 354

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 125/308 (40%), Gaps = 26/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GAD
Sbjct: 18  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHAGEVEPIAVQIAGAD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC-----IAAMCK 113
            + + EAA+     G   I++N+GCP+ +V   + G+ L+ N  +V         A    
Sbjct: 77  PAMMAEAARHNVANGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVQRIVEAVVGAVGAG 136

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           A ++PVT+K R G D          +    + +G++ + +H R         + +    +
Sbjct: 137 ADAVPVTLKIRTGWDRDHKNA--LRIATLAEAAGISMLTVHGRT--------RADLYRGD 186

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +YD +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +D 
Sbjct: 187 AEYDTIAAVK-AAVRIPVVANGDITSPRKAKAVLDATRADALMIGRAAQGRPWLFREIDH 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +  +      P    + +     +      Y          ++   +H+     G   + 
Sbjct: 246 FLQSGELLPPPRIDEIRQVMNEHLEDHYAFYGEF-----TGVRTARKHIGWYTRGLSGAN 300

Query: 292 RCRHILTV 299
             RH +  
Sbjct: 301 GFRHRMNT 308


>gi|56461388|ref|YP_156669.1| tRNA-dihydrouridine synthase [Idiomarina loihiensis L2TR]
 gi|56180398|gb|AAV83120.1| Predicted tRNA-dihydrouridine synthase [Idiomarina loihiensis L2TR]
          Length = 323

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 128/300 (42%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R      T   L  +EM+ ++  +    K+   +  S +    A+QI G++
Sbjct: 17  MAGVTDQPFRQLCYS-TGAGLTVSEMLSSNPKVWQTDKSRQRMDHSGELGIRAVQIAGSE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA++    G   I++N+GCP+ +V++   G+ LM +P +V + + A+  A+ +P
Sbjct: 76  PALMAEAARVNVSMGAQIIDINMGCPAKKVNKKMAGSALMQHPGLVEEILTAVVAAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +       ++ +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKTRTGWDPEHRNGI--DIAQLAERCGIQSLAIHGRT--------RACMYKGIAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK    + +  NG +    QA ++L     D +MIGR A  N  +   +  +    
Sbjct: 186 IKAIKKAV-SIPVVANGDIRTPLQAQQVLEYTGADAIMIGRGAQGNPWLFREIAHFLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P  T V +     +      Y      S   ++   +H+        ++   R  
Sbjct: 245 QELSPPSLTEVAETVIHHVGKLHEFY-----GSYQGVRIARKHVGWYLKEQASNDEFRQT 299


>gi|330963424|gb|EGH63684.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 337

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 132/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L    +   +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRQL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHAGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  AQMMADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L     DG++IGRAA     +   ++ Y    
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARHVLQATGADGLLIGRAAQGRPWIFREIEHYLLTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +   + V++     ++A    Y          ++   +H+       P +R  R
Sbjct: 248 EILPALQSSEVERILLEHLAALHVFY-----GDVMGVRIARKHVGWYLATLPGAREFR 300


>gi|260220081|emb|CBA27263.1| tRNA-dihydrouridine synthase B [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 350

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 68/329 (20%), Positives = 132/329 (40%), Gaps = 25/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G +
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVTSRKDLWNSLKTSRRANHDGEPGPIAVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    D G   I++N+GCP+ +V     G+ LM +  +  + + A+ KA    
Sbjct: 76  AAMMAEAAVYNIDRGAQIIDINMGCPAKKVCNKWAGSALMQDEQLAIEIVDAVVKACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G         +  L ++ + +GV  + +H R         ++       +
Sbjct: 136 NVPVTLKMRTGWCQAEKNAVV--LARAAEAAGVQMVTVHGRT--------REQGYKGAAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A  +L     D +MIGRAA     +   V  + 
Sbjct: 186 YDTIAAVKAAL-RIPVVANGDITTPEKARDVLAATGADAIMIGRAAQGYPWIFREVAHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+ + V K     +    + Y          ++   +H+       P     
Sbjct: 245 ATGTHLAPPLVSEVKKLLVEHLYDHYSLYDEFI-----GVRSARKHIGWYLEDLPGGEDF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  + +   +++    + ET  + + E +
Sbjct: 300 RQRMNLFEDSASQVAAV-ETYLDELNEKM 327


>gi|268596189|ref|ZP_06130356.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA19]
 gi|268549977|gb|EEZ44996.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA19]
          Length = 340

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 23  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 82  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDESLVAAILEAVVKAAGVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 142 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 192 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 251 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 305

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 306 INRLDNAA-AQYDTLAGYLERL 326


>gi|68535448|ref|YP_250153.1| hypothetical protein jk0383 [Corynebacterium jeikeium K411]
 gi|68263047|emb|CAI36535.1| hypothetical protein jk0383 [Corynebacterium jeikeium K411]
          Length = 389

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 73/337 (21%), Positives = 132/337 (39%), Gaps = 36/337 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        +   L   EM+ A A++  + K   +  F+  E P +L
Sbjct: 27  MAGVTNVAFRSLCREQERERMGSVAGLYVCEMVTARALVERNPKTLHMTTFAPDEDPRSL 86

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V     G+ L     + G+ +AA 
Sbjct: 87  QLYTTDPEYTYKAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRKLFGNIVAAA 146

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +   + G   + +H R A          
Sbjct: 147 VKATEGTDIPVTVKMRVGIDDEHH--THLDAGRIAVEEGAAAVALHGRTA--------AQ 196

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   + D++ +  +K+   +  + +  NG +   + A  ++     DGV++GR       
Sbjct: 197 RYSGHADWNEIARLKEHLAHTGIPVLGNGDIFKATDARAMMEQTGCDGVVVGRGCLGRPW 256

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          S P    V +   R       +  A H       + + +HM    
Sbjct: 257 LFAELSAELRGLPIPSEPTLGEVARIILRHA-----ELLAAHDGEQKACRDLRKHMTWYL 311

Query: 285 HGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            GFP     R  L+  +         +++A   + +S
Sbjct: 312 RGFPAGGELRRSLSRVSSLDE-----LKSALAEVWDS 343


>gi|255004171|ref|ZP_05278972.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Virginia]
          Length = 304

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 123/314 (39%), Gaps = 20/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R          LL +EMI + A++   ++++   S      A+Q+ G    
Sbjct: 1   MSGVTDMPFRSIVGEF-GAGLLVSEMIASRAMIIKTRQSLQK-SDVGANTAVQLAGCVPE 58

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAKI +D G   I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVT
Sbjct: 59  IMAEAAKINQDMGARSIDINFGCPVKKIVDGHAGSALMKDEEKAAKIMESVVKAVTIPVT 118

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G       +    L K  +  G+  + +H R         +        D+  + 
Sbjct: 119 VKMRMGWSATD--LNAPRLAKIAEDVGIQMVTVHGRT--------RTQMFSGTADWKFIK 168

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K +   + +  NG +  +        L   DGVMIGR AY    ++     +      
Sbjct: 169 CVK-DCVKIPVIANGDIRTLQDITSALSLSGADGVMIGRGAYGKPWLIKQALHFMKTGEA 227

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P       D   +I     D A  +      ++ + +H+         +   R  + 
Sbjct: 228 LPEPS-----ADEKLRIVLKHYDSAVDYYGKDIGVKILRKHLGWYSVSNAGATYFRAQIN 282

Query: 299 VEAGASTATHHIIE 312
             +        ++E
Sbjct: 283 TMSDPVAIREKLLE 296


>gi|183602388|ref|ZP_02963754.1| possible NifR3-like protein [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|219683297|ref|YP_002469680.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis AD011]
 gi|241191258|ref|YP_002968652.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis Bl-04]
 gi|241196664|ref|YP_002970219.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis DSM
           10140]
 gi|183218307|gb|EDT88952.1| possible NifR3-like protein [Bifidobacterium animalis subsp. lactis
           HN019]
 gi|219620947|gb|ACL29104.1| possible NifR3-like protein [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249650|gb|ACS46590.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis Bl-04]
 gi|240251218|gb|ACS48157.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis DSM
           10140]
 gi|295794251|gb|ADG33786.1| NifR3-like protein [Bifidobacterium animalis subsp. lactis V9]
          Length = 417

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 66/328 (20%), Positives = 125/328 (38%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EM+ A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 57  MAGVTNWPFRVLCEEYGPDGLYVAEMVTARALVERNPKALRLCRFAPSERIRSLQLYGVN 116

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
            S + +AA+ + D G  + ++LN GCP  +V     G+ L    D+  + +    A+C+ 
Sbjct: 117 PSIMEQAARFLVDNGMMDHLDLNFGCPVPKVTRRGGGSALPWKTDLFTEIVQRVVAVCEP 176

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +IPVT K R+G+D +          +  ++ G + + +HAR                + 
Sbjct: 177 ANIPVTAKIRVGLDHE--HETFLEAGRIAQEEGCSAVTLHARTT--------AEYYGGHS 226

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +     A+ ++      GV IGR       +   +   
Sbjct: 227 DWCRIGELV-STLDIPVFGNGDIWGAEDAIAMVNETGCAGVAIGRGCQGRPWLFGNIGNA 285

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+      +P    V +   R        Y      +   +  + +H+     GFP    
Sbjct: 286 FAGSDVRINPTLGEVGRIIMRHAELLTEFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 342

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIE 320
            R               +   A +  IE
Sbjct: 343 TRRAFMECESLKDVREQV--DALDPNIE 368


>gi|289177373|gb|ADC84619.1| tRNA-dihydrouridine synthase [Bifidobacterium animalis subsp.
           lactis BB-12]
          Length = 502

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 66/328 (20%), Positives = 125/328 (38%), Gaps = 24/328 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EM+ A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 142 MAGVTNWPFRVLCEEYGPDGLYVAEMVTARALVERNPKALRLCRFAPSERIRSLQLYGVN 201

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
            S + +AA+ + D G  + ++LN GCP  +V     G+ L    D+  + +    A+C+ 
Sbjct: 202 PSIMEQAARFLVDNGMMDHLDLNFGCPVPKVTRRGGGSALPWKTDLFTEIVQRVVAVCEP 261

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +IPVT K R+G+D +          +  ++ G + + +HAR                + 
Sbjct: 262 ANIPVTAKIRVGLDHE--HETFLEAGRIAQEEGCSAVTLHARTT--------AEYYGGHS 311

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +     A+ ++      GV IGR       +   +   
Sbjct: 312 DWCRIGELV-STLDIPVFGNGDIWGAEDAIAMVNETGCAGVAIGRGCQGRPWLFGNIGNA 370

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+      +P    V +   R        Y      +   +  + +H+     GFP    
Sbjct: 371 FAGSDVRINPTLGEVGRIIMRHAELLTEFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 427

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIE 320
            R               +   A +  IE
Sbjct: 428 TRRAFMECESLKDVREQV--DALDPNIE 453


>gi|229588163|ref|YP_002870282.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens SBW25]
 gi|229360029|emb|CAY46883.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens SBW25]
          Length = 337

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 65/300 (21%), Positives = 132/300 (44%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ +        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRMRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVAEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNKNG--LTVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAAIKQAV-SIPVFANGDIDSAEKARRVLHATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 DVLPAPELIEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATLPGAREFRAH 302


>gi|332970433|gb|EGK09425.1| tRNA-dihydrouridine synthase B [Kingella kingae ATCC 23330]
          Length = 340

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 140/325 (43%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR  R  AR    N    +EM+ +D  L+  +K+        ++  + +QI G+D
Sbjct: 25  MAGITDRPTRQLARQFGAN-WTVSEMLSSDPTLQNTQKSRNRRNHDGEQGVIVVQIAGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++L +AA++  + G   I++N+GCP+ +V     G+ L+ N  +V   + A+ +A S+P
Sbjct: 84  PTQLADAARLNAEHGAQVIDINMGCPAKKVCNVLAGSALLQNEKLVEQILHAVVQAASVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD+   +    + K  +++G+  + IH R         +         YD+
Sbjct: 144 VTLKTRLGWDDEHKNI--LTIAKMAEQAGIVALAIHGRT--------RTQMYKGQAQYDL 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+    L +  NG ++   +A ++L     DG++IGRAA     +   V  +  + 
Sbjct: 194 IAEVKQ-TISLPVWANGDIDSPQKARQVLQQTGADGILIGRAAQGQPWLFADVAHFLQHG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++             + +    Y      +G ++    +H+            CR  
Sbjct: 253 TLPNALTMQAACTTILAHVQSLHEFYGEL---AGTRI--ARKHIGWYLARLDGGEACRQH 307

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
           +     A  A +  +        E+
Sbjct: 308 INRLDDAR-AQYDYLARFLEQQCET 331


>gi|126737682|ref|ZP_01753412.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. SK209-2-6]
 gi|126721075|gb|EBA17779.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. SK209-2-6]
          Length = 313

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 127/310 (40%), Gaps = 24/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G +
Sbjct: 1   MAGITDRPFRDLVRSF-GAGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRE 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+ +A+ IP
Sbjct: 60  AEWMAEAARQVADRGARIIDINMGCPAKKVTNGYSGSALLKTPDHALRLIEAVVEAVDIP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD+   +   ++    + +GV  + IH R         +        D+  
Sbjct: 120 VTLKTRLGWDDK--CLNAASVAARAEDAGVQMVTIHGRT--------RCQFYKGQADWSA 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + + K+    + +  NG +     A + L     DGVM+GR       +L  +       
Sbjct: 170 IRQTKEAIT-VPLLANGDITSTETAKRALEQSGADGVMVGRGTQGKPWLLAQISHDLWGA 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
                P    + +       A +  Y          L+   +H+       G P++ R R
Sbjct: 229 TKPEIPRGNDLIRMVSEHYEAMLEFY-----GQDLGLRVARKHLGWYMDEAGTPSALR-R 282

Query: 295 HILTVEAGAS 304
            ILT +    
Sbjct: 283 QILTEKDPKK 292


>gi|149910034|ref|ZP_01898682.1| putative Dihydrouridine synthase [Moritella sp. PE36]
 gi|149806902|gb|EDM66863.1| putative Dihydrouridine synthase [Moritella sp. PE36]
          Length = 321

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 65/298 (21%), Positives = 127/298 (42%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    +  +EM+ ++  +   +K+   +  + +    ++QI GAD
Sbjct: 17  MAGVTDRPFRQLCRDL-GVGMAVSEMLSSNPRVWSTEKSQQRMDHAGETGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +  AA+     G   I++N+GCP+ +V++   G+ LM +P  V   + A+  A+ +P
Sbjct: 76  PALMAAAAQHNVKNGAQIIDINMGCPAKKVNKKMAGSALMQHPAQVKLILDAVISAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  +++G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDLENRNGI--QIAEIAEQAGIQALAVHGRT--------RACLYKGTAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK  +  + +  NG ++   +A ++L    VDG+MIGR A  N  +   ++ Y    
Sbjct: 186 IKAIK-ASISIPVIANGDIDSPEKAKQVLEYTGVDGLMIGRPAQGNPWIFREINHYLKTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                P    V +   + +      Y          ++   +H+        N    R
Sbjct: 245 EKLPVPTADEVRRVILQHVENLHQFYGEF-----KGVRFARKHVGWYIQHQTNGVEFR 297


>gi|119473198|ref|ZP_01614895.1| tRNA-dihydrouridine synthase B [Alteromonadales bacterium TW-7]
 gi|119444562|gb|EAW25877.1| tRNA-dihydrouridine synthase B [Alteromonadales bacterium TW-7]
          Length = 259

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 114/250 (45%), Gaps = 16/250 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ ++  +   +K++  +  S +    A+QI GAD
Sbjct: 20  MAGITDRPFRQLCRRL-GAGLAVSEMLSSNPKVWKTEKSMNRMDHSGESGIRAVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+     G   I++N+GCP+ +V++   G+ L+  P++V + I A+  A+ IP
Sbjct: 79  PELMAQAAQFNVANGAQIIDINMGCPAKKVNKKLAGSALLQFPELVEEIIDAVVNAVDIP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + +H R         +        +Y  
Sbjct: 139 VTLKIRTGWDPDNRNGV--EIARIAERYGIASLAVHGRT--------RACMYKGEAEYAT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IK+ +  + +  NG +    +A ++L     D +MIGRAA     +   +D Y    
Sbjct: 189 IRDIKR-SVSIPVVANGDITSPEKAKQVLDYTGADAIMIGRAAQGRPWIFREIDHYLRTG 247

Query: 237 LTGSSPIKTR 246
                    R
Sbjct: 248 EHMQPTCYCR 257


>gi|255659250|ref|ZP_05404659.1| tRNA-dihydrouridine synthase [Mitsuokella multacida DSM 20544]
 gi|260848704|gb|EEX68711.1| tRNA-dihydrouridine synthase [Mitsuokella multacida DSM 20544]
          Length = 322

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 135/321 (42%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   +++   +L    +E+PLA+QI    
Sbjct: 17  MAGVTDTAYRIIAHDM-GCPLCFAEMVSSQGIHFRNERTLAMLQSEKEERPLAMQIFANT 75

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                EAA  VE  G  + ++ N+GCP+ ++ +   G+ LM +P+     ++A+ KA+ +
Sbjct: 76  PEMAAEAAAFVEALGTADILDFNMGCPAPKIVKNGEGSALMRDPERAFAILSAIRKAVKM 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D    +V +  + K  +++GV+ I +H R         ++       D++
Sbjct: 136 PVTVKMRKGWD--AASVNVVEMAKLAEEAGVDAIAVHGRT--------REQFYTGRADWE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+    + +  NG +        ++ +   DGVMIGRAA  N  +      Y   
Sbjct: 186 IIGEVKRAV-KIPVIANGDVRTFDDLDKIRAVTGCDGVMIGRAAQGNPWIFRQFTHYLET 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          R +     D   ++       +++ +H      G  +    R 
Sbjct: 245 GERLPGPTMKERAAVILRHL-----DLLLKYKGDYVGPREMRKHATWYTRGIVHGAILRD 299

Query: 296 ILTVEAGASTATHHIIETAFN 316
               +A        I+E  F 
Sbjct: 300 RFN-KAVTREDFVEILEEYFE 319


>gi|24371990|ref|NP_716032.1| hypothetical protein SO_0394 [Shewanella oneidensis MR-1]
 gi|38604872|sp|Q8EJR8|DUSB_SHEON RecName: Full=tRNA-dihydrouridine synthase B
 gi|24345845|gb|AAN53477.1|AE015487_11 conserved hypothetical protein [Shewanella oneidensis MR-1]
          Length = 322

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 139/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAALAVSEMLSSNPEVWDTDKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G + I++N+GCP+ +V++   G+ LM NP +V D + A+  A+ +P
Sbjct: 76  PELMAQAAQFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKDILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +  G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWEPEHRNGV--QIAQIAEDCGIASLAVHGRT--------RQCMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG ++   +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NVSIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +        +     ++     Y          ++   +H+        + R+ R  
Sbjct: 245 NKLAPIEVAEQRQVMLEHLTKLYDLY-----GEYKGIRFARKHIGWYL-DQEDQRQFRAD 298

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 A+   + ++E  F+ ++++
Sbjct: 299 FNQLETAAE-QYSLVEYYFDELVQN 322


>gi|256383848|gb|ACU78418.1| tRNA-dihydrouridine synthase B [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384679|gb|ACU79248.1| tRNA-dihydrouridine synthase B [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455465|gb|ADH21700.1| tRNA-dihydrouridine synthase B [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 324

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 132/290 (45%), Gaps = 23/290 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  ++     +L+Y EM+    ++  +KK   +L  +  E P+++QI G D
Sbjct: 17  MAGVSNEAFRIISKQ-HGASLVYAEMVSVAGMVHDNKKTLNMLNVNEIEHPMSMQIFGND 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           + + ++A + +E     + I+LN+GCP+ +V      G+ L+  PD++ + +  + K  +
Sbjct: 76  VDEFIKATQWIEKNVDCDIIDLNLGCPAPKVAIRSQSGSALLKTPDLIYEIVKNVVKNTT 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R+G D    +V    + K I+K+G + I +HAR         +++    + D+
Sbjct: 136 KPVTAKIRLGWDK--NSVNAVEVAKLIEKAGASAIAVHART--------RNDFYTGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+K+    + +  NG + D   A K+L     D VM+ RA   N  +   ++ Y  
Sbjct: 186 EKIKEVKQAV-SIPVIGNGDVIDAKSAKKMLDETGCDAVMVSRACQGNPWIFDQINHYLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  P          + +   +     +H      +++  +H+    
Sbjct: 245 TGKELEKPSFEEWKTTVLQHLDLLVKLKTEQH-----AIKEFRKHLTWYL 289


>gi|23308951|ref|NP_601768.2| TIM-barrel containing enzyme [Corynebacterium glutamicum ATCC
           13032]
 gi|62391408|ref|YP_226810.1| hypothetical protein cg2841 [Corynebacterium glutamicum ATCC 13032]
 gi|21325342|dbj|BAB99963.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Corynebacterium glutamicum ATCC 13032]
 gi|41326749|emb|CAF21231.1| Predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           [Corynebacterium glutamicum ATCC 13032]
          Length = 381

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 124/314 (39%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNN--ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R      T     L   EM+ A A++  ++K +    F+  E P +L
Sbjct: 19  MAGVTNVAFRTLCREQEMQRTGTISGLYVCEMVTARALVERNEKTMHMTTFAPDENPRSL 78

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAAK++ D    + I++N GCP  +V     G+ +     +  + ++A 
Sbjct: 79  QLYTVDPKYTYEAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSAIPYKRRLFENIVSAA 138

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +    +G   + +HAR A          
Sbjct: 139 VKATEGTDIPVTVKFRVGIDDEHH--THLDAGRIAVDAGAKSVALHARTA--------AQ 188

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R     D++ +  +K+   D  + +  NG +   S A +++     DGV++GR       
Sbjct: 189 RYSGEADWNEIARLKEHLADTGIPVLGNGDIFAASDATRMMEQTGCDGVVVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +   R     M     +H      L+ + +HM    
Sbjct: 249 LFAELSAAVRGEEIPEEPTFGEVTQIILRHAELLM-----QHDGETKGLRDLRKHMGWYL 303

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 304 RGFPVGGEFRSNLA 317


>gi|46190134|ref|ZP_00206339.1| COG0042: tRNA-dihydrouridine synthase [Bifidobacterium longum
           DJO10A]
          Length = 361

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 122/318 (38%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 1   MAGVTNWPFRVICEEYGPDGLYVAEMITARALVAHNPKALRLCHFAKSEKIRSLQLYGVN 60

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---IAAMCKA 114
            S   +AAKIV D    + ++LN GCP  +V     G+ L    DI  +    + A+C+ 
Sbjct: 61  PSITEQAAKIVVDGNMADHVDLNFGCPVPKVTRRGGGSALPWKTDIFTELLQRVVAVCEP 120

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 121 AGIPVTAKIRVGID--HNHETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 170

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K E+ ++ +  NG +     AL+++     DGV IGR       +   +   
Sbjct: 171 DWSRIGELK-EHLNIPVFGNGDIWGAEDALEMVRETGCDGVAIGRGCQGRPWLFANIKNA 229

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F       +P    V +   R        Y    + +   +  + +H+     GFP    
Sbjct: 230 FEGNPERLNPNLGEVCRVIHRHAELLTEFYEGDEMMA---VHDLRKHIAWYLKGFPVGGS 286

Query: 293 CRHILTVEAGASTATHHI 310
            R         +     I
Sbjct: 287 TRKAFMECESLADVDREI 304


>gi|308389527|gb|ADO31847.1| nifR3 protein [Neisseria meningitidis alpha710]
 gi|325130494|gb|EGC53251.1| dihydrouridine synthase [Neisseria meningitidis OX99.30304]
          Length = 374

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 55  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 114 PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 173

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 174 VTLKTRLGWHEDHQNLPV--IAKIAEDCGITALAVHGRT--------RTQMYKGEARYEL 223

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 224 IAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 282

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 283 VLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIGEMPDGEQARRE 337

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 338 IN-RLDSAAAQYDMLAGYLERL 358


>gi|297568450|ref|YP_003689794.1| hypothetical protein [Desulfurivibrio alkaliphilus AHT2]
 gi|296924365|gb|ADH85175.1| TIM-barrel protein, nifR3 family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 313

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 127/316 (40%), Gaps = 31/316 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  +R   R      L Y+EMI    ++R     +  L     E+P+ +Q+ GA+ 
Sbjct: 23  AGFSDLAFRLLCREY-GAGLCYSEMISCHGLVRQQPSTLELLATVPAERPVIMQLFGAEP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + +AA I+     + I++N+GCP  +V +   GA LM  P++    + A+ KA  +PV
Sbjct: 82  EVMGQAAAILSRLPIDGIDINMGCPVKKVVKKGAGAALMRQPELAAAIVTAVVKATELPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G + Q   +      +  +  G   I +H R          D R        ++
Sbjct: 142 TVKIRTGWNHQR--ITAPEFARRCEDCGAAAITVHGRTWSDGFSGRADQR--------LI 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  NG +    +A+ ++     DGVMIGR A     + +        P 
Sbjct: 192 AAVKQAV-KVPVIGNGDVTCHQEAVAMMANTGCDGVMIGRGAIGAPWVFS--------PD 242

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +SP   R      R +   +  Y   H  S     QI R     F G P     R  +
Sbjct: 243 FPTSPTLPRRLAAARRHL-ELLQQYHPHHHPSRIN-NQIGR----YFKGVPGGAAIRKEI 296

Query: 298 TVEAGASTATHHIIET 313
             EA    A   +++ 
Sbjct: 297 -YEAVNPAALAGLLQR 311


>gi|38234473|ref|NP_940240.1| hypothetical protein DIP1903 [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200736|emb|CAE50438.1| Putative exported protein [Corynebacterium diphtheriae]
          Length = 383

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 124/314 (39%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EMI A A++  ++K   +  F  QE   +L
Sbjct: 21  MAGVTNIAFRTLCREQELERTGTVSGLYICEMITARALVERNEKTLHMTTFGPQEDIRSL 80

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ +    + I++N GCP  +V +   G+ L     + G+ +AA 
Sbjct: 81  QLYTVDPEYTYKAAKMIAENNMADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGNIVAAA 140

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            K +    IP+TVK R+G+DD    +   +  +   + G   + +HAR A          
Sbjct: 141 VKGVEGTDIPITVKFRMGIDDD--HLTYLDAGRIAAEEGAAAVTLHARTA--------AE 190

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   +  +D +  +K+   D  + +  NG +     A  +L     DGV++GR       
Sbjct: 191 RYSGDAHWDAIGTLKEHMRDSGIPVLGNGDIFKAEDAKAMLDASGCDGVVVGRGCLGRPW 250

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +  +R       +  A H       + + +HM    
Sbjct: 251 LFAGISAALRGEELPPEPTLGEVTRIIYRHA-----ELLAEHDGEKKASRDMRKHMGWYM 305

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 306 RGFPVGGEFRGALA 319


>gi|260072681|gb|ACX30578.1| tRNA-dihydrouridine synthase [uncultured SUP05 cluster bacterium]
          Length = 324

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 127/287 (44%), Gaps = 21/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D+ +R   R     AL  +EM+V    L G  K+   L FS +  P+++QI G+ 
Sbjct: 19  MAGTSDKPFRAICR-AQGAALTTSEMVVIQKHLLGTNKSKHRLDFSGEPAPISIQIAGSQ 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  +A+    FG + I++N+GCP+ +V   + G+ LM +  +V   + A+  A+ IP
Sbjct: 78  ADELAYSAQQALKFGADIIDINMGCPAKKVCNKAAGSALMQDEALVKSILNAVVSAVDIP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G    +       + K  +++G+  + +H R         ++++     +YD 
Sbjct: 138 VTLKMRTGW--NVSNKNAPTIAKIAEEAGIQMLSVHGRT--------REDKYTGMAEYDT 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +    +A  +L     DGVM+GRA   N  ++  +D Y    
Sbjct: 188 IKAVKSQVG-IPVIANGDITSAKKAQSVLQYTGADGVMVGRATQGNPWIIHEIDHYLKTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
              +        +     I      Y  +    G +L    +H+   
Sbjct: 247 QKATDIPLNVKKQTILDHIKQIHAFYGEKL---GTQLS--RKHIFWY 288


>gi|331703079|ref|YP_004399766.1| hypothetical protein MLC_0590 [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328801634|emb|CBW53787.1| Conserved hypothetical protein, probable tRNA dihydrouridine
           synthase (NifR3 family) [Mycoplasma mycoides subsp.
           capri LC str. 95010]
          Length = 324

 Score =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 132/290 (45%), Gaps = 23/290 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  +R     +L+Y EM+    ++  +KK   +L  +  E P+++QI G D
Sbjct: 17  MAGVSNEAFRIISRQ-HGASLVYAEMVSVAGMVHDNKKTLNMLNVNEIEHPMSMQIFGND 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           + + ++A + +E     + I+LN+GCP+ +V      G+ L+  PD++ + +  + K  +
Sbjct: 76  VDEFIKATQWIEKNVDCDIIDLNLGCPAPKVAIRSQSGSALLKTPDLIYEIVKNVVKNTT 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R+G D    +V    + K I+K+G + I +HAR         +++    + ++
Sbjct: 136 KPVTAKIRLGWDK--NSVNAVEVAKLIEKAGASAIAVHART--------RNDFYTGHANW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+K+    + +  NG + D   A K+L     D VM+ RA   N  +   ++ Y  
Sbjct: 186 EKIKEVKQAV-SIPVIGNGDVIDAKSAKKMLDETGCDAVMVSRACQGNPWIFDQINHYLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  P          + +   +     +H      +++  +H+    
Sbjct: 245 TGKELEKPNFEEWKTTVLQHLGLLVKLKTEQH-----AIKEFRKHLTWYL 289


>gi|218961108|ref|YP_001740883.1| dihydrouridine synthase family protein [Candidatus Cloacamonas
           acidaminovorans]
 gi|167729765|emb|CAO80677.1| dihydrouridine synthase family protein [Candidatus Cloacamonas
           acidaminovorans]
          Length = 321

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 62/317 (19%), Positives = 129/317 (40%), Gaps = 24/317 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  +R   +      +LY+EM+ AD + R   K +  + F   E P  +QI G++ 
Sbjct: 17  AGYSDSAFRQICKNW-GAEVLYSEMVSADGLTRNSAKTLQYVQFDESEHPFGIQIFGSNP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SI 117
             +  A +++     + +++N+GCP  +V     G+ LM  P + G  +  +  AL   I
Sbjct: 76  LIMARAVEVLLPLKPDFMDINMGCPVKKVIRKGAGSALMQTPSLAGKIVKEVKNALLGRI 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P++VK R G + Q            +++ G + + +H R                  +++
Sbjct: 136 PLSVKFRSGWNFQ--NQNYLQFGLMLQECGADFLCLHPRT--------SSQMFSGTSNWE 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+ N  + +  NG ++    A +++     DG+MIGR A     +     +  S 
Sbjct: 186 QIKILKQ-NVQIPVVGNGDIKTPEDAQRMITETNCDGIMIGRGALGKPWLFAQSRQLIST 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T +  I+  + K  +  +     D A  +      ++++  H+     G       R+
Sbjct: 245 G-TYNPVIQKEIVKTIFAHL-----DKALLYKSEDVVVREMRAHLCFYTKGILGGAELRN 298

Query: 296 ILTVEAGASTATHHIIE 312
            +      S     I++
Sbjct: 299 QINHTENISELKAIILK 315


>gi|222475071|ref|YP_002563486.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Florida]
 gi|222419207|gb|ACM49230.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Florida]
          Length = 320

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 123/314 (39%), Gaps = 20/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R          LL +EMI + A++   ++++   S      A+Q+ G    
Sbjct: 17  MSGVTDMPFRSIVGEF-GAGLLVSEMIASRAMIIKTRQSLQK-SDVGANTAVQLAGCVPE 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAKI +D G   I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVT
Sbjct: 75  IMAEAAKINQDMGARSIDINFGCPVKKIVDGHAGSALMKDEEKAAKIMESVVKAVTIPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G       +    L K  +  G+  + +H R         +        D+  + 
Sbjct: 135 VKMRMGWSATD--LNAPRLAKIAEDVGIQMVTVHGRT--------RTQMFSGTADWKFIK 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K +   + +  NG +  +        L   DGVMIGR AY    ++     +      
Sbjct: 185 CVK-DCVKIPVIANGDIRTLQDITSALSLSGADGVMIGRGAYGKPWLIKQALHFMKTGEA 243

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P       D   +I     D A  +      ++ + +H+         +   R  + 
Sbjct: 244 LPEPS-----ADEKLRIVLKHYDSAVDYYGKDIGVKILRKHLGWYSVSNAGATYFRAQIN 298

Query: 299 VEAGASTATHHIIE 312
             +        ++E
Sbjct: 299 TMSDPVAIREKLLE 312


>gi|163845808|ref|YP_001633852.1| NifR3 family TIM-barrel protein [Chloroflexus aurantiacus J-10-fl]
 gi|222523518|ref|YP_002567988.1| TIM-barrel protein, nifR3 family [Chloroflexus sp. Y-400-fl]
 gi|163667097|gb|ABY33463.1| TIM-barrel protein, nifR3 family [Chloroflexus aurantiacus J-10-fl]
 gi|222447397|gb|ACM51663.1| TIM-barrel protein, nifR3 family [Chloroflexus sp. Y-400-fl]
          Length = 350

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 87/329 (26%), Positives = 140/329 (42%), Gaps = 30/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM-----IVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     L    L+ TEM     +   A+ R     +L +  +E+PL +QI 
Sbjct: 33  MAGVTDSIFRRMILRLGGCGLVSTEMTNAASVSPKALRRH---RLLDYLPEERPLTMQIS 89

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   +  AA++VE  G + I++N GCPS +V  G  G+ L+ +   +   + A+ +A+
Sbjct: 90  GNDPDLVANAARVVEQLGADIIDINCGCPSPKVTGGGHGSALLRDLPKMERLLRAVREAV 149

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT+K R G D+Q  ++      K  + +GV+ + +H R         ++       D
Sbjct: 150 QIPVTLKFRAGWDEQ--SLNFIEAGKRAEAAGVSALALHPRT--------REQGYKGQAD 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V  +K+    + +  +G +     AL  L     DGVMIGR A  N  +   + +  
Sbjct: 200 WSRVAALKQAV-SIPVIGSGDVTSAHDALIRLRDSGADGVMIGRGAMANPWIFRQIAD-L 257

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
              +T   P          R +        A  L     L +I + +IG FH G P S  
Sbjct: 258 RRGVTPYVPTPAD-----KRNLLIEYMTICAEELPERLALNKI-KQLIGQFHVGLPGSNH 311

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R  +      + A    IE  F   +ES
Sbjct: 312 LRVAVHTSTSLAEA-RDAIERFFAPFLES 339


>gi|270283991|ref|ZP_05965366.2| putative tRNA-dihydrouridine synthase [Bifidobacterium gallicum DSM
           20093]
 gi|270277877|gb|EFA23731.1| putative tRNA-dihydrouridine synthase [Bifidobacterium gallicum DSM
           20093]
          Length = 422

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 67/304 (22%), Positives = 121/304 (39%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 62  MAGVTNWPFRVLCEQYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVN 121

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            S + +AAKIV D    + ++LN GCP  +V     G+ L    D+  D ++ + +   A
Sbjct: 122 PSIMEQAAKIVVDEQMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFTDVVSRVVRVCDA 181

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 182 AGIPVTAKIRVGIDHE--HETFHEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+ ++  D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 232 DWSRIGELVEQL-DVPVFGNGDIWGAADALAMVEQTGCAGVAIGRGCQGRPWLFADIKHA 290

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+     + P   +V +   R  +     Y      +      + +H+     GFP    
Sbjct: 291 FAGSDERTDPTLGQVCQVIMRHATYLTEFYDGDERMAA---HDMRKHVAWYLKGFPVGGG 347

Query: 293 CRHI 296
            R  
Sbjct: 348 VRRA 351


>gi|54114569|gb|AAV29918.1| NT02FT1147 [synthetic construct]
          Length = 327

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 138/320 (43%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +    +      L+YTEM+   A++  + + +  L     EKPL +QI G D
Sbjct: 19  MAGFCDSAFPTICKE-HGAGLIYTEMVSNKAVVEHNWETMEMLYMENSEKPLGIQIFGTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I+  V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  INSFVGATKYIAENTECDFLDINMGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 302 MKLNQLEH-EQEIFKVLEEY 320


>gi|42528231|ref|NP_973329.1| NifR3 family TIM-barrel protein [Treponema denticola ATCC 35405]
 gi|41819501|gb|AAS13248.1| TIM-barrel protein, putative, NifR3 family [Treponema denticola
           ATCC 35405]
          Length = 333

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 136/326 (41%), Gaps = 28/326 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D+ +R    +       YTEM+ ++A++R   K   ++G +  EK  A+QI G++ 
Sbjct: 23  AGYSDKAFRSIC-VDCGADFTYTEMVSSEALVRDSDKTESLIGRAPNEKAYAVQIFGSNP 81

Query: 60  SKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
             + + A  I E +    I++N GCP A++ +   G+ LM +  ++   + A+  A+   
Sbjct: 82  EYMAKTAVIIAEKYSPECIDINSGCPMAKITKNGAGSALMTDIPLLYRIVKAVNDAMAPY 141

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT+K R G       +  +    +   +GV  + +H R         +        D
Sbjct: 142 KIPVTLKIRSGF--TADKLNWKEAASAAIDAGVKMLTLHPRT--------RSQVYSGKAD 191

Query: 176 YDIVYEIKKENP--DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           ++I+ E+ +      + I  +G L     A K+L      G+M  R A  N  + T   E
Sbjct: 192 WNILAELVQFAKPYQIPIFGSGDLFSPEDAKKMLEETGCAGIMFARGAMGNPFIFTQTRE 251

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +N   G    + ++   F   I      +           +++ +       G P+  
Sbjct: 252 LLTNGTYGEISTEQKIRTGFKELI------FLCDEKGEEKGCREMRKRFAAYTKGIPDGS 305

Query: 292 RCRHILTVEAGASTATHHIIETAFNL 317
           R R  L V+A        II++AFN+
Sbjct: 306 RLRQEL-VQASTIAEYKAIIQSAFNI 330


>gi|88809287|ref|ZP_01124796.1| hypothetical protein WH7805_06326 [Synechococcus sp. WH 7805]
 gi|88787229|gb|EAR18387.1| hypothetical protein WH7805_06326 [Synechococcus sp. WH 7805]
          Length = 338

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 135/327 (41%), Gaps = 29/327 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADIS 60
              +D+ +R   R  + +ALL+TEM+ A ++  G  +  +    QE  P+ +Q+      
Sbjct: 30  AGVSDKIFRALVRRWSRDALLFTEMVNATSLELGHGRGKVEELRQEAGPIGVQLFDHRPE 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  ED G   I++N+GCP  ++     G+ L+ +PD+    + A+  A+ IPVT
Sbjct: 90  SMADAARRAEDAGAFLIDINMGCPVRKIARKGGGSGLIRDPDLACTIVEAVVAAVGIPVT 149

Query: 121 VKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           VK R+G            A     + ++ +G   + +H R         ++ R     D+
Sbjct: 150 VKTRLGWCSVPQGGDSHAAAMAWCRRLEAAGAQLLTLHGRT--------REQRFSGRADW 201

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K+    + +  NG +     A + L     DGVM+GR       ++  +D    
Sbjct: 202 EAIAAVKRAL-RIPVIANGDVFSPEDARECLGVTGADGVMVGRGTMGAPWLVGQIDAALK 260

Query: 235 NPLTGSSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                 +P  +    +  D  + + A+  D+          L    +HM     GF  + 
Sbjct: 261 GLPVPPTPGASERLMIAADQLQALVAARGDH---------GLLIARKHMSWTCTGFNGAS 311

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
           + R  L + A        ++    + +
Sbjct: 312 QFRQQL-MRAPTPDQALSLLRRQHDQL 337


>gi|282891207|ref|ZP_06299710.1| hypothetical protein pah_c048o037 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498900|gb|EFB41216.1| hypothetical protein pah_c048o037 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 342

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 134/317 (42%), Gaps = 24/317 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
              +D  +R  +   +   L+Y EM+  DA++R D     +L F     P+  Q+ G+  
Sbjct: 24  AGCSDFPFRQMSARYS-PGLMYCEMVKMDALVRHDPNTFRMLDFDKDMHPIGGQLCGSKP 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               +AAKI+ED G++ ++LN GCP  +V +   G+ L+ NP ++G+ ++ M  A+ IPV
Sbjct: 83  QLAAKAAKIIEDLGFDVVDLNCGCPVDKVTKDGSGSGLLKNPLLIGEILSEMVAAVKIPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD+   +    + +  +K+G   I IH R         +        ++D +
Sbjct: 143 TVKIRAGWDDE--NLCAEEITQIAEKAGAKAITIHGRT--------RQQAYRGPANWDHI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              K+    + +  NG + D + A ++      D V++ R       +   +  Y     
Sbjct: 193 KASKQVAKHIKVIGNGDVMDPTSAKRMFEYTGCDAVLVARGTMGQPWIAQDILNYLQGGT 252

Query: 238 TG-SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P   R  +  +     +   Y  R +     + ++ R           +R  R +
Sbjct: 253 IRVHTPEDCR--QALYEHFLCTERYYNPRQV-----VIEMRRVGCWYIKSSGGTREFRGL 305

Query: 297 LTVEAGASTATHHIIET 313
           ++  A +      +I+ 
Sbjct: 306 IS-RASSPDQVKDLIQN 321


>gi|221481338|gb|EEE19732.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii GT1]
 gi|221502060|gb|EEE27806.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 394

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 114/351 (32%), Positives = 162/351 (46%), Gaps = 35/351 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+  T+ H+R F R  T  A L+TEM+   AIL    +    L     E P+  Q+GG+D
Sbjct: 20  MLAVTNTHFRNFMRCFTREAQLWTEMVTDGAILNNMDRLQQNLCLEDIEHPIVCQLGGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
              L EA K++E  G++EINLNVGCPS RV     FGA LM  P+ V D +  + + + I
Sbjct: 80  PKTLAEAGKLIEKLGFDEINLNVGCPSNRVVSQGCFGAALMKTPETVRDIVHEIRRHVQI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D       LRN V+++   G     IHARKA LKG+ PK NR +P L Y 
Sbjct: 140 PVTVKTRIGYDHCDSRDVLRNFVQTVSAGGCRHFIIHARKAWLKGVDPKKNRSVPPLLYG 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD----------------------GV 213
            VY++  + P L   LNGG+  + QA+ +      D                      GV
Sbjct: 200 RVYDLCDQFPHLDFSLNGGVRSIQQAIDLAAGKWTDGTAEMDALLRRITRDKTVKPLRGV 259

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GRAA  +  +L  VD  F           +R  +         +  +A    +S   L
Sbjct: 260 MLGRAASADPCILANVDTDFYGADANPPTSHSR--RTVLEAYRNYIKPFAEDGEYSHFAL 317

Query: 274 QQITRHMIGLFHGFPNSRRCR---HILTVEAGASTATHHIIETAFNLMIES 321
               + ++G+F+G P +R  R     L  +         I+      + E+
Sbjct: 318 L---KPVLGVFNGMPGNRLFRFTLDHLMRDQSRVWTAEEILAHTMAAVDET 365


>gi|269958877|ref|YP_003328666.1| dihydrouridine synthase [Anaplasma centrale str. Israel]
 gi|269848708|gb|ACZ49352.1| dihydrouridine synthase [Anaplasma centrale str. Israel]
          Length = 304

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 120/314 (38%), Gaps = 20/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R     L    LL +EMI + A++   ++++   S      ++Q+ G    
Sbjct: 1   MSGVTDMPFRSIVGEL-GAGLLVSEMIASRAMIIKTRQSLQK-SDVGANTSVQLAGCVPE 58

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAKI +D G   I++N GCP  ++ +G  G+ LM +       + ++  A++IPVT
Sbjct: 59  IMAEAAKINQDMGAMSIDINFGCPVKKIVDGHAGSALMKDEAKAAKIMESVVNAVTIPVT 118

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G       +    L K  + +G+  + +H R         +        D+  + 
Sbjct: 119 VKMRMGWSPTD--LNAPRLAKIAEDAGIRMVTVHGRT--------RSQMFSGTADWKFIK 168

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K +   + +  NG +           L   DGVMIGR AY    ++     +      
Sbjct: 169 CVK-DCVKIPVIANGDIRTFQDITDALNLSGADGVMIGRGAYGKPWLIKQALHFIKTREA 227

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P          R       D A  +      ++ + +H+         S   R  + 
Sbjct: 228 LPEPSADEKLNIVLRHY-----DSAIDYYGKDIGVKILRKHLGWYSASNAGSACFRAQVN 282

Query: 299 VEAGASTATHHIIE 312
             +        ++E
Sbjct: 283 TMSDPVAIRERLLE 296


>gi|325204406|gb|ADY99859.1| dihydrouridine synthase [Neisseria meningitidis M01-240355]
          Length = 336

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  KK +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTKKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHEDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERL 320


>gi|240117283|ref|ZP_04731345.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID1]
 gi|240125030|ref|ZP_04737916.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-92-679]
          Length = 364

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++   +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 330 INRLDNAA-AQYDTLAGYLERL 350


>gi|123966327|ref|YP_001011408.1| nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9515]
 gi|123200693|gb|ABM72301.1| putative nitrogen regulation protein NifR3 family-like protein
           [Prochlorococcus marinus str. MIT 9515]
          Length = 335

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 134/320 (41%), Gaps = 21/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD-KKNILGFSTQEKPLALQIGGADIS 60
              TD+ +R   R    ++LL+TEMI A ++  G   + I     ++ P+ +QI      
Sbjct: 26  AGVTDKVFRKLVRKWAPDSLLFTEMINATSLKEGHGTQKIKQLELEQGPIGVQIFDNRPF 85

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N+GCP  ++ +   G+ L+ +  +  + +  + KA+ IPVT
Sbjct: 86  AVSEAAKLAEDSGAFLIDINMGCPVKKISKKGGGSALIKDRLLAVELVKRVSKAVKIPVT 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D++     +   + S++ SG   I +H R    +G S          D+D++ 
Sbjct: 146 VKTRLGWDNKE--ENIEEFLLSLQDSGATMITLHGRTRK-EGFSGA-------ADWDMIG 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            IK E+ ++ +  NG ++    A   L   + DG+MIGR    +   +  +D        
Sbjct: 196 RIK-EHLEIPVIANGDIKTPEDAFNCLKKTNADGLMIGRGILGSPWKIGEIDYAIKKVKG 254

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +           L    +H+      F  +   R+ L 
Sbjct: 255 FKEPNVEEKLLLIIEHLDELIKEKGNH------GLLIARKHISWTCKNFQGANNLRNEL- 307

Query: 299 VEAGASTATHHIIETAFNLM 318
           V A        +I      +
Sbjct: 308 VRAINVKEVKELINKTIERL 327


>gi|237838939|ref|XP_002368767.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211966431|gb|EEB01627.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
          Length = 394

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 113/351 (32%), Positives = 162/351 (46%), Gaps = 35/351 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+  T+ H+R F R  T  A L+TEM+   AIL    +    L     E P+  Q+GG+D
Sbjct: 20  MLAVTNTHFRNFMRCFTREAQLWTEMVTDGAILNNMDRLQQNLCLEDIEHPIVCQLGGSD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
              L EA K++E  G++EINLNVGCPS RV     FGA LM  P+ V D +  + + + I
Sbjct: 80  PKTLAEAGKLIEKLGFDEINLNVGCPSNRVVSQGCFGAALMKTPETVRDIVHEIRRHVQI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D       LRN V+++   G     +HARKA LKG+ PK NR +P L Y 
Sbjct: 140 PVTVKTRIGYDHCDSRDVLRNFVQTVSAGGCRHFIVHARKAWLKGVDPKKNRSVPPLLYG 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD----------------------GV 213
            VY++  + P L   LNGG+  + QA+ +      D                      GV
Sbjct: 200 RVYDLCDQFPHLDFSLNGGVRSIQQAIDLAAGKWTDGTAEMDALLRRITRDKTVKPLRGV 259

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GRAA  +  +L  VD  F           +R  +         +  +A    +S   L
Sbjct: 260 MLGRAASADPCILANVDTDFYGADANPPTSHSR--RTVLEAYRNYIKPFAEDGEYSHFAL 317

Query: 274 QQITRHMIGLFHGFPNSRRCR---HILTVEAGASTATHHIIETAFNLMIES 321
               + ++G+F+G P +R  R     L  +         I+      + E+
Sbjct: 318 L---KPVLGVFNGMPGNRLFRFTLDHLMRDQSRVWTAEEILAHTMAAVDET 365


>gi|271967481|ref|YP_003341677.1| hypothetical protein Sros_6205 [Streptosporangium roseum DSM 43021]
 gi|270510656|gb|ACZ88934.1| conserved hypothetical protein [Streptosporangium roseum DSM 43021]
          Length = 373

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 124/322 (38%), Gaps = 23/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L   EMI   A++  + K   ++ F   EKP ++Q+ G D
Sbjct: 20  MAGITNAPFRTLCREQGG-GLFVCEMITTRALVERNAKTFKMIRFEPAEKPRSIQLYGVD 78

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALS 116
              + +A +++ D    + ++LN GCP  +V     G+ L    +++   +  A+  A +
Sbjct: 79  PVTVGKAVRMIADEDLADHVDLNFGCPVPKVTRRGGGSALPYKRNLLRAILREAVRNAGT 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R G+DD    +   +  +   + GV+ I +H R A+               D+
Sbjct: 139 LPVTMKMRKGIDDD--HLTYLDAGRIAVEEGVSAIALHGRTAV--------QHYGGTADW 188

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K+   ++ +  NG +   + AL+++     DGV++GR       +   +     
Sbjct: 189 EAIARLKEAVTEIPVLGNGDIWSAADALRMMDETGCDGVVVGRGCLGRPWLFRDLAVACE 248

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P    V     R  +      A         +    +H+     GF      R
Sbjct: 249 GGRERLRPPLGEVAATMDRHATL----LAECFGSEPHAVADFRKHVGWYLKGFTVGSDLR 304

Query: 295 HILTVEAGAST--ATHHIIETA 314
             L      +        ++ A
Sbjct: 305 RRLATSVTLAGLREGLAELDAA 326


>gi|312138334|ref|YP_004005670.1| tRNA-dihydrouridine synthase [Rhodococcus equi 103S]
 gi|325674749|ref|ZP_08154436.1| dihydrouridine synthase [Rhodococcus equi ATCC 33707]
 gi|311887673|emb|CBH46985.1| tRNA-dihydrouridine synthase [Rhodococcus equi 103S]
 gi|325554335|gb|EGD24010.1| dihydrouridine synthase [Rhodococcus equi ATCC 33707]
          Length = 380

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 69/309 (22%), Positives = 118/309 (38%), Gaps = 29/309 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      + + L   EM+ A A++       ++  F   E P +L
Sbjct: 20  MAGITNVAFRTLCRELELERAGSTSGLYVCEMVTARALVERHPVTMHMTTFGPTETPRSL 79

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V     G+ L     + G  +AA 
Sbjct: 80  QLYTVDPEITYQAAKMIVDENLADHIDMNFGCPVPKVTRKGGGSALPYKRRLFGQIVAAA 139

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+D +       +  +     G   + +H R A          
Sbjct: 140 VKATEGTDIPVTVKMRVGIDAEHH--THLDAGRIAAAEGAAAVALHGRTA--------AQ 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D+  +  +K+   D+ +  NG +     A K++     DGV++GR       + 
Sbjct: 190 RYSGQADWSEIARLKEHVTDVPVLGNGDIFAAEDAEKMMSETGCDGVVVGRGCLGRPWLF 249

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +    +       P    V     R          A H      ++++ +H+     G
Sbjct: 250 AELSAALNGTEMPVPPNLGEVAAIMMRH-----GRLLADHHGEDKGMREMRKHIAWYMRG 304

Query: 287 FPNSRRCRH 295
           FP     R+
Sbjct: 305 FPAGSELRN 313


>gi|145296565|ref|YP_001139386.1| hypothetical protein cgR_2473 [Corynebacterium glutamicum R]
 gi|140846485|dbj|BAF55484.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 363

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 73/314 (23%), Positives = 124/314 (39%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARL----LTNN--ALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R      T     L   EM+ A A++  ++K +    F+  E P +L
Sbjct: 1   MAGVTNVAFRTLCREQEMQRTGTISGLYVCEMVTARALVERNEKTMHMTTFAPDENPRSL 60

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAAK++ D    + I++N GCP  +V     G+ +     +  + ++A 
Sbjct: 61  QLYTVDPKYTYEAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSAIPYKRRLFENIVSAA 120

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +    +G   + +HAR A          
Sbjct: 121 VKATEGTDIPVTVKFRVGIDDEHH--THLDAGRIAVDAGAKSVALHARTA--------AQ 170

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R     D++ +  +K+   D  + +  NG +   S A +++     DGV++GR       
Sbjct: 171 RYSGEADWNEIARLKEHLADTGIPVLGNGDIFAASDATRMMEQTGCDGVVVGRGCLGRPW 230

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +   R     M     +H      L+ + +HM    
Sbjct: 231 LFAELSAAVRGEEIPEEPTFGEVTQIILRHAELLM-----QHDGETKGLRDLRKHMGWYL 285

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 286 RGFPVGGEFRSNLA 299


>gi|7573334|emb|CAB87804.1| putative protein [Arabidopsis thaliana]
          Length = 456

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 109/380 (28%), Positives = 170/380 (44%), Gaps = 63/380 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL+T +A LYTEMI A+ ++         L FS Q+ P+ LQ+GG++
Sbjct: 44  MMDWTDNHYRTLARLITKHAWLYTEMIAAETLVHQQTNLDRFLAFSPQQHPIVLQLGGSN 103

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPD--------------- 102
           +  L +AAK+ + +GY+EINLN GCPS +V     FG  LML P                
Sbjct: 104 VENLAKAAKLSDAYGYDEINLNCGCPSPKVAGHGCFGVSLMLKPKVRYFTPPHDFKRYLL 163

Query: 103 ---------IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR---------------- 137
                    +VG+ ++A+    ++PVTVKCRIGVD+      L                 
Sbjct: 164 FLNFTLSFKLVGEAMSAIAANTNVPVTVKCRIGVDNHDSYDELCELFLLSVFLKSRMDLP 223

Query: 138 ------------NLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
                       + +  +   S      +H+RKA+L G+SP DNR+IP L Y+  Y + +
Sbjct: 224 LRSNTAFPLLLGDFIYKVSTLSPTRHFIVHSRKALLGGISPADNRRIPPLKYEYYYALVR 283

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFSNPLTGSSP 242
           + PDL   +NGG+  +S+    L     GVM+GRAAY N    L  VD           P
Sbjct: 284 DFPDLRFTINGGITSVSKVNAALKEGAHGVMVGRAAYNNPWQTLGQVDTAVYG-----VP 338

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAG 302
                 +    +           H +    ++ + + ++ LFH    +   +        
Sbjct: 339 SSGLTRRQVLEQYQVYGDSVLGTHGNGRPNVRDLVKPLLNLFHSENGNSLWKRRADAAFK 398

Query: 303 ASTATHHIIETAFNLMIESL 322
              +   ++E +   + + +
Sbjct: 399 ECRSVGSLLEESLRAIPDCV 418


>gi|269468440|gb|EEZ80105.1| tRNA-dihydrouridine synthase [uncultured SUP05 cluster bacterium]
          Length = 306

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 127/287 (44%), Gaps = 21/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D+ +R   R     AL  +EM+V    L G  K+   L FS +  P+++QI G+ 
Sbjct: 1   MAGTSDKPFRAICR-AQGAALTTSEMVVIQKHLLGTNKSKHRLDFSGEPAPISIQIAGSQ 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  +A+    FG + I++N+GCP+ +V   + G+ LM +  +V   + A+  A+ IP
Sbjct: 60  ADELAYSAQQALKFGADIIDINMGCPAKKVCNKAAGSALMQDEALVKSILNAVVSAVDIP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G    +       + K  +++G+  + +H R         ++++     +YD 
Sbjct: 120 VTLKMRTGW--NVSNKNAPTIAKIAEEAGIQMLSVHGRT--------REDKYTGMAEYDT 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +    +A  +L     DGVM+GRA   N  ++  +D Y    
Sbjct: 170 IKAVKSQVG-IPVIANGDITSAKKAQSVLQYTGADGVMVGRATQGNPWIIHEIDHYLKTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
              +        +     I      Y  +    G +L    +H+   
Sbjct: 229 QKATDIPLNVKKQTILDHIKQIHAFYGEKL---GTQLS--RKHIFWY 270


>gi|115314770|ref|YP_763493.1| tRNA-dihydrouridine synthase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|115129669|gb|ABI82856.1| probable tRNA-dihydrouridine synthase [Francisella tularensis
           subsp. holarctica OSU18]
          Length = 327

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 136/320 (42%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  + D  +R   +      ++Y EM+   A++  + + +  L     EKPL +QI   D
Sbjct: 19  MAGFCDSAFRTICKEY-GAGMIYMEMVSNKAVVERNWETMEMLYMENSEKPLGIQIFSTD 77

Query: 59  ISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALS 116
           I   V A K I E+   + +++N+GCP  +V +    GA L+ + + + + + A+ KA+ 
Sbjct: 78  IDSFVGATKYIAENTECDFLDINIGCPMPKVAKKLQAGAALLKDVNRIHEILTAVVKAVH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK RIG D+Q   +    + K+ + +GV+ I IH R         ++       ++
Sbjct: 138 KPVTVKMRIGWDEQ--NINAIEVAKACQDAGVSAIAIHGRT--------REQMYTGKANW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DI+ +++K   D  +  NG +     A  ++    VD VM+GRA+  N  +   + EY +
Sbjct: 188 DIIRDVRKAV-DTVVIGNGDVFCPHSAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLN 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +         +   +   +++I  H        PNS+  R
Sbjct: 247 TGELIPPPTPVERV-----DVLEEHLRRLIKLKTAKVAVKEIRTHASFYLQDLPNSKEFR 301

Query: 295 HILTVEAGASTATHHIIETA 314
             L            ++E  
Sbjct: 302 MKLNQLEH-EQEIFKVLEEY 320


>gi|260578340|ref|ZP_05846255.1| tRNA-dihydrouridine synthase [Corynebacterium jeikeium ATCC 43734]
 gi|258603521|gb|EEW16783.1| tRNA-dihydrouridine synthase [Corynebacterium jeikeium ATCC 43734]
          Length = 374

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 73/337 (21%), Positives = 132/337 (39%), Gaps = 36/337 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        +   L   EM+ A A++  + K   +  F+  E P +L
Sbjct: 12  MAGVTNVAFRSLCREQERERMGSVAGLYVCEMVTARALVERNPKTLHMTTFAPDEDPRSL 71

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V     G+ L     + G+ +AA 
Sbjct: 72  QLYTTDPEYTYKAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRKLFGNIVAAA 131

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +   + G   + +H R A          
Sbjct: 132 VKATEGTDIPVTVKMRVGIDDEHH--THLDAGRIAVEEGAAAVALHGRTA--------AQ 181

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   + D++ +  +K+   +  + +  NG +   + A  ++     DGV++GR       
Sbjct: 182 RYSGHADWNEIARLKEHLAHTGIPVLGNGDIFKATDARAMMEQTGCDGVVVGRGCLGRPW 241

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          S P    V +   R       +  A H       + + +HM    
Sbjct: 242 LFAELSAELRGLPIPSEPTLGEVARIILRHA-----ELLAAHDGEQKACRDLRKHMTWYL 296

Query: 285 HGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            GFP     R  L+  +         +++A   + +S
Sbjct: 297 RGFPAGGELRRSLSRVSSLDE-----LKSALAEVWDS 328


>gi|116075024|ref|ZP_01472284.1| hypothetical protein RS9916_25729 [Synechococcus sp. RS9916]
 gi|116067221|gb|EAU72975.1| hypothetical protein RS9916_25729 [Synechococcus sp. RS9916]
          Length = 339

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 136/321 (42%), Gaps = 20/321 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADIS 60
              +DR +R   R    +ALL+TEM+ A ++  G  +  +    QE  P+ +Q+      
Sbjct: 34  AGVSDRIFRHLVRRWAPDALLFTEMVNATSLELGHGRRKVEELAQEAGPIGVQLFDHRPQ 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+  E  G   I++N+GCP  ++ +   G+ L+  PD+    +  +  A++IPVT
Sbjct: 94  AMAEAARRAEASGAFLIDINMGCPVKKIAKKGGGSGLIREPDLAARIVDTVAAAVAIPVT 153

Query: 121 VKCRIGVDDQI-PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK R+G       A       + ++++G   + +H R         ++ +     D+  +
Sbjct: 154 VKTRLGWCGSDGSAADAVQWCQQLEEAGARLLTLHGRT--------REQKFSGRADWQAI 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +   + +  NG +     AL+ L     DGVM+GR    +  ++  +D   S   
Sbjct: 206 AAVK-DALSIPVIANGDVNTPDDALRCLAETGADGVMVGRGTMGSPWLVGQIDSALSGRP 264

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             ++P           ++ A + D           L    +HM     GFP + + RH L
Sbjct: 265 IPTTPGAAERLTIAREQLVALVAD------RGDHGLLIARKHMSWTCTGFPGAPQLRHAL 318

Query: 298 TVEAGASTATHHIIETAFNLM 318
            + A +      +++     +
Sbjct: 319 -MRAPSPQDALDLLDGQLQQL 338


>gi|90020455|ref|YP_526282.1| cell division protein, FtsL -like protein [Saccharophagus degradans
           2-40]
 gi|89950055|gb|ABD80070.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Saccharophagus
           degradans 2-40]
          Length = 336

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 123/293 (41%), Gaps = 25/293 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R      L  +EM+ +D  L    K+ L   +S +  P+++QI G++
Sbjct: 18  MAGVTDLPFRQICRHY-GVGLATSEMVTSDTRLWQSDKSRLRLTYSAELAPVSVQIAGSE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA      G   +++N+GCP+ +V +   G+ L+ +   V + + A+  A+ +P
Sbjct: 77  PDMMAQAAIECVKLGAQIVDINMGCPAKKVCKKLAGSALLQDEKRVAEILTAVVNAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         ++ R     +YD 
Sbjct: 137 VTLKTRTGWSPENRNGVT--IARMAENIGIAALTVHGRT--------RECRFKGQAEYDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +I + N  + +  NG ++   +A  +L       VM+GRAA  N  +L ++       
Sbjct: 187 LADIVQ-NVSIPVIANGDIDSTDKAKHVLDYTGAQAVMVGRAALGNPWLLQSIAHTLEGG 245

Query: 237 LTGS----SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
            T S    +P    +++     +      Y          ++   +H+     
Sbjct: 246 NTESVEKKAPSWIELNEVITAHLGELHKFYGEYQ-----GVRIARKHLSWYAQ 293


>gi|146340809|ref|YP_001205857.1| putative tRNA-dihydrouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146193615|emb|CAL77632.1| putative tRNA-dihydrouridine synthase (Nitrogen regulation protein
           nifR3) [Bradyrhizobium sp. ORS278]
          Length = 317

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 134/331 (40%), Gaps = 37/331 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A  L    L+ +EM  +D ++RG   + L        P  +Q+ G + 
Sbjct: 1   MSGITDAPFRRLAAEL-GAGLVVSEMTASDDLVRGRWISRLRCEAGGIGPHVVQLAGCEA 59

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK+  D G + I++N+GCP+  V  G  G+ LM + D     I A  +A+ +PV
Sbjct: 60  HWMAEGAKVAADGGADIIDINMGCPARHVTGGQSGSALMRDLDHALTLIEATVEAVDVPV 119

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D++  ++    L +  + +GV  I +H R         +        D+  V
Sbjct: 120 TLKMRLGWDER--SLNAPELARRAEAAGVQLITVHGRT--------RQQFYKGEADWSAV 169

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+   DL + +NG +     A + L     D VMIGR A     +   +        
Sbjct: 170 RAVKQAV-DLPVVVNGDITSYEDAREALDASGADAVMIGRGAQGQPWLPGQIGRRLDGGA 228

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF---------- 287
              +P  T+        +  ++ D   RH      L+   +H+     G           
Sbjct: 229 EEGAPELTQQL-----ALLTALYDEICRHYGERVGLRHARKHLSW---GLDVAAAHAQAP 280

Query: 288 -PNSRRCR-HILTVEAGASTATHHIIETAFN 316
               +  R  ILT E    +  H  +  AF+
Sbjct: 281 AEKLKAWRERILTSE--QPSQVHRALREAFD 309


>gi|58038941|ref|YP_190905.1| nitrogen assimilation regulatory protein NifR3 [Gluconobacter
           oxydans 621H]
 gi|58001355|gb|AAW60249.1| Nitrogen assimilation regulatory protein NifR3 [Gluconobacter
           oxydans 621H]
          Length = 371

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 79/323 (24%), Positives = 138/323 (42%), Gaps = 22/323 (6%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADISK 61
             TD  +R  AR L    L+ +EMI + A++R ++  + +    +  P A+Q+ G D   
Sbjct: 44  GVTDLPFRQLARDL-GAGLVVSEMIASWAMIRENENTMRMARMAERGPNAVQLAGCDPKA 102

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           + +AAKI  D G N I++N GCP  +V      G+ LM +  + G  + A  +A+++PVT
Sbjct: 103 MAQAAKISVDGGANLIDINFGCPVKKVAIGQMAGSALMRDEVLAGKLLEATARAVNVPVT 162

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G D    ++    L K  ++SG+  + +H R         +        D+  V 
Sbjct: 163 LKMRMGWD--HNSLNAPRLAKIAEESGIRLVTVHGRT--------RQMFYNGTADWRFVK 212

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K +   L + +NG +  +  A + L     DGVMIGR  Y        V +       
Sbjct: 213 TVK-DAVSLPVIVNGDINTIRDAREALHQSQADGVMIGRGCYGRPWFTAQVAQSLRTGED 271

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P     D    ++I+         H      L+   +H+     G P S   R  + 
Sbjct: 272 VPDP-----DLATEKEIALRHYRMMLDHFGERPGLRLARKHVSWYSAGLPGSATFRSTIN 326

Query: 299 VEAGASTATHHIIETAFNLMIES 321
               A+ A   ++   ++  I++
Sbjct: 327 GVESAAEA-IALLTAFYDRHIDA 348


>gi|56416705|ref|YP_153779.1| hypothetical protein AM492 [Anaplasma marginale str. St. Maries]
 gi|56387937|gb|AAV86524.1| hypothetical protein AM492 [Anaplasma marginale str. St. Maries]
          Length = 320

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 123/314 (39%), Gaps = 20/314 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R          LL +EMI + A++   ++++   S      A+Q+ G    
Sbjct: 17  MSGVTDMPFRSIVGEF-GAGLLVSEMIASRAMIIKTRQSLQK-SDVGANTAVQLAGCVPE 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAKI +D G   I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVT
Sbjct: 75  IMAEAAKINQDMGARSIDINFGCPVKKIVDGHAGSALMKDEEKATKIMESVVKAVTIPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G       +    L K  +  G+  + +H R         +        D+  + 
Sbjct: 135 VKMRMGWSATD--LNAPRLAKIAEDVGIQMVTVHGRT--------RTQMFSGTADWKFIK 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K +   + +  NG +  +        L   DGVMIGR AY    ++     +      
Sbjct: 185 CVK-DCVKIPVIANGDIRTLQDITSALSLSGADGVMIGRGAYGKPWLIKQALHFMKTGEA 243

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P       D   +I     D A  +      ++ + +H+         +   R  + 
Sbjct: 244 LPEPS-----ADEKLRIVLKHYDSAVDYYGKDIGVKILRKHLGWYSVSNAGATYFRAQIN 298

Query: 299 VEAGASTATHHIIE 312
             +        ++E
Sbjct: 299 TMSDPVAIREKLLE 312


>gi|254773708|ref|ZP_05215224.1| dihydrouridine synthase [Mycobacterium avium subsp. avium ATCC
           25291]
          Length = 377

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN------ALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L          L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERELVGTVSGLYVCEMVTARALVERHPATMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ + G  + I++N GCP  +V +   G+ L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIANEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+D++       +  +  +  G   + +HAR A          
Sbjct: 137 VRATQGTEIPVTVKFRIGIDEEHH--THLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K++   + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQQVRTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P   +V       I        A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPPPTPPTLGQVA-----DIVRRHGRLLAAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAM 314


>gi|323340116|ref|ZP_08080381.1| tRNA-dihydrouridine synthase [Lactobacillus ruminis ATCC 25644]
 gi|323092493|gb|EFZ35100.1| tRNA-dihydrouridine synthase [Lactobacillus ruminis ATCC 25644]
          Length = 329

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 81/323 (25%), Positives = 130/323 (40%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E P+++QI G  
Sbjct: 19  MAGVTNVAFRLICKEF-GAGLVVCEMISDKGIHFRNKKTLGMLFVDPTEHPVSVQIFGGS 77

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V +    + I++N+GCP  +V +   G+  +L+PD V + + A+  ++  
Sbjct: 78  KESLVEAAQFVAENTSADIIDINMGCPVPKVTKTDAGSRWLLDPDKVYEMVDAVTHSIDK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D++
Sbjct: 138 PVTVKMRTGWDEDHIYAVENALA--AQEGGAKALAMHGRT--------RKQLYSGHADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I++E+  +    F+G NG +     A K+L     D VMIGRAA  N  +L     Y   
Sbjct: 188 ILHEVAGKLTIPFMG-NGDVRTPQDAKKMLDEVGCDAVMIGRAALGNPWILKQTVHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL--QQITRHMIGLFHGFPNSRRC 293
                 P   +       KI  +        L  G K+  ++          G P S R 
Sbjct: 247 GELLEEPTPDQ-------KIIVAKEHLHRLVLAKGEKMGPKEFRSQAAYYLKGIPRSARA 299

Query: 294 RHILTVEAGASTATHHIIETAFN 316
           +  L   A      H I +    
Sbjct: 300 KAALNS-ADTEEEMHEIFDGFLA 321


>gi|313665725|ref|YP_004047596.1| TIM-barrel protein, nifR3 family [Mycoplasma leachii PG50]
 gi|312949868|gb|ADR24464.1| TIM-barrel protein, nifR3 family [Mycoplasma leachii PG50]
          Length = 324

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 139/316 (43%), Gaps = 24/316 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  ++     +L+Y EM+    ++  +KK   +L  +  E P+++QI G +
Sbjct: 17  MAGVSNEAFRIISKQ-HGASLVYAEMVSVAGMVHDNKKTLDMLNVNKIEHPISMQIFGNN 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           + + + A K +E+    + I+LN+GCP+ +V      G+ L+  P+++ + +  + K  +
Sbjct: 76  VEEFITATKWIENNVNCDIIDLNLGCPAPKVAIRSQSGSALLKTPELIYEIVKNVVKNTT 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R+G D    +V    + K I+K+G + I +HAR         + +    + D+
Sbjct: 136 KPVTAKIRLGWDK--NSVNAVEVAKLIQKAGASAIAVHART--------RSDFYTGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+K+    + +  NG + D   A K+L     D VMI RA   N  +   ++ Y  
Sbjct: 186 EKIKEVKQAV-SIPVIGNGDVIDAKSAKKMLDETGCDAVMISRACQGNPWIFEQINHYLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P            +   + D     +     +++  +H+        N+++  
Sbjct: 245 TGKELEKPNFDEWKTTVLEHLKL-LVDLKTEPIA----IKEFRKHLTWYL-DVLNNKQLT 298

Query: 295 HILTVEAGASTATHHI 310
            IL  +A        +
Sbjct: 299 KILKEKANKIETVKDV 314


>gi|118466583|ref|YP_880044.1| dihydrouridine synthase [Mycobacterium avium 104]
 gi|118167870|gb|ABK68767.1| dihydrouridine synthase [Mycobacterium avium 104]
          Length = 377

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 129/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN------ALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L          L   EM+ A A++       ++  F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERELVGTVSGLYVCEMVTARALVERHPATMHMTTFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ + G  + I++N GCP  +V +   G+ L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIANEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+D++       +  +  +  G   + +HAR A          
Sbjct: 137 VRATQGTEIPVTVKFRIGIDEEHH--THLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K++   + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQQVRTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P   +V       I        A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPPPTPPTLGQVA-----DIVRRHGRLLAAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAI 314


>gi|323359853|ref|YP_004226249.1| tRNA-dihydrouridine synthase [Microbacterium testaceum StLB037]
 gi|323276224|dbj|BAJ76369.1| tRNA-dihydrouridine synthase [Microbacterium testaceum StLB037]
          Length = 388

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 61/311 (19%), Positives = 113/311 (36%), Gaps = 17/311 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI   A++  +     ++     E P ++Q+ G D
Sbjct: 27  MAGITNTAFRRLCREY-GAGLYVSEMITTRALVERNDTTMRLIRHHESETPRSIQLYGVD 85

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              +  A +I+ D    + I+LN GCP  +V     GA L     +  + +  A+  A  
Sbjct: 86  PGTVEAAVRIIVDEDHADHIDLNFGCPVPKVTRRGGGAALPWKTSLFREIVERAVRAAGE 145

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            P+T+K R G+D     +      +  + +GV  I +HAR A              + D+
Sbjct: 146 KPLTIKMRKGID--ADHLTYLEAGRIAEGAGVASIALHARTASEF--------YSGHADW 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K+    + +  NG +     A +++     DGV++GR       +   +     
Sbjct: 196 SAITKLKETVTSVPVLGNGDIWSADDAARMMAETGCDGVVVGRGCLGRPWLFGDLARALG 255

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            P                +                G   + I +H+   F G+P     R
Sbjct: 256 QPGAAHGEPVDATLGFVAKAFRRHAELLVEFFEDEGRGCRDIRKHVAWYFKGYPVGGELR 315

Query: 295 HILTVEAGAST 305
             L   +  + 
Sbjct: 316 ASLATASTLNE 326


>gi|325474572|gb|EGC77758.1| NifR3 family TIM-barrel protein [Treponema denticola F0402]
          Length = 334

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 133/326 (40%), Gaps = 28/326 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D+ +R    +       YTEM+ ++A++R   K   ++G +  EK  A+QI G++ 
Sbjct: 26  AGYSDKAFRSIC-IDCGADFTYTEMVSSEALVRDSDKTESLIGRAPNEKAYAVQIFGSNP 84

Query: 60  SKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
             + + A  I E +    I++N GCP A++ +   G+ LM +  ++   + A+  A+   
Sbjct: 85  EYMAKTAVIIAEKYSPECIDINSGCPMAKITKNGAGSALMTDIPLLYRIVKAVNDAMAPY 144

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT+K R G       +  +    +   +GV  + +H R         +        D
Sbjct: 145 KIPVTLKIRSGF--TADKLNWKEAASAAIDAGVKMLTLHPRT--------RSQVYSGKAD 194

Query: 176 YDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           ++I+ E+ +      + I  +G L     A K+L      G+M  R A  N  + T   E
Sbjct: 195 WNILAELVQFAKSHQIPIFGSGDLFSPEDAKKMLEETGCAGIMFARGAMGNPFIFTQTRE 254

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +N   G    + ++   F   +      +           +++ +       G P+  
Sbjct: 255 LLTNGTYGEISTEQKIRTGFKELV------FLCDEKGEEKGCREMRKRFATYTKGIPDGS 308

Query: 292 RCRHILTVEAGASTATHHIIETAFNL 317
           R R  L V+A        I++  F L
Sbjct: 309 RLRQEL-VQASTIAEYKTIVQNYFQL 333


>gi|99081204|ref|YP_613358.1| dihydrouridine synthase TIM-barrel protein nifR3 [Ruegeria sp.
           TM1040]
 gi|99037484|gb|ABF64096.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Ruegeria sp.
           TM1040]
          Length = 328

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 134/322 (41%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  ++QI G D
Sbjct: 19  MAGITDRPFRDLVRSF-GAGLVVSEMVASQEMVQAKPGVREKAELSADVENTSVQIAGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+ +A+ +P
Sbjct: 78  AYWMAEAARQVADRGARMIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVQAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD    +   ++ +  + +GV  + IH R         +      + D+  
Sbjct: 138 VTLKTRLGWDD--NCLNAADVARRAEAAGVQMVTIHGRT--------RCQFYKGHADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK     + +  NG + D   A K L     DGVMIGR       +L  +       
Sbjct: 188 ISEIKNAI-SVPLLANGDIVDAKSAGKALSDSGADGVMIGRGVQGRPWLLAQIAHDLWGT 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
                P          +   A +  Y A        L+   +H+       G P + R R
Sbjct: 247 AAPDVPEGRAFIDLVSKHYEAMLAFYGAE-----LGLRVARKHLGWYMDEAGTPAALR-R 300

Query: 295 HILTVEAGASTATHHIIETAFN 316
            +LT  A + +    ++ +A  
Sbjct: 301 EVLT--AKSPSDVLRLLPSALQ 320


>gi|291543545|emb|CBL16654.1| tRNA-U20-dihydrouridine synthase [Ruminococcus sp. 18P13]
          Length = 336

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 122/298 (40%), Gaps = 19/298 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR YR   R      ++ +E+I A  +   D K   +   + +E+P+ALQ+ G++
Sbjct: 20  MASVADRAYRQLCRSF-GACMVTSELISAKGMCYNDSKTAELCTITPEERPMALQLFGSE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +A K++  F  + I+LN+GCP  +V     G+ LM + +   D +AA   A  +P
Sbjct: 79  PKFIQQAVKLLLPFQPDVIDLNMGCPVPKVVNTGAGSALMQDLNTAADLVAAARMASDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G  +    V        + ++G   I IH R         +        D+  
Sbjct: 139 VTVKIRRGWSEDT--VNCVEFACRMAEAGAQAIAIHGRT--------RSQMYSGKADWSC 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +   +  L +      D VM+GRA+Y N  +   +D      
Sbjct: 189 IRAVKQAV-SVPVIGNGDVCSGADCLNMYRETGCDLVMVGRASYGNPWIFQEIDAACRGI 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 ++ R++          M     R      ++++  +H     HG   +   R
Sbjct: 248 PYTPPTVEERMETMLLH---IRMILETGRGKPEPQRMKEARKHAAWYLHGLRGAAGFR 302


>gi|240015904|ref|ZP_04722444.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae FA6140]
 gi|240112253|ref|ZP_04726743.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae MS11]
          Length = 364

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 330 INRLDNAA-AQYDTLAGYLERL 350


>gi|171464157|ref|YP_001798270.1| TIM-barrel protein, nifR3 family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
 gi|171193695|gb|ACB44656.1| TIM-barrel protein, nifR3 family [Polynucleobacter necessarius
           subsp. necessarius STIR1]
          Length = 338

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 136/327 (41%), Gaps = 27/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A+L   +K         + K +A+QI GAD
Sbjct: 17  MAGVTDRPFRQLCKKL-GADYAVSEMVASNALLWKSEKTQRRANHIGEFKLIAVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI- 117
            + +  AAKI  D G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+ I 
Sbjct: 76  PAMMAAAAKINVDHGAQIIDINMGCPAKKVCNVAAGSALLRDEPLVQQILEAVVNAVGIG 135

Query: 118 ----PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
               PVT+K R G D Q        + +  +KSG++ + +H R         + +     
Sbjct: 136 PDAVPVTLKIRTGWDRQNKNAI--EIAQLAEKSGISMLTVHGRT--------RADLYHGE 185

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +Y+ +  +K     + +  NG +    +A ++L     D +MIGRAA     +   ++ 
Sbjct: 186 AEYETITTVKN-YVRIPVVANGDINSPEKAEQVLKITGADAIMIGRAAQGRPWIFREINH 244

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           Y        +P    +       +      Y   H+     L+   +H+     G  +S 
Sbjct: 245 YLETGGKLPTPKINEIQTIMNAHLLDHYEFY-GEHIG----LRTARKHIGWYCKGLRDSH 299

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
             R  +   A        ++   F+ M
Sbjct: 300 AFRQRMNT-ADDCKTQLQMVNDYFDEM 325


>gi|269956952|ref|YP_003326741.1| TIM-barrel protein, nifR3 family [Xylanimonas cellulosilytica DSM
           15894]
 gi|269305633|gb|ACZ31183.1| TIM-barrel protein, nifR3 family [Xylanimonas cellulosilytica DSM
           15894]
          Length = 400

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 117/312 (37%), Gaps = 26/312 (8%)

Query: 1   MVDWTDRHYRFFARLLTN-----NALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQ 53
           M   T+R +R   R           L   EM+ + A++  + +   I+ F   E P + Q
Sbjct: 35  MAGVTNRAFRTLCREAGASGGEHPGLYVAEMVTSRALVERNAEALRIVTFGADETPRSAQ 94

Query: 54  IGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + G D + +  A +I+  +   + ++LN GCP  +V     G  L     +  D + A  
Sbjct: 95  VYGVDPATVGAAVRIIASEDRADHVDLNFGCPVPKVTRKGGGGALPWKRQLFTDIVRAAV 154

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            A     +PVT+K R G+DD    +         +  GV  + +HAR             
Sbjct: 155 DAAAPYGVPVTIKMREGIDDD--HLTYLEAGTIAEGLGVAAVALHART--------VAQH 204

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                 +  +  +K+    + +  NG +     AL+++     DGV++GR       +  
Sbjct: 205 YSGEARWPSIARLKEAVTSVPVLGNGDIWSADDALRMVAETGADGVVVGRGCQGRPWLFA 264

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +   F        P    V    +R     M +Y     H G  ++ + +HM     G+
Sbjct: 265 DLAAAFHGQTVRVQPTLREVADTIYRH-GELMIEYYDGDEHKG--VRDLRKHMAWYLKGY 321

Query: 288 PNSRRCRHILTV 299
                 RH L +
Sbjct: 322 AVGGEARHALAL 333


>gi|189502204|ref|YP_001957921.1| hypothetical protein Aasi_0818 [Candidatus Amoebophilus asiaticus
           5a2]
 gi|189497645|gb|ACE06192.1| hypothetical protein Aasi_0818 [Candidatus Amoebophilus asiaticus
           5a2]
          Length = 327

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 140/326 (42%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M D +D  +R   +      L+YTE I A+ ++R   K+I  L     E+P+ +QI G  
Sbjct: 19  MEDVSDPPFRAVCKE-KGADLMYTEFISAEGLIREADKSIKKLDIYDYERPIGIQIFGEK 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  + EAA I E      +++N GCP   V     GA ++L+   +    A + K +S+P
Sbjct: 78  IESMREAAAIAEAASPALLDINYGCPVNNVACRGAGAGILLDLPKMQTMTAEIVKRVSLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D  + ++ +  + + ++ +G+  + IH R         +        D+  
Sbjct: 138 VTVKTRLGWD--VNSIKIVEVAQRLQDAGIQALTIHGRT--------RQQMYKGEADWSY 187

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + ++K      + I  NG ++   +AL       +DG+MIGRA+     +   +  +F  
Sbjct: 188 IADVKNHPAIRIPIFGNGDIDTPQKALAYRNEYGIDGIMIGRASIGYPWIFQEIKHFFKT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P          + +      +A +       + ++ RH      G P  +  R 
Sbjct: 248 GEQLAPPDLQERIATLQKHL-----QHAIQWKGERTGILEMRRHYTNYLKGLPEVKTYRQ 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +L VEAG       I+    N ++ +
Sbjct: 303 ML-VEAGDLLTVESILAELVNKLMAA 327


>gi|83320047|ref|YP_424779.1| tRNA-dihydrouridine synthase [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|83283933|gb|ABC01865.1| tRNA-dihydrouridine synthase [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 308

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 138/316 (43%), Gaps = 24/316 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  ++     +L+Y EM+    ++  +KK   +L  +  E P+++QI G +
Sbjct: 1   MAGVSNEAFRIISKQ-HGASLVYAEMVSVAGMVHDNKKTLDMLNVNKVEHPISMQIFGNN 59

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           + + + A K +E +   + I+LN+GCP+ +V      G+ L+  P+++ + +  + K  +
Sbjct: 60  VEEFITATKWIESNVDCDIIDLNLGCPAPKVAIRSQSGSALLKTPELIYEIVKNVVKNTT 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R+G D    +V    + K I+K+G + I +HAR         + +    + D+
Sbjct: 120 KPVTAKIRLGWDK--NSVNAVEVAKLIQKAGASAIAVHART--------RSDFYTGHADW 169

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+K+    + +  NG + D   A K+L     D VMI RA   N  +   ++ Y  
Sbjct: 170 EKIKEVKQAV-SIPVIGNGDVIDAKSAKKMLDETGCDAVMISRACQGNPWIFEQINHYLK 228

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P       D W+                   +++  +H+        N+++  
Sbjct: 229 TGKELEKPNF-----DEWKTTVLKHLKLLVDLKTEPIAIKEFRKHLTWYL-DVLNNKQLT 282

Query: 295 HILTVEAGASTATHHI 310
            IL  +A        +
Sbjct: 283 KILKEKANKIETVKDV 298


>gi|319950652|ref|ZP_08024556.1| TIM-barrel protein, nifR3 family [Dietzia cinnamea P4]
 gi|319435694|gb|EFV90910.1| TIM-barrel protein, nifR3 family [Dietzia cinnamea P4]
          Length = 392

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 120/315 (38%), Gaps = 32/315 (10%)

Query: 1   MVDWTDRHYRFFARLLTNN------ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R +          L   EM+ A A++        +  F+  E P +L
Sbjct: 28  MAGVTNVAFRTLCREIEREQQGSVSGLYVCEMVTARALVERQPATLHMATFAPDESPRSL 87

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++ D    + I++N GCP  +V     G+ +     +    +AA 
Sbjct: 88  QLYTVDAEYTYAAARMIVDENLADHIDINFGCPVPKVTRRGGGSAIPYKRRLFRSIVAAA 147

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK R+G+DD+       +  +   + G   + +HAR A          
Sbjct: 148 VRATEGTDIPVTVKMRVGIDDEHH--THLDAGRIAVEEGAKAVALHARTA--------AQ 197

Query: 169 RKIPNLDYDIVYEIKK---ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
           R     D+  +  + +      D+ +  NG +     A+++       GV+IGR      
Sbjct: 198 RYSGEADWSQISRLVEHVGAVSDVPVLGNGDIFSAQDAVRMREQTGCAGVVIGRGCLGRP 257

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            + + +    +     + P    V +  +R       +  A H      ++ I +H+   
Sbjct: 258 WLFSELAARLAGREAPAPPTLGEVARIMYRH-----GELLAEHHGEDKGMRDIRKHVAWY 312

Query: 284 FHGFPNSRRCRHILT 298
             GFP     R  L+
Sbjct: 313 LRGFPAGSEKRVALS 327


>gi|307942245|ref|ZP_07657596.1| tRNA-dihydrouridine synthase B [Roseibium sp. TrichSKD4]
 gi|307774531|gb|EFO33741.1| tRNA-dihydrouridine synthase B [Roseibium sp. TrichSKD4]
          Length = 354

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 127/287 (44%), Gaps = 20/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD  +R FA       ++ +EM+ +++ ++GD +  +    Q   L  +Q+ G + 
Sbjct: 37  MSGVTDLPFRRFAARY-GAGMVVSEMVASESFVKGDAETQMRAEAQNNGLHVVQLAGREA 95

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAK + D G + I++N+GCP+ +V  G  G+ LM + D     I A  +A+ +PV
Sbjct: 96  RWMGEAAKTIADLGADIIDINMGCPAKKVTSGYSGSALMRDLDHALTLIEATVEAVDVPV 155

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D    ++    L +  + +G+  I +H R         ++       D+  +
Sbjct: 156 TLKMRLGWD--HDSINAPELARRAENAGIQLITVHGRT--------RNQFYKGTADWSAI 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+E   + +  NG  +    A ++L     D VMIGR AY    +   +  Y  + +
Sbjct: 206 AAVKQEI-SVPLIANGDCQSYDDASEMLARSGADAVMIGRGAYGRPWLPGHIGTYLKSGI 264

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               P              A +  Y  R   +G ++    +H+   F
Sbjct: 265 RTPQPDANEFADLAREHYDALLIHYGER---AGNRI--ARKHLGWYF 306


>gi|268602979|ref|ZP_06137146.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID1]
 gi|268683619|ref|ZP_06150481.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-92-679]
 gi|268587110|gb|EEZ51786.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID1]
 gi|268623903|gb|EEZ56303.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae SK-92-679]
          Length = 334

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++   +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 300 INRLDNAA-AQYDTLAGYLERL 320


>gi|241766789|ref|ZP_04764615.1| TIM-barrel protein, nifR3 family [Acidovorax delafieldii 2AN]
 gi|241362823|gb|EER58579.1| TIM-barrel protein, nifR3 family [Acidovorax delafieldii 2AN]
          Length = 349

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 117/306 (38%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G +
Sbjct: 17  MAGVTDRPFRQLCKQL-GAGYAVSEMVTSRKDLWNSLKTSRRANHEGEPGPIAVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    + G   I++N+GCP+ +V     G+ LM +  +      A+  A    
Sbjct: 76  AAMMAEAAVYNIERGAQIIDINMGCPAKKVCNKWAGSALMQDEVLAVSIARAVVDACAPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVT+K R G   Q        L +  +  G+  + +H R         ++       +
Sbjct: 136 NVPVTLKMRTGWCQQHKNAVA--LARQFEAVGIQMLTVHGRT--------REQGYKGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG +    +A ++L     D +M+GRAA     +   +  + 
Sbjct: 186 YDTIAAVK-AAVQVPVVANGDIASPEKAREVLAYTGADAIMVGRAAQGRPWIFREIGHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +    + Y       G  ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAEVRRLLLDHLQDHYSLY-----GEGTGVRSARKHIAWYVRQLPGGEDF 299

Query: 294 RHILTV 299
           R  +  
Sbjct: 300 RQHINT 305


>gi|219847108|ref|YP_002461541.1| TIM-barrel protein, nifR3 family [Chloroflexus aggregans DSM 9485]
 gi|219541367|gb|ACL23105.1| TIM-barrel protein, nifR3 family [Chloroflexus aggregans DSM 9485]
          Length = 351

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 86/329 (26%), Positives = 139/329 (42%), Gaps = 30/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM-----IVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   TD  +R     L    L+ TEM     +   A+ R     +L +  +E+PL +QI 
Sbjct: 33  MAGVTDSIFRRMILRLGGCGLVSTEMTNAASVSPKALRRH---RLLDYLPEERPLTMQIS 89

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   +  AA++VE  G + I++N GCPS +V  G  G+ L+ +   +   + A+  A+
Sbjct: 90  GNDPDLVANAARVVEQLGADIIDINCGCPSPKVTGGGHGSALLRDLPKMERLLRAVRAAV 149

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT+K R G D+   ++      +  + +GV  + +H R         ++       D
Sbjct: 150 QIPVTLKLRAGWDE--ASLNFIEAGQRAEAAGVAALTLHPRT--------REQGYKGQAD 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V  +K+    + +  +G +     AL  L     DGVMIGR A  N  +   V +  
Sbjct: 200 WSRVAALKRAV-SIPVIGSGDVVTAQDALIRLRDSGADGVMIGRGAIANPWIFRQVAD-L 257

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
               T   P       D +  +   M  YA   L     L +I + +IG F+ G P S  
Sbjct: 258 RQGRTPFEPTP----ADKYHLLLEYMAIYAEE-LPERLALNKI-KQLIGQFYIGLPGSNH 311

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R  +      + A    IE  F   +E+
Sbjct: 312 LRVAVHTSTSLAAA-QEAIERFFAPYLET 339


>gi|77456843|ref|YP_346348.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pseudomonas
           fluorescens Pf0-1]
 gi|77380846|gb|ABA72359.1| tRNA-U20-dihydrouridine synthase [Pseudomonas fluorescens Pf0-1]
          Length = 336

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 135/320 (42%), Gaps = 21/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ +        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRMRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVTEILNAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNKNG--LTVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG +    +A  +L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAAIKQAV-SIPVFANGDIVSPEKARYVLDATGADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    V++     ++A    Y          ++   +H+       P +R  R  
Sbjct: 248 EKLPAPELIEVERILLEHLAALHAFY-----GDVMGVRIARKHVGWYLATLPGAREFRAH 302

Query: 297 LTVEAGASTATHHIIETAFN 316
                G  T   ++ E    
Sbjct: 303 FNRLDGTETQCANVREFFAE 322


>gi|33861565|ref|NP_893126.1| nitrogen regulation protein NifR3 family protein [Prochlorococcus
           marinus subsp. pastoris str. CCMP1986]
 gi|33634142|emb|CAE19468.1| putative nitrogen regulation protein NifR3 family homolog
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 340

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 73/320 (22%), Positives = 136/320 (42%), Gaps = 21/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADIS 60
              TD+ +R   R     +LL+TEMI A ++  G     +     EK P+ +QI      
Sbjct: 31  AGVTDKIFRKLVRKWAPESLLFTEMINATSLKHGYGTQKIKQLELEKGPIGVQIFDNRPF 90

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N+GCP  ++     G+ L+ +  +  + +  +  A+ +PVT
Sbjct: 91  AVSEAAKLAEDSGAFLIDINMGCPVKKISRKGGGSALINDRLLAIELVKRVSNAVKVPVT 150

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G +++     +   + S++ +G   I +H R    +G S K        D++++ 
Sbjct: 151 VKTRLGWENKE--ENIEEFLLSLQDAGAEMITLHGRTRK-EGFSGK-------ADWEMIG 200

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           +IK E  ++ +  NG +++   A   L   + DG+MIGR    +   +  +D        
Sbjct: 201 KIK-ELLEIPVIANGDIKNPKDAYNCLKKTNADGLMIGRGILGSPWKIGEIDYAVKEIKG 259

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            +   + +  +        L    +H+      FP +   R+ L 
Sbjct: 260 FEEPNIEEKLLLIIEHLDELIKEKGSH------GLLIARKHISWTCKNFPEATSLRNKL- 312

Query: 299 VEAGASTATHHIIETAFNLM 318
           V A  +     +I  A   +
Sbjct: 313 VRAIDANEVKELINKAIKTL 332


>gi|224055152|ref|XP_002298425.1| predicted protein [Populus trichocarpa]
 gi|222845683|gb|EEE83230.1| predicted protein [Populus trichocarpa]
          Length = 378

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 102/302 (33%), Positives = 159/302 (52%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  AR+++ +A LYTEM+ A+ I+   GD    L FS ++ P+ LQIGG +
Sbjct: 16  MMDWTDNHYRTVARIISKHAWLYTEMLAAETIVHQQGDLDRFLAFSPEQHPIVLQIGGNN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   +GY+EINLN GCPS +V     FG  LML+P  VG+ ++ +     +
Sbjct: 76  LDNIAKATRLANSYGYDEINLNCGCPSPKVAGHGCFGVRLMLDPKFVGEAMSVIAANTDV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIG+DD      L + +  +   S      IH+RKA+L G+SP DNR+IP L Y
Sbjct: 136 PVSVKCRIGLDDHDSYNELCDFIYKVSSLSPTKHFIIHSRKALLNGISPADNRRIPPLKY 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  Y + ++ PDL   +NGG+  + +    L     GVM+GRAAY      L  VD    
Sbjct: 196 EYYYALLRDFPDLRFTINGGINCVDEVNAALREGAHGVMVGRAAYNYLWNTLAHVDTAIY 255

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P      +    +           + +S   ++ + + + G F+  P +   +
Sbjct: 256 G-----APSSGLTRRQVLEQYQVYGDAVLGTYGNSRPNIRDLIKPLFGFFYSEPGNNLWK 310

Query: 295 HI 296
             
Sbjct: 311 RK 312


>gi|302339678|ref|YP_003804884.1| hypothetical protein Spirs_3192 [Spirochaeta smaragdinae DSM 11293]
 gi|301636863|gb|ADK82290.1| TIM-barrel protein, nifR3 family [Spirochaeta smaragdinae DSM
           11293]
          Length = 327

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 126/324 (38%), Gaps = 22/324 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TDR +R    +       YTEM+  +A+ RG+ K   +L  +  EK L +QI  +  
Sbjct: 13  AGITDRGFRRIC-IEHGAPFTYTEMVSGEALARGNAKTIALLRRAKGEKLLGVQIFLSSP 71

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +   A  ++E      I+LN GCP  +V +   GA LM +P+ +   ++ + K+ S P+
Sbjct: 72  EQAERALPVIEKADPTLIDLNCGCPVPKVVKTGAGAALMRSPETIYRIVSLLSKSSSRPI 131

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D +   +      ++ + +G + I +H R         +      + D+D +
Sbjct: 132 TVKIRTGWDSKT--INYLEAAQASESAGASMITLHGRS--------RSQGYSGSADWDTI 181

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+ +    + +  NG       A ++L      GVM  R A  N  +         +  
Sbjct: 182 AELVQ-TVRVPVIGNGDAFSPEAAKRLLMETGCSGVMFARGAMGNPFIFEQTRRLLEHDS 240

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           TG  P    + K    ++      Y           +++ + M G   G   S   R  +
Sbjct: 241 TGKIPSVAEIMKAALTQL-----HYTIEEKGERVACREMRKQMTGYTKGLDGSAALRQSI 295

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
                       + E   +L  ES
Sbjct: 296 VTCETEEDYRRTV-EDYLSLRGES 318


>gi|113968744|ref|YP_732537.1| nifR3 family TIM-barrel protein [Shewanella sp. MR-4]
 gi|114049112|ref|YP_739662.1| nifR3 family TIM-barrel protein [Shewanella sp. MR-7]
 gi|117918856|ref|YP_868048.1| nifR3 family TIM-barrel protein [Shewanella sp. ANA-3]
 gi|113883428|gb|ABI37480.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. MR-4]
 gi|113890554|gb|ABI44605.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. MR-7]
 gi|117611188|gb|ABK46642.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. ANA-3]
          Length = 322

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 139/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAALAVSEMLSSNPEVWDTDKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G + I++N+GCP+ +V++   G+ LM NP +V + + A+  A+ +P
Sbjct: 76  PELMAQAAQFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKEILQAVVAAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWEPEHRNGV--QIAQIAEDCGIASLAVHGRT--------RQCMYRGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG ++   +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NVSIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +        +     ++     Y          ++   +H+        + R+ R  
Sbjct: 245 NKLAPIEVAEQRQVMLEHLTKLYDLY-----GEYKGIRFARKHIGWYL-DQEDQRQFRAD 298

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 A+   + ++E  F+ ++++
Sbjct: 299 FNQLETAAE-QYSLVEYYFDELVQN 322


>gi|224106093|ref|XP_002314040.1| predicted protein [Populus trichocarpa]
 gi|222850448|gb|EEE87995.1| predicted protein [Populus trichocarpa]
          Length = 380

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 101/302 (33%), Positives = 163/302 (53%), Gaps = 11/302 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M++WTD+HYR  AR+++ +A LYTEM+ A+ I+   G+    L F +++ P+ LQIGG +
Sbjct: 16  MMEWTDKHYRTVARIISKHAWLYTEMLAAETIVYQQGNLDRFLAFPSEQHPIVLQIGGNN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  + +A ++   +G++EINLN GCPSA+V     FGA LML+P  V + ++ +     +
Sbjct: 76  LDNIAKATQLANAYGFDEINLNCGCPSAKVAGHGCFGARLMLDPKFVSEAMSVIAANTDV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD      L + +  +   S      IH+RKA+L G+SP DNR+IP L Y
Sbjct: 136 PVSVKCRIGVDDHDSYNELCDFIYKVSSLSPTKHFIIHSRKALLNGISPADNRRIPPLKY 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           +  Y + ++ PDL   +NGG++ + +    L     GVM+GRAAY N    L  VD    
Sbjct: 196 EYYYALLRDFPDLRFTINGGIDCVDEVNAALREGAHGVMVGRAAYNNLWNTLAHVDSAVY 255

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +    +           + ++   ++++ R + G F+  P +   +
Sbjct: 256 G-----EPSSGLTRRQVLEQYQVYGDAVLGTYGNNRPNMRELIRPLSGFFYSEPGNSLWK 310

Query: 295 HI 296
             
Sbjct: 311 RK 312


>gi|94967061|ref|YP_589109.1| dihydrouridine synthase TIM-barrel protein nifR3 [Candidatus
           Koribacter versatilis Ellin345]
 gi|94549111|gb|ABF39035.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Candidatus
           Koribacter versatilis Ellin345]
          Length = 370

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 148/329 (44%), Gaps = 32/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK---KNILGFSTQEKPLALQIGGA 57
           M   TD  +R F R L    L+ TE   AD + R  +   +  L F   E+P++ Q+ G+
Sbjct: 39  MAGVTDTVFRRFIRNLGGCGLMMTEFTSADGLARMREAKARRYLTFYGNERPISAQLFGS 98

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   L +AAK+V+D G++ ++LN+GCPS RV + + G+ L+ +   +     ++ KA++I
Sbjct: 99  DAETLADAAKVVQDLGFDLVDLNLGCPSKRVVKCNGGSGLLRDLPQIKVIFESVRKAVTI 158

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R G +++   +    L K  +  G+N + +HAR         ++       ++ 
Sbjct: 159 PFTVKFRAGWNEKE--LVFLELAKLAENCGLNAVAMHART--------REQGYSGQANWG 208

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K+    + +  NG +     A  ++     D VMIGR+A  N  +   +++Y + 
Sbjct: 209 WIADLKQ-VVKIPVIGNGDIRTPEDAAAMVAKTGCDAVMIGRSAASNPWIFRQIEQYTAT 267

Query: 236 PLTGSSPIKTR--VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   + R  + + ++R +  +          + GK++Q         HG P     
Sbjct: 268 GRYDLPTNEDRYEMIRMYFRMLIEN------DTQGAEGKMKQFA---SWFTHGVPGGGVL 318

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R     +A         I  A +   E+L
Sbjct: 319 R-----KAVYEAKKRETILVAVDQFFEAL 342


>gi|15828169|ref|NP_302432.1| NifR3/Smm1 family transcriptional regulator [Mycobacterium leprae
           TN]
 gi|221230646|ref|YP_002504062.1| transcriptional regulator (NifR3/Smm1 family) [Mycobacterium leprae
           Br4923]
 gi|2833435|sp|Q50049|DUS_MYCLE RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|699230|gb|AAA62994.1| ntrB [Mycobacterium leprae]
 gi|13093723|emb|CAC31141.1| transcriptional regulator (NifR3/Smm1 family) [Mycobacterium
           leprae]
 gi|219933753|emb|CAR72283.1| transcriptional regulator (NifR3/Smm1 family) [Mycobacterium leprae
           Br4923]
          Length = 384

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 128/332 (38%), Gaps = 48/332 (14%)

Query: 1   MVDWTDRHYRFFARLLTNN-------------------------ALLYTEMIVADAILRG 35
           M   T+  +R   R   +                           L   EM+ A A++  
Sbjct: 5   MAGVTNVTFRTLCREFGSTRGNLLRPAPPHLRSPLEQSQVGTISGLYVCEMVTARALVER 64

Query: 36  DKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGS 92
           +     +  F+  E P +LQ+   D +    AAK+V D G  + I++N GCP  +V    
Sbjct: 65  NAVTIHMTTFAPDESPRSLQLYTVDPATTYTAAKMVADEGLADHIDMNFGCPMPKVTRRG 124

Query: 93  FGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            GA L     + G  +AA  +A     IPVTVK RIG+DD+       +  +  +  G  
Sbjct: 125 GGAALPYKRRLFGQIVAAAVRATEGTKIPVTVKFRIGIDDEHH--THLDAGRIAEAEGAA 182

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
            + +HAR A          R     D+  + ++K++   + +  NG + D S AL ++  
Sbjct: 183 AVALHARTA--------AQRYSGTADWAQIAQLKQQVRTIPVLGNGDIYDASDALAMMAV 234

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              DGV+IGR       +   +   F+     + P    V      +I          H 
Sbjct: 235 TGCDGVVIGRGCLGRPWLFAELSAAFTGRPAPAPPTLGEVA-----EIVRRHGKLLVAHF 289

Query: 268 HSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                ++ I +H+    HGFP     R+ L +
Sbjct: 290 GEDKGMRDIRKHIAWYLHGFPAGSELRNALAL 321


>gi|223982705|ref|ZP_03632935.1| hypothetical protein HOLDEFILI_00209 [Holdemania filiformis DSM
           12042]
 gi|223965301|gb|EEF69583.1| hypothetical protein HOLDEFILI_00209 [Holdemania filiformis DSM
           12042]
          Length = 333

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 141/326 (43%), Gaps = 26/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   ++  +R  A       L+YTEMI   AI   +KK +     +  E P+A+Q+ G +
Sbjct: 18  MAGISNAAFRTIAHEF-GAGLIYTEMISDKAICYSNKKTMEMTQLAPDEHPIAMQLFGHE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +++AA++++    + I++N+GCP  +V     G+ +M +P+     +  +   +  P
Sbjct: 77  EASMIQAAQVLDKTDCDVIDINMGCPVPKVVNSGSGSAMMKDPEATYQLVRKIVAVVEKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D    ++ +  + + ++ +GV+ + +H R         +        D+  
Sbjct: 137 VTAKIRLGWD--SSSINVLEMARGLEAAGVSALAVHGRT--------RSQLYEGKADWSW 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG L  +  A+  +    VD VMIGR    N  ++  +   FS  
Sbjct: 187 IKKVK-EAVSIPVIGNGDLRSVEDAMARIQETQVDAVMIGRGVLGNPWLIRDLVCAFSGE 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            + + P+      +   + +  +    +  +     ++++  H      G P S R +  
Sbjct: 246 GS-AEPVSDHEKFEIALEHARRLCTLKSERIG----MKEMRGHACWYIQGIPYSNRMKDR 300

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           +      +       ET   L  E+L
Sbjct: 301 INQMTTYAE-----FETMLKLYEEAL 321


>gi|256825031|ref|YP_003148991.1| TIM-barrel protein, nifR3 family [Kytococcus sedentarius DSM 20547]
 gi|256688424|gb|ACV06226.1| putative TIM-barrel protein, nifR3 family [Kytococcus sedentarius
           DSM 20547]
          Length = 419

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 123/316 (38%), Gaps = 33/316 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNAL-----------LYTEMIVADAILRGDK--KNILGFSTQE 47
           M   T+R +R   R   +  L             +EMI   A++        ++ F  +E
Sbjct: 48  MAGITNRAFRRLCREYGSEGLTAGGASGASSLYVSEMITTRALVERTPITMKLVEFDAEE 107

Query: 48  KPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +P ++Q+ G D + +  AA+ IVE+   + I++N GCP  +V     GA +     +  D
Sbjct: 108 QPRSMQLYGVDPATVRAAARDIVENDRADHIDMNFGCPVPKVTRKGGGAAIPWKSTLFRD 167

Query: 107 CIAAMCK---ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            + +  +      IPVTVK RIG+D+           +  +  G   + +HAR A     
Sbjct: 168 IVRSAVEEASKADIPVTVKMRIGIDEDHH--THLEAGRIAEDMGAAAVALHARTA----- 220

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                       +  +  +K+    + +  NG +     AL+++     DGV++GR    
Sbjct: 221 ---SQAYSGQARWGEIARLKQTVTTIPVLGNGDIWSAEDALRMVAETGCDGVVVGRGCLG 277

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T +   F+      +P    V     R+ +  + D+   H       + I +H+ 
Sbjct: 278 RPWLFTDLAAAFAGSDARVTPTLREVTAT-LRRHAEYLADF---HEDENHACRDIRKHIT 333

Query: 282 GLFHGFPNSRRCRHIL 297
               GF      R  L
Sbjct: 334 WYLKGFRVGGELRSQL 349


>gi|226227146|ref|YP_002761252.1| putative tRNA-dihydrouridine synthase [Gemmatimonas aurantiaca
           T-27]
 gi|226090337|dbj|BAH38782.1| putative tRNA-dihydrouridine synthase [Gemmatimonas aurantiaca
           T-27]
          Length = 349

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 129/302 (42%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   ++  +R          ++ TE + A+ I R ++  I  L F+ +E+P+ +QI G++
Sbjct: 21  MAGVSESPFRRLCH-AHGADVVVTEFLSAEGIRRENEATISKLRFAPEERPIGVQIFGSE 79

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            S + +AA +V D F  + +++N GCP  +V   + G+  + + D+V + I A+ KA  +
Sbjct: 80  PSAMADAAALVTDMFSPDFVDINFGCPVKKVVRRNGGSGCLKDLDLVEEIIRAVSKATPL 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G ++++       +   ++ +G     +HAR         +      + ++D
Sbjct: 140 PVTVKTRSGWNEEMRDPV--GIALRMQDAGAKVFALHART--------RTQMYSGSANWD 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +  E  D+ +  NG ++    A ++L     DG+MIGR +Y    +          
Sbjct: 190 EIARVA-EALDIPVLGNGDIKTALDAKRMLDHTKADGIMIGRGSYGQPWVFKQTRALIDG 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P                        + + G   +  +H+     G PNS   R 
Sbjct: 249 TPVPETPGVQERFAIALDHARMVQ----GYEVDAIGAALEFRKHLGWYVKGLPNSAELRA 304

Query: 296 IL 297
            L
Sbjct: 305 KL 306


>gi|38604692|sp|O52532|DUSB_SERMA RecName: Full=tRNA-dihydrouridine synthase B
 gi|3885440|gb|AAC77880.1| yhdG homolog [Serratia marcescens]
          Length = 334

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 17  MAGITDRPFRTLCHAM-GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+I    G   I++N+GCP+ +V+    G+ L+  PD+V   + A+  A+ +P
Sbjct: 76  PDDMAAAARINVASGAQLIDINMGCPAKKVNRKLAGSALLQYPDLVKRILHAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRN--CVEIAQLAEDCGIQALTIHGRT--------RACLFNGDAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRAVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V +     I      Y       G   +   +H+         + + R  
Sbjct: 245 ELLPPLPLGEVKRLLIGHIRELHGFY-----GQGKGFRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|215402614|ref|ZP_03414795.1| transcriptional regulator [Mycobacterium tuberculosis 02_1987]
 gi|215444960|ref|ZP_03431712.1| transcriptional regulator [Mycobacterium tuberculosis T85]
 gi|289744547|ref|ZP_06503925.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           02_1987]
 gi|289756910|ref|ZP_06516288.1| transcriptional regulatory protein [Mycobacterium tuberculosis T85]
 gi|294996303|ref|ZP_06801994.1| transcriptional regulator [Mycobacterium tuberculosis 210]
 gi|289685075|gb|EFD52563.1| transcriptional regulatory protein [Mycobacterium tuberculosis
           02_1987]
 gi|289712474|gb|EFD76486.1| transcriptional regulatory protein [Mycobacterium tuberculosis T85]
 gi|326904957|gb|EGE51890.1| transcriptional regulator [Mycobacterium tuberculosis W-148]
          Length = 388

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 125/313 (39%), Gaps = 30/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  FS  E P +L
Sbjct: 29  MAGVTNVAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSL 88

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA 
Sbjct: 89  QLYTVDPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAA 148

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD        +  +  +  G   + +HAR A          
Sbjct: 149 VRATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQ 198

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       + 
Sbjct: 199 RYSGTADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLF 258

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P    V       I        A H      ++ I +H+    HG
Sbjct: 259 AELSAAFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHG 313

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 314 FPAGSA-RRALAM 325


>gi|259416525|ref|ZP_05740445.1| probable tRNA-dihydrouridine synthase [Silicibacter sp. TrichCH4B]
 gi|259347964|gb|EEW59741.1| probable tRNA-dihydrouridine synthase [Silicibacter sp. TrichCH4B]
          Length = 328

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 131/322 (40%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  ++QI G +
Sbjct: 19  MAGITDRPFRDLVRSF-GAGLVVSEMVASQEMVQAKPGVREKAELSADVENTSVQIAGRE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V   G   I++N+GCP+ +V  G  G+ L+  PD     I A+ KA+ +P
Sbjct: 78  AYWMAEAARRVAGSGARMIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVKAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD    +   ++ +  + +GV  + IH R         +        D+  
Sbjct: 138 VTLKTRLGWDD--NCLNAADVARRAQDAGVQMVTIHGRT--------RCQFYKGQADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E++     + +  NG + D + A + L     DGVMIGR       +L  V       
Sbjct: 188 IAEVRNAI-SVPLLANGDIVDAATAQQALGASGADGVMIGRGVQGKPWLLAQVAHELWGS 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
                P +        R   A +  Y      +   L+   +H+       G P + R R
Sbjct: 247 AAPDIPTQGDFVDMVSRHYEAMLAFY-----GNDLGLRVARKHLGWYMDEAGTPTALR-R 300

Query: 295 HILTVEAGASTATHHIIETAFN 316
            +LT  A        ++  A  
Sbjct: 301 EVLT--AKTPAEVLRLLPAALQ 320


>gi|325136535|gb|EGC59139.1| dihydrouridine synthase [Neisseria meningitidis M0579]
          Length = 336

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D  LR  +K +    F  +   +A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRDF-GAGWAVCEMLTSDPTLRNTRKTLHRSDFVDEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM N  +V   + A+ +A  +P
Sbjct: 76  PQQMADAARYNVSLGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVRAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    + +  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHEDHQNLPV--IAKIAEDCGIAALAVHGRT--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKCRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     ++ A + ++      +
Sbjct: 300 IN-RLDSAAAQYDMLAGYLERL 320


>gi|148255455|ref|YP_001240040.1| putative tRNA-dihydrouridine synthase [Bradyrhizobium sp. BTAi1]
 gi|146407628|gb|ABQ36134.1| tRNA-U20-dihydrouridine synthase [Bradyrhizobium sp. BTAi1]
          Length = 317

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 79/318 (24%), Positives = 130/318 (40%), Gaps = 35/318 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A  L    L+ +EM  +D ++RG   + L        P  +Q+ G + 
Sbjct: 1   MSGITDAPFRRLAADL-GAGLVVSEMTASDDLVRGRWISRLRCEASGVGPHVVQLAGCEA 59

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AK+ ED G + I++N+GCP+  V  G  G+ LM + D     I A  +A+ +PV
Sbjct: 60  HWMAEGAKVAEDGGADVIDINMGCPARHVTGGQSGSALMRDLDHALALIEATVEAVDVPV 119

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D++  ++    L +  + +GV  I +H R         +        D+  V
Sbjct: 120 TLKMRLGWDER--SLNAPELARRAEAAGVQLITVHGRT--------RQQFYKGEADWSAV 169

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+   DL + +NG +     A + L     D VMIGR A     +   +        
Sbjct: 170 RAVKQAV-DLPVVVNGDITSYEDAREALDASGADAVMIGRGAQGQPWLPGQIGRRLDGGA 228

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR----- 292
              +P  ++           ++ D   RH      L+   +H+     G   + R     
Sbjct: 229 EEGAPALSQQL-----AYLTALYDEICRHYGERVGLRHARKHLSW---GLDVAARHAKAP 280

Query: 293 ------CR-HILTVEAGA 303
                  R  ILT E  A
Sbjct: 281 AEKLKAWRERILTSEQPA 298


>gi|238789816|ref|ZP_04633598.1| tRNA-dihydrouridine synthase B [Yersinia frederiksenii ATCC 33641]
 gi|238722175|gb|EEQ13833.1| tRNA-dihydrouridine synthase B [Yersinia frederiksenii ATCC 33641]
          Length = 290

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 117/305 (38%), Gaps = 21/305 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              +  +EM+ ++  +    K+ L     ++P    +QI G D   +  AA+I    G  
Sbjct: 2   GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDDMAAAARINVANGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSPEHRN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  +  G+  + IH R         +        +YD +  +K+    + +  NG
Sbjct: 120 CIEIAQLAESCGIQALTIHGRT--------RSCLFNGEAEYDSIRAVKQ-IVSIPVIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPMPLGEVQRLLNG 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            I      Y       G   +   +H+         + + R        AS      +E 
Sbjct: 231 HIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEA 284

Query: 314 AFNLM 318
            F  +
Sbjct: 285 YFENL 289


>gi|53803919|ref|YP_114184.1| YjbN family TIM-barrel protein [Methylococcus capsulatus str. Bath]
 gi|53757680|gb|AAU91971.1| TIM-barrel protein, yjbN family [Methylococcus capsulatus str.
           Bath]
          Length = 327

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 128/293 (43%), Gaps = 21/293 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R   R      L  +EMI A   L+  +K+ L      +  P+++QI GAD
Sbjct: 17  MAGVTDLPFRRLCRQF-GAGLAVSEMISASPALQATRKSRLRQDHRGEPGPISVQIVGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+   D G + I++N+GCP+ +V   + G+ L+ +  +V + + A+ +A+ +P
Sbjct: 76  PREMAEAARRTVDLGADIIDINMGCPAKKVCNVAAGSALLRDEKLVANILEAVVQAVPVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ K  + +G+  + +H R         +        +Y  
Sbjct: 136 VTLKIRTGWDSASRNAV--SIGKIAESAGIRALTVHGRT--------RACGFAGAAEYST 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+KK    + +  NG ++   +A  +L     D VMIGR A+    +L  +D    + 
Sbjct: 186 ITEVKKAIG-IPVIANGDIDSPGKAEAVLRSTGADAVMIGRGAWGRPWLLREIDARLKDG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                P    + +     + A  + Y  +       ++   +H+       P 
Sbjct: 245 RQPLPPTLDEIRRTVLGHLEALYSFYGEKQ-----GVRIARKHIGWYAARIPG 292


>gi|269140492|ref|YP_003297193.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda EIB202]
 gi|267986153|gb|ACY85982.1| tRNA-dihydrouridine synthase B [Edwardsiella tarda EIB202]
 gi|304560282|gb|ADM42946.1| tRNA dihydrouridine synthase B [Edwardsiella tarda FL6-60]
          Length = 334

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GVGMAVSEMLSSNPEVWRTDKSRLRMVHMDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PDEMAAAARINADNGAQIIDINMGCPAKKVNRKLAGSALLQYPGLVEQILRAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPAHRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQHV-SIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     + +     +      Y      SG  L+   +H+         + + R  
Sbjct: 245 ELLPPMPLGEIKRLLAGHVKELHDFY-----GSGKGLRIARKHVSWYLQAHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFEKL 320


>gi|323703650|ref|ZP_08115292.1| TIM-barrel protein, nifR3 family [Desulfotomaculum nigrificans DSM
           574]
 gi|323531365|gb|EGB21262.1| TIM-barrel protein, nifR3 family [Desulfotomaculum nigrificans DSM
           574]
          Length = 323

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 129/322 (40%), Gaps = 23/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR      L+ TEM+   A++  + +   +L F  +  PL++QI G++
Sbjct: 17  MAGVTDRAYRILARE-QGCGLVVTEMVSDLALIYANPRTYRMLDFRGEAPPLSVQIFGSN 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI-VGDCIAAMCKALSI 117
              + +AA IV + G N +++N+GCP+ ++ +   G+ LM NP +      A +     +
Sbjct: 76  PETMGQAAAIVVERGANIVDINMGCPTPKIVKNGEGSALMKNPGLAARIVAAVVAAVPGV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+                +    +    R     G            D+D
Sbjct: 136 PVTVKMRKGWDETSVNAVELAQAVVEAGAAAVAVHGRTRNQFYSG----------KADWD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E   + +  NG +     A +++     DGVMIGRAA  N  +   +  Y +N
Sbjct: 186 IIRQVK-EAVKVPVIGNGDIWHARDAARMMAETGCDGVMIGRAAMGNPWIFRDIIHYLAN 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          R +     D           + ++ +H      G   + R R 
Sbjct: 245 GEELPPPTPAERIATALRHL-----DLMIESKGEQVAVFEMRKHAAWYTKGIRGAARVRE 299

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +  +A       HI+ +    
Sbjct: 300 FIN-KANTREEIEHILRSLLEH 320


>gi|299144544|ref|ZP_07037623.1| tRNA-dihydrouridine synthase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
 gi|298517632|gb|EFI41372.1| tRNA-dihydrouridine synthase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
          Length = 313

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 65/302 (21%), Positives = 129/302 (42%), Gaps = 25/302 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R       N  +  TEMI A A+  GDKK   +L  S  EK +A+QI G D 
Sbjct: 14  AGYTDIAFREICSQ-KNAYMTVTEMISAKALYYGDKKTNELLKVSPFEKNVAVQIFGDDP 72

Query: 60  SKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +    K  +    ++ I++N+GCP+ ++ + + G+ L+  P++    I ++ +  ++P
Sbjct: 73  DIMGYVVKNSLNSLNFSCIDINMGCPAPKIVKNNNGSALLDQPNLAYSIIRSVVENSNVP 132

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R G+ +         + +  +K+G + I +H R         ++       D++ 
Sbjct: 133 VSVKIRKGIRNTNS----MEVARLAQKAGASFITVHGRT--------REEYYSGLSDWNY 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  E   + +  NG ++    A++      V GV IGR A  N  +   + +  S  
Sbjct: 181 IKSVVDELT-IPVIGNGDVQSYEDAMEKIKFSGVSGVSIGRGAIGNPFIFDEIYKK-SIG 238

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P      +     + ++       +      + ++ +H +G F G   S+  R  
Sbjct: 239 CNYEKPTDLEKIEMALSHLKSNCA-----YKGEKIGILEMRKHFVGYFKGMKGSKELRDK 293

Query: 297 LT 298
           + 
Sbjct: 294 IN 295


>gi|114320555|ref|YP_742238.1| nifR3 family TIM-barrel protein [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226949|gb|ABI56748.1| tRNA-U20-dihydrouridine synthase [Alkalilimnicola ehrlichii MLHE-1]
          Length = 356

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 66/291 (22%), Positives = 116/291 (39%), Gaps = 21/291 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R     AL  +EM+ AD  LR  +K+      +  E P   QI GAD
Sbjct: 44  MAGITDLPFRQLCRQW-GAALAVSEMLSADPTLRKTRKSQWRATLADDECPRVAQIAGAD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+     G   I++N+GCP+ +V     G+ L+ +  +V   + A+  A+ +P
Sbjct: 103 PVALAEAARYNVQRGAQVIDINMGCPAKKVCNRMAGSALLADEPLVRRILTAVVSAVEVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  + +GV  + +H R  +               +Y  
Sbjct: 163 VTLKYRTGPSPERRNAVA--IARMAEDAGVAALTLHGRTRV--------QAYQGQAEYRS 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  + +   D+ +  NG ++   +A ++L     D VM+GRAA     +   +  Y    
Sbjct: 213 VEAVCRAV-DIPVVANGDIDSPDKARQVLDETGADAVMVGRAAQGRPWLFQAIHTYLETG 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
              ++P      +     +      Y       G ++    +H+       
Sbjct: 272 TRVATPSLAVRKQTLLTHLREIHRFYGD---WMGPRI--ARKHIKWYLQAL 317


>gi|300721814|ref|YP_003711092.1| tRNA -dihydrouridine synthase B [Xenorhabdus nematophila ATCC
           19061]
 gi|297628309|emb|CBJ88870.1| tRNA-dihydrouridine synthase B [Xenorhabdus nematophila ATCC 19061]
          Length = 296

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 120/303 (39%), Gaps = 21/303 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              +  +EM+ ++  +    K+ L     ++P   ++QI G+D  ++  AAKI  D G  
Sbjct: 2   GAGMAVSEMLSSNPQVWKTDKSRLRMVHSDEPGVRSVQIAGSDPDEMAAAAKINVDNGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+  P++V   ++A+  A+ +PVT+K R G   +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLRYPELVEKILSAVVNAVDVPVTLKIRTGWSPEERN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  ++ G+  + IH R         +        +YD +  +K+    + I  NG
Sbjct: 120 CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDNIRTVKQ-TVAIPIIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPLKARAVLEYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPMPLGEVQRLMSE 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            +      Y       G  ++   +H+           + R        AS      +E 
Sbjct: 231 HVRELQDFY-----GQGKGVRIARKHVSWYLKEHAPDDQFRRSFNAIEDASE-QLEALEA 284

Query: 314 AFN 316
            F 
Sbjct: 285 YFE 287


>gi|226308278|ref|YP_002768238.1| tRNA-dihydrouridine synthase [Rhodococcus erythropolis PR4]
 gi|229488396|ref|ZP_04382262.1| putative tRNA-dihydrouridine synthase [Rhodococcus erythropolis
           SK121]
 gi|226187395|dbj|BAH35499.1| putative tRNA-dihydrouridine synthase [Rhodococcus erythropolis
           PR4]
 gi|229323900|gb|EEN89655.1| putative tRNA-dihydrouridine synthase [Rhodococcus erythropolis
           SK121]
          Length = 380

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 74/308 (24%), Positives = 122/308 (39%), Gaps = 29/308 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R L      + + L   EM+ A A++      +    F   E P +L
Sbjct: 20  MAGVTNVAFRTLCRELELERAGSTSGLYVCEMVTARALVERQPATMHMTTFGPTETPRSL 79

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK++ D    + I++N GCP  +V     G+ L     + G  +AA 
Sbjct: 80  QLYTVDPDTTYAAAKMIVDENMADHIDMNFGCPVPKVTRKGGGSALPYKRRLFGQIVAAA 139

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK R+G+D +       +  +     G   + +HAR A          
Sbjct: 140 VRATEGTDIPVTVKMRVGIDPEHH--THLDAGRIAAAEGAAAVALHARTA--------SQ 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+   D+ I  NG + D S A +++     DGV++GR       + 
Sbjct: 190 RYSGTADWNEITRLKEHVTDVPILGNGDIFDASDAARMMNETGCDGVVVGRGCLGRPWLF 249

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +    +     + P    V K     I A      A H      L+++ +H+     G
Sbjct: 250 AELSAALNGQQIATPPTLGEVTK-----IIARHAQLLAAHHGEMKGLRELRKHVSWYMRG 304

Query: 287 FPNSRRCR 294
           FP     R
Sbjct: 305 FPVGSDLR 312


>gi|268598315|ref|ZP_06132482.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae MS11]
 gi|268582446|gb|EEZ47122.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae MS11]
          Length = 334

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKSRL-NIPVWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 300 INRLDNAA-AQYDTLAGYLERL 320


>gi|238921361|ref|YP_002934876.1| hypothetical protein NT01EI_3505 [Edwardsiella ictaluri 93-146]
 gi|238870930|gb|ACR70641.1| conserved hypothetical protein [Edwardsiella ictaluri 93-146]
          Length = 334

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCYEM-GVGMAVSEMLSSNPEVWRTDKSRLRMVHMDEPGIRAVQIAGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+I  D G   I++N+GCP+ +V+    G+ L+  P +V   + A+  A+ +P
Sbjct: 76  PDEMAAAARINADNGAQIIDINMGCPAKKVNRKLAGSALLQYPGLVEQILRAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPAHRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQHV-SIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     + +     +      Y      SG  L+   +H+         + + R  
Sbjct: 245 ELLPPMPLGEIKRLLAGHVKELHDFY-----GSGKGLRIARKHVSWYLQAHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFEKL 320


>gi|331701913|ref|YP_004398872.1| TIM-barrel protein, nifR3 family [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129256|gb|AEB73809.1| TIM-barrel protein, nifR3 family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 335

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 131/324 (40%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 19  MAGVTNSAFRIICKEY-GVGLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+     + I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  
Sbjct: 78  KETLVQAAKFVDQNTAADIIDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + + +H R         +      + D+ 
Sbjct: 138 PVTVKMRTGWDEDHIYAVENALA--AERAGASALAMHGRT--------RKQMYEGHADWG 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++ +E   +    NG +     A K+L     D VM+GRA   N  +L     Y   
Sbjct: 188 ILKQVAQEI-HIPFMGNGDVRTPQDAKKMLTEVGTDAVMMGRAVEGNPWILKQTQHYLET 246

Query: 236 PLTGSSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
               + P         K+   ++     DY   H   G               G P+S R
Sbjct: 247 GELLAEPTPEEKVVTAKEHLHRLVELKGDYIGSHEFRGQA--------GYYLKGIPHSAR 298

Query: 293 CRHILTVEAGASTATHHIIETAFN 316
            +  LT  A   +A   I +    
Sbjct: 299 TKVALT-NASGESAMDDIFDEFLE 321


>gi|253991187|ref|YP_003042543.1| tRNA -dihydrouridine synthase B [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782637|emb|CAQ85801.1| tRNA-dihydrouridine synthase B [Photorhabdus asymbiotica]
          Length = 328

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 125/320 (39%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   ++QI G D
Sbjct: 24  MAGITDRPFRSLCYAM-GAGMTVSEMLSSNPQVWKTDKSRLRMVHSDEPGIRSVQIAGND 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA++    G   I++N+GCP+ +V+    G+ L+  P++V   ++A+  A+ +P
Sbjct: 83  PDEMAAAARVNVANGAQIIDINMGCPAKKVNRKLAGSALLRYPELVEKILSAVVNAVDVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 143 VTLKIRTGWSPEERN--CVKIAQLAEHCGIQALTIHGRT--------RACLFNGEAEYDN 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 193 IRTVKQ-TVAIPVIANGDITDPLKARAVLEYTGADALMIGRAAQGRPWIFREIQHYLETG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       I      Y    L  G ++    +H+           + R  
Sbjct: 252 ELLPPMPIGEVQHLMNEHIQELHDFYG---LGKGARI--ARKHVSWYLREHAPDDQFRRT 306

Query: 297 LTVEAGASTATHHIIETAFN 316
                 AS     +++  F 
Sbjct: 307 FNTIEDASE-QLEVLKAYFE 325


>gi|37681322|ref|NP_935931.1| tRNA-dihydrouridine synthase [Vibrio vulnificus YJ016]
 gi|326423811|ref|NP_760162.2| tRNA dihydrouridine synthase B [Vibrio vulnificus CMCP6]
 gi|38604853|sp|Q8CWL2|DUSB_VIBVU RecName: Full=tRNA-dihydrouridine synthase B
 gi|37200073|dbj|BAC95902.1| tRNA-dihydrouridine synthase [Vibrio vulnificus YJ016]
 gi|319999178|gb|AAO09689.2| tRNA dihydrouridine synthase B [Vibrio vulnificus CMCP6]
          Length = 322

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L    K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPQLWKTSKSKQRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+   + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLKYPDIIEQILKAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +       ++ K  +  G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWDTENKN--CIHIAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAVKQAV-SIPVIANGDIDSPEKAKYVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       + A    Y           +   +H+         +   R  
Sbjct: 245 TTMPELPIEEVKSIMLGHVQALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      +E  F+ +
Sbjct: 300 FNA-IDAAMLQLEALEGYFDNV 320


>gi|160944625|ref|ZP_02091852.1| hypothetical protein FAEPRAM212_02138 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443809|gb|EDP20813.1| hypothetical protein FAEPRAM212_02138 [Faecalibacterium prausnitzii
           M21/2]
          Length = 354

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 122/320 (38%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD   R             +EM+ + A++ GD K   +L  +    P  +QI G  
Sbjct: 35  MAGFTDAPCRRLMAQ-HGAGFTVSEMVSSRALVYGDHKTVSLLKAAPNGAPYGVQIFGEV 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA   +E + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  +      P
Sbjct: 94  PEIMGEATAAIEQYEFDFVDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEQVVAHTKRP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     +      K+ +++G   + +HAR         ++    P +D +I
Sbjct: 154 VTVKMRKGWD--ADHITAVECAKACEQAGAALVAVHART--------REQMYTPGIDPEI 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +     AL+++   + DGVMI R A  +  +   V+      
Sbjct: 204 IARVK-DAVKVPVLGNGDIHCAEDALRMVRETNCDGVMIARGALGDPWLFERVNAALEGL 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R++                 + Q     +    G   +   R  
Sbjct: 263 PAPKEPNLQARMNALRRQVEEM-----VEQKGEFVAMPQARAQTMHYMKGLKGAAALRRY 317

Query: 297 ---LTVEAGASTATHHIIET 313
              LT           + E 
Sbjct: 318 CCTLTHLEDLDELIAAVFEE 337


>gi|41406755|ref|NP_959591.1| hypothetical protein MAP0657c [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395105|gb|AAS02974.1| hypothetical protein MAP_0657c [Mycobacterium avium subsp.
           paratuberculosis K-10]
          Length = 377

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 130/313 (41%), Gaps = 29/313 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN------ALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L          L   EM+ A A++       +++ F+  E P +L
Sbjct: 17  MAGVTNVAFRTLCRELERELVGTVSGLYVYEMVTARALVERHPATMHMITFAPDESPRSL 76

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D G  + I++N GCP  +V +   G+ L     + G  +AA 
Sbjct: 77  QLYTVDPATTYAAAKMIADEGLADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGQIVAAA 136

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IPVTVK RIG+DD+       +  +  +  G   + +HAR A          
Sbjct: 137 VRATQGTEIPVTVKFRIGIDDEHH--THLDAGRIAEAEGAAAVALHARTA--------AQ 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K++   + +  NG + D S AL ++     DGV+IGR       + 
Sbjct: 187 RYSGTADWEQIALLKQQVRTIPVLGNGDIYDASDALTMMAATGCDGVVIGRGCLGRPWLF 246

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+     + P   +V       I        A H      ++ I +H+    HG
Sbjct: 247 AELSAAFTGSPPPTPPTLGQVA-----DIVRRHGRLLAAHFGEDKGMRDIRKHIAWYLHG 301

Query: 287 FPNSRRCRHILTV 299
           FP     R  L +
Sbjct: 302 FPAGSELRRALAM 314


>gi|313139725|ref|ZP_07801918.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
 gi|313132235|gb|EFR49852.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
          Length = 413

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 118/317 (37%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 53  MAGVTNWPFRVLCEEYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVN 112

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AA+IV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 113 PAIVEQAARIVVDEDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCSA 172

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 173 ANIPVTAKIRVGID--HSHETFMEAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 222

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +     AL+++      GV IGR       +   +   
Sbjct: 223 DWSRIGELVGAL-DIPVFGNGDIWGADDALEMVRETGCAGVAIGRGCQGRPWLFADIRNA 281

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+      +P    V     R     +  Y      +   +  + +H+     GFP    
Sbjct: 282 FAGSDERVNPTLGAVCDVIMRHARLLVEFYDGDERMA---VHDLRKHIAWYLKGFPVGGT 338

Query: 293 CRHILTVEAGASTATHH 309
            R         +     
Sbjct: 339 TRRAFMECENLADVERE 355


>gi|119026155|ref|YP_910000.1| NifR3-like protein [Bifidobacterium adolescentis ATCC 15703]
 gi|154488945|ref|ZP_02029794.1| hypothetical protein BIFADO_02254 [Bifidobacterium adolescentis
           L2-32]
 gi|118765739|dbj|BAF39918.1| possible NifR3-like protein [Bifidobacterium adolescentis ATCC
           15703]
 gi|154083082|gb|EDN82127.1| hypothetical protein BIFADO_02254 [Bifidobacterium adolescentis
           L2-32]
          Length = 409

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 119/318 (37%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPSEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            S + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 109 PSIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 169 ANVPVTAKIRVGIDHE--HETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 218

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+  E  D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 219 DWSRIGELVSEL-DIPVFGNGDIWGANDALAMVAETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +   R        Y      +   +  + +H+     GFP    
Sbjct: 278 FAGSDERVDPTLGDVCRVIERHAELLTEFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 334

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 335 TRRAFMECENLEDVRREI 352


>gi|111021839|ref|YP_704811.1| tRNA-dihydrouridine synthase [Rhodococcus jostii RHA1]
 gi|110821369|gb|ABG96653.1| probable tRNA-dihydrouridine synthase [Rhodococcus jostii RHA1]
          Length = 380

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 126/326 (38%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R L      + + L   EM+ A A++        +  F   E P +L
Sbjct: 20  MAGITNVAFRTLCRELETERAGSTSGLYVCEMVTARALVERQPATLHMTTFGPTETPRSL 79

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK++ D    + I++N GCP  +V     GA L     + G  +AA 
Sbjct: 80  QLYTVDPDTTYAAAKMIVDENMADHIDMNFGCPVPKVTRKGGGAALPYKRTLFGRIVAAA 139

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     +PVTVK R+G+D +       +  +     G   + +HAR A          
Sbjct: 140 VKATEGTDVPVTVKFRVGIDAEHH--THLDAGRIAAGEGAAAVALHARTA--------SQ 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+   D+ +  NG +     A +++     DGV++GR       + 
Sbjct: 190 RYSGTADWNEIARLKEHVTDVPVLGNGDIFAAEDAARMMEQTGCDGVVVGRGCLGRPWLF 249

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +    +     + P    V     R       +  A H      L+++ +H+     G
Sbjct: 250 AELSAALNGKPQPTPPNLGEVATIIRRHA-----ELLADHHGEDKGLRELRKHVSWYLRG 304

Query: 287 FPNSRRCRHILTVEAGASTATHHIIE 312
           FP     R  + + +  +     +++
Sbjct: 305 FPAGSELRVAMALVSTLTELDDLLVQ 330


>gi|224282569|ref|ZP_03645891.1| NifR3-like protein [Bifidobacterium bifidum NCIMB 41171]
 gi|310287030|ref|YP_003938288.1| TIM-barrel protein [Bifidobacterium bifidum S17]
 gi|309250966|gb|ADO52714.1| putative TIM-barrel protein [Bifidobacterium bifidum S17]
          Length = 426

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 118/317 (37%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 66  MAGVTNWPFRVLCEEYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVN 125

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AA+IV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 126 PAIVEQAARIVVDEDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCSA 185

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 186 ANIPVTAKIRVGID--HSHETFMEAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 235

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +     AL+++      GV IGR       +   +   
Sbjct: 236 DWSRIGELVGAL-DIPVFGNGDIWGADDALEMVRETGCAGVAIGRGCQGRPWLFADIRNA 294

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+      +P    V     R     +  Y      +   +  + +H+     GFP    
Sbjct: 295 FAGSDERVNPTLGAVCDVIMRHARLLVEFYDGDERMA---VHDLRKHIAWYLKGFPVGGT 351

Query: 293 CRHILTVEAGASTATHH 309
            R         +     
Sbjct: 352 TRRAFMECENLADVERE 368


>gi|289670979|ref|ZP_06492054.1| nifR3 family TIM-barrel protein [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 299

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 130/305 (42%), Gaps = 21/305 (6%)

Query: 19  NALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             L  +EM ++D    G +K++  +  + +  P+++QI G +  +L EAA+   D G   
Sbjct: 1   AGLAVSEMTISDRRFWGTRKSLHRMDHAGEPDPISVQIAGTEPQQLAEAARYNVDHGAQL 60

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N+GCP+ +V     G+ LM + D+V   + A+ +A+++PVT+K R G D       +
Sbjct: 61  IDINMGCPAKKVCNAWAGSALMRDEDLVARILIAVVRAVNVPVTLKIRTGWDCDHRNGPV 120

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + +  +  G+  + +H R         +D     + +Y  + +IK     + +  NG 
Sbjct: 121 --IARIAQDCGIAALAVHGRT--------RDQHYTGSAEYATIAQIKAAL-QIPVVANGD 169

Query: 197 LEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           ++   +A ++L     D VMIGRAA     +   V  + +       P    V       
Sbjct: 170 IDSPQKAAQVLRETGADAVMIGRAAQGRPWIFGEVAHFLATGEVLPPPSLAFVRDTLLSH 229

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
           + A    Y          ++   +H+       P S   R ++   A    A   +    
Sbjct: 230 LEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAVVN-RAETPEAQLALTRDY 283

Query: 315 FNLMI 319
           F+ +I
Sbjct: 284 FDALI 288


>gi|313891460|ref|ZP_07825076.1| TIM-barrel protein, nifR3 family [Dialister microaerophilus UPII
           345-E]
 gi|313120235|gb|EFR43411.1| TIM-barrel protein, nifR3 family [Dialister microaerophilus UPII
           345-E]
          Length = 327

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 76/301 (25%), Positives = 133/301 (44%), Gaps = 21/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR     A+   EM+ +  +   ++K   +L  +  E P+ALQ+ G  
Sbjct: 20  MAGVSDLAYRVIARK-HGAAMTTAEMVSSRGLYYKNEKTEEMLKIAPDEHPVALQLFGNQ 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK VE+ G + I++N+GCP  +V +   G  +M + D     + AM KA+ +P
Sbjct: 79  AEIMALAAKEVEEAGADVIDINMGCPMQKVVKNGDGCSMMKDIDNSAKVVEAMVKAVKVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D +   +    L K+++ +G   I +H R         ++       D D 
Sbjct: 139 VTVKMRIGWDRE--NLNSPELAKAVEAAGAAAITVHGRT--------REEMYSGKADLDA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  E   + +  NG + D   A +++      GV IGRAA+ N  +   V+ Y  + 
Sbjct: 189 IRKVV-EAVKIPVFGNGDIVDGPSAKRMMEETGCVGVAIGRAAWGNPWIFNAVNTYLESG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T   P       +    ++ +      +       ++++  H    FHG P +   R  
Sbjct: 248 ETVEEPS-----WEMRLSMARTHLGNLVKEKGEYTAIREMRAHASHYFHGLPKATALRRE 302

Query: 297 L 297
           +
Sbjct: 303 I 303


>gi|296141212|ref|YP_003648455.1| hypothetical protein Tpau_3537 [Tsukamurella paurometabola DSM
           20162]
 gi|296029346|gb|ADG80116.1| TIM-barrel protein, nifR3 family [Tsukamurella paurometabola DSM
           20162]
          Length = 396

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 126/322 (39%), Gaps = 38/322 (11%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T   L   EM+ A A++       ++  F+  E P +L
Sbjct: 25  MAGVTNVAFRSLCRELERARTGTVAGLYVCEMVTARALVERHPVTMHMTTFAPDEDPRSL 84

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAA+++ + G  + +++N GCP  ++     G+ L    ++    + A 
Sbjct: 85  QLYTVDAHYTYEAARMIAEEGLADHLDMNFGCPVPKITRRGGGSALPYKRNLFASIVDAA 144

Query: 112 CKALS-------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + +        IPVTVK RIG+DD+       +  +   + G   + +HAR A      
Sbjct: 145 VRGIEDGGQGGRIPVTVKFRIGIDDEHH--THLDAGRIAAEQGAVAVALHARTA------ 196

Query: 165 PKDNRKIPNLDYDIVYEIKKENPD-----LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
               R     D+D +  +K+         + +  NG +     A+ ++     DGV++GR
Sbjct: 197 --AQRYSGQADWDEIARLKEHVHHHFGDAVPVLGNGDIFAAEDAVTMMDRTGCDGVVVGR 254

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  + + +    +     + P    V +  +R       +  A H      +++I 
Sbjct: 255 GCLGRPWLFSELSAALNGTPMPTPPNLGEVTEIMYRH-----GELLAAHHGEDKGMREIR 309

Query: 278 RHMIGLFHGFPNSRRCRHILTV 299
           +H+     GFP     R  L  
Sbjct: 310 KHVAWYLRGFPAGGELRTRLAT 331


>gi|288559354|ref|YP_003422840.1| tRNA-dihydrouridine synthase DusA1 [Methanobrevibacter ruminantium
           M1]
 gi|288542064|gb|ADC45948.1| tRNA-dihydrouridine synthase DusA1 [Methanobrevibacter ruminantium
           M1]
          Length = 329

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 138/326 (42%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D  +R   + +    L+ TEM+   A++ G+ K   +L  +  E+P++ QI G+D
Sbjct: 19  MAGVCDSAFRTIVKSM-GCGLIETEMVSDKAVMYGNWKTKEMLYMTDYERPISQQIVGSD 77

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALS 116
           I  L  A+K ++D    + I++N+GCP  +V      G+ L+ +PD +   + ++  ++ 
Sbjct: 78  IESLTFASKYIQDNTNVDIIDINMGCPVTKVTNRGKAGSALLKSPDKIKSIVESIVDSVD 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT K R G D     +    + K I+ +G + I +H R         KD       D+
Sbjct: 138 IPVTAKIRSGWDK--SCINAVEIAKIIEDAGASAITVHPRT--------KDQAYSGKADW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            I+ ++K+ + ++ +  NG +     A ++L     D VMIGRAA  N  ++     Y  
Sbjct: 188 SIIKKVKQ-SVNIPVIGNGDVRTCFDAKRMLDETDCDAVMIGRAALGNPWLIRDCVNYLD 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           N                 R ++  + +           + ++  H        P +   +
Sbjct: 247 NGDLPMEVTIEERMDMLKRHVNLLLENKGEE-----FAIPKMRTHAAYYVKKLPRTIELK 301

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
            ++           ++++   + + E
Sbjct: 302 QMIFKMNTKEDL-FNLLDDYVDSLDE 326


>gi|42560628|ref|NP_975079.1| NifR transcriptional regulator [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492124|emb|CAE76721.1| Transcriptional regulator (involved in nitrogen regulation; NifR3
           family [Mycoplasma mycoides subsp. mycoides SC str. PG1]
 gi|301321309|gb|ADK69952.1| TIM-barrel protein, nifR3 family [Mycoplasma mycoides subsp.
           mycoides SC str. Gladysdale]
          Length = 324

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 69/326 (21%), Positives = 144/326 (44%), Gaps = 28/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  ++     +L+Y EM+    ++  +KK   +L  +  E P+++QI G D
Sbjct: 17  MAGVSNEAFRIISKQ-HGASLVYAEMVSVAGMVHDNKKTLNMLNVNKIEYPMSMQIFGND 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAMCKALS 116
           + + ++A + +E     + I+LN+GCP+ +V      G+ L+  P+++ + +  +    +
Sbjct: 76  VDEFIKATQWIEKNVDCDIIDLNLGCPAPKVAIRSQSGSALLKTPELIYEIVKNVVNNTN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R+G D    +V    + K I+K+G + I +HAR         +++    + D+
Sbjct: 136 KPVTAKIRLGWDK--NSVNAVEVAKLIEKAGASAIAVHART--------RNDFYTGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + E+K+    + +  NG + D   A K+L     D VM+ RA   N  +   ++ Y  
Sbjct: 186 EKIKEVKQAV-SIPVIGNGDVIDAKSAKKMLDETGCDAVMVSRACQGNPWIFDQINYYLK 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P         W+       D   +       +++  +H+        N+++  
Sbjct: 245 TGKELEKPSFEE-----WKTTVLQHLDLLVKLKTKQFAIKEFRKHLTWYL-DVLNNKQLT 298

Query: 295 HILTVEAGASTATHHIIETAFNLMIE 320
            IL  +A         I+   +++ E
Sbjct: 299 KILKEKANK----IETIKDVEDIIKE 320


>gi|163855213|ref|YP_001629511.1| dihydrouridine synthase [Bordetella petrii DSM 12804]
 gi|163258941|emb|CAP41240.1| dihydrouridine synthase [Bordetella petrii]
          Length = 349

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 70/306 (22%), Positives = 126/306 (41%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K    L    +  P+A+QI GAD
Sbjct: 25  MAGVTDRPFRQLCKRL-GAGHAVSEMAASNPRLWDSVKTSRRLNHDGEIAPVAVQIAGAD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            + + EAA      G   I++N+GCP  +V   + G+ L+ + D+V   + A+  A   L
Sbjct: 84  PAMMAEAAAFNAARGARIIDINMGCPVKKVCNLASGSALLRDEDLVARILDAVVAACAPL 143

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G D +        + +  +++G+  + +H R         + +      +
Sbjct: 144 GVPVTLKTRTGWDREHRNA--LRVARRAQEAGIAALALHGRT--------RADLYTGTAE 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K E   + +  NG ++   +A ++L     D VMIGRAA     +   +D Y 
Sbjct: 194 YDTIRAVKAEL-SIPVIANGDIDSPQKARRVLDYTGADAVMIGRAAQGRPWIFREIDHYL 252

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               T + P    +       +      Y          ++   +H+     G P +   
Sbjct: 253 RTGDTLAPPSLEEMRDLLLEHLDDHYRFYGEH-----TGVRSARKHIGWYIDGLPGADAF 307

Query: 294 RHILTV 299
           R  + +
Sbjct: 308 RDRMNL 313


>gi|302206819|gb|ADL11161.1| Dihydrouridine synthase-like (DUS-like) FMN-binding domain protein
           [Corynebacterium pseudotuberculosis C231]
 gi|308277071|gb|ADO26970.1| Dihydrouridine synthase-like (DUS-like) FMN-binding domain protein
           [Corynebacterium pseudotuberculosis I19]
          Length = 384

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 127/314 (40%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EMI A A++  ++K   +  F  QE   +L
Sbjct: 22  MAGVTNIAFRTLCREQELERTGTVSGLYICEMITARALVHRNEKTLHMTTFGPQEDVRSL 81

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D G  + I++N GCP  +V +   G+ L     + G+ IAA 
Sbjct: 82  QLYTVDPEYTFKAAKMIADEGIADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGNIIAAA 141

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            K +   +IPVTVK R+G+D     +   +  +   + G   + +HAR A          
Sbjct: 142 VKGVEGTNIPVTVKFRMGID--HDHLTHLDAGRIAAEEGAAAVTLHARTA--------AE 191

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   +  +D + ++K+   +  + +  NG +   + A+ ++     DGV++GR       
Sbjct: 192 RYSGDAHWDEIGKLKEHLAHTGIPVLGNGDIFKPTDAIDMIKASGCDGVVVGRGCLGRPW 251

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +  +R       +    H       + + +HM    
Sbjct: 252 LFAGLSAAMRGKEIPPEPTLGEVTRIIYRHA-----ELLVEHEGETKGCRDMRKHMGWYL 306

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 307 RGFPVGGDFRGALA 320


>gi|226364360|ref|YP_002782142.1| tRNA-dihydrouridine synthase [Rhodococcus opacus B4]
 gi|226242849|dbj|BAH53197.1| putative tRNA-dihydrouridine synthase [Rhodococcus opacus B4]
          Length = 380

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 125/326 (38%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R L      + + L   EM+ A A++        +  F   E P +L
Sbjct: 20  MAGITNVAFRTLCRELETERAGSTSGLYVCEMVTARALVERQPATLHMTTFGPTETPRSL 79

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D      AAK++ D    + I++N GCP  +V     GA L     + G  +AA 
Sbjct: 80  QLYTVDPDTTYAAAKMIVDENMADHIDMNFGCPVPKVTRKGGGAALPYKRTLFGRIVAAA 139

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     +PVTVK R+G+D         +  +     G   + +HAR A          
Sbjct: 140 VKATEGTDVPVTVKFRVGID--ADHHTHLDAGRIAAGEGAAAVALHARTA--------SQ 189

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           R     D++ +  +K+   D+ +  NG +     A +++     DGV++GR       + 
Sbjct: 190 RYSGTADWNEIARLKEHVTDVPVLGNGDIFAAEDAARMMEQTGCDGVVVGRGCLGRPWLF 249

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +    +     + P    V     R       +  A H      L+++ +H+     G
Sbjct: 250 AELSAALNGKPQPTPPNLGEVATIIRRHA-----ELLADHHGEDKGLRELRKHVSWYLRG 304

Query: 287 FPNSRRCRHILTVEAGASTATHHIIE 312
           FP     R  + + +  +     +++
Sbjct: 305 FPAGSELRVAMALVSTLTELDDLLVQ 330


>gi|311063903|ref|YP_003970628.1| tRNA-dihydrouridine synthase [Bifidobacterium bifidum PRL2010]
 gi|310866222|gb|ADP35591.1| tRNA-dihydrouridine synthase [Bifidobacterium bifidum PRL2010]
          Length = 413

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 117/317 (36%), Gaps = 22/317 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E+  +LQ+ G +
Sbjct: 53  MAGVTNWPFRVLCEEYGPDGLYVAEMITARALVARNPKALRLCRFAPSERIRSLQLYGVN 112

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
            + + +AA+IV D    + ++LN GCP  +V     G+ L    D+  + I  + K  S 
Sbjct: 113 PAIVEQAARIVVDEDMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCST 172

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D               ++ G   + +HAR                + 
Sbjct: 173 ANIPVTAKIRVGID--HSHETFMEAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 222

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +     AL+++      GV IGR       +   +   
Sbjct: 223 DWSRIGELVGAL-DIPVFGNGDIWGADDALEMVRETGCAGVAIGRGCQGRPWLFADIRNA 281

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+      +P    V     R     +  Y      +   +  + +H+     GFP    
Sbjct: 282 FAGSDERVNPTLGAVCDVIMRHARLLVEFYDGDERMA---VHDLRKHIAWYLKGFPVGGT 338

Query: 293 CRHILTVEAGASTATHH 309
            R         +     
Sbjct: 339 TRRAFMECENLADVERE 355


>gi|238794627|ref|ZP_04638233.1| tRNA-dihydrouridine synthase B [Yersinia intermedia ATCC 29909]
 gi|238726016|gb|EEQ17564.1| tRNA-dihydrouridine synthase B [Yersinia intermedia ATCC 29909]
          Length = 290

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 118/305 (38%), Gaps = 21/305 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              +  +EM+ ++  +    K+ L     ++P    +QI G D  ++  AA+I    G  
Sbjct: 2   GAGMTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMAAAARINVANGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSTEHRN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  +  G+  + IH R         +        +YD +  +K+    + +  NG
Sbjct: 120 CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDSIRAVKQ-IVSIPVIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPMPLGEVQRLLNG 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            I      Y       G   +   +H+         + + R        AS      +E 
Sbjct: 231 HIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEA 284

Query: 314 AFNLM 318
            F  +
Sbjct: 285 YFENL 289


>gi|325266282|ref|ZP_08132961.1| tRNA-dihydrouridine synthase B [Kingella denitrificans ATCC 33394]
 gi|324982244|gb|EGC17877.1| tRNA-dihydrouridine synthase B [Kingella denitrificans ATCC 33394]
          Length = 336

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 132/302 (43%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD   R  AR         +EM+ +D  L+  +K+        ++  + +QI G+D
Sbjct: 20  MAGITDNPTRRTARQW-GADWTVSEMLSSDPGLQHTQKSRNRRNHEGEDGVIVVQIAGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA+   + G   I++N+GCP  +V     G+ L+ N  +V   + A+ +   +P
Sbjct: 79  PEQMAHAARHNAEHGAQIIDINMGCPVKKVCNVLAGSALLQNEPLVERILHAVVRNAGVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD+   +    + K  +++G+  + IH R         +      N +YD+
Sbjct: 139 VTLKTRLGWDDEHRNI--LTIAKMAEQAGIAALAIHGRT--------RTQMYQGNAEYDL 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     L + +NG ++   +A ++L     DGVM+GRAA     +   + ++  + 
Sbjct: 189 IAQVK-HTVSLPVWVNGDIDSPQKAARVLQQTQADGVMVGRAAQGQPWIFRDIAQFLQHG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P+           I+A    Y      +G ++    +H+        +   CR  
Sbjct: 248 RIPEAPVFDEAADTVLAHIAALHRFYGDT---AGTRI--ARKHIAWYLRRLADGESCRKH 302

Query: 297 LT 298
           + 
Sbjct: 303 IN 304


>gi|172041286|ref|YP_001801000.1| hypothetical protein cur_1606 [Corynebacterium urealyticum DSM
           7109]
 gi|171852590|emb|CAQ05566.1| hypothetical protein cu1606 [Corynebacterium urealyticum DSM 7109]
          Length = 442

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 120/313 (38%), Gaps = 30/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        +   L   EM+ A A++  + K   +  F+  E P +L
Sbjct: 81  MAGVTNVAFRTLCREQERERMGSVAGLYVCEMVTARALVERNPKTLHMTTFAPDEDPRSL 140

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAAK++ D    + I++N GCP  +V     GA L     + G+ +AA 
Sbjct: 141 QLYTTDPKYTYEAAKMIVDENMADHIDMNFGCPMPKVTRRGGGAALPYKRRLFGNIVAAA 200

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK RIG+DD+       +  +     G   + +H R A          
Sbjct: 201 VKATEGTDIPVTVKMRIGIDDEHR--THLDAGRIAADEGAAAVALHGRTA--------AQ 250

Query: 169 RKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
           R   + D+  +  + +     + +  NG +   + A  ++     DGV++GR       +
Sbjct: 251 RYAGDADWSEIARLVEHMDGRVPVLGNGDIFKATDARAMMDQTGCDGVVVGRGCLGRPWL 310

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +          + P    V +   R       +  A H       + + +HM     
Sbjct: 311 FAELSAELRGLPVPAEPPLGEVARIIMRHA-----ELLAEHDGEDRACRDLRKHMTWYMR 365

Query: 286 GFPNSRRCRHILT 298
           GFP     R  L+
Sbjct: 366 GFPAGGELRRSLS 378


>gi|134093535|ref|YP_001098610.1| tRNA-dihydrouridine synthase B [Herminiimonas arsenicoxydans]
 gi|133737438|emb|CAL60481.1| tRNA-dihydrouridine synthase B [Herminiimonas arsenicoxydans]
          Length = 322

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 120/302 (39%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L    K         + +P A+QI GAD
Sbjct: 1   MAGVTDRPFRQLCKQL-GAGYAVSEMAASNPRLWATDKSTRRTNHDGEVEPKAVQIAGAD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L E AK   D G   I++N+GCP  +V     G+ L+ +  +V + + A+  A+ +P
Sbjct: 60  PLMLAECAKFNVDRGAQIIDINMGCPVKKVCNSWCGSALLQHESLVAEILQAVVAAVDVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         N+ +  ++SG+  + +H R         + +      +Y++
Sbjct: 120 VTLKFRTGWDRAHKNA--LNIARIAEQSGIAMLTLHGRT--------RADGYSGEAEYEM 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 170 IAAVK-AAVSIPVVANGDITTPEKAKFVLEATGADAIMIGRAAQGRPWIFREIVHYLRTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P+ + V       + A    Y          ++   +H+        +    R  
Sbjct: 229 THLPAPLISEVRTLMDEHLRAHYAFY-----GEYLGVRTARKHIGWYVRELIDGEAFRQQ 283

Query: 297 LT 298
           + 
Sbjct: 284 MN 285


>gi|261868732|ref|YP_003256654.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261414064|gb|ACX83435.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 349

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R          L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 39  MAGVTDLPFRRICANY-GAGLTFSEMMSTNPQVWYTEKSKLRLAHHQEAGINAVQIAGSD 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ KA+ +P
Sbjct: 98  PDGMAQAAQVNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVRRILEAVVKAVKVP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  ++SG+  + +H R         +  +     +YD 
Sbjct: 158 VTLKIRTGWDMENRN--CVEIAKIAEQSGIQALTVHGRT--------RACKFEGVAEYDS 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  L +  NG +    QA  +L     DG+MIGR A     +  TV       
Sbjct: 208 IKAVKQ-NVSLPVIANGDITSAEQAKFVLDYTGADGIMIGRGALGRPWLFQTVVGLIEQH 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P          + I      Y       G ++    +H+             +  
Sbjct: 267 SIVAEPSLEEKCSVILQHICDLHRFYGEE---KGYRI--ARKHITWYLQDIHPDSVFKQR 321

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A     H +E  F L+
Sbjct: 322 FNALTSAKE-QLHALEQFFKLI 342


>gi|300859124|ref|YP_003784107.1| hypothetical protein cpfrc_01707 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686578|gb|ADK29500.1| hypothetical protein cpfrc_01707 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302331381|gb|ADL21575.1| TIM-barrel containing enzyme [Corynebacterium pseudotuberculosis
           1002]
          Length = 384

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 127/314 (40%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EMI A A++  ++K   +  F  QE   +L
Sbjct: 22  MAGVTNIAFRTLCREQELERTGTVSGLYICEMITARALVHRNEKTLHMTTFGPQEDVRSL 81

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D G  + I++N GCP  +V +   G+ L     + G+ IAA 
Sbjct: 82  QLYTVDPEYTFKAAKMIADEGIADHIDMNFGCPVPKVTKRGGGSALPYKRRLFGNIIAAA 141

Query: 112 CKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            K +   +IPVTVK R+G+D     +   +  +   + G   + +HAR A          
Sbjct: 142 VKGVEGTNIPVTVKFRMGID--HDHLTHLDAGRIAAEEGAAAVTLHARTA--------AE 191

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   +  +D + ++K+   +  + +  NG +   + A+ ++     DGV++GR       
Sbjct: 192 RYSGDAHWDEIGKLKEHLAHTGIPVLGNGDIFKPTDAIDMIKASGCDGVVVGRGCLGRPW 251

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +  +R       +    H       + + +HM    
Sbjct: 252 LFAGLSAAMRGKEIPPEPTLGEVTRIIYRHA-----ELLVEHEGETKGCRDMRKHMGWYL 306

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 307 RGFPVGGDFRGALA 320


>gi|317509475|ref|ZP_07967091.1| dihydrouridine synthase [Segniliparus rugosus ATCC BAA-974]
 gi|316252227|gb|EFV11681.1| dihydrouridine synthase [Segniliparus rugosus ATCC BAA-974]
          Length = 386

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 125/320 (39%), Gaps = 31/320 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L          L   EMI+A +++  + K   ++ F  +E+P ++
Sbjct: 26  MAGVTNLAFRTVCRELETELTGQARGLYVNEMIMARSLVARNPKAMRMVEFGPEERPRSM 85

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D   + EA +++      + ++LN GCP  +V     G+ L     +    I A 
Sbjct: 86  QLYTVDPEAVGEAVRMIVAEDLADHVDLNFGCPVPKVTRNGGGSALPYKRRLFARIIEAA 145

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +PVTVK RIG+DD+       +  +  + SG   + +HAR A           
Sbjct: 146 VRGADGVVPVTVKFRIGIDDEHH--TYLDAGRIARDSGAAAVALHARTA--------AQL 195

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                D+  +  +K+   D+ +  NG +     A +++     DGV++GR       +  
Sbjct: 196 YSGTADWSAIARLKEHVTDIPVLGNGDIFAAEDAARMMAQTGCDGVVVGRGCLGRPWLFA 255

Query: 228 TVDEYFSNPLTGSSPIK--TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
            +    S     + P      V +   R    S  ++A +H      + ++ +H      
Sbjct: 256 ELASALSGGTIPAPPPPNLGEVARIVLRHAQLS-VEHAGKH-----GVAEMRKHFAWYLR 309

Query: 286 GFPNSRRCRHILTVEAGAST 305
           GF      R   +  A  + 
Sbjct: 310 GFSVGSELRTKFSTVASLAE 329


>gi|254787030|ref|YP_003074459.1| tRNA-dihydrouridine synthase B [Teredinibacter turnerae T7901]
 gi|237684325|gb|ACR11589.1| tRNA-dihydrouridine synthase B [Teredinibacter turnerae T7901]
          Length = 330

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 133/321 (41%), Gaps = 25/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK---PLALQIGGA 57
           M   TD  +R   R +    L  +EM+ +D  L   +K     S  E+   P+++QI G+
Sbjct: 18  MAGVTDAPFRRICREM-GAGLATSEMVTSDVNLWQSRKTRARLSALEQELAPVSVQIAGS 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + +AA      G   +++N+GCP+ +V + + G+ L+ +  +V      + +A+ +
Sbjct: 77  EPQMMAQAAVAAVVQGAQIVDINMGCPAKKVCKKAAGSALLRDEALVDAITRTVVEAVDV 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R G D         N+ +  + +G+  + +H R         +  R     +YD
Sbjct: 137 PVTLKIRTGWD--TSQRNAINIARIAENNGIQALAVHGRT--------RACRFNGTAEYD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++   +  + +  NG ++  ++A K+L       VMIGRAA  N  +   ++++   
Sbjct: 187 TIAQVVN-SVAIPVIANGDIDSPAKARKVLQHTGAQAVMIGRAALGNPWLFGQIEQFLEQ 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-- 293
                 P  + V K   R ++     Y          ++   +H      G+ ++     
Sbjct: 246 GEIRELPATSEVCKTIERHLTDLTCFYGEE-----AGVRIARKHTRWYLQGYRDAETFLK 300

Query: 294 -RHILTVEAGASTATHHIIET 313
             + L        A    +E 
Sbjct: 301 HFNTLNTLQSQLMAVRQFLER 321


>gi|312958742|ref|ZP_07773262.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens WH6]
 gi|311287285|gb|EFQ65846.1| tRNA-dihydrouridine synthase B [Pseudomonas fluorescens WH6]
          Length = 337

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 133/298 (44%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L+ +EM+ +D  L   +K+ +        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCKRL-GAGLVVSEMVTSDMSLWNTRKSRMRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+     G   I++N+GCP+ +V   + G+ L+ +  +V + + A+  A+ +P
Sbjct: 79  AQMLADAARANVALGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVAEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNKNG--LTVAKIAEQAGITALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A ++L     DG++IGRAA     +   ++ +    
Sbjct: 189 IAAIKQAV-SMPVFANGDIDSAEKARRVLHATDADGLLIGRAAQGRPWIFREIEHFLRTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            T  +P    V++     ++A  T Y          ++   +H+       P +R  R
Sbjct: 248 ETLPAPELFEVERILLEHLAALHTFY-----GDVMGVRIARKHVGWYLATLPGAREFR 300


>gi|227891607|ref|ZP_04009412.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius ATCC 11741]
 gi|227866754|gb|EEJ74175.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius ATCC 11741]
 gi|300214974|gb|ADJ79390.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 330

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 121/321 (37%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E P+++QI G  
Sbjct: 19  MAGVTNVAFRMICKEF-GAGLVVCEMISDKGIHFRNKKTLDMLFVDPTEHPVSVQIFGGS 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V +    + I++N+GCP  +V +   GA  +L+PD + + + A+  ++  
Sbjct: 78  KETLVEAAQFVAENTATDIIDINMGCPVPKVTKTDAGARWLLDPDKIYEMVHAVTSSIDK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D+ 
Sbjct: 138 PVTVKMRTGWDEDHILAVENALA--AEEGGAKALAMHGRT--------RKQLYTGHADWG 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+      +    NG +    +A K+L     D VMIGRAA  N  ++     Y   
Sbjct: 188 ILKEVADHLTKIPFMGNGDVRTPEEAKKMLDEVGADAVMIGRAALGNPWIVKQTTHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      K     ++        +        ++          G P S R + 
Sbjct: 248 GEILEEPTPAEKIK-----VAKEHLHRLVKAKGEVIGPKEFRSQAAYYLKGIPRSARTKA 302

Query: 296 ILTVEAGASTATHHIIETAFN 316
            L   A        I +    
Sbjct: 303 ALNS-ADTEAEMIDIFDNFLA 322


>gi|256956805|ref|ZP_05560976.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis DS5]
 gi|257078474|ref|ZP_05572835.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis JH1]
 gi|294779307|ref|ZP_06744710.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis PC1.1]
 gi|307268520|ref|ZP_07549895.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4248]
 gi|256947301|gb|EEU63933.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis DS5]
 gi|256986504|gb|EEU73806.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis JH1]
 gi|294453593|gb|EFG21992.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis PC1.1]
 gi|306515181|gb|EFM83721.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4248]
 gi|315032987|gb|EFT44919.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0017]
 gi|315036600|gb|EFT48532.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0027]
          Length = 332

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 137/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  +         I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPSEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|238751413|ref|ZP_04612906.1| tRNA-dihydrouridine synthase B [Yersinia rohdei ATCC 43380]
 gi|238710471|gb|EEQ02696.1| tRNA-dihydrouridine synthase B [Yersinia rohdei ATCC 43380]
          Length = 290

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 118/305 (38%), Gaps = 21/305 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              +  +EM+ ++  +    K+ L     ++P    +QI G D  ++  AA+I    G  
Sbjct: 2   GAGMAVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMAAAARINVANGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSAEHRN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  +  G+  + IH R         +        +YD +  +K+    + +  NG
Sbjct: 120 CIEIAQLAESCGIQALTIHGRT--------RSCLFNGEAEYDSIRAVKQ-IVSIPVIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPMPLGEVQRLLDG 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            I      Y       G   +   +H+         + + R        AS      +E 
Sbjct: 231 HIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEA 284

Query: 314 AFNLM 318
            F  +
Sbjct: 285 YFENL 289


>gi|256848391|ref|ZP_05553834.1| nifR3 family TIM-barrel protein [Lactobacillus coleohominis
           101-4-CHN]
 gi|256714989|gb|EEU29967.1| nifR3 family TIM-barrel protein [Lactobacillus coleohominis
           101-4-CHN]
          Length = 334

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 133/327 (40%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T++ +R   +       +  EMI    I+  +KK   +      E P+ +QI G  
Sbjct: 19  MAGVTNKAFRVICKKF-GAGYVVCEMISDRGIMYHNKKTLSMTTVDPHEHPMGIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVE AK ++     + I++N+GCP  +V     GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEGAKFIDQHTAADVIDINMGCPVNKVVNTDAGARWLLDPNKVYEMVSYVVDAVQK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+   +       + +++G + I +H R         +      + D+D
Sbjct: 138 PVTVKMRTGWDDK--HIFAVENALAAERAGASAIAMHGRT--------RKQMYTGHADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +    F+G NG ++    A ++L     D VMIGRAA  N  MLT  + Y   
Sbjct: 188 ILKEVAGQLTIPFMG-NGDVKTPEDAKRMLDEVGADAVMIGRAAMGNPWMLTRTEHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     +  +     ++A               +++          G P S R + 
Sbjct: 247 GELLPEATPQQKIQTAKGHLAA-----LCDLKGEYVGIREFRGQAAYYLKGIPRSARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L + A        I +   +   E L
Sbjct: 302 AL-MSATKQAEADEIFDRFLDQYEERL 327


>gi|124265679|ref|YP_001019683.1| tRNA-dihydrouridine synthase B [Methylibium petroleiphilum PM1]
 gi|124258454|gb|ABM93448.1| tRNA-dihydrouridine synthase B [Methylibium petroleiphilum PM1]
          Length = 349

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 117/308 (37%), Gaps = 25/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K         +  P+A+QI G +
Sbjct: 20  MAGVTDRPFRQLCKRL-GAGYAVSEMVTSRKELWHSLKTSRRANHDGEVAPIAVQIAGTE 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + EAA    D G   I++N+GCP+ +V     G+ LM +  +    + A+  A    
Sbjct: 79  PLMMAEAAAYNIDRGAQVIDINMGCPAKKVCNVWAGSALMRDESLALRIVEAVVTACAPH 138

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G + Q        L +  +  G+  + +H R         ++     + +
Sbjct: 139 GVPVTLKMRTGWNMQNRNAVA--LARGAESLGIAMLTVHGRT--------REQGYAGSAE 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D V  +K     + +  NG ++   +A  +L     D VM+GRAA     +   +  + 
Sbjct: 189 HDTVRAVKTAV-QVPVVANGDIDSPEKARDVLAATGADAVMVGRAAQGRPWIFREIAHFL 247

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +       P   +        +      Y          ++   +H+    H  P     
Sbjct: 248 ATGERLPPPRTAQAKAWLIEHLHDHYGLY-----GEYAGVRTARKHIGWAVHALPGGALF 302

Query: 294 R-HILTVE 300
           R  + T+E
Sbjct: 303 RARMNTLE 310


>gi|332163158|ref|YP_004299735.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325667388|gb|ADZ44032.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 290

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 118/305 (38%), Gaps = 21/305 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              +  +EM+ ++  +    K+ L     ++P    +QI G D  ++  AA+I    G  
Sbjct: 2   GAGMTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMATAARINVANGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSAEHRN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  +  G+  + IH R         +        +YD +  +K+    + +  NG
Sbjct: 120 CIEIAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDSIRSVKQ-IVSIPVIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPMPLGEVQRLLNG 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            I      Y       G   +   +H+         + + R        AS      +E 
Sbjct: 231 HIRELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEA 284

Query: 314 AFNLM 318
            F  +
Sbjct: 285 YFENL 289


>gi|90962324|ref|YP_536240.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius UCC118]
 gi|90821518|gb|ABE00157.1| tRNA-dihydrouridine synthase [Lactobacillus salivarius UCC118]
          Length = 330

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 121/321 (37%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E P+++QI G  
Sbjct: 19  MAGVTNVAFRMICKEF-GAGLVVCEMISDKGIHFRNKKTLDMLFVDPTEHPVSVQIFGGS 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V +    + I++N+GCP  +V +   GA  +L+PD + + + A+  ++  
Sbjct: 78  KETLVEAAQFVAENTATDIIDINMGCPVPKVTKTDAGARWLLDPDKIYEMVHAVTSSIDK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D+ 
Sbjct: 138 PVTVKMRTGWDEDHILAVENALA--AEEGGAKALAMHGRT--------RKQLYTGHADWG 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+      +    NG +    +A K+L     D VMIGRAA  N  ++     Y   
Sbjct: 188 ILKEVADHLTKIPFMGNGDVRTPEEAKKMLDEVGADAVMIGRAALGNPWIVKQTTHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      K     ++        +        ++          G P S R + 
Sbjct: 248 GEILEEPTPAEKIK-----VAKEHLHRLVKAKGEVIGPKEFRSQAAYYLKGIPRSARTKA 302

Query: 296 ILTVEAGASTATHHIIETAFN 316
            L   A        I +    
Sbjct: 303 ALNS-ADTEAEMIDIFDNFLA 322


>gi|330469566|ref|YP_004407309.1| TIM-barrel protein, nifR3 family [Verrucosispora maris AB-18-032]
 gi|328812537|gb|AEB46709.1| TIM-barrel protein, nifR3 family [Verrucosispora maris AB-18-032]
          Length = 389

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 119/311 (38%), Gaps = 24/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EMI   A++  + K   ++ F   E P +LQ+ G D
Sbjct: 27  MAGITNVGFRQLCREQGG-GIYVCEMITTVALVERNPKTLRMIAFGADESPRSLQLYGTD 85

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
                 A +IV +    + I+LN GCP  +V     GA L     +    +         
Sbjct: 86  PEITAAAVRIVVEKDLADHIDLNFGCPVPKVTRRGGGAALPWRRRLFARLVKAAVDAAAP 145

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+DD         L    + +GV  + +H R A          R     
Sbjct: 146 AGVPVTVKMRKGIDDDHLTYVEAGLA--AQDAGVAAVALHGRTA--------AQRYSGTA 195

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K+   D+ +  NG + +   AL+++    VDGV+IGR       +   ++  
Sbjct: 196 DWDAIATLKQAL-DVPVLGNGDIWEADDALRMVTHTGVDGVVIGRGCLGRPWLFADLEAA 254

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGK--LQQITRHMIGLFHGFP 288
           F+       P    V     R     +  +   AR+   G +       +H+     GFP
Sbjct: 255 FAGRTDRRLPTLGEVALTMRRHAELLVEQFTAGARNPARGERDGCTDFRKHVAWYLKGFP 314

Query: 289 NSRRCRHILTV 299
                R  L +
Sbjct: 315 IGSELRRALAM 325


>gi|329903041|ref|ZP_08273353.1| tRNA-dihydrouridine synthase B [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548519|gb|EGF33185.1| tRNA-dihydrouridine synthase B [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 348

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 122/303 (40%), Gaps = 21/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  ++  L   +K    +    +  P A+QI GAD
Sbjct: 27  MAGVTDRPFRQLCKQL-GAGYAVSEMAASNPRLWQTEKTSRRINHDGEMAPRAVQIAGAD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L + A+   + G   I++N+GCP  +V     G+ L+ +  +VG  + A+  A+ +P
Sbjct: 86  PAMLADCARFNVERGAQVIDINMGCPVKKVCNSWCGSALLQDERLVGQILDAVVAAVDVP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D Q       N+ +  + +G+  + +H R         + +      +Y+ 
Sbjct: 146 VTLKFRTGWDRQHKNA--LNIARLAQSAGIAMLTLHGRT--------RADGYNGAAEYET 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +    +A  +L     D +MIGRAA     +   V  +    
Sbjct: 196 IAAVKAAVT-IPVVANGDITTPEKARHVLAVTGADAIMIGRAAQGRPWIFREVVHFLKTG 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++P+ + V       + A    Y          ++   +H+             R  
Sbjct: 255 THLAAPLVSEVALLMDEHLRAHYAFY-----GEYLGVRTARKHIGWYVRDLAGGEDFRQS 309

Query: 297 LTV 299
           + +
Sbjct: 310 MNL 312


>gi|300780503|ref|ZP_07090359.1| tRNA-dihydrouridine synthase B [Corynebacterium genitalium ATCC
           33030]
 gi|300534613|gb|EFK55672.1| tRNA-dihydrouridine synthase B [Corynebacterium genitalium ATCC
           33030]
          Length = 388

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 67/313 (21%), Positives = 133/313 (42%), Gaps = 30/313 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   TD  +R   R +      T + L   EMI A A++ G++K   +  F+ QE P ++
Sbjct: 27  MAGVTDMPFRVLCREIEEDLTGTVSGLYVCEMITARALVEGNEKTLHMTTFAPQETPRSM 86

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +A +++ +    + +++N GCP  +V     G+ +     +  + ++A 
Sbjct: 87  QLYTVDPEYTYKAVRMIVEGDMADHVDMNFGCPVPKVTRRGGGSAIPYKRGLYRNIVSAA 146

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            KA    +PVTVK R+G+DD+       +  +   + G + + +HAR A          R
Sbjct: 147 VKAADGRVPVTVKFRVGIDDEHK--THLDAGRIAAEEGASAVTLHARTA--------AQR 196

Query: 170 KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
                D+D +  + +  +   + +  NG +   + A +++   + DGV++GR       +
Sbjct: 197 YSGTADWDEISRLVEHMDGTGIPVLGNGDIFASTDAEEMMERTACDGVVVGRGCLGRPWL 256

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +       +  + P   +V +     I A   +  A H       +++ +H+     
Sbjct: 257 FAQLSAQLRGEVVPAEPTLGQVAR-----IMARHGELLAAHNGEERGCRELRKHVGWYLR 311

Query: 286 GFPNSRRCRHILT 298
           GFP   + R  L 
Sbjct: 312 GFPVGGQFRSELA 324


>gi|315171400|gb|EFU15417.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1342]
          Length = 337

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 137/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  +         I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPSEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|225351461|ref|ZP_03742484.1| hypothetical protein BIFPSEUDO_03056 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157805|gb|EEG71088.1| hypothetical protein BIFPSEUDO_03056 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 409

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 119/318 (37%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCHFAPSEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 169 ANVPVTAKIRVGIDHE--HETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 218

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+ +   D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 219 DWSRIGELVEAL-DIPVFGNGDIWGANDALAMVAETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +   R        Y      +   +  + +H+     GFP    
Sbjct: 278 FAGSDKRVDPTLGDVCRVVERHAELLTEFYDGDEQMA---VHDLRKHIAWYLKGFPVGGS 334

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 335 TRRAFMECENLEDVRAEI 352


>gi|257084202|ref|ZP_05578563.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Fly1]
 gi|256992232|gb|EEU79534.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Fly1]
          Length = 332

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLSIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|229824537|ref|ZP_04450606.1| hypothetical protein GCWU000282_01881 [Catonella morbi ATCC 51271]
 gi|229785908|gb|EEP22022.1| hypothetical protein GCWU000282_01881 [Catonella morbi ATCC 51271]
          Length = 357

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 134/325 (41%), Gaps = 22/325 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L     E PL++QI G +
Sbjct: 32  MAGVSNAAFRTIVKQF-GAGLVVCEMISDKGIQFRNDKTLSMLHIEPNEYPLSIQIMGGN 90

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +      I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+  
Sbjct: 91  KETLVEAAKYVAENTECAIIDINMGCPVNKVIKAEAGARWLLDPNKVYEMVAAVVDAVQK 150

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L    +++G + + +H R  +               ++D
Sbjct: 151 PVTVKMRTGWDDEHLYAIENALA--AERAGASMVAMHGRTRV--------QMYEGKANWD 200

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++KKE   +    NG +    +   +L    VDGVM+GRAA  N  ++  +  Y   
Sbjct: 201 ILAQVKKELKTIPFVGNGDVRTPEELKYLLDTTGVDGVMVGRAALGNPWVIQQMVHYVET 260

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                + +  R   D        + D       +    ++          G P S + + 
Sbjct: 261 GELLPA-MTARQKIDTAIDHLERLVDLKGDRTAT----REFRTQAHYYLKGIPRSSKVKV 315

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +  E    T    ++    + + E
Sbjct: 316 AVN-ETEDPTVVKQLLRDFVDQVEE 339


>gi|116625730|ref|YP_827886.1| nifR3 family TIM-barrel protein [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116228892|gb|ABJ87601.1| putative TIM-barrel protein, nifR3 family [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 337

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 139/325 (42%), Gaps = 29/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--------RGDKKNILGFSTQEKPLAL 52
           M   TD  +R F R L    L+ TE   +  +             K  L F   E P++ 
Sbjct: 24  MAGVTDTVFRRFIRNLDGCGLIMTEFTSSHGVSAALKAKKPNKTMKRYLNFEPDEHPISA 83

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ GAD + + +AA++ +D G++ ++LN GCP  +V + + G+ L+ +  +V   + ++ 
Sbjct: 84  QLFGADPAVMADAARVCQDLGFDILDLNFGCPVNKVVKCNGGSGLLRDLPLVEKLLRSVR 143

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            A++IP T+K R G +D+   +    + K  +  G+  I +H R         ++     
Sbjct: 144 AAITIPFTMKFRAGWNDRE--LVAVAMAKLAEDCGLQAIALHPRT--------REQGYAG 193

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             D+  + E+K     + +  NG +     A++++   + D VMIGR A  N  +   + 
Sbjct: 194 KADWTRIAEVK-AAVKIPVIGNGDIVTPEDAVRMVRETNCDAVMIGRGASSNPWIFRQIQ 252

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +Y +           R      R+    +   A R   + GK++Q         HG  + 
Sbjct: 253 QYLATGRYDEPTHGDRY--QMMRQYYDMLI--ARREDDAVGKMKQFA---TYFTHGVRHG 305

Query: 291 RRCRHILTVEAGASTATHHIIETAF 315
              R  +  +A  + A   +++  F
Sbjct: 306 AHLRASI-YQAHETAAILELVDQFF 329


>gi|240120537|ref|ZP_04733499.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae PID24-1]
          Length = 364

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 126/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 47  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 106 PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 166 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++   +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 216 IAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 275 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 329

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 330 INRLDNAA-AQYDTLAGYLERL 350


>gi|254512463|ref|ZP_05124530.1| NifR3 family protein [Rhodobacteraceae bacterium KLH11]
 gi|221536174|gb|EEE39162.1| NifR3 family protein [Rhodobacteraceae bacterium KLH11]
          Length = 364

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 129/322 (40%), Gaps = 26/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R          ++ +EM+ +  +++     +     S   +  A+Q+ G +
Sbjct: 56  MAGITDRPFRDLVMRF-GAGMVVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRE 114

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+ IP
Sbjct: 115 AHWMAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALTLIEAVVAAVDIP 174

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD +  +   ++ +  + +G+  + IH R         +        D+  
Sbjct: 175 VTLKTRLGWDDSL--LNAPDVARRAQDAGIQMVTIHGRT--------RCQFYKGRADWQA 224

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +     A   L     DGVM+GR A     +L  +       
Sbjct: 225 IGAVK-EAVSVPVIANGDITGPGAARTALDQSGADGVMVGRGAQGRPWLLAQICHDLYGI 283

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
                P  + +         A +  Y      +   L+   +H+       G P     R
Sbjct: 284 APPDIPTGSALIDMVRGHYQAMLAFY-----GTDLGLRVARKHLGWYMDDAGTP--ATLR 336

Query: 295 HILTVEAGASTATHHIIETAFN 316
             + + +  +    H++  A N
Sbjct: 337 RAV-LTSRDTGEVLHLLGDALN 357


>gi|308234685|ref|ZP_07665422.1| TIM-barrel protein, nifR3 family [Gardnerella vaginalis ATCC 14018]
 gi|311114396|ref|YP_003985617.1| dihydrouridine synthase [Gardnerella vaginalis ATCC 14019]
 gi|310945890|gb|ADP38594.1| dihydrouridine synthase [Gardnerella vaginalis ATCC 14019]
          Length = 384

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 116/302 (38%), Gaps = 22/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    + L   EMI A A++  + K   +  F+  EK  +LQ+ G D
Sbjct: 24  MAGITNWPFRVICREYGPDGLYVAEMITARALVARNPKALRLCRFAPNEKVRSLQLYGVD 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
            S +  AA+IV D    + ++LN GCP  +V     G+ L    D++ + +  +      
Sbjct: 84  PSIVELAARIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCDP 143

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D+              ++ G   + +HAR                + 
Sbjct: 144 AGIPVTAKFRVGIDE--NHETFMQAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +     AL +       GV IGR       +   +   
Sbjct: 194 DWSRIAELVNAL-DIPVFGNGDIWGADDALAMFKETGCAGVAIGRGCQGRPWIFADIRSA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +      +P   +V K   R +   +  Y      +   +  + +H+     GFP    
Sbjct: 253 CNGSDDRVNPSLGQVCKVILRHLELLVEFYDGDERMA---VHDLRKHIAWYLKGFPVGGG 309

Query: 293 CR 294
            R
Sbjct: 310 TR 311


>gi|152996996|ref|YP_001341831.1| nifR3 family TIM-barrel protein [Marinomonas sp. MWYL1]
 gi|150837920|gb|ABR71896.1| putative TIM-barrel protein, nifR3 family [Marinomonas sp. MWYL1]
          Length = 322

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 126/298 (42%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R          L+ +EM+ +D  L    K+   L    +  P ++QI G D
Sbjct: 19  MAGVTDLPFRRLCHD-QGAGLVVSEMVTSDVRLWNSTKSRHRLIHDAEVSPRSVQIAGGD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V + + ++  ++S+P
Sbjct: 78  PQMMAEAAQQNVELGAQIIDINMGCPAKKVCNKAAGSALLKDEALVREILESVVNSVSVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            + K  +  G+  + IH R         ++ +    ++YD 
Sbjct: 138 VTLKIRTGWSLDQKNG--LAIAKMAEDIGIQALAIHGRT--------RECKFQGQVEYDT 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK  +  + I  NG ++D   A   K     DG+MIGRAA     +   ++ Y    
Sbjct: 188 IAEIK-HHLSIPIFANGDIKDAQSAKFVKDYTQADGIMIGRAAQGRPWIFREINHYLETN 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              + P  + V +     ++A    Y          ++   +H+        +  + R
Sbjct: 247 ELLAPPSLSEVRQLVINHVNALHQFY-----GDYLGVRIARKHVGWYLQTLADKTQFR 299


>gi|256762062|ref|ZP_05502642.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis T3]
 gi|256964190|ref|ZP_05568361.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis HIP11704]
 gi|307274231|ref|ZP_07555439.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0855]
 gi|256683313|gb|EEU23008.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis T3]
 gi|256954686|gb|EEU71318.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis HIP11704]
 gi|306509193|gb|EFM78255.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0855]
          Length = 332

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 137/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGAANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  +         I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPSEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|257088029|ref|ZP_05582390.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis D6]
 gi|256996059|gb|EEU83361.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis D6]
 gi|315026775|gb|EFT38707.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2137]
          Length = 332

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKVSK 324


>gi|148655022|ref|YP_001275227.1| nifR3 family TIM-barrel protein [Roseiflexus sp. RS-1]
 gi|148567132|gb|ABQ89277.1| putative TIM-barrel protein, nifR3 family [Roseiflexus sp. RS-1]
          Length = 349

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 144/327 (44%), Gaps = 24/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV  TD  +R     L    L+ +EM  A A+    +     L +  +E+P+A+Q+ G D
Sbjct: 39  MVGVTDSIFRRMILSLGGCGLVCSEMTSASAVSPRARSRHRQLDYLPEERPIAMQLSGND 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++VE+ G + +++N GCPS +V  G  G+ L+ +   +   + A+C A+ IP
Sbjct: 99  PDLVAAAARVVEELGADILDINCGCPSPKVTGGGHGSALLRDLPTMERLLKAVCAAVQIP 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+   ++   +  K  +++GV  + +H R         +        D+  
Sbjct: 159 VTLKFRAGWDE--ASLNYLDTAKMAEQAGVAALALHPRT--------RAQGYSGVADWTR 208

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+K+    + +  +G + D + AL+ L     DGVMIGR A  N  +   + +  +  
Sbjct: 209 VAEVKRAV-SIPVIGSGDVRDAADALRRLHESGADGVMIGRGAMHNPWIFRQIAQLRTGM 267

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCRH 295
              +     +   DF  +      D     L          + +IG F    P +   R 
Sbjct: 268 QPMTVTPADKY--DFLTRYLEMCCDEMPERLALNK-----LKQLIGQFGIELPGAAALRS 320

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +   +  + A  H +E  F   IE++
Sbjct: 321 AVHHSSSVAEARDH-LERFFAWHIEAM 346


>gi|315172633|gb|EFU16650.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1346]
          Length = 332

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLSIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|21227445|ref|NP_633367.1| NifR3-like protein [Methanosarcina mazei Go1]
 gi|20905814|gb|AAM31039.1| NifR3-like protein [Methanosarcina mazei Go1]
          Length = 323

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 129/303 (42%), Gaps = 26/303 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M D T+  +R   R      L YTEMI  DA+L   +K+ +    S +++P  +Q+ G  
Sbjct: 22  MADVTNLAFRLLCRRY-GADLTYTEMINVDALLNESRKSFIKGLSSEEDRPFGVQLVGGC 80

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             KL  AA  +E+ +    I++N+GCP+  +     G+ L+ +P++V   I  + ++L  
Sbjct: 81  PDKLKRAALFIEEEYRPEIIDVNMGCPARCITGAGCGSALLNSPELVYSIILELTESLDT 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+   ++        + + I+K+G + + +H R A              N + +
Sbjct: 141 PVSAKIRLLGREEKT----LEIARLIEKAGASAVTVHGRTA--------AQMYSGNSNLE 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E   + +  NG ++D   A +   L   DG+MIGRAA  N  +   +  Y   
Sbjct: 189 GIRAVKNEL-SIPVIANGDVKDEESAERTLELTGCDGLMIGRAAMGNPFIFKKIRHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +    R  +DF   IS          ++       +  H      G   SR  R 
Sbjct: 248 GEKLGADKPFRQLEDFNSYISLLEEHNLLSSIN-------LRMHAHWFTKGLRGSRHVRE 300

Query: 296 ILT 298
            + 
Sbjct: 301 KIN 303


>gi|327534064|gb|AEA92898.1| tRNA-dihydrouridine synthase [Enterococcus faecalis OG1RF]
          Length = 332

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTKAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLSIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|284990203|ref|YP_003408757.1| TIM-barrel protein, nifR3 family [Geodermatophilus obscurus DSM
           43160]
 gi|284063448|gb|ADB74386.1| TIM-barrel protein, nifR3 family [Geodermatophilus obscurus DSM
           43160]
          Length = 400

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 115/310 (37%), Gaps = 28/310 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M   T+  +R   R      L   EMI   A++   +K +        +E   ++Q+ G 
Sbjct: 45  MAGITNPAFRTLCREF-GAGLYVCEMITTRALVERTEKTLSMVRATPDEEDAFSVQLYGV 103

Query: 58  DISKLVEAAKIVEDFG-----YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AM 111
           D + +  A +++ D G        ++LN GCP  +V     G+ L     +  D +  A+
Sbjct: 104 DPATVGRAVEMLVDEGVAGTRPAHVDLNFGCPVPKVTRKGGGSALPWRRVLFRDIVRAAV 163

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A  +PVTVK RIG+D     V   +  +  +  G   I +H R A        D    
Sbjct: 164 RAARDVPVTVKTRIGID--ADHVTYLDAGRIAQDEGAAAITLHGRTA--------DQLYS 213

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+  +  +  E  D+ +  NG + +   AL+++      GV+IGR       +   +
Sbjct: 214 GTADWAPIARLV-EAVDIPVLGNGDIWEADDALRMVAETGCAGVVIGRGCLGRPWLFGDL 272

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
              F+     + P    V     R  +    +   RH           +H+     GF  
Sbjct: 273 AAAFAGGTRRALPTLREVAAVMHRHATLLSEEQGERH-----GCTDFRKHVAWYLKGFSV 327

Query: 290 SRRCRHILTV 299
               R  L +
Sbjct: 328 GSDVRRALAM 337


>gi|293391553|ref|ZP_06635887.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952087|gb|EFE02206.1| tRNA-dihydrouridine synthase B [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 349

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 130/324 (40%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R          L ++EM+  +  +   +K+ L      +    A+QI G+D
Sbjct: 39  MAGVTDLPFRRICANY-GAGLTFSEMMSTNPQVWYTEKSKLRLAHHQEAGINAVQIAGSD 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA++  ++G   I++N+GCP+ +V+    G+ L+  PD+V   + A+ KA+ +P
Sbjct: 98  PDGMAQAAQVNVEYGAQIIDINMGCPAKKVNRKMAGSALLQYPDLVRRILEAVVKAVKVP 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + K  ++SG+  + +H R         +  +     +YD 
Sbjct: 158 VTLKIRTGWDMENRN--CVEIAKIAEQSGIQALTVHGRT--------RACKFEGVAEYDS 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  L +  NG +    QA  +L     DG+MIGR A     +  TV       
Sbjct: 208 IKAVKQ-NVSLPVIANGDITSAEQAKFVLDYTGADGIMIGRGALGRPWLFQTVVGLIEQH 266

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P          + I      Y     H     +   +H+             +  
Sbjct: 267 SIVAEPSLEEKCSVILQHIRDLHRFYGEEKGH-----RIARKHITWYLQDIHPDSVFKQR 321

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
                 A     H +E  F L+ +
Sbjct: 322 FNALTSAKE-QLHALEQFFKLIFK 344


>gi|126176129|ref|YP_001052278.1| nifR3 family TIM-barrel protein [Shewanella baltica OS155]
 gi|153002467|ref|YP_001368148.1| nifR3 family TIM-barrel protein [Shewanella baltica OS185]
 gi|160877184|ref|YP_001556500.1| NifR3 family TIM-barrel protein [Shewanella baltica OS195]
 gi|217975034|ref|YP_002359785.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS223]
 gi|304412483|ref|ZP_07394089.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS183]
 gi|307307142|ref|ZP_07586880.1| TIM-barrel protein, nifR3 family [Shewanella baltica BA175]
 gi|125999334|gb|ABN63409.1| putative TIM-barrel protein, nifR3 family [Shewanella baltica
           OS155]
 gi|151367085|gb|ABS10085.1| putative TIM-barrel protein, nifR3 family [Shewanella baltica
           OS185]
 gi|160862706|gb|ABX51240.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS195]
 gi|217500169|gb|ACK48362.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS223]
 gi|304349125|gb|EFM13537.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS183]
 gi|306910381|gb|EFN40812.1| TIM-barrel protein, nifR3 family [Shewanella baltica BA175]
 gi|315269388|gb|ADT96241.1| TIM-barrel protein, nifR3 family [Shewanella baltica OS678]
          Length = 322

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 137/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAALAVSEMLSSNPEVWDTDKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA    + G + I++N+GCP+ +V++   G+ LM NP +V + + A+  A+++P
Sbjct: 76  PDLMAQAALFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKEILQAVVAAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWEPEHKNGV--QIAQIAQDCGIASLAVHGRT--------RQCMYRGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG ++   +A  +L     D +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NVSIPVVANGDIDSPEKARFVLEYTGADALMIGRGAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +        +     ++     Y          ++   +HM          R+ R  
Sbjct: 245 NKLAPIEVAEQRQVMLEHLTKLYDLY-----GEYKGIRFARKHMGWYLDQEAQ-RQFRAD 298

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 A+   + ++E  F+ ++++
Sbjct: 299 FNRLETAAE-QYSLVECYFDELVQN 322


>gi|116871611|ref|YP_848392.1| dihydrouridine synthase family protein [Listeria welshimeri serovar
           6b str. SLCC5334]
 gi|116740489|emb|CAK19609.1| dihydrouridine synthase family protein [Listeria welshimeri serovar
           6b str. SLCC5334]
          Length = 331

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 139/326 (42%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D ++A+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVSAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++   V       + +++G + + +H R  +             + ++D
Sbjct: 137 PVTVKMRIGWDEE--HVFAIENALAAERAGASAVAMHGRTRV--------QMYEGSANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG ++    A +IL     DGVMIGRAA  N  M+    ++   
Sbjct: 187 VLRDVKREL-KIPFMANGDVKTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLPEPEPREKMQTAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A   +    I+        E 
Sbjct: 300 VAANQATKQSEMEAILNEFVLQYEEK 325


>gi|83648649|ref|YP_437084.1| tRNA-dihydrouridine synthase [Hahella chejuensis KCTC 2396]
 gi|83636692|gb|ABC32659.1| tRNA-dihydrouridine synthase [Hahella chejuensis KCTC 2396]
          Length = 336

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 71/289 (24%), Positives = 128/289 (44%), Gaps = 21/289 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L  +EM+ A+  LR  +K+ L      + +P+A+QI GA+
Sbjct: 24  MAGVTDRPFRLLCRSL-GAGLAVSEMMAANPDLRDTRKSRLRMDHDGEGEPIAVQIAGAE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+S+P
Sbjct: 83  PEMLAEAARYNVEHGAQIIDINMGCPAKKVCNKAAGSALLRDEALVKDILTAVVSAVSVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   Q        + +  +  G+  + +H R         ++ +     +YD 
Sbjct: 143 VTLKIRTGWSRQSRNGVT--VARIAEDCGIQSLAVHGRT--------RECKYEGTAEYDT 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK+ +  + +  NG +  + QA  +L    VD +MIGR A     +   ++ + +  
Sbjct: 193 IAEIKQ-SVSIPVVANGDITCVEQARHVLDYTGVDALMIGRGAQGRPWIFREIEHFIATG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
                P      +     I A    Y          ++   +H+     
Sbjct: 252 ERLPEPPMDETKQILIGHIKALHEFY-----GDYQGVRIARKHVGWYLQ 295


>gi|156972542|ref|YP_001443449.1| tRNA-dihydrouridine synthase B [Vibrio harveyi ATCC BAA-1116]
 gi|156524136|gb|ABU69222.1| hypothetical protein VIBHAR_00174 [Vibrio harveyi ATCC BAA-1116]
          Length = 331

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 128/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + K  +  G+  + +H R         K        +YD 
Sbjct: 145 VTLKTRTGWNTENKNCVH--IAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 195 IKAVKQAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+        ++   R  
Sbjct: 254 TTMDELPSEEVKAIMLGHVNALHGFYGEF-----LGPRIARKHVGWYLKEHEHASEFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      +E  F+ +
Sbjct: 309 FNA-IDAAELQLEALEGYFDNV 329


>gi|330993258|ref|ZP_08317194.1| putative tRNA-dihydrouridine synthase [Gluconacetobacter sp.
           SXCC-1]
 gi|329759660|gb|EGG76168.1| putative tRNA-dihydrouridine synthase [Gluconacetobacter sp.
           SXCC-1]
          Length = 353

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 130/302 (43%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M   TD  +R  AR L    L+ +EMI + A++R ++  + +     + P ++Q+ G D 
Sbjct: 26  MAGVTDLPFRRLARRL-GAGLVVSEMIASWAMVRENQTTLRMAEVADDGPNSVQLAGCDP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +AA+I  D G + I++N GCP  +V      G+ LM +       +  + +A+ +P
Sbjct: 85  DAMGQAARIAVDRGADIIDINFGCPVKKVAVGQLAGSALMRDEVQAARLLEGVVRAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D +   +    L +  ++SG+  + +H R         +        D+  
Sbjct: 145 VTLKMRMGWDHE--HLNAPRLARIAQESGIRMVTVHGRT--------RQQFYNGTADWYF 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++  +  DL + +NG +  +  A   L      GVMIGR  Y     L  V     + 
Sbjct: 195 VRKVV-DAVDLPVIVNGDILTVEDARVALERSGARGVMIGRGCYGRPWFLAQVARALMDG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +  + P     +K    +    M D+   H      L+   +H+     G P+S   R  
Sbjct: 254 VAVAEPGLA-AEKAIVLEHYGMMIDHFGAH----PGLRLARKHVSWYSAGLPDSAGFRAA 308

Query: 297 LT 298
           + 
Sbjct: 309 VN 310


>gi|229550492|ref|ZP_04439217.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
 gi|229304349|gb|EEN70345.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
          Length = 332

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 137/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+           I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPLPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|329121393|ref|ZP_08250018.1| tRNA-dihydrouridine synthase [Dialister micraerophilus DSM 19965]
 gi|327469683|gb|EGF15150.1| tRNA-dihydrouridine synthase [Dialister micraerophilus DSM 19965]
          Length = 327

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 133/301 (44%), Gaps = 21/301 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR     A+   EM+ +  +   ++K   +L  +  E P+ALQ+ G  
Sbjct: 20  MAGVSDLAYRVIARK-HGAAMTTAEMVSSRGLYYKNEKTEEMLKIAPDEHPVALQLFGNQ 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK VE+ G + I++N+GCP  +V +   G  +M + D     + AM KA+ +P
Sbjct: 79  AEIMALAAKEVEEAGADVIDINMGCPMQKVVKNGDGCSMMKDIDNSAKVVEAMVKAVKVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D +   +    L K+++ +G   I +H R         ++       D D 
Sbjct: 139 VTVKMRIGWDRE--NLNSPELAKAVEAAGAAAITVHGRT--------REEMYSGKADLDA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  E   + +  NG + D   A +++      GV IGRAA+ N  +   V+ Y  + 
Sbjct: 189 IRKVV-ETVKIPVFGNGDIVDGPSAKRMMEETGCVGVAIGRAAWGNPWIFNAVNTYLESG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T   P       +    ++ +      +       ++++  H    F+G P +   R  
Sbjct: 248 ETVEEPS-----WEMRLSMARTHLGNLVKEKGEYTAIREMRAHASHYFYGLPKATALRRE 302

Query: 297 L 297
           +
Sbjct: 303 I 303


>gi|154498409|ref|ZP_02036787.1| hypothetical protein BACCAP_02398 [Bacteroides capillosus ATCC
           29799]
 gi|150272477|gb|EDM99662.1| hypothetical protein BACCAP_02398 [Bacteroides capillosus ATCC
           29799]
          Length = 307

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 119/304 (39%), Gaps = 23/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R   R L       TEM+ A A+   DKK+  +L     E P A QI G+D
Sbjct: 1   MAGVTDMAFRTICREL-GAGYTITEMVSAKALCYQDKKSIPLLKLGEGEHPCAAQIFGSD 59

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
              + EAA I  +  G + I++N+GCP  +V     G+ LM + D       A+ + A  
Sbjct: 60  EKCMEEAAAIAGEVSGADIIDINMGCPVPKVANSGDGSGLMRDVDKAVRVAEAVVRGAGE 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVTVK R+G D    ++      K+++ +GV+ + +H R         +        ++
Sbjct: 120 RPVTVKFRLGWDKG--SINCVEFAKAMEAAGVSAVAVHGRT--------RTQMYAGTANW 169

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + E+K+    + +  NG + D   A  IL     D  MIGR  + N  +         
Sbjct: 170 DYIREVKQAV-SIPVIANGDVFDGPAAAHILRYTGADMAMIGRGCFGNPWVFQQARAALE 228

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P          R+      + AA H        +  +       G   +   +
Sbjct: 229 GEEIPPLPPLAERVDTAVRQ-----FELAAAHKGEHIACLEARKQYAWYLKGVAFAGYYK 283

Query: 295 HILT 298
             ++
Sbjct: 284 EQIS 287


>gi|289752872|ref|ZP_06512250.1| LOW QUALITY PROTEIN: transcriptional regulatory protein
           [Mycobacterium tuberculosis EAS054]
 gi|289693459|gb|EFD60888.1| LOW QUALITY PROTEIN: transcriptional regulatory protein
           [Mycobacterium tuberculosis EAS054]
          Length = 362

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 77/308 (25%), Positives = 123/308 (39%), Gaps = 29/308 (9%)

Query: 6   DRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGA 57
           D  +R   R L      T + L   EM+ A A++       ++  FS  E P +LQ+   
Sbjct: 7   DIAFRALCRQLEQSKVGTVSGLYVCEMVTARALIERHPVTMHMTTFSADESPRSLQLYTV 66

Query: 58  DISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-- 114
           D      AA+++   G  + I++N GCP  +V +   GA L     + G  +AA  +A  
Sbjct: 67  DPDTTYAAARMIAGEGLADHIDMNFGCPVPKVTKRGGGAALPFKRRLFGQIVAAAVRATE 126

Query: 115 -LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              IPVTVK RIG+DD        +  +  +  G   + +HAR A          R    
Sbjct: 127 GTDIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAAAVALHARTA--------AQRYSGT 176

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            D++ +  +K+    + +  NG + D   AL ++     DGV+IGR       +   +  
Sbjct: 177 ADWEQIARLKQHVRTIPVLGNGDIYDAGDALAMMSTTGCDGVVIGRGCLGRPWLFAELSA 236

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
            F+     + P    V       I        A H      ++ I +H+    HGFP   
Sbjct: 237 AFTGSPAPTPPTLGEVA-----DIIRRHGTLLAAHFGEDKGMRDIRKHIAWYLHGFPAGS 291

Query: 292 RCRHILTV 299
             R  L +
Sbjct: 292 ALRRALAM 299


>gi|29374908|ref|NP_814061.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecalis
           V583]
 gi|227520052|ref|ZP_03950101.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
 gi|227555913|ref|ZP_03985960.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|229546903|ref|ZP_04435628.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|255971767|ref|ZP_05422353.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255974767|ref|ZP_05425353.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256618323|ref|ZP_05475169.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis ATCC 4200]
 gi|256960610|ref|ZP_05564781.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Merz96]
 gi|257081554|ref|ZP_05575915.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis E1Sol]
 gi|257417632|ref|ZP_05594626.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis AR01/DG]
 gi|257418643|ref|ZP_05595637.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257421556|ref|ZP_05598546.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|293382697|ref|ZP_06628622.1| tRNA-dihydrouridine synthase [Enterococcus faecalis R712]
 gi|293388121|ref|ZP_06632648.1| tRNA-dihydrouridine synthase [Enterococcus faecalis S613]
 gi|300862204|ref|ZP_07108284.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TUSoD Ef11]
 gi|307276456|ref|ZP_07557579.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2134]
 gi|307278666|ref|ZP_07559736.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0860]
 gi|307286954|ref|ZP_07567029.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0109]
 gi|307290187|ref|ZP_07570105.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0411]
 gi|312901061|ref|ZP_07760350.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0470]
 gi|312904624|ref|ZP_07763779.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0635]
 gi|312908593|ref|ZP_07767535.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 512]
 gi|312909259|ref|ZP_07768116.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 516]
 gi|312952667|ref|ZP_07771531.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0102]
 gi|29342366|gb|AAO80132.1| zinc-binding TIM-barrel protein, nifR3 family, putative
           [Enterococcus faecalis V583]
 gi|227072600|gb|EEI10563.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
 gi|227174970|gb|EEI55942.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|229307831|gb|EEN73818.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|255962785|gb|EET95261.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255967639|gb|EET98261.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256597850|gb|EEU17026.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis ATCC 4200]
 gi|256951106|gb|EEU67738.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis Merz96]
 gi|256989584|gb|EEU76886.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis E1Sol]
 gi|257159460|gb|EEU89420.1| dihydrouridine synthase TIM-barrel protein nifR3 [Enterococcus
           faecalis ARO1/DG]
 gi|257160471|gb|EEU90431.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257163380|gb|EEU93340.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|291079857|gb|EFE17221.1| tRNA-dihydrouridine synthase [Enterococcus faecalis R712]
 gi|291082497|gb|EFE19460.1| tRNA-dihydrouridine synthase [Enterococcus faecalis S613]
 gi|300848729|gb|EFK76486.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TUSoD Ef11]
 gi|306498743|gb|EFM68242.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0411]
 gi|306501900|gb|EFM71189.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0109]
 gi|306504726|gb|EFM73926.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0860]
 gi|306506936|gb|EFM76083.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2134]
 gi|310625380|gb|EFQ08663.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 512]
 gi|310629455|gb|EFQ12738.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0102]
 gi|310631976|gb|EFQ15259.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0635]
 gi|311290501|gb|EFQ69057.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis DAPTO 516]
 gi|311291807|gb|EFQ70363.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0470]
 gi|315145397|gb|EFT89413.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX2141]
 gi|315147111|gb|EFT91127.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4244]
 gi|315151136|gb|EFT95152.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0012]
 gi|315153549|gb|EFT97565.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0031]
 gi|315156271|gb|EFU00288.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0043]
 gi|315158584|gb|EFU02601.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0312]
 gi|315160787|gb|EFU04804.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0645]
 gi|315165841|gb|EFU09858.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1302]
 gi|315168160|gb|EFU12177.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1341]
 gi|315573575|gb|EFU85766.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0309B]
 gi|315579386|gb|EFU91577.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0630]
 gi|315582077|gb|EFU94268.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX0309A]
 gi|323479480|gb|ADX78919.1| TIM-barrel protein, nifR3 family protein [Enterococcus faecalis 62]
          Length = 332

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|145297864|ref|YP_001140705.1| tRNA-dihydrouridine synthase B [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142850636|gb|ABO88957.1| tRNA-dihydrouridine synthase B [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 321

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 128/320 (40%), Gaps = 22/320 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R     L    +  +EM++A+  +   +K  +    S +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRL-GAGMAVSEMLLANPDVWDTQKTRMRMDHSAEGGLRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G   +++N+GCP+ +V++   G+ L+ +PD+V     A+  A+ +P
Sbjct: 76  PEMMAFAARYNVEQGAQIVDINMGCPAKKVNKKLAGSALLRHPDLVRTICRAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWDPDNRNGE--EIARIAEDCGIAALAVHGRT--------RACLYRGHAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+    + +  NG ++   +A  +L    VD VMIGRAA     +   +  +    
Sbjct: 186 IKAIKQAV-SIPVVANGDIDSPEKARYVLDYTGVDAVMIGRAAQGRPWIFREIRHFLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P +  V       ++     Y A         +   +H+          R  R  
Sbjct: 245 TKLPPPEREEVRTLMNEHVTNLHQFYGA-----YLGARIARKHVGWYLDEEETGREFRKH 299

Query: 297 LTVEAGASTATHHIIETAFN 316
                  + A    +E  F+
Sbjct: 300 FNAL-DCADAQLEALEAYFD 318


>gi|301300310|ref|ZP_07206517.1| TIM-barrel protein, nifR3 family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852083|gb|EFK79760.1| TIM-barrel protein, nifR3 family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 330

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 120/321 (37%), Gaps = 22/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E P+++QI G  
Sbjct: 19  MAGVTNVAFRMICKEF-GAGLVVCEMISDKGIHFRNKKTLDMLFVDPTEHPVSVQIFGGS 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V      + I++N+GCP  +V +   GA  +L+PD + + + A+  ++  
Sbjct: 78  KETLVEAAQFVAKNTATDIIDINMGCPVPKVTKTDAGARWLLDPDKIYEMVHAVTSSIDK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D+ 
Sbjct: 138 PVTVKMRTGWDEDHILAVENALA--AEEGGAKALAMHGRT--------RKQLYTGHADWG 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+      +    NG +    +A K+L     D VMIGRAA  N  ++     Y   
Sbjct: 188 ILKEVADHLTKIPFMGNGDVRTPEEAKKMLDEVGADAVMIGRAALGNPWIVKQTTHYLET 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      K     ++        +        ++          G P S R + 
Sbjct: 248 GEILEEPTPAEKIK-----VAKEHLHRLVKAKGEVIGPKEFRSQAAYYLKGIPRSARTKA 302

Query: 296 ILTVEAGASTATHHIIETAFN 316
            L   A        I +    
Sbjct: 303 ALNS-ADTEAEMIDIFDNFLA 322


>gi|312898246|ref|ZP_07757637.1| TIM-barrel protein, nifR3 family [Megasphaera micronuciformis
           F0359]
 gi|310620743|gb|EFQ04312.1| TIM-barrel protein, nifR3 family [Megasphaera micronuciformis
           F0359]
          Length = 327

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 77/318 (24%), Positives = 132/318 (41%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M    D  YR  AR     AL+  EM+ A  ++ G+K  + +L     E PL++Q+ GA+
Sbjct: 24  MAGVCDLPYRMIARK-HGAALVCAEMVSAKGLVYGNKHTREMLTVHKNEHPLSMQLFGAE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK+ +++G + I++N+GCP  +V +   G+ LM N  +    ++A+ KA+S+P
Sbjct: 83  PEIMARAAKVAQEYGADIIDINMGCPVRKVVQNGEGSALMKNLPLAEKVVSAVVKAVSVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G DD         L +  + +G   + +H R         ++       D + 
Sbjct: 143 VTVKMRTGWDDIE--FVAPELARRCEAAGAAALAVHGRT--------REQFYSGRADLEK 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + K    + +  NG + D     ++        VMIGR A  N  +   V +Y S  
Sbjct: 193 IAAVVKAV-SIPVIGNGDITDGPSCARMFEETGCTAVMIGRGAQGNPWIFEEVRDYLSGR 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                    R       +   S+  +   H+     L+++  H      G   S   R  
Sbjct: 252 TVQKPSAADRYA--VLLEHFESLIRFKGAHIA----LREMRSHASWYTKGLFGSAALRER 305

Query: 297 LTVEAGASTATHHIIETA 314
           +   +        I E A
Sbjct: 306 INRTSTVEEFRQVISEVA 323


>gi|260433535|ref|ZP_05787506.1| NifR3 family protein [Silicibacter lacuscaerulensis ITI-1157]
 gi|260417363|gb|EEX10622.1| NifR3 family protein [Silicibacter lacuscaerulensis ITI-1157]
          Length = 352

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 125/318 (39%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R          ++ +EM+ +  +++     +     S   +  A+Q+ G D
Sbjct: 44  MAGITDRPFRDLVMRF-GAGMVVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRD 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+ +P
Sbjct: 103 AYWMAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALTLIEAVVGAVDVP 162

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD +  +   ++ +  +++GV  + IH R         +        D+  
Sbjct: 163 VTLKTRLGWDDTL--LNAPDVARRAQEAGVQMVTIHGRT--------RCQFYKGEADWAA 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +    +A   L     DGVM+GR A     +L  +       
Sbjct: 213 IRAVK-DAVSIPVVANGDITSPGRAQAALEQSGADGVMVGRGAQGKPWLLAQIAHELWGT 271

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +         A +  Y A        L+   +H+             R  
Sbjct: 272 PAPEVPEGDDLADMVRAHYEAMLGFYGAE-----LGLRVARKHLGWYMDEARTPASLRRA 326

Query: 297 LTVEAGASTATHHIIETA 314
           + + A        +I  A
Sbjct: 327 V-LTARDPAEVLRLIGDA 343


>gi|257088706|ref|ZP_05583067.1| dihydrouridine synthase [Enterococcus faecalis CH188]
 gi|256997518|gb|EEU84038.1| dihydrouridine synthase [Enterococcus faecalis CH188]
          Length = 332

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTKAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +               ++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|298707058|emb|CBJ29860.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 379

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 115/356 (32%), Positives = 171/356 (48%), Gaps = 45/356 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+  TDR++R+  R L+  + LYTEM V   +L    +  N L     E PLA+Q+GG D
Sbjct: 15  MMAVTDRYFRYLFRQLSRRSKLYTEMYVDKTLLHQQDNLHNFLSHRAAEGPLAVQLGGND 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSI 117
              L EAA++ E + ++EINLN GCPS++V +  FGA LML+P+ V +    M  K    
Sbjct: 75  PDTLAEAAEMCEQWAFSEINLNCGCPSSKVSDRCFGARLMLDPERVREITYGMIRKVTRT 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVKCRIGVDD+     L   V+++K +G++ + +HARK +LKGLS   NR IP L YD
Sbjct: 135 PVTVKCRIGVDDKDSYDELTTFVRAVKAAGIDHVVVHARKCLLKGLSTSANRTIPPLRYD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG---------------RAAYKN 222
           +V+ + +E P+L I LNGG++ +    + +        G               RAAY +
Sbjct: 195 VVHRLAQEFPELEIVLNGGIDSLGAVNEHITGT-----GEWGEYGGGVAGVMVGRAAYFD 249

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM-- 280
                  D         S P  TR  ++   +     T+        G +  + TRH+  
Sbjct: 250 PWTFRHTDSAVFGS---SDPGFTR--REIMERCVDRFTEMMQEGRREGPECNR-TRHLCL 303

Query: 281 ------IGLF-HGFPNSRRCRHILTVEAGASTA-------THHIIETAFNLMIESL 322
                 +G    G   SR  R  L+    A +            ++ A  L+ E +
Sbjct: 304 GTVTKPLGYLSSGARGSRTFRQELSRAVQAQSKIDPDTDDFRDAVDRAMALLPEGV 359


>gi|224368016|ref|YP_002602179.1| Dhs2 [Desulfobacterium autotrophicum HRM2]
 gi|223690732|gb|ACN14015.1| Dhs2 [Desulfobacterium autotrophicum HRM2]
          Length = 330

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 129/322 (40%), Gaps = 31/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              T+  +R  A+      L+ +EM+ A  +    +K   +L     E+P+++QI GA+ 
Sbjct: 18  AGITNLPFRIIAK-GCGCTLVCSEMVSAKGLEFNSEKTVQLLRTDACERPVSVQIFGAEA 76

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  AA+ + +    + I++N GC   +V     G  LM + D     I A+ +A+S+P
Sbjct: 77  LSMANAARWIAERNVADIIDINFGCSVKKVARTGAGVALMKDMDNARAIIRAVRRAVSMP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            T+K R G D         ++ +  + +GV+ I IH R A                D+ +
Sbjct: 137 FTIKIRSGWDSSASQAF--DIARMAEDNGVDAIAIHPRTAAQGFR--------GRADWSM 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +    Q + ++     DGVM+GRAA  N  +   ++      
Sbjct: 187 IARLK-EMLTIPVIGNGDITTPEQGVAMIQETGCDGVMVGRAAMGNPFIFGGIEALLRGE 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    +      +I   M +    +L      + +   +     GF  +   R  
Sbjct: 246 -AWNEPSPMEIF-----QIMEEMVESHVAYLGERPACRMMRSRLAWFVKGFAGASVFRRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           LT            ++ A  L+
Sbjct: 300 LT--------GIETLDQAMALI 313


>gi|308188309|ref|YP_003932440.1| dehydrogenase [Pantoea vagans C9-1]
 gi|308058819|gb|ADO10991.1| putative dehydrogenase [Pantoea vagans C9-1]
          Length = 321

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 133/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRTLCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+++P
Sbjct: 76  PSEMAQAARINVEAGAQVIDINMGCPAKKVNRKMAGSALLQYPAVVESILSAVVNAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPENRNCVA--IAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y      SG   +   +H+         + + R  
Sbjct: 245 ELLAPLPMAEVKRLLVSHIRELHDFY-----GSGKGYRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|148726263|emb|CAL07960.2| putative dihydrouridine synthase [Ruminococcus flavefaciens]
          Length = 332

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 128/300 (42%), Gaps = 23/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    DR YR   +     A + +EM+ A  I   D+K   +   + +E+P+A+Q+ G++
Sbjct: 21  MAGVADRAYRLMCKRY-GAAYVVSEMVSAKGICYSDRKTAELCTVTEEERPMAVQLFGSE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSI 117
              + EA KIV D+  + I++N+GCP  +V     G+ LM +P        AA+  A   
Sbjct: 80  PDFMAEAVKIVLDYRPDIIDINMGCPVPKVVGTGAGSALMKDPALAAAITEAAVKAAGDT 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G      ++    + ++++ SG   I +H R         +D       D +
Sbjct: 140 PVTVKIRSGW--SSDSINAPEMARALEASGTAAIAVHGRT--------RDMFYSGQSDMN 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++  +K E   + +  NG + D     ++      D VMIGR +Y N  +   +      
Sbjct: 190 VIKAVK-EAVSVPVIGNGDITDAESCAEMYGRTGCDLVMIGRGSYGNPFIFREIAARMEG 248

Query: 236 PLTGSSPIKTRVDKDFWR-KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  ++ ++       ++ A +++           + +  +H     +G+  S + R
Sbjct: 249 SEYQPPSLEEKMRVMLEHIRLIAGLSEKCEE-----LAMHEARKHAAWYMNGYYGSAKFR 303


>gi|159897989|ref|YP_001544236.1| nifR3 family TIM-barrel protein [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159891028|gb|ABX04108.1| putative TIM-barrel protein, nifR3 family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 362

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 138/324 (42%), Gaps = 24/324 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R     L    L+ +EM  A ++     K   +L +  +E+P+++Q+ G D
Sbjct: 32  MAGVTDSVFRRLVLSLGGCGLVVSEMTNAASVSPKAMKRHRLLDYLPEERPISIQLSGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+ VE+ G + I++N GCPS +V  G  G+ L+ +   +   + A+  A++IP
Sbjct: 92  PDLVATAARFVEELGPDVIDINCGCPSPKVTGGGHGSALLKDLPKMQQMLKAVYAAINIP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            T+K R G D+Q  ++   +  K  + +G   I +H R  +             + D+  
Sbjct: 152 FTLKFRAGWDEQ--SLNYIDTAKIAEDAGCAAITLHPRTKVQG--------YSGDADWSR 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+ +    + +  +G +   + AL  L    V  VMIGRAA  N  +   + +  +  
Sbjct: 202 VAEVVQAV-SIPVIGSGDVRTPADALARLEQTGVAAVMIGRAAMANPWIFRQIAQLRAGE 260

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCRH 295
                P  +       R +         R   + GKL+Q    +IG F  G   S + R 
Sbjct: 261 PIF-VPTPSDKRDLLVRYVDMCAETMVERQ--ALGKLKQ----LIGQFSIGLYASNQLRR 313

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
            +   A    A   II   F   I
Sbjct: 314 DV-QRANEIEAAKAIIANFFEPFI 336


>gi|256855221|ref|ZP_05560582.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecalis
           T8]
 gi|256709734|gb|EEU24781.1| zinc-binding NifR3 family TIM-barrel protein [Enterococcus faecalis
           T8]
 gi|315028814|gb|EFT40746.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX4000]
          Length = 332

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 137/325 (42%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G D
Sbjct: 18  MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSVQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+
Sbjct: 77  KETLVEAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + I +H R  +              +++D
Sbjct: 137 PVTVKMRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTVNWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY   
Sbjct: 187 VLKEVKKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            I+                +++  +H      G   + + + 
Sbjct: 246 GELMPEPSPAEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            +        A   +++     + +
Sbjct: 301 AINQVET-QQAVVDLLDAFVEKISK 324


>gi|153835711|ref|ZP_01988378.1| tRNA-dihydrouridine synthase B [Vibrio harveyi HY01]
 gi|148867644|gb|EDL66932.1| tRNA-dihydrouridine synthase B [Vibrio harveyi HY01]
          Length = 331

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + K  +  G+  + +H R         K        +YD 
Sbjct: 145 VTLKTRTGWNTENKNCVH--IAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 195 IKAVKQAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMDELPSEEVKAIMLGHVNALHGFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      +E  F+ +
Sbjct: 309 FNA-IDAAELQLEALEGYFDNV 329


>gi|254503074|ref|ZP_05115225.1| putative TIM-barrel protein, nifR3 family [Labrenzia alexandrii
           DFL-11]
 gi|222439145|gb|EEE45824.1| putative TIM-barrel protein, nifR3 family [Labrenzia alexandrii
           DFL-11]
          Length = 315

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 122/287 (42%), Gaps = 20/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +++ ++GD +  +    Q+  L  +Q+ G + 
Sbjct: 1   MSGVSDLPFRRLAARF-GAGMVVSEMVASESFVKGDAETQMRAEAQDGGLHVVQLAGREA 59

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAK++   G + I++N+GCP+ +V  G  G+ LM + D     I A  +A+ +PV
Sbjct: 60  RWMGEAAKVIAGLGADIIDINMGCPAKKVTSGYSGSALMRDLDHALTLIEATVEAVDVPV 119

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD    +    L +  + +GV  I +H R         +        D++ +
Sbjct: 120 TLKMRLGWDDTT--INAPELARRAEAAGVQLITVHGRT--------RCQFYKGTADWNAI 169

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG    +  A  +L     D VMIGR AY    +   V  Y     
Sbjct: 170 SAVKSEI-SVPLIANGDCTGIESADAMLVASGADAVMIGRGAYGRPWLPGLVGHYLETGE 228

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             S+P    +         A +  Y          ++   +H+    
Sbjct: 229 ILSAPQGNALGDLVIEHYEAILDLYGV-----LPGVRIARKHLGWYL 270


>gi|113954689|ref|YP_729811.1| dihydrouridine synthase family protein [Synechococcus sp. CC9311]
 gi|113882040|gb|ABI46998.1| dihydrouridine synthase family protein [Synechococcus sp. CC9311]
          Length = 331

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 137/318 (43%), Gaps = 22/318 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADIS 60
              +DR +R   R    +ALL+TEM+ A ++  G  +  + G   +  P+ +Q+      
Sbjct: 24  AGVSDRIFRQLVRRWAPDALLFTEMVNATSLELGHGRLKMDGLQEETGPIGVQLFDHHPD 83

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+   D G   I++N+GCP  ++     G+ L+ +PD+    +  +  A+ +PVT
Sbjct: 84  AMADAARRAADAGAFLIDINMGCPVRKIARKGGGSGLIRDPDLACRIVDTVVAAVGLPVT 143

Query: 121 VKCRIGVDDQIPAV---ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           VK R+G   +  AV   A  N  + ++++G   + +H R         ++ R     D++
Sbjct: 144 VKTRLGWCGEHNAVKAQAAVNWCRRLEEAGARMLTLHGRT--------REQRFSGTADWN 195

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG +    +AL+ L     DGVM+GR +     ++  +D   S+
Sbjct: 196 AIAAVKAAL-SIPVIANGDVNSPEEALRCLRITGADGVMVGRGSMGAPWLVGQIDAALSD 254

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++P           ++ A +             L    +HM     GF  + + R 
Sbjct: 255 RPIPATPKPLARLALAKEQLLALI------EARGDHGLLIARKHMSWTCTGFHGASQFRQ 308

Query: 296 ILTVEAGASTATHHIIET 313
            L + A    A   +++ 
Sbjct: 309 QL-MRAPTPAAALDLLDQ 325


>gi|212715521|ref|ZP_03323649.1| hypothetical protein BIFCAT_00419 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660888|gb|EEB21463.1| hypothetical protein BIFCAT_00419 [Bifidobacterium catenulatum DSM
           16992]
          Length = 409

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 118/318 (37%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  E   +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCHFAPSENIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKMDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 169 ANVPVTAKIRVGIDHE--HETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 218

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+ +   D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 219 DWSRIGELVEAL-DIPVFGNGDIWGANDALAMVAETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +   R        Y      +   +  + +H+     GFP    
Sbjct: 278 FAGSEKRVDPTLGDVCRVVERHAELLTEFYDGDEQMA---VHDLRKHIAWYLKGFPVGGS 334

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 335 TRRAFMECENLEDVRTEI 352


>gi|283782945|ref|YP_003373699.1| TIM-barrel protein, nifR3 family [Gardnerella vaginalis 409-05]
 gi|283441929|gb|ADB14395.1| TIM-barrel protein, nifR3 family [Gardnerella vaginalis 409-05]
          Length = 384

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 65/307 (21%), Positives = 115/307 (37%), Gaps = 22/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 24  MAGITNWPFRVICREFGPDGLYVAEMITARALVARNPKALRLCRFAPSEKVRSLQLYGVN 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            S + +A +IV D    + ++LN GCP  +V     G+ L    D++ + +  +      
Sbjct: 84  PSIVEQATRIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCEP 143

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D+              ++ G   + +HAR                + 
Sbjct: 144 AGIPVTAKFRVGIDE--NHETFIQAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+  E  D+ +  NG +     AL +       GV IGR       +   +   
Sbjct: 194 DWQRIGELV-ETLDIPVFGNGDIWGAEDALAMFKETGCAGVAIGRGCQGRPWLFADIRNA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                   +P    V     R ++  +  Y      +   +  + +H+     GFP    
Sbjct: 253 CEGSDNRVNPTLAEVGSVILRHLNLLVEFYDGDERMA---VHDLRKHIAWYLKGFPVGGG 309

Query: 293 CRHILTV 299
            R     
Sbjct: 310 TRKAFME 316


>gi|254475986|ref|ZP_05089372.1| tRNA-dihydrouridine synthase B [Ruegeria sp. R11]
 gi|214030229|gb|EEB71064.1| tRNA-dihydrouridine synthase B [Ruegeria sp. R11]
          Length = 331

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 77/309 (24%), Positives = 130/309 (42%), Gaps = 22/309 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G D
Sbjct: 19  MAGITDRPFRDLVRGF-GVGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ VED G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+S+P
Sbjct: 78  AYWMAEAARQVEDRGAKVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVGAVSVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD   ++   ++ +  + +GV  + IH R         +      + D+  
Sbjct: 138 VTLKTRLGWDD--NSLNAADVARRAQNAGVQMVTIHGRT--------RCQFYKGSADWGA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K    D+ +  NG + D + A + L     DGVMIGR A     +L  V       
Sbjct: 188 ISEVKAAL-DVPLLANGDIIDTATAREALKRSGADGVMIGRGAQGKPWLLAQVAHDIWGS 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                P  T + +       A +  Y          ++   +H+             R  
Sbjct: 247 EAPQIPTGTDLVRLVSDHYEAMLAFY-----GLDLGIRVARKHLGWYMDEAATPAPLRRD 301

Query: 296 ILTVEAGAS 304
           ILT +    
Sbjct: 302 ILTAKDPKD 310


>gi|153873343|ref|ZP_02001955.1| Dihydrouridine synthase, DuS [Beggiatoa sp. PS]
 gi|152070190|gb|EDN68044.1| Dihydrouridine synthase, DuS [Beggiatoa sp. PS]
          Length = 259

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 113/241 (46%), Gaps = 16/241 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR YR   +      +  +EMI ++++L G +K         + +P  +QI GAD
Sbjct: 17  MAGVTDRPYRQLCKQW-GAGMAVSEMISSNSLLWGSEKTKRRANHEGETEPRCIQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   D G   I++N+GCP+ +V     G+ L+ +  +VG  + A+ KA+ +P
Sbjct: 76  PELMAKAAQYNVDNGAQIIDINMGCPAKKVCHVMAGSALLKDEGLVGKILEAVVKAVEVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++SG+  + +H R    +             +Y+ 
Sbjct: 136 VTLKIRTGWDKEHRNGV--RIAQIAEQSGIQALAVHGRTRACQ--------FSGEAEYET 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK     + +  NG +++  +A  +L     D VM+GRAA     +   ++ Y +  
Sbjct: 186 IAAIK-ATIKIPVIANGDIDNPEKAKSVLDYTGADAVMVGRAALGQPWLFREMEHYLNTG 244

Query: 237 L 237
            
Sbjct: 245 E 245


>gi|259906958|ref|YP_002647314.1| tRNA-dihydrouridine synthase B [Erwinia pyrifoliae Ep1/96]
 gi|224962580|emb|CAX54035.1| tRNA-dihydrouridine synthase B [Erwinia pyrifoliae Ep1/96]
 gi|283476752|emb|CAY72590.1| putative dehydrogenase [Erwinia pyrifoliae DSM 12163]
          Length = 286

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 64/302 (21%), Positives = 125/302 (41%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  +    K+ L     ++P    +QI G D  ++ EAA+I    G   I+
Sbjct: 1   MTVSEMLSSNPEVWASDKSRLRMVHSDEPGIRTVQIAGCDPQEMAEAARINAASGAQVID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+ +P++V   ++A+  A+ +PVT+K R G D          
Sbjct: 61  INMGCPAKKVNRKMAGSALLQHPELVKSILSAVVNAVDVPVTLKIRTGWDSDNRN--CVE 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  ++ G+  + IH R         +      + +YD +  +K+ N  + +  NG + 
Sbjct: 119 IAQLAERCGIQALTIHGRT--------RACLFNGDAEYDSIRTVKQ-NVSIPVIANGDIT 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           D  +A  +L     D +MIGRAA     +   +  Y       +      V +     + 
Sbjct: 170 DPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLAPMPLAEVKRLLIGHLR 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
                Y  R    G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 ELHGFYGQR---KGYRI--ARKHVSWYLQENAPNDQFRRTFNAIEDASE-QLEALEAYFE 283

Query: 317 LM 318
            +
Sbjct: 284 NL 285


>gi|297242773|ref|ZP_06926711.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis AMD]
 gi|296888984|gb|EFH27718.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis AMD]
          Length = 377

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 65/307 (21%), Positives = 115/307 (37%), Gaps = 22/307 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 17  MAGITNWPFRVICREFGPDGLYVAEMITARALVARNPKALRLCRFAPSEKVRSLQLYGVN 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            S + +AA+IV D    + ++LN GCP  +V     G+ L    D++ + +  +      
Sbjct: 77  PSIVEQAARIVVDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCEP 136

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVT K R+G+D+              ++ G   + +HAR                + 
Sbjct: 137 AGIPVTAKFRVGIDE--NHETFIQAGHIAQEEGCAAVTLHARTT--------AEYYGGHS 186

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+  E  ++ +  NG +     AL +       GV IGR       +   +   
Sbjct: 187 DWQRIGELV-EALNIPVFGNGDIWGAEDALAMFKETGCAGVAIGRGCQGRPWLFADIRNA 245

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                   +P    V     R +   +  Y      +   +  + +H+     GFP    
Sbjct: 246 CEGSDNRVNPTLAEVGSVILRHLKLLVEFYDGDERMA---VHDLRKHVAWYLKGFPVGGG 302

Query: 293 CRHILTV 299
            R     
Sbjct: 303 TRKAFME 309


>gi|59800609|ref|YP_207321.1| hypothetical protein NGO0151 [Neisseria gonorrhoeae FA 1090]
 gi|240013465|ref|ZP_04720378.1| hypothetical protein NgonD_02246 [Neisseria gonorrhoeae DGI18]
 gi|260441186|ref|ZP_05795002.1| hypothetical protein NgonDG_08906 [Neisseria gonorrhoeae DGI2]
 gi|59717504|gb|AAW88909.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
          Length = 334

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 126/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 17  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 76  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++   +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 186 IAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 245 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 300 INRLDNAA-AQYDTLAGYLERL 320


>gi|304396993|ref|ZP_07378873.1| TIM-barrel protein, nifR3 family [Pantoea sp. aB]
 gi|304355789|gb|EFM20156.1| TIM-barrel protein, nifR3 family [Pantoea sp. aB]
          Length = 321

 Score =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 133/322 (41%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P   A+QI G D
Sbjct: 17  MAGITDRPFRALCHEM-GAGMAVSEMLSSNPEVWASDKSRLRMVHSDEPGIRAVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ +AA+I  + G   I++N+GCP+ +V+    G+ L+  P +V   ++A+  A+++P
Sbjct: 76  PSEMAQAARINVEAGAQVIDINMGCPAKKVNRKMAGSALLQYPTVVESILSAVVNAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPENRNCVA--IAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +  + I  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-SVSIPIIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     I      Y      SG   +   +H+         + + R  
Sbjct: 245 ELLAPLPMAEVKRLLVSHIRELHDFY-----GSGKGYRIARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|256832754|ref|YP_003161481.1| TIM-barrel protein, nifR3 family [Jonesia denitrificans DSM 20603]
 gi|256686285|gb|ACV09178.1| TIM-barrel protein, nifR3 family [Jonesia denitrificans DSM 20603]
          Length = 380

 Score =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 67/308 (21%), Positives = 123/308 (39%), Gaps = 25/308 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R    +     EM+ + A++  +  ++  + F   E+P + Q+ G D
Sbjct: 21  MAGVTNTAFRRLCRE-QGDGFFVAEMVTSRALVERNDVSLRIVSFEDYEQPRSAQVYGVD 79

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
            + +  A  I+  +   + I+LN GCP  +V     GA L    ++    + A  +A S 
Sbjct: 80  PATVGAAVSIIAGEDRADHIDLNFGCPVPKVTRKGGGAALPWKKELYTRIVDAAVRAASP 139

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R+G+DD    +      K  +  GV+ + +HAR A                
Sbjct: 140 HHVPVTVKMRMGIDDD--HMTYLEAGKIAEDLGVSAVALHARTA--------AQHYSGQA 189

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D +  +K+    + +  NG +     AL ++     DGV++GR       +   +   
Sbjct: 190 RWDAIKNLKEHVTTIPVLGNGDIWSAEDALNMVAHTGCDGVVVGRGCQGRPWLFADLTAA 249

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-SGGKLQQITRHMIGLFHGFPNSR 291
           F+      +P    V +  +R       +Y        G  L+ + +HM     G+    
Sbjct: 250 FAGRDERVTPGLGYVAETIYRH-----GEYLVEFFGDEGRGLRDLRKHMAWYLKGYAVGG 304

Query: 292 RCRHILTV 299
             R  L +
Sbjct: 305 EARQALAL 312


>gi|292669421|ref|ZP_06602847.1| tRNA-dihydrouridine synthase B [Selenomonas noxia ATCC 43541]
 gi|292648942|gb|EFF66914.1| tRNA-dihydrouridine synthase B [Selenomonas noxia ATCC 43541]
          Length = 323

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 134/323 (41%), Gaps = 25/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++  +  L     E+P+A+QI    
Sbjct: 20  MAGVTDTAYRVIAHDM-GCPLAFAEMVSSQGIHYRNEHTMKMLRTEPDERPIAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  + ++ N+GCP+ +V +   G+ LM +P    + + A+ +A  +
Sbjct: 79  AAMAAEAAAYIEEIGTADILDFNMGCPAPKVVKNGEGSALMRDPKRAEEILTAIRRATKL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R+G DD     A   + K  +  GV+ + +H R         ++     N DY 
Sbjct: 139 PFTVKMRLGWDDSSRNAA--EIAKMAEAVGVDAVAVHGRT--------REQFYSGNADYA 188

Query: 178 IVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + E+K+    + + ++G +    D+S+AL +    D VMIGR A  N  +   +  +  
Sbjct: 189 AIAEVKRAVG-IPVIVSGDIRRSADLSRALAV-TEADAVMIGRGAQGNPWIFPQLIHWLR 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +   R +     D    +      ++++ RH      G   S   R
Sbjct: 247 TGEDLPPPTLAERAQVILRHL-----DLLIGYKGEYIGIREMRRHAAWYTRGLAGSAELR 301

Query: 295 HILTVEAGASTATHHIIETAFNL 317
                 A        I+  A+ +
Sbjct: 302 EQFNRAASRED-FAQILHDAWEI 323


>gi|303235002|ref|ZP_07321626.1| TIM-barrel protein, nifR3 family [Finegoldia magna BVS033A4]
 gi|302493857|gb|EFL53639.1| TIM-barrel protein, nifR3 family [Finegoldia magna BVS033A4]
          Length = 310

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 131/302 (43%), Gaps = 32/302 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R     L    L +TEMI A A+   DKK   +L    +EK  ++QI G + 
Sbjct: 18  AGVTDIPFRIICGEL-GAGLCFTEMISAKALYYDDKKTKKLLDTDPREKSTSVQIFGHEP 76

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A + + E++ +  I++N+GCP+ ++ +   G+ LM + ++  D I A      +P
Sbjct: 77  EIIAYATRFLTENYNFKSIDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G+D+   ++    L +  ++  V+ I +HAR   +              D+  
Sbjct: 137 VSVKFRLGIDE--NSMNYMQLAQICERLKVDYITLHARTRKMF--------YSGEADWSH 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  EN D+ +  NG         K +   + DGV++ R A +N  + +         
Sbjct: 187 IKRVV-ENVDIPVFGNGDCFTKEDIRKNMEYSNCDGVLLARGAMQNPFIFSD-------- 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +  K  V     + +   +  Y  R       + ++ +H+     GF NS + ++ 
Sbjct: 238 --DENKSKEEVIDTIKKHMQLKLEFYEERR-----AILEMRKHIQWYLKGFRNSNKVKNK 290

Query: 297 LT 298
           + 
Sbjct: 291 IN 292


>gi|224475660|ref|YP_002633266.1| putative tRNA-dihydrouridine synthase 1 [Staphylococcus carnosus
           subsp. carnosus TM300]
 gi|222420267|emb|CAL27081.1| putative tRNA-dihydrouridine synthase 1 [Staphylococcus carnosus
           subsp. carnosus TM300]
          Length = 331

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 132/318 (41%), Gaps = 23/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L     E+PL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILFNNPKTMNMLYIDENERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V ++   + I++N+GCP  ++     GA  +L+P+ + + ++A+ + +S 
Sbjct: 77  KESLVEAAVYVDQNTTADIIDINMGCPVNKIIRCEAGARWLLDPNKIYEMVSAVTEKVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RIG D+           K+ +++G   I +H R  +             + D+D
Sbjct: 137 PVTCKMRIGWDEDHIYAV--ENAKAAERAGAAAISLHGRTRV--------QMYEGHADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG +     A K+L    VD VMIGR A  N  M+     Y   
Sbjct: 187 IIRQVK-EAVNIPVIGNGDVTSPELAQKMLDETGVDAVMIGREALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     +                 + ++ +H      G   + + R 
Sbjct: 246 GELMDEPTVKEKVEIALLHLRR-----LVELKGEKIGVMEMRKHASWYLKGVKGNGKARK 300

Query: 296 ILTVEAGASTATHHIIET 313
            L  +A        I++ 
Sbjct: 301 ALN-QANTEQEMIDILQN 317


>gi|320527911|ref|ZP_08029078.1| TIM-barrel protein, nifR3 family [Solobacterium moorei F0204]
 gi|320131707|gb|EFW24270.1| TIM-barrel protein, nifR3 family [Solobacterium moorei F0204]
          Length = 328

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 126/318 (39%), Gaps = 24/318 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              ++  YR          L+ +EMI   A+   + K   +   S  E P+ALQ+ G+D 
Sbjct: 19  AGISNPVYREIMHNY-GAGLVVSEMISDKALHYQNAKTQDMCRISEGEHPVALQLFGSDP 77

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EAA+ + ++   + I++N+GCP  +V +   G+ LM  P++  + + A+      P
Sbjct: 78  ITMAEAAEYLTKNTNCDMIDINMGCPVQKVVKAHSGSYLMQKPELAYEVMHAVVTHTDRP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     +    + K  +K+GV+ + +H R    +     +N  I  +    
Sbjct: 138 VTVKMRAGWDSD--HINCVEIAKLAEKAGVSAVTVHGRTRGQQYTGHSNNAYIKAV---- 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                K+  ++ +  NG +     A ++L     D +MIGR        L  VD Y +  
Sbjct: 192 -----KDAVNIPVIGNGDIRIPEDAKRMLEETGCDAIMIGRGLLGRPFFLQEVDAYLNGG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                    ++D  +         +    +      +  +         G P++   ++ 
Sbjct: 247 TYVEPDYNEKLDLAY------HYAEKLCEYEGERNGICMMRGMAGWYITGLPHASEYKNR 300

Query: 297 LTVEAGASTATHHIIETA 314
           L+  +        IIE  
Sbjct: 301 LSSISSLREMK-EIIEEY 317


>gi|88607437|ref|YP_505166.1| putative tRNA-dihydrouridine synthase [Anaplasma phagocytophilum
           HZ]
 gi|88598500|gb|ABD43970.1| putative tRNA-dihydrouridine synthase [Anaplasma phagocytophilum
           HZ]
          Length = 315

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 75/282 (26%), Positives = 124/282 (43%), Gaps = 20/282 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   R L    LL +EM+ + A++   ++++   S      ++Q+ G    
Sbjct: 15  MSGVTDLPFRTTVRKL-GAGLLISEMVASRAMILKTRQSMQK-SEVCPNTSVQLAGCTPE 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAKI ED G   I+LN GCP+ +V +G  G+ LM +  I    + ++ KA+ +PVT
Sbjct: 73  IMAEAAKINEDLGAKSIDLNFGCPAKKVVDGYAGSALMKDEVIATKIMESVVKAVKVPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D     +    L K  +  G+  I IH R         +      + D+  V 
Sbjct: 133 VKMRMGWD--TTNLNAPTLAKVAEDVGIQMITIHGRT--------RSQMFSGSADWKFVK 182

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K E   + + +NG +  +   +  L     DGVMIGR AY    ++     +  N   
Sbjct: 183 RVK-ECVKIPVIVNGDIRTLDDIVVALNESGADGVMIGRGAYGKPWLIKQALSFMKNSEI 241

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
              P K+         I     DYA  +      ++ + +H+
Sbjct: 242 LPEPTKSE-----KLAIILDHYDYALDYYGKDLGVKILRKHL 278


>gi|152990938|ref|YP_001356660.1| tRNA-dihydrouridine synthase [Nitratiruptor sp. SB155-2]
 gi|151422799|dbj|BAF70303.1| tRNA-dihydrouridine synthase [Nitratiruptor sp. SB155-2]
          Length = 308

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 69/304 (22%), Positives = 128/304 (42%), Gaps = 32/304 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EMI ++A++   KK   +L  S +E P  +QI G D 
Sbjct: 16  AGYTDLPFRSVVKKF-GADLTISEMISSNALVYDSKKTYKMLEKSPEENPYFVQIAGGDP 74

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + + +  G + I+LN GCP  +V +   G+ L+ + D +G  +  + +     
Sbjct: 75  LIVKEAVERLNEIEGIDGIDLNCGCPVPKVVKQGAGSALLDDLDRLGKIVQTIKETSEKN 134

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T VK R+G  +      +  +VK ++++G + I IH R         +       +DY+
Sbjct: 135 YTSVKIRLGFTENR----VVEIVKVLEEAGADFITIHGRT--------RSGGFKAPVDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +    KE+  + +  NG + +  +  ++L     DGVMIGR A     +   +      
Sbjct: 183 AIAR-AKESVSIPVIANGDITNFQKTQEVLFITKADGVMIGRGAIGKPWIFYQLKH---- 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   K  VD    ++I         R   + G +    +H+     G+P + + R 
Sbjct: 238 -------GKEDVDASLKKEIILEHFHQMIRFYGTYGAVL-FRKHLHTYSKGYPGATQFRT 289

Query: 296 ILTV 299
            +  
Sbjct: 290 KINE 293


>gi|81429207|ref|YP_396208.1| putative dihydrouridine synthetase [Lactobacillus sakei subsp.
           sakei 23K]
 gi|78610850|emb|CAI55902.1| Putative dihydrouridine synthetase [Lactobacillus sakei subsp.
           sakei 23K]
          Length = 328

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 133/321 (41%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    I+  +KK +  +     E P+++QI G  
Sbjct: 19  MAGITNAAFRVTAKEF-GAGLVVCEMISDRGIMHNNKKTMGMMFVDPNEHPVSIQIFGGS 77

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  +V +   GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KDTLVEAAKFVDQHTQADIIDINMGCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + + +H R         +        D+D
Sbjct: 138 PVTVKMRTGWDEDHIFAVQNALA--AERAGASALAMHGRT--------RKQMYTGKADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E    F+G NG +     A ++L     D VMIGRAA  N  +L  V+ Y  +
Sbjct: 188 ILKQVKAELKIPFMG-NGDVRTPQDAKRMLDEVGADAVMIGRAALGNPWILRQVETYLRS 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P           ++                  ++  +       G P + + + 
Sbjct: 247 GELIAEPTPREKIATAKLQLHR-----LVELKGENVACREFRQQAAYYLKGIPRAAKTKA 301

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +  E     A   I++    
Sbjct: 302 AVN-EVETEQAVGDILDRFVE 321


>gi|33862473|ref|NP_894033.1| nitrogen regulation protein NifR3 family protein [Prochlorococcus
           marinus str. MIT 9313]
 gi|33640586|emb|CAE20375.1| putative nitrogen regulation protein NifR3 family homolog
           [Prochlorococcus marinus str. MIT 9313]
          Length = 336

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 137/323 (42%), Gaps = 21/323 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADIS 60
              +D+ +R   R    +ALL+TEM+ A ++  G   + I   + +  P+ +Q+      
Sbjct: 25  AGVSDQIFRSLVRRWAPDALLFTEMVNATSLELGHGLQKINELANEAGPIGVQLFDHRPE 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    ++ +  A+ IPVT
Sbjct: 85  AMADAAQRAEAAGAFLIDINMGCPVRKIARKGGGSGLIRDPQLAAKIVSTVAAAVKIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G              +S++++G   + +HAR         ++     + D+  + 
Sbjct: 145 VKTRLGWCGSDAKPI--EWCQSLEQAGAQMLTLHART--------REQGFKGSADWHAIA 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K     + +  NG ++    A + L     DGVM+GR +     ++  +D   S    
Sbjct: 195 AVKSAL-QIPVIANGDVKSDIDAKRCLAITGADGVMVGRGSLGAPWLVGQIDAALSGRPV 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P          R+   ++      H      L    +HM     GFP + + RH L 
Sbjct: 254 PATPGAAE-RLTIAREQLEALVQAKGEH-----GLLIARKHMGWTCSGFPGASKLRHAL- 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
           + A        ++E A   ++ +
Sbjct: 307 MRAPTPMDAISLLEQASAELLTA 329


>gi|153827384|ref|ZP_01980051.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-2]
 gi|149738714|gb|EDM53056.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-2]
          Length = 331

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNTIETADQ-QLDALEGYFDNV 329


>gi|291044520|ref|ZP_06570229.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae DGI2]
 gi|293397656|ref|ZP_06641862.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae F62]
 gi|291011414|gb|EFE03410.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae DGI2]
 gi|291611602|gb|EFF40671.1| tRNA-dihydrouridine synthase B [Neisseria gonorrhoeae F62]
          Length = 340

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 126/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M    D+ +R   R          EM+ +D  LR   K +    F+ +   +A+QI G+D
Sbjct: 23  MAGIADKPFRRLCRAF-GAGWAVCEMLASDPTLRNTGKTLHRSDFADEGGIVAVQIAGSD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ +AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+ KA  +P
Sbjct: 82  PEQMADAARYNVGLGAQVIDINMGCPAKKVCNVQAGSALMQDEPLVAAILEAVVKAAGVP 141

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D      L  + K  +  G+  + +H R         +         Y++
Sbjct: 142 VTLKTRLGWHDDHQN--LPAIAKIAEDCGIAALAVHGRA--------RTQMYKGEARYEL 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++   +NG +    +A  +L   + DG+MIGR A         +  Y  + 
Sbjct: 192 IAETKSRL-NIPAWVNGDITSPQKAAAVLKQTAADGIMIGRGAQGRPWFFRDLKHYAEHG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +             I A    Y          ++   +H+       P+  + R  
Sbjct: 251 VLPPALSLAECRAAILNHIRAMHAFY-----GETVGVRIARKHIGWYIGEMPDGEQARRE 305

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     A+ A +  +      +
Sbjct: 306 INRLDNAA-AQYDTLAGYLERL 326


>gi|94266587|ref|ZP_01290270.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
 gi|93452782|gb|EAT03317.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
          Length = 313

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 67/301 (22%), Positives = 118/301 (39%), Gaps = 31/301 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   R      L Y+EM+    ++R       +L  +  E+PL +Q+ GA+ 
Sbjct: 21  AGYSDLPFRLLCREY-GAGLCYSEMLSCHGLVRRQPATIEMLATTAAERPLLMQLFGAEP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             + EAA I+     + I++N+GCP  +V +   GA LM +P++      A+   A  +P
Sbjct: 80  EVMGEAAAILSRLPIDGIDINMGCPVKKVVKKGAGAALMRDPELAAAITGAVTAAAGDLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G       +   +  + +   G   + IHAR           +      D+ +
Sbjct: 140 VTVKIRSGW--NHKQLNAPDFARLLVAHGAAAVTIHARTW--------SDGFAGRADWAV 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    QAL ++     DGVMIGR A     +          P
Sbjct: 190 IAAVKRAV-SVPVIGNGDIGSYEQALAMMAATGCDGVMIGRGALGAPWVF--------TP 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P   +      R +         RH        ++   +   F   P   + R  
Sbjct: 241 GAEQNPPLAQRLAAARRHLELI------RHWRPADNPARVRNQLGRYFKKIPGGAQLRRQ 294

Query: 297 L 297
           +
Sbjct: 295 I 295


>gi|148272765|ref|YP_001222326.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147830695|emb|CAN01635.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 410

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/308 (21%), Positives = 124/308 (40%), Gaps = 21/308 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +++  +     EK  ++Q+ G D
Sbjct: 45  MAGITNTAFRRLCREF-GAGLYVSEMITSRALVERTPESMRLITHHPSEKVRSIQLYGVD 103

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + EA   +V +   + I+LN GCP A+V     GA L     +  D +  A+  A  
Sbjct: 104 PKTVREAVTMLVAEDRADHIDLNFGCPVAKVTRKGGGAALPWKLGLFTDIVEGAVKAAGD 163

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IP+TVK R G+D     +      ++ + +GV  I +HAR A         +    + D+
Sbjct: 164 IPLTVKMRKGID--ADHLTYLEAGRAAEGAGVASIALHARTA--------ADYYSGHADW 213

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K+    + +  NG +     A++++     DGV++GR       +   +   F 
Sbjct: 214 SAIAKLKQAIESVPVLGNGDIWAAEDAIRMMDETGADGVVVGRGCLGRPWLFGDLAAAFH 273

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDY----AARHLHSGGKLQQITRHMIGLFHGFPNS 290
               G  P  T        +++ +   +    A          +   +H+   F G+P  
Sbjct: 274 ARAAGLDPADTPRAHPSQGQVADTFRRHVELLAEFFESEERGCRDARKHVAWYFKGYPVG 333

Query: 291 RRCRHILT 298
              R  L 
Sbjct: 334 GDLRAALA 341


>gi|296875651|ref|ZP_06899720.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC
           15912]
 gi|296433335|gb|EFH19113.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC
           15912]
          Length = 325

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 137/322 (42%), Gaps = 27/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   + D    H+     +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKR-LIDLKGEHIA----VREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            ++  +  +      IE    L
Sbjct: 307 AISQASTLAE-----IEELLQL 323


>gi|116749246|ref|YP_845933.1| nifR3 family TIM-barrel protein [Syntrophobacter fumaroxidans MPOB]
 gi|116698310|gb|ABK17498.1| putative TIM-barrel protein, nifR3 family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 352

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 83/323 (25%), Positives = 138/323 (42%), Gaps = 31/323 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M   TD  YR         A++ TEM+    ++R  +  +           PLA+Q+ G 
Sbjct: 29  MAGVTDSAYRALMADF-GAAMVTTEMVSIQGLVRNQRATLDLCRQQHPVGVPLAVQVFGR 87

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D + + EAA++VE  G   I++N GCP  +V     GA L+ +PD +   + A+ +A+S+
Sbjct: 88  DPAVMAEAARLVEQGGAALIDINAGCPVRKVVRQGAGAILLKDPDRLAAMVEAVKRAVSV 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    VA   L + +  +GV+ I +H R A                D+ 
Sbjct: 148 PVTVKIRVGWDNAANGVA--GLARQLVSAGVDAITVHGRTA--------AQMYSGRADWS 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K     + +  NG +     A +++     DGVMIGRA+  N  +   +   +  
Sbjct: 198 RIAEVK-AAVAVPVIGNGDVTSPELAERMIHETGCDGVMIGRASLGNPWLFAVISRRWGR 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              G+         DF R   A +  +      + G L+++   +I    G P+S   R 
Sbjct: 257 ---GARQGDCPGWNDFLRTAEAHLESFRTMRPRADGHLKKL---LIWYSKGCPDSAGLRC 310

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            +        A    IE+     
Sbjct: 311 RI--------AGPDGIESMLAAF 325


>gi|295104372|emb|CBL01916.1| tRNA-U20-dihydrouridine synthase [Faecalibacterium prausnitzii
           SL3/3]
          Length = 339

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 123/320 (38%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD   R             +EM+ + A++ GD K   +L  +    P  +QI G  
Sbjct: 20  MAGFTDAPCRRLMAQ-HGAGFTVSEMVSSRALVYGDHKTVSLLKAAPNGAPYGVQIFGEV 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EA   +E + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  +      P
Sbjct: 79  PEIMGEATAAIEQYEFDFVDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEQVVAHTKRP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     +      K+ +++G   + +HAR         ++    P +D +I
Sbjct: 139 VTVKMRKGWD--ADHITAVECAKACEQAGAALVAVHART--------REQMYTPGIDPEI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +     AL+++   + DGVMI R+A  +  +   V+      
Sbjct: 189 IARVK-DAVKVPVLGNGDIHCAEDALRMVRETNCDGVMIARSALGDPWLFERVNAALEGL 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R++                 + Q     +    G   +   R  
Sbjct: 248 PAPKEPNLQARMNALRRQVEEM-----VEQKGEFVAMPQARAQTMHYMKGLKGAAALRRY 302

Query: 297 ---LTVEAGASTATHHIIET 313
              LT           + E 
Sbjct: 303 CCTLTHLEDLDELIAAVFEE 322


>gi|148261024|ref|YP_001235151.1| nifR3 family TIM-barrel protein [Acidiphilium cryptum JF-5]
 gi|146402705|gb|ABQ31232.1| tRNA-U20-dihydrouridine synthase [Acidiphilium cryptum JF-5]
          Length = 353

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 136/326 (41%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TD  +R   + +    L+ +EMI + A++R +   +   S  E   P ++Q+ G D
Sbjct: 37  MSGVTDLPFRRLVKSM-GAGLVVSEMIASWAMIRENAATLRMASVDEGTGPNSVQLAGCD 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + + EAA+I    G + +++N GCP  +V      G+ LM +    G  + A  KA+ +
Sbjct: 96  PAAMAEAARIAVAGGADLVDINFGCPVKKVAVGQMAGSALMRDEVQAGRILEATAKAVDV 155

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D Q  ++    L +  ++SG+  + +H R         +        D+D
Sbjct: 156 PVTLKMRMGWDRQ--SLNAPTLARIAQESGIAMVTVHGRT--------RQQFYEGTADWD 205

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG +    +A + L     DGVMIGR AY     L  V  Y + 
Sbjct: 206 FIASVK-AAVAIPVIANGDITTEDEAEEALRRSQADGVMIGRGAYGRPWFLAQVARYLAT 264

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P     D +  R +          H      L+   +H+     G P +   R 
Sbjct: 265 GQKLPAP-----DLEMRRDVLIGHYRAMRAHYGEQPGLRVARKHIGWYVRGLPGAAEFRA 319

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +  +  ++     I +     M E+
Sbjct: 320 AVNRQDDSAAVEAMIHDIYARAMGET 345


>gi|306822377|ref|ZP_07455756.1| possible dihydrouridine synthase [Bifidobacterium dentium ATCC
           27679]
 gi|309802137|ref|ZP_07696246.1| TIM-barrel protein, nifR3 family [Bifidobacterium dentium
           JCVIHMP022]
 gi|304554375|gb|EFM42283.1| possible dihydrouridine synthase [Bifidobacterium dentium ATCC
           27679]
 gi|308221217|gb|EFO77520.1| TIM-barrel protein, nifR3 family [Bifidobacterium dentium
           JCVIHMP022]
          Length = 409

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 117/318 (36%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPGEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 169 ANVPVTAKIRVGIDHE--HETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 218

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 219 DWSRIGELVGAL-DIPVFGNGDVWGANDALAMVSETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V     R        Y      +   +  + +H+     GFP    
Sbjct: 278 FAGSDERIDPTLGDVCTVIERHAQLLTEFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 334

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 335 TRRAFMECENLEDVRREI 352


>gi|92117380|ref|YP_577109.1| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrobacter
           hamburgensis X14]
 gi|91800274|gb|ABE62649.1| tRNA-U20-dihydrouridine synthase [Nitrobacter hamburgensis X14]
          Length = 349

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 74/285 (25%), Positives = 123/285 (43%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADI 59
           M   TDR +R  A  L    L+ +EM  +D ++RG   ++L   +T   P  +Q+ G + 
Sbjct: 33  MSGITDRPFRGLAEAL-GAGLVVSEMTASDDLVRGRPMSVLRCEATGGGPHVVQLAGCET 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 92  HWMAEGARIAEGAGADIIDINMGCPARHVTGGQSGSALMRDLDHALRLIEATVGAVKVPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+  ++    L +  + +GV  + +H R         +      + D+  V
Sbjct: 152 TLKMRLGWDDR--SLNAPALAQRAESAGVQMMTVHGRT--------RCQFYKGSADWQAV 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +  D+ + +NG +     A+  L     D VM+GR A     M   +       +
Sbjct: 202 RAVK-DAVDIPVVVNGDITSFDAAVAALEASGADAVMVGRGAQGQPWMPGQIGRRLETGI 260

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
               P       D    I A   D   RH      L+   +H+  
Sbjct: 261 AEPPPSL----ADQLAYIHALYDDLL-RHYGLRIGLRHARKHLGW 300


>gi|318603958|emb|CBY25456.1| tRNA dihydrouridine synthase B [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|330862841|emb|CBX72982.1| tRNA-dihydrouridine synthase B [Yersinia enterocolitica W22703]
          Length = 286

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 62/302 (20%), Positives = 118/302 (39%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  +    K+ L     ++P    +QI G D  ++  AA+I    G   I+
Sbjct: 1   MTVSEMLSSNPEVWRTDKSRLRMVHSDEPGIRTVQIAGNDPDEMATAARINVANGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+ +PD+V   ++A+  A+ +PVT+K R G   +        
Sbjct: 61  INMGCPAKKVNRKLAGSALLQHPDLVKQILSAVVNAVDVPVTLKIRTGWSAEHRN--CIE 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  +  G+  + IH R         +        +YD +  +K+    + +  NG + 
Sbjct: 119 IAQLAENCGIQALTIHGRT--------RSCLFNGEAEYDSIRSVKQ-IVSIPVIANGDIT 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           D  +A  +L     D +MIGRAA     +   +  Y              V +     I 
Sbjct: 170 DPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPMPLGEVQRLLNGHIR 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
                Y       G   +   +H+         + + R        AS      +E  F 
Sbjct: 230 ELHDFY-----GPGKGFRIARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 283

Query: 317 LM 318
            +
Sbjct: 284 NL 285


>gi|169824686|ref|YP_001692297.1| nitrogen regulation protein [Finegoldia magna ATCC 29328]
 gi|167831491|dbj|BAG08407.1| nitrogen regulation protein [Finegoldia magna ATCC 29328]
          Length = 305

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 130/302 (43%), Gaps = 32/302 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R     L    L +TEMI A  +   DKK   +L    +EK  ++QI G + 
Sbjct: 13  AGVTDIPFRILCGEL-GAGLCFTEMISAKGLYYDDKKTKKLLDTDPREKSTSVQIFGHEP 71

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A + + E++ +  I++N+GCP+ ++ +   G+ LM + ++  D I A      +P
Sbjct: 72  EIIAYATRFLTENYNFKSIDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLP 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G+D+   ++    L +  ++  V+ I +HAR   +              D+  
Sbjct: 132 VSVKFRLGIDE--NSMNYMQLAQICERLKVDYITLHARTRKMF--------YSGEADWLH 181

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  EN D+ +  NG         K +   + DGV++ R A +N  + +         
Sbjct: 182 IKRVV-ENVDIPVFGNGDCFTKEDIRKNMEYSNCDGVLLARGAMQNPFIFSD-------- 232

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +  K  V     + +   +  Y  R       + ++ +H+     GF NS + ++ 
Sbjct: 233 --DENKSKEEVIDTIKKHMQLKLEFYEERR-----AILEMRKHIQWYLKGFRNSNKVKNK 285

Query: 297 LT 298
           + 
Sbjct: 286 IN 287


>gi|83589019|ref|YP_429028.1| dihydrouridine synthase TIM-barrel protein nifR3 [Moorella
           thermoacetica ATCC 39073]
 gi|83571933|gb|ABC18485.1| tRNA-U20-dihydrouridine synthase [Moorella thermoacetica ATCC
           39073]
          Length = 334

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 78/315 (24%), Positives = 126/315 (40%), Gaps = 22/315 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TDR +R  AR     AL YTEMI A  ++  +K    +L    +  P+A+Q+ G +
Sbjct: 21  MAGYTDRVFRLLARE-AGAALTYTEMISAQGLIYNNKNTHALLDLKGEPGPVAVQLFGRE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              +  A +I    G   I+LN+GCP+ ++ +   G+ LM +       +AAM +A   +
Sbjct: 80  PEIMAAATRIAVAAGAAIIDLNMGCPTPKIVKNGEGSALMRDLPRAAAIVAAMVRAAGPV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D+    V           +    I    R     G            D+ 
Sbjct: 140 PVTVKMRLGWDEDSINVVEAARAVVYAGAAAVAIHGRTRSQFYSG----------RADWS 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               +K E  D+ +  NG +     A+ +L     DGVM+GR A  N  +LT +      
Sbjct: 190 YFRRVK-EAVDVPVIGNGDVRTARDAVTMLAETGCDGVMVGRGAVGNPWLLTAIRAVLEG 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    VD      ++                ++++ +H+   F G P + R R 
Sbjct: 249 -----RPEPPPVDVRTRMTMACRHLKLLVELKGETTAVKEMRKHLACYFRGLPGAARLRQ 303

Query: 296 ILTVEAGASTATHHI 310
            +     A+     I
Sbjct: 304 QINTLTTAAEVIAAI 318


>gi|87125619|ref|ZP_01081464.1| putative nitrogen regulation protein NifR3 family-like protein
           [Synechococcus sp. RS9917]
 gi|86166919|gb|EAQ68181.1| putative nitrogen regulation protein NifR3 family-like protein
           [Synechococcus sp. RS9917]
          Length = 343

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 73/324 (22%), Positives = 141/324 (43%), Gaps = 26/324 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADIS 60
              +DR +R   R    +ALL+TEM+ A ++  G  +  +    +E  P+ +Q+     +
Sbjct: 34  AGVSDRVFRSLVRRWAPDALLFTEMVNATSLELGHGRRKVEELAEESGPIGVQLFDHRPA 93

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+  E  G   I++N+GCP  ++     G+ L+  P++    +  +  A+SIPVT
Sbjct: 94  AMAEAARRAEAAGAFLIDINMGCPVRKIARKGGGSGLIQTPELACSIVETVAAAVSIPVT 153

Query: 121 VKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK R+G  ++   + A  +  + ++++G   + +H R         +        D+  +
Sbjct: 154 VKTRLGWSERETGSAAAVHWCRQLERAGAQLLTLHGRS--------RSQGFKGAADWQAI 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN-- 235
             + +E   + +  NG +     A + L      GVM+GR +     ++  +D       
Sbjct: 206 AAV-QEALTIPVIANGDVNSPEDARRCLTITGAAGVMVGRGSMGAPWLVGQIDAALCGRP 264

Query: 236 -PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            P T   P +  + +D    + AS  D+          L    +HM     GFP + + R
Sbjct: 265 IPATPGGPERLELARDQLLALVASRGDH---------GLLIARKHMSWTCTGFPGAPQLR 315

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
           H L + A    A   ++++A   +
Sbjct: 316 HAL-MRAPTPAAALELLDSARQTL 338


>gi|91791809|ref|YP_561460.1| dihydrouridine synthase TIM-barrel protein nifR3 [Shewanella
           denitrificans OS217]
 gi|91713811|gb|ABE53737.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Shewanella
           denitrificans OS217]
          Length = 322

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 135/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +   +K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAALAVSEMLSSNPEVWDTEKSRQRMTHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA+   + G + I++N+GCP+ +V++   G+ LM +P +V D + A+  A+ +P
Sbjct: 76  PDLMANAAQFNVEQGAHIIDINMGCPAKKVNKKFAGSALMQDPALVKDILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWDPEHKNGV--QIAQIAQDCGIASLAVHGRT--------RQCMYKGFAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG ++   +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NISIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFKEIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +              ++     Y          ++   +H     +     R+ R  
Sbjct: 245 KKLAPIEIHEQRLVMLEHLTKLYELY-----GEYKGVRFARKHTGWYLN-QEEQRQFRAD 298

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 A    + ++E  F+ ++++
Sbjct: 299 FNRLESADQ-QYSLVECYFDELVKN 322


>gi|94263194|ref|ZP_01287011.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
 gi|93456412|gb|EAT06532.1| Dihydrouridine synthase TIM-barrel protein nifR3 [delta
           proteobacterium MLMS-1]
          Length = 313

 Score =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 68/301 (22%), Positives = 118/301 (39%), Gaps = 31/301 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   R      L Y+EM+    ++R       +L  +  E+PL +Q+ GA+ 
Sbjct: 21  AGYSDLPFRLLCREY-GAGLCYSEMLSCHGLVRRQPATIEMLATTAAERPLLMQLFGAEP 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             + EAA I+     + I++N+GCP  +V +   GA LM +P++      A+   A  +P
Sbjct: 80  EVMGEAAAILSRLPIDGIDINMGCPVRKVVKKGAGAALMRDPELAAAITGAVTAAAGDLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G       +   +  + +   G   + IHAR           +      D+ +
Sbjct: 140 VTVKIRSGW--NHKQINAPDFARLLVAHGAAAVTIHARTW--------SDGFTGRADWAV 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +    QAL ++     DGVMIGR A     +          P
Sbjct: 190 IAAVKRAV-SVPVIGNGDIGSYEQALAMMAATGCDGVMIGRGALGAPWVF--------TP 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P   +      R +         RH        ++   +   F   P   R R  
Sbjct: 241 GAEQNPPLAQRLAAARRHLELI------RHWRPADNPARVRNQLGRYFKKIPGGARLRRQ 294

Query: 297 L 297
           +
Sbjct: 295 I 295


>gi|15640319|ref|NP_229946.1| NifR3/Smm1 family protein [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121727027|ref|ZP_01680218.1| NifR3/Smm1 family protein [Vibrio cholerae V52]
 gi|153801529|ref|ZP_01956115.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-3]
 gi|153822836|ref|ZP_01975503.1| NifR3/Smm1 family protein [Vibrio cholerae B33]
 gi|254286235|ref|ZP_04961194.1| NifR3/Smm1 family protein [Vibrio cholerae AM-19226]
 gi|254851428|ref|ZP_05240778.1| NifR3/Smm1 family protein [Vibrio cholerae MO10]
 gi|297581755|ref|ZP_06943677.1| NifR3/Smm1 family protein [Vibrio cholerae RC385]
 gi|9654702|gb|AAF93465.1| NifR3/Smm1 family protein [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121630538|gb|EAX62928.1| NifR3/Smm1 family protein [Vibrio cholerae V52]
 gi|124122934|gb|EAY41677.1| NifR3/Smm1 family protein [Vibrio cholerae MZO-3]
 gi|126519654|gb|EAZ76877.1| NifR3/Smm1 family protein [Vibrio cholerae B33]
 gi|150423650|gb|EDN15592.1| NifR3/Smm1 family protein [Vibrio cholerae AM-19226]
 gi|254847133|gb|EET25547.1| NifR3/Smm1 family protein [Vibrio cholerae MO10]
 gi|297534162|gb|EFH73001.1| NifR3/Smm1 family protein [Vibrio cholerae RC385]
          Length = 331

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIETADQ-QLDALEGYFDNV 329


>gi|288940563|ref|YP_003442803.1| TIM-barrel protein, nifR3 family [Allochromatium vinosum DSM 180]
 gi|288895935|gb|ADC61771.1| TIM-barrel protein, nifR3 family [Allochromatium vinosum DSM 180]
          Length = 338

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 135/322 (41%), Gaps = 21/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L    L   EM+ A+  L G +K++  L +  +  P++ QI G+D
Sbjct: 24  MAGITDRPFRTLCRRL-GAGLAVAEMVAANTALWGSRKSLRRLDYRDEPGPISAQIVGSD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAA++  + G + +++N+GCP+ +V + + G+ L+ +   V   + A+  A+  P
Sbjct: 83  PAEMAEAARLNVELGAHIVDINMGCPAKKVCKVAAGSALLRDETRVARILEAVVAAVEAP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  ++SG+  + +H R       +P         +YD 
Sbjct: 143 VTLKIRTGWSPEERNAV--RIARIARESGIAALTVHGRTRACTYGAP--------AEYDT 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I + + D+ +  NG +     A ++L     D +MIGRAA     +   +    ++ 
Sbjct: 193 IRAI-RASVDIPLIANGDIASAQDARRVLDYTGADAIMIGRAAQGRPWIFGDIAAGLASE 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               S             +   +    A H      ++   +H+       P +   R  
Sbjct: 252 PAHPSESPNAPRHWIKDILREHLESLYAFH-GDYAGVRIARKHIAWYCRHLPGAASFRDT 310

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +     AS      +  A   +
Sbjct: 311 INTTESAS----EQLRLALAFL 328


>gi|108801475|ref|YP_641672.1| dihydrouridine synthase TIM-barrel protein nifR3 [Mycobacterium sp.
           MCS]
 gi|119870628|ref|YP_940580.1| nifR3 family TIM-barrel protein [Mycobacterium sp. KMS]
 gi|108771894|gb|ABG10616.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Mycobacterium sp.
           MCS]
 gi|119696717|gb|ABL93790.1| putative TIM-barrel protein, nifR3 family [Mycobacterium sp. KMS]
          Length = 370

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 123/319 (38%), Gaps = 29/319 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F++ E P +L
Sbjct: 10  MAGVTNVAFRTLCRELEVARAGTVSGLYVCEMVTARALVERHPVTMHMTAFASDESPRSL 69

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D    + I++N GCP  +V +   GA L     + G  + A 
Sbjct: 70  QLYTVDPATTYAAAKMIADENMADHIDMNFGCPVPKVTKRGGGAALPYKRKLFGQIVRAA 129

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             A     IPVTVK RIG+DD        +  +   + G   + +HAR A          
Sbjct: 130 VTATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAAEEGAAAVALHARTA--------AQ 179

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKNSAML 226
           R     D+D +  +K     + +  NG +   D + A+      DGV+IGR       + 
Sbjct: 180 RYSGTADWDQIAALKAHVTAVPVLGNGDIFDADDALAMMAATGCDGVVIGRGCLGRPWLF 239

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+       P    V       I     +    H      ++ I +H+    HG
Sbjct: 240 AELSAKFTGRPLPVPPTLGEVA-----DIIRRHGELLTDHFGEDKAMRDIRKHIAWYLHG 294

Query: 287 FPNSRRCRHILTVEAGAST 305
           FP     R  L +    + 
Sbjct: 295 FPAGSDLRRALALVKTRAE 313


>gi|229509284|ref|ZP_04398767.1| tRNA dihydrouridine synthase B [Vibrio cholerae B33]
 gi|229512700|ref|ZP_04402168.1| tRNA dihydrouridine synthase B [Vibrio cholerae TMA 21]
 gi|229516228|ref|ZP_04405676.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC9]
 gi|229527213|ref|ZP_04416606.1| tRNA dihydrouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229606424|ref|YP_002877072.1| tRNA dihydrouridine synthase B [Vibrio cholerae MJ-1236]
 gi|38605062|sp|Q9KV66|DUSB_VIBCH RecName: Full=tRNA-dihydrouridine synthase B
 gi|229335221|gb|EEO00705.1| tRNA dihydrouridine synthase B [Vibrio cholerae 12129(1)]
 gi|229346654|gb|EEO11624.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC9]
 gi|229350210|gb|EEO15162.1| tRNA dihydrouridine synthase B [Vibrio cholerae TMA 21]
 gi|229353599|gb|EEO18536.1| tRNA dihydrouridine synthase B [Vibrio cholerae B33]
 gi|229369079|gb|ACQ59502.1| tRNA dihydrouridine synthase B [Vibrio cholerae MJ-1236]
          Length = 322

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 186 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 300 FNAIETADQ-QLDALEGYFDNV 320


>gi|312796563|ref|YP_004029485.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
 gi|312168338|emb|CBW75341.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
          Length = 233

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 99/203 (48%), Positives = 138/203 (67%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R L+ +  LYTEM+   A+L GD    L F+ QE P+ALQ+GG++  
Sbjct: 30  MMDWTDRHCRYFHRQLSRHVYLYTEMVTTGALLFGDVARHLSFTPQEAPIALQLGGSEPD 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E +GY+E+NLN GCPS RV  G+FGACLM    +V DC+ AMC A+++PVT
Sbjct: 90  ELARCAKLSEQWGYDEVNLNCGCPSERVQRGAFGACLMKEATLVADCVKAMCDAVAVPVT 149

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIGVD       +R+ V ++ + G     +HAR AILKGLSPK+NR+IP L YD  Y
Sbjct: 150 VKHRIGVDAIDDYGFVRDFVGTVAQGGCRVFIVHARNAILKGLSPKENREIPPLKYDYAY 209

Query: 181 EIKKENPDLFIGLNGGLEDMSQA 203
            +K++ P+  I +NGG++ + + 
Sbjct: 210 RLKRDFPEFEIVINGGIKTLDEG 232


>gi|171742467|ref|ZP_02918274.1| hypothetical protein BIFDEN_01579 [Bifidobacterium dentium ATCC
           27678]
 gi|171278081|gb|EDT45742.1| hypothetical protein BIFDEN_01579 [Bifidobacterium dentium ATCC
           27678]
          Length = 409

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 117/318 (36%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 49  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPGEKIRSLQLYGVN 108

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 109 PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 169 ANVPVTAKIRVGIDHE--HETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 218

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 219 DWSRIGELVGAL-DIPVFGNGDVWGANDALAMVSETGCAGVAIGRGCQGRPWLFADIKNA 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V     R        Y      +   +  + +H+     GFP    
Sbjct: 278 FAGSDERIDPALGDVCTVIERHAQLLTEFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 334

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 335 TRRAFMECENLEDVRREI 352


>gi|227512326|ref|ZP_03942375.1| tRNA-dihydrouridine synthase [Lactobacillus buchneri ATCC 11577]
 gi|227084501|gb|EEI19813.1| tRNA-dihydrouridine synthase [Lactobacillus buchneri ATCC 11577]
          Length = 335

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 132/321 (41%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 19  MAGVTNSAFRIICKEF-GAGLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+     + I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  
Sbjct: 78  KETLVQAAKFVDQNTAADIIDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + + +H R         +    + + ++D
Sbjct: 138 PVTVKMRTGWDEDHIYAVENALA--AERAGASALAMHGRT--------RKQMYMGHANWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++  +   +    NG +     A K+L     D VM+GRA   N  +L+ V+ Y   
Sbjct: 188 ILKQVAGQL-HIPFMGNGDVRTPQDAKKMLEDVGADAVMMGRAVEGNPWVLSQVEHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P   +        +   + +    H+ S     +          G  +S R + 
Sbjct: 247 GDILPEPTPEKKVATAKEHLHR-LVELKGDHVGS----HEFRGQAGYYLKGISHSARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFN 316
            L V A    A   I +    
Sbjct: 302 AL-VNADGEQAMDDIFDQFLE 321


>gi|312866800|ref|ZP_07727013.1| TIM-barrel protein, nifR3 family [Streptococcus parasanguinis
           F0405]
 gi|311097583|gb|EFQ55814.1| TIM-barrel protein, nifR3 family [Streptococcus parasanguinis
           F0405]
          Length = 335

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 137/322 (42%), Gaps = 27/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 202 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   + +    H+     +++          G   + + R 
Sbjct: 262 GEILPDLTFEDKMKIAYEHLKR-LINLKGEHIA----VREFRGLAPHYLRGTSGAAKLRG 316

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            ++  +  +      IE    L
Sbjct: 317 AISQASTLAE-----IEELLQL 333


>gi|121609971|ref|YP_997778.1| nifR3 family TIM-barrel protein [Verminephrobacter eiseniae EF01-2]
 gi|121554611|gb|ABM58760.1| putative TIM-barrel protein, nifR3 family [Verminephrobacter
           eiseniae EF01-2]
          Length = 348

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 114/306 (37%), Gaps = 24/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EMI A   L    K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKAL-GAGYAVSEMITARKDLWSSLKTSRRANHDGEPGPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + EAA    + G   I++N+GCP+ +V     G+ LM +  +      A+  A    
Sbjct: 76  AAMMAEAALYNIERGAQIIDINMGCPAKKVCRQWAGSALMQDEALAVAIARAVVAACAPH 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G   Q        L +  +  G+  + +H R         ++       +
Sbjct: 136 RVPVTLKMRTGWCQQHKNA--PQLARQFESVGIQMLTVHGRT--------REQGYGGQAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  +K     + +  NG +    +A  +L     D +MIGRAA     +   V  + 
Sbjct: 186 YETIAAVKAAVG-VPVVANGDITTPEKARAVLAATGADAIMIGRAAQGRPWIFREVGHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   + +     +    + Y          ++   +H+       P     
Sbjct: 245 ATGEHLAPPLVAELRRLLLAHLQDHYSLY-----GEPIGVRSARKHIAWYLRALPGGEAF 299

Query: 294 RHILTV 299
           R  +  
Sbjct: 300 RQHINT 305


>gi|120597327|ref|YP_961901.1| nifR3 family TIM-barrel protein [Shewanella sp. W3-18-1]
 gi|146294528|ref|YP_001184952.1| nifR3 family TIM-barrel protein [Shewanella putrefaciens CN-32]
 gi|120557420|gb|ABM23347.1| putative TIM-barrel protein, nifR3 family [Shewanella sp. W3-18-1]
 gi|145566218|gb|ABP77153.1| putative TIM-barrel protein, nifR3 family [Shewanella putrefaciens
           CN-32]
 gi|319427893|gb|ADV55967.1| TIM-barrel protein, nifR3 family [Shewanella putrefaciens 200]
          Length = 322

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 141/325 (43%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQVFRNLCLRY-GAALAVSEMLSSNPDVWETDKSRQRMMHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G + I++N+GCP+ +V++   G+ LM NP +V   + A+  A+++P
Sbjct: 76  PDLMAQAAQFNVEQGAHIIDINMGCPAKKVNKKLAGSALMQNPPLVKAILQAVVAAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGV--QIAQIAEDCGIASLAVHGRT--------RQCMYKGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG ++   +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NVSIPVVANGDIDSPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +PI+    ++   +    + D    +      ++   +HM          R+ R  
Sbjct: 245 -NKLAPIEVAQQREVMLEHLTKLYDLYGEY----KGIRFARKHMGWYLDQEAQ-RQFRAD 298

Query: 297 LTVEAGASTATHHIIETAFNLMIES 321
                 A+   + ++E  F+ + ++
Sbjct: 299 FNRLETAAE-QYSLVECYFDELAQN 322


>gi|319442510|ref|ZP_07991666.1| hypothetical protein CvarD4_12149 [Corynebacterium variabile DSM
           44702]
          Length = 402

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 116/320 (36%), Gaps = 38/320 (11%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        + + L   EMI A A++  + K   +  F   E P +L
Sbjct: 30  MAGVTNVAFRTLCREQEEQRTGSASGLYVCEMITARALVERNPKTLHMTTFGPDESPRSL 89

Query: 53  QIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AA++  E+   + I++N GCP  +V     G+ L     +    + A 
Sbjct: 90  QLYTTDPEYTYKAARMLAEEDRADHIDMNFGCPVPKVTRRGGGSALPYKRKLFAAVVGAA 149

Query: 112 CKALS----------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            + ++          IPVTVK R+G+DD+       +  +     G   + +H R A   
Sbjct: 150 VRGVADAGRASGPDAIPVTVKFRVGIDDEHH--THLDAGRIAADQGAAAVTLHGRTA--- 204

Query: 162 GLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGR 217
                  R     D+  +  + +  +   + +  NG +     + A+      DGV++GR
Sbjct: 205 -----AQRYSGTADWGEIARLVEHMDGTGIPVLGNGDIFKATDAAAMMEQTGCDGVVVGR 259

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  +   +  +       + P    V       I     +  A H       + I 
Sbjct: 260 GCLGRPWLFAELSAHLRGEEIPAEPTLGEVA-----HIILRHAELLADHDGEKYASRDIR 314

Query: 278 RHMIGLFHGFPNSRRCRHIL 297
           +H+     GFP     R  L
Sbjct: 315 KHIAWYLRGFPAGGEMRRQL 334


>gi|300932473|ref|ZP_07147729.1| hypothetical protein CresD4_00255 [Corynebacterium resistens DSM
           45100]
          Length = 394

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 74/336 (22%), Positives = 127/336 (37%), Gaps = 35/336 (10%)

Query: 1   MVDWTDRHYRFFARLLTNN------ALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R            L   EM+ A A++  + K   +  F   E+P +L
Sbjct: 33  MAGITNVAFRTLCREQEREKIGSVSGLYVCEMVTARALVERNPKTLHMTTFGPDEQPRSL 92

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     EAAK++ D    + I++N GCP  +V     G+ L     + G+ +AA 
Sbjct: 93  QLYTTDPKYTYEAAKMIVDENMADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAA 152

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +     G   + +HAR A          
Sbjct: 153 VKATEGTDIPVTVKFRVGIDDEHH--THLDAGRIAADEGAAAVALHARTA--------AQ 202

Query: 169 RKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
           R   + ++D +  + +     + +  NG +   + A  ++     DGV++GR       +
Sbjct: 203 RYSGDANWDEITRLVEHMDGRVPVLGNGDIFKATDARAMMDRTGCDGVVVGRGCLGRPWL 262

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +          + P    V +   R       +  A H       + + +HM     
Sbjct: 263 FAELAAELQGLPVPAPPTLGEVARIVLRHA-----ELLAEHDGEFKACRDMRKHMTWYMR 317

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           GFP     R  L      +      +  A + + ES
Sbjct: 318 GFPAGGEIRRTLATIESLAD-----LRAALDPIWES 348


>gi|126437460|ref|YP_001073151.1| nifR3 family TIM-barrel protein [Mycobacterium sp. JLS]
 gi|126237260|gb|ABO00661.1| putative TIM-barrel protein, nifR3 family [Mycobacterium sp. JLS]
          Length = 370

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 123/319 (38%), Gaps = 29/319 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLAL 52
           M   T+  +R   R L      T + L   EM+ A A++       ++  F++ E P +L
Sbjct: 10  MAGVTNVAFRTLCRELEVARAGTVSGLYVCEMVTARALVERHPVTMHMTAFASDESPRSL 69

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D +    AAK++ D    + I++N GCP  +V +   GA L     + G  + A 
Sbjct: 70  QLYTVDPATTYAAAKMIADENMADHIDMNFGCPVPKVTKRGGGAALPYKRKLFGQIVRAA 129

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             A     IPVTVK RIG+DD        +  +   + G   + +HAR A          
Sbjct: 130 VTATEGTDIPVTVKFRIGIDD--AHHTHLDAGRIAAEEGAAAVALHARTA--------AQ 179

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKNSAML 226
           R     D+D +  +K     + +  NG +   D + A+      DGV+IGR       + 
Sbjct: 180 RYSGTADWDQIAALKAHVTAVPVLGNGDIFDADDALAMMAATGCDGVVIGRGCLGRPWLF 239

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
             +   F+       P    V       I     +    H      ++ I +H+    HG
Sbjct: 240 AELSAKFTGRPLPVPPTLGEVA-----DIIRRHGELLTDHFGEDKAMRDIRKHIAWYLHG 294

Query: 287 FPNSRRCRHILTVEAGAST 305
           FP     R  L +    + 
Sbjct: 295 FPAGSDLRRALALVKTRAE 313


>gi|329894590|ref|ZP_08270396.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC3088]
 gi|328922944|gb|EGG30272.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC3088]
          Length = 325

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 67/290 (23%), Positives = 122/290 (42%), Gaps = 20/290 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG-FSTQEKPLALQIGGADI 59
           M   +D  +R    L    +    EMI A+   R  +K+         +   +QI G D 
Sbjct: 18  MAGVSDLPFRRLC-LEHGASYAVAEMISANPDTRQTQKSQWRSVIDSNQAHIVQIVGHDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L EAA++ ++ G + I++N+GCP+ +V + + G+ L+ N  +V D + A+  A+ IPV
Sbjct: 77  EQLAEAARLNQEAGADIIDINMGCPAKKVCKKAAGSALLANEALVQDILVAVKSAVDIPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G            L+   + +G+  + IH R         K       ++YD +
Sbjct: 137 TLKIRTGTSPNERNATTIALI--AQDAGIAALTIHGRT--------KACAFKGAVEYDTI 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+     D+ +  NG +    QALK+L      G+M+GR A     +L  +   +    
Sbjct: 187 AEVV-SRVDIPVIANGDITHPDQALKVLNYTGAAGIMVGRGAQGQPWLLGQIKHKWRTGE 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
              +P +       ++ ++A    Y          ++   +H    F   
Sbjct: 246 VLEAPSRETKLHIAYQHVAAIHEFYGDFM-----GVRFARKHASWYFESM 290


>gi|121586356|ref|ZP_01676145.1| NifR3/Smm1 family protein [Vibrio cholerae 2740-80]
 gi|147675018|ref|YP_001218564.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|153820017|ref|ZP_01972684.1| NifR3/Smm1 family protein [Vibrio cholerae NCTC 8457]
 gi|227080505|ref|YP_002809056.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|298500925|ref|ZP_07010727.1| NifR3/Smm1 family protein [Vibrio cholerae MAK 757]
 gi|121549476|gb|EAX59504.1| NifR3/Smm1 family protein [Vibrio cholerae 2740-80]
 gi|126509439|gb|EAZ72033.1| NifR3/Smm1 family protein [Vibrio cholerae NCTC 8457]
 gi|146316901|gb|ABQ21440.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|227008393|gb|ACP04605.1| NifR3/Smm1 family protein [Vibrio cholerae M66-2]
 gi|227012150|gb|ACP08360.1| NifR3/Smm1 family protein [Vibrio cholerae O395]
 gi|297540429|gb|EFH76488.1| NifR3/Smm1 family protein [Vibrio cholerae MAK 757]
          Length = 331

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIETADQ-QLDALEGYFDNV 329


>gi|319891470|ref|YP_004148345.1| tRNA dihydrouridine synthase B [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317161166|gb|ADV04709.1| tRNA dihydrouridine synthase B [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 330

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 139/326 (42%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L     E+PL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILFNNPKTMKMLYIDENERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+ +   + I++N+GCP +++ +   GA  +L+P+ + + ++A+ + +S 
Sbjct: 77  KETLVEAAEYVDKNTTADIIDINMGCPVSKIIKCEAGARWLLDPNKIYEMVSAVTERVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RIG D+    +      K+ +++G   I +H R  +               D+D
Sbjct: 137 PVTCKMRIGWDED--HIFAVENAKAAERAGAAAISLHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG +     A K+L    VD VMIGR A  N  M+     Y   
Sbjct: 187 IIRQVK-EAVNIPVIGNGDVTSPELAEKMLKETGVDAVMIGREALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                + ++ +H+     G   + + R 
Sbjct: 246 GELIDEPQIDEKIEIALLHLNR-----LVDLKGEKVGVMEMRKHVSWYLKGVRGNGKARK 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L      +  T  I+    +  +E 
Sbjct: 301 ALNQAETLAEMT-EILTEFRDEQMEK 325


>gi|148238900|ref|YP_001224287.1| tRNA-dihydrouridine synthase [Synechococcus sp. WH 7803]
 gi|147847439|emb|CAK22990.1| Probable tRNA-dihydrouridine synthase [Synechococcus sp. WH 7803]
          Length = 338

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 133/327 (40%), Gaps = 29/327 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADIS 60
              +D+ +R   R  + +ALL+TEM+ A ++  G  +  +    QE  P+ +Q+      
Sbjct: 30  AGVSDKIFRALVRRWSLDALLFTEMVNATSLELGHGRGKVEELQQEAGPIGVQLFDHRPE 89

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  E  G   I++N+GCP  ++     G+ L+ +PD+    + A+  A+ IPVT
Sbjct: 90  AMADAARRAEAAGAFLIDINMGCPVRKIARKGGGSGLIRDPDLACSIVEAVVAAVGIPVT 149

Query: 121 VKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           VK R+G            A  +  + ++ +G   + +H R         ++ R     ++
Sbjct: 150 VKTRLGWCSDPQTADNHAAAMDWCRRLEAAGAQLLTLHGRT--------REQRFSGRANW 201

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K+    + +  NG +     A   L     DGVM+GR       ++  +D    
Sbjct: 202 EAIAAVKR-TLRIPVIANGDVFSPEDARACLEITGADGVMVGRGTMGAPWLVGQIDAALK 260

Query: 235 NPLTGSSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                 +P       +  D  + + A+  D+          L    +HM     GF  + 
Sbjct: 261 GRPVPPTPSARERLTIAADQLQALVAARGDH---------GLLIARKHMSWTCTGFNGAS 311

Query: 292 RCRHILTVEAGASTATHHIIETAFNLM 318
           + R  L + A        ++    + +
Sbjct: 312 QFRQQL-MRAPTPDQALSLLRQQQDQL 337


>gi|269962458|ref|ZP_06176807.1| tRNA-dihydrouridine synthase B [Vibrio harveyi 1DA3]
 gi|269832754|gb|EEZ86864.1| tRNA-dihydrouridine synthase B [Vibrio harveyi 1DA3]
          Length = 331

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 126/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ A+  L G  K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 85  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + K  +  G+  + +H R         K        +YD 
Sbjct: 145 VTLKTRTGWNTENKNCVH--IAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 195 IKAVKHAI-SIPVIANGDIDSPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMDELPSEEVKTIMLGHVNALHDFYGEF-----LGPRIARKHVGWYLKEHEQASEFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      +E  F+ +
Sbjct: 309 FNA-IDAAELQLEALEGYFDNV 329


>gi|229506911|ref|ZP_04396419.1| tRNA dihydrouridine synthase B [Vibrio cholerae BX 330286]
 gi|229356016|gb|EEO20935.1| tRNA dihydrouridine synthase B [Vibrio cholerae BX 330286]
          Length = 322

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 186 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 300 FNAIETADQ-QLDALEGYFDNV 320


>gi|227509314|ref|ZP_03939363.1| tRNA-dihydrouridine synthase [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227191244|gb|EEI71311.1| tRNA-dihydrouridine synthase [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 335

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 133/324 (41%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 19  MAGVTNSAFRIICKEF-GAGLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+     + I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  
Sbjct: 78  KETLVQAAKFVDQNTAADIIDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + + +H R         +    + + ++D
Sbjct: 138 PVTVKMRTGWDEDHIYAVENALA--AERAGASALAMHGRT--------RKQMYMGHANWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG +     A K+L     D VM+GRA   N  +L+ V+ Y   
Sbjct: 188 ILKEVAGQL-HIPFMGNGDVRTPQDAKKMLEDVGADAVMMGRAVEGNPWVLSQVEHYLET 246

Query: 236 PLTGSSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                 P   +     K+   ++     D+   H   G               G  +S R
Sbjct: 247 GDILPEPTPEKKIATAKEHLHRLVELKGDHVGSHEFRGQS--------GYYLKGISHSAR 298

Query: 293 CRHILTVEAGASTATHHIIETAFN 316
            +  L V A    A   I +    
Sbjct: 299 TKVAL-VNADGEQAMDDIFDQFLE 321


>gi|319946107|ref|ZP_08020355.1| tRNA-dihydrouridine synthase [Streptococcus australis ATCC 700641]
 gi|319747753|gb|EFV99998.1| tRNA-dihydrouridine synthase [Streptococcus australis ATCC 700641]
          Length = 326

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 137/322 (42%), Gaps = 27/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   + +    H+     +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKR-LINLKGEHIA----VREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            ++  +  +      IE    L
Sbjct: 307 AISQASTLAE-----IEELLQL 323


>gi|227833973|ref|YP_002835680.1| hypothetical protein cauri_2149 [Corynebacterium aurimucosum ATCC
           700975]
 gi|262183538|ref|ZP_06042959.1| hypothetical protein CaurA7_06061 [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454989|gb|ACP33742.1| hypothetical protein cauri_2149 [Corynebacterium aurimucosum ATCC
           700975]
          Length = 381

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 72/314 (22%), Positives = 126/314 (40%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  + K   +  F  QE+P +L
Sbjct: 19  MAGVTNVAFRVLCREQEIEKTGTVSGLYVCEMVTARALVERNPKTLHMTTFDPQEQPRSL 78

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V     G+ L     + G+ +AA 
Sbjct: 79  QLYTVDPEYTYKAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAA 138

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+D++       +  +     G   + +H R A          
Sbjct: 139 VKATEGTDIPVTVKMRVGIDEEHK--THLDAGRIAVAEGAAAVALHGRTA--------AQ 188

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   + D+  +  +K+   D  + +  NG +   + A  ++     DGV++GR       
Sbjct: 189 RYSGHADWGEIARLKEHLADTGIPVLGNGDIFKATDAHDMMKQTGCDGVVVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +  +         P    V +   R       +  A+H       + I +H+    
Sbjct: 249 LFAELSAHLRGEPVPEEPTLGEVTRIMIRHA-----ELLAQHEGEAQASRDIRKHIGWYL 303

Query: 285 HGFPNSRRCRHILT 298
            GFP   + R  L+
Sbjct: 304 RGFPVGGQVRAGLS 317


>gi|199598783|ref|ZP_03212195.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus HN001]
 gi|229551627|ref|ZP_04440352.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258509504|ref|YP_003172255.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus GG]
 gi|258540706|ref|YP_003175205.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus Lc 705]
 gi|199590288|gb|EDY98382.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus HN001]
 gi|229315031|gb|EEN81004.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257149431|emb|CAR88404.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus GG]
 gi|257152382|emb|CAR91354.1| tRNA-dihydrouridine synthase 1 [Lactobacillus rhamnosus Lc 705]
 gi|259650775|dbj|BAI42937.1| tRNA-dihydrouridine synthase [Lactobacillus rhamnosus GG]
          Length = 333

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 134/322 (41%), Gaps = 23/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 18  MAGVTNAAFRVTAKEF-GAGLVVCEMISDRGIMYKNKKTLSMLFVDPREHPISIQIFGGT 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+     + I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S 
Sbjct: 77  KETLVNAAKFVDQNTAADIIDINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D++
Sbjct: 137 PVTVKMRTGWDEDHIYAVQNALA--AERGGAAALAMHGRT--------RKQLYSGHADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+     FIG NG +     A ++L     D VM+GRAA  N  +L  +  Y  +
Sbjct: 187 ILKEVKQHLSIPFIG-NGDVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMAAYLDH 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++   +  +          +++          G P S + + 
Sbjct: 246 GELIPEPTPREKIATAKLQLQRLVDLHGEHQ-----AVREFRMQAAYYLKGIPRSAKTKA 300

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            + +    +    HI +     
Sbjct: 301 AVNMVDTQAEVN-HIFDDFVAQ 321


>gi|229524749|ref|ZP_04414154.1| tRNA dihydrouridine synthase B [Vibrio cholerae bv. albensis VL426]
 gi|229338330|gb|EEO03347.1| tRNA dihydrouridine synthase B [Vibrio cholerae bv. albensis VL426]
          Length = 322

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 129/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 186 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y A   + G ++    +H+         +   R  
Sbjct: 245 TTMPELPISEVKDIMLGHVTALHQFYGA---YLGPRI--ARKHVSWYLQEHEQASAFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 300 FNAIETAEQ-QLDALEGYFDNV 320


>gi|227522412|ref|ZP_03952461.1| tRNA-dihydrouridine synthase [Lactobacillus hilgardii ATCC 8290]
 gi|227090470|gb|EEI25782.1| tRNA-dihydrouridine synthase [Lactobacillus hilgardii ATCC 8290]
          Length = 335

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 132/321 (41%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 19  MAGVTNSAFRIICKEF-GAGLVVCEMISDRGIMYKNKKTLDMMFVDPREHPMSIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+     + I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  
Sbjct: 78  KETLVQAAKFVDQNTAADIIDINMGCPVNKVVKTDAGARWLLDPKKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    +++G + + +H R         +    + + ++D
Sbjct: 138 PVTVKMRTGWDEDHIYAVENALA--AERAGASDLAMHGRT--------RKQMYMGHANWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++  +   +    NG +     A K+L     D VM+GRA   N  +L+ V+ Y   
Sbjct: 188 ILKQVAGQL-HIPFMGNGDVRTPQDAKKMLEDVGADAVMMGRAVEGNPWVLSQVEHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P   +        +   + +    H+ S     +          G  +S R + 
Sbjct: 247 GDILPEPTPEKKIATAKEHLHR-LVELKGDHVGS----HEFRGQAGYYLKGISHSARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFN 316
            L V A    A   I +    
Sbjct: 302 AL-VNADGEQAMDDIFDQFLE 321


>gi|322390392|ref|ZP_08063914.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC 903]
 gi|321142903|gb|EFX38359.1| tRNA-dihydrouridine synthase [Streptococcus parasanguinis ATCC 903]
          Length = 325

 Score =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 137/322 (42%), Gaps = 27/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLRDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   + +    H+     +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKR-LINLKGEHIA----VREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            ++  +  +      IE    L
Sbjct: 307 AISQASTLAE-----IEELLQL 323


>gi|259047582|ref|ZP_05737983.1| tRNA-dihydrouridine synthase [Granulicatella adiacens ATCC 49175]
 gi|259035773|gb|EEW37028.1| tRNA-dihydrouridine synthase [Granulicatella adiacens ATCC 49175]
          Length = 348

 Score =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 74/324 (22%), Positives = 128/324 (39%), Gaps = 26/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   ++K   +L     E PL++QI G +
Sbjct: 29  MAGISNSAFRVTVKEF-GAGLVVCEMISDKGIQFRNEKTLSMLHIEPNEYPLSVQIMGGN 87

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +      I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+  
Sbjct: 88  KDTLVEAAKYVAENTEAAIIDINMGCPVNKVIKAEAGAKWLLDPNKVYEMVAAVVDAVDK 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +        L    + +G + + +H R  +               D++
Sbjct: 148 PVTVKMRTGWDHEHLYAVENALA--AEHAGASAVAMHGRTRV--------QMYDGKADWE 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+KK    + +  NG +     A +++    VDGVMIGRAA  N  M+     Y   
Sbjct: 198 ILGEVKKNLTRIPLIGNGDVRSPEDAKRMIDIAGVDGVMIGRAALANPWMIRQTVHYLET 257

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                             +I+       A         ++  +       G P + + + 
Sbjct: 258 GELLPENTVPEKI-----EIAKLHLQRLANLKGEAVATKEFRKLAGYYLKGVPRASKTKV 312

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
            +             +E   +  +
Sbjct: 313 AINE-----AENLQTVEALLDQFV 331


>gi|296130021|ref|YP_003637271.1| TIM-barrel protein, nifR3 family [Cellulomonas flavigena DSM 20109]
 gi|296021836|gb|ADG75072.1| TIM-barrel protein, nifR3 family [Cellulomonas flavigena DSM 20109]
          Length = 442

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 121/305 (39%), Gaps = 23/305 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R  +   L   EM+ + A++    +   I+ F   E P ++Q+ G D
Sbjct: 83  MAGVTNAAFRRLCRE-SGAGLYVAEMLTSRALVERSPESFRIIAFEPDEVPRSVQVYGVD 141

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            + +  A ++ VE+   + ++LN GCP  +V     GA L    ++    + A   A   
Sbjct: 142 PATVGAAVRLLVEEDRADHVDLNFGCPVPKVTRRGGGAVLPWKRELFASIVRAAVDAARP 201

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+D+         L  + + +GV  + +H R A         +      
Sbjct: 202 HGVPVTVKMRKGIDEDHLTYVEAGL--TAQDAGVAAVALHGRTA--------ADYYSGTA 251

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K+   D+ +  NG +     AL ++     DGV++GR       +   +   
Sbjct: 252 DWDAIATLKEAVTDIPVLGNGDIWSAEDALAMVAHTRCDGVVVGRGCQGRPWLFADLAAA 311

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V     R     +  +          L+++ +HM   F G+     
Sbjct: 312 FAGSDVRIRPGLRDVAHVVRRHAELMVDHF----DDENKALREMRKHMAWYFKGYVVGGE 367

Query: 293 CRHIL 297
            R  L
Sbjct: 368 LRAQL 372


>gi|269215618|ref|ZP_06159472.1| tRNA-dihydrouridine synthase B [Slackia exigua ATCC 700122]
 gi|269131105|gb|EEZ62180.1| tRNA-dihydrouridine synthase B [Slackia exigua ATCC 700122]
          Length = 318

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 129/331 (38%), Gaps = 29/331 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    D  +R    L     L YTEMI + A+   ++K   +L  +  E+ +A+Q+ G +
Sbjct: 1   MAGVNDIVFRRLC-LEQGCDLTYTEMISSKALSFANEKTRHLLDLAEGERRVAIQLFGHE 59

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +   A  VED   +    I++N+GCP+ ++ +   G+ LM + D+    +  + +A+
Sbjct: 60  PKVMAREAAWVEDELGDALALIDINMGCPAHKIVKKGDGSALMRDQDLAASIVRDVARAV 119

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S PVTVK R G   +       +    ++ +G   + +H R A      P +        
Sbjct: 120 SCPVTVKFRRGFGAEEETAV--DFGLRMEDAGAAAVTVHGRTAAQMYRGPSE-------- 169

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ V  +K     + +  NG +   + A  ++     DGVMI R A  N  +   V    
Sbjct: 170 WECVARVKAAL-SVPVIGNGDIVSGASAADMVRATGCDGVMIARGAQGNPWIFADVRRVL 228

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   P +    +   R I    +         G  +  + +H++   HG P + R 
Sbjct: 229 DGMPPAPDPTRQDRVEMARRHIHLLSSRL-------GNTVVYMRKHVMWYLHGVPGASRA 281

Query: 294 RHILTVEAGASTATH---HIIETAFNLMIES 321
           R  L               ++  A  +  E 
Sbjct: 282 RAALNACVTVDDFDRVLDELLADAARIEEED 312


>gi|163803826|ref|ZP_02197676.1| DNA-binding protein Fis [Vibrio sp. AND4]
 gi|159172369|gb|EDP57246.1| DNA-binding protein Fis [Vibrio sp. AND4]
          Length = 322

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 127/322 (39%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+ ++  L G  K+   +    +    ++QI GAD
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSSNPKLWGTSKSKQRMVHEGESGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA+   + G   I++N+GCP+ +V++   G+ L+  PDI+ + + A+  A+ +P
Sbjct: 76  PQLMADAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLQYPDIIKEILTAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + K  +  G+  + +H R         K        +YD 
Sbjct: 136 VTLKTRTGWNTENKNCVH--VAKLAEDCGIQALALHGRT--------KACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG ++   +A  +L     D +MIGR A     +   +  Y  N 
Sbjct: 186 IKAVKQAI-SIPVIANGDIDSPEKAKYVLEYTGADALMIGRPAQGRPWIFQEIHHYLENG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T        V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMDELPGEEVKAIMLGHVNALHGFYGEF-----LGPRIARKHVGWYLKAHEQASEFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A+      +E  F+ +
Sbjct: 300 FNA-IDAAELQLEALEGYFDNV 320


>gi|229520989|ref|ZP_04410410.1| tRNA dihydrouridine synthase B [Vibrio cholerae TM 11079-80]
 gi|229341874|gb|EEO06875.1| tRNA dihydrouridine synthase B [Vibrio cholerae TM 11079-80]
          Length = 322

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 125/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G D
Sbjct: 17  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 76  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +++  +A  +L     D +MIGR A     +   +  +  + 
Sbjct: 186 IKAVK-AAVSIPVIANGDIDNPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 245 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 300 FNAIETADQ-QLDALEGYFDNV 320


>gi|153831237|ref|ZP_01983904.1| NifR3/Smm1 family protein [Vibrio cholerae 623-39]
 gi|148873280|gb|EDL71415.1| NifR3/Smm1 family protein [Vibrio cholerae 623-39]
          Length = 331

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 124/322 (38%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R          +  +EM+  +  L    K+   +    +    ++QI G+D
Sbjct: 26  MAGVTDRPFRELCLRY-GAGMAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V++   G+ L+  PD++ D + A+  A+++P
Sbjct: 85  PQLMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  +  G+  + +H R         +        +YD 
Sbjct: 145 VTLKTRTGWD--TDNKNCLSIAQLAEDCGIQALALHGRT--------RACMYKGEAEYDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG ++   +A  +L     D  MIGR A     +   +  +  + 
Sbjct: 195 IKAVK-AAVSIPVIANGDIDSPEKARYVLEYTGADAXMIGRPAQGRPWIFQEIQHFLEHG 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T      + V       ++A    Y           +   +H+         +   R  
Sbjct: 254 TTMPELPISEVKDIMLGHVTALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRT 308

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 A       +E  F+ +
Sbjct: 309 FNAIETADQ-QLDALEGYFDNV 329


>gi|239630367|ref|ZP_04673398.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|301067518|ref|YP_003789541.1| tRNA-dihydrouridine synthase [Lactobacillus casei str. Zhang]
 gi|239526650|gb|EEQ65651.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|300439925|gb|ADK19691.1| tRNA-dihydrouridine synthase [Lactobacillus casei str. Zhang]
          Length = 333

 Score =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 136/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    I+  ++K   +L    +E P+++QI G  
Sbjct: 18  MAGVTNAAFRVTAKEF-GAGLVVCEMISDRGIMYKNEKTLNMLFVDPREHPISIQIFGGT 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+     + I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S 
Sbjct: 77  KETLVNAAKFVDQNTAADIIDINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D++        L    ++ G   + +H R         +      + D++
Sbjct: 137 PVTVKMRTGWDEKHVYAVQNALA--AERGGAAALAMHGRT--------RKQLYSGHADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+     F+G NG +     A ++L     D VM+GRAA  N  +L  +  Y  +
Sbjct: 187 ILKEVKQHLTIPFMG-NGDVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMSAYLED 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++   +  +          +++          G P S + + 
Sbjct: 246 GELIPEPTPREKIATAKLQLQRLVDLHGEHQ-----AVREFRMQAAYYLKGIPRSAKTKA 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            + +    +    HI +       E
Sbjct: 301 AVNMVDTQAEVD-HIFDDFVEQTEE 324


>gi|300718658|ref|YP_003743461.1| tRNA-dihydrouridine synthase B [Erwinia billingiae Eb661]
 gi|299064494|emb|CAX61614.1| tRNA-dihydrouridine synthase B [Erwinia billingiae Eb661]
          Length = 321

 Score =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 130/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R     +    +  +EM+ ++  +    K+ L     ++P    +QI G D
Sbjct: 17  MAGITDRPFRTLCYAM-GAGMTVSEMMSSNPEVWATDKSRLRMVHSDEPGIRTVQIAGCD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA+I    G   I++N+GCP+ +V+    G+ L+ +P++V   + A+  A+ +P
Sbjct: 76  PHEMAEAARINALSGAQVIDINMGCPAKKVNRKLAGSALLQHPELVKSILLAVVDAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + +  ++ G+  + IH R         +        +YD 
Sbjct: 136 VTLKIRTGWDPDNRN--CVEIAQLAERCGIQALTIHGRT--------RACLFNGEAEYDS 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + +  NG + D  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 186 IRTVKQ-NVSIPVIANGDITDPHKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +      V +     +      Y  R    G ++    +H+         + + R  
Sbjct: 245 ELLAPMPLAEVKRLLIGHLRELHDFYGHR---KGYRI--ARKHVSWYLQEHAPNDQFRRT 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
                 AS      +E  F  +
Sbjct: 300 FNAIEDASE-QLEALEAYFENL 320


>gi|283456447|ref|YP_003361011.1| tRNA-dihydrouridine synthase [Bifidobacterium dentium Bd1]
 gi|283103081|gb|ADB10187.1| tRNA-dihydrouridine synthase [Bifidobacterium dentium Bd1]
          Length = 372

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 117/318 (36%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R        + L   EMI A A++  + K   +  F+  EK  +LQ+ G +
Sbjct: 12  MAGVTNWPFRVICESYGPDGLYVAEMITARALVARNPKALRLCRFAPGEKIRSLQLYGVN 71

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---A 114
            + + +AAKIV D    + ++LN GCP  +V     G+ L    D+  + I  + K   A
Sbjct: 72  PAIVEQAAKIVIDENMADHVDLNFGCPVPKVTRRGGGSALPWKTDLFREIIQRVVKVCDA 131

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PVT K R+G+D +             ++ G   + +HAR                + 
Sbjct: 132 ANVPVTAKIRVGIDHE--HETFLEAGHIAQEEGCKAVTLHARTT--------AEYYGGHS 181

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+     D+ +  NG +   + AL ++      GV IGR       +   +   
Sbjct: 182 DWSRIGELVGAL-DIPVFGNGDVWGANDALAMVSETGCAGVAIGRGCQGRPWLFADIKNA 240

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V     R        Y      +   +  + +H+     GFP    
Sbjct: 241 FAGSDERIDPALGDVCTVIERHAQLLTEFYDGDERMA---VHDLRKHVAWYLKGFPVGGS 297

Query: 293 CRHILTVEAGASTATHHI 310
            R               I
Sbjct: 298 TRRAFMECENLEDVRREI 315


>gi|260779561|ref|ZP_05888451.1| tRNA-dihydrouridine synthase B [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260604370|gb|EEX30674.1| tRNA-dihydrouridine synthase B [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 285

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 119/300 (39%), Gaps = 21/300 (7%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  L    K+   +    +    ++QI GAD   + +AA+   + G   I+
Sbjct: 1   MAVSEMMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGADPQLMADAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+  PDI+ D + A+  A+ +PVT+K R G D          
Sbjct: 61  INMGCPAKKVNKKLAGSALLRFPDIIEDILKAVVNAVDVPVTLKTRTGWDPDNKN--CVQ 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K  +  G+  + +H R         K        +YD +  +K+    + +  NG ++
Sbjct: 119 IAKLAEDCGIQALALHGRT--------KACMYKGEAEYDSIRAVKQAI-SIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A ++L     D +MIGR A     +   +  +  N  T        V       ++
Sbjct: 170 SPEKAKRVLEYTGADALMIGRPAQGRPWIFQEIQHFLENGTTMPDLPSAEVKDILLGHVN 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A+      +E  F+
Sbjct: 230 ALHDFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRAFNAIE-AAELQLEALEEYFD 283


>gi|294083784|ref|YP_003550541.1| NifR3-like protein [Candidatus Puniceispirillum marinum IMCC1322]
 gi|292663356|gb|ADE38457.1| NifR3-like protein [Candidatus Puniceispirillum marinum IMCC1322]
          Length = 328

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 71/301 (23%), Positives = 123/301 (40%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGA 57
           M   TD  +R   R      L+ TEMI + A+L   K  +    T+   E PL++Q+ G 
Sbjct: 19  MSGVTDWPFRRAVRRAGG-GLVVTEMIASAAMLAEVKTEMRKLKTEVATEAPLSIQLAGW 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + S + +AAK+  D G + I++N+GCP+ +V     G+ LM +       + A+ KA+ I
Sbjct: 78  EPSVMADAAKVSADLGASIIDINMGCPAKKVTGKQSGSALMRDEHHAAAILDAVVKAVDI 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G DD   ++    L K  +  G+  + +H R         +      + D+ 
Sbjct: 138 PVTLKMRLGWDD--ASLNAPQLAKIAQDVGIRMVAVHGRT--------RCQMYTGSADWQ 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+      + +  NG +  +             GVMIGR A      +    +  + 
Sbjct: 188 KIGEVV-AAVSIPVIANGDIRTLDDVRMALHHSHAAGVMIGRGAQGRPWFVAQAGDLLNG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     +   +T Y          ++   +H+    HG P S   R 
Sbjct: 247 QQVRPEPSIAIRHQFMLAHLEDMLTHYG------SAAMRLARKHIAWYAHGLPGSAELRD 300

Query: 296 I 296
           +
Sbjct: 301 V 301


>gi|328907204|gb|EGG26970.1| TIM-barrel protein, nifR3 family [Propionibacterium sp. P08]
          Length = 418

 Score =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 124/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 64  MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHDMLAFAEGEDVRSVQLYGVD 122

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     I+A  +A   
Sbjct: 123 PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFTAVISAAVQAGDA 182

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D     +   +  ++   SG   + +HAR                + 
Sbjct: 183 HGVPVTVKIRIGIDPD--HITYMDSTRAAVDSGAAAVCLHART--------VAEAYAGHS 232

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + ++ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 233 HWDAIGDLVKAV-DVPVIGNGDIWEASDAMAMVERTGCAGVEVGRGCLGRPWLFRDLADA 291

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 292 FAGRGTTTLPSLGEVCAMI-RRHTELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 345

Query: 293 CRHIL 297
            RH L
Sbjct: 346 IRHAL 350


>gi|191639443|ref|YP_001988609.1| tRNA-dihydrouridine synthase [Lactobacillus casei BL23]
 gi|227533060|ref|ZP_03963109.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|190713745|emb|CAQ67751.1| tRNA-dihydrouridine synthase [Lactobacillus casei BL23]
 gi|227189311|gb|EEI69378.1| tRNA-dihydrouridine synthase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|327383535|gb|AEA55011.1| tRNA-dihydrouridine synthase [Lactobacillus casei LC2W]
 gi|327386728|gb|AEA58202.1| tRNA-dihydrouridine synthase [Lactobacillus casei BD-II]
          Length = 333

 Score =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 135/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    I+  ++K   +L    +E P+++QI G  
Sbjct: 18  MAGVTNAAFRVTAKEF-GAGLVVCEMISDRGIMYKNEKTLNMLFVDPREHPISIQIFGGT 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+     + I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S 
Sbjct: 77  KETLVNAAKFVDQNTAADIIDINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D++
Sbjct: 137 PVTVKMRTGWDENHVYAVQNALA--AERGGAAALAMHGRT--------RKQLYAGHADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+     F+G NG +     A ++L     D VM+GRAA  N  +L  +  Y  +
Sbjct: 187 ILKEVKQHLTIPFMG-NGDVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMSAYLED 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++   +  +          +++          G P S + + 
Sbjct: 246 GELIPEPTPREKIATAKLQLQRLVDLHGEHQ-----AVREFRMQAAYYLKGIPRSAKTKA 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            + +    +    HI +       E
Sbjct: 301 AVNMVDTQAEVD-HIFDDFVEQTEE 324


>gi|323465360|gb|ADX77513.1| dihydrouridine synthase TIM-barrel protein, putative
           [Staphylococcus pseudintermedius ED99]
          Length = 330

 Score =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 138/326 (42%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+   AIL  + K +  L     E+PL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKAILFNNPKTMKMLYIDENERPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V+ +   + I++N+GCP +++ +   GA  +L+P+ + + ++A+ + +S 
Sbjct: 77  KETLVEAAEYVDKNTTADIIDINMGCPVSKIIKCEAGARWLLDPNKIYEMVSAVTERVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RIG D+    +      K+ +++G   I +H R  +               D+D
Sbjct: 137 PVTCKMRIGWDED--HIFAVENAKAAERAGAAAISLHGRTRV--------QMYEGKADWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++K E  ++ +  NG +     A K+L    VD VMIGR A  N  M+     Y   
Sbjct: 187 IIRQVK-EAVNIPVIGNGDVTSPELAEKMLKETGVDAVMIGREALGNPWMIYRTVHYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                + ++ +H      G   + + R 
Sbjct: 246 GELIDEPQIDEKIEIALLHLNR-----LVDLKGEKVGVMEMRKHASWYLKGVRGNGKARK 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L      +  T  I+    +  +E 
Sbjct: 301 ALNQAETLAEMT-EILTEFRDEQMEK 325


>gi|322375163|ref|ZP_08049677.1| TIM-barrel protein, NifR3 family [Streptococcus sp. C300]
 gi|321280663|gb|EFX57702.1| TIM-barrel protein, NifR3 family [Streptococcus sp. C300]
          Length = 336

 Score =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 202 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 262 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 316

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 317 AISQASTLAE 326


>gi|319786120|ref|YP_004145595.1| hypothetical protein Psesu_0506 [Pseudoxanthomonas suwonensis 11-1]
 gi|317464632|gb|ADV26364.1| TIM-barrel protein, nifR3 family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 332

 Score =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 131/322 (40%), Gaps = 22/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R   + L    L  +EM ++D      +K++  +  + +  P+++QI G +
Sbjct: 17  MAGVTDKPFRLLCKQL-GAGLAVSEMTISDPRFWNTRKSLQRMDHAGEPDPVSVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA+     G   I++N+GCP+ +V     G+ LM +  +V   + A+  A+ +P
Sbjct: 76  PEQLAGAARYNVANGAQIIDINMGCPAKKVCNAWAGSALMRDEALVARILEAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   ++       + +  ++SG+  + IH R         ++       +YD 
Sbjct: 136 VTLKIRTGWCAEVRNA--PTIARIAEESGIAALAIHGRT--------RNQHYTGQAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  NG ++  ++A  +L     D VM+GRAA     +   +  Y    
Sbjct: 186 IAEVKSRL-RIPVLANGDIDSPAKAAFVLRHTGADAVMVGRAAQGRPWIFRQIAHYLGTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    V       + A    Y          ++   +H+         +   R +
Sbjct: 245 EELPEPSVAEVRDILLGHLQALHAFYGEEQ-----GVRIARKHLGWYAKDRAENAAFRAV 299

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           +   A  +     +    F+ +
Sbjct: 300 VN-RAQTAAEQLALTRGYFDAL 320


>gi|262283589|ref|ZP_06061354.1| tRNA-dihydrouridine synthase B [Streptococcus sp. 2_1_36FAA]
 gi|262260646|gb|EEY79347.1| tRNA-dihydrouridine synthase B [Streptococcus sp. 2_1_36FAA]
          Length = 325

 Score =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 63/317 (19%), Positives = 132/317 (41%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K     +   + D    H+     +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAHDHLKR-LIDLKGEHIA----VREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGASTATHHIIE 312
            ++ +A        +++
Sbjct: 307 AIS-QANTLAEIEELLQ 322


>gi|163793260|ref|ZP_02187236.1| tRNA-dihydrouridine synthase [alpha proteobacterium BAL199]
 gi|159181906|gb|EDP66418.1| tRNA-dihydrouridine synthase [alpha proteobacterium BAL199]
          Length = 328

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 84/324 (25%), Positives = 141/324 (43%), Gaps = 22/324 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR YR   R      L+ +EMI +DA+LR  ++ +L     T + P  +Q+ G D
Sbjct: 19  MSGVTDRPYRRIVRSF-GVGLVISEMIASDAMLREVREELLKAEIDTDDAPAVVQLAGWD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA++    G   I++N+GCP+ +V     G+ LM +  + G  IAA+  A+ +P
Sbjct: 78  PATMAEAARLAVAGGAAVIDINMGCPAKKVVNRLAGSALMRDEALAGQIIAAVVNAVPVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D+         L +  + +GV  I +H R         +        D++ 
Sbjct: 138 VTLKMRTGWDENDRNA--PRLARIAEDAGVRMITVHGRT--------RCQMYTGQADWEF 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+         NG +     A+  L     DGVMIGR AY    +L  +    +  
Sbjct: 188 IRRVKEVVSVPV-VANGDITSPEDAMACLQQSDADGVMIGRGAYGRPWILKQIAARIAGQ 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +P    +     + + A ++ Y    +HSG  L+   +H+     G P+S   R  
Sbjct: 247 AVVPAPSVGEIKAIIVQHLEAMLSHYG---IHSG--LRNARKHIGWYSQGLPDSAEFRQA 301

Query: 297 LTVEAGASTATHHIIETAFNLMIE 320
           +             I+  F+ +IE
Sbjct: 302 VN-NTVEPMRVFAAIDRYFDPLIE 324


>gi|322391264|ref|ZP_08064735.1| tRNA-dihydrouridine synthase [Streptococcus peroris ATCC 700780]
 gi|321145868|gb|EFX41258.1| tRNA-dihydrouridine synthase [Streptococcus peroris ATCC 700780]
          Length = 326

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAESAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLI-----DLKGEKVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|225874633|ref|YP_002756092.1| putative tRNA-dihydrouridine synthase [Acidobacterium capsulatum
           ATCC 51196]
 gi|225791394|gb|ACO31484.1| putative tRNA-dihydrouridine synthase [Acidobacterium capsulatum
           ATCC 51196]
          Length = 398

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 82/344 (23%), Positives = 144/344 (41%), Gaps = 43/344 (12%)

Query: 1   MVDWTDRHYRFFAR---------------------LLTNNALLYTEMIVADAIL---RGD 36
           M   TD  +R F R                       +   L+ TE   AD +       
Sbjct: 39  MAGVTDTVFRRFIRNASLFAEGGAGAANVDREVTNQQSGCGLIMTEFTSADGLSKMRESK 98

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           +K  L F   E P+A Q+ G++   L E A+IVED G++ ++LN+GCP+ RV   + G+ 
Sbjct: 99  RKRYLTFYEDEHPIAAQLFGSNPETLAEGARIVEDTGFDMVDLNLGCPAKRVVACNGGSG 158

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L+ +  ++     A+  A+ IP TVK R+G +DQ   +    L +  ++SG+N + +HAR
Sbjct: 159 LLRDLPLIAKIFEAVRGAVKIPFTVKFRLGWNDQ--HIICVPLARLAEESGLNAVSLHAR 216

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
                    ++        ++ + E+K +   + +  NG +     A  ++     DGVM
Sbjct: 217 T--------REQGYSGQARWEHIAEVK-DAVRIPVIGNGDVRTPEDACALVAKTGCDGVM 267

Query: 215 IGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           IGRAA  N  +   + +Y +       S   + ++ + ++  +     +       + GK
Sbjct: 268 IGRAAPANPWIFRQIAQYTATGRYDEPSEADRYQMIRTYFEMLLDEGREDEHASRAAEGK 327

Query: 273 LQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           ++Q         HG P     R  +  EA         +E  F 
Sbjct: 328 MKQFA---SWFTHGVPGGAGLRKSI-YEAKTGPKILDAVERFFE 367


>gi|116495964|ref|YP_807698.1| tRNA-dihydrouridine synthase [Lactobacillus casei ATCC 334]
 gi|116106114|gb|ABJ71256.1| tRNA-U20-dihydrouridine synthase [Lactobacillus casei ATCC 334]
          Length = 333

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 135/325 (41%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    I+  ++K   +L    +E P+++QI G  
Sbjct: 18  MAGVTNAAFRVTAKEF-GAGLVVCEMISDRGIMYKNEKTLNMLFVDPREHPISIQIFGGT 76

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+     + I++N+GCP  +V +   GA  +L+P+ V + +AA+  A+S 
Sbjct: 77  KETLVNAAKFVDQNTAADIIDINMGCPVPKVTKTDAGAHWLLDPEKVYEMVAAVTDAVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D+         L    ++ G   + +H R         +      + D++
Sbjct: 137 PVTVKMRTGWDENHVYAVQNALA--AERGGAAALAMHGRT--------RKQLYAGHADWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+     F+G NG +     A ++L     D VM+GRAA  N  +L  +  Y  +
Sbjct: 187 ILKEVKQHLTIPFMG-NGDVRTPQDAKRMLDEVGADAVMVGRAALGNPWVLKQMSAYLED 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           ++   +  +          +++          G P S + + 
Sbjct: 246 GELIPEPTPREKIATAKLQLQRLVDLHGEHQ-----AVREFRMQAAYYLKGIPRSAKTKV 300

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            + +    +    HI +       E
Sbjct: 301 AVNMVDTQAEVD-HIFDDFVEQTEE 324


>gi|327438060|dbj|BAK14425.1| tRNA-dihydrouridine synthase [Solibacillus silvestris StLB046]
          Length = 336

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 130/304 (42%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+Y EMI   A+   +KK   +L    +E P+ LQI G D
Sbjct: 25  MAGICNSAFRLTVKEF-GAGLVYAEMISDKALNTRNKKTLDMLYIDERENPMTLQIFGGD 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  ++ +   GA  +L+P+ + + ++A+  A+  
Sbjct: 84  KENLVEAAKFVDKHTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKIYEMVSAVVDAVDK 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D++               +    +    R  + +G            ++D
Sbjct: 144 PVSVKMRIGWDEERVFAVENAQAAERAGAAAIAMHGRTRVQMYEG----------KANWD 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK N  +    NG +E    A +IL     DGVMIGRAA  N  M+    +Y  +
Sbjct: 194 VLAEVKK-NISIPFIANGDVETPEDAKRILEHTKADGVMIGRAALGNPWMIYQTVKYLES 252

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +    P            +     +           ++++ +H      G   + + R+
Sbjct: 253 GVQIPEPSVRE-----KMDVCLLHFERLKALKGEKVAVREMRKHASWYLKGIRGNGKIRN 307

Query: 296 ILTV 299
            + +
Sbjct: 308 AINL 311


>gi|227878374|ref|ZP_03996329.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus JV-V01]
 gi|293380365|ref|ZP_06626436.1| TIM-barrel protein, nifR3 family [Lactobacillus crispatus 214-1]
 gi|312978416|ref|ZP_07790158.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           crispatus CTV-05]
 gi|227862053|gb|EEJ69617.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus JV-V01]
 gi|290923048|gb|EFD99979.1| TIM-barrel protein, nifR3 family [Lactobacillus crispatus 214-1]
 gi|310894759|gb|EFQ43831.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           crispatus CTV-05]
          Length = 341

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 124/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+ G+KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYGNKKTLSMMDVDPREHPMSIQIFGGS 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EETLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVKK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D +   +       + +++G + I +H R         +        D++
Sbjct: 140 PVSVKMRTGWDKK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 VLHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++ A       +       + +  +       G P S R R 
Sbjct: 249 GEKLKPQTVREKVETAKHQLHA-----LVKIHGEKRAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|332670826|ref|YP_004453834.1| TIM-barrel protein, nifR3 family [Cellulomonas fimi ATCC 484]
 gi|332339864|gb|AEE46447.1| TIM-barrel protein, nifR3 family [Cellulomonas fimi ATCC 484]
          Length = 396

 Score =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 130/325 (40%), Gaps = 25/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R  +   L   EM+ + A++    +   I+ F+  E P ++Q+ G D
Sbjct: 37  MAGVTNAAFRRLCRE-SGAGLYVAEMLTSRALVERSPESFRIISFAPDEVPRSVQVYGVD 95

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            + +  A ++ VE+   + ++LN GCP  +V     GA L    D+    + A   A   
Sbjct: 96  PATVGAAVRMLVEEDLADHVDLNFGCPVPKVTRRGGGAVLPWKRDLFSAIVHAAVDAARP 155

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+D++        L  + + +GV  + +H R A         +      
Sbjct: 156 SGVPVTVKMRKGIDEEHLTYVEAGL--TAQDAGVAAVALHGRTA--------ADYYSGTA 205

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +K+   D+ +  NG +     AL ++     DGV++GR       +   +   
Sbjct: 206 DWDAIATLKEAVTDIPVLGNGDIWSAEDALAMVAHTGCDGVVVGRGCQGRPWLFADLAAA 265

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+       P    V +   R     +  +          L+++ +HM     G+     
Sbjct: 266 FAGSDVRIRPGLGEVAQVVRRHAELMVEHFG----DESKALREMRKHMAWYLKGYVVGGE 321

Query: 293 CRHILTVEAGASTATHHIIETAFNL 317
            R  L + +  +     +   A +L
Sbjct: 322 ARAALGLVSSMADLDDRL--AALDL 344


>gi|297622174|ref|YP_003710311.1| putative tRNA-dihydrouridine synthase B [Waddlia chondrophila WSU
           86-1044]
 gi|297377475|gb|ADI39305.1| putative tRNA-dihydrouridine synthase B [Waddlia chondrophila WSU
           86-1044]
          Length = 326

 Score =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 133/317 (41%), Gaps = 22/317 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R       N  L+Y EM+  DA++R D     IL +     P+  Q+ G+  
Sbjct: 25  AGCSDFPFRQMCAQY-NPGLIYCEMVKMDALIRHDPATFHILDYEEGMHPIGAQLCGSKP 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               +AAKI+ED G++ I+LN GCP  +V +   G+ L+  P+ + + ++ M  A+S+PV
Sbjct: 84  ELAGKAAKILEDLGFDVIDLNCGCPVDKVTKDGSGSGLLKQPEKIAEILSEMVAAVSVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD+         +     +    I    RK   +G          + ++D +
Sbjct: 144 TVKIRAGWDDESIIAEEITRLAEKAGAAAIAIHGRTRKQAYRG----------DANWDYI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              K+    + +  NG + D   A ++      D V++ R       +   +  +     
Sbjct: 194 KACKETAGKIKVIGNGDVFDAEAAEQMFRYTGCDAVLVSRGTMGKPWIAEDIQRHL---- 249

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
            G  P++  ++ D  RK       +A+R+      + ++ +         P +R  R ++
Sbjct: 250 CGLKPVERTLEDD--RKALLEHYRFASRYHSDRRTVLEMRKVGCWYLKKSPGTRDFRGLI 307

Query: 298 TVEAGASTATHHIIETA 314
           + +A        +IE  
Sbjct: 308 S-KAKNLEEVRELIENY 323


>gi|256844417|ref|ZP_05549903.1| transcriptional regulator [Lactobacillus crispatus 125-2-CHN]
 gi|256849195|ref|ZP_05554628.1| transcriptional regulator [Lactobacillus crispatus MV-1A-US]
 gi|262047211|ref|ZP_06020169.1| transcriptional regulator [Lactobacillus crispatus MV-3A-US]
 gi|256613495|gb|EEU18698.1| transcriptional regulator [Lactobacillus crispatus 125-2-CHN]
 gi|256713971|gb|EEU28959.1| transcriptional regulator [Lactobacillus crispatus MV-1A-US]
 gi|260572456|gb|EEX29018.1| transcriptional regulator [Lactobacillus crispatus MV-3A-US]
          Length = 342

 Score =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 124/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+ G+KK   ++    +E P+++QI G  
Sbjct: 22  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYGNKKTLSMMDVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 81  EETLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVKK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D +   +       + +++G + I +H R         +        D++
Sbjct: 141 PVSVKMRTGWDKK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 191 VLHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++ A       +       + +  +       G P S R R 
Sbjct: 250 GEKLKPQTVREKVETAKHQLHA-----LVKIHGEKRAVPEFRQQAAYYLKGIPRSARTRA 304

Query: 296 ILTV 299
            +  
Sbjct: 305 KINE 308


>gi|326404424|ref|YP_004284506.1| putative tRNA-dihydrouridine synthase [Acidiphilium multivorum
           AIU301]
 gi|325051286|dbj|BAJ81624.1| putative tRNA-dihydrouridine synthase [Acidiphilium multivorum
           AIU301]
          Length = 353

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 136/326 (41%), Gaps = 22/326 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TD  +R   + +    L+ +EMI + A++R +   +   S  E   P ++Q+ G D
Sbjct: 37  MSGVTDLPFRRLVKSM-GAGLVVSEMIASWAMIRENAATLRMASVDEGTGPNSVQLAGCD 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + + EAA+I    G + +++N GCP  +V      G+ LM +    G  + A  KA+ +
Sbjct: 96  PAAMAEAARIAVAGGADLVDINFGCPVKKVAVGQMAGSALMRDEVQAGRILEATAKAVDV 155

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D Q  ++    L +  ++SG+  + +H R         +        D+D
Sbjct: 156 PVTLKMRMGWDRQ--SLNAPTLARIAQESGIAMVTVHGRT--------RQQFYEGTADWD 205

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG +    +A + L     DGVMIGR AY     L  V  Y + 
Sbjct: 206 FIASVK-AAVAIPVIANGDITTEDEAEEALRRSQADGVMIGRGAYGRPWFLAQVARYLAT 264

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                +P     D +  R +          H      L+   +H+     G P +   R 
Sbjct: 265 GQKLPAP-----DMEMRRDVLIGHYRAMRAHYGEQPGLRVARKHIGWYVRGLPGAAEFRA 319

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +  +  ++     I E     M E+
Sbjct: 320 AVNRQDDSAAVEAMIHEIHARAMGET 345


>gi|332525538|ref|ZP_08401693.1| NifR3 family TIM-barrel protein [Rubrivivax benzoatilyticus JA2]
 gi|332109103|gb|EGJ10026.1| NifR3 family TIM-barrel protein [Rubrivivax benzoatilyticus JA2]
          Length = 346

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 128/327 (39%), Gaps = 25/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EMI +   LR  +K       + +  P+A+QI G +
Sbjct: 18  MAGVTDRAFRKLCKRL-GAGYAVSEMITSRPDLRDSRKTSRRADHTGEGAPIAVQIAGTE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + +AA+   D G   +++N+GCP+ +V     G+ LM +  +    + A+  A    
Sbjct: 77  PAMMADAARHEIDRGAQIVDINMGCPAKKVCNKWAGSALMQDEALALSIVEAVVGACAPR 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G              ++ + +GV  + +H R         ++       +
Sbjct: 137 GVPVTLKMRTGWCAAERNALRL--ARAAEAAGVAMVTVHGRT--------REQGYQGQAE 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG ++  ++A  +L     D +MIGRAA     +   +  Y 
Sbjct: 187 YDTIAAVKAAL-AIPVVANGDIDSPAKAAAVLARTGADALMIGRAAQGRPWIFREIAHYL 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P    V       +      Y          ++   +H+     G P     
Sbjct: 246 ATGTLLAPPATHEVRGWLLEHLEEHYALYGEH-----AGVRSARKHIGWAVRGLPGGEDF 300

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           R  +   A  + A    ++  F+ + E
Sbjct: 301 RAAMNTIA-EAGAQWRAVDGFFSELAE 326


>gi|148998011|ref|ZP_01825524.1| replicative DNA helicase [Streptococcus pneumoniae SP11-BS70]
 gi|168576061|ref|ZP_02721966.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae MLV-016]
 gi|307068800|ref|YP_003877766.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae AP200]
 gi|147756021|gb|EDK63064.1| replicative DNA helicase [Streptococcus pneumoniae SP11-BS70]
 gi|183578142|gb|EDT98670.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae MLV-016]
 gi|306410337|gb|ADM85764.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae AP200]
 gi|332198603|gb|EGJ12686.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA41317]
          Length = 326

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLI-----DLKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|323454823|gb|EGB10692.1| hypothetical protein AURANDRAFT_22498 [Aureococcus anophagefferens]
          Length = 378

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 111/342 (32%), Positives = 160/342 (46%), Gaps = 24/342 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-------RGDKKNILGFSTQEKPLALQ 53
           M+D+TDRH+R+  RLL+  A+LYTEM+ A  ++        GD    LG+        LQ
Sbjct: 26  MMDYTDRHFRYLLRLLSREAVLYTEMVTAATLVDGAGAPRHGDGARWLGYDDDAGRTVLQ 85

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMC 112
           +GGAD ++L  AA++    GY  +NLN GCPS RV     FGA LM +  +V DC+ A+ 
Sbjct: 86  LGGADPAQLGAAARLAAPRGYAGVNLNCGCPSDRVAGQGCFGAALMRDAALVADCVDALA 145

Query: 113 KALSIPVTVKCRIGV---------DDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +    PV+VKCR+GV         DD+     L N V ++   G      +HAR A+L G
Sbjct: 146 EHA--PVSVKCRVGVCDTVSDMVDDDEALYAGLANFVSTVAARGTCAHFVVHARVAVLSG 203

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYK 221
           LSP  NRK+P L   +V  +  E P+L +  NG +     A       V GVM GR   K
Sbjct: 204 LSPDKNRKVPPLKPRLVSRLADEFPELTVVSNGEISSYESARDRSEGNVAGVMAGRDVCK 263

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                  VD         + P  +R D       + +    A          + + +  +
Sbjct: 264 RPWYYANVDSALFG--ADADPAASRRDVLLGAYAAYAAAFEADHARADWSPRRALLKPAL 321

Query: 282 GLFHGFPNSRRCRHILTVEAGASTATH-HIIETAFNLMIESL 322
           GLFHG P + R +  +   A    A    I+E A  L+ + +
Sbjct: 322 GLFHGSPGAGRFKREVDALAKGGDAGVREILERAAALVPDDV 363


>gi|149006830|ref|ZP_01830511.1| hypothetical protein CGSSp18BS74_11461 [Streptococcus pneumoniae
           SP18-BS74]
 gi|149013437|ref|ZP_01834118.1| hypothetical protein CGSSp19BS75_00095 [Streptococcus pneumoniae
           SP19-BS75]
 gi|169833585|ref|YP_001695544.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Hungary19A-6]
 gi|147761431|gb|EDK68396.1| hypothetical protein CGSSp18BS74_11461 [Streptococcus pneumoniae
           SP18-BS74]
 gi|147762863|gb|EDK69813.1| hypothetical protein CGSSp19BS75_00095 [Streptococcus pneumoniae
           SP19-BS75]
 gi|168996087|gb|ACA36699.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Hungary19A-6]
 gi|332071268|gb|EGI81763.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA17545]
          Length = 326

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|33865189|ref|NP_896748.1| nitrogen regulation protein NifR3 family protein [Synechococcus sp.
           WH 8102]
 gi|33638873|emb|CAE07170.1| putative nitrogen regulation protein NifR3 family homolog
           [Synechococcus sp. WH 8102]
          Length = 333

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 132/318 (41%), Gaps = 27/318 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGA 57
              +DR +R   R    +ALL+TEM+ A ++     RG  K +     ++ P+ +Q+   
Sbjct: 31  AGVSDRVFRHLVRRWAPDALLFTEMVNATSLELGFGRGKVKEL---GDEQGPIGVQLFDH 87

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
               + +AA+  ED G   I++N+GCP  ++     G+ L+ +P +    I A+  A+ +
Sbjct: 88  RPDAMADAARRAEDAGAFLIDINMGCPVRKIARKGGGSGLIRDPHLASRIIEAVANAVRL 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G      A       + ++++G   + +H R         ++       D+ 
Sbjct: 148 PVTVKTRLGWCGSDAAPQT--WCRQLQEAGAQLLTLHGRT--------REQGFKGKADWA 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+    + +  NG +     A + L     DGVM+GR       ++  +D     
Sbjct: 198 AIAAVKQALT-IPVIANGDINTPEDAQRCLAQTGADGVMVGRGTMGAPWLVGQIDAALKG 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++P           ++ A + +    H      L    +HM     GFP + + RH
Sbjct: 257 LPIPATPGPAARLTLAREQLLA-LVEARGEH-----GLLIARKHMGWTCTGFPGAPQLRH 310

Query: 296 ILTVEAGASTATHHIIET 313
            L + A        ++E 
Sbjct: 311 AL-MRAPTPEDALALLEN 327


>gi|148984490|ref|ZP_01817778.1| hypothetical protein CGSSp3BS71_10563 [Streptococcus pneumoniae
           SP3-BS71]
 gi|168494054|ref|ZP_02718197.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC3059-06]
 gi|147923267|gb|EDK74381.1| hypothetical protein CGSSp3BS71_10563 [Streptococcus pneumoniae
           SP3-BS71]
 gi|183575963|gb|EDT96491.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC3059-06]
 gi|301800925|emb|CBW33584.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           OXC141]
          Length = 326

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|295692146|ref|YP_003600756.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus ST1]
 gi|295030252|emb|CBL49731.1| tRNA-dihydrouridine synthase [Lactobacillus crispatus ST1]
          Length = 341

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 124/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+ G+KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYGNKKTLSMMDVDPREHPMSIQIFGGS 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EETLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVKK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D +   +       + +++G + I +H R         +        D++
Sbjct: 140 PVSVKMRTGWDKK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 VLHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++ A       +       + +  +       G P S R R 
Sbjct: 249 GEKLQPQTVREKVETAKHQLHA-----LVKIHGEKRAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|168483984|ref|ZP_02708936.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1873-00]
 gi|225857757|ref|YP_002739268.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae P1031]
 gi|225859959|ref|YP_002741469.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 70585]
 gi|172042699|gb|EDT50745.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1873-00]
 gi|225720185|gb|ACO16039.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 70585]
 gi|225726197|gb|ACO22049.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae P1031]
 gi|301795102|emb|CBW37572.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           INV104]
 gi|332198809|gb|EGJ12891.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA47368]
 gi|332199009|gb|EGJ13090.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA47901]
          Length = 326

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|148988833|ref|ZP_01820248.1| hypothetical protein CGSSp6BS73_07143 [Streptococcus pneumoniae
           SP6-BS73]
 gi|148991954|ref|ZP_01821728.1| replicative DNA helicase [Streptococcus pneumoniae SP9-BS68]
 gi|149003048|ref|ZP_01827957.1| hypothetical protein CGSSp14BS69_11215 [Streptococcus pneumoniae
           SP14-BS69]
 gi|149020105|ref|ZP_01835079.1| hypothetical protein CGSSp23BS72_08719 [Streptococcus pneumoniae
           SP23-BS72]
 gi|168486294|ref|ZP_02710802.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1087-00]
 gi|168489262|ref|ZP_02713461.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae SP195]
 gi|168491720|ref|ZP_02715863.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC0288-04]
 gi|194397168|ref|YP_002038780.1| dihydrouridine synthase [Streptococcus pneumoniae G54]
 gi|221232891|ref|YP_002512045.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225855683|ref|YP_002737195.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae JJA]
 gi|237650706|ref|ZP_04524958.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae CCRI
           1974]
 gi|237821964|ref|ZP_04597809.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae CCRI
           1974M2]
 gi|303253994|ref|ZP_07340113.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae BS455]
 gi|303262142|ref|ZP_07348087.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP14-BS292]
 gi|303266234|ref|ZP_07352126.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS457]
 gi|303268867|ref|ZP_07354653.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS458]
 gi|307128454|ref|YP_003880485.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 670-6B]
 gi|147758789|gb|EDK65785.1| hypothetical protein CGSSp14BS69_11215 [Streptococcus pneumoniae
           SP14-BS69]
 gi|147925644|gb|EDK76720.1| hypothetical protein CGSSp6BS73_07143 [Streptococcus pneumoniae
           SP6-BS73]
 gi|147929003|gb|EDK80014.1| replicative DNA helicase [Streptococcus pneumoniae SP9-BS68]
 gi|147930783|gb|EDK81764.1| hypothetical protein CGSSp23BS72_08719 [Streptococcus pneumoniae
           SP23-BS72]
 gi|183570643|gb|EDT91171.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC1087-00]
 gi|183572275|gb|EDT92803.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae SP195]
 gi|183574050|gb|EDT94578.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           CDC0288-04]
 gi|194356835|gb|ACF55283.1| Dihydrouridine synthase (Dus) [Streptococcus pneumoniae G54]
 gi|220675353|emb|CAR69952.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722760|gb|ACO18613.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae JJA]
 gi|301802853|emb|CBW35631.1| putative tRNA-dihydrouridine synthase [Streptococcus pneumoniae
           INV200]
 gi|302599025|gb|EFL66052.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae BS455]
 gi|302636782|gb|EFL67272.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP14-BS292]
 gi|302641566|gb|EFL71927.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS458]
 gi|302644282|gb|EFL74537.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS457]
 gi|306485516|gb|ADM92385.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae 670-6B]
 gi|332071458|gb|EGI81952.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA41301]
 gi|332071628|gb|EGI82121.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA17570]
          Length = 326

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|302380164|ref|ZP_07268636.1| TIM-barrel protein, nifR3 family [Finegoldia magna ACS-171-V-Col3]
 gi|302311947|gb|EFK93956.1| TIM-barrel protein, nifR3 family [Finegoldia magna ACS-171-V-Col3]
          Length = 310

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 131/302 (43%), Gaps = 32/302 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R     L    L +TEMI A A+   DKK   +L   ++E   ++QI G + 
Sbjct: 18  AGVTDIPFRIICGEL-GAGLCFTEMISAKALYYDDKKTKKLLDTDSRENDTSVQIFGHEP 76

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A + + E++ +  I++N+GCP+ ++ +   G+ LM + ++  D I A      +P
Sbjct: 77  EIIAYATRFLTENYNFKSIDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G+D+   ++    L +  ++  V+ I +HAR   +              D+  
Sbjct: 137 VSVKFRLGIDE--NSMNYMQLAQICERLKVDYITLHARTRKMF--------YSGEADWSH 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  EN D+ +  NG         K +   + DGV++ R A +N  + +         
Sbjct: 187 IKRVV-ENVDIPVFGNGDCFTKEDIRKNMEYSNCDGVLLARGAMQNPFIFSD-------- 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +  K  V     + +   +  Y  R       + ++ +H+     GF NS + ++ 
Sbjct: 238 --DENKSKEEVIDTIKKHMQLKLEFYEERR-----AILEMRKHIQWYLKGFRNSNKVKNE 290

Query: 297 LT 298
           + 
Sbjct: 291 IN 292


>gi|114561641|ref|YP_749154.1| putative TIM-barrel protein, nifR3 family protein [Shewanella
           frigidimarina NCIMB 400]
 gi|114332934|gb|ABI70316.1| putative TIM-barrel protein, nifR3 family protein [Shewanella
           frigidimarina NCIMB 400]
          Length = 320

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 138/323 (42%), Gaps = 23/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+   +  S +E   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAALAVSEMLSSNPDVWDSDKSRQRMMHSGEEGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK   + G + I++N+GCP+ +V++   G+ LM +P +V + + A+  A+ +P
Sbjct: 76  PDLMANAAKFNVEQGAHIIDINMGCPAKKVNKKFAGSALMQSPSLVKEILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G + +        + +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWEPEHRNGV--EIAQIAEDCGIVSLAVHGRT--------RQCMYKGFAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG ++   +A  +L     D +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NVSIPVVANGDIDTPEKAKFVLDYTGADALMIGRGAQGRPWIFKEILHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +PIK    +    +    + D    +      ++   +H+    +     R+ R  
Sbjct: 245 K-KLAPIKAEEQRSVMLEHLKKLYDLYGEY----KGVRFARKHVGWYLNHEEQ-RQFRAD 298

Query: 297 LTVEAGASTATHHIIETAFNLMI 319
                 A+   H ++E  F+ ++
Sbjct: 299 FNRLETAAQ-QHSLVECYFDELV 320


>gi|329118447|ref|ZP_08247153.1| tRNA-dihydrouridine synthase B [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327465493|gb|EGF11772.1| tRNA-dihydrouridine synthase B [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 332

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 137/300 (45%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R  AR         +EM+ +D  LR  KK++    F+ +    A+QI G+D
Sbjct: 18  MAGITDKPFRALARQF-GAGYAVSEMLNSDPALRQTKKSLHRSDFAGEAGIRAVQIAGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             K+ EAA+   + G   I++N+GCP  +V     G+ L+ N  +VGD + A+  A  +P
Sbjct: 77  PQKMAEAARYNVEQGAQIIDINMGCPVKKVCNVLAGSALLQNEKLVGDILRAVVAAAGVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  +    +    + K+ +++G+  I +H R         ++     +  YD+
Sbjct: 137 VTLKTRLGYCEGSKNI--LAIAKTAEQAGIAAIAVHGRT--------REQMYKGSASYDL 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+ +  + +  NG +    +A ++L     DGVM+GRAA     +   +  +  + 
Sbjct: 187 IAEVKQ-SVAIPVWANGDITSPQKAAEVLRQTGADGVMVGRAAQGRPWLFAQIRHFLRHG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            T  +P+  +   D   +   +M  +      +G ++    +H+             R  
Sbjct: 246 -TPPAPLPFQTAADTMLRHLEAMYAFYGE--AAGARI--ARKHIGWYVAPLAGGEAFRKH 300


>gi|15904035|ref|NP_359585.1| hypothetical protein spr1994 [Streptococcus pneumoniae R6]
 gi|182685127|ref|YP_001836874.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae CGSP14]
 gi|15459698|gb|AAL00796.1| Conserved hypothetical protein [Streptococcus pneumoniae R6]
 gi|182630461|gb|ACB91409.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae CGSP14]
          Length = 336

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 202 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 262 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 316

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 317 AISQASTLAE 326


>gi|322387011|ref|ZP_08060624.1| tRNA-dihydrouridine synthase [Streptococcus infantis ATCC 700779]
 gi|321142155|gb|EFX37647.1| tRNA-dihydrouridine synthase [Streptococcus infantis ATCC 700779]
          Length = 326

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 135/310 (43%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   + D    ++     +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKR-LIDLKGENIA----VREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|262392968|ref|YP_003284822.1| tRNA dihydrouridine synthase B [Vibrio sp. Ex25]
 gi|262336562|gb|ACY50357.1| tRNA dihydrouridine synthase B [Vibrio sp. Ex25]
          Length = 287

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 61/302 (20%), Positives = 119/302 (39%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ A+  L G  K+   +    +    ++QI G+D   + +AA+   + G   I+
Sbjct: 1   MAVSEMMSANPKLWGTSKSKQRMVHEGESGIRSVQIAGSDPQLMADAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+  P+I+ + + A+  A+ +PVT+K R G D          
Sbjct: 61  INMGCPAKKVNKKLAGSALLQYPNIIEEILKAVVNAVDVPVTLKTRTGWD--TDNKNCVQ 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K  +  G+  + +H R         K        +YD +  +K+    + +  NG ++
Sbjct: 119 IAKLAENCGIQALALHGRT--------KACMYKGEAEYDSIKAVKEAI-SIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  Y  N  T        V       ++
Sbjct: 170 SPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIHHYLENGTTMEELPTEEVKTIMLGHVN 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A       +E  F+
Sbjct: 230 ALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRTFNAIDAAP-LQIEALEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|212550478|ref|YP_002308795.1| tRNA-dihydrouridine synthase [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|212548716|dbj|BAG83384.1| tRNA-dihydrouridine synthase [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
          Length = 340

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 71/299 (23%), Positives = 130/299 (43%), Gaps = 25/299 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+ ++R   +      ++YTE I ADA++R   K    L     E P+A+QI G D
Sbjct: 25  MEGVTNVYFRSLCKSF-GADMVYTEFISADALIRHVDKIQGKLKIINSEHPIAVQIYGQD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAA+I E+   + ++LN GCP  ++   + GA ++  P  + +    +  +++IP
Sbjct: 84  KDTMVEAARICEEMQPDFLDLNFGCPVKKIVRRNAGAGMLRVPKKMIEITQQVVHSVNIP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R+G D+    +   +L + ++ +G+  + IH R                  D+++
Sbjct: 144 ITVKTRLGWDENSKIIV--DLAERLQDTGIALLTIHGRTG--------SQMYSGKADWNL 193

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +K  NP   + I  NG +    Q  +      VD VMIGRA+     +   V  Y  
Sbjct: 194 IGAVKN-NPRMYIPICGNGDIVSPQQCEQAFNRYGVDAVMIGRASIGAPWIFQEVKYYLK 252

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSR 291
                   +  +   +++  +       +   L     +    RH++   LF    N +
Sbjct: 253 YND-----LAPKKSFEYYLSVLKQQILQSVSQLGERQGILNSRRHIVASPLFKKMSNFK 306


>gi|229495227|ref|ZP_04388962.1| TIM-barrel protein, NifR3 family [Porphyromonas endodontalis ATCC
           35406]
 gi|229317670|gb|EEN83568.1| TIM-barrel protein, NifR3 family [Porphyromonas endodontalis ATCC
           35406]
          Length = 334

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 139/329 (42%), Gaps = 26/329 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M D +D  +R   R     +++Y+E I ADA++R  +   N L     E P  +QI G D
Sbjct: 18  MEDVSDSAFRLLCRGF-GASMVYSEFISADALIRSVRGACNKLFIHPDEHPAVIQIYGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ + EAA I    G   +++N GCP  RV     G+ ++ N  ++ +   A+ KA  +P
Sbjct: 77  VASMAEAAAIASTTGAEILDINFGCPVKRVAGKGAGSGMLRNIPLLLEITRAVVKASRVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D Q   + + +L ++++  G+  + IH R         + +    N D+ +
Sbjct: 137 VTVKTRLGWDHQ--NIIIEDLAEALQDCGIAALTIHGRT--------RSDMYNGNADWSL 186

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K      + I  NG +    +A +      VD VM+GRA+     +   +  Y   
Sbjct: 187 IGAVKNNPRITIPIIGNGDITTPQEAKEAFDRYGVDAVMVGRASIGRPWVFEEMRHYLDT 246

Query: 236 P-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG--LFHGFPNSRR 292
             L    P   R+D          M       L     +    RH+    +F G  N R 
Sbjct: 247 GELLQDRPASERLDTLI------QMIRNNIDKLDERRGILHSRRHLAASPIFKGIANFRP 300

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R I  ++A        I+     ++ + 
Sbjct: 301 WR-IAMLQATTMEQLLDILAQVRTILTQD 328


>gi|227495968|ref|ZP_03926279.1| dihydrouridine synthase [Actinomyces urogenitalis DSM 15434]
 gi|226834456|gb|EEH66839.1| dihydrouridine synthase [Actinomyces urogenitalis DSM 15434]
          Length = 438

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 72/363 (19%), Positives = 133/363 (36%), Gaps = 58/363 (15%)

Query: 1   MVDWTDRHYRFFAR-------------------------LLTNNALLYTEMIVADAILRG 35
           M   T+  +R   R                         LL    L  TEM+   A++  
Sbjct: 43  MAGVTNASFRRLCREQGESALPAHARPAAAGPLPTDDGGLLAPAGLYVTEMVTTRALVER 102

Query: 36  DKKN--ILGFSTQEKPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGS 92
           + K   ++     E+  ++Q+ G D     +AA+I VE+   + I+LN GCP  +V    
Sbjct: 103 NDKTLAMVRTDPTERVRSIQLYGVDPVIAGKAARILVEEDLADHIDLNFGCPVPKVTRKG 162

Query: 93  FGACLMLNPDIVGDCIAAMCKAL-----------SIPVTVKCRIGVDDQIPAVALRNLVK 141
            GA L    D++   +  + +              +PVTVK RIGVD++       +  +
Sbjct: 163 GGAALPWKKDLLHAILREVVRGAEEGVRLGRREREVPVTVKMRIGVDEE--HETYLDAAR 220

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           + + +GV  + +H R A                D+  +  +K+    + +  NG     S
Sbjct: 221 AAQDAGVAALALHGRTA--------RQHYAGKADWSAIARLKEAC-RIPVLGNGDTWTGS 271

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            AL+++     DGV++GR       +   +    S  +  + P     D D       + 
Sbjct: 272 HALEMMRQTGCDGVVVGRGCQGRPWLFADIVHALSGSVERTHP-----DLDAVIATIRAH 326

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMI 319
               A  L     ++ + +H+     G+P   + R  L   +  +      +E     + 
Sbjct: 327 ARLLAAELGEDRGVRDLRKHIGWYLKGYPVGGQARGDLMKVSSLAELDAG-LEAMRARLP 385

Query: 320 ESL 322
           E +
Sbjct: 386 EQV 388


>gi|15901996|ref|NP_346600.1| NifR3 family TIM-barrel protein [Streptococcus pneumoniae TIGR4]
 gi|111657242|ref|ZP_01408011.1| hypothetical protein SpneT_02001540 [Streptococcus pneumoniae
           TIGR4]
 gi|14973700|gb|AAK76240.1| putative TIM-barrel protein, NifR3 family [Streptococcus pneumoniae
           TIGR4]
          Length = 318

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 184 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 244 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 298

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 299 AISQASTLAE 308


>gi|296118884|ref|ZP_06837457.1| putative tRNA-dihydrouridine synthase [Corynebacterium ammoniagenes
           DSM 20306]
 gi|295967982|gb|EFG81234.1| putative tRNA-dihydrouridine synthase [Corynebacterium ammoniagenes
           DSM 20306]
          Length = 400

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 74/314 (23%), Positives = 128/314 (40%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K +    F+  E P +L
Sbjct: 38  MAGVTNVAFRSLCREQEVHRTGTVSGLYVCEMVTARALVERNEKTMKMTTFAPDEDPRSL 97

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  ++     G+ L     + G+ +AA 
Sbjct: 98  QLYTVDPEYTYKAAKMIVDENLADHIDMNFGCPVPKITRRGGGSALPYKRRLFGNIVAAA 157

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +   + G   + +HAR A          
Sbjct: 158 VKATEGTDIPVTVKFRVGIDDE--NHTHLDAGRIAVEEGAAAVALHARTA--------AQ 207

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R     D++ +  +K+   + D+ I  NG +   + A +++     DGV++GR       
Sbjct: 208 RYSGEADWNEIKRLKEHLAHTDVPILGNGDIFKATDAHRMMEETGCDGVVVGRGCLGRPW 267

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          + P    V +   R  +  M  Y      S    + I +H+    
Sbjct: 268 LFAELSAQLRGEEIPAEPTLGEVTQIIIRH-AELMAHYDGEAHAS----RDIRKHIGWYL 322

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 323 RGFPVGGGIRSALA 336


>gi|255003049|ref|ZP_05278013.1| tRNA-dihydrouridine synthase [Anaplasma marginale str. Puerto Rico]
          Length = 298

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 120/308 (38%), Gaps = 20/308 (6%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
             +R          LL +EMI + A++   ++++   S      A+Q+ G     + EAA
Sbjct: 1   MPFRSIVGEF-GAGLLVSEMIASRAMIIKTRQSLQK-SDVGANTAVQLAGCVPEIMAEAA 58

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           KI +D G   I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G
Sbjct: 59  KINQDMGARSIDINFGCPVKKIVDGHAGSALMKDEEKAAKIMESVVKAVTIPVTVKMRMG 118

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
                  +    L K  +  G+  + +H R         +        D+  +  +K + 
Sbjct: 119 WSATD--LNAPRLAKIAEDVGIQMVTVHGRT--------RTQMFSGTADWKFIKCVK-DC 167

Query: 187 PDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             + +  NG +  +        L   DGVMIGR AY    ++     +         P  
Sbjct: 168 VKIPVIANGDIRTLQDITSALSLSGADGVMIGRGAYGKPWLIKQALHFMKTGEALPEPS- 226

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAS 304
                D   +I     D A  +      ++ + +H+         +   R  +   +   
Sbjct: 227 ----ADEKLRIVLKHYDSAVDYYGKDIGVKILRKHLGWYSVSNAGATYFRAQINTMSDPV 282

Query: 305 TATHHIIE 312
                ++E
Sbjct: 283 AIREKLLE 290


>gi|315612212|ref|ZP_07887126.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis ATCC 49296]
 gi|315315605|gb|EFU63643.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis ATCC 49296]
          Length = 326

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 130/303 (42%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AIS 309


>gi|313204550|ref|YP_004043207.1| tRNA-u20-dihydrouridine synthase [Paludibacter propionicigenes WB4]
 gi|312443866|gb|ADQ80222.1| tRNA-U20-dihydrouridine synthase [Paludibacter propionicigenes WB4]
          Length = 341

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 79/309 (25%), Positives = 133/309 (43%), Gaps = 26/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M D TD  +R   +      ++YTE I ADA++R  K+    L    +E+P+A+Q+ G +
Sbjct: 18  MEDVTDPAFRLLCKRF-GVDMVYTEFISADALIRSVKRTEQKLTIYDEERPVAIQLYGRE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I  +     I+LN GCP  +V     GA L+ +   +    + + KA+++P
Sbjct: 77  ADAMAEAARIAAEACPEFIDLNFGCPVKKVAGKGAGAGLLRDIPKMLQITSEVVKAVNLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+    +    L + ++  G+  + IH R         +      + D+ +
Sbjct: 137 VTVKTRLGWDEDSKVIV--ELAERLQDCGIAALAIHGRT--------RSQMYKGDADWTL 186

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K      + I  NG +    +A +      VD VM+GRAA     +   + +YF  
Sbjct: 187 IGEVKNNPRMHIPIIGNGDVTTAERAAECFDRYGVDAVMVGRAAIGRPWVFAEMKQYFQT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISA-----SMTDYAARHLHSGGKLQ---QITRHMIG--LFH 285
                              I A      + D  A    S  +L+      RH+    +F 
Sbjct: 247 GEIHPVLTFEEQKNILKEHIIASVRWLDIDDNTAIESVSNQRLKGIIHSRRHLAATPVFK 306

Query: 286 GFPNSRRCR 294
           G PN +  R
Sbjct: 307 GIPNFKETR 315


>gi|322386176|ref|ZP_08059809.1| tRNA-dihydrouridine synthase [Streptococcus cristatus ATCC 51100]
 gi|321269756|gb|EFX52683.1| tRNA-dihydrouridine synthase [Streptococcus cristatus ATCC 51100]
          Length = 325

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 135/322 (41%), Gaps = 27/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            ++  +  +      IE    L
Sbjct: 307 AISQASTLAE-----IEELLQL 323


>gi|306828659|ref|ZP_07461852.1| tRNA-dihydrouridine synthase [Streptococcus mitis ATCC 6249]
 gi|304429165|gb|EFM32252.1| tRNA-dihydrouridine synthase [Streptococcus mitis ATCC 6249]
          Length = 326

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|332365222|gb|EGJ42985.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1059]
          Length = 325

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 127/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|293189559|ref|ZP_06608279.1| zinc-binding TIM-barrel protein, nifR3 family [Actinomyces
           odontolyticus F0309]
 gi|292821649|gb|EFF80588.1| zinc-binding TIM-barrel protein, nifR3 family [Actinomyces
           odontolyticus F0309]
          Length = 411

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/362 (19%), Positives = 132/362 (36%), Gaps = 78/362 (21%)

Query: 1   MVDWTDRHYRFFARLLT------------------------------------------- 17
           M   TD  +R   R++                                            
Sbjct: 1   MAGVTDVPFRRLCRIMGESGLPDHLRPVGIPSWAAESGEGATASSPKAPGESSNEPRHVT 60

Query: 18  ------NNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV 69
                    L  TEM+ + A++  +++   ++     E+  +LQ+ G + + + +AA ++
Sbjct: 61  IPRVDAPAGLYVTEMVTSRALVEENERTLEMVRPDPAERVRSLQLYGVNPAVMAKAATML 120

Query: 70  EDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---------IPV 119
            +    + I+LN GCP  +V +   GA L    D+  D + A+ +A           IPV
Sbjct: 121 VERDLTDHIDLNFGCPVPKVTKKGGGAALPWKRDLFSDLVGAVVRACDEAGERAGREIPV 180

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+D +       +   S +K G   + +HAR          +     +  +D +
Sbjct: 181 TVKIRIGIDSEHETAT--DAALSAQKLGAAALTLHARTQ--------NQHYAGHAHWDEI 230

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +  D+ +  NG + + + AL +L     DG+ +GR A     +   +   +    
Sbjct: 231 ARLK-DLLDIPVFGNGDVFEAADALAMLEQTGCDGISVGRGAQGRPWIFRDIVAAYHGGS 289

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P    V        +  + D        G  L+++ +H+     GF      RH L
Sbjct: 290 IPPGPSLAEVVSVIECHAAWCVVD----QGDEGRALREMRKHIGWYLRGFAVGGPQRHAL 345

Query: 298 TV 299
           ++
Sbjct: 346 SM 347


>gi|325688860|gb|EGD30868.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK115]
          Length = 325

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 127/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|89900372|ref|YP_522843.1| dihydrouridine synthase TIM-barrel protein nifR3 [Rhodoferax
           ferrireducens T118]
 gi|89345109|gb|ABD69312.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodoferax
           ferrireducens T118]
          Length = 350

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 69/331 (20%), Positives = 122/331 (36%), Gaps = 26/331 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R L       +EM+ +   L    +         +  P+A+QI G +
Sbjct: 17  MAGVTDRPFRQLCRRL-GAGYAVSEMLTSRPDLWHTPQTARRANHDGEAGPIAVQIAGTE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            + + +AA    D G   I++N+GCP+ +V     G+ LM N  +    I A+       
Sbjct: 76  AAMMAQAAAYNIDCGAQIIDINMGCPAKKVCSKWAGSALMQNEPLALSIIEAVVAVCTPR 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G            L ++ + +GV  I +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWCQSHKNAVA--LARAAEGAGVQMITVHGRT--------REQGYSGTAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K     + +  NG ++   QA  +L     D VM+GRAA     +   +  + 
Sbjct: 186 YDTIAAVKAAI-KVPVVANGDIDSPEQARHVLAVTRADAVMVGRAAQGRPWIFREMAHFL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V +     +      Y          ++   +H+       P     
Sbjct: 245 ATGSHLAPPLVAEVKQLLIDHLYDHYALYGDF-----LGVRTARKHIGWYVKNLPGGDAF 299

Query: 294 RHI--LTVEAGASTATHHIIETAFNLMIESL 322
           R    L  + G   A         N  ++ L
Sbjct: 300 RARMNLMEDCGQQAAAVADFFDVLNARMDRL 330


>gi|332685806|ref|YP_004455580.1| tRNA dihydrouridine synthase B [Melissococcus plutonius ATCC 35311]
 gi|332369815|dbj|BAK20771.1| tRNA dihydrouridine synthase B [Melissococcus plutonius ATCC 35311]
          Length = 336

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 82/303 (27%), Positives = 129/303 (42%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  A+      L+  EMI    I   +KK   +L     E PL++QI G D
Sbjct: 18  MAGISNAAFRITAKEF-GAGLVVCEMISDKGIHFRNKKTLDMLYIDENEHPLSIQIFGGD 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V++    + I++N+GCP  +V +   GA  +L+PD V + I A+  A+ I
Sbjct: 77  KDTLVEAAQFVQENTKADIIDINMGCPVNKVIKAEAGAKWLLDPDKVYEMIHAVSSAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DDQ        +      +    +    R  + +G            +++
Sbjct: 137 PVTVKMRTGWDDQHILAIENAIAAEKAGAAAIAMHGRTRTQMYEG----------KANWE 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+K+     FIG NG ++    A K+L  V  DGVMIGRA   N  M+     Y   
Sbjct: 187 ILKEVKQHVAIPFIG-NGDVKTPEDAKKMLEYVKADGVMIGRAILGNPWMIHRTTNYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  T   K     I+                +++  +H      G P + + + 
Sbjct: 246 GTLMVEPTPTEKIK-----IAKVHLQRLIDIKGEKIAVREFRQHAAYYLKGIPRAAKVKV 300

Query: 296 ILT 298
            + 
Sbjct: 301 AIN 303


>gi|116516462|ref|YP_817401.1| TIM-barrel protein, nifR3 family protein, putative [Streptococcus
           pneumoniae D39]
 gi|116077038|gb|ABJ54758.1| TIM-barrel protein, nifR3 family protein, putative [Streptococcus
           pneumoniae D39]
          Length = 318

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 184 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 244 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 298

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 299 AISQASTLAE 308


>gi|322377962|ref|ZP_08052450.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M334]
 gi|321281138|gb|EFX58150.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M334]
          Length = 336

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 202 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 262 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 316

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 317 AISQASTLAE 326


>gi|270291880|ref|ZP_06198095.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M143]
 gi|270279408|gb|EFA25250.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M143]
          Length = 336

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 34  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 92

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++     + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 93  EDSLARAAEFIQKNTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 153 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 202 TLHDVAQALTKIPFIANGDIRTVQDAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   ++            +++          G   + + R 
Sbjct: 262 GEILPDLTFEDKMKIAYEHLKRLIS-----LKGEKIAVREFRGLAPHYLRGTSGAAKLRG 316

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 317 AISQASTLAE 326


>gi|116628953|ref|YP_814125.1| tRNA-dihydrouridine synthase [Lactobacillus gasseri ATCC 33323]
 gi|238853552|ref|ZP_04643924.1| tRNA-dihydrouridine synthase B [Lactobacillus gasseri 202-4]
 gi|311111242|ref|ZP_07712639.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           gasseri MV-22]
 gi|116094535|gb|ABJ59687.1| tRNA-U20-dihydrouridine synthase [Lactobacillus gasseri ATCC 33323]
 gi|238833848|gb|EEQ26113.1| tRNA-dihydrouridine synthase B [Lactobacillus gasseri 202-4]
 gi|311066396|gb|EFQ46736.1| zinc-binding TIM-barrel protein, nifR3 family [Lactobacillus
           gasseri MV-22]
          Length = 335

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 125/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 22  MAGISNAAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V+     + IN+N+GCP  +V +   GA  +L+P+ +   + A+ + +S 
Sbjct: 81  EETLVEAAHYVDTHTAADIININMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +       + +++G + + +H R         +    +   D++
Sbjct: 141 PVTVKMRTGWDQK--HIFAVENALAAQEAGASAVAMHGRT--------RKQMYMGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+       F+G NG +    +A  +L     D VM+GRAA  N  ++  +  Y   
Sbjct: 191 TLKEVADALTIPFVG-NGDVTTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                             ++   + D     +     + +  R       G P S R R 
Sbjct: 250 GEKLRPQTVEEKVATAKEQL-NGLIDLKGEKIA----VPEFRRQAAYYLKGIPRSARTRA 304

Query: 296 ILT 298
            + 
Sbjct: 305 KIN 307


>gi|327463514|gb|EGF09833.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1057]
          Length = 325

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +     A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSAQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|241204538|ref|YP_002975634.1| TIM-barrel protein, nifR3 family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240858428|gb|ACS56095.1| TIM-barrel protein, nifR3 family [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 338

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/290 (24%), Positives = 125/290 (43%), Gaps = 27/290 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++    S    +P  +Q+ G + 
Sbjct: 33  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAESWSRLSAAGFRPHMVQLAGREA 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPV
Sbjct: 92  HWMAEAAKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++   ++ +  + +G+  + IH R  +               D+D +
Sbjct: 152 TLKMRLGWDE--NSINAPDIARRAEAAGIQLVTIHGRTRM--------QFYEGRADWDAI 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG +E  S A +IL     D VMIGR                +  +
Sbjct: 202 RAV-REVISIPLIANGDVETASDAQEILRRSGADAVMIGRGCQGRPWH--------AGVI 252

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +G+   ++    D   +    M D+          ++   +H+      F
Sbjct: 253 SGAPAPQSLKIADIAVEHYRMMLDFYGE----AVAIRHARKHLGWYLQRF 298


>gi|254994912|ref|ZP_05277102.1| hypothetical protein AmarM_02227 [Anaplasma marginale str.
           Mississippi]
          Length = 298

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 120/308 (38%), Gaps = 20/308 (6%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
             +R          LL +EMI + A++   ++++   S      A+Q+ G     + EAA
Sbjct: 1   MPFRSIVGEF-GAGLLVSEMIASRAMIIKTRQSLQK-SDVGANTAVQLAGCVPEIMAEAA 58

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           KI +D G   I++N GCP  ++ +G  G+ LM + +     + ++ KA++IPVTVK R+G
Sbjct: 59  KINQDMGARSIDINFGCPVKKIVDGHAGSALMKDEEKATKIMESVVKAVTIPVTVKMRMG 118

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
                  +    L K  +  G+  + +H R         +        D+  +  +K + 
Sbjct: 119 WSATD--LNAPRLAKIAEDVGIQMVTVHGRT--------RTQMFSGTADWKFIKCVK-DC 167

Query: 187 PDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             + +  NG +  +        L   DGVMIGR AY    ++     +         P  
Sbjct: 168 VKIPVIANGDIRTLQDITSALSLSGADGVMIGRGAYGKPWLIKQALHFMKTGEALPEPS- 226

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAS 304
                D   +I     D A  +      ++ + +H+         +   R  +   +   
Sbjct: 227 ----ADEKLRIVLKHYDSAVDYYGKDIGVKILRKHLGWYSVSNAGATYFRAQINTMSDPV 282

Query: 305 TATHHIIE 312
                ++E
Sbjct: 283 AIREKLLE 290


>gi|307705860|ref|ZP_07642699.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK597]
 gi|307620588|gb|EFN99685.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK597]
          Length = 326

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEYIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|157151554|ref|YP_001451243.1| transcriptional regulator [Streptococcus gordonii str. Challis
           substr. CH1]
 gi|157076348|gb|ABV11031.1| possible transcriptional regulator [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 317

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/317 (19%), Positives = 132/317 (41%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 184 TLHDVAQALTKIPFIANGDIRSVQEAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K     +   + D    H+     +++          G   + + R 
Sbjct: 244 GEILPDLTFEDKMKIAHDHLKR-LIDLKGEHIA----VREFRGLAPHYLRGTSGAAKLRG 298

Query: 296 ILTVEAGASTATHHIIE 312
            ++ +A        +++
Sbjct: 299 AIS-QANTLAEIEELLQ 314


>gi|284030422|ref|YP_003380353.1| TIM-barrel protein, nifR3 family [Kribbella flavida DSM 17836]
 gi|283809715|gb|ADB31554.1| TIM-barrel protein, nifR3 family [Kribbella flavida DSM 17836]
          Length = 381

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 127/307 (41%), Gaps = 25/307 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  YR          L   EMI +  I+ GD+K+  +L F  +E   ++Q+ G D
Sbjct: 26  MAGITNAAYRRLCAE-QGAGLYVCEMITSRGIVEGDQKSLDMLTFDERETVRSVQLYGVD 84

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
              +  A +++ D +G   I+LN GCP  +V     GA L    +++G  + +  KA   
Sbjct: 85  PVYIGRAVELLCDAYGVAHIDLNFGCPVPKVTRKGGGAALPWKRNLLGAILQSAVKAATP 144

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K RIG+D +       +  +  ++SG   I +H R A                
Sbjct: 145 YDVPVTMKTRIGIDSEHQ--TYLDAGRIAEESGAAAIGLHGRTA--------AQAYSGQA 194

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+  E+ D+ +  NG + + S AL+++      GV++GR       +   +   
Sbjct: 195 DWTKIAELV-EHVDIPVLGNGDIWEASDALRMVEQTGCAGVIVGRGCLGRPWLFRDLAVA 253

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+     + P    V     R       +  A  +     L+   +H+     GFP    
Sbjct: 254 FAGGEALNLPTLGEVATVMRRH-----GELLADLMGEQRGLRDFRKHVPWYLKGFPAGGE 308

Query: 293 CRHILTV 299
            R  L +
Sbjct: 309 LRAALGM 315


>gi|227894508|ref|ZP_04012313.1| tRNA-dihydrouridine synthase [Lactobacillus ultunensis DSM 16047]
 gi|227863667|gb|EEJ71088.1| tRNA-dihydrouridine synthase [Lactobacillus ultunensis DSM 16047]
          Length = 341

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 125/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EDTLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVEK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + I +H R         +        D++
Sbjct: 140 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGKADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   ++    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 VLHDVAQAL-NIPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T          +    ++ A       +       + +  +       G P S R R 
Sbjct: 249 GETLPPQTVREKVETAKHQLRA-----LVKIHGEKRAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|307702576|ref|ZP_07639528.1| TIM-barrel protein, nifR3 family protein [Streptococcus oralis ATCC
           35037]
 gi|307623692|gb|EFO02677.1| TIM-barrel protein, nifR3 family protein [Streptococcus oralis ATCC
           35037]
          Length = 326

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRVEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|184201291|ref|YP_001855498.1| putative dihydrouridine synthase [Kocuria rhizophila DC2201]
 gi|183581521|dbj|BAG29992.1| putative tRNA-dihydrouridine synthase [Kocuria rhizophila DC2201]
          Length = 394

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 69/331 (20%), Positives = 131/331 (39%), Gaps = 37/331 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T++ +R   R      L  TEM+ A A++    +++  +     E P ++QI G D
Sbjct: 37  MAGVTNKSFRKLCREYGG-GLYVTEMVTARALVERRPESLRIIHHDPGETPRSIQIYGVD 95

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + +A ++V      + I+LN GCP  +V +   G+ L    D+    ++ A+ +A  
Sbjct: 96  AVNVGKAVRMVAQEDRADHIDLNFGCPVPKVTKRGGGSALPWKTDLFRAIVSTAVREAGD 155

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK RIG+DD+       +  +  +  GV  + +H R          +       ++
Sbjct: 156 IPVTVKMRIGIDDEHQ--TYLDAGRMARDEGVAAVALHGRTL--------EQHYSGTANW 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  +++  PD+ +  NG +     A++++     DGV++GR       +   +   F 
Sbjct: 206 DAIARLREALPDIPVLGNGDIFSAEDAVRMVEHTGVDGVVVGRGCQGRPWLFGDLQAAFE 265

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P   +V    +R       ++           ++I +H+   F G+P     R
Sbjct: 266 GSPRRFRPGVRKVADTVYRHAELLTEEFG----DEAKGCREIRKHVSWYFKGYPVGGELR 321

Query: 295 ----------------HILTVEAGASTATHH 309
                             L ++A    A   
Sbjct: 322 AKMAQVPDLAALRELLDQLDLDAPYPGADVE 352


>gi|303259674|ref|ZP_07345650.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP-BS293]
 gi|303264577|ref|ZP_07350496.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS397]
 gi|307707852|ref|ZP_07644329.1| transcriptional regulator [Streptococcus mitis NCTC 12261]
 gi|307710303|ref|ZP_07646744.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK564]
 gi|307711175|ref|ZP_07647597.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK321]
 gi|302639226|gb|EFL69685.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae SP-BS293]
 gi|302645947|gb|EFL76175.1| TIM-barrel protein, putative, NifR3 family [Streptococcus
           pneumoniae BS397]
 gi|307616112|gb|EFN95308.1| transcriptional regulator [Streptococcus mitis NCTC 12261]
 gi|307617137|gb|EFN96315.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK321]
 gi|307618895|gb|EFN98030.1| TIM-barrel protein, nifR3 family protein [Streptococcus mitis
           SK564]
          Length = 326

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|331267284|ref|YP_004326914.1| tRNA-dihydrouridine synthase, putative [Streptococcus oralis Uo5]
 gi|326683956|emb|CBZ01574.1| tRNA-dihydrouridine synthase, putative [Streptococcus oralis Uo5]
          Length = 326

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHTDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|306826116|ref|ZP_07459452.1| tRNA-dihydrouridine synthase [Streptococcus sp. oral taxon 071 str.
           73H25AP]
 gi|304431832|gb|EFM34812.1| tRNA-dihydrouridine synthase [Streptococcus sp. oral taxon 071 str.
           73H25AP]
          Length = 326

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 132/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHKVAQALTKIPFIANGDIRTVQDAKQRVEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   ++            +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIS-----LKGEKIAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|114771140|ref|ZP_01448580.1| tRNA-dihydrouridine synthase, putative [alpha proteobacterium
           HTCC2255]
 gi|114548422|gb|EAU51308.1| tRNA-dihydrouridine synthase, putative [alpha proteobacterium
           HTCC2255]
          Length = 324

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 76/289 (26%), Positives = 124/289 (42%), Gaps = 25/289 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGGA 57
              TD  YR          L+ +EM+ +  I++       +  LGF+ +   +  QI G 
Sbjct: 17  AGITDLPYRNLVSSF-GAGLVVSEMVASHEIMQKGKDARARAELGFNVEGTSV--QIAGR 73

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   + E AK++E  G   I++N+GCP+  V  G+ G+ LM  PD+    I A+  A+ I
Sbjct: 74  DAFWMSECAKLIEGNGAKIIDINMGCPAKSVVNGASGSALMRTPDLALKLIEAVVNAVDI 133

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D      A  +L  S +K G+  I IH R         +      + D+ 
Sbjct: 134 PVTLKTRLGWDHNDLNAA--DLSSSAEKIGIQMITIHGRT--------RCQFYKGDADWR 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K E  ++ +  NG + D   A   +     DGVMIGR A     +L+ +     N
Sbjct: 184 KIREVK-EAVNIPVIANGDIIDTPTAKLAMKQSKADGVMIGRGAQGKPWLLSQIASEIFN 242

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 P   ++ +         +  Y  +H   G K+    +H+    
Sbjct: 243 TKPPEIPSGNKLLEMISDHYLDMLNFYGEQH---GNKV--ARKHLGWYM 286


>gi|261250467|ref|ZP_05943042.1| tRNA-dihydrouridine synthase B [Vibrio orientalis CIP 102891]
 gi|260939036|gb|EEX95023.1| tRNA-dihydrouridine synthase B [Vibrio orientalis CIP 102891]
          Length = 285

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 120/300 (40%), Gaps = 21/300 (7%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  L    K+   +    +    ++QI GAD   + +AA+   + G   I+
Sbjct: 1   MAVSEMMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGADPQLMADAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+  PDI+ D + A+  A+ +PVT+K R G D          
Sbjct: 61  INMGCPAKKVNKKLAGSALLQYPDIIKDILQAVVNAVDVPVTLKTRTGWD--TDNKNCVQ 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K  +  G+  + +H R         K        +YD +  +K+    + +  NG ++
Sbjct: 119 IAKLAEDCGIQALALHGRT--------KACMYKGEAEYDSIKAVKQAI-SIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  +  N  T      + V       ++
Sbjct: 170 SPEKAKFVLEYTGADALMIGRPAQGRPWIFQEIQHFLENGTTMPDLPYSEVKDILLGHVN 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A  + Y           +   +H+         +   R        A+      +E  F+
Sbjct: 230 ALHSFY-----GEYLGPRIARKHVGWYLKEHEQASEFRPTFNA-IDAAELQLEALEEYFD 283


>gi|227506387|ref|ZP_03936436.1| possible tRNA-dihydrouridine synthase [Corynebacterium striatum
           ATCC 6940]
 gi|227197038|gb|EEI77086.1| possible tRNA-dihydrouridine synthase [Corynebacterium striatum
           ATCC 6940]
          Length = 381

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 74/314 (23%), Positives = 126/314 (40%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EM+ A A++  ++K +    F  +E P +L
Sbjct: 19  MAGVTNVAFRTLCREQEIEKTGTVSGLYVCEMVTARALVERNEKTMHMTTFGPEENPRSL 78

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +AAK++ D    + I++N GCP  +V     G+ L     + G+ IAA 
Sbjct: 79  QLYTVDPEYTYKAAKMIVDENLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIIAAA 138

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            KA     IPVTVK R+G+DD+       +  +   + G   + +H R A          
Sbjct: 139 VKATEGTDIPVTVKMRVGIDDEHH--THLDAGRIAVEEGAAAVALHGRTA--------AQ 188

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R   + D++ +  +K+   D  + +  NG +   + A  ++     DGV++GR       
Sbjct: 189 RYSGHADWNEIARLKEHLADSGIPVLGNGDIFKATDARAMMEQTGCDGVVVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +          + P    V K   R       +  A+H       + I +H+    
Sbjct: 249 LFAELSAELRGEPIPAEPTLGEVTKTMIRHA-----ELLAQHDGERQASRDIRKHVGWYL 303

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 304 RGFPVGGEVRSGLA 317


>gi|297626128|ref|YP_003687891.1| TIM-barrel enzyme, dihydrouridine synthase [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296921893|emb|CBL56453.1| TIM-barrel enzyme, dihydrouridine synthase [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 387

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 115/305 (37%), Gaps = 25/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  YR          L   EMI +  ++ G+ K   +L F   E   ++Q  G +
Sbjct: 28  MAGVTNAAYRTLCYE-QGAGLCVCEMITSRGLVVGNVKTDSMLTFFDDEPHRSVQTYGTN 86

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              L  A  ++   +  + ++LN GCP  +V     G  L    D++ + I    +A   
Sbjct: 87  PRVLARAIDELCTHYRADHVDLNFGCPVPKVTRKGGGGVLPWKLDLIREIIRQSVRAADA 146

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P+TVK R+G+DD        ++ +  ++ G   I +H R                + 
Sbjct: 147 HGVPLTVKTRVGIDDD--HTTFLDVGRIAQEEGAAAICLHGRT--------VAEAYAGHA 196

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+     D+ +  NG + + S AL+++      GV IGR       +   +   
Sbjct: 197 HWDRIGELV-AAVDIPVLGNGDIWEPSDALEMMARTGCAGVEIGRGCLGRPWLFRDLAAA 255

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                  + P    V       I     +   R +     L  + +HM   F GFP    
Sbjct: 256 MHGQQVQTLPTLGEVA-----AIVRRHGELLVRQMGVKHGLTDLRKHMSWYFKGFPVGGE 310

Query: 293 CRHIL 297
            RH L
Sbjct: 311 LRHSL 315


>gi|116493271|ref|YP_805006.1| tRNA-dihydrouridine synthase [Pediococcus pentosaceus ATCC 25745]
 gi|116103421|gb|ABJ68564.1| tRNA-U20-dihydrouridine synthase [Pediococcus pentosaceus ATCC
           25745]
          Length = 332

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 124/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+ G+KK   ++     E P+++QI G  
Sbjct: 19  MAGVTNTAFRMICKKF-GAGLVVCEMISDRGIIYGNKKTLSMMTVDPNEHPMSIQIFGGT 77

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V ++   + I++N+GCP  +V     GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEAAKFVDQNTDADIIDINMGCPVNKVVNTDAGARWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D     +       + +++G + + +H R         +        D++
Sbjct: 138 PVTVKMRTGWD--ANHILAVENALAAERAGASALAMHGRT--------RKQMYTGQADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG +     A ++L     D VMIGRA   N   L  +  Y ++
Sbjct: 188 ILKEVGSQL-HIPFMGNGDVRTPEDAKRMLDEVGADAVMIGRAVLGNPWELQRISAYLND 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P           +I+                 ++          G P+S R + 
Sbjct: 247 GTVIDEPTPREKI-----EIAKEHLHALVELKGENVGPREFRGQAAYYLKGIPHSARTKV 301

Query: 296 ILT 298
            +T
Sbjct: 302 AVT 304


>gi|310778159|ref|YP_003966492.1| TIM-barrel protein, nifR3 family [Ilyobacter polytropus DSM 2926]
 gi|309747482|gb|ADO82144.1| TIM-barrel protein, nifR3 family [Ilyobacter polytropus DSM 2926]
          Length = 311

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 72/324 (22%), Positives = 141/324 (43%), Gaps = 32/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           M   TD  YR   +    + L++TEM+  +A+   ++K    +L     +   A+QI G 
Sbjct: 8   MAGVTDYTYRRIMKEFHPD-LMFTEMVSVNAVEMANEKTINKMLRLLPDD---AVQIFGK 63

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
           DI  +  +AK VE+ G   I++N+GCP  ++ +  +G+ ++ +P+     +  + K+L  
Sbjct: 64  DIEIMKNSAKYVENLGVKHIDVNMGCPVPKIVKNGYGSAMLEDPEHARKMMLELRKSLKP 123

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RIG  +    +      K  +++G   I IH R         K+       D
Sbjct: 124 ETCLSMKIRIGYKNHKDPL---KFAKIAEEAGCEHITIHGRT--------KEQMYSGTAD 172

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D++ ++K +  ++ +  NG +     A    +   VDGVM+ R  Y N  ++  V E F
Sbjct: 173 WDVIKDVKSQV-NIPVIGNGDIFTPEDAYEKAMYSKVDGVMLARGIYGNPWLIKQVREIF 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 + P          + +  +  D+  R  +      +I +H+     G  N+   
Sbjct: 232 QEGTVKTIPTAEDKIDMAIKHVKYAREDHPDRDFY-----FEIRKHLCWYIKGLKNATHG 286

Query: 294 RHILTVEAGASTATHHIIETAFNL 317
           ++++      S +   I+E   NL
Sbjct: 287 KNLIN----RSESYEEILEILENL 306


>gi|327472537|gb|EGF17968.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK408]
 gi|328944686|gb|EGG38847.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1087]
          Length = 325

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 128/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG + ++  A + +     D +MIGRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRNVQDAKQRIEEVGADAIMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSS---PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K +V  D   ++     +Y A     G               G   + +
Sbjct: 252 GEVLPDLSFENKMKVAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|282852631|ref|ZP_06261973.1| TIM-barrel protein, nifR3 family [Lactobacillus gasseri 224-1]
 gi|282556373|gb|EFB61993.1| TIM-barrel protein, nifR3 family [Lactobacillus gasseri 224-1]
          Length = 335

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 126/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 22  MAGISNAAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V+     + IN+N+GCP  +V +   GA  +L+P+ +   + A+ + +S 
Sbjct: 81  EETLVEAAHYVDTHTAADIININMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +       + +++G + + +H R         +    +   D++
Sbjct: 141 PVTVKMRTGWDQK--HIFAVENALAAQEAGASAVAMHGRT--------RKQMYMGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+       F+G NG +    +A  +L     D VM+GRAA  N  ++  +  Y   
Sbjct: 191 TLKEVADALTIPFVG-NGDVTTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                             ++   + D   + +     + +  R       G P S R R 
Sbjct: 250 GEKLRPQTVEEKVATAKEQL-NGLIDLKGQKIA----VPEFRRQAAYYLKGIPRSARTRA 304

Query: 296 ILT 298
            + 
Sbjct: 305 KIN 307


>gi|116252011|ref|YP_767849.1| tRNA-dihydrouridine synthase (nitrogen regulation protein)
           [Rhizobium leguminosarum bv. viciae 3841]
 gi|115256659|emb|CAK07747.1| putative tRNA-dihydrouridine synthase (nitrogen regulation protein)
           [Rhizobium leguminosarum bv. viciae 3841]
          Length = 338

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 118/290 (40%), Gaps = 27/290 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++    S    +P  +Q+ G + 
Sbjct: 33  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAESWSRLSAAGFRPHMVQLAGREA 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPV
Sbjct: 92  HWMAEAAKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHAIGLIEATVKAVDIPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++   ++ +  + +GV  + IH R  +               D+D +
Sbjct: 152 TLKMRLGWDE--NSINAPDIARRAEAAGVQLVTIHGRTRM--------QFYEGRADWDAI 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG +E    A +IL     D VMIGR           +        
Sbjct: 202 RAV-REVISIPLIANGDVETAGDAQEILRRSGADAVMIGRGCQGRPWHAGVI-------S 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               P+   +           +  Y          ++   +H+      F
Sbjct: 254 GAPEPLPPEIADIAIEHYRMMLDFYGEA-----VAIRHARKHLGWYLQRF 298


>gi|320353935|ref|YP_004195274.1| tRNA-U20-dihydrouridine synthase [Desulfobulbus propionicus DSM
           2032]
 gi|320122437|gb|ADW17983.1| tRNA-U20-dihydrouridine synthase [Desulfobulbus propionicus DSM
           2032]
          Length = 329

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/300 (23%), Positives = 123/300 (41%), Gaps = 30/300 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             +TD  +R   R     AL ++EMI    ++   K  +  L    +E+P A+Q+ G++ 
Sbjct: 29  AGYTDLPFRLLCRE-NGAALCFSEMISCHGLVYEQKNTLELLRTVPEERPFAVQLFGSEP 87

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  A  +V     + I++N+GCP  +V +   GA LM +P      I A+C   S+PV
Sbjct: 88  ELMARATAMVSSGPVDLIDINMGCPVRKVIKKGCGAALMKDPQRAEAIIRAVCAQTSLPV 147

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G   +  +V         + +G + + IH R  +       D R        ++
Sbjct: 148 TVKFRSGWTGE--SVNAPQFAAMAEAAGASAVTIHGRTWVQGFGGRADRR--------VI 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +   + +  NG +   + AL+++     DGVM+GR A  N  + +        P 
Sbjct: 198 RAVK-DAVSIPVIGNGDILTRADALEMMAETGCDGVMVGRGALGNPWLFS--------PS 248

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              + +  R+       +       A + L     L ++  H      G   +   RH L
Sbjct: 249 GRPATLANRLP------VIERYLQLAEQFLPLDKVLFKVKNHTAKFLSGLAGAATLRHAL 302


>gi|42518373|ref|NP_964303.1| hypothetical protein LJ0286 [Lactobacillus johnsonii NCC 533]
 gi|41582658|gb|AAS08269.1| hypothetical protein LJ_0286 [Lactobacillus johnsonii NCC 533]
          Length = 335

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 127/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 22  MAGISNAAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V+     + IN+N+GCP  +V +   GA  +L+P+ +   + A+ + +S 
Sbjct: 81  EETLVEAAHYVDTHTAADIININMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +       + +++G + + +H R         +    +   D++
Sbjct: 141 PVTVKMRTGWDQK--HIFAVENALAAQEAGASAVAMHGRT--------RKQMYMGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++       F+G NG +    +A  +L     D VM+GRAA  N  ++  +  Y   
Sbjct: 191 TLKDVADALTIPFVG-NGDVTTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    +++  + D     +     + +  R       G P S R R 
Sbjct: 250 GEKLRPQTVEEKVETAKDQLNR-LIDLKGEKIA----VPEFRRQAAYYLKGIPRSARTRA 304

Query: 296 ILT 298
            + 
Sbjct: 305 KIN 307


>gi|227495137|ref|ZP_03925453.1| dihydrouridine synthase [Actinomyces coleocanis DSM 15436]
 gi|226831589|gb|EEH63972.1| dihydrouridine synthase [Actinomyces coleocanis DSM 15436]
          Length = 410

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 66/328 (20%), Positives = 125/328 (38%), Gaps = 47/328 (14%)

Query: 1   MVDWTDRHYRFFARLLT---------------------NNALLYTEMIVADAILRGDKKN 39
           M   TD  +R  +R                           L   EMI A A++  ++K 
Sbjct: 28  MAGVTDVPFRRLSREFGEAGLPESQQEKLNQATPGIDAPAGLYVCEMITARALVEKNEKT 87

Query: 40  I--LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGAC 96
           +       Q++  +LQ+ G D   L +A  I+ E+   + I+LN GCP  +V +   GA 
Sbjct: 88  MHMAKPDPQDRVRSLQLYGTDPVNLYKATHILLEEDFVDHIDLNFGCPVPKVTKKGGGAA 147

Query: 97  LMLNPDIVGDCIAAMCKAL-----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           L    D+  D + ++ +A+      +PVT+K R+G+DD       R+  +  + +G+  +
Sbjct: 148 LPWKLDLFDDIVNSVVRAVTETGKDVPVTIKMRVGIDD--AHHTFRDAGRIAEDAGIAAV 205

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PS 209
            +H R                + D+D + ++K++   + +  NG +     A  ++    
Sbjct: 206 ALHGRTQ--------AQYYSGHADWDTIAQLKQDLT-VPVLGNGDIFSAQDAKDVMAHTG 256

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS-SPIKTRVDKDFWRKISASMTDYAARHLH 268
            D V++GR A     +   +    +        P + RV +   +          A    
Sbjct: 257 CDAVVVGRGAQGRPWLFHDLVATLTGESVVELEPNQGRVAQIILQHAQMM----IANSRS 312

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               L+ + +H+     GF      R  
Sbjct: 313 ENEALRNMRKHIGWYLRGFKLGGDLRMA 340


>gi|227888863|ref|ZP_04006668.1| tRNA-dihydrouridine synthase [Lactobacillus johnsonii ATCC 33200]
 gi|268318841|ref|YP_003292497.1| tRNA-dihydrouridine synthase B [Lactobacillus johnsonii FI9785]
 gi|227850700|gb|EEJ60786.1| tRNA-dihydrouridine synthase [Lactobacillus johnsonii ATCC 33200]
 gi|262397216|emb|CAX66230.1| tRNA-dihydrouridine synthase B [Lactobacillus johnsonii FI9785]
          Length = 335

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 126/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 22  MAGISNAAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V+     + IN+N+GCP  +V +   GA  +L+P+ +   + A+ + +S 
Sbjct: 81  EETLVEAAHYVDTHTAADIININMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +       + +++G + + +H R         +    +   D++
Sbjct: 141 PVTVKMRTGWDQK--HIFAVENALAAQEAGASAVAMHGRT--------RKQMYMGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++       F+G NG +    +A  +L     D VM+GRAA  N  ++  +  Y   
Sbjct: 191 TLKDVADALTIPFVG-NGDVTTPEKAKAMLEDVGADAVMVGRAALGNPWIIKDMVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P       +  +     + D     +     + +  R       G P S R R 
Sbjct: 250 GE-KLRPQTVEEKVETAKDQLNGLIDLKGEKIA----VPEFRRQAAYYLKGIPRSARTRA 304

Query: 296 ILT 298
            + 
Sbjct: 305 KIN 307


>gi|323189128|gb|EFZ74412.1| TIM-barrel protein, nifR3 family protein [Escherichia coli RN587/1]
          Length = 290

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 61/303 (20%), Positives = 119/303 (39%), Gaps = 21/303 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              L  +EM+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G  
Sbjct: 2   GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  +  G+  + IH R         +        +YD +  +K++   + +  NG
Sbjct: 120 CEEIAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCA 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            +      Y       G ++    +H+         + + R        AS      +E 
Sbjct: 231 HVRELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEA 284

Query: 314 AFN 316
            F 
Sbjct: 285 YFE 287


>gi|116669897|ref|YP_830830.1| nifR3 family TIM-barrel protein [Arthrobacter sp. FB24]
 gi|116610006|gb|ABK02730.1| putative TIM-barrel protein, nifR3 family [Arthrobacter sp. FB24]
          Length = 392

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 59/316 (18%), Positives = 120/316 (37%), Gaps = 41/316 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    +++  +     EK  ++Q+ G D
Sbjct: 33  MAGITNSAFRRLCREYGG-GMYVAEMVTSRALVERTPESLRIISHDDDEKVRSVQLYGVD 91

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + +A ++ VE+   + I+LN GCP  +V     G+ L    D+    +    K  S 
Sbjct: 92  PVTVGQAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTSIVQTAVKEASK 151

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +P+T+K R G+D+    +   +  +  + +GV  + +H R A                
Sbjct: 152 GNVPLTIKMRKGIDED--HLTYLDAGRIARDAGVAAVALHGRTA--------AQFYSGQA 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA-----------AYKNS 223
           D+  +  +++  PD+ +  NG +     A++++         R                 
Sbjct: 202 DWSAIARLREALPDIPVLGNGDIWSAEDAVRMV---------RETGVDGVVVGRGCQGRP 252

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +   F    T   P   +V +  +R     +  +       G  L++I +HM   
Sbjct: 253 WLFGDLQAAFEGSDTRHRPNLRQVAEGVYRHAELMVETFG----DEGKALREIRKHMAWY 308

Query: 284 FHGFPNSRRCRHILTV 299
           F G+      R  L +
Sbjct: 309 FKGYVVGGELRTRLAL 324


>gi|224028635|gb|ACN33393.1| unknown [Zea mays]
          Length = 296

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 97/231 (41%), Positives = 142/231 (61%), Gaps = 5/231 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 63  MMDWTDNHYRTLARLISRHAWLYTEMVVAETIVHQKDNLDRFLAFPEEQHPIVLQIGGSN 122

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++  D+ Y+EINLN GCPS +V     FGA LM +P+ VGD ++ +     +
Sbjct: 123 LENLAKATELANDYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSTIAANCDV 182

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V  +  KS      IHARKA+L GLSP +NRKIP L Y
Sbjct: 183 PVSVKCRIGVDDRDSYEELCEFVDKVISKSPTRHFIIHARKALLSGLSPAENRKIPPLKY 242

Query: 177 DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIGRAAYKNSAML 226
           +  + + ++ P++   LNGG+ ++   +  +     GVM+GRAAY    + 
Sbjct: 243 EYYFALLRDFPEIKFTLNGGITNVSQVSASMRQGAHGVMVGRAAYNKYVLF 293


>gi|170781947|ref|YP_001710279.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156515|emb|CAQ01666.1| putative tRNA-dihydrouridine synthase [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 408

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 67/301 (22%), Positives = 126/301 (41%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +++  +     EK  ++Q+ G D
Sbjct: 43  MAGITNTAFRRLCREF-GAGLYVSEMITSRALVERTPESMRLITHHPSEKVRSIQLYGVD 101

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + EA   +V +   + I+LN GCP A+V     GA L     +  D +  A+  A +
Sbjct: 102 PKTVREAVTMLVAEDRADHIDLNFGCPVAKVTRKGGGAALPWKLGLFTDIVEGAVKAAGN 161

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IP+TVK R G+D     +      ++ + +GV  I +HAR A         +    + D+
Sbjct: 162 IPLTVKMRKGID--ADHLTYLEAGRAAEGAGVASIALHARTA--------ADYYSGHADW 211

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K+   ++ +  NG +     A++++     DGV++GR       +   +   F 
Sbjct: 212 SAIAKLKQAIRNVPVLGNGDIWAAEDAIRMMDETGADGVVVGRGCLGRPWLFGDLAAAFH 271

Query: 235 NPLTGSSPIKTRVD-------KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               G  P  T           D +R+    +T++           +   +H+   F G+
Sbjct: 272 ARAAGLDPADTPRAHPSQGQVADTFRRHVELLTEFFESEE---RGCRDARKHVAWYFKGY 328

Query: 288 P 288
           P
Sbjct: 329 P 329


>gi|86138358|ref|ZP_01056932.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. MED193]
 gi|85824883|gb|EAQ45084.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. MED193]
          Length = 310

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 131/321 (40%), Gaps = 24/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G +
Sbjct: 1   MAGITDRPFRDLVRSF-GVGLMVSEMVASQEMVQSKPGVRERAELSADVENTAVQLAGRE 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+ +A+ IP
Sbjct: 60  ASWMAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVEAVDIP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD    +   ++    + +G+  + IH R         +        D+  
Sbjct: 120 VTLKTRLGWDD--NCLNAASVAARAEAAGIQMVTIHGRT--------RCQFYKGRADWSA 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    L +  NG + D + A   L     DGVMIGR       +L  V       
Sbjct: 170 IRAVKEAVG-LPVLANGDIVDSATATSALERSGADGVMIGRGIQGKPWLLAQVASDLWGS 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCRH 295
              + P    +     +   A +  Y          L+   +H+          +   R 
Sbjct: 229 AAPAIPEGDDLIDMVSKHYEAMLGFYGG-----DLGLRVARKHLGWYMDQAQTPAALRRA 283

Query: 296 ILTVEAGASTATHHIIETAFN 316
           ILT ++   T    ++  A +
Sbjct: 284 ILTEKS--PTEVLRLLPDALS 302


>gi|332365647|gb|EGJ43406.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK355]
          Length = 325

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A   +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKHRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|325695385|gb|EGD37285.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK150]
          Length = 326

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAYDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|160947348|ref|ZP_02094515.1| hypothetical protein PEPMIC_01282 [Parvimonas micra ATCC 33270]
 gi|158446482|gb|EDP23477.1| hypothetical protein PEPMIC_01282 [Parvimonas micra ATCC 33270]
          Length = 316

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 130/304 (42%), Gaps = 24/304 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R  A  +    L +TEM+    +   + K   I     +E P+ LQ+ G+D 
Sbjct: 12  AGVSDVAFRILASEM-GAGLTFTEMVSIKGLYYDNDKTSIITYIDKREGPVGLQVFGSDE 70

Query: 60  SKLVEAA--KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + E    +  +     +++LN+GCP+ ++ +   G+ LM +P  V   ++AM K   +
Sbjct: 71  NIMAEIIQNRFNKRDDIYQLDLNLGCPAPKIVKNHEGSYLMKDPKKVKTIVSAMVKNSKV 130

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R+G D+         +  +I ++G   I +HAR         ++       D++
Sbjct: 131 PVSVKIRLGFDENNKN--FLEVADAIVEAGAYMITLHART--------REMFYSGKADWN 180

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K   P + +  NG +  +   +++      D V IGR A  N  +   + +Y   
Sbjct: 181 AIKTLKNHVP-IKVVGNGDVCSVEDYVRMKEETGADAVAIGRHALGNPFIFKQIKDYNLT 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               SSP    V     R     +     R       ++++ ++++    GF +S + ++
Sbjct: 240 KKY-SSPTLEEVIDTIKRHYKLELEFKPERI-----AIREMRKNILWYLKGFKDSNKVKN 293

Query: 296 ILTV 299
            +  
Sbjct: 294 TINT 297


>gi|293364460|ref|ZP_06611186.1| tRNA-dihydrouridine synthase [Streptococcus oralis ATCC 35037]
 gi|291317306|gb|EFE57733.1| tRNA-dihydrouridine synthase [Streptococcus oralis ATCC 35037]
          Length = 318

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 62/310 (20%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 184 TLHKVAQALTKIPFIANGDIRTVQDAKQRVEEVGADAVMIGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 244 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 298

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 299 AISQASTLAE 308


>gi|327467879|gb|EGF13369.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK330]
          Length = 325

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAADFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAQALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|319956594|ref|YP_004167857.1| tim-barrel protein, nifr3 family [Nitratifractor salsuginis DSM
           16511]
 gi|319418998|gb|ADV46108.1| TIM-barrel protein, nifR3 family [Nitratifractor salsuginis DSM
           16511]
          Length = 320

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 76/323 (23%), Positives = 134/323 (41%), Gaps = 34/323 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + L  +EMI ++A+   + K   +L  S  E P ++QI G+D 
Sbjct: 16  AGFTDLPFRSMVKKFDVD-LTVSEMISSNALAHENAKTLKMLEKSPLEDPYSVQIAGSDP 74

Query: 60  SKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A   I    G + ++LN GCP+ +V     G+ L+ +P+ +G  +  +    + P
Sbjct: 75  ETIKRALDVINAREGIDIVDLNCGCPAPKVFNNLQGSALLGDPEKLGRAVETIKAYSNKP 134

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T VK R+GV ++        L K I+++G + I +H R         +  R    +DYD
Sbjct: 135 YTSVKMRLGVREK----NHVELAKVIEEAGADFIAVHGRT--------RAGRYKAPVDYD 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E+K E   + +  NG ++   +A   +     DG+MIGRAA     +   + E    
Sbjct: 183 AIREVK-EAVRIPVIANGDIDSPQKARWVREYTGCDGIMIGRAAVGRPWIFAQIKEGLDE 241

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCR 294
           P             D  R++     D    H    G +    +H+      G P +   R
Sbjct: 242 PSV-----------DLIREVVLEHFDQMIAHYGDYG-VFLFRKHLHTYSKAGLPGAGAFR 289

Query: 295 HILTVEAGASTATHHIIETAFNL 317
           + +      +      IE  F+ 
Sbjct: 290 NAVNTITDPAKMRGE-IERFFSQ 311


>gi|328543927|ref|YP_004304036.1| TRNA-dihydrouridine synthase [polymorphum gilvum SL003B-26A1]
 gi|326413671|gb|ADZ70734.1| TRNA-dihydrouridine synthase, putative [Polymorphum gilvum
           SL003B-26A1]
          Length = 310

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 125/287 (43%), Gaps = 20/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   +D  +R  A       ++ +EM+ ++++++GD +       +   L  +Q+ G + 
Sbjct: 1   MSGVSDLPFRRLASRF-GAGVVVSEMVASESLVQGDVEMRTRAEGKGIGLHVVQLAGREA 59

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I E  G + I++N+GCP+ RV  G  G+ LM + D     I A   A+S+PV
Sbjct: 60  RWMAEAARIAEGAGASIIDINMGCPAKRVTTGYSGSALMRDLDHALGLIEATVGAVSVPV 119

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D Q  ++    L +  + +GV  + +H R         ++       D+  +
Sbjct: 120 TVKMRLGWDAQ--SINAPELARRAQAAGVQLVTVHGRT--------RNQFYKGAADWAAI 169

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +  E  D+ +  NG       A ++  L    GVMIGR AY    ++  V  Y     
Sbjct: 170 RAVV-EAVDIPVIANGDCLSFDDADRMLALSGAAGVMIGRGAYGRPWLVGHVGAYLQTGE 228

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             + P  + +           ++ Y    L  G ++    +H+    
Sbjct: 229 RQAEPSGSTLCDIVLEHYEDLLSHYG---LDLGRRI--ARKHLGWYL 270


>gi|281492559|ref|YP_003354539.1| tRNA-dihydrouridine synthase [Lactococcus lactis subsp. lactis
           KF147]
 gi|281376223|gb|ADA65714.1| tRNA-dihydrouridine synthase [Lactococcus lactis subsp. lactis
           KF147]
          Length = 334

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 81/321 (25%), Positives = 144/321 (44%), Gaps = 21/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T++ +   A+      L+ TEMI    I   +KK   ++ F     PL++QI G +
Sbjct: 27  MAGITNKAFLTTAKEF-GAGLVVTEMISDKGIEHRNKKTLEMMDFEGVPHPLSMQIFGGE 85

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  LVEAAK VE     + I++N+GCP  +V +   G+ L+L+PD V D ++A+ KA+S 
Sbjct: 86  VDTLVEAAKFVEANTVADIIDINMGCPVPKVTKNEAGSRLLLDPDKVYDVVSAVSKAISR 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK RIG DD    +      K+I+  G   + +HAR                  ++ 
Sbjct: 146 PLTVKIRIGWDDD--HLFAVENAKAIEAGGGAAVSMHARTKAQAYTGNAQE------NWH 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++  EN ++ +  NG ++    A +++    V  VM+GRAA  N  +L   + Y   
Sbjct: 198 WLKKL-TENVNIPVIGNGDVKTPEDAKRMIDETGVTAVMMGRAALGNPWILHRTEHYLRT 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     + A + +    +L S    ++  +H      G   + + + 
Sbjct: 257 GELLPEPTVAEKMEIAKLHL-ARLVELKGDNLAS----REFRQHAAYYLKGASRAAKVKV 311

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +  +A +      I++   N
Sbjct: 312 AVN-QAESQAEIITILDNFVN 331


>gi|152972182|ref|YP_001337328.1| FMN-linked protein [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|150957031|gb|ABR79061.1| conserved protein, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 290

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 119/303 (39%), Gaps = 21/303 (6%)

Query: 18  NNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYN 75
              L  +EM+ ++  +    K+ L     ++P    +QI G+   ++  AA+I  + G  
Sbjct: 2   GAGLTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSVPEEMAAAARINVESGAQ 61

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V+    G+ L+  PD V   + A+  A+ +PVT+K R G + +     
Sbjct: 62  IIDINMGCPAKKVNRKLAGSALLQYPDQVKSILTAVVNAVDVPVTLKIRTGWEPEHRN-- 119

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + +  ++ G+  + IH R         +      + +YD +  +K++   + I  NG
Sbjct: 120 CVEIAQLAEECGIQALTIHGRT--------RACLFNGDAEYDSIRAVKQKV-SIPIIANG 170

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D  +A  +L     D +MIGRAA     +   +  Y              V +    
Sbjct: 171 DITDPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCA 230

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
            +      Y       G ++    +H+           + R        AS      +E 
Sbjct: 231 HVRELHDFYGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRTFNAIEDASE-QLEALEA 284

Query: 314 AFN 316
            F 
Sbjct: 285 YFE 287


>gi|253583466|ref|ZP_04860664.1| dihydrouridine-tRNA ligase [Fusobacterium varium ATCC 27725]
 gi|251834038|gb|EES62601.1| dihydrouridine-tRNA ligase [Fusobacterium varium ATCC 27725]
          Length = 320

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 72/325 (22%), Positives = 139/325 (42%), Gaps = 27/325 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  YR   +      LL+TEM+  +A+    +K +       +  ++Q+ G DI K
Sbjct: 10  AGVTDYTYRGILKEF-KPDLLFTEMVSINALEVACEKTLKVILRLREGDSVQLFGKDIKK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP--V 119
           +VE+AK VE  G   I++N GCP  ++    +GA LM  P++V   ++ +  AL+    +
Sbjct: 69  MVESAKFVESLGVKHIDINSGCPMKKIVNNGYGAALMEQPELVKAMLSEVRSALNDKTDL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G  +    V    + K  +++G   I IH R         ++       D+ I+
Sbjct: 129 SIKIRVGYKESKNPV---EIAKIAQETGCKHITIHGRT--------REQMYTGKADWSII 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K E+ D+ +  NG +     A +      VDG+M+ R  + N  ++  + EYF    
Sbjct: 178 KEVK-ESVDIPVIGNGDIFTAEDAKERVDYSGVDGIMLARGIFGNPWLIRDIREYFEYGK 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                          +    +  ++  R       + ++ +H+     G  N+   +  +
Sbjct: 237 ILHPVTDIEKIDMAIKHTKRTEVEHPERPF-----IFELRKHLCWYLKGIRNTAEIKDKI 291

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
                 +   + I+E   N + ++L
Sbjct: 292 NH----TDNYNEIVE-LLNRVKDNL 311


>gi|197336031|ref|YP_002157182.1| tRNA-dihydrouridine synthase B [Vibrio fischeri MJ11]
 gi|197317521|gb|ACH66968.1| tRNA-dihydrouridine synthase B [Vibrio fischeri MJ11]
          Length = 293

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 59/307 (19%), Positives = 121/307 (39%), Gaps = 25/307 (8%)

Query: 18  NNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
              +  +EM+ ++  L    K+   +    +    ++QI GAD   + EAA+   + G  
Sbjct: 4   GAGMAVSEMMSSNPKLWKTSKSQNRMVHEGESGIRSVQIAGADPKLMAEAAQHCVETGAQ 63

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I++N+GCP+ +V++   G+ L+  PD++ + + A+  A+ +PVT+K R G D       
Sbjct: 64  IIDINMGCPAKKVNKKLAGSALLQRPDLIEEILLAVVNAVDVPVTLKTRTGWDPDNRN-- 121

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
              + K  ++ G+  + +H R         +        +YD +  +K+    + +  NG
Sbjct: 122 CVQVAKMAEQCGIQALALHGRT--------RACMYKGEAEYDNIKAVKEAI-SIPVIANG 172

Query: 196 GLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            ++   +A  +L     D +MIGR A     +   +  Y              V      
Sbjct: 173 DIDSPEKARFVLDYTGADALMIGRPAQGRPWIFKEIQHYLETGELMPPLPIEEVKATLLG 232

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI--I 311
            + A    Y           +   +H+         +   R   +  A    A+  +  +
Sbjct: 233 HVHALHQFYGEF-----LGPRIARKHVGWYLKEHEQANDFRR--SFNAI-EDASLQLSQL 284

Query: 312 ETAFNLM 318
           E+ F+ +
Sbjct: 285 ESYFDHV 291


>gi|255262537|ref|ZP_05341879.1| probable tRNA-dihydrouridine synthase [Thalassiobium sp. R2A62]
 gi|255104872|gb|EET47546.1| probable tRNA-dihydrouridine synthase [Thalassiobium sp. R2A62]
          Length = 325

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 72/289 (24%), Positives = 119/289 (41%), Gaps = 25/289 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGGA 57
              TD  +R          L+ +EM+ +  +++       K  LG    +  +  Q+ G 
Sbjct: 18  AGITDLPFRQLVGGF-GAGLVVSEMVASQEMVQSKPGAREKAELGLGLADTSV--QLAGR 74

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  AA+IVED G   I++N+GCP+ +V  G  G+ LM + D     I A+   + I
Sbjct: 75  DAEWMARAARIVEDSGARLIDINMGCPAKKVTNGYSGSALMRDLDHALTLIDAVVNEVDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G DD +  +    L K  + +GV+ I IH R         +      + D+ 
Sbjct: 135 PVTLKTRLGWDDAM--LNAPTLAKRAENAGVSMITIHGRT--------RCQFYKGHADWT 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K +   + +  NG + D   A + L     DGVMIGR A     +L  V      
Sbjct: 185 AISAVK-DAVTIPVIANGDIVDSESARRALTSSGADGVMIGRGAQGLPWLLAQVAADLHG 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 P  T + +       A M+ Y     +     +   +H+    
Sbjct: 244 TPMPDVPKGTALVRMVSDHYEAMMSFYGIELGN-----RVARKHLGWYM 287


>gi|227903176|ref|ZP_04020981.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus ATCC 4796]
 gi|227868981|gb|EEJ76402.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus ATCC 4796]
          Length = 341

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 127/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ + ++   + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EETLLQAAQYIDQNTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   V       + +++G + I +H R         +        D++
Sbjct: 140 PVSVKMRIGWDRK--HVFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 VLHDVAQ-VLDVPFVANGDIATPELAKKALDDIGCTAVMVGRAALGNPWILKDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T          +    ++   +  +  +       + +  +       G P S R R 
Sbjct: 249 GETLPPQTVREKVETAKHQLQGLIEIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|325686690|gb|EGD28716.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK72]
          Length = 325

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAYDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|118581480|ref|YP_902730.1| nifR3 family TIM-barrel protein [Pelobacter propionicus DSM 2379]
 gi|118504190|gb|ABL00673.1| tRNA-U20-dihydrouridine synthase [Pelobacter propionicus DSM 2379]
          Length = 329

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 70/317 (22%), Positives = 126/317 (39%), Gaps = 27/317 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              T+  +R   R +   AL +TEM+  + ++R     +  L  + ++ PL +Q+ G   
Sbjct: 22  AGITNLPFRVICRRM-GAALAFTEMVSVNGLVRSGSNTLALLKSTPEDHPLGIQLFGDRP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA+ VE  G   +++N+GCP  +V     G+ L+  P  V   I A+  A  +P+
Sbjct: 81  EDLAEAARRVEGTG-ELLDINMGCPVRKVVGTGAGSALLREPLKVAAIIRAVRAATPLPL 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R G      +     + +  +  G + I +H R         +      + D+D +
Sbjct: 140 SVKIRSGWHCGEDS--YLRIAQIAQSEGCDAITLHPRS--------RSQMFSGHADWDQL 189

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +   + +  +G L       ++L     DGVM+ R A     +   V E   +  
Sbjct: 190 RELKSQL-SIPVIGSGDLFTPQDCQRMLAETGCDGVMVARGALGTPWIFRQVLELGESGS 248

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                   R   D  R             + S    +++ +H+     GF  +   R   
Sbjct: 249 FREITNAER--ADMIRLHLELYLQTWGESIAS----REMKKHIGWYAKGFAGAADVRR-- 300

Query: 298 TVEAGASTATHHIIETA 314
             EA  + +T  I+  A
Sbjct: 301 --EANNARSTTDILALA 315


>gi|300814628|ref|ZP_07094879.1| TIM-barrel protein, nifR3 family [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300511247|gb|EFK38496.1| TIM-barrel protein, nifR3 family [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 310

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 135/322 (41%), Gaps = 25/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TDR +R             TEM+ A A+   D+K +  L     EK   +QI  +D
Sbjct: 9   MAGYTDRAFRQLIYE-NGLDHAVTEMVSAKALCFNDRKTLELLKKFPGEKNTGVQIFASD 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + +A+ ++ DF ++ I++N+GCP+ ++ +   G+ L+ NP++V + +    K  +  
Sbjct: 68  VESISKASYLLNDFDFSYIDINMGCPAPKIVKNGCGSALIKNPNLVYELVKGAVKNSNKK 127

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R   D+ +      +++++ + +G   + +H R         ++       D+  
Sbjct: 128 ISIKTRKSFDNTLS----LDIIRAAQDAGAFAVTVHPRS--------REEYYKNKSDWQY 175

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IKK    + +  NG +  +  AL  +    VDG+ IGR A +N  + + + +     
Sbjct: 176 LIKIKK-FLTIPLIGNGDILTVEDALYKIKKYDVDGIAIGRGAIENPLIFSQIKKALKGE 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                    R+D      I          +      +  + +          NS+  R+ 
Sbjct: 235 KYEELNFNQRID------ILLRHLYLEVNYKGQRQAILNMRKTYAYYLKNLKNSKEIRNK 288

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L VE   +     I+E     M
Sbjct: 289 LNVENDYTNV-VKILEEYREQM 309


>gi|282882553|ref|ZP_06291174.1| probable tRNA-dihydrouridine synthase [Peptoniphilus lacrimalis
           315-B]
 gi|281297695|gb|EFA90170.1| probable tRNA-dihydrouridine synthase [Peptoniphilus lacrimalis
           315-B]
          Length = 310

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 135/322 (41%), Gaps = 25/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TDR +R             TEM+ A A+   D+K +  L     EK   +QI  +D
Sbjct: 9   MAGYTDRAFRQLIYE-NGLDHAVTEMVSARALCFNDRKTLELLKKFPGEKNTGVQIFASD 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + +A+ ++ DF ++ I++N+GCP+ ++ +   G+ L+ NP++V + +    K  +  
Sbjct: 68  VESISKASYLLNDFDFSYIDINMGCPAPKIVKNGCGSALIKNPNLVYELVKGAVKNSNKK 127

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R   D+ +      +++++ + +G   + +H R         ++       D+  
Sbjct: 128 ISIKTRKSFDNTLS----LDIIRAAQDAGAFAVTVHPRS--------REEYYKNKSDWQY 175

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +IKK    + +  NG +  +  AL  +    VDG+ IGR A +N  + + + +     
Sbjct: 176 LIKIKK-FLTIPLIGNGDILTVEDALYKIKKYDVDGIAIGRGAIENPLIFSQIKKALKGE 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                    R+D      I          +      +  + +          NS+  R+ 
Sbjct: 235 KYEELNFNQRID------ILLRHLYLEVNYKGQRQAILNMRKTYAYYLKNLKNSKEIRNK 288

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L VE   +     I+E     M
Sbjct: 289 LNVENDYTNV-VKILEEYREQM 309


>gi|58336619|ref|YP_193204.1| transcriptional regulator [Lactobacillus acidophilus NCFM]
 gi|58253936|gb|AAV42173.1| transcriptional regulator [Lactobacillus acidophilus NCFM]
          Length = 342

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 127/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 22  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 80

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ + ++   + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 81  EETLLQAAQYIDQNTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   V       + +++G + I +H R         +        D++
Sbjct: 141 PVSVKMRIGWDRK--HVFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 191 VLHDVAQ-VLDVPFVANGDIATPELAKKALDDIGCTAVMVGRAALGNPWILKDMVHYLET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T          +    ++   +  +  +       + +  +       G P S R R 
Sbjct: 250 GETLPPQTVREKVETAKHQLQGLIEIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 304

Query: 296 ILTV 299
            +  
Sbjct: 305 KINE 308


>gi|312864362|ref|ZP_07724595.1| TIM-barrel protein, nifR3 family [Streptococcus downei F0415]
 gi|311100083|gb|EFQ58294.1| TIM-barrel protein, nifR3 family [Streptococcus downei F0415]
          Length = 326

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 135/324 (41%), Gaps = 27/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L   EM+    IL  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLAVMEMVSDKGILYNNEKTLHMLHIDEGEHPVSIQLFGND 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++     + +++N+GCP  ++ +   GA  + +PD +   I  +   L+I
Sbjct: 83  GDSLARAAEFIQANTKTDLVDINMGCPVNKIVKNEAGAMWLKDPDKIYQVIKTVKSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + +++GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAEEAGVSALTMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ +    +    NG ++ +  A  ++     D VMIGR A  N  + T ++ +F +
Sbjct: 192 TLAQVAQAIKTIPFIGNGDIKTVEDARFMIEEVGCDAVMIGRGALNNPYLFTQINHFFES 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     R  +  +  +S  + D     +     +++          G   + + R 
Sbjct: 252 GEILPDLTFARKLEIAYDHLSR-LVDLKGEKIA----VREFRGLAPYYLRGTSGAAKIR- 305

Query: 296 ILTVEAGASTATHHIIETAFNLMI 319
                A A   T   ++  F+ + 
Sbjct: 306 ----GAVARAETLDQVKEIFDRIP 325


>gi|309791641|ref|ZP_07686133.1| NifR3 family TIM-barrel protein [Oscillochloris trichoides DG6]
 gi|308226263|gb|EFO79999.1| NifR3 family TIM-barrel protein [Oscillochloris trichoides DG6]
          Length = 336

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 73/313 (23%), Positives = 126/313 (40%), Gaps = 21/313 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R     L    L+ TEM  A ++     K   +L F  QE+PL +Q+ G D
Sbjct: 31  MAGVTDSVFRRVILGLGGCGLVCTEMTNAASVTPKALKRHHLLDFLPQERPLTMQLSGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA  VE  G + I++N GCPS +V  G  G+ L+ +   +   + A+  A+ +P
Sbjct: 91  PDLVAAAALSVERLGADMIDINCGCPSPKVTGGGHGSALLKDLPKLERVLRAVTAAVQVP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD    +      +  + +G+  + +H R         ++       D+  
Sbjct: 151 VTLKFRAGWDDAR--LNYLETARIAEDAGIAALTLHPRT--------REQEYHGRADWSR 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+K+    + +  +G ++    AL  L    VDGVMIGR A +N  +   + +     
Sbjct: 201 VAEVKRAVT-IPVVGSGDVKTAEDALLRLHETGVDGVMIGRGAMENPWIFLQIQQLRRGE 259

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                    ++             D     +     L ++ + +     G P S   R  
Sbjct: 260 PIFQPTPADKL------AFLNQYLDLCLSEMPERLALNKLKQLVGQFVVGLPGSALMRGA 313

Query: 297 LTVEAGASTATHH 309
           +   +  + A   
Sbjct: 314 VHRSSTVAAARAE 326


>gi|304437091|ref|ZP_07397054.1| tRNA-dihydrouridine synthase B [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304370042|gb|EFM23704.1| tRNA-dihydrouridine synthase B [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 323

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 128/320 (40%), Gaps = 23/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++  +  L     E+P+A+QI    
Sbjct: 20  MAGVTDTAYRVIAHGM-GCPLAFAEMVSSQGIHYRNEHTMNMLRTEPDERPIAMQIFAKS 78

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   EAA  +E+ G  + ++ N+GCP+ +V     G+ LM +P    + + A+ +A  +
Sbjct: 79  AAMAAEAAAYIEELGTADILDFNMGCPAPKVVRNGEGSALMRDPKRAEEILTAIRRATRL 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R+G DD         + +  +  GV+ + +H R         ++     + DY 
Sbjct: 139 PFTVKMRLGWDDASRNAV--EIARMAEAVGVDAVAVHGRT--------REQFYSGSADYA 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+    + + ++G +   +   + L     D VMIGR A  N  +   +  +   
Sbjct: 189 AIAAVKRAVG-IPVIVSGDVRRPADLKRALEITGADAVMIGRGAQGNPWIFPQLIHWLHT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          R +   +  Y   ++ +    +++ +H      G   S   R 
Sbjct: 248 GEELPPPTLAERAAVILRHLDL-LVGYKGEYIGT----REMRKHAAWYTRGLKGSAELRE 302

Query: 296 ILTVEAGASTATHHIIETAF 315
                A   T    I+  A+
Sbjct: 303 RFNRAASR-TEFAEILHGAW 321


>gi|327388929|gb|EGE87277.1| TIM-barrel , nifR3 family protein [Streptococcus pneumoniae
           GA04375]
          Length = 326

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  +  PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKGPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|225862005|ref|YP_002743514.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|298229280|ref|ZP_06962961.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298254679|ref|ZP_06978265.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|225727928|gb|ACO23779.1| tRNA-dihydrouridine synthase B [Streptococcus pneumoniae
           Taiwan19F-14]
          Length = 326

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 63/310 (20%), Positives = 131/310 (42%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  +  PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKGPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        K  +  +   +             +++          G   + + R 
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 306

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 307 AISQASTLAE 316


>gi|298369297|ref|ZP_06980615.1| tRNA-dihydrouridine synthase B [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298283300|gb|EFI24787.1| tRNA-dihydrouridine synthase B [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 332

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 119/302 (39%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R          EM+ +D   R   K +    F  +E   A+QI G+D
Sbjct: 17  MAGITDKPFRRLCRAF-GAGWAVGEMLHSDPAFRNTAKTLHRSDFGGEEGVAAVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EAA      G   I++N+GCP+ +V     G+ LM N  +V   + A+  A  +P
Sbjct: 76  PRQMAEAAVYNVALGAQLIDINMGCPAKKVCNVQAGSALMQNEPLVAAILEAVVGAAGVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G  D    +    + +  ++SG+  I IH R         +         Y++
Sbjct: 136 VTLKTRLGWHDDHKNI--LTVARIAEESGIAAIAIHGRT--------RTQMYRGEASYEL 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E K    ++ + +NG +    +A  +L     DGVMIGR A     +   +  Y  + 
Sbjct: 186 IAEAKGRL-NIPVWVNGDITSPQKAAAVLRQTGADGVMIGRGAQGRPWLFRDLAHYARHG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +   +       +     + A    Y A       +     +H+       P     R  
Sbjct: 245 VLPEALSLRECGETVLAHVRAMHDFYGAAAGARIAR-----KHIGWYLDSMPEGEAARRE 299

Query: 297 LT 298
           + 
Sbjct: 300 IN 301


>gi|297588656|ref|ZP_06947299.1| NifR3 family TIM-barrel protein [Finegoldia magna ATCC 53516]
 gi|297574029|gb|EFH92750.1| NifR3 family TIM-barrel protein [Finegoldia magna ATCC 53516]
          Length = 310

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 129/302 (42%), Gaps = 32/302 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R     L    L +TEMI A A+   DKK   +L   ++E   ++QI G + 
Sbjct: 18  AGVTDIPFRIICGEL-GAGLCFTEMISAKALYYDDKKTKKLLDTDSRENNTSVQIFGHEP 76

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A + + E++ +  I++N+GCP+ ++ +   G+ LM + ++  D I A      +P
Sbjct: 77  EIIAYATRFLTENYNFKSIDINMGCPAPKIFKNGDGSALMGDLNLAEDVIRACKNNTDLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G+D+   ++    L +  ++  V+ I +HAR   +              D+  
Sbjct: 137 VSVKFRLGIDE--NSMNYMQLGQICERLKVDYITLHARTRKMF--------YSGEADWAH 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  EN D+ +  NG         K +   + DGV++ R A +N  + +         
Sbjct: 187 IKRLV-ENVDIPVFGNGDCFTKEDIRKNMEYSNCDGVLLARGAMQNPFIFSD-------- 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                  K  V     + +   +  Y          + ++ +H+     GF NS + ++ 
Sbjct: 238 --DEIKTKEEVIDTIKKHMQLKLEFY-----EEKRAILEMRKHIQWYLKGFRNSNKVKNE 290

Query: 297 LT 298
           + 
Sbjct: 291 IN 292


>gi|240171884|ref|ZP_04750543.1| transcriptional regulator [Mycobacterium kansasii ATCC 12478]
          Length = 396

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 122/332 (36%), Gaps = 48/332 (14%)

Query: 1   MVDWTDRHYRFFARLLTN-------------------------NALLYTEMIVADAIL-- 33
           M   T+  +R   R   +                           L   EM+ A A++  
Sbjct: 17  MAGVTNVAFRTLCRDFGSMRGDPLRPASPPLRSPREQAKVGTVGGLYVCEMVTARALVER 76

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGS 92
                ++  F+  E P +LQ+   D      AA+++ D G  + I++N GCP  +V +  
Sbjct: 77  HPVTMHMTTFAPDESPRSLQLYTVDPDTTYAAARMIADEGLADHIDMNFGCPVPKVTKRG 136

Query: 93  FGACLMLNPDIVG---DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            GA L     + G          +   IPVTVK RIG+DD        +  +  +  G  
Sbjct: 137 GGAALPFKRRLFGRIVAAAVRAAEGTGIPVTVKFRIGIDD--AHHTHLDAGRIAEAEGAA 194

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
            + +HAR A          R     D+D +  +K++   + +  NG + D S AL ++  
Sbjct: 195 AVALHARTA--------AQRYSGTADWDQISRLKQQVTTIPVLGNGDIYDASDALAMMAT 246

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              DGV+IGR       +   +   F+     + P    V       +        A H 
Sbjct: 247 TGCDGVVIGRGCLGRPWLFAELSAAFTGRPAPTPPTLGEVA-----DVIRRHGALLAAHF 301

Query: 268 HSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                ++ I +H+    HGFP     R  L +
Sbjct: 302 GEDKGMRDIRKHIAWYLHGFPAGSDVRRALAL 333


>gi|126731334|ref|ZP_01747141.1| tRNA-dihydrouridine synthase, putative [Sagittula stellata E-37]
 gi|126708245|gb|EBA07304.1| tRNA-dihydrouridine synthase, putative [Sagittula stellata E-37]
          Length = 314

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 78/309 (25%), Positives = 126/309 (40%), Gaps = 24/309 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              TD  +R          L+ +EMI +   L  R   +       Q +  ++QI G + 
Sbjct: 7   AGITDLPFRTLVSRY-GAGLVVSEMIASGEFLTARPGTREKAELGAQVENTSVQIAGREP 65

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++V D G   I++N+GCP+ +V  G  G+ LM  PD     I A+  A+ +PV
Sbjct: 66  EPMAEAARMVADMGARVIDINMGCPAKKVTGGWSGSALMRVPDHALRLIEAVVAAVDLPV 125

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD    +    L +  + +GV  I IH R         +        D+  +
Sbjct: 126 TLKTRLGWDDTD--LNAPELARRAEGAGVRMIVIHGRT--------RCQFYKGRADWAAI 175

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +   + +  NG + D   A +   L   DGVM+GR A     ML  +        
Sbjct: 176 RPVK-DAVSIPVVANGDITDADTARRALDLSGADGVMVGRGAQGAPWMLAEIASKLHGAP 234

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCRH 295
               P  T +  D   +   +M D+    L +        +H+       G P + R + 
Sbjct: 235 APEIPEGTEL-ADLVAEHYEAMLDFYGPTLGNRVA----RKHLGWYMDRAGTPAALR-KT 288

Query: 296 ILTVEAGAS 304
           +LT    A 
Sbjct: 289 VLTERDPAR 297


>gi|332360096|gb|EGJ37910.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1056]
          Length = 325

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|325697325|gb|EGD39211.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK160]
          Length = 325

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GQVLPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|257462573|ref|ZP_05626984.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D12]
 gi|317060226|ref|ZP_07924711.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D12]
 gi|313685902|gb|EFS22737.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D12]
          Length = 322

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 130/316 (41%), Gaps = 23/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  YR        + LL+TEM+ +DA+   + K I           +Q+ G D  K
Sbjct: 10  AGVTDYTYRGILEEFQPD-LLFTEMVSSDALAALNDKTISQILRLRSGNGVQLFGKDTEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           ++ +AK +E  G   I++N GCP  RV     G+ L+ +P+ + + +  + + L  S  +
Sbjct: 69  MIYSAKYIEKLGVKNIDINAGCPMKRVVHSGHGSALLKSPEKIKEILFTLREQLEESTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G D     +    + K  +++G + I +H R         +        D+ ++
Sbjct: 129 SIKIRVGYDRPENYL---QIAKIAEEAGCSHITVHGRT--------RAQLYTGLADWSLI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            EIK E+  + +  NG +     A + +    VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEIK-EHVTIPVIGNGDIFTAEAAKEKIEDSGVDGVMLARGIFGNPWLIRDIREMLQYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +              I  +  D   R       +  + +H+     G P+S   ++ +
Sbjct: 237 VKTKVSTEDKIDMAIHHILKTEEDNPQREF-----VFDVRKHICWYLKGIPHSAEYKNRI 291

Query: 298 TVEAGASTATHHIIET 313
             ++    A   +++ 
Sbjct: 292 N-QSTDYKAVVQLLQE 306


>gi|171912320|ref|ZP_02927790.1| putative transcriptional regulator [Verrucomicrobium spinosum DSM
           4136]
          Length = 331

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 130/299 (43%), Gaps = 19/299 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L    ++ TE + A+ IL+ D++      F   ++ + +Q+ GAD
Sbjct: 17  MAGVTDMVFRSLCKEL-GADVMVTEFVSAEGILQADERTRKYTEFDDAQRTVGVQLFGAD 75

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             ++ EAA+ + D+   + I++N GCP  +V   + G+ L+ +  ++    A + KA+ +
Sbjct: 76  GQRMGEAARKIVDWKSPDFIDINFGCPVNKVVAKNGGSSLLKDCPLLSSVAAGIVKAVPV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RIG D    ++    + + ++ +G+  I IH R         +        D+ 
Sbjct: 136 PVTAKIRIGWD--ATSINAVEVCRLLEDTGIQAIAIHGRT--------RAQGYTGQADWG 185

Query: 178 IVYEIKKENPDLFIGLNGGLED-MSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E       + I  NG +   M  A +     V GVMIGRAA  N  +      +  +
Sbjct: 186 VIAE-CAAAVKIPIIGNGDIATGMDVARRQRETGVHGVMIGRAAMGNPWVFREAKHFLQH 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P   +  +   R     +  ++ R+      L+ +   ++    G P S+  R
Sbjct: 245 GTHLQPPTTEQRFELMLRHT--RLAVHSKRYGSEIQALRSMRNRLMTYTQGLPGSKHLR 301


>gi|258645918|ref|ZP_05733387.1| tRNA-dihydrouridine synthase [Dialister invisus DSM 15470]
 gi|260403288|gb|EEW96835.1| tRNA-dihydrouridine synthase [Dialister invisus DSM 15470]
          Length = 330

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 135/309 (43%), Gaps = 25/309 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR +   AL   EM+ A  +   ++K   +L  + +E P++LQ+ G+D
Sbjct: 20  MAGVSDLAYRVIARKM-GAALTTAEMVSAKGLYYHNEKTKDMLKIAEEEHPVSLQLFGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +   AK++E  G + +++N+GCP  +V +   G+ LM N  +  + I+A+  A+ IP
Sbjct: 79  PAVMALGAKVMEKAGADIVDINMGCPMQKVVKNGDGSALMKNVTLAAEIISAVTAAVKIP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G       +    L  + + +G   I +H R         +++  +   D+  
Sbjct: 139 VTIKMRLGW--SRDTINAVELAMAAESAGAAAITVHGRT--------REDFYMGTADWRE 188

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++  +   + +  NG + D   ++AL        V IGRAA+ N  +   V+ Y    
Sbjct: 189 IKKVV-DAVRIPVIGNGDVGDGPAAKALMEETGCAAVAIGRAAWGNPWVFGAVNTYLETG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                P          + +     +   R       ++++  H    FHG P +   R  
Sbjct: 248 EILPGPSWEERLAMARKHLHGLCVEKGERI-----AVREMRAHASRYFHGLPKATVLRRE 302

Query: 296 ---ILTVEA 301
               LT E 
Sbjct: 303 IMKALTEEE 311


>gi|313837246|gb|EFS74960.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL037PA2]
 gi|314927734|gb|EFS91565.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL044PA1]
 gi|314972018|gb|EFT16116.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL037PA3]
          Length = 355

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 124/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 1   MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHDMLAFAEGEDVRSVQLYGVD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     I+A  +A   
Sbjct: 60  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFTAVISAAVQAGDA 119

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D     +   +  ++   SG   + +HAR                + 
Sbjct: 120 HGVPVTVKIRIGIDPD--HITYMDSTRAAVDSGAAAVCLHART--------VAEAYAGHS 169

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + ++ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 170 HWDAIGDLVKAV-DVPVIGNGDIWEASDAMAMVERTGCAGVEVGRGCLGRPWLFRDLADA 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 229 FAGRGTTTLPSLGEVCAMI-RRHTELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 282

Query: 293 CRHIL 297
            RH L
Sbjct: 283 IRHAL 287


>gi|329666682|gb|AEB92630.1| tRNA-dihydrouridine synthase [Lactobacillus johnsonii DPC 6026]
          Length = 335

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 126/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 22  MAGISNAAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V+     + IN+N+GCP  +V +   GA  +L+P+ +   + A+ + +S 
Sbjct: 81  EETLVEAAHYVDTHTAADIININMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVSK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +       + +++G + + +H R         +    +   D++
Sbjct: 141 PVTVKMRTGWDQK--HIFAVENALAAQEAGASAVAMHGRT--------RKQMYMGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++       F+G NG +    +A  +L     D VM+GRAA  N  ++  +  Y   
Sbjct: 191 TLKDVADALTIPFVG-NGDVTTPEKAKVMLEDVGADAVMVGRAALGNPWIIKDMVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P       +  +     + D     +     + +  R       G P S R R 
Sbjct: 250 GE-KLRPQTVEEKVETAKDQLNGLIDLKGEKIA----VPEFRRQAAYYLKGIPRSARTRA 304

Query: 296 ILT 298
            + 
Sbjct: 305 KIN 307


>gi|332358130|gb|EGJ35962.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK49]
          Length = 325

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|300362399|ref|ZP_07058575.1| tRNA-dihydrouridine synthase [Lactobacillus gasseri JV-V03]
 gi|300353390|gb|EFJ69262.1| tRNA-dihydrouridine synthase [Lactobacillus gasseri JV-V03]
          Length = 335

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 125/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L    +E P+++QI G  
Sbjct: 22  MAGISNAAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLEMLTVDPREHPMSIQIFGGS 80

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA  V+     + IN+N+GCP  +V +   GA  +L+P+ +   + A+ + ++ 
Sbjct: 81  EETLVEAAHYVDTHTAADIININMGCPVPKVTKTDAGARWLLDPNKIYQMVHAVVRNVNK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +   +       + +++G + + +H R         +    +   D++
Sbjct: 141 PVTVKMRTGWDQK--HIFAVENALAAQEAGASAVAMHGRT--------RKQMYMGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++       F+G NG +    +A  +L     D VM+GRAA  N  ++  +  Y   
Sbjct: 191 TLKDVADALTIPFVG-NGDVTTPEKAKSMLEDVGADAVMVGRAALGNPWIIKDMVHYLDT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                             ++   + D     +     + +  R       G P S R R 
Sbjct: 250 GEKLRPQTVEEKVATAKEQL-NGLIDLKGEKIA----VPEFRRQAAYYLKGIPRSARTRA 304

Query: 296 ILT 298
            + 
Sbjct: 305 KIN 307


>gi|154509409|ref|ZP_02045051.1| hypothetical protein ACTODO_01940 [Actinomyces odontolyticus ATCC
           17982]
 gi|153799043|gb|EDN81463.1| hypothetical protein ACTODO_01940 [Actinomyces odontolyticus ATCC
           17982]
          Length = 411

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 68/362 (18%), Positives = 131/362 (36%), Gaps = 78/362 (21%)

Query: 1   MVDWTDRHYRFFARLLT------------------------------------------- 17
           M   TD  +R   R++                                            
Sbjct: 1   MAGVTDVPFRRLCRIMGESGLPDHLRPVGIPSWAAESGEGATASSPKAPGESSNEPRHVT 60

Query: 18  ------NNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV 69
                    L  TEM+ + A++  +++   ++     E+  +LQ+ G + + + +AA ++
Sbjct: 61  IPRVDAPAGLYVTEMVTSRALVEENERTLEMVRPDPAERVRSLQLYGVNPAVMAKAATML 120

Query: 70  EDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---------IPV 119
            +    + I+LN GCP  +V +   GA L    D+  D + A+ +A           IPV
Sbjct: 121 VERDLTDHIDLNFGCPVPKVTKKGGGAALPWKRDLFSDLVGAVVRACDEAGERAGREIPV 180

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+D +       +   + +K G   + +HAR          +     +  +D +
Sbjct: 181 TVKIRIGIDSEHETAT--DAALNAQKLGAAALTLHARTQ--------NQHYAGHAHWDEI 230

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +  D+ +  NG + + + AL +L     DG+ +GR A     +   +   +    
Sbjct: 231 ARLK-DLLDIPVFGNGDVFEAADALAMLEQTGCDGISVGRGAQGRPWIFRDIVAAYHGGS 289

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P    V        +  + D           L+++ +H+     GF      RH L
Sbjct: 290 IPPGPSLAEVVSVIECHAAWCVVDQGDEERA----LREMRKHIGWYLRGFAVGGPQRHAL 345

Query: 298 TV 299
           ++
Sbjct: 346 SM 347


>gi|222085889|ref|YP_002544420.1| tRNA-dihydrouridine synthase protein [Agrobacterium radiobacter
           K84]
 gi|221723337|gb|ACM26493.1| tRNA-dihydrouridine synthase protein [Agrobacterium radiobacter
           K84]
          Length = 342

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/287 (22%), Positives = 121/287 (42%), Gaps = 27/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-STQEKPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  +++   ++     S   KP  +Q+ G + 
Sbjct: 34  MSGVTDLPFRQLALRY-GAGLVVTEMVASRELVQDTAESWARLKSAGLKPHMVQLAGREA 92

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ +PV
Sbjct: 93  YWMAEAAKIAADNGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDVPV 152

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++   ++ +  +++G+  + IH R  +               D+D +
Sbjct: 153 TLKMRLGWDE--NSINAPHIARRAEEAGIQLVTIHGRTRM--------QFYEGRADWDAI 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + +  NG ++    A +IL     D VM+GR                +  L
Sbjct: 203 RAV-RDVISIPLVANGDVDTPEDASEILRRSGADAVMVGRGCQGRPWH--------AGVL 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            G          D   +    M D+          ++   +H+    
Sbjct: 254 AGHREPDRGEIADIALEHYRMMLDFYGE----AVGIRHARKHLGWYL 296


>gi|257467996|ref|ZP_05632092.1| nitrogen regulation protein NIFR3 [Fusobacterium ulcerans ATCC
           49185]
 gi|317062282|ref|ZP_07926767.1| nitrogen regulation protein NIFR3 [Fusobacterium ulcerans ATCC
           49185]
 gi|313687958|gb|EFS24793.1| nitrogen regulation protein NIFR3 [Fusobacterium ulcerans ATCC
           49185]
          Length = 320

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/325 (21%), Positives = 138/325 (42%), Gaps = 27/325 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  YR   +      LL+TEM+  +A+    +K +       +  ++Q+ G DI K
Sbjct: 10  AGVTDYTYRGILKEF-KPDLLFTEMVSINALEVACEKTLKVILRLREGDSVQLFGKDIKK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP--V 119
           +VE+AK VE  G   I++N GCP  ++    +GA LM  P++V   ++ M  AL     +
Sbjct: 69  MVESAKFVESLGVKHIDINSGCPMKKIVNNGYGAALMEQPELVRAMLSEMRSALDDKTDL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G  +    V    + K  +++G   I +H R         ++       D+ ++
Sbjct: 129 SIKIRVGYKESKNPV---EIAKIAQETGCKHITVHGRT--------REQMYTGKADWSLI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K E+ D+ +  NG +     A +      VDG+M+ R  + N  ++  + EYF +  
Sbjct: 178 KQVK-ESVDIPVIGNGDIFTAEDAKERVDYSGVDGIMLARGIFGNPWLIRDIREYFEHGK 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                               +  ++  R       + ++ +H+     G  N+   +  +
Sbjct: 237 ILHPVTDIEKIDMAIEHTRRTEIEHPERPF-----IFELRKHLCWYLKGIRNTAEIKDKI 291

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
                 +   + I+E   N + ++L
Sbjct: 292 NH----TDNYNEIVE-LLNRVKDNL 311


>gi|229820271|ref|YP_002881797.1| TIM-barrel protein, nifR3 family [Beutenbergia cavernae DSM 12333]
 gi|229566184|gb|ACQ80035.1| TIM-barrel protein, nifR3 family [Beutenbergia cavernae DSM 12333]
          Length = 397

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 64/342 (18%), Positives = 129/342 (37%), Gaps = 41/342 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNAL-----------------LYTEMIVADAILRGDKKNILGF 43
           M   T+  +R   R    + L                   +EM+ + A++    +++   
Sbjct: 20  MAGVTNAPFRALCRAAGRDGLGADASSDVLASDAPEGLYVSEMVTSRALVERTPESMRII 79

Query: 44  S--TQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           +    E+  ++Q+ G D + +  AA+++  +   + I+LN GCP  +V     GA L   
Sbjct: 80  TAAPDERVRSVQLYGVDPATVRLAARMLVTEDRADHIDLNFGCPVPKVTRKGGGAVLPWK 139

Query: 101 PDIVGDCIAAMCKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
            D+    + A         +PVTVK R+G+DD    +   +     +++G   + +HAR 
Sbjct: 140 RDLFAAIVRAAVDEAAPSGVPVTVKMRMGIDDD--HLTYLDAGLLAQEAGAAWVALHART 197

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMI 215
           A        +        ++ +  +K+   D+ +  NG +     AL ++     DGV++
Sbjct: 198 A--------EQYYSGEARWEAIARLKETVTDVPVLGNGDIWSAEDALAMVQQTGCDGVVV 249

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           GR       + T +   F+       P    V   F R     +  +          L++
Sbjct: 250 GRGCQGRPWLFTDLVAGFAGSARRVRPGLADVAATFRRHAELMVDHFGEEERA----LRE 305

Query: 276 ITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
           + +H      G+      R  L + +  +     +   A +L
Sbjct: 306 LRKHASWYLKGYVVGGEARAALGLVSSLAELDDRL--AALDL 345


>gi|114776793|ref|ZP_01451836.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Mariprofundus
           ferrooxydans PV-1]
 gi|114552879|gb|EAU55310.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Mariprofundus
           ferrooxydans PV-1]
          Length = 341

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 128/299 (42%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      L+ TEMI + A+   R   + +      E P+++QI G+D
Sbjct: 25  MAGITDLPFRRICKRF-GVGLMVTEMIASRAVDMGRERTERMAELGDDEHPVSIQIAGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+     G + +++N+GCP  ++ +   G+ ++ +  +V   +AA+  A+ +P
Sbjct: 84  PEFVTEAARWAVGHGADFVDINMGCPVKKICKQVAGSAMLRDEALVARVLAAVVAAVDVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DDQ   V   N+ +  + SG+  + +H R         +      +  ++ 
Sbjct: 144 VTLKIRTGWDDQSKNVQ--NIARIAEDSGIQLLTVHGRT--------RAQMFHGHACWED 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + K    + +  NG + D   A +++   + DGVM+GRA   N  +L  V    +  
Sbjct: 194 IG-LAKAAVSIPVIGNGDIVDAESAREMIRVSNCDGVMVGRAVQGNPWVLGEVHAAIAGL 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                P       + W  +   M  +   H       +   +H+I    G   S   R 
Sbjct: 253 PIPPKPT----AAERWLIVDEHM-RHLVEHHGIRTASKLARKHVIWYSKGLHGSAEFRQ 306


>gi|15673943|ref|NP_268118.1| oxidoreductase [Lactococcus lactis subsp. lactis Il1403]
 gi|12725003|gb|AAK06059.1|AE006426_5 oxidoreductase [Lactococcus lactis subsp. lactis Il1403]
 gi|326407498|gb|ADZ64569.1| oxidoreductase [Lactococcus lactis subsp. lactis CV56]
          Length = 334

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 81/321 (25%), Positives = 144/321 (44%), Gaps = 21/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T++ +   A+      L+ TEMI    I   +KK   ++ F     PL++QI G +
Sbjct: 27  MAGITNKAFLTTAKEF-GAGLVVTEMISDKGIEHRNKKTLEMMDFEGVPHPLSMQIFGGE 85

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  LVEAAK VE     + I++N+GCP  +V +   G+ L+L+PD V D ++A+ KA+S 
Sbjct: 86  VDTLVEAAKFVEANTVADIIDINMGCPVPKVTKNEAGSRLLLDPDKVYDVVSAVSKAISR 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK RIG DD    +      K+I+  G   + +HAR                  ++ 
Sbjct: 146 PLTVKIRIGWDDD--HLFAVENAKAIEAGGGAAVSMHARTKAQAYTGNAQE------NWH 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++  EN ++ +  NG ++    A +++    V  VM+GRAA  N  +L   + Y   
Sbjct: 198 WLKKL-TENVNIPVIGNGDVKTPEDAKRMIDETGVTAVMMGRAALGNPWILHRTEHYLRT 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     + A + +    +L S    ++  +H      G   + + + 
Sbjct: 257 GELLPEPTVAGKMEIAKLHL-ARLVELKGDNLAS----REFRQHAAYYLKGASRAAKVKV 311

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +  +A +      I++   N
Sbjct: 312 AVN-QAESQAEIITILDNFVN 331


>gi|304414074|ref|ZP_07395442.1| fusion of tRNA-dihydrouridine synthase and subunit of Fis DNA
           binding transcriptional dual regulator [Candidatus
           Regiella insecticola LSR1]
 gi|304283288|gb|EFL91684.1| fusion of tRNA-dihydrouridine synthase and subunit of Fis DNA
           binding transcriptional dual regulator [Candidatus
           Regiella insecticola LSR1]
          Length = 440

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 116/300 (38%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R    L     +  +EM+ ++  +    K+ L      +     +QI G+D
Sbjct: 25  MAGITDRPFRALC-LAMGAGMAVSEMLSSNLEVWQTDKSRLRRIHKDEAGIRTVQIAGSD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AAKI    G   I++N+GCP+ +V+    G+ L+  P++V   I A+  A+ +P
Sbjct: 84  PDEMAAAAKINVANGAQIIDINMGCPAKKVNRKLAGSALLKYPNLVKQIITAVVDAVDVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + IH R         +        +YD 
Sbjct: 144 VTLKIRTGWVPENRN--CVEIAQLAECCGIQALTIHGRT--------RSCLFNGEAEYDS 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ N  + +  NG + +  +A  +L     D +MIGRAA     +   +  Y    
Sbjct: 194 IRAVKQ-NVTIPVIANGDITNPHKAKVVLDYTGADALMIGRAAQGRPWIFREIQHYLDTG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                     V       I      Y       G   +   +H+         + + R  
Sbjct: 253 ELLPPMPLETVQHLLNNHIRELHDFY-----GPGKGFRIARKHVSWYLKEHAPNDQFRRT 307


>gi|269123581|ref|YP_003306158.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
 gi|268314907|gb|ACZ01281.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
          Length = 317

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 108/303 (35%), Positives = 161/303 (53%), Gaps = 18/303 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MVD TD H+R F  ++  +  LYTEMI   AIL GD+  IL  +  E P+ LQI  +++ 
Sbjct: 9   MVDRTDIHFRNFISMINKDIELYTEMITTQAILNGDRSKILKITNVENPVVLQIATSNLK 68

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           + +EAAK ++   YN +N+NVGCPS RV   + GA LM  P++V D   A+ +     VT
Sbjct: 69  ESIEAAKYIKYTNYNAVNINVGCPSDRVSGHNMGAYLMSEPELVRDIAQAVKEYSGKDVT 128

Query: 121 VKCRIGVD------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +K RIG+D      +    V    L+  I  + V+   +HAR AILKGLSPK+NR IP L
Sbjct: 129 IKNRIGIDGKGILENDRKIVRYEELLNFIDITNVSKYIVHARIAILKGLSPKENRTIPEL 188

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DY++VY +K++ P+L I +NGG++ +         VD VMIGRA Y N  +   ++    
Sbjct: 189 DYEMVYRLKRDRPNLMIEINGGIKTIEDIKIHHNYVDSVMIGRAFYDNPMLANEINLLND 248

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +   +            +I   M  Y      +  K     RH +GLF+    S+  +
Sbjct: 249 KSVKKHT------------EIVKEMFHYVKMLEENNEKPHHFLRHTLGLFYNTKYSKMWK 296

Query: 295 HIL 297
           +++
Sbjct: 297 NMI 299


>gi|119963532|ref|YP_947259.1| IMP dehydrogenase/GMP reductase domain-containing protein
           [Arthrobacter aurescens TC1]
 gi|119950391|gb|ABM09302.1| putative IMP dehydrogenase / GMP reductase domain protein
           [Arthrobacter aurescens TC1]
          Length = 401

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 60/335 (17%), Positives = 121/335 (36%), Gaps = 45/335 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    +++  +     EK  ++Q+ G D
Sbjct: 41  MAGITNSAFRRLCREYGG-GMYVAEMVTSRALVERTPESLRIISHDEDEKVRSVQLYGVD 99

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              +  A ++ VE+   + I+LN GCP  +V     G+ L    D+    +    K  S 
Sbjct: 100 PVTVGAAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTSIVQTAVKEASK 159

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IP+T+K R G+D+    +   +  +  + +GV  + +H R A                
Sbjct: 160 GGIPLTIKMRKGIDED--HLTYLDAGRIARDAGVAAVALHGRTA--------AQFYSGQA 209

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA-----------AYKNS 223
           D+  +  +++  PD+ +  NG +     A++++         R                 
Sbjct: 210 DWSAIARLREALPDIPVLGNGDIWSAEDAVRMV---------RETGVDGVVVGRGCQGRP 260

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +   F        P    V +  +R     +  +          L++I +HM   
Sbjct: 261 WLFGDLQAAFEGSDQRHRPGLREVAEGVYRHAELMVETFGN---DEYKALREIRKHMAWY 317

Query: 284 FHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           F G+      R  L   A   T    ++    + +
Sbjct: 318 FKGYVVGGELRAKL---ATVPT--LEVLREYLDEL 347


>gi|330721068|gb|EGG99210.1| tRNA dihydrouridine synthase B [gamma proteobacterium IMCC2047]
          Length = 312

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 124/298 (41%), Gaps = 21/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR YR   R      L  +EM+ +D  L   +K+   L  + ++ P ++QI G+D
Sbjct: 1   MAGVTDRPYRALCRHY-GAGLAVSEMVTSDQSLWHTRKSQQRLNHAGEQTPRSVQIAGSD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA    + G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+++P
Sbjct: 60  PKMMAAAAVANVENGAQIIDINMGCPAKKVCNKAAGSALLRDEKLVSHILEAVVAAVNVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G            +    ++SG+  + IH R         +  R     +YD 
Sbjct: 120 VTLKIRTGWCPDSRNA--LTIANIAEQSGIQALTIHGRT--------RACRYNGEAEYDT 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + ++   + I  NG +   ++A  ++     + +MIGR A     +   ++ +    
Sbjct: 170 IAAVVQQ-SRIPIIANGDITTANKAHWVMQRTGANAIMIGRGAQGTPWIFAEINHFLKTG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              + P    + +   + I+   + Y           +   +HM        N+   R
Sbjct: 229 EQLAKPTIAELGEIVSQHIATLHSFYGDF-----LGPRIARKHMGWYLQHLSNASSVR 281


>gi|296392551|ref|YP_003657435.1| hypothetical protein Srot_0113 [Segniliparus rotundus DSM 44985]
 gi|296179698|gb|ADG96604.1| TIM-barrel protein, nifR3 family [Segniliparus rotundus DSM 44985]
          Length = 386

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/336 (19%), Positives = 129/336 (38%), Gaps = 36/336 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLAL 52
           M   T+  +R   R L          L   EM++A +++  + K   ++ F  +E+P ++
Sbjct: 26  MAGVTNLAFRTVCRELETRLTGQARGLYVNEMVMARSLVNRNPKAMRMIEFGPEERPRSM 85

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D   + EA + IV +   + ++LN GCP  +V     GA L     +    I A 
Sbjct: 86  QLYTVDPEAVGEAVRMIVAEDLADHVDLNFGCPVPKVTRNGGGAALPYKRRLFARIIEAA 145

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                 ++P+TVK R+G+DD+       +  +  + SG   + +HAR A           
Sbjct: 146 VNGAQGAVPITVKFRVGIDDEHH--TYLDAGRIAQDSGAASVALHARTA--------AQL 195

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                D+  +  +K+   ++ +  NG +   + A +++     DGV++GR       +  
Sbjct: 196 YSGTADWSAIARLKEHVTEIPVLGNGDIFAAADAKRMMDQTGCDGVVVGRGCLGRPWLFA 255

Query: 228 TVDEYFSNPLTGSSPI--KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
            +    S     + P      V +   R  +  +  +A  H      + ++ +H      
Sbjct: 256 ELAAALSGGAIPAPPPPNLGEVARIVLRH-AQLLVLHAGSH-----GVAEMRKHFAWYLR 309

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           GF      R   +     +      IE     + + 
Sbjct: 310 GFSVGSELRGKFSTVGSLAE-----IEDLLGQLPQE 340


>gi|328949131|ref|YP_004366468.1| TIM-barrel protein, nifR3 family [Treponema succinifaciens DSM
           2489]
 gi|328449455|gb|AEB15171.1| TIM-barrel protein, nifR3 family [Treponema succinifaciens DSM
           2489]
          Length = 336

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/331 (19%), Positives = 133/331 (40%), Gaps = 35/331 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R         +L  TEM+ A+A++RG+KK   ++  +  EK   +QI G + 
Sbjct: 24  AGYSDMAFRSLCVEY-GASLCTTEMVSAEALVRGNKKTELLMRRAPNEKVYCVQIFGGNA 82

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
             + EAAKIV E    + I++N GCP  ++ +   G+ L   P+ +   + A+ ++    
Sbjct: 83  QTMAEAAKIVLEKTDCDCIDINGGCPVPKITKTGAGSVLTKEPERLFSIVKAVKESSIKY 142

Query: 116 --------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                   ++PVT+K R G D     +  +    +  K+G + I IHAR         K 
Sbjct: 143 TSLHPERGNVPVTIKIRSGWD--SSNITWKECADAALKAGADAITIHART--------KA 192

Query: 168 NRKIPNLDYDIVYEIKK-ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                  D++I   + +     + +  +G   +   A  +L    VD VM  R A  +  
Sbjct: 193 QGYSGKADWEIQKRLVEFVAKRIPVFGSGDAFNPETAKLMLEQTGVDAVMFARGAMGDPF 252

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +     ++ +     +   K R++    R++  ++ ++  +          + +      
Sbjct: 253 LFRRTKQFLTEGKYETETPKERLEAG-LRELKMNVAEHGEK-----AACMLMRKKFCAYS 306

Query: 285 HGFPNSRRCRHILTVEAGASTATHHIIETAF 315
            G     R R  + V + +      + +   
Sbjct: 307 SGIKGGARLREQI-VNSRSIKDYEELFKQFL 336


>gi|256396137|ref|YP_003117701.1| hypothetical protein Caci_7030 [Catenulispora acidiphila DSM 44928]
 gi|256362363|gb|ACU75860.1| TIM-barrel protein, nifR3 family [Catenulispora acidiphila DSM
           44928]
          Length = 379

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/316 (20%), Positives = 123/316 (38%), Gaps = 26/316 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM++  A++  ++K   ++ F++ EKP +LQ+ G D
Sbjct: 25  MAGITNVAFRQLCRE-HGAGIYVCEMVMTRALVERNEKTLRMVKFASDEKPRSLQLYGVD 83

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA---AMCKA 114
              + +A +++      + +++N GCP  RV     GA L     + G  +         
Sbjct: 84  PVTVRKAVEMIAAEDLADHVDMNFGCPVPRVTRKGGGAALPYKRRLFGQIVEAAVQAAAP 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVTVK RIG+D++          +  +++G   + +H R A          R     
Sbjct: 144 AGIPVTVKMRIGIDEEHH--TFLEAGRIAQEAGAAWVALHGRTA--------AQRYSGEA 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K E  ++ +  NG + +   AL+++     DGV++GR       +   +   
Sbjct: 194 DWSAIKALKDEL-EVPVLGNGDIWEADDALRMIAETGADGVVVGRGCLGRPWLFADLAAA 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH-SGGKLQQITRHMIGLFHGFPNSR 291
           F        P    V     R       +  A  L      +    +H+     GFP   
Sbjct: 253 FDGRHERKLPALGEVMATMRRHA-----ELLASWLGTEREGVVDFRKHVAWYLKGFPVGG 307

Query: 292 RCRHILTVEAGASTAT 307
             R  L + +  +   
Sbjct: 308 DVRRGLAMSSSLAELD 323


>gi|237746835|ref|ZP_04577315.1| tRNA-dihydrouridine synthase B [Oxalobacter formigenes HOxBLS]
 gi|229378186|gb|EEO28277.1| tRNA-dihydrouridine synthase B [Oxalobacter formigenes HOxBLS]
          Length = 335

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 128/322 (39%), Gaps = 21/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM  A+ +LR   K+        +  P A+QI G+ 
Sbjct: 1   MAGITDRPFRQLCKKL-GAGYAVSEMAAANPLLRDTLKSRKRIIHDGESGPHAIQIVGSV 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + ++A+   D G + I++N+GCP+ +V     G+ L+ N  +VG  + A+  A+ +P
Sbjct: 60  PAIMADSARYHVDQGADIIDINMGCPAKKVCNNWCGSALLQNESLVGQILDAVVHAVPVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D     +    + K  + +G+  + +H R         + +      +Y  
Sbjct: 120 VTLKFRTGWDR--SHINAPAIAKIAESAGIAMLTLHGRT--------RADGYRGEAEYAT 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     + +  NG ++   +A  +L     D +MIGRAA     +   +  +    
Sbjct: 170 IAEVK-SLVSIPVVANGDIDSPQKAKTVLDKTGADALMIGRAARGRPWIFREIGHFLQYG 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    + +     +      Y          ++   +H+       P+  + R  
Sbjct: 229 TPLLPPSLQEIWQILREHLEDHYAFY-----GETLGVRNARKHIGWYAGNLPDGEKLRQK 283

Query: 297 LTVEAGASTATHHIIETAFNLM 318
             +        + +     +L+
Sbjct: 284 TNMADTCEKQINEVDRFFMSLL 305


>gi|254480827|ref|ZP_05094073.1| putative TIM-barrel protein, nifR3 family [marine gamma
           proteobacterium HTCC2148]
 gi|214038622|gb|EEB79283.1| putative TIM-barrel protein, nifR3 family [marine gamma
           proteobacterium HTCC2148]
          Length = 334

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 62/298 (20%), Positives = 129/298 (43%), Gaps = 22/298 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R     +    L+ +EMI ++  LR  +K         + +P ++QI G++
Sbjct: 25  MAGVTDLPFRRLCAEM-GAGLVVSEMISSNPRLRDSRKTAWRSVHDFEVEPRSVQIAGSE 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA+     G   I++N+GCP+ +V + + G+ L+ +  +V D +  + K++ +P
Sbjct: 84  PLELAAAAQYNVSQGAQIIDINMGCPAKKVCKKAAGSALLADEALVKDILHTVVKSVDVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G +         N+ +  + +G+  + +H R         +  +     +YD 
Sbjct: 144 VTLKIRTGANPGERNGI--NIARIAQDAGIAALAVHGRT--------RACKFEGAAEYDT 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I     +  +  NG ++   +A  ++      GVM+GRAA     +   +  + S  
Sbjct: 194 IAAIV-AATEFPVFANGDIDTPEKAAAVIRRTGAAGVMVGRAAQGKPWLCGQIAAHLSGE 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              S   + +      R+   ++ D+    +     ++   +H+     G P+ R  R
Sbjct: 253 TIVSVTPEKQFA--ILRRHLLALHDFYGEFMG----VRIARKHVSWYLQGQPDYRSHR 304


>gi|42521773|ref|NP_967153.1| transcription regulator homolog yacF [Bdellovibrio bacteriovorus
           HD100]
 gi|39574303|emb|CAE77807.1| transcription regulator homolog yacF [Bdellovibrio bacteriovorus
           HD100]
          Length = 337

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 124/301 (41%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R F + L   +++ TE++ A  I     + +  + F   ++P+ +Q+ G +
Sbjct: 17  MAGITDHAFRTFIKKLD-ASVVVTELVSASGIEYKSDRTLKLMSFDESQRPIGIQLFGEE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++ E  G + ++LN GCP  +V +   G+ ++ +P  V   ++ +  A+ IP
Sbjct: 76  PEIVARAAQVAEADGCDFVDLNFGCPVPKVVKKGAGSAILKDPAAVQKMVSTVKAAIKIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G D          +       GV+ + IH R         +        D+D 
Sbjct: 136 LTIKIRTGWDANSRNAT--EICNIAYNEGVSWVAIHGRT--------RAQSYTGLADWDF 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K  N  + I  NG +    QA   L     DGVMIGR   KN  +       +   
Sbjct: 186 IADVK-ANTKIPILGNGDILTPRQANLRLQQSGCDGVMIGRGCLKNPFIFMDALSLWRG- 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                PIK  V +D+   +   +      H        Q+ +       G+  + + R  
Sbjct: 244 ----EPIKD-VKRDYVS-LFQGLQKEIVAHCDEHITGIQLRKFAAWFSTGYSGAAQFRKN 297

Query: 297 L 297
           L
Sbjct: 298 L 298


>gi|324989868|gb|EGC21811.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK353]
          Length = 317

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 184 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 244 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 295

Query: 293 CRHILT 298
            R  ++
Sbjct: 296 LRGAIS 301


>gi|323350640|ref|ZP_08086302.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis VMC66]
 gi|322123322|gb|EFX95007.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis VMC66]
          Length = 325

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVHDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K +V  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKVAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|124023850|ref|YP_001018157.1| nitrogen regulation protein NifR3 family protein [Prochlorococcus
           marinus str. MIT 9303]
 gi|123964136|gb|ABM78892.1| putative nitrogen regulation protein NifR3 family protein
           [Prochlorococcus marinus str. MIT 9303]
          Length = 336

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 137/323 (42%), Gaps = 21/323 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADIS 60
              +D+ +R   R    +ALL+TEM+ A ++  G   + I   + +  P+ +Q+      
Sbjct: 25  AGVSDQIFRSLVRRWAPDALLFTEMVNATSLELGHGLQKIDELANEAGPIGVQLFDHRPE 84

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    ++ +  A+ IPVT
Sbjct: 85  AMADAAQRAEAAGAFLIDINMGCPVRKIARKGGGSGLIRDPQLAAKIVSTVAAAVKIPVT 144

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G      +       + ++++G   + +HAR         ++     + D+  + 
Sbjct: 145 VKTRLGWCGSDASPV--RWCQWLEQAGAQMLTLHART--------REQGFKGSADWLAIA 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K     + +  NG ++    A + L     DGVM+GR +     ++  +D   S    
Sbjct: 195 AVKSAL-QIPVIANGDVKSDMDAKRCLAITGADGVMVGRGSMGAPWLVGQIDAALSGIPV 253

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            ++P          R+   ++      H      L    +HM     GF  + + RH L 
Sbjct: 254 PATPGAAE-RLTIAREQLEALVQAKGEH-----GLLIARKHMGWTCSGFVGASKLRHAL- 306

Query: 299 VEAGASTATHHIIETAFNLMIES 321
           + A   T    ++E A   +I +
Sbjct: 307 MRAPTPTDAISLLEQASAELITA 329


>gi|212696521|ref|ZP_03304649.1| hypothetical protein ANHYDRO_01059 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676457|gb|EEB36064.1| hypothetical protein ANHYDRO_01059 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 321

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 132/305 (43%), Gaps = 28/305 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R  +         +TEM+  +A+   +KK   +L  S  EK   +Q+ G+  
Sbjct: 16  AGVSDVGFRLISERY-GADKTFTEMVSVNALYYDNKKTNDLLFISENEKNCNIQLFGSKP 74

Query: 60  SKLVEAAK----IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             + +  K     +E     EI+ N+GCP A++ +   G+ LM NP +V +    + K+ 
Sbjct: 75  EVIEKVIKDKINYIEK--SKEISFNMGCPVAKITKNGEGSQLMANPKLVEEICKTLRKST 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              + +K R+G+DD+   +   ++ K  + +G++ + +HAR         KD     N +
Sbjct: 133 DKKLNIKFRLGIDDK--HINYLDIGKIAQDTGIDYVILHART--------KDQMYSGNAN 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D + ++K EN  + +  NG +  +   + +  L   DGVM+ R A  N  +   + +Y 
Sbjct: 183 WDHIRKLK-ENLQIPVIANGDIFSVEDFINVIDLTKADGVMLARGAMGNPFLFKEIKDYI 241

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 S P    +      +    +     ++      + Q+ +H+     G  NS + 
Sbjct: 242 KTGKY-SKPSPIEIIDQLIDQYKLEL-----KYKEEKLVVTQMRKHLSWYIKGLENSSKI 295

Query: 294 RHILT 298
           R ++ 
Sbjct: 296 RDLVN 300


>gi|115524762|ref|YP_781673.1| nifR3 family TIM-barrel protein [Rhodopseudomonas palustris BisA53]
 gi|115518709|gb|ABJ06693.1| putative TIM-barrel protein, nifR3 family [Rhodopseudomonas
           palustris BisA53]
          Length = 344

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/285 (23%), Positives = 115/285 (40%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A  L    ++ +EM  +D ++ G   ++         P  +Q+ G + 
Sbjct: 28  MSGITDAPFRRLAASL-GAGVVVSEMTASDDLVNGRPMSVRRCDAGGIGPHVVQLAGCEP 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM +       I A   A+++PV
Sbjct: 87  HWMAEGARIAEAGGADIIDINMGCPARHVTGGQSGSALMRDLAHALTLIEATVNAVNVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+        L +  + +GV  I +H R         +        D+  V
Sbjct: 147 TLKMRLGWDDRCRNA--PELARRAEAAGVQLITVHGRT--------RHQFYKGEADWRAV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K     +   +NG +     A K L     D VMIGR AY    +   +  +    +
Sbjct: 197 REVKNAVT-IPTVVNGDIVSRETAAKALEQSGADAVMIGRGAYGQPWLPGQIGRWLDTGV 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
              +P +     D        +  Y  R       L+   +H+  
Sbjct: 256 VEPTPDRASQLVDLLTLYDELLAHYGVR-----VGLRHARKHLGW 295


>gi|324992591|gb|EGC24512.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK405]
          Length = 317

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 184 TLHDVAHALTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K +V  D   ++     +Y A     G               G   + +
Sbjct: 244 GEVLPDLSFEDKMKVAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 295

Query: 293 CRHILT 298
            R  ++
Sbjct: 296 LRGAIS 301


>gi|116512883|ref|YP_811790.1| tRNA-dihydrouridine synthase [Lactococcus lactis subsp. cremoris
           SK11]
 gi|125624976|ref|YP_001033459.1| tRNA-dihydrouridine synthase B [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|116108537|gb|ABJ73677.1| tRNA-U20-dihydrouridine synthase [Lactococcus lactis subsp.
           cremoris SK11]
 gi|124493784|emb|CAL98776.1| tRNA-dihydrouridine synthase B (EC 1.-.-.-) [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300071776|gb|ADJ61176.1| tRNA-dihydrouridine synthase B [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 334

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 79/321 (24%), Positives = 145/321 (45%), Gaps = 21/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T++ +   A+      L+ TEMI    I   +KK   ++ F     PL++QI G +
Sbjct: 27  MAGITNKAFLTTAKEF-GAGLVVTEMISDKGIEHRNKKTLEMMDFEGVPHPLSMQIFGGE 85

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  LVEAAK VE     + I++N+GCP  +V +   G+ L+L+PD V D ++A+ KA+S 
Sbjct: 86  VDTLVEAAKFVEANTVADIIDINMGCPVPKVTKNEAGSRLLLDPDKVYDVVSAVSKAISR 145

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK RIG DD    +      K+I+  G   + +HAR                  ++ 
Sbjct: 146 PLTVKIRIGWDDD--HLFAVENAKAIEAGGGAAVSMHARTKAQAYTGNAQE------NWH 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++  +N ++ +  NG ++    A +++    V  VM+GRAA  N  +L   + Y   
Sbjct: 198 WLKKL-TDNVNIPVIGNGDVKTPEDAKRMIDETGVTAVMMGRAALGNPWILHRTEHYLRT 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +     + A + +    +L S    ++  +H      G   + + + 
Sbjct: 257 GELLAEPTVAEKMEIAKLHL-ARLVELKGDNLAS----REFRQHAAYYLKGASRAAKVKV 311

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +  +A +      I++   +
Sbjct: 312 AVN-QAESQAEIITILDNFVS 331


>gi|257452894|ref|ZP_05618193.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_5R]
 gi|317059436|ref|ZP_07923921.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_5R]
 gi|313685112|gb|EFS21947.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_5R]
          Length = 314

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 129/316 (40%), Gaps = 23/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  YR        + LL+TEM+ +DA+   + K I           +Q+ G DI K
Sbjct: 10  AGVTDYTYRGILEEFHPD-LLFTEMVSSDALAALNDKTISQILRLRPGNGVQLFGKDIEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           ++ +AK VE  G   I++N GCP  RV     GA L+ +PD + + ++ + + L     +
Sbjct: 69  MLYSAKYVEKLGVKHIDINSGCPMKRVVHSGHGAALLKSPDKIKEILSTLREGLQEDTDL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +     +    + K  ++ G + I +H R         +        D+ ++
Sbjct: 129 SIKIRVGYEKPENYI---QIAKIAEEVGCSHITVHGRT--------RAQLYTGFADWSLI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            EIK EN  + +  NG +     A + +    VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEIK-ENVSIPVIGNGDIFTAEDAKEKIEYSGVDGVMLARGIFGNPWLIREIREILQYGQ 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +              I     D   R       +  + +H+     G  NS  C++ +
Sbjct: 237 VKTKVTAEDKINMAIHHIEEIAKDNPQREF-----VFDVRKHICWYLKGISNSAECKNQI 291

Query: 298 TVEAGASTATHHIIET 313
              +    AT  +++ 
Sbjct: 292 N-RSVDYQATVALLQE 306


>gi|296137143|ref|YP_003644385.1| TIM-barrel protein, nifR3 family [Thiomonas intermedia K12]
 gi|295797265|gb|ADG32055.1| TIM-barrel protein, nifR3 family [Thiomonas intermedia K12]
          Length = 350

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 120/312 (38%), Gaps = 24/312 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR L       +EM+ + A LR   K         +  P+A+QI G D
Sbjct: 36  MAGVTDRPYRRLARQL-GAGYCVSEMVTSRADLRDTLKTSRRANHDGEAAPIAVQIVGTD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
             ++ EA +   + G + I++N+GCP+ +V     G+ LM + D+    + A   A    
Sbjct: 95  PEQIAEATRYNLERGADIIDINMGCPAKKVCNRWAGSALMQDEDLAARLVEAAVAAARPF 154

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PVT+K R G  +   A     + +  + +G   + +H R         ++       +
Sbjct: 155 DAPVTLKMRAGWCE--AARNAPRIARRAEAAGAAMLVVHGRT--------REQGYGGEAE 204

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + E+K+    + +  NG ++   +A  +L     D VMIGRAA     +   V  Y 
Sbjct: 205 YATLAEVKRSVG-IPVVANGDIDSPQKAAAVLRQSGADAVMIGRAAMGRPWLFGQVAAYL 263

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            + +    P   +     +  +      Y          ++   +H+       P     
Sbjct: 264 EHGVLLPDPAPEQWRDWLFAHLDDHYALYGEAI-----GVRTARKHVGWYVAALPEGETF 318

Query: 294 RHILTVEAGAST 305
           R        A+ 
Sbjct: 319 RRQFNTLGSAAE 330


>gi|327459994|gb|EGF06333.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1]
 gi|327488584|gb|EGF20384.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK1058]
          Length = 325

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVHDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|320105775|ref|YP_004181365.1| TIM-barrel protein, nifR3 family [Terriglobus saanensis SP1PR4]
 gi|319924296|gb|ADV81371.1| TIM-barrel protein, nifR3 family [Terriglobus saanensis SP1PR4]
          Length = 413

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 73/362 (20%), Positives = 146/362 (40%), Gaps = 58/362 (16%)

Query: 1   MVDWTDRHYRFFAR----------------------LLTNNALLYTEMIVADAILRGD-- 36
           M   TD  +R F R                        +   L+ TE   AD + R    
Sbjct: 39  MAGVTDTVFRRFIRNASMFTAASTAAPSDVETEVSNQQSGCGLIVTEFTSADGLARMRET 98

Query: 37  -KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
            +K  L +   E P++ Q+ G++   L E+A+IV+D G++ ++LN+GCP+ RV   + G+
Sbjct: 99  KRKRYLTYYEDEHPISAQLFGSNPETLAESARIVQDAGFDMVDLNLGCPAKRVVSSNGGS 158

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            L+ +  ++ +    +  +++IP TVK R+G +D+   +    L K  ++SG+N + +HA
Sbjct: 159 GLLRDLPLIQNIFEKVRASVTIPFTVKFRMGWNDKQ--IVCVELAKMAQESGLNAVALHA 216

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGV 213
           R         +++       ++ +  +K +   + +  NG +     A  ++     D V
Sbjct: 217 RT--------REDGYSGEARWEWIAAVK-DAVSIPVIGNGDVRTPEDAAAMVEKTGCDAV 267

Query: 214 MIGRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVDKDFWRKISASMT----------- 260
           MIGRAA  N  +   + ++ +       +   + R+ + ++  + A M            
Sbjct: 268 MIGRAAPANPWIFRQIAQFTATGNYDRPTEMDRYRMIRGYFEMLLAEMEQEHPEITGPAE 327

Query: 261 ------DYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
                     R       + ++ +      HG       R  +  +A   +     +E  
Sbjct: 328 TDFEKRQKKDRESSRRDAIGKMKQFASWFTHGVVGGAALRRAI-FDAKRGSEVMDAVERF 386

Query: 315 FN 316
           F 
Sbjct: 387 FE 388


>gi|125718973|ref|YP_001036106.1| hypothetical protein SSA_2191 [Streptococcus sanguinis SK36]
 gi|125498890|gb|ABN45556.1| Conserved uncharacterized protein [Streptococcus sanguinis SK36]
          Length = 317

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 16  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 75  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D +
Sbjct: 135 PLTVKMRTGWSDSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGHADLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 184 TLHDVAHSLTKIPFIANGDIRSVQDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 243

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 244 GQVLPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 295

Query: 293 CRHILT 298
            R  ++
Sbjct: 296 LRGAIS 301


>gi|127511264|ref|YP_001092461.1| nifR3 family TIM-barrel protein [Shewanella loihica PV-4]
 gi|126636559|gb|ABO22202.1| putative TIM-barrel protein, nifR3 family [Shewanella loihica PV-4]
          Length = 322

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/328 (19%), Positives = 130/328 (39%), Gaps = 29/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+   +  + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLCLRY-GAALAVSEMLSSNPEVWDTDKSRQRMAHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+  P++V   + A+  A+ +P
Sbjct: 76  PDMMAHAALVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQQPELVKAILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGVH--IAQIAQDCGIASLAVHGRT--------RQCMYKGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG +    +A  +L     D VMIGR A     +   +  Y    
Sbjct: 186 IRAIKQ-NVSIPVVANGDICTPEKARSVLDYTGADAVMIGRGAQGRPWLFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRR-C 293
              +        +     +      Y          L+   +H+          + R   
Sbjct: 245 NKLAPIEVDEKRQVMLEHLKNLYALY-----GEYKGLRIARKHVGWYLDQEAQRSFRADF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
             + TVE   S      +E  F+ ++++
Sbjct: 300 NRLETVEEQRSM-----LERYFDELVKN 322


>gi|260102343|ref|ZP_05752580.1| tRNA-dihydrouridine synthase [Lactobacillus helveticus DSM 20075]
 gi|260083852|gb|EEW67972.1| tRNA-dihydrouridine synthase [Lactobacillus helveticus DSM 20075]
          Length = 341

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 125/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKGF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EETLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D +   V       + +++G + I +H R         +        D++
Sbjct: 140 PVSVKMRTGWDKK--HVFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 ILHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMTHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++ A +  +  +       + +  +       G P S R R 
Sbjct: 249 GKKLPPQTVREKVETAKHQLHALIKIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|324995879|gb|EGC27790.1| tRNA-dihydrouridine synthase [Streptococcus sanguinis SK678]
          Length = 325

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 62/306 (20%), Positives = 126/306 (41%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYKIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +G++ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWSDSSLAVEN---ALAAEAAGISALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++      +    NG +  +  A + +     D VM+GRAA  N  +   ++ YF  
Sbjct: 192 TLHDVAHALTKIPFIANGDIRSVHDAKQRIEEVGADAVMVGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPI---KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                      K ++  D   ++     +Y A     G               G   + +
Sbjct: 252 GEILPDLSFEDKMKIAHDHLSRLVNLKGEYVAIREFRGLAPH--------YLRGTAGAAK 303

Query: 293 CRHILT 298
            R  ++
Sbjct: 304 LRGAIS 309


>gi|161506862|ref|YP_001576816.1| putative tRNA-dihydrouridine synthase [Lactobacillus helveticus DPC
           4571]
 gi|160347851|gb|ABX26525.1| putative tRNA-dihydrouridine synthase [Lactobacillus helveticus DPC
           4571]
          Length = 342

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 125/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 22  MAGVSNSAFRVVCKGF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 80

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 81  EETLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D +   V       + +++G + I +H R         +        D++
Sbjct: 141 PVSVKMRTGWDKK--HVFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 191 ILHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMTHYLET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++ A +  +  +       + +  +       G P S R R 
Sbjct: 250 GKKLPPQTVREKVETAKHQLHALIKIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 304

Query: 296 ILTV 299
            +  
Sbjct: 305 KINE 308


>gi|289449752|ref|YP_003474753.1| TIM-barrel protein [Clostridiales genomosp. BVAB3 str. UPII9-5]
 gi|289184299|gb|ADC90724.1| TIM-barrel protein, nifR3 family [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 367

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/325 (20%), Positives = 120/325 (36%), Gaps = 37/325 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---DKKNILGFSTQEKPLALQIGGAD 58
              +D  +R   +      L  TE++ A  +           L     E P A+Q+ G D
Sbjct: 45  AGASDLPFRHLCQTY-GAGLTCTELVSARGLHYAGVAKSWRYLRLGEDETPRAIQLFGYD 103

Query: 59  ISKLVEAAKIV----EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            +    A +++    E    + I++N+GCP  +V +   G+ LML P++    I+A    
Sbjct: 104 PTDFAAAIELILKTAELPRPDIIDINMGCPVPKVTKTGAGSALMLRPELAAKIISACKNT 163

Query: 115 L---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           L    I VT K R G +      A      ++ ++G   I +H R         ++    
Sbjct: 164 LNGTDILVTCKFRRGYNKDSNIAA--EFALAMAEAGAAMITVHGRT--------REQGYS 213

Query: 172 PNLDYDIVYEIKKEN---------PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
              D++ + E+ +             + +  NG + D   A K L     DGVMIGRAA 
Sbjct: 214 GTADWECIAEVVEAVHGFLARHRYSPIPVIANGDIIDGPTARKALETTGADGVMIGRAAL 273

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
            +  +   +  Y        +P +  +    W +  A ++ Y           +++ + +
Sbjct: 274 GHPWIFREIANYLQGLPKPEAPTRQEIAAAIWGQYQAYLSFY-----DETTATKELRKII 328

Query: 281 IGLFHGFPNSRRCRHILTVEAGAST 305
                G P +   R +    +    
Sbjct: 329 GWYLRGQPGAVEMRRLAVSVSNRDD 353


>gi|295100970|emb|CBK98515.1| tRNA-U20-dihydrouridine synthase [Faecalibacterium prausnitzii
           L2-6]
          Length = 339

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 124/320 (38%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD   R             +EM+ + A++  D K   +L       P  +QI G  
Sbjct: 20  MAGFTDAPCRRLMAQ-HGAGFTVSEMVSSRALVYHDHKTVSLLKAEPNGAPYGVQIFGEV 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA  +E++ ++ +++N+GCP+ ++  G  G+ LML+PD+ G  +  +    + P
Sbjct: 79  PQIMGEAAAAIEEYEFDFLDINMGCPAPKIVSGGAGSKLMLDPDLCGRIVEQVKAHTTRP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D     +      K+ +++G   I +HAR         ++    P +D DI
Sbjct: 139 VTVKMRKGWD--ADHITAVECAKACEQAGAELIAVHART--------REQMYAPGIDPDI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K     + +  NG +     A++++     DGVMI RAA  +  +   V+      
Sbjct: 189 IAKVK-AAVKVPVLGNGDIHTAEDAVEMMQRTGCDGVMIARAALGDPWLFERVNAAIEGL 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                P          R++                 + Q     +    G   +   R  
Sbjct: 248 PAPKEPNLQARMNALRRQVEEM-----VEQKGEYTAMPQARAQTMHYMKGLKGAAALRRC 302

Query: 296 --ILTVEAGASTATHHIIET 313
              L+           + E 
Sbjct: 303 CCTLSRLEDLDELITAVFEE 322


>gi|323465811|gb|ADX69498.1| tRNA-dihydrouridine synthase B [Lactobacillus helveticus H10]
          Length = 342

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 61/321 (19%), Positives = 130/321 (40%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 22  MAGVSNSAFRVVCKGF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 80

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 81  EETLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R G D +   V       + +++G + I +H R         +        D++
Sbjct: 141 PVSVKMRTGWDKK--HVFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 191 ILHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILKDMTHYLET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++ A +  +  +       + +  +       G P S R R 
Sbjct: 250 GKKLPPQTVREKVETAKHQLHALIKIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 304

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +          + +++   +
Sbjct: 305 KINEVWTRQEV-YELLDNFVD 324


>gi|87303078|ref|ZP_01085876.1| Dihydrouridine synthase TIM-barrel protein [Synechococcus sp. WH
           5701]
 gi|87282245|gb|EAQ74205.1| Dihydrouridine synthase TIM-barrel protein [Synechococcus sp. WH
           5701]
          Length = 339

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 134/316 (42%), Gaps = 21/316 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADIS 60
              +DR +R F R    +ALL+TEM+ A ++  G   + + G   +  P+A+Q+      
Sbjct: 32  AGVSDRIFRGFVRRWAPDALLFTEMVNATSLELGHGSDKMAGLEAETGPIAVQLFDHRPG 91

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAA+  E  G   +++N+GCP  ++     G+ L+ +P +    + A+  A+++PVT
Sbjct: 92  AMAEAARRAEGAGAFLVDINMGCPVRKIARKGGGSGLLRDPALACRIVEAVSAAVTVPVT 151

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G               +++++G   + +H R         ++     + D+D + 
Sbjct: 152 VKTRLGWCGDSSDPV--GFALALQEAGAQALTLHGRT--------REQGFSGSADWDAIA 201

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+    + +  NG +    QAL  L     DGVM+GR       ++  +D   S    
Sbjct: 202 RVKQALF-IPLIANGDITGPEQALACLERTGADGVMVGRGTLGAPWLVGRIDAALSGRAL 260

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P            + A +     +       L    +H+     GF  + R RH L 
Sbjct: 261 PPLPGPAERLALAREHLEALVAARGEQ------GLLIARKHLGWTCQGFAGAARLRHQL- 313

Query: 299 VEAGASTATHHIIETA 314
           + A + +A   ++  A
Sbjct: 314 MRAPSPSAALELLAGA 329


>gi|237785022|ref|YP_002905727.1| hypothetical protein ckrop_0405 [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237757934|gb|ACR17184.1| hypothetical protein ckrop_0405 [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 361

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/308 (22%), Positives = 121/308 (39%), Gaps = 31/308 (10%)

Query: 7   RHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
             +R   R L      T + L   EM+ A A++  ++K   +  F+ +E P ++Q+   D
Sbjct: 1   MAFRLLCRELEIEKTGTTSGLYVCEMVTARALVERNEKTLHMTEFAPEETPRSMQLYTTD 60

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
                EAA+++ D    + I++N GCP  +V     GA L     + G+ +AA  + +  
Sbjct: 61  PKWTYEAARMIADDNLADHIDMNFGCPVPKVTRRGGGAALPYKRRLFGEIVAAAVRGVEG 120

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPVTVK R G+DD    +   +        G   + +HAR A          R     
Sbjct: 121 TTIPVTVKMRTGIDDD--HLTFLDAGAIAAAEGAQAVALHARTA--------AQRYSGTA 170

Query: 175 DYDIVYEIKKENP--DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           D++ + E+K+      + +  NG +   + A  ++     DGV++GR       +   + 
Sbjct: 171 DWNRIGELKEHLSGTGVPVLGNGDIFKATDAADMMDQTGCDGVVVGRGCLGRPWLFAELS 230

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                    + P    V     R      T   A H       + + +HM     G+P  
Sbjct: 231 AALRGEPLPAQPTFAEVCDVILRH-----TRLLAAHSGESTACRDMRKHMGWYLRGYPAG 285

Query: 291 RRCRHILT 298
              R  +T
Sbjct: 286 SDLRQKVT 293


>gi|322373801|ref|ZP_08048336.1| tRNA-dihydrouridine synthase family protein [Streptococcus sp.
           C150]
 gi|321277173|gb|EFX54243.1| tRNA-dihydrouridine synthase family protein [Streptococcus sp.
           C150]
          Length = 349

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D++
Sbjct: 167 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGHCDHE 215

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VM+GRAA  N  + T ++ +F  
Sbjct: 216 TLARVAKAITKIPFIGNGDVRSVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFET 275

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 276 GEELPE-LPFDKKLDIAEDHLKRLVDLKGEKIA----VREFRGLAPHYLRGTAGAAKVRG 330

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 331 EVSRAESVAQ-----VEEIFATL 348


>gi|196228193|ref|ZP_03127060.1| TIM-barrel protein, nifR3 family [Chthoniobacter flavus Ellin428]
 gi|196227596|gb|EDY22099.1| TIM-barrel protein, nifR3 family [Chthoniobacter flavus Ellin428]
          Length = 328

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 130/299 (43%), Gaps = 21/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R   +      ++ TE + A+ I R +++ +  L F   E+PL +Q+ G D
Sbjct: 16  MAGITDTIFRQLCKE-QGADVMVTEFVSAEGIFRRNERTLEYLEFIEAERPLGVQLFGGD 74

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
              L EAA++V ++   + I+LN GCP  +V   + G+ L+ +  ++     A+ K A  
Sbjct: 75  PEHLGEAARMVGEWKQPDFIDLNFGCPVNKVVSKNGGSSLLRDCPLLERVARAVVKGAAP 134

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K RIG  +Q          + ++  GV  I +H R         K+       ++
Sbjct: 135 LPVTAKIRIGWCEQTINATTT--ARILEDCGVQAIAVHGRT--------KEQGYSGRANW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D++ E+      L +  NG +   + A+  +   V G+MIGRAA     +   +  Y S 
Sbjct: 185 DVIAEVA-AATSLPVIGNGDIASAADAVGAMKCGVRGLMIGRAAMSTPWIFREIKHYVST 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               + P        F  +      +     LH+   +Q +   ++    G P +++ R
Sbjct: 244 GEILAPPPL-ETQWAFIIRHCRWKVEVEGSELHA---MQSMRTRLMAYSRGMPEAKQLR 298


>gi|325955982|ref|YP_004286592.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus 30SC]
 gi|325332547|gb|ADZ06455.1| tRNA-dihydrouridine synthase [Lactobacillus acidophilus 30SC]
          Length = 341

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 125/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ V+     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EETLLQAAQYVDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + I +H R         +        D+ 
Sbjct: 140 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 VLHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILQDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T          +    ++   +  +  +       + +  +       G P S R R 
Sbjct: 249 GETLPPQTVREKVETAKHQLEGLIKIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|261210422|ref|ZP_05924716.1| tRNA dihydrouridine synthase B [Vibrio sp. RC341]
 gi|260840480|gb|EEX67046.1| tRNA dihydrouridine synthase B [Vibrio sp. RC341]
          Length = 287

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 55/302 (18%), Positives = 117/302 (38%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+  +  L    K+   +    +    ++QI G+D   + EAA+   + G   I+
Sbjct: 1   MAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSDPQLMAEAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+ +PD++   +  +  A+++PVT+K R G D         +
Sbjct: 61  INMGCPAKKVNKKLAGSALLRHPDVIESILKTVVNAVNVPVTLKTRTGWD--TDNKNCVS 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  +  G+  + +H R         +        +YD +  +K     + +  NG ++
Sbjct: 119 IAQLAEDCGIQALALHGRT--------RACMYKGEAEYDSIKAVK-AAVSIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  +  +  T      + V       + 
Sbjct: 170 SPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHGTTMPELPISEVKDIMLGHVK 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A       +E  F+
Sbjct: 230 ALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRTFNAIETADQ-QLDELEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|50954563|ref|YP_061851.1| NifR3/Smm1 family transcriptional regulator [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50951045|gb|AAT88746.1| transcriptional regulator, NifR3/Smm1 family [Leifsonia xyli subsp.
           xyli str. CTCB07]
          Length = 408

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 64/311 (20%), Positives = 121/311 (38%), Gaps = 23/311 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      L  +EMI + A++    +   ++     E P ++Q+ G D
Sbjct: 41  MAGITNTAFRRLCREF-GAGLYVSEMITSRALVERTPESLRLIAHHESETPRSIQLYGVD 99

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + EA   +V +   + I+LN GCP  +V     GA L     +  + +  A+  A  
Sbjct: 100 PKTVREAVTLLVAEDRADHIDLNFGCPVPKVTRKGGGAALPWKLGLFREIVEGAVAAAGD 159

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IP+TVK R G+D     +      ++ + +GV  I +HAR A              + D+
Sbjct: 160 IPLTVKMRKGIDSD--HLTYLEAARAAEGAGVASIALHARTA--------AEFYSGHADW 209

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  +K+      +  NG +   + A++++     DGV++GR       +   +   F 
Sbjct: 210 PAIRTLKETITGTPVIGNGDIWSAADAVRMVEETGCDGVVVGRGCLGRPWLFGDLAAAFK 269

Query: 235 --NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH----SGGKLQQITRHMIGLFHGFP 288
                  +             +++A+   +A   +          + I +H+   F G+P
Sbjct: 270 ARAGELSADEAAAAQAHPALGEVAATFRRHAELLVEFFDSEERGCRDIRKHVAWYFKGYP 329

Query: 289 NSRRCRHILTV 299
                R  L  
Sbjct: 330 VGGDLRASLAT 340


>gi|315037518|ref|YP_004031086.1| transcriptional regulator [Lactobacillus amylovorus GRL 1112]
 gi|312275651|gb|ADQ58291.1| transcriptional regulator [Lactobacillus amylovorus GRL 1112]
 gi|327182814|gb|AEA31261.1| tRNA-dihydrouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 341

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 125/304 (41%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLSMMDVDPREHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ V+     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +  
Sbjct: 80  EETLLQAAQYVDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHAVVQNVQK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + I +H R         +        D+ 
Sbjct: 140 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGEADWG 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y   
Sbjct: 190 VLHDVAQ-VLDVPFVANGDIRTPELAKKALDEIGCTAVMVGRAALGNPWILQDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T          +    ++   +  +  +       + +  +       G P S R R 
Sbjct: 249 GETLPPQTVREKVETAKHQLEGLIKIHGEKR-----AVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|15888769|ref|NP_354450.1| nitrogen regulation protein [Agrobacterium tumefaciens str. C58]
 gi|15156519|gb|AAK87235.1| nitrogen regulation protein [Agrobacterium tumefaciens str. C58]
          Length = 338

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 117/287 (40%), Gaps = 27/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++          P  +Q+ G + 
Sbjct: 31  MSGVTDLPFRQLAWRY-GAGLVVTEMVASRELVANRGESWARLKNAGMVPHMVQLAGREA 89

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G   I++N+GCP+ +V  G  G+ LM +PD     I A   A+ +PV
Sbjct: 90  HFMAEAAKIAADNGAGIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVGAVDVPV 149

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    + +  + +GV  I IH R  +               D+D +
Sbjct: 150 TLKMRLGWDE--NSINAPEIARRAEAAGVQLITIHGRTRM--------QFYEGRADWDAI 199

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG +E    A +IL     D VM+GR A     +   +  +     
Sbjct: 200 RAV-REVISVPLIANGDVETAEDAREILRRSGADAVMVGRGAQGQPWLPAVLAGH----- 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             S+P +  +           +  Y          L+   +H+    
Sbjct: 254 --SAPQRADIPTIAVEHYEMMLEFYGRE-----AGLRHARKHLGWYL 293


>gi|262405017|ref|ZP_06081569.1| tRNA dihydrouridine synthase B [Vibrio sp. RC586]
 gi|262348856|gb|EEY97997.1| tRNA dihydrouridine synthase B [Vibrio sp. RC586]
          Length = 287

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 55/302 (18%), Positives = 118/302 (39%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+  +  L    K+   +    +    ++QI G+D  ++ EAA+   + G   I+
Sbjct: 1   MAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSDPQQMAEAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+ +PD++ + +  +  A+++PVT+K R G D         +
Sbjct: 61  INMGCPAKKVNKKLAGSALLRHPDVIENILKTVVNAVNVPVTLKTRTGWD--TDNKNCVS 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  +  G+  + +H R         +        +YD +  +K     + +  NG ++
Sbjct: 119 IAQLAEDCGIQALALHGRT--------RACMYKGEAEYDSIKAVK-AAVSIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  +  +  T        V       + 
Sbjct: 170 SPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHGTTMPELPILEVKDIMLGHVK 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A       +E  F+
Sbjct: 230 ALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRTFNSIETADQ-QLDELEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|254442182|ref|ZP_05055658.1| putative TIM-barrel protein, nifR3 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198256490|gb|EDY80798.1| putative TIM-barrel protein, nifR3 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 367

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 121/290 (41%), Gaps = 19/290 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             +T+  +R  A+ L    L+ T+++ A ++L G      ++    +E+P+A+Q+ G   
Sbjct: 18  AGYTNLPFRLTAKSLGGLGLVTTDLVNARSLLEGRAVAYKMIATDVREQPMAVQLFGGVA 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++ +AA I ++ G   +++N+GCP  +V +   G+ +M N +   + +  M  A+ IPV
Sbjct: 78  EEMRDAAVICQERGAQSVDINMGCPVKKVVKTGSGSSMMKNHEKTQELVKGMIDAVDIPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T K R+G D     +    L ++++  GV+ I+IH R         +       +D + +
Sbjct: 138 TAKMRLGWDSD--NITAPELARALEDVGVSAIFIHGRT--------RAQGFSGGVDLEGI 187

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K+    + +  NG +     A  +      DGV IGR A+ N  +      Y     
Sbjct: 188 RKVKEAVSSVPVIGNGDVTSPEAARIMFERTGCDGVSIGRGAFYNPWIFRQTVHYLDTGE 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               P      +     +   +  Y            Q  +  +     F
Sbjct: 248 LLPDPTFEERVELMRVHLERMIDFY-----GELKGCIQFRKVAVWYAKRF 292


>gi|218660217|ref|ZP_03516147.1| tRNA-dihydrouridine synthase A [Rhizobium etli IE4771]
          Length = 249

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 119/231 (51%), Positives = 150/231 (64%), Gaps = 25/231 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D  
Sbjct: 13  MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDVAEHPLALQLGGSDPG 72

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  C+AAM    + PVT
Sbjct: 73  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAACVAAMKAVATAPVT 132

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY
Sbjct: 133 VKCRIGVDEQEPEDALPALISRVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVY 192

Query: 181 --------EIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRA 218
                    + + +              + A    P      VDGVM+GR 
Sbjct: 193 RDETALARRLHRAS------------TAASARSTRPRATSAHVDGVMLGRG 231


>gi|114762893|ref|ZP_01442325.1| tRNA-dihydrouridine synthase, putative [Pelagibaca bermudensis
           HTCC2601]
 gi|114544503|gb|EAU47510.1| tRNA-dihydrouridine synthase, putative [Roseovarius sp. HTCC2601]
          Length = 327

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 70/287 (24%), Positives = 117/287 (40%), Gaps = 21/287 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              TD  +R          L+ +EMI +   L  R   +         +  ++QI G   
Sbjct: 20  AGITDLPFRTLVSRW-GAGLVVSEMIASGEFLTARPGTREKAELGAAIENTSVQIAGRAP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++V D G   I++N+GCP+ +V  G  G+ LM +PD     I A+  A+ +PV
Sbjct: 79  EPMAEAARMVADMGARVIDINMGCPAKKVTGGYSGSALMRDPDHALRLIEAVVAAVDLPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD   ++    L    + +G+  I IH R         +        D+  +
Sbjct: 139 TLKTRLGWDDG--SLNAPELAARAEAAGIRMIVIHGRT--------RCQFYKGRADWAAI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K E   + +  NG + D + A +   L   DGVM+GR A      L  +        
Sbjct: 189 RKVK-EAVSVPLVANGDITDAASAREALRLSGADGVMVGRGAQGAPWRLAEIAHALYGAP 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               P +     D  R+    M D+    L     ++   +H+    
Sbjct: 248 LPEIP-EGAALTDLVREHYDRMIDFYGPELG----VRCARKHLGWYM 289


>gi|299820638|ref|ZP_07052527.1| tRNA-dihydrouridine synthase [Listeria grayi DSM 20601]
 gi|299817659|gb|EFI84894.1| tRNA-dihydrouridine synthase [Listeria grayi DSM 20601]
          Length = 335

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 129/318 (40%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 24  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNTKTLDMLYIDEKEKPLSLQIFGGE 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V + ++A+  A+  
Sbjct: 83  KDTLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYEMVSAVVDAVDK 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD                +    +    R  + +G          N D+D
Sbjct: 143 PVTVKMRIGWDDDHIFAIENAQAAERAGAAAVAMHGRTRVQMYEG----------NADWD 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++KKE   +    NG ++    A +IL     DGVMIGRAA  N  M+    +Y   
Sbjct: 193 VLRDVKKEI-KIPFMANGDVKTPEDAKRILEHTNADGVMIGRAALGNPWMIYRTVKYLET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     +   +             +++  +H      G   S   R 
Sbjct: 252 GELLPEPEPREKIETALLHLKRLIA-----LKGENIAVREFRQHAAYYLKGARGS--TRA 304

Query: 296 ILTVEAGASTATHHIIET 313
            +      + A   +I  
Sbjct: 305 KVAANQATTQAEMEMILR 322


>gi|189485309|ref|YP_001956250.1| putative tRNA-dihydrouridine synthase [uncultured Termite group 1
           bacterium phylotype Rs-D17]
 gi|170287268|dbj|BAG13789.1| putative tRNA-dihydrouridine synthase [uncultured Termite group 1
           bacterium phylotype Rs-D17]
          Length = 320

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 78/300 (26%), Positives = 137/300 (45%), Gaps = 21/300 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD   R  A+      L+YT M+ A A++R D+K   +L  +  E+P+A QI G+ 
Sbjct: 20  MAGITDLPLRRLAKS-GGAGLVYTGMLSARALVRSDEKTEKLLKTTEDERPVAAQIFGSA 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAKIV + G + I++N+GCP  +V +   GA L+ +  +V + + ++ K++ +P
Sbjct: 79  AHIMAEAAKIVRNSGADIIDVNLGCPVKKVAKAGAGAKLLADEKLVSEILESVVKSVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G+  +  A     ++K     G+  + +HAR A        D +         
Sbjct: 139 VTVKIRTGLLPEHNAAT--EIIKVAYNCGIKMVAVHARPASQGHSGFPDLK--------- 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++        + +  NGG+ D   A   L  P+  G+MIGR A  N ++   ++ +FS+ 
Sbjct: 188 LFAASCAGAKIPVIANGGVVDEKTAADFLRVPNCAGIMIGRGALGNYSIFKRLEAFFSSG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P KT   +   + +      Y+  +         + +         PN+ + R I
Sbjct: 248 KKLPLPSKTEKVEWLKKHV-----QYSVEYYGEKKGFVVMKKVFHYYVKDLPNAAKIRDI 302


>gi|323492069|ref|ZP_08097231.1| NifR3/Smm1 family protein [Vibrio brasiliensis LMG 20546]
 gi|323313630|gb|EGA66732.1| NifR3/Smm1 family protein [Vibrio brasiliensis LMG 20546]
          Length = 280

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 116/295 (39%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  L    K+   +    +    ++QI GAD   + +AA+   + G   I++N+GC
Sbjct: 1   MMSSNPKLWKTSKSKQRMVHEGESGIRSVQIAGADPQLMADAAQFSVENGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V++   G+ L+  PDI+ D + A+  A+ +PVT+K R G D          + K  
Sbjct: 61  PAKKVNKKLAGSALLQYPDIIEDILKAVVNAVDVPVTLKTRTGWD--TDNKNCVQIAKLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + +H R         K        +YD +  +K+    + +  NG ++   +A
Sbjct: 119 EDCGIQALALHGRT--------KACMYKGEAEYDSIKAVKQAI-SIPVIANGDIDSPEKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGR A     +   +  +  N  T      + V       ++A  + 
Sbjct: 170 KYVLEYTGADALMIGRPAQGRPWIFQEIQHFLENGTTMPDLPYSEVKDILLGHVNALHSF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y           +   +H+         +   R         +      +E  F+
Sbjct: 230 Y-----GEYLGPRIARKHVGWYLKEHEQASEFRRTFNA-IDVAELQLEALEEYFD 278


>gi|317968889|ref|ZP_07970279.1| nitrogen regulation protein NifR3 family protein [Synechococcus sp.
           CB0205]
          Length = 347

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 68/323 (21%), Positives = 137/323 (42%), Gaps = 27/323 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-KNILGFSTQEKPLALQIGGADIS 60
              +DR +R   R    +ALL+TEM+ A ++  G   + +   + ++ P+ +Q+      
Sbjct: 44  AGVSDRIFRGLVRRWAPDALLFTEMVNATSLELGHGLQKVEELALEQGPIGVQLFDHRPQ 103

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  E  G   I++N+GCP  ++ +   G+ L+  PD+    +  +  A+SIP+T
Sbjct: 104 SMADAARRAEAAGAFLIDINMGCPVKKIAKKGGGSGLIREPDLASRIVETVSAAVSIPIT 163

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G              + ++ +G   + +H R         ++     + D+  + 
Sbjct: 164 VKTRLGWCGSDLDPVA--WCRQLESAGAQLLTLHGRT--------REQGFKGSADWQAIA 213

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             K+    + +  NG +   + AL+ L     DGVM+GR +     ++  +D   S    
Sbjct: 214 AFKRAL-AIPVIANGDINSAADALRCLEQTGADGVMVGRGSMGAPWLVGQIDAALSGRPI 272

Query: 239 GSSPIKTR---VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             SP       + K+  + + A+  D+          L    +HM    +GF  + + RH
Sbjct: 273 PESPSALERVLLAKEQLQALVAAKGDH---------GLLIARKHMGWTCNGFTGAPQLRH 323

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            L + A        +++     +
Sbjct: 324 AL-MRAPTPAEAIALLDQTAAAL 345


>gi|257066133|ref|YP_003152389.1| TIM-barrel protein, nifR3 family [Anaerococcus prevotii DSM 20548]
 gi|256798013|gb|ACV28668.1| TIM-barrel protein, nifR3 family [Anaerococcus prevotii DSM 20548]
          Length = 326

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 68/327 (20%), Positives = 130/327 (39%), Gaps = 25/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R            +TEM+  +A+   ++  + I+  +  EK   +QI G D
Sbjct: 15  MAGITDSAFRQICEE-NGCDKTFTEMVSVNALDFNNRATEEIMYTAYSEKNCNIQIFGKD 73

Query: 59  ISKLVEAAK--IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              +    K  I     + EI+ N+GCP+ ++     G+ LM +   V +    + ++  
Sbjct: 74  CDIIERVIKDKINPREDFEEISFNMGCPAPKIFNNGQGSALMRDVKKVYEIGKCLKESTD 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V VK R+G+DD   +V    + K+++ SG++ + +H R    +             ++
Sbjct: 134 KIVNVKIRMGIDDD--SVNYIEVGKALEDSGIDYVILHGRTRKQQ--------YSGKANW 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K E   + +  NG +  +     IL     DGVMI R A  N  +   + +Y  
Sbjct: 184 QAIRKLK-ETLSIPVIANGDVFSVKDYKDILDETGADGVMIARGAMGNPFIFRQIKDYIQ 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T  SPI         ++       Y    L     + Q+ +H+     G P +   R
Sbjct: 243 GKET--SPISYEDILATIKRQYELSLKYKKEKL----VINQMRKHVGWYIKGLPQAASYR 296

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             +  +   S     ++E     + ++
Sbjct: 297 DRVN-KLKTSEEIFDLLEEYRKFLEDN 322


>gi|82617391|emb|CAI64302.1| dihydrouridine synthase like protein [uncultured archaeon]
          Length = 318

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 129/318 (40%), Gaps = 27/318 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M + T+  +R   +     AL Y+EMI A+A++R  +K +        E+P  +Q+ G  
Sbjct: 17  MANVTNLAFRMLCKKY-GAALTYSEMISANAVVRQGEKTMQRGLTCEDEQPFCIQMFGNS 75

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA I+E+ +    I++N+GCP+  +     G+ L+ +P +V D ++++   +S 
Sbjct: 76  TDTMTEAALILEETYRPAIIDVNMGCPAPLIVRQECGSALLNSPSLVHDIVSSLADNIST 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+             + ++I+ +G   I +H R         ++         +
Sbjct: 136 PVSTKIRVF----DNMEKTLEIARTIESAGACAITVHGRT--------REQMYSGTSSLE 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               IKKE   + +  NG ++D   A   L     DG+MIGRAA  +  +   V  Y  +
Sbjct: 184 YAKRIKKEL-SIPVIANGDIKDGESAKHALEYTECDGLMIGRAAIGHPFIFRQVSHYLEH 242

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     R   DF   I                + +  T+       G   SR  R 
Sbjct: 243 GEPLEIDYCNRQVSDFMEYIELLKQYDIFSLGDIKAQSKAFTK-------GVAGSRHIRE 295

Query: 296 ILTVEAGASTATHHIIET 313
            L  EA        +++ 
Sbjct: 296 ELN-EAKTIGPIIDVMDR 312


>gi|78777367|ref|YP_393682.1| dihydrouridine synthase TIM-barrel protein nifR3 [Sulfurimonas
           denitrificans DSM 1251]
 gi|78497907|gb|ABB44447.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sulfurimonas
           denitrificans DSM 1251]
          Length = 318

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 136/321 (42%), Gaps = 33/321 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EM+ ++A++ G  K   ++  S  E P ++QI GA++
Sbjct: 19  AGYTDLPFRSVVKKF-GADLTVSEMLSSNALVHGSSKTLGMIEKSPNEDPYSVQIAGAEV 77

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + +  A +I+ E  G + I+LN GCP  ++     G+ L+LN  ++G+ I  +    +  
Sbjct: 78  NVIRRAVEILNEQDGIDIIDLNCGCPVPKIVGHGSGSSLLLNLPLMGEIIRTIKNTSNKN 137

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +       ++ K ++ SG + I +H R         +  +    +DYD
Sbjct: 138 LTSVKIRLGFEKK----NHVDIAKMVEDSGADFIAVHGRT--------RAGKFKAPVDYD 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + EIK+   ++ +  NG ++   +A  +L     DGVMIGR A     +   +      
Sbjct: 186 AIREIKEAI-NIPVIANGDIDSYEKAEWVLEHTGADGVMIGRGAVGAPWIFHQLK----- 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
              G+  I   +      +    M ++   H      +    +HM     G+  +   R 
Sbjct: 240 --YGTKDIDENIKHAIILEHYDKMIEFHGAH-----GVIMFRKHMHTYSKGYRGASALRD 292

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +            +IE    
Sbjct: 293 GIN-HISDPDKCRELIENFLK 312


>gi|315062559|gb|ADT76886.1| tRNA-dihydrouridine synthase B [Escherichia coli W]
 gi|323183019|gb|EFZ68418.1| TIM-barrel protein, nifR3 family protein [Escherichia coli 1357]
          Length = 286

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 60/300 (20%), Positives = 119/300 (39%), Gaps = 21/300 (7%)

Query: 21  LLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I+
Sbjct: 1   MTVSEMMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        
Sbjct: 61  INMGCPAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEE 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  +  G+  + IH R         +        +YD +  +K++   + +  NG + 
Sbjct: 119 IAQLAEDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDIT 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           D  +A  +L     D +MIGRAA     +   +  Y              V +     + 
Sbjct: 170 DPLKARAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVR 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
                Y       G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 ELHDFYGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 283


>gi|300812108|ref|ZP_07092556.1| TIM-barrel protein, nifR3 family [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496947|gb|EFK32021.1| TIM-barrel protein, nifR3 family [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 342

 Score =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 59/304 (19%), Positives = 123/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      ++  EMI    I+ G++K   +L     E P+++QI G  
Sbjct: 21  MAGVSNMAFRKVCKEF-GAGMVVCEMISDHGIIYGNEKTLSMLDVDPGEHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   +  + + +  
Sbjct: 80  EDSLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMVHKVVQNVEK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + + +H R         +        D++
Sbjct: 140 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y + 
Sbjct: 190 TLHEVAQ-VMDIPFVANGDITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D   +       + +  +       G P S R R 
Sbjct: 249 GEELPKQSVREKVETAKHQL-----DGLVQLHGEKRAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|254464462|ref|ZP_05077873.1| tRNA-dihydrouridine synthase B [Rhodobacterales bacterium Y4I]
 gi|206685370|gb|EDZ45852.1| tRNA-dihydrouridine synthase B [Rhodobacterales bacterium Y4I]
          Length = 319

 Score =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 68/288 (23%), Positives = 123/288 (42%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+Q+ G +
Sbjct: 10  MAGITDRPFRDLVRSF-GVGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRE 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK V   G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+ +P
Sbjct: 69  EYWIAEAAKQVAGQGARIIDINMGCPAKKVTNGYSGSALLKTPDHALRLIEAVVGAVDVP 128

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD    +   ++ +   ++GV  + IH R         +      + D+  
Sbjct: 129 VTLKTRLGWDD--NCLNAPDVARRAAEAGVQMVTIHGRT--------RCQFYKGSADWAA 178

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +  ++ +  NG + D + A + L     DGVMIGR A     +L  V  +    
Sbjct: 179 IRSVK-DAVNVPVLANGDIVDTASARQALELSGADGVMIGRGAEGKPWLLAEVAHHLWGA 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                P    + +       A +T Y      +   ++   +H+    
Sbjct: 238 PAPDVPEGGALIEMVSEHYKAMLTFY-----GTDLGVRVARKHLGWYM 280


>gi|304391548|ref|ZP_07373490.1| tRNA-dihydrouridine synthase B [Ahrensia sp. R2A130]
 gi|303295777|gb|EFL90135.1| tRNA-dihydrouridine synthase B [Ahrensia sp. R2A130]
          Length = 342

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 75/323 (23%), Positives = 138/323 (42%), Gaps = 24/323 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGADI 59
           M   TD  +R  A       ++ +EM+ ++A+  G  + +L  +    P   +Q+ G + 
Sbjct: 28  MSGVTDVPFRRLAWRY-GAGMVVSEMVASEALTTGMDEMVLKAAGAGLPDHMVQLAGREP 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  A ++ ED G   I++N+GCPS RV  G  G+ LM + D     I A+  A  +PV
Sbjct: 87  QWMDRATRMAEDAGATIIDINMGCPSKRVTNGYSGSALMRDLDNAEGLINAVVAATDLPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+Q  ++    L +  + +GV  + +H R         ++       D+D +
Sbjct: 147 TLKMRLGWDEQ--SINAPELARRAENAGVQMLTVHGRT--------RNQFYKGTADWDAI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   L + +NG + D + A   L     DGVMIGRA+Y    +   +    +   
Sbjct: 197 RAV-REASRLPLVVNGDICDEATACAALIASGADGVMIGRASYGAPWLPGQIGAALAGTP 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP-NSRR--CR 294
              +P    +       + A ++ Y          L+   +H+       P + R+   R
Sbjct: 256 VPETPSGEHLAALVCEHVDAMLSHYGLE-----LGLRNARKHIDWYAAHLPKDVRKSPLR 310

Query: 295 HILTVEAGASTATHHIIETAFNL 317
             +      +T    ++E  F+ 
Sbjct: 311 RAIMT-GTDATEVLSMVEKLFSQ 332


>gi|212633320|ref|YP_002309845.1| dihydrouridine synthase [Shewanella piezotolerans WP3]
 gi|212554804|gb|ACJ27258.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Shewanella
           piezotolerans WP3]
          Length = 322

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 67/324 (20%), Positives = 134/324 (41%), Gaps = 26/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R         A+  +EM+ ++  +    K+ L    + ++   ++QI G+D
Sbjct: 17  MAGVTDQPFRNLCIRY-GAAMAVSEMLSSNPDVWDTDKSRLRMTHAGEDGIRSVQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAAVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQDPQQVEAILKAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +        +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGVH--IAQIAENCGIASLAVHGRT--------RQCMYKGEAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK+   + +  NG +    +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKKQI-SIPVVANGDILTPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
               +P++T   +    +    +      +      ++   +H+    +   + R  R  
Sbjct: 245 -NKLAPVETDEKRQLMLEHLKMLYALYGDY----KGIRFARKHVGWYLN-QESQRAFRAE 298

Query: 295 --HILTVEAGASTATHHIIETAFN 316
              ++TVE   S   H+  E A N
Sbjct: 299 FNRLVTVEEQCSMVEHYFDEFAAN 322


>gi|187736076|ref|YP_001878188.1| TIM-barrel protein, nifR3 family [Akkermansia muciniphila ATCC
           BAA-835]
 gi|187426128|gb|ACD05407.1| TIM-barrel protein, nifR3 family [Akkermansia muciniphila ATCC
           BAA-835]
          Length = 334

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 137/327 (41%), Gaps = 28/327 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R   + L  + ++ TE + A+ IL      +         +P+ +Q+ GAD
Sbjct: 24  MAGVTDPIFRTICKELGVDVMV-TEFVSAEGILQAWERNRRYTKIENAHRPIGIQLFGAD 82

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
            + + EAA+I+ D    + I++N GCP  +V   + G+ L+ +  ++      + KA+  
Sbjct: 83  GNHMGEAARIILDHEKPDFIDINFGCPVPKVVGKNGGSSLLKDLPLLASVAGGVVKAVGE 142

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT K RIG D Q  ++   +  + ++  G++ I IH R         +  +     +
Sbjct: 143 RIPVTAKIRIGWDFQ--SLCAMDACRLLENEGISMITIHGRT--------RSQQYSGTAN 192

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +DI+ E  +    + +  NG +        +K   +V GVMIGRAA +N  +      Y 
Sbjct: 193 WDIIDECARAM-SVPVIGNGDISTPQAVAYVKENTAVSGVMIGRAAMENPWIFGDAKYYL 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMT-DYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +     +           R    ++   +    LH+   ++ +   ++    GFP ++ 
Sbjct: 252 LHGTMPPARDPQEKAALILRHARMALESRHYGDELHT---MRHMRSRILAYTKGFPGAKE 308

Query: 293 CRHILTVEAGASTATHHIIETAFNLMI 319
            R  L   +         +E   + + 
Sbjct: 309 MRSRLVRVSSMPE-----LEDLLSKLP 330


>gi|222148571|ref|YP_002549528.1| nitrogen regulation protein [Agrobacterium vitis S4]
 gi|221735557|gb|ACM36520.1| nitrogen regulation protein [Agrobacterium vitis S4]
          Length = 332

 Score =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 121/287 (42%), Gaps = 27/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++          P  +Q+ G D 
Sbjct: 26  MSGVTDLPFRQLAFR-HGAGLVVTEMVASRELVFNAAESWSRLKGAGLTPHMVQLAGRDP 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM  P+I    I A  KA+SIPV
Sbjct: 85  HWMAEAAKIAEANGADIIDINMGCPAKKVIGGYAGSALMREPEIALAMIEATVKAVSIPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D    ++   +L +  + +GV  I +H R  +               D+D +
Sbjct: 145 TVKMRLGWDSD--SINAPDLSRRAQDAGVQAITVHGRTRM--------QFYEGRADWDAI 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + +  NG ++ +  A +IL     D +M+GRA               +  L
Sbjct: 195 AAV-RDAIYIPLIANGDIDTLGDAQEILRRSGADAIMLGRACQGRPWH--------AGVL 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            G +P               +M D+   H      ++   +H+    
Sbjct: 246 AGHAPPSAEEIPAIAVAHYRAMLDHYGAH----VGVRHARKHVGWYL 288


>gi|329943329|ref|ZP_08292103.1| TIM-barrel , nifR3 family protein [Chlamydophila psittaci Cal10]
 gi|313848477|emb|CBY17481.1| putative dihydrouridine synthase [Chlamydophila psittaci RD1]
 gi|328814876|gb|EGF84866.1| TIM-barrel , nifR3 family protein [Chlamydophila psittaci Cal10]
 gi|328915169|gb|AEB56002.1| NifR3/Smm1 family protein [Chlamydophila psittaci 6BC]
          Length = 332

 Score =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 138/322 (42%), Gaps = 23/322 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  YR  +      AL++ EM+  + +     + +  L +S   +P+  Q+ G+  
Sbjct: 22  AGFSDYPYRKMSSFYGPPALMFCEMVKVEGLHYSPSRTLKLLEYSESMRPIGGQLCGSKP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               EAAK++E  G++ I+LN GCP+ R+ +   G+ L+ +P+++G  +  + +A+SIPV
Sbjct: 82  EMAGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGLLKSPELIGKILEKIIEAVSIPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ I+ +G + +++H R         +    +   + + +
Sbjct: 142 TVKIRSGWD--CNNINVEETVRIIRDAGASAVFVHGRT--------RAQGYVGPSNLEYI 191

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K     DL +  NG +     A  ++     DGV++ R       ++  ++ Y ++ 
Sbjct: 192 ARAKAAAGKDLPVFGNGDIFSPEAAKLMMDSTQCDGVLVARGTMGAPWIVRQIESYLASG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCRH 295
                P   R      ++       +   +  S  K    TR + G         R  R 
Sbjct: 252 TYQKVPFSKR------KQAFIQHLQWVEEYYQSEAKFLSETRKLCGHYLISASKVRFLRS 305

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            L+ +A +    + +I+     
Sbjct: 306 ALS-KATSVQEVYQLIDNYEEA 326


>gi|55822169|ref|YP_140610.1| putative transcriptional regulator [Streptococcus thermophilus
           CNRZ1066]
 gi|55738154|gb|AAV61795.1| possible transcriptional regulator [Streptococcus thermophilus
           CNRZ1066]
          Length = 350

 Score =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 125/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 49  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 107

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 108 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D++
Sbjct: 168 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGHCDHE 216

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG + ++  A  ++    VD VM+GRAA  N  + T ++ +F  
Sbjct: 217 TLARVAKAITKIPFIGNGDVRNVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFET 276

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 277 GEELPD-LPFDKKLDIAEDHLKRLVDLKGEMIA----VREFRGLAPHYLRGTAGAAKVRG 331

Query: 296 ILT 298
            ++
Sbjct: 332 EVS 334


>gi|257466741|ref|ZP_05631052.1| nitrogen regulation protein NIFR3 [Fusobacterium gonidiaformans
           ATCC 25563]
 gi|315917890|ref|ZP_07914130.1| nitrogen regulation protein NIFR3 [Fusobacterium gonidiaformans
           ATCC 25563]
 gi|313691765|gb|EFS28600.1| nitrogen regulation protein NIFR3 [Fusobacterium gonidiaformans
           ATCC 25563]
          Length = 314

 Score =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 123/301 (40%), Gaps = 22/301 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  YR        + LL+TEM+ +DA+   + K I           +Q+ G D+ K
Sbjct: 10  AGVTDYTYRGILEEFHPD-LLFTEMVSSDALAALNDKTISQILRLRPGNGVQLFGKDVEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           ++ +AK VE  G   I++N GCP  RV     GA L+ +PD + + ++ + + L     +
Sbjct: 69  MLYSAKYVEKLGVKHIDINSGCPMKRVVHSGHGAALLKSPDKIKEILSTLREGLQEDTDL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG +     +    + K  ++ G + I +H R         +        D+ ++
Sbjct: 129 SIKIRIGYEKPENYI---QIAKIAEEVGCSHITVHGRT--------RAQLYTGFADWSLI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            EIK EN  + +  NG +     A + +    VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEIK-ENVSIPVIGNGDIFTAEDAKEKIEYSGVDGVMLARGIFGNPWLIREIREILQYGQ 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +              I     D   R       +  + +H+     G  NS  C++ +
Sbjct: 237 VKTKVTAEDKIDMAIHHIEEIAKDNPQREF-----VFDVRKHICWYLKGISNSAECKNQI 291

Query: 298 T 298
            
Sbjct: 292 N 292


>gi|163746230|ref|ZP_02153588.1| tRNA-dihydrouridine synthase [Oceanibulbus indolifex HEL-45]
 gi|161380115|gb|EDQ04526.1| tRNA-dihydrouridine synthase [Oceanibulbus indolifex HEL-45]
          Length = 330

 Score =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 67/288 (23%), Positives = 117/288 (40%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  YR          L+ +EM+ +  +L  R   +            ++Q+ G +
Sbjct: 17  MAGITDLPYRSLVARF-GAGLVVSEMVASQELLSRRPGTREKAELGLDVIGTSVQLAGRE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ +V +G+ G+ LM  PD     I A+  A+++P
Sbjct: 76  AEPMAEAARMVEAMGARIIDINMGCPAKKVTQGASGSALMKTPDHALRLIEAVVGAVNVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD +   A   + K  + +GV  I IH R         +        D+  
Sbjct: 136 VTLKTRLGWDDNMLNAA--PIAKRAEDAGVQMITIHGRT--------RCQFYKGRADWAA 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E  ++ +  NG +    +A +   L   DGVM+GR A     +L  +       
Sbjct: 186 IRAVK-ETVNVPVIANGDIIGSDEARQALKLSGADGVMVGRGAQGRPWLLAQIAHDLHGR 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                P    + +         +  Y           +   +H+    
Sbjct: 245 PAPVIPKGRAMAEMVTEHYDEMLRFYGVE-----LGAKVARKHLGWYM 287


>gi|262172604|ref|ZP_06040282.1| tRNA dihydrouridine synthase B [Vibrio mimicus MB-451]
 gi|261893680|gb|EEY39666.1| tRNA dihydrouridine synthase B [Vibrio mimicus MB-451]
          Length = 287

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 55/302 (18%), Positives = 116/302 (38%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+  +  L    K+   +    +    ++QI G+D   + EAA+   + G   I+
Sbjct: 1   MAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSDPQLMAEAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+ +PD++   +  +  A+++PVT+K R G D         +
Sbjct: 61  INMGCPAKKVNKKLAGSALLRHPDVIESILKTVVNAVNVPVTLKTRTGWD--TDNKNCIS 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  +  G+  + +H R         +        +YD +  +K     + +  NG ++
Sbjct: 119 IAQLAEDCGIQALALHGRT--------RACMYKGEAEYDSIKAVK-AAVSIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  +  +  T        V       + 
Sbjct: 170 SPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHGTTMPELPILEVKDIMLGHVK 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A       +E  F+
Sbjct: 230 ALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRTFNAIETADQ-QLDELEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|289427130|ref|ZP_06428846.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J165]
 gi|295130515|ref|YP_003581178.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK137]
 gi|289159599|gb|EFD07787.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J165]
 gi|291376434|gb|ADE00289.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK137]
 gi|315080730|gb|EFT52706.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL078PA1]
 gi|315085740|gb|EFT57716.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL002PA3]
          Length = 409

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 125/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 55  MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 113

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 114 PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 174 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 224 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 283 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 336

Query: 293 CRHIL 297
            RH+L
Sbjct: 337 TRHVL 341


>gi|85715510|ref|ZP_01046491.1| dihydrouridine synthase TIM-barrel protein [Nitrobacter sp.
           Nb-311A]
 gi|85697705|gb|EAQ35581.1| dihydrouridine synthase TIM-barrel protein [Nitrobacter sp.
           Nb-311A]
          Length = 331

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 71/285 (24%), Positives = 117/285 (41%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TDR +R  A  L    L+ +EM  +D ++RG   ++L        P  +Q+ G + 
Sbjct: 15  MSGITDRPFRRLAESL-GAGLVVSEMTASDDLVRGRPMSVLRCEATGYGPHVVQLAGCEA 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 74  RWMAEGARIAEAAGADIIDINMGCPARHVTGGQSGSALMRDLDHALPLIEATVGAVKVPV 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+  ++    L +  +  GV  I +HAR         +        D+  V
Sbjct: 134 TLKMRLGWDDR--SLNAPALAQRAESVGVQMITVHART--------RCQFYKGCADWQAV 183

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + + +NG +     A+  L     D VM+GR A     M   +       +
Sbjct: 184 RAVK-EAVRIPVVVNGDITSFEAAVAALKASGADAVMVGRGAQGRPWMPGQIGRRLETGV 242

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
              +P                +  Y  R       L+   +H+  
Sbjct: 243 EEPNPSLADQLAYIRALYDDLLLHYGLRI-----GLRHARKHLGW 282


>gi|289209406|ref|YP_003461472.1| hypothetical protein TK90_2246 [Thioalkalivibrio sp. K90mix]
 gi|288945037|gb|ADC72736.1| TIM-barrel protein, nifR3 family [Thioalkalivibrio sp. K90mix]
          Length = 330

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 61/289 (21%), Positives = 119/289 (41%), Gaps = 21/289 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +DR  R  AR L   +   +EM+ +D  L G  K+   L    + +P  +Q+ G +
Sbjct: 18  MAGVSDRPLRLIARRL-GASAAVSEMVTSDTRLWGSDKSRHRLDHRQEPRPRIVQLLGNE 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+     G + I+LN+GCP+ +V   + G+ L+  P+ V + + A+ +++ +P
Sbjct: 77  PEPLAEAARENVRRGADVIDLNLGCPAKKVCSKAAGSALLGEPERVRELLTALVESVEVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G+D +        +    +  G+  + +H R         + +      DY+ 
Sbjct: 137 VTLKMRLGLDRERVNAET--IAGIAQDCGIAMLTVHGRT--------RADAYRGTADYEA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +    + +  NG + D+  A + L      G+MIGR A     +   +    +  
Sbjct: 187 IARVVRAV-SIPVLANGDVVDIGSARRALAISGATGLMIGRGAQGRPWLPGQIRASLAGE 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              + P            + A    Y          ++   +H+     
Sbjct: 246 PVPADPAWDARLALIEEHLRALHAQYGEMQ-----GVRIARKHLGWYLQ 289


>gi|190891640|ref|YP_001978182.1| tRNA-dihydrouridine synthase [Rhizobium etli CIAT 652]
 gi|190696919|gb|ACE91004.1| tRNA-dihydrouridine synthase protein [Rhizobium etli CIAT 652]
          Length = 339

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 123/293 (41%), Gaps = 27/293 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++         +P  +Q+ G + 
Sbjct: 34  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAESWSRLKAAGFRPHMVQLAGREA 92

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPV
Sbjct: 93  HWMAEAARIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPV 152

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++   ++ +  + +G+  + IH R  +               D+D +
Sbjct: 153 TLKMRLGWDE--NSINAPDIARRAEAAGIQLVTIHGRTRM--------QFYDGRADWDAI 202

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + +  NG +E    A +IL     D VMIGR                +  L
Sbjct: 203 RAV-RDVISIPLIANGDVETAEDAQEILRRSGADAVMIGRGCQGRPWH--------AGVL 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
            G++  +     D   +    M D+          ++   +H+      F  +
Sbjct: 254 AGAAEPQREDIADIAVEHYRMMLDFYGE----AVAIRHARKHLGWYLERFAPA 302


>gi|89897831|ref|YP_514941.1| dehydrogenases [Chlamydophila felis Fe/C-56]
 gi|89331203|dbj|BAE80796.1| dehydrogenases [Chlamydophila felis Fe/C-56]
          Length = 339

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 138/321 (42%), Gaps = 23/321 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  YR  + L    AL++ EM+  + +     + +  L +S   +P+  Q+ G+  
Sbjct: 22  AGFSDYPYRRMSSLYGLPALMFCEMVKIEGLHYSPSRTLKLLEYSESMRPIGGQLCGSKP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               EAAK++E  G++ I+LN GCP+ R+ +   G+ L+  P+++G  +  +  ++SIPV
Sbjct: 82  EMAGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGLLKTPELIGKVLEKIIGSVSIPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ IK++G + +++H R         +    +   + + +
Sbjct: 142 TVKIRSGWDG--NNINVEETVRIIKEAGASAVFVHGRT--------RAQGYVGPSNLEYI 191

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K     D  +  NG +     A  +L     DGV++ R       +   +++Y +  
Sbjct: 192 ARAKAAAGKDFPVFGNGDVFSPEAAKLMLDSTGCDGVLVARGTMGAPWIARQIEDYLTTG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCRH 295
                P  TR      ++       +   +  S  K    TR + G         R  R 
Sbjct: 252 TYQKMPFSTR------KQAFLQHLHWVEEYYQSEAKFLCETRKLCGHYLISAAKVRFLRS 305

Query: 296 ILTVEAGASTATHHIIETAFN 316
            L+ +A +  A + +IE    
Sbjct: 306 ALS-KATSVQAVYQLIEAYEE 325


>gi|294056396|ref|YP_003550054.1| TIM-barrel protein, nifR3 family [Coraliomargarita akajimensis DSM
           45221]
 gi|293615729|gb|ADE55884.1| TIM-barrel protein, nifR3 family [Coraliomargarita akajimensis DSM
           45221]
          Length = 333

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 135/303 (44%), Gaps = 20/303 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD  +R F +      ++ TE + ADAI RGD +    + F+  ++P+ +QI G++
Sbjct: 17  MARFTDIVFRQFCKE-QGADVMVTEFVQADAITRGDDRLWETVDFTESQRPMGVQIFGSN 75

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
              + +AA+++ D    + I++N GCP+ RV     G+ ++ NP  +G  +AA+ KA+  
Sbjct: 76  PVTMGQAARMIVDRMQPDFIDINFGCPAERVICMDAGSSMLRNPRKLGTVVAAVIKAVPD 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PVT K R G DD    +  + +   ++  G   + IH R  +               ++
Sbjct: 136 TPVTAKIRTGWDDDT--IVAKEVGHIVESEGGQALAIHGRTKMQGYR--------GEANW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            I+ E+ +E   + +  NG +      ++I  +    G+MIGRAA     +   +  Y +
Sbjct: 186 PIIAEVAEELT-IPVIGNGNIRSAEDVIRIRETTRCAGLMIGRAALGYPWIFRDIKHYLA 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +      P      +         M+       HS   L+ +    I L  G P SR+ R
Sbjct: 245 HGTIPEPPTIGERWQTIIDYTRGIMSRPFREQKHSD--LRWMRPKFIALTKGMPGSRKIR 302

Query: 295 HIL 297
             L
Sbjct: 303 TAL 305


>gi|238927136|ref|ZP_04658896.1| dihydrouridine synthase [Selenomonas flueggei ATCC 43531]
 gi|238884918|gb|EEQ48556.1| dihydrouridine synthase [Selenomonas flueggei ATCC 43531]
          Length = 320

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 125/320 (39%), Gaps = 23/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  YR  A  +    L + EM+ +  I   ++  +  L     E+P+A+QI    
Sbjct: 17  MAGVTDTSYRVIAHGM-GCPLAFAEMVSSQGIHYRNEHTMNMLRTEPDERPIAMQIFAKS 75

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                EAA  +E+ G  + ++ N+GCP+ +V     G+ LM +P    + + A+ +A  +
Sbjct: 76  ARMAAEAAAYIEELGTADILDFNMGCPAPKVVRNGEGSALMRDPKRAEEILTAIRRATRL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P TVK R+G DD         + +  +  GV+ + +H R         ++     + DY 
Sbjct: 136 PFTVKMRLGWDDASRNAV--EIARMAEAVGVDAVAVHGRT--------REQFYSGSADYA 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+    + + ++G +   +   + L     D VMIGR A  N  +   +  +   
Sbjct: 186 AIAAVKRAVG-IPVIVSGDVRRPADLKRALEITGADAVMIGRGAQGNPWIFPQLIHWLHT 244

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          R +     D    +      ++++ +H      G   S   R 
Sbjct: 245 GEELPPPTLAERAAVILRHL-----DLLVGYKGEYIGIREMRKHAAWYTRGLKGSAELRE 299

Query: 296 ILTVEAGASTATHHIIETAF 315
                A   T    I+  A+
Sbjct: 300 RFNRAASR-TEFAEILHGAW 318


>gi|55820279|ref|YP_138721.1| putative transcriptional regulator [Streptococcus thermophilus LMG
           18311]
 gi|55736264|gb|AAV59906.1| possible transcriptional regulator [Streptococcus thermophilus LMG
           18311]
          Length = 350

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 126/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+  +   L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 49  MAGVTNSAFRTIAKEFS-AGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 107

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 108 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D++
Sbjct: 168 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGHCDHE 216

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG + ++  A  ++    VD VM+GRAA  N  + T ++ +F  
Sbjct: 217 TLARVAKAITKIPFIGNGDVRNVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFET 276

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 277 GEELPD-LPFDKKLDIAEDHLKRLVDLKGEMIA----VREFRGLAPHYLRGTAGAAKVRG 331

Query: 296 ILT 298
            ++
Sbjct: 332 EVS 334


>gi|289433582|ref|YP_003463454.1| dihydrouridine synthase family protein [Listeria seeligeri serovar
           1/2b str. SLCC3954]
 gi|289169826|emb|CBH26364.1| dihydrouridine synthase family protein [Listeria seeligeri serovar
           1/2b str. SLCC3954]
          Length = 331

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 132/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G          + ++D
Sbjct: 137 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG +     A +IL     DGVMIGRAA  N  M+    +Y   
Sbjct: 187 VLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKYLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLPEPEPREKMQTAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A        I+        E 
Sbjct: 300 VAANQATKQAEMEAILNEFVLQYEEK 325


>gi|227544677|ref|ZP_03974726.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|300909081|ref|ZP_07126544.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri SD2112]
 gi|227185323|gb|EEI65394.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|300894488|gb|EFK87846.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri SD2112]
          Length = 333

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 128/325 (39%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +       +  EMI    I+  +++   ++    +E P+ +QI G  
Sbjct: 19  MAGVTNSAFRVICKRF-GAGYVVCEMISDRGIVYHNQRTLNMMDVDPEEHPMGIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  +V +   GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEAAKYVDQHTAADVIDINMGCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L    +++G + I +H R         +        D++
Sbjct: 138 PVTVKMRTGWDDKHILAVENALA--AERAGASAIAMHGRT--------RKQMYTGQADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG ++    A KIL        MIGRAA  N  ML   + Y   
Sbjct: 188 ILKEVASQL-KIPFMANGDVKTPEDAKKILDMTGATAAMIGRAAMGNPWMLKRTEHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     +  +     ++                +++          G P + R + 
Sbjct: 247 GELLPEATPEQKIEMAKDHLNR-----LVDLKGEYVGVREFRGLSTYYIKGIPRAARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L VEA      + I +       E
Sbjct: 302 AL-VEAETLDEMNDIFDRFAEQTAE 325


>gi|313123089|ref|YP_004033348.1| tRNA-dihydrouridine synthase b [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312279652|gb|ADQ60371.1| tRNA-dihydrouridine synthase B [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 342

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 123/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      ++  EMI    I+ G++K   +L     E P+++QI G  
Sbjct: 21  MAGVSNMAFRKVCKEF-GAGMVVCEMISDHGIIYGNEKTLSMLDVDPGEHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   I  + + +  
Sbjct: 80  EDSLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + + +H R         +        D++
Sbjct: 140 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y + 
Sbjct: 190 TLHEVAQ-VMDIPFVANGDITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D   +       + +  +       G P S R R 
Sbjct: 249 GEELPKQSVREKVETAKHQL-----DGLVQLHGEKRAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|27379597|ref|NP_771126.1| nitrogen regulation protein [Bradyrhizobium japonicum USDA 110]
 gi|27352749|dbj|BAC49751.1| nitrogen regulation protein [Bradyrhizobium japonicum USDA 110]
          Length = 371

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 126/328 (38%), Gaps = 31/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R     L    L+ +EM  +D +  G + + L        P  +Q+ G + 
Sbjct: 55  MSGVTDSPVRRLVAEL-GAGLVVSEMTASDELANGHRMSRLRCEATGIGPHVVQLAGCEA 113

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 114 HWMAEGARIAEAEGADIIDINMGCPARHVTGGQSGSALMRDLDHAVGLIDATIAAVKVPV 173

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+        L +  + +G+  + +H R         +        D+D +
Sbjct: 174 TLKMRLGWDDRSRNA--PELARRAEAAGIKLVTVHGRT--------RCQFYKGEADWDAI 223

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + + +NG +    +AL  L     D VMIGR A     +   +        
Sbjct: 224 RTV-REAISIPLIVNGDITSYEKALAALESSGADAVMIGRGAQGQPWLPGQIGRRLKGGA 282

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR----- 292
             ++P               ++ +           L+   +H+        ++ R     
Sbjct: 283 AEATPSLA-----TQLHYVRTLYEGVCALYGLRVGLKHARKHLGWALDVAADASRAPVEK 337

Query: 293 ---CRH-ILTVEAGASTATHHIIETAFN 316
               R  ILT E       H  ++ AF+
Sbjct: 338 LKSWRRTILTSEDPR--LVHQSLQDAFD 363


>gi|227821859|ref|YP_002825829.1| tRNA-dihydrouridine synthase [Sinorhizobium fredii NGR234]
 gi|227340858|gb|ACP25076.1| tRNA-dihydrouridine synthase [Sinorhizobium fredii NGR234]
          Length = 342

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 121/287 (42%), Gaps = 26/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A        + TEM+ +  ++    ++          P  +Q+ G + 
Sbjct: 33  MSGVTDLPFRMLAWRF-GAGFVVTEMVASRELVGNAAESWARLKNSGIDPHIVQLAGREA 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKIVE  G + +++N+GCP+ +V  G  G+ LM +PD     I A  KA+ +PV
Sbjct: 92  HWMAEAAKIVEANGADIVDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVKAVRVPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+      L  + +  +++GV  I IH R  +             N D+D +
Sbjct: 152 TLKMRLGWDENSINAPL--IARRAEEAGVQAITIHGRTRM--------QFYNGNADWDAI 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + +  NG ++ ++ A++IL     D VM+GR+               +   
Sbjct: 202 RAV-RDVISIPLIANGDVDTIADAMEILRRSGADAVMLGRSCQGRPW------HAGALAG 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               P  T +   F    +  +  Y          L+   +H+    
Sbjct: 255 AADEPAATEIAAIFVEHYAMMLDFYGPEI-----GLRHARKHVGWYL 296


>gi|307720977|ref|YP_003892117.1| TIM-barrel protein, nifR3 family [Sulfurimonas autotrophica DSM
           16294]
 gi|306979070|gb|ADN09105.1| TIM-barrel protein, nifR3 family [Sulfurimonas autotrophica DSM
           16294]
          Length = 317

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 146/322 (45%), Gaps = 35/322 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EM+ ++A+  G +K   +L  S+ E P ++QI GAD+
Sbjct: 18  AGFTDLPFRSVVKKF-GADLTVSEMLSSNALAHGSQKTLHMLEKSSLEDPYSVQIAGADV 76

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +I+ E  G + I+LN GCP  +V     G+ L+L+  ++G+ I  +    +  
Sbjct: 77  DIVRSAVEILNEQEGIDIIDLNCGCPVPKVVGHGSGSSLLLDLPLMGEIIKTIKDTSNKS 136

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G +++       ++ K ++ SG + I +H R         +  +    +DYD
Sbjct: 137 MTSVKIRLGFEEKKHV----DIAKVVQDSGADFIAVHGRT--------RAGKFKAAVDYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + EIK E  D+ +  NG ++   +A  +L     DGVMIGR A     +   +      
Sbjct: 185 AIREIK-EAVDIPVIANGDIDSYEKAKWVLEHTGADGVMIGRGAVGAPWIFHQLK----- 238

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG+  I+  +  +   +    M ++  +H      +    +H      G+  +   R+
Sbjct: 239 --TGNEHIEQSLKHEIIMEHFDKMIEFYGQH-----GVAMFRKHTHTYSKGYRGASALRN 291

Query: 296 ILTVEAGASTATHH-IIETAFN 316
              V +    AT+  +I+  F 
Sbjct: 292 --EVNSIDDIATYRSVIDDFFK 311


>gi|257868307|ref|ZP_05647960.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257874420|ref|ZP_05654073.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|257877912|ref|ZP_05657565.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
 gi|257802421|gb|EEV31293.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257808584|gb|EEV37406.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|257812078|gb|EEV40898.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
          Length = 337

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 129/310 (41%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL++QI G +
Sbjct: 23  MAGITNSAFRVTVKEF-GAGLVVCEMISDRGIQLRNKKTLEMLFIDETEHPLSIQIFGGN 81

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + LVEAA+ V +    + I++N+GCP  ++ +   GA  +L+PD V + + A+  A+  
Sbjct: 82  KASLVEAAQFVAENTTADIIDINMGCPVNKIIKAEAGAKWLLDPDKVYEMVHAVSSAIDK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+Q               +   G+    R  + +G          + D+D
Sbjct: 142 PVTVKMRIGWDEQHVFAVENAQAAEAAGAAAIGMHGRTRVQMYEG----------SADWD 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+     F+G NG ++    A ++L     D VMIGRAA  N  M+    +Y   
Sbjct: 192 VLKQVKQSITIPFMG-NGDVKTPEDAKRMLEEVGADAVMIGRAALGNPWMIHRTKQYLET 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   + D     + S    ++  +H      G   + + + 
Sbjct: 251 GELLPEPTPREKISTAKLHL-ERLADLKGEKIAS----REFRQHAAYYLKGISRAAKVKA 305

Query: 296 ILTVEAGAST 305
            +       T
Sbjct: 306 AINQAEDKQT 315


>gi|50842438|ref|YP_055665.1| NifR3 family TIM-barrel protein [Propionibacterium acnes KPA171202]
 gi|50840040|gb|AAT82707.1| TIM-barrel enzyme, NifR3 family [Propionibacterium acnes KPA171202]
 gi|332675350|gb|AEE72166.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes 266]
          Length = 411

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 125/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 57  MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 115

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 116 PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 175

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 176 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 225

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 226 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 284

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 285 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 338

Query: 293 CRHIL 297
            RH+L
Sbjct: 339 TRHVL 343


>gi|325684701|gb|EGD26855.1| tRNA-dihydrouridine synthase [Lactobacillus delbrueckii subsp.
           lactis DSM 20072]
          Length = 344

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 123/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      ++  EMI    I+ G++K   +L     E P+++QI G  
Sbjct: 23  MAGVSNMAFRKVCKEF-GAGMVVCEMISDHGIIYGNEKTLSMLDVDPGEHPMSIQIFGGT 81

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   I  + + +  
Sbjct: 82  EDSLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + + +H R         +        D++
Sbjct: 142 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y + 
Sbjct: 192 TLHEVAQ-VMDIPFVANGDITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D   +       + +  +       G P S R R 
Sbjct: 251 GEELPKQSVREKVETAKHQL-----DGLVQLHGEKRAVPEFRQQAAYYLKGIPRSARTRA 305

Query: 296 ILTV 299
            +  
Sbjct: 306 KINE 309


>gi|325292774|ref|YP_004278638.1| nitrogen regulation protein [Agrobacterium sp. H13-3]
 gi|325060627|gb|ADY64318.1| nitrogen regulation protein [Agrobacterium sp. H13-3]
          Length = 333

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 117/287 (40%), Gaps = 27/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++          P  +Q+ G + 
Sbjct: 26  MSGVTDLPFRQLAWRY-GAGLVVTEMVASRELVANRGESWARLKNAGMVPHMVQLAGREA 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G   I++N+GCP+ +V  G  G+ LM +PD     I A   A+ +PV
Sbjct: 85  HFMAEAAKIAADNGAGIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVGAVDVPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+    +    + +  + +GV  I IH R  +               ++D +
Sbjct: 145 TLKMRLGWDE--NTINAPEIARRAQAAGVQLITIHGRTRM--------QFYEGRANWDAI 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG +E    A +IL     D VM+GR A     +           L
Sbjct: 195 RAV-REVISVPLIANGDVETAEDAREILSRSGADAVMVGRGAQGQPWLPA--------VL 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            G +  +     D   +    M ++  R       L+   +H+    
Sbjct: 246 AGHAAPQRADIADIAVEHYDMMLEFYGRE----AGLRHARKHLGWYL 288


>gi|306834510|ref|ZP_07467623.1| tRNA-dihydrouridine synthase [Streptococcus bovis ATCC 700338]
 gi|304423312|gb|EFM26465.1| tRNA-dihydrouridine synthase [Streptococcus bovis ATCC 700338]
          Length = 325

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 125/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEFIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIINEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSELAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG + ++  A  ++    VD VM+GRAA  N  + T ++ YF  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRNVHDAKYMIEEIGVDAVMVGRAAMNNPYIFTQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPD-LPFVKKLDIAEDHLKRLIDLKGEKIA----VREFRGLAPHYLRGTAGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|270290207|ref|ZP_06196433.1| tRNA-dihydrouridine synthase B [Pediococcus acidilactici 7_4]
 gi|304385524|ref|ZP_07367868.1| tRNA-dihydrouridine synthase [Pediococcus acidilactici DSM 20284]
 gi|270281744|gb|EFA27576.1| tRNA-dihydrouridine synthase B [Pediococcus acidilactici 7_4]
 gi|304328028|gb|EFL95250.1| tRNA-dihydrouridine synthase [Pediococcus acidilactici DSM 20284]
          Length = 332

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 77/327 (23%), Positives = 125/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+ G+KK   ++     E P+++QI G  
Sbjct: 19  MAGVTNTAFRVICKQF-GAGLVVCEMISDRGIIYGNKKTLSMMQVDPNEHPMSIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  +V     GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEAAKFVDQNTEADIIDINMGCPVNKVVNTDAGARWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L      +    +    RK +  G          + D+D
Sbjct: 138 PVTVKMRTGWDDKHIYAVENALAAQRAGAAALAMHGRTRKQMYTG----------HADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG +     A ++L     D VMIGRA   N   L  V  Y ++
Sbjct: 188 ILKEVASQL-HIPFMGNGDVRTPQDAKRMLDEVGADAVMIGRAVLGNPWELQKVAAYLND 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      K     I+                 ++          G P+S R + 
Sbjct: 247 GTLIDEPTPAEKIK-----IAKEHLHGLVELKGENIGPREFRGQAAYYLKGVPHSARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L   A        I +     +   +
Sbjct: 302 ALNA-AETEQEMIDIFDRFIEKLDSRM 327


>gi|116513521|ref|YP_812427.1| tRNA-dihydrouridine synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116092836|gb|ABJ57989.1| tRNA-U20-dihydrouridine synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
          Length = 342

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 123/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      ++  EMI    I+ G+KK   +L     E P+++QI G  
Sbjct: 21  MAGVSNMAFRKVCKEF-GAGMVVCEMISDHGIIYGNKKTLSMLDVDPGEHPMSIQIFGGA 79

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   I  + + +  
Sbjct: 80  EDSLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + + +H R         +        D++
Sbjct: 140 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y + 
Sbjct: 190 TLHEVAQ-VMDIPFVANGDITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D   +       + +  +       G P S R R 
Sbjct: 249 GEELPKQSVREKVETAKHQL-----DGLVQLHGEKRAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|320547612|ref|ZP_08041897.1| tRNA-dihydrouridine synthase [Streptococcus equinus ATCC 9812]
 gi|320447687|gb|EFW88445.1| tRNA-dihydrouridine synthase [Streptococcus equinus ATCC 9812]
          Length = 325

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 123/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEYIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIIDEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D +
Sbjct: 143 PLTVKMRTGWSDNSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGKCDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VM+GRAA  N  + T ++ YF  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVHDAKYMIEEVGVDAVMVGRAAMNNPYIFTQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPD-LPFVKKLDIAEDHLKRLIDLKGEKIA----VREFRGLAPHYLRGTAGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|116515275|ref|YP_802904.1| tRNA-dihydrouridine synthase A [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116257129|gb|ABJ90811.1| tRNA-dihydrouridine synthase A [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 348

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 101/298 (33%), Positives = 160/298 (53%), Gaps = 11/298 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M  +TD+H  +F R LT    LYTEMI    +L   K        +  P+A+Q+ G +  
Sbjct: 36  MFKYTDQHCLYFYRQLTKKTFLYTEMITIQKMLFSKKLFKKKQIKKNNPIAIQLAGNNPL 95

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   AK     G+ EINLN+GCPS +   G+FG  LM NP +V + I A+   + I ++
Sbjct: 96  FLSLCAKKAYFLGFKEINLNIGCPSKKAKSGNFGIYLMNNPILVYNLIKAIYLTVPIQIS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNG-IWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +K R+G ++      L+N ++ + K+       IHAR A L+  SPK NR IP L+Y  V
Sbjct: 156 IKIRLGTNENKNYRFLKNFIQLVSKNNYCIKYIIHARIANLQINSPKKNRNIPLLNYSYV 215

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           Y+IKK+ P L I +NGG++ +++  + L +VDGVM+GR  YKN   L  +D+        
Sbjct: 216 YKIKKDFPHLIIIINGGIKTINEINEHLKNVDGVMMGREIYKNPLFLRKIDKK------- 268

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              I  +  +   +K    M++Y  + +  G    +I +HM+ +F+  P +++ +H L
Sbjct: 269 ---IFFQKKQIKIKKFIKKMSNYIKKKIIKGVPAIKIIKHMLNIFYKLPQAKKWKHEL 323


>gi|228476444|ref|ZP_04061134.1| tRNA-dihydrouridine synthase B [Streptococcus salivarius SK126]
 gi|228251865|gb|EEK10911.1| tRNA-dihydrouridine synthase B [Streptococcus salivarius SK126]
          Length = 325

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VM+GRAA  N  + T ++ +F  
Sbjct: 192 TLARVAKAITKIPFIGNGDVRSVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPE-LPFDKKLDIAEDHLKRLVDLKGEKIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 EVSRAESVAQ-----VEEIFATL 324


>gi|325831497|ref|ZP_08164751.1| tRNA-dihydrouridine synthase B [Eggerthella sp. HGA1]
 gi|325486751|gb|EGC89199.1| tRNA-dihydrouridine synthase B [Eggerthella sp. HGA1]
          Length = 330

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 112/290 (38%), Gaps = 26/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R      L YTEM+ A  +   ++K   +L  +  E  +A+Q+ G +
Sbjct: 18  MAGVSDEAFRTLCRE-QGADLTYTEMVSAKGLSYANEKTRHLLRLAPGEDQVAVQLFGHE 76

Query: 59  ISKLV-EAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  +AA I  + G     +++N+GCP+ ++     G+ LM +P +    + A+  A+
Sbjct: 77  PDTMAAQAAWIEREMGQSLAYLDINMGCPARKIVSKGDGSALMKDPALAASIVRAVRAAV 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S PVTVK R G  +           + ++ +G   I +H R A        +       +
Sbjct: 137 SRPVTVKFRRGWAEGD--ETAPEFARRMEDAGACAIAVHGRYA--------EQLYRGRAE 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +  +K E   + +  NG +   + A+ I      D VMI RAA  N  +        
Sbjct: 187 WGAIARVK-EAVSVPVVGNGDVRSGADAVAITERTGCDAVMIARAAEGNPWLFAQAKAAL 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +       P          R                G  + ++ +H +  
Sbjct: 246 AGEPEPDGPTVEERIALARRHARLLSA-------REGRNIVRMRKHAMWY 288


>gi|158522876|ref|YP_001530746.1| nifR3 family TIM-barrel protein [Desulfococcus oleovorans Hxd3]
 gi|158511702|gb|ABW68669.1| putative TIM-barrel protein, nifR3 family [Desulfococcus oleovorans
           Hxd3]
          Length = 326

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 130/325 (40%), Gaps = 27/325 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R  A+     AL+Y+EM+ +  +    +K   +L  + +E P A+QI G   
Sbjct: 18  AGITDAPFRRLAK-AAGCALVYSEMVSSHGLFYQSEKTGAMLRTTPEEAPFAVQIFGGKP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + +  AA +V+  G + I++N GC   ++ +   GA LM +  +  + I A+  A+SIP+
Sbjct: 77  AVMGRAAAMVQASGAHMIDINFGCSVKKILKSGAGAALMKDLPLAAEVIQAVRDAVSIPL 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G +          L +  +  GVN + +H R A                D+ ++
Sbjct: 137 TIKMRSGWNPDGSDAFH--LAEIAEARGVNAVALHPRTATQGFG--------GTADWSLI 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    L +  NG +     A ++L     D VM+GRAA     +   ++   +   
Sbjct: 187 AALKQRTG-LPVIGNGDIVLPEDARRMLDQTGCDAVMVGRAAIGAPWIFKQINACLAGKP 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                ++ R       ++ +   +    H       + +   +       P+    R   
Sbjct: 246 VVEPSLEHRF------EVMSEYINAMVAHYGEDLACRVMRSRLGWFTRAMPHGTLFR--- 296

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
             E+     T   +  A +   E L
Sbjct: 297 --ESIRRIETKDQVLAAVSDYRERL 319


>gi|84516240|ref|ZP_01003600.1| tRNA-dihydrouridine synthase, putative [Loktanella vestfoldensis
           SKA53]
 gi|84509936|gb|EAQ06393.1| tRNA-dihydrouridine synthase, putative [Loktanella vestfoldensis
           SKA53]
          Length = 333

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 129/322 (40%), Gaps = 26/322 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
              TD  +R           + +EM+ +  +++     +        ++  A+QI G + 
Sbjct: 28  AGITDLPFRQLVASF-GAGWVVSEMVASQEMVQAKPGVRERAELGYDQQGTAVQIAGREA 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA+++E  G   I++N+GCP+ +V  G  G+ L+ +PD     I A+  A+ +PV
Sbjct: 87  YWLAEAARMIEANGAAMIDINMGCPAKKVTNGYSGSALLRDPDHALRLIEAVVNAVKLPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D     +   ++ +  + +G+  + IH R         +        D+  +
Sbjct: 147 TLKTRLGWD--HDCLNAADVARRAQDAGIRLVTIHGRT--------RCQFYKGAADWRAI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            EIK+    + +  NG +     A +   L   DGVMIGR A     +L  V        
Sbjct: 197 REIKQAV-SIPVIANGDITGPEAAKQALALSGADGVMIGRGAQGRPWVLAQVAARLHGTK 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCRH 295
               P             SA ++ Y    L  G ++    +H+       G P   R + 
Sbjct: 256 MPVIPQGADFIDMVGAHYSAMLSFYG---LDLGRRV--ARKHLGWYMDEAGTPAGLR-KA 309

Query: 296 ILTVEAGASTATHHIIETAFNL 317
           ILT +     A    +  A  +
Sbjct: 310 ILTHD--TPDAVLRDLADALAM 329


>gi|47093172|ref|ZP_00230947.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           4b H7858]
 gi|47097267|ref|ZP_00234827.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           1/2a F6854]
 gi|85700164|ref|YP_012849.2| dihydrouridine synthase family protein [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|226222856|ref|YP_002756963.1| hypothetical protein Lm4b_00225 [Listeria monocytogenes Clip81459]
 gi|254826415|ref|ZP_05231416.1| dihydrouridine synthase [Listeria monocytogenes FSL J1-194]
 gi|254829644|ref|ZP_05234331.1| dihydrouridine synthase [Listeria monocytogenes FSL N3-165]
 gi|254832544|ref|ZP_05237199.1| lysyl-tRNA synthetase [Listeria monocytogenes 10403S]
 gi|254854615|ref|ZP_05243963.1| dihydrouridine synthase [Listeria monocytogenes FSL R2-503]
 gi|254901221|ref|ZP_05261145.1| lysyl-tRNA synthetase [Listeria monocytogenes J0161]
 gi|254914104|ref|ZP_05264116.1| dihydrouridine synthase family protein [Listeria monocytogenes
           J2818]
 gi|254933691|ref|ZP_05267050.1| dihydrouridine synthase [Listeria monocytogenes HPB2262]
 gi|254938416|ref|ZP_05270113.1| dihydrouridine synthase [Listeria monocytogenes F6900]
 gi|254992592|ref|ZP_05274782.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           J2-064]
 gi|255026879|ref|ZP_05298865.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           J2-003]
 gi|284803033|ref|YP_003414898.1| hypothetical protein LM5578_2790 [Listeria monocytogenes 08-5578]
 gi|284996174|ref|YP_003417942.1| hypothetical protein LM5923_2739 [Listeria monocytogenes 08-5923]
 gi|300766504|ref|ZP_07076452.1| dihydrouridine synthase [Listeria monocytogenes FSL N1-017]
 gi|47014367|gb|EAL05340.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           1/2a F6854]
 gi|47018479|gb|EAL09237.1| dihydrouridine synthase family protein [Listeria monocytogenes str.
           4b H7858]
 gi|83316100|gb|AAT03026.2| dihydrouridine synthase family protein [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|225875318|emb|CAS04015.1| unnamed protein product [Listeria monocytogenes serotype 4b str.
           CLIP 80459]
 gi|258602062|gb|EEW15387.1| dihydrouridine synthase [Listeria monocytogenes FSL N3-165]
 gi|258608010|gb|EEW20618.1| dihydrouridine synthase [Listeria monocytogenes FSL R2-503]
 gi|258611030|gb|EEW23638.1| dihydrouridine synthase [Listeria monocytogenes F6900]
 gi|284058595|gb|ADB69536.1| hypothetical protein LM5578_2790 [Listeria monocytogenes 08-5578]
 gi|284061641|gb|ADB72580.1| hypothetical protein LM5923_2739 [Listeria monocytogenes 08-5923]
 gi|293585255|gb|EFF97287.1| dihydrouridine synthase [Listeria monocytogenes HPB2262]
 gi|293592702|gb|EFG00463.1| dihydrouridine synthase family protein [Listeria monocytogenes
           J2818]
 gi|293595656|gb|EFG03417.1| dihydrouridine synthase [Listeria monocytogenes FSL J1-194]
 gi|300512786|gb|EFK39885.1| dihydrouridine synthase [Listeria monocytogenes FSL N1-017]
 gi|328467945|gb|EGF38975.1| dihydrouridine synthase family protein [Listeria monocytogenes
           1816]
 gi|332310638|gb|EGJ23733.1| Putative tRNA-dihydrouridine synthase 1 [Listeria monocytogenes
           str. Scott A]
          Length = 331

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 133/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G          + ++D
Sbjct: 137 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG +     A +IL     DGVMIGRAA  N  M+    ++   
Sbjct: 187 VLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLPEPEPREKMQTAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A   +    I+        E 
Sbjct: 300 VAANQATKQSEMEAILNEFVLQYEEK 325


>gi|224500852|ref|ZP_03669201.1| dihydrouridine synthase family protein [Listeria monocytogenes
           Finland 1988]
          Length = 331

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 133/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G          + ++D
Sbjct: 137 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG +     A +IL     DGVMIGRAA  N  M+    ++   
Sbjct: 187 VLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLPEPEPREKMQTAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A   +    I+        E 
Sbjct: 300 VAANQATKQSEMEAILNEFVLQYEEK 325


>gi|254469483|ref|ZP_05082888.1| tRNA-dihydrouridine synthase B [Pseudovibrio sp. JE062]
 gi|211961318|gb|EEA96513.1| tRNA-dihydrouridine synthase B [Pseudovibrio sp. JE062]
          Length = 308

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 64/281 (22%), Positives = 119/281 (42%), Gaps = 19/281 (6%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEA 65
             +R  A L     L+ +EM+ ++A+  G  ++++    +   P  +Q+ G D   + E 
Sbjct: 1   MPFRRIA-LSYGVGLVVSEMVASEALCTGHPESLMRAEGEGIDPHIVQLAGKDPHWMGEG 59

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A++ E  G + I++N+GCP+ +V  G  G+ LM + D     + A  +A+S+PVT+K R+
Sbjct: 60  ARMAEKAGADVIDINMGCPAKKVTSGYSGSALMKDLDHAMTLVEATLEAVSVPVTLKMRL 119

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D+   ++    L K    +GV  I +H R         +        D+  + +++  
Sbjct: 120 GWDE--ASINAPELAKRAVDAGVKMITVHGRT--------RSQFYKGQADWRAIRQVRDV 169

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
            PD+ +  NG       A ++L     D VM+GR AY    +   +  Y       + P 
Sbjct: 170 IPDVPLVANGDCCSFDDADEMLAQSGADLVMVGRGAYGRPWVPGRIAHYLETGERLADPH 229

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +         A +  Y          ++   +HM    
Sbjct: 230 GEELATLVVGHYDAMLEHYGFEI-----GVRAFRKHMGWYL 265


>gi|330837194|ref|YP_004411835.1| TIM-barrel protein, nifR3 family [Spirochaeta coccoides DSM 17374]
 gi|329749097|gb|AEC02453.1| TIM-barrel protein, nifR3 family [Spirochaeta coccoides DSM 17374]
          Length = 343

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 127/324 (39%), Gaps = 21/324 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             +TD  +R         ++  +EM+ A+ + RG    + +L     E+   +QI G++ 
Sbjct: 29  AGFTDLTFRSICSS-HGASIACSEMVSAEGLARGSAGTEELLERYEGEEQFIIQIFGSET 87

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           +++  A   +  +    I+ N GCP  +V +   G+ LM +P  +   + A+     +PV
Sbjct: 88  NQVERALPRLLCYKPTVIDFNCGCPVPKVVKTGAGSALMKHPQTIYAMVRAVRNQCDVPV 147

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G D    A++ R   ++  + G   + +HAR          D  +I  L    V
Sbjct: 148 SVKFRLGWDKD--AISWREFAQAALEGGAQMLTMHARTRSQGYSGVADWSRIAAL----V 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+ +P++ +  +G +     A  +L    VDGVM  R A  N  +         +  
Sbjct: 202 DMVKQMSPNVPVFGSGDVFTPHDAQHMLEETGVDGVMFARGAIGNPFIFERTKALLLSGQ 261

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +     +     R ++       A         +Q+  H      G P S R R ++
Sbjct: 262 EPEAVPLETIIGTIMRHLTL-----LAERKGEEAACRQMRGHAGSYLKGLPGSSRIRGLI 316

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
           T        T      A + M  +
Sbjct: 317 T-----QATTVEDYRKALDSMEHA 335


>gi|314923074|gb|EFS86905.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL001PA1]
 gi|314966844|gb|EFT10943.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL082PA2]
 gi|314981186|gb|EFT25280.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA3]
 gi|315092006|gb|EFT63982.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA4]
 gi|315093235|gb|EFT65211.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL060PA1]
 gi|315103509|gb|EFT75485.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL050PA2]
 gi|327327670|gb|EGE69446.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL103PA1]
          Length = 409

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 123/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 55  MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 113

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 114 PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D     +   +  ++   SG   + +HAR                + 
Sbjct: 174 HGVPVTVKTRIGIDPD--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 224 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 283 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 336

Query: 293 CRHIL 297
            RH L
Sbjct: 337 TRHAL 341


>gi|171777588|ref|ZP_02919276.1| hypothetical protein STRINF_00111 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171283197|gb|EDT48621.1| hypothetical protein STRINF_00111 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 325

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 123/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEYIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIIDKVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D +
Sbjct: 143 PLTVKMRTGWSDNELAVEN---ALAAESAGVSALAMHGRT--------REQMYTGKCDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VM+GRAA  N  + T ++ YF  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVHDAKYMIEEIGVDAVMVGRAAMNNPYIFTQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPD-LPFVKKLDIAEDHLKRLIDLKGEKIA----VREFRGLAPHYLRGTAGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|325568181|ref|ZP_08144622.1| tRNA-dihydrouridine synthase [Enterococcus casseliflavus ATCC
           12755]
 gi|325158382|gb|EGC70533.1| tRNA-dihydrouridine synthase [Enterococcus casseliflavus ATCC
           12755]
          Length = 337

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 128/310 (41%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL++QI G +
Sbjct: 23  MAGITNSAFRVTVKEF-GAGLVVCEMISDRGIQLRNKKTLEMLFIDETEHPLSIQIFGGN 81

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + LVEAA+ V +    + I++N+GCP  ++ +   GA  +L+PD V + + A+  A+  
Sbjct: 82  KASLVEAAQFVAENTTADIIDINMGCPVNKIIKAEAGAKWLLDPDKVYEMVHAVSSAIDK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D+Q               +   G+    R  + +G          + D+D
Sbjct: 142 PVTVKMRIGWDEQHVFAVENAQAAEAAGAAAIGMHGRTRVQMYEG----------SADWD 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+     F+G NG +     A ++L     D VMIGRAA  N  M+    +Y   
Sbjct: 192 VLKQVKQSITIPFMG-NGDVRTPEDAKRMLEEVGADAVMIGRAALGNPWMIHRTKQYLET 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P            +   + D     + S    ++  +H      G   + + + 
Sbjct: 251 GELLPEPTPREKISTAKLHL-ERLADLKGEKIAS----REFRQHAAYYLKGISRAAKVKA 305

Query: 296 ILTVEAGAST 305
            +       T
Sbjct: 306 AINQAEDKQT 315


>gi|16799336|ref|NP_469604.1| hypothetical protein lin0259 [Listeria innocua Clip11262]
 gi|16412688|emb|CAC95492.1| lin0259 [Listeria innocua Clip11262]
          Length = 331

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 133/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G          + ++D
Sbjct: 137 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG +     A +IL     DGVMIGRAA  N  M+    ++   
Sbjct: 187 VLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLPEPEPREKMETAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A   +    I+        E 
Sbjct: 300 VAANQATKQSEMEAILNEFVLQYEEK 325


>gi|310815776|ref|YP_003963740.1| tRNA-dihydrouridine synthase, putative [Ketogulonicigenium vulgare
           Y25]
 gi|308754511|gb|ADO42440.1| tRNA-dihydrouridine synthase, putative [Ketogulonicigenium vulgare
           Y25]
          Length = 337

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 120/319 (37%), Gaps = 22/319 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              TD  YR           + +EMI +  IL      I        +   A+Q+ G + 
Sbjct: 30  AGITDLPYRQMVGAF-GAGWVVSEMIASQEILTNRPGTIEKAELGLDQANTAVQLAGREA 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAK++E  G   I++N+GCP+ +V  G  G+ LM + D     I A   A+ +PV
Sbjct: 89  EWMAEAAKMIEGNGAQLIDINMGCPAKKVTSGLSGSALMRDLDHALRLIEATVGAVKVPV 148

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD    +    L K  + +G+  + IH R         +        D+  +
Sbjct: 149 TLKMRLGWDDDQ--INAPELAKRAEGAGIKLVTIHGRT--------RCQFYTGRADWAAI 198

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  NG +  +  A   L     DGVMIGR A     +L  V        
Sbjct: 199 RAVKQAV-SIPVIANGDICSVQDARDALEQSGADGVMIGRGAQGRPWLLAEVMADLCGTA 257

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P              A +  Y A   H      ++ R  +G F     +       
Sbjct: 258 APVIPKGAAFADLVLTHYDAVLNFYGATLGH------RVARKHLGWFMDTAGTSDVLRRA 311

Query: 298 TVEAGASTATHHIIETAFN 316
            + A  +     ++ TA +
Sbjct: 312 VLTAPTAADVIALLPTALD 330


>gi|218283931|ref|ZP_03489799.1| hypothetical protein EUBIFOR_02395 [Eubacterium biforme DSM 3989]
 gi|218215510|gb|EEC89048.1| hypothetical protein EUBIFOR_02395 [Eubacterium biforme DSM 3989]
          Length = 321

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 62/325 (19%), Positives = 131/325 (40%), Gaps = 29/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R  A+      L+  EM+   A+     K   +      E P++ Q+ G D
Sbjct: 18  MAGISNIAFRRIAKRF-GAGLVCNEMVSDKALYYDSLKTKQMCAIDENEHPVSFQLFGHD 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  +V AAK ++     + I+ N+GCP  +V +   G+ LM + D   + ++ + + +S 
Sbjct: 77  IDTVVYAAKYLDTQTDCDIIDFNMGCPVNKVIKAQAGSFLMKDIDYAKELVSNIVQNVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D     +    + K+++  GV+ + +H R         ++       D+ 
Sbjct: 137 PVTVKMRLGFD--TYHINCVEMAKAMESVGVSAVAVHGRT--------RNQMYEGKADWS 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K +   + +  NG +  +    +++     D VM+GR    N  ++    +  + 
Sbjct: 187 YIKQVK-DAVSIPVIGNGDVRSVEDFHRMMNETGCDAVMLGRGIVGNPFLIQECVDSITG 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   K     +   +I        A        ++++         G P+SR  ++
Sbjct: 246 Q-------KHEFSMEDRIEICMDHAKGLADTKGEKVAIREMRGLASWYLKGLPSSRIFKN 298

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            ++        T   +E   +  +E
Sbjct: 299 EMS-----QMNTLEDLENILHQFME 318


>gi|289425437|ref|ZP_06427214.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK187]
 gi|289154415|gb|EFD03103.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes SK187]
          Length = 409

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 124/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 55  MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 113

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 114 PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDQFAAVVSAAVQAGDA 173

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 174 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 224 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 282

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +     Y   H      L  + +HM     GFP    
Sbjct: 283 FAGRDTTTLPTLGEVCAMI-RRHAELSVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 336

Query: 293 CRHIL 297
            RH+L
Sbjct: 337 TRHVL 341


>gi|317490541|ref|ZP_07949018.1| dihydrouridine synthase [Eggerthella sp. 1_3_56FAA]
 gi|316910356|gb|EFV31988.1| dihydrouridine synthase [Eggerthella sp. 1_3_56FAA]
          Length = 330

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 112/290 (38%), Gaps = 26/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R      L YTEM+ A  +   ++K   +L  +  E  +A+Q+ G +
Sbjct: 18  MAGVSDEAFRTLCRE-QGADLTYTEMVSAKGLSYANEKTRHLLRLAPGEGQVAVQLFGHE 76

Query: 59  ISKLV-EAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  +AA I  + G     +++N+GCP+ ++     G+ LM +P +    + A+  A+
Sbjct: 77  PDTMAAQAAWIEREMGQSLAYLDINMGCPARKIVSKGDGSALMKDPALAASIVRAVRAAV 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S PVTVK R G  +           + ++ +G   I +H R A        +       +
Sbjct: 137 SRPVTVKFRRGWAEGD--ETAPEFARRMEDAGACAIAVHGRYA--------EQLYRGRAE 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +  +K E   + +  NG +   + A+ +      D VMI RAA  N  +        
Sbjct: 187 WGAIARVK-EAVSVPVVGNGDVRSGADAVAVTERTGCDAVMIARAAEGNPWLFAQAKAAL 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +       P          R                G  + ++ +H +  
Sbjct: 246 AGEPEPDGPTVEERIALARRHARLLSA-------REGRNIVRMRKHAMWY 288


>gi|257791401|ref|YP_003182007.1| TIM-barrel protein, nifR3 family [Eggerthella lenta DSM 2243]
 gi|257475298|gb|ACV55618.1| TIM-barrel protein, nifR3 family [Eggerthella lenta DSM 2243]
          Length = 330

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 112/290 (38%), Gaps = 26/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  +R   R      L YTEM+ A  +   ++K   +L  +  E  +A+Q+ G +
Sbjct: 18  MAGVSDEAFRTLCRE-QGADLTYTEMVSAKGLSYANEKTRHLLRLAPGEDQVAVQLFGHE 76

Query: 59  ISKLV-EAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +  +AA I  + G     +++N+GCP+ ++     G+ LM +P +    + A+  A+
Sbjct: 77  PDTMAAQAAWIEREMGQSLAYLDINMGCPARKIVSKGDGSALMKDPALAASIVRAVRAAV 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S PVTVK R G  +           + ++ +G   I +H R A        +       +
Sbjct: 137 SRPVTVKFRRGWAEGD--ETAPEFARRMEDAGACAIAVHGRYA--------EQLYRGRAE 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +  +K E   + +  NG +   + A+ I      D VMI RAA  N  +        
Sbjct: 187 WGAIARVK-EAVSVPVVGNGDVRSGADAVAITERTGCDAVMIARAAEGNPWLFAQAKAAL 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +       P          R                G  + ++ +H +  
Sbjct: 246 AGEPEPDGPTVEERIALARRHARLLSA-------REGRNIVRMRKHAMWY 288


>gi|89054727|ref|YP_510178.1| dihydrouridine synthase TIM-barrel protein nifR3 [Jannaschia sp.
           CCS1]
 gi|88864276|gb|ABD55153.1| tRNA-U20-dihydrouridine synthase [Jannaschia sp. CCS1]
          Length = 347

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 116/290 (40%), Gaps = 21/290 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R          L+ +EM+ +  ++      +        E   A+Q+ G +
Sbjct: 38  MAGITDLPFRRLVASF-GAGLVVSEMVASQEMVEAKASVRARAELGFGENATAVQLAGRE 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I E  G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+++P
Sbjct: 97  AHWMAEAARIAEGQGARIIDINMGCPAKKVVGGLSGSALMRDLDHALRLIDAVVGAVNVP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD+   +    L +  + +G+  I IH R         +         +  
Sbjct: 157 VTLKTRLGWDDKT--LNAPALAQRAETAGIRMITIHGRT--------RCQFYKGTAKWGA 206

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG + D   A + L     DGVM+GR       ++  +       
Sbjct: 207 IRAVK-DAVSIPVIANGDITDAPAAAQALRCSGADGVMVGRGIQGQPWLVAEIGAALFGT 265

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
            T  +P    +           +  Y       GGK+    +H+     G
Sbjct: 266 PTPVAPQGDALVAMVAAHYEDMLAFYGRDL---GGKV--ARKHLGWYMDG 310


>gi|325125157|gb|ADY84487.1| Transcriptional regulator [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 344

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 123/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      ++  EMI    I+ G+KK   +L     E P+++QI G  
Sbjct: 23  MAGVSNMAFRKVCKEF-GAGMVVCEMISDHGIIYGNKKTLSMLDVDPGEHPMSIQIFGGA 81

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   I  + + +  
Sbjct: 82  EDSLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVQNVEK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + + +H R         +        D++
Sbjct: 142 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y + 
Sbjct: 192 TLHEVAQ-VMDIPFVANGDITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D   +       + +  +       G P S R R 
Sbjct: 251 GEELPKQSVREKVETAKHQL-----DGLVQLHGEKRAVPEFRQQAAYYLKGIPRSARTRA 305

Query: 296 ILTV 299
            +  
Sbjct: 306 KINE 309


>gi|121606249|ref|YP_983578.1| nifR3 family TIM-barrel protein [Polaromonas naphthalenivorans CJ2]
 gi|120595218|gb|ABM38657.1| tRNA-U20-dihydrouridine synthase [Polaromonas naphthalenivorans
           CJ2]
          Length = 356

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 65/330 (19%), Positives = 127/330 (38%), Gaps = 27/330 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TDR +R   + L       +EM+ +   L    K     + + +  P+A+QI G D
Sbjct: 17  MAGVTDRPFRQLCKKL-GAGYAVSEMVTSRRDLWDTLKTSRRANHEGEAAPIAVQIAGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              + +AA    D G   I++N+GCP+ +V     G+ LM +  +    I A+  A    
Sbjct: 76  ARMMADAAAYNLDRGAQIIDINMGCPAKKVCNKWAGSALMQDETLALQIIEAVVAACLPH 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R G           ++ ++ + +G+  + +H R         ++       +
Sbjct: 136 GVPVTLKMRTGWAQSHKNA--LSIARAAESAGIQMLAVHGRT--------REQGYKGLAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD + E+K     + +  NG ++   +A  +L   + D +M+GRAA     +   +  + 
Sbjct: 186 YDTIAEVKAAL-RIPVVANGDIDSPEKARDVLAYTAADALMVGRAAQGRPWIFRELTHFM 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P+   V       +      Y          ++   +H+       P     
Sbjct: 245 ATGTHLAPPLVADVKCLLLDHLLDHYALYGEF-----TGVRTARKHIGWYVKTLPGGEAF 299

Query: 294 R-HILTVEAGASTATHHIIETAFNLMIESL 322
           R  +  +E     A    +   F  + E +
Sbjct: 300 RGQMNGLEDCR--AQLEAVNDYFEALSERM 327


>gi|322517559|ref|ZP_08070428.1| tRNA-dihydrouridine synthase [Streptococcus vestibularis ATCC
           49124]
 gi|322123819|gb|EFX95393.1| tRNA-dihydrouridine synthase [Streptococcus vestibularis ATCC
           49124]
          Length = 325

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 124/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VM+GRAA  N  + T ++ +F  
Sbjct: 192 TLARVAKAITKIPFIGNGDVRSVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPD-LPFDKKLDIAEDHLKRLVDLKGEKIA----VREFRGLAPHYLRGTVGAAKVRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 EVS 309


>gi|169335415|ref|ZP_02862608.1| hypothetical protein ANASTE_01827 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258153|gb|EDS72119.1| hypothetical protein ANASTE_01827 [Anaerofustis stercorihominis DSM
           17244]
          Length = 329

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 67/306 (21%), Positives = 134/306 (43%), Gaps = 28/306 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP---LALQIG 55
           M   T   YR F R +    +  +EM+ A  +    K    ++  +  E       +QI 
Sbjct: 23  MAGVTTLPYRLFMREM-GCKIFISEMVSAKGLYYKSKNTFPLMETNELEHKDSVTGIQIF 81

Query: 56  GADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G++   + E   + + D  ++ I++N+GCP  ++     G+ L+ + D     +  +  A
Sbjct: 82  GSEPEIMGEITERYINDTAFDFIDINMGCPMKKIVNNGDGSALLKDLDKANKVVREVKSA 141

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            S PV+VK R+G ++ I    + +++K+I+  G + I +H R         ++      +
Sbjct: 142 SSKPVSVKVRLGFNENI----IEDIIKAIEDGGADMITVHGRT--------REQVFTGEV 189

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           DYD + +  KE   + +  NG L++  +A + +     DGVMIGR A  +  + +  +E 
Sbjct: 190 DYDGIKK-AKETASVPLIANGDLDNYLKAKEKMDYTGADGVMIGRGANYDPFIFSQFNEC 248

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            S        ++ ++D    RK       Y+        K+ +  +++     G  NS +
Sbjct: 249 ISGKKVSEYSLRDKIDAA--RKHFEIHLKYSKD----KKKVIEFRKYLYWYIKGIKNSAK 302

Query: 293 CRHILT 298
            R+ + 
Sbjct: 303 IRNSIN 308


>gi|295425664|ref|ZP_06818351.1| tRNA-dihydrouridine synthase [Lactobacillus amylolyticus DSM 11664]
 gi|295064680|gb|EFG55601.1| tRNA-dihydrouridine synthase [Lactobacillus amylolyticus DSM 11664]
          Length = 341

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 63/304 (20%), Positives = 124/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   ++    +E P+++QI G  
Sbjct: 21  MAGVSNSAFRMVCKEF-GAGLVVCEMISDHGIIYRNKKTLSMMQVDPREHPMSIQIFGGT 79

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+EAA+ V+     + I++N+GCP  +V +   G+  +L+ + +   + A+ + +S 
Sbjct: 80  EETLLEAAQYVDKHTAADIIDINMGCPVPKVTKTDAGSKWLLDANKIYQMVHAVVQNVSK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D +   +       + +++G + I +H R         +      + D++
Sbjct: 140 PVTVKMRIGWDRK--HIFAVENALAAQEAGASMIAMHGRT--------RKQMYQGHADWE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSN 235
           +++++     D+    NG +     A K L  +    VM+GRAA  N  ++  +  Y   
Sbjct: 190 VLHDVANAL-DIPFVANGDIRTPEDAKKALDEIGSTAVMVGRAALGNPWIIKDMVHYLET 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                             ++     D           + +  +       G P S R R 
Sbjct: 249 GEKLKPQTVRERVATAKHQL-----DGLVELKGEKIAVPEFRQQAAYYLKGIPRSARTRA 303

Query: 296 ILTV 299
            +  
Sbjct: 304 KINE 307


>gi|288906346|ref|YP_003431568.1| tRNA-dihydrouridine synthase [Streptococcus gallolyticus UCN34]
 gi|306832388|ref|ZP_07465541.1| tRNA-dihydrouridine synthase [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325979357|ref|YP_004289073.1| putative tRNA-dihydrouridine synthase [Streptococcus gallolyticus
           subsp. gallolyticus ATCC BAA-2069]
 gi|288733072|emb|CBI14653.1| putative tRNA-dihydrouridine synthase [Streptococcus gallolyticus
           UCN34]
 gi|304425428|gb|EFM28547.1| tRNA-dihydrouridine synthase [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|325179285|emb|CBZ49329.1| putative tRNA-dihydrouridine synthase [Streptococcus gallolyticus
           subsp. gallolyticus ATCC BAA-2069]
          Length = 325

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 125/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  ADGLKRAAEFIQENTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIINEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSELAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG + ++  A  ++    VD VM+GRAA  N  + T ++ YF  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRNVHDAKYMIEEIGVDAVMVGRAAMNNPYIFTQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +     +     +++          G   + + R 
Sbjct: 252 GEELPD-LPFVKKLDIAEDHLKRLINLKGEKIA----VREFRGLAPHYLRGTAGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|313772422|gb|EFS38388.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL074PA1]
 gi|313807433|gb|EFS45920.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL087PA2]
 gi|313809940|gb|EFS47661.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL083PA1]
 gi|313813022|gb|EFS50736.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL025PA1]
 gi|313818478|gb|EFS56192.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL046PA2]
 gi|313820241|gb|EFS57955.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL036PA1]
 gi|313822949|gb|EFS60663.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL036PA2]
 gi|313825122|gb|EFS62836.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL063PA1]
 gi|313830271|gb|EFS67985.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL007PA1]
 gi|313834072|gb|EFS71786.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL056PA1]
 gi|314925128|gb|EFS88959.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL036PA3]
 gi|314960085|gb|EFT04187.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL002PA2]
 gi|314973277|gb|EFT17373.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL053PA1]
 gi|314975952|gb|EFT20047.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL045PA1]
 gi|314978290|gb|EFT22384.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL072PA2]
 gi|314984029|gb|EFT28121.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA1]
 gi|314987792|gb|EFT31883.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA2]
 gi|314990014|gb|EFT34105.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA3]
 gi|315084401|gb|EFT56377.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL027PA2]
 gi|315088841|gb|EFT60817.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL072PA1]
 gi|315096190|gb|EFT68166.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL038PA1]
 gi|315105467|gb|EFT77443.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL030PA1]
 gi|327326106|gb|EGE67896.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL096PA2]
 gi|327330171|gb|EGE71920.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL097PA1]
 gi|327332023|gb|EGE73760.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL096PA3]
 gi|327443226|gb|EGE89880.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL013PA2]
 gi|327446010|gb|EGE92664.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL043PA2]
 gi|327448010|gb|EGE94664.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL043PA1]
 gi|328753553|gb|EGF67169.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL020PA1]
 gi|328760675|gb|EGF74242.1| putative tRNA-dihydrouridine synthase [Propionibacterium acnes
           HL099PA1]
          Length = 355

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 125/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 1   MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 60  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 119

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 120 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 169

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 170 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 229 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 282

Query: 293 CRHIL 297
            RH+L
Sbjct: 283 TRHVL 287


>gi|57239061|ref|YP_180197.1| putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Welgevonden]
 gi|58579004|ref|YP_197216.1| putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Welgevonden]
 gi|57161140|emb|CAH58053.1| conserved hypothetical protein [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417630|emb|CAI26834.1| Putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Welgevonden]
          Length = 317

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 76/300 (25%), Positives = 125/300 (41%), Gaps = 20/300 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L    LL +EMI +  ++    K+ L  S  +   A+Q+ G D  
Sbjct: 17  MSGITDFPFRSLVKNL-GAGLLVSEMIASRGMI-KQTKDSLQKSHIQSNTAVQLAGCDPL 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V     G+ LM +       + A+ KA+ +PVT
Sbjct: 75  IMAEAAKLNEDMGAQIIDINFGCPVKKVVNSYAGSALMKDEITAAKILEAVVKAVKVPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG D Q   +    L K  + +G+  I IH R         +        D+  + 
Sbjct: 135 LKMRIGWDSQ--NLNSPRLAKIAENTGIKMITIHGRT--------RAQMFTGKADWKFIS 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            IKK    + I +NG ++ +      L     DG+MIGR AY    ++    ++  + + 
Sbjct: 185 NIKK-CVRIPIIVNGDIKTLDDIKIALEESQADGIMIGRGAYGKPWIINKALQFIKSGII 243

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P  +        +I  +  D    H      ++   +H+        NS   R  + 
Sbjct: 244 LPDPTVSE-----KLQIIINHYDNIIEHYGKDIGVKISKKHIGWYSACLENSTEFRSKVN 298


>gi|305680317|ref|ZP_07403125.1| TIM-barrel protein, nifR3 family [Corynebacterium matruchotii ATCC
           14266]
 gi|305659848|gb|EFM49347.1| TIM-barrel protein, nifR3 family [Corynebacterium matruchotii ATCC
           14266]
          Length = 384

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 125/337 (37%), Gaps = 36/337 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EMI A A++ G++K   +  F   E P +L
Sbjct: 22  MAGVTNVAFRTLCREQELAKTGTVSGLYVCEMITARALVEGNEKTRHMTTFGPDEHPRSL 81

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---I 108
           Q    D     +AA++V D    + I++N GCP  +V     G+ L     + G+     
Sbjct: 82  QFYTTDPEYTYKAARMVADNNLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAA 141

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                  +IP+TVK RIG+DD        +  +     G   + +HAR A          
Sbjct: 142 VKAVAGTNIPITVKFRIGIDDDHH--THLDAGRIAAAEGAAAVALHARTA--------AQ 191

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R     D+  +  +K+   D  + +  NG +   + A K++     DGV++GR       
Sbjct: 192 RYSGTADWSQIAALKEHLADTGIPVLGNGDIFQATDAQKMMTETGCDGVVVGRGCLGRPW 251

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V     R  +  +T Y           + + +HM    
Sbjct: 252 LFAELSAALRGVDIPPEPTLGEVTGIILRH-AELLTHYDGE----DKACRDLRKHMGWYL 306

Query: 285 HGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            GFP     R  L+  A  + A    +  A     ES
Sbjct: 307 RGFPVGGPLRAQLS--AIKTLAD---LRAALEPWRES 338


>gi|325962747|ref|YP_004240653.1| hypothetical protein Asphe3_13420 [Arthrobacter phenanthrenivorans
           Sphe3]
 gi|323468834|gb|ADX72519.1| putative TIM-barrel protein, nifR3 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 392

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 56/311 (18%), Positives = 119/311 (38%), Gaps = 41/311 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    +++  +     E+  ++Q+ G D
Sbjct: 33  MAGITNSAFRRLCREYGG-GMYVAEMVTSRALVERTPESLRIISHDEDEQVRSVQLYGVD 91

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKAL- 115
              +  A ++ VE+   + I+LN GCP  +V     G+ L    D+    +  A+ +A  
Sbjct: 92  PVTVGAAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTSIVQTAVREAAK 151

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++P+T+K R G+DD    +   +  +  + +GV  + +H R A                
Sbjct: 152 GNVPLTIKMRKGIDDD--HLTYLDAGRIARDAGVAAVALHGRTA--------AQFYSGQA 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA-----------AYKNS 223
           D+  +  +++  PD+ +  NG +     A++++         R                 
Sbjct: 202 DWSAIARLREALPDIPVLGNGDIWSAEDAVRMV---------RETGVDGVVVGRGCQGRP 252

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +   F        P   +V +  +R     +  +       G  L++I +H+   
Sbjct: 253 WLFGDLQAAFEGSDVRHKPNLGQVAQGVYRHAELMVETFG----DEGKALREIRKHIAWY 308

Query: 284 FHGFPNSRRCR 294
           F G+      R
Sbjct: 309 FKGYVVGGELR 319


>gi|313792228|gb|EFS40329.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA1]
 gi|313801823|gb|EFS43057.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL110PA2]
 gi|313827691|gb|EFS65405.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL063PA2]
 gi|313838649|gb|EFS76363.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL086PA1]
 gi|314962886|gb|EFT06986.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL082PA1]
 gi|315078100|gb|EFT50151.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL053PA2]
 gi|315108413|gb|EFT80389.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL030PA2]
 gi|327453057|gb|EGE99711.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL092PA1]
          Length = 355

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 125/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 1   MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 60  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 119

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 120 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 169

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 170 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 229 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 282

Query: 293 CRHIL 297
            RH+L
Sbjct: 283 TRHVL 287


>gi|217965686|ref|YP_002351364.1| transcriptional regulator [Listeria monocytogenes HCC23]
 gi|290894521|ref|ZP_06557473.1| dihydrouridine synthase [Listeria monocytogenes FSL J2-071]
 gi|217334956|gb|ACK40750.1| transcriptional regulator involved in nitrogen regulation [Listeria
           monocytogenes HCC23]
 gi|290555922|gb|EFD89484.1| dihydrouridine synthase [Listeria monocytogenes FSL J2-071]
 gi|307569766|emb|CAR82945.1| dihydrouridine synthase [Listeria monocytogenes L99]
          Length = 331

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 132/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G          + ++D
Sbjct: 137 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG +     A +IL     DGVMIGRAA  N  M+    ++   
Sbjct: 187 VLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLPEPEPREKMQTAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A        I+        E 
Sbjct: 300 VAANQATKQAEMEAILNEFVLQYEEK 325


>gi|237736815|ref|ZP_04567296.1| nitrogen regulation protein NIFR3 [Fusobacterium mortiferum ATCC
           9817]
 gi|229420677|gb|EEO35724.1| nitrogen regulation protein NIFR3 [Fusobacterium mortiferum ATCC
           9817]
          Length = 318

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 128/315 (40%), Gaps = 26/315 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  YR   +   N  +L+TEM+  +A+    +K +       +  ++Q+ G DI K
Sbjct: 10  AGVTDYTYRGILKEF-NPDMLFTEMVSINAMECASEKTLKVILRLREGDSVQLFGKDIPK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +VE+AK VE  G   I++N GCP  ++    +G+ LM NP+ +   ++ +  AL     +
Sbjct: 69  MVESAKFVERLGVKHIDINSGCPMKKITSNGYGSALMANPEHIKAMLSELRSALNDDTGL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R G  +    V    + K  ++ G   I +H R         ++       D+ I+
Sbjct: 129 SIKIRAGYKEFKNPV---EIAKIAEEVGCKHITVHGRT--------REQMYTGKADWSII 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E+  + +  NG +     A +      VDG+M+ R  + N  ++  + EY     
Sbjct: 178 KAVK-ESVGIPVIGNGDIFTAEDAKERIDYSGVDGIMLARGIFGNPWLIRDIREYLEYGK 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +                 +  ++  R       + ++ +H+     G  NS   +  +
Sbjct: 237 ILNPVTPLDRINMAIEHTRRTQIEHPERDF-----IFELRKHICWYLKGIRNSNPIKDKI 291

Query: 298 TVEAGASTATHHIIE 312
                 +     ++E
Sbjct: 292 NH----TDKYEEVLE 302


>gi|314968036|gb|EFT12135.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL037PA1]
          Length = 355

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 76/305 (24%), Positives = 125/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  +L GD K   +L F+  E   ++Q+ G D
Sbjct: 1   MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLLYGDHKTHGMLAFAECEDVRSVQLYGVD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 60  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 119

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 120 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 169

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 170 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 229 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 282

Query: 293 CRHIL 297
            RH+L
Sbjct: 283 TRHVL 287


>gi|294341441|emb|CAZ89858.1| tRNA-dihydrouridine synthase B [Thiomonas sp. 3As]
          Length = 331

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 119/312 (38%), Gaps = 24/312 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TDR YR  AR L       +EM+ + A LR   K         +  P+A+QI G D
Sbjct: 17  MAGVTDRPYRRLARQL-GAGYCVSEMVTSRADLRDTLKTSRRANHDGEAAPIAVQIVGTD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
             ++ EA +   + G + I++N+GCP+ +V     G+ LM + D+    + A   A    
Sbjct: 76  PEQIAEATRYNLERGADIIDINMGCPAKKVCNRWAGSALMQDEDLAARLVEAAVAAARPF 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PVT+K R G  +   A     + +  + +G   + +H R         ++       +
Sbjct: 136 GAPVTLKMRAGWCE--AARNAPRIARRAEAAGAAMLVVHGRT--------REQGYGGEAE 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y  + E+K+    + +  NG ++   +A  +L     D VMIGRAA     +   V  Y 
Sbjct: 186 YATLAEVKRSVG-IPVVANGDIDSPQKAAAVLRQSGADAVMIGRAAMGRPWLFGQVAAYL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              +    P   +     +  +      Y          ++   +H+       P     
Sbjct: 245 ERGVLLPGPAPVQWRDWLFAHLDDHYALYGEAI-----GVRTARKHVGWYVAALPEGETF 299

Query: 294 RHILTVEAGAST 305
           R        A+ 
Sbjct: 300 RRQFNTLGSAAE 311


>gi|163731736|ref|ZP_02139183.1| tRNA-dihydrouridine synthase [Roseobacter litoralis Och 149]
 gi|161395190|gb|EDQ19512.1| tRNA-dihydrouridine synthase [Roseobacter litoralis Och 149]
          Length = 327

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/291 (25%), Positives = 126/291 (43%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M   TDR +R          L+ +EM+ +  IL       +K  LG S +    A+Q+ G
Sbjct: 19  MAGITDRPFRDLVASF-GAGLVVSEMVASADILNARPGSQEKAELGLSAEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+ KA+ 
Sbjct: 76  REPGLMAEAARMVEGQGARIIDINMGCPAKKVTQGYSGSALMRTPDHAMTLIEAVVKAVK 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT+K R+G DD +  +    + +  +++G+  + IH R         +      + D+
Sbjct: 136 IPVTLKTRLGWDDAM--LNAPQIARRAEEAGIRMLTIHGRT--------RCQFYKGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +  +K     + +  NG +       QAL+ L   DGVMIGR A     +L+ +    
Sbjct: 186 AAIAGVK-SVVSIPVIANGDILCSVSAKQALR-LSGADGVMIGRGARGKPWLLSQIAHDL 243

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 + P+            +A +  Y          ++   +H+    
Sbjct: 244 YGAPAPAIPVGEAFSDMVRTHYAAIIRFY-----GHDLGVKVARKHLGWYM 289


>gi|325479557|gb|EGC82653.1| TIM-barrel protein, nifR3 family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 326

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 136/326 (41%), Gaps = 25/326 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R            +TEM+  +A+L  +K    I+  S  EK   +QI G D 
Sbjct: 16  AGVTDAAFRIICEE-NGADKTFTEMVSVNALLYDNKATHEIMYRSDLEKNCNIQIFGNDP 74

Query: 60  SKLVEAAK--IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + +  K  I     + EI+ N+GCP+ ++ +   G+ LM +     +    +  +   
Sbjct: 75  AIIEKVVKEKINPRDDFKEISFNMGCPAPKIFKNGQGSALMGDIKKAQEIAKTLVGSTDK 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V +K R+G+D+   ++   +  K+++ +GV+ + +HAR         +  +     ++D
Sbjct: 135 IVNIKFRLGIDE--NSINYIDFGKALEDAGVDYVILHART--------RAQQYSGKANWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K E   + +  NG    +   +KI+   + DGVMI R A  N  +   + +Y   
Sbjct: 185 DIRKLK-EALSIPVVANGDCFSVDDYIKIIETTNADGVMIARGAMGNPFIFRQIKDYLKG 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    +     R+   S+T Y    L     + Q+ +H+     G P +   R 
Sbjct: 244 KRIK-DPTYDDILDTIKRQYDLSLT-YKEERL----VINQMRKHVGWYIKGLPQAASYRD 297

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +  +   S     +++     + ++
Sbjct: 298 RVN-KLRTSEEIFDLLDEYRKYLEDN 322


>gi|58617063|ref|YP_196262.1| putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Gardel]
 gi|58416675|emb|CAI27788.1| Putative nitrogen regulation protein nifR3 [Ehrlichia ruminantium
           str. Gardel]
          Length = 317

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 76/300 (25%), Positives = 125/300 (41%), Gaps = 20/300 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R   + L    LL +EMI +  ++    K+ L  S  +   A+Q+ G D  
Sbjct: 17  MSGITDFPFRALVKNL-GAGLLVSEMIASRGMI-KQTKDSLQKSHIQSNTAVQLAGCDPL 74

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + EAAK+ ED G   I++N GCP  +V     G+ LM +       + A+ KA+ +PVT
Sbjct: 75  IMAEAAKLNEDMGAQIIDINFGCPVKKVVNSYAGSALMKDEITAAKILEAVVKAVKVPVT 134

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K RIG D Q   +    L K  + +G+  I IH R         +        D+  + 
Sbjct: 135 LKMRIGWDSQ--NLNSPRLAKIAENTGIKMITIHGRT--------RAQMFTGKADWKFIS 184

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            IKK    + I +NG ++ +      L     DG+MIGR AY    ++    ++  + + 
Sbjct: 185 NIKK-CVRIPIIVNGDIKTLDDIKIALEESQADGIMIGRGAYGKPWIINKALQFIKSGII 243

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P  +        +I  +  D    H      ++   +H+        NS   R  + 
Sbjct: 244 LPDPTVSE-----KLQIIINHYDNIIEHYGKDIGVKISKKHIGWYSACLENSTEFRSKVN 298


>gi|260427626|ref|ZP_05781605.1| probable tRNA-dihydrouridine synthase [Citreicella sp. SE45]
 gi|260422118|gb|EEX15369.1| probable tRNA-dihydrouridine synthase [Citreicella sp. SE45]
          Length = 327

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 80/323 (24%), Positives = 129/323 (39%), Gaps = 28/323 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              TD  +R          L+ +EMI +   L  R   +            ++Q+ G   
Sbjct: 20  AGITDLPFRSLVARW-GAGLVVSEMIASGEFLTARPGTREKAELGAGIANTSVQLAGRAP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++V D G   I++N+GCP+ +V  G  G+ LM  PD     I A+  A+ +PV
Sbjct: 79  GPMAEAARMVADMGARVIDINMGCPAKKVTGGYSGSALMREPDHALRLIEAVVGAVDVPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD   ++    L +  + +GV  I IH R         +        D+  +
Sbjct: 139 TLKTRLGWDDG--SLNAPELARRAEAAGVCMIVIHGRT--------RCQFYKGRADWAAI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +   + +  NG + D + A +   L   DGVM+GR A      L  +        
Sbjct: 189 RAVK-DAVSVPVVANGDITDAATAREALDLSGADGVMVGRGAQGAPWRLAEIAHALYGAP 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HG-FPNSRRCR 294
               P K R   D  ++   +M  +    L     ++   +H+       G  P  R  R
Sbjct: 248 RPDVP-KGRALTDIVQEHYEAMIAFYGPELG----VKCARKHLGWYMDHAGTAPEMR--R 300

Query: 295 HILTVE--AGASTATHHIIETAF 315
            +LT    A AS      +E A 
Sbjct: 301 RVLTERDPAQASALLRPALEDAL 323


>gi|116627125|ref|YP_819744.1| putative transcriptional regulator [Streptococcus thermophilus
           LMD-9]
 gi|116100402|gb|ABJ65548.1| tRNA-dihydrouridine synthase [Streptococcus thermophilus LMD-9]
 gi|312277599|gb|ADQ62256.1| tRNA-dihydrouridine synthase B [Streptococcus thermophilus ND03]
          Length = 325

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 125/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGHCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG + ++  A  ++    VD VM+GRAA  N  + T ++ +F  
Sbjct: 192 TLARVAKAITKIPFIGNGDVRNVQDAKLMIEELGVDAVMVGRAAMNNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPD-LPFDKKLDIAEDHLKRLVDLKGEMIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 EVS 309


>gi|326773529|ref|ZP_08232812.1| tRNA-dihydrouridine synthase [Actinomyces viscosus C505]
 gi|326636759|gb|EGE37662.1| tRNA-dihydrouridine synthase [Actinomyces viscosus C505]
          Length = 440

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 132/338 (39%), Gaps = 57/338 (16%)

Query: 1   MVDWTDRHYRFFAR-------------------------LLTNNALLYTEMIVADAILRG 35
           M   T+  +R   R                         LL    L  TEM+   A++  
Sbjct: 45  MAGVTNASFRRLCREMAEAALPESLRPSCPGPLPTFDGGLLAPAGLYVTEMVTTRALVER 104

Query: 36  DKKN--ILGFSTQEKPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGS 92
           +++   ++     E+  ++Q+ G D + +  A +I VE+   + I+LN GCP  +V    
Sbjct: 105 NERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEEDLADHIDLNFGCPVPKVTRKG 164

Query: 93  FGACLMLNPDIVGDC-----------IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            GA L    D++              + A+ +A  +PVT+K R+G+D++       +  +
Sbjct: 165 GGAALPWKRDLLAAILTEAVRASEAAVRAVGRARQVPVTMKMRLGIDEE--HETFLDAAR 222

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           + + +G+  + +HAR A                 ++ +  +K E  DL +  NG +    
Sbjct: 223 AAENAGIAAVALHARSA--------RQHYSGQARWEEIARLK-EATDLPVLGNGDVWLGD 273

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            A++++     DGV++GR       +   +           SP +TR D D   ++    
Sbjct: 274 DAVRMMEATGCDGVVVGRGCQGRPWLFADIVAAMHG-----SPARTRPDLDAVIEVIRRH 328

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               A  +     ++ + +H+     G+P     R  L
Sbjct: 329 GRMLAEEMGEDRGVRDLRKHVGWYLKGYPVGGAARADL 366


>gi|209549216|ref|YP_002281133.1| hypothetical protein Rleg2_1617 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209534972|gb|ACI54907.1| TIM-barrel protein, nifR3 family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 315

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 119/287 (41%), Gaps = 27/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++         +P  +Q+ G + 
Sbjct: 10  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAESWSRLRAAGFRPHMVQLAGREA 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPV
Sbjct: 69  HWMAEAAKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPV 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    + +  + +G+  + IH R  +               D+D +
Sbjct: 129 TLKMRLGWDE--NSINAPEIARRAEAAGIQLVTIHGRTRM--------QFYEGRADWDAI 178

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + +  NG +E    A +IL     D VMIGR                +  L
Sbjct: 179 RPV-RDVISIPLIANGDVETAEDAQEILRRSGADAVMIGRGCQGRPWH--------AGVL 229

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            G +  +     D   +    M D+          ++   +H+    
Sbjct: 230 AGGAEPRREDIADIAVEHYRMMLDFYGE----AVAIRHARKHLGWYL 272


>gi|315604759|ref|ZP_07879822.1| NifR3/Smm1 family transcriptional regulator [Actinomyces sp. oral
           taxon 180 str. F0310]
 gi|315313771|gb|EFU61825.1| NifR3/Smm1 family transcriptional regulator [Actinomyces sp. oral
           taxon 180 str. F0310]
          Length = 423

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 69/360 (19%), Positives = 130/360 (36%), Gaps = 76/360 (21%)

Query: 1   MVDWTDRHYRFFARLLT------------------------------------------- 17
           M   TD  +R   R++                                            
Sbjct: 15  MAGVTDAPFRRLCRIMGESGLPGALRPAGLPAWAADASPGADVSSQMDPEAGTARRVAIP 74

Query: 18  ----NNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
                  L  TEM+ + A++ G+++   ++     E+  +LQ+ G D + +  AA ++ +
Sbjct: 75  RVDAPAGLYVTEMVTSRALVEGNERTLDMVRPDPAERVRSLQLYGVDPAVMARAATMLVE 134

Query: 72  FG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---------SIPVTV 121
               + ++LN GCP  +V +   GA L    D+  D + ++ +A           IPVTV
Sbjct: 135 RDLTDHVDLNFGCPVPKVTKKGGGAALPWKRDLFVDLLDSVVRACRKAGERAGREIPVTV 194

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K RIG+D         +   S ++ G   + +HAR                   ++ +  
Sbjct: 195 KIRIGID--SSHETATDAALSAQRLGAAALTLHARTQT--------QHYAGKAQWEHIAR 244

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K E  D+ +  NG + + + AL +L     DG+ +GR A     +   +   +      
Sbjct: 245 LK-ELLDIPVFGNGDVFEGADALDMLERTGCDGISVGRGAQGRPWIFRDIVAAYHGAPIP 303

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
           + P    V     R  +  + D           L+++ +H+     GF      RH L++
Sbjct: 304 AGPTLADVIAVIERHAAWCVADQGCEERA----LREMRKHIGWYLRGFAVGGAQRHALSM 359


>gi|313764539|gb|EFS35903.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL013PA1]
 gi|313816081|gb|EFS53795.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL059PA1]
 gi|314915535|gb|EFS79366.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL005PA4]
 gi|314918342|gb|EFS82173.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL050PA1]
 gi|314919997|gb|EFS83828.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL050PA3]
 gi|314955880|gb|EFT00280.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL027PA1]
 gi|314958193|gb|EFT02296.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL002PA1]
 gi|315098451|gb|EFT70427.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL059PA2]
 gi|315101191|gb|EFT73167.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL046PA1]
 gi|327450866|gb|EGE97520.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL087PA3]
 gi|327453786|gb|EGF00441.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL083PA2]
 gi|328754285|gb|EGF67901.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL087PA1]
 gi|328754462|gb|EGF68078.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL025PA2]
          Length = 355

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 124/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 1   MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 60  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 119

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 120 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 169

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A  ++      GV +GR       +   + + 
Sbjct: 170 HWDAIGELVK-TVDVPVIGNGDIWEASDATAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 229 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 282

Query: 293 CRHIL 297
            RH+L
Sbjct: 283 TRHVL 287


>gi|16802273|ref|NP_463758.1| hypothetical protein lmo0227 [Listeria monocytogenes EGD-e]
 gi|224503816|ref|ZP_03672123.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           R2-561]
 gi|255029456|ref|ZP_05301407.1| dihydrouridine synthase family protein [Listeria monocytogenes
           LO28]
 gi|16409592|emb|CAD00754.1| lmo0227 [Listeria monocytogenes EGD-e]
          Length = 331

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 132/326 (40%), Gaps = 23/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G            ++D
Sbjct: 137 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEGS----------ANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ ++K+E   +    NG +     A +IL     DGVMIGRAA  N  M+    ++   
Sbjct: 187 VLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +     ++                +++  +H      G   S R + 
Sbjct: 246 GELLLEPEPREKMQTAMLHLNR-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK- 299

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           +   +A   +    I+        E 
Sbjct: 300 VAANQATKQSEMEAILNEFVLQYEEK 325


>gi|148543507|ref|YP_001270877.1| nifR3 family TIM-barrel protein [Lactobacillus reuteri DSM 20016]
 gi|184152914|ref|YP_001841255.1| transcription regulator [Lactobacillus reuteri JCM 1112]
 gi|194467682|ref|ZP_03073669.1| TIM-barrel protein, nifR3 family [Lactobacillus reuteri 100-23]
 gi|227363656|ref|ZP_03847770.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325681851|ref|ZP_08161370.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM4-1A]
 gi|148530541|gb|ABQ82540.1| tRNA-U20-dihydrouridine synthase [Lactobacillus reuteri DSM 20016]
 gi|183224258|dbj|BAG24775.1| transcription regulator [Lactobacillus reuteri JCM 1112]
 gi|194454718|gb|EDX43615.1| TIM-barrel protein, nifR3 family [Lactobacillus reuteri 100-23]
 gi|227071325|gb|EEI09634.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324978942|gb|EGC15890.1| tRNA-dihydrouridine synthase [Lactobacillus reuteri MM4-1A]
          Length = 333

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 129/325 (39%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +       +  EMI    I+  +++   ++    +E P+ +QI G  
Sbjct: 19  MAGVTNSAFRVICKRF-GAGYVVCEMISDRGIMYHNQRTLNMMDVDPEEHPMGIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V+     + I++N+GCP  +V +   GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEAAKYVDQHTAADVIDINMGCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L    +++G + I +H R         +        D++
Sbjct: 138 PVTVKMRTGWDDKHILAVENALA--AERAGASAIAMHGRT--------RKQMYTGQADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG ++    A KIL        MIGRAA  N  ML   + Y + 
Sbjct: 188 ILKEVASQL-KIPFMANGDVKTPEDAKKILDMTGATAAMIGRAAMGNPWMLKRTEHYLAT 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     +  +     ++                +++          G P + R + 
Sbjct: 247 GELLPEATPEQKIEMAKDHLNR-----LVDLKGEYVGVREFRGLSTYYIKGIPRAARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L VEA      + I +       E
Sbjct: 302 AL-VEAETLDEMNDIFDRFAEQTAE 325


>gi|329114574|ref|ZP_08243333.1| Putative tRNA-dihydrouridine synthase [Acetobacter pomorum DM001]
 gi|326696054|gb|EGE47736.1| Putative tRNA-dihydrouridine synthase [Acetobacter pomorum DM001]
          Length = 356

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 123/319 (38%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R  AR L    L+ +EMI + A++R +     +   +    P A+Q+ G D
Sbjct: 26  MSGVTDLPFRRLARKL-GAGLVVSEMIASWAMVRENDTTLRMAEVADAGGPNAVQLAGCD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA+I    G + I++N GCP  +V      G+ LM +       +AA+ KA+ +
Sbjct: 85  PDAMAEAARIAVGRGADLIDINFGCPVKKVAVGQMAGSALMRDEGAAERLLAAVVKAVPV 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D +     +  L +  +  G+  I +H R         +        ++ 
Sbjct: 145 PVTLKMRMGWDHEHLNAPV--LARIAQDVGIRMITVHGRT--------RQQFYNGTANWA 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  +K +  DL + +NG +  +  A + L     DGVMIGR  Y     L  V      
Sbjct: 195 FVKNVK-DAVDLPVIVNGDILTVGDAREALAQSGADGVMIGRGCYGRPWFLAQVAHALRT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P          + I     +    H      L+   +H+     G   S   R 
Sbjct: 254 GQEIPDPALPEE-----KAIVLEHYNMMLEHFGQRPGLRLARKHVSWYSAGLHGSASFRA 308

Query: 296 ILTVEAGASTATHHIIETA 314
                     A   I +  
Sbjct: 309 AFNRVETPEEAIAMIADFY 327


>gi|258542828|ref|YP_003188261.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256633906|dbj|BAH99881.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256636965|dbj|BAI02934.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-03]
 gi|256640018|dbj|BAI05980.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-07]
 gi|256643074|dbj|BAI09029.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-22]
 gi|256646129|dbj|BAI12077.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-26]
 gi|256649182|dbj|BAI15123.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-32]
 gi|256652169|dbj|BAI18103.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-01-42C]
 gi|256655226|dbj|BAI21153.1| tRNA-dihydrouridine synthase NifR3 [Acetobacter pasteurianus IFO
           3283-12]
          Length = 356

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 120/299 (40%), Gaps = 22/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R  AR L    L+ +EMI + A++R +     +   +    P A+Q+ G D
Sbjct: 26  MSGVTDLPFRRLARKL-GAGLVVSEMIASWAMVRENDTTLRMAEVADAGGPNAVQLAGCD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + EAA+I    G + I++N GCP  +V      G+ LM +       +AA+ KA+ +
Sbjct: 85  PDAMAEAARIAVGRGADLIDINFGCPVKKVAVGQMAGSALMRDEGAAERLLAAVVKAVPV 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D +     +  L +  +  G+  I +H R         +        ++ 
Sbjct: 145 PVTLKMRMGWDHEHLNAPV--LARIAQDVGIRMITVHGRT--------RQQFYNGTANWA 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  +K E  DL + +NG +  +  A + L     DGVMIGR  Y     L  V      
Sbjct: 195 FVKNVK-EAVDLPVIVNGDILTVGDAREALAQSGADGVMIGRGCYGRPWFLAQVAHALRT 253

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 P          + I     +    H      L+   +H+     G   S   R
Sbjct: 254 GQEIPDPALPEE-----KAIVLEHYNMMLEHFGQRPGLRLARKHVSWYSAGLHGSASFR 307


>gi|51246454|ref|YP_066338.1| tRNA-dihydrouridine synthase [Desulfotalea psychrophila LSv54]
 gi|50877491|emb|CAG37331.1| tRNA-dihydrouridine synthase [Desulfotalea psychrophila LSv54]
          Length = 328

 Score =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 112/300 (37%), Gaps = 30/300 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R             +EMI    +    ++   +L    +E+P++ Q+ GA+ 
Sbjct: 19  AGYTDLSFRLLCHQF-GADYTVSEMISCHGLFYNQQRTLEMLASLPEERPVSFQLFGAEP 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + +A  I+ DF  + I++N+GCP  +V +   GA LM  P++  D I ++     IPV
Sbjct: 78  DIMAKATLILNDFQPDMIDINMGCPVRKVTKKGAGAALMSTPELAYDVIRSVVDNTDIPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R GV           L+     +    +    R     G+           D  I+
Sbjct: 138 TVKFRAGVSSTELNGVEFGLMTERAGAAAVAVHGRTRAQAFSGV----------ADRGII 187

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K E   + +  NG +      L ++     DGVM+GR A  N  +            
Sbjct: 188 KEVK-EALSIPVIGNGDILSYQDGLDMMAETGCDGVMVGRGALGNPWVF---------QA 237

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           +G       +     + +           +     L  I  HM   F   P S R R  +
Sbjct: 238 SGKPANIHGLAAGALQHLLLMERFNPVERV-----LGLIKNHMSKYFKDMPGSSRLRTAI 292


>gi|295098775|emb|CBK87864.1| tRNA-U20-dihydrouridine synthase [Eubacterium cylindroides T2-87]
          Length = 326

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 62/301 (20%), Positives = 120/301 (39%), Gaps = 28/301 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              ++  +R  A+      L+  EM+   A+    KK   +      E P++ Q+ G DI
Sbjct: 19  AGISNIAFRVIAKEF-GAGLVCNEMVSDKALYYDSKKTFSMCDVDPNEHPVSFQLFGHDI 77

Query: 60  SKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +V AAK ++     + I+ N+GCP  +V +   G+ LM + D   + ++ + + ++ P
Sbjct: 78  DTVVYAAKYLDTQTNCDIIDFNMGCPVNKVIKAKAGSYLMKDIDYAKELVSHIVENVNKP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D     +    + K+++  GV  + +H R         +        D+  
Sbjct: 138 VTVKMRIGFDKD--HINCVEMAKAMEGVGVKAVAVHGRT--------RSQMYEGKADWSY 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K E   + +  NG +  +    ++      D VMIGR    N  ++    +   N 
Sbjct: 188 IKQVK-EAVSIPVIGNGDVRSVDDFFRMQKETGCDAVMIGRGIIGNPFLIQECKDALYNE 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRRCR 294
                        DF  +I   +        + G    ++++         G P S   +
Sbjct: 247 HH---------TYDFNDRIEICLKHANGLIKNKGEVIAIKEMRGLASWYLKGLPGSHYFK 297

Query: 295 H 295
           +
Sbjct: 298 N 298


>gi|29840744|ref|NP_829850.1| nifR3 family TIM-barrel protein [Chlamydophila caviae GPIC]
 gi|29835094|gb|AAP05728.1| putative TIM-barrel protein, nifR3 family [Chlamydophila caviae
           GPIC]
          Length = 339

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 138/322 (42%), Gaps = 23/322 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  YR  + L    AL++ EM+  + +     + +  L +S   +P+  Q+ G+  
Sbjct: 22  AGFSDYPYRRMSSLYGPPALMFCEMVKIEGLHYSPSRTLKLLEYSESMRPIGGQLCGSKP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               EAAK++E  G++ I+LN GCP+ R+ +   G+ ++ +P+++G  +  +  A+SIPV
Sbjct: 82  DMAGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGMLKSPELIGKVLEKIIGAVSIPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ IK +G + I++H R         +    +   + + +
Sbjct: 142 TVKIRSGWDG--NNINVEETVRIIKDAGASAIFVHGRT--------RAQGYVGPSNLEYI 191

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K     D  +  NG +     A  +L     DGV++ R       ++  +++Y +  
Sbjct: 192 TRAKAAAGKDFPVFGNGDVFSPEAAKVMLDTTGCDGVLVARGTMGTPWIVRQIEDYLNTG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCRH 295
                P  TR      ++       +   +  S  K    TR + G         R  R 
Sbjct: 252 TYEKMPFSTR------KQAFIQHLQWVEEYYQSEAKFLCETRKLCGHYLISASKVRFLRS 305

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            L+ +A +    + +I+     
Sbjct: 306 ALS-KATSVQEVYQLIDDYEEA 326


>gi|282854101|ref|ZP_06263438.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J139]
 gi|282583554|gb|EFB88934.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes J139]
          Length = 364

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 123/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 10  MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 68

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 69  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 128

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D     +   +  ++   SG   + +HAR                + 
Sbjct: 129 HGVPVTVKTRIGIDPD--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 178

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D + E+ K   D+ +  NG + + S A+ ++      GV +GR       +   + + 
Sbjct: 179 HWDAIGELVK-TVDVPVIGNGDIWEASDAMAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 237

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 238 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 291

Query: 293 CRHIL 297
            RH L
Sbjct: 292 TRHAL 296


>gi|290476760|ref|YP_003469671.1| tRNA-dihydrouridine synthase B [Xenorhabdus bovienii SS-2004]
 gi|289176104|emb|CBJ82909.1| tRNA-dihydrouridine synthase B [Xenorhabdus bovienii SS-2004]
          Length = 287

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 113/295 (38%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L      +    ++QI G+D  ++  AA+I    G   I++N+GC
Sbjct: 1   MLSSNPQVWKTDKSRLRMVHRDESGVRSVQIAGSDPDEMAAAARINVANGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  P++V   ++A+  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLRYPELVQAILSAVVNAVDVPVTLKIRTGWSPEERN--CVEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           ++ G+  + IH R         +        +YD +  +K+    + I  NG + D  +A
Sbjct: 119 ERCGIQALTIHGRT--------RSCLFNGEAEYDNIRTVKQ-TVAIPIIANGDITDPLKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V       +      
Sbjct: 170 RAVLEYTGADALMIGRAAQGRPWIFREIQHYLETGELLPPMPLGDVQHLMSEHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G  ++   +H+           + R        AS      +E  F 
Sbjct: 230 Y-----GQGKGVRIARKHVSWYLKEHAPDDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|184154699|ref|YP_001843039.1| hypothetical protein LAF_0223 [Lactobacillus fermentum IFO 3956]
 gi|227514339|ref|ZP_03944388.1| tRNA-dihydrouridine synthase [Lactobacillus fermentum ATCC 14931]
 gi|183226043|dbj|BAG26559.1| conserved hypothetical protein [Lactobacillus fermentum IFO 3956]
 gi|227087311|gb|EEI22623.1| tRNA-dihydrouridine synthase [Lactobacillus fermentum ATCC 14931]
          Length = 333

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 127/325 (39%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +       + +EMI    I+  +KK   ++G    E P+ LQI G  
Sbjct: 19  MAGVMNTAFRVICKKF-GAGYVVSEMISDRGIMYHNKKTLQMMGVDPVEHPMGLQIFGGT 77

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V++    + I++N+GCP  ++     G+  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEAAKFVDENTDADVIDINMGCPVNKIVNTEAGSRWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DDQ        L      +    +    RK + +G          + D+D
Sbjct: 138 PVTVKMRTGWDDQHIFAVENALAAQRAGAAAVAMHGRTRKQMYRG----------HADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG ++   +A  +L     D +MIGRAA  N  MLT    Y  N
Sbjct: 188 ILKEVASQLT-IPFMANGDIKTAEEAKYVLEYTGADAIMIGRAAMGNPWMLTQTVHYLEN 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                              ++                +++          G P + R + 
Sbjct: 247 GELLPEATPEEKITTAKEHLAR-----LVDLKGEYAGVREFRGQAAYYMKGIPRAARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L +EA        I +   +   E
Sbjct: 302 AL-MEATEQAQMDEIFDRFIDQYEE 325


>gi|222152337|ref|YP_002561512.1| tRNA-dihydrouridine synthase [Streptococcus uberis 0140J]
 gi|222113148|emb|CAR40571.1| putative tRNA-dihydrouridine synthase [Streptococcus uberis 0140J]
          Length = 325

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 131/323 (40%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   ++ +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVSEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRTVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +    ++     +++          G   + + R 
Sbjct: 252 GEELPD-LPFDKKLDIAEDHLRRLINLKGENIA----VREFRGLAPHYLRGTAGAAKIRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E+ F  +
Sbjct: 307 AVSRAETLAE-----VESIFAQV 324


>gi|300023200|ref|YP_003755811.1| hypothetical protein Hden_1683 [Hyphomicrobium denitrificans ATCC
           51888]
 gi|299525021|gb|ADJ23490.1| TIM-barrel protein, nifR3 family [Hyphomicrobium denitrificans ATCC
           51888]
          Length = 328

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 73/305 (23%), Positives = 125/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A  L     + +EMI ++ +++     +     +E  P  +Q+ G + 
Sbjct: 17  MSGVSDLPFRRLAHRL-GATFVVSEMIASEELVKSRADVLRRAEGRELTPFVMQLAGREE 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + + A+I E  G + I++N+GCP+  V     G+ LM N D     I A+ +A+++PV
Sbjct: 76  RWMADGARIAEAKGADVIDINMGCPAKEVTGKLSGSALMRNLDHAQSLIRAVVQAVNVPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+     A  +L +  +  GV  I +H R         +        D+  V
Sbjct: 136 TLKMRLGWDETSRNAA--DLARRAEAEGVKLITVHGRT--------RCQFFTGTADWQGV 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +  E   L + +NG +   S A K L     DGVM+GR AY    M   +   FS   
Sbjct: 186 RPVV-EATSLPVLVNGDINGPSDARKALDASGADGVMVGRGAYGAPWMPGRIAATFSTGR 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-----RR 292
               P +    +     + A +T Y          L+   +H+         +     + 
Sbjct: 245 DPGDPSRATQREIALEHVDAMLTHYGRE-----LGLKNARKHIGWYLLS-SGADTATVKA 298

Query: 293 CRHIL 297
            R  L
Sbjct: 299 WRARL 303


>gi|86357567|ref|YP_469459.1| tRNA-dihydrouridine synthase protein [Rhizobium etli CFN 42]
 gi|1171717|sp|P41504|DUS_RHILP RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|581522|emb|CAA50567.1| unnamed protein product [Rhizobium phaseoli]
 gi|86281669|gb|ABC90732.1| probable tRNA-dihydrouridine synthase protein [Rhizobium etli CFN
           42]
          Length = 317

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 123/293 (41%), Gaps = 27/293 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++         +P  +Q+ G + 
Sbjct: 12  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAESWSRLKAAGFRPHMVQLAGREA 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPV
Sbjct: 71  HWMAEAAKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPV 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++   ++ +  + SG+  + IH R  +               D+D +
Sbjct: 131 TLKMRLGWDE--NSINAPDIARRAEASGIQLVTIHGRTRM--------QFYEGRADWDAI 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG +E    A +IL     D VMIGR                +  L
Sbjct: 181 RAV-REVISVPLIANGDVETAHDAQEILRRSGADAVMIGRGCQGRPWH--------AGVL 231

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
            G++  +     D   +    M D+          ++   +H+      F  +
Sbjct: 232 AGAAEPRREDIADIAVEHYRMMLDFYGE----AVAIRHARKHLGWYLERFAPA 280


>gi|254458047|ref|ZP_05071474.1| tRNA-dihydrouridine synthase B [Campylobacterales bacterium GD 1]
 gi|207085440|gb|EDZ62725.1| tRNA-dihydrouridine synthase B [Campylobacterales bacterium GD 1]
          Length = 317

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 139/322 (43%), Gaps = 35/322 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EM+ ++A+  G  K   +L  ++ E P ++QI G+  
Sbjct: 18  AGFTDLPFRSVVKKF-GADLTVSEMLSSNALAHGSVKTLHMLQKASIEDPYSVQISGSQS 76

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +++ +  G + I+LN GCP  +V     G+ L+LN  ++G+ I  +    +  
Sbjct: 77  DMIRRAVEVLNEHDGIDIIDLNCGCPVPKVVGHGSGSSLLLNLPLMGEIIRTIKDTSNKS 136

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +        + K ++ SG + + +H R         +  +    +DYD
Sbjct: 137 LTSVKIRLGFEKK----NHIEIAKMVEDSGADFLAVHGRT--------RAGKFKAAVDYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + EIK E   + +  NG ++   +A  +L     DGVMIGR A     +   +      
Sbjct: 185 AIKEIK-EAVSIPVIANGDIDSYEKAKWVLEHTGADGVMIGRGAVGAPWIFHQLR----- 238

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG+  I   +  D   +    M ++   H      +    +H      G+  +   R+
Sbjct: 239 --TGTQEIDNNIKHDIIMEHFDKMIEFYGAH-----GVAMFRKHTHTYSKGYKGASALRN 291

Query: 296 ILTVEAGASTATHH-IIETAFN 316
             +V + +  + +  +I+  F 
Sbjct: 292 --SVNSISDISEYRAVIDDFFK 311


>gi|294142602|ref|YP_003558580.1| tRNA-dihydrouridine synthase B [Shewanella violacea DSS12]
 gi|293329071|dbj|BAJ03802.1| tRNA-dihydrouridine synthase B [Shewanella violacea DSS12]
          Length = 325

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 124/288 (43%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         A+  +EM+ ++  +    K+   +  + ++   ++QI GAD
Sbjct: 20  MAGVTDQAFRNLCVRY-GAAMAVSEMLSSNPDVWDTDKSRQRMSHAGEKGIRSVQIAGAD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ NP +V + + A+  A+ +P
Sbjct: 79  PELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQNPVLVKEILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  +  G+  + +H R         +      N +YD 
Sbjct: 139 VTLKIRTGWDPEHRNGV--QIAQIAEDCGIASLAVHGRT--------RQCMYKGNAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK N  + +  NG +    +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 189 IKAIKK-NISIPVIANGDIVTPEKARYVLDHTGVDALMIGRGAQGRPWIFREIQHYLDTG 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               +P++    +    +   ++ +    +      ++   +H+    
Sbjct: 248 -NKLAPVEMDEKRLVMLEHLKNLYELYGEY----KGIRFARKHVGWYL 290


>gi|220912142|ref|YP_002487451.1| hypothetical protein Achl_1372 [Arthrobacter chlorophenolicus A6]
 gi|219859020|gb|ACL39362.1| TIM-barrel protein, nifR3 family [Arthrobacter chlorophenolicus A6]
          Length = 392

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 60/316 (18%), Positives = 121/316 (38%), Gaps = 41/316 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EM+ + A++    +++  +     EK  ++Q+ G D
Sbjct: 33  MAGITNSAFRRLCREYGG-GMYVAEMVTSRALVERTPESLRIISHDDDEKVRSVQLYGVD 91

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKAL- 115
              +  A ++ VE+   + I+LN GCP  +V     G+ L    D+    +  A+ +A  
Sbjct: 92  AGTVGAAVRMLVEEDRADHIDLNFGCPVPKVTRRGGGSALPWKIDLFTAIVQTAVREASK 151

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +IP+T+K R G+DD    +   +  +  + SGV  + +H R A                
Sbjct: 152 GNIPLTIKMRKGIDDD--HLTYLDAGRIARDSGVAAVALHGRTA--------AQFYSGQA 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA-----------AYKNS 223
           D+  +  +++  PD+ +  NG +     A++++         R                 
Sbjct: 202 DWSAIARLREALPDIPVLGNGDIWSAEDAVRMV---------RETGVDGVVVGRGCQGRP 252

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +   F        P   +V +  +R     +  +       G  L++I +H+   
Sbjct: 253 WLFGDLQAAFEGSDVRHRPNLRQVAEGVYRHAELMVETFG----DEGKALREIRKHIAWY 308

Query: 284 FHGFPNSRRCRHILTV 299
           F G+      R  L +
Sbjct: 309 FKGYVVGGELRTRLAL 324


>gi|104773526|ref|YP_618506.1| putative tRNA-dihydrouridine synthase [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|103422607|emb|CAI97210.1| Putative tRNA-dihydrouridine synthase [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
          Length = 344

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 122/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      ++  EMI    I+ G+KK   +L     E P+++QI G  
Sbjct: 23  MAGVSNMAFRKVCKEF-GAGMVVCEMISDHGIIYGNKKTLSMLDVDPGEHPMSIQIFGGA 81

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L++AA+ ++     + I++N+GCP  +V +   G+  +L+ + +   I  +   +  
Sbjct: 82  EDSLLQAAQYIDQHTDADIIDINMGCPVPKVTKTDAGSKWLLDSNKIYQMIHKVVHNVEK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RIG D +   +       + +++G + + +H R         +        D++
Sbjct: 142 PVSVKMRIGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+ +   D+    NG +     A K L       VM+GRAA  N  +L  +  Y + 
Sbjct: 192 TLHEVAQ-VMDIPFVANGDITTPQLAKKALDEIGCTAVMVGRAALGNPWILKEMTHYLAT 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D   +       + +  +       G P S R R 
Sbjct: 251 GEELPKQSVREKVETAKHQL-----DGLVQLHGEKRAVPEFRQQAAYYLKGIPRSARTRA 305

Query: 296 ILTV 299
            +  
Sbjct: 306 KINE 309


>gi|251781585|ref|YP_002995886.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390213|dbj|BAH80672.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 354

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 53  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 111

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 112 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 171

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 172 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 220

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 221 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 280

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 281 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 335

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 336 AVSRAETLAE-----VEAIFETV 353


>gi|322410957|gb|EFY01865.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 325

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 67/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  TEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLAQVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFEC 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                    T+        I+        +       +++          G   + + R 
Sbjct: 252 GQELPDLPFTK-----KLDIAEEHLRRLIKLKGETIAVREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 AVSRAETLAE-----VEAIFAQV 324


>gi|116326862|ref|YP_796582.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116329809|ref|YP_799527.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116119606|gb|ABJ77649.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116123498|gb|ABJ74769.1| tRNA-dihydrouridine synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 318

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 72/291 (24%), Positives = 122/291 (41%), Gaps = 29/291 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D   R   R     A  YTE +  D ++    K   +  F  +E+P+  QI G  
Sbjct: 18  MAGISDSPTRRICRKF-GAAFSYTEFVNTDELVHKAPKAFKMFRFHPEERPITFQIFGNR 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EA +I+++   + I+LN+GC + +V     GA L+  P + G  I AM K ++IP
Sbjct: 77  LEIISEATEIIQELEPDIIDLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAMKKRVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D          + K +++SG++ + +H R         K+       D+D 
Sbjct: 137 VTAKIRIGWDATSRN--YLEVSKILEESGIDALTVHGRT--------KEMAYTGFADWDA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K  N  + I  NG ++   +A   +    +DGV+IGR A  N  + + V       
Sbjct: 187 IGEVK-VNRKIPIFGNGDIKSFQEANSKINKYSLDGVLIGRNAIGNPWIFSEVK------ 239

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                  K  +       I      +          L    +H++   +G 
Sbjct: 240 -------KEELSWSEISDIILQHARWMIEDYGEEFGLLLFRKHLVKYLNGL 283


>gi|257871359|ref|ZP_05651012.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
 gi|257805523|gb|EEV34345.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
          Length = 336

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 133/321 (41%), Gaps = 23/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G +
Sbjct: 22  MAGITNAAFRVTVKEF-GAGLVVCEMISDRGIQLRNKKTLEMLYIDETEHPLSLQIFGGN 80

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ V E+   + I++N+GCP  ++ +   GA  +L+PD V + + A+  A+  
Sbjct: 81  KESLVEAAQFVSENTAADIIDINMGCPVNKIIKAEAGAKWLLDPDKVYEMVHAVATAIDK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG DD+   +      ++ + +G   I +H R  +               ++ 
Sbjct: 141 PVTVKMRIGWDDE--HIFAVQNAQAAEAAGAAAIGMHGRTRV--------QMYEGAANWS 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+K+     F+G NG +     A ++L     D VMIGRAA  N  M+     Y   
Sbjct: 191 VLREVKQAISIPFMG-NGDVRTPEDAKRMLEEVGADAVMIGRAALGNPWMIHRTKHYLET 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P            +   + D     + S    ++  +H      G   + + + 
Sbjct: 250 GELIAEPTPREKIATAKLHL-ERLADLKGEFVAS----REFRQHAAYYLKGISRAAKVKA 304

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +        A   +++    
Sbjct: 305 AINQTENK-QAIIDLLDAFVE 324


>gi|255994138|ref|ZP_05427273.1| tRNA-dihydrouridine synthase [Eubacterium saphenum ATCC 49989]
 gi|255993806|gb|EEU03895.1| tRNA-dihydrouridine synthase [Eubacterium saphenum ATCC 49989]
          Length = 336

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/309 (21%), Positives = 127/309 (41%), Gaps = 19/309 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADI 59
             +TD   R  A       L+Y+EM+ A  ++    + + +L F   +  +A+QI G+D 
Sbjct: 23  AGFTDNAVRTIALEF-GAGLVYSEMVSAKGLIYEQKNTEELLDFRGADGFIAIQIFGSDP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +    + +E+ G   +++N+GCP  ++ +   GA LM  PDI+ D +    K    PV
Sbjct: 82  DAVAHGIQCIENKGNAIVDINMGCPMQKIVKSGSGAALMKRPDIIYDMVKDAVKITQKPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T K RIG D+    +   +  K+I+ +G + + +H R A  K           +++ D++
Sbjct: 142 TAKIRIGWDN--NNINAVDCAKAIESAGASAVAVHGRTAKQK--------YEGSVNRDVI 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+ +  + +  NG ++   +AL+ +     D VMIGR A     +  + +   S   
Sbjct: 192 ASVKQ-SVSIPVIGNGDIKSAKEALEFMDETGCDMVMIGRGAIGKPWIFKSCNMALSEIR 250

Query: 238 TGS---SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
            G       +     D        + D    +      L ++ + +          +  R
Sbjct: 251 KGKSIDEITEYEPCADEILNTLKKLIDLTVSYKGEKRALLELRKKLSKYLKNTSGVKDYR 310

Query: 295 HILTVEAGA 303
             L      
Sbjct: 311 KRLYEAGTK 319


>gi|254440340|ref|ZP_05053834.1| putative TIM-barrel protein, nifR3 family [Octadecabacter
           antarcticus 307]
 gi|198255786|gb|EDY80100.1| putative TIM-barrel protein, nifR3 family [Octadecabacter
           antarcticus 307]
          Length = 329

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 130/328 (39%), Gaps = 35/328 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
              TD  +R           + +EMI +  +++     +        +   A+Q+ G + 
Sbjct: 20  AGITDLPFRQLVASF-GAGWVVSEMIASQEMVQAKPGVREKAELGLSQASTAVQLAGREA 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+ V   G   I++N+GCP+ +V  G  G+ L+ + D     I A+  A+ IPV
Sbjct: 79  HWMAEAARHVAANGAAMIDINMGCPAKKVTSGYSGSALLRDLDHALTLIDAVVGAVDIPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD++   A   L    + +G+  I IH R         +      + +++ +
Sbjct: 139 TLKTRLGWDDRLLNAA--ELAIRAENAGIARIVIHGRT--------RCQFYKGHANWNAI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K     + +  NG + D   A   L     DGVMIGR A     +L  V    S  +
Sbjct: 189 AQVKNAV-SIPVIANGDIIDAVTAKTALNASGADGVMIGRGAQGRPWILRDVAAQLSGHV 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF---HGFPNSRRCR 294
             + P      +       A ++ Y    + S        +H+          PN R  R
Sbjct: 248 VPAPPQGNTFIRMVSDHYDAMLSFY-GSQMGSKVA----RKHLGWYMDQCDSEPNLR--R 300

Query: 295 HILTVEAGASTATHHIIETAFNLMIESL 322
            +LT             E  F L+ ++L
Sbjct: 301 AVLTERDP---------EQVFKLLPDAL 319


>gi|19745298|ref|NP_606434.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS8232]
 gi|306828200|ref|ZP_07461461.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes ATCC 10782]
 gi|19747397|gb|AAL96933.1| hypothetical protein spyM18_0122 [Streptococcus pyogenes MGAS8232]
 gi|304429578|gb|EFM32626.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes ATCC 10782]
          Length = 325

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 252 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 AVSRAETLAE-----VEAIFETV 324


>gi|71902768|ref|YP_279571.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS6180]
 gi|71801863|gb|AAX71216.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS6180]
          Length = 349

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 124/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 216 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 275

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 276 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 330

Query: 296 ILT 298
            ++
Sbjct: 331 AVS 333


>gi|94987736|ref|YP_595837.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS9429]
 gi|94991604|ref|YP_599703.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS2096]
 gi|94541244|gb|ABF31293.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS9429]
 gi|94545112|gb|ABF35159.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS2096]
          Length = 349

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 216 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 275

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 276 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 330

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 331 AVSRAETLAE-----VEAIFETV 348


>gi|152992909|ref|YP_001358630.1| tRNA-dihydrouridine synthase [Sulfurovum sp. NBC37-1]
 gi|151424770|dbj|BAF72273.1| tRNA-dihydrouridine synthase [Sulfurovum sp. NBC37-1]
          Length = 318

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 74/323 (22%), Positives = 139/323 (43%), Gaps = 34/323 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EMI ++A++   KK   +L  S +E P ++QI G+D+
Sbjct: 17  AGFTDLPFRSVVKKF-GVDLTVSEMISSNALVHNSKKTHKMLEKSPREDPYSIQIAGSDL 75

Query: 60  SKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +I+ E  G + I+LN GCP+ +V     G+ L+ +   +G  I  +    + P
Sbjct: 76  EVIRRAVEIINEQEGVSVIDLNCGCPAPKVVNNLQGSSLLTDLPQMGKVIETIKTHSNKP 135

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T +K R+G +++        + +  + SG + I +H R         +  R    +DYD
Sbjct: 136 YTSMKMRLGFNEK----NHVEIARIAEASGADYIAVHGRT--------RAGRYKAPVDYD 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + EIK E  ++ +  NG ++   +A  +L     DGVMIGRAA     +   + E  + 
Sbjct: 184 AIREIK-EAVNIPVIANGDIDSPEKAQWVLEHTGADGVMIGRAAVGKPWIFKQIKEGMAQ 242

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCR 294
           P        + + K+   +    M DY  ++           +++      G+  +   R
Sbjct: 243 PT-------SELIKEVVLEHFDQMIDYYDKY-----GAIIFRKNLHSYSKAGYQGASLFR 290

Query: 295 HILTVEAGASTATHHIIETAFNL 317
             +            ++E  F+ 
Sbjct: 291 DRVNRIED-PKEMREVVEEFFSQ 312


>gi|312863979|ref|ZP_07724215.1| TIM-barrel protein, nifR3 family [Streptococcus vestibularis F0396]
 gi|311100392|gb|EFQ58599.1| TIM-barrel protein, nifR3 family [Streptococcus vestibularis F0396]
          Length = 325

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 64/323 (19%), Positives = 127/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGYCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VM+GRA   N  + T ++ +F  
Sbjct: 192 TLARVAKAITKIPFIGNGDVRSVQDAKLMIEELGVDAVMVGRAVMNNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + D     +     +++          G   + + R 
Sbjct: 252 GEELPE-LPFDKKLDIAEDHLKRLVDLKGEKIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 EVSRAESVAQ-----VEEIFATL 324


>gi|217976714|ref|YP_002360861.1| TIM-barrel protein, nifR3 family [Methylocella silvestris BL2]
 gi|217502090|gb|ACK49499.1| TIM-barrel protein, nifR3 family [Methylocella silvestris BL2]
          Length = 327

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 75/322 (23%), Positives = 135/322 (41%), Gaps = 23/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A+     +L++TEM+ A+A  +GD +N L    +   P  +QI G D 
Sbjct: 17  MSGVTDIAMRRVAQRF-GASLVFTEMVAAEAYAKGDAENRLKAEGRGVDPHVVQIAGCDA 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  AA+I  D G   +++N+GCP+ +V  G  G+ LM +  +  D I A  +A+ IPV
Sbjct: 76  QSMARAARIAADSGAAILDINMGCPAKKVINGYSGSHLMRDLPLALDLIRATVRAVDIPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  +  G+  + +H R         +        D+  +
Sbjct: 136 TLKMRLGWDE--ASINAAELGRLAEAEGIAMLTVHGRT--------RSQFYNGKADWRAI 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG    ++ A +++     D VMIGRAA     ++  + E  +  +
Sbjct: 186 RAVK-EAVSIPVVANGDCASLADAARMMDVSGADAVMIGRAAIGQPWLVGMIAERLATGV 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCRH 295
            G+ P      +         +  +          ++   +H+       G P +   R 
Sbjct: 245 VGAEPSPAEKSEAAQEHYDGVLRLFGREQ-----GMRHARKHLAAYAERSGSPAAGALRA 299

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            L   A        I+   F+ 
Sbjct: 300 RLVT-ADDPETVRSILSELFDF 320


>gi|94993507|ref|YP_601605.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10750]
 gi|94547015|gb|ABF37061.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10750]
          Length = 349

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 130/323 (40%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 216 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 275

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  +      D  +     + +     +     +++          G   + + R 
Sbjct: 276 GQELAD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 330

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 331 AVSRAETLAE-----VEAIFETV 348


>gi|94989615|ref|YP_597715.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10270]
 gi|94543123|gb|ABF33171.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10270]
          Length = 349

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 130/323 (40%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 48  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 106

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 107 AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 166

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 167 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 215

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 216 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 275

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  +      D  +     + +     +     +++          G   + + R 
Sbjct: 276 GQELTD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 330

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 331 AVSRAETLAE-----VEAIFETV 348


>gi|313672939|ref|YP_004051050.1| dihydrouridine synthase dus [Calditerrivibrio nitroreducens DSM
           19672]
 gi|312939695|gb|ADR18887.1| dihydrouridine synthase DuS [Calditerrivibrio nitroreducens DSM
           19672]
          Length = 315

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 134/298 (44%), Gaps = 26/298 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              T+  +R   RL  N  L++TEM+  + + RG+K+ +  +   ++E P+ +Q+ G + 
Sbjct: 18  AGITNHPFRKLVRLFHN-GLIFTEMVSVEGVKRGNKQTLKLIDVRSEENPVGIQLFGGNP 76

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               EA K++ED F +   ++N+GCP  +V +   GA L+ +       I+A+ KA   P
Sbjct: 77  ESFSEAVKVIEDNFDFFCFDINMGCPVKKVLKSKAGAYLLTDLKTAVGIISAVRKATRKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + VK R+G D++   +  R ++K  +  GV+ + IH R         K       ++YD 
Sbjct: 137 LFVKTRLGWDEK--NLIYREILKICEGEGVDVLTIHGRT--------KSQLYSGKVNYDA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + E+K     + I  NG + D+   AL     VD +MIGR   K+  +   + +    P+
Sbjct: 187 IAEVK-SLSKIPIIGNGDVVDLKMFALMKNTGVDAIMIGRGMMKSPWIFKALMDN-KEPI 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFPNSRRCR 294
               P + R    F  +          +    G   L    ++ +    GF NS   R
Sbjct: 245 NYLKPEEIRYTLLFLLE--------EEKRFREGKYFLAPFKKYAVWFSKGFKNSSDFR 294


>gi|194334749|ref|YP_002016609.1| TIM-barrel protein, nifR3 family [Prosthecochloris aestuarii DSM
           271]
 gi|194312567|gb|ACF46962.1| TIM-barrel protein, nifR3 family [Prosthecochloris aestuarii DSM
           271]
          Length = 347

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 129/318 (40%), Gaps = 22/318 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M + TDR +R   +      ++YTE I A+AI R    ++  + F   E P+ +QI G  
Sbjct: 17  MEEVTDRSFRKICKRF-GADVVYTEFISAEAIRRQVDTSLRKMRFDDDEAPVVVQIFGNS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA I        I++N GCP+ +V     GA L+  PD +    AA+ +A+++P
Sbjct: 76  QEAMAEAAVIAASCSPAWIDINFGCPAKKVAGKGAGAALLKEPDKMVAIAAAVVRAVNLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D    ++ + ++V  ++  GV  + IH R         +        D++ 
Sbjct: 136 VTVKTRLGWDRD--SINIVDIVPRLEDVGVQALAIHGRT--------RSEMYRGVADWEW 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ ++   + +  NG +   + A  +      D VMIGR A  N  +     E     
Sbjct: 186 IRKVTEKA-RIPVIANGDIWSAADARAMFAETGADAVMIGRGAIGNPFIFAQARELLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P     D      ++      +           ++ RH      G P   R R  
Sbjct: 245 RVVTHP-----DYRDRIAVAVEHLKLSVEFKGEKYGSLEMRRHYSTYLKGLPRVSRVRDK 299

Query: 297 LTVEAGASTATHHIIETA 314
           L  E         I++  
Sbjct: 300 LVREPDWRNV-IEILQAY 316


>gi|320184072|gb|EFW58892.1| tRNA dihydrouridine synthase B [Shigella flexneri CDC 796-83]
          Length = 281

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 117/295 (39%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++ ++    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPLVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + +  NG + D  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V +     +      
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 YGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|225022204|ref|ZP_03711396.1| hypothetical protein CORMATOL_02238 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945137|gb|EEG26346.1| hypothetical protein CORMATOL_02238 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 384

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 124/337 (36%), Gaps = 36/337 (10%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R        T + L   EMI A A++ G++K   +  F   E P +L
Sbjct: 22  MAGVTNVAFRTLCREQELAKTGTVSGLYVCEMITARALVEGNEKTRHMTTFGPDEHPRSL 81

Query: 53  QIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC---I 108
           Q    D     +AA++V D    + I++N GCP  +V     G+ L     + G+     
Sbjct: 82  QFYTTDPEYTYKAARMVADNNLADHIDMNFGCPVPKVTRRGGGSALPYKRRLFGNIVAAA 141

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                   IP+TVK RIG+DD        +  +     G   + +HAR A          
Sbjct: 142 VKAVAGTDIPITVKFRIGIDDDHH--THLDAGRIAAAEGAAAVALHARTA--------AQ 191

Query: 169 RKIPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R     D+  +  +K+   D  + +  NG +   + A K++     DGV++GR       
Sbjct: 192 RYSGTADWSQITALKEHLADTGIPVLGNGDVFQATDAQKMMTETGCDGVVVGRGCLGRPW 251

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V     R  +  +T Y           + + +HM    
Sbjct: 252 LFAELSAALRGVDIPPEPTLGEVTGIILRH-AELLTHYDGE----DKACRDLRKHMGWYL 306

Query: 285 HGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            GFP     R  L+  A  + A    +  A     ES
Sbjct: 307 RGFPVGGPLRVQLS--AIKTLAD---LRAALEPWRES 338


>gi|110679975|ref|YP_682982.1| tRNA-dihydrouridine synthase [Roseobacter denitrificans OCh 114]
 gi|109456091|gb|ABG32296.1| tRNA-dihydrouridine synthase [Roseobacter denitrificans OCh 114]
          Length = 327

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/290 (24%), Positives = 125/290 (43%), Gaps = 25/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           M   TDR +R          L+ +EM+ +  IL       +K  LG S +    A+Q+ G
Sbjct: 19  MAGITDRPFRDLVASF-GAGLVVSEMVASADILNARPGTQEKAELGLSAEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     + A+ KA++
Sbjct: 76  REPGLMAEAARMVEGQGARIIDINMGCPAKKVTQGYSGSALMRTPDHAMTLVEAVVKAVN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT+K R+G DD +  +    + +  +++G+  + IH R         +      + D+
Sbjct: 136 IPVTLKTRLGWDDAM--LNAPQIARRAEEAGIRMLTIHGRT--------RCQFYKGHADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  +K     + +  NG +   + A++   L   DGVMIGR A     +L  +     
Sbjct: 186 AAIAGVK-SVVSIPVIANGDILCSATAMEALRLSGADGVMIGRGARGKPWLLAQIAHDVY 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  P+            +A +  Y          ++   +H+    
Sbjct: 245 GTPAPVVPMGGDFADMVRSHYAAMIRFY-----GHDLGVRVARKHLGWYM 289


>gi|298501698|ref|YP_003723638.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|298237293|gb|ADI68424.1| tRNA-dihydrouridine synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 311

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 119/262 (45%), Gaps = 17/262 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  +  PD +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKGPDKIYSIINKVQSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWAD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +Y++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLYKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFNQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISA 257
                        K  +  +  
Sbjct: 252 GEILPDLTFEDKMKIAYEHLKR 273


>gi|86750001|ref|YP_486497.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris HaA2]
 gi|86573029|gb|ABD07586.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodopseudomonas
           palustris HaA2]
          Length = 354

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 64/285 (22%), Positives = 116/285 (40%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST-QEKPLALQIGGADI 59
           M   TD  +R     L    L+ +EM  ++ +++G   ++       + P  +Q+ G + 
Sbjct: 38  MSGITDAPFRKQVAAL-GAGLVVSEMTASEDLVQGRAMSVRRCDAIDDGPHVVQLAGCEP 96

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 97  HWMAEAARIAEAGGADIIDINMGCPARHVTGGQSGSALMRDLDHALTLIEATIGAVRVPV 156

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+        L +  + +GV  + +H R         +        D+  V
Sbjct: 157 TLKMRLGWDDRSRNA--PELARRAEAAGVQLVTVHGRT--------RSQFYKGEADWRAV 206

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + + +NG +     A++ L     D VMIGR A     +   +       +
Sbjct: 207 RAV-RDAVGIPLVVNGDITSYQMAVEALDQSGADAVMIGRGAQGQPWLPGQIGRRLQTGI 265

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             + P  T             +  Y  R       L+   +H+  
Sbjct: 266 AEAMPSLTDQLAYLRALYDGVLGLYGERI-----GLRHARKHLGW 305


>gi|149914887|ref|ZP_01903416.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseobacter sp.
           AzwK-3b]
 gi|149811075|gb|EDM70912.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseobacter sp.
           AzwK-3b]
          Length = 323

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 118/293 (40%), Gaps = 29/293 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGGA 57
              TD  +R          L+ +EM+ +  +++       +  LGF  +    A+Q+ G 
Sbjct: 12  AGITDLPFRNLVSRF-GAGLVVSEMVASQEMVQAKPGVRERAELGFGIENT--AVQLAGR 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHE----GSFGACLMLNPDIVGDCIAAMCK 113
           +   + EAA+ V   G   I++N+GCP+ +V      G+ G+ LM + D     I A+  
Sbjct: 69  EAHWMAEAARKVAANGARIIDINMGCPAKKVTSASGTGASGSALMKDLDHALSLIEAVVG 128

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           A+ IPVT+K R+G DD++       L +  + +G+  I IH R         +       
Sbjct: 129 AVDIPVTLKTRLGWDDRLMNA--PELARRAEGAGIAMITIHGRT--------RCQFYKGR 178

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
            D+  +  +K +  ++ +  NG + D   A     L   DGVMIGR A     +L+ V  
Sbjct: 179 ADWAAIRAVK-DAVEIPVIANGDIVDAGSARDALRLSGGDGVMIGRGAQGRPWLLSQVAA 237

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             +      +P    +           +  Y     +     +   +HM    
Sbjct: 238 ELAGQPVPKAPEAGDLVDIVTGHYDEMLRFYGEELGN-----RVARKHMGWYL 285


>gi|323126378|gb|ADX23675.1| tRNA-dihydrouridine synthase [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 325

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 64/323 (19%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   A+       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADSSLAIEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 252 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 AVSRAETLAE-----VEAIFETV 324


>gi|170724871|ref|YP_001758897.1| NifR3 family TIM-barrel protein [Shewanella woodyi ATCC 51908]
 gi|169810218|gb|ACA84802.1| TIM-barrel protein, nifR3 family [Shewanella woodyi ATCC 51908]
          Length = 322

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/328 (19%), Positives = 127/328 (38%), Gaps = 29/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R         A+  +EM+ ++  +    K+      + ++   ++QI GAD
Sbjct: 17  MAGVTDQAFRNLCLRY-GAAMAVSEMLSSNPDVWDTDKSRQRMLHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V+    G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNRKLAGSALLQDPVQVKAILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGV--QIAQIAEDCGIAALAVHGRT--------RQCMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK N  + +  NG +    +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKK-NVSIPVVANGDITTPQKAQFVLEHTGVDALMIGRGAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF---HGFPNSRRC 293
              +        +     +    + Y          ++   +H+          P     
Sbjct: 245 NMLAPVEVDEKRQVMLEHLKNLYSLY-----GEYKGIRFARKHVGWYLDQDEQRPFRAEF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
             + TVE   S      +E  F+ + ++
Sbjct: 300 NRLETVEEQGSM-----VERYFDEIAQN 322


>gi|15674339|ref|NP_268513.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes M1 GAS]
 gi|21909631|ref|NP_663899.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS315]
 gi|28895009|ref|NP_801359.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes SSI-1]
 gi|71909918|ref|YP_281468.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS5005]
 gi|209558683|ref|YP_002285155.1| putative transcriptional regulator [Streptococcus pyogenes NZ131]
 gi|4033718|gb|AAC97155.1| unknown [Streptococcus pyogenes]
 gi|13621424|gb|AAK33234.1| possible transcriptional regulator [Streptococcus pyogenes M1 GAS]
 gi|21903813|gb|AAM78702.1| putative transcriptional regulator [Streptococcus pyogenes MGAS315]
 gi|28810254|dbj|BAC63192.1| putative transcriptional regulator [Streptococcus pyogenes SSI-1]
 gi|71852700|gb|AAZ50723.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS5005]
 gi|209539884|gb|ACI60460.1| putative transcriptional regulator [Streptococcus pyogenes NZ131]
          Length = 325

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 252 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 AVSRAETLAE-----VEAIFETV 324


>gi|32476561|ref|NP_869555.1| hypothetical protein RB10683 [Rhodopirellula baltica SH 1]
 gi|32447107|emb|CAD76923.1| conserved hypothetical protein-putative protein belonging to the
           NifR3 family [Rhodopirellula baltica SH 1]
          Length = 364

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 63/328 (19%), Positives = 124/328 (37%), Gaps = 27/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR------GDKKNILGFSTQEKPLALQI 54
           M  +T+  +R   R      LL TEM+ A   +            + G + + +PLA+QI
Sbjct: 35  MAGFTNAAFRHIVRQFGGAGLLATEMVNARGFVWLDENEAEHPDRLWGVADEPRPLAVQI 94

Query: 55  GGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC 112
              D   + +   ++ E++  + +++N GCP  +V E    G+ L+  P+ +   I+ + 
Sbjct: 95  WDNDPETMAKVGRRLAEEYRVSVVDINFGCPVRQVTEKAHSGSYLLREPNRMHAIISRLV 154

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           +     PVT K R+G   +   +    + + ++++G   + +H R A         +   
Sbjct: 155 QVCAPTPVTAKIRLGCSRE--NINCNEIARVVEEAGAAALTVHGRTA--------ADMFR 204

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            N D++ + EIK    ++ +  NG L+   + +       VD VMI RA      +    
Sbjct: 205 GNADWERISEIKSHLRNIPLIGNGDLDSAEKVVAAFDQYDVDAVMIARACLGRPWLFAQA 264

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                       P          +     +  +       G  L  + ++      G   
Sbjct: 265 AAALRGEPIPPEPTLPEQRDVMLKHYQLVVDRFGDE---KGTVL--MRKYACCYAQGKHG 319

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNL 317
           +R  R  +  +       H ++E  F L
Sbjct: 320 ARYFRTHVA-KVSTPEEFHSVVEEYFPL 346


>gi|50913499|ref|YP_059471.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10394]
 gi|50902573|gb|AAT86288.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes MGAS10394]
          Length = 325

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSVFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D+D
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHD 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     + +     +     +++          G   + + R 
Sbjct: 252 GQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 AVSRAETLAE-----VEAIFETV 324


>gi|219127844|ref|XP_002184137.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404368|gb|EEC44315.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 330

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 112/332 (33%), Positives = 160/332 (48%), Gaps = 38/332 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGAD 58
           M+++TDRH+R   RL++N  LLYTEM+ A+A+    K   L  G    E P  LQ+GG+D
Sbjct: 6   MMEYTDRHFRHLVRLVSNRTLLYTEMVAANALANERKNRYLAQGRVMPEGPSVLQLGGSD 65

Query: 59  ISKLVEAAKIVEDF------GYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAM 111
             ++ +AA+ V D        Y  INLN GCPS +V     FGA LM  P +V +   A+
Sbjct: 66  PEQMFQAAQTVLDMTARGHCDYTAINLNCGCPSPKVAGKGCFGAALMDEPQLVAELTKAL 125

Query: 112 CKALS--IPVTVKCRI--------------GVDDQIPAVALRNLVKSIKKSG-VNGIWIH 154
            +     +PVTVKCRI               +D +     LR+ ++++   G V    +H
Sbjct: 126 HEGTEGRLPVTVKCRIGTDSDQAFTRQAYAAIDPEQEYSKLRSFIETVASDGIVTDFSVH 185

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSV 210
           AR A+L+   SP DNRKIP L YDIV  + +E PD    LNGG+E +SQA       P +
Sbjct: 186 ARIAVLQKSFSPSDNRKIPPLKYDIVRRLVQEYPDFTFSLNGGVESISQAQAEFATSPGL 245

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
            GVMIGR+   +       D             +  + + F R             L   
Sbjct: 246 KGVMIGRSWAADPWSFAMADRLLYKDENAPR-NRLEILQAFGRHADR------EEELGDP 298

Query: 271 GKLQQ-ITRHMIGLFHGFPNSRRCRHILTVEA 301
            K+++ I + +  LF G  N++R R  L   A
Sbjct: 299 VKIRRFIVKAVTPLFTGEINAKRYRIALNEIA 330


>gi|62185558|ref|YP_220343.1| putative dihydrouridine synthase [Chlamydophila abortus S26/3]
 gi|62148625|emb|CAH64397.1| putative dihydrouridine synthase [Chlamydophila abortus S26/3]
          Length = 339

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/322 (20%), Positives = 138/322 (42%), Gaps = 23/322 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  YR  +      AL++ EM+  + +     + +  L +S   +P+  Q+ G+  
Sbjct: 22  AGFSDYPYRKMSSFYGPPALMFCEMVKVEGVHYSPARTLKLLEYSESMRPIGGQLCGSKP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAK++E  G++ I+LN GCP+ R+ +   G+ L+ +P+++G  +  + +A+S+PV
Sbjct: 82  EMVGEAAKVLEGLGFDLIDLNCGCPTDRITKDGSGSGLLKSPELIGKVLEKIVEAVSVPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ I+ +G + +++H R         +    +   + + +
Sbjct: 142 TVKIRSGWDG--SNINVEETVRIIRDAGASAVFVHGRT--------RAQGYVDPSNLEYI 191

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K     D  +  NG +     A  +L     DGV++ R       ++  ++ Y ++ 
Sbjct: 192 ARAKAAAGKDFPVFGNGDVFSPEAAKLMLDSTQCDGVLVARGTMGAPWIVRQIESYLTSG 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCRH 295
                    +V     ++       +   +  S  K    TR + G         R  R 
Sbjct: 252 TY------QKVLFSQRKQAFIQHLQWVEEYYQSEAKFLSETRKLCGHYLISASKVRFLRS 305

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            L+ +A +    + +IE     
Sbjct: 306 ALS-KATSVQEVYQLIEDYEEA 326


>gi|257439182|ref|ZP_05614937.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii A2-165]
 gi|257198315|gb|EEU96599.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii A2-165]
          Length = 340

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 110/239 (46%), Gaps = 16/239 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD   R             +EM+ + A++ GD K   +L       P  +QI G  
Sbjct: 56  MAGFTDAPARRLMAQ-HGAGFTVSEMVSSRALVYGDHKTVSLLKAEPNGAPYGVQIFGEV 114

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA  VE + ++ +++N+GCP+ ++  G  G+ LML+PD  G  +  + K  S P
Sbjct: 115 PEIMGQAAAAVEQYAFDFLDINMGCPAPKIVSGGAGSKLMLDPDRCGRIVEEVVKNTSRP 174

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D +   V      K+ +++G   I +HAR         ++    P +D  I
Sbjct: 175 VTVKMRKGWDAE--HVTAVECAKACEQAGAVLIAVHART--------REQMYTPGIDPSI 224

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K +   + +  NG +     A++++     DGVMI RAA  +  +   V+     
Sbjct: 225 IAAVK-DAVHVPVLGNGDIRTAEDAVRMVEETGCDGVMIARAALGDPWLFERVNAALEG 282


>gi|329115748|ref|ZP_08244465.1| TIM-barrel protein, nifR3 family [Streptococcus parauberis NCFD
           2020]
 gi|326906153|gb|EGE53067.1| TIM-barrel protein, nifR3 family [Streptococcus parauberis NCFD
           2020]
          Length = 325

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/310 (21%), Positives = 125/310 (40%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  L  AA  ++ +   + +++N+GCP  +V +   GA  + +P+ +   I  +   L I
Sbjct: 83  IEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYQIIKEVTAVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G +D   AV       + + +GV  + +H R         +        D++
Sbjct: 143 PLTVKMRTGWNDSSLAVEN---ALAAESAGVAALAMHGRT--------RKQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG + ++  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITTIPFIGNGDVRNVQDAKFMIEEIGVDAVMIGRAAMSNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                    T+        I+                +++          G   + + R 
Sbjct: 252 GQELPDLPFTK-----KLDIAEDHLTRLVSLKGEMIAVREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGAST 305
           +++     S 
Sbjct: 307 VVSRAETLSE 316


>gi|327543426|gb|EGF29850.1| TIM-barrel protein, nifR3 family [Rhodopirellula baltica WH47]
          Length = 358

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 63/328 (19%), Positives = 123/328 (37%), Gaps = 27/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR------GDKKNILGFSTQEKPLALQI 54
           M  +T+  +R   R      LL TEM+ A   +            + G + + +PLA+QI
Sbjct: 29  MAGFTNAAFRHIVRQFGGAGLLATEMVNARGFVWLDENEAEHPDRLWGVADEPRPLAVQI 88

Query: 55  GGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC 112
              D   + +   ++ E++  + +++N GCP  +V E    G+ L+  P+ +   I+ + 
Sbjct: 89  WDNDPETMAKVGRRLAEEYRVSVVDINFGCPVRQVTEKAHSGSYLLREPNRMHAIISRLV 148

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           +     PVT K R+G       +    + + ++++G   + +H R A         +   
Sbjct: 149 QVCAPTPVTAKIRLGC--SRDNINCNEIARVVEEAGAAALTVHGRTA--------ADMFR 198

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            N D++ + EIK    ++ +  NG L+   + +       VD VMI RA      +    
Sbjct: 199 GNADWERISEIKSHLRNIPLIGNGDLDSAEKVVAAFDQYDVDAVMIARACLGRPWLFAQA 258

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                       P          +     +  +       G  L  + ++      G   
Sbjct: 259 AAALRGEPIPPEPTLPEQRDVMLKHYQLVVDRFGDE---KGTVL--MRKYACCYAQGKHG 313

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNL 317
           +R  R  +  +       H ++E  F L
Sbjct: 314 ARYFRTHVA-KVSTPEEFHSVVEEYFPL 340


>gi|149919781|ref|ZP_01908258.1| hypothetical protein PPSIR1_32512 [Plesiocystis pacifica SIR-1]
 gi|149819388|gb|EDM78819.1| hypothetical protein PPSIR1_32512 [Plesiocystis pacifica SIR-1]
          Length = 406

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 122/322 (37%), Gaps = 36/322 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNAL------------LYTEMIVADAILRGDKK--NILGFSTQ 46
           M   TD  +R   R      L              +EMI A  ++ G++K   +  F   
Sbjct: 29  MAGVTDYPFRALCRRFAREGLESAGSSAAIPGLFVSEMITARPLVEGNQKTARLASFGPD 88

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P +LQ+ G D   +  A + +   G    I++N GCP  ++     G+ +   P ++ 
Sbjct: 89  EAPRSLQLYGVDPFFVRAAVERLVGEGRVEHIDMNFGCPVPKITRRGGGSAIPAKPRLLA 148

Query: 106 DCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             +AA  +     +PVT+K R G+DD++  +  R+  +  ++ G   + +HAR AI    
Sbjct: 149 RIVAAAVEGARGQVPVTIKFRKGIDDRL--ITFRDAGRVAQEEGCAAVGLHARTAIEFYE 206

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                      D+  + E+  +   + +  NG + +   A +++      GV+IGR    
Sbjct: 207 DG--------ADWSCIAELVDQL-SIPVFGNGDIWEAEDAARMMAQTGCAGVIIGRGCLG 257

Query: 222 NSAMLTTVDEYFSN----PLTGSSPIKTRVDKDFWRKISAS--MTDYAARHLHSGGKLQQ 275
              +   +   FS     P     P    V +       A      +   +      L+ 
Sbjct: 258 RPWLFAELARLFSGRPIYPDARCGPTFAEVAQIMVEHARAMVDWDTHRGGYHGEANCLRA 317

Query: 276 ITRHMIGLFHGFPNSRRCRHIL 297
             +H      GF  S + R  L
Sbjct: 318 FRKHASWYTKGFRGSTQLRERL 339


>gi|290579684|ref|YP_003484076.1| hypothetical protein SmuNN2025_0158 [Streptococcus mutans NN2025]
 gi|254996583|dbj|BAH87184.1| hypothetical protein [Streptococcus mutans NN2025]
          Length = 325

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 131/323 (40%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++     + +++N+GCP  ++ +   GA  + +P+ +   I+++   L+I
Sbjct: 83  GDSLARAAEFIQANTKTDLVDINMGCPVNKIVKNEAGAMWLKDPEKIYSVISSVKSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV  + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDASLAVEN---ALAAESAGVAALAMHGRT--------REQMYTGSCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++     D VMIGRAA  N  + T ++ YF  
Sbjct: 192 TLAKVAKAITKVPFIANGDIRSVEDAQFMIDQVGADAVMIGRAARSNPYIFTQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  I   +      +I+                +++          G   + + R 
Sbjct: 252 GE-----ILDNLPFAKMLEIAQDHLRRLVDLKGEKIAVREFRGLAPYYLRGTSGAAKIRS 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++        T   +E  F  +
Sbjct: 307 AVS-----RAETISEVENIFAQI 324


>gi|157960219|ref|YP_001500253.1| nifR3 family TIM-barrel protein [Shewanella pealeana ATCC 700345]
 gi|157845219|gb|ABV85718.1| putative TIM-barrel protein, nifR3 family [Shewanella pealeana ATCC
           700345]
          Length = 322

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 68/326 (20%), Positives = 130/326 (39%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+ L    + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLCLRY-GAALAVSEMLSSNPDVWDTDKSRLRMTHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQDPVQVEAILRAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGVH--IAQIAEDCGIASLAVHGRT--------RQCMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK+   + +  NG +    +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKKQI-SIPVVANGDILTPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF---HGFPNSRRC 293
              +      V+ D  R++                 ++   +H+       +  P     
Sbjct: 245 NKLAP-----VEMDEKRQVMLEHLKLLYNLYGDYKGIRFARKHVGWYLDQENQRPFRAEF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
             + TVE   S      +E  F+  +
Sbjct: 300 NRLETVEEQCSM-----VERYFDEFV 320


>gi|126736292|ref|ZP_01752034.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. CCS2]
 gi|126714113|gb|EBA10982.1| tRNA-dihydrouridine synthase, putative [Roseobacter sp. CCS2]
          Length = 333

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 128/320 (40%), Gaps = 22/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
              TD  +R           + +EM+ +  +++     +        +   A+QI G + 
Sbjct: 28  AGITDLPFRQLVASF-GAGWVVSEMVASQEMVQAKPGVRERAELGYDQAGTAVQIAGRET 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++    G   I++N+GCP+ +V  G  G+ L+  PD     + A+  A+ +PV
Sbjct: 87  YWMAEAARMAAGNGAAIIDINMGCPAKKVTNGYSGSALLRTPDHALRLMEAVVNAVDVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD   ++   N+ K  + +G+  + IH R         +        D+  +
Sbjct: 147 TLKTRLGWDDD--SLNAANVAKRAEDAGIRLVTIHGRT--------RCQFYKGAADWAAI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           ++IK E   + +  NG + D   A     L   DGVMIGR A     +L  V        
Sbjct: 197 HKIK-EAVSIPVIANGDIVDAGTARNALRLSGADGVMIGRGAQGRPWVLAQVAAALHGTP 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P    + +   +   A ++ Y       G K+    +H+         +   R  +
Sbjct: 256 QPQIPQGHALIEVVCKHYEAMLSFYGD---ALGRKVS--RKHLGWYMDDAGTAPALRKAI 310

Query: 298 TVEAGASTATHHIIETAFNL 317
              A  +   H + E A N+
Sbjct: 311 LTHANPADVLHDLPE-ALNM 329


>gi|307321967|ref|ZP_07601348.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti AK83]
 gi|306892391|gb|EFN23196.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti AK83]
          Length = 342

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 118/287 (41%), Gaps = 26/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A        + TEM+ +  ++    ++          P  +Q+ G + 
Sbjct: 33  MSGVTDLPFRMLAWRF-GAGFVVTEMVASRELVGNAAESWARLKNSGIDPHIVQLAGREA 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+IVE  G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA +IPV
Sbjct: 92  HWMAEAARIVEANGADIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVKAATIPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+      L  + +  +++GV  I IH R  +               D+D +
Sbjct: 152 TLKMRLGWDENSINAPL--IARRAEEAGVKAITIHGRTRM--------QFYNGKADWDAI 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG ++ ++ A +IL     D VM+GR+                   
Sbjct: 202 RAV-REVVSIPLIANGDVDSVADAHEILRRSGADAVMVGRSCQGRPW------HAGVLAD 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             + P  + V + F       +  Y          L+   +H     
Sbjct: 255 AAAHPDASGVARIFAEHYEMMLEFYGVE-----VGLRTARKHAGWYL 296


>gi|314932010|gb|EFS95841.1| TIM-barrel protein, nifR3 family [Propionibacterium acnes HL067PA1]
          Length = 355

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 123/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R          L   EMI +  ++ GD K   +L F+  E   ++Q+ G D
Sbjct: 1   MAGVTNAAFRQLCAE-QGAGLYVCEMITSRGLVYGDHKTHGMLAFAECEDVRSVQLYGVD 59

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KA 114
              + EA  I+ E +G N ++LN GCP  +V     G  L    D     ++A      A
Sbjct: 60  PGMVGEATSILCEKYGVNHVDLNFGCPVPKVTRKGGGGVLPWKLDRFAAVVSAAVQAGDA 119

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK RIG+D +   +   +  ++   SG   + +HAR                + 
Sbjct: 120 HGVPVTVKTRIGIDPE--HITYIDSARAAVDSGAAAVCLHART--------VAEAYAGHS 169

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +D   E+ K   D+ +  NG + + S A  ++      GV +GR       +   + + 
Sbjct: 170 HWDATGELVK-TVDVPVIGNGDIWEASDATAMVGQTGCAGVEVGRGCLGRPWLFRDLADA 228

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F+   T + P    V     R+ +  +  Y   H      L  + +HM     GFP    
Sbjct: 229 FAGRDTTTLPTLGEVCAMI-RRHAELLVKYQGMH-----GLVDMRKHMAWYLKGFPVGGE 282

Query: 293 CRHIL 297
            RH+L
Sbjct: 283 TRHVL 287


>gi|313891107|ref|ZP_07824726.1| TIM-barrel protein, nifR3 family [Streptococcus pseudoporcinus SPIN
           20026]
 gi|313120470|gb|EFR43590.1| TIM-barrel protein, nifR3 family [Streptococcus pseudoporcinus SPIN
           20026]
          Length = 325

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 124/304 (40%), Gaps = 24/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     + +++N+GCP  +V +   GA  + +PD +   ++ +   L I
Sbjct: 83  AEGLKRAADFIQTKTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVSQVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV  + +H R         ++       D+D
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVAALAMHGRT--------REQMYTGRCDHD 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKALTKIPFIGNGDVRTVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSS-PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P   ++D      I+        +       +++          G   + + R
Sbjct: 252 GDILPDLPFAKKLD------IAEDHLTRLIKLKGETIAVREFRGLAPHYLRGTAGAAKVR 305

Query: 295 HILT 298
             ++
Sbjct: 306 GAVS 309


>gi|256852018|ref|ZP_05557405.1| transcriptional regulator [Lactobacillus jensenii 27-2-CHN]
 gi|260661413|ref|ZP_05862326.1| transcriptional regulator [Lactobacillus jensenii 115-3-CHN]
 gi|282933690|ref|ZP_06339048.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
 gi|297205110|ref|ZP_06922506.1| tRNA-dihydrouridine synthase [Lactobacillus jensenii JV-V16]
 gi|256615430|gb|EEU20620.1| transcriptional regulator [Lactobacillus jensenii 27-2-CHN]
 gi|260547868|gb|EEX23845.1| transcriptional regulator [Lactobacillus jensenii 115-3-CHN]
 gi|281302180|gb|EFA94424.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
 gi|297149688|gb|EFH29985.1| tRNA-dihydrouridine synthase [Lactobacillus jensenii JV-V16]
          Length = 342

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 122/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L  +  E P+++QI G  
Sbjct: 23  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLDMLQVAPGEHPMSIQIFGGT 81

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+EAA+ ++     + I++N+GCP  +V +   G+  +L+ + +   +  + + +  
Sbjct: 82  EDTLLEAAQYIDQHTAADIIDINMGCPVPKVTKTDAGSKWLLDANKIYQMVHKVVQNVEK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R+G D +   +       + +++G + + +H R         +        D++
Sbjct: 142 PVSVKMRLGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+       F+G NG +     A K++  V    VMIGRAA  N   +  +  Y   
Sbjct: 192 TLHEVANALTIPFVG-NGDITSPELAKKMIDEVGATAVMIGRAALGNPWEIKDMVHYLET 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    ++     D           + +  +       G P S R R 
Sbjct: 251 GEKLRPQTVREKIETAKHQL-----DGLVELKGEKVAVPEFRQQAAYYLKGIPRSARTRA 305

Query: 296 ILTV 299
            +  
Sbjct: 306 KINE 309


>gi|24378701|ref|NP_720656.1| hypothetical protein SMU.187c [Streptococcus mutans UA159]
 gi|24376565|gb|AAN57962.1|AE014869_7 conserved hypothetical protein [Streptococcus mutans UA159]
          Length = 325

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 126/303 (41%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ ++     + +++N+GCP  ++ +   GA  + +P+ +   I+++   L+I
Sbjct: 83  GDSLARAAEFIQANTKTDLVDINMGCPVNKIVKNEAGAMWLKDPEKIYSVISSVKSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV  + +H R         ++     + D++
Sbjct: 143 PLTVKMRTGWSDASLAVEN---ALAAESAGVAALAMHGRT--------REQMYTGSCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++     D VMIGRAA  N  + T ++ YF  
Sbjct: 192 TLAKVAKAITKVPFIANGDIRSVEDAQFMIDQVGADAVMIGRAARSNPYIFTQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  I   +      +I+                +++          G   + + R 
Sbjct: 252 GE-----ILDNLPFAKMLEIAQDHLRRLVDLKGEKIAVREFRGLAPYYLRGTSGAAKIRS 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|77408418|ref|ZP_00785157.1| NifR3/Smm1 family protein [Streptococcus agalactiae COH1]
 gi|77172941|gb|EAO76071.1| NifR3/Smm1 family protein [Streptococcus agalactiae COH1]
          Length = 325

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 122/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  +++    + +++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQNNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++     D +M+GR A  N  + T ++ +F  
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +     +     +++          G   + + R 
Sbjct: 252 GEILPD-LPFEKMLDVAEDHLTRLVNLKGETIA----VREFRGLAPHYLRGKSGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|167625806|ref|YP_001676100.1| nifR3 family TIM-barrel protein [Shewanella halifaxensis HAW-EB4]
 gi|167355828|gb|ABZ78441.1| putative TIM-barrel protein, nifR3 family [Shewanella halifaxensis
           HAW-EB4]
          Length = 322

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 67/326 (20%), Positives = 129/326 (39%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R         AL  +EM+ ++  +    K+ L    + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLCLRY-GAALAVSEMLSSNPDVWDTDKSRLRMTHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQDPAQVEAILRAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGVH--IAQIAEDCGIASLAVHGRT--------RQCMYKGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK+   + +  NG +    +A  +L    VD +MIGR A     +   +  Y    
Sbjct: 186 IKAIKKQI-SIPVVANGDILTPEKARFVLDYTGVDALMIGRGAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSR-RC 293
              +      V+ D  R++                 ++   +H+            R   
Sbjct: 245 NKLAP-----VEMDEKRQVMLEHLKLLYNLYGDYKGIRFARKHVGWYLDQESQRAFRSEF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
             + TVE   S      +E  F+  +
Sbjct: 300 NRLETVEEQCSM-----VERYFDEFV 320


>gi|238855045|ref|ZP_04645373.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 269-3]
 gi|260664829|ref|ZP_05865680.1| transcriptional regulator [Lactobacillus jensenii SJ-7A-US]
 gi|282934831|ref|ZP_06340065.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
 gi|313472617|ref|ZP_07813106.1| zinc-binding TIM-barrel protein [Lactobacillus jensenii 1153]
 gi|238832289|gb|EEQ24598.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 269-3]
 gi|239529432|gb|EEQ68433.1| zinc-binding TIM-barrel protein [Lactobacillus jensenii 1153]
 gi|260561312|gb|EEX27285.1| transcriptional regulator [Lactobacillus jensenii SJ-7A-US]
 gi|281301103|gb|EFA93413.1| tRNA-dihydrouridine synthase B [Lactobacillus jensenii 208-1]
          Length = 342

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 122/304 (40%), Gaps = 22/304 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I+  +KK   +L  +  E P+++QI G  
Sbjct: 23  MAGVSNSAFRVVCKEF-GAGLVVCEMISDHGIIYRNKKTLDMLQVAPNEHPMSIQIFGGT 81

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+EAA+ ++     + I++N+GCP  +V +   G+  +L+ + +   +  + + +  
Sbjct: 82  EDTLLEAAQYIDQNTAADIIDINMGCPVPKVTKTDAGSKWLLDANKIYQMVHKVVQNVEK 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R+G D +   +       + +++G + + +H R         +        D++
Sbjct: 142 PVSVKMRLGWDRK--HIFAVENALAAQEAGASMLAMHGRT--------RKQMYQGEADWE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSN 235
            ++E+       F+G NG +     A K++  V    VMIGRAA  N   +  +  Y   
Sbjct: 192 TLHEVANALTIPFVG-NGDITSPELAKKMIDEVGATAVMIGRAALGNPWEIKDMVHYLET 250

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +    +++                + +  +       G P S R R 
Sbjct: 251 GEKLRPQTVREKIETAKHQLNG-----LVELKGEKVAVPEFRQQAAYYLKGIPRSARTRA 305

Query: 296 ILTV 299
            +  
Sbjct: 306 KINE 309


>gi|257063743|ref|YP_003143415.1| putative TIM-barrel protein, nifR3 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256791396|gb|ACV22066.1| putative TIM-barrel protein, nifR3 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 341

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 123/305 (40%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M    D  YR     +    L +TEM+ + A+   ++K   +L  +  E  + +Q+ G +
Sbjct: 21  MAGVNDVMYRSICVEM-GADLTFTEMVSSKALSFANEKTRRLLDTAPNELHVGVQLFGHE 79

Query: 59  ISKLVEAAKIVED---FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              +   A  VED        I++N+GCP+ ++ +   G+ L+  PD+    +  +   +
Sbjct: 80  PDTMAREAAWVEDSLGEKLVCIDVNMGCPARKIIKKGDGSALLNTPDVAQQIVRQIKSQV 139

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S PVTVK R G           +  K ++ +G + + +H R                + D
Sbjct: 140 SCPVTVKFRKGFAAGEDVA--CDFAKRMEDAGADWMTVHGRTT--------AQMYSGDAD 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +D++  +K+ +  + +  NG ++    A  ++    VDGVMI R A  N  +        
Sbjct: 190 WDVLGRVKR-SVSVPVIGNGDIKRGEDARAMVDATGVDGVMIARGAQGNPWIFPEAAAAL 248

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P          R   ASM D      + G  +  + +H++    G P  R  
Sbjct: 249 AGEPAPAEPTDEERVAMARRH--ASMLD-----GYMGNTIVYMRKHVMWYLRGVPGVREA 301

Query: 294 RHILT 298
           R  L 
Sbjct: 302 RGALN 306


>gi|223937326|ref|ZP_03629232.1| TIM-barrel protein, nifR3 family [bacterium Ellin514]
 gi|223894111|gb|EEF60566.1| TIM-barrel protein, nifR3 family [bacterium Ellin514]
          Length = 369

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 59/319 (18%), Positives = 124/319 (38%), Gaps = 20/319 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             +T+  +R   R +    L  T+++ A ++L  + K   ++  +  ++PLA+Q+ G+  
Sbjct: 19  AGYTNLPFRLALREVGGLDLATTDLVNARSLLEKNPKAFKLIETNAADRPLAVQLFGSVP 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++ +AA  +E  G + I++N+GCP  +V +   G+ +M   D     +  M  A+ IPV
Sbjct: 79  EEMRDAAVFLESIGISSIDINMGCPVRKVCKVGGGSAMMTELDKTSALVKGMVDAVKIPV 138

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T K R+G DD    +   +L ++++  G+  I++H R         ++      +    +
Sbjct: 139 TAKMRLGWDDD--NLTAPDLARALEDVGITAIFVHGRT--------REQGFSGTVKLHGI 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +    + +  NG +     A  +       GV IGR A+ N  +      Y     
Sbjct: 189 RAVVQAVKSIPVIGNGDVTTPEAARMMFDETGCAGVSIGRGAFYNPWIFAHTQHYIKTGE 248

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +   R +     D            +   +        F  +      +
Sbjct: 249 LLPEPAFEERVRVMCRHL-----DLMVEVFGEPLGCRMFRKVAPWYSKRFGPANEFNKKV 303

Query: 298 TVEAGASTATHHIIETAFN 316
            + +  +   H I++    
Sbjct: 304 VLVSTRAE-FHDILDRYIK 321


>gi|331694352|ref|YP_004330591.1| TIM-barrel protein, nifR3 family [Pseudonocardia dioxanivorans
           CB1190]
 gi|326949041|gb|AEA22738.1| TIM-barrel protein, nifR3 family [Pseudonocardia dioxanivorans
           CB1190]
          Length = 391

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 121/306 (39%), Gaps = 23/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R          EMI +  ++  +   + ++ F   E P ++Q+ G D
Sbjct: 39  MAGITNPGFRRLCRE-QGAGYYVCEMITSRGLVERNPLTRRMIAFDADEHPRSMQLYGVD 97

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALS 116
            + +  A +IV +    + ++ N GCP  +V     GA L     +    + A    A  
Sbjct: 98  PATIGAAVRIVAEEDLADHLDFNFGCPVPKVTRRGGGAALPYKRRLFERIVRAAVDNAGG 157

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT+K R+G+DD+       ++ +     GV  I +HAR A          R     D+
Sbjct: 158 IPVTIKMRVGIDDEHH--TFLDVARIAADCGVAAITLHARTA--------AQRYSGTADW 207

Query: 177 DIVYEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +  ++   P +L +  NG +   + AL ++     DGV++GR       +   ++  F
Sbjct: 208 STIARLRDAMPAELPVLGNGDVFSAADALAMVARTGCDGVVVGRGVLGRPWLFADLEAAF 267

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +     + P   +V     R            H+     ++ + +H+     GFP     
Sbjct: 268 AGRPLPTPPRLGQVAATLRRHAVL-----LCEHMGDHKGIRDVRKHIAWYLKGFPVGPEV 322

Query: 294 RHILTV 299
           R  L +
Sbjct: 323 RRRLGM 328


>gi|15642871|ref|NP_227912.1| hypothetical protein TM0096 [Thermotoga maritima MSB8]
 gi|4980586|gb|AAD35190.1|AE001696_4 conserved hypothetical protein [Thermotoga maritima MSB8]
          Length = 306

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/325 (19%), Positives = 132/325 (40%), Gaps = 31/325 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M  +TD  +R  A         ++EM+ A   L   +K   L     E+ +A+QI G++ 
Sbjct: 10  MAGYTDSAFRTLAFEW-GADFAFSEMVSAKGFLMNSQKTEELLPQPHERNVAVQIFGSEP 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   
Sbjct: 69  NELSEAARILSE-KYKWIDLNAGCPVRKVVKKGAGGALLKDLRHFRYIVRELRKSVSGKF 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +       +  + + + + GV+ ++IH R  +       + + +  L+    
Sbjct: 128 SVKTRLGWEKN----EVEEIYRILVEEGVDEVFIHTRTVVQSFTGRAEWKALSVLE---- 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                    +   ++G +     A + L     DG+++ R A     +   + ++  +  
Sbjct: 180 -------KRIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAIGRPWIFKQIKDFLRSGK 232

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             S P +  + + F R +     +   +       + ++ + + G       +RR R   
Sbjct: 233 Y-SEPSREEILRTFERHL-----ELLIKTKGERKAVVEMRKFLAGYTKDLKGARRFR--- 283

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
             E         I++  F   I+ +
Sbjct: 284 --EKVMKIEEVQILKEMFYNFIKEV 306


>gi|126642530|ref|YP_001085514.1| NifR3 family protein [Acinetobacter baumannii ATCC 17978]
          Length = 301

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 69/299 (23%), Positives = 134/299 (44%), Gaps = 23/299 (7%)

Query: 26  MIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ AD  LR  KK++    F  +  P++ QI G+D  +L EAA+     G   +++N+GC
Sbjct: 1   MMTADKTLRMTKKSLYRANFDGELAPISAQIAGSDPEQLAEAARYQVANGAQIVDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V     G+ L+ + D+V   + A+  A+ +PVT+K R+G  +      +  + K  
Sbjct: 61  PAKKVCNKLAGSALLQDEDLVARILDAVVAAVDVPVTLKTRLGFLNGQ--ENILRVAKRA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +++G+  + +H R         +++  +    Y+++  +K E   + +  NG ++   +A
Sbjct: 119 EEAGIAALALHGRT--------REDMYLNTARYELIKHVK-ELIHIPVIANGDIDSPEKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y       ++P    V +     +S     
Sbjct: 170 KYVLDYTGADAIMIGRAAQGRPWIFREIAHYLKTGEHLAAPNIEEVKEVLLGHLSELYQF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH-ILTVEAGASTATHHIIETAFNLMI 319
           Y           +   +H+     G  +S   R  +  VE  A  A   ++E+ FN ++
Sbjct: 230 Y-----GEYSGCRIARKHIAWYTKGLRSSNEFRQNMYKVETTAEQAL--VVESYFNQLL 281


>gi|161529033|ref|YP_001582859.1| nifR3 family TIM-barrel protein [Nitrosopumilus maritimus SCM1]
 gi|160340334|gb|ABX13421.1| putative TIM-barrel protein, nifR3 family [Nitrosopumilus maritimus
           SCM1]
          Length = 320

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 131/309 (42%), Gaps = 32/309 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL------RGDKKNI---LGFSTQEKPLA 51
           M   +D   R   + +    L+ TE     +I+      + + K I   + FS QE+P++
Sbjct: 14  MAGVSDPALRLQCKKM-GAGLVVTEFTSIHSIIAKEEQLKENMKTIQEFIEFSEQERPIS 72

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D+  L +AA IVE + ++ I+ N+GCP+  + +   G  L+   ++       +
Sbjct: 73  VQLFGSDLYALEKAATIVEPY-FDIIDYNMGCPAPHITQQMAGGALLQEVNLTQQIFETL 131

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A+  PVT+K R GV D       R++ +  +  G+  I  H R  + +G S       
Sbjct: 132 VNAVKKPVTLKIRSGVTD-ASKFLFRDIAEIAEDQGIQMITFHPRT-VSQGYS------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            + D+ ++ E+K E  ++ +  NG +     A  +L     D VMIGR A  N  +   +
Sbjct: 183 GSADWKLIKELK-EISNIPVVGNGDITTPEDAKMMLDETGCDYVMIGRGAMGNPFLFEQI 241

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           ++Y           K R+D  F          Y  +   S  K Q +         G   
Sbjct: 242 NDYLKTGSYKEYSFKDRLDSFF--DYLHLTNQYKIK--FSNIKSQAMR-----FTKGLKG 292

Query: 290 SRRCRHILT 298
             + R  +T
Sbjct: 293 GSKLRSKIT 301


>gi|315222400|ref|ZP_07864305.1| TIM-barrel protein, nifR3 family [Streptococcus anginosus F0211]
 gi|315188561|gb|EFU22271.1| TIM-barrel protein, nifR3 family [Streptococcus anginosus F0211]
          Length = 323

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/317 (19%), Positives = 131/317 (41%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTQTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYSIINKVRSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV  + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWADASLAVENA---LAAEAAGVAALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++ + +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHNVAQALTKIPFIANGDIRTVQDAQQRIEEVGADAVMIGRAAMGNPYLFHQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +  +  +   + D    H+     +++          G   + + R 
Sbjct: 252 GEILPDLSFEDKMQVAYDHLKR-LIDLKGEHIA----IREFRGLAPHYLRGTAGAAKLRG 306

Query: 296 ILTVEAGASTATHHIIE 312
            ++ +A +      +++
Sbjct: 307 AIS-QANSLAEIEELLQ 322


>gi|22537964|ref|NP_688815.1| NifR3/Smm1 family protein [Streptococcus agalactiae 2603V/R]
 gi|25011905|ref|NP_736300.1| hypothetical protein gbs1866 [Streptococcus agalactiae NEM316]
 gi|76797858|ref|ZP_00780121.1| possible transcriptional regulator [Streptococcus agalactiae
           18RS21]
 gi|77414267|ref|ZP_00790427.1| NifR3/Smm1 family protein [Streptococcus agalactiae 515]
 gi|22534864|gb|AAN00688.1|AE014274_18 NifR3/Smm1 family protein [Streptococcus agalactiae 2603V/R]
 gi|24413447|emb|CAD47525.1| Unknown [Streptococcus agalactiae NEM316]
 gi|76586761|gb|EAO63256.1| possible transcriptional regulator [Streptococcus agalactiae
           18RS21]
 gi|77159683|gb|EAO70834.1| NifR3/Smm1 family protein [Streptococcus agalactiae 515]
          Length = 325

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 57/303 (18%), Positives = 122/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   A+       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAIEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++     D +M+GR A  N  + T ++ +F  
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +     +     +++          G   + + R 
Sbjct: 252 GEILPD-LPFEKMLDVAEDHLTRLVNLKGETIA----VREFRGLAPHYLRGKSGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|76788535|ref|YP_330442.1| tRNA-dihydrouridine synthase family protein [Streptococcus
           agalactiae A909]
 gi|77405658|ref|ZP_00782746.1| NifR3/Smm1 family protein [Streptococcus agalactiae H36B]
 gi|77411533|ref|ZP_00787876.1| NifR3/Smm1 family protein [Streptococcus agalactiae CJB111]
 gi|76563592|gb|ABA46176.1| tRNA-dihydrouridine synthase family protein [Streptococcus
           agalactiae A909]
 gi|77162387|gb|EAO73355.1| NifR3/Smm1 family protein [Streptococcus agalactiae CJB111]
 gi|77175731|gb|EAO78512.1| NifR3/Smm1 family protein [Streptococcus agalactiae H36B]
          Length = 325

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 122/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++     D +M+GR A  N  + T ++ +F  
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +     +     +++          G   + + R 
Sbjct: 252 GEILPD-LPFEKMLDVAEDHLTRLVNLKGETIA----VREFRGLAPHYLRGKSGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|308807222|ref|XP_003080922.1| nitrogen regulation family protein (ISS) [Ostreococcus tauri]
 gi|116059383|emb|CAL55090.1| nitrogen regulation family protein (ISS) [Ostreococcus tauri]
          Length = 490

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 100/344 (29%), Positives = 164/344 (47%), Gaps = 23/344 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M+++T  H+R   RL++    L+TEM V   +     +       L +  +     LQ+G
Sbjct: 107 MMEYTTAHFRVMCRLMSAKTWLWTEMEVDQTLTHAVLEGTRVDRFLDYPVETAATVLQLG 166

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKA 114
           G+D   L  A  I   +GY EINLN GCPS +V     FGA LM  P +V +C+ AM + 
Sbjct: 167 GSDPEILGRATAIAAPYGYEEINLNSGCPSPKVAGKGCFGAALMTEPRLVAECLQAMNEN 226

Query: 115 --LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV-NGIWIHARKAILKGLSPKDNRKI 171
                PV++KCRIGVD+     AL   V +I ++      ++HARKA+L GLSP +NR +
Sbjct: 227 APSGTPVSIKCRIGVDECDSYDALCEYVDTIVRASATRRFYVHARKALLNGLSPAENRSV 286

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPS----VDGVMIGRAAYKNSA 224
           P L ++  Y + ++ P+    LNGG   L+D+  A+   P     + GVMIGR A+ +  
Sbjct: 287 PPLKHEWAYALARDFPECEFHLNGGLKTLKDVENAIHRGPEGGGPIAGVMIGRQAHADPW 346

Query: 225 -MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGGKLQQITRHMIG 282
            +L+  D       T     +    + +      ++  Y  A+  +    ++ +   +  
Sbjct: 347 GLLSAADTTIFGESTNPCASRRDFLEKYVEYADDTIGRYGTAKDGYRIPSVRHMMHPIQN 406

Query: 283 LFHGFPNSRRCRHILTVEAGASTATHH-----IIETAFNLMIES 321
           LFHG  N++  R ++  E    +         I+E    ++ + 
Sbjct: 407 LFHGCANNKMWRRLVDEELQKRSKKPDTTVRSILEATLGVIEDE 450


>gi|256544716|ref|ZP_05472088.1| tRNA-dihydrouridine synthase [Anaerococcus vaginalis ATCC 51170]
 gi|256399605|gb|EEU13210.1| tRNA-dihydrouridine synthase [Anaerococcus vaginalis ATCC 51170]
          Length = 321

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 130/303 (42%), Gaps = 24/303 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R  A         +TEM+  +A+   +KK   +L  S  EK   +QI G+  
Sbjct: 16  AGVSDVGFRLIAEKY-GADKTFTEMVSVNALYYDNKKTDDLLFISENEKNCNIQIFGSKP 74

Query: 60  SKLVEAAK-IVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             + +  K  +       EI+ N+GCP A++ +   G+ LM  P +V +    + K+   
Sbjct: 75  ELIEKVVKDKINPIEKSKEISFNMGCPVAKITKNGEGSALMAKPKLVEEICKILRKSTDK 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + +K R+G+DD+   +    + K  + +G++ + +HAR         K+       +++
Sbjct: 135 KINIKFRLGIDDK--NLNYLEIGKIAQDAGIDYVILHART--------KEQMYSGKANWN 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I KEN  + +  NG +  +   +K++     DGVM+ R A  N  +   + +Y + 
Sbjct: 185 HIK-ILKENLSIPVIANGDIFCVEDFVKVIDKTKADGVMLARGAMGNPFLFKEIKDYINK 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  T++      +    +     + +     + Q+ +H+     G  NS + R 
Sbjct: 244 GFY-EKPSSTQIIDQLIEQYKLELKYKKEKLV-----VTQMRKHLSWYIKGLENSSKIRD 297

Query: 296 ILT 298
           ++ 
Sbjct: 298 LVN 300


>gi|110633972|ref|YP_674180.1| nifR3 family TIM-barrel protein [Mesorhizobium sp. BNC1]
 gi|110284956|gb|ABG63015.1| tRNA-U20-dihydrouridine synthase [Chelativorans sp. BNC1]
          Length = 354

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 129/316 (40%), Gaps = 23/316 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADI 59
           M   TD  +R  A       L+ +EM+ +  + +G  ++       +  + + QI G + 
Sbjct: 42  MSGVTDLPFRMRA-YAHGAGLVVSEMVASGELAKGRAESARRIRRPDIDVHMVQIAGREA 100

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I  D G + +++N+GCP+ +V  G  G+ LM  PD     I A+ KA+ +PV
Sbjct: 101 RWMAEAARIAVDEGADIVDINMGCPAKKVTGGYSGSALMREPDHALSLIEAVVKAVDVPV 160

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G DD    +    L +  + +GV  + +H R         +        ++  +
Sbjct: 161 TVKMRLGWDD--ACLNAPELARRAEAAGVAMVTVHGRT--------RCQFYTGQANWKAI 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K+    + +  NG  E   +A  +L     D VMIGRA Y        +        
Sbjct: 211 AEVKQAV-SIPVVANGDGEGPLEAATMLTQSGADAVMIGRAHYGAPWKAGALAHAADGSA 269

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCRH 295
               P  T    D+       M      H  +G   +   +H+      H  P+    R 
Sbjct: 270 APGVPAGTAEMADYVAAHYVDML----SHYGTGQGTRHARKHIGWYLDRHSAPDPALRRS 325

Query: 296 ILTVEAGASTATHHII 311
           I+T      +   H+I
Sbjct: 326 IMTE--TDPSKVLHLI 339


>gi|332524006|ref|ZP_08400258.1| putative tRNA-dihydrouridine synthase B [Streptococcus porcinus
           str. Jelinkova 176]
 gi|332315270|gb|EGJ28255.1| putative tRNA-dihydrouridine synthase B [Streptococcus porcinus
           str. Jelinkova 176]
          Length = 317

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 124/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 16  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDETEHPMSIQLFGGD 74

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +PD +   ++ +   L I
Sbjct: 75  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIVSEVTSVLDI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV  + +H R         ++     + D+D
Sbjct: 135 PLTVKMRTGWADSSLAVEN---ALAAESAGVAALAMHGRT--------REQMYTGSCDHD 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 184 TLARVSKALTKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +     +     +++          G   + + R 
Sbjct: 244 GEELPD-LPFAKKLDIAEDHLTRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 298

Query: 296 ILT 298
            ++
Sbjct: 299 AVS 301


>gi|182678493|ref|YP_001832639.1| NifR3 family TIM-barrel protein [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182634376|gb|ACB95150.1| TIM-barrel protein, nifR3 family [Beijerinckia indica subsp. indica
           ATCC 9039]
          Length = 350

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 126/321 (39%), Gaps = 20/321 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A+      L+ +EM+ +D   +GD  N L    Q  +   +QI G D 
Sbjct: 42  MAGITDLGMRRLAQQF-GAGLVVSEMVSSDEYAKGDAANRLKAGGQGIEQSVVQIAGCDP 100

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+  E  G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+ +PV
Sbjct: 101 VAMGEAARQAEGSGAAMIDINMGCPARKVIGGYAGSHLMRDLDRAVALIRAVIGAVRVPV 160

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G DDQ    A  +L +  +  GV  + +H R         +        D+  V
Sbjct: 161 SVKMRLGWDDQQRNAA--DLGRLAEAEGVAMLSVHGRT--------RCQFYRGKADWAAV 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + + +NG     + A  +L     D VMIGRAA     ++  +  Y     
Sbjct: 211 RAVKEAVT-IPVVVNGDCTGPAVASAMLAQSGADAVMIGRAAVGKPWLVGDIAYYLETGE 269

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P      +         ++ Y   H      ++   +H+ G           R  L
Sbjct: 270 VRPEPSAQIQAEATLDHYETLLSLYGTEH-----GVRHARKHLAGYAVHRHAPSDLRRRL 324

Query: 298 TVEAGASTATHHIIETAFNLM 318
                 +     ++  A +  
Sbjct: 325 VTSEHPAEVKSILLSLARDTF 345


>gi|163748710|ref|ZP_02155963.1| hypothetical protein KT99_18942 [Shewanella benthica KT99]
 gi|161331820|gb|EDQ02624.1| hypothetical protein KT99_18942 [Shewanella benthica KT99]
          Length = 322

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 56/288 (19%), Positives = 120/288 (41%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         A+  +EM+ ++  +    K+   +  + +    ++QI GAD
Sbjct: 17  MAGVTDQPFRNLCVRY-GAAMAVSEMLSSNPDVWDTDKSRKRMSHAGENGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V++   G+ L+ NP+ V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNKKLAGSALLQNPEQVKAILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      + +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGV--QIAQIAEDCGIASLAVHGRT--------RQCMYKGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK+ N  + +  NG +    +A  +L     D +MIGR A     +   +  Y    
Sbjct: 186 IKAIKQ-NISIPVIANGDIVTPEKARYVLDHTGADALMIGRGAQGRPWIFREIQHYLDTG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               +P++    +    +   ++ +    +      ++   +H+    
Sbjct: 245 -NKLAPVEMDEKRLVMLEHLENLYELYGEY----KGIRFARKHVGWYL 287


>gi|319940025|ref|ZP_08014379.1| tRNA-dihydrouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319810739|gb|EFW07066.1| tRNA-dihydrouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 323

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 61/317 (19%), Positives = 130/317 (41%), Gaps = 23/317 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L    +E P+++Q+ G+D
Sbjct: 24  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEEEHPVSIQLFGSD 82

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +P+ +   I  +   L I
Sbjct: 83  EDSLARAAEFIQENTQTDIVDINMGCPVNKIVKNEAGAKWLKDPEKIYSIINKVRSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +G   + +H R         ++     + D +
Sbjct: 143 PLTVKMRTGWADASLAVENA---LAAEAAGAAALAMHGRT--------REQMYTGHADLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++ + +    +    NG +  +  A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 192 TLHNVAQALTKIPFIANGDIRTVQDAQQRIEEVGADAVMIGRAAMGNPYLFHQINHYFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                           +  +   + D    H+     +++          G   + + R 
Sbjct: 252 GEILPDLSFEDKMHIAYDHLKR-LIDLKGEHIA----IREFRGLAPHYLRGTAGAAKLRS 306

Query: 296 ILTVEAGASTATHHIIE 312
            ++ +A +      +++
Sbjct: 307 AIS-QANSLAEIEELLQ 322


>gi|15965210|ref|NP_385563.1| putative NIFR3-like protein [Sinorhizobium meliloti 1021]
 gi|307309224|ref|ZP_07588895.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti BL225C]
 gi|15074390|emb|CAC46036.1| tRNA-dihydrouridine synthase B [Sinorhizobium meliloti 1021]
 gi|306900370|gb|EFN30986.1| TIM-barrel protein, nifR3 family [Sinorhizobium meliloti BL225C]
          Length = 342

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 118/287 (41%), Gaps = 26/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A        + TEM+ +  ++    ++          P  +Q+ G + 
Sbjct: 33  MSGVTDLPFRMLAWRF-GAGFVVTEMVASRELVGNAAESWARLKNSGIDPHIVQLAGREA 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+IVE  G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA ++PV
Sbjct: 92  HWMAEAARIVEANGADIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVKAATVPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+      L  + +  +++GV  I IH R  +               D+D +
Sbjct: 152 TLKMRLGWDENSINAPL--IARRAEEAGVKAITIHGRTRM--------QFYNGKADWDAI 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG ++ ++ A +IL     D VM+GR+                   
Sbjct: 202 GAV-REVVSIPLIANGDVDSVADAHEILRRSGADAVMVGRSCQGRPW------HAGVLAG 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             + P  + V + F       +  Y          L+   +H     
Sbjct: 255 AAAHPDASGVARIFAEHYEMMLEFYGVE-----VGLRTARKHAGWYL 296


>gi|329766573|ref|ZP_08258116.1| nifR3 family TIM-barrel protein [Candidatus Nitrosoarchaeum limnia
           SFB1]
 gi|329136828|gb|EGG41121.1| nifR3 family TIM-barrel protein [Candidatus Nitrosoarchaeum limnia
           SFB1]
          Length = 321

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 71/310 (22%), Positives = 134/310 (43%), Gaps = 32/310 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---------NILGFSTQEKPLA 51
           M   +D   R   + +    L+ TE     +I+  + +           L +S +E+PL+
Sbjct: 14  MAGVSDPVLRLQCKKM-GAGLVVTEFTSIHSIIAKEHQLKENKKTIQEFLEYSEKERPLS 72

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D+  L +AAKIVE F ++ I+ N+GCP+  + +   G  L+   ++     + +
Sbjct: 73  VQLFGSDLLALEKAAKIVEPF-FDIIDYNMGCPAPHITQQMAGGALLQEINLTQQIFSTL 131

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A+  PVT+K R GV D    +  +++    +  G+  I +H R  + +G S       
Sbjct: 132 VNAVKKPVTLKIRSGVTDASRYL-FKDIATIAEDEGIQMITLHPRT-VSQGYS------- 182

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            N D+ ++ E+K E  ++ I  NG +     A  ++     D VMIGR A  N  +   +
Sbjct: 183 GNADWKMIKELK-EISNIPIVGNGDITTPEDAKNMIDQTGCDYVMIGRGAMGNPFLFEQI 241

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           ++Y          +K ++D  F+  +S S           G  ++           G   
Sbjct: 242 NDYLKTGTYKQYSLKDKID-SFFEYLSLSTQYKIKFSNIKGQAMR--------FTKGIKG 292

Query: 290 SRRCRHILTV 299
             + R  ++ 
Sbjct: 293 GSKIRPKIST 302


>gi|261228265|ref|ZP_05942546.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|301028291|ref|ZP_07191551.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 196-1]
 gi|307139948|ref|ZP_07499304.1| tRNA-dihydrouridine synthase B [Escherichia coli H736]
 gi|312972471|ref|ZP_07786645.1| TIM-barrel , nifR3 family protein [Escherichia coli 1827-70]
 gi|299878634|gb|EFI86845.1| TIM-barrel protein, nifR3 family [Escherichia coli MS 196-1]
 gi|307625140|gb|ADN69444.1| tRNA-dihydrouridine synthase B [Escherichia coli UM146]
 gi|310334848|gb|EFQ01053.1| TIM-barrel , nifR3 family protein [Escherichia coli 1827-70]
 gi|315617069|gb|EFU97679.1| TIM-barrel , nifR3 family protein [Escherichia coli 3431]
 gi|320189607|gb|EFW64266.1| tRNA dihydrouridine synthase B [Escherichia coli O157:H7 str.
           EC1212]
 gi|320202169|gb|EFW76744.1| tRNA dihydrouridine synthase B [Escherichia coli EC4100B]
 gi|320650932|gb|EFX19389.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H- str. H
           2687]
 gi|320656313|gb|EFX24225.1| tRNA-dihydrouridine synthase B [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320666837|gb|EFX33816.1| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154479|gb|EFZ40680.1| TIM-barrel , nifR3 family protein [Escherichia coli EPECa14]
 gi|323162945|gb|EFZ48780.1| TIM-barrel protein, nifR3 family protein [Escherichia coli E128010]
 gi|323165221|gb|EFZ51011.1| TIM-barrel , nifR3 family protein [Shigella sonnei 53G]
 gi|323173481|gb|EFZ59110.1| TIM-barrel protein, nifR3 family protein [Escherichia coli LT-68]
 gi|323178560|gb|EFZ64136.1| TIM-barrel protein, nifR3 family protein [Escherichia coli 1180]
 gi|325498839|gb|EGC96698.1| tRNA-dihydrouridine synthase B [Escherichia fergusonii ECD227]
 gi|326337955|gb|EGD61789.1| tRNA dihydrouridine synthase B [Escherichia coli O157:H7 str. 1125]
 gi|326347524|gb|EGD71249.1| tRNA dihydrouridine synthase B [Escherichia coli O157:H7 str. 1044]
 gi|327251354|gb|EGE63043.1| TIM-barrel protein, nifR3 family protein [Escherichia coli STEC_7v]
 gi|330909311|gb|EGH37825.1| tRNA dihydrouridine synthase B [Escherichia coli AA86]
 gi|332086518|gb|EGI91665.1| TIM-barrel protein, nifR3 family protein [Shigella dysenteriae
           155-74]
 gi|332087251|gb|EGI92384.1| TIM-barrel protein, nifR3 family protein [Shigella boydii 5216-82]
 gi|332345215|gb|AEE58549.1| TIM-barrel protein, nifR3 family protein [Escherichia coli UMNK88]
          Length = 281

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 116/295 (39%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + +  NG + D  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V +     +      
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 YGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|320194746|gb|EFW69376.1| tRNA dihydrouridine synthase B [Escherichia coli WV_060327]
          Length = 281

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 116/295 (39%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + +  NG + D  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V +     +      
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCVHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 YGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|260663747|ref|ZP_05864635.1| transcription regulator [Lactobacillus fermentum 28-3-CHN]
 gi|260551798|gb|EEX24914.1| transcription regulator [Lactobacillus fermentum 28-3-CHN]
          Length = 333

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 74/325 (22%), Positives = 127/325 (39%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +       + +EMI    I+  +KK   ++G    E P+ LQI G  
Sbjct: 19  MAGVMNTAFRVICKKF-GAGYVVSEMISDRGIMYHNKKTLQMMGVDPVEHPMGLQIFGGT 77

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V++    + I++N+GCP  ++     G+  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVEAAKFVDENTDADVIDINMGCPVNKIVNTEAGSRWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DDQ        L      +    +    RK + +G          + D+D
Sbjct: 138 PVTVKMRTGWDDQHIFAVENALAAQRAGAAAVAMHGRTRKQMYRG----------HADWD 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG ++   +A  +L     + +MIGRAA  N  MLT    Y  N
Sbjct: 188 ILKEVASQLT-IPFMANGDIKTAEEAKYVLEYTGAEAIMIGRAAMGNPWMLTQTVHYLEN 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                              ++                +++          G P + R + 
Sbjct: 247 GELLPEATPEEKITTAKEHLAR-----LVDLKGEYAGVREFRGQAAYYMKGIPRAARTKV 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L +EA        I +   +   E
Sbjct: 302 AL-MEATEQAQMDEIFDRFIDQYEE 325


>gi|58697366|ref|ZP_00372700.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           simulans]
 gi|58536243|gb|EAL59783.1| NifR3 family protein [Wolbachia endosymbiont of Drosophila
           simulans]
          Length = 262

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 64/263 (24%), Positives = 110/263 (41%), Gaps = 19/263 (7%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           A+Q+ G +   + EAAK+ ED G   I++N GCP  +V  G  G+ LM +     + I A
Sbjct: 9   AVQLAGCEPDVMAEAAKLNEDMGAKIIDINFGCPVKKVVNGYAGSALMRDEKKAAEIIEA 68

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + KA+++PVTVK R G +D+        L K  +  G   I +H R         +    
Sbjct: 69  VVKAVNMPVTVKMRTGWNDENRNA--PRLAKIAEDLGAKMITVHGRT--------RAQLY 118

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
               D+  V  +K++   + + +NG +++++     L     DGVMIGR AY    ++  
Sbjct: 119 NGQADWKFVRNVKEQV-KIPVIVNGDIKNLNDIQNALKESGADGVMIGRGAYGKPWLINQ 177

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              + S   T       R+       I     D    +  +   ++   +H+     G  
Sbjct: 178 AMNFLSGSETSEPTASERLS------IILEHYDNILEYYGNDTGIKMARKHIGWYSSGLQ 231

Query: 289 NSRRCRHILTVEAGASTATHHII 311
            S   R  +     ++    +II
Sbjct: 232 GSSEFRVRVNNMTDSTEVKENII 254


>gi|227547980|ref|ZP_03978029.1| possible dihydrouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227079991|gb|EEI17954.1| possible dihydrouridine synthase [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 393

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 119/314 (37%), Gaps = 31/314 (9%)

Query: 1   MVDWTDRHYRFFARLL------TNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
           M   T+  +R   R +      T++ L   EMI A A++  ++K   +  F+  E P +L
Sbjct: 31  MAGVTNMPFRVLCREIEEELTGTSSGLYVCEMITARALVARNQKTLHMTTFADVETPRSL 90

Query: 53  QIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           Q+   D     +A + IVE+   + +++N GCP  +V     G+ +     +  + ++A 
Sbjct: 91  QLYTVDPKFTYDAVRMIVEEDIADHVDMNFGCPVPKVTRKGGGSAIPFKRRLYANIVSAA 150

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A     IP+TVK RIG+DD        +  +   + G   + +HAR A        D 
Sbjct: 151 VRAAEGSGIPITVKFRIGIDD--AHHTHLDAGRIAAEEGAAAVALHARTA--------DQ 200

Query: 169 RKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           R      +  +  + +  +   + +  NG +     A K+L   +  GV +GR       
Sbjct: 201 RYSGQAHWSEIRRLVEHMDGSGVPVIGNGDIFAADDAEKMLETTNCHGVEVGRGCLGRPW 260

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +   +            P    V +  +R            H       + I +H     
Sbjct: 261 LFAQIGAQLRGEEIPPEPTLGEVARIIYRHAELLALHDGEEH-----ACRDIRKHTGWYL 315

Query: 285 HGFPNSRRCRHILT 298
            GFP     R  L 
Sbjct: 316 RGFPVGGEFRKDLA 329


>gi|150396307|ref|YP_001326774.1| nifR3 family TIM-barrel protein [Sinorhizobium medicae WSM419]
 gi|150027822|gb|ABR59939.1| putative TIM-barrel protein, nifR3 family [Sinorhizobium medicae
           WSM419]
          Length = 337

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 68/287 (23%), Positives = 118/287 (41%), Gaps = 26/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A        + TEM+ +  ++    ++          P  +Q+ G + 
Sbjct: 28  MSGVTDLPFRMLAWRF-GAGFVVTEMVASRELVGNAAESWARLKNSGIDPHIVQLAGREA 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+IVE  G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA ++PV
Sbjct: 87  HWMAEAARIVEANGADIIDINMGCPAKKVTGGYSGSALMRDPDHALSLIEATVKAATVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+      L  + +  +++GV  I IH R  +               D+D +
Sbjct: 147 TLKMRLGWDENSINAPL--IARRAEEAGVKAITIHGRTRM--------QFYNGKADWDAI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + +  NG ++ ++ A +IL     D VM+GR+                   
Sbjct: 197 RSV-REVTSVPLIANGDVDSVADAHEILRRSGADAVMVGRSCQGRPW------HAGVLAG 249

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           T + P    V + F       +  Y          L+   +H     
Sbjct: 250 TAAHPDAAGVARIFAEHYETLLEFYGVE-----VGLRTARKHAGWYL 291


>gi|319745777|gb|EFV98072.1| tRNA-dihydrouridine synthase [Streptococcus agalactiae ATCC 13813]
          Length = 325

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 123/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGITNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +P+ +   +  +   L+I
Sbjct: 83  AEGLKRAADFIQSNTKADIVDINMGCPVNKVVKNEAGAKWLRDPEKIYHIVKEVTSVLNI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWSDSSNAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++ K    +    NG +  +  A  ++     D +M+GR A  N  + T ++ +F  
Sbjct: 192 TLGKVAKAVTSIPFIANGDIRTVHDAKFMIEEIGADAIMVGRGARSNPYIFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D        + +     +     +++          G   + + R 
Sbjct: 252 GEILPD-LPFEKMLDVAEDHLTRLVNLKGETIA----VREFRGLAPHYLRGKSGAAKIRG 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|294495034|ref|YP_003541527.1| hypothetical protein Mmah_0350 [Methanohalophilus mahii DSM 5219]
 gi|292666033|gb|ADE35882.1| TIM-barrel protein, nifR3 family [Methanohalophilus mahii DSM 5219]
          Length = 317

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 73/299 (24%), Positives = 130/299 (43%), Gaps = 26/299 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M + T+  YR   R     +  +TEM+ ++AIL G++K+  +      E    +QI G  
Sbjct: 17  MAEVTNLAYRVVCRR-RGASFAFTEMVNSEAILHGNRKSYQMASSCADEGIFGIQIFGNS 75

Query: 59  ISKLVEAAKIVEDFGYN-EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              + +AA I+E+  +   I++N GCPS R+ +   G+ LM  PD++ + +  + +++++
Sbjct: 76  PVSMAKAAGILENTKFPSIIDINAGCPSPRIRKTGAGSMLMEKPDVLENIVRCVVESVTV 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+  D          L   ++ +G + I +H R A  +             D+ 
Sbjct: 136 PVTVKIRVFRD----VSQTVELASRLENAGASAITVHGRTATQQ--------YSGLADHL 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               IK+E   + +  NG + + + A ++L     DG+MIGRAA  +  +   ++ +  N
Sbjct: 184 YARRIKEEL-SIPVIANGDIRNGAFAAQLLEYTGCDGLMIGRAAMGDPDVFLRIETFLEN 242

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                S       K+   +    +  Y    L     L     H      G   SR  R
Sbjct: 243 GTEFPS-ADCDQRKNRLEEYLKLLESYG---LEKNVNLAA---HSAWFTRGLAGSRSFR 294


>gi|227528915|ref|ZP_03958964.1| tRNA-dihydrouridine synthase [Lactobacillus vaginalis ATCC 49540]
 gi|227351189|gb|EEJ41480.1| tRNA-dihydrouridine synthase [Lactobacillus vaginalis ATCC 49540]
          Length = 336

 Score =  221 bits (565), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 128/325 (39%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +       +  EMI    I+  +KK   ++     E P+ +QI G  
Sbjct: 19  MAGVTNSAFRVICKEF-GAGYVVCEMISDRGIMYHNKKTLNMMDVDPSEHPMGIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V++    + I++N+GCP  +V +   GA  +L+P+ V + ++ +  A+  
Sbjct: 78  KETLVQAAKYVDEHTAADVIDINMGCPVNKVVKTDAGARWLLDPNKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L      +    +    RK +  G          + D++
Sbjct: 138 PVTVKMRTGWDDKHIYAVENALAAERAGAAALAMHGRTRKQMYTG----------HADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  ++  +    NG +     A +IL        MIGRAA  N  ML   + Y   
Sbjct: 188 ILKEVA-DHLSIPFMANGDVRTPEDAKRILDETGATAAMIGRAALGNPWMLKRTEHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     +  K     ++  + D    +      +++          G P S R + 
Sbjct: 247 GELLPEATPEQKIKMAKEHLNR-LIDLKGEY----VGVREFRGLSTYYLKGIPRSARTKA 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L VEA      + I +       E
Sbjct: 302 SL-VEAETRQEMNDIFDRFAEQTAE 325


>gi|320095947|ref|ZP_08027566.1| tRNA-dihydrouridine synthase B [Actinomyces sp. oral taxon 178 str.
           F0338]
 gi|319977118|gb|EFW08842.1| tRNA-dihydrouridine synthase B [Actinomyces sp. oral taxon 178 str.
           F0338]
          Length = 441

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 65/364 (17%), Positives = 123/364 (33%), Gaps = 80/364 (21%)

Query: 1   MVDWTDRHYRFFARLLT------------------------------------------- 17
           M   TD  +R   R                                              
Sbjct: 29  MAGVTDAPFRRLCRFFGEAGLPQELRPLDPARPGTGGDEAVAGTDGREGIANLARAGAGR 88

Query: 18  --------NNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
                      L  TEM+ + A++    +   ++     E+  ++Q+ G D + +  AA+
Sbjct: 89  RAVPRVDAPAGLYVTEMVTSRALVEEGARTLDMVRPDPVERVRSIQLYGVDPAVMGAAAR 148

Query: 68  IVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---------I 117
           ++ + G  + I+LN GCP  +V     GA L    D+  D + ++ +A           I
Sbjct: 149 LLVERGLADHIDLNFGCPVPKVTRKGGGAALPWKRDLFVDLVGSVVRACQKAGERAGRQI 208

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG+D         +   + ++ G + + +HAR                   +D
Sbjct: 209 PVTVKIRIGID--SAHETATDAALAAQRLGASALTLHARTQ--------AQHYAGRAHWD 258

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+    + +  NG + +   A+ ++     DGV +GR A     +   +   +  
Sbjct: 259 EIARLKEALT-IPVLGNGDVFEARDAMAMMERTGCDGVCVGRGAQGRPWLFRDIVAAYHG 317

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P    V     R  +       A        ++++ +H+     GF      RH
Sbjct: 318 APVPPGPALAEVVAVIERHAAWV----VADQGDEARAMREMRKHVGWYLRGFAVGGAQRH 373

Query: 296 ILTV 299
            L++
Sbjct: 374 ALSM 377


>gi|269861290|ref|XP_002650357.1| NIFR3-like protein [Enterocytozoon bieneusi H348]
 gi|220066217|gb|EED43710.1| NIFR3-like protein [Enterocytozoon bieneusi H348]
          Length = 321

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 95/302 (31%), Positives = 152/302 (50%), Gaps = 23/302 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M+  T   +R   +L+    +LYTEMI A  I+  + + + +     +    +QIGG++ 
Sbjct: 16  MMKVTTPCFRKLIQLIAPTTILYTEMITASTIINLNDEKLQITLGNPDNQTVVQIGGSNP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +V A K ++  G+   NLN GCPS RV +G FGA LM   ++V + I  +     I +
Sbjct: 76  KDIVNAIKRLKQCGWRLFNLNCGCPSTRVQKGMFGAILMKYKELVIEIINTVYIETQIIL 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++KCR G+D+      L+  ++SI K +  N  +IHARK  L+G++PK NR IP L+YD 
Sbjct: 136 SIKCRTGIDEFDSYEFLKEFIESISKNTPCNIFYIHARKCWLQGINPKQNRNIPPLNYDY 195

Query: 179 VYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++ IKKE P LFIG+NGG+      +    + + DG+MIGR A KN  +   +    + P
Sbjct: 196 IFRIKKEFPHLFIGINGGITYNSYLKYKFQMDTCDGIMIGREAIKNPLIFAEI---INMP 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +                 I   +  Y      S   + +I   +  L  G PNS+  + +
Sbjct: 253 IN----------------IQYIIQSYFKFIEMSNFTIYKILYPLCNLRRGKPNSKHFKQM 296

Query: 297 LT 298
           + 
Sbjct: 297 IN 298


>gi|281412156|ref|YP_003346235.1| TIM-barrel protein, nifR3 family [Thermotoga naphthophila RKU-10]
 gi|281373259|gb|ADA66821.1| TIM-barrel protein, nifR3 family [Thermotoga naphthophila RKU-10]
          Length = 306

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 125/300 (41%), Gaps = 26/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M  +TD  +R  A         ++EM+ A   L   +K   L     E+ +A+QI G++ 
Sbjct: 10  MAGYTDSAFRTLAFEW-GADFAFSEMVSAKGFLMNSQKTEELLPQPHERNVAVQIFGSEP 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S+L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   
Sbjct: 69  SELSEAARILSE-KYKWIDLNAGCPVRKVVKKGAGGALLKDLRHFRYIVRELRKSVSGKF 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +       +  + + + + GV+ ++IH R  +       + + +  L+    
Sbjct: 128 SVKTRLGWEKN----EVEEIYRILVEEGVDEVFIHTRTVVQGFTGKAEWKALSVLE---- 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                    +   ++G +     A + L     DG+++ R A     +   + ++  +  
Sbjct: 180 -------KRVPTFVSGDVFTPEDAKRALEESGCDGLLVARGAIGRPWIFKQIKDFLRSGK 232

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             S P +  + + F R +     +   +       + ++ + + G       +RR R  +
Sbjct: 233 Y-SEPSREEILRTFERHL-----ELLIKTKGERKAVVEMRKFLAGYTKDLKGARRFREKI 286


>gi|182412757|ref|YP_001817823.1| NifR3 family TIM-barrel protein [Opitutus terrae PB90-1]
 gi|177839971|gb|ACB74223.1| TIM-barrel protein, nifR3 family [Opitutus terrae PB90-1]
          Length = 370

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 59/308 (19%), Positives = 131/308 (42%), Gaps = 20/308 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             +T+  +R   R L     + T+++ A ++L  +     ++  S +++P+++Q+ G+  
Sbjct: 18  AGYTNLPFRLTLRELGGLGWVTTDLVNARSLLERNPAALKLVASSAEDRPMSIQLFGSVP 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           +++ +AA+I ED G   +++N+GCP  +V     G+ +M   +     +  M +A+ IPV
Sbjct: 78  TEMRDAARICEDLGAQAVDINMGCPVRKVVRVGGGSAMMTELNQTAALVRGMIEAVKIPV 137

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T K R+G DD+   +   +L + ++ +GV  +++H R         +       ++   +
Sbjct: 138 TAKMRLGWDDE--NLTAPDLARVLEDAGVAAVFVHGRT--------RAQGFSGTVNLAGI 187

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +    + +  NG +     A  ++      GV IGR A+ +  +        ++  
Sbjct: 188 AAVVQAVKRIPVIGNGDVTTPEAARAMIEQTGCAGVSIGRGAFYDPWIFRRTHHLLTSGE 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-RHI 296
               P      +   R        Y       G +L    +        F  ++   R I
Sbjct: 248 LWPEPGFDERVRVMRRHFERYCEFYGEE---KGPRL--FRKVAPWYAKRFGPAKPFKRRI 302

Query: 297 LTVEAGAS 304
           +T+++ A 
Sbjct: 303 ITIDSRAD 310


>gi|329946913|ref|ZP_08294325.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328526724|gb|EGF53737.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 436

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 66/338 (19%), Positives = 129/338 (38%), Gaps = 57/338 (16%)

Query: 1   MVDWTDRHYRFFAR-------------------------LLTNNALLYTEMIVADAILRG 35
           M   T+  +R   R                         LL    L  TEM+   A++  
Sbjct: 39  MAGVTNASFRRLCREMAEATMPKALAPASSGPVAAPDGGLLAPAGLYVTEMVTTRALVER 98

Query: 36  DKKN--ILGFSTQEKPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGS 92
           +++   ++     E+  ++Q+ G D + +  A +I VE+   + I+LN GCP  +V    
Sbjct: 99  NERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEEDLADHIDLNFGCPVPKVTRKG 158

Query: 93  FGACLMLNPDIVGDCIAAMCKAL-----------SIPVTVKCRIGVDDQIPAVALRNLVK 141
            GA L    D++   +    +A             +PVT+K R+G+D++          +
Sbjct: 159 GGAALPWKRDLLAAILTEAVRASEAACRAAGRAREVPVTMKMRLGIDEE--HETFLAAAR 216

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           + + +G+  + +HAR A                 ++ +  +K E  DL +  NG +    
Sbjct: 217 TAENAGIAAVALHARSA--------RQHYSGQARWEEIARLK-EATDLPVLGNGDIWLGD 267

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            A++++     DGV++GR       +   +           S ++TR D D   ++    
Sbjct: 268 DAVRMMETTGCDGVVVGRGCQGRPWLFADIVAAMHG-----SSMRTRPDLDAVIEVIRRH 322

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               A  +     ++ + +H+     G+P     R  L
Sbjct: 323 GRMLAAEMGEDRGVRDLRKHVGWYLKGYPVGGAARADL 360


>gi|260774378|ref|ZP_05883292.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
 gi|260610505|gb|EEX35710.1| tRNA-dihydrouridine synthase [Vibrio metschnikovii CIP 69.14]
          Length = 265

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 54/280 (19%), Positives = 109/280 (38%), Gaps = 19/280 (6%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           +    +    ++QI G+D  ++ EAA+   + G   I++N+GCP+ +V++   G+ L+  
Sbjct: 1   MVHQGESGIRSVQIAGSDPQQMAEAAQFSVENGAQIIDINMGCPAKKVNKKLAGSALLRY 60

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           PD++   + A+  A+ +PVT+K R G D          + +  +  G+    +H R    
Sbjct: 61  PDVIEHILKAVVDAVKVPVTLKTRTGWDTDNKNCVY--IAQLAENCGIQAFALHGRT--- 115

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
                +        +YD +  +K+    + +  NG ++   +A ++L     D +MIGR 
Sbjct: 116 -----RTCMYKGEAEYDSIKAVKQAI-SIPVIANGDIDSPQKAKQVLDYTGADALMIGRP 169

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           A     +   +  Y  +  T        V       + A    Y           + + +
Sbjct: 170 AQGRPWIFQEIQHYLESGTTMPELPAQEVKDILLGHVHALHQFY-----GEYLGPRIVRK 224

Query: 279 HMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           H+         +   R I      A       +E  F+ +
Sbjct: 225 HVGWYLKEHEQASEFRRIFNALEAAP-LQIEALEGYFDNV 263


>gi|16762143|ref|NP_457760.1| hypothetical protein STY3564 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29143632|ref|NP_806974.1| hypothetical protein t3299 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|56415311|ref|YP_152386.1| hypothetical protein SPA3251 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364241|ref|YP_002143878.1| hypothetical protein SSPA3037 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|224585182|ref|YP_002638981.1| hypothetical protein SPC_3455 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|25528230|pir||AE0913 conserved hypothetical protein STY3564 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504446|emb|CAD07899.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139267|gb|AAO70834.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|56129568|gb|AAV79074.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095718|emb|CAR61287.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|224469710|gb|ACN47540.1| hypothetical protein SPC_3455 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|312914412|dbj|BAJ38386.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321225194|gb|EFX50253.1| tRNA dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhimurium str. TN061786]
 gi|322614525|gb|EFY11455.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322618253|gb|EFY15144.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625966|gb|EFY22780.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322626736|gb|EFY23533.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322631304|gb|EFY28064.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322635429|gb|EFY32143.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322647267|gb|EFY43765.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322649731|gb|EFY46158.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322655595|gb|EFY51901.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322658375|gb|EFY54640.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322664401|gb|EFY60597.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667379|gb|EFY63541.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322674627|gb|EFY70719.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675742|gb|EFY71815.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322682378|gb|EFY78401.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|323196165|gb|EFZ81325.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196731|gb|EFZ81876.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323204368|gb|EFZ89377.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323207716|gb|EFZ92663.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323214291|gb|EFZ99044.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323225046|gb|EGA09299.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323230398|gb|EGA14517.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233374|gb|EGA17468.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323239411|gb|EGA23461.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323242338|gb|EGA26364.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323250398|gb|EGA34282.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323256846|gb|EGA40561.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323264109|gb|EGA47617.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323271632|gb|EGA55051.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
          Length = 281

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 115/295 (38%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSDPVEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVPVTLKIRTGWAPEHRN--CVEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + I  NG + +  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPIIANGDITNPHKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V +     +      
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCTHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G ++    +H+           + R        AS      +E  F 
Sbjct: 230 YGQ---AKGYRI--ARKHVSWYLQEHAPDDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|88704576|ref|ZP_01102289.1| tRNA-dihydrouridine synthase B [Congregibacter litoralis KT71]
 gi|88700897|gb|EAQ98003.1| tRNA-dihydrouridine synthase B [Congregibacter litoralis KT71]
          Length = 327

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 122/294 (41%), Gaps = 26/294 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD  +R          LL  EM+ +D  LR  +K+        +  P ++QI G D
Sbjct: 18  MAGVTDLPFRRLCARF-GAGLLVGEMVHSDPRLRESRKSRQRRRHDLEINPRSVQIVGND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+     G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+ +P
Sbjct: 77  PLLMAEAARYNVACGAQIIDINMGCPAKKVCRKAAGSALLADEPLVAAILGAVVSAVDVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  + +G+  + +H R         +       +++D 
Sbjct: 137 VTLKIRTGADPLHRNGT--SIARIAEDAGIALLAVHGRT--------RACAFKGEVEHDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              I  E+ D+ +  NG +     A  +L      GVM+GRAA     +   + +     
Sbjct: 187 TARIV-ESVDIPVLANGDIASARDAQAVLNHTGAAGVMVGRAAQGAPWLPGMIADAIEGR 245

Query: 237 LTGSSPIKTR--VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
            + S  + T+  V ++   ++     ++A   +          +H+     G P
Sbjct: 246 PSSSPDLATQYAVMREHLEELHRFYGEFAGSRIA--------RKHIGWYLDGHP 291


>gi|262066716|ref|ZP_06026328.1| NifR3 family protein [Fusobacterium periodonticum ATCC 33693]
 gi|291379515|gb|EFE87033.1| NifR3 family protein [Fusobacterium periodonticum ATCC 33693]
          Length = 307

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 63/302 (20%), Positives = 122/302 (40%), Gaps = 23/302 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I          A+QI G DI K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLRDGNAVQIFGEDIEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  +A+ +++ G  +INLN GCP  ++    +GA L+ +P+ +   ++ +   L   + +
Sbjct: 69  IKSSAQYIQNLGVKDINLNCGCPMKKIVNCGYGAALVKDPEKIKRILSEIKSILNDDVKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK RIG  +    V    + K  ++ G + I +H R         ++       D+  +
Sbjct: 129 SVKIRIGYKEPENYV---QIAKIAEEVGCDHITVHGRT--------REQLYSGKADWTYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNVSIPVIGNGDIFTAEDALERISYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D   +       +  + +H+     G  N    +  +
Sbjct: 237 VKNPVTKEEKINMAIEHLKRIRIDNDEQF------IFDVRKHISWYLKGLENCAEAKRKI 290

Query: 298 TV 299
             
Sbjct: 291 NT 292


>gi|289168865|ref|YP_003447134.1| tRNA-dihydrouridine synthase [Streptococcus mitis B6]
 gi|288908432|emb|CBJ23274.1| tRNA-dihydrouridine synthase [Streptococcus mitis B6]
          Length = 348

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 60/310 (19%), Positives = 126/310 (40%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 49  MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 107

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 108 EESLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV  + +H R         ++     + D +
Sbjct: 168 PLTVKMRTGWADPSLAVENA---LAAEAAGVAALAMHGRT--------REQMYTGHADLE 216

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++++ +    +    NG +  + +A + +     D VMIGRAA  N  +   ++ YF  
Sbjct: 217 TLHDVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAMGNPYLFHQINHYFET 276

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +  +  +   +             +++          G   + + R 
Sbjct: 277 GEILPDLTFEDKMEIAYEHLKRLIN-----LKGENVAVREFRGLAPHYLRGTSGAAKLRG 331

Query: 296 ILTVEAGAST 305
            ++  +  + 
Sbjct: 332 AISQASTLAE 341


>gi|157377250|ref|YP_001475850.1| nifR3 family TIM-barrel protein [Shewanella sediminis HAW-EB3]
 gi|157319624|gb|ABV38722.1| putative TIM-barrel protein, nifR3 family [Shewanella sediminis
           HAW-EB3]
          Length = 322

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 64/328 (19%), Positives = 125/328 (38%), Gaps = 29/328 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   TD+ +R         A+  +EM+ ++  +    K+   +  + ++   ++QI GAD
Sbjct: 17  MAGVTDQPFRNLCLRY-GAAMAVSEMLSSNPDVWDTDKSRQRMSHAGEDGIRSVQIAGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +    G   I++N+GCP+ +V+    G+ L+ +P  V   + A+  A+ +P
Sbjct: 76  PELMANAAVVNVQQGAQIIDINMGCPAKKVNRKLAGSALLQDPVQVKAILQAVVAAVDVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G   +        + +  +  G+  + +H R         +      N +YD 
Sbjct: 136 VTLKIRTGWAPEHRNGV--QIAQIAEDCGIASLAVHGRT--------RQCMYKGNAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IKK N  + +  NG +    +A  +L     D +MIGR A     +   +  Y    
Sbjct: 186 IKAIKK-NVSIPVVANGDIVTPEKARFVLDQTGADALMIGRGAQGRPWIFREIQHYLETG 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF---HGFPNSRRC 293
              +              +      Y          ++   +H+          P     
Sbjct: 245 NKLAPVEMDEKRLVMLEHLKNLYALY-----GEYKGIRFARKHVGWYLDQDEQRPFRAEF 299

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
             + TVE   S      +E  F+ + ++
Sbjct: 300 NRLETVEEQGSM-----VERYFDEIAQN 322


>gi|227499305|ref|ZP_03929417.1| dihydrouridine--tRNA ligase [Anaerococcus tetradius ATCC 35098]
 gi|227218656|gb|EEI83890.1| dihydrouridine--tRNA ligase [Anaerococcus tetradius ATCC 35098]
          Length = 326

 Score =  221 bits (563), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 65/329 (19%), Positives = 132/329 (40%), Gaps = 29/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R            +TEM+  +A+   ++  + I+  S  EK + +QI G D
Sbjct: 15  MAGVTDSAFRQICEE-NGCDKTFTEMVSVNALDFDNRATEEIMYRSKAEKNVNIQIFGKD 73

Query: 59  ISKLVEAAKI----VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +    K     +E+F   EI+ N+GCP+ ++ +   G+ LM +   V      +  +
Sbjct: 74  TDIIERVVKEKINPIEEF--KEISFNMGCPAPKIFKNGQGSALMADLKKVYAIGKCLVDS 131

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +  V VK R+G+DD         + K+++ +GV+ + +HAR         ++ +     
Sbjct: 132 TNKIVNVKFRLGIDDSSKN--YIEVAKALEDAGVDYVILHART--------RNQQYSGKA 181

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + ++K ++  + +  NG    +     IL     DGVM+ R    N  +   + +Y
Sbjct: 182 DWTAIRKLK-DSLGIPVIANGDCFSVEDYKNILEVTGADGVMLARGVMGNPFLFRQIKDY 240

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                       TR+  D   K      + +  +      + Q+ +H+     G P++  
Sbjct: 241 IQGKEI------TRIGFDDILKTIKRQYELSLAYKDEKLVINQMRKHVGWYIKGLPSAAT 294

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIES 321
            R  +            ++E     + ++
Sbjct: 295 YRARVNKLKTTRE-IFDLLEEYRKNLEDN 322


>gi|315924890|ref|ZP_07921107.1| tRNA-dihydrouridine synthase B [Pseudoramibacter alactolyticus ATCC
           23263]
 gi|315621789|gb|EFV01753.1| tRNA-dihydrouridine synthase B [Pseudoramibacter alactolyticus ATCC
           23263]
          Length = 322

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 61/321 (19%), Positives = 122/321 (38%), Gaps = 24/321 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +++  +R  A+    +A+  TEMI A  +   DKK   ++    +E P  +Q+ G+D 
Sbjct: 18  AGYSNLPFRLMAKKYGADAVT-TEMISAKGLFYRDKKTAKLMATCPEEAPAGIQLFGSDP 76

Query: 60  SKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + +    A+ V    +  I+ N GCP+ ++ +   GA L+ +   +   +  M      P
Sbjct: 77  AIIERVVAEQVNATPFAFIDFNAGCPAPKIVKNGDGAALLKDLSRLEAIVCRMKTVSIKP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R+G D            K I+ +G + + +H R         ++       D+  
Sbjct: 137 VHVKIRLGWDAGHRVAV--EAAKRIEAAGADVLTVHGRT--------REAFYSGAADWPA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K     L +  NG ++      A       DG+M+GR A  N  +   + +  +  
Sbjct: 187 IAEVK-AAVSLPVVANGDIDSPEAAAAALAATGADGLMVGRGAIGNPFIFREMKQALAGK 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 +  R+      + +              G + ++ + ++    G P S   R  
Sbjct: 246 TAAPPSVDERL------QAAIDHVHLVTAMAERVGPMVEMRKQLVAYTRGMPGSAALRQQ 299

Query: 297 LTVEAGASTATHHIIETAFNL 317
           +   +    A   ++E     
Sbjct: 300 IFTRSTG-EALLALLEAYREA 319


>gi|237739609|ref|ZP_04570090.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 2_1_31]
 gi|229423217|gb|EEO38264.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 2_1_31]
          Length = 307

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 64/302 (21%), Positives = 121/302 (40%), Gaps = 23/302 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I          A+QI G DI K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLRDGNAVQIFGEDIEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  +AK +++ G   INLN GCP  ++    +GA L+ +P+ +   ++ +   L   + +
Sbjct: 69  IKLSAKYIQNLGVKHINLNCGCPMKKIVNCGYGAALVKDPEKIKRILSEIKSVLNDDVKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK RIG  +    V    + K  ++ G + I +H R         ++       D+  +
Sbjct: 129 SVKIRIGYKEPENYV---QIGKIAEEVGCDHITVHGRT--------REQLYSGKADWSYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTAEDALEKISYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D      +    +  + +H+     G  N    +  +
Sbjct: 237 VKNPVTKDEKINMAIEHLKRIRVD------NDDQFIFDVRKHISWYLKGLENCAEAKRKI 290

Query: 298 TV 299
             
Sbjct: 291 NT 292


>gi|297571272|ref|YP_003697046.1| hypothetical protein Arch_0694 [Arcanobacterium haemolyticum DSM
           20595]
 gi|296931619|gb|ADH92427.1| TIM-barrel protein, nifR3 family [Arcanobacterium haemolyticum DSM
           20595]
          Length = 407

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 63/335 (18%), Positives = 116/335 (34%), Gaps = 53/335 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNA----------------------LLYTEMIVADAILRGDKK 38
           M   T+  +R   R                            L   EM+ + A++    +
Sbjct: 19  MAGVTNPPFRQLCREFGEAGARAAGVTEVGSGHTTGTVSHAGLYVCEMVTSRALIERVPE 78

Query: 39  NILGF--STQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGA 95
            +        +   ++Q+ G +   +  A +I+      + I++N GCP  +V     G+
Sbjct: 79  TLTMIQPDPADPVRSIQLYGVEPKNIAAAVEILVREDWADHIDINFGCPVPKVTRKGGGS 138

Query: 96  CLMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAVALRNLVKSIK 144
            L     +  D +     A             IPVT K RIG+DD       R++ K  +
Sbjct: 139 ALPWKHQLFSDIVTGAVAASERASREAGRTHTIPVTAKFRIGIDDD--HTTFRDVAKMSE 196

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +G++ + +HAR          +        +D + E+K    +L I  NG + +   A 
Sbjct: 197 DAGISALTLHARTT--------EQHYSGQAQWDYIRELK-ATSNLPIFGNGDVFEAEDAA 247

Query: 205 KILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           ++L     DGV +GR       +   +            P    V     R    S+  +
Sbjct: 248 RMLAHTAADGVCVGRGCQGRPWLFFDLVAASYGSDARYRPSLREVADIIVRHGELSVAHF 307

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              H      ++++ +H+     GF    + RH L
Sbjct: 308 GDEHRA----MRELRKHVGWYMRGFSVGGQMRHQL 338


>gi|139472982|ref|YP_001127697.1| tRNA-dihydrouridine synthase [Streptococcus pyogenes str. Manfredo]
 gi|134271228|emb|CAM29444.1| putative tRNA-dihydrouridine synthase [Streptococcus pyogenes str.
           Manfredo]
          Length = 325

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 64/323 (19%), Positives = 129/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDENEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   + +++N+GCP  +V +   GA  + +P+ +   +  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKADIVDINMGCPVNKVVKNEAGAKWLRDPNKIYHIVKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D+ 
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTCDHK 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  +      D  +     + +     +     +++          G   + + R 
Sbjct: 252 GQELAD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGTAGAAKVRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +E  F  +
Sbjct: 307 AVSRAETLAE-----VEAIFETV 324


>gi|254517397|ref|ZP_05129454.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR5-3]
 gi|219674235|gb|EED30604.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR5-3]
          Length = 327

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 126/294 (42%), Gaps = 26/294 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           M   TD  +R          LL  EM+ +D  LR  +K+    S   +  P ++QI G D
Sbjct: 18  MAGVTDLPFRRLCARF-GTGLLVGEMVHSDPRLRESRKSQQRRSHDLEIDPRSVQIVGND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+   + G   I++N+GCP+ +V   + G+ L+ +  +V   + A+  A+S+P
Sbjct: 77  PLLMAEAARYNVNCGAQVIDINMGCPAKKVCRKAAGSALLADEPLVASILHAVVNAVSVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D         ++ +  + +G+  + +H R         +      ++++D 
Sbjct: 137 VTLKIRTGADPHHRNGV--SIARIAEDAGIALLAVHGRT--------RACAFSGDVEHDT 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              I  E+ D+ +  NG +     A  +L      GVMIGRAA     +   V    +  
Sbjct: 187 TARIV-ESIDIPVLANGDIRSADDARAVLAHTGAAGVMIGRAAQGAPWLPGMVANAIAGG 245

Query: 237 LTGSSPIKTR--VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
              +  + T+  V ++   ++ A   ++A   +          +H+     G P
Sbjct: 246 AYAAPSLATQYAVMREHLEELHAFYGEFAGSRIA--------RKHIGWYLDGHP 291


>gi|75675635|ref|YP_318056.1| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrobacter
           winogradskyi Nb-255]
 gi|74420505|gb|ABA04704.1| tRNA-U20-dihydrouridine synthase [Nitrobacter winogradskyi Nb-255]
          Length = 349

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 73/285 (25%), Positives = 120/285 (42%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           M   TDR +R     L   AL+ +EM  +D ++RG   ++L        P  +Q+ G + 
Sbjct: 33  MSGITDRPFRRLTESL-GAALVVSEMTASDDLVRGRPMSVLRCEATGHGPHVVQLAGCET 91

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I E  G + I++N+GCP+  V  G  G+ LM +PD   D I A   A+++PV
Sbjct: 92  RWMAEAARIAEAAGADIIDINMGCPARHVTGGQSGSALMRDPDHALDLIEATVGAVNVPV 151

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D    +    +L +  + +GV  I +H R         +        D+  V
Sbjct: 152 TLKMRLGWDGH--SFNAPSLARRAESAGVRMITVHGRT--------RCQFYKGRADWRAV 201

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + + +NG +     A+  L     D VM+GR A     +   +       +
Sbjct: 202 RAVK-EAVRVPVVVNGDITSFDAAVAALEASGADAVMVGRGAQGRPWLPGQIGRRLETGI 260

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             S P  T             +  Y  R       L+   +H+  
Sbjct: 261 EESHPSLTDQLAYIRALYDDLLLHYGLRI-----GLRHARKHLGW 300


>gi|254453092|ref|ZP_05066529.1| tRNA-dihydrouridine synthase B [Octadecabacter antarcticus 238]
 gi|198267498|gb|EDY91768.1| tRNA-dihydrouridine synthase B [Octadecabacter antarcticus 238]
          Length = 333

 Score =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 120/289 (41%), Gaps = 25/289 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGGA 57
              +D  +R           + +EMI +  +++       K  LGF   +   A+Q+ G 
Sbjct: 20  AGISDLPFRQLVASF-GAGWVVSEMIASQEMVQAKPGVREKAELGF--NQANTAVQLAGR 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAA+ VE  G   I++N+GCP+ +V  G  G+ L+ + D     I A+  A+ I
Sbjct: 77  EAHWMAEAARHVEANGAAMIDINMGCPAKKVTSGYSGSALLRDLDHALTLIDAVVGAVDI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G DD +  +   +L    + +G+  I IH R         +        ++D
Sbjct: 137 PVTLKTRLGWDDAL--LNAPDLAVRAENAGIARIVIHGRT--------RCQFYKGRANWD 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     + +  NG + D S A   L     DG+MIGR A     ML  V    S 
Sbjct: 187 AIALVKNAV-SIPVIANGDIIDASTAKTALDASGADGLMIGRGAQGCPWMLRDVAAQLSG 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            +  + P  +   +       A ++ Y  +        +   +H+    
Sbjct: 246 NVAPAPPQGSAFIQLVSDHYDAMLSFYGTQMGS-----KAARKHLGWYM 289


>gi|83593011|ref|YP_426763.1| dihydrouridine synthase TIM-barrel protein nifR3 [Rhodospirillum
           rubrum ATCC 11170]
 gi|83575925|gb|ABC22476.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodospirillum
           rubrum ATCC 11170]
          Length = 362

 Score =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 71/301 (23%), Positives = 124/301 (41%), Gaps = 24/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF------STQEKPLALQI 54
           M   TD  +R  A       L +TEM+ +  +LR   + +         + +  P A+Q+
Sbjct: 19  MAGVTDSPFRRLAHDY-GCPLSWTEMVASRELLRERARGVDPRLGGGAEAGRAGPFAVQL 77

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G D   + EAA+ VE  G   I++N+GCP  +V  G  G+ LM +  +    + A+  A
Sbjct: 78  AGCDPLIMAEAARRVEGAGAELIDINMGCPVRKVVGGLGGSALMRDLPLAARILEAVVGA 137

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +++PV++K R+G DD         L +  + +G++ + +H R         +        
Sbjct: 138 VTLPVSLKMRLGWDDASRNAV--ELARLAESAGISRLTVHGRT--------RAQMYDGRA 187

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K+    L +  NG + ++S+A +IL     DGVMIGRAA     +   +   
Sbjct: 188 DWPAIGLVKRAV-SLPVIANGDVTNLSEAREILAVTGADGVMIGRAALGAPWLPGAIARA 246

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +     + P                +   A   L  G  L+   +HM       P    
Sbjct: 247 IAAGTRETPPPALAERAAVMAAHLEGLL--ACHGLERG--LKTSRKHMGWYARTMPQGAD 302

Query: 293 C 293
            
Sbjct: 303 F 303


>gi|303279296|ref|XP_003058941.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460101|gb|EEH57396.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 376

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 110/361 (30%), Positives = 173/361 (47%), Gaps = 40/361 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGGA 57
           M+D+T  H+R   R+L+    LYTEM V   +   D   +   L F  Q  P  LQ+GG+
Sbjct: 13  MMDYTTAHFRAMCRMLSRKTWLYTEMEVDQTLTHVDHPRLDRYLDFPLQTHPSVLQLGGS 72

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKAL- 115
           D   L  AA I   + Y+E+NLN GCPS +V     FGA LML P++V DC+AAM     
Sbjct: 73  DPESLGRAAAIAAPYAYDELNLNCGCPSPKVAGKGNFGAALMLEPELVADCVAAMAANSG 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIK--------KSGVNGIWIHARKAILK------ 161
             PVTVKCRIGVDD     AL   V+++         +       IHARKA+L+      
Sbjct: 133 GAPVTVKCRIGVDDVDSYDALCAFVETVAARMPPRRGEDARPLFAIHARKALLRRVLYTG 192

Query: 162 -----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS------- 209
                GLSP +NR +P L ++ V+ + ++ PD+   +NGG+  + +A+ I          
Sbjct: 193 SHTTAGLSPAENRTVPPLRHEWVHALARDFPDVAFAINGGINTLEEAVAIARGEGTPVGG 252

Query: 210 --VDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-AR 265
             + G MIGR A+ +   +L   D       +     +  + + +     A+   Y   +
Sbjct: 253 GRLVGTMIGRRAHADPWGLLARADTAVFGEASDPCVSRRALLETYAAYADATWARYGTTK 312

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRH----ILTVEAGASTATHH-IIETAFNLMIE 320
             ++   ++ +   +  LF G PN++R R     +L  +A  +T T   ++E    ++ +
Sbjct: 313 DGYAVPSIRHLMHPLQNLFLGEPNAKRWRREVDEVLKRDARRATTTVTGVLEETLRVLSD 372

Query: 321 S 321
            
Sbjct: 373 E 373


>gi|87309552|ref|ZP_01091687.1| hypothetical protein DSM3645_24660 [Blastopirellula marina DSM
           3645]
 gi|87287860|gb|EAQ79759.1| hypothetical protein DSM3645_24660 [Blastopirellula marina DSM
           3645]
          Length = 361

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 64/325 (19%), Positives = 128/325 (39%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M  +T+  +R   R      L  TEM+ A + +  D++      + G   + +PLA+Q+ 
Sbjct: 33  MAGYTNYAFRQIVRDYGGVGLQATEMVSARSFVWLDQQAEFPDRLWGIEDEPRPLAVQMW 92

Query: 56  GADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCK 113
             +   +     ++VE+F  + +++N GCP  +V +    G+ L+  P+ +   I  + +
Sbjct: 93  DNEPDTMARVGERLVEEFQVSVVDINFGCPVKQVTQSAHSGSYLLRWPEKMFSIIRRVVE 152

Query: 114 AL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           A    PVT K R+G       +    + + ++++G   + +H R A         +    
Sbjct: 153 ACAPTPVTAKIRLGC--SRDKINANEIAQVVEEAGAAALTVHGRTA--------ADFFKG 202

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           + D++ + EIK     + +  NG L+  ++ ++      VDGVMI RA      +     
Sbjct: 203 SADWEKISEIKPYLKKIPLIGNGDLDSAAKVVEAFRSYQVDGVMIARACLGRPWLFAQAA 262

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                    + P  T       R     +  +    +  G  L  + +       G   +
Sbjct: 263 AALRGEPVPADPTLTEQRMCLLRHYDLVVQRFG---IEKGTML--MRKFACCYAQGMYGA 317

Query: 291 RRCRHILTVEAGASTATHHIIETAF 315
           R  R     +  +    + I+E  F
Sbjct: 318 RAFRTR-AAKVSSPAEFYEIVENLF 341


>gi|327398323|ref|YP_004339192.1| dihydrouridine synthase DuS [Hippea maritima DSM 10411]
 gi|327180952|gb|AEA33133.1| dihydrouridine synthase DuS [Hippea maritima DSM 10411]
          Length = 320

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 140/317 (44%), Gaps = 31/317 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD+ +R   R      L ++E+I  +AI   +KK +  +     +KP  +Q+ G+D
Sbjct: 17  MAGYTDKPFRKLCREF-GCGLTFSELISVNAIYYKNKKTLKLIERDITDKPYCIQLFGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               + AA+ VE F  + I++N GCP+ +V     G+ L+  P  +      + K L  P
Sbjct: 76  ERLFLYAAQFVEPF-CDCIDINAGCPAPKVIRAKAGSYLLKEPKKLISITQTLRKHLKKP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K RIG +   P      L K +++SG++ I IH R         K       +DY+ 
Sbjct: 135 LSIKMRIGYEKINPV----ELYKELERSGIDFITIHGRL--------KSQYFKGEVDYNH 182

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +I      + +  NGG++   +A ++  +   + +MIG+AA     +   +++     
Sbjct: 183 IGQI-NSVLSIPVVANGGIDSFKKAQQVKRITGCEYLMIGQAAIGKPFIFEDLNK----- 236

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 + T  D  F + +      Y          ++Q  +       G+PN +R  ++
Sbjct: 237 -----KVDTNRDLGFVKAVMKRHLQYMIDFWG-DTAIRQFRKFFHAYLKGYPNIKRFNNM 290

Query: 297 LTVEAGASTATHHIIET 313
           +   +  + A  +II+ 
Sbjct: 291 INNCSTNNEA-LNIIDR 306


>gi|254461960|ref|ZP_05075376.1| tRNA-dihydrouridine synthase B [Rhodobacterales bacterium HTCC2083]
 gi|206678549|gb|EDZ43036.1| tRNA-dihydrouridine synthase B [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 331

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 67/289 (23%), Positives = 115/289 (39%), Gaps = 25/289 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGGA 57
              TD  +R          L+ +EM+ +  +++       K  LGF      +  QI G 
Sbjct: 22  AGITDLPFRNLVCSF-GAGLVVSEMVASQEMVKAKPGVREKAELGFGAARTSV--QIAGR 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAA++    G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+ +
Sbjct: 79  EAYWMAEAARLAAGNGAQIIDINMGCPAKKVTSGYSGSALMKDLDHALTLIEAVVGAVDV 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D+ +   A   L    + +G+  I IH R         +        ++ 
Sbjct: 139 PVTLKTRLGWDNHLLNAA--ELAVRAESAGIQMITIHGRT--------RCQFYKGQANWS 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  IK     + +  NG + D++ A   L     DG+M+GR A     +L  +      
Sbjct: 189 AIKGIK-AAVRIPVIANGDIVDVATARAALSQSGADGIMVGRGAQGRPWILAQIAAELHG 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 P K     D  +   A+M  +    L S        +H+    
Sbjct: 248 LPAPKIP-KGAALIDMVQGHYANMLVFYGEALGSRVA----RKHLGWYM 291


>gi|148269963|ref|YP_001244423.1| nifR3 family TIM-barrel protein [Thermotoga petrophila RKU-1]
 gi|170288648|ref|YP_001738886.1| NifR3 family TIM-barrel protein [Thermotoga sp. RQ2]
 gi|147735507|gb|ABQ46847.1| putative TIM-barrel protein, nifR3 family [Thermotoga petrophila
           RKU-1]
 gi|170176151|gb|ACB09203.1| TIM-barrel protein, nifR3 family [Thermotoga sp. RQ2]
          Length = 306

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 63/325 (19%), Positives = 132/325 (40%), Gaps = 31/325 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           M  +TD  +R  A         ++EM+ A   L   +K   L     E+ +A+QI G++ 
Sbjct: 10  MAGYTDSAFRTLAFEW-GADFAFSEMVSAKGFLMNSQKTEELLPQPHERNVAVQIFGSEP 68

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S+L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   
Sbjct: 69  SELSEAARILSE-KYKWIDLNAGCPVRKVVKKGAGGALLKDLRHFRYIVRELRKSVSGKF 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +       +  + + + + GV+ ++IH R  +       + + +  L+    
Sbjct: 128 SVKTRLGWEKN----EVEEIYRILVEEGVDEVFIHTRTVVQGFTGKAEWKALSVLE---- 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                    +   ++G +     A + L     DG+++ R A     +   + ++  +  
Sbjct: 180 -------KRVPTFVSGDVFTPEDAKRALEESGCDGLLVARGAIGRPWIFKQIKDFLRSGR 232

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             S P +  + + F R +     +   +       + ++ + + G       +RR R   
Sbjct: 233 Y-SEPSREEILRTFERHL-----ELLIKTKGERKAVVEMRKFLAGYTKDLKGARRFR--- 283

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
             E         I++  F   I+ +
Sbjct: 284 --EKVMKIEKVQILKEMFYNFIKEV 306


>gi|265984180|ref|ZP_06096915.1| nifR3 family TIM-barrel protein [Brucella sp. 83/13]
 gi|264662772|gb|EEZ33033.1| nifR3 family TIM-barrel protein [Brucella sp. 83/13]
          Length = 332

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +           +
Sbjct: 193 HAV-RDAVKIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWL---------AGV 242

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 243 IAGSDFAPRDTNGILEYIIRHYED-MLDHYGSKTGIRHARKHLGWYM 288


>gi|254719183|ref|ZP_05180994.1| nitrogen regulation protein Nifr3 [Brucella sp. 83/13]
 gi|306838176|ref|ZP_07471032.1| putative TIM-barrel protein, nifR3 family [Brucella sp. NF 2653]
 gi|306406766|gb|EFM62989.1| putative TIM-barrel protein, nifR3 family [Brucella sp. NF 2653]
          Length = 333

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +           +
Sbjct: 194 HAV-RDAVKIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWL---------AGV 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 IAGSDFAPRDTNGILEYIIRHYED-MLDHYGSKTGIRHARKHLGWYM 289


>gi|149177590|ref|ZP_01856192.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
 gi|148843570|gb|EDL57931.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
          Length = 365

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 63/319 (19%), Positives = 128/319 (40%), Gaps = 19/319 (5%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADI 59
             +T+  +R   R L    L  T+++ A  +L G +K +       ++ P A+QI G++ 
Sbjct: 36  AGYTNLPFRRIVRELGGVGLATTDLVNARGLLEGSEKTLQLTQTCPEDSPFAVQIFGSEP 95

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++ +AA+++E  G + I++N+GCP  R+ +G  GA +M  P      +  + +A+ IPV
Sbjct: 96  QQMKDAAQLLESRGVHSIDINMGCPVNRIVKGGAGASMMCRPSDTVSLVQTVVEAVKIPV 155

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G DD   +       +  +K GV  + IH R         ++      +++D +
Sbjct: 156 SVKMRLGWDDSELSAPF--FSREFEKVGVVAVAIHGRT--------REQGFRGVVNHDGI 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +    + +  NG + ++++A  +L      GV IGR A  N  +   + ++     
Sbjct: 206 RRVVEAVDSIPVIGNGDVTNVAEADFMLKTTGCAGVSIGRGALANPWIFRQLVQWEQTGT 265

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                      +   R+       Y          +    +               RH  
Sbjct: 266 YDPPGNFDDRLELLLRQ-----FRYLLEMTTEKRAISMFRKMGHWYLKSMRVKPAMRHEF 320

Query: 298 TVEAGASTATHHIIETAFN 316
            + +        + + A  
Sbjct: 321 QLASNLDEFGQAVRKIAAE 339


>gi|320534182|ref|ZP_08034711.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320133603|gb|EFW26022.1| TIM-barrel protein, nifR3 family [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 432

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 66/338 (19%), Positives = 129/338 (38%), Gaps = 57/338 (16%)

Query: 1   MVDWTDRHYRFFAR-------------------------LLTNNALLYTEMIVADAILRG 35
           M   T+  +R   R                         LL    L  TEM+   A++  
Sbjct: 37  MAGVTNASFRRLCREMAEAVLPEALTPSCPGPVSAPGGGLLAPAGLYVTEMVTTRALVER 96

Query: 36  DKKN--ILGFSTQEKPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGS 92
           +++   ++     E+  ++Q+ G D + +  A +I VE+   + I+LN GCP  +V    
Sbjct: 97  NERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEEDLSDHIDLNFGCPVPKVTRKG 156

Query: 93  FGACLMLNPDIVGDCI-----------AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            GA L    D++   +            A  +   +PVT+K R+G+D+        +  +
Sbjct: 157 GGAALPWKRDLLAAILTEAVRASEAAARAAGRVRQVPVTMKMRLGIDEG--HETFLDAAR 214

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           + + +G+  + +HAR A                 ++ +  +K E+  L +  NG +    
Sbjct: 215 AAENAGIAAVALHARSA--------RQHYSGQARWEEIARLK-ESTVLPVLGNGDIWLGD 265

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            A++++     DGV++GR       +   +           SP +TR D D   ++    
Sbjct: 266 DAVRMMETTGCDGVVVGRGCQGRPWLFADIVAAMHG-----SPTRTRPDLDAVIEVIRRH 320

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               A  +     ++ + +H+     G+P     R  L
Sbjct: 321 GRMLAEEMGEDRGVRDLRKHVGWYLKGYPVGGAARADL 358


>gi|192291239|ref|YP_001991844.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris TIE-1]
 gi|192284988|gb|ACF01369.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris TIE-1]
          Length = 333

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 127/315 (40%), Gaps = 33/315 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           M   TD  +R     L    L+ +EM  ++ ++ G + ++       + P  +Q+ G + 
Sbjct: 17  MTGITDAPFRRQVAEL-GAGLVVSEMTASEDLVAGRRMSVRRCDKVGQGPHVVQLAGCEP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 76  RWMAEGARIAEAGGADIIDINMGCPARHVTGGLSGSALMRDLDHALTLIEATIGAVRVPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+        L +  + +G+  + +H R         +        D+D V
Sbjct: 136 TLKMRLGWDDRSRNA--PELARRAQDAGIQLVTVHGRT--------RQQFYKGEADWDAV 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + + +NG +   + A++ L     D VMIGR A     +   V    +   
Sbjct: 186 RAV-RDAISIPLVVNGDITCHASAVEALKRSGADAVMIGRGAQGRPWLPGQVGRQLTTGK 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             + P  T       R    ++ D           L+   +H+                L
Sbjct: 245 AEAEPSLT-----MQRDYLRALYDDILALYGVKIGLRHARKHLGW-------------SL 286

Query: 298 TVEAGASTATHHIIE 312
            V A  + A+  +++
Sbjct: 287 EVAASTAGASPDVLK 301


>gi|225871383|ref|YP_002747330.1| tRNA-dihydrouridine synthase [Streptococcus equi subsp. equi 4047]
 gi|225700787|emb|CAW95466.1| putative tRNA-dihydrouridine synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 325

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 67/323 (20%), Positives = 128/323 (39%), Gaps = 27/323 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQSHTKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIQEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 143 PLTVKMRTGWADSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGTCDHE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + +    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSRAITRIPFIGNGDVRTVQDARFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +   +       I+        R       +++          G   + + R 
Sbjct: 252 GE-----VLPELPFAKKLDIAKDHLKRLIRLKGEAIAVREFRGLAPHYLRGTAGAAKIRS 306

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            ++     +      +ET F  +
Sbjct: 307 AVSRAKTLAE-----VETIFAQI 324


>gi|215429674|ref|ZP_03427593.1| transcriptional regulator [Mycobacterium tuberculosis EAS054]
          Length = 330

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 70/282 (24%), Positives = 114/282 (40%), Gaps = 23/282 (8%)

Query: 26  MIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVG 82
           M+ A A++       ++  FS  E P +LQ+   D      AA+++   G  + I++N G
Sbjct: 1   MVTARALIERHPVTMHMTTFSADESPRSLQLYTVDPDTTYAAARMIAGEGLADHIDMNFG 60

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LSIPVTVKCRIGVDDQIPAVALRNL 139
           CP  +V +   GA L     + G  +AA  +A     IPVTVK RIG+DD        + 
Sbjct: 61  CPVPKVTKRGGGAALPFKRRLFGQIVAAAVRATEGTDIPVTVKFRIGIDD--AHHTHLDA 118

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +  +  G   + +HAR A          R     D++ +  +K+    + +  NG + D
Sbjct: 119 GRIAEAEGAAAVALHARTA--------AQRYSGTADWEQIARLKQHVRTIPVLGNGDIYD 170

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              AL ++     DGV+IGR       +   +   F+     + P    V       I  
Sbjct: 171 AGDALAMMSTTGCDGVVIGRGCLGRPWLFAELSAAFTGSPAPTPPTLGEVA-----DIIR 225

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 A H      ++ I +H+    HGFP     R  L +
Sbjct: 226 RHGTLLAAHFGEDKGMRDIRKHIAWYLHGFPAGSALRRALAM 267


>gi|153006747|ref|YP_001381072.1| nifR3 family TIM-barrel protein [Anaeromyxobacter sp. Fw109-5]
 gi|152030320|gb|ABS28088.1| putative TIM-barrel protein, nifR3 family [Anaeromyxobacter sp.
           Fw109-5]
          Length = 348

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 118/322 (36%), Gaps = 23/322 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R +   +  YTEM+ A  ++ G    ++ L     E P A+QI  ++ 
Sbjct: 18  AGVSDRPFRAICRSM-GASFAYTEMVSAHGLVHGTLQTESYLDRDPDEDPFAVQIFASEA 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   A++    G   I++N+ CP  +V     GA L  +P  V + + A+  A+++PV
Sbjct: 77  DVLARGAEVAVRAGAGIIDVNMACPVKKVCGTGAGAALGRDPRRVEEAVRAIRAAVAVPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G DD                +    +    R  +  G             +++V
Sbjct: 137 TVKIRAGWDDAEVNCVEVARAAEAGGAAAVALHGRTRTQMYSG----------RARWELV 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  +G +  +  AL++      D V++ R A  N  +   +        
Sbjct: 187 RAVK-EAVSVPVLGSGDVWTVDDALRMRAETGCDAVLVARGACGNPWIFRELRAAELGAP 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLH------SGGKLQQITRHMIGLFHGFPNSR 291
               P +          +   +     +H            ++++ +H++    G     
Sbjct: 246 RPPPPTRDEWIGTVLHHVRLQVEHRQRQHPGDDPLELERLAIRELRKHLLWYTRGRRGGV 305

Query: 292 RCRHILTVEAGASTATHHIIET 313
             R      A A+     +IE 
Sbjct: 306 HFRRDANRLATAADV-AQVIEE 326


>gi|119502731|ref|ZP_01624816.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2080]
 gi|119461077|gb|EAW42167.1| tRNA-dihydrouridine synthase B [marine gamma proteobacterium
           HTCC2080]
          Length = 352

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 69/289 (23%), Positives = 123/289 (42%), Gaps = 25/289 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD   R     L    +   EM+ +D  L   +K+ L    S +    ++QI G++
Sbjct: 31  MAGVTDLPMRELCVEL-GAGMAVAEMLTSDPKLLASRKSSLRRRHSAKGGLRSVQIVGSE 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA++  D G + I++N+GCP+ +V + + G+ L+ + D V + + A+  A+ +P
Sbjct: 90  PQQLANAARLNADDGADVIDINMGCPAKKVCKKAAGSALLADEDRVAEILKAVVSAVDVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R GV  Q        + K  + +G+  + +H R         + +R     +Y  
Sbjct: 150 VTLKIRTGVSPQQRNGVA--IAKIAEDAGIQLLTVHGRT--------RADRFKGEAEYHT 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I  +   + +  NG +   +QAL +L      G+MIGRAA     +   + +  +  
Sbjct: 200 IERIV-DAVSIPVLANGDITTPAQALAVLQKTGAAGIMIGRAALGRPWLPGAIAQSLAGL 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLF 284
            T    +  R                 A H  H      +I R  +G F
Sbjct: 259 RTPLPSLAERF--------LQMRCHLTALHDFHGDFMGVRIARKHVGWF 299


>gi|195978929|ref|YP_002124173.1| probable tRNA-dihydrouridine synthase Dus [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
 gi|195975634|gb|ACG63160.1| probable tRNA-dihydrouridine synthase Dus [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
          Length = 313

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 124/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G +
Sbjct: 12  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEHPISIQLFGGN 70

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 71  AEGLKRAADFIQSHAKADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIREVTSVLDI 130

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   AV       + + +GV+ + +H R         ++       D++
Sbjct: 131 PLTVKMRTGWADSSLAVEN---ALAAEAAGVSALAMHGRT--------REQMYTGTCDHE 179

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + +    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 180 TLARVSRAITRIPFIGNGDVRTVQDAAFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                    T+   D  R+    +       +     +++          G   + + R 
Sbjct: 240 GEVLPELPFTK-KLDIAREHLKRLIRLKGETIA----VREFRGLAPHYLRGTAGAAKIRS 294

Query: 296 ILT 298
            ++
Sbjct: 295 AVS 297


>gi|296122547|ref|YP_003630325.1| hypothetical protein Plim_2300 [Planctomyces limnophilus DSM 3776]
 gi|296014887|gb|ADG68126.1| TIM-barrel protein, nifR3 family [Planctomyces limnophilus DSM
           3776]
          Length = 351

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 128/321 (39%), Gaps = 24/321 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             +T+  +R     L    L  T+++ A  +L G +K   ++     ++P A+QI G + 
Sbjct: 22  AGFTNLPFRRVVHELGGLGLGTTDLVNARGLLAGSEKTLRLIATHPIDRPFAVQIFGGEA 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           S + +AA+++E  G + I++N+GCP  +V +   GA LM + D   + + A+ +A+ +PV
Sbjct: 82  SIMRDAAQLLEARGVDSIDINMGCPVLKVVKTGAGASLMCHADAATELVKAVVEAVHVPV 141

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D     +      +  ++ GV  + IH R    +G S   NR       D +
Sbjct: 142 TVKMRLGWD--ASQLTAPRFAREFEQVGVAAVAIHGRTRA-QGFSGTVNR-------DGI 191

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++ +    + +  NG +  +  A+ +        + IGR A  N  +   + E+ +   
Sbjct: 192 RQVVEAVDSIPVIANGDIRSVDDAIAMYDETGCQAISIGRGALANPWIFRQLTEWETTGD 251

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +           R+       Y    +     +    +               RH  
Sbjct: 252 WAPAGSFNDRLLLMRRQ-----FRYLQEWVGEETAVSAFRKMSHWYTKAMRVGPALRH-- 304

Query: 298 TVEAGASTATHHIIETAFNLM 318
              A  S  T    E A   +
Sbjct: 305 ---AVQSAKTGEEFEQALQEI 322


>gi|261366358|ref|ZP_05979241.1| tRNA-dihydrouridine synthase B [Subdoligranulum variabile DSM
           15176]
 gi|282571961|gb|EFB77496.1| tRNA-dihydrouridine synthase B [Subdoligranulum variabile DSM
           15176]
          Length = 325

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 126/318 (39%), Gaps = 25/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD   R         A   +EM  A A+  GD+K+  +L         A+Q+ GA+
Sbjct: 17  MAGLTDAACRRMMAD-HGAAWTVSEMASAKALNFGDRKSFALLKDPDPHGIYAIQLFGAE 75

Query: 59  ISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL- 115
              L +A  +V + G  ++ +++N+GCP+ ++     G+ L+L+P + G  +AA  KAL 
Sbjct: 76  PETLAKAILLVREKGIRFDILDINMGCPAPKITSSGAGSHLLLDPPLCGAMVAAARKALG 135

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
              P+TVK RIG D          + +  + +G + + +H R         ++   IP +
Sbjct: 136 DDTPLTVKMRIGWDADHMTGV--EVARQCEANGADLLAVHGRT--------REQMYIPPI 185

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D D +  +K+    + +  NG +     AL +L     DGVMIGR A  +  +   V   
Sbjct: 186 DTDAIAAVKQAV-QIPVLANGDVTTAEGALDLLAKTGCDGVMIGRGALGDPWLFERVRAA 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                  + P   +      R+I                 + Q     +    G   +  
Sbjct: 245 LLGEEPPAEPSLNQRMMALRRQIYEMC-----EEKGEWLAMPQARSQAMHYMKGLRGAAS 299

Query: 293 CRHILTVEAGASTATHHI 310
            R   ++    +     I
Sbjct: 300 LRRYCSMLEHFTDVDKLI 317


>gi|86160208|ref|YP_466993.1| dihydrouridine synthase TIM-barrel protein nifR3 [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85776719|gb|ABC83556.1| tRNA-U20-dihydrouridine synthase [Anaeromyxobacter dehalogenans
           2CP-C]
          Length = 352

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 54/304 (17%), Positives = 108/304 (35%), Gaps = 22/304 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R +   +  YTEM+ A  ++ G     + L     E P A+QI  ++ 
Sbjct: 18  AGVSDRPFRAICRRM-GASFAYTEMVSAHGLMHGALQTSSYLDREPDEDPFAVQIFASEP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   A +    G   I++N+ CP  +V     GA +  +P  V + + A+  A+ +PV
Sbjct: 77  DVLARGAVVAVQAGAGMIDVNMACPVKKVCGSGAGAAMGRDPRKVEEAVRAIRAAVPVPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D+                +    +    R  +  G             +++V
Sbjct: 137 TVKIRAGWDEGEVNCVDVARAAEAGGAAAVALHGRTRSQLYSG----------KARWELV 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  +G +     A+++      D V++ R A  N  +   +    +   
Sbjct: 187 RAVKQAV-AIPVLGSGDVWTAGDAVRMREETGCDAVLVARGACGNPWIFRELKAIEAGRP 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAAR------HLHSGGKLQQITRHMIGLFHGFPNSR 291
               P +          +   +   A               ++++ +H++    G     
Sbjct: 246 PPPPPGRDEWVGTVLEHVRLQVEHRARMAPGEPAEASERHAIRELRKHLLWYTRGRRGGV 305

Query: 292 RCRH 295
             R 
Sbjct: 306 HFRR 309


>gi|39935657|ref|NP_947933.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris CGA009]
 gi|39649510|emb|CAE28032.1| putative nitrogen regulation protein nifR3 [Rhodopseudomonas
           palustris CGA009]
          Length = 333

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 130/322 (40%), Gaps = 33/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           M   TD  +R     L    L+ +EM  ++ ++ G + ++       + P  +Q+ G + 
Sbjct: 17  MTGITDVPFRRQVAEL-GAGLVVSEMTASEDLVAGRRMSVRRCDKVGQGPHVVQLAGCEA 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 76  RWMAEGARIAEAGGADIIDINMGCPARHVTGGLSGSALMRDLDHALTLIEATIGAVRVPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+        L +  + +GV  + +H R         +        D+D V
Sbjct: 136 TLKMRLGWDDRSRNA--PELARRAQDAGVQLVTVHGRT--------RQQFYKGEADWDAV 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + + +NG +   + A++ L     D VMIGR A     +   V    +   
Sbjct: 186 RAV-RDAISIPLVVNGDITCHASAVEALKRSGADAVMIGRGAQGRPWLPGQVGRQLTTGK 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
               P  T       R    ++ D           L+   +H+                L
Sbjct: 245 AEGEPSLT-----MQRDYLRTLYDDILALYGVKIGLRHARKHLGW-------------SL 286

Query: 298 TVEAGASTATHHIIETAFNLMI 319
            V A  + A+  ++++   +++
Sbjct: 287 EVAASTAGASPDVLKSWRAVIL 308


>gi|259501966|ref|ZP_05744868.1| tRNA-dihydrouridine synthase [Lactobacillus antri DSM 16041]
 gi|259170143|gb|EEW54638.1| tRNA-dihydrouridine synthase [Lactobacillus antri DSM 16041]
          Length = 332

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 126/325 (38%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +       +  EMI    I+  ++K   ++     E P+ +QI G  
Sbjct: 19  MAGVTNSAFRVICKEF-GAGYVVCEMISDRGIMYHNQKTLNMMDVDPTEHPMGIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V++    + I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  
Sbjct: 78  KETLVEAAKYVDEHTAADVIDINMGCPVNKVVKTDAGARWLLDPQKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L      +    +    RK +  G          + D++
Sbjct: 138 PVTVKMRTGWDDKHIYAVENALAAERAGAAAIAMHGRTRKQMYTG----------HADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG +     A K+L        MIGRAA  N  MLT    Y   
Sbjct: 188 ILKEVANQLT-IPFMANGDIRTPEDAKKVLEMTGATAAMIGRAAMGNPWMLTRTAHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     +  K     ++  + D    +      +++          G P S R + 
Sbjct: 247 GELLPEASAEKKIKMAKEHLNR-LIDLKGEY----VGVREFRGLSTYYLKGIPRSARTKA 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L VEA      + I +       E
Sbjct: 302 AL-VEAETRQEMNDIFDRFAEKTAE 325


>gi|322437060|ref|YP_004219272.1| TIM-barrel protein, nifR3 family [Acidobacterium sp. MP5ACTX9]
 gi|321164787|gb|ADW70492.1| TIM-barrel protein, nifR3 family [Acidobacterium sp. MP5ACTX9]
          Length = 409

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 74/362 (20%), Positives = 142/362 (39%), Gaps = 58/362 (16%)

Query: 1   MVDWTDRHYRFFARLLT--------------------NNALLYTEMIVADAILRGD---K 37
           M   TD  +R F +  +                       L+ TE   AD + R     +
Sbjct: 39  MAGVTDTVFRRFIKNASKFTPDSGDTDVDVETSNAQSGCGLIMTEFTSADGLSRMREVKR 98

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K  L +   E P++ QI G++   L ++A+I +D G++ ++LN+GCP+ RV   + G+ L
Sbjct: 99  KRYLTYYDDEHPISAQIFGSNPETLADSARICQDAGFDIVDLNLGCPAKRVVACNGGSGL 158

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + +  ++      +  A+SIP TVK R+G +D+   +    L K  +  G+N + +HAR 
Sbjct: 159 LRDLPLIETIFKRVRGAISIPFTVKFRMGWNDK--NIVCVELAKIAEDCGLNAVALHART 216

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMI 215
                   +++       ++ +  +K     + +  NG +     A+        D VMI
Sbjct: 217 --------REDGYSGQARWEYIAAVKDAVG-IPVIGNGDILTPEDAVAMTHQTRCDAVMI 267

Query: 216 GRAAYKNSAMLTTVDEYFSNP--LTGSSPIKTRVDKDFWRKISASMTDYAA--------- 264
           GRAA  N  +   + +Y         +   + R+ K ++  +     ++           
Sbjct: 268 GRAAPANPWIFRQIAQYTETGRYDLATDDDRYRMIKAYFGMLLHEFHEHPEIVGIPGVEL 327

Query: 265 ----------RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
                     +       L ++ +      HG P     R  +  E+ +  A    +E  
Sbjct: 328 TDADKKLQRVKESSLRETLGKMKQFASWFTHGIPGGGGLRKEI-FESKSGDAVLGAVERF 386

Query: 315 FN 316
           F+
Sbjct: 387 FD 388


>gi|312968409|ref|ZP_07782618.1| TIM-barrel , nifR3 family protein [Escherichia coli 2362-75]
 gi|312286627|gb|EFR14538.1| TIM-barrel , nifR3 family protein [Escherichia coli 2362-75]
          Length = 280

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 58/294 (19%), Positives = 115/294 (39%), Gaps = 21/294 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           + ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GCP
Sbjct: 1   MSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGCP 60

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
           + +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  +
Sbjct: 61  AKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEEIAQLAE 118

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
             G+  + IH R         +        +YD +  +K++   + +  NG + D  +A 
Sbjct: 119 DCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKAR 169

Query: 205 KIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
            +L     D +MIGRAA     +   +  Y              V +     +      Y
Sbjct: 170 AVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVRELHDFY 229

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
                  G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 GP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 277


>gi|315640560|ref|ZP_07895668.1| tRNA-dihydrouridine synthase [Enterococcus italicus DSM 15952]
 gi|315483764|gb|EFU74252.1| tRNA-dihydrouridine synthase [Enterococcus italicus DSM 15952]
          Length = 329

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 124/310 (40%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L     E PL+LQI G+ 
Sbjct: 21  MAGISNAAFRVTVKE-AGAGLVVCEMISDKGIQLRNKKTLEMLYIDETEHPLSLQIFGST 79

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAA+ VE +   + I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+SI
Sbjct: 80  KESLVEAAQFVEKNTTADIIDINMGCPVNKIIKAEAGAKWLLDPNKVYEMVQAVASAVSI 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D++        L      +    +    R  + +G            D+ 
Sbjct: 140 PVTVKMRTGWDEEHLFAVENALAAQAAGAAAVAMHGRTRVQMYEG----------KADWS 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+KK+   + +  NG +     A ++      D VMIGRAA  N  M+   + Y   
Sbjct: 190 VLREVKKKL-SIPLMGNGDVRTPEDARRMFEEVGCDAVMIGRAALGNPWMIGRTNHYLQT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P                +     R        ++  +H      G   + + + 
Sbjct: 249 GELIAEPTPEEKIAMAKLHFDRLVALKGERIAA-----REFRQHAAYYLKGISRTAKLKA 303

Query: 296 ILTVEAGAST 305
            +       T
Sbjct: 304 EINKSEDRQT 313


>gi|303272601|ref|XP_003055662.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463636|gb|EEH60914.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 252

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 93/248 (37%), Positives = 139/248 (56%), Gaps = 15/248 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M+D TD H+R   R  +    L+TEMI  DA++        +LG    E PL +Q+GG+ 
Sbjct: 9   MLDCTDAHFRAVCRSFSRRTHLWTEMIHQDAVIHSHASRPEMLGHDASEHPLTVQLGGSS 68

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEG-----SFGACLMLNPDIVGDCIAAMC 112
             +L  AA+I    +GY+E+NLN GCPSA+V         FGA LM +P++VG+C+  M 
Sbjct: 69  PGRLARAAEICDAAYGYDEVNLNAGCPSAKVTSKSDAEKCFGAVLMRDPELVGECLRRMR 128

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKI 171
           +A+ +PVT+K R+G         + + V+ + + SGV    +HAR A+L GLSP  NR I
Sbjct: 129 EAVDVPVTLKHRLG----DNYAYVSDFVQRVHELSGVTHFIVHARAAVLGGLSPAANRSI 184

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
           P L +  V+ +  + P L   LNGG+E +  A++ L    + GVM+GRA Y++  +L  V
Sbjct: 185 PPLRHREVHALASDFPKLGFSLNGGVETVDDAVRHLSSGKLKGVMLGRAVYRDPTILHDV 244

Query: 230 DEYFSNPL 237
           D       
Sbjct: 245 DARVYGDE 252


>gi|90424075|ref|YP_532445.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris BisB18]
 gi|90106089|gb|ABD88126.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodopseudomonas
           palustris BisB18]
          Length = 356

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 116/287 (40%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R     L    L+ +EM  +D + RG   ++    T    P  +Q+ G   
Sbjct: 38  MSGITDAPFRRLTAAL-GAGLVVSEMTASDDLARGRPMSVRRCDTAGIGPHVVQLAGCQA 96

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF--GACLMLNPDIVGDCIAAMCKALSI 117
             + E A+I E  G + I++N+GCP+  V  GS   G+ LM + D     I A   A+ +
Sbjct: 97  RWMAEGARIAEAGGADLIDINMGCPARHVTGGSGQSGSALMRDLDHALTLIEATVGAVRV 156

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D     +    L +  + +GV  I +H R         ++       D+ 
Sbjct: 157 PVTLKMRLGWDRD--CLNAPELARRAEAAGVQLITVHGRT--------RNQFYKGTADWA 206

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  + +E   L + +NG +  +  A + L     D VMIGR A     +   +      
Sbjct: 207 AVRAV-REATSLPLVVNGDITSVEAAREALRQSGADAVMIGRGAQGQPWLPGQIGRQLQT 265

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
            +  + P        + + +   + +    H      L+   +H+  
Sbjct: 266 GIAEAPPSLAE-QLSYLQTLYDELLELYGLH----VGLRHARKHLGW 307


>gi|149194756|ref|ZP_01871851.1| tRNA-dihydrouridine synthase B [Caminibacter mediatlanticus TB-2]
 gi|149135179|gb|EDM23660.1| tRNA-dihydrouridine synthase B [Caminibacter mediatlanticus TB-2]
          Length = 311

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 61/321 (19%), Positives = 133/321 (41%), Gaps = 35/321 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      + ++EMI A+AI   ++K   ++  S++E P  +QI   ++
Sbjct: 19  AGYTDLPFRSVVKEF-GCDMTFSEMINANAIAFNNEKTKKMMQKSSKETPYFIQIAANNV 77

Query: 60  SKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNP--DIVGDCIAAMCKALS 116
              ++A +I+ +  + + I++N+GCP  +     +G  L+ +   + + + ++A+ K   
Sbjct: 78  ENAIKAVEIINEIPWIDGIDINLGCPVNKARRSGYGGVLLKDENKEKLKEIVSAIIKTSK 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+ K R+G ++    V   +  K ++  G+  + +H R                N +Y
Sbjct: 138 KIVSAKMRLGYNE----VVAVDRAKMLEDLGIKFLTVHGRTVK--------QMYKGNANY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++ KE  ++ +  NG + D  +A ++L     +GV IGR       +   + +   
Sbjct: 186 KEIKKVVKEV-NIPVIANGDITDYKKAKEVLEYTEANGVAIGRGVIGKPWIFLEMKQ--Q 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +T     K  V    ++ +     DY          +    +H+     G  N+   R
Sbjct: 243 GEITPYQ--KKEVILTHFKAMIEWYGDY---------GVILFRKHLHQYSKGIKNASEFR 291

Query: 295 HILTVEAGASTATHHIIETAF 315
             +           ++IE  F
Sbjct: 292 SKINSTENK-DEVINLIEEYF 311


>gi|304440037|ref|ZP_07399930.1| tRNA-dihydrouridine synthase B [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304371529|gb|EFM25142.1| tRNA-dihydrouridine synthase B [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 306

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 127/303 (41%), Gaps = 24/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M  +TD  YR        ++ + TEM+ A A+   DKK +  +  S +E+ + LQ+ G +
Sbjct: 8   MAGYTDFVYRSMCMDFGCDSTI-TEMVSAKALYYKDKKTLELMETSDKERDVHLQLFGYE 66

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                  AK +    +  IN+N+GCP+ ++ +   G+ L+ +P+     I A+  +  IP
Sbjct: 67  EDIFEIVAKEI-PNRFKYININMGCPAPKIVKNFSGSYLLNDPEKCKRLIYALKSSTDIP 125

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R G++     + +    K  ++ G + + +H R         K+       D++ 
Sbjct: 126 ISIKIRRGINGGNQGLKV---AKVAEEEGASMVIVHGRT--------KEEYYSGIADWNF 174

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+     ++ +  NG + D    L+      V GV IGR A  N  +   +     N 
Sbjct: 175 IEEVATSL-NIPVIGNGDITDYDSFLERTKDSKVSGVAIGRGAIGNPFIFKEIKSKI-NK 232

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P +    + F   +   M  Y          + ++ +  +G  +G   ++  R  
Sbjct: 233 EEYTPPTEKEKLETFLTHLKMMMEAYP-----KKVAINEMRKQFVGYSNGIYGAKELRQK 287

Query: 297 LTV 299
           L  
Sbjct: 288 LNT 290


>gi|291287718|ref|YP_003504534.1| dihydrouridine synthase DuS [Denitrovibrio acetiphilus DSM 12809]
 gi|290884878|gb|ADD68578.1| dihydrouridine synthase DuS [Denitrovibrio acetiphilus DSM 12809]
          Length = 340

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 72/301 (23%), Positives = 135/301 (44%), Gaps = 25/301 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              T   +R   R    + L+YTEM+  + + R   + +  L  +  ++P+ +Q+ G+  
Sbjct: 26  AGVTTPPFRKLLRKY-FDGLIYTEMVSVEGVRRKADRTLSYLSITESDQPIGVQLFGSKP 84

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
               EA ++V+D+     +++N+GCP  +V +   G  +M +P   G  +AA  KAL  +
Sbjct: 85  EAYTEAIEVVQDYIKAEFVDINMGCPVKKVLKSGSGCAMMKDPVNSGKIVAAAKKALGDV 144

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G D +   +    ++K   + G   + +H R         K       ++YD
Sbjct: 145 PLTVKIRLGWDKK--NLNYNEMIKIAYEEGAEAVTVHGRT--------KTEMFSGVVNYD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++ +  K N  L I  NG + D++   K+L   VDGVMIGR   K   +  ++       
Sbjct: 195 LIAD-AKANAKLPIIGNGDVVDVATYEKMLATGVDGVMIGRGMMKQPWLFESI------- 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           L G  P    +  D   ++   +      +      L+ + ++++    G P +   R+ 
Sbjct: 247 LNGRDP-SGYMTYDKLYELIKELVRNEKIYKGEMFFLETVKKYIVWFLKGMPGAAALRNK 305

Query: 297 L 297
           L
Sbjct: 306 L 306


>gi|153009400|ref|YP_001370615.1| nifR3 family TIM-barrel protein [Ochrobactrum anthropi ATCC 49188]
 gi|151561288|gb|ABS14786.1| putative TIM-barrel protein, nifR3 family [Ochrobactrum anthropi
           ATCC 49188]
          Length = 349

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 124/294 (42%), Gaps = 25/294 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    K+++L  S +      +Q+ G + 
Sbjct: 39  MSGVSDLPFRRRAAE-AGAGMVVSEMVASAELCNRHKESLLRLSGEGLGTHVVQLAGREA 97

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I E  G + I++N+GCP+ +V  G  G+ LM + D     + A   A+ +PV
Sbjct: 98  HWMGEAARIAEGEGADIIDINMGCPAKKVTGGYSGSALMRDLDHAMTLVEATVNAVRVPV 157

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D++  ++    L +  + +G+  + +H R         +        D++ +
Sbjct: 158 TLKMRLGWDEK--SINAPELARRAEGAGIAMVTVHGRT--------RCQFYEGKADWNAI 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +     A +IL     D VM+GRA+Y    +   +        
Sbjct: 208 HAV-RDAVRIPLIANGDVACRPDAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 258

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
              S +  +   +    I     D    H  S   ++   +H+         + 
Sbjct: 259 -AGSDLAPQSRSEILDYIIKHYED-MLEHYGSTTGIRHSRKHLGWYLDRLAGAA 310


>gi|312869850|ref|ZP_07729991.1| TIM-barrel protein, nifR3 family [Lactobacillus oris PB013-T2-3]
 gi|311094629|gb|EFQ52932.1| TIM-barrel protein, nifR3 family [Lactobacillus oris PB013-T2-3]
          Length = 332

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 128/325 (39%), Gaps = 23/325 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +       +  EMI    I+  ++K   ++     E P+ +QI G  
Sbjct: 19  MAGVTNSAFRVICKEF-GAGYVVCEMISDRGIMYHNQKTLNMMDVDPTEHPMGIQIFGGT 77

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V++    + I++N+GCP  +V +   GA  +L+P  V + ++ +  A+  
Sbjct: 78  KETLVEAAKYVDEHTAADVIDINMGCPVNKVVKTDAGARWLLDPQKVYEMVSYVTDAVKK 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD+        L      +    +    RK +  G          + D++
Sbjct: 138 PVTVKMRTGWDDKHIYAVENALAAERAGAAAIAMHGRTRKQMYTG----------HADWN 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+  +   +    NG +     A K+L        MIGRAA  N  MLT  + Y   
Sbjct: 188 ILKEVASQLT-IPFMANGDIRTPEDAKKVLDMTGATAAMIGRAAMGNPWMLTRTEHYLET 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                     +  K     ++  + D    ++     +++          G P S R + 
Sbjct: 247 GELLPEASAEKKIKMAKEHLNR-LIDLKGEYIG----VREFRGLSTYYLKGIPRSARAKA 301

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
            L VEA      + I +       E
Sbjct: 302 AL-VEAETRQEMNDIFDRFAEKTAE 325


>gi|302382892|ref|YP_003818715.1| hypothetical protein Bresu_1781 [Brevundimonas subvibrioides ATCC
           15264]
 gi|302193520|gb|ADL01092.1| TIM-barrel protein, nifR3 family [Brevundimonas subvibrioides ATCC
           15264]
          Length = 352

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 120/287 (41%), Gaps = 21/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   TD  +R  A  L   A + TEM+ +  + RG    +   +     PL  +Q+ G D
Sbjct: 21  MTGITDLPFRQLACRL-GAAYVATEMVASAELARGRPDVMRRAAVGDGLPLTVIQLVGRD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + + A++ E  G + ++LN GCP+  V   + G+ LM  PD+ G  +AA+  A S P
Sbjct: 80  PAAMAQGARMAEAAGADIVDLNFGCPAKEVTGSASGSALMRTPDLAGRIMAAVVAATSRP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD     A   L    +  GV  + +H R         +      + D+D 
Sbjct: 140 VTVKMRLGWDDASRNAA--ELAARAEDLGVKAVTVHGRT--------RQQFYTGHADWDA 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + + +NG +    QA + L     D +M+GR  Y    +   ++    + 
Sbjct: 190 IAAVKTAVG-IPVIVNGDIITADQAREALQKSGADALMLGRGVYGRPWLAAHLERALRDG 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
              + P            + AS+  Y       G  L+   +H+   
Sbjct: 249 TVLTEPGAAERFDIVVDHMRASIAFY-----GPGLGLKMFRKHLGWY 290


>gi|332998380|gb|EGK17979.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri VA-6]
          Length = 281

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 58/295 (19%), Positives = 115/295 (38%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+   ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSAPKEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + +  NG + D  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V +     +      
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 YGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|239832008|ref|ZP_04680337.1| TIM-barrel protein, nifR3 family [Ochrobactrum intermedium LMG
           3301]
 gi|239824275|gb|EEQ95843.1| TIM-barrel protein, nifR3 family [Ochrobactrum intermedium LMG
           3301]
          Length = 335

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 58/294 (19%), Positives = 125/294 (42%), Gaps = 25/294 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRRRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I E  G + I++N+GCP+ +V  G  G+ LM + D     + A   A+++PV
Sbjct: 84  HWMGEAARIAEGEGADIIDINMGCPAKKVTGGYSGSALMRDLDHAMTLVEATVNAVNVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D++  ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDEK--SINAPELARRAESAGIAMVTVHGRT--------RCQFYEGKADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + +  NG +     A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 RAV-RDAVKIPLVANGDVACREDAEEILRRSGADAVMVGRASYGQPWLAGAI-----AGS 247

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +   ++ V +   +     +  Y      S   ++   +H+         + 
Sbjct: 248 DFAPKSRSEVLEYIIKHYEDMLDHY-----GSTTGVRHSRKHLGWYLDRHAGAA 296


>gi|225869383|ref|YP_002745331.1| tRNA-dihydrouridine synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225702659|emb|CAX00744.1| putative tRNA-dihydrouridine synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 325

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 122/303 (40%), Gaps = 22/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+      L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEHPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     + +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQSHTRADIVDINMGCPVNKVVKNEAGAKWLRDPDKIYHIIQEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D   A+       + + +GV+ + +H R         ++       DY+
Sbjct: 143 PLTVKMRTGWSDSSLALENA---LAAEAAGVSALAMHGRT--------REQMYTGTCDYE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T ++ +F  
Sbjct: 192 TLARVSKAITRIPFIGNGDVRTVQDAAFMIEEIGVDAVMIGRAAMNNPYLFTQINHFFET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  +      D  +     +       +     +++          G   + + R 
Sbjct: 252 GEALPE-LPFAKKLDIAKDHLKRLIKLKGETIA----VREFRGLAPHYLRGTAGAAKIRS 306

Query: 296 ILT 298
            ++
Sbjct: 307 AVS 309


>gi|311744088|ref|ZP_07717894.1| NifR3 family TIM-barrel enzyme [Aeromicrobium marinum DSM 15272]
 gi|311313218|gb|EFQ83129.1| NifR3 family TIM-barrel enzyme [Aeromicrobium marinum DSM 15272]
          Length = 432

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 70/368 (19%), Positives = 123/368 (33%), Gaps = 72/368 (19%)

Query: 1   MVDWTDRHYRFFA----------------------------------------------- 13
           M   T+  +R                                                  
Sbjct: 29  MAGVTNAAFRQLCAEQGALRGSQARTSGQALRGSQARTSGQALRGSQARTSGQALRGSQA 88

Query: 14  RLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVE- 70
           R      L   EMI +  ++ GD+ +  +L F+  E+  ++Q+ G D + +  A  I+  
Sbjct: 89  RTSGQAGLYVCEMITSRGVVEGDRTSLGMLTFAPNERVRSVQLYGIDPATVGRAVAILCG 148

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGV 127
           D G + ++LN GCP  +V     GA L     ++G  +     A     +PVT+K R G+
Sbjct: 149 DHGVDHVDLNFGCPVPKVTRKGGGAALPWKATLLGRILTEAVAAAAPFGVPVTMKTRKGI 208

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD    +   +     + SG   I +H R A+       D   I  L             
Sbjct: 209 DDD--HLTYLDAGHIAEDSGCAAIALHGRTAVQHYSGEADWAAIAALK---------AAV 257

Query: 188 DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIK 244
            + +  NG + + + AL+++     DGV++GR       +   +   F+   T  + P  
Sbjct: 258 SIPVLGNGDVWEAADALRMVRETGCDGVVVGRGCLGRPWLFRDLAAAFTGEETVPALPTL 317

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAS 304
             V     R       +     L       +  +H+     GFP     R  L   +  +
Sbjct: 318 GEVMAIMRRHA-----ELLGGWLGEERGCVEFRKHVAWYLKGFPAGPSVRQRLGQVSSYA 372

Query: 305 TATHHIIE 312
                ++E
Sbjct: 373 ALDELLVE 380


>gi|294852457|ref|ZP_06793130.1| tRNA-dihydrouridine synthase B [Brucella sp. NVSL 07-0026]
 gi|294821046|gb|EFG38045.1| tRNA-dihydrouridine synthase B [Brucella sp. NVSL 07-0026]
          Length = 304

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRHSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 288


>gi|114569990|ref|YP_756670.1| nifR3 family TIM-barrel protein [Maricaulis maris MCS10]
 gi|114340452|gb|ABI65732.1| tRNA-U20-dihydrouridine synthase [Maricaulis maris MCS10]
          Length = 356

 Score =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 70/285 (24%), Positives = 117/285 (41%), Gaps = 22/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A+      ++ +EM+ +DA+   R D           KP  +Q+ G  
Sbjct: 43  MSGVTDLPFRRQAQRF-GAGMVVSEMVASDALAAGRRDMIRKAALDASLKPCVIQLAGRQ 101

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+I ED G   I++N+GCP+ +V +G  G+ LM + D     I A   A S P
Sbjct: 102 AHWMSEGARIAEDAGAEVIDINMGCPARQVTKGLSGSALMRDLDHALTLIEATVGATSKP 161

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D    ++    L +  + +GV  + +H R         +        D+  
Sbjct: 162 VTLKMRLGWD--HASLNAPELARRARDAGVKLLTVHGRT--------RQQFYKGQADWAA 211

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++  E  DL + +NG +   + A   L       VM+GRAA     +L  +       
Sbjct: 212 VRKVV-EAVDLPVIVNGDIHTTADARAALDQSGAAAVMVGRAAQGRPWLLGEIGRELLGE 270

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
               +P   ++D            D    H   G  ++ + +H  
Sbjct: 271 PAARTPWNDKIDA------LGQQFDDCLEHYGEGLGIRMMRKHFA 309


>gi|306843984|ref|ZP_07476579.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO1]
 gi|306275739|gb|EFM57463.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO1]
          Length = 333

 Score =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +           +
Sbjct: 194 HAV-RDAVKIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWL---------AGV 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +    R        I     D    H  S   ++   +H+    
Sbjct: 244 IAGNDFAPRDANGILEYIIRHYED-MLDHYGSKTGIRHARKHLGWYM 289


>gi|91201593|emb|CAJ74653.1| strongly similar to tRNA-dihydrouridine synthase [Candidatus
           Kuenenia stuttgartiensis]
          Length = 341

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 70/298 (23%), Positives = 133/298 (44%), Gaps = 29/298 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  YR   R     ++ YTE++    I+  +KK   +L F  +E+P+  Q+ G D
Sbjct: 40  MAGFSDMPYRLICRRF-GMSMSYTEVVSVSGIVWNNKKTFKLLDFKEEERPVTFQVVGND 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ EA K +E  G + I++N+GC  + +     GA ++ +P  +      +  +LS+P
Sbjct: 99  ECQITEACKKIEQLGPDIIDINMGCSVSDIAGKGAGAGMLKHPSKISKMFNNLTGSLSVP 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D +        + + ++++G + I +H R         +        D+D 
Sbjct: 159 VTGKIRLGWDHKTRN--YIEVARILEENGASLIAVHGRT--------RSQYFSGAADWDA 208

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K+ +  + +  NG +  ++    +K   + DGVMIGRAA  +  +    D      
Sbjct: 209 IAEVKQ-SVKIPVIANGDVRSVADIAEIKKRTACDGVMIGRAAIGHPWIFRYKDR---EN 264

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           ++GS  I      +  R     M +Y    +     +    +H +    G P +   R
Sbjct: 265 ISGSEKI------EMIRYHLDCMKEYYGHAIG----VVLFRKHAVKYIVGLPKATELR 312


>gi|28377433|ref|NP_784325.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|254555616|ref|YP_003062033.1| transcription regulator [Lactobacillus plantarum JDM1]
 gi|300768966|ref|ZP_07078857.1| tRNA-dihydrouridine synthase [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308179646|ref|YP_003923774.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28270265|emb|CAD63166.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|254044543|gb|ACT61336.1| transcription regulator [Lactobacillus plantarum JDM1]
 gi|300493487|gb|EFK28664.1| tRNA-dihydrouridine synthase [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308045137|gb|ADN97680.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 335

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 71/310 (22%), Positives = 126/310 (40%), Gaps = 22/310 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I+  ++K   ++    +E P+++QI G  
Sbjct: 21  MAGVTNAAFRVICKDF-GAGLVVCEMISDRGIMYHNRKTLEMMFVDPKEHPMSIQIFGGS 79

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + LV+AA+ V +    + I++N+GCP  +V +   GA  +L+PD V + +AA+  A++ 
Sbjct: 80  KATLVQAAQFVDQQTNADIIDINMGCPVNKVVKTDAGAKWLLSPDKVYEMVAAVTAAVNK 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G D +               +    +    RK + +G          + D+D
Sbjct: 140 PVTVKMRTGWDAEHVYAVENARAAERAGAAAVAMHGRTRKQMYQG----------HADWD 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++  +      + +  NG ++    A ++L     D VMIGRA   N  MLT    Y + 
Sbjct: 190 VLKRVADALT-IPLMGNGDVQTPQDAARMLDEVGADAVMIGRAVEGNPWMLTQTVHYLAT 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P      +     +   +     R     G   +          G P S R + 
Sbjct: 249 GELLTPPTPMAKMQTAMEHLQRLVVLKGER-----GGCHEFREQAPYYLKGIPRSARTKV 303

Query: 296 ILTVEAGAST 305
            L   +  + 
Sbjct: 304 ALMEASSLAE 313


>gi|56696957|ref|YP_167319.1| tRNA-dihydrouridine synthase, putative [Ruegeria pomeroyi DSS-3]
 gi|56678694|gb|AAV95360.1| tRNA-dihydrouridine synthase, putative [Ruegeria pomeroyi DSS-3]
          Length = 327

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 71/319 (22%), Positives = 125/319 (39%), Gaps = 22/319 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R          ++ +EM+ +  +++     +     S   +  A+Q+ G D
Sbjct: 19  MAGITDRPFRDLVMEF-GAGMVVSEMVASQEMVQAKPGVRERAELSADVENTAVQLAGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ V D G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+ +P
Sbjct: 78  THWIAEAARQVADRGARVIDINMGCPAKKVTNGYSGSALLKTPDHALRLIEAVVAAVDVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD +      ++ +   ++GV  + IH R         +        D+  
Sbjct: 138 VTLKTRLGWDDTLMNA--PDVARRAAEAGVRMVTIHGRT--------RCQFYKGRADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +E  D+ +  NG +     A + L     DGVM+GR A     +L  +       
Sbjct: 188 IAAV-REAVDVPLIANGDITCAHTARQALDRSGADGVMVGRGAQGRPWLLAQIAHALYGT 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P    +     R   A +  Y          L+   +H+             R  
Sbjct: 247 PAPEVPQGAELADMVARHYQAMLDFYGRE-----LGLRVARKHLGWYMDEAATPAPLR-K 300

Query: 297 LTVEAGASTATHHIIETAF 315
           L + A       H++  A 
Sbjct: 301 LVLTARDPETVLHLLPEAL 319


>gi|300120278|emb|CBK19832.2| unnamed protein product [Blastocystis hominis]
          Length = 407

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 101/350 (28%), Positives = 155/350 (44%), Gaps = 69/350 (19%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKN-ILGFSTQEKPLALQIGGADISKLVEAAKI 68
           R+  RL++ +  LY+EM V + ++    ++ ++ F   E P+  Q+GG++  K++EAAK+
Sbjct: 16  RYIVRLMSKHTTLYSEMFVDEMLIHSQFRSNLIRFDKSEHPIIAQLGGSNKYKMLEAAKL 75

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           +E  GY+ IN+N GCPS +V EG FGA LML+P  V D +  + + LSIPVTVKCRIGVD
Sbjct: 76  LEAEGYDGININCGCPSPKVAEGCFGARLMLSPWRVYDIVQHLQRHLSIPVTVKCRIGVD 135

Query: 129 --------------DQIPAVALRNLVKSIKKS---------------------------- 146
                         +      L   ++ +  +                            
Sbjct: 136 RIYFLKLCFAHNIVEYDSYEELCRFIRIVSGAGTEQDRKSFASASDDEAESDPLMPPVQS 195

Query: 147 --------------GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                         G     IHARK +L GLS K NR +P L YD VY +  + P +   
Sbjct: 196 ESDGIQRQEIQPCYGAKHFIIHARKCLLSGLSAKQNRSVPPLHYDWVYRLLDDFPCIDFS 255

Query: 193 LNGGLEDMSQALKILP-------SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           +NGG+  + QA  +L         + GVMIGR   K       +D++F      S     
Sbjct: 256 INGGVLSLGQAKDLLERKSQSGRQLRGVMIGRLLTKAPWNFHFIDQFFYGEPNPSLSPFE 315

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            V K +         +   +H  +     ++ + +  +F   P S RCR 
Sbjct: 316 TVMK-YVEYCEQMEKNGYTQHFST----NELLKPLFNIFVDIPGSLRCRR 360


>gi|91774082|ref|YP_566774.1| dihydrouridine synthase, DuS [Methanococcoides burtonii DSM 6242]
 gi|91713097|gb|ABE53024.1| tRNA-dihydrouridine synthase [Methanococcoides burtonii DSM 6242]
          Length = 318

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 137/316 (43%), Gaps = 31/316 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGADI 59
            + T+  +R   +     +L +TEMI +DA++ G+  + +      +E+P  LQ+ G   
Sbjct: 18  AEVTNLAFRLMCKKY-GASLCFTEMISSDAVVYGNASSAMRGITCDEERPFGLQLFGNSP 76

Query: 60  SKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EAA ++ED  Y + I++N+GCP+  +     G+ L+ +P++V D  + +C+ +  P
Sbjct: 77  EVITEAALVLEDMFYPDMIDINLGCPAPVITNAGCGSALLESPELVSDIFSTLCEGVDTP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+         A  ++   ++ +GV  I +H R          +       D+  
Sbjct: 137 VTAKIRVL----ESRAATLDMAHRLEDAGVCAITVHGRTC--------EQGYSGTADHSY 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              IK+E   + + +NG + D   A K+L     DG+MIGRAA  +  +   +  Y  + 
Sbjct: 185 AKLIKEEL-SIPVIVNGDIRDGVSAEKVLEYTGCDGLMIGRAAMGDPHVFHRISRYLDDG 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                  + + D            D     L S   L+    H+     G   SRR R  
Sbjct: 244 EVIGCGCEQKRDDLLEYLDLLEKFD-----LSSHINLKA---HVQWFTRGLKGSRRMRSD 295

Query: 297 LTVEAGASTATHHIIE 312
           +    G + +   I+E
Sbjct: 296 I----GYADSRDSIVE 307


>gi|163741114|ref|ZP_02148506.1| tRNA-dihydrouridine synthase, putative [Phaeobacter gallaeciensis
           2.10]
 gi|161385467|gb|EDQ09844.1| tRNA-dihydrouridine synthase, putative [Phaeobacter gallaeciensis
           2.10]
          Length = 319

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 132/320 (41%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+QI G D
Sbjct: 1   MAGITDRPFRDLVRSF-GAGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQIAGRD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ VE  G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+S+P
Sbjct: 60  AYWMAEAARQVESRGAKVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVAAVSVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD   ++   ++ +  + +GV  + IH R         +        D+  
Sbjct: 120 VTLKTRLGWDD--NSLNAADVARRAQDAGVQMVTIHGRT--------RCQFYKGTADWKA 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K    D+ +  NG + D + A   L     DGVMIGR       +L  V       
Sbjct: 170 IAAVKAAL-DVPLLANGDIVDTATARTALAQSGADGVMIGRGVQGKPWLLAQVAHDIWGS 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                PI + + +       A +  Y A        L+   +H+             R  
Sbjct: 229 AAPEVPIGSDLVQMVSAHYEAMIAFYGA-----DLGLRVARKHLGWYMDEAATPAPLRRE 283

Query: 296 ILTVEAGASTATHHIIETAF 315
           +LT +A  +     ++  A 
Sbjct: 284 VLTAKAPKT--VLQLLPDAL 301


>gi|118475725|ref|YP_891451.1| tRNA-dihydrouridine synthase B [Campylobacter fetus subsp. fetus
           82-40]
 gi|261885859|ref|ZP_06009898.1| tRNA-dihydrouridine synthase B [Campylobacter fetus subsp.
           venerealis str. Azul-94]
 gi|118414951|gb|ABK83371.1| tRNA-dihydrouridine synthase B [Campylobacter fetus subsp. fetus
           82-40]
          Length = 306

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 61/303 (20%), Positives = 129/303 (42%), Gaps = 34/303 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D   R   +      +  +EMI ++A++  + K   ++  +  E P  +Q+ G   
Sbjct: 15  AGFSDLPLRGIVKKF-GCDVTISEMISSNALVYENTKTVSMIEKNPLETPYIVQLAGNGS 73

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +I+ D  G + I+LN GCP  +V + + G+ L+ +   + + +  + K  +  
Sbjct: 74  EIIKQAVQILNDIEGIDGIDLNCGCPVPKVVKQNSGSALLNDIKTLCEIVETIKKTSNKH 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T VK R+G + +       N+ K I+ +G + I +H R         +       +DY+
Sbjct: 134 YTSVKIRLGFNSK----TAHNIAKDIENAGADFICVHGRT--------RAGGYSAKVDYE 181

Query: 178 IVYEIKKENPDLFIGLNGGL--EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+ +  + +  NG +  ++  + L+ L + DGVMIGRA+  N  +   +      
Sbjct: 182 AIGLVKQ-SVSIPVIANGDINAKNADEILR-LTNCDGVMIGRASIGNPWIFYEIKH---- 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P+   + K    +    M +Y   H      +    +H+     G   +   R+
Sbjct: 236 ----KKPVDKNIKKQIVLEHFNEMLNYYGEH-----GIGIFRKHLHEYSKGIDGASSFRN 286

Query: 296 ILT 298
            + 
Sbjct: 287 EIN 289


>gi|261314157|ref|ZP_05953354.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M163/99/10]
 gi|261317754|ref|ZP_05956951.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis B2/94]
 gi|261296977|gb|EEY00474.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis B2/94]
 gi|261303183|gb|EEY06680.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M163/99/10]
          Length = 332

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 288


>gi|254449283|ref|ZP_05062729.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HTCC5015]
 gi|198261092|gb|EDY85391.1| tRNA-dihydrouridine synthase B [gamma proteobacterium HTCC5015]
          Length = 270

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 112/259 (43%), Gaps = 18/259 (6%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           +    +  P+ +QI GAD ++L EAA+   + G + I++N+GCP+ +V   + G+ L+ +
Sbjct: 1   MDHRGEPGPIIVQIAGADPAQLAEAAQFNAEHGADIIDINMGCPAKKVCNVAAGSALLSD 60

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
             +V   +  +  A+ IPVT+K R G            + +  + SG+    +H R    
Sbjct: 61  EPLVSRILTTVVNAVDIPVTLKTRTGPSADTRNAV--RIAQLAEDSGIQMFALHGRT--- 115

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
                +D     + +YD +  +++   D+ +  NG ++   +A ++L     DG+MIGRA
Sbjct: 116 -----RDQLYKGHAEYDTIASVRRAI-DIPLVANGDIDSPERARQVLDHTGADGLMIGRA 169

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           A  N  +   V  +       + P    V       ++A    Y           +   +
Sbjct: 170 AQGNPWIFREVAHFLETGKHLAPPNPDEVRLTLLEHLTALYEFY-----GEVMGPRIARK 224

Query: 279 HMIGLFHGFPNSRRCRHIL 297
           H+   F    + +R +  L
Sbjct: 225 HIGWYFKTRSDFKRHKKTL 243


>gi|256844991|ref|ZP_05550449.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_36A2]
 gi|256718550|gb|EEU32105.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_36A2]
          Length = 307

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 122/316 (38%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       K  A+QI G ++ K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLRKGNAVQIFGENVEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG       V    + K  ++ G + I +H R         ++       D+  +
Sbjct: 129 SIKIRIGYKKPENYV---QIAKIAEEIGCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGEDALEKISYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D      +    +  + +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLRRIRID------NDNKFIFDVRKHISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
              +        I+E 
Sbjct: 291 NTISNY-DEIIKILEE 305


>gi|148560180|ref|YP_001259040.1| nitrogen regulation protein Nifr3 [Brucella ovis ATCC 25840]
 gi|254706696|ref|ZP_05168524.1| TIM-barrel protein nifR3 family protein [Brucella pinnipedialis
           M163/99/10]
 gi|254710196|ref|ZP_05172007.1| TIM-barrel protein nifR3 family protein [Brucella pinnipedialis
           B2/94]
 gi|256031690|ref|ZP_05445304.1| TIM-barrel protein nifR3 family protein [Brucella pinnipedialis
           M292/94/1]
 gi|256061202|ref|ZP_05451354.1| TIM-barrel protein nifR3 family protein [Brucella neotomae 5K33]
 gi|256369546|ref|YP_003107056.1| nitrogen regulation protein Nifr3 [Brucella microti CCM 4915]
 gi|261325210|ref|ZP_05964407.1| nifR3 family TIM-barrel protein [Brucella neotomae 5K33]
 gi|265988785|ref|ZP_06101342.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M292/94/1]
 gi|148371437|gb|ABQ61416.1| nitrogen regulation protein Nifr3 [Brucella ovis ATCC 25840]
 gi|255999708|gb|ACU48107.1| nitrogen regulation protein Nifr3 [Brucella microti CCM 4915]
 gi|261301190|gb|EEY04687.1| nifR3 family TIM-barrel protein [Brucella neotomae 5K33]
 gi|264660982|gb|EEZ31243.1| nifR3 family TIM-barrel protein [Brucella pinnipedialis M292/94/1]
          Length = 333

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 289


>gi|296272247|ref|YP_003654878.1| dihydrouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296096422|gb|ADG92372.1| dihydrouridine synthase DuS [Arcobacter nitrofigilis DSM 7299]
          Length = 316

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 135/305 (44%), Gaps = 34/305 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EMI ++A++   +K   ++  S  E P  +QI G   
Sbjct: 17  AGYTDLPFRAVVKKF-GADLTISEMISSNALVYNSQKTFKMIEKSPSEDPYFVQIAGNKA 75

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSI 117
             + +A +I+ D  G + I+LN GCP+ +V     G+ L+ +   + + +  + K    +
Sbjct: 76  ELVRDAVEILNDMEGIDGIDLNCGCPAPKVFNHGSGSNLLGDLKKLEEILGTVKKYNKKL 135

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             + K RIGV+++IP     ++ K+++  GV+ I +H R         +  +    +DYD
Sbjct: 136 YTSAKVRIGVNEKIPV----DIAKAVESCGVDFISVHGRT--------RAGKYKAPVDYD 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  IK E   + +  NG ++D ++A ++L     DG+MIGR A     +   +    + 
Sbjct: 184 AIKAIK-EAVSIPVIANGDIKDYAKAKEVLAHTKADGLMIGRGAIGKPWIFYQLK---NG 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCR 294
               S  IK  +  + +  +     ++ A           + R ++     G+  +   R
Sbjct: 240 VEDISEDIKKAIILEHYDAVLRFHGEHGA----------IMFRKLLHSYSKGYNGASEFR 289

Query: 295 HILTV 299
            I+  
Sbjct: 290 DIINT 294


>gi|159039340|ref|YP_001538593.1| nifR3 family TIM-barrel protein [Salinispora arenicola CNS-205]
 gi|157918175|gb|ABV99602.1| putative TIM-barrel protein, nifR3 family [Salinispora arenicola
           CNS-205]
          Length = 391

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 72/319 (22%), Positives = 113/319 (35%), Gaps = 40/319 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EMI   A++  + K   ++ F   E P +LQ+ G D
Sbjct: 29  MAGITNVGFRQLCREQGG-GIYVCEMITTVALVERNPKTLRMIAFGGGESPRSLQLYGTD 87

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
                 A +IV +    + I+LN GCP  +V     GA L     +    + A   A S 
Sbjct: 88  PEVTAAAVRIVVERDLADHIDLNFGCPVPKVTRKGGGAALPWRRRLFARLVTAAVDAASP 147

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+DD         L    + +GV  + +H R A          R     
Sbjct: 148 AGVPVTVKMRKGIDDDHLTYVEAGLA--AQDAGVAAVALHGRTA--------AQRYSGTA 197

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG----------RAAYKNSA 224
           D+D +  +K    D+ +  NG + +   AL+        M+           R       
Sbjct: 198 DWDAIATLKAAL-DVPVLGNGDIWEADDALR--------MVAHTGVDGVVVGRGCLGRPW 248

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGK--LQQITRHM 280
           +   ++  FS       P    V     R     +  +   AR    G +       +H+
Sbjct: 249 LFADLEAAFSGSPQRRLPTLGEVATTMRRHAELLVEQFSAGARSAARGERDGCTDFRKHV 308

Query: 281 IGLFHGFPNSRRCRHILTV 299
                GFP     R  L +
Sbjct: 309 AWYLKGFPVGGELRRSLAM 327


>gi|283782299|ref|YP_003373054.1| TIM-barrel protein, nifR3 family [Pirellula staleyi DSM 6068]
 gi|283440752|gb|ADB19194.1| TIM-barrel protein, nifR3 family [Pirellula staleyi DSM 6068]
          Length = 345

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 66/326 (20%), Positives = 119/326 (36%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR------GDKKNILGFSTQEKPLALQI 54
           M  +T+  YR   R      L  TEM+ A                + G   + +PLA+Q+
Sbjct: 20  MAGYTNYAYRQMVREFGGAGLQATEMVNASGFAWLHEHEAEHPDRLWGVKEEARPLAVQM 79

Query: 55  GGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC 112
              D + L +   ++  +   + +++N GCP   V E    G+ L+  PD +   +  + 
Sbjct: 80  WDNDPATLAKVGERLANELHVSVVDINFGCPVKDVTEKAHSGSYLLKFPDRIAQIVERVV 139

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           KA    PVT K R+G      A+    + K ++ +G   + +H R A         +   
Sbjct: 140 KACAPTPVTAKIRLGC--SRDAINAIEIAKVVESAGAAALTVHGRTA--------ADFFR 189

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D++ + EIK     + +  NG L+   + ++      VDGVMI RA+     +    
Sbjct: 190 GTADWNRIAEIKPHLKKIPLIGNGDLDSPEKVIEAFRRYGVDGVMIARASMGRPWLFRQA 249

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                       P          R    +   +  +    G  L  + +       G P 
Sbjct: 250 AAALRGEPVPPDPTAEEQRLTMLRHYELTCARFGEQ---KGTLL--MRKFACNYATGRPG 304

Query: 290 SRRCRHILTVEAGASTATHHIIETAF 315
           +R  R ++           +++E  F
Sbjct: 305 ARTFRAMVANVFTRED-FFNVVERYF 329


>gi|15618677|ref|NP_224963.1| oxidoreductase [Chlamydophila pneumoniae CWL029]
 gi|15836301|ref|NP_300825.1| oxidoreductase [Chlamydophila pneumoniae J138]
 gi|16752273|ref|NP_445641.1| hypothetical protein CP1104 [Chlamydophila pneumoniae AR39]
 gi|33242127|ref|NP_877068.1| nitrogen regulating protein [Chlamydophila pneumoniae TW-183]
 gi|4377076|gb|AAD18906.1| predicted oxidoreductase [Chlamydophila pneumoniae CWL029]
 gi|7190016|gb|AAF38872.1| conserved hypothetical protein [Chlamydophila pneumoniae AR39]
 gi|8979141|dbj|BAA98976.1| oxidoreductase [Chlamydophila pneumoniae J138]
 gi|33236637|gb|AAP98725.1| nitrogen regulating protein [Chlamydophila pneumoniae TW-183]
          Length = 335

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 70/312 (22%), Positives = 135/312 (43%), Gaps = 22/312 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  YR  + L     L++ EM+  + IL   ++   +L ++   +P+  Q+ G++ 
Sbjct: 22  AGFSDYPYRCMSALYQ-PGLMFCEMVKVEGILYAPERTSKLLDYNENMRPIGAQLCGSNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               EAAKI+E  G++ I+LN GCP+ ++ +   G+ L+  P+++G  +  +  ++SIPV
Sbjct: 81  ETSGEAAKILEGLGFDLIDLNCGCPTDKITKDGSGSGLLKTPELIGRILDKIINSVSIPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D +   + + + V+ I+ +G + +++H R        P     I        
Sbjct: 141 TVKIRSGWDME--HINVEDTVRIIRDAGASAVFVHGRTRAQGYHGPSKQEYISRAK---- 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               KE P   +  NG +     A  +L    DGV++ R       +   + +Y +    
Sbjct: 195 AAAGKEFP---VFGNGDIFSPEAAQAMLTTGCDGVLVARGTLGAPWIGKQIQDYLTTGSY 251

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P   R      +            +  S  K    TR + G  H   ++ + R + +
Sbjct: 252 EKIPFIKR------KAAFLEHMRLVEDYYQSETKFLSETRKLCG--HYLISAAKVRFLRS 303

Query: 299 VEAGASTATHHI 310
             A  +T+   +
Sbjct: 304 SLA-KATSYQEV 314


>gi|156740075|ref|YP_001430204.1| nifR3 family TIM-barrel protein [Roseiflexus castenholzii DSM
           13941]
 gi|156231403|gb|ABU56186.1| putative TIM-barrel protein, nifR3 family [Roseiflexus castenholzii
           DSM 13941]
          Length = 335

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 148/326 (45%), Gaps = 24/326 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV  TD  +R     L    L+ +EM  A A+    +     L +  +E+P+A+Q+ G++
Sbjct: 25  MVGVTDSIFRRMILSLGGCGLVCSEMTNASAVSPRARSRHRQLDYLPEERPIAMQLSGSE 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA++VE  G + +++N GCPS +V  G  G+ L+ +   +   + A+C A+ IP
Sbjct: 85  PDLVAAAARVVEALGADILDINCGCPSPKVTGGGHGSALLRDLPKMERLLKAVCAAVQIP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD+   +   +  K  ++ GV  + +H R         +        D+  
Sbjct: 145 VTLKFRAGWDDE--NLNYLDTAKMAEQVGVAALALHPRT--------RAQGYSGVADWRR 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K+    + +  +G + D + AL+ L     DGVMIGRAA  N  +   + +  +  
Sbjct: 195 VADVKRAV-RIPVIGSGDVRDAADALRRLRESGADGVMIGRAAMHNPWIFRQIAQLRAGT 253

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCRH 295
                 + T  DK  +      M   A     +  KL+Q    +IG F    P +   R 
Sbjct: 254 QPM---VVTPSDKYEFLMHYLDMCHEALPERLALNKLKQ----LIGQFGIELPGAAALRS 306

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +   +G + A  H +E  F   +E+
Sbjct: 307 AIHHSSGVAEARDH-LERFFAQYVET 331


>gi|299135626|ref|ZP_07028810.1| dihydrouridine synthase DuS [Acidobacterium sp. MP5ACTX8]
 gi|298601750|gb|EFI57904.1| dihydrouridine synthase DuS [Acidobacterium sp. MP5ACTX8]
          Length = 425

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 72/376 (19%), Positives = 142/376 (37%), Gaps = 66/376 (17%)

Query: 1   MVDWTDRHYRFFAR-------------------------LLTNNALLYTEMIVADAILRG 35
           M   TD  +R F +                          ++   L+ TE   AD + R 
Sbjct: 42  MAGVTDTVFRRFIKNSSMFTAEAATPETQGADIDVETSNEVSGCGLIMTEFTSADGLSRM 101

Query: 36  D---KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
               +K  L +   E P++ Q+ G++ + L E+A I +D G++ ++LN+GCP+ RV   +
Sbjct: 102 RETKRKRYLTYYEDEHPISAQLFGSNPATLAESAIICQDAGFDLVDLNLGCPAKRVVACN 161

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
            G+ L+ +   +      +  A++IP TVK R+G +D    +    L K  +  G+N + 
Sbjct: 162 GGSGLLRDLPAIRTIFERVRAAVTIPFTVKFRMGWND--SNIVCVELAKMAEDCGLNAVA 219

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSV 210
           +HAR         ++        ++ +  +K +   + +  NG +     A  ++     
Sbjct: 220 LHART--------REQGYTGVARWEWIAAVK-DAVTIPVIGNGDIRTPEDAAAMVEATHC 270

Query: 211 DGVMIGRAAYKNSAMLTTVDEY--------FSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           D VMIGRAA  N  +   + +Y               +   + R+ +D++ ++   + ++
Sbjct: 271 DAVMIGRAAPANPWIFRQIAQYTASKQATGVGTYDKPTDMDRYRMIRDYFERLMHEVAEH 330

Query: 263 AA----------------RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTA 306
                                     + ++ +      HG P     R  +  +A     
Sbjct: 331 PEIVGPADSDLEKRLKRNHESAQRDAIGRMKQFASWFTHGVPGGATLRREI-FDAKRGAQ 389

Query: 307 THHIIETAFNLMIESL 322
               +E  F      L
Sbjct: 390 VMEKVEAFFTQRANEL 405


>gi|237741667|ref|ZP_04572148.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 4_1_13]
 gi|294785722|ref|ZP_06751010.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_27]
 gi|229429315|gb|EEO39527.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 4_1_13]
 gi|294487436|gb|EFG34798.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 3_1_27]
          Length = 307

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 122/316 (38%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       K  A+QI G ++ K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLRKGNAVQIFGENVEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG       V +  + + I   G + I +H R         ++       D+  +
Sbjct: 129 SIKIRIGYKKPENYVQIGKIAEEI---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNVSIPVIGNGDIFTGEDALEKISYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D      +    +  + +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLRRIRID------NDNKFIFDVRKHISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
              +        I+E 
Sbjct: 291 NTISNY-DEIIKILEE 305


>gi|254303688|ref|ZP_04971046.1| dihydrouridine--tRNA ligase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323880|gb|EDK89130.1| dihydrouridine--tRNA ligase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 307

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 125/316 (39%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       +  A+QI G DI K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIKK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           + E+AK +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKESAKYIENLGVKHINLNCGCPMKKIVNCGYGAALVREPEKIKKILSEIKSILNDDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK RIG  +    + +  + + I   G + I IH R         ++       D+  +
Sbjct: 129 SVKIRIGYKEPENYIQIGKIAEEI---GCDHITIHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNVSIPVIGNGDIFTGEDALEKISYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D      +    +  + +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLKRIRVD------NDNQFIFDVRKHISWYLKGMENCTEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
              +        I+E 
Sbjct: 291 NTISDY-DEIIKILEE 305


>gi|291299569|ref|YP_003510847.1| TIM-barrel protein, nifR3 family [Stackebrandtia nassauensis DSM
           44728]
 gi|290568789|gb|ADD41754.1| TIM-barrel protein, nifR3 family [Stackebrandtia nassauensis DSM
           44728]
          Length = 394

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 68/328 (20%), Positives = 129/328 (39%), Gaps = 35/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R          +   EM++  A+L  + K   ++ F   E+P +LQ+ G D
Sbjct: 21  MAGITNVAFRRLCAE-QGAGIYTCEMVMTRALLERNPKTTRMIAFGPGERPRSLQLYGVD 79

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALS 116
              + +A +++ D    + I++N GC   +V     G+ +    ++ G  +  A+  A  
Sbjct: 80  PVTVRKAVEMIVDEDLADHIDMNFGCSVPKVTRKGGGSAIPYKRNLFGQIVRSAVEAAGD 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVTVK R G+DD++  +   +  +  + +G   + +HAR A          R     D+
Sbjct: 140 IPVTVKMRKGIDDEL--LTFVDAGRVAQDAGAAWVALHARTA--------AQRYSGTADW 189

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + E+K+   D+ +  NG + + + AL+++     DGV++GR       +   +   F+
Sbjct: 190 DAITELKRAL-DIPVLGNGDIWEATDALRMVEETGCDGVVVGRGCLGRPWLFADLAAAFA 248

Query: 235 NPLTGSSPIKTRVDKDFWRK--ISASMTDYAARHLHSGGKLQ---------------QIT 277
                  P    V     R   +       A   +  G  L+                  
Sbjct: 249 GSSHRVMPSLGEVAAIMRRHAALLVDWYSSAGAPVEEGKSLRPEKRRKISAEEHGVTDFR 308

Query: 278 RHMIGLFHGFPNSRRCRHILTVEAGAST 305
           +H+     GF      R  L + +    
Sbjct: 309 KHVAWYLKGFSVGGELRRSLAMSSSLDE 336


>gi|119716174|ref|YP_923139.1| nifR3 family TIM-barrel protein [Nocardioides sp. JS614]
 gi|119536835|gb|ABL81452.1| putative TIM-barrel protein, nifR3 family [Nocardioides sp. JS614]
          Length = 386

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 124/305 (40%), Gaps = 25/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T+  YR          L   EMI +  ++ GD+  K++L F   E   ++Q+ G+D
Sbjct: 31  MAGITNAAYRRLCAE-QGAGLYVCEMITSRGLVEGDQHTKDMLVFDELETIRSVQLYGSD 89

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            + + +AA+I+  ++G   I+LN GCP  +V     G  L     ++ + + +   A   
Sbjct: 90  PAYVGKAAEILCAEYGVAHIDLNFGCPVPKVTRKGGGGALPWKRGLLAEILESAVAAAAP 149

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R G+D+    +   +  +  ++SG   I +H R                  
Sbjct: 150 YDVPVTMKTRKGIDED--HLTYLDAGRIAQESGCAAIALHGRT--------VAQAYSGAA 199

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
           D+D +  +  E+ D+ +  NG + + + AL+++      GV++GR       +   +   
Sbjct: 200 DWDAIAALV-EHVDIPVLGNGDVWEAADALRMVEETGVAGVVVGRGCLGRPWLFRDLAAA 258

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           F      + P    V     R       +   +HL      ++  +H+     GF     
Sbjct: 259 FGGEDVATLPALGEVAAMMRRHA-----ELLCQHLGEERGCKEFRKHVTWYLKGFGAGGE 313

Query: 293 CRHIL 297
            R  L
Sbjct: 314 MRRSL 318


>gi|209885217|ref|YP_002289074.1| probable tRNA-dihydrouridine synthase [Oligotropha carboxidovorans
           OM5]
 gi|209873413|gb|ACI93209.1| probable tRNA-dihydrouridine synthase [Oligotropha carboxidovorans
           OM5]
          Length = 343

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 66/285 (23%), Positives = 117/285 (41%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A  L    L+ +EM  +D + RG   ++L        P  +Q+ G + 
Sbjct: 27  MSGITDAPLRRVAARL-GAGLVVSEMTASDDLARGRPMSVLRCEASGVGPHVVQLAGCET 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 86  KWMAEGARIAEGGGADIIDINMGCPARHVTGGQSGSALMRDLDHAMALIEATIAAVKVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D    ++    L +  + +G+  + +H R         +        D+  V
Sbjct: 146 TLKMRLGWD--HASLNAPELARRSEVAGIRMVTVHGRT--------RCQFYKGEADWQAV 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + + +NG +     A++ L     D VMIGR A     +   +    +   
Sbjct: 196 RAV-REAIRIPLVVNGDIATYDDAVEALAASGADAVMIGRGAQGRPWLPGQIGRRLAGGA 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
           + + P       D       ++ D    H  +   L+   +H+  
Sbjct: 255 SETDPAL-----DVQLGYLRTLYDDILSHYGARIGLRHARKHLGW 294


>gi|290969239|ref|ZP_06560764.1| TIM-barrel protein, nifR3 family [Megasphaera genomosp. type_1 str.
           28L]
 gi|290780745|gb|EFD93348.1| TIM-barrel protein, nifR3 family [Megasphaera genomosp. type_1 str.
           28L]
          Length = 331

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 119/302 (39%), Gaps = 21/302 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M    D  YR  A+     AL+ TEM+    ++   G  + +L  +  E PL+LQ+ GAD
Sbjct: 25  MAGVCDLPYRRIAK-AHGAALVCTEMVSDKGLVYHNGHTQEMLQIAKDEHPLSLQLFGAD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +  AA   E+ G + +++N+GCP  +V     GA L+ +       I A+ +A+SIP
Sbjct: 84  PASMAYAAAAAEEAGADLVDINMGCPVKKVVRNGAGAALLQDLPRAEAIIRAVVQAVSIP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D                 +    +    R+A   G            D+ +
Sbjct: 144 VTVKMRAGWDAAHVVAPALAERAEAAGAAAVAVHGRTREAFYSG----------KADWRV 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +  +    + +  NG + D   A  +L       VM+ RAA  N  + + +  Y +  
Sbjct: 194 IADTVQAV-SIPVIGNGDVVDGPSARDMLQQTGCAAVMVARAAQGNPWIFSQITHYLTTG 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P            + A +  Y   ++     ++++  H      G   S   R  
Sbjct: 253 EMAAPPTAWERYTQILAHLEA-LVAYKGEYIG----IREMRAHASWYTRGLYGSAALRER 307

Query: 297 LT 298
           + 
Sbjct: 308 IN 309


>gi|326803024|ref|YP_004320842.1| TIM-barrel protein, nifR3 family [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326650489|gb|AEA00672.1| TIM-barrel protein, nifR3 family [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 349

 Score =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 126/317 (39%), Gaps = 26/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL++QI G  
Sbjct: 18  MAGVSNAAFRTIVK-AQGAGLVVCEMISDQGIHFRNKKTLSMLHIEDEEWPLSVQIFGGQ 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L EAA+ +E       I++N+GCP  +V +   G+  +L+P+ V + +  +  A+SI
Sbjct: 77  ADSLAEAAQFIEANTKAAIIDINMGCPVNKVVKTDAGSKALLDPNEVYNRVKMVADAVSI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD         L    +++G   I +H R         ++       +++
Sbjct: 137 PVTVKMRTGWDDDHILAVENALA--AQEAGAKMIAMHGRT--------REQMYTGKANWN 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ ++ ++   +    NG +    +A   L    VDGVM+GR    N  ++  +  Y   
Sbjct: 187 IIKQVSQKL-SVPFYGNGDIRTPEEAKYALDNYGVDGVMVGRGCLGNPWVIHRMVHYVET 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +     ++                +++    +     G P S + + 
Sbjct: 246 GELLPEKTGLERIEACKDHLTR-----LVDLKGESVGVREFRSMVAYYLKGIPRSAKVK- 299

Query: 296 ILTVEAGASTATHHIIE 312
              V    + +   +++
Sbjct: 300 ---VACTQADSYQEVVD 313


>gi|78213546|ref|YP_382325.1| dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9605]
 gi|78198005|gb|ABB35770.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus sp.
           CC9605]
          Length = 333

 Score =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 134/324 (41%), Gaps = 23/324 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R    +ALL+TEM+ A ++    G  K +   + +  P+ +Q+     
Sbjct: 28  AGVSDRVFRSLVRRWAPDALLFTEMVNATSLEMGHGLCK-VESLAEESGPIGVQLFDHRP 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    + A+  A+++PV
Sbjct: 87  QAMADAARRAEASGAFLIDINMGCPVRKIARKGGGSGLIRDPGLAIQIVEAVADAVAVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G              + ++++G   + +H R         ++       D+  +
Sbjct: 147 TVKTRLGWCGSDADPVH--WCQQLEQAGAQLLTLHGRT--------REQGFKGAADWSSI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++ +E   + +  NG +     AL+ L      GVM+GR    +  ++  +D   +   
Sbjct: 197 RQV-REALTIPLIANGDINSPDDALRCLKQTGAAGVMVGRGTMGSPWLVGQIDAALAGRS 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             ++P  +        ++   + D           L    +HM     GFP + R RH L
Sbjct: 256 IPATPDPSARLALARDQLDGLVQD------RGDHGLLIARKHMGWTCTGFPGASRLRHDL 309

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
            + A        ++    + +  S
Sbjct: 310 -MRAPTPAQARDLLTQQIDALAAS 332


>gi|254419994|ref|ZP_05033718.1| putative TIM-barrel protein, nifR3 family [Brevundimonas sp. BAL3]
 gi|196186171|gb|EDX81147.1| putative TIM-barrel protein, nifR3 family [Brevundimonas sp. BAL3]
          Length = 357

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 118/287 (41%), Gaps = 21/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   TD  +R  A  L   A + TEM+ A  + R     +   +     PL  +Q+ G D
Sbjct: 27  MTGVTDLPFRVLASRL-GAAYVATEMVAAKELARERPDVVRRAAVGAGLPLTVIQLVGRD 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++ E A++ E  G + ++LN GCP+  V   + G+ LM  PD+    + A  +A S P
Sbjct: 86  PGQMAEGARMAEKAGADIVDLNFGCPAKEVTGSAAGSALMRTPDLACRIMEAAVQATSRP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD     A   L K  ++ GV  + +H R         +        D+  
Sbjct: 146 VTVKMRLGWDDDSRNAA--ELAKRAEEIGVRAVTVHGRT--------RKQFYTGVADWAA 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+K     + + +NG +     A + L     DG+M+GR  Y    +   ++    + 
Sbjct: 196 VGEVKAAVG-IPVIVNGDITTAEAARQALAQSGADGLMLGRGVYGRPWLAAHLERALIDG 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           ++   P            + AS+  Y          L+   +H+   
Sbjct: 255 VSLDEPGPEARLGIVVEHLRASVEFY-----GLPLGLRMFRKHLGWY 296


>gi|325972614|ref|YP_004248805.1| hypothetical protein SpiBuddy_2803 [Spirochaeta sp. Buddy]
 gi|324027852|gb|ADY14611.1| TIM-barrel protein, nifR3 family [Spirochaeta sp. Buddy]
          Length = 332

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 113/303 (37%), Gaps = 25/303 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             +TD  +R    +       +TEM+ A+ + R  +K +  +  +  EK  A+Q+  ++ 
Sbjct: 27  AGYTDIPFRTLC-IEHGADFTFTEMVSAEGLSREGEKTMELMYRAPNEKQYAIQLFMSNT 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L +A + +  F    I++N GCP  +V +   G+ +M  P ++ D +  +   + IPV
Sbjct: 86  DSLKQALEQLLPFHPEVIDINCGCPVPKVTKTGAGSAMMKTPSLITDVVRTITAEVDIPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R G D Q  +       ++    G + + +HAR         +     P  D+  +
Sbjct: 146 SVKFRTGWDAQ--SENFLEFAQAALDGGASALTLHART--------RSQGYAPFADWSKL 195

Query: 180 YEIKKENP----DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +K+        + +  +G L     A+++L    +D VM  R A  N  + +      
Sbjct: 196 RALKQYCLTHGYTVPVFGSGDLFIAEDAIRMLQETGIDAVMFARGAIGNPFIFSQAKALL 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                       RV+            D              + +H      G  N+   
Sbjct: 256 EGREKPEITKLMRVEAII------RHLDLMIETFGEKTACTLMRKHTCSYLKGIANTSPI 309

Query: 294 RHI 296
           +  
Sbjct: 310 KQA 312


>gi|256027949|ref|ZP_05441783.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D11]
 gi|289765894|ref|ZP_06525272.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D11]
 gi|289717449|gb|EFD81461.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. D11]
          Length = 308

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 125/316 (39%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       +  A+QI G DI+K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIAK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALLREPEKIKRILSEIKSVLNDDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG  +    + +  + + I   G + I +H R         ++       D+  +
Sbjct: 129 SIKIRIGYKEPENYIQIGKIAEEI---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGKDALEKISYSNVDGVMLARGIFGNPWLIRDIREILKYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +  +  D      +    +  I +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLKRTRVD------NDNKFIFDIRKHISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
              +        I+E 
Sbjct: 291 NTISDY-DEIIKILEE 305


>gi|260565621|ref|ZP_05836105.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 1 str.
           16M]
 gi|260151689|gb|EEW86783.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 1 str.
           16M]
          Length = 332

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGTDIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 288


>gi|17987147|ref|NP_539781.1| nitrogen regulation protein NIFR3 [Brucella melitensis bv. 1 str.
           16M]
 gi|225852620|ref|YP_002732853.1| TIM-barrel protein nifR3 family protein [Brucella melitensis ATCC
           23457]
 gi|256044776|ref|ZP_05447680.1| TIM-barrel protein nifR3 family protein [Brucella melitensis bv. 1
           str. Rev.1]
 gi|256113675|ref|ZP_05454486.1| TIM-barrel protein nifR3 family protein [Brucella melitensis bv. 3
           str. Ether]
 gi|256263888|ref|ZP_05466420.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 2 str.
           63/9]
 gi|265991200|ref|ZP_06103757.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995036|ref|ZP_06107593.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 3 str.
           Ether]
 gi|17982812|gb|AAL52045.1| nitrogen regulation protein nifr3 [Brucella melitensis bv. 1 str.
           16M]
 gi|225640985|gb|ACO00899.1| TIM-barrel protein nifR3 family protein [Brucella melitensis ATCC
           23457]
 gi|262766149|gb|EEZ11938.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 3 str.
           Ether]
 gi|263001984|gb|EEZ14559.1| nifR3 family TIM-barrel protein [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263094019|gb|EEZ17953.1| nitrogen regulation protein NifR3 [Brucella melitensis bv. 2 str.
           63/9]
 gi|326538846|gb|ADZ87061.1| TIM-barrel protein nifR3 family protein [Brucella melitensis M5-90]
          Length = 333

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGTDIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 289


>gi|91977059|ref|YP_569718.1| dihydrouridine synthase TIM-barrel protein NifR3 [Rhodopseudomonas
           palustris BisB5]
 gi|91683515|gb|ABE39817.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodopseudomonas
           palustris BisB5]
          Length = 353

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 62/285 (21%), Positives = 119/285 (41%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST-QEKPLALQIGGADI 59
           M   TD  +R     L    L+ +EM  ++ +++G   ++         P  +Q+ G + 
Sbjct: 37  MSGITDAPFRKQVAAL-GAGLVVSEMTASEDLVQGRAMSVRRCDAIDGAPHVVQLAGCEP 95

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 96  HWMAEGARIAEAGGADIIDINMGCPARHVTGGQSGSALMRDLDHALTLIEATIDAVRVPV 155

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D++  ++    L +  + +GV  + +H R         +        D+  V
Sbjct: 156 TLKMRLGWDER--SLNAPELARRAEAAGVQLVTVHGRT--------RSQFYKGEADWRAV 205

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + + +NG +     A++ L     D VMIGR A     +   +       +
Sbjct: 206 RAV-REAISIPLVVNGDITTYHMAVEALDQSGADAVMIGRGAQGQPWLPGQIGRRLQTGI 264

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             + P       D+ R +   +     + +     L+   +H+  
Sbjct: 265 AEAMPSLAEQF-DYLRSLYDGVLSLYGQRIG----LRHARKHLGW 304


>gi|145350035|ref|XP_001419429.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144579660|gb|ABO97722.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 355

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 96/323 (29%), Positives = 156/323 (48%), Gaps = 18/323 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-----DKKNILGFSTQEKPLALQIG 55
           M+++T  H+R  ARL++   +L+TEM V   +             L +        LQ+G
Sbjct: 7   MMEYTTPHFRVMARLMSRRVMLWTEMEVDQTVTHSARDGDRVDKFLDYPAATFGTVLQLG 66

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKA 114
           G+    L  A  I   +GY+EINLN GCPS +V     FGA LM  P +V +C+AAM + 
Sbjct: 67  GSTPEYLGRATAIAAPYGYDEINLNSGCPSPKVAGKGCFGAALMAEPGLVAECLAAMAEN 126

Query: 115 L--SIPVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                PV+VKCRIGVDD      L + V + +  S     ++HARKA+L GLSP +NR +
Sbjct: 127 APEGTPVSVKCRIGVDDVDSYDDLCDYVERIVAGSSTRRFYVHARKALLAGLSPAENRTV 186

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-------VDGVMIGRAAYKNSA 224
           P L ++  Y + ++ P+    LNGGL+ ++    +L         + G MIGR A+ +  
Sbjct: 187 PPLKHEWAYALARDFPECEFHLNGGLKTLNDVKNVLKRGPEDGGPIVGAMIGRQAHADPW 246

Query: 225 -MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA-ARHLHSGGKLQQITRHMIG 282
            +L+  D       +  S  +      +      ++  Y  A+  +    ++ +   +  
Sbjct: 247 GLLSAADTTLFGEASNPSASRRDFLNKYAVYADETIGRYGTAKDGYRIPSVRHMMHPIQN 306

Query: 283 LFHGFPNSRRCRHILTVEAGAST 305
           LFHG  N++  R ++  +    +
Sbjct: 307 LFHGCANNKAWRRLVEEDLQKRS 329


>gi|163736351|ref|ZP_02143770.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Phaeobacter
           gallaeciensis BS107]
 gi|161390221|gb|EDQ14571.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Phaeobacter
           gallaeciensis BS107]
          Length = 319

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 131/320 (40%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TDR +R   R      L+ +EM+ +  +++     +     S   +  A+QI G D
Sbjct: 1   MAGITDRPFRDLVRSF-GAGLMVSEMVASQEMVQAKPGVRERAELSADVENTAVQIAGRD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+ VE  G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+S+P
Sbjct: 60  AYWMAEAARQVESRGAKVIDINMGCPAKKVTNGYSGSALLKTPDHALSLIEAVVAAVSVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD   ++   ++ +  + +GV  + IH R         +        D+  
Sbjct: 120 VTLKTRLGWDD--NSLNAADVARRAQDAGVQMVTIHGRT--------RCQFYKGTADWKA 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K    ++ +  NG + D + A   L     DGVMIGR       +L  V       
Sbjct: 170 IAAVKTAL-NVPLLANGDIVDTATARTALAQSGADGVMIGRGVQGKPWLLAEVAHDIWGS 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH- 295
                P  + + +       A +  Y      +   L+   +H+             R  
Sbjct: 229 AAPEVPTGSDLVQMVSAHYEAMIAFY-----GTDLGLRVARKHLGWYMDEAATPAPLRRE 283

Query: 296 ILTVEAGASTATHHIIETAF 315
           +LT +A  +     ++  A 
Sbjct: 284 VLTAKAPKT--VLQLLPDAL 301


>gi|261752425|ref|ZP_05996134.1| nifR3 family TIM-barrel protein [Brucella suis bv. 5 str. 513]
 gi|261742178|gb|EEY30104.1| nifR3 family TIM-barrel protein [Brucella suis bv. 5 str. 513]
          Length = 332

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELYNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYCSKIGIRHARKHLGWYM 288


>gi|269302558|gb|ACZ32658.1| dihydrouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 335

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 136/312 (43%), Gaps = 22/312 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  YR  + L     L++ EM+  + +L   ++   +L ++   +P+  Q+ G++ 
Sbjct: 22  AGFSDYPYRCMSALYQ-PGLMFCEMVKVEGMLYAPERTSKLLDYNENMRPIGAQLCGSNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               EAAKI+E  G++ I+LN GCP+ ++ +   G+ L+  P+++G  +  +  ++SIPV
Sbjct: 81  ETSGEAAKILEGLGFDLIDLNCGCPTDKITKDGSGSGLLKTPELIGRILDKIINSVSIPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D +   + + + V+ I+ +G + +++H R        P +   I        
Sbjct: 141 TVKIRSGWDME--HINIEDTVRIIRDAGASAVFVHGRTRAQGYHGPSNQEYISRAK---- 194

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               KE P   +  NG +     A  +L    DGV++ R       +   + +Y +    
Sbjct: 195 AAAGKEFP---VFGNGDIFSPEAAQAMLTTGCDGVLVARGTMGAPWIGKQIQDYLTTGSY 251

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
              P   R      +            +  S  K    TR + G  H   ++ + R + +
Sbjct: 252 EKIPFIKR------KAAFLEHMRLVEDYYQSETKFLSETRKLCG--HYLISAAKVRFLRS 303

Query: 299 VEAGASTATHHI 310
             A  +T+   +
Sbjct: 304 SLA-KATSYQEV 314


>gi|254701862|ref|ZP_05163690.1| nitrogen regulation protein NifR3 [Brucella suis bv. 5 str. 513]
          Length = 333

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELYNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYCSKIGIRHARKHLGWYM 289


>gi|34763049|ref|ZP_00144023.1| Nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|27887275|gb|EAA24372.1| Nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
          Length = 307

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 122/316 (38%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       K  A+QI G ++ K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLRKGNAVQIFGENVEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG       V +  + + I   G + I +H R         ++       D+  +
Sbjct: 129 SIKIRIGYKKPENYVQIGKIAEEI---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGEDALEKISYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D      +    +  + +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLRRIRID------NDNKFIFDVRKHISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
              +        I+E 
Sbjct: 291 NTISNY-DEIIKILEE 305


>gi|260494139|ref|ZP_05814270.1| dihydrouridine-tRNA ligase [Fusobacterium sp. 3_1_33]
 gi|260198285|gb|EEW95801.1| dihydrouridine-tRNA ligase [Fusobacterium sp. 3_1_33]
          Length = 299

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 64/302 (21%), Positives = 121/302 (40%), Gaps = 23/302 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       +  A+QI G DI+K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIAK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALLREPEKIKRILSEIKSILNDDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG  +    + +  L + I   G + I +H R         ++       D+  +
Sbjct: 129 SIKIRIGYKEPENYIQIGKLAEEI---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGKDALEKISYSNVDGVMLARGIFGNPWLIRDIREILKYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +  +  D      +    +  I +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLKRTRVD------NDNKFIFDIRKHISWYLKGIENCAEAKRKI 290

Query: 298 TV 299
             
Sbjct: 291 NT 292


>gi|306841846|ref|ZP_07474528.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO2]
 gi|306288073|gb|EFM59470.1| putative TIM-barrel protein, nifR3 family [Brucella sp. BO2]
          Length = 320

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 12  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 71  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 131 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGMADWDAI 180

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +           +
Sbjct: 181 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWL---------AGV 230

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 231 IAGSDFAPRDANGILEYIIRHYED-MLDHYGSKTGIRHARKHLGWYM 276


>gi|316934214|ref|YP_004109196.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris DX-1]
 gi|315601928|gb|ADU44463.1| TIM-barrel protein, nifR3 family [Rhodopseudomonas palustris DX-1]
          Length = 344

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 65/285 (22%), Positives = 116/285 (40%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADI 59
           M   TD  +R     L    L+ +EM  ++ ++ G + ++       + P  +Q+ G + 
Sbjct: 28  MTGITDAPFRRQVAEL-GAGLVVSEMTASEDLVAGRRMSVRRCDKVGQGPHVVQLAGCEA 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ +PV
Sbjct: 87  RWMAEGARIAEAGGADIIDINMGCPARHVTGGLSGSALMRDLDHALTLIEATIGAVRVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD+        L +  + +GV  + +H R         +        D+  V
Sbjct: 147 TLKMRLGWDDRSRNA--PELARRAQDAGVQLVTVHGRT--------RQQFYKGEADWGAV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + ++   + + +NG +     AL+ L     D VMIGR A     +   V    +   
Sbjct: 197 RAV-RDAISIPLVVNGDITCHDTALEALQRSGADAVMIGRGAQGRPWLPGQVGRQLTTGQ 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
            G+ P          R    ++ D           L+   +H+  
Sbjct: 256 AGAEPPLA-----AQRDYLRTLYDDILALYGVRIGLRHARKHLGW 295


>gi|260546585|ref|ZP_05822324.1| nitrogen regulation protein NifR3 [Brucella abortus NCTC 8038]
 gi|260754862|ref|ZP_05867210.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 6 str. 870]
 gi|260758079|ref|ZP_05870427.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 4 str. 292]
 gi|260761903|ref|ZP_05874246.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 2 str.
           86/8/59]
 gi|261214113|ref|ZP_05928394.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 3 str. Tulya]
 gi|297248433|ref|ZP_06932151.1| tRNA-dihydrouridine synthase B [Brucella abortus bv. 5 str. B3196]
 gi|260095635|gb|EEW79512.1| nitrogen regulation protein NifR3 [Brucella abortus NCTC 8038]
 gi|260668397|gb|EEX55337.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 4 str. 292]
 gi|260672335|gb|EEX59156.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260674970|gb|EEX61791.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 6 str. 870]
 gi|260915720|gb|EEX82581.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 3 str. Tulya]
 gi|297175602|gb|EFH34949.1| tRNA-dihydrouridine synthase B [Brucella abortus bv. 5 str. B3196]
          Length = 332

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYVSKIGIRHARKHLGWYM 288


>gi|62290033|ref|YP_221826.1| NifR3, nitrogen regulation protein Nifr3 [Brucella abortus bv. 1
           str. 9-941]
 gi|82699960|ref|YP_414534.1| hypothetical protein BAB1_1142 [Brucella melitensis biovar Abortus
           2308]
 gi|189024273|ref|YP_001935041.1| nitrogen regulation protein NifR3 [Brucella abortus S19]
 gi|237815542|ref|ZP_04594539.1| TIM-barrel protein, nifR3 family [Brucella abortus str. 2308 A]
 gi|254689345|ref|ZP_05152599.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 6 str. 870]
 gi|254693829|ref|ZP_05155657.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697478|ref|ZP_05159306.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254730375|ref|ZP_05188953.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 4 str. 292]
 gi|256257591|ref|ZP_05463127.1| nitrogen regulation protein NifR3 [Brucella abortus bv. 9 str. C68]
 gi|260883874|ref|ZP_05895488.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 9 str. C68]
 gi|62196165|gb|AAX74465.1| NifR3, nitrogen regulation protein Nifr3 [Brucella abortus bv. 1
           str. 9-941]
 gi|82616061|emb|CAJ11098.1| Protein of unknown function UPF0034:FMN/related compound-binding
           core:Putative TIM-barrel protein nifR3 family [Brucella
           melitensis biovar Abortus 2308]
 gi|189019845|gb|ACD72567.1| nitrogen regulation protein NifR3 [Brucella abortus S19]
 gi|237788840|gb|EEP63051.1| TIM-barrel protein, nifR3 family [Brucella abortus str. 2308 A]
 gi|260873402|gb|EEX80471.1| nifR3 family TIM-barrel protein [Brucella abortus bv. 9 str. C68]
          Length = 333

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYVSKIGIRHARKHLGWYM 289


>gi|255079776|ref|XP_002503468.1| predicted protein [Micromonas sp. RCC299]
 gi|226518735|gb|ACO64726.1| predicted protein [Micromonas sp. RCC299]
          Length = 499

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 97/260 (37%), Positives = 142/260 (54%), Gaps = 19/260 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M++ TD H+R   RL++  A L+TEM+  DA++   +    +L +  +E PL +Q+GGA 
Sbjct: 38  MLECTDTHFRRVCRLVSRRAHLWTEMVNQDAVVHSWRSKPEMLAYGDEEHPLTVQLGGAS 97

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEG-----SFGACLMLNPDIVGDCIAAMC 112
             +L  AA +   ++ Y+EINLN GCPS RV         FGA LM +P  VG+C+  M 
Sbjct: 98  PERLALAATVCDAEYRYDEINLNCGCPSNRVVNKKDVATCFGAALMRDPTHVGECLRRMR 157

Query: 113 KALSIPVTVKCRIGV--------DDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGL 163
           +A+ +PVTVK R+GV        D       +   V  + ++ GV    +HAR A+L GL
Sbjct: 158 EAVDVPVTVKHRLGVRPTEKSPDDSMDSYAFVSEFVDVVNQASGVKHFIVHARAAVLSGL 217

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           S   NR +P L +  V+ +  + P L   LNGG+E M QA + L    + GVM+GRA Y+
Sbjct: 218 STTGNRTVPPLRHAEVHALADDFPSLGFTLNGGIETMDQAAEHLESGKLRGVMLGRAVYR 277

Query: 222 NSAMLTTVDEYFSNPLTGSS 241
           N A+L  VD  F       +
Sbjct: 278 NPAVLAEVDARFYGDEPREA 297


>gi|237744277|ref|ZP_04574758.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 7_1]
 gi|229431506|gb|EEO41718.1| nitrogen regulation protein NIFR3 [Fusobacterium sp. 7_1]
          Length = 308

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 125/316 (39%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       +  A+QI G DI+K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIAK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALLREPEKIKRILSEIKSILNDDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K RIG  +    + +  + + I   G + I +H R         ++       D+  +
Sbjct: 129 SIKIRIGYKEPENYIQIGKIAEEI---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGKDALEKISYSNVDGVMLARGIFGNPWLIRDIREILKYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +  +  D      +    +  I +H+     G  N    +  +
Sbjct: 237 IKTPTTKEDKINMAIEHLKRTRVD------NDNKFIFDIRKHISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
              +        I+E 
Sbjct: 291 NTISDY-DEIIKILEE 305


>gi|30064591|ref|NP_838762.1| putative dehydrogenase [Shigella flexneri 2a str. 2457T]
 gi|56480301|ref|NP_709055.2| putative dehydrogenase [Shigella flexneri 2a str. 301]
 gi|30042850|gb|AAP18573.1| putative dehydrogenase [Shigella flexneri 2a str. 2457T]
 gi|56383852|gb|AAN44762.2| putative dehydrogenase [Shigella flexneri 2a str. 301]
          Length = 280

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 57/294 (19%), Positives = 114/294 (38%), Gaps = 21/294 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           + ++  +    K+ L     ++P    +QI G+   ++ +AA+I  + G   I++N+GCP
Sbjct: 1   MSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSAPKEMADAARINVESGAQIIDINMGCP 60

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
           + +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  +
Sbjct: 61  AKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGWAPEHRN--CEEIAQLAE 118

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
             G+  + IH R         +        +YD +  +K++   + +  NG + D  +A 
Sbjct: 119 DCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKAR 169

Query: 205 KIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
            +L     D +MIGRAA     +   +  Y              V +     +      Y
Sbjct: 170 AVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVRELHDFY 229

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
                  G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 GP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 277


>gi|326409138|gb|ADZ66203.1| TIM-barrel protein nifR3 family protein [Brucella melitensis M28]
          Length = 319

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 121/287 (42%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 11  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 70  RWMGEAAKIAEGEGTDIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 130 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 179

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 180 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 230

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 231 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 275


>gi|330444003|ref|YP_004376989.1| putative TIM-barrel protein, nifR3 family [Chlamydophila pecorum
           E58]
 gi|328807113|gb|AEB41286.1| putative TIM-barrel protein, nifR3 family [Chlamydophila pecorum
           E58]
          Length = 327

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 137/320 (42%), Gaps = 23/320 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             ++D  YR  + L    AL++ EM+  + +L   ++ +  L +S + +P+  Q+  ++ 
Sbjct: 22  AGFSDYPYRRMSALYA-PALMFCEMVKVEGLLYSPQRTMKLLEYSEEMRPIGGQLCCSNP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E AKI+ED G++ I+LN GCP+ ++ +   G+ L+  P ++G  +  +   +S+PV
Sbjct: 81  EIVGEGAKILEDLGFDLIDLNCGCPTDKITKDGSGSGLLKTPSLIGVLVEKIVNTVSVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D +   + +  +VK ++++G + +++H R        P +   I        
Sbjct: 141 TVKIRSGWDSE--HINVEEIVKILREAGASAVFVHGRTRAQGYHGPSNREYIARA----- 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             +  E     +  NG +     A ++     DG+++ R       +   ++EY +    
Sbjct: 194 KVVAGEA--FPVFGNGDIFSPEAAKEMFATGCDGLLVARGTMGAPWIGKQIEEYLTTGSY 251

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR--HI 296
              P   R      ++       +   +  S  K    TR + G  H    + + R    
Sbjct: 252 QPVPFTMR------KQAFVQHLQWVEEYYQSEAKFLSETRKLCG--HYLICASKVRFLRA 303

Query: 297 LTVEAGASTATHHIIETAFN 316
               A +    + +IE    
Sbjct: 304 SLARASSYHEVYQLIEAYEE 323


>gi|302024537|ref|ZP_07249748.1| tRNA-dihydrouridine synthase [Streptococcus suis 05HAS68]
 gi|330833584|ref|YP_004402409.1| TIM-barrel protein, nifR3 family [Streptococcus suis ST3]
 gi|329307807|gb|AEB82223.1| TIM-barrel protein, nifR3 family [Streptococcus suis ST3]
          Length = 334

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 65/326 (19%), Positives = 132/326 (40%), Gaps = 27/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++ +   N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQTNTKANIVDINMGCPVNKVVKNEAGAKWLKDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++   AV       + + +GV+ + +H R         ++      +D +
Sbjct: 143 PLTVKMRTGWNNTDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTVDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++      +    NG + ++  A + +     D VM+GR A  N  +   ++ Y   
Sbjct: 192 TLTKVAGSLTKIPFIANGDIRNVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        +  +  ++  +T+     +     +++          G   + + R 
Sbjct: 252 GEVLPDLSFEDKLEVAFDHLTR-LTNLKGESIA----VREFRGLAPHYLRGSAGAAKIR- 305

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
                A A   T   ++  FN   E+
Sbjct: 306 ----GAVARAETIEQVQELFNQAREA 327


>gi|260436473|ref|ZP_05790443.1| probable tRNA-dihydrouridine synthase 1 [Synechococcus sp. WH 8109]
 gi|260414347|gb|EEX07643.1| probable tRNA-dihydrouridine synthase 1 [Synechococcus sp. WH 8109]
          Length = 334

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 133/324 (41%), Gaps = 23/324 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R    +ALL+TEM+ A ++    G  K +   + +  P+ +Q+     
Sbjct: 28  AGVSDRIFRGLVRRWAPDALLFTEMVNATSLEMGHGLCK-VESLAEESGPIGVQLFDHRP 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + +AA+  E  G   I++N+GCP  ++     G+ L+ NP++    + A+  A+++PV
Sbjct: 87  QAMADAARRAEASGAFLIDINMGCPVRKIARKGGGSGLIRNPELAIQIVEAVADAVAVPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G              + ++++G   + +H R         ++       D+  +
Sbjct: 147 TVKTRLGWCGSDADPVH--WCQQLEQAGAQLLTLHGRT--------REQGFKGAADWSAI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+ +E   + +  NG +     AL+ L      GVM+GR       ++  +D   +   
Sbjct: 197 TEV-REALTIPLIANGDINSPDDALRCLKQTSAAGVMVGRGTMGAPWLVGQIDAALAGRA 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             ++P  +        ++   + D           L    +HM     GFP + R RH L
Sbjct: 256 IPTTPNPSARLALARDQLDGLVED------RGDHGLLIARKHMGWTCTGFPGASRLRHAL 309

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
            + A        ++      +  S
Sbjct: 310 -MRAPTPAQARQLLTQQIEALAAS 332


>gi|223933531|ref|ZP_03625513.1| TIM-barrel protein, nifR3 family [Streptococcus suis 89/1591]
 gi|223897791|gb|EEF64170.1| TIM-barrel protein, nifR3 family [Streptococcus suis 89/1591]
          Length = 334

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 62/327 (18%), Positives = 127/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQKNTKANIVDINMGCPVNKVIKNEAGAKWLKDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++   AV       + + +GV+ + +H R         ++      +D +
Sbjct: 143 PLTVKMRTGWNNTDLAVEN---ALAAESAGVSALAMHGRT--------REQMYTGTVDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++      +    NG +  +  A + +     D VM+GR A  N  +   ++ Y   
Sbjct: 192 TLTKVAGSLTKIPFIANGDIRTVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                           +  ++  +T+     +     +++          G   + + R 
Sbjct: 252 GEVLPDLSFDDKLNVAFDHLTR-LTNLKGESIA----VREFRGLAPHYLRGSAGAAKIRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +   A        + + A     E +
Sbjct: 307 AVA-RAETIEQVQELFDQAREAYQERI 332


>gi|15834638|ref|NP_296397.1| NifR3/Smm1 family protein [Chlamydia muridarum Nigg]
 gi|270284804|ref|ZP_06194198.1| NifR3/Smm1 family protein [Chlamydia muridarum Nigg]
 gi|270288833|ref|ZP_06195135.1| NifR3/Smm1 family protein [Chlamydia muridarum Weiss]
 gi|301336184|ref|ZP_07224386.1| NifR3/Smm1 family protein [Chlamydia muridarum MopnTet14]
 gi|7190054|gb|AAF38906.1| NifR3/Smm1 family protein [Chlamydia muridarum Nigg]
          Length = 334

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 74/316 (23%), Positives = 139/316 (43%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             ++D  YR  + L    AL++ EMI  + +    K+   +L FS   +P+  Q+ G+  
Sbjct: 22  AGFSDYPYRRMSALYH-PALMFCEMIKMEGLHYCPKRTLRLLDFSESMRPIGGQLCGSRP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               E+AKI+E  G++ I+LN GCP+ R+ +   G+ ++  P ++G  + ++ +A+S+PV
Sbjct: 81  DLAGESAKILEGLGFDLIDLNCGCPTDRITKDGSGSGMLKTPQLIGKVVESIVEAVSVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D +   + +   V  IK+SG + +++H R         +        + + +
Sbjct: 141 TVKIRSGWDFE--HINVEETVHIIKESGASAVFVHGRT--------RSQGYQGPSNLEFI 190

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K+       +  NG +     A  +L     DGV++ R       +   +++Y +  
Sbjct: 191 ARAKRAAGEHFPVFGNGDVFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRH 295
              S     R      ++       +   +  S  KL   TR + G +    P  R  R 
Sbjct: 251 TYSSPSFSMR------KQAFVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPRVRSLRA 304

Query: 296 ILTVEAGASTATHHII 311
            L  +A +S   + +I
Sbjct: 305 SLA-KASSSQEVYQLI 319


>gi|224372117|ref|YP_002606489.1| tRNA-dihydrouridine synthase B [Nautilia profundicola AmH]
 gi|223588677|gb|ACM92413.1| tRNA-dihydrouridine synthase B [Nautilia profundicola AmH]
          Length = 313

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 124/323 (38%), Gaps = 35/323 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      + ++EM   +AI   ++K   ++  S  E P  +QI   ++
Sbjct: 19  AGYTDLPFRSVVKKF-GCDMTFSEMTNVNAIAYQNEKTQKMMEKSPLENPYFVQIAANNV 77

Query: 60  SKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLN--PDIVGDCIAAMCKALS 116
              V+A +I+ +  + + I++N+GCP  +     FG  L+ +   D + + +  + K   
Sbjct: 78  ENAVKAVEIINELNWIDGIDINLGCPVNKARRSGFGGVLLKDENRDFLKEVVGTIVKTSK 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            PV+ K RIG D       + +  K ++  G+  + IH R                  DY
Sbjct: 138 KPVSAKMRIGFDKS----VVEDRAKLLEDLGIVFLTIHGRTVK--------QMYKGEADY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D + +       + +  NG + D  +A  +L      GV IGR A     +   + +   
Sbjct: 186 DEIKKGVNAV-KIPVIANGDITDYEKAKYVLEYTGASGVSIGRGAVGKPWIFLEMKQ--Q 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +T     K  V  + + ++     +Y          +    +H      G P +   R
Sbjct: 243 GNITSEQ--KKEVILEHFNQMVYWYGEY---------GVILFRKHAHAYSKGIPKASEFR 291

Query: 295 HILTVEAGASTATHHIIETAFNL 317
             +  E         +IE  FN+
Sbjct: 292 SKMN-EVKDPEVARKLIEEYFNV 313


>gi|168704071|ref|ZP_02736348.1| hypothetical protein GobsU_31344 [Gemmata obscuriglobus UQM 2246]
          Length = 346

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 64/308 (20%), Positives = 125/308 (40%), Gaps = 27/308 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADI 59
             +T+  +R   R L    L  T++I A AI+ G +K +L       E+PL +QI G+  
Sbjct: 13  AGYTNLPFRLSVRELGGVGLCTTDLINARAIVDGIQKTMLLLAHDHAERPLFVQIFGSKP 72

Query: 60  SKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-----DIVGDCIAAMCK 113
            ++  AAK +VE+   + I++N+GCP  +V +   G+ LM +       +V   + A+  
Sbjct: 73  HEMAGAAKWLVENRIADGIDINMGCPVRKVVKTGGGSSLMCDTTGATVGLVSQVVEAVR- 131

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PV+VK R+G DD   +       +  +K+GV  + IH R         ++      
Sbjct: 132 --PVPVSVKMRLGWDDDNLSAPY--FAREFEKAGVAALTIHGRT--------REQGFAGG 179

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           ++++ +  + +    + +  NG +  +  A +++      G+ IGR A  N  +    D 
Sbjct: 180 VNHEGIRRVVEAVEKIPVFGNGDVRSVQDAARMITETGCHGIAIGRGALANPWVFRQFDA 239

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
           +      G           F R     + D+     +         +            +
Sbjct: 240 WVRTGDPGPRATYAERLA-FMRLHLKRLVDWRGSERN---GCVHFRKVATWYTKALRFPK 295

Query: 292 RCRHILTV 299
           + +  L +
Sbjct: 296 KVQQRLVM 303


>gi|146329061|ref|YP_001209337.1| dihydrouridine synthase [Dichelobacter nodosus VCS1703A]
 gi|146232531|gb|ABQ13509.1| dihydrouridine synthase [Dichelobacter nodosus VCS1703A]
          Length = 318

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 73/321 (22%), Positives = 133/321 (41%), Gaps = 31/321 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYT--EMIVADAILRGDKKNILG--FSTQEK-PLALQIG 55
           M   +D  YR   +   ++   YT  EM+ A        ++ L   F    + P  +Q+ 
Sbjct: 19  MAGISDLPYRSLCQRFGSH---YTIAEMVDARPQFLAMPESQLRLQFDDDARFPKIVQLV 75

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   + E A++++  G + I++N+GCP+ +V + + G+ L+ +   V   +A + + +
Sbjct: 76  GGDPYLMAETAQVMQALGCDVIDINMGCPAKKVGKQNAGSALLSDLPQVEKILAQVTRVV 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           SIPVT+K R+G ++Q   +    + K  + +GV  + +H R         +  R      
Sbjct: 136 SIPVTLKTRLGFNEQTMTIET--VAKIAENTGVAALTVHGRT--------RAQRFNGTAH 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  +K +   L I +NG +   +QA  ++     DGVMIGRAA  N  +L  +    
Sbjct: 186 YDEIGRVKAQT-SLPIIVNGDITTTAQAQDLIQQFGFDGVMIGRAACGNPWLLAHMRCAL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +  +  V  +    +           L+    L    +H+       P     
Sbjct: 245 DCDFALPAISRRAVISEHISAL---------HQLYQRQGLLIARKHLHWYLAPMPRYDFW 295

Query: 294 RHILTVEAGASTATHHIIETA 314
           R  +   A    A   I+  A
Sbjct: 296 RQEINT-ATDLAAQLAIVAQA 315


>gi|40889946|pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
           Flavin
          Length = 318

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 60/324 (18%), Positives = 129/324 (39%), Gaps = 31/324 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADIS 60
             +TD  +R  A         ++E + A   L   +K   L     E+ +A+QI G++ +
Sbjct: 13  AGYTDSAFRTLAFEW-GADFAFSEXVSAKGFLXNSQKTEELLPQPHERNVAVQIFGSEPN 71

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L EAA+I+ +  Y  I+LN GCP  +V +   G  L+ +       +  + K++S   +
Sbjct: 72  ELSEAARILSE-KYKWIDLNAGCPVRKVVKEGAGGALLKDLRHFRYIVRELRKSVSGKFS 130

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G +       +  + + + + GV+ ++IH R  +       + + +  L+     
Sbjct: 131 VKTRLGWEKN----EVEEIYRILVEEGVDEVFIHTRTVVQSFTGRAEWKALSVLE----- 181

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
                   +   ++G +     A + L     DG+++ R A     +   + ++  +   
Sbjct: 182 ------KRIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAIGRPWIFKQIKDFLRSGKY 235

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
            S P +  + + F R +     +   +       + +  + + G       +RR R    
Sbjct: 236 -SEPSREEILRTFERHL-----ELLIKTKGERKAVVEXRKFLAGYTKDLKGARRFR---- 285

Query: 299 VEAGASTATHHIIETAFNLMIESL 322
            E         I++  F   I+ +
Sbjct: 286 -EKVXKIEEVQILKEXFYNFIKEV 308


>gi|320155028|ref|YP_004187407.1| tRNA dihydrouridine synthase B [Vibrio vulnificus MO6-24/O]
 gi|319930340|gb|ADV85204.1| tRNA dihydrouridine synthase B [Vibrio vulnificus MO6-24/O]
          Length = 287

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 119/302 (39%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  L    K+   +    +    ++QI G+D   + +AA+   + G   I+
Sbjct: 1   MAVSEMMSSNPQLWKTSKSKQRMVHEGESGIRSVQIAGSDPQLMADAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+  PDI+   + A+  A+ +PVT+K R G D +       +
Sbjct: 61  INMGCPAKKVNKKLAGSALLKYPDIIEQILKAVVDAVDVPVTLKTRTGWDTENKN--CIH 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K  +  G+  + +H R         K        +YD +  +K+    + +  NG ++
Sbjct: 119 IAKLAEDCGIQALALHGRT--------KACMYKGEAEYDSIKAVKQAV-SIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  Y  N  T        V       + 
Sbjct: 170 SPEKAKYVLEYTGADALMIGRPAQGRPWIFQEIHHYLENGTTMPELPIEEVKSIMLGHVQ 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A+      +E  F+
Sbjct: 230 ALHEFY-----GEYLGPRIARKHVGWYLKEHEQASEFRRTFNA-IDAAMLQLEALEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|332999337|gb|EGK18923.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-272]
 gi|333014706|gb|EGK34052.1| TIM-barrel protein, nifR3 family protein [Shigella flexneri K-227]
          Length = 281

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 57/295 (19%), Positives = 113/295 (38%), Gaps = 21/295 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+   ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSAPKEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PV +K R G            + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVPLKIRTGWAPVHRN--CEEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + +  NG + D  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPVIANGDITDPLKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             +L     D +MIGRAA     +   +  Y              V +     +      
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCAHVRELHDF 229

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           Y       G ++    +H+         + + R        AS      +E  F 
Sbjct: 230 YGP---AKGYRI--ARKHVSWYLQEHAPNDQFRRTFNAIEDASE-QLEALEAYFE 278


>gi|162452011|ref|YP_001614378.1| dihydrouridine synthase TIM-barrel protein nifR3 [Sorangium
           cellulosum 'So ce 56']
 gi|161162593|emb|CAN93898.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Sorangium
           cellulosum 'So ce 56']
          Length = 328

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 136/322 (42%), Gaps = 21/322 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M D TD  +R   R L    L  TE +  + +LRG K  +  L  +  ++P A+QI GA+
Sbjct: 22  MEDVTDAVFRRIGREL-GAELCVTEFVNVEGLLRGCKTARRKLALADGDQPTAIQIYGAN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L EAA++ E+ G   +++N GC   ++     GA  + +P+ +      + +++++P
Sbjct: 81  PERLAEAARVAEEAGPAFLDINCGCWVPKIAGRGAGAGWLRDPEAMVAMARLVTRSVALP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG   +   + + +L + ++ +GV  + IH R A +              D+  
Sbjct: 141 VTVKTRIGWGPE-SHMPIVDLARRLEDAGVAALTIHCRTAQMGHS--------GAADWGW 191

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                +E   + + +NG ++    A + L      GVM+GRAA  +  +         + 
Sbjct: 192 AAR-AREVVSIPVVVNGDIKTADDAARALRETGCAGVMVGRAAIDHPWIFREARALLDDG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +    P            + A+       H      ++   RH+ G   G P +   R  
Sbjct: 251 VHLPPPTAEERLALCRAHLIANTEARGEPH-----GVRVTRRHLTGYLRGLPGASALRRE 305

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L      S     I+++A   +
Sbjct: 306 LLFCDSLSG-CLDILDSAAQRL 326


>gi|296327905|ref|ZP_06870441.1| NifR3 family protein [Fusobacterium nucleatum subsp. nucleatum ATCC
           23726]
 gi|296155039|gb|EFG95820.1| NifR3 family protein [Fusobacterium nucleatum subsp. nucleatum ATCC
           23726]
          Length = 307

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 123/316 (38%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I          A+QI G DI K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLRAGNAVQIFGEDIEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK RIG  +    + +  + + +   G + I +H R         ++       D+  +
Sbjct: 129 SVKIRIGYKEPENYIQIGKIAEEL---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGEDALEKIFYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K          +     D      +    +  + +H+     G  N    +  +
Sbjct: 237 IKTPTTKADKINMAIEHLKRIRVD------NDNKFVFDVRKHISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
            + +        I+E 
Sbjct: 291 NIISDY-DEIIKILEE 305


>gi|19704027|ref|NP_603589.1| nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714217|gb|AAL94888.1| Nitrogen regulation protein NIFR3 [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 307

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 125/316 (39%), Gaps = 24/316 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              TD  +R          L++TEM+  +A+   + K I       +  A+QI G DI K
Sbjct: 10  AGVTDYTFRGILEDF-KPDLIFTEMVSVNALSVLNDKTISKILKLREGNAVQIFGEDIEK 68

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           +  + K +E+ G   INLN GCP  ++    +GA L+  P+ +   ++ +   L     +
Sbjct: 69  IKASVKYIENLGVKHINLNCGCPMKKIVNCGYGAALVKEPEKIKKILSEIKSVLNNDTKL 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK RIG  +    + +  + + +   G + I +H R         ++       D+  +
Sbjct: 129 SVKIRIGYKEPENYIQIGKIAEEL---GCDHITVHGRT--------REQLYSGKADWKYI 177

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+K +N  + +  NG +     AL+     +VDGVM+ R  + N  ++  + E      
Sbjct: 178 KEVK-DNISIPVIGNGDIFTGEDALEKIFYSNVDGVMLARGIFGNPWLIRDIREILEYGE 236

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   KT         +     D      +    +  + +++     G  N    +  +
Sbjct: 237 IKTPTTKTDKINMAIEHLKRIRVD------NDNKFVFDVRKYISWYLKGIENCAEAKRKI 290

Query: 298 TVEAGASTATHHIIET 313
            + +        I+E 
Sbjct: 291 NIISDY-DEIIKILEE 305


>gi|146319624|ref|YP_001199336.1| tRNA-dihydrouridine synthase [Streptococcus suis 05ZYH33]
 gi|146321822|ref|YP_001201533.1| tRNA-dihydrouridine synthase [Streptococcus suis 98HAH33]
 gi|145690430|gb|ABP90936.1| tRNA-dihydrouridine synthase [Streptococcus suis 05ZYH33]
 gi|145692628|gb|ABP93133.1| tRNA-dihydrouridine synthase [Streptococcus suis 98HAH33]
 gi|292559241|gb|ADE32242.1| Dihydrouridine synthase [Streptococcus suis GZ1]
          Length = 344

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 62/327 (18%), Positives = 126/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 34  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 92

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 93  AEGLKRAADFIQKNTKANIVDINMGCPVNKVIKNEAGAKWLKDPDKIYHIIKEVTSVLDI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++   AV       + +  GV  + +H R         ++      +D +
Sbjct: 153 PLTVKMRTGWNNTDLAVEN---ALAAESGGVAALAMHGRT--------REQMYTGTVDLE 201

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++      +    NG + ++  A + +     D VM+GR A  N  +   ++ Y   
Sbjct: 202 TLTKVAGSLTKIPFIANGDIRNVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLET 261

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                           +  ++  +T+     +     +++          G   + + R 
Sbjct: 262 GEVLPDLSFDDKLNVAFDHLTR-LTNLKGESIA----VREFRGLAPHYLRGSAGAAKIRG 316

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +   A        + + A     E +
Sbjct: 317 AVA-RAETIEQVQELFDQAREAYQERI 342


>gi|166364397|ref|YP_001656670.1| nitrogen regulation protein NifR3-like protein [Microcystis
           aeruginosa NIES-843]
 gi|166086770|dbj|BAG01478.1| nitrogen regulation protein NifR3 homolog [Microcystis aeruginosa
           NIES-843]
          Length = 258

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 50/270 (18%), Positives = 104/270 (38%), Gaps = 22/270 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+       +  AA+     G   I++N+GCP  ++ +   G+ L+  P+I    +  +
Sbjct: 1   MQLFDCRPDFMAVAAEKAVKEGAMTIDINMGCPVNKITKKGGGSSLLRQPEIAEQIVREV 60

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             A+S+PVTVK R+G + Q   + + +  + ++ +G   + +HAR         ++    
Sbjct: 61  VGAVSVPVTVKTRLGWNAQE--INIIDFARRLEDAGAQMLTLHART--------REQGYH 110

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
              D+  +  +K E   + +  NG +  +  A+  L     DGVM  R       ++  +
Sbjct: 111 GPADWQWIKRVK-EVLSIPVIANGDIVSVEAAINCLEFTRADGVMCSRGTLGYPYLVGEI 169

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-LQQITRHMIGLFHGFP 288
           D Y         P    +       +           L+ G + + Q  +H+      F 
Sbjct: 170 DYYLKTGKKLPKPTSIDLLSLAKEHLQ-------GLWLYKGQRGIWQARKHLAWYCQDFT 222

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLM 318
            +   R   +     +     +I+ A   +
Sbjct: 223 GAAVWRDRFSRIESLAE-GCDLIDRAIAQL 251


>gi|299133856|ref|ZP_07027050.1| TIM-barrel protein, nifR3 family [Afipia sp. 1NLS2]
 gi|298591692|gb|EFI51893.1| TIM-barrel protein, nifR3 family [Afipia sp. 1NLS2]
          Length = 344

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 78/333 (23%), Positives = 131/333 (39%), Gaps = 31/333 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A  L    L+ +EM  +D + RG   ++L        P  +Q+ G + 
Sbjct: 28  MSGITDAPLRRVAARL-GAGLVVSEMTASDDLARGRAMSVLRCEAAGIGPHVVQLAGCEA 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I E  G + I++N+GCP+  V  G  G+ LM + D     I A   A+ IPV
Sbjct: 87  KWMAEGARIAESGGADIIDINMGCPARHVTGGQSGSALMRDLDHAMTLIEATIAAVKIPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D    ++    L +  + SG+  + +H R         +      + D++ V
Sbjct: 147 TLKMRLGWD--HASLNAPELARRAEASGIQMVTVHGRT--------RCQFYKGDADWNAV 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + +E   + + +NG +       A       D VMIGR A     +   +    +   
Sbjct: 197 RAV-REAIAIPLVVNGDIASYEDAVAALAASGADAVMIGRGAQGRPWLPGQIARQLAGGA 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--------HGFPN 289
           T + P       D       ++ D    H  +   L+   +H+             G   
Sbjct: 256 TETDPAL-----DVQLGYLRTLYDDILSHYGARIGLRHARKHLGWGLDVAEEGAGAGITA 310

Query: 290 SRRCR-HILTVEAGASTATHHIIETAFNLMIES 321
            +  R  ILT E       H +++ AF+    S
Sbjct: 311 LKEWRGKILTSE--RPDDVHALLDQAFDSFARS 341


>gi|269219506|ref|ZP_06163360.1| putative tRNA-dihydrouridine synthase [Actinomyces sp. oral taxon
           848 str. F0332]
 gi|269211085|gb|EEZ77425.1| putative tRNA-dihydrouridine synthase [Actinomyces sp. oral taxon
           848 str. F0332]
          Length = 432

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 57/340 (16%), Positives = 123/340 (36%), Gaps = 49/340 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALL---------------------YTEMIVADAILRGDKK- 38
           M   T+  +R   R      L                        EM+ + A++  + + 
Sbjct: 46  MAGVTNPPFRQLCREQAEEGLALAGADPAPRGLPGTDAPGGLWVCEMVTSRALVERNPEA 105

Query: 39  -NILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGAC 96
            N++     +   ++Q+ G +      A  ++  +   + I+LN GCP+ +V     G+ 
Sbjct: 106 MNMIKPDPGDPVRSIQLYGVEPKTSAAAVAMLVGENRADHIDLNFGCPAPKVTRKGGGSA 165

Query: 97  LMLNPDIVGDCIAAMCKA---------LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
           L    D+  + ++A  +A         + +PVT K R+G+DD        +  +  + +G
Sbjct: 166 LPWKLDLFREIVSAAVEAARRASADRDVEVPVTAKIRVGIDDG--HTTFLDAARIAEDAG 223

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + G+ +HAR                + D+  + E+  E   L +  NG + ++  A++++
Sbjct: 224 IAGLTLHARTT--------AQHYSGSADWGRIAELA-EATSLPVLGNGDVFEVEDAVRLM 274

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
                 GV +GR       +   +          + P  + V     R    S   +   
Sbjct: 275 AETGCAGVAVGRGCQGRPWLFRELAARLHGCGETARPGLSDVVAMIERHGQLSYEHFNGD 334

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAST 305
              +   ++++ +H+     GF      R  L + +    
Sbjct: 335 EHRA---MRELRKHIGWYLRGFAVGGESRRGLALVSTREE 371


>gi|253752622|ref|YP_003025763.1| tRNA-dihydrouridine synthase [Streptococcus suis SC84]
 gi|253754448|ref|YP_003027589.1| tRNA-dihydrouridine synthase [Streptococcus suis P1/7]
 gi|253756381|ref|YP_003029521.1| tRNA-dihydrouridine synthase [Streptococcus suis BM407]
 gi|251816911|emb|CAZ52560.1| putative tRNA-dihydrouridine synthase [Streptococcus suis SC84]
 gi|251818845|emb|CAZ56688.1| putative tRNA-dihydrouridine synthase [Streptococcus suis BM407]
 gi|251820694|emb|CAR47456.1| putative tRNA-dihydrouridine synthase [Streptococcus suis P1/7]
 gi|319759039|gb|ADV70981.1| tRNA-dihydrouridine synthase [Streptococcus suis JS14]
          Length = 334

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 62/327 (18%), Positives = 126/327 (38%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ +    L+  EMI    +L  ++K   +L     E P+++Q+ G D
Sbjct: 24  MAGVTNSAFRTIAKEM-GAGLVVMEMISEKGLLYNNEKTLHMLHIDDNEYPMSIQLFGGD 82

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA  ++     N +++N+GCP  +V +   GA  + +PD +   I  +   L I
Sbjct: 83  AEGLKRAADFIQKNTKANIVDINMGCPVNKVIKNEAGAKWLKDPDKIYHIIKEVTSVLDI 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G ++   AV       + +  GV  + +H R         ++      +D +
Sbjct: 143 PLTVKMRTGWNNTDLAVEN---ALAAESGGVAALAMHGRT--------REQMYTGTVDLE 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++      +    NG + ++  A + +     D VM+GR A  N  +   ++ Y   
Sbjct: 192 TLTKVAGSLTKIPFIANGDIRNVEDARQRIEEVGADAVMVGRTAMGNPYIFNQINHYLET 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                           +  ++  +T+     +     +++          G   + + R 
Sbjct: 252 GEVLPDLSFDDKLNVAFDHLTR-LTNLKGESIA----VREFRGLAPHYLRGSAGAAKIRG 306

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +   A        + + A     E +
Sbjct: 307 AVA-RAETIEQVQELFDQAREAYQERI 332


>gi|329889586|ref|ZP_08267929.1| putative tRNA-dihydrouridine synthase [Brevundimonas diminuta ATCC
           11568]
 gi|328844887|gb|EGF94451.1| putative tRNA-dihydrouridine synthase [Brevundimonas diminuta ATCC
           11568]
          Length = 349

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 69/288 (23%), Positives = 117/288 (40%), Gaps = 23/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
           M   TD  +R  A  L   A + TEM+ A  + R    +++  +     L    +Q+ G 
Sbjct: 21  MTGITDLPFRVLASKL-GAAYVATEMVAAAELARARP-DVVRRAAVGGGLPLTVIQLVGG 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   + E A++ E  G + I+LN GCP+  V   + G+ LM  PD     + A+  A+S 
Sbjct: 79  DPVAMAEGARMAEAAGADLIDLNFGCPAKEVTGAACGSALMRTPDQAARIMEAVVGAVSR 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R+G D+     A  +L +  +  GV  + +H R         +        D+D
Sbjct: 139 PVSVKMRLGWDENSHNAA--DLARRAETLGVAAVTVHGRT--------RKQFYTGVADWD 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V E+K+    + + +NG +    QA + L     D +M+GR  Y    +   ++     
Sbjct: 189 AVAEVKQ-VVTIPVIVNGDIITAEQAREALDRSGADALMLGRGVYGRPWLAAHLERALIG 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                 P +          + AS   Y          L+   +H+   
Sbjct: 248 GTQLQEPDREERLAIVIEHLRASAAFY-----GLPLGLKMFRKHLGWY 290


>gi|254486875|ref|ZP_05100080.1| tRNA-dihydrouridine synthase B [Roseobacter sp. GAI101]
 gi|214043744|gb|EEB84382.1| tRNA-dihydrouridine synthase B [Roseobacter sp. GAI101]
          Length = 328

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 68/301 (22%), Positives = 119/301 (39%), Gaps = 25/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M   TD  YR          L+ +EM+ ++ ++           LG   +    A+Q+ G
Sbjct: 19  MAGITDLPYRNLVASF-GAGLVVSEMVASEDMINARPGTREKAELGLGIEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            + + L EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+  A+ 
Sbjct: 76  REAAPLAEAARMVEAQGARIIDINMGCPAKKVTQGYSGSALMRTPDYALTLIEAVVNAVK 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R+G DD +  +    +  + + +G+  I IH R         +        D+
Sbjct: 136 VPVTLKTRLGWDDAM--LNAPQIAAAAEAAGITMITIHGRT--------RCQFYKGAADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
             + ++K +   + +  NG + D   A   L     DGVM+GR +     +L  +     
Sbjct: 186 AAISKVK-DAVSIPVIANGDIIDTDSASTALNQSRADGVMVGRGSQGQPWILAEIAHQLY 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P      +         +  Y          L+   +H+          R  R
Sbjct: 245 GTPAPVVPQGADFARMVGDHYEEIIRFYGVTI-----GLRAARKHLGWYMDTCATPRDLR 299

Query: 295 H 295
            
Sbjct: 300 R 300


>gi|169830345|ref|YP_001716327.1| nifR3 family TIM-barrel protein [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637189|gb|ACA58695.1| putative TIM-barrel protein, nifR3 family [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 334

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 135/301 (44%), Gaps = 22/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TDR +R  AR +    L +TEMI A A+++G+++   +L  S  E P+A+Q+ G+D
Sbjct: 19  MAGITDRAFRDLAREM-GCGLTWTEMISAQALIQGNRRTAELLEVSG-EHPIAVQVFGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +V AA++  + G + ++LN+GCP+ ++ +   GA LM +P+  G+ +AA+  A+ +P
Sbjct: 77  PNTMVRAARLAAEAGADIVDLNMGCPTPKIVKSCEGAALMRDPERAGEIVAAVAAAVPVP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G D+  P+        +   +    +    R     G            D+ +
Sbjct: 137 VTVKMRKGWDEGYPSAVELARAVAQAGAAAVTVHGRLRSEFFGG----------RADWSV 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+    + +  NG +     A ++L     D VMIGRAA  N  +   V +     
Sbjct: 187 IGAVKQAV-SIPVIGNGDVRIGPDAARMLAETRCDAVMIGRAALGNPWVFRQVRDCLETG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P          R       D   R+      +Q++ +H      G   S R R  
Sbjct: 246 QEPPPPTMDERVAMALRH-----FDLLIRYKGEARAVQEMRKHAAWYTRGLRGSARLRER 300

Query: 297 L 297
           L
Sbjct: 301 L 301


>gi|119386836|ref|YP_917891.1| nifR3 family TIM-barrel protein [Paracoccus denitrificans PD1222]
 gi|119377431|gb|ABL72195.1| tRNA-U20-dihydrouridine synthase [Paracoccus denitrificans PD1222]
          Length = 349

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 66/325 (20%), Positives = 118/325 (36%), Gaps = 30/325 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG-----FSTQEKPLALQIG 55
           M   TD  +R          L+ +EM+ +  ++               +    P+++QI 
Sbjct: 23  MAGITDLPFRRAVARHGGAGLMVSEMVASTEMVTPRPSTRAAVRAKALTEGALPVSVQIA 82

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +   + E A+IV   G   +++N+GCP+ +V  G  GA LM + D     I A+  A+
Sbjct: 83  GREAGAMAETARIVAGMGARIVDINMGCPAKKVTGGLSGAALMRDLDHALGLIDAVVAAV 142

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVT+K R+G D     +   +L +    +GV  + +H R         +      + 
Sbjct: 143 PDLPVTLKMRLGWDGD--CLNAPDLARRAAGAGVGMLTVHGRT--------RAQFYTGSA 192

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +        +  NG + D + A   L     + VM+GR A      L  +   
Sbjct: 193 DWAAIRAVANLPGRPPLVANGDVVDAASARAALRQSGAEAVMVGRGAQGAPWRLAQIAHE 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL--FHGFPNS 290
                    P   R+ +         ++ Y          L+   +H+      +G PN 
Sbjct: 253 LWGTPAPDVPQGARLAEAVAEHYDDILSLYGRE-----LGLRVARKHLGWYAEANGAPNR 307

Query: 291 RRCRHILTVEAGASTATHHIIETAF 315
                   + A    A    I   F
Sbjct: 308 AEL-----LRAPTPEAALAAIRAGF 327


>gi|269122887|ref|YP_003305464.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
 gi|268314213|gb|ACZ00587.1| dihydrouridine synthase DuS [Streptobacillus moniliformis DSM
           12112]
          Length = 305

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 64/317 (20%), Positives = 128/317 (40%), Gaps = 27/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R            +TEM+  D +L  +   IL          +QI G DI 
Sbjct: 10  MAGVTDYTFRKIIEDF-KPDFTFTEMVSVDKLLYKEVPKILKLRENN---IVQIFGKDIY 65

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-- 118
            + +AAK +E  G  EINLN GCP  ++     G+ L+ +P  + + + A+ + L     
Sbjct: 66  LMQKAAKYIESMGVKEINLNCGCPMKKIVNSGHGSALIKDPRKIEEILTALREVLDPKTA 125

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R+G D     + +  + + +K    + I IH R         ++ +     D+  
Sbjct: 126 LSLKIRVGYDKPENYLEIAKIAEKLK---CSNIIIHGRT--------REQKYSGEADWKY 174

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K +N ++ +  NG + D   A++ +   +VDG+M+ R    N  +++ + E F   
Sbjct: 175 IKEVK-DNVNIKVIGNGDIFDAKNAIEKIRETNVDGIMLARGILGNPWLISQIKELFEFG 233

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +            R +     D      +       I +++I            +++
Sbjct: 234 EIKTIVRDIDRINMAIRHVKEYAID------NENVFFPDIRKYIIWYIENIKGIDETKNL 287

Query: 297 LTVEAGASTATHHIIET 313
           +  ++        ++E 
Sbjct: 288 IN-QSFEYDEIIELLEK 303


>gi|157165335|ref|YP_001466365.1| phosphoribosylamine--glycine ligase [Campylobacter concisus 13826]
 gi|112800093|gb|EAT97437.1| tRNA-dihydrouridine synthase B [Campylobacter concisus 13826]
          Length = 307

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 67/301 (22%), Positives = 129/301 (42%), Gaps = 35/301 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGAD 58
             ++D   R   +      +  +EMI A+A++         +L  S  E+P  +QI G++
Sbjct: 15  AGFSDLPLRSVVKKF-GCDVTVSEMISANALVYESSDKTLEMLKKSPNEEPYVVQIAGSE 73

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  + +A +I+  F G   ++LN GCP  +V     G+ L+ + D + + I+ +    + 
Sbjct: 74  IENIKKAVQIINKFDGIYGLDLNCGCPVPKVVRQGAGSALLNDLDKLQNIISDIKSVSNK 133

Query: 118 P-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             ++VK R+G +D+        + K+ +++G + I +H R         +       +DY
Sbjct: 134 ESLSVKFRLGFNDKNE----EKIAKACEEAGADYIAVHGRT--------RAGGYSAKVDY 181

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  +K  +  + +  NG + +   A +IL     D +MIGRA+  N  +   +     
Sbjct: 182 EAIARVK-ASVKIPVIANGDI-NAQNADEILNFTKCDALMIGRASIGNPWIFHEIK---- 235

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                    K+ VDK   +KI  +  D    H    G L    +H+     G   +   R
Sbjct: 236 --------TKSSVDKALKQKIILAHFDAMIEHYGEHG-LCIFRKHLHQYSKGIDGATSFR 286

Query: 295 H 295
           +
Sbjct: 287 N 287


>gi|313682259|ref|YP_004059997.1| tim-barrel protein, nifr3 family [Sulfuricurvum kujiense DSM 16994]
 gi|313155119|gb|ADR33797.1| TIM-barrel protein, nifR3 family [Sulfuricurvum kujiense DSM 16994]
          Length = 329

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 61/299 (20%), Positives = 121/299 (40%), Gaps = 32/299 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EM+ ++A+  G +K   +L  S  E P ++QI GA+ 
Sbjct: 18  AGYTDLPFRNVVKKF-GADLTVSEMLSSNALAYGSQKTIKMLERSPNEDPYSVQIAGAEE 76

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +++      + I+LN GCP  ++     G+ L+ +   +   I  + K  +  
Sbjct: 77  DIVRRAVEVLNTVDDIDIIDLNCGCPVPKIVCHGSGSALLNDLPRMARIIETIKKTSNKS 136

Query: 119 -VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            ++VK R+G + +        + K ++  G + + +H R         +  +    +DYD
Sbjct: 137 TLSVKIRLGFETK----NHIEIAKLVESCGADFLAVHGRT--------RAGKFKAPVDYD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + EIK     + +  NG ++   +A  +L     DGVMIGR A     +         +
Sbjct: 185 AIGEIKASIG-IPVIANGDIDSFEKAQWVLEHTKADGVMIGRGAVGAPWIF----HQLKS 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +   P+           +   ++ Y AR       +    +H+     G+  +   R
Sbjct: 240 GSSAVDPLIK--HAIIMEHLDGMVSFYGAR------GVVTFRKHVHTYSKGYEGASALR 290


>gi|225619221|ref|YP_002720447.1| dihydrouridine synthase-like FMN-binding domain-containing protein
           [Brachyspira hyodysenteriae WA1]
 gi|225214040|gb|ACN82774.1| Dihydrouridine synthase-like (DUS-like) FMN-binding domain protein
           [Brachyspira hyodysenteriae WA1]
          Length = 325

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 70/292 (23%), Positives = 134/292 (45%), Gaps = 19/292 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD  +R  +R      LL TE++ A A+ R  KK    +     E P++LQ+ GA+
Sbjct: 21  MAGYTDYVFRRLSRKF-GAGLLVTELVSAAALARQVKKTYRYMEHKEDEYPISLQLFGAN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                 A +I +  G++ I++N+GCP+ +V + + GA L+ + D +   + A+     +P
Sbjct: 80  EDDYKRAIEITDLSGFSFIDINMGCPTKKVVKNNGGAGLLEDTDKMISVLNAVKSVSPLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G+         R L   +K++G   + +H R A         +      D++ 
Sbjct: 140 VSVKIRLGLKRGEGGEIERALA--MKENGACFLTLHGRYA--------SDMYRGTADWEA 189

Query: 179 VYEIKKENPDLFI-GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + +IK+   + +I   NG ++    A+K      VDG+M+GR A  N  + T ++  F +
Sbjct: 190 IAKIKEALGEDYILIGNGDIKSKEDAVKAFDISKVDGIMVGRGAIGNPWIFTELNTIFED 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               ++ I    +KD  + I     +           +  + + ++    G+
Sbjct: 250 NDEYNNKID---EKDNLKNIIKEHINGCCELYGEVSGIHFMRKFIMKYLTGY 298


>gi|260770653|ref|ZP_05879584.1| tRNA-dihydrouridine synthase B [Vibrio furnissii CIP 102972]
 gi|260614379|gb|EEX39567.1| tRNA-dihydrouridine synthase B [Vibrio furnissii CIP 102972]
 gi|315178395|gb|ADT85309.1| NifR3/Smm1 family protein [Vibrio furnissii NCTC 11218]
          Length = 287

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 124/302 (41%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+ ++  L    K+   +    +    ++QI G+D   + +AA+   + G   I+
Sbjct: 1   MAVSEMMSSNPALWKTDKSRNRMVHEGESGIRSVQIAGSDPQLMADAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+  P+++ D + A+  A+++PVT+K R G D          
Sbjct: 61  INMGCPAKKVNKKLAGSALLRYPNVIEDILKAVVNAVNVPVTLKTRTGWD--TDNKNCVQ 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K  +  G+  + +H R         +        +YD +  +K     + +  NG ++
Sbjct: 119 IAKLAEDCGIQALALHGRT--------RTCMYKGEAEYDSIKAVKAAI-QIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  Y  N  T      + V       ++
Sbjct: 170 SPEKAKHVLEYTGADALMIGRPAQGRPWIFQEIQHYLENGTTMPELPISEVKDILLGHVN 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y A   + G ++  + +H+         +   R        A       +E  F+
Sbjct: 230 ALHQFYGA---YLGPRI--VRKHVGWYLKEHEQASEFRRTFNAIEAAP-LQLEALEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|260566345|ref|ZP_05836815.1| nitrogen regulation protein NifR3 [Brucella suis bv. 4 str. 40]
 gi|260155863|gb|EEW90943.1| nitrogen regulation protein NifR3 [Brucella suis bv. 4 str. 40]
          Length = 332

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 120/287 (41%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GC + +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 288


>gi|227486471|ref|ZP_03916787.1| dihydrouridine--tRNA ligase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235652|gb|EEI85667.1| dihydrouridine--tRNA ligase [Anaerococcus lactolyticus ATCC 51172]
          Length = 332

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 68/323 (21%), Positives = 128/323 (39%), Gaps = 25/323 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              TD  +R            +TEM+  +A+   +K    I+  S  EK   +QI G+D+
Sbjct: 16  AGVTDTAFRIVCEK-NGCDKTFTEMVSVNALSFDNKATADIMFISDMEKNANIQIFGSDV 74

Query: 60  SKLVEAA--KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            K+      KI       EI+ N+GCP+ ++     G+ L+ NP  V     A+ +A   
Sbjct: 75  DKIKRVVEEKINPLTNIKEISFNMGCPAPKIFNNGEGSALLKNPHQVYKITKALREATDK 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            + +K R+GVDD   A+      K+++++G + + +HAR         +      + D+ 
Sbjct: 135 VINIKFRLGVDDD--AINYLENGKAMEEAGADYLILHART--------RKAMYSGHADWQ 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K E  ++ +  NG +      ++ +     DG MI R A  N  +   + EY   
Sbjct: 185 AIKNLK-EAVNIPVIANGDIFTPEDFIRAMEITGADGAMIARGAMGNPFIFRYIKEYLEK 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                    T+V  D          + A +       + Q+ +H+     G   S   R 
Sbjct: 244 GSY------TKVTFDEIISQIKEHYELALKFKDERLVINQMRKHVGWYIKGLYMSSDYRD 297

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
            +  +   S     +++    ++
Sbjct: 298 RVN-KIHTSKEIFDLLDEYRKIL 319


>gi|161619071|ref|YP_001592958.1| NifR3 family TIM-barrel protein [Brucella canis ATCC 23365]
 gi|161335882|gb|ABX62187.1| TIM-barrel protein, nifR3 family [Brucella canis ATCC 23365]
          Length = 333

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 120/287 (41%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GC + +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 289


>gi|296125339|ref|YP_003632591.1| dihydrouridine synthase DuS [Brachyspira murdochii DSM 12563]
 gi|296017155|gb|ADG70392.1| dihydrouridine synthase DuS [Brachyspira murdochii DSM 12563]
          Length = 324

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 67/292 (22%), Positives = 130/292 (44%), Gaps = 19/292 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD  +R  +R      LL TE++ A A+ R  KK    +     E P++LQ+ GA+
Sbjct: 21  MAGYTDYIFRRLSRRF-GAGLLITELVSAAALARQVKKTYRYMEHKEDEYPISLQLFGAN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                +A +I    G++ I++N+GCP+ +V + + GA L+ +   +   + A+     +P
Sbjct: 80  EDDYKKAIEITNLSGFSFIDINMGCPTKKVVKNNGGAGLLEDTGKMVSILNAVKSVSPLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G+         R L   +K++G   + +H R A         +      D++ 
Sbjct: 140 VSVKIRLGLKRGEGGEIERALA--LKENGACFLTLHGRYA--------SDLYRGTADWEA 189

Query: 179 VYEIKKENPDLFI-GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K+     +I   NG ++    ALK     +VDG+M+GR A  N  +   ++  F +
Sbjct: 190 IARVKEALGKDYILIGNGDIKTKEDALKAFNISNVDGIMVGRGAVGNPWIFRELNTIFED 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               ++ I    + D  + I     +           +  + + ++    G+
Sbjct: 250 NDDYNNDI---TENDSLKNIIKEHINGCCELYGEISGIHFMRKFVMKYLTGY 298


>gi|317050642|ref|YP_004111758.1| dihydrouridine synthase DuS [Desulfurispirillum indicum S5]
 gi|316945726|gb|ADU65202.1| dihydrouridine synthase DuS [Desulfurispirillum indicum S5]
          Length = 324

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 63/304 (20%), Positives = 119/304 (39%), Gaps = 26/304 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLAL-QIGGAD 58
               +  +R  AR       ++TEM+ ++A+ R   K +  L    +E+     Q+ GA+
Sbjct: 22  AGVCNIPFRVIARE-QGCPNIFTEMVSSEALSRHIPKTVEFLRVGAEERLRPFVQLFGAN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            + + ++A+I  + G+  I++N+GCP  +V     G  LM +P + G+ ++ M  A    
Sbjct: 81  PATMAQSARICTEEGFTLIDINMGCPVKKVVRSGSGVELMQHPQLAGEIVSQMVAAAGAC 140

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             +TVK R+G+        L  L   ++++G + + +HAR             ++  +  
Sbjct: 141 ADITVKTRLGLIHGD--ELLPELALQVQQAGASMLTVHARTRSDGFGGQARWHEVAPI-- 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
                  K    + + +NG + D   A   +     DG MI R  Y    +   +     
Sbjct: 197 -------KSLLHIPLIINGDITDYPSACLAMEQSRADGAMIAREGYTRPWIFREILSQVR 249

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T   P   ++ +   R +   +  Y     H       + +H      G P S   R
Sbjct: 250 GQATC-EPTPRQIREILLRHLDL-LCQYMPERAHIL-----MRKHGSWYSKGTPGSSEFR 302

Query: 295 HILT 298
             L 
Sbjct: 303 QALN 306


>gi|83952210|ref|ZP_00960942.1| tRNA-dihydrouridine synthase, putative [Roseovarius nubinhibens
           ISM]
 gi|83837216|gb|EAP76513.1| tRNA-dihydrouridine synthase, putative [Roseovarius nubinhibens
           ISM]
          Length = 331

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 76/330 (23%), Positives = 125/330 (37%), Gaps = 35/330 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
              TD  +R          L+ +EM+ +  +++     +         +  A+Q+ G D 
Sbjct: 20  AGITDLPFRNLVSRF-GAGLVVSEMVASQEMVQAKPGVRERAELGFGVENTAVQLAGCDA 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVH----EGSFGACLMLNPDIVGDCIAAMCKAL 115
             L EAA++VE  G   I++N+GCP+ +V      G+ G+ LM  PD     I A+ +A+
Sbjct: 79  EWLAEAARMVEANGAKIIDINMGCPAKKVTSASGNGASGSALMKTPDHALRLIEAVVEAV 138

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT+K R+G D+ +  +    +    + +GV  I IH R         +        D
Sbjct: 139 EVPVTLKTRLGWDEDL--LNAPEIAARAEAAGVQMITIHGRT--------RCQFYKGRAD 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +  +K E   + +  NG +    +A   L     DGVMIGR A     +L  V    
Sbjct: 189 WAAIARVK-EAVAVPVIANGDITGPDEARTALAQSGGDGVMIGRGAQGRPWVLAQVAAEL 247

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   P    +           +  Y          L+   +H+     G       
Sbjct: 248 WGAAPPDVPQGAELVDLVSDHYDEMLRFYGG-----DLGLRVARKHLGWYMDGVGTPANL 302

Query: 294 RH-ILTVEAGASTATHHIIETAFNLMIESL 322
           R  ILT  A          E  F  + E+L
Sbjct: 303 RRPILTARAP---------EEVFARLPEAL 323


>gi|320103323|ref|YP_004178914.1| tRNA-U20-dihydrouridine synthase [Isosphaera pallida ATCC 43644]
 gi|319750605|gb|ADV62365.1| tRNA-U20-dihydrouridine synthase [Isosphaera pallida ATCC 43644]
          Length = 393

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 53/284 (18%), Positives = 117/284 (41%), Gaps = 18/284 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +T   +R   R      L+ T+++   ++L   ++   +      ++P+A+Q+ G+ 
Sbjct: 65  MAGFTSLAFRLSVRERGGLGLVTTDLVNCRSLLENRQRALELTETDPADRPVAMQLYGSK 124

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I ++  AA  + + G   +++N+GCP  +V +   G+ LM   D     +  M KA+ +P
Sbjct: 125 IEEMTAAAARLVERGATLVDINMGCPVRKVVKTGGGSALMCEVDNAARLVEEMVKAVEVP 184

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D+   +    +L ++ +++G   + +H R         +       ++ + 
Sbjct: 185 VTIKTRLGWDEHTLSA--PDLARAFEQAGAAALVVHGRT--------RAQGFKGPVNREG 234

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +    + +  NG +  +  A  +        V +GR A  N  +   +D +    
Sbjct: 235 IRAVVEAVKTMPVVGNGDIRTIHDAETMFRETGCAAVSLGRGALANPFIFRHLDHWARTG 294

Query: 237 LTGSSPIKTR----VDKDFWRKISASMTDYAARHLHSGGKLQQI 276
             G  P        V + F R ++     +         K   +
Sbjct: 295 EAGPEPEFAERVDLVRRHFRRLVALRGERFGCLQFRKLVKWYSM 338


>gi|300869979|ref|YP_003784850.1| dihydrouridine synthase like protein [Brachyspira pilosicoli
           95/1000]
 gi|300687678|gb|ADK30349.1| dihydrouridine synthase like, DUS like/ FMN binding domain protein
           [Brachyspira pilosicoli 95/1000]
          Length = 323

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 66/292 (22%), Positives = 124/292 (42%), Gaps = 21/292 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  +TD  +R  +R      LL TE++ A A+ R  KK    +     E P++LQI G  
Sbjct: 21  MAGYTDYVFRRLSRRF-GAGLLVTELVSAAALARMIKKTYRYMEHKEDEYPISLQIFGNK 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                +A ++ +  G++ I++N+GCP+ +V   + GA L+ + D +   +  +     +P
Sbjct: 80  EDDFKKAIELTDLSGFSFIDINMGCPTKKVVRNNGGAGLLSDTDKMVSILNTVKSVSPLP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G          R L   +K++G   + +H R A         +      D++ 
Sbjct: 140 VSVKIRLGFQRGEGGEIERALA--LKENGAVFLTLHGRYA--------SDLYRGVADWEA 189

Query: 179 VYEIKKENPDLFI-GLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +K+   D +I   NG ++    A +      VDG+M+GRAA  N  +   ++  F +
Sbjct: 190 IANVKEALGDDYILIGNGDIKTKEDAKRAFEISKVDGIMVGRAAIGNPWVFRELNTIFDD 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
               +      +       I+     Y          +  + + ++    GF
Sbjct: 250 NAEYNDDDTRNLKSVLIEHINGCCELY-----GEVSGIHFMRKFIMKYLTGF 296


>gi|302335762|ref|YP_003800969.1| tRNA-U20-dihydrouridine synthase [Olsenella uli DSM 7084]
 gi|301319602|gb|ADK68089.1| tRNA-U20-dihydrouridine synthase [Olsenella uli DSM 7084]
          Length = 350

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 67/328 (20%), Positives = 123/328 (37%), Gaps = 33/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   TD  YR  AR      L Y+EM+    I  G +K       +  E  LA+Q+ G+ 
Sbjct: 43  MAGVTDAAYRLMAR-AGGAGLAYSEMVSVAGIHYGGEKTWDLVCPRDGESELAVQLFGSK 101

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  EAA  V++        I++N+ CP  +V     G+ L+ +P +    + A     
Sbjct: 102 PEQFREAAARVQERLGRRLALIDVNMACPVPKVTRKGEGSALLDDPALAASIVRACKAEA 161

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++ VT K R G   +          ++++++G + I +H R A                D
Sbjct: 162 TVDVTCKIRRG--RRAGEEVAPEFARAMEQAGASAIAVHGRTA--------SQLYRGEAD 211

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V  + +   D+ +  +G + D + A ++L       VM+ R +Y N  +        
Sbjct: 212 WGTVSRVARAV-DVPVIGSGDVTDAATARRMLAETGAAAVMVARGSYGNPWLFAQARGI- 269

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P       +   ++  +   + AR     G            F G P++   
Sbjct: 270 --SAASGTPSSRLSAFECHLRLLEATGAHMARARSLAG----------WYFRGLPHAAAW 317

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           R   ++         H+IE    L+ +S
Sbjct: 318 RER-SMHCADLGDYLHVIEELRTLLAQS 344


>gi|86153597|ref|ZP_01071800.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           HB93-13]
 gi|85842558|gb|EAQ59770.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           HB93-13]
          Length = 305

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 126/300 (42%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAS-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFHEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+ F ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKFKKEIILTHFDEMIKH-YKDQGISIFRKHLHEYSKGHKDASAFR 285


>gi|46204191|ref|ZP_00050361.2| COG0042: tRNA-dihydrouridine synthase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 324

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 132/318 (41%), Gaps = 25/318 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISK 61
             TD H R  A+ L   + + +EM+ A  + +GD ++ +        P  +Q+ G     
Sbjct: 12  GVTDLHMRRLAQGL-GASAVVSEMVAAAELAKGDAESRVRAEGAGVSPHIVQLAGCAPEP 70

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+ +A+ +PVTV
Sbjct: 71  MAEAARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVREAVEVPVTV 130

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    ++   +L +  +  G++G+ +H R         +        D+  +  
Sbjct: 131 KMRLGWD--HASLNAPDLARRAESLGLDGVTVHGRT--------RQQFYKGRADWSAIRS 180

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   L +  NG +  + +A   L      GVMIGRAA     ++  +    +     
Sbjct: 181 VV-EAVSLPVIANGDIASLEEARACLAASGATGVMIGRAAVGRPWLVGAIAAGLAGRTVM 239

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL--FHGFPNSRRCRHIL 297
               + +       +++ +  +       +   ++   +H+       G   +   R ++
Sbjct: 240 PLSPERQA------EVATAHYEGLIALYGASMGVRHARKHLAAYADAAGGLGADDRRRLV 293

Query: 298 TVEAGASTATHHIIETAF 315
           T           ++  AF
Sbjct: 294 TT--TDPAEALRLLRRAF 309


>gi|163843386|ref|YP_001627790.1| NifR3 family TIM-barrel protein [Brucella suis ATCC 23445]
 gi|163674109|gb|ABY38220.1| TIM-barrel protein, nifR3 family [Brucella suis ATCC 23445]
          Length = 333

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 119/287 (41%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GC + +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H      ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYGGKIGIRHARKHLGWYM 289


>gi|57505594|ref|ZP_00371521.1| NifR3 family protein [Campylobacter upsaliensis RM3195]
 gi|57016141|gb|EAL52928.1| NifR3 family protein [Campylobacter upsaliensis RM3195]
          Length = 305

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/304 (22%), Positives = 133/304 (43%), Gaps = 34/304 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   +      +  +EMI ++A++   +K+  +L  +  E P  +QI G D
Sbjct: 14  MAGFTDPPFRSVVKQF-GADVTISEMISSNALVYESQKSLKMLEKTPFETPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A  I+ +  + + I+ N GCP  +V +   G+ L+ + D+    +  +      
Sbjct: 73  EDILKKAVLILNELDFIDGIDFNCGCPVNKVVKQCAGSALLEDLDLFKRLVGVIKTHNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             T VK R+G +D+ P      + K  ++ GV+ I IH R         +      + DY
Sbjct: 133 QFTSVKFRLGFNDKYP----EKMAKICEELGVDFISIHGRT--------RKQLYSGSADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + + KK +  + +  NG + +   A K+L   + +G+MIGRA+  N  +   + E   
Sbjct: 181 NSIAKAKK-SVKIPVIANGDI-NAQNAKKVLKITACEGLMIGRASVGNPWIFYEIKE--- 235

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD    ++I  +  +   +H  + G +    +H+     G+ ++   R
Sbjct: 236 ---------GKSVDGALKKRIILTHFEEMIKHYKAMG-VSIFRKHLHEYSKGYKDASAFR 285

Query: 295 HILT 298
            ++ 
Sbjct: 286 DMIN 289


>gi|83858330|ref|ZP_00951852.1| putative nitrogen regulation protein [Oceanicaulis alexandrii
           HTCC2633]
 gi|83853153|gb|EAP91005.1| putative nitrogen regulation protein [Oceanicaulis alexandrii
           HTCC2633]
          Length = 339

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 130/322 (40%), Gaps = 25/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD   R  A       L+ +EM+  + + +G +     +       P  +Q+ G +
Sbjct: 27  MSGVTDWPIRKQAHRF-GAGLVVSEMVACETLAQGREDVIRRMRADGDCGPHVIQLAGRE 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A++ E+ G + I++N+GCP+ +V  G  G+ LM + D     + A  KA+S+P
Sbjct: 86  AHWMDVGARLAEEVGADIIDINMGCPARQVTRGLSGSALMRDLDHALTLVEATVKAVSVP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D    ++    L +  + +GV  + +H R         +        D+  
Sbjct: 146 VTLKMRLGWD--HDSLNAPELARRAEAAGVQMVTVHGRT--------RQQFYKDKADWSA 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K +   + + +NG ++   QA +   L   DGVM+GRA+     +   + +   + 
Sbjct: 196 VARVK-DAVSIPLVVNGDIQTPQQAREALRLSGADGVMVGRASQGRPWLPGAIADVLCDG 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPN---SRR 292
                P   RV  D   +  A        HL     ++ + +H         P    +R 
Sbjct: 255 AAFKEPSL-RVGADALCQALADSVTLYGEHLG----VRTMRKHFASFVDWAIPEPEAARE 309

Query: 293 CRHILTVEAGASTATHHIIETA 314
            R  L        A   ++  A
Sbjct: 310 WRGRLCRAQNRLEAEAALMAFA 331


>gi|156387454|ref|XP_001634218.1| predicted protein [Nematostella vectensis]
 gi|156221299|gb|EDO42155.1| predicted protein [Nematostella vectensis]
          Length = 570

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 113/285 (39%), Gaps = 26/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G +    ++   + E    +Q+ GA    + 
Sbjct: 230 NLPFRRICKQY-GADITCGEMAMCTNLLQGQQSEWALVKRHSSEDIFGVQLCGAFPDTMT 288

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A++++ +   + I++N GCP   V     G+ LM     +   +  M   + IP+TVK
Sbjct: 289 KCAELLQKETDVDFIDINTGCPIDLVFNKGAGSALMERKGKLQQIVQGMKSVIDIPLTVK 348

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G+ D+        LV +++  G + + IH R         ++ R   + D+D + E+
Sbjct: 349 IRAGIHDKKYTWNAHKLVGNLRDWGTDMVTIHGRS--------REQRYTKSADWDYISEV 400

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            K    + +  NG +     A++      V GVMI R A     + T + E     ++ S
Sbjct: 401 AKLASPMPVFGNGDILSFEDAMQHRKQAGVAGVMIARGAIIKPWIFTEIKEQRHWDISSS 460

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
             +           I     +    H  S  +  + TR  +   L
Sbjct: 461 ERL----------DILRQFVNAGLEHWGSDTQGVEKTRRFLLEWL 495


>gi|325107227|ref|YP_004268295.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
 gi|324967495|gb|ADY58273.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
          Length = 376

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 59/318 (18%), Positives = 122/318 (38%), Gaps = 23/318 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
             +T+  +R   R      L   +++ A A++ G  K++  +    ++ P A+QI G+D 
Sbjct: 46  AKYTNLPFRLVVRACGGLGLGTCDLVNARALMAGSSKSLALIRTEPEDTPFAVQIFGSDP 105

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + + +AA+ +E  G  + I++N+GCP   V +   GA +M   D     +  + +A  +P
Sbjct: 106 AYMRDAAQYLEGLGTVDAIDINMGCPVDHVTKNGAGAGMMCERDKTCQLVQTVVEATRLP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD    +      +  ++ G+  + IH R         +      ++D   
Sbjct: 166 VTVKMRLGWDDTQ--LTAPRFAREFEQIGIKAVAIHGRT--------RAQGFKGSVDLGG 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +    + +  NG +  +  A ++        V +GR A  N  +   + ++  + 
Sbjct: 216 IRRVVEAVESIPVIGNGDVRTIPDAARMFERTGCHAVSVGRGALANPWIFRQLAQWEQDG 275

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-- 294
                    +      ++      +Y A        L    R +             R  
Sbjct: 276 WYDPPGNFEQRLDLVLKQ-----FEYHAELDGEKYGLIAYRRTVHWYLKAMRVKAALRDQ 330

Query: 295 -HILTVEAGASTATHHII 311
               +  A  + A   I+
Sbjct: 331 VQHASNAAEFNAAIREIV 348


>gi|315499857|ref|YP_004088660.1| tim-barrel protein, nifr3 family [Asticcacaulis excentricus CB 48]
 gi|315417869|gb|ADU14509.1| TIM-barrel protein, nifR3 family [Asticcacaulis excentricus CB 48]
          Length = 327

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 70/287 (24%), Positives = 116/287 (40%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   +D  +R  A  L   A   TEM+    + RG    +  F+  E      +Q+ G D
Sbjct: 21  MTGVSDLPFRRMASKL-GAAYAATEMVACAELERGRPDVVRKFALGEHAGLKIVQLIGKD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +   A + E  G + ++LN GCP+  V     G+ LM + D     + A   A S P
Sbjct: 80  PAFIARGAALAEASGAHIVDLNFGCPAKEVTGVLCGSALMRDLDAASRLMEAAVSATSRP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G D+Q        L +  +  G+  + +H R         +        D+  
Sbjct: 140 VTVKMRMGWDNQSRNA--PELARRAEAIGIQAVTVHGRT--------RQQFYKGEADWAF 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K E   + + +NG + D  +A + L     DG+MIGR  Y    +   +D   S  
Sbjct: 190 VQQVK-EAVSIPVIVNGDITDGEKAREALAQSGADGLMIGRGVYGRPWLAAQLDAALSGE 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                P  +   +     +  S++ Y      SG  L+   +H+   
Sbjct: 249 -NEPEPTGSARLELILEHMHDSLSFY-----GSGLGLKMFKKHLGWY 289


>gi|257784603|ref|YP_003179820.1| TIM-barrel protein, nifR3 family [Atopobium parvulum DSM 20469]
 gi|257473110|gb|ACV51229.1| TIM-barrel protein, nifR3 family [Atopobium parvulum DSM 20469]
          Length = 363

 Score =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 63/301 (20%), Positives = 115/301 (38%), Gaps = 28/301 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR  AR      L Y+EM+    I  G +K   ++   + E  +A+Q+ G+ 
Sbjct: 44  MAGVSDGVYRTMAR-AGGAGLAYSEMVSVAGIHFGGEKTWELVEPLSTEPDIAVQLFGSK 102

Query: 59  ISKLVEAAKIVED---FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  EAA  + +        I++N+ CP  +V +   G+ L+  P++  + + A    +
Sbjct: 103 PEQFKEAAAQISERLGNKLALIDINMACPVPKVVKKGEGSALLDTPELAANLVKACLSEV 162

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           ++PVTVK R G   +          ++++ +G + I +H R A                +
Sbjct: 163 TVPVTVKIRRG--RRQDEEVAPEFARAMEAAGASAIAVHGRFAT--------QMYRGQAE 212

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ V  +  +   + +  +G +         L    V  VMI R  Y N  +        
Sbjct: 213 WETVNRVC-DAVSIPVIGSGDMLSAEDVAHALKETGVTAVMIARGTYGNPWIFKNTQALL 271

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
               T   P   ++   F   +   + D A  H+     L          F G PN+   
Sbjct: 272 EGK-TPFVPSVDQMLASFMMHV--KLLDAAHIHIARARSLS------TWYFRGIPNAAYW 322

Query: 294 R 294
           R
Sbjct: 323 R 323


>gi|121612695|ref|YP_999847.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|167004818|ref|ZP_02270576.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81-176]
 gi|87250431|gb|EAQ73389.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81-176]
          Length = 305

 Score =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 125/300 (41%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ I IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFISIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAS-AKASVSIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285


>gi|220926307|ref|YP_002501609.1| TIM-barrel protein, nifR3 family [Methylobacterium nodulans ORS
           2060]
 gi|219950914|gb|ACL61306.1| TIM-barrel protein, nifR3 family [Methylobacterium nodulans ORS
           2060]
          Length = 357

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 114/284 (40%), Gaps = 21/284 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISK 61
             TD H R  AR L     + +EM+ A+   RG  +  L    +   P  +Q+ G D   
Sbjct: 40  GVTDLHLRRIARRL-GATAVVSEMVAAEDFARGTAEARLRAEGEGVLPHVVQLAGCDPHW 98

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + E A++ E  G + I++N+GCP+ +V  G  G+ LM + D     +AA+  A+++PVTV
Sbjct: 99  MAEGARLAEANGADVIDVNMGCPAKKVTGGEAGSALMRDLDHAARLLAAVRGAVAVPVTV 158

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    A+    L +  +  G+  + +H R         +        D+  +  
Sbjct: 159 KMRLGWD--HAALNAPELARRAEDLGLAAVTVHGRT--------RQQFYTGRADWAAIRA 208

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   + +  NG ++ +  A   L       VMIGRAA     ++  V          
Sbjct: 209 VV-ETVSIPVVANGDVDGLEAARACLNASGAAAVMIGRAAVGRPWLVGAVAAGLQGRDAP 267

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                 + D               AR+      ++   +H+   
Sbjct: 268 DLTPAEQADL-----AVEHYEGLLARY-GVPMGVRHARKHLAAY 305


>gi|170743988|ref|YP_001772643.1| NifR3 family TIM-barrel protein [Methylobacterium sp. 4-46]
 gi|168198262|gb|ACA20209.1| TIM-barrel protein, nifR3 family [Methylobacterium sp. 4-46]
          Length = 358

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 65/284 (22%), Positives = 122/284 (42%), Gaps = 21/284 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISK 61
             TD H R  AR     + + +EM+ A+ + RG  +  L    +  +P  +Q+ G D   
Sbjct: 37  GVTDLHLRRIARR-CGASAVVSEMVAAEDLARGSAEARLRAEGEGVRPHVVQLAGCDPRW 95

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + E A++ E  G + I++N+GCP+ +V  G  G+ LM + D     +AA+ +A+++PVTV
Sbjct: 96  MAEGARLAEANGADVIDVNMGCPAKKVTGGEAGSALMRDLDHAARLLAAVREAVAVPVTV 155

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD        +L +  +  G++ + +H R         +        D+  +  
Sbjct: 156 KMRLGWDDASRNA--PDLARRAEALGLSAVTVHGRT--------RQQFYAGRADWAAIRA 205

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   + +  NG +  +++A   L       VMIGRAA     ++  V          
Sbjct: 206 VV-EAVSIPVVANGDVGSLAEARACLAESGAAAVMIGRAAVGRPWLVGAVAAGLRG---A 261

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +P  TR  +     ++    +           ++   +H+   
Sbjct: 262 PAPALTRAAQA---DLAGEHYEGLLALYGVAMGVRHARKHLAAY 302


>gi|225164984|ref|ZP_03727193.1| TIM-barrel protein, nifR3 family [Opitutaceae bacterium TAV2]
 gi|224800406|gb|EEG18793.1| TIM-barrel protein, nifR3 family [Opitutaceae bacterium TAV2]
          Length = 389

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 118/302 (39%), Gaps = 21/302 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             +T+   R   R L       T+++ A +++   K    ++  +  ++PLA+Q+ G+  
Sbjct: 18  AGYTNLPMRLTVRELGGLGWATTDLVNARSLIERSKGAMKLVETAPGDQPLAIQLFGSVP 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--I 117
            ++ +AA I ++ G   +++N+GCP  +V     GA +M   +     +  M +A+   I
Sbjct: 78  EEMRDAAVICKELGAQSVDVNMGCPVKKVVGIGGGAAMMTELNKTAALVRGMVEAVGNKI 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R+G DD    +   +L + +   GV  I++H R         +       ++  
Sbjct: 138 PVTAKMRLGWDD--ANITAPDLARVLADVGVAAIFVHGRT--------RAQGFSGTVNLA 187

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + +  P L +  NG +     A  ++      GV +GR A+ +  +    +     
Sbjct: 188 GIRAVVEAVPGLPVIGNGDVTTPESARHMIAETGCAGVSVGRGAFYDPWIFKRTEHLLRT 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P      +   R        Y   H   G +L    R        F  S+  + 
Sbjct: 248 GELLPEPTFAERLRVMTRHFERYCEFYGEEH---GARL--FRRVAPWYARRFGPSKLFKQ 302

Query: 296 IL 297
            +
Sbjct: 303 KI 304


>gi|154253571|ref|YP_001414395.1| nifR3 family TIM-barrel protein [Parvibaculum lavamentivorans DS-1]
 gi|154157521|gb|ABS64738.1| putative TIM-barrel protein, nifR3 family [Parvibaculum
           lavamentivorans DS-1]
          Length = 341

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 72/288 (25%), Positives = 120/288 (41%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A  L    L+ +EM+ +D ++R           + +  PLA+Q+ G +
Sbjct: 19  MAGVTDLPFRRVAHRL-GAGLVVSEMVASDELVRARPDVVRRAAGAGEFAPLAIQLAGRE 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A++    G + I++N+GCP+ +V  G  G+ LM + D     I A   A+S+P
Sbjct: 78  AHWMAEGARVAAAAGADIIDINMGCPAKQVTTGLSGSALMRDLDHAESLIEATVGAVSLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD         L +  +  GV  + +H R       S          D++ 
Sbjct: 138 VTLKMRTGWDDTKRNA--PELAQRAEALGVKMVTVHGRTRCQFYKS--------RADWNF 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+KK    + +  NG +     A  IL     DGVMIGR A      L  V ++    
Sbjct: 188 ISEVKKAV-SIPVIANGDVTSEEDARAILDASGADGVMIGRGAQGRPWFLAQVAQFLWTG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              ++P       +   +I A        H      ++   +H++   
Sbjct: 247 EKRAAP-----AWETQAEIVAGHYRDMLDHYGEALGIRVARKHLVWYL 289


>gi|261755085|ref|ZP_05998794.1| nifR3 family TIM-barrel protein [Brucella suis bv. 3 str. 686]
 gi|261744838|gb|EEY32764.1| nifR3 family TIM-barrel protein [Brucella suis bv. 3 str. 686]
          Length = 332

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 120/287 (41%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLSFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GC + +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 193 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 244 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 288


>gi|254704408|ref|ZP_05166236.1| NifR3 family TIM-barrel protein [Brucella suis bv. 3 str. 686]
          Length = 333

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 120/287 (41%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLSFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GC + +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++   +H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHARKHLGWYM 289


>gi|305432665|ref|ZP_07401826.1| tRNA-dihydrouridine synthase B [Campylobacter coli JV20]
 gi|304444376|gb|EFM37028.1| tRNA-dihydrouridine synthase B [Campylobacter coli JV20]
          Length = 308

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 132/327 (40%), Gaps = 43/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++    +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKSLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAN-AKASVKIPVIANGDI-NAQNAKEVYEITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKNVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285

Query: 295 ----HILTVEAGASTATHHIIETAFNL 317
                I  VE          IE  F+L
Sbjct: 286 DSVNRIDNVEEMRKK-----IEEFFSL 307


>gi|315639099|ref|ZP_07894266.1| tRNA-dihydrouridine synthase B [Campylobacter upsaliensis JV21]
 gi|315480803|gb|EFU71440.1| tRNA-dihydrouridine synthase B [Campylobacter upsaliensis JV21]
          Length = 305

 Score =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 129/304 (42%), Gaps = 34/304 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  +TD  +R   +      +  +EMI ++A++   +K+  +L  +  E P  +QI G D
Sbjct: 14  MAGFTDPPFRSVVKQF-GADVTISEMISSNALVYESQKSLKMLEKTPFETPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A  I+ +  + + I+ N GCP  +V +   G+ L+ N ++    +  +      
Sbjct: 73  EDILKKAVLILNELDFIDGIDFNCGCPVNKVVKQCAGSALLENLELFRKLVGVIKTHNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             T VK R+G +D+ P      + +  ++ GV+ I IH R         +      + DY
Sbjct: 133 QFTSVKFRLGFNDKYP----EKMAQICEELGVDFISIHGRT--------RKQLYSGSADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + + KK +  + +  NG + +   A ++L   + +G+MIGRA+  N  +   + E   
Sbjct: 181 NSIAKAKK-SVKIPVIANGDI-NAQNAKEVLKITACEGLMIGRASVGNPWIFYEIKE--- 235

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               G S  +    +         +  Y A        +    +H+     G+ ++   R
Sbjct: 236 ----GKSVNEALKKRIILTHFEEMIKHYKAM------GVSIFRKHLHEYSKGYKDASAFR 285

Query: 295 HILT 298
            ++ 
Sbjct: 286 DMIN 289


>gi|157414436|ref|YP_001481692.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81116]
 gi|157385400|gb|ABV51715.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           81116]
 gi|307747080|gb|ADN90350.1| Probable tRNA-dihydrouridine synthase [Campylobacter jejuni subsp.
           jejuni M1]
 gi|315931517|gb|EFV10484.1| dihydrouridine synthase (Dus) family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 305

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 60/300 (20%), Positives = 125/300 (41%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAS-AKASVSIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285


>gi|262199164|ref|YP_003270373.1| hypothetical protein Hoch_6005 [Haliangium ochraceum DSM 14365]
 gi|262082511|gb|ACY18480.1| TIM-barrel protein, nifR3 family [Haliangium ochraceum DSM 14365]
          Length = 348

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 122/303 (40%), Gaps = 23/303 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R          L  TE + A A+  GD +  + L  S       +QI G +
Sbjct: 23  MAAVTDLPFRTICERF-GVGLTITEFLKATALCDGDAEVVDKLTASLDGVRFGVQIYGRE 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
           +  LV+AA++  D G + I++N+GCP+ RV  G  GA LM  P++  + + A+  ++  S
Sbjct: 82  VEPLVQAAQLALDIGASLIDINMGCPAKRVVAGECGAALMQWPELSAELVRAVVASVPDS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVTVK R G +             ++ ++G   + +H R         +      ++D 
Sbjct: 142 VPVTVKHRAGWNPLNRNA--PEFACAMVEAGAQMVTVHGRT--------RTQGFAGSVDL 191

Query: 177 DIVYEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +++  +++  P  + +  NG +  +   L++      D VMIGR A  N  +  ++    
Sbjct: 192 EVIRRVREAVPARVPVVGNGDVVCVDDYLRMREHTGCDAVMIGRGALGNPWLFRSLHALA 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   P      + F   ++          L     + ++ +       G   +   
Sbjct: 252 HGLPDPGRPDMAERYRVFCEHVALLYALKGGPKL-----IHEVRKACAWYAKGLDGADGF 306

Query: 294 RHI 296
           R  
Sbjct: 307 RQH 309


>gi|255744093|ref|ZP_05418047.1| tRNA dihydrouridine synthase B [Vibrio cholera CIRS 101]
 gi|262161983|ref|ZP_06031000.1| tRNA dihydrouridine synthase B [Vibrio cholerae INDRE 91/1]
 gi|262167985|ref|ZP_06035684.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC27]
 gi|262192555|ref|ZP_06050705.1| tRNA dihydrouridine synthase B [Vibrio cholerae CT 5369-93]
 gi|255738358|gb|EET93749.1| tRNA dihydrouridine synthase B [Vibrio cholera CIRS 101]
 gi|262023518|gb|EEY42220.1| tRNA dihydrouridine synthase B [Vibrio cholerae RC27]
 gi|262028361|gb|EEY47017.1| tRNA dihydrouridine synthase B [Vibrio cholerae INDRE 91/1]
 gi|262031600|gb|EEY50188.1| tRNA dihydrouridine synthase B [Vibrio cholerae CT 5369-93]
 gi|327483164|gb|AEA77571.1| tRNA dihydrouridine synthase B [Vibrio cholerae LMA3894-4]
          Length = 287

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 57/302 (18%), Positives = 119/302 (39%), Gaps = 21/302 (6%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +  +EM+  +  L    K+   +    +    ++QI G+D   + EAA+   + G   I+
Sbjct: 1   MAVSEMMSCNPALWKTAKSQNRMVHEGESGIRSVQIAGSDPQLMAEAAQFSVENGAQIID 60

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+GCP+ +V++   G+ L+  PD++ D + A+  A+++PVT+K R G D         +
Sbjct: 61  INMGCPAKKVNKKLAGSALLRYPDVIEDILKAVVNAVNVPVTLKTRTGWD--TDNKNCLS 118

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +  +  G+  + +H R         +        +YD +  +K     + +  NG ++
Sbjct: 119 IAQLAEDCGIQALALHGRT--------RACMYKGEAEYDSIKAVK-AAVSIPVIANGDID 169

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +A  +L     D +MIGR A     +   +  +  +  T      + V       ++
Sbjct: 170 SPEKARYVLEYTGADALMIGRPAQGRPWIFQEIQHFLEHGTTMPELPISEVKDIMLGHVT 229

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           A    Y           +   +H+         +   R        A       +E  F+
Sbjct: 230 ALHQFY-----GEYLGPRIARKHVSWYLQEHEQASAFRRTFNAIETADQ-QLDALEGYFD 283

Query: 317 LM 318
            +
Sbjct: 284 NV 285


>gi|57237130|ref|YP_178142.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni RM1221]
 gi|57165934|gb|AAW34713.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni RM1221]
 gi|284925416|gb|ADC27768.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           IA3902]
 gi|315057563|gb|ADT71892.1| tRNA dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           S3]
          Length = 308

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 68/327 (20%), Positives = 132/327 (40%), Gaps = 43/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ I IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFISIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 GSIAS-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285

Query: 295 ----HILTVEAGASTATHHIIETAFNL 317
                I  VE          IE  F+L
Sbjct: 286 DTVNRIDNVEEMRKK-----IEEFFSL 307


>gi|163852236|ref|YP_001640279.1| NifR3 family TIM-barrel protein [Methylobacterium extorquens PA1]
 gi|163663841|gb|ABY31208.1| TIM-barrel protein, nifR3 family [Methylobacterium extorquens PA1]
          Length = 342

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 131/320 (40%), Gaps = 29/320 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISK 61
             TD H R  A+ L   + + +EM+ A  + +GD ++ +        P  +Q+ G     
Sbjct: 30  GVTDLHMRRLAQRL-GASAVVSEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPEP 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + E A+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTV
Sbjct: 89  MAEGARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    ++    L +  +  G++G+ +H R         +        D+  +  
Sbjct: 149 KMRLGWD--HASLNAAELAQRAEALGLDGVTVHGRT--------RQQFYKGRADWSAIRP 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   + +  NG +  + +A   L      GVMIGRAA     ++  +    +  +  
Sbjct: 199 VV-EAVRIPVIANGDITGLEEARACLSQSGAAGVMIGRAAVGRPWLVGEIAVGLAGRVAP 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FHGF-PNSRRCRH 295
               + R        ++A           +   ++   +H+        G  P+ R  R 
Sbjct: 258 PLSAEQRA------AVAAEHYQGLIALYGAAMGVRHARKHLAAYADAAGGLTPDDR--RR 309

Query: 296 ILTVEAGASTATHHIIETAF 315
           ++T           +++ AF
Sbjct: 310 LVTT--HDPAEALRLLQRAF 327


>gi|315929909|gb|EFV09068.1| dihydrouridine synthase (Dus) family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 308

 Score =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 68/327 (20%), Positives = 132/327 (40%), Gaps = 43/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ I IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFISIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 GSIAS-AKASVSIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASTFR 285

Query: 295 ----HILTVEAGASTATHHIIETAFNL 317
                I  VE          IE  F+L
Sbjct: 286 DTVNRIDNVEEMRKK-----IEEFFSL 307


>gi|167519967|ref|XP_001744323.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163777409|gb|EDQ91026.1| predicted protein [Monosiga brevicollis MX1]
          Length = 353

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 61/281 (21%), Positives = 111/281 (39%), Gaps = 26/281 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +  +EM +A ++L+G   +  ++     E    +QI G     L 
Sbjct: 19  NLPFRRLCKRL-GADVTCSEMAMASSLLQGSSSDWALVRRHESEDLFGIQICGNQPDMLA 77

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ E+   + I+LN GCP  ++ +   G+ L+     + D +  M     IP+TVK
Sbjct: 78  RCAELLSEETDASFIDLNCGCPIDQIFQKGCGSALLARRQRLKDIVQGMRVCSKIPITVK 137

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV    P      +V  ++  GV+ + IH R         +  R     ++D + + 
Sbjct: 138 VRTGVHGDRP--TTHKMVHEMRSWGVSALTIHGRS--------RQQRYTKYANWDYIKDC 187

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +  PDL I  NG +     A++      V GVM+ R A     + T + E  +  ++  
Sbjct: 188 VEAAPDLPIFGNGDILSWEHAVQHQASTGVSGVMLARGALIKPWLFTEIKEQRTWDISSM 247

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              +                 Y   H  S     + TR  +
Sbjct: 248 ERFEQ----------LQEFCKYGLEHWGSDHAGVERTRRFL 278


>gi|205356497|ref|ZP_03223261.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|205345684|gb|EDZ32323.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8421]
          Length = 308

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 125/304 (41%), Gaps = 34/304 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ I IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFISIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 GSIAS-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285

Query: 295 HILT 298
             + 
Sbjct: 286 DTVN 289


>gi|261415070|ref|YP_003248753.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261371526|gb|ACX74271.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302327170|gb|ADL26371.1| dihydrouridine synthase family protein [Fibrobacter succinogenes
           subsp. succinogenes S85]
          Length = 392

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 126/299 (42%), Gaps = 28/299 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN--ALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGG 56
           M   TD  +R   R+L+ +   LL +E +  D  A+   D    L F  +E+P  +QI G
Sbjct: 29  MDGVTDAPFRRLCRVLSGDRMGLLVSEFVPTDGDAVFNPDGHKQLKFFPEERPFGVQIFG 88

Query: 57  ADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
               ++  AA KI E +    I +N GCP+ +V     G+ L+ +   + + +  +   L
Sbjct: 89  RFPDRMAAAAGKIAERYHPEFIEVNAGCPAPKVAGKGSGSGLLRDLPRLQEILHDVKAVL 148

Query: 116 S-----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                 IP+T+KCRIG DD   ++ +   +K  +  GV  + +H R  +           
Sbjct: 149 DAKTPEIPLTLKCRIGWDDD--SINVMETLKIAEGEGVEMLTVHGRTRLQGYN------- 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
               ++D + ++      + +  NG +  +  A + +    V GV IGR A  N  +   
Sbjct: 200 -GLANWDWIGKVAAAA-KIPVIGNGDVNSVECARERINTYGVSGVSIGRGAMHNPWIFGQ 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           + + +         I  +   D +        +  A  +++ G+++Q+      L  GF
Sbjct: 258 IADAWEGRE--KHVITAQEALDVFPLYYKFKIEDGATEMNAMGRMKQLA---ARLCKGF 311


>gi|319940882|ref|ZP_08015221.1| nifR3 family TIM-barrel protein [Sutterella wadsworthensis 3_1_45B]
 gi|319805764|gb|EFW02545.1| nifR3 family TIM-barrel protein [Sutterella wadsworthensis 3_1_45B]
          Length = 323

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 129/320 (40%), Gaps = 23/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M  ++DR +R   R          EM  +   LR   K++  +  +++P    +Q+ GAD
Sbjct: 17  MAGYSDRSFREIVREW-GADYAVAEMTASREDLRCRAKSLTRWVERDEPGLHVVQLLGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAAK  ED G + +++N+GCP+ +V     G+ LM N  +  + + A+  A+ IP
Sbjct: 76  PVVMAEAAKAAEDDGADVVDINMGCPAKKVLNTDCGSALMKNECLTAEILEAVRAAVEIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D +        + +  ++ G+  + IH R         + +    + +YD 
Sbjct: 136 VTLKIRTGWDREHKNA--PEIARIAEECGIAMLVIHGRT--------RADGFRGDAEYDT 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK E   + +  NG +    +A  +L     DG+MIGR A     +   V       
Sbjct: 186 IARIKAERG-IPVVANGDIVSGVKAQAVLRACGADGLMIGRGAVGRPWLFAEVRAALEGR 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P++            A   DY      +   +    +H+      F +    R  
Sbjct: 245 AWK--PLENGAVLRHLLHHRAKHFDYY----GARRGIVTFRKHLCAYLKPFSDPLELRPK 298

Query: 297 LTVEAGASTATHHIIETAFN 316
           L +          ++E  F+
Sbjct: 299 L-LRETDPQVQKALVEQFFS 317


>gi|221116753|ref|XP_002163197.1| PREDICTED: similar to tRNA-dihydrouridine synthase 3-like [Hydra
           magnipapillata]
          Length = 679

 Score =  208 bits (531), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 56/285 (19%), Positives = 115/285 (40%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  +L+G +    ++   + E    +Q+ G     + 
Sbjct: 345 NLPFRRVCKNF-GADITCGEMAMATNLLQGHQSEWALVKRHSSEDIFGVQLCGGYPDSMA 403

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +A +++  +   + I++N+GCP   V +   G+ LM     + + +  M +   +P+T+K
Sbjct: 404 KAVEMLNKECQIDFIDINMGCPIDLVFKKGEGSALMGRMKKLEEVVKGMVQVSDVPITIK 463

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G+ +         ++  +K+ GV+ I +H R         ++ R     D+D + + 
Sbjct: 464 MRTGIQENKSIA--HKIIPLVKEWGVDLITLHGRS--------REQRYTKAADWDYINQC 513

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            K +  +    NG +     A+K      VDG+MI R A     + T + E     ++  
Sbjct: 514 AKLSHPVPFFGNGDIFSYEDAIKRQENFGVDGLMIARGALIKPWIFTEIKEKRHWDISSQ 573

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        ++    T+Y   H  S  K  + TR  +   L
Sbjct: 574 ERF----------ELLKCFTNYGLEHWGSDTKGVENTRRFLLEWL 608


>gi|86149700|ref|ZP_01067930.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88597178|ref|ZP_01100413.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|218561804|ref|YP_002343583.1| putative tRNA-dihydrouridine synthase [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|85839968|gb|EAQ57227.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           CF93-6]
 gi|88190239|gb|EAQ94213.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           84-25]
 gi|112359510|emb|CAL34294.1| putative tRNA-dihydrouridine synthase [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|315926939|gb|EFV06301.1| dihydrouridine synthase (Dus) family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
          Length = 308

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 68/327 (20%), Positives = 132/327 (40%), Gaps = 43/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ I IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFISIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 GSIAS-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASTFR 285

Query: 295 ----HILTVEAGASTATHHIIETAFNL 317
                I  VE          IE  F+L
Sbjct: 286 DTVNRIDNVEEMRKK-----IEEFFSL 307


>gi|57168706|ref|ZP_00367838.1| probable transcription regulator Cj0123c [Campylobacter coli
           RM2228]
 gi|57019987|gb|EAL56667.1| probable transcription regulator Cj0123c [Campylobacter coli
           RM2228]
          Length = 308

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 66/327 (20%), Positives = 132/327 (40%), Gaps = 43/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +Q+ G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQVAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++    +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKSLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAN-AKASVKIPVIANGDI-NAQNAKEVYEITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKNVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285

Query: 295 ----HILTVEAGASTATHHIIETAFNL 317
                I  VE          IE  F+L
Sbjct: 286 DSVNRIDNVEEMRKK-----IEEFFSL 307


>gi|86151249|ref|ZP_01069464.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           260.94]
 gi|315123725|ref|YP_004065729.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|85841596|gb|EAQ58843.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           260.94]
 gi|315017447|gb|ADT65540.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
          Length = 308

 Score =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 133/327 (40%), Gaps = 43/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSIHGRT--------RKQLYSGKTDY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAN-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285

Query: 295 ----HILTVEAGASTATHHIIETAFNL 317
                I  VE          IE  F+L
Sbjct: 286 DTVNRIDNVEEMRKK-----IEEFFSL 307


>gi|283955300|ref|ZP_06372800.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           414]
 gi|283793214|gb|EFC31983.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           414]
          Length = 311

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 60/304 (19%), Positives = 126/304 (41%), Gaps = 34/304 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++    +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFTSLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMTKICESLGVDFVSIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + +  K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 NSIAK-AKASVKIPVIANGDI-NAQNAKEVYEITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVGIFRKHLHEYSKGRKDASAFR 285

Query: 295 HILT 298
             + 
Sbjct: 286 DEIN 289


>gi|23501997|ref|NP_698124.1| nitrogen regulation protein Nifr3 [Brucella suis 1330]
 gi|23347948|gb|AAN30039.1| nitrogen regulation protein Nifr3 [Brucella suis 1330]
          Length = 333

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 119/287 (41%), Gaps = 25/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GC + +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCLAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + + ++   + +  NG +   + A +IL     D VM+GRA+Y    +   +        
Sbjct: 194 HAV-RDAVRIPLVANGDVSSRADAEEILRRSGADAVMVGRASYGQPWLAGAI-------- 244

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              S    R        I     D    H  S   ++    H+    
Sbjct: 245 -AGSDFAPRDANGILDYIIRHYED-MLDHYGSKIGIRHAREHLGWYM 289


>gi|158424712|ref|YP_001526004.1| nitrogen regulation protein [Azorhizobium caulinodans ORS 571]
 gi|158331601|dbj|BAF89086.1| nitrogen regulation protein [Azorhizobium caulinodans ORS 571]
          Length = 365

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 65/285 (22%), Positives = 113/285 (39%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A       L  +EM+ ++A+L G  +  L          A+Q+ G + 
Sbjct: 49  MAGITDAPVRRMALRY-GAGLTVSEMVASEALLTGHAEMTLRAEGAGVDIHAVQLAGNEP 107

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++ E  G   I++N+GCP+ RV  G+ GA L+ +  +    + A+  A+S+PV
Sbjct: 108 HWMAEAARLAEASGAAIIDINMGCPAKRVTTGAAGAALLRDLPLATRILEAVRAAISVPV 167

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D     +    + +  +  G+  + IH R         +        D+  +
Sbjct: 168 TLKTRLGWDG--AEMTAPEIARRAEAIGIAMVTIHGRT--------RCQFYTGTADWAAI 217

Query: 180 YEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +   + +  NG L       A+      DGVMIGR A         V +++    
Sbjct: 218 RAVK-DAVSIPVIANGDLTQTHDAAAMLAASGADGVMIGRGAQGRPWFPGAVAQHWRTGR 276

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             + P                +  Y          L+Q  +H+  
Sbjct: 277 APADPDLAEQRDVLLELYDGWLALYGVE-----LGLRQARKHVGW 316


>gi|157363261|ref|YP_001470028.1| dihydrouridine synthase DuS [Thermotoga lettingae TMO]
 gi|157313865|gb|ABV32964.1| dihydrouridine synthase DuS [Thermotoga lettingae TMO]
          Length = 305

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 136/322 (42%), Gaps = 36/322 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGADI 59
           M   T+R +R            +TEMI A++++R + K +     +++P +A+Q+ G D 
Sbjct: 1   MAGITNRAFRKIC-TFWGAQFSFTEMISAESVVR-NFKTVQRMLPKDEPNVAVQLFGNDP 58

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L +AAKIVE +    I++N  CP  +V + + G  L+ + + +   I ++  ++  PV
Sbjct: 59  KTLAQAAKIVEPY-AAWIDINAACPVKKVIKKNSGGALLNDLERLEKIIGSVKSSVQKPV 117

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG +  I    L  +V S  K+G +GI +H R  + K              +D  
Sbjct: 118 TVKIRIGFEKNI----LDQIVHSCIKAGADGIEVHGRTVVQK--------YSGKAFWD-- 163

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K     +   ++G + +     K L     +  +I R A +   +   + +      
Sbjct: 164 --LKLSQYGISTAVSGDIFEAEDFHKALEMSGANSALIARGALRKPWIFAQITQ------ 215

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +P  T + + F + +   + D   R ++       + + + G  HG   +R  R   
Sbjct: 216 -KRTPKITEIKETFTKHLKMQIEDEGERSIYK------MRQFVAGYTHGMRGAREFREKF 268

Query: 298 TVEAGASTATHHIIETAFNLMI 319
            ++          IE  FN  +
Sbjct: 269 -MKLNKPEDMEKAIEEFFNSFL 289


>gi|332287905|ref|YP_004422806.1| dihydrouridine synthase family protein [Chlamydophila psittaci 6BC]
 gi|325507219|gb|ADZ18857.1| dihydrouridine synthase family protein [Chlamydophila psittaci 6BC]
          Length = 291

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 63/302 (20%), Positives = 130/302 (43%), Gaps = 23/302 (7%)

Query: 22  LYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ EM+  + +     + +  L +S   +P+  Q+ G+      EAAK++E  G++ I+L
Sbjct: 1   MFCEMVKVEGLHYSPSRTLKLLEYSESMRPIGGQLCGSKPEMAGEAAKVLEGLGFDLIDL 60

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N GCP+ R+ +   G+ L+ +P+++G  +  + +A+SIPVTVK R G D     + +   
Sbjct: 61  NCGCPTDRITKDGSGSGLLKSPELIGKILEKIIEAVSIPVTVKIRSGWD--CNNINVEET 118

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLE 198
           V+ I+ +G + +++H R         +    +   + + +   K     DL +  NG + 
Sbjct: 119 VRIIRDAGASAVFVHGRT--------RAQGYVGPSNLEYIARAKAAAGKDLPVFGNGDIF 170

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               A  ++     DGV++ R       ++  ++ Y ++      P   R      ++  
Sbjct: 171 SPEAAKLMMDSTQCDGVLVARGTMGAPWIVRQIESYLASGTYQKVPFSKR------KQAF 224

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
                +   +  S  K    TR + G         R  R  L+ +A +    + +I+   
Sbjct: 225 IQHLQWVEEYYQSEAKFLSETRKLCGHYLISASKVRFLRSALS-KATSVQEVYQLIDNYE 283

Query: 316 NL 317
             
Sbjct: 284 EA 285


>gi|148926294|ref|ZP_01809978.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|145844686|gb|EDK21791.1| putative transcriptional regulator [Campylobacter jejuni subsp.
           jejuni CG8486]
          Length = 300

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 61/304 (20%), Positives = 125/304 (41%), Gaps = 34/304 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ I IH R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFISIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 GSIAS-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285

Query: 295 HILT 298
             + 
Sbjct: 286 DTVN 289


>gi|45655921|ref|YP_000007.1| nifR3-like protein [Leptospira interrogans serovar Copenhageni str.
           Fiocruz L1-130]
 gi|45599154|gb|AAS68644.1| nifR3-like protein [Leptospira interrogans serovar Copenhageni str.
           Fiocruz L1-130]
          Length = 329

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 75/291 (25%), Positives = 129/291 (44%), Gaps = 29/291 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D   R   R     A  YTE +  D ++    K   +  + ++E+P+  QI G  
Sbjct: 18  MAGISDSPTRRICRKF-GAAFSYTEFVNTDELVHRAPKALKMFRYKSEERPITFQIFGNR 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I+++   + I+LN+GC + +V     GA L+  P + G  I A+ K ++IP
Sbjct: 77  LEIIAEAAEIIQELKPDIIDLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAIKKRVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D          + K +++SGV+ + +H R         K+       D+D 
Sbjct: 137 VTAKIRIGWDSTSRN--YLEVSKILEESGVDALTVHGRT--------KEMAYTGFADWDA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK  N  + I  NG ++   +A   +    +DGV+IGR A  N  + + V +     
Sbjct: 187 IGEIK-VNRKIPIFGNGDIKSFQEANFKIDKYLLDGVLIGRNAIGNPWIFSGVKK----- 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                   + V     + +   + DY          L    +H++   +GF
Sbjct: 241 ---EELSWSEVLDVILQHLRWMIEDYGEE-----FGLVLFRKHLVKYLNGF 283


>gi|85703153|ref|ZP_01034257.1| tRNA-dihydrouridine synthase, putative [Roseovarius sp. 217]
 gi|85672081|gb|EAQ26938.1| tRNA-dihydrouridine synthase, putative [Roseovarius sp. 217]
          Length = 339

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 121/294 (41%), Gaps = 29/294 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M   TD  +R          L+ +EM+ +  +++       K  LGF  +   +  Q+ G
Sbjct: 18  MAGITDLPFRTVVAGF-GAGLVVSEMVASQEMVQAKPSARGKAELGFGIENTSV--QLAG 74

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVH----EGSFGACLMLNPDIVGDCIAAMC 112
            D   + EAA++V D G   I++N+GCP+ +V      G+ G+ LM + D     I A+ 
Sbjct: 75  CDPHWMAEAARVVADHGARIIDINMGCPAKKVVSAAGAGASGSALMRDLDHALRLIEAVV 134

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            A+ +PVT+K R+G D+     A   L K  + +GV  I +H R         +      
Sbjct: 135 GAVDVPVTLKTRLGWDEGCSNAA--ELAKRAEAAGVAMITVHGRT--------RCQFYRG 184

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             D+ ++ +I +   ++ +  NG +  ++ A + +   +  GVMIGR A     +L  V 
Sbjct: 185 AADWAMISDIAQAV-NIPVIANGDIVGVASACRAMAQSNAAGVMIGRGARGRPWLLAEVA 243

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               +      P    +         A +  Y          L+   +H+    
Sbjct: 244 AAMGHGTAPEVPRGAVLADLVAGHYEAMLGFY-----GRDLGLRVARKHLGWYM 292


>gi|258405203|ref|YP_003197945.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
 gi|257797430|gb|ACV68367.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
          Length = 328

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 65/325 (20%), Positives = 125/325 (38%), Gaps = 28/325 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             +TD  +R   R      + +TEMI    ++   +   ++L  +  + PL +Q+ GAD 
Sbjct: 25  AGFTDLPFRLLCRE-NGARVAHTEMISVKGLIYNSQGTWDLLATAPADTPLVVQLFGADP 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               +  + + + G++ I+LN GCP  +V +   GA LM +P  +   +  + +A  +  
Sbjct: 84  DCFAQPVRWLTERGFHWIDLNAGCPVRKVIKTGAGAALMEDPQRLVRIMQTIGRAAPVQA 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            VK R+  D       L  L  ++ ++GV+ I +H R A                 +  +
Sbjct: 144 GVKLRLPADG--STDGLLRLRDTLARAGVSWITLHPRTA--------RQGYGGLAQWSAL 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             + + +P + I  +G L +   A +      VDG+M  R A  N  +           L
Sbjct: 194 SRMAESSP-VPIVASGDLWNAQAARRCFEQTGVDGIMFARGALHNPRIFK-------ADL 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +      D      +         R+  S   L ++   +     GFP +++ R   
Sbjct: 246 ATGAEEDPCTDTASIAALVRRHGQLCRRYDPSRSMLLKMRSFIPRYVKGFPGAKQAR--- 302

Query: 298 TVEAGASTATHHIIETAFNLMIESL 322
             +   +       E   + + E+L
Sbjct: 303 --KGIIACQDWEAFEQYADQLEEAL 325


>gi|323452300|gb|EGB08174.1| hypothetical protein AURANDRAFT_12844 [Aureococcus anophagefferens]
          Length = 329

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 149/322 (46%), Gaps = 27/322 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M+  TDRH+R+ AR ++   LLYTEM+V +A+            LG    E P+A+Q+GG
Sbjct: 16  MMGVTDRHWRWMARQMSRKTLLYTEMVVDNALNHNAHNLGGTQFLGHDACEAPVAVQLGG 75

Query: 57  ADISKLVEAAKIVEDF---GYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAA-M 111
            D   L +AA +  D+      EINLN GCPS  V     FGA LML+P+ V   +   +
Sbjct: 76  NDAKALGDAAALCVDYFGDSCVEINLNCGCPSNVVAARNEFGARLMLDPEKVRGIVHELI 135

Query: 112 CKALSIPVTVKCRIGVD-DQIPAVALRNLVKSIKKSGVNGIWIHARKAIL-KGLSPKDNR 169
            +  S PVTVK R+G D            V++ + +G     +HAR+A+L K  S + NR
Sbjct: 136 RRCPSTPVTVKHRLGTDLSGSDYATTLAFVRASRAAGCRHFVLHAREAVLDKKFSTQQNR 195

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS------VDGVMIGRAAYKNS 223
            IP L  D+ + + ++ PD    +NG L  +      L        V   M+GRAA+   
Sbjct: 196 TIPPLKPDVAHRLARDLPDCTFAMNGMLRSLEDCAAHLSGWNGLPPVHSTMVGRAAWYQP 255

Query: 224 A-MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ-ITRHMI 281
             +L T D         S P  +R      R +  +  DYA     +    +  + R + 
Sbjct: 256 WDLLATADTALYG--AASDPAASR------RDVLEAYLDYADEQYAALDVAEDCLYRPLF 307

Query: 282 GLFHGFPNSRRCRHILTVEAGA 303
            LF G  NS++ R  L  E   
Sbjct: 308 YLFGGEQNSKKFRVRLADEVTR 329


>gi|153952282|ref|YP_001397382.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. doylei
           269.97]
 gi|152939728|gb|ABS44469.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. doylei
           269.97]
          Length = 308

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 59/300 (19%), Positives = 124/300 (41%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++    + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNKMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + +H R         +        DY
Sbjct: 133 SLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSVHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAS-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASAFR 285


>gi|157736711|ref|YP_001489394.1| tRNA-dihydrouridine synthase [Arcobacter butzleri RM4018]
 gi|315635883|ref|ZP_07891145.1| tRNA-dihydrouridine synthase B [Arcobacter butzleri JV22]
 gi|157698565|gb|ABV66725.1| probable tRNA-dihydrouridine synthase [Arcobacter butzleri RM4018]
 gi|315479862|gb|EFU70533.1| tRNA-dihydrouridine synthase B [Arcobacter butzleri JV22]
          Length = 309

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 134/304 (44%), Gaps = 34/304 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      L  +EMI ++A++    +   ++  S  E P  +QI G  +
Sbjct: 17  AGYTDLPFRSVVKKF-GADLTISEMISSNALVYKSARTLKMVEKSPTEDPYFVQIAGNSV 75

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +I+ D  G + I+LN GCP+ +V     G+ L+ +   + + ++ + K     
Sbjct: 76  DLVKAAVEILNDVEGIDGIDLNCGCPAPKVFNHGSGSNLLGDLKKLEEILSTVKKYSKKQ 135

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T  K R+GV+++IP      + K+++  GV+ + +H R         +  +    +DYD
Sbjct: 136 YTSAKVRLGVNEKIPV----EIGKAVEACGVDFVSVHGRT--------RAGKYKAPVDYD 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + ++K+    + +  NG ++D ++A ++L     +GVMIGR A     +   +      
Sbjct: 184 AIKQMKEAI-SIPVIANGDIKDYAKAKEVLEYTKANGVMIGRGAIGKPWVFYQLKH---- 238

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCR 294
              G   I   + K+   +   SM ++   H         + R ++     G+  +   R
Sbjct: 239 ---GIEDISNEMKKEIILEHFDSMINFHGNHGA------IMFRKLLHSYSKGYTGANEFR 289

Query: 295 HILT 298
            I+ 
Sbjct: 290 DIVN 293


>gi|301100330|ref|XP_002899255.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262104172|gb|EEY62224.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 377

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/326 (22%), Positives = 132/326 (40%), Gaps = 34/326 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R L      YT M+ +       +    +     Q++PL +Q  G D
Sbjct: 31  MVDQSELAFRMLCRKL-GADCCYTPMLHSRLFAESAEYREKMFEHHIQDRPLVVQFCGND 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ AAK+VE    + ++LN+GCP     +G +G+ LM + + V   +  +   L+IP
Sbjct: 90  PKTVLAAAKMVEGH-CDAVDLNLGCPQGIARKGHYGSFLMHDKETVKATVKTLSAGLNIP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+  DD             ++++G + + +H R   +   + ++      +++DI
Sbjct: 149 VTVKIRVFPDDN----ETLEFADMLQEAGCDLLTVHGRTKEMNKTAVRE------VNWDI 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK E   + +  NGG+E      + L     DGVM      +N A+           
Sbjct: 199 IRRIK-ERLTIPVIANGGIETHEDIARCLEATGCDGVMSSEGLLENPALFAD-------- 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG-LFHGFPNSRRCRH 295
            T ++P +     +  R+     T Y           + +  H+   LF         R 
Sbjct: 250 -TNNTPGEDTSFLELARQYLECATLYPPASD------KIVRAHLFKILFQDLRVHSDLRD 302

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L   A +      I++     + E+
Sbjct: 303 ALAA-AKSQQEMVEIVDELAVRLKEA 327


>gi|195443038|ref|XP_002069246.1| GK21069 [Drosophila willistoni]
 gi|194165331|gb|EDW80232.1| GK21069 [Drosophila willistoni]
          Length = 519

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 123/305 (40%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 37  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFANDVKYRKDALQTCAEDRPLIIQFCGND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA + +    + I++N+GCP A    G +G+ L    +++   ++ + + LSIP
Sbjct: 96  SQQILEAALLAQGH-CDAIDINLGCPQAIAKRGHYGSFLQDEWELLEKIVSTLHEKLSIP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            D+  
Sbjct: 155 VTCKIRIFEDREKT----IRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVADWSY 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  ++KE   + +  NG +  +    + L    VDGVM       N A+   +       
Sbjct: 205 IRSVRKEI-KIPMFANGNILGLEDVHRCLDTTGVDGVMSAEGNLHNPAIFRGI------- 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               SP   ++ K++   ++       Y   HL    KL     H++ +          R
Sbjct: 257 ----SPPVWQIAKEYLELVNQYPCPTSYIRGHL---FKLFH---HIMNINQN----AELR 302

Query: 295 HILTV 299
             L  
Sbjct: 303 EQLAT 307


>gi|24212707|ref|NP_710188.1| tRNA-dihydrouridine synthase [Leptospira interrogans serovar Lai
           str. 56601]
 gi|24193338|gb|AAN47206.1| tRNA-dihydrouridine synthase [Leptospira interrogans serovar Lai
           str. 56601]
          Length = 329

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 74/291 (25%), Positives = 128/291 (43%), Gaps = 29/291 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D   R   R     A  YTE +  D ++    K   +  + ++E+P+  QI G  
Sbjct: 18  MAGISDSPTRRICRKF-GAAFSYTEFVNTDELVHRAPKALKMFRYKSEERPITFQIFGNR 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I+++   + I+LN+GC + +V     GA L+  P + G  I A+ K ++IP
Sbjct: 77  LEIIAEAAEIIQELKPDIIDLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAIKKRVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D          + K +++SGV+ + +H R         K+       D+D 
Sbjct: 137 VTAKIRIGWDSTSRN--YLEVSKILEESGVDALTVHGRT--------KEMAYTGFADWDA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK  N  + I  NG ++   +A   +    +DGV+IGR A  N  + + V +     
Sbjct: 187 IGEIK-VNRKIPIFGNGDIKSFQEANFKIDKYLLDGVLIGRNAIGNPWIFSGVKK----- 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                   + V     + +   + DY          L    +H++   +G 
Sbjct: 241 ---EELSWSEVLDVILQHLRWMIEDYGEE-----FGLVLFRKHLVKYLNGL 283


>gi|198476736|ref|XP_002132430.1| GA25459 [Drosophila pseudoobscura pseudoobscura]
 gi|198137829|gb|EDY69832.1| GA25459 [Drosophila pseudoobscura pseudoobscura]
          Length = 507

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 123/305 (40%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 34  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFAHDPKYRKDALQTCPEDRPLIIQFCGND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ D +  + + LS+P
Sbjct: 93  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTDIVRTLHEKLSVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            D+  
Sbjct: 152 VTCKIRIFEDREKT----LRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVADWSY 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E++K    + +  NG +  +    + L    VDGVM       N A+           
Sbjct: 202 IQEVRKHL-KIPMFANGNILGLEDVHRCLDETGVDGVMTAEGNLHNPAIFQ--------- 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             G +P   +V K++   +        Y   HL    KL     H++ +          R
Sbjct: 252 --GLAPPVWQVAKEYLEFVDLYPCPSSYIRGHL---FKLFH---HIMNIRQN----SELR 299

Query: 295 HILTV 299
             L  
Sbjct: 300 DTLAT 304


>gi|300706178|ref|XP_002995385.1| hypothetical protein NCER_101742 [Nosema ceranae BRL01]
 gi|239604450|gb|EEQ81714.1| hypothetical protein NCER_101742 [Nosema ceranae BRL01]
          Length = 336

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 98/310 (31%), Positives = 164/310 (52%), Gaps = 20/310 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGGADI 59
           M+D T  ++R F RL + + +L+TE+IVA+ ++  DK+ ++      ++   +QIGG+D+
Sbjct: 22  MLDVTTANFRRFVRLTSEHTILFTELIVANTVIHIDKEKLIERLGDIDERTVVQIGGSDV 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           +++V A  +++D G    NLNVGCPS RV +G FGA LM N +++ + I ++ K   I +
Sbjct: 82  NEIVNAICVLKDVGCKHFNLNVGCPSTRVQKGCFGAVLMKNKELISEIINSVYKKCDIVL 141

Query: 120 TVKCRIGVDDQIPAVALRNLVK-SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++K R GVD+       R+ V   +K + V   ++HARK  L GLSPK NR IP L+Y  
Sbjct: 142 SLKIRTGVDNYDTYEFFRDFVHFLVKNTPVKKFYVHARKCWLLGLSPKQNRNIPPLNYSF 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS----VDGVMIGRAAYKNSAMLTTVDEYFS 234
           VY+IK+E P +   LNGGL+ ++   K+  +    +DG+MIGR A KN  +  + + Y  
Sbjct: 202 VYKIKEEFPHVLFILNGGLKKIADFNKLFCNNNLTLDGIMIGREAIKNILVFRSFENYLH 261

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                +              I + +  Y  +   S     +I   +  + HG   +++ +
Sbjct: 262 ESSQDT--------------IFSVVKKYLNKFELSKPITFRILNPLQNILHGQKGTKKWK 307

Query: 295 HILTVEAGAS 304
             L       
Sbjct: 308 IFLNESVHKK 317


>gi|224087931|ref|XP_002195720.1| PREDICTED: dihydrouridine synthase 3-like (S. cerevisiae)
           [Taeniopygia guttata]
          Length = 718

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 112/284 (39%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 385 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQSSEWALLKRHHTEDIFGVQLEGAFPDTMT 443

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +PVTVK
Sbjct: 444 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPVTVK 503

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  I++ G + + +H R         ++ R   + D+  + E 
Sbjct: 504 IRTGVQEKVNVA--HKLIPRIREWGASMVTLHGRS--------REQRYTRSADWHYIAEC 553

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A + +   V G+MI R A     + T + E     ++ S 
Sbjct: 554 ARLASPMPLFGNGDILSYEDANRAMQMGVSGIMIARGALIKPWLFTEIKEQRHWDISSSE 613

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                       +I    T+Y   H  S  +  + TR  +   L
Sbjct: 614 RF----------EILKDFTNYGLEHWGSDTQGVEKTRKFLLEWL 647


>gi|118103122|ref|XP_425899.2| PREDICTED: similar to Dihydrouridine synthase 3-like protein
           [Gallus gallus]
          Length = 660

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 110/284 (38%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 327 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQSSEWALLKRHHTEDIFGVQLEGAFPDTMT 385

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +P+TVK
Sbjct: 386 KCAELLNQTIDVDFVDINVGCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPLTVK 445

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       ++  I++ G + + +H R         ++ R     D+D + E 
Sbjct: 446 IRTGVQEKMNVA--HKIIPKIREWGASMVTLHGRS--------REQRYTRVADWDYIAEC 495

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 496 AKIASPMPLFGNGDILSYEDANQAMQTGVSGIMIARGALIKPWLFTEIKEQRHWDISSSE 555

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        I    T+Y   H  S  +  + TR  +   L
Sbjct: 556 RF----------DILRDFTNYGLEHWGSDTQGVEKTRKFLLEWL 589


>gi|195155541|ref|XP_002018662.1| GL25830 [Drosophila persimilis]
 gi|194114815|gb|EDW36858.1| GL25830 [Drosophila persimilis]
          Length = 507

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 123/305 (40%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 34  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFAHDPKYRKDALQTCPEDRPLIIQFCGND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ D +  + + LS+P
Sbjct: 93  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTDIVRTLHEKLSVP 151

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            D+  
Sbjct: 152 VTCKIRIFEDREKT----LRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVADWSY 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+++    + +  NG +  +    + L    VDGVM       N A+           
Sbjct: 202 IQEVRQHL-KIPMFANGNILGLEDVHRCLDETGVDGVMTAEGNLHNPAIFQ--------- 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             G +P   +V K++   +        Y   HL    KL     H++ +          R
Sbjct: 252 --GLAPPVWQVAKEYLEFVDLYPCPSSYIRGHL---FKLFH---HIMNIRQN----SELR 299

Query: 295 HILTV 299
             L  
Sbjct: 300 DTLAT 304


>gi|196000454|ref|XP_002110095.1| hypothetical protein TRIADDRAFT_21776 [Trichoplax adhaerens]
 gi|190588219|gb|EDV28261.1| hypothetical protein TRIADDRAFT_21776 [Trichoplax adhaerens]
          Length = 427

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 101/231 (43%), Gaps = 17/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ +   +R        F    +++PL +Q  G D
Sbjct: 18  MVDQSELAWRLLCRRY-GAQLCYTPMLHSAVFIRDATYRRENFKTCPEDRPLIVQFCGND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE    + ++LN+GCP A    G +GA L  +  ++   ++ + + L IP
Sbjct: 77  PDTLLKAAKIVEPH-CDAVDLNLGCPQAIAKRGHYGAFLQDDWKLLEKIVSHLHQNLKIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            + ++K+G   + +H R    K             D++ 
Sbjct: 136 VTCKIRIFNDLDKTV----KYAQLLEKAGCQLLTVHGRTREQK------KELTGLADWNF 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  + K++  + +  NG ++      +      VDG+M       N A+ +
Sbjct: 186 IK-VIKDSLSIPVFANGNIQYFEDLERCFTATGVDGIMSAEGILTNPALFS 235


>gi|326934323|ref|XP_003213240.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Meleagris
           gallopavo]
          Length = 667

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 110/284 (38%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 334 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQSSEWALLKRHHTEDVFGVQLEGAFPDTMT 392

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +P+TVK
Sbjct: 393 KCAELLNQTIDVDFVDINVGCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPLTVK 452

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       ++  I++ G + + +H R         ++ R     D+D + E 
Sbjct: 453 IRTGVQEKMNVA--HKIIPKIREWGASMVTLHGRS--------REQRYTRVADWDYIAEC 502

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 503 AKIASPMPLFGNGDILSYEDANQAMQTGVSGIMIARGALIKPWLFTEIKEQRHWDISSSE 562

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        I    T+Y   H  S  +  + TR  +   L
Sbjct: 563 RF----------DILKDFTNYGLEHWGSDTQGVEKTRKFLLEWL 596


>gi|217076849|ref|YP_002334565.1| NifR3 family protein [Thermosipho africanus TCF52B]
 gi|217036702|gb|ACJ75224.1| NifR3 family protein [Thermosipho africanus TCF52B]
          Length = 296

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 131/326 (40%), Gaps = 45/326 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M   T+  +R            YTEMI A++++R  K N   F    ++  +A+QI G+D
Sbjct: 10  MAGVTNWSFRKLCFGF-GAEFAYTEMISAESVIRNLKINEYYFPKPEEKDKVAIQIFGSD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA ++E+ G   I++N GCP  +V +   G+ L+ + + + + I  +  A+S  
Sbjct: 69  PFVMAKAASMLENMGA-WIDINAGCPVKKVVKKGAGSALLKDLNRLKNIIMQVKSAVSCK 127

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK RIG +          +  ++  +G + I +H R A                 ++I
Sbjct: 128 VSVKVRIGFEKD----EFEKIYDTVVDAGADMIAVHGRTAK--------QMYSGKATWNI 175

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                K    + + +NG +  +S A + +     DGV+I RA+     +           
Sbjct: 176 -----KNKGYIPLYINGDIHSLSDAKRAMEISKADGVLIARASIGKPWVFND-------- 222

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P  + + K     I    ++   R        Q+  + + G     PNSR+ R  
Sbjct: 223 ---KPPSLSEIKKIILYHIDLLYSEIGER------AAQEFRKFVAGYTKNLPNSRQFRAK 273

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           +             ++ AF   + S+
Sbjct: 274 VM-----KINDVETLKKAFEEYLTSI 294


>gi|83953578|ref|ZP_00962299.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. NAS-14.1]
 gi|83841523|gb|EAP80692.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. NAS-14.1]
          Length = 328

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 67/290 (23%), Positives = 118/290 (40%), Gaps = 25/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M   TD  +R          L+ +EM+ +  ++      +    LG   +    A+Q+ G
Sbjct: 19  MAGITDLPFRTLVASF-GAGLVVSEMVASVDMINARPGTLEKAELGLGVEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            + + + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+  A++
Sbjct: 76  REAAPMAEAARMVEGQGARVIDINMGCPAKKVTQGYSGSALMKTPDHALRLIEAVVNAVN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R+G DD +  +    +    + +G+  I IH R         +      + D+
Sbjct: 136 VPVTLKTRLGWDDNM--LNAPQIAARAEAAGITMITIHGRT--------RCQFYKGSADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  +K+    + +  NG +     A + L     DGVMIGR A     +L  V     
Sbjct: 186 AAIAGVKQAV-SVPVIANGDIISTDAARQALAQSGADGVMIGRGAQGKPWLLAQVAHDLF 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  P      +       A +  Y          L+   +H+    
Sbjct: 245 GAPAPVIPQGADFARMVSDHYEAIIRFY-----GEVIGLRVARKHLGWYM 289


>gi|145595944|ref|YP_001160241.1| nifR3 family TIM-barrel protein [Salinispora tropica CNB-440]
 gi|145305281|gb|ABP55863.1| putative TIM-barrel protein, nifR3 family [Salinispora tropica
           CNB-440]
          Length = 368

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 113/319 (35%), Gaps = 40/319 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EMI   A++  + K   ++ F + E P +LQ+ G D
Sbjct: 6   MAGITNVGFRQLCREQGG-GIYVCEMITTVALVERNPKTLRMIAFGSGESPRSLQLYGTD 64

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
                 A +IV +    + I+LN GCP  +V     GA L     +    + A   A S 
Sbjct: 65  PDTTAAAVRIVVERDLADHIDLNFGCPVPKVTRRGGGAALPWRRRLFARLVRAAVDAASP 124

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+DD    +       + + +G   + +H R A          R     
Sbjct: 125 AGVPVTVKMRKGIDDD--HLTYVEAGLAAQDAGAAAVALHGRTA--------AQRYSGTA 174

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG----------RAAYKNSA 224
           D+D +  +K    D+ +  NG + +   AL+        M+           R       
Sbjct: 175 DWDAIATLKTAL-DVPVLGNGDIWEADDALR--------MVAHTGVDGVVVGRGCLGRPW 225

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY--AARHLHSGGK--LQQITRHM 280
           +   ++  F+       P    V     R     +  +    R    G +       +H+
Sbjct: 226 LFADLEAAFTGSPHRRLPTLGEVATTMRRHAELLVEQFTVGGRDAARGERDGCTDFRKHV 285

Query: 281 IGLFHGFPNSRRCRHILTV 299
                GFP     R  L +
Sbjct: 286 AWYLKGFPVGSELRRALAM 304


>gi|283955568|ref|ZP_06373062.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           1336]
 gi|283792911|gb|EFC31686.1| tRNA-dihydrouridine synthase B [Campylobacter jejuni subsp. jejuni
           1336]
          Length = 305

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 60/300 (20%), Positives = 125/300 (41%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   +      +  +EMI ++A++    K   +L  +  E P  +QI G D
Sbjct: 14  MAGFSDLPFRNVVKKF-GADITISEMISSNALVYESSKTLHMLERAELENPYIVQIAGGD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L +A +++ +  + + I+ N GCP  +V +   G+ L+ N ++  + +  + +    
Sbjct: 73  KEVLKKAVQMLNEMDFVDGIDFNCGCPVNKVVKQCAGSALLENLELFKNLVGVIKENNKK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++ P      + K  +  GV+ + IH R         +        DY
Sbjct: 133 NLTSVKFRLGFNEKYP----EKMAKICESLGVDFVSIHGRT--------RKQLYSGKADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    K +  + +  NG + +   A ++      DG+MIGRA+  N  +   +     
Sbjct: 181 ESIAN-AKASVKIPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK---- 234

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                       VD+   ++I  +  D   +H +    +    +H+     G  ++   R
Sbjct: 235 --------SGKSVDEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLHEYSKGHKDASVFR 285


>gi|154175306|ref|YP_001408795.1| dihydrouridine synthase (Dus) superfamily protein [Campylobacter
           curvus 525.92]
 gi|112803746|gb|EAU01090.1| dihydrouridine synthase (Dus) superfamily [Campylobacter curvus
           525.92]
          Length = 307

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 68/304 (22%), Positives = 129/304 (42%), Gaps = 35/304 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGAD 58
             ++D   R   +      +  +EMI A+A++         +L  S  E P  +QI G+D
Sbjct: 15  AGFSDLPLRSVVKRF-GCDVTISEMISANALVYESGAKTLEMLKKSPNETPYIVQIAGSD 73

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           I  + +A  I+  F G + I+LN GCP  +V +   G+ L+ + + +   I A+ K  + 
Sbjct: 74  IENIKKAVAIINKFDGIDGIDLNCGCPVPKVVKQCAGSALLNDLENLKRIIEAIKKISNK 133

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            +T VK R+G +++       ++ K+ +++G + I IH R         +       +DY
Sbjct: 134 TMTSVKFRLGFNEKNQV----DIAKACEEAGADYIAIHGRT--------RAGGYSAKVDY 181

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + +  K +  + +  NG +     A +I  L S D +MIGRA+  +  + + +     
Sbjct: 182 EAIAQ-AKASVKIPVVANGDINS-QNASEILALTSCDALMIGRASIGSPWVFSEIKN--- 236

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                    K  V K+  ++I  +  D    H    G      +H+     G       R
Sbjct: 237 ---------KQGVSKELKKEIILAHFDAMLEHYGEHGA-NIFRKHLHQYSKGLDGGSAFR 286

Query: 295 HILT 298
           + + 
Sbjct: 287 NEIN 290


>gi|70929895|ref|XP_736939.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56511905|emb|CAH87272.1| hypothetical protein PC302401.00.0 [Plasmodium chabaudi chabaudi]
          Length = 265

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 82/197 (41%), Positives = 124/197 (62%), Gaps = 3/197 (1%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M++ T+RH+R   R+++    L+TEMIV + +L    + +  LGF+  E P+  Q+GG+D
Sbjct: 69  MINVTNRHFRALVRIISKKVQLWTEMIVDNTLLYNINNLEEHLGFNKNEHPIVCQLGGSD 128

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
            + L EAA ++E  GY+EIN+NVGCPS +V     FGA LM  P++V + +  + K + I
Sbjct: 129 PTSLSEAAVLIEQAGYDEININVGCPSTKVANKGAFGAYLMKKPELVKNIVYEIKKKVQI 188

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R GVDD      L++ ++++   G     IH+RKA LKGL PK NR +P L+Y+
Sbjct: 189 PVTVKIRTGVDDLDSFSFLKSFIETVSSVGCEHFIIHSRKAWLKGLDPKQNRSVPPLEYN 248

Query: 178 IVYEIKKENPDLFIGLN 194
            V+++ K  P+L   LN
Sbjct: 249 KVFDLCKLYPNLKFTLN 265


>gi|188582181|ref|YP_001925626.1| hypothetical protein Mpop_2936 [Methylobacterium populi BJ001]
 gi|179345679|gb|ACB81091.1| TIM-barrel protein, nifR3 family [Methylobacterium populi BJ001]
          Length = 342

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 62/284 (21%), Positives = 119/284 (41%), Gaps = 21/284 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISK 61
             TD H R  A+ L   + + +EM+ A  + +GD ++ +        P  +Q+ G   + 
Sbjct: 30  GVTDLHMRRLAQRL-GASAVVSEMVAAAELAKGDAESQVRAEGAGISPHVVQLAGCAPAP 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+++PVTV
Sbjct: 89  MAEAARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVAVPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    ++   +L    +  G+NG+ +H R         +        D+  +  
Sbjct: 149 KMRLGWD--HASLNAPDLACRAEALGLNGVTVHGRT--------RQQFYKGRADWSAIRA 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + +    + +  NG +  + +A   L      GVMIGRAA     ++  +    +     
Sbjct: 199 VVEAVG-IPVIANGDITSLDEARVCLRESGAAGVMIGRAAVGRPWLVGEIAAGLAGR--A 255

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
             P+          +    +         +   ++   +H+   
Sbjct: 256 VVPLSAEARAAAACEHYEGLIALY----GAAMGVRHARKHLAAY 295


>gi|319783399|ref|YP_004142875.1| hypothetical protein Mesci_3706 [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317169287|gb|ADV12825.1| TIM-barrel protein, nifR3 family [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 342

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 120/287 (41%), Gaps = 19/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADI 59
           M   TD  +R  A       L+ +EM+ +  + +G     L       P+ + Q+ G + 
Sbjct: 27  MSGITDEPFRQRAH-AHGAGLVVSEMVASGELAKGRAGFNLRIRHSGLPVHMVQLAGREA 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I    G + I++N+GCP+ +V  G  G+ LML+ D     I A+  A+ +PV
Sbjct: 86  VHMAEGARIAAGEGADIIDINMGCPAKKVTGGYAGSALMLDLDHALSLIDAVVGAVEVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D+   A+    L +  +++GV+ + +H R         +        D+  +
Sbjct: 146 TVKMRLGWDEG--ALNAPMLARRAEQAGVSMVTVHGRT--------RCQFYQGKADWRAI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG +   ++A  IL     D VMIGRA Y    +   +    +   
Sbjct: 196 ARVK-ETVSIPVVANGDVSSPAEAADILDQSGADAVMIGRAHYGAPWIAGGIAAAATGEA 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           T + P       D+       M             L+Q  +H+    
Sbjct: 255 TPNIPQNPTALADYIVAHYEDMLALYGAE----SGLRQARKHLGWYL 297


>gi|118399013|ref|XP_001031833.1| dihydrouridine synthase [Tetrahymena thermophila]
 gi|89286167|gb|EAR84170.1| dihydrouridine synthase [Tetrahymena thermophila SB210]
          Length = 444

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 105/232 (45%), Gaps = 18/232 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           MVD ++  +R   R      L YT MI +  +     G   ++     +++PL  Q  G 
Sbjct: 79  MVDQSELAFRMLCRKY-GTTLAYTPMIHSKVLQDQGYGYLNSVFSTCQEDRPLFAQFCGN 137

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   L+  A+ VED   + I++N GCP      G +G+ L+  PD +   +  + + LSI
Sbjct: 138 NPDALLAGARYVED-KCDAIDINFGCPQGIAKRGRYGSYLLSEPDTIVALVKKLHENLSI 196

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RI  + Q        L K I+ +G + + +H R          +   +   D+D
Sbjct: 197 PVTCKIRILPNRQ----QTIELAKKIEAAGCSILTVHGRTKEQ------NKDTVGLCDWD 246

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           I+  IK+E   + +  NGG+       K L    VDGVM   +  +N A+ +
Sbjct: 247 IIKIIKEEL-SIPVFANGGIYTYEDVQKCLEYTGVDGVMSAESLLENPALFS 297


>gi|320535329|ref|ZP_08035448.1| TIM-barrel protein, nifR3 family [Treponema phagedenis F0421]
 gi|320147829|gb|EFW39326.1| TIM-barrel protein, nifR3 family [Treponema phagedenis F0421]
          Length = 334

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 119/305 (39%), Gaps = 29/305 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R  A         YTEM+ ++A++R  +K   +   +  E+  A+QI G++ 
Sbjct: 27  AGYSDVTFRSVAVEW-GADFTYTEMVSSEAMVRDSQKTENLFKRAPNEQAYAVQIFGSNP 85

Query: 60  SKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
           + + E AK I+E    + I++N GCP  ++ +   G+ LM NP  +     A+  A+   
Sbjct: 86  NHMAETAKKILEKASPSCIDINAGCPMPKITKTGAGSALMRNPQNLYTVTKAVRDAVDTV 145

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              +PVTVK R G       +  ++  ++   +G   I IH R A               
Sbjct: 146 NISVPVTVKIRSGW--NTEHLTWKDAAQAAVDAGAAAITIHPRTA--------SQCYGGK 195

Query: 174 LDYDIVYEIKKENP--DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            D+ I+ ++ +      + +  +G L     A  +L     D VM  R A  N  +    
Sbjct: 196 ADWTILAQLAQMLHPQGISVFGSGDLFTPEDAKAMLEQTDCDAVMFARGAMGNPFIFKRT 255

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            E   +  + +     R  K  W ++         + L      +++ +       G   
Sbjct: 256 KELLLHG-SYADISFERKLKTGWDELL-----ILTQELGEERACKEMRKRFAAYTKGLEG 309

Query: 290 SRRCR 294
               R
Sbjct: 310 GAELR 314


>gi|303390009|ref|XP_003073236.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
 gi|303302381|gb|ADM11876.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
          Length = 357

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 105/338 (31%), Positives = 169/338 (50%), Gaps = 32/338 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL-GFSTQEKPLALQIGGADI 59
           M+D T  H+R   RL +++ +L+TEMIV++ ++   +  +       +    +QIGG+D 
Sbjct: 20  MMDVTTAHFRRLIRLTSSSTILFTEMIVSNTVIHISRDRLREKLGEYDDKTVVQIGGSDA 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++VEA KI++D GY   NLN GCPS+RV +GSFGA LMLN ++V + I  + K     +
Sbjct: 80  GQIVEAVKILQDLGYRMFNLNCGCPSSRVKKGSFGAVLMLNKELVAEIINKVYKETGEIL 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGV-NGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++K R+GVD+      L+  V  IK++      ++HARK  L+GLSP+ NRK+P LDYD 
Sbjct: 140 SLKIRVGVDNHEGIDFLKEFVGYIKENTPNRTFYVHARKCWLEGLSPEQNRKLPPLDYDS 199

Query: 179 VYEIKKENPDLFIGLNG--GLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           VY IK+  P+L I LNG  G+ ++ +       +DGVM+GR A ++  +   +D   S  
Sbjct: 200 VYMIKRLYPELKIVLNGCIGINNLDRIKD----LDGVMVGREAIRDILVFWDIDRKLSMK 255

Query: 237 LTGSSPIKTRVDKDFWRKI--SASMTDYAARHLHSGGKLQQITR---------------- 278
                         F   +      +D  A+   +  K++ + R                
Sbjct: 256 CDKGERRDCEELFPFDMDMKKIECRSDSEAKEWRA-QKIRSVVREYFEGFPPSDQLKSIH 314

Query: 279 --HMIGLFHGFPNSRRCRHILT---VEAGASTATHHII 311
              +I L  G    +  R  L    +E   +   + +I
Sbjct: 315 IQPIINLMRGKKGCKEYRRKLNSLLMERVKAGEAYGLI 352


>gi|224438190|ref|ZP_03659125.1| hypothetical protein HcinC1_09430 [Helicobacter cinaedi CCUG 18818]
 gi|313144635|ref|ZP_07806828.1| transcriptional regulator [Helicobacter cinaedi CCUG 18818]
 gi|313129666|gb|EFR47283.1| transcriptional regulator [Helicobacter cinaedi CCUG 18818]
          Length = 328

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 138/322 (42%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EMI + A++  +K+   +   S QE+P ++QI G+  
Sbjct: 14  AGYTDLPFRSVVKGF-GVDITVSEMISSHALVYSNKRTLKMTEKSPQEQPYSVQISGSKE 72

Query: 60  SKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +I+      + I+LN GCP+ +V     G+ L+ + +++      + +    P
Sbjct: 73  EVIKQAVEILNTQKDIDIIDLNCGCPAPKVANHGNGSGLLKDLNLLVKIANLIKENAKTP 132

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T +K R+G D +IP      + +++K    + + +H R          D  K   +DYD
Sbjct: 133 YTSLKVRLGFDKKIP----HEIAQALKDVKSDFVVVHGRTR-------ADGYKKEKIDYD 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  IK+  P + +  NG ++ + +A K+L     +GVMIGRAA  +  +   +      
Sbjct: 182 AIAYIKQNIP-MPLIANGEIDSVEKAQKVLEHTGANGVMIGRAAITSPWIFWQIK----- 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  I   V K+   +    M ++               +++     G   +   R+
Sbjct: 236 --NNTQEIPPIVKKELVLEHFHKMIEFYGERGAIM-----FRKNLHAYTKGHEGASEFRN 288

Query: 296 ILTVEAGASTATHHIIETAFNL 317
           ++   +     T H IE  F+ 
Sbjct: 289 LINSLSDVKQITQH-IENFFSH 309


>gi|24753769|gb|AAN64017.1|AF434658_14 NifR [Leptospira interrogans]
          Length = 329

 Score =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 74/291 (25%), Positives = 127/291 (43%), Gaps = 29/291 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   +D   R   R     A  YTE +  D ++    K   +  +  +E+P+  QI G  
Sbjct: 18  MAGISDSPTRRICRKF-GAAFSYTEFVNTDELVHRAPKALKMFRYKLEERPITFQIFGNR 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  + EAA+I+++   + I+LN+GC + +V     GA L+  P + G  I A+ K ++IP
Sbjct: 77  LEIIAEAAEIIQELKPDIIDLNMGCSTRKVSLRGAGAGLLRRPLLAGKIIEAIKKRVNIP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RIG D          + K +++SGV+ + +H R         K+       D+D 
Sbjct: 137 VTAKIRIGWDSTSRN--YLEVSKILEESGVDALTVHGRT--------KEMAYTGFADWDA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK  N  + I  NG ++   +A   +    +DGV+IGR A  N  + + V +     
Sbjct: 187 IGEIK-VNRKIPIFGNGDIKSFQEANFKIDKYLLDGVLIGRNAIGNPWIFSGVKK----- 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                   + V     + +   + DY          L    +H++   +G 
Sbjct: 241 ---EELSWSEVLAVILQHLRWMIEDYGEE-----FGLVLFRKHLVKYLNGL 283


>gi|254294026|ref|YP_003060049.1| dihydrouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042557|gb|ACT59352.1| dihydrouridine synthase DuS [Hirschia baltica ATCC 49814]
          Length = 337

 Score =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 75/285 (26%), Positives = 124/285 (43%), Gaps = 22/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           M   TD  +R  A       ++ TEMI    +  G +  +   +  E   P  +Q+ G D
Sbjct: 18  MSGATDAPFRRQASRF-GAPVVITEMIAGSELATGRQDMVWRITKPENTFPFVVQLAGRD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA+I    G + I++N+GCPS +V  G  GA LM + D+  + I A  +   +P
Sbjct: 77  PKWMYEAARISASAGADIIDINMGCPSRQVTGGQSGAALMRDLDLARELIIAAREGGGLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G DD    +    L K  ++  V  I +H R         +        D++ 
Sbjct: 137 VSVKMRLGWDDDT--LNAPALAKICEEEHVKLITVHGRT--------RCQFYTGKADWNK 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+K    +L + +NG ++    A +  +L   DGVMIGRAA     +L  +    +N 
Sbjct: 187 VKEVK-LASNLPLIVNGDIDSSKTAKQAILLSQADGVMIGRAALGRPWLLGKIASDLANR 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                P  +        ++S S+  Y  R       ++   +H+ 
Sbjct: 246 -PYIEPTWSEKLSSLCEQVSDSVLLYGDR-----LGVRVFRKHLA 284


>gi|46447621|ref|YP_008986.1| hypothetical protein pc1987 [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46401262|emb|CAF24711.1| conserved hypothetical protein [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 297

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 127/293 (43%), Gaps = 27/293 (9%)

Query: 26  MIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+  DA++R D     IL ++    P+  Q+ G+  S   +AAKI+E+ G++ ++LN GC
Sbjct: 1   MVKMDALIRHDPHTYHILDYAANMHPIGGQLCGSKPSIAGQAAKIIEELGFDIVDLNCGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P  ++ +   G+ L+  P+++G+ +  M  A+ IPVTVK R G D+Q   + + N+V+ +
Sbjct: 61  PVDKITKDGSGSGLLKTPELIGEIVCNMVSAVKIPVTVKIRAGWDEQQ--IQVENIVQIV 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +++G   I IH R         +        +++ +   K     + I  NG + D   A
Sbjct: 119 EQAGAQAICIHGRT--------RQQGYRGPANWEYIKRGKLAAKSIKIIGNGDVLDGPSA 170

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
            K+      D V++ R       ++  +  Y          ++    +  ++    ++  
Sbjct: 171 AKMFCETGCDAVLVARGTLGQPWIVQDILRYLEGKTAICHSLED-CRQALYQHFLETL-- 227

Query: 262 YAARHLHSGGKL-QQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
               H H   ++   + R           +R  R +++       +   +I+ 
Sbjct: 228 ----HYHPDQRVCIDMRRVGCWYLKKSSGTRLFRELIS-----KASDVEVIKN 271


>gi|257456062|ref|ZP_05621265.1| tRNA-dihydrouridine synthase B [Treponema vincentii ATCC 35580]
 gi|257446520|gb|EEV21560.1| tRNA-dihydrouridine synthase B [Treponema vincentii ATCC 35580]
          Length = 340

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 62/307 (20%), Positives = 117/307 (38%), Gaps = 28/307 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++DR +R    +       YTEM+ ++A +R   K   ++  +  E+  A+QI GA+ 
Sbjct: 34  AGYSDRSFRSVC-VDWGADFTYTEMVSSEAYIRNSVKTEKLIARAYNEQRYAVQIFGANP 92

Query: 60  SKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-----CK 113
             + E A +I+E +  + I++N GCP  ++ +   G+ LM  P+ +   + A+       
Sbjct: 93  DYMAETAVRIIERYRPDCIDINAGCPMPKITKTGAGSALMRKPERLYAVVKAVAEAAGKT 152

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +  IPVTVK R G       +  +    +  ++G   + IH R                 
Sbjct: 153 SSGIPVTVKIRSGWSQTE--LTWKEAADAAVEAGAAALTIHPRTC--------SQCYSGA 202

Query: 174 LDYDIVYEIKK-ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
            D+DI+ ++ +     + +  +G L     A  +L      GVM  R A  N  +     
Sbjct: 203 ADWDILAQLVQMMRGRVPVFGSGDLFSPQAAQDMLASTQCAGVMFARGAMGNPFIFRQTK 262

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           E             T +  +   + +    D     +      +++ +       G    
Sbjct: 263 ELLQTGAY------TGILPEDKIRTAKKELDLLCEEVGEQIACREMRKRFAAYTKGIAGG 316

Query: 291 RRCRHIL 297
            R R  L
Sbjct: 317 ARLREQL 323


>gi|160902971|ref|YP_001568552.1| dihydrouridine synthase DuS [Petrotoga mobilis SJ95]
 gi|160360615|gb|ABX32229.1| dihydrouridine synthase DuS [Petrotoga mobilis SJ95]
          Length = 301

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 64/300 (21%), Positives = 130/300 (43%), Gaps = 31/300 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           M D+TD  +R   R        +TEMI  D+I+R ++K   +     E  + +Q+ G + 
Sbjct: 11  MADYTDYPFREICRRF-GAKFTFTEMISVDSIIRENEKVEKMLPQKGEDNIGVQLFGNET 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           +K +EAAK ++    + I++N  CP  +V +   GA L+ NP ++GD +  + K++ +PV
Sbjct: 70  TKFIEAAKSIQHL-ASWIDINAACPVNKVVKKGSGAALLKNPKLLGDIVFNLKKSIDLPV 128

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            VK R+G D     + +  + ++++K+G + I +H R         +        + +I+
Sbjct: 129 GVKVRLGYDQ----INIEEVAETVEKAGADYIIVHGRT--------RSQMYSGIANREIL 176

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K +   + +G +G +         L     D V++ R A  N  + T          
Sbjct: 177 KKLKAKIT-IPLGASGDVFSKKDIDDYLLNYGADFVLVARGAIGNPWIFTK--------- 226

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +P            +   +  Y +        +++  + ++  F G   ++  R  L
Sbjct: 227 NNYNPTIDERIDTCLEHLKLMIEFYGSEVYA----VKKFRKVLMKYFSGIEGAKEIRRNL 282


>gi|83942358|ref|ZP_00954819.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. EE-36]
 gi|83846451|gb|EAP84327.1| tRNA-dihydrouridine synthase, putative [Sulfitobacter sp. EE-36]
          Length = 328

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 119/290 (41%), Gaps = 25/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           M   TD  +R          L+ +EM+ +  ++      +    LG   +    A+Q+ G
Sbjct: 19  MAGITDLPFRTLVASF-GAGLVVSEMVASVDMINARPGTLEKAELGLGVEGT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            + + + EAA++VE  G   I++N+GCP+ +V +G  G+ LM  PD     I A+  A++
Sbjct: 76  REAAPMAEAARMVEGQGARVIDINMGCPAKKVTQGYSGSALMKTPDHALRLIEAVVNAVN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R+G DD +  +    +    + +G+  I IH R         +      + D+
Sbjct: 136 VPVTLKTRLGWDDNM--LNAPQIAARAEAAGITMITIHGRT--------RCQFYKGSADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  +K+    + +  NG +     A + L     DGVMIGR A     +L  V     
Sbjct: 186 AAIAGVKQAV-SVPVIANGDIISTDAARQALAQSGADGVMIGRGAQGKPWLLAQVAYDLF 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  P  T   +       A +  Y          L+   +H+    
Sbjct: 245 GAPAPVIPQGTDFARMVSDHYEAIIRFY-----GEVIGLRVARKHLGWYM 289


>gi|291276558|ref|YP_003516330.1| putative Dihydrouridine synthase [Helicobacter mustelae 12198]
 gi|290963752|emb|CBG39587.1| putative Dihydrouridine synthase [Helicobacter mustelae 12198]
          Length = 327

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 73/326 (22%), Positives = 137/326 (42%), Gaps = 36/326 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EMI + A++    K   +L  S QE P A+QI G+ I
Sbjct: 13  AGYTDLPFRSVVKQF-GVDITVSEMISSHALVYQSAKTLKMLCKSPQESPYAVQISGSKI 71

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A + + +  G + I+ N GCP+ +V     G+ L+ N  ++   +  + +  + P
Sbjct: 72  EIIKQAVERINEIDGIDIIDFNCGCPAPKVANHGNGSGLLKNLSLLVKLLNTIKETSNKP 131

Query: 119 V-TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             +VK R+G D +IP      +  ++K + V+ + +H R          D  K   +DY+
Sbjct: 132 YSSVKVRLGFDQKIP----EEIANALKDANVDYVVVHGRTR-------SDGYKKERIDYE 180

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +IK+      +  NG + D + A ++L     +G+MIGRAA     +   +     N
Sbjct: 181 SIAKIKQILSA-PVIANGEITDYASARRVLEITGANGLMIGRAAISTPWIFWQIK----N 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             T   PI   + K+   K   +M  +   H    G +    +++     G   +   R 
Sbjct: 236 KTTEIPPI---IKKELVLKHFDAMVGFYGEH----GAIL-FRKNLHAYAKGHQGASEYRD 287

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
           I+            I+  +     E 
Sbjct: 288 IVN-----KIIDPKIMRESIEHFFEK 308


>gi|222823251|ref|YP_002574824.1| tRNA-dihydrouridine synthase B [Campylobacter lari RM2100]
 gi|222538472|gb|ACM63573.1| tRNA-dihydrouridine synthase B [Campylobacter lari RM2100]
          Length = 308

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 129/299 (43%), Gaps = 32/299 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M  ++D   R   +      +  +EMI ++A++    K   +L  +  E P  +QI G+D
Sbjct: 14  MAGFSDLPLRNLVKQF-GADITISEMISSNALVYESSKTLKMLEKAELENPYIVQIAGSD 72

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            S + +A +I+  F + + I+ N GCP  +V +   G+ L+ + D +   +  + K  + 
Sbjct: 73  ESVICKAVEILNRFDFIDGIDFNCGCPVNKVIKQCAGSALLQDLDKLQRILELIKKTSNK 132

Query: 118 PVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             T VK R+G D + P      + K+ + +GV+ I +H R         +      N DY
Sbjct: 133 KSTSVKVRLGFDKKDPIA----IAKACENAGVDFISMHGRT--------RKQMYSGNADY 180

Query: 177 DIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + +  + KEN  + +  NG + ED ++ +  + + D +MIGRA+     +   +      
Sbjct: 181 EAIA-LAKENIKIPLVANGDISEDNAKEVFKITNCDALMIGRASVGKPWIFYEIK----- 234

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             TG    K   +K  +      +  Y  +       +    +H+     G+ ++   R
Sbjct: 235 --TGKKIEKAMKNKIIFAHFEEMLKHYKEQ------GISIFRKHLHEYSKGYDDASNFR 285


>gi|298253423|ref|ZP_06977215.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis 5-1]
 gi|297532818|gb|EFH71704.1| tRNA-dihydrouridine synthase [Gardnerella vaginalis 5-1]
          Length = 336

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 61/282 (21%), Positives = 107/282 (37%), Gaps = 22/282 (7%)

Query: 26  MIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVG 82
           MI A A++  + K   +  F+  EK  +LQ+ G + S + +AA+IV D    + ++LN G
Sbjct: 1   MITARALVARNPKALRLCRFAPSEKVRSLQLYGVNPSIVEQAAQIVVDENMADHVDLNFG 60

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGVDDQIPAVALRNL 139
           CP  +V     G+ L    D++ + +  +        IPVT K R+G+D+          
Sbjct: 61  CPVPKVTRRGGGSALPWKTDLLQEILHRVVSVCEPAGIPVTAKFRVGIDE--NHETFIQA 118

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
               ++ G   + +HAR                + D+  + E+  E  D+ +  NG +  
Sbjct: 119 GHIAQEEGCAAVTLHARTT--------AEYYGGHSDWTRIGELV-EALDIPVFGNGDIWG 169

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              AL +       GV IGR       +   +           +P  T V     R +  
Sbjct: 170 AEDALAMFKETGCAGVAIGRGCQGRPWLFADIRNACEGSDNRVNPTLTEVGSVILRHLKL 229

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
            +  Y      +   +  + +H+     GFP     R     
Sbjct: 230 LVEFYDGDERMA---VHDLRKHVAWYLKGFPVGGGTRKAFME 268


>gi|242013989|ref|XP_002427681.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212512111|gb|EEB14943.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 557

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 122/286 (42%), Gaps = 29/286 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM +A ++L+G K    ++     E    +Q+ G +   + 
Sbjct: 221 NLPFRRICKEF-GADITCSEMAMATSLLQGLKYEWALIKRHESEDLFGIQLCGNNPFVMT 279

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++E+    + I++N+GCP   V++   G+ L+    ++   I +M K +S+P+TVK
Sbjct: 280 KCAQLLEESTNVDYIDINLGCPIDLVYQKGGGSGLLRREKVLESVIKSMSKVMSLPLTVK 339

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV           L+     SGV+ I +H R         ++ R     D++ + E 
Sbjct: 340 TRTGVYADKNVA--HRLIPMFVDSGVSLITVHGRS--------REQRYTRTADWNYINEC 389

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            K    + +  NG +   ED ++ALK   +V GVM+GR A     +   + E  +  ++ 
Sbjct: 390 GKAASPIPVFGNGDVLSFEDYNRALKENNNVSGVMVGRGALYKPWIFKEIKEQKNWDISS 449

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
           S              I     +Y   H  S     ++TR      L
Sbjct: 450 SERF----------DIIKKFVNYGLDHWGSDTMGVELTRKFTLEWL 485


>gi|220919018|ref|YP_002494322.1| TIM-barrel protein, nifR3 family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219956872|gb|ACL67256.1| TIM-barrel protein, nifR3 family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 348

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 54/304 (17%), Positives = 109/304 (35%), Gaps = 22/304 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R +   +  YTEM+ A  ++ G     + L     E P A+QI  ++ 
Sbjct: 18  AGVSDRPFRAICRRM-GASFAYTEMVSAHGLMHGALQTSSYLDREPDEDPFAVQIFASEP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   A +    G   I++N+ CP  +V     GA +  +P  V + + A+  A+ +PV
Sbjct: 77  EVLARGAAVAVAAGAGMIDVNMACPVKKVCGSGAGAAMGRDPRRVEEAVRAIRAAVPVPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D+                +    +    R  +  G             +++V
Sbjct: 137 TVKIRAGWDEGEVNCVDVARAAEAGGAAAVALHGRTRSQLYSG----------KARWELV 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  +G +   + A+++      D V++ R A  N  +   +    +   
Sbjct: 187 RAVKQAV-AIPVLGSGDVWTAADAVRMREETGCDAVLVARGACGNPWIFRELRAIEAGRP 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAAR------HLHSGGKLQQITRHMIGLFHGFPNSR 291
               P +          +   +   A               ++++ +H++    G     
Sbjct: 246 PPPPPGRDEWVGTVLEHVRLQVEHRARMAPGEPAEASERHAIRELRKHLLWYTRGRRGGV 305

Query: 292 RCRH 295
             R 
Sbjct: 306 HFRR 309


>gi|56751238|ref|YP_171939.1| nitrogen regulation protein NifR3-like protein [Synechococcus
           elongatus PCC 6301]
 gi|81299094|ref|YP_399302.1| dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus
           elongatus PCC 7942]
 gi|56686197|dbj|BAD79419.1| nitrogen regulation protein NifR3 homolog [Synechococcus elongatus
           PCC 6301]
 gi|81167975|gb|ABB56315.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Synechococcus
           elongatus PCC 7942]
          Length = 334

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 128/320 (40%), Gaps = 24/320 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISK 61
              +DR +R   R     +L++ EM  A   L G  ++   F   E+P+  Q+ G   + 
Sbjct: 36  AGVSDRSFRQLVRRSAPQSLIFAEMAHAGLQLAG--RDRWEFLPHEQPIGAQLFGDQPAT 93

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L  AA+  E  G   I+LN+GCP ++V     G+ L+  P++    + A+  A+SIPVTV
Sbjct: 94  LAAAAQQAEAAGAVCIDLNMGCPVSKVTRKRGGSALLREPELAIAIVQAVAAAVSIPVTV 153

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G +     V + +  + ++ +G   + +H R         +        D++ +  
Sbjct: 154 KTRLGWEQ----VTILDFAQQLEAAGAQLLTLHGRS--------RSQGYSGQADWNWITR 201

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K     + +  NG +   + A+  L     DGVM GR +  N  ++  +D         
Sbjct: 202 VKSRL-SIPVIANGDINSPADAIACLQQTGADGVMCGRGSLGNPGLVGAIDRSLKTGEQT 260

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                    +     +     D  A        L Q  +H+       P+ +  R  L  
Sbjct: 261 PELELRDRLQLAREHLLLLWEDKGAA------GLLQARKHLGWYLADQPDYQDLRQHLLR 314

Query: 300 EAGASTATHHIIETAFNLMI 319
               S +   +++ A   ++
Sbjct: 315 SEDLSQS-LDLLDAAIASVV 333


>gi|154248321|ref|YP_001419279.1| nifR3 family TIM-barrel protein [Xanthobacter autotrophicus Py2]
 gi|154162406|gb|ABS69622.1| putative TIM-barrel protein, nifR3 family [Xanthobacter
           autotrophicus Py2]
          Length = 345

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 75/285 (26%), Positives = 123/285 (43%), Gaps = 20/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD   R  A       L+ +EM+ ++A+L G  + +L    +  PL A+QI G D 
Sbjct: 28  MAGITDAPVRRMAVRY-GAGLVISEMVASEALLEGHPEMVLRAEGEGVPLHAVQIAGNDP 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA++ E  G   I++N+GCP+ RV  G+ GA L+ +  +    + A+  A+SIPV
Sbjct: 87  YLMGEAARVAEAAGAGIIDINMGCPAKRVTTGAAGAALLRDLPLAQAILEAVRGAVSIPV 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G DD        +L +  ++SG+  + IH R         +        D+  +
Sbjct: 147 TVKTRLGWDDTASTAV--DLARMAQESGLAMVTIHGRT--------RCQFYTGRADWTAI 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K +   + +  NG +   S    IL     DGVMIGR A         V    +   
Sbjct: 197 RAVK-DAVSIPVIANGDVTAPSDGPAILDASGADGVMIGRGAQGRPWFPGRVARAIAGQH 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             + P     D D    +   + +           ++Q  +H+  
Sbjct: 256 DTADP-----DLDEQHAVLLELYEGWLELYGRALGVRQARKHVGW 295


>gi|197124236|ref|YP_002136187.1| hypothetical protein AnaeK_3847 [Anaeromyxobacter sp. K]
 gi|196174085|gb|ACG75058.1| TIM-barrel protein, nifR3 family [Anaeromyxobacter sp. K]
          Length = 348

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 54/304 (17%), Positives = 108/304 (35%), Gaps = 22/304 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R +   +  YTEM+ A  ++ G     + L     E P A+QI  ++ 
Sbjct: 18  AGVSDRPFRAICRRM-GASFAYTEMVSAHGLMHGALQTSSYLDREPDEDPFAVQIFASEP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   A +    G   I++N+ CP  +V     GA +   P  V + + A+  A+ +PV
Sbjct: 77  EVLARGAAVAVAAGAGMIDVNMACPVKKVCGSGAGAAMGREPRRVEEAVRAIRAAVPVPV 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D+                +    +    R  +  G             +++V
Sbjct: 137 TVKIRAGWDEGEVNCVDVARAAEAGGAAAVALHGRTRSQLYSG----------KARWELV 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  +G +   + A+++      D V++ R A  N  +   +    +   
Sbjct: 187 RAVKQAV-AIPVLGSGDVWTAADAVRMREETGCDAVLVARGACGNPWIFRELRAIEAGRP 245

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAAR------HLHSGGKLQQITRHMIGLFHGFPNSR 291
               P +          +   +   A               ++++ +H++    G     
Sbjct: 246 PPPPPGRDEWVATVLEHVRLQVEHRARMAPGEPAEASERHAIRELRKHLLWYTRGRRGGV 305

Query: 292 RCRH 295
             R 
Sbjct: 306 HFRR 309


>gi|260459491|ref|ZP_05807746.1| TIM-barrel protein, nifR3 family [Mesorhizobium opportunistum
           WSM2075]
 gi|259035045|gb|EEW36301.1| TIM-barrel protein, nifR3 family [Mesorhizobium opportunistum
           WSM2075]
          Length = 340

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 120/287 (41%), Gaps = 19/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADI 59
           M   TD+ +R  A       L+ +EM+ +  + +G     L       P+ + Q+ G + 
Sbjct: 27  MSGITDQPFRQRAH-AHGAGLVVSEMVASGELAKGRAGFDLRIRHSGLPVHMVQLAGREA 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I    G + I++N+GCP+ +V  G  G+ LML+ D     I A+  A+ +PV
Sbjct: 86  IHMAEGARIAAGEGADIIDINMGCPAKKVTGGYAGSALMLDLDHALSLIEAVVGAVKVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D+   A+    L +  +++GV+ + +H R         +        D+  +
Sbjct: 146 TVKMRLGWDEG--ALNAPTLARRAEQAGVSMVTVHGRT--------RCQFYQGKADWRAI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG +   ++A  IL     D VM+GRA Y    +   +    +  +
Sbjct: 196 ARVK-EAVSIPVVANGDVCSPAEAAAILDQSGADAVMVGRAHYGAPWIAGGIAAAAAGEM 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               P       D+       M             L+Q  +H+    
Sbjct: 255 AVGVPQDPTALADYVVAHYEDMLALYGVE----SGLRQARKHLGWYL 297


>gi|116333187|ref|YP_794714.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
 gi|116098534|gb|ABJ63683.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
          Length = 340

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 129/327 (39%), Gaps = 23/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   +      L+  EMI    I   +++   ++  + QE P+++QI G  
Sbjct: 22  MAGVTNVAFRMICKAF-GAGLVECEMISGQGIHYHNQRTLRMMAVNAQEHPMSIQIFGGT 80

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AA+ V +    + I++N+GCP  +V     GA  +L+P  V D +AA+  A+  
Sbjct: 81  QETLVQAAQFVDQQTAADIIDINMGCPVNKVVNTDAGAKWLLDPQKVHDMVAAVVAAVKK 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R G DD         L      +    +    RK + +G            D+ 
Sbjct: 141 PVTVKMRTGWDDHHIFAVDNALAAQRAGAAAVAMHGRTRKQMYQG----------QADWQ 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+ E+ +     F+G NG +     A ++L     D VMIGRA   N  +L  ++ Y + 
Sbjct: 191 ILAEVAQHLTIPFMG-NGDVRTPQDAQRMLNEVGADAVMIGRAVMGNPWLLQRINHYLAT 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P            +                  +     +     G P++ R + 
Sbjct: 250 DELLAEPTPQEKTTIALEHLHKLCVAKGPVE-----GPRDFRNQVAYYLKGIPHTARTKV 304

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            +T +A      H ++      M  ++
Sbjct: 305 AIT-DATEEAVMHDLLVKFLERMTATI 330


>gi|325295522|ref|YP_004282036.1| dihydrouridine synthase DuS [Desulfurobacterium thermolithotrophum
           DSM 11699]
 gi|325065970|gb|ADY73977.1| dihydrouridine synthase DuS [Desulfurobacterium thermolithotrophum
           DSM 11699]
          Length = 310

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 132/299 (44%), Gaps = 30/299 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADIS 60
             +T   +R   + L  +   Y+E++ A  I+  G++K +  F+ +E+P+ LQ+ G +  
Sbjct: 15  AGYTHSAFRRLCKRLGAHR-TYSELMNATGIIYKGEEKELAYFTDEERPIHLQVYGRNPE 73

Query: 61  KLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---LS 116
           ++ EAA KI E +    I++N GC   +V +      L+  P  +G  +AA  KA   L+
Sbjct: 74  EIAEAARKIAEKYKPEAIDINFGCSVKKVLKAKAAGYLLQFPKEMGKIVAATAKALKPLN 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+G  +      L  + + + K+ V+ I +H R A  +G S        N ++
Sbjct: 134 VPVTAKIRLGFYED----TLEEIAEELLKANVSAIALHPRTAK-QGFS-------GNANW 181

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + V ++KK   D  I  +G +    +  +       DGVMIGRAA  N  +     E   
Sbjct: 182 ERVKDLKKIAGDTPIIGSGDIRSWKEIDQKFEETGCDGVMIGRAALANPWIFKEFKE--- 238

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                   ++ +   +F  +    M ++  +        + I   +  +F G     + 
Sbjct: 239 ---KKDIEVRLKERIEFILRELQLMWEFFEKERA----CKVIKSQISQIFKGIRGKAKL 290


>gi|301167381|emb|CBW26963.1| tRNA-dihydrouridine synthase [Bacteriovorax marinus SJ]
          Length = 363

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 66/297 (22%), Positives = 127/297 (42%), Gaps = 29/297 (9%)

Query: 8   HYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLVEA 65
            +R     L       +E+I    I  G++K   +L     EK + +Q+ G D   + +A
Sbjct: 50  PFRLLMEELGCGG-TVSELISCHGINYGNEKTIRMLSIHPDEKNIGIQLFGEDAESMAKA 108

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+  +     I++N+GCP  +V     G+ LM +   +G+    + KA+ +P+T+K R 
Sbjct: 109 AKVALESRPKFIDINMGCPVRKVVSKGSGSALMKDTSKLGNFFGTIKKAIDVPLTIKIRT 168

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G DD   ++    ++   K+ GV  + IH R    +             +++++ E+   
Sbjct: 169 GWDDD--SINANEIIHIAKEEGVEFVAIHGRTRTQQ--------YKGKANWELLEELAST 218

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT--VDEYFSNPLTGSS 241
           +P L I  NG L   S   K +     D  M+ R   ++  +     ++E  +   T S 
Sbjct: 219 SP-LPIIGNGDLHSASLVKKRMRNSKCDAFMLARGPLRDPFIFLESYIEEGENINFTPS- 276

Query: 242 PIKTRVDKDFWRKISASMTDYAARHL-HSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
                   D+W +I+  + +Y   +       L  + +HM+    G  N+   R+++
Sbjct: 277 --------DYW-EITNRLFEYNQMYTDRERTLLVMMRKHMVWFAAGLSNAANFRNMI 324


>gi|84684884|ref|ZP_01012784.1| tRNA-dihydrouridine synthase, putative [Maritimibacter alkaliphilus
           HTCC2654]
 gi|84667219|gb|EAQ13689.1| tRNA-dihydrouridine synthase, putative [Rhodobacterales bacterium
           HTCC2654]
          Length = 327

 Score =  203 bits (518), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 131/327 (40%), Gaps = 26/327 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   TD  +R          L+ +EM+ +  +++     +       +    A+Q+ G D
Sbjct: 20  MAGITDLPFRDLVSSF-GAGLVVSEMVASQEMVQAKPGTRERAELGIEVANTAVQLAGRD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ +V  G  G+ L+ +  +    I A+ +A+ +P
Sbjct: 79  PYWIGEAARMVEANGARMIDINMGCPAKKVVGGLSGSALLRDLPLALRLIEAVVEAVEVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G DD +       L    + +G+  I IH R         +        D+  
Sbjct: 139 VTLKTRLGWDDDLMNA--PTLAAQAEAAGIRMITIHGRT--------RCQFYKGRADWGA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +  D+ +  NG +     A   L     DGVM+GR       ++  +     + 
Sbjct: 189 IRAVK-DAVDIPVIANGDICSTPDARSALNASGADGVMVGRGTGGRPWLIAEIASELFDA 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSRRCR 294
                P    +         AS+  Y       G ++  I +H+       G P   R R
Sbjct: 248 PAPDVPEGAALIDMVQGHYEASLRFYGD---ALGKRV--IRKHLGWYMDEAGTPPDLR-R 301

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
            +L+    A      +I TA N   E+
Sbjct: 302 RVLSEPEPAR--VLDLIPTALNAAKEA 326


>gi|254561982|ref|YP_003069077.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens DM4]
 gi|254269260|emb|CAX25226.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens DM4]
          Length = 342

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 69/320 (21%), Positives = 132/320 (41%), Gaps = 29/320 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISK 61
             TD H R  A+ L   + + +EM+ A  + +GD ++ +        P  +Q+ G     
Sbjct: 30  GVTDLHMRRLAQRL-GASAVVSEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPEP 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + E A+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTV
Sbjct: 89  MAEGARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    ++    L +  +  G++G+ +H R         +        D+  +  
Sbjct: 149 KMRLGWD--HASLNAAELARRAEALGLDGVTVHGRT--------RQQFYKGRADWSAIRP 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   + +  NG +  + +A   L      GVM+GRAA     ++  +    +  +T 
Sbjct: 199 VV-EAVRIPVIANGDITGLEEARACLSQSGAAGVMVGRAAVGRPWLVGEIAAGLAGRVTA 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FHGF-PNSRRCRH 295
               + R        ++A           +   ++   +H+        G  P+ R  R 
Sbjct: 258 PLSAEQRA------AVAAEHYQGLIALYGAAMGVRHARKHLAAYADAAGGLTPDDR--RR 309

Query: 296 ILTVEAGASTATHHIIETAF 315
           ++T           +++ AF
Sbjct: 310 LVTT--HDPAEALRLLQRAF 327


>gi|149202616|ref|ZP_01879588.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseovarius sp.
           TM1035]
 gi|149143898|gb|EDM31932.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Roseovarius sp.
           TM1035]
          Length = 333

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 118/294 (40%), Gaps = 29/294 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M   TD  +R          L+ +EM+ +  +++       K  LG   +    A+Q+ G
Sbjct: 18  MAGITDLPFRNVVASF-GAGLVVSEMVASQEMVQAKPSARGKAELGLGAEST--AVQLAG 74

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVH----EGSFGACLMLNPDIVGDCIAAMC 112
            D   + EAA++V D G   I++N+GCP+ +V      G+ G+ LM +PD     I A+ 
Sbjct: 75  CDAQWMAEAARVVADHGARIIDINMGCPAKKVVSGSGSGASGSALMRDPDHALRLIEAVV 134

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            A+ +PVT+K R+G D     +    L +  + +GV  + +H R         +      
Sbjct: 135 GAVDVPVTLKMRLGWD--HDCLNAPELARRAESAGVAMVTVHGRT--------RCQFYTG 184

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
             D+  + +I     ++ + +NG + D + A K +      GVMIGR A     +L  V 
Sbjct: 185 AADWAAISDIV-AAVNIPVIVNGDIVDSATARKAVAQSGAAGVMIGRGARGRPWVLAEVA 243

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                      P    +         A +  Y          L+   +H+    
Sbjct: 244 AAMGQGAAPLVPQGAALADLVAGHYEAMLGFYGG-----DLGLRVARKHLGWYM 292


>gi|163760105|ref|ZP_02167188.1| probable tRNA-dihydrouridine synthase protein [Hoeflea
           phototrophica DFL-43]
 gi|162282504|gb|EDQ32792.1| probable tRNA-dihydrouridine synthase protein [Hoeflea
           phototrophica DFL-43]
          Length = 304

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 115/281 (40%), Gaps = 30/281 (10%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEA 65
             +R+         L+ TEM+ +  ++   +++ +        P  +Q+ G +   + +A
Sbjct: 1   MAWRY------GAGLVVTEMVASRELVTERRESQVRLRGDGINPHVVQLAGREADWMAKA 54

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I E  G   I++N+GCP+ +V  G  G+ LM +PD   + I A  KA+S+PVT+K R+
Sbjct: 55  ARIAEGEGAAMIDINMGCPAKKVTGGYSGSALMRDPDHALELIEATVKAVSVPVTLKMRL 114

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D       L  +    + +G+  I IH R  +             + D+  + ++ +E
Sbjct: 115 GWDHDNINAPL--IAARAEAAGIQMITIHGRTRM--------QFYEGSADWVAIAKV-RE 163

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              + +  NG +   +     L     D VMIGRA+     +   + E    P  GS   
Sbjct: 164 AVSVPLVANGDVASRADIEACLKHSGADAVMIGRASRGRPWICGDLAESDKAPAPGSQ-- 221

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    R I+         H      ++   +H+    
Sbjct: 222 --------QRAIAVEHYWMMIEHYGEDVGVRHARKHIGWYL 254


>gi|325188155|emb|CCA22696.1| tRNAdihydrouridine synthase putative [Albugo laibachii Nc14]
          Length = 367

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M  +       +     F    +++PL +Q  G D
Sbjct: 26  MVDQSELAFRMLCR-HHGAQLCYTPMFHSRLFAESQEYRTRMFEQHVRDRPLIVQFCGND 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V AAK VE    + +++N+GCP     +G++GA LM     V + +  +   +++P
Sbjct: 85  GDTMVAAAKYVEGH-CDAVDINLGCPQGIARKGNYGAFLMKEKTRVCEIVEKLVAEVAVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D+           + ++K+G + + IH R   +      +   +  +D++I
Sbjct: 144 VTCKIRVFPDE----AETIEFSRMLEKAGCDLLVIHGRTKEM------NKVTVGQVDWEI 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK     + +  NGG+E     +K L +   DGVM   A   N A+      + ++P
Sbjct: 194 IKRIK-STLSIPVIANGGIETADDIVKCLEATSADGVMSSEAILGNPALFDE--PFRNDP 250

Query: 237 LTGSSPIKTRVDKDFW 252
           L    P    + K++ 
Sbjct: 251 LDPKGPRYFDLAKEYM 266


>gi|15606718|ref|NP_214098.1| hypothetical protein aq_1598 [Aquifex aeolicus VF5]
 gi|39930814|sp|O67533|DUS_AQUAE RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|2983958|gb|AAC07506.1| hypothetical protein aq_1598 [Aquifex aeolicus VF5]
          Length = 316

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 78/321 (24%), Positives = 139/321 (43%), Gaps = 32/321 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M  +T   +R   R L      YTE+I A  +LR G    +  F+ +E+P+ +Q+ G++ 
Sbjct: 13  MASYTHSAFRRLCRRL-GADRTYTELISAVGVLRNGIPMKLAYFTEEERPIHIQVFGSNP 71

Query: 60  SKLVEA-AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            ++ +A   I ++   + I++N GC   +V        ++  P ++G+ +    +AL   
Sbjct: 72  EEIAQASVVIAKELKPDFIDINFGCSVPKVLRNKAAGYMLQCPPLMGEVVKETVEALKPY 131

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPV+ K R+G +       +  +V+ ++K+GV+ I IHAR A  +G S K         
Sbjct: 132 GIPVSAKIRLGFEKD----EVERIVEELQKAGVSLIAIHARTAK-QGFSGK-------AL 179

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  + E KK    + I  +G ++      ++      DGVM+GRAA  N  +     E  
Sbjct: 180 WHRIKEAKK-VASVPIIGSGDVKSWRDIERMFEETECDGVMVGRAALSNPWIFKEFKEKR 238

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              +            DF  +  + MT+Y +R         +I   ++ +  G PNSR  
Sbjct: 239 DIEVGLKE------RMDFILEELSMMTEYMSRE----KACAEIKSQIVQILKGVPNSREL 288

Query: 294 RHILTVEAGASTATHHIIETA 314
           +  +             IE A
Sbjct: 289 KTYIVHAENCKELVKR-IEEA 308


>gi|19074540|ref|NP_586046.1| similarity to HYPOTHETICAL PROTEINS YJBN_ECOLI and Y926_YEAST
           [Encephalitozoon cuniculi GB-M1]
 gi|19069182|emb|CAD25650.1| similarity to HYPOTHETICAL PROTEINS YJBN_ECOLI and Y926_YEAST
           [Encephalitozoon cuniculi GB-M1]
          Length = 357

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 104/320 (32%), Positives = 162/320 (50%), Gaps = 24/320 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGGADI 59
           M+D T  H+R F RL +   +L+TEMIV++ ++   +  +     + +    +QIGG+D 
Sbjct: 20  MMDVTTAHFRRFIRLTSEKTVLFTEMIVSNTVIHVPRDKLRERLGEYDDRTVVQIGGSDA 79

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + +VEA +I++  GY   NLN GCPS+RV +GSFGA LMLN ++V + I  +       +
Sbjct: 80  TSMVEAVRILQGLGYRMFNLNCGCPSSRVKKGSFGAVLMLNRELVAEIINRVYGETGAVL 139

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++K R GVD+      L   V  IKK +     ++HAR+  L+GLSP+ NRK P LDY  
Sbjct: 140 SLKIRTGVDEHDGVDFLDGFVSHIKKNTPTRTFYVHARRCWLEGLSPQQNRKAPPLDYAS 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS---- 234
           VY IK  +P+L I LNG +      L  + ++DGVMIGR A +N  +   ++   S    
Sbjct: 200 VYAIKSLHPELRIILNGSI--GEGNLDKIHNLDGVMIGRGAIRNVFVFWDIENRMSMCGA 257

Query: 235 ----------NPLTGSSPIKTRVDKDFW----RKISASMTDYAARHLHSGGKLQQI-TRH 279
                      P TG   I+    +D      RK+ + + +Y         +L+ I  + 
Sbjct: 258 ERRCKDGRECQPDTGIQKIECSDVEDHKSRRARKVLSVVKEYF-DWFSPSEQLKPIHVQP 316

Query: 280 MIGLFHGFPNSRRCRHILTV 299
           ++ L       +  R  L  
Sbjct: 317 VLNLMVAKRGCKAYRRRLNE 336


>gi|195114456|ref|XP_002001783.1| GI15082 [Drosophila mojavensis]
 gi|193912358|gb|EDW11225.1| GI15082 [Drosophila mojavensis]
          Length = 510

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 124/305 (40%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 30  MVDQSELAWRMLCRRY-GAQLCYSPMYHANLFATDLKYRKDALQTCPEDRPLIIQFCGND 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA   +D   + +++N+GCP A    G +G+ L    +++ D +  + + LS+P
Sbjct: 89  PQQILEAALAAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTDIVRTLHEKLSVP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R   D +          K ++ +G   + IH R    KG            D+  
Sbjct: 148 VTCKIRRFEDREKT----IQYAKMLEAAGCQLLTIHGRTREQKG------PLTGIADWSY 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ +E+  + +  NG +  +    + L    VDGVM       N A+   +       
Sbjct: 198 IKDV-REHIKIPMFANGNILGLDDVHRCLDETGVDGVMSAEGNLHNPAIFQGI------- 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               +P   ++ K++   +        Y   HL    KL     H++       ++ + R
Sbjct: 250 ----APPVWQMAKEYLEFVDQYPCPTSYIRGHL---FKLFH---HIMN----IRSNSQLR 295

Query: 295 HILTV 299
             L  
Sbjct: 296 EQLAT 300


>gi|149173427|ref|ZP_01852057.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
 gi|148847609|gb|EDL61942.1| predicted TIM-barrel enzyme, possibly dehydrogenase, nifR3 family
           protein [Planctomyces maris DSM 8797]
          Length = 355

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 137/325 (42%), Gaps = 40/325 (12%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +T   +R   R L    L  T++++A  +L G +K+  +L  S  ++PL +QI G   
Sbjct: 31  AGYTQHAFRVAIRELGGVGLCTTDLVLASHLLSGSRKSKALLTTSPADRPLTIQIFGGIT 90

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++LV AA+ +E  GY  ++LN+GCP A+++    GA +M  PD     +A +  A+SIPV
Sbjct: 91  AELVAAARWLEQHGYAAVDLNMGCPMAKINGNGGGARIMCAPDAACQLVAEVVDAVSIPV 150

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D       L  L +  +++GV  I +H R         ++      +D   +
Sbjct: 151 TVKMRLGWDRDSITAPL--LAREFEQAGVAAITVHGRT--------RNQGFGGTVDLQGI 200

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            +  +    + +  NG +  +  A ++      + V IGR A  +  +   + +   +  
Sbjct: 201 RQTVEAVQQIPVIGNGDVCTVEDAFRMREQTGCEAVSIGRGAMLDPWIFRKISQAVRDEP 260

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR------ 291
             + P +    +   R  S        +H   G +L  I +           +R      
Sbjct: 261 V-TEPTRDEQIQFLERHFSLMF----EQHELYGCRL--IRKFAAWY-----GARLGIPED 308

Query: 292 ---RCRHILTVEAGASTATHHIIET 313
              R R + + E         IIE 
Sbjct: 309 LEDRLRRLESDEEFK-----DIIEQ 328


>gi|257460864|ref|ZP_05625965.1| tRNA-dihydrouridine synthase B [Campylobacter gracilis RM3268]
 gi|257442195|gb|EEV17337.1| tRNA-dihydrouridine synthase B [Campylobacter gracilis RM3268]
          Length = 308

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 130/320 (40%), Gaps = 33/320 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D   R   +    +A   +EMI A+A++   +K   +L  +  E P  +QI G+D 
Sbjct: 17  AGFSDPPLRGVVKKFGCDA-TVSEMISANALVFEGEKTLKMLEKNAAETPFFVQIAGSDA 75

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A  ++  F G + I+LN GCP  +V +   G+ L+L+   +   +  + K  +  
Sbjct: 76  EIIKKAVLLINKFDGIDGIDLNCGCPVPKVVKQGAGSALLLDLPRLSRLVETIKKYSNKK 135

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T  K R+G      AV + N+ ++++ +G + I IH R         +       +DY 
Sbjct: 136 FTSAKVRLGF----SAVDIENIARAVQSAGADFIAIHGRT--------RAGGYSAAVDYG 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +    +    + +  NG +    + A++ L   D +MIGRA      +   +       
Sbjct: 184 AIARAGR-VLQIPVIANGDINSANAPAVRDLSGADALMIGRAVIGRPWIFREIK------ 236

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            TG         +      +  ++ Y  R       +    +H+     G  N+   R  
Sbjct: 237 -TGEQASDALKKEVVLYHFAQMLSHYGVR------GVAIFRKHLHEYSKGRENAASFREQ 289

Query: 297 LTVEAGASTATHHIIETAFN 316
           +   A A + T  +IE  F+
Sbjct: 290 INHVA-AESETTRLIEEFFS 308


>gi|218530995|ref|YP_002421811.1| hypothetical protein Mchl_3045 [Methylobacterium chloromethanicum
           CM4]
 gi|218523298|gb|ACK83883.1| TIM-barrel protein, nifR3 family [Methylobacterium chloromethanicum
           CM4]
          Length = 342

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 131/320 (40%), Gaps = 29/320 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISK 61
             TD H R  A+ L   + + +EM+ A  + +GD ++ +        P  +Q+ G     
Sbjct: 30  GVTDLHMRRLAQRL-GASAVVSEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPEP 88

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + E A+I    G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTV
Sbjct: 89  MAEGARIAVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D    ++    L +  +  G++G+ +H R         +        D+  +  
Sbjct: 149 KMRLGWD--HASLNAAELARRAEALGLDGVTVHGRT--------RQQFYKGQADWSAIRP 198

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  E   + +  NG +  + +A   L      GVM+GRAA     ++  +    +  +  
Sbjct: 199 VV-EAVRIPVIANGDITGLEEARACLSQSGAAGVMVGRAAVGRPWLVGEIAAGLAGRVAS 257

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FHGF-PNSRRCRH 295
               + R        ++A           +   ++   +H+        G  P+ R  R 
Sbjct: 258 PLSAEQRA------AVAAEHYQGLIALFGAAMGVRHARKHLAAYADAAGGLTPDDR--RR 309

Query: 296 ILTVEAGASTATHHIIETAF 315
           ++T           +++ AF
Sbjct: 310 LVTT--HDPAEALRLLQRAF 327


>gi|159044125|ref|YP_001532919.1| tRNA-dihydrouidine synthase [Dinoroseobacter shibae DFL 12]
 gi|157911885|gb|ABV93318.1| tRNA-dihydrouidine synthase [Dinoroseobacter shibae DFL 12]
          Length = 333

 Score =  201 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 126/325 (38%), Gaps = 30/325 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           M   TD  +R          L+ +EM+ +  +++       +  LGF  Q    A+Q+ G
Sbjct: 19  MAGITDLPFRNVVSRF-GAGLVVSEMVASQEMVQAKASVRARAELGFGAQAT--AVQLAG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   + EAA+ V D G   I++N+GCP+ +V  G+ G+ LM + D     I A+  A+ 
Sbjct: 76  REAYWMGEAARYVADQGARVIDINMGCPAKKVVNGASGSALMRDLDHALTLIDAVVAAVD 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT+K R+G DD    +   +L +  + +G+  + IH R         +        D+
Sbjct: 136 VPVTLKTRLGWDDD--CLNAPDLARRAEAAGIAMVTIHGRT--------RCQFYKGAADW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  +K+    + +  NG + D   +   +     DG+M+GR A      L  +     
Sbjct: 186 TAIGRVKRAV-SIPVIANGDIVDTAAAAQARAASGADGLMVGRGAQGRPWRLAEIAAALY 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS---- 290
                  P    +         A +  Y          L+   +H+       P+     
Sbjct: 245 GAPAPDIPSGDALVDLVLAHFEAMLAFYGPE-----LGLRTARKHLGWYMEARPDGFSPP 299

Query: 291 RRCRHILTVEAGASTATHHIIETAF 315
           +  R  + + A        ++  A 
Sbjct: 300 KSLRRAI-LTATDPATVRRLVPAAL 323


>gi|294677333|ref|YP_003577948.1| tRNA-dihydrouridine synthase B [Rhodobacter capsulatus SB 1003]
 gi|1171718|sp|Q08111|DUS_RHOCA RecName: Full=Probable tRNA-dihydrouridine synthase; AltName:
           Full=Nitrogen regulation protein nifR3
 gi|581498|emb|CAA51073.1| nifR3 [Rhodobacter capsulatus SB 1003]
 gi|294476153|gb|ADE85541.1| tRNA-dihydrouridine synthase B [Rhodobacter capsulatus SB 1003]
          Length = 324

 Score =  201 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 123/321 (38%), Gaps = 25/321 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGA 57
           M   TD  +R          L+ +EM+ +  +L            +     P ++Q+ G 
Sbjct: 19  MAGITDLPFRRMVARF-GAGLVVSEMVASGEMLTAKPSVRAKAQAELTAGLPTSVQLAGR 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + + + EAAKIV D G   I++N+GCP+ +V  G  GA LM NPD     I A+  A+ +
Sbjct: 78  EAAPMAEAAKIVADMGAEIIDINMGCPAKKVTGGLSGAALMRNPDHALRLIEAVVGAVDL 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G D+     A        + +GV  I IH R  +       D R I  +   
Sbjct: 138 PVTLKMRLGWDEDQLNAAEI--AARAEAAGVKMIVIHGRTRMQFYTGAADWRAIAAVRAA 195

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +   +           NG + D + A + L      GVM+GR A      L  +      
Sbjct: 196 VSVPVV---------ANGDITDAASARRALDQSGAAGVMVGRGAQGAPWRLAQIAAALFG 246

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                 P  +           A ++ Y          L+   +H+         +   R 
Sbjct: 247 KADPKLPSGSEFSDFVSEHYEAILSFY-----GRDLGLRIARKHLGWYA--EAAAAPLR- 298

Query: 296 ILTVEAGASTATHHIIETAFN 316
              + A    AT  +I +AF+
Sbjct: 299 AEMMRATDPAATLALIRSAFS 319


>gi|223038738|ref|ZP_03609031.1| tRNA-dihydrouridine synthase B [Campylobacter rectus RM3267]
 gi|222880140|gb|EEF15228.1| tRNA-dihydrouridine synthase B [Campylobacter rectus RM3267]
          Length = 512

 Score =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 124/318 (38%), Gaps = 39/318 (12%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D   R   +      +  +EMI A+A++    K   +L  S  E P  +QI G+D 
Sbjct: 16  AGFSDLPLRSVVKRF-GCDVTVSEMISANALVYEGSKTLEMLKKSPLETPYIVQIAGSDA 74

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +I+    G + I+LN GCP  +V + S G+ L+ +   +   +  + K  +  
Sbjct: 75  DIVKKAVEILNGIEGIDGIDLNCGCPVPKVVKQSAGSALLKDISNLKRIVETIKKTSNKQ 134

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D++IP +    L  + + +G + I  H R         +       +DY 
Sbjct: 135 MTSVKLRLGFDEKIPEI----LALAAQDAGADYIAFHGRT--------RAGGYTATVDYA 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +    KE   + +  NG +     A     L + D +MIGRA      +   +      
Sbjct: 183 AIGR-AKEAVTIPVIANGDI-SPENAADALNLTNADALMIGRACIGKPWVFHEIK----- 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             TG S     +D    + I  +  D    H    G      +H+     G P +   R 
Sbjct: 236 --TGES-----IDAATKKAIILAHFDAMIEHYGEHGA-AIFRKHLHRYSKGTPGAGAFRD 287

Query: 296 ILTVEAGASTATHHIIET 313
            +        A   I+  
Sbjct: 288 EIN-----RIAEPDILRQ 300


>gi|45361515|ref|NP_989334.1| tRNA-dihydrouridine synthase 3-like [Xenopus (Silurana) tropicalis]
 gi|110808214|sp|Q28BT8|DUS3L_XENTR RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|39850298|gb|AAH64263.1| dihydrouridine synthase 3-like protein [Xenopus (Silurana)
           tropicalis]
          Length = 639

 Score =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 112/284 (39%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      +L     E    +Q+ GA    + 
Sbjct: 306 NLPFRRLCKRF-GADITCGEMAMCTNLLQGQPSEWALLKRHHSEDIFGVQLEGAFPDTMT 364

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +P+TVK
Sbjct: 365 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCGLMNRTNKFEQIVKGMNSVLDVPLTVK 424

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV ++I       L+ +++  GV+ + +H R         ++ R     D++ + + 
Sbjct: 425 IRTGVQEKINIA--HKLIPNLRDWGVSLVTLHGRS--------REQRYTKLADWEYIAQC 474

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 L +  NG +     A + L   V G+M+ R A     + T + E     ++ + 
Sbjct: 475 ADIASPLPLFGNGDIISYEDANRALQTGVSGIMLARGALLKPWLFTEIKEQRHWDISSTE 534

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI-GL 283
                        I    T+Y   H  S    +++  R M+  L
Sbjct: 535 RF----------DILKDFTNYGLEHWGSDCQGVEKTRRFMLEWL 568


>gi|89272495|emb|CAJ83250.1| dihydrouridine synthase 3-like protein [Xenopus (Silurana)
           tropicalis]
          Length = 639

 Score =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 112/284 (39%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      +L     E    +Q+ GA    + 
Sbjct: 306 NLPFRRLCKRF-GADITCGEMAMCTNLLQGQPSEWALLKRHHSEDIFGVQLEGAFPDTMT 364

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +P+TVK
Sbjct: 365 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCGLMNRTNKFEQIVKGMNSVLDVPLTVK 424

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV ++I       L+ +++  GV+ + +H R         ++ R     D++ + + 
Sbjct: 425 IRTGVQEKINIA--HKLIPNLRDWGVSLVTLHGRS--------REQRYTKLADWEYIAQC 474

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 L +  NG +     A + L   V G+M+ R A     + T + E     ++ + 
Sbjct: 475 ADIASPLPLFGNGDIISYEDANRALQTGVSGIMLARGALLKPWLFTEIKEQRHWDISSTE 534

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI-GL 283
                        I    T+Y   H  S    +++  R M+  L
Sbjct: 535 RF----------DILKDFTNYGLEHWGSDCQGVEKTRRFMLEWL 568


>gi|330800078|ref|XP_003288066.1| hypothetical protein DICPUDRAFT_152274 [Dictyostelium purpureum]
 gi|325081890|gb|EGC35390.1| hypothetical protein DICPUDRAFT_152274 [Dictyostelium purpureum]
          Length = 402

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 105/231 (45%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MVD T   +R   R      L+YT M  +   +         F+   +++PL +Q  G D
Sbjct: 57  MVDHTYLAFRMLTRKY-GADLVYTPMFHSKNFVTCKTYRKDNFTTCPEDRPLVVQFCGND 115

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V+AAK+VED   + I+LN+GCP      G++G+ L+  P I+   +  + K + +P
Sbjct: 116 PEWVVKAAKLVEDR-CDAIDLNLGCPQQIARRGNYGSFLLDKPHIILPIVRELHKNIKVP 174

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +  K R+  D +        L   ++++G   + +H R    KG      +   + ++D 
Sbjct: 175 IFCKIRLLPDLKDT----IKLALDLQEAGCQLLTVHGRTKEQKG------QYSGHANWDA 224

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
           + +IK E   + +  NG +   +D+ + L+     DG+M       N +  
Sbjct: 225 IRQIK-EVLHIPVIANGSVVKFDDIDRCLEA-SKADGIMSAEGLLANPSFF 273


>gi|255321994|ref|ZP_05363144.1| tRNA-dihydrouridine synthase B [Campylobacter showae RM3277]
 gi|255301098|gb|EET80365.1| tRNA-dihydrouridine synthase B [Campylobacter showae RM3277]
          Length = 306

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 121/318 (38%), Gaps = 39/318 (12%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D   R   +      +  +EMI A+A++    K   +L  S  E P  +QI G+D 
Sbjct: 16  AGFSDLPLRSVVKQF-GCDVTVSEMISANALVYEGSKTLEMLKKSPLETPYIVQIAGSDA 74

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +I+    G + I+LN GCP  +V + S G+ L+ +   +   +  + K  +  
Sbjct: 75  DIVKKAVEILNGIDGIDGIDLNCGCPVPKVVKQSAGSALLKDISNLKRIVETIKKTSNKQ 134

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D++IP +    L  + + +G + I  H R         +       +DY 
Sbjct: 135 MTSVKLRLGFDEKIPEI----LAIAAQDAGADYIAFHGRT--------RAGGYTTAVDYA 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +    KE   + +  NG +     A +   L + D +MIGRA      +   +      
Sbjct: 183 AIGR-AKEAVTIPVIANGDI-SPENAAQTLNLTNADALMIGRACIGKPWVFHEIK----- 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                      +D    + I  +  D    H    G      +H+     G   +   R 
Sbjct: 236 -------TGGSIDAATKKAIILAHFDAMIEHYGEHGA-AIFRKHLHRYSKGIDGASAFRD 287

Query: 296 ILTVEAGASTATHHIIET 313
            +        A   I+  
Sbjct: 288 EINH-----IAEPEILRQ 300


>gi|13470630|ref|NP_102199.1| nitrogen reguration protein nifR3 protein [Mesorhizobium loti
           MAFF303099]
 gi|14021372|dbj|BAB47985.1| nitrogen reguration protein; NifR3 [Mesorhizobium loti MAFF303099]
          Length = 357

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 67/287 (23%), Positives = 119/287 (41%), Gaps = 19/287 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADI 59
           M   TD  +R  A       L+ +EM+ +  + +G     L       P+ + Q+ G + 
Sbjct: 42  MSGITDEPFRRRAH-AHGAGLVVSEMVASGELAKGRAGFDLRIRHSGLPVHMVQLAGREA 100

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + E A+I    G + I++N+GCP+ +V  G  G+ LML+ D     I A+  A+ +PV
Sbjct: 101 IHMAEGARIAAGEGADIIDINMGCPAKKVTGGYAGSALMLDLDHALSLIEAVVGAVKVPV 160

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D+   A+    L +  +++GV  + +H R         +        D+  +
Sbjct: 161 TVKMRLGWDEG--ALNAPILARRAEQAGVKMVTVHGRT--------RCQFYQGKADWRAI 210

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG +   ++A  IL     D VM+GRA Y    +   +    +  +
Sbjct: 211 ARVK-EAVSIPVVANGDVCSPAEAAAILDQSGADAVMVGRAHYGAPWIAGGIAAAAAGEV 269

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             + P       D+       M             L+Q  +H+    
Sbjct: 270 AANVPENRAALADYIVGHYEDMLALYGVE----SGLRQARKHLGWYL 312


>gi|302342599|ref|YP_003807128.1| dihydrouridine synthase DuS [Desulfarculus baarsii DSM 2075]
 gi|301639212|gb|ADK84534.1| dihydrouridine synthase DuS [Desulfarculus baarsii DSM 2075]
          Length = 326

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 74/322 (22%), Positives = 130/322 (40%), Gaps = 25/322 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFS-TQEKPLALQIGGAD 58
           M   +   +R  A+      L+YTEMI A  ++RG KK + L  +  +E+P+ALQ+ GAD
Sbjct: 17  MAGVSSPAFRLMAKR-GGAGLVYTEMISAVGLVRGHKKTLELCLTLPEERPVALQLFGAD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AA +      + I++N+GCP+ +V     G+ L+ +       +AA+ +A S+P
Sbjct: 76  PEIMGRAAALASRMPVDLIDINMGCPARKVRRQGAGSALLEDIPRAAAVMAAVAQAASLP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TVK R+G  D      L  +V  +  +G   + +HAR                  D+  
Sbjct: 136 ATVKLRLGPSDDD----LERIVPPLLAAGAKAVCLHARTT--------RQAFAGQADWAA 183

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +    P + +  NG +     AL +L   +   VMIGR A  +  +     +  +  
Sbjct: 184 IARLSAWCP-VPVIGNGDVRGEQDALGMLRQTNCQAVMIGRGAMGDPWIFGRAADLLAGR 242

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               + +  R      R+     T+ A              + M+    G P +   R  
Sbjct: 243 AVERASLAQR------RQSLLQHTELALSLGGDKLAAHFAKQFMMWHAKGLPGAADFRR- 295

Query: 297 LTVEAGASTATHHIIETAFNLM 318
           L  +         + E  F+ +
Sbjct: 296 LACQERELGRLLTLCEEFFDQL 317


>gi|195035293|ref|XP_001989112.1| GH10224 [Drosophila grimshawi]
 gi|193905112|gb|EDW03979.1| GH10224 [Drosophila grimshawi]
          Length = 503

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 116/289 (40%), Gaps = 36/289 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 33  MVDQSELAWRMLCRRY-GAQLCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA +      + +++N+GCP A    G +GA L    +++   +  + + LSIP
Sbjct: 92  PQQILEAA-LAAQNYCDAVDINLGCPQAIAKRGHYGAFLQDEWELLTQIVRTLHEKLSIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R   D            K ++ +G   + +H R    KG            D+  
Sbjct: 151 VTCKIRRFEDR----AKTIEYAKMLEAAGCQLLTVHGRTREQKG------PLTGIADWSY 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++ +E+  + +  NG +  +    + L    VDGVM       N A+   +       
Sbjct: 201 IKDV-REHIKIPMLANGNILGVEDVHRCLTETGVDGVMTAEGNLHNPALFEGI------- 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGL 283
               SP   ++  ++   +        Y   HL    KL     H++ +
Sbjct: 253 ----SPPVWQMANEYLEFVDLYPCPTSYIRGHL---FKLFH---HIMNI 291


>gi|221639223|ref|YP_002525485.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides KD131]
 gi|221160004|gb|ACM00984.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides KD131]
          Length = 317

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 110/288 (38%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R  A       L+ +EM+ +  ++    +          E   A+Q+ G D
Sbjct: 10  MAGITDLPFRRLAVRF-GAGLVVSEMVASREVVCAGAEARARAEIGAAEGRTAVQLAGCD 68

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     I A+  A+++P
Sbjct: 69  PHWMAEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALIEAVVGAVAMP 128

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D+ +  +    + +  + +GV  I IH R         +        D+  
Sbjct: 129 VTLKMRLGWDEGM--LNAPEIARRAEAAGVAMITIHGRT--------RCQFYTGRADWGA 178

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +         NG +    +  A        GVM+GR A     +L  V       
Sbjct: 179 IRPVVEAVSVPV-VANGDITGPKEAQAALAASGAAGVMVGRGAQGRPWLLGQVASGLDGR 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                P    +           ++ Y          L+   +H+    
Sbjct: 238 AAPDVPEGEALADLVVAHYEEMLSFY-----GRDLGLRVARKHLTWYL 280


>gi|298291769|ref|YP_003693708.1| hypothetical protein Snov_1785 [Starkeya novella DSM 506]
 gi|296928280|gb|ADH89089.1| TIM-barrel protein, nifR3 family [Starkeya novella DSM 506]
          Length = 343

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 125/308 (40%), Gaps = 28/308 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADI 59
           M   TD   R  A      +L  +EM+ + A+  G ++ +L    +   L A+Q+ G + 
Sbjct: 27  MAGITDAPMRRMALRY-GASLAVSEMVASAALETGHEETVLRAEGEGVALHAVQLAGNEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + +  AA+I E  G   I++N+GCP+ RV  G  G+ L+ + D+    I ++  A+ +PV
Sbjct: 86  ASMARAARIAEAAGAAIIDINMGCPAKRVTTGLAGSALLRDLDLATSIIESVVAAVKVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G DD    +    L +  +  GV  + IH R         +        D+  +
Sbjct: 146 TLKTRLGWDD--NVLVAPELARRAEAIGVQLVTIHGRT--------RCQFYTGRADWAAI 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K+    + +  NG L +   A  +L     DG+MIGR A         V E   +  
Sbjct: 196 RQVKQAV-SIPVLANGDLVEAEDAPAMLAASGTDGLMIGRGAQGRPWFPGQVVERLRSGR 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF------HGFP--N 289
           T + P                +T Y          ++   +H+           G P   
Sbjct: 255 TPADPGLDEQHDVLVELYEGWLTHYGRE-----LGMRCARKHIGWSLAAATASAGRPPEA 309

Query: 290 SRRCRHIL 297
           ++  R  L
Sbjct: 310 AKGWRQRL 317


>gi|84501088|ref|ZP_00999323.1| tRNA-dihydrouridine synthase, putative [Oceanicola batsensis
           HTCC2597]
 gi|84391155|gb|EAQ03573.1| tRNA-dihydrouridine synthase, putative [Oceanicola batsensis
           HTCC2597]
          Length = 326

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 69/288 (23%), Positives = 115/288 (39%), Gaps = 24/288 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD   R          L+ +EM+ +  +L  R   +            ++Q+ G D
Sbjct: 19  MAGITDLPMRDLVSGF-GADLVVSEMVASGELLTDRPGTRERAELGLGRAATSVQLAGRD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + + EAA+ V D G   I++N+GCP+ +V  G  G+ LM +PD+    IAA+  A+ +P
Sbjct: 78  PAVMAEAARQVADLGARVIDINMGCPAKKVTGGLSGSALMRDPDLALSLIAAVAGAVDLP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD        +L +  + +GV  + +H R         +        D+  
Sbjct: 138 VTVKMRLGWDDDTRNA--PDLARRAEAAGVRMVVVHGRT--------RCQFYKGRADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V E+  E   + + +NG + D   + A        GVM+GR       +L  +    +  
Sbjct: 188 VREVV-EAVSIPVLVNGDIVDGATAAAALSASGAAGVMVGRGIQGQPWLLAGLIASLTGG 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                     V     R   A +  Y A        L+   +H+    
Sbjct: 247 AFAP---PHDVPGLIARHYEAVLGFYGA-----DLGLRVARKHLGWYM 286


>gi|298715097|emb|CBJ27785.1| dihydrouridine synthase [Ectocarpus siliculosus]
          Length = 450

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 127/288 (44%), Gaps = 31/288 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF------STQEKPLALQI 54
           MV+ ++  +R+  R      L YT+M+ A+     + +             +++PL +Q 
Sbjct: 101 MVEQSEAAFRYLVRR-HGCGLAYTQMLHAEKFAPDNAEKFRRRRFDGVDDEEDRPLIVQF 159

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G +   +V AA+ VE    + ++LN+GCP     +G++GA L+ NP +  D +AAM + 
Sbjct: 160 CGNNPDTVVRAARHVE-HRCDAVDLNLGCPQKIAKKGNYGAYLLPNPQLCEDIVAAMSRE 218

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           LS+PVTVK R     Q       +L + ++ +G   + +H R             K    
Sbjct: 219 LSVPVTVKIRA----QDRESDTLDLARRLEGAGAQLLTVHGRTV------SSQKTKQGAA 268

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+DI+ ++K E  D+ +  NGG+E  + A ++L     D VM      +N A+       
Sbjct: 269 DWDIIRKVK-EVVDIPVVANGGIETGADAERLLEETGADAVMSSEGLLENPALF------ 321

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
                +   P++     +   +I +  T+Y          +  I  H+
Sbjct: 322 ----DSDLIPMEELQGLEVAHRILSFTTEYMELVKRYPAPMISIKGHL 365


>gi|139439601|ref|ZP_01773014.1| Hypothetical protein COLAER_02041 [Collinsella aerofaciens ATCC
           25986]
 gi|133774942|gb|EBA38762.1| Hypothetical protein COLAER_02041 [Collinsella aerofaciens ATCC
           25986]
          Length = 347

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 57/301 (18%), Positives = 109/301 (36%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R    N L Y+EM+    +     K   ++  + +E+ + +Q+ G+ 
Sbjct: 24  MAGVTDPAYRIMCRRRGAN-LAYSEMVSVAGLAYASNKTWRLVLPADEEQQICVQLFGSK 82

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A   VE+   +    I++N+ CP+ +V     G+ LM  PD+    + A   A 
Sbjct: 83  PEQFASAVAAVEERVGDRLSLIDINMACPARKVVTKGEGSALMRTPDLAEKIVEAAVGAA 142

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVTVK R G   +    A     + ++ +G   + +H R A                D
Sbjct: 143 HVPVTVKIRKGFYAEDRNAAT--FAQMLEGAGAAAVAVHGRCAT--------QLYTGQAD 192

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +V E+  +  ++ +  +G +     A + L       V I R  Y N  +        
Sbjct: 193 WSVVDEVA-DAVEIPVIGSGDVFSAEDAAEHLQGSGASAVFIARGIYGNPWVFGDARALA 251

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            +     S       +     ++ +              + +   +      G P++   
Sbjct: 252 LDGTPVPSRSSVERLEALREHLTLTHELLPL--------MSRARTYASWYLKGMPHAAAW 303

Query: 294 R 294
           R
Sbjct: 304 R 304


>gi|328767911|gb|EGF77959.1| hypothetical protein BATDEDRAFT_13578 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 296

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 105/232 (45%), Gaps = 19/232 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  A       K     FST E  +PL +Q    D
Sbjct: 28  MVDQSEYAWRILSRRY-GAQLCYTPMFHAKLFSEHHKYRKQVFSTGEFDRPLIVQFCAND 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE    + I+LN+GCP     +G +G+ L    D++   + A+ + +S+P
Sbjct: 87  PETLLSAAKLVEAQ-CDAIDLNLGCPQGIAKKGHYGSFLQDEWDLIASMVKAVHEHISVP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K RI  D +            ++ +G   + +H R    KG      +     D+D 
Sbjct: 146 ITCKIRIFPDVKKT----IEYALMLQNAGCQLLTVHGRLREQKG------QLTGLADWDQ 195

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           + ++K E   + +  NG +   +D+ + +K    VDGVM       N A+ +
Sbjct: 196 IRQVK-EALSIPVFANGNILYHDDVERCIKE-TGVDGVMTAEGNLYNPAIFS 245


>gi|291080756|ref|ZP_06534880.2| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 205

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 50/216 (23%), Positives = 98/216 (45%), Gaps = 15/216 (6%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSDPVEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVPVTLKIRTGWAPEHRN--CVEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G+  + IH R         +        +YD +  +K++   + I  NG + +  +A
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPIIANGDITNPHKA 169

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +L     D +MIGRAA     +   +  Y     
Sbjct: 170 RAVLDYTGADALMIGRAAQGRPWIFREIQHYLDTGE 205


>gi|170748588|ref|YP_001754848.1| NifR3 family TIM-barrel protein [Methylobacterium radiotolerans JCM
           2831]
 gi|170655110|gb|ACB24165.1| TIM-barrel protein, nifR3 family [Methylobacterium radiotolerans
           JCM 2831]
          Length = 341

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 68/284 (23%), Positives = 117/284 (41%), Gaps = 21/284 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISK 61
             TD H R  AR    +A++ +EM+ A    RG  +  L        L  +Q+ G +   
Sbjct: 33  GVTDLHMRRIARRCGADAVI-SEMVAAREFTRGSGEATLRAEGSGVDLHVVQLAGCEAGP 91

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAA++ E  G + I++N+GCP+  V   + G+ LM + D     +A++  A+SIPVTV
Sbjct: 92  MAEAARLAEAGGADVIDVNMGCPAKIVTGIASGSALMRDLDHAERLLASVRGAVSIPVTV 151

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G DD     A  +L    ++ G+N + +H R         +        D+     
Sbjct: 152 KMRLGWDDASRNAA--DLAARAERLGLNAVTVHGRT--------RQQFYKGRADWAA-IR 200

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
                  + +  NG + D + A   L      GVMIGRAA     ++  V          
Sbjct: 201 AVVAAVSIPVIANGDVTDFASARACLDASGAAGVMIGRAATGRPWLVGQVAAAL-TGRPA 259

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           + P ++          +  ++ Y          ++   +H+   
Sbjct: 260 AEPSRSEQAALAAEHYAGLLSLY-----GRDMGVRHARKHLAAY 298


>gi|147903417|ref|NP_001079662.1| tRNA-dihydrouridine synthase 3-like [Xenopus laevis]
 gi|82176436|sp|Q7ZWS1|DUS3L_XENLA RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|28436916|gb|AAH46730.1| MGC53781 protein [Xenopus laevis]
          Length = 640

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 113/284 (39%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L     E    +Q+ GA    + 
Sbjct: 307 NLPFRRICKRL-GADITCGEMAMCTNLLQGQPSEWALLKRHHSEDIFGVQLEGAFPDTMT 365

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +P+TVK
Sbjct: 366 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCGLMNRTNKFEQIVKGMNSVLDVPLTVK 425

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+ +++  GV+ + +H R         ++ R     +++ + + 
Sbjct: 426 IRTGVQEKVNIA--HKLIPNLRDWGVSLVTLHGRS--------REQRYTKLANWEYIDQC 475

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A + L   V GVM+ R A     + T + E     ++ + 
Sbjct: 476 AKIASPVPLFGNGDIISYEDANRALQTGVAGVMLARGALFKPWLFTEIKEQRHWDISSTE 535

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        I    T+Y   H  S  +  + TR  +   L
Sbjct: 536 RF----------DILKDFTNYGLEHWGSDCQGVEKTRKFMLEWL 569


>gi|89069985|ref|ZP_01157317.1| tRNA-dihydrouridine synthase, putative [Oceanicola granulosus
           HTCC2516]
 gi|89044433|gb|EAR50564.1| tRNA-dihydrouridine synthase, putative [Oceanicola granulosus
           HTCC2516]
          Length = 331

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 108/287 (37%), Gaps = 21/287 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              TD  +R           + +EM+ +  ++  R   +        E   A+QI G + 
Sbjct: 26  AGITDLPFRQLVARF-GAGWVVSEMVASQEMVQARPGTREKAELGFGEHDTAVQIAGREA 84

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+I E  G   I++N+GCP+ +V  G  G+ L+  PD     I A+  A+++PV
Sbjct: 85  HWMAEAARIAEANGARLIDINMGCPAKKVTNGWSGSALLRTPDHALRLIEAVVGAVTVPV 144

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D    ++    +    + +GV  + IH R         +        D+  +
Sbjct: 145 TLKTRLGWD--HDSLNAAQVAARAEAAGVRMVTIHGRT--------RCQFYKGRADWAAI 194

Query: 180 YEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             I  E   + +  NG + D   ++A        GVMIGR A      +  V        
Sbjct: 195 RPIV-EAVSIPVVANGDITDAATARAALAASGARGVMIGRGAQGAPWRIAEVAHALYGSP 253

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               P    +         A +  Y      +    +   +H+    
Sbjct: 254 APRIPTGAALADMVAEHYEAMLGFY-----GTDLGARVARKHLGWYM 295


>gi|47219443|emb|CAG10807.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 614

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 104/277 (37%), Gaps = 25/277 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G +    +L     E    +QI G     + 
Sbjct: 281 NLPFRRVCKRF-GADITCGEMAMCTNLLQGQQSEWALLKRHESEDVFGVQIEGCFPDTMT 339

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ +    + +++N GCP   V +   G  LM       + +  M   L +P+TVK
Sbjct: 340 RCAELINNNTEVDFVDINSGCPIDLVFKKGGGCGLMTRTRKFEEIVKGMNYVLDVPLTVK 399

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV ++        L+  +KK GV+ I +H R         ++ R     D+D +   
Sbjct: 400 IRTGVQEKTNIA--HKLIPEMKKWGVSMITLHGRS--------REQRYTKLADWDYISTC 449

Query: 183 KKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A+      V G+MI R A     + T + E     ++   
Sbjct: 450 SKLASPVPLFGNGDILSYEDAMMAKETGVSGIMIARGALIKPWIFTEIKEKRHWDISSGE 509

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                        I    T++   H  S  +  + TR
Sbjct: 510 ----------RLDILRDFTNFGLEHWGSDTRGVEKTR 536


>gi|194853320|ref|XP_001968141.1| GG24669 [Drosophila erecta]
 gi|190660008|gb|EDV57200.1| GG24669 [Drosophila erecta]
          Length = 505

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 121/306 (39%), Gaps = 42/306 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L+IP
Sbjct: 94  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            +++ 
Sbjct: 153 VTCKIRIFEDLEKT----IRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVANWNY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +++    + +  NG +  +    + L    VDGVM       N A+   +       
Sbjct: 203 IKSVRQHI-KIPMLANGNILGLEDVHRCLAETGVDGVMSAEGNLHNPAIFRGI------- 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRRC 293
               SP   ++  ++   +       +            I  H+  LFH       +   
Sbjct: 255 ----SPPVWQMAHEYLELVQLHPCPSSF-----------IRGHLFKLFHHIMNIRQNSEL 299

Query: 294 RHILTV 299
           R  L  
Sbjct: 300 RQYLAT 305


>gi|323508721|dbj|BAJ77254.1| cgd1_3440 [Cryptosporidium parvum]
          Length = 407

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 123/306 (40%), Gaps = 32/306 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   +      L Y+ M  +     L+G ++       ++ P+ +Q  G D
Sbjct: 24  MVDGSELAFRLICKKY-GCDLGYSPMYHSGLFSKLQGYRETNFQTCEEDDPMIVQFCGND 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSI 117
              LV+A+K ++D     I++N GCP      G++GA L+ NPD++   I+ + ++ L  
Sbjct: 83  PETLVKASKFIDD-KVKGIDINFGCPQNIAKRGNYGAFLLSNPDLMERIISTLSESDLKC 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K RI   D        NL+K ++ +G   I +H R    +G+           +++
Sbjct: 142 PVSCKIRIL--DHHDLQPTINLIKRLESAGACMIAVHGRTMTSRGV------LTGPANWE 193

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     +    NGG+ +     K L     D VM      +N  +        + 
Sbjct: 194 ALKILKSRC-SIPFIANGGISNYEDIQKCLNYTGADAVMSAEGILENPWLFQGFK---TP 249

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRR 292
               + P + ++  ++               L+    +  I  H+  +FH     P +  
Sbjct: 250 EAINNKPSQFQIALEYLDYCI----------LYPPPNVGIIRTHLYRIFHTIFSLPGAHI 299

Query: 293 CRHILT 298
            R  + 
Sbjct: 300 FRDEIN 305


>gi|309799512|ref|ZP_07693742.1| tRNA-dihydrouridine synthase [Streptococcus infantis SK1302]
 gi|308116868|gb|EFO54314.1| tRNA-dihydrouridine synthase [Streptococcus infantis SK1302]
          Length = 234

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 111/225 (49%), Gaps = 17/225 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T+  +R  A+ L    L+  EM+    I   ++K   +L     E P+++Q+ G+D
Sbjct: 1   MAGVTNSAFRTIAKEL-GAGLVVMEMVSDKGIQYNNEKTLHMLHIDEGENPVSIQLFGSD 59

Query: 59  ISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  AA+ +++    + +++N+GCP  ++ +   GA  + +PD +   I  +   L I
Sbjct: 60  EDSLARAAEFIQENTKTDIVDINMGCPVNKIVKNEAGAMWLKDPDKIYSIINKVQSVLDI 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G  D  P++A+ N + + + +GV+ + +H R         ++     + D +
Sbjct: 120 PLTVKMRTGWSD--PSLAVENAL-AAEAAGVSALAMHGRT--------REQMYTGHADLE 168

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
            ++++ +    +    NG +  + +A + +     D VMIGRAA 
Sbjct: 169 TLHKVAQALTKIPFIANGDIRTVQEAKQRIEEVGADAVMIGRAAM 213


>gi|67588468|ref|XP_665355.1| ENSANGP00000019228 [Cryptosporidium hominis TU502]
 gi|54656003|gb|EAL35125.1| ENSANGP00000019228 [Cryptosporidium hominis]
          Length = 384

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 123/306 (40%), Gaps = 32/306 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   +      L Y+ M  +     L+G ++       ++ P+ +Q  G D
Sbjct: 1   MVDGSELAFRLICKKY-GCDLGYSPMYHSGLFSKLQGYRETNFQTCEEDDPMIVQFCGND 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSI 117
              LV+A+K ++D     I++N GCP      G++GA L+ NPD++   I+ + ++ L  
Sbjct: 60  PETLVKASKFIDD-KVKGIDINFGCPQNIAKRGNYGAFLLSNPDLMERIISTLSESDLKC 118

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K RI   D        NL+K ++ +G   I +H R    +G+           +++
Sbjct: 119 PVSCKIRIL--DHHDLQPTINLIKRLESAGACMIAVHGRTMTSRGV------LTGPANWE 170

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     +    NGG+ +     K L     D VM      +N  +        + 
Sbjct: 171 ALKILKSRC-SIPFIANGGISNYEDIQKCLNYTGADAVMSAEGILENPWLFQGFK---TP 226

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRR 292
               + P + ++  ++               L+    +  I  H+  +FH     P +  
Sbjct: 227 EAINNKPSQFQIALEYLDYCI----------LYPPPNVGIIRTHLYRIFHTIFSLPGAHI 276

Query: 293 CRHILT 298
            R  + 
Sbjct: 277 FRDEIN 282


>gi|66362388|ref|XP_628158.1| Dus1p, tRNA dihydrouridine synthase [Cryptosporidium parvum Iowa
           II]
 gi|46227613|gb|EAK88548.1| Dus1p, tRNA dihydrouridine synthase [Cryptosporidium parvum Iowa
           II]
          Length = 409

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 123/306 (40%), Gaps = 32/306 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   +      L Y+ M  +     L+G ++       ++ P+ +Q  G D
Sbjct: 26  MVDGSELAFRLICKKY-GCDLGYSPMYHSGLFSKLQGYRETNFQTCEEDDPMIVQFCGND 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSI 117
              LV+A+K ++D     I++N GCP      G++GA L+ NPD++   I+ + ++ L  
Sbjct: 85  PETLVKASKFIDD-KVKGIDINFGCPQNIAKRGNYGAFLLSNPDLMERIISTLSESDLKC 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K RI   D        NL+K ++ +G   I +H R    +G+           +++
Sbjct: 144 PVSCKIRIL--DHHDLQPTINLIKRLESAGACMIAVHGRTMTSRGV------LTGPANWE 195

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K     +    NGG+ +     K L     D VM      +N  +        + 
Sbjct: 196 ALKILKSRC-SIPFIANGGISNYEDIQKCLNYTGADAVMSAEGILENPWLFQGFK---TP 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRR 292
               + P + ++  ++               L+    +  I  H+  +FH     P +  
Sbjct: 252 EAINNKPSQFQIALEYLDYCI----------LYPPPNVGIIRTHLYRIFHTIFSLPGAHI 301

Query: 293 CRHILT 298
            R  + 
Sbjct: 302 FRDEIN 307


>gi|50289099|ref|XP_446979.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49526288|emb|CAG59912.1| unnamed protein product [Candida glabrata]
          Length = 412

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 66/290 (22%), Positives = 117/290 (40%), Gaps = 24/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL------RGDKKNILGFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A          R    ++ G S  ++PL +Q 
Sbjct: 29  MVDQSELAWRVLSRRY-GATLCYTPMFHAKLFATSEKYRREMWCDLDGDSKLDRPLVVQF 87

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK+VED   + ++LN+GCP     +G +G+ LM   D++   I  + + 
Sbjct: 88  CANDPEYLLQAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHKLIKTLHEN 146

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L+IPVT K R+  D Q       +  K +  +G   + +H R    KG      ++    
Sbjct: 147 LNIPVTAKIRVFPDRQKT----LDYAKMVLDAGAQFLTVHGRLREQKG------QQTGLA 196

Query: 175 DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           D+DI+  +++  PD      NG +       + +     D VM       N  +      
Sbjct: 197 DWDIIKYLRENLPDNTVFFANGNILYPEDIDRCISQIKCDAVMSAEGNLYNPGVFN--VH 254

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           Y       + P    + ++++  I     +  A          ++ R  +
Sbjct: 255 YI-GDKDKTYPRVDVLLREYFEIIRNECKESLASRKAMKSHFFKLLRPFL 303


>gi|195470200|ref|XP_002087396.1| GE16327 [Drosophila yakuba]
 gi|194173497|gb|EDW87108.1| GE16327 [Drosophila yakuba]
          Length = 505

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 63/306 (20%), Positives = 121/306 (39%), Gaps = 42/306 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L+IP
Sbjct: 94  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAQLAIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            D++ 
Sbjct: 153 VTCKIRIFEDLEKT----IRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVADWNY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +++    + +  NG +  +    + L    VDGVM       N A+   V       
Sbjct: 203 IKSVRQHV-KIPMLANGNILGLEDVHRCLAETGVDGVMSAEGNLHNPAIFQGV------- 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRRC 293
               SP   ++  ++   +       +            I  H+  LFH       +   
Sbjct: 255 ----SPPVWQMAHEYLELVQLYPCPSSF-----------IRGHLFKLFHHIMNIRQNSEL 299

Query: 294 RHILTV 299
           R  L  
Sbjct: 300 RQYLAT 305


>gi|297624504|ref|YP_003705938.1| dihydrouridine synthase DuS [Truepera radiovictrix DSM 17093]
 gi|297165684|gb|ADI15395.1| dihydrouridine synthase DuS [Truepera radiovictrix DSM 17093]
          Length = 362

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 122/318 (38%), Gaps = 30/318 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M  ++D  +R   R    +A   TEM+ A A+  GD++   I      E+ L +Q+ G +
Sbjct: 69  MAGFSDAPFRRLCRRF-GSAWAVTEMVSAKALTVGDERGLEISAPYEGERDLVIQVFGGE 127

Query: 59  ISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +    +++ E F    ++LN+GCP  +V   S GA LM +P      I  + +A+ +
Sbjct: 128 PEVVAAGGRLLYERFSPAALDLNMGCPVKKVTGRSCGAKLMNDPGRAAAIIGQLARAVPV 187

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+G D     V    +  +++++G   I IH R A  K             D++
Sbjct: 188 PVSAKLRLGYDR----VNALEVALALQEAGAALITIHGRTAAQK--------YTGEADWE 235

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            V EI      + +  +G +    Q  +      GVM+GR A     +   +        
Sbjct: 236 AVAEIA-ARLAIPVVGSGDVTTQEQFRRYRAWGLGVMVGRGALGRPWVFRELR------- 287

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
              +P    +         +    Y   H      + ++  H+      FP     R  L
Sbjct: 288 GEPAPPLPEIKDLILEHARSMRAWYGTDH-----AVIKMRGHLARYAQAFPEPEALRKAL 342

Query: 298 TVEAGASTATHHIIETAF 315
              +    A   ++  A 
Sbjct: 343 MQVSTL-GALERVLACAL 359


>gi|195386396|ref|XP_002051890.1| GJ17247 [Drosophila virilis]
 gi|194148347|gb|EDW64045.1| GJ17247 [Drosophila virilis]
          Length = 504

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 121/305 (39%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L     ++PL +Q  G D
Sbjct: 32  MVDQSELAWRMLCRRY-GAQLCYSPMYHANLFATDLKYRKDALQTCPADRPLIIQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++EAA   +D   + +++N+GCP A    G +GA L     ++   +  + + LS+P
Sbjct: 91  PQQMLEAALAAQDH-CDAVDINLGCPQAIAKRGHYGAFLQDEWQLLTQIVRTLHEQLSVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +       N  K ++ +G   + +H R    KG            D+  
Sbjct: 150 VTCKIRIFEDREKT----INYAKMLEAAGCQLLTVHGRTREQKG------PLTGIADWSY 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++++    + +  NG +  +    + L    VDGVM       N A+   +       
Sbjct: 200 IKDVRQHI-KIPMFANGNILGLEDVHRCLEATGVDGVMTAEGNLHNPAIFQGI------- 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
               SP   ++  ++   +        Y   HL    KL     H++       ++ + R
Sbjct: 252 ----SPPVWQMAHEYLEFVDLYPCPTSYIRGHL---FKLFH---HIMN----IRSNAQLR 297

Query: 295 HILTV 299
             L  
Sbjct: 298 EQLAT 302


>gi|329850670|ref|ZP_08265515.1| putative tRNA-dihydrouridine synthase [Asticcacaulis biprosthecum
           C19]
 gi|328840985|gb|EGF90556.1| putative tRNA-dihydrouridine synthase [Asticcacaulis biprosthecum
           C19]
          Length = 326

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 66/290 (22%), Positives = 110/290 (37%), Gaps = 20/290 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   +D  +R  A  L       TEM+    + R +               +Q+ G D  
Sbjct: 21  MTGVSDLPFRRVAAKL-GAPYAATEMVACADMSRPEIVRKAQLGDHAGLKIVQLVGRDPE 79

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +   A++ E+ G + ++LN GCP+  V     G+ LM + D     + A  KA S PVT
Sbjct: 80  HIAHGARLAEESGADIVDLNFGCPAKEVIGVLCGSALMRDLDQAERIMTAALKATSRPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G DD         L +  +K G+  + +H R         +        ++  V 
Sbjct: 140 VKMRLGWDDDSQNA--PELAQRAEKLGIKALTVHGRT--------RQQFYKGEANWHAVA 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K     + + +NG + D+  A         DG+MIGR  Y        ++   ++   
Sbjct: 190 HVKSAV-RIPVIVNGDIVDLGSARDALHQSGADGLMIGRGIYGRPWFAHDLNHALNDNDM 248

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
            S  +  R D      +   M D  A +      L+   +H+     G P
Sbjct: 249 PSRDVADRADI-----VVEHMNDSLAFY-GKALGLRMFKKHLGAYVEGAP 292


>gi|291279750|ref|YP_003496585.1| tRNA-dihydrouridine synthase [Deferribacter desulfuricans SSM1]
 gi|290754452|dbj|BAI80829.1| tRNA-dihydrouridine synthase [Deferribacter desulfuricans SSM1]
          Length = 320

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 67/324 (20%), Positives = 134/324 (41%), Gaps = 29/324 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADI 59
              T   +R   R    + L+YTEM+ A+ + R  K  +  +     ++P+ +Q+ G++ 
Sbjct: 21  AGVTTPPFRKIVRKF-FDGLIYTEMVSAEGLKRKVKATLDYIKIQPIDRPIFIQVFGSNP 79

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA KI ED       +LN GCP  +V + + G+ L+ + + + + I  M KA   P
Sbjct: 80  DTIYEAIKICEDLASPEGYDLNAGCPVKKVIKANAGSYLLKDLNNLTNIIKNMRKATDKP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++VK R+G D    ++  + ++   +  GV+ + IHAR         K      ++ +D 
Sbjct: 140 ISVKTRLGWD--YNSLVYKEILNMCENEGVDILTIHART--------KTEMFSGDIHFDA 189

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + E+     ++ +  NG + D +   K++   VD +MIGRA  K   +   +        
Sbjct: 190 LSELATLKKNVTLIGNGNVVDKTSFDKMIETGVDAIMIGRAYMKAPWIFQAIKHNLDIHN 249

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             +   K  +  +      +   +Y             I ++ +    G+  S   R  +
Sbjct: 250 FLTLKQKINILMELLTFEKSFRRNYIDF----------IRKYSVWFLKGYKGSTELRKKI 299

Query: 298 TVEAGASTATHHIIETAFNLMIES 321
                       I++T    + ++
Sbjct: 300 ----YKINTEQEIVKTLEEFLEQN 319


>gi|34556610|ref|NP_906425.1| putative transcriptional regulator [Wolinella succinogenes DSM
           1740]
 gi|34482324|emb|CAE09325.1| PUTATIVE TRANSCRIPTIONAL REGULATOR [Wolinella succinogenes]
          Length = 346

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 71/329 (21%), Positives = 138/329 (41%), Gaps = 36/329 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R  A+      +  +EMI   A+   +++   ++  +  E P ++QI G  +
Sbjct: 43  AGYTDLPFRSVAKSF-GADITVSEMISVHALAYKNRRTAKMVEKAPNENPYSVQIAGNHL 101

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +++  F G + ++LN GCP+ +V     G+ L+ + D + + +  + K  +IP
Sbjct: 102 DIIQRAVEVLNAFEGIDILDLNGGCPAPKVSGHGSGSSLLKDLDKMVEILRLIKKTTTIP 161

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T VK RIG + +IPA     +  ++  + ++ + +H R          D  K   +DYD
Sbjct: 162 YTSVKVRIGFETKIPA----EIAHALNDAPIDFVVVHGRTK-------SDGYKKERIDYD 210

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK    + +  NG ++  S+A ++L     DG+MIGRAA     +   + E    
Sbjct: 211 SIALMKK-ILKVPLIANGEIDSFSKAQEVLAHTGADGLMIGRAAVAKPWIFRQIKEGIH- 268

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR- 294
                       D +  R ++    D         G +    +++     G   +   R 
Sbjct: 269 ----------EADLELRRAVALEHFDKTIAFRGEFGAV-MFRKNLHAYSKGLAGASDFRD 317

Query: 295 --HILTVEAGASTATHHIIETAFNLMIES 321
             + LT       A         + ++ES
Sbjct: 318 KVNHLTSPVLMREAIEEFFLA--SQVLES 344


>gi|195350041|ref|XP_002041550.1| GM16688 [Drosophila sechellia]
 gi|194123323|gb|EDW45366.1| GM16688 [Drosophila sechellia]
          Length = 503

 Score =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 62/306 (20%), Positives = 121/306 (39%), Gaps = 42/306 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L++P
Sbjct: 94  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            D++ 
Sbjct: 153 VTCKIRIFEDLEKT----IRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVADWNY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +++    + +  NG +  +    + L    VDGVM       N A+   V       
Sbjct: 203 IKNVRQHI-KIPMLANGNILALDDVHRCLTETGVDGVMSAEGNLHNPAIFKGV------- 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRRC 293
               SP   ++  ++   +       +            I  H+  LFH       +   
Sbjct: 255 ----SPPVWQMAHEYLEFVQLHPCPSSF-----------IRGHLFKLFHHIMNIRQNSEL 299

Query: 294 RHILTV 299
           R  L  
Sbjct: 300 RQYLAT 305


>gi|66815915|ref|XP_641974.1| tRNA-dihydrouridine synthase 1-like protein [Dictyostelium
           discoideum AX4]
 gi|60470022|gb|EAL68003.1| tRNA-dihydrouridine synthase 1-like protein [Dictyostelium
           discoideum AX4]
          Length = 435

 Score =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 104/235 (44%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD T   +R   R      ++YT M  +   A  +  +++      +++PL +Q  G +
Sbjct: 59  MVDHTFLAFRMLCRKY-GADMVYTPMFHSKNFATCKTYRRDYWSTCPEDRPLVVQFCGNE 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +V+AAK +ED   + I+LN+GCP      G++G+ L+  P I+   +  + K + +P
Sbjct: 118 PEWVVKAAKYIEDH-CDAIDLNLGCPQQIARRGNYGSFLLDKPHIILPIVQELHKHIKVP 176

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +  K R+  +          L   ++++G   + IH R    KG            ++  
Sbjct: 177 IFCKIRLLPNLDDT----IKLALQLQEAGCQLLTIHGRTKEQKG------HNSGIANWKA 226

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +  I+++   + +  NG +   ED+ + L+     DGVM       N +  + + 
Sbjct: 227 IRTIREQL-SIPVIANGSVVQYEDIDRCLEE-TGADGVMSAEGILANPSFFSGLK 279


>gi|332701296|ref|ZP_08421384.1| TIM-barrel protein, nifR3 family [Desulfovibrio africanus str.
           Walvis Bay]
 gi|332551445|gb|EGJ48489.1| TIM-barrel protein, nifR3 family [Desulfovibrio africanus str.
           Walvis Bay]
          Length = 322

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 127/314 (40%), Gaps = 26/314 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   R L   A+  TEMI A  ++   +    IL   + + PL  Q+ G++ 
Sbjct: 18  AGFSDLPFRLLCREL-GAAVTVTEMISARGLVYDSRNTQPILATDSADSPLVAQLFGSEP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
             + +A  ++   G+   +LN GC   +V +   GA LM +PD++     AM + A    
Sbjct: 77  KFMGQATDMLLARGFTWFDLNCGCSVPKVVKTGSGAALMKDPDLLLAVAKAMVERASPFR 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R+G +          + K+++++GV  + +H R A  +G S          D+  
Sbjct: 137 VGVKMRLGWNP--SGENYLEVAKALEQAGVGWLTLHPRYA-QQGFS-------GQADWAA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  + +++  + +  +G L     A++ L      GVM  R A ++ A+   +    +  
Sbjct: 187 VARL-RQSVSIPVLASGDLFTAEDAVRCLQETGASGVMFARGALRDPAVFMRLQAALNGG 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              S P    + +   + I       +   L     + +  RH+          +  R  
Sbjct: 246 Q-ASVPSLAWIIRRHVQLIHEHGLP-SRELLKMRTIVPRYVRHI-------DGCKELRQR 296

Query: 297 LTVEAGASTATHHI 310
           L + +      H +
Sbjct: 297 LVMCSSWEELEHIV 310


>gi|296232631|ref|XP_002761660.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Callithrix jacchus]
          Length = 651

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 109/284 (38%), Gaps = 26/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 318 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDVFGIQLEGAFPDTMT 376

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 377 KCAELLNRTVEVDFVDINVGCPIDLVYKKGGGCALMNRLAKFQQIVRGMNQVLDVPLTVK 436

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D++ + + 
Sbjct: 437 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWEYIAQC 486

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V GVMI R A     + T + E     ++ S 
Sbjct: 487 VKAASPMPLFGNGDILSFEDANHAMQTGVAGVMIARGALLKPWLFTEIKEQRHWDISSSE 546

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                        I    T+Y   H  S    +++  R ++   
Sbjct: 547 ----------RLDILRDFTNYGLEHWGSDTQGVEKTRRFLLQWL 580


>gi|90419633|ref|ZP_01227543.1| nitrogen regulation protein Nifr3 [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90336570|gb|EAS50311.1| nitrogen regulation protein Nifr3 [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 341

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 57/286 (19%), Positives = 116/286 (40%), Gaps = 25/286 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISK 61
             +D  +R  AR      ++ +EM+ +   ++G +++ L        L  +Q+ G D + 
Sbjct: 21  GISDVPFRRLARRF-GAGMVVSEMVASGEFVKGCEESALRAMRDGPGLHVVQLAGRDPAW 79

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVT 120
           +  AA  + D G + I++N+GCP+ +V  G  G+ LM  P++    + A    A  +PVT
Sbjct: 80  MQRAAAQLADNGTDIIDINMGCPAKKVVGGLSGSALMREPELALRIVEATVAGAGGVPVT 139

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G D +  ++    L  + + +GV  I +H R         + +      D+  + 
Sbjct: 140 LKMRLGWDRE--SINAPELAAAAEAAGVAMITVHGRT--------RSDFYDGQADWPAIA 189

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + +    + +  NG L    Q   +L     D VM+GR +     +           L 
Sbjct: 190 AV-RAAVSVPLVANGDLVSPEQITAMLAQSGADAVMVGRGSQGRPWL---------PGLL 239

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             +  +  + +     + A        H  +   ++   +H+    
Sbjct: 240 AGAIGEDELARLPLGDLVAEHYAAMLDHYGARVGVRHARKHLGWYL 285


>gi|195575487|ref|XP_002077609.1| GD22975 [Drosophila simulans]
 gi|194189618|gb|EDX03194.1| GD22975 [Drosophila simulans]
          Length = 505

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 62/306 (20%), Positives = 121/306 (39%), Gaps = 42/306 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L++P
Sbjct: 94  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            D++ 
Sbjct: 153 VTCKIRIFEDLEKT----IRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVADWNY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +++    + +  NG +  +    + L    VDGVM       N A+   V       
Sbjct: 203 IKNVRQHI-KIPMLANGNILALDDVHRCLTETGVDGVMSAEGNLHNPAIFKGV------- 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRRC 293
               SP   ++  ++   +       +            I  H+  LFH       +   
Sbjct: 255 ----SPPVWQMAHEYLEFVQLHPCPSSF-----------IRGHLFKLFHHIMNIRQNSEL 299

Query: 294 RHILTV 299
           R  L  
Sbjct: 300 RQYLAT 305


>gi|194765691|ref|XP_001964960.1| GF22874 [Drosophila ananassae]
 gi|190617570|gb|EDV33094.1| GF22874 [Drosophila ananassae]
          Length = 509

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 121/305 (39%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R    + L YT M  A+        +K+ L     ++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRYGAH-LCYTPMYHANLFATDPKYRKDALQTCAGDRPLVIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA   +D   + +++N+GCP A    G +G+ L    +++ + ++ + K LSIP
Sbjct: 94  AQQILDAALAAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHKKLSIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            + ++ +G   + +H R    KG            D+  
Sbjct: 153 VTCKIRIFEDR----AKTIRYAQMLEAAGCQLLTVHGRTREQKG------PLTGVADWSY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+++    + +  NG +  +    + L    VDGVM       N A+           
Sbjct: 203 IKEVRQHI-KIPMFANGNILGLEDVHRCLEETGVDGVMSAEGNLHNPAIFQ--------- 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             G +P    + K++   +        Y   HL    KL     H++ +          R
Sbjct: 253 --GLAPPVWHMAKEYLEFVDLYPCPSSYIRGHL---FKLFH---HIMNIRQN----SELR 300

Query: 295 HILTV 299
             L  
Sbjct: 301 ETLAT 305


>gi|291242586|ref|XP_002741186.1| PREDICTED: CG3645-like [Saccoglossus kowalevskii]
          Length = 599

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 59/285 (20%), Positives = 106/285 (37%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      ++     E    +Q+ G+    + 
Sbjct: 265 NLPFRRICKRY-GADITCGEMAMCTNLLQGQLSEWALVKRHHTEDLFGVQLCGSFPDTMT 323

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+I+ D    + I++NVGCP   V +   G  LM         I  M   + IP+TVK
Sbjct: 324 KCAEILNDKMDIDFIDVNVGCPIDLVFKKGGGCALMGRLSRFEHIITGMSSVMDIPITVK 383

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G+  Q        ++  ++  GV+ + +H R         ++ R     D+D + + 
Sbjct: 384 MRAGI--QDNNFTAHKVLPRLRDWGVSMVTLHGRS--------REQRYTKIADWDYISKC 433

Query: 183 KKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +    + +  NG +     A   +    V GVMI R A     + T + E     ++ S
Sbjct: 434 AEIAKPMPLYGNGDILSYEDANRQRQHTGVSGVMIARGALIKPWVFTEIKEQRHWDISSS 493

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                         I    T+Y   H  S  +    TR  +   L
Sbjct: 494 ERF----------DILRDFTNYGLEHWGSDQQGVDRTRRFLLEWL 528


>gi|319789225|ref|YP_004150858.1| dihydrouridine synthase DuS [Thermovibrio ammonificans HB-1]
 gi|317113727|gb|ADU96217.1| dihydrouridine synthase DuS [Thermovibrio ammonificans HB-1]
          Length = 316

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 73/327 (22%), Positives = 135/327 (41%), Gaps = 34/327 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADI 59
           M  +T   +R   R L      Y+E++ A  I R G++K +  F+  E+P+ LQ+ G + 
Sbjct: 14  MAGYTHSAFRLLCREL-GADRTYSELMNATGIARRGEEKELSFFTDSERPIHLQVYGQNP 72

Query: 60  SKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---L 115
            ++ + A  +   +    I++N GC   +V +      L+  P+ +G  +    KA   L
Sbjct: 73  EEIAQGAYVLASKYRPEAIDINFGCSVKKVLKAKAAGYLLQYPEEMGRIVEETVKALKPL 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVTVK R+G  +      L  + +++ K+GV+ I +H R A+ +G S        + D
Sbjct: 133 GIPVTVKIRLGFYED----TLEEIAENLLKAGVSAIALHPRLAV-QGFS-------GSAD 180

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V  +K+    + +  +G +    Q  +       +GVM+GRAA  N  +     E  
Sbjct: 181 WSRVKALKEIAGSVPVIGSGDVRSWRQIDEKFEQTGCNGVMVGRAAVSNPWIFKEYKERR 240

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              ++ +  +      DF  +    M  Y  +        + I   +  LF G       
Sbjct: 241 DIEVSLAERV------DFILRELELMWGYFPKE----KACKAIKAQISQLFKGVRG---- 286

Query: 294 RHILTVEAGASTATHHIIETAFNLMIE 320
           +  L      S +   ++     +  E
Sbjct: 287 KAKLNDAIMRSKSCEELVSNLLRIKEE 313


>gi|301784767|ref|XP_002927798.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Ailuropoda
           melanoleuca]
          Length = 646

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 105/280 (37%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 316 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQTSEWALLRRHPCEDVFGVQLEGAFPDTMT 374

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 375 KCAELLNRTIEVDFVDINVGCPIDLVYKKGGGCALMNRAAKFQQIVRGMNQVLDVPLTVK 434

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  G   + +H R         ++ R     D++ + + 
Sbjct: 435 IRTGVQERMNLA--HRLLPELRDWGAALVTLHGRS--------REQRYTKLADWEYIAQC 484

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 + +  NG +     A   +   V GVM+ R A     + T + E     ++ S 
Sbjct: 485 VTAASPMPLFGNGDILSYEDANRAMQTGVAGVMVARGALLKPWLFTEIKEQRHWDISSSE 544

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T Y   H  S  +  + TR  +
Sbjct: 545 ----------RLAILQDFTHYGLEHWGSDTQGVEKTRRFL 574


>gi|151946084|gb|EDN64315.1| tRNA dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|259148496|emb|CAY81741.1| Dus1p [Saccharomyces cerevisiae EC1118]
          Length = 423

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 78/316 (24%), Positives = 128/316 (40%), Gaps = 36/316 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L YT M+ A         R D  + L  S+ ++PL +Q  
Sbjct: 36  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L
Sbjct: 95  ANDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNL 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D +       N  K +  +G   + +H R    KG      +K    +
Sbjct: 154 KVPVTAKIRIFDDCEKS----LNYAKMVLDAGAQFLTVHGRVREQKG------QKTGLAN 203

Query: 176 YDIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ +  ++   P       NG +   ED+S+ ++ +   D VM       N  +   VD+
Sbjct: 204 WETIKYLRDNLPKETVFFANGNILYPEDISRCMEHI-GADAVMSAEGNLYNPGVFN-VDQ 261

Query: 232 YFSNPLTGSSPIKTRVDKDFWR--KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                      I  RVDK      +I     +  A          +I R  +      P+
Sbjct: 262 -----TKNKEKIFPRVDKIIREYFQIVKECQESKASKTAMKSHFFKILRPFL------PH 310

Query: 290 SRRCRHILTVEAGAST 305
               R  L      +T
Sbjct: 311 HTDIRSTLATMNAKAT 326


>gi|260575061|ref|ZP_05843062.1| TIM-barrel protein, nifR3 family [Rhodobacter sp. SW2]
 gi|259022683|gb|EEW25978.1| TIM-barrel protein, nifR3 family [Rhodobacter sp. SW2]
          Length = 332

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 60/296 (20%), Positives = 110/296 (37%), Gaps = 23/296 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
              TD  +R          L+ +EM+ +  +++     +        +   A+Q+ G + 
Sbjct: 27  AGITDLPFRRLVAGF-GAGLVVSEMVASQEVVQARPLARARAELGFDQASTAVQLAGREA 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAA+ V   G   I++N+GCP+ +V  G  G+ LM + D     I A+  A+ +PV
Sbjct: 86  HWMAEAARFVAGQGARVIDINMGCPARKVTNGYSGSALMRDLDHALRLIEAVVGAVEVPV 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+ +  +    L +  + +GV  I IH R         +        D+  +
Sbjct: 146 TLKTRLGWDEAL--LNAPELAQRAESAGVAMITIHGRT--------RCQFYKGAADWAAI 195

Query: 180 YEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +      + +  NG + D   +QA        GVM+GR A     +L  +        
Sbjct: 196 AGVTSAVG-VPVIANGDIVDAASAQAALAASGAAGVMVGRGAQGRPWLLAQISAEVYGTP 254

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF--HGFPNSR 291
               P    +           +  Y          ++   +H+       G    R
Sbjct: 255 QPLVPQGAALADLVIGHYQDMLGFY-----GRDLGVKVARKHLGWYLEAAGVAGQR 305


>gi|268679177|ref|YP_003303608.1| dihydrouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268617208|gb|ACZ11573.1| dihydrouridine synthase DuS [Sulfurospirillum deleyianum DSM 6946]
          Length = 312

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 125/303 (41%), Gaps = 32/303 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      + ++EMI A+A+    +K   +L  S  E P  +QI G+D+
Sbjct: 18  AGFTDLPFRSVVKKF-GADVTFSEMISANALRFKSEKTFKMLTKSPLEIPYIVQIVGSDL 76

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + + EA  I+ D  G   I+LN GCP  ++     G+ L+LN D +   I  +    +  
Sbjct: 77  TSIKEAVLILNDMEGIAGIDLNCGCPVPKMVAQEAGSSLLLNLDHMQRVIETIKTYSNKR 136

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T  K R+G + +IP +    + K+ + +G + + +H R         +       +DY 
Sbjct: 137 YTSAKVRLGFNTKIPEL----IAKACENAGADFMSMHGRT--------RSGAYKAEVDYQ 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + E  +    + +  NG +  + +AL ++       +MIGR A  N  +   +     +
Sbjct: 185 AIAE-ARAAVKIPVIANGDITSLEKALHVMSVTGCKNLMIGRGALGNPWIFYQLKNGLHH 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   KT++ +       A +  Y  +       +    +H+     GF  +   R 
Sbjct: 244 VE------KTKILEIVLEHYDAMVEFYGEK------GVSIFRKHLHTYSKGFREASEFRD 291

Query: 296 ILT 298
            + 
Sbjct: 292 KIN 294


>gi|254282370|ref|ZP_04957338.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR51-B]
 gi|219678573|gb|EED34922.1| tRNA-dihydrouridine synthase B [gamma proteobacterium NOR51-B]
          Length = 319

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 131/319 (41%), Gaps = 27/319 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP--LALQIGGAD 58
           M   TDR +R    L    A+  +EMI  D  L   +K  L      +    ++QI G D
Sbjct: 1   MAGVTDRPFRELC-LDLGAAMAVSEMISDDPELAQSRKTRLRREHSPRAALRSVQIVGND 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++  AA      G + I++N+GCP+ +V + + G+ L+ +  +V   + A+   +S+P
Sbjct: 60  PERMAAAALRNAKDGADIIDINMGCPAKKVCKKAAGSALLGDEALVTAILEAVVSTVSVP 119

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G+D          + K  + +GV  + +H R         + ++   + +Y  
Sbjct: 120 VTLKIRTGLDRSRRNGV--RIAKIAEDAGVQMLAVHGRT--------RADKFAGDAEYHT 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +I  +   + +  NG +  +++A ++L      GVMIGR A     +   +       
Sbjct: 170 IEQIV-DAVTIPVLANGDINSITRARRVLETTGAAGVMIGRGAQGQPWLPGMIARALRGQ 228

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG----LFHGFP-NSR 291
            T +   +T+V +     +   +  Y       G K+    +H+       F   P  +R
Sbjct: 229 STAAPSPETQV-QIIQGHLLELIAFYGEFM---GTKI--ARKHVGWFADGWFTNEPTTAR 282

Query: 292 RCRHILTVEAGASTATHHI 310
           R +              H+
Sbjct: 283 RWKQQFNRLDHYKDQLEHL 301


>gi|281348023|gb|EFB23607.1| hypothetical protein PANDA_017628 [Ailuropoda melanoleuca]
          Length = 610

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 105/280 (37%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 280 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQTSEWALLRRHPCEDVFGVQLEGAFPDTMT 338

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 339 KCAELLNRTIEVDFVDINVGCPIDLVYKKGGGCALMNRAAKFQQIVRGMNQVLDVPLTVK 398

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  G   + +H R         ++ R     D++ + + 
Sbjct: 399 IRTGVQERMNLA--HRLLPELRDWGAALVTLHGRS--------REQRYTKLADWEYIAQC 448

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 + +  NG +     A   +   V GVM+ R A     + T + E     ++ S 
Sbjct: 449 VTAASPMPLFGNGDILSYEDANRAMQTGVAGVMVARGALLKPWLFTEIKEQRHWDISSSE 508

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T Y   H  S  +  + TR  +
Sbjct: 509 ----------RLAILQDFTHYGLEHWGSDTQGVEKTRRFL 538


>gi|126726844|ref|ZP_01742683.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodobacterales
           bacterium HTCC2150]
 gi|126703802|gb|EBA02896.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Rhodobacterales
           bacterium HTCC2150]
          Length = 329

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 71/322 (22%), Positives = 125/322 (38%), Gaps = 26/322 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGA 57
              TD  +R          L+ +EM+ +  +++     +    LGF +     A+QI G 
Sbjct: 22  AGITDLPFRNLVSQF-GAGLVVSEMVASHEMMQAKPSTLAKAELGFDSANT--AVQIAGR 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + EAAK+    G   I++N+GCP+ +V  G  G+ L+ + D+    IAA+  A+ +
Sbjct: 79  EAYWMSEAAKLCAANGAKIIDINMGCPAKKVTSGYSGSALLRDLDLAVSLIAAVVAAVDV 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G DD     A   L K  +  G+  I IH R         +      + D++
Sbjct: 139 PVTLKTRLGWDDDSHNAA--ELAKRAEAEGIAWITIHGRT--------RCQFYKGSADWE 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +IK+    + +  NG + D   A + L     DG+M+GR A      L T+      
Sbjct: 189 AISKIKQAV-KIPVFANGDIVDDFSAKQALKVSGADGIMVGRGAQGRPWQLATIASKLWG 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               + P                ++ Y A         +   +H+             R 
Sbjct: 248 ASAPNVPKGQARADLISGHYQDMLSFYGAE-----LGGRNARKHLGWYLDDVECPPELRR 302

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +  +         +I  A + 
Sbjct: 303 EIMTQKSV-ELVPQLISEAMSF 323


>gi|242072234|ref|XP_002446053.1| hypothetical protein SORBIDRAFT_06g001050 [Sorghum bicolor]
 gi|241937236|gb|EES10381.1| hypothetical protein SORBIDRAFT_06g001050 [Sorghum bicolor]
          Length = 679

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 109/287 (37%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM ++  +L+G      +L     E    +QI G     + 
Sbjct: 338 NLPFRRLCKTL-GADVTCGEMAMSTNLLQGQASEWALLRRHPSEDLFGVQICGPYPDTVA 396

Query: 64  EAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++V++    + I++N+GCP   V     G+ L+  P  +   + A       P+TVK
Sbjct: 397 RTVELVDNECPVDFIDINMGCPIDIVVNKGAGSSLLTKPMRIRSIVQAASSVTEKPLTVK 456

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +        ++V  I   G + I IH R         +  R     D+D +Y+ 
Sbjct: 457 VRTAFFEGRNRA--DSIVSDIYDWGASAITIHGRS--------RQQRYSKLADWDYIYQC 506

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +   +   K +     +   MI R A     + T + E     +T
Sbjct: 507 AQKAPDYLHVIGNGDVFSFTDWNKHVSDCSKISTCMIARGALIKPWLFTEIKEQRHWDIT 566

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                +  + KDF R        +   H  S  K  + TRH +   L
Sbjct: 567 SGE--RLNILKDFVR--------FGLEHWGSDSKGVETTRHFLLEWL 603


>gi|281207360|gb|EFA81543.1| tRNA-dihydrouridine synthase 1-like protein [Polysphondylium
           pallidum PN500]
          Length = 430

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 118/287 (41%), Gaps = 24/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M+D T   +R   R      L+YT M  +          +  F  + +++PL +Q  G +
Sbjct: 81  MIDHTFLAFRMLCRKY-GADLVYTPMFHSKNYATNATYRLENFEIAKEDRPLVVQFCGNE 139

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +V+AAK+VE    + ++LN+GCP      G++GA L+  PD++   + A+ K LS+P
Sbjct: 140 VDYIVQAAKMVE-SQCDAVDLNLGCPQGIARRGNYGAFLLEKPDVILPMVRALHKELSVP 198

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +  K R+  +          L   ++++G   + +H R    KG         P+ ++  
Sbjct: 199 IFCKIRLLPNLDDT----IKLALQLQEAGCQLLTVHGRTKEQKG------HTQPHANWKA 248

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN- 235
           +  IK+    + +  NG + +     + L     DGVM       N AM    +   S  
Sbjct: 249 IRAIKEALV-IPVIANGSVGEWGDIEECLKETGADGVMSADGILNNPAMFNGAERIGSTT 307

Query: 236 ------PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                  +    P   ++ +  + K+     ++          L ++
Sbjct: 308 LCREYLEMVKKYPTPYQIVRSHFYKMLKKECEHYEDLRDKLAHLYEM 354


>gi|222099569|ref|YP_002534137.1| TIM-barrel protein, nifR3 family [Thermotoga neapolitana DSM 4359]
 gi|221571959|gb|ACM22771.1| TIM-barrel protein, nifR3 family [Thermotoga neapolitana DSM 4359]
          Length = 273

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 59/272 (21%), Positives = 111/272 (40%), Gaps = 25/272 (9%)

Query: 26  MIVADAILRGDKKNI-LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           M+ A   L   +K   L  S +EK +A+QI G+D  +L  AA ++ D  Y  I+LN GCP
Sbjct: 1   MVSAKGFLMNSEKTRELLPSPEEKNVAVQIFGSDPEELSRAADVLSDE-YPWIDLNAGCP 59

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
             +V +   G  L+ + D+    +  + K +    TVK R+G ++      +  + + + 
Sbjct: 60  VRKVVKKGAGGGLLRDLDLFRAVVKELRKHVKGKFTVKTRLGWNEN----QISKIYEILV 115

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           + GV+ ++IH R          D + +  LD             +   ++G +     A 
Sbjct: 116 EEGVDEVFIHTRTVAQAFTGKADWKSLSVLD-----------KKIPTFVSGDIFSPEDAK 164

Query: 205 KILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           + L      GV++ R A     +   + ++       S P    + + F   +S  + D 
Sbjct: 165 RALEESGCHGVLVARGAIGRPWLFKQIKDFLERGKY-SEPSTDEILRSFEMHLSLLVEDK 223

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                     +++I + + G       +RR R
Sbjct: 224 GEE-----KAIKEIKKFVAGYTKNLKGARRFR 250


>gi|15807427|ref|NP_296160.1| nifR3 protein [Deinococcus radiodurans R1]
 gi|6460259|gb|AAF11984.1|AE002074_2 nifR3 protein [Deinococcus radiodurans R1]
          Length = 406

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 64/280 (22%), Positives = 108/280 (38%), Gaps = 26/280 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGA 57
           M  ++D   R  A          +EMI A  ++ G ++  L        E+  A+Q+ GA
Sbjct: 99  MAGYSDAPMRQLAAE-QGALWTVSEMISARGLVLGSEQESLSLGRPYPGEQGRAVQLFGA 157

Query: 58  DISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D   L +A    E  F    I+LN+GCP  +V     GACL+  P++  + + AM +A  
Sbjct: 158 DPDVLADAVGKAEAWFAPAAIDLNLGCPVPKVRGKG-GACLLQTPEVAYELVRAMRQATG 216

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V+ K R+G D+         + + ++ +G   + +H R            R   N D+
Sbjct: 217 LDVSAKIRLGWDENRSV----EIAQGLEAAGAAVVTVHGRT--------SAQRYTGNADW 264

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  + +    + +  +G +    QA + +    V  VMIGR A  N  M   +     
Sbjct: 265 DAIGRVAQAV-RIPVIGSGDVLSPVQARERMQQSGVAAVMIGRGAVGNPWMFRAIASGEE 323

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                  P      +   R        Y   H     +L 
Sbjct: 324 T-----LPPAQERARTALRHAELQHDFYTTPHRRDPSRLH 358


>gi|19920448|ref|NP_608507.1| CG3645, isoform A [Drosophila melanogaster]
 gi|24580595|ref|NP_722619.1| CG3645, isoform B [Drosophila melanogaster]
 gi|15292203|gb|AAK93370.1| LD42056p [Drosophila melanogaster]
 gi|22945600|gb|AAF51525.2| CG3645, isoform A [Drosophila melanogaster]
 gi|22945601|gb|AAN10512.1| CG3645, isoform B [Drosophila melanogaster]
 gi|220955978|gb|ACL90532.1| CG3645-PA [synthetic construct]
 gi|295293325|gb|ADF87928.1| MIP22167p [Drosophila melanogaster]
          Length = 505

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 121/306 (39%), Gaps = 42/306 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L Y+ M  A+        +K+ L    +++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRY-GAELCYSPMYHANLFATDPKYRKDALQTCPEDRPLIIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA + +D   + +++N+GCP A    G +G+ L    +++ + ++ +   L++P
Sbjct: 94  AQQILDAALLAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIVSTLHAKLAVP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G   + +H R    KG            +++ 
Sbjct: 153 VTCKIRIFEDLEKT----IRYAKMLEAAGCQLLTVHGRTREQKG------PLTGVANWNY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +++    + +  NG +  +    + L    VDGVM       N A+   V       
Sbjct: 203 IKNVRQHI-KIPMLANGNILALDDVHRCLTETGVDGVMSAEGNLHNPAIFKGV------- 254

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRRC 293
               SP   ++  ++   +       +            I  H+  LFH       +   
Sbjct: 255 ----SPPVWQMAHEYLELVQLHPCPSSF-----------IRGHLFKLFHHIMNIRQNSEL 299

Query: 294 RHILTV 299
           R  L  
Sbjct: 300 RQYLAT 305


>gi|6323560|ref|NP_013631.1| Dus1p [Saccharomyces cerevisiae S288c]
 gi|1730621|sp|P53759|DUS1_YEAST RecName: Full=tRNA-dihydrouridine synthase 1
 gi|587531|emb|CAA86498.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285813922|tpg|DAA09817.1| TPA: Dus1p [Saccharomyces cerevisiae S288c]
          Length = 423

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 125/316 (39%), Gaps = 36/316 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L YT M+ A         R D  + L  S+ ++PL +Q  
Sbjct: 36  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L
Sbjct: 95  ANDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNL 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D +       N  K +  +G   + +H R    KG      +K    +
Sbjct: 154 KVPVTAKIRIFDDCEKS----LNYAKMVLDAGAQFLTVHGRVREQKG------QKTGLAN 203

Query: 176 YDIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ +  ++   P       NG +   ED+S+ ++ +   D VM       N  +      
Sbjct: 204 WETIKYLRDNLPKETVFFANGNILYPEDISRCMEHI-GADAVMSAEGNLYNPGVFN---- 258

Query: 232 YFSNPLTGSSPIKTRVDKDFWR--KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                      I  RVDK      +I     +  A          +I R  +      P+
Sbjct: 259 --VGQTKNKEKIFPRVDKIIREYFQIVKECQESKASKTAMKSHFFKILRPFL------PH 310

Query: 290 SRRCRHILTVEAGAST 305
               R  L      +T
Sbjct: 311 HTDIRSTLATMNAKAT 326


>gi|168057686|ref|XP_001780844.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667700|gb|EDQ54323.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 401

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 126/300 (42%), Gaps = 24/300 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MVD ++  +R   R        Y+ M+ +    +  K  +  FS   +++PL +Q    +
Sbjct: 51  MVDQSELPFRMLCRKY-GATAAYSPMLHSRLFAQDAKYRLKEFSTCPEDRPLFIQFCANN 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAAK+V+D   + +++N GCP      G++GA LM +  +V   +  +   L+ P
Sbjct: 110 PDTLLEAAKLVQD-DCDYVDINFGCPQRIAKRGNYGAFLMDDLPLVRSLVEKLSSGLTTP 168

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+    +          + I+++G + + +H R         KD + I   D+ +
Sbjct: 169 VSCKIRMFPKLEDT----LAYARMIEEAGCSLLAVHGRTRDQ-----KDGKSI-RADWGV 218

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +  +    + +    VDGVM   +  +N A+      Y   P
Sbjct: 219 IKAVKSAL-RIPVVANGNIRWLEDVDECIRATGVDGVMSAESLLENPALFAG---YRMKP 274

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH---MIG-LFHGFPNSRR 292
           L  S+      DK +       + +Y           + I  H   M+G  F  +P+ R 
Sbjct: 275 LDSSAAEPDDHDKKYSLNEPTLVLEYLDFCDKYPVPARMIRAHVHRMLGPWFRQYPHLRE 334


>gi|294932843|ref|XP_002780469.1| tRNA-dihydrouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
 gi|239890403|gb|EER12264.1| tRNA-dihydrouridine synthase A, putative [Perkinsus marinus ATCC
           50983]
          Length = 403

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 109/350 (31%), Positives = 164/350 (46%), Gaps = 31/350 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-----KNILGFSTQEKPLALQIG 55
           MVD +DR +R F RLL++   ++TEM+V  A++  +      + I+GF+  E P+  Q+G
Sbjct: 1   MVDVSDRDFRMFMRLLSSKCEVWTEMLVDQALVHNEDIPRQLEKIIGFTEAEHPIVCQLG 60

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKA 114
           G D SKL  AA+I    GY+E+NLNVGCPS+RV      G  LM  P++V DC+  +   
Sbjct: 61  GHDPSKLAAAARIAHRRGYDEVNLNVGCPSSRVAGHGLMGVALMKTPELVRDCLRTLDDE 120

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSI-------KKSGVNGIWIHARKAILKGLSPKD 167
           +   V++K R+GVDD       R+ + +I              + +H RKA L+GLSP +
Sbjct: 121 VPH-VSIKTRLGVDDLDTEEFTRSFLGTILPPLASSAAQQPYRVIMHCRKAWLQGLSPAE 179

Query: 168 NRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP------SVDGVMIGRAAY 220
           NR +P LDY     +       +   LNGG+E + QA  +L       +++GVMIGRAAY
Sbjct: 180 NRTVPPLDYPRACRVLGAFGSRVRWTLNGGIETLWQAKDVLTSEIAPANLEGVMIGRAAY 239

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT--- 277
            N  ML   D Y        +P+            +  + D       S           
Sbjct: 240 NNPCMLHDADVYLYG--CDENPVSAESRGALLEAYADYLHDRYPLESDSPLTPGTFATSL 297

Query: 278 RHMIGLFHGFPNSRRCRHILT--VEAGASTATH---HIIETAFNLMIESL 322
           +  +G F     +R  RH +   ++A           ++  A   M E L
Sbjct: 298 KPTLGTFANKSGNRMYRHTIDGLIKAHKRDREVGPGDVVRMAMREMPEEL 347


>gi|194212507|ref|XP_001916859.1| PREDICTED: similar to dihydrouridine synthase 3-like [Equus
           caballus]
          Length = 784

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 104/280 (37%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 451 NLPFRRVCKRF-GADVTCGEMAVCTNLLQGQTSEWALLRRHQCEDIFGVQLEGAFPDTMT 509

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 510 KCAELLNRTVDVDFVDINVGCPIDLVYKKGGGCALMQRSGKFQQIVRGMSQVLDVPLTVK 569

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV ++ P      L+  ++  G   + +H R         ++ R     D+  + + 
Sbjct: 570 LRTGVQERTPLA--HRLLPELRTWGAALVTLHGRS--------REQRYTKLADWRYIEQC 619

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 + +  NG +     A   +   V GVMI R A     + T + E     ++ S 
Sbjct: 620 VAAASPMPLFGNGDILSYEDANRAMQTGVAGVMIARGALLKPWLFTEIKEQRHWDISASE 679

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T Y   H  S  +  + TR  +
Sbjct: 680 ----------RLDILRDFTHYGLEHWGSDTQGVERTRRFL 709


>gi|213401397|ref|XP_002171471.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|211999518|gb|EEB05178.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 403

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 74/335 (22%), Positives = 138/335 (41%), Gaps = 38/335 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS----TQEKPLALQIGG 56
           MVD ++  +R  AR  +   + +T M  +             FS     +EKPL +Q  G
Sbjct: 26  MVDQSELPWRILARR-SGADMCFTPMFHSRLFSESKDYRDKVFSTKDIPEEKPLIVQFCG 84

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            ++  +++AAK+ E +    ++LN+GCP     +G +G+ +  N +++   I+ +   LS
Sbjct: 85  NEVETMLQAAKLAEPYCVA-VDLNLGCPQGIARKGKYGSFMQDNWELIEAIISKLHAELS 143

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K RI  D            K I ++G + + +H R    +G++          D+
Sbjct: 144 VPVTAKIRIFPDPSRT----LEYAKMILRAGASILTVHGRTREQRGINT------GIADW 193

Query: 177 DIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D +  ++++ P D  +  NG +    D+ + L+    VDGVM    +  N  +  +    
Sbjct: 194 DQIKMLREKLPADTVLFANGNILHSSDIERCLE-YTGVDGVMSAEGSLYNPKVFLS---- 248

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH--LHSGGKLQQITRHMIGLFHGF-PN 289
              P    + +  RVDK           D    H        L  +  H+  + H F   
Sbjct: 249 ---PSRPYTELYPRVDKM-----CEEYFDIVREHGLTKDYSSLSAMKGHLFKILHSFLSK 300

Query: 290 SRRCRHILTVEAGAST--ATHHIIETAFNLMIESL 322
               R +L V+   +   +   +++     +  SL
Sbjct: 301 HTDLRQVLGVKCTPTDFESFVQLVQEVRERIETSL 335


>gi|126323260|ref|XP_001376181.1| PREDICTED: similar to Dihydrouridine synthase 3-like (S.
           cerevisiae) [Monodelphis domestica]
          Length = 666

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 109/284 (38%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 333 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQSSEWALLKRHHTEDLFGVQLEGAFPDTMT 391

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M + L +P+TVK
Sbjct: 392 KCAELLNQTVEVDFVDINVGCPIDLVYKKGGGCALMNRSNKFEQIVRGMNQVLDVPLTVK 451

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  +++ GV    +H R         ++ R     D+  +   
Sbjct: 452 IRTGVQEKVNLA--HRLLPELREWGVALATLHGRS--------REQRYTKGADWQYIQHC 501

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A + L   V G+MI R A     + T + E     ++   
Sbjct: 502 AEVAHPMPLFGNGDILSYEDANRALQTGVSGIMIARGALIKPWLFTEIKEQRHWDISSGE 561

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T+Y   H  S  +  + TR  +   L
Sbjct: 562 RL----------DILRDFTNYGLEHWGSDTQGVEKTRKFLLEWL 595


>gi|256269754|gb|EEU05021.1| Dus1p [Saccharomyces cerevisiae JAY291]
          Length = 423

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 76/316 (24%), Positives = 125/316 (39%), Gaps = 36/316 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L YT M+ A         R D  + L  S+ ++PL +Q  
Sbjct: 36  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L
Sbjct: 95  ANDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNL 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D +       N  K +  +G   + +H R    KG      +K    +
Sbjct: 154 KVPVTAKIRIFDDCEKS----LNYAKMVLDAGAQFLTVHGRVREQKG------QKTGLAN 203

Query: 176 YDIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ +  ++   P       NG +   ED+S+ ++ +   D VM       N  +      
Sbjct: 204 WETIKYLRDNLPKETVFFANGNILYPEDISRCMEHI-GADAVMSAEGNLYNPGVFN---- 258

Query: 232 YFSNPLTGSSPIKTRVDKDFWR--KISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                      I  RVDK      +I     +  A          +I R  +      P+
Sbjct: 259 --VGQTKNKEKIFPRVDKIIREYFRIVKECQESKASKTAMKSHFFKILRPFL------PH 310

Query: 290 SRRCRHILTVEAGAST 305
               R  L      +T
Sbjct: 311 HTDIRSTLATMNAKAT 326


>gi|78355436|ref|YP_386885.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
 gi|78217841|gb|ABB37190.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 378

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 123/320 (38%), Gaps = 24/320 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   R      ++ +EM+ A  ++        +L    Q+ P+ LQ+ G ++
Sbjct: 50  AGFTDLAFRLLCREF-GARVVCSEMVSAKGLVYRSPGTHALLETCPQDAPMVLQLFGNEV 108

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
             +  A + + D GY   +LN+GC   +V +   GA ++ +         AM   A +  
Sbjct: 109 PIMDAAMRELVDKGYRWFDLNMGCSVRKVVKTGCGAGMLRDVPNAVRVARAMTAVAGAGR 168

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G +    A    +L + ++ +G   + +H R A                D+D 
Sbjct: 169 VGFKFRLGWEQG--AQVCMDLARRLEDAGAGWLTLHPRFA--------RQGFSGTADWDA 218

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E+  + +  +G L     A++ +    VDGVM  R A  N A+        S  
Sbjct: 219 LARLK-EHVTIPVIASGDLFTAGDAVRCMRASGVDGVMFARGALANPAVFEDFSAMMSGG 277

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                P   R  +   R ++      A         L ++   +      FP +R  R+ 
Sbjct: 278 E-QPQPDPERTVRIIRRHVAL-----ARALCAEKTALFKMRTFVPRYVRQFPGARALRNH 331

Query: 297 LTVEAGASTATHHIIETAFN 316
           L           H+++T F 
Sbjct: 332 LASCLTWEGLD-HLLDTFFE 350


>gi|114704555|ref|ZP_01437463.1| nitrogen regulation protein nifr3 [Fulvimarina pelagi HTCC2506]
 gi|114539340|gb|EAU42460.1| nitrogen regulation protein nifr3 [Fulvimarina pelagi HTCC2506]
          Length = 344

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 59/286 (20%), Positives = 108/286 (37%), Gaps = 25/286 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLAL-QIGGADISK 61
             +D  +R  +R      L+ +EM+ +   ++G ++  L        +   Q+ G D   
Sbjct: 27  GISDVPFRRLSRRF-GAGLVVSEMVASGEFVKGAEEGKLRALRDGPGVHTVQLAGRDPIW 85

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVT 120
           + EAA+ + D G + I++N+GCP+ +V  G  G+ LM  PD+    + A +  A + PV+
Sbjct: 86  MEEAARRLADEGADLIDINMGCPAKKVVGGLSGSALMREPDLAFSIVEATVRGAGATPVS 145

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+G        A   +    + +GV  I +H R         +        D+  + 
Sbjct: 146 LKMRLGWCRDSMNAA--EIAVRAEAAGVTMITVHGRT--------RAEFYEGTADWRAIC 195

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+    + +  NG L + +Q   IL     D VM GR                   L 
Sbjct: 196 SVKRSVG-VPVVANGDLTEANQLSAILAASGADAVMTGRGMQGRPW---------FAGLL 245

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  R+             +    H      ++   +H+   F
Sbjct: 246 AGRVTMERLSAIDAADFVGGHYEAMLSHYGVTTGVRHARKHLGWYF 291


>gi|196230050|ref|ZP_03128913.1| dihydrouridine synthase DuS [Chthoniobacter flavus Ellin428]
 gi|196225647|gb|EDY20154.1| dihydrouridine synthase DuS [Chthoniobacter flavus Ellin428]
          Length = 330

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 70/306 (22%), Positives = 126/306 (41%), Gaps = 25/306 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE--MIVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +           L  TE   +  D+ L  D    +  +   +P+  Q+ G D
Sbjct: 1   MQDVTDLPFWQLLTRYGGADLCVTEYFRVHPDSRLDPDILASITKNPTGRPVVAQMMGND 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  LV AAK +E      I+LN+GCP   V+    G  L+ +P+ V   + A+ +A++IP
Sbjct: 61  IPSLVRAAKELEQHPVAAIDLNLGCPVPVVYRKCAGGGLLRDPERVDSILGALREAVTIP 120

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TVK RIG DD         ++    +  ++ + +H R       S         + Y+ 
Sbjct: 121 FTVKTRIGFDDPS---VFEQMLPIYARHSLDLLTVHGRTVKEMYRS--------EVHYEY 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +       P   +  NG +  +  A ++  L    G+MIGRAA +N  +   + ++    
Sbjct: 170 IARAVAAMP-CPVVANGNVSSVHSAEEVLNLTGARGLMIGRAAIRNPWIFQQIRQHRR-- 226

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC--- 293
              S PI     ++    I A         +    ++Q++ +++  +  G   + +    
Sbjct: 227 ---SEPIYQPTGREVLEYIQALYEAVCDPQVRETSQVQKMKKYLTYISDGVEPTGQFQHS 283

Query: 294 -RHILT 298
            R ++T
Sbjct: 284 IRRVIT 289


>gi|41056139|ref|NP_956968.1| tRNA-dihydrouridine synthase 3-like [Danio rerio]
 gi|34784014|gb|AAH58066.1| Zgc:63779 [Danio rerio]
          Length = 660

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 107/284 (37%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      +L     E    +Q+ G     + 
Sbjct: 327 NLPFRRVCKRF-GADITCGEMAMCTNLLQGQASEWALLKRHASEDLFGVQLEGCFPDTMT 385

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++      + +++N GCP   V++   G  LM         +  M   L +P+TVK
Sbjct: 386 RCAELLNQNIDVDFVDINSGCPIDLVYKKGGGCGLMTRTSKFEQIVRGMNSVLDVPLTVK 445

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV  Q  +     L+  +KK GV+ I +H R         ++ R     D+D +   
Sbjct: 446 IRTGV--QQNSNIAHKLIPEMKKWGVSLITLHGRS--------REQRYTKLADWDYINTC 495

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A+K     V G+M+ R A     + T + E     ++ + 
Sbjct: 496 AQLAAPVPLFGNGDILSYEDAMKARETGVSGIMVARGALIKPWLFTEIKESRHWDISSTE 555

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T +   H  S  +  + TR+ +   L
Sbjct: 556 RL----------DILRDFTHFGLEHWGSDTQGVEKTRNFLLEWL 589


>gi|126308862|ref|XP_001379483.1| PREDICTED: similar to DUS1L protein [Monodelphis domestica]
          Length = 480

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 61/284 (21%), Positives = 113/284 (39%), Gaps = 37/284 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVKAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----KYAQLLEKAGCQLLTVHGRTKEQKG------PLSGIASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  ++K   ++ +  NG ++   D+ + ++    V GVM       N A+        
Sbjct: 192 EHIKAVRKAV-NIPVFANGNIQYLHDVEKCIQE-TGVHGVMSAEGNLHNPALF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
                G +P+   + +++   +        Y   HL    KL  
Sbjct: 243 ----EGRNPLVWEMAEEYLEIVQQHPCPLSYVRAHL---FKLWH 279


>gi|225438801|ref|XP_002283225.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 424

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 68/300 (22%), Positives = 123/300 (41%), Gaps = 27/300 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 99  MVDNSELPFRMLCRKYGAQA-AYTPMLHSRIFSENEKYRSQEFTTCKEDRPLFVQFCAND 157

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA+ VE +  + +++N+GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 158 PDTLLEAAQRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLHVP 216

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+  + Q       N  + ++ +G + + +H R         KD +K    D++ 
Sbjct: 217 VSCKIRVFPNLQDT----INYARMLEDAGCSLLAVHGRT-----RDEKDGKKF-RADWNA 266

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +  M    + L     DGV+   +  +N A+           
Sbjct: 267 IKAVKNAV-SIPVLANGDIRHMDDVQRCLEETGADGVLSAESLLENPALFAGFQTA-EWA 324

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH---MIG-LFHGFPNSRR 292
           L G        +KD     +  + +Y           + I  H   ++G  F   P  R 
Sbjct: 325 LGGE-----EGNKDGELDQANLLVEYLKLCEKYPVPWRMIRSHVHKLLGEWFRIQPQVRD 379


>gi|190408164|gb|EDV11429.1| tRNA dihydrouridine synthase [Saccharomyces cerevisiae RM11-1a]
          Length = 423

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 74/314 (23%), Positives = 130/314 (41%), Gaps = 32/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L YT M+ A         R D  + L  S+ ++PL +Q  
Sbjct: 36  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ +    + K L
Sbjct: 95  ANDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLTNTLHKNL 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D +       N  K +  +G   + +H R    KG      +K    +
Sbjct: 154 KVPVTAKIRIFDDCEKS----LNYAKMVLDAGAQFLTVHGRVREQKG------QKTGLAN 203

Query: 176 YDIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ +  ++   P       NG +   ED+S+ ++ +   D VM       N  +   VD+
Sbjct: 204 WETIKYLRDNLPKETVFFANGNILYPEDISRCMEHI-GADAVMSAEGNLYNPGVFN-VDQ 261

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +       P   ++ ++++R I     +  A          +I R  +      P+  
Sbjct: 262 TKNKEKIF--PRVDKIIREYFR-IVKECQESKASKTAMKSHFFKILRPFL------PHHT 312

Query: 292 RCRHILTVEAGAST 305
             R  L      +T
Sbjct: 313 DIRSTLATMNAKAT 326


>gi|157127436|ref|XP_001654979.1| t-diRNAhydrouridine synthase [Aedes aegypti]
 gi|108882414|gb|EAT46639.1| t-diRNAhydrouridine synthase [Aedes aegypti]
          Length = 581

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 73/330 (22%), Positives = 131/330 (39%), Gaps = 49/330 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +    +K+ L    +++PL +Q  G D
Sbjct: 100 MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFSKDPKYRKDSLQTCPEDRPLIIQFCGND 158

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA + +D   + I++N+GCP A    G +GA L    D++ + ++ +   LS+P
Sbjct: 159 PKVLLEAALLAQDH-CDAIDINLGCPQAIAKRGHYGAFLQDEWDLLKEIVSTLHSKLSVP 217

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            K ++ +G   + +H R    KG            D+  
Sbjct: 218 VTCKIRIFEDMNKT----IRYAKMLEAAGCQMLTVHGRTRDQKG------PLTGIADWKY 267

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V ++K E   + +  NG +   ED+ + ++    V+G+M       N  +   V+     
Sbjct: 268 VKKLK-EILKIPVLSNGNIMGVEDVHRCMEE-TGVNGIMTAEGNLFNPFLFEGVN----- 320

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS----- 290
                 P    V  ++   +      Y A   +  G L +I  H++ L    PN+     
Sbjct: 321 ------PTAWSVALEYLDIVEQ----YPAPMSYIRGHLFKILHHLMNL---KPNAVLRER 367

Query: 291 -------RRCRHILTVEAGASTATHHIIET 313
                     R I+          H  ++ 
Sbjct: 368 MASCHSVSEFRAIVKEIEAKYAPIHEGLQQ 397


>gi|311248426|ref|XP_003123132.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Sus scrofa]
 gi|311248450|ref|XP_003123140.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Sus scrofa]
          Length = 652

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 56/284 (19%), Positives = 106/284 (37%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 319 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQTSEWALLKRHPCEDVFGVQLEGAFPDTMT 377

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 378 KCAELLNRTIEVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGMNQVLDVPLTVK 437

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  G   + +H R         ++ R     D+  + + 
Sbjct: 438 IRTGVQERVNLA--HRLLPELRDWGAALVTLHGRS--------REQRYTKLADWQYIEQC 487

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 488 VTAASPMPLFGNGDILSYEDANRAMKTGVAGIMIARGALLKPWLFTEIKEQRHWDISSSE 547

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T Y   H  S  +  + TR  +   L
Sbjct: 548 RL----------DILRDFTHYGLEHWGSDTQGVEKTRRFLLEWL 581


>gi|308233986|ref|ZP_07664723.1| TIM-barrel protein, nifR3 family [Atopobium vaginae DSM 15829]
 gi|328944005|ref|ZP_08241470.1| tRNA-dihydrouridine synthase [Atopobium vaginae DSM 15829]
 gi|327491974|gb|EGF23748.1| tRNA-dihydrouridine synthase [Atopobium vaginae DSM 15829]
          Length = 390

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 62/348 (17%), Positives = 124/348 (35%), Gaps = 43/348 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T+  YR   RL       Y+EM+    +   ++  + +    T E  L +Q+ G+D
Sbjct: 42  MAGVTNSAYRIMNRL-GGAQYAYSEMVSVAGLCMKNQATRELCLPHTAEPNLIVQLFGSD 100

Query: 59  ISKLVEAAKIVEDFGYN---EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A  +V +   +    I++N+ CP  +V +   G+ LM +P      + A  + +
Sbjct: 101 PVQFQRACALVGELLGDKLSCIDINMACPVPKVTKRGEGSALMCDPHRACALVRACLREV 160

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K R G      + A     ++++ +G + + +H R A                +
Sbjct: 161 RVPVTCKIRRGYYMDHESAA--EFGRALQDAGASALAVHGRFAK--------QLYKGEAN 210

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +  E  D+ +  +G +     A +IL       V+I R  Y N  +     + F
Sbjct: 211 WESIKRVV-EAVDIPVIASGDVMSAEDACRILYKTQAHAVLIARGTYGNPWIFDDALKIF 269

Query: 234 SNP----LTGSSPIKTRVDKDFWRKISASMTDYAA-----------RHLHSGGKLQQITR 278
           +          S +   +D   +   +     +A              L    +L   T 
Sbjct: 270 NKKKLLLKGNPSDLSALLDAGLYNSSAREHNRHAHITDTHSISARLNALELHLRLLAATH 329

Query: 279 -HMI-------GLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            HM           +G  ++   R      A       H+++     +
Sbjct: 330 AHMARARSLCSWYLYGLSHAALWRQKFMT-ATTLDEFLHLLQAFKEQV 376


>gi|32266316|ref|NP_860348.1| hypothetical protein HH0817 [Helicobacter hepaticus ATCC 51449]
 gi|32262366|gb|AAP77414.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 328

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 136/322 (42%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EMI + A++  + +   ++  S +E+P ++QI G+  
Sbjct: 14  AGYTDLPFRSVVKSF-GVDITVSEMISSHALVYNNARTLKMIEKSPEEQPYSVQISGSKE 72

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +I+   G  + I+LN GCP+ +V     G+ L+ +  ++      +    + P
Sbjct: 73  EVIKKAVEILNAQGGIDVIDLNCGCPAPKVANHGNGSGLLKDLHLLVKIANLIKDRATTP 132

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T +K R+G D +IP      + +++K    + + +H R          D  K   +DYD
Sbjct: 133 YTSLKVRLGFDKKIPN----EIAQALKDVRSDFVVVHGRTR-------ADGYKKERIDYD 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  IK+    + +  NG ++ + +A K+      +GVMIGRAA  +  +   +  +  +
Sbjct: 182 AIAHIKQHI-SMPLIANGEIDSVDKAQKVFSHTGANGVMIGRAAITSPWIFWQIKNHTHD 240

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                  I   V K+   K    M ++               +++     G   +   R+
Sbjct: 241 -------IPPIVKKELILKHFKKMVEFYGERGAIM-----FRKNLHAYAKGHEGASVFRN 288

Query: 296 ILTVEAGASTATHHIIETAFNL 317
           ++   +   +   H IE  F  
Sbjct: 289 VINNVSDVPSIMRH-IEEFFAC 309


>gi|239618483|ref|YP_002941805.1| dihydrouridine synthase DuS [Kosmotoga olearia TBF 19.5.1]
 gi|239507314|gb|ACR80801.1| dihydrouridine synthase DuS [Kosmotoga olearia TBF 19.5.1]
          Length = 314

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 63/299 (21%), Positives = 121/299 (40%), Gaps = 26/299 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M  +TD   R  + L      +++EM+  + +LR D+         E P  +Q+ G DI+
Sbjct: 11  MAGYTDEAMRAIS-LEWGADFVFSEMLSVEGVLRNDRTTQKIIP--ETPCRIQLFGNDIA 67

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L  AAK V D      ++N GCP  +V +   GA L+  P+ +   I  +     +PV+
Sbjct: 68  RLAMAAKAVLD-KATWFDINAGCPVKKVVKRGAGAALLREPEKLNAMIQTLKGISDLPVS 126

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D       +  +V+ + +S    I +H R  +               D++ + 
Sbjct: 127 VKIRLGWDKN----EVVKIVERLVESRPFAIMVHGRTVVQG--------YSGVADWESIG 174

Query: 181 EIKKENP--DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++ K      + +  +G +    + ++      VDGV++ R A  N  + +   E     
Sbjct: 175 KVVKICKPHGIKVYGSGDVFSPEKIVEAFEKYGVDGVLVARGAIGNPWIFSQYKE-LKQK 233

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            + + P      K F + +   +             + +  +H +G   G  N+ + R 
Sbjct: 234 GSYTVPDPHERLKVFAKHLKKLIELKGEER-----AIIESRKHFVGYCKGLLNATKMRR 287


>gi|320164949|gb|EFW41848.1| tRNA-dihydrouridine synthase 1-like protein [Capsaspora owczarzaki
           ATCC 30864]
          Length = 563

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 101/232 (43%), Gaps = 19/232 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  A             FST  +++PL +Q    D
Sbjct: 39  MVDQSELAWRMLSRRY-GADLCYTPMFNARLFAESQLYRDEMFSTCAEDRPLVVQFCAND 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE+   + ++LN+GCP      G +G+ LM   D++   +  + + L +P
Sbjct: 98  PDHLLAAAKLVEN-DCDAVDLNLGCPQHIARRGHYGSFLMEEWDLIERMVRKLHENLKVP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI               + ++++G   + +H R    KG       K    D+  
Sbjct: 157 VTCKIRIFP----SVEKTVQYAQMLERAGCQLLTVHGRLREQKG------HKTGLADWSY 206

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  + +E   + +  NG +   E++ + ++    V GVM       N A+ +
Sbjct: 207 IRAV-REAVKIPVFANGNILYNENVEECIRQ-TGVQGVMTAEGNLYNPALFS 256


>gi|110003924|emb|CAK98264.1| probable trna-dihydrouridine synthase n-terminal truncated protein
           [Spiroplasma citri]
          Length = 262

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 105/247 (42%), Gaps = 20/247 (8%)

Query: 52  LQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIA 109
           +QI G DI   V A K V+     + I++N+G  + ++  +   G+ L+ +P  V + + 
Sbjct: 1   MQIFGTDIETFVAAEKYVDQHSDCDIIDINMGYSAPKIAIKSQAGSYLLKHPQRVYEVVK 60

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ + ++ PVTVK RIG D++   +    + K  +++G   I +H R         ++  
Sbjct: 61  AVVENVTKPVTVKIRIGWDEE--NINCVEIAKYCEQAGAQAIAVHVRT--------RNQF 110

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                D++ + ++K EN  + +  NG +     A ++L     D +M+ R A  N  +  
Sbjct: 111 YSGKADWNWIRKVK-ENVAIPVIGNGDVFTCEDAERMLKETGCDAIMLARGAQGNPWVFK 169

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +  +       + P         +R     +     R   S     ++ +++   F G 
Sbjct: 170 QIQHFLDTGEKIAQPPLDEWQNIIFRHAELLLNLKGERISAS-----EMWKNLAFYFKGK 224

Query: 288 PNSRRCR 294
           P +   +
Sbjct: 225 PEATSYK 231


>gi|73987294|ref|XP_542144.2| PREDICTED: similar to dihydrouridine synthase 3-like [Canis
           familiaris]
          Length = 645

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 56/280 (20%), Positives = 105/280 (37%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 312 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQTSEWALLRRHPCEDVFGVQLEGAFPDTMT 370

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 371 KCAELLNRTIEVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGMNQVLDVPLTVK 430

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  +++ G   + +H R         ++ R     D+  + + 
Sbjct: 431 IRTGVQERVNLA--HRLLPELREWGAALVTLHGRS--------REQRYTKLADWQYIEQC 480

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 + +  NG +     A   +   V GVMI R A     + T + E     ++ S 
Sbjct: 481 VTAASPMPLFGNGDILSYEDANRAMQTGVAGVMIARGALLKPWLFTEIKEQRHWDISSSE 540

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T Y   H  S  +  + TR  +
Sbjct: 541 ----------RLAILQDFTRYGLEHWGSDTQGVEKTRRFL 570


>gi|46447213|ref|YP_008578.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Candidatus Protochlamydia amoebophila UWE25]
 gi|46400854|emb|CAF24303.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Candidatus Protochlamydia amoebophila UWE25]
          Length = 326

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 70/289 (24%), Positives = 122/289 (42%), Gaps = 24/289 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M    DR +R     +       TE   + ++A +           T   P A Q+ G+D
Sbjct: 19  MEGVGDRSFRKAMASVGGFDEACTEFMRVPSNAHVPSLANRYEANETFPIPQAAQLMGSD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A+ VE  G   I+LN GCPS  V     G+ L+  PD +     +M +A+++P
Sbjct: 79  PELMAEMARAVERRGAQRIDLNCGCPSNTVTGRGAGSSLLKEPDHLYKVAKSMVEAVNVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G  D        + + + + SG+  + +H R  +            P   +++
Sbjct: 139 VTAKLRSGFTDTSL---FHDNLLAAQASGIKYLTLHPRTKVDGYG--------PPAKWEL 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + + K+    + +  NG +  +  AL +L     DG+MIGR +  N  +   +  +FS  
Sbjct: 188 IAQAKQ-LLKIPVVGNGDILTVQDALNMLKQTKCDGLMIGRGSVINPFIFHEIKSHFS-- 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              + P + + D  F R I     D   + +   G+L ++ + M  LF 
Sbjct: 245 ---AQPFEKKWD-VFSRYIDVFTEDL--KEMSVKGQLNKLKQLMSFLFK 287


>gi|325108020|ref|YP_004269088.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
 gi|324968288|gb|ADY59066.1| tRNA-U20-dihydrouridine synthase [Planctomyces brasiliensis DSM
           5305]
          Length = 362

 Score =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 70/286 (24%), Positives = 122/286 (42%), Gaps = 21/286 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +T    R   R L    L  T++I+A  +L   KK+  +L  S  ++PL++QI G   
Sbjct: 38  AGYTHLPLRTALRELGGIGLATTDLILAPQLLADSKKSRILLSTSEADRPLSVQIFGGRT 97

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             LV AA+ +E+ GY  I++N+GCP  +V+    GA LM + D      AA+ +A+ IPV
Sbjct: 98  EDLVRAAQRLEERGYEGIDINMGCPMGKVNSSGGGARLMCDCDNATQMTAAVVEAVDIPV 157

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D     +    L ++ +  GV  I IH R         +      +++ + +
Sbjct: 158 TVKMRLGWD--ADNITAPILARAFEDVGVAAITIHGRT--------RQQGFHGSVNLEGI 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            +  +    + I  NG +  +  A+ +  +   D + IGR A  +  +   + ++  N L
Sbjct: 208 RKTVEAVDRIPIIGNGDVRSVDDAIHMRKVTGCDAIAIGRGAMLDPWLFRKLWQH-ENGL 266

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
             + P +        R       D  A             + +   
Sbjct: 267 PITEPTRDEQIAFLVRH-----FDLMAEQRG-DYACVLFRKFVGWY 306


>gi|198436587|ref|XP_002123151.1| PREDICTED: similar to PP3111 protein [Ciona intestinalis]
          Length = 474

 Score =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 105/231 (45%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ A   LR  +  I  L    +++PL +Q    D
Sbjct: 26  MVDQSELAWRMLSRKY-GAELCYTPMLHASVFLRDPQYRIDGLASCPEDRPLIVQFCAND 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L ++A + +D   + +++N+GCP      G++GA L  N ++V   I A  + LS+P
Sbjct: 85  PDILTKSALLAQDH-CDAVDINLGCPQTIAKRGNYGAFLGENWELVTKLIKACHEKLSVP 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K I+++G   + +H R   +KG             ++ 
Sbjct: 144 VTCKIRIFTDVEKTV----QYAKMIERAGCQLLTVHGRTKEMKG------PMTGLASWEH 193

Query: 179 VYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAML 226
           +  +K +   + +  NG ++   D+ + +     VDGVMI      +  + 
Sbjct: 194 IKAVK-DAVKIPVFANGNIQYKADVDRCINQ-TGVDGVMIAEGNLHDPCLF 242


>gi|329663208|ref|NP_001193247.1| tRNA-dihydrouridine synthase 3-like [Bos taurus]
 gi|297476780|ref|XP_002688932.1| PREDICTED: Dihydrouridine synthase 3-like (S. cerevisiae)-like [Bos
           taurus]
 gi|296485774|gb|DAA27889.1| Dihydrouridine synthase 3-like protein [Bos taurus]
          Length = 650

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 104/280 (37%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 317 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQTSEWALLKRHPCEDIFGVQLEGAFPDTMT 375

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V +   G  LM         +  M + L +P+TVK
Sbjct: 376 KCAELLNRTIEVDFVDINVGCPIDLVFKKGGGCALMNRLAKFQQIVRGMNQVLDVPLTVK 435

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  G   + +H R         ++ R     D+  + + 
Sbjct: 436 LRTGVQERVNLA--HRLLPDLRDWGAALVTLHGRS--------REQRYTKLADWQYIEQC 485

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                 + +  NG +     A + L   V GVMI R A     + T + E     ++ S 
Sbjct: 486 VAAARPMPLFGNGDVLSYEDANRALQTGVAGVMIARGALLKPWLFTEIKEQRHWDISSSE 545

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T Y   H  S  +  + TR  +
Sbjct: 546 ----------RLDILRDFTHYGLEHWGSDTQGVEKTRRFL 575


>gi|237752877|ref|ZP_04583357.1| conserved hypothetical protein [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375144|gb|EEO25235.1| conserved hypothetical protein [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 319

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 141/323 (43%), Gaps = 35/323 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D   R  A+      +  +EMI   A+   +KK   ++  S  E P ALQI G D 
Sbjct: 18  AGYSDLPLREVAKKF-GADITVSEMISVHALAFKNKKTLKMVEKSPLENPFALQIAGNDF 76

Query: 60  SKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             +  A + +  +  G   ++LN GCP+ +V     G+ L+ + + + + +  + K   I
Sbjct: 77  GIIARAVEYLNTQKDGIQILDLNCGCPAPKVSSHGSGSSLLKDLNKLVEILKLIRKVSEI 136

Query: 118 P-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P ++VK R+G D +IP      + +++K + ++ + +H R  +       D  K   +DY
Sbjct: 137 PYLSVKVRLGFDQKIP----LEIAQALKDTPIDYVVVHGRTKV-------DGYKKEKIDY 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  IK+ N  + +  NG +  + ++ ++L     DGVMIGRAA +   +   + E  +
Sbjct: 186 DSIALIKQ-NLKVPLIANGEINSVKKSQEVLEKTGADGVMIGRAAVEKPWIFAQIKEGLT 244

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                S  ++ RV  + + +  +   DY A             +++     G   +   R
Sbjct: 245 ED---SVKLRERVVLEHFDRTISFRGDYGAIMF---------RKNLHAYSKGLKGASEFR 292

Query: 295 ---HILTVEAGASTATHHIIETA 314
              +++T       A     + A
Sbjct: 293 SKVNVITEPILMREAISEFFKKA 315


>gi|94987210|ref|YP_595143.1| tRNA-dihydrouridine synthase [Lawsonia intracellularis PHE/MN1-00]
 gi|94731459|emb|CAJ54822.1| tRNA-dihydrouridine synthase [Lawsonia intracellularis PHE/MN1-00]
          Length = 330

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 61/321 (19%), Positives = 131/321 (40%), Gaps = 26/321 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             W+D  +R   R     A+ YTEMI A  ++  +   +++L    ++ PL +Q+ G++ 
Sbjct: 20  AGWSDLPFRLLCRE-HGAAVCYTEMISAKGLIYNNPGTESLLKTIPEDNPLIVQLCGSEA 78

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP- 118
           S + +A  I+ + GY   + N+GC   ++     GA +M N D       AM   ++   
Sbjct: 79  SCMKDALTILLEKGYKWFDCNMGCSVPKITRTGSGASMMKNIDNSIKIAEAMIHTVNKKS 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +  K R+G D++        L K ++++G   I +H R A                +++ 
Sbjct: 139 IGFKLRLGWDEK--HETWPILAKLLEEAGAGWITLHPRTA--------QQGFTGTANWEK 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+K++   + +  +G L   S  +  +    VD VM  R A K+  + T  ++     
Sbjct: 189 LLELKQQV-KIPVIASGDLLTASHGVDCIKKTHVDTVMYARGALKDPNIFTKHNQILKGK 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-H 295
              ++   +         +    +  A ++      L ++   +         +++ R +
Sbjct: 248 QITTTNSNS------LFSMIMRHSYLACKYSSYDTALLKMRTIVPRYIRHLKGAKQLRLN 301

Query: 296 ILTVEAGASTATHHIIETAFN 316
           I++    +S     I++    
Sbjct: 302 IISCRTWSS--FEDILQQFLK 320


>gi|328955422|ref|YP_004372755.1| tRNA-U20-dihydrouridine synthase [Coriobacterium glomerans PW2]
 gi|328455746|gb|AEB06940.1| tRNA-U20-dihydrouridine synthase [Coriobacterium glomerans PW2]
          Length = 328

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 64/326 (19%), Positives = 118/326 (36%), Gaps = 29/326 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R      L Y+EM+    +     +   +     +E  L++Q+ G+ 
Sbjct: 17  MAGVTDAAYRIMCRR-HGAVLAYSEMVSVAGLAFASARTIELAEPHAEEPQLSVQLFGSK 75

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            ++   A ++++         +++N+ CP  +V     GA LM  PD+    + A     
Sbjct: 76  PAQFAAAVEMIQQRVGERLSLVDINMACPVRKVVSKGEGAALMDKPDLAARIVRACVSVA 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RIG            L + +++ G+  + +H R A                D
Sbjct: 136 RVPVTAKIRIGTRSGTR--TAPELARRLEQEGLAAVAVHGRTA--------AQLYRGRAD 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + I+ E+      + +  +G +     A+ +L   +   VMI R +Y    +        
Sbjct: 186 WSIIDEVACGVT-IPVIGSGDVLTAEAAVAMLRDTAASAVMIARGSYGEPWIFEDAASIA 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                      +R+     R+  A   D+A         + +          G PN+   
Sbjct: 245 RGNAPRPRSRLSRLAA--LREHLALARDHA-------PHMSRARTFSAWYLKGMPNAAAW 295

Query: 294 RHILTVEAGASTATHHIIETAFNLMI 319
           R  L V  G   A   +I+   N ++
Sbjct: 296 RARL-VRCGDYDAFCALIDEIENDVV 320


>gi|70726229|ref|YP_253143.1| hypothetical protein SH1228 [Staphylococcus haemolyticus JCSC1435]
 gi|68446953|dbj|BAE04537.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 325

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 70/332 (21%), Positives = 130/332 (39%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSFGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYD---IEEWRDWLKHVFKQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK+      P+  + +NG + D      L +   VDGVMIGR  + N        
Sbjct: 187 ELIAAIKQLRDDIAPNTLLTINGDIPDRKTGHELAMKYGVDGVMIGRGIFNNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   + +R   +    Y++       +L++  +       G   +
Sbjct: 243 ------EKEPREHTSKELLNLFRLHLSLFEKYSSDESQQFKRLRRFFKI---YVKGIKGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            + RH L        A   +++   + + E +
Sbjct: 294 SQLRHQLMSTESVDEA-RDLLDEFESKIEEDV 324


>gi|213514710|ref|NP_001133911.1| tRNA-dihydrouridine synthase 3-like [Salmo salar]
 gi|209155790|gb|ACI34127.1| tRNA-dihydrouridine synthase 3-like [Salmo salar]
          Length = 654

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 59/277 (21%), Positives = 108/277 (38%), Gaps = 25/277 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      +L     E    +Q+ G     + 
Sbjct: 321 NLPFRRICKRF-GADITCGEMAMCTNLLQGQSSEWALLKRHESEDLFGVQVEGCFPDTMT 379

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ +    + +++N GCP   V++   G  LM   +     I  M   L +P+TVK
Sbjct: 380 RCAELLNNKIDVDFVDINSGCPIDLVYKKGGGCGLMTRTNKFEQIIRGMNSVLDVPLTVK 439

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV  Q  A     L+  +KK GV+ I +H R         ++ R   + D+D +   
Sbjct: 440 IRTGV--QEKANIAHKLIPEMKKWGVSMITLHGRS--------REQRYTKSADWDYINTC 489

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A+K   + V G+M+ R A     + T + E     ++ S 
Sbjct: 490 SQLASPIPLFGNGDILSYYDAMKARETDVSGIMLARGALIKPWVFTEIKERRDWDISSSE 549

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
            +           +    T Y   H  S  +  + TR
Sbjct: 550 RL----------DVLRDFTHYGLEHWGSDTQGLEKTR 576


>gi|332263177|ref|XP_003280631.1| PREDICTED: tRNA-dihydrouridine synthase 3 isoform 1 [Nomascus
           leucogenys]
          Length = 649

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 107/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 316 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 374

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 375 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 434

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 435 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 484

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 485 VKAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHWDISSSE 544

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T+Y   H  S  +  + TR  +
Sbjct: 545 ----------RLDILRDFTNYGLEHWGSDTQGVEKTRRFL 574


>gi|321476981|gb|EFX87940.1| hypothetical protein DAPPUDRAFT_305459 [Daphnia pulex]
          Length = 484

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 63/273 (23%), Positives = 112/273 (41%), Gaps = 30/273 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ A   +R  +  +  L   T+++PL  Q    D
Sbjct: 25  MVDASELPWRLLSRKY-GTQLAYTPMMNAGIFIREPRYRREHLESCTEDRPLIAQFCAND 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               ++AAK+ E    + I+LN+GCP +   +G +GA L    D++   +  + + LSIP
Sbjct: 84  TDIFLKAAKMAEQH-CDAIDLNLGCPQSIAKKGHYGAFLQDEWDLISKMVKLIHRELSIP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R+  D            K +++SG   + +H R    KG             +  
Sbjct: 143 ITCKVRVFPDINKSIA----YAKMLEESGCYALTVHGRTREQKG------PLTGLASWKH 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K    ++ +  NG ++  S   + L     D VM+      N A+   +       
Sbjct: 193 IQAVK-AAVNIPVIANGNIQYWSDVERCLESTGADAVMVAEGNLTNPALFANL------- 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHL 267
                P+   + K++   +        YA  HL
Sbjct: 245 ----QPLVWDMGKEYLDLVERFPCPMSYARGHL 273


>gi|226492326|ref|NP_001145737.1| hypothetical protein LOC100279244 [Zea mays]
 gi|219884231|gb|ACL52490.1| unknown [Zea mays]
 gi|224031411|gb|ACN34781.1| unknown [Zea mays]
          Length = 686

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 107/287 (37%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L     E    +QI G     + 
Sbjct: 345 NLPFRRLCKTL-GADVTCGEMAMCTNLLQGQASEWALLRRHPSEDLFGVQICGPYPDTVA 403

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++V  +   + I++N+GCP   V     G+ L+  P  +   + A       P+TVK
Sbjct: 404 RTVELVDNECSVDFIDINMGCPIDIVVNKGAGSSLLTKPMRIRSIVQAASTVTEKPLTVK 463

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +        +LV  I   G + I IH R         +  R     D+D +Y+ 
Sbjct: 464 VRTAFFEGRNRA--DSLVSDIYNWGASAITIHGRS--------RQQRYSKLADWDYIYQC 513

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +   +   K +     +   MI R A     + T + E     +T
Sbjct: 514 AQKAPDYLHVIGNGDVFSFTDWNKHVSDCSKISTCMIARGALIKPWLFTEIKEQRHWDIT 573

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                +  + KDF R        +   H  S  K  + TRH +   L
Sbjct: 574 SGE--RLNILKDFVR--------FGLEHWGSDFKGVETTRHFLLEWL 610


>gi|158296576|ref|XP_316960.4| AGAP008484-PA [Anopheles gambiae str. PEST]
 gi|157014776|gb|EAA12777.4| AGAP008484-PA [Anopheles gambiae str. PEST]
          Length = 560

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 64/287 (22%), Positives = 120/287 (41%), Gaps = 32/287 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +    +K+ L    +++PL +Q  G D
Sbjct: 48  MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFTKDPKYRKDSLQTCPEDRPLIIQFCGND 106

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++EAA + +D   + I++N+GCP A    G +GA L    +++ + ++ + + L+IP
Sbjct: 107 PKIMLEAALLAQDH-CDAIDINLGCPQAIAKRGHYGAFLQDEWELLREIVSTLHRHLAIP 165

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            + ++ +G   + +H R    KG            D+  
Sbjct: 166 VTCKIRIFEDM----AKTIRYARMLQDAGAQMLTVHGRTRDQKG------PLTGLADWKY 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD------ 230
           V  ++++   + I  NG +  +    + +    V+GVM       N A+   V+      
Sbjct: 216 VRVLRQQL-SIPIFSNGNIMSVHDVERCIAETGVNGVMTAEGNLHNPALFEGVNPTAWSM 274

Query: 231 --EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
             EY        +PI       + R     +  +   HL S   L++
Sbjct: 275 AHEYLDLVEQYPAPIS------YIRGHLFKLFHHL-MHLKSNAALRE 314


>gi|183219434|ref|YP_001837430.1| putative tRNA-dihydrouridine synthase [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
 gi|189909580|ref|YP_001961135.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167774256|gb|ABZ92557.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167777856|gb|ABZ96154.1| Putative tRNA-dihydrouridine synthase [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 337

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 72/294 (24%), Positives = 124/294 (42%), Gaps = 29/294 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  YR   +    +A  YTE +  + +  G+ K+  +  F   E+P+  QI G+D
Sbjct: 18  MAGISDSPYRQITKRF-GSAFSYTEFVSTEQLKLGNAKSLDMFRFVEMERPIVFQIFGSD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +V A++I  +   + I+LN+GC  ++V     GA L+ N  + G  I  +    ++P
Sbjct: 77  LDTVVNASEIAAEQKPDIIDLNMGCSVSKVSHNGSGAGLLKNIRLAGKMIEGIRNRTNLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+G D    ++     +K ++ SGV+ I +H R         K        D++ 
Sbjct: 137 VTAKIRLGWD--ANSLNYLETLKVLEDSGVSAISVHGRT--------KAMAYTGIADWNA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK    ++ I  NG ++   +AL+      VD V+IGR A  N  +     + F   
Sbjct: 187 IGEIKSRA-NVPIYGNGDVQSYKEALEKKKTYGVDLVLIGRKAIGNPWVFGKTPKQFF-- 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH--GFP 288
                    ++       +   +  Y          L    +H I      GFP
Sbjct: 244 ------PWYQIKDVILEHLDLMLNFYPT---SDDYALILFRKHFIKYIENIGFP 288


>gi|123288584|emb|CAM27542.1| dihydrouridine synthase 1-like (S. cerevisiae) [Mus musculus]
          Length = 482

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PMAGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAVG-IPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVRQHPCPLSYVRAHL---FKLWH 279


>gi|14249957|gb|AAH08362.1| DUS3L protein [Homo sapiens]
          Length = 613

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 58/284 (20%), Positives = 109/284 (38%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 280 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 338

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 339 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 398

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 399 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 448

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 449 VQAASPMPLFGNGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE 508

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T+Y   H  S  +  + TR  +   L
Sbjct: 509 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFLLEWL 542


>gi|145551887|ref|XP_001461620.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124429455|emb|CAK94247.1| unnamed protein product [Paramecium tetraurelia]
          Length = 360

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 126/317 (39%), Gaps = 40/317 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ +  +               +++PL  Q+ G D
Sbjct: 25  MVDQSELAFRMLTRKY-GTTLAYTPMLHSRIMTESKSYKDEFFTTCPEDRPLFAQLCGHD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AA +++D   + I++N+GCP     +G +GA L+   + V   +  + + +++P
Sbjct: 84  PQVLIKAALMIQDQ-CDAIDINLGCPQGIARKGLYGAYLLEKREQVLTIVKELKQNINVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +       +L K I+++G + + +H R          +   +   D+ I
Sbjct: 143 VTCKIRMFKDRKRT----LDLTKDIQEAGCSILTVHGRTKEQ------NKDFVGQCDWTI 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIK+    + +  NGG+   S   + L    VD VM   A  +N A+ +         
Sbjct: 193 IAEIKQ-ILQIPVFANGGIYTWSDVERCLQETKVDAVMSSEALLENPALFSG-------- 243

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-GLFHGFPNSRRCRH 295
                           + ++    +Y         +L +I  H+   L+ G       R 
Sbjct: 244 --------------EIKDLNDLALEYMQFAKQYNARLAEIKAHLFKLLYTGLQIFTDLRS 289

Query: 296 ILTVEAGASTATHHIIE 312
            L            +IE
Sbjct: 290 KLGSAKTYEEHLEVVIE 306


>gi|14602971|gb|AAH09973.1| Dihydrouridine synthase 3-like (S. cerevisiae) [Homo sapiens]
 gi|190690551|gb|ACE87050.1| dihydrouridine synthase 3-like (S. cerevisiae) protein [synthetic
           construct]
 gi|190691915|gb|ACE87732.1| dihydrouridine synthase 3-like (S. cerevisiae) protein [synthetic
           construct]
          Length = 650

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 58/284 (20%), Positives = 109/284 (38%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 317 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 375

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 376 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 435

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 436 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 485

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 486 VQAASPMPLFGNGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE 545

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T+Y   H  S  +  + TR  +   L
Sbjct: 546 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFLLEWL 579


>gi|289742295|gb|ADD19895.1| uncharacterized conserved protein [Glossina morsitans morsitans]
          Length = 582

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 56/289 (19%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM     +++G   +  +      E    +Q+ G   + + 
Sbjct: 247 NLPFRRICKEF-GADITCGEMACCVPLVKGLTQEWALTKRHESEDVFGIQLCGNSPNIVA 305

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTV 121
           +AA++V++    + ++LN+GCP   +++   G+ LM   +I+   + +       IP TV
Sbjct: 306 QAAQLVQETTEVDYLDLNIGCPIDLIYQQGGGSALMRRTNILELIVRSCANLNTKIPFTV 365

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV          +L+  +++ G   + +H R         ++ R   N ++  + E
Sbjct: 366 KMRTGVYADKSTA--HDLMPLVEEWGAAAVTLHGRS--------REQRYTKNANWTYIEE 415

Query: 182 IKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +   ED ++   I P V  VMIGR A     +   + +      T
Sbjct: 416 CAAKVKTIPVVGNGDILSYEDYNEKRDIAPHVSSVMIGRGALIKPWIFQEIKQQKHWSPT 475

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            S             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 476 SSERF----------ELLRKYVNYGLEHWGSDTKGVENTRRFLLEWQSF 514


>gi|189055070|dbj|BAG38054.1| unnamed protein product [Homo sapiens]
          Length = 650

 Score =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 108/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 317 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 375

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 376 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 435

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 436 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 485

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 486 VQAASPMPLFGNGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE 545

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T+Y   H  S  +  + TR  +
Sbjct: 546 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFL 575


>gi|260828450|ref|XP_002609176.1| hypothetical protein BRAFLDRAFT_92533 [Branchiostoma floridae]
 gi|229294531|gb|EEN65186.1| hypothetical protein BRAFLDRAFT_92533 [Branchiostoma floridae]
          Length = 578

 Score =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 111/285 (38%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +A  +L+G      +L     E    +QI G+    + 
Sbjct: 244 NLPFRRICKGL-GADITCGEMAMASNLLQGQSSEWALLKRHQSEDVFGVQICGSHPEVMS 302

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ D    + +++NVGCP   V +   G  LM         +  M   L +P+TVK
Sbjct: 303 HVAELLNDTISVDFVDVNVGCPIDLVFKRGGGCALMGRLTKFEQVVKGMIGMLDVPLTVK 362

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G+ ++ P      +V  ++  GV+ + +H R         ++ R     D+D + E 
Sbjct: 363 MRTGIYEEKP--FAYRVVPHLRDWGVSLVTLHGRS--------REQRYTKLADWDYISEC 412

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            K    + +  NG +     A +      V G+MI R A     + T + E     ++  
Sbjct: 413 AKAASPMPLFGNGDILSFEDANRHRESTGVAGLMIARGALIKPWIFTEIKEQRHWDISSH 472

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI-GL 283
                        +I    ++Y   H  S    +++  R M+  L
Sbjct: 473 ERF----------QILKDFSNYGLEHWGSDTQGVEKTRRFMLEWL 507


>gi|40807366|ref|NP_071439.3| tRNA-dihydrouridine synthase 1-like [Homo sapiens]
 gi|74749069|sp|Q6P1R4|DUS1L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 1-like
 gi|38511481|gb|AAH62566.1| DUS1L protein [Homo sapiens]
 gi|40787788|gb|AAH64918.1| Dihydrouridine synthase 1-like (S. cerevisiae) [Homo sapiens]
 gi|313883632|gb|ADR83302.1| dihydrouridine synthase 1-like (S. cerevisiae) [synthetic
           construct]
          Length = 473

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 279


>gi|31980834|ref|NP_081100.2| tRNA-dihydrouridine synthase 1-like [Mus musculus]
 gi|81898593|sp|Q8C2P3|DUS1L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 1-like
 gi|26353202|dbj|BAC40231.1| unnamed protein product [Mus musculus]
 gi|148702860|gb|EDL34807.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_b [Mus
           musculus]
          Length = 475

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PMAGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAVG-IPVFANGNIQCLQDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVRQHPCPLSYVRAHL---FKLWH 279


>gi|296123913|ref|YP_003631691.1| dihydrouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296016253|gb|ADG69492.1| dihydrouridine synthase DuS [Planctomyces limnophilus DSM 3776]
          Length = 322

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 124/299 (41%), Gaps = 23/299 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M + T   +R   +     +L+ +E I A  +   DK+   +L  ++ E+P   QI G D
Sbjct: 17  MEEHTSLPFRLICKQ-QGASLVCSERIDAKDVAERDKRAIKLLSTTSAERPAVGQISGND 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++ EAA+++E+ G++ ++LN  CP  R+     G  LM  P  + + +AA  +A+SIP
Sbjct: 76  AAQIGEAARVIEELGFSMVDLNFECPIRRLVGRGEGGALMGQPQRIAELVAAAKQAVSIP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R G              + ++++G   I +HAR          +   +   D+  
Sbjct: 136 VTVKLRTGPKAGEDTAV--ETAQRVEQAGGAAIILHARS--------VEQAYLGGPDWQH 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K E   + +  +GG+     A+  L     DGV IGR    N  +           
Sbjct: 186 VTRVK-EAVSIPVLGSGGVRTPQDAISFLESSGADGVAIGRGCLGNPWIFQQARTLLFGS 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCR 294
                P      K     +      Y+A HL      +++ R     F  F P+    +
Sbjct: 245 REIIEPSPAERGKVLLALVEHEFEFYSA-HLAQ----KRLAR-TACYFAKFLPDFAEFK 297


>gi|303390091|ref|XP_003073277.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
 gi|303302422|gb|ADM11917.1| tRNA-dihydrouridine synthase [Encephalitozoon intestinalis ATCC
           50506]
          Length = 341

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 105/233 (45%), Gaps = 19/233 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           MV  ++  +R  ++      L YTEM+  ++ LRG +          S  ++PL +QI G
Sbjct: 18  MVGNSEEAWRRLSKR-HGANLFYTEMVHCESFLRGSRNPVKNRWYTTSESDRPLVIQICG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                ++EAA I+++   + I++N GCP     +G +GA L  N D+    +  +   L+
Sbjct: 77  NSPKTMLEAALIMQNH-CDAIDINFGCPQKVARKGGYGAYLQENWDLTERIVKVLSTGLN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+ K R+               K I+K+G + + +H R    KG +      +    +
Sbjct: 136 VPVSCKIRVF----ESIEKTVEYAKMIEKAGCSLLAVHGRTRDQKGPA------MGLASW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           D +  +K EN  + +  NG +       K L     DGVM+G A   N  + T
Sbjct: 186 DHIKAVK-ENLKIPVLSNGNIMTHEDVWKCLEYTKCDGVMVGEAHLYNPLIFT 237


>gi|114671084|ref|XP_001167358.1| PREDICTED: PP3111 protein isoform 1 [Pan troglodytes]
 gi|114671086|ref|XP_001167386.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 2 [Pan
           troglodytes]
          Length = 473

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 279


>gi|10436076|dbj|BAB14740.1| unnamed protein product [Homo sapiens]
          Length = 650

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 107/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 317 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 375

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 376 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 435

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 436 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 485

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 486 VQAASPMPLFGNGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE 545

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T+Y   H  S  +  + TR  +
Sbjct: 546 ----------RLDILRDFTNYGLEHWGSDTQGVEKTRRFL 575


>gi|239788462|ref|NP_064560.2| tRNA-dihydrouridine synthase 3-like isoform 1 [Homo sapiens]
 gi|110808212|sp|Q96G46|DUS3L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 3-like
          Length = 650

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 107/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 317 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 375

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 376 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 435

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 436 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 485

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 486 VQAASPMPLFGNGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE 545

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                        I    T+Y   H  S  +  + TR  +
Sbjct: 546 ----------RLDILRDFTNYGLEHWGSDTQGVEKTRRFL 575


>gi|255079532|ref|XP_002503346.1| tRNA-dihydrouridine synthase [Micromonas sp. RCC299]
 gi|226518612|gb|ACO64604.1| tRNA-dihydrouridine synthase [Micromonas sp. RCC299]
          Length = 353

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 119/297 (40%), Gaps = 20/297 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R        YT MI A   +     +K I      ++PL +Q    D
Sbjct: 42  MVDQSELAFRELCRR-HGATCAYTPMIHARLFVEDLKYRKEIFTTHINDRPLLVQFCAND 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AA IV     + +++N GCP      G +GA LM + + V + I  + K LS+P
Sbjct: 101 PDMLLKAASIVAPH-CDGVDINFGCPQRIAKRGRYGAFLMDDWETVHNLINKLDKHLSVP 159

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +          K ++ +G   I +H R    K  +          ++  
Sbjct: 160 VTAKIRVYDDLETS----LKYAKMVEAAGAQLIAVHGRTREQKRAADV------RANWAF 209

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EIKK+   + +  NG +  +++A K L     DGV+      +N ++ +    Y  + 
Sbjct: 210 IREIKKQL-KVPVLANGDIRTLAEAEKCLEATGADGVLSAEPLLENPSLFSDPPLYSPSD 268

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                P++  V+ +   +       Y        G +  +   +      F + R  
Sbjct: 269 PAHPLPVEGDVNCELLHEYLEITRTYQTPLRMVKGHVHNM---VGSWLKEFTDLRDW 322


>gi|291060336|gb|ADD73071.1| probable tRNA-dihydrouridine synthase [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 351

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 62/326 (19%), Positives = 132/326 (40%), Gaps = 31/326 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R  A      +  YTEM+ ++A++R   + K ++  ++ E   A+QI G++ 
Sbjct: 38  AGYSDSAFRSIAIEW-EASFTYTEMVSSEAMVRDSLNTKRLIRRASNETHYAIQIFGSNP 96

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
           + + E AK++ D    + I++N GCP  ++ +   GA L   P  + + + A+  A+   
Sbjct: 97  AVMAETAKLIVDSAQPSCIDINAGCPMPKITKTGAGAALTREPTRLYEVVKAVADAVYAQ 156

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              IPVTVK R G ++    +  +   ++   +G   + +H R                 
Sbjct: 157 DARIPVTVKIRAGWEE--AHLTWKEAARAAVDAGAQALALHPRTC--------AQCYAGE 206

Query: 174 LDYDIVYEIKKEN---PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            ++DI+ ++ +      ++ +  +G L     A  +L      GVM  R A  N  +   
Sbjct: 207 ANWDIIADLVQCARGWGEVPVFGSGDLHAPEDARAMLEHTACAGVMFARGAMGNPFIFRQ 266

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             +  +         + ++ +  WR++        A+ +      +Q+ +  +    G  
Sbjct: 267 TRQLLTEGYYTPVTFEQKL-RAAWREL-----HLLAQDVGESSACKQMRKRFVSYAKGER 320

Query: 289 NSRRCRHILTVEAGASTATHHIIETA 314
              +      V A +      +I  A
Sbjct: 321 GKTQWCQR-AVHASSFADFAAVIRDA 345


>gi|114650483|ref|XP_001146302.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Pan troglodytes]
          Length = 473

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKT----MRYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 279


>gi|296419375|ref|XP_002839286.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295635409|emb|CAZ83477.1| unnamed protein product [Tuber melanosporum]
          Length = 483

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 64/331 (19%), Positives = 123/331 (37%), Gaps = 23/331 (6%)

Query: 1   MVDWTDRHYRFFARLLTN-NALLYTEMIVADAILRGDKKNI------LGFSTQEKPLALQ 53
           MV+ ++  +R  +R  +  N L YT M  +                 L  S  ++PL +Q
Sbjct: 32  MVEQSELAWRLLSRRHSPPNTLCYTPMFHSRLFATTPIYRSQSFYPPLDGSKPDRPLFVQ 91

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
                   L  AA+ V     + ++LN+GCP     +G +GA L  +  ++   ++ + K
Sbjct: 92  FCSNTPEDLFSAAQHVAPH-CDGVDLNLGCPQGIARKGKYGAFLQEDWGLIRSLVSKLHK 150

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L +PVT K RI    +          + +  +G   + +H R    KG           
Sbjct: 151 DLEVPVTAKIRILETRERS----LEYARMVVDAGAQVLTVHGRTRDQKG------HNTGM 200

Query: 174 LDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
            D+ ++  I+   P  + +  NG +       + L     DGVM       N A+  + D
Sbjct: 201 ADWGVIRYIRDNLPKEVVLFANGNILWHEDVQRCLDATGADGVMSAEGNLYNPAIFQS-D 259

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG-FPN 289
           E +         +         +++   + +   + L     +  I  H+  L+H   P 
Sbjct: 260 EDWEKRFPRMDILGREYLDIVRKEVLPGLEERGRKLLLQDPSITAIKPHLFKLWHALLPK 319

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIE 320
               R +L   +  ++    ++E     ++E
Sbjct: 320 YTDVRALLAKSSARASEGGDVLEPYETCLME 350


>gi|269120324|ref|YP_003308501.1| dihydrouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268614202|gb|ACZ08570.1| dihydrouridine synthase DuS [Sebaldella termitidis ATCC 33386]
          Length = 309

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 61/293 (20%), Positives = 123/293 (41%), Gaps = 20/293 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M   TD  +R      + + +++TEM+  +A+   +++       +    A+QI G    
Sbjct: 8   MAGITDYSFRKILYEFSPD-IIFTEMVDVNALKYSNQRTQDEILRKAGNEAVQIFGNKNE 66

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP 118
             +EA K++ + G++ I++N+GCP  ++     G+ L+L  D V + +  + K     I 
Sbjct: 67  DFLEAVKLLIERGFDHIDINLGCPVKKIIRAGKGSALLLESDFVKELLLKLKKEFRNDIK 126

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R G  +          VK  ++ G+  I IH R          +       D++I
Sbjct: 127 LSMKIRTGYKNFSDPEYY---VKLAEEYGLFQICIHGRTQ--------EQLYSGQADWNI 175

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + ++K+++ ++ I  NG L D+    +   S   DG+M+ R    N  +L    +YF   
Sbjct: 176 IKKMKQKHKNVKIIGNGDLTDLKTIKEKTDSAKPDGIMLARGLLGNPWLLKEAKDYFKTG 235

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
           +   S     V ++  +       +Y             + +H+      F N
Sbjct: 236 VFHES----EVGREEIKNTLIKHINYCIEDKGEIRANLDMRKHIFWYLKEFEN 284


>gi|323347278|gb|EGA81552.1| Dus1p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 301

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 66/267 (24%), Positives = 118/267 (44%), Gaps = 25/267 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L YT M+ A         R D  + L  S+ ++PL +Q  
Sbjct: 36  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L+ AAK+VED   + ++LN+GCP     +G +G+ LM   D++ + I  + K L
Sbjct: 95  ANDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLIHNLINTLHKNL 153

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D +       N  K +  +G   + +H R    KG      +K    +
Sbjct: 154 KVPVTAKIRIFDDCEKS----LNYAKMVLDAGAQFLTVHGRVREQKG------QKTGLAN 203

Query: 176 YDIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           ++ +  ++   P       NG +   ED+S+ ++ +   D VM       N  +   VD+
Sbjct: 204 WETIKYLRDNLPKETVFFANGNILYPEDISRCMEHI-GADAVMSAEGNLYNPGVFN-VDQ 261

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISAS 258
             +       P   ++ ++++  +   
Sbjct: 262 TKNKEKIF--PRVDKIIREYFXIVKEC 286


>gi|150020274|ref|YP_001305628.1| dihydrouridine synthase, DuS [Thermosipho melanesiensis BI429]
 gi|149792795|gb|ABR30243.1| dihydrouridine synthase, DuS [Thermosipho melanesiensis BI429]
          Length = 295

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 60/299 (20%), Positives = 120/299 (40%), Gaps = 44/299 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   ++  +R            YTEMI A++I+R     +       ++K +A+QI G++
Sbjct: 11  MAGISNWSFRTLCFKF-GAEFAYTEMISAESIVRNLKINEKYFPKDIEKKRVAVQIFGSE 69

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA +V+  G   I++N GCP  +V +   G+ L+ +   +   I  +   +   
Sbjct: 70  PYIMSQAASMVDGKGA-WIDINAGCPVKKVIKKGAGSALLKDLKKLKKIIEGVKNNVKSK 128

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+G D+         +  +  ++G + I +H R A                 + I
Sbjct: 129 VSVKVRLGFDED----NFERIYDAAVEAGADMIAVHGRTAK--------QMYSGRAKWQI 176

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                K    + + +NG +   +++  A++ L   DGV+I R A  N  + + +      
Sbjct: 177 -----KNKGYIPLYINGDIYNSDNIKIAME-LSGADGVLIARGAIGNPWIFSNI------ 224

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                +P          + I     +         G +++  + + G   G P +R+ R
Sbjct: 225 -----TPSIFERKNVVLQHIDLLYLEV--------GDIREFRKFVAGYTKGLPGARQFR 270


>gi|73964669|ref|XP_848227.1| PREDICTED: similar to PP3111 protein isoform 2 [Canis familiaris]
          Length = 475

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG------PLSGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLRDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVRQHPCPLSYVRAHL---FKLWH 279


>gi|50303583|ref|XP_451733.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640865|emb|CAH02126.1| KLLA0B04499p [Kluyveromyces lactis]
          Length = 425

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 75/332 (22%), Positives = 138/332 (41%), Gaps = 34/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQ-EKPLALQI 54
           MVD ++  +R  +R      L YT M  A         R D    L    + ++PL +Q 
Sbjct: 25  MVDQSELAWRILSRKY-GATLAYTPMFHAKLFATSEKYRKDMWCELDGDEKIDRPLVVQF 83

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK+V++   + ++LN+GCP     +G +GA LM + D++   I+ + + 
Sbjct: 84  CANDPEYLLQAAKLVQN-KCDAVDLNIGCPQGIARKGKYGAFLMEDWDLISRLISTLHEH 142

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K R+  + +          K I KSG   + +H R    KG      ++    
Sbjct: 143 LDVPVTAKIRVFPEREKT----LEYAKMILKSGAQFLTVHGRLREQKG------QQTGLA 192

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           D++I+  ++   P D     NG +       + +     DGVM       N  +  T   
Sbjct: 193 DWEIIKYLRDNLPQDTVFFANGNILYPEDISRCMNKIHCDGVMSAEGNLYNPGIFNT--- 249

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             +N      P   ++ ++++  + +    +A++ +       +I R  +      P + 
Sbjct: 250 EHTNEKDKIFPRVDKLLREYFEIVKSCEGSHASK-IAMKSHFFKILRPFL------PLNT 302

Query: 292 RCR-HILTVEAGASTATHHIIETAFNLMIESL 322
             R +I T++A  S       E    L+ E +
Sbjct: 303 DIRSNIATMKATTSFNDWE--EKVVKLVEERV 332


>gi|297702082|ref|XP_002828013.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 2 [Pongo
           abelii]
 gi|297702084|ref|XP_002828014.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 3 [Pongo
           abelii]
          Length = 473

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + ++LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAVDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 279


>gi|255003775|ref|NP_659107.2| tRNA-dihydrouridine synthase 3-like [Mus musculus]
 gi|74186083|dbj|BAE34157.1| unnamed protein product [Mus musculus]
 gi|148706257|gb|EDL38204.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_d [Mus
           musculus]
          Length = 637

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 107/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 304 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMT 362

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  + + L +P+TVK
Sbjct: 363 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGVNEVLDVPLTVK 422

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + + 
Sbjct: 423 MRTGVQERVSLA--HRLLPELRDWGVALVTLHGRS--------REQRYTRLADWPYIEQC 472

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+M+ R A     + T + E     ++ S 
Sbjct: 473 AKVASPMPLFGNGDILSFEDANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSE 532

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T Y   H  S  +  + TR  +
Sbjct: 533 RL----------DILRDFTHYGLEHWGSDTQGVERTRRFL 562


>gi|15639964|ref|NP_219417.1| histidine phosphokinase/phophatase (ntrB) [Treponema pallidum
           subsp. pallidum str. Nichols]
 gi|189026203|ref|YP_001933975.1| histidine phosphokinase/phophatase [Treponema pallidum subsp.
           pallidum SS14]
 gi|6136586|sp|O83945|DUS_TREPA RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|3323302|gb|AAC65935.1| histidine phosphokinase/phophatase (ntrB) [Treponema pallidum
           subsp. pallidum str. Nichols]
 gi|189018778|gb|ACD71396.1| histidine phosphokinase/phophatase [Treponema pallidum subsp.
           pallidum SS14]
          Length = 340

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 62/326 (19%), Positives = 132/326 (40%), Gaps = 31/326 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R  A      +  YTEM+ ++A++R   + K ++  ++ E   A+QI G++ 
Sbjct: 27  AGYSDSAFRSIAIEW-EASFTYTEMVSSEAMVRDSLNTKRLIRRASNETHYAIQIFGSNP 85

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
           + + E AK++ D    + I++N GCP  ++ +   GA L   P  + + + A+  A+   
Sbjct: 86  AVMAETAKLIVDSAQPSCIDINAGCPMPKITKTGAGAALTREPTRLYEVVKAVADAVYAQ 145

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              IPVTVK R G ++    +  +   ++   +G   + +H R                 
Sbjct: 146 DARIPVTVKIRAGWEE--AHLTWKEAARAAVDAGAQALALHPRTC--------AQCYAGE 195

Query: 174 LDYDIVYEIKKEN---PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            ++DI+ ++ +      ++ +  +G L     A  +L      GVM  R A  N  +   
Sbjct: 196 ANWDIIADLVQCARGWGEVPVFGSGDLHAPEDARAMLEHTACAGVMFARGAMGNPFIFRQ 255

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
             +  +         + ++ +  WR++        A+ +      +Q+ +  +    G  
Sbjct: 256 TRQLLTEGYYTPVTFEQKL-RAAWREL-----HLLAQDVGESSACKQMRKRFVSYAKGER 309

Query: 289 NSRRCRHILTVEAGASTATHHIIETA 314
              +      V A +      +I  A
Sbjct: 310 GKTQWCQR-AVHASSFADFAAVIRDA 334


>gi|315453289|ref|YP_004073559.1| tRNA Dihydrouridine synthase [Helicobacter felis ATCC 49179]
 gi|315132341|emb|CBY82969.1| tRNA Dihydrouridine synthase [Helicobacter felis ATCC 49179]
          Length = 332

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 57/322 (17%), Positives = 134/322 (41%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + A++   +K   +L  S  E P ++QI G+ +
Sbjct: 19  AGYTDLPFRSVVKRF-GVDVTVSEMVSSHALVHAFEKTAKMLEKSPHENPFSVQIAGSKV 77

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +  A +++    G + ++ N GCP+ +V     G+ L+ + + +   +  + +  + P
Sbjct: 78  EIVQRAVELLNQVEGIDIVDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKVVREHTNKP 137

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T VK R+G + +IP      +  ++  + V+ + +HAR          D  K   +DY+
Sbjct: 138 YTSVKVRLGFERKIP----EEIAHALNDAPVDFVVVHARTR-------ADRYKKEKIDYE 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  + +   +  + +NG ++ +++A ++       GVMIGRA+     +   +      
Sbjct: 187 SV-RLMRSILNKPLIVNGEIDSVAKAQEVRAYTGAQGVMIGRASLIKPWIFWQIKH---- 241

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  +   + KD   +    M ++          +    +++     G   +   + 
Sbjct: 242 ---NTQELPPVLKKDLVLEHFDKMVEFYGVR-----GVVMFRKNLHAYAKGHAGASAFKG 293

Query: 296 ILTVEAGASTATHHIIETAFNL 317
           ++   +    A   + E  F+ 
Sbjct: 294 VVNSMSDPLVARAQV-EEFFSQ 314


>gi|304319857|ref|YP_003853500.1| dihydrouridine synthase TIM-barrel protein [Parvularcula
           bermudensis HTCC2503]
 gi|303298760|gb|ADM08359.1| dihydrouridine synthase TIM-barrel protein [Parvularcula
           bermudensis HTCC2503]
          Length = 368

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 123/315 (39%), Gaps = 27/315 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R  A L     L+ +EM+ ++  +R      L     T +    +Q+ G +
Sbjct: 35  MSGITDLPFRR-AALRAGAPLVVSEMVASEEWVRERPDVALRAALPTGDSLNVIQLAGRE 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + E A   E  G + I++N+GCP+ +V     G+ LM + D     I A     S P
Sbjct: 94  ARWMREGAAKAEALGADIIDINMGCPARKVTGLLSGSALMRDVDHALSLIKATLSGTSRP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D     +    + K    +GV  I +H R         +        D+  
Sbjct: 154 VTLKMRLGWD--HGHLNAPEIAKGAADAGVAVITVHGRT--------RQQFYKGTADWRA 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V     E   + + +NG + D   A   L      GVMIGRAA     +   + E  ++ 
Sbjct: 204 VRATV-EAVSVPVIVNGDIVDDVTARAALAQSGAAGVMIGRAAEGRPWLPAALAEALASG 262

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI-----TRHMIGLFHGFP--- 288
               +P      +   R    +++ YAA H  S  + +Q+      +H+     G P   
Sbjct: 263 TPMIAPSFVDQIQGVRRLYDETLSHYAAGHGRSAAQGRQLGARMARKHLAAFIDGAPAPW 322

Query: 289 ---NSRRCRHILTVE 300
                R  R +L  E
Sbjct: 323 SSAARREWRRVLCAE 337


>gi|194216507|ref|XP_001490768.2| PREDICTED: dihydrouridine synthase 1-like (S. cerevisiae) [Equus
           caballus]
          Length = 475

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLRDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVRQHPCPLSYVRAHL---FKLWH 279


>gi|242278643|ref|YP_002990772.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
 gi|242121537|gb|ACS79233.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
          Length = 323

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 65/321 (20%), Positives = 120/321 (37%), Gaps = 27/321 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+    +    K  K +L    ++ PL +Q+ G + 
Sbjct: 17  AGYSDLPFRMLCRK-RGCAVACTEMVSVKGLKYDGKGTKALLATCPEDNPLVVQLFGGEP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
               +    + D GY+  +LN GCP  +V +   G+ L L+PD + +  +AM + A    
Sbjct: 76  QDYSDTMPQLIDEGYSFFDLNSGCPVKKVLKTGGGSALHLDPDRLVETASAMVRVAGEGK 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R+G  +         + K ++ +GV  + +H R A        D  K+       
Sbjct: 136 VGVKIRLGFMNGEDN--FLEIAKRLEDTGVAWLTMHPRYAKQMFSGQADWSKL------- 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              + K+N  + +  +G L      ++ +    +DG+M  R A  +  +     +   +P
Sbjct: 187 --AVLKQNVSIPVIGSGDLFTAEDGMECIKQTGIDGIMFARGALFDPEIFARYLKLLDDP 244

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P           K      +       S    ++I   +     G    R  R  
Sbjct: 245 KCATLPPFD------LGKTMEEHINMTRDFDGSNRSFRKIRSILPRYAKGMDGIRSIRTK 298

Query: 297 LTVEAGASTATHHIIETAFNL 317
           LT           ++E A  +
Sbjct: 299 LTACEDW----EELLEAAREV 315


>gi|194765697|ref|XP_001964963.1| GF22885 [Drosophila ananassae]
 gi|190617573|gb|EDV33097.1| GF22885 [Drosophila ananassae]
          Length = 513

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 65/289 (22%), Positives = 118/289 (40%), Gaps = 36/289 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R    + L YT M  A+        +K+ L     ++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRYGAH-LCYTPMYHANLFATDPKYRKDALQTCAGDRPLVIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             ++++AA   +D   + +++N+GCP A    G +G+ L    +++ +  + + K LSIP
Sbjct: 94  AQQILDAALAAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEIESTLHKKLSIP 152

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            + ++ +G   + +H R    KG            D+  
Sbjct: 153 VTCKIRIFEDR----AKTIRYAQMLEAAGCQLLTVHGRTREQKG------PLTGVADWSY 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+++    + +  NG +  +    + L    VDGVM       N A+           
Sbjct: 203 IKEVRQHI-KIPMFANGNILGLEDVHRCLEETGVDGVMSAEGNLHNPAIFQ--------- 252

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGL 283
             G +P    + K++   +        Y   HL    KL     H++ +
Sbjct: 253 --GLAPPVWHMAKEYLEFVDLYPCPSSYIRGHL---FKLFH---HIMNI 293


>gi|239788483|ref|NP_001155091.1| tRNA-dihydrouridine synthase 3-like isoform 2 [Homo sapiens]
 gi|13528705|gb|AAH04549.1| DUS3L protein [Homo sapiens]
 gi|119589550|gb|EAW69144.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
 gi|325463133|gb|ADZ15337.1| dihydrouridine synthase 3-like (S. cerevisiae) [synthetic
           construct]
          Length = 408

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 57/280 (20%), Positives = 108/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 75  NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 133

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 134 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 193

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 194 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 243

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 244 VQAASPMPLFGNGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE 303

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T+Y   H  S  +  + TR  +
Sbjct: 304 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFL 333


>gi|242003652|ref|XP_002422814.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212505672|gb|EEB10076.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 540

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 61/314 (19%), Positives = 127/314 (40%), Gaps = 46/314 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M  +  ++  + +      L    +++PL +Q  G
Sbjct: 19  MVDASELAWRLLSRR-HGAQLCYTPMFHS--LIFANNERYRKEGLASVPEDRPLIVQFCG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   +++AA++ E +  + +++N+GCP A    G +GA L  +  ++ + +  + K+L 
Sbjct: 76  NEPDSILKAAQLAEPY-CDAVDINLGCPQAIAKRGHYGAFLQDDWPLLKEIVGTLKKSLK 134

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT K R+  D +          K ++++G   + +H R    KG            ++
Sbjct: 135 IPVTCKIRVFEDVKKTV----KYAKMLEEAGCQLLTVHGRTKEQKG------PLTGLANW 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  + +EN  + +  NG ++ +    + L     +GVM       N A+         
Sbjct: 185 EHIKAV-RENVRIPVLANGNIQCVQDIFRCLEVTKCNGVMSAEGNLYNPAIF-------- 235

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF---PNSR 291
               G  P    +  ++   +                 L  I  H+  +FH     P+++
Sbjct: 236 ---EGRYPPSWEMATEYLDLVEKY-----------PCPLSYIRGHLFKIFHHILCEPDNK 281

Query: 292 RCRHILTVEAGAST 305
             R  L  ++    
Sbjct: 282 DVRAELANKSTLED 295


>gi|332263179|ref|XP_003280632.1| PREDICTED: tRNA-dihydrouridine synthase 3 isoform 2 [Nomascus
           leucogenys]
          Length = 408

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 108/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 75  NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 133

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 134 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 193

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E 
Sbjct: 194 IRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEEC 243

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 244 VKAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHWDISSSE 303

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T+Y   H  S  +  + TR  +
Sbjct: 304 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFL 333


>gi|296120472|ref|YP_003628250.1| dihydrouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296012812|gb|ADG66051.1| dihydrouridine synthase DuS [Planctomyces limnophilus DSM 3776]
          Length = 362

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 132/311 (42%), Gaps = 35/311 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             +T R +R   R L    L  T+++ A  +L  +   + ++  S  ++PL++Q+ GAD 
Sbjct: 38  AGYTQRPFRVALRELGGMGLATTDLVHAVKLLSNNAFSQQLIATSLLDQPLSVQLFGADP 97

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + +  AA+ +ED GY  ++LN+GCP A+V+    GA LM +P      +A +  ++SIPV
Sbjct: 98  THVATAARWLEDLGYEGVDLNMGCPMAKVNSQGGGARLMCDPTGATRLVALVVASVSIPV 157

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G D Q  +  L  L +  ++ G   I IH R    +G S K +R       + +
Sbjct: 158 TVKMRLGWDAQSLSAPL--LARQFEEVGAAAITIHGRTRA-QGFSGKVSR-------EGI 207

Query: 180 YEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                    + +  NG +  +  A  ++       V IGR A  +  +   + ++     
Sbjct: 208 AATVAAVQSIPVIGNGDVRTVEDAISMRRETGCAAVAIGRGAMLDPWIFRKLHDFEMTGQ 267

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR------ 291
                 + ++   F       M D             ++ R   G +     +R      
Sbjct: 268 YAEPGPEEQI--QFLVTHFREMVDLFGEQA------TRLFRKFAGWY----GARLGIPQD 315

Query: 292 ---RCRHILTV 299
              R R + ++
Sbjct: 316 LEDRLRRVESL 326


>gi|169845921|ref|XP_001829678.1| tRNA-dihydrouridine synthase 1 [Coprinopsis cinerea okayama7#130]
 gi|116509234|gb|EAU92129.1| tRNA-dihydrouridine synthase 1 [Coprinopsis cinerea okayama7#130]
          Length = 561

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 110/255 (43%), Gaps = 28/255 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-----------TQEKP 49
           MVD ++  +R   R      L+YT MI A        K+    +             ++P
Sbjct: 41  MVDQSELAFRRLCRQY-GAQLIYTPMINAKMFTDPVNKSYRASAFDIASGEEGDMASDRP 99

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L +Q    D  +L+++AK+VE +  + +++N+GCP      G +G+ L  +  ++   I 
Sbjct: 100 LIVQFCANDPDQLLQSAKVVEKY-CDAVDINLGCPQDIAKRGRYGSFLQDDWPLIYSMIN 158

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +   LSIPVT K R+  D +          K ++++G   +  H R    +G      +
Sbjct: 159 TLHVNLSIPVTAKFRVFPDVEKTV----EYAKMLERAGAQILTCHGRIREQRG------Q 208

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
                D+  +  +K E   + +  NG +   +D+++ L+     DGVM       N A+ 
Sbjct: 209 NTGLADWSKIRAVK-EAVKVPVFANGNILFQDDIARCLEE-TGCDGVMSAEGILYNPALF 266

Query: 227 TTVDEYFSNPLTGSS 241
             +D   S+P   ++
Sbjct: 267 YGLDAPSSSPKPPTT 281


>gi|328789228|ref|XP_623799.3| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 2 [Apis
           mellifera]
          Length = 478

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 102/230 (44%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K     L  + +++PL +Q  G D
Sbjct: 37  MVDASELAWRLLSRR-HGAHLCYTPMLHSSVFCRDPKYRREALASTAEDRPLVVQFCGND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S L+EAA + E +  + +++N+GCP A    G +GA L  + +++   ++ + K L +P
Sbjct: 96  PSTLLEAALLAEPY-CDAVDINIGCPQAIAKRGHYGAFLQDDWNLLQQIVSTLSKKLHVP 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  +            + ++ +G   + +H R    KG             +D 
Sbjct: 155 VTCKLRVFAEIDKTV----KYAQMLEAAGAQLLTVHGRTREQKG------PLTGVASWDH 204

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           +  +++    + +  NG ++ +    K +    V+GVM       N  + 
Sbjct: 205 IKAVRQAVT-IPVFANGNIQCLQDIQKCIEETGVNGVMSAEGNLYNPYIF 253


>gi|126340537|ref|XP_001363271.1| PREDICTED: similar to dihydrouridine synthase 4-like [Monodelphis
           domestica]
          Length = 317

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 123/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKY-NCDLCYTPMIVAADFVRSTKARDSEFTTNKGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  AQLLSDAARIVCPY-ANGIDINCGCPQRWAITEGYGACLINKPELVQDMVKQVRSQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 NFSVSIKIRIHDDLTRT----IDLCRKAEATGVSWITVHGRNIEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + I  NG ++ + +A   + +   +G+M+ R    N AM     E  
Sbjct: 199 YDAIK-IIKENLSIPIIANGDIKSLKEAENVQEMTGTNGIMVARGLLANPAMFAGYKE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKI-SASMTDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I     T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALEHGTPFMCFHHHLMYMMERIT 290


>gi|301754165|ref|XP_002912927.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Ailuropoda
           melanoleuca]
          Length = 475

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG------PLSGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLRDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVRQHPCPLSYVRAHL---FKLWH 279


>gi|87309530|ref|ZP_01091665.1| hypothetical protein DSM3645_24550 [Blastopirellula marina DSM
           3645]
 gi|87287838|gb|EAQ79737.1| hypothetical protein DSM3645_24550 [Blastopirellula marina DSM
           3645]
          Length = 362

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 117/322 (36%), Gaps = 25/322 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGAD 58
            ++D   R  AR     +    E+++   ++    R   K+ L  + +E P+  Q+ GA+
Sbjct: 35  GYSDMSMRVIARRF-GASYAVCEVMLDQFLVTFKDRSKNKHFLAIADEEHPVGGQLMGAE 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
             +    A  +   GY+ I++N GCP  +V     G   +  P++  + I+    A    
Sbjct: 94  PIQFAAGAVKLAQAGYDVIDINFGCPVRKVLGRCRGGFHLSQPEVALEVISRTRDATPPE 153

Query: 117 IPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           IPVTVK R G+DD          ++      GV  I +H R          + R +    
Sbjct: 154 IPVTVKMRRGIDDTAASRDNFFRILDGAFDLGVAAITVHGRT--------VEQRYVGPSR 205

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ + E+K+      I  +G L      L ++    VDGV + R A  N  +       +
Sbjct: 206 WEFLREVKEHVGSRVILGSGDLFSAQDCLDMMRQTGVDGVTVARGAIGNPWIFQQCRALY 265

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +       P          R +       A         + Q+ +  I      P+   C
Sbjct: 266 AGEPLPPPPTVFE-----QRDVINEHLRLAEELYGEKRGITQMRKFGIKYSFLHPDMEEC 320

Query: 294 RHILTVEAGASTATHHIIETAF 315
           R   T     + A  H I   F
Sbjct: 321 RAKFTK--MRTLADWHAIRETF 340


>gi|320333337|ref|YP_004170048.1| dihydrouridine synthase DuS [Deinococcus maricopensis DSM 21211]
 gi|319754626|gb|ADV66383.1| dihydrouridine synthase DuS [Deinococcus maricopensis DSM 21211]
          Length = 312

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 65/296 (21%), Positives = 106/296 (35%), Gaps = 30/296 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLALQIGGADI 59
           M  ++D   R             +EM+ A  +L GD    LG     E+   LQ+ GAD 
Sbjct: 20  MAGYSDAPMRALCSE-QGALWTVSEMLSARGLLEGDLAVDLGQPYPGEQGRVLQLFGADP 78

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             L   A+     F    ++LN+GCP  ++     GACL+  PD+    + AM  A++I 
Sbjct: 79  DILAAGAQEAVRLFQPAALDLNMGCPVPKIKGKG-GACLLQTPDVAYTLVKAMRDAVNID 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+G D          + + ++ +G   I +H R            R     D+D 
Sbjct: 138 VSAKIRLGWDTNRSV----EIAQGLEAAGAALITVHGRT--------SAQRYTGYADWDA 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +   +    +  +G +       A +    V  VMIGR A  N  +           
Sbjct: 186 IAHVA-ASVRAPVIGSGDVTSAEQAHARRAHSGVAAVMIGRGAVGNPWVFRQ------TA 238

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            TG +P          R    +              + Q+ + +   F   P  R 
Sbjct: 239 GTGGAPTPDDRLCTALRHAELN-----VHWYGERRGMLQLRKVLHRYFPDQPERRD 289


>gi|154148885|ref|YP_001406121.1| NifR3 family protein [Campylobacter hominis ATCC BAA-381]
 gi|153804894|gb|ABS51901.1| NifR3 family protein [Campylobacter hominis ATCC BAA-381]
          Length = 310

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 65/304 (21%), Positives = 124/304 (40%), Gaps = 32/304 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D   R   +    +A   +EMI A+A++   +K+  ++  S  E P  +QI G+D 
Sbjct: 15  AGFSDLPLRSVVKRFGCDA-TVSEMISANALVFCSEKSLKMIKKSENETPYFVQIAGSDP 73

Query: 60  SKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +I+    G + I+LN GCP  +V   + G+ L+ N D++   I  + K  +  
Sbjct: 74  KIIKQAVEILNKIDGIDGIDLNCGCPVPKVVRQNAGSALLQNLDLLSKLIEIIKKTSNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T  K R+G D + P     N+  +++ +G + I +HAR         +        DY+
Sbjct: 134 YTSAKVRLGFDTKNPV----NIALAVQNAGADFIAMHART--------RAGGYSAKPDYE 181

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +   K     + +  NG +     A +I  L   D +MIGRA   N  +   +      
Sbjct: 182 AIAAAKSAV-KIPLIANGNINS-QNANQILNLTKADALMIGRATIGNPWVFYEIKNQ--- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  +  ++ K+        M  +   H           +H+     G+ ++   R 
Sbjct: 237 ---KTVAVDEKIKKEIILAHFDEMIKFYGDH-----GAVIFRKHLHEYSKGYADATNFRC 288

Query: 296 ILTV 299
            +  
Sbjct: 289 EINT 292


>gi|307206649|gb|EFN84621.1| tRNA-dihydrouridine synthase 1-like [Harpegnathos saltator]
          Length = 304

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 103/230 (44%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K     L  +++++PL +Q  G+D
Sbjct: 36  MVDASELPWRLLSRR-HGAELCYTPMLHSSVFCRDPKYRREALTSTSEDRPLIVQFCGSD 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA++ E +  + +++N+GCP A    G +GA L  + D++   ++ + + L IP
Sbjct: 95  PEVLLEAARLAEPY-CDAVDINIGCPQAIAKRGHYGAFLQDDWDLLQKIVSTLKRGLRIP 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  +            + ++ +G + + +H R    KG             ++ 
Sbjct: 154 VTCKLRVFPEVGRTV----EYARMLENAGASLLTVHGRTREQKG------PLTGLASWEH 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           +  +K     + +  NG ++ M    + +    V GVM       N  + 
Sbjct: 204 IKAVK-AAVKIPVIANGNIQCMQDLQRCIKETQVQGVMSAEGNLYNPYIF 252


>gi|256088793|ref|XP_002580509.1| tRNA-dihydrouridine synthase [Schistosoma mansoni]
 gi|238666091|emb|CAZ36748.1| tRNA-dihydrouridine synthase, putative [Schistosoma mansoni]
          Length = 441

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 122/298 (40%), Gaps = 29/298 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L +T MI + A L   K     L F+++++PL +Q     
Sbjct: 17  MVDGSELAWRMLGRKY-GVQLTFTPMINSTAFLINMKYRRSCLQFASEDRPLIVQFCANS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               V  AK+V+ F  + ++LN+GCP      G +GA L    + + + I+     L++P
Sbjct: 76  PDTFVRCAKLVQPF-CDAVDLNLGCPQGIAKRGHYGAFLQDEWNSLKEIISRASLELNVP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D +          K ++ +G + + +H R   +KG      +K    D++ 
Sbjct: 135 VTCKIRIFSDVERTV----QYAKLLEAAGASMLTVHGRTREMKG------QKTGLADWNQ 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN- 235
           +  +K E   + +  NG ++ +S   + L     D VM       N A+   +     + 
Sbjct: 185 IRAVK-EAVKIPVIANGNIQYLSDVHQCLDSTKADAVMSAEGHLHNPALFLGIQPCIYDM 243

Query: 236 -----PLTGSSPIKTRVDKDFWRKISASMTDYAARHL------HSGGKLQQITRHMIG 282
                 L    P   ++ +    K+     D  + +        S   +++I + M  
Sbjct: 244 CFEYLDLVEKYPTSMQIIRGHIFKLCHHALDEHSEYRSLIGTSQSTKGIKEILQKMAN 301


>gi|281348632|gb|EFB24216.1| hypothetical protein PANDA_000684 [Ailuropoda melanoleuca]
          Length = 478

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 109/283 (38%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG------PLSGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLRDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVRQHPCPLSYVRAHL---FKLWH 279


>gi|308808940|ref|XP_003081780.1| Dihydrouridine synthase TIM-barrel protein yjbN (ISS) [Ostreococcus
           tauri]
 gi|116060246|emb|CAL56305.1| Dihydrouridine synthase TIM-barrel protein yjbN (ISS) [Ostreococcus
           tauri]
          Length = 418

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 100/304 (32%), Positives = 147/304 (48%), Gaps = 28/304 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKL 62
           D T  H+R  AR +T  A L+TEM   D + R     +      E  +  Q+GG+  S L
Sbjct: 16  DVTTPHHRALARAMTTRARLWTEMAHHDCVTRMCSSTMTR---SETHVTAQVGGSRPSGL 72

Query: 63  VEAAKIVE-DFGYNEINLNVGCPSARVHEG-----SFGACLMLNPDIVGDCIAAMCKALS 116
             AA+I+E ++GY+E+NLN GCPS RV        SFGA +M++ +   +C+  M +A+ 
Sbjct: 73  ARAAEILESEYGYDEVNLNCGCPSERVCRKDDETSSFGAAMMIDVENTAECVRRMVEAVD 132

Query: 117 -IPVTVKCRIGV---------DDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGLSP 165
              +TVK R+GV         ++      +   +++IK + GV+   +HAR A++ GLSP
Sbjct: 133 ATKITVKHRLGVRFDKTMTVKEETDSYEHVVKFIEAIKDAAGVDHFIVHARSAVMGGLSP 192

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAAYK 221
             NRKIP L YD V+ +  E       LNGG+E + QA  +L   D    GVM+GRA YK
Sbjct: 193 DANRKIPPLRYDEVFALCDEFSKCDFTLNGGVETLEQAKGLLEREDGKLAGVMMGRAFYK 252

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           +  ML  +D       T   P   R     +     S+       +H   +     R   
Sbjct: 253 HPCMLADIDRVIFGEPTADPPPTRRSLVKMYGDYGDSVFAGLGSDVHYKVRKSMARR--- 309

Query: 282 GLFH 285
            LF 
Sbjct: 310 -LFK 312


>gi|47937507|gb|AAH72076.1| MGC78973 protein [Xenopus laevis]
          Length = 465

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 99/233 (42%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 18  MVDQSELAWRLLSRR-HGVQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +G+ L    D++   I    + LS
Sbjct: 77  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGSFLQDEWDLLEKMIQLAHQKLS 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  + +          K ++K+G   + +H R    KG             +
Sbjct: 136 VPVTCKIRVFPEIEKTV----EYAKMLEKAGCQLLTVHGRTKEQKG------PLTGIASW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAML 226
           + +  ++     + +  NG ++   D+ + ++   +V GVM       N A+ 
Sbjct: 186 EHIKAVRNAV-IIPVFANGNIQYLNDVERCMRE-TAVQGVMSAEGNLHNPALF 236


>gi|149028168|gb|EDL83606.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_c
           [Rattus norvegicus]
          Length = 640

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 107/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      +L     E    +Q+ GA    + 
Sbjct: 307 NLPFRRICKRF-GADVTCGEMAMCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMT 365

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 366 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGMNEVLDVPLTVK 425

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + + 
Sbjct: 426 MRTGVQERVSLA--HRLLPELRNWGVALVTLHGRS--------REQRYTRLADWPYIEQC 475

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+M+ R A     + T + E     ++ S 
Sbjct: 476 AKVASPMPLFGNGDILSFEDANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSE 535

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T Y   H  S  +  + TR  +
Sbjct: 536 RL----------DILRDFTHYGLEHWGSDTQGVERTRRFL 565


>gi|307182359|gb|EFN69626.1| tRNA-dihydrouridine synthase 1-like [Camponotus floridanus]
          Length = 468

 Score =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 102/230 (44%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K     L  +++++PL +Q  G D
Sbjct: 30  MVDASELAWRLLSRR-HGAQLCYTPMLHSTVFCRDPKYRREALASTSEDRPLIVQFCGND 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA++ E +  + I++N+GCP A    G +GA L  +  ++   ++ +   L IP
Sbjct: 89  PDVLLEAARLAEPY-CDAIDINIGCPQAIAKRGHYGAFLQDDWILLNRIVSTLKNGLHIP 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  +            + ++ +G + + IH R    KG             ++ 
Sbjct: 148 VTCKLRVFSEINRTV----EYARMLQDAGASLLTIHGRTREQKGS------LTGLASWEH 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           +  + ++  ++ +  NG ++ M    + +    V GVM       N  + 
Sbjct: 198 IKAV-RDAVEIPVIANGNIQCMQDLQRCIEEIQVQGVMSAEGNLYNPYIF 246


>gi|148223341|ref|NP_001085224.1| hypothetical protein LOC432319 [Xenopus laevis]
 gi|80477797|gb|AAI08778.1| MGC78973 protein [Xenopus laevis]
          Length = 465

 Score =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 99/233 (42%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 18  MVDQSELAWRLLSRR-HGVQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +G+ L    D++   I    + LS
Sbjct: 77  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGSFLQDEWDLLEKMIQLAHQKLS 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  + +          K ++K+G   + +H R    KG             +
Sbjct: 136 VPVTCKIRVFPEIEKTV----EYAKMLEKAGCQLLTVHGRTKEQKG------PLTGIASW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAML 226
           + +  ++     + +  NG ++   D+ + ++   +V GVM       N A+ 
Sbjct: 186 EHIKAVRNAV-IIPVFANGNIQYLNDVERCMRE-TAVQGVMSAEGNLHNPALF 236


>gi|77917548|ref|NP_001030095.1| tRNA-dihydrouridine synthase 3-like [Rattus norvegicus]
 gi|110808213|sp|Q3KRC5|DUS3L_RAT RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|77415407|gb|AAI05781.1| Dihydrouridine synthase 3-like (S. cerevisiae) [Rattus norvegicus]
          Length = 640

 Score =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 107/280 (38%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +L+G      +L     E    +Q+ GA    + 
Sbjct: 307 NLPFRRICKRF-GADVTCGEMAMCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMT 365

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 366 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGMNEVLDVPLTVK 425

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + + 
Sbjct: 426 MRTGVQERVSLA--HRLLPELRNWGVALVTLHGRS--------REQRYTRLADWPYIEQC 475

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+M+ R A     + T + E     ++ S 
Sbjct: 476 AKVASPMPLFGNGDILSFEDANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSE 535

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T Y   H  S  +  + TR  +
Sbjct: 536 RL----------DILRDFTHYGLEHWGSDTQGVERTRRFL 565


>gi|81902404|sp|Q91XI1|DUS3L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|15192726|gb|AAK84684.1| putative zinc finger protein [Mus musculus]
          Length = 637

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 106/280 (37%), Gaps = 25/280 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 304 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMT 362

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  +   L +P+TVK
Sbjct: 363 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMNRSAKFQQIVRGVNGVLDVPLTVK 422

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +++       L+  ++  GV  + +H R         ++ R     D+  + + 
Sbjct: 423 MRTGVQERVSLA--HRLLPELRDWGVALVTLHGRS--------REQRYTRLADWPYIEQC 472

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            K    + +  NG +     A   +   V G+M+ R A     + T + E     ++ S 
Sbjct: 473 AKVASPMPLFGNGDILSFEDANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSE 532

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           I    T Y   H  S  +  + TR  +
Sbjct: 533 RL----------DILRDFTHYGLEHWGSDTQGVERTRRFL 562


>gi|327265085|ref|XP_003217339.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Anolis
           carolinensis]
          Length = 485

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 58/284 (20%), Positives = 113/284 (39%), Gaps = 37/284 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + ++LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEIFVQAALLAQDY-CDAVDLNLGCPQMIAKRGHYGAFLQEEWDLLRRMIMLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T K R+  +            + ++++G   + +H R    KG             +
Sbjct: 142 VPITCKIRVFPE----IAKTVKYAQLLEEAGCQLLTVHGRTKEQKG------PLAGVASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  ++K   ++ +  NG ++   D+ + ++    V GVM       N A+        
Sbjct: 192 EHIQAVRKAV-NIPVFANGNVQYLNDVEKCIQK-TGVQGVMSAEGNLHNPALF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
                G +P+   + +++   +        Y   HL    KL  
Sbjct: 243 ----EGRNPVVWEMAEEYLEIVQQYPCPLSYVRAHL---FKLWH 279


>gi|255714418|ref|XP_002553491.1| KLTH0D18084p [Lachancea thermotolerans]
 gi|238934871|emb|CAR23053.1| KLTH0D18084p [Lachancea thermotolerans]
          Length = 430

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 71/315 (22%), Positives = 129/315 (40%), Gaps = 33/315 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE------KPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K     +   +      +PL +Q 
Sbjct: 37  MVDQSELAWRILSRRY-GATLAYTPMFHAKMFATSEKYRRDMWCKDDGSQELDRPLVVQF 95

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L+ AAK++ED   + ++LN+GCP     +G +G+ LM + D++   I  +   
Sbjct: 96  CANDSDYLLAAAKLIED-KCDAVDLNLGCPQGIAKKGHYGSFLMEDWDLIHKLIRTLHDN 154

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L IPVT K R+  +            K +  +G   + +H R    KG      +K    
Sbjct: 155 LKIPVTAKIRVFSER----AKTLEYAKMVLDAGAQFLTVHGRLREQKG------QKTGLA 204

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           D+DI+  +++E P D     NG +   ED+S+ +  +   D VM       N  +  T  
Sbjct: 205 DWDIIQYLRQELPKDTVFFANGNILYPEDISRCMNEI-HCDAVMSAEGNLYNPGVFNT-- 261

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F      + P   ++ ++++  + +    +A++ +       +I R  +      P  
Sbjct: 262 -DFIGDKEMTFPRVDKLLREYFEVVKSCEGSHASK-VAMKSHFFKILRPFL------PEH 313

Query: 291 RRCRHILTVEAGAST 305
              R  L   +  S+
Sbjct: 314 TDIRSNLATMSAKSS 328


>gi|302795500|ref|XP_002979513.1| hypothetical protein SELMODRAFT_444257 [Selaginella moellendorffii]
 gi|300152761|gb|EFJ19402.1| hypothetical protein SELMODRAFT_444257 [Selaginella moellendorffii]
          Length = 378

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 65/324 (20%), Positives = 129/324 (39%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A       K     F+   +++PL +Q    +
Sbjct: 59  MVDQSELPFRMLCRKYGATG-AYTPMLHARLFSEDRKYRNYEFTTCPEDRPLLIQFCANN 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE F  + I++N+GCP      G++GA LM +  +V   +  +   L +P
Sbjct: 118 PDTLLAAAKLVEPF-CDYIDINLGCPQRIAKRGNYGAFLMDDLPLVQALVTKLVSNLDVP 176

Query: 119 VTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   +DD I         K ++ SG + + +H R    K        +    D+
Sbjct: 177 VSCKIRMFPSLDDTISY------AKMLESSGCSLLAVHGRTREQK------CSRTVRADW 224

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +++  +K+    + +  NG +  +  A + +    VDGV+   +  +N A+      +  
Sbjct: 225 EVIRAVKQAL-RIPVLANGNIRSLEDAERCIQETGVDGVLSAESLLENPALFAGYRTFKP 283

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +         +++  D    +   + D   ++      ++     ++G +  F      R
Sbjct: 284 SDSEDDEQGSSKLMIDPVTLLMEYL-DQCEKYPAPDKCIRAHVHRLLGEW--FRVHPDLR 340

Query: 295 HILTVEAGAS-----TATHHIIET 313
             L  E              ++E 
Sbjct: 341 EKLNREHKVDSTWLRDLGREMLER 364


>gi|149704573|ref|XP_001491222.1| PREDICTED: dihydrouridine synthase 4-like (S. cerevisiae) [Equus
           caballus]
          Length = 317

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 72/284 (25%), Positives = 119/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVQDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDLTRTV----DLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  I K+N  + +  NG +  + +A   + +   DGVM+ R    N AM    +E  
Sbjct: 199 YEAIK-IIKDNASIPVIANGDIRSLKEAENVRHITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +   D+        T Y   H H    +++IT
Sbjct: 256 ---------TPLKCVSDWVDIALELGTPYICFHQHLMYMMEKIT 290


>gi|237751061|ref|ZP_04581541.1| transcriptional regulator [Helicobacter bilis ATCC 43879]
 gi|229373506|gb|EEO23897.1| transcriptional regulator [Helicobacter bilis ATCC 43879]
          Length = 320

 Score =  191 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 141/326 (43%), Gaps = 36/326 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   +    + +  +EMI + A++  ++K   +   S  E P +LQI G+  
Sbjct: 8   AGFSDVPFRKVVKDFGVD-ITVSEMISSHALVYENEKTLKMALKSPNETPFSLQISGSKE 66

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             L  A + + +    + I+ N GCP+ +V     G+ L+ + D     +  + K  +  
Sbjct: 67  EILKRAVEKINELSWVDIIDFNCGCPAPKVANHGNGSALLKDLDKFVSLLQIIRKYGNKQ 126

Query: 119 V-TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           V +VK R+G D +IP     +L ++I +S V+   +HAR  +       D  K   +DYD
Sbjct: 127 VYSVKVRLGFDKKIP----LDLAEAINESSVDYCVVHARTKM-------DAYKKDKIDYD 175

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KEN  + +  NG ++ +    K++   + DG MIGRAA K+  +   +      
Sbjct: 176 SLA-LMKENLKIPMIANGEIDGLESFQKVMQITNADGAMIGRAALKSPWIFWQIQA---- 230

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++     + +D   K   SM ++          +    +++     G  +S + R 
Sbjct: 231 ---KTNDFPLALKRDLVLKHLDSMFEFYGER-----GVIMFRKNLHAYAKGQKDSSKYRE 282

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            +  E       +H+I  +     ++
Sbjct: 283 FVNNE-----KDYHLIRESIKDFFDT 303


>gi|170034571|ref|XP_001845147.1| t-diRNAhydrouridine synthase [Culex quinquefasciatus]
 gi|167875928|gb|EDS39311.1| t-diRNAhydrouridine synthase [Culex quinquefasciatus]
          Length = 609

 Score =  191 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 65/287 (22%), Positives = 117/287 (40%), Gaps = 32/287 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +    +K+ L    +++PL +Q  G D
Sbjct: 112 MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFTKDPKYRKDSLQTCPEDRPLIIQFCGND 170

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EA  + +D   + I++N+GCP A    G +GA L    D++   ++ + + LS+P
Sbjct: 171 PKVLLEAGLLAQDH-CDAIDINLGCPQAIAKRGHYGAFLQDEWDLLKKIVSTLHQNLSVP 229

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            K ++ +G   + +H R    KG            D+  
Sbjct: 230 VTCKVRIFEDM----AKTIRYAKMLESAGCQMLVVHGRTRDQKG------PLTGVADWKY 279

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  + KE   + +  NG +  +    + +    V+GVM       N  +   ++      
Sbjct: 280 VK-VLKEIMKIPVLSNGNIMSVEDVHRCIEETGVNGVMTAEGNLFNPFLFEGIN------ 332

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                P    V  ++   +      Y A   +  G L +I  H++ L
Sbjct: 333 -----PTSWTVALEYLDIVEK----YPAPISYIRGHLFKILHHLMNL 370


>gi|218515463|ref|ZP_03512303.1| tRNA-dihydrouridine synthase A [Rhizobium etli 8C-3]
          Length = 156

 Score =  191 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 92/156 (58%), Positives = 114/156 (73%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D  
Sbjct: 1   MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDAAEHPLALQLGGSDPV 60

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           KL EA +I E +GY+EINLNVGCPS RV  G+FGACLML P+ V  CIAAM    + PVT
Sbjct: 61  KLAEAVRIAEPYGYDEINLNVGCPSDRVQSGTFGACLMLTPETVAGCIAAMKAVSTAPVT 120

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           VKCRIGVD+Q P  AL  L+  +  +G + IWIHAR
Sbjct: 121 VKCRIGVDEQEPEEALPALITRVLDAGADAIWIHAR 156


>gi|254431919|ref|ZP_05045622.1| tRNA-dihydrouridine synthase B [Cyanobium sp. PCC 7001]
 gi|197626372|gb|EDY38931.1| tRNA-dihydrouridine synthase B [Cyanobium sp. PCC 7001]
          Length = 342

 Score =  191 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 130/320 (40%), Gaps = 21/320 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADIS 60
              +DR +R   R    +ALL+TEM+ A ++  G     +     E  P+ +Q+     +
Sbjct: 41  AGVSDRIFRSLVRRWAPDALLFTEMVNATSLELGHGVQKVEELGSESGPIGVQLFDHRPA 100

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + +AA+  E  G   I++N+GCP  ++     G+ L+ +P +    + A+  A++IPVT
Sbjct: 101 AMADAARRAEAAGAFLIDINMGCPVKKIARKGGGSGLIRDPHLAARIVEAVAAAVAIPVT 160

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G           +  + ++ +G   + +H R         ++       D+  + 
Sbjct: 161 VKTRLGWCGSDADPV--SWCRQLQDAGAQLLTLHGRT--------REQGFRGRADWGAIA 210

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            +K+    + +  NG +     AL  L     DG+M+GR +     ++  +D   S    
Sbjct: 211 AVKRALT-IPVVANGDVNTPEGALHCLAATGCDGLMVGRGSMGAPWLVGQIDAALSGQPI 269

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +P           ++ A +             L    +HM     GFP + + RH L 
Sbjct: 270 PPTPGAAERIALAAEQLQALVAAKG------DHGLLIARKHMGWTCTGFPGAPQLRHDL- 322

Query: 299 VEAGASTATHHIIETAFNLM 318
           + A        ++E A   +
Sbjct: 323 MRAPTPAEALALLERARQSL 342


>gi|311232399|gb|ADP85253.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris RCH1]
          Length = 441

 Score =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 116/303 (38%), Gaps = 25/303 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+ A  ++      +++L  + ++ PL +Q+ G D 
Sbjct: 40  AGYSDLSFRLLCRE-AGAAVCCTEMVSAKGLIYCSPGTRDLLATTPEDAPLVVQLFGCDP 98

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             +V A + + + G+   +LN+GC   +V +   GA ++ +         AM   A +  
Sbjct: 99  DIMVRAMEPLLEQGFRWFDLNMGCSVPKVVKTGCGAAMLRDVPQALAVARAMLRTAGAGR 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G D  +      +L +++   G   + +H R A                 +  
Sbjct: 159 VGFKFRLGWD--VGQEVWADLGRALADLGAGWVTLHPRYA--------RQGFSGEARWSA 208

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN- 235
           + E+ +    + +  +G L   +  ++ L    V  VM  R A  +  +     E  +  
Sbjct: 209 LGELVRAV-SVPVIASGDLFTAADGVRCLRETGVASVMYARGALNDPGVFHAHRERVAGR 267

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P  G +P + R       +++       +  L     + +  RH        P +R  R 
Sbjct: 268 PDPGYTPQRLRALITRHAELARQYAPGRSALLKMRTFVPRYVRH-------LPGARALRQ 320

Query: 296 ILT 298
            L 
Sbjct: 321 HLA 323


>gi|318042395|ref|ZP_07974351.1| nitrogen regulation protein NifR3 family protein [Synechococcus sp.
           CB0101]
          Length = 331

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 141/324 (43%), Gaps = 29/324 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADI 59
              +DR +R   R    +ALL+TEM+ A ++    G  K +   +++  P+ +Q+     
Sbjct: 29  AGVSDRIFRGLVRRWAPDALLFTEMVNATSLELGHGLIK-VEELASEPGPIGVQLFDHRP 87

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + + +AA+  E  G   I++N+GCP  ++ +   G+ L+ +P +    + A+  A++IPV
Sbjct: 88  AAMADAARRAEAAGAFLIDINMGCPVKKIAKKGGGSGLIRDPSLAARIVEAVAAAVAIPV 147

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G      ++      + ++ +G   + +H R         ++       D+D +
Sbjct: 148 TVKTRLGWCG--SSLDPVGWCRELEDAGAQLLTLHGRT--------REQGFKGQADWDAI 197

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K+    + +  NG +     AL+ L     DGVM+GR A     ++  +D   S   
Sbjct: 198 AAVKQAL-QIPVIANGDVNSADDALRCLAHTGADGVMVGRGAMGAPWLVGQIDAALSGRP 256

Query: 238 TGSSP---IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              SP    + ++  +  + + A+  D+          L    +HM     GF  + + R
Sbjct: 257 VPPSPGALERIQLASEQLQALVAARGDH---------GLLIARKHMSWTCTGFSGAPQLR 307

Query: 295 HILTVEAGASTATHHIIETAFNLM 318
           H L + A        ++  A   +
Sbjct: 308 HAL-MRAPTPADALALLHHAATQL 330


>gi|120603945|ref|YP_968345.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
 gi|120564174|gb|ABM29918.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
          Length = 449

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 116/303 (38%), Gaps = 25/303 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+ A  ++      +++L  + ++ PL +Q+ G D 
Sbjct: 40  AGYSDLSFRLLCRK-AGAAVCCTEMVSAKGLIYYSPGTRDLLATTPEDAPLVVQLFGCDP 98

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             +V A + + + G+   +LN+GC   +V +   GA ++ +         AM   A +  
Sbjct: 99  DIMVRAMEPLLEQGFRWFDLNMGCSVPKVVKTGCGAAMLRDVPQALAVARAMLRTAGAGR 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G D  +      +L +++   G   + +H R A                 +  
Sbjct: 159 VGFKFRLGWD--VGQEVWADLGRALADLGAGWVTLHPRYA--------RQGFSGEARWST 208

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN- 235
           + E+ +    + +  +G L   +  ++ L    V  VM  R A  +  +     E  +  
Sbjct: 209 LGELVRAV-SVPVIASGDLFTAADGVRCLRETGVASVMYARGALNDPGVFHAHRERVAGR 267

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P  G +P + R       +++       +  L     + +  RH        P +R  R 
Sbjct: 268 PDPGYTPQRLRALITRHAELARQYAPGRSALLKMRTFVPRYVRH-------LPGARALRQ 320

Query: 296 ILT 298
            L 
Sbjct: 321 HLA 323


>gi|68482886|ref|XP_714669.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68483082|ref|XP_714575.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436155|gb|EAK95523.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436256|gb|EAK95622.1| likely tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|238883810|gb|EEQ47448.1| tRNA-dihydrouridine synthase 1 [Candida albicans WO-1]
          Length = 467

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 73/301 (24%), Positives = 124/301 (41%), Gaps = 35/301 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKN--ILGFSTQEKPLALQ 53
           MVD ++  +R  +R      L YT M  A         R       + G    ++PL +Q
Sbjct: 65  MVDQSELAWRILSRRY-GAQLCYTPMFHAKLFATQEKYRNSMWTTNLDGNKDLDRPLVVQ 123

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
               D   L++AAK++E+   + I+LN+GCP     +G +GA LM + D+V   I  +  
Sbjct: 124 FCANDPDYLLQAAKLIENE-CDAIDLNLGCPQGIARKGKYGAFLMDDWDLVYKLIKNLHD 182

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            LSIPVT K RI  D            K +  +G   I +H R   +KG +         
Sbjct: 183 NLSIPVTAKIRIYDD----YEKSLKYAKMVLDAGAQFITVHGRTREMKGQAT------GL 232

Query: 174 LDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
            ++ I+  ++   P D     NG +   S   +     + D VM       N  +  T+D
Sbjct: 233 ANWKILKYLRDNLPQDQVFFSNGNILYPSDIQRCQSETACDAVMSAEGNLYNPGVFWTLD 292

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH---------LHSGGKLQQITRHMI 281
           +          P   ++ ++++  +  +    A+RH         LH+  ++ +  R +I
Sbjct: 293 DNKDKQF----PRVDKILREYFEIVKENYDSLASRHAMKSHFFKLLHAFLEVHKELRPII 348

Query: 282 G 282
           G
Sbjct: 349 G 349


>gi|205374743|ref|ZP_03227537.1| tRNA-dihydrouridine synthase [Bacillus coahuilensis m4-4]
          Length = 334

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 76/332 (22%), Positives = 131/332 (39%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+PL   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNTESYCHPDGIQSVRGRLTFTEDEQPLVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V +   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGMAEMGFKGIDLNMGCPVPNVTQNGKGSGLILRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGFSDL---EEWRGWLTHILKQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK++    VDGVMIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRETGLKLVEQYGVDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   D  R        YA + + S   L +  +       GF  +
Sbjct: 243 ------EVEPKDHTSKELLDLLRLHLDLYDQYAEQVMRSFKSLHRFFKI---YVKGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+ L +   ++     +++   +  ++ L
Sbjct: 294 SELRNHL-MNTESTDEVRALLDEFESKNLDEL 324


>gi|241952224|ref|XP_002418834.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223642173|emb|CAX44140.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 463

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/301 (24%), Positives = 124/301 (41%), Gaps = 35/301 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKN--ILGFSTQEKPLALQ 53
           MVD ++  +R  +R      L YT M  A         R       + G  T ++PL +Q
Sbjct: 63  MVDQSELAWRILSRRY-GAQLCYTPMFHAKLFATQEKYRNSMWTTNLDGNQTLDRPLVVQ 121

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
               D   L++AAK++ED   + I+LN+GCP     +G +GA LM + D+V   I  +  
Sbjct: 122 FCANDPDYLLQAAKLIEDE-CDAIDLNLGCPQGIARKGKYGAFLMDDWDLVYKLIKNLHD 180

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            LSIPVT K RI  D            K +  +G   I +H R   +KG +         
Sbjct: 181 NLSIPVTAKIRIYDD----YEKSLKYAKMVLDAGAQFITVHGRTREMKGQAT------GL 230

Query: 174 LDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVD 230
            ++ I+  ++   P D     NG +   S   +       D VM       N  +  T+D
Sbjct: 231 ANWKILKYLRDNLPQDQVFFSNGNVLYPSDLQRCQSETSCDAVMSAEGNLYNPGVFWTLD 290

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH---------LHSGGKLQQITRHMI 281
           +          P   ++ ++++  +  +    A+RH         LH+  ++ +  R +I
Sbjct: 291 DNKDKQF----PRVDKILREYFEIVKENYDSLASRHAMKSHFFKLLHAFLEVHKELRPII 346

Query: 282 G 282
           G
Sbjct: 347 G 347


>gi|319654161|ref|ZP_08008250.1| tRNA-dihydrouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317394095|gb|EFV74844.1| tRNA-dihydrouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 325

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 131/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSDSYCHPEGINSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+  P++  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAELGFKGLDINMGCPVPNVAQHGKGSGLIRRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +K I +  +  + IH R         +D        +
Sbjct: 138 LPVSVKTRLGFTE---VDEWKVWLKHILEQDIANLSIHLRT--------RDEMSKVPAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D  + L++     +DGVMIGR  + N        
Sbjct: 187 ELIPEIKKLRDQVAPDTLLTINGDIPDRQKGLELAEKYGIDGVMIGRGIFHNPFAFEREK 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +  S          +    D  R        Y+   L     L +  +       GFP +
Sbjct: 247 KDHS----------SEELLDLLRLHMDLHDQYSHLELRPFTALHRFFKIYA---KGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++   +  +E+
Sbjct: 294 SALRNQL-MNTRSTDEVRELLDAFVSKNLEN 323


>gi|322780739|gb|EFZ09996.1| hypothetical protein SINV_07882 [Solenopsis invicta]
          Length = 1167

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 100/230 (43%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K     L  +++++PL +Q  G D
Sbjct: 732 MVDASELAWRLLSRR-HGAQLCYTPMLHSSVFCRDPKYRREALASTSEDRPLIVQFCGND 790

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA + E +  + I++N+GCP A    G +GA L  + D++   ++ +   L IP
Sbjct: 791 PDILLEAAHLAEPY-CDAIDINIGCPQAIAKRGHYGAFLQDDWDLLKKIVSTLKNGLRIP 849

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  + +            ++ +G + + +H R    KG             +  
Sbjct: 850 VTCKLRVFSEIERTV----EYACMLEDAGASLLTVHGRTREQKG------PLTGLASWKH 899

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           +  + ++   + +  NG ++ +    + +    V GVM       N  + 
Sbjct: 900 IKAV-RDAVKIPVIANGNIQCVQDLERCIEEIQVHGVMSAEGNLYNPYIF 948


>gi|46578471|ref|YP_009279.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46447882|gb|AAS94538.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
          Length = 419

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 58/303 (19%), Positives = 116/303 (38%), Gaps = 25/303 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+ A  ++      +++L  + ++ PL +Q+ G D 
Sbjct: 18  AGYSDLSFRLLCRE-AGAAVCCTEMVSAKGLIYCSPGTRDLLATTPEDAPLVVQLFGCDP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             +V A + + + G+   +LN+GC   +V +   GA ++ +         AM   A +  
Sbjct: 77  DIMVRAMEPLLEQGFRWFDLNMGCSVPKVVKTGCGAAMLRDVPQALAVARAMLRTAGAGR 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G D  +      +L +++   G   + +H R A                 +  
Sbjct: 137 VGFKFRLGWD--VGQEVWADLGRALADLGAGWVTLHPRYA--------RQGFSGEARWSA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN- 235
           + E+ +    + +  +G L   +  ++ L    V  VM  R A  +  +     E  +  
Sbjct: 187 LGELVRAV-SVPVIASGDLFTAADGVRCLRETGVASVMYARGALNDPGVFHAHRERVAGR 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
           P  G +P + R       +++       +  L     + +  RH        P +R  R 
Sbjct: 246 PDPGYTPQRLRALITRHAELARQYAPGRSALLKMRTFVPRYVRH-------LPGARALRQ 298

Query: 296 ILT 298
            L 
Sbjct: 299 HLA 301


>gi|31742496|ref|NP_853559.1| tRNA-dihydrouridine synthase 4-like [Homo sapiens]
 gi|114615410|ref|XP_001164272.1| PREDICTED: tRNA-dihydrouridine synthase 4-like isoform 5 [Pan
           troglodytes]
 gi|332868275|ref|XP_519306.3| PREDICTED: tRNA-dihydrouridine synthase 4-like isoform 6 [Pan
           troglodytes]
 gi|110808215|sp|O95620|DUS4L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 4-like; AltName:
           Full=pp35
 gi|51095148|gb|EAL24391.1| protein similar to E.coli yhdg and R. capsulatus nifR3 [Homo
           sapiens]
 gi|119603807|gb|EAW83401.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
 gi|119603808|gb|EAW83402.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
 gi|119603810|gb|EAW83404.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_c [Homo
           sapiens]
          Length = 317

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 78/285 (27%), Positives = 127/285 (44%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   ++  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVQDMVKQVRNQVETP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R A  +            + 
Sbjct: 152 GFSVSIKIRIHDDLKRTV----DLCQKAEATGVSWITVHGRTAEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSIK-IIKENMSIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|66818553|ref|XP_642936.1| hypothetical protein DDB_G0277081 [Dictyostelium discoideum AX4]
 gi|60471072|gb|EAL69042.1| hypothetical protein DDB_G0277081 [Dictyostelium discoideum AX4]
          Length = 392

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/237 (30%), Positives = 117/237 (49%), Gaps = 17/237 (7%)

Query: 1   MVDWTDRHYRFF-ARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGA 57
           M D TD  +RF  A  +    +++ E + AD + R  +   + LG+STQEKP+  Q  G 
Sbjct: 18  MADVTDISFRFLLANCMGKPNVIFNEFVSADGLARNREALIDKLGYSTQEKPIVAQFFGN 77

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVH--EGSFGACLMLNPDIVGDCIAAMCKAL 115
                 E+AKI  + GY+ +++N+GCPS +V   + + GA L+ NP +  + +    +AL
Sbjct: 78  KPEYFYESAKIANELGYDGVDINMGCPSRKVLSPKQASGAALITNPSLAKEIVKITKEAL 137

Query: 116 S--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +   PV+VK RIG D     + +   +  I +S    + +H R      L P        
Sbjct: 138 NFEKPVSVKTRIGFD----KIEIDEWIPLILESEPACLTLHLRTKKELSLVPAHWEHQV- 192

Query: 174 LDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
              D V E++ + +P+  +  NG +E   Q +  +    +DGVMIGRA Y N  +  
Sbjct: 193 --LDRVVELRNQISPNTLLVGNGDVETYEQGIDYINQFGIDGVMIGRAVYGNPWLFN 247


>gi|314936531|ref|ZP_07843878.1| dihydrouridine synthase family protein [Staphylococcus hominis
           subsp. hominis C80]
 gi|313655150|gb|EFS18895.1| dihydrouridine synthase family protein [Staphylococcus hominis
           subsp. hominis C80]
          Length = 324

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 68/328 (20%), Positives = 121/328 (36%), Gaps = 30/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFKEMSFGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          +  ++ + K  +  + IH R              I     
Sbjct: 138 LPVSVKTRLGY---YNIEEWKEWLRHVFKQDIANLSIHLRTRKEMSKVDAHWELI----- 189

Query: 177 DIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           + + E++ E  P   + +NG + D  + +++     +DGVMIGR  + N           
Sbjct: 190 EAIKEMRDEVAPQTLLTINGDIPDRQKGMELATKYGIDGVMIGRGIFHNPFAF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                      ++   D +R        Y+         L++  +       G   +   
Sbjct: 243 ---EKDPREHTSKELLDLFRLHLELFEKYSNEETQQFKSLRRFFKI---YVRGIRGASEL 296

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           RH L        A   +++     M + 
Sbjct: 297 RHQLMSTETVDEA-RALLDDFEANMEDK 323


>gi|109067839|ref|XP_001093588.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Macaca mulatta]
          Length = 317

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 78/285 (27%), Positives = 127/285 (44%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   ++  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVETP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R A  +            + 
Sbjct: 152 GFSVSIKIRIHDDLKRTV----DLCRKAEATGVSWITVHGRTAEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSIK-IIKENMSIPVIANGDIRSLKEAENVWQITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|299473005|emb|CBN77406.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 461

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 99/232 (42%), Gaps = 17/232 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R   +N L YT M  +             F    +++PL +Q  G D
Sbjct: 93  MVDQSELAFRRLCRRYGSN-LCYTPMYNSKCFAVSSAYRKSNFDPHPEDRPLIVQFCGHD 151

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L+ +AK VE    + I+LN+GCP     +G +GA L+    ++ D ++ + K LSIP
Sbjct: 152 PALLLASAKFVEKE-CDAIDLNLGCPQGIARKGRYGAFLLEEWALLRDIVSTLAKNLSIP 210

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+             + K +  +G   I +H R    K  +          ++D 
Sbjct: 211 VTCKVRLL----DSVEDTITMCKMLVAAGARIITVHGRTKEQKSKATA------GCNWDA 260

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
           +  IK+  P + +  NG +  +    + L     DGVM      +   + + 
Sbjct: 261 IRRIKEALP-VPVFSNGAISSLEDVERCLRETGCDGVMSSEGVLERPGLFSD 311


>gi|301755675|ref|XP_002913683.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Ailuropoda
           melanoleuca]
 gi|281349138|gb|EFB24722.1| hypothetical protein PANDA_001508 [Ailuropoda melanoleuca]
          Length = 317

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 125/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDLTRTV----DLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  I KEN  + +  NG + ++ +A     +   DGVM+ R    N AM    +E  
Sbjct: 199 YEAIK-IIKENLSIPVIANGDIRNLKEAENVWHITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|253827463|ref|ZP_04870348.1| putative transcriptional regulator [Helicobacter canadensis MIT
           98-5491]
 gi|313141671|ref|ZP_07803864.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
 gi|253510869|gb|EES89528.1| putative transcriptional regulator [Helicobacter canadensis MIT
           98-5491]
 gi|313130702|gb|EFR48319.1| conserved hypothetical protein [Helicobacter canadensis MIT
           98-5491]
          Length = 328

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 127/317 (40%), Gaps = 33/317 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   +      +  +EMI   A+   +KK   ++  S  E P ALQI G D 
Sbjct: 28  AGYSDLPFREVVKKF-GADITVSEMISVHALAFQNKKTIKMIEKSPLENPFALQIAGNDF 86

Query: 60  SKLVEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             +  A + +  F      ++LN GCP+ +V     G+ L+ + + +   +  + K    
Sbjct: 87  EIIQRAVEFLNQFRDSIQILDLNCGCPAPKVSSHGSGSSLLKDLNKLVKILNLLRKISLF 146

Query: 118 P-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P ++VK R+G D +IP      + K++  S ++ + +H R          D  K   +DY
Sbjct: 147 PYLSVKVRLGFDKKIP----LEIAKALSDSPIDYVVVHGRTK-------SDGYKKDKIDY 195

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  IK+  P   +  NG +     A K+      DG+MIGR+A +   + T +     
Sbjct: 196 DSIKIIKENIPH-PLIANGEINSPETAKKVQEFTGADGIMIGRSAIEKPWIFTQIKNNLE 254

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +     ++ +V  + + +      DY A             +++     G   +   R
Sbjct: 255 ESVE----LRKQVALEHFDRTIEFRGDYGAIMF---------RKNLHAYSKGLKGASEFR 301

Query: 295 HILTVEAGASTATHHII 311
             +      +     I+
Sbjct: 302 SKVNAITNPTAMREEIL 318


>gi|224074477|ref|XP_002197358.1| PREDICTED: dihydrouridine synthase 1-like (S. cerevisiae)
           [Taeniopygia guttata]
          Length = 486

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/293 (21%), Positives = 116/293 (39%), Gaps = 38/293 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   LR               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRRENLYGEACPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T K RI  D            + ++K+G   + +H R    KG             +
Sbjct: 142 VPITCKIRIFPDIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG------PLAGVASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K   ++ +  NG ++ +S   + +    V GVM       N A+         
Sbjct: 192 EHIQAVRKAV-NIPVFANGNIQCLSDVQECIRKTGVHGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFH 285
               G +P+   + +++   +        Y   HL    KL     H + ++ 
Sbjct: 243 ---EGRNPLVWEMAEEYLEIVRKYPCPLSYVRAHL---FKLWH---HTLQVYQ 286


>gi|156364501|ref|XP_001626386.1| predicted protein [Nematostella vectensis]
 gi|156213260|gb|EDO34286.1| predicted protein [Nematostella vectensis]
          Length = 288

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/281 (22%), Positives = 111/281 (39%), Gaps = 29/281 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  A   +R       ++     ++PL +Q    D
Sbjct: 33  MVDQSELAWRMLSRRY-GAELCYTPMFHAGMFIRDPIYRSEMMQTCVGDRPLIVQFCAND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               V+AA +VE    + ++LN+GCP      G +GA L    +++   +    + LS+P
Sbjct: 92  PEVFVQAALLVESE-CDGVDLNLGCPQHIAKRGHYGAFLQDEWELLEKMVKLAHEKLSVP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R+  D Q          K ++ +G   + +H R    K             D+D 
Sbjct: 151 ITCKIRVFDDVQKTIA----YAKMLESAGCQLLTVHGRTREQK------RELTGLADWDQ 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +EN ++ +  NG ++ +S   + L     +GVM       N A+           
Sbjct: 201 IKAV-RENLNIPVFANGNIQYLSDVTRCLEYTGCNGVMTAEGNLSNPALF---------- 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            TGS P    +  ++    +      +A   H   +L    
Sbjct: 250 -TGSQPYVWSMANEYLELATKHKASLSAVRAH-LFRLWHKR 288


>gi|302792084|ref|XP_002977808.1| hypothetical protein SELMODRAFT_443602 [Selaginella moellendorffii]
 gi|300154511|gb|EFJ21146.1| hypothetical protein SELMODRAFT_443602 [Selaginella moellendorffii]
          Length = 378

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 65/324 (20%), Positives = 129/324 (39%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A       K     F+   +++PL +Q    +
Sbjct: 59  MVDQSELPFRMLCRKYGATG-AYTPMLHARLFSEDRKYRNYEFTTCPEDRPLLIQFCANN 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AAK+VE F  + I++N+GCP      G++GA LM +  +V   +  +   L +P
Sbjct: 118 PDTLLAAAKLVEPF-CDYIDINLGCPQRIAKRGNYGAFLMDDLPLVQALVTKLVSNLDVP 176

Query: 119 VTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R+   +DD I         K ++ SG + + +H R    K        +    D+
Sbjct: 177 VSCKIRMFPSLDDTISY------AKMLESSGCSLLAVHGRTREQK------CSRTVRADW 224

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +++  +K+    + +  NG +  +  A + +    VDGV+   +  +N A+      +  
Sbjct: 225 EVIRAVKQAL-RIPVLANGNIRWLEDAERCIQETGVDGVLSAESLLENPALFAGYRTFKP 283

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
           +         +++  D    +   + D   ++      ++     ++G +  F      R
Sbjct: 284 SDSEDEEQGSSKLMIDPVTLLMEYL-DQCEKYPAPDKCIRAHVHRLLGEW--FRVHPDLR 340

Query: 295 HILTVEAGAS-----TATHHIIET 313
             L  E              ++E 
Sbjct: 341 EKLNREHKVDSTWLRDLGREMLER 364


>gi|73981937|ref|XP_540383.2| PREDICTED: similar to dihydrouridine synthase 4-like [Canis
           familiaris]
          Length = 317

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 117/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKY-GCDLCYTPMIVAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDLTRT----IDLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  I KEN  + +  NG +  + +A     +   DGVM+ R    N AM    +E  
Sbjct: 199 YEAIK-IIKENMSIPVIANGDIRSLKEAENVWHITGTDGVMVARGLLANPAMFAGYNE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +   D+        T Y   H H    +++IT
Sbjct: 256 ---------TPLQCIWDWIDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|118099691|ref|XP_415637.2| PREDICTED: similar to DUS1L protein isoform 2 [Gallus gallus]
          Length = 486

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/294 (21%), Positives = 116/294 (39%), Gaps = 40/294 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   LR               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRRENLYGEACPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPITCKIRVFPEIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG------PLAGVASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  ++K    + +  NG ++   D+ + ++    V GVM       N A+        
Sbjct: 192 EHIQAVRKAV-SIPVFANGNIQCLSDVEECIRK-TGVHGVMSAEGNLHNPALF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFH 285
                G +P+   + +++   +        Y   HL    KL     H + ++ 
Sbjct: 243 ----EGRNPLVWEMAEEYLEIVQKYPCPLSYVRAHL---FKLWH---HTLQVYQ 286


>gi|118099689|ref|XP_001232803.1| PREDICTED: similar to DUS1L protein isoform 1 [Gallus gallus]
          Length = 473

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/294 (21%), Positives = 116/294 (39%), Gaps = 40/294 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   LR               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRRENLYGEACPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPITCKIRVFPEIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG------PLAGVASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  ++K    + +  NG ++   D+ + ++    V GVM       N A+        
Sbjct: 192 EHIQAVRKAV-SIPVFANGNIQCLSDVEECIRK-TGVHGVMSAEGNLHNPALF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFH 285
                G +P+   + +++   +        Y   HL    KL     H + ++ 
Sbjct: 243 ----EGRNPLVWEMAEEYLEIVQKYPCPLSYVRAHL---FKLWH---HTLQVYQ 286


>gi|193788568|ref|NP_001123329.1| zinc finger protein ZF(C3H)-5 [Ciona intestinalis]
 gi|93003036|tpd|FAA00101.1| TPA: zinc finger protein [Ciona intestinalis]
          Length = 609

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 54/285 (18%), Positives = 112/285 (39%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM VA  +L+  G +  ++     E    +Q+ GA    + 
Sbjct: 275 NLPFRVVCKRL-GADITCGEMAVATNVLQAKGGEWALMKRHPCEDIFGVQLCGAFPDTMS 333

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++      + I++N+GCP   +++   G+ LM   + + D +  M +++ +P+T K
Sbjct: 334 RCAELISKTCEVDFIDINMGCPIDLIYKKGAGSALMRRTNKLFDIVNCMNRSIDVPLTCK 393

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV+ +       N++  ++  GV    +H R         ++ R     D+  + E 
Sbjct: 394 VRAGVETKKNCA--HNILPKLRDYGVAMTTVHGRS--------REARYTKAADWGYISEC 443

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                 + +  NG +      + ++ +  V GVMI R A     + T + E     ++  
Sbjct: 444 AALADPMPVFGNGDILSYHDYMSVMENTTVSGVMIARGALIKPWVFTEIKERRDWDISSG 503

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
             +           I     +    H  S  +  + TR  +   L
Sbjct: 504 ERL----------DILRQFVNEGFVHWGSDTRGVENTRRFLLEWL 538


>gi|25282413|ref|NP_742015.1| tRNA-dihydrouridine synthase 1-like [Rattus norvegicus]
 gi|81866863|sp|Q8K582|DUS1L_RAT RecName: Full=tRNA-dihydrouridine synthase 1-like; AltName:
           Full=Liver regeneration-related protein LRRG08/LRRG09
 gi|21105480|gb|AAM34683.1|AF508021_1 embryo-related protein [Rattus norvegicus]
 gi|33187773|gb|AAP97740.1| liver regeneration-related protein LRRG08 [Rattus norvegicus]
 gi|33187775|gb|AAP97741.1| liver regeneration-related protein LRRG09 [Rattus norvegicus]
          Length = 438

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/281 (20%), Positives = 102/281 (36%), Gaps = 29/281 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGRYGAFLQEEWDLLQRMILLAHERLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PMAGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT------ 228
           + +  ++K    + +  NG +  +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAVG-IPVFANGNIRCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVW 250

Query: 229 --VDEYFSNPLTGSSPIKTRVDKDF--WRKISASMTDYAAR 265
              DEY         P+       F  W             
Sbjct: 251 ELADEYLDIVRQHPCPLSYVRAHLFKLWHHTLQVHQQLREE 291


>gi|210633854|ref|ZP_03297869.1| hypothetical protein COLSTE_01786 [Collinsella stercoris DSM 13279]
 gi|210159023|gb|EEA89994.1| hypothetical protein COLSTE_01786 [Collinsella stercoris DSM 13279]
          Length = 330

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 56/301 (18%), Positives = 108/301 (35%), Gaps = 27/301 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R      L YTEM+    +     K   ++    +E  + +Q+ G  
Sbjct: 18  MAGVTDAAYRIMCRR-RGAELAYTEMVSVAGLSYKSAKTWVLVEPEPEEPQICVQLFGTK 76

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A   V++   ++   I++N+ CP+ +V     G+ LM  P++    + A  +  
Sbjct: 77  PEQFAYAVDSVQERVGDKLSLIDINMACPARKVITKGEGSALMKTPELAASLVEASVREA 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVTVK R G        A  +    ++++G   + +H R A                D
Sbjct: 137 RVPVTVKIRRGFAAGENTAA--DFAARMEQAGAAAVAVHGRTA--------SQLYTGQAD 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  + E+      + +  +G +     A ++L   + D V I R  Y N  +        
Sbjct: 187 WSTIDEVAGRV-SVPVIGSGDVFSAEDAARMLSDTAADAVFIARGTYGNPWVFGDARAL- 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  +P+  R  ++    +   +T            + +          G P++   
Sbjct: 245 ---ALEGTPVPERSARERIEALREHLTLLHETQ----PFMARARAFASWYLKGLPHAAAW 297

Query: 294 R 294
           R
Sbjct: 298 R 298


>gi|224418136|ref|ZP_03656142.1| putative transcriptional regulator [Helicobacter canadensis MIT
           98-5491]
          Length = 317

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 127/317 (40%), Gaps = 33/317 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   +      +  +EMI   A+   +KK   ++  S  E P ALQI G D 
Sbjct: 17  AGYSDLPFREVVKKF-GADITVSEMISVHALAFQNKKTIKMIEKSPLENPFALQIAGNDF 75

Query: 60  SKLVEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             +  A + +  F      ++LN GCP+ +V     G+ L+ + + +   +  + K    
Sbjct: 76  EIIQRAVEFLNQFRDSIQILDLNCGCPAPKVSSHGSGSSLLKDLNKLVKILNLLRKISLF 135

Query: 118 P-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P ++VK R+G D +IP      + K++  S ++ + +H R          D  K   +DY
Sbjct: 136 PYLSVKVRLGFDKKIP----LEIAKALSDSPIDYVVVHGRTK-------SDGYKKDKIDY 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  IK+  P   +  NG +     A K+      DG+MIGR+A +   + T +     
Sbjct: 185 DSIKIIKENIPH-PLIANGEINSPETAKKVQEFTGADGIMIGRSAIEKPWIFTQIKNNLE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +     ++ +V  + + +      DY A             +++     G   +   R
Sbjct: 244 ESVE----LRKQVALEHFDRTIEFRGDYGAIMF---------RKNLHAYSKGLKGASEFR 290

Query: 295 HILTVEAGASTATHHII 311
             +      +     I+
Sbjct: 291 SKVNAITNPTAMREEIL 307


>gi|326433345|gb|EGD78915.1| hypothetical protein PTSG_01890 [Salpingoeca sp. ATCC 50818]
          Length = 459

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 111/247 (44%), Gaps = 27/247 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R  AR    + L YT M+ +   +R      L F+T  +++PL +Q  G D
Sbjct: 25  MVDQSELSWRLLARAYGAH-LCYTPMLHSGVFVRDANYRKLNFTTCAEDRPLIVQFCGND 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++EAAK VED   + ++LN+GCP      G +GA L    D +   +  +   LS+P
Sbjct: 84  PDTVLEAAKYVED-KCDAVDLNLGCPQNIARRGRYGAFLQDEWDTISAIVKRLHAELSVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K RI  D            + +++SG   + +H R  + KG       +    ++D 
Sbjct: 143 VTCKIRIFDDLDKT----LAYARMLEESGCQLLTVHGRTRVQKG------PRSGLANWDY 192

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTT------- 228
           +  IK     + +  NG +    D+ + ++    VDGVM       N A+ +        
Sbjct: 193 IKAIKNAV-SIPVVANGNILYTSDIDKCIE-YTGVDGVMSSETHLVNPAVFSGQYPLLWE 250

Query: 229 -VDEYFS 234
            VDEY  
Sbjct: 251 MVDEYMG 257


>gi|328875032|gb|EGG23397.1| nuclear receptor coactivator NC0A-62 [Dictyostelium fasciculatum]
          Length = 1243

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 122/310 (39%), Gaps = 36/310 (11%)

Query: 1    MVDWTDRHYRFFARLLTNNALL----------------YTEMIVADAILRGD---KKNIL 41
            M D TD  +R    L +   L                 +TE +  + +        K  L
Sbjct: 795  MADVTDYSFRQLIALKSKGHLYKNSSNSTTPPQSTHISWTEFVNVNGMNYYPERFIKQDL 854

Query: 42   GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
             F   ++P+  Q+ G D     +AA +V+D G++ +++N+GCP  +V + S G+ L++ P
Sbjct: 855  AFHEIQRPIVAQLFGCDPEAFKKAASLVKDLGFDAVDINMGCPVRKVLKQSAGSALIVQP 914

Query: 102  DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            D+  D I A  + +   IPV VK RIG ++      +   +  +  +  + I +H R   
Sbjct: 915  DLARDIIIATREGVDNSIPVFVKTRIGFEEN----EMDRWIPQLVDAQPDAISLHLRTKK 970

Query: 160  LKGLSPKDNRKIPNLD---YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGV 213
                 P     +        D V           +  NG ++   +A + L S   ++GV
Sbjct: 971  ELSDCPAHWELVDKFISTVEDRVGGSASTLRRPLLIANGDIDSRHEAKEKLESYKRLNGV 1030

Query: 214  MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            M+GR  Y N       D+Y          I ++   D   ++  ++ +++        K+
Sbjct: 1031 MVGRGLYGNPWFFCEDDKYNFGRDQPIPSINSQEAVDTIYEVFKTLIEFSIILEQRQKKV 1090

Query: 274  Q-----QITR 278
                   I R
Sbjct: 1091 GPSLSAHIRR 1100


>gi|228474963|ref|ZP_04059691.1| conserved hypothetical protein [Staphylococcus hominis SK119]
 gi|228270948|gb|EEK12336.1| conserved hypothetical protein [Staphylococcus hominis SK119]
          Length = 324

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 68/328 (20%), Positives = 122/328 (37%), Gaps = 30/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFKEMSFGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          +  ++ + K  +  + IH R              I     
Sbjct: 138 LPVSVKTRLGY---YNIEEWKEWLRHVFKQDIANLSIHLRTRKEMSKVDAHWELI----- 189

Query: 177 DIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           + + E++ E  P   + +NG + D  + +++     +DGVMIGR  + N           
Sbjct: 190 EAIKEMRDEVAPQTLLTINGDIPDRQKGMELATKYGIDGVMIGRGIFHNPFAF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                      ++   D +R        Y+         L++  +       G   +   
Sbjct: 243 ---EKDPREHTSKELLDLFRLHLELFEKYSNEETQQFKSLRRFFKI---YVRGIRGASEL 296

Query: 294 RHILTVEAGASTATHHIIETAFNLMIES 321
           RH L        A   +++     M ++
Sbjct: 297 RHQLMSTETVDEA-RALLDDFEANMEDN 323


>gi|149199028|ref|ZP_01876068.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Lentisphaera araneosa HTCC2155]
 gi|149137817|gb|EDM26230.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Lentisphaera araneosa HTCC2155]
          Length = 330

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/327 (21%), Positives = 143/327 (43%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGGA 57
           M   T    R          LL TE I        +R  KK I+   + + PL++QI G 
Sbjct: 14  MEGVTHPLMRHQIAQHGGLDLLCTEFIRISSHKPSMRSLKKQIVK--SGDIPLSVQIMGN 71

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + E+AK+V D G + +++N+GCP+ R  +G  G+ ++ +P +    +A+M + +  
Sbjct: 72  NAELMAESAKLVVDCGADAVDVNMGCPTKRAVKGGVGSAMLKDPKLCYQVLASMREQVPC 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            ++ K R G D++        ++++I  SG + + +H R+ +        +    + D+ 
Sbjct: 132 ALSAKIRAGFDNKEGVF---EILQAIVDSGADYLAVHPRRRV--------DHYEGHSDWR 180

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           I+  +K+++P + +  NG +   + A+++      DGVMIGR A  N  +     +  S+
Sbjct: 181 IISALKEKSP-IPVIGNGDVRTAADAVRMFKETQCDGVMIGRGALSNPWIFLQTSQVLSD 239

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRRCR 294
                   +      F+  I+ + +D+      +  K    T+ M+  F    P     R
Sbjct: 240 QEVFIPNWEDIYH--FYHGIAQAFSDFCDNEQGTLNK----TKEMLMYFSVNLPEPAPFR 293

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
             +    G S +   ++    + + E 
Sbjct: 294 KAI----GRSQSIDEMMNKLHSFLKEK 316


>gi|291391307|ref|XP_002712160.1| PREDICTED: dihydrouridine synthase 4-like [Oryctolagus cuniculus]
          Length = 317

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 126/285 (44%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L YT MIVA   ++  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKY-NCDLCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSEAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I IH R    +            + 
Sbjct: 152 RFSVSIKIRIHEDLRRTV----DLCQKAEATGVSWITIHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIK-IIKENISIPVIANGDIRSLKEAENVWQVTGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|301615796|ref|XP_002937362.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Xenopus (Silurana)
           tropicalis]
          Length = 486

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 101/232 (43%), Gaps = 19/232 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R              ++++PL +Q   
Sbjct: 37  MVDQSELAWRLLSRR-HGVQLCYTPMLHAQVFVRDANYRKENLYCEVCSEDRPLIVQFCA 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   +    + LS
Sbjct: 96  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLEKMVQLAHQKLS 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  + +          K ++K+G   + +H R    KG             +
Sbjct: 155 VPVTCKIRVFPEIEKTV----EYAKMLEKAGCQLLTVHGRTKEQKG------PLTGIASW 204

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           + +  ++    ++ +  NG ++ ++ A + +   +V GVM       N A+ 
Sbjct: 205 EHIKAVRNAV-NIPVFANGNIQYLNDAERCMRETAVQGVMSAEGNLHNPALF 255


>gi|50547431|ref|XP_501185.1| YALI0B21516p [Yarrowia lipolytica]
 gi|49647051|emb|CAG83438.1| YALI0B21516p [Yarrowia lipolytica]
          Length = 423

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 126/333 (37%), Gaps = 41/333 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE------KPLALQI 54
           MVD ++  +R  +R      L YT M  A      ++     F   +      +PL +Q 
Sbjct: 35  MVDQSELAWRILSRR-HGADLCYTPMFHAKLFGTSERYREEMFGPMDGDQTTDRPLVVQF 93

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D  +L+ AAK+VED   + ++LN+GCP     +G +G+ LM + D++   I  +   
Sbjct: 94  CANDPDELLAAAKLVEDR-CDAVDLNLGCPQGIARKGHYGSFLMEDWDLIHKLINKLHLE 152

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K R+  D            K I  +G   + IH R   +KG      ++    
Sbjct: 153 LKVPVTAKMRVFDDRDKT----LEYAKMIINAGAQFLTIHGRTREMKG------QQTGLA 202

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           D++I+  +++  P D  +  NG +   ED+ + ++   + D VM       N A+     
Sbjct: 203 DWEIIKYVRENLPKDTVVFANGNVLYSEDIEKCMEE-TTTDAVMSAEGNLYNPAIF---- 257

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PN 289
               N  T       RVDK               +          +  H   + H F P 
Sbjct: 258 ----NKPTDKDVNFPRVDKMLREYFE------IVKETPGKASNTAMKSHFFKILHSFLPV 307

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
               R         S A   + E     + E +
Sbjct: 308 ETELR---AEIGRTSKAGFDVWEKIVQKVEEKV 337


>gi|229009817|ref|ZP_04167037.1| tRNA-dihydrouridine synthase [Bacillus mycoides DSM 2048]
 gi|228751435|gb|EEM01241.1| tRNA-dihydrouridine synthase [Bacillus mycoides DSM 2048]
          Length = 336

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R       +  + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGSPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++     +
Sbjct: 301 AELRNQL-MNTKSTDEVRALLDKFEASV 327


>gi|255543897|ref|XP_002513011.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
 gi|223548022|gb|EEF49514.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
          Length = 686

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 109/287 (37%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +LL    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 345 NLPFRRLCKLL-GADITCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYSDTVA 403

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++ ++   + I++N+GCP   V     G+CL+  P  +   I A    +  P+TVK
Sbjct: 404 RTVELIDQECTVDFIDINMGCPIDIVVSKGAGSCLLTKPMRMKSIIHAASSTVDTPITVK 463

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +      + +L+  I   G N + IH R         +  R     D++ +Y  
Sbjct: 464 VRTGYFEGKN--RIDSLIADISNWGTNAVTIHGRS--------RQQRYSKLADWEYIYHC 513

Query: 183 KKENPDLF-IGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            K+ P+ F +  NG +   +   K     P +   MI R A     + T + E     + 
Sbjct: 514 AKKAPESFQVLGNGDIFSYTDWNKHKSDCPELSSCMIARGALIKPWLFTEIKEQRHWDIR 573

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
               +           I      +   H  S  K  + TRH +   L
Sbjct: 574 SGERL----------DILKDYVHFGLEHWGSDTKGIETTRHFLLEWL 610


>gi|193636409|ref|XP_001949454.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Acyrthosiphon
           pisum]
          Length = 578

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 58/286 (20%), Positives = 120/286 (41%), Gaps = 29/286 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM+++ ++L+G  +   +      E    +Q+ G +   L 
Sbjct: 243 NLPFRRICKEF-GADITCSEMVLSSSLLQGHNQEWALTKRHETEDIFGIQVCGNNPYMLA 301

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           ++A+++++    + ++LN+GCP  ++++   G+ L+L    +  C+ +M   L +P+TVK
Sbjct: 302 KSAQVLQENVDMDFLDLNLGCPLDQIYKQGAGSGLLLRSKKLEVCLKSMRTVLDVPLTVK 361

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV+         +L+   K SGV+ I +H R         +D R     D++ V E 
Sbjct: 362 TRSGVNKDQNVA--HDLIPMFKDSGVSLITVHGRS--------RDQRYTKMADWNYVNEC 411

Query: 183 KKENPDLFIGLNGGLEDMSQALK---ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            K    + +  +G +      +      P + G MIGR A     +   + E     ++ 
Sbjct: 412 AKLASPVQVFSSGDIMSYEDYVDSKLQFPDITGAMIGRGALIKPWIFKELKENCHWDISS 471

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
           +  +          +I      Y   H  S  +  + TR  +   L
Sbjct: 472 NERL----------EILKKYVKYGLEHWGSDTRGVETTRKFLLEWL 507


>gi|298528412|ref|ZP_07015816.1| dihydrouridine synthase DuS [Desulfonatronospira thiodismutans
           ASO3-1]
 gi|298512064|gb|EFI35966.1| dihydrouridine synthase DuS [Desulfonatronospira thiodismutans
           ASO3-1]
          Length = 328

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 75/327 (22%), Positives = 127/327 (38%), Gaps = 36/327 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R L   A   TEMI A  +     +   +L    Q+ PL +Q+ G+D 
Sbjct: 24  AGYSDLSFRLLCRNLGCRA-ACTEMISAKGLFFSTANTMRLLETCDQDLPLVVQLYGSDP 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
             +  A   +   G+   +LN GC   +V +   GA L+ +  ++   +AAM   A    
Sbjct: 83  DIMGRAVSTLSSKGFRYFDLNCGCSVKKVVKTGAGAALLKDTGLLLQMVAAMADMAGPGR 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R+G   +       +L   +  +G   I +H R A+ +             D+  
Sbjct: 143 VGVKLRLGWSSEQK--VYLDLAAPLADAGAGWITLHPRTAVQQ--------FTGKADWQA 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K+ +P + +  +G L     AL  +    VD VM  R A  + A+           
Sbjct: 193 LKNLKEISP-VPVVASGDLFTARDALDCVRQTGVDTVMFARGALMDPAIGMRYKNLLQGL 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG--KLQQITRHMIGLFHGFPNSRR-- 292
                      D++F  ++     D   RH  S    KL+ +   MI    G P ++   
Sbjct: 252 EDLPR------DQEFTLRLCMETIDTYRRHASSRAVLKLRTLLPRMI---RGLPGAKDLR 302

Query: 293 -----CRHILTVEAGASTATHHIIETA 314
                CR    +E   ++A  H +E A
Sbjct: 303 KKIILCRQWAELEEVMNSARKH-LEQA 328


>gi|330799310|ref|XP_003287689.1| hypothetical protein DICPUDRAFT_151810 [Dictyostelium purpureum]
 gi|325082309|gb|EGC35795.1| hypothetical protein DICPUDRAFT_151810 [Dictyostelium purpureum]
          Length = 324

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 120/276 (43%), Gaps = 35/276 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      + YT MI+A    R +      ++T   E  + +Q G  +
Sbjct: 42  MVRFSRLPFRMLCRKW-GCDITYTPMIMAAEFNRSESARDSDYTTNQFEDQMIVQFGVNN 100

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA+ V +   + I++N GCP   V +  +GA L+LNPD + D +  +   + +P
Sbjct: 101 AEELCAAAEKVAN-TCSGIDINCGCPQRWVMKEGYGANLLLNPDKIYDMVKQLNNRVPVP 159

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            ++K RI  D          LVK  +K GV+ I +H R + ++   P        +DYD 
Sbjct: 160 CSIKIRIQPDLNKT----IELVKRAEKIGVSWITVHGRTSAMRSSHP--------VDYDA 207

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDE----- 231
           +  +K EN  L +  NG +  + QA  +K    V+GVM  R    N A+    D+     
Sbjct: 208 IKLVK-ENTSLPVFANGDVFTLEQANTIKEKTGVNGVMAARGLLSNPALFMGYDKTPIEC 266

Query: 232 -----YFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                   +   G  PI       F R +   + +Y
Sbjct: 267 IEDFINIYSEYGGLHPI------IFHRHLIYMLYEY 296


>gi|125589164|gb|EAZ29514.1| hypothetical protein OsJ_13588 [Oryza sativa Japonica Group]
          Length = 685

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 104/287 (36%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 344 NLPFRRLCKTL-GADITCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVA 402

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++V  +   + I++N+GCP   V     G+ L+  P  +   + A       P+TVK
Sbjct: 403 RTVELVDNECSVDFIDINMGCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVK 462

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +        ++V  I   G + I +H R         +  R     D+D +Y+ 
Sbjct: 463 VRTAFFEGRNRA--DSIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQC 512

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +   +   K +     +   MI R A     + T V E     +T
Sbjct: 513 AQKAPDQLHVVGNGDVFSFTDWNKHVSGCSKISTSMIARGALIKPWIFTEVKEQRHWDIT 572

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                           I      +   H  S  K  + TR+ +   L
Sbjct: 573 SGERFN----------ILKDFVSFGLEHWGSDSKGVETTRYFLLEWL 609


>gi|125547021|gb|EAY92843.1| hypothetical protein OsI_14644 [Oryza sativa Indica Group]
          Length = 685

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 104/287 (36%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 344 NLPFRRLCKTL-GADITCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVA 402

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++V  +   + I++N+GCP   V     G+ L+  P  +   + A       P+TVK
Sbjct: 403 RTVELVDNECSVDFIDINMGCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVK 462

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +        ++V  I   G + I +H R         +  R     D+D +Y+ 
Sbjct: 463 VRTAFFEGRNRA--DSIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQC 512

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +   +   K +     +   MI R A     + T V E     +T
Sbjct: 513 AQKAPDQLHVVGNGDVFSFTDWNKHVSGCSKISTCMIARGALIKPWIFTEVKEQRHWDIT 572

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                           I      +   H  S  K  + TR+ +   L
Sbjct: 573 SGERFN----------ILKDFVSFGLEHWGSDSKGVETTRYFLLEWL 609


>gi|115456906|ref|NP_001052053.1| Os04g0117600 [Oryza sativa Japonica Group]
 gi|75233055|sp|Q7XT07|DUS3L_ORYSJ RecName: Full=tRNA-dihydrouridine synthase 3-like; AltName:
           Full=Zinc finger CCCH domain-containing protein 26;
           Short=OsC3H26
 gi|38344118|emb|CAE01725.2| OSJNBb0050O03.15 [Oryza sativa Japonica Group]
 gi|113563624|dbj|BAF13967.1| Os04g0117600 [Oryza sativa Japonica Group]
          Length = 685

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 104/287 (36%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 344 NLPFRRLCKTL-GADITCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVA 402

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++V  +   + I++N+GCP   V     G+ L+  P  +   + A       P+TVK
Sbjct: 403 RTVELVDNECSVDFIDINMGCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVK 462

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +        ++V  I   G + I +H R         +  R     D+D +Y+ 
Sbjct: 463 VRTAFFEGRNRA--DSIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQC 512

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +   +   K +     +   MI R A     + T V E     +T
Sbjct: 513 AQKAPDQLHVVGNGDVFSFTDWNKHVSGCSKISTSMIARGALIKPWIFTEVKEQRHWDIT 572

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                           I      +   H  S  K  + TR+ +   L
Sbjct: 573 SGERFN----------ILKDFVSFGLEHWGSDSKGVETTRYFLLEWL 609


>gi|4097493|gb|AAD00100.1| PP35 [Homo sapiens]
          Length = 307

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 78/285 (27%), Positives = 127/285 (44%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   ++  K     F+T   + PL +Q    D
Sbjct: 24  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 83  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVQDMVKQVRNQVETP 141

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R A  +            + 
Sbjct: 142 GFSVSIKIRINDDLKRTV----DLCQKAEATGVSWITVHGRTAEERHQ---------PVH 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 189 YDSIK-IIKENMCIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE-- 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 246 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 280


>gi|194760465|ref|XP_001962460.1| GF14432 [Drosophila ananassae]
 gi|190616157|gb|EDV31681.1| GF14432 [Drosophila ananassae]
          Length = 606

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 57/290 (19%), Positives = 117/290 (40%), Gaps = 30/290 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + + 
Sbjct: 271 NLPFRRICKEF-GADITCGEMACALPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNTIS 329

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVT 120
           +AA+++E+    + I+LN+GCP   +++   G+ LM   +I+   + + C ALS  +P T
Sbjct: 330 QAAQLIEETAKVDYIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRS-CSALSERLPFT 388

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G+           L+  +++ G + + +H R         ++ R   + +++ + 
Sbjct: 389 VKMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWNYIE 438

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           E   +   + +  NG +      L+       V  VMIGR A     +   + E  +   
Sbjct: 439 ECAAKAKQMPVIGNGDILSYEDYLERRTLAPHVSSVMIGRGALIKPWIFQEIKEQKAWAP 498

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           + S             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 499 SSSQRF----------ELMRKFCNYGLEHWGSDTKGVETTRRFLLEWQSF 538


>gi|126651951|ref|ZP_01724143.1| hypothetical protein BB14905_03460 [Bacillus sp. B14905]
 gi|126591220|gb|EAZ85329.1| hypothetical protein BB14905_03460 [Bacillus sp. B14905]
          Length = 325

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 128/321 (39%), Gaps = 35/321 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    D     +N L F+  E+P+   I G
Sbjct: 20  MEDVTDVVFRHVISEAGRPDVFFTEFTNTTSYCHPDGMDSVRNRLAFTEDEQPIVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  +++ G+  I++N+GCP   V E   GA L+L+P++  + I A  KA  
Sbjct: 80  DNPEHFRQMSIGMKELGFKGIDINMGCPVDNVAERGKGAGLILHPELASEIIQA-AKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         ++        +
Sbjct: 139 LPVSVKTRLGFTD---VAEWREWLTHILKQNIANLSIHLRT--------REEMSKVPAHW 187

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +IKK      PD  + +NG + D    LK+     +DGVMIGR  + N        
Sbjct: 188 ELIADIKKLRDEIAPDTLLTINGDIPDRVTGLKLAEQYGIDGVMIGRGVFSNPYAFEQ-- 245

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                P   S+     +             ++  R   +  +  +I         GF  +
Sbjct: 246 ----EPKEHSAEEYLSLLSLHLDLHDQYSKEFETRSFKALQRFFKI------YVRGFKGA 295

Query: 291 RRCRHILTVEAGASTATHHII 311
            + R  L + A ++     ++
Sbjct: 296 SQLRIQL-INAHSTDEVRELL 315


>gi|332028941|gb|EGI68959.1| tRNA-dihydrouridine synthase 3-like protein [Acromyrmex echinatior]
          Length = 665

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 56/283 (19%), Positives = 117/283 (41%), Gaps = 28/283 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  IL+G ++   ++     E    +Q+ G +   L 
Sbjct: 322 NLPFRRICKEY-GADITCGEMALAPNILKGTQEEWALVKRHESEDIFGVQLCGNNPGVLA 380

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++  +   + I+LN+GCP   +++   G+ ++   +++   I ++ + L IP++VK
Sbjct: 381 RCAQLLNHEIDADYIDLNLGCPIDMIYKNGGGSGMLNRLNVLETVIKSVSQVLDIPLSVK 440

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV    P     NL+   +  GV+ I +H R         ++ R     D++ + + 
Sbjct: 441 TRTGVYIDKPIA--HNLMPRFRDWGVSMITVHGRS--------REQRYTKLADWEYIEKC 490

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
                 + +  NG +   +D  +A +   +V G+ IGR A     + T + E     ++ 
Sbjct: 491 AMAAQPIPVFGNGDILSFDDYRRAKETYSTVQGITIGRGALIKPWIFTEIKERKLIDISS 550

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ-ITRHMI 281
           +              I     +Y   H  S  +  +   R M+
Sbjct: 551 AERF----------DILKKYANYGLEHWGSDTRGVENTRRFML 583


>gi|193699924|ref|XP_001951016.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Acyrthosiphon
           pisum]
          Length = 471

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 98/230 (42%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           MV+ ++  +R  +R      L +  M+ +   +  R  +K       +++PL +Q  G D
Sbjct: 21  MVEQSELPWRMLSRK-HGVQLCFAPMLHSQNFVQDRKYRKEFFTTCPEDRPLVVQFCGND 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++EA K+VED   + I+LN+GCP A    G +G+ L     ++ D +  +   L +P
Sbjct: 80  PKVILEAGKLVED-SCDVIDLNLGCPQAIAKRGFYGSFLQDEWKLIFDIVKTLRDNLKVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI  D            K ++++G   + +H R    KG      R     D+  
Sbjct: 139 VSCKIRIFEDLTKTIS----YAKMLEEAGCQMLSVHGRTRDQKG------RLTGIADWSQ 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           +  +K EN  + +  NG +       + L     +GVM       N  + 
Sbjct: 189 IKAVK-ENVTIPVLANGNILIYQDIERCLKDTLCEGVMSAEGHLHNPYIF 237


>gi|116308867|emb|CAH66003.1| H0613H07.1 [Oryza sativa Indica Group]
          Length = 685

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 108/287 (37%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 344 NLPFRRLCKTL-GADITCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVA 402

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++V  +   + I++N+GCP   V     G+ L+  P  +   + A       P+TVK
Sbjct: 403 RTVELVDNECSVDFIDINMGCPIDIVVNKGAGSSLLTKPMRIKSIVQAASTVTEKPLTVK 462

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +        ++V  I   G + I +H R         +  R     D+D +Y+ 
Sbjct: 463 VRTAFFEGRNRA--DSIVSDIYDWGASAITVHGRS--------RQQRYSKLADWDYIYQC 512

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +   +   K +     +   MI R A     + T V E     +T
Sbjct: 513 AQKAPDQLHVVGNGDVFSFTDWNKHVSGCSKISTCMIARGALIKPWIFTEVKEQRHWDIT 572

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                +  + KDF          +   H  S  K  + TR+ +   L
Sbjct: 573 SGE--RFNILKDFVT--------FGLEHWGSDSKGVETTRYFLLEWL 609


>gi|54295685|ref|YP_128100.1| hypothetical protein lpl2773 [Legionella pneumophila str. Lens]
 gi|53755517|emb|CAH17016.1| hypothetical protein lpl2773 [Legionella pneumophila str. Lens]
          Length = 328

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 108/232 (46%), Gaps = 18/232 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             ++   +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G + 
Sbjct: 26  AGYSCAPFRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKLLAYQISGNEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA  ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+
Sbjct: 86  HVLAEAAAKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISKVRAAISIPL 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RI  +++        L K I+ +G + + +H R+       P + ++I N+     
Sbjct: 146 TIKIRIQNNEKD-----LTLAKQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI----- 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               K   ++ + +NG + ++S   K L   + DG MI RA      +   +
Sbjct: 196 ----KNAVNIPVIVNGDISNISSLRKALEISACDGFMISRAGTGKPWLYRDL 243


>gi|168050219|ref|XP_001777557.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162671042|gb|EDQ57600.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 324

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 61/309 (19%), Positives = 126/309 (40%), Gaps = 21/309 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M+D ++  +R   R        YT M  +           + F+   +++PL +Q G  D
Sbjct: 21  MMDQSELPFRMLCRKY-GATAAYTPMFHSRPFALQPGYRRVEFTTCPEDRPLFVQFGAND 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV+AA  V++   + +++N+GCP      G +GA LM +  ++   +  +  +L+ P
Sbjct: 80  PELLVKAAMFVQE-DCDYVDINLGCPQRVAKRGFYGAFLMDDLPLIQLMVTQLVSSLTTP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI  D +          + ++ +G + + +H R         KD R     D++ 
Sbjct: 139 VSCKIRIFPDLEDT----LAYARMLENAGCSLLAVHGRTRDQ-----KDGRTT-RADWEA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K E   + +  NG +  +    +   +  VDGV+   +  +N A+ +       + 
Sbjct: 189 IKAVK-EAVRIPVLANGNIRWLEDVHECIRMTGVDGVLSAESLLENPALFSGHRMRPVDA 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ-QITRHMIGLFHGFPNSRRCRH 295
           +TG     ++        +     +   ++      ++  + + +   F  +P     R 
Sbjct: 248 VTGGLVELSKEGSLNEPSLVLEYLELCEKYPIPQRMIRSHVYKMLCAWFKRYP---ELRD 304

Query: 296 ILTVEAGAS 304
            L  E GAS
Sbjct: 305 ELNFEQGAS 313


>gi|147906386|ref|NP_001086550.1| dihydrouridine synthase 1-like [Xenopus laevis]
 gi|49903669|gb|AAH76792.1| MGC83715 protein [Xenopus laevis]
          Length = 464

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 101/233 (43%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R              ++++PL +Q   
Sbjct: 18  MVDQSELAWRLLSRR-HGVQLCYTPMLHAQVFVRDANYRKENLYCERCSEDRPLIVQFCA 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 77  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLEKMIQLAHQKLS 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  + +          K ++K+G   + +H R    KG             +
Sbjct: 136 VPVTCKIRVFPEMEKTV----QYAKMLEKAGCQLLTVHGRTKEQKGS------LTGIASW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAML 226
           + +  ++    ++ +  NG ++   D+ + ++   +V GVM       N A+ 
Sbjct: 186 EHIKAVRNAV-NIPVFANGNIQYLNDVERCMRE-TAVQGVMSAEGNLHNPALF 236


>gi|302308179|ref|NP_985016.2| AER158Cp [Ashbya gossypii ATCC 10895]
 gi|299789331|gb|AAS52840.2| AER158Cp [Ashbya gossypii ATCC 10895]
          Length = 434

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 121/312 (38%), Gaps = 31/312 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQ-EKPLALQI 54
           MVD ++  +R  +R      L YT M+ A         R D  + L      ++PL +Q 
Sbjct: 34  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSEKYRRDMWSDLDGDESIDRPLVVQF 92

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AA++VE+   + ++LN+GCP     +G +G+ LM   D+V + I  +   
Sbjct: 93  CANDPEYLLKAAQLVEN-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLVANLINTLHTK 151

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L++PVT K RI  D +          K +  +G   + +H R    KG      ++    
Sbjct: 152 LAVPVTAKIRIFPDREKT----LAYAKMVLDAGAQFLTVHGRLREQKG------QQTGLA 201

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           D+  +  ++   P D     NG +       + +     D VM       N  +   ++ 
Sbjct: 202 DWATIKYLRDNLPSDTVFFANGNILYPEDIPRCMTELGCDAVMSAEGNLYNPGVFN-IEH 260

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                   + P   +V ++++  +       A+R         +I R  +      PN  
Sbjct: 261 I--GDKEKTFPRVDKVLREYFEIVKQHNCSVASR-TAMKNHFFKILRPFL------PNHV 311

Query: 292 RCRHILTVEAGA 303
             R  L   +  
Sbjct: 312 DIRSQLAQLSPK 323


>gi|145545963|ref|XP_001458665.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124426486|emb|CAK91268.1| unnamed protein product [Paramecium tetraurelia]
          Length = 358

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 62/277 (22%), Positives = 116/277 (41%), Gaps = 18/277 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ +  +               +++PL  Q+ G D
Sbjct: 25  MVDQSELAFRMQTRKY-GTTLAYTPMLHSRIMTESKSYKDEFFTTCPEDRPLFAQLCGHD 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +++AA +++D   + I+LN GCP     +G +GA L+   + V   +  + + + +P
Sbjct: 84  PQVIIKAALMIQDQ-CDAIDLNFGCPQGIARKGLYGAFLLEKREQVLTIVKELKQNIKVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +       +L K I+ +G + + +H R          +   +   D++I
Sbjct: 143 VTCKIRVFKDRKRT----LDLTKDIQSAGCSILTVHGRTKEQ------NKDFVGQCDWNI 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT-TVDEYFSN 235
           + EIK+    + +  NGG+   S   + L    VD VM   A  +N A+ +  + +    
Sbjct: 193 IAEIKQ-LLQIPVFANGGIYTWSDVERCLQETKVDAVMSSEALLENPALFSGEIKDLNEL 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
            L      K    +    K       Y    +H+  +
Sbjct: 252 ALEYMQLAKQYDARLVEIKAHLFKLLYTGLQIHTDQR 288


>gi|321468855|gb|EFX79838.1| hypothetical protein DAPPUDRAFT_304378 [Daphnia pulex]
          Length = 663

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 64/289 (22%), Positives = 117/289 (40%), Gaps = 26/289 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +A+ ++ G ++   ++     E    +QI GA+   L 
Sbjct: 329 NLPFRRLCKAL-GADITCGEMAMAETLVGGGQQEWALVRKHKSEDLFGVQICGANPYILG 387

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + ++++E+    + I+LN+GCP   V++   G+ LM     +   I  M + L IP TVK
Sbjct: 388 KCSQLLEENTEIDFIDLNLGCPIDMVYQKGAGSGLMRRKGPLESSIKTMSQLLKIPFTVK 447

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+GV    P      LV+  +  GV+ + +H R         ++ R     D+D +   
Sbjct: 448 MRMGVYTDHP--FAHQLVEKCRDWGVSMVTVHGRS--------REQRYTRLADWDYIGNC 497

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            K    + I  NG L       +++      GVMI R A     + T + E     ++ S
Sbjct: 498 VKAADPMPIFGNGDLMSYEDYERVVDQSGAAGVMIARGALIKPWIFTEIKERRHWDISSS 557

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                        +      +Y   H  S  +  + TR  +  +  F +
Sbjct: 558 ERF----------QYMKDFCNYGLEHWGSDSQGVERTRRFLLEWQSFAH 596


>gi|240139568|ref|YP_002964044.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens AM1]
 gi|240009541|gb|ACS40767.1| tRNA-dihydrouridine synthase B [Methylobacterium extorquens AM1]
          Length = 307

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 65/313 (20%), Positives = 128/313 (40%), Gaps = 29/313 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADISKLVEAAKI 68
           R  A+ L   + + +EM+ A  + +GD ++ +        P  +Q+ G     + E A+I
Sbjct: 2   RRLAQRL-GASAVVSEMVAAAELAKGDAESQVRAEGAGVDPHVVQLAGCAPELMAEGARI 60

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
               G + I++N+GCP+  V  G  G+ LM + D     +AA+  A+ +PVTVK R+G D
Sbjct: 61  AVANGADAIDINMGCPAKTVTGGESGSALMRDLDHAARLLAAVRGAVDVPVTVKMRLGWD 120

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
               ++    L +  +  G++G+ +H R         +        D+  +  +  E   
Sbjct: 121 --HASLNAAELARRAEALGLDGVTVHGRT--------RQQFYKGRADWSAIRPVV-EAVR 169

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           + +  NG +  + +A   L      GVM+GRAA     ++  +    +  +      + R
Sbjct: 170 IPVIANGDITGVEEARACLSQSGAAGVMVGRAAVGRPWLVGEIAAGLAGRVAAPLSAEQR 229

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FHGF-PNSRRCRHILTVEAG 302
                   ++A           +   ++   +H+        G  P+ R  R ++T    
Sbjct: 230 A------AVAAEHYQGLIALYGAAMGVRHARKHLAAYADAAGGLTPDDR--RRLVTT--H 279

Query: 303 ASTATHHIIETAF 315
                  +++ AF
Sbjct: 280 DPAEALRLLQRAF 292


>gi|322378794|ref|ZP_08053223.1| Putative tRNA-dihydrouridine synthase [Helicobacter suis HS1]
 gi|322380643|ref|ZP_08054795.1| tRNA-dihydrouridine synthase [Helicobacter suis HS5]
 gi|321146965|gb|EFX41713.1| tRNA-dihydrouridine synthase [Helicobacter suis HS5]
 gi|321148824|gb|EFX43295.1| Putative tRNA-dihydrouridine synthase [Helicobacter suis HS1]
          Length = 350

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 61/321 (19%), Positives = 131/321 (40%), Gaps = 32/321 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EMI + A++    K   +L  S +E P ++QI G+ +
Sbjct: 37  AGYTDLPFRSVVKRF-GVDVTVSEMISSHALVHAFDKTSKMLQKSPEESPFSVQIAGSKM 95

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +A +++    G + ++ N GCP+ +V     G+ L+ +   +   +  +    + P
Sbjct: 96  EVVKQAVELLNTTTGIDILDFNCGCPAPKVANHGNGSGLLKDLKHLVKLLELIKTTTNKP 155

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            T VK R+G D++IP      +  ++  + V+ + +HAR          D  K   +DYD
Sbjct: 156 YTSVKVRLGFDEKIP----LEIAHALNDAPVDFVVVHARTR-------SDRYKKERIDYD 204

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  + ++     +  NG ++   +A ++L     +GVMIGR++     +   +      
Sbjct: 205 SV-RLMRQILHKPLIANGEIDSPKKAREVLEYTGANGVMIGRSSLTQPWIFWQIKH---- 259

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +  +   + KD   +    M  +          +    +++     G   +   R 
Sbjct: 260 ---NTEELPAILKKDLVLEHFDKMVAFYG-----DRGVIMFRKNLHAYAKGHVGAGAFRS 311

Query: 296 ILTVEAGASTATHHIIETAFN 316
            +      + +    IE  F+
Sbjct: 312 AVNAMVMPAQSRAQ-IEDFFS 331


>gi|219870355|ref|YP_002474730.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis SH0165]
 gi|219690559|gb|ACL31782.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis SH0165]
          Length = 306

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 128/328 (39%), Gaps = 40/328 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       GF+    P+ +
Sbjct: 1   MQGVLDPFVRQLLTAVNDYDLCISEFVRVVDQKLPKKTFYRLCPELHNNGFTLSGTPVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A +  + G + ++LN GCPS  V+  + G  L+  P ++     AM 
Sbjct: 61  QLLGQHPQWLAENAALAVELGSHGVDLNCGCPSKTVNGSNGGVSLLKQPKLIYRATKAMR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D    A     +  ++ + G   I +H R  +       D  +
Sbjct: 121 EAVPSHLPVSVKVRLGWDSSEQAF---EIADAVVQGGATEITVHGRTKM-------DGYR 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EIKK  P + +  NG + D   A K   + + D +MIGR A  N   L+ 
Sbjct: 171 AERINWQAIGEIKKRLP-IPVIANGEIWDYLSAKKCREVTACDALMIGRGAL-NVPNLSK 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                K  W ++   +  Y             + R    +  L  
Sbjct: 229 VVKY-------------NQPKMAWNEVLQLLFQYVHMENELDTGFYHVARIKQWLRYLDK 275

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIET 313
            +P + +   IL  E G      HII+ 
Sbjct: 276 EYPEAVQLFDILKTEHGYEGLKQHIIQA 303


>gi|69245524|ref|ZP_00603488.1| Dihydrouridine synthase, DuS [Enterococcus faecium DO]
 gi|257879771|ref|ZP_05659424.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257891612|ref|ZP_05671265.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257894880|ref|ZP_05674533.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|260559446|ref|ZP_05831627.1| dihydrouridine synthase [Enterococcus faecium C68]
 gi|293564087|ref|ZP_06678493.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1162]
 gi|293570023|ref|ZP_06681103.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1071]
 gi|294618242|ref|ZP_06697824.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1679]
 gi|314940100|ref|ZP_07847283.1| dihydrouridine synthase [Enterococcus faecium TX0133a04]
 gi|314942492|ref|ZP_07849331.1| dihydrouridine synthase [Enterococcus faecium TX0133C]
 gi|314949401|ref|ZP_07852742.1| dihydrouridine synthase [Enterococcus faecium TX0082]
 gi|314952861|ref|ZP_07855833.1| dihydrouridine synthase [Enterococcus faecium TX0133A]
 gi|314993706|ref|ZP_07859051.1| dihydrouridine synthase [Enterococcus faecium TX0133B]
 gi|314994770|ref|ZP_07859902.1| dihydrouridine synthase [Enterococcus faecium TX0133a01]
 gi|68195775|gb|EAN10212.1| Dihydrouridine synthase, DuS [Enterococcus faecium DO]
 gi|257813999|gb|EEV42757.1| dihydrouridine synthase [Enterococcus faecium 1,230,933]
 gi|257827972|gb|EEV54598.1| dihydrouridine synthase [Enterococcus faecium 1,231,410]
 gi|257831259|gb|EEV57866.1| dihydrouridine synthase [Enterococcus faecium 1,231,408]
 gi|260074545|gb|EEW62866.1| dihydrouridine synthase [Enterococcus faecium C68]
 gi|291587395|gb|EFF19279.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1071]
 gi|291595458|gb|EFF26769.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1679]
 gi|291604005|gb|EFF33533.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1162]
 gi|313590954|gb|EFR69799.1| dihydrouridine synthase [Enterococcus faecium TX0133a01]
 gi|313591806|gb|EFR70651.1| dihydrouridine synthase [Enterococcus faecium TX0133B]
 gi|313595095|gb|EFR73940.1| dihydrouridine synthase [Enterococcus faecium TX0133A]
 gi|313598713|gb|EFR77558.1| dihydrouridine synthase [Enterococcus faecium TX0133C]
 gi|313640700|gb|EFS05280.1| dihydrouridine synthase [Enterococcus faecium TX0133a04]
 gi|313644232|gb|EFS08812.1| dihydrouridine synthase [Enterococcus faecium TX0082]
          Length = 327

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 126/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKNPYAFEKDPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I+ET
Sbjct: 297 RVQL-MNTKSTDEVREILET 315


>gi|332237993|ref|XP_003268188.1| PREDICTED: tRNA-dihydrouridine synthase 4 isoform 1 [Nomascus
           leucogenys]
 gi|332237995|ref|XP_003268189.1| PREDICTED: tRNA-dihydrouridine synthase 4 isoform 2 [Nomascus
           leucogenys]
          Length = 317

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 127/285 (44%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MI+A   ++  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIIAADFVKSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVRDMVKQVRNQVETP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R A  +            + 
Sbjct: 152 GFSVSIKIRIHDDLKRTV----DLCRKAEATGVSWITVHGRTAEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSIK-IIKENMSIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|165975764|ref|YP_001651357.1| putative nitrogen regulator protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|165875865|gb|ABY68913.1| putative nitrogen regulator protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 320

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 125/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       G +    P+ +
Sbjct: 13  MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRLAPELLQGGLTDSGTPVRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 73  QLLGQHPQWLAENARLAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 132

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++ + G N I +H R         +D  +
Sbjct: 133 EAVPSDQTVSVKVRLGWD---SAAQCFEIADAVAQGGANEITVHGRTK-------QDGYR 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 183 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 238

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 239 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 287

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 288 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 318


>gi|229815224|ref|ZP_04445560.1| hypothetical protein COLINT_02270 [Collinsella intestinalis DSM
           13280]
 gi|229809234|gb|EEP45000.1| hypothetical protein COLINT_02270 [Collinsella intestinalis DSM
           13280]
          Length = 330

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 58/326 (17%), Positives = 117/326 (35%), Gaps = 30/326 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  YR   R      + YTEM+    +     K   ++    +E  + +Q+ G  
Sbjct: 18  MAGVTDAAYRIMCRR-RGAEMAYTEMVSVAGLSYKSAKTWVLVEPEPEEPQICVQLFGTK 76

Query: 59  ISKLVEAAKIVEDFGYNE---INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   A   V++   ++   I++N+ CP+ +V     G+ LM  P++    + A  +  
Sbjct: 77  PEQFAFAVNAVQERVGDKLTLIDINMACPARKVITKGEGSALMKEPELAASLVEACVREA 136

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVTVK R G        A       ++++G   + +H R A        +       D
Sbjct: 137 RVPVTVKIRRGFAAGENTAA--EFAARMEQAGAAAVAVHGRTA--------NQLYTGEAD 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  + E+      + +  +G +     A ++L   + D V I R  Y N  +        
Sbjct: 187 WSTIDEVAARVG-VPVIGSGDVFSAEDAARMLAKTAADAVFIARGTYGNPWVFGDARALA 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARH-LHSGGKLQQITRHMIGLFHGFPNSRR 292
            + +    P+  R   +    +   +T         + G+             G P++  
Sbjct: 246 LDGV----PVPERGALERIEALREHLTLLHETQPFMARGRAFS-----SWYLKGLPHAAA 296

Query: 293 CRHILTVEAGASTATHHIIETAFNLM 318
            R  + V+         +++ A   +
Sbjct: 297 WRGRV-VQCTTYDEFMALLDEAEAEL 321


>gi|224093091|ref|XP_002192992.1| PREDICTED: similar to dihydrouridine synthase 4-like [Taeniopygia
           guttata]
          Length = 316

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 71/284 (25%), Positives = 119/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   +R  K     F+T   + PL +Q    +
Sbjct: 32  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVRSAKARDSEFTTNKGDHPLIVQFAAKE 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA I+  F  + I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 91  AQVLCDAACIICPF-ADGIDVNCGCPQRWAISEGYGACLINKPELVKDMVRHVRNQIDNP 149

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R    +            + 
Sbjct: 150 KFSVSIKIRIHEDLKRTV----DLCQKAEAAGVSWITVHGRTIEERHQ---------PVH 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK+    + I  NG ++ + +A     L   DGVM+ R    N AM    +E  
Sbjct: 197 YDAIKIIKQSM-SIPIVANGDIKSLKEAENVHHLTEADGVMVARGLLANPAMFAGYEE-- 253

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +  +D+        T +   H H    +++IT
Sbjct: 254 ---------TPFQCIQDWVDIALEHGTPFTCFHHHLMYMMERIT 288


>gi|223043632|ref|ZP_03613676.1| tRNA-dihydrouridine synthase [Staphylococcus capitis SK14]
 gi|222442910|gb|EEE49011.1| tRNA-dihydrouridine synthase [Staphylococcus capitis SK14]
          Length = 325

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 126/330 (38%), Gaps = 43/330 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  + +  +++ G+  I+LN+GCP A V +   G+ L+L P+   + I A  +   
Sbjct: 79  DKPEQFRKMSIGLKEMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQATKEG-G 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RREMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P   + +NG + D  + L++     VDGVMIGR  + N        
Sbjct: 187 ELIEAIKTMRDEIAPHTLLTINGDIPDRQKGLELANKYGVDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         +    D +R   +    Y+         L++  +       G   +
Sbjct: 243 ------EKEPREHTSEELLDLFRLHLSLYEKYSNEETQQFKALRRFFKI---YIRGIKGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
            + RH L             I+ A  L+ E
Sbjct: 294 SQLRHKLMS--------TETIDEARELLDE 315


>gi|209882914|ref|XP_002142892.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209558498|gb|EEA08543.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 469

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 106/412 (25%), Positives = 160/412 (38%), Gaps = 114/412 (27%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK---------KNILGFSTQEKPLA 51
           M+D T+ H+R F RLL+ N  L+TEM+V+D I+             +  L  S  ++P+ 
Sbjct: 17  MLDVTNIHFRHFCRLLSTNVQLWTEMVVSDTIIYCHNDPDREILLREGSLQKSDVDEPIV 76

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV-HEGSFGACLMLNPDIVGDCIAA 110
           LQIGG D +K+ +A +I   +G+   NLN+GCPS RV  +G+FGA L  +PD+V   +  
Sbjct: 77  LQIGGNDPTKVADAIEIAIKYGFRSFNLNIGCPSQRVACKGNFGAYLYKDPDLVAKIVGT 136

Query: 111 M---CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS-----------------GVNG 150
           +    K+L+  ++VK RIGVDD      L N +  +  +                 G   
Sbjct: 137 VNHRIKSLNTRISVKTRIGVDDCDSYDILHNFISVVSGTTPRIGKSQGVGSEEDFLGATC 196

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN-------------GGL 197
             IH+RKA L GL P+ NR IP+L Y  VY++  + P L   +N              G+
Sbjct: 197 YIIHSRKAWLDGLDPQKNRTIPSLKYTWVYKLVCDFPHLDFVINGGIDSLDKAEELLWGV 256

Query: 198 E-----------DMSQALKILP--------SVD--------------------------- 211
                             K L          VD                           
Sbjct: 257 WKPTCKDTGESYTPEYNDKYLAIEKLSKRVKVDDNSNTITDYDSEVIERARKLKNGLPLY 316

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG- 270
           GVMIGR    N  +L  VD  F N     + +  +V  + + +    +        H   
Sbjct: 317 GVMIGREIMNNPCILANVDRKFYNSEAPKTSLNRKVLIESYIEYLNKLKPRNNNKYHQKN 376

Query: 271 ------------------------GKLQQITRHMIGLFHGFPNSRRCRHILT 298
                                   G+L    + + G+      ++  R ILT
Sbjct: 377 NDINLTNSNIHLDIIDNVPNKFSIGELFNCLKPVFGVLCRLKGAKVWRRILT 428


>gi|229055160|ref|ZP_04195587.1| tRNA-dihydrouridine synthase [Bacillus cereus AH603]
 gi|228721152|gb|EEL72682.1| tRNA-dihydrouridine synthase [Bacillus cereus AH603]
          Length = 336

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 130/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++     +
Sbjct: 301 AELRNQL-MNTKSTDEVRALLDKFEASV 327


>gi|195433972|ref|XP_002064980.1| GK14924 [Drosophila willistoni]
 gi|194161065|gb|EDW75966.1| GK14924 [Drosophila willistoni]
          Length = 579

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  I++G   +  +      E    +Q+ G + + + 
Sbjct: 244 NLPFRRICKEF-GADITCGEMACALPIVKGLSQEWALTKRHESEDFFGVQLCGNNPNIIS 302

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTV 121
           +AA+++ D    + I+LN+GCP   +++   G+ LM   +I+   + +    +  +P TV
Sbjct: 303 QAAQVLHDTAKVDYIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCSNLSPQLPFTV 362

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G   + +H R         ++ R   + +++ + E
Sbjct: 363 KMRTGIYADKSVA--HELLPLVEEWGAAAVTLHGRS--------REQRYTKHANWEYIEE 412

Query: 182 IKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +          +I P V  VMIGR A     +   + E  +   +
Sbjct: 413 CASKAKSIPVIGNGDILSYEDYVERRQIAPHVSSVMIGRGALIKPWIFQEIKEKRAWSPS 472

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            S             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 473 SSQ----------RYELLQKYCNYGLEHWGSDTKGVENTRRFLLEWQSF 511


>gi|72127067|ref|XP_793440.1| PREDICTED: similar to MGC53781 protein [Strongylocentrotus
           purpuratus]
 gi|115710885|ref|XP_001202768.1| PREDICTED: similar to MGC53781 protein [Strongylocentrotus
           purpuratus]
          Length = 655

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 56/285 (19%), Positives = 102/285 (35%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L     E    +Q+ G     + 
Sbjct: 294 NLPFRAVCKKL-GADITCGEMAMCTNLLQGQSSEWALLRRHPSEDIFGVQLCGGFPDTMT 352

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ D    + I++NVGCP   V+    G+ LM       + +  M   L IP+TVK
Sbjct: 353 RCAELLNDRLDIDFIDINVGCPIDLVYHKGAGSGLMNRMGKFQEIVRGMSSVLDIPLTVK 412

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +  P      +V+ I   G + + +H R         ++ R     D+D + + 
Sbjct: 413 MRTGVHNDNPVA--HKIVRRIYDWGASVVTVHGRT--------REQRYSKLADWDYLKDC 462

Query: 183 KKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +         NG +         +      G MI R A     + T + E     ++ S
Sbjct: 463 VQAADPHPFIGNGDILSYEDSNFFREQSGATGQMIARGALIKPWIFTEIKEQRHWDISSS 522

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQITRHMI-GL 283
                         I     +    H  S    +++  R ++  L
Sbjct: 523 ERF----------DILQDYINLGLLHWGSDSEGVRKTRRFLLEWL 557


>gi|166153985|ref|YP_001654103.1| putative oxidoreductase [Chlamydia trachomatis 434/Bu]
 gi|166154860|ref|YP_001653115.1| putative oxidoreductase [Chlamydia trachomatis L2b/UCH-1/proctitis]
 gi|301335182|ref|ZP_07223426.1| putative oxidoreductase [Chlamydia trachomatis L2tet1]
 gi|165929973|emb|CAP03456.1| putative oxidoreductase [Chlamydia trachomatis 434/Bu]
 gi|165930848|emb|CAP06410.1| putative oxidoreductase [Chlamydia trachomatis L2b/UCH-1/proctitis]
          Length = 334

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 140/317 (44%), Gaps = 24/317 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             ++D  YR  +      AL++ EM+  + +    ++   +L F+   +P+  Q+ G+  
Sbjct: 22  AGFSDFPYRRMSAEY-RPALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSRP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               E+AKI+E  G++ I+LN GCP+ R+ +   G+ ++  P+++G  +  M + +S+PV
Sbjct: 81  DLAGESAKILEGLGFDLIDLNCGCPTDRITKDGSGSGMLKTPELIGKVVEKMVEVVSVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ IK+SG + +++H R         +        + + +
Sbjct: 141 TVKIRSGWD--FDHINVEETVRIIKESGASAVFVHGRT--------RSQGYQGPSNLEFI 190

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K+    D  +  NG +     A  +L     DGV++ R       +   +++Y +  
Sbjct: 191 SRAKQAAGDDFPVFGNGDVFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRH 295
              S    TR      ++       +   +  S  KL   TR + G +    P  R  R 
Sbjct: 251 TYSSPSFSTR------KQAFVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRA 304

Query: 296 ILTVEAGASTATHHIIE 312
            L  +A +S   + +I+
Sbjct: 305 NLA-KASSSQEVYQLID 320


>gi|257882496|ref|ZP_05662149.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|294620960|ref|ZP_06700160.1| tRNA-dihydrouridine synthase [Enterococcus faecium U0317]
 gi|257818154|gb|EEV45482.1| dihydrouridine synthase [Enterococcus faecium 1,231,502]
 gi|291599490|gb|EFF30507.1| tRNA-dihydrouridine synthase [Enterococcus faecium U0317]
          Length = 327

 Score =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 126/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKNPYAFEKEPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I++T
Sbjct: 297 RVQL-MNTKSTDEVREILDT 315


>gi|254579200|ref|XP_002495586.1| ZYRO0B14872p [Zygosaccharomyces rouxii]
 gi|238938476|emb|CAR26653.1| ZYRO0B14872p [Zygosaccharomyces rouxii]
          Length = 406

 Score =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKK-NILGFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A         R D    + G S  ++PL +Q 
Sbjct: 26  MVDQSELAWRILSRKY-GATLAYTPMFHAKLFATSPKYRKDMWCEMDGDSKIDRPLVVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AA++V+D   + ++LN+GCP     +G +G+ LM   D+V   I  + + 
Sbjct: 85  CANDPEYLLQAARLVQD-KCDAVDLNLGCPQGIAKKGHYGSFLMEEWDLVHKLIRNLHEN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K RI  + +          +++  +G   + +H R    KG      ++    
Sbjct: 144 LDVPVTAKIRIFPEKEKS----LQYARTVLDAGAQFLTVHGRLREQKG------QQSGLA 193

Query: 175 DYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           D++ +  ++    PD     NG L   +   + +     D VM       N  +    D 
Sbjct: 194 DWETIKYLRDNLPPDTVFFSNGNLLYPNDISRCMDQINCDAVMSAEGNLYNPGIFNAED- 252

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
             S       P    + ++++  + +    +A+R       L +I R  +      PN  
Sbjct: 253 --SQDKEKVFPRVDVICREYFEIVKSYEFSHASR-TAMKSHLFKILRPFL------PNHT 303

Query: 292 RCRHILTVEAGASTATHHIIETAFNLMI 319
             R  L +    S+     ++   N ++
Sbjct: 304 DIRSSLALLNAKSS-----LDDYENAVV 326


>gi|314934906|ref|ZP_07842265.1| dihydrouridine synthase family protein [Staphylococcus caprae C87]
 gi|313652836|gb|EFS16599.1| dihydrouridine synthase family protein [Staphylococcus caprae C87]
          Length = 325

 Score =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 67/330 (20%), Positives = 126/330 (38%), Gaps = 43/330 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  + +  +++ G+  I+LN+GCP A V +   G+ L+L P+   + I A  +   
Sbjct: 79  DKPEQFRKMSIGLKEMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQATKEG-G 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RREMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P   + +NG + D  + L++     VDGVMIGR  + N        
Sbjct: 187 ELIEAIKTMRDEIAPHTLLTINGDIPDRQKGLELANKYGVDGVMIGRGLFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         +    D +R   +    Y+         L++  +       G   +
Sbjct: 243 ------EKEPREHTSEELLDLFRLHLSLYEKYSNEETQQFKALRRFFKI---YIRGIKGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
            + RH L             I+ A  L+ E
Sbjct: 294 SQLRHKLMS--------TETIDEARELLDE 315


>gi|170017367|ref|YP_001728286.1| tRNA-dihydrouridine synthase [Leuconostoc citreum KM20]
 gi|169804224|gb|ACA82842.1| tRNA-dihydrouridine synthase [Leuconostoc citreum KM20]
          Length = 378

 Score =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 134/329 (40%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + YTE   A +++    K      L  +  E     QI G
Sbjct: 36  MEAVTDTIFRRVVAQAGPPDVYYTEFTNASSMVHPKAKFSVQGRLAVAENEAQPVAQIWG 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +    +  AAKI+   GY  +++N+GCP A V +   G+ L+ + D+    I+A  K   
Sbjct: 96  SRPEDIAGAAKILPTMGYRAVDINMGCPDATVIKNGAGSDLIRHDDLAEKIISA-AKTSG 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G      A   R+ +  I +  V  + +H R       +P     I     
Sbjct: 155 LPVSVKTRLGF---YHAEEFRDWLPIILRQNVAVLTVHLRSRKEMSKAPAHVEYID---- 207

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +I+    K  P   I +NG ++  ++ L   KI P +DG+MIGR  ++N      +    
Sbjct: 208 EILAMRDKLAPKTLIQINGDIKTRAEGLALAKIHPGIDGIMIGRGIFENPYAFEKIPR-- 265

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S    +   D +  ++A++T      L    K+            GF ++   
Sbjct: 266 -QHTLEESIALLKRQLDLFDDVNANVTPKHFEALKRYFKI---------YLRGFAHASSL 315

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R +L +E  ++T    I+      + E++
Sbjct: 316 RQLL-METHSTTEVRQILTRELARVYEAV 343


>gi|242372562|ref|ZP_04818136.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis M23864:W1]
 gi|242349779|gb|EES41380.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis M23864:W1]
          Length = 326

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  +   
Sbjct: 79  DKPEQFREMSIGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPERAAEIIQATKEG-G 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYDID---EWKDWLKHVFEQDIANLSIHLRS--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  PD  + +NG + D    +++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPDTLLTINGDIPDRQTGMELATKYGIDGVMIGRGIFNNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   D +R        ++         L++  +       G   +
Sbjct: 243 ------EKEPREHTSKELLDLFRLHLTLFEKHSTEETQQFKALRRFFKI---YVRGIKGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            + RH L        A   +++     M  S+
Sbjct: 294 SQLRHQLMSTETVDEA-RALLDEFEARMDSSV 324


>gi|229159471|ref|ZP_04287488.1| tRNA-dihydrouridine synthase [Bacillus cereus R309803]
 gi|228623979|gb|EEK80788.1| tRNA-dihydrouridine synthase [Bacillus cereus R309803]
          Length = 336

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 131/331 (39%), Gaps = 37/331 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L   +  ST    ++   F   ++ 
Sbjct: 301 AELRNQLM--STKSTDEVRVLLDKFEASVDK 329


>gi|330873874|gb|EGH08023.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 228

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 57/220 (25%), Positives = 107/220 (48%), Gaps = 16/220 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
           +  IK+    + +  NG ++   +A ++L     DG++IG
Sbjct: 189 IAMIKQAV-SIPVFANGDIDSPEKARRVLQATGADGILIG 227


>gi|73661474|ref|YP_300255.1| hypothetical protein SSP0165 [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72493989|dbj|BAE17310.1| conserved hypothetical protein [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 324

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 122/332 (36%), Gaps = 37/332 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNTESYCHPEGVHSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V     G+ L+  P+I  + I A  KA  
Sbjct: 79  DKPDHFREMSIGMAEMGFKGIDLNMGCPVPNVATKGKGSGLIQRPEIAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPV+VK R+G  +       R+ ++ + +  +  + IH R         +      +  +
Sbjct: 138 IPVSVKTRLGYSEID---EWRDWLRHVFEQDIANLSIHLRT--------RREMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIGEIKKLRDEIAPDTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPY------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +  +          +    T+   R      +  +I         G   +
Sbjct: 241 -AFEKEPREHTSEELLGLLRLHLDLFDQYTENEPRQFKPLRRFFKI------YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L        A   + E  F    E +
Sbjct: 294 SELRHQLMSTNTTDDARKLLDE--FEAQTEQV 323


>gi|229015715|ref|ZP_04172697.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1273]
 gi|229021912|ref|ZP_04178476.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1272]
 gi|228739384|gb|EEL89816.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1272]
 gi|228745572|gb|EEL95592.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1273]
          Length = 336

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 72/333 (21%), Positives = 130/333 (39%), Gaps = 37/333 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLELLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGAST--ATHHIIETAFNLMIES 321
              R+ L          A     E + +++  S
Sbjct: 301 AELRNQLMSTKSTDEVRALLDKFEASVDVVENS 333


>gi|325282430|ref|YP_004254971.1| dihydrouridine synthase DuS [Deinococcus proteolyticus MRP]
 gi|324314239|gb|ADY25354.1| dihydrouridine synthase DuS [Deinococcus proteolyticus MRP]
          Length = 314

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/272 (22%), Positives = 105/272 (38%), Gaps = 24/272 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFS-TQEKPLALQIGGAD 58
           M  ++D   R  A          +EMI A  ++  D  ++ LG     E    +Q+ GA 
Sbjct: 19  MAGYSDAPMRQLAAE-QGALWTVSEMISARGLMEHDGPDLTLGRPYPGESARVVQLFGAI 77

Query: 59  ISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L  A +  E+ F    I+LN+GCP  +VH    GACL+  P++    I AM  A ++
Sbjct: 78  PEYLAAAVQRTEEWFAPAAIDLNMGCPVPKVHGKG-GACLLQTPEVAYSLIRAMKSATTL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ K R+G D+         + + ++ +G   I +H R +          R     D+D
Sbjct: 137 DVSAKIRLGWDENRAV----EVAQGLEAAGAAMITVHGRTSK--------QRYTGEADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            + ++     ++ +  +G +  +  A +     V  VMIGR A  N  +   +       
Sbjct: 185 AIAQVA-AAVNIPVIGSGDITTLDAARQRQSSGVAAVMIGRGAVGNPWLFAAL-----AS 238

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            +   P      +   R        Y      
Sbjct: 239 GSDEYPSAQVRARTALRHAELQAEFYGEDRYG 270


>gi|317153973|ref|YP_004122021.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
 gi|316944224|gb|ADU63275.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
          Length = 339

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 66/338 (19%), Positives = 120/338 (35%), Gaps = 38/338 (11%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             ++D  +R   +     A+  +EM+    +  G+   + ++    ++ P+ LQ+ GAD 
Sbjct: 17  AGYSDLPFRLLVKR-HGCAVACSEMVSVKGMTFGNEGTQRLIATCPEDDPMVLQLFGADP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-----A 114
                    + D GY   +LN GCP  +V +   G  LM +PD +    + M +     A
Sbjct: 76  DLFGPVMDWLVDLGYRNFDLNAGCPVRKVLKSGSGVKLMEDPDTLVRIASVMVERATAHA 135

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
               V VK R+G D          L + ++ +GV+ + +H R                  
Sbjct: 136 RGGQVGVKFRLGFDKG--NDTYLELARRLEDAGVHWVTLHPR--------YGRQMFAGQA 185

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  +  +K+    + +  +G L      ++ +    VD VM  R A  + A+       
Sbjct: 186 DWSKLGLLKRAV-SIPVVASGDLFTAEDGVRCVEETGVDAVMFARGALYDPAIFDRYRTL 244

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +         ++        +I              G   ++I   +     G    R 
Sbjct: 245 LAGGQPEPRSGES------LARIVREHIRLTREFEGDGRSFRKIRSIIPRYAKGLRGIRA 298

Query: 293 CRHIL--------TVEAGASTATHHIIETAFNLMIESL 322
            R  L          EA A+ A    +E A N   E+L
Sbjct: 299 LRGSLLECRDWEALEEAAATIAG---LEPADNATPETL 333


>gi|242002314|ref|XP_002435800.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215499136|gb|EEC08630.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 483

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 51/231 (22%), Positives = 98/231 (42%), Gaps = 17/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M+ A   L+  K     L    +++PL +Q    D
Sbjct: 25  MVDQSELAWRLLGRR-HGAQLCYTPMLHASVFLKDPKYRRDALASCDEDQPLVVQFCAND 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV+A+++V       ++LN+GCP A    G +GA L  + D++   +  +   + +P
Sbjct: 84  PEVLVQASRLVVGHCCA-VDLNLGCPQAIARAGHYGAFLQDDWDLLARMVQRVHTQVDVP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R+  + +          + ++ +G   + +H R    KG             ++ 
Sbjct: 143 ITCKVRVFPEVEKTV----RYAQMLEAAGCQVLTVHGRTREQKGPHT------GLASWEH 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  +K+ +  + +  NG ++ +  A + L     D VM       N  + T
Sbjct: 193 IRAVKR-SVKIPVIANGNIQYLEDAERCLRETGADAVMSAEGHLHNPYLFT 242


>gi|54298852|ref|YP_125221.1| hypothetical protein lpp2919 [Legionella pneumophila str. Paris]
 gi|53752637|emb|CAH14072.1| hypothetical protein lpp2919 [Legionella pneumophila str. Paris]
          Length = 328

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 107/232 (46%), Gaps = 18/232 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             ++   +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G + 
Sbjct: 26  AGYSCAPFRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKLLAYQISGNEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA  ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+
Sbjct: 86  HVLAEAAAKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISRVRAAISIPL 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RI  +++        L K I+ +G + + +H R+       P + ++I N+     
Sbjct: 146 TIKIRIQNNEKD-----LTLAKQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI----- 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               K   ++ + +NG + ++S   K L     DG MI RA      +   +
Sbjct: 196 ----KNAVNIPVIVNGDISNISSLRKALEISMCDGFMISRAGTGKPWLYRDL 243


>gi|30018573|ref|NP_830204.1| nitrogen regulation protein NIFR3 [Bacillus cereus ATCC 14579]
 gi|29894114|gb|AAP07405.1| Nitrogen regulation protein NIFR3 [Bacillus cereus ATCC 14579]
          Length = 329

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 132/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++     + E+
Sbjct: 294 AELRNQL-MSTKSTDEVRALLDKFEASVDEA 323


>gi|307256335|ref|ZP_07538118.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307260774|ref|ZP_07542461.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306865161|gb|EFM97061.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306869500|gb|EFN01290.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
          Length = 313

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 125/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       G +    P+ +
Sbjct: 6   MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRLAPELLQGGLTDSGTPVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 66  QLLGQHPQWLAENARLAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 125

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++ + G N I +H R         +D  +
Sbjct: 126 EAVPSDQTVSVKVRLGWD---SAAQCFEIADAVAQGGANEITVHGRTK-------QDGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 176 AERINWQAIGEIQKRLL-IPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 231

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 232 -----------SRVVKFNQPKMPWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 280

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 281 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 311


>gi|150866685|ref|XP_001386359.2| dihydrouridine synthase [Scheffersomyces stipitis CBS 6054]
 gi|149387941|gb|ABN68330.2| dihydrouridine synthase [Scheffersomyces stipitis CBS 6054]
          Length = 369

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 113/271 (41%), Gaps = 23/271 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D      F+T +  + + +Q+G  +
Sbjct: 60  MVRYSKLPFRELVRNY-NTDIVYTPMILAREFVRNDIARSSDFTTNDKDRCVIVQVGSNN 118

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++  +++  +  + I LN GCP         GA LM  PD+V   + A+ +     
Sbjct: 119 VEDLLKFVEMIHPY-VDGIGLNCGCPIKEQVREGIGAALMSEPDLVASMVKAVKEKYGNT 177

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I +   +        VK ++ SGV+ I +H R         K+ R     ++D 
Sbjct: 178 VCIETKIRIHPNLD--ETIAFVKKVEASGVDFITVHGRT--------KNTRSSQPANWDA 227

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDE----- 231
           +  IK E   + +  NG    +  A  +     VDGVM  R    N A+     +     
Sbjct: 228 IKLIK-ETVSVPVVANGDCFSLEDAYSIAEHTGVDGVMSARGILSNPALFAGYKKTPWAA 286

Query: 232 -YFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             F   L  S  +  R+ +    ++   +  
Sbjct: 287 VEFFWDLATSYGLPFRIIQHHLSEMLDKVIP 317


>gi|163938324|ref|YP_001643208.1| dihydrouridine synthase DuS [Bacillus weihenstephanensis KBAB4]
 gi|163860521|gb|ABY41580.1| dihydrouridine synthase DuS [Bacillus weihenstephanensis KBAB4]
          Length = 329

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 129/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DTPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++     +
Sbjct: 294 AELRNQL-MNTKSTDEVRALLDKFEASV 320


>gi|293553600|ref|ZP_06674224.1| probable tRNA-dihydrouridine synthase [Enterococcus faecium E1039]
 gi|291602175|gb|EFF32403.1| probable tRNA-dihydrouridine synthase [Enterococcus faecium E1039]
          Length = 327

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 126/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKNPYAFEKDPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I++T
Sbjct: 297 RVQL-MNTKSTDEVREILDT 315


>gi|52843056|ref|YP_096855.1| nitrogen regulation protein [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52630167|gb|AAU28908.1| nitrogen regulation protein [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 329

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 107/232 (46%), Gaps = 18/232 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             ++   +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G + 
Sbjct: 27  AGYSCAPFRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKFLAYQISGNEP 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA  ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+
Sbjct: 87  HVLAEAAAKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISRVRAAISIPL 146

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RI  +++        L K I+ +G + + +H R+       P + ++I N+     
Sbjct: 147 TIKIRIQNNEKD-----LTLAKQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI----- 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               K   ++ + +NG + ++    K L   + DG MI RA      +   +
Sbjct: 197 ----KNAVNIPVIVNGDINNIFSLRKALEISACDGFMISRAGTGKPWLYRDL 244


>gi|50554003|ref|XP_504410.1| YALI0E26059p [Yarrowia lipolytica]
 gi|49650279|emb|CAG80011.1| YALI0E26059p [Yarrowia lipolytica]
          Length = 359

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 77/286 (26%), Positives = 125/286 (43%), Gaps = 33/286 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      ++Y+ M++A    R     +  F+T   + PL +Q+GG +
Sbjct: 51  MVRYSKLPFRALVRHFD-CDVVYSPMMLAREFCRNQTARLCDFTTNKDDFPLIVQLGGNN 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              +V+A K+++ +  + + +N GCP         GA LM  PD+V + +AA+ K     
Sbjct: 110 AEDMVKAVKMLQPY-VDGVGINCGCPIKEQIREGVGAALMTAPDLVAEMVAAIRKECGAE 168

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I V VK RI  D            K ++ +G + I +H R      L P+ +R  PN  Y
Sbjct: 169 IYVEVKMRIHKDLNDTVH----FAKLVEAAGADSISVHGR------LVPQRSRTAPN--Y 216

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  I K++ D+ +  NG     +   +I  L   DGVM  R    N AM         
Sbjct: 217 DGIK-IVKDSVDVPVIANGDAFTTTNIEEIVELTGCDGVMAARGILSNPAMFA------- 268

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL-QQITRH 279
               G +    R  + FW  ++A    YA    H    L  ++TR+
Sbjct: 269 ----GYTKTPWRAVELFWDYVTAYGLPYALTIHHFSEMLEAELTRY 310


>gi|302687524|ref|XP_003033442.1| hypothetical protein SCHCODRAFT_256941 [Schizophyllum commune H4-8]
 gi|300107136|gb|EFI98539.1| hypothetical protein SCHCODRAFT_256941 [Schizophyllum commune H4-8]
          Length = 467

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 120/299 (40%), Gaps = 33/299 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-LRGDKKNILGFSTQE---------KPL 50
           MVD ++  +R   R      + YT MI A      G K+    F   E         +PL
Sbjct: 43  MVDQSELAFRILCRRY-GAQVAYTPMINAHVFPFYGKKQQDKNFDVSEGEEGAQGLDRPL 101

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q  G +  +L+ +A+IVE    + ++LN+GCP     +G +G+ L    ++V   +  
Sbjct: 102 VVQFCGNNPDELLASARIVEAH-CDAVDLNLGCPQDIAKKGHYGSWLQDEWELVYKLVNT 160

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + + LSIPVT K RI  D +          K ++++G   + +H R    +G+       
Sbjct: 161 LHENLSIPVTAKFRIFSDPERT----LAYAKMLERAGAQILTVHGRTRDQRGV------N 210

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
               D+  +  +K+    + +  NG +   ED+   L+     DG+M       N A+  
Sbjct: 211 SGLADWKQIAMVKQAV-SVPVLANGNMLYQEDIEACLQA-TGADGIMSAEGLLYNPALFV 268

Query: 228 TVDEYFSNPLTGSSPIKTRV----DKDFWRKISASMTDY--AARHLHSGGKLQQITRHM 280
            +        + S             +    ++A   +Y    R L++   L  I  H+
Sbjct: 269 GLAPPPRPSSSSSVHPLLATSSGSAPNLHPSVTALAFEYLTICRELNTHTSLGAIRGHL 327


>gi|229131322|ref|ZP_04260223.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228652143|gb|EEL08079.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 336

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 130/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DTPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++    ++
Sbjct: 301 AELRNQL-MNTKSTDEVRALLDKFEAIV 327


>gi|307611733|emb|CBX01438.1| hypothetical protein LPW_31271 [Legionella pneumophila 130b]
          Length = 328

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 107/232 (46%), Gaps = 18/232 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             ++   +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G + 
Sbjct: 26  AGYSCAPFRDLFNIYTPPAYCVSEMCSAIDILHKHSPQSRYIYRAPTEKLLAYQISGNEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA  ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+
Sbjct: 86  HVLAEAAAKLQSLGADLIDINCGCPKSKICKKGAGSALLEDPQKLIAIISKVRAAISIPL 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RI  +++        L K I+ +G + + +H R+       P + ++I N+     
Sbjct: 146 TIKIRIQNNEKD-----LTLAKQIEGAGAHALIVHGRRWTEDYDIPCNWQQIANI----- 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               K   ++ + +NG + ++S   K L     DG MI RA      +   +
Sbjct: 196 ----KNAVNIPVIVNGDISNISSLRKALEISVCDGFMISRAGTGKPWLYRDL 243


>gi|169825841|ref|YP_001695999.1| hypothetical protein Bsph_0238 [Lysinibacillus sphaericus C3-41]
 gi|168990329|gb|ACA37869.1| conserved hypothetical protein [Lysinibacillus sphaericus C3-41]
          Length = 322

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/330 (21%), Positives = 130/330 (39%), Gaps = 36/330 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    + +      L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRQVVSEAGRPDVFFTEFTNSDSYCHPEGQKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + ++ + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSRGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D          +  I K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYKD---VEEWEEWLTHIFKQDIANLSIHLRT--------RKEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDCIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +  S+             +D + ++       +   LH   K+            GF  +
Sbjct: 247 KEHSSKEYLDLLRLQLDLQDQYEEVL----PRSITGLHRFFKI---------YVKGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
              R  L +   ++     +++      +E
Sbjct: 294 SELRSQL-MNTKSTDEVRALLDRFEANHVE 322


>gi|218674123|ref|ZP_03523792.1| tRNA-dihydrouridine synthase A [Rhizobium etli GR56]
          Length = 182

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/177 (45%), Positives = 109/177 (61%), Gaps = 9/177 (5%)

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +  +G + IWIHARKA LKGLSPK+NR+IP LDY+IVY +K+  P++FIG+NGG+  + 
Sbjct: 1   RVLDAGADAIWIHARKAWLKGLSPKENREIPPLDYEIVYRMKQRWPEVFIGINGGIRTLD 60

Query: 202 QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           +A   L  VDGVM+GRAAY+N+A+L  VD  F                  W  +   M  
Sbjct: 61  EAASHLAHVDGVMLGRAAYQNAAVLADVDHRFFGAPAAEPD---------WPALCERMMA 111

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           YA RH+  GG+LQ + RHM+GLF G P +RR R IL+ +A  S A   ++  AF  +
Sbjct: 112 YAERHIAGGGRLQHVARHMVGLFTGLPGARRYRQILSTDAAKSGAGPEVLAAAFAAV 168


>gi|66802582|ref|XP_635163.1| tRNA-dihydrouridine synthase 4-like protein [Dictyostelium
           discoideum AX4]
 gi|60463479|gb|EAL61664.1| tRNA-dihydrouridine synthase 4-like protein [Dictyostelium
           discoideum AX4]
          Length = 344

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +      + YT MI+A    R +      F+    ++PL +Q G  +
Sbjct: 62  MVRFSRLPFRMLVKKW-GCDITYTPMIMAAEFNRSEAARDSDFTINKLDEPLIVQFGVNN 120

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +LV AA+ V+D+    I++N GCP   V +  FGA L+L+P+ + D +  +   + IP
Sbjct: 121 AEELVSAAEKVKDY-CQGIDINCGCPQRWVMKEGFGANLLLHPERIYDMVKQINNRVPIP 179

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R+  D +        L K  ++ GV+ I +H R + +K   P        +DYD 
Sbjct: 180 ISIKIRVQSDLKDT----IELAKRAERIGVSWITVHGRTSAMKSSHP--------VDYDA 227

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +  +K +N  L +  NG +  +SQ+ +I     V+GVM  R    N A+    D+
Sbjct: 228 IKLVK-DNVTLPVFANGDVFTLSQSNEIREKTGVNGVMSARGLLTNPALFQGYDK 281


>gi|229165352|ref|ZP_04293139.1| tRNA-dihydrouridine synthase [Bacillus cereus AH621]
 gi|228618177|gb|EEK75215.1| tRNA-dihydrouridine synthase [Bacillus cereus AH621]
          Length = 336

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 129/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGCPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DTPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++     +
Sbjct: 301 AELRNQL-MNTKSTDEVRALLDKFEASV 327


>gi|261206596|ref|ZP_05921294.1| dihydrouridine synthase [Enterococcus faecium TC 6]
 gi|289564958|ref|ZP_06445412.1| tRNA dihydrouridine synthase B [Enterococcus faecium D344SRF]
 gi|294617006|ref|ZP_06696726.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1636]
 gi|260079089|gb|EEW66782.1| dihydrouridine synthase [Enterococcus faecium TC 6]
 gi|289163165|gb|EFD11011.1| tRNA dihydrouridine synthase B [Enterococcus faecium D344SRF]
 gi|291590160|gb|EFF21949.1| tRNA-dihydrouridine synthase [Enterococcus faecium E1636]
          Length = 327

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 126/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSSAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKNPYAFEKDPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I++T
Sbjct: 297 RVQL-MNTKSTDEVREILDT 315


>gi|229125817|ref|ZP_04254843.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|228657674|gb|EEL13486.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-Cer4]
          Length = 336

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 132/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++     + E+
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEASVDEA 330


>gi|52144914|ref|YP_081915.1| dihydrouridine synthase [Bacillus cereus E33L]
 gi|51978383|gb|AAU19933.1| conserved hypothetical protein; probable dihydrouridine synthase
           [Bacillus cereus E33L]
          Length = 329

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 132/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++     + E+
Sbjct: 294 AELRNQL-MSTKSTDEVRALLDKFEASVSET 323


>gi|195995959|ref|XP_002107848.1| hypothetical protein TRIADDRAFT_49631 [Trichoplax adhaerens]
 gi|190588624|gb|EDV28646.1| hypothetical protein TRIADDRAFT_49631 [Trichoplax adhaerens]
          Length = 581

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 55/285 (19%), Positives = 110/285 (38%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM +   +L+G +    ++     E    LQ+ GA    L 
Sbjct: 247 NLPFRRICKTF-GADVTCSEMALCTNLLQGQQSEWALVKRHESEDLFGLQVCGAWPDTLA 305

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             ++ + D    + ++LN+GCP   V     G+ LM   + +   +  M   LS+P+TVK
Sbjct: 306 RLSEYINDRVNVDFVDLNLGCPIDLVFHQGAGSALMGRANKLQQIVTGMSSILSVPLTVK 365

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G+  +        L+  I++ G + + +H R         ++ R     D+  + E 
Sbjct: 366 LRTGILAKKSTA--HKLIPQIREWGASLVTLHGRS--------REQRYTKLADWSYINEC 415

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                 + +  NG +      L+ +   +V GVMI R A     + T + E     ++ +
Sbjct: 416 ATAADPMPLIGNGDILSFEDYLEHMNNTNVAGVMIARGALIKPWLFTEIKERRHWDISAN 475

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI-GL 283
                        +      +Y   H  S    +++  R ++  L
Sbjct: 476 ERF----------EFLRKYVNYGLEHWGSDSLGVEKTRRFLLEWL 510


>gi|242309035|ref|ZP_04808190.1| conserved hypothetical protein [Helicobacter pullorum MIT 98-5489]
 gi|239524459|gb|EEQ64325.1| conserved hypothetical protein [Helicobacter pullorum MIT 98-5489]
          Length = 317

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 66/317 (20%), Positives = 129/317 (40%), Gaps = 33/317 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   +      +  +EMI   A+   +KK   ++  S  E P ALQI G D 
Sbjct: 17  AGYSDLPFREVVKKF-GADITVSEMISVHALAFKNKKTIKMIEKSPLENPFALQIAGNDF 75

Query: 60  SKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
             + +A + + +F      ++LN GCP+ +V     G+ L+ + + +   +  + +    
Sbjct: 76  GIIQKAVEFLNEFKNEIQILDLNCGCPAPKVSSHGSGSSLLKDLNKLVKILQLLRETSVF 135

Query: 118 P-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P ++VK R+G D +IP      +  ++  S ++ + +H R          D  K   +DY
Sbjct: 136 PYLSVKVRLGFDKKIP----LEIANALNDSPIDYVVVHGRTK-------SDGYKKDKIDY 184

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D +  IK+      +  NG +     A K+  L   +GVMIGRAA +   + T +     
Sbjct: 185 DSIRLIKQNIQH-PLIANGEITSPQIAKKVQELTGAEGVMIGRAAIEKPWIFTQIKNNLE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             +     ++ +V  + + +  +   DY A             +++     G   +   R
Sbjct: 244 ESIE----LRKQVALEHFDRTISFRGDYGAIMF---------RKNLHAYSKGLKGASDFR 290

Query: 295 HILTVEAGASTATHHII 311
           + +      +     I 
Sbjct: 291 NKVNAITNPALMREEIF 307


>gi|221142266|ref|ZP_03566759.1| hypothetical protein SauraJ_11637 [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|304380055|ref|ZP_07362778.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|269939624|emb|CBI47992.1| probable tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus TW20]
 gi|302749979|gb|ADL64156.1| tRNA dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           str. JKD6008]
 gi|304341375|gb|EFM07291.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           BAA-39]
 gi|329312793|gb|AEB87206.1| tRNA dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           T0131]
          Length = 328

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPVVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTCKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|255349030|ref|ZP_05381037.1| putative oxidoreductase [Chlamydia trachomatis 70]
 gi|255503568|ref|ZP_05381958.1| putative oxidoreductase [Chlamydia trachomatis 70s]
 gi|255507248|ref|ZP_05382887.1| putative oxidoreductase [Chlamydia trachomatis D(s)2923]
 gi|289525687|emb|CBJ15168.1| putative oxidoreductase [Chlamydia trachomatis Sweden2]
 gi|296435255|gb|ADH17433.1| putative oxidoreductase [Chlamydia trachomatis E/150]
 gi|296438974|gb|ADH21127.1| putative oxidoreductase [Chlamydia trachomatis E/11023]
          Length = 334

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/317 (23%), Positives = 145/317 (45%), Gaps = 24/317 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             ++D  YR  +     +AL++ EM+  + +    ++   +L F+   +P+  Q+ G+  
Sbjct: 22  AGFSDFPYRRMSAEY-RSALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSRP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               E+AKI+E  G++ I+LN GCP+ R+ +   G+ ++  P+++G  +  M + +S+PV
Sbjct: 81  DLAGESAKILEGLGFDLIDLNCGCPTDRITKDGSGSGMLKTPELIGKVVEKMVEVVSVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ IK+SG + +++H R         +        + + +
Sbjct: 141 TVKIRSGWD--FDHINVEETVRIIKESGASAVFVHGRT--------RSQGYQGPSNLEFI 190

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K+    D  +  NG +     A  +L     DGV++ R       +   +++Y +  
Sbjct: 191 SRAKQAAGNDFPVFGNGDVFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRH 295
            T SSP  +   + F + +      +   +  S  KL   TR + G +    P  R  R 
Sbjct: 251 -TYSSPSFSTKKQAFVQHL-----QWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRA 304

Query: 296 ILTVEAGASTATHHIIE 312
            L  +A +S   + +I+
Sbjct: 305 NLA-KASSSQEVYQLID 320


>gi|118082094|ref|XP_001231915.1| PREDICTED: similar to Dihydrouridine synthase 4-like (S.
           cerevisiae) isoform 1 [Gallus gallus]
          Length = 317

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 118/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT M+VA   +R  K     F+T   + PL +Q    +
Sbjct: 32  MVRYSKLAFRTLVRRY-GCDLCYTPMVVAADFVRSAKARDSEFTTNRGDNPLIVQFAAKE 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 91  AQVLCDAALLVCPF-ADGVDLNCGCPQRWAMAEGYGACLINKPELVRDMVRHVRNQIDNP 149

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L K  + +GV+ I +H R    +            + 
Sbjct: 150 RFSVSIKIRIHEDLKKTV----DLCKKAEATGVSWITVHGRNIEERHQ---------PVH 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  + KE+  + +  NG ++ +  A     L   DGVM+ R    N AM    +E  
Sbjct: 197 YDAIK-VIKESIHIPVVANGDIKTLKDAENVHHLTGADGVMVARGLLANPAMFAGYEE-- 253

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +  +D+        T +   H H    +++IT
Sbjct: 254 ---------TPLKCIQDWVDIALEHGTPFTCFHHHLMYMMERIT 288


>gi|42779507|ref|NP_976754.1| hypothetical protein BCE_0426 [Bacillus cereus ATCC 10987]
 gi|42735423|gb|AAS39362.1| hypothetical conserved protein [Bacillus cereus ATCC 10987]
          Length = 329

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 131/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     ++      + E+
Sbjct: 294 AELRNQL-MSTKSTDEVRTLLNQFEASVSET 323


>gi|167516252|ref|XP_001742467.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163779091|gb|EDQ92705.1| predicted protein [Monosiga brevicollis MX1]
          Length = 291

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 102/230 (44%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L YT M  +   +R    +K +      ++PL +Q  G D
Sbjct: 17  MVDQSELAWRMLCRR-KGAVLCYTPMFNSKVFVRDASYRKRMFKAIEGDRPLVVQFCGDD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + L+EAAK VE +  + I+LN GCP      G +GA L    +++ + ++ + K LSI 
Sbjct: 76  AATLLEAAKHVEPY-CDAISLNCGCPQGIARRGHYGAFLQDEWELLAEIVSTLSKNLSIA 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K RI  D    A       K  + +G + + +H R    KG            D+ +
Sbjct: 135 VECKIRIHDD----AERTLAYAKMFEAAGCDLLTVHGRTREQKGTRT------GLADWSL 184

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           V  IK+E   + +  NG +   +  L  L    VDG+M   +   N AM 
Sbjct: 185 VKRIKEEL-KIPVVSNGNILYRADCLACLEETGVDGIMSSESNLSNPAMF 233


>gi|41054535|ref|NP_955911.1| tRNA-dihydrouridine synthase 1-like [Danio rerio]
 gi|37589069|gb|AAH58873.1| Dihydrouridine synthase 1-like (S. cerevisiae) [Danio rerio]
          Length = 479

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 105/265 (39%), Gaps = 32/265 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R             + +++PL  Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAELCYTPMLHAQVFVRDANYRRENLYSEVNQEDRPLITQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    ++AA + +D+  + I+LN+GCP      G +G  L    D++   I    + LS
Sbjct: 83  NDPEVFIQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGVFLQDEWDLLEKMIKLANEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T K R+  + +          K ++K+G   + +H R    KG             +
Sbjct: 142 VPITCKIRVFPEIEKTV----KYAKMLEKAGCQLLTVHGRTKDQKGA------LTGIASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +  + +E  ++ +  NG ++   D+   ++    V GVM       N A+        
Sbjct: 192 KHIKAV-REAVNIPVFANGNIQHLSDVHHCMEE-TGVQGVMSAEGNLHNPALF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISAS 258
                G SP    + +++   +   
Sbjct: 243 ----EGRSPPVWEMAEEYLDIVEKH 263


>gi|229176913|ref|ZP_04304309.1| tRNA-dihydrouridine synthase [Bacillus cereus 172560W]
 gi|228606586|gb|EEK64011.1| tRNA-dihydrouridine synthase [Bacillus cereus 172560W]
          Length = 336

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 133/331 (40%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++   + + E+
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSVGEA 330


>gi|198428499|ref|XP_002130384.1| PREDICTED: similar to dihydrouridine synthase 1-like [Ciona
           intestinalis]
          Length = 626

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 112/283 (39%), Gaps = 31/283 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGG 56
           MVD ++  +R  +R      L ++ M  A+  +              ST++ PL +Q   
Sbjct: 22  MVDQSELPWRLLSRR-HGAQLCFSPMYSANTFVHDHTYRNKVVQDLSSTEDHPLIVQFCS 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +EA+K+VE      ++LN+GCP      G FGA L  + D++ + I+   + + 
Sbjct: 81  NSAENFLEASKLVEGL-CEGVDLNLGCPQHIAKRGHFGAYLQEDWDLIIEIISTTKQHIG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I VT K R+  +            + ++ +G + I +H R    KG             +
Sbjct: 140 IGVTAKIRVFNEIDKTV----KYAQMLETAGCDIITVHGRTREQKG------PNTGLASW 189

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT------ 228
           D +  +K +N D+ +  NG ++     ++ +    VDGVM+      N  +         
Sbjct: 190 DHIKAVK-DNVDIPVFANGNIQYYCDIMRCMETTGVDGVMVAEGNLTNPMIFQDLSTPCN 248

Query: 229 ----VDEYFSNPLTGSSPIKTRVDKDF--WRKISASMTDYAAR 265
               V+EYF+       P+ +     F  W +      D   R
Sbjct: 249 VYDVVEEYFALVAQYPCPLSSARSHMFRIWARTLLIHKDMRER 291


>gi|148361172|ref|YP_001252379.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|296108507|ref|YP_003620208.1| tRNA-dihydrouridine synthase B [Legionella pneumophila 2300/99
           Alcoy]
 gi|148282945|gb|ABQ57033.1| tRNA-dihydrouridine synthase [Legionella pneumophila str. Corby]
 gi|295650409|gb|ADG26256.1| tRNA-dihydrouridine synthase B [Legionella pneumophila 2300/99
           Alcoy]
          Length = 328

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 107/232 (46%), Gaps = 18/232 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADI 59
             ++   +R    + T  A   +EM  A  IL     +   +  +  EK LA QI G + 
Sbjct: 26  AGYSCAPFRDLFNIYTPPAYCVSEMCSAIDILHKHSSQSRYIYRAPTEKLLAYQISGNEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L EAA  ++  G + I++N GCP +++ +   G+ L+ +P  +   I+ +  A+SIP+
Sbjct: 86  YLLAEAAAKLQSLGADLIDINCGCPKSKIRKKGAGSALLEDPQKLIAIISRVRAAISIPL 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K RI  +++        L K I+ +G + + +H R+       P + ++I N+     
Sbjct: 146 TIKIRIQNNEKD-----LTLAKQIEDAGAHALIVHGRRWTEDYDIPCNWQQIANI----- 195

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               K   ++ + +NG + ++    K L   + DG MI RA      +   +
Sbjct: 196 ----KNAVNIPVIVNGDINNIFSLRKALEISACDGFMISRAGTGKPWLYRDL 243


>gi|293572798|ref|ZP_06683752.1| tRNA-dihydrouridine synthase [Enterococcus faecium E980]
 gi|291607148|gb|EFF36516.1| tRNA-dihydrouridine synthase [Enterococcus faecium E980]
          Length = 327

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 126/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRRTGEELAEKYGVDGIMIGRGIFKNPYAFEKEPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I++T
Sbjct: 297 RVQL-MNTKSTDEVREILDT 315


>gi|255585121|ref|XP_002533266.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
 gi|223526922|gb|EEF29128.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
          Length = 426

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 125/302 (41%), Gaps = 31/302 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 98  MVDNSELPFRMLCRKYGADA-AYTPMLHSRIFTENEKYRTQEFTTCNEDRPLFVQFCAND 156

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA+ VE +  + +++N+GCP      G++GA LM N  +V   +  +   L++P
Sbjct: 157 PDILLEAARKVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLNVP 215

Query: 119 VTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           V+ K R    +DD I         + ++++G + + +H R         KD +K    D+
Sbjct: 216 VSCKIRLFPKLDDTISY------ARMLEEAGCSLLAVHGRT-----RDEKDGKKF-RADW 263

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  ++     + +  NG +  M      L     DGV+   +  +N A+         
Sbjct: 264 KAIKAVRNAV-KIPLLANGNVRHMDDVRNCLEETGADGVLSAESLLENPALFAGFRTAEW 322

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH---MIG-LFHGFPNS 290
                 S    ++D+      +  + +Y           + I  H   M+G  F   P+ 
Sbjct: 323 VVGDEESTRDGKLDQ------ADLLVEYLKLCEEYPVPWRMIRAHVHKMLGDWFRIHPHV 376

Query: 291 RR 292
           R 
Sbjct: 377 RE 378


>gi|323136427|ref|ZP_08071509.1| TIM-barrel protein, nifR3 family [Methylocystis sp. ATCC 49242]
 gi|322398501|gb|EFY01021.1| TIM-barrel protein, nifR3 family [Methylocystis sp. ATCC 49242]
          Length = 331

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 121/328 (36%), Gaps = 31/328 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-----PLALQIG 55
           M   TD   R  A      ++  +EMI A  + RGD++  L  S         P  +QI 
Sbjct: 15  MAGVTDPAMRRIAERY-GASVTISEMITAAGVARGDRETALRLSGSNDEANSAPRVIQIA 73

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D +++  AA+  E  G   +++N+GCP  RV  G  GA LM + D     IAA   A+
Sbjct: 74  ARDATEIAAAARHAEAAGAQWVDINMGCPCKRVTGGLAGAALMRDLDQATSLIAAARAAI 133

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IP+++K R+G DD         L +  +  G   + +H R         +        D
Sbjct: 134 RIPLSIKMRLGWDDASRNA--PELARRAEGEGAALVTVHGRT--------RQQFYTGRAD 183

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +  +K+    + +  NG       A ++L     D VM+GRAA     ++  +  Y 
Sbjct: 184 WAAIAAVKQAV-KIPVVANGDCASAGDAAEMLRASGADAVMVGRAAQGRPWLVGDISHYL 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL----FHG-FP 288
           +       P            +   ++            L+   +H+       F G   
Sbjct: 243 ATGRLRPQPSSKERGAIAREHLEGLLSQMGQA------GLRHARKHLAAYVDEAFGGACE 296

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFN 316
              + R  L        A   +I+  F 
Sbjct: 297 QVSQLRRALVTTNSPEEAG-RLIDAIFA 323


>gi|282892092|ref|ZP_06300567.1| hypothetical protein pah_c207o016 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281497987|gb|EFB40331.1| hypothetical protein pah_c207o016 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 304

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 133/325 (40%), Gaps = 27/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M    DR +R     +       TE   + ++A +    K      T   P A+QI G++
Sbjct: 1   MEGLGDRPFRKAMAKMGGFNEACTEFLRVPSNAHVASLAKQYQKDDTFPIPQAVQIMGSN 60

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +   A+ +   G + I+LN GCPS  V     G+ L+ +P  +     AM +A+S+P
Sbjct: 61  PELMAAMAQELAQRGAHRIDLNCGCPSNTVTGRGAGSSLLKDPSQLYRIAKAMVEAVSVP 120

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R G +D   ++   NL+ + ++SG+  + +H R  +            P   +D+
Sbjct: 121 VTAKLRSGYED--ISLFKENLL-AAQESGIKFMTLHPRTKVDG--------YTPPARWDL 169

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E  K    + +  NG + ++  A+++L     D +M+GR +  N  +   +  +F+  
Sbjct: 170 IAE-AKALLKIPVVGNGDILNVDDAVRMLKETGCDALMVGRGSVINPLIFHQIRAFFAGQ 228

Query: 237 LT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        ++F   ++       +  L+   +L      M  LF G  N+R    
Sbjct: 229 QYVPEKNALQNFVQNFLCAMAEGTP--ISTQLNKLKQL------MSFLFKG--NARLLER 278

Query: 296 ILTVEAGASTATHHIIETAFNLMIE 320
              + +         +   F +++E
Sbjct: 279 RGEMLSKRCANPAEFLAFVFPMLLE 303


>gi|224003889|ref|XP_002291616.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220973392|gb|EED91723.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 333

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/295 (23%), Positives = 124/295 (42%), Gaps = 26/295 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----RGDKKNILGFSTQEKPLALQIG 55
           MVD +D  YR   R   N +L +T MI A   +     R     I G  +Q++PL  Q  
Sbjct: 3   MVDASDLPYRLLTRRY-NTSLCFTPMIHAKMFIDKPKYREKFWKIEGMPSQDRPLIAQFC 61

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP--DIVGDCIAAMCK 113
           G D + L++A K++E    + +++N GCP      G +GA LM     D + + +  +  
Sbjct: 62  GHDKNVLLQAMKVLEPH-VDGVDINCGCPQNIAKRGRYGAFLMEEDNGDKIVEIVQHLTA 120

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L++PV+VK RI       ++AL    K +  +G   + IH R          +      
Sbjct: 121 NLNVPVSVKLRILPTGIEDSLALY---KRLVDAGAAMLTIHGRTRFQ------NKVDTGT 171

Query: 174 LDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
            ++D + ++     D + +  NG + ++ +  K      VDGVM      +   + T  +
Sbjct: 172 ANWDYIRQVVDLVGDRVPVIANGNICNLDEVRKCFEVTGVDGVMSSEGILEYPPLFTETN 231

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              S     + P + ++ +D+         +Y +     G  L+ I  H+    H
Sbjct: 232 -VESTGFKRTGPGRLQMAEDYL----ELCKEYPSEEGGQGSGLKCIRAHLHRFLH 281


>gi|303249533|ref|ZP_07335740.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|303252549|ref|ZP_07338712.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302648517|gb|EFL78710.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|302651607|gb|EFL81756.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 320

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 13  MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 73  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 132

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    +     +  ++ + G N I +H R         +D  +
Sbjct: 133 EAVPSDQIVSVKVRLGWDSADQSF---EIADAVAQGGANEITVHGRTK-------QDGYR 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 183 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 238

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 239 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 287

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 288 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 318


>gi|296447367|ref|ZP_06889294.1| TIM-barrel protein, nifR3 family [Methylosinus trichosporium OB3b]
 gi|296255146|gb|EFH02246.1| TIM-barrel protein, nifR3 family [Methylosinus trichosporium OB3b]
          Length = 331

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/313 (23%), Positives = 119/313 (38%), Gaps = 23/313 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD   R  A      A    EM+ A A+ RGD +              +QI   D 
Sbjct: 17  MAGVTDSAMRRIALRFGAAA-AVGEMVGASALARGDLEARQRLDGAGLDAHIVQIAARDP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           + + E A+  E  G   I++N+GCP  RV  G  GA LM +P +    + A   A+++PV
Sbjct: 76  ASIAETARRAEAAGAKLIDINMGCPCKRVTGGLAGAALMRDPALAASLVRAAVGAVTVPV 135

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G DD     A   L + ++  G   + +H R         +        D+  +
Sbjct: 136 SVKMRLGWDDASRNAA--ELARLVESEGAAMVTVHGRT--------RAQFYEGRADWSAI 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            E+++    + +  NG       A  +L     D VMIGRAA     ++  V  + ++  
Sbjct: 186 AEVRRAL-RIPLVANGDCASPEDAAVMLERSGADAVMIGRAALGRPWLVGEVAHFLASG- 243

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS---RRCR 294
               P  +R  +    + +    D     +     L+   +H+       P     R  R
Sbjct: 244 -HRRPALSRAAR---LEAALEHLDGLLGLMGEAAGLRHARKHLAAYADHAPEGGERRALR 299

Query: 295 HILTVEAGASTAT 307
             L     A  A 
Sbjct: 300 QALVCTTTAEEAK 312


>gi|19112778|ref|NP_595986.1| tRNA dihydrouridine synthase Dus1 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74638589|sp|Q9HGN6|DUS1_SCHPO RecName: Full=tRNA-dihydrouridine synthase 1
 gi|9967699|emb|CAC05725.1| tRNA dihydrouridine synthase Dus1 (predicted) [Schizosaccharomyces
           pombe]
          Length = 399

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/296 (23%), Positives = 127/296 (42%), Gaps = 38/296 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS----TQEKPLALQIGG 56
           MVD ++  +R  AR  +   L Y+ M  +      +      FS     +E+PL +Q  G
Sbjct: 25  MVDQSELPWRILARR-SGADLCYSPMFHSRLFGESEDYRNKVFSTRTIPEERPLIIQFCG 83

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D   +++AAKI   +  + +++N+GCP     +G +G+ L  N +++   I  +   LS
Sbjct: 84  NDPEIMLKAAKIAAPY-CDAVDVNLGCPQGIAKKGKYGSFLQENWNLIESIITKLHTELS 142

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPVT K RI  D Q       +  K I K+G + + +H R    KG            D+
Sbjct: 143 IPVTAKIRIFPDPQKT----LDYAKMILKAGASILAVHGRLREQKG------HFTGIADW 192

Query: 177 DIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           + +  ++K  P    +  NG +   +D+ + +K    VDGV+    +  N  +       
Sbjct: 193 EQIQMLRKNLPSETVLFANGNILHAQDIDRCIK-YTGVDGVLSAEGSLYNPRIF------ 245

Query: 233 FSNPLTGSSPIKTRVDK--DFWRKISASMTDYAARHLHS-----GGKLQQITRHMI 281
               L  SSP+ T   +  D   +    + ++     +S      G L ++ R ++
Sbjct: 246 ----LPPSSPLMTLYPRIDDMCEEYLNIIREFKLESDYSSLSAIKGHLFKLMRPLL 297


>gi|167855021|ref|ZP_02477795.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis 29755]
 gi|167853869|gb|EDS25109.1| tRNA-dihydrouridine synthase C [Haemophilus parasuis 29755]
          Length = 317

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 125/328 (38%), Gaps = 40/328 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       GF+    P+ +
Sbjct: 12  MQGVLDPFVRQLLTAVNDYDLCISEFVRVVDQKLPKKTFYRLCPELHNNGFTPSGTPVRV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G     L E A +  + G + ++LN GCPS  V+  + G  L+  P ++     AM 
Sbjct: 72  QILGQHPQWLAENAALAVELGSHGVDLNCGCPSKTVNGSNGGVSLLKQPKLIYRATKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D    A     +  ++ + G   I +H R  +       D  +
Sbjct: 132 EAVPSHLPVSVKVRLGWDSSEQAF---EIADAVVQGGATEITVHGRTKM-------DGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTT 228
              +++  + EIKK  P + +  NG + D   A K       D +MIGR A  N   L+ 
Sbjct: 182 AERINWQAIGEIKKRLP-IPVIANGEIWDYLSAKKCREVTARDALMIGRGAL-NVPNLSK 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                K  W  +   +  Y             + R    +  L  
Sbjct: 240 VVKY-------------NQPKMAWNDVLQLLFQYVHMENELDTGFYHVARIKQWLRYLDK 286

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIET 313
            +P + +   IL  E G      HII+ 
Sbjct: 287 EYPEAVQLFDILKTEHGYEGLKQHIIQA 314


>gi|330718778|ref|ZP_08313378.1| probable tRNA-dihydrouridine synthase [Leuconostoc fallax KCTC
           3537]
          Length = 314

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 137/325 (42%), Gaps = 28/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R       +  + YTE   A +++    K      L +   E+    QI G
Sbjct: 1   MEAVTDTIFRRVVEKAASPDVYYTEFTNASSMVHPKAKFSVQGRLAYMPDEQIPVAQIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +    +  A K++ + GY  ++LN+GCP   V +   G+ L+ + D+  D I+A  K+  
Sbjct: 61  SRPDDIAGAVKLLPEMGYQAVDLNMGCPDGTVIKNGGGSDLIRHQDLACDIISA-AKSTP 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G +     +  R  +  I K  V  + +H R        P     I     
Sbjct: 120 LPVSVKTRLGFN---SPLEFREWLPLILKQDVAVLTVHLRSRKEMSKVPAHYEYID---- 172

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +I+    +  P   I  NG ++D  + L   K  P +DG+MIGR  ++N      V +  
Sbjct: 173 EILAMRDELAPKTLIQFNGDIKDRQEGLAIAKAHPGIDGIMIGRGIFENPFAFEKVQQ-- 230

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            +     S    +     + +++A++T    +H  +  +  +I         GFP++   
Sbjct: 231 -SHTLRESIELLKCQLTLFDEVNATVTP---KHFEALKRFFKI------YLRGFPHASGL 280

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R  L +E  A+     I++ A   +
Sbjct: 281 RQAL-METHATDEVRTILDEAVPQI 304


>gi|187251875|ref|YP_001876357.1| dihydrouridine synthase DuS [Elusimicrobium minutum Pei191]
 gi|186972035|gb|ACC99020.1| Dihydrouridine synthase DuS [Elusimicrobium minutum Pei191]
          Length = 318

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/297 (23%), Positives = 127/297 (42%), Gaps = 25/297 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD  +R    L     ++  EM+ A A+   +KK+  +L    +E P+++QI G D
Sbjct: 24  MAGITDTPFRIHC-LNNGAGIVCAEMVSAKAVEYDNKKSVKMLAVDKKEHPVSMQIFGGD 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  AAK  E  G + I++N GCP  +++    G  L+ +  ++   + A   ++SIP
Sbjct: 83  AESISIAAKAAEAAGADIIDINAGCPVKKINRAGAGCVLIKDEKLLASIVNAAVNSVSIP 142

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K RIG+           + K  +  G   + +HAR A         N      D + 
Sbjct: 143 VTLKTRIGLTAGD--FKGDKIAKLAENEGAAAVIMHARYA--------GNVHGGPADLEA 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + ++      + +  NGG+ D++ A K+    V G+M+GR A  N  +  ++       L
Sbjct: 193 LAKVVSAV-KIPVIGNGGIVDVNTADKMFETGVRGIMVGRGAIGNINIFKSIINGCDIEL 251

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                +     K F+  I  ++  Y  +       + +  + +     GFP +   R
Sbjct: 252 NPKENV-----KIFFNLIKQNVNFYGEK-----NGIARSRKTVGFWIKGFPMAGEIR 298


>gi|257484387|ref|ZP_05638428.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 187

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/192 (36%), Positives = 111/192 (57%), Gaps = 9/192 (4%)

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           ++ +     L + V  + ++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + 
Sbjct: 2   INGRDSYAELSDFVGKVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKSDF 61

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           PDL I LNGG++ + Q  + L + DGVM+GR AY N  +L  VD+   +    ++P+ +R
Sbjct: 62  PDLEIVLNGGIKTLDQCGEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---TAPVISR 118

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTA 306
            D         SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+   +  
Sbjct: 119 YDA------LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVDIHKAEN 172

Query: 307 THHIIETAFNLM 318
              +++ A   +
Sbjct: 173 PMLLLDQAAAFL 184


>gi|229095037|ref|ZP_04226033.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-29]
 gi|229113990|ref|ZP_04243416.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-3]
 gi|228669449|gb|EEL24865.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-3]
 gi|228688367|gb|EEL42249.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-29]
          Length = 336

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|218235838|ref|YP_002365163.1| hypothetical protein BCB4264_A0382 [Bacillus cereus B4264]
 gi|218163795|gb|ACK63787.1| conserved hypothetical protein [Bacillus cereus B4264]
 gi|326938108|gb|AEA14004.1| nitrogen regulation protein NIFR3 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 329

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 294 AELRNQL-MSTKSTDEVRALLDKFEDSV 320


>gi|242277846|ref|YP_002989975.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
 gi|242120740|gb|ACS78436.1| dihydrouridine synthase DuS [Desulfovibrio salexigens DSM 2638]
          Length = 348

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 99/234 (42%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK---PLALQIGGA 57
           M   T   +R       +  L +TEM  A A+   + +    FS  E     L  QI GA
Sbjct: 36  MAGLTHSAFRQVLAHYGSCGLAFTEMCSARAVPTENPRISPVFSWHEWELPSLVCQIVGA 95

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  ++V AA+ VE  G+  +++N+GC +  + +   GA L+  P+     + A+ KA+SI
Sbjct: 96  EPEEMVIAAERVEREGFFGVDINMGCSARGMIKREAGAALLKTPEKAVAIVEAVRKAVSI 155

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G   +I       L K ++ +G + +  H R A  K   P           D
Sbjct: 156 PVFVKFRTGWSKEIGPAVA--LAKDLEAAGADCLVFHPRVAPDKRTRPPYI--------D 205

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            +  IKK    + +  NG +        +L     DG+ IGR A     +    
Sbjct: 206 HIRYIKKAV-SIPVFGNGDVTTPQHCQNMLERTGCDGISIGRMAVARPWIFAQW 258


>gi|209447024|ref|NP_001129275.1| tRNA-dihydrouridine synthase 4-like [Rattus norvegicus]
 gi|149051085|gb|EDM03258.1| dihydrouridine synthase 4-like (S. cerevisiae) (predicted) [Rattus
           norvegicus]
          Length = 321

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 125/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA IV  +  + I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALIVCPY-ASGIDINCGCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L + ++ +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDL----ARTIDLCRKVEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK EN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMIK-ENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T +   H H    +++IT
Sbjct: 256 -------TPLKCVWD---WVDIALELGTPFMCFHQHLMYMMEKIT 290


>gi|311033028|ref|ZP_07711118.1| histidine phosphokinase/phophatase, putative [Bacillus sp. m3-13]
          Length = 322

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 128/321 (39%), Gaps = 32/321 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   R      + +TE   +D+    + K      L F+ +E+P+   I G
Sbjct: 19  MEDVTDVVFRTVVRKAGRPDVFFTEFTNSDSYCHPEGKESVRGRLLFTEEEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+  PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVATRGKGSGLIQRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +K I +  +  + IH R              IP    
Sbjct: 138 LPVSVKTRLGFTE---VDEWKEWLKHILEQDIANLSIHLRTRKEMSEVDAHWELIPE--- 191

Query: 177 DIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML-TTVDEY 232
             + E++ +  P+  I +NG + +     ++     +DGVMIGR  +KN         E+
Sbjct: 192 --IKELRDRIAPETLITINGDIPNRQVGQELAEKYDIDGVMIGRGIFKNPFAFEKEAKEH 249

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            S        ++  +   +   +  +M+      LH   K+            GF  +  
Sbjct: 250 TSKEYLDLLRLQLDLQDHYAEIVPRNMSK-----LHRFFKI---------YVKGFRGAGE 295

Query: 293 CRHILTVEAGASTATHHIIET 313
            R+ L +    +     +++ 
Sbjct: 296 LRNQL-MNTKTTDEVRALLDE 315


>gi|169154846|emb|CAQ15427.1| dihydrouridine synthase 1-like (S. cerevisiae) [Danio rerio]
          Length = 496

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 105/265 (39%), Gaps = 32/265 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R             + +++PL  Q   
Sbjct: 41  MVDQSELAWRLLSRR-HGAELCYTPMLHAQVFVRDANYRRENLYSEVNQEDRPLITQFCA 99

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    ++AA + +D+  + I+LN+GCP      G +G  L    D++   I    + LS
Sbjct: 100 NDPEVFIQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGVFLQDEWDLLEKMIKLANEKLS 158

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+T K R+  + +          K ++K+G   + +H R    KG             +
Sbjct: 159 VPITCKIRVFPEIEKTV----KYAKMLEKAGCQLLTVHGRTKDQKGA------LTGIASW 208

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +  + +E  ++ +  NG ++   D+   ++    V GVM       N A+        
Sbjct: 209 KHIKAV-REAVNIPVFANGNIQHLSDVHHCMEE-TGVQGVMSAEGNLHNPALF------- 259

Query: 234 SNPLTGSSPIKTRVDKDFWRKISAS 258
                G SP    + +++   +   
Sbjct: 260 ----EGRSPPVWEMAEEYLDIVEKH 280


>gi|126207791|ref|YP_001053016.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           L20]
 gi|126096583|gb|ABN73411.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 320

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 13  MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 73  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 132

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    +     +  ++ + G N I +H R         +D  +
Sbjct: 133 EAVPQDQIVSVKVRLGWDSADQSF---EIADAVAQGGANEITVHGRTK-------QDGYR 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 183 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 238

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 239 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 287

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 288 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 318


>gi|304390914|ref|ZP_07372866.1| possible dihydrouridine synthase [Mobiluncus curtisii subsp.
           curtisii ATCC 35241]
 gi|315656297|ref|ZP_07909188.1| dihydrouridine synthase [Mobiluncus curtisii subsp. holmesii ATCC
           35242]
 gi|304325797|gb|EFL93043.1| possible dihydrouridine synthase [Mobiluncus curtisii subsp.
           curtisii ATCC 35241]
 gi|315493299|gb|EFU82899.1| dihydrouridine synthase [Mobiluncus curtisii subsp. holmesii ATCC
           35242]
          Length = 438

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 59/349 (16%), Positives = 119/349 (34%), Gaps = 54/349 (15%)

Query: 1   MVDWTDRHYRFFARLLTN-----------------------NALLYTEMIVADAILRGDK 37
           M   T+  +R      +                          +   EMI A A++    
Sbjct: 29  MAGVTNAPFRDLCAAFSRQGLPSESDSSLRRDGETGAFRSVEGMFVNEMITAKALMMNST 88

Query: 38  KN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFG 94
           ++  +      +    LQ+ G   + L  AA+ ++     + I+LN GCP  +V     G
Sbjct: 89  RSWVMAQSGPGQTVRVLQLYGVVGADLAWAARELIARDLVDVIDLNFGCPVPKVTRKGGG 148

Query: 95  ACLMLNP----DIVGDCI-------AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           A L        D++G  +        A  + + +PVTVK R+G+D+      + +  ++ 
Sbjct: 149 AALPWKTAYFGDLIGQVVQAAQESSQAARREVEVPVTVKIRVGIDE--SHETMLDAGRAA 206

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           + +G   + +HAR          +     + D+  + ++     D+ +  NG +   S A
Sbjct: 207 QDAGAAALTLHARTT--------NQYYSGHSDWSRIGQLVN-TLDIPVLGNGDVFSASDA 257

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           L++       G+ IGRA      +   +          + P    + +         +  
Sbjct: 258 LEMFAQTGCAGIEIGRAVQGRPWIFREITAALWGQPIPAGPTLGEIVEVIRAHACGLVEH 317

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHI 310
           +     +    L+ + +H+     GF      R  LT           +
Sbjct: 318 FG----NEKAALRDMRKHVGWYLRGFHLGGDTRAELTRVETLDDLERRL 362


>gi|229171166|ref|ZP_04298760.1| tRNA-dihydrouridine synthase [Bacillus cereus MM3]
 gi|228612344|gb|EEK69572.1| tRNA-dihydrouridine synthase [Bacillus cereus MM3]
          Length = 336

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R       +  + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGSPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEEWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|307247299|ref|ZP_07529347.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307251840|ref|ZP_07533741.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306856143|gb|EFM88298.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306860532|gb|EFM92544.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 313

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 6   MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 66  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 125

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    +     +  ++ + G N I +H R         +D  +
Sbjct: 126 EAVPSDQIVSVKVRLGWDSADQSF---EIADAVAQGGANEITVHGRTK-------QDGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 176 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 231

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 232 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 280

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 281 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 311


>gi|149174914|ref|ZP_01853538.1| hypothetical protein PM8797T_11079 [Planctomyces maris DSM 8797]
 gi|148846251|gb|EDL60590.1| hypothetical protein PM8797T_11079 [Planctomyces maris DSM 8797]
          Length = 355

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 55/284 (19%), Positives = 115/284 (40%), Gaps = 23/284 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGADI 59
            ++D   R  A  L   A    E+++   I++   G + +++     E P+  Q+ G++ 
Sbjct: 27  GYSDYPMRVIAARL-GAAYTLCEVMIDRMIIQTKQGKQHSMMYCHQDEFPVGGQLMGSEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--I 117
            +   AA+ + + G++ I++N GCP  +V     G   +  P++  D I+ +   +   I
Sbjct: 86  EEFGPAARRLVEAGFHVIDINFGCPVKKVMSRCRGGYHLSQPEVALDIISRVRDTVPAEI 145

Query: 118 PVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PVT+K R G+DD    A     +       G++ I +H R          D + +   ++
Sbjct: 146 PVTLKMRRGIDDSSESADNFFMIFDGAYARGLSAITVHGRT--------VDQKYVGPSNW 197

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + + ++K+   +  +  +G L      L +L    VDGV I R A  N  +     +   
Sbjct: 198 EFLKQVKQHAGEKTVIGSGDLFSPQSCLDMLRVTGVDGVSIARGAIGNPWIFQQTADLLR 257

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                   +  +      R++ ++  + A            + +
Sbjct: 258 GKSISPPDVTEQ------REVISAHFELAREFYGDKKVCNTMRK 295


>gi|15645347|ref|NP_207521.1| transcriptional regulator, putative [Helicobacter pylori 26695]
 gi|39930813|sp|O25427|DUS_HELPY RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|2313849|gb|AAD07774.1| transcriptional regulator, putative [Helicobacter pylori 26695]
          Length = 328

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      N I+ N GCP+ +V     G+ L+ + + +   +  + +  S  
Sbjct: 74  SVVKEAVEKINALEHVNGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTSKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYGDM-----GVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|19074582|ref|NP_586088.1| similarity to HYPOTHETICAL PROTEIN YM10_yeast [Encephalitozoon
           cuniculi GB-M1]
 gi|19069224|emb|CAD25692.1| similarity to HYPOTHETICAL PROTEIN YM10_yeast [Encephalitozoon
           cuniculi GB-M1]
          Length = 341

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 105/237 (44%), Gaps = 19/237 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           MV  ++  +R  ++      + YTEM+  D+ LRG +          S  ++PL +QI G
Sbjct: 18  MVGNSEEAWRRLSKR-HGANIFYTEMVHCDSFLRGSRNPVKNRWYTTSEGDRPLVVQICG 76

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                ++EAA I++D   + I++N GCP     +G +GA L  N  + G+ +  +   L+
Sbjct: 77  NSPEVMLEAALIIQDH-CDAIDVNFGCPQKVARKGGYGAYLQENWKLTGEIVKVLSSGLN 135

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV  K R+               K I+++G + + +H R    +G +      +    +
Sbjct: 136 VPVFCKIRVF----GSIEKTVEYAKMIEEAGCSLLAVHGRTRDQRGAA------MGFASW 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             +  IK EN  + +  NG +       + L     DGVM+G A   N  + T  D 
Sbjct: 186 KHIRAIK-ENLRIPVLSNGNIMTHHDVWRCLEYTGCDGVMVGEAHLHNPLIFTGEDR 241


>gi|303278204|ref|XP_003058395.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459555|gb|EEH56850.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 440

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 73/306 (23%), Positives = 121/306 (39%), Gaps = 23/306 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE----KPLALQIGG 56
           MVD ++  +R   R      L YT MI A   +   K     F+T E    +PL +Q   
Sbjct: 54  MVDQSELAFRTLCRRY-GATLAYTPMIHARLFVEDLKYRAEIFTTVEGIADRPLLVQFCA 112

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D + L+ AAK+V     + +++N GCP     +G +GA LM +   V D I+ + K LS
Sbjct: 113 NDPATLLAAAKLVAPH-CDGVDINFGCPQRIAKKGRYGAFLMDDWKTVHDLISILDKELS 171

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  D +          + ++ +G   + IH R    K  S          ++
Sbjct: 172 VPVTAKIRVYDDLETS----IQYAEMVQNAGAQLVAIHGRTREQKRASDV------RANW 221

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  IK E   + +  NG +  +++A K L     DGVM      +N ++ +      +
Sbjct: 222 AFIKAIK-ERLTVPVIANGDVRTLAEARKCLEATGADGVMSADPLLENPSLFSDPPFAPT 280

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
             L    PI+   +     +           H      ++     M+G +         R
Sbjct: 281 RDLANPLPIEGDANCRLLMEYLDITQ--LPGHHTPLRMIKAHVFKMVGHW--LAEFTDLR 336

Query: 295 HILTVE 300
             L  E
Sbjct: 337 DWLNRE 342


>gi|109947333|ref|YP_664561.1| putative transcriptional regulator [Helicobacter acinonychis str.
           Sheeba]
 gi|109714554|emb|CAJ99562.1| putative transcriptional regulator [Helicobacter acinonychis str.
           Sheeba]
          Length = 328

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 134/322 (41%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  ST E    +QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSTLEDHFMVQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  + P
Sbjct: 74  SVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKVIRENTNKP 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + ++ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPIDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  + KE     +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIA-LMKEILKKPVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|46143827|ref|ZP_00133954.2| COG0042: tRNA-dihydrouridine synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307249523|ref|ZP_07531510.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306858378|gb|EFM90447.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 313

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 6   MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 66  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 125

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    +     +  ++ + G N I +H R         +D  +
Sbjct: 126 EAVPQDQIVSVKVRLGWDSADQSF---EIADAVAQGGANEITVHGRTK-------QDGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 176 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 231

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 232 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 280

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 281 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 311


>gi|190149581|ref|YP_001968106.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|189914712|gb|ACE60964.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
          Length = 320

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 72/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 13  MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 73  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 132

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++ + G N I +H R         +D  +
Sbjct: 133 EAVPQDQIVSVKVRLGWD---SADQCFEIADAVAQGGANEITVHGRTK-------QDGYR 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 183 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNATACSSLMIGRGALNTPNL--- 238

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 239 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 287

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 288 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 318


>gi|229068075|ref|ZP_04201383.1| tRNA-dihydrouridine synthase [Bacillus cereus F65185]
 gi|229077679|ref|ZP_04210309.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock4-2]
 gi|228705620|gb|EEL57976.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock4-2]
 gi|228715083|gb|EEL66950.1| tRNA-dihydrouridine synthase [Bacillus cereus F65185]
          Length = 336

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 133/331 (40%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++   + + E+
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSVGEA 330


>gi|258544513|ref|ZP_05704747.1| tRNA-dihydrouridine synthase B [Cardiobacterium hominis ATCC 15826]
 gi|258520248|gb|EEV89107.1| tRNA-dihydrouridine synthase B [Cardiobacterium hominis ATCC 15826]
          Length = 314

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 74/311 (23%), Positives = 125/311 (40%), Gaps = 29/311 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA--ILRGDKKNILGFSTQEK-PLALQIGGA 57
           M   +D  +R   +          EMI A    +        L F    + P  +Q+ G 
Sbjct: 20  MAGVSDLPFRRLCQQ-NGADYSTAEMISAKPELLHTAYSAARLQFDLDPRYPKIVQLVGG 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D + L EAA +++  G + I+LN+GCP+  V +   G+ L+ +   V   +AA+ +A++I
Sbjct: 79  DAALLAEAALLMQAKGADIIDLNMGCPAKTVAKQQAGSALLADLRQVEKILAAVVRAVNI 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G  D  P +A   + +  +  G+  + +H R         +  R     DY 
Sbjct: 139 PVTLKTRLGYHDGEPVIA--EVARIAEACGIAALAVHGRS--------RAQRYQGEADYA 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                 K    L +  NG ++   QA  +L     DG+MIGRAA  +  +        + 
Sbjct: 189 T-IAAAKAKTRLPVIANGDIKSAEQAKTLLDRYGFDGIMIGRAALGDPWLFARCQALING 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI-TRHMIGLFHGFPNSRRCR 294
               ++   T        +I A + D    H H G +   I  +H+       P+    R
Sbjct: 248 RDIPAAAKNT--------QIRAHLRDL---HQHYGAQATAIARKHLHAYLRPHPDYPALR 296

Query: 295 HILTVEAGAST 305
             +   A    
Sbjct: 297 PAINHAAHLDA 307


>gi|307245120|ref|ZP_07527213.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307254076|ref|ZP_07535923.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307258531|ref|ZP_07540268.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306854009|gb|EFM86221.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306863001|gb|EFM94948.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306867435|gb|EFM99286.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 313

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 6   MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 66  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 125

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    +     +  ++ + G N I +H R         +D  +
Sbjct: 126 EAVPQDQIVSVKVRLGWDSADQSF---EIADAVAQGGANEITVHGRTK-------QDGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 176 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 231

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 232 -----------SRVVKFNQPKIAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 280

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 281 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 311


>gi|229028175|ref|ZP_04184316.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1271]
 gi|228733123|gb|EEL83964.1| tRNA-dihydrouridine synthase [Bacillus cereus AH1271]
          Length = 336

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDIPDRKVGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLNLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|145351179|ref|XP_001419962.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580195|gb|ABO98255.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 361

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 55/283 (19%), Positives = 105/283 (37%), Gaps = 26/283 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM +A  +L+GD+K   +L     EK   +Q+ G     + 
Sbjct: 20  NLPFRRVCTDL-GADITVSEMAMASNLLKGDRKEWALLRRHPSEKCYGIQVCGGYPDLMA 78

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++  +   + I++N+GCP   V     G+ LM + D + + +  M    S PVT+K
Sbjct: 79  RCAELIDNEVSCDFIDVNMGCPIDGVCAKGAGSSLMRDTDRLKNVVRTMAAVSSTPVTIK 138

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G  D        +++   K  G     +H R         ++ R     D+  ++  
Sbjct: 139 LRMGYFDDPSKYVAHDIIPRAKAWGAFAATLHGRT--------REQRYSRLADWSYIHRC 190

Query: 183 --KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
                  +  +  NG +         +    V   MIGR A     ++T + E     ++
Sbjct: 191 ADVAAKSEFTLIGNGDVYTYEDYNAQVADNKVATCMIGRGAIIKPWLMTEIKEQRHWDIS 250

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +  +           +      Y   H  S     + TR  +
Sbjct: 251 ANERL----------DLFKDFCQYGLEHWGSDSMGVEKTRRYL 283


>gi|270158229|ref|ZP_06186886.1| putative tRNA-dihydrouridine synthase [Legionella longbeachae
           D-4968]
 gi|289163514|ref|YP_003453652.1| tRNA-dihydrouridine synthase B [Legionella longbeachae NSW150]
 gi|269990254|gb|EEZ96508.1| putative tRNA-dihydrouridine synthase [Legionella longbeachae
           D-4968]
 gi|288856687|emb|CBJ10498.1| putative tRNA-dihydrouridine synthase B [Legionella longbeachae
           NSW150]
          Length = 319

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 101/232 (43%), Gaps = 18/232 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             ++   +R         A   TEM  A  IL    +    +  + +E+ LA Q+ G + 
Sbjct: 26  AGYSCAPFRTLFHNYRPPAYCVTEMSSAIDILYKHSRSSRYIYRAPEEQILAYQLAGTEP 85

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L +AA+ ++ +G + I++N GCP  ++ +   G+ L+  PD +   +  +  A++IP+
Sbjct: 86  HLLAQAAQNLQRYGADIIDINCGCPKPKIRKKGAGSALLEAPDQLVKIVKEVRAAITIPL 145

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RI  ++Q        L K I+++G + + +H R+ +       D  +I        
Sbjct: 146 TVKIRIQGNEQDFI-----LAKKIQEAGADALIVHGRRWMDDYEVTPDLHQI-------- 192

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTV 229
               K+   + +  NG + D+    K   L   D  MI RA      +   +
Sbjct: 193 -ACIKQRLVIPVIANGDIHDLDSLKKTIALSGCDAYMISRAGSGKPWLYQEL 243


>gi|225427796|ref|XP_002275411.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 692

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 108/287 (37%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   ++L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 351 NLPFRRVCKML-GADVTCGEMAMCTNLLQGQASEWALLRRHSAEDLFGVQICGAYPDTVA 409

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++ ++   + I++N+GCP   V     G+ L+  P  + + I A    +  P+TVK
Sbjct: 410 RTVELIDQECEVDFIDINMGCPIDIVVNKGAGSALLTKPMRMKNIIEAASGIVDKPITVK 469

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +    V   +L+  I + G N + IH R         +  R     D++ +Y+ 
Sbjct: 470 VRTGFLEGRNRV--DSLIADIGQWGANVVTIHGRS--------RQQRYSKLADWEYIYQC 519

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSV---DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ P+ L +  NG +       K           MI R A     + T + E     ++
Sbjct: 520 ARKAPEALQVLGNGDIFSYLDWNKHKSGCPELSTCMIARGALVKPWIFTEIKEQRHWDIS 579

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
               +           I          H  S  K  + TRH +   L
Sbjct: 580 SGERLN----------ILKDYVRCGLEHWGSDTKGVETTRHFMLEWL 616


>gi|222628527|gb|EEE60659.1| hypothetical protein OsJ_14110 [Oryza sativa Japonica Group]
          Length = 257

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 82/180 (45%), Positives = 115/180 (63%), Gaps = 4/180 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 70  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 129

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V     FGA LM +P+ VGD ++A+    ++
Sbjct: 130 LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 189

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           PV+VKCRIGVDD+     L   V   + KS      IHARKA+L GLSP +NR +P L Y
Sbjct: 190 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRNVPPLKY 249


>gi|15923079|ref|NP_370613.1| hypothetical protein SAV0089 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15925793|ref|NP_373326.1| hypothetical protein SA0085 [Staphylococcus aureus subsp. aureus
           N315]
 gi|148266519|ref|YP_001245462.1| hypothetical protein SaurJH9_0077 [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150392555|ref|YP_001315230.1| hypothetical protein SaurJH1_0079 [Staphylococcus aureus subsp.
           aureus JH1]
 gi|156978419|ref|YP_001440678.1| hypothetical protein SAHV_0088 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253733809|ref|ZP_04867974.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|254664018|ref|ZP_05143490.1| hypothetical protein SauraM_00430 [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257794441|ref|ZP_05643420.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9781]
 gi|258407597|ref|ZP_05680733.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9763]
 gi|258419873|ref|ZP_05682835.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9719]
 gi|258438612|ref|ZP_05689835.1| dihydrouridine synthase DuS [Staphylococcus aureus A9299]
 gi|258443931|ref|ZP_05692269.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|258445131|ref|ZP_05693368.1| dihydrouridine synthase DuS [Staphylococcus aureus A6300]
 gi|258447736|ref|ZP_05695875.1| dihydrouridine synthase [Staphylococcus aureus A6224]
 gi|258455641|ref|ZP_05703596.1| dihydrouridine synthase DuS [Staphylococcus aureus A5937]
 gi|282894311|ref|ZP_06302541.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8117]
 gi|282928341|ref|ZP_06335944.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A10102]
 gi|295405362|ref|ZP_06815172.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8819]
 gi|297244698|ref|ZP_06928578.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8796]
 gi|54037013|sp|P67717|DUS_STAAN RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|54040779|sp|P67716|DUS_STAAM RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|13700005|dbj|BAB41304.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14245856|dbj|BAB56251.1| probable dehydrogenases, nifR3 family [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|147739588|gb|ABQ47886.1| dihydrouridine synthase, DuS [Staphylococcus aureus subsp. aureus
           JH9]
 gi|149945007|gb|ABR50943.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           JH1]
 gi|156720554|dbj|BAF76971.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|253728112|gb|EES96841.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257788413|gb|EEV26753.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9781]
 gi|257840822|gb|EEV65279.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9763]
 gi|257844155|gb|EEV68542.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9719]
 gi|257848171|gb|EEV72163.1| dihydrouridine synthase DuS [Staphylococcus aureus A9299]
 gi|257850815|gb|EEV74759.1| conserved hypothetical protein [Staphylococcus aureus A8115]
 gi|257856039|gb|EEV78958.1| dihydrouridine synthase DuS [Staphylococcus aureus A6300]
 gi|257859018|gb|EEV81882.1| dihydrouridine synthase [Staphylococcus aureus A6224]
 gi|257861853|gb|EEV84626.1| dihydrouridine synthase DuS [Staphylococcus aureus A5937]
 gi|282589925|gb|EFB95008.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A10102]
 gi|282763356|gb|EFC03486.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8117]
 gi|285815814|gb|ADC36301.1| tRNA dihydrouridine synthase B [Staphylococcus aureus 04-02981]
 gi|294969437|gb|EFG45456.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8819]
 gi|297178215|gb|EFH37462.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A8796]
 gi|312828608|emb|CBX33450.1| dihydrouridine synthase (Dus) family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315129069|gb|EFT85065.1| hypothetical protein CGSSa03_13652 [Staphylococcus aureus subsp.
           aureus CGS03]
          Length = 328

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEHPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|328873275|gb|EGG21642.1| tRNA-dihydrouridine synthase 1-like protein [Dictyostelium
           fasciculatum]
          Length = 426

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 62/277 (22%), Positives = 120/277 (43%), Gaps = 17/277 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFSTQEKPLALQIGGADI 59
           MV+ +   +R   R      ++YT M  +               + Q++P+ +Q  G ++
Sbjct: 61  MVEHSLLAFRLLTRKF-GADVVYTPMYNSKIFSHDATYRCNFSTNPQDRPMVVQFCGNEV 119

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +V++AK+VED   + +++N+GCP     +G +GA L+  PDIV   + A+ K L +P+
Sbjct: 120 DHIVKSAKMVEDH-CDAVDINLGCPQGIARKGFYGAFLLERPDIVLPMVRALHKELKVPI 178

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
             K R+  D          L   ++++G   + +H R    KG        + + D+  +
Sbjct: 179 FCKIRLLPDIDDT----IKLALQLQEAGCQLLTVHGRTKEQKG------EFLCHADWKAI 228

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   + +  NG +++    +  L     DGVM       N AM + +D   ++  
Sbjct: 229 RRVK-EAVSIPVFANGSVDEYKDIVPCLEESGADGVMSADGILANPAMFSGLDMTLTDVC 287

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                I  ++  DF+  I +       RH+     ++
Sbjct: 288 REYLDICDQIPTDFFL-IRSHCYKMLKRHMDDYEDIR 323


>gi|257886417|ref|ZP_05666070.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822273|gb|EEV49403.1| dihydrouridine synthase [Enterococcus faecium 1,231,501]
          Length = 327

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 125/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L  +  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTITEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  KA  
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFKNPYAFEKDPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I++T
Sbjct: 297 RVQL-MNTKSTDEVREILDT 315


>gi|224094282|ref|XP_002310123.1| predicted protein [Populus trichocarpa]
 gi|222853026|gb|EEE90573.1| predicted protein [Populus trichocarpa]
          Length = 358

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/279 (21%), Positives = 112/279 (40%), Gaps = 17/279 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 91  MVDNSELPFRMLCRKYGAEA-AYTPMLHSRIFSENEKYRREEFTTCKEDRPLFVQFCAND 149

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AA+ VE +  + +++N+GCP      G +GA LM N  +V   +  +   L++P
Sbjct: 150 PDILLQAARRVEPY-CDYVDINLGCPQRIARRGYYGAFLMDNLLLVKSLVEKLAINLNVP 208

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+    +       N  + ++++G + + +H R         KD +K    D+  
Sbjct: 209 VSCKIRVFPKLEDT----INYARMLEEAGCSLLAVHGRT-----RDEKDGKKF-RADWKA 258

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + +  NG +  M      L     DGV+      +N A+           
Sbjct: 259 IKAVKSAL-RIPVLANGNIRHMDDVKTCLEETGTDGVLSAETLLENPALFAGFRTAEWAD 317

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           L              WR I + +            ++++
Sbjct: 318 LLVEYLKFCERHPVPWRMIRSHVHKMLGEWFRIHPQVRE 356


>gi|317127197|ref|YP_004093479.1| dihydrouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315472145|gb|ADU28748.1| dihydrouridine synthase DuS [Bacillus cellulosilyticus DSM 2522]
          Length = 323

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 119/307 (38%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++          K  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSAAARPDVFFTEFANSESYCHPEGNKSVKGRLTFTDDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPENFRKMSIGMAEQGFKGLDINMGCPVPNVARHGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFTELD---EWREWLTHILKQDIANLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDGVMIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDILDRQTGLKLANQYGVDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   D  R        Y+   L     L +  +       GFP +
Sbjct: 243 ------EKEPREHSSKELLDLLRLHMDLHDKYSGLELRPFKALHRFFKI---YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 SGLRNHL 300


>gi|317177444|dbj|BAJ55233.1| transcriptional regulator [Helicobacter pylori F16]
          Length = 328

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 132/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S+ E    +QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSSLEDHFMVQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ I +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYIVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIK----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|228937614|ref|ZP_04100252.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228970501|ref|ZP_04131152.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977070|ref|ZP_04137473.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis Bt407]
 gi|228782687|gb|EEM30862.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis Bt407]
 gi|228789233|gb|EEM37161.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228822095|gb|EEM68085.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 336

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSV 327


>gi|229101138|ref|ZP_04231904.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-28]
 gi|228682266|gb|EEL36377.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-28]
          Length = 336

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 74/333 (22%), Positives = 130/333 (39%), Gaps = 37/333 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R       +  + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGSPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEEWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGAST--ATHHIIETAFNLMIES 321
              R+ L          A     E + N++  S
Sbjct: 301 AELRNQLMSTKSTDEVRALLDKFEASVNVVESS 333


>gi|254567437|ref|XP_002490829.1| tRNA-dihydrouridine synthase 1 [Pichia pastoris GS115]
 gi|238030625|emb|CAY68549.1| tRNA-dihydrouridine synthase 1 [Pichia pastoris GS115]
 gi|328351211|emb|CCA37611.1| tRNA-dihydrouridine synthase 1 [Pichia pastoris CBS 7435]
          Length = 407

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 117/274 (42%), Gaps = 26/274 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQ-EKPLALQI 54
           MVD ++  +R  +R      L YT M  A         R D  + L    + ++PL +Q 
Sbjct: 26  MVDQSELAWRILSRRY-GADLCYTPMFHAKLFATQEKYRKDMMSELDGDEKVDRPLIVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AA++V D   + ++LN+GCP     +G++G+ LM +  +V   I  + + 
Sbjct: 85  CANDPEYLLQAARLVAD-KCDAVDLNLGCPQGIAKKGNYGSFLMDDWKLVHRLIKHLHEN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           LSIPVT K R+  D +          K +  +G   + IH R   +KG      ++    
Sbjct: 144 LSIPVTAKIRVYDDKEKS----LEYAKMVLDAGAQFLTIHGRTREMKG------QQTGLA 193

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDE 231
           +++ +  I+   P D     NG +       + L  V  D VM       N  +  T  E
Sbjct: 194 NWETLKYIRDNLPDDTVFFANGNILYSDDLGRCLEKVNADAVMSAEGNLFNPGVFWTATE 253

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
                     P   R+ ++++ ++  +   YA+R
Sbjct: 254 DKEKQF----PRLDRIVREYF-EVLKTTPGYASR 282


>gi|149055089|gb|EDM06906.1| PP3111 protein, isoform CRA_b [Rattus norvegicus]
 gi|149055090|gb|EDM06907.1| PP3111 protein, isoform CRA_b [Rattus norvegicus]
          Length = 326

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/281 (20%), Positives = 102/281 (36%), Gaps = 29/281 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGRYGAFLQEEWDLLQRMILLAHERLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PMAGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT------ 228
           + +  ++K    + +  NG +  +    + +    V GVM       N A+         
Sbjct: 192 EHIKAVRKAVG-IPVFANGNIRCLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVW 250

Query: 229 --VDEYFSNPLTGSSPIKTRVDKDF--WRKISASMTDYAAR 265
              DEY         P+       F  W             
Sbjct: 251 ELADEYLDIVRQHPCPLSYVRAHLFKLWHHTLQVHQQLREE 291


>gi|307262900|ref|ZP_07544524.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|306871805|gb|EFN03525.1| tRNA-dihydrouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 313

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 72/332 (21%), Positives = 124/332 (37%), Gaps = 41/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     + +  L  +E +          A  R   + + G  +    P+ +
Sbjct: 6   MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRRAPELLQGGLTDSGTPVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   ++LN GCPS  V+  + GA L+ +PD++     AM 
Sbjct: 66  QLLGQHPQWLAENARLAIELGSQGVDLNCGCPSKTVNGSNGGASLLKDPDLIYRATKAMR 125

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++ + G N I +H R         +D  +
Sbjct: 126 EAVPQDQIVSVKVRLGWD---SADQCFEIADAVAQGGANEITVHGRTK-------QDGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 176 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNATACSSLMIGRGALNTPNL--- 231

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 232 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 280

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
            +P ++    IL  E G      H IE A N 
Sbjct: 281 EYPQAKDLFQILKTEHGYDGLKTH-IERAVNQ 311


>gi|30260504|ref|NP_842881.1| hypothetical protein BA_0334 [Bacillus anthracis str. Ames]
 gi|47525601|ref|YP_016950.1| hypothetical protein GBAA_0334 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49183347|ref|YP_026599.1| hypothetical protein BAS0319 [Bacillus anthracis str. Sterne]
 gi|165871396|ref|ZP_02216044.1| conserved hypothetical protein [Bacillus anthracis str. A0488]
 gi|167640100|ref|ZP_02398367.1| conserved hypothetical protein [Bacillus anthracis str. A0193]
 gi|170688341|ref|ZP_02879550.1| conserved hypothetical protein [Bacillus anthracis str. A0465]
 gi|170708765|ref|ZP_02899202.1| conserved hypothetical protein [Bacillus anthracis str. A0389]
 gi|190567484|ref|ZP_03020397.1| conserved hypothetical protein [Bacillus anthracis Tsiankovskii-I]
 gi|227812999|ref|YP_002813008.1| hypothetical protein BAMEG_0394 [Bacillus anthracis str. CDC 684]
 gi|229602511|ref|YP_002864949.1| hypothetical protein BAA_0391 [Bacillus anthracis str. A0248]
 gi|254686718|ref|ZP_05150576.1| hypothetical protein BantC_23150 [Bacillus anthracis str.
           CNEVA-9066]
 gi|254724794|ref|ZP_05186577.1| hypothetical protein BantA1_20374 [Bacillus anthracis str. A1055]
 gi|254739057|ref|ZP_05196759.1| hypothetical protein BantWNA_28205 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254742322|ref|ZP_05200008.1| hypothetical protein BantKB_15138 [Bacillus anthracis str. Kruger
           B]
 gi|254756097|ref|ZP_05208126.1| hypothetical protein BantV_26846 [Bacillus anthracis str. Vollum]
 gi|254761915|ref|ZP_05213764.1| hypothetical protein BantA9_25851 [Bacillus anthracis str.
           Australia 94]
 gi|30253872|gb|AAP24367.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
 gi|47500749|gb|AAT29425.1| conserved hypothetical protein [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49177274|gb|AAT52650.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
 gi|164712880|gb|EDR18409.1| conserved hypothetical protein [Bacillus anthracis str. A0488]
 gi|167511911|gb|EDR87290.1| conserved hypothetical protein [Bacillus anthracis str. A0193]
 gi|170126344|gb|EDS95234.1| conserved hypothetical protein [Bacillus anthracis str. A0389]
 gi|170667673|gb|EDT18427.1| conserved hypothetical protein [Bacillus anthracis str. A0465]
 gi|190561271|gb|EDV15243.1| conserved hypothetical protein [Bacillus anthracis Tsiankovskii-I]
 gi|227003040|gb|ACP12783.1| conserved hypothetical protein [Bacillus anthracis str. CDC 684]
 gi|229266919|gb|ACQ48556.1| conserved hypothetical protein [Bacillus anthracis str. A0248]
          Length = 329

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 131/332 (39%), Gaps = 40/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+ L      ST +   +    N   ES+
Sbjct: 294 AELRNQLM-----STKSTDEVRALLNKFEESV 320


>gi|195156385|ref|XP_002019081.1| GL26174 [Drosophila persimilis]
 gi|194115234|gb|EDW37277.1| GL26174 [Drosophila persimilis]
          Length = 577

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 114/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM  A  +L+G   +  +      E    +Q+ G + + + 
Sbjct: 242 NLPFRRICKEL-GADITCGEMACAVPLLKGLGQEWALTKRHESEDIFGVQLCGNNPNVIT 300

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++++    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 301 QAAQVLQETAKVDYIDLNIGCPIDLIYQQGGGSALMRRTNILELVVRSCSSLSEQLPFTV 360

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           LV  +++ G + + +H R         ++ R   + +++ + +
Sbjct: 361 KMRTGIYADKSVA--HELVPLVEEWGASAVTLHGRS--------REQRYTKHANWEYIEQ 410

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
                  + I  NG +      ++     P V  VMIGR A     +   + +  +   T
Sbjct: 411 CAATAKQMPIIGNGDILSYEDYVERRALAPHVSSVMIGRGALIKPWIFQEIKQQKAWSPT 470

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 471 STQRF----------EMLRRYCNYGLEHWGSDTKGVESTRRFLLEWQSF 509


>gi|297744713|emb|CBI37975.3| unnamed protein product [Vitis vinifera]
          Length = 678

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 108/287 (37%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   ++L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 337 NLPFRRVCKML-GADVTCGEMAMCTNLLQGQASEWALLRRHSAEDLFGVQICGAYPDTVA 395

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++ ++   + I++N+GCP   V     G+ L+  P  + + I A    +  P+TVK
Sbjct: 396 RTVELIDQECEVDFIDINMGCPIDIVVNKGAGSALLTKPMRMKNIIEAASGIVDKPITVK 455

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +    V   +L+  I + G N + IH R         +  R     D++ +Y+ 
Sbjct: 456 VRTGFLEGRNRV--DSLIADIGQWGANVVTIHGRS--------RQQRYSKLADWEYIYQC 505

Query: 183 KKENPD-LFIGLNGGLEDMSQALKILPSV---DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ P+ L +  NG +       K           MI R A     + T + E     ++
Sbjct: 506 ARKAPEALQVLGNGDIFSYLDWNKHKSGCPELSTCMIARGALVKPWIFTEIKEQRHWDIS 565

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
               +           I          H  S  K  + TRH +   L
Sbjct: 566 SGERLN----------ILKDYVRCGLEHWGSDTKGVETTRHFMLEWL 602


>gi|282902679|ref|ZP_06310572.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus C160]
 gi|282921360|ref|ZP_06329078.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|283767833|ref|ZP_06340748.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           H19]
 gi|282315775|gb|EFB46159.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282597138|gb|EFC02097.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus C160]
 gi|283461712|gb|EFC08796.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           H19]
 gi|302331835|gb|ADL22028.1| tRNA dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           JKD6159]
          Length = 328

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|110808216|sp|Q32M08|DUS4L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 4-like
 gi|80478497|gb|AAI09352.1| Dihydrouridine synthase 4-like (S. cerevisiae) [Mus musculus]
          Length = 324

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 124/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MI+A   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALLVCPY-ANGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDL----ARTIDLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK EN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMIK-ENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLANPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 290


>gi|51011069|ref|NP_001003490.1| tRNA-dihydrouridine synthase 4-like [Danio rerio]
 gi|50417946|gb|AAH78413.1| Zgc:92033 [Danio rerio]
          Length = 285

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 124/284 (43%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+A   +R  K     F+T   ++PL +Q    D
Sbjct: 1   MVRYSKLAFRSLVRKYD-CDVCFTPMIIAADFMRSAKARDSEFTTNKNDRPLIVQFAAKD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 60  AQTLADAACVVSPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQIDNP 118

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L + ++ +GV+ I +H R AI +            + 
Sbjct: 119 NYAVSIKIRIHKDVRQTV----DLCQKVEAAGVSYITVHGRTAIERHQ---------PVH 165

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK ++  + +  NG ++ M    A+  L  VDGVM  R    N AM +  +E  
Sbjct: 166 YDTIKTIK-DSLSIPVIANGDIKSMQDVEAVCELTGVDGVMSARGLLSNPAMFSGFEE-- 222

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +   D+    +   T +   H H    L++IT
Sbjct: 223 ---------TPLQCVWDWVDIAAEHGTPFTCFHHHLIHMLERIT 257


>gi|91092412|ref|XP_967539.1| PREDICTED: similar to t-diRNAhydrouridine synthase [Tribolium
           castaneum]
 gi|270004747|gb|EFA01195.1| hypothetical protein TcasGA2_TC010522 [Tribolium castaneum]
          Length = 461

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 95/230 (41%), Gaps = 17/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M+ +    R  K     L     +KPL +Q  G D
Sbjct: 18  MVDASELPWRLLSRKY-GAQLCYTPMLHSAIFARDAKYRNEALASCEIDKPLIVQFCGND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++EAA + +D     I++N+GCP A    G +GA L     ++ + ++ + + L +P
Sbjct: 77  PKVMLEAALLAQDHCCA-IDINLGCPQAIAKRGHYGAFLQDEWPLLHEIVSLLSQRLKVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R             +  K +  +G   + +H R    KG            D+  
Sbjct: 136 ITCKVRRF----ESVEKTVDYAKMLVSAGCKMLTVHGRTREQKG------PLTGLADWSY 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           V  + +E  D+ +  NG ++ M    + L      GVM       N A+ 
Sbjct: 186 VKAV-REAVDIPVISNGNIQCMQDVDRCLEETGAVGVMTAEGNLYNPALF 234


>gi|49482339|ref|YP_039563.1| hypothetical protein SAR0099 [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257424237|ref|ZP_05600666.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257426913|ref|ZP_05603315.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257429551|ref|ZP_05605938.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257432197|ref|ZP_05608560.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257435157|ref|ZP_05611208.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282907090|ref|ZP_06314938.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282910084|ref|ZP_06317892.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282912336|ref|ZP_06320132.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282912954|ref|ZP_06320746.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M899]
 gi|282922580|ref|ZP_06330270.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C101]
 gi|283959546|ref|ZP_06376987.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|293498009|ref|ZP_06665863.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293511598|ref|ZP_06670292.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|293550207|ref|ZP_06672879.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M1015]
 gi|295426642|ref|ZP_06819281.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589157|ref|ZP_06947798.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|81652014|sp|Q6GKK9|DUS_STAAR RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|49240468|emb|CAG39125.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257273255|gb|EEV05357.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257276544|gb|EEV07995.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257280032|gb|EEV10619.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257283076|gb|EEV13208.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257285753|gb|EEV15869.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282314801|gb|EFB45187.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           C101]
 gi|282323054|gb|EFB53373.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M899]
 gi|282324032|gb|EFB54348.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326150|gb|EFB56455.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282329989|gb|EFB59510.1| dihydrouridine synthase DuS [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|283789138|gb|EFC27965.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|290919254|gb|EFD96330.1| dihydrouridine synthase family protein [Staphylococcus aureus
           subsp. aureus M1015]
 gi|291096940|gb|EFE27198.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291465556|gb|EFF08088.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|295129094|gb|EFG58721.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297577668|gb|EFH96381.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus MN8]
 gi|312436792|gb|ADQ75863.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus TCH60]
 gi|315194550|gb|EFU24939.1| hypothetical protein CGSSa00_00231 [Staphylococcus aureus subsp.
           aureus CGS00]
          Length = 328

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTCKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|149180942|ref|ZP_01859444.1| hypothetical protein BSG1_00885 [Bacillus sp. SG-1]
 gi|148851461|gb|EDL65609.1| hypothetical protein BSG1_00885 [Bacillus sp. SG-1]
          Length = 332

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 123/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    + +      L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPNGRQSVRGRLTFTEDEQPIVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  I++N+GCP A V     G+ L+  P++  + I A  KA  
Sbjct: 86  DKPEFFREMSIGMAKEGFRGIDINMGCPVANVAGNGKGSGLIRRPEVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R+ +  + K  +  + IH R         K      +  +
Sbjct: 145 LPVSVKTRLGYSE---VDEWRDWLTHLLKQDIVNLSIHLRT--------KKEMSKVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    L+++    VDGVMIGR  + N        
Sbjct: 194 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLELVEKYGVDGVMIGRGIFHNPFAFEKEK 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +  S+              D +          A R                    GF  +
Sbjct: 254 KEHSSKELLDLLRLHLDLYDKYSTEEEPRPFIALRRFFKI------------YVKGFRGA 301

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+ L      STA    +   F    E L
Sbjct: 302 SELRNQLME--TQSTAEVRSLLNTFEAENEVL 331


>gi|300118953|ref|ZP_07056664.1| histidine phosphokinase/phophatase, putative [Bacillus cereus SJ1]
 gi|298723569|gb|EFI64300.1| histidine phosphokinase/phophatase, putative [Bacillus cereus SJ1]
          Length = 329

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 129/327 (39%), Gaps = 37/327 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNL 317
              R+ L   +  ST    ++   F  
Sbjct: 294 AELRNQLM--STKSTDEVRVLLDKFEA 318


>gi|229148723|ref|ZP_04276973.1| tRNA-dihydrouridine synthase [Bacillus cereus m1550]
 gi|228634731|gb|EEK91310.1| tRNA-dihydrouridine synthase [Bacillus cereus m1550]
          Length = 336

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 132/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     +++     + E+
Sbjct: 301 AELRNQL-MSTKSTDEVRGLLDKFEASVGEA 330


>gi|320168070|gb|EFW44969.1| tRNA-dihydrouridine synthase 3 [Capsaspora owczarzaki ATCC 30864]
          Length = 741

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 52/287 (18%), Positives = 114/287 (39%), Gaps = 26/287 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  YR   +    + +  +EM +A  +++G+ +   +      E    +Q+ G ++  + 
Sbjct: 406 NLPYRRLCKEFGVD-ITCSEMAMAVKLIQGEAQEWALTKRHASEDIFGVQLCGGNVEVMG 464

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            AA+++ +    + I++N GCP   V E   G+ L+  P  +      M +  ++P+T+K
Sbjct: 465 NAAELLSNHCELDFIDVNCGCPIDLVVERGQGSALLSRPSRLETIAKGMLQVSTVPITIK 524

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +    +    L+  +   GV+ + +H R         +  R     D+  + + 
Sbjct: 525 LRTGFSEDR--LVAHTLIPRLANLGVSLVTLHGRT--------RAQRYSRLADWQYINQC 574

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +  P L +  NG +    +A++      V G+M+ R A     + T + E  +  ++  
Sbjct: 575 AEAAPTLPVYGNGDIMSYQEAMEHREKTKVSGLMLARGALIKPWVFTEIKESRTWDISSG 634

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                         +     +Y   H  S  +  + TR  +  +  F
Sbjct: 635 ERF----------DMLKKFVNYGLEHWGSDTRGVETTRRFLLEWQSF 671


>gi|269201723|ref|YP_003280992.1| hypothetical protein SAAV_0037 [Staphylococcus aureus subsp. aureus
           ED98]
 gi|262074013|gb|ACY09986.1| hypothetical protein SAAV_0037 [Staphylococcus aureus subsp. aureus
           ED98]
          Length = 310

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E P+   I G
Sbjct: 1   MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEHPMVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 61  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 120 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 168

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 169 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 224

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 225 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 275

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 276 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 306


>gi|29377655|ref|NP_816809.1| dihydrouridine synthase family protein [Enterococcus faecalis V583]
 gi|29345123|gb|AAO82879.1| dihydrouridine synthase family protein [Enterococcus faecalis V583]
          Length = 324

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 138 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 193 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 244 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 297

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 298 AQL-MNTKSTDEVRQLL 313


>gi|296501149|ref|YP_003662849.1| nitrogen regulation protein NIFR3 [Bacillus thuringiensis BMB171]
 gi|296322201|gb|ADH05129.1| nitrogen regulation protein NIFR3 [Bacillus thuringiensis BMB171]
          Length = 329

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|21281788|ref|NP_644874.1| hypothetical protein MW0059 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49484964|ref|YP_042185.1| hypothetical protein SAS0059 [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|82749810|ref|YP_415551.1| hypothetical protein SAB0033c [Staphylococcus aureus RF122]
 gi|151220242|ref|YP_001331065.1| hypothetical protein NWMN_0030 [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|161508354|ref|YP_001574013.1| hypothetical protein USA300HOU_0096 [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|258424849|ref|ZP_05687722.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|258452233|ref|ZP_05700247.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282923748|ref|ZP_06331425.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9765]
 gi|284023097|ref|ZP_06377495.1| hypothetical protein Saura13_00779 [Staphylococcus aureus subsp.
           aureus 132]
 gi|294850441|ref|ZP_06791172.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9754]
 gi|297209414|ref|ZP_06925812.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|300911413|ref|ZP_07128862.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus TCH70]
 gi|39930905|sp|Q8NYV4|DUS_STAAW RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|81650227|sp|Q6GD38|DUS_STAAS RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|84028932|sp|Q5HJT5|DUS_STAAC RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|21203223|dbj|BAB93924.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49243407|emb|CAG41827.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|82655341|emb|CAI79721.1| probable nitrogen regulation protein [Staphylococcus aureus RF122]
 gi|150373042|dbj|BAF66302.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160367163|gb|ABX28134.1| possible tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|257844941|gb|EEV68982.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|257860070|gb|EEV82904.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282592990|gb|EFB97991.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9765]
 gi|294822711|gb|EFG39149.1| tRNA-dihydrouridine synthase [Staphylococcus aureus A9754]
 gi|296885875|gb|EFH24810.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus ATCC
           51811]
 gi|298693361|gb|ADI96583.1| hypothetical protein SAOV_0041 [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300887592|gb|EFK82788.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus TCH70]
 gi|315196066|gb|EFU26425.1| possible tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320139505|gb|EFW31376.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320142108|gb|EFW33928.1| dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329731636|gb|EGG67996.1| dihydrouridine synthase (Dus) [Staphylococcus aureus subsp. aureus
           21189]
 gi|329732272|gb|EGG68622.1| dihydrouridine synthase (Dus) [Staphylococcus aureus subsp. aureus
           21193]
          Length = 328

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|239907298|ref|YP_002954039.1| putative tRNA-dihydrouridine synthase [Desulfovibrio magneticus
           RS-1]
 gi|239797164|dbj|BAH76153.1| putative tRNA-dihydrouridine synthase [Desulfovibrio magneticus
           RS-1]
          Length = 337

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 117/300 (39%), Gaps = 20/300 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R  +R L   A+  TEM+ A  +     + K +L     + PL +Q+ GA+ 
Sbjct: 23  AGFSDLPFRLLSREL-GAAVAVTEMVSAKGLFYDSRNTKRLLDTCPADSPLVVQLFGAEP 81

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L  AA  + + GY   +LN GC   +V +   GA L+ +PD +  C  AM +A+  P 
Sbjct: 82  DYLERAAVALAEAGYTYFDLNCGCSVRKVVKTGAGAALLGDPDRLVACARAMVRAVG-PG 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            V  ++ +  + PA     L   + ++G   + +H R A        D + +        
Sbjct: 141 RVGVKLRLGPKPPARVDLELAIRLAEAGAAWLALHPRHASQGFAGTADRQALGEFV---- 196

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                    L +  +G L   +    +L      GVM  R A  +  +       F+N  
Sbjct: 197 -----AASTLPVIASGDLMTAADGRAVLAQTGAQGVMYARGALADPRVFARHAALFANE- 250

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
             ++P +     D  R+ +A   +YA         L ++   +       P  R  R  L
Sbjct: 251 GQTTPREVPSVCDVIRRHAALCREYADDR----QALLRMRTAVPRYLRDLPGCRALRDRL 306


>gi|315172916|gb|EFU16933.1| dihydrouridine synthase [Enterococcus faecalis TX1346]
          Length = 337

 Score =  185 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 206 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 257 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 310

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 311 AQL-MNTKSTDEVRQLL 326


>gi|218895442|ref|YP_002443853.1| probable tRNA-dihydrouridine synthase 2 [Bacillus cereus G9842]
 gi|218543849|gb|ACK96243.1| probable tRNA-dihydrouridine synthase 2 [Bacillus cereus G9842]
          Length = 329

 Score =  185 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|198471850|ref|XP_001355747.2| GA10329 [Drosophila pseudoobscura pseudoobscura]
 gi|198139493|gb|EAL32806.2| GA10329 [Drosophila pseudoobscura pseudoobscura]
          Length = 615

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 114/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM  A  +L+G   +  +      E    +Q+ G + + + 
Sbjct: 280 NLPFRRICKEL-GADITCGEMACAVPLLKGLGQEWALTKRHESEDIFGVQLCGNNPNVIT 338

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++++    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 339 QAAQVLQETAKVDYIDLNIGCPIDLIYQQGGGSALMRRTNILELVVRSCSSLSEQLPFTV 398

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           LV  +++ G + + +H R         ++ R   + +++ + +
Sbjct: 399 KMRTGIYADKSVA--HELVPLVEEWGASAVTLHGRS--------REQRYTKHANWEYIEQ 448

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
                  + I  NG +      ++     P V  VMIGR A     +   + +  +   T
Sbjct: 449 CAATAKKMPIIGNGDILSYEDYVEKRALSPHVSSVMIGRGALIKPWIFQEIKQQKAWSPT 508

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 509 STQRF----------EMLRRYCNYGLEHWGSDTKGVESTRRFLLEWQSF 547


>gi|217033055|ref|ZP_03438523.1| hypothetical protein HPB128_5g8 [Helicobacter pylori B128]
 gi|298736427|ref|YP_003728953.1| tRNA-dihydrouridine synthase B [Helicobacter pylori B8]
 gi|216945227|gb|EEC23910.1| hypothetical protein HPB128_5g8 [Helicobacter pylori B128]
 gi|298355617|emb|CBI66489.1| tRNA-dihydrouridine synthase B [Helicobacter pylori B8]
          Length = 328

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 131/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKILKVIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R          D  +   +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTR-------SDRYQKDKIDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|164661924|ref|XP_001732084.1| hypothetical protein MGL_0677 [Malassezia globosa CBS 7966]
 gi|159105986|gb|EDP44870.1| hypothetical protein MGL_0677 [Malassezia globosa CBS 7966]
          Length = 473

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 74/351 (21%), Positives = 123/351 (35%), Gaps = 50/351 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL------------------- 41
           MVD ++  +R   R      L+YT MI A   ++  +                       
Sbjct: 41  MVDQSELAWRILCRRY-GADLVYTPMINAKIYVQQGRGTHRVREGFFNQDVGEEGAHTLD 99

Query: 42  ---GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
                   ++PL +Q    D   L+EAA+ V+D   + ++LN+GCP      G FGA LM
Sbjct: 100 LCDDRKDSDRPLIVQFCANDPDMLLEAAQAVQD-KCDAVDLNLGCPQQIAKRGKFGAFLM 158

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            + D+V   I  +   L +PVT K R+               + I+++G   + +H R  
Sbjct: 159 DDWDLVFRLINTLHLNLKVPVTAKFRVY----DSVEKSIAYARMIQRAGAQIVTVHGRTR 214

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
            +KG       K    D+ I+  +K+    + +  NG +         L     DGVM  
Sbjct: 215 EMKG------HKTGLADWSIMRAVKEAL-AIPVFANGNILYAQDWRDCLAYTGCDGVMSA 267

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR------HLHSG 270
                N  +         + L   +    + +     +I+    D  AR      H    
Sbjct: 268 EGNLYNPTLFHRELGRDLSVLCDPAADHAQFEPMQLIRIAHEYLDIVARLKTPTSHSALK 327

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHIL-TVEAGASTATHHIIETAFNLMIE 320
           G + +ITR  + +          R +L            H I      + E
Sbjct: 328 GHMFKITRPALCI------HTDLRPVLGNAHTYDDGDGEHQIREYRAFVHE 372


>gi|206968108|ref|ZP_03229064.1| conserved hypothetical protein [Bacillus cereus AH1134]
 gi|206737028|gb|EDZ54175.1| conserved hypothetical protein [Bacillus cereus AH1134]
          Length = 329

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 294 AELRNQL-MSTKSTDEVRALLDKFEDSV 320


>gi|257083126|ref|ZP_05577487.1| dihydrouridine synthase [Enterococcus faecalis Fly1]
 gi|256991156|gb|EEU78458.1| dihydrouridine synthase [Enterococcus faecalis Fly1]
          Length = 326

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 194

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 195 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 246 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 299

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 300 AQL-MNTKSTDEVRQLL 315


>gi|65317756|ref|ZP_00390715.1| COG0042: tRNA-dihydrouridine synthase [Bacillus anthracis str.
           A2012]
 gi|167634108|ref|ZP_02392430.1| conserved hypothetical protein [Bacillus anthracis str. A0442]
 gi|177653669|ref|ZP_02935808.1| conserved hypothetical protein [Bacillus anthracis str. A0174]
 gi|167530422|gb|EDR93137.1| conserved hypothetical protein [Bacillus anthracis str. A0442]
 gi|172081249|gb|EDT66324.1| conserved hypothetical protein [Bacillus anthracis str. A0174]
          Length = 336

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 131/332 (39%), Gaps = 40/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+ L      ST +   +    N   ES+
Sbjct: 301 AELRNQLM-----STKSTDEVRALLNKFEESV 327


>gi|229547942|ref|ZP_04436667.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
 gi|293385258|ref|ZP_06631074.1| dihydrouridine synthase family protein [Enterococcus faecalis R712]
 gi|293389729|ref|ZP_06634173.1| dihydrouridine synthase family protein [Enterococcus faecalis S613]
 gi|307284767|ref|ZP_07564923.1| dihydrouridine synthase [Enterococcus faecalis TX0860]
 gi|312906609|ref|ZP_07765609.1| dihydrouridine synthase [Enterococcus faecalis DAPTO 512]
 gi|312910930|ref|ZP_07769765.1| dihydrouridine synthase (Dus) [Enterococcus faecalis DAPTO 516]
 gi|312953310|ref|ZP_07772153.1| dihydrouridine synthase [Enterococcus faecalis TX0102]
 gi|229306963|gb|EEN72959.1| tRNA-dihydrouridine synthase [Enterococcus faecalis ATCC 29200]
 gi|291077458|gb|EFE14822.1| dihydrouridine synthase family protein [Enterococcus faecalis R712]
 gi|291080976|gb|EFE17939.1| dihydrouridine synthase family protein [Enterococcus faecalis S613]
 gi|306503026|gb|EFM72283.1| dihydrouridine synthase [Enterococcus faecalis TX0860]
 gi|310627257|gb|EFQ10540.1| dihydrouridine synthase [Enterococcus faecalis DAPTO 512]
 gi|310628768|gb|EFQ12051.1| dihydrouridine synthase [Enterococcus faecalis TX0102]
 gi|311288798|gb|EFQ67354.1| dihydrouridine synthase (Dus) [Enterococcus faecalis DAPTO 516]
 gi|315144170|gb|EFT88186.1| dihydrouridine synthase [Enterococcus faecalis TX2141]
 gi|315152877|gb|EFT96893.1| dihydrouridine synthase [Enterococcus faecalis TX0031]
 gi|315154625|gb|EFT98641.1| dihydrouridine synthase [Enterococcus faecalis TX0043]
 gi|315159573|gb|EFU03590.1| dihydrouridine synthase [Enterococcus faecalis TX0312]
 gi|315161258|gb|EFU05275.1| dihydrouridine synthase [Enterococcus faecalis TX0645]
 gi|315167078|gb|EFU11095.1| dihydrouridine synthase [Enterococcus faecalis TX1341]
 gi|315579569|gb|EFU91760.1| dihydrouridine synthase [Enterococcus faecalis TX0630]
 gi|327536326|gb|AEA95160.1| dihydrouridine synthase [Enterococcus faecalis OG1RF]
          Length = 337

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 206 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 257 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 310

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 311 AQL-MNTKSTDEVRQLL 326


>gi|326692782|ref|ZP_08229787.1| probable tRNA-dihydrouridine synthase [Leuconostoc argentinum KCTC
           3773]
          Length = 374

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 136/329 (41%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + +TE   A +++    K      L  +  E     QI G
Sbjct: 36  MEAVTDTIFRRVVEKAGAPDVYFTEFTNASSMIHPKAKFSVQGRLAVAENETQPVAQIWG 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +    +  AAK++ D GY  ++LN+GCP   V +   G+ L+ + D+    ++A  +   
Sbjct: 96  SRPEDIAGAAKLLPDMGYRAVDLNMGCPDPTVVKNGAGSDLIRHQDLAAQLVSAAKE-SG 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D +     R+ +  I +  V  + +H R       +P     I     
Sbjct: 155 LPVSVKTRLGFYDPM---EFRDWLPVILQQDVAVLTVHLRSRKEMSKAPAHFELID---- 207

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +IV       P++ + +NG ++  ++     K  P VDG+MIGR  ++N       ++  
Sbjct: 208 EIVAMRDAIAPNILLQINGDIKSRAEGEALAKAHPGVDGIMIGRGIFENPYAF---EKSP 264

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S    ++  D + +++A++T      L    K+            GF ++   
Sbjct: 265 RQHTLEESIALLKLQLDLFDEVNATVTPKHFEALKRYFKI---------YLRGFAHASAL 315

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R +L +E  A+     +++     +  ++
Sbjct: 316 RQML-METHATDEVREVLDRELARVYAAV 343


>gi|261838041|gb|ACX97807.1| transcriptional regulator [Helicobacter pylori 51]
          Length = 328

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 128/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEVKSM-RESIEEFFNQ 310


>gi|57652431|ref|YP_184972.1| hypothetical protein SACOL0067 [Staphylococcus aureus subsp. aureus
           COL]
 gi|87161344|ref|YP_492806.1| hypothetical protein SAUSA300_0089 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88193860|ref|YP_498645.1| hypothetical protein SAOUHSC_00039 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|57286617|gb|AAW38711.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           COL]
 gi|87127318|gb|ABD21832.1| Probable tRNA-dihydrouridine synthase [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87201418|gb|ABD29228.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
          Length = 310

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 1   MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 61  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 120 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 168

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 169 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 224

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 225 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 275

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 276 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 306


>gi|21312100|ref|NP_082278.1| tRNA-dihydrouridine synthase 4-like [Mus musculus]
 gi|12845370|dbj|BAB26724.1| unnamed protein product [Mus musculus]
          Length = 324

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 124/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MI+A   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALLVCPY-ANGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDL----ARTIDLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK EN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMIK-ENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLTNPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 290


>gi|317014140|gb|ADU81576.1| tRNA-dihydrouridine synthase B [Helicobacter pylori Gambia94/24]
          Length = 328

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 131/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + + + +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVEILKVIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R          D  +   +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTR-------SDRYQKDKIDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMAEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|323341866|ref|ZP_08082099.1| dihydrouridine synthase [Erysipelothrix rhusiopathiae ATCC 19414]
 gi|322464291|gb|EFY09484.1| dihydrouridine synthase [Erysipelothrix rhusiopathiae ATCC 19414]
          Length = 327

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/322 (21%), Positives = 123/322 (38%), Gaps = 29/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG----FSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++      +  L     F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVAKAAQPDVYFTEFTNSESYFHAKGRESLRGRLLFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP+  V +   G+ L+L P++  + I +  KA  
Sbjct: 79  DNPDYFRDMSIGLAEMGFQGIDINMGCPAPNVFKHGRGSGLILRPEVAAEIIQS-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       ++ +  + +  ++ + IH R              IP    
Sbjct: 138 LPVSVKTRLGHRD---VQEYKSWIAHVLRQDISNLSIHLRTKTEMSKVDAHWELIP---- 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+    +  PD  I +NG + D     ++  L  VDGVMIGR  + N            
Sbjct: 191 EILKLRDEIAPDTLITINGDIMDYKMGKELADLYGVDGVMIGRGIFHNPFAF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                      +   D +R        Y+A+       L +  +  I  F G   +   R
Sbjct: 243 --EKEPQEHSAKELLDLFRYHLDQYDLYSAQEPGLSKPLHRFFKIYIREFKG---ANDLR 297

Query: 295 HILTVEAGASTATHHIIETAFN 316
             L        A    I  AF 
Sbjct: 298 TALMDTKTTDDART--ILDAFE 317


>gi|321314532|ref|YP_004206819.1| putative tRNA-dihydrouridine synthase [Bacillus subtilis BSn5]
 gi|320020806|gb|ADV95792.1| putative tRNA-dihydrouridine synthase [Bacillus subtilis BSn5]
          Length = 325

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 68/332 (20%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRKMSIGMAELGFKGLDINMGCPVPNVTQNGKGSGLIRRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGFTD---VDEWREWLTHILKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I         GF  +
Sbjct: 241 -AFEKEPKEHSSKELLDLLRLHLDLHDKYSALEARPYKPLPRFFKI------YLRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 294 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGI 324


>gi|295114506|emb|CBL33143.1| tRNA-dihydrouridine synthase [Enterococcus sp. 7L76]
 gi|323479133|gb|ADX78572.1| dihydrouridine synthase (Dus) family protein [Enterococcus faecalis
           62]
          Length = 324

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 138 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 193 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 244 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 297

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 298 AQL-MNTKSTDEVRQLL 313


>gi|229143117|ref|ZP_04271550.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228640390|gb|EEK96787.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST24]
          Length = 336

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|282915420|ref|ZP_06323192.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           D139]
 gi|282320523|gb|EFB50861.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           D139]
          Length = 330

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|229002247|dbj|BAH57713.1| conserved hypothetical protein orfY [Staphylococcus aureus]
          Length = 312

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 3   MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 62

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 63  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 121

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 122 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 170

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 171 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 226

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 227 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 277

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 278 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 308


>gi|57865821|ref|YP_189958.1| hypothetical protein SERP2413 [Staphylococcus epidermidis RP62A]
 gi|293367518|ref|ZP_06614173.1| dihydrouridine synthase [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|81672956|sp|Q5HKD5|DUS_STAEQ RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|57636479|gb|AAW53267.1| conserved hypothetical protein [Staphylococcus epidermidis RP62A]
 gi|291318346|gb|EFE58737.1| dihydrouridine synthase [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329732120|gb|EGG68474.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU144]
 gi|329733723|gb|EGG70050.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU028]
 gi|329737784|gb|EGG74023.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU045]
          Length = 326

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 72/328 (21%), Positives = 126/328 (38%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSDDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSIGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYDID---EWRDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DG+MIGR  + N        
Sbjct: 187 ELIEAIKTLRDEIAPNTLLTINGDIPDRQTGLELANKYGIDGIMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +        ARH  S  +  +I         G   +
Sbjct: 241 -AFEKEPREHSSKELLGLLRLHLSLFEKYDKDEARHFKSLRRFFKI------YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              RH L +   +      +++T    M
Sbjct: 294 SELRHQL-MNTQSIAEARELLDTFEARM 320


>gi|304405943|ref|ZP_07387601.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
 gi|304345186|gb|EFM11022.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
          Length = 312

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 117/307 (38%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+P+   I G
Sbjct: 5   MEDVTDVVFRHVVSEAGRPDVFFTEFTNTESYCHPDGNQSVRGRLAFTEDEQPIVAHIWG 64

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V +   G+ L+  P+     I A  KA  
Sbjct: 65  DKPEYFRQMSIGMAQQGFKGIDINMGCPVANVAQNGQGSGLICRPETAAAIIQAT-KAGG 123

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G D        R+ +  I K G+  + IH R         +      +  +
Sbjct: 124 LPVSVKTRLGFD---AIEEWRDWLTHILKQGIANLSIHLRT--------RAEMSKVDAHW 172

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 173 ELIPEIKKLRDEVAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFNNPFAF---- 228

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         +       R        Y+A  L      + ITR       GF  +
Sbjct: 229 ------EKEPREHSSEELLSLLRLHLDLHDHYSALEL---RPFKHITRFFKIYVRGFRGA 279

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 280 SELRNNL 286


>gi|149240295|ref|XP_001526023.1| tRNA-dihydrouridine synthase 1 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146450146|gb|EDK44402.1| tRNA-dihydrouridine synthase 1 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 516

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 105/266 (39%), Gaps = 25/266 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL------RGDKKNILGFSTQEKPLALQI 54
           MVD ++  +R  +R      L YT M  +          +       G    ++PL +Q 
Sbjct: 97  MVDHSELAWRILSRRY-GADLCYTPMFHSRLFATDPKYRQSMWNEKDGSRDNDRPLIVQF 155

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK+VE+   + ++LN+GCP      G +GA LM + ++V   I  +   
Sbjct: 156 CANDPDYLLQAAKLVENQ-CDAVDLNLGCPQGIARRGKYGAFLMDDWELVHKLIRTLHDN 214

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           LS+PVT K R+  D +          K +  +G   I IH R   +KG      +     
Sbjct: 215 LSVPVTAKIRVYDDWEKS----LEYAKMVLDAGAQFITIHGRTREMKG------QNTGLA 264

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           D+ I+  ++   P D     NG +   S   +       D VM       N  +  T D 
Sbjct: 265 DWKILKHLRDNLPEDQVFFANGNILYPSDLKRCADEVGCDAVMSAEGNLYNPGVFWTKDN 324

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISA 257
                     P   ++ ++++  +  
Sbjct: 325 DIEKQF----PRVDKLLREYFEIVKE 346


>gi|49480076|ref|YP_034652.1| dihydrouridine synthase [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|49331632|gb|AAT62278.1| conserved hypothetical protein, probable dihydrouridine synthase
           [Bacillus thuringiensis serovar konkukian str. 97-27]
          Length = 329

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 131/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     ++      + E+
Sbjct: 294 AELRNQL-MSTKSTDEVRTLLNKFEASVSET 323


>gi|315031899|gb|EFT43831.1| dihydrouridine synthase [Enterococcus faecalis TX0017]
          Length = 337

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 206 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 257 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 310

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 311 AQL-MNTKSTDEVRQLL 326


>gi|296436182|gb|ADH18356.1| putative oxidoreductase [Chlamydia trachomatis G/9768]
 gi|297140544|gb|ADH97302.1| putative oxidoreductase [Chlamydia trachomatis G/9301]
          Length = 334

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 139/317 (43%), Gaps = 24/317 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             ++D  YR  +      AL++ EM+  + +    ++   +L F+   +P+  Q+ G+  
Sbjct: 22  AGFSDFPYRRMSAEY-RPALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSHP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               E+AKI+E  G++ I+LN GCP+ R+ +   G+ ++   +++G  +  M + +S+PV
Sbjct: 81  DLAGESAKILEGLGFDLIDLNCGCPTDRITKDGSGSGMLKTSELIGKVVEKMVEVVSVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ IK+SG + +++H R         +        + + +
Sbjct: 141 TVKIRSGWD--FDHINVEETVRIIKESGASAVFVHGRT--------RSQGYQGPSNLEFI 190

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K+    D  +  NG +     A  +L     DGV++ R       +   +++Y +  
Sbjct: 191 SRAKQAAGNDFPVFGNGDVFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRH 295
              S    TR      ++       +   +  S  KL   TR + G +    P  R  R 
Sbjct: 251 TYSSPSFSTR------KQAFVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRA 304

Query: 296 ILTVEAGASTATHHIIE 312
            L  +A +S   + +I+
Sbjct: 305 NLA-KASSSQEVYQLID 320


>gi|228899051|ref|ZP_04063324.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|228970175|ref|ZP_04130851.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228789541|gb|EEM37446.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228860626|gb|EEN05013.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 336

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|196034769|ref|ZP_03102177.1| conserved hypothetical protein [Bacillus cereus W]
 gi|218901524|ref|YP_002449358.1| hypothetical protein BCAH820_0366 [Bacillus cereus AH820]
 gi|195992812|gb|EDX56772.1| conserved hypothetical protein [Bacillus cereus W]
 gi|218535642|gb|ACK88040.1| conserved hypothetical protein [Bacillus cereus AH820]
          Length = 329

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 131/332 (39%), Gaps = 40/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+ L      ST +   +    N   ES+
Sbjct: 294 AELRNQLM-----STKSTDEVRALLNKFEESV 320


>gi|315655777|ref|ZP_07908675.1| tRNA-dihydrouridine synthase B [Mobiluncus curtisii ATCC 51333]
 gi|315489841|gb|EFU79468.1| tRNA-dihydrouridine synthase B [Mobiluncus curtisii ATCC 51333]
          Length = 438

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 61/337 (18%), Positives = 122/337 (36%), Gaps = 54/337 (16%)

Query: 1   MVDWTDRHYRFFARLLTN-----------------------NALLYTEMIVADAILRGDK 37
           M   T+  +R      +                          +   EMI A A++    
Sbjct: 29  MAGVTNAPFRDLCAAFSRQGLPSESDSSLRRDGETGALCSVEGMFVNEMITAKALMMNST 88

Query: 38  KN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFG 94
           ++  +      +   ALQ+ G   + L  AA+ ++     + I+LN GCP  +V     G
Sbjct: 89  RSWVMAQSGPGQTVRALQLYGVVGADLAWAARELIARDLVDVIDLNFGCPVPKVTRKGGG 148

Query: 95  ACLMLNP----DIVGDCI-------AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           A L        D++G  +        A  + + +PVTVK R+G+D+      + +  ++ 
Sbjct: 149 AALPWKTTYFGDLIGQVVQAAQESSQAARREVEVPVTVKIRVGIDE--AHETMLDAGRAA 206

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           + +G   + +HAR          +     + D+  + ++     D+ +  NG +   S A
Sbjct: 207 QDAGAAALTLHARTT--------NQYYSGHSDWSRIGQLVN-TLDIPVLGNGDVFSASDA 257

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           L++       G+ IGRA      +   +          + P    + +   R  +  + +
Sbjct: 258 LEMFAQTGCAGIEIGRAVQGRPWIFREITAALWGQPIPAGPTLGEIVEVI-RAHARGLVE 316

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +     +    L+ + +H+     GF      R  LT
Sbjct: 317 HFG---NEKAALRDMRKHVGWYLRGFHLGGDTRAELT 350


>gi|253730438|ref|ZP_04864603.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253725822|gb|EES94551.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 328

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKIGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|15605376|ref|NP_220162.1| oxidoreductase [Chlamydia trachomatis D/UW-3/CX]
 gi|76789383|ref|YP_328469.1| oxidoreductase [Chlamydia trachomatis A/HAR-13]
 gi|237803073|ref|YP_002888267.1| putative oxidoreductase [Chlamydia trachomatis B/Jali20/OT]
 gi|237804994|ref|YP_002889148.1| putative oxidoreductase [Chlamydia trachomatis B/TZ1A828/OT]
 gi|255311468|ref|ZP_05354038.1| putative oxidoreductase [Chlamydia trachomatis 6276]
 gi|255317769|ref|ZP_05359015.1| putative oxidoreductase [Chlamydia trachomatis 6276s]
 gi|3329093|gb|AAC68821.1| predicted oxidoreductase [Chlamydia trachomatis D/UW-3/CX]
 gi|76167913|gb|AAX50921.1| predicted oxidoreductase [Chlamydia trachomatis A/HAR-13]
 gi|231273294|emb|CAX10209.1| putative oxidoreductase [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231274307|emb|CAX11102.1| putative oxidoreductase [Chlamydia trachomatis B/Jali20/OT]
 gi|296437111|gb|ADH19281.1| putative oxidoreductase [Chlamydia trachomatis G/11222]
 gi|296438042|gb|ADH20203.1| putative oxidoreductase [Chlamydia trachomatis G/11074]
 gi|297748774|gb|ADI51320.1| tRNA-dihydrouridine synthase [Chlamydia trachomatis D-EC]
 gi|297749654|gb|ADI52332.1| tRNA-dihydrouridine synthase [Chlamydia trachomatis D-LC]
          Length = 334

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 71/317 (22%), Positives = 139/317 (43%), Gaps = 24/317 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADI 59
             ++D  YR  +      AL++ EM+  + +    ++   +L F+   +P+  Q+ G+  
Sbjct: 22  AGFSDFPYRRMSAEY-RPALMFCEMVKMEGLHYCPQRTLRLLDFAESMRPIGGQLCGSRP 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               E+AKI+E  G++ I+LN GCP+ R+ +   G+ ++   +++G  +  M + +S+PV
Sbjct: 81  DLAGESAKILEGLGFDLIDLNCGCPTDRITKDGSGSGMLKTSELIGKVVEKMVEVVSVPV 140

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G D     + +   V+ IK+SG + +++H R         +        + + +
Sbjct: 141 TVKIRSGWD--FDHINVEETVRIIKESGASAVFVHGRT--------RSQGYQGPSNLEFI 190

Query: 180 YEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K+    D  +  NG +     A  +L     DGV++ R       +   +++Y +  
Sbjct: 191 SRAKQAAGNDFPVFGNGDVFSPEAAKTMLETTHCDGVLVARGTMGAPWIGKQIEDYLTTG 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF-PNSRRCRH 295
              S    TR      ++       +   +  S  KL   TR + G +    P  R  R 
Sbjct: 251 TYSSPSFSTR------KQAFVQHLQWIEEYYQSEEKLLTDTRKLCGHYLILSPKVRSLRA 304

Query: 296 ILTVEAGASTATHHIIE 312
            L  +A +S   + +I+
Sbjct: 305 NLA-KASSSQEVYQLID 320


>gi|329577778|gb|EGG59203.1| dihydrouridine synthase [Enterococcus faecalis TX1467]
          Length = 342

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 127/321 (39%), Gaps = 36/321 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 37  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 96

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 97  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 155

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R         +      +  +
Sbjct: 156 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRT--------RKEMSKVDAHW 204

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN        
Sbjct: 205 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY------ 258

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +P +          +     +   R +    +  +I         GFP +
Sbjct: 259 -AFEKEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGA 311

Query: 291 RRCRHILTVEAGASTATHHII 311
              R  L +   ++     ++
Sbjct: 312 SDLRAQL-MNTKSTDEVRQLL 331


>gi|242243139|ref|ZP_04797584.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis W23144]
 gi|242233391|gb|EES35703.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis W23144]
 gi|319399949|gb|EFV88191.1| dihydrouridine synthase (Dus) family protein [Staphylococcus
           epidermidis FRI909]
          Length = 326

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 126/328 (38%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSDDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSIGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYDID---EWRDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DG+MIGR  + N        
Sbjct: 187 ELIEAIKTLRDEIAPNTLLTINGDIPDRQTGLELANKYGIDGIMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +        ARH  S  +  +I         G   +
Sbjct: 241 -AFEKEPREHSSKELLGLLRLHLSLFEKYDKDEARHFKSLRRFFKI------YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              RH L +   +      +++T    M
Sbjct: 294 SELRHQL-MNTQSIAEARELLDTFEARM 320


>gi|229107992|ref|ZP_04237619.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-15]
 gi|228675495|gb|EEL30712.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock1-15]
          Length = 336

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|227554623|ref|ZP_03984670.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|227176236|gb|EEI57208.1| tRNA-dihydrouridine synthase [Enterococcus faecalis HH22]
 gi|315573226|gb|EFU85417.1| dihydrouridine synthase [Enterococcus faecalis TX0309B]
 gi|315581272|gb|EFU93463.1| dihydrouridine synthase [Enterococcus faecalis TX0309A]
          Length = 362

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 230

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 231 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 281

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 282 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 335

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 336 AQL-MNTKSTDEVRQLL 351


>gi|312905510|ref|ZP_07764624.1| dihydrouridine synthase [Enterococcus faecalis TX0635]
 gi|310631239|gb|EFQ14522.1| dihydrouridine synthase [Enterococcus faecalis TX0635]
          Length = 337

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 67/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV++K RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 151 LPVSIKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 206 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 257 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 310

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 311 AQL-MNTKSTDEVRQLL 326


>gi|210134928|ref|YP_002301367.1| transcriptional regulator [Helicobacter pylori P12]
 gi|210132896|gb|ACJ07887.1| transcriptional regulator [Helicobacter pylori P12]
          Length = 328

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  S  
Sbjct: 74  GVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTSKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R          D  +   +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTR-------SDRYQKDKIDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|294779128|ref|ZP_06744538.1| dihydrouridine synthase (Dus) [Enterococcus faecalis PC1.1]
 gi|294453761|gb|EFG22153.1| dihydrouridine synthase (Dus) [Enterococcus faecalis PC1.1]
          Length = 324

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 127/321 (39%), Gaps = 36/321 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN        
Sbjct: 187 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +P +          +     +   R +    +  +I         GFP +
Sbjct: 241 -AFEKEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGA 293

Query: 291 RRCRHILTVEAGASTATHHII 311
              R  L +   ++     ++
Sbjct: 294 SDLRAQL-MNTKSTDEVRQLL 313


>gi|228919255|ref|ZP_04082625.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228956783|ref|ZP_04118568.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229188590|ref|ZP_04315629.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 10876]
 gi|228594779|gb|EEK52559.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 10876]
 gi|228802824|gb|EEM49657.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228840362|gb|EEM85633.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 336

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSV 327


>gi|283781134|ref|YP_003371889.1| dihydrouridine synthase DuS [Pirellula staleyi DSM 6068]
 gi|283439587|gb|ADB18029.1| dihydrouridine synthase DuS [Pirellula staleyi DSM 6068]
          Length = 354

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 55/271 (20%), Positives = 106/271 (39%), Gaps = 19/271 (7%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAIL-----RGDKKNILGFSTQEKPLALQIGGA 57
            ++D   R  AR     +    E+++   ++     R   ++ L  + ++ P+A Q+ GA
Sbjct: 23  GYSDWPMRVIARR-HGASYALCEVMLDKFLVTLKGDRKKNRHFLYLTDEDHPVAGQLMGA 81

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
           + ++  + A  + + G++ I++N GCP  +V     G   +  PD+  + +      +  
Sbjct: 82  EPAEFAQGALRLAEAGFDVIDINFGCPVKKVLGRCRGGFHLSQPDVALEIVRRTRDIVPA 141

Query: 117 -IPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            IPVTVK R G+DD Q+       ++     +GV  I +H R  +         R +   
Sbjct: 142 HIPVTVKMRRGLDDTQLSRDRFFEILDGAFAAGVAAITVHGRTVV--------QRYVGPS 193

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
            +  + E+K+      I  +G L      L ++    VDGV + R A  N  + +     
Sbjct: 194 RWSFLTEVKRHVGSRVILGSGDLFSAQDCLAMMRETGVDGVTVARGAIGNPWIFSQCRAL 253

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            +       P               +   Y 
Sbjct: 254 DAGEPLPPPPTLFEQKATILEHYRLAAELYG 284


>gi|311067292|ref|YP_003972215.1| histidine phosphokinase/phophatase [Bacillus atrophaeus 1942]
 gi|310867809|gb|ADP31284.1| histidine phosphokinase/phophatase, putative [Bacillus atrophaeus
           1942]
          Length = 327

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 118/305 (38%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +  + K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYTD---VDEWRDWLTHVLKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAQQYGVDGIMIGRGIFTNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I         GF  +
Sbjct: 241 -AFEKEPKEHSSKELLDLLRLHLDLHDKYSKLEARPYKPLPRFFKI------YLRGFRGA 293

Query: 291 RRCRH 295
              R+
Sbjct: 294 SELRN 298


>gi|307637408|gb|ADN79858.1| tRNA di hydro uridine synthase B [Helicobacter pylori 908]
 gi|325995999|gb|ADZ51404.1| tRNA dihydrouridine synthase B [Helicobacter pylori 2018]
 gi|325997594|gb|ADZ49802.1| putative tRNA dihydrouridine synthase B [Helicobacter pylori 2017]
          Length = 328

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 131/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKRFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R          D  +   +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTR-------SDRYQKDKIDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|229194708|ref|ZP_04321501.1| tRNA-dihydrouridine synthase [Bacillus cereus m1293]
 gi|228588811|gb|EEK46836.1| tRNA-dihydrouridine synthase [Bacillus cereus m1293]
          Length = 336

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 131/331 (39%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R+ L +   ++     ++      + E+
Sbjct: 301 AELRNQL-MSTKSTDEVRALLNKFEASVSET 330


>gi|327273572|ref|XP_003221554.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Anolis
           carolinensis]
          Length = 325

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 72/284 (25%), Positives = 119/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L YT MIVA   +R +K     F+T   ++PL +Q    +
Sbjct: 41  MVRYSKLSFRTLVRKY-NCDLCYTPMIVAADFVRSEKARHSEFTTNQGDRPLIVQFAAKE 99

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA IV  F  + I+LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 100 AQVLADAACIVSPF-ADGIDLNCGCPQRWAMAEGYGACLINKPELVQDMVKLVKNQVENP 158

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV+ I +H R    +            + 
Sbjct: 159 LFSVSIKIRIHDDLKRT----IDLCQKAEAAGVSWITVHGRNVEERHQ---------PVH 205

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            D +  I KE+  + +  NG ++ +     +  +   DGVM+ R    N AM    +E  
Sbjct: 206 CDAIK-IIKESVSIPVVANGDMKSLKDVEDVHQITGTDGVMVARGLLANPAMFAGYEE-- 262

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                          +D+        T +   H H    L++IT
Sbjct: 263 ---------TPLECVQDWVHIALEHGTPFMCFHHHLMYMLERIT 297


>gi|315150824|gb|EFT94840.1| dihydrouridine synthase [Enterococcus faecalis TX0012]
          Length = 337

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 151 LPVSVKTRIGFTEM---AEMDAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 206 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 257 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 310

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 311 AQL-MNTKSTDEVRQLL 326


>gi|260818049|ref|XP_002603897.1| hypothetical protein BRAFLDRAFT_129997 [Branchiostoma floridae]
 gi|229289221|gb|EEN59908.1| hypothetical protein BRAFLDRAFT_129997 [Branchiostoma floridae]
          Length = 347

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 111/238 (46%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L ++ MI+A++ ++  K     F+T   ++PL +Q    D
Sbjct: 33  MVRYSKLPFRALVRRY-NCDLAFSPMIIAESFVKSLKARDSEFTTNSADRPLVVQFAARD 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              L +AA+IV  +  + ++LN GCP        +G+CL+ NP++V D +      +   
Sbjct: 92  GVTLADAAEIVAPYS-DGVDLNCGCPQRWAMAEGYGSCLLKNPELVSDMVRQAKARVSDK 150

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K R+  D +       ++ +  + +GV+ I +H R    +G           ++
Sbjct: 151 DFSVSIKIRLHKDLRETV----DMCQKAEHAGVSWIAVHGRTPSQRG---------EPVN 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
            + +  IK+    + +  NG ++++    ++  L  VDGVM  R   +N  M    D+
Sbjct: 198 TEAISLIKQSL-SIPVIANGDIKNLEDVKRVQSLTGVDGVMAARGILQNPGMYAGYDQ 254


>gi|255970603|ref|ZP_05421189.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255974183|ref|ZP_05424769.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256618039|ref|ZP_05474885.1| dihydrouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256760977|ref|ZP_05501557.1| dihydrouridine synthase [Enterococcus faecalis T3]
 gi|256960544|ref|ZP_05564715.1| dihydrouridine synthase [Enterococcus faecalis Merz96]
 gi|257080404|ref|ZP_05574765.1| dihydrouridine synthase [Enterococcus faecalis E1Sol]
 gi|257088308|ref|ZP_05582669.1| dihydrouridine synthase [Enterococcus faecalis D6]
 gi|257091440|ref|ZP_05585801.1| dihydrouridine synthase [Enterococcus faecalis CH188]
 gi|257417325|ref|ZP_05594319.1| dihydrouridine synthase [Enterococcus faecalis AR01/DG]
 gi|257418042|ref|ZP_05595036.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257420355|ref|ZP_05597345.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|307276567|ref|ZP_07557685.1| dihydrouridine synthase [Enterococcus faecalis TX2134]
 gi|255961621|gb|EET94097.1| dihydrouridine synthase [Enterococcus faecalis T1]
 gi|255967055|gb|EET97677.1| dihydrouridine synthase [Enterococcus faecalis T2]
 gi|256597566|gb|EEU16742.1| dihydrouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256682228|gb|EEU21923.1| dihydrouridine synthase [Enterococcus faecalis T3]
 gi|256951040|gb|EEU67672.1| dihydrouridine synthase [Enterococcus faecalis Merz96]
 gi|256988434|gb|EEU75736.1| dihydrouridine synthase [Enterococcus faecalis E1Sol]
 gi|256996338|gb|EEU83640.1| dihydrouridine synthase [Enterococcus faecalis D6]
 gi|257000252|gb|EEU86772.1| dihydrouridine synthase [Enterococcus faecalis CH188]
 gi|257159153|gb|EEU89113.1| dihydrouridine synthase [Enterococcus faecalis ARO1/DG]
 gi|257159870|gb|EEU89830.1| dihydrouridine synthase [Enterococcus faecalis T11]
 gi|257162179|gb|EEU92139.1| dihydrouridine synthase [Enterococcus faecalis X98]
 gi|306506677|gb|EFM75829.1| dihydrouridine synthase [Enterococcus faecalis TX2134]
          Length = 326

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 194

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 195 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 246 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 299

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 300 AQL-MNTKSTDEVRQLL 315


>gi|227552753|ref|ZP_03982802.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257888745|ref|ZP_05668398.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897323|ref|ZP_05676976.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|257899874|ref|ZP_05679527.1| dihydrouridine synthase [Enterococcus faecium Com15]
 gi|293378937|ref|ZP_06625092.1| dihydrouridine synthase (Dus) [Enterococcus faecium PC4.1]
 gi|227178153|gb|EEI59125.1| tRNA-dihydrouridine synthase [Enterococcus faecium TX1330]
 gi|257824799|gb|EEV51731.1| dihydrouridine synthase [Enterococcus faecium 1,141,733]
 gi|257833888|gb|EEV60309.1| dihydrouridine synthase [Enterococcus faecium Com12]
 gi|257837786|gb|EEV62860.1| dihydrouridine synthase [Enterococcus faecium Com15]
 gi|292642478|gb|EFF60633.1| dihydrouridine synthase (Dus) [Enterococcus faecium PC4.1]
          Length = 327

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 125/320 (39%), Gaps = 30/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V E   G+ L+L P++    I A  K   
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKGSGLILRPEVAAQLIEA-AKTGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  +    +  + +H R              IP    
Sbjct: 138 LPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSKVDAHWEVIPK--- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
            I+    +  P   I +NG + D     ++     VDG+MIGR  +KN         E+ 
Sbjct: 192 -IIALRDQIAPQTLITINGDIPDRRTGEELAEKYGVDGIMIGRGIFKNPYAFEKEPREHT 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
              L G   ++  +   +   I  S+T      LH   K+            GFP +   
Sbjct: 251 EKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI---------YIKGFPGANDL 296

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +   ++     I++T
Sbjct: 297 RVQL-MNTKSTDEVREILDT 315


>gi|206974138|ref|ZP_03235055.1| conserved hypothetical protein [Bacillus cereus H3081.97]
 gi|217957892|ref|YP_002336436.1| hypothetical protein BCAH187_A0408 [Bacillus cereus AH187]
 gi|222094091|ref|YP_002528148.1| dihydrouridine synthase family protein [Bacillus cereus Q1]
 gi|206747378|gb|EDZ58768.1| conserved hypothetical protein [Bacillus cereus H3081.97]
 gi|217065496|gb|ACJ79746.1| conserved hypothetical protein [Bacillus cereus AH187]
 gi|221238146|gb|ACM10856.1| dihydrouridine synthase family protein [Bacillus cereus Q1]
          Length = 329

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     E +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFREMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|53792892|dbj|BAD54069.1| putative PP35 [Oryza sativa Japonica Group]
 gi|53793348|dbj|BAD54568.1| putative PP35 [Oryza sativa Japonica Group]
 gi|125598482|gb|EAZ38262.1| hypothetical protein OsJ_22639 [Oryza sativa Japonica Group]
          Length = 396

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 61/282 (21%), Positives = 113/282 (40%), Gaps = 21/282 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 69  MVDNSELPFRMLCRRYGATG-AYTPMLHSRIFSENEKHRAMEFTTCKEDRPLFVQFCAND 127

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE +  + +++N GCP      G +GA LM N  +V   +  +   L +P
Sbjct: 128 PDILLQAAKIVEPY-CDYVDINFGCPQRIARRGYYGAFLMNNLPLVKSLVQNLSANLHVP 186

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI    +          K ++++G + + +H R         KD +K    D+D 
Sbjct: 187 VSCKIRIFPRLEDT----LAYAKMLEEAGASLVAVHGRT-----RDEKDGKKF-RADWDA 236

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT--TVDEYFS 234
           +  +K +   + +  NG +  +      L     DGV+      +N A+       E+  
Sbjct: 237 IKAVK-DALRIPVLANGNIRHLDDVKDCLEHTGADGVLSAETLLENPALFAGFRTKEWKE 295

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           N     +    + D     +       Y          + ++
Sbjct: 296 NGDEDEASGLDQADLVI--EYLKLCEQYPVPWRMVRSHVHKM 335


>gi|56207834|emb|CAI20920.1| novel protein similar to human and mouse protein similar to E. coli
           yhdg and R. capsulatus nifR3 (PP35) [Danio rerio]
          Length = 307

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 124/284 (43%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+A   +R  K     F+T   ++PL +Q    D
Sbjct: 23  MVRYSKLAFRTLVRKYD-CDVCFTPMIIAADFMRSAKARDSEFTTNKNDRPLIVQFAAKD 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 82  AQTLADAACVVSPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQIDNP 140

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L + ++ +GV+ I +H R AI +            + 
Sbjct: 141 NYAVSIKIRIHKDVRQTV----DLCQKVEAAGVSYITVHGRTAIERHQ---------PVH 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK ++  + +  NG ++ M    A+  L  VDGVM  R    N AM +  +E  
Sbjct: 188 YDTIKTIK-DSLSIPVIANGDIKSMQDVEAVCELTGVDGVMSARGLLSNPAMFSGFEE-- 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +   D+    +   T +   H H    L++IT
Sbjct: 245 ---------TPLQCVWDWVDIAAEHGTPFTCFHHHLIHMLERIT 279


>gi|296209951|ref|XP_002751783.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Callithrix jacchus]
          Length = 317

 Score =  185 bits (469), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 125/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MIVA   ++  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIVAADFVKSIKARDSEFTTNRGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARVLSDAARIVSPY-ANGIDINCGCPQRWAMAEGYGACLINKPELVRDMVTQVRNQVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  +  GV+ I +H R    +            + 
Sbjct: 152 GFSVSIKIRIHDDLKRTV----DLCRKAEAIGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  I KEN  + +  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDSIK-IIKENMSIPVIANGDIRSLKEAENVWQITGTDGVMVARGLLTNPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  I+  + T Y   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDIALELGTPYMCFHQHLMYMMEKIT 290


>gi|109119167|ref|XP_001113015.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Macaca mulatta]
          Length = 476

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 114/293 (38%), Gaps = 35/293 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    +G  P     +     
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGR--WSQGC-PGPGGVLGRWR- 193

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D  + + ++   + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 194 DRCFSVNRKAVAIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFH 285
               G SP    + +++   +        Y   HL    KL     H + ++ 
Sbjct: 246 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH---HTLQVYQ 289


>gi|307288357|ref|ZP_07568349.1| dihydrouridine synthase [Enterococcus faecalis TX0109]
 gi|306500657|gb|EFM69982.1| dihydrouridine synthase [Enterococcus faecalis TX0109]
 gi|315026494|gb|EFT38426.1| dihydrouridine synthase [Enterococcus faecalis TX2137]
 gi|315146498|gb|EFT90514.1| dihydrouridine synthase [Enterococcus faecalis TX4244]
 gi|315164353|gb|EFU08370.1| dihydrouridine synthase [Enterococcus faecalis TX1302]
 gi|315171103|gb|EFU15120.1| dihydrouridine synthase [Enterococcus faecalis TX1342]
          Length = 362

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 230

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 231 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 281

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 282 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 335

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 336 AQL-MNTKSTDEVRQLL 351


>gi|302769496|ref|XP_002968167.1| hypothetical protein SELMODRAFT_89139 [Selaginella moellendorffii]
 gi|300163811|gb|EFJ30421.1| hypothetical protein SELMODRAFT_89139 [Selaginella moellendorffii]
          Length = 540

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 112/287 (39%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L     E    +QI G+    L 
Sbjct: 199 NLPFRRLCKKL-GADVTCGEMAMCTNLLQGHASEWALLRRHPVEDCFGVQICGSYADSLT 257

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  +++E +   + I++N+GCP   V +   G+CL+  P  +   + A    +  P+T+K
Sbjct: 258 KTVELIERECTVDFIDINLGCPIDIVVKKGAGSCLLTKPTRLEQIVRATASIVEKPLTLK 317

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +        +++  +   GV+ + +H R         +  R     D+  +Y+ 
Sbjct: 318 MRTGYFEGKNCA--HSMISELSNWGVSAVTVHGRT--------RQQRYSKLADWVYIYDC 367

Query: 183 KKENP-DLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            K  P DL +  NG +   S   + +    ++   M+ R A     +LT + E     ++
Sbjct: 368 AKRAPDDLQVLGNGDIFSYSDWNEHMLPDLNLSSCMLARGALIKPWLLTEIKEQRHWDIS 427

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +  +           +    T +   H  S  K  + TR  +   L
Sbjct: 428 SNERL----------DLLRDYTQFGLEHWGSDSKGVETTRKFLLEWL 464


>gi|270007852|gb|EFA04300.1| hypothetical protein TcasGA2_TC014592 [Tribolium castaneum]
          Length = 548

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/286 (21%), Positives = 115/286 (40%), Gaps = 29/286 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +  ++L+G  +   ++     E    +Q+   +   L 
Sbjct: 213 NLPFRRICKEF-GADVTCGEMAMCSSLLQGAPQEWALVKRHHSEDIFGVQLCANNPHLLT 271

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  ++++ +   + I+LN+GCP   V++   G  L+    ++  CI  + + L+IP+TVK
Sbjct: 272 KCGQVLQQEAEIDFIDLNLGCPIELVYKEGGGCGLLRRQRVLESCIKNLSQLLTIPMTVK 331

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV        +  L    +  G + I IH R         ++ R     D+  + ++
Sbjct: 332 TRTGVYSNENLAHI--LAPKFRDWGASLITIHGRS--------REQRYTKLADWTYIRQV 381

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            +    L +  NG +   ED   A +  P + GVMIGR A     + T + E     ++ 
Sbjct: 382 AQAAAPLPVLGNGDVLSYEDYKIARETCPELAGVMIGRGALIKPWIFTEIKEQKLWDISS 441

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
           S              +    T+Y   H  S  K  + TR  +   L
Sbjct: 442 SERF----------DLLKKYTNYGLEHWGSDNKGVENTRRFLLEWL 477


>gi|256958478|ref|ZP_05562649.1| dihydrouridine synthase [Enterococcus faecalis DS5]
 gi|257078210|ref|ZP_05572571.1| dihydrouridine synthase [Enterococcus faecalis JH1]
 gi|256948974|gb|EEU65606.1| dihydrouridine synthase [Enterococcus faecalis DS5]
 gi|256986240|gb|EEU73542.1| dihydrouridine synthase [Enterococcus faecalis JH1]
          Length = 326

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 127/321 (39%), Gaps = 36/321 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R         +      +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRT--------RKEMSKVDAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN        
Sbjct: 189 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY------ 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +P +          +     +   R +    +  +I         GFP +
Sbjct: 243 -AFEKEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGA 295

Query: 291 RRCRHILTVEAGASTATHHII 311
              R  L +   ++     ++
Sbjct: 296 SDLRAQL-MNTKSTDEVRQLL 315


>gi|228944129|ref|ZP_04106508.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229119980|ref|ZP_04249235.1| tRNA-dihydrouridine synthase [Bacillus cereus 95/8201]
 gi|228663446|gb|EEL19031.1| tRNA-dihydrouridine synthase [Bacillus cereus 95/8201]
 gi|228815518|gb|EEM61760.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 336

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/332 (22%), Positives = 131/332 (39%), Gaps = 40/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+ L      ST +   +    N   ES+
Sbjct: 301 AELRNQLM-----STKSTDEVRALLNKFEESV 327


>gi|115469926|ref|NP_001058562.1| Os06g0712900 [Oryza sativa Japonica Group]
 gi|113596602|dbj|BAF20476.1| Os06g0712900 [Oryza sativa Japonica Group]
          Length = 421

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/282 (21%), Positives = 113/282 (40%), Gaps = 21/282 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 94  MVDNSELPFRMLCRRYGATG-AYTPMLHSRIFSENEKHRAMEFTTCKEDRPLFVQFCAND 152

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE +  + +++N GCP      G +GA LM N  +V   +  +   L +P
Sbjct: 153 PDILLQAAKIVEPY-CDYVDINFGCPQRIARRGYYGAFLMNNLPLVKSLVQNLSANLHVP 211

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI    +          K ++++G + + +H R         KD +K    D+D 
Sbjct: 212 VSCKIRIFPRLEDT----LAYAKMLEEAGASLVAVHGRT-----RDEKDGKKF-RADWDA 261

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT--TVDEYFS 234
           +  +K +   + +  NG +  +      L     DGV+      +N A+       E+  
Sbjct: 262 IKAVK-DALRIPVLANGNIRHLDDVKDCLEHTGADGVLSAETLLENPALFAGFRTKEWKE 320

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           N     +    + D     +       Y          + ++
Sbjct: 321 NGDEDEASGLDQADLVI--EYLKLCEQYPVPWRMVRSHVHKM 360


>gi|196040201|ref|ZP_03107503.1| conserved hypothetical protein [Bacillus cereus NVH0597-99]
 gi|196029056|gb|EDX67661.1| conserved hypothetical protein [Bacillus cereus NVH0597-99]
          Length = 329

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|148704962|gb|EDL36909.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_b [Mus
           musculus]
          Length = 324

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 124/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MI+A   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLAFRTLVRKYS-CDLCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAALLVCPY-ANGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDL----ARTIDLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK EN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 199 YDAIKMIK-ENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLTNPAMFAGYEE-- 255

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 256 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 290


>gi|283469330|emb|CAQ48541.1| tRNA-dihydrouridine synthase [Staphylococcus aureus subsp. aureus
           ST398]
          Length = 328

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/331 (19%), Positives = 126/331 (38%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              RH L +   +      +++     M E 
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDED 323


>gi|71032309|ref|XP_765796.1| hypothetical protein [Theileria parva strain Muguga]
 gi|68352753|gb|EAN33513.1| hypothetical protein, conserved [Theileria parva]
          Length = 327

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/282 (21%), Positives = 112/282 (39%), Gaps = 22/282 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R  +   L YT M+ A      +    + F T   +KPL  Q  G D
Sbjct: 33  MVDQSELPFRLLCRRYS-ADLAYTPMLHAKIFSENENYRNIHFHTSSDDKPLIAQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +  + A+  +     + I++N+GCP     +G +G+ L+  P ++ + + ++ +   I 
Sbjct: 92  PNAFILASSYI-KNDVSAIDINLGCPQGIARKGRYGSFLLEYPQLINEIVRSLTQ-TGIN 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R    D + +    NL  S++ SG   + +H R             +I   D+D 
Sbjct: 150 VTCKIRKVEKDCLQST--LNLCYSLEASGCKALTVHGRHRSET------KTRISECDWDS 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT-----VDE 231
           +  IK +  ++ +  NGG+E      + L     D VM   A  +N  + +      +D 
Sbjct: 202 IKIIKSKV-NIPVIANGGIETFEDVKRCLEYTGADAVMSSEAILENPYLFSGKIYNNID- 259

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            F   L+       +            +  Y  +H      +
Sbjct: 260 IFEEYLSILKGSPRQKISCIKGHAFKILYKYINQHHDIRTAI 301


>gi|228906094|ref|ZP_04069983.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228853503|gb|EEM98271.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis IBL 200]
          Length = 336

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSV 327


>gi|322514831|ref|ZP_08067850.1| tRNA-dihydrouridine synthase C [Actinobacillus ureae ATCC 25976]
 gi|322119213|gb|EFX91354.1| tRNA-dihydrouridine synthase C [Actinobacillus ureae ATCC 25976]
          Length = 319

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/334 (21%), Positives = 125/334 (37%), Gaps = 41/334 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       G +    P+ +
Sbjct: 12  MQGVLDPFVRKLLTAVNDYDLCISEFVRVVDQKLPKKAFYRLAPELLQGGLTDSGTPVRV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ + D++     AM 
Sbjct: 72  QLLGQHPQWLAENAQLAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDLDLIYRATKAMR 131

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++ + G N I +H R         +D  +
Sbjct: 132 EAVPQDQIVSVKVRLGWD---SADQCFEIADAVAQGGANEITVHGRTK-------QDGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A       +   +MIGR A     +   
Sbjct: 182 AERINWQAIGEIQKRL-SIPVIANGEIWDFESAKNCQNTTACSSLMIGRGALNTPNL--- 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 238 -----------SRVVKFNQPKMAWNEVLQLLFQYVNMENEDDSGFYHVARIKQWLHYLDK 286

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLMI 319
            +P ++    IL  E G      H IE A N  I
Sbjct: 287 EYPEAKDLFQILKTEHGYDGLNAH-IERAVNQEI 319


>gi|15611731|ref|NP_223382.1| putative transcriptional regulator [Helicobacter pylori J99]
 gi|39930913|sp|Q9ZLB6|DUS_HELPJ RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|4155212|gb|AAD06235.1| putative TRANSCRIPTIONAL REGULATOR [Helicobacter pylori J99]
          Length = 328

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 131/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + + + +  + +  +  
Sbjct: 74  SVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVEILKVIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R          D  +   +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTR-------SDRYQKDKIDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRA  +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRATLRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|323440393|gb|EGA98106.1| hypothetical protein SAO11_0837 [Staphylococcus aureus O11]
 gi|323443127|gb|EGB00746.1| hypothetical protein SAO46_0916 [Staphylococcus aureus O46]
          Length = 328

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 65/332 (19%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DG+MIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGIMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    K+    +   ++ +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSKELLNLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              RH L +   +      +++     M E +
Sbjct: 294 SELRHQL-MNTQSIAEARALLDEFEAQMDEDV 324


>gi|227517187|ref|ZP_03947236.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
 gi|227075410|gb|EEI13373.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX0104]
          Length = 337

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 123/317 (38%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+      K+     L F+  E+P+   I G
Sbjct: 32  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPAGKDSVRGRLVFTEDEQPMVAHIWG 91

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 92  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 150

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 151 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 205

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 206 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 257 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 310

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 311 AQL-MNTKSTDEVRQLL 326


>gi|47569585|ref|ZP_00240263.1| dihydrouridine synthase family protein [Bacillus cereus G9241]
 gi|47553768|gb|EAL12141.1| dihydrouridine synthase family protein [Bacillus cereus G9241]
          Length = 329

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|295398418|ref|ZP_06808458.1| tRNA-dihydrouridine synthase [Aerococcus viridans ATCC 11563]
 gi|294973371|gb|EFG49158.1| tRNA-dihydrouridine synthase [Aerococcus viridans ATCC 11563]
          Length = 339

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 130/331 (39%), Gaps = 35/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG----FSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +++ +    ++ L     F+  EKP+   I G
Sbjct: 34  MEDVTDTVFRHVVQKAAKPDVYFTEFTNSESYVHPKGRDSLNSRLLFTEDEKPIVAHIWG 93

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +       AK + + GY  +++N+GCP+  V +   G+ L+L PD+  + I A  +   
Sbjct: 94  DNPDHFAAMAKGMNEMGYAGLDINMGCPAPNVFKHGRGSGLILRPDVAVELIQAAKEG-G 152

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +  + K  +  + IH R         K      +  +
Sbjct: 153 LPVSVKTRLGHQNTEEY---KEWLSLLLKQDIANLSIHLRT--------KTEMSKVDAHW 201

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P   + +NG + +     +++    VDGVMIGR  + N        
Sbjct: 202 ELIPEIKKLRDEIAPQTLLTINGDIPNRQVGQELVDKYGVDGVMIGRGIFHNPF------ 255

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +P   +   D +R       + AA+    G   + + R        F  +
Sbjct: 256 -AFEEEARDHTP---KELLDLFRYHLDLFDENAAK---DGRPYKPLRRFFKIYIRSFRGA 308

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIES 321
              R  L        A   + E     + E+
Sbjct: 309 NDLRIGLMETESTEEARALLDEFEEKYLAEA 339


>gi|282874789|ref|ZP_06283668.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis SK135]
 gi|281296505|gb|EFA89020.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis SK135]
          Length = 326

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 126/328 (38%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D T+  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTNIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSDDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSIGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYDID---EWRDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DG+MIGR  + N        
Sbjct: 187 ELIEAIKTLRDEIAPNTLLTINGDIPDRQTGLELASKYGIDGIMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +        ARH  S  +  +I         G   +
Sbjct: 241 -AFEKEPREHSSKELLGLLRLHLSLFEKYDKDEARHFKSLRRFFKI------YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              RH L +   +      +++T    M
Sbjct: 294 SELRHQL-MNTQSIAEARELLDTFEARM 320


>gi|330685277|gb|EGG96938.1| dihydrouridine synthase (Dus) [Staphylococcus epidermidis VCU121]
          Length = 326

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 63/324 (19%), Positives = 123/324 (37%), Gaps = 30/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTASFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P++  + I A  KA  
Sbjct: 79  DQPEQFREMSIGLAEMGFKGIDLNMGCPVANVAQKGKGSGLILRPEVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R+ +K + +  +  + IH R              I     
Sbjct: 138 LPVSVKTRLGFYEID---EWRDWLKHVFEQDIANLSIHLRTRKEMSKVDAHWELI----- 189

Query: 177 DIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           + + +++ E  P+  + +NG + D    L++     +DGVMIGR  + N           
Sbjct: 190 EAIKQLRDEIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFHNPFAF------- 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                     +    ++    +   ++ +         + + + R       G   + + 
Sbjct: 243 ------EKEPREHTSEELLGLLRLHLSLFQKYDKDEDRQFKSLRRFFKIYVRGIKGASQL 296

Query: 294 RHILTVEAGASTATHHIIETAFNL 317
           RH L +   +      +++     
Sbjct: 297 RHQL-MNTQSIAEARELLDEFEAQ 319


>gi|229916707|ref|YP_002885353.1| dihydrouridine synthase DuS [Exiguobacterium sp. AT1b]
 gi|229468136|gb|ACQ69908.1| dihydrouridine synthase DuS [Exiguobacterium sp. AT1b]
          Length = 330

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/327 (22%), Positives = 123/327 (37%), Gaps = 32/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+       G  +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVAHAGRPDVFFTEFANSDSYCHPEGKGSLRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + GY  +++N+GCP   V +   G+ L+L P++  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAEMGYKGLDINMGCPVPNVAKRGKGSGLILRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           IPV+VK R+G          R+ +  + K  +  + IH R              IP    
Sbjct: 138 IPVSVKTRLGFAKLD---EWRDWLTHLLKQDIANLSIHLRTRNEMSKVDAHWEMIP---- 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           DIV    +  PD  I +NG + D    L+++    VDGVMIGR  +KN          F 
Sbjct: 191 DIVKLRDEIAPDTLITINGDILDRQMGLELVEKYGVDGVMIGRGIFKNPF-------AFE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 S  +          +     +   R + +  +  +I         GF  +   R
Sbjct: 244 KEPREHSMEEHLDLLRLQLDLQDKFQEDVPRSISNLHRFFKI------YVKGFRGASELR 297

Query: 295 HILTVEAGASTATHHIIETAFNLMIES 321
           H L             +    +  +E 
Sbjct: 298 HNLMETKSTDE-----VRALLDAFVEK 319


>gi|163789796|ref|ZP_02184233.1| hypothetical protein CAT7_06176 [Carnobacterium sp. AT7]
 gi|159875018|gb|EDP69085.1| hypothetical protein CAT7_06176 [Carnobacterium sp. AT7]
          Length = 326

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 119/322 (36%), Gaps = 35/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    D ++     L F+  E+PL   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFTNTVSYCHPDGRDSVRGRLTFTEDEQPLVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+   ++  + I A  KA  
Sbjct: 79  DEPKYFRQMSIGMAEEGFKGIDINMGCPVPNVAGKGKGSGLIRRSEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R+ +  I +  +  + IH R         +         +
Sbjct: 138 LPVSVKTRLGY---TNIEEWRDWLTHIFEQDIANLSIHLRT--------RKEMSKGAAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ E+KK      P   + +NG + D    LK++    VDGVMIGR  ++N        
Sbjct: 187 EMISEVKKLRDEIAPQTLLTINGDIPDRETGLKLVEEYGVDGVMIGRGIFQNPYAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   + +R        Y      S   L++  +       G   +
Sbjct: 243 ------EKEPREHSSKELLELFRLHLDLFDKYTVDEPRSFRPLRRFFKI---YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIE 312
              R  L      + A   + E
Sbjct: 294 SDLRVQLMESETTNEARILLDE 315


>gi|148704961|gb|EDL36908.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_a [Mus
           musculus]
          Length = 327

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 124/285 (43%), Gaps = 36/285 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   L YT MI+A   +R  K     F+T   + PL +Q    D
Sbjct: 37  MVRYSKLAFRTLVRKYS-CDLCYTPMIIAADFVRSIKARDSEFTTNQGDCPLIVQFAAND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 96  ARLLSDAALLVCPY-ANGIDINCGCPQRWAMADGYGACLINKPELVHDMVRQVRNRVESP 154

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 155 RFSVSIKIRIHDDL----ARTIDLCRKAEATGVSWITVHGRTVEERHQ---------PVH 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK EN  + I  NG +  + +A  +  +   DGVM+ R    N AM    +E  
Sbjct: 202 YDAIKMIK-ENVSIPIVANGDIRSLKEAENVWQMTGTDGVMVARGLLTNPAMFAGYEE-- 258

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
                  +P+K   D   W  IS  + T +   H H    +++IT
Sbjct: 259 -------TPLKCIWD---WVDISLELGTPFMCFHQHLMYMMEKIT 293


>gi|229547370|ref|ZP_04436095.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|307270477|ref|ZP_07551776.1| dihydrouridine synthase [Enterococcus faecalis TX4248]
 gi|307292224|ref|ZP_07572088.1| dihydrouridine synthase [Enterococcus faecalis TX0411]
 gi|229307519|gb|EEN73506.1| tRNA-dihydrouridine synthase [Enterococcus faecalis TX1322]
 gi|306496730|gb|EFM66283.1| dihydrouridine synthase [Enterococcus faecalis TX0411]
 gi|306513178|gb|EFM81811.1| dihydrouridine synthase [Enterococcus faecalis TX4248]
 gi|315028673|gb|EFT40605.1| dihydrouridine synthase [Enterococcus faecalis TX4000]
 gi|315034772|gb|EFT46704.1| dihydrouridine synthase [Enterococcus faecalis TX0027]
          Length = 362

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 67/321 (20%), Positives = 127/321 (39%), Gaps = 36/321 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R         +      +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRT--------RKEMSKVDAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN        
Sbjct: 225 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY------ 278

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +P +          +     +   R +    +  +I         GFP +
Sbjct: 279 -AFEKEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGA 331

Query: 291 RRCRHILTVEAGASTATHHII 311
              R  L +   ++     ++
Sbjct: 332 SDLRAQL-MNTKSTDEVRQLL 351


>gi|195484562|ref|XP_002090745.1| GE13280 [Drosophila yakuba]
 gi|194176846|gb|EDW90457.1| GE13280 [Drosophila yakuba]
          Length = 609

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 115/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + + 
Sbjct: 274 NLPFRRICKEF-GADITCGEMACAQPLLKGMGQEWALTKRHQSEDIFGVQLCGNNPNMIN 332

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ E    + I+LN+GCP   +++   G+ LM   +I+   + +     + +P TV
Sbjct: 333 QAAQVIYETAQVDFIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSNRLPFTV 392

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G + + +H R         ++ R   + ++  + E
Sbjct: 393 KMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWAYIEE 442

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++       V  VMIGR A     +   + E   +  +
Sbjct: 443 CAAKAKRMPVIGNGDILSYEDYIERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KHSWS 500

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            SS  +  + + F         +Y   H  S  K  + TR  +  +  F
Sbjct: 501 PSSGQRYEMLQKF--------CNYGLEHWGSDTKGVETTRRFLLEWQSF 541


>gi|299541815|ref|ZP_07052138.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
 gi|298725553|gb|EFI66194.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
          Length = 325

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/332 (21%), Positives = 132/332 (39%), Gaps = 37/332 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE     +    D     +N L F+  E+P+   I G
Sbjct: 20  MEDVTDVVFRHVIQEAGRPDVYFTEFTNTTSYCHPDGLDNVRNRLAFTEDEQPIVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  +++ G+  I++N+GCP   V E   GA L+L+P++  D I A  KA  
Sbjct: 80  DNPEHFRQMSIGMKELGFKGIDINMGCPVDNVAERGKGAGLILHPELAADIIQA-AKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         ++        +
Sbjct: 139 LPVSVKTRLGFTD---VTEWREWLTHILKQDIANLSIHLRT--------REEMSKVAAHW 187

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +IKK      P   + +NG + D    LK++    +DG+MIGR  + N        
Sbjct: 188 ELIGDIKKLRDEVAPHTLLTINGDIPDRLTGLKLVEQYGIDGIMIGRGVFSNPFAFE--- 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                P   S+     +             ++  R   +  +  +I         GF  +
Sbjct: 245 ---KEPKEHSAKEYLNLLYLHLNLHDHYSKEFETRSFKALQRFFKI------YVRGFKGA 295

Query: 291 RRCR-HILTVEAGASTATHHIIETAFNLMIES 321
            + R  +L+  A ++     ++       ++ 
Sbjct: 296 SQLRVQLLS--AHSTVEVRELLAAYIAHELKE 325


>gi|229142705|ref|ZP_04271179.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST26]
 gi|228640768|gb|EEK97125.1| tRNA-dihydrouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 336

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     E +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFREMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|239635868|ref|ZP_04676891.1| dihydrouridine synthase DuS [Staphylococcus warneri L37603]
 gi|239598492|gb|EEQ80966.1| dihydrouridine synthase DuS [Staphylococcus warneri L37603]
          Length = 326

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 67/324 (20%), Positives = 121/324 (37%), Gaps = 30/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTASFCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P++  + I A  KA  
Sbjct: 79  DQPEQFREMSIGLAEMGFKGIDLNMGCPVANVAQKGKGSGLILRPEVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R+ +K + +  +  + IH R              I     
Sbjct: 138 LPVSVKTRLGFYEID---EWRDWLKHVFEQDIANLSIHLRTRKEMSKVDAHWELI----- 189

Query: 177 DIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
           + + +++ E  P+  + +NG + D    L++     +DGVMIGR  + N          F
Sbjct: 190 EAIKQLRDEIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFHNPF-------AF 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S  +          +         R   S  +  +I         G   + + 
Sbjct: 243 EKEPREHSSEELLGLLRLHLSLFQKYDKDEDRQFKSLRRFFKI------YVRGIKGASQL 296

Query: 294 RHILTVEAGASTATHHIIETAFNL 317
           RH L +   +      +++     
Sbjct: 297 RHQL-MNTQSIAEARELLDEFEAQ 319


>gi|228950876|ref|ZP_04112999.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228808805|gb|EEM55301.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 336

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 131/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSV 327


>gi|108563136|ref|YP_627452.1| transcriptional regulator [Helicobacter pylori HPAG1]
 gi|107836909|gb|ABF84778.1| transcriptional regulator [Helicobacter pylori HPAG1]
          Length = 328

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/322 (18%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + D +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLDHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +KK      +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKKILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-REGIEEFFNQ 310


>gi|300706707|ref|XP_002995598.1| hypothetical protein NCER_101453 [Nosema ceranae BRL01]
 gi|239604766|gb|EEQ81927.1| hypothetical protein NCER_101453 [Nosema ceranae BRL01]
          Length = 327

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 107/233 (45%), Gaps = 21/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           MV  ++  +R  AR      + YTEM+  D  +R             +  ++PL +QI G
Sbjct: 17  MVGNSELAWRILARRY-GADICYTEMVNCDTFIRSKINPLSNRWYTTNKIDRPLIIQICG 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D++K+++ + I++++  + I++N+GCP     +G++G+ LM +   V + +  +   L 
Sbjct: 76  NDVNKMLKVSLILQEY-CDAIDINLGCPQEIARKGNYGSFLMDDLLKVKEIVTVLSNNLK 134

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K RI    +          K I+++G   + +H R    +GL+           +
Sbjct: 135 VPVTCKIRIFESIEKSV----EYAKMIEQAGCKMLTVHGRTRDQRGLNT------GLASW 184

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
           D +  IK  + ++ +  NG +    D+   ++     DGVM+      N  + 
Sbjct: 185 DHIRAIK-ASLNIPVISNGNIINNSDIDNCVE-YTKCDGVMVAETHLYNPLIF 235


>gi|308808596|ref|XP_003081608.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
 gi|116060073|emb|CAL56132.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
          Length = 639

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 54/284 (19%), Positives = 110/284 (38%), Gaps = 27/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM +A  +L+GD+K   ++     EK   +QI G     + 
Sbjct: 281 NLPFRRICTDL-GADITVSEMAMASNLLKGDRKEWALVRRHPIEKCFGIQICGGYPDLMT 339

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++  +   + I++N+GCP   V     G  LM + D +   + +M    S PVT+K
Sbjct: 340 RCAELLDNEVHCDFIDVNMGCPIDGVCAKGAGGSLMRDTDRLKRVVRSMTSVSSTPVTIK 399

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G  D        +++   K  G     +H R         ++ R     D+  ++  
Sbjct: 400 LRMGYFDDPSRYVAHDIISKAKSWGAYAATLHGRT--------REQRYSRLADWSYIHRC 451

Query: 183 KKENP--DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   +L +  NG +       + +    +   MIGR A     ++T + E     ++
Sbjct: 452 ADASALNNLPLIGNGDVYTYQDWNEQIANEKISTCMIGRGAIIKPWLMTEIKEQRHWDIS 511

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQITRHMI 281
            +  +           +      Y   H  S    +++  R+++
Sbjct: 512 ANERL----------DLFKDFVHYGLEHWGSDSVGVEKTRRYLL 545


>gi|302848098|ref|XP_002955582.1| hypothetical protein VOLCADRAFT_43118 [Volvox carteri f.
           nagariensis]
 gi|300259205|gb|EFJ43435.1| hypothetical protein VOLCADRAFT_43118 [Volvox carteri f.
           nagariensis]
          Length = 320

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 92/312 (29%), Positives = 145/312 (46%), Gaps = 25/312 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR-GDKKNILGFSTQEKPLALQIGGADIS 60
           +DWTD H+R  ARLL+    L+TEM+V   IL   +    L F  +++PL LQ+GG+D +
Sbjct: 10  MDWTDMHFRQLARLLSRRTWLWTEMVVDKTILHTQNLDKFLWFPPEQRPLVLQLGGSDPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSIP- 118
            L  AA    ++GY+EINLN GCPS RV     FGA LM+ P +V  C AAM +A+    
Sbjct: 70  TLAAAAARAVEYGYDEINLNCGCPSDRVASAGCFGAALMMRPHLVARCTAAMAEAMKGDL 129

Query: 119 --VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V + C  G        ++R       +S            +++GLSP  NR +P L +
Sbjct: 130 RLVMMTCYPGGRYLGAIFSVRCCTILTARSPPPLPPGVRPPWVVQGLSPHQNRTVPPLRH 189

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI------------GRAAYKNSA 224
              + + ++ P L   LNGG+ +  +A        G+ +            GR AY +  
Sbjct: 190 QWAWALARDFPHLQFSLNGGVLNCHEARFQ-----GLSVGGNGGGIVGVMIGRGAYNDPW 244

Query: 225 -MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
             L   D          +P +  V + +     + +  Y   H  +   ++ + R ++ L
Sbjct: 245 GCLADADRAVYGEPYNPAPSRRWVIERYREYAESMVGRYPDGH--ADPSIRTLMRPLLNL 302

Query: 284 FHGFPNSRRCRH 295
           FHG P  +R ++
Sbjct: 303 FHGEPGCKRWKN 314


>gi|256831223|ref|YP_003159951.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
 gi|256580399|gb|ACU91535.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
          Length = 324

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 59/299 (19%), Positives = 116/299 (38%), Gaps = 23/299 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R        +A   TEM+ A  ++        +L    Q+ PL +Q+ G++ 
Sbjct: 19  AGFSDLPFRLLCHEYGCHA-AVTEMVSAKGLIYDSPGTNELLQTCDQDSPLVVQLFGSEE 77

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             LV++ + +   G+   +LN GCP  +V +   GA L+  P+ +     +M  A   P 
Sbjct: 78  PFLVQSIERLRKAGFRYFDLNCGCPVRKVIKTGSGAALLKEPENLLKIAKSMIDAAE-PG 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            +  +I +   +       +   +++ G   + +H R                + D+  +
Sbjct: 137 CMGFKIRLGWYVGQPVYLQVATKLEELGAGWVTMHPRFG--------AQGFTGHADWSHL 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             +K E   L +  +G L     A+K +    VD +M  R A  + ++ T    Y     
Sbjct: 189 KTLK-ERVTLPVIASGDLFHAEDAIKCIEQTSVDSIMFARGALNDPSIFT---RYLQLRR 244

Query: 238 TGSSPIKT-RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               P K+ +  +D  R++S     +    L     L ++   +     G P +R  R 
Sbjct: 245 HEEPPAKSWQQMEDMVRRLSELYPQHGMDRLG----LLKMRTLVPRFLKGLPGARALRR 299


>gi|326435888|gb|EGD81458.1| DUS3L protein [Salpingoeca sp. ATCC 50818]
          Length = 612

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 62/285 (21%), Positives = 109/285 (38%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +A  +L G K    +L     E    +QI G       
Sbjct: 273 NLPFRRLCKRL-GADITCGEMAMARNLLEGQKSEWALLRRHESEDVFGVQICGNHPRLTT 331

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  +++  +   + I+LN GCP   V     G+ L+     +GD +  M  A  +P+TVK
Sbjct: 332 KCVELLSNETDVDFIDLNCGCPIDLVFNHGSGSALLARKRRLGDILRGMSFASRVPITVK 391

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV +   +     L+   + +GV+ + IH R         +  R     D+  V + 
Sbjct: 392 IRAGVTNT--SWTSHTLMPIFRDAGVSLVSIHGRS--------RQQRYARLADWGYVRKC 441

Query: 183 KKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +E   L +  NG +    +A++      V G+M+ R A     + T + E     ++ S
Sbjct: 442 VEEAKGLPVYGNGDILSFEEAMQHKATTGVSGLMLARGALIKPWLFTEIKEQRHWDISSS 501

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        +      DY   H  S  +  + TR  +   L
Sbjct: 502 ERF----------QFLKDFADYGLTHWGSDQQGVETTRRFLLEWL 536


>gi|78358129|ref|YP_389578.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
 gi|78220534|gb|ABB39883.1| dihydrouridine synthase family protein [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 376

 Score =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 98/238 (41%), Gaps = 16/238 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKP-LALQIGGA 57
           M       YR          L++T M  A A+   +      FS   +E P L  Q+ GA
Sbjct: 64  MAGLGHIAYRQVLESFGGCGLVFTGMCSARAVPTENPARSPVFSWRPEELPALVCQLFGA 123

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  AA+ VE  G+  +++N+GC  A + +   GA L+ +P+     + A+ +A+S+
Sbjct: 124 DPQDMAAAARRVESEGFFGVDINMGCSVAPIVKKGCGADLLRDPERAVRMVDAVRRAVSV 183

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G           NL + ++ +G + +  H R A  +         I      
Sbjct: 184 PVFVKMRTGWSPDPEPAV--NLARRLQDAGADALVFHPRVAPDRRTHRPRTAHIG----- 236

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
               + K+  D+ +  NG + D +    +L     DGV +GR A     +       F
Sbjct: 237 ----LVKDAVDIPVIGNGDVFDAADCAAMLERTGCDGVSLGRLAIARPWIFAQWTRGF 290


>gi|229083615|ref|ZP_04215942.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-44]
 gi|228699693|gb|EEL52351.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-44]
          Length = 332

 Score =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        N +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWENWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    +++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGMELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|195118882|ref|XP_002003961.1| GI20204 [Drosophila mojavensis]
 gi|193914536|gb|EDW13403.1| GI20204 [Drosophila mojavensis]
          Length = 614

 Score =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 57/289 (19%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G   +  +      E    +Q+ G + + + 
Sbjct: 279 NLPFRRICKEF-GADITCGEMACAVPLLKGLGQEWALTKRHESENVFGVQLCGNNPNVIS 337

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 338 QAAQVLHETSRVDFIDLNIGCPIDLIYQQGGGSALMHRTNILELTVRSCSALSDRLPFTV 397

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV           L+  +++ G + + +H R         ++ R     ++  + E
Sbjct: 398 KMRTGVYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTRQANWTYIEE 447

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             K+   + +  NG +      ++     P V  VMIGR A     +   + E       
Sbjct: 448 CAKQAKHIPVIGNGDILSYEDYVERRALAPHVSSVMIGRGALIKPWIFQEIKEQ-----K 502

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
             SP  T+  +   R       +Y   H  S  K  + TR  +  +  F
Sbjct: 503 ACSPSSTQRFEMMRR-----YCNYGLEHWGSDTKGVESTRRFLLEWQSF 546


>gi|324324412|gb|ADY19672.1| putative tRNA-dihydrouridine synthase [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 329

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        N +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWENWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|126649588|ref|ZP_01721829.1| hypothetical protein BB14905_06608 [Bacillus sp. B14905]
 gi|126593913|gb|EAZ87836.1| hypothetical protein BB14905_06608 [Bacillus sp. B14905]
          Length = 324

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 71/330 (21%), Positives = 129/330 (39%), Gaps = 36/330 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    + +      L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRQVVSEAGRPDVFFTEFTNSDSYCHPEGQKSVRGRLIFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 81  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D          +  I K  +  + IH R         +      +  +
Sbjct: 140 LPVSVKTRLGYKD---VEEWEEWLTHIFKQDIANLSIHLRT--------RKEMSQVDAHW 188

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 189 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 248

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +  S+             +D + ++       +   LH   K+            GF  +
Sbjct: 249 KEHSSKEYLDLLRLQLNLQDQYEEVL----PRSITGLHRFFKI---------YVKGFRGA 295

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIE 320
              R  L +   ++     +++      IE
Sbjct: 296 GELRSQL-MNTKSTDEVRALLDRFEANHIE 324


>gi|228913068|ref|ZP_04076707.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228846473|gb|EEM91486.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 336

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|21430920|gb|AAM51138.1| SD26982p [Drosophila melanogaster]
          Length = 604

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + L 
Sbjct: 269 NLPFRRICKEF-GADITCGEMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMLN 327

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 328 QAAQVIHETAQVDFIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSDRLPFTV 387

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G + + +H R         ++ R   + ++  + E
Sbjct: 388 KMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWAYIEE 437

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++       V  VMIGR A     +   + E      +
Sbjct: 438 CAAKAKRMPVIGNGDILSYEDYMERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWS 495

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            SS  +  + + F         +Y   H  S  K  + TR  +  +  F
Sbjct: 496 PSSGQRYEMLQKF--------CNYGLEHWGSDTKGVETTRRFLLEWQSF 536


>gi|288555000|ref|YP_003426935.1| tRNA-dihydrouridine synthase [Bacillus pseudofirmus OF4]
 gi|288546160|gb|ADC50043.1| tRNA-dihydrouridine synthase [Bacillus pseudofirmus OF4]
          Length = 327

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 67/332 (20%), Positives = 131/332 (39%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++    D     +  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGMKSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+  P++  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAELGFKGLDINMGCPVPNVVQNGKGSGLIRRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +       R+ +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRIGFAE---VDEWRDWLTHILKQDIVNLSIHLRT--------RNEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P   + +NG + D    LK++    VDGVMIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPHTLLTINGDIPDRQTGLKLVEQYGVDGVMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +    R   +  +  +I         GF  +
Sbjct: 241 -AFEKEPKDHSSKELLDLLRLHLDLYDKYSHLELRPFKALHRFFKI------YVKGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            + R+ L +   ++     +++   +  +E +
Sbjct: 294 GQLRNEL-MNTESTDEVRDLLDQFESANLEGM 324


>gi|329577257|gb|EGG58721.1| TIM-barrel protein, nifR3 family [Enterococcus faecalis TX1467]
          Length = 252

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 60/260 (23%), Positives = 108/260 (41%), Gaps = 20/260 (7%)

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           EAAK VE+      I++N+GCP  ++ +   GA  +L+P+ V + + A+  A+S+PVTVK
Sbjct: 2   EAAKFVEENTQAAIIDINMGCPVNKIIKAEAGAKWLLDPNKVHEMVHAVSSAVSLPVTVK 61

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G D+         L    +++G + I +H R  +               ++D++ E+
Sbjct: 62  MRTGWDEDHLYAVDNALA--AEQAGASAIAMHGRTRV--------QMYEGTANWDVLKEV 111

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           KK     F+G NG ++    A ++L     DGVMIGRAA  N  M+    EY        
Sbjct: 112 KKHLTIPFMG-NGDVKTPEDAKRMLEYVGADGVMIGRAALGNPWMIQRTKEYLETGELMP 170

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
            P  +         I+                +++  +H      G   + + +  +   
Sbjct: 171 EPSPSEKIN-----IAKVHLQRLVDLKGEKIAVREFRQHASYYLKGISRAAKVKVAINQV 225

Query: 301 AGASTATHHIIETAFNLMIE 320
                A   +++     + +
Sbjct: 226 ET-QQAVVDLLDAFVEKISK 244


>gi|327438626|dbj|BAK14991.1| tRNA-dihydrouridine synthase [Solibacillus silvestris StLB046]
          Length = 322

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 117/304 (38%), Gaps = 29/304 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDLVFRHVVAEAGRPDVFFTEFTNSESYCHPDGIKSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPDNFRKMSIGMAELGFKGIDINMGCPVPNVAGRGKGSGLILRPDVAAELIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       +  +  I K  +  + IH R              IP    
Sbjct: 138 LPVSVKTRLGYKEID---EWKEWLTHILKQDIANLSIHLRTRKEMSAVDAHWELIPE--- 191

Query: 177 DIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
             +  ++ E  P+  + +NG + D    L++     +DG+MIGR  +KN      V    
Sbjct: 192 --IKALRDEIAPNTLLTINGDIPDRQVGLELAEKYGIDGIMIGRGIFKNPFAFEKV---- 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  SP +          +     +   R +    +  +I         GF  +   
Sbjct: 246 ---PKEHSPEEYLDLLKLQLDLQDKYAEELPRSMSGLHRFFKI------YVKGFRGAGEL 296

Query: 294 RHIL 297
           R+ L
Sbjct: 297 RNQL 300


>gi|195345193|ref|XP_002039157.1| GM17377 [Drosophila sechellia]
 gi|194134287|gb|EDW55803.1| GM17377 [Drosophila sechellia]
          Length = 605

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + + 
Sbjct: 270 NLPFRRICKEF-GADITCGEMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMIN 328

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 329 QAAQVIHETAQVDFIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSDRLPFTV 388

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G + + +H R         ++ R   + ++  + E
Sbjct: 389 KMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWAYIEE 438

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++       V  VMIGR A     +   + E      +
Sbjct: 439 CAAKAKRMPVIGNGDILSYEDYIERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWS 496

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            SS  +  + + F         +Y   H  S  K  + TR  +  +  F
Sbjct: 497 PSSGQRYEMLQKF--------CNYGLEHWGSDTKGVETTRRFLLEWQSF 537


>gi|157691447|ref|YP_001485909.1| tRNA-dihydrouridine synthase [Bacillus pumilus SAFR-032]
 gi|157680205|gb|ABV61349.1| tRNA-dihydrouridine synthase [Bacillus pumilus SAFR-032]
          Length = 324

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 121/324 (37%), Gaps = 28/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++    D     K  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGIQSVKGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFQGLDINMGCPVPNVTQNGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + ++ I +  +  + IH R              IP    
Sbjct: 138 LPVSVKTRLGFTE---VDEWHDWLRHILEQDIVNLSIHLRTRKEMSQVDAHWELIP---- 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +I+    +  PD  + +NG + D    LK+     VDGVMIGR  + N          F 
Sbjct: 191 EIIKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGVMIGRGIFHNPF-------AFE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +  +          +    +    R   +  +  +I         GF  +   R
Sbjct: 244 KEPKEHTSDELLGLLRLHLDLHDQYSSLGLRPFKALHRFFKI------YVKGFRGASFLR 297

Query: 295 HILTVEAGASTATHHIIE-TAFNL 317
           + L   +        + E  A N 
Sbjct: 298 NQLMNTSSTDEVRAMLDEFEARNQ 321


>gi|228925577|ref|ZP_04088666.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228983574|ref|ZP_04143779.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229154086|ref|ZP_04282211.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 4342]
 gi|228629366|gb|EEK86068.1| tRNA-dihydrouridine synthase [Bacillus cereus ATCC 4342]
 gi|228776170|gb|EEM24531.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228834055|gb|EEM79603.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 336

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|196045371|ref|ZP_03112603.1| conserved hypothetical protein [Bacillus cereus 03BB108]
 gi|301052047|ref|YP_003790258.1| putative dihydrouridine synthase [Bacillus anthracis CI]
 gi|196023955|gb|EDX62630.1| conserved hypothetical protein [Bacillus cereus 03BB108]
 gi|300374216|gb|ADK03120.1| probable dihydrouridine synthase [Bacillus cereus biovar anthracis
           str. CI]
          Length = 329

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|329117282|ref|ZP_08245999.1| dihydrouridine synthase (Dus) [Streptococcus parauberis NCFD 2020]
 gi|326907687|gb|EGE54601.1| dihydrouridine synthase (Dus) [Streptococcus parauberis NCFD 2020]
          Length = 319

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 128/323 (39%), Gaps = 39/323 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   + +    D     K  L ++  E+PL   I G
Sbjct: 20  MEDVTDVAFRHVVAKAGRPDVFFTEFTNSASYCHPDGIESVKGRLTYTHDEQPLVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E AK +++ G+  +++N+GCP+  V +   G+ L+L P++    I A  +   
Sbjct: 80  DVPDNFAEMAKGMKEMGFAGVDINMGCPAPNVFKHGRGSGLILRPEVAAQLIHATKEG-G 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G             +K + + G+  + IH R         K      +  +
Sbjct: 139 LPVSVKTRLGHAKPEEYKV---WLKHVLEQGIANLSIHLRT--------KTEMSKVDAHW 187

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIK    +  PD  + +NG + +    L+++    VDGVMIGR  + N      V 
Sbjct: 188 EMIGEIKELRDRIAPDTLLTINGDIPNRQVGLELVEKYGVDGVMIGRGIFHNPYAFEKVQ 247

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S           +   D +R        Y  R   S  +  +I         GF  +
Sbjct: 248 SAHS----------PKELIDLFRYHLDQFDKYQLRPFPSMKRSFKI------YIRGFAGA 291

Query: 291 RRCRHILTVEAGASTATHHIIET 313
              R  L ++A  +     +++ 
Sbjct: 292 NELRIAL-MDAKNTDECRKLVDE 313


>gi|223995337|ref|XP_002287352.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220976468|gb|EED94795.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 353

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 92/327 (28%), Positives = 134/327 (40%), Gaps = 79/327 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------------GDKKNILGF 43
           M+D +   +R+F RLLT  A ++TEM+VA+ +                    D K   G+
Sbjct: 14  MLDVSTVEFRYFMRLLTKRAFIWTEMVVAETLWHQSNQKGVLSSGDDLELEPDLKRHCGW 73

Query: 44  STQE----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
              +     P+  QIG  D  +   A ++V   GY+ I+LN  CPS RV    FGA LM 
Sbjct: 74  YEDQYLNPHPVVCQIGTNDPKQAEFATRVVHKLGYDRIDLNAECPSDRVAGREFGAALMR 133

Query: 100 NPDIVGDCIAAMCKAL-------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           + D   + + AM            IPV+VK RIGVD+      L   V+ +  +G     
Sbjct: 134 DHDTAIEVVRAMVDTAQSTKSDNPIPVSVKTRIGVDEFDTFEHLEGWVQRLVDAGCTWFI 193

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI------ 206
           IHARK   +GLSP  NR +P L+Y  VY + +  P      NGG+  +  A ++      
Sbjct: 194 IHARKVYTQGLSPAQNRTVPPLNYPRVYRLLQRFPSCDFWFNGGIMSLEHAKQVAFGYTG 253

Query: 207 -------------------------------------------LPSVDGVMIGRAAYKNS 223
                                                      LP++ GVM+GR A  + 
Sbjct: 254 VGDSDLIRETSSEETDCIDDDHTVPCQRCGVPHGSCIAPPRMSLPNLKGVMVGRLARDHP 313

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           + L T+D +F      S P K R +  
Sbjct: 314 SELATIDSHFYGE--ASDPCKNRRELM 338


>gi|312079658|ref|XP_003142269.1| tRNA-dihydrouridine synthase 4 [Loa loa]
 gi|307762565|gb|EFO21799.1| tRNA-dihydrouridine synthase 4 [Loa loa]
          Length = 333

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/281 (21%), Positives = 115/281 (40%), Gaps = 34/281 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   RL   + + +T MI A   +  ++     FS    + P  +Q    +
Sbjct: 37  MVRYSKLPFRMLVRLYAVD-VAFTPMIYAKHFIASEQCRSAEFSTCPGDNPTIVQFATNN 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +   AA  +  +    I+LN GCP   V +  +G+ L+++P+ + D +A   + +S P
Sbjct: 96  PEEFFTAAMFISRYS-RGIDLNCGCPQRDVMKEGYGSSLLVDPERIADIVATARRRISKP 154

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K R+  + Q+         +  +K+GV+ I +H R    +             D
Sbjct: 155 DFTVSIKIRLKTNRQLT----LETCRQAEKAGVSFITVHGRTPEQRS---------EPAD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+++  IK     + +  NG ++   QAL++     VDGVM      +N AM        
Sbjct: 202 YEMIKLIKSSL-SIPVIANGNIKSYEQALQVVKYTGVDGVMSANGLLENPAMFA------ 254

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                G +    +   D+ R  +     +   H      L+
Sbjct: 255 -----GYTSTPKQCVADWVRLATEYGCPFDLFHQQLMFMLR 290


>gi|229042218|ref|ZP_04189972.1| tRNA-dihydrouridine synthase [Bacillus cereus AH676]
 gi|228727153|gb|EEL78356.1| tRNA-dihydrouridine synthase [Bacillus cereus AH676]
          Length = 336

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 130/328 (39%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGF---KALSEWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  I +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLITINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              R+ L +   ++     +++   + +
Sbjct: 301 AELRNQL-MSTKSTDEVRALLDKFEDSV 327


>gi|77463371|ref|YP_352875.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides 2.4.1]
 gi|126462226|ref|YP_001043340.1| nifR3 family TIM-barrel protein [Rhodobacter sphaeroides ATCC
           17029]
 gi|77387789|gb|ABA78974.1| tRNA-dihydrouridine synthase, nifR3 [Rhodobacter sphaeroides 2.4.1]
 gi|126103890|gb|ABN76568.1| putative TIM-barrel protein, nifR3 family [Rhodobacter sphaeroides
           ATCC 17029]
          Length = 326

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 110/288 (38%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R  A       L+ +EM+ +  ++    +          E   A+Q+ G D
Sbjct: 19  MAGITDLPFRRLAVRF-GAGLVVSEMVASREVVCAGAEARARAEIGAAEGRTAVQLAGCD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     I A+  A+++P
Sbjct: 78  PHWMAEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALIEAVVGAVAVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D+ +  +    + +  + +GV  I IH R         +        D+  
Sbjct: 138 VTLKMRLGWDEGM--LNAPEIARRAEAAGVAMITIHGRT--------RCQFYTGRADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +         NG +    +  A        GVM+GR A     +L  V       
Sbjct: 188 IRPVVEAVSVPV-VANGDITGPEEAQAALAASGAAGVMVGRGAQGRPWLLGQVASALDGR 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                P    +           ++ Y          L+   +H+    
Sbjct: 247 AAPDVPEGEALADLVVAHYEEMLSFY-----GRDLGLRVARKHLNWYL 289


>gi|89098483|ref|ZP_01171366.1| hypothetical protein B14911_09737 [Bacillus sp. NRRL B-14911]
 gi|89086728|gb|EAR65846.1| hypothetical protein B14911_09737 [Bacillus sp. NRRL B-14911]
          Length = 304

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 121/307 (39%), Gaps = 34/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 1   MEDVTDVVFRHVVSEAARPDVFFTEFTNTESYCHPEGNQSVRGRLTFTEDEQPMVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  V + G+  I++N+GCP   V +   G+ L+L PD+  D + A  KA  
Sbjct: 61  DKPEFFRQTSIGVAEQGFRGIDINMGCPVPNVAQRGKGSGLILRPDVAADIVQA-AKAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +  I +  +  + IH R         +      +  +
Sbjct: 120 LPVSVKTRLGYTE---VDEWQDWLTHILEQDIANLSIHLRT--------RKEMSEVDAHW 168

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D     +++    VDGVMIGR  +KN        
Sbjct: 169 ELIPEIKKLRDRVAPDTLLTINGDILDRQAGQQLVDQYGVDGVMIGRGIFKNPFAFE--- 225

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                P   +      + +           +  AR   +  +  +I         GF  +
Sbjct: 226 ---KEPKDHTPKELLDLLRLHLDLHDKYSKELEARPFRALHRFFKI------YVKGFRGA 276

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 277 GELRNQL 283


>gi|317180488|dbj|BAJ58274.1| transcriptional regulator [Helicobacter pylori F32]
          Length = 328

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/322 (18%), Positives = 128/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      N I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVNGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRTPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEVKSM-RESIEEFFNQ 310


>gi|225862371|ref|YP_002747749.1| hypothetical protein BCA_0408 [Bacillus cereus 03BB102]
 gi|225786832|gb|ACO27049.1| conserved hypothetical protein [Bacillus cereus 03BB102]
          Length = 329

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSMGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGFKELS---EWEDWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|307203528|gb|EFN82561.1| tRNA-dihydrouridine synthase 3-like [Harpegnathos saltator]
          Length = 660

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 56/282 (19%), Positives = 116/282 (41%), Gaps = 27/282 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  IL+G ++   ++     E    +Q+ G +   L 
Sbjct: 325 NLPFRRICKEY-GADITCGEMALAPKILKGTQEEWALVKRHECEDVFGVQLCGNNPGVLT 383

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++  +   + I+LN+GCP   ++    G+ ++   +++   + ++ + L IP+++K
Sbjct: 384 RCAQLLNREIDVDYIDLNLGCPIDLIYRQGGGSGMLNRLNVLETVVKSVSQVLDIPLSIK 443

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV    P     NL+    + GV+ I +H R         ++ R     D++ + + 
Sbjct: 444 TRTGVYIDKPIA--HNLMPKFHEWGVSMITVHGRS--------REQRYTKLADWEYIEKC 493

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
                 + +  NG +   +D  +  +   +V G+ IGR A     + T + E     +  
Sbjct: 494 AVAASPVPVFGNGDILSFDDYQRMKETYSTVQGITIGRGALIKPWIFTEIKERKLIDI-- 551

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             P   R D      I     +Y   H  S  +  + TR  +
Sbjct: 552 --PSGERFD------ILRKYANYGLEHWGSDTRGVETTRRFM 585


>gi|304405948|ref|ZP_07387606.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
 gi|304345191|gb|EFM11027.1| dihydrouridine synthase DuS [Paenibacillus curdlanolyticus YK9]
          Length = 326

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 124/327 (37%), Gaps = 36/327 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFTNTESYCHPDGHQSVRGRLAFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V +   G+ L+  P+     I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAQQGFKGIDINMGCPVANVAQNGQGSGLICRPETAAAIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G D        R+ +  I K G+  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGFD---AIEEWRDWLTHILKQGIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFNNPFAFE--K 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           E   +       +            +  +  +           + ITR       GF  +
Sbjct: 245 EPREHGSEELLSLLRLHLDLHDHYSALELRPF-----------KHITRFFKIYVRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNL 317
              R+ L +   ++     +++   + 
Sbjct: 294 SELRNNL-MNTKSTNEVRAMLDEFISQ 319


>gi|218887109|ref|YP_002436430.1| dihydrouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218758063|gb|ACL08962.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris str. 'Miyazaki
           F']
          Length = 351

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/302 (19%), Positives = 108/302 (35%), Gaps = 23/302 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A   TEM+ A  +L      +++L  + ++ PL LQ+ GAD 
Sbjct: 28  AGYSDLPFRLLCRE-HGAAACCTEMVSAKGLLYHSPGTRDLLASTPEDAPLVLQLFGADA 86

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIP 118
             +      + + G+   +LN+GC   +V +   G+ +  + D       AM + A    
Sbjct: 87  DIMRTVMPGLLEQGFRWFDLNMGCSVPKVVKTGCGSAMSRDMDNALSVARAMVEVAGEGR 146

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G   Q      R +   ++ +G   I +H R A                 +  
Sbjct: 147 VGFKMRLGW--QAGEETWREMALRLQDAGAGWITLHPRFA--------RQGFGGEARWSA 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + E+      + +  +G L   + A++ +    V  VM  R A  N A+        +  
Sbjct: 197 LRELA-ATLTIPVIASGDLFTAADAVRCVRETGVATVMFARGAMNNPAVFDEYRVLLAGG 255

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                      D D  + +     + A  H      L ++   +       P  R  R+ 
Sbjct: 256 QPPPP------DADRLKALIRRHLELALAHSGERTALLKMRTFVPRYVRHIPGVRALRNR 309

Query: 297 LT 298
           L 
Sbjct: 310 LA 311


>gi|289549381|ref|YP_003470285.1| tRNA dihydrouridine synthase B [Staphylococcus lugdunensis
           HKU09-01]
 gi|315659951|ref|ZP_07912809.1| dihydrouridine synthase [Staphylococcus lugdunensis M23590]
 gi|289178913|gb|ADC86158.1| tRNA dihydrouridine synthase B [Staphylococcus lugdunensis
           HKU09-01]
 gi|315494852|gb|EFU83189.1| dihydrouridine synthase [Staphylococcus lugdunensis M23590]
          Length = 326

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 66/327 (20%), Positives = 123/327 (37%), Gaps = 37/327 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + + G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSFGLAEMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYDID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    +++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKHMRDEIAPNTLLTINGDIPDRKTGMELATKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                        +    ++        +T +         + + + R       G   +
Sbjct: 243 ---------EKEPREHTSEELLSLFRLHLTLFDKHSSDETQQFKSLRRFFKIYVRGIKGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNL 317
            + RH L        A    +  AF  
Sbjct: 294 SQLRHQLMDTQTTDEARA--LLDAFEA 318


>gi|283851081|ref|ZP_06368365.1| dihydrouridine synthase DuS [Desulfovibrio sp. FW1012B]
 gi|283573477|gb|EFC21453.1| dihydrouridine synthase DuS [Desulfovibrio sp. FW1012B]
          Length = 329

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 119/301 (39%), Gaps = 22/301 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R L   A   TEM+ A  +     + + +L  +  + PLA+Q+ GA+ 
Sbjct: 18  AGFSDLPFRLLCRELGACA-AVTEMVSAKGLFYDSKNTRRLLATTPADAPLAVQLFGAEP 76

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             L  A   +   GY   +LN GC   +V +   GA L+ +PD + DC  AM   AL   
Sbjct: 77  EYLFRAVASLAGDGYALFDLNCGCSVRKVVKTGAGAALLGDPDRLVDCARAMARAALPGR 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R+G   + P+ A  +L + +  +GV  + +H R A  +G S          D + 
Sbjct: 137 VGVKLRLG--PKPPSFAALDLARRLADAGVAWLTLHPRHAS-QGFS-------GTADQEA 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +      +P L +  +G L     A   L      GVM  R A  +  +           
Sbjct: 187 LAAFVAASP-LPVLASGDLLTAGDAEACLTRTGAAGVMYARGALADPRVFGRHANLIRQT 245

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
               +    R+  D  R+ +A   +YA         L ++   +       P  R  R  
Sbjct: 246 RGLPALPLPRLC-DVIRRHAALCREYADDRRA----LLRMRTAVPRYLREMPGCRALRDR 300

Query: 297 L 297
           L
Sbjct: 301 L 301


>gi|125556734|gb|EAZ02340.1| hypothetical protein OsI_24443 [Oryza sativa Indica Group]
          Length = 396

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 60/282 (21%), Positives = 113/282 (40%), Gaps = 21/282 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 69  MVDNSELPFRMLCRRYGATG-AYTPMLHSRIFSENEKHRAMEFTTCKEDRPLFVQFCAND 127

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAKIVE +  + +++N GCP      G +GA LM N  ++   +  +   L +P
Sbjct: 128 PDILLQAAKIVEPY-CDYVDINFGCPQRIARRGYYGAFLMDNLPLIKSLVQNLSANLHVP 186

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI    +          K ++++G + + +H R         KD +K    D+D 
Sbjct: 187 VSCKIRIFPRLEDT----LAYAKMLEEAGASLVAVHGRT-----RDEKDGKKF-RADWDA 236

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT--TVDEYFS 234
           +  +K +   + +  NG +  +      L     DGV+      +N A+       E+  
Sbjct: 237 IKAVK-DALRIPVLANGNIRHLDDVKDCLEHTGADGVLSAETLLENPALFAGFRTKEWKE 295

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           N     +    + D     +       Y          + ++
Sbjct: 296 NGDEDEASGLDQADLVI--EYLKLCEQYPVPWRMVRSHVHKM 335


>gi|27467074|ref|NP_763711.1| hypothetical protein SE0156 [Staphylococcus epidermidis ATCC 12228]
 gi|251811498|ref|ZP_04825971.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|39930886|sp|Q8CU07|DUS_STAES RecName: Full=Probable tRNA-dihydrouridine synthase
 gi|27314616|gb|AAO03753.1|AE016744_156 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251805002|gb|EES57659.1| tRNA-dihydrouridine synthase [Staphylococcus epidermidis
           BCM-HMP0060]
          Length = 326

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 126/328 (38%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D T+  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTNIVFRHVVSEAARPDVFFTEFTNTESYCHPEGIHSVRGRLTFSDDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  + D G+  I+LN+GCP A V +   G+ L+L P+   + I A  KA  
Sbjct: 79  DKPEQFREMSIGLADMGFKGIDLNMGCPVANVAKKGKGSGLILRPETAAEIIQA-SKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R+ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYDID---EWRDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DG+MIGR  + N        
Sbjct: 187 ELIEAIKTLRDEIAPNTLLTINGDIPDRQTGLELANKYGIDGIMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +        ARH  S  +  +I         G   +
Sbjct: 241 -AFEKEPREHSSKELLGLLRLHLSLFEKYDKDEARHFKSLRRFFKI------YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLM 318
              RH L +   +      +++T    M
Sbjct: 294 SELRHQL-MNTQSIAEARELLDTFEARM 320


>gi|208434637|ref|YP_002266303.1| transcriptional regulator [Helicobacter pylori G27]
 gi|208432566|gb|ACI27437.1| transcriptional regulator [Helicobacter pylori G27]
          Length = 328

 Score =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 128/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKVIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEVKSM-RESIEEFFNQ 310


>gi|223041930|ref|ZP_03612115.1| tRNA-dihydrouridine synthase C [Actinobacillus minor 202]
 gi|223017284|gb|EEF15711.1| tRNA-dihydrouridine synthase C [Actinobacillus minor 202]
          Length = 319

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 70/331 (21%), Positives = 128/331 (38%), Gaps = 41/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNI------LGFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + R     +       G +    P+ +
Sbjct: 12  MQGVLDPFLRKLLTTVNDYDLCISEFVRVVDQKLPRKTFYRLCPELYQAGKTDSGTPVRV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +P+++     A+ 
Sbjct: 72  QLLGQYPQWLAENAELAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPELIYRATQAIR 131

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++++ G N I +H R          D  +
Sbjct: 132 QAVPKEQVVSVKVRLGWD---SAEQCFEIADAVQRGGANEITVHGRTKT-------DGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I+K   ++ +  NG + D   A K   + +   +MIGR A     +   
Sbjct: 182 AERINWQAIGDIQKRL-NIPVIANGEIWDFESAKKCQEITACQALMIGRGALNTPNL--- 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  WR++   +  Y             + R    +  L  
Sbjct: 238 -----------SRVVKFNQPKLAWREVLKLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 286

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
            +P +     IL  E G +    H IE A  
Sbjct: 287 EYPEAIALFQILKTEHGYAGLKRH-IEQAVE 316


>gi|39546256|emb|CAD39831.3| OSJNBa0079F16.4 [Oryza sativa Japonica Group]
          Length = 1708

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 81/179 (45%), Positives = 114/179 (63%), Gaps = 4/179 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+    +    L F  ++ P+ LQIGG++
Sbjct: 70  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQKDNLDRFLAFPAEQHPIVLQIGGSN 129

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           +  L +A ++   + Y+EINLN GCPS +V     FGA LM +P+ VGD ++A+    ++
Sbjct: 130 LDNLAKATELANAYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIAANCNV 189

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           PV+VKCRIGVDD+     L   V   + KS      IHARKA+L GLSP +NR +P L 
Sbjct: 190 PVSVKCRIGVDDRDSYEELCEFVDKVVSKSPTRHFIIHARKALLSGLSPAENRNVPPLK 248


>gi|146277526|ref|YP_001167685.1| nifR3 family TIM-barrel protein [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555767|gb|ABP70380.1| putative TIM-barrel protein, nifR3 family [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 326

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 113/288 (39%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R  A       L+ +EM+ +  ++    + +        E   A+Q+ G D
Sbjct: 19  MAGITDLPFRRLAVRF-GAGLVVSEMVASREMVCAGTEARARAEIGAAEGRTAVQLAGCD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     + A+  A+++P
Sbjct: 78  PHWMAEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALVEAVVAAVTVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D+ +  +    + +  + +GV  I IH R         +        D+  
Sbjct: 138 VTLKMRLGWDEGM--LNAPEIARRAEAAGVAMITIHGRT--------RCQFYTGRADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +         NG +    +A   L      GVM+GR A     +L  +       
Sbjct: 188 IRPVVEAVSVPV-VANGDITGPGEARAALEASEAAGVMVGRGAQGRPWLLGRIGAALEGR 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               +P    +           ++ Y          L+   +H+    
Sbjct: 247 ALPDAPFGAALADLVVSHYEEMLSFY-----GRDLGLRVARKHLNWYL 289


>gi|118476082|ref|YP_893233.1| dihydrouridine synthase family protein [Bacillus thuringiensis str.
           Al Hakam]
 gi|228931824|ref|ZP_04094720.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|229089448|ref|ZP_04220719.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-42]
 gi|229182715|ref|ZP_04309956.1| tRNA-dihydrouridine synthase [Bacillus cereus BGSC 6E1]
 gi|118415307|gb|ABK83726.1| conserved hypothetical protein [Bacillus thuringiensis str. Al
           Hakam]
 gi|228600800|gb|EEK58379.1| tRNA-dihydrouridine synthase [Bacillus cereus BGSC 6E1]
 gi|228693925|gb|EEL47617.1| tRNA-dihydrouridine synthase [Bacillus cereus Rock3-42]
 gi|228827804|gb|EEM73542.1| tRNA-dihydrouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 336

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 123/307 (40%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +        + +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELS---EWEDWLTHIFKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDILDRKMGLELAEKYGIDGVMIGRGIFKNPFAFEKEP 253

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GFP +
Sbjct: 254 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFPGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|187607636|ref|NP_001120313.1| hypothetical protein LOC100145375 [Xenopus (Silurana) tropicalis]
 gi|156914833|gb|AAI52625.1| Zgc:92033 protein [Danio rerio]
 gi|170285083|gb|AAI60936.1| LOC100145375 protein [Xenopus (Silurana) tropicalis]
          Length = 306

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 124/284 (43%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+A   +R  K     F+T   ++PL +Q    D
Sbjct: 22  MVCYSKLAFRSLVRKYD-CDVCFTPMIIAADFMRSAKARDSEFTTHKNDRPLIVQFAAKD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 81  AQTLADAACVVSPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQIDNP 139

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L + ++ +GV+ I +H R AI +            + 
Sbjct: 140 NYAVSIKIRIHKDVRQTV----DLCQKVEAAGVSYITVHGRTAIERHQ---------PVH 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK ++  + +  NG ++ M    A+  L  VDGVM  R    N AM +  +E  
Sbjct: 187 YDTIKTIK-DSLSIPVIANGDIKSMQDVEAVCELTGVDGVMSARGLLSNPAMFSGFEE-- 243

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                       +   D+    +   T +   H H    L++IT
Sbjct: 244 ---------TPLQCVWDWVDIAAEHGTPFTCFHHHLIHMLERIT 278


>gi|156085996|ref|XP_001610407.1| dihydrouridine synthase [Babesia bovis T2Bo]
 gi|154797660|gb|EDO06839.1| dihydrouridine synthase, putative [Babesia bovis]
          Length = 355

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 109/233 (46%), Gaps = 15/233 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MV+ ++  +R   R   N  L YT M+     +  +K   + F  S  ++PL  Q+ G D
Sbjct: 19  MVNQSELPFRLLCRRY-NVDLTYTPMLHGRIFVENEKYRAVHFQTSDDDRPLIAQVCGDD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + +AA++++    + ++LN+GCP A   +G +G+ L+  PD+V   ++ + + + I 
Sbjct: 78  AGTITQAARLLKGH-VSAVDLNLGCPQAIAKDGHYGSFLLDEPDLVTGIVSRVTREVGIA 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R    D+    +  NL  S+++SG   + +H R    KG        +   D+D 
Sbjct: 137 VTCKIRKV--DKDSLQSTLNLCYSLEQSGCKALTVHGRHRSEKGT------NVGAADWDA 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
           +  I K    + +  NGG+E  +   + L     D VM   +  +   + + +
Sbjct: 189 I-RIIKSRLRIPVIANGGIETFADVERCLSYTGADAVMSSESLLERPYLFSGI 240


>gi|16077870|ref|NP_388684.1| tRNA-dihydrouridine synthase 2 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221308639|ref|ZP_03590486.1| hypothetical protein Bsubs1_04473 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312963|ref|ZP_03594768.1| hypothetical protein BsubsN3_04424 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317889|ref|ZP_03599183.1| hypothetical protein BsubsJ_04368 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322162|ref|ZP_03603456.1| hypothetical protein BsubsS_04464 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|39930914|sp|O31546|DUS2_BACSU RecName: Full=Probable tRNA-dihydrouridine synthase 2
 gi|2633127|emb|CAB12632.1| tRNA-dihydrouridine synthase 2 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|2780398|dbj|BAA24299.1| YfjN [Bacillus subtilis]
          Length = 325

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 67/332 (20%), Positives = 125/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P +  + I A  KA  
Sbjct: 79  DKPENFRKMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPAVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYTD---VDEWREWLTHILKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   D  R       +Y+         L +  +       GF  +
Sbjct: 243 ------EKEPKEHSSKELLDLLRLHLDLHDEYSKEEARPYKPLPRFFKI---YLRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 294 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGI 324


>gi|256963036|ref|ZP_05567207.1| dihydrouridine synthase [Enterococcus faecalis HIP11704]
 gi|256953532|gb|EEU70164.1| dihydrouridine synthase [Enterococcus faecalis HIP11704]
          Length = 326

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 194

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 195 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 245

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 246 KEPKTHTPQELMGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 299

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 300 AQL-MNTKSTDEVRQLL 315


>gi|326502988|dbj|BAJ95927.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 430

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 113/288 (39%), Gaps = 24/288 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 101 MVDNSELPFRMLCRRYGADA-AYTPMLHSRIFSENEKHRDMEFTTCKEDRPLFVQFCAND 159

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAK+VE    + ++LN GCP      G +GA LM N  +V   +  +   L +P
Sbjct: 160 PDILLQAAKMVEA-NCDYVDLNFGCPQRIAKRGYYGAFLMDNLPLVKSLVQNLAGNLRVP 218

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI    +          K ++++G   + +H R         KD +K    D+D 
Sbjct: 219 VSCKIRIFPRLEDT----LAYAKMLEEAGAALVAVHGRT-----RDEKDGKKF-RADWDA 268

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +  M      L     DGV+      +N A+           
Sbjct: 269 IKAVK-DALRIPVLANGNIRHMEDVKSCLQHTGADGVLSAEPLLENPALFAGFR------ 321

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            T         D D     +    +Y           + I  H+  L 
Sbjct: 322 -TKEWKEDGNEDGDGGLDPADLAIEYLKLCEQYPVPWRMIRSHLHKLL 368


>gi|195580263|ref|XP_002079972.1| GD24232 [Drosophila simulans]
 gi|194191981|gb|EDX05557.1| GD24232 [Drosophila simulans]
          Length = 605

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + + 
Sbjct: 270 NLPFRRICKEF-GADITCGEMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMIN 328

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 329 QAAQVIHETAQVDFIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSDRLPFTV 388

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G + + +H R         ++ R   + ++  + E
Sbjct: 389 KMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWAYIEE 438

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++       V  VMIGR A     +   + E      +
Sbjct: 439 CAAKAKRMPVIGNGDILSYEDYVERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWS 496

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            SS  +  + + F         +Y   H  S  K  + TR  +  +  F
Sbjct: 497 PSSGQRYEMLQKF--------CNYGMEHWGSDTKGVETTRRFLLEWQSF 537


>gi|315586603|gb|ADU40984.1| tRNA-dihydrouridine synthase B [Helicobacter pylori 35A]
 gi|332673473|gb|AEE70290.1| tRNA-dihydrouridine synthase B [Helicobacter pylori 83]
          Length = 328

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|317009261|gb|ADU79841.1| transcriptional regulator [Helicobacter pylori India7]
          Length = 328

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|307273704|ref|ZP_07554932.1| dihydrouridine synthase [Enterococcus faecalis TX0855]
 gi|306509717|gb|EFM78759.1| dihydrouridine synthase [Enterococcus faecalis TX0855]
          Length = 362

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 230

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 231 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY-------AFE 281

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 282 KEPKTHTPQELMGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 335

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 336 AQL-MNTKSTDEVRQLL 351


>gi|298245190|ref|ZP_06968996.1| dihydrouridine synthase DuS [Ktedonobacter racemifer DSM 44963]
 gi|297552671|gb|EFH86536.1| dihydrouridine synthase DuS [Ktedonobacter racemifer DSM 44963]
          Length = 404

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 69/375 (18%), Positives = 126/375 (33%), Gaps = 77/375 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           M   TD   R    L     ++ TE    + + +G  +    F  +  E+P   QI G  
Sbjct: 20  MDGVTDAPCRTMHGLHGRPDIVLTEFTNVEGLWKGSDRIFRDFLYTPAERPAIAQIFGCR 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                 AA +  + G++ +++N+GCP+ ++     GA L+  PD     I A    +   
Sbjct: 80  PEYFYLAAHVACELGFDGVDINMGCPATKIANKGGGAALIRVPDTAKAIIRATQAGVRDW 139

Query: 117 ----------------------------------------IPVTVKCRIGVDDQIPAVAL 136
                                                   +PV+VK R+G D    ++ +
Sbjct: 140 ANGQTLEELGMEPERIQRIRQMNEERVRIWGDKAVIERRLLPVSVKTRLGYD----SITI 195

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLN 194
            + VK + +     I +H R                  ++D + +  +     D  I  N
Sbjct: 196 TDWVKDLLEMEPANISLHGRTL--------AQHYKGEANWDAIAQAAEIVRQTDTLILGN 247

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML---TTVDEYFSNPLTGSS-------P 242
           G + ++  A K +    V GV+IGRA Y N  +      + E  +N +  +        P
Sbjct: 248 GDIHNLYDAAKRIRETGVHGVLIGRATYGNPWLFQNKAQMKEILNNDVEPTPENIPSIMP 307

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAG 302
            +    +   +            H        ++ +HM      F  +++ R+ L     
Sbjct: 308 SREERLRMALKHARVHARLKGEDHF------VELRKHMGWYLGHFAGAKQVRNELVRINS 361

Query: 303 ASTATHHIIETAFNL 317
            +     IIE A   
Sbjct: 362 LADV-EEIIERALTQ 375


>gi|242097028|ref|XP_002439004.1| hypothetical protein SORBIDRAFT_10g029830 [Sorghum bicolor]
 gi|241917227|gb|EER90371.1| hypothetical protein SORBIDRAFT_10g029830 [Sorghum bicolor]
          Length = 421

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 113/280 (40%), Gaps = 17/280 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 94  MVDNSELPFRMLCRRYGADA-AYTPMLHSRIFSENEKYRSMEFTTCKEDRPLFVQFCAND 152

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAK+VE    + +++N GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 153 PDILLQAAKMVEPH-CDYVDINFGCPQRIARRGNYGAFLMDNLPLVKSLVQNLAANLHVP 211

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+    +          K ++++G + + +H R         KD +K    D+D 
Sbjct: 212 VSVKIRVFPRLEDT----LAYAKMLEEAGASLVAVHGRT-----RDEKDGKKF-RADWDA 261

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +  M      L     DGV+      +N A+           
Sbjct: 262 IKAVK-DALRVPVLANGNIRHMEDVKNCLEHTGADGVLSAETLLENPALFAGFRTKEWKE 320

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
            +  +        D   +       Y          + ++
Sbjct: 321 DSDENGDSGLDQADLVIEYLKLCEQYPVPWRMVRSHVHKM 360


>gi|312901978|ref|ZP_07761240.1| dihydrouridine synthase [Enterococcus faecalis TX0470]
 gi|311290914|gb|EFQ69470.1| dihydrouridine synthase [Enterococcus faecalis TX0470]
          Length = 362

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 127/321 (39%), Gaps = 36/321 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 57  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 116

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 117 DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 175

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R         +      +  +
Sbjct: 176 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRT--------RKEMSKVDAHW 224

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +I     +  P   I +NG + +  + L++     VDG+MIGR  +KN        
Sbjct: 225 EVIPQIMSIRDRVAPQTTITINGDIPNRQKGLELAEQYGVDGIMIGRGIFKNPY------ 278

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +P +          +     +   R +    +  +I         GFP +
Sbjct: 279 -AFEKEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGA 331

Query: 291 RRCRHILTVEAGASTATHHII 311
              R  L +   ++     ++
Sbjct: 332 SDLRAQL-MNTKSTDEVRQLL 351


>gi|16125983|ref|NP_420547.1| nitrogen regulation protein Nifr3 [Caulobacter crescentus CB15]
 gi|13423159|gb|AAK23715.1| nitrogen regulation protein Nifr3 [Caulobacter crescentus CB15]
          Length = 315

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 121/293 (41%), Gaps = 23/293 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   +D  +R  A  L     + TEM+ +    +G    +   +  +  PL  +Q+ G D
Sbjct: 1   MTGVSDLPFRETASAL-GAPYVATEMVASAEFAKGRPDVVRRAAVGEGLPLTVIQLVGRD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSI 117
           +  + + A++ ++ G   I+LN GCP+  V  G+  G+ LM  PD+    +AA  +A+ +
Sbjct: 60  VDFMAQGARMAQEAGAEIIDLNFGCPAKEVAAGAACGSALMREPDLAEALVAAAVEAVDV 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D  I  +   ++ +  + +G   + +H R         ++       D+ 
Sbjct: 120 PVTVKMRLGWD--IDCLNAPDIARRAEAAGAKAVTVHGRT--------RNQFYKGVADWT 169

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  +K+    + + +NG + D   A + L     DGVMIGR  Y    +   ++     
Sbjct: 170 AVAAVKQAV-SVPVLVNGDIVDGETARQALEQSGADGVMIGRGVYGRPWIAGAIEAALEG 228

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                 P               S++ Y  R       L+   +H+       P
Sbjct: 229 R-GFQEPEAEERLAIAITHFRRSLSFYGER-----LGLKMFRKHLASYIEAAP 275


>gi|221234750|ref|YP_002517186.1| tRNA-dihydrouridine synthase [Caulobacter crescentus NA1000]
 gi|220963922|gb|ACL95278.1| tRNA-dihydrouridine synthase [Caulobacter crescentus NA1000]
          Length = 335

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 121/293 (41%), Gaps = 23/293 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   +D  +R  A  L     + TEM+ +    +G    +   +  +  PL  +Q+ G D
Sbjct: 21  MTGVSDLPFRETASAL-GAPYVATEMVASAEFAKGRPDVVRRAAVGEGLPLTVIQLVGRD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSI 117
           +  + + A++ ++ G   I+LN GCP+  V  G+  G+ LM  PD+    +AA  +A+ +
Sbjct: 80  VDFMAQGARMAQEAGAEIIDLNFGCPAKEVAAGAACGSALMREPDLAEALVAAAVEAVDV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D  I  +   ++ +  + +G   + +H R         ++       D+ 
Sbjct: 140 PVTVKMRLGWD--IDCLNAPDIARRAEAAGAKAVTVHGRT--------RNQFYKGVADWT 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V  +K+    + + +NG + D   A + L     DGVMIGR  Y    +   ++     
Sbjct: 190 AVAAVKQAV-SVPVLVNGDIVDGETARQALEQSGADGVMIGRGVYGRPWIAGAIEAALEG 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                 P               S++ Y  R       L+   +H+       P
Sbjct: 249 R-GFQEPEAEERLAIAITHFRRSLSFYGER-----LGLKMFRKHLASYIEAAP 295


>gi|217033784|ref|ZP_03439210.1| hypothetical protein HP9810_7g65 [Helicobacter pylori 98-10]
 gi|216943833|gb|EEC23273.1| hypothetical protein HP9810_7g65 [Helicobacter pylori 98-10]
          Length = 328

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVVANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEVKSM-RESIEEFFNQ 310


>gi|257871421|ref|ZP_05651074.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
 gi|257805585|gb|EEV34407.1| dihydrouridine synthase [Enterococcus gallinarum EG2]
          Length = 319

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 118/305 (38%), Gaps = 27/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D     +  L F+  E+P+   I G
Sbjct: 1   MEDVTDVVFRHVVQTAGAPDVFFTEFTNSDSYCHPDGIESVRGRLTFTEDEQPIVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 61  DKPEFFRQMSIGMAEMGFKGIDINMGCPVPNVAGRGKGSGLILRPDVAAELIEA-AKAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + +H R        P     IP    
Sbjct: 120 LPVSVKTRIGYTEM---AEMEAWITHLLQQDIANLSVHLRTRKEMSKVPAHWDLIP---- 172

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +++    +  P   I +NG + D     AL     VDG+MIGR  +KN        E   
Sbjct: 173 EVLAIRDRVAPQTLITINGDIPDRQAGLALAQQYGVDGIMIGRGIFKNPYAF----EKEP 228

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              +    +     +   +   A+M   +   LH   K+            GFP +   R
Sbjct: 229 KEHSSEELLGLLQLQLDLQDHYATMVPRSIAGLHRFFKI---------YVKGFPGASDLR 279

Query: 295 HILTV 299
             L  
Sbjct: 280 AQLMT 284


>gi|194879304|ref|XP_001974213.1| GG21206 [Drosophila erecta]
 gi|190657400|gb|EDV54613.1| GG21206 [Drosophila erecta]
          Length = 609

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + + 
Sbjct: 274 NLPFRRICKEF-GADITCGEMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMIN 332

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 333 QAAQVIHETAQVDFIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSDRLPFTV 392

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G + + +H R         ++ R   + ++  + E
Sbjct: 393 KMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWAYIEE 442

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++       V  VMIGR A     +   + E      +
Sbjct: 443 CAAKAKRMPVIGNGDILSYEDYIERRTLAPHVSSVMIGRGALIKPWIFQEIKE--KQAWS 500

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            SS  +  + + F         +Y   H  S  K  + TR  +  +  F
Sbjct: 501 PSSGQRYEMLQKF--------CNYGLEHWGSDTKGVETTRRFLLEWQSF 541


>gi|261404875|ref|YP_003241116.1| dihydrouridine synthase DuS [Paenibacillus sp. Y412MC10]
 gi|261281338|gb|ACX63309.1| dihydrouridine synthase DuS [Paenibacillus sp. Y412MC10]
          Length = 329

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 126/323 (39%), Gaps = 36/323 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    D  +     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPDGNHSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V E   G+ L+  PDI  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPDIAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R+ +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGF---SAVDEWRDWLTHILKQDIVNLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +    R   +  +  +I         GF  +
Sbjct: 241 -AFEKEPRDHSSEELLDLLRLHLDLHDQYSAQMRRSFSALVRFFKI------YVRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIET 313
              R+ L + A +++    +++ 
Sbjct: 294 SELRNNL-MNAKSTSEVRALLDE 315


>gi|302773960|ref|XP_002970397.1| hypothetical protein SELMODRAFT_267436 [Selaginella moellendorffii]
 gi|300161913|gb|EFJ28527.1| hypothetical protein SELMODRAFT_267436 [Selaginella moellendorffii]
          Length = 634

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 112/287 (39%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L     E    +QI G+    L 
Sbjct: 293 NLPFRRLCKKL-GADVTCGEMAMCTNLLQGHASEWALLRRHPVEDCFGVQICGSYADSLT 351

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  +++E +   + I++N+GCP   V +   G+CL+  P  +   + A    +  P+T+K
Sbjct: 352 KTVELIERECTVDFIDINLGCPIDIVVKKGAGSCLLTKPTRLEQIVRATASIMEKPLTLK 411

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +        +++  +   GV+ + +H R         +  R     D+  +Y+ 
Sbjct: 412 MRTGYFEGKNCA--HSMISELSNWGVSAVTVHGRT--------RQQRYSKLADWVYIYDC 461

Query: 183 KKENP-DLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            K  P DL +  NG +   S   + +    ++   M+ R A     +LT + E     ++
Sbjct: 462 AKRAPDDLQVLGNGDIFSYSDWNEHMLPDLNLSSCMLARGALIKPWLLTEIKEQRHWDIS 521

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +  +           +    T +   H  S  K  + TR  +   L
Sbjct: 522 SNERL----------DLLRDYTQFGLEHWGSDSKGVETTRKFLLEWL 558


>gi|332298957|ref|YP_004440879.1| TIM-barrel protein, nifR3 family [Treponema brennaborense DSM
           12168]
 gi|332182060|gb|AEE17748.1| TIM-barrel protein, nifR3 family [Treponema brennaborense DSM
           12168]
          Length = 408

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 58/381 (15%), Positives = 115/381 (30%), Gaps = 105/381 (27%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++DR +R   R        YTEM+ ++A++RG  K   ++  +  E   A+Q+ G + 
Sbjct: 23  AGYSDRAFRSVCRE-GGADFAYTEMVSSEALVRGSDKTALLMARAPNETQYAIQLFGGEP 81

Query: 60  SKLVEAAKIV-----EDFG--------------------------YNEINLNVGCPSARV 88
           + +  A +++      + G                             I++N GCP  ++
Sbjct: 82  AVMAAAVRLILNGASAERGDAGTFGSADACGDAAERSFSARRFDVPEVIDINAGCPVPKI 141

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKAL--------------------------------- 115
            +   G+ L  +PD +     A  +A                                  
Sbjct: 142 TKTGAGSALTRDPDRLYKITEAAVRASAECAVAAKNIAADNAAAAKNGDEVKSLDAEAKN 201

Query: 116 ---------------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
                           +P+TVK R G D     +  +    +  ++G + I +H R    
Sbjct: 202 GAEAKISDAEVTIAGPVPITVKIRAGWD--ADHITWKEAACAAIEAGASAITLHGRT--- 256

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKEN-----PDLFIGLNGGLEDMSQALKIL--PSVDGV 213
                +        D+D + E+           + +  +G +     A ++L      GV
Sbjct: 257 -----RAQGYEGAADWDALAELTALVAGETGGKVPVFGSGDVFSPEAAARMLEQTGCAGV 311

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M  R A  N  +                P+  R++          + + A          
Sbjct: 312 MFARGAMGNPFIFIQTRRLLQTGSYEEIPVSVRMEAGLRE--LRCLIEDAGEE----SAC 365

Query: 274 QQITRHMIGLFHGFPNSRRCR 294
           +Q+ +       G       R
Sbjct: 366 RQMRKRFCAYSKGVAGGAALR 386


>gi|224105275|ref|XP_002313751.1| predicted protein [Populus trichocarpa]
 gi|222850159|gb|EEE87706.1| predicted protein [Populus trichocarpa]
          Length = 362

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 113/287 (39%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L   + E    +QI GA    + 
Sbjct: 27  NLPFRRVCKAL-GADVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGAYPDTVT 85

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++ ++   + I++N+GCP   V     G+ L+  P  +   I A    +  P+TVK
Sbjct: 86  RTVELIDQECTVDFIDINMGCPIDIVVNKGAGSSLLTKPMRMKSIIEATSGTVEKPITVK 145

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G  +      + +L+  I K G + + IH R         +  R     D+D +Y+ 
Sbjct: 146 VRTGYFEGKS--RIDSLIVDIGKWGASAVTIHGRS--------RQQRYSKLADWDYIYQC 195

Query: 183 KKENPD-LFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            ++ PD L +  NG +    D +      P +   MI R A     + T + E     ++
Sbjct: 196 ARKAPDSLQVLGNGDVFSFVDWNNHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDIS 255

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                +  + KD+ R            H  S  K  + TRH +   L
Sbjct: 256 SGE--RLNILKDYVRS--------GLEHWGSDTKGVETTRHFLLEWL 292


>gi|332661587|gb|AEE86987.1| tRNA-dihydrouridine synthase 3-like protein [Arabidopsis thaliana]
          Length = 691

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 61/295 (20%), Positives = 114/295 (38%), Gaps = 33/295 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   ++L    +   EM +   +L+G      +L   + E    +QI G+    + 
Sbjct: 350 NLPFRRLCKVL-GADVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGSYPDTVS 408

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++++ +   + I++N+GCP   V   S G+ L+  P  + + +      +  P+T+K
Sbjct: 409 RVVELIDRECTVDFIDINMGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSIVETPITIK 468

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +      + +L+  I   G   + IH R         +  R   + D+D +Y+ 
Sbjct: 469 VRTAFFEGKN--RIDSLIADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQC 518

Query: 183 -KKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            K    +L +  NG +       K     P +   MI R A     + T + E     +T
Sbjct: 519 TKNATTNLQVIGNGDVYSYLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDIT 578

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL---FHGFP 288
                +  + KDF R        +  +H  S  K  + TRH +   L   F   P
Sbjct: 579 SGE--RLNIMKDFVR--------FGLQHWGSDTKGVETTRHFLLEWLSYTFRYIP 623


>gi|154685282|ref|YP_001420443.1| YfjN [Bacillus amyloliquefaciens FZB42]
 gi|154351133|gb|ABS73212.1| YfjN [Bacillus amyloliquefaciens FZB42]
          Length = 327

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 67/332 (20%), Positives = 127/332 (38%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYTDID---EWRGWLTHILKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   D  R       +Y+     +   L +  +       GF  +
Sbjct: 243 ------EKEPREHSSKELLDLLRLHLDLHDEYSKAEARAYKPLPRFFKI---YLRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 294 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGM 324


>gi|15234862|ref|NP_195600.1| dihydrouridine synthase family protein [Arabidopsis thaliana]
 gi|75266821|sp|Q9T0J6|DUS3L_ARATH RecName: Full=tRNA-dihydrouridine synthase 3-like; AltName:
           Full=Zinc finger CCCH domain-containing protein 50;
           Short=AtC3H50
 gi|4490341|emb|CAB38623.1| putative protein [Arabidopsis thaliana]
 gi|7270872|emb|CAB80552.1| putative protein [Arabidopsis thaliana]
          Length = 700

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 61/295 (20%), Positives = 114/295 (38%), Gaps = 33/295 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   ++L    +   EM +   +L+G      +L   + E    +QI G+    + 
Sbjct: 359 NLPFRRLCKVL-GADVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGSYPDTVS 417

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++++ +   + I++N+GCP   V   S G+ L+  P  + + +      +  P+T+K
Sbjct: 418 RVVELIDRECTVDFIDINMGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSIVETPITIK 477

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +      + +L+  I   G   + IH R         +  R   + D+D +Y+ 
Sbjct: 478 VRTAFFEGKN--RIDSLIADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQC 527

Query: 183 -KKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            K    +L +  NG +       K     P +   MI R A     + T + E     +T
Sbjct: 528 TKNATTNLQVIGNGDVYSYLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDIT 587

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL---FHGFP 288
                +  + KDF R        +  +H  S  K  + TRH +   L   F   P
Sbjct: 588 SGE--RLNIMKDFVR--------FGLQHWGSDTKGVETTRHFLLEWLSYTFRYIP 632


>gi|302848343|ref|XP_002955704.1| hypothetical protein VOLCADRAFT_106923 [Volvox carteri f.
           nagariensis]
 gi|300259113|gb|EFJ43344.1| hypothetical protein VOLCADRAFT_106923 [Volvox carteri f.
           nagariensis]
          Length = 396

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 62/337 (18%), Positives = 134/337 (39%), Gaps = 51/337 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   +   YR    +    +L  +EM++A A+L  +++ +    ++  E   ++Q+ G  
Sbjct: 1   MAGISCAPYRQLC-IEHGASLSTSEMVIASALLLRNRRTLKLASYAPDESLRSVQLYGVR 59

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
             ++ +A +++  +   + ++LN GCP  ++     G+ L L P +    +AA  +    
Sbjct: 60  PDQVEQAVRMLVSERNVHHVDLNFGCPVRKITARGGGSALPLRPMLFARLVAAAVRGAGG 119

Query: 117 -IPVTVKCRIGVDDQIPAV---------ALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +PVTVK R+G+  ++P            + +  +  +  G   + +HAR A        
Sbjct: 120 QVPVTVKLRVGLTSELPTHLQASVGWCGDMVDAGRIAEAEGAAALTLHARTA-------- 171

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           D      + +  + ++ K    + +  NG + + S A++++      GVM+GRAA     
Sbjct: 172 DQLYSAPVMWHAIRDLVK-TVQIPVIGNGDVYEASDAVQLMEQTGCAGVMVGRAALGRPW 230

Query: 225 MLTTVDEYFSNPLTG-------------------SSPIKTRVDKDFWRKI---SASMTDY 262
           +   V E   +                       + P+  +V     R +        DY
Sbjct: 231 VFREVAEALHDNKDDHDDASITTPAAAGAAGAVLAPPVLGKVVATALRHVEAEVEWYRDY 290

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 S   + +  + +    +GF ++ + +  L V
Sbjct: 291 DPEERDS---ILRFRKFISLYLYGFKSATQLKARLMV 324


>gi|315640501|ref|ZP_07895609.1| dihydrouridine synthase [Enterococcus italicus DSM 15952]
 gi|315483705|gb|EFU74193.1| dihydrouridine synthase [Enterococcus italicus DSM 15952]
          Length = 331

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 71/324 (21%), Positives = 131/324 (40%), Gaps = 31/324 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVQQAGAPDVFFTEFTNSDSYCHPDGIESVRGRLVFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFRQMSLGMAEMGFKGIDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G ++       ++ ++ + +  +  + IH R              IP +  
Sbjct: 138 LPVSVKTRLGFEEL---AEHQDWIEHLLRQDIANLSIHLRTRKEMSKVAAHWEMIPLV-- 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTVDEYF 233
             + +  +  P   I +NG + D +  L +     VDG+MIGR  +KN         ++ 
Sbjct: 193 TAIRD--RVAPQTTITINGDIPDRATGLALAEKYGVDGIMIGRGIFKNPFAFEKEPRQHS 250

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           ++ L     ++  +   +  ++   +       LH   K+            GFP +   
Sbjct: 251 ASELLDLLRLQLDLQDTYKERVPRPIV-----GLHRFFKI---------YVKGFPGASEL 296

Query: 294 RHILTVEAGASTATHHIIETAFNL 317
           R  L      STA    +  AF  
Sbjct: 297 RVRLM--GTKSTAQVRELLDAFEQ 318


>gi|256827198|ref|YP_003151157.1| putative TIM-barrel protein, nifR3 family [Cryptobacterium curtum
           DSM 15641]
 gi|256583341|gb|ACU94475.1| putative TIM-barrel protein, nifR3 family [Cryptobacterium curtum
           DSM 15641]
          Length = 331

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 129/329 (39%), Gaps = 31/329 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   TD   R    L    +L +TEM+ A  +   +++   +L  S  E  + +Q+ G +
Sbjct: 17  MAGVTDPVMRKLC-LEQGASLTFTEMVSAKGLSYENQRTEDLLTLSPDETQVGVQLFGHE 75

Query: 59  ISKLV-EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            + +  +AA++ E  G     I++N+GCP+ ++     G+ LM  PD     +AA+  A+
Sbjct: 76  PATMAHQAARVREMLGEALAVIDINMGCPARKIITKGDGSALMQQPDRAVHIVAAVVDAV 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVTVK R G    +      +L + ++++G  G+ +H R A                 
Sbjct: 136 DVPVTVKMRRGF--ALGCETAGDLARRVEQAGAAGVTVHGRFA--------QQLYRGTSC 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +  +K E   + +  NG +   + A+ ++   + D +MI RAA  N  +   V    
Sbjct: 186 HATIRRVK-EAVAIPVVGNGDVCCGADAVTLMRETACDAIMIARAAEGNPWVFADVAAAL 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +       P          R            +      L ++ +       G P + + 
Sbjct: 245 AGKPAPQPPSLRERVALARRHAREL-------YRWEPRTLVRMRKQGSWYCKGQPGASQA 297

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R  L      +       E AF+ M   L
Sbjct: 298 REALNRCRSLAE-----FEAAFDEMDRRL 321


>gi|290982753|ref|XP_002674094.1| predicted protein [Naegleria gruberi]
 gi|284087682|gb|EFC41350.1| predicted protein [Naegleria gruberi]
          Length = 450

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 95/235 (40%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQ-EKPLALQIGGA 57
           MVD ++  +R  ++      L YT M      A  +  +     F+   E P+  Q    
Sbjct: 110 MVDQSEMAFRLLSKEY-GATLAYTPMFHGMYFAYHKKYRARFYQFNPDLEGPVFAQFCTN 168

Query: 58  DISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           D    V+  K V D    +I   +LN+GCP      G +G+ LM +   V   I      
Sbjct: 169 DPETFVQCGKRVWDLSKQKISAIDLNLGCPQRIARRGRYGSFLMEDLQTVHSIINKAHLE 228

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K RI  D ++      N VK++  +G   + +H R    KG +          
Sbjct: 229 LPMPVTAKIRIFEDLELT----MNYVKTVVDAGAQVLCVHGRTREQKGANQNY------A 278

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           D+ ++  I+++ P + +  NG +         L    VD VM G    +N A+  
Sbjct: 279 DWTVIRAIREQFPQIPMIANGNIRTFQDVQDCLEYTRVDAVMSGEGLLENPALFN 333


>gi|291483244|dbj|BAI84319.1| hypothetical protein BSNT_01340 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 332

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 68/332 (20%), Positives = 125/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P +  + I A  KA  
Sbjct: 86  DKPENFRKMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPAVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         +      +  +
Sbjct: 145 LPVSVKTRLGYTD---VDEWREWLTHILKQDIANLSIHLRT--------RAEMSKVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 194 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPF------ 247

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I         GF  +
Sbjct: 248 -AFEKEPKEHSSKELLDLLRLHLDLHEKYSALEARPYKPLPRFFKI------YLRGFRGA 300

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 301 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGV 331


>gi|303232252|ref|ZP_07318951.1| TIM-barrel protein, nifR3 family [Atopobium vaginae PB189-T1-4]
 gi|302481662|gb|EFL44723.1| TIM-barrel protein, nifR3 family [Atopobium vaginae PB189-T1-4]
          Length = 456

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 65/333 (19%), Positives = 115/333 (34%), Gaps = 53/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           M   +D+ YR            Y+EM+    +     K          EKPL +Q+ G+ 
Sbjct: 76  MASVSDKSYR-IVNECAGAGFAYSEMVSVAGLHYDSDKTWDLICPSDVEKPLVVQLFGSK 134

Query: 59  ISKLVEAAKIVEDFGYN---EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +   AA  + +   +     ++N+ CP A+V +   G+ LM  P+   D + A+C   
Sbjct: 135 PDQFRAAAARIAERLSDRLLFFDVNMACPVAKVTKKGEGSALMCTPEKAADIVRALCAET 194

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPN 173
           S+ VT K R G +            + ++ +G   I +H R  K +  G S         
Sbjct: 195 SVAVTCKIRRGYEQG--NETASEFARVLEDAGAAAITVHGRYAKQLYSGNSC-------- 244

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
              D   E       +    +G +    +A  +  +P V GVMI R  Y N  + +    
Sbjct: 245 ---DACIERVARAISVPTIASGDILTPERACTLASIPGVAGVMIARGTYGNPWIFSDAYT 301

Query: 232 YFSNPLTGS-------------SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT- 277
            FS     +             + +    D D    +SA ++        +  ++  +  
Sbjct: 302 LFSQLQQANTHDSASNVVVCADTAMPFARDADELTDMSADVSTLVPFRRSTPARIAAMRL 361

Query: 278 ---------RHMI-------GLFHGFPNSRRCR 294
                     HM             FP+++  R
Sbjct: 362 SVHLLAAHGSHMARARSIMSWYLAAFPHAKAWR 394


>gi|299535227|ref|ZP_07048551.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
 gi|298729348|gb|EFI69899.1| histidine phosphokinase/phophatase, putative [Lysinibacillus
           fusiformis ZC1]
          Length = 322

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 119/307 (38%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+    + K      L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGKKSVRGRLLFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     E +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  K   
Sbjct: 79  DNPVYFREMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKVGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D        + +  I K  +  + IH R         +    + +  +
Sbjct: 138 LPVSVKTRLGYKD---VNEWEDWLTHILKQDIANLSIHLRT--------RKEMSLVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEQYGIDGVMIGRGIFKNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   +  R        YA     S   L +  +       GF  +
Sbjct: 243 ------EKEPKEHSSKEYLNLLRLQLDLQDQYAEELPRSITGLHRFFKI---YVKGFRGA 293

Query: 291 RRCRHIL 297
              R  L
Sbjct: 294 GELRSQL 300


>gi|33152782|ref|NP_874135.1| putative nitrogen regulator protein [Haemophilus ducreyi 35000HP]
 gi|38604730|sp|Q7VKU5|DUSC_HAEDU RecName: Full=tRNA-dihydrouridine synthase C
 gi|33149006|gb|AAP96524.1| putative nitrogen regulator protein [Haemophilus ducreyi 35000HP]
          Length = 325

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 69/329 (20%), Positives = 128/329 (38%), Gaps = 41/329 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R       +  L  +E +  V   + +     +       G +    P+ +
Sbjct: 13  MQGVLDPFMRKLLTAYNDYDLCVSEFVRVVDQRLPKKTFYRLAPELLQGGLTDSGTPIRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G   I+ N GCPS  V+    GA L+ +P+++     A+ 
Sbjct: 73  QLLGQYPQWLAENAQLAIELGSYGIDFNCGCPSKTVNGSHGGAALLKDPELIYCATKAIR 132

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G D    A     +  +I+++G + I +H R         +D  +
Sbjct: 133 EAVPKAQPVSVKMRLGWD---CASQCFEIADAIQQAGADEITVHGRTK-------QDGYR 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I ++  ++ +  NG + D + A K   + +  G+MIGR A     +   
Sbjct: 183 AERINWQAIGQI-QQRLNIPVIANGEILDFNSAQKCREITACCGLMIGRGALNTPNL--- 238

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  IK  V K  W ++   + +Y             + R    +  L  
Sbjct: 239 -----------SKVIKYNVAKMAWSEVLQLLYEYVNMPNERDSGFYHVARIKQWLHYLDK 287

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETA 314
            +P +     I+  E        H IE A
Sbjct: 288 AYPEAVDLFQIVKTEHSYDGVKAH-IEKA 315


>gi|145349324|ref|XP_001419086.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144579317|gb|ABO97379.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 307

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 106/248 (42%), Gaps = 18/248 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MVD ++  +R   +      L YT MI A   +   K     FST   ++PL  Q    D
Sbjct: 23  MVDQSELAFRELCKRY-GATLGYTPMIHARLFVESPKYRREIFSTSTRDRPLLAQFCAND 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AA ++  +  + +++N GCP      G++GA LM +   V   I  + + L +P
Sbjct: 82  PEILLRAATMIAPY-CDGVDINFGCPQRIAKRGNYGAFLMDDWKTVEALIRKLDEELPVP 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +          K ++ +G   + +H R    K     D R     ++  
Sbjct: 141 VTAKIRVYDDLE----TTLKYAKMVEAAGAQIVAVHGRTREQK--RCADIR----ANWAY 190

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK +   + +  NG +  +++A   L     DGV+       N A+ +    +++ P
Sbjct: 191 IRAIK-DALKVPVLANGDIRSLAEARACLEATGADGVLSAEPLLSNPALFSD-PPFYAAP 248

Query: 237 LTGSSPIK 244
             G +PI 
Sbjct: 249 TDGYAPIP 256


>gi|254779294|ref|YP_003057399.1| putative transcriptional regulator [Helicobacter pylori B38]
 gi|254001205|emb|CAX29173.1| Putative transcriptional regulator [Helicobacter pylori B38]
          Length = 328

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-REGIEEFFNQ 310


>gi|94984185|ref|YP_603549.1| dihydrouridine synthase, DuS [Deinococcus geothermalis DSM 11300]
 gi|94554466|gb|ABF44380.1| tRNA-U20-dihydrouridine synthase [Deinococcus geothermalis DSM
           11300]
          Length = 333

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 71/330 (21%), Positives = 124/330 (37%), Gaps = 39/330 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGA 57
           M  ++D   R  A          +EMI A  ++ G     L        E    +Q+ GA
Sbjct: 22  MAGYSDAPMRQLAAE-QGALWTVSEMISARGLVLGGDSEKLTLGRPYPGEVGRVVQLFGA 80

Query: 58  DISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   L +A    E  F    ++LN+GCP  +V +G  GACL+  P++    + AM  A +
Sbjct: 81  EPDVLAQAVARAESWFAPAALDLNMGCPVPKV-KGRGGACLLQTPEVAYTLVRAMRSATT 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V+ K R+G D          + + +  +G   I +H R ++         R     D+
Sbjct: 140 LDVSAKIRLGWDTDRSV----EIAQGLAAAGAALITVHGRTSV--------QRYSGEADW 187

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D +  +   +  + +  +G ++   QA   L   V  VMIGR A  N  +   +      
Sbjct: 188 DAIARVA-ASVKVPVVGSGDVKSAEQARARLNTGVAAVMIGRGAVGNPWLFRAL-----A 241

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLH--SGGKLQQITRHMIGLFHGFPNSRRC 293
                 P      +   R     +T Y        S   L+++  H +      P+    
Sbjct: 242 SGDDVVPSAQERARTALRHAQLHVTFYGPDRFGLLSVRPLRKVLPHYL------PDHPEL 295

Query: 294 RHILTVEAGASTATHHIIETAFN-LMIESL 322
           R  L      +      +E A   L++++L
Sbjct: 296 RAALVQVNTVAD-----VEQALAPLLVDAL 320


>gi|297801970|ref|XP_002868869.1| dihydrouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297314705|gb|EFH45128.1| dihydrouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 691

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/295 (21%), Positives = 115/295 (38%), Gaps = 33/295 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   ++L    +   EM +   +L+G      +L   + E    +QI G+    + 
Sbjct: 350 NLPFRRLCKVL-GADVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQICGSYPDTVS 408

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              ++++ +   + I++N+GCP   V   S G+ L+  P  + + +      L  P+T+K
Sbjct: 409 RTVELIDRECTVDFIDINMGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSILETPITIK 468

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R    +      + +L+  I   G   + IH R         +  R   + D+D +Y+ 
Sbjct: 469 VRTAFFEGKN--RIDSLIADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQC 518

Query: 183 -KKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            K  + +L +  NG +       K     P +   MI R A     + T + E     +T
Sbjct: 519 TKNASTNLQVIGNGDVYSYLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDIT 578

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL---FHGFP 288
                +  + KDF R        +  +H  S  K  + TRH +   L   F   P
Sbjct: 579 SGE--RLNIMKDFVR--------FGLQHWGSDTKGVETTRHFLLEWLSYTFRYIP 623


>gi|261839452|gb|ACX99217.1| transcriptional regulator [Helicobacter pylori 52]
          Length = 328

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 128/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFIAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLTIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|194015963|ref|ZP_03054578.1| probable tRNA-dihydrouridine synthase [Bacillus pumilus ATCC 7061]
 gi|194012318|gb|EDW21885.1| probable tRNA-dihydrouridine synthase [Bacillus pumilus ATCC 7061]
          Length = 324

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 70/328 (21%), Positives = 125/328 (38%), Gaps = 36/328 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M + TD  +R          + +TE   +++    D     K  L F+  E+P+   I G
Sbjct: 19  MEEVTDVVFRHVVSEAARPDVFFTEFTNSESYCHPDGIQSVKGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFQGLDINMGCPVPNVTQNGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  ++ I +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGFTE---VDEWRGWLRHILEQDIVNLSIHLRT--------RKEMSQVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDGVMIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGVMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +  +          +    +    R   +  +  +I         GF  +
Sbjct: 241 -AFEKEPKDHTSDELLGLLRLHLDLHDQYSSLGLRPFKALHRFFKI------YVKGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIE-TAFNL 317
              R+ L   +        + E  A N 
Sbjct: 294 SFLRNQLMNTSSTDEVRAMLDEFEARNQ 321


>gi|320354884|ref|YP_004196223.1| dihydrouridine synthase DuS [Desulfobulbus propionicus DSM 2032]
 gi|320123386|gb|ADW18932.1| dihydrouridine synthase DuS [Desulfobulbus propionicus DSM 2032]
          Length = 347

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 73/292 (25%), Positives = 127/292 (43%), Gaps = 22/292 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   T    R          LL TEM+ A  +     D    L  +T+E PL+ Q+   D
Sbjct: 17  MAGLTHSALRTTLLHFGGVGLLSTEMLSAARLPAESVDHSPYLFRTTKESPLSHQLMLTD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +  A   +   G + I+LN+GCP+ ++     G+ LM +P  V   +A+  +  S+P
Sbjct: 77  EKHIAPAFAALHRLGADVIDLNLGCPAPQIRRSGGGSRLMEDPARVRRLVASARQHTSLP 136

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R+G  + + A  LR+  + ++  GV+ I +HAR   L+G S           ++ 
Sbjct: 137 LTAKIRLG--ETLDAAKLRDFCRMLEGEGVDMITVHAR---LRGESFARRP-----RWEW 186

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN- 235
           V  +K+   D+ +  NGG++ ++ A   L     DG+MIGRAA ++  +   +       
Sbjct: 187 VANVKRWI-DIPVVANGGIDSIASARTCLEQSGADGLMIGRAAARSPWIFAVLARALYAV 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-GLFHG 286
             T       ++ + F   +    +          G+L++ T H     F G
Sbjct: 246 DCTEPHICLPQLYQGFATALVERFSP-----ERRLGRLKEFTHHFATNYFFG 292


>gi|228989497|ref|ZP_04149482.1| tRNA-dihydrouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228770222|gb|EEM18801.1| tRNA-dihydrouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 336

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 119/307 (38%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELN---EWEEWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKNPF------ 247

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +     +   R +    +  +I         GF  +
Sbjct: 248 -AFEKEPKEHSSKEYLDLLRLQLDLQDQYAEVLPRSITGLHRFFKI------YVKGFHGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|317178919|dbj|BAJ56707.1| transcriptional regulator [Helicobacter pylori F30]
          Length = 328

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 127/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY 
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYK 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEVKSM-RESIEEFFNQ 310


>gi|326930780|ref|XP_003211519.1| PREDICTED: LOW QUALITY PROTEIN: tRNA-dihydrouridine synthase
           1-like, partial [Meleagris gallopavo]
          Length = 487

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 63/303 (20%), Positives = 115/303 (37%), Gaps = 51/303 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG-------------FSTQE 47
           MVD ++  +R  +R      L YT M+ A   LR     + G             F +  
Sbjct: 21  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFLRDANYRLRGKKNNYCLLILLVXFCSSL 79

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P   Q    D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   
Sbjct: 80  SP--SQFCANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRM 136

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I    + LS+P+T K R+  +            + ++K+G   + +H R    KG     
Sbjct: 137 ILLANEKLSVPITCKIRVFPEIDKTV----KYAQMLEKAGCQLLTVHGRTKEQKG----- 187

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSA 224
                   ++ +  ++K    + +  NG ++   D+ + ++    V GVM       N A
Sbjct: 188 -PLAGVASWEHIQAVRKAV-SIPVFANGNIQCLSDVEECIRK-TGVHGVMSAEGNLHNPA 244

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIG 282
           +             G +P+   + +++   +        Y   HL    KL     H + 
Sbjct: 245 LF-----------EGRNPLVWEMAEEYLEIVQKYPCPLSYVRAHL---FKLWH---HTLQ 287

Query: 283 LFH 285
           ++ 
Sbjct: 288 VYQ 290


>gi|24585320|ref|NP_610000.1| CG10463 [Drosophila melanogaster]
 gi|7298625|gb|AAF53841.1| CG10463 [Drosophila melanogaster]
          Length = 604

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 54/289 (18%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G  +   +      E    +Q+ G + + L 
Sbjct: 269 NLPFRRICKEF-GADITCGEMACAQPLLKGMGQEWALTKRHQSEDVFGVQLCGNNPNMLN 327

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 328 QAAQVIHETAQVDFIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSDRLPFTV 387

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G + + +H R         ++ R   + ++  + E
Sbjct: 388 KMRTGIYADKSVA--HELLPLVEEWGASAVTLHGRS--------REQRYTKHANWAYIEE 437

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++       V  VMIGR A     +   + E      +
Sbjct: 438 CAAKAKCMPVIGNGDILSYEDYMERRTLAPHVCSVMIGRGALIKPWIFQEIKE--KQAWS 495

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            SS  +  + + F         +Y   H  S  K  + TR  +  +  F
Sbjct: 496 PSSGQRYEMLQKF--------CNYGLEHWGSDTKGVETTRRFLLEWQSF 536


>gi|317182037|dbj|BAJ59821.1| transcriptional regulator [Helicobacter pylori F57]
          Length = 328

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKTIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R          D  +   +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTR-------SDKYQKDRIDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVVANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|332558248|ref|ZP_08412570.1| tRNA-dihydrouridine synthase B [Rhodobacter sphaeroides WS8N]
 gi|332275960|gb|EGJ21275.1| tRNA-dihydrouridine synthase B [Rhodobacter sphaeroides WS8N]
          Length = 326

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 110/288 (38%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R  A       L+ +EM+ +  ++    +          E   A+Q+ G D
Sbjct: 19  MAGITDLPFRRLAVRF-GAGLVVSEMVASREVVCAGAEARARAEIGATEGRTAVQLAGCD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + EAA++VE  G   I++N+GCP+ RV  G  G+ LM  PD     I A+  A+++P
Sbjct: 78  PHWMTEAARLVEAQGARIIDINMGCPAKRVTNGWSGSALMREPDRALALIEAVVGAVAVP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R+G D+ +  +    + +  + +GV  I IH R         +        D+  
Sbjct: 138 VTLKMRLGWDEGM--LNAPEIARRAEAAGVAMITIHGRT--------RCQFYTGRADWAA 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +         NG +    +  A        GVM+GR A     +L  V       
Sbjct: 188 IRPVVEAVSVPV-VANGDITGPEEAQAALAASGAAGVMVGRGAQGRPWLLGQVASALDGR 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                P    +           ++ Y          L+   +H+    
Sbjct: 247 AAPDVPEGEALADLVVAHYEEMLSFY-----GRDLGLRVARKHLNWYL 289


>gi|329927628|ref|ZP_08281775.1| dihydrouridine synthase (Dus) [Paenibacillus sp. HGF5]
 gi|328938326|gb|EGG34717.1| dihydrouridine synthase (Dus) [Paenibacillus sp. HGF5]
          Length = 329

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 72/323 (22%), Positives = 126/323 (39%), Gaps = 36/323 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +  +     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V E   G+ L+  PDI  D I A  KA  
Sbjct: 79  DKPEFFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPDIAADIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R+ +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGF---TAVDEWRDWLTHILKQDIVNLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFHNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +    R   +  +  +I         GF  +
Sbjct: 241 -AFEKEPKDHSSEELLGLLRLHLDLHDQYSAQMRRSFSALVRFFKI------YVRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIET 313
              R+ L + A +++    +++ 
Sbjct: 294 GELRNQL-MNAKSTSEVRALLDE 315


>gi|209882371|ref|XP_002142622.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209558228|gb|EEA08273.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 405

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 61/307 (19%), Positives = 120/307 (39%), Gaps = 33/307 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  YR   R      L +T M  +     L G +         +KPL LQ  G +
Sbjct: 21  MVDASELAYRLLCRKY-GCDLAFTPMYHSGLFSKLSGYRNTNFQTCDDDKPLILQFCGNN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSI 117
              +++A+K + D     I+LN GCP      G +GA L+  P+++   ++ +  + L  
Sbjct: 80  PEVILQASKYI-DNKVQGIDLNFGCPQNIAKRGHYGAFLLEEPELMESLVSKLVNSDLKC 138

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+   + +      N++  ++++G++ + +H R    KG          + D++
Sbjct: 139 PVSCKIRLVCKNDLQKTI--NIMYRLEQAGISMLTVHGRTLKDKGT------LTGSCDWE 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I K+  ++    NGG+       K       D VM      ++  +       F N
Sbjct: 191 SLK-IMKQRCNIPFIANGGIHTFEDIQKCFDYTGADAVMSAEGILEDPWLF----YRFKN 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH---GFPNSRR 292
               + P +  +  ++   +                    +  H+  +FH     P + +
Sbjct: 246 NQNINRPSQFDLVGEYI-DVCKKYPPPNNSI---------VRSHLYRIFHTILNTPGANK 295

Query: 293 CRHILTV 299
            R  + V
Sbjct: 296 FRDKINV 302


>gi|320168879|gb|EFW45778.1| tRNA-dihydrouridine synthase 4-like protein [Capsaspora owczarzaki
           ATCC 30864]
          Length = 432

 Score =  181 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 101/231 (43%), Gaps = 20/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      L YT M VA+  +   +     FST E   P+ +Q     
Sbjct: 90  MVRYSKLGFRELVRAF-GCDLAYTPMTVAENFILSKRGRDNDFSTNEYDHPVIVQFAAKH 148

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA++V  +  + I++N GCP        +G+ L+  P ++ D + A    ++IP
Sbjct: 149 TEMLCTAAEMVAPY-VDGIDINCGCPQRWAMSEGYGSALLRKPQLIYDMVRAAKSRITIP 207

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK RI +D +        L ++ +++G + I +H R   ++            +  + 
Sbjct: 208 VSVKIRINLDFKKT----IELAQTAERAGADWIAVHGRTPSMRH---------EPVILEG 254

Query: 179 VYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLT 227
           +  +K +N  + +  NG +  M    A+     VDGVM  R    N A+  
Sbjct: 255 IKAVK-DNVSIPVVANGDINSMLDVNAVAAATGVDGVMSARGLLANPALFG 304


>gi|317012537|gb|ADU83145.1| putative transcriptional regulator [Helicobacter pylori
           Lithuania75]
          Length = 328

 Score =  181 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + + + +  + +  +  
Sbjct: 74  SVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVNLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-REGIEEFFNQ 310


>gi|257877859|ref|ZP_05657512.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
 gi|257812025|gb|EEV40845.1| dihydrouridine synthase [Enterococcus casseliflavus EC20]
          Length = 328

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 123/320 (38%), Gaps = 27/320 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + ++     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVQAAGAPDVFFTEFTNSDSYCHPEGRDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEYFREMSIGLAEMGFKGIDLNMGCPVPNVAGRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +      +   +  + +  +  + IH R              IP    
Sbjct: 138 LPVSVKTRLGYTELG---EMEAWLTHVLQQDIANLSIHLRTRKEMSKVDAHWELIP---- 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           ++V    +  P   + +NG + D ++ L++     VDG+MIGR  +KN        E   
Sbjct: 191 EVVALRDRIAPQTKLTINGDIPDRTKGLELAEKYGVDGIMIGRGIFKNPYAF----EKEP 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T    +     +   +   A M   +   LH   K+            GFP +   R
Sbjct: 247 KEHTSEELLGLLQLQLDLQDHYAKMVPRSIAGLHRFFKI---------YVKGFPGASDLR 297

Query: 295 HILTVEAGASTATHHIIETA 314
             L            + E A
Sbjct: 298 AKLMNTKSTDEVRQLLAEFA 317


>gi|127513170|ref|YP_001094367.1| dihydrouridine synthase, DuS [Shewanella loihica PV-4]
 gi|126638465|gb|ABO24108.1| dihydrouridine synthase, DuS [Shewanella loihica PV-4]
          Length = 309

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 66/306 (21%), Positives = 115/306 (37%), Gaps = 31/306 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     +    ++ +E   +V   +       +         +    P+ L
Sbjct: 8   MEGVADAPMRALLTSVGGYDMVISEFIRVVDQLLPEKVFYRLCAELKYQCRTASGTPVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G   ++LN GCP+  V+    GA L+  P+ +     A+ 
Sbjct: 68  QLLGQEPNWMAENAIRAVELGSRGVDLNYGCPAPMVNRSKGGAALLKEPETIYRVTQAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+ K R+G DD+        + ++I+ +G   + +HAR         K+   
Sbjct: 128 QAVPKDKPVSAKIRLGWDDKSRCT---EIAQAIEAAGATELTVHART--------KEEAY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +IK     L I  NG +      LK       D VM+GR A      L  
Sbjct: 177 RPPAHWEYIAQIK-SVTRLPIIANGEIWGREDYLKCREASGCDDVMLGRGALTIP-NLAH 234

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V +    P+     +   +    +  +S     Y AR       L+ I RH      G  
Sbjct: 235 VVKGEQTPMPWPEVLALLLQYSEFEIVSEKEKYYPARIKQW---LRFIARH---YEEGEA 288

Query: 289 NSRRCR 294
             R+ R
Sbjct: 289 LFRQVR 294


>gi|228995691|ref|ZP_04155354.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock3-17]
 gi|228764068|gb|EEM12952.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock3-17]
          Length = 336

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 119/307 (38%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELN---EWEEWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKNPF------ 247

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +     +   R +    +  +I         GF  +
Sbjct: 248 -AFEKEPKEHSSKEYLDLLRLQLDLQDQYAEVLPRSITGLHRFFKI------YVKGFHGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|207093032|ref|ZP_03240819.1| transcriptional regulator, putative [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 323

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 62/322 (19%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      N I+ N GCP+ +V     G+ L+ + + +   +  + +  S  
Sbjct: 74  SVVKEAVEKINALEHVNGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTSKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|308184510|ref|YP_003928643.1| putative transcriptional regulator [Helicobacter pylori SJM180]
 gi|308060430|gb|ADO02326.1| putative transcriptional regulator [Helicobacter pylori SJM180]
          Length = 328

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 130/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSPLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-REGIEDFFNQ 310


>gi|229003320|ref|ZP_04161150.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock1-4]
 gi|228757938|gb|EEM07153.1| tRNA-dihydrouridine synthase [Bacillus mycoides Rock1-4]
          Length = 336

 Score =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 119/307 (38%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 26  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPMVAHIWG 85

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 86  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 144

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++     +  +
Sbjct: 145 LPVSVKTRLGFKELN---EWEEWLTHILKQDIANLSIHLRT--------REEMSQVDAHW 193

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 194 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKNPF------ 247

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +     +   R +    +  +I         GF  +
Sbjct: 248 -AFEKEPKEHSSKEYLDLLRLQLDLQDQYAEVLPRSITGLHRFFKI------YVKGFHGA 300

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 301 AELRNQL 307


>gi|224002192|ref|XP_002290768.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974190|gb|EED92520.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 615

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 95/235 (40%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFSTQEKPLALQIGGAD 58
           MV  ++  +R   R      L YT M+ +   ++     KN +  S   +PL        
Sbjct: 98  MVGASELAFRLLCRKY-GATLSYTPMMSSSQFVQEAASMKNTVADSNLYRPLVCHFSANQ 156

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCIAAMCKALS 116
                +AAK+VE +  + I+LN+GCP      G FG+ L+   +  +V   + A  KA+S
Sbjct: 157 PQDFAKAAKLVEKY-CDAIDLNLGCPQRTAFIGHFGSYLLGQKDRKLVLSIVRAGSKAVS 215

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSPKDNRKIPN 173
           IP+ VK R+             L   ++ +G + I IHAR        G   +D      
Sbjct: 216 IPIFVKIRLL----DTVEETTKLCHELRDAGASLIAIHARYRATWERTGPGARD----GP 267

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAML 226
              D V  +K+  PD  I  NG +      +  K     DG+M       N A+ 
Sbjct: 268 ALLDQVAVVKQSMPDFPIIANGNVITYDDVISNKQSTGADGIMSAEGILDNPALF 322


>gi|159473569|ref|XP_001694906.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158276285|gb|EDP02058.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 368

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 65/294 (22%), Positives = 116/294 (39%), Gaps = 19/294 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +   YR  A      A+  +EM++A  +L  +++   +  F+  E+  ++Q+ G  
Sbjct: 1   MAGISSAPYRRLA-TSHGAAMATSEMVIASTLLVKNRRTRKLASFADDERVRSVQLYGVK 59

Query: 59  ISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--IAAMCKAL 115
             +L +A ++ V + G   ++LN GCP  ++     G+ L L P +       A      
Sbjct: 60  PEQLEQAVRLLVCEHGVQHVDLNFGCPVRKITARGGGSALPLRPRLFAKLVAAAVAGAGG 119

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PVTVK R+G+  ++P        +  +  G   + +HAR A        D      +D
Sbjct: 120 EAPVTVKFRVGLTPELP--THLQAGRIAEAEGAAALVLHARTA--------DQLYASPVD 169

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  V  +  E   + +  NG + + + AL++L      GVM+GRAA     +   V    
Sbjct: 170 WAAVRALV-EAVRIPVVGNGDVFEGADALRLLRETGCAGVMVGRAAVGRPWVFDEVAAAL 228

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +       P    V     R     +  Y   H      L +  + +     GF
Sbjct: 229 TGAPPPPPPRLGEVVAAALRHAEMEVDWYRGYHDSERDTLLRFRKFIKLYLLGF 282


>gi|290474025|ref|YP_003466899.1| tRNA-dihydrouridine synthase C [Xenorhabdus bovienii SS-2004]
 gi|289173332|emb|CBJ80109.1| tRNA-dihydrouridine synthase C [Xenorhabdus bovienii SS-2004]
          Length = 313

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 63/286 (22%), Positives = 113/286 (39%), Gaps = 24/286 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +    P+ +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDSLLPVKSFYRLCPELEHQSRTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAVRAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 128 DAVPEELPVTVKVRLGWDSGDHQF---EIADAVQQAGATELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +D+  + EI++    + +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AERIDWQAIGEIRRRL-AIPVIANGEIWDWHSAQECMKVTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           + +Y    +  +  ++      +  K   +   + AR     G L+
Sbjct: 236 IIKYNEPKMPWNGVLQLLQKYTYLEKRGDTGMYHVARIKQWLGYLR 281


>gi|308182888|ref|YP_003927015.1| putative transcriptional regulator [Helicobacter pylori PeCan4]
 gi|308065073|gb|ADO06965.1| putative transcriptional regulator [Helicobacter pylori PeCan4]
          Length = 328

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSLLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALDHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKEK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTKLPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-REGIEEFFNQ 310


>gi|300173156|ref|YP_003772322.1| tRNA-dihydrouridine synthase [Leuconostoc gasicomitatum LMG 18811]
 gi|299887535|emb|CBL91503.1| tRNA-dihydrouridine synthase [Leuconostoc gasicomitatum LMG 18811]
          Length = 376

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 70/325 (21%), Positives = 129/325 (39%), Gaps = 28/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + YTE   A +++    K      L  +  EK    QI G
Sbjct: 36  MEAVTDTVFRRVIAQAGGPDVYYTEFTNASSMVHPQAKFSVQGRLAVAENEKQPVAQIWG 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   ++  AAK++   GY  +++N+GCP   V +   G+ L+ + ++  + I+A  K   
Sbjct: 96  SRPEEIAGAAKVLATMGYQAVDINMGCPDTTVIKNGAGSDLIRHQELAKEIISAAKK-SG 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V+VK R+G      A   R  +  I +  V  + IH R       +P     I     
Sbjct: 155 LAVSVKTRLGF---YQAEEFREWLPIILRQQVAVLTIHLRSRKEMSKAPAHEEYID---- 207

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +I+       P   I +NG ++     ++++   P +DG+MIGR  ++N      V    
Sbjct: 208 EILAMRDAIAPQTLIQINGDIKTRQSGMQLVKNHPGIDGIMIGRGIFENPYAF-EVKP-- 264

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S    ++  D +  ++A++       L    K+            GF ++   
Sbjct: 265 KQHTLEESIALLKLQLDLFDDVNANIAPKHFEALKRYFKI---------YLRGFAHASAL 315

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R +L +E  A+     I++     +
Sbjct: 316 RQLL-METHATEEVRDILDRELAKV 339


>gi|152974153|ref|YP_001373670.1| dihydrouridine synthase DuS [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152022905|gb|ABS20675.1| dihydrouridine synthase DuS [Bacillus cytotoxicus NVH 391-98]
          Length = 319

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 68/307 (22%), Positives = 120/307 (39%), Gaps = 35/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +D+          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSDSYCHPEGMKSVRGRLIFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+L PD+  + I A  KA  
Sbjct: 79  DNPEYFRQMSIGMAELGFKGIDINMGCPVPNVASRGKGSGLILRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +          +  I K  +  + IH R         ++        +
Sbjct: 138 LPVSVKTRLGFKE---VNEWEEWLTHIFKQDIANLSIHLRT--------REEMSQVAAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D    L++     +DGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDRIAPNTLLTINGDIPDRQTGLQLAEKYGIDGVMIGRGIFKNPFAFEKEP 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
              S+             +D + ++       +   LH   K+            GF  +
Sbjct: 247 REHSSKEHLDLLRLQLDLQDQYAEVL----PRSITGLHRFFKI---------YVKGFHGA 293

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 294 AELRNQL 300


>gi|308062049|gb|ADO03937.1| transcriptional regulator [Helicobacter pylori Cuz20]
          Length = 328

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKEK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|257868259|ref|ZP_05647912.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257874468|ref|ZP_05654121.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|325568131|ref|ZP_08144572.1| dihydrouridine synthase [Enterococcus casseliflavus ATCC 12755]
 gi|257802373|gb|EEV31245.1| dihydrouridine synthase [Enterococcus casseliflavus EC30]
 gi|257808632|gb|EEV37454.1| dihydrouridine synthase [Enterococcus casseliflavus EC10]
 gi|325158332|gb|EGC70483.1| dihydrouridine synthase [Enterococcus casseliflavus ATCC 12755]
          Length = 328

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 71/320 (22%), Positives = 123/320 (38%), Gaps = 27/320 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + ++     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVQAAGAPDVFFTEFTNSDSYCHPEGRDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I+LN+GCP   V     G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEYFREMSIGLAEMGFKGIDLNMGCPVPNVAGRGKGSGLILRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +      +   +  + +  +  + IH R              IP    
Sbjct: 138 LPVSVKTRLGYTELG---EMEAWLTHVLQQDIANLSIHLRTRKEMSKVDAHWELIP---- 190

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           ++V    +  P   + +NG + D ++ L++     VDG+MIGR  +KN        E   
Sbjct: 191 EVVALRDRIAPQTKLTINGDIPDRTKGLELAEKYGVDGIMIGRGIFKNPYAF----EKEP 246

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
              T    +     +   +   A M   +   LH   K+            GFP +   R
Sbjct: 247 KEHTSEELLGLLQLQLDLQDHYAKMVPRSIAGLHRFFKI---------YVKGFPGASDLR 297

Query: 295 HILTVEAGASTATHHIIETA 314
             L            + E A
Sbjct: 298 AKLMNTKSTDEVRQLLAEFA 317


>gi|304395766|ref|ZP_07377649.1| dihydrouridine synthase DuS [Pantoea sp. aB]
 gi|304357060|gb|EFM21424.1| dihydrouridine synthase DuS [Pantoea sp. aB]
          Length = 309

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 1   MEGVLDSLVRQLLSEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHNASRTPSGTRVRM 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 61  QLLGQHPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAMR 120

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D    +     +  +++++G + + +H R          +  +
Sbjct: 121 EAVPADLPVTVKVRLGWD---SSARSLEIADAVQQAGASELTVHGRTKE-------EGYR 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +       VMIGR A  N   L+ 
Sbjct: 171 AEAINWQAIGEIRQRL-RIPVIANGEIWDWQSAQNCMAVTGCSAVMIGRGAL-NIPNLSR 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y   P+              W  +   +  Y+         L  + R
Sbjct: 229 VVKYNEPPMA-------------WTDVVRLLQKYSRLEKQGDTGLYHVAR 265


>gi|256854872|ref|ZP_05560236.1| dihydrouridine synthase [Enterococcus faecalis T8]
 gi|256710432|gb|EEU25476.1| dihydrouridine synthase [Enterococcus faecalis T8]
          Length = 326

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 126/321 (39%), Gaps = 36/321 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 21  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 81  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R         +      +  +
Sbjct: 140 LPVSVKTRIGFTEM---AEMEAWITHLLEQDIANLSIHLRT--------RKEMSKVDAHW 188

Query: 177 DIVYEI----KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +I     +  P   I +NG + D  + L++     VDG+MIGR  +KN        
Sbjct: 189 EVIPQIMSIRDRVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNPY------ 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       +  +          +     +   R +    +  +I         GFP +
Sbjct: 243 -AFEKEPKTHTLQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGA 295

Query: 291 RRCRHILTVEAGASTATHHII 311
              R  L +   ++     ++
Sbjct: 296 SDLRAQL-MNTKSTDEVRQLL 315


>gi|328910783|gb|AEB62379.1| tRNA-dihydrouridine synthase 2 [Bacillus amyloliquefaciens LL3]
          Length = 309

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/332 (19%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D ++     L F+  E+P+   I G
Sbjct: 1   MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGRDSVRGRLTFTEDEQPMVAHIWG 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 61  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 119

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  + K  +  + IH R         +      +  +
Sbjct: 120 LPVSVKTRLGYTD---VDEWRGWLTHVLKQDIANLSIHLRT--------RAEMSKVDAHW 168

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIK    +  PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 169 ELIPEIKNLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTNPF------ 222

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I         GF  +
Sbjct: 223 -AFEKEPREHSSKELLDLLRLHLDLHDKYSKLEARPYKPLPRFFKI------YLRGFRGA 275

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 276 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGM 306


>gi|312382630|gb|EFR28023.1| hypothetical protein AND_04540 [Anopheles darlingi]
          Length = 708

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 115/280 (41%), Gaps = 29/280 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L Y+ M  +    +    +K+ L    +++PL +Q  G D
Sbjct: 165 MVDASELAWRLLSRR-HGAQLCYSPMFHSSCFSKDPKYRKDSLQTCPEDRPLIIQFCGND 223

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC----IAAMCKA 114
              +++AA + +D   + I++N+GCP A    G +GA L    +++ +     ++ +   
Sbjct: 224 PKVMLQAALLAQDH-CDAIDINLGCPQAIAKRGHYGAFLQDEWELLREIGQQTMSTLHCH 282

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L+IPVT K RI  D            + ++ +G   + +H R    KG            
Sbjct: 283 LAIPVTCKIRIFEDMSKT----IRYARMLQDAGAQLLTVHGRTREQKG------PLTGLA 332

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV--- 229
           D+  V  ++K+   + I  NG +  +    + +    V+GVM       N A+   +   
Sbjct: 333 DWKYVTVLRKQL-SVPIFSNGNIMSVHDVERCIEETGVNGVMTAEGNLYNPALFEGINPV 391

Query: 230 -----DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
                +EY        +PI           +  S+ ++ A
Sbjct: 392 SWEMANEYLDLVEHFPAPISYIRALREELAVCRSVAEFRA 431


>gi|296331895|ref|ZP_06874360.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii ATCC 6633]
 gi|296150973|gb|EFG91857.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii ATCC 6633]
          Length = 327

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 67/332 (20%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       RN +  + K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYTD---VDEWRNWLTHVLKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I          F  +
Sbjct: 241 -AFEKEPKEHSSKELLDLLRLHLDLHDKYSKLEARPYKPLPRFFKI------YLRRFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 294 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGV 324


>gi|330938356|gb|EGH41984.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 216

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 53/209 (25%), Positives = 101/209 (48%), Gaps = 14/209 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD+ +R   R L    L+ +EM+ +D  L   +K+ L        +P ++QI G D
Sbjct: 20  MAGVTDQPFRQLCRRL-GAGLVVSEMVTSDMSLWNSRKSRLRMIHEGDPEPRSVQIAGGD 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+   + G   I++N+GCP+ +V   + G+ L+ +  +V D + A+  A+ +P
Sbjct: 79  PQMLADAARANVELGAQIIDINMGCPAKKVCNKAAGSALLKDEQLVNDILQAVVAAVDVP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G D          + K  +++G+  + +H R         + +      +YD 
Sbjct: 139 VTLKIRTGWDRDNRNG--LTVAKIAEQAGIQALAVHGRT--------RADLYTGEAEYDT 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + +IK+    + +  NG ++   +A  +L
Sbjct: 189 IAQIKQAV-SIPVFANGDIDSPEKARHVL 216


>gi|169830145|ref|YP_001700303.1| tRNA-dihydrouridine synthase 2 [Lysinibacillus sphaericus C3-41]
 gi|168994633|gb|ACA42173.1| Probable tRNA-dihydrouridine synthase 2 [Lysinibacillus sphaericus
           C3-41]
          Length = 325

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 127/321 (39%), Gaps = 35/321 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    D     +N L F+  E+P+   I G
Sbjct: 20  MEDVTDVVFRHVISEAGRPDVFFTEFTNTTSYCHPDGMDSVRNRLAFTEDEQPMVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +++ G+  I++N+GCP   V E   GA L+L+P +  + I A  KA  
Sbjct: 80  DTPEHFRQMSIGMKELGFKGIDINMGCPVDNVAERGKGAGLILHPALASEIIQA-AKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  I K  +  + IH R         ++        +
Sbjct: 139 LPVSVKTRLGFTD---VAEWREWLTHILKQNIANLSIHLRT--------REEMSKVPAHW 187

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ +IKK      P+  + +NG + D    LK+     +DG+MIGR  + N        
Sbjct: 188 ELIADIKKLRDDIAPETLLTINGDIPDRVTGLKLAEQYGIDGIMIGRGVFSNPYAFEQ-- 245

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               +P   S+     +             ++  R   +  +  +I         GF  +
Sbjct: 246 ----DPKEHSAEEYLNLLYLHLDLHDQYSKEFETRSFKALQRFFKI------YVRGFKGA 295

Query: 291 RRCRHILTVEAGASTATHHII 311
            + R  L + A ++     ++
Sbjct: 296 NQLRIQL-INAHSTDEVRELL 315


>gi|308067621|ref|YP_003869226.1| tRNA-dihydrouridine synthase 2 [Paenibacillus polymyxa E681]
 gi|305856900|gb|ADM68688.1| Probable tRNA-dihydrouridine synthase 2 [Paenibacillus polymyxa
           E681]
          Length = 329

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 127/323 (39%), Gaps = 36/323 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNKSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  I++N+GCP A V E   G+ L+  P+I  D I A  KA  
Sbjct: 79  DKPEYFREMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPEIAADIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R+ +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGF---TTVDEWRDWLTHILKQDIVNLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  ++N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFQNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         +    +  R        Y+A+   S   L +  +       GF  +
Sbjct: 243 ------EKEPKEHSSEELLELLRLHLDLHDHYSAQEPRSFSPLARFFKI---YVRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIET 313
              R+ L + A +++    +++ 
Sbjct: 294 SELRNSL-MNAKSTSEVRTLLDE 315


>gi|297794265|ref|XP_002865017.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297310852|gb|EFH41276.1| nitrogen regulation family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 423

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 70/301 (23%), Positives = 124/301 (41%), Gaps = 28/301 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   +     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 95  MVDNSELPFRLLCQKYGAQA-AYTPMLHSRIFTETEKYRNQEFTTCKEDRPLFVQFCAND 153

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAAK VE +  + +++N+GCP      G++GA LM N  +V   +  + + L++P
Sbjct: 154 PDTLLEAAKRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLAQNLNVP 212

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI  + Q          K ++ +G + + +H R         KD +K+   D+  
Sbjct: 213 VSCKIRIFPNLQDT----LKYAKMLEDAGCSLLAVHGRT-----RDEKDGKKL-RADWSA 262

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K     + +  NG    +ED+   +K    V+GV+      +N A        F  
Sbjct: 263 IKEVKNAL-RIPVLGNGNVRCIEDVDNCIKE-TGVEGVLSAETLLENPAAFAG----FRT 316

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH---MIG-LFHGFPNSR 291
               S   +         +    + +Y           + I  H   M+G  F   P  R
Sbjct: 317 AEWVSENEEEGFVDGGLDQ-GDLVVEYLKLCEKHPVPWRMIRSHVHKMLGEWFRIHPQVR 375

Query: 292 R 292
            
Sbjct: 376 E 376


>gi|308172670|ref|YP_003919375.1| tRNA-dihydrouridine synthase 2 [Bacillus amyloliquefaciens DSM 7]
 gi|307605534|emb|CBI41905.1| tRNA-dihydrouridine synthase 2 [Bacillus amyloliquefaciens DSM 7]
 gi|328552438|gb|AEB22930.1| probable tRNA-dihydrouridine synthase [Bacillus amyloliquefaciens
           TA208]
          Length = 327

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/332 (19%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D ++     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGRDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       R  +  + K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYTD---VDEWRGWLTHVLKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIK    +  PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKNLRDEIAPDTLLTINGDIPDRETGLKLAEQYGVDGIMIGRGIFTNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I         GF  +
Sbjct: 241 -AFEKEPREHSSKELLDLLRLHLDLHDKYSKLEARPYKPLPRFFKI------YLRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 294 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGM 324


>gi|308063487|gb|ADO05374.1| transcriptional regulator [Helicobacter pylori Sat464]
          Length = 328

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E    +QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMVQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +        I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVIGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKEK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEKFFNQ 310


>gi|195053116|ref|XP_001993476.1| GH13829 [Drosophila grimshawi]
 gi|193900535|gb|EDV99401.1| GH13829 [Drosophila grimshawi]
          Length = 582

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 50/289 (17%), Positives = 113/289 (39%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G   +  +      E    +Q+ G + + + 
Sbjct: 247 NLPFRRICKEF-GADITCGEMACAVPLLKGLGQEWALTKRHETEDIFGVQVCGNNPNVIA 305

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +    +  +P TV
Sbjct: 306 QAAQVLHETSRVDYIDLNIGCPIDLIYQQGGGSALMRRTNILELVVRSCSSLSPQLPFTV 365

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G   + +H R         ++ R +   ++  + +
Sbjct: 366 KMRTGIYADKSVA--HELMPLVEEWGAAAVTLHGRS--------REQRYMKQANWTYIEQ 415

Query: 182 IKKENPDLFIGLNGGLEDMSQALK---ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++   + P V  VMIGR A     +   + +  +   T
Sbjct: 416 CAAQAKQMPVIGNGDILSYEDYVEKRAMAPHVSSVMIGRGALIKPWIFQEIKQQRAWAPT 475

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 476 STQRF----------ELMRRYCNYGLEHWGSDTKGVENTRRFLLEWQSF 514


>gi|226498556|ref|NP_001142214.1| hypothetical protein LOC100274382 [Zea mays]
 gi|194707636|gb|ACF87902.1| unknown [Zea mays]
          Length = 420

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 60/280 (21%), Positives = 112/280 (40%), Gaps = 17/280 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R    +A  YT M+ +      +K   + F+T  +++PL +Q    D
Sbjct: 96  MVDNSELPFRMLCRRYGADA-AYTPMLHSRIFSENEKYRSMEFTTCKEDRPLFVQFCAND 154

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L++AAK VE +  + +++N GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 155 PDILLQAAKKVEPY-CDYVDINFGCPQRIARRGNYGAFLMDNLPLVKSLVQNLAANLHVP 213

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R+    +          K ++++G + + +H R         KD +K    D+D 
Sbjct: 214 VSVKIRVFPRLEDT----LAYAKMLEEAGASLVAVHGRT-----RDEKDGKKF-RADWDA 263

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K +   + +  NG +  M      L     DGV+      +N A+           
Sbjct: 264 IKAVK-DALRVPVLANGNIRHMEDVKNCLEHTGADGVLSAETLLENPAVFAGFRTKEWKE 322

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
               +        D   +       Y          + ++
Sbjct: 323 DGDENGDGGLDQADLVIEYLKLCEQYPVPWRMVRSHVHKM 362


>gi|224368204|ref|YP_002602367.1| dihydrouridine synthase family protein [Desulfobacterium
           autotrophicum HRM2]
 gi|223690920|gb|ACN14203.1| dihydrouridine synthase family protein [Desulfobacterium
           autotrophicum HRM2]
          Length = 350

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/289 (22%), Positives = 114/289 (39%), Gaps = 29/289 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQE-KPLALQIGGA 57
           M       +R          LL+T M  A A+   +     +  +  QE   L  QI G 
Sbjct: 39  MAGLGHVAFRELVAEFGGYGLLFTGMCSAKALPHENPATSPVFKWRKQELATLVCQIFGP 98

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  AA+ +E  G+  ++LN GC  A + +   GA ++  PD+  + +A +  ++SI
Sbjct: 99  DPQSMAAAAQRIEAEGFFGVDLNFGCSVAAICKRGCGAEILKTPDLAVEILARVRASVSI 158

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G  +        +L K  + +G + +  H R A  +   P    +I      
Sbjct: 159 PVFVKFRTGWINDPRPAI--DLAKRFEDNGADALVFHPRVAPDRRSRPPRWEQI------ 210

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               + KE   + +  NG + D +    ++     DG+ IGR A     +     + F  
Sbjct: 211 ---SLIKEAVTIPVFGNGNVFDANDLSTVVKQTGCDGIAIGRMAVSRPWIFAQWTKGF-T 266

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           P  G+           +   +  MT+  A+H      ++ + +  I  F
Sbjct: 267 PTIGT-----------YHHTAIRMTELLAKHHGERFAVK-LYKKFIPYF 303


>gi|268590285|ref|ZP_06124506.1| tRNA-dihydrouridine synthase [Providencia rettgeri DSM 1131]
 gi|291314193|gb|EFE54646.1| tRNA-dihydrouridine synthase [Providencia rettgeri DSM 1131]
          Length = 313

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 117/288 (40%), Gaps = 28/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEKP---------L 50
           M    D   R     + N  L  TE + V D +L    K       + K          +
Sbjct: 8   MEGVLDPLVRCLLSEVNNYDLCITEFVRVVDTLL--PAKTFYRLCPELKHGSRTPSGTLV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  PD++     +
Sbjct: 66  RVQLLGQHPQWLAENASRAVELGSWGVDLNCGCPSKTVNGHGGGATLLKQPDLIYQAAKS 125

Query: 111 MCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M +A+    P++VK R+G D    +     +  +++++G   + +H R          D 
Sbjct: 126 MREAVPKELPISVKVRLGWD---SSEFAYEIADAVQQAGATELTVHGRTKE-------DG 175

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            K  ++++  + EI+++   + +  NG + D + A + L     D VMIGR A      L
Sbjct: 176 YKAESINWSAIGEIRRKL-SIPVIANGEIWDYASAQRCLEITGCDAVMIGRGALNTP-NL 233

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           + V ++  + +      +  +      K   +   +AAR     G L+
Sbjct: 234 SRVVKFNESKMPWEQVGRLLLKYTELEKQGDTGHYHAARIKQWLGYLR 281


>gi|188534377|ref|YP_001908174.1| tRNA-dihydrouridine synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029419|emb|CAO97296.1| Putative dihydrouridine synthase [Erwinia tasmaniensis Et1/99]
          Length = 310

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V DA+L       L         +    P+ +
Sbjct: 8   MEGVLDSLVRELLTDVNDYDLCITEFLRVVDALLPVKCFQRLCPELDNASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R          D  +
Sbjct: 128 AAVPSHLPVTVKIRLGWDSGSRQF---EIADAVQQAGASELAVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  +  I++    + +  NG + D   A   +     D VMIGR A     +   
Sbjct: 178 AEAINWQAIGAIRQRL-SIPVIANGEIWDWQSAQDCMAITGCDAVMIGRGALNVPNLSRV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           +          + P      +  WR++   +  Y          L  + R
Sbjct: 237 IKH--------NEP------RMAWRQVVQLLQRYVRLEKQGDTGLYHVAR 272


>gi|300861503|ref|ZP_07107587.1| dihydrouridine synthase (Dus) [Enterococcus faecalis TUSoD Ef11]
 gi|300848964|gb|EFK76717.1| dihydrouridine synthase (Dus) [Enterococcus faecalis TUSoD Ef11]
          Length = 324

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 124/317 (39%), Gaps = 28/317 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    + K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKEAGAPDVFFTEFTNSDSYCHPEGKDSVRGRLVFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  V + G+  +++N+GCP   V E   G+ L+L P++  + I A  KA  
Sbjct: 79  DKPEFFREMSIGVAEMGFQGLDINMGCPVPNVAERGKGSGLILRPEVAAELIDA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG  +      +   +  + +  +  + IH R              IP +  
Sbjct: 138 LPVSVKTRIGFTEM---AEMDAWITHLLEQDIANLSIHLRTRKEMSKVDAHWEVIPQI-- 192

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + +  +  P   I +NG + D  + L++     VDG+MIGR  +KN          F 
Sbjct: 193 MAIRD--RVAPQTTITINGDIPDRQKGLELAEQYGVDGIMIGRGIFKNLY-------AFE 243

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 +P +          +     +   R +    +  +I         GFP +   R
Sbjct: 244 KEPKTHTPQELLGLLRLQLDLQDKYAELVPRSIVGLHRFFKI------YVKGFPGASDLR 297

Query: 295 HILTVEAGASTATHHII 311
             L +   ++     ++
Sbjct: 298 AQL-MNTKSTDEVRQLL 313


>gi|284043141|ref|YP_003393481.1| dihydrouridine synthase [Conexibacter woesei DSM 14684]
 gi|283947362|gb|ADB50106.1| dihydrouridine synthase DuS [Conexibacter woesei DSM 14684]
          Length = 333

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 66/285 (23%), Positives = 115/285 (40%), Gaps = 32/285 (11%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQE------KPLALQIGGADIS 60
           R  A+      L  +EM+ + AI  G++K    +L     E       P+++Q+ G D  
Sbjct: 34  RLQAKRY-GAGLAVSEMVSSHAIHYGNEKTCTELLRVHPDEWRAGAGGPVSIQLFGNDPD 92

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            +  AA    + G N I+LN+GCP  +V +   GA L+ +PD+  +   A  +   +PVT
Sbjct: 93  IMRSAAARAAETGANLIDLNMGCPVPKVCKTGAGAALVKDPDLAVEIARAAAEGSGLPVT 152

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R G+             + +  +G+ G+ IH R A  +             DY++  
Sbjct: 153 VKLRPGLRPGDRNGIELAY-RLVADAGIAGLCIHPRHASQQHS--------GRPDYELAK 203

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + +E P + + ++GGL       ++      + V++ R +  N  +   V        T
Sbjct: 204 RLVEELP-VPVLISGGLRSAELVREVFEFTGAEAVLLARGSLGNPWLFEQVLGDRVGEPT 262

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
               I T VD          + D A  HL  G   + + +     
Sbjct: 263 REE-ILTEVD---------WILDRAVEHLGEGRAARYLRKFYPWY 297


>gi|313203243|ref|YP_004041900.1| dihydrouridine synthase dus [Paludibacter propionicigenes WB4]
 gi|312442559|gb|ADQ78915.1| dihydrouridine synthase DuS [Paludibacter propionicigenes WB4]
          Length = 326

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 69/315 (21%), Positives = 121/315 (38%), Gaps = 40/315 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNA---LLYTEMIVADAIL----RGDKKNILGFSTQEK----- 48
           M D TD  +R   R ++ +    +++TE   AD +     R      L  S  E+     
Sbjct: 18  MEDVTDTVFREVIRSVSESDALHVMFTEFTSADGLCNEKGREFVATRLHVSETERELLKA 77

Query: 49  ---PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
               L  QI G+D  K  E+AK++   G ++ I++N+GCP  +V +    + L+ +P++ 
Sbjct: 78  TNTKLVAQIWGSDPVKFHESAKLISAMGLFDGIDINMGCPVKKVVKNHSCSDLINHPEMA 137

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
              + A  +  ++PV+VK RIG      ++     +  + +     I IH R   +    
Sbjct: 138 KQIVVATREGTNLPVSVKTRIGF----SSIVTEEWIGQLLEVHPAAITIHGRTRSMMSNG 193

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                +I       V    +      I  NG ++  + AL  +    VDGVM+GR  +KN
Sbjct: 194 LALWDEIGKA----VQLRNQSKSSTLILGNGDVDSHATALAKVRDFGVDGVMVGRGVFKN 249

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             M   VD+               + +     +               G    + R    
Sbjct: 250 PWMFNAVDK--------------EISRQMRIDLVVKHIQLYDTTWKEKGNFNVLKRFFKI 295

Query: 283 LFHGFPNSRRCRHIL 297
             +GF  + + R  L
Sbjct: 296 YLNGFDGAAQWRDQL 310


>gi|58041830|gb|AAW63417.1| Orf2 [Klebsiella pneumoniae]
          Length = 312

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHNNSLTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPTHLPVTVKVRLGWDSGERRF---EIADAVQQAGASELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +D+  + EI++    + +  NG + D   A   L     D VMIGR A  N   L+ 
Sbjct: 178 AERIDWQAIGEIRQRLT-IPVVANGEIWDWQSAQDCLAATGCDSVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPQVVELLQKYTRLEKQGDTGLYHVAR 272


>gi|126135962|ref|XP_001384505.1| hypothetical protein PICST_58121 [Scheffersomyces stipitis CBS
           6054]
 gi|126091703|gb|ABN66476.1| tRNA dihydrouridine synthase [Scheffersomyces stipitis CBS 6054]
          Length = 415

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 98/235 (41%), Gaps = 21/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFS-TQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A         R +  + L     +++PL +Q 
Sbjct: 26  MVDQSELAWRILSRRY-GADLCYTPMFHAKLFATEQKYRDNMWSELDGDFEKDRPLIVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK VED   + ++LN+GCP     +G +GA LM + D+V   I  +   
Sbjct: 85  CANDPDYLLQAAKFVED-KCDAVDLNLGCPQGIAKKGKYGAFLMDDWDLVHTLIKNLHDN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L +PVT K RI  D +          K I  +G   I +H R   +KG +          
Sbjct: 144 LKVPVTAKIRIYDDWEKS----LQYAKMILDAGAQFITVHGRTRDMKGQAT------GLA 193

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAML 226
           ++ ++  +++  P D     NG +   S     +     D VM       N  + 
Sbjct: 194 NWKVLRYLRENLPKDQVFFANGNILYPSDLGRCENETQCDAVMSAEGNLYNPGVF 248


>gi|170572143|ref|XP_001891998.1| tRNA-dihydrouridine synthase 4 [Brugia malayi]
 gi|158603133|gb|EDP39179.1| tRNA-dihydrouridine synthase 4, putative [Brugia malayi]
          Length = 321

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 57/281 (20%), Positives = 113/281 (40%), Gaps = 34/281 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   RL + + + +T MI A   +  ++     F+    + P  +Q    +
Sbjct: 37  MVRYSKLPFRMLVRLYSVD-VAFTPMIYAKHFIASEQCRSAEFTTCPGDNPTVVQFASNE 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +   AA  +  +    I+LN GCP   V    +G+ L+ +P  + D ++   + +S P
Sbjct: 96  PEEFSTAAMFISRY-CRGIDLNCGCPQRDVMREGYGSSLLTDPVRIADIVSTTRRRISRP 154

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K R+  + Q+         +  +++GV+ + +H R    +             D
Sbjct: 155 DFTISIKIRLKPNRQLT----LETCRQAERAGVSFVTVHGRTPEQRS---------EPAD 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD++  IK     + +  NG ++   QAL++     VDGVM      +N AM        
Sbjct: 202 YDMIKLIKSSL-SIPVIANGNIKSYEQALQVVKYTGVDGVMSANGLLENPAMFA------ 254

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                G +    +   D+ R  +     +   H      L+
Sbjct: 255 -----GYTSTPKQCVADWVRLATEHGCPFDLFHQQLMFMLR 290


>gi|66801291|ref|XP_629571.1| CCCH-type zinc finger-containing protein [Dictyostelium discoideum
           AX4]
 gi|74850928|sp|Q54CU9|DUS3L_DICDI RecName: Full=tRNA-dihydrouridine synthase 3-like
 gi|60462949|gb|EAL61146.1| CCCH-type zinc finger-containing protein [Dictyostelium discoideum
           AX4]
          Length = 671

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 108/285 (37%), Gaps = 28/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L G K  +  L     E    +QI G+ +   V
Sbjct: 336 NLPFRRICKRL-GADITIGEMALTTKLLEGTKSELALLKRHPCEDKFGVQICGSYVDAAV 394

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+ +E +   + +++N GCP   V     GA LM  P  V   +  +  +LS P T+K
Sbjct: 395 KCAEFIENEIDADFVDINSGCPIDLVCNMGAGAALMERPKKVEQLLRGISSSLSCPTTIK 454

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG  +  P      L+ S+ + G   + +H R         +  R     ++D V + 
Sbjct: 455 IRIGKSEDAPTA--HKLIPSLGEWGACAVTLHGRS--------RAQRYSRLANWDYVKQ- 503

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             E   + +  NG + +    + I     V  +MI R A     + T + E     ++ S
Sbjct: 504 CSEVSSIPLIGNGDIYNYQDVVNIYDSSKVSSIMIARGALIKPWIFTEIKEKREWDISAS 563

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                    DF R       +Y   H  S    +    + ++   
Sbjct: 564 E------RLDFIRD----FANYGLDHWGSDRIGVDNTRKFLLNWL 598


>gi|308186130|ref|YP_003930261.1| tRNA-dihydrouridine synthase [Pantoea vagans C9-1]
 gi|308056640|gb|ADO08812.1| tRNA-dihydrouridine synthase [Pantoea vagans C9-1]
          Length = 316

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 61/286 (21%), Positives = 113/286 (39%), Gaps = 24/286 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRQLLSEVNDYDLCITEFLRVVDQLLPVKSFTRLCPELHHASRTPSGTRVRM 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 68  QLLGQHPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAMR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D    +     +  +++++G + + +H R          +  +
Sbjct: 128 EAVPADLPVTVKVRLGWD---SSARSLEIADAVQQAGASELTVHGRTKE-------EGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGDIRQRL-RIPVIANGEIWDWQSAQNCMAVTGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           V +Y   P+     ++         K   +   + AR     G L+
Sbjct: 236 VVKYNEPPMAWPDVVRLLQKYSRLEKQGDTGLYHVARIKQWLGYLR 281


>gi|195997917|ref|XP_002108827.1| hypothetical protein TRIADDRAFT_52208 [Trichoplax adhaerens]
 gi|190589603|gb|EDV29625.1| hypothetical protein TRIADDRAFT_52208 [Trichoplax adhaerens]
          Length = 309

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 64/284 (22%), Positives = 124/284 (43%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      + +T MI++++ ++ +K     F+T   ++PL +Q   ++
Sbjct: 23  MVRYSKLPFRSLVRKY-GCDVAFTPMIISESFIKSEKARASEFTTVASDRPLIVQFAASN 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
              L +A +++  +  + ++LN GCP        +GA L+ +P++V + +      +   
Sbjct: 82  AFDLADATELIVPY-ADGVDLNCGCPQRWAMHEGYGAHLINHPELVKEMVRHTRSKICNE 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +  +++K RI  D         +L +  + +GV+ I +H R    K            + 
Sbjct: 141 NFSISIKIRIHNDINTTV----DLCRKAEAAGVSWITVHGRTTSEKHT---------PVH 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK ++  + +  NG +  +  A +I    +VDGVM  R   +N A+        
Sbjct: 188 YDAIKTIK-DSVSIPVIANGNVFTVDDAQEIYDKTNVDGVMSARGILRNPALYA------ 240

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                G S       +DF R  S   T +   H H    L++IT
Sbjct: 241 -----GYSKTPICCVEDFVRITSELETHFTPFHRHLIFMLEKIT 279


>gi|297379926|gb|ADI34813.1| tRNA-dihydrouridine synthase B [Helicobacter pylori v225d]
          Length = 328

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 127/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +      +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKF-GVDVTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGR A +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQADGLMIGRTALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEVKSM-RESIEEFFNQ 310


>gi|295098151|emb|CBK87241.1| tRNA-U20a,U20b-dihydrouridine synthase [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 311

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 106/290 (36%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPEKSFYRLCPELHRQSRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 128 EAVPSHLPVTVKVRLGWDSDDKQF---EIADAVQQAGATELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A   L     + VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRKRLT-IPVIANGEIWDYESAQACLKETGCNAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W  +   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWADVVKLLQKYTRLEKQGDTGLYHVAR 272


>gi|305673507|ref|YP_003865179.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|305411751|gb|ADM36870.1| histidine phosphokinase/phophatase, putative [Bacillus subtilis
           subsp. spizizenii str. W23]
          Length = 327

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 126/332 (37%), Gaps = 36/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D K+     L F+  ++P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAGRPDVFFTEFTNSESYCHPDGKDSVRGRLTFTEDDQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP   V     G+ L+  P++  + I A  KA  
Sbjct: 79  DKPENFRQMSIGMAELGFKGLDINMGCPVPNVAGNGKGSGLICRPEVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       RN +  + K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYTD---VDEWRNWLTHVLKQDIANLSIHLRT--------RAEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFTNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +    +   AR      +  +I          F  +
Sbjct: 241 -AFEKEPKEHSSKELLDLLRLHLDLHDKYSKLEARPYKPLPRFFKI------YLRRFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R+   +   ++     +++      ++ +
Sbjct: 294 SELRNQ-CMNTKSTDEVRALLDDFERKYLDGV 324


>gi|56118841|ref|NP_001007929.1| dihydrouridine synthase 4-like [Xenopus (Silurana) tropicalis]
 gi|51513200|gb|AAH80375.1| MGC79829 protein [Xenopus (Silurana) tropicalis]
          Length = 308

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 71/284 (25%), Positives = 121/284 (42%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT MI+A   ++  K     F+T   ++PL +Q    +
Sbjct: 24  MVRYSKLAFRTLVRKYD-CDLCYTPMIIAADFVKSVKARDSEFTTNQGDRPLIVQFAAKE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + I+LN GCP        +GACL+ NP++V D +  +   +  P
Sbjct: 83  AQVLADAASLVSPF-ASGIDLNCGCPQRWAMAEGYGACLINNPELVSDMVKQVRNQVGDP 141

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 142 GFTISIKIRIHADISRTV----DLCRKAEAAGVSWITVHGRTHDERHQ---------PVH 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK E+  + +  NG ++ + +A  ++ +   DGVM  R    N AM      Y 
Sbjct: 189 YDAIKSIK-ESLSIPVVANGDVKSLKEAENIREITGADGVMAARGLLANPAMFAG---YE 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
             PL           +D+        T +   H H    +++IT
Sbjct: 245 ETPLA--------CIQDWIDITLEHGTPFTCLHHHLIYMMERIT 280


>gi|146312384|ref|YP_001177458.1| tRNA-dihydrouridine synthase C [Enterobacter sp. 638]
 gi|145319260|gb|ABP61407.1| tRNA-U20a,U20b-dihydrouridine synthase [Enterobacter sp. 638]
          Length = 310

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +T    + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPAKSFYRLCPELHRQSRTTSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 128 EAVPSHLPVTVKVRLGWDSGDRQF---EIADAVQQAGATELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++   ++ +  NG + D   A   L     D VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIRDIRQRL-NIPVIANGEIWDYESAQACLHATGCDSVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W  +   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPDVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|296112003|ref|YP_003622385.1| transcription regulator [Leuconostoc kimchii IMSNU 11154]
 gi|295833535|gb|ADG41416.1| transcription regulator [Leuconostoc kimchii IMSNU 11154]
          Length = 374

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 131/329 (39%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + YTE   A +++    K      L  +  E+    QI G
Sbjct: 36  MEAVTDTIFRRVVAQAGAPDVYYTEFTNASSMVHPQAKFSVQGRLAVAEHEQQPVAQIWG 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   ++  AAK +   GY  +++N+GCP + V + + G+ L+  PD+  + +AA  K   
Sbjct: 96  SHPEEIAGAAKKLPSMGYQAVDINMGCPDSSVIKNNAGSALIRTPDLASEIVAA-AKLSG 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R  +  I K  V  + +H R       +P     I     
Sbjct: 155 LPVSVKTRLGF---YKPEEFREWLPIILKQNVAVLTVHLRSRKEMSKAPAHEEYID---- 207

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +I+       P   I +NG ++  S  L+++     +DG+MIGR  ++N       ++  
Sbjct: 208 EILAMRDAIAPQTLIQINGDIKTRSAGLQLVKRHSGIDGIMIGRGIFENPYAF---EKQE 264

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S     +  D + +++ ++T      L    K+            GF ++   
Sbjct: 265 RQHTLSESIALLNLQLDLFDEVNETITPKHFEALKRYFKI---------YLRGFAHASAL 315

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R +L +E   +     I+      +  ++
Sbjct: 316 RQML-METHTTQEVRAILSQELPKVYAAV 343


>gi|317010947|gb|ADU84694.1| putative transcriptional regulator [Helicobacter pylori
           SouthAfrica7]
          Length = 328

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 129/322 (40%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSALEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           S + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  SVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKVIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G + +IP      +  ++  + V+ + +H R    K    K       +DY+
Sbjct: 134 ITSVKVRLGFEKKIPQ----EIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     DG+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLEITQADGLMIGRAALRVPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVVMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|240949296|ref|ZP_04753639.1| putative nitrogen regulator protein [Actinobacillus minor NM305]
 gi|240296247|gb|EER46896.1| putative nitrogen regulator protein [Actinobacillus minor NM305]
          Length = 319

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 125/331 (37%), Gaps = 41/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     + +  L  +E +  V   + R     +         +    P+ +
Sbjct: 12  MQGVLDPFLRKLLTTVNDYDLCISEFVRVVDQKLPRKTFYRLCPELYQGSKTDSGTPVRV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++  + G + ++LN GCPS  V+  + GA L+ +P+++     A+ 
Sbjct: 72  QLLGQYPQWLAENAELAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPELIYRATQAIR 131

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D    A     +  ++++ G N I +H R          D  +
Sbjct: 132 QAVPQDQVVSVKVRLGWD---SAEQCFEIADAVQQGGANEITVHGRTKT-------DGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I+K    + +  NG + D   A K   + +   +MIGR A     +   
Sbjct: 182 AERINWQAIGDIQKRLT-IPVIANGEIWDFESAKKCQEITACQALMIGRGALNTPNL--- 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K    K  W ++   +  Y             + R    +  L  
Sbjct: 238 -----------SRVVKFNQPKLAWCEVLKLLFQYVNMENEHDSGFYHVARIKQWLHYLDK 286

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
            +P +     IL  E G +    H IE A  
Sbjct: 287 EYPEAIALFQILKTEHGYAGLKRH-IEQAVE 316


>gi|195384997|ref|XP_002051195.1| GJ13589 [Drosophila virilis]
 gi|194147652|gb|EDW63350.1| GJ13589 [Drosophila virilis]
          Length = 590

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 50/289 (17%), Positives = 110/289 (38%), Gaps = 28/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  +L+G   +  +      E    +Q+ G + + + 
Sbjct: 255 NLPFRRICKEF-GADITCGEMACAVPLLKGLGQEWALTKRHESEDIFGVQVCGNNPNVIT 313

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           +AA+++ +    + I+LN+GCP   +++   G+ LM   +I+   + +       +P TV
Sbjct: 314 QAAEVLHETARVDYIDLNIGCPIDLIYQQGGGSALMRRTNILELTVRSCAALSDRLPFTV 373

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+           L+  +++ G   + +H R         ++ R     ++  + +
Sbjct: 374 KMRTGIYADKSVA--HELLPLVEQWGAAAVTLHGRS--------REQRYTRQANWAYIEQ 423

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
              +   + +  NG +      ++     P V  VMIGR A     +   + +  +   T
Sbjct: 424 CAAQARHMPVIGNGDIISYEDYVERRALAPHVSSVMIGRGALIKPWIFQEIKQQKAWAPT 483

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +             ++     +Y   H  S  K  + TR  +  +  F
Sbjct: 484 STQRF----------ELLRRYCNYGLEHWGSDTKGVENTRRFLLEWQSF 522


>gi|15240243|ref|NP_201523.1| nitrogen regulation family protein [Arabidopsis thaliana]
 gi|10177609|dbj|BAB10956.1| unnamed protein product [Arabidopsis thaliana]
 gi|15146316|gb|AAK83641.1| AT5g67220/K21H1_18 [Arabidopsis thaliana]
 gi|20908082|gb|AAM26724.1| AT5g67220/K21H1_18 [Arabidopsis thaliana]
 gi|332010932|gb|AED98315.1| tRNA-dihydrouridine synthase 4 [Arabidopsis thaliana]
          Length = 423

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 68/301 (22%), Positives = 122/301 (40%), Gaps = 28/301 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   +     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 95  MVDNSELPFRLLCQKYGAQA-AYTPMLHSRIFTETEKYRNQEFTTCKEDRPLFVQFCAND 153

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAAK VE +  + +++N+GCP      G++GA LM N  +V   +  + + L++P
Sbjct: 154 PDTLLEAAKRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLAQNLNVP 212

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K RI  + +          K ++ +G + + +H R         KD +K    D+  
Sbjct: 213 VSCKIRIFPNLEDT----LKYAKMLEDAGCSLLAVHGRT-----RDEKDGKKF-RADWSA 262

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + E+K     + +  NG    +ED+   +K    V+GV+      +N A        F  
Sbjct: 263 IKEVKNAM-RIPVLANGNVRCIEDVDNCIKE-TGVEGVLSAETLLENPAAFAG----FRT 316

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH---MIG-LFHGFPNSR 291
                   +         +    + +Y           + I  H   M+G  F   P  R
Sbjct: 317 AEWAKDNEEEGFVDGGLDQ-GDLVVEYLKLCEKHPVPWRMIRSHVHKMLGEWFRIHPQVR 375

Query: 292 R 292
            
Sbjct: 376 E 376


>gi|23098238|ref|NP_691704.1| hypothetical protein OB0783 [Oceanobacillus iheyensis HTE831]
 gi|22776463|dbj|BAC12739.1| hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
          Length = 326

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 119/305 (39%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   +++    D +      L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVTEAARPDVFFTEFTNSESYCHPDGRQSVRGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  +++N+GCP A V     G+ L+  P+I  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAEMGFKGLDINMGCPVANVAGNGKGSGLINRPEIAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          +  +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGY---TYIDEWKEWLKHVLEQDIVNLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK++    VDGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDEIAPDTLLTINGDIPDRQTGLKLVEEYGVDGVMIGRGVFKNPF------ 240

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
             F       S  +          +     +  +R      +  +I         GF  +
Sbjct: 241 -AFEKEQKEHSSQEMLDLLRLHLDLHDKYDELESRSFKPLHRFFKI------YVKGFRGA 293

Query: 291 RRCRH 295
              R+
Sbjct: 294 SELRN 298


>gi|89266831|emb|CAJ83965.1| dihydrouridine synthase 4-like (S. cerevisiae) [Xenopus (Silurana)
           tropicalis]
          Length = 324

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 71/284 (25%), Positives = 121/284 (42%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT MI+A   ++  K     F+T   ++PL +Q    +
Sbjct: 40  MVRYSKLAFRTLVRKYD-CDLCYTPMIIAADFVKSVKARDSEFTTNQGDRPLIVQFAAKE 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + I+LN GCP        +GACL+ NP++V D +  +   +  P
Sbjct: 99  AQVLADAASLVSPF-ASGIDLNCGCPQRWAMAEGYGACLINNPELVSDMVKQVRNQVGDP 157

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 158 GFTISIKIRIHADISRTV----DLCRKAEAAGVSWITVHGRTHDERHQ---------PVH 204

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK E+  + +  NG ++ + +A  ++ +   DGVM  R    N AM      Y 
Sbjct: 205 YDAIKSIK-ESLSIPVVANGDVKSLKEAENIREITGADGVMAARGLLANPAMFAG---YE 260

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
             PL           +D+        T +   H H    +++IT
Sbjct: 261 ETPLA--------CIQDWIDITLEHGTPFTCLHHHLIYMMERIT 296


>gi|238794075|ref|ZP_04637692.1| tRNA-dihydrouridine synthase C [Yersinia intermedia ATCC 29909]
 gi|238726580|gb|EEQ18117.1| tRNA-dihydrouridine synthase C [Yersinia intermedia ATCC 29909]
          Length = 310

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 62/286 (21%), Positives = 114/286 (39%), Gaps = 24/286 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +     + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHHQSRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWQAISEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           V +Y    ++    +K         K   +   + AR     G L+
Sbjct: 236 VVKYNEPRMSWPEVVKLLQKYVLLEKQGDTGLYHVARIKQWLGYLR 281


>gi|238763826|ref|ZP_04624784.1| tRNA-dihydrouridine synthase C [Yersinia kristensenii ATCC 33638]
 gi|238697956|gb|EEP90715.1| tRNA-dihydrouridine synthase C [Yersinia kristensenii ATCC 33638]
          Length = 303

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         ++    + +
Sbjct: 1   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHYQSRTSSGTQVRI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 61  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 121 EAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 171 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLSR 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 229 VVKYNE-------------PRMPWPEVVKLLKKYVQLEKQGDTGLYHVAR 265


>gi|238798925|ref|ZP_04642390.1| tRNA-dihydrouridine synthase C [Yersinia mollaretii ATCC 43969]
 gi|238717235|gb|EEQ09086.1| tRNA-dihydrouridine synthase C [Yersinia mollaretii ATCC 43969]
          Length = 310

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + L
Sbjct: 8   MEGVLDSLVRQLLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHNQSRTQSGTLVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPEHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|296237888|ref|XP_002763931.1| PREDICTED: tRNA-dihydrouridine synthase 1-like [Callithrix jacchus]
          Length = 471

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 55/283 (19%), Positives = 107/283 (37%), Gaps = 35/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L  T  + A   +                +++PL +Q   
Sbjct: 24  MVDQSELGWRLLSRR-HGAQLCCTPTLHAQVFVCDANYRKENLYCEACPEDRPLIMQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    +++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQTIAKRGHYGAFLQDEWNLLQRIILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT + R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCRIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLAGAASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  +G ++ +    + +    V GVM       N A+         
Sbjct: 192 ERIKAVRKAV-AIPVFADGNIQSLQDVERCIQDTGVQGVMSAEGNLHNPALF-------- 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +   +    Y   HL    KL  
Sbjct: 243 ---EGRSPAVWELAEEYLDIVREHLCPLSYVWAHL---FKLWH 279


>gi|152997627|ref|YP_001342462.1| dihydrouridine synthase DuS [Marinomonas sp. MWYL1]
 gi|150838551|gb|ABR72527.1| dihydrouridine synthase DuS [Marinomonas sp. MWYL1]
          Length = 335

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 70/315 (22%), Positives = 126/315 (40%), Gaps = 31/315 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R           L +E I      I     K+++        +T   P+  
Sbjct: 26  MEGVMDHTMRALLSQTGGMDYLVSEFIRVTQYPIPAATFKHLVPENTNKARTTHNHPVHT 85

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G++   + E+A      G   I++N GCP+ RV+    G+ L+  PD + D ++A+ 
Sbjct: 86  QLLGSNAELMAESALNATKAGAKHIDVNFGCPAKRVNGHGGGSVLLQTPDALYDIMSAIR 145

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IPV+ K R+G +D+     L + V +I+ +GV  + IH R         K +  
Sbjct: 146 DTLPSDIPVSAKIRLGFEDE---ALLFDNVAAIEAAGVGTLTIHGRT--------KKDGY 194

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + EI +    + +  NG + D    L+   +      MIGR +  N  +   
Sbjct: 195 KPPARWEKIGEI-QAKTKMTVVANGDITDTKSLLRCQSITGCQHFMIGRGSLNNPFVFQQ 253

Query: 229 VDEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           + +  +    T  +    R+   + R++     + AA      G+L+Q   H+   F   
Sbjct: 254 IRKELNGQESTADTTNLNRLFISYSRELQEHYDEVAA-----LGRLKQWCGHLRFEFKEI 308

Query: 288 P-NSRRCRHILTVEA 301
             N +  R   +V  
Sbjct: 309 KENLQTLRRCKSVNE 323


>gi|134114502|ref|XP_774081.1| hypothetical protein CNBH0060 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50256713|gb|EAL19434.1| hypothetical protein CNBH0060 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 725

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 108/250 (43%), Gaps = 13/250 (5%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM +A  ++ G K+   ++     EK   +Q+ G   +++V
Sbjct: 370 NLPFRRLCVDY-GATITVSEMALAQPLVYGAKEEWALVRRHESEKMFGVQVAGGFPNRMV 428

Query: 64  EAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            AA+++ +      G + +++N+GCP   V     G+ LM +P  +G  +  M +AL  I
Sbjct: 429 PAAEVIANTIGKGGGVDFVDVNMGCPIDLVFNQGAGSALMDSPGRLGKLLVGMNRALGDI 488

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R GV    P  A + + + + + G   + IH R    +   P D   I      
Sbjct: 489 PLTVKFRTGVAHGKPN-AHKLIPRFVTEWGAGALTIHGRSRQQRYSKPADWEYIKTCVTA 547

Query: 178 IVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +   +   N P + I  NG     +   + +    VDGVM+ R A     + T + E   
Sbjct: 548 LRESVADANLPPVPIFGNGDCFSAASYYEEMDRSGVDGVMVARGALIKPWIFTEIKERRE 607

Query: 235 NPLTGSSPIK 244
             ++    ++
Sbjct: 608 WDISAVERLE 617


>gi|212712155|ref|ZP_03320283.1| hypothetical protein PROVALCAL_03237 [Providencia alcalifaciens DSM
           30120]
 gi|212685202|gb|EEB44730.1| hypothetical protein PROVALCAL_03237 [Providencia alcalifaciens DSM
           30120]
          Length = 319

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 66/329 (20%), Positives = 118/329 (35%), Gaps = 44/329 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L       L         +     + +
Sbjct: 8   MEGVLDSLVRRLLSEVNDYDLCITEFVRVVDTLLPAKTFYRLCPELQYGSRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  PD++     A+ 
Sbjct: 68  QLLGQYPEWLAENANRAVELGSWGVDLNCGCPSKTVNGSGGGATLLKQPDLIYHAAKAIR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PV+VK R+G D    +     +  +++++G   + +H R          D  K
Sbjct: 128 AAVPKELPVSVKVRLGWD---SSQFAHEIADAVQQAGATELTVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+++   + +  NG + D   A +   +   D +MIGR A     +   
Sbjct: 178 AECINWQAIGEIRQKL-SIPVIANGEIWDYESAKRCMEMTGCDSIMIGRGALNTPNLSRV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           +                 V K  W ++   +  Y               R    +  L  
Sbjct: 237 IKH--------------NVPKMPWEQVGKILFKYTELEKQGDTGHYHAARIKQWLSYLRK 282

Query: 286 GFPNS----RRCRHILTVEAGASTATHHI 310
            +  +     + R + T E  A    HH+
Sbjct: 283 EYQQADVLFSQVRALKTAEQIADIIAHHV 311


>gi|290991278|ref|XP_002678262.1| predicted protein [Naegleria gruberi]
 gi|284091874|gb|EFC45518.1| predicted protein [Naegleria gruberi]
          Length = 292

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 61/273 (22%), Positives = 102/273 (37%), Gaps = 22/273 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  A     + L YT M      ++ +  +K    F   E P+  Q    D
Sbjct: 19  MVDQSELAFRLLA-QNHGSTLAYTPMFHGRIFVQDETYQKTHFQFLESEGPVFAQFCAND 77

Query: 59  ISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            +  VE   +  +    +I   +LN+GCP     +G +G+ LM + D++   I    K L
Sbjct: 78  PNIFVECGWLAWELSNQKIAAVDLNLGCPQRIAKKGRYGSYLMEDIDLICSMIEKAHKEL 137

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K RI  D    A      V  I ++G   + +H R    +G +          D
Sbjct: 138 PVPVTAKIRIFED----AEHTLKYVDRILEAGAQVLCVHGRTRDQRGHNQNY------AD 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + ++  I++  P + +  NG +      +  L     D VM       N A+        
Sbjct: 188 WKMIKLIREHVPHIPVIANGNIRMYQDVIDCLEFTGADAVMSADPLLCNPALFNGGQHVN 247

Query: 234 SNPLTGSSPIKTR----VDKDFWRKISASMTDY 262
              L              D  F ++    M D+
Sbjct: 248 GIDLCEEYINICEKYPPPDHSFIKRHLFQMLDH 280


>gi|58271188|ref|XP_572750.1| tRNA dihydrouridine synthase [Cryptococcus neoformans var.
           neoformans JEC21]
 gi|74683549|sp|Q5KC68|DUS3_CRYNE RecName: Full=tRNA-dihydrouridine synthase 3
 gi|57229009|gb|AAW45443.1| tRNA dihydrouridine synthase, putative [Cryptococcus neoformans
           var. neoformans JEC21]
          Length = 725

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 108/250 (43%), Gaps = 13/250 (5%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM +A  ++ G K+   ++     EK   +Q+ G   +++V
Sbjct: 370 NLPFRRLCVDY-GATITVSEMALAQPLVYGAKEEWALVRRHESEKMFGVQVAGGFPNRMV 428

Query: 64  EAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
            AA+++ +      G + +++N+GCP   V     G+ LM +P  +G  +  M +AL  I
Sbjct: 429 PAAEVIANTIGKGGGVDFVDVNMGCPIDLVFNQGAGSALMDSPGRLGKLLVGMNRALGDI 488

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R GV    P  A + + + + + G   + IH R    +   P D   I      
Sbjct: 489 PLTVKFRTGVAHGKPN-AHKLIPRFVTEWGAGALTIHGRSRQQRYSKPADWEYIKTCVTA 547

Query: 178 IVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +   +   N P + I  NG     +   + +    VDGVM+ R A     + T + E   
Sbjct: 548 LRESVADANLPPVPIFGNGDCFSAASYYEEMDRSGVDGVMVARGALIKPWIFTEIKERRE 607

Query: 235 NPLTGSSPIK 244
             ++    ++
Sbjct: 608 WDISAVERLE 617


>gi|308453103|ref|XP_003089301.1| hypothetical protein CRE_11589 [Caenorhabditis remanei]
 gi|308241223|gb|EFO85175.1| hypothetical protein CRE_11589 [Caenorhabditis remanei]
          Length = 548

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 123/298 (41%), Gaps = 30/298 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +   EM +A +IL G   + ++L     EK   +Q+ G     + 
Sbjct: 211 NLPFRRICVDY-GADITCGEMALATSILSGAASEYSLLKRHPSEKIFGVQLAGGFADTMA 269

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTV 121
           +AA+IV E+F  + +++N+GCP   V++   G  L   P+ + + +AA    L   P+TV
Sbjct: 270 KAAQIVVENFDVDFVDINMGCPIDVVNQKGGGCALPSRPNKLYEVLAATKSVLGDCPMTV 329

Query: 122 KCRIGVDDQI-PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R G  + +  A      +K       + I  H R         K+ R     ++D  +
Sbjct: 330 KIRTGQKEGVLKAPETVEFMKKSPWHCPDLITFHPRS--------KEQRYTKLANWDYTH 381

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + + +  + + + G +       + L +  V+G+MIGR A     + T +DE  +  ++
Sbjct: 382 AVAEASKQVPLWVCGDVLSWEDYYERLENHPVNGIMIGRGALIKPWIFTEIDERRTWDIS 441

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            +              +    T+Y   H  S     + TR  +  F  F    +CR+I
Sbjct: 442 ATERF----------DLLKKFTNYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 485


>gi|288549865|ref|ZP_05968436.2| tRNA-dihydrouridine synthase [Enterobacter cancerogenus ATCC 35316]
 gi|288316988|gb|EFC55926.1| tRNA-dihydrouridine synthase [Enterobacter cancerogenus ATCC 35316]
          Length = 303

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         ++    + +
Sbjct: 1   MEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPVKSFHRLCPELHNQSRTSSGTLVRI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 61  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYRGAKAMR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 121 EAVPSHLPVTVKVRLGWDSGARQF---EIADAVQQAGATELVVHGRTKE-------DGYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   L     D VMIGR A  N   L+ 
Sbjct: 171 AERINWQAIGEIRQRLT-IPVIANGEIWDYESAQACLKETGCDAVMIGRGAL-NVPNLSR 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W  + A +  Y+         L  + R
Sbjct: 229 VVKY-------------NAPRMPWADVVALLQKYSRLEKQGDTGLYHVAR 265


>gi|238788774|ref|ZP_04632565.1| tRNA-dihydrouridine synthase C [Yersinia frederiksenii ATCC 33641]
 gi|238723079|gb|EEQ14728.1| tRNA-dihydrouridine synthase C [Yersinia frederiksenii ATCC 33641]
          Length = 310

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         ++   P+ +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHQQSRTSSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTK-------DDGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 ADRINWPAIGEIRQRLT-IPVIANGEIWDYHSAQQCMKVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMAWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|332161013|ref|YP_004297590.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318604885|emb|CBY26383.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325665243|gb|ADZ41887.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859407|emb|CBX69752.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica W22703]
          Length = 310

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         ++    + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPTKSFYRLCPELHQQSRTSSGTQVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRAAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPAHFPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|220905344|ref|YP_002480656.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869643|gb|ACL49978.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 331

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 111/301 (36%), Gaps = 23/301 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+ A  ++        +L    +++PL +Q+ GA+ 
Sbjct: 30  AGYSDLPFRLLCRQY-GAAVCVTEMVSAKGLVYQSPGTNELLASLPEDQPLVVQLFGAEA 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IP 118
             L  A  ++ D GY   +LN+GC  A+V     GA ++ +   + +    M  A     
Sbjct: 89  PFLSRAVSLLRDAGYGWFDLNMGCSVAKVLRQGAGAAMLGDTGNILEVARGMIAAAGPGR 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G+DD  P   L +L   ++ +G   + +H R A            + +L    
Sbjct: 149 VGFKLRLGLDDTRP--VLPDLALRLEDAGAGWLVLHPRTARQGFGGTAQWEALADL---- 202

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                     + +  +G L   ++ +  L      G+M  R A  N A+        +  
Sbjct: 203 -----APRLSIPLLASGDLFSAAEGMACLEQTGAAGLMYARGAMYNPAIFADHAALCAGG 257

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +       D    + +     + A  H      + ++   +       P +R  R  
Sbjct: 258 HPQAH------DAASLKAMILRHMELARLHCPGKAAVWKMRSVVPRYVRALPGARALRQE 311

Query: 297 L 297
           L
Sbjct: 312 L 312


>gi|310640378|ref|YP_003945136.1| dihydrouridine synthase dus [Paenibacillus polymyxa SC2]
 gi|309245328|gb|ADO54895.1| Dihydrouridine synthase DuS [Paenibacillus polymyxa SC2]
          Length = 329

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 73/323 (22%), Positives = 127/323 (39%), Gaps = 36/323 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNKSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  I++N+GCP A V E   G+ L+  P+I  D I A  KA  
Sbjct: 79  DKPEYFREMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPEIAADIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R+ +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGF---TAVDEWRDWLTHILKQDIVNLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  ++N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFQNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         +    +  R        Y+A+   S   L +  +       GF  +
Sbjct: 243 ------EKEPKEHSSEELLELLRLHLDLHDHYSAQEPRSFSPLARFFKI---YVRGFRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIET 313
              R+ L + A +++    +++ 
Sbjct: 294 SELRNSL-MNAKSTSEVRTLLDE 315


>gi|294501960|ref|YP_003565660.1| dihydrouridine synthase (Dus) [Bacillus megaterium QM B1551]
 gi|294351897|gb|ADE72226.1| dihydrouridine synthase (Dus) [Bacillus megaterium QM B1551]
          Length = 332

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 114/322 (35%), Gaps = 34/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M   TD  +R          + +TE    ++      K+     L F+  E+P+   I G
Sbjct: 19  MEAVTDVVFRHVVTEAARPDVFFTEFTNTESYCHPKGKDSVKGRLTFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+  PD   + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAEMGFRGIDINMGCPVQNVAGNGKGSGLIRRPDTAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + +K I +  +  + IH R         K      +  +
Sbjct: 138 LPVSVKTRLGY---TQVDEWYDWLKHILEQDIVNLSIHLRT--------KKEMSDVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P   + +NG + D  + L++     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEIAPHTLLTINGDIPDRQKGLELAEKYGVDGIMIGRGIFHNPFAFEKEK 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +  ++              D + +          R                    GF  +
Sbjct: 247 KEHTSEELLELLRLQLDLHDKYSEELEPRPFKPLRRFFKI------------YVRGFRGA 294

Query: 291 RRCRHILTVEAGASTATHHIIE 312
              R++L            + E
Sbjct: 295 SELRNLLMSTETTDEVRALLDE 316


>gi|294886251|ref|XP_002771632.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
 gi|239875338|gb|EER03448.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
          Length = 720

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 96/237 (40%), Gaps = 18/237 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A +     K     F  +  + PLA Q  G D
Sbjct: 317 MVDQSELAFRMMTRKY-GAQFCYTPMMHAKSFATSKKYREKNFETAPGDSPLAAQFCGDD 375

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAK +ED   + I+LN+GCP      G +G+ L+  P++V   +  M K +  P
Sbjct: 376 GDVIVEAAKHIEDQ-VSCIDLNLGCPQGIARRGHYGSFLLEEPELVLRIVEKMVKGIKCP 434

Query: 119 VTVKCRIGVDDQI------PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           V+VK R+               A +  VK +   GV+ I +H R    KG   +      
Sbjct: 435 VSVKIRLMTAKDDDGSGRPDVAATKEFVKRLDSLGVDLIALHPRTKEWKGQLTQACW--- 491

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              +    E++   PD+   +NGG+       K       D VM      +   +  
Sbjct: 492 ---WQAAAEVRACVPDIPFIVNGGISCFEDVEKCFEVTKCDAVMSSECILEVPTLFR 545


>gi|67479621|ref|XP_655192.1| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
 gi|56472312|gb|EAL49806.1| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
          Length = 339

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 109/230 (47%), Gaps = 18/230 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           MVD +D  +R   R    N L YT M+++   +         +     +E+P+ +QI G+
Sbjct: 29  MVDGSDLTFRILVRRHGVN-LCYTPMVLSKMFVESKVYRNEVVNSLDPKEQPIIIQIVGS 87

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D +++   AK ++ +  + I++N+GCP     +G++GA L L+ D   + + A+ +A++I
Sbjct: 88  DANEMARTAKFLQSY-CDAIDINLGCPQKIAQKGNYGAYLALDFDHTKEIVNAVIEAVNI 146

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV  K R+  D++         V+ +++ G+ GI +H R    K           +  ++
Sbjct: 147 PVYCKVRVFEDEEKT----MRFVEMLQECGIWGIAVHGRTITEK------QSMNYHARWN 196

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAM 225
            + +IK E   + +  NG +    +  +   +   DG MIG     N  M
Sbjct: 197 YIAKIK-ERLKIPVIANGEMRSREKIEECKKVTHSDGYMIGFGLLMNPGM 245


>gi|328778500|ref|XP_393458.4| PREDICTED: tRNA-dihydrouridine synthase 3-like [Apis mellifera]
          Length = 642

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 57/282 (20%), Positives = 113/282 (40%), Gaps = 27/282 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  IL+G  +   ++     E    +Q+ G +   L 
Sbjct: 307 NLPFRRICKEY-GADITCGEMALAPRILKGAHEEWALVKRHESEDIFGIQLCGNNPGVLT 365

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ E    + I+LN+GCP   ++    G+ ++   +++   + ++ + ++IP+TVK
Sbjct: 366 RCAQLLNEQIDVDFIDLNLGCPIDLIYRQGGGSGMLNRLNVLETVVKSVNQVMNIPLTVK 425

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV    P      L+   +  GV+ I +H R         ++ R     D+D + + 
Sbjct: 426 TRTGVYIDKPIA--HTLMPKFRDWGVSMITVHGRS--------REQRYTKLADWDYIEKC 475

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            K    + +  NG +   +D  +      S+ GV IGR A     + T + E        
Sbjct: 476 AKTAHPIPVYGNGDILSFDDYQRVQDTYNSIYGVTIGRGALIKPWIFTEIKE-------- 527

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                  +      +I    + Y   H  S  +  + TR  +
Sbjct: 528 --KKLIDISSTERFEILKKYSKYGLEHWGSDTRGVETTRRFM 567


>gi|254360707|ref|ZP_04976855.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
 gi|153091277|gb|EDN73251.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica PHL213]
          Length = 306

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 67/331 (20%), Positives = 124/331 (37%), Gaps = 41/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       G +    P+ +
Sbjct: 1   MQGVLDPFVRNLLTSVNDYDLCISEFVRVVDQRLPKKTFYRLAPELYQGGLTDSGTPVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A +  + G + ++LN GCPS  V+  + GA L+ +P+++     AM 
Sbjct: 61  QLLGQHPQWLAENAALAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPELIYRATKAMR 120

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D          +  ++++ G N I +H R  +       D  +
Sbjct: 121 EAVPSDKIVSVKVRLGWD---SVSQCFEIADAVEQGGANEITVHGRTKV-------DGYR 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI ++   + +  NG + D   A     + +   +M+GR A     +   
Sbjct: 171 AERINWQAIGEI-QQRLSIPVIANGEIWDFESAKNCQKITACKALMMGRGALNTPNL--- 226

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K  V K  W ++   +  Y             + R    +  L  
Sbjct: 227 -----------SKVVKYNVPKMAWNEVLQLLFKYVQMENQFDTGFYHVARIKQWLRYLDK 275

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
            +P +     IL  E G      H IE A  
Sbjct: 276 EYPQAVELFDILKTEHGYDGLKAH-IEKAVE 305


>gi|323700791|ref|ZP_08112703.1| dihydrouridine synthase DuS [Desulfovibrio sp. ND132]
 gi|323460723|gb|EGB16588.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans ND132]
          Length = 339

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 64/329 (19%), Positives = 123/329 (37%), Gaps = 34/329 (10%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R  AR     A+  +EM+     A      + ++    ++ P+ LQ+ G++ 
Sbjct: 17  AGYSDLPFRLLARRF-GCAVACSEMVSVKGMAFKNSGTRRLIATCPEDDPMVLQLFGSEP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALSIP 118
                  + +   GY   +LN GCP  +V +   G  LM + D +    A M  KA   P
Sbjct: 76  QYFPPVMEKLVSLGYRNFDLNAGCPVRKVLKSGSGVQLMEDLDRLVGLAAIMVAKAAEHP 135

Query: 119 ----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
               V VK R+G +         +L + ++ +GVN + +H R                + 
Sbjct: 136 EGGRVGVKFRLGFNKGED--VYLDLARRLEDAGVNWVTLHPR--------YGRQMFGGSA 185

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + E+K+    + +  +G L      ++ +    +D +M  R A  + ++ +     
Sbjct: 186 DWSKLAELKRAV-SIPVIGSGDLFSAEDGVRCIEETGIDAIMFARGALYDPSIFSR---- 240

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
               L    P+  R D  F  +I          +       ++I   +     G    R 
Sbjct: 241 -YTALRRGEPMPVR-DGAFLAEIVREHIRLTRLYEGDTRSFRKIRSIVPRYAKGLKGIRS 298

Query: 293 CR-HILTVEAGASTATHHIIETAFNLMIE 320
            R  +L  E      T   +E A  ++ +
Sbjct: 299 LRASMLQCE------TWEDLEEAARVIRD 321


>gi|321261612|ref|XP_003195525.1| tRNA dihydrouridine synthase [Cryptococcus gattii WM276]
 gi|317461999|gb|ADV23738.1| tRNA dihydrouridine synthase, putative [Cryptococcus gattii WM276]
          Length = 725

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 114/288 (39%), Gaps = 25/288 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM +A  ++ G K+   ++     EK   LQ+ G   +++V
Sbjct: 370 NLPFRRLCVDY-GATITISEMALAQPLVYGAKEEWALVRRHESEKMFGLQVAGGFPNRMV 428

Query: 64  EAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
            AA+I+ +      G + +++N+GCP   V     G+ LM +P  +G  +  M +AL  I
Sbjct: 429 PAAEIIANTIGKGGGVDFVDVNMGCPIDLVFNQGAGSALMDSPGRLGKLLVGMNRALGEI 488

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P+TVK R GV    P      L+     + GV  + IH R    +   P D   I     
Sbjct: 489 PLTVKFRTGVAHGKPNA--HKLIPRFATEWGVRALTIHGRSRQQRYSKPADWDYIKTCVT 546

Query: 177 DIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
            +   +   N P + I  NG     +   + +    VDGVM+ R A     + T + E  
Sbjct: 547 TLRESVADANLPPVPIFGNGDCFSAASYYEEMEKSGVDGVMVARGALIKPWIFTEIKERR 606

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              ++    ++                ++   H  S  +    TR  +
Sbjct: 607 EWDISAVERLEG----------IRKFAEFGLSHWGSDTQGVNTTRRFL 644


>gi|149200474|ref|ZP_01877488.1| dihydrouridine synthase family protein [Lentisphaera araneosa
           HTCC2155]
 gi|149136436|gb|EDM24875.1| dihydrouridine synthase family protein [Lentisphaera araneosa
           HTCC2155]
          Length = 334

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 124/332 (37%), Gaps = 40/332 (12%)

Query: 1   MVDWTDRHYRFF---ARLLTNNALLYTEMIVADAILR--GDKKNILGF--STQEKP---- 49
           M D TD  +R          N  ++++E I  D +    G  K I  F  S +E+     
Sbjct: 18  MEDVTDTVFRQILLETAQPKNLQVVFSEFISTDGLCHPIGHDKVIHRFLISDEERKLLKE 77

Query: 50  ----LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
               +  Q+ G +  K  EA  K V+   ++ +++N+GCP A++ +    + L+  P+I 
Sbjct: 78  KNIKIVAQVWGKNPDKFSEAISKYVDPEVFDGVDINMGCPVAKIVKQGGCSALINTPEIA 137

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + + A   A  +PV+VK R G+     A      +  + +     I +H R    +   
Sbjct: 138 KELVLAAKAATKLPVSVKTRTGI----TAHKTEEWMTHLLEVEPAAIILHGRTQKQQSEG 193

Query: 165 PKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
                +I          ++ +  P +    NG +  + QA ++     +DG MIGR  + 
Sbjct: 194 LASWDEIAKG-----ARVRDRLKPHIPFWGNGDVRSIEQAHQLCQEHKLDGAMIGRGVFH 248

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           N  +        ++ L  +           WR  S   + +      S      + R   
Sbjct: 249 NPWIFN------TDLLGDNVLPPEEKIALLWRHASLYTSFW-----GSQKNFLTLRRFFK 297

Query: 282 GLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
               GFP +   R  + ++         ++E 
Sbjct: 298 IYAQGFPGANAFRSEI-MQTKKLDEVRALLEK 328


>gi|225715276|gb|ACO13484.1| tRNA-dihydrouridine synthase 4-like PP35 [Esox lucius]
          Length = 320

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 106/238 (44%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      + +T MIVA   LR  K     F+T   ++PL +Q   +D
Sbjct: 28  MVRYSKLAFRSLVRKYD-CDICFTPMIVAPDFLRSVKARDSEFTTNKADRPLIVQFAASD 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 87  AQTLADAACVVAPFS-DGVDLNCGCPQRWAMSEGYGACLINKPELVKDMVRHVRNQVDNP 145

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K RI  + +       ++ +  + +GV+ I +H R A  +            + 
Sbjct: 146 NYTTSIKIRIHKELRRTV----DMCQKAEAAGVSWITVHGRTAEERHQ---------PVH 192

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +D +  IK ++  + +  NG ++ +        L  VDGVM  R    N AM    +E
Sbjct: 193 FDAIKTIK-DSLSVPVIANGDIKSLQDVETTHQLTGVDGVMAARGLLANPAMFAGYNE 249


>gi|73964671|ref|XP_533136.2| PREDICTED: similar to PP3111 protein isoform 1 [Canis familiaris]
          Length = 507

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 109/315 (34%), Gaps = 67/315 (21%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--------- 107
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++            
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMSESAVCCGW 141

Query: 108 -----------------------IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
                                  +    + LS+PVT K R+  +            + ++
Sbjct: 142 GGQAGSWRRTNATLLRSPLSFPAVLLAHEKLSVPVTCKIRVFPEIDKTV----KYAQMLE 197

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K+G   + +H R    KG             ++ +  ++K    + +  NG ++ +    
Sbjct: 198 KAGCQLLTVHGRTKEQKG------PLSGTASWEHIKAVRKAV-AIPVFANGNIQCLRDVE 250

Query: 205 KIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD- 261
           + +    V GVM       N A+             G SP    + +++   +       
Sbjct: 251 RCIQDTGVQGVMSAEGNLHNPALF-----------EGRSPAVWELAEEYLDIVRQHPCPL 299

Query: 262 -YAARHLHSGGKLQQ 275
            Y   HL    KL  
Sbjct: 300 SYVRAHL---FKLWH 311


>gi|50420411|ref|XP_458741.1| DEHA2D06512p [Debaryomyces hansenii CBS767]
 gi|49654408|emb|CAG86885.1| DEHA2D06512p [Debaryomyces hansenii]
          Length = 423

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 72/296 (24%), Positives = 119/296 (40%), Gaps = 27/296 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQ-EKPLALQI 54
           MVD ++  +R  +R      L YT M  A         R +  + L    + ++PL +Q 
Sbjct: 26  MVDQSELAWRILSRRY-GADLCYTPMFHARLFATEEKYRNNMWSELDGDKEKDRPLIVQF 84

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK VED   + ++LN+GCP     +G++GA LM + D+V   I  +   
Sbjct: 85  CANDSDYLLKAAKFVED-KCDAVDLNLGCPQGIAKKGNYGAFLMDDWDLVYKLIKNLHDN 143

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L  PVT K R+  D +          K +  +G   I IH R   +KG +          
Sbjct: 144 LKCPVTAKIRVYDDWEKS----LEYAKLVLNAGAQFITIHGRTRDMKGQAT------GLA 193

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML---- 226
           +++I+  +K   P D     NG +    D+ +   ++   D VM       N  +     
Sbjct: 194 NWEILKYLKDNLPKDQVFFANGNILYPSDLERCTNVVR-CDAVMSAEGNLYNPGVFWTKS 252

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             +D+ F+            V          SM  +  + LH+   +    R +IG
Sbjct: 253 DDIDKQFARVDRMLREYFEIVKSCPGEASKHSMKAHFFKLLHAFLSVHTELRPVIG 308


>gi|307299179|ref|ZP_07578980.1| dihydrouridine synthase DuS [Thermotogales bacterium mesG1.Ag.4.2]
 gi|306914975|gb|EFN45361.1| dihydrouridine synthase DuS [Thermotogales bacterium mesG1.Ag.4.2]
          Length = 312

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 56/298 (18%), Positives = 119/298 (39%), Gaps = 26/298 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M  +TD   R  +        +++EMI  + +LR   +          P  +Q+ G+  S
Sbjct: 10  MAGYTDAVMRELSAEW-GADFVFSEMISVEGVLRASGRT--EEIVPVTPTRIQLFGSSAS 66

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ +AA  + +     I++N GCP  +V     G+ L+  P+ + + I A+  ++ +PV+
Sbjct: 67  RMAKAAMRLSEV-ATWIDINAGCPVKKVTRKGAGSALLRTPEKIAEMITALKNSIDVPVS 125

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G D    A     ++  I ++  + +++H R  +L+G S K        ++D + 
Sbjct: 126 VKIRLGND----ATDTEKIIYQIIEAKPDAVFVHGRT-VLQGYSGK-------ANWDEIE 173

Query: 181 EIKKENPD--LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            I K      +    +G + +       L +  +DGV++ R A  +  +     +     
Sbjct: 174 RITKLLHSEGILSFGSGDMFNPEAIAYALENYFIDGVLVARGAIGSPWIFKQAKDLIKFG 233

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                    R+   F R          +  +     ++ + +   G      ++   R
Sbjct: 234 SYEELAPHERLAL-FLRHFRR-----LSEAVGEDQAVRDLRKSFAGYTRNIRHAASLR 285


>gi|320583070|gb|EFW97286.1| tRNA-dihydrouridine synthase 1 [Pichia angusta DL-1]
          Length = 402

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 116/267 (43%), Gaps = 26/267 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-----LGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L Y+ M+ +      DK        +  S  ++PL +Q  
Sbjct: 25  MVDGSELAWRMISRKY-GADLCYSPMLHSRLFATDDKYREKMFGPMDGSEVDRPLIVQFC 83

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             D   L++AAK VED   + ++LN+GCP     +G +G+ LM + D++   I  + + L
Sbjct: 84  ANDPDYLLQAAKHVEDR-CDAVDLNLGCPQGIARKGHYGSFLMEDWDLISKLINTLHRNL 142

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT K R+  DD   ++A     K    +G   + +H R   +KG      +K    +
Sbjct: 143 KIPVTAKIRV-YDDWEKSLAY---AKMCLDAGAQFLTVHGRTREMKG------QKTGFAN 192

Query: 176 YDIVYEIKKEN-PDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + +V  IK    P+     NG +   ED+ + +K +   D VM       N  +  T  E
Sbjct: 193 WKLVKYIKDNLPPETVFLSNGNILYPEDIDRCIKEV-GCDAVMSAEGNLYNPGIFWTETE 251

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISAS 258
                     P   R  ++++  ++  
Sbjct: 252 DIEKQF----PRIDRFVREYFEVVAQC 274


>gi|15802690|ref|NP_288717.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 EDL933]
 gi|38604938|sp|Q8XEC6|DUSC_ECO57 RecName: Full=tRNA-dihydrouridine synthase C
 gi|12516448|gb|AAG57272.1|AE005445_9 putative regulator protein [Escherichia coli O157:H7 str. EDL933]
          Length = 316

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 64/311 (20%), Positives = 118/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQECMAISGCDSVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y      S   L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQSDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|313651246|gb|EFS15644.1| dihydrouridine synthase (Dus) family protein [Shigella flexneri 2a
           str. 2457T]
 gi|332755178|gb|EGJ85542.1| dihydrouridine synthase family protein [Shigella flexneri K-671]
          Length = 313

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 127/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 6   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 66  QLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 125

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 126 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 176 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 234 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 280

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 281 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 313


>gi|172059012|ref|YP_001815472.1| dihydrouridine synthase DuS [Exiguobacterium sibiricum 255-15]
 gi|171991533|gb|ACB62455.1| dihydrouridine synthase DuS [Exiguobacterium sibiricum 255-15]
          Length = 331

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 124/324 (38%), Gaps = 29/324 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++      K      L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVAKAARPDVFFTEFTNTESYCHPKGKQSVRGRLEFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  + + G+  I++N+GCP   V     G+ L+  PD+  + I A  KA  
Sbjct: 79  DKPEYFREMSIGMAEMGFKGIDINMGCPVQNVAVNGKGSGLINRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + ++ I +  +  + IH R        P     IP    
Sbjct: 138 LPVSVKTRLGY---SKVEEWHDWLRHILEQDIANLSIHLRTRKEMSAVPAHFELIPE--- 191

Query: 177 DIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
             + +++ E  P   + +NG + D    L+++    VDGVMIGR  + N      V++  
Sbjct: 192 --IKKLRDEVAPQTLLTINGDINDRQHGLELVEQYGVDGVMIGRGIFHNPFAF-EVEK-- 246

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
            +  +       R+  D   + S+       + L    K+            GF  +   
Sbjct: 247 KDHSSEELLDLLRLQLDLHDQYSSEFEPRLFKPLRRFFKI---------YVRGFRGASEL 297

Query: 294 RHILTVEAGASTATHHIIETAFNL 317
           R  L ++  ++     +++     
Sbjct: 298 RARL-MDTNSTDDVRALLDEFVEQ 320


>gi|167381962|ref|XP_001735922.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165901877|gb|EDR27854.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 340

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 121/283 (42%), Gaps = 18/283 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           MVD +D  +R   R    N L YT M+++   +         +     +E+P+ +Q+ G+
Sbjct: 30  MVDGSDLTFRILVRRHGVN-LCYTPMVLSKMFVESKVYRNEVVNSLDPKERPIIIQVVGS 88

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D +++   AK ++ +  + I++N+GCP     +G++GA L L+ D   + + A+ +A++I
Sbjct: 89  DANEMARTAKFLQSY-CDAIDINLGCPQKIAQKGNYGAYLALDFDHTKEIVNAVIEAVNI 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV  K R+  D+          V+ +++ G+ GI +H R    K           +  ++
Sbjct: 148 PVYCKVRVFEDEDKT----MKFVEMLQECGIWGIAVHGRTINEK------QSMNYHARWN 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +IK++   + +  NG +    +  +   +   DG MIG     N  M   + +    
Sbjct: 198 YIAKIKEQL-KIPVIANGEMRSREKIEECKKVTHSDGYMIGFGLLMNPGMCEGIIDNNEQ 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                  I          ++S          L+   + + + +
Sbjct: 257 IAEEYINIVFEYKDKNLVRLSDVKGHLIKMMLYKIKQKKDLLK 299


>gi|261493422|ref|ZP_05989947.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
 gi|261496889|ref|ZP_05993257.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261307413|gb|EEY08748.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. OVINE]
 gi|261310916|gb|EEY12094.1| tRNA-dihydrouridine synthase [Mannheimia haemolytica serotype A2
           str. BOVINE]
          Length = 317

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/331 (20%), Positives = 124/331 (37%), Gaps = 41/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   + +     +       G +    P+ +
Sbjct: 12  MQGVLDPFVRNLLTSVNDYDLCISEFVRVVDQRLPKKTFYRLAPELYQGGLTDSGTPVRV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A +  + G + ++LN GCPS  V+  + GA L+ +P+++     AM 
Sbjct: 72  QLLGQHPQWLAENAALAIELGSHGVDLNCGCPSKTVNGSNGGASLLKDPELIYRATKAMR 131

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D          +  ++++ G N I +H R  +       D  +
Sbjct: 132 EAVPSDKIVSVKVRLGWD---SVSQCFEIADAVEQGGANEITVHGRTKV-------DGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI ++   + +  NG + D   A     + +   +M+GR A     +   
Sbjct: 182 AERINWQAIGEI-QQRLSIPVIANGEIWDFESAKNCQKITACKALMMGRGALNTPNL--- 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K  V K  W ++   +  Y             + R    +  L  
Sbjct: 238 -----------SKVVKYNVPKMAWNEVLQLLFKYVQMENQFDTGFYHVARIKQWLRYLDK 286

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
            +P +     IL  E G      H IE A  
Sbjct: 287 EYPQAVELFDILKTEHGYDGLKAH-IEKAVE 316


>gi|315645321|ref|ZP_07898446.1| histidine phosphokinase/phophatase, putative [Paenibacillus vortex
           V453]
 gi|315279363|gb|EFU42669.1| histidine phosphokinase/phophatase, putative [Paenibacillus vortex
           V453]
          Length = 329

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 73/324 (22%), Positives = 130/324 (40%), Gaps = 38/324 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +  +     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSEAARPDVFFTEFANTESYCHPEGNHSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP A V E   G+ L+  PDI  + I A  KA  
Sbjct: 79  DKPEYFRQMSIGMAKEGFKGIDINMGCPVANVAENGKGSGLICRPDIAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R  +  I K  +  + IH R         ++     +  +
Sbjct: 138 LPVSVKTRLGF---SSVDEWRGWLTHILKQDIVNLSIHLRT--------REEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTV 229
           +++ EIKK      PD  + +NG + D    LK+     VDG+MIGR  ++N        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFQNPFAFEKEP 246

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            E+ S  L     +   +   +  ++  S +  A        +  +I         GF  
Sbjct: 247 KEHSSEELLDLLRLHLDLHDHYSAQLPRSFSPLA--------RFFKI------YVRGFRG 292

Query: 290 SRRCRHILTVEAGASTATHHIIET 313
           +   R+ L + A ++     +++ 
Sbjct: 293 ASELRNSL-MNAKSTREVRALLDE 315


>gi|110806117|ref|YP_689637.1| tRNA-dihydrouridine synthase C [Shigella flexneri 5 str. 8401]
 gi|110615665|gb|ABF04332.1| putative regulator protein [Shigella flexneri 5 str. 8401]
          Length = 315

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 70/338 (20%), Positives = 128/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +P    D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMPISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYND-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|333001275|gb|EGK20843.1| dihydrouridine synthase family protein [Shigella flexneri VA-6]
          Length = 327

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 305 EYDEATELFQH 315


>gi|323977672|gb|EGB72758.1| dihydrouridine synthase [Escherichia coli TW10509]
          Length = 316

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|308493062|ref|XP_003108721.1| hypothetical protein CRE_11115 [Caenorhabditis remanei]
 gi|308248461|gb|EFO92413.1| hypothetical protein CRE_11115 [Caenorhabditis remanei]
          Length = 548

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/298 (21%), Positives = 122/298 (40%), Gaps = 30/298 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +   EM +A +IL G   + ++L     EK   +Q+ G     + 
Sbjct: 211 NLPFRRICVDY-GADITCGEMALATSILSGAASEYSLLKRHPSEKIFGVQLAGGFADTMA 269

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTV 121
           +AA+IV E+F  + +++N+GCP   V++   G  L   P+ + + +AA    L   P+TV
Sbjct: 270 KAAQIVVENFDVDFVDINMGCPIDVVNQKGGGCALPSRPNKLYEVLAATKSVLGDCPMTV 329

Query: 122 KCRIGVDDQI-PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R G  + +  A      +K       + I  H R         K+ R     ++D  +
Sbjct: 330 KIRTGQKEGVLKAPETVEFMKKSPWHCPDLITFHPRS--------KEQRYTKLANWDYTH 381

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            + + +  + + + G +       + L +  V+G+MIGR A     + T +DE  +  ++
Sbjct: 382 AVAEASKPVPLWVCGDVLSWEDYYERLENHPVNGIMIGRGALIKPWIFTEIDERRTWDIS 441

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
            +              +     +Y   H  S     + TR  +  F  F    +CR+I
Sbjct: 442 ATERF----------DLLKKFINYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 485


>gi|30063584|ref|NP_837755.1| tRNA-dihydrouridine synthase C [Shigella flexneri 2a str. 2457T]
 gi|56480050|ref|NP_708040.2| tRNA-dihydrouridine synthase C [Shigella flexneri 2a str. 301]
 gi|38604724|sp|Q7UC91|DUSC_SHIFL RecName: Full=tRNA-dihydrouridine synthase C
 gi|30041837|gb|AAP17564.1| putative regulator protein [Shigella flexneri 2a str. 2457T]
 gi|56383601|gb|AAN43747.2| putative regulator protein [Shigella flexneri 2a str. 301]
 gi|281601597|gb|ADA74581.1| tRNA-dihydrouridine synthase C [Shigella flexneri 2002017]
 gi|332756520|gb|EGJ86871.1| dihydrouridine synthase family protein [Shigella flexneri 2747-71]
 gi|332765951|gb|EGJ96161.1| tRNA dihydrouridine synthase [Shigella flexneri 2930-71]
 gi|333016719|gb|EGK36048.1| dihydrouridine synthase family protein [Shigella flexneri K-304]
          Length = 315

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 127/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|328877006|gb|EGG25369.1| CCCH-type zinc finger-containing protein [Dictyostelium
           fasciculatum]
          Length = 699

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 54/284 (19%), Positives = 112/284 (39%), Gaps = 28/284 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +A  I+ G +  +        E    +Q+ G  +  ++
Sbjct: 364 NLPFRRLCKDL-GVDITCGEMALASNIVIGQQSELALFKRHASEDKFGVQVCGPHLDSMI 422

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+ + ++   + +++N GCP   V     GA +M  P+ +   +  M   L +P+T+K
Sbjct: 423 HTAEFINEYMDVDFVDINSGCPIDLVCNMGAGAAMMERPNRMETLVRGMSSVLDVPLTIK 482

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG  ++ P      L+ ++K+ G   + +H R         +  R     +++ + E 
Sbjct: 483 IRIGKSEESPNA--HKLIPNLKEWGAQAVTLHGRS--------RAQRYTRLANWEYIREC 532

Query: 183 KKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
              +P L +  NG + +     K+    +  +M+ R A     + T + E     ++ S 
Sbjct: 533 ADISP-LPLIANGDIYNWRDIEKVKESKISSLMVARGALIKPWIFTEIKERRDWDISASE 591

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           +     +Y   H  S  +    TRH +   L
Sbjct: 592 RL----------DLIKDFVNYGLTHWGSDQQGVDNTRHFLLNWL 625


>gi|157115267|ref|XP_001658172.1| tRNA-dihydrouridine synthase [Aedes aegypti]
 gi|108883495|gb|EAT47720.1| tRNA-dihydrouridine synthase [Aedes aegypti]
          Length = 578

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 109/291 (37%), Gaps = 30/291 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +    + +   EM  +  I+ G  +   +      E    +QI G +   + 
Sbjct: 241 NLPFRRICKEYGVD-ITCGEMACSVPIINGMMQEWALTKRHPSEDLFGVQICGHNQKLVS 299

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPV 119
            A +++ +    + ++LN+GCP   +     G+ L+   +I+   I +  + L       
Sbjct: 300 YATQVIAEHADVDFVDLNLGCPIDLIFNQGGGSALLRRRNILEVMIQSCSRILADYDKEF 359

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R+G+           LV   ++ G + + IH R         K+ R     D+D +
Sbjct: 360 TVKTRMGIY--ANKYVAHELVPKFEEWGASLVTIHGRT--------KEQRYTKKADWDYI 409

Query: 180 YEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +  ++   + I  NG +    D   A +  P + GVM+GR A     +   + E     
Sbjct: 410 RQCAQQAKSIPIYGNGDIFCYQDYLDAKERAPELAGVMVGRGALIKPWVFQEIKEQ---- 465

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                P  +       R +     +Y   H  S  K  + TR  +  +  F
Sbjct: 466 -KNLDPSSSERMDMLKRYV-----NYGLEHWGSDTKGVENTRRFLLEWQSF 510


>gi|190346080|gb|EDK38084.2| hypothetical protein PGUG_02182 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 347

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/287 (20%), Positives = 116/287 (40%), Gaps = 24/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D      F+T   ++ + +Q+G  +
Sbjct: 38  MVRYSKLPFRELVRHY-NTDIVYTPMILAREFVRNDVARASDFTTNPADRSVIVQVGCNN 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++  +++  +  + I LN GCP         GA LM  P++V   + A+ +     
Sbjct: 97  VEDLLKFVEMIHPY-VDGIGLNCGCPIKEQVREGIGAALMSEPELVSSMVKAVKQKYGDK 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I +   I        VK +++SGV+ I +H R         K+ R    ++ D 
Sbjct: 156 ICIETKIRIHPDIK--ETLKFVKMVEESGVDFITVHGRT--------KNTRSSVPVNLDA 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY---- 232
           +  +K E   + +  NG    +  A  +     VDGVM  R    N A+           
Sbjct: 206 IKAVK-EAVSVPVVANGDCFSLQDAYDIAEYTGVDGVMAVRGILANPALFAGYKSAPWSA 264

Query: 233 --FSNPLTGSSPIKTRVDKDFWRKISASMTDYAA-RHLHSGGKLQQI 276
                 L  S  +  R+ +    ++          + ++    L  +
Sbjct: 265 VERFWDLATSYGLPFRIIQHHLSQMLEKKIPKKVLKEMNETTSLVDM 311


>gi|330891419|gb|EGH24080.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
          Length = 172

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/177 (38%), Positives = 105/177 (59%), Gaps = 9/177 (5%)

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            + ++G     +HAR AIL+GLSPK+NR IP L YD+V ++K + PDL I LNGG++ + 
Sbjct: 2   KVHEAGCESFTVHARIAILEGLSPKENRDIPPLRYDVVAQLKSDFPDLEIVLNGGIKTLD 61

Query: 202 QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           Q  + L + DGVM+GR AY N  +L  VD+   +    ++P+ +R D         SM  
Sbjct: 62  QCGEHLQTFDGVMLGREAYHNPYLLAHVDQQLFDS---TAPVISRYDA------LESMRP 112

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+   +     +++ A   +
Sbjct: 113 YIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVDIHKAENPMLLLDQAAAFL 169


>gi|294937192|ref|XP_002782004.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
 gi|239893217|gb|EER13799.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
          Length = 438

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 96/237 (40%), Gaps = 18/237 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A +     K     F  +  + PLA Q  G D
Sbjct: 35  MVDQSELAFRMMTRKY-GAQFCYTPMMHAKSFATSKKYREKNFETAPGDSPLAAQFCGDD 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +VEAAK +ED   + I+LN+GCP      G +G+ L+  P++V   +  M K +  P
Sbjct: 94  GDVIVEAAKHIEDQ-VSCIDLNLGCPQGIARRGHYGSFLLEEPELVLGIVEKMVKGIKCP 152

Query: 119 VTVKCRIGVDDQI------PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           V+VK R+               A +  VK +   GV+ I +H R    KG   +      
Sbjct: 153 VSVKIRLMTAKDDDGSGRPDVAATKEFVKRLDALGVDLIALHPRTKEWKGQLTQACW--- 209

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              +    E++   PD+   +NGG+       K       D VM      +   +  
Sbjct: 210 ---WQAAAEVRACVPDIPFIVNGGISCFEDVEKCFKVTKCDAVMSSECILEVPTLFR 263


>gi|302039230|ref|YP_003799552.1| putative tRNA-dihydrouridine synthase [Candidatus Nitrospira
           defluvii]
 gi|300607294|emb|CBK43627.1| putative tRNA-dihydrouridine synthase [Candidatus Nitrospira
           defluvii]
          Length = 394

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/344 (18%), Positives = 123/344 (35%), Gaps = 62/344 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   TD  +R          + +TE    + I RG       L +S  E+P+  Q+ G D
Sbjct: 17  MDGVTDAAFRRVVASQGQPDITFTEFTNVNEICRGPDHLLESLIYSEAERPIVAQLYGKD 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
             +   AA++V + G++ +++N+GCPS  V     GA L+  PD+    + A  + L   
Sbjct: 77  PDQFYRAAQVVCELGFDGLDINMGCPSKSVAASGSGAALIKTPDLAHAIVRAARQGLEDW 136

Query: 117 ------------------------------------IPVTVKCRIGVDDQIPAVALRNLV 140
                                               +P+++K R+G D     V +   V
Sbjct: 137 AAGQSIHSQGFKPSRIEFIHTLNHSRSGVPVVPRRLLPLSIKTRLGFD----CVVVERWV 192

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGLE 198
           + + ++    I +H R                  D+  + E           +  NG L 
Sbjct: 193 EHLLEARPAAITLHGRTL--------QQMYRGAADWSAIAEAATVARGTGTLMLGNGDLN 244

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE----YFSNPLTGSSPIKTRVDKDFW 252
            +  A++ +   +V GV++GR    +       ++    +       + P      +   
Sbjct: 245 TLVDAMRRVAESNVQGVLVGRGTLGSPWFFREKEQARRAFSERRDLAALPATAWEPQVSV 304

Query: 253 RKISASMTDYAARH--LHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                 M D+A ++  +    + + I +H+     GFP++   R
Sbjct: 305 SHRMQVMLDHARQYEAIAGLERFRSIRKHLGWYCKGFPHAAAMR 348


>gi|312377328|gb|EFR24184.1| hypothetical protein AND_11402 [Anopheles darlingi]
          Length = 633

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 111/291 (38%), Gaps = 30/291 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM  A  I+ G  +   +      E    +Q+ G     + 
Sbjct: 281 NLPFRRICKEY-GVDITCGEMACAIPIINGAIQEWALTKRHASEDLFGVQLCGHKPKLVT 339

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPV 119
            AA+I+ +    + I+LN+GCP   +     G+ L+   +++   + +  + L       
Sbjct: 340 YAAQIIAEKADVDFIDLNIGCPIDLIFNQGGGSALLRRQNVLQVMVQSCSRLLADYGKEF 399

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+ +  P      LV   ++ G + I IH R         K+ R   + D++ V
Sbjct: 400 TVKTRIGIYNNKPIA--HELVPRFEEWGASLITIHGRT--------KEQRYTKHADWEFV 449

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                +   + +  NG +    D   A +  P+V GVM+GR A     +   + E     
Sbjct: 450 QRCAAQASSVPVYGNGDIYCYSDYESARERCPNVGGVMVGRGALIKPWVFQEIKER---- 505

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                P  +   +   R +     +Y   H  S  K  + TR  +  +  F
Sbjct: 506 -KNLDPSSSERFEMLKRYV-----NYGLEHWGSDTKGVENTRRFLLEWQSF 550


>gi|323968058|gb|EGB63468.1| dihydrouridine synthase [Escherichia coli M863]
 gi|327253266|gb|EGE64920.1| dihydrouridine synthase family protein [Escherichia coli STEC_7v]
          Length = 315

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|317486330|ref|ZP_07945160.1| dihydrouridine synthase [Bilophila wadsworthia 3_1_6]
 gi|316922400|gb|EFV43656.1| dihydrouridine synthase [Bilophila wadsworthia 3_1_6]
          Length = 335

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 56/301 (18%), Positives = 108/301 (35%), Gaps = 24/301 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             W+D  +R   R     A+  TEMI A  ++        +     ++ P+ +Q+ G++ 
Sbjct: 24  AGWSDLPFRLLCRRF-GAAVCCTEMISAKGLIYKSPGTAELFATCPEDGPVVVQLFGSEA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI-P 118
             +  AA  + D G+   + N+GC   +V     GA +  + D       A+ +A     
Sbjct: 83  PFMEAAAGQLRDKGFVWFDCNMGCSVPKVARTGSGAAMCKDIDNALAVAEALIRAAGRGR 142

Query: 119 VTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           V  K R+G D+      A   R L  +++  G   + +H R A                 
Sbjct: 143 VGFKLRLGWDEPGRSPAAETWRVLAPALEALGAGWLTLHPRTAKQG--------FTGTAR 194

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ + E+K     L +  +G L      ++ L    VD VM  R A ++ A+     +  
Sbjct: 195 WEYLSELK-ALVSLPVIASGDLFTAEDGVRCLAETGVDTVMYARGALRDPAIFKAHLDLL 253

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +      + + T + +             A         L ++   +         S++ 
Sbjct: 254 AGREPEVADVATLLAR------IREHARLARELSTEKVALLKMRTIVPRYVRHIEGSKQL 307

Query: 294 R 294
           R
Sbjct: 308 R 308


>gi|300918780|ref|ZP_07135349.1| dihydrouridine synthase [Escherichia coli MS 115-1]
 gi|300414023|gb|EFJ97333.1| dihydrouridine synthase [Escherichia coli MS 115-1]
          Length = 337

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 305 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 337


>gi|327393212|dbj|BAK10634.1| tRNA-dihydrouridine synthase C DusC [Pantoea ananatis AJ13355]
          Length = 328

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + L
Sbjct: 8   MEGVLDSLVRQLLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHASRTPSGTLVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 68  QLLGQHPDWLAENAARAVTLGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRAAKAMR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  S+PVTVK R+G D    +     +  +++++G + + +H R          D  +
Sbjct: 128 AAVPASLPVTVKVRLGWD---SSARSMEIADAVQQAGASELVVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A   L     D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGDIRQRL-RIPVIANGEIWDWQTAQDCLRTTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y   P+              W ++ A +  Y          +  + R
Sbjct: 236 VIKYNDAPMP-------------WPEVVALLQKYTRLEKQGDTGMYHVAR 272


>gi|295689377|ref|YP_003593070.1| NifR3 family TIM-barrel protein [Caulobacter segnis ATCC 21756]
 gi|295431280|gb|ADG10452.1| TIM-barrel protein, nifR3 family [Caulobacter segnis ATCC 21756]
          Length = 335

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 116/293 (39%), Gaps = 23/293 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   +D  +R  A  L     + TEM+ +    +G    +   +     PL  +Q+ G D
Sbjct: 21  MTGVSDLPFRETATAL-GAPYVATEMVASAEFAKGRPDVVRRAAVGDGLPLTVIQLVGRD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-GACLMLNPDIVGDCIAAMCKALSI 117
           I  + + A++  + G   I+LN GCP+  V  G+  G+ LM  PD+    +AA  +A+ +
Sbjct: 80  IDCMAQGARMAAEAGAEIIDLNFGCPAKEVAAGAACGSALMREPDLAEALVAAAVRAVDV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD         +    +  G   I +H R         ++       D+ 
Sbjct: 140 PVTVKMRLGWDDGSRNA--PEIAARAEAVGAKAITVHGRT--------RNQFYKGVADWS 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V ++KK    + + +NG + D   A   L     DGVMIGR  Y    +   ++     
Sbjct: 190 AVAQVKKAV-SVPVLVNGDIVDGESARAALEQSGADGVMIGRGVYGRPWIAGAIEAALDG 248

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
               + P               S++ Y  R       L+   +H+       P
Sbjct: 249 R-GFAEPEAEERLAIALTHFRRSLSFYGERQ-----GLKMFRKHLASYIEAAP 295


>gi|26248520|ref|NP_754560.1| tRNA-dihydrouridine synthase C [Escherichia coli CFT073]
 gi|91211426|ref|YP_541412.1| tRNA-dihydrouridine synthase C [Escherichia coli UTI89]
 gi|191169962|ref|ZP_03031516.1| tRNA-dihydrouridine synthase C [Escherichia coli F11]
 gi|218690289|ref|YP_002398501.1| tRNA-dihydrouridine synthase C [Escherichia coli ED1a]
 gi|227887195|ref|ZP_04005000.1| tRNA-dihydrouridine synthase C [Escherichia coli 83972]
 gi|300981485|ref|ZP_07175566.1| dihydrouridine synthase [Escherichia coli MS 200-1]
 gi|300982854|ref|ZP_07176318.1| dihydrouridine synthase [Escherichia coli MS 45-1]
 gi|306814745|ref|ZP_07448907.1| tRNA-dihydrouridine synthase C [Escherichia coli NC101]
 gi|26108925|gb|AAN81128.1|AE016763_87 Hypothetical protein yohI [Escherichia coli CFT073]
 gi|91073000|gb|ABE07881.1| hypothetical protein YohI [Escherichia coli UTI89]
 gi|190909478|gb|EDV69063.1| tRNA-dihydrouridine synthase C [Escherichia coli F11]
 gi|218427853|emb|CAR08768.2| tRNA-dihydrouridine synthase C [Escherichia coli ED1a]
 gi|227835545|gb|EEJ46011.1| tRNA-dihydrouridine synthase C [Escherichia coli 83972]
 gi|300307558|gb|EFJ62078.1| dihydrouridine synthase [Escherichia coli MS 200-1]
 gi|300408654|gb|EFJ92192.1| dihydrouridine synthase [Escherichia coli MS 45-1]
 gi|305852139|gb|EFM52591.1| tRNA-dihydrouridine synthase C [Escherichia coli NC101]
 gi|307626319|gb|ADN70623.1| tRNA-dihydrouridine synthase C [Escherichia coli UM146]
 gi|312946758|gb|ADR27585.1| tRNA-dihydrouridine synthase C [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315285789|gb|EFU45229.1| dihydrouridine synthase [Escherichia coli MS 110-3]
 gi|315294495|gb|EFU53843.1| dihydrouridine synthase [Escherichia coli MS 153-1]
 gi|324013979|gb|EGB83198.1| dihydrouridine synthase [Escherichia coli MS 60-1]
          Length = 338

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 305 EYDEATELFQH 315


>gi|322833772|ref|YP_004213799.1| dihydrouridine synthase DuS [Rahnella sp. Y9602]
 gi|321168973|gb|ADW74672.1| dihydrouridine synthase DuS [Rahnella sp. Y9602]
          Length = 310

 Score =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +     + +
Sbjct: 8   MEGVLDPLVRELLTEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHHASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D    +     +  +++++G   + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKVRLGWDSLEHSF---EIADAVQQAGATELTVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D       L     D VM+GR A  N   L+ 
Sbjct: 178 PERINWAAIGEIRQRL-SIPVIANGEIWDYESGQACLHTTGCDAVMLGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVITLLQKYTRLEKQGDTGLYHVAR 272


>gi|123443101|ref|YP_001007075.1| tRNA-dihydrouridine synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090062|emb|CAL12925.1| conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 312

 Score =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         ++    + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPTKSFYRLCPELHQQSRTSSGTQVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPAHQPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|291616786|ref|YP_003519528.1| DusC [Pantoea ananatis LMG 20103]
 gi|291151816|gb|ADD76400.1| DusC [Pantoea ananatis LMG 20103]
          Length = 328

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + L
Sbjct: 8   MEGVLDSLVRQLLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHASRTPSGTLVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 68  QLLGQHPDWLAENAARAVTLGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRAAKAMR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  S+PVTVK R+G D    +     +  +++++G + + +H R          D  +
Sbjct: 128 AAVPASLPVTVKVRLGWD---SSARSMEIADAVQQAGASELVVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A   L     D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGDIRQRL-RIPVIANGEIWDWQTAQDCLRTTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y   P+              W ++ A +  Y          +  + R
Sbjct: 236 VIKYNDAPMP-------------WPEVVALLQKYTRLEKQGDTGMYHVAR 272


>gi|15832280|ref|NP_311053.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           Sakai]
 gi|168750514|ref|ZP_02775536.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|168757716|ref|ZP_02782723.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|195935510|ref|ZP_03080892.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208809098|ref|ZP_03251435.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813928|ref|ZP_03255257.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208818944|ref|ZP_03259264.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209400918|ref|YP_002271543.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|217326717|ref|ZP_03442800.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254794033|ref|YP_003078870.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261223407|ref|ZP_05937688.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261259043|ref|ZP_05951576.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291283388|ref|YP_003500206.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str.
           CB9615]
 gi|13362495|dbj|BAB36449.1| putative regulator protein [Escherichia coli O157:H7 str. Sakai]
 gi|188015333|gb|EDU53455.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|189355352|gb|EDU73771.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|208728899|gb|EDZ78500.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735205|gb|EDZ83892.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208739067|gb|EDZ86749.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209162318|gb|ACI39751.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|209766348|gb|ACI81486.1| putative regulator protein [Escherichia coli]
 gi|209766350|gb|ACI81487.1| putative regulator protein [Escherichia coli]
 gi|209766352|gb|ACI81488.1| putative regulator protein [Escherichia coli]
 gi|209766356|gb|ACI81490.1| putative regulator protein [Escherichia coli]
 gi|217319084|gb|EEC27509.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254593433|gb|ACT72794.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|290763261|gb|ADD57222.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str.
           CB9615]
 gi|320192243|gb|EFW66888.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|320641205|gb|EFX10683.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           G5101]
 gi|320646593|gb|EFX15504.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320651848|gb|EFX20223.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H- str. H
           2687]
 gi|320657572|gb|EFX25370.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320663178|gb|EFX30487.1| tRNA-dihydrouridine synthase C [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320667929|gb|EFX34832.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|326339484|gb|EGD63295.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str. 1125]
 gi|326343945|gb|EGD67706.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str. 1044]
          Length = 316

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQECMAISGCDSVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|324114444|gb|EGC08413.1| dihydrouridine synthase [Escherichia fergusonii B253]
          Length = 312

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +     + I         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFQRICPELQNSSRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENALRAVELGSFGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEQKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A +   L   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQQCMALSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWAQVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|189404356|ref|ZP_02788797.2| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189405202|ref|ZP_02813951.2| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC869]
 gi|189406070|ref|ZP_02826184.2| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC508]
 gi|189366104|gb|EDU84520.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189371342|gb|EDU89758.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC869]
 gi|189376618|gb|EDU95034.1| tRNA-dihydrouridine synthase C [Escherichia coli O157:H7 str.
           EC508]
          Length = 335

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 27  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 147 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQECMAISGCDSVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 255 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 301

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 302 EYDEATELFQH 312


>gi|51246252|ref|YP_066136.1| hypothetical protein DP2400 [Desulfotalea psychrophila LSv54]
 gi|50877289|emb|CAG37129.1| conserved hypothetical protein [Desulfotalea psychrophila LSv54]
          Length = 354

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 120/285 (42%), Gaps = 19/285 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           MV  +    R     L    L YTEM+ A  +   +    + L  +  E+PL  Q+  AD
Sbjct: 49  MVGLSHSALRSLIADLGGCGLFYTEMLAARRLPHENPAVSSYLHTTPCERPLIYQLFIAD 108

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  +  A   +   G + +++N+GCP+  V  G  GA L  + D V D +++  +   + 
Sbjct: 109 VKYVAPALDKIHRLGGDGVDINLGCPAPSVRRGGAGAALAEDWDRVRDIVSSARRHTDLT 168

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R+G   +     L +  K ++  GV+ + +HAR    K       + +  +    
Sbjct: 169 LSAKIRVGHVGKEAH--LLDFCKMLEAEGVDLLAVHARYHGEKFCRKPRWQLLAPI---- 222

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                 E  D+ I  NGG+  +  A + L      G+M+GR A +   +   +       
Sbjct: 223 -----CEQLDIPIFANGGIFSVDDARRCLELSGAAGLMLGRGAVERPWLFNEIAREVYGL 277

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
               +  ++R  + ++R +   +  +A       G++++ T ++ 
Sbjct: 278 DLPVA--ESRPVEIYFRFVQKMVEIFAPER--QLGRIKEFTHYIA 318


>gi|146417549|ref|XP_001484743.1| hypothetical protein PGUG_02472 [Meyerozyma guilliermondii ATCC
           6260]
 gi|146390216|gb|EDK38374.1| hypothetical protein PGUG_02472 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 416

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 72/296 (24%), Positives = 121/296 (40%), Gaps = 27/296 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE------KPLALQI 54
           MVD ++  +R  +R      L YT M  A      +K     +S Q+      +PL +Q 
Sbjct: 25  MVDQSELAWRIISRRY-GAELCYTPMFHARLFATEEKYRQNMWSEQDGDRELDRPLIVQF 83

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D + L+EAAK+VED   + ++LN+GCP     +G +GA LM + D+V   I  +   
Sbjct: 84  CANDPNYLLEAAKLVED-KCDAVDLNLGCPQGIAKKGKYGAFLMDDWDLVHKLIRTLHDN 142

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L  PVT K R+  DD   ++A     K +  +G   I +H R   +KG +          
Sbjct: 143 LKCPVTAKIRV-YDDWEKSLAY---AKMVLDAGAQFITVHGRTRDMKGQAT------GLA 192

Query: 175 DYDIVYEIKKENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML---- 226
           ++ ++  ++   P D     NG +    D+ +  +     D VM       N  +     
Sbjct: 193 NWKVLKYLRDNLPKDQVFFANGNILYPSDLQRCREE-TGADAVMSAEGNLYNPGVFWTKT 251

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             +D+ F             V          +M  +  + LH+   + +  R +IG
Sbjct: 252 DNIDKQFPRVDKLLREYFEIVKSCAGEASKHAMKAHFFKILHAFLNVHKELRPVIG 307


>gi|293415423|ref|ZP_06658066.1| tRNA-dihydrouridine synthase C [Escherichia coli B185]
 gi|291433071|gb|EFF06050.1| tRNA-dihydrouridine synthase C [Escherichia coli B185]
          Length = 316

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 118/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI+++  ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQQL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|300930369|ref|ZP_07145778.1| dihydrouridine synthase [Escherichia coli MS 187-1]
 gi|300461691|gb|EFK25184.1| dihydrouridine synthase [Escherichia coli MS 187-1]
          Length = 337

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 305 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 337


>gi|188527429|ref|YP_001910116.1| transcriptional regulator [Helicobacter pylori Shi470]
 gi|188143669|gb|ACD48086.1| transcriptional regulator [Helicobacter pylori Shi470]
          Length = 328

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 128/322 (39%), Gaps = 32/322 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             +TD  +R   +    + +  +EM+ + +++    K   +L  S  E     QI G+  
Sbjct: 15  AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKTSKMLEKSHLEDHFMAQISGSKE 73

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + EA + +      + I+ N GCP+ +V     G+ L+ + + +   +  + +  +  
Sbjct: 74  GVVKEAVEKINALEHVSGIDFNCGCPAPKVANHGNGSGLLKDLNHLVKLLKIIRENTNKK 133

Query: 119 VT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           +T VK R+G D +IP    + +  ++  + V+ + +H R    K    K       +DY 
Sbjct: 134 ITSVKVRLGFDQKIP----KEIAHALNDAPVDYVVVHGRTRSDKYQKDK-------IDYK 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K       +  NG ++ + +A ++L     +G+MIGRAA +   +   +      
Sbjct: 183 SIALMKGILKK-PVIANGEIDSVKKAFEVLQITQAEGLMIGRAALRAPWIFWQIR----- 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               ++ +   V KD   +    M ++          +    +++     G   +   R+
Sbjct: 237 --NNTTELPAVVKKDLVLEHFDKMVEFYG-----DRGVIMFRKNLHAYAKGEMQASAFRN 289

Query: 296 ILTVEAGASTATHHIIETAFNL 317
            +       +     IE  FN 
Sbjct: 290 CVNTLTEIKSM-RESIEEFFNQ 310


>gi|306818269|ref|ZP_07451998.1| dihydrouridine synthase [Mobiluncus mulieris ATCC 35239]
 gi|304648914|gb|EFM46210.1| dihydrouridine synthase [Mobiluncus mulieris ATCC 35239]
          Length = 471

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 19  NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YN 75
             +   EM+ A A+  G +++  ++     +   ++Q+ G     L  AA  +   G  +
Sbjct: 117 EGMFVGEMVTAKALRMGSERSWVMVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGLAD 176

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVKCR 124
            I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK R
Sbjct: 177 HIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVKIR 236

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G+D +       ++ +  + +GV  + +HAR                +  ++ +  +  
Sbjct: 237 SGIDAEHR--IFLDVARVAEDNGVAAVTLHARTT--------SEYYGGHSHWEDIAALV- 285

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           E  D+ +  NG +   + AL++       GV IGRA      +   +            P
Sbjct: 286 EVLDIPVLGNGDVFCAADALEMFRETGCAGVEIGRAVQGRPWIFREITAALWGLPVPVGP 345

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT---V 299
               V     R     +  Y     +    L+ + +H+   F GF      R  L     
Sbjct: 346 SLGEVANVARRHAEGLVAHYG----NELVALRDMRKHLGWYFRGFGLGGEMRGRLARVES 401

Query: 300 EAGASTATHHIIET 313
            AG   ATH +IE 
Sbjct: 402 LAGLEQATHELIER 415


>gi|218549553|ref|YP_002383344.1| tRNA-dihydrouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|218357094|emb|CAQ89727.1| tRNA-dihydrouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|325497953|gb|EGC95812.1| tRNA-dihydrouridine synthase C [Escherichia fergusonii ECD227]
          Length = 316

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +     + I         +     + +
Sbjct: 12  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFQRICPELQNSSRTPSGTLVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQYPQWLAENALRAVELGSFGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 132 EAVPAHLPVSVKVRLGWDSGEQKF---EIADAVQQAGATELVVHGRTKE-------QGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A +   L   D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQQCMALSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWAQVVALLQKYTRLEKQGDTGLYHVAR 276


>gi|331653569|ref|ZP_08354570.1| tRNA-dihydrouridine synthase C [Escherichia coli M718]
 gi|331048418|gb|EGI20494.1| tRNA-dihydrouridine synthase C [Escherichia coli M718]
          Length = 294

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|317491241|ref|ZP_07949677.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
 gi|316920788|gb|EFV42111.1| dihydrouridine synthase [Enterobacteriaceae bacterium 9_2_54FAA]
          Length = 314

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D++L       L         +     + +
Sbjct: 12  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDSLLPEKVYYRLCPELAHQSRTPSGTAVRV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKMVNGSGGGATLLKDPEMIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   I +H R          D  K
Sbjct: 132 EAVPAHLPVTVKVRLGWDSGDRQF---EIADAVEQAGATEITVHGRTKE-------DGYK 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++   ++ +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEKINWAAIGKIRQRL-NIPVIANGEIWDWQSAQDCMATTGCDSVMIGRGAL-NVPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                K  W ++   +  Y          L  + R
Sbjct: 240 VIKYHE-------------PKMLWPEVMLLLKKYVRLEKQGDTGLYHVAR 276


>gi|300935056|ref|ZP_07150087.1| dihydrouridine synthase [Escherichia coli MS 21-1]
 gi|331663636|ref|ZP_08364546.1| tRNA-dihydrouridine synthase C [Escherichia coli TA143]
 gi|300459637|gb|EFK23130.1| dihydrouridine synthase [Escherichia coli MS 21-1]
 gi|320199735|gb|EFW74324.1| tRNA-dihydrouridine synthase C [Escherichia coli EC4100B]
 gi|331059435|gb|EGI31412.1| tRNA-dihydrouridine synthase C [Escherichia coli TA143]
 gi|333002858|gb|EGK22414.1| dihydrouridine synthase family protein [Shigella flexneri K-272]
 gi|333016862|gb|EGK36186.1| dihydrouridine synthase family protein [Shigella flexneri K-227]
          Length = 315

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|206577930|ref|YP_002237438.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae 342]
 gi|288934362|ref|YP_003438421.1| dihydrouridine synthase [Klebsiella variicola At-22]
 gi|206566988|gb|ACI08764.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae 342]
 gi|288889091|gb|ADC57409.1| dihydrouridine synthase DuS [Klebsiella variicola At-22]
          Length = 310

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHQSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPDHLPVTVKVRLGWDSGERRF---EIADAVQQAGASELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVVANGEIWDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPQVVQLLQKYTRLEKQGDTGLYHVAR 272


>gi|323184237|gb|EFZ69614.1| dihydrouridine synthase family protein [Escherichia coli 1357]
          Length = 313

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 6   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 66  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 125

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 126 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 176 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 234 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 270


>gi|253575078|ref|ZP_04852417.1| dihydrouridine synthase DuS [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251845534|gb|EES73543.1| dihydrouridine synthase DuS [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 324

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/331 (19%), Positives = 122/331 (36%), Gaps = 36/331 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D T   +R          + +TE    ++    +  +     L F+  E+P+   I G
Sbjct: 19  MEDVTHVVFRHVVSQAGRPDVFFTEFANTESYCHPEGNHSVRGRLLFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP   V     G+ L+L P +  + I A  KA  
Sbjct: 79  DKPEYFAKMSIGMAKQGFQGIDINMGCPVPNVATNGMGSGLILRPTVAAEVIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G ++       R+ +  I K  +  + IH R         ++        +
Sbjct: 138 LPVSVKTRLGFNE---VEEWRDWLTHILKQDIVNLSIHLRT--------REEMSQVAAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTV 229
           +++ EIK    +  P   + +NG + D    LK+     VDG+MIGR  +KN        
Sbjct: 187 ELIPEIKALRDQVAPQTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFKNPFAFEKEP 246

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            E+ +        +   +   +  ++ A    + A                     GF  
Sbjct: 247 REHSTTEYLDLLRLHLDLHDQYSEQLEA--RPFKALQRFFKV-----------YVKGFRG 293

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLMIE 320
           +   R+ L            + E A   + +
Sbjct: 294 ASELRNQLMSTTSTDEVRKMLDEFAEQTVSD 324


>gi|331673664|ref|ZP_08374427.1| tRNA-dihydrouridine synthase C [Escherichia coli TA280]
 gi|331068937|gb|EGI40329.1| tRNA-dihydrouridine synthase C [Escherichia coli TA280]
          Length = 315

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 125/338 (36%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPIKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + L     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCLAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|320196009|gb|EFW70633.1| tRNA-dihydrouridine synthase C [Escherichia coli WV_060327]
          Length = 315

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMTISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + +   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRMLNNSPD-----IARAIQAIDIEKL 315


>gi|300821757|ref|ZP_07101902.1| dihydrouridine synthase [Escherichia coli MS 119-7]
 gi|300924857|ref|ZP_07140792.1| dihydrouridine synthase [Escherichia coli MS 182-1]
 gi|301328613|ref|ZP_07221674.1| dihydrouridine synthase [Escherichia coli MS 78-1]
 gi|309793018|ref|ZP_07687446.1| dihydrouridine synthase [Escherichia coli MS 145-7]
 gi|331668839|ref|ZP_08369687.1| tRNA-dihydrouridine synthase C [Escherichia coli TA271]
 gi|331678088|ref|ZP_08378763.1| tRNA-dihydrouridine synthase C [Escherichia coli H591]
 gi|300418974|gb|EFK02285.1| dihydrouridine synthase [Escherichia coli MS 182-1]
 gi|300525599|gb|EFK46668.1| dihydrouridine synthase [Escherichia coli MS 119-7]
 gi|300845005|gb|EFK72765.1| dihydrouridine synthase [Escherichia coli MS 78-1]
 gi|308123304|gb|EFO60566.1| dihydrouridine synthase [Escherichia coli MS 145-7]
 gi|331064033|gb|EGI35944.1| tRNA-dihydrouridine synthase C [Escherichia coli TA271]
 gi|331074548|gb|EGI45868.1| tRNA-dihydrouridine synthase C [Escherichia coli H591]
          Length = 315

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|154249065|ref|YP_001409890.1| dihydrouridine synthase DuS [Fervidobacterium nodosum Rt17-B1]
 gi|154153001|gb|ABS60233.1| dihydrouridine synthase DuS [Fervidobacterium nodosum Rt17-B1]
          Length = 322

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 115/300 (38%), Gaps = 44/300 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           M   TD  +R    L       +TEMI A +++   K N + F    ++  + +Q+ G+D
Sbjct: 16  MAGVTDYPFRKLC-LQHGAYFAFTEMISAKSVIINVKINEIYFPRQDEKDRVGVQLFGSD 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            ++L EAA IV++ G   ++LN GCP ++V +   G+ L+ +       + AM   L   
Sbjct: 75  YAELSEAAAIVQEKGL-WVDLNAGCPVSKVIKKGAGSALLKDLGEFRKVVRAMRSVL-KR 132

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TVK RIG +          +   + +  V+ +++H R A                    
Sbjct: 133 FTVKTRIGWEKD----EFEKIYNILLEENVDAVFVHGRTAKQMYSGKATW---------- 178

Query: 179 VYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
               K  NP  + + ++G +   ED+  A++      GV++ R +  N  + + + E   
Sbjct: 179 ----KIYNPGFVPLYISGDIYTKEDIKNAMEQ-SGATGVIVARGSIGNPWIFSEIGE--- 230

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                  P   +      + +     +Y               + + G       +R  R
Sbjct: 231 -------PNCEQRLCTILKHLEYLYDEY------KDYGAVVFRKFVAGYTKNMLGARDFR 277


>gi|328956746|ref|YP_004374132.1| tRNA-dihydrouridine synthase [Carnobacterium sp. 17-4]
 gi|328673070|gb|AEB29116.1| tRNA-dihydrouridine synthase [Carnobacterium sp. 17-4]
          Length = 326

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 117/322 (36%), Gaps = 35/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE     +    + ++     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSAAGKPDVFFTEFTNTVSYCHPEGRDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +     + +  + + G+  I++N+GCP   V     G+ L+    +  D I A  K   
Sbjct: 79  DEPEHFRQMSIGMAEQGFKGIDINMGCPVPNVAGKGKGSGLIRRATVAADLIQA-AKTGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R+ +  + +  +  + IH R         +      N  +
Sbjct: 138 LPVSVKTRLGY---TNIDEWRDWLTHVFEQDIANLSIHLRT--------RKEMSKGNAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P   + +NG + D    LK++    VDGVMIGR  + N        
Sbjct: 187 EMISEIKKLRDEIAPQTLLTINGDIPDRETGLKLVEEYGVDGVMIGRGVFHNPYAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                         ++   + +R        Y      +   L++  +       G   +
Sbjct: 243 ------EKEPKEHSSQELLNLFRLHLDLFDKYTVDEPRAFRPLRRFFKI---YVRGIRGA 293

Query: 291 RRCRHILTVEAGASTATHHIIE 312
              R  L      + A   + E
Sbjct: 294 SDLRVQLMETETTNQARALLDE 315


>gi|163750237|ref|ZP_02157479.1| NifR3/Smm1 family protein [Shewanella benthica KT99]
 gi|161330093|gb|EDQ01077.1| NifR3/Smm1 family protein [Shewanella benthica KT99]
          Length = 303

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 59/281 (20%), Positives = 108/281 (38%), Gaps = 25/281 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQE------KPLAL 52
           M    D   R     +    L+ +E   +V   +       +      E       P+ L
Sbjct: 1   MEGVADASMRALLTGVGGYDLVISEFIRVVDQLLPERVFYRLCAELANESKTRSGTPVRL 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     + E A    + G   ++LN GCP+  V+  + GA L+  P+ +   + A+ 
Sbjct: 61  QLLGQHPQWMAENALRAVELGSLGVDLNFGCPAPMVNRNNGGAALLKEPETIYRIVKAVR 120

Query: 113 KALSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  P+  T K R+G DD+   V    + ++I+ +G   + +HAR         K+   
Sbjct: 121 EAVPEPLPATAKIRLGWDDKSRCV---EIAQAIEAAGATELTVHART--------KEEGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +IK+    + +  NG +      L+   +   D VMIGR A      L  
Sbjct: 170 KPPAHWEYIRQIKQAI-SIPVIANGEVWSREDYLECQQVSQCDDVMIGRGALAVP-NLAQ 227

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
           V +     +     ++  +       +S     Y AR    
Sbjct: 228 VIKGCQTKMPWPEVLRLLLQYSDDEIVSEKEKYYPARIKQW 268


>gi|238784237|ref|ZP_04628249.1| tRNA-dihydrouridine synthase C [Yersinia bercovieri ATCC 43970]
 gi|238714804|gb|EEQ06804.1| tRNA-dihydrouridine synthase C [Yersinia bercovieri ATCC 43970]
          Length = 310

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRQLLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHNQSRTQSGSLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPKWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMNVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|110642349|ref|YP_670079.1| tRNA-dihydrouridine synthase C [Escherichia coli 536]
 gi|117624342|ref|YP_853255.1| tRNA-dihydrouridine synthase C [Escherichia coli APEC O1]
 gi|215487361|ref|YP_002329792.1| tRNA-dihydrouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218559058|ref|YP_002391971.1| tRNA-dihydrouridine synthase C [Escherichia coli S88]
 gi|312967433|ref|ZP_07781648.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           2362-75]
 gi|331683817|ref|ZP_08384413.1| tRNA-dihydrouridine synthase C [Escherichia coli H299]
 gi|38604879|sp|Q8FFV5|DUSC_ECOL6 RecName: Full=tRNA-dihydrouridine synthase C
 gi|110343941|gb|ABG70178.1| tRNA-dihydrouridine synthase C [Escherichia coli 536]
 gi|115513466|gb|ABJ01541.1| tRNA-dihydrouridine synthase C [Escherichia coli APEC O1]
 gi|215265433|emb|CAS09834.1| tRNA-dihydrouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218365827|emb|CAR03568.1| tRNA-dihydrouridine synthase C [Escherichia coli S88]
 gi|222033901|emb|CAP76642.1| tRNA-dihydrouridine synthase C [Escherichia coli LF82]
 gi|281179232|dbj|BAI55562.1| putative regulator protein [Escherichia coli SE15]
 gi|294493936|gb|ADE92692.1| tRNA-dihydrouridine synthase C [Escherichia coli IHE3034]
 gi|307554209|gb|ADN46984.1| tRNA-dihydrouridine synthase C [Escherichia coli ABU 83972]
 gi|312287630|gb|EFR15535.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           2362-75]
 gi|320186769|gb|EFW61491.1| tRNA-dihydrouridine synthase C [Shigella flexneri CDC 796-83]
 gi|323188135|gb|EFZ73430.1| dihydrouridine synthase family protein [Escherichia coli RN587/1]
 gi|323951936|gb|EGB47810.1| dihydrouridine synthase [Escherichia coli H252]
 gi|323955905|gb|EGB51658.1| dihydrouridine synthase [Escherichia coli H263]
 gi|331078769|gb|EGI49971.1| tRNA-dihydrouridine synthase C [Escherichia coli H299]
          Length = 316

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|213403071|ref|XP_002172308.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
 gi|212000355|gb|EEB06015.1| tRNA-dihydrouridine synthase [Schizosaccharomyces japonicus yFS275]
          Length = 347

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 108/231 (46%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   L  +      FST E  + L +Q G  D
Sbjct: 27  MVRYSKLPFRQLVRDY-NADIVYTPMILAKEFLHPEG-RYFDFSTNEKDRSLVVQFGVED 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +A++IV  +  + I +N GCP     +   G+ L+  P  V + + ++  AL   
Sbjct: 85  PVILAQASEIVAPYT-DAIGINCGCPQPWAIQEGIGSALLKQPQKVHELVRSVKSALGET 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
             V+ +I +D+ +     R L+++ +++G + I +H R+        + +R    +D + 
Sbjct: 144 FCVEVKIRLDNDL--EKTRQLMQTAERAGADFITVHGRR--------RADRSSFPVDLEA 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  + +    + +  NG + D+   LKI    + DGVM  R   +N A+  
Sbjct: 194 IRSV-RPCVSIPVVANGDVNDLDTGLKIAEYTNTDGVMSARGLMENPALFA 243


>gi|124808213|ref|XP_001348259.1| tRNA-dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
 gi|23497150|gb|AAN36698.1| tRNA-dihydrouridine synthase, putative [Plasmodium falciparum 3D7]
          Length = 340

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 104/246 (42%), Gaps = 24/246 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ +   +  +K           +KP+  Q  G D
Sbjct: 33  MVDLSELPFRLLCRKY-NCDLTFTPMLHSKNFVEHEKYRKGYFKSCDMDKPVIAQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EA   ++D   N +++N+GCP     +G++GA L+   D V + I+ +     IP
Sbjct: 92  SKILLEAINFIKD-DVNAVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLISDITNNCVIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R   +D        NL   ++  G+  I +H R    KG+       I   DY+I
Sbjct: 151 ITCKIRKIDND---YQKTLNLCYDLQSRGIKMITVHGRTKEEKGI------NIKQCDYEI 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT-------- 228
           +  I KE  ++ I  NG +E      K L     D VM      +     +         
Sbjct: 202 I-RIIKERLNIPIIANGSIEHFEDIKKCLNYTKADAVMCAEILLEKPYFFSNKNIDAVNI 260

Query: 229 VDEYFS 234
           V+EYF 
Sbjct: 261 VNEYFE 266


>gi|74312663|ref|YP_311082.1| tRNA-dihydrouridine synthase C [Shigella sonnei Ss046]
 gi|73856140|gb|AAZ88847.1| putative regulator protein [Shigella sonnei Ss046]
 gi|323171791|gb|EFZ57435.1| dihydrouridine synthase family protein [Escherichia coli LT-68]
          Length = 315

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|327539746|gb|EGF26351.1| tRNA-dihydrouridine synthase [Rhodopirellula baltica WH47]
          Length = 374

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 64/325 (19%), Positives = 115/325 (35%), Gaps = 29/325 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGAD 58
            ++D   R  AR   + +    E+++   +L    R   ++ L  + +E P+  Q+ GA+
Sbjct: 47  GYSDLPMRVIARR-HSASYTICEVMLDQFLLSLTKREKTRHFLDIADEEHPVGGQLMGAE 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
             +    A  + + G++ I++N GCP  +V     G   +  P +  + +      +   
Sbjct: 106 PEQFSAGALKLVEAGFDVIDVNFGCPVKKVLGRCRGGFHLSQPAVAIEILRRTRDVVPDH 165

Query: 117 IPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           IPVTVK R G+DD          ++     +G+ G+ +H R  +         R I    
Sbjct: 166 IPVTVKMRRGMDDTPESREQFFEILDGAIDAGLAGVTVHGRTVM--------QRYIGPSR 217

Query: 176 YDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +  + E+K+   D L I  +G L      L+++    +DGV I R A  N  +       
Sbjct: 218 WAFLKEVKQHVGDRLKILGSGDLFAAVDGLEMMHQTGIDGVTIARGAIGNPWIFQQSRAL 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +     + P             +     Y             + +  I      PN R 
Sbjct: 278 ANGEPLPAPPTIAEQAAVMREHFALCEETYTVERAPLL-----MRKFCIKYSQSHPNYRE 332

Query: 293 CRHILTVEAGASTATHHIIETAFNL 317
            R   T             E A   
Sbjct: 333 VRMAFTRLRTR-----EEFEAALEQ 352


>gi|47216250|emb|CAG05946.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 505

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/320 (19%), Positives = 110/320 (34%), Gaps = 72/320 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL----GFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M  A   +R               +++PL  Q   
Sbjct: 1   MVDQSELAWRLLSRR-HGAQLCYTPMFHAQVFVRDANYRRDNLYNEVCEEDRPLITQFCA 59

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--------- 107
            D    V+AA + +D+  + I+LN+GCP      G +GA L     ++            
Sbjct: 60  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWGLLEKMGKLDFMSGF 118

Query: 108 ---------------------------IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
                                      +    + LS+P+T K R+  + +          
Sbjct: 119 WKNTHSEFIRGIPLFFPSHALLFAWFPVRLASEKLSVPITCKIRVFKEMEKTV----RYA 174

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           + ++K+G   + +H R    KG             ++ +  +++   ++ +  NG ++ +
Sbjct: 175 QMLEKAGCQLLTVHGRTKEQKGAMT------GVASWEHIRAVRQAV-NIPVFANGNIQHL 227

Query: 201 SQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW---RKI 255
           S   + L    V GVM       N A+             G SP    + +++    RK 
Sbjct: 228 SDVTRCLQETGVQGVMSAEGNLHNPALF-----------EGRSPPVWEMAEEYLEVVRKH 276

Query: 256 SASMTDYAARHLHSGGKLQQ 275
                 Y   HL    KL  
Sbjct: 277 PPCSLSYVRAHL---FKLWH 293


>gi|270260822|ref|ZP_06189095.1| tRNA-dihydrouridine synthase C [Serratia odorifera 4Rx13]
 gi|270044306|gb|EFA17397.1| tRNA-dihydrouridine synthase C [Serratia odorifera 4Rx13]
          Length = 309

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHHASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLGENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D    +     +  +++++G   + +H R          D  K
Sbjct: 128 AAVPDHLPVTVKVRLGWDSDSRSF---EIADAVQQAGATELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A   L     D VM+GR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRKRLT-IPVIANGEIWDYQSAQDCLQTTGCDAVMLGRGAL-NVPNLSQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPQVVQLLQKYVHLEKQGDTGLYHVAR 272


>gi|191165389|ref|ZP_03027231.1| tRNA-dihydrouridine synthase C [Escherichia coli B7A]
 gi|209919598|ref|YP_002293682.1| tRNA-dihydrouridine synthase C [Escherichia coli SE11]
 gi|218554705|ref|YP_002387618.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI1]
 gi|218695751|ref|YP_002403418.1| tRNA-dihydrouridine synthase C [Escherichia coli 55989]
 gi|293446490|ref|ZP_06662912.1| tRNA-dihydrouridine synthase C [Escherichia coli B088]
 gi|300818860|ref|ZP_07099065.1| dihydrouridine synthase [Escherichia coli MS 107-1]
 gi|190904552|gb|EDV64259.1| tRNA-dihydrouridine synthase C [Escherichia coli B7A]
 gi|209912857|dbj|BAG77931.1| putative regulator protein [Escherichia coli SE11]
 gi|218352483|emb|CAU98260.1| tRNA-dihydrouridine synthase C [Escherichia coli 55989]
 gi|218361473|emb|CAQ99062.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI1]
 gi|291323320|gb|EFE62748.1| tRNA-dihydrouridine synthase C [Escherichia coli B088]
 gi|300528479|gb|EFK49541.1| dihydrouridine synthase [Escherichia coli MS 107-1]
 gi|323944956|gb|EGB41021.1| dihydrouridine synthase [Escherichia coli H120]
 gi|324020608|gb|EGB89827.1| dihydrouridine synthase [Escherichia coli MS 117-3]
 gi|324118020|gb|EGC11919.1| dihydrouridine synthase [Escherichia coli E1167]
          Length = 315

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|242208769|ref|XP_002470234.1| predicted protein [Postia placenta Mad-698-R]
 gi|220730684|gb|EED84537.1| predicted protein [Postia placenta Mad-698-R]
          Length = 260

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 118/240 (49%), Gaps = 27/240 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS------TQEKPLALQI 54
           MV+ +D  +R   R   N  L+YT+M+++D +L     + L F         ++P+ +Q+
Sbjct: 6   MVNQSDLPFRRLVRRY-NATLVYTQMLLSDRLLNDH--DYLQFHLRGLGEPNDRPVVVQL 62

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCIAAMC 112
            G D   +V A K V+    + I+ N+GCP     +  +GA L+   +  +V +  A+M 
Sbjct: 63  CGNDPELVVRAGKQVQSH-CDAIDFNLGCPQEAARDAHYGAYLLGQNDWPLVENIAASMS 121

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            +L++PV+ K R+      PA A  +L + ++ +G + + +HAR   ++       R+  
Sbjct: 122 NSLTVPVSAKLRLCQ----PASATLDLARRLEHAGASWVTLHARTVSVR------RRRQG 171

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
             D + +  +K +N  + +  NG +   ED+ + L  L   DG+M+G +   N  +   +
Sbjct: 172 AADLEQIKTLK-DNLSIPVISNGNVRVWEDVERNLA-LTGADGIMVGESLLANPCLFADI 229


>gi|315297996|gb|EFU57266.1| dihydrouridine synthase [Escherichia coli MS 16-3]
          Length = 337

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDRQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 305 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 337


>gi|302682790|ref|XP_003031076.1| hypothetical protein SCHCODRAFT_82562 [Schizophyllum commune H4-8]
 gi|300104768|gb|EFI96173.1| hypothetical protein SCHCODRAFT_82562 [Schizophyllum commune H4-8]
          Length = 701

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 110/293 (37%), Gaps = 38/293 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +   EM +A + L G  ++ +++     EK   +Q+ G   + +V
Sbjct: 352 NLPFRRICVDY-GVDITCGEMGLATSFLSGSKEEWSLVRRHPSEKMFGVQMAGNKPNTMV 410

Query: 64  EAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            AA+++++      + +++N GCP   V++   G+ L+ +P  +G  I  M KAL   PV
Sbjct: 411 RAAELLKNEIGPHVDFVDINCGCPIDLVYKTGSGSALLDSPGKLGRIIVGMNKALGDTPV 470

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R GV D         L+  + + G   + +H R         +  R     D+D V
Sbjct: 471 SVKLRTGVKDGKNNA--HRLMPRVAEWGAGMMTLHGRT--------RQQRYTKLADWDYV 520

Query: 180 YEIKKEN---------PDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTT 228
            E  +           P + I   G                VDGVMIGR A     + T 
Sbjct: 521 RECVQAVRAYEAEKNLPKVPIFGGGDCYSSQDYWTDVETTGVDGVMIGRGALIKPWIFTE 580

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           + E     ++    +          +      +Y   H  +       TR  +
Sbjct: 581 IKERREWDISSRERL----------EHVRKFVEYGLNHFGADTPGVNTTRRYL 623


>gi|229543049|ref|ZP_04432109.1| dihydrouridine synthase DuS [Bacillus coagulans 36D1]
 gi|229327469|gb|EEN93144.1| dihydrouridine synthase DuS [Bacillus coagulans 36D1]
          Length = 327

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 69/307 (22%), Positives = 117/307 (38%), Gaps = 34/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVSKAGRPDVFFTEFTNTESYCHPEGNQSVRGRLAFTADEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G++ +++N+GCP   V     G+ L+  PD+  + I A  KA  
Sbjct: 79  DKPEYFRQMSMGMAKLGFSGVDINMGCPVPNVATKGKGSGLIRRPDVAAELIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + +  I K  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGY---TYVEEWWDWLTHILKQDIVNLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  + +NG + D    LK+     VDGVMIGR  +KN        
Sbjct: 187 ELIPEIKKLRDEVAPDTLLTINGDVPDRQTGLKLARQYGVDGVMIGRGIFKNPFAFE--- 243

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                P   SS     + +          T+   R      +  +I         GF  +
Sbjct: 244 ---KEPKEHSSKELLDLLRLHLDLFDKYSTELEQRPFPPLRRFFKI------YVKGFRGA 294

Query: 291 RRCRHIL 297
              R+ L
Sbjct: 295 SELRNQL 301


>gi|213852323|ref|ZP_03381855.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 316

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 12  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 132 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 276


>gi|238753348|ref|ZP_04614711.1| tRNA-dihydrouridine synthase C [Yersinia ruckeri ATCC 29473]
 gi|238708301|gb|EEQ00656.1| tRNA-dihydrouridine synthase C [Yersinia ruckeri ATCC 29473]
          Length = 309

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +     + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHHQSRTQSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D+         +  +++++G   + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDNDSRQF---EIADAVQQAGATELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + L     D VM+GR A  N   L+ 
Sbjct: 178 AELINWAAIGEIRQRLT-IPVIANGEIWDYQSAQECLKVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|295707311|ref|YP_003600386.1| dihydrouridine synthase [Bacillus megaterium DSM 319]
 gi|294804970|gb|ADF42036.1| dihydrouridine synthase (Dus) [Bacillus megaterium DSM 319]
          Length = 332

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 114/322 (35%), Gaps = 34/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M   TD  +R          + +TE    ++      K+     L F+  E+P+   I G
Sbjct: 19  MEAVTDVVFRHVVTEAARPDVFFTEFTNTESYCHPKGKDSVKGRLTFTDDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  + + G+  I++N+GCP   V     G+ L+  PD   + I A  KA  
Sbjct: 79  DKAEYFRQMSIGMAEMGFRGIDINMGCPVQNVAGNGKGSGLIRRPDTAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G           + +K I +  +  + IH R         K      +  +
Sbjct: 138 LPVSVKTRLGY---TQVDEWYDWLKHILEQDIVNLSIHLRT--------KKEMSDVDAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P   + +NG + D  + L++     VDG+MIGR  + N        
Sbjct: 187 ELIPEIKKLRDEIAPHTLLTINGDIPDRQKGLELAEKYGVDGIMIGRGIFHNPFAFEKEK 246

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +  ++              D + +          R                    GF  +
Sbjct: 247 KEHTSEELLELLRLQLDLHDKYSEELEPRPFKPLRRFFKI------------YVRGFRGA 294

Query: 291 RRCRHILTVEAGASTATHHIIE 312
              R++L            + E
Sbjct: 295 SELRNLLMSTETTDEVRALLDE 316


>gi|260856113|ref|YP_003230004.1| tRNA-dihydrouridine synthase C [Escherichia coli O26:H11 str.
           11368]
 gi|260868842|ref|YP_003235244.1| tRNA-dihydrouridine synthase C [Escherichia coli O111:H- str.
           11128]
 gi|257754762|dbj|BAI26264.1| tRNA-dihydrouridine synthase C [Escherichia coli O26:H11 str.
           11368]
 gi|257765198|dbj|BAI36693.1| tRNA-dihydrouridine synthase C [Escherichia coli O111:H- str.
           11128]
 gi|323176964|gb|EFZ62554.1| dihydrouridine synthase family protein [Escherichia coli 1180]
          Length = 316

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|195873972|ref|ZP_02700016.2| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|195631197|gb|EDX49757.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
          Length = 331

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|324006553|gb|EGB75772.1| dihydrouridine synthase [Escherichia coli MS 57-2]
          Length = 338

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGERKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRIPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 305 EYDEATELFQH 315


>gi|237704605|ref|ZP_04535086.1| tRNA-dihydrouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|226900971|gb|EEH87230.1| tRNA-dihydrouridine synthase C [Escherichia sp. 3_2_53FAA]
          Length = 332

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 24  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 83

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 84  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 143

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 144 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 193

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 194 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 251

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 252 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 298

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 299 EYDEATELFQH 309


>gi|256017692|ref|ZP_05431557.1| tRNA-dihydrouridine synthase C [Shigella sp. D9]
 gi|307311281|ref|ZP_07590925.1| dihydrouridine synthase DuS [Escherichia coli W]
 gi|332278706|ref|ZP_08391119.1| tRNA-dihydrouridine synthase C [Shigella sp. D9]
 gi|306908787|gb|EFN39284.1| dihydrouridine synthase DuS [Escherichia coli W]
 gi|315061449|gb|ADT75776.1| tRNA-dihydrouridine synthase C [Escherichia coli W]
 gi|323377970|gb|ADX50238.1| dihydrouridine synthase DuS [Escherichia coli KO11]
 gi|332101058|gb|EGJ04404.1| tRNA-dihydrouridine synthase C [Shigella sp. D9]
          Length = 316

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|168229529|ref|ZP_02654587.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205335746|gb|EDZ22510.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
          Length = 312

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G N + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGANELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|170680883|ref|YP_001744334.1| tRNA-dihydrouridine synthase C [Escherichia coli SMS-3-5]
 gi|218700612|ref|YP_002408241.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI39]
 gi|170518601|gb|ACB16779.1| tRNA-dihydrouridine synthase C [Escherichia coli SMS-3-5]
 gi|218370598|emb|CAR18405.1| tRNA-dihydrouridine synthase C [Escherichia coli IAI39]
          Length = 315

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 67/338 (19%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + +   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWNWQSAQQCMTISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + +   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRMLNNSPD-----IARAIQAIDIEKL 315


>gi|271500980|ref|YP_003334005.1| dihydrouridine synthase DuS [Dickeya dadantii Ech586]
 gi|270344535|gb|ACZ77300.1| dihydrouridine synthase DuS [Dickeya dadantii Ech586]
          Length = 311

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 117/319 (36%), Gaps = 43/319 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDSRLPVKAFYRLCPELRHGSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYQAAKAMR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  S+PVTVK R+G D          +  ++ ++G + + +H R          D  +
Sbjct: 128 DAVPLSLPVTVKVRLGWDSGERQF---EIADAVAQAGASELVVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRQRL-RIPVIANGEIWDWQSAQDCMAVTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y             R  +  W ++   +  Y          L  + R    +  L  
Sbjct: 236 VIKY-------------REARMPWAEVVQLLQKYVRLEKQGDTGLYHVARIKQWLGYLRK 282

Query: 286 GFPNSRRCR---HILTVEA 301
            + ++         LT  A
Sbjct: 283 EYDDASELFSQIRALTTSA 301


>gi|293410501|ref|ZP_06654077.1| tRNA-dihydrouridine synthase C [Escherichia coli B354]
 gi|291470969|gb|EFF13453.1| tRNA-dihydrouridine synthase C [Escherichia coli B354]
          Length = 315

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 70/338 (20%), Positives = 125/338 (36%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKEPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   M IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAMDIEKL 315


>gi|313884075|ref|ZP_07817841.1| dihydrouridine synthase (Dus) [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620522|gb|EFR31945.1| dihydrouridine synthase (Dus) [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 320

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 72/332 (21%), Positives = 130/332 (39%), Gaps = 43/332 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE   + +    D     K  L F+  E+PL   I G
Sbjct: 20  MEDVTDVAFRHVIARAGRPDVFFTEFTNSASYCHPDGIESVKGRLTFTEDEQPLVAHIWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + AK +++ G+  +++N+GCP+  V +   G+ L+L   +  + I A  +   
Sbjct: 80  DVPEYFSQMAKGMQEMGFAGVDINMGCPAPNVFKHGRGSGLILRSQVAAELIQATKEG-G 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          +  +K +    +  + IH R         K      +  +
Sbjct: 139 LPVSVKTRLG---HAKPEEYKEWLKHLFDQDIVNLSIHLRT--------KTEMSKVDAHW 187

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT--T 228
           D++ +IK    +  P   + +NG + +    L ++    VDGVMIGR  + N        
Sbjct: 188 DMIGDIKALRDQIAPQTLLTINGDIPNRQVGLDLVDQYGVDGVMIGRGVFTNPYAFAKEE 247

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           VD          SP+      + +R        Y  R   S  +  +I         GF 
Sbjct: 248 VDH---------SPLD---LINLFRYHLDLFDKYRLRPFPSLKRSFKI------YIRGFA 289

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
            +   R  L +EA ++    H+++      ++
Sbjct: 290 GANELRIQL-MEAKSTQEVRHLLDKFEAAYLK 320


>gi|120603342|ref|YP_967742.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
 gi|120563571|gb|ABM29315.1| dihydrouridine synthase, DuS [Desulfovibrio vulgaris DP4]
          Length = 332

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 109/288 (37%), Gaps = 24/288 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGAD 58
                  +R     L    LL+T M  A A+   +      F+    + +    Q+ GAD
Sbjct: 18  AGVGHVAFREVIDNLGGCGLLFTGMCNARAVPTENPARSNAFTWRAEELERCVCQLFGAD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ EAA+ VE  G+  +++N+GC  A +     GA L+ + +     + ++ +A+  P
Sbjct: 78  PSEMAEAARRVEAEGFFGVDINMGCSVAAIVRRGCGADLLRDEERAVRMVESVRRAVDCP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R G            L +  + +G + +  H R A        D R  P L + I
Sbjct: 138 VLVKFRTGWSPDPQGAVA--LARRFEDAGADALVFHPRVAP-------DRRTRPPLRHHI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              + KE   + +  NG +     A  +L     DG+ +GR A     +         + 
Sbjct: 189 --RLVKEAVAIPVLGNGEVFTPGDAASMLETTGCDGISLGRIALGRPWVFAGWTGLVDDN 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +         D WR I  ++ D   R         ++ +  +  F
Sbjct: 247 PASNP--------DLWRDIPLALLDALERRHADRKYAARLFKKFLLYF 286


>gi|331647791|ref|ZP_08348883.1| tRNA-dihydrouridine synthase C [Escherichia coli M605]
 gi|330911973|gb|EGH40483.1| tRNA-dihydrouridine synthase C [Escherichia coli AA86]
 gi|331043515|gb|EGI15653.1| tRNA-dihydrouridine synthase C [Escherichia coli M605]
          Length = 316

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|256022176|ref|ZP_05436041.1| tRNA-dihydrouridine synthase C [Escherichia sp. 4_1_40B]
 gi|300950101|ref|ZP_07164048.1| dihydrouridine synthase [Escherichia coli MS 116-1]
 gi|300955838|ref|ZP_07168179.1| dihydrouridine synthase [Escherichia coli MS 175-1]
 gi|301024370|ref|ZP_07188059.1| dihydrouridine synthase [Escherichia coli MS 196-1]
 gi|301644157|ref|ZP_07244165.1| dihydrouridine synthase [Escherichia coli MS 146-1]
 gi|307138799|ref|ZP_07498155.1| tRNA-dihydrouridine synthase C [Escherichia coli H736]
 gi|331642765|ref|ZP_08343900.1| tRNA-dihydrouridine synthase C [Escherichia coli H736]
 gi|299880467|gb|EFI88678.1| dihydrouridine synthase [Escherichia coli MS 196-1]
 gi|300317305|gb|EFJ67089.1| dihydrouridine synthase [Escherichia coli MS 175-1]
 gi|300450591|gb|EFK14211.1| dihydrouridine synthase [Escherichia coli MS 116-1]
 gi|301077455|gb|EFK92261.1| dihydrouridine synthase [Escherichia coli MS 146-1]
 gi|331039563|gb|EGI11783.1| tRNA-dihydrouridine synthase C [Escherichia coli H736]
          Length = 337

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 305 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 337


>gi|317047410|ref|YP_004115058.1| dihydrouridine synthase DuS [Pantoea sp. At-9b]
 gi|316949027|gb|ADU68502.1| dihydrouridine synthase DuS [Pantoea sp. At-9b]
          Length = 318

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + L
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPVKSFHRLCPELQHHSRTPSGTRVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R          +  +
Sbjct: 128 AAVPDHLPVTVKVRLGWDSSDRRF---EIADAVQQAGASELVVHGRTKE-------EGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++++  + EI++    + +  NG + +   A   L     D VM+GR A  N   L+ 
Sbjct: 178 AESINWQAIGEIRQRL-RIPVIANGEIWNWQDAQDCLRITGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y   P+              W ++ A +  Y          L  + R
Sbjct: 236 VVKYNEAPMA-------------WPQVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|302676381|ref|XP_003027874.1| hypothetical protein SCHCODRAFT_60830 [Schizophyllum commune H4-8]
 gi|300101561|gb|EFI92971.1| hypothetical protein SCHCODRAFT_60830 [Schizophyllum commune H4-8]
          Length = 282

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 112/260 (43%), Gaps = 29/260 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS----------TQEKPL 50
           MV+ +D  +R   R        YT+M+  D IL  + ++ L F               P 
Sbjct: 13  MVNQSDLPFRMLVRKY-GATATYTQMLNPDKIL--NDRDYLEFHQRDLELASNAPDGSPT 69

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCI 108
            +Q+ G D   +V+AAK V+      I+LN+GCP     EG +GA L+   +  +V D +
Sbjct: 70  IVQVCGNDTELVVQAAKRVQTL-CQGIDLNLGCPQDAAREGHYGAYLLGQKDWPLVNDIV 128

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +++  +L+IPV+ K R+      P++       +++ SG + + +H R            
Sbjct: 129 SSLSYSLTIPVSAKLRLCQ----PSIKTLAFATALEASGASWVTLHPRTV------SARR 178

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
           R+    D ++V  +K     + +  NG +       K   L   DGVM+G     N   +
Sbjct: 179 RRQGAADLEVVRALKSALT-VPVVSNGNVRHWDDVPKNLALTGADGVMVGETLLGNPWSV 237

Query: 227 TTVDEYFSNPLTGSSPIKTR 246
             +  +    LT +S   +R
Sbjct: 238 LQIRAFSKRALTHASKASSR 257


>gi|261330856|emb|CBH13841.1| tRNA-dihydrouridine synthase 1, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 520

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 94/258 (36%), Gaps = 43/258 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--------------- 45
           MVD ++  +R   R      L YT M  A +  +        FST               
Sbjct: 80  MVDQSELPFRLLCRRY-GATLAYTPMFHAKSFAQSAHYRQRYFSTTTFPPHSAMESGGNV 138

Query: 46  -------------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         + PL  Q  G D   ++ AA+ VED+    ++ N+GCP      G 
Sbjct: 139 AANDSTSNDGALDNDHPLFAQFCGNDPETILAAARHVEDY-CEAVDFNIGCPQGIARRGH 197

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +G+ LM + +++ + + A+   L +PVT K RI  D+           + ++ +G+  + 
Sbjct: 198 YGSFLMEDWELLHNILHALAVELRVPVTAKMRIFDDE----ALTLKYAEMLRDTGIYVLC 253

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKIL--PS 209
           +H R    KG   +        D  ++  + +     + I  NG +       + L    
Sbjct: 254 VHGRTRENKGQQQQ------PADLRMIRRVHEHLRGSIPIIANGNVLTFEDVPRNLAITG 307

Query: 210 VDGVMIGRAAYKNSAMLT 227
            +G M       +  +  
Sbjct: 308 CEGYMCAEPLLWDPKLFA 325


>gi|218778247|ref|YP_002429565.1| dihydrouridine synthase DuS [Desulfatibacillum alkenivorans AK-01]
 gi|218759631|gb|ACL02097.1| dihydrouridine synthase DuS [Desulfatibacillum alkenivorans AK-01]
          Length = 328

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 66/287 (22%), Positives = 112/287 (39%), Gaps = 24/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
           M   T   +R    L     LLYT M  A ++   + K    FS +EK L     QI G+
Sbjct: 17  MAGLTHIAFREVMALYGGYGLLYTGMAGAKSVPHENPKVSTVFSWREKELDHTVCQIFGS 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
               + +AA+ +E  G+  +++N GC +  +     GA L+  PD+    + A+ KA++I
Sbjct: 77  VPETMAKAAERIEAEGFFGVDINCGCSARAICRFDSGAALLAKPDLAAQVVRAVRKAVNI 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G  D        ++ +     G + +  H R A      P     I      
Sbjct: 137 PVIVKFRTGWKDDPAHAV--SMARLFCDEGADALIFHPRVAPDLRTRPPKWEYIG----- 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE---- 231
               + K+   + +  NG +  +  A K+L     DGV +GR A     ++    +    
Sbjct: 190 ----LVKDAVKVPVFGNGNVISLDDAAKMLSMSGCDGVALGRIALAQPWIMAQWSQGMKP 245

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQ 274
              +  T  + + +   K F  + +       + Y   +   G  L 
Sbjct: 246 ALEDYKTAGAAMASFCAKRFEPRTAFLRFMKFSPYYCANFQFGHALH 292


>gi|157369580|ref|YP_001477569.1| tRNA-dihydrouridine synthase C [Serratia proteamaculans 568]
 gi|157321344|gb|ABV40441.1| dihydrouridine synthase DuS [Serratia proteamaculans 568]
          Length = 309

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHHASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D    +     +  +++++G   + +H R          D  K
Sbjct: 128 AAVPAHLPVTVKIRLGWDSDSRSF---EIADAVQQAGATELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   L     D VM+GR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRQRLT-IPVIANGEIWDYQSAQDCLQTTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPQVVQLLQKYVHLEKQGDTGLYHVAR 272


>gi|296411986|ref|XP_002835709.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295629498|emb|CAZ79866.1| unnamed protein product [Tuber melanosporum]
          Length = 459

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 66/293 (22%), Positives = 117/293 (39%), Gaps = 38/293 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFST--QEKPLALQIGG 56
           MV ++   +R   R      L YT M+    +      KK +L F+T   ++PL  Q G 
Sbjct: 36  MVRYSKLPFRALVRDY-GVDLCYTPMVSLKRLYWIASAKKLLLDFTTNASDRPLIAQFGA 94

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL- 115
                   AA++V+ +  + ++LN GCP +   +   G  LM  P +V + + A      
Sbjct: 95  HSSIDFSRAAELVKPYT-DGVDLNCGCPQSWAIQEGIGCRLMQQPQLVKEMVRAAKDRCG 153

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
               V++K R+  D +       + VK ++ SGV+ I IH R+        +  R    +
Sbjct: 154 EDFCVSIKIRVHHDLRETV----DFVKMVESSGVDYITIHGRR--------RSQRSSEPV 201

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD-- 230
           + + +  +K     + I  NG +  +  A +I  +  VDGVM  R   +N A+       
Sbjct: 202 NSEAIALVKSLAG-VPIVANGDVFSLGDAERIVGITGVDGVMAARGLMENPALFAGFKKT 260

Query: 231 -----EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                E F +      P+  ++      ++   M     R         ++TR
Sbjct: 261 PWGAVERFLHYNANYGPLPYQLALHNVGEMLRDMMTKKER--------AEMTR 305


>gi|32471326|ref|NP_864319.1| NifR3 family protein [Rhodopirellula baltica SH 1]
 gi|32443167|emb|CAD71998.1| conserved hypothetical protein-putative NifR3 family protein
           [Rhodopirellula baltica SH 1]
          Length = 374

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 63/325 (19%), Positives = 114/325 (35%), Gaps = 29/325 (8%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAIL----RGDKKNILGFSTQEKPLALQIGGAD 58
            ++D   R  AR   + +    E+++   +L    R   ++ L  + +E P+  Q+ GA+
Sbjct: 47  GYSDLPMRVIARR-HSASYTICEVMLDQFLLSLTKREKTRHFLDIADEEHPVGGQLMGAE 105

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
             +    A  + + G++ I++N GCP  +V     G   +  P +  + +      +   
Sbjct: 106 PEQFSAGALKLVEAGFDVIDVNFGCPVKKVLGRCRGGFHLSQPAVAIEILRRTRDVVPDH 165

Query: 117 IPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           IPVTVK R G+DD          ++     +G+ G+ +H R  +         R I    
Sbjct: 166 IPVTVKMRRGMDDTPESREQFFEILDGAIDAGLAGVTVHGRTVM--------QRYIGPSR 217

Query: 176 YDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +  + E+K+   D L I  +G L      L+++    +DGV I R A  N  +       
Sbjct: 218 WAFLKEVKQHVGDRLKILGSGDLFAAVDGLEMMRQTGIDGVTIARGAIGNPWIFQQSRAL 277

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            +       P             +     Y             + +  I      P+ R 
Sbjct: 278 AAGEPLPPPPTIAEQAAVMREHFALCEETYTVERAPLL-----MRKFCIKYSQSHPDYRE 332

Query: 293 CRHILTVEAGASTATHHIIETAFNL 317
            R   T             E A   
Sbjct: 333 VRMAFTRLRTR-----EEFEAALEQ 352


>gi|300897804|ref|ZP_07116197.1| dihydrouridine synthase [Escherichia coli MS 198-1]
 gi|300358519|gb|EFJ74389.1| dihydrouridine synthase [Escherichia coli MS 198-1]
          Length = 337

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 125/338 (36%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPIKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 305 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 337


>gi|331658219|ref|ZP_08359181.1| tRNA-dihydrouridine synthase C [Escherichia coli TA206]
 gi|331056467|gb|EGI28476.1| tRNA-dihydrouridine synthase C [Escherichia coli TA206]
          Length = 315

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDRQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|307130591|ref|YP_003882607.1| tRNA-dihydrouridine synthase C [Dickeya dadantii 3937]
 gi|306528120|gb|ADM98050.1| tRNA-dihydrouridine synthase C [Dickeya dadantii 3937]
          Length = 311

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 67/331 (20%), Positives = 122/331 (36%), Gaps = 42/331 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDSRLPVKAFYRLCPELRHGSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKMVNGSGGGATLLKDPDLIYRAARAMR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  S+PVTVK R+G D          +  +++++G + + +H R          D  +
Sbjct: 128 EAVPSSLPVTVKVRLGWDSGERQF---EIADAVQQAGASELVVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRRRL-RIPVIANGEIWDWQSAQDCMAATGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y             R  +  W ++   +  Y          L  + R    +  L  
Sbjct: 236 VIKY-------------REARMPWPEVVQLLQKYVRLEKQGDTGLYHVARIKQWLGYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
            +  +      +   A  ++A    +  A  
Sbjct: 283 EYDEASDLFSRI--RALNTSADIERVIDAIE 311


>gi|255732059|ref|XP_002550953.1| tRNA-dihydrouridine synthase 4 [Candida tropicalis MYA-3404]
 gi|240131239|gb|EER30799.1| tRNA-dihydrouridine synthase 4 [Candida tropicalis MYA-3404]
          Length = 342

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 58/272 (21%), Positives = 102/272 (37%), Gaps = 27/272 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R +      F+T +  K + +Q+G  +
Sbjct: 33  MVRYSKLPFRELCRFY-NVDIVYTPMILAREFVRNETARYTDFTTNDIDKSVIVQVGVNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   ++   ++  F  + I +N GCP         GA LM  PD+V D I A        
Sbjct: 92  VEDFMKFVDMIHPF-VDAIGINCGCPIKEQVREGIGAALMSEPDLVADLIKAAKAKYGES 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + +  +I +   I         K +  +G + I +H R         K  R    ++ + 
Sbjct: 151 ICIDTKIRIHSDINQTV--EFAKKVVAAGTDMITVHGRT--------KSTRSTVPVNLEA 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I+     + +  NG    +     +     VDGVM  R    N A+ T +D+     
Sbjct: 201 IKIIRDNVKTIPVIANGDCFTLDDCNRIAEFTGVDGVMSARGILANPALFTGLDK----- 255

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
                       + F    +A    Y     H
Sbjct: 256 ------TPWSAVEMFMHLATAYGLPYKLAQYH 281


>gi|193071073|ref|ZP_03051999.1| tRNA-dihydrouridine synthase C [Escherichia coli E110019]
 gi|300902211|ref|ZP_07120211.1| dihydrouridine synthase [Escherichia coli MS 84-1]
 gi|301306542|ref|ZP_07212606.1| dihydrouridine synthase [Escherichia coli MS 124-1]
 gi|192955596|gb|EDV86073.1| tRNA-dihydrouridine synthase C [Escherichia coli E110019]
 gi|300405730|gb|EFJ89268.1| dihydrouridine synthase [Escherichia coli MS 84-1]
 gi|300838243|gb|EFK66003.1| dihydrouridine synthase [Escherichia coli MS 124-1]
 gi|315255348|gb|EFU35316.1| dihydrouridine synthase [Escherichia coli MS 85-1]
          Length = 325

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 18  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 77

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 78  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 137

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 138 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 188 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 245

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 246 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 292

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 293 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 325


>gi|194469675|ref|ZP_03075659.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194456039|gb|EDX44878.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
          Length = 331

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G N + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGANELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|16761116|ref|NP_456733.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29141188|ref|NP_804530.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|289824273|ref|ZP_06543868.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|38604947|sp|Q8Z5B2|DUSC_SALTI RecName: Full=tRNA-dihydrouridine synthase C
 gi|25311313|pir||AD0779 conserved hypothetical protein STY2404 [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16503414|emb|CAD02554.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29136814|gb|AAO68379.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
          Length = 312

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|300722436|ref|YP_003711724.1| tRNA -dihydrouridine synthase C [Xenorhabdus nematophila ATCC
           19061]
 gi|297628941|emb|CBJ89524.1| tRNA-dihydrouridine synthase C [Xenorhabdus nematophila ATCC 19061]
          Length = 324

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +    P+ +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDSLLPVKSFYRLCPELHSQSRTPSGAPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAVRAIELGSWGVDLNCGCPSKTVNGSGGGASLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVTVK R+G D          +  +I+++G   + +H R          D  K
Sbjct: 128 EAVPDCFPVTVKVRLGWDSGARQF---EIADAIQQAGATELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              ++++ + EI++    + +  NG + D   A   +     + VMIGR A      L+ 
Sbjct: 178 AERINWEAIGEIRRRL-SIPVVANGEIWDWQSAQACIKTTGCNAVMIGRGALHVP-NLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                K  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PKMPWDRVLNLLQKYTILEKQDDTGLYHVAR 272


>gi|311232920|gb|ADP85774.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris RCH1]
          Length = 400

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 109/288 (37%), Gaps = 24/288 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGAD 58
                  +R     L    LL+T M  A A+   +      F+    + +    Q+ GAD
Sbjct: 86  AGVGHVAFREVIDNLGGCGLLFTGMCNARAVPTENPARSNAFTWRAEELERCVCQLFGAD 145

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ EAA+ VE  G+  +++N+GC  A +     GA L+ + +     + ++ +A+  P
Sbjct: 146 PSEMAEAARRVEAEGFFGVDINMGCSVAAIVRRGCGADLLRDEERAVRMVESVRRAVDCP 205

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R G            L +  + +G + +  H R A        D R  P L + I
Sbjct: 206 VLVKFRTGWSPDPQGAVA--LARRFEDAGADALVFHPRVAP-------DRRTRPPLRHHI 256

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              + KE   + +  NG +     A  +L     DG+ +GR A     +         + 
Sbjct: 257 --RLVKEAVAIPVLGNGEVFTPGDAASMLETTGCDGISLGRIALGRPWVFAAWTGLVDDN 314

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +         D WR I  ++ D   R         ++ +  +  F
Sbjct: 315 PASNP--------DLWRDIPLALLDALERRHADRKYAARLFKKFLLYF 354


>gi|46579075|ref|YP_009883.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46448488|gb|AAS95142.1| dihydrouridine synthase family protein [Desulfovibrio vulgaris str.
           Hildenborough]
          Length = 332

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 109/288 (37%), Gaps = 24/288 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGAD 58
                  +R     L    LL+T M  A A+   +      F+    + +    Q+ GAD
Sbjct: 18  AGVGHVAFREVIDNLGGCGLLFTGMCNARAVPTENPARSNAFTWRAEELERCVCQLFGAD 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S++ EAA+ VE  G+  +++N+GC  A +     GA L+ + +     + ++ +A+  P
Sbjct: 78  PSEMAEAARRVEAEGFFGVDINMGCSVAAIVRRGCGADLLRDEERAVRMVESVRRAVDCP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V VK R G            L +  + +G + +  H R A        D R  P L + I
Sbjct: 138 VLVKFRTGWSPDPQGAVA--LARRFEDAGADALVFHPRVAP-------DRRTRPPLRHHI 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              + KE   + +  NG +     A  +L     DG+ +GR A     +         + 
Sbjct: 189 --RLVKEAVAIPVLGNGEVFTPGDAASMLETTGCDGISLGRIALGRPWVFAAWTGLVDDN 246

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +         D WR I  ++ D   R         ++ +  +  F
Sbjct: 247 PASNP--------DLWRDIPLALLDALERRHADRKYAARLFKKFLLYF 286


>gi|323961604|gb|EGB57210.1| dihydrouridine synthase [Escherichia coli H489]
          Length = 311

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 62/311 (19%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|325090797|gb|EGC44107.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus H88]
          Length = 583

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 112/325 (34%), Gaps = 68/325 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNA------LLYTEMIVADAILRGDKKNILGFSTQ-------- 46
           MVD ++  +R   R   N        L Y+ M  +          +  F           
Sbjct: 29  MVDRSEFAWRMLTRSFMNPDSDSPPLLAYSPMFHSRLFKESPNYRLQHFEATRPRSKTPT 88

Query: 47  --------------------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
                                     ++PL +Q    +   L++AA+ VE F  + ++LN
Sbjct: 89  TPAANGIDGGAPQSNTVPYLDGNPSFDRPLIVQFCANNPDDLLQAARAVEPF-CDAVDLN 147

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G +GA L  +PD++ + I  +   LSIPVT K RI    Q          
Sbjct: 148 LGCPQGIARKGHYGAFLQEHPDLIYELINTLHTHLSIPVTAKFRI----QETKEKTLEYA 203

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLED 199
           + I  +G + I +H R+   KG            D+  +  +++  P D  I  NG + +
Sbjct: 204 RIILSAGASIITVHGRRREQKG------HNTGLADWSYIRYLRENLPADTVIFANGNILN 257

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
                K L     DGVM    +  +  + +              P  + V     R    
Sbjct: 258 HGDIEKCLEATGADGVMSAEGSLCDPTIFSG------------PPPPSSVGGSGMRGERR 305

Query: 258 SMTDYAARHLHSGGKLQQ--ITRHM 280
              +Y       GG      + R+M
Sbjct: 306 DGAEYWVGRDGKGGYRVDFVLRRYM 330


>gi|16130078|ref|NP_416645.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           MG1655]
 gi|89108957|ref|AP_002737.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           W3110]
 gi|157161621|ref|YP_001458939.1| tRNA-dihydrouridine synthase C [Escherichia coli HS]
 gi|170019543|ref|YP_001724497.1| tRNA-dihydrouridine synthase C [Escherichia coli ATCC 8739]
 gi|170081763|ref|YP_001731083.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188495359|ref|ZP_03002629.1| tRNA-dihydrouridine synthase C [Escherichia coli 53638]
 gi|194436141|ref|ZP_03068243.1| tRNA-dihydrouridine synthase C [Escherichia coli 101-1]
 gi|238901322|ref|YP_002927118.1| tRNA-dihydrouridine synthase C [Escherichia coli BW2952]
 gi|253772933|ref|YP_003035764.1| tRNA-dihydrouridine synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162154|ref|YP_003045262.1| tRNA-dihydrouridine synthase C [Escherichia coli B str. REL606]
 gi|297521104|ref|ZP_06939490.1| tRNA-dihydrouridine synthase C [Escherichia coli OP50]
 gi|312973611|ref|ZP_07787783.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           1827-70]
 gi|466094|sp|P33371|DUSC_ECOLI RecName: Full=tRNA-dihydrouridine synthase C
 gi|405871|gb|AAA60503.1| yohI [Escherichia coli]
 gi|1788462|gb|AAC75201.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           MG1655]
 gi|85675254|dbj|BAE76617.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K12 substr.
           W3110]
 gi|157067301|gb|ABV06556.1| tRNA-dihydrouridine synthase C [Escherichia coli HS]
 gi|169754471|gb|ACA77170.1| dihydrouridine synthase DuS [Escherichia coli ATCC 8739]
 gi|169889598|gb|ACB03305.1| tRNA-dihydrouridine synthase C [Escherichia coli str. K-12 substr.
           DH10B]
 gi|188490558|gb|EDU65661.1| tRNA-dihydrouridine synthase C [Escherichia coli 53638]
 gi|194424869|gb|EDX40854.1| tRNA-dihydrouridine synthase C [Escherichia coli 101-1]
 gi|238863715|gb|ACR65713.1| tRNA-dihydrouridine synthase C [Escherichia coli BW2952]
 gi|242377782|emb|CAQ32545.1| tRNA dihydrouridine synthase [Escherichia coli BL21(DE3)]
 gi|253323977|gb|ACT28579.1| dihydrouridine synthase DuS [Escherichia coli 'BL21-Gold(DE3)pLysS
           AG']
 gi|253974055|gb|ACT39726.1| tRNA-dihydrouridine synthase C [Escherichia coli B str. REL606]
 gi|253978223|gb|ACT43893.1| tRNA-dihydrouridine synthase C [Escherichia coli BL21(DE3)]
 gi|260448766|gb|ACX39188.1| dihydrouridine synthase DuS [Escherichia coli DH1]
 gi|309702453|emb|CBJ01779.1| tRNA-dihydrouridine synthase C [Escherichia coli ETEC H10407]
 gi|310332206|gb|EFP99441.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           1827-70]
 gi|315136773|dbj|BAJ43932.1| tRNA-dihydrouridine synthase C [Escherichia coli DH1]
 gi|315615379|gb|EFU96011.1| dihydrouridine synthase (Dus) family protein [Escherichia coli
           3431]
 gi|323936754|gb|EGB33039.1| dihydrouridine synthase [Escherichia coli E1520]
 gi|323940791|gb|EGB36979.1| dihydrouridine synthase [Escherichia coli E482]
 gi|323972978|gb|EGB68175.1| dihydrouridine synthase [Escherichia coli TA007]
 gi|332343918|gb|AEE57252.1| dihydrouridine synthase [Escherichia coli UMNK88]
 gi|744179|prf||2014253AN yohI gene
          Length = 315

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|229366234|gb|ACQ58097.1| tRNA-dihydrouridine synthase 4-like PP35 [Anoplopoma fimbria]
          Length = 318

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 69/283 (24%), Positives = 116/283 (40%), Gaps = 34/283 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      + ++ MIVA   +R  K     F+T E  +PL +Q    D
Sbjct: 29  MVRYSKLAFRSLVRKYD-CDICFSPMIVASDFMRSVKARDSEFTTNESDRPLIVQFAAPD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        FGACL+  P++V D +  +   +  P
Sbjct: 88  AQTLADAACVVAPFS-DGVDLNCGCPQRWAMSAGFGACLINKPELVKDMVRHVRNQVDNP 146

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K RI  D +       +L +  + +GV+ I +H R A  +            ++
Sbjct: 147 NYTASIKIRIHKDLRQTV----DLCQKAESAGVSWITVHGRTAEERHQ---------PVN 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +  IK ++  + +  NG ++ +        L  VDGVM  R    N AM +      
Sbjct: 194 YDAIKTIK-DSVSIPVIANGDIKHLRDVESTYQLTGVDGVMAARGLLTNPAMFS------ 246

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                G          D+        T +   H H    L+++
Sbjct: 247 -----GYEDTPLECIWDWVDIAIEQGTQFTCFHHHLIYMLERV 284


>gi|323168721|gb|EFZ54401.1| dihydrouridine synthase family protein [Shigella sonnei 53G]
          Length = 315

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 126/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKAVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|301021095|ref|ZP_07185136.1| dihydrouridine synthase [Escherichia coli MS 69-1]
 gi|300398276|gb|EFJ81814.1| dihydrouridine synthase [Escherichia coli MS 69-1]
          Length = 337

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 62/311 (19%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPIKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 200 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 257

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 258 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 304

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 305 EYDEATELFQH 315


>gi|238895707|ref|YP_002920442.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae NTUH-K2044]
 gi|238548024|dbj|BAH64375.1| tRNA-dihydrouridine synthase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 310

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHQSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVALGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPEHLPVTVKVRLGWDSGERRF---EIADAVQQAGASELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVVANGEIWDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPQVVQLLQKYTRLEKQGDTGLYHVAR 272


>gi|209766354|gb|ACI81489.1| putative regulator protein [Escherichia coli]
          Length = 316

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 62/311 (19%), Positives = 116/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D     + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSTQECMAISGCDSVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 283 EYDEATELFQH 293


>gi|294141562|ref|YP_003557540.1| tRNA-dihydrouridine synthase C [Shewanella violacea DSS12]
 gi|293328031|dbj|BAJ02762.1| tRNA-dihydrouridine synthase C [Shewanella violacea DSS12]
          Length = 310

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 59/299 (19%), Positives = 117/299 (39%), Gaps = 44/299 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     +    L+ +E   +V   +       +         +    P+ L
Sbjct: 8   MEGVADAPMRALLTGVGGYDLVISEFIRVVDQLLPEKVFYRLCAELAHGSKTKSGTPVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     + E A+   + G   ++LN GCP+  V+  + GA ++  P+ +   + A+ 
Sbjct: 68  QLLGQHPQWMAENAQRAIELGSLGVDLNFGCPAPMVNRSNGGAAMLKEPETIYRVVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +P T K R+G DD+   V    + ++I+ +G   + +HAR         K+   
Sbjct: 128 EAVPEQLPATAKIRLGWDDKSRCV---EIAQAIEAAGATELTVHART--------KEEGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +IK+    + +  NG +      LK   +   D VMIGR A     +   
Sbjct: 177 RPPAHWEYIQQIKQAI-SIPVIANGEVWSREDYLKCQQVSQCDDVMIGRGALAVPNL--- 232

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY------AARHLHSGGKLQQITRHMI 281
                      +  IK   DK  W ++   +  Y      + +  +   +++Q  + + 
Sbjct: 233 -----------AHVIKGSQDKMPWSEVLLLLLQYSDYEIVSEKEKYYPARIKQWLKFIA 280


>gi|152971120|ref|YP_001336229.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|262040158|ref|ZP_06013411.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|329999116|ref|ZP_08303320.1| tRNA-dihydrouridine synthase [Klebsiella sp. MS 92-3]
 gi|150955969|gb|ABR77999.1| conserved protein, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|259042511|gb|EEW43529.1| tRNA-dihydrouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328538446|gb|EGF64564.1| tRNA-dihydrouridine synthase [Klebsiella sp. MS 92-3]
          Length = 310

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHQSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVALGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPEHLPVTVKVRLGWDSGERRF---EIADAVQQAGASELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVVANGEIWDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPQVVQLLQKYTRLEKQGDTGLYHVAR 272


>gi|300176192|emb|CBK23503.2| unnamed protein product [Blastocystis hominis]
          Length = 311

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 89/274 (32%), Positives = 130/274 (47%), Gaps = 46/274 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L  AAKI++D GYNEINLN GCPS  V   +FGA LML+P +V   I +M   ++IP+T
Sbjct: 1   MLAYAAKILQDRGYNEINLNCGCPSKTVSSHNFGAKLMLDPPLVRRIIESMKAEVTIPIT 60

Query: 121 VKCRIGVDDQIPAVALRNLVK-----------------------SIKKSG-VNGIWIHAR 156
           VKCRIGVD+     +L + +                        +   +  V+   +HAR
Sbjct: 61  VKCRIGVDNCDSYESLVHFISVVSGVSPSSDSSAEEATEPTDASAASAAPLVSHFIVHAR 120

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----- 211
           K  L G++ ++NR+IP+L  D V+ +  + P L   LNGG++  ++A + L  +      
Sbjct: 121 KCWLNGVNTRENRRIPDLRPDWVFRLLDDFPTLDFTLNGGIKSFAEAQRYLDELSPKRGR 180

Query: 212 ---GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
              GVMIGR A +   M   VDE F        P  +R      R+I     DY  +   
Sbjct: 181 KLRGVMIGRMAMQCPWMFRHVDEIFYG---CKGPGLSR------RQIVERYCDYVEKLQE 231

Query: 269 SGGKLQQ----ITRHMIGLFHGFP-NSRRCRHIL 297
           +  K +     + R +  LF G P      R +L
Sbjct: 232 THQKWKPKNDVVFRPLCTLFSGAPRGGAVFRGVL 265


>gi|171911693|ref|ZP_02927163.1| Dihydrouridine synthase, DuS [Verrucomicrobium spinosum DSM 4136]
          Length = 366

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 63/285 (22%), Positives = 116/285 (40%), Gaps = 22/285 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE--MIVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +           L YTE   + AD+ L       +  +   +P+A Q+ G D
Sbjct: 39  MQDVTDLPFWRLMADYGGADLYYTEYFRVHADSNLEKPILRSVTENPTGRPVAAQMIGND 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSI 117
           I+ LV  A+ +++     ++LN+GCP+  V++   G  L+ +P  V   + A+  A +  
Sbjct: 99  IASLVRTARELQEHPIAAVDLNLGCPAPVVYKKCAGGGLLRDPRHVDAILGALRDAVVKC 158

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             TVK RIG DD   A      +    K  ++ + +H R       S         + YD
Sbjct: 159 KFTVKTRIGFDD---AGVFEQFLPLFAKHDIDLLTVHGRTVAEMYRS--------EVHYD 207

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +    +      +  NG +   ++A +I  L    G+MIGR A +N  M   + ++   
Sbjct: 208 FIARAVEAM-KCPVLANGNVSSAAKAEEILQLTGARGLMIGRGAIRNPWMFRQIRQHL-- 264

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
                 P+      +    I        +  +    ++Q++ +++
Sbjct: 265 ---ARQPVIVPRGGEVLDYIHRLYEAVTSPEVPETLQVQKMKKYL 306


>gi|72393571|ref|XP_847586.1| tRNA-dihydrouridine synthase 1 [Trypanosoma brucei TREU927]
 gi|62176372|gb|AAX70483.1| tRNA-dihydrouridine synthase 1, putative [Trypanosoma brucei]
 gi|70803616|gb|AAZ13520.1| tRNA-dihydrouridine synthase 1, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 520

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 94/258 (36%), Gaps = 43/258 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--------------- 45
           MVD ++  +R   R      L YT M  A +  +        FST               
Sbjct: 80  MVDQSELPFRLLCRRY-GATLAYTPMFHAKSFAQSAHYRQRYFSTTTFPPHSAMESGGNV 138

Query: 46  -------------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         + PL  Q  G D   ++ AA+ VED+    ++ N+GCP      G 
Sbjct: 139 AANDSTSNDGALDNDHPLFAQFCGNDPETVLAAARHVEDY-CEAVDFNIGCPQGIARRGH 197

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +G+ LM + +++ + + A+   L +PVT K RI  D+           + ++ +G+  + 
Sbjct: 198 YGSFLMEDWELLHNILHALAVELRVPVTAKMRIFDDE----ALTLKYAEMLRDTGIYVLC 253

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKIL--PS 209
           +H R    KG   +        D  ++  + +     + I  NG +       + L    
Sbjct: 254 VHGRTRENKGQQQQ------PADLRMIRRVHEHLRGSIPIIANGNVLTFEDVPRNLAITG 307

Query: 210 VDGVMIGRAAYKNSAMLT 227
            +G M       +  +  
Sbjct: 308 CEGYMCAEPLLWDPKLFA 325


>gi|159465759|ref|XP_001691090.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158279776|gb|EDP05536.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 336

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 66/301 (21%), Positives = 116/301 (38%), Gaps = 43/301 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R   R        YT M+ A    +  K      +L   T+++PL +Q   
Sbjct: 52  MVDQSELPFRMLCRN-HGATCAYTPMLHARIFTQDKKYRCAAEMLTTCTEDRPLFVQFCS 110

Query: 57  ADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            +   L++AA++VE  G  + I++N GCP      G +GA LM +   V   +  + + L
Sbjct: 111 NEPQHLLKAARMVEAMGICDAIDINFGCPQRIAKRGGYGAFLMDDLPKVEAMVRGLAQGL 170

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPVT K RI  D            + ++++G   + +H R    K LS          D
Sbjct: 171 RIPVTAKIRIFPDL----AKTVEYARMVERAGAWLVAVHGRLREQKDLS------ATRAD 220

Query: 176 YDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           +D +  +K     + +  NG +    D+   L      DGV+       + A+     E 
Sbjct: 221 WDAIRAVKAAL-SVPVLANGNIRHLGDVDACLA-YTGCDGVLSAEGLLADPALFAPRREP 278

Query: 233 FSNP-------------------LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
            ++                    L  + P+  R+ +     +   M D+ A H     ++
Sbjct: 279 VASGDVSEVGGRDGGTLAAEYLALVAAHPVPLRMVRG---HVHKLMWDWLAEHTDLRERI 335

Query: 274 Q 274
            
Sbjct: 336 N 336


>gi|193062350|ref|ZP_03043445.1| tRNA-dihydrouridine synthase C [Escherichia coli E22]
 gi|194427149|ref|ZP_03059700.1| tRNA-dihydrouridine synthase C [Escherichia coli B171]
 gi|260844746|ref|YP_003222524.1| tRNA-dihydrouridine synthase C [Escherichia coli O103:H2 str.
           12009]
 gi|192932016|gb|EDV84615.1| tRNA-dihydrouridine synthase C [Escherichia coli E22]
 gi|194414770|gb|EDX31041.1| tRNA-dihydrouridine synthase C [Escherichia coli B171]
 gi|257759893|dbj|BAI31390.1| tRNA-dihydrouridine synthase C [Escherichia coli O103:H2 str.
           12009]
 gi|323161767|gb|EFZ47648.1| dihydrouridine synthase family protein [Escherichia coli E128010]
          Length = 316

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|333002068|gb|EGK21634.1| dihydrouridine synthase family protein [Shigella flexneri K-218]
          Length = 315

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 128/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSQVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A+ N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISDCDAVMIGRGAF-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|323488887|ref|ZP_08094126.1| probable tRNA-dihydrouridine synthase [Planococcus donghaensis
           MPA1U2]
 gi|323397450|gb|EGA90257.1| probable tRNA-dihydrouridine synthase [Planococcus donghaensis
           MPA1U2]
          Length = 331

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 71/337 (21%), Positives = 121/337 (35%), Gaps = 39/337 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD----KKNILGFSTQEKPLALQIGG 56
           M D T+  +R          + +TE    ++    +     +  L F+  E+P+   I G
Sbjct: 19  MEDVTNVVFRHVVAEAARPDVFFTEFTNTESYCHPEGIFSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  E +  +   G+  +++N+GCP   V     G+ L+  PD   + I A  KA  
Sbjct: 79  NKPEHFREMSIGMAKQGFKGVDINMGCPVPNVAAKGKGSGLIRYPDNAAEIIQA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  D       +  +  + +  +  + IH R         K         +
Sbjct: 138 LPVSVKTRLGYTD---VEEWKGWLTHVFEQDIANLSIHLRT--------KKEMSAVPAHW 186

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      PD  I +NG + D    L++     +DGVMIGR  + N       +
Sbjct: 187 ELIPEIKKLRDKIAPDTLITINGDIPDRQVGLELAEKYGIDGVMIGRGIFHNPFAF---E 243

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           E              R+  D   K S  +   A + L    K+            G    
Sbjct: 244 EEPKEHSPKELFDLLRLHLDLHDKYSTDIEPIAFKPLRRFFKI---------YVRGVRGV 294

Query: 291 RRCRHILTVEAGAST-----ATHHIIETAFNLMIESL 322
              R+ L             A   +   A N +  ++
Sbjct: 295 GELRNQLMYTETTDQVRALLAEFEVTNEAENSVETNV 331


>gi|218705668|ref|YP_002413187.1| tRNA -dihydrouridine synthase C [Escherichia coli UMN026]
 gi|293405608|ref|ZP_06649600.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1412]
 gi|298381290|ref|ZP_06990889.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1302]
 gi|218432765|emb|CAR13659.1| tRNA-dihydrouridine synthase C [Escherichia coli UMN026]
 gi|291427816|gb|EFF00843.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1412]
 gi|298278732|gb|EFI20246.1| tRNA-dihydrouridine synthase C [Escherichia coli FVEC1302]
          Length = 315

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 68/338 (20%), Positives = 125/338 (36%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPIKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|320176621|gb|EFW51663.1| tRNA-dihydrouridine synthase C [Shigella dysenteriae CDC 74-1112]
          Length = 326

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 63/311 (20%), Positives = 117/311 (37%), Gaps = 40/311 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 18  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 77

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 78  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 137

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 138 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 188 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 245

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 246 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 292

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 293 EYDEATELFQH 303


>gi|296103788|ref|YP_003613934.1| tRNA-dihydrouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295058247|gb|ADF62985.1| tRNA-dihydrouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 310

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +T    + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCVTEFLRVVDMLLPVKSFYRLCPELHRQSRTTSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKVRLGWDSDARQF---EIADAVQQAGATELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+K    + +  NG + D   A   L     + VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRKRL-SIPVIANGEIWDYQSAQACLKATGCEAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W  +   +  Y+         L  + R
Sbjct: 236 VIKYNE-------------PRMPWADVVTLLQKYSRLEKQGDTGLYHVAR 272


>gi|213428225|ref|ZP_03360975.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
          Length = 331

 Score =  175 bits (444), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|227874944|ref|ZP_03993095.1| possible tRNA-dihydrouridine synthase [Mobiluncus mulieris ATCC
           35243]
 gi|227844464|gb|EEJ54622.1| possible tRNA-dihydrouridine synthase [Mobiluncus mulieris ATCC
           35243]
          Length = 471

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 117/314 (37%), Gaps = 34/314 (10%)

Query: 19  NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YN 75
             +   EM+ A A+  G +++  ++     +   ++Q+ G     L  AA  +   G  +
Sbjct: 117 EGMFVGEMVTAKALRMGSERSWVMVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGLAD 176

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVKCR 124
            I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK R
Sbjct: 177 HIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVKIR 236

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G+D +       ++ +  + +GV  + +HAR                +  ++ +  +  
Sbjct: 237 SGIDAEHR--IFLDVARVAEDNGVAAVTLHARTT--------SEYYGGHSHWEDIAALV- 285

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           E  D+ +  NG +   + AL++       GV IGRA      +   +            P
Sbjct: 286 EVLDIPVLGNGDVFCAADALEMFRETGCAGVEIGRAVQGRPWIFREITAALWGLPVPVGP 345

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT---V 299
               V     R     +  Y     +    L+ + +H+   F GF      R  L     
Sbjct: 346 SLGEVANVARRHAEGLVAHYG----NELVALRDMRKHLGWYFRGFGLGGEMRGRLARVES 401

Query: 300 EAGASTATHHIIET 313
            A    ATH +IE 
Sbjct: 402 LAELEQATHELIER 415


>gi|170767246|ref|ZP_02901699.1| tRNA-dihydrouridine synthase C [Escherichia albertii TW07627]
 gi|170123580|gb|EDS92511.1| tRNA-dihydrouridine synthase C [Escherichia albertii TW07627]
          Length = 316

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 118/312 (37%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYLGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   D+ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-DIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHIL 297
            +  +      +
Sbjct: 283 EYDEATELFQHI 294


>gi|153950443|ref|YP_001401772.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|229841115|ref|ZP_04461274.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229843219|ref|ZP_04463365.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229894163|ref|ZP_04509349.1| tRNA-dihydrouridine synthase C [Yersinia pestis Pestoides A]
 gi|229903397|ref|ZP_04518510.1| tRNA-dihydrouridine synthase C [Yersinia pestis Nepal516]
 gi|38604952|sp|Q8ZGV2|DUSC_YERPE RecName: Full=tRNA-dihydrouridine synthase C
 gi|152961938|gb|ABS49399.1| tRNA-dihydrouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|229679167|gb|EEO75270.1| tRNA-dihydrouridine synthase C [Yersinia pestis Nepal516]
 gi|229689566|gb|EEO81627.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229697481|gb|EEO87528.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229704048|gb|EEO91061.1| tRNA-dihydrouridine synthase C [Yersinia pestis Pestoides A]
 gi|320015990|gb|ADV99561.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 312

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 107/290 (36%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHNQSRTQSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 AAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWLEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|262038887|ref|ZP_06012232.1| nitrogen regulation protein nifr3 [Leptotrichia goodfellowii F0264]
 gi|261747090|gb|EEY34584.1| nitrogen regulation protein nifr3 [Leptotrichia goodfellowii F0264]
          Length = 311

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 126/294 (42%), Gaps = 25/294 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK---KNILGFSTQEKPLALQIGGA 57
           M  +TD  YR   +   N  LL+TEM+ A  +   D+   K +L    +E    +Q+ G+
Sbjct: 8   MAGYTDYSYRKILKKF-NPDLLFTEMVSAHLLNENDEATEKELLKCDDKE-NEGVQVFGS 65

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
           D ++L++A   +E+ G+  +NLN+GCP  ++ +   G+ L+   D V   ++ +   LS 
Sbjct: 66  DKNELIKAFLKLENKGFKNLNLNMGCPQTKIIKNGAGSALLPQTDFVDSLLSELKSKLSD 125

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RIG  D        +L     K  ++ I IH R         ++       D
Sbjct: 126 KTKLSIKIRIGYRDFSSPELYIDLAN---KYNLDFICIHGRT--------REQLYNGKAD 174

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +DIV E+      +    NG L +    + ++   ++DG+M+ R    N  +++ + E  
Sbjct: 175 WDIVSELSNRPRKIDFIGNGDLFEAKDIVSLIKKSNLDGIMLSRGIIGNPWLISQIRELL 234

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +     + P    V       IS     Y   +        +I +++   F  F
Sbjct: 235 NLGEITTFPDFDTVKNAVLEHIS-----YLEENKGKIVAALEINKYLQPYFKRF 283


>gi|157157351|ref|YP_001463486.1| tRNA-dihydrouridine synthase C [Escherichia coli E24377A]
 gi|157079381|gb|ABV19089.1| tRNA-dihydrouridine synthase C [Escherichia coli E24377A]
          Length = 315

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     A  
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKATR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|260947234|ref|XP_002617914.1| conserved hypothetical protein [Clavispora lusitaniae ATCC 42720]
 gi|238847786|gb|EEQ37250.1| conserved hypothetical protein [Clavispora lusitaniae ATCC 42720]
          Length = 415

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 96/235 (40%), Gaps = 21/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFS-TQEKPLALQI 54
           MVD ++  +R  +R      L YT M  A         R    +       +++PL +Q 
Sbjct: 25  MVDQSELAWRILSRRY-GAELCYTPMFHARLFATEEKYRNKMWSEWDGDREKDRPLVVQF 83

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D   L++AAK VED   + ++LN+GCP     +G++GA LM + D+V   I  +   
Sbjct: 84  CANDPEYLLQAAKFVED-KCDAVDLNLGCPQGIARKGNYGAFLMDDWDLVYKLIRKLHDN 142

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L  PVT K R+  D +          K +  +G   I IH R   +KG +          
Sbjct: 143 LKCPVTAKIRVYDDWEKS----LEYAKMVLSAGAQFITIHGRTRDMKGQAT------GLA 192

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           ++ I+  ++   P D     NG +   S   + +     D VM       N  + 
Sbjct: 193 NWKILRYLRDNLPSDQVFFANGNILYPSDINRCIDEVSCDAVMSAEGNLYNPGVF 247


>gi|167551130|ref|ZP_02344885.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205324041|gb|EDZ11880.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
          Length = 312

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|119589547|gb|EAW69141.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
 gi|119589548|gb|EAW69142.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
          Length = 315

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 102/260 (39%), Gaps = 24/260 (9%)

Query: 26  MIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVG 82
           M V   +L+G      +L     E    +Q+ GA    + + A+++      + +++NVG
Sbjct: 1   MAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMTKCAELLSRTVEVDFVDINVG 60

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP   V++   G  LM         +  M + L +P+TVK R GV +++       L+  
Sbjct: 61  CPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERVNLA--HRLLPE 118

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++  GV  + +H R         ++ R     D+  + E  +    + +  NG +     
Sbjct: 119 LRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFGNGDILSFED 170

Query: 203 A-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           A   +   V G+MI R A     + T + E     ++ S  +           I    T+
Sbjct: 171 ANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSERL----------DILRDFTN 220

Query: 262 YAARHLHSGGKLQQITRHMI 281
           Y   H  S  +  + TR  +
Sbjct: 221 YGLEHWGSDTQGVEKTRRFL 240


>gi|307171073|gb|EFN63116.1| tRNA-dihydrouridine synthase 3-like [Camponotus floridanus]
          Length = 592

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 100/233 (42%), Gaps = 17/233 (7%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  IL+  ++   ++     E    +Q+ G +   L 
Sbjct: 289 NLPFRRICKEY-GADITCGEMALAPKILKAAQEEWALVKRHESEDIFGVQLCGNNPGVLT 347

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ ++   + I+LN+GCP   ++    G+ ++    ++   + ++ + L IP+TVK
Sbjct: 348 RCAQLLNQEIDVDFIDLNLGCPIDLIYRKGGGSGMLNRLHVLESVVKSISQVLDIPLTVK 407

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV    P      L+   +  G + I +H R         ++ R     +++ + + 
Sbjct: 408 TRTGVYIDKPIA--HKLMPRFRDWGASMITVHGRS--------REQRYTKLANWEYIEKC 457

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
                 + +  NG +   +D  +  KI  +V G+ IGR A     + T + E 
Sbjct: 458 ALAAQPIPVFGNGDVLSFDDYQRMKKICGTVQGITIGRGALIKPWIFTEIKER 510


>gi|258404616|ref|YP_003197358.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
 gi|257796843|gb|ACV67780.1| dihydrouridine synthase DuS [Desulfohalobium retbaense DSM 5692]
          Length = 341

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/292 (22%), Positives = 116/292 (39%), Gaps = 25/292 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQE-KPLALQIGGA 57
           MV  T    R          L +TEM  A A+L+ D +   +  F   E   L  QI G+
Sbjct: 29  MVGVTHVALRRLLHDFGGFGLHWTEMCSASAVLQEDPRISPVFRFHRDELATLVCQIMGS 88

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   +  AA+ ++D G+  +++N+GC  A V +   GA L+ +       + A+ +A+ I
Sbjct: 89  EPETMAAAARRIQDEGFFGVDINMGCCVAAVRQQGAGAALLRDISRAAAIVDAVRQAVDI 148

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+ VK R G  DQ P V       +   +  + + +H R A  +   P   R        
Sbjct: 149 PLFVKLRSGWTDQGPVVVHAARACAKAGA--DALIVHPRLAPDRRTRPPQWRD------- 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +  E  DL +  NG +     A  +L      G+ +GR A     +      +F  
Sbjct: 200 -IRAVC-EAVDLPVFGNGNVFTADDATAMLRQTGCQGIALGRMAAARPWIAAEWLGHFHP 257

Query: 236 PLTGSSPIKTRVDKDFW--------RKISASMTDYAARHLHSGGKLQ-QITR 278
                  +  R+ +  W         ++     +Y A +   G +L+  +TR
Sbjct: 258 APETYPKVAQRMVELLWTSFPEGQALRLYRKFMNYFAANFAFGHRLRSDLTR 309


>gi|170049778|ref|XP_001870922.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
 gi|167871506|gb|EDS34889.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
          Length = 590

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 106/291 (36%), Gaps = 30/291 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +    + +   EM  +  I+ G  +   +      E    +QI G       
Sbjct: 253 NLPFRRICKEYGVD-ITCGEMACSVPIINGMMQEWALTKRHPSEDLFGVQICGYSGKLAA 311

Query: 64  EAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPV 119
            A++ I E+   + +++N+GCP   +     G+ L+    ++   + +  + L       
Sbjct: 312 YASQLIAENADVDFVDINLGCPIELIFNQGGGSALLRREKVLEVLVQSCSRLLADYGKEF 371

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R GV           LV   ++ G + + IH R         K+ R     D++ +
Sbjct: 372 TVKTRTGVYAGKNVA--HELVPKFEEWGASLVTIHGRT--------KEQRYTKRADWNYI 421

Query: 180 YEIKKENPDLFIGLNGGLEDMSQ---ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++  +    + I  NG +        A K  P + GVMIGR A     +   + E     
Sbjct: 422 WQCAQTVKSVPIYGNGDIFSYEDYVEAKKCAPELAGVMIGRGALVKPWIFQEIKEQ---- 477

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                P  +   +   R +     +Y   H  S  K  + TR  +  +  F
Sbjct: 478 -KALDPSSSERMEMLKRYV-----NYGLEHWGSDTKGVENTRRFLLEWQSF 522


>gi|192360796|ref|YP_001981875.1| dihydrouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686961|gb|ACE84639.1| dihydrouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
          Length = 321

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/333 (19%), Positives = 118/333 (35%), Gaps = 47/333 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGF------STQEKPLAL 52
           M    + H R     L       TE   +    +                 +    P+ +
Sbjct: 8   MEGVVEHHVRDILTRLGGLDGCVTEFIRVTDQKLPYKVFYKYAQELENHCQTPNGTPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+    +   A+ +  +G   I+LN GCP+  V+    GACL+  PD V   I A+ 
Sbjct: 68  QLLGSKPEPMALNAQELVRYGAKAIDLNFGCPAKTVNSHEGGACLLRTPDRVYSIIKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D+          ++++ +G + + +HAR         K +  
Sbjct: 128 DAVPRAIPVSAKIRLGFEDRTSY---MENAQAVEAAGADELTVHARS--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   +  + +IK     + +  NG +  +   L+         VM+GR       +   
Sbjct: 177 KPPAYWHYIADIKAAL-KIPVIANGEIWSVEDYLRCREQSQCADVMLGRGLLSCPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA------RHLHSGGKLQQITRHMIG 282
           +  Y +                 W ++   + DY           + G +++Q    ++ 
Sbjct: 236 IKAYLAGEEYRP---------LTWGEVCQILFDYYRLTTPLYETRNCGNRVKQW---LMY 283

Query: 283 LFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
           L   +P +         EA     T   IE  F
Sbjct: 284 LSRQYPEANVFF-----EAVKRKTTPADIEACF 311


>gi|146421120|ref|XP_001486511.1| hypothetical protein PGUG_02182 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 347

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 17/234 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D      F+T   ++ + +Q+G  +
Sbjct: 38  MVRYSKLPFRELVRHY-NTDIVYTPMILAREFVRNDVARASDFTTNPADRLVIVQVGCNN 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++  +++  +  + I LN GCP         GA LM  P++V   + A+ +     
Sbjct: 97  VEDLLKFVEMIHPY-VDGIGLNCGCPIKEQVREGIGAALMSEPELVSSMVKAVKQKYGDK 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I +   I        VK +++SGV+ I +H R         K+ R    ++ D 
Sbjct: 156 ICIETKIRIHPDIK--ETLKFVKMVEESGVDFITVHGRT--------KNTRSSVPVNLDA 205

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +  +K+    + +  NG    +  A  +     VDGVM  R    N A+     
Sbjct: 206 IKAVKEAVL-VPVVANGDCFSLQDAYDIAEYTGVDGVMAVRGILANPALFAGYK 258


>gi|22126892|ref|NP_670315.1| tRNA-dihydrouridine synthase C [Yersinia pestis KIM 10]
 gi|45440801|ref|NP_992340.1| tRNA-dihydrouridine synthase C [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51595560|ref|YP_069751.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|108806882|ref|YP_650798.1| tRNA-dihydrouridine synthase C [Yersinia pestis Antiqua]
 gi|108812963|ref|YP_648730.1| tRNA-dihydrouridine synthase C [Yersinia pestis Nepal516]
 gi|145599791|ref|YP_001163867.1| tRNA-dihydrouridine synthase C [Yersinia pestis Pestoides F]
 gi|149366830|ref|ZP_01888864.1| tRNA-dihydrouridine synthase C [Yersinia pestis CA88-4125]
 gi|162420578|ref|YP_001605884.1| tRNA-dihydrouridine synthase C [Yersinia pestis Angola]
 gi|165924670|ref|ZP_02220502.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165938395|ref|ZP_02226953.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166009907|ref|ZP_02230805.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166211701|ref|ZP_02237736.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167400320|ref|ZP_02305833.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167419917|ref|ZP_02311670.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167424368|ref|ZP_02316121.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167466751|ref|ZP_02331455.1| tRNA-dihydrouridine synthase [Yersinia pestis FV-1]
 gi|170025109|ref|YP_001721614.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis YPIII]
 gi|186894623|ref|YP_001871735.1| tRNA-dihydrouridine synthase C [Yersinia pseudotuberculosis PB1/+]
 gi|218928338|ref|YP_002346213.1| tRNA-dihydrouridine synthase C [Yersinia pestis CO92]
 gi|270487207|ref|ZP_06204281.1| dihydrouridine synthase (Dus) [Yersinia pestis KIM D27]
 gi|294503193|ref|YP_003567255.1| hypothetical protein YPZ3_1083 [Yersinia pestis Z176003]
 gi|21959928|gb|AAM86566.1|AE013903_3 putative regulator protein [Yersinia pestis KIM 10]
 gi|45435659|gb|AAS61217.1| Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family
           [Yersinia pestis biovar Microtus str. 91001]
 gi|51588842|emb|CAH20456.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108776611|gb|ABG19130.1| hypothetical protein YPN_2803 [Yersinia pestis Nepal516]
 gi|108778795|gb|ABG12853.1| hypothetical protein YPA_0885 [Yersinia pestis Antiqua]
 gi|115346949|emb|CAL19839.1| conserved hypothetical protein [Yersinia pestis CO92]
 gi|145211487|gb|ABP40894.1| hypothetical protein YPDSF_2522 [Yersinia pestis Pestoides F]
 gi|149291204|gb|EDM41279.1| tRNA-dihydrouridine synthase C [Yersinia pestis CA88-4125]
 gi|162353393|gb|ABX87341.1| tRNA-dihydrouridine synthase [Yersinia pestis Angola]
 gi|165913773|gb|EDR32392.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165923730|gb|EDR40862.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165991303|gb|EDR43604.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166207472|gb|EDR51952.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962658|gb|EDR58679.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167050269|gb|EDR61677.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167057217|gb|EDR66980.1| tRNA-dihydrouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169751643|gb|ACA69161.1| dihydrouridine synthase DuS [Yersinia pseudotuberculosis YPIII]
 gi|186697649|gb|ACC88278.1| dihydrouridine synthase DuS [Yersinia pseudotuberculosis PB1/+]
 gi|262361232|gb|ACY57953.1| hypothetical protein YPD4_1044 [Yersinia pestis D106004]
 gi|262365231|gb|ACY61788.1| hypothetical protein YPD8_1103 [Yersinia pestis D182038]
 gi|270335711|gb|EFA46488.1| dihydrouridine synthase (Dus) [Yersinia pestis KIM D27]
 gi|294353652|gb|ADE63993.1| hypothetical protein YPZ3_1083 [Yersinia pestis Z176003]
          Length = 314

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 107/290 (36%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 10  MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHNQSRTQSGTLVRI 69

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 70  QLLGQYPEWLAENAARAVALGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 129

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 130 AAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 179

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 180 AERINWQAIGEIRQRLT-IPVIANGEIWDYQSAQECMKVTGCDAVMLGRGAL-NVPNLSR 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 238 VVKYNE-------------PRMPWLEVVKLLQKYVQLEKQGDTGLYHVAR 274


>gi|260582845|ref|ZP_05850630.1| RNA polymerase factor sigma-32 [Haemophilus influenzae NT127]
 gi|260094058|gb|EEW77961.1| RNA polymerase factor sigma-32 [Haemophilus influenzae NT127]
          Length = 310

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A    D G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQNPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ GV  I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGVTEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+ V+K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNVEKMPWYEIQKILQKYANVENEYDSGFYHVAR 272


>gi|307701794|ref|ZP_07638808.1| TIM-barrel protein, nifR3 family [Mobiluncus mulieris FB024-16]
 gi|307613052|gb|EFN92307.1| TIM-barrel protein, nifR3 family [Mobiluncus mulieris FB024-16]
          Length = 458

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 117/314 (37%), Gaps = 34/314 (10%)

Query: 19  NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YN 75
             +   EM+ A A+  G +++  ++     +   ++Q+ G     L  AA  +   G  +
Sbjct: 104 EGMFVGEMVTAKALRMGSERSWVMVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGLAD 163

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVKCR 124
            I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK R
Sbjct: 164 HIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVKIR 223

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G+D +       ++ +  + +GV  + +HAR                +  ++ +  +  
Sbjct: 224 SGIDAEHR--IFLDVARVAEDNGVAAVTLHARTT--------SEYYGGHSHWEDIAALV- 272

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           E  D+ +  NG +   + AL++       GV IGRA      +   +            P
Sbjct: 273 EVLDIPVLGNGDVFCAADALEMFRQTGCAGVEIGRAVQGRPWIFREITAALWGLPVPVGP 332

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT---V 299
               V     R     +  Y     +    L+ + +H+   F GF      R  L     
Sbjct: 333 SLGEVANVARRHAEGLVAHYG----NELVALRDMRKHLGWYFRGFGLGGEMRGRLARVES 388

Query: 300 EAGASTATHHIIET 313
            A    ATH +IE 
Sbjct: 389 LAELEQATHELIER 402


>gi|68478245|ref|XP_716864.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68478366|ref|XP_716804.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46438488|gb|EAK97818.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46438550|gb|EAK97879.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|238882442|gb|EEQ46080.1| tRNA-dihydrouridine synthase 4 [Candida albicans WO-1]
          Length = 339

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 57/272 (20%), Positives = 110/272 (40%), Gaps = 27/272 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R +      F+T   +K + +Q+G  +
Sbjct: 33  MVRYSKLPFRELCRFYDVD-IVYTPMILAREFVRNEVARSTDFTTNDSDKCVIVQVGVNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   ++  +++  F  + I +N GCP         GA LM +PD+V + I          
Sbjct: 92  VDDFMKFIEMIHPF-VDGIGINCGCPIKEQVREGIGAALMSDPDLVAELIKTAKDKYGDS 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + +  +I +   I      + V  + ++G + + +H R         K+ R    ++ D 
Sbjct: 151 ICIDTKIRIHRDINQTI--DFVNKVVEAGTDTLTVHGRT--------KNTRSSVPVNLDA 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I++    + +  NG    ++   KI     VDGVM  R    N A+ T +D+     
Sbjct: 201 IKIIRENVTTIPVIANGDCFTLTDFQKIVDYTGVDGVMSARGVLANPALFTGLDK----- 255

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
                       + F   ++A    Y     H
Sbjct: 256 ------TPWSAVEMFLHLVTAYGLPYKLAQYH 281


>gi|213648444|ref|ZP_03378497.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
          Length = 331

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPKLLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|324509339|gb|ADY43931.1| tRNA-dihydrouridine synthase 1-like protein [Ascaris suum]
          Length = 503

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 103/231 (44%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L ++ MI A   ++    +++ L     ++PL +Q    +
Sbjct: 59  MVDQSELAFRMMMRQ-HGADLCFSPMIHAQLFVKDLTYRRSALSSCPSDRPLIVQFCANE 117

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ A  +VED   + ++LN+GCP      G +GA L  + D+V + ++ +     +P
Sbjct: 118 PHMLLTACLLVEDI-CDGVDLNLGCPQLIAKRGHYGAYLEEDLDLVCEMVSLVHSHCRVP 176

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K RI  +         N  ++++K+G   + +H R    +G S          D++ 
Sbjct: 177 LSCKIRILDEIGKTV----NYARALEKAGACMLTVHGRTRQQRGAST------GLADWNA 226

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
           +  +K+    + +  NG +   +D+ + LK+    + VM       N  + 
Sbjct: 227 IRIVKRAI-SIPLLANGSIQMPDDVERCLKM-TGANAVMSAEGVLSNPLLF 275


>gi|329295989|ref|ZP_08253325.1| tRNA-dihydrouridine synthase C [Plautia stali symbiont]
          Length = 315

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 65/296 (21%), Positives = 121/296 (40%), Gaps = 24/296 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLSGVNDYDLCVTEFLRVVDQLLPVKSFYRLCPELHHHSRTPSGTRVRM 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R       + +D  +
Sbjct: 128 EAVPAHLPVTVKVRLGWDSGARRF---EIADAVQQAGASELVVHGR-------AKEDGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++++  + EI++    + +  NG + +   A   L     D VM+GR A  N   L  
Sbjct: 178 AESINWQAIGEIRQRLT-IPVIANGEIWNWQDAQDCLRITGCDAVMLGRGAL-NVPNLGR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           V +Y   P+  S  ++  +      K   +   + AR     G L++    + GLF
Sbjct: 236 VVKYNEAPMPWSQVVELLLRYTQLEKQGDTGNYHVARIKQWLGYLRKAYHEVDGLF 291


>gi|253990396|ref|YP_003041752.1| tRNA -dihydrouridine synthase C [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253781846|emb|CAQ85009.1| tRNA-dihydrouridine synthase C [Photorhabdus asymbiotica]
          Length = 310

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 117/298 (39%), Gaps = 28/298 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEKP---------L 50
           M    D   R     +    L  TE + V D++L    K+      +            +
Sbjct: 8   MEGVLDSLVRELLSEINEYDLCITEFLRVVDSLL--PVKSFYKLCPELHNQSRTLSGTLV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     A
Sbjct: 66  RIQLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYQGAKA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M +A+   +PVTVK R+G D          +  +++++G   I IH R          D 
Sbjct: 126 MREAVPSHLPVTVKVRLGWDSSERQF---EIADAVQQAGATEITIHGRTKE-------DG 175

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            K   +++  + EI++    + +  NG + D   A   +     + VMIGR A  N   L
Sbjct: 176 YKAERINWQAIGEIRRRL-SIPVIANGEIWDWQSAQDCMDVTGCNAVMIGRGAL-NVPNL 233

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           + V +Y    +     ++         K   +   + AR     G L++  +    LF
Sbjct: 234 SRVVKYNEPRMHWQEVVQLLQKYVRLEKQGDTGQYHVARIKQWLGYLRKEYKEAATLF 291


>gi|332754772|gb|EGJ85137.1| dihydrouridine synthase family protein [Shigella flexneri 4343-70]
          Length = 315

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 69/338 (20%), Positives = 128/338 (37%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G+  ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGFWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A+ N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISDCDAVMIGRGAF-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|68076617|ref|XP_680228.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56501126|emb|CAH94784.1| conserved hypothetical protein [Plasmodium berghei]
          Length = 338

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 101/231 (43%), Gaps = 16/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ +   +   K          Q+KPL  Q  G D
Sbjct: 32  MVDLSELPFRLLCRNY-NCDLAFTPMLHSKNFVEHSKYRTGYFKKCDQDKPLIAQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S ++ A   ++D   N +++N+GCP     +G++GA L+   D V + I+ +    ++P
Sbjct: 91  PSTILRAIDYIKDE-VNGVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLISDITNNCNVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R   +D        NL   ++   V  I +H R    KG+       I   DY+I
Sbjct: 150 ISCKIRKIDND---YQKTLNLCYDLQSRNVKMITVHGRTKEEKGV------NIKECDYEI 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  I KE  ++ I  NG +E+     K L     D VM      +  +  +
Sbjct: 201 IK-IIKERLNIPIIANGSIENFEDIEKCLNYTKTDAVMCAEILLEKPSFFS 250


>gi|158290529|ref|XP_312125.3| AGAP002791-PA [Anopheles gambiae str. PEST]
 gi|157017939|gb|EAA07861.3| AGAP002791-PA [Anopheles gambiae str. PEST]
          Length = 396

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 99/231 (42%), Gaps = 15/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      L +T MI+AD+  + +K  +  F+T E   PL  Q    +
Sbjct: 30  MVRYSKLEFRHLVRSY-GTDLAFTSMIMADSFCKSEKARLNEFTTNEEDTPLIAQFAANN 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               + A+++V  +  + ++LN GCP        +G+ L+  P+++ D +  + + +   
Sbjct: 89  TIDFLSASEMVYPY-VDGVDLNCGCPQRWAMAEGYGSALLKTPELIADMLGTVRRNMPST 147

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +V  ++ +          ++ + ++ +G+  + +H R A               +  D 
Sbjct: 148 FSVSVKVRLLSSTDHKRTIDMCRQLEATGITFLTVHGRTAPE--------MTKVPVHKDA 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           + EIK+    + +  NG +  +  A ++      DGVM  R    N A+  
Sbjct: 200 LQEIKQSIG-IPMVANGDIFTLDDAEQMYLQTKCDGVMTARGILSNPALFA 249


>gi|169862298|ref|XP_001837779.1| zinc finger dihydrouridine synthase [Coprinopsis cinerea
           okayama7#130]
 gi|187471053|sp|A8NZY7|DUS3_COPC7 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|116501141|gb|EAU84036.1| zinc finger dihydrouridine synthase [Coprinopsis cinerea
           okayama7#130]
          Length = 676

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/294 (22%), Positives = 109/294 (37%), Gaps = 39/294 (13%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +   EM +A + L G  ++ +++     EK   +Q+ G     LV
Sbjct: 323 NLPFRRMCVKL-GADITCGEMGLATSFLAGSKEEWSLVRRHPSEKIFGIQVAGNKPHTLV 381

Query: 64  EAAKIVE---DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
             A+++      G + ++LN GCP   V +   G+ L+ N   +G  I  M +AL  IP+
Sbjct: 382 PTAEVIAKEFPTGVDFVDLNCGCPIDLVFKAGSGSALLDNAGKLGKIIQGMNRALGEIPL 441

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R GV +         L+  I  +   + I +H R         +  R     D+D 
Sbjct: 442 TVKIRTGVKEGRNNA--HKLMPRISAEWSASAITLHGRT--------RQQRYTKLADWDY 491

Query: 179 VYEIKKEN---------PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           + E              P + I   G         + +    VDGVMIGR A     + T
Sbjct: 492 IKECVAAVRAREADEDLPPVPIFGGGDCFSSQDYWEKINNYGVDGVMIGRGALIKPWIFT 551

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            + E     ++ +             ++     +Y   H  S       TR  +
Sbjct: 552 EIKERREWDISATE----------RLQLIRDYVEYGLNHFGSDTAGVNTTRRYL 595


>gi|218662153|ref|ZP_03518083.1| tRNA-dihydrouridine synthase protein [Rhizobium etli IE4771]
          Length = 241

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 54/227 (23%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI  D G + I++N+GCP+ +V  G  G+ LM +PD+    I A  KA+ IPVT+K R+
Sbjct: 1   AKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDLALGLIEATVKAVDIPVTLKMRL 60

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D+   ++   ++ +  + +G+  + IH R  +               D+D ++ + ++
Sbjct: 61  GWDE--NSINAPDIARRAEAAGIQLVTIHGRTRM--------QFYEGRADWDAIHAV-RD 109

Query: 186 NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              + +  NG +E  + A +IL     D VMIGR                +  L G++  
Sbjct: 110 VISIPLIANGDVETAADAQEILRRSGADAVMIGRGCQGRPWH--------AGVLAGAAEP 161

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +     D   +    M D+          ++   +H+      F  +
Sbjct: 162 RREDIADIAVEHYRMMLDFYGE----AVAIRHARKHLGWYLERFAPA 204


>gi|260943748|ref|XP_002616172.1| hypothetical protein CLUG_03413 [Clavispora lusitaniae ATCC 42720]
 gi|238849821|gb|EEQ39285.1| hypothetical protein CLUG_03413 [Clavispora lusitaniae ATCC 42720]
          Length = 367

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/288 (22%), Positives = 114/288 (39%), Gaps = 35/288 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   RL  N  L+Y+ MI+A   +R        FST   + PL +Q+G ++
Sbjct: 50  MVRYSKLPFRELVRLY-NTDLVYSPMILAREFVRNGTARATDFSTNSRDSPLVVQVGASN 108

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV    ++ +   + I LN GCP         GA LM  P+ V   + A+ +     
Sbjct: 109 AQDLVRFVDLIHEH-VDAIGLNCGCPIRDQVREGIGAALMSQPENVASMVRAVKEKYGAR 167

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V V+ +I +   +        VK ++++GV+ I +H R    +   P         ++  
Sbjct: 168 VLVETKIRIHPDLQ--ETLRWVKLVEEAGVDWITVHGRTRTTRSSQP--------ANWAA 217

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT-------- 228
           + E+KK    + +  NG    +  A ++      DGVM  R    N A+ +         
Sbjct: 218 IAEVKKAA-SVPVVANGDCFSLEDARRMARETGCDGVMAVRGILANPALFSGRARPPWGA 276

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           V+ +F    +   P +          ++          L S   L++ 
Sbjct: 277 VEHFFDLAASYGLPFR----------VAQHHLAQMMEQLVSRRYLREF 314


>gi|303325730|ref|ZP_07356173.1| dihydrouridine synthase family protein [Desulfovibrio sp. 3_1_syn3]
 gi|302863646|gb|EFL86577.1| dihydrouridine synthase family protein [Desulfovibrio sp. 3_1_syn3]
          Length = 334

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 110/301 (36%), Gaps = 23/301 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+ A  ++       ++L    +++PL +Q+ GA+ 
Sbjct: 30  AGYSDLPFRLLCREY-GAAVCVTEMVSAKGLVYQSPGTNDLLVSLPEDQPLVVQLFGAEA 88

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
             L  A  ++ + GY   +LN+GC   +V     GA ++ + +       AM  +A    
Sbjct: 89  DFLRRAVGLLREAGYGWFDLNMGCSVPKVLRQGAGAAMLGDLENSLAVAGAMLKEAGPGR 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G+DD      L +L   ++  G   + +H R A                D++ 
Sbjct: 149 VGFKLRLGLDDART--VLPDLALRLEDLGAGWLTLHPRTA--------RQGFGGTADWEA 198

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     L +  +G L + +  L+ L      GVM  R A     +           
Sbjct: 199 LARLK-PRLSLPLLASGDLFNAADGLRCLEQTGATGVMYARGAMHGPGIFA-AHLALCRG 256

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              + P    +     R       D A         L ++   +       P +R  R  
Sbjct: 257 ERIAEPTPAALRAMILRH-----MDLARSLCPGKAALWKMRSVVPRYVRALPGTRTLRRE 311

Query: 297 L 297
           L
Sbjct: 312 L 312


>gi|293397165|ref|ZP_06641439.1| tRNA-dihydrouridine synthase C [Serratia odorifera DSM 4582]
 gi|291420636|gb|EFE93891.1| tRNA-dihydrouridine synthase C [Serratia odorifera DSM 4582]
          Length = 311

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/319 (20%), Positives = 118/319 (36%), Gaps = 43/319 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D    ++    +  +++++G + + +H R          D  K
Sbjct: 128 AAVPAELPVTVKVRLGWDSPQHSL---EIADAVQQAGASELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D + A + +     D VM+GR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRQRLT-IPVIANGEIWDYASAQQCMQITGCDVVMLGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y    L              W ++   +  Y          L  + R    +  L  
Sbjct: 236 VVKYNEPRLP-------------WPQVVQLLKKYVRLEKQGDTGLYHVARIKQWLGYLRK 282

Query: 286 GFPNSRRCR---HILTVEA 301
            +  +         L   A
Sbjct: 283 EYAEASDLFAEVRALATSA 301


>gi|145631054|ref|ZP_01786829.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           R3021]
 gi|144983339|gb|EDJ90821.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           R3021]
          Length = 310

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF+    P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    D G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPEYLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ G   I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGRTKT-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + ++ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  WR+I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWREIQKILQKYAKVENEYDSGFYHVAR 272


>gi|72008833|ref|XP_786210.1| PREDICTED: similar to MGC79829 protein [Strongylocentrotus
           purpuratus]
 gi|115930963|ref|XP_001189238.1| PREDICTED: similar to MGC79829 protein [Strongylocentrotus
           purpuratus]
          Length = 351

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 107/238 (44%), Gaps = 23/238 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      L +T MIV D+ ++  K     F++ E  +PL +Q   ++
Sbjct: 25  MVRYSKLAFRTLVRSYD-CDLTFTPMIVCDSFVKSAKARDSEFTSNEGDRPLIVQFAASN 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CKAL 115
              L +AA++V  +  + ++LN GCP        +GACL+ +PD++ D +          
Sbjct: 84  AKDLADAAELVARYT-DGVDLNCGCPQRWAVAEGYGACLIKHPDLIKDMVQQTWNRVDRS 142

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K R+  D +        L +  + +GV+ I +H R    +G            D
Sbjct: 143 DFTTSIKIRLHKDIRETV----ELCRRAEHAGVSWITVHGRTKEQRG---------EPAD 189

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +D +  I KE   + +  NG ++ M    +I+    VDGVM  R   +N AM    D+
Sbjct: 190 HDAI-RIIKEGVGVPVVANGDVKLMEDVRRIVEQTGVDGVMSARGILRNPAMYAGYDD 246


>gi|168236343|ref|ZP_02661401.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194735562|ref|YP_002115264.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|204929001|ref|ZP_03220144.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|194711064|gb|ACF90285.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197290619|gb|EDY29974.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|204321545|gb|EDZ06744.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|322615201|gb|EFY12123.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617792|gb|EFY14688.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322624614|gb|EFY21445.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322626935|gb|EFY23731.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322634121|gb|EFY30857.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322635688|gb|EFY32398.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322640177|gb|EFY36841.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322646400|gb|EFY42912.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322649367|gb|EFY45803.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322656488|gb|EFY52777.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322661464|gb|EFY57688.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322665648|gb|EFY61832.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667172|gb|EFY63339.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322671178|gb|EFY67306.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322675182|gb|EFY71259.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322680790|gb|EFY76825.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322686965|gb|EFY82942.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323192729|gb|EFZ77956.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323198839|gb|EFZ83938.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323205151|gb|EFZ90129.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323208194|gb|EFZ93138.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323215781|gb|EGA00524.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323221280|gb|EGA05703.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323223854|gb|EGA08157.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323231227|gb|EGA15342.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233661|gb|EGA17753.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237731|gb|EGA21791.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323245714|gb|EGA29708.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323248921|gb|EGA32845.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323253007|gb|EGA36840.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323258683|gb|EGA42345.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323259515|gb|EGA43150.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323268298|gb|EGA51773.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323271913|gb|EGA55329.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
          Length = 312

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMAASGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 272


>gi|268553095|ref|XP_002634530.1| Hypothetical protein CBG08326 [Caenorhabditis briggsae]
 gi|187032698|emb|CAP28172.1| hypothetical protein CBG_08326 [Caenorhabditis briggsae AF16]
          Length = 551

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 119/299 (39%), Gaps = 31/299 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +   EM +A +IL G   + ++L     EK   +Q+ G     + 
Sbjct: 213 NLPFRRLCVDY-GADITCGEMALATSILSGAASEYSLLKRHPSEKIFGVQLAGGFADTMA 271

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTV 121
           +AA+IV E+F  + +++N+GCP   V++   G  L   P+ + + + A    L   P+TV
Sbjct: 272 KAAQIVVENFDVDFVDINMGCPIDVVNQKGGGCALPSRPNKLYEVLTATKSVLGDTPMTV 331

Query: 122 KCRIGVDDQI-PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           K R G  + I  A      +K       + I  H R         K+ R     ++D   
Sbjct: 332 KIRTGQKEGILKAPETVEFMKKNPWHCPDLITFHPRS--------KEQRYTKLANWDYTI 383

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            + +    + + + G +       + L    +V+G+MIGR A     + T +DE  +  +
Sbjct: 384 PVAEAAAPVPLWVCGDVLSWEDYYERLEKYPNVNGIMIGRGALIKPWIFTEIDERRTWDI 443

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           T +              +    T Y   H  S     + TR  +  F  F    +CR+I
Sbjct: 444 TATERF----------DLLKKFTSYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 488


>gi|237732187|ref|ZP_04562668.1| tRNA-dihydrouridine synthase C [Citrobacter sp. 30_2]
 gi|226907726|gb|EEH93644.1| tRNA-dihydrouridine synthase C [Citrobacter sp. 30_2]
          Length = 314

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 118/312 (37%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L     + L         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPAKVFHRLCPELHNNSRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAIELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D+         +  +++++G + + +H R             K
Sbjct: 128 EAVPAHLPVTVKVRLGWDNSDRQF---EIADAVQQAGASELAVHGRTKE-------QGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHINWQAIGEIRQRL-SIPVIANGEIWDWQSAQDCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++   +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVARIKQWLGYLRK 282

Query: 286 GFPNSRRCRHIL 297
            +  +      +
Sbjct: 283 EYSEATELFQEI 294


>gi|225717662|gb|ACO14677.1| tRNA-dihydrouridine synthase 4-like [Caligus clemensi]
          Length = 308

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/280 (23%), Positives = 117/280 (41%), Gaps = 33/280 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGA 57
           MV ++   +R    L     + ++ MI+AD+ +   +     F+T    ++PL +Q    
Sbjct: 20  MVRYSKLPFRRLI-LSYGADVAFSPMILADSFVSSPEARFNEFTTDPLRDRPLIVQFASK 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            +   V AA++V       ++LN GCP         GA L+  P+ + D + +       
Sbjct: 79  SVDDFVSAAQLVAPH-AEGVDLNCGCPQGWAIREGIGAALLQRPEFISDVVRSTKNRTQH 137

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           S+ V+VK R+  D +       +LVK+++ +G + I +H R         KD +    +D
Sbjct: 138 SLSVSVKIRLQKDHRRTW----DLVKAVENAGADFITVHGRT--------KDQQSGDPVD 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + V  +K E+  + +  NG ++ +     ++ L  VDGVM  R   +N AM        
Sbjct: 186 LEGVKYVK-ESLSIPVVANGDIKSLHEAHCVRELTGVDGVMAARGLLENPAMYA------ 238

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
                G         +D+ R    + T +   H H    L
Sbjct: 239 -----GYGITPKECVEDWLRISLETGTPFQTFHHHLSYML 273


>gi|261343438|ref|ZP_05971083.1| tRNA-dihydrouridine synthase [Providencia rustigianii DSM 4541]
 gi|282568584|gb|EFB74119.1| tRNA-dihydrouridine synthase [Providencia rustigianii DSM 4541]
          Length = 319

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/305 (20%), Positives = 110/305 (36%), Gaps = 40/305 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRSLLSEVNDYDLCITEFVRVVDTLLPEKTFYRLCPELRHGSRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  P+ +     AM 
Sbjct: 68  QLLGQHPEWLAENANRAIELGSWGVDLNCGCPSKTVNGSGGGATLLKQPESIYRAAKAMR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PV+VK R+G D    +     +  + +++GV  + +H R          D  K
Sbjct: 128 DAVPKELPVSVKVRLGWD---SSQFSHEIADAAQQAGVTELTVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A + +     D +MIGR A     +   
Sbjct: 178 AECINWQAIGDIRQRL-SIPVIANGEIWDYESAKRCMEITGCDSIMIGRGALNTPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA-RHLHSGGKLQQIT-RHMIGLF-H 285
                      S  IK  V +  W ++   +  Y     L   G       +  +G    
Sbjct: 234 -----------SRVIKQNVAQMPWEQVGKLLFKYTELEKLGDTGHYHAARIKQWLGYLRK 282

Query: 286 GFPNS 290
            +P +
Sbjct: 283 EYPQA 287


>gi|251790102|ref|YP_003004823.1| tRNA-dihydrouridine synthase C [Dickeya zeae Ech1591]
 gi|247538723|gb|ACT07344.1| dihydrouridine synthase DuS [Dickeya zeae Ech1591]
          Length = 311

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDSRLPVKAFYRLCPELRHGSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKMVNGSGGGATLLKDPDLIYRAAKAMR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  S+PVTVK R+G D          +  ++ ++G + + +H R          D  +
Sbjct: 128 EAVPSSLPVTVKVRLGWDSGERRF---EIADAVAQAGASELVVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRRRL-RIPVIANGEIWDWQSAQDCMAATGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y             R  +  W  +   +  Y          L  + R
Sbjct: 236 VIKY-------------REARMPWPDVVQLLQKYVRLEKQGDTGLYHVAR 272


>gi|168259485|ref|ZP_02681458.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205350920|gb|EDZ37551.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 312

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|198242215|ref|YP_002216259.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|197936731|gb|ACH74064.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
          Length = 312

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHYASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|225561353|gb|EEH09633.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus G186AR]
          Length = 583

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 113/325 (34%), Gaps = 68/325 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNA------LLYTEMIVADAILRGDKKNILGFSTQ-------- 46
           MVD ++  +R   R   N        L Y+ M  +          +  F           
Sbjct: 29  MVDRSEFAWRMLTRSFMNPDSDSPPLLAYSPMFHSRLFKESPNYRLQHFEATRPRSKTPT 88

Query: 47  --------------------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
                                     ++PL +Q    +  +L++AA+ VE F  + ++LN
Sbjct: 89  TPAANDIDGGAPQSNTIPYLDGNPSFDRPLIVQFCANNPDELLQAARAVEPF-CDAVDLN 147

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G +GA L  +PD++ + I  +   LSIPVT K RI    Q          
Sbjct: 148 LGCPQGIARKGHYGAFLQEHPDLIYELINTLHTQLSIPVTAKFRI----QETKEKTLEYA 203

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLED 199
           + I  +G + I +H R+   KG            D+  +  +++  P D  I  NG + +
Sbjct: 204 RIILSAGASIITVHGRRREQKG------HNTGLADWSYIRYLRENLPADTVIFANGNILN 257

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
                K L     DGVM    +  +  + +              P  + V     R    
Sbjct: 258 HGDIEKCLEATGADGVMSAEGSLCDPTIFSG------------PPPSSSVGGSGMRGEKR 305

Query: 258 SMTDYAARHLHSGGKLQQ--ITRHM 280
              +Y       GG      + R+M
Sbjct: 306 DGAEYWVGRDGKGGYRVDFVLRRYM 330


>gi|323213523|gb|EFZ98314.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
          Length = 331

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMAASGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++ A +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVAR 291


>gi|290508567|ref|ZP_06547938.1| tRNA-dihydrouridine synthase C [Klebsiella sp. 1_1_55]
 gi|289777961|gb|EFD85958.1| tRNA-dihydrouridine synthase C [Klebsiella sp. 1_1_55]
          Length = 310

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKSFYRLCPELHHQSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPDHLPVTVKVRLGWDSGERRF---EIADAVQQAGASELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRLT-IPVVANGEIGDWQSAQDCMAVTGCDSVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPQVVQLLQKYTRLEKQGDTGLYHVAR 272


>gi|221194516|ref|ZP_03567573.1| tRNA-dihydrouridine synthase B [Atopobium rimae ATCC 49626]
 gi|221185420|gb|EEE17810.1| tRNA-dihydrouridine synthase B [Atopobium rimae ATCC 49626]
          Length = 361

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 60/301 (19%), Positives = 113/301 (37%), Gaps = 28/301 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   +D  Y          AL YTEM+    I  G +K   ++     E  +A+Q+ G+ 
Sbjct: 45  MAGVSDGAY-RLLARAGGAALAYTEMVSVAGIHFGGEKTWQLVYPLDPEPDIAVQLFGSK 103

Query: 59  ISKLVEAA-KIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  EAA +I E  G     I++N+ CP  +V +   G+ L+ NP    + + A    +
Sbjct: 104 PEQFREAASQIAERLGPKLALIDINMACPVPKVVKKGEGSALLDNPVRAAEIVRACISEV 163

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PVT K R G    + +       ++++ +G   + +H R A                D
Sbjct: 164 DVPVTAKIRRG--RTVGSECAPEFARALEAAGAAAVTVHGRFA--------SQLYQGKAD 213

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ V  +      + +  +G +     A ++L    +  VM+ R  Y +  +        
Sbjct: 214 WNCVERVVCAV-SIPVIGSGDVMSAHDAARVLKTTGISAVMLARGTYGDPWIFANTRRAC 272

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           +       P  ++    F   +   + + A  H+     L          F G P++   
Sbjct: 273 AEKELFC-PTLSQRLSAFKLHV--HLLEAAHIHIARARSLS------TWYFRGVPHAAYW 323

Query: 294 R 294
           R
Sbjct: 324 R 324


>gi|307110102|gb|EFN58339.1| hypothetical protein CHLNCDRAFT_16859 [Chlorella variabilis]
          Length = 308

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 98/232 (42%), Gaps = 17/232 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A   L         F+T  Q++PL  Q    D
Sbjct: 18  MVDQSELAFRQLTRRHGATG-AYTPMLHARLFLETPSYRAEHFTTTQQDRPLLAQFCAND 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ AA++V     + ++LN+GCP      G +G+ LM +  +V   +  +   L++P
Sbjct: 77  PDILLSAARLVAPH-VDGVDLNLGCPQRIAKRGKYGSFLMDDLPLVERLVRQLAANLAVP 135

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R                + ++++G + + IH R    K  S          + + 
Sbjct: 136 VTVKIRRF----DCVQRTVQYAQMLERAGASLLAIHGRTREQKRASEV------RAEVEY 185

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
           +  +K+    + +  NG +  ++    ++    VDGVM   +   + A+ + 
Sbjct: 186 IRAVKQGL-RIPVLGNGNIRTLADCEALMAATGVDGVMSAESLLADPALFSQ 236


>gi|148228148|ref|NP_001089272.1| dihydrouridine synthase 4-like [Xenopus laevis]
 gi|58702004|gb|AAH90192.1| MGC85035 protein [Xenopus laevis]
          Length = 308

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 118/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT MI+A   ++  K     F+T   + PL +Q    +
Sbjct: 24  MVRYSKLAFRTLVRKYD-CDLCYTPMIIAADFVKSVKARDSEFTTNQGDCPLIVQFAAKE 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
              L +AA +V  F  + I+LN GCP        +GACL+ NP++V D +  +   +   
Sbjct: 83  AQVLADAASLVSPF-ASGIDLNCGCPQRWAMAEGYGACLINNPELVSDMVRQVRNQVGSS 141

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              +++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 142 EFTISIKIRIHADISRTV----DLCRKAEAAGVSWITVHGRTHDERHQ---------PVH 188

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  IK E+  + I  NG ++ + +A  +  +   DGVM  R    N AM      Y 
Sbjct: 189 YNAIKNIK-ESLSIPIVANGDIKSLKEAENIHQITGADGVMAARGLLANPAMFAG---YE 244

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
             PL           +D+        T +   H H    +++IT
Sbjct: 245 ETPLA--------CIQDWVDIALEHGTPFTCLHHHLMYMMERIT 280


>gi|322715236|gb|EFZ06807.1| Dihydrouridine synthase, DuS [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 312

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|292487710|ref|YP_003530583.1| putative regulator protein [Erwinia amylovora CFBP1430]
 gi|292898945|ref|YP_003538314.1| tRNA-dihydrouridine synthase C [Erwinia amylovora ATCC 49946]
 gi|291198793|emb|CBJ45902.1| tRNA-dihydrouridine synthase C [Erwinia amylovora ATCC 49946]
 gi|291553130|emb|CBA20175.1| putative regulator protein [Erwinia amylovora CFBP1430]
          Length = 310

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 114/290 (39%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V DA+L       L         +     + +
Sbjct: 8   MEGVLDSLVRELLTDVNDYDLCITEFLRVVDALLPVKCFQRLCPELNNASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R          +  +
Sbjct: 128 AAVPDHLPVTVKVRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------EGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGEIRQRL-NIPVIANGEIRDWQSAQECMAMTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y   P+              W ++   +  Y          L  + R
Sbjct: 236 VIKYREPPMA-------------WPQVVQLLQRYVRLEKQGDTGLYHVAR 272


>gi|83032642|ref|XP_729128.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]
 gi|23486029|gb|EAA20693.1| Drosophila melanogaster CG3645 gene product [Plasmodium yoelii
           yoelii]
          Length = 338

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 103/231 (44%), Gaps = 16/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ +   +   K  I  F    Q+KPL  Q  G D
Sbjct: 32  MVDLSELPFRLLCRNY-NCDLAFTPMLHSKNFVEHSKYRIGYFKKCDQDKPLIAQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S +++A   ++D   N +++N+GCP     +G++GA L+   D V + I+ +    ++P
Sbjct: 91  PSTILKAIDYIKD-DVNGVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLISDITNNCNVP 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R   +D        NL   ++   V  I +H R    KG+       I   DY+I
Sbjct: 150 ISCKIRKIDND---YQKTLNLCYDLQSRNVKMITVHGRTKEEKGV------NIKECDYEI 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  I KE  ++ I  NG +E      K L     D VM      +  +  +
Sbjct: 201 IK-IIKERLNIPIIANGSIEHFEDIEKCLNYTKTDAVMCAEILLEKPSFFS 250


>gi|326624009|gb|EGE30354.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
          Length = 316

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 12  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHYASRTPSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 132 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 276


>gi|326484320|gb|EGE08330.1| tRNA-dihydrouridine synthase [Trichophyton equinum CBS 127.97]
          Length = 566

 Score =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 59/283 (20%), Positives = 103/283 (36%), Gaps = 54/283 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGFST---------- 45
           MVD ++  +R   R           L Y+ M  A             F            
Sbjct: 57  MVDRSEFAWRMLTRSFMKEGSPTPILAYSPMFHARFFNDAPTYRTQHFEPVRQTKKAGTD 116

Query: 46  -------------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         ++PL +Q    D  +L++AA+ VE+   + ++LN+GCP     +G 
Sbjct: 117 ENTTEPYLDGNPKHDRPLIVQFCANDPDELLKAARHVEEH-CDAVDLNLGCPQGIAKKGH 175

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L  +PD++   I  +   LSIPVT K RI               + I  +G + + 
Sbjct: 176 YGAFLQEDPDLIYKLINKLHNELSIPVTAKFRIL----ETKEKTLEYARMILSAGASILS 231

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PS 209
           +H R+   KG S          +++ +  ++    P+  I  NG + + S   + L    
Sbjct: 232 VHGRRREQKGHST------GVANWEYIRYLRDNLPPETVIFANGNILNHSDINRCLEVTG 285

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
            DGVM       +  + +            + P      + +W
Sbjct: 286 ADGVMSAEGNLSDPTIFS------------TPPAPGEEGRIYW 316


>gi|294655199|ref|XP_002770100.1| DEHA2B07942p [Debaryomyces hansenii CBS767]
 gi|199429763|emb|CAR65470.1| DEHA2B07942p [Debaryomyces hansenii]
          Length = 364

 Score =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 103/231 (44%), Gaps = 17/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R D   +  F+T   ++ + +Q+G  +
Sbjct: 55  MVRYSKLPFRELVRNF-NTDIVYTPMILAREFVRNDIARLSDFTTNAGDRSVIVQVGCNN 113

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++   ++  +  + I LN GCP         GA LM  P++V   + A+       
Sbjct: 114 VKDLLKFVDMIHPY-VDGIGLNCGCPIKEQVREGIGAALMSEPELVSSMVKAVKDKYKDS 172

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I +   I        VK ++K+GV+ I +H R         K+ R     ++D 
Sbjct: 173 VVIETKIRIHPDIN--ETIKFVKLVEKNGVDFITVHGRT--------KNTRSSQPANFDA 222

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  IK E+  + +  NG    +  A +I     VDG+M  R    N  +  
Sbjct: 223 IKAIK-ESVAVPVVANGDCFSLKDAYEIAEYTGVDGIMAVRGILSNPGLFG 272


>gi|212704120|ref|ZP_03312248.1| hypothetical protein DESPIG_02175 [Desulfovibrio piger ATCC 29098]
 gi|212672480|gb|EEB32963.1| hypothetical protein DESPIG_02175 [Desulfovibrio piger ATCC 29098]
          Length = 332

 Score =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 115/299 (38%), Gaps = 25/299 (8%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
             ++D  +R   R     A+  TEM+ A  ++        +L    +++PL +Q+ GA+ 
Sbjct: 31  AGYSDLPFRLLCRRY-GAAVCVTEMVSAKGLVYRSPGTGELLQSLPEDQPLVVQLFGAEA 89

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIP 118
           S L  + +++ D GY   +LN+GC  A+V +   GA ++ +     +   AM   A    
Sbjct: 90  SFLQRSVEMLRDVGYGWFDLNMGCSVAKVLKQGAGAAMLGDVPNALEVARAMLRAAGPGR 149

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  K R+G+D +      R+L   ++  G   I +H R A                 +++
Sbjct: 150 VGFKIRLGLDSRRH--VWRDLSLRLQDLGAGWITLHPRTA--------RQGFGGEAAHEV 199

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE-YFSN 235
           + E+K+   D+ +  +G L      L++L    VD VM  R A    A+    D      
Sbjct: 200 LAELKQAL-DIPLIASGDLFSARDGLRVLDQTGVDTVMYARGAMHGPAIFD--DHLRLCR 256

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR 294
                SP    +     R       + A         L ++   +       P  +  R
Sbjct: 257 GEEPQSPTPAALRAMVLRH-----MELAQELCPGRAALWKMRSVVPRYVRSLPGVKALR 310


>gi|308485393|ref|XP_003104895.1| hypothetical protein CRE_24419 [Caenorhabditis remanei]
 gi|308257216|gb|EFP01169.1| hypothetical protein CRE_24419 [Caenorhabditis remanei]
          Length = 304

 Score =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 64/282 (22%), Positives = 111/282 (39%), Gaps = 36/282 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   RL   + + YT MI A   +     + + L    ++ PL +Q    D
Sbjct: 20  MVRYSKLAFRQLVRLYDVD-VCYTPMIYAKNFIESEKCRNSELSICERDSPLIVQFATDD 78

Query: 59  ISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
              L EAA++V  +G +  +++N GCP   V    FG+ L+  P+++ D I      +S 
Sbjct: 79  PIVLAEAAEMV--YGCSTGVDVNCGCPKHDVRSKGFGSALLNKPELLADMIRQTRARISD 136

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
               V++K R+  D +       +L +  + +GV  + +H R                 +
Sbjct: 137 TEFSVSLKIRVNSDIERTV----DLCRKAESAGVTHLTVHGRTPSQH---------AEPI 183

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           D   +  I KE+  + +  NGG+    +A  L     VDG+M       N A+       
Sbjct: 184 DIQAI-RIVKESVSVPVIANGGITTREEALFLAEQTGVDGIMAANGLLDNPALFA----- 237

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                 G     +   + F R       D+   H H    L+
Sbjct: 238 ------GYEYTPSDCVEHFMRLSREHGLDWLLYHQHLQYMLR 273


>gi|62180761|ref|YP_217178.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|197264574|ref|ZP_03164648.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|62128394|gb|AAX66097.1| putative nitrogen regulation protein [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|197242829|gb|EDY25449.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
          Length = 312

 Score =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|296476150|gb|DAA18265.1| PP3111 protein [Bos taurus]
          Length = 266

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 96/230 (41%), Gaps = 19/230 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAHLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           + +  ++K    + +  NG ++ +    + +    V GVM    A  + A
Sbjct: 192 EHIKAVRKAVT-IPVFANGNIQCLRDVERCIQDTGVQGVMSAGEAVPSPA 240


>gi|223938646|ref|ZP_03630536.1| dihydrouridine synthase DuS [bacterium Ellin514]
 gi|223892634|gb|EEF59105.1| dihydrouridine synthase DuS [bacterium Ellin514]
          Length = 340

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 59/287 (20%), Positives = 109/287 (37%), Gaps = 22/287 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE--MIVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +        +  + YTE   +   + L       +  +   +P+  Q+ G D
Sbjct: 14  MQDVTDLPFMKVISSYGSADVYYTEYFRVHGSSNLEKWILESITKNPTGQPVIAQMIGND 73

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  LV +AK ++ +    ++LN+GCP+  V+    G  L+  P  V   + A+  A+S+ 
Sbjct: 74  IPSLVRSAKELQQYPIVAVDLNLGCPAPIVYRKCAGGGLLREPKRVDSILGALRDAISVK 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TVK RIG D          L+    K  ++ + +H R       S         + YD 
Sbjct: 134 FTVKTRIGFD---STGVFDELLPIFAKHSIDLLTVHGRTVQEMYRS--------EVHYDF 182

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +    +      +  NG +    +A ++L      G+MIGR   +N  +   +  +    
Sbjct: 183 IARAAQAV-SCPVLANGNVYSAKKAEEVLQFTGARGLMIGRGVIRNPWLFHQIRHHRRG- 240

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
                PI      D  + I           +    ++Q++ +  +  
Sbjct: 241 ----EPIFIPKGHDVLQYIRTLYDAVRPPDIRELAQVQKM-KKYLNY 282


>gi|71004722|ref|XP_757027.1| hypothetical protein UM00880.1 [Ustilago maydis 521]
 gi|46096397|gb|EAK81630.1| hypothetical protein UM00880.1 [Ustilago maydis 521]
          Length = 527

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 73/356 (20%), Positives = 129/356 (36%), Gaps = 62/356 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---------NILGFSTQE---- 47
           MVD ++  +R  +R   ++ L+YT MI A      + K         N      +E    
Sbjct: 56  MVDQSELAWRILSRRYGSD-LVYTPMINAKLFADENSKKKKVKYQEVNFNREHAEEGASS 114

Query: 48  ------------------KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
                             +PL +Q    D   L++AAK+VED   + ++LN+GCP     
Sbjct: 115 PIASLLSNEGEGSSKDTDRPLFVQFCSNDPETLLKAAKVVEDR-CDAVDLNLGCPQHIAR 173

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +G+ LM +  ++   I  +   L +PVT K R+               + ++++G  
Sbjct: 174 RGHYGSYLMEDWSLIFSLINILHVNLKVPVTAKMRVY----ESVEKTITYARLLERAGAQ 229

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
            I +H R   +KG            D+  +  +K E  ++ +  NG +         L  
Sbjct: 230 IITVHGRTRNMKG------HLTGLADWAKIRAVK-EAVNVPVFANGNVLYPQDFYDALAA 282

Query: 208 PSVDGVMIGRAAYKNSAML-----TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
              DGVM       N A++           F N      P   ++  ++   + +  T  
Sbjct: 283 TGADGVMSAEGNLYNPAIMLPNPPKQPSAMFPNAPELPLPSIVKMAHEYLDIVCSLRTPT 342

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV---EAGASTATHHIIETAF 315
            +  + +   L ++ R  +         R  R  L     +  AS A   +   AF
Sbjct: 343 QSSAIKA--HLFRLCRPAL------EVHRDLREQLGKSHFDHTASGADKIVTYRAF 390


>gi|194444008|ref|YP_002041446.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|200388326|ref|ZP_03214938.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|194402671|gb|ACF62893.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|199605424|gb|EDZ03969.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
          Length = 331

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|260773041|ref|ZP_05881957.1| tRNA-dihydrouridine synthase C [Vibrio metschnikovii CIP 69.14]
 gi|260612180|gb|EEX37383.1| tRNA-dihydrouridine synthase C [Vibrio metschnikovii CIP 69.14]
          Length = 348

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/312 (18%), Positives = 124/312 (39%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILG------FSTQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 41  MEGVLDHLMRQMLTEINDYDFCVTEFVRVVNLLLPDHVFYRLCPELKHASRTQSGTPIKV 100

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 101 QLLGQEPQWMAENAVRAAELGAYGVDLNFGCPAKMVNKSKGGAALLQHPELIYQVVKACR 160

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D        ++V ++ ++G + + +HAR             K
Sbjct: 161 DAVPKHIPVSAKIRLGWEDPNDCF---DIVDAVTQAGADELTVHARTK-------AGGYK 210

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++++  + +  NG + + + A   +    VD +M+ R A  N   L  
Sbjct: 211 ASEIQWDYIDQIRQKST-IPLIANGEIWNYADAQACISTTGVDSLMVCRGAL-NIPNLGN 268

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           + +Y   P+              W ++   + +Y+A  +          ++ +    L  
Sbjct: 269 IVKYNHAPMP-------------WNQVVELLLEYSAYEVRGDKGRYYPNRVKQWFSYLRQ 315

Query: 286 GFPNSRRCRHIL 297
            +P +      +
Sbjct: 316 AYPEAAELFREI 327


>gi|161613134|ref|YP_001587099.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|161362498|gb|ABX66266.1| hypothetical protein SPAB_00842 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 331

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHYASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|224583325|ref|YP_002637123.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|224467852|gb|ACN45682.1| hypothetical protein SPC_1528 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
          Length = 316

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 12  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 132 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 276


>gi|168242260|ref|ZP_02667192.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194448667|ref|YP_002046228.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194406971|gb|ACF67190.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205338332|gb|EDZ25096.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 312

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|56412912|ref|YP_149987.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197361843|ref|YP_002141479.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56127169|gb|AAV76675.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197093319|emb|CAR58767.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 312

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMSWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|114563584|ref|YP_751097.1| dihydrouridine synthase, DuS [Shewanella frigidimarina NCIMB 400]
 gi|114334877|gb|ABI72259.1| dihydrouridine synthase, DuS [Shewanella frigidimarina NCIMB 400]
          Length = 314

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 70/338 (20%), Positives = 135/338 (39%), Gaps = 50/338 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D H R     +    L+ TE +      + D +       +L  G +    P+ +
Sbjct: 8   MEGVVDDHMREILSAINPFDLVVTEFVRVVNQLIPDKVFYKLCPELLHQGLTASGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + + A    + G N ++ N GCP+  V++   GA L+  P+ +   + AM 
Sbjct: 68  QLLGQEPEWMAQNAIRAIELGSNGVDANFGCPAKTVNKSKGGAVLLQYPENIYSIVKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PVT K R+G +D+           ++ ++G   + IHAR         K +  
Sbjct: 128 DAVPSEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARS--------KTDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E+++  P + +  NG + + + A + +     D +MIGR A     +  T
Sbjct: 177 KPPAYWEYITEVRQRLP-IPVIANGEIWNAADAQRCMDVTGCDSIMIGRGAISLPNLGDT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGLFH 285
           +        TG++P         W++  + +  Y  + L+   S     +I +    L  
Sbjct: 236 IK-------TGATPFS-------WQQTLSLLMAYTDKELNGRKSDYYPSRIKQWFSYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETAFNLMI 319
            +P +    R  R   T E         +++ A   +I
Sbjct: 282 QYPEADTLFRELRVFKTTEEIVK-----VLQHAHRSLI 314


>gi|284922125|emb|CBG35206.1| tRNA-dihydrouridine synthase C [Escherichia coli 042]
          Length = 315

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 67/338 (19%), Positives = 124/338 (36%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPIKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+       L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLSQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EVVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 236 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM-IESL 322
            +  +      + V   +       I  A   + IE L
Sbjct: 283 EYDEATELFQHVRVLNNSPD-----IARAIQAIDIEKL 315


>gi|320086613|emb|CBY96384.1| tRNA-dihydrouridine synthase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 316

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 12  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQYPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 132 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 276


>gi|312171823|emb|CBX80080.1| putative regulator protein [Erwinia amylovora ATCC BAA-2158]
          Length = 310

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 113/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V DA+L       L         +     + +
Sbjct: 8   MEGVLDSLVRELLTDVNDYDLCITEFLRVVDALLPVKCFQRLCPELNNASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R          +  +
Sbjct: 128 AAVPDHLPVTVKVRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------EGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A +   +   D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGEIRQRLT-IPVIANGEIRDWQSAQECMAMTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y   P+              W ++   +  Y          L  + R
Sbjct: 236 VIKYREPPMA-------------WPQVVQLLQRYVRLEKQGDTGLYHVAR 272


>gi|205353310|ref|YP_002227111.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207857608|ref|YP_002244259.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|238912616|ref|ZP_04656453.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|205273091|emb|CAR38045.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|206709411|emb|CAR33752.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
          Length = 312

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|156536943|ref|XP_001608232.1| PREDICTED: similar to MGC79829 protein [Nasonia vitripennis]
          Length = 346

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/278 (22%), Positives = 119/278 (42%), Gaps = 31/278 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R      + +T MI+AD+ ++  K     FST E   PL +Q    +
Sbjct: 21  MVRYSKLPFRTLVRKYD-CDICFTPMILADSFVQSSKARDSEFSTNEGDSPLIVQFAAKE 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   VEA ++V  +  N ++LN GCP     +  +GA L+  P +V + ++ +   +  P
Sbjct: 80  VDDFVEATEMVAPYS-NGVDLNCGCPQRWALKDGYGADLLTKPQLVKELVSNVRNRIPKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I         ++I+ +GV+ + +HAR   ++            +D D 
Sbjct: 139 FTVSVKIRILKDIKKTI--EFSRAIEHAGVSFLTVHARTPDMRN---------EPIDLDS 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  + +    L +  NG +     A  +      +GVM+      N A+ +         
Sbjct: 188 LK-LVRSCVHLPMIANGNVRSFEDAKTLYEESKCNGVMVAGGILTNPAIFSGYK------ 240

Query: 237 LTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGKL 273
              ++P++   D   W  I+++M T +   H H    L
Sbjct: 241 ---NTPVECIQD---WLDITSTMSTQFMCMHHHLVFML 272


>gi|241955235|ref|XP_002420338.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223643680|emb|CAX41413.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 340

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 57/272 (20%), Positives = 108/272 (39%), Gaps = 27/272 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R +      F+T   +K + +Q+G  +
Sbjct: 33  MVRYSKLPFRELCRFYDVD-IVYTPMILAREFVRNEVARSTDFTTNDSDKCVIVQVGVNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   ++  +++  F  + I +N GCP         GA LM +PD+V + I          
Sbjct: 92  VEDFMKFIEMIHPF-VDGIGINCGCPIKEQVREGIGAALMSDPDLVAELIKTAKCKYGDS 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + +  +I +   I      + V  + ++G + + +H R         K+ R    ++ D 
Sbjct: 151 ICIDTKIRIHRDINQTI--DFVNKVVEAGTDMLTVHGRT--------KNTRSSVPVNLDA 200

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I+     + +  NG    ++   KI     VDGVM  R    N A+           
Sbjct: 201 IKIIRDNVSSIPVIANGDCFTLTDFQKIVAYTGVDGVMSARGVLANPALF---------- 250

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            TG +       + F   ++A    Y     H
Sbjct: 251 -TGLNKTPWSAVEMFLHLVTAYGLPYKLAQYH 281


>gi|197105195|ref|YP_002130572.1| tRNA-dihydrouridine synthase, nifR3 [Phenylobacterium zucineum
           HLK1]
 gi|196478615|gb|ACG78143.1| tRNA-dihydrouridine synthase, nifR3 [Phenylobacterium zucineum
           HLK1]
          Length = 334

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 112/292 (38%), Gaps = 22/292 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   +D  +R  A      A + TEM+      +G    +   +  +  PL  +Q+ G D
Sbjct: 21  MTGVSDLPFRKAAS-AQGAAYVATEMVACAEFSKGRPDVVRRAAVGEGLPLMVVQLVGRD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              + + A++    G   ++LN GCP+  V     G+ LM  P++    +AA  +A+ +P
Sbjct: 80  PEHIRQGARLAAQAGAQIVDLNFGCPAKEVTGVLSGSALMREPELAARLMAAAVEAVDVP 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK R+G DD            + +  GV  + +H R         +        D+  
Sbjct: 140 VTVKMRLGWDDASRNAPEI--AAAAEAIGVQAVTVHGRT--------RCQFYKGAADWSA 189

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V  +K     + + +NG + D   ++A       D VM+GR  Y    +   ++   +  
Sbjct: 190 VRAVK-AAVSIPVIVNGDIVDGTTAKAALAASGADAVMVGRGVYGKPWVAAQIEAELAGR 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                    R+      +I+ S    + +       L+   +H+       P
Sbjct: 249 RFEEPDAPARL------EIALSHFRESLKFYGDRLGLRIFRKHLASYIENAP 294


>gi|154282457|ref|XP_001542024.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
 gi|150410204|gb|EDN05592.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
          Length = 584

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 68/325 (20%), Positives = 111/325 (34%), Gaps = 68/325 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNA------LLYTEMIVADAILRGDKKNILGFSTQ-------- 46
           MVD ++  +R   R   N        L Y+ M  +          +  F           
Sbjct: 29  MVDRSEFAWRMLTRSFMNPDSDSPPLLAYSPMFHSRLFKESPNYRLQHFEATRPRSKTHN 88

Query: 47  --------------------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
                                     ++PL +Q    +   L++AA+ VE F  + ++LN
Sbjct: 89  PPAANDIDGGAPQSNTIPYLDGNPSFDRPLIVQFCANNPDDLLQAARAVEPF-CDAVDLN 147

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G +GA L  +PD++ + I  +   LSIPVT K RI    Q          
Sbjct: 148 LGCPQGIARKGHYGAFLQEHPDLIYELINTLHTQLSIPVTAKFRI----QETKEKTLEYA 203

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLED 199
           + I  +G + I +H R+   KG            D+  +  +++  P D  I  NG + +
Sbjct: 204 RMILSAGASIITVHGRRREQKG------HNTGLADWSYIRYLRENLPADTVIFANGNILN 257

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
                K L     DGVM       +  + +              P  + V     R    
Sbjct: 258 HGDIEKCLEATGADGVMSAEGNLCDPTIFSG------------PPPSSSVGGSGMRGEER 305

Query: 258 SMTDYAARHLHSGGKLQQ--ITRHM 280
              +Y       GG      + R+M
Sbjct: 306 DGAEYWVGRDRKGGYRVDFVLRRYM 330


>gi|145640201|ref|ZP_01795785.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|145274787|gb|EDK14649.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 22.4-21]
          Length = 310

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A    D G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQNPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ GV  I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGVTEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWYEIQKILQKYANVENEYDSGFYHVAR 272


>gi|15603745|ref|NP_246819.1| hypothetical protein PM1880 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|38605040|sp|Q9CJW1|DUSC_PASMU RecName: Full=tRNA-dihydrouridine synthase C
 gi|12722310|gb|AAK03964.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 312

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/314 (19%), Positives = 116/314 (36%), Gaps = 40/314 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +    L  +E +  V   +       +       G +    P+ +
Sbjct: 8   MQGVLDPFVRQLLTQVNQYDLCVSEFVRVVDQLLPTKVFYRLCPELYQQGLTASGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A+   + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPQWLAENAQRAIELGSHGIDLNCGCPSKTVNGSNGGASLLKQPELIYHATKALR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PV+VK R+G D+   A     +  ++++ G   I IH R  +       D  +
Sbjct: 128 AAVPKALPVSVKVRLGWDNSEQAF---EIADAVQQGGATEITIHGRTKM-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + ++++    + +  NG + D       L       +MIGR A  N   L+ 
Sbjct: 178 ADRINWAKINDVRQRL-SIPVIANGEIWDWQSGQACLAETGCQDLMIGRGAL-NIPNLSQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR--HMIGLF-H 285
           V ++                K  W ++   +  YA            + R    +G    
Sbjct: 236 VVKF-------------NQAKMPWAEVLILLHQYAHTENQFDTGFYHVARIKQWLGYLKK 282

Query: 286 GFPNSRRCRHILTV 299
            +P +     ++  
Sbjct: 283 AYPQADALFQLIKT 296


>gi|328868434|gb|EGG16812.1| tRNA-dihydrouridine synthase 4-like protein [Dictyostelium
           fasciculatum]
          Length = 346

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 64/275 (23%), Positives = 114/275 (41%), Gaps = 28/275 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +      L ++ M++A++  R +      F+T   +  L +Q    D
Sbjct: 63  MVRFSKLPFRLLCKKW-GCDLTFSPMLLAESFNRSEFARDSDFTTNQFDNSLIVQFAAND 121

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSI 117
             +L  A + V +     +++N GCP   +   + GA L+  P+ + + I     +  +I
Sbjct: 122 GEELSAAVEKVANH-CQGVDINCGCPQKWIIRENMGAGLLTTPEKIEEMIKTTTRRITNI 180

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+++K RI  D          L K  +++GV+ I +H R            R    +DYD
Sbjct: 181 PLSIKIRIQKDMS----QTIELAKRAERAGVSWITVHGRT--------SSQRSSHPVDYD 228

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +K+    + +  NG +  + QA  ++    V+GVM  R    N A+      Y   
Sbjct: 229 AIKLVKESIG-IPVFANGDIFTLDQANDIRDKTKVNGVMSARGILCNPAL------YMGY 281

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
             T    IK  +  D   +I    TD   RHL   
Sbjct: 282 DTTPIECIKEFI--DINSQIGGLNTDIFHRHLMYM 314


>gi|253687922|ref|YP_003017112.1| dihydrouridine synthase DuS [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251754500|gb|ACT12576.1| dihydrouridine synthase DuS [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 310

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 57/290 (19%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCVTEFLRVVDQCLPVKSFYRLCPELHHASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGASELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A   +     D +M+GR A  N   L+ 
Sbjct: 178 AECINWQAIGKIRQRL-RIPVIANGEIWDWQSAQDCMATTGCDAIMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          +  + R
Sbjct: 236 VIKYNE-------------PRMPWPEVMLLLQKYVQLEKQGDTGMYHVAR 272


>gi|218887737|ref|YP_002437058.1| dihydrouridine synthase [Desulfovibrio vulgaris str. 'Miyazaki F']
 gi|218758691|gb|ACL09590.1| dihydrouridine synthase DuS [Desulfovibrio vulgaris str. 'Miyazaki
           F']
          Length = 383

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 91/234 (38%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---TQEKPLALQIGGA 57
           M       +R          LL+T M  A A+     +    FS    +   L  Q+ GA
Sbjct: 54  MAGLGHAAFREVVEDYGGCGLLFTGMCNARAVPTERPEKSEAFSWRAGEPPRLVCQLFGA 113

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   + E A+ V+  G+  ++LN+GC  + + +   GA L+ +P+     +AA+ +A+ I
Sbjct: 114 EPEHMAEGARRVQAEGFFGVDLNMGCSVSAIIKRGCGADLLRDPERAVRMVAAVRRAVDI 173

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G           +L +  + +G + +  H R A  +   P     I      
Sbjct: 174 PVFVKFRTGWSPDPQPAV--DLARRFEDAGADCLVFHPRVAPDRRTQPPRRAHIG----- 226

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
               + K    + +  NG +        +L     DGV +GR A     +    
Sbjct: 227 ----LVKAAVSIPVMGNGDVFTPEDCANLLDDTGCDGVSLGRIAVARPWVFAAW 276


>gi|313218109|emb|CBY41424.1| unnamed protein product [Oikopleura dioica]
          Length = 283

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 100/238 (42%), Gaps = 25/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----------EKPL 50
           MVD ++  +R  +R  +   L YT M  A   ++        F             ++PL
Sbjct: 47  MVDASELPWRVLSRRYSAE-LCYTPMFHAANYIKDATYRRENFPDTGDLEQGSPEFDRPL 105

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q    DI+    AAK+VED   + ++LN+GCP      G +GA +M +   +   I  
Sbjct: 106 FVQFCANDINAFSTAAKMVEDR-CDAVDLNLGCPQMIAKRGHYGAHMMEDWSNIRKMIEE 164

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             K   + +T K R   D+ I         K ++ +GV+ + IH R    +G        
Sbjct: 165 ARKVAKVRITAKIRKFEDESIT----LRYAKMLENAGVSLLTIHGRTRDQRG------PN 214

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
               D+ I+ ++K E   + +  NG ++ +  A+  +    VDG+M       N A+ 
Sbjct: 215 TGLADWQIIKKVK-EALRVPVVANGNIQCLQNAIDCMEQTGVDGIMTAEGNLYNPALF 271


>gi|145637129|ref|ZP_01792791.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           PittHH]
 gi|145269574|gb|EDK09515.1| Dna-J like membrane chaperone protein [Haemophilus influenzae
           PittHH]
          Length = 310

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A    D G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQNPECLAENAIRAIDLGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ G   I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L        M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDFMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWYEIQKILQKYANVENEYDSGFYHVAR 272


>gi|326628399|gb|EGE34742.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 316

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 12  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 132 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 276


>gi|323152368|gb|EFZ38657.1| dihydrouridine synthase family protein [Escherichia coli EPECa14]
          Length = 306

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/302 (20%), Positives = 115/302 (38%), Gaps = 40/302 (13%)

Query: 10  RFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLALQIGGADISK 61
           R     + +  L  TE + V D +L           +     +     + +Q+ G     
Sbjct: 7   RELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQW 66

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPV 119
           L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM +A+   +PV
Sbjct: 67  LAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPV 126

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G D          +  +++++G   + +H R             +  ++D+  +
Sbjct: 127 SVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYRAEHIDWQAI 176

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            EI++   ++ +  NG + D   A +   +   D VMIGR A  N   L+ V +Y     
Sbjct: 177 GEIRQRL-NIPVIANGEIWDWQSAQQCIAISGCDAVMIGRGAL-NIPNLSRVVKYNE--- 231

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFHGFPNSRRCR 294
                      +  W ++ A +  Y          L  + R    +  L   +  +    
Sbjct: 232 ----------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELF 281

Query: 295 HI 296
             
Sbjct: 282 QH 283


>gi|297582892|ref|YP_003698672.1| dihydrouridine synthase DuS [Bacillus selenitireducens MLS10]
 gi|297141349|gb|ADH98106.1| dihydrouridine synthase DuS [Bacillus selenitireducens MLS10]
          Length = 343

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 72/320 (22%), Positives = 122/320 (38%), Gaps = 29/320 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M   TD  +R          + +TE   +D+      +      L F+  E+P+   I G
Sbjct: 19  MEAVTDVVFRHVVSEAAAPDVFFTEFANSDSFCHPKGRESLKGRLMFTEDEQPIVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                    +  + + GY  I++N+GCP   V     GA L+  PD+  + I A  KA  
Sbjct: 79  DKPEHFRTMSVAMAEMGYKGIDINMGCPVHNVAGDGKGAGLIKRPDVAAELIEA-AKAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK RIG          +N ++ I +  +  + IH R        P     IP+   
Sbjct: 138 LPVSVKTRIGF---SKIDEWQNWLRHILEQDIVNLSIHLRTKKEMSDVPAHWELIPD--- 191

Query: 177 DIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYF 233
             +  ++ E  P+  + +NG ++D    L++     VDG+MIGR  +KN           
Sbjct: 192 --IKALRDEVAPNTLLTINGDIDDRQTGLELAEKYGVDGIMIGRGIFKNPFAFE------ 243

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
           + P   +S     + +           D   R      +  +I          FP +   
Sbjct: 244 TEPKEHTSEELLGLLRLQLDLHDKYSKDLENRPFTPLQRFFKI------YVRSFPKAGEL 297

Query: 294 RHILTVEAGASTATHHIIET 313
           R  L +E   +     I++T
Sbjct: 298 RKKL-METKTTDEVRAILDT 316


>gi|319638462|ref|ZP_07993224.1| tRNA-dihydrouridine synthase C [Neisseria mucosa C102]
 gi|317400211|gb|EFV80870.1| tRNA-dihydrouridine synthase C [Neisseria mucosa C102]
          Length = 321

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 100/253 (39%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +    P  +
Sbjct: 8   MQGLVDDVMRDLLTRIGGFDECVSEFVRITHTVHSRATWLKYVPEIAHANRTPAGTPCTV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +  + 
Sbjct: 68  QLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIVRTLR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  +           
Sbjct: 128 QRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ V +I ++   + +  NG +  +   L  K +   D VM+GR A     +   
Sbjct: 177 EPPAHWEWVRKI-RDAVSIPVTANGDVFSLQDYLDIKTVSGCDSVMLGRGAVIRPDLARQ 235

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 236 IKQYENGETVKDT 248


>gi|291239208|ref|XP_002739522.1| PREDICTED: dihydrouridine synthase 4-like [Saccoglossus
           kowalevskii]
          Length = 367

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/284 (22%), Positives = 119/284 (41%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      + +T MIV+D+ ++  K     FST   ++PL +Q    +
Sbjct: 39  MVRYSKLAFRTLVRKY-GCDVTFTPMIVSDSFIKSIKARDNEFSTHKGDQPLIVQFAANN 97

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
               V A +++  F  + ++LN GCP        FGA L+ +P++V D +      +   
Sbjct: 98  TKDFVTATELIAPF-ADGVDLNCGCPQRWAMANGFGANLIKHPELVKDMVQQTRNKIQDE 156

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K R+  + +       +L +  + +GV+ I +H R    +            ++
Sbjct: 157 KFSVSIKIRLRHNLRDT----LDLCQKAEHAGVSWITVHGRTTEQR---------TEPVN 203

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           Y+ +  I KEN  + +  NG ++ +    ++  L  VDGVM  R    N AM      Y 
Sbjct: 204 YEDIK-IIKENLSIPVIANGDVKSLKDVNRVHELTKVDGVMAARGMLHNPAMYAG---YE 259

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
             PL           +D+        T +   H H    ++ +T
Sbjct: 260 FTPL--------ECIQDWVDISLQLGTQFQCFHHHLIQMMEHVT 295


>gi|197250762|ref|YP_002147146.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|205359500|ref|ZP_02830116.2| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|197214465|gb|ACH51862.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|205344872|gb|EDZ31636.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
          Length = 331

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQYPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 197 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 254

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 255 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 291


>gi|310767077|gb|ADP12027.1| tRNA-dihydrouridine synthase C [Erwinia sp. Ejp617]
          Length = 310

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V DA+L       L         +     + +
Sbjct: 8   MEGVLDSLVRELLTDVNDYDLCITEFLRVVDALLPVKCFQRLCPELDNASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R          D  +
Sbjct: 128 AAVPAHLPVTVKVRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGEIRQRLT-IPVIANGEIWDWHSAQDCMAVTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y             +  +  W ++   +  Y          L  + R
Sbjct: 236 VIKY-------------KEPRMAWPQVVQLLQRYVRLEKQGDTGLYHVAR 272


>gi|269967333|ref|ZP_06181394.1| tRNA-dihydrouridine synthase C [Vibrio alginolyticus 40B]
 gi|269828041|gb|EEZ82314.1| tRNA-dihydrouridine synthase C [Vibrio alginolyticus 40B]
          Length = 319

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 61/324 (18%), Positives = 125/324 (38%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQLLPDHVFHRLCPELLQGSQTASGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G   I++N GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQEPNWMAENAIKAANLGARGIDINFGCPAKMVNKSKGGAALLQHPELIHRVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 EAVPEAIPVTAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++   D+ +  NG + +     + +    V  +M+ R A+    +   
Sbjct: 178 ASEIKWDYINQIRERF-DIPLIANGEIWNYEDGQRCIETTGVSSLMVCRGAFNIPNLGNM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKHNLQ--------------PMSWPEVVELLIYYSKFEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATH 308
            +P ++   R I T    A    H
Sbjct: 283 AYPEAKDLFREIRTFNKAAPIVEH 306


>gi|145628600|ref|ZP_01784400.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 22.1-21]
 gi|144979070|gb|EDJ88756.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 22.1-21]
          Length = 310

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   +     +  ++++ G   I +H R          D  +
Sbjct: 128 RAVPSEFPVSVKVRLGWDDISQSF---EIADAVEQGGATEITVHGRTKT-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + ++ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  WR+I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWREIQKILQKYAKVENEYDSGFYHVAR 272


>gi|158299928|ref|XP_319936.4| AGAP009171-PA [Anopheles gambiae str. PEST]
 gi|157013754|gb|EAA14958.4| AGAP009171-PA [Anopheles gambiae str. PEST]
          Length = 599

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 110/291 (37%), Gaps = 30/291 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +    + +   EM  A  I+ G  +   +    + E    +Q+ G +   + 
Sbjct: 262 NLPFRRICKEYGVD-ITCGEMACAIPIINGAIQEWALTKRHSSEDLFGVQLCGHNPKLVT 320

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPV 119
            AA+I+ +    + I+LN GCP   +     G+ L+   +++   + +  + L       
Sbjct: 321 YAAQIIAEKADVDFIDLNTGCPIDLIFNQGGGSALLRRQNVLKVMVQSCSRLLADYGKEF 380

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK RIG+ +    +    +V   +  G + I IH R         K+ R     D++ +
Sbjct: 381 TVKTRIGIYN--NKLIAHEMVPKFEDWGASLITIHGRT--------KEQRYTKRADWEYL 430

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +   +   + +  NG +   ED        P++ GVM+GR A     +   + E     
Sbjct: 431 QQCATQAQSVPVFGNGDIFGYEDYEHIRTKCPNIAGVMVGRGALIKPWVFQEIKER---- 486

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
                P      +   R +     +Y   H  S  K  + TR  +  +  F
Sbjct: 487 -KTLDPSSGERFEMLKRYV-----NYGLEHWGSDTKGVETTRRFLLEWQSF 531


>gi|183598227|ref|ZP_02959720.1| hypothetical protein PROSTU_01611 [Providencia stuartii ATCC 25827]
 gi|188020396|gb|EDU58436.1| hypothetical protein PROSTU_01611 [Providencia stuartii ATCC 25827]
          Length = 320

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/290 (20%), Positives = 104/290 (35%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A    R   +      +     + +
Sbjct: 8   MEGVLDSLVRSLLSEVNDYDLCITEFVRVVDTLLPAKTFYRLCPELRHGSRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+  P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAYRAVSLGSWGVDLNCGCPSKTVNGHGGGATLLKQPELIYRAAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D    +     +  +++++G   + +H R          D  +
Sbjct: 128 EAVPEELPVSVKVRLGWD---NSQFCHEIADAVEQAGATELTVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A   L     D +MIGR A     +   
Sbjct: 178 AEKINWQAIGDIRRRL-SIPVIANGEVWDYESAQHCLAITGCDAIMIGRGALHTPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  IK+   K  W  + + +  Y               R
Sbjct: 234 -----------SHVIKSNQPKMAWEHVGSLLLKYTELEKQGDTGNYHAAR 272


>gi|37525463|ref|NP_928807.1| tRNA-dihydrouridine synthase C [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784891|emb|CAE13805.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 310

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 57/290 (19%), Positives = 104/290 (35%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     +    L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLSEINEYDLCITEFLRVVDSLLPVKSFYRLCPELRNQSRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     A+ 
Sbjct: 68  QLLGQYPQWLAENAARAIELGSYGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAIR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R             +
Sbjct: 128 EAVPAHLPVTVKVRLGWDSGDRQF---EIADAVQQAGATEMTVHGRTKE-------HGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A     +   D VMIGR A      L+ 
Sbjct: 178 AERINWQAIGEIRQRL-SIPVIANGEIWDWQSAQNCQSVTGCDAVMIGRGALHVP-NLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                K  W+ +   +  Y             + R
Sbjct: 236 VVKYNE-------------PKMCWQDVVQLLQKYIRLEKQGDTGQYHVAR 272


>gi|254229857|ref|ZP_04923262.1| dihydrouridine synthase (Dus) superfamily [Vibrio sp. Ex25]
 gi|262393748|ref|YP_003285602.1| tRNA-dihydrouridine synthase C [Vibrio sp. Ex25]
 gi|151937626|gb|EDN56479.1| dihydrouridine synthase (Dus) superfamily [Vibrio sp. Ex25]
 gi|262337342|gb|ACY51137.1| tRNA-dihydrouridine synthase C [Vibrio sp. Ex25]
          Length = 319

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 64/334 (19%), Positives = 131/334 (39%), Gaps = 43/334 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQLLPDHVFHRLCPELLQGSQTASGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A      G   I++N GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQEPNWMAENAIKAASLGARGIDINFGCPAKMVNKSKGGAALLQHPELIHRVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 EAVPEAIPVTAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++   D+ +  NG + +     + +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWDYINQIRERF-DIPLIANGEIWNYEDGQRCIETTGVDSLMVCRGAFNIPNLGNM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V            P+        W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKH-------NHQPMS-------WPEVVELLIYYSKFEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATHHIIETAFNLM 318
            +P ++   R I T    A    H  I+   + +
Sbjct: 283 AYPEAKDLFREIRTFNKAAPIVEH--IQRYRDEL 314


>gi|118151248|ref|NP_001071552.1| tRNA-dihydrouridine synthase 1-like [Bos taurus]
 gi|117306348|gb|AAI26847.1| Dihydrouridine synthase 1-like (S. cerevisiae) [Bos taurus]
          Length = 270

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 96/230 (41%), Gaps = 19/230 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAHLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGTASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           + +  ++K    + +  NG ++ +    + +    V GVM    A  + A
Sbjct: 192 EHIKAVRKAVT-IPVFANGNIQCLRDVERCIQDTGVQGVMSAGEAVPSPA 240


>gi|328779117|ref|XP_623545.2| PREDICTED: tRNA-dihydrouridine synthase 4-like [Apis mellifera]
          Length = 349

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 107/231 (46%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+AD+ ++ +K     FST   +KPL +Q    +
Sbjct: 21  MVRYSKLQFRTLVRQYD-CDICFTPMILADSFIQSEKARNNEFSTNNSDKPLIVQFAAKN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   + AA++V  +  + ++LN GCP     +  +GA L+  PD V D I  +   +  P
Sbjct: 80  VYDFLNAAELVAPY-CSGVDLNCGCPQRWALKEGYGADLLKKPDFVKDLIYQVRNRIPHP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I      N  + ++K+G + + IHAR   ++            ++ D 
Sbjct: 139 FTVSVKIRLLKDIHKTI--NFCRILEKAGASFLTIHARTPEMR---------CEPINLDN 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  + +++  L +  NG ++ +  A  +    + D VM  R    N A+ +
Sbjct: 188 LK-LIRDSVKLPLIANGDVKSLENAENLYRESNCDAVMSARGILTNPALFS 237


>gi|238749854|ref|ZP_04611358.1| tRNA-dihydrouridine synthase C [Yersinia rohdei ATCC 43380]
 gi|238711783|gb|EEQ03997.1| tRNA-dihydrouridine synthase C [Yersinia rohdei ATCC 43380]
          Length = 310

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +        A +  R   + +    +     + +
Sbjct: 8   MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHHQSRTQSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 AAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D + A + +     D +M+GR A  N   L+ 
Sbjct: 178 AERINWQAIGEIRQRL-SIPVIANGEIWDYASAQECMKVTGCDALMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVKLLQKYVQLEKQGDTGLYHVAR 272


>gi|145351342|ref|XP_001420040.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580273|gb|ABO98333.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 425

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 90/265 (33%), Positives = 132/265 (49%), Gaps = 24/265 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKL 62
           D T  +YR  AR +T  A ++TEM   DA+ R     +      E     Q+GGAD S L
Sbjct: 24  DVTTPYYRALARAMTKRARVWTEMAHHDAVERLKSNTLTR---GETLATAQLGGADPSGL 80

Query: 63  VEAAKIVE-DFGYNEINLNVGCPSARVHEGS-----FGACLMLNPDIVGDCIAAMCKALS 116
             A ++ E ++GY+E+NLN GCPS RV         FGA +ML+ +   +C   M +A  
Sbjct: 81  ARAVEVCEGEYGYDEVNLNCGCPSDRVCGKGETEKRFGASMMLDVERAAECARRMAEASD 140

Query: 117 I-PVTVKCR---------IGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSP 165
              +T+K R         +  ++      + N V++I + +GV    +HAR A++ GL+P
Sbjct: 141 RAKITIKHRLGVRYDKTMMKHEETDCYDYVVNFVEAIHEAAGVEHFIVHARSAVMGGLNP 200

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG----VMIGRAAYK 221
             NRKIP L YD V+ +  E       LNGG+  ++QA ++L   DG    VM+GRA YK
Sbjct: 201 DANRKIPPLRYDEVFALCDEFGRCDFTLNGGVNSLAQAKELLDREDGKLAGVMMGRAFYK 260

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTR 246
           +  ML  VD            +  R
Sbjct: 261 HPCMLADVDRVIFGDAACEPALTRR 285


>gi|302499246|ref|XP_003011619.1| hypothetical protein ARB_02173 [Arthroderma benhamiae CBS 112371]
 gi|302667563|ref|XP_003025363.1| hypothetical protein TRV_00424 [Trichophyton verrucosum HKI 0517]
 gi|291175171|gb|EFE30979.1| hypothetical protein ARB_02173 [Arthroderma benhamiae CBS 112371]
 gi|291189471|gb|EFE44752.1| hypothetical protein TRV_00424 [Trichophyton verrucosum HKI 0517]
          Length = 567

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/283 (20%), Positives = 101/283 (35%), Gaps = 54/283 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGFST---------- 45
           MVD ++  +R   R           L Y+ M  A             F            
Sbjct: 57  MVDRSEFAWRMLTRSFMGEGNPTPILAYSPMFHARFFNEAPAYRTQHFEPVRQAKTVGTD 116

Query: 46  -------------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         ++PL +Q    D  +L++AA+ VE    + ++LN+GCP     +G 
Sbjct: 117 ETTAEPYLDGNPKHDRPLIVQFCANDPDELLKAARHVEAH-CDAVDLNLGCPQGIAKKGH 175

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L  +PD++   I  +   LSIPVT K RI               + I  +G + + 
Sbjct: 176 YGAFLQEDPDLIYKLINKLHNELSIPVTAKFRIL----ETKEKTLEYARMILSAGASILS 231

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PS 209
           +H R+   KG            +++ +  ++    P+  I  NG + + S   + L    
Sbjct: 232 VHGRRREQKG------HNTGVANWEYIRYLRDNLPPETVIFANGNILNHSDISRCLEVTG 285

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
            DGVM       +  + +            + P      + +W
Sbjct: 286 ADGVMSAEGNLSDPTIFS------------TPPAPGEEGRMYW 316


>gi|119185991|ref|XP_001243602.1| hypothetical protein CIMG_03043 [Coccidioides immitis RS]
          Length = 538

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 109/312 (34%), Gaps = 65/312 (20%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R        N  L Y+ M+ A             F            
Sbjct: 40  MVDRSEFAWRMLTRSFMKDNSRNPLLAYSPMLHARLFKDRAGYRSQHFEPVRPKADAVET 99

Query: 47  --------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         ++PL +Q    D  +L+EAA+ V+ +  + ++LN+GCP     +G 
Sbjct: 100 SADTVPFLDGNPAIDRPLIVQFCANDPDELLEAARHVQQY-CDAVDLNLGCPQGIAKKGR 158

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L   PD++   I  +   LSIPVT K RI               K I  +G + I 
Sbjct: 159 YGAFLQEEPDLIYRLINKLHTGLSIPVTAKFRIL----ETKEKTLEYAKMILSAGASFIT 214

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PS 209
           +H R+   KG            D+  +  ++    PD  I  NG + +     K L    
Sbjct: 215 VHGRRREQKG------HNTGVADWSYIRYLRDNLPPDTVIFANGNILNHDDIQKCLDATG 268

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
            DGVM       +  + +              P       ++WR           R    
Sbjct: 269 ADGVMSAEGNLSDPTIFSE------------PPPVGEEGCEYWR----------GRDGKG 306

Query: 270 GGKL-QQITRHM 280
           G +L   + R+M
Sbjct: 307 GYRLDFILRRYM 318


>gi|90410806|ref|ZP_01218821.1| putative regulator protein [Photobacterium profundum 3TCK]
 gi|90328437|gb|EAS44735.1| putative regulator protein [Photobacterium profundum 3TCK]
          Length = 322

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 66/332 (19%), Positives = 123/332 (37%), Gaps = 47/332 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + + D++L       L       G +T   P+ +
Sbjct: 8   MEGVLDPLMREMLTNINDYDLCVTEFVRIIDSLLPSSVFYRLCPELHHGGKTTSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   I++N GCP+  V++   GA L+  P+ +   +  + 
Sbjct: 68  QLLGQEPVWMAENAYRASNLGSAGIDINFGCPAKSVNKNRGGAVLLKEPEKIYQIVKEVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  + PVT K R+G DD         +V ++ ++G + I IHAR  +       D  K
Sbjct: 128 SAVCPTKPVTAKVRLGWDDPTHCF---EIVDAVAQAGGDEIAIHARTKV-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + ++K E   + I  NG + +       L     D +MI R A     +   
Sbjct: 178 AETIKWDYIRQVK-EKSSIPIIANGEVWNYQDGQACLNVTQTDALMICRGALNLPNLCNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           +                      W  +   +  ++   +     L    ++ +    L H
Sbjct: 237 IKR--------------NEAHMPWSHVIQLLLKFSEFEIKGDKGLYYPNRVKQWFAYLRH 282

Query: 286 GFPNSRRCR---HILTVEAGASTATHHIIETA 314
            +P ++        L   A        I++ A
Sbjct: 283 EYPEAKDLFVDIRSLNKAAP----IVEILQRA 310


>gi|195484353|ref|XP_002090658.1| GE13230 [Drosophila yakuba]
 gi|194176759|gb|EDW90370.1| GE13230 [Drosophila yakuba]
          Length = 395

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 108/235 (45%), Gaps = 17/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + +AL   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVRQVVQEVRRALPAD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+   +Q     + +L + ++++GV  + +H R    K            LD 
Sbjct: 148 FSVSVKMRLLGGEQSLERTI-DLARQLEQAGVTFLTLHGRTPAQKH-------SKDTLDI 199

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
             + E++K    + + +NG +E    A  +       GVM  R    N A+  ++
Sbjct: 200 PAMAEVRKSL-QIPLIVNGNVESYRDACDMHDQTGAAGVMAARGLLANPALFNSI 253


>gi|302833555|ref|XP_002948341.1| hypothetical protein VOLCADRAFT_80128 [Volvox carteri f.
           nagariensis]
 gi|300266561|gb|EFJ50748.1| hypothetical protein VOLCADRAFT_80128 [Volvox carteri f.
           nagariensis]
          Length = 422

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 64/293 (21%), Positives = 115/293 (39%), Gaps = 33/293 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R        YT M+ A      R  ++ +L   ++++PL +Q    +
Sbjct: 54  MVDQSELPFRLLCRR-HGATCAYTPMLHARIFSQDRKYREEMLTTCSEDRPLLVQFCAHE 112

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+ AA++V+D G  + I++N GCP      G +GA LM +   V   +  + + L I
Sbjct: 113 PQHLLAAARLVQDSGVADAIDINFGCPQRIAKRGGYGAFLMDDLPRVESLVRVLAQNLRI 172

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K RI  D            + ++ +G + + +H R    K  S          D+D
Sbjct: 173 PVTAKIRIFPDL----AKTVAYARMVEAAGASLVAVHGRLREQKDNSST------RADWD 222

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT-------T 228
            +  +K     + +  NG +  +      L     DGV+   +   + A+          
Sbjct: 223 AIRAVKAAL-SVPVLANGNIRHLGDVGACLSYTGADGVLSAESLLADPALFDVPARASVA 281

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           V +        S+P   R+       ++A   D    H      L+ +  H+ 
Sbjct: 282 VGDVSGRGRWYSAPPLERLS------LAAQYMDLVRAH---PVPLRMVRGHVH 325


>gi|261377469|ref|ZP_05982042.1| tRNA-dihydrouridine synthase C [Neisseria cinerea ATCC 14685]
 gi|269146198|gb|EEZ72616.1| tRNA-dihydrouridine synthase C [Neisseria cinerea ATCC 14685]
          Length = 333

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 102/247 (41%), Gaps = 24/247 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--------QEKPLAL 52
           M    D   R     +       +E +     +      +                P  +
Sbjct: 20  MQGLIDDVMRDLLTRIGGYDECVSEFVRITHTVHSRATWLKYIPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   + E A     FG ++I+LN GCP+  V++   GA L+  P ++   +  M 
Sbjct: 80  QLLGSDADNMAENALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIVKTMR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+IPA+       +I + G  G+ +HAR         K    
Sbjct: 140 ERLPAHIPLTGKMRLGYEDKIPAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I ++N D+ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDNVDIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSN 235
           + +Y S 
Sbjct: 248 IKQYESG 254


>gi|283832436|ref|ZP_06352177.1| tRNA-dihydrouridine synthase [Citrobacter youngae ATCC 29220]
 gi|291072092|gb|EFE10201.1| tRNA-dihydrouridine synthase [Citrobacter youngae ATCC 29220]
          Length = 316

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L     + L         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPAKVFHRLCPELHNDSRTLSGTRVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D+         +  +++++G + + +H R             K
Sbjct: 128 EAVPDHLPVTVKVRLGWDNSDRQF---EIADAVQQAGASELAVHGRTKE-------QGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHINWQAIGEIRQRLT-IPVIANGEIWDWQSAQDCMAISGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W  +   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPDVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|149188159|ref|ZP_01866454.1| putative regulator protein [Vibrio shilonii AK1]
 gi|148838147|gb|EDL55089.1| putative regulator protein [Vibrio shilonii AK1]
          Length = 320

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 67/338 (19%), Positives = 134/338 (39%), Gaps = 43/338 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +     +    P+ +
Sbjct: 8   MEGVLDHLMREILTEINDYDLCVTEFVRVVDQTLPDHVFHRLCPELAQGSMTKSGTPVHI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A      G   I+LN GCP+  V++   GA L+ +P+++ + + A  
Sbjct: 68  QLLGQDPRWMAENAVRAASLGAKGIDLNFGCPAKLVNKSKGGAALLQHPELIHNVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++         +V +I+++G N + +HAR             K
Sbjct: 128 EAVDRNIPVTAKIRLGWENPDDCF---EIVDAIEQAGANELTVHARTKT-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + EI+K+   + +  NG + +     + +    VD +M+ R A+ N   L  
Sbjct: 178 ASEIKWEYINEIRKKT-SVPLIANGEIWNFEDGQRCIETTGVDSLMVCRGAF-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V ++    +              W+ +   +  Y+   +     L    ++ +    L  
Sbjct: 236 VVKHNHTVMP-------------WQDVVDLLLVYSTYEIKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATHHIIETAFNLMIESL 322
            +P +    R I T         H  I+   + ++E+L
Sbjct: 283 QYPQANELFREIRTFNKAVPIVEH--IQNYRDNVLETL 318


>gi|259909025|ref|YP_002649381.1| tRNA-dihydrouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224964647|emb|CAX56161.1| tRNA-dihydrouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|283479041|emb|CAY74957.1| putative regulator protein [Erwinia pyrifoliae DSM 12163]
          Length = 310

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 65/290 (22%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V DA+L       L         +     + +
Sbjct: 8   MEGVLDSLVRELLTDVNDYDLCITEFLRVVDALLPVKCFQRLCPELDNASRTPSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPEWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R          D  +
Sbjct: 128 AAVPAHLPVTVKVRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEAINWQAIGEIRQRLT-IPVIANGEIWDWHSAQDCMAVTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V             IK +  +  W ++   +  Y          L  + R
Sbjct: 236 V-------------IKCKEPRMAWPQVVQLLQRYVRLEKQGDTGLYHVAR 272


>gi|330797093|ref|XP_003286597.1| hypothetical protein DICPUDRAFT_31125 [Dictyostelium purpureum]
 gi|325083422|gb|EGC36875.1| hypothetical protein DICPUDRAFT_31125 [Dictyostelium purpureum]
          Length = 561

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 56/281 (19%), Positives = 104/281 (37%), Gaps = 27/281 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R  A+ L    +   EM +   IL G +  +  L     E    +QI G+ +   +
Sbjct: 226 NLPFRRIAKKL-GADITIGEMALTTKILEGSRSELALLKKHPCEDKFGIQICGSYVDTAI 284

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+ +E +   + +++N GCP   V     GA LM  P  V   +  +   LS P T+K
Sbjct: 285 RCAEFIENEVECDFVDINSGCPIDMVCNMGAGAALMEKPKKVEQLLKGISSTLSCPTTIK 344

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG  +  P      ++  +   G + + +H R         ++ R     +++ V + 
Sbjct: 345 IRIGKLEDAPTA--HKIIPFLGDYGASAVTLHGRS--------RNQRYSRLANWEYVKQ- 393

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             E   + +  NG + +    + I     V  VM+ R A     + T + E     ++ +
Sbjct: 394 CSEVSKIPLIGNGDIYNYRDVVNIYDTSKVSSVMVARGALIKPWIFTEIKEKRDWDISAT 453

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             +           +      Y   H  S       TR  +
Sbjct: 454 ERL----------DLIRDYVHYGLDHWGSDKIGVDNTRKFL 484


>gi|261380252|ref|ZP_05984825.1| tRNA-dihydrouridine synthase [Neisseria subflava NJ9703]
 gi|284797111|gb|EFC52458.1| tRNA-dihydrouridine synthase [Neisseria subflava NJ9703]
          Length = 321

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 100/253 (39%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +    P  +
Sbjct: 8   MQGLVDDVMRDLLTRIGGFDECVSEFVRITHTVHSRATWLKYVPEIAHANRTPAGTPCTV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +  + 
Sbjct: 68  QLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIVHTLR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  +           
Sbjct: 128 QRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ V +I ++   + +  NG +  +   L  K +   D VM+GR A     +   
Sbjct: 177 EPPAHWEWVRKI-RDAVSIPVTANGDVFSLQDYLDIKTVSGCDSVMLGRGAVIRPDLARQ 235

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 236 IKQYENGETVKDT 248


>gi|332289088|ref|YP_004419940.1| tRNA-dihydrouridine synthase C [Gallibacterium anatis UMN179]
 gi|330431984|gb|AEC17043.1| tRNA-dihydrouridine synthase C [Gallibacterium anatis UMN179]
          Length = 314

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 117/290 (40%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R       N  L  +E +  V   + +     +       G++    P+ +
Sbjct: 8   MQGVLDPFMRQLLTSCNNYDLCVSEFVRVVDQLLPKKVFYRLCPELYQQGYTDSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A +  + G + I+LN GCPS  V+    GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPQWLAENANLAIELGSHGIDLNCGCPSKTVNGSCGGASLLKQPELIYQATKAIR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+S    V+VK R+G DD+  A+    +  ++++ G + I IH R  +       D  +
Sbjct: 128 QAVSSEKTVSVKVRLGWDDKQKAL---EIADAVQQGGADEIAIHGRTKM-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +D+  + E++++   + +  NG + +  QA + L     + +M+ R A +   +   
Sbjct: 178 ADKIDWQKIGEVRQKL-SIPVIANGEIFNAQQAQECLAVTGCEDLMVARGALQIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  IK   +   W+ I   +  Y+            + R
Sbjct: 234 -----------SYVIKDNSEVMSWQNILMLLQYYSRVDNQWDSGWYHLAR 272


>gi|225076728|ref|ZP_03719927.1| hypothetical protein NEIFLAOT_01779 [Neisseria flavescens
           NRL30031/H210]
 gi|224952004|gb|EEG33213.1| hypothetical protein NEIFLAOT_01779 [Neisseria flavescens
           NRL30031/H210]
          Length = 328

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 100/253 (39%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +    P  +
Sbjct: 15  MQGLVDDVMRDLLTRIGGFDECVSEFVRIAHTVHSRATWLKYVPEIAHANRTPAGTPCTV 74

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +  + 
Sbjct: 75  QLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIVHTLR 134

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  +           
Sbjct: 135 QRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKVEG--------Y 183

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ V +I ++   + +  NG +  +   L  K +   D VM+GR A     +   
Sbjct: 184 EPPAHWEWVRKI-RDAVSIPVTANGDVFSLQDYLDIKTVSGCDSVMLGRGAVIRPDLARQ 242

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 243 IKQYENGETVKDT 255


>gi|169767132|ref|XP_001818037.1| dihydrouridine synthase family protein [Aspergillus oryzae RIB40]
 gi|83765892|dbj|BAE56035.1| unnamed protein product [Aspergillus oryzae]
          Length = 536

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 98/279 (35%), Gaps = 49/279 (17%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R           L Y+ M  A       +  +  F            
Sbjct: 50  MVDRSEFAWRMLTRSFMPPDDPKPMLAYSPMYHARLFREQLQMRLQHFHPTRAAIKGDDT 109

Query: 47  ---------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
                    ++PL +Q    +    +EAA+ V  +  + ++LN+GCP      G +GA L
Sbjct: 110 PYLDGNPAIDRPLFVQFCANNPDDFLEAARHVAPY-CDAVDLNLGCPQGIARRGHYGAFL 168

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             + D++   I  +   L +PVT K RI    Q          K I  +G + I +H R 
Sbjct: 169 QEDWDLIYKLINKLHTELDVPVTAKFRI----QETKEKTLEYAKMILSAGASIITLHGRT 224

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
              KG            D+  +  ++    P+  I  NG + +     + L     DGVM
Sbjct: 225 REQKG------HNTGVADWSYIRYLRDNLPPETVIFANGNILNYDDLERCLEETGADGVM 278

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                  + ++ +              P      +++WR
Sbjct: 279 SAEGNLSDPSVFS------------KPPPVGSEGREYWR 305


>gi|227326968|ref|ZP_03830992.1| tRNA-dihydrouridine synthase C [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 310

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQCLPVKSFYRLCPELQHASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AECINWQAIGEIRQRL-RIPVIANGEIWDWQSAQDCMATTGCDAVMIGRGAL-NLPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPEVMLLLQKYVQLEKQGDTGLYHVAR 272


>gi|290982534|ref|XP_002673985.1| predicted protein [Naegleria gruberi]
 gi|284087572|gb|EFC41241.1| predicted protein [Naegleria gruberi]
          Length = 427

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 98/239 (41%), Gaps = 19/239 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      ++YT MI++D   +  K     F+T   + PL +Q    +
Sbjct: 131 MVRYSKLAFRLLCREY-GCDVVYTPMIMSDCFHKSQKARDSDFTTHYYDSPLVVQFAANN 189

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---- 114
            +    A ++   +  + I+LN GCP   V + S GA L+  P  + D +          
Sbjct: 190 PTDFSLACQLAAPY-CDGIDLNCGCPQPYVMKESLGAALVTKPQKIFDMVHEANNKFISG 248

Query: 115 LSIPVTVKCRIGV-DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +S P+ VK R+   DD +       L + I+ +G + + +H R    +  + K N   P 
Sbjct: 249 MSRPIGVKIRLHPEDDTLEFRKTIELARQIEMAGASWVTVHGRTHKQRTKNTKVNPDGPK 308

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                     K+  ++ +  NG +  +  S         DGVM  R    N A+ +  D
Sbjct: 309 T--------IKQILNVPVMHNGDIFTLGDSDRFAKETGCDGVMSARGLLSNPALFSGYD 359


>gi|300715941|ref|YP_003740744.1| tRNA-dihydrouridine synthase C [Erwinia billingiae Eb661]
 gi|299061777|emb|CAX58893.1| tRNA-dihydrouridine synthase C [Erwinia billingiae Eb661]
          Length = 320

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     +    L  TE   +V   +     + +         ++    + +
Sbjct: 8   MEGVLDSLVRELLTDVNEYDLCITEFLRVVDQLLPVKSFQRLCPELHHASRTSSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G +          +  +++++G   + +H R          D  K
Sbjct: 128 DAVPAHLPVTVKVRLGWESGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 PERINWQAIGEIRQRLT-IPVIANGEIWDWQSAQDCMQVTGCDAVMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPEVVMLLKKYVLLEKEGDTGLYHVAR 272


>gi|269860977|ref|XP_002650205.1| tRNA-dihydrouridine synthase 1 [Enterocytozoon bieneusi H348]
 gi|220066379|gb|EED43863.1| tRNA-dihydrouridine synthase 1 [Enterocytozoon bieneusi H348]
          Length = 309

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 110/238 (46%), Gaps = 21/238 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           MV +++  +R   R    + + YTEM+      +      K      +  ++PL +QI G
Sbjct: 1   MVSFSEEAFRILVRRYAVD-VCYTEMVNCKVFNQNKADPRKNRWYTTNDNDRPLVIQICG 59

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D S+++     ++ +  + I++N+GCP     +G++G+ LM + + V + I+ + + L+
Sbjct: 60  NDPSEMLATCLQIQQY-CDAIDINLGCPQNIAKKGNYGSYLMDDFEKVKNIISTLAEQLT 118

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+  K R+               K I+KSG + + +H R    KG      +    + +
Sbjct: 119 VPIFCKIRVF----ESIEKTITYAKMIEKSGCSLLAVHGRTREQKG------QNTGYVSF 168

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           D +  +K     + +  NGG+    D+  A++I    DG+MIG       ++   +++
Sbjct: 169 DHIRAVKNAL-SIPVVSNGGVLTHRDIKNAVEI-TGCDGIMIGEPILFIPSIFVDIEK 224


>gi|303247058|ref|ZP_07333333.1| dihydrouridine synthase DuS [Desulfovibrio fructosovorans JJ]
 gi|302491484|gb|EFL51369.1| dihydrouridine synthase DuS [Desulfovibrio fructosovorans JJ]
          Length = 331

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 69/319 (21%), Positives = 114/319 (35%), Gaps = 25/319 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADI 59
             ++D  +R   R L   A+  TEM+ A  +     + K +L     + PL +Q+ GAD 
Sbjct: 17  AGFSDLPFRLLCREL-GAAVAMTEMVSAKGLFYDSRNTKRLLATLPPDSPLVVQLFGADP 75

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIP 118
             L  A   +   GY   +LN GC   +V +   GA L+ +PD +  C  AM +A     
Sbjct: 76  DYLSRAVTALSGEGYGFFDLNCGCSVRKVVKTGAGAALLGDPDKLVACARAMVEAAGDAH 135

Query: 119 VTVKCRI-GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           V VK R+        A+ALR+    + ++GV  + +H R A  +G S          D+D
Sbjct: 136 VGVKLRLGPKPPDFCALALRD---RLTEAGVAWLTLHPRHAS-QGFS-------GRADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +     +   + +  +G L         L      G+M  R A  +  + T       +
Sbjct: 185 SLAAFTADA-KVPVLASGDLMTAGDGADCLARTGAAGLMYARGALADPRIFTRHANRLRS 243

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                      +     R  +         +      L ++   +       P  R  R 
Sbjct: 244 AQGLPELPLPPICDVIRRHAALC-----RGYADDRRALLRMRTAVPRYLRDLPGCRALRD 298

Query: 296 ILTVEAGASTATHHIIETA 314
            L            II+ A
Sbjct: 299 RLCHCTSWEELDA-IIDAA 316


>gi|298345359|ref|YP_003718046.1| putative dihydrouridine synthase [Mobiluncus curtisii ATCC 43063]
 gi|298235420|gb|ADI66552.1| possible dihydrouridine synthase [Mobiluncus curtisii ATCC 43063]
          Length = 367

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 56/306 (18%), Positives = 113/306 (36%), Gaps = 31/306 (10%)

Query: 21  LLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEI 77
           +   EMI A A++    ++  +      +    LQ+ G   + L  AA+ ++     + I
Sbjct: 1   MFVNEMITAKALMMNSTRSWVMAQSGPGQTVRVLQLYGVVGADLAWAARELIARDLVDVI 60

Query: 78  NLNVGCPSARVHEGSFGACLMLNP----DIVGDCI-------AAMCKALSIPVTVKCRIG 126
           +LN GCP  +V     GA L        D++G  +        A  + + +PVTVK R+G
Sbjct: 61  DLNFGCPVPKVTRKGGGAALPWKTAYFGDLIGQVVQAAQESSQAARREVEVPVTVKIRVG 120

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +D+      + +  ++ + +G   + +HAR          +     + D+  + ++    
Sbjct: 121 IDE--SHETMLDAGRAAQDAGAAALTLHARTT--------NQYYSGHSDWSRIGQLVN-T 169

Query: 187 PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
            D+ +  NG +   S AL++       G+ IGRA      +   +          + P  
Sbjct: 170 LDIPVLGNGDVFSASDALEMFAQTGCAGIEIGRAVQGRPWIFREITAALWGQPIPAGPTL 229

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAS 304
             + +         +  +     +    L+ + +H+     GF      R  LT      
Sbjct: 230 GEIVEVIRAHACGLVEHFG----NEKAALRDMRKHVGWYLRGFHLGGDTRAELTRVETLD 285

Query: 305 TATHHI 310
                +
Sbjct: 286 DLERRL 291


>gi|313237639|emb|CBY12783.1| unnamed protein product [Oikopleura dioica]
          Length = 460

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 100/238 (42%), Gaps = 25/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----------EKPL 50
           MVD ++  +R  +R  +   L YT M  A   ++        F             ++PL
Sbjct: 47  MVDASELPWRVLSRRYSAE-LCYTPMFHAANYIKDATYRRENFPDTGDLEQGSPEFDRPL 105

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q    DI+    AAK+VED   + ++LN+GCP      G +GA +M +   +   I  
Sbjct: 106 FVQFCANDINAFSTAAKMVEDR-CDAVDLNLGCPQMIAKRGHYGAHMMEDWSNIRKMIEE 164

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             K   + +T K R   D+ I         K ++ +GV+ + IH R    +G        
Sbjct: 165 ARKVAKVRITAKIRKFEDESIT----LRYAKMLENAGVSLLTIHGRTRDQRG------PN 214

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
               D+ I+ ++K E   + +  NG ++ +  A+  +    VDG+M       N A+ 
Sbjct: 215 TGLADWQIIKKVK-EALRVPVVANGNIQCLQNAIDCMEQTGVDGIMTAEGNLYNPALF 271


>gi|167465717|ref|ZP_02330806.1| transcriptional regulator involved in nitrogen regulation
           (NifR3/Smm1 family) protein [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 201

 Score =  171 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 54/195 (27%), Positives = 100/195 (51%), Gaps = 14/195 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M    +  +R  A+      L+  EM+   AI+ G+ + +  L    +EKPL+LQI G D
Sbjct: 18  MAGVCNPAFRLIAKEF-GCGLVCAEMVSDKAIVHGNSRTMEMLYVDEREKPLSLQIFGGD 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV AAK V+ +   + I++N+GCP  +V +   GA  +L+P  + + ++A+ + +S 
Sbjct: 77  KETLVAAAKYVDLNTNADIIDINMGCPVPKVTKCDAGARWLLDPQKIEEMVSAVVEVVSK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G D +          ++++++G + + +H R         ++       ++D
Sbjct: 137 PVTVKMRMGWDSEHIYAVRN--AQAVERAGGSAVSLHGRT--------REQLYTGTANWD 186

Query: 178 IVYEIKKENPDLFIG 192
           I+ E+K+      IG
Sbjct: 187 IIREVKQSISIPLIG 201


>gi|148706255|gb|EDL38202.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_b [Mus
           musculus]
          Length = 351

 Score =  171 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 99/260 (38%), Gaps = 31/260 (11%)

Query: 24  TEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVG 82
           TEM          +  +L     E    +Q+ GA    + + A+++      + +++NVG
Sbjct: 46  TEM---------SEWALLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINVG 96

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP   V++   G  LM         +  + + L +P+TVK R GV +++       L+  
Sbjct: 97  CPIDLVYKKGGGCALMNRSAKFQQIVRGVNEVLDVPLTVKMRTGVQERVSLA--HRLLPE 154

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++  GV  + +H R         ++ R     D+  + +  K    + +  NG +     
Sbjct: 155 LRDWGVALVTLHGRS--------REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFED 206

Query: 203 A-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           A   +   V G+M+ R A     + T + E     ++ S  +           I    T 
Sbjct: 207 ANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSERL----------DILRDFTH 256

Query: 262 YAARHLHSGGKLQQITRHMI 281
           Y   H  S  +  + TR  +
Sbjct: 257 YGLEHWGSDTQGVERTRRFL 276


>gi|321249423|ref|XP_003191451.1| tRNA dihydrouridine synthase [Cryptococcus gattii WM276]
 gi|317457918|gb|ADV19664.1| tRNA dihydrouridine synthase, putative [Cryptococcus gattii WM276]
          Length = 623

 Score =  171 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 60/285 (21%), Positives = 108/285 (37%), Gaps = 60/285 (21%)

Query: 1   MVDWTDRHYRFFARLL------------------------TNNALLYTEMIVADAIL--- 33
           MVD ++  +R  +R                              + YT MI A   +   
Sbjct: 63  MVDQSELAWRLLSRSPLPPALAGPSETVKTPQGKTYIRHPGGAHVCYTPMIHAKVFVDAK 122

Query: 34  -----RGDKKNILGFSTQ------------EKPLALQIGGADISKLVEAAKIVEDFGYNE 76
                 GD +  L    +            ++PL +Q    D   L+ AAK VE    + 
Sbjct: 123 GEGGRNGDGQFCLSLDEEGGEGTIGGVEGGDRPLIVQFCANDPDILLAAAKKVE-HRCDA 181

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N GCP      G +G+ L    +++   I+ + + LS+PVT K RI  D        
Sbjct: 182 VDINFGCPQGIAKRGHYGSFLQDEWELIHKLISTLHENLSVPVTAKFRIFADLDKTIA-- 239

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
               + ++ +G   +  H R   +KG      +     D++ + E+K     + +  NG 
Sbjct: 240 --YARMMEAAGAQILTCHGRTREMKG------QNTGLADWEYIREVKNAV-KVPVFANGN 290

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           +   ED+ + +++    DGVM       N A+    D  +++P  
Sbjct: 291 ILYREDVDRCMEV-TGCDGVMTAEGNLSNPAIFMPPDHPYAHPPI 334


>gi|255074587|ref|XP_002500968.1| predicted protein [Micromonas sp. RCC299]
 gi|226516231|gb|ACO62226.1| predicted protein [Micromonas sp. RCC299]
          Length = 662

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 52/289 (17%), Positives = 105/289 (36%), Gaps = 33/289 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +    + +   EM +   +L+G      +L     E     Q+ G     + 
Sbjct: 317 NLPFRRICKRYGVD-ITCGEMAMVTNLLQGQPAEWALLRRHPSEDIFGAQVCGGYSDSMS 375

Query: 64  EAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              +++ED      G + I++N+GCP   V     G+ L+  P  +   + A    LS P
Sbjct: 376 RCMQLLEDEVVSKGGLDFIDINMGCPIDLVCNKGAGSMLLEKPARMEQLVRASAPLLSCP 435

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R+G  D         ++  +   G+ G+ +H R         +  R     D+D 
Sbjct: 436 LTLKTRMGYFDNKRVA--HEIIPKMVDWGLAGMTLHGRS--------RQQRYSRLADWDY 485

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +  + +P + +  NG +      +K +    V   MI R A     + T + E     
Sbjct: 486 INQCARASP-IQLIGNGDVFSYHDYVKNVEGQGVATCMIARGALIKPWIFTEIKERRDWD 544

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
           ++ +  +           +      +   H  +  +    TR  +   L
Sbjct: 545 ISATERL----------DMLKDYAAFGLEHWGADARGVANTRRFLLEWL 583


>gi|238060527|ref|ZP_04605236.1| nifR3 family TIM-barrel protein [Micromonospora sp. ATCC 39149]
 gi|237882338|gb|EEP71166.1| nifR3 family TIM-barrel protein [Micromonospora sp. ATCC 39149]
          Length = 239

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 58/221 (26%), Positives = 90/221 (40%), Gaps = 20/221 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T+  +R   R      +   EMI   A++  + K   ++ F   E+P +LQ+ G D
Sbjct: 31  MAGITNVGFRRLCREQGG-GIYVCEMITTVALVERNPKTLRMIAFGDDERPRSLQLYGTD 89

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
                 A +IV +    + I+LN GCP  +V     G+ L     +    + A   A S 
Sbjct: 90  PEITAAAVRIVVEKDLADHIDLNFGCPVPKVTRKGGGSALPWRRRLFARLVRAAVDAASP 149

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             +PVTVK R G+DD         L    + +GV  + +H R A          R     
Sbjct: 150 AGVPVTVKMRKGIDDDHLTYVEAGLA--AQDAGVAAVALHGRTA--------AQRYSGTA 199

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGV 213
           D+D +  +K+   D+ +  NG +     A        VDGV
Sbjct: 200 DWDAIATLKQSL-DVPVLGNGDIWKADDAAANGRPHWVDGV 239


>gi|91793740|ref|YP_563391.1| dihydrouridine synthase, DuS [Shewanella denitrificans OS217]
 gi|91715742|gb|ABE55668.1| dihydrouridine synthase, DuS [Shewanella denitrificans OS217]
          Length = 319

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 75/336 (22%), Positives = 133/336 (39%), Gaps = 46/336 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +    LL TE + V D +L   +K  L    +           P+
Sbjct: 10  MEGVVDPLMRDILSKINPYDLLVTEFVRVVDQLL--PEKVFLKLCPELHQQGMTANGTPV 67

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G +   + E A    + G N ++ N GCP+  V+    GA L+  PD V D + A
Sbjct: 68  RVQLLGQEPQCMAENAVRAIELGSNGVDANFGCPAKMVNRSKGGAVLLQCPDKVHDIVKA 127

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M +A+S   PVT K R+G +D+           ++ ++G   + IHAR         K +
Sbjct: 128 MRQAVSSEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARS--------KTD 176

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              P   ++ + E+++  P + +  NG +     A + +     D VMIGR A     + 
Sbjct: 177 GYKPPAYWEYITEVRQRLP-IPVIANGEIWSAEDARRCIEVTGCDSVMIGRGAISLPNLA 235

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGL 283
            T+        TG++P         W +  + +  Y+   L+   S     +I +    L
Sbjct: 236 DTIK-------TGAAPY-------TWEQTLSLLMSYSELELNGRKSDYYPARIKQWFCYL 281

Query: 284 FHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMI 319
              +P +      L V    +     +++ A   ++
Sbjct: 282 NRQYPEADALFRELRV-FKTTDEIRAVLDKAHRALL 316


>gi|329119847|ref|ZP_08248521.1| tRNA-dihydrouridine synthase C [Neisseria bacilliformis ATCC
           BAA-1200]
 gi|327464003|gb|EGF10314.1| tRNA-dihydrouridine synthase C [Neisseria bacilliformis ATCC
           BAA-1200]
          Length = 315

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 62/334 (18%), Positives = 117/334 (35%), Gaps = 35/334 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M   TD   R     +       +E +       + A        +     +    P  +
Sbjct: 1   MQGLTDAPMRDLLTRIGGFDECVSEFVRITHTVHSRAAWLKYAPEMARGSRTPSGIPCTV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + +   A     FG  +I+LN GCP+  V++   GA L+  P  V   +  + 
Sbjct: 61  QLLGSDAANMAANALEAVRFGAEKIDLNFGCPAPTVNKHQGGAVLLKEPQRVHAIVKTLR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +AL   I +T K R+G DD+  A+      ++I + G   + +HAR  +           
Sbjct: 121 EALPAHILLTGKMRLGFDDKTLALEN---AQAIAEGGACALTVHARTKVEG--------Y 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +  V +I     D+ +  NG +  +    A++      GVMIGR A     +   
Sbjct: 170 EPPAHWAWVKKIA-AAVDIPVTANGDVFTLQDYLAIRRESGCAGVMIGRGAVIRPGLARQ 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GF 287
           +  Y  N             +     +   +        ++  +L+Q     +G+     
Sbjct: 229 IKAY-ENGEDAPEMAFAETLQWMRLFVDLCLNAAGGSEKYALARLKQW----LGMMKQAE 283

Query: 288 PNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           P +R        +A  +      ++       + 
Sbjct: 284 PQARDLF-----DAVRTLKEADAVKRVLAAFADK 312


>gi|319896605|ref|YP_004134798.1| tRNA-dihydrouridine synthase c [Haemophilus influenzae F3031]
 gi|317432107|emb|CBY80458.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae F3031]
          Length = 310

 Score =  171 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDSFVRQLFTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A    D G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQNPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQPELIYCATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           KA+    PV+VK R+G DD   A     +  ++++ G   I +H R          D  +
Sbjct: 128 KAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWCEIQKILQKYANVENEYDSGFYHVAR 272


>gi|229846358|ref|ZP_04466466.1| hypothetical protein CGSHi7P49H1_06795 [Haemophilus influenzae
           7P49H1]
 gi|229810451|gb|EEP46169.1| hypothetical protein CGSHi7P49H1_06795 [Haemophilus influenzae
           7P49H1]
          Length = 310

 Score =  171 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRELLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    D G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ GV  I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGVTEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+ V+K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNVEKMPWYEIQKILQKYANVENEYDSGFYHVAR 272


>gi|145632514|ref|ZP_01788248.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 3655]
 gi|144986709|gb|EDJ93261.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 3655]
          Length = 310

 Score =  171 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSSTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ G   I +H R          D  +
Sbjct: 128 RAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGRTK-------SDGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + ++ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  WR+I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWREIQKILQKYAKVENEYDSGFYHVAR 272


>gi|58258725|ref|XP_566775.1| tRNA dihydrouridine synthase [Cryptococcus neoformans var.
           neoformans JEC21]
 gi|134106771|ref|XP_777927.1| hypothetical protein CNBA3960 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50260627|gb|EAL23280.1| hypothetical protein CNBA3960 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|57222912|gb|AAW40956.1| tRNA dihydrouridine synthase, putative [Cryptococcus neoformans
           var. neoformans JEC21]
          Length = 610

 Score =  171 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 59/273 (21%), Positives = 104/273 (38%), Gaps = 60/273 (21%)

Query: 1   MVDWTDRHYRFFARLL------------------------TNNALLYTEMIVADAIL--- 33
           MVD ++  +R  +R                              + YT MI A   +   
Sbjct: 59  MVDQSELAWRLLSRSPLPPALAGPSETVTTPQGKAYIRHPGGAHVCYTPMIHAKVFVDAK 118

Query: 34  -----RGDKKNILGFSTQ------------EKPLALQIGGADISKLVEAAKIVEDFGYNE 76
                 GD +  L    +            ++PL +Q    D   L+ AAK VE    + 
Sbjct: 119 GEGGRNGDGQFCLSLDEEGGEGTIGGVEGGDRPLIVQFCANDPDILLAAAKKVE-HRCDA 177

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N GCP      G +G+ L    +++   I+ + + LS+PVT K RI  D        
Sbjct: 178 VDINFGCPQGIAKRGHYGSFLQDEWELIHKLISTLHENLSVPVTAKFRIFPDLDKTIA-- 235

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
               + ++ +G   +  H R   +KG      +     D++ + E+KK    + +  NG 
Sbjct: 236 --YARMMEAAGAQILTCHGRTREMKG------QNTGLADWEYIREVKKAV-KVPVFANGN 286

Query: 197 L---EDMSQALKILPSVDGVMIGRAAYKNSAML 226
           +   ED+ + +++    DGVM       N A+ 
Sbjct: 287 ILYREDVDRCMEV-TGCDGVMTAEGNLSNPAIF 318


>gi|303318106|ref|XP_003069055.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
 gi|240108736|gb|EER26910.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
          Length = 538

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 109/312 (34%), Gaps = 65/312 (20%)

Query: 1   MVDWTDRHYRFFARLLT-----NNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R        N  L Y+ M+ A             F            
Sbjct: 40  MVDRSEFAWRMLTRSFMKDNSPNPLLAYSPMLHARLFKDRAGYRSQHFEPVRPKADAVET 99

Query: 47  --------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         ++PL +Q    D  +L+EAA+ V+ +  + ++LN+GCP     +G 
Sbjct: 100 SADTVPFLDGNPAIDRPLIVQFCANDPDELLEAARHVQQY-CDAVDLNLGCPQGIAKKGR 158

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L   PD++   I  +   LSIPVT K RI               K I  +G + I 
Sbjct: 159 YGAFLQEEPDLIYRLINKLHTGLSIPVTAKFRIL----ETKEKTLEYAKMILSAGASFIT 214

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PS 209
           +H R+   KG            D+  +  ++    PD  I  NG + +     K L    
Sbjct: 215 VHGRRREQKG------HNTGVADWSYIRYLRDNLPPDTVIFANGNILNHDDIQKCLDATG 268

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
            DGVM       +  + +              P       ++WR           R    
Sbjct: 269 ADGVMSAEGNLSDPTIFSE------------PPPVGEEGCEYWR----------GRDGKG 306

Query: 270 GGKL-QQITRHM 280
           G +L   + R+M
Sbjct: 307 GYRLDFILRRYM 318


>gi|119610149|gb|EAW89743.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
          Length = 415

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 52/222 (23%), Positives = 93/222 (41%), Gaps = 19/222 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKLS 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 142 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
           + +  ++K    + +  NG ++ +    + L    V GVM  
Sbjct: 192 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSA 232


>gi|269976450|ref|ZP_06183435.1| tRNA-dihydrouridine synthase B [Mobiluncus mulieris 28-1]
 gi|269935251|gb|EEZ91800.1| tRNA-dihydrouridine synthase B [Mobiluncus mulieris 28-1]
          Length = 462

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 65/314 (20%), Positives = 116/314 (36%), Gaps = 34/314 (10%)

Query: 19  NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YN 75
             +   EM+ A A+  G  ++  ++     +   ++Q+ G     L  AA  +   G  +
Sbjct: 108 EGMFVGEMVTAKALRMGSARSWVMVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGLAD 167

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVKCR 124
            I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK R
Sbjct: 168 HIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVKIR 227

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G+D +       ++ +  + +GV  + +HAR                +  ++ +  +  
Sbjct: 228 SGIDAEHR--IFLDVARVAEDNGVVAVTLHARTT--------SEYYGGHSHWEDIAALV- 276

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           E  D+ +  NG +   + AL++       GV IGRA      +   +            P
Sbjct: 277 EVLDIPVLGNGDVFCAADALEMFRETGCAGVEIGRAVQGRPWIFREITAALWGLPVPVGP 336

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT---V 299
               V     R     +  Y     +    L+ + +H+   F GF      R  L     
Sbjct: 337 SLGEVANVARRHAEGLVAHYG----NELVALRDMRKHLGWYFRGFGLGGEMRGRLARVES 392

Query: 300 EAGASTATHHIIET 313
            A    ATH +IE 
Sbjct: 393 LAELEQATHELIER 406


>gi|16579860|gb|AAL26675.1| unknown [Staphylococcus aureus]
          Length = 289

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/286 (22%), Positives = 114/286 (39%), Gaps = 43/286 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E+P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESCCHPEGIHSVRGRLTFSEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+    I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAKIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR  + N        
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF---- 242

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                            +K+     S  + D    H H    ++++
Sbjct: 243 -----------------EKEPREHTSKELLDLLRLHYHCLTNMKKM 271


>gi|238759753|ref|ZP_04620911.1| tRNA-dihydrouridine synthase C [Yersinia aldovae ATCC 35236]
 gi|238701985|gb|EEP94544.1| tRNA-dihydrouridine synthase C [Yersinia aldovae ATCC 35236]
          Length = 314

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 58/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 10  MEGVLDSLVRELLSEVNDYDLCITEFLRVVDQLLPAKSFYRLCPELHNQSRTQSGTLVRI 69

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 70  QLLGQYPEWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 129

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 130 EAVPAHLPVTVKIRLGWDSGDRQF---EIADAVQQAGATELAVHGRTKE-------DGYQ 179

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A + +     + VM+GR A  N   L+ 
Sbjct: 180 AERINWQAISEIRQRLT-IPVIANGEIWDYRSAQECMSVTGCNTVMLGRGAL-NVPNLSR 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 238 VVKYNE-------------PRMAWPEVVKLLQKYVQLEKQGDTGLYHVAR 274


>gi|242239833|ref|YP_002988014.1| tRNA-dihydrouridine synthase C [Dickeya dadantii Ech703]
 gi|242131890|gb|ACS86192.1| dihydrouridine synthase DuS [Dickeya dadantii Ech703]
          Length = 320

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVA-----DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE   +V       A  R   +      +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQRLPVKAFYRLCPELRHDSRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A+     G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAERAVSLGSWGVDLNCGCPSKMVNGSGGGATLLKDPELIYQAAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 128 EAVPAALPVTVKIRLGWDSGARRF---EIADAVQQAGATELVVHGRTKE-------DGYQ 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   L     D VM+GR A  N   L+ 
Sbjct: 178 AERINWAAIGEIRRRLT-IPVIANGEIWDWQSAQDCLAATGCDAVMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y             R  +  W  +   +  Y          L  + R
Sbjct: 236 VIKY-------------REARMPWADVVRLLQKYVRLEKQGDTGLYHVAR 272


>gi|218768088|ref|YP_002342600.1| hypothetical protein NMA1207 [Neisseria meningitidis Z2491]
 gi|38605054|sp|Q9JUP6|DUSC_NEIMA RecName: Full=tRNA-dihydrouridine synthase C
 gi|121052096|emb|CAM08407.1| hypothetical protein NMA1207 [Neisseria meningitidis Z2491]
 gi|319410331|emb|CBY90676.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis WUE 2594]
          Length = 333

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 103/254 (40%), Gaps = 26/254 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +       L +  +           P  
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRA-TWLKYVPEIANGNKTFSGTPCT 78

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D   +   A     FG ++I+LN GCP+  V+    GA L+  P+++   +  +
Sbjct: 79  VQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNRHKGGAILLKEPELIFHIVKTL 138

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K   
Sbjct: 139 RERLPAHIPLTAKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEG 187

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
             P   ++ + +I +++ D+ +  NG +  +     +K +   + VM+GR A     +  
Sbjct: 188 YEPPAHWEWIRKI-RDSVDIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLAR 246

Query: 228 TVDEYFSNPLTGSS 241
            + +Y +      +
Sbjct: 247 QIKQYENGGPVKDT 260


>gi|16765504|ref|NP_461119.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167991101|ref|ZP_02572200.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|38604956|sp|Q8ZNM4|DUSC_SALTY RecName: Full=tRNA-dihydrouridine synthase C
 gi|16420711|gb|AAL21078.1| putative nitrogen regulation protein [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|205330623|gb|EDZ17387.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261247388|emb|CBG25213.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994239|gb|ACY89124.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301158735|emb|CBW18247.1| conserved hypothetical protein [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913164|dbj|BAJ37138.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321224828|gb|EFX49891.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. TN061786]
 gi|332989108|gb|AEF08091.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 312

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 8   MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 128 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEILDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 272


>gi|261822179|ref|YP_003260285.1| tRNA-dihydrouridine synthase C [Pectobacterium wasabiae WPP163]
 gi|261606192|gb|ACX88678.1| dihydrouridine synthase DuS [Pectobacterium wasabiae WPP163]
          Length = 310

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQCLPVKSFYRLCPELQHASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D +M+GR A  N   L+ 
Sbjct: 178 AECINWQAIGEIRQRL-RIPVIANGEIWDWQSAQDCMATTGCDAIMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W  +   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPDVMLLLQKYVRLEKQGDTGLYHVAR 272


>gi|156975206|ref|YP_001446113.1| hypothetical protein VIBHAR_02933 [Vibrio harveyi ATCC BAA-1116]
 gi|156526800|gb|ABU71886.1| hypothetical protein VIBHAR_02933 [Vibrio harveyi ATCC BAA-1116]
          Length = 319

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/338 (18%), Positives = 129/338 (38%), Gaps = 43/338 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQLLPDHVFHRLCPELLQGSQTASGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G   I+LN GCP+  V++   GA L+ +P+ + + + A  
Sbjct: 68  QLLGQEPNWMAENAVKAAELGARGIDLNFGCPAKLVNKSKGGAALLQHPEFIHNIVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +IPVT K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 DAVPSNIPVTAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + +I+     + +  NG + +     + +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWEYITQIRDRF-SIPLIANGEIWNYEDGQRCIETTGVDSLMVCRGAFNIPNLGNM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKH--------------NQQPMAWPEVVELLIYYSQFEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATHHIIETAFNLMIESL 322
            +P +    R I T    A    H  I+   + ++  +
Sbjct: 283 AYPEANELFREIRTFNKAAPIVEH--IQRYRDELLSRV 318


>gi|90579253|ref|ZP_01235063.1| putative regulator protein [Vibrio angustum S14]
 gi|90440086|gb|EAS65267.1| putative regulator protein [Vibrio angustum S14]
          Length = 313

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/335 (19%), Positives = 124/335 (37%), Gaps = 47/335 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D++L       L       G +    P+ +
Sbjct: 8   MEGVLDHLMREMLTEINDYDLCVTEFVRVIDSLLPSSVFYRLCPELRQGGKTRSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D + + E A+     G   +++N GCP+  V++   GA L+  P+ +   + A  
Sbjct: 68  QILGQDPNWMAENAQRACSLGSAGVDINFGCPAKAVNKSRGGAVLLKEPERIYQIVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A++   P+T K R+G DD         +  +I ++G + + +HAR          D  +
Sbjct: 128 AAVNPVKPLTAKVRLGWDD---PAQCFEIADAIAQAGADEMVVHARTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + ++K+ +  + I  NG + +       L   + D +M+ R A     +   
Sbjct: 178 AETIKWDYIKQLKQ-SVAIPIIANGEVWNYQDGQACLSTTNTDALMVCRGALNLPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W  + A +  Y+   +     L    ++ +    L H
Sbjct: 237 VKH--------------NQAHMSWEDVLALLLVYSQFEIKGDKGLYYPNRVKQWFSYLRH 282

Query: 286 GFPNSRRCR---HILTVEAGASTATHHIIETAFNL 317
            +P ++        L   A        +++ A   
Sbjct: 283 EYPQAKLLFTDIRALNKAAP----IIEVLQRAQQQ 313


>gi|260801020|ref|XP_002595394.1| hypothetical protein BRAFLDRAFT_119015 [Branchiostoma floridae]
 gi|229280640|gb|EEN51406.1| hypothetical protein BRAFLDRAFT_119015 [Branchiostoma floridae]
          Length = 212

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 49/199 (24%), Positives = 93/199 (46%), Gaps = 15/199 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R  +R      L YT M  A    R +   ++ +    +++PL +Q    D
Sbjct: 27  MVDQSELPWRLLSRR-HGCQLAYTPMFHAALFSREETYFRDAMQTCPEDRPLIVQFCAND 85

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV+AA + +D   + I+LN+GCP +    G +GA L  + D++   ++A+ +  S+P
Sbjct: 86  PDILVQAALLAQDH-CDAIDLNLGCPQSIARRGHYGAFLQDDWDLIRRLVSAVHERCSVP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  D +          + ++K+G   + +H R    KG             +D 
Sbjct: 145 VTCKIRVFQDVKRTV----EYAQMLEKAGCQLLTVHGRTKEQKGS------LTGLASWDH 194

Query: 179 VYEIKKENPDLFIGLNGGL 197
           +  +K ++  + +  NG +
Sbjct: 195 IKAVK-DSVKIPVFANGNI 212


>gi|91227370|ref|ZP_01261759.1| putative regulator protein [Vibrio alginolyticus 12G01]
 gi|91188634|gb|EAS74924.1| putative regulator protein [Vibrio alginolyticus 12G01]
          Length = 319

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/324 (19%), Positives = 127/324 (39%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQLLPDHVFHRLCPELLQGSQTASGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G   I++N GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQEPNWMAENAIKAANLGARGIDINFGCPAKMVNKSKGGAALLQHPELIHRVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 EAVPEAIPVTAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++   D+ +  NG + +     + +    V  +M+ R A+    +   
Sbjct: 178 ASEIKWDYINQIRERF-DIPLIANGEIWNYEDGQRCIETTGVSSLMVCRGAFNIPNLGNM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V            P+        W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKH-------NHQPMS-------WPEVVELLIYYSKFEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATH 308
            +P ++   R I T    A    H
Sbjct: 283 AYPEAKDLFREIRTFNKAAPIVEH 306


>gi|328773713|gb|EGF83750.1| hypothetical protein BATDEDRAFT_21188 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 327

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 103/244 (42%), Gaps = 29/244 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGA 57
           MV ++   +R   R   N  L YT MI++D            F T    + P+ +Q   +
Sbjct: 32  MVRYSKLAFRELVRGY-NVDLAYTPMILSDVFKHSQISRETEFRTHQITDDPVIVQFAAS 90

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-------- 109
           + + L +AA++V  +  N ++LN GCP         G+ LM +P++V D +         
Sbjct: 91  NPTDLADAAELVARYT-NGVDLNCGCPQKWAISEGIGSYLMEHPELVRDMVKQVKSRTSS 149

Query: 110 -AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             M    S P ++K RI  D +         V+  +  GV+ I +H R    K   P + 
Sbjct: 150 VKMANGTSFPCSIKIRIHSDLKKTV----EFVRRAESIGVDWITVHGRTRKQKNTEPLNM 205

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
             I          I KE+  + +  NG +  +  A +++    VDGVM  R   +N A+ 
Sbjct: 206 DGI---------RIAKESVGVPVFANGNVLTLGDADRLVEETRVDGVMAARGLLENPALF 256

Query: 227 TTVD 230
           +  D
Sbjct: 257 SGYD 260


>gi|323130501|gb|ADX17931.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
          Length = 316

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-------DAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  TE +             R   + +    +    P+ +
Sbjct: 12  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELHHASRTPSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 72  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLKDPELIYQGAKAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 132 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 182 AEHIDWQAIGEIRQRLT-IPVIANGEILDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 240 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 276


>gi|294670948|ref|ZP_06735804.1| hypothetical protein NEIELOOT_02654 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307435|gb|EFE48678.1| hypothetical protein NEIELOOT_02654 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 313

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/254 (22%), Positives = 100/254 (39%), Gaps = 24/254 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M   TD   R     +       +E +       + A        I     +    P  +
Sbjct: 1   MQGLTDAPMRDLLTRIGGFDECVSEFVRITHTVHSRATWLKYAPEIANSNRTPSGVPCTV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D  K+ E A     FG  +I+LN GCP+  V++   GA L+  P+ +   +  + 
Sbjct: 61  QLLGSDEEKMAENALEAVRFGVRKIDLNFGCPAPTVNKHQGGAVLLKEPERIHRIVRTLR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +AL   IP++ K R+G +D+  A+      ++I + G   + +HAR  +           
Sbjct: 121 RALPDHIPLSGKMRLGFEDKTLALEN---AQAIAEGGACSLTVHARTKVEG--------Y 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTT 228
            P   +  V +I  +   + +  NG +  +   L  K     + VMIGR A     +   
Sbjct: 170 EPPAHWSWVKKIA-DAVSIPVTANGDVFTLRDYLDIKRESGCNSVMIGRGAVMCPDLARQ 228

Query: 229 VDEYFSNPLTGSSP 242
           + +Y +       P
Sbjct: 229 IKQYENGEEVCEMP 242


>gi|269962061|ref|ZP_06176415.1| tRNA-dihydrouridine synthase C [Vibrio harveyi 1DA3]
 gi|269833145|gb|EEZ87250.1| tRNA-dihydrouridine synthase C [Vibrio harveyi 1DA3]
          Length = 319

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 65/338 (19%), Positives = 134/338 (39%), Gaps = 43/338 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQLLPDHVFHRLCPELLQGSQTASGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G   I+LN GCP+  V++   GA L+ +P+++ + + A  
Sbjct: 68  QLLGQEPNWMAENAIKAAELGARGIDLNFGCPARLVNKSKGGAALLQHPELIHNVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 DAVPSDIPVSAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + +I++   D+ +  NG + +     + +    VD +M+ R A+ N   L  
Sbjct: 178 ASEIKWEYITQIRERF-DIPLIANGEIWNYEDGQRCIETTGVDSLMVCRGAF-NIPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           + +Y   P               W ++   +  Y+   +     L    ++ +    L  
Sbjct: 236 MVKYNHKP-------------MVWAEVVELLIYYSQFEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATHHIIETAFNLMIESL 322
            +P +    R I T    A    H  I+   + +   +
Sbjct: 283 AYPEANELFREIRTFNKAAPIVEH--IQRYRDELQSRV 318


>gi|238483959|ref|XP_002373218.1| dihydrouridine synthase family protein, putative [Aspergillus
           flavus NRRL3357]
 gi|220701268|gb|EED57606.1| dihydrouridine synthase family protein, putative [Aspergillus
           flavus NRRL3357]
          Length = 474

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 98/279 (35%), Gaps = 49/279 (17%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R           L Y+ M  A       +  +  F            
Sbjct: 50  MVDRSEFAWRMLTRSFMPPDDPKPMLAYSPMYHARLFREQLQMRLQHFHPTRAAIKGDDT 109

Query: 47  ---------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
                    ++PL +Q    +    +EAA+ V  +  + ++LN+GCP      G +GA L
Sbjct: 110 PYLDGNPAIDRPLFVQFCANNPDDFLEAARHVAPY-CDAVDLNLGCPQGIARRGHYGAFL 168

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             + D++   I  +   L +PVT K RI    Q          K I  +G + I +H R 
Sbjct: 169 QEDWDLIYKLINKLHTELDVPVTAKFRI----QETKEKTLEYAKMILSAGASIITLHGRT 224

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
              KG            D+  +  ++    P+  I  NG + +     + L     DGVM
Sbjct: 225 REQKG------HNTGVADWSYIRYLRDNLPPETVIFANGNILNYDDLERCLEETGADGVM 278

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                  + ++ +              P      +++WR
Sbjct: 279 SAEGNLSDPSVFS------------KPPPVGSEGREYWR 305


>gi|219117564|ref|XP_002179575.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408628|gb|EEC48561.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 233

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 101/236 (42%), Gaps = 17/236 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD +D  +R   R    N L +T MI A       +      +     Q++PL  QI G
Sbjct: 6   MVDQSDLPFRLLCRSYGTN-LCFTPMIHARLFTTNVEYRRKFTLQYGPPQDRPLIAQICG 64

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D+  +V  A  ++ +  + I++N GCP      G++GA L+   D++   +  + + LS
Sbjct: 65  GDVQAVVACALAMQPY-CDGIDINCGCPQNIAKRGNYGAFLLEQEDVLLPLVHTLLQHLS 123

Query: 117 IPVTVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +P++VK R+   +   A   A   L   +  +GV+ + IH R    KG            
Sbjct: 124 VPLSVKVRLLPAETRQASLEASLRLYTKLVDAGVHLLTIHGRTRHHKG------PLTGAA 177

Query: 175 DYDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           D+D +  +       + I  NGG+  +  A   L     DGVM   A  +  A+  
Sbjct: 178 DWDAIRVVVDRLGQRIPIFANGGVASLRDAQACLATTHADGVMSSEALLEYPALFA 233


>gi|304387694|ref|ZP_07369877.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis ATCC 13091]
 gi|304338263|gb|EFM04390.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis ATCC 13091]
          Length = 341

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 103/247 (41%), Gaps = 24/247 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 28  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 87

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 88  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 147

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K    
Sbjct: 148 ERLPAHIPLTAKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEGY 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 197 EPPAHWEWIRKI-RDTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 255

Query: 229 VDEYFSN 235
           + +Y S 
Sbjct: 256 IKQYESG 262


>gi|50121723|ref|YP_050890.1| tRNA-dihydrouridine synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612249|emb|CAG75699.1| putative dihydrouridine synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 310

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQCLPVKSFYRLCPELEHASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G + + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGARQF---EIADAVQQAGASELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D +M+GR A  N   L+ 
Sbjct: 178 AECINWQAIGEIRQRL-QIPVIANGEIWDWQSAQDCMATTGCDAIMLGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          +  + R
Sbjct: 236 VIKYNE-------------PRMPWPEVMLLLQKYVRLEKQGDTGMYHVAR 272


>gi|320036772|gb|EFW18710.1| dihydrouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 538

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 96/259 (37%), Gaps = 42/259 (16%)

Query: 1   MVDWTDRHYRFFARLLT-----NNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R        N  L Y+ M+ A             F            
Sbjct: 40  MVDRSEFAWRMLTRSFMKDNSPNPLLAYSPMLHARLFKDRAGYRSQHFEPVRPKADAVET 99

Query: 47  --------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                         ++PL +Q    D  +L+EAA+ V+ +  + ++LN+GCP     +G 
Sbjct: 100 SADPVPFLDGNPAIDRPLIVQFCANDPDELLEAARHVQQY-CDAVDLNLGCPQGIAKKGR 158

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA L   PD++   I  +   LSIPVT K RI               K I  +G + I 
Sbjct: 159 YGAFLQEEPDLIYRLINKLHTGLSIPVTAKFRIL----ETKEKTLEYAKMILSAGASFIT 214

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PS 209
           +H R+   KG            D+  +  ++    PD  I  NG + +     K L    
Sbjct: 215 VHGRRREQKG------HNTGVADWSYIRYLRDNLPPDTVIFANGNILNHDDIQKCLDATG 268

Query: 210 VDGVMIGRAAYKNSAMLTT 228
            DGVM       +  + + 
Sbjct: 269 ADGVMSAEGNLSDPTIFSE 287


>gi|294102360|ref|YP_003554218.1| dihydrouridine synthase DuS [Aminobacterium colombiense DSM 12261]
 gi|293617340|gb|ADE57494.1| dihydrouridine synthase DuS [Aminobacterium colombiense DSM 12261]
          Length = 339

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 64/306 (20%), Positives = 118/306 (38%), Gaps = 32/306 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T    R F R L   A  +TEM+    ++R + K+  +L    +E+P+ LQ+   D
Sbjct: 23  MAGVTIPPLRLFFRKLGAAA-THTEMVSCAGLMRSNTKSGNMLEICHKEEPVILQLFAGD 81

Query: 59  ISKLVEAAKIV---EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              L+ AA+         +  + +N+ CP  +V +   G+ L+ +P+     + ++ + L
Sbjct: 82  TKTLLTAAEKAMSEAPGRFAALGINMACPMPKVLKKGAGSRLLEDPEKATSMVKSLKE-L 140

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PV VK RI  +      A  +  + +  +G + + +H R            R     +
Sbjct: 141 GAPVWVKTRIYSERGFSMTA--SFCEKLLSAGADNVCVHGRTP--------SQRYAGVAN 190

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKNSAMLTTVDEYFS 234
              V+++ +  PD+ I  +G +    +AL  L      V I R A K+  +         
Sbjct: 191 RQSVFDLAETFPDM-ISASGDVFTPQEALDYLEKRCVSVFIARGALKDPFIFPQTLAALG 249

Query: 235 -----NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                  L  S  ++  +  +    I+   +   A  L        I R + G+F   P 
Sbjct: 250 FSVDNRLLCPSIGLQISLLVELGDHIAEMASPRLAEIL--------IKRLLSGMFKSIPG 301

Query: 290 SRRCRH 295
               R 
Sbjct: 302 IAELRR 307


>gi|319775859|ref|YP_004138347.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae F3047]
 gi|329123704|ref|ZP_08252264.1| tRNA-dihydrouridine synthase C [Haemophilus aegyptius ATCC 11116]
 gi|317450450|emb|CBY86666.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae F3047]
 gi|327469903|gb|EGF15368.1| tRNA-dihydrouridine synthase C [Haemophilus aegyptius ATCC 11116]
          Length = 310

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + N  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNNYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    D G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIDLGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A  + +   ++++ G   I +H R          D  +
Sbjct: 128 QAVPGEFPVSVKVRLGWDDISQAFEITD---AVEQGGATEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKIGEV-RERLFIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWCEIQKILQKYANVENEYDSGFYHVAR 272


>gi|311278876|ref|YP_003941107.1| dihydrouridine synthase DuS [Enterobacter cloacae SCF1]
 gi|308748071|gb|ADO47823.1| dihydrouridine synthase DuS [Enterobacter cloacae SCF1]
          Length = 345

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 112/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L     + L         +     + +
Sbjct: 35  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRLCPELHHNSRTPSGTLVRV 94

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 95  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYQGAKAMR 154

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  +
Sbjct: 155 EAVPAHLPVTVKVRLGWDSGDKRF---EIADAVQQAGATELVVHGRTKE-------DGYR 204

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + +I++    + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 205 AERINWQAIGDIRRRL-SIPVVANGEIWDWQSAQDCMAATGCDAVMIGRGAL-NIPNLSR 262

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y+         L  + R
Sbjct: 263 VVKY-------------NAPRMPWPEVMTLLQKYSRLEKQGDTGLYHVAR 299


>gi|116617846|ref|YP_818217.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
 gi|116096693|gb|ABJ61844.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           mesenteroides ATCC 8293]
          Length = 365

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/329 (20%), Positives = 136/329 (41%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + YTE   A +++    K      L  +  E+    QI G
Sbjct: 33  MEAVTDTVFRRVVAKAAAPDVYYTEFTNASSMVHPKAKFSVQGRLAVAEGEQQPVAQIWG 92

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   ++  + +++ D GY  +++N+GCP   V + S G+ L+ +PD+  + I A  ++ S
Sbjct: 93  SRPKEIAGSIEVLADMGYQAVDINMGCPDGTVIKNSSGSDLIRHPDLAEEIIVA-AQSGS 151

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R  +  I +  V  + +H R       +P     I     
Sbjct: 152 LPVSVKTRLGF---YKPEEFREWLPIILRHQVAVLTVHLRSRKEMSKAPAHYEHID---- 204

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +I+    +  P+  I +NG ++  +Q +   +  P +DG+MIGR  ++N       ++  
Sbjct: 205 EILAMRDEIAPNTLIQINGDIKTRAQGIALVQEHPGIDGIMIGRGIFENPYAF---EKEP 261

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S     +  D + ++S ++T      L    K+            GF ++   
Sbjct: 262 RQHTLEESIALLNLQLDLFDEVSETVTTKHFEALKRYFKI---------YLRGFAHASAL 312

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R +L ++   +T    I+      +  ++
Sbjct: 313 RQML-MDTHTTTEVREILTRELAKVYAAV 340


>gi|59712245|ref|YP_205021.1| tRNA-dihydrouridine synthase C [Vibrio fischeri ES114]
 gi|59480346|gb|AAW86133.1| tRNA-dihydrouridine synthase C [Vibrio fischeri ES114]
          Length = 315

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 60/287 (20%), Positives = 118/287 (41%), Gaps = 24/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +     TE + V D +L           +L    +    P+ L
Sbjct: 8   MEGVLDHLMRELLTEINDYDFCVTEFVRVVDQLLPPHVFHRICPELLNNSKTKSGTPIRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G + I+LN GCP+  V++   GA L+  P+++   + A  
Sbjct: 68  QLLGQEPNWMAENAARAIELGSDGIDLNFGCPAKAVNKSRGGAALLKEPELIYQVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     VT K R+G ++         +  +IK++G + + IHAR  +       D  K
Sbjct: 128 DAVSKDKKVTAKIRLGWENPEECFV---IADAIKQAGADELTIHARTKV-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +++++  D+ I  NG + +     + +    +D +M+ R A+ N   L  
Sbjct: 178 AEEIKWDYINQVRQKI-DIPIIANGEIWNYDDGQRCIAATGIDSLMVCRGAF-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           V ++  + +     I   +     +        Y+ R       L+Q
Sbjct: 236 VVKHNHSKMPWPEVIALLIHYSKLQMAGDKGQYYSNRVKQWLVYLRQ 282


>gi|148825450|ref|YP_001290203.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           PittEE]
 gi|148715610|gb|ABQ97820.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           PittEE]
          Length = 310

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRELLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSSTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ G   I +H R          D  +
Sbjct: 128 RAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGRTK-------SDGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + ++ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  WR+I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWREIQKILQKYAKVENEYDSGFYHVAR 272


>gi|255956875|ref|XP_002569190.1| Pc21g22200 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211590901|emb|CAP97117.1| Pc21g22200 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 536

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 105/281 (37%), Gaps = 52/281 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAI-----LR-----------GDKKN 39
           MVD ++  +R   R           L Y+ M  A        +R           G  K+
Sbjct: 44  MVDRSEFAWRMLTRSFMPPDDPKPLLAYSPMFHARLFGEQENVRTKHFQPTRKAIGGSKD 103

Query: 40  ILGFSTQ---EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            L        ++PL +Q    +  + +EAA+ V     + ++LN+GCP     +G +GA 
Sbjct: 104 ELFLDGNPAIDRPLFVQFCTNNPDEFLEAARHVAPH-CDAVDLNLGCPQGIAKKGHYGAF 162

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L  + D++   +  +   LSIPVTVK RI    Q          K I  +G + I +H R
Sbjct: 163 LQEDWDLIYRLVNRLHTELSIPVTVKFRI----QETKEKTLEYAKMILSAGASIIAVHGR 218

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLE---DMSQALKILPSVDG 212
           +   KG            D+  +  ++   P D  I  NG +    D+   L+     D 
Sbjct: 219 RREQKG------HNTGIADWSYIRYLRDNLPADTVIFANGNILNYGDIDTCLEA-TGADA 271

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           VM       + ++ +              P      +++WR
Sbjct: 272 VMSAEGNLSDPSIFS------------KPPPPGAEGREYWR 300


>gi|203284633|ref|YP_002222373.1| histidine phosphokinase/phophatase, putative [Borrelia duttonii Ly]
 gi|201084076|gb|ACH93667.1| histidine phosphokinase/phophatase, putative [Borrelia duttonii Ly]
          Length = 339

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 21/241 (8%)

Query: 1   MVDWTDRHYRFFARLLT----NNALLYTEMIVADAILRGDKKNILGF----STQEKPLAL 52
           M D TD  +R    L+        + +TE I    +L   K ++           +PL  
Sbjct: 25  MEDVTDTVFRNLVNLIGNGKDGPDIYFTEFISVKGLLNKSKNSMQHILTKNDELSRPLIA 84

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D  K V+A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 85  QIWGDDPDKFVKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAHEIIIASK 144

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A     +P++VK R G         + + +  + K G++ + +H R  I +   P D  
Sbjct: 145 EACLKYGLPLSVKTRHGFF----CSEVEDWLGFLLKLGIDMLTVHPRLVINQSEGPID-- 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
              N+  ++V    K NP + I  NG +  ++QA +++    +DG+M GR   KN  +  
Sbjct: 199 --VNVFDELVKLRNKINPYVVIIGNGDVLSLNQAYQMINKYSIDGIMFGRGILKNLNLFR 256

Query: 228 T 228
            
Sbjct: 257 R 257


>gi|303278554|ref|XP_003058570.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459730|gb|EEH57025.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 430

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 53/290 (18%), Positives = 104/290 (35%), Gaps = 35/290 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +   +L+G      +L     E    +QI G     + 
Sbjct: 75  NLPFRRVCKGL-GADITCGEMAMCTNLLQGQPNEWALLRRHPSEDLFGVQICGGYSDSVA 133

Query: 64  EAAKIVEDF-----GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++++D      G + +++N+GCP   V     G+ L+   + +     +    LS P
Sbjct: 134 RCSQLIDDVIVSQGGCDFVDINMGCPIDLVCNKGGGSMLLERHNRMEQIARSASSLLSCP 193

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R G  D        ++V  +K  GV  + +H R         +  R     D++ 
Sbjct: 194 LTLKTRTGYYDNKRVA--HDIVPKLKDWGVAAVTLHGRS--------RQQRYSRLADWEY 243

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSN 235
           +         + +  NG + +     K +    GV   MI R A     + T + E    
Sbjct: 244 IKNTAN-VSSVPLIGNGDVFNFRDYEKNVEGT-GVMTCMIARGALIKPWIFTEIKERRDW 301

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            ++ +  +           +      Y   H  S  +  + TR  +   L
Sbjct: 302 DISATERL----------DMLKRFAAYGLEHWGSDERGVENTRRFLLEWL 341


>gi|327288843|ref|XP_003229134.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Anolis
           carolinensis]
          Length = 624

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 49/282 (17%), Positives = 104/282 (36%), Gaps = 28/282 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD---KKNILGFSTQEKPLALQIGGAD 58
             W +  +R   +      +  +E+I +  + +GD             E    +Q+ G+ 
Sbjct: 261 AKWGNLPFRRICKRF-GADITCSEVISSQDLCQGDLEKCAEFFHRHESEDFFGIQVEGSA 319

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              +V+ A+ + +    + +++N   P   + E   G+ LM++P+   + +  M    ++
Sbjct: 320 PEHMVKCAEFLNERIQVDFVDINAEGPV--LFEKGSGSALMMHPNTFENIVRGMDYVSNV 377

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R G+           L+  + + G   + +H R         K++      D++
Sbjct: 378 PITVKLRSGISLDENLA--HTLIPDLHRWGAAMVTLHGRV--------KESTFRSPADWN 427

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +    +    + +   G +      LK     V GVMIGR A     + T + E     
Sbjct: 428 YISHCAQIAKPMPLFGCGDIFSFEDVLKAKQTGVSGVMIGRGALVKPWIFTEIKEMRHWD 487

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           ++    +           +    TDY   +  +     + TR
Sbjct: 488 ISAQERL----------DMLKEFTDYGLEYWGTDTNGVEKTR 519


>gi|254572950|ref|XP_002493584.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|238033383|emb|CAY71405.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|328354588|emb|CCA40985.1| potential tRNA dihydrouridine synthase similar to S. cerevisiae
           DUS4 (YLR405W) [Pichia pastoris CBS 7435]
          Length = 352

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 96/231 (41%), Gaps = 17/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  L+YT MI+A   +R        F+T   + P  +QIG  +
Sbjct: 44  MVRYSKLPFRELVRFY-NVDLVYTPMILAREFVRNKVARYSDFTTNIRDTPTIVQIGCNN 102

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+    ++  +  + I+LN GCP         GA LM  P+ V   +  + +     
Sbjct: 103 SVDLLRMVDMIHSY-VDGISLNCGCPIKEQVREGIGAALMTEPEKVSQMVRVVKEKYGDS 161

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I + + I        VK ++ +GV+ I +H R    +   P D   I       
Sbjct: 162 VCIETKIRIHNDIQ--ETIRFVKQVQDAGVDYITVHGRTKTTRSSKPVDLESI------- 212

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              I KE   + +  NG   D+     IL     DGVM  R   +N ++ +
Sbjct: 213 --RIIKEVARVPVIANGDCVDVKSFEHILDVTKCDGVMSVRGLLENPSLFS 261


>gi|281204195|gb|EFA78391.1| CCCH-type zinc finger-containing protein [Polysphondylium pallidum
           PN500]
          Length = 664

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 52/283 (18%), Positives = 113/283 (39%), Gaps = 27/283 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L  + +   EM +A  I++G K  +  L     E    +Q+ G  +  ++
Sbjct: 330 NLPFRRICKSLGVD-ITCGEMALASNIVQGHKGELALLKRHPSEDKFGVQLCGPHLDSMM 388

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            +A+ +ED    + +++N GCP   +     GA +M   + +   +  M   L+ P+T+K
Sbjct: 389 SSAEFIEDNLNVDFVDVNSGCPIDLICNMGAGAAMMDRQNRMEMILRGMSSVLTCPLTIK 448

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G  ++ P      ++ ++   G   + +H R         +  R     +++ + + 
Sbjct: 449 LRVGRTEENPNA--HKIIPNLGSWGAQAVTVHGRS--------RTQRYTRLANWEYIKQC 498

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            + +P + +  NG + +     K   S+  +M+ R A     + T + E     ++ S  
Sbjct: 499 AEISP-IPVIGNGDIYNWRDIEKSSDSISALMVARGALIKPWIFTEIKEKRDWDISASER 557

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
           +           +     +Y   H  S       TRH +   L
Sbjct: 558 L----------DLVKQFANYGLDHWGSDQLGVDNTRHFLLNWL 590


>gi|17543114|ref|NP_500379.1| hypothetical protein Y37E11B.5 [Caenorhabditis elegans]
 gi|4226107|gb|AAD12825.1| Hypothetical protein Y37E11B.5 [Caenorhabditis elegans]
          Length = 554

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 121/299 (40%), Gaps = 31/299 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +   EM +A +IL G   + ++L     EK   +Q+ G     + 
Sbjct: 216 NLPFRRICVDY-GADITCGEMALATSILSGTASEYSLLKRHPCEKIFGVQLAGGFADTMA 274

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVT 120
           +A++IV E+F  + I++N+GCP   V++   G  L   P  + + +AA    L    P+T
Sbjct: 275 KASQIVVENFDVDFIDINMGCPIDVVNQKGGGCALPSRPQKLFEVLAATKSVLGGCCPLT 334

Query: 121 VKCRIGVDDQI-PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           VK R G+ + +  A      +K       + I  H R         K+ R     ++D  
Sbjct: 335 VKIRTGMKEGVLKAPEYVEHMKKHSWHTPDLITFHPRS--------KEQRYTRLANWDFT 386

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + +++    + + + G +       + L    V+G+MIGR A     + T +DE  +  +
Sbjct: 387 FPVQEATKPVPLWVCGDILSWEDYYERLEQYPVNGIMIGRGALIKPWIFTEIDERRTWDI 446

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           + +              +     DY   H  S     + TR  +  F  F    +CR+I
Sbjct: 447 SSTERF----------DLLKKFVDYGLDHWGSDDAGVERTRRFLLEFLSF----QCRYI 491


>gi|315043678|ref|XP_003171215.1| hypothetical protein MGYG_07214 [Arthroderma gypseum CBS 118893]
 gi|311345004|gb|EFR04207.1| hypothetical protein MGYG_07214 [Arthroderma gypseum CBS 118893]
          Length = 568

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 56/282 (19%), Positives = 101/282 (35%), Gaps = 53/282 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGFST---------- 45
           MVD ++  +R   R  T        L Y+ M  A             F            
Sbjct: 57  MVDRSEFAWRMLTRSFTGEESSPPILAYSPMFHARFFNEAPAYRTQHFEPIRQTKAGTDE 116

Query: 46  ------------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
                        ++P  +Q    +  +L++AA+ VE+   + ++LN+GCP     +G +
Sbjct: 117 ATAEAYLDGNPKYDRPFIVQFCANNPDELLKAARHVEEH-CDAVDLNLGCPQGIAKKGHY 175

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           GA L  +PD++   I  +   LSIPVT K RI               + I  +G + + +
Sbjct: 176 GAFLQEDPDLIYKLINKLHTELSIPVTAKFRIL----ETKEKTLEYARMIISAGASILSV 231

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSV 210
           H R+   KG            +++ +  ++    P+  I  NG + +     + L     
Sbjct: 232 HGRRREQKG------HNTGVANWEYIRYLRDNLPPETVIFANGNILNHDDLSRCLEATGA 285

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           DGVM       +  + +            + P      + +W
Sbjct: 286 DGVMSAEGNLSDPTIFS------------TPPALGEEGRMYW 315


>gi|261253437|ref|ZP_05946010.1| tRNA-dihydrouridine synthase C [Vibrio orientalis CIP 102891]
 gi|260936828|gb|EEX92817.1| tRNA-dihydrouridine synthase C [Vibrio orientalis CIP 102891]
          Length = 317

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/320 (19%), Positives = 121/320 (37%), Gaps = 41/320 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDQLLPDHVFHRLCPELLQGSHTKSGVPVHI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++ + + A  
Sbjct: 68  QLLGQDPKWMAENAIRAAELGARGIDLNFGCPAKLVNKSKGGAALLQHPELIHNVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G ++         +V +I+ +G N + +HAR             K
Sbjct: 128 EAVPQGTPVTAKIRLGWENPDDCF---EIVDAIQSAGANELTVHARTKT-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++    + +  NG + +       +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWDYINQIRQRF-SIPLIANGEIWNYQDGQACIETTGVDSLMVCRGAFNVPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V    S                 W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKHNHS--------------VMPWTEVVELLLIYSQYEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGAS 304
            +P +    R I T    A 
Sbjct: 283 QYPEAAELFREIRTFNKAAP 302


>gi|28898849|ref|NP_798454.1| putative regulatory protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|153838187|ref|ZP_01990854.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
 gi|260364849|ref|ZP_05777427.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus K5030]
 gi|260879477|ref|ZP_05891832.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|260898224|ref|ZP_05906720.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|260903223|ref|ZP_05911618.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|38604770|sp|Q87N01|DUSC_VIBPA RecName: Full=tRNA-dihydrouridine synthase C
 gi|28807068|dbj|BAC60338.1| putative regulator protein [Vibrio parahaemolyticus RIMD 2210633]
 gi|149748446|gb|EDM59305.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
 gi|308088364|gb|EFO38059.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|308093520|gb|EFO43215.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|308106538|gb|EFO44078.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|308113931|gb|EFO51471.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus K5030]
          Length = 322

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/334 (18%), Positives = 129/334 (38%), Gaps = 43/334 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       ++    +T   P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQVLPDHVFHRLCPELMQGSQTTSGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQEPHWMAENAIRAAELGARGIDLNFGCPAKMVNKSKGGAALLQHPELIHSVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +IPV+ K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 DAVPANIPVSAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + +I++    + +  NG + +     + +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWEYINKIRERF-SIPLIANGEIWNFEDGQRCIETTGVDSLMVCRGAFNIPNLGNM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V           +P         W  +   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKH-------NHTP-------MVWSDVVDLLIYYSKFEMKGDKGLYYPNRVKQWFAYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATHHIIETAFNLM 318
            +P +    R I T    A    H  I+   + +
Sbjct: 283 SYPEANELFREIRTFNKAAPIVEH--IQRYRDEL 314


>gi|89093255|ref|ZP_01166205.1| NifR3/Smm1 family protein [Oceanospirillum sp. MED92]
 gi|89082551|gb|EAR61773.1| NifR3/Smm1 family protein [Oceanospirillum sp. MED92]
          Length = 298

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 120/283 (42%), Gaps = 27/283 (9%)

Query: 10  RFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLALQIGGADISK 61
           R     +       TE + V+D++L       L       G +    P+ LQ+ G+D S 
Sbjct: 2   RDLLTQVGGIDHCVTEFLRVSDSVLPAKVFRRLCPELHNGGRTPSGTPVILQLLGSDPSV 61

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           L   A+     G   I+LN GCP+  V+    GA L+  P+++ + + A+ +A+   +PV
Sbjct: 62  LAGNARKGAKLGAPGIDLNFGCPAKTVNRSKGGAVLLDTPELIYEIVKAVREAVPEGVPV 121

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           + K R+G  D+  A        +IK +G + + +HAR         K     P   ++ +
Sbjct: 122 SAKMRLGNKDKSLA---MENAHAIKDAGADSLAVHART--------KLEGYKPPAHWEWI 170

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             I +E  D+ +  NG +       +       D VMIGR       +   +  +  N  
Sbjct: 171 SRI-REAIDIPVVANGEVWSWDDYQRCREVSGCDDVMIGRGLIAKPDLAKVIKHHQVNE- 228

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           + +S     V K     ++    D AA+++H  G+++Q   H+
Sbjct: 229 SFTSFNWDHVLKLVELYLNRIEQDIAAKYVH--GRIKQWLHHL 269


>gi|156933286|ref|YP_001437202.1| tRNA-dihydrouridine synthase C [Cronobacter sakazakii ATCC BAA-894]
 gi|156531540|gb|ABU76366.1| hypothetical protein ESA_01098 [Cronobacter sakazakii ATCC BAA-894]
          Length = 310

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 117/324 (36%), Gaps = 43/324 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTGVNDYDLCITEFLRVVDSLLPVKSFYKLCPELHHESRTPSGTRVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 68  QLLGQHPQWLAENAARAVELGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGARRF---EIADAVQQAGATELVVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI +E   + +  NG + D + A   +     D +MIGR A  N   L+ 
Sbjct: 178 AERINWAAIGEI-RERLTIPVIANGEIWDYASAQACMAETGCDAIMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W  +   +  Y          +  + R    +  L  
Sbjct: 236 VIKYNE-------------PRMPWPDVVQLLQQYTRLEKQGDTGMYHVARIKQWLGYLRK 282

Query: 286 GFPNSRRCR---HILTVEAGASTA 306
            +  +         LT  A  + A
Sbjct: 283 EYAEATELFSEIRALTTSAAIADA 306


>gi|309972569|gb|ADO95770.1| tRNA-dihydrouridine synthase YohI [Haemophilus influenzae R2846]
          Length = 310

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 111/290 (38%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRELLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    D G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIDLGSHGVDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ GV  I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGVTEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWYEIQKILQKYANVENEYDSGFYHVAR 272


>gi|156102342|ref|XP_001616864.1| tRNA-dihydrouridine synthase [Plasmodium vivax SaI-1]
 gi|148805738|gb|EDL47137.1| tRNA-dihydrouridine synthase, putative [Plasmodium vivax]
          Length = 340

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 99/231 (42%), Gaps = 16/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ A   +  +K     F    +++P+  Q  G +
Sbjct: 33  MVDLSELAFRLLCRNY-NCHLTFTPMLHAKNFVEHEKYRKSYFQSCEKDEPVIAQFCGNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ A + +++   N ++LN+GCP     +G++GA L+   D V + ++ +    +IP
Sbjct: 92  SKIILNAIEYIKNE-VNAVDLNLGCPQQIAKKGNYGAFLLQKHDEVVNLVSDITNNCNIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R    D        NL   ++   V  I +H R    KG        I   DY+I
Sbjct: 151 ITCKIRKIDQD---YQKTLNLCYDLQSRNVKMITVHGRTKEEKGT------NIKQCDYEI 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  I KE  ++ I  NG +E      K L     D VM      +     +
Sbjct: 202 IK-IIKERLNIPIIANGSIEHFEDIQKCLNYTKADAVMCAEILLEKPYFFS 251


>gi|260598603|ref|YP_003211174.1| tRNA-dihydrouridine synthase C [Cronobacter turicensis z3032]
 gi|260217780|emb|CBA32227.1| tRNA-dihydrouridine synthase C [Cronobacter turicensis z3032]
          Length = 320

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 68/324 (20%), Positives = 118/324 (36%), Gaps = 43/324 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 18  MEGVLDSLVRELLTGVNDYDLCITEFLRVVDSLLPVKSFYKLCPELHHESRTPSGTRVRV 77

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +PD++     AM 
Sbjct: 78  QLLGQHPQWLAENAARAVALGSWGVDLNCGCPSKLVNGSGGGATLLKDPDLIYRGAKAMR 137

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 138 EAVPAHLPVTVKIRLGWDSGARRF---EIADAVQQAGATELVVHGRTKE-------DGYK 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI +E   + +  NG + D + A   +     D VMIGR A  N   L+ 
Sbjct: 188 AERINWAAIGEI-RERLTIPVIANGEIWDYASAQACMAETGCDAVMIGRGAL-NVPNLSR 245

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++   +  Y          +  + R    +  L  
Sbjct: 246 VIKYNE-------------PRMPWPEVVQLLQQYTRLEKQGDTGMYHVARIKQWLGYLRK 292

Query: 286 GFPNSRR-CR--HILTVEAGASTA 306
            +  +    R    LT  A  + A
Sbjct: 293 EYAEATELFREIRALTTSAAIADA 316


>gi|197336215|ref|YP_002156459.1| tRNA-dihydrouridine synthase C [Vibrio fischeri MJ11]
 gi|197317705|gb|ACH67152.1| tRNA-dihydrouridine synthase C [Vibrio fischeri MJ11]
          Length = 315

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/287 (20%), Positives = 118/287 (41%), Gaps = 24/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +     TE + V D +L           +L    +    P+ L
Sbjct: 8   MEGVLDHLMRELLTEINDYDFCVTEFVRVVDQLLPPHVFHRICPELLNDSKTKSGTPIRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G + I+LN GCP+  V++   GA L+  P+++   + A  
Sbjct: 68  QLLGQEPNWMAENAARAIELGSDGIDLNFGCPAKAVNKSRGGAALLKEPELIYQVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     VT K R+G ++         +  +IK++G + + IHAR  +       D  K
Sbjct: 128 DAVSKDKKVTAKIRLGWENPEECFV---IADAIKQAGADELTIHARTKV-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +++++  D+ I  NG + +     + +    +D +M+ R A+ N   L  
Sbjct: 178 AEEIKWDYINQVRQKI-DIPIIANGEIWNYDDGQRCIAATGIDSLMVCRGAF-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           V ++  + +     I   +     +        Y+ R       L+Q
Sbjct: 236 VVKHNHSKMPWPEVIALLIHYSKLQMAGDKGQYYSNRVKQWLVYLRQ 282


>gi|157144926|ref|YP_001452245.1| tRNA-dihydrouridine synthase C [Citrobacter koseri ATCC BAA-895]
 gi|157082131|gb|ABV11809.1| hypothetical protein CKO_00655 [Citrobacter koseri ATCC BAA-895]
          Length = 312

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       I         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQLLPVKVFHRICPELHNASRTASGTVVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKMVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R             K
Sbjct: 128 EAVPAHLPVTVKVRLGWDSGERKF---EIADAVQQAGATELVVHGRTKE-------QGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + EI++    + +  NG + D   A + +     D VM+GR A  N   L+ 
Sbjct: 178 AEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQECMAVSGCDAVMMGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VVKYNE-------------PRMPWPEVVLLLQKYTRLEKQGDTGLYHVAR 272


>gi|114799466|ref|YP_760712.1| putative tRNA-dihydrouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114739640|gb|ABI77765.1| putative tRNA-dihydrouridine synthase [Hyphomonas neptunium ATCC
           15444]
          Length = 345

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 63/286 (22%), Positives = 111/286 (38%), Gaps = 23/286 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGAD 58
           M   TD   R  A        + +EM+  + +   R D               +Q+    
Sbjct: 28  MSGATDAPMRRQAVHF-GAPAVVSEMVAGEMLAKARADVVRRTCRHEGAGYWIVQLAARR 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSI 117
              ++  A ++ + G + I++N+GCPS +V  G  G+ LM +  + G+ I AA+  A   
Sbjct: 87  PEDMLAGAVLMAEAGVDVIDINMGCPSKQVTGGQSGSALMRDLPLAGEIIDAALQGAAGR 146

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT+K R+G DD+   +    L    +  GV  + +H R         +        ++ 
Sbjct: 147 PVTLKMRLGWDDE--NLNAPELAVMAQDRGVQMLTVHGRT--------RCQFYTGGANWA 196

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            V     +   L + +NG + D + A + L      GVM+GRAA     ++  V      
Sbjct: 197 AVRATV-DAVSLPVIVNGDISDTASAREALAQSGAYGVMLGRAAMGRPWLVGEVAAALEG 255

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                 P           +I+ S+  Y A        L+ + +H+ 
Sbjct: 256 R-AWRRPALNEQLASLCEQITDSIDLYGAS-----LGLRMVRKHVS 295


>gi|25144369|ref|NP_498078.2| hypothetical protein C45G9.2 [Caenorhabditis elegans]
 gi|21431919|sp|Q09504|YQI2_CAEEL RecName: Full=Uncharacterized tRNA-dihydrouridine synthase-like
           protein C45G9.2
 gi|16259260|gb|AAA62547.2| Hypothetical protein C45G9.2 [Caenorhabditis elegans]
          Length = 284

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 61/281 (21%), Positives = 109/281 (38%), Gaps = 34/281 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           MV ++   +R   R+   + + +T MI A   +     + + L     + PL +Q    D
Sbjct: 1   MVRYSKLAFRQLVRVYDVD-VCFTPMIYAKNFIESEKCRSSELSVCEGDSPLIVQFATDD 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L EAA++V       ++LN GCP   V    FG+ L+  P+++ D +      +  P
Sbjct: 60  PFVLSEAAEMVYK-CSTGVDLNCGCPKHDVRSKGFGSALLSKPELLADMVRQTRARIPDP 118

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L +  + +GV  + +H R    +            +D
Sbjct: 119 DFSVSLKIRINHDIEKTV----DLCRKAEAAGVTHLTVHGRTPSQR---------AEPID 165

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              +  I K++  + I  NGG+    +A  L     VDG+M       N A+    +   
Sbjct: 166 IQAL-RIVKDSVSVPIIANGGITTREEALFLAEQTGVDGIMAANGLLDNPALFAGHEH-- 222

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                      +   ++F R       D+   H H    L+
Sbjct: 223 ---------TPSDCVENFMRLSREYGLDWLLYHQHLQYMLR 254


>gi|313234425|emb|CBY24624.1| unnamed protein product [Oikopleura dioica]
          Length = 636

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 101/259 (38%), Gaps = 12/259 (4%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +    + +   EM     ++ G      ++     E    +QI GA   +L 
Sbjct: 295 NMPFRRVCKDYGVD-ITCGEMATCRNLVMGKMSEWALVQRHASEDFFGVQIAGAWPDELS 353

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++ +F   + I++N GCP   + +   G  L   PD +  CI++M     +PVT K
Sbjct: 354 KTAELISEFCDVDFIDINCGCPLDLICKTGGGCRLGKAPDKLAGCISSMKTTSGLPVTCK 413

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G + Q        L+  +K++    I +H R  I +         I     +   E+
Sbjct: 414 IRTGWEPQHDMA--HKLIAKLKEAQPALITLHGRSRICRYTGVARWDYINECS-EASSEV 470

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            KE  D+    NG +   S   + +     DG MIGR A     +   + E     +  S
Sbjct: 471 AKEI-DVPFFGNGDVLSYSDYAEAIEKYGTDGAMIGRGALIKPWVFEEIKE--QKVMDPS 527

Query: 241 SPIKTRVDKDFWRKISASM 259
           S  +  + K F R      
Sbjct: 528 SSERMDMLKKFVRYGLEHW 546


>gi|321469164|gb|EFX80145.1| hypothetical protein DAPPUDRAFT_304174 [Daphnia pulex]
          Length = 303

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 136/326 (41%), Gaps = 51/326 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      L +T MI++D+ ++  K   + F+T +  +PL +Q    +
Sbjct: 18  MVRYSKLPFRLLVRKY-GCDLAFTPMIISDSFIQAPKARDIEFTTCDADQPLIVQFAAHN 76

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
            +    AA++V     N ++LN GCP     +  +GACL+  P+++ D +      +   
Sbjct: 77  STDFATAAELVA-STCNGVDLNCGCPQKWAMQQGYGACLINKPELLRDVVLQTRNRIPSN 135

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  + +        L + ++ +G++ + +H R         KD R    ++
Sbjct: 136 DFTVSIKIRIHPEIRKTV----ELCQQVEAAGLSFLTVHGRT--------KDQRS-DPVN 182

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + V  IK E+  + +  NG +  +  A   + + +V+GVM  R   +N AM     E  
Sbjct: 183 LEGVKLIK-ESVRVPVIANGDICSLQDAEHVQQITNVNGVMSARGILENPAMFAGFSE-- 239

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNS-R 291
                  +PI               + D+    L +G        H+I +         R
Sbjct: 240 -------TPI-------------ECIKDWMKLSLETGISFTHFHHHLIYMCEKNMSRVDR 279

Query: 292 RCRHILTVEAGASTATHHIIETAFNL 317
           R  + L+    ++TA    +E   +L
Sbjct: 280 RYFNALS----STTAVIDYMENYLSL 301


>gi|253576271|ref|ZP_04853602.1| dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251844398|gb|EES72415.1| dihydrouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 326

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 65/329 (19%), Positives = 122/329 (37%), Gaps = 37/329 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D T   +R          + +TE    ++    +  +     L F+  E+P+   I G
Sbjct: 21  MEDVTHVVFRHVVSKAGRPDVFFTEFANTESYCHPEGNHSVRGRLLFTEDEQPMVAHIWG 80

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  +   G+  I++N+GCP   V     G+ L+L P +  + I A  KA  
Sbjct: 81  DKPEYFEKMSIDMAKLGFQGIDINMGCPVPNVATNGKGSGLILRPSVAAEVIQA-AKAGG 139

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  +  I K  +  + IH R         ++        +
Sbjct: 140 LPVSVKTRLGFTE---VEEWREWLTHILKQDIVNLSIHLRT--------REEMSQVAAHW 188

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML-TTV 229
           +++ EIK    +  P   + +NG + D    LK+     VDG+MIGR  +KN        
Sbjct: 189 ELIPEIKALRDQVAPQTLLTINGDIPDRQTGLKLAEQYGVDGIMIGRGIFKNPFAFEKEP 248

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
            E+ +        +   +   +  ++ A    + A                     GF  
Sbjct: 249 REHSTTEYLDLLRLHLDLHDQYSNQLEA--RPFKALQRFFKV-----------YVKGFRG 295

Query: 290 SRRCRHILTVEAGASTATHHIIETAFNLM 318
           +   R+ L +   ++     +++     M
Sbjct: 296 ASELRNQL-MSTSSTDEVREMLDEFTQQM 323


>gi|328855959|gb|EGG05082.1| hypothetical protein MELLADRAFT_48857 [Melampsora larici-populina
           98AG31]
          Length = 448

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 102/252 (40%), Gaps = 27/252 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +   EM +   ++    ++ +++     EK   +Q+ G+    LV
Sbjct: 99  NLPFRRLCSTLGCE-ITCGEMALCQDLIGANTNEWSLVKRHPSEKIFGVQVAGSRPQLLV 157

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
            AA+++  +   + +++N GCP   V +   GA L+ +   +G  +  M K L  IP+T+
Sbjct: 158 PAAEMIGNELKVDFVDVNCGCPIDLVFKKGSGAALLEHTQRLGKSLIGMSKVLKEIPLTI 217

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+ +         ++  ++  GV    +H R         +  R     D++ + E
Sbjct: 218 KLRTGITEGKNLA--HKIIPQLQHWGVGATTLHGRS--------RQQRYSKRADWNYISE 267

Query: 182 IKK----------ENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTV 229
             K          + P + I  NG   D  +  +   +  VDG+MI R A     + T +
Sbjct: 268 CVKTLHRTFEEEPDLPQIPIFGNGDCYDYREYYENMEMSGVDGIMIARGALTKPWIFTEI 327

Query: 230 DEYFSNPLTGSS 241
            E     ++   
Sbjct: 328 KERRDWDISSRE 339


>gi|330810804|ref|YP_004355266.1| tRNA-dihydrouridine synthase C [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327378912|gb|AEA70262.1| tRNA-dihydrouridine synthase C [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 319

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 64/322 (19%), Positives = 121/322 (37%), Gaps = 34/322 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE I      +  A        +L    +    PL +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVNDRLLTPAYFHKLAPELLTGAQTAAGVPLRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++ + +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGSEVIDLNFGCPAKTVNKSRGGAVLLKEPELLNEIVEHVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D    A+       ++ + G   I +HAR  +           
Sbjct: 128 RAVPKHIPVTAKMRLGFDSPDGALV---CATALAEGGAAHIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + +E   + +  NG +  +    +      V+ +M+GR       +   
Sbjct: 177 KPPAHWEWIPRV-QEVVKVPVFANGDIWSVEDWRRCREISGVEDIMLGRGLVSRPDLARQ 235

Query: 229 VDEYFSNP--LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +    +    +  S      + +DFW ++   +T        + G+L+Q    +  L   
Sbjct: 236 IAAARAGEDVVEMSWAELQPMLQDFWVQVVEQLTP-----RQAPGRLKQW---LAMLTRN 287

Query: 287 FPNSRRCRHILTVEAGASTATH 308
           +P +      L  E       H
Sbjct: 288 YPEAVALFTALRRETDLDAVGH 309


>gi|281355584|ref|ZP_06242078.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
 gi|281318464|gb|EFB02484.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
          Length = 334

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 118/293 (40%), Gaps = 27/293 (9%)

Query: 1   MV---DWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIG 55
           M     +TD  YR  AR        +TEM+   ++    +++  +L    +E+ L +Q+ 
Sbjct: 11  MAPLSGFTDLPYRRAAR-AGGCRFAFTEMVDVASLTYARERSAGMLRRGPEEEFLGVQLV 69

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           GAD   +  AA +V ++ ++ ++ N+GCP  +V +   GA L  + D    C A + +  
Sbjct: 70  GADHEFIRRAADVVNEYEFSVVDFNLGCPVPKVAKKGAGAELGRHLDAALACFAIIAERS 129

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             PVT K RI VD + PA  L  L K + + G   I +H R         K+      ++
Sbjct: 130 RHPVTAKIRI-VDAEDPAPTLA-LAKGLAELGAQAITVHGRI--------KEAFYSGPVN 179

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + ++  +++  P + +  NGG+    +  +I        VM+ R A  N  +        
Sbjct: 180 FGMIRAVREALPGVQVIANGGVTGRVKYQEIRRETGCSLVMLARGAMGNPWLFNE----L 235

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           S       P     D D W  +     +           ++   + +     G
Sbjct: 236 SLGDAYVPP-----DIDEWFGVIREHVEGMIELYGEESAMRMARKILHDYLKG 283


>gi|325204077|gb|ADY99530.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M01-240355]
          Length = 333

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 104/253 (41%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   + E A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAENALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|300175488|emb|CBK20799.2| unnamed protein product [Blastocystis hominis]
          Length = 562

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 59/292 (20%), Positives = 109/292 (37%), Gaps = 33/292 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM +   +L+G      +L     E+   +QI      +  
Sbjct: 219 NLPFRRLCVEF-GADITCSEMAITTNLLKGQVSEWALLRRHPCERVFGVQIATGRPDEAR 277

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTV 121
           + A+++  +F  + ++LN GCP   + +   GA LM +P  +   +  +      +PV  
Sbjct: 278 KTAELLRREFRCDFLDLNCGCPIDVLDKMGAGAALMGHPSKLRRILTGVLDGAETLPVVC 337

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           K R G  +      + +L     + G  V+ + IH R  +         R     D++ V
Sbjct: 338 KLRTGDRENSLEKFVGSLAALQGRRGNRVSALTIHGRTKV--------GRYTKLADWEYV 389

Query: 180 YEI----KKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
            +     K+   D+ +  NG + D     + L S  + GVMIGR A     + T + E  
Sbjct: 390 EKCAALAKQSASDVQVIGNGDVFDHEMYYEHLQSGVLSGVMIGRGALIKPWICTEIKERR 449

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
              ++    +          +I     DY   H  S  +    TR  +   L
Sbjct: 450 HWDISAGERL----------EIVKRFCDYGLEHWGSDEQGVDRTRRFLLEWL 491


>gi|149028167|gb|EDL83605.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_b
           [Rattus norvegicus]
          Length = 304

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 95/244 (38%), Gaps = 22/244 (9%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLM 98
           +L     E    +Q+ GA    + + A+++      + +++NVGCP   V++   G  LM
Sbjct: 6   LLKRHPCEDIFGVQLEGAFPDTMTKCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALM 65

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
                    +  M + L +P+TVK R GV +++       L+  ++  GV  + +H R  
Sbjct: 66  NRSAKFQQIVRGMNEVLDVPLTVKMRTGVQERVSLA--HRLLPELRNWGVALVTLHGRS- 122

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGR 217
                  ++ R     D+  + +  K    + +  NG +     A   +   V G+M+ R
Sbjct: 123 -------REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFEDANCAMQTGVAGIMVAR 175

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            A     + T + E     ++ S  +           I    T Y   H  S  +  + T
Sbjct: 176 GALLKPWLFTEIKEQRHWDISSSERL----------DILRDFTHYGLEHWGSDTQGVERT 225

Query: 278 RHMI 281
           R  +
Sbjct: 226 RRFL 229


>gi|255714144|ref|XP_002553354.1| KLTH0D14806p [Lachancea thermotolerans]
 gi|238934734|emb|CAR22916.1| KLTH0D14806p [Lachancea thermotolerans]
          Length = 348

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 105/237 (44%), Gaps = 18/237 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R     +  FS+ E   PL +Q+G  +
Sbjct: 38  MVRYSKLPFRQVCRHY-NVDIVYTPMILAREYVRNCHARMADFSSNESDSPLIVQVGVNN 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L+   ++V  +  + I +N GCP         G+ L+ NP+++   ++A+       
Sbjct: 97  VTDLLRFVEMVSPY-CDGIGINCGCPIKEQVREGIGSALIYNPELLSSMVSAVKTKYGDK 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I + D        +L   +  +GV+ I IH R         +  R    ++ D 
Sbjct: 156 VRLETKIRIHDNWDQTV--DLCNQLCDAGVDWITIHGRT--------RTTRSSEPVNLDA 205

Query: 179 VYEI--KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +  I  K ++ ++ +  NG   DMS   KIL     DGVM  R    N A+      
Sbjct: 206 IKFITQKIKSRNVPVIANGDCFDMSDFQKILDYTGADGVMAVRGLLDNPALFGGFKA 262


>gi|213025593|ref|ZP_03340040.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 146

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 73/128 (57%), Positives = 92/128 (71%), Gaps = 1/128 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VKCRIGVD 128
           VK RIG+D
Sbjct: 139 VKTRIGID 146


>gi|254804888|ref|YP_003083109.1| putative dihydrouridine synthase [Neisseria meningitidis alpha14]
 gi|254668430|emb|CBA05633.1| putative dihydrouridine synthase [Neisseria meningitidis alpha14]
          Length = 333

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 61/324 (18%), Positives = 122/324 (37%), Gaps = 36/324 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + +I       I     +    P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTPVGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V+    GA L+  P ++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNRHKGGAILLKEPQLIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 ERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ---ITRHMIG--- 282
           + +Y +      +         + R+         A + +   +L+Q   + +   G   
Sbjct: 248 IKQYENGGPVKDTDFAE--VSKWIRQFFELCLTKEANNKYPIARLKQWLGMMKKTSGPAQ 305

Query: 283 -LF---HGFPNSRRCRHILTVEAG 302
            LF       ++   R IL     
Sbjct: 306 TLFDRVRTVKDADEVRRILNAFEH 329


>gi|183220020|ref|YP_001838016.1| tRNA-dihydrouridine synthase C [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910141|ref|YP_001961696.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167774817|gb|ABZ93118.1| tRNA-dihydrouridine synthase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167778442|gb|ABZ96740.1| tRNA-dihydrouridine synthase C [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 316

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 107/251 (42%), Gaps = 24/251 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--------FSTQEKPLAL 52
           M    D   R     +       +E I  +  L    +             +  + P+ +
Sbjct: 8   MEGLLDFRLREILTQIGGYDECVSEFIRVNDTLLPPHRFFRTAPELKNSSRTKSDTPVKI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G+D +++ + A +V   G   I++N GCP+  V+    GA L+  P+++   + A+ 
Sbjct: 68  QILGSDPNRMADNAHLVASLGAYGIDINFGCPAPTVNRNRGGAALLKEPNLMYSIVKAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             +  +IPVT K R+G +    A+   +  K++++ G   I +HAR         K +  
Sbjct: 128 NVVPENIPVTAKMRLGYESTELAL---DCAKALEEGGAKEIVVHART--------KTDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +IK     + +  NG +  +  A++   +   D +MIGR A  N ++   
Sbjct: 177 KPPAYWEWIAKIK-SILKINVIANGEIWTVQDAIQCQKISGCDDIMIGRGAVTNPSIALL 235

Query: 229 VDEYFSNPLTG 239
           + +     ++ 
Sbjct: 236 IKKKLEERMSW 246


>gi|320583735|gb|EFW97948.1| dihydrouridine synthase [Pichia angusta DL-1]
          Length = 338

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 102/236 (43%), Gaps = 17/236 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      ++Y+ MI+A   +R        FST   ++PL +QIG  +
Sbjct: 29  MVRYSKLPFRELVRDY-KVDIVYSPMILAREFVRNHNARASDFSTNHRDRPLIVQIGANN 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L+    ++  +  + + LN GCP         GA LM   ++V + + A+ +     
Sbjct: 88  VTDLLRMIDMIHPY-VDGVGLNCGCPIKDQVREGIGAALMSKKELVAEMVHAVKEKYGSK 146

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I V   I        VK ++ +GV+ I +H R         K+ R     +++ 
Sbjct: 147 LVIETKIRVHHDIQ--ETIEFVKMVEAAGVDFITVHGRT--------KNTRSSEPCNFEK 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +  IK E   + +  NG    +  A +I      DGVM  R    N AM    ++ 
Sbjct: 197 IKAIK-EAVSVPVIANGDCRSLEDAFRIAKDTGCDGVMAARGILNNPAMFAGYEKA 251


>gi|54309774|ref|YP_130794.1| putative regulator protein [Photobacterium profundum SS9]
 gi|46914212|emb|CAG20992.1| putative regulator protein [Photobacterium profundum SS9]
          Length = 301

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 64/316 (20%), Positives = 120/316 (37%), Gaps = 47/316 (14%)

Query: 20  ALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLALQIGGADISKLVEAAKIVED 71
            L  TE + + D++L       L       G +T   P+ +Q+ G +   + E A    +
Sbjct: 12  DLCVTEFVRIIDSLLPSSVFYRLCPELHHGGKTTSGTPVRVQLLGQEPVWMAENAYRASN 71

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDD 129
            G   I++N GCP+  V++   GA L+  P+ +   +  +  A+  + PVT K R+G DD
Sbjct: 72  LGSAGIDINFGCPAKSVNKNRGGAVLLKEPEKIYQIVKEVRSAVCPTKPVTAKVRLGWDD 131

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                    +V ++ ++G + I IHAR  +       D  K   + +D ++++K E   +
Sbjct: 132 PTHCF---EIVDAVAQAGGDEIAIHARTKV-------DGYKAETIKWDYIHQVK-EKSSI 180

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
            I  NG + +       L     D +MI R A     +   +                  
Sbjct: 181 PIIANGEVWNYQDGQACLNVTQTDALMICRGALNLPNLCNVIKR--------------NE 226

Query: 248 DKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFHGFPNSRRCR---HILTVEA 301
               W  +   +  ++   +     L    ++ +    L H +P ++        L   A
Sbjct: 227 AHMPWHHVIQLLLKFSEFEIKGDKGLYYPNRVKQWFAYLRHEYPEAKDLFVDIRSLNKAA 286

Query: 302 GASTATHHIIETAFNL 317
                   I++ A  L
Sbjct: 287 P----IVEILQRAQAL 298


>gi|229844973|ref|ZP_04465110.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           6P18H1]
 gi|229812107|gb|EEP47799.1| DnaJ-like membrane chaperone protein [Haemophilus influenzae
           6P18H1]
          Length = 310

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPECLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G D+   A     +  ++++ G   I +H R          D  +
Sbjct: 128 QAVPSEFPVSVKVRLGWDNISQAF---EIADAVEQGGATEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E+  + +  NG +         L       +M GR A     +   
Sbjct: 178 ADRINWKKIGEV-REHLSIPVIANGEIWHWQNGQDCLSQTGCQDLMAGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWCEIQKILQKYAKVENEYDSGFYHVAR 272


>gi|203288167|ref|YP_002223182.1| histidine phosphokinase/phophatase, putative [Borrelia recurrentis
           A1]
 gi|201085387|gb|ACH94961.1| histidine phosphokinase/phophatase, putative [Borrelia recurrentis
           A1]
          Length = 339

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 21/241 (8%)

Query: 1   MVDWTDRHYRFFARLLT----NNALLYTEMIVADAILRGDKKNILGF----STQEKPLAL 52
           M D TD  +R    L+        + +TE I    +L   K ++           +PL  
Sbjct: 25  MEDVTDTVFRNLINLIGNGKDGPDIYFTEFISVKGLLNKSKNSMQHILTKNDELSRPLIA 84

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D  K V+A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 85  QIWGDDPDKFVKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAHEIIIASK 144

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A     +P++VK R G         + + +  + K G++ + +H R  I +   P D  
Sbjct: 145 EACLKYGLPLSVKTRHGFF----CSEVEDWLGFLLKLGIDMLTVHPRLVINQSEGPID-- 198

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
              N+  ++V    K NP + I  NG +  ++QA +++    +DG+M GR   KN  +  
Sbjct: 199 --VNVFDELVKLRNKINPYVVIIGNGDVLSLNQAYQMINKYSIDGIMFGRGILKNLNLFR 256

Query: 228 T 228
            
Sbjct: 257 R 257


>gi|330446569|ref|ZP_08310221.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328490760|dbj|GAA04718.1| tRNA dihydrouridine synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 298

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 63/323 (19%), Positives = 121/323 (37%), Gaps = 47/323 (14%)

Query: 10  RFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLALQIGGADISK 61
           R     + +  L  TE + V D++L       L       G +    P+ +QI G D   
Sbjct: 2   REMLTEINDYDLCVTEFVRVIDSLLPNSVFYRLCPELHQGGKTRSGTPVRVQILGQDPDW 61

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPV 119
           + E A+     G   +++N GCP+  V++   GA L+  P+ +   + A   A++   P+
Sbjct: 62  MAENAQRACSLGSAGVDINFGCPAKAVNKSRGGAVLLKEPERIYQIVKACRAAVNPVKPL 121

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T K R+G DD         +  +I ++G + + +HAR          D  +   + +D +
Sbjct: 122 TAKVRLGWDDPSQCF---EIADAIAQAGADELVVHARTKE-------DGYRADTIKWDYI 171

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++K++   L I  NG + +       L +   D +M+ R A     +   V        
Sbjct: 172 NQLKQQV-KLPIIANGEVWNYQDGQNCLTATDTDALMVCRGALNLPNLGNVVKH------ 224

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFHGFPNSRRCR 294
                         W ++   +  Y+   +     L    ++ +    L H +P ++   
Sbjct: 225 --------DAPHMTWEEVLDLLLVYSQYEIKGDKGLYYPNRVKQWFSYLRHEYPQAKALF 276

Query: 295 ---HILTVEAGASTATHHIIETA 314
                L   A        I++ A
Sbjct: 277 TDLRALNKAAP----IIEILQQA 295


>gi|145635178|ref|ZP_01790883.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittAA]
 gi|145267599|gb|EDK07598.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittAA]
          Length = 310

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 109/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPEYLAENAIRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   +     +  ++++ G   I +H R          D  +
Sbjct: 128 RAVPSEFPVSVKVRLGWDDISQSF---EIADAVEQGGATEITVHGRTKT-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + ++ +E   + +  NG +         L       +M GR A     +   
Sbjct: 178 ADRINWKKIGKV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMAGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWCEIQKVLQKYAKVENEYDSGFYHVAR 272


>gi|134055604|emb|CAK37250.1| unnamed protein product [Aspergillus niger]
          Length = 466

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 94/238 (39%), Gaps = 22/238 (9%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILR--GDKKNILGFSTQ-EKPLAL 52
           MVD ++  +R   R           L Y+ M  A        D+   L  +   ++PL +
Sbjct: 50  MVDRSEFAWRMLTRSFMTPEDQKKVLAYSPMYHARLFREQANDESPYLDGNPSFDRPLFV 109

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q    D    +EAA+ V  +  + ++LN+GCP      G +GA L  + D++   I  + 
Sbjct: 110 QFCANDPDDFLEAARHVAPY-CDAVDLNLGCPQGIAKRGHYGAFLQEDWDLIYRLINRLH 168

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             LSIPVT K RI    Q          K I  +G N I +H R+   KG          
Sbjct: 169 NELSIPVTAKFRI----QETKEKTLEYAKMILSAGANIITVHGRRREQKG------HNTG 218

Query: 173 NLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
             D+  +  ++    P+  I  NG   +     + L     DGVM       + ++ +
Sbjct: 219 LADWSYIRYLRDNLPPETVIFANGNNLNYEDLDRCLEETGADGVMSAEGNLSDPSIFS 276


>gi|325128142|gb|EGC51035.1| dihydrouridine synthase, Dus family [Neisseria meningitidis N1568]
          Length = 333

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 104/253 (41%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   + E A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAENALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|256829559|ref|YP_003158287.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
 gi|256578735|gb|ACU89871.1| dihydrouridine synthase DuS [Desulfomicrobium baculatum DSM 4028]
          Length = 340

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 56/285 (19%), Positives = 108/285 (37%), Gaps = 28/285 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI---LRGDKKNILGFSTQEKPLALQIGGA 57
           M       YR           + TEM  A A+    R           +   L  QI G 
Sbjct: 28  MAGLGHVAYREVLGRFGGFGFMVTEMCNARAVPQESRHHSPVFRWRDEEAASLVCQIFGG 87

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +   +  AA+ +E  G   +++N+GC  A + +  +GA L+ +P+     + A+ +A+  
Sbjct: 88  EPEVMAAAARRIEAEGLMGVDINMGCSVAAICKKGYGAALLKDPERAVAMVRAVRRAVRC 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G ++        +L +  + +G + +  H R A         +R+     + 
Sbjct: 148 PVMVKFRSGWENSPDLAV--DLARRFEDAGADLLTFHPRIAP--------DRRSRPPKWA 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  +  E   + +  NG     +  L+++     DGV IGR A     +   +   F  
Sbjct: 198 HIRAVV-EAVSIPVLGNGNAFCAADCLRMMEETGCDGVSIGRMAIARPWIFAQLAHGF-- 254

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
                       D+D + + +  + D   RH      ++   +++
Sbjct: 255 ----------EPDEDIFLRTALELIDAIWRHFEQARAIKMYKKYL 289


>gi|145341388|ref|XP_001415794.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576017|gb|ABO94086.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 608

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 53/283 (18%), Positives = 102/283 (36%), Gaps = 30/283 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L    +   EM +  ++L+G      +L     E    +QI G     + 
Sbjct: 259 NLPFRRVCKTL-GADITCGEMALCTSLLQGLPSEWALLRRHKSEDIFGVQICGGYPDSVT 317

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI-PVTV 121
              +++ED    + I++N+GCP   V +  +G+ ++  P  +   I A   AL    +T 
Sbjct: 318 RCCQLLEDTIDVDFIDINMGCPIDSVCQKGYGSMMLEKPKKMETVIRAASAALGKCSLTF 377

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+   D+            + + G   + +H R    +  S  D             +
Sbjct: 378 KTRMAYTDKSRVA--HTFAPKVAEWGAAAMTLHGRTRAQRYRSVADWEYT---------K 426

Query: 182 IKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           + KE+  + +  NG +   +D    L+    VD  M+ R A     + T + E     ++
Sbjct: 427 LTKESSSVPLIGNGDVYMQKDYYTHLEEHS-VDTCMLARGALIKPWLFTEIKERRDWDIS 485

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                           I  S   +   H  S  +  + TR  +
Sbjct: 486 SRERF----------DILKSFASFGLEHWGSDTRGVESTRKYL 518


>gi|16272228|ref|NP_438439.1| hypothetical protein HI0270 [Haemophilus influenzae Rd KW20]
 gi|260580847|ref|ZP_05848672.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae RdAW]
 gi|1176627|sp|P44606|DUSC_HAEIN RecName: Full=tRNA-dihydrouridine synthase C
 gi|1573236|gb|AAC21936.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092470|gb|EEW76408.1| tRNA-dihydrouridine synthase C [Haemophilus influenzae RdAW]
          Length = 310

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 62/290 (21%), Positives = 110/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +       GF++   P+ +
Sbjct: 8   MQGVLDPFVRELLTEVNDYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTSSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    D G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPKCLAENAIRAIDLGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYRATQALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PV+VK R+G DD   A     +  ++++ G   I +H R          D  +
Sbjct: 128 RAVPSEFPVSVKVRLGWDDISQAF---EIADAVEQGGATEITVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+ +E   + +  NG +         L       +M+GR A     +   
Sbjct: 178 ADRINWKKISEV-RERLSIPVIANGEIWHWQDGQDCLSQTGCQDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                      S  +K+  +K  W +I   +  YA            + R
Sbjct: 234 -----------SHVLKSNAEKMPWYEIQKILQKYANVENEYDSGFYHVAR 272


>gi|194289473|ref|YP_002005380.1| tRNA-dihydrouridine synthase c [Cupriavidus taiwanensis LMG 19424]
 gi|193223308|emb|CAQ69313.1| tRNA-dihydrouridine synthase C [Cupriavidus taiwanensis LMG 19424]
          Length = 318

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 109/286 (38%), Gaps = 26/286 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA------ILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R             +E +          +   D   IL  G +    P+ +
Sbjct: 9   MEGLADYVLRDVLTATGGYDGCVSEFVRVTGSLLPARVYERDTPEILSGGHTRSGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+ NP ++   +A++ 
Sbjct: 69  QLLGSDPEWLARNAAYAATLSPHGIDLNFGCPAKVVNRHGGGAMLLTNPALLNRIVASVR 128

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPVT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPATIPVTAKMRLGVSDTALAI---DCATALAEGGAASLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I     D+ +  NG +  ++  ++       D VMIGR A  +  +   
Sbjct: 178 RPPAHWDWIARIA-AAVDIPVIANGDVWTVADWVRCREVSGCDDVMIGRGAVSDPFLALR 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +      P T S      V       ++      A+ H H   KL 
Sbjct: 237 IRGQM--PGTPSDQEWPLVLGQIAAYLNKLHARIASCHEHGRVKLW 280


>gi|170057436|ref|XP_001864482.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
 gi|167876880|gb|EDS40263.1| tRNA-dihydrouridine synthase [Culex quinquefasciatus]
          Length = 378

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 53/266 (19%), Positives = 112/266 (42%), Gaps = 16/266 (6%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGADISK 61
            T   +R   R    + L ++ MI+AD+    +K  +  F+T   + P+ +Q    +   
Sbjct: 11  VTKLEFRNLVRTFDTD-LTFSSMIMADSFCHSEKARLNEFTTNKDDTPMIVQFAANNTID 69

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            + AA++V  +  + ++LN GCP     +  +G+ L+  P+++ D +A + + L    +V
Sbjct: 70  FLSAAEMVYPYS-DGVDLNCGCPQRWAMQDGYGSALLKTPELIADMLATVRRNLPCSFSV 128

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
             ++ +  Q    A  ++ + ++  G+  + +H R A  K   P        ++ D + E
Sbjct: 129 SVKVRL-LQKSLAATVDMCRQLEACGITFLTVHGRTAADKTNVP--------VNKDALKE 179

Query: 182 IKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           IK  +  + +  NG +  +  A ++  +   DGVM  R    N  +     +     +  
Sbjct: 180 IK-ASLSIPMVANGDIFSLQDADEMHRITGCDGVMSARGILSNPGLYAGHRQTPRECIQR 238

Query: 240 SSPIKTRVDKDFWRKISASMTDYAAR 265
              I  + D D   +       + A 
Sbjct: 239 WLDITAQADTDITYQAMHHHLSFMAE 264


>gi|227432272|ref|ZP_03914267.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
 gi|227351971|gb|EEJ42202.1| tRNA-dihydrouridine synthase [Leuconostoc mesenteroides subsp.
           cremoris ATCC 19254]
          Length = 365

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 135/329 (41%), Gaps = 28/329 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + YTE   A +++    K      L  +  E+    QI G
Sbjct: 33  MEAVTDTVFRRVVAKAAAPDVYYTEFTNASSMVHHKAKFSVQGRLAVAEGEQQPVAQIWG 92

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   ++  + +++   GY  +++N+GCP   V + S G+ L+ +PD+  + I A  ++ S
Sbjct: 93  SRPKEIAGSIEVLAGMGYQAVDINMGCPDGTVIKNSSGSDLIRHPDLAEEIIVA-AQSGS 151

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G          R  +  I +  V  + +H R       +P     I     
Sbjct: 152 LPVSVKTRLGF---YKPEEFREWLPIILRHQVAVLTVHLRSRKEMSKAPAHYEHID---- 204

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +I+    +  P+  I +NG ++  +Q +   +  P +DG+MIGR  ++N       ++  
Sbjct: 205 EILAMRDEIAPNTLIQINGDIKTRAQGIALVQEHPGIDGIMIGRGIFENPYAF---EKES 261

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                  S     +  D + KIS ++T      L    K+            GF ++   
Sbjct: 262 RQHTLEESIALLNLQLDLFDKISETVTTKHFEALKRYFKI---------YLRGFAHASAL 312

Query: 294 RHILTVEAGASTATHHIIETAFNLMIESL 322
           R +L ++   +T    I+      +  ++
Sbjct: 313 RQML-MDTHTTTEVREILTRELAKVYAAV 340


>gi|308499933|ref|XP_003112152.1| hypothetical protein CRE_29758 [Caenorhabditis remanei]
 gi|308268633|gb|EFP12586.1| hypothetical protein CRE_29758 [Caenorhabditis remanei]
          Length = 529

 Score =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 95/234 (40%), Gaps = 19/234 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R F R      L +T MI A   +         L     ++PL +Q     
Sbjct: 80  MVDQSELAFRLFTRKY-GAQLTFTPMIHAHLFVNDGTYRRNSLALVKADRPLVVQFCANK 138

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   + A ++VED   + ++LN+GCP      G +G+ L    D++ + ++A+     +P
Sbjct: 139 VETFLAACRLVEDV-CDGVDLNLGCPQMVAKRGRYGSWLQDEVDLICEMVSAVRDYCKLP 197

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+  D Q          K +  +G   + +H R   +KG       +    D+  
Sbjct: 198 VSCKIRVRDDRQQTV----EYAKRLVDAGATMLTVHGRTRDMKGA------ETGLADWSR 247

Query: 179 VYEIKKENPD-LFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
           + ++ +     + +  NG ++   D+ + ++       VM       N  +   
Sbjct: 248 IRDVVEAVGSRVPVMANGNIQFPGDVERCMEA-TGAVAVMSAEGLLYNPLIFDD 300


>gi|120598516|ref|YP_963090.1| dihydrouridine synthase, DuS [Shewanella sp. W3-18-1]
 gi|146293405|ref|YP_001183829.1| dihydrouridine synthase, DuS [Shewanella putrefaciens CN-32]
 gi|120558609|gb|ABM24536.1| dihydrouridine synthase, DuS [Shewanella sp. W3-18-1]
 gi|145565095|gb|ABP76030.1| dihydrouridine synthase, DuS [Shewanella putrefaciens CN-32]
 gi|319426708|gb|ADV54782.1| dihydrouridine synthase DuS [Shewanella putrefaciens 200]
          Length = 317

 Score =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 76/338 (22%), Positives = 133/338 (39%), Gaps = 46/338 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +    LL TE + V D +L   +K  L    +           P+
Sbjct: 8   MEGVVDDLMRDILSAINPYDLLVTEFVRVVDQLL--PEKVFLKLCPELHNQGNTPSGTPV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G +   + E A    + G + ++ N GCP+  V+  + GA L+  PD + D + A
Sbjct: 66  RVQLLGQEPQCMGENALRAVELGSHGVDANFGCPAKMVNRSNGGAVLLQYPDSIHDIVRA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M +A+    PVT K R+G +D+           ++ ++G   + IHAR  +         
Sbjct: 126 MRQAVPSEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARSKVDG------- 175

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              P   ++ + E++K  P + +  NG + +   A + +     D +MIGR A     + 
Sbjct: 176 -YKPPAYWEYITEVRKRLP-IPVIANGEIWNSDDAKRCMAVTGCDSIMIGRGAISLPNLA 233

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGL 283
            T+        TG++P         W +  A M  Y  R L+   S     +I +    L
Sbjct: 234 DTIK-------TGAAPY-------TWAQTLALMLSYTQRELNGRKSDYYPARIKQWFTYL 279

Query: 284 FHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
              +P +      L V           +E A N + ++
Sbjct: 280 NRQYPEADTLFRTLRVHKTTEDIVRE-LEAAHNALPKT 316


>gi|330899152|gb|EGH30571.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 314

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 120/314 (38%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 1   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHQGAKTNAGTPLRL 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 61  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 121 RAVPKHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 170 KPPAHWEWIARI-QEVVKVPVVANGEIWTVEDWQRCREICGARDIMIGRGLVARPDLARQ 228

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+   A MT      + + G+L+Q    ++ L   
Sbjct: 229 IAAAQKGEEVVPMTWDELQPMLRVFWQDCLAKMT-----LIQAPGRLKQW---LVLLTKS 280

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 281 YPEATLMFNTLRRE 294


>gi|269102154|ref|ZP_06154851.1| tRNA-dihydrouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162052|gb|EEZ40548.1| tRNA-dihydrouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 314

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/333 (17%), Positives = 125/333 (37%), Gaps = 41/333 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  TE +  V           +       G +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDRLFPNSVFYRLCPELHNGGKTRAGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D + + E  +   + G   +++N GCP+  V++   GA L+  P+++   + ++ 
Sbjct: 68  QILGQDPNWMAENGRRAVELGSPGVDINFGCPAKLVNKSKGGAVLLKEPELIHQIVKSVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G DD         +  +I ++G + I +H R          D  +
Sbjct: 128 QAVDPTKPVTAKIRLGWDDPNHCF---EIADAIAQAGADEITVHGRTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D ++++++ +P + I  NG + +     + +       +M+ R A     +   
Sbjct: 178 AEEIKWDYIHQLQQHSP-ISIVANGEVWNYQDGQQCIATTGTQSLMVCRGAINLPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
                       + IK   D   W ++   +  Y+   +     L    +I +    L H
Sbjct: 234 -----------GNVIKYNADHMPWTEVLDLLLHYSTFEIKGDKGLYYPNRIKQWFAYLRH 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
            +P ++     +      +     I+  A   +
Sbjct: 283 EYPQAKALFADI-RRHNKAQPIVDILTQARAAL 314


>gi|119774440|ref|YP_927180.1| NifR3/Smm1 family protein [Shewanella amazonensis SB2B]
 gi|119766940|gb|ABL99510.1| NifR3/Smm1 family protein [Shewanella amazonensis SB2B]
          Length = 322

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 101/242 (41%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L       L       G +    P+ +
Sbjct: 13  MEGVLDHLMRELLSSINPYDLLVTEFVRVVDQLLPEKVYYRLCPELKNNGLTKSGTPVRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G +   + E A      G   ++ N GCP+  V+    GA L+  P+++ D + AM 
Sbjct: 73  QILGQEPGWMAENALRAVTLGSRGVDANFGCPAKMVNRSKGGAVLLQYPELIHDIVKAMR 132

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 133 QAVPSEQPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARSKVDG--------Y 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E+++  P + +  NG + +   AL+ +     D +MIGR A     +  +
Sbjct: 182 KPPAYWEYITEVRERLP-IPVIANGEIWNRDDALRCMEVTGCDSIMIGRGALSMPNLAAS 240

Query: 229 VD 230
           + 
Sbjct: 241 IK 242


>gi|224825374|ref|ZP_03698479.1| dihydrouridine synthase DuS [Lutiella nitroferrum 2002]
 gi|224602295|gb|EEG08473.1| dihydrouridine synthase DuS [Lutiella nitroferrum 2002]
          Length = 310

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/328 (17%), Positives = 120/328 (36%), Gaps = 37/328 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +       TE +   +  +       +         +     + +
Sbjct: 8   MEGLVDDIMRDVLTRIGGIDWCVTEFVRVTSTLLPPKMFYRLAPELHRAARTRAGTSVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L + A    + G   ++LN GCP+  V+    GA L+  P+++   +AA+ 
Sbjct: 68  QLLGSDPVCLADNAVRAVELGAPAVDLNFGCPAPTVNRHRGGAVLLTEPELLFQIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            ++   +PVT K R+G +D+  A+      ++I+++G + + +H R  +           
Sbjct: 128 ASVPKEVPVTAKMRLGYEDKSLAL---ECAQAIERAGADELVVHGRTKVEGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I +E+ +L +  NG +  +    A++     D VMIGR       +   
Sbjct: 178 -PPAHWDWIARI-RESVNLPVIANGEVWTVEDYHAIRRESGCDTVMIGRGLIAAPDLARR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +         G+ P+       + R       + A    +   +L+Q    +  L   +P
Sbjct: 236 IKA-----GPGAEPMPWDEMMIWLRDFFEQCRERAEESAYPASRLKQW---LGQLKRSYP 287

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFN 316
            +         E         +I     
Sbjct: 288 EAGELF-----EQVRREKQSAVIAQILA 310


>gi|328474591|gb|EGF45396.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus 10329]
          Length = 322

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/334 (18%), Positives = 129/334 (38%), Gaps = 43/334 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       ++    +T   P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQVLPDHVFHRLCPELMQGSQTTSGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQEPHWMAENAIRAAELGARGIDLNFGCPAKMVNKSKGGAALLQHPEVIHSVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +IPV+ K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 DAVPANIPVSAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + +I++    + +  NG + +     + +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWEYINKIRERF-SIPLIANGEIWNFEDGQRCIETTGVDSLMVCRGAFNIPNLGNM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V           +P         W  +   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKH-------NHTP-------MIWSDVVDLLIYYSKFEMKGDKGLYYPNRVKQWFAYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATHHIIETAFNLM 318
            +P +    R I T    A    H  I+   + +
Sbjct: 283 SYPEANELFREIRTFNKAAPIVEH--IQRYRDEL 314


>gi|89073254|ref|ZP_01159784.1| putative regulator protein [Photobacterium sp. SKA34]
 gi|89050964|gb|EAR56428.1| putative regulator protein [Photobacterium sp. SKA34]
          Length = 313

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/335 (19%), Positives = 123/335 (36%), Gaps = 47/335 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D++L       L       G +    P+ +
Sbjct: 8   MEGVLDHLMREMLTEINDYDLCVTEFVRVIDSLLPSSVFYRLCPELRQDGKTRSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D + + E A+     G   +++N GCP+  V++   GA L+  P+ +   + A  
Sbjct: 68  QILGQDPNWMAENAQRACSLGSAGVDINFGCPAKAVNKSRGGAVLLKEPERIYQIVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A++   P+T K R+G DD         +  +I ++G + + +HAR          D  +
Sbjct: 128 AAVNPIKPLTAKVRLGWDD---PAQCFEIADAIAQAGADEMVVHARTKE-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + ++K  +  + I  NG + +       L   + D +M+ R A     +   
Sbjct: 178 AETIKWDYIKQLKN-SVAIPIIANGEVWNYHDGQACLTATNTDALMVCRGALNLPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W  + A +  Y+   +     L    ++ +    L H
Sbjct: 237 VKH--------------NQAHMSWEDVLALLLVYSQFEIKGDKGLYYPNRVKQWFSYLRH 282

Query: 286 GFPNSRRCR---HILTVEAGASTATHHIIETAFNL 317
            +P ++        L   A        +++ A   
Sbjct: 283 EYPQAKLLFTDIRALNKAAP----IIEVLQRAHQQ 313


>gi|241759875|ref|ZP_04757975.1| tRNA-dihydrouridine synthase C [Neisseria flavescens SK114]
 gi|241319883|gb|EER56279.1| tRNA-dihydrouridine synthase C [Neisseria flavescens SK114]
          Length = 321

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +T   P  +
Sbjct: 8   MQGLVDDVMRDLLTRIGGFDECVSEFVRITHTVHSRATWLKYVPEIAHANRTTAGTPCTV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +  + 
Sbjct: 68  QLLGSDAENMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIYHIVHTLR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I+  G   + +HAR  +           
Sbjct: 128 QRLPQHIPLTAKMRLGYEDKSLAL---ECASAIENGGACALTVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ V +I ++  ++ +  NG + ++   L I  +   + VM+GR A     +   
Sbjct: 177 EPPAHWEWVRKI-RDAVNIPVTANGDVFNLQDYLDIKSVSGCNSVMLGRGAVIRPDLARQ 235

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 236 IKQYENGETVKDT 248


>gi|307166837|gb|EFN60767.1| tRNA-dihydrouridine synthase 4-like [Camponotus floridanus]
          Length = 748

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 109/231 (47%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+AD+ +R  K     F+T  ++ PL +Q     
Sbjct: 21  MVRYSKLQFRTLVRRY-GCDICFTPMILADSFVRSLKARENEFTTHKEDNPLIVQFAAKT 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  V AA++V  +  N ++LN GCP     +  +GA L+  P++V D I  +   +  P
Sbjct: 80  VNDFVGAAEMVAPY-CNGVDLNCGCPQRWAIKEGYGADLLKKPELVKDLIYEIRNHIPRP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I    +  L + ++K+G + + +HAR   ++            +D D 
Sbjct: 139 FTVSVKIRLLKDIRQTIM--LCQVLEKAGASFLTVHARTPEMRN---------EPIDLDN 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           +  + +++  L +  NG ++++  A  +      +GVM  R    N A+ +
Sbjct: 188 LK-LLRDHIQLPLVANGDVKNLEDAEFLFKESRCEGVMSARGILNNPALFS 237


>gi|325134156|gb|EGC56806.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M13399]
 gi|325144337|gb|EGC66640.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M01-240013]
 gi|325206171|gb|ADZ01624.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M04-240196]
          Length = 333

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 ERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEAY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|296314205|ref|ZP_06864146.1| tRNA-dihydrouridine synthase [Neisseria polysaccharea ATCC 43768]
 gi|296839101|gb|EFH23039.1| tRNA-dihydrouridine synthase [Neisseria polysaccharea ATCC 43768]
          Length = 314

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 102/254 (40%), Gaps = 26/254 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +       L +  +           P  
Sbjct: 1   MQGLIDDVMRDLLTRIGGYDECVSEFVRITHTVHSRA-TWLKYVPEIANGNKTFSGTPCT 59

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P ++   +  M
Sbjct: 60  VQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIVKTM 119

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K   
Sbjct: 120 RERLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEG 168

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
             P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     +  
Sbjct: 169 YEPPAHWEWIRKI-RDTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLAR 227

Query: 228 TVDEYFSNPLTGSS 241
            + +Y +      +
Sbjct: 228 QIKQYENGGPVKDT 241


>gi|330796961|ref|XP_003286532.1| hypothetical protein DICPUDRAFT_87182 [Dictyostelium purpureum]
 gi|325083513|gb|EGC36964.1| hypothetical protein DICPUDRAFT_87182 [Dictyostelium purpureum]
          Length = 399

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 76/258 (29%), Positives = 121/258 (46%), Gaps = 23/258 (8%)

Query: 1   MVDWTDRHYRFFARLL-------TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQ 53
           M D T+  +RF    +        NN +L+ E +  + + R      L +S  EKP+  Q
Sbjct: 17  MADVTEVSFRFLIANVINKYWIKPNNVVLFNEFLATEGVCRDHIAQQLEYSEIEKPIVAQ 76

Query: 54  IGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVH--EGSFGACLMLNPDIVGDCIAA 110
             G        +A+I  + + Y+ I++N+GCPS +V   + + GA L+ NP +  + I A
Sbjct: 77  FFGCRPEAFKISAEIACNKYNYDGIDINMGCPSRKVVSPKQAAGAALITNPKLAQEIIYA 136

Query: 111 MCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             + A S PV+VK RIG D    ++ + + +  I ++  + + +H R      L P    
Sbjct: 137 TKEGAGSKPVSVKTRIGFD----SIDIESWIPKILEAKPSCLTLHLRTKKELSLVPAHWE 192

Query: 170 KIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
              +   D V E++   +P+  I  NG +E M QA +      +DGVMIGRA Y N  +L
Sbjct: 193 ---HEILDRVLEMRNSISPETLIMGNGDVETMEQAYQYSKEFGIDGVMIGRANYGNPWLL 249

Query: 227 --TTVDEYFSNPLTGSSP 242
               V EY     T   P
Sbjct: 250 NPNLVFEYIEPRTTDCGP 267


>gi|268566179|ref|XP_002639655.1| Hypothetical protein CBG12371 [Caenorhabditis briggsae]
 gi|187029504|emb|CAP31359.1| hypothetical protein CBG_12371 [Caenorhabditis briggsae AF16]
          Length = 527

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 52/283 (18%), Positives = 107/283 (37%), Gaps = 22/283 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R F R      L +T MI A   +         L     ++PL +Q     
Sbjct: 80  MVDQSELAFRLFTRKY-GAQLTFTPMIHAHLFVNDGTYRRNALALVKADRPLVVQFCANK 138

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   + A ++VED   + ++LN+GCP      G +G+ L    D++ + ++A+     IP
Sbjct: 139 VDTFLAACRLVEDV-CDGVDLNLGCPQMVAKRGRYGSWLQDEVDLICEMVSAVRDYCKIP 197

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+  D Q        LV     +G   + +H R   +KG       +    D+  
Sbjct: 198 VSCKIRVRDDRQETISYATRLV----DAGATMLTVHGRTRDMKGA------ETGLADWTR 247

Query: 179 VYEIKKENPD-LFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++ +     + +  NG ++   D+ + ++       VM       N  +    + +  
Sbjct: 248 IRDVVEAVGSRVPVMANGNIQFPGDVERCMEA-TGAVAVMSAEGLLYNPLIFDDANAHVE 306

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARH---LHSGGKLQ 274
                +  ++   D         +       H    +   +++
Sbjct: 307 TWKIAAEYLEYARDFHAGTSAIRAHVFRICHHSLLEYEDLRMR 349


>gi|324517466|gb|ADY46829.1| tRNA-dihydrouridine synthase-like protein [Ascaris suum]
          Length = 348

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 100/235 (42%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   RL     L+YT MI A+  +  ++     F+T   + P  +Q    D
Sbjct: 63  MVRYSKLPFRSLVRLY-GADLVYTPMINANNFITSEECRSSEFTTNKYDSPTIVQFASND 121

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
             +   A ++V  +  + ++LN GCP   V  G +G+ L+  P+ + D IA   + +   
Sbjct: 122 PVEFAAATELVYRY-CSGVDLNCGCPKRDVMRGGYGSSLLSTPERIADMIAHARRRIADT 180

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             T+  +I +++ I       L + ++ +G + I +H R    +             +++
Sbjct: 181 QFTISVKIRLNNDIRRTV--ELCRQVESAGASYICVHGRTPTQRS---------EPANHE 229

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
            +  +K     + I  NG +    +AL++      DGVM       N AM    D
Sbjct: 230 AIALVKSAM-RIPIIANGAIGSYQEALQVAKRTQTDGVMAANGLLDNPAMFAGHD 283


>gi|195156341|ref|XP_002019059.1| GL26162 [Drosophila persimilis]
 gi|194115212|gb|EDW37255.1| GL26162 [Drosophila persimilis]
          Length = 398

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 117/255 (45%), Gaps = 19/255 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   R +    L +T M+++D+I   +K     FS    ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVR-MNGVQLAFTPMMISDSINNSEKARQNEFSTDPDDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  L+  P+ V + +  + + L   
Sbjct: 89  ATEFVTSAQLIYPY-VDGIDLNCGCPQSWAMSKGYGCGLLRQPEQVREVVQQVRRTLPSD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G  ++       +L + ++++GV  + +H R    K            L+
Sbjct: 148 FSVSVKMRLLGGSEEDSVERTIDLARQLERAGVTFLTLHGRTPAQKH-------SKDTLN 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
              + E++K    + + +NG +E  S A ++       GVM  R    N A+  +  +Y 
Sbjct: 201 VSAMEEVRKSL-QIPLIVNGNVESWSDACELHAQTGAAGVMAARGLLANPALFNS--DYP 257

Query: 234 SNPLTGSSPIKTRVD 248
           +   T S+ ++  +D
Sbjct: 258 TATTTPSACVEQWLD 272


>gi|330980698|gb|EGH78801.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 321

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHQGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + + FW+   A MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPITWDELQPMLRVFWQDCLAKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLIFNTLRRE 301


>gi|70729433|ref|YP_259171.1| NifR3/Smm1 family protein [Pseudomonas fluorescens Pf-5]
 gi|68343732|gb|AAY91338.1| NifR3/Smm1 family protein [Pseudomonas fluorescens Pf-5]
          Length = 362

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/321 (19%), Positives = 118/321 (36%), Gaps = 34/321 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE I      +  A        +L    +    PL +
Sbjct: 51  MEGLVDNILRDVLTRVGGIDWCVTEFIRVNDRLLTPAYFHKLAPELLHGAHTAAGVPLRV 110

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 111 QLLGSDPVCLAENAALACELGSEVIDLNFGCPAKTVNKSRGGAVLLKEPELLNQIVEHVR 170

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D    ++       ++ + G   I +HAR  +           
Sbjct: 171 RAVPAHIPVTAKMRLGFDSPDGSLV---CATALAEGGAEHIVVHARTKVDG--------Y 219

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + +E   + +  NG +  +    +      V+ +M+GR       +   
Sbjct: 220 KPPAHWEWIPRV-QEVVKVPVFANGDIWSVEDWRRCREISGVEDIMLGRGLVSRPDLARQ 278

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +    +       S      + +DFW ++   +T        + G+L+Q    +  L   
Sbjct: 279 IAAARAGEEVVEMSWADLQPMLQDFWAQVVVQLTP-----RSAPGRLKQW---LAMLTRN 330

Query: 287 FPNSRRCRHILTVEAGASTAT 307
           +P +      L  E       
Sbjct: 331 YPEAVELFTALRRETELDQVG 351


>gi|194879780|ref|XP_001974300.1| GG21157 [Drosophila erecta]
 gi|190657487|gb|EDV54700.1| GG21157 [Drosophila erecta]
          Length = 396

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 113/254 (44%), Gaps = 19/254 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVRQVVQEVRRTLPAD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+   ++     + +L + ++++GV  + +H R    K            LD 
Sbjct: 148 FSVSVKMRLLGGEKSLESTI-DLARQLEQAGVTFLTLHGRTPAQKH-------SKDTLDI 199

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E++K    + + +NG +E    A  I       GVM  R    N A+  +   Y  
Sbjct: 200 AAMAEVRKSL-QIPLIVNGNVESYRDACDIHDQTGAAGVMAARGLLANPALFNS--NYPE 256

Query: 235 NPLTGSSPIKTRVD 248
              T  S ++  +D
Sbjct: 257 GKTTPLSCVQQWLD 270


>gi|254508473|ref|ZP_05120592.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus 16]
 gi|219548585|gb|EED25591.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus 16]
          Length = 317

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 61/324 (18%), Positives = 122/324 (37%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDQLLPDHVFHRLCPELLQGSQTKSGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPVWMAENAIKAAELGARGVDLNFGCPAKLVNKSKGGAALLQHPELIHQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++         +V +I+K+G N + +HAR             K
Sbjct: 128 EAVPSEIPVTAKIRLGWENPDDCF---EIVDAIEKAGANELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + ++++    + +  NG + +       +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWEYIGQLRERFT-IPLIANGEIWNYEDGQACIETTGVDSLMVCRGAFNVPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKH--------------NHAVMPWSEVVELLLVYSQYEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATH 308
            +P +    R I T    A    H
Sbjct: 283 QYPQAAELFREIRTFNKAAPIVEH 306


>gi|121700723|ref|XP_001268626.1| dihydrouridine synthase family protein, putative [Aspergillus
           clavatus NRRL 1]
 gi|119396769|gb|EAW07200.1| dihydrouridine synthase family protein, putative [Aspergillus
           clavatus NRRL 1]
          Length = 538

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/308 (21%), Positives = 110/308 (35%), Gaps = 60/308 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVAD------------------AILRGDK 37
           MVD ++  +R   R           L Y+ M  A                    I + D 
Sbjct: 50  MVDRSEFAWRMLTRSFMPADDPKPLLSYSPMYHARLFREQPNVRWQHFQPTRAGINKNDN 109

Query: 38  KNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            + L  +   ++PL +Q    D    +EAA+ V  +  + ++LN+GCP     +G +GA 
Sbjct: 110 SSYLDGNPAIDRPLFVQFCANDPDDFIEAARHVAPY-CDAVDLNLGCPQGIARKGHYGAF 168

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L  + D++   I  + K LSIPVT K RI    Q          K I  +G + I +H R
Sbjct: 169 LQEDWDLIYKLINRLHKELSIPVTAKFRI----QESKEKTLEYAKMILSAGASIITLHGR 224

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGV 213
               KG            D+  +  ++    P+  I  NG   +     + L     DGV
Sbjct: 225 TREQKG------HNTGLADWSYIRYLRDNLPPETVIFANGNNLNHDDLERCLEATGADGV 278

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M       + A+ +              P      +++WR           +    G ++
Sbjct: 279 MSAEGNLSDPAIFS------------KPPPVGTHTREYWR----------GKDGKGGYRI 316

Query: 274 QQITRHMI 281
             I R  +
Sbjct: 317 DAIVRRYL 324


>gi|161869911|ref|YP_001599080.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis 053442]
 gi|161595464|gb|ABX73124.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis 053442]
 gi|261392649|emb|CAX50215.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis 8013]
 gi|325130157|gb|EGC52936.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           OX99.30304]
 gi|325132113|gb|EGC54809.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M6190]
 gi|325136420|gb|EGC59028.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis M0579]
 gi|325138046|gb|EGC60619.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           ES14902]
 gi|325202214|gb|ADY97668.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           M01-240149]
 gi|325208031|gb|ADZ03483.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis NZ-05/33]
          Length = 333

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|75908388|ref|YP_322684.1| dihydrouridine synthase, DuS [Anabaena variabilis ATCC 29413]
 gi|75702113|gb|ABA21789.1| tRNA-U20a,U20b-dihydrouridine synthase [Anabaena variabilis ATCC
           29413]
          Length = 378

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 53/250 (21%), Positives = 107/250 (42%), Gaps = 17/250 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M D T+  +        +    +TE    +   R ++  +   +  +  +P+  Q+ G  
Sbjct: 24  MQDVTNLWFMKVIAHYGSPDYFFTEYFRVNDTSRLNRGILAAITENDTGRPVFAQMIGES 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
           I  LV  AK +  +    ++LN+GCP+ R++  + G  L+L+P  V   +A + +A+   
Sbjct: 84  IPDLVRTAKELCHYDIAGVDLNMGCPAPRIYRKNVGGGLLLSPGKVEQILAELRQAVSDR 143

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G ++         ++  + +  ++ + +H R           +     + YD
Sbjct: 144 PLTVKMRVGFENTD---TFYEILDIVNRHNIDLLSLHGRTVK--------DMYHGAVKYD 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E  K   D  +  NG +   + AL++L      GVM+GR A  N  +   + +    
Sbjct: 193 LIAEAVKRV-DCPVLANGNIHSATTALEVLERTGAAGVMVGRWAIGNPWLFNQIRQALRG 251

Query: 236 PLTGSSPIKT 245
                 P+  
Sbjct: 252 EPITPVPLVE 261


>gi|330951649|gb|EGH51909.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae Cit 7]
          Length = 321

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 121/314 (38%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHQGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRPIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E  ++ +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVNVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+   A MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGDEVVPMTWNELQPMLRVFWQDCLAKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNTLRRE 301


>gi|324510450|gb|ADY44369.1| tRNA-dihydrouridine synthase-like protein [Ascaris suum]
          Length = 560

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 100/235 (42%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   RL     L+YT MI A+  +  ++     F+T   + P  +Q    D
Sbjct: 275 MVRYSKLPFRSLVRLY-GADLVYTPMINANNFITSEECRSSEFTTNKYDSPTIVQFASND 333

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
             +   A ++V  +  + ++LN GCP   V  G +G+ L+  P+ + D IA   + +   
Sbjct: 334 PVEFAAATELVYRY-CSGVDLNCGCPKRDVMRGGYGSSLLSTPERIADMIAHARRRIADT 392

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             T+  +I +++ I       L + ++ +G + I +H R    +             +++
Sbjct: 393 QFTISVKIRLNNDIRRTV--ELCRQVESAGASYICVHGRTPTQRS---------EPANHE 441

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
            +  +K     + I  NG +    +AL++      DGVM       N AM    D
Sbjct: 442 AIALVKSAM-RIPIIANGAIGSYQEALQVAKRTQTDGVMAANGLLDNPAMFAGHD 495


>gi|329898406|ref|ZP_08272396.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC3088]
 gi|328920835|gb|EGG28282.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC3088]
          Length = 313

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 113/280 (40%), Gaps = 33/280 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M    D   R     L       TE + V D +L           +   G ++   P+ L
Sbjct: 1   MEGVIDHTMRALLTRLGPYQRCVTEFLRVTDKLLPERVFHKICPELKQAGVTSNNTPVYL 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G++   L + A    D G   I+LN GCP+  V++   GA L+  PD+VGD +A + 
Sbjct: 61  QLLGSNPQILAKNALRAVDLGAKGIDLNFGCPAKTVNKSKGGASLLQTPDLVGDIVACVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             +   IPVT K R+G  D         L++ + K+    I +HAR  +           
Sbjct: 121 DQVPSHIPVTAKVRLGFSDD---TLFETLIRRLDKAAPTEITVHARTKVQG--------Y 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +  + ++K    D+ I  NG +   + AL+   +   D +M+ R A     +   
Sbjct: 170 KPPAHWHRINDVK-SLTDIPIVANGEVWSTADALQCANVSGCDRLMLARGALMRPELGRL 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
           + +  +N      P         WR+I+A + ++     H
Sbjct: 229 IRQEQNNQQQEVLP---------WRQIAALLLEFFEAQGH 259


>gi|149237573|ref|XP_001524663.1| tRNA-dihydrouridine synthase 4 [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146451260|gb|EDK45516.1| tRNA-dihydrouridine synthase 4 [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 342

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 52/235 (22%), Positives = 100/235 (42%), Gaps = 16/235 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   +R +      F+T +K   + +Q+G  +
Sbjct: 36  MVRYSKLPFRELCRFY-NVDIIYTPMILAREFVRNEMARYSDFTTNDKDTCVIVQVGVNN 94

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   ++  +++  +  + I +N GCP         GA LM  PD+V + IA   K     
Sbjct: 95  VEDFMKFIEMIHPY-VDGIGINCGCPIRDQIREGIGAALMSEPDLVAEMIATAKKQYGDS 153

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + +  +I + + +        VK ++ +G + I IH R         K  R    ++ D 
Sbjct: 154 ICIDTKIRIHNDLS--ETIEFVKKVEAAGTDIITIHGRT--------KTTRSSIPVNLDA 203

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           +  ++     + +  NG    +    +I     V+GVM  R    N A+    ++
Sbjct: 204 IKLVRSHITKVPVIANGDCFTLEDCERIADYTGVNGVMSARGILANPALFQGFNQ 258


>gi|163802863|ref|ZP_02196752.1| putative regulator protein [Vibrio sp. AND4]
 gi|159173403|gb|EDP58226.1| putative regulator protein [Vibrio sp. AND4]
          Length = 319

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/324 (19%), Positives = 126/324 (38%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMRQILTEINDYDLCVTEFVRVIDQLLPDHVFHRLCPELLQDSQTASGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + L E A      G   I+LN GCP+  V++   GA L+ +P+++   +    
Sbjct: 68  QLLGQEPNWLAENAIKAAKLGARGIDLNFGCPAKLVNKSKGGAALLQHPELIHSIVKTCR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +IPV+ K R+G ++         +V +I+ +G N + +HAR         +   K
Sbjct: 128 DAVPSNIPVSAKIRLGWENPEDCF---EIVDAIQAAGANELTVHARTK-------QGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++    + +  NG + +     + +    VD +M+ R A+ N   L  
Sbjct: 178 ASEIKWDYITQIRERFT-IPLIANGEIWNFKDGQRCIETTGVDSLMVCRGAF-NIPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           + +Y   P+              W  +   +  Y+   +     L    ++ +    L  
Sbjct: 236 MVKYNHQPMA-------------WPDVVELLIYYSQFEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATH 308
            +P +    R I T    A    H
Sbjct: 283 AYPEANELFREIRTFNKAAPIVEH 306


>gi|330893302|gb|EGH25963.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
          Length = 139

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/136 (49%), Positives = 91/136 (66%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 3   MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 62

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM +P +V DC+ AM  A+ IPVT
Sbjct: 63  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAHPQLVADCVKAMRDAVGIPVT 122

Query: 121 VKCRIGVDDQIPAVAL 136
           VK RIG++ +     L
Sbjct: 123 VKHRIGINGRDSYAEL 138


>gi|261364482|ref|ZP_05977365.1| tRNA-dihydrouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288567413|gb|EFC88973.1| tRNA-dihydrouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 321

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 101/250 (40%), Gaps = 26/250 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +       L ++ +           P  
Sbjct: 8   MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSR-STWLKYAPEIANGNKTPAGTPCT 66

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  PD++   +  +
Sbjct: 67  VQLLGSDADNMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPDLIHHIVKTL 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + L   IP+T K R+G +D+  A+       +I + G   + +HAR  I          
Sbjct: 127 RQRLPEHIPLTGKMRLGYEDKSLAL---ECAAAIAEGGACALTVHARTKIEG-------- 175

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
             P   ++ + +I +E+  + I  NG +  +     +K +   + VM+GR A     +  
Sbjct: 176 YEPPAHWEWIRKI-REHVAIPITANGDVFSLKDYIGIKEMTGCNSVMLGRGAVIRPDLAR 234

Query: 228 TVDEYFSNPL 237
            + +Y +   
Sbjct: 235 QIKQYENGET 244


>gi|121634803|ref|YP_975048.1| hypothetical protein NMC0986 [Neisseria meningitidis FAM18]
 gi|120866509|emb|CAM10257.1| hypothetical protein NMC0986 [Neisseria meningitidis FAM18]
          Length = 341

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 28  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 87

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 88  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 147

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 148 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 197 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 255

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 256 IKQYENGGPVKDT 268


>gi|302188293|ref|ZP_07264966.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. syringae
           642]
          Length = 326

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 120/314 (38%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHQGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKAIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+   A MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRVFWQDCLAKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|227113025|ref|ZP_03826681.1| tRNA-dihydrouridine synthase C [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 310

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 108/290 (37%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE   +V   +       +         +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCITEFLRVVDQCLPVKSFYRLCPELHHASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQYPQWLAENAARAVELGSYGVDLNCGCPSKLVNGSGGGATLLKDPELIYQGAKAMR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 128 EAVPAHLPVTVKIRLGWDSGARQF---EIADAVQQAGATELAVHGRTKE-------DGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D   A   +     D +MIGR A  N   L+ 
Sbjct: 178 AECINWLAIGEIRQRL-RIPVIANGEIWDWQSAQDCMATTGCDAMMIGRGAL-NVPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 236 VIKYNE-------------PRMPWPEVMLLLQKYVQLEKQGDTGLYHVAR 272


>gi|299066646|emb|CBJ37839.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum CMR15]
          Length = 319

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/336 (20%), Positives = 126/336 (37%), Gaps = 44/336 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +       +E + V  ++L               G++    P+ +
Sbjct: 1   MEGVADYVMRDVLTSVGGYDGCVSEFVRVTGSLLPARTYERETPEIRNGGYTASGTPMVI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++   ++A+ 
Sbjct: 61  QLLGSDPEWLARNAAQAATVSPHGIDLNFGCPAKVVNRHGGGAMLLSTPELLHRIVSAVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             +   I VT K R+GV D   A+A      ++ + G   + +HAR         +D+  
Sbjct: 121 ATVPARIAVTAKMRLGVSDTSLAIA---CATALAEGGAASLVVHART--------RDHGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +   + +  NG +  +      + +   D VM+GR A  +  +   
Sbjct: 170 RPPAHWDWIARIA-DAVRVPVVANGEVWTVDDWARCRAVSGCDDVMVGRGAVSDPFLALR 228

Query: 229 VDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG- 286
           +    +  P     P+      D+ +K+ A +   A +H H   KL       +G     
Sbjct: 229 IRGQMAPQPSDAEWPLVLGCLADYLKKLRARI---AIQHEHGRVKLW------LGYLKRT 279

Query: 287 FPNSRRC----RHILTVEAGASTATHHIIETAFNLM 318
           +P +       R +       S     +IE A   +
Sbjct: 280 WPQAAELHDAIRRL-----QDSAEILGVIEQALAQI 310


>gi|221090632|ref|XP_002157580.1| PREDICTED: similar to MGC79829 protein [Hydra magnipapillata]
          Length = 311

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 105/231 (45%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++ + +R   R   N  L YT MI+AD+ ++  +     F+T   ++PL +Q    +
Sbjct: 16  MVRYSKQPFRHLVRRY-NCDLAYTPMIMADSFIKSIEARDSDFTTNKDDRPLVVQFAANN 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+I+  +  + + LN GCP        +GA L+  P+++ D I    + L   
Sbjct: 75  AEDLALAAEIIYPY-ADGVGLNCGCPQRWAMAEGYGAQLISKPELINDMIKQTRQRLPQD 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            + + +I +   I      +L +  + +GV+ I +H R    +            ++YD 
Sbjct: 134 FSCEIKIRIHSDIRKTV--DLCQKAEHAGVSWITVHGRLPSQRN---------EPVNYDA 182

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  IK ++  + +  NG +++   A  ++    V+GVM  +    N AM  
Sbjct: 183 IKTIK-DSLQIPVVANGDIKNKEDAWDVVKKTGVNGVMAAQGMLNNPAMYA 232


>gi|170579239|ref|XP_001894741.1| dihydrouridine synthase domain containing protein [Brugia malayi]
 gi|158598545|gb|EDP36417.1| dihydrouridine synthase domain containing protein [Brugia malayi]
          Length = 832

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/286 (20%), Positives = 110/286 (38%), Gaps = 28/286 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM +    L G   + ++L     EK   +Q+ G     + 
Sbjct: 479 NLPFRRLCVDF-GAEITCSEMGICTNYLNGTSSEWSLLKRHPNEKYFGVQLAGGYPDSMS 537

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTV 121
            AA+I+ E+   + I++N GCP   V+E   G  L L  + + + +  M K + + P+T+
Sbjct: 538 RAAQIIAENEQIDFIDINCGCPIDLVNEKGGGCSLALRSNKLVEVMKTMSKVIGNTPLTL 597

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G+ + +   A + + K +K      I +H R         K  R     D+    +
Sbjct: 598 KLRTGIKEGV-YTAHQTISKVVKYCPPQLITLHPRS--------KAQRYTKLADWSYTQQ 648

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             +   ++     G +   +   + L    V+GVMIGR A     + T + E     +T 
Sbjct: 649 CSEACQNIPFWACGDVLSYTDYYEKLEKYPVNGVMIGRGALMKPWIFTEIKECRHWDITA 708

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
           S  +                 +Y   H  S  +  + TR  +   L
Sbjct: 709 SERL----------DYIQRFVNYGLEHWGSDDEGVEKTRRFLLEWL 744


>gi|307208699|gb|EFN85989.1| tRNA-dihydrouridine synthase 4-like [Harpegnathos saltator]
          Length = 351

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 108/231 (46%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+A++ ++  K     F+T  ++KPL +Q     
Sbjct: 21  MVRYSKLQFRTLVRRYA-CDICFTPMIMANSFVQSSKARENEFTTYKEDKPLIVQFAANT 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  + A +++  +  N ++LN GCP     +  +GA L+  P++V D I  +   +  P
Sbjct: 80  VNDFISATEMIAPYS-NGVDLNCGCPQRWAIKDGYGADLLRKPELVSDLIYQVRNRIPKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I    +  L ++++K+G + + IHAR   ++            ++ D 
Sbjct: 139 FTVSVKIRLLKDICKTIM--LCQTLEKAGASFLTIHARTPEMRN---------EPIELDN 187

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           +  + ++   L    NG ++D+  A  +      +GVM  R    N A+ +
Sbjct: 188 LK-LLRDCVQLPFIANGDVKDLESAEVLFRESRCEGVMSARGILTNPALFS 237


>gi|255018963|ref|ZP_05291089.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           F2-515]
          Length = 200

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/210 (27%), Positives = 99/210 (47%), Gaps = 15/210 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 3   MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 61

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  
Sbjct: 62  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDK 121

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK RIG D++        L      +    +    R  + +G          + ++D
Sbjct: 122 PVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWD 171

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           ++ ++K+E   +    NG +     A +IL
Sbjct: 172 VLRDVKREL-KIPFMANGDVRTPEDAKRIL 200


>gi|125986951|ref|XP_001357238.1| GA10353 [Drosophila pseudoobscura pseudoobscura]
 gi|54645569|gb|EAL34307.1| GA10353 [Drosophila pseudoobscura pseudoobscura]
          Length = 398

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   R +    L +T M+++D+I   +K     FS    ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVR-MNGVQLAFTPMMISDSINNSEKARQNEFSTDPDDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  L+  P+ V + +  + + L   
Sbjct: 89  ATEFVTSAQLIYPY-VDGIDLNCGCPQSWAMSKGYGCGLLRQPEQVREVVQQVRRTLPSD 147

Query: 117 IPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R +G  ++       +L + ++++GV  + +H R    K            L+
Sbjct: 148 FSVSVKMRLLGGSEEDSVERTIDLARQLERAGVTFLTLHGRTPAQKH-------SKDTLN 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              + E++K    + + +NG +E  S A ++       GVM  R    N A+  
Sbjct: 201 VSAMEEVRKSL-QIPLIVNGNVESWSDACELHAQTGAAGVMAARGLLANPALFN 253


>gi|221060526|ref|XP_002260908.1| tRNA-dihydrouridine synthase [Plasmodium knowlesi strain H]
 gi|193810982|emb|CAQ42880.1| tRNA-dihydrouridine synthase, putative [Plasmodium knowlesi strain
           H]
          Length = 340

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 98/231 (42%), Gaps = 16/231 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M+ A   +  +K     F    +++P+  Q  G +
Sbjct: 33  MVDLSELAFRLLCRNY-NCHLAFTPMLHAKNFVEHEKYRKGYFQSCKKDEPVIAQFCGNN 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              ++ A + +     N ++LN+GCP     +G++GA L+   D V + ++ +    +IP
Sbjct: 92  SKIILSAIEYI-KNDVNAVDLNLGCPQQIAKKGNYGAFLLHKHDEVVNLVSDITNNCNIP 150

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T K R    D        NL   ++   V  I +H R    KG+       I   DY+I
Sbjct: 151 ITCKIRKIDQD---YQKTLNLCYDLQSRNVKMITVHGRTKEEKGV------NIKECDYEI 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +  I KE  ++ I  NG +E      K L     D VM      +     +
Sbjct: 202 IK-IIKERLNIPIIANGSIEHFEDVQKCLNYTKADAVMCAEILLEKPYFFS 251


>gi|161502677|ref|YP_001569789.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160864024|gb|ABX20647.1| hypothetical protein SARI_00724 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 305

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 107/290 (36%), Gaps = 37/290 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +     TE   +V   +       +         +     + +
Sbjct: 1   MEGVLDSLVRELLTEVNDYDHCITEFLRVVDQLLPEKSFYRLCPELHNHSRTKSGTLVRI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G + ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 61  QLLGQHPGWLAENAVRAVELGSHGVDLNCGCPSKLVNGSGGGATLLKDPELIYRGAKAMR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G D          +  +++++G   + +H R          D  K
Sbjct: 121 EAVPAHLPVTVKVRLGWDSDARQF---EIADAVQQAGATELVVHGRTKE-------DGYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+     + +  NG + D   A   +     D VMIGR A  N   L+ 
Sbjct: 171 AECINWSAIGEIRNRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSR 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           V +Y                +  W ++   +  Y          L  + R
Sbjct: 229 VVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 265


>gi|66045219|ref|YP_235060.1| dihydrouridine synthase, DuS [Pseudomonas syringae pv. syringae
           B728a]
 gi|63255926|gb|AAY37022.1| Dihydrouridine synthase, DuS [Pseudomonas syringae pv. syringae
           B728a]
          Length = 321

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHNGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDALQPMLRVFWQDCLVKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNTLRRE 301


>gi|308389562|gb|ADO31882.1| NifR3/SMM1 family protein [Neisseria meningitidis alpha710]
          Length = 333

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|225677726|gb|EEH16010.1| tRNA-dihydrouridine synthase C [Paracoccidioides brasiliensis Pb03]
          Length = 526

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 99/268 (36%), Gaps = 52/268 (19%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFS----------- 44
           MVD ++  +R   R       +N  L Y+ M  +          +  F            
Sbjct: 28  MVDRSEFAWRMLTRSFIDPQSSNPLLAYSPMFHSRLFNESANYRLQHFEATRPKPNSKIS 87

Query: 45  ----------------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
                                 T ++PL +Q    D  +L+ AA+ VE F  + ++LN+G
Sbjct: 88  TADGKEPQLPDSPVIPYLDGNPTIDRPLIVQFCANDPDELLHAARTVEPF-CDAVDLNLG 146

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     +G +G+ L   P+++   I  +   LSIPVT K RI    Q          + 
Sbjct: 147 CPQGIARKGHYGSFLQEEPELIYKLINTLHTQLSIPVTAKFRI----QETKEKTLEYARM 202

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMS 201
           I  +G + I +H R+   KG            D+  +  ++   P D  I  NG + D  
Sbjct: 203 ILSAGASFISVHGRRRDQKG------HNTGLADWSYIRYLRDNLPADTVIFANGNILDHG 256

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLT 227
             ++ L     DGVM       +  + T
Sbjct: 257 DIIRCLEATGADGVMSAEGNLCDPTIFT 284


>gi|170726139|ref|YP_001760165.1| dihydrouridine synthase DuS [Shewanella woodyi ATCC 51908]
 gi|169811486|gb|ACA86070.1| dihydrouridine synthase DuS [Shewanella woodyi ATCC 51908]
          Length = 315

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 62/308 (20%), Positives = 119/308 (38%), Gaps = 47/308 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     +    L+ +E   +V   +       +         +    P+ L
Sbjct: 8   MEGVADAPMRSLLTSVGGYDLVISEFIRVVDQLLPEKVFYRLCAELAYGSKTKAGTPVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G   + + E A    + G   ++LN GCP+  V+  + GA L+  P+ +     A+ 
Sbjct: 68  QLLGQHPNWMAENAIRAIELGSLGVDLNYGCPAPMVNRSNGGAALLKEPETIYKVTKAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  S PV+ K R+G DD+   V    + ++I+ +G   + +HAR         K+   
Sbjct: 128 EAVPSSHPVSAKIRLGWDDKSRCV---EIAQAIESAGATELTVHART--------KEEGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + +E   + +  NG +      LK       D VMIGR A     +   
Sbjct: 177 RPPAHWEYIN-LIREAIAIPVIANGEVWCHQDYLKCQAASGCDDVMIGRGALAVPNL--- 232

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA------RHLHSGGKLQQITRHMIG 282
                      +  IKT   K  W ++   +  Y+       +  +   +++Q  + M+ 
Sbjct: 233 -----------AHVIKTNQVKMPWNQVMQLLVQYSEYEIVSVKEKYYPARIKQWLKFMV- 280

Query: 283 LFHGFPNS 290
               +P +
Sbjct: 281 --KQYPQA 286


>gi|317025631|ref|XP_001389487.2| dihydrouridine synthase family protein [Aspergillus niger CBS
           513.88]
          Length = 542

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/309 (20%), Positives = 105/309 (33%), Gaps = 61/309 (19%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R           L Y+ M  A          +  F            
Sbjct: 50  MVDRSEFAWRMLTRSFMTPEDQKKVLAYSPMYHARLFREQANVRVQHFHPTRAAAGKGED 109

Query: 47  -----------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
                      ++PL +Q    D    +EAA+ V  +  + ++LN+GCP      G +GA
Sbjct: 110 ESPYLDGNPSFDRPLFVQFCANDPDDFLEAARHVAPY-CDAVDLNLGCPQGIAKRGHYGA 168

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            L  + D++   I  +   LSIPVT K RI    Q          K I  +G N I +H 
Sbjct: 169 FLQEDWDLIYRLINRLHNELSIPVTAKFRI----QETKEKTLEYAKMILSAGANIITVHG 224

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDG 212
           R+   KG            D+  +  ++    P+  I  NG   +     + L     DG
Sbjct: 225 RRREQKG------HNTGLADWSYIRYLRDNLPPETVIFANGNNLNYEDLDRCLEETGADG 278

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           VM       + ++ +              P      +++WR           R    G +
Sbjct: 279 VMSAEGNLSDPSIFS------------KPPPVGSEGREYWR----------GRDGKGGYR 316

Query: 273 LQQITRHMI 281
           +  + R  +
Sbjct: 317 IDAMLRRYL 325


>gi|261400872|ref|ZP_05986997.1| tRNA-dihydrouridine synthase C [Neisseria lactamica ATCC 23970]
 gi|269209349|gb|EEZ75804.1| tRNA-dihydrouridine synthase C [Neisseria lactamica ATCC 23970]
          Length = 333

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 99/247 (40%), Gaps = 24/247 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +    P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRATWLKYVPEIANGNKTPVGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P ++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 ERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I ++  ++ +  NG +  +     +K     + VM+GR A     +   
Sbjct: 189 EPPAHWEWIKKI-RDAVNIPVTANGDVFSLQDYIGIKTASGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSN 235
           + +Y S 
Sbjct: 248 IKQYESG 254


>gi|281211889|gb|EFA86051.1| hypothetical protein PPL_01287 [Polysphondylium pallidum PN500]
          Length = 334

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 112/263 (42%), Gaps = 42/263 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNA---------LLYTEMIVADAILRG--DKKNILGFSTQEKP 49
           MVD TD  +R    L + +          + +TE +  D +L      K++L +S  ++P
Sbjct: 19  MVDVTDHPFRQLVSLYSKSKDQSSSKSSFITWTEFVSVDGLLANPNRFKSLLDYSEIQRP 78

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCI 108
           +  Q+ G+D  K   A KIV D G++ +++N+GCP  +V    S G+ L+++       I
Sbjct: 79  IVCQLFGSDPDKFNRATKIVADLGFDGVDINMGCPVRKVVERQSSGSALIVDKPTAVSII 138

Query: 109 AAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A  +A+    + V+VK RIG D+    + +   + ++ ++  + + +H R        P
Sbjct: 139 NATKQAVAGTDMSVSVKTRIGFDE----IEIEQWIPTLLQTNPDLLTLHLRTKKELSNCP 194

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLF-----------------IGLNGGLED---MSQALK 205
                        V E+ K++ D                   +  NG +E    + +  +
Sbjct: 195 AHWENEVMGR---VTELLKQHRDEHQQQKSNNNNNNKTTTTRLFGNGDIESRLQIDEMFR 251

Query: 206 ILPSVDGVMIGRAAYKNSAMLTT 228
               +DG+M+GR  Y      + 
Sbjct: 252 RYSLLDGIMVGRGIYGKPWFFSD 274


>gi|307105362|gb|EFN53612.1| hypothetical protein CHLNCDRAFT_25754 [Chlorella variabilis]
          Length = 385

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 53/280 (18%), Positives = 93/280 (33%), Gaps = 29/280 (10%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK 67
           R   + L    +   EM +A  +L+G      +L     E    +Q+ G     L   A+
Sbjct: 7   RRVCKGL-GADVTCGEMALATNLLQGQPSEWALLKRHPSEDCFGVQLCGGYADSLARCAQ 65

Query: 68  IVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +VE+    + +++N GCP   V     G+  +L P  +   +  M   LS PVT K R G
Sbjct: 66  LVEEQCCVDFVDVNFGCPIDVVCSKGAGSACLLKPQRMQAIVRGMSSVLSCPVTFKSRKG 125

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
             D         L+      G   + +H R         ++ R     D+  +    +  
Sbjct: 126 YHDGQDMA--HTLIPQAAGWGAAAVTLHGRT--------REQRYSRLADWPYIKRCVEAA 175

Query: 187 --PDLFIGLNGGLEDMSQALKILPSVDGVM---IGRAAYKNSAMLTTVDEYFSNPLTGSS 241
               L +  NG +       + L    G+    I R A     + T + E     ++   
Sbjct: 176 EGTGLQVVGNGDVFSFEDHYRHLEECPGLATTYIARGALIKPWIFTEIKERRHWDISAGE 235

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +           +          H  S  +  + TR  +
Sbjct: 236 RL----------DMFKRFCSNGLEHWGSDSRGVETTRRFL 265


>gi|117920895|ref|YP_870087.1| dihydrouridine synthase, DuS [Shewanella sp. ANA-3]
 gi|117613227|gb|ABK48681.1| dihydrouridine synthase, DuS [Shewanella sp. ANA-3]
          Length = 315

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 76/339 (22%), Positives = 133/339 (39%), Gaps = 50/339 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  GF+    P+ +
Sbjct: 8   MEGVVDDLMRDILSSINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNGGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P+ + D + AM 
Sbjct: 68  QLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYPNTIHDIVRAMR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPAEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARSKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E+++  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 177 KPPAYWEYITEVRERLP-IPVIANGEIWNREDAKRCMAVTGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGKLQQITRHMIGLFH 285
           +        TG++P         W      M  Y  R L    S     +I +    L  
Sbjct: 236 IK-------TGAAPYS-------WADTLGLMLSYTQRELSGRKSDYYPARIKQWFSYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETAFNLMIE 320
            +P +    R  R   T E         ++E A   + E
Sbjct: 282 QYPEADTLFRELRIYKTTEEI-----VRVLEEAQQRLGE 315


>gi|19921524|ref|NP_609939.1| CG10495 [Drosophila melanogaster]
 gi|7298533|gb|AAF53752.1| CG10495 [Drosophila melanogaster]
 gi|17862030|gb|AAL39492.1| LD05576p [Drosophila melanogaster]
 gi|220942934|gb|ACL84010.1| CG10495-PA [synthetic construct]
 gi|220953160|gb|ACL89123.1| CG10495-PA [synthetic construct]
          Length = 396

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 105/233 (45%), Gaps = 17/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVHQVVQEVRRTLPGD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+   ++     + +L + ++ +GV  + +H R    K    KD   IP +  
Sbjct: 148 FSVSVKMRLLGGEESLQRTI-DLARQLESAGVTFLTLHGRTPAQKH--SKDTLDIPAM-- 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                  +++  + + +NG +E    A  +       GVM  R    N A+  
Sbjct: 203 ----SQVRQSLQIPLIVNGNVESYRDACDMHEQTGAAGVMAARGLLANPALFN 251


>gi|77458109|ref|YP_347614.1| dihydrouridine synthase, DuS [Pseudomonas fluorescens Pf0-1]
 gi|77382112|gb|ABA73625.1| tRNA-U20a,U20b-dihydrouridine synthase [Pseudomonas fluorescens
           Pf0-1]
          Length = 319

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE I      +  A        +L    +    PL +
Sbjct: 8   MEGLVDDILRDVLTRVGGIDWCVTEFIRVNDQLLTPAYFHKFGPELLNGARTASGVPLRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGSEVIDLNFGCPAKTVNKSRGGAVLLKEPELLNRIVEHVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D    ++       ++ + G   I +HAR  +           
Sbjct: 128 RAVPAHIPVTAKMRLGFDSPDGSLV---CATALAEGGAEHIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + ++   + +  NG +  +    +      V+ +M+GR       +   
Sbjct: 177 KPPAHWEWIPRV-QDVVKVPVFANGDIWSVEDWRRCREISGVEDIMLGRGLVSRPDLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +    +              + +DFW +  A MT        S G+L+Q    +  L   
Sbjct: 236 IAAARAGEEVVEMTWAELMPLIQDFWLQAKAQMTA-----RQSPGRLKQW---LAMLTRN 287

Query: 287 FPNSRRCRHILTVE 300
           +P +     +L  E
Sbjct: 288 YPEAVELFTVLRRE 301


>gi|24373569|ref|NP_717612.1| NifR3/Smm1 family protein [Shewanella oneidensis MR-1]
 gi|38604869|sp|Q8EFG7|DUSC_SHEON RecName: Full=tRNA-dihydrouridine synthase C
 gi|24347891|gb|AAN55056.1|AE015643_3 NifR3/Smm1 family protein [Shewanella oneidensis MR-1]
          Length = 315

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 74/333 (22%), Positives = 131/333 (39%), Gaps = 50/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  G++    P+ +
Sbjct: 8   MEGVVDDLMRDILSSINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLSGGYTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P+ + D + AM 
Sbjct: 68  QLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYPNTIHDIVRAMR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPAEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARSKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E+++  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 177 KPPAYWEYITEVRERLP-IPVIANGEIWNRDDAKRCMQVTGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGKLQQITRHMIGLFH 285
           +        TG++P         W      M  Y  R L    S     +I +    L  
Sbjct: 236 IK-------TGATPYS-------WADTLQLMLSYTQRELSGRKSDYYPARIKQWFSYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETA 314
            +P +    R  R   T E         ++E A
Sbjct: 282 QYPEADTLFRELRIYKTTEEI-----VRVLEQA 309


>gi|309379684|emb|CBX21673.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 333

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 99/248 (39%), Gaps = 26/248 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +       L +  +           P  
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHS-HATWLKYVPEIANGNKTPVGTPCT 78

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P ++   +  +
Sbjct: 79  VQLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPQLIFHIVKTL 138

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K   
Sbjct: 139 RERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEA 187

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
             P   ++ + +I ++  ++ +  NG +  +     +K     + VM+GR A     +  
Sbjct: 188 YEPPAHWEWIKKI-RDAVNIPVTANGDVFSLQDYIGIKTASGCNSVMLGRGAVIRPDLAR 246

Query: 228 TVDEYFSN 235
            + +Y S 
Sbjct: 247 QIKQYESG 254


>gi|325142309|gb|EGC64723.1| dihydrouridine synthase, Dus family [Neisseria meningitidis
           961-5945]
 gi|325198237|gb|ADY93693.1| dihydrouridine synthase, Dus family [Neisseria meningitidis G2136]
          Length = 333

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKGRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|195580071|ref|XP_002079879.1| GD24181 [Drosophila simulans]
 gi|194191888|gb|EDX05464.1| GD24181 [Drosophila simulans]
          Length = 396

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 58/254 (22%), Positives = 113/254 (44%), Gaps = 19/254 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVHQVVQEVRRTLPGD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+   ++     + +L + ++ +GV  + +H R    K    KD   IP++  
Sbjct: 148 FSVSVKMRLLGGEESLQRTI-DLARQLEHAGVTFLTLHGRTPAQKH--SKDTLDIPSM-- 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  +++  + + +NG +E    A  +       GVM  R    N A+      Y  
Sbjct: 203 ----SQVRQSLQIPLIVNGNVESYRDACDMHEQTGAAGVMAARGLLANPALFNR--SYPE 256

Query: 235 NPLTGSSPIKTRVD 248
              T  S ++  +D
Sbjct: 257 GKTTPLSCVQQWLD 270


>gi|304409222|ref|ZP_07390843.1| dihydrouridine synthase DuS [Shewanella baltica OS183]
 gi|307303225|ref|ZP_07582980.1| dihydrouridine synthase DuS [Shewanella baltica BA175]
 gi|304353043|gb|EFM17440.1| dihydrouridine synthase DuS [Shewanella baltica OS183]
 gi|306913585|gb|EFN44007.1| dihydrouridine synthase DuS [Shewanella baltica BA175]
          Length = 310

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 75/333 (22%), Positives = 130/333 (39%), Gaps = 50/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  G +    P+ +
Sbjct: 1   MEGVVDALMRDILSTINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNNGNTPSGTPVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P+ V D + AM 
Sbjct: 61  QLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYPESVHDIVKAMR 120

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     VT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 121 QAVPKEHAVTAKIRLGYEDKSL---FMENAIAVYEAGATELAIHARSKVDGYR------- 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E++K  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 171 -PPAYWEYIKEVRKRLP-IPVIANGEIWNSDDAKRCIEVTGCDSIMIGRGAISLPNLADT 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGLFH 285
           +        TG++P         W +    M  Y  R L+   S     +I +    L  
Sbjct: 229 IK-------TGATPY-------TWAQTLGLMLSYTQRELNGRKSDYYPARIKQWFTYLNR 274

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETA 314
            +P +    R  R   T E   +     ++E A
Sbjct: 275 QYPEADTLFRELRVFKTTEEIVA-----VLEAA 302


>gi|187928992|ref|YP_001899479.1| dihydrouridine synthase DuS [Ralstonia pickettii 12J]
 gi|187725882|gb|ACD27047.1| dihydrouridine synthase DuS [Ralstonia pickettii 12J]
          Length = 318

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 114/287 (39%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R             +E + V  ++L               G++    P+ +
Sbjct: 1   MEGVADYVMRDVLTQAGGYDGCVSEFVRVTGSLLPARTYERETPEIRNGGYTASGTPMTI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++ D + A+ 
Sbjct: 61  QLLGSDPEWLARNAAYAATLTPHGIDLNFGCPAKVVNRHGGGAMLLATPEVLHDIVRAVR 120

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 121 AAVPANISVTAKMRLGVSDTSRAI---DCATALAEGGAESLVVHART--------RDHGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +   + +  NG +  ++   +   +     VMIGR A  +  +   
Sbjct: 170 RPPAHWDWIARIA-DAVSIPVTANGEVWTVADWERCRAVSGCSDVMIGRGAVSDPFLAQR 228

Query: 229 VDEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       P     PI      D+ +K+ A ++   A+H H   KL 
Sbjct: 229 IRAQMDQAPSAAEWPIVLGYLADYLKKLHARIS---AKHEHGRVKLW 272


>gi|330959087|gb|EGH59347.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 317

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVTVK R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKDIPVTVKMRLGYENTDLAL---DCARALADGGAAQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPVTWAELQPILRTFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNTLRRE 301


>gi|15676890|ref|NP_274035.1| NifR3/SMM1 family protein [Neisseria meningitidis MC58]
 gi|38605055|sp|Q9JZL5|DUSC_NEIMB RecName: Full=tRNA-dihydrouridine synthase C
 gi|7226240|gb|AAF41402.1| NifR3/SMM1 family protein [Neisseria meningitidis MC58]
 gi|316985877|gb|EFV64818.1| dihydrouridine synthase (Dus) family protein [Neisseria
           meningitidis H44/76]
 gi|325140199|gb|EGC62725.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis CU385]
 gi|325200316|gb|ADY95771.1| tRNA-dihydrouridine synthase C [Neisseria meningitidis H44/76]
          Length = 333

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +++ ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDSVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|315268000|gb|ADT94853.1| dihydrouridine synthase DuS [Shewanella baltica OS678]
          Length = 327

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 76/339 (22%), Positives = 133/339 (39%), Gaps = 50/339 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  G +    P+ +
Sbjct: 20  MEGVVDALMRDILSTINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNKGNTPSGTPVRV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P+ V D + AM 
Sbjct: 80  QLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYPESVHDIVKAMR 139

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+ I   VT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 140 QAVPIEHAVTAKIRLGYEDKSL---FMENAIAVYEAGATELAIHARSKVDG--------Y 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E++K  P + +  NG + +   A +   +   D +MIGR A     +  T
Sbjct: 189 KPPAYWEYITEVRKRLP-IPVIANGEIWNRDDAKRCIDITGCDSIMIGRGAISLPNLADT 247

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGLFH 285
           +        TG++P         W +    M  Y  R L+   S     +I +    L  
Sbjct: 248 IK-------TGATPY-------TWAQTLGLMLSYTQRELNGRKSDYYPARIKQWFTYLNR 293

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETAFNLMIE 320
            +P +    R  R   T E   +     ++E A   + +
Sbjct: 294 QYPEADTLFRELRVFKTTEEIVA-----VLEAAQRNLAD 327


>gi|119504827|ref|ZP_01626905.1| hypothetical protein MGP2080_09206 [marine gamma proteobacterium
           HTCC2080]
 gi|119459432|gb|EAW40529.1| hypothetical protein MGP2080_09206 [marine gamma proteobacterium
           HTCC2080]
          Length = 342

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 119/305 (39%), Gaps = 30/305 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE + V+  IL           +L  G +    P+ L
Sbjct: 28  MEGVIDSVMRDLLTTIGGYDRCVTEFVRVSQTILPSRVFHRLCPELLTGGRTPAGTPVFL 87

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   +   A++ E  G   I+LN GCP+  V++   GA L+  PD++G   A + 
Sbjct: 88  QLLGNNPDLMARNAQVAEALGAPGIDLNFGCPAKTVNKSQGGAVLLKTPDLLGAVCAEVR 147

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPVT K R+G +D     A   +VK+    GV+ + +HA+         +    
Sbjct: 148 AAVAPEIPVTAKIRLGFEDDDSFEA---IVKAAVDGGVSELTVHAKT--------RRQGY 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +  + +I  +   L I  NG L   S  ++   +      M+ R A     +   
Sbjct: 197 RPPAHWSRLAQIANDA-RLPIIANGELWSPSDVIRCGTVSHCKDFMLARGALCRPDLARA 255

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V   +      ++P  T  +     +I      +A    H+   L+Q    ++ L H FP
Sbjct: 256 VRHAWHG---LNTPAMTWAEVFPLLQIFLRSNAHAYEPRHACNPLKQW---LVYLKHYFP 309

Query: 289 NSRRC 293
            +   
Sbjct: 310 QAGAL 314


>gi|157867470|ref|XP_001682289.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68125742|emb|CAJ03495.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 595

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 51/283 (18%), Positives = 103/283 (36%), Gaps = 29/283 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM V   +  L+  + ++L     E    +Q+  +   +  
Sbjct: 247 NLPFRRICKSF-GADVTLSEMAVVFNLNRLQKSEWSLLRRHESEDIFGIQLAVSRPQEAA 305

Query: 64  EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             A+ +E  G  Y+ +++N GCP  ++ +   G  L    + + D + ++    S PV +
Sbjct: 306 TFAQALEASGFSYDFLDINCGCPVEKIVKSGCGCGLWQRTERLRDVVESLAIYQSRPVAI 365

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIG+D+ IP   L   +      G   + +H R         +  R     ++D V +
Sbjct: 366 KCRIGLDEDIP--TLHQQIHRYSAWGAAAVTVHGRS--------RKQRYTKFANWDYVDQ 415

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             +    L +  NG +  +   L+       +   MIGR A     +   +         
Sbjct: 416 CAQ-LTSLPVIGNGDIMSLEDVLEHRERQPHIASHMIGRGALIKPWLFEEIK----TGQV 470

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                  R+D      +      +   H  +  +    TR  +
Sbjct: 471 KDISSSERLD------MLKKFCAHGMAHWGADERGVMTTRRFL 507


>gi|238920710|ref|YP_002934225.1| tRNA-dihydrouridine synthase C [Edwardsiella ictaluri 93-146]
 gi|238870279|gb|ACR69990.1| tRNA-dihydrouridine synthase C [Edwardsiella ictaluri 93-146]
          Length = 318

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/312 (20%), Positives = 114/312 (36%), Gaps = 41/312 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILGFST--QEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +   S      P+ +
Sbjct: 12  MEGVLDALVRELLSEVNDYDLCITEFVRVVDRLLPERVFYRLCPELYRRSQTLSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++ N GCPS  V+    GA L+ +P ++   + AM 
Sbjct: 72  QLLGQSPHWLAENALRAVTLGSPGVDFNCGCPSKAVNGSGGGATLLKDPALIYAGVQAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +P+TVK R+G            +  ++++ G   + +H R          D  +
Sbjct: 132 QAIPAHLPLTVKVRLGWACDSQRF---EIADAVQQGGATELVVHGRTKE-------DGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              ++++ + EI++    + +  NG + D + A   L     D +MIGR A     +   
Sbjct: 182 ADRINWEAIGEIRRRL-RIPVIANGEIWDYASAQACLAQSGCDALMIGRGALNIPNL--- 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  IK    K  W ++   +  Y          L  + R    +  L  
Sbjct: 238 -----------SRVIKANAPKMPWLQVVTLLQRYVRLEKQGDTGLYHVARIKQWLSYLRK 286

Query: 286 GFPNS-RRCRHI 296
            +P +    R I
Sbjct: 287 EYPQADALFRQI 298


>gi|254669503|emb|CBA03423.1| tRNA-dihydrouridine synthase [Neisseria meningitidis alpha153]
          Length = 333

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSQSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG N+I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGANKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEAY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKI-RDTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|156400870|ref|XP_001639015.1| predicted protein [Nematostella vectensis]
 gi|156226140|gb|EDO46952.1| predicted protein [Nematostella vectensis]
          Length = 317

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 102/232 (43%), Gaps = 21/232 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L +T MI++++ ++  K     F+T   ++P+ +Q     
Sbjct: 35  MVRYSKLSFRELVRRYD-CDLCFTPMIISESFVKSQKARDSEFTTNSGDRPIVVQFAANC 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
              L +A +I+  F  + ++LN GCP     +  +GA L+  P++V D +      +  I
Sbjct: 94  AKDLADATEIISPF-VDGVDLNCGCPQRWAIQERYGAHLINQPELVKDMVRQTKSRVTGI 152

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV++K RI  D +       +L K  + +G + I IH R +  +   P           +
Sbjct: 153 PVSIKIRIHQDKRKTV----DLCKRAEHAGASWITIHGRTSKQRTEPPSM---------E 199

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
            +  +K EN  + +  NG +      LK+      +GVM  R    N AM  
Sbjct: 200 TIKLVK-ENLSIPVVANGDIRCTDDFLKVCEATGANGVMAARGILSNPAMYA 250


>gi|241663179|ref|YP_002981539.1| dihydrouridine synthase DuS [Ralstonia pickettii 12D]
 gi|240865206|gb|ACS62867.1| dihydrouridine synthase DuS [Ralstonia pickettii 12D]
          Length = 326

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 114/287 (39%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R             +E + V  ++L               G++    P+ +
Sbjct: 9   MEGVADYVMRDVLTQAGGYDGCVSEFVRVTGSLLPARTYERETPEIRNGGYTASGTPMTI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++ D + A+ 
Sbjct: 69  QLLGSDPEWLARNAAYAATLTPHGIDLNFGCPAKVVNRHGGGAMLLATPEVLYDIVRAVR 128

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPANISVTAKMRLGVSDTSRAI---DCATALAEGGAESLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +   + +  NG +  ++     + +     VMIGR A  +  +   
Sbjct: 178 RPPAHWDWIARIA-DAVSIPVTANGEVWTVADWARCRAVSGCSDVMIGRGAVSDPFLAQR 236

Query: 229 VDEYF-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       P     PI      D+ +K+ A ++   A+H H   KL 
Sbjct: 237 IRGQMDEAPSAAEWPIVLGYLADYLKKLHARIS---AKHEHGRVKLW 280


>gi|160875809|ref|YP_001555125.1| dihydrouridine synthase DuS [Shewanella baltica OS195]
 gi|160861331|gb|ABX49865.1| dihydrouridine synthase DuS [Shewanella baltica OS195]
          Length = 315

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 76/339 (22%), Positives = 133/339 (39%), Gaps = 50/339 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  G +    P+ +
Sbjct: 8   MEGVVDALMRDILSTINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNKGNTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P+ V D + AM 
Sbjct: 68  QLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYPESVHDIVKAMR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+ I   VT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPIEHAVTAKIRLGYEDKSL---FMENAIAVYEAGATELAIHARSKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E++K  P + +  NG + +   A +   +   D +MIGR A     +  T
Sbjct: 177 KPPAYWEYITEVRKRLP-IPVIANGEIWNRDDAKRCIDITGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGLFH 285
           +        TG++P         W +    M  Y  R L+   S     +I +    L  
Sbjct: 236 IK-------TGATPY-------TWAQTLGLMLSYTQRELNGRKSDYYPARIKQWFTYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETAFNLMIE 320
            +P +    R  R   T E   +     ++E A   + +
Sbjct: 282 QYPEADTLFRELRVFKTTEEIVA-----VLEAAQRNLAD 315


>gi|157111456|ref|XP_001651572.1| tRNA-dihydrouridine synthase [Aedes aegypti]
 gi|108878341|gb|EAT42566.1| tRNA-dihydrouridine synthase [Aedes aegypti]
          Length = 391

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 55/273 (20%), Positives = 110/273 (40%), Gaps = 20/273 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      L +T MI+AD+  + +K  +  F+T   + P+  Q    +
Sbjct: 30  MVRYSKLEFRNLVRSY-GTDLTFTSMIMADSFCQSEKARLNEFTTNRDDTPVIAQFAAKN 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
               + A ++   +  + ++LN GCP     +  +G+ L+  P+++ D ++ + + L   
Sbjct: 89  AVDFLSATEMTFPY-VDGVDLNCGCPQRWAMQDGYGSALLRTPELIADMLSTVRRNLPST 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+    Q    A  ++ + ++  G+  I +H R    K   P +   +  +  
Sbjct: 148 FSVSVKVRLL---QKSLSATIDMCRQLEACGITFITVHGRTPAQKTNIPVNQEALKEI-- 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  K +  + +  NG +  +    A+    + DGVM  R    N AM    +    
Sbjct: 203 -------KSSLGIPVVANGDIFSLQDADAMHCKTNCDGVMSARGILSNPAMYAGFERTPL 255

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
             +     I  + D D   +       + A  L
Sbjct: 256 ECIQRWLNITAQADTDITYQAMHHHLTFMAESL 288


>gi|242774281|ref|XP_002478411.1| dihydrouridine synthase family protein, putative [Talaromyces
           stipitatus ATCC 10500]
 gi|218722030|gb|EED21448.1| dihydrouridine synthase family protein, putative [Talaromyces
           stipitatus ATCC 10500]
          Length = 524

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 61/257 (23%), Positives = 101/257 (39%), Gaps = 37/257 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAI-------------LRGDKKN--- 39
           MVD ++  +R   R           L Y+ M  A                +R D  N   
Sbjct: 33  MVDRSEFAWRMLTRSFMAKDEPQRLLAYSPMFHARLYNETEGFRAQHFQPVRRDDPNVPF 92

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           + G    ++PL +Q    D +  +EAA++V  +  + ++LN+GCP     +G +GA L  
Sbjct: 93  LDGNPAIDRPLFVQFCANDPNDFLEAARLVAPY-CDAVDLNLGCPQGIARKGHYGAFLQE 151

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + D++   I  +   L +PVT K RI    Q          K I  +G + I +H R+  
Sbjct: 152 DWDLIYKLINRLHTELPVPVTAKFRI----QETKEKTLEYAKMILSAGASIITVHGRRRE 207

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLE---DMSQALKILPSVDGVMI 215
            KG            D+  +  +++   P   I  NG +    D+   L+     DGVM 
Sbjct: 208 QKG------HNTGVADWSYIKYLRENLPPKTVIFANGNILNHGDIEHCLEA-TGADGVMS 260

Query: 216 GRAAYKNSAMLTTVDEY 232
                 +  + + V E 
Sbjct: 261 AEGNLSDPTIFSKVPEI 277


>gi|195116601|ref|XP_002002842.1| GI17600 [Drosophila mojavensis]
 gi|193913417|gb|EDW12284.1| GI17600 [Drosophila mojavensis]
          Length = 397

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 62/292 (21%), Positives = 114/292 (39%), Gaps = 29/292 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      L +T M++AD+I   +K     F+T   ++PL  Q    D
Sbjct: 29  MVRYSKLEFRRLLRQ-NGVQLAFTPMMIADSINNSEKARQNEFTTGLDDQPLIAQFAAKD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
             + V A++++  +  + ++LN GCP        +G  L+  P+ V D I ++ + L   
Sbjct: 88  ALEFVTASQLIYPY-VDGVDLNCGCPQGWAIAKGYGCGLLRQPEQVRDIIQSLRRTLPTD 146

Query: 117 IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             V+VK R+    D+Q        L + ++  GV  + +H R    K            L
Sbjct: 147 FSVSVKMRLLNSSDNQTSVNKTIQLAQQLEYCGVTFLTLHGRTPAQKH-------SKDTL 199

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           + + + E+ K    + + +NG +E    A ++       GVM  R    N A+  + D  
Sbjct: 200 NVEAMAEVAKSL-QIPLIVNGNVESYQDACELHKQTQAAGVMAARGLLANPALFNS-DYQ 257

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISA---SMTDYAARHLHSGGKLQQITRHMI 281
                        +V    W  I+       ++   H H         +  +
Sbjct: 258 LETAT-------PKVCVQQWLDIAESAGHNLNFQCFHHHLSFMWNSTMKRAL 302


>gi|332022244|gb|EGI62559.1| tRNA-dihydrouridine synthase 4-like protein [Acromyrmex echinatior]
          Length = 745

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 104/231 (45%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      + +T MI+AD+ ++  K     F+T E  +PL +Q     
Sbjct: 21  MVRYSKLQFRTLVRRY-GCDICFTPMILADSFVQSSKARDNEFTTHEGDEPLIVQFAAKT 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  V A+ +V  +  N ++LN GCP     +  +GA L+  P++V D +  +   +  P
Sbjct: 80  VNDFVSASVMVAPY-CNGVDLNCGCPQRWAMQEGYGADLLKKPELVKDLVYQVRNRIPKP 138

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I       L ++++K+G + + IHAR   ++      N          
Sbjct: 139 FTVSAKIRLLKDIRKTIT--LCQTLEKAGASFLTIHARTPEMRNEPIDLNNL-------- 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             ++ ++   L +  NG ++ +  A  +      +GVM  R    N A+ +
Sbjct: 189 --KLLRDYVQLPLIANGDVKSLENAEFLFKESRCEGVMSARGILTNPALFS 237


>gi|17507177|ref|NP_492379.1| hypothetical protein F36A2.2 [Caenorhabditis elegans]
 gi|3876775|emb|CAB03067.1| C. elegans protein F36A2.2, confirmed by transcript evidence
           [Caenorhabditis elegans]
          Length = 527

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 98/247 (39%), Gaps = 19/247 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R F R      L +T MI A   +         L     ++PL +Q     
Sbjct: 80  MVDQSELAFRMFTRKY-GAQLTFTPMIHAHLFVNDGTYRRNSLALVKADRPLVVQFCANK 138

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   + A ++VED   + ++LN+GCP      G +G+ L    D++ + ++A+     +P
Sbjct: 139 VDTFLAACRLVEDV-CDGVDLNLGCPQMVAKRGRYGSWLQDEVDLICEMVSAVRDYCRLP 197

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R+  D Q          K +  +G   + +H R   +KG       +    D+  
Sbjct: 198 ISCKIRVRDDRQQTV----EYAKRLVDAGATMLTVHGRTRDMKGA------ETGLADWSR 247

Query: 179 VYEIKKENPD-LFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++ +     + +  NG ++   D+ + ++       +M       N  +    + +  
Sbjct: 248 IRDVVEAVGSRVPVMANGNIQFPGDVERCMQA-TGAVAIMSAEGLLYNPLIFDDANAHVD 306

Query: 235 NPLTGSS 241
                + 
Sbjct: 307 TWKIAAE 313


>gi|317152055|ref|YP_004120103.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
 gi|316942306|gb|ADU61357.1| dihydrouridine synthase DuS [Desulfovibrio aespoeensis Aspo-2]
          Length = 352

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 64/281 (22%), Positives = 110/281 (39%), Gaps = 24/281 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF---STQEKPLALQIGGA 57
           M       +R          L +TEM  A A+   +++    F     +   L  QI GA
Sbjct: 36  MAGLGHVAFREVLGHYGGCGLAFTEMCSARAVPTENRRVSAVFRWRDPELDRLVCQIAGA 95

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D ++L  AA+ VED G+  +++N+GC  + + +   GA L+ + D     + A+  A++I
Sbjct: 96  DPAELAVAARRVEDEGFFGVDINMGCSVSGIVKKGAGAALLRDHDAALAALDAVRSAVAI 155

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV VK R G    I      +L + ++ +G + +  H R A  K   P     I      
Sbjct: 156 PVFVKFRTGWSADIAPAI--SLARRLESAGADCLVFHPRVAPDKRTRPPMRDHI------ 207

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               +  E   + +  NG +      L +L      GV +GR A     +          
Sbjct: 208 ---RVLAEAVSIPVFGNGDVVTPEDCLDMLQGTGCAGVSVGRMAIARPWIFAEW------ 258

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
             TG       ++ D ++  +  + D   RH      L++ 
Sbjct: 259 --TGGDLPAEVLEGDGFKDYALRLADALDRHFDPIRALKRF 297


>gi|59801293|ref|YP_208005.1| hypothetical protein NGO0894 [Neisseria gonorrhoeae FA 1090]
 gi|194098476|ref|YP_002001536.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae NCCP11945]
 gi|239998870|ref|ZP_04718794.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 35/02]
 gi|240014216|ref|ZP_04721129.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI18]
 gi|240016652|ref|ZP_04723192.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA6140]
 gi|240080841|ref|ZP_04725384.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA19]
 gi|240117840|ref|ZP_04731902.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID1]
 gi|240121779|ref|ZP_04734741.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID24-1]
 gi|240123398|ref|ZP_04736354.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID332]
 gi|240125646|ref|ZP_04738532.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-92-679]
 gi|254493655|ref|ZP_05106826.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 1291]
 gi|268594711|ref|ZP_06128878.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 35/02]
 gi|268596959|ref|ZP_06131126.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA19]
 gi|268603542|ref|ZP_06137709.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID1]
 gi|268682020|ref|ZP_06148882.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID332]
 gi|268684231|ref|ZP_06151093.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-92-679]
 gi|59718188|gb|AAW89593.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933766|gb|ACF29590.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae NCCP11945]
 gi|226512695|gb|EEH62040.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 1291]
 gi|268548100|gb|EEZ43518.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae 35/02]
 gi|268550747|gb|EEZ45766.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae FA19]
 gi|268587673|gb|EEZ52349.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID1]
 gi|268622304|gb|EEZ54704.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID332]
 gi|268624515|gb|EEZ56915.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-92-679]
 gi|317164158|gb|ADV07699.1| hypothetical protein NGTW08_0728 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 333

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MRGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  +  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKIH-DTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|111115566|ref|YP_710184.1| histidine phosphokinase/phophatase, putative [Borrelia afzelii PKo]
 gi|216263364|ref|ZP_03435359.1| putative histidine phosphokinase/phophatase [Borrelia afzelii
           ACA-1]
 gi|110890840|gb|ABH02008.1| histidine phosphokinase/phophatase, putative [Borrelia afzelii PKo]
 gi|215980208|gb|EEC21029.1| putative histidine phosphokinase/phophatase [Borrelia afzelii
           ACA-1]
          Length = 334

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 118/270 (43%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKN----ILGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K++    +L  +   +PL  
Sbjct: 17  MEDVTDSVFRNLIHLIGSKEGEPHIYFTEFISVKGILNGSKQSIQHILLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +  +A +I+   G+  I++N+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYKAIEILGSMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + N +  +   G++ + ++ R A+        N+
Sbjct: 137 EACAKFNLPLSVKTRHGF----SYPEIDNWLGFLLGFGIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +D+DI YE+ K      P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 185 SKGPVDFDIFYELVKLRNNISPSTLIIGNGDVWSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLT-TVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   +   +  N L     I     KDF 
Sbjct: 245 NLFKFSSKHFLDNNLNFRLNILKFHIKDFH 274


>gi|260776361|ref|ZP_05885256.1| tRNA-dihydrouridine synthase C [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260607584|gb|EEX33849.1| tRNA-dihydrouridine synthase C [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 317

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 55/312 (17%), Positives = 119/312 (38%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +         +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDQLLPEHVFYRLCPELKQGSHTKSGVPVHI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   +++N GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAVRAAELGAKGVDINFGCPAKLVNKSKGGAALLQHPELIHRVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    P+T K R+G D+         +V +I+ +G + + +HAR             K
Sbjct: 128 EAVPEGTPLTAKIRLGWDNPEDCF---EIVDAIQSAGADELTVHARTKT-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + +I++    + +  NG + +       +    VD +M+ R A+ N   L  
Sbjct: 178 ASEIKWNYINQIRQRFT-IPLIANGEIWNYEDGQACIKATGVDSLMVCRGAF-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V ++    +              W ++   +  Y+   +     L    ++ +    L H
Sbjct: 236 VVKHNHTVMP-------------WTEVVKLLLLYSQYEMKGDKGLYYPNRVKQWFSYLRH 282

Query: 286 GFPNSRRCRHIL 297
            +P +      +
Sbjct: 283 EYPEANELFREI 294


>gi|225155097|ref|ZP_03723593.1| dihydrouridine synthase DuS [Opitutaceae bacterium TAV2]
 gi|224804267|gb|EEG22494.1| dihydrouridine synthase DuS [Opitutaceae bacterium TAV2]
          Length = 360

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 58/287 (20%), Positives = 118/287 (41%), Gaps = 24/287 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +             YTE   + + +       + +  +   +P+  Q+ G D
Sbjct: 18  MQDVTDHAFMHVIARTGAPDYFYTEFFRVHSQSRPEKHILHAIDHNATGRPIFAQLIGED 77

Query: 59  ISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  L   A +I+++     ++LN+GCP+ +V++ + G  L+ +P  + + +A +  AL  
Sbjct: 78  LQHLARTATEILKNHPAAALDLNLGCPAPKVYKKNVGGGLLRDPARIDEILATLRAALPP 137

Query: 118 P--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           P  +TVK RIG +D     A+ +L+ +     V+ + +H R       S         + 
Sbjct: 138 PRLLTVKMRIGFEDTSNYDAILDLINA---HRVDLLTVHGRTVRELYRS--------EVH 186

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           YD +    +      +  NG +   + A ++L      GVMIGR A +N  +     + F
Sbjct: 187 YDAIAHAVRRV-RCPVLANGNITSAATATRVLAETGAAGVMIGRHAIRNPWIFAQCRQAF 245

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           +       P+      +  R I+          +     + ++ +++
Sbjct: 246 AG-----QPVTPVTLGEVRRYITDLHAATRTPGIPELAHISKMKKYL 287


>gi|270700755|ref|ZP_06223017.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae HK1212]
 gi|270315907|gb|EFA27986.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae HK1212]
          Length = 145

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 72/146 (49%), Positives = 94/146 (64%), Gaps = 1/146 (0%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M+ A AI+     + L F  QE P+ALQ+GG+D  +L   AK+ E+ GY+EINLNVGCPS
Sbjct: 1   MVTAPAIIHAKY-DHLDFDLQENPVALQLGGSDPEQLKHCAKLAEERGYHEINLNVGCPS 59

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            RV  G FGACLM   D+V DC+  M  A+ IPVTVK RIG+D+      L + ++ ++ 
Sbjct: 60  DRVQNGMFGACLMAKADLVADCVEQMQSAVKIPVTVKTRIGIDELDSYEFLCDFIEKVQG 119

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKI 171
            G     IHARK  L GLSPK+NR+I
Sbjct: 120 KGCQEFIIHARKVWLSGLSPKENREI 145


>gi|323495036|ref|ZP_08100125.1| tRNA-dihydrouridine synthase C [Vibrio brasiliensis LMG 20546]
 gi|323310693|gb|EGA63868.1| tRNA-dihydrouridine synthase C [Vibrio brasiliensis LMG 20546]
          Length = 317

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 122/324 (37%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L     + L         +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDQLLPDHVFHRLCPELQQGSQTKSGVPIHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++ + + A  
Sbjct: 68  QLLGQDPHWMAENAVKAAELGAKGIDLNFGCPAKLVNKSKGGAALLQHPELIHNVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PVT K R+G D+         +V +I+ +G N + +HAR             K
Sbjct: 128 DAVDPATPVTAKIRLGWDNPEDCF---EIVDAIQTAGANELTVHARTKT-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++    + +  NG + +       +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWDYINQIRQRF-SIPLIANGEIWNYQDGQACIETTGVDSLMVCRGAFNVPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W ++   +  Y+   +     L    ++ +    L H
Sbjct: 237 VKH--------------DHAVMPWSEVVELLLVYSQYEMKGDKGLYYPNRVKQWFSYLRH 282

Query: 286 GFPNS-RRCRHILTVEAGASTATH 308
            +P +    R I T    A    H
Sbjct: 283 QYPQADALFREIRTFNKAAPIVEH 306


>gi|297702080|ref|XP_002828012.1| PREDICTED: tRNA-dihydrouridine synthase 1-like isoform 1 [Pongo
           abelii]
          Length = 456

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 55/283 (19%), Positives = 101/283 (35%), Gaps = 52/283 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + ++LN+GCP                       +    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAVDLNLGCPQMIAKR-----------------VLLAHEKLS 124

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 125 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 174

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 175 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 225

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 226 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 262


>gi|261191538|ref|XP_002622177.1| dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239589943|gb|EEQ72586.1| dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239612649|gb|EEQ89636.1| dihydrouridine synthase [Ajellomyces dermatitidis ER-3]
 gi|327351718|gb|EGE80575.1| dihydrouridine synthase [Ajellomyces dermatitidis ATCC 18188]
          Length = 564

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 100/265 (37%), Gaps = 49/265 (18%)

Query: 1   MVDWTDRHYRFFARLL----TNNALL-YTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R      + + LL Y+ M  A          +  F            
Sbjct: 31  MVDRSEFAWRMLTRSFMDSNSPHPLLAYSPMFHARLFKESPGYRLQHFEATRPKPPRSPC 90

Query: 47  ---------------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
                                ++PL +Q    D   L++AA+ VE F  + ++LN+GCP 
Sbjct: 91  TDDGESPLPGDIRYLDGNPALDRPLIVQFCANDPDDLLQAARTVEPF-CDAVDLNLGCPQ 149

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
               +G +GA L  +PD++   I  + + LSIPVT K RI    Q          + I  
Sbjct: 150 GIARKGHYGAFLQEHPDLIYKLINTLHRELSIPVTAKFRI----QETKEKTLEYARMILS 205

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQAL 204
           +G + I +H R+   KG            D+  +  ++    PD  I  NG + +     
Sbjct: 206 AGASIIAVHGRRREQKG------HNTGLADWSYIRYLRDNLPPDTVIFANGNILNHGDIE 259

Query: 205 KIL--PSVDGVMIGRAAYKNSAMLT 227
           + L     DGVM       +  + T
Sbjct: 260 RCLEATGADGVMSAEGNLCDPTIFT 284


>gi|288572811|ref|ZP_06391168.1| dihydrouridine synthase DuS [Dethiosulfovibrio peptidovorans DSM
           11002]
 gi|288568552|gb|EFC90109.1| dihydrouridine synthase DuS [Dethiosulfovibrio peptidovorans DSM
           11002]
          Length = 345

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 115/318 (36%), Gaps = 24/318 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   T    R     L    L +TEM+    + R ++K   +L  +  E PL LQ+   D
Sbjct: 30  MAGVTLPAVRRMFWRL-GAGLAHTEMVSCAGLTRKNRKTTEMLFRAPGEGPLVLQLFAGD 88

Query: 59  ISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              L+  A+I    G  ++ + +N+ CP  +V +   GA L+   D+  D +  + + L 
Sbjct: 89  SDTLMRGAEIALSLGVPFDALGINMACPMPKVLKKGAGARLLSRLDLAVDMVRRLNR-LG 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV  K R  V D      L     ++ ++G   + +H R A          R     D+
Sbjct: 148 LPVWPKIRKIVPDGSGPDTL-EFASALVEAGAANVGVHGRTA--------SQRYEGTSDF 198

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS- 234
           D V  + +  P   I  +G +       K L      V + R    +  +L  +  +   
Sbjct: 199 DEVRRVARALPG-VISASGDISGPEDVSKALAGGCVSVFLARGGVTDPFVLPRILSHLGY 257

Query: 235 --NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                    P         +  ++  ++ +          +  + R M G+F G P    
Sbjct: 258 NIGDSVYDDPPSIETRAALFSDLAEDLSTF----HGERVAMVLLKRLMSGVFRGVPGCSS 313

Query: 293 CRHILTVEAGASTATHHI 310
            R  +   +   T   HI
Sbjct: 314 YRRAIASASDWGTMCAHI 331


>gi|157375994|ref|YP_001474594.1| dihydrouridine synthase, DuS [Shewanella sediminis HAW-EB3]
 gi|157318368|gb|ABV37466.1| dihydrouridine synthase, DuS [Shewanella sediminis HAW-EB3]
          Length = 308

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 56/299 (18%), Positives = 118/299 (39%), Gaps = 44/299 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     +    ++ +E   +V   +       +         +    P+ L
Sbjct: 8   MEGVADAPMRSLLTSVGGYDMVISEFIRVVDQLLPEKVFYRLCAELANNSQTQAGTPVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G   S + E A    + G   ++LN GCP+  V+  + GA L+  PD +     ++ 
Sbjct: 68  QLLGQHPSWMAENALRAVELGSRGVDLNFGCPAPMVNRSNGGAALLKEPDTIYRVTHSVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  + PV+ K R+G DD+   V    + ++I+ +G   + +HAR         K+   
Sbjct: 128 EAVPSNHPVSAKIRLGWDDKSRCV---EIAQAIEAAGATELTVHART--------KEEGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +IK+    + +  NG + +     +   +   + VM+GR A     +   
Sbjct: 177 RPPAHWEYINQIKEAI-SIPVIANGEVWNREDYQRCQVVSGCNDVMVGRGALAVPNL--- 232

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY------AARHLHSGGKLQQITRHMI 281
                      +  +K   D   W ++   +  Y      +A+  +   +++Q  R ++
Sbjct: 233 -----------AHVLKGTQDAMPWDEVKQLLLQYSEYEIVSAKEKYYPARIKQWLRFIV 280


>gi|293399153|ref|ZP_06643318.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae F62]
 gi|291610567|gb|EFF39677.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae F62]
          Length = 341

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 28  MRGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 87

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 88  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 147

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K    
Sbjct: 148 GRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEGY 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  +  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 197 EPPAHWEWIRKIH-DTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 255

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 256 IKQYENGGPVKDT 268


>gi|73541045|ref|YP_295565.1| dihydrouridine synthase, DuS [Ralstonia eutropha JMP134]
 gi|72118458|gb|AAZ60721.1| Dihydrouridine synthase, DuS [Ralstonia eutropha JMP134]
          Length = 324

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 62/287 (21%), Positives = 112/287 (39%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA------ILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     L       +E +          +   D   IL  G +    P+ +
Sbjct: 9   MEGLADYVLRDVLTGLGGYDGCVSEFVRVTGSLLPPRVYERDTPEILQGGHTPSGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+ +P+ +   ++A+ 
Sbjct: 69  QLLGSDPEWLARNATYAATLSPHGIDLNFGCPAKVVNRHGGGAMLLAHPEQLHSIVSAVR 128

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPPHIAVTAKMRLGVSDTALAL---DCATALAEGGAASLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I  +  D+ +  NG +  ++   +   +     VMIGR A  +  +   
Sbjct: 178 RPPAHWEWIARIA-DTVDIPVIANGDVWSVADWERCRAVSGCADVMIGRGAVSDPFLALR 236

Query: 229 VDEYF-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +     S P     P+  +    + RK+   ++     H H   KL 
Sbjct: 237 IRGLMDSTPSDADWPLVLQQIAAYLRKLHDRISSC---HEHGRVKLW 280


>gi|17232390|ref|NP_488938.1| transcriptional regulator [Nostoc sp. PCC 7120]
 gi|17134036|dbj|BAB76597.1| transcriptional regulator [Nostoc sp. PCC 7120]
          Length = 349

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 105/250 (42%), Gaps = 17/250 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE--MIVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D T+  +        +    +TE   +   + L     + +  +   +P+  Q+ G  
Sbjct: 32  MQDVTNLWFMKVIAHYGSPDYFFTEYFRVNDTSRLNRGILSAITENDTGRPVFAQMIGES 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
           I  LV  AK +  +    ++LN+GCP+ R++  + G  L+L+P  V   +  + +A+   
Sbjct: 92  IPDLVRTAKELCGYNIAGVDLNMGCPAPRIYRKNVGGGLLLSPAKVEQILEELRQAVNDR 151

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G ++         ++  + +  ++ + +H R           +     + YD
Sbjct: 152 PLTVKMRVGFENTD---TFYEILDIVNRHNIDLLSLHGRTVK--------DMYHGAVKYD 200

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E  +   D  +  NG +   + AL++L      GVM+GR A  N  +   + +    
Sbjct: 201 LIAEAVRRV-DCPVLANGNIHSATTALEVLERTGAAGVMVGRWAIGNPWLFNQIRQALQG 259

Query: 236 PLTGSSPIKT 245
                 P+  
Sbjct: 260 ETITPVPLVE 269


>gi|240115548|ref|ZP_04729610.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID18]
 gi|260440642|ref|ZP_05794458.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI2]
 gi|268601220|ref|ZP_06135387.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID18]
 gi|268585351|gb|EEZ50027.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae PID18]
          Length = 333

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MRGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  +  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKIH-DTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|268576246|ref|XP_002643103.1| Hypothetical protein CBG23028 [Caenorhabditis briggsae]
          Length = 279

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 64/307 (20%), Positives = 117/307 (38%), Gaps = 46/307 (14%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISK 61
           ++   +R   RL   + + YT MI A   +     + + L     + PL +Q    D   
Sbjct: 1   FSRLAFRQLVRLYDVD-VCYTPMIYAKNFIESEKCRNSELSVCEGDSPLIVQFATDDPFV 59

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IP 118
           L EAA++V     + ++LN GCP   V    FG+ L+  P+++ D +      +S     
Sbjct: 60  LAEAAEMVY-SCSSGVDLNCGCPKHDVRSKGFGSALLSKPELLADMVRQTRARISDENFS 118

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V++K R+  + +       +L +  + +GV  + +H R                 +D + 
Sbjct: 119 VSLKIRVNKEIEKTV----DLCRKAESAGVTHLTVHGRTPSQH---------AEPIDIEA 165

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +K     + I  NGG+ ++ +A+ +     VDG+M       N A+           
Sbjct: 166 IRLVKSAV-KVPIIANGGITNLQEAMNLAEKTGVDGIMAANGLLDNPALFA--------- 215

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             G     +   + F R       D+   H H    LQ + R ++        S + R I
Sbjct: 216 --GYEYTPSDCVESFMRLSREHGLDWLLYHQH----LQYMLRPLL--------SAQQRRI 261

Query: 297 LTVEAGA 303
                G 
Sbjct: 262 FNELNGR 268


>gi|300703947|ref|YP_003745549.1| tRNA-dihydrouridine synthase c [Ralstonia solanacearum CFBP2957]
 gi|299071610|emb|CBJ42934.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum CFBP2957]
          Length = 326

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 113/287 (39%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R             +E + V  ++L               G +    P+ +
Sbjct: 9   MEGVADFVMRDVLTRAGGYDGCVSEFVRVTGSLLPARFYERETPEIRNGGCTASGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++   ++A+ 
Sbjct: 69  QLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLATPELLHTIVSAVR 128

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPADIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +  ++ +  NG +  ++   +   +   D VMIGR A  +  +   
Sbjct: 178 RPPAHWDWIARIA-DAVEVPVVANGEVWTVADWERCRAVSGCDDVMIGRGAVSDPFLAQR 236

Query: 229 VDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       P     P+  R   D+ + + A +   AA H H   KL 
Sbjct: 237 IRGQMEQTPSDAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKLW 280


>gi|195434933|ref|XP_002065456.1| GK14658 [Drosophila willistoni]
 gi|194161541|gb|EDW76442.1| GK14658 [Drosophila willistoni]
          Length = 404

 Score =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 64/295 (21%), Positives = 124/295 (42%), Gaps = 23/295 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L +T M+++++I   +K     FST   ++PL  Q    D
Sbjct: 34  MVRYSKFEFRKLLRQ-NGVQLCFTPMMISESINNSEKARQNEFSTDQDDQPLVAQFAAKD 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            S+ V +A+++  +  + I+LN GCP +      +G  L+  P+ V D +  + + L   
Sbjct: 93  ASEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGLLRQPEQVKDIVREVRRVLPTD 151

Query: 117 IPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
             V+VK R+    Q  ++    +L + ++ +GV  + +H R    K    KD   IP ++
Sbjct: 152 FSVSVKMRLLGGSQETSLERTIDLARQLEHTGVTFLTLHGRTPAQKH--SKDTLNIPAMN 209

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
                   +++  + + +NG +E    A+++       GVM  R    N A+  +     
Sbjct: 210 E------VQKSLQIPLIVNGNVESWEDAIELQSQTGAAGVMAARGLLANPALFNS----- 258

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL-QQITRHMIGLFHGF 287
           + P    +P+            +     +   H H       Q+ R +   F+G 
Sbjct: 259 NYPEAKVTPLSCVQQWLDIACAAGDNLHFQCFHHHLTFMWSSQMKRKLRVQFNGL 313


>gi|295657937|ref|XP_002789532.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb01]
 gi|226283236|gb|EEH38802.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb01]
          Length = 563

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 62/269 (23%), Positives = 98/269 (36%), Gaps = 53/269 (19%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFS----------- 44
           MVD ++  +R   R        N  L Y+ M  +          +  F            
Sbjct: 28  MVDRSEFAWRMLTRSFIDPQSPNPLLAYSPMFHSRLFKESANYRLQHFEATRPKLNSKFS 87

Query: 45  -----------------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
                                  T ++PL +Q    D  +L+ AA+ VE F  + ++LN+
Sbjct: 88  TPADGKEPQLPDSPVIPYLDGNPTIDRPLIVQFCANDPDELLHAARTVEPF-CDAVDLNL 146

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP     +G +GA L   P+++   I  +   LSIPVT K RI    Q          +
Sbjct: 147 GCPQGIARKGHYGAFLQEEPELIYKLINTLHTELSIPVTAKFRI----QETKEKTLEYAR 202

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDM 200
            I  +G + I +H R+   KG            D+  +  ++   P D  I  NG + D 
Sbjct: 203 MILSAGASFISVHGRRRDQKG------HNTGLADWSYIRYLRDNLPADTVIFANGNILDN 256

Query: 201 SQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              ++ L     DGVM       +  + T
Sbjct: 257 RDIMRCLEATGADGVMSAEGNLCDPTIFT 285


>gi|322795085|gb|EFZ17930.1| hypothetical protein SINV_15746 [Solenopsis invicta]
          Length = 357

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 108/231 (46%), Gaps = 18/231 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R      + +T MI+AD+ ++  K     F+T   ++PL +Q     
Sbjct: 28  MVRYSKLQFRTLVRQY-GCDICFTPMILADSFVQSSKARDNEFTTHKNDQPLIVQFAANT 86

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++  V+A+ +V  +  N ++LN GCP     +  +GA L+  P++V D +  +   +  P
Sbjct: 87  VNDFVDASVMVAPY-CNGVDLNCGCPQRWAMQEGYGADLLKKPELVKDLVYQVRNRIPRP 145

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  +I +   I    L  L ++++K+G + + +HAR   ++            +D D 
Sbjct: 146 FTVSAKIRLLKDIRQTIL--LCQTLEKAGASFLTVHARTPKMRN---------EPIDLDS 194

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           +  + +++  L +  NG  + +  A  +      +GVM  R    N A+ +
Sbjct: 195 LKFL-RDHVQLPLVANGDAKSLETAKSLFKESRCEGVMSARGILTNPALFS 244


>gi|330720421|gb|EGG98739.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC2047]
          Length = 325

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 103/279 (36%), Gaps = 28/279 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       TE I      R  +K    +  +           P+ 
Sbjct: 12  MQGVVDHPMREMLTRIGGYDRCVTEFIRVTN-TRFPEKVFKRYCPELLQGGKTLAGTPVY 70

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G D   L + A      G + I+LN GCP+  V+    G+ L+  P  V   + A+
Sbjct: 71  IQLLGGDPHWLSQNAAKAARLGAHGIDLNFGCPAKIVNRNDGGSVLLKEPSRVAGIVRAV 130

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PVT K R+G  D   A  L  +   I+ +G + + IHAR         +++ 
Sbjct: 131 RDAVDPAVPVTAKIRLGFSD---ASLLPEIAGGIEAAGASELCIHART--------REDG 179

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
             P   +  +  I+++   + +  NG +   + AL+         +M+GR A     +  
Sbjct: 180 YKPPAYWQHINAIRQQL-SIPVIANGEIWAPADALEAQRQSGCTDLMLGRGALACPDLAR 238

Query: 228 TVDEYFSNPLTGSSPIKTRVD--KDFWRKISASMTDYAA 264
            + +     +    P    ++   DF+         Y  
Sbjct: 239 AIKQQAVGDVPELMPWSDVLEGLTDFFENADQPCPKYIG 277


>gi|332971837|gb|EGK10783.1| tRNA-dihydrouridine synthase C [Kingella kingae ATCC 23330]
          Length = 322

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 60/327 (18%), Positives = 123/327 (37%), Gaps = 30/327 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +       L    +           P  
Sbjct: 11  MQGLCDPVMRDLLTRIGGYDECVSEFVRITHTVHSRP-TWLRHVPEIATQNQTFSGVPCV 69

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+ G+D   + + A      G N+I+LN GCP+  V++   GA L+  P+ V   +A +
Sbjct: 70  TQLLGSDADMMAQNALEAVKLGANKIDLNFGCPAPTVNKHQGGAVLLREPERVRHIVATL 129

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
              L   +T+  ++ +  +   +AL N  ++I++ G + + +HAR  +            
Sbjct: 130 RDRLPSHITLTAKMRLGFENKELALEN-AQAIEQGGASLLTVHARTKVEG--------YQ 180

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTV 229
           P   +D V +I++    + +  NG +  +S  +A++       VMIGR A     +   +
Sbjct: 181 PPAHWDWVNKIRQAV-QIPVVANGDVFTLSDYRAIREQSGCQDVMIGRGAVIRPDLARQI 239

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFP 288
            +Y       ++     +  D+ R   A   +   +  ++  +L+Q     +G+    +P
Sbjct: 240 KQYLHGQTVQAACFHGEIM-DWIRLFFALCLEKEPQGKYAIARLKQW----LGMMRDAYP 294

Query: 289 NSRRCRHILTVEAGASTATHHIIETAF 315
            +      +        A    I  +F
Sbjct: 295 EAETLFQAI--RTQREVADIQRILQSF 319


>gi|291043950|ref|ZP_06569666.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI2]
 gi|291012413|gb|EFE04402.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae DGI2]
          Length = 341

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 102/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 28  MRGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 87

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 88  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 147

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR         K    
Sbjct: 148 GRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEGY 196

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  +  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 197 EPPAHWEWIRKIH-DTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 255

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 256 IKQYENGGPVKDT 268


>gi|156847371|ref|XP_001646570.1| hypothetical protein Kpol_1055p69 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156117248|gb|EDO18712.1| hypothetical protein Kpol_1055p69 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 346

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 14/234 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R     +  F+T   + PL +Q+G  +
Sbjct: 38  MVRYSKLPFRQVCRDYDVD-IVYTPMILAREFVRNGHARLADFTTCSTDSPLIVQVGVNN 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L++  ++V  +  + I +N GCP         G  L+ NP+++   ++A+ +     
Sbjct: 97  VADLLKFVEMVSPY-CDGIGINCGCPIKEQIREGIGCALIYNPELLASMVSAVKQKYGDK 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I + D +       L   +  +GV+ I IH R    +   P +   I      I
Sbjct: 156 VRLETKIRIHDDLEQTV--ELCNKVCDAGVDWITIHGRTRTTRSSQPVNLDAIKY----I 209

Query: 179 VYEIKKENPDLFIGLNGG--LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           + +IK  N  + +  NG   +E     +      DGVM  R    N A+    D
Sbjct: 210 ISQIKGRN--VPVVANGDCFVETDLAKISECTGADGVMAVRGLLANPALFAKYD 261


>gi|229591631|ref|YP_002873750.1| hypothetical protein PFLU4202 [Pseudomonas fluorescens SBW25]
 gi|229363497|emb|CAY50729.1| conserved hypothetical protein [Pseudomonas fluorescens SBW25]
          Length = 325

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 56/275 (20%), Positives = 106/275 (38%), Gaps = 26/275 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE I      +  A        +L    +    PL +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVNDRLLTPAYFHKLAPELLHGAHTAAGVPLRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGSQVIDLNFGCPAKTVNKSRGGAVLLKEPELLNQIVEHVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D    A+       ++ + G   I +HAR         K +  
Sbjct: 128 RAVPAHIPVTAKMRLGFDSPDGALV---CATALAEGGAAHIVVHART--------KTDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + ++   + +  NG +  +    +      V+ +M+GR       +   
Sbjct: 177 KPPAHWEWIPRV-QDVVKVPVFANGDIWSVEDWRRCREISGVEDIMLGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIKT--RVDKDFWRKISASMTD 261
           +    +              + +DFW +  A +T+
Sbjct: 236 IAAARAGEEVVEMTWAEMQPMLQDFWTQSVAQLTE 270


>gi|309782621|ref|ZP_07677343.1| tRNA-dihydrouridine synthase C [Ralstonia sp. 5_7_47FAA]
 gi|308918596|gb|EFP64271.1| tRNA-dihydrouridine synthase C [Ralstonia sp. 5_7_47FAA]
          Length = 322

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 114/287 (39%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R             +E + V  ++L               G++    P+ +
Sbjct: 5   MEGVADYVMRDVLTRAGGYDGCVSEFVRVTGSLLPARTYERETPEIRNGGYTASGTPMTI 64

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++ D + A+ 
Sbjct: 65  QLLGSDPEWLARNAAYAATLTPHGIDLNFGCPAKVVNRHGGGAMLLATPEVLYDIVHAVR 124

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 125 AAVPANISVTAKMRLGVSDTSRAI---DCATALAEGGAESLVVHART--------RDHGY 173

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +   + +  NG +  ++   +   +     VMIGR A  +  +   
Sbjct: 174 RPPAHWDWIARIA-DAVSIPVTANGEVWTVADWERCRAVSGCSDVMIGRGAVSDPFLAQR 232

Query: 229 VDEYF-SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       P     PI      D+ +K+ A ++   A+H H   KL 
Sbjct: 233 IRGQMDEAPSAAEWPIVLGYLADYLKKLHARIS---AKHEHGRVKLW 276


>gi|83745889|ref|ZP_00942946.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
 gi|83727579|gb|EAP74700.1| tRNA-dihydrouridine synthase [Ralstonia solanacearum UW551]
          Length = 369

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 114/287 (39%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R             +E + V  ++L               G +    P+ +
Sbjct: 52  MEGVADFVMRDVLTRAGGYDGCVSEFVRVTGSLLPARFYERETPEIRNGGCTASGTPMVI 111

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++   ++A+ 
Sbjct: 112 QLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLSTPELLHTIVSAVR 171

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 172 AAVPANIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART--------RDHGY 220

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +  ++ +  NG +  ++   +   +   D VMIGR A  +  +   
Sbjct: 221 RPPAHWDWIARIA-DAVEVPVIANGEVWTVADWERCRAVSGCDDVMIGRGAVSDPFLAQR 279

Query: 229 VDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       P     P+  R   D+ + + A +   AA H H   KL 
Sbjct: 280 IRGQMERTPSNAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKLW 323


>gi|322702122|gb|EFY93870.1| dihydrouridine synthase family protein, putative [Metarhizium
           acridum CQMa 102]
          Length = 543

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 124/321 (38%), Gaps = 63/321 (19%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIVADAILRGDKKNILGF------------ 43
           MVD ++  +R   R    +      L YT M  A    +  K     F            
Sbjct: 41  MVDQSEFAWRMLTRSFLTDEEKKKMLAYTPMFHARLFSQERKYRKTHFQSTKPDSQEPWL 100

Query: 44  ---STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
               + ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  +
Sbjct: 101 DGNPSIDRPLFVQFCANDPEALLSAAKQVSPY-CDAVDLNLGCPQGIARKGHYGAFLQED 159

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + K LSIPVT K RI  D +          +++ ++G + + +H R+   
Sbjct: 160 QDLIFRLINTLHKELSIPVTAKIRILEDKEKT----LEYAQNVLRAGASILTVHGRRREQ 215

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLE---DMSQALKILPSVDGVMIG 216
           KG            D+ ++  ++    P+  I  NG +    D+ + L      DGVM  
Sbjct: 216 KG------HLTGVADWKVLRFLRDSLPPETVIFANGNILQGGDIDECLAA-TGADGVMSA 268

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                + A+               +P      +++WR           +    G ++  I
Sbjct: 269 EGNLSDPALFA------------KAPPVGEEGREYWR----------GKDGRGGWRVDAI 306

Query: 277 TRHMIGLFHGF-----PNSRR 292
           TR  + + H +     P +RR
Sbjct: 307 TRRYLDILHRYALGVEPPARR 327


>gi|209695593|ref|YP_002263522.1| tRNA-dihydrouridine synthase C [Aliivibrio salmonicida LFI1238]
 gi|208009545|emb|CAQ79837.1| tRNA-dihydrouridine synthase C [Aliivibrio salmonicida LFI1238]
          Length = 315

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 117/292 (40%), Gaps = 34/292 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAI-----------LRGDKKNILGFSTQE 47
           M    D   R     + +     TE +  V   +           L  D K         
Sbjct: 8   MEGVLDHLMRELLTEINDYDFCVTEFVRIVDQLLPPHVFHRICPELHNDSKT-----KSG 62

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ LQ+ G + + + E A    D G + ++LN GCP+  V++   GA L+ +P+++   
Sbjct: 63  TPIRLQLLGQEPNWMAENAARAIDLGSDGLDLNFGCPAKAVNKSRGGAALLKDPELIYQI 122

Query: 108 IAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A  +A+     VT K R+G ++     A   +  +IK++G N + IHAR         
Sbjct: 123 VKACREAVPQDKKVTAKIRLGWENPEECFA---IADAIKQAGANELTIHARTKT------ 173

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            D  +   + +D + +++++  D+ I  NG + + +   + +    +D +M+ R A+   
Sbjct: 174 -DGYRAEEIKWDYINQVRQKI-DIPIIANGEIWNYADGQRCIAATGIDSLMVCRGAFNMP 231

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
             L  V ++    +     I   +     +        YA R       L+Q
Sbjct: 232 -NLGNVVKHNHPKMPWPEVIALLIHYSKLQMAGDKGQYYANRVKQWLVYLRQ 282


>gi|221486656|gb|EEE24917.1| tRNA-dihydrouridine synthase, putative [Toxoplasma gondii GT1]
          Length = 1220

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 107/285 (37%), Gaps = 30/285 (10%)

Query: 6    DRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLV 63
            +  +R     L    +  +EM VA +I+ G +   ++L     E    +QI G     L 
Sbjct: 831  NLPFRRLCVEL-GAEVTVSEMAVAKSIVDGKQSELSLLKRHKSETFFGVQIAGGTPEVLN 889

Query: 64   EAAKIV--EDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC-KALSIPV 119
                I+  ED   + I+LN  CP  ++H     GAC++ +P  +   + +M  +   +PV
Sbjct: 890  ACTDILASEDVSCDFIDLNAACPLVQLHRRFKAGACMLDHPKRLESLVESMTTRHPEVPV 949

Query: 120  TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            TVK R    +Q     L + ++ +  +G   + +H R A          R     D+  V
Sbjct: 950  TVKLRTA--NQGKKQVLHSFIRRLGDAGAAALIVHGRTA--------QQRYTKAADWSYV 999

Query: 180  YEIKKEN-PDLFIGLNGGLE-DMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + ++       +   G +        ++     DG+MI RAA     + T + E     
Sbjct: 1000 AQCREALDSSTPLIGCGDIFSSPEFEFRLASGASDGLMIARAALVKPWVFTEISERKVWD 1059

Query: 237  LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            ++ S  +           +      +   H  S  +    TR  +
Sbjct: 1060 ISASERL----------DLLKRFVRFGLEHWGSDSRGVATTRRFL 1094


>gi|113970596|ref|YP_734389.1| dihydrouridine synthase, DuS [Shewanella sp. MR-4]
 gi|113885280|gb|ABI39332.1| dihydrouridine synthase, DuS [Shewanella sp. MR-4]
          Length = 315

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 75/333 (22%), Positives = 132/333 (39%), Gaps = 50/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  GF+    P+ +
Sbjct: 8   MEGVVDDLMRDILSSINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNGGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P+ + D + AM 
Sbjct: 68  QLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYPNTIHDIVRAMR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPAEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARSKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E+++  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 177 KPPAYWEYITEVRERLP-IPVIANGEIWNREDAERCMAVTGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGKLQQITRHMIGLFH 285
           +        TG++P +       W      M  Y  R L    S     +I +    L  
Sbjct: 236 IK-------TGAAPYR-------WADTLGLMLSYTQRELSGRKSDYYPARIKQWFSYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETA 314
            +P +    R  R   T E         ++E A
Sbjct: 282 QYPEADTLFRELRIYKTTEEI-----VRVLEEA 309


>gi|300691378|ref|YP_003752373.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum PSI07]
 gi|299078438|emb|CBJ51090.1| tRNA-dihydrouridine synthase C [Ralstonia solanacearum PSI07]
          Length = 326

 Score =  165 bits (419), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 115/287 (40%), Gaps = 28/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +       +E + V  ++L               G++    P+ +
Sbjct: 9   MEGVADFVLRDVLTRVGGYDGCVSEFVRVTGSLLPARTYERETPEIRNGGYTASGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++   ++++ 
Sbjct: 69  QLLGSDPEWLARNAAQAATVSPHGIDLNFGCPAKVVNRHGGGAMLLATPELLHRIVSSVR 128

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   I VT K R+GV D   A+A      ++++ G   + +HAR         +D+  
Sbjct: 129 AAVPAHIAVTAKMRLGVSDTSLAIA---CATALEEGGAASLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +   + +  NG +  +    +   +   D VMIGR A  +  +   
Sbjct: 178 RPPAHWDWIARIA-DAVHVPVVANGEVWTVDDWERCRAVSGCDDVMIGRGAVSDPFLALR 236

Query: 229 VDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +    +  P     P+  R   D+ +K+ A +   A  H H   KL 
Sbjct: 237 IRGQMARAPSDAEWPLVLRCLVDYLKKLHARI---AVHHEHGRVKLW 280


>gi|66358732|ref|XP_626544.1| YjbN-like Dus1p tRNA dihydouriding synthase Tim barrel
           [Cryptosporidium parvum Iowa II]
 gi|46227752|gb|EAK88672.1| YjbN-like Dus1p tRNA dihydouriding synthase Tim barrel
           [Cryptosporidium parvum Iowa II]
          Length = 519

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 111/262 (42%), Gaps = 53/262 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---------ILGFSTQEKPLA 51
           M+D T+ H+R   R+++    L+TEM+V D I+                   +  E PL 
Sbjct: 33  MLDVTNSHFRMLCRIISKKTELWTEMVVDDTIIHCYNDENRRKILQDVHFKKNDIENPLV 92

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAA 110
           LQ+GG +  K+ +A +I   +G+   NLNVGCPS +V     FGA L  NP  V   +  
Sbjct: 93  LQLGGNNPQKMEKAIEIAYKYGFQNFNLNVGCPSCKVASKGSFGASLFKNPLRVAKIVDT 152

Query: 111 MCKA------LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS------------------ 146
             K       ++  ++VK RIGVD       L N +  +                     
Sbjct: 153 CNKKLIHLGLVNKRISVKTRIGVDQYDTYQHLYNFISLVSGCNINNQNKKDYSCIFPQSD 212

Query: 147 -------------------GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                              G N   IHARKA L G++P  NR IP L Y  VY +  + P
Sbjct: 213 DDSDSNILESIDYTENNFIGANVFIIHARKAWLNGINPSKNRTIPKLKYYWVYMLTLDFP 272

Query: 188 DLFIGLNGGLEDMSQALKILPS 209
           +L   LNGG+  + + + IL  
Sbjct: 273 NLTFILNGGVTSIQECISILTG 294



 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/110 (18%), Positives = 36/110 (32%), Gaps = 22/110 (20%)

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR-----------------VDKDFWRK 254
           GVMIGR    N  +L+ VD                                   +    +
Sbjct: 369 GVMIGREVMNNPFILSKVDSMIYGINYNQVNNNNNNNNNCINTNGNNSSIHLTRRIVLER 428

Query: 255 ISASMTDYAARHLHS-----GGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
               ++ +  R++        G+L    + + G+FHGF  ++  R  L+ 
Sbjct: 429 YVEYLSKFKPRNIKDQGQFTIGELNMYLKPVFGIFHGFSGTKFWRRTLSE 478


>gi|227356698|ref|ZP_03841084.1| tRNA-dihydrouridine synthase C [Proteus mirabilis ATCC 29906]
 gi|227163206|gb|EEI48137.1| tRNA-dihydrouridine synthase C [Proteus mirabilis ATCC 29906]
          Length = 303

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 110/288 (38%), Gaps = 28/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     + +  L  TE I V D++L    K       +            +
Sbjct: 1   MEGVLDPLVRDLLTAINHYDLCITEFIRVVDSLL--PPKAFYRLCPELHTQSRTQSGTLV 58

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G +   L E A      G   ++LN GCPS  V+    GA L+  P+ +     A
Sbjct: 59  RVQLLGQNPQWLAENAFRAVSLGSWGVDLNCGCPSKTVNGNGGGASLLKQPETIYQATKA 118

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M  A+   +PV+VK R+G D          +  ++++ G   I IH R          D 
Sbjct: 119 MRGAVPADLPVSVKVRLGWDCSSYC---HEIADAVEQGGATEITIHGRTKE-------DG 168

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            +   +++  + EI+++   + +  NG +     A+  L     D +MIGR A      L
Sbjct: 169 YRADKINWQAIGEIRQKLT-IPVIANGEIWCREDAISCLKITGCDAIMIGRGAMHTP-NL 226

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           + V +     +  S  I+         K   +   +A+R     G L+
Sbjct: 227 SNVIKGIEEKMPWSQVIQLLKRYIRLEKQGDTTYYHASRIKQWLGYLR 274


>gi|221508413|gb|EEE34000.1| tRNA-dihydrouridine synthase, putative [Toxoplasma gondii VEG]
          Length = 1220

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 107/285 (37%), Gaps = 30/285 (10%)

Query: 6    DRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLV 63
            +  +R     L    +  +EM VA +I+ G +   ++L     E    +QI G     L 
Sbjct: 831  NLPFRRLCVEL-GAEVTVSEMAVAKSIVDGKQSELSLLKRHKSETFFGVQIAGGTPEVLN 889

Query: 64   EAAKIV--EDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC-KALSIPV 119
                I+  ED   + I+LN  CP  ++H     GAC++ +P  +   + +M  +   +PV
Sbjct: 890  ACTDILASEDVSCDFIDLNAACPLVQLHRRFKAGACMLDHPKRLESLVESMTTRHPEVPV 949

Query: 120  TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            TVK R    +Q     L + ++ +  +G   + +H R A          R     D+  V
Sbjct: 950  TVKLRTA--NQGKKQVLHSFIRRLGDAGAAALIVHGRTA--------QQRYTKAADWSYV 999

Query: 180  YEIKKEN-PDLFIGLNGGLE-DMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + ++       +   G +        ++     DG+MI RAA     + T + E     
Sbjct: 1000 AQCREALDSSTPLIGCGDIFSSPEFEFRLASGASDGLMIARAALVKPWVFTEISERKVWD 1059

Query: 237  LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            ++ S  +           +      +   H  S  +    TR  +
Sbjct: 1060 ISASERL----------DLLKRFVRFGLEHWGSDSRGVATTRRFL 1094


>gi|313668540|ref|YP_004048824.1| trna-dihydrouridine synthase c [Neisseria lactamica ST-640]
 gi|313006002|emb|CBN87461.1| trna-dihydrouridine synthase c (ec 1.-.-.-) [Neisseria lactamica
           020-06]
          Length = 333

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 99/247 (40%), Gaps = 24/247 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +    P  +
Sbjct: 20  MQGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRATWLKYVPEIANGNKTPVGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V+    GA L+  P ++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAIRFGADKIDLNFGCPAPTVNRHKGGAILLKEPQLIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   IP+T K R+G +D+  A+       +I + G  G+ +HAR         K    
Sbjct: 140 ERLPAHIPLTAKMRLGYEDKSRAL---ECACAIAEGGACGLTVHART--------KAEAY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I ++  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIKKI-RDAVNIPVTANGDVFTLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSN 235
           + +Y S 
Sbjct: 248 IKQYESG 254


>gi|323699589|ref|ZP_08111501.1| dihydrouridine synthase DuS [Desulfovibrio sp. ND132]
 gi|323459521|gb|EGB15386.1| dihydrouridine synthase DuS [Desulfovibrio desulfuricans ND132]
          Length = 348

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 60/281 (21%), Positives = 113/281 (40%), Gaps = 28/281 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKP-LALQIGGAD 58
              +   +R          L +TEM  A ++         +  +   E P L  Q+ GA 
Sbjct: 37  AGLSHVAFREVLDGYGGCGLTFTEMCGAKSLPTESPLVSPVFRWRAAELPRLVCQVAGAT 96

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +++ AA+ V++ G+   ++N+GC  + + + + GA L+ +PD     +  + +A+SIP
Sbjct: 97  PEQMIPAARRVQECGFFGFDINMGCSVSGIIKKNAGAALLRDPDAALRVVEGVRRAISIP 156

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + VK R G    I       L +  + +GV+ +  H R A        D R  P +  + 
Sbjct: 157 LFVKFRTGWTPDIGPAVA--LARRFEDAGVDCLVFHPRVAP-------DKRTRPPVR-EH 206

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  +  +   + +  NG +      L +L      GV +GR A     +           
Sbjct: 207 IRAVV-DAVSIPVFGNGDVVSPEDCLDMLRTTGCAGVSVGRTAIARPWLFAQW------- 258

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            TG +P  T      +R  + ++ D  +RH      L++  
Sbjct: 259 TTGQTPPAT-----CFRDYALNLADALSRHFDPVRALKRYR 294


>gi|320178912|gb|EFW53875.1| tRNA-dihydrouridine synthase C [Shigella boydii ATCC 9905]
 gi|332093245|gb|EGI98305.1| dihydrouridine synthase family protein [Shigella boydii 5216-82]
          Length = 315

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 61/311 (19%), Positives = 116/311 (37%), Gaps = 41/311 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L   E + V D +L           +     +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNDYDLCIIEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 68  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSG-GATLLKDPELIYQGAKAMR 126

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 127 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
             ++D+  + +I++   ++ +  NG + D   A + +     D VMIGR A  N   L+ 
Sbjct: 177 AEHIDWQAIGDIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSR 234

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
           V +Y                +  W ++ A +  Y          L  + R    +  L  
Sbjct: 235 VVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRK 281

Query: 286 GFPNSRRCRHI 296
            +  +      
Sbjct: 282 EYDEATELFQH 292


>gi|269139890|ref|YP_003296591.1| tRNA-dihydrouridine synthase C [Edwardsiella tarda EIB202]
 gi|267985551|gb|ACY85380.1| tRNA-dihydrouridine synthase C [Edwardsiella tarda EIB202]
 gi|304559726|gb|ADM42390.1| tRNA-dihydrouridine synthase C [Edwardsiella tarda FL6-60]
          Length = 318

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 63/312 (20%), Positives = 113/312 (36%), Gaps = 41/312 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +         +    P+ +
Sbjct: 12  MEGVLDALVRELLSEVNDYDLCITEFVRVVDRLLPERVFYRLCPELHRRSQTLSGTPVRI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++ N GCPS  V+    GA L+ +P ++   + AM 
Sbjct: 72  QLLGQSPHWLAENALRAVTLGSPGVDFNCGCPSKAVNGSGGGATLLKDPALIYAGVQAMR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +P+TVK R+G       V    +  ++++ G   + +H R          D  +
Sbjct: 132 QAIPAHLPLTVKVRLGWACDSQRV---EIADAVQQGGATELVVHGRTKE-------DGYR 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG + D + A   L     D +MIGR A     +   
Sbjct: 182 ADRINWAAIGEIRRRL-RIPVIANGEIWDYASAQACLAQTGCDALMIGRGALNIPNL--- 237

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  IK    K  W ++   +  YA         L  + R    +  L  
Sbjct: 238 -----------SRVIKENAPKMPWPQVVTLLQRYARLEKQGDTGLYHVARIKQWLSYLRK 286

Query: 286 GFPNS-RRCRHI 296
            +P +    R +
Sbjct: 287 EYPQADALFRQV 298


>gi|237834267|ref|XP_002366431.1| hypothetical protein TGME49_028080 [Toxoplasma gondii ME49]
 gi|211964095|gb|EEA99290.1| hypothetical protein TGME49_028080 [Toxoplasma gondii ME49]
          Length = 1220

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 107/285 (37%), Gaps = 30/285 (10%)

Query: 6    DRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLV 63
            +  +R     L    +  +EM VA +I+ G +   ++L     E    +QI G     L 
Sbjct: 831  NLPFRRLCVEL-GAEVTVSEMAVAKSIVDGKQSELSLLKRHKSETFFGVQIAGGTPEVLN 889

Query: 64   EAAKIV--EDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC-KALSIPV 119
                I+  ED   + I+LN  CP  ++H     GAC++ +P  +   + +M  +   +PV
Sbjct: 890  ACTDILASEDVSCDFIDLNAACPLVQLHRRFKAGACMLDHPKRLESLVESMTTRHPEVPV 949

Query: 120  TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            TVK R    +Q     L + ++ +  +G   + +H R A          R     D+  V
Sbjct: 950  TVKLRTA--NQGKKQVLHSFIRRLGDAGAAALIVHGRTA--------QQRYTKAADWSYV 999

Query: 180  YEIKKEN-PDLFIGLNGGLE-DMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + ++       +   G +        ++     DG+MI RAA     + T + E     
Sbjct: 1000 AQCREALDSSTPLIGCGDIFSSPEFEFRLASGASDGLMIARAALVKPWVFTEISERKVWD 1059

Query: 237  LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            ++ S  +           +      +   H  S  +    TR  +
Sbjct: 1060 ISASERL----------DLLKRFVRFGLEHWGSDSRGVATTRRFL 1094


>gi|114047827|ref|YP_738377.1| dihydrouridine synthase, DuS [Shewanella sp. MR-7]
 gi|113889269|gb|ABI43320.1| dihydrouridine synthase, DuS [Shewanella sp. MR-7]
          Length = 315

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 75/333 (22%), Positives = 131/333 (39%), Gaps = 50/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  GF+    P+ +
Sbjct: 8   MEGVVDDLMRDILSSINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNDGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + + E A    + G + ++ N GCP+  V+  + GA L+  P+ + D + AM 
Sbjct: 68  QLLGQEPNCMAENAMRAIELGSHGVDANFGCPAKMVNRSNGGAVLLQYPNTIHDIVRAMR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPAEHPVTAKIRLGYEDKSL---FMENALAVYEAGATELAIHARSKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E+++  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 177 KPPAYWEYITEVRERLP-IPVIANGEIWNREDAERCMAVTGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGKLQQITRHMIGLFH 285
           +        TG++P         W      M  Y  R L    S     +I +    L  
Sbjct: 236 IK-------TGAAPYS-------WADTLGLMLSYTQRELSGRKSDYYPARIKQWFSYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETA 314
            +P +    R  R   T E         ++E A
Sbjct: 282 QYPEADTLFRELRIYKTTEEI-----VRVLEEA 309


>gi|261329882|emb|CBH12865.1| tRNA-dihydrouridine synthase 3, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 528

 Score =  165 bits (418), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 90/233 (38%), Gaps = 20/233 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +  L+  + ++L   + E    LQI  +     +
Sbjct: 178 NLPFRRVCKEY-GADITVGEMAIVHNLNRLQKSEWSLLRRHSSEDIFGLQIAVSRPHDAI 236

Query: 64  EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSIPVT 120
             A+ VE+ G  Y+ +++N GCP  +V     G  L     + + D + ++    S PVT
Sbjct: 237 TWAQAVEESGFSYDFVDINCGCPVDKVVLSGCGCGLWERKGNRLRDVVQSLVAHQSKPVT 296

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCR+G D++ P   L   +   +  G   + IH R         +  R     ++  + 
Sbjct: 297 IKCRMGPDEENP--DLHKHIADYETWGAAAVTIHGRS--------RRQRYTKLANWSYID 346

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVD 230
                   L +  NG +      ++      +V   MIGR A     +   + 
Sbjct: 347 N-CASLTSLPVIGNGDIFSCEDIVEHRAQSKNVSSFMIGRGALIKPWIFEEIK 398


>gi|315635015|ref|ZP_07890296.1| tRNA-dihydrouridine synthase C [Aggregatibacter segnis ATCC 33393]
 gi|315476277|gb|EFU67028.1| tRNA-dihydrouridine synthase C [Aggregatibacter segnis ATCC 33393]
          Length = 312

 Score =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 65/339 (19%), Positives = 129/339 (38%), Gaps = 55/339 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     + +  L  +E +      +   +       +L  G +    P+ +
Sbjct: 8   MQGVLDPLVRQLLTEVNDYDLCISEFVRVVDQRLPPKVFYRLCPELLQQGCTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPQWLAENAELAIQLGSHGVDLNCGCPSKTVNGSNGGASLLKQPELIYQATKAIR 127

Query: 113 KALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A+  P   VTVK R+G D    A    ++  ++++ G   I IH R  +       D  
Sbjct: 128 QAVP-PEQAVTVKVRLGWDSTDFAF---DIADAVQQGGATEIAIHGRTKV-------DGY 176

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           +   +++  + EI+++   + +  NG +       + L     + +M+GR A      L+
Sbjct: 177 RADRINWQKIGEIRQKL-HIPVIANGEIWRWEDGQRCLEMTGCEDLMVGRGALNMP-NLS 234

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            V ++   PL+             W +I   +  YA            + R         
Sbjct: 235 RVLKHNDAPLS-------------WSEILPILRKYATLENCHDSGFYHVAR--------- 272

Query: 288 PNSRRCRHILTVEAGASTATHHIIETA-----FNLMIES 321
              ++    L  E   +TA   +++          ++E+
Sbjct: 273 --IKQWLQYLKYEYEEATALFEVVKRCHDGDELRALLEA 309


>gi|148977641|ref|ZP_01814217.1| putative regulator protein [Vibrionales bacterium SWAT-3]
 gi|145963156|gb|EDK28424.1| putative regulator protein [Vibrionales bacterium SWAT-3]
          Length = 311

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/312 (20%), Positives = 124/312 (39%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     L +  L  TE + V D +L     + L         +    P+ +
Sbjct: 1   MEGVLDHLMREILTELNDYDLCVTEFVRVTDQLLPPHVFHRLCPELHQGSQTMAGVPVHV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     + E A    + G   I+LN GCP+  V++ + GA L+  P+++   + A  
Sbjct: 61  QLLGQHPKWMAENAIQAANLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVVKATR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPV+ K R+G +          +V +I+++  + + +HAR             K
Sbjct: 121 EAVPKHIPVSAKIRLGWEHPDECF---EIVDAIEQAKADELTVHARTKT-------GGYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I+++   L +  NG + +       +    VD +M+ R A+ N   L  
Sbjct: 171 ASEIKWDYINQIRQKT-SLPLIANGEIWNYQDGQDCIKTTGVDSLMVCRGAF-NVPNLGN 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V ++   P+              W +I A +  Y+   +     L    ++ +  + L  
Sbjct: 229 VVKHNHQPMP-------------WIEIIALLLRYSEFEIEGDKGLYYPNRVKQWFVYLRK 275

Query: 286 GFPNSRRCRHIL 297
            +P +      +
Sbjct: 276 EYPEAEELFREI 287


>gi|320583736|gb|EFW97949.1| Dihydrouridine synthase [Pichia angusta DL-1]
          Length = 618

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/302 (21%), Positives = 112/302 (37%), Gaps = 47/302 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +      E P   +QI  A   + 
Sbjct: 262 NLPYRRLMRTL-GADVTYSEMALALPLIQGSNSEWALPRAHESEYPGFGVQIATAKHWQA 320

Query: 63  VEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALSIPV 119
            +AA+ ++    +  E+NLN GCP   ++    G+ L+ NP  +   +  M   +  IPV
Sbjct: 321 CKAAEAIQTLTSHVSELNLNCGCPIDMLYRKGEGSALLDNPSRMLRILKGMSYSSGEIPV 380

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R+GV D  P     NLV+ +  ++ V  I +H R         +  R     D+D 
Sbjct: 381 TVKIRMGVKDDKPVAE--NLVRRVLNETDVAAITLHGRS--------RQQRYTRAADWDY 430

Query: 179 VYEI----------------KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           +  +                K + P ++   NG         + +    +D VM+ R A 
Sbjct: 431 ISRVGAVVKDYNEQQEEDKDKVDRPPVYFVGNGDCFTHEDWHRAVSDEGIDSVMVARGAL 490

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRH 279
               +   V+       + S  +                  +A  H  S    +    R+
Sbjct: 491 IKPWIFEEVEAQQYLDKSASERL----------AYLEKYAKFALEHWGSDEYGVNSARRY 540

Query: 280 MI 281
           + 
Sbjct: 541 LC 542


>gi|72391948|ref|XP_846268.1| tRNA-dihydrouridine synthase 3 [Trypanosoma brucei TREU927]
 gi|62359888|gb|AAX80315.1| tRNA-dihydrouridine synthase 3, putative [Trypanosoma brucei]
 gi|70802804|gb|AAZ12709.1| tRNA-dihydrouridine synthase 3, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 528

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 90/233 (38%), Gaps = 20/233 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +   +  L+  + ++L   + E    LQI  +     +
Sbjct: 178 NLPFRRVCKEY-GADITVGEMAIVHNLNRLQKSEWSLLRRHSSEDIFGLQIAVSRPHDAI 236

Query: 64  EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSIPVT 120
             A+ VE+ G  Y+ +++N GCP  +V     G  L     + + D + ++    S PVT
Sbjct: 237 TWAQAVEESGFSYDFVDINCGCPVDKVVLSGCGCGLWERKGNRLRDVVQSLVAHQSKPVT 296

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCR+G D++ P   L   +   +  G   + IH R         +  R     ++  + 
Sbjct: 297 IKCRMGPDEENP--ELHKHIADYETWGAAAVTIHGRS--------RRQRYTKLANWSYID 346

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVD 230
                   L +  NG +      ++      +V   MIGR A     +   + 
Sbjct: 347 N-CASLTSLPVIGNGDIFSCEDIVEHRAQSKNVSSFMIGRGALVKPWIFEEIK 398


>gi|330875733|gb|EGH09882.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 344

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 116/314 (36%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHNGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I ++   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QDVVKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + + FW+     MT      + + G+L+Q    +  L   
Sbjct: 236 IAAAQKGEEVVPMTWAELQPILRVFWQHCLIKMT-----LIQAPGRLKQW---LALLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +      L  E
Sbjct: 288 YPEATVLFDTLRRE 301


>gi|195345007|ref|XP_002039067.1| GM17321 [Drosophila sechellia]
 gi|194134197|gb|EDW55713.1| GM17321 [Drosophila sechellia]
          Length = 316

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 58/254 (22%), Positives = 113/254 (44%), Gaps = 19/254 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     FST   ++PL  Q    D
Sbjct: 30  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFSTGADDQPLIAQFAAKD 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  ++  P++V   +  + + L   
Sbjct: 89  PTEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGMLRQPELVHQVVQEVRRTLPGD 147

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+   ++     + +L + ++ +GV  + +H R    K    KD   IP +  
Sbjct: 148 FSVSVKMRLLGGEESLQRTI-DLARQLEHAGVTFLTLHGRTPAQKH--SKDTLDIPAM-- 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  +++  + + +NG +E    A  +       GVM  R    N A+  +   Y  
Sbjct: 203 ----SQVRQSLQIPLIVNGNVESYRDACDMHEQTGAAGVMAARGLLANPALFNS--SYPE 256

Query: 235 NPLTGSSPIKTRVD 248
              T  S ++  +D
Sbjct: 257 GKTTPLSCVQQWLD 270


>gi|262274594|ref|ZP_06052405.1| tRNA-dihydrouridine synthase C [Grimontia hollisae CIP 101886]
 gi|262221157|gb|EEY72471.1| tRNA-dihydrouridine synthase C [Grimontia hollisae CIP 101886]
          Length = 317

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/325 (20%), Positives = 123/325 (37%), Gaps = 52/325 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +    L  TE + V DA L       L       G +     + +
Sbjct: 1   MEGVLDPLMRQILTEINPYDLCVTEFVRVVDAKLPPRVYYKLSPELENGGKTRSGTSVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     + E A +V + G + +++N GCPS  V+    GA L+  P+++   + A+ 
Sbjct: 61  QLLGQSPHYMAENAALVAELGSSGVDINFGCPSKTVNGNKGGAALLKEPELMYQVVKAVR 120

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+ K R+G DD     A R +  +++  G N I +H R       S  D  K
Sbjct: 121 EAVPYDQVVSAKVRLGFDD---VSAYREIADAVQSGGANEIVVHGR-------SKADAYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
              + +D++ ++ K    + +  NG +     ALK       + +M+ R A     + T 
Sbjct: 171 AGTIRWDLIGDLTKRL-SIPVVANGDIWCREDALKCAEVSGCETLMVCRGALNMPNLATH 229

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +        T ++P+        W ++   +  Y+   +     L             +P
Sbjct: 230 IK-------TDAAPMS-------WHQVLVLLVRYSEFEIRGDKGLY------------YP 263

Query: 289 N-SRRCRHILTVEAGASTATHHIIE 312
           N  ++    L  +A    A    + 
Sbjct: 264 NRVKQWFRYL--QAQYPEAKALFVR 286


>gi|307110528|gb|EFN58764.1| hypothetical protein CHLNCDRAFT_140504 [Chlorella variabilis]
          Length = 451

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/284 (19%), Positives = 114/284 (40%), Gaps = 27/284 (9%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVE 64
             +R          + Y+EM  A  +L+G++K +  L  +  E+   +QI    I + V 
Sbjct: 81  LPFRRLC-AAHGAKVTYSEMAFARQLLKGNRKELAILRRAGNEQCYGVQIATNVIDEGVR 139

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           A  +V + G + ++LN GCP         GA L+  P  +   +  +   L +P+TVK R
Sbjct: 140 AGVLVAEAGADFLDLNCGCPIYEATRRGLGAALLRKPHKLARLVNGIAARLPLPLTVKIR 199

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +G  +    + +  +V  ++++G   + +H R          + R     D+++V ++  
Sbjct: 200 LG--ESADKINVHEMVGLLEQAGAAAVTVHGRTM--------EQRYKKAADWELVQQVAA 249

Query: 185 ENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           ++  + +  NG +    +  + L    +  VM+GR A     +   V E      T S  
Sbjct: 250 QH-SVPLVGNGDVLTHYEVRRRLDSHGLLTVMVGRGALIKPWLFQEVKEGRELCPTASER 308

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-GLFH 285
           +           I   +  Y   H     + ++   + +   F+
Sbjct: 309 VG----------IYRQLVAYMKEHFRDDARGKRAAFYFLPWHFN 342


>gi|331006519|ref|ZP_08329818.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC1989]
 gi|330419687|gb|EGG94054.1| tRNA-dihydrouridine synthase C [gamma proteobacterium IMCC1989]
          Length = 333

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 118/297 (39%), Gaps = 33/297 (11%)

Query: 1   MVDWTDRHY-RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPL 50
           M    D H+ R     +    +  TE I  +  +    K    F  +           P+
Sbjct: 8   MEGVVD-HFLRELLTNIGGIDVCVTEFIRVNDQVL-PPKVFQRFCPELFTQCKTPSGVPV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G     +   A      G N I+LN GCP+  V++   GACL+  P  + D I A
Sbjct: 66  RIQLLGGKPEPIALNAVKAVSIGANAIDLNFGCPAKTVNKSDGGACLLRTPHRLYDIIKA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +A+   IPVT K R+G +D+   +       +  ++G   I +HAR         K +
Sbjct: 126 TRQAVPAHIPVTAKMRLGFEDRSNYLEN---ALAAYEAGATEITVHARS--------KAD 174

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
              P   +D + +IK+   D+ +  NG +  +   ++   +   D  M+GR       + 
Sbjct: 175 GYRPPAYWDSLADIKQAI-DIPVIANGEIWTVDDFIRCKEVSQCDDFMLGRGLLSCPDLA 233

Query: 227 TTVDEYFSNPLTGSSPIK-TRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHM 280
             +    +   T   P++ + +     R   A+   Y+ RH+ +  K  L  + RH 
Sbjct: 234 LQIKAREAG--TDYQPMEWSAICHMLQRFFDATTEQYSPRHVGNRLKQWLNYLRRHY 288


>gi|219121577|ref|XP_002181140.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217407126|gb|EEC47063.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 545

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 53/264 (20%), Positives = 101/264 (38%), Gaps = 20/264 (7%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM VA  +L G      +L    +E    +QI         
Sbjct: 199 NLPFRRIMKKF-GADITCGEMAVATNLLSGQSSEWALLKRHPEEDIFGVQIAAGYPDVFA 257

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++E +   + ++LN+GCP   V     GA LM+    +   +  + + L+ P+++K
Sbjct: 258 RTCELIENEMNVDFVDLNLGCPLDIVCNKGSGAALMMRDKRLRSSVEGILETLTCPISIK 317

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G +   P     NLV+ I+  G++GI      A++     +  R     D+D +  +
Sbjct: 318 MRTGWEMTKP--FAHNLVQKIQSWGLDGI-----SAVMIHGRSRLQRYAKEADWDYISMV 370

Query: 183 KK----ENPDLFIGLNGGLEDMSQALK--ILPSVDGV-MIGRAAYKNSAMLTTVDEYFSN 235
            K        + +  NG +       +      V+   M+ R A     + T + E    
Sbjct: 371 AKSQDMSLTTIPVIGNGDIFSYQDFEEKIAREGVNSCAMLARGALIKPWLPTEIKERRHW 430

Query: 236 PLTGSSPIKTRVDKDFWRKISASM 259
            ++ S   +  + KDF R      
Sbjct: 431 DISASE--RLDILKDFARFGMEHW 452


>gi|260913194|ref|ZP_05919676.1| tRNA-dihydrouridine synthase C [Pasteurella dagmatis ATCC 43325]
 gi|260632781|gb|EEX50950.1| tRNA-dihydrouridine synthase C [Pasteurella dagmatis ATCC 43325]
          Length = 312

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/325 (19%), Positives = 118/325 (36%), Gaps = 40/325 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   +       +       G +    P+ +
Sbjct: 8   MQGVLDPFVRELLTAVNSYDLCISEFVRVVDQLLPTKVFYRLCPELQHQGLTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A+   + G   ++LN GCPS  V+  + GA L+  P+++     ++ 
Sbjct: 68  QLLGQYPEWLAENAQRAIELGSYGVDLNCGCPSKTVNGSNGGASLLKQPELIYRATTSLR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PV+VK R+G DD   A     +  ++++ G   I IH R          D  +
Sbjct: 128 AAVPAHLPVSVKVRLGWDDVNQAF---EIADAVQQGGATEITIHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E+++    + +  NG + D       L     + +MIGR A  N   L+ 
Sbjct: 178 ADRINWRKINEVRQRL-SIPVIANGEVWDWQSGQDCLVQTGCEDLMIGRGAL-NVPNLSN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR--HMIGLFH- 285
           V ++                K  W  + A +  Y             + R    +G    
Sbjct: 236 VVKFNH-------------PKMPWVDVLAILHRYTHTENQFDTGFYHVARIKQWLGYLKQ 282

Query: 286 GFPNSRRCRHILTVEAGASTATHHI 310
            +  +     ++     A    H I
Sbjct: 283 EYSEASDLFQLIKTCHDAHELRHKI 307


>gi|312882490|ref|ZP_07742231.1| tRNA-dihydrouridine synthase C [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309369890|gb|EFP97401.1| tRNA-dihydrouridine synthase C [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 317

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/324 (19%), Positives = 119/324 (36%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L       L         +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDQLLPDHVFYRLCPELKQGSKTRSGVPVHI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D + + E A      G   I++N GCP+  V++   GA L+ +PD++   + A  
Sbjct: 68  QLLGQDPNWMAENAVKAATLGAKGIDINFGCPAKLVNKSKGGAALLRHPDVIYQVVKACR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  S PV+ K R+G +D         +V +I+ +G N + +HAR             K
Sbjct: 128 EAVPSSTPVSAKIRLGWEDPEDCF---EIVDAIQSAGANELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++    + +  NG + +         L   D +M+ R A+    +   
Sbjct: 178 ASEIKWDYIRQIRQRF-SIPVIANGEIWNHQDGQDCMSLTGADSLMVCRGAFNVPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V                      W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKHAHQ--------------VMPWDEVVELLLLYSQYEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNS-RRCRHILTVEAGASTATH 308
            +P +    R I T         H
Sbjct: 283 QYPQADALFREIRTFNKAQPIVEH 306


>gi|323498303|ref|ZP_08103305.1| tRNA-dihydrouridine synthase C [Vibrio sinaloensis DSM 21326]
 gi|323316731|gb|EGA69740.1| tRNA-dihydrouridine synthase C [Vibrio sinaloensis DSM 21326]
          Length = 317

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/324 (19%), Positives = 122/324 (37%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE +      + D +       +L    +    P+ +
Sbjct: 8   MEGVLDHLMREILTDINDYDLCVTEFVRVVDQLLPDHVFHRLCPELLQGSQTKSGVPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    D G   I+LN GCP+  V++   GA L+ +P+++   + +  
Sbjct: 68  QLLGQDPKWMAENAIRAADLGAKGIDLNFGCPAKLVNKSKGGAALLQHPELIHQVVKSCR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +IPVT K R+G ++         +V +I+ +G N + +HAR             K
Sbjct: 128 DAVPSNIPVTAKIRLGWENPDDCF---EIVDAIELAGANELTVHARTKT-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + ++ + +I++    + +  NG + +       +    VD +M+ R A+    +   
Sbjct: 178 ASEIKWEYIGQIRERF-SIPLIANGEIWNHQDGQACIETTGVDSLMVCRGAFNVPNLGNV 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V    S                 W ++   +  Y+   +     L    ++ +    L  
Sbjct: 237 VKHDHS--------------VMPWHEVVELLLVYSQYEMKGDKGLYYPNRVKQWFSYLRQ 282

Query: 286 GFPNSRR-CRHILTVEAGASTATH 308
            +P +    R I T    A    H
Sbjct: 283 QYPEAAALFREIRTFNKAAPIVEH 306


>gi|182415683|ref|YP_001820749.1| dihydrouridine synthase DuS [Opitutus terrae PB90-1]
 gi|177842897|gb|ACB77149.1| dihydrouridine synthase DuS [Opitutus terrae PB90-1]
          Length = 384

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 103/250 (41%), Gaps = 17/250 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D TD  +             +TE   + + + L       L  +T  +P+  Q+ G D
Sbjct: 24  MQDVTDLTFMRVIAHYGAPDYFFTEFFRVHSQSRLEKHIVRCLDDNTTGRPIFAQVIGED 83

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           + +LV  A+ ++      I+LN+GCP+ +V++ + G  L+ +   V   + A+  A    
Sbjct: 84  LEQLVRTARELQQHPIAGIDLNLGCPAPKVYKKNVGGGLLRDLAHVDRILGALRAATPGG 143

Query: 119 -VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             TVK RIG DD  P   + +LV +     V+ + +H R       S         + YD
Sbjct: 144 LFTVKMRIGFDDTTPFEPMLDLVNA---HRVDLLSVHGRTVKEMYRS--------RVHYD 192

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +    +      +  NG +    +A+ IL      GVMIGR A +N  +     E F  
Sbjct: 193 FIARAVQRV-RCPVLANGNVTSAPRAVAILRETGAAGVMIGRHAIRNPWIFRQCRELFHP 251

Query: 236 PLTGSSPIKT 245
           P    S  + 
Sbjct: 252 PPALQSTTEP 261


>gi|149909476|ref|ZP_01898130.1| hypothetical protein PE36_16760 [Moritella sp. PE36]
 gi|149807381|gb|EDM67332.1| hypothetical protein PE36_16760 [Moritella sp. PE36]
          Length = 312

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R          L  TE I      + + I       +     +    P+ +
Sbjct: 8   MEGVVDNLMRELLTAQGGYDLCVTEFIRVVEQLLPEKIFYRYCAELNHGSRTQAGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     + E A    D G + +++N GCP+ +V++ S GA  +  P++V   +  + 
Sbjct: 68  QLLGQHPQWMAENAVRAIDLGSHGLDINFGCPAKQVNKSSGGAACLREPELVYQIVKQVR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     V+ K R+G +D    +    +  +++++G N + +H R          D  +
Sbjct: 128 DAVPAEHTVSAKIRLGWEDSNQKL---EIADAVQQAGANELTVHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI++    + +  NG +   + A + L     + +M+GR A  N   L  
Sbjct: 178 AAAINWQAIAEIRQHV-SIPVIANGEIWSHADAQRCLEVTGCNDLMVGRGAL-NLPNLGE 235

Query: 229 VDEYFSNPLTGSS 241
           V +Y   P+  + 
Sbjct: 236 VVKYNKAPMPWAD 248


>gi|251793338|ref|YP_003008066.1| tRNA-dihydrouridine synthase C [Aggregatibacter aphrophilus NJ8700]
 gi|247534733|gb|ACS97979.1| tRNA-dihydrouridine synthase C [Aggregatibacter aphrophilus NJ8700]
          Length = 312

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 65/338 (19%), Positives = 128/338 (37%), Gaps = 53/338 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     + +  L  +E +        A    R   + +  GF+    P+ +
Sbjct: 8   MQGVLDPLVRQLLTEVNDYDLCISEFVRVVDQRLPAKVFYRLCPELHQQGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPQWLAENAELAIQLGSHGVDLNCGCPSKTVNGSNGGASLLKQPELIYQATKAIR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D         ++  ++++ G   I IH R          D  +
Sbjct: 128 QAVPQEQAVSVKVRLGWD---STEFAYDIADAVQQGGATEIAIHGRTKT-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + EI+++  ++ +  NG +       + L     D +M+GR A      L+ 
Sbjct: 178 ADRINWQKIGEIRQKL-NIPVIANGEIWRWEDGQRCLTMTGCDDLMVGRGALNMP-NLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++   PL+             W +I   +  YA            + R          
Sbjct: 236 VLKHNDVPLS-------------WAEIMPILRKYATLENCHDSGFYHVAR---------- 272

Query: 289 NSRRCRHILTVEAGASTATHHIIE-----TAFNLMIES 321
             ++    L  E   +T    +++      A   ++E+
Sbjct: 273 -IKQWLQYLKCEYEEATGLFEVVKRCHDGEALRGLLEA 309


>gi|197284518|ref|YP_002150390.1| tRNA-dihydrouridine synthase C [Proteus mirabilis HI4320]
 gi|194682005|emb|CAR41473.1| tRNA-dihydrouridine synthase C [Proteus mirabilis HI4320]
          Length = 310

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 110/288 (38%), Gaps = 28/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     + +  L  TE I V D++L    K       +            +
Sbjct: 8   MEGVLDPLVRDLLTAINHYDLCITEFIRVVDSLL--PPKAFYRLCPELHTQSRTQSGTLV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G +   L E A      G   ++LN GCPS  V+    GA L+  P+ +     A
Sbjct: 66  RVQLLGQNPQWLAENAFRAVSLGSWGVDLNCGCPSKTVNGNGGGASLLKQPETIYQATKA 125

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M  A+   +PV+VK R+G D          +  ++++ G   I IH R          D 
Sbjct: 126 MRGAVPADLPVSVKVRLGWDCSSYC---HEIADAVEQGGATEITIHGRTKE-------DG 175

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            +   +++  + EI+++   + +  NG +     A+  L     D +MIGR A      L
Sbjct: 176 YRADKINWQAIGEIRQKLT-IPVIANGEIWCREDAISCLKITGCDAIMIGRGAMHTP-NL 233

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           + V +     +  S  I+         K   +   +A+R     G L+
Sbjct: 234 SNVIKGIEEKMPWSQVIQLLKRYIRLEKQGDTTYYHASRIKQWLGYLR 281


>gi|301155565|emb|CBW15033.1| tRNA-dihydrouridine synthase C [Haemophilus parainfluenzae T3T1]
          Length = 303

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/325 (19%), Positives = 116/325 (35%), Gaps = 48/325 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +    L  TE +  V   +       +       GF+  + P+ +
Sbjct: 1   MQGVLDPFVRQLLTEVNEYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTPSKTPVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G   + L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 61  QLLGQHPNCLAENANRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYQATLALR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   +PV+VK R+G D    A     +  ++++ G   I IH R          D  +
Sbjct: 121 QTVPSHLPVSVKVRLGWDCTSQAF---EIADAVQQGGATEITIHGRTK-------ADGYR 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              ++++ + E++     + +  NG +         L     + +M+GR A     +   
Sbjct: 171 ADRINWEKIGEVRSRLT-IPVIANGEIWRWEDGQACLKATGCEDLMVGRGALNIPNL--- 226

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                      S  +K   +K  W  I   +  YA            + R          
Sbjct: 227 -----------SLVLKQNCEKMPWVDIQKILQKYAEMENFHDSGFYHVAR---------- 265

Query: 289 NSRRCRHILTVEAGASTATHHIIET 313
             ++    L  E   +      I+T
Sbjct: 266 -IKQWLRYLNKEYPEADIVFERIKT 289


>gi|322707292|gb|EFY98871.1| dihydrouridine synthase family protein, putative [Metarhizium
           anisopliae ARSEF 23]
          Length = 534

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 72/321 (22%), Positives = 123/321 (38%), Gaps = 63/321 (19%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIVADAILRGDKKNILGF------------ 43
           MVD ++  +R   R    +      L YT M  A    +  K     F            
Sbjct: 32  MVDQSEFAWRMLTRSFLTDEEKKKMLAYTPMFHARLFSQESKYRKAHFQSTKPDSQEPWL 91

Query: 44  ---STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
               + ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  +
Sbjct: 92  DGNPSIDRPLFVQFCANDPEALLSAAKQVSPY-CDAVDLNLGCPQGIARKGHYGAFLQED 150

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + K LSIPVT K RI  D +          +++ K+G + + +H R+   
Sbjct: 151 QDLIFRLINTLHKELSIPVTAKIRILEDKEKT----LAYAQNVLKAGASILTVHGRRREQ 206

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLE---DMSQALKILPSVDGVMIG 216
           KG            D+  +  ++    P+  I  NG +    D+ + L      DGVM  
Sbjct: 207 KG------HLTGVADWKTLRFLRDSLPPETVIFANGNILQGGDIDECLAA-TGADGVMSA 259

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                + A+               +P      +++WR           +    G ++  I
Sbjct: 260 EGNLSDPALFA------------KAPPVGEEGREYWR----------GKDGRGGWRVDAI 297

Query: 277 TRHMIGLFHGF-----PNSRR 292
           TR  + + H +     P +RR
Sbjct: 298 TRRYLDILHRYALGVEPPARR 318


>gi|67594542|ref|XP_665807.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54656648|gb|EAL35578.1| uncharacterized protein family UPF0034 [Cryptosporidium hominis]
          Length = 531

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 111/262 (42%), Gaps = 53/262 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---------ILGFSTQEKPLA 51
           M+D T+ H+R   R+++    L+TEM+V D I+                   +  E PL 
Sbjct: 33  MLDVTNSHFRMLCRIISKKTELWTEMVVDDTIIHCYNDENRRKILQDVHFKKNDIENPLV 92

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAA 110
           LQ+GG +  K+ +A +I   +G+   NLNVGCPS +V     FGA L  NP  V   +  
Sbjct: 93  LQLGGNNPQKMEKAIEIAYKYGFQNFNLNVGCPSCKVASKGSFGASLFKNPLRVAKIVDQ 152

Query: 111 MCKA------LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS------------------ 146
             K       ++  ++VK RIGVD       L N +  +                     
Sbjct: 153 CNKKLIDLGLVNKRISVKTRIGVDQYDTYQHLYNFISLVSGCNINNQNKKDYSCIFPQSD 212

Query: 147 -------------------GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                              G N   IHARKA L G++P  NR IP L Y  VY +  + P
Sbjct: 213 DHSDQNILESIDYTENKFIGANVFIIHARKAWLNGINPSKNRTIPKLKYYWVYMLTLDFP 272

Query: 188 DLFIGLNGGLEDMSQALKILPS 209
           +L   LNGG+  + + + IL  
Sbjct: 273 NLTFILNGGVTSIQECISILTG 294



 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 37/122 (30%), Gaps = 34/122 (27%)

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSN-------------------------PLTGSSPIKTR 246
           GVMIGR    N  +L+ VD                                + ++     
Sbjct: 369 GVMIGREVMNNPFILSKVDSMIYGISYNQVSNNNNNNNNNNNSNSNGSNTNSNNTNGNNS 428

Query: 247 VDKDFWRKISASMTDYAARHLHSG---------GKLQQITRHMIGLFHGFPNSRRCRHIL 297
                 R +     +Y ++              G+L    + + G+FHGF  ++  R  L
Sbjct: 429 SIHLTRRIVLERYVEYLSKFKPRNIKDQGQFTIGELNMYLKPVFGIFHGFSGTKFWRRTL 488

Query: 298 TV 299
           + 
Sbjct: 489 SE 490


>gi|71278711|ref|YP_267655.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
 gi|71144451|gb|AAZ24924.1| NifR3/Smm1 family protein [Colwellia psychrerythraea 34H]
          Length = 310

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/302 (20%), Positives = 120/302 (39%), Gaps = 48/302 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM------IVADAILRGDKKNILG------FSTQEK 48
           M    D   R     + +  L  TE       ++ D +       ++        +    
Sbjct: 8   MEGVLDYRMRDLLTQVGSYDLCVTEFIRVVDQVLPDRVFHRYCPELIDADVYGSCTKAGT 67

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G     + E A  V + G + I+LN GCPS  V++   G+ L+ +P+ +   I
Sbjct: 68  PVRVQLLGQYPEYMAENAAKVIELGSSGIDLNFGCPSKTVNKSRGGSILLKDPENLYQII 127

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +A+     V+ K R+G +D+  A+      ++++ +G N + IHAR         K
Sbjct: 128 KAVKEAVPSDTIVSAKIRLGYEDKTLAIENG---QAVEAAGANELTIHART--------K 176

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                P   +  + ++K    ++ +  NG + ++  A+K         +M+GR A     
Sbjct: 177 LEGYKPPAHWHWIAKVKNAI-NIPVIANGEIWNLEDAIKCREISGCTDLMVGRGALTIP- 234

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG------KLQQITR 278
            L  V             IK   D   W ++ A ++ Y     H         +++Q  +
Sbjct: 235 NLGQV-------------IKQESDNMPWLEVRAILSAYTEFETHGDKSKYYCNRIKQWLK 281

Query: 279 HM 280
           ++
Sbjct: 282 YL 283


>gi|224007851|ref|XP_002292885.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971747|gb|EED90081.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 233

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 85/228 (37%), Positives = 119/228 (52%), Gaps = 34/228 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-------PLALQ 53
           M+++TDRH+R   RL+++  LLYTEM+ A+AI       +LG    +           LQ
Sbjct: 6   MMEYTDRHFRHLVRLISDRTLLYTEMVAANAIAHERNDALLGIEISDTLNTHSLGASVLQ 65

Query: 54  IGGADISKLVEAAK-IVEDFGYNEI-------NLNVGCPSARVHEGS-FGACLMLNPDIV 104
           +GG+D  +L  AAK +++   Y  I       NLN GCPS +V     FGA LM  PD+V
Sbjct: 66  LGGSDPEQLFLAAKTLMQQSNYPAIYCDYTALNLNCGCPSPKVAGKGCFGAALMSEPDLV 125

Query: 105 GDCIAAMCKALS--IPVTVKCRIGVDD--------------QIPAVALRNLVKSIKKSG- 147
                +M K     IP+TVKCRIG D+              +    +L+N ++++   G 
Sbjct: 126 RQLTTSMHKGSEGTIPITVKCRIGTDEGYTFTHKDYLSRSQEEEYSSLKNFIETVASDGI 185

Query: 148 VNGIWIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           V    IHAR A+L K  SP DNRK+P L Y  V  + +E P+L I LN
Sbjct: 186 VTDFQIHARIAVLGKSYSPADNRKVPPLRYHHVQRLAQEFPELNISLN 233


>gi|126174794|ref|YP_001050943.1| dihydrouridine synthase DuS [Shewanella baltica OS155]
 gi|217972939|ref|YP_002357690.1| dihydrouridine synthase DuS [Shewanella baltica OS223]
 gi|125997999|gb|ABN62074.1| dihydrouridine synthase, DuS [Shewanella baltica OS155]
 gi|217498074|gb|ACK46267.1| dihydrouridine synthase DuS [Shewanella baltica OS223]
          Length = 317

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 75/333 (22%), Positives = 130/333 (39%), Gaps = 50/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  G +    P+ +
Sbjct: 8   MEGVVDALMRDILSTINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNNGNTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P+ V D + AM 
Sbjct: 68  QLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYPESVHDIVKAMR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     VT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPKEHAVTAKIRLGYEDKSL---FMENAIAVYEAGATELAIHARSKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E++K  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 178 -PPAYWEYITEVRKRLP-IPVIANGEIWNSDDAKRCIEVTGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGLFH 285
           +        TG++P         W +    M  Y  R L+   S     +I +    L  
Sbjct: 236 IK-------TGATPY-------TWAQTLGLMLSYTQRELNGRKSDYYPARIKQWFTYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETA 314
            +P +    R  R   T E   +     ++E A
Sbjct: 282 QYPEADTLFRELRVFKTTEEIVA-----VLEAA 309


>gi|218460042|ref|ZP_03500133.1| tRNA-dihydrouridine synthase protein [Rhizobium etli Kim 5]
          Length = 174

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 49/165 (29%), Positives = 83/165 (50%), Gaps = 13/165 (7%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + EAAKI  D G + I++N+GCP+ +V  G  G+ LM +PD     I A  KA+ IPVT+
Sbjct: 1   MAEAAKIAADHGADIIDINMGCPAKKVIGGYSGSALMRDPDHALGLIEATVKAVDIPVTL 60

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G D+   ++   ++ +  + +G+  + IH R  +               D+D ++ 
Sbjct: 61  KMRLGWDE--NSINAPDIARRAEAAGIQLVTIHGRTRM--------QFYEGRADWDAIHA 110

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           + ++   + +  NG +E  + A +IL     D VMIGR       
Sbjct: 111 V-RDVISIPLIANGDVETAADAQEILRRSGADAVMIGRGCQGRPW 154


>gi|28869372|ref|NP_791991.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|213968214|ref|ZP_03396359.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato T1]
 gi|301383780|ref|ZP_07232198.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tomato
           Max13]
 gi|302060777|ref|ZP_07252318.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tomato
           K40]
 gi|302131876|ref|ZP_07257866.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|38604775|sp|Q884C6|DUSC_PSESM RecName: Full=tRNA-dihydrouridine synthase C
 gi|28852613|gb|AAO55686.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|213927194|gb|EEB60744.1| dihydrouridine synthase family protein [Pseudomonas syringae pv.
           tomato T1]
 gi|331018629|gb|EGH98685.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 317

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHNGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHTIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKDIPVTAKMRLGYENTDGAL---DCARALADGGAAQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWAELQPMLRTFWQACLVKMT-----LVQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNTLRRE 301


>gi|153001139|ref|YP_001366820.1| dihydrouridine synthase DuS [Shewanella baltica OS185]
 gi|151365757|gb|ABS08757.1| dihydrouridine synthase DuS [Shewanella baltica OS185]
          Length = 317

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 75/333 (22%), Positives = 130/333 (39%), Gaps = 50/333 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGD-----KKNIL--GFSTQEKPLAL 52
           M    D   R     +    LL TE + V D +L           +L  G +    P+ +
Sbjct: 8   MEGVVDALMRDILSTINPYDLLVTEFVRVVDQLLPEKVFLKLCPELLNKGNTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G + ++ N GCP+  V+    GA L+  P+ V D + AM 
Sbjct: 68  QLLGQEPQCMGENALRAIELGSHGVDANFGCPAKIVNRSKGGAVLLQYPESVHDIVKAMR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     VT K R+G +D+           ++ ++G   + IHAR  +           
Sbjct: 128 QAVPKEHAVTAKIRLGYEDKSL---FMENAIAVYEAGATELAIHARSKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + E++K  P + +  NG + +   A + +     D +MIGR A     +  T
Sbjct: 178 -PPAYWEYITEVRKRLP-IPVIANGEIWNSDDAKRCIEVTGCDSIMIGRGAISLPNLADT 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH---SGGKLQQITRHMIGLFH 285
           +        TG++P         W +    M  Y  R L+   S     +I +    L  
Sbjct: 236 IK-------TGATPY-------TWAQTLGLMLSYTQRELNGRKSDYYPARIKQWFTYLNR 281

Query: 286 GFPNS----RRCRHILTVEAGASTATHHIIETA 314
            +P +    R  R   T E   +     ++E A
Sbjct: 282 QYPEADTLFRELRVFKTTEEIVA-----VLEAA 309


>gi|253316294|ref|ZP_04839507.1| hypothetical protein SauraC_09171 [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
          Length = 234

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 100/228 (43%), Gaps = 22/228 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEHPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           +++  IK    +  P+  + +NG + D    L++     +DGVMIGR 
Sbjct: 187 ELIEAIKNLRDEIAPNTLLTINGDIPDRKTGLELAEKYGIDGVMIGRG 234


>gi|242011621|ref|XP_002426546.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212510683|gb|EEB13808.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 332

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 108/237 (45%), Gaps = 22/237 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L +T MI+AD+ ++ +K  I  F+T   + P+ +Q    +
Sbjct: 19  MVRYSKLEFRSLVRQYD-CDLCFTPMIMADSFIKSEKARINEFTTSSNDSPVIVQFAANN 77

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI- 117
                EAAK+V  F  + ++LN GCP     +   GA L+  P+ + D +  +   +S  
Sbjct: 78  TFDFSEAAKLVFPFS-DGVDLNCGCPQRWAMKIGIGAQLLSEPETIKDIVLNVKNQISCN 136

Query: 118 -PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+  D +       +L K ++K+GV  + IH R    +            ++ 
Sbjct: 137 YSVSVKLRLLNDIKSTV----DLCKKLEKTGVTFLTIHGRTKEQRS---------EPVNI 183

Query: 177 DIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
             + +I  ++  + I  NG ++    +Q L+ L    GVM  R   +N ++    +E
Sbjct: 184 AAIKDIV-DSVQIPIIANGDVKTLQDAQLLQQLTGCQGVMSARGLLQNPSLFQGYNE 239


>gi|309355062|emb|CAP39416.2| hypothetical protein CBG_23028 [Caenorhabditis briggsae AF16]
          Length = 283

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 115/304 (37%), Gaps = 46/304 (15%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVE 64
             +R   RL   + + YT MI A   +     + + L     + PL +Q    D   L E
Sbjct: 5   LAFRQLVRLYDVD-VCYTPMIYAKNFIESEKCRNSELSVCEGDSPLIVQFATDDPFVLAE 63

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTV 121
           AA++V     + ++LN GCP   V    FG+ L+  P+++ D +      +S     V++
Sbjct: 64  AAEMVY-SCSSGVDLNCGCPKHDVRSKGFGSALLSKPELLADMVRQTRARISDENFSVSL 122

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+  + +       +L +  + +GV  + +H R                 +D + +  
Sbjct: 123 KIRVNKEIEKTV----DLCRKAESAGVTHLTVHGRTPSQH---------AEPIDIEAIRL 169

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +K     + I  NGG+ ++ +A+ +     VDG+M       N A+             G
Sbjct: 170 VKSAV-KVPIIANGGITNLQEAMNLAEKTGVDGIMAANGLLDNPALFA-----------G 217

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                +   + F R       D+   H H    LQ + R ++        S + R I   
Sbjct: 218 YEYTPSDCVESFMRLSREHGLDWLLYHQH----LQYMLRPLL--------SAQQRRIFNE 265

Query: 300 EAGA 303
             G 
Sbjct: 266 LNGR 269


>gi|34497784|ref|NP_901999.1| hypothetical protein CV_2329 [Chromobacterium violaceum ATCC 12472]
 gi|34103640|gb|AAQ60001.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 315

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/298 (19%), Positives = 118/298 (39%), Gaps = 35/298 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +    L  TE +   ++L    +  +  + +           P+ 
Sbjct: 8   MEGLVDDVMRDVLTRVGGIDLCVTEFVRVTSVLL-PTRTFMRLAPELDHQGKTRAGVPVR 66

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D+S L E        G   ++LN GCP+  V+    GA L+  P+++   +AA+
Sbjct: 67  VQLLGSDVSCLAENGAKAASLGAPGVDLNFGCPAPTVNRHRGGAVLLNEPELLNQIVAAV 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PVT K R+G +D+  A+      ++I  +G + + +H R  +          
Sbjct: 127 RRAVPPEVPVTAKMRLGFEDKSRAL---ECAQAIASAGADELTVHGRTKVEG-------- 175

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLT 227
             P   +D +  I +E+  + +  NG +  ++  +A++     D VMIGR       +  
Sbjct: 176 YKPPAHWDWIARI-RESVTIPVTANGEVWTLADYRAIREESGCDTVMIGRGLVACPDLAL 234

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
            + E        + P+       +           +    +   +L+Q     +GL  
Sbjct: 235 RIAE-----GGPAEPMSWGEMMPWVLDFFRLCRQKSGEERYPAARLKQW----LGLLK 283


>gi|330941969|gb|EGH44666.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 321

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHQGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E      + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENGAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW    A MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRVFWHDCLAKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNTLRRE 301


>gi|226295110|gb|EEH50530.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 556

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/268 (22%), Positives = 98/268 (36%), Gaps = 52/268 (19%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFS----------- 44
           MVD ++  +R   R        N  L Y+ M  +          +  F            
Sbjct: 28  MVDRSEFAWRMLTRSFIDPQSPNPLLAYSPMFHSRLFNESANYRLQHFEATRPKPNSKIS 87

Query: 45  ----------------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
                                 T ++PL +Q    D  +L+ AA+ VE F  + ++LN+G
Sbjct: 88  TADGKEPQLPDSPVIPYLDGNPTIDRPLIVQFCANDPDELLHAARTVEPF-CDAVDLNLG 146

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     +G +G+ L   P+++   I  +   LSIPVT K RI    Q          + 
Sbjct: 147 CPQGIARKGHYGSFLQEEPELIYKLINILHTHLSIPVTAKFRI----QETKEKTLEYARM 202

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMS 201
           I  +G + I +H R+   KG            D+  +  ++   P D  I  NG + D  
Sbjct: 203 ILSAGASFISVHGRRRDQKG------HNTGLADWSYIRYLRDNLPADTVIFANGNILDHG 256

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLT 227
             ++ L     DGVM       +  + T
Sbjct: 257 DIIRCLEATGADGVMSAEGNLCDPTIFT 284


>gi|46125679|ref|XP_387393.1| hypothetical protein FG07217.1 [Gibberella zeae PH-1]
          Length = 510

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/277 (22%), Positives = 108/277 (38%), Gaps = 48/277 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGF------------ 43
           MVD ++  +R   R   +       L YT M+ A    + DK     F            
Sbjct: 35  MVDQSEFAWRMLTRSFISPTEQKSLLAYTPMLHARLFSQDDKYRKAHFQAVKTDGETPWL 94

Query: 44  ---STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
               + ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  +
Sbjct: 95  DGNPSIDRPLFVQFCANDPDALLSAAKQVAPY-CDAVDLNLGCPQGIARKGKYGAFLQED 153

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + K L +PVT K RI               +++ K+G + + +H RK   
Sbjct: 154 QDLIFRLINILHKELPVPVTAKIRIL----DTKEETLAYAQNVLKAGASILTVHGRKREQ 209

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE---DMSQALKILPSVDGVMIG 216
           KG            ++ ++  ++   P    I  NG +    D+ + L+     DGVM  
Sbjct: 210 KG------HLTGLAEWQMIRFLRDSLPKETVIFANGNILQEGDIEKCLEA-TGADGVMSA 262

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                + A+ T              P      +++WR
Sbjct: 263 EGNLSDPAIFT------------KPPPVGEEGREYWR 287


>gi|320155949|ref|YP_004188328.1| tRNA-dihydrouridine synthase C [Vibrio vulnificus MO6-24/O]
 gi|319931261|gb|ADV86125.1| tRNA-dihydrouridine synthase C [Vibrio vulnificus MO6-24/O]
          Length = 311

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 53/307 (17%), Positives = 114/307 (37%), Gaps = 34/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     + +     TE +  V+  +       +         +    P+ +
Sbjct: 1   MEGVLDHLMREMLTEINDYDFCVTEFVRVVSQPLPDHVFYRLCPELKQGSKTKNGVPVKV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A      G + I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 61  QLLGQDPRWMAENAIRAAQLGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G ++         +V ++++   + + +HAR             K
Sbjct: 121 DAVPSHIPVSAKIRLGWENPEDCF---EIVDAVEQGKADELTVHARTK-------AGGYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++ +  + +  NG + + +     +    +D +M+ R A  N   L  
Sbjct: 171 ASEIKWDYIDQIRQRST-IPLIANGEIWNYADGQACIETTGIDSLMVCRGAL-NVPNLGN 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + ++    +     +           +    T Y  R         +I +    L   +P
Sbjct: 229 IVKHNHRAMPWHEVV----------DLLLKYTQYEVRGDKGKYYPNRIKQWFAYLRQAYP 278

Query: 289 NSRRCRH 295
            +     
Sbjct: 279 QAADLFR 285


>gi|326423970|ref|NP_761082.2| tRNA-dihydrouridine synthase C [Vibrio vulnificus CMCP6]
 gi|38604855|sp|Q8DAH1|DUSC_VIBVU RecName: Full=tRNA-dihydrouridine synthase C
 gi|319999348|gb|AAO10609.2| tRNA-dihydrouridine synthase C [Vibrio vulnificus CMCP6]
          Length = 318

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 53/307 (17%), Positives = 114/307 (37%), Gaps = 34/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     + +     TE +  V+  +       +         +    P+ +
Sbjct: 8   MEGVLDHLMREMLTEINDYDFCVTEFVRVVSQPLPDHVFYRLCPELKQGSKTKNGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A      G + I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAQLGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G ++         +V ++++   + + +HAR             K
Sbjct: 128 DAVPSHIPVSAKIRLGWENPEDCF---EIVDAVEQGKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++ +  + +  NG + + +     +    +D +M+ R A  N   L  
Sbjct: 178 ASEIKWDYIDQIRQRST-IPLIANGEIWNYADGQACIETTGIDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + ++    +     +           +    T Y  R         +I +    L   +P
Sbjct: 236 IVKHNHRAMPWHEVV----------DLLLKYTQYEVRGDKGKYYPNRIKQWFAYLRQAYP 285

Query: 289 NSRRCRH 295
            +     
Sbjct: 286 QAADLFR 292


>gi|113461433|ref|YP_719502.1| tRNA-dihydrouridine synthase C [Haemophilus somnus 129PT]
 gi|170718461|ref|YP_001783677.1| dihydrouridine synthase [Haemophilus somnus 2336]
 gi|112823476|gb|ABI25565.1| tRNA-U20a,U20b-dihydrouridine synthase [Haemophilus somnus 129PT]
 gi|168826590|gb|ACA31961.1| dihydrouridine synthase DuS [Haemophilus somnus 2336]
          Length = 309

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 65/325 (20%), Positives = 115/325 (35%), Gaps = 49/325 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +    L  +E +  V   +       +       GF+    P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNQYDLCISEFVRVVDQRLPNKVFYRLCPELHHQGFTLSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A+   + G   I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQYPQWLAENAQRAVELGSQGIDLNCGCPSKAVNGSNGGASLLKQPELIYQATKAIR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+ +  PV+VK R+G D       +  +  ++++ G   I IH R          D  +
Sbjct: 128 QAVPMEQPVSVKVRLGWD---NVDQVFEIADAVQQGGATEITIHGRTK-------SDGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  + E++K+   + +  NG +         L       +MIGR A     +   
Sbjct: 178 ADRINWYKIAEVRKKL-RIPVIANGEIWHWQDGQNCLAITGCQDLMIGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD-YAARHLHSGGKLQQITRHMIGLFHGF 287
                      S  IK   +K  W++    M   YA            I R         
Sbjct: 234 -----------SYVIKFNAEKLDWQQGVMPMLHKYAHVENEFDKGFYHIAR--------- 273

Query: 288 PNSRRCRHILTVEAGASTATHHIIE 312
              ++    L  E   +      I+
Sbjct: 274 --IKQWLQYLKKEYPQAGTLFERIK 296


>gi|38605039|sp|Q9AMN9|DUSC_PSEAC RecName: Full=tRNA-dihydrouridine synthase C
 gi|12965136|gb|AAK11471.1|AF323438_3 unknown [Pseudomonas alcaligenes]
          Length = 315

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 56/278 (20%), Positives = 108/278 (38%), Gaps = 26/278 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V++ +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRIGGIDWCVTEFIRVSERLLPAATYHKLAPELFNGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QFLGSDPQCLADNAAFACTLGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   IPVT K R+G + +  A+   +  +++ + G + I +HAR  +           
Sbjct: 128 RTVPAEIPVTAKMRLGFEGKEGAL---DCARALAEGGASQIVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + +E   + +  NG +  +    +      VD +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QEVVGVPVFANGEVWTLDDWRRCREISGVDDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSN--PLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +    +   P   S      +  DFW++    +    A
Sbjct: 236 IAAVRAGEEPEDMSWAELQPLLLDFWQQARRKLAPRYA 273


>gi|37680310|ref|NP_934919.1| putative regulator protein [Vibrio vulnificus YJ016]
 gi|37199057|dbj|BAC94890.1| putative regulator protein [Vibrio vulnificus YJ016]
          Length = 318

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 53/307 (17%), Positives = 114/307 (37%), Gaps = 34/307 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILGF------STQEKPLAL 52
           M    D   R     + +     TE +  V+  +       +         +    P+ +
Sbjct: 8   MEGVLDHLMREMLTEINDYDFCVTEFVRIVSQPLPDHVFYRLCPELKQGSKTKNGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A      G + I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAQLGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G ++         +V ++++   + + +HAR             K
Sbjct: 128 DAVPSHIPVSAKIRLGWENPEDCF---EIVDAVEQGKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I++ +  + +  NG + + +     +    +D +M+ R A  N   L  
Sbjct: 178 ASEIKWDYIDQIRQRST-IPLIANGEIWNYADGQACIETTGIDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + ++    +     +           +    T Y  R         +I +    L   +P
Sbjct: 236 IVKHNHRAMPWHEVV----------DLLLKYTQYEVRGDKGKYYPNRIKQWFAYLRQAYP 285

Query: 289 NSRRCRH 295
            +     
Sbjct: 286 QAADLFR 292


>gi|195398221|ref|XP_002057721.1| GJ17945 [Drosophila virilis]
 gi|194141375|gb|EDW57794.1| GJ17945 [Drosophila virilis]
          Length = 399

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 110/290 (37%), Gaps = 30/290 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   R      L +T M+++D++   +K     F+    ++PL  Q    D
Sbjct: 29  MVRYSKLEFRRLLRQ-NGVQLAFTPMMISDSVNNSEKARQNEFTTGPDDQPLIAQFAAKD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
             + V +A++V  +  + ++LN GCP        +G  L+  P+ V D +  + + L   
Sbjct: 88  AMEFVTSAQLVYPY-VDGVDLNCGCPQGWAISKGYGCGLLRQPEQVRDIVQCLRRTLPTD 146

Query: 117 IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             V+VK R     D Q        L + ++  GV  + +H R    K            L
Sbjct: 147 FSVSVKMRLLQSSDSQTSLQRTIQLAQQLEHCGVTFLTLHGRTPSQKH-------SKDTL 199

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEY 232
           +   + ++ +    + + +NG +E    A ++       GVM  R    N A+       
Sbjct: 200 NVAAMADVCQSL-QIPLIVNGNVESFQDACELHARTHAAGVMAARGLLANPALF------ 252

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYA---ARHLHSGGKL-QQITR 278
             N     +    +     W  I+ S  D+      H H       ++ R
Sbjct: 253 --NSDYPQATTTPKACVQQWLDIAQSAGDHLQFQCFHHHLSFMCSSEMKR 300


>gi|119953515|ref|YP_945724.1| histidine phosphokinase/phophatase, putative [Borrelia turicatae
           91E135]
 gi|119862286|gb|AAX18054.1| histidine phosphokinase/phophatase, putative [Borrelia turicatae
           91E135]
          Length = 331

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 105/240 (43%), Gaps = 21/240 (8%)

Query: 1   MVDWTDRHYRFFARLLT----NNALLYTEMIVADAILRGDKKNILGF----STQEKPLAL 52
           M D TD  +R    L+        + +TE I    +L   K+++           +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGNGKDGPDIYFTEFISVKGLLNKSKQSMQHILTKNDELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G +  +  +A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNEPDEFFKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAREIIMASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A     + ++VK R G         + + +  + K G++ + +H R AI +     D  
Sbjct: 137 EACLKFGLSLSVKTRHGFF----YSEVEDWLGFLLKLGIDMLTVHPRLAINQSEGSIDIS 192

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
               L    V    + NP   I  NG +  + QA +I+    +DGVM GR  ++N  +  
Sbjct: 193 VFDKL----VNLRDQINPSALIIGNGDILSLEQAHQIVEKHSIDGVMFGRGIFRNLNLFR 248


>gi|17546354|ref|NP_519756.1| hypothetical protein RSc1635 [Ralstonia solanacearum GMI1000]
 gi|38604943|sp|Q8XYX1|DUSC_RALSO RecName: Full=tRNA-dihydrouridine synthase C
 gi|17428651|emb|CAD15337.1| probable trna-dihydrouridine synthase c protein [Ralstonia
           solanacearum GMI1000]
          Length = 326

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 69/336 (20%), Positives = 125/336 (37%), Gaps = 44/336 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +       +E + V  ++L               G++    P+ +
Sbjct: 9   MEGVADFVMRDVLTSVGGYDGCVSEFVRVTGSLLPARTYERETPEIRNGGYTASGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 69  QLLGSDPEWLARNAAQAATVSPHGIDLNFGCPAKVVNRHGGGAMLLATPELLHRIVSTVR 128

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   I VT K R+GV D   A+A      ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPARIAVTAKMRLGVSDTSLAIA---CATALAEGGAASLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +   + +  NG +  +      + +   D VMIGR A  +  +   
Sbjct: 178 RPPAHWDWIARIA-DAVRVPVVANGEVWTVDDWARCRAVSGCDDVMIGRGAVSDPFLALR 236

Query: 229 VDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG- 286
           +    +  P     P+      D+ +K+ A +   A  H H   KL       +G     
Sbjct: 237 IRGQMARQPSDAEWPLVLGCLADYLKKLRARI---AIHHEHGRVKLW------LGYLKRT 287

Query: 287 FPNSRRC----RHILTVEAGASTATHHIIETAFNLM 318
           +P +       R +       S     +IE A   +
Sbjct: 288 WPQAAELHDAIRRL-----QDSAEILGVIEHALARI 318


>gi|186682399|ref|YP_001865595.1| dihydrouridine synthase, DuS [Nostoc punctiforme PCC 73102]
 gi|186464851|gb|ACC80652.1| dihydrouridine synthase, DuS [Nostoc punctiforme PCC 73102]
          Length = 340

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 106/250 (42%), Gaps = 17/250 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M D T+  +        +    +TE    +   R ++  +   +  +  +P+  Q+ G  
Sbjct: 23  MQDVTNLWFMKVIAHYGSPDYFFTEYFRVNDTSRLNRNILAAITENDTGRPVFAQMIGES 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
           I  LV  A  +  +    ++LN+GCP+ R++  + G  L+L+P+ V   +A + +A+   
Sbjct: 83  IPDLVRTAIDLCRYNIAGVDLNMGCPAPRIYRKNVGGGLLLSPEKVDRILAELRQAVNDR 142

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G ++         ++  I +  ++ + +H R           +     + YD
Sbjct: 143 PLTVKMRVGFENTDN---FYKILDIINRHNIDLLSLHGRTVK--------DMYHGAVRYD 191

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E  +   D  +  NG +     A+++L      GVM+GR A  N  +   + +    
Sbjct: 192 LIAEAVRRV-DCPVLANGNINSAKTAIEVLSQTGAAGVMVGRWAIGNPWIFNQIRQALRF 250

Query: 236 PLTGSSPIKT 245
                 P+  
Sbjct: 251 EPIAPVPLVE 260


>gi|187918594|ref|YP_001884157.1| histidine phosphokinase/phophatase, putative [Borrelia hermsii DAH]
 gi|119861442|gb|AAX17237.1| histidine phosphokinase/phophatase, putative [Borrelia hermsii DAH]
          Length = 331

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 111/240 (46%), Gaps = 21/240 (8%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKNILGF----STQEKPLAL 52
           M D TD  +R    L+ N      + +TE I    +L   K+++           +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGNGKDVPDIYFTEFISVKGLLNKSKQSMQHILTKNDELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G +  +  +A +I+ + G+  I+LN+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGKEPDEFFKAIEILSNLGFWGIDLNMGCPKKKIVKKGVCSALINNKSLAREIIMASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A     +P++VK R G         + + +  + + G++ + +H R A+ +   P D  
Sbjct: 137 EACLKFGLPLSVKTRHGFF----YSEVEDWLGFLLELGIDMLIVHPRLAVNQSEGPID-- 190

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
               + +++V    + NP   I  NGG+  + QA +I+    +DGVM G   ++N  +  
Sbjct: 191 --VAVFHELVKLRDQINPSALIIGNGGILSLEQAHQIVREYSIDGVMFGCGIFRNLNLFR 248


>gi|312962068|ref|ZP_07776564.1| NifR3/Smm1 family protein [Pseudomonas fluorescens WH6]
 gi|311283678|gb|EFQ62263.1| NifR3/Smm1 family protein [Pseudomonas fluorescens WH6]
          Length = 319

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE I      +  A        +L    +    PL +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVNDRLLTPAYFHKLAPELLHGAHTAAGVPLRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGSQVIDLNFGCPAKTVNKSRGGAVLLKEPELLNQIVEHVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D    A+       ++ + G   I +HAR         K +  
Sbjct: 128 RAVPAHIPVTAKMRLGFDSPDGALV---CATALAEGGAAHIVVHART--------KTDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + ++   + +  NG L  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWIPRV-QDVVKVPVFANGDLWSVEDWQRCREISGAEDIMLGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIK--TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +    +              + +DFW +  A +T+       + G+L+Q    +  L   
Sbjct: 236 IAAARAGEEVVEMTWAQMQPMLQDFWTQCVAQLTE-----KQAPGRLKQW---LAMLTRN 287

Query: 287 FPNSRRCRHILTVE 300
           +P +      L  E
Sbjct: 288 YPQAVELFTALRRE 301


>gi|325579218|ref|ZP_08149174.1| tRNA-dihydrouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
 gi|325159453|gb|EGC71587.1| tRNA-dihydrouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
          Length = 307

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 63/325 (19%), Positives = 116/325 (35%), Gaps = 48/325 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +    L  TE +  V   +       +       GF+  + P+ +
Sbjct: 8   MQGVLDPFVRQLLTEVNEYDLCITEFVRVVDQLLPEKVFYRLCPELKNQGFTPSKTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G   + L E A    + G + I+LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPNCLAENANRAIELGSHGIDLNCGCPSKTVNGSNGGAALLKQPELIYQATLALR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   +PV+VK R+G D    A     +  ++++ G   I IH R          D  +
Sbjct: 128 QTVPSHLPVSVKVRLGWDCTSQAF---EIADAVQQGGATEITIHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              ++++ + E++     + +  NG +         L     + +M+GR A     +   
Sbjct: 178 ADRINWEKIGEVRSRLT-IPVIANGEIWRWEDGQACLKATGCEDLMVGRGALNIPNL--- 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                      S  +K   +K  W  I   +  YA            + R          
Sbjct: 234 -----------SLVLKQNCEKMPWVDIQKILQKYAEMENFHDSGFYHVAR---------- 272

Query: 289 NSRRCRHILTVEAGASTATHHIIET 313
             ++    L  E   +      I+T
Sbjct: 273 -IKQWLRYLNKEYPEADIVFERIKT 296


>gi|257126332|ref|YP_003164446.1| dihydrouridine synthase [Leptotrichia buccalis C-1013-b]
 gi|257050271|gb|ACV39455.1| dihydrouridine synthase DuS [Leptotrichia buccalis C-1013-b]
          Length = 325

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/290 (19%), Positives = 116/290 (40%), Gaps = 24/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           M   TD  +R        +  L+TEM+ A+ + R D      +L    +EK    QI G 
Sbjct: 8   MAGITDYSFRKILEKFEPD-FLFTEMVNANLLNREDDTTINELLKCDNKEK-TGTQIFGG 65

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D ++LV     +++FG+ +IN+N+GCP  ++ +   G+ L+ N ++V   +    + +  
Sbjct: 66  DKNELVSGILKLKNFGFRKININMGCPQPKIVKNGAGSALLENYELVEQVLLET-QNIDA 124

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K R+G  D        NL     K  ++ I +H R                  +++
Sbjct: 125 KISIKIRVGYKDFDNPEIFLNLAN---KHNLDFICVHGRTQK--------QMYSGTANWE 173

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           IV ++ K   ++    NG L + S+  + + S   DG+++ R    N  +++   E+   
Sbjct: 174 IVEKLSKMPRNINFFGNGDLFEPSEIKRKIASCNLDGIILSRGIIGNPWLISQTREFLKT 233

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
               +              +          +      + +I + +   F 
Sbjct: 234 GKINTIQTFDETKSLVLEHLQN-----IVENKGEKKAVLEINKFLRPYFQ 278


>gi|52425959|ref|YP_089096.1| hypothetical protein MS1904 [Mannheimia succiniciproducens MBEL55E]
 gi|52308011|gb|AAU38511.1| unknown [Mannheimia succiniciproducens MBEL55E]
          Length = 311

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/286 (21%), Positives = 111/286 (38%), Gaps = 24/286 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNI------LGFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   +       +       G +T   P+ +
Sbjct: 8   MQGVLDAFVRQLLTEVNDYDLCISEFVRVVDQLLPEKVFYRLCPELKNAGKTTTGTPIRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+  P+++     A+ 
Sbjct: 68  QLLGQFPEWLAENAVRAVELGSFGVDLNCGCPSKTVNGSHGGASLLKQPELIYQATRAIR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PV+VK R+G D    A    ++  ++++ G N I IH R          D  K
Sbjct: 128 TAVPKHLPVSVKVRLGWD---SADFAFDIADAVQQGGANEITIHGRTK-------ADGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              ++++ + E++++   + +  NG + +       L     + +MIGR A  N   L+ 
Sbjct: 178 AERINWEKIGELRRKL-AIPVIANGEIWNWQDGQNCLAVTGCEDLMIGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           V +     L     I+          I  +   + AR       L+
Sbjct: 236 VVKRNEEKLPWHKVIRILQKYAHLENIHDTGFYHVARIKQWLQYLK 281


>gi|146083263|ref|XP_001464693.1| hypothetical protein [Leishmania infantum JPCM5]
 gi|134068787|emb|CAM59721.1| conserved hypothetical protein [Leishmania infantum JPCM5]
 gi|322498112|emb|CBZ33187.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 595

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 90/232 (38%), Gaps = 19/232 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM V   +  L+  + ++L     E    +Q+  +   +  
Sbjct: 247 NLPFRRICKSF-GADVTLSEMAVVFNLNRLQKSEWSLLRRHESEDIFGIQLAVSRPQEAA 305

Query: 64  EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             A+ +E  G  Y+ +++N GCP  ++ +   G  L      + D + ++    S PV +
Sbjct: 306 TFAQALEASGFSYDFLDINCGCPVEKIVKSGCGCGLWKRTGRLRDVVESLAIHQSRPVAI 365

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIG+D+  P   L   +      G   + +H R         +  R     ++D V +
Sbjct: 366 KCRIGLDEDTP--TLHQQIHRYSTWGAAAVTVHGRS--------RKQRYTKFANWDYVDQ 415

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVD 230
             +    L +  NG +  +   L+       +   MIGR A     +   + 
Sbjct: 416 CAQ-LTSLPVIGNGDIMSLEDVLEHRERQPHITSHMIGRGALIKPWLFEEIK 466


>gi|237801118|ref|ZP_04589579.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331023975|gb|EGI04032.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 326

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/304 (20%), Positives = 116/304 (38%), Gaps = 34/304 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPGCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVNQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +   L+         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKIPVVANGEIWTVDDWLRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIKT--RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +              +    + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWEELQPMLRTFWQDCLVKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNS 290
           +P +
Sbjct: 288 YPQA 291


>gi|219685551|ref|ZP_03540368.1| putative histidine phosphokinase/phophatase [Borrelia garinii
           Far04]
 gi|219672950|gb|EED29972.1| putative histidine phosphokinase/phophatase [Borrelia garinii
           Far04]
          Length = 329

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 119/270 (44%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISVKGILNGSKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D  +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNDPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +   G++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVNDWLGFLLGFGIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 185 SEGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLT-TVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   +   +  + L     I     KDF 
Sbjct: 245 NLFKFSSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|294637389|ref|ZP_06715682.1| tRNA-dihydrouridine synthase [Edwardsiella tarda ATCC 23685]
 gi|291089436|gb|EFE21997.1| tRNA-dihydrouridine synthase [Edwardsiella tarda ATCC 23685]
          Length = 337

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 117/324 (36%), Gaps = 41/324 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     + +  L  TE +  V   +       +         +     + +
Sbjct: 31  MEGVLDALVRELLSEVNDYDLCITEFVRVVDRLLPEKVFYRLCPELHRHSRTRSGTLVRI 90

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A+     G   ++ N GCPS  V+    GA L+ +P  +   + AM 
Sbjct: 91  QLLGQSPHWLAENAQRAVALGSPGVDFNCGCPSKAVNGSGGGATLLKDPAQIYAGVLAMR 150

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVTVK R+G +    A     +  + +++G   + +H R          D  +
Sbjct: 151 QAVPAALPVTVKVRLGWE---SASQRFEIADAAQQAGATELVVHGRTKE-------DGYR 200

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +D+  + EI++    + +  NG + D + A   L     D VMIGR A     +   
Sbjct: 201 ADRIDWVAIGEIRQRLT-IPVIANGEIWDYASAQACLAQTGCDAVMIGRGALNIPNL--- 256

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFH 285
                      S  +K       W ++ A +  Y          L  + R    +  L  
Sbjct: 257 -----------SRVVKDNAAPMAWPEVVALLQRYVRLEKQGDTGLYHVARIKQWLSYLRK 305

Query: 286 GFPNS-RRCRHILTVEAGASTATH 308
            +P +    R +  + A  + A H
Sbjct: 306 VYPEAETLFRQVRPLMATPAIAAH 329


>gi|289806468|ref|ZP_06537097.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 195

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 51/207 (24%), Positives = 89/207 (42%), Gaps = 18/207 (8%)

Query: 34  RGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
                 +L    +    P+ +Q+ G     L E A      G   ++LN GCPS  V+  
Sbjct: 1   HRICPELLHASRTPSGTPVRIQLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGS 60

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             GA L+ +P+++     AM  A+   +PVTVK R+G D          +  +++++G +
Sbjct: 61  GGGATLLTDPELIYQGAKAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGAS 117

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
            + +H R             +  ++D+  + EI++    + +  NG + D   A   +  
Sbjct: 118 ELVVHGRTK-------AQGYRAEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMAT 169

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
              D VMIGR A  N   L+ V +Y  
Sbjct: 170 SGCDAVMIGRGAL-NIPNLSRVVKYNE 195


>gi|325118549|emb|CBZ54100.1| Dihydrouridine synthase, related [Neospora caninum Liverpool]
          Length = 1295

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/285 (21%), Positives = 111/285 (38%), Gaps = 30/285 (10%)

Query: 6    DRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGADISKLV 63
            +  +R     L    +  +EM VA +I+ G +   ++L     EK   +QI G     L 
Sbjct: 905  NLPFRRLCVEL-GAEVTVSEMAVAKSIVEGKQSELSLLKRHKSEKFFGVQIAGGTPEVLN 963

Query: 64   EAAKIV--EDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMC-KALSIPV 119
              A ++  E+   + I+LN  CP  ++H     GAC++ +P  +   I  +  +   I +
Sbjct: 964  ACADVLASEEVSCDFIDLNAACPLVQLHRRFKAGACMLDHPARLESLIEGVTMRQPEIAL 1023

Query: 120  TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            TVK R    +Q     L N ++ + ++G   + IH R A          R     D+  V
Sbjct: 1024 TVKLRTA--NQGKKQVLHNFIQRLGQAGAAALIIHGRTA--------QQRYTKAADWGYV 1073

Query: 180  YEIKKEN-PDLFIGLNGGLED-MSQALKILPSV-DGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + ++   P + I   G +        ++     D +MI RAA     + T + E     
Sbjct: 1074 AQCREALDPSVPIIGCGDIFSSPEFEFRLSSGAADALMIARAALIKPWVFTEISEQKVWD 1133

Query: 237  LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            ++ S  +          ++      +   H  S G+    TR  +
Sbjct: 1134 ISASERL----------ELLKRFVGFGLEHWGSDGRGVATTRRFL 1168


>gi|240128100|ref|ZP_04740761.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-93-1035]
 gi|268686488|ref|ZP_06153350.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-93-1035]
 gi|268626772|gb|EEZ59172.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae SK-93-1035]
          Length = 333

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 101/253 (39%), Gaps = 24/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MRGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   IP+  K R+G +D+ PA+       +I + G  G+ +HAR         K    
Sbjct: 140 GRLPAHIPLAGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART--------KAEGY 188

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  +  ++ +  NG +  +     +K +   + VM+GR A     +   
Sbjct: 189 EPPAHWEWIRKIH-DTVNIPVTANGDVFSLQDYIGIKTISGCNSVMLGRGAVIRPDLARQ 247

Query: 229 VDEYFSNPLTGSS 241
           + +Y +      +
Sbjct: 248 IKQYENGGPVKDT 260


>gi|71422193|ref|XP_812059.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70876795|gb|EAN90208.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 529

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 56/284 (19%), Positives = 102/284 (35%), Gaps = 29/284 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  + M  +     L+  + ++L     E    LQI  +      
Sbjct: 182 NLPFRRVCKSY-GADITVSSMSLVHNLNRLQKGEWSLLRRHESEDVFGLQIAVSQPQSAQ 240

Query: 64  EAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLNPD-IVGDCIAAMCKALSIPVT 120
             AK +E  GY  + I++N GCP   +     G  L    D  + D ++++ +  S PV+
Sbjct: 241 TWAKAIEASGYSYDFIDINCGCPVQMIMSAGCGCGLWERRDNRLRDIVSSLVQHQSKPVS 300

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIG      A +L   +   +  G + + IH R         +  R     +++ + 
Sbjct: 301 IKCRIGAGANSSA-SLHEKIGDYEGWGADAVTIHGRF--------RAQRYTKLANWEYID 351

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                   L +  NG +      +      P V   MIGR A     +   + +    P 
Sbjct: 352 S-CAARTSLPVIGNGDIFSYEDIIDHRERYPHVSSYMIGRGALIKPWIFEEIKQ--EQPR 408

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             SS  +  + + F         +Y   H  S  +    TR  +
Sbjct: 409 DISSQERFEMLRSF--------CNYGLSHWGSDERGVLTTRRFL 444


>gi|330888122|gb|EGH20783.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. mori str.
           301020]
          Length = 321

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLWL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRAFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|219684394|ref|ZP_03539338.1| putative histidine phosphokinase/phophatase [Borrelia garinii PBr]
 gi|219672383|gb|EED29436.1| putative histidine phosphokinase/phophatase [Borrelia garinii PBr]
          Length = 329

 Score =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 64/270 (23%), Positives = 119/270 (44%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISVKGILNGSKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D  +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNDPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P+++K R G         + + +  +   G++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSIKTRHGF----SYPEVNDWLGFLLGFGIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 185 SEGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLT-TVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   +   +  + L     I     KDF 
Sbjct: 245 NLFKFSSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|212531921|ref|XP_002146117.1| dihydrouridine synthase family protein, putative [Penicillium
           marneffei ATCC 18224]
 gi|210071481|gb|EEA25570.1| dihydrouridine synthase family protein, putative [Penicillium
           marneffei ATCC 18224]
          Length = 526

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 61/296 (20%), Positives = 109/296 (36%), Gaps = 43/296 (14%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVAD--------------AILRGDKKN-- 39
           MV+ ++  +R   R       +   + Y+ M  A                I   D+ +  
Sbjct: 33  MVERSEFAWRMLTRSFMEKDQSQRLIAYSPMFHARLYKESEGHRTQCMQPIRHNDQTDTD 92

Query: 40  ---ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
              + G    ++PL +Q    D    +EAA++   +  + ++LN+GCP     +G +GA 
Sbjct: 93  VPYLDGNPAIDRPLFVQFCANDPDDFLEAARLAAPY-CDAVDLNLGCPQGIARKGHYGAF 151

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L  + D++ + I  +   L IPVT K RI    Q          K I  +G + I +H R
Sbjct: 152 LQEDWDLIYNLINKLHTELPIPVTAKFRI----QETKEKTLEYAKMILSAGASIITVHGR 207

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGL---EDMSQALKILPSVDG 212
           +   KG            D+  V  ++    P+  I  NG +    D+ + L+     DG
Sbjct: 208 RREQKG------HNTGVADWSYVRYLRDNLPPETVIFANGNILGQADIERCLEA-TGADG 260

Query: 213 VMIGRAAYKNSAMLT---TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           VM       + ++      +         G            +R+    + +Y  R
Sbjct: 261 VMSAEGNLSDPSIFGKAPEIGNEGREYWRGRDGRGGYRMDAVFRRYMNIIHEYVLR 316


>gi|330502905|ref|YP_004379774.1| dihydrouridine synthase, DuS [Pseudomonas mendocina NK-01]
 gi|328917191|gb|AEB58022.1| dihydrouridine synthase, DuS [Pseudomonas mendocina NK-01]
          Length = 316

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 56/278 (20%), Positives = 108/278 (38%), Gaps = 26/278 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V++ +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRIGGIDWCVTEFIRVSERLLPAATYHKLAPELFNGSRTQAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QFLGSDPQCLADNAAFACTLGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   IPVT K R+G + +  A+   +  +++ + G + I +HAR  +           
Sbjct: 128 RTVPADIPVTAKMRLGFEGKEGAL---DCARALAEGGASQIVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + +E   + +  NG +  +    +      VD +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QEVVGVPVFANGEVWTLDDWHRCREISGVDDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSN--PLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +    +   P   S      +  DFW++    +    A
Sbjct: 236 IAAVRAGEAPAEMSWAELQPLLLDFWQQARRKLAPRYA 273


>gi|89901795|ref|YP_524266.1| dihydrouridine synthase [Rhodoferax ferrireducens T118]
 gi|89346532|gb|ABD70735.1| dihydrouridine synthase, DuS [Rhodoferax ferrireducens T118]
          Length = 335

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 110/254 (43%), Gaps = 24/254 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDK-----KNIL--GFSTQEKPLAL 52
           M    D   R     +       +E I V++ +L           +L  G +    P+A 
Sbjct: 8   MEGLLDFVLRDILTRVGGVDRCVSEFIRVSNTLLPDQVFIRVVPELLNGGRTFAGVPVAA 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A  +   G + I+LN GCP+  V+    GA L+  P+++   +AA+ 
Sbjct: 68  QLLGSDPVCLAENAARLAALGPHGIDLNFGCPAKTVNRHGGGAALLDEPELLLAIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+ K R+GV D   A+       +++  G + + +HAR         + +  
Sbjct: 128 RAVPKTMPVSAKMRLGVHDDSRAL---ECALALEGGGASELVVHART--------RADAY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +   ++ +  NG + ++  AL+       D +M+GR    N  +   
Sbjct: 177 RPPAYWERIADI-RAVVNIPVVANGEIWNVQDALRCREESGCDSLMLGRGMVTNPGLALA 235

Query: 229 VDEYFSNPLTGSSP 242
           +    + P    +P
Sbjct: 236 IRAAMAGPDASPAP 249


>gi|322828617|gb|EFZ32349.1| hypothetical protein TCSYLVIO_1313 [Trypanosoma cruzi]
          Length = 529

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 56/284 (19%), Positives = 102/284 (35%), Gaps = 29/284 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  + M  +     L+  + ++L     E    LQI  +      
Sbjct: 182 NLPFRRVCKGY-GADITVSSMSLVHNLNHLQKSEWSLLRRHESEDVFGLQIAVSQPQSAQ 240

Query: 64  EAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLNPD-IVGDCIAAMCKALSIPVT 120
             AK +E  GY  + I++N GCP   +     G  L    D  + D ++++ +  S PV+
Sbjct: 241 TWAKAIEASGYSYDFIDINCGCPVQMIMSAGCGCGLWERRDNRLRDIVSSLVQHQSKPVS 300

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIG      A +L   +   +  G + + IH R         +  R     +++ + 
Sbjct: 301 IKCRIGAGANSNA-SLHEKIGDYEGWGADAVTIHGRF--------RAQRYTKLANWEYID 351

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                   L +  NG +      +      P V   MIGR A     +   + +    P 
Sbjct: 352 S-CAARTSLPVIGNGDIFSYEDIIDHRERYPHVSSYMIGRGALIKPWIFEEIKQ--EQPR 408

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             SS  +  + + F         +Y   H  S  +    TR  +
Sbjct: 409 DISSQERFEMLRSF--------CNYGLSHWGSDERGVLTTRRFL 444


>gi|302916105|ref|XP_003051863.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256732802|gb|EEU46150.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 509

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 117/308 (37%), Gaps = 57/308 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGF------------ 43
           MVD ++  +R   R   +       L YT M+ A    + +K     F            
Sbjct: 36  MVDQSEFAWRMLTRSFLSPTEQSSLLAYTPMLHARLFSQDEKYRQAHFQAVRSNEDPWLD 95

Query: 44  --STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
              + ++PL +Q    D   L+ AAK V  +  + ++LN+GCP     +G +GA L  + 
Sbjct: 96  GNPSIDRPLFVQFCANDPDALLAAAKQVAPY-CDAVDLNLGCPQGIARKGKYGAFLQEDQ 154

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++   I  + K L +PVT K RI               +++ K+G + + +H R+   K
Sbjct: 155 DLIFRLINILHKELPVPVTAKIRIL----ETEEQTLAYAQNVLKAGASILTVHGRRREQK 210

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE---DMSQALKILPSVDGVMIGR 217
           G            ++ ++  ++   P    I  NG +    D+ + L+     DGVM   
Sbjct: 211 G------HLTGLAEWKMIKFLRDSLPKETVIFANGNILQEGDIERCLEA-TGADGVMSAE 263

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
               + A+ +              P      +++WR           +    G ++  + 
Sbjct: 264 GNLSDPAIFS------------KPPPVGEEGREYWRD----------KDGKGGYRVDAVM 301

Query: 278 RHMIGLFH 285
           R  + + H
Sbjct: 302 RRYMNILH 309


>gi|189208310|ref|XP_001940488.1| tRNA-dihydrouridine synthase C [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187976581|gb|EDU43207.1| tRNA-dihydrouridine synthase C [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 801

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 101/265 (38%), Gaps = 50/265 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAI----------------------- 32
           MV+ ++  +R  +R     +     L YT M  +                          
Sbjct: 52  MVEQSEFAWRLLSRSFLPESQQKNLLAYTPMFHSKMFGEKSNYRDAHFQPLKSTVPSPID 111

Query: 33  ------LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
                 LR   +++ G    ++PL +Q    D    + AAK V  F  + ++LN+GCP  
Sbjct: 112 DYHLSQLRDSDRHLDGNPVFDRPLTVQFCSNDPDDFLRAAKHVAPF-CDAVDLNLGCPQG 170

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
               G +GA L  + D++   I  + + L +PVT K R+               K++  +
Sbjct: 171 IAKRGKYGAFLQEDWDLISRMIRKLHEELDVPVTAKMRVL----ETPEKTLAYAKTLLDA 226

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGL---EDMSQ 202
           G + I +H R+   KG            D+ ++  +++  P    I  NG +   ED+++
Sbjct: 227 GASIITVHGRRREQKG------HNTGLADWKMIRHLRENLPKETVIFANGNILQHEDIAK 280

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLT 227
            L+     DGVM       +  +  
Sbjct: 281 CLEA-TGADGVMSAEGNLYDPTIFA 304


>gi|119494427|ref|XP_001264109.1| dihydrouridine synthase family protein, putative [Neosartorya
           fischeri NRRL 181]
 gi|119412271|gb|EAW22212.1| dihydrouridine synthase family protein, putative [Neosartorya
           fischeri NRRL 181]
          Length = 527

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 65/308 (21%), Positives = 107/308 (34%), Gaps = 60/308 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAI-------LRGDKKNILGFSTQE- 47
           MVD ++  +R   R           L Y+ M  A           +  +    G    + 
Sbjct: 44  MVDRSEFAWRMLTRSFMPPDDPKPILAYSPMYHARLFREQANVRWQHFQPTRAGLDKNDN 103

Query: 48  -----------KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
                      +PL +Q    D    +EAA+ V  +  + ++LN+GCP     +G +GA 
Sbjct: 104 SLYLDGNPAFDRPLFVQFCANDPDDFLEAARHVAPY-CDAVDLNLGCPQGIARKGHYGAF 162

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L  + D++   I  + K L IPVT K RI    Q          K I  +G + I +H R
Sbjct: 163 LQEDWDLIYKLINRLHKELPIPVTAKFRI----QESKEKTLEYAKMILSAGASIITLHGR 218

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGV 213
               KG            D+  +  ++    P+  I  NG   +     + L     DGV
Sbjct: 219 TREQKG------HNTGLADWSYIRYLRDNLPPETVIFANGNNLNHDDLERCLEATGADGV 272

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M       + A+ +              P      +++WR           R+   G ++
Sbjct: 273 MSAEGNLSDPAIFS------------KPPPVGSEGREYWR----------GRNGKGGYRI 310

Query: 274 QQITRHMI 281
             I R  +
Sbjct: 311 DAIFRRYL 318


>gi|328713887|ref|XP_001951826.2| PREDICTED: tRNA-dihydrouridine synthase 4-like [Acyrthosiphon
           pisum]
          Length = 350

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 110/233 (47%), Gaps = 22/233 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MV ++   +R   R+     L +T MI+AD  ++  K     F   T ++PL +Q G  +
Sbjct: 24  MVRYSRLQFRKLIRMY-ECDLCFTPMIMADCYVKSAKARAHEFQTDTDDRPLIVQFGANN 82

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            S  V A+ ++  +  + ++LN GCP        +GA L+ NP+I+ DC+  +   L  +
Sbjct: 83  SSDFVNASNLIIPY-CDGVDLNCGCPQRWALNEGYGAQLLKNPEIIKDCVRQLRNHLPTN 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             ++VK R+  D +       +L + I+ +GV+ I +H R A+ K   P D   +     
Sbjct: 142 KTISVKLRLLDDHRKSV----DLCQQIEATGVSFITVHGRTALQK-NEPIDQECL----- 191

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLT 227
               ++  E+  + + LNG ++++S A  ++      G+M  R    N  +  
Sbjct: 192 ----KLINESVSVPVILNGDIKNLSDAITMQEYTGCRGMMSARGILHNPGLFA 240


>gi|154335122|ref|XP_001563801.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134060830|emb|CAM37846.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 590

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 92/232 (39%), Gaps = 19/232 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM V   +  L+  + ++L     E    +Q+  +   +  
Sbjct: 242 NLPFRRICKSF-GADVTLSEMAVVFNLNRLQKSEWSLLRRHESEDIFGIQLAVSRPQEAA 300

Query: 64  EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             A+++E  G  Y+ +++N GCP  ++ +   G  L      + D +  +    S PVT+
Sbjct: 301 TFAQVLEASGFSYDFLDINCGCPVEKLVKSGCGCGLWERTGRLRDVVENLAIHQSRPVTI 360

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIG D+ +P   L   +      G   + +H R         +  R     ++D V +
Sbjct: 361 KCRIGFDEAMP--TLHQQIHQYSTWGAAAVTVHGRS--------RKQRYTKFANWDYVDQ 410

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVD 230
             +    L +  NG +  +   L+     P +   MIGR A     +   + 
Sbjct: 411 CAQ-LSLLPVIGNGDIMSLEDVLEHRRRQPHITSHMIGRGALIKPWLFEEIK 461


>gi|213420476|ref|ZP_03353542.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 181

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 69/122 (56%), Positives = 87/122 (71%), Gaps = 1/122 (0%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+D +
Sbjct: 20  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGSDPA 78

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           +L   AK+ E  GY+EINLNVGCPS RV  G FGACLM N  +V DC+ AM   +SIPVT
Sbjct: 79  QLAHCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAQLVADCVKAMRDVVSIPVT 138

Query: 121 VK 122
           VK
Sbjct: 139 VK 140


>gi|322490130|emb|CBZ25391.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 660

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 89/232 (38%), Gaps = 19/232 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +EM V   +  L+  + ++L     E    +Q+  +   +  
Sbjct: 312 NLPFRRVCKSF-GADVTLSEMAVVFNLNRLQKSEWSLLRRHESEDIFGIQLAVSRPEEAA 370

Query: 64  EAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             A  +E  G  Y+ +++N GCP  ++ +   G  L      + D + ++    S PV +
Sbjct: 371 TFAHALEASGFSYDFLDINCGCPVEKIVKSGCGCGLWKRTGRLRDVVESLAIHQSRPVAI 430

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           KCRIG+D+  P   L   +      G   + +H R         +  R     ++D V +
Sbjct: 431 KCRIGLDEDTP--TLHQQIHRYSTWGAAAVTVHGRS--------RKQRYTKLANWDYVDQ 480

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP---SVDGVMIGRAAYKNSAMLTTVD 230
             +    L +  NG +  +   L+       +   MIGR A     +   + 
Sbjct: 481 CAQ-LTSLPVIGNGDIMSLEDVLEHRERQPHITSHMIGRGALIKPWLFEEIK 531


>gi|71734038|ref|YP_274172.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71554591|gb|AAZ33802.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|320324866|gb|EFW80938.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329231|gb|EFW85228.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330880875|gb|EGH15024.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 321

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLYSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRAFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|146307749|ref|YP_001188214.1| dihydrouridine synthase, DuS [Pseudomonas mendocina ymp]
 gi|145575950|gb|ABP85482.1| tRNA-U20a,U20b-dihydrouridine synthase [Pseudomonas mendocina ymp]
          Length = 318

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 58/278 (20%), Positives = 108/278 (38%), Gaps = 26/278 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V+D +L     + L         +     + +
Sbjct: 8   MEGLVDEILRDVLTRIGGIDWCVTEFIRVSDRLLPAATYHKLAPELFAGARTQAGTLMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QFLGSDPQCLADNAAFACGLGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   IPVT K R+G +D+  A+   +  +++ + G + I +HAR  +           
Sbjct: 128 RTVPAEIPVTAKMRLGFEDKSVAL---DCARALAEGGASQIVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + +E   + +  NG +  +    +      VD +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QEVVAVPVFANGEVWTLQDWRRCREISGVDDIMLGRGLVSRPGLARQ 235

Query: 229 VD--EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +        P   S      + +DFWR+    +    A
Sbjct: 236 IAAVRAGEQPQEMSWEELQPLLQDFWRQARRKLAPRYA 273


>gi|119476924|ref|ZP_01617205.1| hypothetical protein GP2143_10237 [marine gamma proteobacterium
           HTCC2143]
 gi|119449731|gb|EAW30968.1| hypothetical protein GP2143_10237 [marine gamma proteobacterium
           HTCC2143]
          Length = 321

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 59/305 (19%), Positives = 115/305 (37%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     +       TE +        +    R   + +  G +    P+ +
Sbjct: 1   MEGVVDHTMRTMLTKVGGIDRCVTEFVRVTTTRLPSRVFYRYCPELHNRGMTPSGVPVYI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   +   A      G   I++N GCP+  V+    G+ L+  P  + D +AA+ 
Sbjct: 61  QLLGGNAESMAINAAKAASLGAPGIDINFGCPAKSVNRNDGGSVLLKEPQRLHDIVAAVR 120

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPVT K R+G +D      L ++ ++I  +  + + IHAR         K +  
Sbjct: 121 DAVPLDIPVTAKIRLGFNDSSL---LTDISQAIFSANASELTIHART--------KSDGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I + N  + +  NG +  ++     +     D VM+GR       +   
Sbjct: 170 KPPAYWEAIADI-QANSPVPVIANGEIWTVNDYHSCIKQSGCDDVMLGRGLLACPDLAVQ 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMT---DYAARHLHSGGKLQQ----ITRHMI 281
           +       +TGS      +       + A      +      + G +++Q    + +H +
Sbjct: 229 IRA--GRSMTGSQQDIPALSWPQVLDLVAQFCIVTEAMYERKYVGNRVKQWLAYLRQHYV 286

Query: 282 GLFHG 286
             F G
Sbjct: 287 --FAG 289


>gi|260768108|ref|ZP_05877042.1| tRNA-dihydrouridine synthase C [Vibrio furnissii CIP 102972]
 gi|260616138|gb|EEX41323.1| tRNA-dihydrouridine synthase C [Vibrio furnissii CIP 102972]
          Length = 308

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 52/312 (16%), Positives = 118/312 (37%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +     TE +      + D +       +     +    P+ +
Sbjct: 1   MEGVLDHLMREMLTQINDYDFCVTEFVRVINLPLPDHVFYRLCPELKQGSRTKAGVPVKV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   ++LN GCP+  V++   GA L+ +P+++   I A  
Sbjct: 61  QLLGQEPHWMAENAVRAAELGACGVDLNFGCPAKMVNQSKGGAALLQHPELIYQVIKACR 120

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G ++         +V +++++G + + +HAR             K
Sbjct: 121 DAVPADIPVSAKIRLGWENPDDCF---EIVDAVQQAGADELTVHARTK-------AGGYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +D + +I+++   + +  NG + + +     +    +D +M+ R A     +   
Sbjct: 171 ASEIKWDYINQIRQKT-HIPLIANGEIWNYADGQACIDTTGIDSLMVCRGALNVPNLGNI 229

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG---GKLQQITRHMIGLFH 285
           V    S                 W ++   + +Y+A  +          ++ +    L  
Sbjct: 230 VKHNHS--------------AMPWHEVVDLLLEYSAYEVRGDKGKYYPNRVKQWFAYLRQ 275

Query: 286 GFPNSRRCRHIL 297
            +P +      +
Sbjct: 276 AYPQAADLFREI 287


>gi|167646566|ref|YP_001684229.1| NifR3 family TIM-barrel protein [Caulobacter sp. K31]
 gi|167348996|gb|ABZ71731.1| TIM-barrel protein, nifR3 family [Caulobacter sp. K31]
          Length = 335

 Score =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 75/325 (23%), Positives = 119/325 (36%), Gaps = 26/325 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPL-ALQIGGAD 58
           M   +D  +R  A  L   A + TEM+      RG    +   +     PL  +Q+ G D
Sbjct: 21  MTGVSDLPFRETATRL-GAAYVATEMVACAEFARGRPDAVRRAAVGDGLPLMVVQLVGRD 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-SFGACLMLNPDIVGDCIAAMCKALSI 117
            + + + A++  + G   I+LN GCPS +V  G + G+ LM  PD+    +AA  +A+ +
Sbjct: 80  PTFMGQGARMAAEAGAQIIDLNFGCPSKQVTGGVASGSALMREPDLAEALVAAAVRAVDV 139

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVTVK R+G DD     A  ++ +    +G   I +H R          D   +  +   
Sbjct: 140 PVTVKMRLGWDDDSRNAA--DIARRAVDAGAQAITVHGRTRCQFYKGVADWSAVAAVKAA 197

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +   +          +NG + D   A   L     DGVMIGR  Y    +   ++    N
Sbjct: 198 VSVPV---------LVNGDIIDGDTARLALEQSGADGVMIGRGVYGRPWIAQAIEAAL-N 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF--PNSRRC 293
                 P               S+  Y          L+   +H+         P+S   
Sbjct: 248 GEGFREPDAEERLAIAVTHFRRSLGFY-----GQNLGLKMFRKHLASYIEAAPWPDSEEL 302

Query: 294 RHILTVEAGASTATHHIIETAFNLM 318
           R      A         IE     +
Sbjct: 303 RRT-ARAALCRLEDPAAIEDGLAAL 326


>gi|71414125|ref|XP_809176.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70873517|gb|EAN87325.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 529

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 56/284 (19%), Positives = 102/284 (35%), Gaps = 29/284 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  + M  +     L+  + ++L     E    LQI  +      
Sbjct: 182 NLPFRRVCKGY-GADITVSSMSLVSNLNRLQKGEWSLLRRHESEDVFGLQIAVSQPQSAQ 240

Query: 64  EAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLNPD-IVGDCIAAMCKALSIPVT 120
             AK +E  GY  + I++N GCP   +     G  L    D  + D ++++ +  S PV+
Sbjct: 241 TWAKAIEASGYSYDFIDINCGCPVQMIMSAGCGCGLWERRDNRLRDIVSSLVQHQSKPVS 300

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +KCRIG      A +L   +   +  G + + IH R         +  R     +++ + 
Sbjct: 301 IKCRIGAGANSNA-SLHEKIGDYEGWGADAVTIHGRF--------RAQRYTKLANWEYID 351

Query: 181 EIKKENPDLFIGLNGGLEDMSQ---ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                   L +  NG +          +  P V   MIGR A     +   + +    P 
Sbjct: 352 S-CAARTSLPVIGNGDIFSYEDIIGHRERYPHVSSYMIGRGALIKPWIFEEIKQ--EQPR 408

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             SS  +  + + F         +Y   H  S  +    TR  +
Sbjct: 409 DISSQERFEMLRSF--------CNYGLSHWGSDERGVLTTRRFL 444


>gi|312880306|ref|ZP_07740106.1| tRNA-U20-dihydrouridine synthase [Aminomonas paucivorans DSM 12260]
 gi|310783597|gb|EFQ23995.1| tRNA-U20-dihydrouridine synthase [Aminomonas paucivorans DSM 12260]
          Length = 340

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 112/298 (37%), Gaps = 22/298 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              T    R F R L    L +TEM+ A  +    KK   +L     E PLA Q+ G D 
Sbjct: 29  AGITVPALRRFHRRL-GAGLAHTEMVSALGLAYRGKKTRELLTVLEGEGPLAAQLFGPDA 87

Query: 60  SKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             L E A++ +    +  + +N+ CP  +V     GA L+  PD     + + C AL +P
Sbjct: 88  PSLAEGARLTLAVHPFQALEINMACPMPKVARKGAGAALLERPDEAVRAVRS-CAALGVP 146

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + VK R+       A A     +++  +G   + +H R            R     D D 
Sbjct: 147 LWVKVRLL--PGGAATATARFCEALLDAGAAFLLVHGRTP--------GQRYEGTADRDA 196

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           V  + +  P L +G +G L     A   L      V++ R   K+  ++  + E    PL
Sbjct: 197 VCALARLYPGL-LGASGDLFTPEDARAYLEGGCASVLVARGLLKDPLLVPRILEELGFPL 255

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               P+     ++    +     D   R       L    R + G F G   +   RH
Sbjct: 256 ----PLGGEGRRNPREALLELGDDLFLRE-GERTALLLAKRMVAGWFRGGHGAAERRH 308


>gi|226330863|ref|ZP_03806381.1| hypothetical protein PROPEN_04784 [Proteus penneri ATCC 35198]
 gi|225201658|gb|EEG84012.1| hypothetical protein PROPEN_04784 [Proteus penneri ATCC 35198]
          Length = 244

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 98/263 (37%), Gaps = 33/263 (12%)

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G     L E A      G   ++LN GCPS  V+    GA L+  P+ +     AM
Sbjct: 1   MQLLGQHPQWLAENAFRAVSLGSWGVDLNCGCPSKTVNGSGGGASLLKQPETIYQATKAM 60

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PV+VK R+G D    +     +  ++ + G   I IH R          D  
Sbjct: 61  RDAVPSALPVSVKVRLGWD---SSAYSHEIADAVAQGGATEITIHGRTKE-------DGY 110

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
               +++  + +I++    + +  NG + +   AL  L     D +MIGR A     +  
Sbjct: 111 NAEKINWQAIGDIRQRL-SIPVIANGEIWNREDALACLATTGCDAIMIGRGAMNTPNL-- 167

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLF 284
                       S  +K    +  W+++   +  Y          +   +R       L 
Sbjct: 168 ------------SRVVKGIEARMPWQEVIELLKRYVRLEKRGDTTIYHASRIKQWFSYLR 215

Query: 285 HGFPNSRR-CRHILTVEAGASTA 306
             +P +    R I T++     A
Sbjct: 216 KEYPEADELFRQIRTLKTSPEIA 238


>gi|330919514|ref|XP_003298646.1| hypothetical protein PTT_09419 [Pyrenophora teres f. teres 0-1]
 gi|311328059|gb|EFQ93260.1| hypothetical protein PTT_09419 [Pyrenophora teres f. teres 0-1]
          Length = 578

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 99/265 (37%), Gaps = 50/265 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAI----------------------- 32
           MV+ ++  +R  +R     +     L YT M  +                          
Sbjct: 45  MVEQSEFAWRLLSRSFLPESQQKNLLAYTPMFHSKMFGEKSNYRDAHFQPLKSTVPSPVD 104

Query: 33  ------LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
                 LR   +++ G    ++PL +Q    D    + AAK V  F  + ++LN+GCP  
Sbjct: 105 DYHLSQLRDSDRHLDGNPAFDRPLTVQFCSNDPEDFLRAAKHVAPF-CDAVDLNLGCPQG 163

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
               G +GA L  +  ++   I  + + L +PVT K R+               K++  +
Sbjct: 164 IAKRGKYGAFLQEDWGLISSMIRKLHEELDVPVTAKMRVL----ETPEKTLAYAKTLLDA 219

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGL---EDMSQ 202
           G + I +H R+   KG            D+ ++  +++  P    I  NG +   ED++ 
Sbjct: 220 GASIITVHGRRREQKG------HNTGLADWKMIRYLRENLPKETVIFANGNILQHEDIAA 273

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLT 227
            L+     DGVM       +  +  
Sbjct: 274 CLEA-TGADGVMSAEGNLYDPTIFA 297


>gi|121595495|ref|YP_987391.1| dihydrouridine synthase [Acidovorax sp. JS42]
 gi|120607575|gb|ABM43315.1| tRNA-U20a,U20b-dihydrouridine synthase [Acidovorax sp. JS42]
          Length = 342

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 108/277 (38%), Gaps = 30/277 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       +E I V  ++L    K  L +  +           P+
Sbjct: 18  MEGLLDFVLRDVLTRVGGVDRCVSEFIRVTGSLL--PDKVFLRYIPELNHGGRTLAGVPV 75

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+ G+D   + E A  + + G   I+LN GCP+  V+    GA L+  P+ +   + A
Sbjct: 76  RAQLLGSDPVSMAENAARLAELGPEGIDLNFGCPAKTVNRHGGGAALLREPERIAAVVEA 135

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +PV+ K R+G DD   A   R   +++ + G   + +HAR        P   
Sbjct: 136 VRRAVPAHVPVSAKMRLGYDD---AGLARECAQAMARGGACELVVHARTKADGYRPPAYW 192

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
            +IP +         +E   + +  NG +  +  AL+   +   D +M+GR    +  + 
Sbjct: 193 EQIPAI---------REAVGIPVVANGEIWTVQDALRCRSVSGCDALMLGRGIVADPGLA 243

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKD--FWRKISASMTD 261
            ++  +         P +  +     FW  +   +  
Sbjct: 244 LSIRAHDRGAPALGLPWEDLLPHMARFWHLVCEDLEP 280


>gi|330967041|gb|EGH67301.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. actinidiae
           str. M302091]
          Length = 321

 Score =  162 bits (410), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHNGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHSIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVIKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVACPDLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWAELQPMLRTFWQACLVKMT-----LVQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNTLRRE 301


>gi|254369301|ref|ZP_04985313.1| Nif3 family protein [Francisella tularensis subsp. holarctica
           FSC022]
 gi|157122251|gb|EDO66391.1| Nif3 family protein [Francisella tularensis subsp. holarctica
           FSC022]
          Length = 242

 Score =  161 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 96/235 (40%), Gaps = 21/235 (8%)

Query: 84  PSARVHEGSF--GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           P A   + +F  GA L+ + + + + + A+ KA+  PVTVK RIG D+Q   +    + K
Sbjct: 18  PMAGFCDSAFRAGAALLKDVNRIHEILTAVVKAVHKPVTVKMRIGWDEQ--NINAIEVAK 75

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           + + +GV+ I IH R         ++       ++DI+ +++K   D  +  NG +    
Sbjct: 76  ACQDAGVSAIAIHGRT--------REQMYTGKANWDIIRDVRKAV-DTVVIGNGDVFCPH 126

Query: 202 QALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            A  ++    VD VM+GRA+  N  +   + EY +       P            +   +
Sbjct: 127 SAKAMMEHTGVDAVMVGRASRGNPWIFRQIAEYLNTGELIPPPTPVERVDVLGEHLRRLI 186

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
               A+       +++I  H        PNS+  R  L            ++E  
Sbjct: 187 KLKTAK-----VAVKEIRTHASFYLQDLPNSKEFRMKLNQLEH-EQEIFKVLEEY 235


>gi|237836529|ref|XP_002367562.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211965226|gb|EEB00422.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
          Length = 540

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 58/297 (19%), Positives = 100/297 (33%), Gaps = 79/297 (26%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----RGDKKNILGFSTQ--------- 46
           MVD ++  +R   R    + L YT M+ +   L     R      L  S           
Sbjct: 44  MVDASELAFRLLGRRYGVD-LAYTPMLHSRLFLDDSKYRALHWQTLRSSPSWTQASCSEE 102

Query: 47  -------------------------------------EKPLALQIGGADISKLVEAAKIV 69
                                                ++P+ +Q  G   + L+ AA++V
Sbjct: 103 EDVQEEEEGEEEEGEEGEREVSEGGRSQWTGDESQEFDEPVFVQFCGDSPATLLAAAQLV 162

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI---- 125
           ED     +++N GCP      G +GA L+  P+++ D ++ + K L  PVT K R     
Sbjct: 163 EDE-VEAVDVNFGCPQGIARRGHYGAFLLNEPELLVDIVSTLHKHLKTPVTCKMRKVSPR 221

Query: 126 -------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
                         +D++        L  + + +G   + IH R    K         + 
Sbjct: 222 NPRDALPRSEAALVLDEERRLQDTLRLCDAFEAAGCACLCIHGRTKEEK------AAFVG 275

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
             D+  +  +K+    + +  NG +E    AL+ L     D VM       N  +  
Sbjct: 276 PCDWLAIRHVKQRL-SIPVIANGAVETYEDALRCLEFTGADAVMSAEGLLDNPMLFA 331


>gi|289621184|emb|CBI51967.1| unnamed protein product [Sordaria macrospora]
          Length = 614

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 59/288 (20%), Positives = 107/288 (37%), Gaps = 59/288 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKN---------------- 39
           MVD ++  +R   R           L YT M  A       K                  
Sbjct: 57  MVDQSEFVWRMLTRSFLPTEEQHKLLCYTPMFHARLFTEAPKYRDSHYQPIRGPLTENSP 116

Query: 40  ----------ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
                     + G  + ++ L +Q    D S L+ AAK+V  +  + ++LN+GCP     
Sbjct: 117 RPGSPDYVPFLDGNPSIDRSLFVQFCANDPSYLLSAAKLVAPY-CDAVDLNLGCPQGIAK 175

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +G+ L  N +++ + I  + K L IPVT K RI         A     +++ ++G +
Sbjct: 176 RGQYGSFLQENQELIFELINTLHKELDIPVTAKIRIL----ETKEATLKYAQNVLRAGAS 231

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGL---EDMSQALK 205
            + +H R+   KG       +    +++ +  +++  P    I  NG +    D+ + L+
Sbjct: 232 ILTVHGRRREQKG------HQTGLANWEYIRYLRENLPKETVIFANGNILQYSDLEKCLE 285

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                DGVM       +  +                P      +++WR
Sbjct: 286 A-TGADGVMSAEGNLSDPGLFA------------KPPAVGEEGREYWR 320


>gi|330987411|gb|EGH85514.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 321

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++    +   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGTL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRAFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|219130876|ref|XP_002185580.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402988|gb|EEC42945.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 216

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 74/214 (34%), Positives = 114/214 (53%), Gaps = 11/214 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-------KNILGFS-TQEKPLAL 52
           M+  + R +R   R+L+   +L+TEM+V + +    +       +  LG+  T E P+  
Sbjct: 4   MLHVSTREFRQLFRILSKRVVLWTEMVVDELVYHNHEDRSNGTLETHLGYDDTNEHPVIC 63

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH-EGSFGACLMLNPDIVGDCIAAM 111
           Q+GG   S    A ++  + GY+EINLNVGCPS RV  +  FGA LM     +   + AM
Sbjct: 64  QLGGIVPSHTALATQLAVERGYDEINLNVGCPSDRVSGKREFGAVLMKQLSRLLLLVQAM 123

Query: 112 CK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            + A   P++VKCR+GVDD      L   V +++       ++HARK +L+ LSP  NR 
Sbjct: 124 RENAGDTPISVKCRLGVDDWDSWEVLEEFVDTLRPY-CRIFYVHARKCLLQVLSPAQNRL 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           +P L+Y  VY + +  PD    +NGG+  +  A 
Sbjct: 183 VPPLNYPRVYRLCERFPDCDFYINGGIPGLRAAK 216


>gi|289626961|ref|ZP_06459915.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289650795|ref|ZP_06482138.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330869806|gb|EGH04515.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 321

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRAFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|51598988|ref|YP_073176.1| histidine phosphokinase/phophatase, putative [Borrelia garinii PBi]
 gi|51573559|gb|AAU07584.1| histidine phosphokinase/phophatase, putative [Borrelia garinii PBi]
          Length = 329

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/270 (23%), Positives = 117/270 (43%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL   K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISVKGILNESKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D  +   A +I+   G+  I++N+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNDPEQFYRAIEILGGMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +   G++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVNDWLGFLLGFGIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 185 SEGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLT-TVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   +   +  + L     I     KDF 
Sbjct: 245 NLFKLSSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|327480372|gb|AEA83682.1| NifR3/Smm1 family protein [Pseudomonas stutzeri DSM 4166]
          Length = 324

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 55/313 (17%), Positives = 113/313 (36%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +       TE   +    + +     +         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRMGGVDWCVTEFIRVSDRLLPQSSFGKLAPELKNGALTRAGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L + A      G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPICLADNAAFACTLGAPAIDLNFGCPAKTVNKSRGGAVLLKEPELLHAILCEVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPVT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 SAVPAHIPVTAKMRLGFDSPDGAL---DCARALVAGGAEQLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +++  P + +  NG +  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARVQEIVP-VPVYANGDIWSLEDWRRCREVSGAEDIMLGRGLVSRPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIKT--RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +    +         +    V  DFW++    +        ++ G+L+Q    +  L   
Sbjct: 236 IAAAKAGQQIAPMSWEEFRPVLLDFWQQARGKIAP-----RYAPGRLKQW---LALLTRN 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVALFAELRR 300


>gi|297703228|ref|XP_002828550.1| PREDICTED: tRNA-dihydrouridine synthase 3-like [Pongo abelii]
          Length = 645

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 55/281 (19%), Positives = 104/281 (37%), Gaps = 36/281 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 321 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 379

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGAC-LMLNPDIVGDCIAAMCKALSIPVTV 121
           + A+++      + +++NVGCP   V++        +  P  V          L +P+TV
Sbjct: 380 KCAELLSRTVEVDFVDINVGCPIDLVYKKVAALDVCLGFPIWV----------LDVPLTV 429

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV +++       L+  ++  GV  + +H R         ++ R     D+  + E
Sbjct: 430 KIRTGVQERVNLA--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEE 479

Query: 182 IKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S
Sbjct: 480 CVQAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHWDISSS 539

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                         I    T+Y   H  S  +  + TR  +
Sbjct: 540 E----------RLDILRDFTNYGLEHWGSDTQGVEKTRRFL 570


>gi|302879006|ref|YP_003847570.1| dihydrouridine synthase DuS [Gallionella capsiferriformans ES-2]
 gi|302581795|gb|ADL55806.1| dihydrouridine synthase DuS [Gallionella capsiferriformans ES-2]
          Length = 309

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 115/289 (39%), Gaps = 32/289 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     L    L   E +      + +  +      +   G +    P+ +
Sbjct: 8   MEGLADPSLRDILTRLGGIDLCVAEFVRVTNHLLTEKFVLRTVPELDHGGCTPSGVPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A  +   G   I+LN GCP+  V+    GA L+  P+ +   +AA  
Sbjct: 68  QLLGSDPVCLAENAAFIASLGAPGIDLNFGCPAPTVNRHGGGAVLLAFPEQIHAIVAATR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G+ D    +      ++I+  G + I +HAR         + +  
Sbjct: 128 RAVPEGIPVTAKMRLGLSDTSLTL---ECARAIEAGGADEITVHART--------RSDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +E   L + +NG +        ++ +   + VM+GR       ++  
Sbjct: 177 RPPARWEWLSQI-REVVTLPMVVNGDVWTPEDGQNIRRVSGCEDVMVGRGVILRPDLMRR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
           + E        S         D++  + A M      H H+ G+L+Q  
Sbjct: 236 IKE---GGEAMSWEALRPWVLDYFDLLCARM-----EHRHAPGRLKQWM 276


>gi|207743024|ref|YP_002259416.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           IPO1609]
 gi|206594421|emb|CAQ61348.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           IPO1609]
          Length = 310

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 104/238 (43%), Gaps = 20/238 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P
Sbjct: 42  GCTASGTPMVIQLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLSTP 101

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   ++A+  A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 102 ELLHTIVSAVRAAVPANIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 156

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                 +D+   P   +D +  I  +  ++ +  NG +  ++   +   +   D VMIGR
Sbjct: 157 ------RDHGYRPPAHWDWIARIA-DAVEVPVIANGEVWTVADWERCRAVSGCDDVMIGR 209

Query: 218 AAYKNSAMLTTVDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            A  +  +   +       P     P+  R   D+ + + A +   AA H H   KL 
Sbjct: 210 GAVSDPFLAQRIRGQMERTPSNAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKLW 264


>gi|257485510|ref|ZP_05639551.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|331010686|gb|EGH90742.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 321

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/314 (19%), Positives = 118/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++    +   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGTL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRAFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|42522830|ref|NP_968210.1| nitrogen regulation protein nifR3 [Bdellovibrio bacteriovorus
           HD100]
 gi|39574026|emb|CAE79203.1| Nitrogen regulation protein nifR3 [Bdellovibrio bacteriovorus
           HD100]
          Length = 352

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/294 (20%), Positives = 114/294 (38%), Gaps = 26/294 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY---TEMIVADAI----LRGDKKNILGFSTQEKPLALQ 53
           MV  T    R   R            TEM+ +  I    L    + +   +  E  L  Q
Sbjct: 23  MVGLTHVALREVMRDYLPAEAYTIWPTEMLNSRRIPGENLEKTPETM--RAAYEPGLVPQ 80

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           I G +   + E+ K + ++G   I++N+GCP  +  + ++G  LM +P    + +    K
Sbjct: 81  ILGNEEDAIAESVKRLVEWGAEAIDINMGCPVQKALKHNYGVALMGDPAYAAEVVRMTVK 140

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             ++PV+VK R  V        L   V  +++SG   + +H R A  K        +  N
Sbjct: 141 NSTVPVSVKLRA-VGSTKEFDELLTFVSGLRQSGAAWVCLHPRTAAQK--------RRGN 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            D++ + ++ K   D  +  NG ++    A+ +L     D  M GR       M+  + E
Sbjct: 192 ADWEQIKQLHKAV-DFPVIGNGDVQTYDDAINMLKETGCDMAMAGRGLAARPWMMWQLGE 250

Query: 232 YF-----SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
                  +      +P  +  +   + K    + D    +      ++++  ++
Sbjct: 251 ELGFAPPAGKEGQKAPRTSEEEGAEYGKCLLRLIDRCRFYFGEDLAMRKVRFYV 304


>gi|325265681|ref|ZP_08132370.1| tRNA-dihydrouridine synthase C [Kingella denitrificans ATCC 33394]
 gi|324982812|gb|EGC18435.1| tRNA-dihydrouridine synthase C [Kingella denitrificans ATCC 33394]
          Length = 330

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 50/273 (18%), Positives = 107/273 (39%), Gaps = 24/273 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       +E +       + A        I     +    P  +
Sbjct: 18  MQGLCDFVMRDLLTRIGGYDECVSEFVRITHTVHSRATWLRHVPEIATANKTHAGIPCVV 77

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +V+ A +    G ++I+LN GCP+  V++   GA L+  P+ +   ++A+ 
Sbjct: 78  QMLGSDAEMMVKNALVAVGLGAHQIDLNFGCPAPTVNKHQGGAVLLQTPERIYHIVSAIR 137

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   IP++ K R+G +++  A+       +I ++G + + +HAR  I           
Sbjct: 138 QGVPEHIPISAKMRLGFENKDLALEN---ADAIAQAGASVLTVHARTKIEGYR------- 187

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +  V +I++    + +  NG +  +     ++     D VM+GR A     +   
Sbjct: 188 -PPAHWGWVDKIRRHV-AIPVIANGDVFCLQDYIDIRAQSGCDDVMLGRGAVMRPDLARQ 245

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           + +Y       ++     +     + I   +  
Sbjct: 246 IRQYLRGEEVQAALFDDEIIVWIAQFIELCLQH 278


>gi|152987650|ref|YP_001347379.1| hypothetical protein PSPA7_2003 [Pseudomonas aeruginosa PA7]
 gi|150962808|gb|ABR84833.1| conserved hypothetical protein [Pseudomonas aeruginosa PA7]
          Length = 319

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 111/288 (38%), Gaps = 27/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I + D +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRVGGIDWCVTEFIRITDRLLPATAFHKLAPELRDGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +AA+ 
Sbjct: 68  QLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 RAVPGETPVTSKMRLGYDSPDGAL---DCARALADGGSVHVVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +  E   + +  NG +  +   L+      V+ +M+GR       +   
Sbjct: 177 KPPAHWEWVARVA-EAVRVPVFANGEVWTLDDYLRCREISGVEDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD-YAARHLHSGGKL 273
           +  +         P      + +DFW +    +   YA   L     +
Sbjct: 236 IAAWRDGGEIREMPWSELLPLLRDFWLQARRKLAPRYAPGRLKQWLGM 283


>gi|255725686|ref|XP_002547772.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
 gi|240135663|gb|EER35217.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
          Length = 252

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 93/226 (41%), Gaps = 22/226 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-------GDKKNILGFSTQEKPLALQ 53
           MVD ++  +R  +R     AL YT M  A               K + G    ++PL +Q
Sbjct: 37  MVDHSELAWRILSRRY-GAALCYTPMFNAKLFATQEKYRDSMWTKGLDGNEKLDRPLVVQ 95

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
               D   L+ AA+ +ED   + +++N+GCP     +G +GA LM + +++   I  +  
Sbjct: 96  FCANDPDYLLTAARFIEDQ-CDAVDINLGCPQGIARKGRYGAFLMDDWELIHKLIRNLHD 154

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L IPVT K RI  D            K +  +G   I IH R   +KG      +K   
Sbjct: 155 NLKIPVTAKIRIYDD----YEKSLEYAKMVLDAGAQFITIHGRTREMKG------QKTGL 204

Query: 174 LDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
            ++ I+  ++   P D     NG +   S   +       D VM  
Sbjct: 205 ANWKILKYLRDNLPKDQVFFANGNILYPSDLKRCEEQIECDAVMSA 250


>gi|325849659|ref|ZP_08170862.1| dihydrouridine synthase (Dus) [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325480000|gb|EGC83078.1| dihydrouridine synthase (Dus) [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 220

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 42/208 (20%), Positives = 88/208 (42%), Gaps = 19/208 (9%)

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
           +  +   G+ LM NP +V +    + K+    + +K R+G+DD+   +   ++ K  + +
Sbjct: 3   KSQKNGEGSQLMANPKLVEEICKTLRKSTDKKLNIKFRLGIDDK--HINYLDIGKIAQDT 60

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G++ + +HAR         KD     + ++D + ++K EN  + +  NG +  +   +K+
Sbjct: 61  GIDYVILHART--------KDQMYSGHANWDHIRKLK-ENLQIPVIANGDIFSVEDFIKV 111

Query: 207 --LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
             L   DGVM+ R A  N  +   + +Y              VD+   +           
Sbjct: 112 IDLTKADGVMLARGAMGNPFLFKEIKDYIKTGNYNKPSPIEIVDQLIDQYKLE------L 165

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRR 292
           ++      + Q+ +H+     G  NS +
Sbjct: 166 KYKEEKLVVTQMRKHLSWYIKGLENSSK 193


>gi|50294732|ref|XP_449777.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49529091|emb|CAG62755.1| unnamed protein product [Candida glabrata]
          Length = 344

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 104/235 (44%), Gaps = 14/235 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R  +  I   +T   + PL +Q+G  +
Sbjct: 37  MVRYSKLPFRQTCRQYDTD-IVYTPMILAREFVRNQQARIADLTTNKNDTPLIVQVGVNN 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++ A++V  F  + I +N GCP         G  L+ NPD++ + + ++       
Sbjct: 96  VGDLMKFAEMVAPF-CDGIGINCGCPIREQIREGIGCALIYNPDLLCEMVKSVKSKYGAK 154

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I + D        NL + +  SGV+ I IH R    +   P +   I      I
Sbjct: 155 LRLETKIRIHDDWDVTV--NLCRRLCDSGVDWITIHGRTRTTRSSQPVNLEAIKY----I 208

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           V +IK +N  + +  NG    M     I     V GVM  R    N A+    D+
Sbjct: 209 VDKIKDKN--VPVVANGDCFTMKDFKHISDYTGVQGVMAVRGVLANPALFAGHDK 261


>gi|240274458|gb|EER37974.1| dihydrouridine synthase [Ajellomyces capsulatus H143]
          Length = 545

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 105/315 (33%), Gaps = 68/315 (21%)

Query: 11  FFARLLTNNA------LLYTEMIVADAILRGDKKNILGFSTQ------------------ 46
              R   N        L Y+ M  +          +  F                     
Sbjct: 1   MLTRSFMNPDSDSPPLLAYSPMFHSRLFKESPNYRLQHFEATRPRSKTPTTPAANGIDGG 60

Query: 47  ----------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
                           ++PL +Q    +   L++AA+ VE F  + ++LN+GCP     +
Sbjct: 61  APQSNTVPYLDGNPSFDRPLIVQFCANNPDDLLQAARAVEPF-CDAVDLNLGCPQGIARK 119

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G +GA L  +PD++ + I  +   LSIPVT K RI    Q          + I  +G + 
Sbjct: 120 GHYGAFLQEHPDLIYELINTLHTQLSIPVTAKFRI----QETKEKTLEYARIILSAGASI 175

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL-- 207
           I +H R+   KG            D+  +  +++  P D  I  NG + +     K L  
Sbjct: 176 ITVHGRRREQKG------HNTGLADWSYIRYLRENLPADTVIFANGNILNHGDIEKCLEA 229

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              DGVM    +  +  + +              P  + V     R       +Y     
Sbjct: 230 TGADGVMSAEGSLCDPTIFSG------------PPPPSSVGGSGMRGERRDGAEYWVGRD 277

Query: 268 HSGGKLQQ--ITRHM 280
             GG      + R+M
Sbjct: 278 GKGGYRVDFVLRRYM 292


>gi|119510895|ref|ZP_01630018.1| transcriptional regulator [Nodularia spumigena CCY9414]
 gi|119464423|gb|EAW45337.1| transcriptional regulator [Nodularia spumigena CCY9414]
          Length = 339

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 105/250 (42%), Gaps = 17/250 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           M D T+  +        +    +TE    +   R ++  +   +  +  +P+  Q+ G  
Sbjct: 22  MQDVTNLWFMKVIAHYGSPDYFFTEYFRVNDTSRLNRSILAAITENDTGRPVFAQMIGES 81

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
           I  LV  AK +  +    ++LN+GCP+ R++  + G  L+L+P+ V   +A + + +   
Sbjct: 82  IPDLVRTAKELCGYNIAGVDLNMGCPAPRIYRKNVGGGLLLSPEKVDRILAELRQTVNDR 141

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+TVK R+G ++         ++  I +  ++ + +H R           +     + YD
Sbjct: 142 PLTVKMRLGFENTD---TFYEILDIINRHSIDLLSLHGRTVK--------DMYHGAVKYD 190

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E  +      +  NG +     AL++L      GVM+GR A  N  +   + +    
Sbjct: 191 LIAEAVRRV-QCPVLANGNIHSAKTALEVLSQTGAAGVMVGRWAIGNPWLFNQIRQALRF 249

Query: 236 PLTGSSPIKT 245
                 P+  
Sbjct: 250 EPITPVPLVE 259


>gi|195031103|ref|XP_001988289.1| GH11083 [Drosophila grimshawi]
 gi|193904289|gb|EDW03156.1| GH11083 [Drosophila grimshawi]
          Length = 398

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 68/320 (21%), Positives = 126/320 (39%), Gaps = 39/320 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   R      L +T M+++D+I   +K     F+    ++PL  Q    D
Sbjct: 29  MVRYSKLEFRRLLRQ-NGVQLAFTPMMISDSINNSEKARQNEFTTGPDDQPLIAQFAAKD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI- 117
            ++ V +A+++  +  + I+LN GCP +      +G  L+  PD + D I  + + L   
Sbjct: 88  ATEFVTSAQLIYPY-VDGIDLNCGCPQSWAIAKGYGCGLLRQPDQMRDMIQCLRRTLPTG 146

Query: 118 -PVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             V+VK R   G D  I       L + ++  GV  + +H R    K            L
Sbjct: 147 FSVSVKMRLLQGSDSDISLQKTIQLAQQLEHCGVTFLTLHGRTPAQKH-------SKDTL 199

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           +   + ++ +    + + +NG +E    A ++       GVM  R    N A+  +    
Sbjct: 200 NVAAMADVAQSL-QIPLIVNGNVESYRDACELHANTQAAGVMAARGLLANPALFNS---- 254

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
              PL  ++P   +     W  I+ S    A   LH       +T   +        S  
Sbjct: 255 -DYPLAETTP---KSCVQQWLDIAQS----AGERLHFQCFHHHLT--FMW-------SSE 297

Query: 293 CRHILTVEAGASTATHHIIE 312
            +  L V+  +  +   ++E
Sbjct: 298 MKRALRVQFNSLGSKSQVLE 317


>gi|170095681|ref|XP_001879061.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164646365|gb|EDR10611.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 632

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 108/295 (36%), Gaps = 33/295 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +   EM +A++ L G  ++ +++     E    +Q+ G   + LV
Sbjct: 272 NLPFRRLCVQL-GAEITCGEMGLANSFLAGSKEEWSLVRRHPSESIFGVQVAGNKPANLV 330

Query: 64  EAAKIVEDFGY---NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
             A+++        + +++N GCP   V     G+ L+     +G  +  M KAL  IPV
Sbjct: 331 PTAEVIAKECAGGIDFVDVNCGCPIDLVFRTGSGSALLDTVGKLGKILIGMNKALGEIPV 390

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIK-KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R GV D         L+  +  +     I +H R         +  R     D+D 
Sbjct: 391 TVKLRTGVKDGKNTA--HKLMPRLSTEWNAGCITLHGRT--------RQQRYTKLADWDY 440

Query: 179 VYEIKKEN---------PDLFIGLNGGLED-MSQALKIL-PSVDGVMIGRAAYKNSAMLT 227
           + E  +           P + I   G           +    VDG+M+GR A     + T
Sbjct: 441 IKECVRAVRAQEADEDLPPVPIFGGGDCFSSYDYWTNVENTGVDGIMVGRGALIKPWIFT 500

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI 281
            + E     ++    ++   +       +    +Y   H  S    +    R++ 
Sbjct: 501 EIKERREWDISARERLELIRNASGS---ALFYAEYGLNHFGSDTAGVNATRRYLC 552


>gi|88857879|ref|ZP_01132521.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas tunicata D2]
 gi|88819496|gb|EAR29309.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas tunicata D2]
          Length = 311

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 94/242 (38%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M    D   R     L    L  TE I V D +L           +   G +    P+ +
Sbjct: 1   MEGVVDFQMRQLLTDLGGFDLCVTEFIRVVDQLLPPRVFYRYCAELNQAGLTRSGTPVRI 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   L E A    + G + ++LN GCP+  V +   GA L+  P+++   + A+ 
Sbjct: 61  QLLGQDPDWLSENAVRAVELGSHGVDLNFGCPAKAVMKNKGGAVLLKEPEVIYQIVKAVR 120

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     VT K R+G DD   +  + +   ++  +  + I IHAR        P    K
Sbjct: 121 DAVPAHHEVTAKVRLGFDDDSLSQEIFD---AVVSAKASSIAIHARTKKDGYRPPAYWEK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
           I  L         K + +L    NG +  +      KI    D VM+GR A     +   
Sbjct: 178 IKPL---------KNSSNLKTIANGEVWSVEDYTLCKIRSGCDDVMLGRGALAQPDLAKQ 228

Query: 229 VD 230
           + 
Sbjct: 229 IK 230


>gi|213027525|ref|ZP_03341972.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 160

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 64/160 (40%), Positives = 90/160 (56%), Gaps = 12/160 (7%)

Query: 129 DQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DQ     L + + ++   G      IHARKA L GLSPK+NR+IP LDY  VY++K++ P
Sbjct: 11  DQDSYAFLCDFINTVSGQGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFP 70

Query: 188 DLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD-EYFSNPLTGSSPIKTR 246
            L + +NGG++ + +A + L  +DGVM+GR AY+N  +L  VD E F    T + P+   
Sbjct: 71  HLTMSINGGIKSLEEAKEHLRHMDGVMVGREAYQNPGILAAVDREIFGADTTDTDPV--- 127

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                   +  +M  Y  R L  G  L  ITRHM+GLF G
Sbjct: 128 -------AVVRAMYPYIERELSQGAYLGHITRHMLGLFQG 160


>gi|167519230|ref|XP_001743955.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163777917|gb|EDQ91533.1| predicted protein [Monosiga brevicollis MX1]
          Length = 328

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 93/231 (40%), Gaps = 21/231 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
           MV ++   +R   R      L YT MIVAD+  +        F T E  +PL  Q    +
Sbjct: 30  MVRYSRLAFRRTVRK-HGIDLAYTPMIVADSFTKSQWAREADFHTAEDDRPLVAQFAANN 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
              L  A +++  +  +   LN GCP     +   G  L LNPD + D +     A+   
Sbjct: 89  GPVLAHAVELMAPY-ADAFCLNCGCPQRWAIQDGLGCALTLNPDAMVDLVRHARAAVPHH 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK RI    +  A     LV+  +  G   I +H R    +            + YD
Sbjct: 148 PVSVKVRI----RDTAAETVELVRRAEAMGAAWISVHGRTPAERHQ---------PVHYD 194

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           ++  +K ++  + +  NG +  +  A ++      DG+M  R    N  + 
Sbjct: 195 MLKLVK-DSVSVPVVANGDIFTLKDADRVWNETGCDGIMAARGLLANPGLF 244


>gi|207724169|ref|YP_002254567.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           MolK2]
 gi|206589379|emb|CAQ36341.1| trna-dihydrouridine synthase c protein [Ralstonia solanacearum
           MolK2]
          Length = 315

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 115/287 (40%), Gaps = 31/287 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M D+     R             +E + V  ++L               G +    P+ +
Sbjct: 1   MADF---VMRDVLTRAGGYDGCVSEFVRVTGSLLPARFYERETPEIRNGGCTASGTPMVI 57

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L   A        + I+LN GCP+  V+    GA L+  P+++   ++A+ 
Sbjct: 58  QLLGSDPVWLARNAAQAATISPHGIDLNFGCPAKVVNRHGGGAMLLSTPELLHTIVSAVR 117

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 118 AAVPANIAVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART--------RDHGY 166

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I  +  ++ +  NG +  ++   +   +   D VMIGR A  +  +   
Sbjct: 167 RPPAHWDWIARIA-DAVEVPVIANGEVWTVADWERCRAVSGCDDVMIGRGAVSDPFLAQR 225

Query: 229 VDEYFS-NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       P     P+  R   D+ + + A +   AA H H   KL 
Sbjct: 226 IRGQMERTPSDAEWPLVLRYLVDYLKMLHARI---AACHEHGRVKLW 269


>gi|94501272|ref|ZP_01307793.1| hypothetical protein RED65_02629 [Oceanobacter sp. RED65]
 gi|94426543|gb|EAT11530.1| hypothetical protein RED65_02629 [Oceanobacter sp. RED65]
          Length = 321

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 98/242 (40%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILGFS------TQEKPLAL 52
           M    D H R             TE   +    +     + I   S          P+ L
Sbjct: 8   MEGLVDVHMRTLLTRGGYFDYCVTEFLRVTTQLLPERSFRRICPESDHQWKTPAGTPVHL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   + E A    + G   +N+N GCPS  V+    GA L+  PD +   + ++ 
Sbjct: 68  QLLGSDPVAMAENACRAAELGAPVVNINFGCPSRFVNGRCGGAYLLQFPDQIHTILESVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           KAL   +P+T K R+G  D   A+A     ++++ +GV  I IHAR  +           
Sbjct: 128 KALPEHVPLTAKMRLGFKDDALALAN---AQAMESAGVRDICIHARTKVQGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +  +  IK++   + I  NG + +     A K     + VM+GR A  +  +  T
Sbjct: 178 -PPAHWHQIKNIKQQV-KVPIIANGEIWNRRDYEACKAASHCEHVMLGRGAVADPELAAT 235

Query: 229 VD 230
           + 
Sbjct: 236 IK 237


>gi|312075878|ref|XP_003140612.1| hypothetical protein LOAG_05027 [Loa loa]
 gi|307764220|gb|EFO23454.1| hypothetical protein LOAG_05027 [Loa loa]
          Length = 463

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 62/327 (18%), Positives = 118/327 (36%), Gaps = 41/327 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R      L ++ MI A   +          ST   ++PL +Q    D
Sbjct: 51  MVDQSELAFRMMLRK-HGAHLCFSPMIHAQLFITDATYRRTALSTSLDDRPLIVQFCAND 109

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ A ++VE F  + ++LN+GCP      G +GA L  +  ++ + +A +   L +P
Sbjct: 110 PVTLLTACQLVESF-CDGVDLNLGCPQLIAKRGHYGAYLQEDQKLICEMVALLHSRLQLP 168

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K RI  +          LVK    +G   + +H R    +G            D+  
Sbjct: 169 LSCKIRILQNINETIAYAVALVK----AGACMLTVHGRTREQRG------PNTGLADWYA 218

Query: 179 VYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  +     D+ +  NG ++   D+ + L+I      +M       N  +          
Sbjct: 219 MRAVVNAV-DVPVLANGNIQLPGDVDRCLEI-TGASAIMSAEGILSNPYLFEK------- 269

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                   +  V+    R+       Y +        L +I  H +  +         R 
Sbjct: 270 --------RHEVNWTAAREYLDFAERYESTISAVRAHLFRICHHSLLEY------SDLRE 315

Query: 296 ILTVEAGASTATHHIIETAFNLMIESL 322
            L+         H I++     + +S+
Sbjct: 316 RLSYVCSMKG-FHQIVDDLEERVFQSV 341


>gi|170592763|ref|XP_001901134.1| PP3111 protein [Brugia malayi]
 gi|158591201|gb|EDP29814.1| PP3111 protein, putative [Brugia malayi]
          Length = 513

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 93/231 (40%), Gaps = 19/231 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R      L ++ MI A   +          ST   ++PL +Q    D
Sbjct: 67  MVDQSELAFRMMLRK-HGAHLCFSPMIHAQLFVTDATYRRTALSTCLDDRPLVVQFCAND 125

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+ A ++VE F  + ++LN+GCP      G +GA L  +  ++ + I  +     +P
Sbjct: 126 PVILLNACQLVESF-CDGVDLNLGCPQLIAKRGHYGAYLQEDLKLICEMITLLHSHSRLP 184

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K RI  D            +++ K+G   + +H R    +G            D+  
Sbjct: 185 LSCKIRILQDINETVA----YARALVKAGACMLTVHGRTREQRG------PNTGLADWYA 234

Query: 179 VYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAML 226
           +  +     D+ +  NG ++   D+ + L+I      +M       N  + 
Sbjct: 235 MRAVVSAV-DVPVLANGNIQLPGDVDRCLEI-TGASAIMSAEGILSNPYLF 283


>gi|226355126|ref|YP_002784866.1| tRNA-dihydrouridine synthase [Deinococcus deserti VCD115]
 gi|226317116|gb|ACO45112.1| putative tRNA-dihydrouridine synthase [Deinococcus deserti VCD115]
          Length = 346

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 117/326 (35%), Gaps = 35/326 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGA 57
           M  ++D   R  A          +EMI A  ++ G     L        E    +Q+ GA
Sbjct: 32  MAGYSDAPLRQLAAE-QGALWTVSEMISARGLVLGGDSENLSLGRPFEGETNRVVQLFGA 90

Query: 58  DISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +   L  A + VE  F    I+LN+GCP  ++     GACL+  P++  + I AM  A +
Sbjct: 91  ESELLARAVQKVEAWFAPAAIDLNMGCPVPKIRGKG-GACLLQTPEVAFELIQAMKAATT 149

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V+ K R+G D          + + +  +GVN I +H R            R     D+
Sbjct: 150 LDVSAKIRLGWDHDRSV----EVAQGLAAAGVNLITVHGRT--------SAQRYTGEADW 197

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + +  +        +G  G +   +QA       V  VMIGR A  N  +   +      
Sbjct: 198 EAIARVAAAVDVPVVGS-GDIRSAAQARARQALGVAAVMIGRGAVGNPWLFRALAT--GG 254

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               S+  + R         +    D   R       L+ + + +       P+    R 
Sbjct: 255 DQYPSAQERARTALRHAELQTRFYDDNTGR-----LTLRPLRKVLPQY---LPDHPELRD 306

Query: 296 ILTVEAGASTATHHIIETAFNLMIES 321
            L      +      +E A   ++ S
Sbjct: 307 DLVQVVTLAD-----VERALAPLLTS 327


>gi|221217908|ref|ZP_03589375.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           72a]
 gi|221192214|gb|EEE18434.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           72a]
          Length = 329

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYCVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|300122290|emb|CBK22863.2| unnamed protein product [Blastocystis hominis]
          Length = 516

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 59/288 (20%), Positives = 106/288 (36%), Gaps = 31/288 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM +   +L        +L     E+   +QI    +    
Sbjct: 169 NLPFRRICVEL-GADITCSEMAMCGNLLHSCASEWALLRRHPSEQCFGVQITTGKVEDAG 227

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTV 121
              +++   G  + ++LN GCP   V +   GA L+     +   +  M  +L ++P+ V
Sbjct: 228 YVCELLRREGTVDFVDLNAGCPIDAVEKAGAGAGLLTKVGRLKRIVRCMLGSLENVPLMV 287

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           K R G  +      +  L +     G  V+G+ IH R         K  R   + D++ +
Sbjct: 288 KVRTGDHENTSHRLVPQLQRIRGNRGNRVSGVIIHGRT--------KQGRYTKSADWEYI 339

Query: 180 YEIKK----ENPDLFIGLNGGLEDMS-QALKILPSV-DGVMIGRAAYKNSAMLTTVDEYF 233
               K    + P L +  NG + D      ++   V DG+MIGR A     + T + E  
Sbjct: 340 KACAKSQDADLPRLQVIGNGDVFDNEDYWNRMEDGVLDGIMIGRGALIKPWICTEIKERR 399

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              ++    +          +I     DY   H  S  +    TR  +
Sbjct: 400 HWDISAGERL----------EIVKRFCDYGLEHWGSDAQGVDRTRRFL 437


>gi|254445896|ref|ZP_05059372.1| Dihydrouridine synthase superfamily [Verrucomicrobiae bacterium
           DG1235]
 gi|198260204|gb|EDY84512.1| Dihydrouridine synthase superfamily [Verrucomicrobiae bacterium
           DG1235]
          Length = 352

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 109/284 (38%), Gaps = 21/284 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE--MIVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D TDR +              TE   +   + L       +  +   +P+  Q+ G D
Sbjct: 29  MQDVTDRPFMAVIANCGAPDYFVTEYFRVHVQSRLEKHILEAVTENETGRPVFAQMIGED 88

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           I  L   AK ++      ++LN+GCP+  V++   G  L+ +P  +   + A+ + +   
Sbjct: 89  IHHLTRTAKDLQSHPIAGVDLNMGCPAPTVYKKHCGGGLLRDPQKIDQVLGALRQTIPGL 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TVK RIG ++      + +LV   +   V+ + +H R       S         + YD 
Sbjct: 149 FTVKMRIGFENTENFETILDLVNKHQ---VDLLSLHGRTVKEMYRS--------EVHYDF 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +     E  +  +  NG +   ++A +IL      GVM+GR A +N  +   + E     
Sbjct: 198 IKR-AAERINCPLLANGDVTSAAKARQILDYTGAAGVMVGRHAIRNPWIFRQIRE----- 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
                P+         R +          H     ++ ++ +++
Sbjct: 252 DQAGLPVSKISLNQVNRYVKDLYAAVERPHAPEQAQVNKMKKYL 295


>gi|258621727|ref|ZP_05716758.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM573]
 gi|258585958|gb|EEW10676.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM573]
          Length = 326

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 117/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +     TE + V + +L       L         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNQLLPDHVFYRLCPELQHGSKTPAGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPQWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPEHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +          ++    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHTAMPWHEVV----------ELLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANDLFGEL 294


>gi|212634541|ref|YP_002311066.1| NifR3/Smm1 family protein [Shewanella piezotolerans WP3]
 gi|212556025|gb|ACJ28479.1| NifR3/Smm1 family protein [Shewanella piezotolerans WP3]
          Length = 311

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/287 (19%), Positives = 115/287 (40%), Gaps = 26/287 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +    L+ TE +  V   +       I       G +    P+ +
Sbjct: 1   MEGVVDDLMREILSAINPYDLMVTEFVRVVDQLLPEKVFYRICPELKTNGETASGTPVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   +++N GCP+  V+  + GA ++  P+ + + + AM 
Sbjct: 61  QLLGQEPGWMAENAIRAIEMGSKGVDVNFGCPAKMVNRSNGGAVMLQYPEQLYNVVKAMR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+    PVT K R+G +D+          ++I ++G + + +HAR  +           
Sbjct: 121 EAVPEQHPVTAKIRLGFNDKSLY---MENAQAIYEAGASELAVHARSKVDG--------Y 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  + P + +  NG + ++  A +   L   D +M+GR A     +  +
Sbjct: 170 KPPAYWEYITDINAKLP-IPVIANGEIWNVDDARRCMELTGCDSIMVGRGAISLPNLAAS 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           +      P T    +   ++      ++   T Y AR       L +
Sbjct: 229 IKGA--APYTWQQSLALMLEYTNRELVARKSTYYPARIKQWFNYLNR 273


>gi|42522835|ref|NP_968215.1| dihydrouridine synthase family protein [Bdellovibrio bacteriovorus
           HD100]
 gi|39574031|emb|CAE79208.1| Dihydrouridine synthase family protein [Bdellovibrio bacteriovorus
           HD100]
          Length = 323

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 50/280 (17%), Positives = 107/280 (38%), Gaps = 26/280 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     L       TE +        +++   +   +     +    P+ +
Sbjct: 8   MEGVVDWVMRDTLTRLGGIDQCVTEFLRVTDRLHPESVFYKNCPELKTGSRTRWGTPVFV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L   A+     G   ++LN GCP+  V+    GA L+ + D V + +  + 
Sbjct: 68  QLLGGQAEPLALNAQRAVKLGALGVDLNFGCPAKTVNRHDGGASLLKSCDRVFNIVDTVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           KA+   +PVT K R+G DD    +    + ++++++    + +H R         K +  
Sbjct: 128 KAVPADVPVTAKIRLGFDDPTKCL---EIAQAVEEANATWLTVHCRT--------KTDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D + +IK++   + +  NG + +++   +   +   +  MIGR    N  + + 
Sbjct: 177 KPPAYWDWIPKIKEKT-KIKLIANGEIWNVADFNRCVEVTQCEDYMIGRGVMSNPFIFSQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
           + +  +        +     +    +   S T Y   +  
Sbjct: 236 IKQSLNQQ--PVEDMSWERARPLLPQFFESSTLYINDYFA 273


>gi|225712694|gb|ACO12193.1| tRNA-dihydrouridine synthase 4-like [Lepeophtheirus salmonis]
          Length = 301

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 104/238 (43%), Gaps = 25/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST---QEKPLALQIGGA 57
           MV ++   +R    L     + ++ MI+AD+ +   +     F++   ++ PL +Q    
Sbjct: 16  MVRYSKLPFRRLI-LSHGADVAFSPMILADSFVSSSEARDNEFTSDPKEDHPLVVQFAAN 74

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            +   V+A+ +V  +    ++LN GCP +   +   GA L+  P+ + D + +    +  
Sbjct: 75  KVQDFVDASVLVAPY-AEGVDLNCGCPQSWALKEGIGASLLQKPEFICDVVKSTKSVIPY 133

Query: 118 P---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           P   V+VK R+  D +         +  ++ SGV+ I +H R                 +
Sbjct: 134 PDFSVSVKIRLHRDKRRTID-----LCKVENSGVDFITVHGRTKDQHS---------DPV 179

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
           D + V  IK +   + +  NG ++ +  A ++  +  VDGVM  R   +N AM    D
Sbjct: 180 DLEGVKMIK-DALSIPVVANGDIKSLDDAYRVREVTGVDGVMAARGLLENPAMYAGFD 236


>gi|115397477|ref|XP_001214330.1| tRNA-dihydrouridine synthase 1 [Aspergillus terreus NIH2624]
 gi|114192521|gb|EAU34221.1| tRNA-dihydrouridine synthase 1 [Aspergillus terreus NIH2624]
          Length = 536

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 94/280 (33%), Gaps = 50/280 (17%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R           L Y+ M  A             F            
Sbjct: 46  MVDRSEFAWRMLTRSFMTPEEQKQLLAYSPMYHARLFREQLSFRQQHFHPTRAAVGKDDD 105

Query: 47  ----------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
                     ++PL +Q    +    +EAA+ V  +  + ++LN+GCP      G +G+ 
Sbjct: 106 APYLDGNPAIDRPLFVQFCANNPDDFLEAAQHVAPY-CDAVDLNLGCPQGIAKRGHYGSF 164

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           L  + D++   I  +   L IPVT K RI               K I  +G + I +H R
Sbjct: 165 LQEDWDLIYKLINKLHTELPIPVTAKFRIL----ESKEKTLEYAKMILSAGASIITLHGR 220

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGV 213
               KG            D+  +  ++    P+  I  NG   +     + L     DGV
Sbjct: 221 TREQKG------HNTGVADWSYIRYLRDNLPPETVIFANGNNLNHDDLERCLEATGADGV 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           M       + A+ +              P      +D+WR
Sbjct: 275 MSAEGNLSDPAIFS------------KPPPIGSEGRDYWR 302


>gi|254579030|ref|XP_002495501.1| ZYRO0B12826p [Zygosaccharomyces rouxii]
 gi|238938391|emb|CAR26568.1| ZYRO0B12826p [Zygosaccharomyces rouxii]
          Length = 348

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 102/237 (43%), Gaps = 20/237 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R     +  FST   + PL +Q+G  +
Sbjct: 41  MVRYSKLPFRQVCRQYDTD-IVYTPMILAREFVRNPHARLADFSTNSSDSPLMVQVGTNN 99

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++  ++V  +  + I +N GCP         G  L+ N +++   + A+ +     
Sbjct: 100 VMDLLKFVEMVAPY-CDGIGINCGCPIKEQVREGIGCALIYNRELLCSMVKAVKEKYGDL 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I + +         L + +  +GV+ I IH R         K+ R     +++ 
Sbjct: 159 VRLETKIRIHEDWDQTV--KLCRDLCSAGVDWITIHGRT--------KNTRSSHTANFEA 208

Query: 179 VYEIKKENPD--LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +  +     D  + +  NG     ED+ + +  +   DGVM  R    N A+ +   
Sbjct: 209 IRYVVDRIRDKQVPVVANGDCLQSEDVQK-IAEITGADGVMAVRGVLSNPALFSGFK 264


>gi|313235191|emb|CBY25064.1| unnamed protein product [Oikopleura dioica]
          Length = 286

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/284 (19%), Positives = 108/284 (38%), Gaps = 34/284 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  + ++ M+++D+ +         L  + ++ PL +Q     
Sbjct: 1   MVRYSRLPFRALCRKF-NVDVCFSPMLISDSFINSASARDADLRSNAEDGPLVVQFAANK 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                + A+++       I+LN GCP   V+  ++G  LM  P+++ D +    +A+   
Sbjct: 60  GEDFAKVAQMLYGH-CEGIDLNCGCPQRWVNALNYGDILMKQPELLADIVLQARRAIPDS 118

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              ++VK R+  D          + + I+K+G   + IH R             +   + 
Sbjct: 119 EFSISVKTRVFDDLH----TTIEMARRIEKAGATMLSIHGRT---------HGERDHPVR 165

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + +  I  E   + +  NG +     A        V GVM+ R    N  +    D   
Sbjct: 166 IETISTIV-ETLSIPVNYNGSIRTREDAQLAYESTGVGGVMVARGLLHNPGLFD--DRRL 222

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            +P          V  ++ +        Y++ H H    L ++T
Sbjct: 223 GDP---------EVLTEWTKIALELGIPYSSYHKHLMYMLDKVT 257


>gi|31789402|gb|AAP58518.1| hypothetical protein [uncultured Acidobacteria bacterium]
          Length = 355

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/280 (19%), Positives = 103/280 (36%), Gaps = 26/280 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  YR     L    +  +EM +A  + +       ++     E    +Q+ G  
Sbjct: 4   MTKGSNLPYRRLCVEL-GARITVSEMTLARRLKQKRNSEFALIRRFPGEPCFGVQLAGNK 62

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
             +   AA +VE  G + +++N GCP         GA +   P  +   + A+  ++ +I
Sbjct: 63  PDETAWAAALVESRGADFVDINFGCPIDYFTRKGLGASIGRQPQRMRRLVEAIKGSVTNI 122

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PVT K R+G +D           ++    G   +++H R         ++ R     D+D
Sbjct: 123 PVTAKIRLGWNDDDRN--YLQQAQAAVDGGAAALFVHGRT--------RNARYRFAADWD 172

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT-VDEYFS 234
            +  I    P + +  NG L    +  A +       VM+ RAA     +    VD Y+ 
Sbjct: 173 AIARIVAAVP-VPVIGNGDLLFPHEIAAARERSGCAAVMVARAALIKPWIFREAVDGYWD 231

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                   I        +R+      ++     H   +++
Sbjct: 232 --------ITAEERVGLYRRYVTLAREHWGDDEHGLARIR 263


>gi|170720730|ref|YP_001748418.1| dihydrouridine synthase DuS [Pseudomonas putida W619]
 gi|169758733|gb|ACA72049.1| dihydrouridine synthase DuS [Pseudomonas putida W619]
          Length = 323

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 61/315 (19%), Positives = 125/315 (39%), Gaps = 42/315 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPASSFDKLAPELRKGARTAAGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D    A+   +   ++ + G   + +HAR  +           
Sbjct: 128 RAVPAHIPVTSKMRLGFDTPDGAL---DCATALAEGGSAHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVDDWRRCREVSGAEDIMLGRGLVSRPDLALQ 235

Query: 229 V----DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +    D     P++  + +   + ++FWR+  A ++       ++ G+++Q    +  L 
Sbjct: 236 IAAARDGREYQPMSWEALLP--LLREFWRQAQAKLSP-----RYAPGRMKQW---LAMLT 285

Query: 285 HGFPNS----RRCRH 295
             +P +       R 
Sbjct: 286 RSYPEAVLLFAELRR 300


>gi|3046395|gb|AAC38320.1| unknown [Ralstonia eutropha H16]
          Length = 322

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 105/249 (42%), Gaps = 26/249 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+ NP
Sbjct: 58  GYTRSGTPMVIQLLGSDPEWLARNAAYAATLSPHGIDLNFGCPAKVVNRHGGGAMLLTNP 117

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   +A++  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 ELLNRIVASVRAAVPAHIAVTAKMRLGVSDASLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                 +D+   P   +D +  I     D+ +  NG +  ++   +   +     VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIA-AAVDVPVIANGDVWTVADWERCRAVSGCADVMIGR 225

Query: 218 AAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
            A  +  +   +       P     P+  R    + +K+ A +   A+ H H   KL   
Sbjct: 226 GAVSDPFLALRIRGLMDGSPSDQEWPLVLRQIATYLKKLHARI---ASCHEHGRVKLW-- 280

Query: 277 TRHMIGLFH 285
               +  F 
Sbjct: 281 ----LSYFK 285


>gi|218708996|ref|YP_002416617.1| tRNA-dihydrouridine synthase C [Vibrio splendidus LGP32]
 gi|218322015|emb|CAV18052.1| tRNA-dihydrouridine synthase C [Vibrio splendidus LGP32]
          Length = 318

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 59/310 (19%), Positives = 117/310 (37%), Gaps = 44/310 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEK---------PL 50
           M    D   R     + +  L  TE + V D +L     +      +           P+
Sbjct: 8   MEGVLDHLMREILTEINDYDLCVTEFVRVVDQLLPPHVFH--RICPELHQGSQTMAGVPI 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            LQ+ G   + + E A      G   I+LN GCP+  V++ + GA L+  P+++   + +
Sbjct: 66  HLQLLGQHPNWMAENAFQAASLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVVKS 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
              A+   IPV+ K R+G +          +V +I+++  + + +HAR  +         
Sbjct: 126 CRDAVPAHIPVSAKIRLGWER---PEECFEIVDAIEQAKADELTVHARTKV-------GG 175

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            K   + +D + +I +E   L +  NG + +       +    VD +M+ R A+    + 
Sbjct: 176 YKASEIKWDYINQI-REKTSLPLIANGEIWNYQDGQDCIEATGVDSLMVCRGAFNIPNLG 234

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGL 283
             V                   K  W K+   +  Y+   +     +    ++ +  + L
Sbjct: 235 NVVKH--------------NHPKMPWNKVIELLLRYSEFQIKGDKGMYYPNRVKQWFVYL 280

Query: 284 FHGFPNSRRC 293
             G+P +   
Sbjct: 281 SKGYPEANEL 290


>gi|84999472|ref|XP_954457.1| hypothetical protein [Theileria annulata]
 gi|65305455|emb|CAI73780.1| hypothetical protein, conserved [Theileria annulata]
          Length = 359

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/285 (20%), Positives = 103/285 (36%), Gaps = 39/285 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R  +   L YT M+ A      +    + F T   +KPL  Q  G D
Sbjct: 33  MVDQSELPFRLLCRRYS-ADLAYTPMLHAKIFSENENYRNIHFHTSSDDKPLIAQFCGND 91

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            S  + A+  +     + I++N+GCP     +G +G+ L+  P ++    A++       
Sbjct: 92  PSAFILASSYI-KNDVSAIDINLGCPQGIAKKGRYGSFLLEYPQLITKGFASV------- 143

Query: 119 VTVKCRIGVDDQIPAVALRNL---VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
                     D    +  R     V+S + +G   + +H R             +I   D
Sbjct: 144 ----------DTKFMLFTRGWLFSVQSCQANGCKALTVHGRHRSET------KTRISECD 187

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT----- 228
           +D +  I K   ++ +  NGG+E      + L     D VM   A  +N  + +      
Sbjct: 188 WDSIK-IIKSRVNIPVIANGGIETFEDVKRCLDYTGADAVMSSEAILENPYLFSGKMYNN 246

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           +D  F   L+       +            +  Y  +H      +
Sbjct: 247 ID-IFEEYLSILKGSPRQKISCIKGHAFKILYKYINQHHDIRTAI 290


>gi|71660993|ref|XP_817524.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70882721|gb|EAN95673.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 428

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 62/297 (20%), Positives = 103/297 (34%), Gaps = 34/297 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL     + YT MI+AD+    D      FS    E+ L  QI    
Sbjct: 83  MVRCSRPAFRKLCRLW-GTDVSYTHMIMADSFTCSDAARHADFSMYAGEERLVAQIASCS 141

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK----A 114
                EAA ++  +  + I+LN GCP   + +   G+ L+  P++V D +  +       
Sbjct: 142 GPVAAEAATLLAPY-CDAIDLNCGCPQRWIIKEGLGSALLQKPEVVADMVRCIHNGLSGG 200

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + +P  VK R+  D         +  +  + +G   I +H R       +P        +
Sbjct: 201 VDLPCVVKMRVSNDVGRSV----DFARQCEAAGCGWITVHGRTPSCSAHAP--------V 248

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             D +  I +E   + +  NGG+ +   ALK  +      VM       N A        
Sbjct: 249 RLDAIRTI-RECVSVPVVANGGVNNPQTALKTSLTTGAGAVMSATGLLANPACF------ 301

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
              P  G   +     +     + ASM         +     +          G P 
Sbjct: 302 -YVPREGELLLFAPQRRGVDVALEASMGPCRGADEGASTAGSEN----SAWLKGLPG 353


>gi|262171859|ref|ZP_06039537.1| tRNA-dihydrouridine synthase C [Vibrio mimicus MB-451]
 gi|261892935|gb|EEY38921.1| tRNA-dihydrouridine synthase C [Vibrio mimicus MB-451]
          Length = 326

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 117/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +     TE + V + +L       L         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNQLLPDHVFYRLCPELQHGSKTPAGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPQWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQATGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +          ++    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHTAMPWHEVV----------ELLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANDLFGEL 294


>gi|322822399|gb|EFZ28459.1| hypothetical protein TCSYLVIO_5308 [Trypanosoma cruzi]
          Length = 428

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 63/297 (21%), Positives = 104/297 (35%), Gaps = 34/297 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL     + YT MI+AD+    D      FS    E+ L  QI    
Sbjct: 83  MVRCSRPAFRKLCRLW-GTDVSYTHMIMADSFTCSDAARHADFSIYAGEERLVAQIASCS 141

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK----A 114
                EAA ++  +  + I+LN GCP   + +   G+ L+  P++V D +  +       
Sbjct: 142 GPVAAEAATLLAPY-CDAIDLNCGCPQRWIIKEGLGSALLQKPEVVADMVRCIHNGLSGG 200

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +S+P  VK R+  D         +  +  + +G   I +H R       +P        +
Sbjct: 201 VSLPCVVKMRVNNDVGRSV----DFARHCEAAGCGWITVHGRTPSCSAHAP--------V 248

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             D +  I +E   + +  NGG+ +   ALK  +      VM       N A        
Sbjct: 249 RLDAIRTI-RECVSVPVVANGGVNNPQTALKTSLTTGAGAVMSATGLLANPACF------ 301

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
              P  G   +     +     + ASM         +     +          G P 
Sbjct: 302 -YVPREGELLLFAPQRRGVDVALEASMGPCQGADEGASTAGSEN----SAWLKGLPG 353


>gi|119610150|gb|EAW89744.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
          Length = 378

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/283 (19%), Positives = 101/283 (35%), Gaps = 52/283 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP                       +    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKR-----------------VLLAHEKLS 124

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 125 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASW 174

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 175 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF-------- 225

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 226 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 262


>gi|251797245|ref|YP_003011976.1| dihydrouridine synthase [Paenibacillus sp. JDR-2]
 gi|247544871|gb|ACT01890.1| dihydrouridine synthase DuS [Paenibacillus sp. JDR-2]
          Length = 341

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 70/332 (21%), Positives = 124/332 (37%), Gaps = 35/332 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    D+          +  L F+  E+P+   + G
Sbjct: 20  MEDVTDVVFRHVVSTAAKPDVFFTEFTSTDSYCNPAGIESTRGRLTFTEDEQPIVAHLWG 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  + +  ++  G+  I++N+GCP   V     GA L+ +P+          KA  
Sbjct: 80  NKPELFEQMSIDMKKLGFRGIDINMGCPVQNVASNGKGAGLIRHPEAAAAI-IQAAKAGG 138

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       R  +  I K  +  + IH R         K      +  +
Sbjct: 139 LPVSVKTRLGYSE---VDEWRGWLTHILKQDIANLSIHLRT--------KKEMSKVDAHW 187

Query: 177 DIVYEIKKE----NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +++ EIKK      P+  + +NG + D +  LK++    VDGVMIGR  + N        
Sbjct: 188 ELIPEIKKLRDEIAPNTLLTINGDIPDRATGLKLVEQYGVDGVMIGRGIFTNPFAFE--- 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                P   S+    ++            T+   R      +  +I         GF  +
Sbjct: 245 ---KEPKEHSARDFLQLLLLQLDLHDKYSTEVLPRSFKPLLRFFKI------YVRGFRGA 295

Query: 291 RRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              R  L +E  ++     ++    + +  SL
Sbjct: 296 NELRIQL-METKSTDEVRRLVNAVLDQIDASL 326


>gi|145352754|ref|XP_001420702.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144580937|gb|ABO98995.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 287

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 96/234 (41%), Gaps = 19/234 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE----KPLALQIGGADISK 61
           +  +R          ++ +EM  A  + +G +         E         QI    I +
Sbjct: 14  NAPFRRLCASEFGAEVVVSEMAFARFLAKGARVERARVRRHEGDAGDCFGAQIATNAIEE 73

Query: 62  LVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            V AA I   +FG + ++LN GCP     +   GA L+  P  +   +  +   + +P+T
Sbjct: 74  GVNAALIASGEFGADFVDLNCGCPIHETWKRGLGAALLKKPAKLERLVEGIASRIDVPLT 133

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G+D    A   R + + ++ +G + + +H R         K+ R     DYD++ 
Sbjct: 134 VKIRLGIDSSSQA---RRIAEGLENAGASAVVVHGRT--------KEQRYTKAADYDVIR 182

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +I +E  ++ I  NG +     A   +    V  +M+GR A     +     E 
Sbjct: 183 DIVRER-NIPIIGNGDVLTWYDARDRMEHSGVAAMMVGRGALIKPWIFKEYRER 235


>gi|239993480|ref|ZP_04714004.1| NifR3/Smm1 family protein [Alteromonas macleodii ATCC 27126]
          Length = 309

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 59/279 (21%), Positives = 112/279 (40%), Gaps = 38/279 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +       TE +  V   + +     +       G +    P+ +
Sbjct: 5   MEGVVDHLMRDMLTRVGGFDQCVTEFVRVVDQKLPKKTFYRLCPELHNGGKTPAGVPVRV 64

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A+   + G   ++LN GCP+  V++   GA L+     + D + A+ 
Sbjct: 65  QLLGQHPQWLAENAQTAIELGSPGVDLNFGCPAKTVNKSKGGAVLLKETQTLYDIVKAVR 124

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D+  A+       +I ++G + + +HAR         K    
Sbjct: 125 DAVPAEIPVSAKIRLGFEDKSLAIEN---AIAITEAGASELVVHART--------KTEGY 173

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            P   +D + +IK+   D+ +  NG + +   A +         +MIGR A     +  +
Sbjct: 174 KPPAYWDWIAKIKQHT-DIPLVANGEIWNAEDAQRCQSQSECTNLMIGRGALAMPNLAMS 232

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
           + E       G +P+        W +++A +  Y+   +
Sbjct: 233 IKE-------GVAPMP-------WSELAALLIQYSGYEI 257


>gi|326794052|ref|YP_004311872.1| dihydrouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326544816|gb|ADZ90036.1| dihydrouridine synthase DuS [Marinomonas mediterranea MMB-1]
          Length = 319

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 59/324 (18%), Positives = 122/324 (37%), Gaps = 44/324 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNILG------FSTQEKPLAL 52
           M    D   R     +     L +E   +  + I     + ++        +    P+ +
Sbjct: 6   MEGVMDHIMRSLLSSIGGMDYLVSEFIRVSQNPIPVTGFRRLVPEIDKNSRTEHGHPVHI 65

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G++  ++ ++A      G   I++N GCP+ RV+    G+ L+  P+ +   ++++ 
Sbjct: 66  QLLGSNAERIAQSAINAVAAGAKHIDMNFGCPAKRVNGHGGGSVLLQTPEQLHLIMSSLQ 125

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L   I ++ K R+G +D+     L   V +I+++G + + +H R         K +  
Sbjct: 126 QVLPSHIGLSAKIRLGYEDESL---LFENVSAIEEAGTHALTVHGRT--------KKDGY 174

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + EI      + I  NG ++D    ++   +      MIGR +  N  +   
Sbjct: 175 KPPARWEKIGEI-NARSKMRIIANGDIDDFETLMRCHEMTGCVDFMIGRGSLSNPFVFRQ 233

Query: 229 VDEYFS-------NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----IT 277
           +                   P+ T +D+                   + G+L+Q    + 
Sbjct: 234 LKHRLESEGHTVKTEQNKKEPLLTLIDQ------YQKNLRGECDEFATVGRLKQWCAYLK 287

Query: 278 RHMIGLFHGFPNSRRCRHILTVEA 301
           RH   +     N R  R   T E 
Sbjct: 288 RHYPYI---EANLRELRQTTTAEE 308


>gi|224534532|ref|ZP_03675108.1| putative histidine phosphokinase/phophatase [Borrelia spielmanii
           A14S]
 gi|224514209|gb|EEF84527.1| putative histidine phosphokinase/phophatase [Borrelia spielmanii
           A14S]
          Length = 334

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 117/270 (43%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL   K++I    L  +   +PL  
Sbjct: 17  MEDVTDSVFRNLIHLIGSGEGEPHIYFTEFISVKGILNRSKQSIQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP  ++ +    + L+ N  + G+ I A  
Sbjct: 77  QIWGNIPEQFYRAIEILGGMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAGEIILASK 136

Query: 113 KALSI---PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A S    P++VK R G         + + +  +   G++ + ++ R A+        N+
Sbjct: 137 EACSKFNLPLSVKTRHGF----SYPEVDDWLGFLLGFGIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 185 SEGPVNFDIFYELVKLRNNISPSTLIIGNGDVLSLKDARYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLT-TVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   +   +  N L     I     KDF+
Sbjct: 245 NLFKFSSKHFLDNNLNFRLNILKFHIKDFY 274


>gi|294892129|ref|XP_002773909.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239879113|gb|EER05725.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 606

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 55/285 (19%), Positives = 115/285 (40%), Gaps = 24/285 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM +A+++L+G++    +L     EK   +Q+ G     + 
Sbjct: 248 NLPFRRLCVSLGCE-VTVSEMALAESLLKGNRAEHALLKKHPDEKIFGIQVAGGFPDMMS 306

Query: 64  EAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSIP 118
             A+++  E   ++ +++N+GCP   +H+   G+ LM         +++M K   A    
Sbjct: 307 RCAEMLCREMDDFDFLDINMGCPLEGLHKKGAGSALMTRLGKAEGVMSSMAKVCHAYDKN 366

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R     Q        +      SGV+G+ +H R A  +   P D          +
Sbjct: 367 LTVKIRTAHYGQ--NHVYDKVAARAVSSGVDGVVLHGRTAQQRYSRPADWTFHTKCRTAM 424

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              +      + +   G + D  +A++ +    V+G+MIGR A     + T + E+    
Sbjct: 425 DSAVPGNA--VPLVGCGDIIDWREAIERMETPGVEGLMIGRGALIKPWIFTEIKEHRDWD 482

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           ++ +  +          ++      Y   H  +  +  + TR  +
Sbjct: 483 ISSAERL----------ELLKRFVSYGLTHWGTDTRGVESTRRFL 517


>gi|221505283|gb|EEE30937.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 544

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 101/301 (33%), Gaps = 83/301 (27%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----RGDKKNILGFSTQ--------- 46
           MVD ++  +R   R    + L YT M+ +   L     R      L  S           
Sbjct: 44  MVDASELAFRLLGRRYGVD-LAYTPMLHSRLFLDDSKYRALHWQTLRSSPSWTQASCSEE 102

Query: 47  -----------------------------------------EKPLALQIGGADISKLVEA 65
                                                    ++P+ +Q  G   + L+ A
Sbjct: 103 EDVQEEGEEEGEEEEEGEEGEEGEVSEGGRSQWTGDESQEFDEPVFVQFCGDSPATLLAA 162

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A++VED     +++NVGCP      G +GA L+  P+++ D ++ + K L  PVT K R 
Sbjct: 163 AQLVEDE-VEAVDVNVGCPQGIARRGHYGAFLLNEPELLVDIVSTLHKHLKTPVTCKMRK 221

Query: 126 -----------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                             +D++        L  + + +G   + IH R    K       
Sbjct: 222 VSPRNPRDALPRSEAALVLDEERRLQDTLRLCDAFEAAGCACLCIHGRTKEEK------A 275

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
             +   D+  +  +K+    + +  NG +E    AL+ L     D VM       N  + 
Sbjct: 276 AFVGPCDWLAIRHVKQRL-SIPVIANGAVETYEDALRCLEFTGADAVMSAEGLLDNPMLF 334

Query: 227 T 227
            
Sbjct: 335 A 335


>gi|146282133|ref|YP_001172286.1| NifR3/Smm1 family protein [Pseudomonas stutzeri A1501]
 gi|145570338|gb|ABP79444.1| NifR3/Smm1 family protein [Pseudomonas stutzeri A1501]
          Length = 302

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 53/298 (17%), Positives = 109/298 (36%), Gaps = 38/298 (12%)

Query: 16  LTNNALLYTEM--IVADAILRGDKKNIL------GFSTQEKPLALQIGGADISKLVEAAK 67
           +       TE   +    + +     +         +    P+ +Q+ G+D   L + A 
Sbjct: 1   MGGVDWCVTEFIRVSDRLLPQSSFGKLAPELQNGALTRAGTPVRVQLLGSDPICLADNAA 60

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRI 125
                G   I+LN GCP+  V++   GA L+  PD++   +  +  A+   IPVT K R+
Sbjct: 61  FACTLGAPAIDLNFGCPAKTVNKSRGGAVLLKEPDLLHAILCEVRSAVPAHIPVTAKMRL 120

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G D    A+   +  +++   G   + +HAR  +            P   ++ V  + +E
Sbjct: 121 GFDSPDGAL---DCARALVAGGAEQLVVHARTKVEG--------YKPPAHWEWVARV-QE 168

Query: 186 NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              + +  NG +  +    +       + +M+GR       +   +    +         
Sbjct: 169 VVPVPVYANGDIWSLEDWRRCREVSGAEDIMLGRGLVSRPDLARQIAAAKAGQQIAPMSW 228

Query: 244 KT--RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS----RRCRH 295
           +    V  DFW++    +        ++ G+L+Q    +  L   +P +       R 
Sbjct: 229 EEFRPVLLDFWQQARGKIAP-----RYAPGRLKQW---LALLTRNYPEAVALFAELRR 278


>gi|167623514|ref|YP_001673808.1| dihydrouridine synthase DuS [Shewanella halifaxensis HAW-EB4]
 gi|167353536|gb|ABZ76149.1| dihydrouridine synthase DuS [Shewanella halifaxensis HAW-EB4]
          Length = 327

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 98/242 (40%), Gaps = 24/242 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +    L+ TE +  V   +       +       G +    P+ +
Sbjct: 21  MEGVVDDLMREILSAINPYDLMVTEFVRVVDQLLPEKVFYRLCPELQTGGQTLSGTPVRV 80

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G   +++N GCP+  V+  + GA ++  P+ + + + AM 
Sbjct: 81  QLLGQNPDWMAENAARAIELGSKGVDVNFGCPAKMVNRSNGGAVMLQYPEQLYNVVKAMR 140

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PVT K R+G +D+           +I ++G + + +HAR  +           
Sbjct: 141 DAVPSDQPVTAKIRLGFNDKSLY---MENALAIYEAGASELAVHARSKVDG--------Y 189

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  + P + +  NG + +   A + +     D VM+GR A     +   
Sbjct: 190 KPPAYWEYITDINAKLP-IPVIANGEIWNRDDAERCMSITGCDSVMVGRGAISLPNLAAN 248

Query: 229 VD 230
           + 
Sbjct: 249 IK 250


>gi|71402428|ref|XP_804129.1| dihydrouridine synthase (Dus) [Trypanosoma cruzi strain CL Brener]
 gi|70866933|gb|EAN82278.1| dihydrouridine synthase (Dus), putative [Trypanosoma cruzi]
          Length = 547

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 59/329 (17%), Positives = 111/329 (33%), Gaps = 57/329 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---------------- 44
           MVD ++  +R   R      L Y+ M+ A +  +  +     FS                
Sbjct: 102 MVDQSELPFRMLCRRY-GATLAYSPMLHARSFAQSAQYRARYFSTTPHRAEPAMTATVSG 160

Query: 45  ---------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
                            + PL +Q  G D   L+ AA+ VED     +++N+GCP     
Sbjct: 161 EGEAAEDAGRTSDGKETDHPLFVQFCGNDADTLLAAARHVED-DCEAVDVNLGCPQGIAR 219

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +G+ LM + D V + +  +   L +PVT K R+  DD           + ++ +G+ 
Sbjct: 220 RGHYGSFLMEDWDRVHNILHCLAVELRVPVTAKMRVFDDD----ALTLKYAEMLRDTGIA 275

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKIL- 207
            + +H R           + K    D + +  +++     + +  NG +       + + 
Sbjct: 276 VLCVHGRT---------RHNKRGLADMEKIRRVREHLRGSIPVIGNGNVLTFEDVRRNMS 326

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWRKISASMTDYAAR 265
               DG M       +  +         N    +   + R+D     ++    +  Y   
Sbjct: 327 VTMTDGYMCAEPLLWDPRLFAAPLHPVRNGRCFAECCEARLDAIRTAQEYLQLVQRYPVD 386

Query: 266 HLHSGGKLQQITRH-------MIGLFHGF 287
                  L ++  H       M G    F
Sbjct: 387 LAFVKAHLFKMLFHSYEMHPVMHGWLTNF 415


>gi|71411788|ref|XP_808128.1| dihydrouridine synthase (Dus) [Trypanosoma cruzi strain CL Brener]
 gi|70872267|gb|EAN86277.1| dihydrouridine synthase (Dus), putative [Trypanosoma cruzi]
          Length = 548

 Score =  159 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 59/329 (17%), Positives = 111/329 (33%), Gaps = 57/329 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---------------- 44
           MVD ++  +R   R      L Y+ M+ A +  +  +     FS                
Sbjct: 103 MVDQSELPFRMLCRRY-GATLAYSPMLHARSFAQSAQYRARYFSTTPHRAELAMTATASG 161

Query: 45  ---------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
                            + PL +Q  G D   L+ AA+ VED     +++N+GCP     
Sbjct: 162 EGEAAEDAGRTSDGEETDHPLFVQFCGNDADTLLAAARHVED-DCEAVDVNLGCPQGIAR 220

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +G+ LM + D V + +  +   L +PVT K R+  DD           + ++ +G+ 
Sbjct: 221 RGHYGSFLMEDWDRVHNILHCLAVELRVPVTAKMRVFDDD----ALTLKYAEMLRDTGIA 276

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKIL- 207
            + +H R           + K    D + +  +++     + +  NG +       + + 
Sbjct: 277 VLCVHGRT---------RHNKRGIADMEKIRRVREHLRGSIPVIGNGNVLTFEDVRRNMS 327

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWRKISASMTDYAAR 265
               DG M       +  +         N    +   + R+D     ++    +  Y   
Sbjct: 328 ATMTDGYMCAEPLLWDPRLFAAPLHPVRNGRCFAERREARLDAIRTAQEYLQFVQRYPVD 387

Query: 266 HLHSGGKLQQITRH-------MIGLFHGF 287
                  L ++  H       M G    F
Sbjct: 388 LAFVKAHLFKMLFHSYEMHPVMHGWLTNF 416


>gi|298486487|ref|ZP_07004547.1| tRNA-dihydrouridine synthase C [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298158964|gb|EFI00025.1| tRNA-dihydrouridine synthase C [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 321

 Score =  159 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 63/314 (20%), Positives = 119/314 (37%), Gaps = 34/314 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDK--KNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRDALTKVGGIDWCVTEFIRVSERLMPAPYFYKYASEFHKGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAILLKEPELLHSIVSQVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +           
Sbjct: 128 RAVPRHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVHARTKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I +E   + +  NG +  +    +         +MIGR       +   
Sbjct: 177 KPPAHWEWIARI-QEVVKVPVVANGEIWTVDDWRRCREICGARDIMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            +      + + FW+     MT      + + G+L+Q    ++ L   
Sbjct: 236 IAAAQKGEEVVPMTWDELQPMLRAFWQACLIKMT-----LIQAPGRLKQW---LVLLTKS 287

Query: 287 FPNSRRCRHILTVE 300
           +P +    + L  E
Sbjct: 288 YPEATLMFNALRRE 301


>gi|113867457|ref|YP_725946.1| hypothetical protein H16_A1443 [Ralstonia eutropha H16]
 gi|124106281|sp|O68273|DUSC_RALEH RecName: Full=tRNA-dihydrouridine synthase C
 gi|113526233|emb|CAJ92578.1| conserved hypothetical protein [Ralstonia eutropha H16]
          Length = 322

 Score =  159 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 103/238 (43%), Gaps = 20/238 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G++    P+ +Q+ G+D   L   A        + I+LN GCP+  V+    GA L+ NP
Sbjct: 58  GYTRSGTPMVIQLLGSDPEWLARNAAYAATLSPHGIDLNFGCPAKVVNRHGGGAMLLTNP 117

Query: 102 DIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +++   +A++  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 ELLNRIVASVRAAVPAHIAVTAKMRLGVSDASLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                 +D+   P   +D +  I     D+ +  NG +  ++   +   +     VMIGR
Sbjct: 173 ------RDHGYRPPAHWDWIARIA-AAVDVPVIANGDVWTVADWERCRAVSGCADVMIGR 225

Query: 218 AAYKNSAMLTTVDEYFSN-PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            A  +  +   +       P     P+  R    + +K+ A +   A+ H H   KL 
Sbjct: 226 GAVSDPFLALRIRGLMDGSPSDQEWPLVLRQIATYLKKLHARI---ASCHEHGRVKLW 280


>gi|39953378|ref|XP_363980.1| hypothetical protein MGG_08825 [Magnaporthe oryzae 70-15]
 gi|145021243|gb|EDK05372.1| hypothetical protein MGG_08825 [Magnaporthe oryzae 70-15]
          Length = 614

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 104/283 (36%), Gaps = 54/283 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKN---------------- 39
           MVD ++  +R   R     +     L YT M  A                          
Sbjct: 45  MVDQSEFAWRMLTRSFMPESQRSTVLGYTPMFHARLFGENPSYRDSHFQAIRKDAASPDA 104

Query: 40  -----ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
                + G    ++PL +Q    D S L+EAAK V  +  + ++LN+GCP     +G +G
Sbjct: 105 QPTPWLDGNPAIDRPLFVQFCANDPSALLEAAKHVAPY-CDAVDLNLGCPQGIARKGHYG 163

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           A L  + +++   I  +   LSIPVT K RI         A     +++  +G + + +H
Sbjct: 164 AFLQEDQELIHKLIRQLHDGLSIPVTAKIRIL----DTPEATLAYARNVLDAGASILTVH 219

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLE---DMSQALKILPSV 210
            R+   KG            D+  +  +++   P+  I  NG +    D+ + L+     
Sbjct: 220 GRRREQKG------HLTGVADWSAIRHLRENLPPETVIFANGNILQRGDLERCLEA-TGA 272

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           D VM       +  +                P      +++WR
Sbjct: 273 DAVMSAEGNLSDPTLFA------------PEPPVGEEGREYWR 303


>gi|282856150|ref|ZP_06265433.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pyramidobacter
           piscolens W5455]
 gi|282585909|gb|EFB91194.1| dihydrouridine synthase TIM-barrel protein nifR3 [Pyramidobacter
           piscolens W5455]
          Length = 333

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 59/310 (19%), Positives = 108/310 (34%), Gaps = 19/310 (6%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +    R   R L   AL +TEM+ +  +L    K   +   + +E+PL LQ+   D 
Sbjct: 22  AGVSVAAVRRLFRRL-GAALTHTEMVSSAGLLYAGTKTWQMTECTDEERPLVLQLFTGDA 80

Query: 60  SKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             L  +A+  ++   Y    +N+ CP  +VH+   G+ L+ NPD+    +  + K   +P
Sbjct: 81  DSLCRSAERCLQSRSYAAFGVNMACPMPKVHKKGAGSRLLQNPDVAFAMVRELKK-FGLP 139

Query: 119 VTVKCRIGVDDQIPA-VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           V  K R  V D     +      + + ++G + + IH R    +     D  ++      
Sbjct: 140 VWPKIRKIVPDGREYRLDTLQFAEGLLEAGADNVTIHGRTPQQRYEGKADKSEVVRAARR 199

Query: 178 IVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              +         I  +G +      A  +      V+  R A  +  M   V       
Sbjct: 200 FEGK---------ITASGDVYAAADVAFYLDNGCAAVLCARGAIADPFM---VVHSLRVL 247

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
              +  +          +I   + D   R       L  + R + G F G   +   +  
Sbjct: 248 GYNNRILHGDPSLQERAEILTGLADDLYRLHGGRAALVLLRRFLSGFFRGQAGTAEFKRT 307

Query: 297 LTVEAGASTA 306
           L       +A
Sbjct: 308 LASAKDWDSA 317


>gi|307546327|ref|YP_003898806.1| dihydrouridine synthase, DuS [Halomonas elongata DSM 2581]
 gi|307218351|emb|CBV43621.1| dihydrouridine synthase, DuS [Halomonas elongata DSM 2581]
          Length = 344

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 68/313 (21%), Positives = 116/313 (37%), Gaps = 36/313 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ----------EKP 49
           M    D   R             TE + V DA  R   +  L    +            P
Sbjct: 26  MEGVIDAATRDLLTRTAGIDWTVTEFVRVVDA--RLPPRVFLRHCPELAGGDPRTPSGAP 83

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + LQ+ G+D   L   A+     G   ++LN GCP+  V+    GA ++  P  +   ++
Sbjct: 84  VHLQLLGSDPVALAANARQALALGATSLDLNFGCPAKLVNRHDGGASMLRTPWRLRTAVS 143

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A+  A+   IPVT K R+G  D+  A+   +  ++ +  G + + +HAR         ++
Sbjct: 144 AVHDAVGDVIPVTAKIRLGFADRRLAL---DCARATEDGGASQLVVHART--------RN 192

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAM 225
               P   ++ +  I++    + +  NG +  +    K   L     VM+GR A  +S +
Sbjct: 193 EGYRPPAHWEWIGRIRRRL-SIPVIANGDIWTLEDYWKARTLSGCRDVMLGRGALADSGL 251

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              +  +         P     DK       A+M            +L+Q   HM     
Sbjct: 252 APRIRHWQGTGEHL--PPTPWADKASLLLDYAAMQRSILSSKTVVARLKQWMNHM----R 305

Query: 286 GF-PNSRRCRHIL 297
           G  P + RC   L
Sbjct: 306 GRDPEAARCFQAL 318


>gi|262369265|ref|ZP_06062593.1| tRNA-dihydrouridine synthase C [Acinetobacter johnsonii SH046]
 gi|262315333|gb|EEY96372.1| tRNA-dihydrouridine synthase C [Acinetobacter johnsonii SH046]
          Length = 317

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 114/292 (39%), Gaps = 28/292 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM------IVADAILRGDKKNIL--GFSTQEKPLAL 52
           M   TD   R     + +     TE       ++ D I       +L  G +    P+ +
Sbjct: 14  MEGLTDPIMRDVLTSVGSFDWCVTEFIRVTNSVLPDHIYHQYCPELLNGGKTAAGTPVHV 73

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G D   L   A      G   I++N GCP+  V+    G+ L+  P++V + + A+ 
Sbjct: 74  QFLGNDPEMLAANAIRAVKLGAPAIDMNFGCPAKTVNRHRGGSVLLDEPEVVHELVKAVR 133

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+     + +   +I+ +G   + +HAR         K +  
Sbjct: 134 DAVPAHIPVSAKMRLGYMDRH---FMLDNAHAIEDAGAAWVTVHART--------KADGY 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I +E   + +  NG + + + A +       + +MIGR A     +   
Sbjct: 183 TPPAFWDQLRPI-REALKINVIANGEIWNNADAKQCRLESGCEDLMIGRGAVTTPDLTQC 241

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           + +    PL   + + T   + F         +   R+    G    +++H 
Sbjct: 242 IRQNIDTPLLTWNELLTLQIR-FLNGGYKKEMNMVGRYKQWLGM---MSKHY 289


>gi|120553985|ref|YP_958336.1| dihydrouridine synthase, DuS [Marinobacter aquaeolei VT8]
 gi|120323834|gb|ABM18149.1| tRNA-U20a,U20b-dihydrouridine synthase [Marinobacter aquaeolei VT8]
          Length = 325

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 120/318 (37%), Gaps = 43/318 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +       TE I V   +L           +     +    P+A+
Sbjct: 8   MEGLVDAPIRETLTKVGGIDRCVTEFIRVTHGMLPPRIFYKYAPELYNGALTEVGTPVAV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G++   +        + G  ++++N GCP+  V++   G  LM  P+++ +  AA+ 
Sbjct: 68  QLLGSNADMMGRHGAKAAELGAGQVDINFGCPAKTVNKHKGGCVLMREPELMYEITAAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           KA+   IPVT K R+G DD+   VA     ++++ +G + I IHAR  +           
Sbjct: 128 KAVPADIPVTAKMRLGYDDRSMGVA---CGQALEAAGASEIVIHARSKVDG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + ++ K      +  NG +  +    +   +   D VMIGR       +   
Sbjct: 177 KPPAYWEEIAKVCKAVKS-HVIANGEIWTVEDYWRCRKVSGCDDVMIGRGLIARPDLAAQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR---HLHSGGKLQQITRHMIGLFH 285
           +                      W ++   + +YAA     L       +I + +  L  
Sbjct: 236 IKASQRGETREP---------MSWAEVVVLVREYAAALQTRLEDKYVTGRIKQWLNYLRQ 286

Query: 286 GF-------PNSRRCRHI 296
           GF       P +R+ R +
Sbjct: 287 GFAEAEALWPQARKIREV 304


>gi|313679501|ref|YP_004057240.1| dihydrouridine synthase dus [Oceanithermus profundus DSM 14977]
 gi|313152216|gb|ADR36067.1| dihydrouridine synthase DuS [Oceanithermus profundus DSM 14977]
          Length = 313

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 60/315 (19%), Positives = 112/315 (35%), Gaps = 32/315 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   TD  +R  +           EM++A ++L+   +   +L    +E+   +Q+ GAD
Sbjct: 18  MASLTDAPFRLVSERF-GALWAVGEMVMAGSLLQESVEGWRLLRLHPEERSRVVQLAGAD 76

Query: 59  I-SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                  AA++ E  G   I+LN+GCP  +V     GA LM +P      +A + +A  +
Sbjct: 77  PGEVARAAARVRERVGPRAIDLNMGCPMPKVTARGAGAALMDDPARAARMVAGVREATGL 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+VK R+G            + ++++++G   + +H R A          R     D+D
Sbjct: 137 PVSVKLRLGF----SRANAVEVARALEQAGAALLRVHGRTA--------QQRYGGRADWD 184

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            V E+ +    + +   G +  +           G  + R A         V        
Sbjct: 185 AVREVARAV-RIPVVGTGDVRSVEDYRARRGLGVGAAVARGALGRPWFFAEV-----RRE 238

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-HI 296
              +  +    ++      A   D           L+    H+       P     R   
Sbjct: 239 RVDAAARRAAAREHLSLHLAWYADRGEVW-----ALRAFRGHLKAYLSAAP--AEVRARA 291

Query: 297 LTVEAGASTATHHII 311
           L +E   +     ++
Sbjct: 292 LALE--RAEEVAEVL 304


>gi|328771087|gb|EGF81127.1| hypothetical protein BATDEDRAFT_10653 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 624

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 96/255 (37%), Gaps = 39/255 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +    + +  +EM +A  +LRG  +   +      E    +Q+   D ++  
Sbjct: 274 NIPFRRVCKSYGVD-ITCSEMAIARQLLRGSPQEWALTRRHASEDMFGIQLASNDPTQFT 332

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  +I+ +    + I+LN+GCP   + +   G+ L+   + V   +       S+P+T+K
Sbjct: 333 QTVEILSQKVDCDFIDLNMGCPIDTMTKSGNGSALLERKNKVRGMLLGAVHVSSVPITIK 392

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG+ ++        ++   +  GV  I +H R         K+ R     D+D   E 
Sbjct: 393 MRIGLSNKKKIG--HKIIPLARDCGVAAITVHGRS--------KEQRYTKLSDWDYTMEC 442

Query: 183 KK------ENPD------------LFIGLNGGLEDMSQALKILPS-VD------GVMIGR 217
            K       +PD                 NG +    +    +    D      G+M+GR
Sbjct: 443 AKMTKMTWHSPDASTVTPDWVTEPPAFFGNGDVFSPQEYWDHVDHSTDSELPLAGIMVGR 502

Query: 218 AAYKNSAMLTTVDEY 232
            A     +   + E 
Sbjct: 503 GALSKPWIFKEIKER 517


>gi|145299064|ref|YP_001141905.1| tRNA-dihydrouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142851836|gb|ABO90157.1| tRNA-dihydrouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 314

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 64/283 (22%), Positives = 112/283 (39%), Gaps = 42/283 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     + +  L  +E I V D +L    K     + +           P+
Sbjct: 8   MQGVLDHLMREVLTSVNDYDLCVSEFIRVVDQLL--PAKVFYRIAPELKQGGKTRAGTPV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G     L E A    + G   ++LN GCP+  V++   GA L+  PD V   + A
Sbjct: 66  RVQLLGQHPEWLAENAVRAIELGSPGVDLNFGCPAPTVNKSKGGAVLLKEPDAVYRIVKA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +PV+ K R+G DD+   +      +++ ++G N + +HAR         K  
Sbjct: 126 VREAVPAHLPVSAKIRLGYDDKDLYLEN---AQAVYQAGANELAVHART--------KRE 174

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
                  ++ V  I++  P + +  NG + D   AL    +   D +M+GR A     + 
Sbjct: 175 GYKAPAHWEYVDAIRRALP-IPVTANGEIWDHQDALTCASVSGCDALMVGRGAISLPNL- 232

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
                        ++ +KT      W  +   M  Y  + L S
Sbjct: 233 -------------ANVMKTGCTHMSWAAVLQLMVSYTEQDLAS 262


>gi|257484388|ref|ZP_05638429.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 148

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 62/121 (51%), Positives = 82/121 (67%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L   +++ E+ GY+E+NLNVGCPS RV     GACLM  P +V DC+ AM  A+ IPVT
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVGCPSDRVQNNMIGACLMAYPQLVADCVKAMRDAVGIPVT 147

Query: 121 V 121
           V
Sbjct: 148 V 148


>gi|153824959|ref|ZP_01977626.1| conserved hypothetical protein [Vibrio cholerae MZO-2]
 gi|149741471|gb|EDM55501.1| conserved hypothetical protein [Vibrio cholerae MZO-2]
          Length = 323

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 117/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPDWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR  +          K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTKV-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|312148418|gb|ADQ31077.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           JD1]
          Length = 329

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|223889346|ref|ZP_03623932.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           64b]
 gi|223885032|gb|EEF56136.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           64b]
          Length = 329

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|216264467|ref|ZP_03436459.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           156a]
 gi|224533271|ref|ZP_03673865.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           CA-11.2a]
 gi|225548971|ref|ZP_03769948.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           94a]
 gi|215980940|gb|EEC21747.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           156a]
 gi|224513436|gb|EEF83793.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           CA-11.2a]
 gi|225370574|gb|EEH00011.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           94a]
          Length = 329

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|15595082|ref|NP_212871.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           B31]
 gi|2688667|gb|AAC67079.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           B31]
          Length = 335

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 23  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHVFLKPNELNRPLIA 82

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 83  QIWGNVPEQFYRAIEILGSMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 142

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 143 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 190

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 191 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 250

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 251 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 280


>gi|255071937|ref|XP_002499643.1| dihydrouridine synthase-like family protein [Micromonas sp. RCC299]
 gi|226514905|gb|ACO60901.1| dihydrouridine synthase-like family protein [Micromonas sp. RCC299]
          Length = 495

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/279 (21%), Positives = 107/279 (38%), Gaps = 21/279 (7%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLV 63
           +  +R        N +  +EM+ A  +LR +   K  L     EK   +Q+    I + V
Sbjct: 123 NLPFRRLCVDFGCN-VTVSEMVFARFLLRRNPVEKARLRRHPSEKLFGVQLATNQIVEGV 181

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA +  D G + I+LN GCP     +   GA L+  P  +   +  +     +P+TVK 
Sbjct: 182 NAAALAADAGADFIDLNCGCPIHETWKRGLGAALLKKPKKLERLVRGIADGTRLPLTVKI 241

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G          R L ++++ +G   + IH R         K+ R     ++D++ EI+
Sbjct: 242 RLGA--GGSEAPARQLAEAVENAGAAAVIIHGRT--------KEQRYTRAANWDLIGEIQ 291

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +E   + +  NG +    +    L        M GR A     +   V E         +
Sbjct: 292 RERG-IPVVGNGDILTHYEHRDRLARSGAHAAMTGRGALIKPWIFKEVAEGVEW-----A 345

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           P      + + R  S     +    +  G  L+ +  H 
Sbjct: 346 PTPEERVEVYLRLCSYFKEHFFTDEMGRGRYLEFMPWHF 384


>gi|224532602|ref|ZP_03673224.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           WI91-23]
 gi|224512458|gb|EEF82837.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           WI91-23]
          Length = 329

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|195941555|ref|ZP_03086937.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           80a]
 gi|218249652|ref|YP_002375235.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           ZS7]
 gi|225549995|ref|ZP_03770956.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           118a]
 gi|226321434|ref|ZP_03796961.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           Bol26]
 gi|218164840|gb|ACK74901.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           ZS7]
 gi|225369454|gb|EEG98906.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           118a]
 gi|226233230|gb|EEH31982.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           Bol26]
 gi|312148972|gb|ADQ29043.1| histidine phosphokinase/phophatase, putative [Borrelia burgdorferi
           N40]
          Length = 329

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|262402534|ref|ZP_06079095.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC586]
 gi|262351316|gb|EEZ00449.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC586]
          Length = 331

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|255745518|ref|ZP_05419466.1| tRNA-dihydrouridine synthase C [Vibrio cholera CIRS 101]
 gi|255736593|gb|EET91990.1| tRNA-dihydrouridine synthase C [Vibrio cholera CIRS 101]
          Length = 316

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 115/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGF------STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 1   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELQQGSKTPSGVPVKV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 61  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 121 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 170

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 171 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 229 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 278

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 279 QANELFGEL 287


>gi|254291529|ref|ZP_04962320.1| conserved hypothetical protein [Vibrio cholerae AM-19226]
 gi|150422593|gb|EDN14549.1| conserved hypothetical protein [Vibrio cholerae AM-19226]
          Length = 323

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 117/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR  +          K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTKV-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|118443329|ref|YP_877508.1| transcriptional regulator [Clostridium novyi NT]
 gi|118133785|gb|ABK60829.1| probable transcriptional regulator [Clostridium novyi NT]
          Length = 321

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 123/294 (41%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV +        + +++L  + + K +  QI  
Sbjct: 8   MEGITGYIYRNAYEKFFGNVDKYFTPFIVTNKNIGFKAKELRDVLPENNEVKNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  + +  A+ +++ GYNEINLN+GCPS  V     G+  +   + +   +  + K   
Sbjct: 68  NDSERFINIARKLQELGYNEINLNLGCPSGTVVSKYRGSGFLAKREELDRFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G D          L+K   K  +  + IH R            +  PNL  
Sbjct: 128 MKISIKTRLGKD---SPEEFYELIKIFNKYPLEELIIHPRTREDFY------KNKPNL-- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
               E+ K+   L    I  NG +    D  Q  +  P V+ VMIGR    N  ++  + 
Sbjct: 177 ----EVFKDALSLSVNPICYNGDIFTSTDYKQLTEAFPQVETVMIGRGILANPGLINEIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           E        +  +  +V ++F  ++  +  +      ++  +++++  +MI +F
Sbjct: 233 E--------NKTLDKKVLREFHDEVLNNYRELFNEDRNAMFRMKELWGYMIYIF 278


>gi|148548985|ref|YP_001269087.1| dihydrouridine synthase, DuS [Pseudomonas putida F1]
 gi|148513043|gb|ABQ79903.1| dihydrouridine synthase, DuS [Pseudomonas putida F1]
          Length = 323

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 120/313 (38%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPASSFDKLAPELRQGARTASGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  +IPVT K R+G D    A+       ++ + G   + +HAR  +           
Sbjct: 128 RAVPANIPVTSKMRLGFDSPDGAL---ECATALAEGGSAHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  ++   +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVNDWRRCREVSGAEDIMLGRGLVSRPDLGLQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + ++FWR+  A ++       ++ G+++Q    +  L   
Sbjct: 236 IAAARDGRDYQPMSWHELLPLLREFWRQAQAKLSP-----RYAPGRMKQW---LAMLTRS 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVVLFAELRR 300


>gi|330829416|ref|YP_004392368.1| tRNA-dihydrouridine synthase C [Aeromonas veronii B565]
 gi|328804552|gb|AEB49751.1| tRNA-dihydrouridine synthase C [Aeromonas veronii B565]
          Length = 314

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 113/281 (40%), Gaps = 38/281 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNIL--GFSTQEKPLAL 52
           M    D   R     + +  L  +E I V D +L           +L  G +    P+ +
Sbjct: 8   MQGVLDHLMREVLTSVNDYDLCVSEFIRVVDQLLPAKVFYRLCPELLQDGKTRAGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCP+  V++   GA L+  P+ +   + A+ 
Sbjct: 68  QLLGQHPEWLAENALRAIELGSPGVDLNFGCPAPTVNKSKGGAVLLKEPETIYRIVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+ K R+G DD+   +      +++ + G N + +HAR         K    
Sbjct: 128 EAVPAHLPVSAKIRLGYDDKDLYLEN---AQAVFQGGANELAVHART--------KREGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
                ++ V  I++  P + +  NG + D   AL    +   D +M+GR A     +   
Sbjct: 177 KAPAHWEYVDAIRRALP-IPVTANGEIWDHKDALACARVSGCDALMVGRGAISLPNL--- 232

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
                      ++ +KT      W ++   M  Y  + L S
Sbjct: 233 -----------ANVMKTGCPHMSWAEVLQLMVSYTEQDLAS 262


>gi|119945939|ref|YP_943619.1| dihydrouridine synthase, DuS [Psychromonas ingrahamii 37]
 gi|119864543|gb|ABM04020.1| dihydrouridine synthase, DuS [Psychromonas ingrahamii 37]
          Length = 314

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/300 (20%), Positives = 115/300 (38%), Gaps = 36/300 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA-----DAILRGDKKNILG---FSTQEKPLAL 52
           M    D   R     +    L  TE I        A +       L     +    P+ +
Sbjct: 8   MEGVMDHQMRQLLTAIGGYDLCITEFIRVVDMQLPAKVYRRHSPELYNDSKTASGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A      G + I+LN GCP+  V++   GA L+ +P+ +   +  + 
Sbjct: 68  QLLGQNPQCLAENAHQAISIGSDGIDLNFGCPAKTVNKNKGGAVLLKSPEALYQIVTEVR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           KA+ +   ++VK R+G +D+  A+      ++I+ +G + + +HAR         K    
Sbjct: 128 KAVPVFQTLSVKIRLGYEDKSLAIEN---AQAIQAAGADELAVHART--------KAEGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +  + +IK     + +  NG +  +  A + +     + +MIGR A      L  
Sbjct: 177 RPPAHWHWIAKIKDAIT-IPVTANGDIFSVDDAKRCMEITGCERLMIGRGALATP-NLAQ 234

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWR-----------KISASMTDYAARHLHSGGKLQQIT 277
             +   +P +    +       F +           +I   +    A+H  +   LQQ+ 
Sbjct: 235 AIKGIESPNSWPEILNILEKYMFVQTHGDQEKYLPSRIKQWLIFIKAQHPQAAVFLQQVR 294


>gi|149924148|ref|ZP_01912526.1| Dihydrouridine synthase family protein [Plesiocystis pacifica
           SIR-1]
 gi|149814994|gb|EDM74553.1| Dihydrouridine synthase family protein [Plesiocystis pacifica
           SIR-1]
          Length = 321

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/297 (20%), Positives = 106/297 (35%), Gaps = 40/297 (13%)

Query: 1   MVDWTDRHYRF-FARLLTNNA---LLYTEMI--VADAILRGDKKNILGFSTQ-------- 46
           M   TD  YR     L    +   L  +E +      ++    +  L    +        
Sbjct: 1   MDGVTDGSYRECLTALFGGRSGISLCVSEFVRVTRQPVVE---RVFLRHCPELARGGKTR 57

Query: 47  -EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
              P+ +Q+ G +   +  AA+     G   I+LN GCP+  V+    GA L+ +P  V 
Sbjct: 58  AGVPVFVQLLGGEPHWMARAAETAVALGAPGIDLNFGCPAKTVNSSDGGATLLKDPCRVE 117

Query: 106 DCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               A+  A+   +PVTVK R+G +D  P V    + ++ +  G + + IH R       
Sbjct: 118 AVTRAVRAAVPAELPVTVKIRVGWEDPSPVV---EIARAAEAGGASWLTIHGRT------ 168

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYK 221
             +     P +DY+ +    +    + +  NG L  +    +          MIGR A  
Sbjct: 169 --RRQLYKPPVDYEAIGR-AQAAVSMAVVANGDLFGVPSLFEAAQRSGCTAFMIGRGAMG 225

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
              +                P       D +     +     A   ++ G+L+Q  R
Sbjct: 226 RPELFARAR---GTQRAALDPRPFEALLDVYADTLLAS---GANERNTLGRLKQWLR 276


>gi|49083690|gb|AAT51107.1| PA3129 [synthetic construct]
          Length = 320

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 111/288 (38%), Gaps = 27/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I + D +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRVGGIDWCVTEFIRITDRLLPATAFHKLAPELRDGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +AA+ 
Sbjct: 68  QLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   I VT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 RAVPSEIAVTSKMRLGYDSPDGAL---DCARALADGGSAHVVVHARTKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +  E   + +  NG +  +   L+      V+ +M+GR       +   
Sbjct: 178 -PPAHWEWVARVA-EAVRVPVFANGEVWTLDDYLRCREVSGVEDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSNPLTGSSPIKT--RVDKDFWRKISASMTD-YAARHLHSGGKL 273
           +  +         P      + +DFW +    +   YA   L     +
Sbjct: 236 IAAWRDGGEIREMPWSKLLPLLRDFWLQARRKLAPRYAPGRLKQWLGM 283


>gi|15598325|ref|NP_251819.1| hypothetical protein PA3129 [Pseudomonas aeruginosa PAO1]
 gi|107102678|ref|ZP_01366596.1| hypothetical protein PaerPA_01003743 [Pseudomonas aeruginosa PACS2]
 gi|254236099|ref|ZP_04929422.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|254241823|ref|ZP_04935145.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
 gi|38605051|sp|Q9HZ95|DUSC_PSEAE RecName: Full=tRNA-dihydrouridine synthase C
 gi|9949242|gb|AAG06517.1|AE004737_3 conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
 gi|126168030|gb|EAZ53541.1| conserved hypothetical protein [Pseudomonas aeruginosa C3719]
 gi|126195201|gb|EAZ59264.1| conserved hypothetical protein [Pseudomonas aeruginosa 2192]
          Length = 319

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 111/288 (38%), Gaps = 27/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I + D +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRVGGIDWCVTEFIRITDRLLPATAFHKLAPELRDGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +AA+ 
Sbjct: 68  QLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   I VT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 RAVPSEIAVTSKMRLGYDSPDGAL---DCARALADGGSAHVVVHARTKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +  E   + +  NG +  +   L+      V+ +M+GR       +   
Sbjct: 178 -PPAHWEWVARVA-EAVRVPVFANGEVWTLDDYLRCREVSGVEDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD-YAARHLHSGGKL 273
           +  +         P      + +DFW +    +   YA   L     +
Sbjct: 236 IAAWRDGGEIREMPWSELLPLLRDFWLQARRKLAPRYAPGRLKQWLGM 283


>gi|45190681|ref|NP_984935.1| AER075Wp [Ashbya gossypii ATCC 10895]
 gi|44983660|gb|AAS52759.1| AER075Wp [Ashbya gossypii ATCC 10895]
          Length = 352

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 100/236 (42%), Gaps = 18/236 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   +  F+T   + PL +Q+G  +
Sbjct: 41  MVRYSKLPFRQLCRHF-NVDIVYSPMILAREFVRNEHARMADFTTNSRDTPLIVQVGVNN 99

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L+   ++V  +  + I +N GCP         G+ L+ N  ++ + + A+ +     
Sbjct: 100 VVDLLRFVEMVSPY-CDGIGINCGCPIREQVREGIGSALIYNQPLLCEMVRAVKEKYKDT 158

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I + D +       L  ++  +GV+ I IH R         +  R     +   
Sbjct: 159 VRLETKIRIHDDLAQTVT--LCNALASAGVDWITIHGRT--------RTTRSSVPANIAA 208

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           +  IK+   D  L I  NG    +    +I      DG+M  R    N A+ +   
Sbjct: 209 IRYIKEHITDKELPIVANGDCFTLDDCHRIAAETGADGIMAVRGLLANPALFSGYK 264


>gi|120609942|ref|YP_969620.1| dihydrouridine synthase [Acidovorax citrulli AAC00-1]
 gi|120588406|gb|ABM31846.1| tRNA-U20a,U20b-dihydrouridine synthase [Acidovorax citrulli
           AAC00-1]
          Length = 323

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 57/277 (20%), Positives = 107/277 (38%), Gaps = 29/277 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E I     L  D K  L +  +           P+ 
Sbjct: 12  MEGLLDFVLRDVLTRVGGVDRCVSEFIRVTGTLLPD-KVFLRYIPELRNGGRTAAGVPVR 70

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+ G+D S + E A  +   G   I+LN GCP+  V+    GA L+  P+ +   ++A+
Sbjct: 71  AQLLGSDPSSMAENAARLAALGPEGIDLNFGCPAKVVNRHGGGAALLREPERIAAVVSAV 130

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+ K R+G DD   A   R   ++ +  G   + +HAR         K + 
Sbjct: 131 RRAVPPEMPVSAKMRLGYDDTSLA---RECAQAAEAGGACELVVHART--------KADG 179

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
             P   +++V  + +    + +  NG +  +  A++   L   D +M+GR    +  +  
Sbjct: 180 YRPPAYWELVAPL-RAAVRIPVIANGEIWTVEDAMRCRALSGGDALMLGRGIVADPGLAL 238

Query: 228 TVDEYFSNPLTGSSPIKTRVDKD---FWRKISASMTD 261
            +    +      +     +      FWR +   +  
Sbjct: 239 AIRAAEAGRAHAPALAWEALLPQLGVFWRTVCEDLEP 275


>gi|258626327|ref|ZP_05721174.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM603]
 gi|258581379|gb|EEW06281.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM603]
          Length = 326

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/333 (18%), Positives = 124/333 (37%), Gaps = 35/333 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +     TE + V + +L       L         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNQLLPDHVFYRLCPELQHGSKTPAGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDSQWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +          ++    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHTAMPWHEVV----------ELLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            +      L       +   H ++     ++ S
Sbjct: 286 QANDLFGELRTLTQVESIVSH-LQHYLESLLNS 317


>gi|294789807|ref|ZP_06755036.1| tRNA-dihydrouridine synthase C [Simonsiella muelleri ATCC 29453]
 gi|294482249|gb|EFG29947.1| tRNA-dihydrouridine synthase C [Simonsiella muelleri ATCC 29453]
          Length = 331

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 50/260 (19%), Positives = 107/260 (41%), Gaps = 26/260 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +    +  L    +           P  
Sbjct: 20  MQGLCDDVMRHLLTHIGGFDECVSEFVRITHTVHSR-QTWLRHIPEIATNNQTVAGTPCT 78

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +QI G+D + +   A      G N+I++N GCP+  V++   GA L+  PD++   +  +
Sbjct: 79  VQILGSDENMMAINALEAIKLGANKIDINFGCPAPTVNKHKGGAILLQEPDLIYQIVRTL 138

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + L  +IP+T K R+G +++  A+      ++I  +GV+ + +HAR  +          
Sbjct: 139 RERLPENIPLTAKMRLGYENKDLALEN---AQAIASAGVSALTVHARTKVEG-------- 187

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
             P   ++ V +I +++ D+ +  NG +  +    A+K     + +M+GR A     +  
Sbjct: 188 YEPPAHWNWVKKI-QQSIDIPVIANGDVFSLDDFIAIKNETGCNQIMLGRGAVMRPDLAR 246

Query: 228 TVDEYFSNPLTGSSPIKTRV 247
            + ++    +   +     +
Sbjct: 247 QIRQFERREIVQQAEFNEEI 266


>gi|153802134|ref|ZP_01956720.1| conserved hypothetical protein [Vibrio cholerae MZO-3]
 gi|124122327|gb|EAY41070.1| conserved hypothetical protein [Vibrio cholerae MZO-3]
          Length = 323

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|45946028|gb|AAH17081.4| DUS1L protein [Homo sapiens]
          Length = 406

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 92/238 (38%), Gaps = 30/238 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
               +++PL +Q    D    V+AA + +D+  + I+LN+GCP      G +GA L    
Sbjct: 1   EVCPEDRPLIVQFCANDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEW 59

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D++   I    + LS+PVT K R+  +            + ++K+G   + +H R    K
Sbjct: 60  DLLQRMILLAHEKLSVPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQK 115

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           G             ++ +  ++K    + +  NG ++ +    + L    V GVM     
Sbjct: 116 G------PLSGAASWEHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGN 168

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
             N A+             G SP    + +++   +        Y   HL    KL  
Sbjct: 169 LHNPALF-----------EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 212


>gi|26988707|ref|NP_744132.1| NifR3/Smm1 family protein [Pseudomonas putida KT2440]
 gi|38604780|sp|Q88LF2|DUSC_PSEPK RecName: Full=tRNA-dihydrouridine synthase C
 gi|24983496|gb|AAN67596.1|AE016389_4 NifR3/Smm1 family protein [Pseudomonas putida KT2440]
          Length = 323

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 119/313 (38%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPASSFDKLAPELRQGARTAAGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  +IPVT K R+G D    A+       ++ + G   + +HAR  +           
Sbjct: 128 RAVPANIPVTSKMRLGFDSPDGAL---ECATALAEGGSAHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVDDWRRCREVSGAEDIMLGRGLVSRPDLGLQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + ++FWR+  A ++       ++ G+++Q    +  L   
Sbjct: 236 IAAARDGRDYQPMSWHDLLPLLREFWRQAQAKLSP-----RYAPGRMKQW---LAMLTRS 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVVLFAELRR 300


>gi|15641118|ref|NP_230750.1| hypothetical protein VC1105 [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121591280|ref|ZP_01678575.1| conserved hypothetical protein [Vibrio cholerae 2740-80]
 gi|153816887|ref|ZP_01969554.1| conserved hypothetical protein [Vibrio cholerae NCTC 8457]
 gi|227081278|ref|YP_002809829.1| hypothetical protein VCM66_1061 [Vibrio cholerae M66-2]
 gi|229505299|ref|ZP_04394809.1| tRNA-dihydrouridine synthase C [Vibrio cholerae BX 330286]
 gi|229511031|ref|ZP_04400510.1| tRNA-dihydrouridine synthase C [Vibrio cholerae B33]
 gi|229518152|ref|ZP_04407596.1| tRNA-dihydrouridine synthase C [Vibrio cholerae RC9]
 gi|229608318|ref|YP_002878966.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254848235|ref|ZP_05237585.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MO10]
 gi|298498790|ref|ZP_07008597.1| conserved hypothetical protein [Vibrio cholerae MAK 757]
 gi|38605060|sp|Q9KT00|DUSC_VIBCH RecName: Full=tRNA-dihydrouridine synthase C
 gi|9655575|gb|AAF94264.1| conserved hypothetical protein [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121546864|gb|EAX57022.1| conserved hypothetical protein [Vibrio cholerae 2740-80]
 gi|126512474|gb|EAZ75068.1| conserved hypothetical protein [Vibrio cholerae NCTC 8457]
 gi|227009166|gb|ACP05378.1| conserved hypothetical protein [Vibrio cholerae M66-2]
 gi|229344867|gb|EEO09841.1| tRNA-dihydrouridine synthase C [Vibrio cholerae RC9]
 gi|229350996|gb|EEO15937.1| tRNA-dihydrouridine synthase C [Vibrio cholerae B33]
 gi|229357522|gb|EEO22439.1| tRNA-dihydrouridine synthase C [Vibrio cholerae BX 330286]
 gi|229370973|gb|ACQ61396.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254843940|gb|EET22354.1| tRNA-dihydrouridine synthase C [Vibrio cholerae MO10]
 gi|297543123|gb|EFH79173.1| conserved hypothetical protein [Vibrio cholerae MAK 757]
          Length = 323

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 115/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGF------STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELQQGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|229525717|ref|ZP_04415122.1| tRNA-dihydrouridine synthase C [Vibrio cholerae bv. albensis VL426]
 gi|229339298|gb|EEO04315.1| tRNA-dihydrouridine synthase C [Vibrio cholerae bv. albensis VL426]
          Length = 323

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 115/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGF------STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRQGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|90407636|ref|ZP_01215816.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
 gi|90311227|gb|EAS39332.1| NifR3/Smm1 family protein [Psychromonas sp. CNPT3]
          Length = 313

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 100/253 (39%), Gaps = 25/253 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----VADAILRGDKKNILG---FSTQEKPLAL 52
           M    D H R     L    L  TE I        A +       L     +    P+ +
Sbjct: 8   MEGVMDHHMRALLTSLGGIDLCVTEFIRVISLTLPAKVYRRVSPELFNQSKTPSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   L   A+     G + I+LN GCP+  V++   GA L+ +P+ +   +  + 
Sbjct: 68  QLLGQDPQCLANNARKALLVGSDGIDLNFGCPAKAVNKSKGGAILLKSPETLYKIVKEVR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            ++     ++VK R+G  D+  A+      ++I ++G N + +HAR         K+   
Sbjct: 128 ASMHTCETLSVKIRLGYADKSLAIEN---AQAICEAGANELAVHART--------KEEGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   +  + +I +E+ D+ +  NG +     A +         +MIGR A      L  
Sbjct: 177 APPAHWHWIAKI-RESIDIPVTANGDIFSAEDAKRCHEISGCHSLMIGRGALATP-NLAQ 234

Query: 229 VDEYFSNPLTGSS 241
           V +    P +   
Sbjct: 235 VIKGIEEPYSWPQ 247


>gi|67471577|ref|XP_651736.1| hypothetical protein [Entamoeba histolytica HM-1:IMSS]
 gi|56468508|gb|EAL46349.1| hypothetical protein, conserved [Entamoeba histolytica HM-1:IMSS]
          Length = 515

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 103/289 (35%), Gaps = 27/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  TEMI+A++++ G      ++   + E    +Q+   +     
Sbjct: 182 NLPFRKVVKRF-GCDVTMTEMIMAESLVEGKTSEWALVKRDSSEDIFGIQLCVGNSMLAA 240

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +A +++     +   LN  CP   V++   GA L+  P  +   + AM      PV +K 
Sbjct: 241 KACQVLNSVDCDFYELNCACPIDYVYKKGMGAQLIERPKRIESLLHAMRSVTERPVAIKV 300

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G            L+ +    G   + IH R         +D R   + D+D + +  
Sbjct: 301 RTGKSSNTIQDV---LLPNCADYGAAMVSIHGRT--------RDQRYTKSADWDFIKQ-A 348

Query: 184 KENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                  +   G +   +D  +AL     V  V IGR A     + T + E     ++ S
Sbjct: 349 TTITQCPVIGVGDIYGYKDYQKALDC--GVATVAIGRGALIKPWIYTEIKEKRDWDISSS 406

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ-ITRHMIGLFHGFP 288
                    D  R+ +     +         K ++ +  H+  +    P
Sbjct: 407 E------RLDILRQYALDGLSHWGSDAQGISKTREFMCHHLTFMTRYVP 449


>gi|297578707|ref|ZP_06940635.1| conserved hypothetical protein [Vibrio cholerae RC385]
 gi|297536301|gb|EFH75134.1| conserved hypothetical protein [Vibrio cholerae RC385]
          Length = 323

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGF------STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELQHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +  +  +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWNEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|303278930|ref|XP_003058758.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459918|gb|EEH57213.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 440

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 54/287 (18%), Positives = 103/287 (35%), Gaps = 30/287 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM +A  +L+GD+    +L     EK    Q+ G     L 
Sbjct: 64  NLPFRRVCVGL-GADVTISEMAMASNVLKGDRGEWALLRRHPSEKLFGAQVCGGWPDLLA 122

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----SIP 118
              ++++D    + +++N+GCP   V     G+ L+ + + V      +  A       P
Sbjct: 123 RCGELLDDELDCDFVDVNMGCPIDGVCAKGAGSSLLRDAEGVARMERVVRAASRSMRRAP 182

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R+G DD         +V   K  G + + +H R         +  R     D+  
Sbjct: 183 LTIKLRMGYDDDPSKHVAHEIVARAKSWGAHAVTLHGRT--------RQQRYSRAADWAY 234

Query: 179 VYEIKKEN--PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           V             +  NG +   +   + +   S+   MIGR A     +LT + E   
Sbjct: 235 VERCAAAARETSTPLIGNGDVFSSADYERHMSSGSLATCMIGRGALIKPWVLTEIKERRV 294

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             ++    +           +      +   H  +  K  + TR  +
Sbjct: 295 WDISARERL----------DLFERFGAFGLEHWGADEKGVETTRRFM 331


>gi|153213536|ref|ZP_01948826.1| conserved hypothetical protein [Vibrio cholerae 1587]
 gi|124115872|gb|EAY34692.1| conserved hypothetical protein [Vibrio cholerae 1587]
          Length = 323

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|84393366|ref|ZP_00992125.1| putative regulator protein [Vibrio splendidus 12B01]
 gi|84375975|gb|EAP92864.1| putative regulator protein [Vibrio splendidus 12B01]
          Length = 303

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 118/301 (39%), Gaps = 44/301 (14%)

Query: 10  RFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEK---------PLALQIGGADI 59
           R     + +  L  TE + V D +L     +      +           P+ LQ+ G   
Sbjct: 2   REILTEINDYDLCVTEFVRVVDQLLPPHVFH--RICPELHQGSQTMAGVPIHLQLLGQHP 59

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--I 117
           + + E A    + G   I+LN GCP+  V++ + GA L+  P+++   + A  +A+   I
Sbjct: 60  NWMAENAFQAANLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVVNACREAVPAHI 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+G +          +V +I+++  + + +HAR  +          K   + +D
Sbjct: 120 PVSAKIRLGWE---HPEECFEIVDAIEQAKADELTVHARTKV-------GGYKASEIKWD 169

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +I +E   L +  NG + +       +    VD +M+ R A+    +   V      
Sbjct: 170 YINQI-REKTSLPLIANGEIWNYQDGQDCIEATGVDSLMVCRGAFNIPNLGNVVKH---- 224

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFHGFPNSRR 292
                        K  W K+ A +  Y+   +     +    ++ +  + L  G+P +  
Sbjct: 225 ----------NHQKMPWDKVIALLLRYSEFQIKGDKGMYYPNRVKQWFVYLSKGYPEANE 274

Query: 293 C 293
            
Sbjct: 275 L 275


>gi|254225500|ref|ZP_04919110.1| conserved hypothetical protein [Vibrio cholerae V51]
 gi|125621970|gb|EAZ50294.1| conserved hypothetical protein [Vibrio cholerae V51]
          Length = 323

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|116051125|ref|YP_790044.1| hypothetical protein PA14_23640 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|313108452|ref|ZP_07794456.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
 gi|115586346|gb|ABJ12361.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|310880958|gb|EFQ39552.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           39016]
          Length = 319

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 111/288 (38%), Gaps = 27/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I + D +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRVGGIDWCVTEFIRITDRLLPATAFHKLAPELRDGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +AA+ 
Sbjct: 68  QLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   I VT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 RAVPSEIAVTSKMRLGYDSPDGAL---DCARALADGGSAHVVVHARTKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +  E   + +  NG +  +   L+      V+ +M+GR       +   
Sbjct: 178 -PPAHWEWVARVA-EAVRVPVFANGEVWTLDDYLRCREVSGVEDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD-YAARHLHSGGKL 273
           +  +         P      + +DFW +    +   YA   L     +
Sbjct: 236 IAAWRDGGEIHEMPWSELLPLLRDFWLQARRKLAPRYAPGRLKQWLGM 283


>gi|260655068|ref|ZP_05860556.1| dihydrouridine synthase family protein [Jonquetella anthropi E3_33
           E1]
 gi|260630179|gb|EEX48373.1| dihydrouridine synthase family protein [Jonquetella anthropi E3_33
           E1]
          Length = 317

 Score =  158 bits (401), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 106/301 (35%), Gaps = 23/301 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           M   T    R  A  L    L +TEM  A  ++RG ++ +  L  +   +PL  Q+   D
Sbjct: 1   MASVTTAAVRRLAVRL-GAGLTHTEMASATGLVRGGRQTLRVLDQTNDTRPLVAQLFAGD 59

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV  A++    G ++ + +N+ CP  +V +   G+ L+  PD     +  +C+    
Sbjct: 60  AESLVRGAEVALTCGPFDALGINMACPMPKVLKRGAGSALLDRPDEAASMVRELCR-FGF 118

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV  K R   +     +     V+ + ++G + + +H R            R     D  
Sbjct: 119 PVWPKVRK--EPAGSGITTEEFVQILFEAGASCVAVHGRTP--------GQRYEGQADRK 168

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            V E+ +  P   I  +G +      L  L      V++ R    +  ++    +  S  
Sbjct: 169 SVKELCRAFPG-RILASGDVFTAEDVLDYLSAGAGAVLLARGFIADPFIVPRSLDLLSGR 227

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                 + +R       +I         R       L  + R   G F     +   R  
Sbjct: 228 PEARPSLASRY------EIFCEFAGELERLHGPKMALGMVKRFAPGFFKFQAGAGALRRT 281

Query: 297 L 297
           L
Sbjct: 282 L 282


>gi|242210427|ref|XP_002471056.1| predicted protein [Postia placenta Mad-698-R]
 gi|220729846|gb|EED83713.1| predicted protein [Postia placenta Mad-698-R]
          Length = 513

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 100/258 (38%), Gaps = 57/258 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILGFS-------------- 44
           MVD ++              L+YT MI A A +R  G    +L                 
Sbjct: 31  MVDQSEL-------------LVYTPMINAKACMRYAGPHNILLSHHYQMFAEGARKGYRD 77

Query: 45  ------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                        +++PL +Q       +L+++AK+VE +  + +++N+GCP      G 
Sbjct: 78  QNFNITLGEEGGPEDRPLIVQFCANSPEQLLKSAKVVEPY-CDAVDVNLGCPQDIARRGH 136

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +G+ L    D++ + I  + + LSIPVT K R+               K ++++G   + 
Sbjct: 137 YGSFLQDEWDLIYELINTLHRNLSIPVTAKFRVFP----TVEKTVEYAKMLERAGAQILT 192

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPS 209
            H R    +G            D++ +  +K E   + +  NG +    D+ + L     
Sbjct: 193 CHGRLREQRG------HNTGLADWEKIRAVK-EAVSIPVFANGNVLFHSDIERCLAA-TG 244

Query: 210 VDGVMIGRAAYKNSAMLT 227
            D +M       N A+ +
Sbjct: 245 ADAIMSAEGNLYNPAIFS 262


>gi|297568054|ref|YP_003689398.1| dihydrouridine synthase DuS [Desulfurivibrio alkaliphilus AHT2]
 gi|296923969|gb|ADH84779.1| dihydrouridine synthase DuS [Desulfurivibrio alkaliphilus AHT2]
          Length = 335

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 118/289 (40%), Gaps = 19/289 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T    R   +      LL TEM+ A  +   +      L     E+PL+ Q+    
Sbjct: 25  MAGLTHSALRRLVQEQGGVGLLSTEMLAAKRLPHENPTLSPYLVRHPSEQPLSFQLLLTS 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +++  A    E+ G   I+LN+GCP+  +     G+ LM  P +V   +    +  ++P
Sbjct: 85  PAEVAAAVASAEELGAAAIDLNLGCPAPDIRRQGGGSRLMEEPQMVRRLVQETRRRTALP 144

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++ K R+G  +++ A  LR     ++ +GV+ + +HAR   L+G             ++ 
Sbjct: 145 LSAKIRLG--EELNAERLRAFCLLLEDAGVDLLTVHAR---LRG-----EPYGRKPRWEW 194

Query: 179 VYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           V ++K     + +  NGG+     + A       DG+MIGRAA     +   + E ++  
Sbjct: 195 VGKVK-HWLRIPVVANGGIFSAADAAACLAASGADGLMIGRAAAATPWLFRQLAEGWATD 253

Query: 237 L-TGSSPIKTRVDKDFWRKISASMTDYAARHL---HSGGKLQQITRHMI 281
              G   + T   ++    I     +            G+L++ T +  
Sbjct: 254 FAPGHDELSTAPSQEQKAAIYRRFCELLKESFTPERRLGRLKEFTHYYA 302


>gi|313499911|gb|ADR61277.1| TRNA-dihydrouridine synthase C [Pseudomonas putida BIRD-1]
          Length = 323

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 119/313 (38%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPASSFDKLAPELRQGARTAAGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+  +IPVT K R+G D    A+       ++ + G   + +HAR  +           
Sbjct: 128 RAVPANIPVTSKMRLGFDSPDGAL---ECATALAEGGSAHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVDDWRRCREVSGAEDIMLGRGLVSRPDLGLQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + ++FWR+  A ++       ++ G+++Q    +  L   
Sbjct: 236 IAAARDGRDYQPMSWHDLLPLLREFWRQAQAKLSP-----RYAPGRMKQW---LAMLTRS 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVVLFAELRR 300


>gi|121726268|ref|ZP_01679558.1| conserved hypothetical protein [Vibrio cholerae V52]
 gi|229529805|ref|ZP_04419195.1| tRNA-dihydrouridine synthase C [Vibrio cholerae 12129(1)]
 gi|121631214|gb|EAX63587.1| conserved hypothetical protein [Vibrio cholerae V52]
 gi|229333579|gb|EEN99065.1| tRNA-dihydrouridine synthase C [Vibrio cholerae 12129(1)]
          Length = 323

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|238021955|ref|ZP_04602381.1| hypothetical protein GCWU000324_01860 [Kingella oralis ATCC 51147]
 gi|237866569|gb|EEP67611.1| hypothetical protein GCWU000324_01860 [Kingella oralis ATCC 51147]
          Length = 320

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 107/288 (37%), Gaps = 25/288 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--------FSTQEKPLAL 52
           M   TD   R     +       +E +     +      +           +    P   
Sbjct: 9   MQGLTDAPMRDLLTRIGGYDECVSEFVRITHTVHSRVTWLRHVPEIARQNRTPSGIPCTT 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   + + A      G   I+LN GCP+  V++   GA L+  P+ +   +  + 
Sbjct: 69  QLLGSDADMMAKNALEAVRLGVQTIDLNFGCPAPTVNKHQGGAILLREPERIHQIVHELR 128

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             L   I +T K R+G ++   AVA     ++I   G + I IHAR  +           
Sbjct: 129 FRLPEHINLTAKMRLGFENTDLAVANA---QAIAAGGASQITIHARTKVQG--------Y 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +  +  I +E+ ++ +  NG +  +    A++     D VMIGR A     +   
Sbjct: 178 EPPAHWHWLKTI-REHVNIPVIANGDVFTLDDYLAIRQTSGCDDVMIGRGAVMRPDLARQ 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           + ++       ++     +  D+ R        +  +  ++  +L+Q 
Sbjct: 237 IKQHLRGEPVQAAAFNAEIM-DWIRLFFDLCLAHEPQGKYAVARLKQW 283


>gi|209520559|ref|ZP_03269315.1| dihydrouridine synthase DuS [Burkholderia sp. H160]
 gi|209498996|gb|EDZ99095.1| dihydrouridine synthase DuS [Burkholderia sp. H160]
          Length = 347

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 99/232 (42%), Gaps = 26/232 (11%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +    P+ +Q+ G+D   +   A          I+LN GCP+  V++   GA L+ NP++
Sbjct: 60  TASGTPMVIQLLGSDPEWMARNAAHAATLSPYGIDLNFGCPAKVVNQHGGGAMLLANPEL 119

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   ++A+  A+  ++ VT K R+GV D   A+      +++   G   + +HAR     
Sbjct: 120 LNRIVSAVRAAVPANVAVTAKMRLGVSDTSRAI---ECAQALADGGAASLVVHART---- 172

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
               +D+R  P   ++ +  I  +  ++ +  NG +  ++   +   +     VMIGR A
Sbjct: 173 ----RDDRYRPPAHWEWIARI-DDAVEVPVIANGEVWSVADWERCRSVSGCADVMIGRGA 227

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
             +  +   +            P  +    D W+++  S+  Y  +    G 
Sbjct: 228 VSDPFLAQRIRGLM-------DPCPS---ADEWQQVLRSIVGYMHKLRERGT 269


>gi|19075762|ref|NP_588262.1| tRNA dihydrouridine synthase Dus4 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74626875|sp|O74553|DUS4_SCHPO RecName: Full=tRNA-dihydrouridine synthase 4
 gi|3560252|emb|CAA20719.1| tRNA dihydrouridine synthase Dus4 (predicted) [Schizosaccharomyces
           pombe]
          Length = 326

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 104/235 (44%), Gaps = 18/235 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK--PLALQIGGAD 58
           MV ++   +R   R   N  ++YT MI+A   L         FST +    L LQ G  D
Sbjct: 27  MVRYSKLPFRQLVRDY-NTDIVYTPMILAKEFLHPKG-RYFDFSTNDADASLILQFGVDD 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA++V  +  + I +N GCP     +   G+ L+  P+ V   + A+   L   
Sbjct: 85  PVILEKAAQLVGPY-VDGIGINCGCPQTWAIQEGIGSALLDEPEKVHKLVRAVKSTLGES 143

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
              + +I +   +     R+L++ I+KSG + I +H R         + +R    ++ D 
Sbjct: 144 FCTEVKIRIAKDLNKT--RHLMQVIEKSGADIITVHGRT--------RQDRSSFPVNLDA 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
           + E+ +    + +  NG ++ + + L+I       G+M  R   +N A+    +E
Sbjct: 194 IREV-RPCVQIPVVANGDVKSLRKGLEIAKYTETQGIMSARGLLENPALFAGYEE 247


>gi|225551868|ref|ZP_03772811.1| putative histidine phosphokinase/phophatase [Borrelia sp. SV1]
 gi|225371663|gb|EEH01090.1| putative histidine phosphokinase/phophatase [Borrelia sp. SV1]
          Length = 329

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSTEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P+++K R G         + + +  +    ++ + ++ R A+        N+
Sbjct: 137 EACARFNLPLSIKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAV--------NQ 184

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI YE+ K      P   I  NG +  + +A   +    +DG+M GR  + N 
Sbjct: 185 SKGPVNFDIFYELVKLRNNLSPSTLIIGNGDVLSLKEARYYVDKYLIDGIMFGRGIFDNL 244

Query: 224 AMLTTV-DEYFSNPLTGSSPIKTRVDKDFW 252
            +       +  + L     I     KDF 
Sbjct: 245 NLFKPFSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|71668150|ref|XP_821014.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70886380|gb|EAN99163.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 428

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/297 (21%), Positives = 103/297 (34%), Gaps = 34/297 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL     + YT MI+AD+    D      FS    E+ L  QI    
Sbjct: 83  MVRCSRPAFRKLCRLW-GTDVSYTHMIMADSFTCSDAARHADFSMYAGEERLVAQIASCS 141

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK----A 114
                EAA ++  +  + I+LN GCP   + +   G+ L+  P++V D +  +       
Sbjct: 142 GPVAAEAATLLAPY-CDAIDLNCGCPQRWIIKEGLGSALLQKPEVVADMVRCIHNGLSGG 200

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +S+P  VK R+  D         +  +  + +G   I +H R       +P        +
Sbjct: 201 VSLPCVVKMRVDNDVGRSV----DFARHCEAAGCGWITVHGRTPSCSAHAP--------V 248

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             D +  I +E   + +  NGG+ +   ALK  +      VM       N A        
Sbjct: 249 RLDAIRTI-RECVSVPVVANGGVNNPQTALKTSLTTGAGAVMSATGLLANPACF------ 301

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
              P  G   +           + ASM         +     +          G P 
Sbjct: 302 -YVPREGELLLFAPQRHGIDVALEASMGPCRGADEGASTAGSEN----SAWLKGLPG 353


>gi|262165382|ref|ZP_06033119.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM223]
 gi|262025098|gb|EEY43766.1| tRNA-dihydrouridine synthase C [Vibrio mimicus VM223]
          Length = 326

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 121/313 (38%), Gaps = 37/313 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +     TE + V + +L       L         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNQLLPDHVFYRLCPELQHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G + I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPLWMAENAIRAAELGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPV+ K R+G ++         +V ++ ++  + + +HAR             K
Sbjct: 128 EAVPAHIPVSAKIRLGWENPEDCF---EIVDAVVQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYTDGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +          ++    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHTAMPWHEVV----------ELLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCR---HILT 298
            +        ILT
Sbjct: 286 QANDLFGELRILT 298


>gi|315179807|gb|ADT86721.1| tRNA-dihydrouridine synthase C [Vibrio furnissii NCTC 11218]
          Length = 305

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 46/262 (17%), Positives = 106/262 (40%), Gaps = 32/262 (12%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            +    P+ +Q+ G +   + E A    + G   ++LN GCP+  V++   GA L+ +P+
Sbjct: 48  RTKAGVPVKVQLLGQEPHWMAENAVRAAELGACGVDLNFGCPAKMVNQSKGGAALLQHPE 107

Query: 103 IVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           ++   I A   A+   IPV+ K R+G ++         +V +++++G + + +HAR    
Sbjct: 108 LIYQVIKACRDAVPADIPVSAKIRLGWENPDDCF---EIVDAVQQAGADELTVHARTK-- 162

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
                    K   + +D + +I+++   + +  NG + + +     +    +D +M+ R 
Sbjct: 163 -----AGGYKASEIKWDYIDQIRQKT-HIPLIANGEIWNYADGQACIETTGIDSLMVCRG 216

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG---GKLQQ 275
           A     +   V    S                 W ++   + +Y+A  +          +
Sbjct: 217 ALNVPNLGNIVKHNHS--------------AMPWHEVVDLLLEYSAYEVRGDKGKYYPNR 262

Query: 276 ITRHMIGLFHGFPNSRRCRHIL 297
           + +    L   +P +      +
Sbjct: 263 VKQWFAYLRQAYPQAADLFREI 284


>gi|167032522|ref|YP_001667753.1| dihydrouridine synthase DuS [Pseudomonas putida GB-1]
 gi|166859010|gb|ABY97417.1| dihydrouridine synthase DuS [Pseudomonas putida GB-1]
          Length = 323

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 118/313 (37%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPPSSFDKLAPELRQGARTAAGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  +IPVT K R+G D    A+       ++ + G   + +HAR  +           
Sbjct: 128 HAVPANIPVTSKMRLGFDSPDGAL---ECATALAEGGSAHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVDDWRRCREVSGAEDIMLGRGLVSRPDLGLQ 235

Query: 229 VDEYFSNP--LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +            S      + ++FWR+    ++       ++ G+++Q    +  L   
Sbjct: 236 IAAAREGRDYQPMSWDDLLPLLREFWRQAQNKLSP-----RYAPGRMKQW---LAMLTRS 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVVLFAELRR 300


>gi|253682545|ref|ZP_04863342.1| dihydrouridine synthase family protein [Clostridium botulinum D
           str. 1873]
 gi|253562257|gb|EES91709.1| dihydrouridine synthase family protein [Clostridium botulinum D
           str. 1873]
          Length = 319

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 123/294 (41%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV +        + +++L  + + K +  QI  
Sbjct: 8   MEGITGYIYRNAYEKFFGNVDKYFTPFIVTNKNIGFKAKELRDVLPENNEVKNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  + +  A+ +++ GYNEINLN+GCPS  V     G+  +   + +   +  + K  +
Sbjct: 68  NDSERFINIARKLQELGYNEINLNLGCPSGTVVSKYRGSGFLAKREELDRFLDEIFKIDN 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R            +  PNLD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIFNKYPLEELIIHPRTREDFY------KNKPNLD- 177

Query: 177 DIVYEIKKENPDL---FIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                + K+   L    I  NG +    D  + ++    V+ VMIGR    N  ++  + 
Sbjct: 178 -----VFKDALSLSVNPICYNGDIFTATDYKKLIETFKEVETVMIGRGILANPGLINEIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           E           +  +V K+F  ++  +  +      ++  +++++  +MI +F
Sbjct: 233 E--------DKTLDKKVLKEFHDEVLNNYRELFNEDRNAMFRMKELWGYMIYIF 278


>gi|255724312|ref|XP_002547085.1| hypothetical protein CTRG_01391 [Candida tropicalis MYA-3404]
 gi|240134976|gb|EER34530.1| hypothetical protein CTRG_01391 [Candida tropicalis MYA-3404]
          Length = 619

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/307 (20%), Positives = 109/307 (35%), Gaps = 46/307 (14%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +++G      +      E P   +QI  +     
Sbjct: 263 NLPYRRLMKTL-GADVTYSEMALSVPLIQGHNPEWALPKAHISEYPGFGVQIASSRHWPA 321

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ +       +E+NLN GCP   +++   G+ LM  P  +   +  M  +   IPV
Sbjct: 322 AKAAEAIYRNTNHVSELNLNCGCPIDLLYKQGQGSALMDQPSKLLRILHGMSASSGDIPV 381

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R GV +         LV+ + + G    I +H R         +  R     D+D 
Sbjct: 382 TVKIRTGVREGKNTAKT--LVRRVLQEGNTAAITLHGRS--------RQQRYSREADWDY 431

Query: 179 VYEI-------------KKENPDL---FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           + E+              K+  D+   +   NG +         +    +D VM+ R A 
Sbjct: 432 IAEVGSVVKEWNENQKEDKDATDIQPVYFVGNGDVYSHEDWYNHVNTDGIDSVMVARGAL 491

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               +   V+       + S              +      YA  H  S      + R  
Sbjct: 492 IKPWIFEEVEAQQYLDKSSSE----------RLDMLGKFAKYAVEHWGSDEYGVGMARRY 541

Query: 281 IGLFHGF 287
           +  F GF
Sbjct: 542 MCEFLGF 548


>gi|67517419|ref|XP_658560.1| hypothetical protein AN0956.2 [Aspergillus nidulans FGSC A4]
 gi|40746829|gb|EAA65985.1| hypothetical protein AN0956.2 [Aspergillus nidulans FGSC A4]
 gi|259488751|tpe|CBF88446.1| TPA: dihydrouridine synthase family protein, putative
           (AFU_orthologue; AFUA_1G16550) [Aspergillus nidulans
           FGSC A4]
          Length = 563

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 55/257 (21%), Positives = 88/257 (34%), Gaps = 41/257 (15%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R       + + L Y+ M  A             F            
Sbjct: 49  MVDRSEFAWRMLTRSFMTPEESKSVLAYSPMYHARLFEEHAGYRAKAFHPTRAWGDTKCK 108

Query: 47  -------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
                        ++PL +Q    D      AA+ V  +  + ++LN+GCP      G +
Sbjct: 109 GDDSPYLDGNPAIDRPLFVQFCANDPDDFFNAARHVAPY-CDAVDLNLGCPQGIARRGHY 167

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           GA L  + D++   I  +   L +PVT K RI    Q          K I  +G + I +
Sbjct: 168 GAFLQEDWDLIYKLINKLHMELEVPVTAKFRI----QESKEKTLEYAKMILSAGASIITL 223

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSV 210
           H R    KG            D+  +  ++    PD  I  NG   +     + L     
Sbjct: 224 HGRTREQKG------HNTGLADWSYIRYLRDNLPPDTVIFANGNNLNHDDLARCLEATGA 277

Query: 211 DGVMIGRAAYKNSAMLT 227
           DGVM       + ++  
Sbjct: 278 DGVMSAEGNLSDPSIFA 294


>gi|261210733|ref|ZP_05925025.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC341]
 gi|260840218|gb|EEX66798.1| tRNA-dihydrouridine synthase C [Vibrio sp. RC341]
          Length = 323

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 118/309 (38%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGF------STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELQHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G + I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAHGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPV+ K R+G ++         +V ++ ++  + + +HAR             K
Sbjct: 128 EAVPAHIPVSAKIRLGWENPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWYYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +  S T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLSYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|167394491|ref|XP_001740985.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165894630|gb|EDR22551.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 515

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 103/289 (35%), Gaps = 27/289 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  TEMI+A++++ G      ++     E    +Q+   +     
Sbjct: 182 NLPFRKAVKRF-GCDVTMTEMIMAESLVEGKTSEWALVKRDPSEDIFGIQLCVGNSLLAA 240

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +A +++     +   LN  CP   V++   GA L+  P  +   + AM      PV +K 
Sbjct: 241 KACQVLNSVDCDFYELNCACPIDYVYKKGMGAQLIERPKRIESLLHAMRSVTERPVAIKV 300

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R G            L+ +    G   + IH R         +D R   + D+D + +  
Sbjct: 301 RTGKSSNTIQDV---LLPNCANYGAAMVSIHGRT--------RDQRYTKSADWDFIKQ-A 348

Query: 184 KENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                  +   G +   +D  +AL+    V  V IGR A     + T + E     ++ S
Sbjct: 349 TTITQCPVIGVGDIYGYKDYQKALEC--GVATVAIGRGALIKPWIYTEIKEKRDWDISSS 406

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ-ITRHMIGLFHGFP 288
                    D  R+ +     +         K ++ +  H+  +    P
Sbjct: 407 E------RLDILRQYALDGLSHWGSDAQGISKTREFMCHHLTFMTRYVP 449


>gi|187923837|ref|YP_001895479.1| dihydrouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187715031|gb|ACD16255.1| dihydrouridine synthase DuS [Burkholderia phytofirmans PsJN]
          Length = 340

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/281 (19%), Positives = 111/281 (39%), Gaps = 30/281 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           G +    P+ +Q+ G+D   +   A        + ++LN GCP+  V++   GA L+ +P
Sbjct: 58  GHTPNGTPMVVQLLGSDPEWMALNAAHAATLSPHGVDLNFGCPAKVVNQHGGGAMLLADP 117

Query: 102 DIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +   ++A+  A+   I VT K R+GV D   A+   +   ++ + G   + +HAR   
Sbjct: 118 EQLNRIVSAVRAAVPADILVTAKMRLGVSDTSLAI---DCATALAEGGAASLVVHART-- 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
                 +D+   P   ++ +  I     D+ +  NG +  ++   +   +   D VMIGR
Sbjct: 173 ------RDHGYRPPAHWEWIARI-DAAVDVPVIANGEVWTVTDWERCRAVSGCDDVMIGR 225

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR---HLHSGGKLQ 274
            A  +  +   +        +             WR +   M  Y  +    + S  +  
Sbjct: 226 GAVSDPFLALRIRGLMDRSPSNED----------WRDVLGHMAGYLRKLQARVASRHEHG 275

Query: 275 QITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
           ++ + +  L   +P +    H        S     +IE A 
Sbjct: 276 RVKKWLSYLQRTWPQAAEL-HAAIRRVQDSQEIQDVIERAL 315


>gi|71908499|ref|YP_286086.1| dihydrouridine synthase, DuS [Dechloromonas aromatica RCB]
 gi|71848120|gb|AAZ47616.1| tRNA-U20a,U20b-dihydrouridine synthase [Dechloromonas aromatica
           RCB]
          Length = 319

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 104/240 (43%), Gaps = 29/240 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             P+ +Q+ G+D   + E A+ +       ++LN GCP+  V     G+ L+  P+++ +
Sbjct: 63  GTPMRVQLLGSDPHFMAENARRLVALNPAGVDLNFGCPAPTVFRHRGGSALLGEPELLNE 122

Query: 107 CIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             +A+   +   IP T K R+G+DD   A+   +  ++++ +G+N + +H R        
Sbjct: 123 ITSAVRSVVPAHIPFTAKMRLGIDDTSRAI---DCAQALEAAGINELIVHGRT------- 172

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKN 222
            + +   P   ++ + ++ ++   + +  NG +  +      ++      +M+GR A  +
Sbjct: 173 -RSDGYRPPARWEWIDKV-RDAIHIPLIANGEVWTVEDFRNCQLATGCADIMVGRGAVAD 230

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----ITR 278
             +   V    +       P        +W  +   +       +H+GG+++Q    + R
Sbjct: 231 PLLARRVRGEETGGWDEIRPTV----ATYWLGVRKKVVP-----VHAGGRVKQWLAMMRR 281


>gi|293390935|ref|ZP_06635269.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951469|gb|EFE01588.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 322

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 57/300 (19%), Positives = 117/300 (39%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   +       +       GF+    P+ +
Sbjct: 8   MQGVLDPLVRQLLTEVNDYDLCISEFVRVVDQRLPPKVFYRLCPELHQRGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPQWLAENAELAVQLGSHGVDLNCGCPSKTVNGSNGGASLLKQPELIYQATKAIR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     V+VK R+G D         ++  ++++ G   I IH R          D  +
Sbjct: 128 QAVPQHHTVSVKVRLGWD---STEFAYDIADAVQQGGATEIAIHGRTKT-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
           +  +++  + EI+++   + +  NG +   +   +   +   + +M+GR A  N   L+ 
Sbjct: 178 VDRINWQKIGEIRQKL-KIPVIANGEIWRWADGQQCRDVTGCEDLMVGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSS--PIKTRVDKD--------FWRKISASMTDYAARHLHSGGKLQQITR 278
           V +  + PL+ +   PI  +            +          Y          L ++ +
Sbjct: 236 VLKRNAAPLSWAEIMPILRKYAALENCHDSGFYHVARIKQWLQYLKYEYAEAADLFEMVK 295


>gi|298368946|ref|ZP_06980264.1| tRNA-dihydrouridine synthase C [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282949|gb|EFI24436.1| tRNA-dihydrouridine synthase C [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 338

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 104/248 (41%), Gaps = 26/248 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E +     +    +  L +  +           P  
Sbjct: 24  MQGLVDDVMRDLLTRIGGFDECVSEFVRITHTVHSR-QTWLKYVPEIANGNKTFAGTPCT 82

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  +
Sbjct: 83  VQLLGSDADNMAVNALEAVRFGADKIDLNFGCPAPTVNKHKGGAVLLKEPELIYRIVRTL 142

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + L   IP+T K R+G +D+ PA+       +I  +G   + +HAR         K+  
Sbjct: 143 RRRLPPHIPLTAKMRLGYEDKSPALECA---AAIAAAGACALTVHART--------KNEG 191

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
             P   ++ + +I +++ D+ +  NG +  +   L+I  +   D VM+GR A     +  
Sbjct: 192 YEPPAHWEWIRKI-RDSVDIPVTANGDVFTLEDYLEIKAVSGCDSVMLGRGAVIRPYLAR 250

Query: 228 TVDEYFSN 235
            + +Y   
Sbjct: 251 QIKQYEDG 258


>gi|296388369|ref|ZP_06877844.1| tRNA-dihydrouridine synthase C [Pseudomonas aeruginosa PAb1]
          Length = 319

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 111/288 (38%), Gaps = 27/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I + D +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRVGGIDWCVTEFIRITDRLLPATAFHKLAPELRDGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P+++ D +AA+ 
Sbjct: 68  QLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPELMHDIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   I VT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 RAVPSEIAVTSKMRLGYDSPDGAL---DCARALADGGSAHVVVHARTKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +  E   + +  NG +  +   L+      V+ +M+GR       +   
Sbjct: 178 -PPAHWEWVARVA-EAVRVPVLANGEVWTLDDYLRCREVSGVEDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD-YAARHLHSGGKL 273
           +  +         P      + +DFW +    +   YA   L     +
Sbjct: 236 IAAWRDGGEIHEMPWSELLPLLRDFWLQARRKLAPRYAPGRLKQWLGM 283


>gi|312214198|emb|CBX94192.1| hypothetical protein [Leptosphaeria maculans]
          Length = 623

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/266 (20%), Positives = 96/266 (36%), Gaps = 50/266 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MV+ ++  +R  +R     A     L YT M  +    +  K     F            
Sbjct: 45  MVEQSEFAWRLLSRSFLPPAQQRNLLAYTPMFHSKMFGKESKYRDAHFQPLKSTILSPTD 104

Query: 47  --------------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
                               ++PL +Q    D   L+ AAK V  F  + ++LN+GCP  
Sbjct: 105 SHHLSTLDESQRYLDGNPAFDRPLTVQFCSNDPDDLLAAAKHVAPF-CDAVDLNLGCPQG 163

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
               G +GA L  + D++   I    + L +P+T K RI               K++  +
Sbjct: 164 IAKRGKYGAFLQEDWDLIARMIRKCHEELDVPITAKMRIL----ETREKTLEYAKTLLDA 219

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGL---EDMSQ 202
           G + + +H R+   KG            D+ ++  ++   P D  +  NG +   +D++ 
Sbjct: 220 GASILTVHGRQREQKG------HNTGLADWTVIRYLRDNLPKDTVLFANGNILQHDDIAT 273

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLTT 228
            L+     D VM       +  +   
Sbjct: 274 CLRA-TGADAVMSAEGNLYDPTIFAE 298


>gi|254557522|ref|YP_003063939.1| transcription regulator [Lactobacillus plantarum JDM1]
 gi|254046449|gb|ACT63242.1| transcription regulator [Lactobacillus plantarum JDM1]
          Length = 334

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 74/333 (22%), Positives = 119/333 (35%), Gaps = 37/333 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPL-ALQIG 55
           M   T   +R          + YTE   A +I     K      L     E P   +Q+ 
Sbjct: 27  MEAVTGSVFRRVVMRAAAPDVFYTEFTNALSITHPKAKFTTRGRLYVDEAESPRPIVQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G       +AA  V++ GY  I+LN+GCP   V +   G+ L+ + D   + I    +A 
Sbjct: 87  GNSGEDFTKAAHEVKNQGYQAIDLNMGCPDMAVIKNHSGSDLIRHFDRAKEVIEGARQA- 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PV+VK R+G DD          +  + +  V  + +H R  +     P     I NL 
Sbjct: 146 ELPVSVKTRLGFDDVHEYET---WIPFLLQQQVPVLTVHVRTKMEMSKVPAHYELIDNL- 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEY 232
              V       P   + +NG + D    LK+    P VDG+MIGR  ++N      +   
Sbjct: 202 ---VQMRDTLAPATLLQINGDILDYQAGLKLAKAHPGVDGIMIGRGIFQNPYAFEPI--- 255

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAA----RHLHSGGKLQQITRHMIGLFHGFP 288
                    P  TR   +  R        +       H     +  +I         G  
Sbjct: 256 -------PQPHSTRDMLELLRYQVDLYDQFIGLGLQGHFAPLQRFFKI------YVRGMR 302

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           ++   R+ L ++   +     II+     + E 
Sbjct: 303 HAAELRNEL-MQTKTTDDVRAIIDRLEAKLPED 334


>gi|295112160|emb|CBL28910.1| tRNA-dihydrouridine synthase [Synergistetes bacterium SGP1]
          Length = 344

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 116/321 (36%), Gaps = 30/321 (9%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
              T    R FF RL    +L +TEM+    ++R ++K   +L  S  E P+ LQ+    
Sbjct: 28  AGVTSLPIREFFTRL--GASLTHTEMVSCAGLVRHNRKTLSMLHTSPSEAPVILQLFAPA 85

Query: 59  ISKLVEAAKIVEDF-------GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              LV  A+   D         +  + +N+ CP  +V +   GA L+ +P      +  +
Sbjct: 86  ADVLVRGAEAALDLVHQSGEVPFAGLGINMACPMPKVTKRGAGAALLKSPSDAFAMVRGL 145

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            K L  PV VK R     +    A    ++ +  SG + + IH R A          R  
Sbjct: 146 -KGLGFPVWVKIRRIEAGEAGIEATVRFIEGLLNSGADNVCIHGRTAT--------QRYE 196

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVD 230
              D  +     +  P  FI  +G + ++    + L      VM  R A  N  +     
Sbjct: 197 GVADRTVHAAAARLFPG-FISASGDVREVGDVREYLEMGCVLVMAARGALGNPWLFAEAL 255

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                 +   +  +T   +         + + A         +  + R M G+  G   +
Sbjct: 256 NALGYAVPEMARDRTPAGRMT---ALRWLGERAMGTSGEAQAVILLKRLMGGVLRGISGA 312

Query: 291 RRCRHILTVEAGASTATHHII 311
              RH    +AG S +   I+
Sbjct: 313 AELRH----QAGCSGSVEEIL 329


>gi|91789280|ref|YP_550232.1| dihydrouridine synthase [Polaromonas sp. JS666]
 gi|91698505|gb|ABE45334.1| tRNA-U20a,U20b-dihydrouridine synthase [Polaromonas sp. JS666]
          Length = 344

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 63/333 (18%), Positives = 125/333 (37%), Gaps = 31/333 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +       +E I      +       I+      G +    P+  
Sbjct: 14  MEGLLDFVLRDILTRVGGIDRCVSEFIRITDQLLPERVFTRIVPELHNGGRTLAGVPVRA 73

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + + E A  +   G   I+LN GCP+A V+    GA L+  P+ +   ++A+ 
Sbjct: 74  QLLGSDPACMAENAARLATLGPAGIDLNFGCPAAVVNRHGGGASLLKEPETLLAIVSAVR 133

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+ K R+G +D   AV       +I + G   + +HAR         K    
Sbjct: 134 RAVPAGMPVSAKMRLGYNDDSRAV---ECALAIAEGGAGELVVHART--------KAQAY 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +    + +  NG +  +  A +         +MIGR A  +  +   
Sbjct: 183 KPPAYWERIADI-RAAVQIPVVANGEIWTVDDARRCREASGCSMLMIGRGAVADPGLGLA 241

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +    S+P  G    +  +       + A         L +  +  ++ + +  L   FP
Sbjct: 242 IKAAMSHPAAGGQ--EPGITWAELVPLLADFWHVVCARLDARARPGRLKQWLNFLRRRFP 299

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            +     +L      +     +I+     ++E+
Sbjct: 300 QAEAAYQVL-----KTITDPALIDEWLAALVEA 327


>gi|322823915|gb|EFZ29514.1| dihydrouridine synthase (Dus), putative [Trypanosoma cruzi]
          Length = 548

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 59/329 (17%), Positives = 111/329 (33%), Gaps = 57/329 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---------------- 44
           MVD ++  +R   R      L Y+ M+ A +  +  +     FS                
Sbjct: 103 MVDQSELPFRMLCRRY-GATLAYSPMLHARSFAQSAQYRARYFSTTPHRAEPAMTATASG 161

Query: 45  ---------------TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
                            + PL +Q  G D   L+ AA+ VED     +++N+GCP     
Sbjct: 162 EGEAAEDAGRTSDGEETDHPLFVQFCGNDADTLLAAARHVED-DCEAVDVNLGCPQGIAR 220

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G +G+ LM + D V + +  +   L +PVT K R+  DD           + ++ +G+ 
Sbjct: 221 RGYYGSFLMEDWDRVHNILHCLAVELRVPVTAKMRVFDDD----ALTLKYAEMLRDTGIA 276

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKIL- 207
            + +H R           + K    D + +  +++     + +  NG +       + + 
Sbjct: 277 VLCVHGRT---------RHNKRGLADMEKIRRVREHLRGSIPVIGNGNVLTFEDVRRNMS 327

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWRKISASMTDYAAR 265
               DG M       +  +         N    +   + R+D     ++    +  Y   
Sbjct: 328 ATMTDGYMCAEPLLWDPRLFAAPLHPVRNGRCFAECREARLDAIRTAQEYLQLVQRYPVD 387

Query: 266 HLHSGGKLQQITRH-------MIGLFHGF 287
                  L ++  H       M G    F
Sbjct: 388 LAFVKAHLFKMLFHSYEMHPVMHGWLTNF 416


>gi|170099590|ref|XP_001881013.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164643692|gb|EDR07943.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 234

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 108/235 (45%), Gaps = 25/235 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--------NILGFSTQEKPLAL 52
           MV   D  +R   R     +L YT+M++ D IL             +I      E+P+ +
Sbjct: 13  MVKQADGPFRLLVRKY-GASLTYTQMLLPDRILNDQDYLEYHLRDLSIASDDGLERPVVI 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCIAA 110
           Q+ G D   +V+A + ++    + I+LN+GCP     +G FGA L+   N  +V + ++A
Sbjct: 72  QLCGHDPQTIVKAGRKLQGH-CDAIDLNLGCPQESARDGHFGAYLLGQKNWPLVEEIVSA 130

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           M  + S+PVT K R+      P+ A  +L + ++  GV+ + +HAR            R+
Sbjct: 131 MSSSFSVPVTAKLRLCQ----PSHATLDLSQRLEACGVSWVTLHARNV------SARRRR 180

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNS 223
             + + D V  +K  N  + +  NG + + S   A       DGVM+G     N 
Sbjct: 181 QGSANLDEVKRLKG-NLQVPVVSNGNVREFSDLLANTEYTGADGVMVGETLLGNP 234


>gi|328851127|gb|EGG00285.1| hypothetical protein MELLADRAFT_93719 [Melampsora larici-populina
           98AG31]
          Length = 321

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 102/261 (39%), Gaps = 43/261 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-------------- 46
           MV ++   +R        + + +T MI+A       K     FST               
Sbjct: 1   MVRYSKLPFRQLVSEYETH-ITFTPMILAKEFSLSQKARDSDFSTNPFERGTFSMIDSSN 59

Query: 47  ------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
                 +  L  Q+GG +   +  AA++++ +  + I++N GCP +  ++   G+ L+  
Sbjct: 60  QSTRLVKGSLVAQLGGNESFYMAHAAELLQPY-VDGIDINCGCPQSWAYKEGIGSALLRK 118

Query: 101 PDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           PD+V D +  +        PV++K R+  D Q  +     L+K+   + V+ I +H R  
Sbjct: 119 PDLVRDLVRGIKTKCGETFPVSIKIRVDDDLQHTS----RLIKTALAANVSFITVHGRT- 173

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKEN-----PDLFIGLNGGLEDMSQAL--KILPSVD 211
                  +       + YD +    +E        +    NG +  ++ A   + L  V 
Sbjct: 174 -------RHQASSEPVSYDSIKFAAEEATTGSDGGVPTAANGNVFTLADAQKTRELCGVK 226

Query: 212 GVMIGRAAYKNSAMLTTVDEY 232
           GVM  R   +N A+    +  
Sbjct: 227 GVMSARGLQENPALFAGYERI 247


>gi|254496630|ref|ZP_05109495.1| nitrogen regulation protein [Legionella drancourtii LLAP12]
 gi|254354152|gb|EET12822.1| nitrogen regulation protein [Legionella drancourtii LLAP12]
          Length = 268

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 48/209 (22%), Positives = 91/209 (43%), Gaps = 20/209 (9%)

Query: 26  MIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M  A  IL         +  + QE+ LA QI G +   L +AA+ ++  G + I++N GC
Sbjct: 1   MSSAADILHKHTVNSRYIYRAAQEQILAYQISGTEPQVLAQAARQLQMQGADLIDINCGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P  ++ +   G+ L+  P+ +   + A+  A++IP+T+K RI  +D         L + I
Sbjct: 61  PKPKIRKKGAGSALLERPEQLVSLVHAVRAAITIPLTIKIRIQGNDHDLL-----LAQKI 115

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDM 200
             +G + + +H R+                 ++  + +IK     + +  NG +     +
Sbjct: 116 AAAGADALIVHGRRWFDG--------YDVAANWQQIAQIKN-VLTIPVIANGDIADGTSL 166

Query: 201 SQALKILPSVDGVMIGRAAYKNSAMLTTV 229
            QA+      D  MI RA   +  +   +
Sbjct: 167 QQAVA-YSGCDAYMISRAGSGHPWLYQEL 194


>gi|156037856|ref|XP_001586655.1| hypothetical protein SS1G_12642 [Sclerotinia sclerotiorum 1980]
 gi|154698050|gb|EDN97788.1| hypothetical protein SS1G_12642 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 587

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 59/288 (20%), Positives = 103/288 (35%), Gaps = 58/288 (20%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R  +R         + L YT M+ A       K     F            
Sbjct: 53  MVDQSEFAWRMLSRSFMSPESNKSLLAYTPMLHARMFSETPKFRDAHFQPMKSSLVSQLD 112

Query: 47  ------------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
                             ++PL +Q    D  +L+E AK V  F  + ++LN+GCP    
Sbjct: 113 SSCPIPKEDIFLDGNPAFDRPLFVQFCANDEKELLEGAKYVAPF-CDAVDLNLGCPQGIA 171

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
             G +GA L  +  ++   I  + K L +PVT K RI               K +  +G 
Sbjct: 172 RRGKYGAFLQEDQGLIYKLINTLHKELDVPVTAKIRIL----ETREKTLEYAKMVVSAGA 227

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL 207
           + + +H R   +KG       K    D+ ++  +++  P  + +  NG +       + L
Sbjct: 228 SILTVHGRTREMKG------HKTGLADWAVLRFLRESLPKEVVLFANGNILSREDIDECL 281

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                DGVM       +  + +             +P      +++WR
Sbjct: 282 KVTGADGVMSAEGNLYDPTIFSD------------APTLREEGREYWR 317


>gi|71023677|ref|XP_762068.1| hypothetical protein UM05921.1 [Ustilago maydis 521]
 gi|74699222|sp|Q4P1U2|DUS3_USTMA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|46101502|gb|EAK86735.1| hypothetical protein UM05921.1 [Ustilago maydis 521]
          Length = 867

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 57/296 (19%), Positives = 103/296 (34%), Gaps = 33/296 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKL- 62
           +  +R       ++ +   EM +A++ L G+  + +++     E+    Q+ G     L 
Sbjct: 502 NLPFRRICTGYGSD-IHCGEMGLAESFLHGNAAEWSLVRRHESERIFGTQLCGGKPDLLV 560

Query: 63  --VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
              EA K     G + +++N GCP   V     G+ L+ +P  +   +  M   L   P+
Sbjct: 561 PVAEALKAEVGDGLDFVDINCGCPIDLVFNKGAGSALLDHPTKLSKIVRGMNAVLGDTPL 620

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R G   +     +    K+  +  V    +H R    +  +  D   I      + 
Sbjct: 621 TIKLRTGTGAKQTTHKI--FAKAQTEWRVAAATLHGRSRKQRYKNDADWGYIATCANTLR 678

Query: 180 YEIKK-----------ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
             + +           E   + +  NG +       + +    VDG MI R A     + 
Sbjct: 679 ESVSEWNESSRFADEPEMVPIPVYGNGDVYSWQDYYERIERTHVDGEMIARGALIKPWLF 738

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI 281
           T + E           I +R   D  RK      +Y   H  S    +    R M 
Sbjct: 739 TEIKERRDWD------ISSRERLDMMRK----FAEYGLTHWGSDTHGVNTTRRFMC 784


>gi|326492876|dbj|BAJ90294.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326526215|dbj|BAJ97124.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 320

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 114/303 (37%), Gaps = 49/303 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----------------VADAILRGDKKNILGF 43
           MV      +R  A       + Y E I                   D + RG    +   
Sbjct: 12  MVRAGTLPFRLLAAEY-GADITYGEEIIDHKFVHCQRVTNESLGTTDFLERGTDSVVFRT 70

Query: 44  STQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             QE+  +  Q+G +D  + ++AA+IV +     I++N+GCP A    G  G+ L+  P+
Sbjct: 71  CPQERDRVVFQMGTSDAVRALKAAEIVCN-DVAAIDINMGCPKAFSVSGGMGSALLSKPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L+ PVT K R+    Q        L + I+K GV  + +H RK   + 
Sbjct: 130 LIHDILTTLRRNLNTPVTCKIRLLNTRQDTV----ELARRIEKCGVPALAVHGRKVKDRP 185

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAY 220
             P          +D + ++      + +  NG + +     +I        VM  R A 
Sbjct: 186 RDP--------AKWDEIADVVSAL-SIPVIANGDVFEYEDFKRIKDATGATSVMAARGAL 236

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
            N+++ +              P      +DF R+       +      +   L++I  H 
Sbjct: 237 WNASIFS--------------PNGKVPWEDFKREYVRKTILWDNCIKSTKTTLREIIMHY 282

Query: 281 IGL 283
           I L
Sbjct: 283 ICL 285


>gi|229520462|ref|ZP_04409887.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TM 11079-80]
 gi|229342560|gb|EEO07553.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TM 11079-80]
          Length = 323

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGF------STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +         +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRQGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR  +          K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTKV-------GGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QTNELFGEL 294


>gi|229515488|ref|ZP_04404947.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TMA 21]
 gi|229347257|gb|EEO12217.1| tRNA-dihydrouridine synthase C [Vibrio cholerae TMA 21]
          Length = 323

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 116/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+++   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQVCIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|326911232|ref|XP_003201965.1| PREDICTED: tRNA-dihydrouridine synthase 4-like [Meleagris
           gallopavo]
          Length = 262

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 103/250 (41%), Gaps = 31/250 (12%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           +    + ++     + PL +Q    +   L +AA +V  F  + ++LN GCP        
Sbjct: 10  VHTSVQQLVTLHDSDNPLIVQFAAKEAQVLCDAALLVCPF-ADGVDLNCGCPQRWAMAEG 68

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +GACL+  P++V D +  +   +  P   V++K RI  D +       +L K  + +GV+
Sbjct: 69  YGACLINKPELVQDMVRHVRNRIDNPRFSVSIKIRIHEDLKKTV----DLCKKAEATGVS 124

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--L 207
            I +H R    +            + YD +  + KE+  + +  NG ++ +  A  +  L
Sbjct: 125 WITVHGRNTEERHQ---------PVHYDAIK-VIKESMHIPVVANGDIKSLKDAENVHRL 174

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              DGVM+ R    N AM    +E              +  +D+        T +   H 
Sbjct: 175 TGADGVMVARGLLANPAMFAGYEE-----------TPLKCIQDWVDIALEHGTPFTCFHH 223

Query: 268 HSGGKLQQIT 277
           H    +++IT
Sbjct: 224 HLMYMMERIT 233


>gi|289522351|ref|ZP_06439205.1| dihydrouridine synthase family protein [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289504187|gb|EFD25351.1| dihydrouridine synthase family protein [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 329

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 123/323 (38%), Gaps = 35/323 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGA 57
           M D T    R  F R      L +TEM+ + A++ G       L     E PL LQ+   
Sbjct: 14  MADITSWPVRKMFFR--VGVGLAHTEMVASRALMEGHSSAFYSLQRHHDEGPLVLQLFSG 71

Query: 58  DISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           D++ L+EAA+       +  +++N+ CPS +V     GA L+  P +  + I    K L 
Sbjct: 72  DVASLLEAAQEAFRISSFEALSINMACPSKKVMASGGGASLINRPHVAAEMIRQ-AKNLG 130

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            P+ VK RI   +     +  +L   +  +G   + +H R                + D 
Sbjct: 131 FPIWVKTRIPSRNLKDVASWCDL---LISAGAKNVALHGRT--------VSQGYKGSSDR 179

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +I+ E+ +  P   I   G +      L  L     GV++ R A K+  ++  +D     
Sbjct: 180 NIIGEVARAFPG-KITGTGDVFTSDDVLDYLEKGCIGVLVARGALKDPFIV--LDALAKL 236

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
                        ++ +R   + +       +     +  + R +  +F G P + + R 
Sbjct: 237 GFRNDRKATFEFQREIFRSFLSDLC-----QVKDNLAMHLLRRFLSCIFKGMPGASQLR- 290

Query: 296 ILTVEAGASTATHHIIETAFNLM 318
                  +S A  H I  AF + 
Sbjct: 291 -------SSMARAHGITQAFEIF 306


>gi|110835023|ref|YP_693882.1| dihydrouridine synthase (Dus) superfamily protein [Alcanivorax
           borkumensis SK2]
 gi|110648134|emb|CAL17610.1| Dihydrouridine synthase protein family, putative [Alcanivorax
           borkumensis SK2]
          Length = 314

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 114/270 (42%), Gaps = 30/270 (11%)

Query: 20  ALLYTEMIVADAIL--------RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
               +E +    +L           +  +   +    P+ LQ+ G+D + + + A+   +
Sbjct: 30  DWCVSEFVRVSGLLLPPKVFYRWCPELKLGARTRAGTPVHLQLLGSDPACMADNAERAVE 89

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDD 129
            G   I+LN GCP+  V+    GA L+  PD+V    AA+ +A+   +PV+VK R+G +D
Sbjct: 90  LGAPAIDLNFGCPAKTVNRHRGGAVLLDEPDVVHAVTAAVRQAVPSQVPVSVKMRLGNED 149

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
              A+   +  +++  +G   + +H R         K     P   +D +  I +E   +
Sbjct: 150 DARAL---DNARAVVDAGAAWLTVHGRT--------KRQGYKPPAFWDRIGHI-REVVSI 197

Query: 190 FIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
            +  NG +     A   +     + +M+GR A  N  +++ +   F       + +   +
Sbjct: 198 PVIANGEIWTPDDAGRAQRESGCEDLMLGRGAVANPLLVSLLR--FGGETNWDAILP--I 253

Query: 248 DKDFWRKISASMTD--YAARHLHSGGKLQQ 275
            + FW  ++ + TD   A R       L++
Sbjct: 254 LQQFWMDVADTGTDAQLAGRIKQWLSYLRR 283


>gi|86147938|ref|ZP_01066242.1| putative regulator protein [Vibrio sp. MED222]
 gi|85834263|gb|EAQ52417.1| putative regulator protein [Vibrio sp. MED222]
          Length = 303

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 57/301 (18%), Positives = 115/301 (38%), Gaps = 44/301 (14%)

Query: 10  RFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEK---------PLALQIGGADI 59
           R     + +  L  TE + V D +L     +      +           P+ LQ+ G   
Sbjct: 2   REILTEINDYDLCVTEFVRVVDQLLPPHVFH--RICPELHQGSQTMAGVPIHLQLLGQHP 59

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--I 117
           + + E A      G   I+LN GCP+  V++ + GA L+  P+++   + +   A+   I
Sbjct: 60  NWMAENAFQAASLGAKGIDLNFGCPAKAVNKSNGGASLLKEPELIYQVVKSCRDAVPAHI 119

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV+ K R+G +          +V +I+++  + + +HAR  +          K   + +D
Sbjct: 120 PVSAKIRLGWE---HPEECFEIVDAIEQAKADELTVHARTKV-------GGYKASEIKWD 169

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +I +E   L +  NG + +       +    VD +M+ R A+    +   V      
Sbjct: 170 YINQI-REKTSLPLIANGEIWNYQDGQDCIEATGVDSLMVCRGAFNIPNLGNVVKH---- 224

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFHGFPNSRR 292
                        K  W K+   +  Y+   +     +    ++ +  + L  G+P +  
Sbjct: 225 ----------NHPKMPWNKVIELLLRYSEFQIKGDKGMYYPNRVKQWFVYLSKGYPEANE 274

Query: 293 C 293
            
Sbjct: 275 L 275


>gi|104294976|gb|ABF71992.1| hypothetical protein MA4_111B14.10 [Musa acuminata]
          Length = 220

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 65/139 (46%), Positives = 93/139 (66%), Gaps = 3/139 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+DWTD HYR  ARL++ +A LYTEM+VA+ I+   +     L FS  + P+ LQIGG++
Sbjct: 11  MMDWTDNHYRTLARLISKHAWLYTEMVVAETIVHQSENLDRFLAFSPIQHPIVLQIGGSN 70

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKALSI 117
           ++ L +AA++   + Y+EINLN GCPS +V     FGA LM +P+ VGD ++A+     +
Sbjct: 71  LTNLAKAAELANSYSYDEINLNCGCPSGKVAGHGCFGARLMFDPEFVGDAMSAIASNCDV 130

Query: 118 PVTVKCRIGVDDQIPAVAL 136
           PV+VKCRIGVDD+     L
Sbjct: 131 PVSVKCRIGVDDRDSYDEL 149


>gi|70996530|ref|XP_753020.1| dihydrouridine synthase family protein [Aspergillus fumigatus
           Af293]
 gi|66850655|gb|EAL90982.1| dihydrouridine synthase family protein, putative [Aspergillus
           fumigatus Af293]
 gi|159131754|gb|EDP56867.1| dihydrouridine synthase family protein, putative [Aspergillus
           fumigatus A1163]
          Length = 541

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 108/318 (33%), Gaps = 70/318 (22%)

Query: 1   MVDWTD----------RHYRFFARLLTNNA-----LLYTEMIVADAI-------LRGDKK 38
           MVD ++          + +R   R           L Y+ M  A           +  + 
Sbjct: 44  MVDRSEFRIRTNHSISQAWRMLTRSFMPPDDPKPILAYSPMYHARLFREQANVRWQHFQP 103

Query: 39  NILGFSTQE------------KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
              G    +            +PL +Q    D    +EAA+ V  +  + ++LN+GCP  
Sbjct: 104 TRAGLDKNDNSLYLDGNPAFDRPLIVQFCANDPDDFLEAARHVAPY-CDAVDLNLGCPQG 162

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
              +G +GA L  + D++   I  + K L IPVT K RI    Q          K I  +
Sbjct: 163 IARKGHYGAFLQEDWDLIYKLINRLHKELPIPVTAKFRI----QESKEKTLEYAKMILSA 218

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALK 205
           G + I +H R    KG            D+  +  ++    P+  I  NG   +     +
Sbjct: 219 GASIITLHGRTREQKG------HNTGLADWSYIRYLRDNLPPETVIFANGNNLNHDDLER 272

Query: 206 IL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            L     DGVM       + A+ +              P      +++WR          
Sbjct: 273 CLEATGADGVMSAEGNLSDPAIFS------------KPPPVGSEGREYWR---------- 310

Query: 264 ARHLHSGGKLQQITRHMI 281
            R+   G ++  I R  +
Sbjct: 311 GRNGKGGYRIDAIFRRYL 328


>gi|260890147|ref|ZP_05901410.1| putative dihydrouridine synthase [Leptotrichia hofstadii F0254]
 gi|260860170|gb|EEX74670.1| putative dihydrouridine synthase [Leptotrichia hofstadii F0254]
          Length = 325

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 55/290 (18%), Positives = 117/290 (40%), Gaps = 24/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKPLALQIGGA 57
           M   TD  +R   +    +  L+TEM+ A+ + R D      +L    +++    QI G 
Sbjct: 8   MAGTTDYSFRKILKKFEPD-FLFTEMVNANLLNREDDTTINELLKCDDKQR-TGTQIFGG 65

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D  +L+     +++FG+ +IN+N+GCP  ++ +   G+ L+ NPD+V   +    + +  
Sbjct: 66  DKDELISGILKLKNFGFKKINVNMGCPQPKIIKNGAGSALLENPDLVDQVLLET-QNIGA 124

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K R+G  D        NL     K  ++ I +H R                  +++
Sbjct: 125 EISIKIRVGYKDFNNPEIFLNLAN---KHNLDFICVHGRTQK--------QMYSGTANWE 173

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFSN 235
           IV ++ K   ++    NG L + ++  +   S   DG+++ R    N  +++   E+   
Sbjct: 174 IVEKLSKMPRNINFFGNGDLFEPTEIKRKTSSCNLDGIILSRGIIGNPWLISQTREFLQI 233

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
               +              +         ++      + +I + +   F 
Sbjct: 234 GKINTIQTFDETKSLVLEHLQN-----IVKNKGEMKAVLEINKFLRPYFQ 278


>gi|223590199|sp|A5DBS1|DUS3_PICGU RecName: Full=tRNA-dihydrouridine synthase 3
 gi|190344863|gb|EDK36628.2| hypothetical protein PGUG_00726 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 607

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 112/299 (37%), Gaps = 30/299 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +L+       +    + E P   +QI  +     
Sbjct: 251 NLPYRRLMKTL-GADVTYSEMALSLPLLQATNSEWALPKAHSSEYPGFGVQIATSKHWAA 309

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+++  E    +E+NLN GCP   ++    G+ LM  P  +   +  M   +  IPV
Sbjct: 310 AKAAEVIYKETTHVSELNLNCGCPIDLLYRQGQGSALMEQPARLLRILKGMNASSGDIPV 369

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNL---- 174
           TVK R G  D       ++LV+ +  ++ V  I +H R    +     D   I  +    
Sbjct: 370 TVKIRTGTKDNKNTA--KSLVERVLAENDVAAITLHGRSRQQRYTKDADWEYIKEVGAVV 427

Query: 175 -DYDIVYEIKKENP---DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            +++   E  KE+          NG +         +    VD VM+ R A     +   
Sbjct: 428 TEWNNKKEEDKESSETNRTNFVGNGDVFTHEDWYNAVNTEGVDSVMVARGALIKPWIFEE 487

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           V+       + +  +           I     D++  H  S      ++R  +  F  F
Sbjct: 488 VEAQQYLDKSATERL----------DILRKFADFSLEHWGSDEYGVGLSRRFMCEFLSF 536


>gi|146422829|ref|XP_001487349.1| hypothetical protein PGUG_00726 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 607

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 62/299 (20%), Positives = 112/299 (37%), Gaps = 30/299 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +L+       +    + E P   +QI  +     
Sbjct: 251 NLPYRRLMKTL-GADVTYSEMALSLPLLQATNSEWALPKAHSSEYPGFGVQIATSKHWAA 309

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+++  E    +E+NLN GCP   ++    G+ LM  P  +   +  M   +  IPV
Sbjct: 310 AKAAEVIYKETTHVSELNLNCGCPIDLLYRQGQGSALMEQPARLLRILKGMNASSGDIPV 369

Query: 120 TVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPNL---- 174
           TVK R G  D       ++LV+ +  ++ V  I +H R    +     D   I  +    
Sbjct: 370 TVKIRTGTKDNKNTA--KSLVERVLAENDVAAITLHGRSRQQRYTKDADWEYIKEVGAVV 427

Query: 175 -DYDIVYEIKKENP---DLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            +++   E  KE+          NG +         +    VD VM+ R A     +   
Sbjct: 428 TEWNNKKEEDKESSETNRTNFVGNGDVFTHEDWYNAVNTEGVDSVMVARGALIKPWIFEE 487

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           V+       + +  +           I     D++  H  S      ++R  +  F  F
Sbjct: 488 VEAQQYLDKSATERL----------DILRKFADFSLEHWGSDEYGVGLSRRFMCEFLSF 536


>gi|224531764|ref|ZP_03672396.1| putative histidine phosphokinase/phophatase [Borrelia valaisiana
           VS116]
 gi|224511229|gb|EEF81635.1| putative histidine phosphokinase/phophatase [Borrelia valaisiana
           VS116]
          Length = 329

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 116/270 (42%), Gaps = 30/270 (11%)

Query: 1   MVDWTDRHYRFFARLLTN----NALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I A  IL G K++I    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSKEGEPHIYFTEFISAKGILNGSKQSIQHVFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP  ++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKNKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A    ++P++VK R G         +   +  +    ++ + ++ R A+ +   P    
Sbjct: 137 EACAKFNLPLSVKTRHGF----SYPEVDAWLGFLLSFKIDMLTVYPRLAVDQSKGP---- 188

Query: 170 KIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +++DI +E+ K      P   I  NG +  +  A   +    +DG+M GR  +KN 
Sbjct: 189 ----VNFDIFHELVKLRNNISPSTLIIGNGDVLSLKDAKYYVDKYLIDGIMFGRGIFKNL 244

Query: 224 AMLT-TVDEYFSNPLTGSSPIKTRVDKDFW 252
            +   +   +  + L     I     KDF 
Sbjct: 245 NLFKLSSKHFLDSNLNFRLNILKFHIKDFH 274


>gi|50303445|ref|XP_451664.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49640796|emb|CAH02057.1| KLLA0B02959p [Kluyveromyces lactis]
          Length = 351

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 53/235 (22%), Positives = 106/235 (45%), Gaps = 14/235 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV ++   +R   R    + ++YT MI+A   +R     +  F+T  ++ PL +Q+G  +
Sbjct: 40  MVRYSKLAFRQTCRQYDVD-IVYTPMILAREFVRNGHARMADFTTCDEDSPLIVQVGVNN 98

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  L++  ++V  +  + I +N GCP         G+ L+ N +++ D + A+       
Sbjct: 99  VPDLLKFTEMVYPY-CDGIGINCGCPIREQVREGIGSALIYNGELLCDMVKAVKDKYRDS 157

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++ +I + D +       L   + ++GV+ I +H R    +   P +   I  +  ++
Sbjct: 158 VRLETKIRIHDDVKDTV--KLCDDLCEAGVDWITVHGRTRTTRSSVPVNLDAIKFIRENM 215

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDE 231
            Y+      D+ +  NG    ++   +I     VDGVM  R    N A+    D+
Sbjct: 216 KYQ------DVPLVANGDCFTLNDCYRISEYTKVDGVMAVRGLLCNPALFDGYDK 264


>gi|302840690|ref|XP_002951897.1| hypothetical protein VOLCADRAFT_105302 [Volvox carteri f.
           nagariensis]
 gi|300262798|gb|EFJ47002.1| hypothetical protein VOLCADRAFT_105302 [Volvox carteri f.
           nagariensis]
          Length = 894

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 53/300 (17%), Positives = 101/300 (33%), Gaps = 45/300 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   + L  + +   EM +A  +L+G      +L     E    +Q+ G     L 
Sbjct: 481 NLPFRRVCKSLGVD-VTCGEMALATNLLQGQAAEWALLKRHPCEDLFGVQVCGGYPDALA 539

Query: 64  EAAKIVED-FGYNEINLNVGCPSA--------RVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              +++ +    + +++N+GCP           V + + G+ L+  P  +   + A   A
Sbjct: 540 RVGQLLNERLVVDFVDINMGCPIDLVGVWAGVGVCDKNAGSALLRQPRRIEQILRATSAA 599

Query: 115 L-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           L  IP+T K R G +D          +      G   + +H R         +  R    
Sbjct: 600 LGDIPLTFKTRKGFNDGEDVA--HTFLPKAAGWGAAAVTLHGRT--------RQQRYSKL 649

Query: 174 LDYDIVYEIKKENPD--LFIGLNGGLEDM-----SQALKILPSVDG-----VMIGRAAYK 221
            D+D +        +  L +  NG +            +      G     +MIGR A  
Sbjct: 650 ADWDYIQRCAAPCSEAGLQLIGNGDVFSYLDWNRQMDRRETEGEGGGSLASIMIGRGALI 709

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              + T + E     ++ S  +           +          H  S G+  + TR  +
Sbjct: 710 KPWIFTEIKEQRHWDISASERL----------DLYKQFCTAGLEHWGSDGRGVETTRRFL 759


>gi|254428569|ref|ZP_05042276.1| Dihydrouridine synthase superfamily [Alcanivorax sp. DG881]
 gi|196194738|gb|EDX89697.1| Dihydrouridine synthase superfamily [Alcanivorax sp. DG881]
          Length = 315

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 63/298 (21%), Positives = 116/298 (38%), Gaps = 37/298 (12%)

Query: 20  ALLYTEMIVADAIL--------RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
               +E +    +L           +  +   +    P+ LQ+ G++   + E A     
Sbjct: 30  DWCVSEFVRVSGLLLPPRVFYRWCPELKLGARTRAGTPVHLQLLGSEPDCMAENAVRAVA 89

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDD 129
            G   I+LN GCP+  V+    GA L+  P++V    AA+  A+  ++PV+VK R+G +D
Sbjct: 90  LGAPAIDLNFGCPAKTVNRHRGGAVLLDEPEVVHAVTAAVRDAVPANVPVSVKMRLGNED 149

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
              A+   +  +++ ++G   + +H R         K     P   +D +  I +E   +
Sbjct: 150 DARAL---DNARAVVEAGAAWLTVHGRT--------KRQGYKPPAFWDRIGHI-REVVSI 197

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
            +  NG +     A +       D +M+GR A  N  +++ +            PI  + 
Sbjct: 198 PVIANGEIWTADDAARARQESGCDDLMLGRGAVANPRLVSVLRHGGEPGWDAILPILQQ- 256

Query: 248 DKDFWRKISASMTD--YAARHLHSGGKLQQITRHMIGLFHGFPNSRRCR-----HILT 298
              FW  ++ + TD   A R       L++       L       R  R      IL+
Sbjct: 257 ---FWVDVAGTGTDAQLAGRIKQWLSYLRRRWPQAAQLLEQLK--RETRPEVIARILS 309


>gi|294054269|ref|YP_003547927.1| dihydrouridine synthase DuS [Coraliomargarita akajimensis DSM
           45221]
 gi|293613602|gb|ADE53757.1| dihydrouridine synthase DuS [Coraliomargarita akajimensis DSM
           45221]
          Length = 356

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/301 (20%), Positives = 110/301 (36%), Gaps = 36/301 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE--MIVADAILRGDKKNILGFSTQEKPLALQIGGAD 58
           M D T   +           LL+TE   +   + L     + +     ++P+  Q+ G  
Sbjct: 22  MQDVTTLPFMRLLGAYGAPDLLFTEYFRVHGHSNLESHIVDSICKHGTDRPVFAQLIGES 81

Query: 59  ISKLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
              L    K + D       I+LN+GCP+ +V++ + G  L+  P+ +   +  + +++ 
Sbjct: 82  HPDLKRTVKAIHDAQLPVAGIDLNMGCPAPKVYKKNVGGGLLREPEKIDGILGLLRESVE 141

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
              TVK RIG +D     A+ +L+   +K  V+ + +HAR       S      I     
Sbjct: 142 GRFTVKMRIGFEDDRHFEAILDLI---EKHEVDLLSLHARTVKEAYRSEVHYAYIKRA-- 196

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                   E     +  NG +  +++   +L      G+MIGR+  +N  +     E+F+
Sbjct: 197 -------AERLACPVLANGNVTSVAKGQWVLDETKCAGLMIGRSCIRNPWIFRQHREHFA 249

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD-----YAARHLHS------------GGKLQQIT 277
                  P    V +       A+        Y   HL              G  L  + 
Sbjct: 250 GQTVFK-PTLADVRQYVEDLYEATTLPDRKGVYHVNHLKKFLNFVGLGVDIDGQFLHDMR 308

Query: 278 R 278
           R
Sbjct: 309 R 309


>gi|148654121|ref|YP_001281214.1| dihydrouridine synthase, DuS [Psychrobacter sp. PRwf-1]
 gi|148573205|gb|ABQ95264.1| dihydrouridine synthase, DuS [Psychrobacter sp. PRwf-1]
          Length = 323

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 103/247 (41%), Gaps = 30/247 (12%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEM------IVADAILRGDKKNIL--GFSTQE 47
           M   TD   R     + ++         +E       ++ + +       +L  G +   
Sbjct: 18  MEGLTDPLMRQILTQIASDLGRPYDWSVSEFIRITHHVLPEHVFYRFVPELLQSGTTDSG 77

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ +Q+ G++   +   A    + G   I+LN GCP+  V+    G+ L+  P ++ D 
Sbjct: 78  TPIHVQLLGSEPKLMGANALAAAELGAPAIDLNFGCPAKTVNNHRGGSVLLDEPRLMRDI 137

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I+A+ +A+   IPV+ K R+G +D      + ++ ++I  SG + + IHAR         
Sbjct: 138 ISAVREAVPAHIPVSAKIRLGYNDTNN---IDDIRQAIADSGADWLTIHART-------- 186

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
           K     P   ++ +  +      + I  NG + +   A + +       VM+GR A    
Sbjct: 187 KTQGYKPPAYWEKI--VAFTELPIPIIANGEIWNAQHAHQCIAQSHTSHVMLGRGAVTRP 244

Query: 224 AMLTTVD 230
            ++  +D
Sbjct: 245 DLVAQID 251


>gi|295318114|gb|ADF98491.1| dihydrouridine synthase family protein [Clostridium botulinum F
           str. 230613]
          Length = 287

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 62/296 (20%), Positives = 121/296 (40%), Gaps = 27/296 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFHNIDKYFTPFIVPNKSTSLKTKELRDILPENNEGINIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  + +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSERFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               P+LD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYG------NKPDLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +++         I  NG +  +S     +K  P V  +M+GR    N  ++  +    
Sbjct: 178 --IFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLINEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                 ++ I   V K+F  +I     +      ++  +++++  +MI +F    N
Sbjct: 233 -----NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIFSNIKN 283


>gi|284007122|emb|CBA72398.1| tRNA-dihydrouridine synthase C [Arsenophonus nasoniae]
          Length = 313

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 60/286 (20%), Positives = 110/286 (38%), Gaps = 24/286 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     +    L  TE +        A A  R   +      +     + +
Sbjct: 8   MEGVLDSLVRELLTEVNEYDLCITEFLRVVDSLLPAKAFYRICPELYQARKTVSGTLVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++ N GCPS  V+    GA L+ +P+ +     A+ 
Sbjct: 68  QLLGQHPQWLAENAARAVELGSWGVDFNCGCPSPTVNGHGGGATLLKDPERIYQAAKAIR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  ++P +VK R+G DD+  A     +  +++++G   I IH R          +  +
Sbjct: 128 AAVPANLPTSVKVRLGWDDRCLAF---EIADAVQQAGATEIIIHGRTK-------AEGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTT 228
              +D   +  I+++   + +  NG + D   +   + +   D +MIGR        L  
Sbjct: 178 AEKIDSLTIGRIRQKLT-IPVIANGEIWDWCSANECRTITGCDALMIGRGGLHVP-NLAQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           V +Y + P+  S  ++         K   +   + AR     G L+
Sbjct: 236 VIKYQTEPMAWSQVMQLLFKYIQLEKQGDTGQYHTARIKQWLGYLR 281


>gi|118082096|ref|XP_001231946.1| PREDICTED: similar to Dihydrouridine synthase 4-like (S.
           cerevisiae) isoform 2 [Gallus gallus]
          Length = 301

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 57/219 (26%), Positives = 96/219 (43%), Gaps = 23/219 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT M+VA   +R  K     F+T   + PL +Q    +
Sbjct: 32  MVRYSKLAFRTLVRRY-GCDLCYTPMVVAADFVRSAKARDSEFTTNRGDNPLIVQFAAKE 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + ++LN GCP        +GACL+  P++V D +  +   +  P
Sbjct: 91  AQVLCDAALLVCPF-ADGVDLNCGCPQRWAMAEGYGACLINKPELVRDMVRHVRNQIDNP 149

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D +       +L K  + +GV+ I +H R    +            + 
Sbjct: 150 RFSVSIKIRIHEDLKKTV----DLCKKAEATGVSWITVHGRNIEERHQ---------PVH 196

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDG 212
           YD +  + KE+  + +  NG ++ +  A     L   DG
Sbjct: 197 YDAIK-VIKESIHIPVVANGDIKTLKDAENVHHLTGADG 234


>gi|93007131|ref|YP_581568.1| dihydrouridine synthase, DuS [Psychrobacter cryohalolentis K5]
 gi|92394809|gb|ABE76084.1| dihydrouridine synthase, DuS [Psychrobacter cryohalolentis K5]
          Length = 340

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 102/261 (39%), Gaps = 30/261 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIVAD-----AILRGDKKNILGFSTQ---E 47
           M   TD   R     + ++         +E I        A +       L    +    
Sbjct: 28  MEGLTDPLMRQILTQIASDLGRPYDWSVSEFIRVTQHVLPAHVFYKYVPELRHDAKTACG 87

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ +Q+ G++   + + A      G   I++N GCP+  V+    G+ L+  P+ +   
Sbjct: 88  TPIHIQLLGSEAQLMADNAAYACALGAPAIDINFGCPAKTVNSHRGGSVLLDEPETMYQI 147

Query: 108 IAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I+A+ +A+   IPV+ K R+G  D      + ++  +IK SG + + +HAR         
Sbjct: 148 ISAVRQAVPADIPVSAKIRLGYTDTSL---MDDIRGAIKDSGADWLTVHART-------- 196

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           K     P   +D +        D+ +  NG + +   A   +     + +M+GR A    
Sbjct: 197 KTQGYKPPAYWDKIQSF--NALDIPVIANGEIWNAEHAQNCMTQSGTEHLMLGRGAVTRP 254

Query: 224 AMLTTVDEYFSNPLTGSSPIK 244
            ++  VD   S  L   + + 
Sbjct: 255 DLIAQVDREHSQTLNNETTLL 275


>gi|153828105|ref|ZP_01980772.1| conserved hypothetical protein [Vibrio cholerae 623-39]
 gi|148876347|gb|EDL74482.1| conserved hypothetical protein [Vibrio cholerae 623-39]
          Length = 323

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 115/309 (37%), Gaps = 34/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G +D         +V ++ ++  + + +HAR             K
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK-------AGGYK 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              + +  + +I+ +   + +  NG + + +     +    VD +M+ R A  N   L  
Sbjct: 178 ASEIKWHYIDQIRPKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGAL-NVPNLGN 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V ++    +     +           +    T +  R         +I +    L H +P
Sbjct: 236 VVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQWFAYLRHAYP 285

Query: 289 NSRRCRHIL 297
            +      L
Sbjct: 286 QANELFGEL 294


>gi|326436672|gb|EGD82242.1| dihydrouridine synthase [Salpingoeca sp. ATCC 50818]
          Length = 434

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 66/295 (22%), Positives = 105/295 (35%), Gaps = 33/295 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEK---PLAL 52
           MV  ++  +R          L YT M+ AD +L  +         L    +     PL  
Sbjct: 34  MVWQSETAFRRLVTAEGGCDLAYTPMMHADQLLENNLAAQSHLTDLRQDMERGRPYPLLG 93

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+   +    V+AA++VE +  + ++LN+GCP      G FGA LM +PD V   +    
Sbjct: 94  QLCATNADDFVQAAQLVEPY-VDAVDLNLGCPQRTAQAGGFGAFLMEHPDTVAAIVQRAS 152

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             L +PV  K R+  D            + +++SG + + +H R    +           
Sbjct: 153 TTLQVPVCCKIRVFTDVDKTVA----FARMLQESGCSMLAVHGRTRAQRHHE-------G 201

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
              YD V  I  E  D+ + +NGG+    QA  IL        M          M T V 
Sbjct: 202 TPHYDTVRAIV-EALDIPVVVNGGIATRQQADAILRHTGACATMSATGLLACPLMYTGVA 260

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
              + P   +         ++  +       Y   H+     L     H     H
Sbjct: 261 ASETTPFEHAHKYL-----EYACRYPPPCARYIRDHV-----LALFRSHFANYAH 305


>gi|92112823|ref|YP_572751.1| dihydrouridine synthase, DuS [Chromohalobacter salexigens DSM 3043]
 gi|91795913|gb|ABE58052.1| tRNA-U20a,U20b-dihydrouridine synthase [Chromohalobacter salexigens
           DSM 3043]
          Length = 340

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 60/296 (20%), Positives = 106/296 (35%), Gaps = 29/296 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-------ADAILRGDKK--NILGFSTQEKPLA 51
           M    D   R             TE +        A   LR   +       +    P+ 
Sbjct: 14  MEGVIDVVTRELLSADGALDWTVTEFVRVVDTRLPARVFLRHCPELETAACATASGTPVH 73

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           LQ+ G+D   L   A   +  G  +++LN GCP+  V+    GA L+  P+ V   + A+
Sbjct: 74  LQLLGSDPEALAANAVRAQALGARQVDLNFGCPAKTVNRHDGGASLLRQPERVHTVVRAV 133

Query: 112 CKA---LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A   L I VT K R+G DD+  A+A     ++ +  G   + +HAR         +  
Sbjct: 134 AEALAPLGIAVTAKIRLGFDDKHVALA---CAEAAESGGAAHLVVHART--------RRE 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
              P   ++ +  I +    + +  NG +  +    K   L     VM+GR    +  + 
Sbjct: 183 GYRPPAHWEWIGRI-QARLSIPVIANGDIWTLEDYWKARTLSGCADVMLGRGMLADPWLA 241

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQIT-RH 279
             +  +  +     +   +   +               + + S  K  L Q+  RH
Sbjct: 242 RRIKHWQRHGEMLPATPWSARAEILHAYAQRMRAHLPEKVVVSLLKQWLNQMRGRH 297


>gi|302854216|ref|XP_002958618.1| hypothetical protein VOLCADRAFT_108215 [Volvox carteri f.
           nagariensis]
 gi|300256079|gb|EFJ40355.1| hypothetical protein VOLCADRAFT_108215 [Volvox carteri f.
           nagariensis]
          Length = 508

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 103/249 (41%), Gaps = 25/249 (10%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIVADAILRGDKKNILGFST-------QEKPLAL 52
           M +  DR +R  F  ++       TE I           +I G S         + PL +
Sbjct: 92  MENLADRAFRRAFLAVIGGFDEACTEFIRIPGRSENPLGSIRGVSCWYEAGELGQVPLGV 151

Query: 53  QIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           QI G++   +  AAK +    G   ++LN GCP+  V     G+ L+  P ++G  +A M
Sbjct: 152 QIMGSNPELMGLAAKYLVQVRGAPRVDLNCGCPANTVTGRGAGSSLLRTPHLLGQVVAEM 211

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + +    PV+VK R G DD      L + + + +++G   + +H R         +   
Sbjct: 212 VRQVDGAAPVSVKLRAGFDDTSL---LEDNLLAAQEAGAAFVTLHPRT--------RRQA 260

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
                ++ ++     E  ++ +  NG +  + +A ++L      G+MIGR A  +  +  
Sbjct: 261 YSGAAEWGLIARAV-ELLEIPVVGNGDVVSVERAHQLLRETGCHGLMIGRGAVHDPLIFH 319

Query: 228 TVDEYFSNP 236
            +   F   
Sbjct: 320 RIRHSFGEE 328


>gi|323303732|gb|EGA57518.1| Dus4p [Saccharomyces cerevisiae FostersB]
 gi|323307899|gb|EGA61159.1| Dus4p [Saccharomyces cerevisiae FostersO]
          Length = 367

 Score =  156 bits (394), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 99/233 (42%), Gaps = 18/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I  L  + ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L++  ++V  +  + I +N GCP         G  L+ N D++   + A+       
Sbjct: 105 VADLLKFVEMVAPY-CDGIGINCGCPIKEQIREGIGCALIYNSDLLCSMVHAVKDKYGDK 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I + + +       L + +  +GV+ I IH R         +  R     + D 
Sbjct: 164 LRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRT--------RRTRSSQPANLDA 213

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  I +   D  + +  NG    +S   +I       GVM  R    N A+  
Sbjct: 214 IKYIIENISDKNVPVIANGDCFKLSDLERITKYTGAHGVMAVRGLLSNPALFA 266


>gi|295676479|ref|YP_003605003.1| dihydrouridine synthase DuS [Burkholderia sp. CCGE1002]
 gi|295436322|gb|ADG15492.1| dihydrouridine synthase DuS [Burkholderia sp. CCGE1002]
          Length = 347

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 45/195 (23%), Positives = 85/195 (43%), Gaps = 16/195 (8%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +    P+ +Q+ G+D   +   A          I+LN GCP+  V++   GA L+  P++
Sbjct: 60  TASGTPMVIQLLGSDPQWMARNAAYAATLSPYGIDLNFGCPAKVVNQHGGGAMLLATPEL 119

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   ++A+  A+   I VT K R+GV D   A+      +++   G   + +HAR     
Sbjct: 120 LNQIVSAVRAAVPADIAVTAKMRLGVSDTSRAI---ECAQALVDGGAASLVVHART---- 172

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
               +D+R  P   ++ V  I  +  D+ +  NG +  ++   +   +     VMIGR A
Sbjct: 173 ----RDDRYRPPAHWEWVARI-DDAVDVPVIANGEVWTVADWQRCRSVSGCADVMIGRGA 227

Query: 220 YKNSAMLTTVDEYFS 234
             +  +   +     
Sbjct: 228 VSDPFLAQRIRGLMD 242


>gi|294788400|ref|ZP_06753643.1| tRNA-dihydrouridine synthase B [Simonsiella muelleri ATCC 29453]
 gi|294483831|gb|EFG31515.1| tRNA-dihydrouridine synthase B [Simonsiella muelleri ATCC 29453]
          Length = 218

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 46/200 (23%), Positives = 90/200 (45%), Gaps = 18/200 (9%)

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           ++ N  +V + +  + KA+ IPVT+K R+G +D+   ++   + K  +++G+  + IH R
Sbjct: 1   MLQNEPLVEEILNTVVKAVPIPVTLKTRLGWNDEHKNIST--IAKIAEQAGIAALAIHGR 58

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
                    +         YD++ EIK+ + +L I  NG +    +A+++L     DG+M
Sbjct: 59  T--------RTQMYNGEAQYDLIAEIKQ-SVNLPIWANGDITSPQKAVQVLQQTGADGIM 109

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           IGR A     +   + +YF         ++ +   D      A+M D+        G ++
Sbjct: 110 IGRGAQGQPWLFADI-QYFLQHHELPEKMRFQAACDVILAHLAAMHDFYGDV----GGVR 164

Query: 275 QITRHMIGLFHGFPNSRRCR 294
              +H+       P+S   R
Sbjct: 165 IARKHIGWYLARVPHSADFR 184


>gi|256075605|ref|XP_002574108.1| tRNA-dihydrouridine synthase [Schistosoma mansoni]
 gi|238659304|emb|CAZ30341.1| tRNA-dihydrouridine synthase, putative [Schistosoma mansoni]
          Length = 370

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 53/278 (19%), Positives = 102/278 (36%), Gaps = 54/278 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV +T   +R   R   N  L++T MI+A++ ++ +K   + F+    ++PL +Q+   D
Sbjct: 21  MVRYTKLPFRLLLRQ-HNVDLVHTPMILANSFIQSEKARNIEFTTCPNDRPLIVQLASND 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI- 117
             +   A +++  +  + I+LN GCP         G+ L+  P+ + + + A    +   
Sbjct: 80  PCEFAIATEMLAPY-CDGIDLNCGCPQPWAIGSGLGSALLKEPEKIANIVHAARNTIPRW 138

Query: 118 -----------------------------------PVTVKCRIGVDDQ-----------I 131
                                              P ++  +I +               
Sbjct: 139 RNSHMESCKMSDDIEDLDKNNKLGNKFKSITRSHGPFSISAKIRIPTTSNRSVGEGLSCD 198

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           P      LV+ +   GV+ + +HAR    +         +  L    +        D+ I
Sbjct: 199 PIKLTVELVRRLAVMGVDWVTLHARTPQQRSRDCASWNVVQELVDCKIKHCY-LGTDIPI 257

Query: 192 GLNGGLEDMSQAL--KILPSVDGVMIGRAAYKNSAMLT 227
            LNG +  ++ A   +      GVM+GRA  K   + T
Sbjct: 258 ILNGDVRGLNDAYDAQETTGCHGVMVGRALLKFPHLFT 295


>gi|219130828|ref|XP_002185557.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402965|gb|EEC42922.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 243

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 71/216 (32%), Positives = 110/216 (50%), Gaps = 23/216 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK---------NILGFSTQEK--- 48
           M+  +   +R F R+LT  A L+TEM+V + +               ++    + +    
Sbjct: 29  MIRVSTPEFRAFVRILTKKATLWTEMVVDETLWYHRNDPGALQTYLGSLKRTDSNDHEIS 88

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV-----HEGSFGACLM 98
                P+  Q+GG       +A +I+  FGY+EINLN+ CPSARV         FGA LM
Sbjct: 89  AQQRNPIVCQLGGITPKHTAKATQIITAFGYDEINLNMDCPSARVSPQPRRRRQFGAILM 148

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
              D   + +  + +   +PV+VKCR+GVD++     L  +V+S++       +IHARK 
Sbjct: 149 KETDRAVELVKTIWENTHLPVSVKCRVGVDNEDSWEFLEAIVRSLRPY-CQRFYIHARKC 207

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           +L+GLSP  NR +P L+Y  VY + +  PD    LN
Sbjct: 208 LLQGLSPAQNRIVPPLNYPCVYRLCESFPDCEFYLN 243


>gi|151940924|gb|EDN59306.1| dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|256269148|gb|EEU04483.1| Dus4p [Saccharomyces cerevisiae JAY291]
          Length = 367

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 99/233 (42%), Gaps = 18/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I  L  + ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L++  ++V  +  + I +N GCP         G  L+ N D++   + A+       
Sbjct: 105 VADLLKFVEMVAPY-CDGIGINCGCPIKEQIREGIGCALIYNSDLLCSMVHAVKDKYGDK 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I + + +       L + +  +GV+ I IH R         +  R     + D 
Sbjct: 164 LRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRT--------RRTRSSQPANLDA 213

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  I +   D  + +  NG    +S   +I       GVM  R    N A+  
Sbjct: 214 IKYIIENISDKNVPVIANGDCFKLSDLERITKYTGAHGVMAVRGLLSNPALFA 266


>gi|156120523|ref|NP_001095407.1| dihydrouridine synthase 4-like [Bos taurus]
 gi|151555764|gb|AAI49230.1| DUS4L protein [Bos taurus]
 gi|296488502|gb|DAA30615.1| dihydrouridine synthase 4-like [Bos taurus]
          Length = 238

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 59/219 (26%), Positives = 95/219 (43%), Gaps = 23/219 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R      L YT MIVA   +R  K     F+T   + PL +Q    D
Sbjct: 34  MVRYSKLSFRTLVRKYD-CDLCYTPMIVAADFVRSAKARDSEFTTNQGDCPLIVQFAAND 92

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA+IV  +  N I++N GCP        +GACL+  P++V D +  +   +  P
Sbjct: 93  ARLLSDAARIVCPY-ANGIDINCGCPQRWALAEGYGACLINKPELVRDMVKQVRNQVENP 151

Query: 119 ---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              V++K RI  D         +L +  + +GV+ I +H R    +            + 
Sbjct: 152 RFSVSIKIRIHDDLTRTV----DLCRKAEATGVSWITVHGRTVEERHQ---------PVH 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDG 212
           Y+ +  I KE+  + I  NG +  + +A         DG
Sbjct: 199 YEAIK-IIKESMSIPIVANGDIRSLKEAENVWHTTGTDG 236


>gi|261222286|ref|ZP_05936567.1| nitrogen regulation protein [Brucella ceti B1/94]
 gi|260920870|gb|EEX87523.1| nitrogen regulation protein [Brucella ceti B1/94]
          Length = 228

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 43/187 (22%), Positives = 87/187 (46%), Gaps = 12/187 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L    +      +Q+ G + 
Sbjct: 25  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLFGEGLGTHVVQLAGREA 83

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 84  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 143

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 144 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 193

Query: 180 YEIKKEN 186
           + ++   
Sbjct: 194 HAVRDAV 200


>gi|193690494|ref|XP_001952087.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Acyrthosiphon
           pisum]
          Length = 456

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 102/251 (40%), Gaps = 38/251 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A L     ++YTE ++   ++R  +K                      
Sbjct: 21  MVRINTLPMRLLA-LDYGADIVYTEELIDHRLIRCYRKVNETLESVDFIDKSDATVVFRT 79

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            S ++  + LQIG +D  +  +AA++VE      I++N+GCP     +G  GA L+ +PD
Sbjct: 80  CSREKHNVVLQIGTSDPERAAKAAQVVEQ-DVAGIDINMGCPKDFSLKGGMGAALLFHPD 138

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                ++A+  A+ IPVT K R+  D          L K +  +GV  I +H R    + 
Sbjct: 139 KACAILSAVVSAVKIPVTCKIRVLQDIDDTVA----LCKKLAATGVAAICVHGRTINERP 194

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDGVMIGR 217
           +    N  I  +          E  D+ +  NGG +++     I     +     VMI R
Sbjct: 195 MHSNRNHFIKAI---------SEALDIPVIANGGSKEIKVFEDIIKFKNITGCSSVMIAR 245

Query: 218 AAYKNSAMLTT 228
            A KN ++   
Sbjct: 246 TAEKNCSIFKR 256


>gi|262158407|ref|ZP_06029523.1| tRNA-dihydrouridine synthase C [Vibrio cholerae INDRE 91/1]
 gi|262029848|gb|EEY48496.1| tRNA-dihydrouridine synthase C [Vibrio cholerae INDRE 91/1]
          Length = 313

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 103/258 (39%), Gaps = 26/258 (10%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +    P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P++
Sbjct: 49  TPSGVPVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPEL 108

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A   A+   IPV+ K R+G +D         +V ++ ++  + + +HAR     
Sbjct: 109 IYQVVKACRDAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK--- 162

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                   K   + +  + +I+++   + +  NG + + +     +    VD +M+ R A
Sbjct: 163 ----AGGYKASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGA 217

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
             N   L  V ++    +     +           +    T +  R         +I + 
Sbjct: 218 L-NVPNLGNVVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQW 266

Query: 280 MIGLFHGFPNSRRCRHIL 297
              L H +P +      L
Sbjct: 267 FAYLRHAYPQANELFGEL 284


>gi|6323437|ref|NP_013509.1| Dus4p [Saccharomyces cerevisiae S288c]
 gi|2833204|sp|Q06063|DUS4_YEAST RecName: Full=tRNA-dihydrouridine synthase 4
 gi|625099|gb|AAB82341.1| Ylr405wp [Saccharomyces cerevisiae]
 gi|45271062|gb|AAS56912.1| YLR405W [Saccharomyces cerevisiae]
 gi|285813808|tpg|DAA09704.1| TPA: Dus4p [Saccharomyces cerevisiae S288c]
          Length = 367

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 99/233 (42%), Gaps = 18/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I  L  + ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L++  ++V  +  + I +N GCP         G  L+ N D++   + A+       
Sbjct: 105 VADLLKFVEMVAPY-CDGIGINCGCPIKEQIREGIGCALIYNSDLLCSMVHAVKDKYGDK 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I + + +       L + +  +GV+ I IH R         +  R     + D 
Sbjct: 164 LRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRT--------RRTRSSQPANLDA 213

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  I +   D  + +  NG    +S   +I       GVM  R    N A+  
Sbjct: 214 IKYIIENISDKNVPVIANGDCFKLSDLERITKYTGAHGVMAVRGLLSNPALFA 266


>gi|325275792|ref|ZP_08141661.1| tRNA-dihydrouridine synthase C [Pseudomonas sp. TJI-51]
 gi|324099063|gb|EGB97040.1| tRNA-dihydrouridine synthase C [Pseudomonas sp. TJI-51]
          Length = 322

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/313 (19%), Positives = 117/313 (37%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPPASFHKLAPELRQGALTAAGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   + A+ 
Sbjct: 68  QLLGSDPLCLAENAALACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVHAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IPVT K R+G D         +   ++   G   + +HAR  +           
Sbjct: 128 RAVPAHIPVTAKMRLGFD---SPAGALDCAMALADGGSAHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  +    +       + +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVDDWRRCREVSGAEDIMLGRGLVSRPDLGLQ 235

Query: 229 VDEYFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + ++FWR+  A ++       ++ G+L+Q    +  L   
Sbjct: 236 IAAARDGRDYQPLGWQDLQPLLREFWRQAQAKLSP-----RYAPGRLKQW---LAMLTRS 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVLLFAELRR 300


>gi|260949371|ref|XP_002618982.1| hypothetical protein CLUG_00141 [Clavispora lusitaniae ATCC 42720]
 gi|238846554|gb|EEQ36018.1| hypothetical protein CLUG_00141 [Clavispora lusitaniae ATCC 42720]
          Length = 611

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 65/297 (21%), Positives = 115/297 (38%), Gaps = 32/297 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM +A  +L+G K    +      E P   +Q+      + 
Sbjct: 255 NLPYRRLMKTL-GADVTYSEMALALPLLQGTKPEWALPKAHASEYPGFGIQLATNHHQQA 313

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPV 119
            +AA+ +  E    +E+NLN GCP   ++    G+ L+  P  +   +  M   +  IPV
Sbjct: 314 SKAAEAISREAPNVSELNLNCGCPIDLLYRQGQGSALLDQPSKMVRILNGMNACSGDIPV 373

Query: 120 TVKCRI-GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL---- 174
           T+K R    D++  A+ L N  + +  + V  I +H R    +     D   I  +    
Sbjct: 374 TLKIRTGTKDNKNTAIPLIN--RMLADTHVAAITLHGRSRQQRYTREADWNYIAEVGKTV 431

Query: 175 -DYDIVYEIKKE----NPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
            +++   E  K+    NP  FIG NG      Q    +    +D VM+ R A     +  
Sbjct: 432 QEWNHKKEEDKDSSETNPTWFIG-NGDCFTYEQWHNAVNTEGIDSVMVARGALIKPWIFE 490

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            VD       + +             +   +  ++A  H  S     ++ R  +  F
Sbjct: 491 EVDAEQYLDKSATE----------RLEYLRTFANFAVEHWGSDEYGIEVARRYMCEF 537


>gi|332638352|ref|ZP_08417215.1| probable tRNA-dihydrouridine synthase [Weissella cibaria KACC
           11862]
          Length = 353

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 100/233 (42%), Gaps = 15/233 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + YTE   A +I     K      L     EK   +QI G
Sbjct: 36  MEAVTDTVFRRVVDKAAAPDVYYTEFTNARSITHPKAKFTVQGRLHVDKSEKVPVVQIWG 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                  +++  + D GYN I+LN+GCP + V +   G+ L+ + +   + I A   A  
Sbjct: 96  NRGEDFEKSSLELRDRGYNAIDLNMGCPDSTVIKNGGGSDLIRHYESAQEVIQAAKTA-G 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G +D       R  +  + K  +  + +H R        P     I     
Sbjct: 155 LPVSVKTRLGFNDL---ETFREWIPFLLKQDIQVLTVHLRTRKEMSKVPAHYEYID---- 207

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAML 226
           +IV    +  PD  + +NG ++   + L+++   P VDGVMIGR  ++N    
Sbjct: 208 EIVKMRDEIAPDTLLQINGDVKTRQEGLELVRQHPGVDGVMIGRGVFENPFAF 260


>gi|261867320|ref|YP_003255242.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412652|gb|ACX82023.1| tRNA-dihydrouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 334

 Score =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 56/300 (18%), Positives = 115/300 (38%), Gaps = 34/300 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     + +  L  +E +  V   +       +       GF+    P+ +
Sbjct: 8   MQGVLDPLVRQLLTEVNDYDLCISEFVRVVDQRLPPKVFYRLCPELHQRGFTPSGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A++    G + ++LN GCPS  V+  + GA L+  P+++     A+ 
Sbjct: 68  QLLGQHPQWLAENAELAVQLGSHGVDLNCGCPSKTVNGSNGGASLLKQPELIYQATKAIR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     V+VK R+G D         ++  ++++ G   I IH R          D  +
Sbjct: 128 LAVPQHHTVSVKVRLGWD---STEFAYDIADAVQQGGATEIAIHGRTKT-------DGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
              +++  + E++++   + +  NG +   +   +   +   + +M+GR A  N   L+ 
Sbjct: 178 ADRINWQKIGEVRQKL-KIPVIANGEIWRWADGQQCRDVTGCEDLMVGRGAL-NIPNLSR 235

Query: 229 VDEYFSNPLTGSS--PIKTRVDKD--------FWRKISASMTDYAARHLHSGGKLQQITR 278
           V +  + PL+ +   PI  +            +          Y          L ++ +
Sbjct: 236 VLKRNAAPLSWAEIMPILRKYAALENCHDSGFYHVARIKQWLQYLKYEYAEAADLFEMVK 295


>gi|190405444|gb|EDV08711.1| dihydrouridine synthase 4 [Saccharomyces cerevisiae RM11-1a]
 gi|259148383|emb|CAY81630.1| Dus4p [Saccharomyces cerevisiae EC1118]
 gi|323332436|gb|EGA73845.1| Dus4p [Saccharomyces cerevisiae AWRI796]
 gi|323336419|gb|EGA77687.1| Dus4p [Saccharomyces cerevisiae Vin13]
 gi|323347323|gb|EGA81596.1| Dus4p [Saccharomyces cerevisiae Lalvin QA23]
          Length = 367

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 99/233 (42%), Gaps = 18/233 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I  L  + ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L++  ++V  +  + I +N GCP         G  L+ N D++   + A+       
Sbjct: 105 VADLLKFVEMVAPY-CDGIGINCGCPIKEQIREGIGCALIYNSDLLCSMVHAVKDKYGDK 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I + + +       L + +  +GV+ I IH R         +  R     + D 
Sbjct: 164 LRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRT--------RRTRSSQPANLDA 213

Query: 179 VYEIKKENPD--LFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
           +  I +   D  + +  NG    +S   +I       GVM  R    N A+  
Sbjct: 214 IKYIIENISDKNVPVIANGDCFKLSDLERITKYTGAHGVMAVRGLLSNPALFA 266


>gi|258578427|ref|XP_002543395.1| tRNA-dihydrouridine synthase 1 [Uncinocarpus reesii 1704]
 gi|237903661|gb|EEP78062.1| tRNA-dihydrouridine synthase 1 [Uncinocarpus reesii 1704]
          Length = 514

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 61/278 (21%), Positives = 103/278 (37%), Gaps = 56/278 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-----AILRGDKKNILGFSTQ--------- 46
           MVD +D          +N  L Y+ M  A      A  R      +  S           
Sbjct: 30  MVDRSDGS--------SNPLLAYSPMFHARLFKDRAAYRSQHFEAVRPSPVAGETAEPVP 81

Query: 47  --------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
                   ++PL +Q    D  +L+ AA++V+ +  + ++LN+GCP     +G +GA L 
Sbjct: 82  FLDGNPAIDRPLIVQFCANDPDELLAAARLVQPY-CDAVDLNLGCPQGIAKKGHYGAFLQ 140

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            +P+++   I  +   LSIPVT K RI            +  K I  +G + I +H R+ 
Sbjct: 141 EDPELIYKLIHTLHTGLSIPVTAKFRIL----ETREKTLDYAKMILSAGASFISVHGRRR 196

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL--PSVDGVMI 215
             KG            D+  +  ++    P+  I  NG + +     K L     D VM 
Sbjct: 197 EQKG------HNTGVADWSYIRYLRDNLPPETVIFANGNILNHDDIQKCLEATGADAVMS 250

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                 +  + +              P   +   ++WR
Sbjct: 251 AEGNLSDPTIFS------------PPPPVGKEGCEYWR 276


>gi|257093932|ref|YP_003167573.1| dihydrouridine synthase DuS [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
 gi|257046456|gb|ACV35644.1| dihydrouridine synthase DuS [Candidatus Accumulibacter phosphatis
           clade IIA str. UW-1]
          Length = 327

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 60/274 (21%), Positives = 107/274 (39%), Gaps = 30/274 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     +    L  +E + V+  +L     R     +     +    P+A+
Sbjct: 9   MEGLVDDVLRDVLTRVGTYDLAVSEFVRVSGNLLPPRAFRRICPELARGCRTAAGTPVAV 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A  + +     I+LN GCP+  V+    GA L+ +P+ +   +AA+ 
Sbjct: 69  QLLGSDPGCLAENAAQLAELSPAGIDLNFGCPAPTVNRHGGGARLLADPEQLFRIVAAVR 128

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   IP T K R+GV D        +  +++   G++ + +HAR         +    
Sbjct: 129 RAVPAGIPFTAKMRLGVSDT---ARTLDCARALAAGGIDSLVVHART--------RAEGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKIL-PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  I  E     +  NG +      A   L    D VMIGR A  +  ++  
Sbjct: 178 RPPAHWEWVARI-GEVVQRPVTANGEVWTTADHARCCLVSGSDDVMIGRGAVADPFLVRH 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           +    +     +           WR++   +  Y
Sbjct: 237 IRSRVAGETIAADRSAD------WRQLQPLLASY 264


>gi|255600129|ref|XP_002537390.1| tRNA-dihydrouridine synthase C, putative [Ricinus communis]
 gi|223516517|gb|EEF24993.1| tRNA-dihydrouridine synthase C, putative [Ricinus communis]
          Length = 329

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 60/282 (21%), Positives = 116/282 (41%), Gaps = 36/282 (12%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            +    P+ LQ+ G+D   + E A      G   I++N GCP+  V+    GA L+  P+
Sbjct: 71  RTPAGVPVRLQLLGSDPVCMAENAAKAASLGAAGIDINFGCPAKIVNRHRGGAALLKEPE 130

Query: 103 IVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           ++ + +AA+  A+  S+ VT K R+G +    AV      ++++  G + I +HAR    
Sbjct: 131 LMREIVAAIRAAVPASVSVTAKMRLGYEVPDYAV---ECAQALQDGGADEITVHART--- 184

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
                K +   P   ++ + +I +E   + +  NG +   + A +         +MIGR 
Sbjct: 185 -----KTDGYKPPAYWEWIAQI-REALQIPVIANGEIWTAADARRCREISGCTDIMIGRG 238

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA---RHLHSGGKLQQ 275
           A  N A+   +     +PL              W ++   +  Y A   RH+    +  +
Sbjct: 239 AVANPALALMIRGELESPLP-------------WSEVIVLLHRYWATVSRHISERHRNGR 285

Query: 276 ITRHMIGLFHGFPNSRRC----RHILTVEAGASTATHHIIET 313
           I + ++ L   +P +       R ++           H++  
Sbjct: 286 IKQWLLYLGRTYPEAEALFDAIRRVIAPAEIEQLVFPHLLRE 327


>gi|28379386|ref|NP_786278.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|300768771|ref|ZP_07078667.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|28272225|emb|CAD65133.1| transcription regulator [Lactobacillus plantarum WCFS1]
 gi|300493728|gb|EFK28900.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 334

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 118/331 (35%), Gaps = 37/331 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPL-ALQIG 55
           M   T   +R          + YTE   A +I     K      L     E P   +Q+ 
Sbjct: 27  MEAVTGSVFRRVVMRAAAPDVFYTEFTNALSITHPKAKFTTRGRLYVDEAESPRPIVQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G       +AA  V++ GY  I+LN+GCP   V +   G+ L+ + D   + I    +A 
Sbjct: 87  GNSGEDFTKAAHEVKNQGYQAIDLNMGCPDMAVIKNHSGSDLIRHFDRAKEVIEGARQA- 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PV+VK R+G DD          +  + +  V  + +H R  +     P     I NL 
Sbjct: 146 ELPVSVKTRLGFDDVHEYET---WIPFLLQQQVPVLTVHVRTKMEMSKVPAHYELIDNL- 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEY 232
              V       P   + +NG + D    LK+    P VDG+MIGR  ++N      +   
Sbjct: 202 ---VQMRDTLAPATLLQINGDILDYQAGLKLAKAHPGVDGIMIGRGIFQNPYAFEPI--- 255

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAA----RHLHSGGKLQQITRHMIGLFHGFP 288
                    P  TR   +  R        +       H     +  +I         G  
Sbjct: 256 -------PQPHSTRDMLELLRYQVDLYDQFIGLGLQGHFAPLQRFFKI------YVRGMR 302

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLMI 319
           ++   R+ L ++   +     II+     + 
Sbjct: 303 HAAELRNEL-MQTKTTDDVRAIIDRLEAKLP 332


>gi|157961327|ref|YP_001501361.1| dihydrouridine synthase DuS [Shewanella pealeana ATCC 700345]
 gi|157846327|gb|ABV86826.1| dihydrouridine synthase DuS [Shewanella pealeana ATCC 700345]
          Length = 319

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 110/280 (39%), Gaps = 39/280 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +    L+ TE + V D +L     + L       G +    P+ +
Sbjct: 13  MEGVVDDLMREILSAINPYDLMVTEFVRVVDQLLPEKVFHRLCPELQTGGQTLSGTPVRV 72

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   + E A    + G N +++N GCP+  V+  + GA ++  P+ + + + AM 
Sbjct: 73  QLLGQNPDWMAENAVRAIELGSNGVDVNFGCPAKMVNRSNGGAVMLQYPEQLYNVVKAMR 132

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+    PVT K R+G +D+           +I ++G + + +HAR  +           
Sbjct: 133 DAVPSEQPVTAKIRLGFNDKSLY---MENALAIYEAGASELAVHARSKVDG--------Y 181

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I  + P + +  NG + +   A + +     D +M+GR A     +   
Sbjct: 182 KPPAYWEYITDINAKLP-IPVIANGEIWNRDDAERCMSVTGCDNIMVGRGAISLPNLAAH 240

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
           +                  D   W +    M +Y  R L 
Sbjct: 241 IKGD---------------DTYTWEQSLNLMLEYTNRELE 265


>gi|117620179|ref|YP_856732.1| tRNA-dihydrouridine synthase C [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117561586|gb|ABK38534.1| tRNA-dihydrouridine synthase C [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 314

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 123/327 (37%), Gaps = 44/327 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     + +  L  +E I V D +L     + L       G +    P+ +
Sbjct: 8   MQGVLDHLMREVLTSVNDYDLCVSEFIRVVDQLLPAKVFHRLCPELKQDGKTRAGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   I+LN GCP+  V++   GA L+  P  +   + A+ 
Sbjct: 68  QLLGQHPEWLAENALRAIELGSPGIDLNFGCPAPTVNKSKGGAVLLKEPGTIYRIVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+ K R+G DD+   +       ++ + G N + +HAR         K    
Sbjct: 128 EAVPAHLPVSAKIRLGYDDKELYLEN---AHAVHQGGANELAVHART--------KREGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
                ++ V  I++  P + +  NG + D + AL    +   D +M+GR A     +   
Sbjct: 177 KAPAHWEYVDAIRRALP-IPVTANGEIWDHADALACAQVSGCDTLMVGRGAISLPNL--- 232

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS---GGKLQQITRHMIGLFH 285
                      ++ +KT      W ++   M  Y  + L S        +I +    L  
Sbjct: 233 -----------ANVMKTGCAHMSWAEVLQLMVSYTEQDLASEKADYYPSRIKQWFSYLKR 281

Query: 286 GFPNSRRCR---HILTVEAGASTATHH 309
            +P + R      +L        A   
Sbjct: 282 EYPEADRLFGEIRVLKETHPIRDALLQ 308


>gi|226940983|ref|YP_002796057.1| tRNA-dihydrouridine synthase C [Laribacter hongkongensis HLHK9]
 gi|226715910|gb|ACO75048.1| tRNA-dihydrouridine synthase C [Laribacter hongkongensis HLHK9]
          Length = 323

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 117/290 (40%), Gaps = 26/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IV-----ADAILRGDKKNILG-FSTQEKPLAL 52
           M    D   R     +       TE   +      A A  R   ++  G  +    P+ L
Sbjct: 8   MEGLVDAPLRDLITRMGGVDWCVTEFLRVTGSLLPAAAFRRIAPEHAHGWRTPAGTPVRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   ++LN GCP+  V++   GA L+ NP  +    +A+ 
Sbjct: 68  QLLGSDPASLADNAARGAELGAPVLDLNFGCPAPTVNKHGGGAALLDNPGQLYRIASAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            AL   +P+T K R+G+ D    +   +  +++  +G++ + +HAR  +           
Sbjct: 128 AALPAGVPLTAKMRLGLRDTELTL---DCARALDSAGISELVVHARTKVEGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +  V ++K E     +  NG + ++     I     VD +MIGR       +   
Sbjct: 178 -PPAHWQWVAQVK-EVVAARVWANGEVWNLQDWQDIRRESGVDDIMIGRGLVVRPDLAYR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           +    +N      P+      +   +++  M D A +  +   +L+Q  +
Sbjct: 236 IAA--TNSGAEVVPLDWHGMLELLEEMARHMHDAAPQGNYLPFRLKQWLK 283


>gi|189239358|ref|XP_974445.2| PREDICTED: similar to tRNA-dihydrouridine synthase [Tribolium
           castaneum]
          Length = 401

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 100/232 (43%), Gaps = 18/232 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +   N  L YT MI+AD+  +  K     F+T   + PL  Q     
Sbjct: 31  MVRYSKLQFRNLVKSY-NCDLCYTPMILADSFCKSGKARANEFTTNMNDTPLITQFAANK 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +   V AA +V  F  + ++LN GCP         G  ++  P+++ D +      +  P
Sbjct: 90  VYDFVGAAYMVSPF-CDGVDLNCGCPQRWAKLQGLGCIMLEKPEVIYDLVKQCRNVIPKP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            TV  ++ +   +       + + ++  GV+ + +H R      L+ + N++  NL   I
Sbjct: 149 FTVSVKLRLQKDLRRSV--EICRQLEHCGVSFLTVHGRTPDQ--LTGEVNKEALNL---I 201

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
           V  +     ++ +  NGG++ +   L++    +  GVM+      N  + T 
Sbjct: 202 VGSV-----NVPVVANGGVKSLEDCLELQEKTNCKGVMVANGLLTNPTLFTE 248


>gi|315187425|gb|EFU21181.1| dihydrouridine synthase DuS [Spirochaeta thermophila DSM 6578]
          Length = 334

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 120/292 (41%), Gaps = 20/292 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGDKKN-ILGFSTQEKPLALQIGGAD 58
           M + T   +R         ++  TEMI A  +L +G  +   L FS       +Q+ G D
Sbjct: 21  MAELTHSGFRTLIHTWGGCSVYATEMISAPGLLSKGPYERFYLDFSPDPSRTIVQLVGYD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           +  LV+AA I+ +     +++N+GC +  + +   GA  +L  +     +  + + L   
Sbjct: 81  MDSLVQAAGILAEHPILGVDINMGCAAPEIRKRGGGAGWLLRGEEAVRLVGEVRRLLPPH 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++  +I + + +P       ++ + K G++ I +H      KGL  K +R      +D+
Sbjct: 141 LSLSVKIRIPESLPLEEFILFLQRLAKQGLSFITVHP-----KGLKEKHDR---PARWDL 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  + +E P + +  NG +  +       + LP + G+MIGR A +       +      
Sbjct: 193 IPPLLEEIP-IPVVGNGNITSLDVYRKKREELPRLAGIMIGRKAVEAPWFFAYLRSRERG 251

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-GLFHG 286
                +       + F   +S         HL    + ++  R+    LF G
Sbjct: 252 GGGPFTVNLEETARSFLELLSRHQPP--EFHLS---RARRFFRYYTRNLFFG 298


>gi|91082415|ref|XP_970120.1| PREDICTED: similar to tRNA-dihydrouridine synthase [Tribolium
           castaneum]
 gi|270007514|gb|EFA03962.1| hypothetical protein TcasGA2_TC014107 [Tribolium castaneum]
          Length = 455

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 104/250 (41%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-----------------ILGF 43
           MV       R  + L     ++YTE ++    L+  ++                  +   
Sbjct: 19  MVRVGTLPMRLLS-LDHGADIVYTEELIDWKFLKSIRRENDVLGTVDYLDKSDGTVVFRT 77

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  + +Q+G  D  + ++ AK++E+     I++N+GCP     +G  GA L+  P+
Sbjct: 78  CPREKNRVVVQLGTCDPQRALKVAKMIEN-DVAGIDINMGCPKEFSLKGGMGAALLKQPE 136

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                ++ + + + IP+T K R+       A    +LVK +  +G++ I IH R    + 
Sbjct: 137 KAKSILSTLTQNVKIPITCKIRVF----ESAEETLDLVKELVSTGISAIAIHGRTKAERP 192

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
             P  N  I  +          EN  + +  NGG +++ +   I+          VMI R
Sbjct: 193 QHPNRNATIKFI---------AENVSIPVVANGGSKEIEKYQDIIKFKEECGCSSVMIAR 243

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 244 AAEANCSIFR 253


>gi|332305787|ref|YP_004433638.1| dihydrouridine synthase DuS [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332173116|gb|AEE22370.1| dihydrouridine synthase DuS [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 310

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/279 (20%), Positives = 110/279 (39%), Gaps = 38/279 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNI--LGFSTQEKPLAL 52
           M    D   R     +    L  TE +      +   +       +   G++    P+ +
Sbjct: 8   MEGVVDHLMRDMLSKVGGFDLCVTEFVRVVNCLLPKKVFHRICPELHNDGYTPNGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A    + G + ++LN GCP+  V++   GA L+  P  + D ++A+ 
Sbjct: 68  QLLGQNPQPLAENAVRAVELGSHGVDLNFGCPAKTVNKSKGGAVLLREPQTLYDIVSAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     VT K R+G DD+  A        +I+ +G + + IHAR  +           
Sbjct: 128 QAVPSEHKVTAKMRLGFDDKSLAFENA---AAIEAAGADLLVIHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   +  + +IK++  ++ I  NG +     A   +   +   +M+GR       +   
Sbjct: 177 KPPAYWSWIADIKQKV-NIPIIANGEIWSYEDAINCQAQSNCQDIMLGRGILAMPNLARV 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
           V              + + +   W +++  + DY+   L
Sbjct: 236 V--------------RGQQEVMNWSQVNQLLIDYSGYEL 260


>gi|104780807|ref|YP_607305.1| tRNA-dihydrouridine synthase C [Pseudomonas entomophila L48]
 gi|95109794|emb|CAK14499.1| putative tRNA-dihydrouridine synthase C [Pseudomonas entomophila
           L48]
          Length = 323

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 56/313 (17%), Positives = 116/313 (37%), Gaps = 38/313 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V D +L     + L         +    P+ +
Sbjct: 8   MEGLVDNILRDVLTRVGGIDWCVTEFIRVCDRLLPESSFDKLAPELRRGARTAAGVPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A +  + G   I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPVCLAENAVLACELGAPVIDLNFGCPAKTVNKSRGGAVLLKEPELLHAIVREVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +   IPVT K R+G +    A+   +   ++ + G   + +HAR  +           
Sbjct: 128 RQVPAHIPVTAKMRLGFETPDGAL---DCATALAEGGAEHLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  + ++   + +  NG +  +    +         +M+GR       +   
Sbjct: 177 KPPAHWEWVARV-QDVVKVPVFANGEIWTVDDWRRCREVSGATDIMLGRGLVSRPDLALQ 235

Query: 229 VDEYFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           +                   + ++FWR+    ++       ++ G+++Q    +  L   
Sbjct: 236 IAAARDGVEYQPMAWDDLLPLLREFWRQAQDKLSP-----RYAPGRMKQW---LAMLTRS 287

Query: 287 FPNS----RRCRH 295
           +P +       R 
Sbjct: 288 YPEAVVLFAELRR 300


>gi|327483810|gb|AEA78217.1| tRNA-dihydrouridine synthase C [Vibrio cholerae LMA3894-4]
          Length = 313

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 103/258 (39%), Gaps = 26/258 (10%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +    P+ +Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P++
Sbjct: 49  TPSGVPVKVQLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPEL 108

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A   A+   IPV+ K R+G +D         +V ++ ++  + + +HAR     
Sbjct: 109 IYQVVKACRDAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK--- 162

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                   K   + +  + +I+++   + +  NG + + +     +    VD +M+ R A
Sbjct: 163 ----AGGYKASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGA 217

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
             N   L  V ++    +     +           +    T +  R         +I + 
Sbjct: 218 L-NVPNLGNVVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQW 266

Query: 280 MIGLFHGFPNSRRCRHIL 297
              L H +P +      L
Sbjct: 267 FAYLRHAYPQANELFGEL 284


>gi|308181599|ref|YP_003925727.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308047090|gb|ADN99633.1| transcription regulator [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 334

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 111/309 (35%), Gaps = 36/309 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPL-ALQIG 55
           M   T   +R          + YTE   A +I     K      L     E P   +Q+ 
Sbjct: 27  MEAVTGSVFRRVVMRAAAPDVFYTEFTNALSITHPKAKFTTRGRLYVDEAESPRPIVQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G       +AA  V++ GY  I+LN+GCP   V +   G+ L+ + D   + I    +A 
Sbjct: 87  GNSGEDFTKAAHEVKNQGYQAIDLNMGCPDMAVIKNHSGSDLIRHFDRAKEVIEGARQA- 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PV+VK R+G DD          +  + +  V  + +H R  +     P     I NL 
Sbjct: 146 ELPVSVKTRLGFDDVHEYET---WIPFLLQQQVPVLTVHVRTKMEMSKVPAHYELIDNL- 201

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEY 232
              V       P   + +NG + D    LK+    P VDG+MIGR  ++N      +   
Sbjct: 202 ---VQMRDTLAPATLLQINGDILDYQAGLKLAKAHPGVDGIMIGRGIFQNPYAFEPI--- 255

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAA----RHLHSGGKLQQITRHMIGLFHGFP 288
                    P  TR   +  R        +       H     +  +I         G  
Sbjct: 256 -------PQPHSTRDMLELLRYQVDLYDQFIGLGLQGHFAPLQRFFKI------YVRGMR 302

Query: 289 NSRRCRHIL 297
           ++   R+ L
Sbjct: 303 HAAELRNEL 311


>gi|241895343|ref|ZP_04782639.1| tRNA-dihydrouridine synthase [Weissella paramesenteroides ATCC
           33313]
 gi|241871317|gb|EER75068.1| tRNA-dihydrouridine synthase [Weissella paramesenteroides ATCC
           33313]
          Length = 353

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/321 (19%), Positives = 120/321 (37%), Gaps = 30/321 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPLALQIGG 56
           M   TD  +R          + +TE   A +I     K      L     EK    Q+ G
Sbjct: 36  MEAVTDSVFRRVVAAAGGPDVYFTEFTNARSITHPKAKFTVQGRLHVDKSEKMPVAQLWG 95

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                   A   +++ GY  +++N+GCP+A V +   G+ L+ + D   + I A  KA  
Sbjct: 96  DRAIDFEAACFDLKERGYEAVDINMGCPAATVVKNGGGSDLIRHFDKAEEIIVAAKKA-G 154

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V+VK R+G +           +  I K  V  + +H R        P     I  L  
Sbjct: 155 LAVSVKTRLGFNQID---TFEEWIPFILKQDVPLLTVHMRTRKEMSKVPAHFEYIDRL-- 209

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +    +  P+  + +NG ++D ++ L+++   P V+G+MIGR  ++N      +    
Sbjct: 210 --IQLRDEIAPNTLLQINGDIKDRTEGLELVRQHPGVNGIMIGRGIFENPFAF-EI---- 262

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI-TRHMIGLFHGFPNSRR 292
             P   +      + +           ++   H     +  +I  RH          +  
Sbjct: 263 -TPKEHTLDETLTLLRMQLDLYDQFTAEFGPMHFQKLKRFFKIYVRHFSY-------ASD 314

Query: 293 CRHILTVEAGASTATHHIIET 313
            R  L ++   +T    +++ 
Sbjct: 315 LRVAL-MDTTNTTQVRELLDQ 334


>gi|95931069|ref|ZP_01313796.1| dihydrouridine synthase, DuS [Desulfuromonas acetoxidans DSM 684]
 gi|95132878|gb|EAT14550.1| dihydrouridine synthase, DuS [Desulfuromonas acetoxidans DSM 684]
          Length = 320

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 64/280 (22%), Positives = 116/280 (41%), Gaps = 21/280 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI----VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T+R  R     +    +++TE +    VA   +  + +  +     + PL +Q+ G
Sbjct: 18  MQGLTNRAMRAVQCDIGQPDVVFTEFVRVSHVARQRITPNDRREILAGVDDVPLVVQLIG 77

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                L EAA+IV D G   +NLN+GCP  R   G  G  ++  P+ +GDC+ A+  A  
Sbjct: 78  HRSESLAEAAQIVADLGGAHVNLNMGCPFGRTTTGKTGGAMLQEPEKIGDCLRAIRAAFH 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R G DD      + +L+   +K GV+ I +H R  + K           + D+
Sbjct: 138 GSVSVKVRAGYDD---PEQIFDLLPVFEKYGVDFIVLHPRTVVQK--------YADDADH 186

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +   +      L +  NG L    +A ++       G+M+GR A  +  +   +     
Sbjct: 187 AVTARVV-AATALPVIANGDLFSEERARQVAEQTGAAGLMLGRGAIADPWLFQRIR---G 242

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
             +      + +    ++ ++S +             KL+
Sbjct: 243 RGVEPDISQRLQQMVVYFDRLSENYVPLFCGEQQVLSKLK 282


>gi|301092882|ref|XP_002997292.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262111427|gb|EEY69479.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 199

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 50/210 (23%), Positives = 97/210 (46%), Gaps = 22/210 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-----LGFSTQEKPLALQIG 55
           M + TD  +R     +   ++++TE +  +A+             L ++ QE+P+  Q+ 
Sbjct: 1   MANVTDTAFRRLISEIAKPSVMWTEFVSCEALTHDPDSRRRMMTTLKYAEQERPVVAQLF 60

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-A 114
           G+   +  E+A IV D G++ I++N+GCP   V+    GA L+L PD+  D +AA  + A
Sbjct: 61  GSKPEQFYESAMIVRDLGFDGIDINMGCPETNVNSQGSGAALILQPDLAVDIVAACKRGA 120

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            ++PV++K RIG       +   + +  +  +    + IH R         +D       
Sbjct: 121 GNLPVSIKTRIGFH----HIDYTDWILRLLGTDPEVLTIHGRT--------RDEMSKVPA 168

Query: 175 DYDIVYEIKKENPDL----FIGLNGGLEDM 200
            +D++ E+      +     I  NG ++ +
Sbjct: 169 HWDVIGEVVALAKLVGSPALILGNGDVKSL 198


>gi|325115288|emb|CBZ50843.1| hypothetical protein NCLIV_039180 [Neospora caninum Liverpool]
          Length = 491

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 87/324 (26%), Positives = 124/324 (38%), Gaps = 89/324 (27%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M+  T+ H+R F R LT  A L+TEM+   AIL    +    L     E P+  Q+    
Sbjct: 20  MLAVTNTHFRNFMRCLTREAQLWTEMVTDGAILNNMDRLQQNLRLEDIEHPIVCQL---- 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                                  GC         FGA LM  P++V D +  + + + IP
Sbjct: 76  -----------------------GC---------FGAALMKTPELVRDIVHEIGRQVQIP 103

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VTVK RIG D       LRN V                    +G+ PK NR +P L Y  
Sbjct: 104 VTVKTRIGYDYYDSFDVLRNFV--------------------QGVDPKRNRSVPPLLYGR 143

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD----------------------GVM 214
           VY +  + PDL   LNGG+  + +A+ +      D                      GVM
Sbjct: 144 VYNLCDQFPDLDFTLNGGVTSIQEAIDLAAGKWTDGTTEMDALLRRITRDKTVQPLRGVM 203

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK-L 273
           +GRAA  +  +L +VD  F           +R      R +  +  DY       GG  L
Sbjct: 204 LGRAASNDPCILGSVDTDFYGASANPPSSHSR------RTVLEAYGDYLKPFAEDGGYSL 257

Query: 274 QQITRHMIGLFHGFPNSRRCRHIL 297
             + + ++G+ +G P  R  R  L
Sbjct: 258 FALLKPVLGVLNGMPGHRLFRFTL 281


>gi|227202714|dbj|BAH56830.1| AT3G63510 [Arabidopsis thaliana]
          Length = 261

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 104/228 (45%), Gaps = 8/228 (3%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK-SGVNGIWIHAR 156
           ML P +VG+ ++A+    ++PVTVKCRIGVD+      L + +  +   S      +H+R
Sbjct: 1   MLKPKLVGEAMSAIAANTNVPVTVKCRIGVDNHDSYDELCDFIYKVSTLSPTRHFIVHSR 60

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMI 215
           KA+L G+SP DNR+IP L Y+  Y + ++ PDL   +NGG+  +S+    L     GVM+
Sbjct: 61  KALLGGISPADNRRIPPLKYEYYYALVRDFPDLRFTINGGITSVSKVNAALKEGAHGVMV 120

Query: 216 GRAAYKNSAM-LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           GRAAY N    L  VD           P      +    +           H +    ++
Sbjct: 121 GRAAYNNPWQTLGQVDTAVYG-----VPSSGLTRRQVLEQYQVYGDSVLGTHGNGRPNVR 175

Query: 275 QITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
            + + ++ LFH    +   +           +   ++E +   + + +
Sbjct: 176 DLVKPLLNLFHSENGNSLWKRRADAAFKECRSVGSLLEESLRAIPDCV 223


>gi|221121780|ref|XP_002165230.1| PREDICTED: similar to tRNA-dihydrouridine synthase 2-like, partial
           [Hydra magnipapillata]
          Length = 246

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 98/248 (39%), Gaps = 37/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVAD----------AILRGDKKNILGFS 44
           MV      +R  A       ++YTE      MI               L  D   +    
Sbjct: 14  MVRIGTLPFRLLALRY-GADIVYTEEIIDYKMIECKRIENKLLDTIDFLLADGTVVFRTC 72

Query: 45  TQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            +EK  L  Q+G  +  + +  A+++E    + I++N+GCP     +G  GA L+  PD 
Sbjct: 73  KEEKGKLVFQMGTNNAERALSVAQMLEK-DIDGIDINMGCPKEFSVKGGMGAALLTQPDK 131

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V   +  + + LSIPVT K RI             L K I+ +GV  I IH R    +  
Sbjct: 132 VKQILTGLVQNLSIPVTCKIRILPQLSDT----IELAKLIEATGVKAIAIHGRTKDERSS 187

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-----LKILPSVDGVMIGRA 218
           SP  N        D +  +  +  ++ +  NGG +D+         K       VMI R+
Sbjct: 188 SPCHN--------DYIKAVA-DAVNIPVIANGGSQDIKTYFNIAKFKEETGCSSVMIARS 238

Query: 219 AYKNSAML 226
           A  N ++ 
Sbjct: 239 AQWNPSVF 246


>gi|116491410|ref|YP_810954.1| tRNA-dihydrouridine synthase [Oenococcus oeni PSU-1]
 gi|290890989|ref|ZP_06554053.1| hypothetical protein AWRIB429_1443 [Oenococcus oeni AWRIB429]
 gi|116092135|gb|ABJ57289.1| tRNA-dihydrouridine synthase [Oenococcus oeni PSU-1]
 gi|290479388|gb|EFD88048.1| hypothetical protein AWRIB429_1443 [Oenococcus oeni AWRIB429]
          Length = 330

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/322 (18%), Positives = 122/322 (37%), Gaps = 32/322 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   TD  +R          L YTE   A ++     K      +     +++P+  Q+ 
Sbjct: 26  MEAVTDSVFRRVVFKAAPPDLFYTEFTNAISVTHPKAKFSVMGRLYVKKDEQRPIV-QLW 84

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G   S   +AA  V++ G+  I++N+GCP + V +   G+ L+ +     + I A  +A 
Sbjct: 85  GNHASDFAKAALSVKNQGFKAIDINMGCPDSTVVKNGGGSDLIRHRSAAAEVIQASKEA- 143

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +P++ K R+G         + + +  + K  +  + +H R        P     I    
Sbjct: 144 GLPISAKTRLGF---SKIDEMYDWLPWLLKQDLQVLTVHLRTRKEMSKVPAHFELID--- 197

Query: 176 YDIVYEIKKENPDLFIGLNGGLED----MSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +I+    +  P+  + +NG +++    +  A K  P +DG+MIGR  ++N         
Sbjct: 198 -EIIKMRDQIAPETLLQINGDIKNRSEGIELAKKH-PGIDGIMIGRGVFENPYCF----- 250

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
                 T ++        D +         Y         + + + R       G  ++ 
Sbjct: 251 -----ETKAATHSLNDCLDLFEMQLDLYDQYVQEV--GLKRFETLRRFFKIYIRGIRDAA 303

Query: 292 RCRHILTVEAGASTATHHIIET 313
           + R +L +   ++     II  
Sbjct: 304 KYRDLL-INTHSTDEARKIINE 324


>gi|254284133|ref|ZP_04959101.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR51-B]
 gi|219680336|gb|EED36685.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR51-B]
          Length = 320

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 117/305 (38%), Gaps = 30/305 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     +       TE + V+  +L           +LG   +    P+ +
Sbjct: 8   MEGVIDAVMRDLLTRIGGYNRCVTEFVRVSQTVLPKRVFYRLAPELLGDGKTAAGIPVYV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + + + A +    G   I+LN GCP+  V++ S GA L+  P  +     A+ 
Sbjct: 68  QLLGSDPALMADNAAVAARLGAPGIDLNFGCPAKTVNKSSGGAILLRQPQRIAAICTAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             +  SIPVT K R+G  D        ++V ++  SGV+ I IHAR         ++   
Sbjct: 128 ATVPASIPVTAKIRLGYADDDG---FEDVVDAVADSGVSEITIHART--------REQGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +D + +       + +  NG L   +   +   +   D  M+ R A     +   
Sbjct: 177 RPPAYWDRIADAVN-RSSIPVIANGELWSPADVDRCAAVTGCDRFMLARGALCRPDLGLA 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +       L       T ++      ++ +   Y+ RH      +  + + ++ L H +P
Sbjct: 236 IRARIEA-LDYPVLQWTDIEALLLEFLTTNAHRYSERH-----AVNPVKQWLMYLKHHYP 289

Query: 289 NSRRC 293
            +   
Sbjct: 290 QAAAL 294


>gi|164663047|ref|XP_001732645.1| hypothetical protein MGL_0420 [Malassezia globosa CBS 7966]
 gi|190359304|sp|A8PTG4|DUS3_MALGO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|159106548|gb|EDP45431.1| hypothetical protein MGL_0420 [Malassezia globosa CBS 7966]
          Length = 766

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 62/295 (21%), Positives = 114/295 (38%), Gaps = 32/295 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLV 63
           +  +R       ++ +   EM +A++ L+G   + +++     E+    Q+ GA    LV
Sbjct: 407 NLPFRRLCASFGSD-IHCGEMGMAESFLQGHASEWSLVRRWEGERIFGTQVCGAKPELLV 465

Query: 64  EAAKIVED---FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
             A+++      G + +++N GCP   V+    G+ L+ + + +G  +  M +AL  IP+
Sbjct: 466 PTAEVLAREVGRGLDFVDVNCGCPIDLVYNKGAGSALLDHANKLGRIVRGMSEALGEIPL 525

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL---DY 176
           T+K R G   +     +    ++  + GV G+ +H R    +  +  D   I       +
Sbjct: 526 TIKLRTGTTSKPTTHKI--FARAQTEWGVGGLSLHGRSRKQRYKNDADWAYIRTCVDTLH 583

Query: 177 DIVYEIKKE--------NPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           D V    +E           + +  NG +         L    VDG MI R A     + 
Sbjct: 584 DAVRTWNEEPQHADEPDMVPVPVYGNGDVYGWRDYYDHLEHAHVDGTMIARGALIKPWIF 643

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           T + E           I +R   D  R+       Y   H  S  +    TR  +
Sbjct: 644 TEIKERRDWD------ISSRERLDMIRQ----YASYGLTHWGSDTQGVNTTRRFL 688


>gi|265998250|ref|ZP_06110807.1| nitrogen regulation protein [Brucella ceti M490/95/1]
 gi|262552718|gb|EEZ08708.1| nitrogen regulation protein [Brucella ceti M490/95/1]
          Length = 214

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 43/187 (22%), Positives = 87/187 (46%), Gaps = 12/187 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L    +      +Q+ G + 
Sbjct: 11  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLFGEGLGTHVVQLAGREA 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 70  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+K R+G D+   ++    L +  + +G+  + +H R         +        D+D +
Sbjct: 130 TLKMRLGWDE--NSINAPELARRAEDAGIAMVTVHGRT--------RCQFYEGTADWDAI 179

Query: 180 YEIKKEN 186
           + ++   
Sbjct: 180 HAVRDAV 186


>gi|126135514|ref|XP_001384281.1| dihydrouridine synthase of tRNA [Scheffersomyces stipitis CBS 6054]
 gi|187471049|sp|A3LUK5|DUS3_PICST RecName: Full=tRNA-dihydrouridine synthase 3
 gi|126091479|gb|ABN66252.1| dihydrouridine synthase of tRNA [Scheffersomyces stipitis CBS 6054]
          Length = 613

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 63/307 (20%), Positives = 112/307 (36%), Gaps = 46/307 (14%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +L+             T+     +QI  +     
Sbjct: 256 NLPYRRLMKKL-GADITYSEMALSVPLLQATNAEWALPKAHRTEYPGYGVQIATSKHWAA 314

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            + A+I+  E    +E+NLN GCP   ++    G+ L+  P  +   + AM   +  IPV
Sbjct: 315 AKVAEIISRETEHVSELNLNCGCPIDLLYRQGQGSALLEQPARLVRILKAMNASSGDIPV 374

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G  +         + + + ++ V  I +H R         +  R     D++ +
Sbjct: 375 TVKIRTGSKENKNTAKTL-VERLLAENDVAAITLHGRS--------RQQRYTKEADWNYI 425

Query: 180 YEI----------KKENPD-------LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
            E+          K+EN D        F+G NG +         +    +D VM+ R A 
Sbjct: 426 AEVGQVVQQWNDKKEENKDSRDTQRTCFVG-NGDVFSHVDWYNAVNTDGIDSVMVARGAL 484

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               +   V+       T +              I  + +DYA  H  +      + R  
Sbjct: 485 IKPWIFEEVEAQQYLDKTATE----------RLDILKTFSDYALEHWGTDEYGVGLARRF 534

Query: 281 IGLFHGF 287
           +  F  F
Sbjct: 535 MCEFLSF 541


>gi|219123999|ref|XP_002182301.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|219128682|ref|XP_002184536.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403986|gb|EEC43935.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406262|gb|EEC46202.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 229

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 92/235 (39%), Gaps = 19/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MV  ++  +R   R      + YT M+ A             F     ++PL       D
Sbjct: 5   MVGASELAFRLLCRKY-GAQVAYTPMMSAPKFATDPSYRSAEFQTCAADRPLVCHFAAND 63

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCIAAMCKALS 116
            +    AA   + F  + I+LN+GCP    + G FG+ L+   +  ++ D + A   A+S
Sbjct: 64  AADFAAAAIAAQPF-CDAIDLNLGCPQRTAYLGHFGSYLLDRKDRSLICDIVRAGAAAVS 122

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSPKDNRKIPN 173
           IP+ VK R+             L + ++++G + I +HAR       KG   +D      
Sbjct: 123 IPIFVKIRLL----DKVEETIELCQQLERAGASLIAVHARYRASWERKGAGARD----GP 174

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAML 226
              D +  +K+    + I  NG +       K   L   DGVM       N A+ 
Sbjct: 175 ALLDQIAVLKQHITSIPIIANGNVITYDDVEKNLELTGADGVMSAEGILDNPALF 229


>gi|307717822|ref|YP_003873354.1| tRNA-dihydrouridine synthase C [Spirochaeta thermophila DSM 6192]
 gi|306531547|gb|ADN01081.1| tRNA-dihydrouridine synthase C [Spirochaeta thermophila DSM 6192]
          Length = 334

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 118/291 (40%), Gaps = 18/291 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGDKKN-ILGFSTQEKPLALQIGGAD 58
           M + T   +R         ++  TEMI A  +L +G  +   L FS       +Q+ G D
Sbjct: 21  MAELTHSGFRALLHTWGGCSVYATEMISAPGLLSKGPYERFYLDFSPDPSRTIVQLVGYD 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              LV+AA I+ ++    +++N+GC +  + +   GA  +L  +     +  + + L   
Sbjct: 81  TDSLVQAAGILAEYPILGVDINMGCAAPEIRKRGGGAGWLLRGEEAVRLVGEVRRVLPPH 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++  +I + + +P       ++ +   G++ I +H      KGL  K +R      +D+
Sbjct: 141 LSLSVKIRIPESLPLEEFIAFLQGLMGQGLSFITVHP-----KGLKEKHDR---PARWDL 192

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  + +E P + +  NG +          + +P + G+MIGR A +          Y  +
Sbjct: 193 IPPLLEEIP-IPVVGNGNITSFDVYRKRREEIPGLAGIMIGRKAVQAPWFFA----YLRS 247

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
              G     T   ++  R     ++ +     H     +    +   LF G
Sbjct: 248 RDRGEREPFTVNLEEAARSFLELLSRHQPPEFHLSRARRFFRYYTRNLFFG 298


>gi|218890670|ref|YP_002439534.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
 gi|218770893|emb|CAW26658.1| putative tRNA-dihydrouridine synthase [Pseudomonas aeruginosa
           LESB58]
          Length = 319

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 110/288 (38%), Gaps = 27/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I + D +L     + L         +    P+ +
Sbjct: 8   MEGLVDEILRDVLTRVGGIDWCVTEFIRITDRLLPATAFHKLAPELRDGSRTRAGTPMRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L + A    + G   I+LN GCP+  V+    GA L+  P ++ D +AA+ 
Sbjct: 68  QLLGSDPACLADNAAFACELGAPVIDLNFGCPAKTVNRSRGGAVLLKEPKLMHDIVAAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   I VT K R+G D    A+   +  +++   G   + +HAR  +           
Sbjct: 128 RAVPSEIAVTSKMRLGYDSPDGAL---DCARALADGGSAHVVVHARTKVDGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ V  +  E   + +  NG +  +   L+      V+ +M+GR       +   
Sbjct: 178 -PPAHWEWVARVA-EAVRVPVFANGEVWMLDDYLRCREVSGVEDIMLGRGLVSRPGLARQ 235

Query: 229 VDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD-YAARHLHSGGKL 273
           +  +         P      + +DFW +    +   YA   L     +
Sbjct: 236 IAAWRDGGEIREMPWSELLPLLRDFWLQARRKLAPRYAPGRLKQWLGM 283


>gi|153940547|ref|YP_001390029.1| dihydrouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
 gi|152936443|gb|ABS41941.1| dihydrouridine synthase family protein [Clostridium botulinum F
           str. Langeland]
          Length = 312

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/291 (20%), Positives = 120/291 (41%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFHNIDKYFTPFIVPNKSTSLKTKELRDILPENNEGINIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  + +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSERFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               P+LD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYG------NKPDLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             +++         I  NG +  +S     +K  P V  +M+GR    N  ++  +    
Sbjct: 178 --IFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLINEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 -----NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|304313177|ref|YP_003812775.1| Dihydrouridine synthase [gamma proteobacterium HdN1]
 gi|301798910|emb|CBL47146.1| Dihydrouridine synthase [gamma proteobacterium HdN1]
          Length = 313

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 66/310 (21%), Positives = 113/310 (36%), Gaps = 36/310 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE I V  ++L       L         +    PL +
Sbjct: 15  MEGLVDAPMRAALTAMGGVDWCVTEFIRVTQSVLPTRTYQRLAPELEQQWKTASGTPLHV 74

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G+D   L   A      G  EI+LN GCP+  V+    GA L+  P+++   + A+ 
Sbjct: 75  QFLGSDPEFLAANAVRAAKLGAKEIDLNFGCPAKAVNRHRGGAVLLEEPELLNTIVTAVR 134

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   I VT K R+G  D+     + +  +++ ++G   I +HAR         K    
Sbjct: 135 AAVPEPIKVTAKMRLGYLDKSL---MLDCARALDEAGAARIVVHART--------KAEGY 183

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +  + +I  +     +  NG +  +   L+       + VM+GR       +   
Sbjct: 184 RPPAHWHCIAQIA-DVVRAPVMANGEIWTVEDYLQCRRESGCNDVMLGRGLVARPDLALQ 242

Query: 229 VDEYFSNPLTGSS---PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           +           S   PI   V + F++   A +   AA      G+L+     +  L H
Sbjct: 243 IRTALLGEHQAPSSWDPIFAAV-QVFYQHSLAQLNPTAAA-----GRLKSW---LAHLRH 293

Query: 286 GFPNSRRCRH 295
            +P +     
Sbjct: 294 TYPEASELYQ 303


>gi|198429785|ref|XP_002120440.1| PREDICTED: similar to MGC79829 protein [Ciona intestinalis]
          Length = 305

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 106/257 (41%), Gaps = 31/257 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MV ++   +R   R      + YT MIVA + L  D      F  S  + PL +Q    +
Sbjct: 21  MVRYSKHAFRLLVRKYD-CDIAYTPMIVAKSFLESDSCRQNEFITSKDDTPLIVQFAAKN 79

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKAL 115
             +  EA++++  F  + + LN GCP        +GA L+  P+ + D I    A+    
Sbjct: 80  AKEFSEASELIYPF-ASGVGLNCGCPQRWAMAEGYGAKLLQKPEEIVDFIRFTKALVSDE 138

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              ++VK R+             + + ++K+G + + +H R +  +            + 
Sbjct: 139 KFTISVKIRLH----EELARTVEMCRGLEKAGASFVSVHGRTSKERHQ---------PVH 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML------- 226
           YD +  I KE+  + I  NGG+       K+  +   +GVM+ +    N A+        
Sbjct: 186 YDAIK-ILKESVSIPIVANGGVNTYKDFDKVHKMTGANGVMVAQGLLNNPALFQGYKTTP 244

Query: 227 -TTVDEYFSNPLTGSSP 242
            + V ++    L+  +P
Sbjct: 245 LSCVKDWLDISLSYGTP 261


>gi|315126902|ref|YP_004068905.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas sp. SM9913]
 gi|315015416|gb|ADT68754.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas sp. SM9913]
          Length = 326

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 95/243 (39%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNI--LGFSTQEKPLAL 52
           M    D   R     +    L  TE I      + D +       +   G +    P+ +
Sbjct: 8   MEGVVDFKMRQLLTDIGGFDLCVTEFIRVVDTCLPDKVFHRYCPELKNAGLTRSGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G + ++LN GCP+  V++   GA L+ +PD +   I  + 
Sbjct: 68  QLLGQVADVLAENAVKAIGLGSHGVDLNFGCPAKTVNKSKGGAVLLKDPDHMYSIIKTVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     V+ K R+G DD   +     +V ++  +G N I IHAR         K +  
Sbjct: 128 DAVDDEHEVSAKIRLGFDDDSNSQ---EIVDAVVSAGANSIAIHART--------KRDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + K+   + +  NG +  +  A   +       +MIGR A  +  +   
Sbjct: 177 NPPAYWEKIPPLVKD-KKIAVVANGEIWQVEDALLCQKRSGCTDLMIGRGALSHPDLARK 235

Query: 229 VDE 231
           +  
Sbjct: 236 IKA 238


>gi|308048892|ref|YP_003912458.1| tRNA-U20a,U20b-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
 gi|307631082|gb|ADN75384.1| tRNA-U20a,U20b-dihydrouridine synthase [Ferrimonas balearica DSM
           9799]
          Length = 310

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 56/312 (17%), Positives = 109/312 (34%), Gaps = 40/312 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     L    L  TE   ++   I       +       G +    P+ +
Sbjct: 8   MEGVLDHRMRQLLSELNPYDLCVTEFIRVIEQPIPDKVFYRLAPELENGGKTRNGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   L   A+     G   +++N GCP+  V++   GA L+  P+ +   ++AM 
Sbjct: 68  QLLGQDPDWLAYNAERAIALGSPGVDINFGCPAKTVNKSKGGAVLLKEPETLYRIVSAMR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     ++ K R+G +          + ++I+ +G N + IH R          D  +
Sbjct: 128 QAVPADQVLSAKIRLGWECTSQ---TMEIAQAIESAGANELAIHGRTK-------ADGYR 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
              +++  +  + K    + +  NG +   S   +         +MIGR A     +   
Sbjct: 178 ADAINWGAIAPVAKAL-SIPVIANGEINGFSDGQRCQAESGCQDLMIGRGALCRPNLGAM 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL---QQITRHMIGLFH 285
           V E                +   W  I   + +Y    ++   +     +I +    L  
Sbjct: 237 VKE--------------NAELLSWDAIREVLNEYVTLEVYGDKQRYFPNRIKQWFGYLRQ 282

Query: 286 GFPNSRRCRHIL 297
            +P +      L
Sbjct: 283 AYPQANELFREL 294


>gi|328947505|ref|YP_004364842.1| dihydrouridine synthase DuS [Treponema succinifaciens DSM 2489]
 gi|328447829|gb|AEB13545.1| dihydrouridine synthase DuS [Treponema succinifaciens DSM 2489]
          Length = 331

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 58/273 (21%), Positives = 107/273 (39%), Gaps = 23/273 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   +   +R            +TEMI A ++L      K  L      + +  Q+ G  
Sbjct: 8   MATLSHEAFRISVEEFGGCDEYFTEMINASSLLNMGPFEKYYLMNGPCPEKIVWQLTGTS 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSI 117
              L +AA+IV + G   I+LN+GC + ++++   G   ML P     + ++ + K+L +
Sbjct: 68  AESLAKAAEIVCEKGGIGIDLNMGCSAPQIYKIGAGIAWMLKPLKETAEAVSKVKKSLDL 127

Query: 118 ---------PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                      +VKCR+G ++        N    + ++GV  I +HAR    K       
Sbjct: 128 IEEKTQNHFRFSVKCRLG-NENFTEQTFFNFTDMLVENGVELITLHARTIKEKYRGLPRY 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAM 225
                L      +IK       + +NG ++D      A++  P  DG+MI RAA +   +
Sbjct: 187 EFAKKLSQRYEKKIK-------VYVNGCIKDTASAKFAIQKAPEADGIMIARAAAERPWI 239

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
              +     +     +  + +   +F   +   
Sbjct: 240 FAQIKNGLEDSAEKITIDRMQTALNFIDNVEKF 272


>gi|283768232|ref|ZP_06341145.1| TIM-barrel protein, nifR3 family [Bulleidia extructa W1219]
 gi|283105109|gb|EFC06480.1| TIM-barrel protein, nifR3 family [Bulleidia extructa W1219]
          Length = 234

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 38/215 (17%), Positives = 81/215 (37%), Gaps = 19/215 (8%)

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            ++ +   G+ L+ +P        A+      PVTVK R G D Q        + K +++
Sbjct: 13  KKIIKSHAGSYLLQDPRQAQKVAKAVVDHSKKPVTVKIRTGWDHQHKNAV--EVAKVLEE 70

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +GV+ I IH R         K       +D +++ ++K+    + +  NG ++ +    +
Sbjct: 71  AGVSAITIHGRT--------KSQMYSGTVDLEMIKQVKQAV-SIPVIGNGDIKTVEDGKR 121

Query: 206 IL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
           +L    VD +MIGR        ++ +  + +           R+       +      + 
Sbjct: 122 MLEETGVDAIMIGRGLLGRPYFMSEMVAFLNGEEFIEPSFLKRI------HLLEEYAIHL 175

Query: 264 ARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           +  +     +Q +         G PN  + +  L+
Sbjct: 176 SARMGEKNGIQMMRGMASWYVTGMPNCSQIKKALS 210


>gi|91783478|ref|YP_558684.1| putative tRNA-dihydrouridine synthase C, DuS [Burkholderia
           xenovorans LB400]
 gi|91687432|gb|ABE30632.1| tRNA-U20a,U20b-dihydrouridine synthase [Burkholderia xenovorans
           LB400]
          Length = 340

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 51/277 (18%), Positives = 104/277 (37%), Gaps = 34/277 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +       +E + V  ++L               G +    P+ +
Sbjct: 9   MEGLADYVLRDVLTGIGGFDGCVSEFVRVTGSLLPSRVYEREAPEVLDGGHTPNGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A        + I+LN GCP+  V++   GA L+ +P+ +   ++++ 
Sbjct: 69  QLLGSDPEWMARNAAHAASLSPHGIDLNFGCPAKVVNQHGGGAMLLADPEQLNRIVSSVR 128

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVT K R+GV D   A+       ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPAGVPVTAKMRLGVSDTSLAI---ECAVALAEGGAASLVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I     D+ +  NG +  ++   +   +     VM+GR A  +  +   
Sbjct: 178 RPPAHWEWIARI-DAAVDVPVVANGEVWTVADWERCRAVSGCANVMLGRGAVSDPFLALR 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           +        +             WR +   +  Y  +
Sbjct: 237 IRGLMERTPSHGE----------WRHVLGHIAGYLRK 263


>gi|3859982|gb|AAC72941.1| unknown [Homo sapiens]
          Length = 223

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 45/209 (21%), Positives = 81/209 (38%), Gaps = 21/209 (10%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + +++NVGCP   V++   G  LM         +  M + L +P+TVK R GV +++  
Sbjct: 11  VDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERVNL 70

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                L+  ++  GV  + +H R         ++ R     D+  + E  +    + +  
Sbjct: 71  A--HRLLPELRDWGVALVTLHGRS--------REQRYTKLADWQYIEECVQAASPMPLFG 120

Query: 194 NGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           NG +     A   +   V G+MI R A     + T + E     ++ S            
Sbjct: 121 NGDILSFEDANRAMQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSE----------R 170

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMI 281
             I    T+Y   H  S  +  + TR  +
Sbjct: 171 LDILRDFTNYGLEHWGSDTQGVEKTRRFL 199


>gi|126667330|ref|ZP_01738303.1| hypothetical protein MELB17_15347 [Marinobacter sp. ELB17]
 gi|126628275|gb|EAZ98899.1| hypothetical protein MELB17_15347 [Marinobacter sp. ELB17]
          Length = 335

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 67/318 (21%), Positives = 118/318 (37%), Gaps = 43/318 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFSTQ-----EKPLAL 52
           M    D   R     +       TE I V   +L  R   K               P+A+
Sbjct: 8   MEGLVDAPIRETLTKVGGIDRCVTEFIRVTHGMLPPRIFYKYAPELHNNSLTRVGVPVAV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +        + G  ++++N GCP+  V++   G  LM  P+++ +  AA+ 
Sbjct: 68  QLLGSDPHMMARHGAKAAELGATQVDINFGCPAKTVNKHKGGCVLMREPELMHEITAAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   I VT K R+G DD+   VA     +++  +G   I IHAR         K +  
Sbjct: 128 QAVPADILVTAKMRLGYDDRSMGVA---CAQALDAAGAGEIVIHARS--------KTDGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +  +E     +  NG +  ++   +       D VMIGR       +   
Sbjct: 177 KPPAYWEEIAK-AREAVKAKVIANGDIFTVADYWRCREVSGCDDVMIGRGLVARPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA---ARHLHSGGKLQQITRHMIGLFH 285
           +                 ++   W +  A + +Y       L       +I + M  L  
Sbjct: 236 IRASQRGES---------IELMTWPEALALVQEYGYALQGWLEDKYVTGRIKQWMNYLRQ 286

Query: 286 GF-------PNSRRCRHI 296
           GF       P +R+ R +
Sbjct: 287 GFSEAEALWPQARKIREV 304


>gi|257455770|ref|ZP_05620996.1| tRNA-dihydrouridine synthase C [Enhydrobacter aerosaccus SK60]
 gi|257446784|gb|EEV21801.1| tRNA-dihydrouridine synthase C [Enhydrobacter aerosaccus SK60]
          Length = 337

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 57/312 (18%), Positives = 114/312 (36%), Gaps = 42/312 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD--------------AILRGDKKNILGFSTQ 46
           M   TD   R     + +     +E I                  +L  D   + G +  
Sbjct: 22  MEGLTDPLMRDILTSIGHYDWTVSEFIRVTQHVLPAHVFYKFVPELLHKDG--LKGKTIH 79

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             P+ +Q+ G++   +   A    + G   I++N GCP+  V+    G+ L+  P+ +  
Sbjct: 80  GTPVHVQLLGSEPDLMAGNAVRAVELGALAIDINFGCPAKTVNSHRGGSVLLTEPETLYQ 139

Query: 107 CIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            I A+ +A+    PV+ K R+G +D      + +   +++ +  + + IHAR        
Sbjct: 140 IIHAVRQAVPSDTPVSAKIRLGYEDTSLTQEIGD---AVQSANASWLTIHART------- 189

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKN 222
            K     P   ++++  + +    L I  NG +    QA++     +   +M+GR A   
Sbjct: 190 -KTQGYKPPAYWELIAPLTQRL-SLPIIANGEIWQTEQAMRCRKQANTPHIMLGRGAVTR 247

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             ++  +     N           V    W+ +      +   H  S   L    +  +G
Sbjct: 248 PDLVNQIKAMDKNDT---------VKNMAWQALLKLQIAFLQGHARSDNMLVGRYKQWLG 298

Query: 283 -LFHGFPNSRRC 293
            L  G+  +   
Sbjct: 299 MLTQGYEEASEL 310


>gi|332993814|gb|AEF03869.1| NifR3/Smm1 family protein [Alteromonas sp. SN2]
          Length = 312

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 108/284 (38%), Gaps = 38/284 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +       TE +  V   +       +       G +    P+ +
Sbjct: 8   MEGVVDHLMRDMLTHVGGFDQCVTEFVRVVDQKLPNKTFYKLCPELHNGGKTPNGVPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    D G   ++LN GCP+  V++   GA L+     + D + A+ 
Sbjct: 68  QLLGQHPQWLAENAHTAVDLGSPGVDLNFGCPAKTVNKSKGGAVLLKETQALYDIVKAVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+  S PV+ K R+G +D+  AV       +I ++G + + +HAR         K    
Sbjct: 128 DAVPASQPVSAKIRLGFEDKSLAVEN---AIAITEAGASELVVHART--------KTEGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            P   +D + +IK+ N D+ +  NG + +     +         +M+GR A     +   
Sbjct: 177 KPPAYWDWIAKIKQ-NTDIPLVANGEIWNEEDGKRCQEQSACTNLMVGRGALAMPNLARC 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           + +       G  P+        W  ++A +  Y+   ++    
Sbjct: 236 IRD-------GEPPMA-------WEDVAALLIRYSGYEIYGDKG 265


>gi|50084050|ref|YP_045560.1| hypothetical protein ACIAD0837 [Acinetobacter sp. ADP1]
 gi|49530026|emb|CAG67738.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. ADP1]
          Length = 310

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 113/305 (37%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M   TD   R     + +     TE I V D++L               G +    P+ +
Sbjct: 8   MEGLTDPIMRDVLTHVGSFDWCVTEFIRVTDSVLPDHVYYTYCPELKNNGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A+ V   G   I+LN GCP+  V+    G+ L+  PD+V   + A+ 
Sbjct: 68  QFLGNNPDMLAANAEKVVALGAPAIDLNFGCPAKTVNRHRGGSILLDEPDVVHLLVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+       +   +I+++G N + +HAR         K +  
Sbjct: 128 DAVPAHIPVSAKMRLGYLDENH---TMDNAYAIQEAGANWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK +   + +  NG +     A         + +MIGR A     +   
Sbjct: 177 TPPAYWEKIQPIK-DALSINVIANGEIWTNQDAKACQQQSGCEDLMIGRGAVTTPDLTLC 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + +     L   +     + + F      +      R+    G +             +P
Sbjct: 236 IRQNVDEALMNWA-ALIELQQRFLNGEYKTEIGMIGRYKQWLGMM----------TKAYP 284

Query: 289 NSRRC 293
            +++ 
Sbjct: 285 EAKQL 289


>gi|297819610|ref|XP_002877688.1| FAD binding protein [Arabidopsis lyrata subsp. lyrata]
 gi|297323526|gb|EFH53947.1| FAD binding protein [Arabidopsis lyrata subsp. lyrata]
          Length = 543

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 105/247 (42%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE------------- 47
           MV      +R  A       + Y+E I+   +++ +++  + + T E             
Sbjct: 226 MVRVGTLSFRMLAAEY-GADITYSEEIIDHKLVKCERRINVAYGTTEFVEKGTDNVVFST 284

Query: 48  -----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                  +  Q+G +D  + ++AA+IV +     +++N+GCP A   +G  GA L+  P+
Sbjct: 285 CKEERNRVVFQMGTSDAVRALKAAEIVCN-DVATVDINMGCPKAFSIQGGMGAALLSKPE 343

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +A + + L +PVT K R+             L + I+K GV  + +H RK     
Sbjct: 344 LIHDILATLKRNLDVPVTCKIRLLKSPADTV----ELARRIEKLGVPALAVHGRKI---- 395

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +      +K       VM+ R A 
Sbjct: 396 ----ADRPRDPAKWDEIADVVAAL-SIPVIANGDVLEYDDFSRIKTATGAASVMVARGAM 450

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 451 WNASIFS 457


>gi|170755297|ref|YP_001780311.1| dihydrouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
 gi|169120509|gb|ACA44345.1| dihydrouridine synthase family protein [Clostridium botulinum B1
           str. Okra]
          Length = 312

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 119/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + +++L  + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYKKFFNNIDKYFTPFIVPNKSTSLRTKELRDMLPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               PNLD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYG------NKPNLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++         I  NG +  +S     +K  P V  +M+GR    N  ++  +    
Sbjct: 178 --VFKDALSLSSNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLINEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 -----NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|221068625|ref|ZP_03544730.1| dihydrouridine synthase DuS [Comamonas testosteroni KF-1]
 gi|220713648|gb|EED69016.1| dihydrouridine synthase DuS [Comamonas testosteroni KF-1]
          Length = 347

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 59/301 (19%), Positives = 115/301 (38%), Gaps = 42/301 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       +E I ++ ++L    K  L    +           P+
Sbjct: 8   MEGLLDFVLRDVLTRVGGADRCVSEFIRISGSLL--PDKVYLRTMPELRYGSRTLAGVPV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+ +P  +   + A
Sbjct: 66  RAQLLGSDPVSMAENAANLARLGPEGIDLNFGCPAKVVNRHGGGASLLQDPMQIARVVEA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + KA+   +PV+ K R+G +D+     +    ++++  G   I +HAR  +     P   
Sbjct: 126 VRKAVPAQLPVSAKMRLGFNDR---ALMTECAQAMESGGACEIVVHARTKLDGYRPPAYW 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +IP +         +E   + +  NG +  + +AL+       D +M+GR    +  + 
Sbjct: 183 EEIPRI---------REAVGVNVVANGEIWTVEEALRCREVSGCDDLMLGRGIVADPGLA 233

Query: 227 TTVDEYFSNPLTGSSPIKTRVD-----KDFWRKISASMTDYAARHLHSGGKLQQ----IT 277
             V          ++     ++     + FW  +   +           G+L+Q    + 
Sbjct: 234 LAVRRAVEQGSGTAAAGIDWLELVPQVQRFWHMVCEDLEP-----RQRAGRLKQWLNLMR 288

Query: 278 R 278
           R
Sbjct: 289 R 289


>gi|109899222|ref|YP_662477.1| dihydrouridine synthase, DuS [Pseudoalteromonas atlantica T6c]
 gi|109701503|gb|ABG41423.1| tRNA-U20a,U20b-dihydrouridine synthase [Pseudoalteromonas atlantica
           T6c]
          Length = 310

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 58/279 (20%), Positives = 109/279 (39%), Gaps = 38/279 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     +    L  TE +      +   +       +   GF+    P+ +
Sbjct: 8   MEGVVDHLMRDMLSKVGGFDLCVTEFVRVVNCLLPKKVFYRICPELHHGGFTPNGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G +   L E A    + G + ++LN GCP+  V++   GA L+  P  + D ++A+ 
Sbjct: 68  QLLGQNPQPLAENAVRAVELGSHGVDLNFGCPAKTVNKSKGGAILLREPQALYDIVSAVR 127

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+     VT K R+G +D+  A        +I+ +G + + +HAR  +           
Sbjct: 128 EAVPKEHKVTAKMRLGFEDKSLAFENA---AAIEAAGADLLVVHARTKVEG--------Y 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            P   +  + +IK++  ++ I  NG +     AL          +M+GR        L  
Sbjct: 177 KPPAYWSWIADIKQKV-NVPIIANGEIWSQEDALNCQTQSNCQDIMLGRGILAMP-NLAQ 234

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
           V             ++   D   W +++  + DY+   L
Sbjct: 235 V-------------VRGEQDVMSWSQVNQLLIDYSGYEL 260


>gi|332852106|ref|ZP_08433933.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013150]
 gi|332867504|ref|ZP_08437657.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013113]
 gi|332872645|ref|ZP_08440613.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6014059]
 gi|332729478|gb|EGJ60817.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013150]
 gi|332733921|gb|EGJ65066.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6013113]
 gi|332739174|gb|EGJ70033.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii 6014059]
          Length = 318

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 116/308 (37%), Gaps = 41/308 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 12  MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 71

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 72  QFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 131

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 132 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 180

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +     ++A +     + +MIGR A     +   
Sbjct: 181 TPPAYWEKILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 239

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FH 285
           + +     L              W ++      +      +  ++  + R+   L     
Sbjct: 240 IRQNMDEALF------------TWEQLVDLQIRFLNGQ--AKTEIGMVGRYKQWLGMMTK 285

Query: 286 GFPNSRRC 293
            +P ++  
Sbjct: 286 AYPQAKEL 293


>gi|262373327|ref|ZP_06066606.1| tRNA-dihydrouridine synthase C [Acinetobacter junii SH205]
 gi|262313352|gb|EEY94437.1| tRNA-dihydrouridine synthase C [Acinetobacter junii SH205]
          Length = 310

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 55/243 (22%), Positives = 96/243 (39%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     +       TE I      + D I       +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDVLTHVGRFDWCVTEFIRITDSILPDHIYYSFCPELKTDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  P+ V   + A+ 
Sbjct: 68  QFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPETVHLLVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+   +   +   +I+ +G + + +HAR         K +  
Sbjct: 128 DAVPKHIPVSAKMRLGYLDENHTL---DNAHAIEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I  E   + +  NG + + + A   L       +MIGR A     +   
Sbjct: 177 TPPAYWEKIQPI-TEALKINVIANGEIWNNTDAKACLTQSHCTDLMIGRGAVTTPDLTQC 235

Query: 229 VDE 231
           + +
Sbjct: 236 IRQ 238


>gi|184157069|ref|YP_001845408.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|239501250|ref|ZP_04660560.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii AB900]
 gi|183208663|gb|ACC56061.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii ACICU]
 gi|322506968|gb|ADX02422.1| dusC [Acinetobacter baumannii 1656-2]
 gi|323516835|gb|ADX91216.1| tRNA-dihydrouridine synthase [Acinetobacter baumannii TCDC-AB0715]
          Length = 307

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 116/308 (37%), Gaps = 41/308 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 1   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 61  QFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 121 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +     ++A +     + +MIGR A     +   
Sbjct: 170 TPPAYWEKILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FH 285
           + +     L              W ++      +      +  ++  + R+   L     
Sbjct: 229 IRQNMDEALF------------TWEQLVDLQIRFLNGQ--AKTEIGMVGRYKQWLGMMTK 274

Query: 286 GFPNSRRC 293
            +P ++  
Sbjct: 275 AYPQAKEL 282


>gi|226953507|ref|ZP_03823971.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. ATCC 27244]
 gi|226835748|gb|EEH68131.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. ATCC 27244]
          Length = 309

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 97/249 (38%), Gaps = 24/249 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M   TD   R     + +     TE I      + D I       +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDVLTHVGSFDWCVTEFIRITDSILPDHIYYNFCPELQTDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  P+ V   + A+ 
Sbjct: 68  QFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPETVHLLVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +I+ +G + + +HAR         K +  
Sbjct: 128 DAVPSHIPVSAKMRLGYLDENH---TMENAHAIEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I  E   + +  NG + + + A   L       +MIGR A     +   
Sbjct: 177 TPPAYWEKIQPI-TEALKINVIANGEIWNNTDAKACLTQSHCTDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPL 237
           + +   + L
Sbjct: 236 IRQNVDHAL 244


>gi|187777797|ref|ZP_02994270.1| hypothetical protein CLOSPO_01389 [Clostridium sporogenes ATCC
           15579]
 gi|187774725|gb|EDU38527.1| hypothetical protein CLOSPO_01389 [Clostridium sporogenes ATCC
           15579]
          Length = 319

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 120/291 (41%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRSSYEKFFNNIDKYFTPFIVPNKSTSLKTKELRDILPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               P+LD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYGHK------PDLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++         I  NG +    D ++ +K  P V  +M+GR    N  ++  +    
Sbjct: 178 --VFKDALSLSSNPICYNGDIFTVSDYNRLIKTFPKVKTIMLGRGILANPGLINEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 -----NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIHIF 278


>gi|148378675|ref|YP_001253216.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. ATCC 3502]
 gi|153932290|ref|YP_001383059.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|153935524|ref|YP_001386608.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. Hall]
 gi|148288159|emb|CAL82227.1| putative dihydrouridine synthase (tRNA modification protein)
           [Clostridium botulinum A str. ATCC 3502]
 gi|152928334|gb|ABS33834.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. ATCC 19397]
 gi|152931438|gb|ABS36937.1| dihydrouridine synthase family protein [Clostridium botulinum A
           str. Hall]
          Length = 319

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 120/291 (41%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRSSYEKFFNNIDKYFTPFIVPNKSTSLKTKELRDILPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               P+LD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYGHK------PDLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++         I  NG +    D ++ +K  P V  +M+GR    N  ++  +    
Sbjct: 178 --VFKDALSLSSNPICYNGDIFTVSDYNRLIKTFPKVKTIMLGRGILANPGLINEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 -----NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIHIF 278


>gi|241763268|ref|ZP_04761325.1| dihydrouridine synthase DuS [Acidovorax delafieldii 2AN]
 gi|241367543|gb|EER61830.1| dihydrouridine synthase DuS [Acidovorax delafieldii 2AN]
          Length = 317

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 55/277 (19%), Positives = 101/277 (36%), Gaps = 29/277 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK---------PLA 51
           M    D   R     +       +E I     L  D K  L +  +           P+ 
Sbjct: 8   MEGLLDFVLRDVLTRVGGVDRCVSEFIRITGTLLPD-KVFLRYVPELHHGGRTLAGVPVR 66

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+  P  +   ++A+
Sbjct: 67  AQLLGSDPVCMAENAARLAALGPEGIDLNFGCPAKVVNRHGGGAALLQEPQRIAAVVSAV 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+ K R+G +D   A   R   ++++  G   + +HAR        P    
Sbjct: 127 RRAVPAHLPVSAKMRLGFND---ASLARECAQAMEAGGACELVVHARTKADGYRPPAYWE 183

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +IP +         +    + +  NG +  ++ AL+       D +M+GR    +  +  
Sbjct: 184 QIPAI---------RAAVRIPVVANGEIWTVADALRCREVSGCDALMLGRGMVADPGLAH 234

Query: 228 TVDEYFSNPLTG---SSPIKTRVDKDFWRKISASMTD 261
            +    +          P        FW  +   +  
Sbjct: 235 AIRAADAGVPGLGGVEWPALVPQLAVFWDLVCQDLEP 271


>gi|296421752|ref|XP_002840428.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295636644|emb|CAZ84619.1| unnamed protein product [Tuber melanosporum]
          Length = 707

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 62/284 (21%), Positives = 104/284 (36%), Gaps = 35/284 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  +R     L   AL Y+EM ++  +L+G K    +L     E P    QI G  I   
Sbjct: 336 NLPFRRLCSRL-GAALTYSEMAMSVPLLQGHKPEWALLRAHASEIPNFGAQICGTKIGTA 394

Query: 63  VEAAKIV---------EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A +++            G + ++LN GCP   V+    G+ L+  P  +   +  M  
Sbjct: 395 VRATEVLTTLFPSAASSRHGLSLVDLNCGCPIDLVYRQGGGSALLDQPSKLIKMLKGMNY 454

Query: 114 ALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKI 171
                P+T K R+G  D  P    + LV+ I  +G V  I +H R    +     D   I
Sbjct: 455 VSGETPITCKIRLGTRDSSPVA--KKLVQRIYDAGDVQAITLHGRSRQQRYSRDADWTYI 512

Query: 172 PNLDY--------------DIVYEIKKENPDLFIGLNGGLED-MSQALKILPS-VDGVMI 215
                                + +  ++ P++F   NG     +     I    VDGVM+
Sbjct: 513 AETAALIKDFKRRSDTTADTAIDKEARDKPNVFFVGNGDCYSHVDYYNSIDQGNVDGVML 572

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            R A     +   + +     L  S+  +    +++ R      
Sbjct: 573 ARGALIKPWLFEEIQK--GQYLDKSATERLDYIREYVRYGLECW 614


>gi|310791648|gb|EFQ27175.1| dihydrouridine synthase [Glomerella graminicola M1.001]
          Length = 555

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 113/302 (37%), Gaps = 63/302 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGF------------ 43
           MVD ++  +R  +R     A     + YT M  A      +      F            
Sbjct: 43  MVDQSEFAWRMLSRSFIPPAEQKNLVAYTPMFHARLFKDTENYRQCHFQAVRPGDANDST 102

Query: 44  ----------STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
                      + ++PL +Q    D   L+ AA  V  +  + ++LN+GCP     +G +
Sbjct: 103 STPQAWLDGNPSIDRPLFVQFCANDPDALLGAALRVAPY-CDAVDLNLGCPQGIAKKGKY 161

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           GA L  + +++   I  + + L IPVT K RI    +    A     K++  +G + + +
Sbjct: 162 GAFLQEDQELIFKLINTLHRNLPIPVTAKIRILPTRE----ATLAYAKNVLSAGASILTV 217

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGL---EDMSQALKILPS 209
           H R    KG            D+  +  ++++  P+  +  NG +   +D+ +AL+    
Sbjct: 218 HGRLREQKG------HLTGLADWSTIKWLREQLPPETVLFANGNILQHDDLQRALEA-TG 270

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR--------KISASMTD 261
            DG+M       +  + +              P      +++WR        ++ A M  
Sbjct: 271 ADGIMSAEGNLSDPTIFSR------------PPEPGTETREYWRGKDGKGGYRVDAVMRR 318

Query: 262 YA 263
           Y 
Sbjct: 319 YM 320


>gi|193076570|gb|ABO11229.2| hypothetical protein A1S_0789 [Acinetobacter baumannii ATCC 17978]
          Length = 307

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 62/308 (20%), Positives = 114/308 (37%), Gaps = 41/308 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 1   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 61  QFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 121 DAVPAHIPVSAKMRLGYLDENH---TMENAYAVEDAGASWLTVHART--------KADGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK+    + +  NG +   + A         + +MIGR A     +   
Sbjct: 170 TPPAYWEKILPIKEAL-KINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FH 285
           + +     L              W ++      +      +  ++  + R+   L     
Sbjct: 229 IRQNMDEALF------------TWEQLVDLQIRFLNGQ--AKTEIGMVGRYKQWLGMMTK 274

Query: 286 GFPNSRRC 293
            +P ++  
Sbjct: 275 AYPQAKEL 282


>gi|169634141|ref|YP_001707877.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii SDF]
 gi|169152933|emb|CAP01974.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii]
          Length = 321

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 66/336 (19%), Positives = 125/336 (37%), Gaps = 45/336 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 68  QFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 128 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +     ++A +     + +MIGR A     +   
Sbjct: 177 TPPAYWEKILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FH 285
           + +     L              W ++      +      +  ++  + R+   L     
Sbjct: 236 IRQNMDEALF------------TWEQLVDLQIRFLNGQ--AKTEIGMVGRYKQWLGMMTK 281

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            +P ++     L  +     A   I++    ++ + 
Sbjct: 282 AYPQAKE----LWDQVKRIKALDEIVQQLEQMITKK 313


>gi|325121123|gb|ADY80646.1| tRNA-dihydrouridine synthase C [Acinetobacter calcoaceticus PHEA-2]
          Length = 307

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 112/305 (36%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 1   MEGLTDPIMRDTLTSVGDFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 61  QFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHLLIKAVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 121 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +   + A         + +MIGR A     +   
Sbjct: 170 TPPAYWEKILPIK-EALKINVIANGEIWSNADARACQQQSGCEDLMIGRGAVTTPDLTQC 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + +     L     +     + F    + +      R+    G +             +P
Sbjct: 229 IRQNMDEALFNWEQLVDLQIR-FLNGQAKTEIGMVGRYKQWLGMM----------TKAYP 277

Query: 289 NSRRC 293
            ++  
Sbjct: 278 QAKEL 282


>gi|169797018|ref|YP_001714811.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AYE]
 gi|213156578|ref|YP_002318239.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB0057]
 gi|215484478|ref|YP_002326713.1| Dihydrouridine synthase (Dus) family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260555690|ref|ZP_05827910.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii ATCC 19606]
 gi|301347725|ref|ZP_07228466.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB056]
 gi|301512473|ref|ZP_07237710.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB058]
 gi|301594395|ref|ZP_07239403.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB059]
 gi|169149945|emb|CAM87839.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AYE]
 gi|213055738|gb|ACJ40640.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii AB0057]
 gi|213987092|gb|ACJ57391.1| Dihydrouridine synthase (Dus) family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260410601|gb|EEX03899.1| tRNA-dihydrouridine synthase C [Acinetobacter baumannii ATCC 19606]
          Length = 314

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 116/308 (37%), Gaps = 41/308 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 68  QFLGNNPEMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 128 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +     ++A +     + +MIGR A     +   
Sbjct: 177 TPPAYWEKILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL---FH 285
           + +     L              W ++      +      +  ++  + R+   L     
Sbjct: 236 IRQNMDEALF------------TWEQLVDLQIRFLNGQ--AKTEIGMVGRYKQWLGMMTK 281

Query: 286 GFPNSRRC 293
            +P ++  
Sbjct: 282 AYPQAKEL 289


>gi|77360138|ref|YP_339713.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875049|emb|CAI86270.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 326

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 71/328 (21%), Positives = 121/328 (36%), Gaps = 42/328 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-------RGDKKNILGFSTQEKPLAL 52
           M    D   R     +    L  TE + V DA L          + +  G ++   P+ +
Sbjct: 8   MEGVVDFKMRQLLTNVGGFDLCVTEFVRVVDACLPDKVFYRYCPELSNNGLTSAGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G + I+LN GCP+  V++   GA L+ +P+ + + I A+ 
Sbjct: 68  QLLGQVAGALAENAVKAISLGSHGIDLNFGCPAKTVNKSKGGAVLLKDPEHMYEIIKAVR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     V+ K R+G DD   +     +V ++  +G + I IHAR        P    K
Sbjct: 128 DAVDSKHQVSAKIRLGFDDDSNSQ---EIVDAVVSAGASSIAIHARTKRDGYNPPAYWEK 184

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
           IP L  D          D+ +  NG +  ++ A   +       +M+GR A  +  +   
Sbjct: 185 IPPLIKD---------KDIAVVANGEIWQVADAMLCQKRSGCTDLMLGRGALSHPDLAKK 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG--GKLQQITRHMIGLFHG 286
           +    +N                W  I   + + A  H  +         T+  +G    
Sbjct: 236 IKANINNEHY---------VGLEWEHILYHLINSAIHHDPAKDEKYFASRTKQWLGYLK- 285

Query: 287 FPNSRRCRHILTV--EAGASTATHHIIE 312
               R+    +T+  E     A   + E
Sbjct: 286 ----RQYPQAITLFDEIRRLKAKEDVAE 309


>gi|260550991|ref|ZP_05825196.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. RUH2624]
 gi|260405939|gb|EEW99426.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. RUH2624]
          Length = 314

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 62/305 (20%), Positives = 111/305 (36%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 68  QFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHILIKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 128 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK+    + +  NG +   + A         + +MIGR A     +   
Sbjct: 177 TPPAYWEKILPIKEAL-KINVIANGEIWTNADAKACQQQSGCEDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +       L     +     + F    + +      R+    G +             +P
Sbjct: 236 IRNNMDEALFSWEQLVDLQIR-FLNGQAKTEIGMVGRYKQWLGMM----------TKAYP 284

Query: 289 NSRRC 293
            ++  
Sbjct: 285 QAKEL 289


>gi|262280104|ref|ZP_06057889.1| tRNA-dihydrouridine synthase C [Acinetobacter calcoaceticus
           RUH2202]
 gi|262260455|gb|EEY79188.1| tRNA-dihydrouridine synthase C [Acinetobacter calcoaceticus
           RUH2202]
          Length = 314

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 102/249 (40%), Gaps = 24/249 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 68  QFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 128 DAVPPHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +     ++A +     + +MIGR A     +   
Sbjct: 177 TPPAYWEKILPIK-EALKINVIANGEIWSNSDARACQQQSGCEDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPL 237
           + E  +  L
Sbjct: 236 IRENMNEAL 244


>gi|255078812|ref|XP_002502986.1| predicted protein [Micromonas sp. RCC299]
 gi|226518252|gb|ACO64244.1| predicted protein [Micromonas sp. RCC299]
          Length = 361

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 53/285 (18%), Positives = 103/285 (36%), Gaps = 26/285 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM +A  IL+G++  +  L     E+   +Q+ G     + 
Sbjct: 19  NLPFRRVCVAL-GADVTISEMAMASNILKGERSELALLRRHPSERLFGVQVCGGHPDLMA 77

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNP---DIVGDCIAAMCKAL-SIP 118
              + +  D   + +++N+GCP   V     G+ L+ +      +   + AM  ++   P
Sbjct: 78  RCGEFLDNDVDCDFVDVNMGCPIDGVCAKGAGSTLLRDEVGLARMKKLVQAMSGSMQRTP 137

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +T+K R+G DD        +++K  +  G     +H R    +     D R I       
Sbjct: 138 LTIKVRMGYDDDPSKYVAHDVLKDARAWGAAAATLHGRTRAQRYSRLADWRYIRRC---- 193

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                     L +  NG +       + +    +   MIGR A     +LT + E     
Sbjct: 194 --AAVAAPSGLPLVGNGDVFSFKDYERHMRGGTLATCMIGRGALIKPWVLTEIKERRVWD 251

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           ++ S  +           I      +   H  S  +  + TR  +
Sbjct: 252 ISASERL----------AIFGDFARHGLEHWGSDERGVETTRRFM 286


>gi|164428803|ref|XP_956375.2| hypothetical protein NCU00065 [Neurospora crassa OR74A]
 gi|157072287|gb|EAA27139.2| conserved hypothetical protein [Neurospora crassa OR74A]
          Length = 576

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 55/257 (21%), Positives = 104/257 (40%), Gaps = 33/257 (12%)

Query: 5   TDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGGADIS 60
           T  H R F   + +   +   M+   +  R D  + + F       ++ L +Q    D +
Sbjct: 36  TKLHGRAFYESIGSPKYIVAPMV-DQSDPRPDSSDYVPFLDGNPEFDRSLFVQFCANDPA 94

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            L+ AAK+V  +  + ++LN+GCP      G +G+ L  N +++ + I  + K L IPVT
Sbjct: 95  YLLSAAKLVAPY-CDAVDLNLGCPQGIAKRGQYGSFLQENQELIFELINTLHKELDIPVT 153

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K RI         A     +++ ++G + + +H R+   KG       +    D++ + 
Sbjct: 154 AKIRIL----DTKEATLKYAQNVLRAGASILTVHGRRREQKG------HQTGLADWEYIR 203

Query: 181 EIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +++  P    I  NG +    D+ + L      DGVM       +  +           
Sbjct: 204 YLRENLPKETVIFANGNILQHADLEKCLAA-TGADGVMSAEGNLSDPGLFAR-------- 254

Query: 237 LTGSSPIKTRVDKDFWR 253
                P      +++WR
Sbjct: 255 ----PPAVGEEGREYWR 267


>gi|299742242|ref|XP_001832336.2| t-diRNAhydrouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|298405094|gb|EAU89497.2| t-diRNAhydrouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 349

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 105/238 (44%), Gaps = 30/238 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE---------KPLA 51
           MV+ +D  +R         +  YT+M++ + +L  + +  L F  ++         +P+ 
Sbjct: 1   MVNQSDLPFRLLVEQYGATS-TYTQMLLPEKLL--NDQEYLEFHLRDLQTFAKLKTRPVV 57

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--LNPDIVGDCIA 109
           +Q+GG D   +V+A + ++ +  + I+LN+GCP     +  +GA L+   +  +V   ++
Sbjct: 58  VQLGGNDPDLVVQAGRKMQQW-CDGIDLNLGCPQEAARDAHYGAYLLGQRDWPLVEQIVS 116

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +M  + ++P + K R+      P        + ++  G + I +HAR            R
Sbjct: 117 SMATSFTVPCSAKIRLCQ----PVGKTSEFSQRLEAQGASWITLHARTV------SARRR 166

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSA 224
           +    D  IV E+K     + +  NG +    D+   L      DG+M+G A   N  
Sbjct: 167 RQGAADLSIVQELKSSL-RVPVISNGNVRAFPDLQVNLD-YTGADGLMVGEALLDNPW 222


>gi|293609101|ref|ZP_06691404.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292829674|gb|EFF88036.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 307

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 112/305 (36%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 1   MEGLTDPIMRDTLTSVGDFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 61  QFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHLLIKAVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 121 DAVPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +   + A         + +MIGR A     +   
Sbjct: 170 TPPAYWEKILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + +     L     +     + F    + +      R+    G +             +P
Sbjct: 229 IRQNMDEALFSWEQLVDLQIR-FLNGQAKTEIGMVGRYKQWLGMM----------TKAYP 277

Query: 289 NSRRC 293
            ++  
Sbjct: 278 QAKEL 282


>gi|255576019|ref|XP_002528905.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
 gi|223531659|gb|EEF33485.1| tRNA-dihydrouridine synthase, putative [Ricinus communis]
          Length = 330

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 67/341 (19%), Positives = 127/341 (37%), Gaps = 54/341 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-----------------ILGF 43
           MV      +R  A       + Y E I+   +L+ ++K                  +   
Sbjct: 12  MVRVGTLPFRLLAAEY-GADITYGEEIIDHKLLKCERKVNEYIGCTDFVEKGTENVVFRT 70

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  +  Q+G +D  + + AA++V       I++N+GCP +    G  GA L+  P+
Sbjct: 71  CNEEKNRVVFQMGTSDAVRALTAAQMVCK-DVAAIDINMGCPKSFSISGGMGAALLTKPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L  PVT K R+    Q        L + I+K+GV+ + +H RK     
Sbjct: 130 LIHDILTTLKRNLDSPVTCKIRLLKSPQDTV----ELARRIEKTGVSALAVHGRK----- 180

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAY 220
                +R      +  + +I      + +  NG + D     +I        VM+ R A 
Sbjct: 181 ---VADRPRDPAKWSEIADIV-STLSIPVIANGDVFDYGDFERIKAATGASSVMVARGAL 236

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
            N+++ +              P      +D  R+       +      +   L+++  H 
Sbjct: 237 WNASIFS--------------PKGKVHWEDVKREYVRKSILWDNDVKSTKHTLKEMIMHY 282

Query: 281 IGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
             L    P  +    ++  E  A  A  +  E  + L+ E 
Sbjct: 283 SCL--ELPEGKG---VIKSETLADIAKFYGEERYYQLVNEK 318


>gi|332534960|ref|ZP_08410779.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332035633|gb|EGI72124.1| tRNA-dihydrouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 326

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 112/299 (37%), Gaps = 35/299 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNI--LGFSTQEKPLAL 52
           M    D   R     +    L  TE +      + D +       +   GF+    P+ +
Sbjct: 8   MEGVVDFKMRQLLTDIGGFDLCVTEFVRVVETCLPDKVFHRFCPELHNNGFTRAGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + L E A      G + ++LN GCP+  V+    GA L+ +PD +   I A+ 
Sbjct: 68  QLLGQEANPLAENAIRAIALGSHGVDLNFGCPAKTVNRSRGGAVLLKDPDHMYTIIKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     V+ K R+G DD   +     +V ++  +G N + IHAR        P    K
Sbjct: 128 DAVDDEHEVSAKIRLGFDDDSNSQ---EIVDAVVSAGANSVAIHARTKRDGYNPPAYWEK 184

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
           IP +       IK +N  + +  NG +  +  A   +       +M+GR A  +  +   
Sbjct: 185 IPPI-------IKGKN--IAVVANGEIWQVEDAMLCQKRSGCTDLMLGRGALSHPDLAKK 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG--GKLQQITRHMIGLFH 285
           +  + +N          + D   W  I   +   A     +         T+  +G   
Sbjct: 236 IKAHVNNE---------QYDGLEWEHIIYHLIHSAIHQDPAKDEKYFASRTKQWLGYLK 285


>gi|331268768|ref|YP_004395260.1| dihydrouridine synthase, DuS [Clostridium botulinum BKT015925]
 gi|329125318|gb|AEB75263.1| dihydrouridine synthase, DuS [Clostridium botulinum BKT015925]
          Length = 323

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 119/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV +  +R   K +   L  + +   +  QI  
Sbjct: 8   MEGITGYIYRNAYEKFFGNVDKYFTPFIVTNKNIRFKAKELRDVLPENNEGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  +  ++  GYNEINLN+GCPS  V     G+  +   + +   +  + K  +
Sbjct: 68  NDSEGFISISTKLQQLGYNEINLNLGCPSGTVVSKYRGSGFLAKREELDRFLDEIFKIDN 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R            +  PNL  
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIFNKYPLEELIIHPRTREDFY------KNKPNL-- 176

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++         +  NG +    D  + ++  P V+ VMIGR    N  ++  + E  
Sbjct: 177 -YVFKDALSLSVNPVCYNGDIFTVTDYKKLIETFPEVETVMIGRGILANPGLINEIKE-- 233

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +  +V +DF  +I  +  +      ++  +++++  +MI +F
Sbjct: 234 ------NKNLDKKVLEDFHDEILNNYRELFNEDRNAMFRMKELWGYMIYIF 278


>gi|67587982|ref|XP_665290.1| hypothetical protein [Cryptosporidium hominis TU502]
 gi|54655895|gb|EAL35060.1| hypothetical protein Chro.50134 [Cryptosporidium hominis]
          Length = 677

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 56/320 (17%), Positives = 113/320 (35%), Gaps = 49/320 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM++ + IL G    +  L  S +EK   +Q+ G + S ++
Sbjct: 298 NLPFRRLCLKF-GADVTVSEMVLCNEILSGKASELALLKKSPEEKHFGIQLAGGNKSTII 356

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTV 121
           +  + + +   ++ I++N  CP   +H+   G+ L+     +   +  + K +    VTV
Sbjct: 357 KTGEFINEHCEFDFIDINAACPLKSLHDKGAGSILVDRVSELETMVKGLKKVMDGKLVTV 416

Query: 122 KCRI---------------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           K R+                             +    ++  +  SG++ + IH R +  
Sbjct: 417 KVRMSHGGSPINKNLSEKDYFENFENWPVIYHNMKTHKILNILCDSGIDALTIHGRTSFQ 476

Query: 161 KGLSPKDNRKIPNLDY--------DIVYEIKKENPDLF---IGLNGGLEDMSQALKILPS 209
           +     D   I              +   I+  N  LF   I   G + +     + + +
Sbjct: 477 RYTKEADWSYIKYCSVLNSKLYSNKVANNIQSSNHSLFCPSIIGCGDIINFQDYQQHIQN 536

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
             VD VMIGR A     + T + E  +  ++ S              I     +    H 
Sbjct: 537 DLVDSVMIGRGALLKPWIFTEIKENRNWDISASERF----------DIIKQYVNLGLEHW 586

Query: 268 HSGGKLQQITRHMIGLFHGF 287
            +  +   +TR  +  F  F
Sbjct: 587 GTDKRGIALTRRFLLEFLSF 606


>gi|66358006|ref|XP_626181.1| Ylr401cp-like protein with 2 CCCH domains plus Dus1p tRNA
           dihydrouridine synthase Tim barrel [Cryptosporidium
           parvum Iowa II]
 gi|46227017|gb|EAK87967.1| Ylr401cp-like protein with 2 CCCH domains plus Dus1p tRNA
           dihydrouridine synthase Tim barrel [Cryptosporidium
           parvum Iowa II]
          Length = 707

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 56/320 (17%), Positives = 113/320 (35%), Gaps = 49/320 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R          +  +EM++ + IL G    +  L  S +EK   +Q+ G + S ++
Sbjct: 328 NLPFRRLCLKF-GADVTVSEMVLCNEILSGKASELALLKKSPEEKYFGIQLAGGNKSTII 386

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTV 121
           +  + + +   ++ I++N  CP   +H+   G+ L+     +   +  + K +    VTV
Sbjct: 387 KTGEFINEHCEFDFIDINAACPLKSLHDKGAGSILVDRVSELETMVKGLKKVMDGKLVTV 446

Query: 122 KCRI---------------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           K R+                             +    ++  +  SG++ + IH R +  
Sbjct: 447 KVRMSHGGSPINKNLSEKDYFENFENWPVIYHNMKTHKILNILCDSGIDALTIHGRTSFQ 506

Query: 161 KGLSPKDNRKIPNLDY--------DIVYEIKKENPDLF---IGLNGGLEDMSQALKILPS 209
           +     D   I              +V  I+  N  L    I   G + +     + + +
Sbjct: 507 RYTKEADWSYIKYCSVLNSKLYSNKVVNNIQNSNHSLICPSIIGCGDIINFQDYQQHIQN 566

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
             VD VMIGR A     + T + E  +  ++ S              I     +    H 
Sbjct: 567 DLVDSVMIGRGALLKPWIFTEIKENRNWDISASERF----------DIIKQYVNLGLEHW 616

Query: 268 HSGGKLQQITRHMIGLFHGF 287
            +  +   +TR  +  F  F
Sbjct: 617 GTDKRGIALTRRFLLEFLSF 636


>gi|46206232|ref|ZP_00047549.2| COG0042: tRNA-dihydrouridine synthase [Magnetospirillum
           magnetotacticum MS-1]
          Length = 182

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 90/174 (51%), Gaps = 9/174 (5%)

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +G +G+ +HARKA LKGLSP++NR +P LDY  V  +K  +P+L I +NGG+ D+S A 
Sbjct: 7   AAGXDGLIVHARKAWLKGLSPRENRDVPPLDYGRVARLKAAHPNLPIAINGGIADLSAAK 66

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
             L  VDGVM+GRAAY + A+L  VD          +     ++          +    A
Sbjct: 67  ARLAEVDGVMMGRAAYTDPALLLAVDPELFGEPPPVADAFAAIEA---------LEPTLA 117

Query: 265 RHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
             L  G +L   TRHM+GLF+G P +R  R  L     A  A    +  A   +
Sbjct: 118 EGLARGLRLHAYTRHMLGLFNGRPGARAYRRHLATAGMAPEAGLATLREAVARV 171


>gi|254786760|ref|YP_003074189.1| tRNA-dihydrouridine synthase C [Teredinibacter turnerae T7901]
 gi|237685547|gb|ACR12811.1| tRNA-dihydrouridine synthase C [Teredinibacter turnerae T7901]
          Length = 320

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/296 (19%), Positives = 117/296 (39%), Gaps = 32/296 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNA------LLYTEMIVADAILRGDKKNILGFSTQ-----EKP 49
           M    D H R     +  NA      L  TE +         +K  L    +       P
Sbjct: 8   MEGVVDHHMRRTLHAVKGNAQQSGIDLCVTEFVRVTE-HTLPRKVFLRACPELNEANAYP 66

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + +Q+ G++ + L   A      G   ++LN GCP+  V++   GACL+    ++G+ ++
Sbjct: 67  VRVQLLGSNPATLASNANKAAQLGAPAVDLNFGCPAKTVNKSRGGACLLNETSLLGEIVS 126

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A+ +A+   IPVT K R+G +++ P +       +I  +G + + +HAR  +        
Sbjct: 127 AVREAVPAEIPVTAKIRLGYENREPYLKNA---LAIAAAGADELVVHARSKVDG------ 177

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAM 225
               P   ++ + EI++    + +  NG +  +   ++   +   +  M+GR       +
Sbjct: 178 --YKPPAYWEYIAEIRQAL-SIPVVANGEIWTLEDFIRCREVTGCEDFMLGRGLLARPDL 234

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              +  Y +    G  P+                 D   +  + G +L+Q   H +
Sbjct: 235 ALQIKAYTAGE--GYLPLSWADFAPLVHAFFEQTCDAYPK-KYMGNRLKQWL-HYL 286


>gi|237666036|ref|ZP_04526024.1| dihydrouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237658983|gb|EEP56535.1| dihydrouridine synthase family protein [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 320

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 128/333 (38%), Gaps = 45/333 (13%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNI---LGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  I+ +   R + K +   L  + +   +  QI  
Sbjct: 8   MEGITGHIYRNAYEKFFHNIDKYFTPFIIPNESKRLNTKELIDVLPENNKGISIVSQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  +K +++ GY+EINLN+GCPS  V     G+  +   + +   +  + +  +
Sbjct: 68  NDSEGFILTSKKLQELGYSEINLNLGCPSGTVVGKGRGSGFLAKREELDKFLYEIFEKNN 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I +++K RIG D +       +L+K   K  +  + IH R       +  D         
Sbjct: 128 IKISIKTRIGKDSRD---EFYDLIKIYNKYPLEELIIHPRTQKDFYGNKPDW-------- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQALK---ILPSVDGVMIGRAAYKNSAMLTTVD 230
               E+ K+   L    +  NG +       K   + P VD +MIGR    N  ++  + 
Sbjct: 177 ----EVFKDALSLSNNPVCYNGDIFTNDNYTKFTNLFPEVDRIMIGRGILANPGLINEI- 231

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                   G+  I     K F  +I  +  D     + +  K++++  +MI +F    N 
Sbjct: 232 -------IGNDMISKEKMKAFHDEILNAYIDLYPEDIGALFKMKELWSYMIYIFS---NG 281

Query: 291 RRC----RHILTVEAGAST-----ATHHIIETA 314
           +      R    +E          +   II+ A
Sbjct: 282 KEYLKNIRRGKNIEEYKEGVYSLFSEQEIIKGA 314


>gi|221484010|gb|EEE22314.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii GT1]
          Length = 608

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/298 (18%), Positives = 95/298 (31%), Gaps = 83/298 (27%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAIL-----RGDKKNILGFSTQ------------ 46
            +   +R   R      L YT M+ +   L     R      L  S              
Sbjct: 111 VSVAVFRLLGRRY-GVDLAYTPMLHSRLFLDDSKYRALHWQTLRSSPSWTQASCSEEEDV 169

Query: 47  --------------------------------------EKPLALQIGGADISKLVEAAKI 68
                                                 ++P+ +Q  G   + L+ AA++
Sbjct: 170 QEEGEEEGEEEEEGEEGEEGEVSEGGRSQWTGDESQEFDEPVFVQFCGDSPATLLAAAQL 229

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--- 125
           VED     +++N GCP      G +GA L+  P+++ D ++ + K L  PVT K R    
Sbjct: 230 VEDE-VEAVDVNFGCPQGIARRGHYGAFLLNEPELLVDIVSTLHKHLKTPVTCKMRKVSP 288

Query: 126 --------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                          +D++        L  + + +G   + IH R    K         +
Sbjct: 289 RNPRDALPRSEAALVLDEERRLQDTLRLCDAFEAAGCACLCIHGRTKEEK------AAFV 342

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
              D+  +  +K+    + +  NG +E    AL+ L     D VM       N  +  
Sbjct: 343 GPCDWLAIRHVKQRL-SIPVIANGAVETYEDALRCLEFTGADAVMSAEGLLDNPMLFA 399


>gi|294649504|ref|ZP_06726925.1| tRNA-dihydrouridine synthase C [Acinetobacter haemolyticus ATCC
           19194]
 gi|292824565|gb|EFF83347.1| tRNA-dihydrouridine synthase C [Acinetobacter haemolyticus ATCC
           19194]
          Length = 309

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 97/249 (38%), Gaps = 24/249 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M   TD   R     + +     TE I      + D I       +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDVLTHVGSFDWCVTEFIRITDSILPDHIYYNFCPELQTDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  P+ V   + A+ 
Sbjct: 68  QFLGNNPDMLAANASKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPETVHLLVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+           +I+ +G + + +HAR         K +  
Sbjct: 128 DAVPSHIPVSAKMRLGYLDENH---TMENAHAIEDAGASWLTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I  E   + +  NG + + + A   L       +MIGR A     +   
Sbjct: 177 TPPAYWEKIQPI-TEALKINVIANGEIWNNTDAKACLTQSHCTDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPL 237
           + +   + L
Sbjct: 236 IRQNVDHAL 244


>gi|326435349|gb|EGD80919.1| DUS4L protein [Salpingoeca sp. ATCC 50818]
          Length = 558

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/292 (19%), Positives = 111/292 (38%), Gaps = 33/292 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF--STQEKPLALQIGGAD 58
           MV ++   +R   R      + +T MIV+D+ ++  +     F  STQ++P+  Q   A+
Sbjct: 31  MVRYSQLAFRHVVRR-HGVDVAFTPMIVSDSFVQSWRAREADFATSTQDEPVVAQFAAAN 89

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                 AA ++  +  + I+LN GCP     +   G+ L+  P++V D +        IP
Sbjct: 90  ARDFAHAAALMAPY-ADAIDLNCGCPQKWAMQDGLGSHLVSKPELVADMVKQARALSGIP 148

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V++K R+    +        L +  ++ G   I +H R       SPK+ R    + YD 
Sbjct: 149 VSIKIRL----RNTTAETVELCRRAEQMGAAWISVHGR-------SPKERRC--PVHYDE 195

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG-----VM-------IGRAAYKNSAML 226
           +  +K    ++ +  NG    +  A  I+          VM       +   A       
Sbjct: 196 IAAVKAAM-NVPVVANGDAFSLDDARMIVDKTGAEVSSTVMKHMHQLEVAVEAKGQP--- 251

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           + V   F  PL         +++   R ++               ++  + +
Sbjct: 252 SHVGSQFQEPLERIEEQLRELEQRTLRDMTKLRETMKKDRTAIVMRVDHLRK 303


>gi|121604209|ref|YP_981538.1| dihydrouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120593178|gb|ABM36617.1| tRNA-U20a,U20b-dihydrouridine synthase [Polaromonas
           naphthalenivorans CJ2]
          Length = 318

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/271 (20%), Positives = 104/271 (38%), Gaps = 27/271 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLAL 52
           M    D   R     +       +E I      +       I+      G +    P+  
Sbjct: 7   MEGLLDFVLRDILTRVGGIDRCVSEFIRITDQLLPERVFTRIVPELHNGGRTLAGVPVRA 66

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A  + + G   I+LN GCP+  V+    GA L+  P+ V   +AA+ 
Sbjct: 67  QLLGSDPVCLAENAGRLAELGPAGIDLNFGCPAKIVNRHGGGAALLDEPETVFAIVAAVR 126

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+ K R+G +D   AV       +I  +G + + +HAR         K    
Sbjct: 127 RAVPNHMPVSAKMRLGFNDDSRAV---ECALAIAGAGADELVVHART--------KAQAY 175

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ + +I +    + +  NG +  +  A +       + +M+GR    +  +   
Sbjct: 176 RPPAYWERIADI-RAAVRIPVVANGEIWTVDDARRCREASGCESLMLGRGVVTDPGLGLA 234

Query: 229 VDEYFSNPLTG---SSPIKTRVDKDFWRKIS 256
           +    +   +    + P    +   FW  + 
Sbjct: 235 IKAAMNGAASPAGVAWPQLVPLLAQFWHIVC 265


>gi|225024872|ref|ZP_03714064.1| hypothetical protein EIKCOROL_01760 [Eikenella corrodens ATCC
           23834]
 gi|224942352|gb|EEG23561.1| hypothetical protein EIKCOROL_01760 [Eikenella corrodens ATCC
           23834]
          Length = 320

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 59/288 (20%), Positives = 111/288 (38%), Gaps = 26/288 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILG--FSTQEKPLAL 52
           M    D   R     +   +   TE +       + A  R     I     +    P  L
Sbjct: 8   MQGLLDPVMRRLLTDIGGYSECVTEFVRITHTLHSRATWRRHMPEIDHSCRTHAGTPCTL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A+     G  +I+LN GCP+  V++   GA L+  P+ +   +A + 
Sbjct: 68  QLLGSDPDNMAANAQAAVAAGAQKIDLNFGCPAPTVNKHQGGAILLREPERIRQIVATVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + L  +IP+T K R+G +D   A+      K+I + G + + +HAR  I           
Sbjct: 128 QRLPENIPLTAKMRLGYEDGSLAL---ECAKAIAQGGASALAVHARTKIEGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I++   ++ +  NG +  ++   A++       VM+GR A     +   
Sbjct: 178 -PPAHWEQIAPIRQAL-NIPVVANGDVFSLADYLAIRQTSGCQHVMLGRGAVITPDLARQ 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           +     N      P        + R+       +A    +   +L+Q 
Sbjct: 236 IQR--HNQGLPPQPAGFADYLVWIRRFFQLCRQHAGDTPYPAARLKQW 281


>gi|119469539|ref|ZP_01612443.1| tRNA-dihydrouridine synthase C [Alteromonadales bacterium TW-7]
 gi|119447074|gb|EAW28344.1| tRNA-dihydrouridine synthase C [Alteromonadales bacterium TW-7]
          Length = 326

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 61/299 (20%), Positives = 113/299 (37%), Gaps = 35/299 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     L    L  TE +      + + +       +   G++    P+ +
Sbjct: 8   MEGVVDFKMRQLLTDLGGFDLCVTEFVRVVQARLPEKVFYRYCPELNNNGYTRAGTPVRI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G + + L E A    D G + ++LN GCP+  V+    GA L+ +P+ +   I A+ 
Sbjct: 68  QLLGQEANPLAENAVRAIDLGSHGVDLNFGCPAKTVNRSRGGAVLLKDPEHMYTIIKAVR 127

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+     V+ K R+G DD   +     ++ ++  +G N + IHAR        P    K
Sbjct: 128 DAVDSKHEVSAKIRLGFDDDSNSQ---EIIDAVVSAGANSVAIHARTKRDGYNPPAYWEK 184

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
           IP +       IK +N  + +  NG +  +  A   +       +M+GR A  +  +   
Sbjct: 185 IPPI-------IKGKN--IAVVANGEIWQVEDAMLCQKRSGCSDLMLGRGALSHPDLAKK 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG--GKLQQITRHMIGLFH 285
           +  + +N            +   W  +   +   A  H  +         T+  +G   
Sbjct: 236 IKAHVNNEHY---------EGLEWEHVLYHLIHSAIHHDPAKDEKYFASRTKQWLGYLK 285


>gi|209875549|ref|XP_002139217.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209554823|gb|EEA04868.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 716

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 103/269 (38%), Gaps = 34/269 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    + ++EM + + IL G    +  L   ++E+   +Q+ G +   + 
Sbjct: 343 NLPFRRLCVRL-GADITFSEMTLCNEILAGKSSELALLRRHSEERCFGIQLAGGNFETIA 401

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           +  + + ++  Y+ +++NV CP   +H+   G+ L+  P ++   I  + K +  P+T+K
Sbjct: 402 KTGEFINEYCDYDFLDINVACPLKSLHDRGAGSILIDRPKLLESIITGLKKVIDKPLTIK 461

Query: 123 CRI---------------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            R+                       D     +A   L+K +    +NGI IH R +  +
Sbjct: 462 LRMANSASPPNLKFYENTYINNPLNWDIIYSNMAAHKLIKPLVNYNINGIIIHGRTSSQR 521

Query: 162 GLSPKDNRK------IPNLDYDIVYEIKKENPDLF-IGLNGGLEDMSQALKILPS--VDG 212
                D         I   +Y    +  K       +   G + +     K L    V+ 
Sbjct: 522 YNKSADWNYLRYCSKILKNEYLTYKDTNKNITYCPSLIGCGDVLNYCDYYKHLNEDDVNA 581

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           VMIGR A     + T + E     ++   
Sbjct: 582 VMIGRGALLKPWIFTEIKEQRIWDISAGE 610


>gi|325475241|gb|EGC78426.1| dihydrouridine synthase [Treponema denticola F0402]
          Length = 337

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 52/265 (19%), Positives = 94/265 (35%), Gaps = 26/265 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   T   +R  A         ++EMI A + + G   +K     +   + L  QI   D
Sbjct: 8   MAAITHSAFRRLAACFKEPDEYFSEMIHAPSAISGGGFEKWYFRSNPSPEKLVWQITSPD 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKAL-- 115
                    ++   G   I+LN+GC + ++     G   M  P       ++ + KA+  
Sbjct: 68  EDAAAACVPLLLRHGGFGIDLNMGCCAPQIVNTGAGFAWMKKPLSETASLVSKVKKAVLL 127

Query: 116 ---------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                    + P+ +  ++ + ++     L +  K +   GV+ I +H R    K   P 
Sbjct: 128 YDEQKAGPQTAPIRLSVKLRLGEEENYDRLLSFCKMLVSEGVSLITLHPRTQKQKYSRPC 187

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            +     L YD+          + +  NG +  +    KI       G MIGRAA +   
Sbjct: 188 KHEYTARLAYDL---------PIPVYGNGDINSIETLKKISSKYPCSGWMIGRAAVQKPW 238

Query: 225 MLTTV-DEYFSNPLTGSSPIKTRVD 248
           +   +      N +      K  +D
Sbjct: 239 IFYELSKGILKNGIAEDKDEKIEID 263


>gi|254572948|ref|XP_002493583.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|238033382|emb|CAY71404.1| Dihydrouridine synthase [Pichia pastoris GS115]
 gi|328354589|emb|CCA40986.1| tRNA-dihydrouridine synthase 3 [Pichia pastoris CBS 7435]
          Length = 618

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 110/302 (36%), Gaps = 47/302 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +++G      +    + E P   +QI  +     
Sbjct: 263 NLPYRRLMKTL-GADITYSEMALSLPLIQGTNSEWALPKAHSSEYPGFGVQIATSKHWTG 321

Query: 63  VEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALSIPV 119
            +AA+ +        EINLN GCP   ++    G+ LM  P  +   +  M   +  IPV
Sbjct: 322 AKAAEAIAKLTPQVSEINLNCGCPIDLLYRQGQGSALMEQPPKLLRVLKGMNYCSGEIPV 381

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           T K RIG  D  P     NLVK + + G +  + +H R         +  R     D+  
Sbjct: 382 TFKLRIGTRDNHPLAE--NLVKRVCEEGDIGCVTLHGRT--------RQQRYTKEADWSY 431

Query: 179 VYEIKKENPD----------------LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           + ++ +   D                ++   NG         K +  P++D VM+ R A 
Sbjct: 432 ISKVGQVVRDYNHNQLDDKEQSDRDPIYFVGNGDCFTHEDWHKAVSDPNIDSVMVARGAL 491

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS-GGKLQQITRH 279
               +   ++       + +  +           +    + +A +H  S    +    R 
Sbjct: 492 IKPWIFEEINSEQYIDKSATERL----------ALLEQYSKFALQHWGSDDYGVNTARRF 541

Query: 280 MI 281
           M 
Sbjct: 542 MC 543


>gi|169599118|ref|XP_001792982.1| hypothetical protein SNOG_02375 [Phaeosphaeria nodorum SN15]
 gi|160704540|gb|EAT90587.2| hypothetical protein SNOG_02375 [Phaeosphaeria nodorum SN15]
          Length = 491

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 114/290 (39%), Gaps = 42/290 (14%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           + D H++     + +    Y       + +   ++++ G    ++PL +Q    D    +
Sbjct: 8   YRDAHFQPLKSGMASPPDAY-----HVSQVEDGERHLDGNPAFDRPLTVQFCSNDPDDFL 62

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AAK V  F  + ++LN+GCP      G +GA L  +  ++   I  + + L +PVT K 
Sbjct: 63  RAAKHVAPF-CDAVDLNLGCPQGIAKRGKYGAFLQEDQGLIARMINKLHEELEVPVTAKM 121

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+               K+I  +G + I +H R+   KG            D+ ++  ++
Sbjct: 122 RVL----ETKEKTLEYAKTILDAGASIITVHGRRREQKG------HNTGLADWQMIRYLR 171

Query: 184 KENP-DLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  P D  I  NG +   ED++  L+     DGVM       +  +              
Sbjct: 172 ESLPKDTVIFANGNILQHEDIAACLEA-TGADGVMSAEGNLYDPTIFA------------ 218

Query: 240 SSPIKTRVDKDFWR--------KISASMTDYA-ARHLHSGGKLQQITRHM 280
             P   +  +++WR        ++ A M  Y    H H+ G+   + + +
Sbjct: 219 PPPPVGQEGQEYWRDRNGKGGYRVDAVMRRYMDIIHKHALGQQPPVRKPL 268


>gi|168185494|ref|ZP_02620129.1| dihydrouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
 gi|169296460|gb|EDS78593.1| dihydrouridine synthase family protein [Clostridium botulinum C
           str. Eklund]
          Length = 319

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 63/294 (21%), Positives = 123/294 (41%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV +        + +++L  + + K +  Q+  
Sbjct: 8   MEGITGYIYRNAYEKFFGNVDKYFTPFIVTNKNIGFKAKELRDVLPENNEVKNIVPQVLT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D  + +  A+ +++ GYNEINLN+GCPS  V     G+  +   + +   +  + K   
Sbjct: 68  NDSERFINIARKLQELGYNEINLNLGCPSGTVVSKYRGSGFLAKREELDRFLEEIFKIDH 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G D          L+K   K  +  + IH R            +  PNL  
Sbjct: 128 MKISIKTRLGKD---SPEEFYELIKIFNKYSLEELIIHPRTREDFY------KNKPNL-- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
               E+ K+   L    I  NG +    D  Q  +  P V+ VMIGR    N+ ++  + 
Sbjct: 177 ----EVFKDALSLSVNPICYNGDIFTSTDYKQLTEAFPQVETVMIGRGILANTGLINEIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           E           +  +V ++F  ++  +  +      ++  +++++  +MI +F
Sbjct: 233 E--------DKTLDKKVLREFHDEVLNNYRELFNEDRNAMFRMKELWGYMIYIF 278


>gi|299530726|ref|ZP_07044141.1| dihydrouridine synthase, DuS [Comamonas testosteroni S44]
 gi|298721242|gb|EFI62184.1| dihydrouridine synthase, DuS [Comamonas testosteroni S44]
          Length = 340

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/301 (19%), Positives = 115/301 (38%), Gaps = 42/301 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       +E I ++ ++L    K  L    +           P+
Sbjct: 1   MEGLLDFVLRDVLTRVGGADRCVSEFIRISGSLL--PDKVYLRTMPELRNGSRTLAGVPV 58

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+ +P+ +   + A
Sbjct: 59  RAQLLGSDPVSMAENAANLARLGPEGIDLNFGCPAKVVNRHGGGASLLQDPEQIVRVVDA 118

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +PV+ K R+G +D+     +    +++++ G   I +HAR  +     P   
Sbjct: 119 VRRAVPAQLPVSAKMRLGFNDR---ALMTECAQAMEQGGACEIVVHARTKLDGYRPPAYW 175

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +IP +         +E   + +  NG +  + +AL+       D +M+GR    +  + 
Sbjct: 176 EEIPRI---------REAVGVNVVANGEIWTVEEALRCREVSGCDDLMLGRGIVADPGLA 226

Query: 227 TTVDEYFSNPLTGSSP-----IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----IT 277
             V     +    +             + FW  +   +           G+L+Q    + 
Sbjct: 227 LAVRRAVEHGSVSAVAGIDWLALVPQVQRFWHMVCEDLEP-----RQRAGRLKQWLNLMR 281

Query: 278 R 278
           R
Sbjct: 282 R 282


>gi|299771376|ref|YP_003733402.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. DR1]
 gi|298701464|gb|ADI92029.1| tRNA-dihydrouridine synthase C [Acinetobacter sp. DR1]
          Length = 307

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 114/305 (37%), Gaps = 35/305 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNI--LGFSTQEKPLAL 52
           M   TD   R     + +     TE I V D+IL           +   G +    P+ +
Sbjct: 1   MEGLTDPIMRDTLTSVGHFDWCVTEFIRVTDSILPDHIYYSFCPELKNDGKTAAGTPVHV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+ 
Sbjct: 61  QFLGNNPDMLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVR 120

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            AL   IPV+ K R+G  D+           +++ +G + + +HAR         K +  
Sbjct: 121 DALPAHIPVSAKMRLGYLDENH---TMENAHAVEDAGASWLTVHART--------KADGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLED--MSQALKILPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  IK E   + +  NG +     ++A +     + +MIGR A     +   
Sbjct: 170 TPPAYWEKILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQC 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           + +     L     +     + F    + +      R+    G +             +P
Sbjct: 229 IRQNMDEALFSWEQLVDLQIR-FLNGQAKTEIGMVGRYKQWLGMM----------TKAYP 277

Query: 289 NSRRC 293
            ++  
Sbjct: 278 QAKEL 282


>gi|71066558|ref|YP_265285.1| tRNA-dihydrouridine synthase [Psychrobacter arcticus 273-4]
 gi|71039543|gb|AAZ19851.1| possible tRNA-dihydrouridine synthase [Psychrobacter arcticus
           273-4]
          Length = 350

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 103/261 (39%), Gaps = 30/261 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIVADAIL---RGDKK-----NILGFSTQE 47
           M   TD   R     +  +         +E I     +       K     +    +   
Sbjct: 38  MEGLTDPLMRQILTQIAADLGRPYDWSVSEFIRVTQHVLPAHVFYKYVPELHHDAKTASG 97

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
             + +Q+ G++   + E A    + G   I++N GCP+  V+    G+ L+  P+++ D 
Sbjct: 98  TSIHIQLLGSEAQLMAENAAHACELGAPAIDINFGCPAKTVNSHRGGSVLLDEPEVMYDI 157

Query: 108 IAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I+A+ +A+  +IPV+ K R+G  D      + ++  +I  SG + + IHAR         
Sbjct: 158 ISAVRQAVPANIPVSAKIRLGYTDTSR---MDDIRGAIAASGADWLTIHART-------- 206

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
           K     P   +D +      +  + +  NG + +   A   +       +M+GR A    
Sbjct: 207 KTQGYKPPAYWDKIQAF--NSLKIPVIANGEIWNSEHAQNCMAQSGTTHLMLGRGAVTRP 264

Query: 224 AMLTTVDEYFSNPLTGSSPIK 244
            ++  VD    + ++ +  + 
Sbjct: 265 DLIAQVDCGLDSEMSNTPTLL 285


>gi|6561964|emb|CAB62468.1| putative protein [Arabidopsis thaliana]
          Length = 519

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 102/247 (41%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------------------NILG 42
           MV      +R  A       + Y E I+   +++ +++                      
Sbjct: 228 MVRVGTLSFRMLAAEY-GADITYGEEIIDHKLVKCERRLNVASGTSEFVEKGTDNVVFST 286

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              ++  +  Q+G +D  + ++A++IV +     I++N+GCP A   +G  GA L+  P+
Sbjct: 287 CDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPE 345

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +A + + L +PVT K R+             L + I+K GV  + +H RK     
Sbjct: 346 LIHDILATLKRNLDVPVTCKIRLLKSPADTV----ELARRIEKLGVPALAVHGRKI---- 397

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +      +K       VM+ R A 
Sbjct: 398 ----ADRPRDPAKWDEIADVVAAL-SIPVIANGDVLEYDDFSRIKTATGAASVMVARGAM 452

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 453 WNASIFS 459


>gi|152978301|ref|YP_001343930.1| dihydrouridine synthase DuS [Actinobacillus succinogenes 130Z]
 gi|150840024|gb|ABR73995.1| dihydrouridine synthase DuS [Actinobacillus succinogenes 130Z]
          Length = 326

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/297 (19%), Positives = 111/297 (37%), Gaps = 44/297 (14%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMI--VADAILRGDKKNIL------GFSTQEKPLALQIG 55
           W D   R     + +  L  +E +  V   +       +       G +    P+ +Q+ 
Sbjct: 22  WLDPLVRRLLTEVNDYDLCISEFVRVVDRLLPDKVFYRLCPELQNQGKTPSGTPVRVQLL 81

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G     L E A    + G + I+ N GCPS  V+  + GA L+ NP+++     A+ +A+
Sbjct: 82  GQYPDWLAENAVRAIELGSHGIDFNCGCPSKTVNGSNGGASLLKNPELIYRATRAIRQAV 141

Query: 116 SIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           + P   V+VK R+G DD         +  ++++ G + I +H R          D  +  
Sbjct: 142 T-PEQTVSVKVRLGWDDISQVF---EIADAVQQGGADEIAVHGRTKT-------DGYRAD 190

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
            +++  + +++ +   + +  NG +       K   +   + +MIGR A     +     
Sbjct: 191 RINWQQIGKVRSKL-RIPVIANGEIRHWEDGEKCRQITGCEDLMIGRGALNIPNL----- 244

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR-----HMIG 282
                    S  IK    K  W +I   +  YA            + R     H + 
Sbjct: 245 ---------SRVIKFNAPKMPWSEIIPILQKYAQMENIHDTGFYHVARIKQWLHYLN 292


>gi|298710301|emb|CBJ31922.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 743

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/304 (19%), Positives = 113/304 (37%), Gaps = 37/304 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM ++  +L+G+     +L     E    +Q+ GA   ++ 
Sbjct: 367 NLPFRRVMKD-QGADITCGEMALSHHLLKGNGSEWALLRRHPSEDVFGVQVAGAHPDQMT 425

Query: 64  EAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++E +   + +++N+GCP   V +   GA LM     +   IA M   L+ P+TVK
Sbjct: 426 RVAELLEKNAKMDFVDINMGCPIDLVCDKGMGAALMGRSRKLRGIIAGMSSQLTCPLTVK 485

Query: 123 CRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            R+G D++ P   V +R + +   +    G      + ++ G S +  R     D+D V 
Sbjct: 486 MRVGWDEKKPNADVVVRTVQREADRCRKRGFPGSVARVMIHGRS-RLQRYSKLADWDYVR 544

Query: 181 EIKK----ENPDLFIGLNGGLEDMSQALKILPSV----------------DGVMIGRAAY 220
           ++          L +  NG +       + L                      M+ R A 
Sbjct: 545 QVAVSQDPALRPLPVIGNGDILSWRDHEERLEQARELQSQQGEGEGSQWSTCCMLARGAL 604

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               + T V E     ++ S         D +RK      +Y          + +  R +
Sbjct: 605 IKPWLPTEVKEKRDWDISSSE------RLDIYRKFVNFGLEYWGSDQM---GVNKTRRFL 655

Query: 281 I-GL 283
           +  L
Sbjct: 656 LEWL 659


>gi|78221481|ref|YP_383228.1| dihydrouridine synthase, DuS [Geobacter metallireducens GS-15]
 gi|78192736|gb|ABB30503.1| tRNA-U20a,U20b-dihydrouridine synthase [Geobacter metallireducens
           GS-15]
          Length = 331

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 58/271 (21%), Positives = 110/271 (40%), Gaps = 24/271 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV-----ADAILRGDKKNILGFSTQEKPLALQIG 55
           M   T+R  R          +++TE +      A   +R      +       PL +Q+ 
Sbjct: 30  MQGLTNRALRALFINWVRPDVVFTEFMRVNPGGARQPIRAGDLREVAAVEGGVPLVVQLI 89

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D   LV AA+  ++ G   INLN+GCP  R+  G  G  ++  P+ + + I A+ +A+
Sbjct: 90  GHDHKALVAAARTAQEAGAVHINLNLGCPYGRMTSGLTGGGMLHRPEALEELIPALRRAI 149

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +   +VK R G DD      +  L+   +++GV+ + +H R  +             + D
Sbjct: 150 AGTFSVKVRAGYDDSGQ---IMTLLPLFEEAGVDFLVLHPRTVV--------QEYTGHAD 198

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  E+ ++   L +  NG +   +  L++L      G+M+GR A  +  +   +    
Sbjct: 199 HAVTAEVVRQT-RLPVIANGDVRSAADGLRVLRKTGATGLMLGRGAIADPLLFQRLR--- 254

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
                 + P          R +   +  Y  
Sbjct: 255 --GKAPAEPTGEERVAMLKRYLGELLEGYGE 283


>gi|303277773|ref|XP_003058180.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460837|gb|EEH58131.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 229

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 91/229 (39%), Gaps = 16/229 (6%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLV 63
           +  +R     L    +  +EM+ A   L+ +   +  L     E    +QI    I++ V
Sbjct: 13  NLPFRRLCVSLGCE-VTVSEMVFARFALKKNPVELARLRKHDSETLFGVQIATNQITEGV 71

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            A ++  + G + ++LN GCP     +   GA L+  P  +   +  +   + IP+TVK 
Sbjct: 72  NAGRLAHEAGADFVDLNCGCPIHETWKRGLGAALLKKPRKLERLVRGIADGIPIPLTVKI 131

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R+G            L ++++ +G   + IH R         K+ R     +++ +  I+
Sbjct: 132 RLGA--GSSEAPAHALAEAVENAGAAAVVIHGRT--------KEARYTKAANWETIGAIQ 181

Query: 184 KENPDLFIGLNGGLED-MSQALKI-LPSVDGVMIGRAAYKNSAMLTTVD 230
            E   + +  NG +        ++ + +    ++GR A     +     
Sbjct: 182 AERG-IPVVGNGDILTRYELNDRMGISNAHAAIVGRGALIKPWIFKEAK 229


>gi|291545851|emb|CBL18959.1| tRNA-U20a,U20b-dihydrouridine synthase [Ruminococcus sp. SR1/5]
          Length = 320

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 60/305 (19%), Positives = 113/305 (37%), Gaps = 28/305 (9%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGG 56
           M   T+  YR  +          +T  I A    R   K I   S +   + P+  QI  
Sbjct: 8   MEGVTNWVYRNAYHDCFYPMDKYFTPFITAKPNKRLSSKEIKEVSPETNGDLPVIPQILT 67

Query: 57  ADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
            +    V+ A I  +++G+ E+NLN+GCPS  V     GA  +  PD +   +  + +  
Sbjct: 68  NNAEDFVKTAHIFRDEYGHREVNLNLGCPSGTVTAKGKGAGFLGEPDKLERFLDEIFEKT 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            + +++K R+G D +        L++   +  +  + IH R      L     + IP   
Sbjct: 128 GMEISIKTRVGTDYEED---WERLLEIYGRYPLKELIIHPR------LLKDHYKGIPRYG 178

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEY 232
              +YE  +E   + +G NG +  +    +I       D VM GR       +L  + + 
Sbjct: 179 ---LYEEAREKLKVPLGYNGDIFSVEAYQEIREKFPDADSVMYGRGLIARPYLLDAIMQK 235

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                        +  + F  ++      Y +   +   +++++  +M       P    
Sbjct: 236 EDGEDHREE--YRKKLRQFHDRLYRDYQRYLSGERNVLFRMKELWSYMA------PGFTN 287

Query: 293 CRHIL 297
               L
Sbjct: 288 YARYL 292


>gi|115459590|ref|NP_001053395.1| Os04g0531300 [Oryza sativa Japonica Group]
 gi|38346764|emb|CAD41143.2| OSJNBa0081C01.15 [Oryza sativa Japonica Group]
 gi|113564966|dbj|BAF15309.1| Os04g0531300 [Oryza sativa Japonica Group]
 gi|116312037|emb|CAJ86402.1| OSIGBa0125M19.5 [Oryza sativa Indica Group]
 gi|125549126|gb|EAY94948.1| hypothetical protein OsI_16753 [Oryza sativa Indica Group]
 gi|215737387|dbj|BAG96316.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 319

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 59/298 (19%), Positives = 109/298 (36%), Gaps = 39/298 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----------------VADAILRGDKKNILGF 43
           MV      +R  A       + Y E I                   D + RG    +   
Sbjct: 12  MVRVGTLPFRLLAAEY-GADITYGEEIIDHKFLKCERVTNESLGTTDFLERGTDTVVFRT 70

Query: 44  STQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             QE+  +  Q+G +D  + ++AA++V +     I++N+GCP +    G  GA L+  P+
Sbjct: 71  CPQERDRVVFQMGTSDAVRALKAAQLVCN-DVAAIDINMGCPKSFSLSGGMGAALLSKPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L   VT K R+    Q        L + ++K GV  + +H RK   + 
Sbjct: 130 LIHDILTTLRRNLDTTVTCKIRLLNTRQDTV----ELARRVEKIGVPALAVHGRKVKDRP 185

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAY 220
             P          +D + ++      + +  NG + +     +I        VM+ R A 
Sbjct: 186 RDP--------AKWDEIADVVSAL-SIPVIANGDVFEYEDFKRIKDATGAASVMVARGAM 236

Query: 221 KNSAML----TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            N+++      T  E         S +     K   + I   +  Y+      G  + 
Sbjct: 237 WNASIFCPKGKTPWEDVKREYVRKSILWDNDLKSTKQTIKEMIMHYSCLEFPEGKGVN 294


>gi|149377033|ref|ZP_01894784.1| Dihydrouridine synthase, DuS [Marinobacter algicola DG893]
 gi|149358691|gb|EDM47162.1| Dihydrouridine synthase, DuS [Marinobacter algicola DG893]
          Length = 314

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/323 (19%), Positives = 123/323 (38%), Gaps = 53/323 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL------------RGDKKNILGFSTQE 47
           M    D   R     +       TE I V   +L                +  +G     
Sbjct: 1   MEGLVDAPIRETLTAVGGIDRCVTEFIRVTQGMLPPRIFYKYAPELHNGCETRVGV---- 56

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+A+Q+ G+D  ++        + G  ++++N GCP+  V++   G  LM  P+++   
Sbjct: 57  -PVAVQLLGSDPVQMGRHGAKAVELGATQVDINFGCPAKTVNKHKGGCVLMREPELMQQI 115

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             A+  A+   +PVT K R+G DD+   VA     ++++ +G + I +HAR  +      
Sbjct: 116 TEAVRAAVPAHVPVTAKMRLGYDDRSMGVA---CGQALEAAGASEIVVHARSKVDG---- 168

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 P   ++ V  + +E  D  + +NG +  ++   +       D VMIGR      
Sbjct: 169 ----YKPPAYWEDVARV-REAVDAHVIVNGEIWTVADYWRCREVSGCDDVMIGRGLIARP 223

Query: 224 AMLTTVDEYFSNPLTG--SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
            +   +     N      + P   R+ + +   +   + D         G+++Q     +
Sbjct: 224 DLARRIRASQRNESVPDMTWPEVVRLVEGYAVALQDRLEDRFVT-----GRIKQW----L 274

Query: 282 GLFHG--------FPNSRRCRHI 296
               G        +P +R+ R +
Sbjct: 275 NYLRGGYGEAQRLWPEARKIRDV 297


>gi|194759368|ref|XP_001961921.1| GF14697 [Drosophila ananassae]
 gi|190615618|gb|EDV31142.1| GF14697 [Drosophila ananassae]
          Length = 395

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 55/254 (21%), Positives = 113/254 (44%), Gaps = 19/254 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV ++   +R   RL     L +T M+++D+I   +K     F+    ++PL  Q    D
Sbjct: 29  MVRYSKLEFRRLVRL-NGVQLAFTPMMISDSINNSEKARQNEFTTGPDDQPLVAQFAAKD 87

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--S 116
            ++ V +A+++  +  + I+LN GCP +      +G  L+  P++V + +  + + L   
Sbjct: 88  ATEFVTSAQLIYPY-VDGIDLNCGCPQSWAMAKGYGCGLLRQPEVVREVVQQVRRTLPSD 146

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+VK R+ +  +        L + ++++G   + +H R    K            LD 
Sbjct: 147 FSVSVKMRL-LGGESSLERTIELARQLEQAGATFLTLHGRTPAQKH-------SKDTLDI 198

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             + E+++    + + +NG +E  + A ++       GVM  R    N A+  +   Y  
Sbjct: 199 GAMSEVRQSL-RIPLIVNGNVESWADACELSEKTGAAGVMAARGLLANPALFNS--AYPE 255

Query: 235 NPLTGSSPIKTRVD 248
              T S+ ++  +D
Sbjct: 256 ATTTPSACVQQWLD 269


>gi|264677182|ref|YP_003277088.1| dihydrouridine synthase, DuS [Comamonas testosteroni CNB-2]
 gi|262207694|gb|ACY31792.1| dihydrouridine synthase, DuS [Comamonas testosteroni CNB-2]
          Length = 347

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 58/301 (19%), Positives = 115/301 (38%), Gaps = 42/301 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       +E I ++ ++L    K  L    +           P+
Sbjct: 8   MEGLLDFVLRDVLTRVGGADRCVSEFIRISGSLL--PDKVYLRTMPELRNGSRTLAGVPV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+ +P+ +   + A
Sbjct: 66  RAQLLGSDPVSMAENAANLARLGPEGIDLNFGCPAKVVNRHGGGASLLQDPEQIVRVVDA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +PV+ K R+G +D+     +    +++++ G   I +HAR  +     P   
Sbjct: 126 VRRAVPAQMPVSAKMRLGFNDR---ALMTECAQAMEQGGACEIVVHARTKLDGYRPPAYW 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +IP +         +E   + +  NG +  + +AL+       D +M+GR    +  + 
Sbjct: 183 EEIPRI---------REAVGVNVVANGEIWTVEEALRCREVSGCDDLMLGRGIVADPGLA 233

Query: 227 TTVDEYFSNPLTGSSP-----IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----IT 277
             V     +    +             + FW  +   +           G+L+Q    + 
Sbjct: 234 LAVRRAVEHGSVSAVAGIDWLALVPQVQRFWHMVCEDLEP-----RQRAGRLKQWLNLMR 288

Query: 278 R 278
           R
Sbjct: 289 R 289


>gi|226947931|ref|YP_002803022.1| dihydrouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
 gi|226843334|gb|ACO86000.1| dihydrouridine synthase family protein [Clostridium botulinum A2
           str. Kyoto]
          Length = 312

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/294 (21%), Positives = 120/294 (40%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   +  +   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFNNIDKYFTPFIVPNKSTNLKTKELRDILPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R       +       P+LD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYGNE------PDLD- 177

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVD 230
                + K+   L    I  NG +  +S     +K  P V  +M+GR    N  ++  + 
Sbjct: 178 -----VFKDALSLSRNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLINEIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 --------NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|168178053|ref|ZP_02612717.1| dihydrouridine synthase family protein [Clostridium botulinum NCTC
           2916]
 gi|182671610|gb|EDT83584.1| dihydrouridine synthase family protein [Clostridium botulinum NCTC
           2916]
          Length = 319

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/294 (21%), Positives = 120/294 (40%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   +  +   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFNNIDKYFTPFIVPNKSTNLKTKELRDILPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R       +       P+LD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYGNE------PDLD- 177

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVD 230
                + K+   L    I  NG +  +S     +K  P V  +M+GR    N  ++  + 
Sbjct: 178 -----VFKDALSLSRNPICYNGDIFTVSGYNKLIKTFPKVKTIMLGRGILANPGLINEIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    ++ I   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 --------NNTTIDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|168702483|ref|ZP_02734760.1| dihydrouridine synthase DuS [Gemmata obscuriglobus UQM 2246]
          Length = 326

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 99/256 (38%), Gaps = 18/256 (7%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ +Q+ G D  ++ E+A    + G   +++N GCP+  V+    GA L+ +P  + + +
Sbjct: 49  PVQVQLLGGDSGRMAESAVRAHELGATAVDVNFGCPAPTVNRHDGGAALLRHPLRIREIV 108

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+  AL   +PV+ K R+G D      A+        + G   I IH R  +       
Sbjct: 109 GAIRAALPPHVPVSAKLRLGWD---TLDAIHENATMAAEGGAAWITIHGRTRVAG----- 160

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSA 224
                P + ++ +  + +E   + +  NG +  +    +   +      M+GR A  +  
Sbjct: 161 ---YAPPIHWEPIGRV-RERLGIPVVANGDIWTVEDFKRCRDVTGCKHFMLGRGALADPR 216

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY-AARHLHSGGKLQQITRHMIGL 283
           +   V              +        R +      +   R   +  +L+Q  R +   
Sbjct: 217 LARRVAAELGLVPPVEETDEPFDWAAQLRNLVEWSHRFDMLRSDKNVSRLKQWLR-LASQ 275

Query: 284 FHGFPNSRRCRHILTV 299
           F  F +  R + I +V
Sbjct: 276 FGSFAHFDRVKRIESV 291


>gi|168205517|ref|ZP_02631522.1| dihydrouridine synthase family protein [Clostridium perfringens E
           str. JGS1987]
 gi|170662991|gb|EDT15674.1| dihydrouridine synthase family protein [Clostridium perfringens E
           str. JGS1987]
          Length = 321

 Score =  149 bits (377), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 56/291 (19%), Positives = 117/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   +  + K   
Sbjct: 68  NDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHKEELDKFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I +++K R+G+D          L+K   K  +  + IH R           N+    +  
Sbjct: 128 IKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG----NKPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +  +      ++    VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----PVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +  +V K+F  ++     +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKKVLKEFHDEVFNKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|307169925|gb|EFN62434.1| tRNA-dihydrouridine synthase 2-like [Camponotus floridanus]
          Length = 467

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 99/250 (39%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-----------------ILGF 43
           MV       R  A L     ++YTE ++   +LR  ++                  +   
Sbjct: 24  MVRIGTLPMRLLA-LDYGADIVYTEELIDRKLLRSIRRENDVLSTIDYIDKTDGTVVFRT 82

Query: 44  STQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +E+  + LQIG +D  +  E A++VE      I++N+GCP      G  GA L+ +P 
Sbjct: 83  CPREREHVVLQIGTSDPLRAAEVARMVEK-DVAGIDVNMGCPKKFSILGGMGASLLSDPR 141

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              + +  M + ++IPVT K R+             L  ++  +G+  I IH R    + 
Sbjct: 142 KATNILRKMIETVTIPVTCKIRVLF----SLEETLQLCDTLASTGIEAIAIHGRTIEERP 197

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGR 217
             P  N+ +  +          +   + +  NGG +D+ Q   I           VM+ R
Sbjct: 198 QHPNRNQVLKQI---------SDRLSIPVIANGGSKDIQQHSDIFRFKEKTGCSSVMLAR 248

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 249 AAQWNCSIFR 258


>gi|223997918|ref|XP_002288632.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220975740|gb|EED94068.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 378

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 60/274 (21%), Positives = 109/274 (39%), Gaps = 30/274 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +AD +L+G      +L   + E    +QI      +  
Sbjct: 25  NLPFRRIMKGF-GADITCGEMAIADQLLQGKPSEWALLKRHSSEDVFGVQIATGHADQYT 83

Query: 64  EAAKIVE---DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
             A+++    +   + +++N+GCP   V E   GA LML    +   +  + K L+ PVT
Sbjct: 84  RVAELIANEPEIEVDFVDMNLGCPIDLVCEKGAGASLMLRERKLKGSVEGLTKTLNCPVT 143

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R G ++  P      LV++I+  G +GI      A++     +  R     ++D + 
Sbjct: 144 IKIRTGWNENEPIA--HKLVQTIQAWGYDGI-----GAVMIHGRSRLQRYSRLANWDYIA 196

Query: 181 EIKK---ENPD-LFIGLNGGLEDM----SQALKILPSVDG-------VMIGRAAYKNSAM 225
           E+ K    N   + +  NG L          LK +   D         M+GR A     +
Sbjct: 197 EVAKCQAANLHQIPVIGNGDLFSYTDYEQNVLKRVNDCDDSNCLSPTAMLGRGALIKPWL 256

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            T + E     ++ +   +  + KDF R      
Sbjct: 257 PTEIKERRHWDISATE--RLDMLKDFVRFGLEHW 288


>gi|226479846|emb|CAX73219.1| dihydrouridine synthase 2-like, SMM1 homolog [Schistosoma
           japonicum]
          Length = 511

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 116/299 (38%), Gaps = 47/299 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI----------------VADAILRGDKKNILGFS 44
           MV  +    R        + ++  E+I                  D IL          +
Sbjct: 22  MVRVSTHPMRLLCLEYGADYVISEELIDQRVIRSSRIANDELNTVDFILPDGSVTFRTSA 81

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            ++  + +Q+G ++    ++AAK++E+     I++N+GCP A   +G  GA L+  PD V
Sbjct: 82  EEKNRVIVQLGTSNPETALKAAKVLEN-DVMAIDVNMGCPKAYSVKGGMGAALLTKPDTV 140

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + +  +   L IPVT K RI  +          L K I+ +GV  I IH R    + + 
Sbjct: 141 KEILTTLTTNLRIPVTCKMRILPELDKTVA----LAKLIESTGVVAITIHGRTIHERSMH 196

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ------ALKILPSVDGVMIGRA 218
              N        +++  I + +  + I  NGG  D+ +        + L    GV+I RA
Sbjct: 197 RNRN--------EVIQAIAQ-SVSIPILANGGSRDIIRNHEDIEYFRQLTGAAGVVIARA 247

Query: 219 AYKNSAMLT--TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           A  N A+     VDE         SP    +   +   ++     + A   +   ++  
Sbjct: 248 AMWNPAIFKSLQVDE--------PSPKLEEIICRYLT-LAVRYDHHIAGAKYCVLRMLH 297


>gi|126304888|ref|XP_001373897.1| PREDICTED: hypothetical protein [Monodelphis domestica]
          Length = 495

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 103/250 (41%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEKP----- 49
           MV       R  A L     ++Y E      M+    ++      I   +  E+      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMLQCKRVVNEVLDTIDFVAPNERIIFRTC 77

Query: 50  ------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK+VE+     I++N+GCP     +G  G  L+ +PD 
Sbjct: 78  ERERNKVVFQMGSADAERALAVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGVALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K +  PVT K RI    +       NLVK I+++GV  I +H RK      
Sbjct: 137 IEKILSTLVKGICKPVTCKIRILPSLEDT----LNLVKRIERTGVAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS------QALKILPSVDGVMIGR 217
             K+ R    +  DI+  I  E   + I  NGG  D         A + + S   VM+ R
Sbjct: 187 --KEERPQHPVHCDIIKAIA-EAVSIPIIANGGSHDHIKVYSDLDAFRQVTSASSVMVAR 243

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 244 AAMWNPSIFR 253


>gi|328770050|gb|EGF80092.1| hypothetical protein BATDEDRAFT_35061 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 507

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 99/249 (39%), Gaps = 34/249 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---------------DKKNI-LGFS 44
           MV  +    R  A       ++Y+  IV   ++R                D  ++ L   
Sbjct: 188 MVRVSTLPLRLLALKY-GADIVYSPEIVDRRLMRSQRIQNDKFGTIDYVDDSGSLNLRIH 246

Query: 45  TQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             E+  L +Q+G ++    V AA+ V     + I+LN GCP      G  G+ L+ NPD 
Sbjct: 247 PNERGRLVVQLGSSNPVFAVLAAQKVAG-DVDGIDLNCGCPKKFSVSGGMGSALLENPDT 305

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A+  ++SIPVT K R+    +          L++ ++K+G++ I +H R     
Sbjct: 306 LEAILTALVSSVSIPVTCKIRLLDPREGKTSIERTIELMQRLEKTGISAIAVHCRFI--- 362

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL----PSVDGVMIGR 217
                  R      +D+  +I      + +  NG L  M    K       +V   MI R
Sbjct: 363 -----HERPRQPAHWDVFEQISNCI-SIPVIANGDLWTMEDIHKFRATSGSAVSSFMIAR 416

Query: 218 AAYKNSAML 226
            A  N ++ 
Sbjct: 417 GAQDNVSVF 425


>gi|168183356|ref|ZP_02618020.1| dihydrouridine synthase family protein [Clostridium botulinum Bf]
 gi|237793992|ref|YP_002861544.1| dihydrouridine synthase family protein [Clostridium botulinum Ba4
           str. 657]
 gi|182673465|gb|EDT85426.1| dihydrouridine synthase family protein [Clostridium botulinum Bf]
 gi|229262625|gb|ACQ53658.1| dihydrouridine synthase family protein [Clostridium botulinum Ba4
           str. 657]
          Length = 319

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 60/292 (20%), Positives = 115/292 (39%), Gaps = 29/292 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   +  +   + ++IL  + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFNNIDKYFTPFIVPNKSTNLKTKELRDILPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYNEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI-LKGLSPKDNRKIPNLD 175
           + +++K RIG D          L+K   K  +  + IH R      G  P        L 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYGNEPNLGVFKDAL- 183

Query: 176 YDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
                          I  NG +    D ++ +K  P V  +M+GR    N  ++  +   
Sbjct: 184 ---------SLSSNPICYNGDIFTVSDYNRLIKTFPKVKTIMLGRGILANPGLINEIK-- 232

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  ++ +   V K+F  +I     +      ++  +++++  +MI +F
Sbjct: 233 ------NNTTVDKEVLKEFHDEILNKYIELYNEDRNALFRMKELWGYMIYIF 278


>gi|156553630|ref|XP_001600195.1| PREDICTED: similar to CG10463-PA [Nasonia vitripennis]
          Length = 584

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 51/221 (23%), Positives = 93/221 (42%), Gaps = 17/221 (7%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  +L+G ++   ++     E    +QI G +   L 
Sbjct: 302 NLPFRRICKEF-GADITCGEMALAPRLLKGVREEWALVKRHESEDLFGVQIAGNNPGVLT 360

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++ D    + ++LNVGCP   V++   G  ++   +I+   + +  + L IP TVK
Sbjct: 361 RCCQLLNDETEVDFVDLNVGCPIDLVYKQGGGCGMLNRLNILESVVKSATEVLDIPFTVK 420

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R GV    P      L+   K  G + I IH R         ++ R     D+D + + 
Sbjct: 421 TRTGVYADKPIA--HKLMSKFKDWGASMINIHGRS--------REQRYTKLADWDYIEKC 470

Query: 183 KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAY 220
            +    + +   G +   +D  +  K  P+V GV I R A 
Sbjct: 471 AQVASPIPVYGTGDILSWDDYQRVRKTYPTVQGVSIARGAL 511


>gi|116332915|ref|YP_794442.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
 gi|116098262|gb|ABJ63411.1| tRNA-dihydrouridine synthase [Lactobacillus brevis ATCC 367]
          Length = 331

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 116/319 (36%), Gaps = 29/319 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK----NILGFSTQEKPL-ALQIG 55
           M   T+  +R          + +TE   A +I     K      L  + +E  +   Q+ 
Sbjct: 27  MEAVTNAIFRRVVARAAAPDVFFTEFTNAISITHPKAKFTVAGRLYVAPEEAHMPVAQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G D      AA+ V+D GY  I++N+GCP + V +   G+ L+ N D     I A  K  
Sbjct: 87  GNDGEAFARAAEAVKDLGYEAIDINMGCPDSTVIKNHGGSDLICNFDSAAAVI-AGAKTA 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PV+VK R+G          R+ +  + +  +  + IH R        P     I    
Sbjct: 146 GLPVSVKTRLGYSRLD---EWRDWLTFLFQQDIPLLTIHLRTKKEMSRVPAHYEMID--- 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            DIV    +  PD  + LNG +E+ +  +   +  P VDG+MIGR  + +          
Sbjct: 200 -DIVKLRDEIAPDTLLQLNGDIENYTDGVTLAQAHPGVDGIMIGRGIFTSPFAFE----- 253

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
            + P          +              +      S  +  +I            N+  
Sbjct: 254 -ATPQEHDIKELLGLLNYQLDLYDEFAQRFDTSRFASLKRFFKI------YVRNQRNAAS 306

Query: 293 CRHILTVEAGASTATHHII 311
            R+ + +E   +     ++
Sbjct: 307 LRNAM-METHTTDEVRQLL 324


>gi|18310257|ref|NP_562191.1| dihydrouridine synthase family protein [Clostridium perfringens
           str. 13]
 gi|168213028|ref|ZP_02638653.1| dihydrouridine synthase family protein [Clostridium perfringens CPE
           str. F4969]
 gi|18144936|dbj|BAB80981.1| probable transcriptional regulator [Clostridium perfringens str.
           13]
 gi|170715388|gb|EDT27570.1| dihydrouridine synthase family protein [Clostridium perfringens CPE
           str. F4969]
          Length = 321

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 118/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   +  + K   
Sbjct: 68  NDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHKEELDKFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I +++K R+G+D          L+K   K  +  + IH R           N+    +  
Sbjct: 128 IKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG----NKPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +  +      ++    VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----PVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGVLANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +  +V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKKVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|225438161|ref|XP_002262652.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 349

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 99/247 (40%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------------GDKKNILGF 43
           MV      +R  A       + Y E I+   +++                 G    +   
Sbjct: 12  MVRVGTLPFRLLAAQY-GADITYGEEIIDHKLIKCERRLNEDIGSIDFVEKGTHNVVFRT 70

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  +  Q+G ++  + + AA+IV       +++N+GCP +    G  GA L+  P+
Sbjct: 71  CHEEKNRVVFQMGTSNAERALTAAQIVCK-DVAAVDINMGCPKSFSISGGMGAALLTRPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L IPVT K R+    Q        L + I+K+GV  + +H R+     
Sbjct: 130 LIHDILTILKRNLDIPVTCKIRLLKSSQETV----ELAQQIEKTGVAALAVHGRRI---- 181

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAY 220
                +R      ++ + ++      + +  NG +       +  +      VM+ R A 
Sbjct: 182 ----ADRPRDPAKWNEIADVVAAL-SIPVIANGDVFGYDDFQRIKVATGASSVMVARGAL 236

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 237 WNASVFS 243


>gi|302386025|ref|YP_003821847.1| dihydrouridine synthase DuS [Clostridium saccharolyticum WM1]
 gi|302196653|gb|ADL04224.1| dihydrouridine synthase DuS [Clostridium saccharolyticum WM1]
          Length = 320

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 124/320 (38%), Gaps = 28/320 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNA-LLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR    +  +   + +T  IV          +  + L    ++  +  QI  
Sbjct: 8   MEGITGYIYRNAHHMFFDQMDVYFTPFIVPTQNRKFTSREINDFLPEHNKDLHVIPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 + AAK ++ +GY E+NLN+GCPS  V     GA  +  PD++      +  AL 
Sbjct: 68  NKGDDFIWAAKELKRYGYEEVNLNLGCPSPTVVSKGRGAGFLGEPDLLEAFFDQIFSALD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V+VK RIG D    +     L++   K  +  + +H R       +  D + + +   
Sbjct: 128 MKVSVKTRIGKD---SSEEFGRLMEIYNKYPIEELIVHPRIQKDFYRNEPDWKSVKDAV- 183

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
                      +  +  NG L   ED  +     PS+D VM+GR    N  ++  +    
Sbjct: 184 --------SISNFPLCYNGNLFSAEDFERFTADFPSIDRVMLGRGLVANPGLVRKIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
                G   ++    K F  ++     +  +   +   K++++  +MI +F  G  + +R
Sbjct: 233 -----GGENLEKGRLKAFHDEVLRGYEEIMSGDRNVLFKMKELWAYMIRMFEGGEKHGKR 287

Query: 293 CRHILTVEAGASTATHHIIE 312
            R    +    + A    +E
Sbjct: 288 IRKSQNLLEYRTAADRLFVE 307


>gi|168217080|ref|ZP_02642705.1| dihydrouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
 gi|182380794|gb|EDT78273.1| dihydrouridine synthase family protein [Clostridium perfringens
           NCTC 8239]
          Length = 321

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 54/291 (18%), Positives = 117/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCPS  V     G+  + + + +   +  + K   
Sbjct: 68  NDSEGFISTARKLKQLGYNEINLNLGCPSGTVVGKKRGSGFLAHREELDKFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+D          L+K   K  +  + IH R           NR    +  
Sbjct: 128 MKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG----NRPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +  +      ++    VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----PVCYNGDIFTLEDHNKLVETFKEVDKIMLGRGVLANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +  +V K+F  ++ +   +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKKVLKEFHDEVFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|147797460|emb|CAN64677.1| hypothetical protein VITISV_024917 [Vitis vinifera]
          Length = 326

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 99/247 (40%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------------GDKKNILGF 43
           MV      +R  A       + Y E I+   +++                 G    +   
Sbjct: 12  MVRVGTLPFRLLAAQY-GADITYGEEIIDHKLIKCERRLNEDIGSIDFVEKGTHNVVFRT 70

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  +  Q+G ++  + + AA+IV       +++N+GCP +    G  GA L+  P+
Sbjct: 71  CHEEKNRVVFQMGTSNAERALTAAQIVCK-DVAAVDINMGCPKSFSISGGMGAALLTRPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L IPVT K R+    Q        L + I+K+GV  + +H R+     
Sbjct: 130 LIHDILTILKRNLDIPVTCKIRLLKSSQETV----ELAQQIEKTGVAALAVHGRRI---- 181

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAY 220
                +R      ++ + ++      + +  NG +       +  +      VM+ R A 
Sbjct: 182 ----ADRPRDPAKWNEIADVVAAL-SIPVIANGDVFGYDDFQRIKVATGASSVMVARGAL 236

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 237 WNASVFS 243


>gi|242073810|ref|XP_002446841.1| hypothetical protein SORBIDRAFT_06g023500 [Sorghum bicolor]
 gi|241938024|gb|EES11169.1| hypothetical protein SORBIDRAFT_06g023500 [Sorghum bicolor]
          Length = 320

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 99/245 (40%), Gaps = 33/245 (13%)

Query: 1   MVDWTDRHYRFFARLLTN----------NALLYTEMIVADAI------LRGDKKNILGFS 44
           MV      +R  A               + LL  E +  +++       +G    +    
Sbjct: 12  MVRVGTLPFRLLAAEYGADITYGEEIIDHKLLKCERVTNESLGTTDFVEKGTDSVVFRTC 71

Query: 45  TQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            +E+  +  Q+G ++  + ++AA++V       I++N+GCP +    G  GA L+  P++
Sbjct: 72  PEERGRVVFQMGTSNAVRALKAAQLVCQ-DVTAIDINMGCPKSFSLSGGMGAALLSKPEL 130

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + D +  + + L   VT K R+    +        L + I+K+GV  + +H RK   +  
Sbjct: 131 IHDILTTLRRNLDTTVTCKIRLLNTPKDTV----ELARRIEKTGVPALAVHGRKIKDRPR 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYK 221
            P          +D + ++      + +  NG + +     +I        +M+ R A  
Sbjct: 187 DP--------AKWDEIADVVSAL-SIPVIANGDVFEYEDFKRIKDATGAASIMVARGAMW 237

Query: 222 NSAML 226
           N+++ 
Sbjct: 238 NASIF 242


>gi|225468696|ref|XP_002269969.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 326

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 99/247 (40%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------------GDKKNILGF 43
           MV      +R  A       + Y E I+   +++                 G    +   
Sbjct: 12  MVRVGTLPFRLLAAQY-GADITYGEEIIDHKLIKCERRLNEDIGSIDFVEKGTHNVVFRT 70

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  +  Q+G ++  + + AA+IV       +++N+GCP +    G  GA L+  P+
Sbjct: 71  CHEEKNRVVFQMGTSNAERALTAAQIVCK-DVAAVDINMGCPKSFSISGGMGAALLTRPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L IPVT K R+    Q        L + I+K+GV  + +H R+     
Sbjct: 130 LIHDILTILKRNLDIPVTCKIRLLKSSQETV----ELAQQIEKTGVAALAVHGRRI---- 181

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAY 220
                +R      ++ + ++      + +  NG +       +  +      VM+ R A 
Sbjct: 182 ----ADRPRDPAKWNEIADVVAAL-SIPVIANGDVFGYDDFQRIKVATGASSVMVARGAL 236

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 237 WNASVFS 243


>gi|182624205|ref|ZP_02951991.1| dihydrouridine synthase family protein [Clostridium perfringens D
           str. JGS1721]
 gi|177910619|gb|EDT72987.1| dihydrouridine synthase family protein [Clostridium perfringens D
           str. JGS1721]
          Length = 321

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/291 (19%), Positives = 117/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   +  + K   
Sbjct: 68  NDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHREELDKFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+D          L+K   K  +  + IH R           N+    +  
Sbjct: 128 MKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG----NKPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +  +      ++    VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----PVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +   V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKNVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|168209608|ref|ZP_02635233.1| dihydrouridine synthase family protein [Clostridium perfringens B
           str. ATCC 3626]
 gi|170712244|gb|EDT24426.1| dihydrouridine synthase family protein [Clostridium perfringens B
           str. ATCC 3626]
          Length = 321

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 119/294 (40%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  AK ++D GYNEINLN+GCPS  V     G+  + + + +   +  + K   
Sbjct: 68  NDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGSGFLAHREELDKFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+D          L+K   K  +  + IH R               PNL  
Sbjct: 128 MKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG------NKPNL-- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVD 230
               E+ KE   L    I  NG +  +      ++    VD +M+GR    N A++  + 
Sbjct: 177 ----EVFKEAISLSKNPICYNGDIFTLEDHNKLVEEFKEVDKIMLGRGVLANPALMNEI- 231

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    +  +  +V K+F  ++     +      ++  +++++  +MI +F
Sbjct: 232 -------LNNEFMDKKVLKEFHDEVFNKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|88798296|ref|ZP_01113882.1| NifR3/Smm1 family protein [Reinekea sp. MED297]
 gi|88779072|gb|EAR10261.1| NifR3/Smm1 family protein [Reinekea sp. MED297]
          Length = 314

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 58/292 (19%), Positives = 115/292 (39%), Gaps = 31/292 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-------RGDKKNILGFSTQEKPLAL 52
           M    D + R          L  +E + V D +L       +  + +  G +    P+ +
Sbjct: 8   MEGLADHYLRKLITQCGGYDLAVSEFVRVVDQLLPKRVFLEQVPELHQQGRTGAGTPVRV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+    L E A    + G + ++LN GCPS  V+    GA L+  P+ +   + ++ 
Sbjct: 68  QLLGSHPQALAENALRAIELGSHGLDLNFGCPSKTVNASKGGAVLLTEPESIYAVVRSVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            AL     ++ K R+G +D      +     +I+  G N I +HAR        P     
Sbjct: 128 DALPGDQTLSAKMRLGFEDNSL---MWECAHAIRDGGANEIIVHARTKQQGYTPPAYWHL 184

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYKNSAMLTT 228
               D++           + + +NG +   + A   +   +   +M+GR A +N  + + 
Sbjct: 185 --PADFE-------ARLGIPMIINGEIWTPADAGRAQHEANCSSIMLGRGAVRNPWLASE 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           +    +     S     ++   FW++++  M+          G+L+Q   H+
Sbjct: 236 ITGRHNQKSDWSQ--VHQLVVQFWQEVTQQMSPRYCA-----GRLKQWLNHL 280


>gi|50294738|ref|XP_449780.1| hypothetical protein [Candida glabrata CBS 138]
 gi|74637232|sp|Q6FJ14|DUS3_CANGA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49529094|emb|CAG62758.1| unnamed protein product [Candida glabrata]
          Length = 640

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/298 (20%), Positives = 109/298 (36%), Gaps = 51/298 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +      E P   +Q+  +   + 
Sbjct: 279 NLPYRRLMRTL-GADVTYSEMALAVPLVQGTNSEWALPKAHESEYPGFGVQVACSKGWQA 337

Query: 63  VEAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIP 118
            +AA+ +  +   G +EINLN GCP   ++    G+ L+ NP  +  C+ AM      IP
Sbjct: 338 SKAAEALATYIPNGISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSGDIP 397

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +TVK R G  +  P      + + + ++ V  I +H R         +  R     D+D 
Sbjct: 398 ITVKIRTGTKEGHPIADTL-VRRLVFETDVAAITLHGRS--------RQQRYTKVADWDY 448

Query: 179 VYEIKKEN----------------------PDLFIGLNGGLEDMSQALKILP--SVDGVM 214
           V ++ K                               NG + + +   + L    VD  M
Sbjct: 449 VSQVAKALRQAEADFMESPQGKESHHDEKTRHTQFVGNGDIFNYTDWYQHLEDPEVDSCM 508

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           + R A     +   ++       T S  +          +I  + + +A  H  +   
Sbjct: 509 VARGALIKPWIFEEINAQQHLDKTSSERL----------EILKTYSKFAMDHWGTDEY 556


>gi|326927225|ref|XP_003209793.1| PREDICTED: tRNA-dihydrouridine synthase 2-like, partial [Meleagris
           gallopavo]
          Length = 497

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 62/254 (24%), Positives = 101/254 (39%), Gaps = 46/254 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQE------- 47
           MV       R  A L     ++Y E      M+    ++    + +   +  E       
Sbjct: 18  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMMQCKRVVNEVLETVDFVAPNERVVFRTC 76

Query: 48  ----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK+VE      I++N+GCP     +G  GA L+ +PD 
Sbjct: 77  ERERHRVVFQMGSADAERALAVAKLVE-SDVAGIDINMGCPKEYSTKGGMGAALLSDPDK 135

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +  + K +  PVT K RI    +       NLVK I+K+G+  I +H RK      
Sbjct: 136 IESILTTLVKGICKPVTCKIRILPSVEDTV----NLVKRIEKTGIAAIAVHGRK------ 185

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             K+ R    +  D++  I  E   + +  NG           +E   +A     +   V
Sbjct: 186 --KEERPQHPVHCDVIKAI-SEAVSIPVIANGGSHDFIKEYTDIETFQKA----TAASSV 238

Query: 214 MIGRAAYKNSAMLT 227
           MI RAA  N ++  
Sbjct: 239 MIARAAMWNPSIFR 252


>gi|270009693|gb|EFA06141.1| hypothetical protein TcasGA2_TC008984 [Tribolium castaneum]
          Length = 418

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 99/248 (39%), Gaps = 33/248 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +   N  L YT MI+AD+  +  K     F+T   + PL  Q     
Sbjct: 31  MVRYSKLQFRNLVKSY-NCDLCYTPMILADSFCKSGKARANEFTTNMNDTPLITQFAANK 89

Query: 59  ISKLVEAAKIVEDF----------------GYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           +   V AA +V                     + ++LN GCP         G  ++  P+
Sbjct: 90  VYDFVGAAYMVSPLVFGLNLANFYRFFIFSFCDGVDLNCGCPQRWAKLQGLGCIMLEKPE 149

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +      +  P TV  ++ +   +       + + ++  GV+ + +H R      
Sbjct: 150 VIYDLVKQCRNVIPKPFTVSVKLRLQKDLRRSV--EICRQLEHCGVSFLTVHGRTPDQ-- 205

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           L+ + N++  NL   IV  +     ++ +  NGG++ +   L++    +  GVM+     
Sbjct: 206 LTGEVNKEALNL---IVGSV-----NVPVVANGGVKSLEDCLELQEKTNCKGVMVANGLL 257

Query: 221 KNSAMLTT 228
            N  + T 
Sbjct: 258 TNPTLFTE 265


>gi|188589378|ref|YP_001920726.1| dihydrouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
 gi|188499659|gb|ACD52795.1| dihydrouridine synthase family protein [Clostridium botulinum E3
           str. Alaska E43]
          Length = 321

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 67/327 (20%), Positives = 130/327 (39%), Gaps = 33/327 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + +++L  + +   +  QI  
Sbjct: 8   MEGITGYIYRNTYEKFFHNIDKYFTPFIVTNKSRSLKSKELRDVLPENNKGMSIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +   + ++  GYNE+NLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFINTTRKLQQLGYNEVNLNLGCPAGTVVSKNRGSGFLAKREELDIFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               PNLD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPLEELIIHPRTQKDFYG------NKPNLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++      +  +  NG +  ++      +  P V  +M+GR    N  ++  +    
Sbjct: 178 --VFKDALSLSNNPVCYNGDIFTVADHNKFEETFPKVKTLMLGRGILANPGLMNEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
                 +  I   + KDF  +I     D      ++  +++++  +MI +F      +++
Sbjct: 233 -----NNDFINKELLKDFHDEIFNKYIDLFNEEKNAMFRMKELWGYMIYIFSDNKKYAKK 287

Query: 293 CR--HILTV--EAGAST-ATHHIIETA 314
            R    L+   EA  S      IIE A
Sbjct: 288 IRKAQKLSDYNEAVLSLFEEQEIIEGA 314


>gi|110801357|ref|YP_695925.1| dihydrouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
 gi|110676004|gb|ABG84991.1| dihydrouridine synthase family protein [Clostridium perfringens
           ATCC 13124]
          Length = 321

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 55/291 (18%), Positives = 117/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GYNEINLN+GCPS  V     G+  + + + +   +  + K   
Sbjct: 68  NDSEGFISTARKLKQLGYNEINLNLGCPSGTVVGKKRGSGFLAHKEELDKFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+D          L+K   K  +  + IH R           N+    +  
Sbjct: 128 MKLSIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFY----ANKPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       I  NG +  +      ++  P VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----PICYNGDIFTVEDHNKLIETFPEVDKIMLGRGILANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +  +V K+F  ++     +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKKVLKEFHDEVFNKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|90020951|ref|YP_526778.1| RecR protein [Saccharophagus degradans 2-40]
 gi|89950551|gb|ABD80566.1| dihydrouridine synthase, DuS [Saccharophagus degradans 2-40]
          Length = 318

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 60/253 (23%), Positives = 100/253 (39%), Gaps = 29/253 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRG------------DKKNILGFSTQE 47
           M    D H R     +    +  TE I V D +L              + +    +    
Sbjct: 8   MEGVVDHHMRNIISSVGGVDICVTEFIRVTDHVLPNKIFKKACPELDENSETPALYRGAH 67

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ +Q+ G++ S L   A    + G   I+LN GCP+  V+    GACL+   D V D 
Sbjct: 68  CPVRVQLLGSNPSALAANAARAAELGAVAIDLNFGCPAKTVNRHKGGACLLDETDTVFDI 127

Query: 108 IAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A+ KA   S PVT K R+G  ++     LRN  K+I+ +G N + +HAR        P
Sbjct: 128 VNAVRKATPASTPVTAKIRLGYLNRDSY--LRN-AKAIEAAGANELCVHARSKTDGYQPP 184

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                I ++         ++N  + +  NG +  +    +          M+GR      
Sbjct: 185 AYWHYIGDI---------RDNLSIPVVANGEIWSLEDFKRCAEQSKCSDFMLGRGLLAKP 235

Query: 224 AMLTTVDEYFSNP 236
            +   + +Y +  
Sbjct: 236 DLALEIKQYMAGE 248


>gi|330801859|ref|XP_003288940.1| hypothetical protein DICPUDRAFT_34883 [Dictyostelium purpureum]
 gi|325080971|gb|EGC34504.1| hypothetical protein DICPUDRAFT_34883 [Dictyostelium purpureum]
          Length = 384

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 102/245 (41%), Gaps = 31/245 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-----------MIVADAI-----LRGDKKNILGFS 44
           MV  +    R  A+      ++Y+E            +V + +     ++ D   +   S
Sbjct: 25  MVRVSTYPMRILAQRY-GCDIVYSEELIDFKVKSSHRVVNEKLNTIDFVQKDNNLVYRTS 83

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
             +K   +Q+G       +EAA IV       I++N+GCP     +G  G+ L+  P+ +
Sbjct: 84  AIDKNNVMQLGTGSAVTALEAASIVA-RDVCAIDINMGCPKYFSIQGGMGSALLSKPETI 142

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            D +  + + L+ P+T K R+   DQ       +L++ I+ +GV+ I +H R    +   
Sbjct: 143 KDILTTLKRNLNKPITCKIRLLSTDQ----ETIDLLRVIESTGVSAIGVHCRMIPERPRD 198

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P    ++ N+       +   +  + I  NG +         L     + VMI R A KN
Sbjct: 199 PAHWDRLENI-------LSNASFSVPIIANGDIWKHEDIDACLKKTKANSVMIARGAIKN 251

Query: 223 SAMLT 227
            ++ +
Sbjct: 252 VSIFS 256


>gi|327276491|ref|XP_003223003.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Anolis
           carolinensis]
          Length = 488

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    I+      +   +  E+      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMVQCKRIVNEVLGTVDFVAPNERVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK+VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREKDSVVFQMGTADAERALAVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSHPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +  + K +  PVT K RI    +        LVK I+++GV  I +H RK      
Sbjct: 137 IESILTTLVKGVCKPVTCKIRILPTKEETIS----LVKRIERTGVAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM------SQALKILPSVDGVMIGR 217
             K+ R   ++  D++  I  E   + +  NGG  D        +A +       VM+ R
Sbjct: 187 --KEERPQHSVHCDVIKAI-SETVSIPVIANGGSHDFIKEHSDIEAFREATGASSVMVAR 243

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 244 AAMWNPSVFR 253


>gi|186510837|ref|NP_190533.3| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|332645048|gb|AEE78569.1| tRNA-dihydrouridine synthase 2 [Arabidopsis thaliana]
          Length = 329

 Score =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 102/247 (41%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------------------NILG 42
           MV      +R  A       + Y E I+   +++ +++                      
Sbjct: 12  MVRVGTLSFRMLAAEY-GADITYGEEIIDHKLVKCERRLNVASGTSEFVEKGTDNVVFST 70

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              ++  +  Q+G +D  + ++A++IV +     I++N+GCP A   +G  GA L+  P+
Sbjct: 71  CDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +A + + L +PVT K R+             L + I+K GV  + +H RK     
Sbjct: 130 LIHDILATLKRNLDVPVTCKIRLLKSPADTV----ELARRIEKLGVPALAVHGRKI---- 181

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +      +K       VM+ R A 
Sbjct: 182 ----ADRPRDPAKWDEIADVVAAL-SIPVIANGDVLEYDDFSRIKTATGAASVMVARGAM 236

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 237 WNASIFS 243


>gi|251780591|ref|ZP_04823511.1| dihydrouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243084906|gb|EES50796.1| dihydrouridine synthase family protein [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 321

 Score =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 68/330 (20%), Positives = 130/330 (39%), Gaps = 39/330 (11%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + +++L  + +   +  QI  
Sbjct: 8   MEGITGYIYRNTYEKFFHNIDKYFTPFIVTNKSRSLKSKELRDVLPENNKGMSIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +   + ++  GYNE+NLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFINTTRKLQQLGYNEVNLNLGCPAGTVVSKNRGSGFLAKREELDIFLEEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R               PNLD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPLEELIIHPRTQKDFYG------NKPNLD- 177

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVD 230
                + K+   L    +  NG +  ++      +  P V  +M+GR    N  ++  + 
Sbjct: 178 -----VFKDTLSLSNNPVCYNGDIFTVADHNKFEETFPKVKTLMLGRGILANPGLMNEIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPN 289
                    +  I   + KDF  +I     D      ++  +++++  +MI +F      
Sbjct: 233 --------NNDFINKELLKDFHDEIFNKYIDLFNEEKNAMFRMKELWGYMIYIFSDNKKY 284

Query: 290 SRRCR--HILTV--EAGAST-ATHHIIETA 314
           +++ R    L+   EA  S      IIE A
Sbjct: 285 AKKIRKAQKLSDYNEAVLSLFEEQEIIEGA 314


>gi|269792729|ref|YP_003317633.1| dihydrouridine synthase DuS [Thermanaerovibrio acidaminovorans DSM
           6589]
 gi|269100364|gb|ACZ19351.1| dihydrouridine synthase DuS [Thermanaerovibrio acidaminovorans DSM
           6589]
          Length = 318

 Score =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 61/299 (20%), Positives = 116/299 (38%), Gaps = 27/299 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
           M   T    R F R +   +L++TEM+ A  +    +K   IL     E+P+  Q+ G  
Sbjct: 23  MAGITTPSVRLFQRRI-GVSLVHTEMVSALGLKYRGEKSRRILIPLPGEEPVIPQLFGPS 81

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              L+E A+I   ++ +  + +N+ CP  +V     GA ++ +PD+    + A+ K L +
Sbjct: 82  GEDLLEGARIALGEYPFRAVEVNMACPMPKVVSKGSGAAMLKDPDLAARAV-ALLKGLGV 140

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V VK R+                 + ++G++ + +H R +          R     D +
Sbjct: 141 SVWVKARVLP---GGFEETLRFCGRLFEAGLDLLLLHGRTSP--------QRYEGRADVE 189

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            V  + +  P   +G  G +     AL+ L      V++ R   ++  +           
Sbjct: 190 QVIRLSRAFPGRVVGS-GDVFSPDDALRYLEGGCVAVLLARGFVRDPLLALRCARRLGLR 248

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
             G + +K  + +         + D  A H      L  + R + G   G P+    R+
Sbjct: 249 PPGDADLKGALLE---------LGDMLASHEGERTCLILVKRMVAGALKGHPHDAERRN 298


>gi|110801933|ref|YP_698595.1| dihydrouridine synthase family protein [Clostridium perfringens
           SM101]
 gi|110682434|gb|ABG85804.1| dihydrouridine synthase family protein [Clostridium perfringens
           SM101]
          Length = 321

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 118/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  AK ++D GYNEINLN+GCPS  V     GA  + + + +   +  + K   
Sbjct: 68  NDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGAGFLAHREELDKFLEEIFKINH 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+D          L+K   K  +  + IH R           N+    +  
Sbjct: 128 MKISIKTRLGMD---KPEEFYELIKIYNKYPMEELIIHPRTRQDFYG----NKPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +  +      ++    VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----PVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +  +V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKKVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|160900633|ref|YP_001566215.1| dihydrouridine synthase DuS [Delftia acidovorans SPH-1]
 gi|160366217|gb|ABX37830.1| dihydrouridine synthase DuS [Delftia acidovorans SPH-1]
          Length = 329

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 56/305 (18%), Positives = 111/305 (36%), Gaps = 26/305 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E I     +  D K  L    +           P+ 
Sbjct: 8   MEGLLDFVLRDVLTRVGGADRCVSEFIRVTGTVLPD-KVFLRTMPELNNGSRTLAGVPVR 66

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+ G+D   +   A  +   G   I+LN GCP+  V+    GA L+ +P+ +   + A+
Sbjct: 67  AQLLGSDPDSMAANAANLARLGPEGIDLNFGCPAKVVNRHGGGAALLQDPEQIARVVGAV 126

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             A+   +PV+ K R+G +D      +    ++++  G   I +HAR         K + 
Sbjct: 127 RAAVPAAMPVSAKMRLGFNDTTL---MTECAQAMQAGGACEIVVHART--------KLDG 175

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
             P   +D++  I +E+  + +  NG +  +  AL+         +M+GR    +  +  
Sbjct: 176 YRPPAYWDMIPRI-RESVTVPVVANGEIWTVEDALRCREQSGCGDLMLGRGIVADPGLAL 234

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            +          +  +  +V             D     L    +  ++ + +  L   F
Sbjct: 235 AIRAAVEGGQMPAEHVAAQVSWSDLVPQVQRFWDMVCEDLEPRQRAGRLKQWLNLLRRRF 294

Query: 288 PNSRR 292
           P + +
Sbjct: 295 PEAEQ 299


>gi|332022994|gb|EGI63259.1| tRNA-dihydrouridine synthase 2-like protein [Acromyrmex echinatior]
          Length = 461

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 100/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A L     ++YTE ++   +LR  ++                      
Sbjct: 22  MVRIGTLPMRLLA-LDYGADIVYTEELIDRKLLRSIRRENDVLGTVDYIDKTDGTVVFRT 80

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            S + + + LQIG +D ++  + A++VE+     I++N+GCP      G  GA L+  P 
Sbjct: 81  CSREREHVVLQIGTSDPARAAQVARMVEN-DVAGIDINMGCPKKFSILGGMGASLLREPQ 139

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              D +  + + ++IP+T K RI  D +   +    L  ++  +G+  I +H R    + 
Sbjct: 140 KAIDILRKLIETVTIPITCKIRILPDLEETLL----LCDTLASTGIAAIAVHGRTIEERP 195

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGR 217
             P  N  +  +              + +  NGG +D+ +   I           VM+ R
Sbjct: 196 QHPNRNHVLKQI---------SARLSIPVIANGGSKDIQKHSDIFRFKKETGCSSVMLAR 246

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 247 AAEWNCSVFR 256


>gi|42525641|ref|NP_970739.1| dihydrouridine synthase, putative [Treponema denticola ATCC 35405]
 gi|41815652|gb|AAS10620.1| dihydrouridine synthase, putative [Treponema denticola ATCC 35405]
          Length = 337

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 51/265 (19%), Positives = 93/265 (35%), Gaps = 26/265 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGAD 58
           M   T   +R  A         ++EMI A + + G   +K     +   + L  QI   D
Sbjct: 8   MAAITHSAFRRLAACFKEPDEYFSEMIHAPSAISGGGFEKWYFRANPSPEKLVWQITSPD 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSI 117
                    ++  +G   I+LN+GC + ++     G   M  P       ++ + KA+ +
Sbjct: 68  EKSAAACVPLLLQYGGFGIDLNMGCCAPQIVNTGAGFAWMKKPLSETASLVSKVKKAVLL 127

Query: 118 -----------PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                      P+ +  ++ + ++     L +  K +   GV+ I +H R    K   P 
Sbjct: 128 YDEQKAGPQTEPIRLSVKLRLGEEENYDRLLSFCKMLVSEGVDLITLHPRTQKQKYSRPC 187

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            +     L  D+          + +  NG +  +    KI       G MIGRAA +   
Sbjct: 188 KHEYTARLASDL---------SVPVYGNGDINSLETLEKIASKYPCAGWMIGRAAVQKPW 238

Query: 225 MLTTV-DEYFSNPLTGSSPIKTRVD 248
           +   +      N        K  +D
Sbjct: 239 IFYELSKGILKNGTAEDKDEKIEID 263


>gi|154416301|ref|XP_001581173.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121915398|gb|EAY20187.1| hypothetical protein TVAG_021320 [Trichomonas vaginalis G3]
          Length = 312

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 115/283 (40%), Gaps = 24/283 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF----STQEKPLALQIGG 56
           M D  D  +R   R     +L +T  I A   +   K+            EK L +Q+ G
Sbjct: 20  MADVNDYSFRKLCRQ-NGVSLCWTGFINAHHWVTRTKQRDRDVWFTTRDNEKNLVVQLLG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---LNPDIVGDCIAAMCK 113
           +++ +LV  AK VE+F  + I LN GC          G  L+    + D     I  + K
Sbjct: 79  SNLEELVSCAKDVENF-CDMIELNCGCTHCFASRSGCGFFLIDTQKHRDSALILIQNLIK 137

Query: 114 ALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           +++ PV++K R+  DD             + +++ GV+ I +HAR             K 
Sbjct: 138 SINKPVSIKIRLISDDNSVPSLERTVKFAQDLERVGVSLITVHARTQ--------QADKK 189

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
            ++DYD +  + +    + +  NGG+  + QA +I+       VM G+  +KN   LTT 
Sbjct: 190 GDVDYDAIKAVVQAV-SVPVIANGGISSLEQAQEIIQRTGAYAVMAGQCFFKNPTCLTTN 248

Query: 230 D--EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
              +  S      +       +   + + A + D   +H   G
Sbjct: 249 KNPKEISLEYLNLAKENNEDLQRSRKHVYAFLGDVLRQHPEYG 291


>gi|322804995|emb|CBZ02555.1| nitrogen regulation protein NIFR3 [Clostridium botulinum H04402
           065]
          Length = 300

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 55/269 (20%), Positives = 110/269 (40%), Gaps = 26/269 (9%)

Query: 22  LYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
            +T  IV   +  +   + +++L  + +   +  QI   D    +  A+ ++  GY+EIN
Sbjct: 11  YFTPFIVPNKSTNLKTKELRDVLPENNKGMNIVPQILTNDSEGFIITARKLQQLGYDEIN 70

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCP+  V   + G+  +   + +   +  + K   + +++K RIG D          
Sbjct: 71  LNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDDMKISIKTRIGKD---SPEEFYE 127

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L+K      +  + IH R               PNLD   V++         I  NG + 
Sbjct: 128 LIKIYNNYPIEELIIHPRTQKDFYG------NKPNLD---VFKDALSLSSNPICYNGDIF 178

Query: 199 DMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
            +S     +K  P V  +M+GR    N  ++  +          ++ I   V K+F  +I
Sbjct: 179 TVSGYNKLIKTFPKVKTIMLGRGILANPGLINEIK--------NNTTIDKEVLKEFHDEI 230

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLF 284
                +      ++  +++++  +MI +F
Sbjct: 231 LNKYIELYNEDRNALFRMKELWGYMIYIF 259


>gi|311694289|gb|ADP97162.1| tRNA-dihydrouridine synthase C [marine bacterium HP15]
          Length = 323

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 65/320 (20%), Positives = 121/320 (37%), Gaps = 47/320 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       TE + V   +L    +    ++ +           P+
Sbjct: 8   MEGLVDAPIRETLTGVGGIDRCVTEFVRVTHGML--PPRVFYKYAPELYNRSLTQVGTPV 65

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           A+Q+ G+D  ++        + G  ++++N GCP+  V++   G  LM  P+++ + +AA
Sbjct: 66  AVQLLGSDPHQMARHGVRAAELGATQVDINFGCPAKTVNKHKGGCVLMREPELMHEIVAA 125

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +PVT K R+G DD+   VA     ++++ +G   I IHAR  +     P   
Sbjct: 126 VRQAVPAHVPVTAKMRLGYDDRSMGVA---CAQALEAAGAAEIVIHARSKVDGYKPPAYW 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +I            +E     +  NG +  ++   +       D VMIGR       + 
Sbjct: 183 EEIARA---------REAVKAHVIANGEIWSVADYWRCREVSGCDDVMIGRGLIARPDLA 233

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA---ARHLHSGGKLQQITRHMIGL 283
             +                 V    W +  A + +YA      L       +I + +  L
Sbjct: 234 RQIKASQQGET---------VPDMTWPEAVALVREYATVLQGWLEDRYVTGRIKQWLNFL 284

Query: 284 FHGF-------PNSRRCRHI 296
             GF       P +R+ R +
Sbjct: 285 RQGFAEAEALWPEARKIRQV 304


>gi|302785397|ref|XP_002974470.1| hypothetical protein SELMODRAFT_174143 [Selaginella moellendorffii]
 gi|300158068|gb|EFJ24692.1| hypothetical protein SELMODRAFT_174143 [Selaginella moellendorffii]
          Length = 319

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 55/280 (19%), Positives = 105/280 (37%), Gaps = 40/280 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILG---------------- 42
           MV      +R  A       L Y E IV   +L+  +   ++LG                
Sbjct: 16  MVRVGTLPFRMLAAGY-GADLTYGEEIVDHKMLKCSRVVNDVLGSIDFVEKGTNDVVFRT 74

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   +  Q+G +D  + +  A+++       +++N+GCP      G  G+ L+  P+
Sbjct: 75  CKAERDHVVFQMGTSDPYRALTVAQLLCKDIAA-VDINMGCPKPFSVTGGMGSALLSQPE 133

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +V + +  + + L IPVT K R+             L + I+K+GV+ I +H R+     
Sbjct: 134 LVSEILTTLRRNLDIPVTCKIRLL----KSTQETVELARRIEKTGVSAIAVHGRRIP--- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +      +K       VM+ R A 
Sbjct: 187 -----DRPKDRAKWDGIADVVSAL-SIPVIANGDVFEPPDIPRIKAATGASSVMVARGAL 240

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMT 260
            N+++           L     I    D  F +    +M 
Sbjct: 241 WNASIFRP-----EGKLDWEECILWENDIKFTKYTVNNMI 275


>gi|255318636|ref|ZP_05359867.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SK82]
 gi|262379139|ref|ZP_06072295.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SH164]
 gi|255304318|gb|EET83504.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SK82]
 gi|262298596|gb|EEY86509.1| tRNA-dihydrouridine synthase C [Acinetobacter radioresistens SH164]
          Length = 313

 Score =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 54/249 (21%), Positives = 100/249 (40%), Gaps = 24/249 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM------IVADAILRGDKKNIL--GFSTQEKPLAL 52
           M   TD   R     + +     TE       ++ D I       +   G +    P+ +
Sbjct: 8   MEGLTDPIMRDVLTHVGSFDWCVTEFIRVTDSVLPDHIYYSYCPELKTEGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A      G   I++N GCP+  V+    G+ L+  P++V + + A+ 
Sbjct: 68  QFLGNNPEMLAANAVRAAILGAPAIDMNFGCPAKTVNRHRGGSVLLDEPEVVYELVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+     + +   +I+ +G + + +HAR         K +  
Sbjct: 128 DAVPAHIPVSAKMRLGYMDRN---FMLDNAHAIEDAGASWVTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I +E   + +  NG + + + A +       + +MIGR A     +   
Sbjct: 177 TPPAFWDQLQPI-REALKINVIANGEIWNNTDARQCQLESGCEDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPL 237
           +      PL
Sbjct: 236 IRNNSDEPL 244


>gi|123414609|ref|XP_001304522.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121885980|gb|EAX91592.1| hypothetical protein TVAG_323330 [Trichomonas vaginalis G3]
          Length = 322

 Score =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 59/271 (21%), Positives = 119/271 (43%), Gaps = 27/271 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
           D  +R   R   N  L +T M+ +   AI    + +     +Q++PL +Q+ G D S+L+
Sbjct: 28  DLAFRMLVRKY-NVKLCWTGMVNSHMWAIQPSSRNSYFQTCSQDRPLIIQMSGNDESELI 86

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI---VGDCIAAMCKALSIPVT 120
             AK ++ F    I++N GC       G +G  ++ N +    V + +  +  ++++P++
Sbjct: 87  ACAKDLQQF-AVGIDINCGCTQHIARRGQYGYFMVNNENKRKNVIEMVKNIVASINVPLS 145

Query: 121 VKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +K R+    D +          K ++ +GV+ I +H R         K++ K   +D + 
Sbjct: 146 IKFRLIDGEDGKPDVDITCKFAKELEDAGVSLISVHGRA--------KNSNKAGPVDAEA 197

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + +I  E+  + +  NGG+    +A+++       GVM+G+    N        + FS+ 
Sbjct: 198 IRKIA-ESVSIPVMANGGVRTKEEAIEMFKESHAAGVMVGQGLLMNP-------KAFSDT 249

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
                   +R     W++        A RH+
Sbjct: 250 PEHDPVAISREYLQLWKEYPDPNFFIARRHI 280


>gi|169845315|ref|XP_001829377.1| tRNA-dihydrouridine synthase 2 [Coprinopsis cinerea okayama7#130]
 gi|116509442|gb|EAU92337.1| tRNA-dihydrouridine synthase 2 [Coprinopsis cinerea okayama7#130]
          Length = 454

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 103/242 (42%), Gaps = 30/242 (12%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILR---------------GDKKNILGFSTQEKP-L 50
              R FA L     L++   IV  AIL                G  + I      EKP L
Sbjct: 64  LPTRLFA-LKHGATLVWGPEIVDKAILHAKREVDPVTGVVSYNGVSRAIFTTHPIEKPYL 122

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG AD    V+AAK V+    + I+LN GCP         GA L+ NPD++   + A
Sbjct: 123 IYQIGSADPELAVQAAKTVQQ-DVSGIDLNCGCPKPFSTHAGMGAALLTNPDLLISILEA 181

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + KA+   I VT K R+    +        LV+ I  +GV+ + +H R   ++    KD 
Sbjct: 182 LRKAMPPEITVTAKIRLLPSQEDT----LKLVERIVNTGVSALTVHCRTRNMR---EKDR 234

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
             I  L+ +IV  ++K    + +  NG   D   A ++  +     VMI R A  N +  
Sbjct: 235 AVIERLN-EIVEFVEKMGKGIAVIENGDCLDWEDAKRVRRVTGAHSVMIARGAEANPSCF 293

Query: 227 TT 228
           + 
Sbjct: 294 SE 295


>gi|332975732|gb|EGK12615.1| tRNA-dihydrouridine synthase C [Psychrobacter sp. 1501(2011)]
          Length = 347

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 97/247 (39%), Gaps = 30/247 (12%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEM------IVADAILRGDKKNILG--FSTQE 47
           M   TD   R     + ++         +E       ++ D +       +     +   
Sbjct: 38  MEGLTDPLMRRILTQVASDLGRPYDWSVSEFIRVTQNVLPDHVFYRFVPELRNDSRTNSG 97

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ +Q+ G++   + E A      G   I++N GCP+  V+    G+ L+  P ++ D 
Sbjct: 98  TPIHVQLLGSNPELMGENALAACALGAPAIDINFGCPAKTVNNHRGGSVLLDEPSLMRDI 157

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I+A+       IPV+ K R+G  D      ++   K+I  SG N + IHAR        P
Sbjct: 158 ISAVRNKTPSHIPVSAKIRLGYTDTSNMDGIK---KAIADSGANWLTIHARTKTQGYKPP 214

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               KI             E P + +  NG + +  QAL+ +       +M+GR A    
Sbjct: 215 AYWEKITGF---------TELP-IPVVANGEIWNHEQALRCITQSNTPHLMLGRGAVTRP 264

Query: 224 AMLTTVD 230
            ++  +D
Sbjct: 265 DLVAQID 271


>gi|292628574|ref|XP_001342694.3| PREDICTED: tRNA-dihydrouridine synthase 2-like [Danio rerio]
          Length = 504

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 59/251 (23%), Positives = 103/251 (41%), Gaps = 38/251 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M   + +     + I   +  E+      
Sbjct: 24  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMAQCERVENDVLQTIDFVAPDERVMFRTC 82

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK+VE+     +++N+GCP     +G  G+ L+ +P+ 
Sbjct: 83  SKESGRVVFQMGTADPERALAVAKLVEN-DVAAVDVNMGCPKEYSTKGGMGSALLSDPEK 141

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +  + K +S PVT K RI    +       NLVK I+K+GV  I +H R       
Sbjct: 142 IEAILTTLVKGISKPVTCKIRILSTIEDTV----NLVKRIEKTGVAAIAVHGRM------ 191

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL------PSVDGVMIGR 217
             KD R    +  D +  + + +  + +  NGG  D+ +  + +           VM+ R
Sbjct: 192 --KDERPRHPVHCDYIQAVAQ-SVSVPVIANGGSSDIVKEFEDIETFRESTGASSVMLAR 248

Query: 218 AAYKNSAMLTT 228
           AA  N ++   
Sbjct: 249 AAMWNPSVFRQ 259


>gi|50554001|ref|XP_504409.1| YALI0E26048p [Yarrowia lipolytica]
 gi|74633334|sp|Q6C4K3|DUS3_YARLI RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49650278|emb|CAG80010.1| YALI0E26048p [Yarrowia lipolytica]
          Length = 622

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 55/307 (17%), Positives = 100/307 (32%), Gaps = 52/307 (16%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFS----TQEKPLALQIGGADI 59
           +  YR   + L    + Y EM +   +++G K    +        T+     +Q+     
Sbjct: 259 NLPYRRLMKDL-GADVTYGEMALTLPLIQGHKAEWALTRCHSSEVTEGNHFGVQVTAPKH 317

Query: 60  SKLVEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
            + ++AA+ V +   G +EINLN GCP   V+    G+ LM         +  M      
Sbjct: 318 WQAIKAAQAVSELCTGISEINLNCGCPIDLVYRQGAGSALMDQQGKTARIVRGMSMVSGD 377

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+TVK R G      A  L    + + +       +H R         +  R     D+
Sbjct: 378 VPITVKMRTGTGSTPTAKKLT--ARLLAEGQTAAFTLHGRS--------RAQRYTKLADW 427

Query: 177 DIVYEIKKENPD-------------------LFIGLNGGLEDMSQALKILP--SVDGVMI 215
           + + E+     +                    ++  NG     S   + +    VD VM+
Sbjct: 428 NYIREVADSVVNTRDDVREKSELDDHVISHPTWVVGNGDCYTWSDWHRAVDEAHVDSVMV 487

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQ 274
            R A     +   V+       + +             +       Y   H  S    + 
Sbjct: 488 ARGALIKPWIFEEVESRQHIDKSATE----------RLEYFQKFAQYGLEHWGSDQYGVN 537

Query: 275 QITRHMI 281
           Q  R++ 
Sbjct: 538 QTRRYLC 544


>gi|150017944|ref|YP_001310198.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
 gi|149904409|gb|ABR35242.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
          Length = 321

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 63/327 (19%), Positives = 131/327 (40%), Gaps = 33/327 (10%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T+  YR  + +   N    +T  IV   + ++   +  ++L  + +   +  QI  
Sbjct: 8   MEGITEYIYRNSYEKFFGNVDKYFTPFIVPNESRSLKTKELVDVLPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  ++ ++  GY+E+NLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDAEGFINTSRKLQQLGYSEVNLNLGCPAKTVVSKNRGSGFLAKREELDSFLDEIFKMDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG   +        L+K   K  +  + IH R               PNL  
Sbjct: 128 MKISIKTRIG---KENPEEFYELIKIYNKYPLEELIIHPRTQKDFYG------NKPNL-- 176

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V+       +  +  NG +    D ++ +   P V+ VM+GR    N  ++  +    
Sbjct: 177 -CVFRDALSLSNNPVCYNGDIFTINDYNKLVADFPEVNTVMLGRGILANPGLINVIKNNI 235

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN-SRR 292
           +            + KDF  +I     +     +++  +++++  +MI +F      +++
Sbjct: 236 NTS--------KNILKDFHDEILNRYIEVFPEDIYAINRMKELFGYMIYIFSDNKEYAKK 287

Query: 293 CR--HILT--VEAGAST-ATHHIIETA 314
            R    L+   EA  S      II+ A
Sbjct: 288 VRSAQKLSDYTEAVQSLFTEQEIIKEA 314


>gi|302694715|ref|XP_003037036.1| hypothetical protein SCHCODRAFT_37482 [Schizophyllum commune H4-8]
 gi|300110733|gb|EFJ02134.1| hypothetical protein SCHCODRAFT_37482 [Schizophyllum commune H4-8]
          Length = 284

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 102/241 (42%), Gaps = 30/241 (12%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILR---------------GDKKNILGFSTQEKP-L 50
              R FA L    +L++   IV  AIL                G  ++I   S  EKP L
Sbjct: 17  LPTRLFA-LKHGASLVWGPEIVDKAILHAERVVDPDTGIISYNGKSRSIYQCSPVEKPYL 75

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG AD    V+AAK V     + I+LN GCP         GA L+  PD++   + A
Sbjct: 76  IYQIGSADPELAVQAAK-VVMHDVSGIDLNCGCPKPFSTHAGMGAALLSTPDLLCSILRA 134

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   I V+ K R+             LV  I ++G++ + +H R   ++       
Sbjct: 135 LREAMPPEIAVSCKIRLL----STQEETLALVGKIIETGISALTVHCRTRSMRDRDAAMI 190

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
            ++     +IV  +K    D+ +  NG  +    A +I  +   D VMI RAA  N +  
Sbjct: 191 ERLK----EIVDFVKASGKDIAVVENGDCKGYEDAKRIREMTGCDSVMIARAAESNPSCF 246

Query: 227 T 227
           +
Sbjct: 247 S 247


>gi|260223243|emb|CBA33610.1| tRNA-dihydrouridine synthase C [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 345

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 60/302 (19%), Positives = 113/302 (37%), Gaps = 37/302 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-------VADAILRGDKK-NILGFSTQEKPLAL 52
           M    D   R     +       +E I          A+LR   +      +    P+  
Sbjct: 29  MEGLLDFVLRDILTRVGGVEKCVSEFIRITHSLMSEKALLRTVPELEFGARTFAGVPVWP 88

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--IAA 110
           Q+ G+D   + E A  + + G   I+LN GCP+  V+    GA L+ +P+I+        
Sbjct: 89  QLLGSDAPCMAENAARLAEMGSPGIDLNFGCPAKVVNRHGGGATLLQDPEILHTIVAAVR 148

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                 IPVT K R+G +D   A+   +  ++++  G   I +HAR         K    
Sbjct: 149 AAVPAQIPVTAKMRLGYNDDSLAL---DCARALEAGGAAEIVVHART--------KAQGY 197

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +D V +++     + + +NG + ++  A   +     + +M+GR      A+  +
Sbjct: 198 RPPAYWDRVADVRGAV-QVPVVVNGEIWNVQDAQAAVSQSGCNALMLGRGIVARPALARS 256

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA------RHLHSGGKLQQ----ITR 278
           +    +   T    +    D   W+ +   M  +              G+++Q    + R
Sbjct: 257 I---LAAMGTAEGSMAQPGDDWTWQDLGPLMHAFWQVASTRLEQKQQAGRVKQWLNLLRR 313

Query: 279 HM 280
           H 
Sbjct: 314 HY 315


>gi|170759302|ref|YP_001786033.1| dihydrouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
 gi|169406291|gb|ACA54702.1| dihydrouridine synthase family protein [Clostridium botulinum A3
           str. Loch Maree]
          Length = 312

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 118/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   +  +I   + +   +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFHNIDKYFTPFIVPNKSTSLKTKELSDISPKNNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GY+EINLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFIITARKLQQLGYDEINLNLGCPAGTVVSKNRGSGFLAKREELDIFLDEIFKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D          L+K   K  +  + IH R       +       PNLD 
Sbjct: 128 MKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYGNE------PNLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++         I  NG +    D ++ +K  P V  +M+GR    N  ++  +    
Sbjct: 178 --VFKDALSLSSNPICYNGDIFTISDYNRLIKTFPKVKTIMLGRGILANPGLINEMK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 ++ I   V K+F  +I     +      ++  K++++  +MI  F
Sbjct: 233 -----NNTNIDKEVLKEFHDEILNKYIELYNEDRNALFKMKELWGYMIYTF 278


>gi|118096265|ref|XP_414079.2| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 518

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 101/254 (39%), Gaps = 46/254 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQE------- 47
           MV       R  A L     ++Y E      M+    ++    + +   +  E       
Sbjct: 46  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMMQCKRVVNEILETVDFVAPNERVVFRTC 104

Query: 48  ----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK+VE      I++N+GCP     +G  GA L+ +PD 
Sbjct: 105 ERERHRVIFQMGSADAGRALAVAKLVE-SDVAGIDINMGCPKEYSTKGGMGAALLSDPDK 163

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +  + K +  PVT K RI    +       +LVK I+K+G+  I +H RK      
Sbjct: 164 IESILTTLVKGICKPVTCKIRILPSVEDTV----DLVKRIEKTGIAAIAVHGRK------ 213

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLN----------GGLEDMSQALKILPSVDGV 213
             K+ R    +  D++  I  E   + +  N          G +E   +A     +   V
Sbjct: 214 --KEERPQHPVHCDVIKAI-SEAVSIPVIANGGSHDFIKEYGDIETFQKA----TAASSV 266

Query: 214 MIGRAAYKNSAMLT 227
           MI RAA  N ++  
Sbjct: 267 MIARAAMWNPSIFR 280


>gi|321458641|gb|EFX69706.1| hypothetical protein DAPPUDRAFT_300841 [Daphnia pulex]
          Length = 459

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 97/250 (38%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILG---------------- 42
           MV       R  A       ++YTE IV   ++R  +    ILG                
Sbjct: 15  MVRMGTLPLRLLALRY-GADIVYTEEIVDKKMVRTKRVVNEILGTVDFIDEFDGSVVFRT 73

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   +  Q+G +D    +  AK+VE       ++N+GCP     +G  GA L+  P+
Sbjct: 74  CNEESSRVVFQVGTSDAELALNVAKLVEK-DVAGFDVNMGCPKEFSIKGGMGAALLKQPE 132

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            V D +  +    SIP+T K R+            +L   I+  GV  + +H R    + 
Sbjct: 133 KVKDILTNLVSNTSIPITCKMRLLP----TIEETISLANIIQNCGVAAVAVHGRTKEERP 188

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALK--ILPSVDGVMIGR 217
             P +N  I  +          EN  + +  NGG   +E   Q L+         VMI R
Sbjct: 189 QHPNNNEAIKTIV---------ENLKIPVIANGGSKEIETYEQILRFHKATGASSVMIAR 239

Query: 218 AAYKNSAMLT 227
           AA  NS++  
Sbjct: 240 AAQYNSSVFR 249


>gi|219121503|ref|XP_002185974.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|209582823|gb|ACI65444.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 321

 Score =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 85/267 (31%), Positives = 123/267 (46%), Gaps = 46/267 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+  T+RHYR+F RL +    LYTEM+ A  I++  ++          P+ LQIGG D  
Sbjct: 62  MMGHTNRHYRYFVRLFSERTHLYTEMVPASQIVQAFRR---------APVVLQIGGGDPE 112

Query: 61  KLVEAAKIVEDFGYN-EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK------ 113
            L +AA I   +G   +INLN GCPS  V   S GA LM +P  V  C+ AM +      
Sbjct: 113 VLRQAAAIGAAYGGYVDINLNCGCPSNAVRGRSAGAALMRDPSHVAHCVEAMQEGIFEMG 172

Query: 114 ----ALSIPVTVKCRIGV--------------DDQIPAVALRNLVKSIKKSG-VNGIWIH 154
                L   VTVK R+GV              DD     + R  V +I  +G V    +H
Sbjct: 173 QGTNKLKPNVTVKHRLGVRDAATFDASADRSKDDAEAYRSCRQFVNAIALTGAVAKCHVH 232

Query: 155 ARKAILKGLSPK--DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--- 209
           AR  +L   +P    NR +P L   IV ++ ++ P +    NGG++ + +  +++     
Sbjct: 233 ARYGLLGDFTPTTIQNRNVPPLRPSIVNQLAEDFPSVEFVTNGGVKSLDEVSQVVRGGRH 292

Query: 210 ------VDGVMIGRAAYKNSAMLTTVD 230
                 V G M+GRAA  +       D
Sbjct: 293 GSGVNNVVGAMVGRAAINHPCSFAAAD 319


>gi|302818315|ref|XP_002990831.1| hypothetical protein SELMODRAFT_132390 [Selaginella moellendorffii]
 gi|300141392|gb|EFJ08104.1| hypothetical protein SELMODRAFT_132390 [Selaginella moellendorffii]
          Length = 299

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 98/247 (39%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILG---------------- 42
           MV      +R  A       L Y E IV   +L+  +   ++LG                
Sbjct: 16  MVRVGTLPFRMLAAGY-GADLTYGEEIVDHKMLKCSRVVNDVLGSIDFVENGTNDVVFRT 74

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   +  Q+G +D  + +  A+++       +++N+GCP      G  G+ L+  P+
Sbjct: 75  CKAERDHVVFQMGTSDPYRALTVAQLLC-RDIAAVDINMGCPKPFSVTGGMGSALLSQPE 133

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +V + +  + + L IPVT K R+             L + I+K+GV+ I +H R+     
Sbjct: 134 LVSEILTTLRRNLDIPVTCKIRLL----KSTQETVELARRIEKTGVSAIAVHGRRIP--- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +      +K       VM+ R A 
Sbjct: 187 -----DRPKDRAKWDGIADVVSAL-SIPVIANGDVFEPPDIPRIKAATGASSVMVARGAL 240

Query: 221 KNSAMLT 227
            N+++  
Sbjct: 241 WNASIFR 247


>gi|316974141|gb|EFV57667.1| tRNA-dihydrouridine synthase 2 [Trichinella spiralis]
          Length = 724

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 112/302 (37%), Gaps = 47/302 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILG---FSTQEKP------ 49
           MV  +   +R    L     L++TE IV   I+  R      LG   F ++         
Sbjct: 1   MVRISTLPFRLMC-LDYGADLVFTEEIVDQKIIGCRRKINEHLGTIDFCSEGDNFPRFRT 59

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                  L  QIG +D  K + AA++VE      I++N+GCP      G  GA L+   +
Sbjct: 60  SSKETNKLVFQIGTSDGEKALAAARVVEQ-DVAGIDVNMGCPKPFSLLGGMGAALLEQRE 118

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            V   +  + + +S PV+ K R+    +       +L + I++ GV  I IH R    + 
Sbjct: 119 KVRSILTMLVENISKPVSCKIRVLPSVEDTV----DLCRLIEECGVQAITIHGRTTSERA 174

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---------GLEDMSQALKILPSVDGV 213
             P  +        D + E+ +    + +  NG          +E+              
Sbjct: 175 QHPNRD--------DFIAEVARAV-RIPVICNGGSSEIRHHTDIENFRL-KCHATHA--- 221

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MI RAA  + ++  + D +       S  I   V  +   ++        +R  H   K+
Sbjct: 222 MIARAAIVSPSIFQS-DGFDDFKTVVSRYISYAVKYEECVQLVKYTIQRMSRERHDFVKI 280

Query: 274 QQ 275
            Q
Sbjct: 281 IQ 282


>gi|328871537|gb|EGG19907.1| tRNA-dihydrouridine synthase 2-like protein [Dictyostelium
           fasciculatum]
          Length = 375

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 104/245 (42%), Gaps = 31/245 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-----------MIVADAI-----LRGDKKNILGFS 44
           MV  +    R  A L     + Y+E            +V + +     +  D+  +    
Sbjct: 4   MVRVSTLPMRLLA-LRQGCDIAYSEELIDVKLSSTKRVVNEKLNTIDYISKDRAVVYRTC 62

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            Q++   LQ+G A     ++AA+ V +     I++N+GCP     +G  G+ L+  P+ +
Sbjct: 63  EQDRNNVLQLGTASSVSALKAAQHVVN-DICAIDINMGCPKFFSVQGGMGSALLSKPETI 121

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            D +  + + L +PVT K R+   DQ       +L+K I+ +GV+ I +H R+   +   
Sbjct: 122 KDILTTLIRNLPVPVTCKIRLLKTDQ----ETIDLLKIIESTGVSAIGVHMREIPERPKD 177

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P    ++  +  +  Y +        I  NG +        +L     + VMI R A +N
Sbjct: 178 PAHWDRLATILANSSYSV-------PIIANGDIYTHQDIDNVLNQTKANSVMIARGAIRN 230

Query: 223 SAMLT 227
            ++ +
Sbjct: 231 VSVFS 235


>gi|317497926|ref|ZP_07956235.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894805|gb|EFV16978.1| dihydrouridine synthase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 312

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 62/284 (21%), Positives = 112/284 (39%), Gaps = 27/284 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR     L       YT  I+ +        + +++L    +   +  QI  
Sbjct: 8   MESITIYLYRNIYEQLFGEIDKYYTPFIMPNGKRTFKTREFQDVLPEHNEGLHIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +  AK +++ GY+E+NLN+GCPS  V     G+  +  P+++ D +  + +AL 
Sbjct: 68  KSSEDFIRTAKELKELGYDEVNLNLGCPSRTVVAKQKGSGFLREPEVLDDFLTEIFEALD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG+ D         ++    +  V  + IH R               P+LD 
Sbjct: 128 MKISIKTRIGLRDT---EEFEEILSIYNRHPVYELTIHPRLQQEFYKGK------PHLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V+E    + +  +  NG +   ED        P VD VMIGR   +N A++  +   +
Sbjct: 178 --VFEYAVNHSENPLCYNGDIVTKEDYDNITTRFPDVDAVMIGRGLLRNPALVREIK--Y 233

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
              LT       R        +  +   Y +   +   K+++  
Sbjct: 234 GQKLTK------RELLKMHDTLYEAYQGYLSGDKNVLYKMKEFW 271


>gi|71003213|ref|XP_756287.1| hypothetical protein UM00140.1 [Ustilago maydis 521]
 gi|46096292|gb|EAK81525.1| hypothetical protein UM00140.1 [Ustilago maydis 521]
          Length = 364

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 60/290 (20%), Positives = 113/290 (38%), Gaps = 53/290 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----------------KNILGF- 43
           MV  +D  +R          L +T+M +A  +                     KN+  + 
Sbjct: 19  MVGQSDLAFRLQTVQ-NGATLTWTQMYLAPELSSDQYMLESLLKSLEMGSNATKNMARYR 77

Query: 44  ----STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM- 98
                 Q  P  +Q+ G ++ +LVEAA+ V  +  + I+LN+GCP     +G +GACL+ 
Sbjct: 78  ASPLHDQSAPQVVQLAGNNVQQLVEAARRVAPY-ADAIDLNLGCPQRHAEQGHYGACLLP 136

Query: 99  -LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             N  +V + ++ M +A+ +P+T K R+ V    P      L   +  +G + + +H R 
Sbjct: 137 KQNWPLVAEIVSGMVQAVDVPITTKIRLPV----PKEQTAQLAVMLAHAGSSLVTVHPR- 191

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKE-------------NPDLFIGLNGGLEDMSQAL 204
                 +    R+    D D V ++++              + D  +  NG ++     +
Sbjct: 192 -----FASSARRRKGLADLDQVVKVREALQAQGLLRSAEQPHKDTAVVSNGNVQCWQDVV 246

Query: 205 K--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
               L    GVM+G    +N A+         +      P    +  ++ 
Sbjct: 247 NNLELTGASGVMVGETLLQNPALFR---PALRDCEHARLPTAKEMAIEYL 293


>gi|313233300|emb|CBY24415.1| unnamed protein product [Oikopleura dioica]
          Length = 355

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 101/249 (40%), Gaps = 36/249 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV------ADAILRGDKKNILGFSTQEKPL---- 50
           MV       R    L     L+YTE I+             +       + ++ P+    
Sbjct: 10  MVRIGTLPTRLLC-LEEGADLVYTEEIIDHRLMDCRKFEHKNGLVEFKLTAEDNPVLQTC 68

Query: 51  -------ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                   LQ+G AD ++ V+AAK+ +D   + +++N+GCP A   +G  GA ++  PD+
Sbjct: 69  AKEKEKVILQLGTADPNRAVKAAKLCQDH-ISGVDVNMGCPKAYSTKGGMGAAMLKTPDL 127

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               + A+ + L IPVT K R     +          K ++K+G+  + IH R+   +  
Sbjct: 128 AESILKALVQELDIPVTCKIRCLKTLEETV----EFAKRMEKTGIAALAIHGRQKTERSR 183

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMS--QALKILPSVDGVMIGRA 218
           +              + E+ K    + +  NGG   ++  S     +      GV++ RA
Sbjct: 184 A-------DPCRSLWIAEVAKSL-KIPVLANGGSGEIKSRSDIDEFQEKTGTAGVLVARA 235

Query: 219 AYKNSAMLT 227
           A  N ++  
Sbjct: 236 AMWNPSVFN 244


>gi|212722480|ref|NP_001132459.1| hypothetical protein LOC100193915 [Zea mays]
 gi|194694448|gb|ACF81308.1| unknown [Zea mays]
          Length = 320

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 98/246 (39%), Gaps = 35/246 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----------------VADAILRGDKKNILGF 43
           MV      +R  A       + Y E I                   D + +G    +   
Sbjct: 12  MVRVGTLPFRLLAAEY-GADITYGEEIIDHKFLKCERVTNESLGTTDFVEKGTDSVVFRT 70

Query: 44  STQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             QE+  +  Q+G ++  + ++AA+IV     + I++N+GCP +    G  GA L+  P+
Sbjct: 71  CPQERGRVVFQMGTSNAVRALKAAQIVC-RDVSAIDINMGCPKSFSLSGGMGAALLSKPE 129

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L   VT K R+    +        L + I+K+GV  + +H RK     
Sbjct: 130 LIHDILTTLRRNLDTTVTCKIRLLNTPKDTV----ELARRIEKTGVPALAVHGRKIK--- 182

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +     +I        VM+ R A 
Sbjct: 183 -----DRPRDLAKWDEIADVVSAL-SIPVIANGDVFEYEDFKRIKDATGAASVMVARGAM 236

Query: 221 KNSAML 226
            N+++ 
Sbjct: 237 WNASIF 242


>gi|301048876|ref|ZP_07195869.1| dihydrouridine synthase [Escherichia coli MS 185-1]
 gi|300299252|gb|EFJ55637.1| dihydrouridine synthase [Escherichia coli MS 185-1]
          Length = 236

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 46/218 (21%), Positives = 90/218 (41%), Gaps = 21/218 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 30  MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 89

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 90  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMR 149

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PV+VK R+G D          +  +++++G   + +H R             +
Sbjct: 150 EAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QGYR 199

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
             ++D+  + EI++   ++ +  NG + D   A + + 
Sbjct: 200 AEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMA 236


>gi|45190676|ref|NP_984930.1| AER070Cp [Ashbya gossypii ATCC 10895]
 gi|74693589|sp|Q757E3|DUS3_ASHGO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|44983655|gb|AAS52754.1| AER070Cp [Ashbya gossypii ATCC 10895]
          Length = 647

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 63/274 (22%), Positives = 110/274 (40%), Gaps = 38/274 (13%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  +R   R L    + Y+EM +A  +++G      +      E P   +Q+  +   + 
Sbjct: 287 NLPFRRLMRQL-GADVTYSEMALAVPLIQGTNSEWALPKAHCSELPGFGVQLACSKPWQA 345

Query: 63  VEAAKIVEDF---GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIP 118
            +AA+ + D    G +EINLN GCP   ++    G+ L+ NP  +  C+ AM      +P
Sbjct: 346 AKAAEALADNVGDGLSEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDVP 405

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VK R G  D  P +AL    + + ++ V  I +H R         +  R   + D+D 
Sbjct: 406 VSVKLRTGTRDGHP-IALGLCKRLVMETDVAAITLHGRT--------RQQRYTRSADWDY 456

Query: 179 VYEIKKENPD-----------------LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           V ++                       +    NG   +     + L   +VD VM+ R A
Sbjct: 457 VGQVADALRSYETERAEKLKDREGKLRIQFVGNGDCNNWEDWYRHLENENVDSVMVARGA 516

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                +   VD      +  SS  +  + +D+ R
Sbjct: 517 LIKPWIFEEVDA--RQYIDKSSSERLEILRDYAR 548


>gi|169344007|ref|ZP_02864998.1| dihydrouridine synthase family protein [Clostridium perfringens C
           str. JGS1495]
 gi|169297915|gb|EDS80010.1| dihydrouridine synthase family protein [Clostridium perfringens C
           str. JGS1495]
          Length = 321

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 118/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +        +   +    + ++   + +++L  + +   L  QI  
Sbjct: 8   MEGITGFIYRNSYEKFFGGIDKYFAPFVVPNSSKSLKTKELRDVLPENNKGINLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  AK ++D GYNEINLN+GCPS  V     GA  + + + +   +  + K   
Sbjct: 68  NDSEGFILTAKKLKDLGYNEINLNLGCPSGTVVGKKRGAGFLAHREELDKFLEEIFKIDH 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+D    +     L+K   K  +  + IH R           N+    +  
Sbjct: 128 MKISIKTRLGMD---KSEEFYELIKIYNKYPMEELIIHPRTRQDFYG----NKPNLEVFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +  +      ++    VD +M+GR    N A++  +    
Sbjct: 181 DAISLSKN-----TVCYNGDIFTLEDHNKLVEEFKEVDKIMLGRGILANPALMNEI---- 231

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 +  +   V K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 232 ----LNNEFMDKNVLKEFHDEIFSKYREVFNEDRNAMFRMKELWGYMIYMF 278


>gi|296112348|ref|YP_003626286.1| dihydrouridine synthase [Moraxella catarrhalis RH4]
 gi|295920042|gb|ADG60393.1| dihydrouridine synthase [Moraxella catarrhalis RH4]
 gi|326561856|gb|EGE12191.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 7169]
 gi|326563291|gb|EGE13558.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 46P47B1]
 gi|326563404|gb|EGE13669.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 12P80B1]
 gi|326565945|gb|EGE16106.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 103P14B1]
 gi|326568920|gb|EGE18989.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis BC1]
 gi|326569221|gb|EGE19282.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis BC7]
 gi|326571895|gb|EGE21900.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis BC8]
 gi|326575406|gb|EGE25331.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis 101P30B1]
 gi|326576507|gb|EGE26415.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis CO72]
 gi|326577976|gb|EGE27840.1| tRNA-dihydrouridine synthase C [Moraxella catarrhalis O35E]
          Length = 323

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 89/242 (36%), Gaps = 30/242 (12%)

Query: 1   MVDWTDRHYRFFARLLTNN-----ALLYTEMIV-------ADAILRGDKK-NILGFSTQE 47
           M   TD   R     +  +         +E I        A    +   + +  G +   
Sbjct: 17  MEGLTDPLMRRVLTQIAYDLGSPYDWAVSEFIRVTHYPLPAHVFYKYVPELHTKGCTASG 76

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ +Q+ G +   +  +A +    G   I+LN GCP+  V+    G+ L+  P  +   
Sbjct: 77  TPVHVQLLGNNPETMAASALVAVSLGAKAIDLNFGCPAKTVNNHKGGSVLLEEPKTLYTI 136

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I  +  A+   IPV+ K R+G  D   +     +  ++  +  + + +HAR  +     P
Sbjct: 137 IRTVRDAIPTQIPVSAKIRLGYTDTSQSA---EIGHAVADARADWLTVHARTKVDGYKPP 193

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
               KI   +          +  L I  NG + +   A + +       +M+GR A    
Sbjct: 194 AYWEKIAPFN----------DLGLPIIANGEIWNAEHARRCIAQSQTHHLMLGRGAVTRP 243

Query: 224 AM 225
            +
Sbjct: 244 DL 245


>gi|224064274|ref|XP_002192167.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog (S.
           cerevisiae) [Taeniopygia guttata]
          Length = 490

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 61/254 (24%), Positives = 102/254 (40%), Gaps = 46/254 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++    + +   +  ++      
Sbjct: 18  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMMQCKRVINEVLETVDFVAPNDRVVFRTC 76

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK+VE      I++N+GCP     +G  GA L+ +PD 
Sbjct: 77  ERERERVVFQMGSADAERALAVAKLVE-SDVAGIDINMGCPKEYSTKGGMGAALLSDPDK 135

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +  + K +  PVT K RI    +       NLVK I+K+G+  I +H RK      
Sbjct: 136 IESILTTLVKGICKPVTCKIRILPSVEDTV----NLVKRIEKTGIAAIAVHGRK------ 185

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             K+ R    +  D++  I  E   + +  NG           +E   +A     +   V
Sbjct: 186 --KEERPQHPVHCDVIKAI-SEAVSIPVIANGGSHDFIKEYADIETFQKA----TAASSV 238

Query: 214 MIGRAAYKNSAMLT 227
           MI RAA  N ++  
Sbjct: 239 MIARAAMWNPSVFR 252


>gi|331238599|ref|XP_003331954.1| tRNA dihydrouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309310944|gb|EFP87535.1| tRNA dihydrouridine synthase [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 1548

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 70/361 (19%), Positives = 125/361 (34%), Gaps = 80/361 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--------LGFSTQ-----E 47
           MVD ++  +R  +R      L YT MI A   L  D + I        L    +     +
Sbjct: 92  MVDGSELAWRILSR-YYGAELCYTPMIHAG--LYSDDRQIKYRVEQLDLDSHEEGSEGLD 148

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG---------------YNEINLNVGCPSARVHEGS 92
           +PL +Q        L++AA +V +                  + ++LN+GCP     +G 
Sbjct: 149 RPLIVQFCANHPDTLLKAANLVINHPSSSSDFLAGNMDRLPVDAVDLNLGCPQGIAKKGK 208

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +GA LM +PD++   +           T K R     +        L++    +G   + 
Sbjct: 209 YGAFLMDHPDLITQLM-----------TAKYRRFETLEKTEQYTERLIE----AGAQMLS 253

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLE--DMSQALKILP 208
           IH R    KG      +     +++++    +        +  NG +        L    
Sbjct: 254 IHGRTREQKG------QFTGLANWEMIRGAVQRGHARGRPMLGNGNILIGSDVSELMSQT 307

Query: 209 SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
             DGVM+      N A+   ++  F        P + +V      ++     D     L 
Sbjct: 308 GADGVMVAEGNLYNPAIFAPLNPDFMARYRAGLPTRFKVA---LARVDEEYDDECLEQLG 364

Query: 269 SGGKLQQITRHMIGLFHGFPNSRR--------CRHILTVEAGASTATHHIIETAFNLMIE 320
           S   L +           FPN+ +        CR ++T  A ++   H  +   F  + E
Sbjct: 365 SLESLLE-----------FPNATKVASQYLAICRTLVTRTASSAIKGH--LYKLFRPVFE 411

Query: 321 S 321
           +
Sbjct: 412 T 412


>gi|145632062|ref|ZP_01787801.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
 gi|144982266|gb|EDJ89879.1| tRNA-dihydrouridine synthase A [Haemophilus influenzae R3021]
          Length = 152

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/141 (41%), Positives = 83/141 (58%), Gaps = 9/141 (6%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L+K  K+ G     IHARKA L GLSPK+NR+IP LDY  VY++K++ P L I +NGG++
Sbjct: 7   LLKRFKEKGSKEFIIHARKAWLSGLSPKENREIPPLDYIRVYQLKRDFPHLTIAINGGIK 66

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            + +  + L  VDGVM+GR AY+N ++L  +D+   +P   ++PI T        +   S
Sbjct: 67  TIEEMKQHLQYVDGVMVGREAYQNPSLLGQIDQALFDP---NAPIVTA------HEAVES 117

Query: 259 MTDYAARHLHSGGKLQQITRH 279
           M  Y  + L  G  L  I RH
Sbjct: 118 MLPYIEQQLSQGIHLNHIVRH 138


>gi|320536169|ref|ZP_08036218.1| dihydrouridine synthase [Treponema phagedenis F0421]
 gi|320146976|gb|EFW38543.1| dihydrouridine synthase [Treponema phagedenis F0421]
          Length = 323

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/326 (17%), Positives = 116/326 (35%), Gaps = 43/326 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-RGDKKN-ILGFSTQEKPLALQIGGAD 58
           M   T    R       +    +TEMI   +++ +G  ++  L  +   + L  Q+   D
Sbjct: 8   MAALTHAGLRLLIHQFADPDEYFTEMIHCPSLVCKGQFEDWYLHTAPAPEKLVWQLTSND 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALS- 116
                +A  IV + G   ++LN+GC + ++ +   G   M  P       +  + +A++ 
Sbjct: 68  AEYAAKAVPIVLEKGGIGVDLNMGCCAPQIVQSGAGFAWMQKPLTETAHFVRTVRQAINE 127

Query: 117 --------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                     ++VK R+ +        L + V+ +   GV  I +H R    K   P   
Sbjct: 128 YEKTQGRAFRLSVKLRLEI--TENTAFLHSFVQMLIDEGVELITLHPRTQKQKYSRP--- 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
                  ++  + + +E P + I  NG +    +  ++  S    G MIGRA  +   + 
Sbjct: 183 -----AKHEFTHRLAEEFP-IPIYGNGDINSFQKLQRMQSSYPCAGWMIGRAMIQKPWIF 236

Query: 227 TTVD--------EYFSNPLTGSSPIKTRVDKDFWRKISAS----------MTDYAARHLH 268
             +         + +   L     ++    K+FW+                  Y    L 
Sbjct: 237 AELRGEQFEKPIDLYQTALLFLEFLQQEQPKEFWKTRMQRFFALYCDNFTFAHYCKTLLL 296

Query: 269 SGGKLQQITRHMIGLFHGFPNSRRCR 294
           +   + ++ + +   F   P  R  R
Sbjct: 297 NAEDIPEVEKRLQHYFAEVPEDRFLR 322


>gi|309788022|ref|ZP_07682631.1| dihydrouridine synthase (Dus) family protein [Shigella dysenteriae
           1617]
 gi|308924156|gb|EFP69654.1| dihydrouridine synthase (Dus) family protein [Shigella dysenteriae
           1617]
          Length = 225

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 48/227 (21%), Positives = 93/227 (40%), Gaps = 32/227 (14%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAV 134
           ++LN GCPS  V+    GA L+ +P+++     AM +A+   +PV+VK R+G D      
Sbjct: 1   MDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKF 60

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               +  +++++G   + +H R             +  ++D+  + EI+++  ++ +  N
Sbjct: 61  ---EIADAVQQAGATELVVHGRTKE-------QGYRAEHIDWQAIGEIRQQL-NIPVIAN 109

Query: 195 GGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           G + D   A + +     D VMIGR A  N   L+ V +Y                +  W
Sbjct: 110 GEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNLSRVVKYNE-------------PRMPW 155

Query: 253 RKISASMTDYAARHLHSGGKLQQITR---HMIGLFHGFPNSRRCRHI 296
            ++ A +  Y          L  + R    +  L   +  +      
Sbjct: 156 PEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQH 202


>gi|88705806|ref|ZP_01103515.1| tRNA-dihydrouridine synthase C [Congregibacter litoralis KT71]
 gi|88699877|gb|EAQ96987.1| tRNA-dihydrouridine synthase C [Congregibacter litoralis KT71]
          Length = 328

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 120/323 (37%), Gaps = 42/323 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     L       TE + V+  +L     + L       G ++   P+ L
Sbjct: 14  MEGVIDHTMRDLLTQLGGVDRCVTEFVRVSQELLPPRVFHRLCPELANGGCTSSGVPVYL 73

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D S + E A    + G   ++LN GCP+  V+    G+ ++  P+ V   +AA  
Sbjct: 74  QILGGDPSVVAENASRAAELGAPGVDLNFGCPAKTVNRSDGGSIILREPERVHRIVAATR 133

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +AL  S+P++VK R+G D         ++V  I  +  + + IHAR         + +  
Sbjct: 134 QALPPSVPLSVKIRLGFDSSDR---FLDIVSGIDAARPSELVIHART--------RADGY 182

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            P   ++ +  + +    L +  NG +    D   A +       +M+GR       +  
Sbjct: 183 RPPAYWEHIA-LARSKTRLPLIANGEIWGVGDAKLAREK-SGTRDLMLGRGVLCRPDLPR 240

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA---RHLHSGGKLQQITRHMIGLF 284
            +    S            VD   W +I   +  Y A       +   +  I + +  L 
Sbjct: 241 LLRAADSG---------VEVDALTWHEIRGYLLKYLAITLESYDARYAVNPIKQWLGYLR 291

Query: 285 HGFPNSRR----CRHILTVEAGA 303
           H +P +       + IL  E   
Sbjct: 292 HYYPQAAAMFVVIKRILDPEELR 314


>gi|149247657|ref|XP_001528237.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|187471054|sp|A5DTS1|DUS3_LODEL RecName: Full=tRNA-dihydrouridine synthase 3
 gi|146448191|gb|EDK42579.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 642

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 66/320 (20%), Positives = 108/320 (33%), Gaps = 72/320 (22%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISK- 61
           +  YR   + L    + Y+EM +A  + +G +          T+     +QI  +     
Sbjct: 286 NLPYRRLMKTL-GADVTYSEMALAVPLSQGHRPEWALPKAHVTEYPGFGVQIASSKHWAA 344

Query: 62  ------LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKA 114
                 L +    V +     INLN GCP   + +   G+ L+ +P  +   + AM   +
Sbjct: 345 AKAAEALYKTTLHVSE-----INLNCGCPIDLLFKQGQGSALLDSPPRLIRIVKAMNASS 399

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
             IPVT+K R GV +         LV  + +++ V  I +H R         +  R    
Sbjct: 400 GDIPVTIKIRTGVKENKNTAVH--LVNRVLEETQVAAITLHGRS--------RQQRYTKE 449

Query: 174 LDYDIVYEI---------KKE---------NPDLFIGLNGGLEDMSQALK--ILPSVDGV 213
            D+D + E+         K+E         NP  F+G NG +              VD V
Sbjct: 450 ADWDYIEEVGKVVKTWNEKREDEDKEGRDTNPTWFVG-NGDVYSHEDWYNGVNREGVDSV 508

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+ R A     +   V+       + +              +      YA  H  S    
Sbjct: 509 MVARGALIKPWIFEEVEAQQYLDKSSTE----------RLAMLEKYAKYAVEHWGSDEY- 557

Query: 274 QQITRHMIGLFHGFPNSRRC 293
                       G  N+RR 
Sbjct: 558 ------------GVSNARRF 565


>gi|145346004|ref|XP_001417487.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144577714|gb|ABO95780.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 371

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 102/233 (43%), Gaps = 23/233 (9%)

Query: 6   DRHYRFFARLLTN--NALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKL 62
           D   R F R+     N    T+++    +      + L F+   + PL  QI G++   L
Sbjct: 22  DEACREFIRIPGALPNGADPTKLV--KNLCANYDADELRFNATARVPLGAQIMGSEPWLL 79

Query: 63  VEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CKALSIP 118
             AA+ +  +     I+LN GCP+  V     G+ L+ +P+ V  C+ A+    +     
Sbjct: 80  ELAARHLATEKSAPRIDLNCGCPANVVTGKGAGSSLLRDPEYVYACVKAVADGARGSGAH 139

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT+K R G DD      LR  + + +++G   + +HAR         +        +++ 
Sbjct: 140 VTMKLRSGYDDSSL---LRENLLAAREAGARFVSLHART--------RAQGYSGRANWEE 188

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
           +    K+  D+ +  NG +    +A ++L     DG+M+GR A ++  +   +
Sbjct: 189 IA-FAKDVLDIPVLGNGDVTSPQRAAELLRVSDADGIMLGRGAVQDPLIFRRI 240


>gi|8923374|ref|NP_060273.1| tRNA-dihydrouridine synthase 2-like [Homo sapiens]
 gi|73620832|sp|Q9NX74|DUS2L_HUMAN RecName: Full=tRNA-dihydrouridine synthase 2-like; Short=hDUS2;
           AltName: Full=Up-regulated in lung cancer protein 8;
           Short=URLC8
 gi|7020473|dbj|BAA91143.1| unnamed protein product [Homo sapiens]
 gi|16306804|gb|AAH06527.1| Dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae) [Homo
           sapiens]
 gi|71006842|dbj|BAE07219.1| up-regulated in lung cancer 8 [Homo sapiens]
 gi|119603613|gb|EAW83207.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae),
           isoform CRA_a [Homo sapiens]
 gi|119603614|gb|EAW83208.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae),
           isoform CRA_a [Homo sapiens]
 gi|119603615|gb|EAW83209.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae),
           isoform CRA_a [Homo sapiens]
 gi|158254588|dbj|BAF83267.1| unnamed protein product [Homo sapiens]
 gi|312152458|gb|ADQ32741.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           [synthetic construct]
          Length = 493

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 103/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKILSTLVKGTRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEVIKAIA-DTLSIPVIANGGSHDHIQQYSDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|114663240|ref|XP_001166638.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 1
           [Pan troglodytes]
 gi|114663242|ref|XP_001166736.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 3
           [Pan troglodytes]
 gi|114663244|ref|XP_001166768.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 4 [Pan
           troglodytes]
 gi|114663246|ref|XP_001166835.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 6
           [Pan troglodytes]
 gi|114663248|ref|XP_001166866.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 7
           [Pan troglodytes]
 gi|114663250|ref|XP_001166896.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 8
           [Pan troglodytes]
 gi|114663252|ref|XP_001166928.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 9
           [Pan troglodytes]
          Length = 493

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 103/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKILSTLVKGTHRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEVIKAIA-DTLSIPVIANGGSHDHIQQYSDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|50420831|ref|XP_458956.1| DEHA2D11286p [Debaryomyces hansenii CBS767]
 gi|74631711|sp|Q6BS64|DUS3_DEBHA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49654623|emb|CAG87117.1| DEHA2D11286p [Debaryomyces hansenii]
          Length = 622

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 63/300 (21%), Positives = 115/300 (38%), Gaps = 32/300 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +L+G            T+     +QI  +     
Sbjct: 266 NLPYRRLMKTL-GADVTYSEMALSVPLLQGTNAEWALPKAHRTEYPGYGVQIATSKHWAA 324

Query: 63  VEAAKIV--EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+ +  E    +E+NLN GCP   ++    G+ LM  P  +   +  M   +  IPV
Sbjct: 325 AKAAEAIYKEATHVSELNLNCGCPIDLLYRQGQGSALMEQPARLLRILKGMNASSGDIPV 384

Query: 120 TVKCRI-GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL---- 174
           TVK R    +++  A AL    + + ++ V  I +H R    +     D   + ++    
Sbjct: 385 TVKIRTGTKENKNTAKALVE--RILSENEVAAITLHGRSRQQRYTKEADWSYVQDVANIV 442

Query: 175 -DY----DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
            D+    +   E++   P  F+G NG +           +P VD VM+ R A     +  
Sbjct: 443 QDWNNKKEDNKELRDTQPTCFVG-NGDVYTHEDWYNAVNIPGVDSVMVARGALIKPWIFE 501

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            V+       + +  +          ++      +A  H  S      + R  +  F GF
Sbjct: 502 EVEAQQYLDKSSTERL----------EMIGQYAKFAIEHWGSDEYGVGLARRFMCEFLGF 551


>gi|241950946|ref|XP_002418195.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223641534|emb|CAX43495.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 613

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/307 (19%), Positives = 110/307 (35%), Gaps = 46/307 (14%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +++G      +      E P   +QI  +     
Sbjct: 257 NLPYRRLMKTL-GADVTYSEMALSVPLIQGHNPEWALPKAHISEYPGFGVQIASSKHWAA 315

Query: 63  VEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+ +       +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPV
Sbjct: 316 AKAAEAIYRNTTHVSELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPV 375

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G+ +        NLV  +   G    I +H R         +  R     D++ 
Sbjct: 376 TVKIRTGIKEGKNTAV--NLVSRVLDEGNAAAITLHGRS--------RQQRYSKEADWNY 425

Query: 179 VYEI----------------KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           + E+                 ++   ++   NG +       K +    +D VM+ R A 
Sbjct: 426 IAEVGTVVKNWNEQQKEDKEARDRDPVYFVGNGDVYSHEDWYKHVNTEGIDSVMVARGAL 485

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               +   V+       + S  +           I      YA  H  S      ++R  
Sbjct: 486 IKPWIFEEVEAQQYLDKSASERL----------DILGKFAKYAIEHWGSDEYGVGLSRRF 535

Query: 281 IGLFHGF 287
           +  F  F
Sbjct: 536 MCEFLSF 542


>gi|73957464|ref|XP_546866.2| PREDICTED: similar to dihydrouridine synthase 2-like (SMM1, S.
           cerevisiae) [Canis familiaris]
          Length = 560

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 62/289 (21%), Positives = 112/289 (38%), Gaps = 56/289 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++      +   +  E+      
Sbjct: 86  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMLQCKRVVNEVLSTVDFVAPDERVVFRTC 144

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  AK+VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 145 EREQSRVVFQMGTSDADRALAVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 203

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K +  PVT K RI    +       +LVK I+++G+  + +H RK      
Sbjct: 204 IEKILSTLVKGIRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAVTVHGRK------ 253

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  + +  I  E   + +  NG           +ED  QA     +   V
Sbjct: 254 --REERPQHPVSCEAIKAIA-ETVSIPVIANGGSHDHIQKYLDIEDFRQA----TAASSV 306

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           M+ RAA  N ++             G  P++  V + + R        Y
Sbjct: 307 MVARAAMWNPSIFLK---------EGLRPLE-EVMQKYIRYAVQYENHY 345


>gi|226322662|ref|ZP_03798180.1| hypothetical protein COPCOM_00434 [Coprococcus comes ATCC 27758]
 gi|225208999|gb|EEG91353.1| hypothetical protein COPCOM_00434 [Coprococcus comes ATCC 27758]
          Length = 311

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 56/301 (18%), Positives = 105/301 (34%), Gaps = 32/301 (10%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  +          +T  +  +      R +   IL  + +      QI  
Sbjct: 8   MEGITGEVYRRAYHTFFEPMDKYFTPFLNPNPKGKFSRQEWNEILPENNEGMYTVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +  A+ +++FGY E+NLN+GCPS  V     G+  +  PD +   +A +   L 
Sbjct: 68  NRAEDFIRLARQLKEFGYEEVNLNLGCPSKTVVNRKRGSGFLFYPDELNHFLAEVFDQLD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R G  DQ        L+    +  +  + +H R       +  D         
Sbjct: 128 MKISIKTRSGKYDQ---EEFEELLDIYNQYPLEELILHPRVQQDYYKNKPDW-------- 176

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            I +     N    +  NG +   ED     +  P  + +M+GR    N  +   +    
Sbjct: 177 -ITFAYACRNSINPLVYNGDIFCAEDYKIFQEKFPEAECIMLGRGILMNPFLPAVIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRR 292
                G S   T+    F   +  +  + +    ++  K++++           F NS  
Sbjct: 233 -----GKSTFDTKKIATFCDHLLDAYIEKSPEEKNAVVKMKELW----WYLGKNFKNSEE 283

Query: 293 C 293
            
Sbjct: 284 Y 284


>gi|325116870|emb|CBZ52423.1| dihydrouridine synthase domain-containing protein [Neospora caninum
           Liverpool]
          Length = 568

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 93/239 (38%), Gaps = 36/239 (15%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G     L+ AA++VED   + ++LN GCP      G +GA L+   +++ D ++ + K 
Sbjct: 174 AGDSPETLLAAAQLVEDE-VDAVDLNFGCPQGIARRGHYGAFLLHESELLIDIVSTLHKH 232

Query: 115 LSIPVTVKCRI----------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           L  PVT K R                  +D++        L  + + +G   + IH R  
Sbjct: 233 LRTPVTCKMRKVSPRPTAALPRSTTALVLDEERRLQDTLRLCDAFEAAGCACLCIHGRTK 292

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
             K         +   D+  +    KE   + +  NGG+E    AL+ L     D VM  
Sbjct: 293 EEK------ASLVGPCDWLAIRH-AKERLSIPVIANGGVETYEDALRCLEFTGADAVMSA 345

Query: 217 RAAYKNSAMLT-------TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
                N  +         +V    S  L   SP+ +   +D  R+    ++  A RHLH
Sbjct: 346 EGLLDNPLLFAPSRFAAPSVYALLSPSLFALSPLLSSSWRDHLRR---RLSLPARRHLH 401



 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN 39
          MVD ++  +R   R      L YT M+ +   +   K  
Sbjct: 46 MVDASELAFRLLGRRY-GVDLAYTPMMHSRLFVDDPKYR 83


>gi|296231397|ref|XP_002761126.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 1
           [Callithrix jacchus]
 gi|296231399|ref|XP_002761127.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 2
           [Callithrix jacchus]
          Length = 493

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 103/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKILSTLVKGTHRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEVIKAIA-DTLSIPVIANGGSHDHIQRYSDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|156537077|ref|XP_001602214.1| PREDICTED: similar to tRNA-dihydrouridine synthase [Nasonia
           vitripennis]
          Length = 505

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 101/252 (40%), Gaps = 38/252 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--------NILGFST------- 45
           MV       R  A       ++YTE ++   +LR  ++        + +  +        
Sbjct: 64  MVRIGTLPMRLLALEY-GADIVYTEELIDWKLLRSVRRVNEVLGTVDYIDRTDGTIVFRT 122

Query: 46  ---QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   + LQ+G  D ++ ++ AK+VE      I++N+GCP      G  GA L+  P+
Sbjct: 123 SPIERDRVVLQLGTCDANRALKVAKLVEQ-DVAGIDVNMGCPKRFSILGGMGAALLKQPE 181

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              + +  +   LSIPVT K R+  + +        LV ++  +G++ I +H R      
Sbjct: 182 KASEILRTLVGGLSIPVTCKIRVLGNVEDT----LKLVDTLVDTGISAITVHGRT----- 232

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGR 217
               D R       + +  + +    + +  NGG +++ +   I           VMI R
Sbjct: 233 ---VDERPQHPNRSEFIKRVAEHA-KIPVIANGGSKEIEKRADIFKFKKETGCSSVMIAR 288

Query: 218 AAYKNSAMLTTV 229
           AA  N ++    
Sbjct: 289 AAEWNCSIFREA 300


>gi|90083447|dbj|BAE90806.1| unnamed protein product [Macaca fascicularis]
          Length = 493

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 104/253 (41%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K +  PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKILSTLVKGIRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEVIKAIA-DTLSIPVIANGGSHDHIQRYSDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|332251618|ref|XP_003274943.1| PREDICTED: tRNA-dihydrouridine synthase 1 [Nomascus leucogenys]
          Length = 438

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 52/283 (18%), Positives = 93/283 (32%), Gaps = 70/283 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCEVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D              
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQDEWD-------------- 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                                     +++  +  + +H R    KG             +
Sbjct: 128 -------------------------LLQRMILLLLTVHGRTKEQKG------PLSGAASW 156

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  ++K    + +  NG ++ +    + L    V GVM       N A+         
Sbjct: 157 EHIKAVRKAV-AIPVFANGNIQCLQDVERCLQDTGVQGVMSAEGNLHNPALF-------- 207

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
               G SP    + +++   +        Y   HL    KL  
Sbjct: 208 ---EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 244


>gi|313212119|emb|CBY16141.1| unnamed protein product [Oikopleura dioica]
          Length = 250

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 101/249 (40%), Gaps = 36/249 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV------ADAILRGDKKNILGFSTQEKPL---- 50
           MV       R    L     L+YTE I+             +       + ++ P+    
Sbjct: 10  MVRIGTLPTRLLC-LEEGADLVYTEEIIDHRLMDCRKFEHKNGLVEFKLTAEDNPVLQTC 68

Query: 51  -------ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                   LQ+G AD ++ V+AAK+ +D   + +++N+GCP A   +G  GA ++  PD+
Sbjct: 69  AKEKEKVILQLGTADPNRAVKAAKLCQDH-ISGVDVNMGCPKAYSTKGGMGAAMLKTPDL 127

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               + A+ + L IPVT K R     +          K ++K+G+  + IH R+   +  
Sbjct: 128 AESILKALVQELDIPVTCKIRCLKTLEETV----EFAKRMEKTGIAALAIHGRQKTERSR 183

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQA--LKILPSVDGVMIGRA 218
           +              + E+ K    + +  NGG   ++  S     +      GV++ RA
Sbjct: 184 A-------DPCRSLWIAEVAKSL-KIPVLANGGSGEIKSRSDIGQFQEKTGTAGVLVARA 235

Query: 219 AYKNSAMLT 227
           A  N ++  
Sbjct: 236 AMWNPSVFN 244


>gi|195166832|ref|XP_002024238.1| GL14922 [Drosophila persimilis]
 gi|198468810|ref|XP_002134128.1| GA26573 [Drosophila pseudoobscura pseudoobscura]
 gi|194107611|gb|EDW29654.1| GL14922 [Drosophila persimilis]
 gi|198146581|gb|EDY72755.1| GA26573 [Drosophila pseudoobscura pseudoobscura]
          Length = 463

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 64/299 (21%), Positives = 116/299 (38%), Gaps = 39/299 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A  +    ++YTE +V   +++  +++                     
Sbjct: 21  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLIKSIRRHNPALGTVDFVDPSDGTVVFRT 79

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   L LQ+G +D ++ +   K+++    + +++N+GCP     +G  GA L+ +PD
Sbjct: 80  CALETSRLVLQMGTSDATRALAVGKLLQQ-DISGLDINMGCPKEFSIKGGMGAALLADPD 138

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IPVT K RI  D          LV+ +  +G+  I IHAR      
Sbjct: 139 KAALILRTLCSNLDIPVTCKIRILPDLDDTIS----LVQKLADTGIAAIGIHART----- 189

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              +D R       D++  + K    + I  NGG  ++ +   IL        D VM+ R
Sbjct: 190 ---RDERPQHPPHPDVLRAVAKAV-SIPIIANGGSRNVQKYEDILKFQLECGADSVMVAR 245

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           AA  N ++    D            ++  VD D     +        + L    + ++ 
Sbjct: 246 AAQINVSIFRR-DGLLPMDELIERYLRLCVDYDNAPHNAKYCVQNMLKELQETPRGKRF 303


>gi|157818491|ref|NP_001099651.1| tRNA-dihydrouridine synthase 2-like [Rattus norvegicus]
 gi|149038072|gb|EDL92432.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           (predicted), isoform CRA_a [Rattus norvegicus]
 gi|165971659|gb|AAI58729.1| Dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           [Rattus norvegicus]
          Length = 493

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 103/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMLQCRRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQSRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       NLVK I+++G++ I +H R       
Sbjct: 137 IEKILSTLVKGTHRPVTCKIRILPSLEDT----LNLVKRIERTGISAIAVHGRN------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             +D R    +  +++  I  E   + +  NG           +ED  QA     +   V
Sbjct: 187 --RDERPQHPVSCEVIRAIA-ETLSIPVIANGGSHDHIQQHLDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|262375633|ref|ZP_06068865.1| tRNA-dihydrouridine synthase C [Acinetobacter lwoffii SH145]
 gi|262309236|gb|EEY90367.1| tRNA-dihydrouridine synthase C [Acinetobacter lwoffii SH145]
          Length = 311

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 58/249 (23%), Positives = 104/249 (41%), Gaps = 24/249 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNIL--GFSTQEKPLAL 52
           M   TD   R     + +     TE I V D++L           +L  G +    P+ +
Sbjct: 8   MEGLTDPIMRDVLTSVGSFDWCVTEFIRVTDSLLPDHIYHTYCPELLNDGKTAAGTPVHV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q  G +   L   A  V   G   I++N GCP+  V+    G+ L+  P++V + + A+ 
Sbjct: 68  QFLGNNPEMLAANAAKVAAMGAPAIDMNFGCPAKTVNRHRGGSVLLDEPEVVHELVKAVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   IPV+ K R+G  D+     +     +I+ +G + + +HAR         K +  
Sbjct: 128 DAVPAHIPVSAKMRLGYMDRN---FMLENAHAIEDAGASWVTVHART--------KADGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +D +  I +E   + +  NG + + + A +       + +MIGR A     +   
Sbjct: 177 TPPAFWDQLQPI-REALKINVIANGEIWNNADAKQCRLESGCEDLMIGRGAVTTPDLTQC 235

Query: 229 VDEYFSNPL 237
           + +    PL
Sbjct: 236 IRQNSDAPL 244


>gi|110625595|ref|NP_079794.1| tRNA-dihydrouridine synthase 2-like [Mus musculus]
 gi|73620836|sp|Q9D7B1|DUS2L_MOUSE RecName: Full=tRNA-dihydrouridine synthase 2-like
 gi|12844161|dbj|BAB26260.1| unnamed protein product [Mus musculus]
 gi|109733553|gb|AAI16937.1| Dihydrouridine synthase 2-like (SMM1, S. cerevisiae) [Mus musculus]
 gi|109733887|gb|AAI16935.1| Dihydrouridine synthase 2-like (SMM1, S. cerevisiae) [Mus musculus]
 gi|148679394|gb|EDL11341.1| mCG20459, isoform CRA_b [Mus musculus]
          Length = 493

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 103/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMLQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQSRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       NLVK I+++G++ I +H R       
Sbjct: 137 IEKILSTLVKGTHRPVTCKIRILPSLEDT----LNLVKRIERTGISAIAVHGRN------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             +D R    +  +++  I  E   + +  NG           +ED  QA     +   V
Sbjct: 187 --RDERPQHPVSCEVIRAIA-ETLSIPVIANGGSHDHIQQHVDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|50303455|ref|XP_451669.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|74637047|sp|Q6CWM0|DUS3_KLULA RecName: Full=tRNA-dihydrouridine synthase 3
 gi|49640801|emb|CAH02062.1| KLLA0B03069p [Kluyveromyces lactis]
          Length = 665

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 66/298 (22%), Positives = 110/298 (36%), Gaps = 45/298 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +      E P   +QI  +   + 
Sbjct: 309 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHCSEFPGFGVQIACSKTWQA 367

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ +     G +EINLN GCP   ++    G+ L+ NP  +  C+  M      IPV
Sbjct: 368 AKAAEALAANVTGVSEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNGMNYVSNDIPV 427

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G  +  P +AL    + + ++ V  I +H R         +  R   + D+D V
Sbjct: 428 TVKIRTGTREGHP-IALSITKRLVLETDVAAITLHGRT--------RQQRYTKSADWDYV 478

Query: 180 YEIKKENP----------------DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
            E+                      +    NG   +     K L   ++D VM+ R A  
Sbjct: 479 GEVANAVRTYEAERQENKNLRDGQKIQFVGNGDCNNWEDWYKHLENKNMDSVMVARGALI 538

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQITR 278
              +   VD       +    +          +I      +A  H  +    + Q  R
Sbjct: 539 KPWIFEEVDAQQYMDKSSKERL----------EILKDYCKFAMDHWGTDQYGISQCRR 586


>gi|168056695|ref|XP_001780354.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162668196|gb|EDQ54808.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 332

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 56/300 (18%), Positives = 117/300 (39%), Gaps = 55/300 (18%)

Query: 1   MVDWTDRHYRFFA----------RLLTNNALLYTEMIVADAI-----LRGDKKNIL--GF 43
           MV      +R  A            + ++ +L  E +  +A+     +    K+I+    
Sbjct: 12  MVRVGGLPFRMLAAGYGADITYGEEIVDHKMLCCERVENEALGTVDFVDKKSKDIIFRTC 71

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             ++  +  Q+G AD  + ++ A +V        ++N+GCP +    G  G+ L+  P++
Sbjct: 72  DAEKHRVVFQVGTADAVRCLKVANMVAGDIAA-FDVNMGCPKSFSTSGGMGSALLDKPEL 130

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + D +  + + L+IPVT K R+             L + I+K+GV+ + +H R+      
Sbjct: 131 IHDILTTLRRNLNIPVTCKVRLL----KTCGETVELSRRIEKTGVSALAVHGRR------ 180

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYK 221
               +R     ++D + E+      + +  NG + D S   ++        VM+ R A  
Sbjct: 181 --VADRPRDPANWDGIREVVSAL-SIPVIANGDVFDYSDFQRMKDATGASSVMVARGAVW 237

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           N+++                         +W  +    T+Y  R +     +   T+H +
Sbjct: 238 NASVFR------------------PEGMLYWEDV---KTEYVKRCIEWDNNV-HWTKHTL 275


>gi|76156585|gb|AAX27767.2| SJCHGC04037 protein [Schistosoma japonicum]
          Length = 181

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 45/167 (26%), Positives = 78/167 (46%), Gaps = 8/167 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R      L +T MI + + L   K     L F+++++P+ +Q     
Sbjct: 17  MVDGSELAWRMLGRKY-GVQLTFTPMINSTSFLVNKKYRHSCLQFASEDRPIIVQFCANS 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               ++ AK+V+ F  + ++LN+GCP     +G +GA L    D +   I+     LS+P
Sbjct: 76  PDTFIKCAKLVQPF-CDAVDLNLGCPQGIAKKGHYGAFLQDEWDCLKHIISRASSELSVP 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           VT K RI  D            K ++ +G + + +H R   +KG   
Sbjct: 135 VTCKIRIFSDVDRTV----QYAKLLEAAGASMLTVHGRTREMKGQKT 177


>gi|217970411|ref|YP_002355645.1| dihydrouridine synthase [Thauera sp. MZ1T]
 gi|217507738|gb|ACK54749.1| dihydrouridine synthase DuS [Thauera sp. MZ1T]
          Length = 336

 Score =  142 bits (359), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 110/295 (37%), Gaps = 34/295 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-RGDKKNILG------FSTQEKPLAL 52
           M    D   R     +    L  +E + V+  +L R   + I         +    P+A+
Sbjct: 8   MEGVADFVLRDVLTAIGGYDLAVSEFVRVSGTLLPRRMFERICPEILAGSRTAAGTPVAV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--IAA 110
           Q+ G+D   L E A  +     + I+LN GCP+  V+    GA L+  P ++ D      
Sbjct: 68  QLLGSDPVLLAENAARLAALSPHGIDLNFGCPAKVVNRHGGGAMLLDRPRLLHDIAAAVR 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                +IPV+ K R+G+ D   A+   +  +++   G   I +HAR         ++   
Sbjct: 128 AAVPAAIPVSAKMRLGIADPSRAL---DCAQALADGGAQAIVVHART--------REQGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
                ++ V  I  +   + +  NG +  +    +     + + VMIGR A  +  +   
Sbjct: 177 RAPAHWEWVARI-GDAVRVPVTANGEVWSVRDWARCREVSAAEDVMIGRGAVSDPWLARR 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +         G+ P     D+  W ++   +  Y          +    R  + L
Sbjct: 236 IR-----GERGTEP-----DERDWVELHPHLLRYWEGVQGRAAPVHACGRLKLWL 280


>gi|168053249|ref|XP_001779050.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162669612|gb|EDQ56196.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 336

 Score =  142 bits (359), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 57/303 (18%), Positives = 114/303 (37%), Gaps = 49/303 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-----------------GDKKNILGF 43
           MV      +R  A       + Y E IV   ++R                    + +   
Sbjct: 16  MVRVGGLPFRMLAAEY-GADITYGEEIVDHKMVRCARVVNEDLGTVDFVEKSSNEVVFRT 74

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  +  Q+G ++  + ++AA +V        ++N+GCP +    G  G+ L+  PD
Sbjct: 75  CDEEKHRVVFQVGTSEAVRCLKAANLVAGDIAA-FDVNMGCPKSFSTSGGMGSALLSKPD 133

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +  + + L+IPVT K R+             L + I+K+GV+ + +H R+   + 
Sbjct: 134 VIHDILTTLKRNLNIPVTCKIRLL----KTYGETVELARRIEKTGVSALAVHGRRVPDRP 189

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAY 220
             P          +D + E+      + +  NG + + S   +I        VM+ R A 
Sbjct: 190 RDPAQ--------WDGIQEVVSAL-SIPVIANGDVFEYSDFQRIKDATGAASVMVARGAM 240

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
            N ++                P      +D  R+      ++      +   L+++ ++ 
Sbjct: 241 WNVSVFR--------------PEGKHFWEDVKREYVRKCIEWDNDVRWTKHTLKEMIQYH 286

Query: 281 IGL 283
             L
Sbjct: 287 SCL 289


>gi|323484713|ref|ZP_08090072.1| dihydrouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401950|gb|EGA94289.1| dihydrouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 325

 Score =  142 bits (359), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 60/299 (20%), Positives = 106/299 (35%), Gaps = 32/299 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR    R        +T  +       +   +K +IL        L  QI  
Sbjct: 8   MEGITGYVYRNAHHRFFPGADQYFTPFLSPAQNHKLSSREKNDILPGHNAGISLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 + AAK +  +GY E+NLN+GCPSA V   + GA  +  P+ +   +  +   L 
Sbjct: 68  NKAEDFIWAAKELSSYGYREVNLNLGCPSATVTAKNKGAGFLSVPNELDRFLEQVFSGLE 127

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              + V+VK R G++          L+K   +  +  + IH R          D      
Sbjct: 128 TEAVQVSVKTRTGMESHD---EFEELLKIYNRYPLKELIIHPRVR-------SDFYANKP 177

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--------ILPSVDGVMIGRAAYKNSAM 225
                   ++  N    +  NG +    +  +          P +  +M+GR A  N  +
Sbjct: 178 EREVFCRGVRGSNN--PVCYNGDIFTKEECARFRSDFPEDEFPMLKSIMLGRGAVANPWL 235

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              V       +   S       + F  +I     +  +   ++  K++++  +M GLF
Sbjct: 236 FAEVK-----GIKERSKPDKATLRAFHDQIFYGYQEIMSGDRNTLFKMKELWFYMAGLF 289


>gi|254579020|ref|XP_002495496.1| ZYRO0B12716p [Zygosaccharomyces rouxii]
 gi|238938386|emb|CAR26563.1| ZYRO0B12716p [Zygosaccharomyces rouxii]
          Length = 645

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 61/278 (21%), Positives = 105/278 (37%), Gaps = 36/278 (12%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +      E P   +QI  +   + 
Sbjct: 292 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHVSEYPGFGVQIACSKAWQA 350

Query: 63  VEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
            +A + +        E+NLN GCP   ++    G+ L+ NP  +  C+ AM      IPV
Sbjct: 351 AKATEALAAHTSQVSEVNLNCGCPIDLLYRQGSGSALLDNPARMIRCLNAMSYVSGEIPV 410

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R G  D  P   L    + + ++ V  + +H R         +  R   N D+D V
Sbjct: 411 SVKIRTGTKDGHPVAGLLAR-RLVNETDVAAMTLHGRS--------RAQRYTKNADWDYV 461

Query: 180 YEIKKENPD---------------LFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYK 221
             + +E                  +    NG + +       +    ++D VM+ R A  
Sbjct: 462 VRVAEELRSCEDEYDREGRQRSQRIQFVGNGDVNNFEDWYAHVNRSDAIDSVMVARGALI 521

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
              +   VD      L  SS  +  + KD+ +      
Sbjct: 522 KPWIFEEVDA--QQHLDKSSTERMDILKDYIQFALEHW 557


>gi|219128482|ref|XP_002184441.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217404242|gb|EEC44190.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 323

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 119/314 (37%), Gaps = 30/314 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE----------- 47
           MV  +D  +R   R      L YT+MI A  +L  +   K+ L                 
Sbjct: 4   MVGASDFAFRCLCRQ-HGVDLTYTQMIHAKNLLGDNTFSKSHLDMHEHRSLPPELKPFTN 62

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG---YNEINLNVGCPSARVHEGSFGACLM-LNPDI 103
            PL +Q+ G  +  ++ AA+ V D      +  +LN GCP     +G +GA LM  + D+
Sbjct: 63  GPLMVQLAGNSVDMVLRAAQYVLDQTDGKVDGFDLNCGCPQGIARKGRYGAFLMEEDTDL 122

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAIL 160
           V   ++A+ + L  +I V+ K R+ V D++    +  L+ + +    ++G  +H  K  +
Sbjct: 123 VCRILSALRQELPANIAVSAKIRLPVTDEMLVARMPKLLDTGVDFMTIHGRTLHENKTKV 182

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRA 218
           +G+     R         +  + K+ P   I  NGG+E M     L+       VM   +
Sbjct: 183 RGVHTDRIRL-------AIETVHKQRPGFPIVANGGVEHMPDVANLQARTGAVAVMSSES 235

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
             +   + +      +        I    D   W ++   +   A            + +
Sbjct: 236 LLEFPNIFSIDTRKLTPRQILEQQIGFARDYLGWCRVYPPLPGVAGNGGSFNAIKGHLYK 295

Query: 279 HMIGLFHGFPNSRR 292
            +      FP  R 
Sbjct: 296 FLHRYLQEFPELRD 309


>gi|221501948|gb|EEE27699.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii VEG]
          Length = 653

 Score =  142 bits (358), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 92/248 (37%), Gaps = 37/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG------DKKNILGFSTQEK------ 48
           MV      +R          L+YTE  +   +L        D   I      EK      
Sbjct: 261 MVRIGILPFRLECLKY-GADLVYTEETIDHKLLNSVRTFNEDFSTIDFLHKSEKTCVFST 319

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                  + +Q+G +D ++ ++AA +V       +++N+GCP +    G  GA L+  P 
Sbjct: 320 CLEERGKVVMQLGTSDATRALKAAMLVAQ-DVAAVDVNMGCPKSFSINGGMGAALLKTPL 378

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           I  D +  + + L IPVT K R+            +  +  +  G+  I IHAR+     
Sbjct: 379 IATDILKTLRRNLDIPVTCKIRLL----DTIHKTIDFARLCENCGIEAIAIHARET---- 430

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
                 R      +D+   +K     + +  NG      D     + +   D +M  R A
Sbjct: 431 ----HERPSHRAHWDLFPALKSSL-AIPLIANGDFLTRRDADVFQEKI-GADSLMFARGA 484

Query: 220 YKNSAMLT 227
             + ++ +
Sbjct: 485 MWDPSIFS 492


>gi|19115484|ref|NP_594572.1| tRNA dihydrouridine synthase Dus3 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74638894|sp|Q9UTH9|DUS3_SCHPO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|6013094|emb|CAB57402.1| tRNA dihydrouridine synthase Dus3 (predicted) [Schizosaccharomyces
           pombe]
          Length = 617

 Score =  141 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 57/276 (20%), Positives = 102/276 (36%), Gaps = 56/276 (20%)

Query: 2   VDWTDR------------HYRFFARLLTNNALLYTEMIVA----------DAILRG-DKK 38
           +DW DR             +R     L  +   Y+EM +            A++RG + +
Sbjct: 235 IDWRDRKILAPLTTVGNPPFRRLCGSLGADT-FYSEMAMCYPLMQGHQPEWALVRGLNYE 293

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGAC 96
             +    +   L +Q+    + +  + A+++ +   G + ++LN GCP   V     G+ 
Sbjct: 294 REMMRGGRRGILGVQLATGKLWQATKTAQVIAEQCDGVDFLDLNCGCPIDLVFRQGAGSS 353

Query: 97  LMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           L+ NP  +   +  M  A+S  IPVTVK R+G  D  P V    + +   ++  +   +H
Sbjct: 354 LLENPGRLLRNLQGM-DAVSGQIPVTVKLRMGNKDDHPVVKNL-IGRIFNETNTSAATLH 411

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-----------------LFIGLNGGL 197
            R         +  R   N ++D + EI  +                    L +  NG  
Sbjct: 412 GRS--------RQQRYSKNANWDYIGEIASKVKSMNERIDELPEDSLRTQPLSLIGNGDC 463

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEY 232
                    +   VD VMI R A     +   ++  
Sbjct: 464 YSWQDWYDGVNKGVDTVMIARGALVKPWIFEEIEAR 499


>gi|237808200|ref|YP_002892640.1| dihydrouridine synthase DuS [Tolumonas auensis DSM 9187]
 gi|237500461|gb|ACQ93054.1| dihydrouridine synthase DuS [Tolumonas auensis DSM 9187]
          Length = 327

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 97/237 (40%), Gaps = 23/237 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNIL--GFSTQEKPLAL 52
           M    D   R     + +  L  TE +      +    L      +L  G +T   P+ +
Sbjct: 20  MEGVLDSLLREILTAVNHYDLCVTEFVRVVDQLLTRKTLYRLCPELLHGGKTTSGTPVRV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A +  + G   I++N GCP+ RV+    GA L+  P+ +   +  + 
Sbjct: 80  QLLGQHPQWLAENAVLATELGSPGIDINFGCPARRVNNSCGGAALLKEPESIYRILRTVR 139

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            AL     ++ K R+G            ++ ++ + G   + IHAR          D  K
Sbjct: 140 DALPAEQLLSAKVRLGW---SSPDECHEIIDAVIQGGAGELAIHARTKE-------DGYK 189

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAM 225
              + ++ +  ++ +  ++ +  NG + + + A++   +   + +M+GR A +   +
Sbjct: 190 ADAIKWEWINTLRPKI-NIPLIANGEIWNAADAMRCRQITGCNDLMVGRGALQLPNL 245


>gi|323691781|ref|ZP_08106038.1| dihydrouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323504147|gb|EGB19952.1| dihydrouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 325

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 60/299 (20%), Positives = 106/299 (35%), Gaps = 32/299 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR    R        +T  +       +   +K +IL        L  QI  
Sbjct: 8   MEGITGYVYRNAHHRFFPGADQYFTPFLSPAQNHKLSSREKNDILPGHNAGISLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 + AAK +  +GY E+NLN+GCPSA V   + GA  +  P+ +   +  +   L 
Sbjct: 68  NKAEDFIWAAKELSSYGYREVNLNLGCPSATVTAKNKGAGFLSVPNELDRFLEQVFSGLE 127

Query: 117 ---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
              + V+VK R G++          L+K   +  +  + IH R          D      
Sbjct: 128 TEAVQVSVKTRTGMESHD---EFVELLKIYNRYPLKELIIHPRVR-------SDFYANKP 177

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--------ILPSVDGVMIGRAAYKNSAM 225
                   ++  N    +  NG +    +  +          P +  +M+GR A  N  +
Sbjct: 178 EREVFCRGVRGSNN--PVCYNGDIFTKEECARFRSDFPEDEFPMLKSIMLGRGAVANPWL 235

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              V       +   S       + F  +I     +  +   ++  K++++  +M GLF
Sbjct: 236 FAEVK-----GIKERSKPDKATLRAFHDQIFYGYQEIMSGDRNTLFKMKELWFYMAGLF 289


>gi|46107564|ref|XP_380841.1| hypothetical protein FG00665.1 [Gibberella zeae PH-1]
          Length = 767

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/306 (18%), Positives = 101/306 (33%), Gaps = 60/306 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE-KP------------- 49
           +  +R     L    L Y+EM+++  +++G      ++     E  P             
Sbjct: 368 NLPFRRLCVEL-GAQLTYSEMVLSMPLIQGTKADWTLVKAHESEITPPKFNPGSVPIFDN 426

Query: 50  --------LALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLML 99
                      QI G +   + +AA ++  F  +   I+LN GCP   V +   G+ L+ 
Sbjct: 427 YNHSKDIKFGAQISGNNHWVVTKAADVLNRFCPHLRLIDLNCGCPIDMVFKSGGGSALLE 486

Query: 100 NPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA---------LRNLVKSIKKSGVN 149
           N   +   I  M      +P+T K R G+ +  P             R   + +   G  
Sbjct: 487 NSGKLERMIRGMNAVSGEVPITAKIRTGIRNSRPTATQLIGKLAFGAREHRERLGAPGCA 546

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN------PDLF 190
            + +H R    +     D   I                  D + E    +        ++
Sbjct: 547 ALTLHGRSREQRYTKKADWGYISECAALIKTYNKEKDSLTDTIAEPDASSLPNAKDGRMY 606

Query: 191 IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG      +  + +    VD VMIGR A     +   +++     L  SS  + R  
Sbjct: 607 FLGNGDCYSHVEYYEHIEKARVDTVMIGRGALIKPWLFEEIEK--GQYLDKSSSERLRYI 664

Query: 249 KDFWRK 254
           + F R 
Sbjct: 665 EKFVRY 670


>gi|296418297|ref|XP_002838778.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295634739|emb|CAZ82969.1| unnamed protein product [Tuber melanosporum]
          Length = 689

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 56/284 (19%), Positives = 96/284 (33%), Gaps = 51/284 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  +R     L   AL Y+EM ++  +L+G K    +L     E P    QI G  I   
Sbjct: 334 NLPFRRLCSRL-GAALTYSEMAMSVPLLQGHKPEWALLRAHASEIPNFGAQICGTKIGTA 392

Query: 63  VEAAKIV---------EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A +++            G + ++LN GCP   V+    G+ L+  P  +   +  M  
Sbjct: 393 VRATEVLTTLFPSAASSRHGLSLVDLNCGCPVDLVYRQGGGSALLDQPSKLIKMLKGMNY 452

Query: 114 ALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
                P+T K R                       V  I +H R    +     D   I 
Sbjct: 453 VSGETPITCKIR-----------------IYDAGDVQAITLHGRSRQQRYSRDADWTYIA 495

Query: 173 NLDYDIVYEIKKEN---------------PDLFIGLNGGLED-MSQALKILPS-VDGVMI 215
                ++ ++K+ +               P++F   NG     +     I    VDGVM+
Sbjct: 496 ETA-ALIKDLKRRSDTTADTAIDKEARDKPNVFFVGNGDCYSHVDYYNSIDQGNVDGVML 554

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            R A     +   + +     L  S+  +    +++ R      
Sbjct: 555 ARGALIKPWLFEEIQK--GQYLDKSATERLDYIREYVRYGLECW 596


>gi|291390365|ref|XP_002711677.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog
           [Oryctolagus cuniculus]
          Length = 493

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 103/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMLQCRRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQSRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       +LVK I+K+G+  I +H RK      
Sbjct: 137 IEKILSTLVKGTRRPVTCKIRILPSLEDT----LSLVKRIEKTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  E   + +  NG           +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEVIKAIA-ETLSIPVIANGGSHDHIQQHLDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|222054277|ref|YP_002536639.1| dihydrouridine synthase DuS [Geobacter sp. FRC-32]
 gi|221563566|gb|ACM19538.1| dihydrouridine synthase DuS [Geobacter sp. FRC-32]
          Length = 306

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 63/290 (21%), Positives = 125/290 (43%), Gaps = 24/290 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM--IVADAILR----GDKKNILGFSTQEKPLALQI 54
           M   T+R  R     L     ++TE   + A A +R    GD K +   + ++ PL +Q+
Sbjct: 5   MQGVTNRAMRSLFIELVRPDTVFTEFIRVNAAAPVRRISAGDLKEMAA-AEKDVPLVVQL 63

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G     LV AA+  +  G   INLN+GCP  R+  G  G  L+ +P+++ + I ++ + 
Sbjct: 64  IGHGRDALVSAAEAAQATGAIHINLNMGCPYGRMTSGPTGGGLLRHPEVLSEIIPSLRRV 123

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +    ++K R G DD      +  L+   + + V+ + +H R  + +             
Sbjct: 124 IKGTFSLKMRAGYDD---PEQILRLLPLFEAAKVDFLVLHPRTVLQQ--------YQGLA 172

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+ I   + +E  ++ +  NG +   S  L++L      G+M+GR A  +  +   + + 
Sbjct: 173 DHAITARVVRET-EIPVIANGDIRTASAGLQLLEETGAAGLMLGRGAIADPFIFQRLRQ- 230

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
            S P       ++ + + +  ++ A              K++++  H I 
Sbjct: 231 -SAPSEPDQHDRSAMLQSYLLELLARYGKLFCGEAQVLAKIKEVL-HFIN 278


>gi|323449937|gb|EGB05821.1| hypothetical protein AURANDRAFT_1138 [Aureococcus anophagefferens]
          Length = 367

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/290 (17%), Positives = 103/290 (35%), Gaps = 25/290 (8%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R          +   EM +   +  G      +L     EK   +Q+  A   +  
Sbjct: 21  NLPFRRVLTKY-GADITCGEMALCPNLNDGQSSEWALLRRHKDEKCFGVQLSAAHGDQFG 79

Query: 64  EAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            A ++V+ +G  + ++LN+GCP   V     GA LM     V   +    + LS+P+T+K
Sbjct: 80  RACEVVDKYGDVDFVDLNMGCPIDLVCSKGGGAALMRRNKKVRSILEMGLERLSVPMTLK 139

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R G D+      L + +    ++  + +   +   +      +  R     ++  V  +
Sbjct: 140 MRTGWDEDPK---LAHTMAGYAQAWAHELGPGSVACVFVHGRSRTARYSRAANWAYVETV 196

Query: 183 KK----ENPDLFIGLNGGLEDMSQALKIL----PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +      P L I  NG +   +   +       + D  M+ R A     + T + E  +
Sbjct: 197 ARCQDDAIPKLPIIGNGDIMSYADWEEKRKTAPSTCDCAMLARGALIKPWLPTELHEKRA 256

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-GL 283
             ++ S         D  R  +    D+          + +  R ++  L
Sbjct: 257 WDISASE------RLDILRDFAKFGLDHWG---ADDCGVGRCRRFLLEWL 297


>gi|195566706|ref|XP_002106918.1| GD17163 [Drosophila simulans]
 gi|194204313|gb|EDX17889.1| GD17163 [Drosophila simulans]
          Length = 460

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 59/250 (23%), Positives = 102/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A  +    ++YTE +V   +LR  ++                      
Sbjct: 18  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLLRSIRRPNPALGTVDFVDPSDGTIVFRT 76

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   L LQ+G +D  +   A  ++     + +++N+GCP     +G  GA L+ +PD
Sbjct: 77  CAQETSRLVLQMGTSDARR-ALAVGMLLQRDISGLDINMGCPKEFSIKGGMGAALLADPD 135

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              + +  +C  L IPVT K RI  D         +LV+ +  +G+  I IHAR      
Sbjct: 136 KAANILRTLCSGLDIPVTCKIRILPD----VERTIDLVQKLAATGIAAIGIHART----- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              +D R       +++  + +   D+ I  NGG ++M     +         D VM+ R
Sbjct: 187 ---RDERPQHPAHPEVLRAVAQAV-DIPIIANGGSKNMHCYEDLRKFQLECGADSVMVAR 242

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 243 AAQINVSIFR 252


>gi|322417631|ref|YP_004196854.1| dihydrouridine synthase DuS [Geobacter sp. M18]
 gi|320124018|gb|ADW11578.1| dihydrouridine synthase DuS [Geobacter sp. M18]
          Length = 340

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/271 (21%), Positives = 105/271 (38%), Gaps = 26/271 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA------ILRGDKKNILGFSTQEKPLALQI 54
           M   T+R  R           ++TE +  +A      ++ GD + I   +    PL +Q+
Sbjct: 36  MQGLTNRALRELFTKWVRPDAVWTEFMRVNAQSEKKLLMPGDLREIAP-AENGVPLVVQL 94

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G     LV AAK  +D G   INLN+GCP  R+  G  G  ++  P+++ + I A+   
Sbjct: 95  IGHGRDALVAAAKTAQDAGAVHINLNMGCPYGRMTSGLTGGGMLKRPELLEEIIPALRHV 154

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           +    ++K R G ++     +   L+   + + V+ + +H R                  
Sbjct: 155 IQGSFSIKLRAGYEEPQQVFS---LLPLFEAARVDFLVLHPRT--------VRQAYDGFA 203

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+ I  E+ K+   + +  NG +      LK+L      G+M+GR       +   +   
Sbjct: 204 DHAITAEVVKQT-SIPVIANGDIRSSRFGLKVLEETGAAGLMLGRGGIGEPMLFERLR-- 260

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
                  + P          R +S  +  Y 
Sbjct: 261 ---GRAAAEPDCAERRAMLHRYLSDLLPLYC 288


>gi|301119491|ref|XP_002907473.1| tRNA-dihydrouridine synthase 3 [Phytophthora infestans T30-4]
 gi|262105985|gb|EEY64037.1| tRNA-dihydrouridine synthase 3 [Phytophthora infestans T30-4]
          Length = 681

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/318 (16%), Positives = 118/318 (37%), Gaps = 55/318 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +  T   +   EM +A  +L+  +    +L     E    +Q+ G+   ++ 
Sbjct: 301 NLPFRRLMKQ-TGADITCGEMAMATNLLKAQQSEWALLRRHKSEDVFGVQLAGSFSDQMT 359

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA----------AMC 112
              +++  +   + +++N+GCP   V     G+ LM  P  + + ++           M 
Sbjct: 360 RVCELLTRETDIDFVDINMGCPIDIVCRAGAGSALMTRPPRLLEVVSGALTGLELGTRMR 419

Query: 113 KA--LSIP-VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR------------- 156
               ++ P +TVK R G  ++ P      L+  ++    +  ++++              
Sbjct: 420 TGGIVNTPGLTVKLRTGWSEKQPTA--HKLIPKLQAVRASQAYVNSAVVTADFKLRATQS 477

Query: 157 -KAILKGLSPKDNRKIPNLDYDIVYEI---------KKENPDLFIGLNGGLEDMSQALKI 206
             AI      +  R   + D+D +++           K   ++     G +    +  + 
Sbjct: 478 IDAITVHGRSRLQRYTKHADWDYIFQCSDAQKGSIDDKPLSNIPFVGGGDVLSYEEFDEH 537

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           L +  +D  M+ R A     + T + E     ++ S   +  + KDF R        +  
Sbjct: 538 LQNGKLDTCMLARGALIKPWLPTEIKERRHWDISASE--RLDLLKDFVR--------FGL 587

Query: 265 RHLHSGGK-LQQITRHMI 281
            H  S  K + +  R+++
Sbjct: 588 EHWGSDQKGVNRTRRYLL 605


>gi|186510839|ref|NP_001118800.1| FAD binding / catalytic/ tRNA dihydrouridine synthase [Arabidopsis
           thaliana]
 gi|26452531|dbj|BAC43350.1| unknown protein [Arabidopsis thaliana]
 gi|332645049|gb|AEE78570.1| tRNA-dihydrouridine synthase 2 [Arabidopsis thaliana]
          Length = 290

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 43/187 (22%), Positives = 86/187 (45%), Gaps = 16/187 (8%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              ++  +  Q+G +D  + ++A++IV +     I++N+GCP A   +G  GA L+  P+
Sbjct: 32  CDEEKSRVVFQMGTSDAVRALKASEIVCN-DVATIDINMGCPKAFSIQGGMGAALLSKPE 90

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++ D +A + + L +PVT K R+             L + I+K GV  + +H RK     
Sbjct: 91  LIHDILATLKRNLDVPVTCKIRLLKSPADTV----ELARRIEKLGVPALAVHGRKI---- 142

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                +R      +D + ++      + +  NG + +      +K       VM+ R A 
Sbjct: 143 ----ADRPRDPAKWDEIADVVAAL-SIPVIANGDVLEYDDFSRIKTATGAASVMVARGAM 197

Query: 221 KNSAMLT 227
            N+++ +
Sbjct: 198 WNASIFS 204


>gi|242005452|ref|XP_002423579.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212506727|gb|EEB10841.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 409

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 82/183 (44%), Gaps = 19/183 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + LQ+G  D  + ++  K+VE+     I++N+GCP     +G  GA L+  PD   + + 
Sbjct: 39  VILQLGTNDPERALKVGKLVEN-DVAGIDINMGCPKEFSIKGGMGAALLDKPDKAVEILE 97

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +   L IPVT K R+  D          L + ++K+G+  I IH R    +   P  N 
Sbjct: 98  KLVNNLKIPVTCKVRVLKDKNKT----IELCQRLEKTGIAAIAIHGRTKDERPQHPNKN- 152

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGRAAYKNSA 224
                  DI+  +  E   + +  NGG +++     IL          +M+ RAA  N +
Sbjct: 153 -------DIIKAVA-EVLKIPVIANGGSKEIDNYNDILKFKEATGCSSIMLARAAEWNCS 204

Query: 225 MLT 227
           + +
Sbjct: 205 VFS 207


>gi|146098870|ref|XP_001468493.1| hypothetical protein [Leishmania infantum]
 gi|134072861|emb|CAM71577.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 493

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 98/255 (38%), Gaps = 44/255 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   R      + YT M++A++ ++        F+    E  L +Q+    
Sbjct: 103 MVRCSRPAFRQVCRAW-GARVSYTHMLIAESFVKSPHARHAEFARYEGEDRLVVQLAAKS 161

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                +AA ++  +  + I+LN GCP     +   G+ L+  P+ V D + ++  A+   
Sbjct: 162 GPAAAQAAVLLRPY-CDGIDLNCGCPQRWAMKEGIGSALLDQPERVADMVRSIRNAMPDG 220

Query: 117 -----------------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                                  +P  VK RI  D +       +  +  + +GV+ + +
Sbjct: 221 STASTIVGNGCEYGSCTSTVPPFLPCVVKMRIKDDLRRSV----DFARQCEAAGVSWLTV 276

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVD 211
           H R       +      +         ++ +EN  + + LNGG+ D+S A++  +     
Sbjct: 277 HGRTPTCHPSAAVQFEAV---------KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCG 327

Query: 212 GVMIGRAAYKNSAML 226
           G+M       N AM 
Sbjct: 328 GLMSANGLLDNPAMF 342


>gi|302843625|ref|XP_002953354.1| hypothetical protein VOLCADRAFT_105870 [Volvox carteri f.
           nagariensis]
 gi|300261451|gb|EFJ45664.1| hypothetical protein VOLCADRAFT_105870 [Volvox carteri f.
           nagariensis]
          Length = 307

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 90/236 (38%), Gaps = 27/236 (11%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+    I+  + A+K+ ++ G   +++N GCP         G+ ++  P  +   +A 
Sbjct: 3   GFQVACKTIADGIAASKLAKEAGAQFLDINCGCPIHEATRRGMGSAMLRKPRALAKMVAG 62

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +     +PVTVK R+G  +    + + ++V+ ++++G   + +H R A        + R 
Sbjct: 63  IAAESELPVTVKVRLG--ENDKKINVDSVVRFLERAGAAAVTVHGRTA--------EQRY 112

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
               D+  V E+ + +  + I  NG +    +A   L       VM GR A     +   
Sbjct: 113 KKAADWGRVGELAR-SSSVPIIGNGDILTHYEARARLEESGCAAVMAGRGALIKPWLFLE 171

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             E     LT S  +           +   +  Y   H     + +   +     F
Sbjct: 172 FKEGRELLLTTSERVG----------VYRLLVSYMKEHFGDDERGR--RK--AWYF 213


>gi|303282165|ref|XP_003060374.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
 gi|226457845|gb|EEH55143.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
          Length = 424

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 99/244 (40%), Gaps = 28/244 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGADISKLV 63
           D   R F R+        ++   A+ +LRG    + G+  +E  +P    + G++   L 
Sbjct: 63  DEACREFTRVPGTL----SQGAKAEKLLRGIA--LNGYDAEELSRPANASLMGSNPDLLE 116

Query: 64  EAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----IP 118
             A+ +  +     ++LN GCP+  V     G+ L+ +P+ V  C++A+ +       +P
Sbjct: 117 HCARVLARETRAPRVDLNCGCPANVVTGKGAGSSLLRDPNDVYACVSAIRRGCEGTGCVP 176

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            T+K R G DD      LR  + + ++ G   + +H R         +        ++  
Sbjct: 177 -TLKLRSGYDDDSL---LRENLLAAQEGGAAFVTLHPRT--------RRQGYSGRANWKD 224

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I  E  D+ +  NG +    +A  +L      G+M+GR A ++  +   +       
Sbjct: 225 IA-IAVETLDVPVIGNGDVTSPERARALLFETGCAGIMVGRGAVQDPLVFRRIKAELRAG 283

Query: 237 LTGS 240
               
Sbjct: 284 DWSE 287


>gi|237844349|ref|XP_002371472.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|211969136|gb|EEB04332.1| dihydrouridine synthase domain-containing protein [Toxoplasma
           gondii ME49]
 gi|221481251|gb|EEE19648.1| dihydrouridine synthase domain-containing protein, putative
           [Toxoplasma gondii GT1]
          Length = 653

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 92/248 (37%), Gaps = 37/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG------DKKNILGFSTQEK------ 48
           MV      +R          L+YTE  +   +L        D   I      EK      
Sbjct: 261 MVRIGILPFRLECLKY-GADLVYTEETIDHKLLNSVRTFNEDFSTIDFLHKSEKTCVFST 319

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                  + +Q+G +D ++ ++AA +V       +++N+GCP +    G  GA L+  P 
Sbjct: 320 CLEERGKVVMQLGTSDATRALKAAMLVAQ-DVAAVDVNMGCPKSFSINGGMGAALLKTPL 378

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           I  D +  + + L IPVT K R+            +  +  +  G+  I IHAR+     
Sbjct: 379 IATDILKTLRRNLDIPVTCKIRLL----DTIHKTIDFARLCENCGIEAIAIHARET---- 430

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
                 R      +D+   +K     + +  NG      D     + +   D +M  R A
Sbjct: 431 ----HERPSHRAHWDLFPALKSSL-AIPLIANGDFLTRRDADVFQEKI-GADSLMFARGA 484

Query: 220 YKNSAMLT 227
             + ++ +
Sbjct: 485 MWDPSIFS 492


>gi|238882041|gb|EEQ45679.1| hypothetical protein CAWG_04010 [Candida albicans WO-1]
          Length = 613

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/307 (19%), Positives = 111/307 (36%), Gaps = 46/307 (14%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +++G      +      E P   +QI  +     
Sbjct: 257 NLPYRRLMKTL-GADVTYSEMALSVPLIQGHNPEWALPKAHVSEYPGFGVQIASSKHWAA 315

Query: 63  VEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+ +       +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPV
Sbjct: 316 AKAAEAIYRNTTHVSELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPV 375

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G+ +        NLV  + + G    I +H R         +  R     D++ 
Sbjct: 376 TVKIRTGIKEGKNTAV--NLVSRVLEEGNAAAITLHGRS--------RQQRYSKEADWNY 425

Query: 179 VYEI----------------KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           + E+                 ++   ++   NG +       + +    +D VM+ R A 
Sbjct: 426 IAEVGTVVKNWNEQQKEDKEGRDRDPVYFVGNGDVYSHEDWYEHVNTDGIDSVMVARGAL 485

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               +   V+       + S  +           I      YA  H  S      ++R  
Sbjct: 486 IKPWIFEEVEAQQYLDKSSSERL----------DILGKFAKYAIEHWGSDEYGVGLSRRF 535

Query: 281 IGLFHGF 287
           +  F  F
Sbjct: 536 MCEFLSF 542


>gi|115495449|ref|NP_001068887.1| tRNA-dihydrouridine synthase 2-like [Bos taurus]
 gi|111308646|gb|AAI20343.1| Dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae) [Bos
           taurus]
 gi|296477934|gb|DAA20049.1| dihydrouridine synthase 2-like, SMM1 homolog [Bos taurus]
          Length = 493

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 60/289 (20%), Positives = 111/289 (38%), Gaps = 56/289 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELVDLKMLQCKRVVNEALSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQSKVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKILSTLVKGTRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  + +  I  E   + +  NG           +ED  +A     +   V
Sbjct: 187 --REERPQHPVSCEAIKAIA-ETLSIPVIANGGSHDHIQGYLDIEDFRRA----TAASSV 239

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           M+ RAA  N ++             G  P++  V + + R        Y
Sbjct: 240 MVARAAMWNPSIFLK---------EGPRPLE-EVMQKYIRYAVQYDNHY 278


>gi|68466823|ref|XP_722607.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68467102|ref|XP_722466.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|74587613|sp|Q5ALL3|DUS3_CANAL RecName: Full=tRNA-dihydrouridine synthase 3
 gi|46444444|gb|EAL03719.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46444594|gb|EAL03868.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
          Length = 613

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/307 (19%), Positives = 111/307 (36%), Gaps = 46/307 (14%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +++G      +      E P   +QI  +     
Sbjct: 257 NLPYRRLMKTL-GADVTYSEMALSVPLIQGHNPEWALPKAHVSEYPGFGVQIASSKHWAA 315

Query: 63  VEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+ +       +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPV
Sbjct: 316 AKAAEAIYRNTTHVSELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPV 375

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G+ +        NLV  + + G    I +H R         +  R     D++ 
Sbjct: 376 TVKIRTGIKEGKNTAV--NLVSRVLEEGNAAAITLHGRS--------RQQRYSKEADWNY 425

Query: 179 VYEI----------------KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
           + E+                 ++   ++   NG +       + +    +D VM+ R A 
Sbjct: 426 IAEVGTVVKNWNEQQKEDKEGRDRDPVYFVGNGDVYSHEDWYEHVNTDGIDSVMVARGAL 485

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
               +   V+       + S  +           I      YA  H  S      ++R  
Sbjct: 486 IKPWIFEEVEAQQYLDKSSSERL----------DILGKFAKYAIEHWGSDEYGVGLSRRF 535

Query: 281 IGLFHGF 287
           +  F  F
Sbjct: 536 MCEFLSF 542


>gi|196250795|ref|ZP_03149482.1| dihydrouridine synthase DuS [Geobacillus sp. G11MC16]
 gi|196209745|gb|EDY04517.1| dihydrouridine synthase DuS [Geobacillus sp. G11MC16]
          Length = 188

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 45/150 (30%), Positives = 80/150 (53%), Gaps = 6/150 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M    +  +R   +      L+  EM+    I+  ++K   +L    +EKPL+LQI G +
Sbjct: 18  MAGVCNSAFRLTVKEF-GAGLVCAEMVSDKGIVYNNEKTLNMLYIDEREKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
              LV+AAK V+ +   + I++N+GCP  +V     GA  +L+P+ + D +A++  A+  
Sbjct: 77  KETLVKAAKFVDKNTNADIIDINMGCPVPKVTNCDAGAKWLLDPNKIYDVVASIVDAVEK 136

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
           PVTVK RIG D+           ++++++G
Sbjct: 137 PVTVKMRIGWDEHHIYAV--ENAQAVERAG 164


>gi|149699255|ref|XP_001498775.1| PREDICTED: similar to tRNA-dihydrouridine synthase 2-like (hDUS2)
           (Up-regulated in lung cancer) (URLC8) isoform 1 [Equus
           caballus]
          Length = 493

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 102/253 (40%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      M+    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMLQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQSRVIFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K    PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKILSTLVKGTRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 186

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  + +  I  E   + +  NG           +ED  QA     +   V
Sbjct: 187 --REERPQHPVSCEAIKAIA-ETLSIPVIANGGSYDHIQEYLDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|322502519|emb|CBZ37602.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 493

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 98/255 (38%), Gaps = 44/255 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   R      + YT M++A++ ++        F+    E  L +Q+    
Sbjct: 103 MVRCSRPAFRQVCRAW-GARVSYTHMLIAESFVKSPHARHAEFARYEGEDRLVVQLAAKS 161

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                +AA ++  +  + I+LN GCP     +   G+ L+  P+ V D + ++  A+   
Sbjct: 162 GPAAAQAAVLLRPY-CDGIDLNCGCPQRWAMKEGIGSALLDQPERVADMVRSIRNAMPDG 220

Query: 117 -----------------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                                  +P  VK RI  D +       +  +  + +GV+ + +
Sbjct: 221 STASTIVGNGCEYGSCTSTVPPFLPCVVKMRIKDDLRRSV----DFARQCEAAGVSWLTV 276

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVD 211
           H R       +      +         ++ +EN  + + LNGG+ D+S A++  +     
Sbjct: 277 HGRTPTCHPSAAVQFEAV---------KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCG 327

Query: 212 GVMIGRAAYKNSAML 226
           G+M       N AM 
Sbjct: 328 GLMSANGLLDNPAMF 342


>gi|166033391|ref|ZP_02236220.1| hypothetical protein DORFOR_03117 [Dorea formicigenerans ATCC
           27755]
 gi|166027748|gb|EDR46505.1| hypothetical protein DORFOR_03117 [Dorea formicigenerans ATCC
           27755]
          Length = 338

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 67/343 (19%), Positives = 123/343 (35%), Gaps = 44/343 (12%)

Query: 2   VDWTDRHYRF-FARLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGA 57
              T   YR  + +        +T  +V          +K +++   +    L  QI   
Sbjct: 9   EGITTYIYRRAYHQHFAPMDKYFTPFLVPHTKKGFSTKEKNDVMPEHSPGMNLVPQIMSN 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                +   + ++ +GY E+NLN+GCPS  V     G+  + +PD +   +  + K   +
Sbjct: 69  QADSFLHTVEKLKVYGYEEVNLNLGCPSKTVVSKGRGSGFLADPDGLDRFLDEIFKKCDV 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K RIG DD         L+    +  V  + IH R           N+      +D
Sbjct: 129 KISIKTRIGKDD---PEEFARLLDIYNQYPVEELIIHPRVQKDFYK----NQPNLGAFHD 181

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAML-------- 226
            V E K     + +  NG +   E   +  +  P VD  M+GR    N A+L        
Sbjct: 182 AVEESK-----IPLCYNGDIFTPESYEEMKREFPQVDTFMLGRGILMNPALLDLIRMREK 236

Query: 227 ------TTVD--EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG---GKLQQ 275
                 T +D  E+     +       R  K+    +     DY    +       KL++
Sbjct: 237 TDVKKTTDIDVTEWKKEETSRKMQSADRYKKEIHAFLEQIKCDYLEVGMGEKNTLFKLKE 296

Query: 276 ITRHMIGLFHGFPNSRR-CRHILTVE--AGASTATHHIIETAF 315
           +  +M       P +++  + I   +  A   +A+   +E   
Sbjct: 297 LWAYMG---QNAPEAKKALKRIRKSQSMADYDSASREALEDFI 336


>gi|255505161|ref|ZP_05344831.3| dihydrouridine synthase family protein [Bryantella formatexigens
           DSM 14469]
 gi|255269367|gb|EET62572.1| dihydrouridine synthase family protein [Bryantella formatexigens
           DSM 14469]
          Length = 285

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 112/291 (38%), Gaps = 34/291 (11%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMI-----VADAILRGDKKNILGFSTQEKPLALQIG 55
              T   +R    +        +   I             +  +IL    +      QI 
Sbjct: 13  EGITGYIFRSAHHKYFPGADKYFIPFIEPKPNSKKIFSARELNDILPEHNRGMRTVPQIL 72

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
                  V  AK ++++GY+E+N+N+GCPS  V     GA  + +P+ V D +A +  AL
Sbjct: 73  TNKWEDFVWTAKHLQEYGYDEVNINLGCPSKTVVSKKRGAGFLADPEGVDDFLAHIFDAL 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI-LKGLSPKDNRKIPNL 174
            + ++VK R+G +D    V  R L++   K  +  + IH R      G +P         
Sbjct: 133 DMKISVKTRLGRED---PVEFRWLLEIYNKYPLAELIIHPRTQKEFYGFTP--------- 180

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDE 231
            Y++  E  +E   L +  NG +       +I    P + GVM+GR   +N  ++  +  
Sbjct: 181 HYEMFAEALEET-SLPVCYNGDVNTKEDCREIEKRFPQITGVMMGRGILRNPGLIGEIR- 238

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT---RH 279
                  G      R  + F  ++ A+             K++++    RH
Sbjct: 239 -------GEEKADIRRLRSFHDELYAAYQQEMPGDTQVLFKMKELWTYLRH 282


>gi|254519722|ref|ZP_05131778.1| dihydrouridine synthase [Clostridium sp. 7_2_43FAA]
 gi|226913471|gb|EEH98672.1| dihydrouridine synthase [Clostridium sp. 7_2_43FAA]
          Length = 319

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/294 (20%), Positives = 117/294 (39%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  I    + +    + ++IL  + +   +  QI  
Sbjct: 8   MEGITGFIYRNTYKKFFDNVDKYFTPFIVPTSSKSFKTKELRDILPENNKGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  A+ ++  GY+EINLN+GCPS  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSDGFITTARKLQQLGYSEINLNLGCPSGTVVSKNRGSGFLAKREELDKFLDEIYKIDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG D    +     L+K   K  +  + IH R               PNL  
Sbjct: 128 MKISIKTRIGKD---SSEEFYELIKIYNKYPLEELIIHPRTREDFYG------NKPNL-- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVD 230
               E+ K+   L    +  NG +  +    K+    P ++ +M+GR    N  ++  + 
Sbjct: 177 ----EVFKDALTLSNSPVCYNGDIFTLDDYNKLSKEFPELNTIMLGRGVLANPGLINEIR 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    ++ +   V K F  +I     +       +  +++++  +MI +F
Sbjct: 233 --------NNANLNKEVLKKFHDEIFNDYRNVFKDDKIAIYRMKELWGYMIYIF 278


>gi|45549423|ref|NP_572950.2| CG1434 [Drosophila melanogaster]
 gi|45446950|gb|AAF48360.2| CG1434 [Drosophila melanogaster]
 gi|162944734|gb|ABY20436.1| GH10289p [Drosophila melanogaster]
          Length = 473

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 104/250 (41%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A  +    ++YTE +V   +++  ++                      
Sbjct: 31  MVRVGTLPMRLLALEM-GADIVYTEELVDIKLIKSIRRPNPALGTVDFVDPSDGTIVFRT 89

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+ +PD
Sbjct: 90  CAQETSRLVLQMGTSDAGRALAVGKLLQ-RDISGLDINMGCPKEFSIKGGMGAALLADPD 148

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IPVT K RI  D         +LV+ +  +G+  I IHAR      
Sbjct: 149 KAAHILRTLCSGLDIPVTCKIRILPD----VEGTIDLVQKLAATGIAAIGIHART----- 199

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-----LKILPSVDGVMIGR 217
              +D R       +++  + +   D+ I  NGG ++M         ++    D VM+ R
Sbjct: 200 ---RDERPQHPAHPEVLRAVAQAV-DIPIIANGGSKNMHCYDDLRKFQMECGADSVMVAR 255

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 256 AAQINVSIFR 265


>gi|328787042|ref|XP_393745.3| PREDICTED: tRNA-dihydrouridine synthase 2-like [Apis mellifera]
          Length = 460

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 98/251 (39%), Gaps = 38/251 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------------------NILG 42
           MV       R  A L     ++YTE ++   +LR  ++                      
Sbjct: 20  MVRIGTLPMRLLA-LDYGADVVYTEELIDWKLLRSFRRENDVLGTIDYIDKTDGTVTFRT 78

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              ++  + LQIG  D ++ ++ AK+VE      I+LN+GCP      G  GA L+  P+
Sbjct: 79  CPKEKDKVVLQIGTCDAARALKVAKMVEQ-DVAGIDLNMGCPKLFSLIGKMGAALLKEPE 137

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              + +  +   L+IPVT K R+  D          L + ++ +G+  I +H R    + 
Sbjct: 138 TATNILKTLVDNLNIPVTCKIRVLPDIDKT----IELCELLQSTGIAAIAVHGRTVHERP 193

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-----LKILPSVDGVMIGR 217
                N  +  +              + +  NGG +++ +       K +     VM+ R
Sbjct: 194 QHMNRNEVLKKI---------SNRLSIPVIANGGSKEIQKYSDIFKFKEITGCSSVMLAR 244

Query: 218 AAYKNSAMLTT 228
           AA  N ++ + 
Sbjct: 245 AAEWNCSIFSE 255


>gi|187935292|ref|YP_001886306.1| dihydrouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
 gi|187723445|gb|ACD24666.1| dihydrouridine synthase family protein [Clostridium botulinum B
           str. Eklund 17B]
          Length = 321

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 59/291 (20%), Positives = 118/291 (40%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + +   N    +T  IV   + ++   + +++L  +     +  QI  
Sbjct: 8   MEGITGYIYRNSYEKFFNNIDKYFTPFIVTNKSRSLKTKELRDVLPENNNGMNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    +  +  ++  GYNE+NLN+GCP+  V   + G+  +   + +   +  + K   
Sbjct: 68  NDSEGFINTSGKLKQLGYNEVNLNLGCPAGTVVSKNRGSGFLAKREELDMFLDEIFKMDD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I +++K RIG D          L+K   K  +  + IH R               PNLD 
Sbjct: 128 IKISIKTRIGKD---SPEEFYELIKIYNKYPIEELIIHPRTQKDFYG------NKPNLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             V++      +  I  NG +  +    K+    P V  +M+GR    N  ++  +    
Sbjct: 178 --VFKDALSLSNNPICYNGDIFTVKDHDKLTRDFPEVKTLMLGRGILANPGLMNEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                 ++ I   + K+F  +I +   +      ++  +++++  +MI +F
Sbjct: 233 -----NNTFIDKEILKEFHDEILSKYIELFNEDRNAIFRMKELWGYMIYMF 278


>gi|17863006|gb|AAL39980.1| SD08006p [Drosophila melanogaster]
          Length = 460

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 104/250 (41%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A  +    ++YTE +V   +++  ++                      
Sbjct: 18  MVRVGTLPMRLLALEM-GADIVYTEELVDIKLIKSIRRPNPALGTVDFVDPSDGTIVFRT 76

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+ +PD
Sbjct: 77  CAQETSRLVLQMGTSDAGRALAVGKLLQ-RDISGLDINMGCPKEFSIKGGMGAALLADPD 135

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IPVT K RI  D         +LV+ +  +G+  I IHAR      
Sbjct: 136 KAAHILRTLCSGLDIPVTCKIRILPD----VEGTIDLVQKLAATGIAAIGIHART----- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-----LKILPSVDGVMIGR 217
              +D R       +++  + +   D+ I  NGG ++M         ++    D VM+ R
Sbjct: 187 ---RDERPQHPAHPEVLRAVAQAV-DIPIIANGGSKNMHCYDDLRKFQMECGADSVMVAR 242

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 243 AAQINVSIFR 252


>gi|222111715|ref|YP_002553979.1| dihydrouridine synthase dus [Acidovorax ebreus TPSY]
 gi|221731159|gb|ACM33979.1| dihydrouridine synthase DuS [Acidovorax ebreus TPSY]
          Length = 338

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 55/277 (19%), Positives = 102/277 (36%), Gaps = 30/277 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       +E I +  ++L    K  L +  +           P+
Sbjct: 12  MEGLLDFVLRDVLTQVGGVDRCVSEFIRITGSLL--PDKVFLRYIPELKNGGRTLAGVPV 69

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCI 108
             Q+ G+D   + E A  + + G   I+LN GCP+  V+    GA L+  P+        
Sbjct: 70  RAQLLGSDPVSMAENAARLAELGPEGIDLNFGCPARTVNRHGGGAALLREPEAIAAVVAA 129

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                   +PV+ K R+G DD   A   R   +++++ G   + +HAR        P   
Sbjct: 130 VRRAVPAHLPVSAKMRLGYDD---ASLARECAQAMEQGGACELVVHARTKADGYRPPAYW 186

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            +IP +         +    + +  NG +  +  AL+       D +M+GR    +  + 
Sbjct: 187 EQIPAI---------RAAVRIPLVANGEIWTVQDALRCRAASGCDALMLGRGIVADPGLA 237

Query: 227 TTVDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD 261
             +  +     T + P        + FW+ + A +  
Sbjct: 238 LAIRAHDVGRHTIALPWAALLPQLERFWQLVCADLEP 274


>gi|261219467|ref|ZP_05933748.1| nifR3 family TIM-barrel protein [Brucella ceti M13/05/1]
 gi|261321963|ref|ZP_05961160.1| nifR3 family TIM-barrel protein [Brucella ceti M644/93/1]
 gi|260924556|gb|EEX91124.1| nifR3 family TIM-barrel protein [Brucella ceti M13/05/1]
 gi|261294653|gb|EEX98149.1| nifR3 family TIM-barrel protein [Brucella ceti M644/93/1]
          Length = 171

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 40/151 (26%), Positives = 76/151 (50%), Gaps = 4/151 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           T+K R+G D+   ++    L +  + +G+  
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAEDAGIAW 171


>gi|296808361|ref|XP_002844519.1| tRNA-dihydrouridine synthase 3 [Arthroderma otae CBS 113480]
 gi|238844002|gb|EEQ33664.1| tRNA-dihydrouridine synthase 3 [Arthroderma otae CBS 113480]
          Length = 737

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 45/283 (15%), Positives = 93/283 (32%), Gaps = 60/283 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------KPLA--- 51
           +  +R     L      Y+EM ++  +++G K    ++     E         +P+    
Sbjct: 338 NLPFRRLCVEL-GAQFTYSEMAMSLPLMQGTKGEWALMKAHESEIQPPTISPKQPVVKGY 396

Query: 52  ---------LQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G    + ++A +I+     +   ++LN GCP   V+    G+ L+ +
Sbjct: 397 DNSRDLKFGAQIAGNRPWQALKATEILTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 456

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M      +P+T K R+G  D         L + +              +G
Sbjct: 457 PSKLEKILRGMNSVSGEVPITAKIRMGTKD--NYPTALKLAERLVIGGYESNELGQGPAG 514

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNL----------DYDIVYEIKK-------ENPDLF 190
           +  + +H R    +     D   I               ++V  +++           ++
Sbjct: 515 IGALTLHGRSRQQRYTREADWGYISECSALVKRLNVKRDEVVDTVREPDERLLPSAGKVY 574

Query: 191 IGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
              NG     +     +    VD VM+ R A     +   +  
Sbjct: 575 FIGNGDCYSHADYNNAITNSGVDSVMVARGALIKPWIFEEIQA 617


>gi|260834651|ref|XP_002612323.1| hypothetical protein BRAFLDRAFT_265495 [Branchiostoma floridae]
 gi|229297700|gb|EEN68332.1| hypothetical protein BRAFLDRAFT_265495 [Branchiostoma floridae]
          Length = 444

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 58/251 (23%), Positives = 106/251 (42%), Gaps = 40/251 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILG---------------- 42
           MV       R  A L     ++Y E ++  ++L+  +    +L                 
Sbjct: 23  MVRIGTLPARLLA-LDYGADVVYCEELIDHSMLQCQRVENELLDTIDFIKEQAHHPVFRT 81

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   +  Q+G AD  + ++ AK+VE+     I++N+GCP     +G  GA L+ NP+
Sbjct: 82  CAKERDRVVFQMGTADPERALKVAKLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSNPE 140

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +   +  +   +SIPVT K RI    +       +LV+ I+ +GV  + +H R      
Sbjct: 141 KIKQILTTLVNGVSIPVTCKIRILPKLEDT----LSLVQLIESTGVAAVAVHGR------ 190

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL------EDMSQALKILPSVDGVMIG 216
              K+ R    +  D++  I +    + +  NGG       ED+ +  +       VM+ 
Sbjct: 191 --YKEERPRHPVHADVIKAISQAV-SIPVIANGGSGVINRYEDLQRFRED-TGASSVMVA 246

Query: 217 RAAYKNSAMLT 227
           RAA  N ++  
Sbjct: 247 RAAQWNFSIFR 257


>gi|254481818|ref|ZP_05095061.1| Dihydrouridine synthase superfamily protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037947|gb|EEB78611.1| Dihydrouridine synthase superfamily protein [marine gamma
           proteobacterium HTCC2148]
          Length = 325

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 65/327 (19%), Positives = 127/327 (38%), Gaps = 34/327 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     L       TE + V++ +L       L       G +    P+ +
Sbjct: 8   MEGVIDHTMRELLTSLGGVDRCVTEFVRVSERLLPPRVFYRLCPELHTAGKTRFGVPVYI 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI--AA 110
           Q+ G D + + E A    + G   I+LN GCP+  V+    G+ L+  P+ V        
Sbjct: 68  QLLGGDPTVVAENAARAAELGAPGIDLNFGCPAKTVNRSDGGSILLRQPERVAAITAAVR 127

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                ++PVTVK R+G +DQ   +   ++V  I ++G   + +HAR         K +  
Sbjct: 128 RAVPAAVPVTVKTRLGYEDQ---LQFLDIVAGIAEAGATELTVHART--------KRHGY 176

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   +  +    +E   + +  NG + + + AL+   +   + +M+GR A     +   
Sbjct: 177 RPPAYWQEIAR-AREQVRMPVIANGEIWNPADALRCQQVTGCEDLMLGRGALCRPDLPRL 235

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           V    +          + V     +    ++  Y A H+  G  ++Q    ++ L   +P
Sbjct: 236 VKAAVNGEAVNPL-CWSNVVPLVLQFYQLTLEHYDACHV--GNPIKQW---LVYLRAYYP 289

Query: 289 NSR----RCRHILTVEAGASTATHHII 311
            +     + + +   EA  +   + ++
Sbjct: 290 QAASLFEKIKRLRDSEAIGNGLRNEML 316


>gi|115680276|ref|XP_001190481.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115717833|ref|XP_784269.2| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 278

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 95/249 (38%), Gaps = 36/249 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-----MIVADAILRGDKKNILGFSTQE-------- 47
           MV       R  A     + +   E     M+     +      +   S  +        
Sbjct: 16  MVRIGTLPTRLLALEYGADIVYCQELIDFKMLTCRRHVNRVLDTVDYISKDDVVIFRTCS 75

Query: 48  ---KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                L  Q+G AD  + +  AK+VE    + I++N+GCP     +G  GA L+  PD +
Sbjct: 76  KETDRLVFQMGTADAQRALRVAKMVEK-DVSGIDINMGCPKDFSLKGGMGAALLQKPDTI 134

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + +  + + + IPVT K RI    +        L K I+++GV  + +H R        
Sbjct: 135 KEILTTLVQGVKIPVTCKIRILPKLEDTIA----LAKMIEQTGVAALAVHGRLT------ 184

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----LEDMSQAL--KILPSVDGVMIGRA 218
             + R    +  D +  +  ++  + +  NGG    ++  +     + +     VMI R 
Sbjct: 185 --EERPRHPVHCDAIKAVA-DSISIPLITNGGSQDIIKSYADIERFREMTGASSVMIARE 241

Query: 219 AYKNSAMLT 227
           A  N ++  
Sbjct: 242 AQWNPSIFR 250


>gi|301513184|ref|ZP_07238421.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB058]
          Length = 221

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 43/219 (19%), Positives = 89/219 (40%), Gaps = 21/219 (9%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V   + A+  A+ +PVT+K R+G  +      +  + K  +++G+  + +H R       
Sbjct: 1   VARILDAVVAAVDVPVTLKTRLGFLNGQ--ENILRVAKRAEEAGIAALALHGRT------ 52

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
             +++  +    Y+++  +K E   + +  NG ++   +A  +L     D +MIGRAA  
Sbjct: 53  --REDMYLNTARYELIKHVK-ELIHIPVIANGDIDSPEKAKYVLDYTGADAIMIGRAAQG 109

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              +   +  Y       ++P    V +     +S     Y           +   +H+ 
Sbjct: 110 RPWIFREIAHYLKTGEHLAAPNIEEVKEVLLGHLSELYQFY-----GEYSGCRIARKHIA 164

Query: 282 GLFHGFPNSRRCRH-ILTVEAGASTATHHIIETAFNLMI 319
               G  +S   R  +  VE  A  A   ++E+ FN ++
Sbjct: 165 WYTKGLRSSNEFRQNMYKVETTAEQAL--VVESYFNQLL 201


>gi|156052667|ref|XP_001592260.1| hypothetical protein SS1G_06500 [Sclerotinia sclerotiorum 1980]
 gi|154704279|gb|EDO04018.1| hypothetical protein SS1G_06500 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 342

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 89/238 (37%), Gaps = 26/238 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL--ALQIGGAD 58
           MV ++   +R          L +T MI+A    R        F+T         Q G   
Sbjct: 37  MVRYSKLAFRETVAQY-GVDLCWTPMILAKEFNRSVFARDSDFTTSPTSTPTIAQFGVCS 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--- 115
             ++  +  ++  +  N I++N GCP +     S GA LM   ++V + +     AL   
Sbjct: 96  PLEISRSTTLIAPY-INGIDINCGCPQSWACACSIGAALMHKRELVAEMVKEAKSALKRE 154

Query: 116 ----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                  V+VK RI  D +       + +K+++ +GV+ I IH R        P +   I
Sbjct: 155 GYEGKKTVSVKIRIHRDLRDTV----DFIKTVQDAGVDFITIHGRMRSTPSSHPVNLEAI 210

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             L+          +  +    NG +  +  A +      V GVM  R    N A+  
Sbjct: 211 KLLN---------THTTVPTVSNGDITSLRSAHEHTQQTSVSGVMSARGLLSNPALFA 259


>gi|159474720|ref|XP_001695473.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158275956|gb|EDP01731.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 241

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 44/193 (22%), Positives = 81/193 (41%), Gaps = 21/193 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL  Q+ G+    +  AA+ + +     I+LN GCP+  V     G+ L+  P  + D +
Sbjct: 60  PLGAQVMGSSPELMGLAAQYLAER-APRIDLNCGCPANTVTGNGAGSSLLRTPQRIHDIV 118

Query: 109 AAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +AM   +        PV+VK R G DD        + + + +++G + I +H R      
Sbjct: 119 SAMVAGVRASAAPHTPVSVKLRAGFDDTSL---FEDNLLAAQEAGASFITLHPRT----- 170

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
              K        D+ +     +    + +  NG +  + +A  +L      GVM+GR A 
Sbjct: 171 ---KRQCYDGAADWSLTARAVQ-LLRVPVIGNGDVVCVERAHALLRQTGCHGVMVGRGAV 226

Query: 221 KNSAMLTTVDEYF 233
           ++  +   +   F
Sbjct: 227 QDPLLFHRIRHSF 239


>gi|315043164|ref|XP_003170958.1| hypothetical protein MGYG_06949 [Arthroderma gypseum CBS 118893]
 gi|311344747|gb|EFR03950.1| hypothetical protein MGYG_06949 [Arthroderma gypseum CBS 118893]
          Length = 734

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 48/284 (16%), Positives = 95/284 (33%), Gaps = 62/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------KPLA--- 51
           +  +R     L      Y+EM ++  +++G K    ++     E         +P+    
Sbjct: 336 NLPFRRLCVEL-GAQFTYSEMAMSLPLMQGTKGEWALMKAHESEILPPTISPKQPIVKGY 394

Query: 52  ---------LQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G    + ++A +I+     +   ++LN GCP   V+    G+ L+ +
Sbjct: 395 DHSRDLKFGAQIAGNRPWQALKATEILTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 454

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M      +P++ K R+G  D         L + +              +G
Sbjct: 455 PSKLEKILRGMNAVSGEVPISAKIRMGTKD--NYPTALKLAERLVIGGYESNELRQGPAG 512

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLF 190
           +  + +H R    +     D   I                  D + E  + +      +F
Sbjct: 513 IGALTLHGRSRQQRYTREADWEYISECSALVKRLNAKGDEVSDTIREPDERHLPPDGKVF 572

Query: 191 IGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              NG      D + A++    VD VM+ R A     +   +  
Sbjct: 573 FIGNGDCYSHADYNSAVEK-SGVDSVMVARGALIKPWIFEEIQA 615


>gi|123975618|ref|XP_001330358.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121896476|gb|EAY01626.1| hypothetical protein TVAG_292590 [Trichomonas vaginalis G3]
          Length = 333

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 67/298 (22%), Positives = 121/298 (40%), Gaps = 41/298 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---------------ILGFST 45
           MV  ++  +R    L      +Y      D+IL                      + F T
Sbjct: 18  MVRASNLPFRLMC-LENGADGVYGPATSVDSILASHYDENEDPYTMYFGWPKNPHVHFHT 76

Query: 46  QEK---PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             K    L  QI   D SK V+AA +V  F  + I+LN GCP +       G+ LM  P+
Sbjct: 77  DPKEKGKLIFQILTNDASKAVQAASVVVKF-ADAIDLNCGCPESFATSRGTGSSLMSEPE 135

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           IV D ++A+ +  ++P++VK RI  + +           + + +G + I +H R      
Sbjct: 136 IVADVVSALRRNYNVPISVKHRIHHNIEES----IQFAVACENAGASAIAVHGRL----- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
              K+ +   ++ YD +  +  ++  +    NGG+++   A +++     + V+I  AA 
Sbjct: 187 ---KEQKNKGSVAYDNMK-LVFDHLHVAKIGNGGVKNREMAKEMMEKTGCESVIISSAAL 242

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           KN  + +       +P T    +  R  +   +   +   +Y        GK + ITR
Sbjct: 243 KNPTIFS------GHPETDPVKLARRYLEIAKQYGCSDRHEYRWSVNTMLGKYRHITR 294


>gi|118581317|ref|YP_902567.1| dihydrouridine synthase, DuS [Pelobacter propionicus DSM 2379]
 gi|118504027|gb|ABL00510.1| tRNA-U20a,U20b-dihydrouridine synthase [Pelobacter propionicus DSM
           2379]
          Length = 342

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 123/322 (38%), Gaps = 41/322 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIV---ADAILRGDKKNIL--GFSTQEKPLALQIG 55
           M   T+   R          +++TE +    A A  R    ++   G +  + PL +Q+ 
Sbjct: 41  MQGVTNSALRSLFIDWVRPDVVFTEFMRVNPAAAQRRLSAADLAEAGSAGDDVPLVVQLI 100

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G     LV  ++  +D G   INLN+GCP  R+  G  G  ++ +P  +   I A+ K +
Sbjct: 101 GHGREALVSGSQAAQDAGAAHINLNMGCPYGRMTSGQTGGGMLRSPQELSSIIPALRKTI 160

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K R G D+      + +L+   + SGV+ + +H R  + K             D
Sbjct: 161 RGTFSIKLRSGYDNPRQ---IFDLLPLFEASGVDFLVLHPRTVLQK--------YAGFAD 209

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + I  E  + +  L I  NG +  ++    +L      G+M+GR A  +  +   +    
Sbjct: 210 HGITAEAVQRST-LPIIANGDIRSVATGRHVLRETGAAGLMLGRGAISDPLLFQRLRN-- 266

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYA---ARHLHSGGKLQQITRHMIGL------- 283
                   P          R +   +T Y           GK+++I   +  +       
Sbjct: 267 ---CAPPDPQPQERAAMLSRYLDELLTRYQTLFCGEAQILGKIKEI---VSTIHEPAFEK 320

Query: 284 -FHGFPNSRR---CRHILTVEA 301
            FH    +RR    R +L   A
Sbjct: 321 GFHRLKKARRIEAFRELLAELA 342


>gi|237833185|ref|XP_002365890.1| hypothetical protein TGME49_072570 [Toxoplasma gondii ME49]
 gi|211963554|gb|EEA98749.1| hypothetical protein TGME49_072570 [Toxoplasma gondii ME49]
          Length = 668

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 121/328 (36%), Gaps = 95/328 (28%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----------VADAILRGDKKNILGFSTQ--- 46
           M+D+T+RH+R    L++    LYTEM+            +  +    K+ +L  +     
Sbjct: 106 MMDYTNRHWRRLISLMSRRLTLYTEMVPVPPAPCESPDSSQDLPFSVKRKLLEEAGSLAS 165

Query: 47  -EKPLALQIGGADISKLVEAAKIVEDFGYNE----------------INLNVGCPSARVH 89
               + LQ+G          A+++ +F  +                 +NLN GCPS RV 
Sbjct: 166 VPNDVVLQVGVGSAQSATAVARVLNEFSVDRDHAEPVTRMRGKRTFLVNLNCGCPSPRVA 225

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL---------------------------------- 115
           +GSFG  LM +P  V +    +                                      
Sbjct: 226 KGSFGLILMEDPKRVAEMCQILVDGANNREGQKRCSLDVMGKSARGDTKDRTVHTNDSPE 285

Query: 116 --SIPVTVKCRIGVDDQI----------------------PAVALRNLVKS-IKKSGVNG 150
             S+ V+VKCR+G+++                            L   V + ++ S V  
Sbjct: 286 TDSVAVSVKCRVGIEEDKQFLRSGSSPISSATTPYSSSSCTYDKLAEFVGTVVETSPVRH 345

Query: 151 IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
             IHAR  IL G LSPK N +IP    + VY +  + P +    NGG++    A + L  
Sbjct: 346 FIIHARPGILVGKLSPKQNLQIPQRRPEWVYRLCSDFPTVSFTFNGGVKSFQNAEEHLLN 405

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYF 233
               + G+M+GR   +      +  + F
Sbjct: 406 TNDKLAGIMVGRDMLERPWYWGSHADAF 433


>gi|302499860|ref|XP_003011925.1| hypothetical protein ARB_01907 [Arthroderma benhamiae CBS 112371]
 gi|291175479|gb|EFE31285.1| hypothetical protein ARB_01907 [Arthroderma benhamiae CBS 112371]
          Length = 911

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 94/284 (33%), Gaps = 62/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------KPLA--- 51
           +  +R     L      Y+EM ++  +++G K    ++     E         +P+    
Sbjct: 357 NLPFRRLCVEL-GAQFTYSEMAMSLPLMQGTKGEWALMKAHESEILPPTISPKQPVVKEY 415

Query: 52  ---------LQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G    + ++A +I+     +   ++LN GCP   V+    G+ L+ +
Sbjct: 416 DHSRDLKFGAQIAGNRPWQALKATEILTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 475

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M      +P++ K R+G  D         L + +              +G
Sbjct: 476 PSKLEKILRGMNAVSGEVPISAKIRMGTKD--NYPTALKLAERLVIGGYESNELGQGPAG 533

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLF 190
           +  + +H R    +     D   I                  D + E  + +      ++
Sbjct: 534 IGALTLHGRSRQQRYTREADWEYISECSALVKRLNAKRDEVSDTIREPDERHLPPGGKVY 593

Query: 191 IGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              NG      D + A+     VD VM+ R A     +   +  
Sbjct: 594 FIGNGDCYSHADYNTAIDK-SGVDSVMVARGALIKPWIFEEIQA 636


>gi|326316090|ref|YP_004233762.1| dihydrouridine synthase duS [Acidovorax avenae subsp. avenae ATCC
           19860]
 gi|323372926|gb|ADX45195.1| dihydrouridine synthase DuS [Acidovorax avenae subsp. avenae ATCC
           19860]
          Length = 323

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 99/242 (40%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---------EKPLA 51
           M    D   R     +       +E I     L  D K  L +  +           P+ 
Sbjct: 12  MEGLLDFVLRDVLTRVGGVDRCVSEFIRVTGTLLPD-KVFLRYIPELRNGGRTAAGVPVR 70

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+ G+D S + E A  +   G   I+LN GCP+  V+    GA L+  P+ +   +AA+
Sbjct: 71  AQLLGSDPSSMAENAARLAALGPEGIDLNFGCPANVVNRHGGGAALLREPERIAAVVAAV 130

Query: 112 CKA--LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A    +PV+ K R+G DD   A   R   ++ +  G   + +HAR         K + 
Sbjct: 131 RRAVPAGMPVSAKMRLGYDDTSLA---RECAQAAEAGGACELVVHART--------KADG 179

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLT 227
             P   +++V  + +    + +  NG +  ++ A++   L   D +M+GR    +  +  
Sbjct: 180 YRPPAYWELVAPL-RAAVHIPVIANGEIWTVADAMRCRALSGGDALMLGRGIVADPGLAL 238

Query: 228 TV 229
            +
Sbjct: 239 AI 240


>gi|154505842|ref|ZP_02042580.1| hypothetical protein RUMGNA_03383 [Ruminococcus gnavus ATCC 29149]
 gi|153793860|gb|EDN76280.1| hypothetical protein RUMGNA_03383 [Ruminococcus gnavus ATCC 29149]
          Length = 312

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 96/252 (38%), Gaps = 23/252 (9%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +IL    Q      QI        ++ A+ + ++GY E+NLN+GCPS  V     GA
Sbjct: 48  EKNDILPMHNQGMCAIPQILTNSAEDFIKTAERLGEYGYEEVNLNLGCPSKTVVSKGRGA 107

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  PD +   +  + +   I ++VK RIG   +        L++   +  +  + IH 
Sbjct: 108 GFLAEPDRLNAFLEELFEKTPIRISVKTRIG---KESPEEWIRLLEIYNQYPMEELIIHP 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDG 212
           R       +  +            Y +K  N    +  NG +   E+          V  
Sbjct: 165 RIQTDFYKNTPNLEMFE-------YAVK--NSKNPLCYNGDICTKEEYEIICNRFQEVPS 215

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           VMIGR   KN  ++  + +          P++    + F  ++     +          K
Sbjct: 216 VMIGRGILKNPGLVRKIRQGI--------PVEKDRIRAFHDELYREYQEVLFGEKTVLFK 267

Query: 273 LQQITRHMIGLF 284
           ++++  +M  LF
Sbjct: 268 MKELWFYMAPLF 279


>gi|301168352|emb|CBW27942.1| putative tRNA-dihydrouridine synthease [Bacteriovorax marinus SJ]
          Length = 345

 Score =  139 bits (350), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 53/285 (18%), Positives = 99/285 (34%), Gaps = 24/285 (8%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEM--------IVADAILRGDKKNILGFSTQEKPLA 51
           M   TD  YR    R       L T+              I+    + +L      K   
Sbjct: 32  MEGVTDEPYRIAIERAFPEWDYLCTDFLRVPTVGSFSTQKIIGHYGEKVLSTPELRKKTG 91

Query: 52  LQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            QI  +  ++  E    +        ++LN+GCPS +V+    GA L+   D + + I  
Sbjct: 92  FQILTSYRAQTKEMVSRLNSIEEIEHLDLNLGCPSKKVNAHKGGAYLLSEMDELREIIKI 151

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +      TVK RIG  +        + +K  +  GV  I IH R         +D   
Sbjct: 152 IRENFKRTFTVKIRIGYKNTDR---FLDSLKLFEDEGVEAITIHGRT--------RDQLY 200

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
               ++D + +  K + ++ I  NG +  +    ++      D +M+GR A K   + + 
Sbjct: 201 RGLANWDYIKQAVK-SVNIPIIGNGDVWTVHDIDRMFDYCECDSIMLGRGALKTPWLASL 259

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
             +   +             K F +     +     +  +   ++
Sbjct: 260 YYQNKDSLDDLDDYTLLEARKTFIQNYFDELEREYKKEENQNIRI 304


>gi|295103975|emb|CBL01519.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii SL3/3]
          Length = 316

 Score =  139 bits (350), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 52/303 (17%), Positives = 107/303 (35%), Gaps = 33/303 (10%)

Query: 1   MVDWTDRHYRFFARLL----TNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQ 53
           M  +TDR +R   +            Y   I       +++     +   +    P+  Q
Sbjct: 8   MEGFTDRVWRQTHQKWFGAQGAADRYYAPFISPPENRVLIKKKMAELAPEANPGAPVIPQ 67

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   D    V     +   GY E+NLN+GCP+  V     G+ ++ +   V   +  +  
Sbjct: 68  LLAKDGELAVWMIGQLRALGYTEVNLNLGCPAGTVTAKGKGSGMLRDLAKVDAFLDGVFS 127

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
               PV+VK R+GV+          +++   +  ++ + IH R    +     D      
Sbjct: 128 RTEGPVSVKTRLGVE---KPEEFAAILEIYSRYPISELTIHPRVMRQQYRGQADR----- 179

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQ---ALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                 + +      + +  NG +   +Q     +  P++ G+M+GR    + A+   V 
Sbjct: 180 ----AAFAVALPRCTMPVCYNGDVTTAAQLHALEEEFPALSGIMVGRGLIADPALFRRVR 235

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                   G +P      + +   +    T+       +G  + ++  H   L H F  +
Sbjct: 236 --------GGAPATKEDLRGYLTDLYHGYTELFG---SAGCAISRMKGHWFYLIHCFAGA 284

Query: 291 RRC 293
            + 
Sbjct: 285 EKL 287


>gi|290985846|ref|XP_002675636.1| dihydrouridine synthase, DuS [Naegleria gruberi]
 gi|284089233|gb|EFC42892.1| dihydrouridine synthase, DuS [Naegleria gruberi]
          Length = 388

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 55/310 (17%), Positives = 106/310 (34%), Gaps = 51/310 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFSTQEK------ 48
           MV      +R  A       ++Y+E +V   +++         K I              
Sbjct: 41  MVRVNGLPFRRLAARF-GADIVYSEELVDKKLIKCKPVYNEKLKTIDYIGHDGNIVYQVE 99

Query: 49  ---------------PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
                          P  LQ+G +     ++ A+++ D GY+ I++N+GCP     +G  
Sbjct: 100 VVDKESDSPTASQKVPTVLQLGTSSPELALQVAELMID-GYDAIDVNMGCPKKFSVKGGM 158

Query: 94  GACLML--NPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
           G+ L+   N +     + A+ K +      PVT K R+             L + ++ +G
Sbjct: 159 GSALLRPENQENAFAILRALVKGIQEKHGKPVTCKIRLL----DTTENTIELYEKLQATG 214

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LK 205
           V  I +HAR    +      +  +  +          +   + I  NG +        +K
Sbjct: 215 VTAICVHARYIPQRPREKAHSHLVDPV---------SKITKVPIIANGDVFKPEDIDRIK 265

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            L     VMI R A  N ++           +     +   +  ++   +S  +      
Sbjct: 266 DLTGCSSVMIARGAMWNLSIFRKEKVLLDKLVVAKELLDELIKYNYHSGLSKYILKRMFE 325

Query: 266 HLHSGGKLQQ 275
             H+  KL +
Sbjct: 326 -THAKTKLYE 334


>gi|297699046|ref|XP_002826610.1| PREDICTED: LOW QUALITY PROTEIN: tRNA-dihydrouridine synthase 2-like
           [Pongo abelii]
          Length = 493

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 100/253 (39%), Gaps = 46/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD 
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDK 136

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++   K    PVT   RI    +       +LVK I+++G+  I +H RK      
Sbjct: 137 IEKLLSLFVKGTRRPVTCNIRILPSLEDT----LSLVKRIERTGIAAITVHGRKQ----- 187

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
              + R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 188 ---EERPQHPVSCEVIKAIA-DTVSIPVIANGGSHDHIQRYSDIEDFRQA----TAASSV 239

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 240 MVARAAMWNPSIF 252


>gi|268570080|ref|XP_002640687.1| Hypothetical protein CBG19749 [Caenorhabditis briggsae]
 gi|187023917|emb|CAP36964.1| hypothetical protein CBG_19749 [Caenorhabditis briggsae AF16]
          Length = 436

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 95/248 (38%), Gaps = 35/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFST 45
           MV       R    L     L+YTE IV   ++               R     IL  + 
Sbjct: 14  MVRAGRTPLRLLC-LKYGADLVYTEEIVDKKLIEATRVVNEALGTIDYRNGDDIILRLAP 72

Query: 46  QEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           +EK    LQIG     K  + A+IV D     I++N+GCP         GA L+   + +
Sbjct: 73  EEKGKCILQIGTNSGEKAAKIAEIVGD-DVAGIDVNMGCPKPFSIHCGMGAALLTQTEKI 131

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
              + A+  A  +PVT K R+  + +        LV+ I+K GV  + +H R+       
Sbjct: 132 VGILTALKAAAKVPVTCKIRVLDNPEDT----LKLVREIEKCGVVALGVHGRR------- 180

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALKILP--SVDGVMIGRAA 219
            +D R+     Y+ + E+ K    + I  N   G +E      K         +MI R A
Sbjct: 181 -RDERQPDRCRYEEIREVVKTIQSIPIIANGFSGEIERYEDIEKWRDAAGTSSIMIARKA 239

Query: 220 YKNSAMLT 227
               ++  
Sbjct: 240 LSTPSIFR 247


>gi|296082372|emb|CBI21377.3| unnamed protein product [Vitis vinifera]
          Length = 316

 Score =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 41/154 (26%), Positives = 75/154 (48%), Gaps = 8/154 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MVD ++  +R   R     A  YT M+ +      +K     F+T  +++PL +Q    D
Sbjct: 75  MVDNSELPFRMLCRKYGAQA-AYTPMLHSRIFSENEKYRSQEFTTCKEDRPLFVQFCAND 133

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L+EAA+ VE +  + +++N+GCP      G++GA LM N  +V   +  +   L +P
Sbjct: 134 PDTLLEAAQRVEPY-CDYVDINLGCPQRIARRGNYGAFLMDNLPLVKSLVEKLALNLHVP 192

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           V+ K R+  + Q       N  + ++ +G + + 
Sbjct: 193 VSCKIRVFPNLQDT----INYARMLEDAGCSLLA 222


>gi|66810311|ref|XP_638879.1| tRNA-dihydrouridine synthase 2-like protein [Dictyostelium
           discoideum AX4]
 gi|60467531|gb|EAL65553.1| tRNA-dihydrouridine synthase 2-like protein [Dictyostelium
           discoideum AX4]
          Length = 402

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 106/248 (42%), Gaps = 36/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-------MIVADAILRGDKKNI--------LGFST 45
           MV       R  A       + Y+E       M     ++    K I        L + T
Sbjct: 39  MVRVGTYPMRILAYNY-GCDIAYSEELIDLKLMKSTR-VVNEKLKTIDFIAKDQTLCYRT 96

Query: 46  QEKPL--ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            EK +   LQ+G A     +EAAK+V +     +++N+GCP     +G  G+ L+  P+ 
Sbjct: 97  SEKDVRNVLQLGTASSMTALEAAKVVCN-DICALDINMGCPKFFSVQGGMGSALLSKPET 155

Query: 104 VGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + D +  + + L+ IP+T K R+   DQ       +L++ I+ +GV+ I +H R    + 
Sbjct: 156 IKDILTTLKRNLNGIPITCKIRLLSTDQ----ETIDLLRIIESTGVSAIGVHCRMIPERP 211

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAA 219
             P    ++ N+       +   +  + I  NG +    D+ +  K    VD +MI R  
Sbjct: 212 RDPAHWDRLENI-------LSNASFSVPIIANGDIFEHADIEKIKKQ-TKVDSIMIARGV 263

Query: 220 YKNSAMLT 227
            KN ++ +
Sbjct: 264 VKNVSIFS 271


>gi|308470958|ref|XP_003097711.1| hypothetical protein CRE_14205 [Caenorhabditis remanei]
 gi|308239829|gb|EFO83781.1| hypothetical protein CRE_14205 [Caenorhabditis remanei]
          Length = 436

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 95/253 (37%), Gaps = 43/253 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFST 45
           MV       R    L     L YTE IV   ++               R     IL  + 
Sbjct: 14  MVRAGRTPLRLLC-LKYGADLCYTEEIVDKKLIESTRVINDALGTIDYRNGDDIILRLAP 72

Query: 46  QEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           +EK    LQIG     K  + A+IV D     I++N+GCP         GA L+   + +
Sbjct: 73  EEKGRCILQIGTNSGEKAAKIAEIVGD-DVAGIDVNMGCPKPFSIHCGMGAALLTQTEKI 131

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            D + ++  A  +PVT K R+  + +        LV+ I+K GV+ + +H R+       
Sbjct: 132 IDILKSLKAAAKVPVTCKIRVLDNPEDT----LKLVREIEKCGVSALGVHGRR------- 180

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---------GLEDMSQALKILPSVDGVMI 215
            +D R+      + + E+ +    + I  NG          +E    A         +MI
Sbjct: 181 -RDERQPDQCRIEEIREVSRTITTIPIIANGFSGEIEQFSDIEKWRSA----TETSSIMI 235

Query: 216 GRAAYKNSAMLTT 228
            R A    ++   
Sbjct: 236 ARKALSTPSIFRE 248


>gi|154336333|ref|XP_001564402.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134061437|emb|CAM38463.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 512

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 100/255 (39%), Gaps = 44/255 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   R      + YT M++A++ ++        F+    E  L +Q+    
Sbjct: 122 MVRCSRPAFRQVCRSW-GTRIGYTHMLIAESFVKSPHARHAEFALYEGENRLVVQLAAKS 180

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
            +   EAA ++  +  + I+LN GCP     +   GA L+  P+ V D + ++  A+   
Sbjct: 181 GTDAAEAALLLRPY-CDAIDLNCGCPQRWAMKDGIGAVLLDQPERVADMVRSIRNAMPDG 239

Query: 117 -----------------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                                  +P  VK RI  D +       +  +  + +G + + +
Sbjct: 240 NTAPMMVSIGGACSSCPATAPPFLPCVVKMRIKDDLRNSV----DFARQCEAAGASWLTV 295

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVD 211
           H R A  +  +      +         ++ +EN  + + LNGG+ D+S A++  +     
Sbjct: 296 HGRSATSQPSAAVQFEAV---------KLIRENLSVPVVLNGGVRDVSTAMEAALRTGCG 346

Query: 212 GVMIGRAAYKNSAML 226
           G+M       N AM 
Sbjct: 347 GLMSANGLLDNPAMF 361


>gi|148262356|ref|YP_001229062.1| dihydrouridine synthase, DuS [Geobacter uraniireducens Rf4]
 gi|146395856|gb|ABQ24489.1| tRNA-U20a,U20b-dihydrouridine synthase [Geobacter uraniireducens
           Rf4]
          Length = 333

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/271 (20%), Positives = 108/271 (39%), Gaps = 24/271 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEK--PLALQIG 55
           M   T+R  R          +++TE +    A  I R    ++   +  E   PL +Q+ 
Sbjct: 32  MQGVTNRAMRSLFIDWVRPDVVFTEFMRVNAAAPIRRLSAGDLREITASEGNVPLVVQLI 91

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G     LV AA+  +  G   INLN+GCP  R+  G  G  ++  P+ + + I A+ +A+
Sbjct: 92  GHGREALVSAAQAAQAAGAVHINLNMGCPYGRMTSGLTGGGMLQRPEDLAEIIPALRRAI 151

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K R G DD      + +L+   + + V+ + +H R  + K             D
Sbjct: 152 DGTFSIKLRAGYDDHGQ---IFDLLPLFETASVDFLVLHPRTVVQKYG--------GAAD 200

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +  ++ +    L +  NG +   +  L++L      G+M+GR A  +  +   +    
Sbjct: 201 HAVTAQVVRHT-RLPVIANGDIRSAAVGLRVLQETGAAGLMLGRGAIADPLLFERLR--- 256

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
                 + P +          +   +  Y  
Sbjct: 257 --GGANAEPDQDERAAMLHHYLRELLARYGE 285


>gi|167526006|ref|XP_001747337.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774172|gb|EDQ87804.1| predicted protein [Monosiga brevicollis MX1]
          Length = 487

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 100/249 (40%), Gaps = 34/249 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAI----------LRGDKKNILGFS 44
           MV       R  A       L+Y+E      M+    +          + GD +      
Sbjct: 14  MVRAGTLPTRLLALRY-GADLVYSEELIDHRMLACRRVENPVLQTIDYIDGDGEVAFRTC 72

Query: 45  TQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            +EK  + LQIG +D  +    A+++       I++N+GCP     +G  GA L+  PD 
Sbjct: 73  AEEKNRVILQIGTSDPDRAARVAQMMAA-DVAGIDVNMGCPKPFSIKGDMGAALLRQPDR 131

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V D + ++    + P+T K R+    +       NLV  I+ +GV  + IH R    +  
Sbjct: 132 VRDILTSLVATTTKPITCKIRVLPTLE----ETLNLVNIIQDAGVAALGIHGRVPNQRPR 187

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRA 218
            P     I +  Y+ +  + K    + +  NGG  DM     IL          VM+ RA
Sbjct: 188 EP-----ITDYQYEAIRAVAKAC-RIPVICNGGSLDMDSYDDILAFRDKCGCSSVMVARA 241

Query: 219 AYKNSAMLT 227
           A  N ++ +
Sbjct: 242 AQYNMSIFS 250


>gi|302664204|ref|XP_003023736.1| hypothetical protein TRV_02123 [Trichophyton verrucosum HKI 0517]
 gi|291187746|gb|EFE43118.1| hypothetical protein TRV_02123 [Trichophyton verrucosum HKI 0517]
          Length = 957

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 94/284 (33%), Gaps = 62/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------KPLA--- 51
           +  +R     L      Y+EM ++  +++G K    ++     E         +P+    
Sbjct: 356 NLPFRRLCVEL-GAQFTYSEMAMSLPLMQGTKGEWALMKAHESEILPPTISPKQPVVKGY 414

Query: 52  ---------LQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G    + ++A +I+     +   ++LN GCP   V+    G+ L+ +
Sbjct: 415 DHSRDLKFGAQIAGNRPWQALKATEILTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 474

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M      +P++ K R+G  D         L + +              +G
Sbjct: 475 PSKLEKILRGMNAVSGEVPISAKIRMGTKD--NYPTALKLAERLVIGGYESNELGQGPAG 532

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLF 190
           +  + +H R    +     D   I                  D + E  + +      ++
Sbjct: 533 IGALTLHGRSRQQRYTREADWEYISECSALVKRLNAKRDEVSDTIREPDERHLPPGGKVY 592

Query: 191 IGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              NG      D + A+     VD VM+ R A     +   +  
Sbjct: 593 FIGNGDCYSHADYNTAVDK-SGVDSVMVARGALIKPWIFEEIQA 635


>gi|296157786|ref|ZP_06840620.1| dihydrouridine synthase DuS [Burkholderia sp. Ch1-1]
 gi|295892032|gb|EFG71816.1| dihydrouridine synthase DuS [Burkholderia sp. Ch1-1]
          Length = 340

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 60/331 (18%), Positives = 122/331 (36%), Gaps = 38/331 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +       +E + V  ++L G             G +    P+ +
Sbjct: 9   MEGLADYVLRDVLTGMGGFDGCVSEFVRVTGSLLPGRVYEREAPEVLDGGHTPCGTPMVI 68

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A        + I+LN GCP+  V++   GA L+ +P+ +   ++++ 
Sbjct: 69  QLLGSDPEWMALNAAHAASLSPHGIDLNFGCPAKVVNQHGGGAMLLADPEQLNRIVSSVR 128

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   I VT K R+GV D   A+   +   ++ + G   + +HAR         +D+  
Sbjct: 129 AAVPAGIAVTAKMRLGVSDTSLAI---DCAVALAEGGAAALVVHART--------RDHGY 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  I     D+ +  NG +  ++   +   +     VM+GR A  +  +   
Sbjct: 178 RPPAHWEWIARIDSAV-DVPVVANGEVWTVADWERCRAVSGCADVMLGRGAVSDPFLALR 236

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR---HLHSGGKLQQITRHMIGLFH 285
           +        +             WR +   +  Y  +    + S  +  ++ + +  L  
Sbjct: 237 IRGLMDRSPSDGE----------WRHVLGHIAGYLRKLQARVASRHEHGRVKKWLSYLQR 286

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFN 316
            +P +    H        S     +IE A  
Sbjct: 287 TWPQAAEL-HAAIRRLQDSHEILAVIERALE 316


>gi|327295134|ref|XP_003232262.1| tRNA-dihydrouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326465434|gb|EGD90887.1| tRNA-dihydrouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 755

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/292 (16%), Positives = 97/292 (33%), Gaps = 78/292 (26%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------KPLA--- 51
           +  +R     L      Y+EM ++  +++G K    ++     E         +P+    
Sbjct: 357 NLPFRRLCVEL-GAQFTYSEMAMSLPLMQGTKGEWALMKAHESEILPPTISPKQPVVKGY 415

Query: 52  ---------LQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G    + ++A +I+     +   ++LN GCP   V+    G+ L+ +
Sbjct: 416 DHSRDLKFGAQIAGNRPWQALKATEILTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 475

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M      +P++ K R+G  D         L + +              +G
Sbjct: 476 PSKLEKILRGMNAVSGEVPISAKIRMGTKD--NYPTALKLAERLVIGGYESNELGQGPAG 533

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE----IKKEN----------------- 186
           +  + +H R         +  R     D++ + E    +K+ N                 
Sbjct: 534 IGALTLHGRS--------RQQRYTREADWEYISECSALVKRLNTKRDEVSDTVREPDERL 585

Query: 187 ----PDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                 ++   NG      D + A+     VD VM+ R A     +   +  
Sbjct: 586 LPPGGKVYFIGNGDCYSHADYNTAIDK-SGVDSVMVARGALIKPWIFEEIQA 636


>gi|195478541|ref|XP_002100554.1| GE17129 [Drosophila yakuba]
 gi|194188078|gb|EDX01662.1| GE17129 [Drosophila yakuba]
          Length = 473

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 103/250 (41%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLAL-- 52
           MV       R  A  +    ++YTE +V   +++  ++       +      +  +    
Sbjct: 31  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLIKSIRRPNPALGTVDFVDPSDGTIVFRT 89

Query: 53  ----------QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                     Q+G +D  + +   K+++    + +++N+GCP     +G  GA L+ +PD
Sbjct: 90  CAQETSRLVLQMGTSDAGRALAVGKLLQ-RDISGLDINMGCPKEFSIKGGMGAALLADPD 148

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IPVT K RI  D         +LV+ +  +G+  I IHAR      
Sbjct: 149 KAALILRTLCSGLDIPVTCKIRILPD----VEGTIDLVQKLAATGIAAIGIHART----- 199

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              +D R   +   +++  + +   D+ I  NGG ++M     +         D VM+ R
Sbjct: 200 ---RDERPQHSAHPEVLRAVAQAV-DIPIIANGGSKNMHCYEDLRKFQLECGADSVMVAR 255

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 256 AAQINVSIFR 265


>gi|195352556|ref|XP_002042778.1| GM17665 [Drosophila sechellia]
 gi|194126809|gb|EDW48852.1| GM17665 [Drosophila sechellia]
          Length = 473

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 58/252 (23%), Positives = 102/252 (40%), Gaps = 38/252 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A  +    ++YTE +V   ++R  ++                      
Sbjct: 31  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLIRSIRRPNPALGTVDFVDPSDGTIVFRT 89

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   L LQ+G +D  +   A  ++     + +++N+GCP     +G  GA L+ +PD
Sbjct: 90  CAQETSRLVLQMGTSDARR-ALAVGMLLQRDISGLDINMGCPKEFSIKGGMGAALLADPD 148

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              + +  +C  L IPVT K RI  D         +LV+ +  +G+  I IHAR      
Sbjct: 149 KAANILRTLCSGLDIPVTCKIRILPD----VERTIDLVQKLAATGIAAIGIHART----- 199

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              +D R       +++  + +   D+ I  NGG ++M     +           VM+ R
Sbjct: 200 ---RDERPQHPAHPEVLRAVAQAV-DIPIIANGGSKNMHCYEDLRKFQLECGAASVMVAR 255

Query: 218 AAYKNSAMLTTV 229
           AA  N ++   V
Sbjct: 256 AAQINVSIFRPV 267


>gi|291087414|ref|ZP_06571931.1| dihydrouridine synthase family protein [Clostridium sp. M62/1]
 gi|291075096|gb|EFE12460.1| dihydrouridine synthase family protein [Clostridium sp. M62/1]
          Length = 319

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/324 (17%), Positives = 123/324 (37%), Gaps = 32/324 (9%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  + R        +T  +      A+   ++ ++L    +   L  QI  
Sbjct: 1   MEGITGYVYRNAYHRHFGRIGKYFTPFLSPHLNKAMTSRERNDVLPEHNRGILLVPQILT 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-----LNPDIVGDCIAAM 111
            D      A + + + GY E+NLN+GCPS  V     G+  +        +   D I   
Sbjct: 61  NDAEAFCSAMRGLWELGYREVNLNLGCPSGTVAAKGKGSGFLAAQLRERLECFLDEIFDC 120

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            + + + V++K R+G   +  +     L++   +  ++ + IH R       +       
Sbjct: 121 AENMGMRVSIKTRLG---KESSEGFEELLELYLRFPLSELIIHPRVQTDFYKNTPH---- 173

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMS---QALKILPSVDGVMIGRAAYKNSAMLTT 228
               ++     K+    + +  NG +       +     P  + VM+GR    N  +   
Sbjct: 174 ----WEAFRLAKERACGVKLCYNGDIFTPEELSRFRAEFPETECVMLGRGVIANPGLA-- 227

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-HGF 287
                    TG +P+  +  +DF   +     +  + + ++  K++++  +M+ LF    
Sbjct: 228 -----EWMETGKNPLDEKRFRDFHEDLLNGYREVMSGNRNTLFKMKELWTYMLTLFPDSE 282

Query: 288 PNSRRCRHILTVEAGASTATHHII 311
             +++ R   ++EA  + A   ++
Sbjct: 283 KEAKKIRKAGSMEAYLA-AVEELL 305


>gi|195998315|ref|XP_002109026.1| hypothetical protein TRIADDRAFT_2009 [Trichoplax adhaerens]
 gi|190589802|gb|EDV29824.1| hypothetical protein TRIADDRAFT_2009 [Trichoplax adhaerens]
          Length = 300

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 68/292 (23%), Positives = 108/292 (36%), Gaps = 42/292 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL----------------RGDKKNILGFS 44
           MV       R  + L     L+Y E I+   ++                  D + +    
Sbjct: 10  MVRMGTLPLRLLS-LDYGADLVYCEEIIDHKLVKCKRVENEVLNSIDFVHPDGQCVFRTC 68

Query: 45  TQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            QE   + LQ+G AD  + +  AK+VE+     I++N+GCP     +G  GA L+  P  
Sbjct: 69  RQETDKVILQLGTADPERALLTAKLVEN-DVAGIDINMGCPKEYSTKGGMGAALLTEPQK 127

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V + +  +      PVT K RI    Q       +L K I+ +GV  + IH R  + +  
Sbjct: 128 VYNILKKLVDNCLKPVTCKIRILPKLQDT----LDLAKVIESTGVAAVAIHGRLKVERPR 183

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSV--DGVMIGRA 218
            P        +  DI+  I      + +  NGG   ++  S   K         VMI RA
Sbjct: 184 QP--------VHKDIIRTISNSL-SIPVIANGGSLEIKSFSDIEKFKQETNSSSVMIARA 234

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
           A  + ++           L     +K+ +        S S + Y   H   G
Sbjct: 235 AQWDPSIFRK-----EGSLPTDEIVKSYIKYAIDYDNSWSNSKYCITHFMRG 281


>gi|194770353|ref|XP_001967258.1| GF15959 [Drosophila ananassae]
 gi|190614534|gb|EDV30058.1| GF15959 [Drosophila ananassae]
          Length = 460

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 101/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A  +    ++YTE +V   +++  +++                     
Sbjct: 18  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLIKSIRRHNPALGTVDFVDPSDGTIVFRT 76

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            + +   L LQ+G +D  + +   K+++    + +++N+GCP     +G  GA L+  PD
Sbjct: 77  CAQETSRLVLQMGTSDADRALAVGKLLQ-RDISGLDINMGCPKEFSIKGGMGAALLSEPD 135

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IPVT K RI  D          LV+ +  +G+  I IHAR      
Sbjct: 136 KAAVILRTLCSNLDIPVTCKIRILPDVDDT----IRLVQKLADTGIAAIGIHART----- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              +D R       D++  + +    + I  NGG  DM +   +         D VM+ R
Sbjct: 187 ---RDERPQHKPHPDVLRAVAQAV-SIPIIANGGSRDMHKYEDLRKFQEDCGADSVMVAR 242

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 243 AAQLNVSIFR 252


>gi|319763927|ref|YP_004127864.1| dihydrouridine synthase dus [Alicycliphilus denitrificans BC]
 gi|330823809|ref|YP_004387112.1| dihydrouridine synthase DuS [Alicycliphilus denitrificans K601]
 gi|317118488|gb|ADV00977.1| dihydrouridine synthase DuS [Alicycliphilus denitrificans BC]
 gi|329309181|gb|AEB83596.1| dihydrouridine synthase DuS [Alicycliphilus denitrificans K601]
          Length = 339

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/277 (21%), Positives = 112/277 (40%), Gaps = 30/277 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQ---------EKPL 50
           M    D   R     +       +E I V  ++L    K  L +  +           P+
Sbjct: 16  MEGLLDFVLRDVLTRVGGVDRCVSEFIRVTGSLL--PDKVFLRYLPELRNGGRTLAGVPV 73

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+ G+D   + E A  +   G   I+LN GCP+  V+    GA L+  P+++   +AA
Sbjct: 74  RAQLLGSDPVSMAENAARLAALGPEGIDLNFGCPARTVNRHGGGAALLREPEVIAAVVAA 133

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +PV+ K R+G DD   A   R   +++++ G   + +HAR         K +
Sbjct: 134 VRRAVPAHLPVSAKMRLGYDD---AGRARECAQAMEQGGACELVVHART--------KAD 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
              P   ++ + EI +E   + +  NG +  ++ AL+   +   D +M+GR    +  + 
Sbjct: 183 GYRPPAYWERIPEI-REAVAIPVVANGEIWTVADALRCRGVSGCDALMLGRGMVADPGLA 241

Query: 227 TTVDEYFSNPLTGSSP--IKTRVDKDFWRKISASMTD 261
             +          + P          FW+ +   +  
Sbjct: 242 LAIRAQDVGQGAFALPWAALLPQLARFWQLVCEDLEP 278


>gi|326476902|gb|EGE00912.1| tRNA-dihydrouridine synthase [Trichophyton tonsurans CBS 112818]
 gi|326481010|gb|EGE05020.1| tRNA-dihydrouridine synthase [Trichophyton equinum CBS 127.97]
          Length = 755

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/284 (16%), Positives = 94/284 (33%), Gaps = 62/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------KPLA--- 51
           +  +R     L      Y+EM ++  +++G K    ++     E         +P+    
Sbjct: 357 NLPFRRLCVEL-GAQFTYSEMAMSLPLMQGTKGEWALMKAHESEILPPAISPKQPIVKGY 415

Query: 52  ---------LQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G    + ++A +I+     +   ++LN GCP   V+    G+ L+ +
Sbjct: 416 DHSRDLKFGAQIAGNRPWQALKATEILTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 475

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M      +P++ K R+G  D         L + +              +G
Sbjct: 476 PSKLEKILRGMNAVSGEVPISAKIRMGTKD--NYPTALKLAERLVIGGYESNELGQGSAG 533

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLF 190
           +  + +H R    +     D   I                  D V E  + +      ++
Sbjct: 534 IGALTLHGRSRQQRYTREADWEYISECSALVKRLNAKRDEVSDTVREPDERHLPPGGKVY 593

Query: 191 IGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              NG      D + A+     VD VM+ R A     +   +  
Sbjct: 594 FIGNGDCYSHADYNTAIDK-SGVDSVMVARGALIKPWIFEEIQA 636


>gi|325264707|ref|ZP_08131436.1| dihydrouridine synthase family protein [Clostridium sp. D5]
 gi|324029999|gb|EGB91285.1| dihydrouridine synthase family protein [Clostridium sp. D5]
          Length = 313

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 51/287 (17%), Positives = 98/287 (34%), Gaps = 27/287 (9%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKK---NILGFSTQEKPLALQIGGA 57
              T   YR  + +        +   I  +       K   +IL    +      QI   
Sbjct: 9   EGITGYVYRNAYYKCFGEMDRYFIPFISPNQFGHLSSKEKNDILPEHNEGMDAVPQILTN 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                +  A  ++ +GY+E+NLN+GCPS  V     G+  +  PD +   +  + +   +
Sbjct: 69  SAEDFIRTAGKLKKYGYSEVNLNLGCPSKTVVSKGRGSGFLAFPDKLDRFLKEIFEYTDM 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            ++VK RIG D         +L+    +  ++ + IH R       +  + +        
Sbjct: 129 KISVKTRIGKDGPD---EFESLLDIYNQYPISELIIHPRLQADMYRNTPNWQVFGEAL-- 183

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK---ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  E     +  NG +       +     P VD VM+GR    N  ++T++     
Sbjct: 184 -------ERCRCRVCYNGDIFTPQDFERFTVTFPKVDCVMLGRGILSNPGLVTSIR---- 232

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
               G   ++      F  +I                K++++  +M 
Sbjct: 233 ----GKGKMRKDTLLAFHDQIYRDYQKILYGEKTILFKMKEMWFYMS 275


>gi|325189578|emb|CCA24064.1| tRNAdihydrouridine synthase putative [Albugo laibachii Nc14]
          Length = 427

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 52/248 (20%), Positives = 92/248 (37%), Gaps = 36/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI------------------LRGDKKNILG 42
           MV       R  +       L+Y+E I+   I                  +      +  
Sbjct: 14  MVRAGTLPLRLLSLRY-GADLVYSEEIIDKKIIATERIENPILNTVDFVSVNNRDSVVFR 72

Query: 43  FSTQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
            S +EK  +  Q+G +D    ++AA+ V       I++N+GCP     +G  GA L+  P
Sbjct: 73  TSKEEKDRVVFQMGTSDPILAIKAAQKVA-RDVAAIDVNMGCPKHFSIQGGMGAALLQKP 131

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            +  D I A+ + L IPV+ K R+  D      A    VK ++++G + I +H R+    
Sbjct: 132 QLAFDIIKALKQNLEIPVSCKIRVLEDTN----ATIEFVKKMEQAGADAIGVHGRQT--- 184

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAA 219
                  R      +D +  +        +  NG L         +    +   ++ R A
Sbjct: 185 -----HERPEDPASWDSIKPVVSAVSVPVL-ANGDLFTQTAIAKCREQTGLSSFLVARGA 238

Query: 220 YKNSAMLT 227
             N ++  
Sbjct: 239 LSNPSIFR 246


>gi|257456040|ref|ZP_05621245.1| putative dihydrouridine synthase [Treponema vincentii ATCC 35580]
 gi|257446563|gb|EEV21601.1| putative dihydrouridine synthase [Treponema vincentii ATCC 35580]
          Length = 347

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 90/236 (38%), Gaps = 22/236 (9%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGADISKLVEAAK 67
           R       +    +TEMI A +++ G +  +  L  +   + L  Q+        V+A  
Sbjct: 17  RMLIHTFGDPDEYFTEMIHAPSLIAGGRFEQWYLRTNPVPEKLVWQLTSPKGEAFVQAVP 76

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALSI-------PV 119
           +V   G   ++LN+GC +  +     GA  ML P +   + + ++ +AL +         
Sbjct: 77  LVLQQGGIGVDLNMGCSAPPIVRTGAGAAWMLKPLNETAEAVRSVKQALDVYAAAQSRSF 136

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            +  ++ +        L      + + GV  I IH R        P          ++  
Sbjct: 137 RLSVKLRIGAAADYAYLLRFCTMLVEEGVQLITIHPRLQRQSYARP--------ALHEYT 188

Query: 180 YEIKKENPDLFIGLNGGLEDMSQ---ALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
             + K+ P + +  NG ++   +   A    P+  G MIGRAA +   +   + + 
Sbjct: 189 AALAKDLP-IPVYGNGDIDSAEKLQTAAARYPACTGWMIGRAAVQKPWIFKEIRKR 243


>gi|326428503|gb|EGD74073.1| tRNA-dihydrouridine synthase [Salpingoeca sp. ATCC 50818]
          Length = 521

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 102/249 (40%), Gaps = 37/249 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----------------ILGFS 44
           MV       R  A       L+Y E IV   ILR  +                  +    
Sbjct: 34  MVRMGTLPTRLLALRY-GADLVYGEEIVDYKILRCSRVENPVLDTVDFVMPSGLVVFRTC 92

Query: 45  TQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            +EK  +  Q+G AD  + VE AK+VE+     I++N+GCP     +G  GA L+  PD+
Sbjct: 93  KEEKDRVIFQMGTADPQRAVEVAKLVEN-DVAGIDVNMGCPKNFSIKGGMGAALLREPDL 151

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             D +AA+ KA+ +PVT K R+    +    A  + +K ++ +G+  I +H R    +  
Sbjct: 152 AYDIMAALTKAVKVPVTCKIRLLPTRE----ATMSFMKRMQSTGIAAIGLHGRLREQRPR 207

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM-----SQALKILPSVDGVMIGRA 218
            P     +     D+          + +  NGG  D      + A       D +MI RA
Sbjct: 208 EPVQLDAMTAAIGDM---------HIPVIANGGSLDFKNYSEAHAWMEKTGCDSLMIARA 258

Query: 219 AYKNSAMLT 227
           A  N ++  
Sbjct: 259 AQNNLSVFR 267


>gi|213029657|ref|ZP_03344104.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 153

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 63/163 (38%), Gaps = 13/163 (7%)

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  +  G+
Sbjct: 2   NRKLAGSALLQYPDLVKSILIGVVNAVDVPVTLKIRTGWAPEHRN--CVEIAQLAEDCGI 59

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
             + IH R         +        +YD +  +K++   + I  NG + +  +A  +L 
Sbjct: 60  QALTIHGRT--------RACLFNGEAEYDSIRAVKQKV-SIPIIANGDITNPHKARAVLD 110

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
               D +MIGRAA     +   +  Y              V +
Sbjct: 111 YTGADALMIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKR 153


>gi|62859019|ref|NP_001016230.1| dihydrouridine synthase 2-like, SMM1 homolog [Xenopus (Silurana)
           tropicalis]
 gi|89268176|emb|CAJ82133.1| similar to dus2l (dihydrouridine synthase 2-like) [Xenopus
           (Silurana) tropicalis]
          Length = 495

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 68/301 (22%), Positives = 119/301 (39%), Gaps = 52/301 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQE------- 47
           MV       R  A L     ++Y+E      M+    ++      +   S  E       
Sbjct: 15  MVRVGTLPMRLLA-LDYGADIVYSEELVDIKMLQCKRVVNDVLHTVDYVSPTERVIFQTC 73

Query: 48  ----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G AD  + +  AK++++     I++N+GCP     +G  GA L+L P+ 
Sbjct: 74  ERERHSVVFQMGTADAERALTVAKLIQNDIAA-IDINMGCPKEYSTKGGMGAALLLCPEK 132

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   ++ + K +S P+T K RI            +LVK I+K+GV  I +H R       
Sbjct: 133 IEMILSTLVKGISKPITCKIRILP----SLTETISLVKLIEKTGVAAIAVHGRS------ 182

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----LEDMSQ--ALKILPSVDGVMIGR 217
             K+ R    +  D++  I +    + +  NGG    +       A + + S   VM+ R
Sbjct: 183 --KNERPQHPVHCDVIKAISQAV-SIPVIANGGSQEFIRQFQDISAFRSVTSASSVMLAR 239

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
           AA  N ++             G  P++T +     R   A    Y   + ++   L Q+ 
Sbjct: 240 AAMWNPSVFR---------PEGMLPVETVI-----RDYIAYAVQYDNHYTNTKYCLCQML 285

Query: 278 R 278
           R
Sbjct: 286 R 286


>gi|114674845|ref|XP_001146312.1| PREDICTED: dihydrouridine synthase 3-like isoform 2 [Pan
           troglodytes]
          Length = 678

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 87/284 (30%), Gaps = 54/284 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 321 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 379

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   +++   G  L                         
Sbjct: 380 KCAELLSRTVEVDFVDINVGCPIDLMYKKGQGCGL------------------------- 414

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
                        L   V          +        L G S ++ R     D+  + E 
Sbjct: 415 ------KSWLFWYLSLCVSLSASYPAWRL-----LPQLHGRS-REQRYTKLADWQYIEEC 462

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 463 VQAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHWDISSSE 522

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        I    T+Y   H  S  +  + TR  +   L
Sbjct: 523 ----------RLDILRDFTNYGLEHWGSDTQGVEKTRRFLLEWL 556


>gi|316970336|gb|EFV54297.1| conserved hypothetical protein [Trichinella spiralis]
          Length = 747

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 48/307 (15%), Positives = 106/307 (34%), Gaps = 55/307 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG-----------------------DKKNILG 42
           +  +R          +  +EM+++ ++ +G                        +   L 
Sbjct: 191 NLPFRRLCVEF-GAEVTCSEMVLSTSLFQGTVLKKSFSDKFTCKKVLNSIGLQSEWARLV 249

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNP 101
               EK   +QI     ++     KI++ F  ++ +++N  CP   +     GA L++ P
Sbjct: 250 RHESEKCFGIQICVNKPAQAWTVTKIIKKFAEFDFLDINAACPLDDICRAGGGANLLVRP 309

Query: 102 DIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
             + + + +   AL  +P+T+K R        +  +   +  +   GV+ + +H R    
Sbjct: 310 KKLKEVVQSTKAALGDVPLTLKLRT------DSNVVHQFLPDVYSWGVDRVVLHGRS--- 360

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
                ++ R I   D+  + +    +P + +   G +       + L    V GV + R 
Sbjct: 361 -----RNQRYINKSDWHYIDQCASVSP-VPLYGIGDVLSYEDYYQHLNCGKVQGVAVARG 414

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG-GKLQQIT 277
           A     + T + +     +  S  +          +I      Y   H  S    +    
Sbjct: 415 ALIKPWIFTEIIQQRHWDIRSSERL----------EILKKFVKYGLLHWGSDSTGVNCTR 464

Query: 278 RHMI-GL 283
           R ++  L
Sbjct: 465 RFLLEWL 471


>gi|167768596|ref|ZP_02440649.1| hypothetical protein CLOSS21_03155 [Clostridium sp. SS2/1]
 gi|167710120|gb|EDS20699.1| hypothetical protein CLOSS21_03155 [Clostridium sp. SS2/1]
 gi|291560550|emb|CBL39350.1| tRNA-U20a,U20b-dihydrouridine synthase [butyrate-producing
           bacterium SSC/2]
          Length = 314

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 57/284 (20%), Positives = 113/284 (39%), Gaps = 27/284 (9%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR     L       YT  I+ +        + +++L    +   +  QI  
Sbjct: 8   MESITIYLYRNIYEQLFGEIDKYYTPFIMPNGKRTFKTREFQDVLPEHNEGLNIVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +    +  AK +++ GYNE+NLN+GCPS  V     G+  +  P+++ D +  + +AL 
Sbjct: 68  KNAQDFIRTAKELKELGYNEVNLNLGCPSRTVVAKQKGSGFLREPEVLDDFLTEIYEALD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG+ +         ++    +  V  + IH R               P+LD 
Sbjct: 128 MKISIKTRIGLRE---PEEFEEILSIYNRHPVYELTIHPRLQQEFYKGK------PHLD- 177

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
             ++E   ++    +  NG +   +D          ++ VMIGR   +N A++  +   +
Sbjct: 178 --IFEYATKHSGNPLCYNGDIVTKQDYDHITDRFKDINAVMIGRGLLRNPALVREIK--Y 233

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
              LT       R        +  +  +Y +   +   K+++  
Sbjct: 234 GQKLTK------RELLKMHDTLYVAYQEYLSGDKNVLYKMKEFW 271


>gi|115492659|ref|XP_001210957.1| hypothetical protein ATEG_00871 [Aspergillus terreus NIH2624]
 gi|121742521|sp|Q0CZL3|DUS3_ASPTN RecName: Full=tRNA-dihydrouridine synthase 3
 gi|114197817|gb|EAU39517.1| hypothetical protein ATEG_00871 [Aspergillus terreus NIH2624]
          Length = 719

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/340 (17%), Positives = 102/340 (30%), Gaps = 73/340 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQE---------------- 47
           +  +R     L     +Y+EM ++  +++G K    +L     E                
Sbjct: 322 NLPFRRLCVEL-GAQFVYSEMAMSMPLIQGTKSEWALLRSHETELTPPTISPSDKIVQGY 380

Query: 48  -----KPLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI      + ++A +++  F      I+LN GCP   +     G+ L+ +
Sbjct: 381 DNSKDMKFGAQIAANKPWQALKATEVLSKFTPNLRVIDLNCGCPIDLLFREGAGSALLEH 440

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
              +   +  M      IP++VK R+GV D  P      LV+ +               G
Sbjct: 441 HSKLEKILRGMNAVSEEIPISVKIRLGVRDNAPNAQ--KLVERLVLGGHESHLLGLGPCG 498

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLF 190
              I +H R    +     D   I                  D +YE  +        ++
Sbjct: 499 TAAITLHGRSRQQRYTKQADWGYIAETAALIKNLNKRKDELTDTIYEPDERMLPNGGKVY 558

Query: 191 IGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG           +    VD VMIGR A     +   +        + S  +     
Sbjct: 559 FLGNGDCFSHQDYDDHINNAGVDSVMIGRGALIKPWLFEEIQTGQYLDKSASERLS---- 614

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL-FH 285
                 +      Y      S      ITR  +   L FH
Sbjct: 615 ------LVEKFAKYGLDTWGSDEYGVGITRRFLLEWLSFH 648


>gi|221488352|gb|EEE26566.1| conserved hypothetical protein [Toxoplasma gondii GT1]
 gi|221508854|gb|EEE34423.1| conserved hypothetical protein [Toxoplasma gondii VEG]
          Length = 668

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 121/328 (36%), Gaps = 95/328 (28%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-----------VADAILRGDKKNILGFSTQ--- 46
           M+D+T+RH+R    L++    LYTEM+            +  +    K+ +L  +     
Sbjct: 106 MMDYTNRHWRCLISLMSRRLTLYTEMVPVPPAPCESPDSSQDLPFSVKRKLLEEAGSLAS 165

Query: 47  -EKPLALQIGGADISKLVEAAKIVEDFGYNE----------------INLNVGCPSARVH 89
               + LQ+G          A+++ +F  +                 +NLN GCPS RV 
Sbjct: 166 IPNDVVLQVGVGSAQSATAVARVLNEFSVDRDHAEPVTRMRGKRTFLVNLNCGCPSPRVA 225

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL---------------------------------- 115
           +GSFG  LM +P  V +    +                                      
Sbjct: 226 KGSFGLILMEDPKRVAEMCQILVDGANNREGQKRCSLDVMGKSARGDTKDRTVHTNDSPE 285

Query: 116 --SIPVTVKCRIGVDDQI----------------------PAVALRNLVKS-IKKSGVNG 150
             S+ V+VKCR+G+++                            L   V + ++ S V  
Sbjct: 286 TDSVAVSVKCRVGIEEDKQFLRSGSSPISRATTPYSSSSCTYDKLAEFVGTVVETSPVRH 345

Query: 151 IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
             IHAR  IL G LSPK N +IP    + VY +  + P +    NGG++    A + L  
Sbjct: 346 FIIHARPGILVGKLSPKQNLQIPQRRPEWVYRLCSDFPTVSFTFNGGVKSFQNAEEHLLN 405

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYF 233
               + G+M+GR   +      +  + F
Sbjct: 406 TNDKLAGIMVGRDMLERPWYWGSHADAF 433


>gi|332227763|ref|XP_003263057.1| PREDICTED: tRNA-dihydrouridine synthase 2 [Nomascus leucogenys]
          Length = 540

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/244 (22%), Positives = 101/244 (41%), Gaps = 46/244 (18%)

Query: 10  RFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK-----------PLAL 52
           R  A L     ++Y E      MI    ++      +   +  ++            +  
Sbjct: 75  RLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTCEREQNRVVF 133

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++ + 
Sbjct: 134 QMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKILSTLV 192

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           K    PVT K RI    +       +LVK I+++G+  I +H RK        ++ R   
Sbjct: 193 KGTRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK--------REERPQH 240

Query: 173 NLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGVMIGRAAYKN 222
            +  +++  I  +   + +  NG           +ED  QA     +   VM+ RAA  N
Sbjct: 241 PVSCEVIKAIA-DTLSIPVIANGGSHDHIQRYSDIEDFRQA----TAASSVMVARAAMWN 295

Query: 223 SAML 226
            ++ 
Sbjct: 296 PSIF 299


>gi|170085799|ref|XP_001874123.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164651675|gb|EDR15915.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 308

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 98/241 (40%), Gaps = 30/241 (12%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILR---------------GDKKNILGFSTQEKP-L 50
              R FA L     L++   IV  AIL                G  + I      EKP L
Sbjct: 43  LPTRLFA-LKHGATLVWAPEIVDKAILHSTREVDPITGVISYNGVSRAIFATHPVEKPYL 101

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG +D    V+AAK+V     + I+LN GCP         GA L+ NPD++   + A
Sbjct: 102 IYQIGSSDPELAVQAAKMVMQ-DVSGIDLNCGCPKPFSTHAGMGAALLTNPDLLCSILTA 160

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + + +   I VT K R+    +        LV+ I  +G++ + +H R   ++    KD 
Sbjct: 161 LRREMPPEITVTAKIRLLPSQEDT----LKLVERIVNTGISALTVHCRTRNMR---EKDR 213

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
             I  L  +IV  ++     + +  NG       A ++        VMI R A  N +  
Sbjct: 214 AVIERLR-EIVEFVEGLGRGIAVIENGDCMSWEDAKRVRETTGAHSVMIARGAEANPSCF 272

Query: 227 T 227
           +
Sbjct: 273 S 273


>gi|213407250|ref|XP_002174396.1| tRNA dihydrouridine synthase Dus2 [Schizosaccharomyces japonicus
           yFS275]
 gi|212002443|gb|EEB08103.1| tRNA dihydrouridine synthase Dus2 [Schizosaccharomyces japonicus
           yFS275]
          Length = 462

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 60/255 (23%), Positives = 102/255 (40%), Gaps = 39/255 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--------------------KKNI 40
           MV   +   R  A       L++   IV  A++ G+                     K I
Sbjct: 1   MVRIGELPTRLLALRY-GADLVWGPEIVDKALVSGEKAQRVVNDHCQTIDFVKPPSNKVI 59

Query: 41  LGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
                 EK  L  Q+G  +    VEAAK+V +   + I+LN GCP         GA L+ 
Sbjct: 60  FRLHPLEKGRLIFQLGSCNPELAVEAAKLVVN-DVSAIDLNCGCPKHFSVHAGMGAGLLK 118

Query: 100 NPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
           N D +   + A+ + +  P    ++ K R+         A  ++V+ + K+G+  I +H 
Sbjct: 119 NLDRLESILRALVEQVGQPNNIGISCKIRLL----DTHEATLDMVRRLCKTGIRAITVHC 174

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
           R   ++   P     + +     + EI      + I +NG +++   A ++     VDG 
Sbjct: 175 RTTPMRNTEPAIRTSLRD-----IAEICHSY-HVSILVNGDVDNRKMAKELCEEYGVDGA 228

Query: 214 MIGRAAYKNSAMLTT 228
           +I RAA KN +    
Sbjct: 229 VIARAAEKNVSCFRE 243


>gi|156839540|ref|XP_001643460.1| hypothetical protein Kpol_483p21 [Vanderwaltozyma polyspora DSM
           70294]
 gi|187471051|sp|A7TQ73|DUS3_VANPO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|156114071|gb|EDO15602.1| hypothetical protein Kpol_483p21 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 664

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 62/283 (21%), Positives = 107/283 (37%), Gaps = 41/283 (14%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G           ST+     +QI  +   + 
Sbjct: 303 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHSTEIPGFGVQIACSKAWQA 361

Query: 63  VEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPV 119
            +AA+ +  F  +   INLN GCP   ++    G+ L+ NP  +  C+ AM      IP+
Sbjct: 362 AKAAEALAKFTPDINEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSDSIPI 421

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TVK R G  D  P      + + + ++ V  I +H R         +  R     D+D V
Sbjct: 422 TVKIRTGTRDSHPVADTL-VKRLVYETDVAAITLHGRS--------RQQRYTRVADWDYV 472

Query: 180 YEIKKEN--------------------PDLFIGLNGGLEDMSQALKIL---PSVDGVMIG 216
             + K                        +    NG + +     +IL    ++D +M+ 
Sbjct: 473 STVAKSLRESEASFLESAEGKESRESKRRIQFVGNGDVNNFEDWHRILNNDENIDSIMVA 532

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
           R A     +   VD      L  SS  +  + +D+ +      
Sbjct: 533 RGALIKPWVFEEVDA--QQHLDKSSTERLEILRDYAQFSMEHW 573


>gi|256080282|ref|XP_002576411.1| tRNA-dihydrouridine synthase [Schistosoma mansoni]
 gi|238661678|emb|CAZ32648.1| tRNA-dihydrouridine synthase, putative [Schistosoma mansoni]
          Length = 492

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 61/258 (23%), Positives = 107/258 (41%), Gaps = 40/258 (15%)

Query: 1   MVDWTDRHYRFFA----------------RLLTNNALLYTEMIVADAILRGDKKNILGFS 44
           MV  +    R                   R++ ++ ++  E+   D +L           
Sbjct: 1   MVRVSTHPMRLLCLEYGADYVISEELIDQRIIRSSRVVNAELNTIDFVLPDGSVTFRTSM 60

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            ++  + +Q+G  +    ++AAK++E+     I++N+GCP A   +G  GA L+  P+IV
Sbjct: 61  EEKNRVIVQLGTPEPGTALQAAKMLEN-DVMGIDVNMGCPKAYSIKGGMGAALLTKPEIV 119

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + +  +   L IPVT K RI  + +        L K I+ +GV  I +H R    + + 
Sbjct: 120 KEILTTLTTNLRIPVTCKIRILPELEKTIA----LAKLIESTGVAAITVHGRTINERPVH 175

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GL----EDMSQALKILPSVDGVMIGR 217
              N        +++  I      + +  NG    +    ED+    + L S  GV+I R
Sbjct: 176 RNRN--------EVIQTIANSVG-IPVLANGGSHDIIRNHEDIEYFRQ-LTSAAGVVIAR 225

Query: 218 AAYKNSAMLT--TVDEYF 233
           AA  N A+     VDE  
Sbjct: 226 AAMSNPAIFKSFQVDEPL 243


>gi|307207077|gb|EFN84886.1| tRNA-dihydrouridine synthase 2-like [Harpegnathos saltator]
          Length = 512

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 97/250 (38%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN------------------ILG 42
           MV       R  A L     ++YTE ++   +LR  ++                      
Sbjct: 69  MVRIGTLPMRLLA-LDYGADIVYTEELIDWKLLRSIRRENDVLGTIDYIDKTDRTVAFRT 127

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            S +   + LQIG +D ++ V+ A +VE      I++N+GCP      G  GA L+ NP 
Sbjct: 128 CSRERDNVVLQIGTSDPTRAVQVASMVEK-DVAGIDVNMGCPKKFSILGGMGAALLTNPQ 186

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  + + +SIPVT K R+  + +        L  ++  +G+  I +H R    + 
Sbjct: 187 QATSILRKLIETVSIPVTCKIRVLPNLE----ETFQLCDTLTSTGIEAIAVHGRTIDERP 242

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGR 217
                N          V ++  +   + +  NGG +D+     I           VM+ R
Sbjct: 243 QHSNRNH---------VLKLISDRLSIPVIANGGSKDVQNHSDIFRFKEETGCSSVMLAR 293

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 294 AAEWNCSVFR 303


>gi|114674843|ref|XP_001146147.1| PREDICTED: dihydrouridine synthase 3-like isoform 1 [Pan
           troglodytes]
          Length = 632

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 88/284 (30%), Gaps = 54/284 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 321 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 379

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   +++   G  L                         
Sbjct: 380 KCAELLSRTVEVDFVDINVGCPIDLMYKKGQGCGL------------------------- 414

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
                        L   V          +        L G S ++ R     D+  + E 
Sbjct: 415 ------KSWLFWYLSLCVSLSASYPAWRL-----LPQLHGRS-REQRYTKLADWQYIEEC 462

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 463 VQAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHWDISSSE 522

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T+Y   H  S  +  + TR  +   L
Sbjct: 523 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFLLEWL 556


>gi|313114319|ref|ZP_07799854.1| dihydrouridine synthase [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310623374|gb|EFQ06794.1| dihydrouridine synthase [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 314

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 53/305 (17%), Positives = 101/305 (33%), Gaps = 37/305 (12%)

Query: 1   MVDWTDRHYRFFARLL----TNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQ 53
           M   TDR +R   +       N    Y   I       +++     +   +    P+  Q
Sbjct: 8   MEGLTDRVWRQAHQKWFGPAGNADRYYAPFISPPENRVLIKKKMAELAPAANPGAPVIPQ 67

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   D          +   GY E+NLN+GCPS  V     G+ ++ +P  +   +AA+  
Sbjct: 68  LLAKDGELAAWMIGELRGLGYTEVNLNLGCPSGTVTAKGKGSGMLRDPVKLDAFLAAVFA 127

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
               P++VK R+GV+          ++    +  +  + IH R          D      
Sbjct: 128 NAEGPISVKTRLGVE---KPEEFAAILDIYNRYPICELTIHPRVMRQLYRGQADR----- 179

Query: 174 LDYDIVYEIKKENPDL--FIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
                        P     +  NG +    D+       P + G+M+GR    + A+   
Sbjct: 180 ------AAFAASLPGCRMPVCYNGDVTTAADLHTLEAQYPQLSGIMVGRGIIADPALFRE 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                     G +P      + +   +    ++       +G  + ++  H   L H F 
Sbjct: 234 AR--------GGAPAAREELRGYLDDLYHGYSELFG---SAGCAVSRMKGHWFYLIHKFE 282

Query: 289 NSRRC 293
            + + 
Sbjct: 283 GAEKL 287


>gi|323451531|gb|EGB07408.1| hypothetical protein AURANDRAFT_71832 [Aureococcus anophagefferens]
          Length = 557

 Score =  136 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 51/239 (21%), Positives = 90/239 (37%), Gaps = 20/239 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MV  ++  +R   R        YT M+ A   +         L    +++PL     G D
Sbjct: 132 MVGGSELAFRLLCRR-HGATAAYTPMMEATRFVEDAAFRAQYLQTHAEDRPLVAHFCGND 190

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMCKAL 115
              +  A  +    G  + ++LN+GCP      G +G+ LM   + D+V   +AAM +++
Sbjct: 191 PGVVGRACALAAATGGVDAVDLNLGCPQRVAFAGHYGSYLMREEDRDLVKSIVAAMRRSV 250

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              + V  +I + D  P  A   LV+ ++ +G   + IH RK           R     D
Sbjct: 251 PREIAVCVKIRLMDDFP--ATLKLVEDLRDAGAQVVAIHGRKRATWHRKGPGARD-GPAD 307

Query: 176 YDIVYEIKKENPDLFIG-------LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            D +  + +   D  +          G ++    A        GVM       + A+ +
Sbjct: 308 LDSIARVVRAVGDSVVVVSNGNVRDRGDVD----AGLATTGAAGVMSAEGLLDDPALFS 362


>gi|160942572|ref|ZP_02089819.1| hypothetical protein FAEPRAM212_00047 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446156|gb|EDP23159.1| hypothetical protein FAEPRAM212_00047 [Faecalibacterium prausnitzii
           M21/2]
          Length = 316

 Score =  136 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 53/305 (17%), Positives = 104/305 (34%), Gaps = 37/305 (12%)

Query: 1   MVDWTDRHYRFFARLL----TNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQ 53
           M  +TDR +R   +          L Y   I       +++     +   +    P+  Q
Sbjct: 8   MEGFTDRVWRQTHQKWFGAQGAADLYYAPFISPPENRVLIKKKMAELAPEANPGAPVIPQ 67

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   D          +   GY E+NLN+GCP+  V     G+ ++ +   V   +  +  
Sbjct: 68  LLAKDGELAAWMIGQLRALGYTEVNLNLGCPAGTVTAKGKGSGMLRDLAKVDAFLDGVFS 127

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
               PV+VK R+GV+          +++   +  ++ + IH R    +     D      
Sbjct: 128 HAEGPVSVKTRLGVE---KPEEFAAILEIYSRYPISELTIHPRVMRQQYRGQADRAAFAA 184

Query: 174 LDYDIVYEIKKENPDL--FIGLNGGLEDMSQ---ALKILPSVDGVMIGRAAYKNSAMLTT 228
                        P     +  NG +   +Q     K  P++ G+M+GR    + A+   
Sbjct: 185 -----------ALPRCTMPVCYNGDVTTAAQLHALEKEFPALSGIMVGRGLIADPALFRK 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                     G +P      + +   +    T+       +G  + ++  H   L H F 
Sbjct: 234 AR--------GGAPATKEELRGYLTDLYHGYTELFG---SAGCAISRMKGHWFYLIHCFA 282

Query: 289 NSRRC 293
            + + 
Sbjct: 283 GAEKL 287


>gi|207727952|ref|YP_002256346.1| trna-dihydrouridine synthase c (partial sequence n terminus)
           protein [Ralstonia solanacearum MolK2]
 gi|206591195|emb|CAQ56807.1| probable trna-dihydrouridine synthase c (partial sequence n
           terminus) protein [Ralstonia solanacearum MolK2]
          Length = 146

 Score =  136 bits (344), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 39/130 (30%), Positives = 68/130 (52%), Gaps = 6/130 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   + L       +EM+ ++A L   +K +     + + +P+A+QI GA+
Sbjct: 17  MAGVTDRPFRQLCKRL-GAGYAVSEMVASNAQLWKSEKTMRRANHTGEVEPIAVQIAGAE 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALS- 116
              + EAA+   D G   I++N+GCP+ +V   + G+ L+ N  +V   + A    A+  
Sbjct: 76  PMMMAEAARYNVDRGAQIIDINMGCPAKKVCNVAAGSALLQNEPLVARIVEAGGRGAVGD 135

Query: 117 -IPVTVKCRI 125
            +PVT+K R 
Sbjct: 136 RVPVTLKIRT 145


>gi|320587574|gb|EFX00049.1| dihydrouridine synthase family [Grosmannia clavigera kw1407]
          Length = 556

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 111/316 (35%), Gaps = 49/316 (15%)

Query: 1   MVDWTDRHYRFFARLL-----TNNALLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R   R        ++ L Y+ M+ A   +   +     F            
Sbjct: 36  MVDQSEFAWRMLVRSFLAPEKRSSVLAYSPMLHARLFVDSQRYRESHFEAMRSGVDGAEG 95

Query: 47  ----------------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
                           ++PL +Q    D + L+ AA++V     + ++LN+GCP     +
Sbjct: 96  IAAAAATPHLDGNPAVDRPLFVQFCANDPTALLAAARLVAPH-CDAVDLNLGCPQGIARK 154

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G +GA L  + +++   I A+ + L +PVT K RI         A     +++  +G + 
Sbjct: 155 GRYGAFLQEDRELIVRLIRALHEGLDVPVTAKIRIL----DTREATLQYAQAVLAAGASI 210

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKIL-- 207
           + +H R+   KG            D+  +  ++    P+  +  NG +       + L  
Sbjct: 211 LTVHGRRRDQKG------HLTGIADWATLRFLRDSLPPETVLFANGNVLQPRDLQRCLDA 264

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              DGVM       +  +  +  E   +    +           W        +Y     
Sbjct: 265 TGFDGVMSAEGLLSDPGLFGS--EPAGDADDAAETDTATFTATAWWPTPDVQREYWTSRD 322

Query: 268 HSGGKLQ---QITRHM 280
              G  +    + R++
Sbjct: 323 GQRGGWRVDAVMRRYL 338


>gi|302924043|ref|XP_003053802.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256734743|gb|EEU48089.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 770

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 51/291 (17%), Positives = 93/291 (31%), Gaps = 74/291 (25%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE-KP------------- 49
           +  +R     L    L Y+EM +   +++G      +L     E  P             
Sbjct: 371 NLPFRRLCVEL-GAQLTYSEMAIGMPLIQGTKADWTLLKVHDSELTPPKMNTGSVPIFED 429

Query: 50  --------LALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLML 99
                      QI G +   + +AA ++  +  +   I+LN GCP   V +   G+ L+ 
Sbjct: 430 YDHSRDLKFGAQISGNNHWVVSKAADVLNRYCPHLRLIDLNCGCPIDMVFKSGGGSALLE 489

Query: 100 NPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVA---------LRNLVKSIKKSGVN 149
           N   +   I  M   +  IP+T K R G+ +  P             R   + +   G  
Sbjct: 490 NHGKMERMIRGMNAMSGEIPITAKIRTGIRNNRPTATQLIGRLAFGAREHRERLGAPGCA 549

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----------------------- 186
            + +H R         ++ R     D+  + E                            
Sbjct: 550 ALTLHGRS--------REQRYTKKADWGYIGECAALIKSYNKQKDSLTDTAAEPDESSLP 601

Query: 187 ----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
                 ++   NG     ++  + +    VD VMIGR A     +   +++
Sbjct: 602 NAKDGRMYFLGNGDCYSHTEYYENIEKARVDTVMIGRGALIKPWIFEEIEK 652


>gi|312375539|gb|EFR22895.1| hypothetical protein AND_14041 [Anopheles darlingi]
          Length = 512

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 102/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILG---------------- 42
           MV       R  A       L+YTE I+   +LR +++  ++LG                
Sbjct: 20  MVRVGTLPMRLLALEY-GADLVYTEEIIDWKLLRAERRVNDVLGTIDYIDTTDGTVVFRT 78

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   + LQIG A   +     +++++   + I++N+GCP     +G  G  L+ +  
Sbjct: 79  CPAERGKVVLQIGTAAAERAAAVGRMLQE-DVSAIDVNMGCPKDFSIKGGMGVALLYDLP 137

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                + A+ + +SIPVT K R+  D          L + ++ +G++ I +H R      
Sbjct: 138 RAKSILEALVQTVSIPVTCKIRLMPDVDDT----IKLARELQSTGISAIGVHGRT----- 188

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              K  R    ++   +  + K   D+ +  NGG + +++   IL           M+ R
Sbjct: 189 ---KTERPRDPVNEAAIARVAKSL-DIPVIANGGSQSITRRCDILKFARQCGTGSAMVAR 244

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 245 AAEWNVSVFR 254


>gi|295664322|ref|XP_002792713.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb01]
 gi|226278827|gb|EEH34393.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb01]
          Length = 744

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 53/339 (15%), Positives = 92/339 (27%), Gaps = 75/339 (22%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++  +++G K    ++     E                
Sbjct: 345 NLPFRRLCVDL-GAQLTYSEMAMSMNLVQGSKSEWALMKAHESETLPPTVNPNQTIVKDY 403

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      ++A + +         I++N GCP   V     G+ L+ +
Sbjct: 404 DNSRDLKFGAQITGNKPWVALKATEALTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 463

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
              +   +  M      IP+T K R+G  D  P      L++ +              +G
Sbjct: 464 ASKLEKILRGMNAVSGEIPITAKIRMGTKDSNPNAT--KLIERLVLGGVESHEIGRGPAG 521

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-----------------DIVYEIKKENPDLF 190
           V  I +H R    +     D   I                      +     +     +F
Sbjct: 522 VAAITLHGRSRQQRYSRQADWGYIGQCAALVKRLNEQINSGTDTAKEADARYQSSAGKVF 581

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTR 246
              NG                VD VMI R A     +   +   +Y     T        
Sbjct: 582 FLGNGDCYSHEDYFNGIRNSGVDTVMIARGALMKPWIFEEIKKGQYLDKSATER------ 635

Query: 247 VDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                   +      Y      S    +    R ++   
Sbjct: 636 ------LALVEKFAKYGLEAWGSDEYGIGNTRRFLLEYL 668


>gi|332852051|ref|XP_001146456.2| PREDICTED: tRNA-dihydrouridine synthase 3-like isoform 4 [Pan
           troglodytes]
          Length = 654

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 50/290 (17%), Positives = 98/290 (33%), Gaps = 39/290 (13%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 321 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 379

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP                 D++   +AA+   L  P+ V 
Sbjct: 380 KCAELLSRTVEVDFVDINVGCPI----------------DLMYKKVAALDVCLGFPIWVG 423

Query: 123 CR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDY 176
                  G      +++L   +       V+    +   R         ++ R     D+
Sbjct: 424 VSWWEPPGSRGLCLSLSLSAWLFWYLSLCVSLSASYPAWRLLPQLHGRSREQRYTKLADW 483

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             + E  +    + +  NG +     A   +   V G+MI R A     + T + E    
Sbjct: 484 QYIEECVQAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHW 543

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            ++ S  +           I    T+Y   H  S  +  + TR  +   L
Sbjct: 544 DISSSERL----------DILRDFTNYGLEHWGSDTQGVEKTRRFLLEWL 583


>gi|281208917|gb|EFA83092.1| chaperonin containing TCP1 beta subunit [Polysphondylium pallidum
           PN500]
          Length = 853

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 49/207 (23%), Positives = 91/207 (43%), Gaps = 17/207 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   +      + Y+ MI+A+A  R        FST   +  L +Q     
Sbjct: 74  MVRFSRLPFRLLCKKW-GCDITYSPMILAEAFNRSAYARDSDFSTNIFDDSLIVQFAANS 132

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             +L  AA+ V       +++N GCP   V +  +GA L+ +P  + D +  +   + IP
Sbjct: 133 AEELAAAAEKVAKH-CQGVDINCGCPQKWVMKEGYGANLLQHPQKITDMVKQVNNRVGIP 191

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            ++K R+  + Q        LV+  + SGV+ + +H R            R    +DY+ 
Sbjct: 192 CSIKIRVDKNLQKTV----ELVRQAEASGVSWLAVHGRT--------SSQRSSHPVDYEA 239

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALK 205
           +  +K E+  + +  NG +  + QA +
Sbjct: 240 IKLVK-ESVSIPVFANGDIFTLEQANE 265


>gi|156054034|ref|XP_001592943.1| hypothetical protein SS1G_05865 [Sclerotinia sclerotiorum 1980]
 gi|187471050|sp|A7EKL8|DUS3_SCLS1 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|154703645|gb|EDO03384.1| hypothetical protein SS1G_05865 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 750

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 60/345 (17%), Positives = 100/345 (28%), Gaps = 86/345 (24%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQE-KP------------- 49
           +  +R     L    L Y+EM ++  + +G K    ++     E  P             
Sbjct: 349 NLPFRRLCVEL-GAQLTYSEMAMSIPLFQGQKSEWALMKAHESEITPPRINPDRSSIVQN 407

Query: 50  --------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLML 99
                      QI      + ++AA+I+  F  +   I+LN GCP   V+    G+ L+ 
Sbjct: 408 YNNSKDLKFGTQISANKPFQAIKAAEILSRFVPHLRVIDLNCGCPIELVYRQGAGSALLD 467

Query: 100 NPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAV--ALRNLV-------KSIKKSGVN 149
            P  +   I  M      +P+T K R+G     P     +  L        + +   G  
Sbjct: 468 APSKLEKMIRGMNAVSGEVPITAKIRMGTMTGKPTALKTIERLAFGGVESRERLGAPGCA 527

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----------------------- 186
            I +H R         +  R   N D+  + E                            
Sbjct: 528 AITLHGRS--------RQQRYTKNADWSYIAECAALVKSYNQKKDDLTDTIMEPDARTLP 579

Query: 187 ----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                 L    NG        L  + +  VD VM+ R A     +   +        T  
Sbjct: 580 NAPDGKLHFIGNGDCYSHVDYLDHIQNASVDSVMVARGALIKPWLFEEI----EKGQTLD 635

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI-GL 283
                R+      +       Y      S    + Q  R ++  L
Sbjct: 636 KSASERL------QYIEKFARYGLEAWGSDEMGVGQTRRFLLEWL 674


>gi|253580729|ref|ZP_04857993.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848100|gb|EES76066.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 326

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 52/288 (18%), Positives = 113/288 (39%), Gaps = 28/288 (9%)

Query: 3   DWTDRHYRFFARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T R  R   +        +   I+ +    +   +KK+I+  + +      QI   + 
Sbjct: 13  GYTYR--RALYQCFGGFDKYFIPFILPNQKGHLSTREKKDIMPENNEGMYAVPQILTKNA 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              ++ A+ ++++GYNE+NLN+GCPS  V     GA  +  PD +   +  + +   + +
Sbjct: 71  EDFIQTAETLQEYGYNEVNLNLGCPSKTVVTKGRGAGFLDRPDELDKFLDEIFRKCDMKI 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G+DD        +L+    K  +  + +HAR       +            + V
Sbjct: 131 SIKTRLGMDD---PEEFEDLLTIYNKYPLEELIVHARVQKDYYKNTPRLETFG----EAV 183

Query: 180 YEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              K       +  NG +           + P++D +M GR   KN A+   +       
Sbjct: 184 ERAKS-----PVCYNGDIVTAKDCTRLQDMFPTLDCIMTGRGTLKNPALAREIR------ 232

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             G +P      + F   +     +  +   +   +++++  ++  +F
Sbjct: 233 --GGAPASKEEIRRFHDMMYNEYCEDLSGDRNILFRMKELWSYLAPMF 278


>gi|323144809|ref|ZP_08079382.1| putative tRNA-dihydrouridine synthase C [Succinatimonas hippei YIT
           12066]
 gi|322415429|gb|EFY06190.1| putative tRNA-dihydrouridine synthase C [Succinatimonas hippei YIT
           12066]
          Length = 320

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 90/236 (38%), Gaps = 25/236 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---------DKKNILGFSTQEKPLA 51
           M    D   R       N    ++E I    ++           + K     +     + 
Sbjct: 11  MEGVADPPLRKVLTAHGNYDECFSEFIRVTDVVLPYKTLEREVPELKENNARTASGTLVR 70

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +Q+ G +   +   A      G   I++N GCPS  VH G  GA L+  PD++ + ++ +
Sbjct: 71  VQLLGDNPQTIAATAVRAVKLGAKSIDINFGCPSRFVHHG--GAMLLKEPDLMHEIVSTV 128

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
             AL   I ++VK R G    +       +V +I   GV+ I +HAR         KD  
Sbjct: 129 RDALLPEIFLSVKVRTGF---LSKEEAPEIVSAIAVDGVDEIIMHARTR-------KDLY 178

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               LD+ ++  +++    + +  NG +       +       D +M+GR A    
Sbjct: 179 SEAALDWSVIGRVREYAHGIPMVANGDILSFEDGQQCSEAAKTDRLMVGRGALSIP 234


>gi|313238054|emb|CBY13173.1| unnamed protein product [Oikopleura dioica]
          Length = 575

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 103/240 (42%), Gaps = 33/240 (13%)

Query: 1   MVDWTDRHYRFFAR----LLTNNA--LLYTEMIVADAILRGDKKN---ILGFSTQEKPLA 51
           MVD +   +R  ++    ++ +    L YT M  A  I+   K     +       +P+ 
Sbjct: 18  MVDLSWLPFRTRSKSDFKIIHSKGVNLSYTPMHNAHLIVNDLKYRQNVLADLRNSPRPVF 77

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML-NPDIVGDCIAA 110
           +Q+   D+   +EA +IV+DF  + ++LN+GCP      G +GA +ML + +++ + I A
Sbjct: 78  VQMAANDVKLFLEAIRIVKDF-CDAVDLNLGCPQHIARRGGYGAFMMLGSWELISELIQA 136

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             K   I V ++    ++  +     R L           + +H R    K         
Sbjct: 137 GSKIHRITVKIRVFEEIEKSVKYAKERFL-----------LTVHGRTIEQK------REL 179

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
               +++ +  +K++   + + LNG +   ED+ +A +    VDGVM       N  + T
Sbjct: 180 TGLANWEHIKAVKRKLT-IPVILNGNIRYFEDIERAFQE-TRVDGVMSAEGILSNPGIFT 237


>gi|114674849|ref|XP_001146377.1| PREDICTED: dihydrouridine synthase 3-like isoform 3 [Pan
           troglodytes]
          Length = 381

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 47/284 (16%), Positives = 88/284 (30%), Gaps = 54/284 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 75  NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 133

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   +++   G  L                         
Sbjct: 134 KCAELLSRTVEVDFVDINVGCPIDLMYKKGQGCGL------------------------- 168

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
                        L   V          +        L G S ++ R     D+  + E 
Sbjct: 169 ------KSWLFWYLSLCVSLSASYPAWRL-----LPQLHGRS-REQRYTKLADWQYIEEC 216

Query: 183 KKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +    + +  NG +     A   +   V G+MI R A     + T + E     ++ S 
Sbjct: 217 VQAASPMPLFGNGDILSFEDANRAMQTGVAGIMIARGALLKPWLFTEIKEQRHWDISSSE 276

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
            +           I    T+Y   H  S  +  + TR  +   L
Sbjct: 277 RL----------DILRDFTNYGLEHWGSDTQGVEKTRRFLLEWL 310


>gi|210630846|ref|ZP_03296620.1| hypothetical protein COLSTE_00505 [Collinsella stercoris DSM 13279]
 gi|210160280|gb|EEA91251.1| hypothetical protein COLSTE_00505 [Collinsella stercoris DSM 13279]
          Length = 317

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 63/293 (21%), Positives = 109/293 (37%), Gaps = 38/293 (12%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVA----DAILRGDKKNILGFSTQEKPLALQIG 55
           M   T   +R             YT  +       +      K I   + +   +  Q+ 
Sbjct: 8   MEGITGHAFRRVHAECFGALDRYYTPFLAPPRVGSSFGGKAFKEIDPANNEGLNVIPQLL 67

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  + V A K++ D GY E+NLN+GCPS  V     G+  + N D +   +  +C+  
Sbjct: 68  TKNAEEFVWATKLLADMGYREVNLNLGCPSGTVVSKGKGSGFLRNLDELEVFLRDVCERS 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNL 174
            IPV+VK R+G++D      + +L +S+    +  + +H R    +   SP+  R    L
Sbjct: 128 PIPVSVKTRLGLEDDAEYERILDLYRSL---PLAELIVHPRVQKDRYTGSPRQGRYGDTL 184

Query: 175 DYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                           +  NG +   ED S      P+   VM+GR    N A++     
Sbjct: 185 ----------ARAPFPVAYNGDIFVPEDASALCAAYPATRHVMLGRGLLANPALVR---- 230

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                L G  P      K F  K+  +  D      ++  ++++        F
Sbjct: 231 ----MLAGGVPATASELKQFHDKLFHAYVDEIGG--NAVFRMKE------WWF 271


>gi|154321557|ref|XP_001560094.1| hypothetical protein BC1G_01653 [Botryotinia fuckeliana B05.10]
 gi|187471047|sp|A6RMI1|DUS3_BOTFB RecName: Full=tRNA-dihydrouridine synthase 3
 gi|150852191|gb|EDN27383.1| hypothetical protein BC1G_01653 [Botryotinia fuckeliana B05.10]
          Length = 750

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 58/345 (16%), Positives = 102/345 (29%), Gaps = 86/345 (24%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQE-KP------------- 49
           +  +R     L    L Y+EM ++  +L+G K    ++     E  P             
Sbjct: 349 NLPFRRLCVEL-GAQLTYSEMAMSIPLLQGQKSEWALMKAHKSEVTPPRVNSDRTSIVRK 407

Query: 50  --------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLML 99
                      QI  +     ++AA+++  F  +   I+LN GCP   V+    G+ L+ 
Sbjct: 408 YDNSKDLKFGTQISASKPFMAIKAAEVLSRFVPHLRVIDLNCGCPIELVYRQGAGSALLD 467

Query: 100 NPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA--LRNLV-------KSIKKSGVN 149
            P  +   I  M      +P+T K R+G     P     +  L        + +   G  
Sbjct: 468 APSKLEKMIRGMNAVSGEVPITAKIRMGTMTGKPTAFKTIERLAFGGVESRERLGAPGCA 527

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN----------------------- 186
            I +H R         +  R   + D+  + E                            
Sbjct: 528 AITLHGRS--------RQQRYTKSADWSYIAECAALVKSYNQKKDDLTDTVMEPDARTLP 579

Query: 187 ----PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                 +    NG        L  +    VD VM+ R A     +   +++      + S
Sbjct: 580 NAPDGKIHFIGNGDCYSHIDYLDHIQNAGVDSVMVARGALIKPWLFEEIEKGQVLDKSAS 639

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMI-GL 283
                        +     T Y      S    + Q  R ++  L
Sbjct: 640 E----------RLEYVEKFTRYGLEAWGSDEIGVGQTRRFLLEWL 674


>gi|154501072|ref|ZP_02039110.1| hypothetical protein BACCAP_04760 [Bacteroides capillosus ATCC
           29799]
 gi|150269900|gb|EDM97428.1| hypothetical protein BACCAP_04760 [Bacteroides capillosus ATCC
           29799]
          Length = 311

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 54/291 (18%), Positives = 108/291 (37%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   +R   +R        Y   +         R +  +IL    +      Q+  
Sbjct: 1   MEGITGYIFRNCHSRYFPGVDRYYMPFLSPRQDHNFTRRELDDILPEHNEGVHAVPQLLT 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 + AA  +   GY E+NLN+GCPS  V     G+ L+   + +   +  +  A  
Sbjct: 61  RQPEDFLWAAGELAAMGYREVNLNLGCPSGTVTAKGKGSGLLARREELEQLLDGIFAAAP 120

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G+ D        +L++   +  V  + +H R        P          +
Sbjct: 121 MAISIKTRLGMHD---PEEFGHLLELYNRYPVAELTVHPRIRGDFYKKPVRPEY-----F 172

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D+   + +      +  NG +    D  +A +  P V+ VMIGR    + ++        
Sbjct: 173 DLAVRMSRA----PLCYNGDIITPGDWEKASQRWPGVETVMIGRGLVADPSL-------- 220

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +  L G  P      + F  ++  +         ++  ++++I  ++I LF
Sbjct: 221 AGRLKGEQPAGLDTLRAFHHELYETYAQAFGSRRNAMLRMKEIWVYLIHLF 271


>gi|289824091|ref|ZP_06543688.1| hypothetical protein Salmonellentericaenterica_02632 [Salmonella
           enterica subsp. enterica serovar Typhi str. E98-3139]
          Length = 164

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 38/163 (23%), Positives = 78/163 (47%), Gaps = 12/163 (7%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHVDEPGIRTVQIAGSDPVEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G   +        + +  
Sbjct: 61  PAKKVNRKLAGSALLQYPDLVKSILIGVVNAVDVPVTLKIRTGWAPEHRN--CVEIAQLA 118

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +  G+  + IH R         +        +YD +  +K+E+
Sbjct: 119 EDCGIQALTIHGRT--------RACLFNGEAEYDSIRAVKQES 153


>gi|308802842|ref|XP_003078734.1| putative protein involved in tRNA-dihydrouridine (ISS)
           [Ostreococcus tauri]
 gi|116057187|emb|CAL51614.1| putative protein involved in tRNA-dihydrouridine (ISS)
           [Ostreococcus tauri]
          Length = 424

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 56/219 (25%), Positives = 95/219 (43%), Gaps = 18/219 (8%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSA 86
           VA+ I++              PL  QI G+D   L  AAK + ED     ++LN GCP++
Sbjct: 95  VAEKIVKNLCARYDADELGNVPLGAQIMGSDAELLTLAAKHLGEDKNAPRVDLNCGCPAS 154

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSI 143
            V     G+ L+ +P  V D + A+ + +      VT+K R G DD   +  LR  + + 
Sbjct: 155 VVTGKGAGSSLLKDPKFVYDAVRAVARGVEGTNAIVTMKLRTGYDD---SGLLRENLCAA 211

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQ 202
           + +G   I +HAR         +        ++D +   K+    D+ I  NG +    +
Sbjct: 212 RDAGARFISLHART--------RAQGYSGRANWDDIAFAKEVLGDDVPIIGNGDVTSPLR 263

Query: 203 ALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             ++L   + DGV IGR A ++  +   +       + G
Sbjct: 264 CAELLRVSNADGVGIGRGAVQDPLIFRRIAATVKRDVNG 302


>gi|326200913|ref|ZP_08190785.1| dihydrouridine synthase DuS [Clostridium papyrosolvens DSM 2782]
 gi|325988481|gb|EGD49305.1| dihydrouridine synthase DuS [Clostridium papyrosolvens DSM 2782]
          Length = 312

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 126/323 (39%), Gaps = 33/323 (10%)

Query: 1   MVDWTDRHYRFFAR-LLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR   R L       ++  I+A   D     D ++IL  + Q   L  Q+  
Sbjct: 8   MEGLTGYIYRNAHRALFDGMDKYFSPFIIANQIDGFKTRDLRDILPENNQGLVLVPQVLT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +    +  +K +   GYNEINLN+GCPS  V   + G+  +   + +   +  +     
Sbjct: 68  NNAKDFIYTSKKINSMGYNEINLNLGCPSGTVVSKNRGSGFLAKKEELDAFLEEIFSQAM 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             ++VK RIG D         +L+    K  V  + IH R           N+    +  
Sbjct: 128 TKISVKTRIGKD---HPEEFYDLINIFNKYPVEELIIHPRIQKDFYK----NKPNLQIFK 180

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D +   K       +  NG +   +D  +  +  PSVD +M+GR    N A++  +    
Sbjct: 181 DALGLSKN-----TVCYNGDIFTSKDYVKFHEDFPSVDTLMLGRGLLMNPALVHEIK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
                  + ++  + K+F  KI     D  +   +   K++++  +MI +F     ++++
Sbjct: 233 -----NGTKLEKNLLKEFHNKIYNDYKDILSGERNVLFKMKELWFYMINVFTDNEKHAKK 287

Query: 293 CR--HILTVEAGASTATHHIIET 313
            +    L+       A   + E 
Sbjct: 288 IKKSQRLS---DYDEAVSRLFEE 307


>gi|291535651|emb|CBL08763.1| tRNA-U20a,U20b-dihydrouridine synthase [Roseburia intestinalis
           M50/1]
          Length = 335

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 60/310 (19%), Positives = 112/310 (36%), Gaps = 46/310 (14%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           M   T   +R  + +   N    +T  I    +   + K+IL    +   +  QI     
Sbjct: 11  MEGLTGFVFRNAYQKHFGNIDTYFTPFINNKKMNYKEIKDILPEHNEGMHVVPQILTNRA 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +  AK + ++GY  +NLN+GCPS  V     GA  +  P+ +   +  +     + +
Sbjct: 71  EDFLAIAKELGNYGYESVNLNLGCPSGTVVAKHRGAGFLAVPEELDHFLEEIFAECPLRI 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+GV+D   A    +L+   +K  +  + IH R       +  D           +
Sbjct: 131 SVKTRVGVND---AGEWEHLLSIYEKYPMEELIIHPRVQKDFYNNTPDMEA-------FL 180

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPS----------------------VDGVM 214
           Y +  EN    +  NG +   ED     + +                        V  +M
Sbjct: 181 YAV--ENSRHTLCYNGDICSVEDYRTWRQQMEEKRECAFMQESGHQTDPEDTGSLVSHLM 238

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +GR   KN  ++          LTG +PI       F   +     D  +   ++  +++
Sbjct: 239 LGRGVLKNPGLIGE--------LTGHAPITKDQLHAFHDDVLKGYLDVMSGERNTLFRMK 290

Query: 275 QITRHMIGLF 284
           ++  +    F
Sbjct: 291 ELWFYFAKYF 300


>gi|301091909|ref|XP_002896129.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
 gi|262094949|gb|EEY53001.1| tRNA-dihydrouridine synthase, putative [Phytophthora infestans
           T30-4]
          Length = 480

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 91/247 (36%), Gaps = 35/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL------------------RGDKKNILG 42
           MV       R  +       L+Y E I+   I+                   GD      
Sbjct: 14  MVRSGTLPLRLLSLRY-GADLVYGEEIIDKRIISAVRVPNDVVNAVDFVSRNGDSVVFRT 72

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            S +   +  QIG AD    ++AA+         +++N+GCP     +G  GA L+  P+
Sbjct: 73  CSEEAGKVVFQIGTADAVLALKAAE-AVARDVAAVDINMGCPKHFSVQGGMGAALLRKPE 131

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +  D +  + + L+IPV+ K R+  + Q       +L + ++ +G   + +H R+     
Sbjct: 132 VACDIMKTLRRNLNIPVSCKIRLLPEIQDTV----DLARRLEDAGACAVGVHMRQT---- 183

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAY 220
                 R      +D +  +      + +  NG +        L+ L      +I R A 
Sbjct: 184 ----HERPHDKASWDRLAPVVSAL-SVPVLANGDVFMHEDINKLRKLSGASSFLIARGAL 238

Query: 221 KNSAMLT 227
            N ++  
Sbjct: 239 ANPSIFR 245


>gi|321251331|ref|XP_003192028.1| hypothetical protein CGB_B2580W [Cryptococcus gattii WM276]
 gi|317458496|gb|ADV20241.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 408

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 49/299 (16%), Positives = 96/299 (32%), Gaps = 82/299 (27%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR--------------------------- 34
           V  +   +R    L   + + +T MI+A+   R                           
Sbjct: 40  VRCSKLPFRHLTSLYETH-ITHTPMILAEEFSRAQIARTSDFSTSSNERGIYWMTPKNGK 98

Query: 35  ----GDKKNILGFSTQEKPL----------------------------------ALQIGG 56
               G  +  +G     +P+                                    Q   
Sbjct: 99  SEDKGGYQTHIGHPEDARPVKEPWKTYHSPPSTNRLPPSPAPPNSQAQLVRGCLIAQFAS 158

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL- 115
            +   L +AA+++  +  + I+LN GCP    +    G  L+  P++V D +      + 
Sbjct: 159 PNAKSLADAAELISPY-VDGIDLNCGCPQRWAYNEGIGCALLRKPELVRDMVRGAKDRMG 217

Query: 116 -SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
              PV++K RI  + +        L+ +  ++G++ + IH R        P +   I   
Sbjct: 218 WGWPVSIKIRIDSEQK----NTEQLISNALQAGISHLTIHGRTRHQPSTDPVNLPGIK-- 271

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                + ++     +    NG + ++  A ++     V GVM  R    N A+    D 
Sbjct: 272 -----FAVECVKGQVPCVANGDVWELEDARRMRLQTGVQGVMAARGLLANPALFAGYDR 325


>gi|157131542|ref|XP_001655871.1| tRNA-dihydrouridine synthase [Aedes aegypti]
 gi|108871488|gb|EAT35713.1| tRNA-dihydrouridine synthase [Aedes aegypti]
          Length = 461

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 58/279 (20%), Positives = 110/279 (39%), Gaps = 47/279 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-----------------ILGF 43
           MV       R  A       ++YTE I+   +L+ +++                  I   
Sbjct: 16  MVRVGTLPMRLLALSF-GADIVYTEEIIDWKLLKSERRVNDVLKTVDYVDKTDGTIIFRT 74

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             QE+  + LQ+G A+  + ++    ++      +++N+GCP     +G  G  L+ + +
Sbjct: 75  CEQERGKVVLQLGTANAERALQVGLKLQG-DIAGLDVNMGCPKDFSIKGGMGVALLYDLE 133

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +   LSIPVT K RI    +         V+ ++ +G+  I +H R  + + 
Sbjct: 134 RAKGILKTLVDNLSIPVTCKIRIMPQLEDTIRT----VQELESTGIAAIAVHGRTKVERP 189

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
             P        +  D++ E+ K    + +  NGG ++M++   IL          VM+ R
Sbjct: 190 RHP--------VHPDVIREVAKIA-KIPVIANGGSQEMNKRSDILKFRDACGASSVMVAR 240

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           AA  N ++             G  PI+  +D+     I 
Sbjct: 241 AAQWNCSIFRD---------EGPLPIEEIIDRYLRLAIE 270


>gi|195045040|ref|XP_001991926.1| GH12926 [Drosophila grimshawi]
 gi|193901684|gb|EDW00551.1| GH12926 [Drosophila grimshawi]
          Length = 460

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 105/266 (39%), Gaps = 47/266 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-----------------ILGF 43
           MV       R  A  +    ++YTE ++   +++  ++                  I   
Sbjct: 18  MVRVGTLPMRLLALEM-GADIVYTEELIDLKLIKSIRRPNPALGTVDFVDPSDGTIIFRT 76

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              E   + LQ+G +D ++ +   K+V+      +++N+GCP     +G  GA L+  PD
Sbjct: 77  CPLETSKVVLQMGTSDAARALAVGKLVQ-CDIAGLDINMGCPKEFSIKGGMGAALLAEPD 135

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IP+T K RI  D         NLV+ +  +G+  I IHAR      
Sbjct: 136 KAAHILRTLCSQLDIPITCKIRILPDPMDT----INLVQKLAATGIAAIGIHART----- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-----KILPSVDGVMIGR 217
              +D R       D++  +     D+ I  NGG  +M         + L   D VM+ R
Sbjct: 187 ---RDERPQHRPHPDVLRAVASAV-DIPIIANGGSREMHTFEDLHKFQELCGADSVMVAR 242

Query: 218 AAYKNSAMLTT---------VDEYFS 234
           AA  N ++            +D+Y  
Sbjct: 243 AAQLNVSIFRREGVLPIDEVIDKYLR 268


>gi|323507663|emb|CBQ67534.1| related to tRNA dihydrouridine synthase [Sporisorium reilianum]
          Length = 362

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 74/365 (20%), Positives = 140/365 (38%), Gaps = 79/365 (21%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMI------VADAILRGDKKNI-LGFSTQEK---- 48
           MV  +D  +R    R        +T+M           +L    K++ LG +  E     
Sbjct: 19  MVGQSDLPFRLQTVR--NGATSTWTQMYLASDLNSDRDMLDTLCKSLELGKAAPENIIPD 76

Query: 49  ----------PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
                     P  +Q+ G D+ +LVEA++ V  F  + I+LN+GCP     +G +GA L+
Sbjct: 77  KDSPLVGQAAPQIVQLAGNDVQQLVEASRKVAPF-ADAIDLNLGCPQRHAEQGHYGAYLL 135

Query: 99  --LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
              N  ++ + ++ + +A+ +P+T K R+ V    P    + L  ++ ++G + + +H R
Sbjct: 136 PKQNWPLLAEIVSGLAQAVDVPITTKIRLTV----PKEQTQQLAVTLARAGSSLVTLHPR 191

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKEN-------------PDLFIGLNGGLEDMSQA 203
                  +    R+    D D V  +++                D  +  NG +      
Sbjct: 192 ------FASSVRRRKGLADLDQVVHVREALQAEGLLRSADQPCGDTAVVSNGNVRCWCDI 245

Query: 204 LKIL--PSVDGVMIGRAAYKNSAML----TTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +  L      GVM+G    +N A+     + +D        G+SP          + ++ 
Sbjct: 246 VDNLASTGASGVMVGETLLENPALFHPSISEIDR------VGTSP----------KDMAL 289

Query: 258 SMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
              D   R+ H    L+   +H+  +    P         T     + A HH    +   
Sbjct: 290 EYLDLRDRYDHFESPLKVAKQHLQSILGSIP-------YTTSTGPDNIAEHHRFAASMTH 342

Query: 318 MIESL 322
           +I+S+
Sbjct: 343 IIKSM 347


>gi|158296416|ref|XP_316826.3| AGAP000856-PA [Anopheles gambiae str. PEST]
 gi|157015286|gb|EAA12065.3| AGAP000856-PA [Anopheles gambiae str. PEST]
          Length = 469

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 64/340 (18%), Positives = 118/340 (34%), Gaps = 65/340 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN-----------------ILGF 43
           MV       R  A       L+YTE I+   +LR ++                   +   
Sbjct: 16  MVRVGTLPMRLLALEY-GADLVYTEEIIDWKLLRAERHTNEVLGTIDYIDTTDGTVVFRT 74

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              E+  + LQIG A   + V   +++++     I++N+GCP     +G  G  L+ +  
Sbjct: 75  CPHERGKVVLQIGTASAERAVAVGQMMQN-DVAAIDVNMGCPKDFSIKGGMGVALLYDLP 133

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  + + + IPVT K R+  D          L K ++ +G+  I +H R  + + 
Sbjct: 134 RAKAILEGLVQGVRIPVTCKIRVMPDLDETVA----LAKELQSTGIRAIGVHGRTKMERP 189

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGR 217
             P        ++   +  +      + +  NGG + +++   IL      S   VM+ R
Sbjct: 190 RDP--------VNEGAIARVANAL-HIPVIANGGSQSITRRHDILRFAQRCSTTSVMVAR 240

Query: 218 AAYKNSAMLTT---------VDEYFSNPL-TGSSPIKTRVDKDFW-----------RKIS 256
           AA  N ++            +  Y    +   +SP  T+                 R + 
Sbjct: 241 AAEWNCSVFRADGPLPLDDVIRRYLELSVRYDNSPSNTKYCVQMMLRSLQESPIGRRLLD 300

Query: 257 ASMTDYAARHLHSGGKLQQ--ITRHMIGLFHGFPNSRRCR 294
           +            G   ++  +  H    F G    R CR
Sbjct: 301 SQTMQQICDIWEMGEYCRETQLRYH----FAGIKGRRACR 336


>gi|300120824|emb|CBK21066.2| unnamed protein product [Blastocystis hominis]
          Length = 225

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 50/206 (24%), Positives = 85/206 (41%), Gaps = 17/206 (8%)

Query: 26  MIVADAILR--GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M  +  +    G           + PL +Q+ G D   L +AA   E      ++LN+GC
Sbjct: 1   MYHSRVMFEDSGYLDRYFHTCDGDSPLIVQLCGNDPEFLQKAALKFEG-KCMAVDLNLGC 59

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P     +G +G+ L+ N ++V     A+  + +  P TVK R+    +        L K 
Sbjct: 60  PQGIARKGKYGSYLLPNYNLVEQIAKALGGEEVQFPFTVKIRLLPSLEDT----IKLCKM 115

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           +++ G   I IH R          +  +    D+  +  I+KE   + +  NGG+  +  
Sbjct: 116 LEREGAQMITIHGRTREQ------NKDRTGACDWQAIATIRKEL-SIPVFANGGICSLED 168

Query: 203 ALKIL--PSVDGVMIGRAAYKNSAML 226
             K +    V GVM+G A  +N A  
Sbjct: 169 VTKCIEETGVCGVMVGEAILENPAFF 194


>gi|224368002|ref|YP_002602165.1| Dhs1 [Desulfobacterium autotrophicum HRM2]
 gi|223690718|gb|ACN14001.1| Dhs1 [Desulfobacterium autotrophicum HRM2]
          Length = 320

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 56/306 (18%), Positives = 109/306 (35%), Gaps = 36/306 (11%)

Query: 3   DWTDRHYRFFA-RLLTNNALLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGGAD 58
            +TD  +R    R  T         I      R      K++L  +    P+  QI G  
Sbjct: 12  GFTDAPFRQVYPRHFTGFDEALAPFISTMGQARLKPSRIKDVLPENNPLLPVVPQILGNV 71

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               +  A+ + D GY  +N N+GCP +++ +   G+ L+  PD++   +  +  A+   
Sbjct: 72  AEDFIFLARYLADKGYTRVNWNLGCPHSKITKKLRGSGLLCRPDLIDAFLEQVVPAIPCS 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++VK R+G   +  +  + +L+    +  ++ I +H R  +               D D 
Sbjct: 132 LSVKVRLG---RKTSHEIFDLLPVFDRYPLDEIIVHPRTGV--------QLYTGTADIDA 180

Query: 179 VYEIKKENPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
              +  ++  + +  NG + D       +   P +   MIGR    +  +  T+      
Sbjct: 181 FERVLAQSRHILV-YNGDITDKKGFQVLVDRFPEIRSFMIGRGVLADPFLPATIKG---- 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH----GFPNS- 290
                   + R       +I A   D    +  +      I   M G +      FP   
Sbjct: 236 --------EVRDRTMDLERIKAFHDDLFTTYDGNFYGPSHIAGRMKGFWSYLGPSFPGGE 287

Query: 291 RRCRHI 296
           +  + I
Sbjct: 288 KLFKQI 293


>gi|293115531|ref|ZP_05791959.2| dihydrouridine synthase family protein [Butyrivibrio crossotus DSM
           2876]
 gi|292809467|gb|EFF68672.1| dihydrouridine synthase family protein [Butyrivibrio crossotus DSM
           2876]
          Length = 298

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 58/282 (20%), Positives = 105/282 (37%), Gaps = 25/282 (8%)

Query: 1   MVDWTDRHYRFFA-RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           M   T   +R    R   +    +T  I +  +   +K ++L    Q   +  QI     
Sbjct: 1   MEALTGYIFRNVYNRYFGDADRYFTPFIASRKLNSKEKNDVLPEHNQNMDVIPQILTNKS 60

Query: 60  SKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +    A+++ E +GY E+NLN+GCPS  V   + G+  +  PD +      +     + 
Sbjct: 61  EEFCYIASRLKEYYGYEEVNLNLGCPSGTVVAKNRGSGFLAVPDELNRFFEEVFSMTDVR 120

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           ++VK R GV++        N++K   +  ++ + IH R         KD         D 
Sbjct: 121 ISVKTRTGVENNEN---WENILKIYNEYPISELIIHPRCR-------KDGYGGKPNLEDF 170

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
              +      L    NG +   ED +   K  P+VD +M GR    N  + + +      
Sbjct: 171 KKAVLISRHSL--CYNGDINSVEDYNAITKEFPTVDKIMCGRGILMNPGLFSEIK----- 223

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
              GS         +F   +     +  +   +   KL++  
Sbjct: 224 ---GSRKASPETLYNFANDLYKGYKEIMSGDRNVLFKLKEFW 262


>gi|226945483|ref|YP_002800556.1| tRNA-dihydrouridine synthase C [Azotobacter vinelandii DJ]
 gi|226720410|gb|ACO79581.1| tRNA-dihydrouridine synthase C [Azotobacter vinelandii DJ]
          Length = 326

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 56/278 (20%), Positives = 108/278 (38%), Gaps = 26/278 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE + V D +L   +   L         +    P+ L
Sbjct: 8   MEGLVDELLRDLLTRVGGIDWCVTEFVRVCDRLLPVAQFEKLAPELRHGWRTRAGTPMHL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L E A +  + G   I+LN GCP+  V+    GA L+  P+++   +  + 
Sbjct: 68  QLLGSDPACLAENAALAAELGAPAIDLNFGCPAKTVNRSRGGAVLLDEPELLHAIVREVR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A+   +PVT K R+G      A+      +++ + GV  + +HAR  +           
Sbjct: 128 RAVPAHVPVTAKMRLGYARPEGAL---ECARALVEGGVAHLVVHARTKVEGYR------- 177

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
            P   ++ +  + +E   + +  NG +   +  L+      V+ VM+GR       +   
Sbjct: 178 -PPAHWEWLARV-REAVAVPVYANGEIWTPADWLRCREISGVEDVMLGRGLVSRPDLARQ 235

Query: 229 VDEYFSNPLTGSS--PIKTRVDKDFWRKISASMTDYAA 264
           +    +              + ++FWR+    +    A
Sbjct: 236 IAMACAGRTLEPQGWGEVQPLVREFWRRARQRIAPRYA 273


>gi|255522703|ref|ZP_05389940.1| dihydrouridine synthase family protein [Listeria monocytogenes FSL
           J1-175]
          Length = 219

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 86/230 (37%), Gaps = 19/230 (8%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           GA  +L+P+ V D +AA+  A+  PVTVK RIG D++        L      +    +  
Sbjct: 1   GAKWLLDPNKVYDMVAAVVDAVDKPVTVKMRIGWDEEHVFAIENALAAERAGAAAVAMHG 60

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVD 211
             R  + +G          + ++D++ ++K+E   +    NG +     A +IL     D
Sbjct: 61  RTRVQMYEG----------SANWDVLRDVKREL-KIPFMANGDVRTPEDAKRILEHTGAD 109

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           GVMIGRAA  N  M+    ++         P      +     ++               
Sbjct: 110 GVMIGRAALGNPWMIYRTVKFLETGELLPEPEPREKMQTAMLHLNR-----LVELKGENI 164

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            +++  +H      G   S R + +   +A   +    I+        E 
Sbjct: 165 AVREFRQHAAYYLKGARGSTRAK-VAANQATKQSEMEAILNEFVLQYEEK 213


>gi|219118875|ref|XP_002180204.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408461|gb|EEC48395.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 231

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 93/234 (39%), Gaps = 18/234 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI---LRGDKKNILGFSTQEKPLALQIGGA 57
           MV  +    R  A L      +YTE +V  A+   +R + K +     +   L  Q+G  
Sbjct: 4   MVRASTTPLRTLA-LSYGADWVYTEELVDRALTGTIRVENKELGTIDYERGKLVCQLGSG 62

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS- 116
           +   L  AA +      + I+LN+GCP      G  G+ L+ +P+     I  + + LS 
Sbjct: 63  EP-DLALAAALHVHQDVDAIDLNMGCPKKFSVSGGMGSALLSDPERACRIIRTLTENLSS 121

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             IPV+ K R+  D           +  + ++G   I +H R+       P     +   
Sbjct: 122 KGIPVSAKIRLLKDVSSTVA----FIAGLVEAGAKAIAVHGRQVSDDCTVPARWSMLR-- 175

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
             +++ E     P +   LNG      + +  +      GV++ R A  N+++ 
Sbjct: 176 --EVIKEAVHRFPHIPFLLNGDFYTRDEFVSFMRDTGARGVLLARPALFNTSIF 227


>gi|19112231|ref|NP_595439.1| tRNA dihydrouridine synthase Dus2 (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|74582543|sp|O74731|DUS2_SCHPO RecName: Full=tRNA-dihydrouridine synthase 2
 gi|3738144|emb|CAA21245.1| tRNA dihydrouridine synthase Dus2 (predicted) [Schizosaccharomyces
           pombe]
          Length = 479

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 95/250 (38%), Gaps = 31/250 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--------------------DKKNI 40
           MV   +   R  A     N L++   IV  A+L G                      K +
Sbjct: 15  MVRIGELPMRLLALRYGAN-LVWGPEIVDKALLSGTPVERVVNDRINCIDFVKPPSNKVL 73

Query: 41  LGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
                 E   L  Q+G A     VEAAK+V +     I+LN GCP         GA L+ 
Sbjct: 74  FRVHPLEANRLIFQLGSASPELAVEAAKLVAN-DVAGIDLNCGCPKHFSVHAGMGAGLLK 132

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           N D +   + A+   +  P  +     +           LV+ I  +GV  I +H R   
Sbjct: 133 NQDRLVSILDALVNEIGKPYKISISCKIRLLETKEDTLKLVERICDTGVRAITVHCRTTP 192

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           ++   P D   +       +  + + N D+ I +NG +   +  L ++    VDGV+I R
Sbjct: 193 MRNTEPADRSYLSE-----IVGVCR-NKDVSILVNGDVLSYNDGLDVIEKYGVDGVLIAR 246

Query: 218 AAYKNSAMLT 227
           AA +N +   
Sbjct: 247 AAERNVSCFR 256


>gi|240144438|ref|ZP_04743039.1| dihydrouridine synthase family protein [Roseburia intestinalis
           L1-82]
 gi|257203546|gb|EEV01831.1| dihydrouridine synthase family protein [Roseburia intestinalis
           L1-82]
          Length = 335

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/310 (19%), Positives = 112/310 (36%), Gaps = 46/310 (14%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           M   T   +R  + +   N    +T  I    +   + K+IL    +   +  QI     
Sbjct: 11  MEGLTGFVFRNAYQKHFGNIDTYFTPFINNKKMNYKEIKDILPEHNEGMHVVPQILTNRA 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +  AK + ++GY  +NLN+GCPS  V     GA  +  P+ +   +  +     + +
Sbjct: 71  EDFLAIAKELGNYGYESVNLNLGCPSGTVVAKHRGAGFLAVPEELDHFLEEIFAECPLRI 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+GV+D   A    +L+   +K  +  + IH R       +  D           +
Sbjct: 131 SVKTRVGVND---AGEWEHLLSIYEKFPMEELIIHPRVQKDFYNNTPDMEA-------FL 180

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPS----------------------VDGVM 214
           Y +  EN    +  NG +   ED     + +                        V  +M
Sbjct: 181 YAV--ENSRHTLCYNGDICSVEDYRTWRQQMEEKRKCAFMQESGQQTDPEDTGSLVSHLM 238

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           +GR   KN  ++          LTG +PI       F   I     D  +   ++  +++
Sbjct: 239 LGRGVLKNPGLIGE--------LTGHAPITKDQFHAFHDDILKGYLDVMSGERNTLFRMK 290

Query: 275 QITRHMIGLF 284
           ++  +    F
Sbjct: 291 ELWFYFAKYF 300


>gi|327357988|gb|EGE86845.1| tRNA-dihydrouridine synthase 3 [Ajellomyces dermatitidis ATCC
           18188]
          Length = 737

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/337 (16%), Positives = 98/337 (29%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 338 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESEILPPTVNPQQTIVKNY 396

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI G      + A + +     +   I++N GCP   V     G+ L+ +
Sbjct: 397 DNSRDLKFGVQITGNKPWVALRATEALTALCPHLRVIDMNCGCPIDMVFREGSGSALLDH 456

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA---LRNLVKSIKK-------SGVN 149
              +   +  M      IP+T K R+G  D  P       R +   ++        +GV 
Sbjct: 457 ASKLEKMLRGMNAVSGEIPITAKIRMGTKDSNPTATKLVERLICGGVESHEIGQGPAGVA 516

Query: 150 GIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKK----ENPDLFIG 192
            I +H R    +     D   I              ++  D + E           +F  
Sbjct: 517 AITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIAIDTIKEPDARYQPAAGKVFFL 576

Query: 193 LNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTRVD 248
            NG                VD VM+ R A     +   V+  +Y     T          
Sbjct: 577 GNGDCYSHEDYFNGIQKSGVDTVMVARGALMKPWIFEEVEKGQYLDKSATER-------- 628

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 629 ----LALVEKFAKYGLEAWGSDEYGIGNTRRFLLEYL 661


>gi|328861733|gb|EGG10836.1| hypothetical protein MELLADRAFT_60122 [Melampsora larici-populina
           98AG31]
          Length = 377

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 102/248 (41%), Gaps = 28/248 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----------------RGDKKNILGF 43
           MV       R  A      AL++   IV  AI+                      +I   
Sbjct: 107 MVRIGTLTTRLLALEY-GAALVWGPEIVDKAIIGSERIVNERTGTIQYTKNNGTTSIWQT 165

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +EK  L  QIG AD    ++AA+ V     + I+LN GCP     +G  GA L+  P+
Sbjct: 166 HPREKSRLIYQIGSADPELALKAAQTVLQ-DVSGIDLNCGCPKDFSLKGGMGAALLKEPE 224

Query: 103 IVGDCIAAMCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            +   ++ + K +   P++ K R+  D +       NLVK I  +G++ + +H R  +++
Sbjct: 225 KLCGILSHLVKNIPTHPISAKIRLLPDQEDT----LNLVKQISATGISCLTVHCRTQLMR 280

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAA 219
              P    ++  +  + V   +  +  L +  NG   +      +K L  V  +MI R A
Sbjct: 281 STEPALLHRLKEI-VETVNRSRSSSVPLPVVANGDCFEYKDMEKIKALTGVQRIMIARGA 339

Query: 220 YKNSAMLT 227
            +N +  +
Sbjct: 340 ERNVSCFS 347


>gi|239612845|gb|EEQ89832.1| tRNA-dihydrouridine synthase 3 [Ajellomyces dermatitidis ER-3]
          Length = 737

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/337 (16%), Positives = 98/337 (29%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 338 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESEILPPTVNPQQTIVKDY 396

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI G      + A + +     +   I++N GCP   V     G+ L+ +
Sbjct: 397 DNSRDLKFGVQITGNKPWVALRATEALTALCPHLRVIDMNCGCPIDMVFREGSGSALLDH 456

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA---LRNLVKSIKK-------SGVN 149
              +   +  M      IP+T K R+G  D  P       R +   ++        +GV 
Sbjct: 457 ASKLEKMLRGMNAVSGEIPITAKIRMGTKDSNPTATKLVERLICGGVESHEIGQGPAGVA 516

Query: 150 GIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKK----ENPDLFIG 192
            I +H R    +     D   I              ++  D + E           +F  
Sbjct: 517 AITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIAIDTIKEPDARYQPAAGKVFFL 576

Query: 193 LNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTRVD 248
            NG                VD VM+ R A     +   V+  +Y     T          
Sbjct: 577 GNGDCYSHEDYFNGIQKSGVDTVMVARGALMKPWIFEEVEKGQYLDKSATER-------- 628

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 629 ----LALVEKFAKYGLEAWGSDEYGIGNTRRFLLEYL 661


>gi|325116599|emb|CBZ52152.1| GH10224, related [Neospora caninum Liverpool]
          Length = 663

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/248 (21%), Positives = 93/248 (37%), Gaps = 37/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS---------------- 44
           MV      +R          L+YTE  +   +L   +K    FS                
Sbjct: 272 MVRIGILPFRLECLKY-GADLVYTEETIDHKLLNSVRKINEDFSTIDFVHKGEKTCVFST 330

Query: 45  --TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   + +Q+G +D ++ + AA +V       I++N+GCP +    G  GA L+  P 
Sbjct: 331 CLEERGKVVMQLGTSDATRALRAAALVAQ-DVAAIDVNMGCPKSFSINGGMGAALLKTPL 389

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           I  D +  + + L IPVT K R+            +  +  +  GV  I IHAR+     
Sbjct: 390 IATDILKTLRRNLDIPVTCKIRLL----DTIHKTIDFARMCENCGVEAIAIHARET---- 441

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
                 R      +DI   +K     + +  NG      D+    + +   D +M  R A
Sbjct: 442 ----HERPSHRAHWDIFPALKSSL-SIPVIANGDFLTHRDVDVFQEKI-GADSIMFARGA 495

Query: 220 YKNSAMLT 227
             + ++ +
Sbjct: 496 MWDPSIFS 503


>gi|261189953|ref|XP_002621387.1| tRNA-dihydrouridine synthase 3 [Ajellomyces dermatitidis SLH14081]
 gi|239591623|gb|EEQ74204.1| tRNA-dihydrouridine synthase 3 [Ajellomyces dermatitidis SLH14081]
          Length = 737

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/337 (16%), Positives = 98/337 (29%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 338 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESEILPPTVNPQQTIVKDY 396

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI G      + A + +     +   I++N GCP   V     G+ L+ +
Sbjct: 397 DNSRDLKFGVQITGNKPWVALRATEALTALCPHLRVIDMNCGCPIDMVFREGSGSALLDH 456

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA---LRNLVKSIKK-------SGVN 149
              +   +  M      IP+T K R+G  D  P       R +   ++        +GV 
Sbjct: 457 ASKLEKMLRGMNAVSGEIPITAKIRMGTKDSNPTATKLVERLICGGVESHEIGQGPAGVA 516

Query: 150 GIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKK----ENPDLFIG 192
            I +H R    +     D   I              ++  D + E           +F  
Sbjct: 517 AITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIAIDTIKEPDARYQPAAGKVFFL 576

Query: 193 LNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTRVD 248
            NG                VD VM+ R A     +   V+  +Y     T          
Sbjct: 577 GNGDCYSHEDYFNGIQKSGVDTVMVARGALMKPWIFEEVEKGQYLDKSATER-------- 628

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 629 ----LALVEKFAKYGLEAWGSDEYGIGNTRRFLLEYL 661


>gi|197116498|ref|YP_002136925.1| tRNA dihydrouridine synthase-like flavin mononucleotide-binding
           domain-containing protein [Geobacter bemidjiensis Bem]
 gi|197085858|gb|ACH37129.1| tRNA dihydrouridine synthase-like flavin mononucleotide-binding
           domain protein [Geobacter bemidjiensis Bem]
          Length = 341

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/271 (20%), Positives = 106/271 (39%), Gaps = 24/271 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM-----IVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   T+R  R          +++TE      + A   L       +  S    PL +Q+ 
Sbjct: 39  MQGLTNRALRSLFTKWVRPDVVWTEFMRVNPVSAKKRLMPGDLREISASEDGIPLVVQLI 98

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G     LV AA+  +D G   +NLN+GCP  R+  G  G  ++  P+++ + I A+ +A+
Sbjct: 99  GHGREALVSAAQAAQDAGAVHLNLNMGCPYGRMTSGLTGGGMLKKPELLEEIIPALREAI 158

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K R G +D     +   L+   ++SGV+ + +H R                  D
Sbjct: 159 HGSFSIKLRAGYEDPQQVFS---LLPLFERSGVDFLVLHPRT--------VRQAYNGWAD 207

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +++  E+ ++   + +  NG +   +   ++L      G+M+GR       +   +    
Sbjct: 208 HEVTAEVVRQT-SIPVIANGDIRSAAGGQRLLEQTGAAGLMLGRGGIGEPMLFERLR--- 263

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
                 + P          R +   +  Y A
Sbjct: 264 --GRAAAEPDLAERKAMLHRYLIDLLPLYCA 292


>gi|312073196|ref|XP_003139411.1| dihydrouridine synthase domain-containing protein [Loa loa]
 gi|307765423|gb|EFO24657.1| dihydrouridine synthase domain-containing protein [Loa loa]
          Length = 439

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/249 (21%), Positives = 99/249 (39%), Gaps = 37/249 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGFST------------- 45
           MV       R  A       L+YTE I+   +L  +    +ILG +              
Sbjct: 16  MVRAGRTPLRTLALEY-GADLVYTEEIIDQKLLGSQRTINDILGTTDYTYEDDVVLRICN 74

Query: 46  --QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             +++   LQIG  D  +     K VE+     I++N+GCP      G  GA L+ +P+ 
Sbjct: 75  RIEKQKCVLQIGTNDAQRAANVVKKVEN-DVAAIDINMGCPKPFSIAGGMGAALLGSPER 133

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             + +       +IPV+ K R+    +         VK +++ GV+ I IH R+      
Sbjct: 134 AKEIVQTCVSISTIPVSCKMRVLDKREDT----LEFVKMLERCGVSAIGIHGRR------ 183

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALK--ILPSVDGVMIGRA 218
             +  R+      + ++E+ +    + +  N   G +++ +  ++         VMI R 
Sbjct: 184 --RSERQSDMNRLNEIHEVTR-VVSVPVIANGFSGSIKEYADIMRFWKQSGASSVMIARK 240

Query: 219 AYKNSAMLT 227
           A  N ++  
Sbjct: 241 ALSNPSIFR 249


>gi|325090975|gb|EGC44285.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus H88]
          Length = 741

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/337 (16%), Positives = 98/337 (29%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 342 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESETLPPAVNPKQTIVKDY 400

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      + A + +         I++N GCP   V     G+ L+ +
Sbjct: 401 DNSRDLKFGAQITGNKPWVALRATEAMTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 460

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSI------------KKSG 147
              +   +  M      IP+TVK R+G  D  P      L++ +              +G
Sbjct: 461 ASKLEKMLRGMNAVSGEIPITVKIRMGTKDSNPTAT--KLIERLIMGGVESHEIGRGPAG 518

Query: 148 VNGIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKKE----NPDLF 190
           V  I +H R    +     D   I              ++  D + E           +F
Sbjct: 519 VAAITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIGTDTIKEPDARDQPSAGKVF 578

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG        L       VD VM+ R A     +   +++      + S        
Sbjct: 579 FLGNGDCYSHEDYLSGIQKSGVDTVMVARGALVKPWIFEEIEKGQYLDKSASE------- 631

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 632 ---RLALVEKFAQYGLEAWGSDEYGVGNTRRFLLEYL 665


>gi|15896694|ref|NP_350043.1| hypothetical protein CA_C3454 [Clostridium acetobutylicum ATCC 824]
 gi|15026545|gb|AAK81383.1|AE007843_1 Predicted TIM-barrel enzyme, nifR3 family [Clostridium
           acetobutylicum ATCC 824]
 gi|325510859|gb|ADZ22495.1| TIM-barrel enzyme, nifR3 family [Clostridium acetobutylicum EA
           2018]
          Length = 311

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/278 (19%), Positives = 108/278 (38%), Gaps = 26/278 (9%)

Query: 14  RLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           +        +T  I    + ++   + K++L  + +   L  QI   D +K +   + + 
Sbjct: 22  KFFGGIDKYFTPFIVPTSSKSLTSRELKDVLPENNKVTFLVPQILTNDANKFIFTTEKLM 81

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           + GY+E+NLN+GCPS  V     GA  +     + + +  +       +++K RIG D  
Sbjct: 82  NLGYSEVNLNLGCPSGTVVSKGRGAGFLKKRQELDEFLEKIFSKSPAKISIKTRIGKD-- 139

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                   L+K   K  +  + IH R       +  + +   +           E     
Sbjct: 140 -SPDEFYELIKIFNKYPLEELIIHPRIQTDFYNNKPNMKVFKDAL---------ELSKST 189

Query: 191 IGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           +  NG +    D  + ++   ++  VM+GR    N  ++  ++         ++ ++  V
Sbjct: 190 VCYNGDIFQSNDYIKLIEEFSNLGVVMLGRGIISNPNIIKKIN--------SNNVLEKEV 241

Query: 248 DKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
            K F   I     D  +   +   K+++I  +MI LF 
Sbjct: 242 LKKFHDAIYEEYQDILSGEKNVLFKMKEIWFYMIHLFK 279


>gi|325118139|emb|CBZ53690.1| conserved hypothetical protein [Neospora caninum Liverpool]
          Length = 654

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 126/331 (38%), Gaps = 98/331 (29%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADA---------------ILRGDKKNILGFST 45
           M+D+T+RH+R    L++    LYTEM+                   I R   + I   ST
Sbjct: 104 MMDYTNRHWRHLISLMSRRVTLYTEMVSVPPAPCESSECSQDLPPSIKRKLWEEISSLST 163

Query: 46  QEKPLALQIGGADISKLVEAAK------IVEDFGYNE------------INLNVGCPSAR 87
               + LQ+G   ++  +  A+        E+ G  E            +NLN GCPS R
Sbjct: 164 VPNHVVLQVGVGSVASAIAVARAFNSHEFSENRGQCEQGTGTGRQRTFSVNLNCGCPSPR 223

Query: 88  VHEGSFGACLMLNPDIVGDC--------------------------------IAAMCKAL 115
           V +GSFG  LM +P  V +                                 +  M K  
Sbjct: 224 VAKGSFGLILMEDPKRVAEICQVLLDGANSRESQQGRNVADEATGMCAGGDTMNRMAKTD 283

Query: 116 SI------PVTVKCRIGVDDQ---------------------IPAVALRNLVKSI-KKSG 147
            +       V+VKCR+G+++                           L + + ++ + S 
Sbjct: 284 EVLRMDNSAVSVKCRVGIEEDRRFLRSGSNLFSATTFSSSSTCTYEKLASFIATVTEASP 343

Query: 148 VNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           V    IHAR  IL G LSPK+N +IP    + VY + ++ P++    NGG++   +A   
Sbjct: 344 VRHFIIHARPGILVGKLSPKENLQIPQRRPEWVYRLCQDFPNVSFTFNGGVKSFHEAEGH 403

Query: 207 L----PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L      + GVM+GR          +  + F
Sbjct: 404 LLNTNDKLGGVMVGRDILDRPWYWGSCADAF 434


>gi|322712093|gb|EFZ03666.1| tRNA-dihydrouridine synthase 3 [Metarhizium anisopliae ARSEF 23]
          Length = 782

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/292 (18%), Positives = 92/292 (31%), Gaps = 75/292 (25%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE------KP-------- 49
           +  +R     L    L Y+EM +   +L+G      +L     E      KP        
Sbjct: 359 NLPFRRLCVELGCE-LTYSEMAMGMPLLQGTKADWTLLKAHESEIQPPAFKPSSNNYVFE 417

Query: 50  ---------LALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLM 98
                       QI G     + +AA ++  +  +   I+LN GCP   V +   G+ L+
Sbjct: 418 NYDNSRDLRFGAQISGNQPWIVTKAADVLNRYCPHLRLIDLNCGCPIDMVFKSGGGSALL 477

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIP---------AVALRNLVKSIKKSGV 148
            +   +   I  M   +  IP+T K R GV    P         A   R   + +   G 
Sbjct: 478 ESQGKLERMIRGMNAMSGEIPITAKIRTGVKSSRPTAPSVISKLAFGSREHRERLGAPGC 537

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---------------------- 186
             + +H R         ++ R     D+  + E                           
Sbjct: 538 AALTLHGRS--------REQRYTKRADWSYIGECAALIKTYNEQRDALADTAAEPDASTL 589

Query: 187 -----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
                  ++   NG     ++  + +    VD VMIGR A     +   + +
Sbjct: 590 PNSKDGRMYFLGNGDCYSHTEYFEHVSKSRVDTVMIGRGALIKPWLFEEIQQ 641


>gi|195132199|ref|XP_002010531.1| GI14629 [Drosophila mojavensis]
 gi|193908981|gb|EDW07848.1| GI14629 [Drosophila mojavensis]
          Length = 458

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 100/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLAL-- 52
           MV       R  A  +    ++YTE +V   +++  ++       I      +  +    
Sbjct: 17  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLIKSLRRPNPALNTIDFVDPSDGTIVFRT 75

Query: 53  ----------QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                     Q+G +D ++ +   K+V++     +++N+GCP     +G  GA L+  P 
Sbjct: 76  CSLETSRVVLQLGTSDAARALAVGKLVQN-DIAGLDINMGCPKEFSIKGGMGAALLSEPA 134

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +   L IP+T K RI  D     +    LV+ +  +G+  I IHAR      
Sbjct: 135 KAAHILRTLTTHLDIPITCKIRILPD----TLETIKLVQELAATGIAAIGIHART----- 185

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-----KILPSVDGVMIGR 217
              +D R   +   D++  +     D+ I  NGG  +M         + L   D VM+ R
Sbjct: 186 ---RDERPQHHPHPDVLRAVASAV-DIPIIANGGSRNMHTYEDLHKFQELCGADSVMVAR 241

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 242 AAQLNVSIFR 251


>gi|194895115|ref|XP_001978186.1| GG17837 [Drosophila erecta]
 gi|190649835|gb|EDV47113.1| GG17837 [Drosophila erecta]
          Length = 473

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 102/250 (40%), Gaps = 38/250 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLAL-- 52
           MV       R  A  +    ++YTE +V   +++  ++       +      +  +    
Sbjct: 31  MVRVGTLPMRLLALEM-GADIVYTEELVDLKLIKSIRRPNPALGTVDFVDPSDGTIVFRT 89

Query: 53  ----------QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                     Q+G +D  + +   K+++    + +++N+GCP     +G  GA L+  PD
Sbjct: 90  CAQETSRLVLQMGTSDAGRALAVGKLLQ-RDISGLDINMGCPKEFSIKGGMGAALLAVPD 148

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                +  +C  L IPVT K RI  D      +  +LV+ +  +G+  I IHAR ++   
Sbjct: 149 KAALILRTLCSGLDIPVTCKIRILPD----VESTIDLVQKLAATGIAAIGIHARTSVE-- 202

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
                 R       +++  + +   D+ I  NGG ++M     +         D VM+ R
Sbjct: 203 ------RPQHAAHPEVLRAVAQAV-DIPIIANGGSKNMHCYEDLRKFQLECGADSVMVAR 255

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 256 AAQINVSIFR 265


>gi|126663428|ref|ZP_01734425.1| hypothetical protein FBBAL38_08769 [Flavobacteria bacterium BAL38]
 gi|126624376|gb|EAZ95067.1| hypothetical protein FBBAL38_08769 [Flavobacteria bacterium BAL38]
          Length = 314

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 117/293 (39%), Gaps = 38/293 (12%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMI--VADAILRGDKKN-ILGFSTQEKPLALQIGGAD 58
            +TD  +R  F +        Y+  I      I++G  +  IL  +     +  QI   D
Sbjct: 12  GFTDFRFRNAFHKYFGGIDTFYSPYIKLNGKMIIKGSYERDILPENNSTLEVIPQIITND 71

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +  AK V+ FGY E+N N+GCP   V +   G+ L+ N D +   +  +     I 
Sbjct: 72  AEEFLFVAKYVQQFGYKELNWNLGCPYPMVAKCGMGSGLIKNTDQIEHILKRVHNETDII 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD--NRKIPNL 174
           V++K R+G +       + ++   +++  +  I IHAR  K + KG    D   + + + 
Sbjct: 132 VSMKMRMGYE---NPSEILDVFPILEQYPIKNIAIHARIGKQLYKGGVDLDSFQKCLDHS 188

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDE 231
            + + Y             NG +  +++  ++    PS+D  MIGR    +  + + +  
Sbjct: 189 KHKLYY-------------NGDITSVTKFKEMQERFPSIDHFMIGRGLIADPFLPSMIK- 234

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              N  T     + ++ ++F   I      Y             I   M+G +
Sbjct: 235 ---NNTTEYPKNRYQLFEEFHDTIYQEYDAYLQ-------GPTPIRMKMLGFW 277


>gi|322782637|gb|EFZ10516.1| hypothetical protein SINV_13804 [Solenopsis invicta]
          Length = 401

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 43/190 (22%), Positives = 84/190 (44%), Gaps = 19/190 (10%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            S + + + LQIG +D ++  + A++VE+     I++N+GCP      G  GA L+ + +
Sbjct: 21  CSREREHIVLQIGTSDPARAAQVARMVEN-DVAGIDVNMGCPKKFSMLGGMGAALLSDME 79

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              D +  + + ++IP++ K R+  D +        L  ++  +G+  I +H R    + 
Sbjct: 80  KATDILRKLIETVTIPISCKIRVLPDLE----ETLRLCNTLASTGIAAIAVHGRTIEERP 135

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-----PSVDGVMIGR 217
             P  N  +  +              + +  NGG +D+ +   IL          VM+ R
Sbjct: 136 QHPNRNHILKQI---------STALSIPVIANGGSKDIQKHSDILRFKTETGCSSVMLAR 186

Query: 218 AAYKNSAMLT 227
           AA  N ++  
Sbjct: 187 AAEWNCSVFR 196


>gi|158320020|ref|YP_001512527.1| dihydrouridine synthase DuS [Alkaliphilus oremlandii OhILAs]
 gi|158140219|gb|ABW18531.1| dihydrouridine synthase DuS [Alkaliphilus oremlandii OhILAs]
          Length = 321

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 56/293 (19%), Positives = 120/293 (40%), Gaps = 33/293 (11%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGGA 57
              T   YR  +A+   +    +T  IV +   ++   + +++   + Q   +  QI   
Sbjct: 9   EGVTGFIYRNAYAKFFNHIDKYFTPFIVTNQGTSLKNKELRDVFPENNQGLHVVPQILTN 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +    +  +K ++  GY EINLN+GCPS  V   + G+  +   + +   +  + K   +
Sbjct: 69  NSEGFISVSKKLKQLGYAEINLNLGCPSGTVVSKNRGSGFLAKREELDRFLEEIFKIEDM 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K RIG D          L+K   K  +  + IH R               PNL   
Sbjct: 129 KISIKTRIGKD---HPEEFYELIKIYNKYPLEELIIHPRTRQDFYG------NQPNL--- 176

Query: 178 IVYEIKKENPDL---FIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              E+ K+   L    +  NG +    D ++ ++  P VD +M+GR    N  ++  +  
Sbjct: 177 ---EVFKDALLLSTNPVCYNGDIFTVGDHNRLVETFPDVDTMMLGRGVLANPGLMKEIR- 232

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                   ++ ++  V ++F  ++     +      ++  +++++  +M  +F
Sbjct: 233 -------NNTLMEKEVLREFIDEVLYQYVELFQEERNALYRMKELWSYMAYIF 278


>gi|322695939|gb|EFY87739.1| tRNA-dihydrouridine synthase 3 [Metarhizium acridum CQMa 102]
          Length = 764

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 54/292 (18%), Positives = 92/292 (31%), Gaps = 75/292 (25%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE------KP-------- 49
           +  +R     L    L Y+EM +   +L+G      +L     E      KP        
Sbjct: 364 NLPFRRLCVELGCE-LTYSEMAMGMPLLQGTKADWTLLKAHESEIQPPAFKPSSNNYVFE 422

Query: 50  ---------LALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLM 98
                       QI G     + +AA ++  +  +   I+LN GCP   V +   G+ L+
Sbjct: 423 NYDNSRDLRFGAQISGNQPWVVTKAADVLNRYCPHLRLIDLNCGCPIDMVFKSGGGSALL 482

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIP---------AVALRNLVKSIKKSGV 148
            +   +   I  M   +  IP+T K R GV    P         A   R   + +   G 
Sbjct: 483 ESQGKLERMIRGMNAMSGEIPITAKIRTGVKSSRPTAPSVISKLAFGSREHRERLGAPGC 542

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---------------------- 186
             + +H R         ++ R     D+  + E                           
Sbjct: 543 AALTLHGRS--------REQRYTKRADWSYIGECAALIKTYNEQKDALADTAAEPDASTL 594

Query: 187 -----PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
                  ++   NG     ++  + +    VD VMIGR A     +   + +
Sbjct: 595 PNSKDGRMYFLGNGDCYSHTEYFEHVSKSRVDTVMIGRGALIKPWLFEEIQQ 646


>gi|303317776|ref|XP_003068890.1| hypothetical protein CPC735_009210 [Coccidioides posadasii C735
           delta SOWgp]
 gi|240108571|gb|EER26745.1| hypothetical protein CPC735_009210 [Coccidioides posadasii C735
           delta SOWgp]
          Length = 724

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 50/283 (17%), Positives = 94/283 (33%), Gaps = 60/283 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE------KP-------- 49
           +  +R     L      Y+EM ++  I++G K    ++     E      KP        
Sbjct: 327 NLPFRRLCVEL-GAQFTYSEMAMSLPIVQGHKGEWALMKAHQSEVLPPTIKPNQGVVKDY 385

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI      + ++A +++     +   ++LN GCP   V+    G+ L+ +
Sbjct: 386 DHSRDLKFGVQISANKPWQALKATEVMTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 445

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M    + +PV+ K R+G  D  P      L++ +              +G
Sbjct: 446 PSKLEKILRGMNAVSNEVPVSAKIRMGTKDNSPTA--LKLIERLVLGGPEFSEIGQGPAG 503

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYE----IKKENPDLF 190
           V  I +H R    +     D   I                  D + E    ++     ++
Sbjct: 504 VAAITLHGRSRQQRYTREADWSYISECAALIKRLNERSDDLTDTIREPDDRLQAPGRRVY 563

Query: 191 IGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
              NG         + +    VD VMI R A     +   +  
Sbjct: 564 FLGNGDCYSHEDYYRAIGESGVDTVMIARGALMKPWIFEEIQA 606


>gi|253698736|ref|YP_003019925.1| dihydrouridine synthase [Geobacter sp. M21]
 gi|251773586|gb|ACT16167.1| dihydrouridine synthase DuS [Geobacter sp. M21]
          Length = 341

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/271 (21%), Positives = 107/271 (39%), Gaps = 24/271 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEM-----IVADAILRGDKKNILGFSTQEKPLALQIG 55
           M   T+R  R          +++TE      + A   L       +  S    PL +Q+ 
Sbjct: 39  MQGLTNRALRSLFTKWVRPDVVWTEFMRVNPVSAKKRLMPGDLREISASEDGIPLVVQLI 98

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G     LV AA+  +D G   +NLN+GCP  R+  G  G  ++  P+++ + I A+ +A+
Sbjct: 99  GHGREALVSAAQAAQDAGAKHLNLNMGCPYGRMTSGLTGGGMLKKPELLEEIIPALREAI 158

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
               ++K R G +D     +   L+   ++SGV+ + +H R                  D
Sbjct: 159 HGSFSIKLRAGYEDPRQVFS---LLPLFERSGVDFLVLHPRT--------VRQAYNGWAD 207

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +++  E+ +    + +  NG +   +  L +L      G+M+GR       +   +    
Sbjct: 208 HEVTAEVVRSTG-IPVIANGDIRSAAGGLHLLEQTGAAGLMLGRGGIGEPMLFERLR--- 263

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
                 + P  +       R +S  +  Y A
Sbjct: 264 --GRAAAEPDLSERRAMLHRYLSDLLPLYCA 292


>gi|261758310|ref|ZP_06002019.1| nitrogen regulation protein NifR3 [Brucella sp. F5/99]
 gi|261738294|gb|EEY26290.1| nitrogen regulation protein NifR3 [Brucella sp. F5/99]
          Length = 189

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 39/150 (26%), Positives = 72/150 (48%), Gaps = 4/150 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   +D  +R  A       ++ +EM+ +  +    ++++L  S +      +Q+ G + 
Sbjct: 24  MSGVSDLPFRKRAAE-AGAGMVVSEMVASAELCNRHRESLLRLSGEGLGTHVVQLAGREA 82

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + EAAKI E  G + I++N+GCP+ +V  G  G+ LM N D     + A   A+ +PV
Sbjct: 83  RWMGEAAKIAEGEGADIIDINMGCPAKKVTGGYSGSALMRNLDHAMTLVEATVAAVKVPV 142

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           T+K R+G D+   ++    L +        
Sbjct: 143 TLKMRLGWDE--NSINAPELARRAGACQAR 170


>gi|17510279|ref|NP_493554.1| hypothetical protein Y54E5A.6 [Caenorhabditis elegans]
 gi|3925277|emb|CAA21662.1| C. elegans protein Y54E5A.6, partially confirmed by transcript
           evidence [Caenorhabditis elegans]
          Length = 436

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 95/249 (38%), Gaps = 35/249 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFST 45
           MV       R          L YTE IV   ++               R     IL  + 
Sbjct: 14  MVRAGRTPLRLLCLKY-GADLCYTEEIVDKKLIEATRVVNEALGTIDYRNGDDIILRLAP 72

Query: 46  QEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           +EK    LQIG     K  + A+IV D     I++N+GCP         GA L+   + +
Sbjct: 73  EEKGRCILQIGTNSGEKAAKIAQIVGD-DVAGIDVNMGCPKPFSIHCGMGAALLTQTEKI 131

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            D + ++  A  +PVT K R+  D +        LV+ I+K  V+ + +H R+       
Sbjct: 132 VDILTSLKSAAKVPVTCKIRVLDDPEDT----LKLVQEIEKCRVSALGVHGRR------- 180

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALK--ILPSVDGVMIGRAA 219
            +D R+      D + ++ +    + +  NG    +E  S   K  +L      MI R A
Sbjct: 181 -RDERQPDKCRIDEIRDVAQAVQSIPVISNGLSDEIEQYSDFEKYQLLTETSSTMIARKA 239

Query: 220 YKNSAMLTT 228
               ++   
Sbjct: 240 LSTPSIFRR 248


>gi|240274641|gb|EER38157.1| tRNA dihydrouridine synthase 3-like protein [Ajellomyces capsulatus
           H143]
          Length = 741

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 54/337 (16%), Positives = 97/337 (28%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 342 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESETLPPAVNPKQTIVKDY 400

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      + A + +         I++N GCP   V     G+ L+ +
Sbjct: 401 DNSRDLKFGAQITGNKPWVALRATEAMTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 460

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSI------------KKSG 147
              +   +  M      IP+TVK R+G  D  P      L++ +              +G
Sbjct: 461 ASKLEKMLRGMNAVSGEIPITVKIRMGTKDSNPTAT--KLIERLIMGGVESHEIGRGPAG 518

Query: 148 VNGIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKKE----NPDLF 190
           V  I +H R    +     D   I              ++  D + E           +F
Sbjct: 519 VAAITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIGTDTIKEPDARDQPSAGKVF 578

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG                VD VM+ R A     +   +++      + S        
Sbjct: 579 FLGNGDCYSHEDYFSGIQKSGVDTVMVARGALVKPWIFEEIEKGQYLDKSASE------- 631

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 632 ---RLALVEKFAQYGLEAWGSDEYGVGNTRRFLLEYL 665


>gi|153846110|ref|ZP_01993830.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
 gi|149744985|gb|EDM56303.1| tRNA-dihydrouridine synthase C [Vibrio parahaemolyticus AQ3810]
          Length = 158

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 78/165 (47%), Gaps = 15/165 (9%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +Q+ G +   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A
Sbjct: 1   HVQLLGQEPHWMAENAIRAAELGARGIDLNFGCPAKMVNKSKGGAALLQHPELIHSVVKA 60

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
              A+  +IPV+ K R+G ++         +V +I+ +G N + +HAR         +  
Sbjct: 61  CRDAVPANIPVSAKIRLGWENPEDCF---EIVDAIQSAGANELTVHARTK-------QGG 110

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVD 211
            K   + ++ + +I++    + +  NG + +     + +    VD
Sbjct: 111 YKASEIKWEYINKIRERF-SIPLIANGEIWNFEDGQRCIETTGVD 154


>gi|225561539|gb|EEH09819.1| tRNA-dihydrouridine synthase 3-like protein [Ajellomyces capsulatus
           G186AR]
          Length = 741

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 54/337 (16%), Positives = 97/337 (28%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 342 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESETLPPAVNPKQTIVKDY 400

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      + A + +         I++N GCP   V     G+ L+ +
Sbjct: 401 DNSRDLKFGAQITGNKPWVALRATEAMTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 460

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSI------------KKSG 147
              +   +  M      IP+TVK R+G  D  P      L++ +              +G
Sbjct: 461 ASKLEKMLRGMNAVSGEIPITVKIRMGTKDSNPTAT--KLIERLIMGGVESHEIGRGPAG 518

Query: 148 VNGIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKKE----NPDLF 190
           V  I +H R    +     D   I              ++  D + E           +F
Sbjct: 519 VAAITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIGTDTIKEPDARDQPSAGKVF 578

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG                VD VM+ R A     +   +++      + S        
Sbjct: 579 FLGNGDCYSHEDYFSGIQKSGVDTVMVARGALVKPWIFEEIEKGQYLDKSASE------- 631

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 632 ---RLALVEKFARYGLEAWGSDEYGVGNTRRFLLEYL 665


>gi|58258399|ref|XP_566612.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57222749|gb|AAW40793.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 407

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 39/186 (20%), Positives = 77/186 (41%), Gaps = 16/186 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q    +   L +AA+++  +  + I+LN GCP    +    G  L+  P++V D + 
Sbjct: 152 LIAQFASPNAKSLADAAELISPY-VDGIDLNCGCPQRWAYNEGIGCALLRKPELVRDMVR 210

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +   +    PV++K RI  + +        L+ +  ++G++ + IH R        P +
Sbjct: 211 GVKDRMGWGWPVSIKIRIDSEQEKT----EQLISNALQAGISHLTIHGRTRHQPSTDPVN 266

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
              I        + +     ++    NG + ++  A ++     V GVM  R    N A+
Sbjct: 267 LPGIK-------FAVDCVKGEVPCVANGDVWELEDARQMRLHTGVQGVMAARGLLANPAL 319

Query: 226 LTTVDE 231
               D+
Sbjct: 320 FAGYDK 325


>gi|119186423|ref|XP_001243818.1| hypothetical protein CIMG_03259 [Coccidioides immitis RS]
 gi|121927069|sp|Q1E2F4|DUS3_COCIM RecName: Full=tRNA-dihydrouridine synthase 3
          Length = 724

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 49/284 (17%), Positives = 95/284 (33%), Gaps = 62/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE------KP-------- 49
           +  +R     L      Y+EM ++  I++G K    ++     E      KP        
Sbjct: 327 NLPFRRLCVEL-GAQFTYSEMAMSLPIVQGHKGEWALMKAHQSEVLPPTIKPNQGVVKDY 385

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI      + ++A +++     +   ++LN GCP   V+    G+ L+ +
Sbjct: 386 DHSRDLKFGVQISANKPWQALKATEVMTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 445

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M    + +PV+ K R+G  D  P      L++ +              +G
Sbjct: 446 PSKLEKILRGMNAVSNEVPVSAKIRMGTKDNSPTA--LKLIERLVLGGPEFTEIGQGPAG 503

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD------------------L 189
           V  I +H R    +     D   I      ++  + + + D                  +
Sbjct: 504 VAAITLHGRSRQQRYTREADWSYISECA-ALIRRLNERSDDLTDTIREADDRLQAPGRRV 562

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +   NG         + +    VD VMI R A     +   +  
Sbjct: 563 YFLGNGDCYSHEDYYRAIGESGVDTVMIARGALMKPWIFEEIQA 606


>gi|160880024|ref|YP_001558992.1| dihydrouridine synthase DuS [Clostridium phytofermentans ISDg]
 gi|160428690|gb|ABX42253.1| dihydrouridine synthase DuS [Clostridium phytofermentans ISDg]
          Length = 318

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 56/288 (19%), Positives = 111/288 (38%), Gaps = 21/288 (7%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR        N    +T  IVA+   +    + ++I     Q   +  QI  
Sbjct: 8   MEGVTGYIYRNIHHSYFPNVDKYFTPFIVANQSNSFKTRELQDIKPEHNQGMYVVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +    ++ ++ + +FGY+EINLN+GCPS  V     G+  ++  D +   +  + +A  
Sbjct: 68  NNAQDFIQTSRKIAEFGYDEINLNLGCPSGTVVAKGKGSGFLVMKDELNRFLEEVFQASV 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             +++K RIG D         +L+    +  +  + IH R            +  PNL  
Sbjct: 128 TKISIKTRIGRD---NPEEFHDLMSIFNQYPLEELIIHPRIQKDMY------KNTPNLPV 178

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                +  ++   + G    ++D    +   P V  VM+GR    N A++  +       
Sbjct: 179 FAEGLLLSKHEVCYNGDIFTVDDYKNFIANFPQVKAVMLGRGIIANPAIIQEI------- 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            T    +   + K+F  ++        +       K++++  +   +F
Sbjct: 232 -TLGKGLDKSILKEFHSRLVIDYQRILSGDRDVLFKMKEVWHYWSFIF 278


>gi|320038928|gb|EFW20863.1| dihydrouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 698

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 50/283 (17%), Positives = 94/283 (33%), Gaps = 60/283 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE------KP-------- 49
           +  +R     L      Y+EM ++  I++G K    ++     E      KP        
Sbjct: 327 NLPFRRLCVEL-GAQFTYSEMAMSLPIVQGHKGEWALMKAHQSEVLPPTIKPNQGVVKDY 385

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI      + ++A +++     +   ++LN GCP   V+    G+ L+ +
Sbjct: 386 DHSRDLKFGVQISANKPWQALKATEVMTALCPHLRVVDLNCGCPIDLVYRDGAGSALLEH 445

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
           P  +   +  M    + +PV+ K R+G  D  P      L++ +              +G
Sbjct: 446 PSKLEKILRGMNAVSNEVPVSAKIRMGTKDNSPTA--LKLIERLVLGGPEFSEIGQGPAG 503

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYE----IKKENPDLF 190
           V  I +H R    +     D   I                  D + E    ++     ++
Sbjct: 504 VAAITLHGRSRQQRYTREADWSYISECAALIKRLNERSDDLTDTIREPDDRLQAPGRRVY 563

Query: 191 IGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
              NG         + +    VD VMI R A     +   +  
Sbjct: 564 FLGNGDCYSHEDYYRAIGESGVDTVMIARGALMKPWIFEEIQA 606


>gi|255714134|ref|XP_002553349.1| KLTH0D14696p [Lachancea thermotolerans]
 gi|238934729|emb|CAR22911.1| KLTH0D14696p [Lachancea thermotolerans]
          Length = 667

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 63/301 (20%), Positives = 110/301 (36%), Gaps = 49/301 (16%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +      E P   +QI  +   + 
Sbjct: 310 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHVSETPGFGVQIACSKAWQA 368

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ +       +EINLN GCP   ++    G+ L+ NP  +  C+ +M      IPV
Sbjct: 369 AKAAEALAANVQDVSEINLNSGCPIDLLYRQGSGSALLDNPARMFRCLNSMSYVSGDIPV 428

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G  D  P      LV+  + ++ V  I +H R         +  R   N D+D 
Sbjct: 429 TVKIRTGTKDGHPMAE--GLVRRLVSETDVAAITLHGRT--------RQQRYTRNADWDY 478

Query: 179 VYEI------------------KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
           + ++                  ++         NG + +     K +   ++D VM+ R 
Sbjct: 479 ISKVASTLREAEHEVEEKDKERREGKLRTQFVGNGDVNNFEDWYKHVEDENIDSVMVARG 538

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQQIT 277
           A     +   V+       + +              I      +A  H  +    + Q  
Sbjct: 539 ALVKPWIFEEVEAQQHLDKSSAE----------RLDILKDYAHFAMDHWGTDEYGISQSR 588

Query: 278 R 278
           R
Sbjct: 589 R 589


>gi|167526513|ref|XP_001747590.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163774036|gb|EDQ87670.1| predicted protein [Monosiga brevicollis MX1]
          Length = 1116

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 65/288 (22%), Positives = 110/288 (38%), Gaps = 41/288 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR------------------GDKKNILG 42
           MV  ++  +R   R      L YT M  A  + +                  G   ++  
Sbjct: 37  MVWNSEAAFRCLVRD-HGAHLAYTPMWRAAIVCQYRDSPEWTPRTPAEKEAAGILYDVQC 95

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              Q++PL  Q+    +   V AA+I+E F  + I+LN+GCP        FGA LM +  
Sbjct: 96  APEQDRPLIAQLCATKVEDFVAAAQILEPF-VDAIDLNLGCPQNTAKREGFGAYLMDDLP 154

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            V   + A    L  P+T K R+         A R  ++ ++ +G + I IHAR    + 
Sbjct: 155 RVEAMLRAARAVLHKPITAKVRLFP----TLTATRAYLQMLEAAGCSLIAIHARLRGQRH 210

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
                       D+ +V E  ++  D+ + +NGG+  + QA  +L    V GVM+  A  
Sbjct: 211 -------HQGQPDFAMVRE-ARDAVDIPLLVNGGVRSLRQAESVLEYTGVAGVMVAGALL 262

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
           +   +           +  +     R+   +  +       Y   HL 
Sbjct: 263 ELPRLFA-------GQMDLARLADARLYLQYAERYPPPAIRYVRDHLM 303


>gi|225677569|gb|EEH15853.1| tRNA-dihydrouridine synthase B [Paracoccidioides brasiliensis Pb03]
          Length = 795

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 53/339 (15%), Positives = 92/339 (27%), Gaps = 75/339 (22%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++  +++G K    ++     E                
Sbjct: 345 NLPFRRLCVDL-GAQLTYSEMAMSMNLVQGSKSEWALMKAHESETLPPTVNPNQTIVKDY 403

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      ++A + +         I++N GCP   V     G+ L+ +
Sbjct: 404 DNSRDLKFGAQITGNKPWVALKATEALTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 463

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
              +   +  M      IP+T K R+G  D  P      L++ +              +G
Sbjct: 464 ASKLEKMLRGMNAVSGEIPITAKIRMGTKDSNPNAT--KLIERLVLGGVESHEIGQGPAG 521

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-----------------DIVYEIKKENPDLF 190
           V  I +H R    +     D   I                      +     +     +F
Sbjct: 522 VAAITLHGRSRQQRYSRQADWGYIGQCAALVKRLNEQINSGTDTAKEADARYQSSAGKVF 581

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTR 246
              NG                VD VMI R A     +   +   +Y     T        
Sbjct: 582 FLGNGDCYSHDDYFNGIRNSGVDTVMIARGALMKPWIFEEISKGQYLDKSATER------ 635

Query: 247 VDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                   +      Y      S    +    R ++   
Sbjct: 636 ------LALVEKFAKYGLEAWGSDEYGIGNTRRFLLEYL 668


>gi|148702859|gb|EDL34806.1| dihydrouridine synthase 1-like (S. cerevisiae), isoform CRA_a [Mus
           musculus]
          Length = 228

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 40/153 (26%), Positives = 68/153 (44%), Gaps = 10/153 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 40  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 98

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 99  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERLS 157

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +PVT K R+  +            + ++K+G  
Sbjct: 158 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQ 186


>gi|281200935|gb|EFA75149.1| tRNA-dihydrouridine synthase 2-like protein [Polysphondylium
           pallidum PN500]
          Length = 437

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 96/245 (39%), Gaps = 31/245 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-----------MIVADAILRGDK----KNILGFST 45
           MV       R  A+      + Y+E            ++  ++   D       I   + 
Sbjct: 52  MVRVGTLPMRLLAKEY-GCDIAYSEELIDLKVSQTKRVINKSLGTIDFIAKDNTITYRTC 110

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            E  L +   G   +    AA  V       I++N+GCP     +G  G+ L+  PD + 
Sbjct: 111 AEDTLNVLQLGTASATTALAAAQVVVNDVCAIDINMGCPKFFSVQGGMGSALLSKPDTIK 170

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           D +  + + L +PVT K R+  DD        +L++ I+ +GV  I +H R    +   P
Sbjct: 171 DILTTLIRNLPLPVTCKIRLLEDDNKT----IDLMRIIENTGVKAIGVHMRTIPERPRDP 226

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKN 222
               ++ N+       +      + I  NG +   ED+ +  K+    + VM+ R A KN
Sbjct: 227 AHWDRLKNI-------LDNAKFSVPIIANGDIFVNEDIEKVKKM-TGANSVMVARGAIKN 278

Query: 223 SAMLT 227
            ++  
Sbjct: 279 ISVFK 283


>gi|154282833|ref|XP_001542212.1| hypothetical protein HCAG_02383 [Ajellomyces capsulatus NAm1]
 gi|187471044|sp|A6QYC6|DUS3_AJECN RecName: Full=tRNA-dihydrouridine synthase 3
 gi|150410392|gb|EDN05780.1| hypothetical protein HCAG_02383 [Ajellomyces capsulatus NAm1]
          Length = 741

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 53/337 (15%), Positives = 96/337 (28%), Gaps = 71/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++ ++++G K    ++     E                
Sbjct: 342 NLPFRRLCVDL-GAQLTYSEMAMSMSLVQGSKSEWALMKAHESETLPPAVNPKQTIVKDY 400

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      + A + +         I++N GCP   V     G+ L+ +
Sbjct: 401 DNSRDLKFGAQITGNKPWVALRATEAMTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 460

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSI------------KKSG 147
              +   +  M      IP+T K R+G  D  P      L++ +              +G
Sbjct: 461 ASKLEKMLRGMNAVSGEIPITAKIRMGTKDSNPTAT--KLIERLIMGGVESHEIGRGPAG 518

Query: 148 VNGIWIHARKAILKGLSPKDNRKIP-------------NLDYDIVYEIKKE----NPDLF 190
           V  I +H R    +     D   I              ++  D + E           +F
Sbjct: 519 VAAITLHGRSRQQRYSRQADWEYISQCAALVKRLNEQTDIGTDTIKEPDARDQPSAGKVF 578

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG                VD VM+ R A     +   +++      + S        
Sbjct: 579 FLGNGDCYSHEDYFNGIQKSGVDTVMVARGALVKPWIFEEIEKGQYLDKSASE------- 631

Query: 249 KDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                 +      Y      S    +    R ++   
Sbjct: 632 ---RLALVEKFARYGLEAWGSDEYGVGNTRRFLLEYL 665


>gi|134106399|ref|XP_778210.1| hypothetical protein CNBA2100 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50260913|gb|EAL23563.1| hypothetical protein CNBA2100 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 407

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 39/186 (20%), Positives = 77/186 (41%), Gaps = 16/186 (8%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q    +   L +AA+++  +  + I+LN GCP    +    G  L+  P++V D + 
Sbjct: 152 LIAQFASPNAKSLADAAELISPY-VDGIDLNCGCPQRWAYNEGIGCALLRKPELVRDMVR 210

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +   +    PV++K RI  + +        L+ +  ++G++ + IH R        P +
Sbjct: 211 GVKDRMGWGWPVSIKIRIDSEQEKT----EQLISNALQAGISHLTIHGRTRHQPSTDPVN 266

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
              I        + +     ++    NG + ++  A ++     V GVM  R    N A+
Sbjct: 267 LPGIK-------FAVDCVKGEVPCVANGDVWELEDARQMRLHTGVQGVMAARGLLANPAL 319

Query: 226 LTTVDE 231
               D+
Sbjct: 320 FAGYDK 325


>gi|323452795|gb|EGB08668.1| hypothetical protein AURANDRAFT_13024 [Aureococcus anophagefferens]
          Length = 224

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 97/230 (42%), Gaps = 32/230 (13%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF-----STQEKPLALQIGG 56
           VD ++  YR   R      + +T M+ A   +         F     +  ++PL  Q  G
Sbjct: 16  VDQSELAYRLLCRSY-GAGICWTPMMDATRFVADAAYRRAVFEAGAGAPADRPLVAQFAG 74

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D + ++ AA++VE    + + LN GCP      G FGA L+  P+++   + A+ + L+
Sbjct: 75  DDPAAILAAARLVE-HRVDVVELNCGCPQKVAKRGHFGAFLLDEPEVIVAVVRALKRGLA 133

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V+              A   L + ++ +G + + +H R   +K       +     D+
Sbjct: 134 CAVS-------------AATVALARRLEAAGADLLTVHGRTRAMK-------KCGFPCDF 173

Query: 177 DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNS 223
             +  +K+    + +  NGG+E   D ++A + L   D VM G  A  + 
Sbjct: 174 AAIAAVKRAV-RVPVVANGGVERHADFARARE-LTGCDCVMSGELALAHP 221


>gi|296276940|ref|ZP_06859447.1| histidine phosphokinase/phophatase, putative [Staphylococcus aureus
           subsp. aureus MR1]
          Length = 193

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 80/187 (42%), Gaps = 16/187 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----GDKKNILGFSTQEKPLALQIGG 56
           M D TD  +R          + +TE    ++          +  L FS  E P+   I G
Sbjct: 19  MEDVTDIVFRHVVSEAARPDVFFTEFTNTESFCHPEGIHSVRGRLTFSEDEHPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +  E +  +   G+  I+LN+GCP A V +   G+ L+L PD+  + I A  KA  
Sbjct: 79  DKPEQFRETSIQLAKMGFKGIDLNMGCPVANVAKKGKGSGLILRPDVAAEIIQAT-KAGG 137

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV+VK R+G  +       ++ +K + +  +  + IH R         +      +  +
Sbjct: 138 LPVSVKTRLGYYEID---EWKDWLKHVFEQDIANLSIHLRT--------RKEMSKVDAHW 186

Query: 177 DIVYEIK 183
           +++  IK
Sbjct: 187 ELIEAIK 193


>gi|70996182|ref|XP_752846.1| tRNA dihydrouridine synthase [Aspergillus fumigatus Af293]
 gi|74672269|sp|Q4WRX4|DUS3_ASPFU RecName: Full=tRNA-dihydrouridine synthase 3
 gi|66850481|gb|EAL90808.1| tRNA dihydrouridine synthase, putative [Aspergillus fumigatus
           Af293]
 gi|159131599|gb|EDP56712.1| tRNA dihydrouridine synthase, putative [Aspergillus fumigatus
           A1163]
          Length = 726

 Score =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 53/281 (18%), Positives = 89/281 (31%), Gaps = 56/281 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R            Y+EM +  ++++G K    ++     E                
Sbjct: 329 NLPFRRLCIDY-GCQFTYSEMAMGMSLIQGQKSEWALMKAHESEALPPTISSTADVVQGY 387

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      ++A +++         I+LN GCP  +V     G+ L+ +
Sbjct: 388 DNSKDFKFGAQIAGNKPWHAIKATELLSRLTPNLRVIDLNCGCPIDQVFREGAGSALLDH 447

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA--LRNLVKSIKKSGVNGIWIHARK 157
           P  +   +  M      IP+TVK R G  D  P     +  LV    +SG+  I      
Sbjct: 448 PSKLEKMLRGMNAVSEMIPITVKIRTGTRDNSPNATKLIERLVLGGHESGILNIGPPGVA 507

Query: 158 AILKGLSPKDNRKIPNLDYDIVYE----IKKEN---------------------PDLFIG 192
           A+      +  R     D+  + E    IK+ N                       +F  
Sbjct: 508 AVTLHGRSRQQRYTKMADWSYIAECAALIKRLNEKKDDVTDTVREPDERMLPNGGKVFFL 567

Query: 193 LNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            NG           +    VD VM+GR A     +   +  
Sbjct: 568 GNGDCYSHYDYDDHINNAGVDAVMVGRGAIIKPWVFEEIQA 608


>gi|325188682|emb|CCA23213.1| tRNAdihydrouridine synthase 3 putative [Albugo laibachii Nc14]
          Length = 637

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/326 (15%), Positives = 107/326 (32%), Gaps = 69/326 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +  T   +   EM ++  IL+  +    +L     E    +QI GA   ++ 
Sbjct: 237 NLPFRRLLKQ-TGADITCGEMAMSSNILQAQRSEWALLRRHKSEDVFGVQIAGAHGDQMA 295

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI----- 117
              +++  +   + I++N+GCP   V +   G+ LM  P  + + I+     + I     
Sbjct: 296 RVCELLTRETDVDFIDINMGCPIDIVCKSGSGSALMTRPARLLEVISGALTGIQIGQQHR 355

Query: 118 ---------------P-VTVKCRIGVDDQIPAV-------------------ALRNLVKS 142
                          P ++VK R G  ++ P+                       +  K 
Sbjct: 356 LQSRKIVANSSAFCYPALSVKLRTGWSEKQPSAHKVVSKIISTRSSHTYVSMNTAHWCKL 415

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF----IGLNGGLE 198
                V  I IH R  +         R     D+D +Y     + D+         G + 
Sbjct: 416 DDSQSVRAIAIHGRSRL--------QRYTKEADWDYIYRCADTSSDIVSGTSFIGGGDVL 467

Query: 199 DMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              +  + L +  +D  M+ R A     +   + E     ++ S              + 
Sbjct: 468 SFVEFDEHLKNGKLDTCMVARGALIKPWLPIEIKERRHFDISASERF----------DLL 517

Query: 257 ASMTDYAARHLHSGGK-LQQITRHMI 281
                +   H  +  K + +  R+++
Sbjct: 518 KDFVKFGLEHWGTDQKGVNRTRRYLL 543


>gi|259148380|emb|CAY81627.1| Dus3p [Saccharomyces cerevisiae EC1118]
          Length = 668

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 65/304 (21%), Positives = 113/304 (37%), Gaps = 52/304 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +    T E P   +Q+  +   + 
Sbjct: 305 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHTSEFPGFGVQVACSKAWQA 363

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ + +     +EINLN GCP   ++    G+ L+ NP  +  C+ AM      IP+
Sbjct: 364 AKAAEALANSVSEISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPI 423

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R    +  P      LVK  + ++ V  I +H R         +  R   + D+D 
Sbjct: 424 TVKIRTSTKEGHPIAE--GLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDY 473

Query: 179 VYEIK----------------KENPD----LFIGLNGGLEDMSQALKILPS---VDGVMI 215
           V ++                 KE  D    +    NG + +     + L     +D VM+
Sbjct: 474 VSQVADTLRSAEADFIETEQGKEGRDSKNRIQFVGNGDVNNFEDWYRYLDGNENIDSVMV 533

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQ 274
            R A     +   V+       T +  +           I      ++  H  +    + 
Sbjct: 534 ARGALIKPWIFEEVESQQYLDKTSTERL----------DILRDYAQFSMEHWGTDEYGIS 583

Query: 275 QITR 278
           Q  R
Sbjct: 584 QCRR 587


>gi|242207487|ref|XP_002469597.1| predicted protein [Postia placenta Mad-698-R]
 gi|220731401|gb|EED85246.1| predicted protein [Postia placenta Mad-698-R]
          Length = 313

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 100/244 (40%), Gaps = 33/244 (13%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILR---------------GDKKNILGFSTQEKP-L 50
              R +A L    +L++    V  AIL                G  K +      EKP L
Sbjct: 17  LPTRLYA-LKHGASLVWGPETVDKAILHTERVVDPTTGVISYVGKTKALFTTHPIEKPYL 75

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG AD    V+AA+ V        +LN GCP         GA L+ NPD++   + A
Sbjct: 76  IYQIGSADPELAVQAARTVVQ-DVAGFDLNCGCPKPFSTHSGMGAALLSNPDLLCSILTA 134

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   I ++ K R+    +        LV+ I  +GVN + +H R   ++    ++ 
Sbjct: 135 LREAMPPEISISAKIRLLPSQEDT----LKLVERIVNTGVNALTVHCRTRNMR---KREK 187

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNS 223
             I  L  +IV  ++    D+ +  NG  ED   A++I         D VMI  AA  N 
Sbjct: 188 AHIDRLR-EIVDFVRGLGRDVALIENGDCEDYQDAIRIREITGYVGADSVMIATAAEANP 246

Query: 224 AMLT 227
              +
Sbjct: 247 TCFS 250


>gi|207342736|gb|EDZ70406.1| YLR405Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 247

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 42/202 (20%), Positives = 88/202 (43%), Gaps = 16/202 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  ++Y+ MI+A   +R +   I  L  + ++ PL +Q+G  +
Sbjct: 46  MVRYSKLPFRQLCREY-NVDIVYSPMILAREYVRNEHARISDLSTNNEDTPLIVQVGVNN 104

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           ++ L++  ++V  +  + I +N GCP         G  L+ N D++   + A+       
Sbjct: 105 VADLLKFVEMVAPY-CDGIGINCGCPIKEQIREGIGCALIYNSDLLCSMVHAVKDKYGDK 163

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + ++ +I + + +       L + +  +GV+ I IH R         +  R     + D 
Sbjct: 164 LRIETKIRIHEALDETV--ELCRKLCDAGVDWITIHGRT--------RRTRSSQPANLDA 213

Query: 179 VYEIKKENPD--LFIGLNGGLE 198
           +  I +   D  + +  NG   
Sbjct: 214 IKYIIENISDKNVPVIANGDCF 235


>gi|226295293|gb|EEH50713.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 897

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 53/339 (15%), Positives = 92/339 (27%), Gaps = 75/339 (22%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L    L Y+EM ++  +++G K    ++     E                
Sbjct: 498 NLPFRRLCVDL-GAQLTYSEMAMSMNLVQGSKSEWALMKAHESETLPPTVNPNQTIVKDY 556

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      ++A + +         I++N GCP   V     G+ L+ +
Sbjct: 557 DNSRDLKFGAQITGNKPWVALKATEALTALCPQLRVIDMNCGCPIDMVFREGSGSALLDH 616

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
              +   +  M      IP+T K R+G  D  P      L++ +              +G
Sbjct: 617 ASKLEKILRGMNAVSGEIPITAKIRMGTKDSNPNAT--KLIERLVLGGVESHEIGQGPAG 674

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-----------------DIVYEIKKENPDLF 190
           V  I +H R    +     D   I                      +     +     +F
Sbjct: 675 VAAITLHGRSRQQRYSRQADWGYIGQCAALVKRLNEQINSGTDTAKEADARYQSSAGKVF 734

Query: 191 IGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIKTR 246
              NG                VD VMI R A     +   +   +Y     T        
Sbjct: 735 FLGNGDCYSHGDYFNGIRDSGVDTVMIARGALMKPWIFEEISKGQYLDKSATER------ 788

Query: 247 VDKDFWRKISASMTDYAARHLHSGG-KLQQITRHMIGLF 284
                   +      Y      S    +    R ++   
Sbjct: 789 ------LALVEKFVKYGLEAWGSDEYGIGNTRRFLLEYL 821


>gi|242778111|ref|XP_002479173.1| tRNA dihydrouridine synthase, putative [Talaromyces stipitatus ATCC
           10500]
 gi|218722792|gb|EED22210.1| tRNA dihydrouridine synthase, putative [Talaromyces stipitatus ATCC
           10500]
          Length = 712

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 57/333 (17%), Positives = 97/333 (29%), Gaps = 70/333 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQE---------------- 47
           +  +R     L      Y+EM +   +++G K    +L     E                
Sbjct: 313 NTPFRRLCTDL-GAQFTYSEMAMGMPLVQGHKPEWALLKAHASELTPPTISSKANVVQGY 371

Query: 48  -----KPLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI        ++  +I+     +   I+LN GCP   V +   G+ L+ +
Sbjct: 372 DHSRDMKFGAQIAANKPHVALKTVEILAALTPHLRVIDLNCGCPIDLVFKEGSGSALLDS 431

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           P  +   +  M      IP+TVK R+G  D  P      L + +   G +          
Sbjct: 432 PSKLEKILRGMNAVSGEIPITVKIRMGTKDNQPTA--LRLAERLVLGGADAQTMGIGPPG 489

Query: 150 --GIWIHARKAILKGLSPKDNRKIPN-------------LDYDIVYEIKKEN----PDLF 190
              I +H R    +     D   I                  D V E ++        ++
Sbjct: 490 IAAITLHGRSRQQRYTRSADWGYISECAALVKRLRSQSDALADTVREPEERLQPNGSKIY 549

Query: 191 IGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG           +   +VD VMIGR A     +   +        + S        
Sbjct: 550 FLGNGDCYSHEDYYGHVQNANVDTVMIGRGALIKPWLFEEIQAGQYLDKSASE------- 602

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                 +      Y   +  S      +TR  +
Sbjct: 603 ---RLALVEKFARYGMENWGSDEHGLGMTRRFL 632


>gi|207342739|gb|EDZ70408.1| YLR401Cp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 668

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 114/304 (37%), Gaps = 52/304 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +    T E P   +Q+  +   + 
Sbjct: 305 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHTSEFPGFGVQVACSKAWQA 363

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ + +     +EINLN GCP   ++    G+ L+ NP  +  C+ AM      IP+
Sbjct: 364 AKAAEALANSVSEISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPI 423

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G  +  P      LVK  + ++ V  I +H R         +  R   + D+D 
Sbjct: 424 TVKIRTGTKEGHPIAE--GLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDY 473

Query: 179 VYEIK----------------KENPD----LFIGLNGGLEDMSQALKILPS---VDGVMI 215
           V ++                 KE  D    +    NG + +     + L     +D VM+
Sbjct: 474 VSQVADTLRSAEADFIETEQGKEGRDSKNRIQFVGNGDVNNFEDWYRYLDGNENIDSVMV 533

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQ 274
            R A     +   V+       T +  +           I      ++  H  +    + 
Sbjct: 534 ARGALIKPWIFEEVESQQYLDKTSTERL----------DILRDYAQFSMEHWGTDEYGIS 583

Query: 275 QITR 278
           Q  R
Sbjct: 584 QCRR 587


>gi|299472929|emb|CBN80498.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 569

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 56/306 (18%), Positives = 114/306 (37%), Gaps = 55/306 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFST------------- 45
           MV      +R  A     +  ++TE ++   ++   +    +LG                
Sbjct: 20  MVRAGTLPFRALALRYGADT-VFTEEVIDRRVVNAVRTENPVLGTVDYVEKRGKKGIATP 78

Query: 46  -------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
                  +   L  QIG  D +  + AA+ VE      +++N+GCP     +G  GA L+
Sbjct: 79  FQTCPALERGRLVYQIGTGDATNALRAAQHVE-RDVAAVDINMGCPKRFSLQGGMGAALL 137

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             P +  D +  + + LS+PV+VK R+               + ++K+G   + +H RK 
Sbjct: 138 KQPQVAADIVGTLRRNLSVPVSVKIRLL----ETPGETVEFARRMEKAGACALSVHVRK- 192

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIG 216
              G +P          ++ +  +  +  ++ +  NG +   +    +K L     VM+ 
Sbjct: 193 --VGDTPAS-----KARWEELRPVV-DAVNIPVIANGDVYTRADMAGIKALSGCSSVMLA 244

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           R A  N ++             G       V + + R+       Y + + ++   + ++
Sbjct: 245 RPALLNCSIFK---------PDGHVLPLKEVIQQYLRE----CFRYDSVYQNAKYTVMEM 291

Query: 277 ---TRH 279
               RH
Sbjct: 292 LTKRRH 297


>gi|123288585|emb|CAM27543.1| dihydrouridine synthase 1-like (S. cerevisiae) [Mus musculus]
          Length = 194

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 43/194 (22%), Positives = 77/194 (39%), Gaps = 27/194 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQ--- 79

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                   AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 80  --------AALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERLS 130

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PVT K R+  +            + ++K+G   + +H R    KG             +
Sbjct: 131 VPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PMAGTASW 180

Query: 177 DIVYEIKKENPDLF 190
           + +  ++K      
Sbjct: 181 EHIKAVRKAVGIPV 194


>gi|26451942|dbj|BAC43063.1| unknown protein [Arabidopsis thaliana]
 gi|30017287|gb|AAP12877.1| At4g38890 [Arabidopsis thaliana]
          Length = 265

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 48/217 (22%), Positives = 80/217 (36%), Gaps = 29/217 (13%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP   V   S G+ L+  P  + + +      +  P+T+K R    +      + +L+
Sbjct: 1   MGCPIDMVVNKSAGSALLNKPLRMKNIVEVSSSIVETPITIKVRTAFFEGKN--RIDSLI 58

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGLED 199
             I   G   + IH R         +  R   + D+D +Y+  K    +L +  NG +  
Sbjct: 59  ADIGNWGATAVTIHGRS--------RQQRYSKSADWDYIYQCTKNATTNLQVIGNGDVYS 110

Query: 200 MSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
                K     P +   MI R A     + T + E     +T     +  + KDF R   
Sbjct: 111 YLDWNKHKSDCPELSSCMIARGALIKPWIFTEIKEQRHWDITSGE--RLNIMKDFVR--- 165

Query: 257 ASMTDYAARHLHSGGKLQQITRHMI--GL---FHGFP 288
                +  +H  S  K  + TRH +   L   F   P
Sbjct: 166 -----FGLQHWGSDTKGVETTRHFLLEWLSYTFRYIP 197


>gi|39950340|ref|XP_363279.1| hypothetical protein MGG_01205 [Magnaporthe oryzae 70-15]
 gi|187471055|sp|A4RLF4|DUS3_MAGO7 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|145020996|gb|EDK05125.1| hypothetical protein MGG_01205 [Magnaporthe oryzae 70-15]
          Length = 739

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 59/340 (17%), Positives = 102/340 (30%), Gaps = 73/340 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------P 49
           +  +R     L      Y+EM +A  I++G +    ++     E               P
Sbjct: 336 NLPFRRLCVDLGAQG-TYSEMAMAKPIVQGQQSEWALMKAHESETRPPTLSPETLASNSP 394

Query: 50  LA------------LQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGA 95
           +              QI  +     ++AA+ +  F  +   I+LN GCP   +++   G+
Sbjct: 395 IVKVYDNSRDLRFGAQISASSHPLAIKAAECLTTFLPHLRLIDLNCGCPIDMIYKAGAGS 454

Query: 96  CLMLNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIP---------AVALRNLVKSIKK 145
            L+   + +   I  M      +P+T K RIGV +  P              +    +  
Sbjct: 455 ALLEQHNKIERIIRGMNAVSGEVPITCKLRIGVKENHPLAKKNIERAVFGSPDFRNQLGA 514

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKE----NPD 188
            G   I +H R    +   P D   I                  D V E        + +
Sbjct: 515 PGCAAITLHGRTRQQRYKKPADWGYIAECAALIQSYRDKRDELTDTVREPDASTLAPSSE 574

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLTGSSPIK 244
           +F   NG     +   K +    VD VMIGR A     +   +   +Y     T      
Sbjct: 575 VFFLGNGDCYSHADYYKAIDESHVDTVMIGRGALIKPWVFEEIAAGQYLDKSST------ 628

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                +    I                 +    R ++   
Sbjct: 629 -----ERLGYIERFCRYGMEAWGADEMGIGTTRRFLLEYL 663


>gi|300767086|ref|ZP_07076999.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300495624|gb|EFK30779.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 357

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 92/234 (39%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   ++  +R            ++E + A +I   + K      +   + + +   +Q+ 
Sbjct: 47  MEAVSNTVFRQVISHAAAPDTFFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPVVQLW 106

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G + +    A   + D G+  +++N+GCP   V +   G+ L+ NP    D IAA  K  
Sbjct: 107 GNEAADFASATAELRDRGFKAVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTS 165

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            + V+ K R+G           + + ++    V  + +H R        P     I    
Sbjct: 166 GLAVSAKTRLGY---SKVAEYHDWIATLLSQHVAVLTVHLRTKQEMSKVPAHFEVID--- 219

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAML 226
            D++       P+  + +NG + D    +   K  P +DG+MIGR  + N    
Sbjct: 220 -DLIKMRDAIAPETLLQINGDVADYQAGVALAKAHPGLDGIMIGRGVFANPFAF 272


>gi|625116|gb|AAB82358.1| Ylr401cp [Saccharomyces cerevisiae]
          Length = 609

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 114/304 (37%), Gaps = 52/304 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +    T E P   +Q+  +   + 
Sbjct: 305 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHTSEFPGFGVQVACSKAWQA 363

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ + +     +EINLN GCP   ++    G+ L+ NP  +  C+ AM      IP+
Sbjct: 364 AKAAEALANSVSEISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPI 423

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G  +  P      LVK  + ++ V  I +H R         +  R   + D+D 
Sbjct: 424 TVKIRTGTKEGHPIAE--GLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDY 473

Query: 179 VYEIK----------------KENPD----LFIGLNGGLEDMSQALKILPS---VDGVMI 215
           V ++                 KE  D    +    NG + +     + L     +D VM+
Sbjct: 474 VSQVADTLRSAEADFIETEQGKEGRDSKNRIQFVGNGDVNNFEDWYRYLNGNENIDSVMV 533

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQ 274
            R A     +   V+       T +  +           I      ++  H  +    + 
Sbjct: 534 ARGALIKPWIFEEVESQQYLDKTSTERL----------DILRDYAQFSMEHWGTDEYGIS 583

Query: 275 QITR 278
           Q  R
Sbjct: 584 QCRR 587


>gi|85666121|ref|NP_013505.2| Dus3p [Saccharomyces cerevisiae S288c]
 gi|187471052|sp|A7A1S5|DUS3_YEAS7 RecName: Full=tRNA-dihydrouridine synthase 3
 gi|187608869|sp|Q06053|DUS3_YEAST RecName: Full=tRNA-dihydrouridine synthase 3
 gi|151940921|gb|EDN59303.1| dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|285813805|tpg|DAA09701.1| TPA: Dus3p [Saccharomyces cerevisiae S288c]
          Length = 668

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 114/304 (37%), Gaps = 52/304 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +    T E P   +Q+  +   + 
Sbjct: 305 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHTSEFPGFGVQVACSKAWQA 363

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ + +     +EINLN GCP   ++    G+ L+ NP  +  C+ AM      IP+
Sbjct: 364 AKAAEALANSVSEISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPI 423

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G  +  P      LVK  + ++ V  I +H R         +  R   + D+D 
Sbjct: 424 TVKIRTGTKEGHPIAE--GLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDY 473

Query: 179 VYEIK----------------KENPD----LFIGLNGGLEDMSQALKILPS---VDGVMI 215
           V ++                 KE  D    +    NG + +     + L     +D VM+
Sbjct: 474 VSQVADTLRSAEADFIETEQGKEGRDSKNRIQFVGNGDVNNFEDWYRYLNGNENIDSVMV 533

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQ 274
            R A     +   V+       T +  +           I      ++  H  +    + 
Sbjct: 534 ARGALIKPWIFEEVESQQYLDKTSTERL----------DILRDYAQFSMEHWGTDEYGIS 583

Query: 275 QITR 278
           Q  R
Sbjct: 584 QCRR 587


>gi|256269134|gb|EEU04469.1| Dus3p [Saccharomyces cerevisiae JAY291]
          Length = 668

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 66/304 (21%), Positives = 114/304 (37%), Gaps = 52/304 (17%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   R L    + Y+EM +A  +++G      +    T E P   +Q+  +   + 
Sbjct: 305 NLPYRRLMRKL-GADVTYSEMALAVPLIQGTNSEWALPKAHTSEFPGFGVQVACSKAWQA 363

Query: 63  VEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
            +AA+ + +     +EINLN GCP   ++    G+ L+ NP  +  C+ AM      IP+
Sbjct: 364 AKAAEALANSVSEISEINLNSGCPIDLLYRQGSGSALLDNPARMIRCLNAMNYVSKDIPI 423

Query: 120 TVKCRIGVDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G  +  P      LVK  + ++ V  I +H R         +  R   + D+D 
Sbjct: 424 TVKIRTGTKEGHPIAE--GLVKRLVNETDVAAITLHGRS--------RQQRYTKSADWDY 473

Query: 179 VYEIK----------------KENPD----LFIGLNGGLEDMSQALKILPS---VDGVMI 215
           V ++                 KE  D    +    NG + +     + L     +D VM+
Sbjct: 474 VSQVADTLRSAEADFIETEQGKEGRDSKNRIQFVGNGDVNNFEDWYRYLNGNDNIDSVMV 533

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG-KLQ 274
            R A     +   V+       T +  +           I      ++  H  +    + 
Sbjct: 534 ARGALIKPWIFEEVESQQYLDKTSTERL----------DILRDYAQFSMEHWGTDEYGIS 583

Query: 275 QITR 278
           Q  R
Sbjct: 584 QCRR 587


>gi|308179559|ref|YP_003923687.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308045050|gb|ADN97593.1| dihydrouridine synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 337

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 92/234 (39%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   ++  +R            ++E + A +I   + K      +   + + +   +Q+ 
Sbjct: 27  MEAVSNTVFRQVISHAAAPDTFFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPVVQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G + +    A   + D G+  +++N+GCP   V +   G+ L+ NP    D IAA  K  
Sbjct: 87  GNEAADFASATAELRDRGFKAVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTS 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            + V+ K R+G           + + ++    V  + +H R        P     I    
Sbjct: 146 GLAVSAKTRLGY---SKVAEYHDWIATLLSQHVAVLTVHLRTKQEMSKVPAHFEVID--- 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAML 226
            D++       P+  + +NG + D    +   K  P +DG+MIGR  + N    
Sbjct: 200 -DLIKMRDAIAPETLLQINGDVADYQAGVALAKAHPGLDGIMIGRGVFANPFAF 252


>gi|119494964|ref|XP_001264280.1| tRNA dihydrouridine synthase, putative [Neosartorya fischeri NRRL
           181]
 gi|187471056|sp|A1D1U0|DUS3_NEOFI RecName: Full=tRNA-dihydrouridine synthase 3
 gi|119412442|gb|EAW22383.1| tRNA dihydrouridine synthase, putative [Neosartorya fischeri NRRL
           181]
          Length = 726

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/291 (18%), Positives = 91/291 (31%), Gaps = 76/291 (26%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R    +       Y+EM +  ++++G K    ++     E                
Sbjct: 329 NLPFRRLC-IDHGCQFTYSEMAMGMSLIQGQKSEWALMKAHESEALPPTISSTADVVQGY 387

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI G      ++A +++         I+LN GCP  +V     G+ L+ +
Sbjct: 388 DNSKDLKFGAQIAGNKPWHAIKATELLGRLTPNLRVIDLNCGCPIDQVFREGAGSALLDH 447

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKS------------G 147
           P  +   +  M      IP+TVK R G  D  P      L++ +               G
Sbjct: 448 PSKLEKMLRGMNAVSEMIPITVKIRTGTRDNSPNAT--KLIERLVLGGHESSMLNIGPPG 505

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE----IKKEN----------------- 186
           V  I +H R         +  R   + D+  + E    IK+ N                 
Sbjct: 506 VAAITLHGRS--------RQQRYTKSADWSYIAECAALIKRLNEKKDDVTDTVREPDERM 557

Query: 187 ----PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
                 +F   NG           +    VD VM+GR A     +   +  
Sbjct: 558 LPNGGKVFFLGNGDCYSHHDYDDHINNAGVDAVMVGRGAIIKPWVFEEIQA 608


>gi|331091090|ref|ZP_08339932.1| hypothetical protein HMPREF9477_00575 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330405312|gb|EGG84848.1| hypothetical protein HMPREF9477_00575 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 314

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 57/285 (20%), Positives = 108/285 (37%), Gaps = 27/285 (9%)

Query: 4   WTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            T   +R  + R        +T  IV          +KK +         +  Q+     
Sbjct: 11  VTTYIFRNAYHRYFLPLDKYFTPFIVPHPNKKFNTREKKELSTEHNHGLYVVPQLLTNKA 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +  AK +E+ GY EINLN+GCPS  V     G+  +  P+ +   +  +   L + +
Sbjct: 71  EDFITTAKEIENMGYKEINLNLGCPSGTVVAKGKGSGFLAYPEELDRFLDNIYSKLDMKI 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK RIG   +        L++   K  +  + +H R      L     +  PNL    +
Sbjct: 131 SVKTRIG---KTSPDEFYRLIEIYNKYPLEELIVHPR------LQTDFYKNKPNLQ---I 178

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           ++   E     +  NG +   ED  +  +  P+V+ +M GR A  N ++   +       
Sbjct: 179 FKEAVEMSRHSLCYNGDIYTVEDFQKFSEHFPTVEKIMCGRGAVANPSLFDAI------- 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                 +     K F   I     + ++   +   K++++  ++I
Sbjct: 232 -ANGKKLDINTLKKFHDDIYMDYQEISSGERNVLFKMKELWSYLI 275


>gi|255524904|ref|ZP_05391852.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
 gi|255511382|gb|EET87674.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
          Length = 236

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/256 (20%), Positives = 91/256 (35%), Gaps = 29/256 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + + A+      ++ I++N+GCP   V +   G+ L+ +       I    K+  + +TV
Sbjct: 1   MEKMARSDYFSKFDIIDINMGCPVPNVFKSGQGSALLGDLKKASSIIKGCKKSGKV-ITV 59

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R+G+ +     A     K  + SG + I IH R   +         +I          
Sbjct: 60  KFRVGIKEDEMIAA--EFAKMCEASGADMITIHGRTRNMMYHGTPYFDQIEQA------- 110

Query: 182 IKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
             K    + +  NGG+     A K+  L   DGVMI R A +N  + + +          
Sbjct: 111 --KSVVRIPVIANGGIFSKEDADKMMKLTGADGVMIARYAIENPFIFSELTH-------- 160

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTV 299
                 ++ KD    I     D A +       +  I R    L  G   + + +  L  
Sbjct: 161 -----KKIKKDKHTIIFEQ-IDLATKCYDETFAISYIKRLASFLMRGKKGNNKYKTELYK 214

Query: 300 EAGASTATHHIIETAF 315
                     I+E  F
Sbjct: 215 SGNIPEL-RDILEEIF 229


>gi|210630809|ref|ZP_03296610.1| hypothetical protein COLSTE_00495 [Collinsella stercoris DSM 13279]
 gi|210160312|gb|EEA91283.1| hypothetical protein COLSTE_00495 [Collinsella stercoris DSM 13279]
          Length = 317

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 59/285 (20%), Positives = 108/285 (37%), Gaps = 30/285 (10%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVA----DAILRGDKKNILGFSTQEKPLALQIG 55
           M   T   +R             YT  +       +    + K I   + +   +  Q+ 
Sbjct: 8   MEGITGHTFRRVHAECFGALDRYYTPFLAPPRVGSSFGGKNLKEIDPANNEGLNVIPQLL 67

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +    V AA+ + + GY E+NLN+GCPS  V     G+  + N D +   +  +C+  
Sbjct: 68  TKNADAFVWAARELAELGYAEVNLNLGCPSGTVVSKGKGSGFLRNLDELEVFLRDVCERS 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IPV+VK R+G++D      +  L +S+    +  + +H R           +R      
Sbjct: 128 PIPVSVKTRLGLEDDAEYERILELYRSL---PLAELIVHPRVQK--------DRYQGKPR 176

Query: 176 YDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++   E     P   +  NG +   ED +  +   P    +M+GR    N A+       
Sbjct: 177 WEPYGETLARAP-FPVAYNGDIFGEEDQAALVAAYPQTRHIMLGRGLLANPALAR----- 230

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
               LTG +P      K F  K+  +  D      ++  ++++  
Sbjct: 231 ---MLTGGAPASASELKRFHDKLFCAYLDEIGG--NAVFRMKEWW 270


>gi|28377345|ref|NP_784237.1| hypothetical protein lp_0443 [Lactobacillus plantarum WCFS1]
 gi|28270177|emb|CAD63076.1| unknown [Lactobacillus plantarum WCFS1]
          Length = 337

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 92/234 (39%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   ++  +R            ++E + A +I   + K      +   + + +   +Q+ 
Sbjct: 27  MEAVSNTVFRQVISHAAAPDTFFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPVVQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G + +    A   + D G+  +++N+GCP   V +   G+ L+ NP    D IAA  K  
Sbjct: 87  GNEAADFASATAELRDRGFEAVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTS 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            + V+ K R+G           + + ++    V  + +H R        P     I    
Sbjct: 146 GLAVSAKTRLGY---SKVAEYHDWIATLLSQHVAVLTVHLRTKQEMSKVPAHFEVID--- 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAML 226
            D++       P+  + +NG + D    +   K  P +DG+MIGR  + N    
Sbjct: 200 -DLIKMRDAIAPETLLQINGDVADYQAGVALAKAHPGLDGIMIGRGVFANPFAF 252


>gi|270687218|ref|ZP_06222867.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae HK1212]
 gi|270316153|gb|EFA28138.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae HK1212]
          Length = 132

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 33/143 (23%), Positives = 68/143 (47%), Gaps = 11/143 (7%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + +AA I  ++G   I++N+GCP+ +V+    G+ L+  PD+V   +  +  A+++PVT+
Sbjct: 1   MAQAAAINVEYGAQIIDINMGCPAKKVNRKLAGSALLQFPDLVEKILREVVSAVNVPVTL 60

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R G D          + K  ++ G+  + +H R         +        +YD +  
Sbjct: 61  KIRTGWDK--SNRNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDNIKA 110

Query: 182 IKKENPDLFIGLNGGLEDMSQAL 204
           +K+    + +  NG ++   +A 
Sbjct: 111 VKQAI-AIPVIANGDIDSARKAK 132


>gi|195448673|ref|XP_002071763.1| GK10156 [Drosophila willistoni]
 gi|194167848|gb|EDW82749.1| GK10156 [Drosophila willistoni]
          Length = 458

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/295 (20%), Positives = 110/295 (37%), Gaps = 39/295 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLAL-- 52
           MV       R  A  +    ++YTE ++   +++  ++       +      +  +    
Sbjct: 18  MVRVGTLPMRLLALEM-GADIVYTEELIDLKLIKSIRRPNHALGTVDFVDPSDGTVVFRT 76

Query: 53  ----------QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                     Q+G +D  + +   K+++    + +++N+GCP     +G  GA L+  PD
Sbjct: 77  CAQETSQLVLQMGTSDAERALAVGKLLQ-RDISGLDINMGCPKEFSIKGGMGAALLAEPD 135

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                ++ +C  L IPVT K RI  D          LV+ +  +G+  I IHAR      
Sbjct: 136 KAAQILSTLCSNLEIPVTCKIRILPD----VADTIALVQKLAATGIAAIGIHART----- 186

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGR 217
              +D R       D++ E+ +    + +  NGG   M     +L          VM+ R
Sbjct: 187 ---RDERPQHQPHPDVLREVAQSVT-IPVIANGGSRHMHCYDDLLKFQLECGAASVMVAR 242

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           AA  N ++    D         +  ++  VD D     +        R L    +
Sbjct: 243 AAQLNVSIFRR-DGLLPMDEIITKYLRLCVDYDNAPHNAKYCVQSILRELQETPR 296


>gi|158522669|ref|YP_001530539.1| dihydrouridine synthase DuS [Desulfococcus oleovorans Hxd3]
 gi|158511495|gb|ABW68462.1| dihydrouridine synthase DuS [Desulfococcus oleovorans Hxd3]
          Length = 324

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/294 (20%), Positives = 107/294 (36%), Gaps = 27/294 (9%)

Query: 1   MV---DWTDRHYRF-FARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQ 53
           M      TD  +R  FA             + +     I     K++L       P+  Q
Sbjct: 7   MAPIRGITDHIFRTAFAEHFGGFDTAVAPFVSSRKDRKIKSAHLKDLLPEYNTALPVVPQ 66

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           I        V  A  + D GY+  N N+GCP   V +   GA L+ + D + + +  +  
Sbjct: 67  ILSNSGEDFVYLADHLYDLGYSVTNWNLGCPYPMVAKKYRGAGLLPHTDRIAEFLDTVMS 126

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            +   ++VK R+G  D      L  L+  + +  +  + +H R  I +     D      
Sbjct: 127 RMKGGLSVKIRLGWADT---TELMGLLPVLHRYPLAELIVHPRTGIQRYEGTVDL----- 178

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVD 230
                 +E   EN  L +  NG ++ ++    +     +VD  MIGR A  +  +   + 
Sbjct: 179 ----AAFERVLENTGLPVMYNGDIQTVADFAYLSGRFKAVDRWMIGRGALADPFLPAAI- 233

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                        K    ++F   + A  T      +H   +++ + R+ I LF
Sbjct: 234 ----GGSQPEEKEKVARMRNFHDDLMARYTLRLNGPVHLLDRMKGLWRYFILLF 283


>gi|254555542|ref|YP_003061959.1| hypothetical protein JDM1_0373 [Lactobacillus plantarum JDM1]
 gi|254044469|gb|ACT61262.1| conserved hypothetical protein [Lactobacillus plantarum JDM1]
          Length = 337

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 92/234 (39%), Gaps = 16/234 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQEKPLALQIG 55
           M   ++  +R            ++E + A +I   + K      +   + + +   +Q+ 
Sbjct: 27  MEAVSNTVFRQVISHAAAPDTFFSEFVYAKSITNPNTKFPVHGRLYVAAAESQKPVVQLW 86

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G + +    A   + D G+  +++N+GCP   V +   G+ L+ NP    D IAA  K  
Sbjct: 87  GNEAADFASATAELRDRGFEAVDINMGCPDGTVIKNHGGSDLIRNPQWAEDVIAA-AKTS 145

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            + V+ K R+G           + + ++    V  + +H R        P     I    
Sbjct: 146 GLAVSAKTRLGY---SKVAEYHDWIATLLSQHVAVLTVHLRTKQEMSKVPAHFEVID--- 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAML 226
            D++       P+  + +NG + D    +   K  P +DG+MIGR  + N    
Sbjct: 200 -DLIKMRDAIAPETLLQINGDVADYQAGVALAKAHPGLDGIMIGRGVFANPFAF 252


>gi|226292672|gb|EEH48092.1| tRNA-dihydrouridine synthase [Paracoccidioides brasiliensis Pb18]
          Length = 475

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 103/256 (40%), Gaps = 38/256 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L    +   L  QIG A     VEAAKI+       I++N GCP      G  GA L+ 
Sbjct: 115 RLDPHRERGKLIFQIGTASPILAVEAAKIIAP-DVAGIDVNAGCPKPFSTSGGMGAALLQ 173

Query: 100 NPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            PD++   + A+   +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H 
Sbjct: 174 KPDLLVSILTALVTEVGAPHQISISVKIRLLSDPERT----RDLVTRLCATGITGLTVHC 229

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
           R   ++        ++P     ++  I +    + I +NG +E    ALK++    VDG 
Sbjct: 230 RTTPMRPRERAIRDQLP-----MIASICRNAG-VAILMNGDVESRDHALKLMKEYGVDGA 283

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MI  +A  NS+                     +     WR++     D   +  +  G  
Sbjct: 284 MIATSAEANSSCFR---------------TGGQGGLVHWRELVREYMDLCLQCENKWGN- 327

Query: 274 QQITRHMIGLFHGFPN 289
              T++++ +    P 
Sbjct: 328 ---TKYLLNML--IPG 338


>gi|225680962|gb|EEH19246.1| tRNA dihydrouridine synthase [Paracoccidioides brasiliensis Pb03]
          Length = 484

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 103/256 (40%), Gaps = 38/256 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L    +   L  QIG A     VEAAKI+       I++N GCP      G  GA L+ 
Sbjct: 115 RLDPHRERGKLIFQIGTASPILAVEAAKIIAP-DVAGIDVNAGCPKPFSTSGGMGAALLQ 173

Query: 100 NPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            PD++   + A+   +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H 
Sbjct: 174 KPDLLVSILTALVTEVGAPHQISISVKIRLLSDPERT----RDLVTRLCATGITGLTVHC 229

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
           R   ++        ++P     ++  I +    + I +NG +E    ALK++    VDG 
Sbjct: 230 RTTPMRPRERAIRDQLP-----MIASICRNAG-VAILMNGDVESRDHALKLMKEYGVDGA 283

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MI  +A  NS+                     +     WR++     D   +  +  G  
Sbjct: 284 MIATSAEANSSCFR---------------TGGQGGLVHWRELVREYMDLCLQCENKWGN- 327

Query: 274 QQITRHMIGLFHGFPN 289
              T++++ +    P 
Sbjct: 328 ---TKYLLNML--IPG 338


>gi|187736134|ref|YP_001878246.1| dihydrouridine synthase DuS [Akkermansia muciniphila ATCC BAA-835]
 gi|187426186|gb|ACD05465.1| dihydrouridine synthase DuS [Akkermansia muciniphila ATCC BAA-835]
          Length = 352

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 56/296 (18%), Positives = 110/296 (37%), Gaps = 24/296 (8%)

Query: 1   MVDWTDRHYRFFARLLTN-NALLYTEMIVADAILRGDKKNILG---FSTQEKPLALQIGG 56
           M D TD  +    + L +      TE     A  +     IL     +   +P+  Q+ G
Sbjct: 12  MKDVTDLAFLNTLKDLNSLPDYFITEYFRTVAHHKKMSPYILRSIDENPTGRPIYGQLVG 71

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +   L   A+++ +     ++LN+GCP+  V   + G  ++ +   +   + A+   L 
Sbjct: 72  HEPEYLARDAQVLMEHACAGVDLNMGCPAPIVCRRNAGGGMLRSLKAMDAALGALRDVLP 131

Query: 117 IP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            P   TVKCR+G +          ++  I     + + IHAR       SP     +   
Sbjct: 132 -PGAFTVKCRLGYE---TPDEFERILPVIASHSPDRVCIHARTVREGYRSPVHPEWVKWA 187

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEY 232
                           +  NG + D + A   +      G+MIGRAA +N  + + +   
Sbjct: 188 ---------AGMLKCPVVANGNIVDAATAEAWVRLARPAGLMIGRAALRNPWIFSQLHSR 238

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           F      ++ +  R    + R++     +    H      + ++ ++++    G P
Sbjct: 239 FQG--HPAADLTFRNVLHYIRRLYERTRE-MQEHYVEEKHIHRMKKYLVYTARGLP 291


>gi|212533435|ref|XP_002146874.1| tRNA dihydrouridine synthase, putative [Penicillium marneffei ATCC
           18224]
 gi|210072238|gb|EEA26327.1| tRNA dihydrouridine synthase, putative [Penicillium marneffei ATCC
           18224]
          Length = 716

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 58/337 (17%), Positives = 98/337 (29%), Gaps = 72/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L      Y+EM +   +++G K    +L     E                
Sbjct: 317 NTPFRRLCMDL-GAQFTYSEMAMGMPLVQGHKPEWALLKAHESELAPPTISSKANIVQGY 375

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI        ++  +I+     +   I+LN GCP   V +   G+ L+ +
Sbjct: 376 DNSRDFKFGAQIAANKPHVALKTVEILAALTPHLRVIDLNCGCPIDLVFKEGSGSALLDS 435

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----GIWIHA 155
           P  +   +  M      IP+TVK R+G  D  P      L + +   G++    GI    
Sbjct: 436 PSKLEKILRGMNAVSGEIPITVKIRMGTKDNQPTA--LKLAERLVLGGIDSQTMGIGPPG 493

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-------------------------PDLF 190
             AI      +  R   N D+  + E                                ++
Sbjct: 494 IAAITLHGRSRQQRYTKNADWGYISECAALVKRLRSESDVLADTVREPDERLQPNGGKIY 553

Query: 191 IGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG           +   +VD VMIGR A     +   +        + S  +     
Sbjct: 554 FLGNGDCYSHEDYNDHVQNANVDTVMIGRGALIKPWLFEEIQTGQYLDKSASERLS---- 609

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                 +      Y      S      +TR  +   L
Sbjct: 610 ------LVEKFARYGMDAWGSDEHGLGMTRRFLLEWL 640


>gi|51246763|ref|YP_066647.1| hypothetical protein DP2911 [Desulfotalea psychrophila LSv54]
 gi|50877800|emb|CAG37640.1| conserved hypothetical protein [Desulfotalea psychrophila LSv54]
          Length = 318

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/304 (17%), Positives = 111/304 (36%), Gaps = 38/304 (12%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGGAD 58
             T   +R  F +            I      +      K++L  +    P+  Q+   +
Sbjct: 14  GLTTASFRSLFCKHFAGFNSSIAPFINPQKRASFDNKMLKDVLPEANMVVPVIPQLLHNN 73

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               +  A  + + GY EIN N+GCP+  V +   G+ ++ +PD++ + +  +   + + 
Sbjct: 74  AEDFIALAGRLAELGYKEINWNLGCPAPMVAKKKRGSGMLAHPDLIVEFLEEVLPQIPVK 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDY 176
           +++K R+G          + L+  + +  +  I IHAR  K + KG +          D 
Sbjct: 134 LSIKTRLGY---SNTAQTKELLPRLDQFPLTEIIIHARLGKQMYKGTT----------DP 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D   E  + +    I  NG +  +    ++    P V+  MIGR A  +  +   +    
Sbjct: 181 DTFAECLQLSQH-RIAYNGDITTLEHFHELQTRFPQVEHWMIGRGALADPFLAERIK--- 236

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI--TRHMIGLFHG--FPN 289
              +   +P +         ++     +    +         I     M+  + G  FP 
Sbjct: 237 --GIGKLTPTQE------LLRLEKFHAELFEIYREELSGPSHIVGRMKMLWQYLGASFPK 288

Query: 290 SRRC 293
            ++ 
Sbjct: 289 QKKL 292


>gi|255525292|ref|ZP_05392233.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
 gi|296187797|ref|ZP_06856191.1| dihydrouridine synthase (Dus) [Clostridium carboxidivorans P7]
 gi|255511057|gb|EET87356.1| dihydrouridine synthase DuS [Clostridium carboxidivorans P7]
 gi|296047754|gb|EFG87194.1| dihydrouridine synthase (Dus) [Clostridium carboxidivorans P7]
          Length = 313

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 59/291 (20%), Positives = 112/291 (38%), Gaps = 33/291 (11%)

Query: 1   MVDWTDRHYRFFA-RLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR        N    ++  IVA+   +    + +++L  + Q   L  Q+  
Sbjct: 8   MEGLTGYIYRNAHNAFFNNVDKYFSPFIVANQSNSFKTKELRDVLPENNQGLVLIPQLLT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +       +K ++  GYNE+NLN+GCPS  V   + G+  +     + + +  +     
Sbjct: 68  NNAKDFTHMSKKLKQLGYNEVNLNLGCPSGTVVSKNRGSGFLSKTKELDEFLEEIFSEAV 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             +++K RIG D         NL++   K  +  + IH R       +  +         
Sbjct: 128 TKISIKTRIGKD---SPEEFYNLIEIFNKYPMEELIIHPRIQKDFYKNKPNM-------- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
               EI KE   L    I  NG +   +D     K   SV  +M+GR    N  ++  + 
Sbjct: 177 ----EIFKEALILSKNPICYNGDIFKVKDYENFSKDFTSVQTLMLGRGLLANPGLIGDIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                    ++  + ++ KDF  KI     +      +   +++++  +M+
Sbjct: 233 --------NNTKPEKKLLKDFHDKIYEDYKEVLFGDKNVLFRMKELWFYML 275


>gi|241615739|ref|XP_002406800.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215500870|gb|EEC10364.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 449

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 111/300 (37%), Gaps = 56/300 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVA--------------DAILRGDKKNILGFSTQ 46
           MV       R  A L     L+Y+E ++                 +   D  + + F T 
Sbjct: 16  MVRIGTLPMRLLA-LHYGADLVYSEELIDYRLLKCQRLENQVLGTVDYIDDDHQIVFRTC 74

Query: 47  EKPL---ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           EK      LQIG     + V+ AK+VE      I++N+GCP     +G  GA L+   D 
Sbjct: 75  EKERGKNILQIGTCSPERAVQVAKLVEK-DVAGIDVNMGCPKEFSLKGGMGAALLTQLDK 133

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V   + A+ ++ ++PVT K R+    +        L K I+ +GV  + +H R    +  
Sbjct: 134 VKAILTALVQSTTLPVTCKIRVLDRLEDT----LALGKLIESTGVKALGVHGRTKEERPQ 189

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQAL--KILPSVDGVMIGRA 218
               N  I  L          E+  + +  NGG   + D       ++      VM+ R 
Sbjct: 190 HKNRNATIKAL---------AEHLTIPVIANGGSSEIVDYEDIERFRVATGATSVMLARQ 240

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL-QQIT 277
           A  N ++ +           G  PI           +      Y + HL    +L +QIT
Sbjct: 241 AESNCSIFSKA---------GRKPI---------DDVIVQYLHYVSAHLKYLCRLSKQIT 282


>gi|223992807|ref|XP_002286087.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977402|gb|EED95728.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 451

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 69/360 (19%), Positives = 118/360 (32%), Gaps = 51/360 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS-TQEKPLALQIGGADI 59
           MV  +D  +R     L N  L YT+MI A      + +          KP  +QI   D 
Sbjct: 31  MVAQSDLPFRLMCEQLYNVDLSYTQMIHASNFADVNGEPFRTNHLDVIKPTVVQIAAHDP 90

Query: 60  SKLVEAAKIVEDFG-------------YNEINLNVGCPSARVHEGSFGACLMLN-PDIVG 105
              VEAA ++ +                   +LN+GCP     +G +GA L    P    
Sbjct: 91  DVAVEAALMILEKSESTGSSVNGSISPVVAFDLNLGCPQGIARKGKYGAFLHDEYPQSAY 150

Query: 106 DCIAAMCKALS--IPVTVKCRIGVDDQIPAV-------------ALRNLVKSIKKSGVNG 150
           D +  +   L   I VT K R+                           ++ +   GV+ 
Sbjct: 151 DVLIKLRAMLPREIGVTAKVRLPPTKADAEAGKLGNMSELSHLPTPEERIQRLIDCGVDL 210

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIV------YEIKKENPDLFIGLNGGLEDMSQAL 204
           I +H R          +   +   D++ +        +   N    +  NGG+E  +   
Sbjct: 211 ITVHGRTRFE------NKVAVGKADWNSIERCVQTARVYSGNAQYPLIANGGIETYNDVE 264

Query: 205 KIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           K L      GVM   +  +N  + + + E  +        ++ ++         A++   
Sbjct: 265 KCLEQTQASGVMSSESLLENPGLFSNLSEETACDTVARGMLERQLGYACMYLDYATLFPP 324

Query: 263 AARHLHSGGKL-QQITRHMIGLFH-GFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
               L + G     I  H+  + H     +   R +L      ST     I+    L+ E
Sbjct: 325 IPGSLGARGGCFNVIRTHLFKILHRYLEENPELRSLLGDNGALST-----IKQGRELVQE 379


>gi|332526992|ref|ZP_08403077.1| dihydrouridine synthase, DuS [Rubrivivax benzoatilyticus JA2]
 gi|332111427|gb|EGJ11410.1| dihydrouridine synthase, DuS [Rubrivivax benzoatilyticus JA2]
          Length = 311

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 66/294 (22%), Positives = 106/294 (36%), Gaps = 37/294 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNIL-------GFSTQEKPLAL 52
           M    D   R     +    L  +E I V D +L       +       G +    P+  
Sbjct: 1   MEGLLDCSLRDVLTRVGGVELCVSEFIRVTDQLLPARVFTRIAPELLAGGRTAAGTPVRA 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--IAA 110
           Q+ G D   L E A  + +     I+LN GCP+  V+    GA L+  P++V        
Sbjct: 61  QLLGGDPVCLAENAARLAELSPAGIDLNFGCPAPVVNRHRGGAVLLDEPELVHAIVAAVR 120

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                ++PVT K R+G  D      + +   +I   G   + +HAR         K    
Sbjct: 121 RAVPAAVPVTAKMRLGHLDTSR---MLDCAHAIADGGAAELVVHART--------KAEGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
            P   +  + EI +E   L +  NG +  +  A + L     D +M+GR    +  +   
Sbjct: 170 RPPAHWHRIAEI-REAVALPVVANGEVWTVDDARRCLAESGCDALMLGRGMVADPGLARA 228

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ----ITR 278
           +            P   R    FW  +SA +        H  G+L+Q    + R
Sbjct: 229 IRAEPVPGWAALQPELRR----FWASVSARVEP-----RHRAGRLKQWLGLMRR 273


>gi|182417542|ref|ZP_02948869.1| dihydrouridine synthase family protein [Clostridium butyricum 5521]
 gi|237665938|ref|ZP_04525926.1| dihydrouridine synthase, DuS [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182378711|gb|EDT76238.1| dihydrouridine synthase family protein [Clostridium butyricum 5521]
 gi|237658885|gb|EEP56437.1| dihydrouridine synthase, DuS [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 311

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 49/290 (16%), Positives = 108/290 (37%), Gaps = 27/290 (9%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGGA 57
              T   YR  + +        +T  +   +       +  +IL    +   +  QI   
Sbjct: 9   EGVTGYIYRNAYEKYFGKIDKYFTPFVAPTSNMCFTSRELNDILPEHNKGINVIPQILTN 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +    +     +++ GY+E+NLN+GCPS  V     G+  + + D +   + A+     I
Sbjct: 69  NSEYFIYTMNEMKNMGYDEVNLNLGCPSGTVVAKGRGSGFLAHKDELDRFLEAIFSKTEI 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K RIGV+         +++    K  +  + IH R       +  +         D
Sbjct: 129 KISIKTRIGVNSSDD---FNDIMNIYNKYPLEELIIHPRIQKDFYKNTPNM--------D 177

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---GVMIGRAAYKNSAMLTTVDEYFS 234
           +  E  K + +  +  NG + +     +++        VM+GR    N  ++  +     
Sbjct: 178 VFKEALKSSKN-PVCYNGDIFNSHHYKRVVDECSDINAVMLGRGIITNPGLIKEI----- 231

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              T +     +  K F  ++     +  +   +   K+++   +MI +F
Sbjct: 232 ---TDNEFTDKKNLKKFHNQVYLGYKEILSGDKNVLFKMKEFWFYMINIF 278


>gi|260589646|ref|ZP_05855559.1| dihydrouridine synthase family protein [Blautia hansenii DSM 20583]
 gi|260539886|gb|EEX20455.1| dihydrouridine synthase family protein [Blautia hansenii DSM 20583]
          Length = 314

 Score =  129 bits (326), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 57/291 (19%), Positives = 113/291 (38%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIV--ADAILR-GDKKNILGFSTQEKPLALQIGG 56
           M   T   YR             +T  I   +  ++   + ++IL  + +   L  QI  
Sbjct: 8   MEGITGYIYRQVHHQFFQGIDKYFTPFITPGSKKLMTPKELRDILPENNEGYHLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +  A+ + ++GY E+NLN+GCPS  V     G+  +  P  +   +  + + L 
Sbjct: 68  NQAQDFIRLAEELREYGYEEVNLNLGCPSGTVTAKKKGSGFLEFPAQLEKFLNEVFENLD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + ++VK RIG D+         L++   +  +  + +H R       +     +      
Sbjct: 128 MKISVKTRIGKDE---PEEFTELLRIYNRFPLEELIVHPRIQSDYYKNEPRMEQFQ---- 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEYF 233
           + V     +N   +   NG L   S+  K       ++ VM+GR    N A++  V +  
Sbjct: 181 EAVR--CSQNSLCY---NGDLFTRSKCEKFFEEYPSIEKVMLGRGLLVNPALVQQVQK-- 233

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  + ++    K F  K+    T+  +   +   K++++  +M  LF
Sbjct: 234 ------GTVLEKVTLKAFHDKLCEEYTEVMSGDKNVLFKMKELWFYMGNLF 278


>gi|258563178|ref|XP_002582334.1| potential tRNA dihydrouridine synthase [Uncinocarpus reesii 1704]
 gi|237907841|gb|EEP82242.1| potential tRNA dihydrouridine synthase [Uncinocarpus reesii 1704]
          Length = 726

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 45/284 (15%), Positives = 89/284 (31%), Gaps = 62/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L      Y+EM ++  +++G K    ++     E                
Sbjct: 329 NMPFRRLCAEL-GAQFTYSEMAMSLPLIQGHKSEWALVKAHESEVLPPTINPNQAVVKDY 387

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLN 100
                    +QI      + ++A +++     +   ++LN GCP   V+    G+ L+ +
Sbjct: 388 DRTRDLKFGVQISANKPWQALKATEVITTLCPHIRVVDLNCGCPIDLVYRDGAGSALLEH 447

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKS------------G 147
           P  +   +  M      +PV+ K R+G  D+ P      L + +               G
Sbjct: 448 PSKLEKILRGMNAVSGEVPVSAKIRMGTKDKSPTA--LKLAERLILGGPEFRKIGQGPPG 505

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN------------------PDL 189
           V  + +H R    +     D   I      ++  + +                      +
Sbjct: 506 VAALTLHGRSRQQRYTRQADWGYISECA-ALIKRLNERTDEVTDTVQEPDERHQAPGRKV 564

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           F   NG         + +    VD VMI R A     +   +  
Sbjct: 565 FFLGNGDCYSHEDYYRDIRESGVDTVMIARGALMKPWIFEEIQA 608


>gi|220928485|ref|YP_002505394.1| dihydrouridine synthase [Clostridium cellulolyticum H10]
 gi|219998813|gb|ACL75414.1| dihydrouridine synthase DuS [Clostridium cellulolyticum H10]
          Length = 311

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 66/291 (22%), Positives = 115/291 (39%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRFFA-RLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR        +    ++  I+A   D     D K+I   + QE  L  Q+  
Sbjct: 8   MEGLTGYIYRNAHNAFFNSIDKYFSPFIIANQIDGFKTRDLKDISPENNQELVLIPQVLT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +    +  +K ++  GY EINLN+GCPS  V   + G+  +   + +   +  +     
Sbjct: 68  NNAKDFIYTSKKIKSMGYTEINLNLGCPSGTVVSKNRGSGFLAKKEELDVFLEEIFSQAI 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             +++K RIG D         +L++   K  +N + IH R       + K N KI     
Sbjct: 128 TKISIKTRIGKD---QPEEFYDLIRIFNKYPINELIIHPRIQKDFYKN-KPNMKIFR--- 180

Query: 177 DIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D + E K       +  NG +   +D  +     P VD +M+GR    N A+   V    
Sbjct: 181 DALAESKN-----PVCYNGDIFTAKDYKEFCNDFPGVDTLMLGRGLLMNPALAGYVK--- 232

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    ++  + K F  K+     D  +   +   K++++  +MI +F
Sbjct: 233 -----NGRKLEKSLLKKFHDKVYNDYKDILSGERNVLFKMKELWFYMINVF 278


>gi|295672502|ref|XP_002796797.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
 gi|226282169|gb|EEH37735.1| conserved hypothetical protein [Paracoccidioides brasiliensis Pb01]
          Length = 475

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 103/256 (40%), Gaps = 38/256 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L    +   L  QIG A     VEAAKI+       I++N GCP      G  GA L+ 
Sbjct: 106 RLDPHRERGKLIFQIGTASPILAVEAAKIIAP-DVAGIDVNAGCPKPFSTSGGMGAALLQ 164

Query: 100 NPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            PD++   + A+   +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H 
Sbjct: 165 KPDLLVSILTALVTEVGAPHQISISVKIRLLSDPERT----RDLVTRLCATGITGLTVHC 220

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
           R   ++        ++P     ++  I +    + I +NG +E    ALK++    VDG 
Sbjct: 221 RTTPMRPRERAIRDQLP-----MIASICRNAG-VAILMNGDVESRDHALKLMKEYGVDGA 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MI  +A  NS+                     +     WR++     D   +  +  G  
Sbjct: 275 MIATSAEANSSCFR---------------TGGQGGLVHWRELVREYMDLCLQCENKWGN- 318

Query: 274 QQITRHMIGLFHGFPN 289
              T++++ +    P 
Sbjct: 319 ---TKYLLNML--IPG 329


>gi|308801569|ref|XP_003078098.1| unnamed protein product [Ostreococcus tauri]
 gi|116056549|emb|CAL52838.1| unnamed protein product [Ostreococcus tauri]
          Length = 343

 Score =  129 bits (325), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 92/248 (37%), Gaps = 36/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----------------NILGF 43
           MV  +    R  A       L+Y+E +V    ++  ++                      
Sbjct: 20  MVRVSTLATRLVAHEY-GADLVYSEELVDKRFVKCRREENAELGTIDFLDSKGVLTFRTI 78

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             +++ L  Q+G +  +  +++A++V       I++N+GCP      G  GA L+  PD+
Sbjct: 79  PEEKERLVFQVGTSSAALALQSAQLVAG-DVAAIDVNMGCPKHFSTSGGMGARLLSQPDL 137

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + D +  + + L     VT K R+   ++  A     L K I+  GV+   +H R     
Sbjct: 138 IRDILTTLRRNLPETTHVTCKIRLLECEKSTA----ELAKMIESCGVSAFAVHGR----- 188

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                  R      ++++  +  E  D  +  NG +       +I         M  R A
Sbjct: 189 ---YISQRPREPAHWNLIKNVV-EAVDCPVIANGDVMRYEDFERIRKETGAASAMCARMA 244

Query: 220 YKNSAMLT 227
             N ++  
Sbjct: 245 QWNLSIFR 252


>gi|317501236|ref|ZP_07959441.1| dihydrouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897412|gb|EFV19478.1| dihydrouridine synthase [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 311

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 63/285 (22%), Positives = 107/285 (37%), Gaps = 29/285 (10%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+IL    +      QI        V+ AK +E +GY EINLNVGCPS  V     GA
Sbjct: 47  EKKDILPEHNKGMHAVPQILTNCAEDFVQTAKKLEQYGYKEINLNVGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  P+ +   +  + +   I ++VK RIG            L+    K  +  + IH 
Sbjct: 107 GFLAFPERLDLFLEEVFQNCPIDISVKTRIG---TESGEEFPKLMDIYNKYPIKELIIHP 163

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDG 212
           R            + IP++D   V+E         I  NG L          +  P V+ 
Sbjct: 164 RTQKDFY------KNIPHMD---VFEKALGTGRHKICYNGDLTSEEDVRNLSEQFPEVES 214

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           +MIGR    + A+   +         G         + F   +  +  +  +       K
Sbjct: 215 IMIGRGVLADPAIARKIK--------GGDGADKAEMRHFHDMLYEAYCEEMSGERTVLYK 266

Query: 273 LQQITRHMIGLF-HGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           ++++  ++   F +  P +++ +     +A        IIE  F 
Sbjct: 267 MKELWFYLASSFTNSRPYAKKIK-----KAEKCAVYEKIIEELFA 306


>gi|255088371|ref|XP_002506108.1| predicted protein [Micromonas sp. RCC299]
 gi|226521379|gb|ACO67366.1| predicted protein [Micromonas sp. RCC299]
          Length = 353

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 95/253 (37%), Gaps = 41/253 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MI-------VADAIL--------RGDKKN 39
           MV       R  A       ++Y+E      M+        A   +          D   
Sbjct: 16  MVRVNTMPTRLLAAEY-GADIVYSEELIDRKMMKVKRVENTAWGTVDFIDPDATNDDTAV 74

Query: 40  ILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           +   + +EK  L +Q+G  D ++ +++A +V       I++N+GCP         G+ L+
Sbjct: 75  VFQTTPEEKNRLVMQLGTGDATRALQSA-MVAVNDVAAIDINMGCPLKFSTASGAGSALL 133

Query: 99  LNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             P+ V D +  + + L     VT K R+             L + I+K GV+   +H R
Sbjct: 134 KKPETVHDILTTLRRNLPAETHVTCKIRLL----ETIEQTVELARVIEKCGVSAFGVHGR 189

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
                G  P+D        +D + ++  E+    +  NG + + S   KI         M
Sbjct: 190 ---YVGQRPRD-----AAHWDKIKQVV-ESVSCPVIANGDVFEYSDFEKIRAETGAAAAM 240

Query: 215 IGRAAYKNSAMLT 227
            GR A  N ++  
Sbjct: 241 CGRGAMWNQSIFR 253


>gi|255085626|ref|XP_002505244.1| dihydrouridine synthase [Micromonas sp. RCC299]
 gi|226520513|gb|ACO66502.1| dihydrouridine synthase [Micromonas sp. RCC299]
          Length = 465

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 80/226 (35%), Gaps = 18/226 (7%)

Query: 50  LALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           LA Q+ G++   L   A+ +    G   ++LN GCP+  V     G+ L+ +P  V    
Sbjct: 134 LAAQLMGSNEDLLERCARFLAHQGGAPRVDLNCGCPANVVTGKGAGSSLLRDPRDVEAMT 193

Query: 109 AAMCKAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A+ + +      VTVK R G DD+     LR  + + +  G + + +H R         
Sbjct: 194 RAVARGVAGTGCAVTVKLRSGFDDRGL---LRENLLAAQAGGASFVTLHPRTRAQGYSGH 250

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                I             +   + +  NG +   + A K+L      GVMIGR A ++ 
Sbjct: 251 AAWEDIGFAV---------DLLSVPVVGNGDVTSAALASKMLRDTGCAGVMIGRGAVQDP 301

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
            +        S+                W   +    D     L  
Sbjct: 302 LVFRRCRAALSDENFRRGTSGDASVGYAWEMTAEEEADEIRGFLRR 347


>gi|239625676|ref|ZP_04668707.1| dihydrouridine synthase [Clostridiales bacterium 1_7_47_FAA]
 gi|239519906|gb|EEQ59772.1| dihydrouridine synthase [Clostridiales bacterium 1_7_47FAA]
          Length = 322

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/327 (18%), Positives = 123/327 (37%), Gaps = 33/327 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  +    T   L YT  I   A   +   +  +IL    +   +  QI  
Sbjct: 8   MEGLTGYIYRNAYHTCFTPMDLYYTPFISPKARGCLSSREINDILPEHNKGLHVVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARV---HEGSFGACLMLNPDIVGDCIAAMCK 113
                 +  A+I++D+GY E+NLN+GCPS  V   H+G+    L    +     +    +
Sbjct: 68  NQAEDFLTVARILKDYGYQEVNLNLGCPSGTVVSKHKGAGFLALTCGLNSFLSTVTEQLE 127

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L + ++VK R+G+   +       L+    +  +  + IH R       +  +     +
Sbjct: 128 VLGMELSVKTRLGM---VTPDEFYELLDIYNQYHLKRLIIHPRIRTDYYRNTPNWEMFRH 184

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVD 230
                      EN    +  NG +  +    ++    P +D VM+GR    N  ++  + 
Sbjct: 185 GL---------ENSANHVCYNGDIFTVEDFKRLSRSYPELDEVMLGRGIIANPGLVGEIR 235

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPN 289
                      P+  +  ++F + +        +   +   K+++I   MI +F     +
Sbjct: 236 T--------GRPVDKKQLREFHQLLYEGYRGIMSGDRNVLFKMKEIWASMIQIFADSEKH 287

Query: 290 SRRCR--HILTVEAGASTATHHIIETA 314
            ++ +    LT    A ++    ++ A
Sbjct: 288 GKKIKKAQHLTEYEAAVSSIFSELDIA 314


>gi|330925066|ref|XP_003300902.1| hypothetical protein PTT_12265 [Pyrenophora teres f. teres 0-1]
 gi|311324785|gb|EFQ91034.1| hypothetical protein PTT_12265 [Pyrenophora teres f. teres 0-1]
          Length = 473

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 9/180 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    V+AAK+V       I++N GCP      G  GA L+  PD++ + + 
Sbjct: 107 LIYQIGTANPELAVQAAKMVAA-DVAGIDVNSGCPKPFSTSGGMGAALLKTPDLLCNILT 165

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +           LVK + ++G+ G+ +H R   ++        
Sbjct: 166 SLVEEVGKPYEIGISVKIRILDTPEETAALVKRLVRTGITGLTVHCRTTPMRPRERAIRH 225

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           ++      ++ EI +E   +   +NG +   ++ALK++    VDG MI   A KN +   
Sbjct: 226 QLK-----MIGEICREAG-VACVMNGDVTSRTEALKLMEEFNVDGAMIATEAEKNPSCFR 279


>gi|327293319|ref|XP_003231356.1| dihydrouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326466472|gb|EGD91925.1| dihydrouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 456

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 50/225 (22%), Positives = 89/225 (39%), Gaps = 52/225 (23%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
            A+  L G+ K        ++PL +Q    D  +L++AA+ VE++  + ++LN+GCP   
Sbjct: 33  TAEPYLDGNPK-------YDRPLIVQFCANDPDELLKAARHVEEY-CDAVDLNLGCPQGI 84

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
             +G +GA L  +PD++   I  +   LSIPVT K RI               + I  +G
Sbjct: 85  AKKGHYGAFLQEDPDLIYKLINKLHNELSIPVTAKFRIL----ETKEKTLEYARMILSAG 140

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + + +H R+   KG            ++D                     D+S+ L++ 
Sbjct: 141 ASILSVHGRRREQKG------HNTGVANWD---------------------DISRCLEV- 172

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
              DGVM       +  + +            + P      + +W
Sbjct: 173 TGADGVMSAEGNLSDPTIFS------------TPPASGEEGRMYW 205


>gi|114663256|ref|XP_001166706.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 2
           [Pan troglodytes]
          Length = 406

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 46/183 (25%), Positives = 84/183 (45%), Gaps = 28/183 (15%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +G +D  + +  A++VE+     I++N+GCP     +G  GA L+ +PD +   ++ + K
Sbjct: 1   MGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTKGGMGAALLSDPDKIEKILSTLVK 59

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
               PVT K RI    +       +LVK I+++G+  I +H RK        ++ R    
Sbjct: 60  GTHRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK--------REERPQHP 107

Query: 174 LDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGVMIGRAAYKNS 223
           +  +++  I  +   + +  NG           +ED  QA     +   VM+ RAA  N 
Sbjct: 108 VSCEVIKAIA-DTLSIPVIANGGSHDHIQQYSDIEDFRQA----TAASSVMVARAAMWNP 162

Query: 224 AML 226
           ++ 
Sbjct: 163 SIF 165


>gi|168049709|ref|XP_001777304.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162671280|gb|EDQ57834.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 266

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 45/210 (21%), Positives = 75/210 (35%), Gaps = 27/210 (12%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           VGCP   V     G+ L+  P  + + + A   +++ P+TVK R+G  +        +L+
Sbjct: 1   VGCPIDVVVNKGGGSSLLTKPQRLQEIVRAASGSINTPLTVKLRMGFFEGRNCA--HSLL 58

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLED 199
             +   G   + IH R         +  R     D+D + +     P D+ +  NG +  
Sbjct: 59  PDLGSWGATAVTIHGRT--------RQQRYSKLADWDYINQCVTNGPSDVQLIGNGDVFS 110

Query: 200 MSQALKILPSVDG----VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
            +     L S  G     MI R A     + T + E     +T    +           I
Sbjct: 111 YTDYNGHLESSGGKLATCMIARGALIKPWLFTEIKEQRHWDITAEERLN----------I 160

Query: 256 SASMTDYAARHLHSGGKLQQITRHMI--GL 283
                 +   H  S  K  + TRH +   L
Sbjct: 161 LRDYVKFGLIHWGSDSKGVETTRHFLLEWL 190


>gi|331090015|ref|ZP_08338905.1| hypothetical protein HMPREF1025_02488 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330402929|gb|EGG82495.1| hypothetical protein HMPREF1025_02488 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 311

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 63/285 (22%), Positives = 107/285 (37%), Gaps = 29/285 (10%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+IL    +      QI        V+ AK +E +GY EINLNVGCPS  V     GA
Sbjct: 47  EKKDILPEHNKGMHAVPQILTNCAEDFVQTAKKLEQYGYKEINLNVGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  P+ +   +  + +   I ++VK RIG            L+    K  +  + IH 
Sbjct: 107 GFLAFPERLDLFLEEVFQNCPIDISVKTRIG---TESGEEFPKLMDIYNKYPIKELIIHP 163

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDG 212
           R            + IP++D   V+E         I  NG L          +  P V+ 
Sbjct: 164 RTQKDFY------KNIPHMD---VFEKALGTGRHKICYNGDLTSEEDVRNLSEQFPEVES 214

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           +MIGR    + A+   +         G         + F   +  +  +  +       K
Sbjct: 215 IMIGRGVLADPAIARKIK--------GGDGADKAEMRHFHDMLYEAYCEEMSGERTVLYK 266

Query: 273 LQQITRHMIGLF-HGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
           ++++  ++   F +  P +++ +     +A        IIE  F 
Sbjct: 267 MKELWFYLASSFTNSRPYAKKIK-----KAEKCAVYEKIIEELFA 306


>gi|229815921|ref|ZP_04446244.1| hypothetical protein COLINT_02976 [Collinsella intestinalis DSM
           13280]
 gi|229808474|gb|EEP44253.1| hypothetical protein COLINT_02976 [Collinsella intestinalis DSM
           13280]
          Length = 317

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 58/285 (20%), Positives = 106/285 (37%), Gaps = 30/285 (10%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVA----DAILRGDKKNILGFSTQEKPLALQIG 55
           M   T   +R             YT  +      ++      K I   + +   +  Q+ 
Sbjct: 8   MEGITGHTFRRVHAECFGALDRYYTPFLAPPRVGNSFGGKAFKEIDPANNEGLNVIPQLL 67

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  + V AA+ + + GY E+NLN+GCPS  V     G+  + N D +   +  +C   
Sbjct: 68  TKNADEFVWAARELAELGYREVNLNLGCPSGTVVSKGKGSGFLRNLDELEVFLRDVCDRS 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PV+VK R+G++D      +  L  S+    +  + +H R           +R      
Sbjct: 128 PLPVSVKTRLGLEDDAEYERILELYCSL---PLAELIVHPRVQK--------DRYQGKPR 176

Query: 176 YDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++   E     P   +  NG +   EDM   ++  P    VM+GR    N A+       
Sbjct: 177 WEPYGETLARAP-FPVAYNGDIFGTEDMDVLMEAHPRTRHVMLGRGLLANPALAR----- 230

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
               L G         + F  K+ A+  D      ++  ++++  
Sbjct: 231 ---MLAGGPAASADELRQFHDKLYAAYLDEIGG--NAVFRMKEWW 270


>gi|117558547|gb|AAI27296.1| LOC548984 protein [Xenopus (Silurana) tropicalis]
          Length = 451

 Score =  128 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 103/242 (42%), Gaps = 34/242 (14%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   +  Q+G AD  + +  AK++++     I++N+GCP     +G  GA L+L P+
Sbjct: 29  CERERHSVVFQMGTADAERALTVAKLIQNDIAA-IDINMGCPKEYSTKGGMGAALLLCPE 87

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +   ++ + K +S P+T K RI            +LVK I+K+GV  I +H R      
Sbjct: 88  KIEMILSTLVKGISKPITCKIRILP----SLTETISLVKLIEKTGVAAIAVHGRS----- 138

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG----LEDMSQ--ALKILPSVDGVMIG 216
              K+ R    +  D++  I +    + +  NGG    +       A + + S   VM+ 
Sbjct: 139 ---KNERPQHPVHCDVIKAISQAV-SIPVIANGGSQEFIRQFQDISAFRSVTSASSVMLA 194

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           RAA  N ++             G  P++T +     R   A    Y   + ++   L Q+
Sbjct: 195 RAAMWNPSVFR---------PEGMLPVETVI-----RDYIAYAVQYDNHYTNTKYCLCQM 240

Query: 277 TR 278
            R
Sbjct: 241 LR 242


>gi|119897813|ref|YP_933026.1| hypothetical protein azo1522 [Azoarcus sp. BH72]
 gi|119670226|emb|CAL94139.1| conserved hypothetical protein [Azoarcus sp. BH72]
          Length = 366

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 50/261 (19%), Positives = 100/261 (38%), Gaps = 32/261 (12%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQ---------EKPLALQIGGADISKLVEAAKIVEDF 72
             TE +     +    +     + +           PL +Q+ G+D + L   A ++   
Sbjct: 67  AVTEFVRVSG-VMLPPRTYRRIAPELDNGSRTVGGTPLRVQLLGSDPALLAANAAVLARL 125

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQ 130
               ++LN GCP+  V+    GA L+  P+++ +   ++  AL   +P+T K R+G+ D 
Sbjct: 126 APTAVDLNFGCPAPTVNRHRGGAALLDEPELLHEIACSVRAALPPEMPLTAKMRLGIAD- 184

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
             A    +  +++   G+  + +HAR         K     P   ++ V  I  E   + 
Sbjct: 185 --AGRALDCARALADGGIAELVVHART--------KQQGYRPPAHWEWVGRIASEV-QVP 233

Query: 191 IGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG +   +   +   +  V  VM+GR A  +  +   +            P +  V 
Sbjct: 234 VVANGEVWSAADWRRCRAVSGVADVMLGRGAVADPFLAGRIRR------GELEPPEPAVR 287

Query: 249 KDFWRKISASMTDYAARHLHS 269
            + W  +   + D+  R    
Sbjct: 288 AEEWAAVLDLLGDFRVRVRAK 308


>gi|71000116|ref|XP_754775.1| tRNA dihydrouridine synthase (Smm1) [Aspergillus fumigatus Af293]
 gi|66852412|gb|EAL92737.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus
           fumigatus Af293]
          Length = 443

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 100/258 (38%), Gaps = 31/258 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    VEAAK+V       I+LN GCP      G  GA L+  PD +   + 
Sbjct: 104 LVFQIGSANPELAVEAAKLVAG-DVAGIDLNSGCPKPFSTSGGMGAALLRTPDKLVSILE 162

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +          +LVK +  +G+ G+ +H R   ++        
Sbjct: 163 SLVREVGNPYQIGISVKIRILETPEKTESLVKRLVATGITGLTVHCRTTPMRPRERAIRD 222

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           ++      ++  I +E   +   +NG +    +AL ++    VDG MI  AA  N +   
Sbjct: 223 QLA-----MIARICREAG-VACVMNGDVTSRDEALALMKEFGVDGAMIATAAEANPSCFR 276

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +               +       WR++       A    +  G     T+ ++ +    
Sbjct: 277 S---------------EAEGGLLPWREVVHDYLQAAIECENRFGN----TKFLLNIL--I 315

Query: 288 PN-SRRCRHILTVEAGAS 304
           P  +R  +   T ++ + 
Sbjct: 316 PGKNREFKDAKTAKSYSD 333


>gi|197302990|ref|ZP_03168039.1| hypothetical protein RUMLAC_01717 [Ruminococcus lactaris ATCC
           29176]
 gi|197297939|gb|EDY32490.1| hypothetical protein RUMLAC_01717 [Ruminococcus lactaris ATCC
           29176]
          Length = 352

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 104/252 (41%), Gaps = 23/252 (9%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK++L  + +      QI        +E AK + ++GY E+NLN+GCPS  V     GA
Sbjct: 86  EKKDVLPENNRGVLAVPQILTNQAEDFIETAKKLAEYGYEEVNLNLGCPSRTVVTKGRGA 145

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  PD +   +  + K     ++VK RIG+ +         L+K   +  +  + +H 
Sbjct: 146 GFLEEPDRLDRFLDEIFKKREWKISVKTRIGMSE---PEEFEELLKIYNRYPLEELIVHP 202

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDG 212
           R            +  PNLD   V+ +  E     +  NG +   ED+ +  +  P +D 
Sbjct: 203 RLQKDFY------KNTPNLD---VFAMAAEESRNPLCYNGDICNAEDLKRLRERFPKLDC 253

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           VM+GR    + A+           L G    +    + F   +  +  +  +       K
Sbjct: 254 VMVGRGVLADPAL--------GRVLKGGGQAEKAELRKFHDLLYRAYCEEMSGDRTVLYK 305

Query: 273 LQQITRHMIGLF 284
           ++++  +  GLF
Sbjct: 306 MKELWFYFSGLF 317


>gi|159116295|ref|XP_001708369.1| Embryo-related protein [Giardia lamblia ATCC 50803]
 gi|157436480|gb|EDO80695.1| Embryo-related protein [Giardia lamblia ATCC 50803]
          Length = 406

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 96/230 (41%), Gaps = 30/230 (13%)

Query: 23  YTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE---- 76
           +T+M  ADA+L        +L  +   + + LQ+ G + S    AA+++ D         
Sbjct: 86  FTQMYTADALLHNSPLRDAVLSTAAPGEKIILQLCGNNPSTFRAAAELLHDSPIASQLVA 145

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N+GCP++      +G  +  N  +V   I+    A   PVT K R            
Sbjct: 146 LDINLGCPASCASSKGYGFYVAQNWPLVHQIISETSSARLFPVTCKIRPL----NSIEKT 201

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY---------------- 180
            + +  +  SG +GI IH R    +G   +  R       ++V                 
Sbjct: 202 IDYMVLLVMSGASGITIHMRHTTRQGKHAQAVRPAYQEFEELVRAFRQRLDTLFTGLGGS 261

Query: 181 EIKKENPD--LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           E  +ENP     I LNGG+++  +A  +L +   DGVM+G    KN A L
Sbjct: 262 ETAQENPHVYPVIILNGGIKNRQEADHLLATYPADGVMLGVGLLKNPACL 311


>gi|159110447|ref|XP_001705482.1| tRNA dihydrouridine synthase, putative [Giardia lamblia ATCC 50803]
 gi|157433567|gb|EDO77808.1| tRNA dihydrouridine synthase, putative [Giardia lamblia ATCC 50803]
          Length = 462

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 52/237 (21%), Positives = 92/237 (38%), Gaps = 31/237 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQ-EKPLALQI 54
           MVD ++  YR   R      L +T M   + ++   K      + L      ++PL LQ+
Sbjct: 24  MVDGSELPYRLLTRRYGVE-LAWTPMHSTNTLVTSSKAMTQLVDELKHGESIDRPLVLQL 82

Query: 55  GGADISKLVEA----AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            G + S    A     ++     ++ + LN+GCP A    G +GA LM + D+  + +  
Sbjct: 83  SGNNPSNFELAYNTLVQMGAGCCFDVVELNMGCPQAVALRGKYGAYLMGHLDLAEEILRT 142

Query: 111 MCKA-----LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +        L   V VK R+ + D+        L  +    G+    +H R  + +  S 
Sbjct: 143 LVAVTARSGLGHKVAVKTRLDISDKDTVKMCLRLCST----GIAMFTLHGRTRLQRTGS- 197

Query: 166 KDNRKIPNLDYDIVYEI----KKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIG 216
                +   D+  +  I    +   P L    NGG+ ++   + L+ L    G M  
Sbjct: 198 ----AVGLPDWQALASILNNLRASYPHLIFFANGGVWNLETHEHLRSLTGCHGTMSA 250


>gi|189460249|ref|ZP_03009034.1| hypothetical protein BACCOP_00886 [Bacteroides coprocola DSM 17136]
 gi|189433110|gb|EDV02095.1| hypothetical protein BACCOP_00886 [Bacteroides coprocola DSM 17136]
          Length = 313

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/289 (20%), Positives = 111/289 (38%), Gaps = 29/289 (10%)

Query: 3   DWTDRHYRFFARL-LTNNALLYTEMI-VADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
            +T+  +R             YT  I +    +R   K  +L        L  Q+  ++ 
Sbjct: 15  GFTEAAWRNAHEQTFGGVDAYYTPFIRLEKGEIRNKDKREVLPRQNTVSHLIPQLVASEP 74

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L + A  +   GY EI++N+GCP   +     G+ ++  P+ V   + AM +   I  
Sbjct: 75  EELNQLAGFLASKGYREIDVNMGCPFPLIANRGKGSGILPYPEKVAALLDAMRQLPEIRF 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G    + A   + ++  +  SGV+ I +H R    +      NR      YD  
Sbjct: 135 SVKMRLGW---LHADEWKQVLPLLNGSGVSQITLHPRIGKQQYKGEV-NRVAFKEFYDSC 190

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                   +L +  NG L  +    ++L     + GVM+GR    + ++  +V +     
Sbjct: 191 --------ELPLVYNGDLCTLETVQELLEEYPRLKGVMLGRGLLADPSLALSVRK----- 237

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYA----ARHLHSGGKLQQITRHMI 281
             G SP KT + +            Y             KL+ +  +++
Sbjct: 238 --GQSPDKTTLYRQVSAMHGLMYEHYCRIIEGGEAQLLAKLKTMWEYLL 284


>gi|159127783|gb|EDP52898.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus
           fumigatus A1163]
          Length = 443

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 100/258 (38%), Gaps = 31/258 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    VEAAK+V       I+LN GCP      G  GA L+  PD +   + 
Sbjct: 104 LVFQIGSANPELAVEAAKLVAG-DVAGIDLNSGCPKPFSTSGGMGAALLRTPDKLVSILE 162

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +          +LVK +  +G+ G+ +H R   ++        
Sbjct: 163 SLVREVGNPYQIGISVKIRILETPEKTESLVKRLVATGITGLTVHCRTTPMRPRERAIRD 222

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           ++      ++  I +E   +   +NG +    +AL ++    VDG MI  AA  N +   
Sbjct: 223 QL-----TMIARICREAG-VACVMNGDVTSRDEALALMKEFGVDGAMIATAAEANPSCFR 276

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +               +       WR++       A    +  G     T+ ++ +    
Sbjct: 277 S---------------EAEGGLLPWREVVHDYLQAAIECENRFGN----TKFLLNIL--I 315

Query: 288 PN-SRRCRHILTVEAGAS 304
           P  +R  +   T ++ + 
Sbjct: 316 PGKNREFKDAKTAKSYSD 333


>gi|171695442|ref|XP_001912645.1| hypothetical protein [Podospora anserina S mat+]
 gi|170947963|emb|CAP60127.1| unnamed protein product [Podospora anserina S mat+]
          Length = 769

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 52/289 (17%), Positives = 91/289 (31%), Gaps = 57/289 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEK---------PLAL-- 52
           +  +R     L    L Y+EM +   +L+G      ++     E          P+A   
Sbjct: 322 NLPFRRLCVDLGCE-LTYSEMAMGMPLLQGAKSDWTLMRAHKSETTPPRFNGDGPVAQGY 380

Query: 53  ----------QIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLN 100
                     QI        +++ + +  F  +   I+LN GCP   +++   G+ L+  
Sbjct: 381 DNSKDLKFGAQIAANVPWVAIKSTEALARFLPHLRLIDLNCGCPIDMLYKSGAGSALLDA 440

Query: 101 PDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAV--ALRNLV-------KSIKKSGVNG 150
           P  +   I  M      +P+T K R+GV D        +  L          +   G   
Sbjct: 441 PSKLERMIRGMNAVSDDVPITAKIRMGVRDDKFTAQKNIERLALGSEEHRDILGAPGCAA 500

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLFIGL 193
           + +H R    +     +   I                  D + E+ +        +F   
Sbjct: 501 VTLHGRTRQQRYTRAANWEYIAETAAMIKRLNEKTDSLTDTIREVDERTLPNGGRMFFIG 560

Query: 194 NGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLT 238
           NG           +    VD VMIGR A     +   +   +Y     T
Sbjct: 561 NGDCYSHIDYFDHVDNTKVDTVMIGRGAIIKPWIYEEIQTGQYLDKSAT 609


>gi|119492469|ref|XP_001263600.1| tRNA dihydrouridine synthase (Smm1), putative [Neosartorya fischeri
           NRRL 181]
 gi|119411760|gb|EAW21703.1| tRNA dihydrouridine synthase (Smm1), putative [Neosartorya fischeri
           NRRL 181]
          Length = 443

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 100/258 (38%), Gaps = 31/258 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    VEAAK+V       I+LN GCP      G  GA L+  PD +   + 
Sbjct: 104 LVFQIGSANPELAVEAAKLVAG-DVAGIDLNSGCPKPFSTSGGMGAALLRTPDKLVSILE 162

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +          +LVK +  +G+ G+ +H R   ++        
Sbjct: 163 SLVREVGNPYQIGISVKIRILETPEKTESLVKRLVATGITGLTVHCRTTPMRPRERAIRD 222

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           ++      ++  I +E   +   +NG +    +AL ++    VDG MI  AA  N +   
Sbjct: 223 QLA-----MIARICREAG-VACVMNGDVTSRDEALALMKEFGVDGAMIATAAEANPSCFR 276

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
           +               +       WR++       A    +  G     T+ ++ +    
Sbjct: 277 S---------------EAEGGLLPWREVVHDYLQAAIECENRFGN----TKFLLNIL--I 315

Query: 288 PN-SRRCRHILTVEAGAS 304
           P  +R  +   T ++ + 
Sbjct: 316 PGKNREFKDAKTAKSYSD 333


>gi|139438091|ref|ZP_01771644.1| Hypothetical protein COLAER_00632 [Collinsella aerofaciens ATCC
           25986]
 gi|133776288|gb|EBA40108.1| Hypothetical protein COLAER_00632 [Collinsella aerofaciens ATCC
           25986]
          Length = 317

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 93/238 (39%), Gaps = 20/238 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMI----VADAILRGDKKNILGFSTQEKPLALQIG 55
           M   T   +R             YT  +    V +       K I   + Q   +  Q+ 
Sbjct: 8   MEGITGHVFRRVHAECFGALDCYYTPFLPPPRVGNRFGGKAFKEIDPANNQGLNVVPQLM 67

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             +  + V A +++ D GY E+NLN+GCPS  V     G+  + N D +   ++ +C+  
Sbjct: 68  SKNADEFVWAVQVLADMGYREVNLNLGCPSGTVVAKGKGSGFLRNLDELEAFLSDVCERS 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +PV+VK R+G+++      + +L     +  +  + +H R           +R      
Sbjct: 128 PLPVSVKTRLGLENDDEYERVLDL---YCRMPLAELIVHPRVQK--------DRYTGLPR 176

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQA---LKILPSVDGVMIGRAAYKNSAMLTTVD 230
            +   E  +  P   +  NG + D+      ++  P    VM+GR    N A+   V 
Sbjct: 177 KEFYGETLERAP-FPVAYNGDIFDLEDMDALVEAYPGTRHVMLGRGLLANPALARMVK 233


>gi|67517075|ref|XP_658422.1| hypothetical protein AN0818.2 [Aspergillus nidulans FGSC A4]
 gi|74598677|sp|Q5BF62|DUS3_EMENI RecName: Full=tRNA-dihydrouridine synthase 3
 gi|40746492|gb|EAA65648.1| hypothetical protein AN0818.2 [Aspergillus nidulans FGSC A4]
 gi|259488899|tpe|CBF88723.1| TPA: tRNA-dihydrouridine synthase 3 (EC 1.-.-.-)
           [Source:UniProtKB/Swiss-Prot;Acc:Q5BF62] [Aspergillus
           nidulans FGSC A4]
          Length = 714

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 59/337 (17%), Positives = 100/337 (29%), Gaps = 72/337 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQE---------------- 47
           +  +R     L    L Y+EM ++  +++G K    ++     E                
Sbjct: 317 NLPFRRLCVEL-GAQLTYSEMALSMPLIQGHKPEWALMRAHETEALPPTVSARASVVQDY 375

Query: 48  -----KPLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI G     +++A +++         I+LN GCP   ++    G+ L+  
Sbjct: 376 DNSKDMKFGAQIAGNKYRWVMKATEVLSSLTPNLRVIDLNCGCPIDLLYREGSGSALLDA 435

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSI------------KKSG 147
           P  +   +  M      IP+TVK R G  D  P      LV+ +              SG
Sbjct: 436 PSKLEKMLRGMNAVSEQIPITVKIRTGTRDNTPNAQ--KLVERLILGGHEASMLNCGPSG 493

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLF 190
           V  I +H R    +     +   I                  D + E ++         +
Sbjct: 494 VAAITLHGRSRQQRYTREANWEYISETAALIKRLNEKSDEVTDTIREPEERMRPNGGKTW 553

Query: 191 IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
              NG           + +  VD VM+GR A     +   +        + S  +     
Sbjct: 554 FLGNGDCYSHVDYEDHIKNAKVDSVMVGRGALIKPWLFEEIQAGQYLDKSASERL----- 608

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                        Y      S      ITR  +   L
Sbjct: 609 -----AYVEKFARYGMETWGSDEYGIGITRRFLLEWL 640


>gi|189203793|ref|XP_001938232.1| hypothetical protein PTRG_07900 [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187985331|gb|EDU50819.1| hypothetical protein PTRG_07900 [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 434

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 83/180 (46%), Gaps = 9/180 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A+    V+AAK+V       I++N GCP      G  GA L+  PD++ + + 
Sbjct: 107 LIYQIGTANPELAVQAAKMVAA-DVAGIDVNSGCPKPFSTSGGMGAALLKTPDLLCNILT 165

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +           LVK + ++G+ G+ +H R   ++        
Sbjct: 166 SLVEEVGKPYEIGISVKIRILDTPEETAALVKRLVRTGITGLTVHCRTTPMRPRERAIRH 225

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           ++      ++ EI +E   +   +NG +   ++ALK++    VDG MI   A KN +   
Sbjct: 226 QLK-----MIGEICREAG-VACVMNGDVTSRTEALKLMEEFNVDGAMIATEAEKNPSCFR 279


>gi|332140763|ref|YP_004426501.1| multifunctional fatty acid oxidation complex subunit alpha
           [Alteromonas macleodii str. 'Deep ecotype']
 gi|327550785|gb|AEA97503.1| multifunctional fatty acid oxidation complex subunit alpha
           [Alteromonas macleodii str. 'Deep ecotype']
          Length = 629

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 102/244 (41%), Gaps = 31/244 (12%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
             D + +  KK  +  S  +K LAL  G  D S   +   IV +  + +++LN GCP+  
Sbjct: 361 SYDILNKKVKKRFMRNSEMQKQLALLTGTLDYSGYQD-VDIVVEAVFEDLDLNFGCPAKT 419

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
           V++   GA L+     + D + A+  A+   IPV+ K R+G +D+  AV       +I +
Sbjct: 420 VNKSKGGAVLLKETQTLYDIVKAVRDAVPAEIPVSAKIRLGFEDKSLAVEN---AVAITE 476

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G + + +HAR         K     P   +D + +IK+   ++ +  NG +     A +
Sbjct: 477 AGASELVVHART--------KTEGYKPPAYWDWIAKIKQHT-NIPLVANGEIWSAEDAQR 527

Query: 206 ILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
                    +M+GR A     +   +                R     W +++A +  Y+
Sbjct: 528 CQEQSECTNLMVGRGALAMPNLALCIK--------------GRQAPMPWPELAALLIQYS 573

Query: 264 ARHL 267
              +
Sbjct: 574 GYEI 577


>gi|289615723|emb|CBI57464.1| unnamed protein product [Sordaria macrospora]
          Length = 739

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/278 (18%), Positives = 95/278 (34%), Gaps = 55/278 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE------------KPL- 50
           +  +R     L    + Y+EM +   +L+G      ++     E             PL 
Sbjct: 340 NLPFRRLCVEL-GAEITYSEMALGLPLLQGQKADWTLMRAHESEITPPRYTPTGMVDPLY 398

Query: 51  --------ALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI        +++A+ +  +  +   I+LN GCP   V++   G+ L+  
Sbjct: 399 DNSKDLKFGVQITANAPWIAIKSAETLSRYLPHLRVIDLNCGCPIDMVYKSGAGSALLDA 458

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGV-DDQIPAVALRNL-------VKSIKKS-GVNG 150
           P  +   I  M      +PVT K R+G+ DD++ A  L          ++++  + G   
Sbjct: 459 PSKLERMIRGMNTVSGEVPVTAKIRMGIRDDRLTAQKLVERLALGAPDIRAVSGAPGCAA 518

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLFIGL 193
           + +H R    +     D   I                  D + E  +        ++   
Sbjct: 519 VTLHGRTRQQRYTKAADWSYIAECAALVKSFNKTSNSLQDTIREADERTLPNGGRMYFVG 578

Query: 194 NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
           NG           +    VD VM+GR A     +   +
Sbjct: 579 NGDCYSHVDYFNHVDNAGVDSVMVGRGAIIKPWIFEEI 616


>gi|109126451|ref|XP_001113869.1| PREDICTED: tRNA-dihydrouridine synthase 3-like, partial [Macaca
           mulatta]
          Length = 246

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 40/191 (20%), Positives = 70/191 (36%), Gaps = 21/191 (10%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             G  LM         +  M + L +P+TVK R GV +++       L+  ++  GV  +
Sbjct: 1   GGGCALMNRSTKFQQIVRGMNQVLDVPLTVKIRTGVQERVNLA--HRLLPELRDWGVALV 58

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSV 210
            +H R         ++ R     D+  + E  K    + +  NG +     A   +   V
Sbjct: 59  TLHGRS--------REQRYTKLADWQYIEECVKAASPMPLFGNGDILSFEDANRAMQTGV 110

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
            G+MI R A     + T + E     ++ S  +           I    T+Y   H  S 
Sbjct: 111 AGIMIARGALLKPWLFTEIKEQRHWDISSSERL----------DILRDFTNYGLEHWGSD 160

Query: 271 GKLQQITRHMI 281
            +  + TR  +
Sbjct: 161 TQGVEKTRRFL 171


>gi|218132878|ref|ZP_03461682.1| hypothetical protein BACPEC_00739 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991751|gb|EEC57755.1| hypothetical protein BACPEC_00739 [Bacteroides pectinophilus ATCC
           43243]
          Length = 321

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/314 (19%), Positives = 119/314 (37%), Gaps = 44/314 (14%)

Query: 1   MVDWTDRHYRFF---ARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQI 54
           M   T   YR               +T  I  +        ++++I   + + + +  QI
Sbjct: 16  MEGVTGYIYRNIIDDC--FGGADRYFTPFISTNTNKTFTEQERRDIDSGNNRPRDVIPQI 73

Query: 55  GGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              +    ++  + + +++GY+E+NLN+GCPS  V     GA  +  PD +   +  +  
Sbjct: 74  LSNNSCDCIKVIRALHDEYGYDEVNLNLGCPSPTVVTKHKGAGFLAFPDKLDSFLNDVFV 133

Query: 114 AL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           A     + V+VK R GV+          ++    +  ++ + +H R         KD  K
Sbjct: 134 AAGKDGVRVSVKTRTGVESHD---EFIKILDIYNQYPLSELIVHPRVQ-------KDLYK 183

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
               DYD ++E    N    +  NG +   +D  +       ++ VM GR    N A+  
Sbjct: 184 NSP-DYD-IFEYAYTNSKAPVCYNGDICSVDDYQRITSRFNGLNAVMCGRGMITNPAIFA 241

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI------ 281
           T++        G   + +R  + F   +            ++  K++++  +MI      
Sbjct: 242 TIN--------GGDKLSSRALRTFHNAVFKEYCAVMGER-NALFKMKELWYYMIRNFDGA 292

Query: 282 -GLFHGFPNS-RRC 293
              +     + RRC
Sbjct: 293 DRYYKSIRKAQRRC 306


>gi|225390252|ref|ZP_03759976.1| hypothetical protein CLOSTASPAR_04003 [Clostridium asparagiforme
           DSM 15981]
 gi|225043677|gb|EEG53923.1| hypothetical protein CLOSTASPAR_04003 [Clostridium asparagiforme
           DSM 15981]
          Length = 322

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 58/291 (19%), Positives = 106/291 (36%), Gaps = 25/291 (8%)

Query: 1   MVDWTDRHYRFFAR-LLTNNALLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGG 56
           M   T   YR   R         +T  +  +   R    ++K++     +   L  QI  
Sbjct: 8   MEGLTGYVYRNAHRACFGGVDKYFTPFLSPNQNHRFTAKEEKDVRPEHNEGISLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 + AA  ++  GY E+NLN+GCPS  V     GA  +   + +   +  + + + 
Sbjct: 68  NRAEDFIWAAGEMKARGYREVNLNLGCPSGTVVSKYKGAGFLARQEALNRFLDQIFQEVD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG+           L++   +  +  + +H R       +  D         
Sbjct: 128 LEISIKTRIGI---AAPEEFPELMEIFNRYPIRELIVHPRLRTDFYKNTPDRESFG---- 180

Query: 177 DIVYEIKKENPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              Y +K+    L    NG +        A    PSV+ VM+GR    N A+   +    
Sbjct: 181 ---YAVKESRASL--CYNGDIFTEEAFRSAASRFPSVERVMLGRGLLANPALAERIRGIE 235

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
             PLT S          F R +            +   K++++  ++I +F
Sbjct: 236 EAPLTASR------LAAFHRALYEGYRLAIPEERNVLFKMKEMWTYLICMF 280


>gi|308159955|gb|EFO62469.1| tRNA dihydrouridine synthase, putative [Giardia lamblia P15]
          Length = 471

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 95/237 (40%), Gaps = 31/237 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK-----NILGFSTQ-EKPLALQI 54
           MVD ++  YR   R      L +T M   + ++   K      + L +    ++PL LQ+
Sbjct: 36  MVDGSELPYRLLTRRYNVE-LSWTPMYNTNTLVMSPKAMTQLVDELKYGESIDRPLVLQL 94

Query: 55  GGADISKLVEA----AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            G + S    A     ++     ++ + LN+GCP A    G +G+ LM + ++  + +  
Sbjct: 95  SGNNPSNFELAYSTLVQMGAGCCFDIVELNMGCPQAVALRGKYGSYLMEHLELAEEILHT 154

Query: 111 MCKA-----LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +  A     L   V VK R+    +  +     +   +  +G+    +H R  + +  S 
Sbjct: 155 LVAATTRFGLGHKVAVKTRL----ETSSKDTLKMCLRLCNTGIAMFTLHGRTRLQRTGS- 209

Query: 166 KDNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKI--LPSVDGVMIG 216
                +   ++ ++  + K+     P L    NGG+ ++    ++  L    G M  
Sbjct: 210 ----AVGPPNWQMLASVLKDLRASYPHLIFFANGGVWNLETHERLRSLTGCHGTMSA 262


>gi|291550701|emb|CBL26963.1| tRNA-U20a,U20b-dihydrouridine synthase [Ruminococcus torques L2-14]
          Length = 313

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/287 (20%), Positives = 110/287 (38%), Gaps = 21/287 (7%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGGA 57
              T   YR    +        +   I  +        +KK+++  + +      QI   
Sbjct: 9   EGITGHIYRNALHQCFDGFDKYFIPFISPNQKGHFSTREKKDVMPENNEGMYAVPQILTN 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           ++   +  AK + D+GY E+NLN+GCPS  V     GA  +  P  +   + A+ +  ++
Sbjct: 69  NVEDFLCTAKKLGDYGYKEVNLNLGCPSRTVVTKGRGAGFLDEPQKLDRFLDAVFEKCNL 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K RIG++D         ++    K  +  + IH R            +  P LD  
Sbjct: 129 EISIKTRIGMED---PEEFETILPIYNKYPLKELIIHPRVQKEFY------KNTPKLDTY 179

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                  E+P  + G    +EDM Q     P  D VM+GR    + A+           L
Sbjct: 180 AWAVEHSEHPLCYNGDICSVEDMEQLKIRFPQTDTVMMGRGVLADPAL--------GRKL 231

Query: 238 TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            G S       K F   + A+  +  +       K++++  ++  +F
Sbjct: 232 KGGSAATIEELKKFHDVLYAAYCEEMSGDRTILYKMKEMWFYLHPIF 278


>gi|187471073|sp|Q2HDP2|DUS3_CHAGB RecName: Full=tRNA-dihydrouridine synthase 3
          Length = 713

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 49/280 (17%), Positives = 91/280 (32%), Gaps = 55/280 (19%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQE---------KPLAL-- 52
           +  +R     L    + Y+EM +   +L+G      ++     E          P+    
Sbjct: 315 NLPFRRLCVEL-GAQVTYSEMALGLPLLQGLKADWTLMRAHESEIVPPRFNPGGPIVQGY 373

Query: 53  ----------QIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLN 100
                     QI        V+A + +     +   ++LN GCP   V +   G+ L+ +
Sbjct: 374 DNSKDVKFGAQIAANAPWVAVKATEALSQLLPHLRLVDLNCGCPVDAVFKSGSGSALLDS 433

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDD---------QIPAVALRNLVKSIKKSGVNG 150
              +   I  M      +P+T K R+G  D         +  A+   +L   I   G   
Sbjct: 434 HSKLERMIRGMNAVSGEVPITAKIRMGSRDGKLTAQKLVERLALGSEDLRDMIGAPGCAA 493

Query: 151 IWIHARKAILKGLSPKDNRKIPNLD-------------YDIVYEIKKEN----PDLFIGL 193
           + +H R  + +     D   I                  D + E  +        ++   
Sbjct: 494 VTLHGRTRLQRYTKAADWGYIAECAALIKQFNEKSNDLADTIREADENTLPNGGKMYFLG 553

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           NG      +    + +  VD VMIGR A     +   +++
Sbjct: 554 NGDCYSHVEYFDHVDNAKVDSVMIGRGALVKPWVFEEIEK 593


>gi|72388074|ref|XP_844461.1| tRNA-dihydrouridine synthase 4 [Trypanosoma brucei TREU927]
 gi|62359403|gb|AAX79841.1| tRNA-dihydrouridine synthase 4, putative [Trypanosoma brucei]
 gi|70800994|gb|AAZ10902.1| tRNA-dihydrouridine synthase 4, putative [Trypanosoma brucei brucei
           strain 927/4 GUTat10.1]
          Length = 419

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/211 (26%), Positives = 92/211 (43%), Gaps = 21/211 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL     + YT MI+AD+    +      FS  + E  L  Q+  + 
Sbjct: 66  MVRCSRPAFRKLCRLW-GTDISYTHMIMADSFACSEAARQAEFSIYSGETRLITQLASSS 124

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---- 114
                 AA IV  +  + I+LN GCP  RV     GA L+ NP++V D +  +  A    
Sbjct: 125 GPTAATAAAIVAPW-CDAIDLNCGCPQRRVMADGLGAALLRNPEVVADTVRCVRNALEGG 183

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + +P  VK R+  D ++      +  +  + +G   I +H R       +P        +
Sbjct: 184 VELPCVVKMRVKDDVRLSV----DFARQCEAAGAAWITVHGRTPNCSAHAP--------V 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            +D +  I++    + +  NGG+ D S AL+
Sbjct: 232 RFDAINTIREALG-VPVVANGGVRDPSTALQ 261


>gi|224160922|ref|XP_002199744.1| PREDICTED: hypothetical protein, partial [Taeniopygia guttata]
          Length = 435

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 35/154 (22%), Positives = 67/154 (43%), Gaps = 6/154 (3%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 284 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQSSEWALLKRHHTEDIFGVQLEGAFPDTMT 342

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM   +     +  M   L +PVTVK
Sbjct: 343 KCAELLNRTIDVDFVDINVGCPIDLVYKKGGGCALMTRSNKFEQIVRGMNSVLDVPVTVK 402

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            R GV +++       L+  I++ G + + +  R
Sbjct: 403 IRTGVQEKVNVA--HKLIPRIREWGASMVTVRGR 434


>gi|261327635|emb|CBH10611.1| tRNA-dihydrouridine synthase 4, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 419

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 55/211 (26%), Positives = 92/211 (43%), Gaps = 21/211 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   RL     + YT MI+AD+    +      FS  + E  L  Q+  + 
Sbjct: 66  MVRCSRPAFRKLCRLW-GTDISYTHMIMADSFACSEAARQAEFSIYSGETRLITQLASSS 124

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA---- 114
                 AA IV  +  + I+LN GCP  RV     GA L+ NP++V D +  +  A    
Sbjct: 125 GPTAATAAAIVAPW-CDAIDLNCGCPQRRVMADGLGAALLRNPEVVADTVRCVRNALEGG 183

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           + +P  VK R+  D ++      +  +  + +G   I +H R       +P        +
Sbjct: 184 VELPCVVKMRVKDDVRLSV----DFARQCEAAGAAWITVHGRTPNCSAHAP--------V 231

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            +D +  I++    + +  NGG+ D S AL+
Sbjct: 232 RFDAINTIREALG-VPVVANGGVRDPSTALQ 261


>gi|301166477|emb|CBW26053.1| putative dihydrouridine synthase (tRNA modification protein)
           [Bacteriovorax marinus SJ]
          Length = 322

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 60/250 (24%), Positives = 105/250 (42%), Gaps = 32/250 (12%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           F+    P   QI   ++ + + AAK  +D G  ++NLN+GCP   V   + G+ L+L+P 
Sbjct: 58  FTKNLIPTTAQILTKEVDQFIHAAKHFKDLGVQKVNLNMGCPYPMVANRTKGSGLLLHPG 117

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAIL 160
            V   +  + +   + ++VK R+G + +     ++ ++  I    +    IHAR  K + 
Sbjct: 118 RVEKLLTEIKERCPLELSVKIRLGRESKD---EIKEIIPIINALDIKDFTIHARLGKQLY 174

Query: 161 KGLSPKDNRK--IPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMI 215
           KG+   D  +  +P L Y   Y             NG ++   D     K  P +   MI
Sbjct: 175 KGVVDLDGFEECLPLLKYTPCY-------------NGDIKTPSDFENISKRFPQIKRWMI 221

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           GRAA  N A+L+ +         G    + +    F +       +Y +R       LQ+
Sbjct: 222 GRAALSNPALLSQIR--------GEEYNEQKYRALFIKMHKLMSEEYLSRENAKSDYLQR 273

Query: 276 ITRHMIGLFH 285
           +  H +  F 
Sbjct: 274 MREHWL-YFK 282


>gi|160938134|ref|ZP_02085490.1| hypothetical protein CLOBOL_03028 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438938|gb|EDP16694.1| hypothetical protein CLOBOL_03028 [Clostridium bolteae ATCC
           BAA-613]
          Length = 335

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 68/332 (20%), Positives = 119/332 (35%), Gaps = 35/332 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR  +          +T  +   A   +   +  +IL    Q   +  QI  
Sbjct: 16  MEGLTGYIYRNAYHACYHAMDKYFTPFLSPKANSKLSFRELNDILPEHNQGMYVVPQILT 75

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---K 113
                 ++ AK ++++GY+EINLN+GCPS  V     GA  +  PD +   +  +C    
Sbjct: 76  NQAGDFIQTAKELQEYGYSEINLNLGCPSGTVVSKHKGAGFLGRPDSLDRFLDEVCGKMD 135

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            + + V+VK R+G+   I       L++   +  +  + +H R       +   N     
Sbjct: 136 EMGMEVSVKTRLGL---ISPDEFTGLLEIYNRYPLKELILHPRVRTDYYKNTP-NMPAFR 191

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
             +D             +  NG +    D        P +D VM+GR    N  +L  + 
Sbjct: 192 GGFDGSRS--------PVCYNGDIFTISDYETLCGDYPELDRVMLGRGIISNPGLLDRIA 243

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                  +G         K F + I        +   +   K++++   MI +F    N 
Sbjct: 244 A---GRNSGGPGTDKETLKRFHQMIYEGYRQIMSGDRNVLFKMKELWACMIQIFSD--NG 298

Query: 291 RRCRHI-----LTVEAGASTA---THHIIETA 314
           +  + I     L     A+ A      I+E A
Sbjct: 299 KYIKRIKKSQRLEEYETAAAAVFRDLDILEGA 330


>gi|322494951|emb|CBZ30254.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 493

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 98/255 (38%), Gaps = 44/255 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   R      + YT M++A++ ++        F+    E  L +Q+    
Sbjct: 103 MVRCSRPAFRQVCRAW-GTRVSYTHMLIAESFVKSPHARHAEFARYEGEDRLVVQLAAKS 161

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                +AA ++  +  + I+LN GCP     +   GA L+  P+ V D + ++  A+   
Sbjct: 162 GPAAAQAALLLRPY-CDGIDLNCGCPQRWAMKEGIGAALLDQPERVADIVRSIRNAMPDG 220

Query: 117 -----------------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                                  +P  VK RI  D +       +  +  + +GV+ + +
Sbjct: 221 STAPTIVGNGGEHSSCTSAAPPFLPCVVKMRIKDDLRRSV----DFARQCEAAGVSWLTV 276

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVD 211
           H R       +      +         ++ +EN  + + LNGG+ D+S A++  +     
Sbjct: 277 HGRTPTCHPSAAVQFEAV---------KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCG 327

Query: 212 GVMIGRAAYKNSAML 226
           G+M       N AM 
Sbjct: 328 GLMSANGLLDNPAMF 342


>gi|109128993|ref|XP_001097732.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Macaca mulatta]
          Length = 492

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 101/253 (39%), Gaps = 47/253 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +G  GACL   P  
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKEYSTKGG-GACLKTLPQK 135

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               ++ + K +  PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 136 KKKILSTLVKGIRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 185

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 186 --REERPQHPVSCEVIKAIA-DTLSIPVIANGGSHDHIQRYSDIEDFRQA----TAASSV 238

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 239 MVARAAMWNPSIF 251


>gi|213407258|ref|XP_002174400.1| tRNA dihydrouridine synthase Dus3 [Schizosaccharomyces japonicus
           yFS275]
 gi|212002447|gb|EEB08107.1| tRNA dihydrouridine synthase Dus3 [Schizosaccharomyces japonicus
           yFS275]
          Length = 617

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/282 (18%), Positives = 107/282 (37%), Gaps = 45/282 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVA----------DAILRGDKKNILGFSTQEKPL-ALQI 54
           +  +R        +   Y+EM +            A++RG +       T  + +  +Q+
Sbjct: 249 NPAFRQLCASFGADT-FYSEMALCYPLMQGHQPEWALVRGVESERQTMKTGRRGIFGIQL 307

Query: 55  GGADISKLVEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM- 111
               + + V+ A+++ ++  G + ++LN GCP   V+    G+ L+ N   +   +  + 
Sbjct: 308 ACGKLWQGVKTAQVLSEYCDGLDFLDLNCGCPIDLVYRQGAGSALLDNHTRLIRSLQGID 367

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
             + S+P TVK R+G  D  P +A R + +   ++ V+ + +H R         +  R  
Sbjct: 368 TISGSLPTTVKLRMGCRDDHP-IAKRLMTRIFHETNVSAVTLHGRS--------RQQRYS 418

Query: 172 PNLDYDIVYEIKKE------------------NPDLFIGLNGGLEDMSQALK-ILPSVDG 212
              D+D V +   E                  N  + +  NG           +   VD 
Sbjct: 419 KLADWDYVRQCATEIRTLNEALEEKPDAFPMRNQRMAVIGNGDCFTYKDWYDGMETGVDT 478

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           VMI R A     +   ++      +  SS  +  + ++F   
Sbjct: 479 VMIARGALVKPWIFEEIEA--RQSIDKSSTQRLEMLQEFCNH 518


>gi|134057270|emb|CAK37884.1| unnamed protein product [Aspergillus niger]
          Length = 446

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 80/184 (43%), Gaps = 17/184 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LIYQIGTATPEIAVQAAKLVAG-DVAGIDVNSGCPKPFSTSGGMGAALLKTPDKLVAILE 163

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +  P    ++VK RI  D +      R LV  + K+G+ G+ +H R   ++    
Sbjct: 164 ALVKEVGTPFQIGISVKIRILKDPE----ETRALVSRLVKTGITGLTVHCRTPPMRPRER 219

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               ++      ++ +I  E   +   +NG +    +   ++    VDG MI  AA  N 
Sbjct: 220 AIRDQV-----RMIADICHEAG-VACVINGDVTSKDEGHALMKEFGVDGAMIATAAEANP 273

Query: 224 AMLT 227
           +   
Sbjct: 274 SCFR 277


>gi|46124971|ref|XP_387039.1| hypothetical protein FG06863.1 [Gibberella zeae PH-1]
          Length = 416

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 48/180 (26%), Positives = 80/180 (44%), Gaps = 9/180 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + VEAA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 104 LIFQIGTADPDRAVEAARLVAA-DVAGIDVNAGCPKPFSTSGGMGAALLQTPDKLCAILE 162

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ K ++    +   + +     A     LV+ +  +G+ G+ IH R   ++   P++  
Sbjct: 163 ALVKNITPEFEIGISVKIRLLDTAAETEALVRRLCATGITGLTIHCRTTPMR---PRERA 219

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
               L   ++ E+  E   +   +NG +E     L++      DG MI  AA KN +   
Sbjct: 220 IRGQLR--MIAEVCHEFG-VACLVNGDVEGRDHGLQLAEEFGADGAMIAVAAEKNPSCFR 276


>gi|71017671|ref|XP_759066.1| hypothetical protein UM02919.1 [Ustilago maydis 521]
 gi|46098858|gb|EAK84091.1| hypothetical protein UM02919.1 [Ustilago maydis 521]
          Length = 766

 Score =  126 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/249 (21%), Positives = 93/249 (37%), Gaps = 27/249 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFST 45
           MV       R  +       L++   IV  AI+                 D K I     
Sbjct: 83  MVRIGTLPTRLLSLEY-GADLVWGPEIVDRAIIGCERKVNPHTGVVEYLKDHKQIFSCHP 141

Query: 46  QEKP-LALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            E+P L  Q+G AD     +A K I +      ++LN GCP         GA ++  P +
Sbjct: 142 IERPYLVYQLGSADPHLAFQAIKTITQADDVAAVDLNCGCPKPFSTHAGMGANMLSTPIL 201

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + + AM +A    + VT K R+    +     +  +V++     +  + +H R   ++
Sbjct: 202 LCNTLKAMRRAAPAHVAVTCKIRLLPTQEKTLELVDKIVRT---GAIECLTVHCRTKDMR 258

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQA--LKILPSVDGVMIGRA 218
              P    ++  +  D V  +  E    + +  NG + D +    +K L  V   MI R 
Sbjct: 259 PREPALLHRLREI-VDHVNSVATEMGRTIPVVCNGDVWDAATVPRIKELTGVTSTMIARG 317

Query: 219 AYKNSAMLT 227
           A  N +   
Sbjct: 318 AEANPSCFR 326


>gi|327404377|ref|YP_004345215.1| dihydrouridine synthase DuS [Fluviicola taffensis DSM 16823]
 gi|327319885|gb|AEA44377.1| dihydrouridine synthase DuS [Fluviicola taffensis DSM 16823]
          Length = 309

 Score =  126 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 59/326 (18%), Positives = 120/326 (36%), Gaps = 34/326 (10%)

Query: 4   WTDRHYRFFARL-LTNNALLYTEMI--VADAILRGDKK-NILGFSTQEKPLALQIGGADI 59
           +TD H+R   +   +N    Y   +    D  ++ + K +IL  +   + +  Q+   + 
Sbjct: 11  YTDYHFRNAHQQVYSNVDKFYAPYLKLNNDGTIKNNPKIDILVKNNPFQKIVPQLMACNK 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
                 A  +E  GY E+N N+GCP   V   + GA ++  PD +   + ++     + +
Sbjct: 71  DDFFVMADYIESLGYTEVNWNMGCPYPMVTNKNLGAGILNKPDEILRLLDSILPKTKLGI 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            +K R+G++       +   + ++    +  I IHAR A        D+ +         
Sbjct: 131 GIKMRMGLE---STQEIIEFLPALNNYPLTEIIIHARNAKQLYNGTCDHERFLE------ 181

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                   D  +  NG +   ED     K    ++  MIGR A  N  +   +       
Sbjct: 182 ---CISLTDHSLTYNGDIQSKEDFEFLQKKFSGINNWMIGRGAMINPCIFDEIK----TG 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +  SS +       F   ++ S+ +      ++  K++    ++     G  + ++    
Sbjct: 235 IFDSSEVYRNKLLKFSGLLTESLLECNPDRGYALSKMKSYWEYLS---EGLSDGKQLYRK 291

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           L            +IE     +IE +
Sbjct: 292 LK--------KAKLIEDFNEFIIEMV 309


>gi|322505439|emb|CAM42636.2| putative dihydrouridine synthase (Dus) [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 666

 Score =  126 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 53/417 (12%), Positives = 111/417 (26%), Gaps = 145/417 (34%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------- 39
           MVD ++  +R   R      + YT M+ A +   G                         
Sbjct: 120 MVDQSELPFRMLCRQY-GATVAYTPMLHAKSFAEGAAYRSHFLSVTPPGEVKAAMEAPFA 178

Query: 40  --------------------------ILGFSTQEKPLALQIGGADISKLVEAAKIV---- 69
                                     +   +  ++P  +Q  G D   ++ AA++     
Sbjct: 179 SPSVSAGEHSGGSNTRTGVGTDGDDAVADVALVDRPCIVQFCGNDPDIVLRAARLAVLGE 238

Query: 70  --------------------------------ED-----FGYNEINLNVGCPSARVHEGS 92
                                           E+     +  + ++LN+GCP      G 
Sbjct: 239 QAAAGEQTAANYRVSTAPVYPVPVRVNGSSLEEEPVHRLYQCDAVDLNLGCPQGIARRGH 298

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN-------------- 138
           +G+ LM + + +   +  +   L +PVTVK R+         A  +              
Sbjct: 299 YGSFLMEDWESIHTIVHTLHVELEVPVTVKIRVFDRPGHAEAADNDHECATHCSPAACVE 358

Query: 139 --------------------------------LVKSIKKSGVNGIWIHARKAILKGLSPK 166
                                             + I+ +G   + IH R   +KG    
Sbjct: 359 EEEEDAAAAATAVVGTLPKPLEEGFDEALTILYARMIRDAGAQVLCIHGRTREMKGQHT- 417

Query: 167 DNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   + +++  ++   +  + +  NG +      +  L     +G M       + 
Sbjct: 418 -----GTANMELIRRVRLALSGTIPVISNGNVRTYDDVIAHLQETRCEGHMCAEPLLWDP 472

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQQITRH 279
            + +   +      T S+   TR+       +    +  Y          L ++  H
Sbjct: 473 KLFSNPSQPVMPGRTHSADKATRLSALHTALVYMQWVRHYPVDIGFVKAHLFKMCFH 529


>gi|154342528|ref|XP_001567212.1| dihydrouridine synthase (Dus) [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 666

 Score =  126 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 53/417 (12%), Positives = 111/417 (26%), Gaps = 145/417 (34%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------- 39
           MVD ++  +R   R      + YT M+ A +   G                         
Sbjct: 120 MVDQSELPFRMLCRQY-GATVAYTPMLHAKSFAEGAAYRSHFLSVTPPGEVKAAMEAPFA 178

Query: 40  --------------------------ILGFSTQEKPLALQIGGADISKLVEAAKIV---- 69
                                     +   +  ++P  +Q  G D   ++ AA++     
Sbjct: 179 SPSVSAGEHSGGSNTRTGVGTDGDDAVADVALVDRPCIVQFCGNDPDIVLRAARLAVLGE 238

Query: 70  --------------------------------ED-----FGYNEINLNVGCPSARVHEGS 92
                                           E+     +  + ++LN+GCP      G 
Sbjct: 239 QAAAGEQTAANYRVSTAPVYPVPVRVNGSSLEEEPEHRLYQCDAVDLNLGCPQGIARRGH 298

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN-------------- 138
           +G+ LM + + +   +  +   L +PVTVK R+         A  +              
Sbjct: 299 YGSFLMEDWESIHTIVHTLHVELEVPVTVKIRVFDRPGHAEAADNDHECATHCSPAACVE 358

Query: 139 --------------------------------LVKSIKKSGVNGIWIHARKAILKGLSPK 166
                                             + I+ +G   + IH R   +KG    
Sbjct: 359 EEEEDAAAAATAVVGTLPKPLEEGFDEALTILYARMIRDAGAQVLCIHGRTREMKGQHT- 417

Query: 167 DNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   + +++  ++   +  + +  NG +      +  L     +G M       + 
Sbjct: 418 -----GTANMELIRRVRLALSGTIPVISNGNVRTYDDVIAHLQETRCEGHMCAEPLLWDP 472

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQQITRH 279
            + +   +      T S+   TR+       +    +  Y          L ++  H
Sbjct: 473 KLFSNPSQPVMPGRTHSADKATRLSALHTALVYMQWVRHYPVDIGFVKAHLFKMCFH 529


>gi|157875645|ref|XP_001686207.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|68129281|emb|CAJ07821.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 493

 Score =  126 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 97/255 (38%), Gaps = 44/255 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS--TQEKPLALQIGGAD 58
           MV  +   +R   R      + YT M++A++ ++        F+    E  L  Q+    
Sbjct: 103 MVRCSRPAFRQVCRAW-GTRVSYTHMLMAESFVKSPHARHAEFARYEGENRLVAQLAAKS 161

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                +AA ++  +  + I+LN GCP     +   GA L+  P+ V D + ++  A+   
Sbjct: 162 GPAAAQAALLLRPY-CDGIDLNCGCPQRWAMKEGIGAALLDQPERVADMVRSIRNAMPDG 220

Query: 117 -----------------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                                  +P  VK RI  D +       +  +  + +GV+ + +
Sbjct: 221 STAPMIVGNGGEYSSCTSAVPPFLPCVVKMRIKDDLRRSV----DFARQCEAAGVSWLTV 276

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVD 211
           H R       +      +         ++ +EN  + + LNGG+ D+S A++  +     
Sbjct: 277 HGRTPTCHSSTAVQFEAV---------KLIRENLSVPVVLNGGVTDVSTAMEAALRTGCG 327

Query: 212 GVMIGRAAYKNSAML 226
           G+M       N AM 
Sbjct: 328 GLMSANGLLDNPAMF 342


>gi|296421665|ref|XP_002840385.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295636600|emb|CAZ84576.1| unnamed protein product [Tuber melanosporum]
          Length = 386

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 9/179 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAKI+       I++N GCP         GA L+ NPD + D + 
Sbjct: 82  LIFQLGTASPELAVEAAKIIVG-DVAGIDVNSGCPKHFSIHSGMGAALLKNPDKLIDILT 140

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++   + +P +V   + +    P      LV+ +  +G++ + +H R   ++   P    
Sbjct: 141 SLVTEVGVPNSVPISVKIRLLEPHTDTIGLVQRLCTTGISRVTVHCRTIPMRPREPAIRG 200

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
            +       +  +  E   +    NG +   + A +++    VDG MI RAA  N ++ 
Sbjct: 201 VLSE-----IANVCHEAG-IECFANGDVTSRAHAEELIEKHGVDGCMIARAAETNPSVF 253


>gi|224160043|ref|XP_002338164.1| predicted protein [Populus trichocarpa]
 gi|222871075|gb|EEF08206.1| predicted protein [Populus trichocarpa]
          Length = 335

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 97/261 (37%), Gaps = 27/261 (10%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQ 130
           G   I+LN GCP+  V+    GA L+ +P+ +   + A+  A+   +PV+ K R+G +D 
Sbjct: 12  GPEGIDLNFGCPAKVVNRHGGGAALLQDPEQIARVVGAVRAAVPAAMPVSAKMRLGFNDT 71

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
                +    ++++  G   I +HAR         K +   P   +D++  I +E+  + 
Sbjct: 72  ---ALMTECAQAMQAGGACEIVVHART--------KLDGYRPPAYWDMIPRI-RESVTVP 119

Query: 191 IGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +  NG +  +  AL+         +M+GR    +  +   +          +  +  +V 
Sbjct: 120 VVANGEIWTVEDALRCREQSGCGDLMLGRGIVADPGLALAIRAAVEGGRMPAEHVAAQVF 179

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC-------RHILTVEA 301
                       D     L    +  ++ + +  L   FP + +        R       
Sbjct: 180 WSDLVPQVQRFWDMVCEDLEPRQRAGRLKQWLNLLRRRFPEAEQAYQEQMVGRQRANELE 239

Query: 302 GASTA----THHIIETAFNLM 318
             + A       ++ TA  + 
Sbjct: 240 HQAQAPAGIGLAVLVTALTVF 260


>gi|160893898|ref|ZP_02074677.1| hypothetical protein CLOL250_01452 [Clostridium sp. L2-50]
 gi|156864276|gb|EDO57707.1| hypothetical protein CLOL250_01452 [Clostridium sp. L2-50]
          Length = 325

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 54/277 (19%), Positives = 101/277 (36%), Gaps = 21/277 (7%)

Query: 14  RLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE 70
           +        +T  I           +  ++         +  QI        ++AAK + 
Sbjct: 34  KYFGGIDRYFTPFIAPAKGKPFRHRELADVRPEHNTGITVIPQILTNHSEGFIKAAKALA 93

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           D GY+EIN+N+GCPS  V     G+ ++ +P  +   +  +  A    ++VK R+G++  
Sbjct: 94  DMGYDEININMGCPSGTVVSKGKGSGMLADPVKLDHFLEEIFAADICKISVKTRLGME-- 151

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
             A    +++  + K     + IH R          D        +D+  E   E  +  
Sbjct: 152 -FADEFPDILDVLMKYPFTEVIIHPRTREDYYGGSVDL-----AMFDLAVERYGEQTESV 205

Query: 191 IGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           +  NG + D        +  P VD +MIGR    N  +   + E       G       +
Sbjct: 206 LCYNGDITDAAGYKNIQERYPQVDKIMIGRGIIGNPFLPQEIAEQRCCYNAG-------I 258

Query: 248 DKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              F  ++ A   +      +   K++++   M  LF
Sbjct: 259 LLAFHDELFAGYMEAGLGARNVMFKMKELWSFMECLF 295


>gi|312215880|emb|CBX95832.1| hypothetical protein [Leptosphaeria maculans]
          Length = 448

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 44/180 (24%), Positives = 81/180 (45%), Gaps = 9/180 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A+    V+AAK+V       I++N GCP      G  GA L+  PD++   + 
Sbjct: 107 LIYQMGTANPELAVQAAKMVAA-DVAGIDVNSGCPKPFSTAGGMGAALLKTPDLLCSILT 165

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + + +  P  +   + +           LVK + ++G+ G+ +H R   ++        
Sbjct: 166 RLVEEVGKPFEIGISVKIRILELPEETEALVKRLVRTGITGLTVHCRTTPMRPRERAIRD 225

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           ++      +V EI +E   +   +NG +   ++AL+++    VDG MI   A KN +   
Sbjct: 226 QLK-----MVGEICREAG-VACVMNGDVTSRTEALQLMQEFHVDGAMIATEAEKNPSCFR 279


>gi|291519623|emb|CBK74844.1| tRNA-U20a,U20b-dihydrouridine synthase [Butyrivibrio fibrisolvens
           16/4]
          Length = 245

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 88/239 (36%), Gaps = 21/239 (8%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
              TD  +R  F +        YT  I  ++  +   +       ++  +     Q+   
Sbjct: 13  EGVTDSIFRNTFKKYFGGVDKYYTPFISPNSTFKFTTREFKDIDPEKNDINTTVPQLLTN 72

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
                + AA  +   G+ EIN N+GCPS  V     G+ L+  P+ +   +  +   L  
Sbjct: 73  KAEHFLWAAGEIASLGFKEINFNLGCPSGTVVAKKKGSGLLYYPEELDSMLYEIFAGLKN 132

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            I V++K R+G   ++ +     +++   K  ++ + IH R        P     I    
Sbjct: 133 DIQVSIKTRLG---KLESDEFYEILEIYNKYPISELTIHPRVQKDFYREP-----IHPDF 184

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDE 231
           +   Y   K      +  NG ++ +S       +   ++ VMIGR    N  +     +
Sbjct: 185 FQYAYSNAKA----PLVFNGDVKTISDIDDTFNNYPLINAVMIGRGLISNPKLALEFKK 239


>gi|303258014|ref|ZP_07344023.1| dihydrouridine synthase family protein [Burkholderiales bacterium
           1_1_47]
 gi|302859357|gb|EFL82439.1| dihydrouridine synthase family protein [Burkholderiales bacterium
           1_1_47]
          Length = 315

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 113/322 (35%), Gaps = 31/322 (9%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   +R           L Y   I             K +        P+  Q+  
Sbjct: 1   MEGLTTAVFRRLHHQYFGGTDLYYIPFITPTVEPKFTDRHLKELSPEVNAGIPVVPQLLS 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-L 115
              +  + AAK ++D GY E+NLN+GCPS  V     G+  + +   +   +  +  A +
Sbjct: 61  NRSADFIWAAKALQDLGYKEVNLNLGCPSGTVVAKGKGSGFLRDLYALERFLDEIFSAGI 120

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IP+++K R+G           +++   KK  ++ + +H R         K ++    + 
Sbjct: 121 DIPISIKTRLGW---ANTEEFGDILNLYKKYPLSLLIVHMRL--------KTDQYKGEVR 169

Query: 176 YDIVYEIKKENPDLFIGLNGG-LEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
            + + E   E P   +G+NG  +             D   +M+GRA   + A+       
Sbjct: 170 KEALLEHLDEIP-FPLGVNGDMITTADMIDFSKTFRDPKMLMVGRALMADPALFRKYK-- 226

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                 G         K+F   +  + T+      ++  ++++       LF   P  + 
Sbjct: 227 ------GGPAASLEEIKNFTTALFDAYTEAFQNRRNAMMRMKEFWFFQANLFEENP--KA 278

Query: 293 CRHILTVEAGAS-TATHHIIET 313
            ++I   +      A    IE 
Sbjct: 279 FKNIFKSKTEEDFLAAIEEIEA 300


>gi|254674273|emb|CBA10057.1| tRNA-dihydrouridine synthase [Neisseria meningitidis alpha275]
          Length = 272

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 35/165 (21%), Positives = 74/165 (44%), Gaps = 16/165 (9%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN 138
            GCP+  V++   GA L+  P+++   +  +   L   IP+T K R+G +D+  A+    
Sbjct: 47  FGCPAPTVNKHKGGAILLKEPELIFHIVKTLRGRLPAHIPLTAKMRLGYEDKSRAL---E 103

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
              +I + G  G+ +HAR         K     P   ++ + +I +++ ++ +  NG + 
Sbjct: 104 CACAIAEGGACGLTVHART--------KAEGYEPPAHWEWIRKI-RDSVNIPVTANGDVF 154

Query: 199 DMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +     +K +   + VM+GR A     +   + +Y +      +
Sbjct: 155 SLQDYIGIKTISGCNSVMLGRGAVIRPDLARQIKQYENGGPVKDT 199


>gi|169770417|ref|XP_001819678.1| tRNA-dihydrouridine synthase 3 [Aspergillus oryzae RIB40]
 gi|121804085|sp|Q2UL89|DUS3_ASPOR RecName: Full=tRNA-dihydrouridine synthase 3
 gi|83767537|dbj|BAE57676.1| unnamed protein product [Aspergillus oryzae]
          Length = 730

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 50/282 (17%), Positives = 92/282 (32%), Gaps = 58/282 (20%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKP------------- 49
           +  +R     L      Y+EM ++  ++   RG+   +    T+  P             
Sbjct: 331 NLPFRRLCIEL-GAQFTYSEMALSMPLIQGQRGEWALMRAHETEMLPPTISPGADVVQGY 389

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI      + ++A +++  +      I+LN GCP   +     G+ L+ +
Sbjct: 390 DHSKDFRFGAQIAANKHWQALKATEVLSAYTPNLRVIDLNCGCPIDLLFREGAGSALLEH 449

Query: 101 PDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAV---ALRNLVKSIKKS-------GVN 149
           P  +   +  M      IP+T K R+G  D  P     A R ++   + S       GV 
Sbjct: 450 PSKLERILRGMNAVSQEIPITAKIRMGTRDNSPNALKLAERLILGGYESSTLGLGAPGVA 509

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---------PDL---------FI 191
            + +H R    +     D   I      ++  + ++          PD          + 
Sbjct: 510 ALTLHGRSRQQRYTRQADWGYISECA-ALIKRLNEKTDQVTDTVREPDPRTQPNGGKTWF 568

Query: 192 GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             NG           +    VD VM+GR A     +   +  
Sbjct: 569 LGNGDCYSHLDYDDHVNNAGVDTVMVGRGALIKPWLFEEIQA 610


>gi|255941804|ref|XP_002561671.1| Pc16g13720 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211586294|emb|CAP94042.1| Pc16g13720 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 729

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/292 (18%), Positives = 88/292 (30%), Gaps = 62/292 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEK--------------- 48
           +  +R     L      Y+EM ++  +++G K    +L     E                
Sbjct: 332 NMPFRRLCADL-GAQFTYSEMAMSMPLIQGSKSEWTLLKAHESEMAPPTVIPGDNIVQGY 390

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI      + ++A +++  F      I+LN GCP   V     G+ L+ +
Sbjct: 391 DNSKDCRFGAQIAANKPWQALKATEVLSKFTPNLRVIDLNCGCPIELVFRDGAGSALLDH 450

Query: 101 PDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG------------ 147
              +   I  M      IP+TVK R+G  D  P      LV+ +   G            
Sbjct: 451 HSKLEKMIRGMNTVSQEIPITVKIRMGTKDNQPTAQ--KLVERMVLGGYESSVLDLGPPG 508

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-------------LDYDIVYEIKKEN----PDLF 190
              I +H R    +     D   I +                D + E    +       +
Sbjct: 509 AAAITLHGRSRQQRYTRQADWGYISDCAALIKRLNKKQDALSDTIREPDARHMPNGGKTY 568

Query: 191 IGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD--EYFSNPLT 238
              NG           +    VD VM+ R A     +   +   +Y     T
Sbjct: 569 FIGNGDCYSHVDYDDHVNNAGVDSVMVARGALIKPWIFEEIQTGQYLDKSAT 620


>gi|317027955|ref|XP_001400331.2| tRNA dihydrouridine synthase (Smm1) [Aspergillus niger CBS 513.88]
          Length = 454

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 80/184 (43%), Gaps = 17/184 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 113 LIYQIGTATPEIAVQAAKLVAG-DVAGIDVNSGCPKPFSTSGGMGAALLKTPDKLVAILE 171

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +  P    ++VK RI  D +      R LV  + K+G+ G+ +H R   ++    
Sbjct: 172 ALVKEVGTPFQIGISVKIRILKDPE----ETRALVSRLVKTGITGLTVHCRTPPMRPRER 227

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               ++      ++ +I  E   +   +NG +    +   ++    VDG MI  AA  N 
Sbjct: 228 AIRDQV-----RMIADICHEAG-VACVINGDVTSKDEGHALMKEFGVDGAMIATAAEANP 281

Query: 224 AMLT 227
           +   
Sbjct: 282 SCFR 285


>gi|121701031|ref|XP_001268780.1| tRNA dihydrouridine synthase, putative [Aspergillus clavatus NRRL
           1]
 gi|187471045|sp|A1CNY3|DUS3_ASPCL RecName: Full=tRNA-dihydrouridine synthase 3
 gi|119396923|gb|EAW07354.1| tRNA dihydrouridine synthase, putative [Aspergillus clavatus NRRL
           1]
          Length = 728

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 51/290 (17%), Positives = 90/290 (31%), Gaps = 76/290 (26%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-------------- 49
           +  +R     L      Y+EM +  ++++G K    ++     E                
Sbjct: 331 NLPFRRLCTDL-GAQFTYSEMAMGMSLIQGQKSEWALMKAHETEAIPPTISSGANIVQGY 389

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                     QI        ++A +++     +   I+LN GCP  +V+    G+ L+ +
Sbjct: 390 DNSQDLKFGAQIAANKPWHAIKATELLGRLTPHLRVIDLNCGCPIDQVYRDGAGSALLDH 449

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKS------------G 147
              +   +  M      IP+TVK R G  D  P      L++ +               G
Sbjct: 450 QSKLEKILRGMNAVSEAIPITVKIRTGTRDASPNA--LKLIERLTLGGHESSMLNIGPPG 507

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE----IKKEN----------------- 186
           V  I +H R         +  R     D+  + E    IK+ N                 
Sbjct: 508 VAAITLHGRT--------RQQRYTKQADWSYIAECAALIKRLNEKTDEVTDTVREPDART 559

Query: 187 ----PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
                 ++   NG           +    VD VM+GR A     +   + 
Sbjct: 560 LPNGGKVYFLGNGDCYSHKDYEDHINNAGVDAVMVGRGAIIKPWVFEEIQ 609


>gi|238487170|ref|XP_002374823.1| tRNA dihydrouridine synthase, putative [Aspergillus flavus
           NRRL3357]
 gi|220699702|gb|EED56041.1| tRNA dihydrouridine synthase, putative [Aspergillus flavus
           NRRL3357]
          Length = 730

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 50/282 (17%), Positives = 92/282 (32%), Gaps = 58/282 (20%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKP------------- 49
           +  +R     L      Y+EM ++  ++   RG+   +    T+  P             
Sbjct: 331 NLPFRRLCIEL-GAQFTYSEMALSMPLIQGQRGEWALMRAHETEMLPPTISPGADVVQGY 389

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI      + ++A +++  +      I+LN GCP   +     G+ L+ +
Sbjct: 390 DHSKDFRFGAQIAANKHWQALKATEVLSAYTPNLRVIDLNCGCPIDLLFREGAGSALLEH 449

Query: 101 PDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAV---ALRNLVKSIKKS-------GVN 149
           P  +   +  M      IP+T K R+G  D  P     A R ++   + S       GV 
Sbjct: 450 PSKLERILRGMNAVSQEIPITAKIRMGTRDNSPNALKLAERLILGGYESSTLGLGAPGVA 509

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN---------PDL---------FI 191
            + +H R    +     D   I      ++  + ++          PD          + 
Sbjct: 510 ALTLHGRSRQQRYTRQADWGYISECA-ALIKRLNEKTDHVTDTVREPDPRTQPNGGKTWF 568

Query: 192 GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             NG           +    VD VM+GR A     +   +  
Sbjct: 569 LGNGDCYSHLDYDDHVNNAGVDTVMVGRGALIKPWLFEEIQA 610


>gi|167760575|ref|ZP_02432702.1| hypothetical protein CLOSCI_02949 [Clostridium scindens ATCC 35704]
 gi|167661796|gb|EDS05926.1| hypothetical protein CLOSCI_02949 [Clostridium scindens ATCC 35704]
          Length = 279

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 61/296 (20%), Positives = 110/296 (37%), Gaps = 26/296 (8%)

Query: 22  LYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
            +T  +V          +  +IL  + +   L  QI   D    ++  K +ED+GY E+N
Sbjct: 4   YFTPFLVPHTKRGFNTRELNDILPENNEGMRLVPQILTNDAKGFLQTVKKLEDYGYEEVN 63

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCPS  V   + G+  +  PD +   +  +     + +++K RIG   +        
Sbjct: 64  LNLGCPSKTVVSKNRGSGFLAMPDELDRFLDEIYSGTQVRISIKTRIG---KHSPDEFGR 120

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L++   +  V  + IH R            +  PNL+       +  NP  + G    + 
Sbjct: 121 LLEIYNQYPVEELIIHPRLQQDFY------KNTPNLEVFAEAVRESRNPLCYNGDIFSVT 174

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
           D  +  +  P V   M+GR    N  +        +  L G  P      + F  +I   
Sbjct: 175 DRDRIKERFPEVKTYMMGRGILVNPGL--------AGELAGEEPADWDRIRRFHDQIYED 226

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-RRCRHILTVE--AGASTATHHII 311
               +    +   K++++      L H FP   ++ + I   E       A   I+
Sbjct: 227 YQRISMGDKNVLFKMKELW---CYLGHHFPGCEKQLKKIRKAERLDRYEAAVAEIL 279


>gi|159489528|ref|XP_001702749.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158280771|gb|EDP06528.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 198

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 73/211 (34%), Gaps = 27/211 (12%)

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            +++N GCP         G+ ++  P  +   +A +     +PVTVK R+G  +    + 
Sbjct: 1   FLDINCGCPIYEATRRGMGSAMLRKPRALAKMVAGIAADSELPVTVKIRLG--ENDKKIV 58

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  +V  + ++G   + +H R A        + R     D+  V E+ +  P + I  NG
Sbjct: 59  VDTVVDYLHRAGAAAVTVHGRTA--------EQRYKKAADWAKVGEVARSTP-VPIIGNG 109

Query: 196 GLEDM--SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            +     + A +       VM GR A     +     E      +    +          
Sbjct: 110 DILTHYEAHARRTESGCTAVMAGRGALIKPWIFQEYKEGREWLPSTEERVG--------- 160

Query: 254 KISASMTDYAARHLHSGGKLQQITRHMIGLF 284
            +   +  Y   H     + +   +     F
Sbjct: 161 -VYRLLVSYMKEHFGDDERGR--RK--AWYF 186


>gi|225026778|ref|ZP_03715970.1| hypothetical protein EUBHAL_01030 [Eubacterium hallii DSM 3353]
 gi|224955897|gb|EEG37106.1| hypothetical protein EUBHAL_01030 [Eubacterium hallii DSM 3353]
          Length = 329

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/280 (18%), Positives = 108/280 (38%), Gaps = 24/280 (8%)

Query: 16  LTNNALLYTEMIVADA---ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
                  +T  +       +   +K +I     +  P+  QI     +  ++ A ++E+ 
Sbjct: 30  FQGVDKYFTPFVTPKPKKGLNTREKNDIAPEHNKNIPVVPQILTNKAADFIKVAGMMEEL 89

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           GY E+NLN+GCPS  V     G+  + + + +      +   ++I V+VK R+GV++   
Sbjct: 90  GYKEVNLNLGCPSGTVVSKKKGSGFLADLEGMKYFFDEVFSQVNIEVSVKTRLGVENPDE 149

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            +   +L+       ++ + +HAR        P +                       + 
Sbjct: 150 VI---DLMNIYNAFPISEVIVHARVREDYYKRPVNQEAFAQ---------CLAISKHPVC 197

Query: 193 LNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
            NG    ++D+       P +  VM+GR    N  +        ++  + S   +  +D 
Sbjct: 198 YNGDLFTVQDIENLTAKFPDIKAVMLGRGMIANPQLTEVFCGREAHGDSTSVENRQGLDY 257

Query: 250 DFWRKISASMTDYAARHLHSGGK-----LQQITRHMIGLF 284
             W+     +  Y   H+ SGG+     L+++  +MI  F
Sbjct: 258 VRWKAFLDELC-YGYEHIMSGGRNVLFKLKEVWSYMITFF 296


>gi|126640847|ref|YP_001083831.1| hypothetical protein A1S_0789 [Acinetobacter baumannii ATCC 17978]
          Length = 239

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 44/181 (24%), Positives = 76/181 (41%), Gaps = 16/181 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
            L   A  V + G   I+LN GCP+  V+    G+ L+  PD+V   I A+  A+   IP
Sbjct: 1   MLAANAAKVVELGAPAIDLNFGCPAKTVNRHRGGSVLLDEPDVVHMLIKAVRDAVPAHIP 60

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+ K R+G  D+           +++ +G + + +HAR         K +   P   ++ 
Sbjct: 61  VSAKMRLGYLDENH---TMENAYAVEDAGASWLTVHART--------KADGYTPPAYWEK 109

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  IK E   + +  NG +   + A         + +MIGR A     +   + +     
Sbjct: 110 ILPIK-EALKINVIANGEIWTNADARACQQQSGCEDLMIGRGAVTTPDLTQCIRQNMDEA 168

Query: 237 L 237
           L
Sbjct: 169 L 169


>gi|302670253|ref|YP_003830213.1| tRNA dihydrouridine synthase A DusA1 [Butyrivibrio proteoclasticus
           B316]
 gi|302394726|gb|ADL33631.1| tRNA dihydrouridine synthase A DusA1 [Butyrivibrio proteoclasticus
           B316]
          Length = 343

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 60/293 (20%), Positives = 106/293 (36%), Gaps = 33/293 (11%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKN--------ILGFSTQEKPLA 51
           M   T    R     +       YT  + A   +   K+         I GF      + 
Sbjct: 24  MEGITLYPLRNVHHEIFGGIDKYYTPFLTAHHNMHFKKREKRDVMPEFIKGFEDYGNEIV 83

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            QI    +   V AAK + + GYNE+NLN+GCP+A V     G+ L+ + + +   +  +
Sbjct: 84  PQIMSNRVDTFVWAAKEMWNLGYNEVNLNLGCPAATVTNSHKGSGLLTDTEYLDSMLDGI 143

Query: 112 CKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            + L +  +++K R+G  D+  A  L  +     K  ++ + IHAR              
Sbjct: 144 FEDLGNKSISIKTRLGFSDESEADRLMEI---YAKYPISELTIHARVREDFYKGEPRIDA 200

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--------SVDGVMIGRAAYKN 222
                   V   +       I  NG +  +    KI          S   VMIGR    N
Sbjct: 201 FKRA----VEVYRNAGGKADIVYNGDINSIDDLKKIESFDSIGSSISCTSVMIGRGLLSN 256

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
            A+           L G  P++    +++ +++    + +     +   K+ +
Sbjct: 257 PALARQ--------LQGGKPLEAGELREYLKRLYEEYSLFIPEDRNVIFKMLE 301


>gi|123475588|ref|XP_001320971.1| dihydrouridine synthase [Trichomonas vaginalis G3]
 gi|121903787|gb|EAY08748.1| dihydrouridine synthase, putative [Trichomonas vaginalis G3]
          Length = 318

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 101/237 (42%), Gaps = 22/237 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           M + +D  +R   R      + +T M+ A    +G   +        ++ PL  QI G++
Sbjct: 25  MAEISDLSWRMLIRN-HGVKVCWTGMLNAHQWSQGSGYQNKFFNTCPEDHPLIAQIAGSN 83

Query: 59  ISK--LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---LNPDIVGDCIAAMCK 113
             +  +V AAK +  +  + +++N+GC         +G  ++      +   +    +CK
Sbjct: 84  EDQDLIVAAAKDLAKY-ADGVDVNLGCTQKIASRSEYGYFMVDNCQKREKTLELFRRLCK 142

Query: 114 ALSIPVTVKCRIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            ++ P+  K RI +DD  ++      +  K ++++GV+ + +H R             K 
Sbjct: 143 EVNCPICAKIRIFIDDSGEVSEKITIDFAKKLEEAGVSLLQVHGRAE--------HRNKQ 194

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++  +I+  I +   ++ +  NGG+  +  A K +      GV + +A  K+    
Sbjct: 195 ADVYNEIIKHIVQAV-NIPVVANGGINTVEDAHKFMEETGAAGVSVAQALLKDPTAF 250


>gi|330999429|ref|ZP_08323143.1| dihydrouridine synthase [Parasutterella excrementihominis YIT
           11859]
 gi|329574855|gb|EGG56414.1| dihydrouridine synthase [Parasutterella excrementihominis YIT
           11859]
          Length = 325

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 59/322 (18%), Positives = 113/322 (35%), Gaps = 31/322 (9%)

Query: 1   MVDWTDRHYRFFARLL-TNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   +R           L Y   I             K +        P+  Q+  
Sbjct: 11  MEGLTTAVFRRLHHQYFGGTDLYYIPFITPTVEPKFTDRHLKELSPEVNAGIPVVPQLLS 70

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-L 115
              +  + AAK ++D GY E+NLN+GCPS  V     G+  + +   +   +  +  A +
Sbjct: 71  NRSADFIWAAKALQDLGYKEVNLNLGCPSGTVVAKGKGSGFLRDLYALERFLDEIFSAGI 130

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            IP+++K R+G           +++   KK  ++ + +H R         K ++    + 
Sbjct: 131 DIPISIKTRLGW---ANTEEFGDILNLYKKYPLSLLIVHMRL--------KTDQYKGEVR 179

Query: 176 YDIVYEIKKENPDLFIGLNGG-LEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEY 232
            + + E   E P   +G+NG  +             D   +M+GRA   + A+       
Sbjct: 180 KEALLEHLDEIP-FPLGVNGDMITTADMIDFSKTFRDPKMLMVGRALMADPALFRKYK-- 236

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRR 292
                 G         K+F   +  + T+      ++  ++++       LF   P  + 
Sbjct: 237 ------GGPAASLEEIKNFTTALFDAYTEAFQNRRNAMMRMKEFWFFQANLFEENP--KA 288

Query: 293 CRHILTVEAGAS-TATHHIIET 313
            ++I   +      A    IE 
Sbjct: 289 FKNIFKSKTEEDFLAAIEEIEA 310


>gi|189196893|ref|XP_001934784.1| tRNA-dihydrouridine synthase B [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187980732|gb|EDU47358.1| tRNA-dihydrouridine synthase B [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 643

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 51/282 (18%), Positives = 95/282 (33%), Gaps = 58/282 (20%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-------------- 49
           +  YR          + ++EM +   +++GDK    ++     E                
Sbjct: 272 NMPYRRLCVDF-GCQVTWSEMAMGMPLIQGDKGEWPLMKAHESEISPPKFLGKNTVVQGY 330

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI         +  +++ ++      I+LN GCP   V E   G+ L+ +
Sbjct: 331 DNSKDLKFGAQIAANKPWLATKTVEVLTEYCPKLRAIDLNCGCPINLVCEKGSGSALLDS 390

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA--LRNLV----KSIKK----SGVN 149
              +   +  M      +P+TVK R+G  D  P     ++ LV    ++++     SGV 
Sbjct: 391 EAKLEHILRGMSYVSKEVPITVKIRMGTKDNHPTAQKLIKRLVLGGHEAVESGKGTSGVA 450

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN------------------PDLFI 191
            I +H R    +     D   I      ++  ++KE                     ++ 
Sbjct: 451 AITLHGRSKQQRYSRSADWSYIAECS-ALISRLRKEQAAATDTAAEIDPRDLANGGHVYF 509

Query: 192 GLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             NG           L    VD VM+GR A     +   +++
Sbjct: 510 VGNGDCYSHEDYYTHLANAGVDTVMVGRGALIKPWLFEEIEK 551


>gi|315042544|ref|XP_003170648.1| hypothetical protein MGYG_06634 [Arthroderma gypseum CBS 118893]
 gi|311344437|gb|EFR03640.1| hypothetical protein MGYG_06634 [Arthroderma gypseum CBS 118893]
          Length = 420

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 106/246 (43%), Gaps = 38/246 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 116 LIFQLGTASPDLAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 174

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ IH R   ++    
Sbjct: 175 ALVREVGQPWQIGISVKIRLLKDPKDT----ERLVTALCATGITGLTIHCRTTPMRPREA 230

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    + + +NG ++    AL+++    VDG MI  +A  N 
Sbjct: 231 AIRDQLP-----MIAAICRSAG-VAVLMNGDVKSRDHALELMSQYDVDGAMIATSAESNF 284

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +   +  +    PL+             WR+++      A    +  G     T++++ +
Sbjct: 285 SCFRSAAD--GGPLS-------------WRELAHEYISVAMECENKWGN----TKYLLNI 325

Query: 284 FHGFPN 289
           F   P 
Sbjct: 326 F--LPG 329


>gi|123469809|ref|XP_001318114.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121900865|gb|EAY05891.1| hypothetical protein TVAG_353310 [Trichomonas vaginalis G3]
          Length = 321

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 97/235 (41%), Gaps = 20/235 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV+  D  +R          + +T MI      R        + +S +++PL +QI G+ 
Sbjct: 20  MVEMGDIAFRILCHR-HGCDVCWTGMINGSQWNRSKTYRQQQIEYSEEDRPLVIQISGSI 78

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---LNPDIVGDCIAAMCKAL 115
              L+  AK + +FG   I++N+GC       G +G  ++        V + I ++   +
Sbjct: 79  DVDLLTTAKSMSEFGV-PIDINLGCCQKVAKRGEYGYFMVDSEQKRQNVVNLIKSIPSEI 137

Query: 116 SIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           ++P+ VK R   D+          +  K ++++G + I IH R A           K   
Sbjct: 138 TVPLYVKIRALTDESGIPSIPITVDFAKHLEEAGASLITIHGRSA--------AQDKHGP 189

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           L+ ++V  + +    + + +NGG+  +  A  ++        M  ++   +  + 
Sbjct: 190 LNKELVKAVVQAV-SIPVIVNGGINSLDDARNMIRETGAIAAMSAQSLLMDPTLF 243


>gi|121705192|ref|XP_001270859.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus clavatus
           NRRL 1]
 gi|119399005|gb|EAW09433.1| tRNA dihydrouridine synthase (Smm1), putative [Aspergillus clavatus
           NRRL 1]
          Length = 444

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 51/210 (24%), Positives = 87/210 (41%), Gaps = 16/210 (7%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     VEAAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LVFQIGTASPELAVEAAKLVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILE 163

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +           LV+ +  +G+ G+ +H R   ++   P++  
Sbjct: 164 SLVREVGNPFQIGISVKIRILETPEKTEALVRRLVATGITGLTVHCRTTPMR---PRERA 220

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
               L   +V  I ++   +   +NG +    +AL ++    VDG MI  AA  N +   
Sbjct: 221 IRDQLR--MVASICRDAG-VACVMNGDVTSRDEALALMKEFEVDGAMIATAAESNPSCFR 277

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
                 S    G  P +  V +D+ R    
Sbjct: 278 ------SEAEGGLLPWR-EVVRDYLRACIE 300


>gi|253742273|gb|EES99116.1| tRNA-dihydrouridine synthase [Giardia intestinalis ATCC 50581]
          Length = 409

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 95/230 (41%), Gaps = 30/230 (13%)

Query: 23  YTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVED--FGYNEI- 77
           +T+M  ADA+L     +  +L  +   + + LQ+ G + S  + AAK++         I 
Sbjct: 86  FTQMYTADALLHNSLLRDTVLSAAAPGENIILQLCGNNPSNFLAAAKVLSSSSLAPQIIA 145

Query: 78  -NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
            ++N+GCP++      +G  +  N  +V   ++ +  A   PVT K R            
Sbjct: 146 LDVNLGCPASCASSRGYGLYIAQNWPLVHQILSEVSSAQLFPVTCKIRPL----GTIEET 201

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE----------- 185
            + +  +  SG +GI IH R    +G   +  +       +IVY  ++            
Sbjct: 202 VDYMLLLALSGASGITIHMRHTTRQGKHAQSVKPAYLEFEEIVYAFRRRLDVFLDSIGKR 261

Query: 186 -------NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
                  N    I LNGG++   +A  +L S   DG+MIG    K+   L
Sbjct: 262 KPTKREPNLYPVIILNGGVKSRQEADDLLSSYPADGIMIGVGLLKDPTCL 311


>gi|319954975|ref|YP_004166242.1| tRNA-u20a,u20b-dihydrouridine synthase [Cellulophaga algicola DSM
           14237]
 gi|319423635|gb|ADV50744.1| tRNA-U20a,U20b-dihydrouridine synthase [Cellulophaga algicola DSM
           14237]
          Length = 342

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 53/266 (19%), Positives = 99/266 (37%), Gaps = 23/266 (8%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVADA--ILRGDKKNILGFSTQEK-PLALQIGGAD 58
            +TD  +R  F          Y   I  D   +++   +  L         L  Q+   D
Sbjct: 36  GFTDFRFRNAFHHFFGGIDTFYAPYIRLDGKLVIKSSYQRDLQLENNAALNLIPQVMTND 95

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + +   K ++D GY E+N N+GCP   V +   G+ L+   D +   +  +    ++ 
Sbjct: 96  ADEFLFVVKYIQDLGYTELNWNLGCPYPMVTKRGMGSGLVKEADKIDHILDRVHAETNVT 155

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDY 176
           V++K R+G +D      + +    ++K  +  I IHAR  K + KG           +D 
Sbjct: 156 VSMKMRMGYEDSS---EILDTFPVLEKYPIKNIAIHARIGKQLYKGG----------VDL 202

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           D      +      +  NG +  +    K+    PS+D  MIGR    +  + + +    
Sbjct: 203 DAFQRCVESTSH-KLYYNGDITTVDAFKKMQERFPSIDHWMIGRGLIADPFLPSMIKANT 261

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASM 259
                    I +      ++   A +
Sbjct: 262 FEYPENRWAIFSEFHDTIYQDYDAFL 287


>gi|312217914|emb|CBX97861.1| similar to tRNA-dihydrouridine synthase 3 [Leptosphaeria maculans]
          Length = 725

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 53/293 (18%), Positives = 92/293 (31%), Gaps = 64/293 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQE---------------- 47
           +  YR     L    + ++EM +   +++G++    ++     E                
Sbjct: 326 NMPYRRLCVDL-GCQVTWSEMAMGMPLIQGERGEWALMKAHESEITPPAFQSKNKVVQGY 384

Query: 48  -----KPLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI         +  +++ D       I+LN GCP   V E   G+ L+  
Sbjct: 385 DNSTDMKFGAQIAANKPWLATKTVEVLTDHCPKLRAIDLNCGCPINLVCEKGAGSALLDQ 444

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK------------KSG 147
              +   +  M      +P+TVK R+G  D  P      L+K +               G
Sbjct: 445 EAKLEQILRGMNYVSKEVPITVKIRMGTKDNQPTAQ--KLIKRLVLGGRESIETGKGTCG 502

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN------------------PDL 189
           +  I +H R    +     D   I      ++  +KKE                     +
Sbjct: 503 IAAITLHGRSKQQRYSRSADWSYIAECA-SLITRLKKERDAQIDTLAEPDARDQPNGGTV 561

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV--DEYFSNPLT 238
           +   NG     +     L    VD VMIGR A     +   +  ++Y     T
Sbjct: 562 YFVGNGDCYSHTDYYNALDSAHVDSVMIGRGALIKPWIFEEITTNQYLDKSAT 614


>gi|295102082|emb|CBK99627.1| tRNA-dihydrouridine synthase [Faecalibacterium prausnitzii L2-6]
          Length = 313

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/323 (17%), Positives = 103/323 (31%), Gaps = 39/323 (12%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQ 53
           M   TDR +R   +         A  Y   I       +++     +   +    P+  Q
Sbjct: 8   MEGLTDRIWRQAHQRWFGAPGAPARYYAPFISPPENRVLIKKKMAELDPAANPGAPVIPQ 67

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   D +        +   GY E+NLN GCPS  V     GA ++ +   +   +  +  
Sbjct: 68  LLAKDGALAAWMIGELRKMGYTEVNLNFGCPSGTVTAKGKGAGMLRDLSKLEVFLDEVFS 127

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
               P++VK R+GV       A+ +L        +  + +H R          D      
Sbjct: 128 QAEGPISVKTRLGVTSPEEFEAILDLYDRF---PICELTVHPRVMRQLYRGEADR----- 179

Query: 174 LDYDIVYEIKKENPDL--FIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTT 228
                     K  P     +  NG +   +Q   +    P++ G+M+GR    + A+L  
Sbjct: 180 ------AAFAKYLPHCRMPVCYNGDITTPAQLKALEAEFPNLSGIMVGRGIIADPALLRQ 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                     G +P      + +  ++      Y      +   + ++  H   L   F 
Sbjct: 234 A--------VGGAPASKEELRGYLDEL---YHGYTGAFGMASCAVSRMKAHWHYLIQRFE 282

Query: 289 NSRRCRHILTVEAGASTATHHII 311
            S      L          + ++
Sbjct: 283 GSEAFEKQL--RKAREGWEYEVV 303


>gi|294940939|ref|XP_002782932.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
 gi|239895114|gb|EER14728.1| Dus1p, putative [Perkinsus marinus ATCC 50983]
          Length = 413

 Score =  125 bits (315), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 57/298 (19%), Positives = 105/298 (35%), Gaps = 53/298 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----------------RGDKKNILGF 43
           MV       R          L+Y+E I+   I                  + D   +   
Sbjct: 27  MVRACTLPLRRLTANY-GADLVYSEEIIDQKIYSSKRVWDPYFNTWDYISQRDNSLVFQT 85

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           + +EKP L  Q+G        +AA +         ++N+GCP +   +G  G+ L+  P+
Sbjct: 86  AEEEKPKLIFQMGTNSGPGAQKAA-MALLQDVAGFDVNMGCPKSFSIKGGMGSALLKKPE 144

Query: 103 IVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALR--------NLVKSIKKSGVNGIW 152
           +  D +  + + +   +PVT K R+  D Q P               +K    +G   + 
Sbjct: 145 VAVDILKTLRRTVPETMPVTCKVRLICDTQQPTEEELQDATKRTSEFIKGCSDAGACAVA 204

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-----QALKIL 207
           +H R   ++  +P          +    ++++  PD+ +  NG   D       +AL   
Sbjct: 205 LHTRTIPMRPRNP--------AIWPTFAQVQRLCPDVLLIPNGDFFDRKAIEAFRALMDQ 256

Query: 208 PSV---DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
             V   +  MI R    N  M            +   P K +V +++ R  +   + Y
Sbjct: 257 TGVPWSNSFMIARGGLYNPQMFD------KTGASMLLP-KRQVLQEYMRLATQYGSPY 307


>gi|302876216|ref|YP_003844849.1| dihydrouridine synthase DuS [Clostridium cellulovorans 743B]
 gi|307686948|ref|ZP_07629394.1| dihydrouridine synthase DuS [Clostridium cellulovorans 743B]
 gi|302579073|gb|ADL53085.1| dihydrouridine synthase DuS [Clostridium cellulovorans 743B]
          Length = 321

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 102/253 (40%), Gaps = 29/253 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
            +IL    +   +  QI   +    +   K +  FGY EINLN+GCP+  V   + G+  
Sbjct: 49  NDILPEHNEGLNVVPQILTNNSEYFIHTMKDLMKFGYKEINLNLGCPAGTVVAKNKGSGF 108

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   + +   +  +       +++K RIG D          L++   K  +  + IH R 
Sbjct: 109 LAQREQLDQFLEEIFLKAETKISIKTRIGKD---SPGEFYKLIEIFNKYPLEELIIHPRI 165

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDL---FIGLNGGL---EDMSQALKILPSVD 211
                         PN+D      + K+   L    I  NG +   +D ++ ++  P++D
Sbjct: 166 QKDLYN------NKPNMD------VFKDAVSLSKNPICYNGDIFNAKDYTELIETYPNLD 213

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            VM+GR    N A++  +    S           +V K+F  K+  S  +  +   +   
Sbjct: 214 AVMLGRGLIANPALIGEIKNNNSAD--------KKVMKEFHDKVYNSYQEILSGERNVLF 265

Query: 272 KLQQITRHMIGLF 284
           K+ +   +MI LF
Sbjct: 266 KMMEFWFYMIHLF 278


>gi|240281112|gb|EER44615.1| tRNA dihydrouridine synthase [Ajellomyces capsulatus H143]
          Length = 495

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 58/268 (21%), Positives = 102/268 (38%), Gaps = 39/268 (14%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
            + A        +       K L  QIG A     V+AAKI+       I++N GCP   
Sbjct: 101 NSQAAKESIIYRLDPRRESGK-LVFQIGTASPDLAVQAAKIIAA-DVAGIDVNAGCPKPF 158

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSI 143
              G  GA L+  PD +   + A+ + +  P    ++VK R+  D +      R+LV  +
Sbjct: 159 STTGGMGAALLQTPDRLVSILTALVQQVGTPYQIGISVKIRLLADPERT----RDLVTRL 214

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
             +G+ G+ +H R   ++        ++P     ++  I +    + I +NG +E     
Sbjct: 215 CATGITGLTVHCRTTPMRPRERAIRDQLP-----MIASICRAAG-VAILVNGDVESRDHG 268

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           L ++    VDG MI   A  NS+   +  +                    WR I     D
Sbjct: 269 LALMAEYGVDGAMIATCAEANSSCFRSAAD---------------GSLLPWRAIVRDYMD 313

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPN 289
              +  +  G     T++++ +    P 
Sbjct: 314 LCLQCENKWGN----TKYLLNML--IPG 335


>gi|291562170|emb|CBL40986.1| tRNA-dihydrouridine synthase [butyrate-producing bacterium SS3/4]
          Length = 385

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 96/241 (39%), Gaps = 24/241 (9%)

Query: 2   VDWTDRHYRFFA-RLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGA 57
              T   YR    +        +T  +       +   + +++L  +    P+  QI   
Sbjct: 42  EGITTYPYRNLHHKYFGGVDKYFTPFLAPGPEQGMSVKEMRDVLPENNAGVPVVPQILTN 101

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
                + A+K + + GY EINLN+GCPS  V     G+  +L PD +      +    S+
Sbjct: 102 RAGDFLLASKKLAEMGYREINLNLGCPSGTVTAKKKGSGFLLYPDDLDRFFDEVFSDASV 161

Query: 118 P-----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
                 ++VK RIG ++         ++    +  ++ + +H R              +P
Sbjct: 162 RNGEFQISVKTRIGKNE---VEEWPEIMAIYNRYPISELTVHPRIQKEFYKG------VP 212

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTV 229
           +LD  +  +I KE+ +  I  NG L          +  P+V+ VMIGR   +N A+   +
Sbjct: 213 HLD--VFADILKESRN-PIVYNGDLFTAEHMKKFREKFPTVENVMIGRGLIRNPALAELI 269

Query: 230 D 230
            
Sbjct: 270 K 270


>gi|154279318|ref|XP_001540472.1| hypothetical protein HCAG_04312 [Ajellomyces capsulatus NAm1]
 gi|150412415|gb|EDN07802.1| hypothetical protein HCAG_04312 [Ajellomyces capsulatus NAm1]
          Length = 461

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 100/256 (39%), Gaps = 38/256 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L    +   L  QIG A     V+AAKI+       I++N GCP      G  GA L+ 
Sbjct: 78  RLDPHRESGKLVFQIGTASPDLAVQAAKIIAA-DVAGIDVNAGCPKPFSTTGGMGAALLQ 136

Query: 100 NPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            PD +   + A+ + +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H 
Sbjct: 137 TPDRLVSILTALVQQVGTPYQIGISVKIRLLADPERT----RDLVTRLCATGITGLTVHC 192

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
           R   ++        ++P     ++  I +    + I +NG +E     L ++    VDG 
Sbjct: 193 RTTPMRPRERAIRDQLP-----MIASICRAAG-VAILVNGDVESRDHGLALMAEYGVDGA 246

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MI   A  NS+   +  +                    WR I     D   +  +  G  
Sbjct: 247 MIATCAEANSSCFRSAAD---------------GSLLPWRAIVRDYMDLCLQCENKWGN- 290

Query: 274 QQITRHMIGLFHGFPN 289
              T++++ +    P 
Sbjct: 291 ---TKYLLNML--IPG 301


>gi|325092392|gb|EGC45702.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus H88]
          Length = 495

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 58/268 (21%), Positives = 102/268 (38%), Gaps = 39/268 (14%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
            + A        +       K L  QIG A     V+AAKI+       I++N GCP   
Sbjct: 101 NSQAAKESIIYRLDPRRESGK-LVFQIGTASPDLAVQAAKIIAA-DVAGIDVNAGCPKPF 158

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSI 143
              G  GA L+  PD +   + A+ + +  P    ++VK R+  D +      R+LV  +
Sbjct: 159 STTGGMGAALLQTPDRLVSILTALVQQVGTPYQIGISVKIRLLADPERT----RDLVTRL 214

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
             +G+ G+ +H R   ++        ++P     ++  I +    + I +NG +E     
Sbjct: 215 CATGITGLTVHCRTTPMRPRERAIRDQLP-----MIASICRAAG-VAILVNGDVESRDHG 268

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
           L ++    VDG MI   A  NS+   +  +                    WR I     D
Sbjct: 269 LALMAEYGVDGAMIATCAEANSSCFRSAAD---------------GSLLPWRAIVRDYMD 313

Query: 262 YAARHLHSGGKLQQITRHMIGLFHGFPN 289
              +  +  G     T++++ +    P 
Sbjct: 314 LCLQCENKWGN----TKYLLNML--IPG 335


>gi|153855570|ref|ZP_01996686.1| hypothetical protein DORLON_02704 [Dorea longicatena DSM 13814]
 gi|149751991|gb|EDM61922.1| hypothetical protein DORLON_02704 [Dorea longicatena DSM 13814]
          Length = 288

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 53/269 (19%), Positives = 105/269 (39%), Gaps = 25/269 (9%)

Query: 22  LYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
            +T  +V          +K +IL        L  QI   D    ++  + ++ +GY+E+N
Sbjct: 4   YFTPFLVPHTKKDFNTREKNDILPAHNPGMNLVPQILTNDAKGFLDTVEKLKGYGYDEVN 63

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCPS  V     G+  +++ + +   +  +     + +++K RIG  D   A     
Sbjct: 64  LNLGCPSKTVVSKGRGSGFLIHTEELNWFLDEIYAKADVKISIKTRIGKFD---ADEWGE 120

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL- 197
           L++   +  +  + +H R                + D D   +  KE     +  NG + 
Sbjct: 121 LLRIYNQYPLEELIVHPRVQ--------QQFYKGHPDLDAFADAVKECKHT-LCYNGDIF 171

Query: 198 --EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             EDM +  K  P    +M+GR   +N        E      +G   I  +  + F  +I
Sbjct: 172 TTEDMEKLKKRFPEASCIMLGRGILRNP-------ELIEIMESGEKKIDAKKLRAFHDQI 224

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLF 284
                + +    +   K++++  ++  LF
Sbjct: 225 YQDYQEVSCGDKNVLFKMKELWCYLGTLF 253


>gi|224023532|ref|ZP_03641898.1| hypothetical protein BACCOPRO_00234 [Bacteroides coprophilus DSM
           18228]
 gi|224016754|gb|EEF74766.1| hypothetical protein BACCOPRO_00234 [Bacteroides coprophilus DSM
           18228]
          Length = 308

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/326 (19%), Positives = 123/326 (37%), Gaps = 34/326 (10%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMI-VADAILRGDKKN-ILGFSTQEKPLALQIGGADI 59
            +T+  +R   A++       YT  + +    +R   K  +L        L  QI  A+ 
Sbjct: 11  GFTELAWRNAHAQVFGGIDAYYTPFVRLEKGEIRNKDKRELLPAGNTVSRLIPQIIAAEP 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +     + +  +GY EI+LN+GCP   +     G+ ++  PD V   +  M     I  
Sbjct: 71  DEFRMLVEQISGWGYREIDLNMGCPFPLIVNRRKGSGILPFPDKVAALLHEMETFPEIRF 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    A   R ++  + +S V  I +H R    +     D R+     Y+  
Sbjct: 131 SVKMRLGWER---ADEWREILPLLNESCVRQITLHPRIGRQQYKGTVD-REAFTAFYESC 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                    L +  NG L    +  ++L   P ++G+M+GR    N A+     +     
Sbjct: 187 R--------LPLVYNGDLRTQEEMQELLLAYPRLEGLMLGRGLLANPALAAGFRQ----- 233

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
             G++   + + +   +       +YA        ++ Q  + M       P+       
Sbjct: 234 --GNTLPVSELYRKIGQMHQLIYAEYARTLEGGEAQILQKLKPMWEYC--LPD------- 282

Query: 297 LTVEAGASTATHHIIETAFNLMIESL 322
           L  +A  +    + ++     + E+L
Sbjct: 283 LDKKARKAILKSNKLDAYLRAVREAL 308


>gi|332653747|ref|ZP_08419491.1| dihydrouridine synthase family protein [Ruminococcaceae bacterium
           D16]
 gi|332516833|gb|EGJ46438.1| dihydrouridine synthase family protein [Ruminococcaceae bacterium
           D16]
          Length = 317

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 56/295 (18%), Positives = 108/295 (36%), Gaps = 29/295 (9%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP---LALQIGG 56
           M   T   +R    ++       Y   +          + + G   +  P   +  Q+  
Sbjct: 1   MEGVTGAEFRRAHHQVFGGVDAYYMPFLSPTQDHVFTPRELRGILPENNPGFRVVPQLLT 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            ++   + AA  +   GY+E+NLN+GCPS  V     GA L+   D + + +  +     
Sbjct: 61  RNVEDFLWAAGELAAMGYDEVNLNLGCPSGTVTAKGKGAGLLQRRDTLEELLEGIFAKTP 120

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K R+G +D    V    L++   +  V+ + IH R         + +     +  
Sbjct: 121 VKLSIKTRLGWED---PVEFGPLLELFSRYPVSLLIIHPRV--------RQDFYREKVRL 169

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAM-------- 225
           D   +  +  P   +  NGGL             P V+ VMIG+    + A+        
Sbjct: 170 DAFAQALEVYPG-PVCFNGGLVTPEDCKAFHARFPQVEHVMIGQGLLADPALTRKAKGGS 228

Query: 226 LTTVDE--YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
             TVDE   F + L  +       ++     +    +  +     S   L++I +
Sbjct: 229 AATVDELRAFHDLLYRTYLSLFSGERSTVFHMKELWSYLSRLFEDSARPLKKIRK 283


>gi|331083077|ref|ZP_08332194.1| hypothetical protein HMPREF0992_01118 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330405079|gb|EGG84616.1| hypothetical protein HMPREF0992_01118 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 314

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 54/291 (18%), Positives = 112/291 (38%), Gaps = 27/291 (9%)

Query: 1   MVDWTDRHYRFFARLLT-NNALLYTEMIV--ADAILR-GDKKNILGFSTQEKPLALQIGG 56
           M   T   YR             +T  +   +  ++   + ++IL  + +   L  QI  
Sbjct: 8   MEGITGYIYRQVHHQFFPGIDKYFTPFLTPGSKKLMTPKELRDILPDNNEGYHLVPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +  A+ + ++GY E+NLN+GCPS  V     G+  +  P  +   +  + + L 
Sbjct: 68  NQAQDFIRLAEELREYGYEEVNLNLGCPSGTVTAKKKGSGFLEFPAQLEKFLDEVFENLD 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + ++VK RIG D+         L++   +  +  + +H R       +     +      
Sbjct: 128 MKISVKTRIGKDE---PEEFTELLRIYNRFPLEELIVHPRIQSDYYKNEPRMEQFQ---- 180

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEYF 233
           + V     +N   +   NG L   ++  K       ++ VM+GR    N A++  V +  
Sbjct: 181 EAVR--CSQNSLCY---NGDLFTKARCEKFFEEYPSIEKVMLGRGLLVNPALVQQVQK-- 233

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                  + ++    K F  K+     +  +   +   K++++  +M  LF
Sbjct: 234 ------GTVLEKATLKAFHDKLCEEYIEVMSGDKNVLFKMKELWFYMGNLF 278


>gi|315651846|ref|ZP_07904849.1| dihydrouridine synthase [Eubacterium saburreum DSM 3986]
 gi|315485848|gb|EFU76227.1| dihydrouridine synthase [Eubacterium saburreum DSM 3986]
          Length = 310

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/287 (21%), Positives = 106/287 (36%), Gaps = 29/287 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T+  +R  + R  +     +T  I         + +   +     + + L  QI  
Sbjct: 8   MEGVTNYVFRKVYIRHFSGVDKFFTPFITPHMKKGFSKSELMELDKDYNKGQYLIPQILT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KAL 115
             +    + +  ++  GYNE+N+N+GCPSA V     G+  + +   +      +  K +
Sbjct: 68  NSVQDFFKLSGEIKQMGYNELNINIGCPSATVTSKGRGSGFLQDTKAIDKFFYEIFEKTV 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            I +++K RIG  D        +LVK  +K     I IH R   L+    K+   IP   
Sbjct: 128 DIKISIKTRIGFCD---YSEWDDLVKVYEKYNFCEIIIHPR---LRSDFYKNKVYIPA-- 179

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPS--VDGVMIGRAAYKNSAMLTTVD 230
              +   K     L    NG +  M       + L    VD VMIGR   +N  +   + 
Sbjct: 180 --FIEACKILKSKLV--YNGDINTMDDFKILNEQLKENKVDTVMIGRGLVRNPLLPEAIK 235

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  TG+     R   DF   I            ++  KL+++ 
Sbjct: 236 -------TGAKITDLRKTVDFLDDIKEEYLSLDFGERNTLFKLKELW 275


>gi|294655111|ref|XP_457209.2| DEHA2B05720p [Debaryomyces hansenii CBS767]
 gi|199429699|emb|CAG85204.2| DEHA2B05720p [Debaryomyces hansenii]
          Length = 446

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 56/254 (22%), Positives = 94/254 (37%), Gaps = 37/254 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----------------DKKNILGFS 44
           MV   +   R  A       L++T  IV   +++                 +KK +    
Sbjct: 85  MVRSGEIPTRLMALRY-GADLVWTPEIVDKKLIKCERVINDDLGTVDFLDPNKKVVFRTY 143

Query: 45  TQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             E+   L  QIG AD    V+AAKIV     + I+LN GCP         GA L+  PD
Sbjct: 144 PAEESGKLIFQIGSADPELAVQAAKIVAQ-DVDGIDLNCGCPKPFSTHSGMGAALLTTPD 202

Query: 103 IVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           ++   +  +   +     IP++ K R+   D         L+  + K+G++ + +H R  
Sbjct: 203 LLESILRNLVSEVGKVYDIPISAKIRLL--DDTDVTPSLELIDRLCKTGISNLTLHCRTP 260

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA----LKILPSVDGVM 214
            ++         +P     I+  +   N      +NG +    +      K    V G M
Sbjct: 261 RMRNRDTPVRDFLP----SIIDTVHANNVS--FIINGSIRSRREFHLLQRKYGEKVGG-M 313

Query: 215 IGRAAYKNSAMLTT 228
           I  +A  N  +   
Sbjct: 314 IAESAESNPTVFAE 327


>gi|302915835|ref|XP_003051728.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256732667|gb|EEU46015.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 407

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 50/192 (26%), Positives = 87/192 (45%), Gaps = 10/192 (5%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
             +L    ++K L  QIG AD  + V+AA++V       I++N GCP      G  GA L
Sbjct: 93  YRMLPEIEKDK-LIFQIGTADPDRAVQAARLVAA-DVAGIDVNAGCPKPFSTSGGMGAAL 150

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +  PD +   + A+ K ++    +   + +     A     LV+ +  +G+ G+ +H R 
Sbjct: 151 LKTPDKLCAILEALVKNITPEFEIGISVKIRILDTAAETEALVRRLCATGITGLTVHCRT 210

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMI 215
             ++   P++      L   +V E+  E   +   +NG +E+  + LK+      DG MI
Sbjct: 211 TPMR---PRERAIRGQLR--MVAEVCHEYG-VACLMNGDVENRDEGLKLAEEFGADGAMI 264

Query: 216 GRAAYKNSAMLT 227
             AA KN +   
Sbjct: 265 ATAAEKNPSCFR 276


>gi|169616904|ref|XP_001801867.1| hypothetical protein SNOG_11628 [Phaeosphaeria nodorum SN15]
 gi|187471071|sp|Q0U9D6|DUS3_PHANO RecName: Full=tRNA-dihydrouridine synthase 3
 gi|160703286|gb|EAT81336.2| hypothetical protein SNOG_11628 [Phaeosphaeria nodorum SN15]
          Length = 739

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/282 (18%), Positives = 90/282 (31%), Gaps = 58/282 (20%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEK--------------- 48
           +  YR     L    + ++EM +   +++G++    ++     E                
Sbjct: 340 NMPYRRLCVDL-GCQVTWSEMAMGMPLIQGERGEWALMKAHESEIAAPRFQSKGTVVQGY 398

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI         +  +++ D       I+LN GCP   V E   G+ L+ +
Sbjct: 399 DNAADIRFGAQIAANKPWLANKTVEVLTDNCPKLRAIDLNCGCPINLVCEKGSGSALLDS 458

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA----------LRNLVKSIKKSGVN 149
              + + +  M      +P+TVK R+G  D  P                L      SGV 
Sbjct: 459 EAKLENILRGMNYVSKEVPITVKVRMGTKDNHPTAQKLIKRLVLGGYEALASDKGTSGVA 518

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN------------------PDLFI 191
            I +H R    +     D   I      ++  +KKE                     ++ 
Sbjct: 519 AITLHGRSKQQRYSKSADWSYIAECA-SLINRLKKEKDAQTDTAAEADPRDQANGGHVYF 577

Query: 192 GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             NG           +   +VD VMIGR A     +   +++
Sbjct: 578 VGNGDCYSHEDYYNHMNNANVDSVMIGRGALIKPWIFEEIEK 619


>gi|225562406|gb|EEH10685.1| tRNA-dihydrouridine synthase [Ajellomyces capsulatus G186AR]
          Length = 495

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 100/256 (39%), Gaps = 38/256 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L    +   L  QIG A     V+AAKI+       I++N GCP      G  GA L+ 
Sbjct: 112 RLDPRRESGKLVFQIGTASPDLAVQAAKIIAA-DVAGIDVNAGCPKPFSTTGGMGAALLQ 170

Query: 100 NPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            PD +   + A+ + +  P    ++VK R+  D +      R+LV  +  +G+ G+ +H 
Sbjct: 171 TPDRLVSILTALVQQVGTPYQIGISVKIRLLADPERT----RDLVTRLCATGITGLTVHC 226

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
           R   ++        ++P     ++  I +    + I +NG +E     L ++    VDG 
Sbjct: 227 RTTPMRPRERAIRDQLP-----MIASICRAAG-VAILVNGDVESRDHGLALMAEYGVDGA 280

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MI   A  NS+   +  +                    WR I     D   +  +  G  
Sbjct: 281 MIATCAEANSSCFRSAAD---------------GSLLPWRAIVRDYMDLCLQCENKWGN- 324

Query: 274 QQITRHMIGLFHGFPN 289
              T++++ +    P 
Sbjct: 325 ---TKYLLNML--IPG 335


>gi|327348456|gb|EGE77313.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis ATCC 18188]
          Length = 508

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 67/284 (23%), Positives = 113/284 (39%), Gaps = 44/284 (15%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N     T    A          I       K L  QIG A  +  V+AAKI+  
Sbjct: 91  FTRLPSNGGRQNTP--NAK---ESVIYRIDPHRESGK-LIFQIGTASPNLAVQAAKIIAA 144

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD++   + A+ + +  P    ++VK R+  
Sbjct: 145 -DVAGIDVNAGCPKPFSTSGGMGAALLQTPDLLVSILTALVQQIGNPYQIGISVKIRLLA 203

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 204 DPERT----RDLVTRLCATGITGLTVHCRTTPMRPRERAIRAQLP-----MIASICRAAG 254

Query: 188 DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
            + I +NG +E     L ++    VDG MI  +A  NS+         S    G  P   
Sbjct: 255 -VAILMNGDVESRDHGLALMSEYGVDGAMIATSAEANSSCFR------SGAQGGLLP--- 304

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                 WR I  +  D+  +  +  G     T++++ +    P 
Sbjct: 305 ------WRDIVYAYMDFCLQCENKWGN----TKYLLNML--IPG 336


>gi|156058113|ref|XP_001594980.1| hypothetical protein SS1G_04788 [Sclerotinia sclerotiorum 1980]
 gi|154702573|gb|EDO02312.1| hypothetical protein SS1G_04788 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 513

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 63/288 (21%), Positives = 116/288 (40%), Gaps = 44/288 (15%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + K L  QIG +D  K V+ A++V       I++N GCP      G  GA L+  PD + 
Sbjct: 187 EGKKLIFQIGTSDPEKAVQCARMVAA-DVAGIDVNAGCPKPFSTSGGMGAALLQTPDKLC 245

Query: 106 DCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ K +     I ++VK R+    +        LV+ +  +G+ G+ IH R   ++
Sbjct: 246 AILEALVKEIVPEFEIGISVKIRLLETPERTEA----LVRKLCATGITGLTIHCRTTPMR 301

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P++      L   ++ +I +E+  +   +NG +E+  QALK+      +G MI  AA
Sbjct: 302 ---PRERAIRGQLK--MIADICRESG-IACLMNGDVENRDQALKLAEEYGTNGAMIAVAA 355

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
             NS+         S    G +P         W ++      ++    +  G     T++
Sbjct: 356 EANSSCFR------SEADGGLAP---------WEEVVLQYMKFSLDMENRFGN----TKY 396

Query: 280 MIGLFHGFPNSRRCRHILTVEAGASTATHH-----IIETAFNLMIESL 322
           ++      P        +           H     ++E A + + E +
Sbjct: 397 LLNHL--IPGKSPIYRAIQQSKNYQQLCDHLGHKSLLEQAID-VDEKI 441


>gi|261205036|ref|XP_002627255.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239592314|gb|EEQ74895.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis SLH14081]
 gi|239611532|gb|EEQ88519.1| tRNA dihydrouridine synthase [Ajellomyces dermatitidis ER-3]
          Length = 464

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 67/284 (23%), Positives = 113/284 (39%), Gaps = 44/284 (15%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
           F RL +N     T    A          I       K L  QIG A  +  V+AAKI+  
Sbjct: 47  FTRLPSNGGRQNTP--NAK---ESVIYRIDPHRESGK-LIFQIGTASPNLAVQAAKIIAA 100

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP----VTVKCRIGV 127
                I++N GCP      G  GA L+  PD++   + A+ + +  P    ++VK R+  
Sbjct: 101 -DVAGIDVNAGCPKPFSTSGGMGAALLQTPDLLVSILTALVQQIGNPYQIGISVKIRLLA 159

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D +      R+LV  +  +G+ G+ +H R   ++        ++P     ++  I +   
Sbjct: 160 DPERT----RDLVTRLCATGITGLTVHCRTTPMRPRERAIRAQLP-----MIASICRAAG 210

Query: 188 DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
            + I +NG +E     L ++    VDG MI  +A  NS+         S    G  P   
Sbjct: 211 -VAILMNGDVESRDHGLALMSEYGVDGAMIATSAEANSSCFR------SGAQGGLLP--- 260

Query: 246 RVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPN 289
                 WR I  +  D+  +  +  G     T++++ +    P 
Sbjct: 261 ------WRDIVYAYMDFCLQCENKWGN----TKYLLNML--IPG 292


>gi|300857022|ref|YP_003782006.1| putative tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
 gi|300437137|gb|ADK16904.1| putative tRNA-dihydrouridine synthase [Clostridium ljungdahlii DSM
           13528]
          Length = 313

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 57/294 (19%), Positives = 109/294 (37%), Gaps = 33/294 (11%)

Query: 1   MVDWTDRHYRFFA-RLLTNNALLYTEMI---VADAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR             ++  I    +D     +  +IL  + Q   L  Q+  
Sbjct: 8   MEGLTGYIYRNAHNAFFNKIDKYFSPFIFANQSDKFKTKELNDILPENNQGIVLIPQLLT 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +    +  +K ++  GY E+NLN+GCPS  V   + G+  +     +   +  +    +
Sbjct: 68  NNAKDFIHTSKKIKQMGYTEVNLNLGCPSGTVVSKNRGSGFLSKTKELDAFLDEIFSEAA 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             ++VK RIG D         NL++   K  +  + IH R            +  PNL  
Sbjct: 128 TKISVKTRIGKD---SPEEFYNLIEIFNKYPIEELIIHPRIQKDFY------KNKPNL-- 176

Query: 177 DIVYEIKKENPDL---FIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVD 230
               ++ K+   L    I  NG +  +    K   +   V   M+GR    N  ++  + 
Sbjct: 177 ----KVFKDALSLSKNPICYNGDIFSVKDYKKFTTNFHSVETLMLGRGLLINPGLINDIK 232

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    ++ +  ++ K+F  KI            +   +++++  +MI +F
Sbjct: 233 --------NNTKLDKKLLKNFHDKIYEDYKKVLFGDRNVLFRMKELWSYMIQIF 278


>gi|326791078|ref|YP_004308899.1| dihydrouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326541842|gb|ADZ83701.1| dihydrouridine synthase DuS [Clostridium lentocellum DSM 5427]
          Length = 324

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 62/329 (18%), Positives = 114/329 (34%), Gaps = 37/329 (11%)

Query: 1   MVDWTDRHYRFFARLLTNN-ALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR       N+    +T  I           +  +IL    Q   +  QI  
Sbjct: 8   MEGLTGYIYRNAHATFFNHVDKYFTPFIATTQHGKFTTRELHDILPEHNQGLVVIPQILS 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            +    +     ++ FGY E+NLN+GCPS  V   + G+  +   + +   +  +     
Sbjct: 68  NNAEDFMTTVTQLKAFGYEEVNLNLGCPSGTVVSKNKGSGFLAEKEALDQFLEEIFSKAI 127

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             +++K RIG   +        L+    K  +  + IH R       +  +         
Sbjct: 128 TKISIKTRIG---KERPEEFEELIHIFNKYPLEELIIHPRVQKDYYRNTPNWESFST--- 181

Query: 177 DIVYEIKKENPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
                   +  +  +G NG +          K  PSVD +M+GR    N  +++ + +  
Sbjct: 182 ------GVQLSNNSVGYNGDIFTAQRYELFAKQFPSVDTIMLGRGLVANPGLISDIKDNI 235

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF-------HG 286
           +        +  ++ K F  KI     +  +   +   K+++   +MI +F         
Sbjct: 236 T--------LDKQLLKAFHDKIYEDYQEVLSGERNVLFKMKENWFYMIHMFSNADRYAKK 287

Query: 287 FPNSRRCRHILTVEAGAST-ATHHIIETA 314
              S+R R     EA         I+E A
Sbjct: 288 IKKSQRLRDY--EEAVTELFKEQEIVEGA 314


>gi|85116240|ref|XP_965022.1| hypothetical protein NCU02619 [Neurospora crassa OR74A]
 gi|74629110|sp|Q7SG01|DUS3_NEUCR RecName: Full=tRNA-dihydrouridine synthase 3
 gi|28926822|gb|EAA35786.1| hypothetical protein NCU02619 [Neurospora crassa OR74A]
 gi|38567151|emb|CAE76445.1| conserved hypothetical protein [Neurospora crassa]
          Length = 737

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 50/280 (17%), Positives = 92/280 (32%), Gaps = 59/280 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE------KP-------- 49
           +  +R     L    + Y+EM +   +L+G      ++     E       P        
Sbjct: 338 NLPFRRLCVEL-GAEITYSEMALGLPLLQGQKADWTLMRAHESEITPPRYTPTGIVDPAY 396

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLN 100
                    +QI        +++A+ +  +  +   I+LN GCP   V++   G+ L+  
Sbjct: 397 DNSKDLKFGVQITAHAPWIAIKSAETLARYLPHLRVIDLNCGCPIDMVYKSGAGSALLDA 456

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIK-----------KSGV 148
           P  +   I  M      +PVT K R+GV D    +  + LV+ +              G 
Sbjct: 457 PSKLERMIRGMNTVSGEVPVTAKIRMGVRD--NHLTAQKLVERLALGAPDIRAVSGAPGC 514

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLFI 191
             + +H R    +     D   I                  D + E  + +      ++ 
Sbjct: 515 AAVTLHGRTRQQRYTKAADWSYIAECAALVKSFNEKADSLQDTIREADERSLPNGGRMYF 574

Query: 192 GLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
             NG           + +  VD VM+GR A     +   +
Sbjct: 575 VGNGDCYSHVDYFNHVDNAKVDSVMVGRGAIIKPWIFEEI 614


>gi|157873334|ref|XP_001685179.1| dihydrouridine synthase (Dus) [Leishmania major strain Friedlin]
 gi|68128250|emb|CAJ08381.1| putative dihydrouridine synthase (Dus) [Leishmania major strain
           Friedlin]
          Length = 661

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 52/412 (12%), Positives = 109/412 (26%), Gaps = 140/412 (33%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQE---------- 47
           MVD ++  +R   R      + YT M+ A +   G       +     +E          
Sbjct: 120 MVDQSELPFRMLCRQY-GATVAYTPMLHAKSFADGAVYRSHFLSVCPPEEVKAAMQAPLA 178

Query: 48  ----------------------------------KPLALQIGGADISKLVEAAKIVED-- 71
                                             +P  +Q  G D   ++ AA+      
Sbjct: 179 SPSVAAGTHGGGSSMRGGVGAGSEAAVADTALVDRPCIVQFCGNDADTVLRAARFAVLGE 238

Query: 72  ----------------------------------------FGYNEINLNVGCPSARVHEG 91
                                                   +  + +++N+GCP      G
Sbjct: 239 QAAAAEQTGSSRGASAAPVYPVHVRVNGLSCSEKAPEHLLYQCDAVDVNLGCPQGIARRG 298

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN------------- 138
            +G+ LM + +++   +  +   L +PVTVK R+         A  N             
Sbjct: 299 HYGSFLMEDWELIHTIVHTLHVELEVPVTVKIRVFDHPGHAEAAGDNRECATDCSFAAFE 358

Query: 139 ---------------------------LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                                        + I+ +G   + IH R   +KG      ++ 
Sbjct: 359 ENDAVCAAAGTSREPLKEAFDEALTILYARMIRDAGAQMLCIHGRTREMKG------QQT 412

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
              + +++  ++      + +  NG +      +  L     +G M       +  + + 
Sbjct: 413 GLANMELIRRVRDALGGTIPVISNGNVRTYDDVIAHLQETRCEGHMCAEPLLWDPKLFSN 472

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQQITRH 279
             +      T  +   TR+       +    +  Y          L ++  H
Sbjct: 473 PSQPVMPGRTHGADKATRLSALHTALVYMQWVRHYPVDIGFVKAHLFKMCFH 524


>gi|295093806|emb|CBK82897.1| tRNA-U20a,U20b-dihydrouridine synthase [Coprococcus sp. ART55/1]
          Length = 322

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/283 (19%), Positives = 109/283 (38%), Gaps = 25/283 (8%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR    +        +   I       +   + +++L  + Q   +  Q+  
Sbjct: 13  MEGITGYIYRNAHHKYFGGVDKYFMPFIAPAKGRPLRNRELRDVLPENNQGINVVPQLLT 72

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 V AAK +++ GYNE+N+N+GCPS  V     G+ L+ + + + + +  +  A  
Sbjct: 73  NSGEGFVTAAKFLKELGYNEVNINLGCPSKTVVTKYKGSGLIYDTERLDNFLYEVFAADV 132

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V++K RIG D    +V   ++++  KK  ++ + IH R            +  PN++ 
Sbjct: 133 MDVSIKTRIGRD---SSVEFEDIIEIYKKYPISELIIHPRIQTDFY------KNTPNMEV 183

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK---ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
                     PD  +  NG +  ++   +     P +  VMIGR    +  +   ++E  
Sbjct: 184 FAEGVASYGRPDT-VCYNGDINSVADYDRFTGDFPDISKVMIGRGIIADPCLAERINEEC 242

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
            +               F+        +Y    +  G  + ++
Sbjct: 243 GDSTYDW--------NRFFIFHDELYRNYCESDVGRGNTMFKM 277


>gi|320582810|gb|EFW97027.1| Dihydrouridine synthase [Pichia angusta DL-1]
          Length = 367

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 106/260 (40%), Gaps = 45/260 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR------------------GDKK---- 38
           MV   +   R  A L     L++   I+   ++R                  G+KK    
Sbjct: 13  MVRIGELPTRLLA-LKYGADLVWGPEIIDKRLVRAERVYNPILNTVDFIQKDGNKKVPGT 71

Query: 39  NILGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
             L F T    ++  L  Q+G A     V+AAKIV     + I++N GCP         G
Sbjct: 72  TDLVFRTYRKLEQGKLIFQLGTASPELAVQAAKIVAA-DVDGIDINAGCPKHFSVHSGMG 130

Query: 95  ACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           A L+  PD++   ++++ + +      P++VK R+  + +       +LV+ + K+G+  
Sbjct: 131 AALLKTPDVLCSILSSLVEQVGKPFQKPISVKIRLLPEQE----QTLDLVRKLVKTGIAN 186

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           + +H R   ++   P     I     D + EI  E  D+ + +NGG++   +  ++    
Sbjct: 187 LTVHCRTREMRNGQPPIRDYI-----DKIKEICDEA-DVSLIINGGIKSYQEFKEMQEKY 240

Query: 209 SVD-GVMIGRAAYKNSAMLT 227
             D   MI   A  N  +  
Sbjct: 241 GSDISCMIASKAETNPTVFN 260


>gi|123288586|emb|CAM27544.1| dihydrouridine synthase 1-like (S. cerevisiae) [Mus musculus]
          Length = 166

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 39/144 (27%), Positives = 64/144 (44%), Gaps = 8/144 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           MVD ++  +R  +R      L YT M+ A   +R               +++PL +Q   
Sbjct: 24  MVDQSELAWRLLSRR-HGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCA 82

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D    V+AA + +D+  + I+LN+GCP      G +GA L    D++   I    + LS
Sbjct: 83  NDPEVFVQAALLAQDY-CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHERLS 141

Query: 117 IPVTVKCR--IGVDDQIPAVALRN 138
           +PVT K R    +D  +    +  
Sbjct: 142 VPVTCKIRVFPEIDKTVRYAQMLE 165


>gi|255725494|ref|XP_002547676.1| hypothetical protein CTRG_01983 [Candida tropicalis MYA-3404]
 gi|240135567|gb|EER35121.1| hypothetical protein CTRG_01983 [Candida tropicalis MYA-3404]
          Length = 428

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 104/260 (40%), Gaps = 43/260 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---------------------DKKN 39
           MV   +   R  A       L+++  +V   +++                      DKK 
Sbjct: 17  MVRSGELPMRLLALKY-GADLVWSPELVDKKVIQSKRIVNQDLNTIDYISENHQNPDKKT 75

Query: 40  -ILGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
            IL    +E   L  Q+G +D    VEAAK V D   + I+LN GCP         GA L
Sbjct: 76  VILRKHPEESGKLICQLGSSDPELAVEAAKKVID-DVDGIDLNCGCPKNFSTHSGMGAEL 134

Query: 98  MLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +  P+I+   +  + + +      P++ K R+  +        + L++ I ++G+  + I
Sbjct: 135 LKTPEILCSILTNLVENVGKPKGKPISCKIRLFNNFDKS----KELIEKICQTGITNLTI 190

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD-- 211
           H R  I++         +P L    +  I+K    L   LNG  ++      +  ++D  
Sbjct: 191 HCRTPIMRNRQDPVWNYLPKL----IPIIEKSGVSLV--LNGNFQNKQDLKIVQKALDND 244

Query: 212 --GVMIGRAAYKNSAMLTTV 229
              +M G AA  N ++ + V
Sbjct: 245 KLSIMFGEAAEANPSVFSDV 264


>gi|224013536|ref|XP_002296432.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220968784|gb|EED87128.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 242

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 100/241 (41%), Gaps = 23/241 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILG----------FSTQEK 48
           MV  +    R  A L    +L+YTE ++  +I+         LG          +S ++ 
Sbjct: 10  MVRASTTPLRTLA-LSYGASLVYTEELIDRSIVPTERIINTELGTIDYRTPKHCYSAKQD 68

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
            L  Q+G  +    ++AA  V +         +GCP      G  G+ L+ +     D I
Sbjct: 69  KLIYQMGTGEGHLALDAANKVVNDVNGVDVN-MGCPKKFSVTGGMGSALLSDVKRACDII 127

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + + + L+ PV+ K R+   D        + V+++ K+G N I IH R    +  +    
Sbjct: 128 STLRRNLNKPVSAKIRLLDPDNPKPT--LDFVRALIKAGANAIAIHGRIVGDESHTMARW 185

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
             +     ++V ++K+    + I +NG L   +   ++      DGVM+ R A  N ++ 
Sbjct: 186 ETLI----EVVRQLKQ-TESVPIIVNGDLYTRADIQEMKSRTGCDGVMLARPALYNISIF 240

Query: 227 T 227
            
Sbjct: 241 R 241


>gi|156379115|ref|XP_001631304.1| predicted protein [Nematostella vectensis]
 gi|156218342|gb|EDO39241.1| predicted protein [Nematostella vectensis]
          Length = 440

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 64/304 (21%), Positives = 107/304 (35%), Gaps = 41/304 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR--GDKKNILG---------------F 43
           MV       R  A       L+YTE I+   +LR    K  +L                 
Sbjct: 11  MVRIGTLPARLLALRY-GADLVYTEEIIDFKMLRTTRVKNELLNTVDFVMSDGTVVFRTC 69

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             +   +  Q+G AD  + ++ AK+VE       ++N+GCP     +G  GA L+  P+ 
Sbjct: 70  QEETTHVVFQVGTADADRALQVAKMVEKDIAA-FDVNMGCPKDYSVKGGMGAALLTEPEK 128

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V   +  + K LSIPVT K RI             L K I+ +GV  + +H R+   +  
Sbjct: 129 VKKILTTLVKGLSIPVTCKIRILP----TIAETVQLCKLIESTGVTALAVHGREKHERSR 184

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSVDGVMIGRAAYK 221
            P         +Y          P +  G +  ++  S     ++      +M+ RAA  
Sbjct: 185 QPVHT------EYIQAVAAAVAIPVIANGGSLDIKTFSDMEQFRLQAGCASIMVARAAQW 238

Query: 222 NSAMLTT---------VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           N ++            V  Y    +               R +    T  AA    +   
Sbjct: 239 NLSVFRREGPLSHLDVVKAYIKTAIEC-DNSFGNTKYCVLRLMHEQYTSEAAAEFTAAKD 297

Query: 273 LQQI 276
           ++++
Sbjct: 298 IREM 301


>gi|242822853|ref|XP_002487972.1| tRNA dihydrouridine synthase (Smm1), putative [Talaromyces
           stipitatus ATCC 10500]
 gi|218712893|gb|EED12318.1| tRNA dihydrouridine synthase (Smm1), putative [Talaromyces
           stipitatus ATCC 10500]
          Length = 787

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 46/202 (22%), Positives = 86/202 (42%), Gaps = 9/202 (4%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
            AD + +      +    ++  L  QIG A     V+AAK+V       I++N GCP   
Sbjct: 428 SADQLPKESVIYRIDPENEKGKLIFQIGTASPEFAVQAAKVVAG-DVAGIDVNSGCPKPF 486

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G  GA L+  PD +   + ++ + +  P  +   + +         ++LV  +  +G
Sbjct: 487 STSGGMGAALLRTPDKLVSILESLVREVGTPYKIGISVKIRLLETPELTKSLVTRLVATG 546

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + G+ IH R   ++        ++      ++ E+ +    +   +NG +    QAL+++
Sbjct: 547 ITGLTIHCRTTPMRPRERAIRDQL-----SMIAEVCRNAG-VACVMNGDVTSRDQALELM 600

Query: 208 PS--VDGVMIGRAAYKNSAMLT 227
               VDG MI  AA  NS+   
Sbjct: 601 KEYNVDGAMIATAAEANSSCFR 622


>gi|77918513|ref|YP_356328.1| tRNA-dihydrouridine synthase [Pelobacter carbinolicus DSM 2380]
 gi|77544596|gb|ABA88158.1| tRNA-U20a,U20b-dihydrouridine synthase [Pelobacter carbinolicus DSM
           2380]
          Length = 303

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/282 (21%), Positives = 116/282 (41%), Gaps = 18/282 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEK-PLALQIGGAD 58
           M   T+   R     L +  +L+TE + VA   +             E  PL +Q+ G D
Sbjct: 5   MQGLTNMALRAVLAGLGHPDVLFTEFVRVAPGRMPVFPGRQWSADCCEMLPLVVQLIGHD 64

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L  AA+  +  G   INLN+GCP  R+   + G  L+  P+ +   +A + K +S  
Sbjct: 65  DRSLAIAAQSAQQAGARHINLNLGCPHGRMTSAAVGGNLLAQPERIAPMLAGLRKVVSGS 124

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R G +D      + +L+  ++ +GV+   +H R  +L+G            D+ I
Sbjct: 125 FSVKLRAGYED---PTQIFSLLPMLEDAGVDFFILHPRT-VLQG-------YDGQADHAI 173

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAYKNSAMLTTVDEYFSNP 236
              + K    L +  NG +   +   ++L   D  G+M+GR A  +  +   +       
Sbjct: 174 TAAVAKRT-CLPLIANGDIRKPADGCRLLEQTDIAGLMLGRGAIADPLLFERLRRRAPAR 232

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
                  +  + + +  +++    +         GKL++I +
Sbjct: 233 PNRRQ--RAVLLRRYLTEVADRYAERFCGDTQVLGKLREILK 272


>gi|302665254|ref|XP_003024239.1| hypothetical protein TRV_01589 [Trichophyton verrucosum HKI 0517]
 gi|291188286|gb|EFE43628.1| hypothetical protein TRV_01589 [Trichophyton verrucosum HKI 0517]
          Length = 640

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 102/246 (41%), Gaps = 38/246 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 328 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 386

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 387 ALVREVGRPWQIGISVKIRLLKDPKDT----ERLVTALCATGITGLTVHCRTTPMRPREA 442

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    +   +NG ++    AL+++    VDG MI  +A  N 
Sbjct: 443 AIRDQLP-----MIASICRSAG-VACLMNGDVKSRDHALELMSQYDVDGAMIATSAESNF 496

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +   +  +                    WR+++      A    +  G     T++++ +
Sbjct: 497 SCFRSAAD---------------GGCVSWRELAHEYVAVAMECENKWGN----TKYLLNI 537

Query: 284 FHGFPN 289
           F   P 
Sbjct: 538 F--LPG 541


>gi|225572095|ref|ZP_03780959.1| hypothetical protein RUMHYD_00389 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040429|gb|EEG50675.1| hypothetical protein RUMHYD_00389 [Blautia hydrogenotrophica DSM
           10507]
          Length = 316

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 52/281 (18%), Positives = 105/281 (37%), Gaps = 26/281 (9%)

Query: 10  RFFARLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
           R  A L       +   +V     +    + K I   + +      QI        +  A
Sbjct: 18  RIHAHLFPGIDKYFMPFLVPHVKRSFNSKELKEIAPENNKGLYAVPQIMTNKAEDFISTA 77

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K + D GY+E+NLN+GCPS  V     G+  +  P  +   +  + + L + ++VK R G
Sbjct: 78  KKLRDLGYDEVNLNLGCPSKTVVSKGRGSGFLAYPKELERFLDEIFEKLDMKISVKTRAG 137

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           V+++   + L ++     +  +  + +H R        P             V+      
Sbjct: 138 VEEEEEFLTLLDI---YNRFPMEELIVHPRLQTDYYKKPVRFS---------VFLQASAA 185

Query: 187 PDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
               +  NG L   +D+ +  +  P VD VMIGR   +N  ++    +           +
Sbjct: 186 SRNPLCYNGDLIYAQDIERFAREFPQVDRVMIGRGLLRNPGLVREAAQGI--------VL 237

Query: 244 KTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                +++  +I  +  +      +   +++++   M  LF
Sbjct: 238 DKETLREYHDQIYEAYQEVLYGDRNILFRMKELWCFMGSLF 278


>gi|291523511|emb|CBK81804.1| tRNA-dihydrouridine synthase [Coprococcus catus GD/7]
          Length = 329

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 48/295 (16%), Positives = 100/295 (33%), Gaps = 35/295 (11%)

Query: 1   MVDWTDRHYRF-FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGG 56
           M   T   YR    R+       Y   I  +   +  KK++L  + +      +  Q+  
Sbjct: 11  MEGITGSIYRRAHHRIFGGVDRYYAPFIFTNPKGKISKKDLLEIAPEYNEGCRVVPQLLS 70

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +  A  ++  GY+E+NLN+GCPS+ V     G+  +   + +   +A +     
Sbjct: 71  NCAEDFIATAHTLKGLGYDEVNLNLGCPSSTVASKGRGSGFLGEKEALKAFLADIFDKTD 130

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + +++K RIG++    A    +++   +   V  + +H R  +       D         
Sbjct: 131 MKISLKTRIGLNR---ADEFDDILDIYQAFPVEMLIVHPRIRMDYYSGKPDMEAFEKA-- 185

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYF 233
                         +  NG +   +   ++      +   MIGR    N A+   +    
Sbjct: 186 -------SARMPFPVCYNGDIFTAAAYGRVSEKYSDIRHWMIGRGLLSNPALCREIR--- 235

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQITRHMIGLF 284
                G          D++     +M D     L    K    +++   ++  + 
Sbjct: 236 -----GGDCASREELADYYH----TMRDEYEVRLQGNKKVVFLMKEFWHYISWIL 281


>gi|322493958|emb|CBZ29249.1| putative dihydrouridine synthase (Dus) [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 660

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 53/395 (13%), Positives = 103/395 (26%), Gaps = 139/395 (35%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQE---------- 47
           MVD ++  +R   R      + YT M+ A +   G       +      E          
Sbjct: 120 MVDQSELPFRMLCRQY-GATVAYTPMLHAKSFADGAAYRSHFLSVCLPDEVKAAMEAALA 178

Query: 48  ----------------------------------KPLALQIGGADISKLVEAAKIVE--- 70
                                             +P  +Q  G D   ++ AA+      
Sbjct: 179 SPSVAAGEHGGGGSMRAGVGADSEDAVADTVLVDRPCIVQFCGNDADTVLRAARFAVLGE 238

Query: 71  ---------DFG------------------------------YNEINLNVGCPSARVHEG 91
                    D G                               + ++LN+GCP      G
Sbjct: 239 QAAATEQTGDNGGASAAPVYPVHVRVNGLSSSEKAPAHLLYQCDAVDLNLGCPQGIARRG 298

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN------------- 138
            +G+ LM + +++   +  +   L +PVTVK R+         A  N             
Sbjct: 299 HYGSFLMEDWELIHTIVHTLHVELEVPVTVKIRVFDHPGHVEAAGDNRECATDCSSAGCE 358

Query: 139 ---------------------------LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                                        + I+ +G   + IH R   +KG      ++ 
Sbjct: 359 ENGAACATADTSREPLKAVFDEALTILYARMIRDAGAQMLCIHGRTREMKG------QQT 412

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
              +  ++  ++      + +  NG +      +  L     +G M       +  + + 
Sbjct: 413 GLANMALIRRVRDALGGTIPVISNGNVRTYDDVIAHLQETRCEGHMCAEPLLWDPKLFSN 472

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
             +      T  +   TR+       +      Y 
Sbjct: 473 PSQPVMPGRTHGADKATRLSALHTALVYMQWVRYY 507


>gi|327292817|ref|XP_003231106.1| tRNA dihydrouridine synthase [Trichophyton rubrum CBS 118892]
 gi|326466736|gb|EGD92189.1| tRNA dihydrouridine synthase [Trichophyton rubrum CBS 118892]
          Length = 414

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 102/246 (41%), Gaps = 38/246 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 108 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLISILE 166

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 167 ALVREVGRPWQIGISVKIRLLKDPKDT----ERLVTALCATGITGLTVHCRTTPMRPREA 222

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    +   +NG ++    AL+++    VDG MI  +A  N 
Sbjct: 223 AIRDQLP-----MIASICRSAG-VACLMNGDVKSRDHALELMSQYDVDGAMIATSAESNF 276

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +   +  +                    WR+++      A    +  G     T++++ +
Sbjct: 277 SCFRSAAD---------------GGCVSWRELAHEYVAIAMECENKWGN----TKYLLNI 317

Query: 284 FHGFPN 289
           F   P 
Sbjct: 318 F--LPG 321


>gi|229828623|ref|ZP_04454692.1| hypothetical protein GCWU000342_00688 [Shuttleworthia satelles DSM
           14600]
 gi|229793217|gb|EEP29331.1| hypothetical protein GCWU000342_00688 [Shuttleworthia satelles DSM
           14600]
          Length = 338

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 56/308 (18%), Positives = 113/308 (36%), Gaps = 44/308 (14%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--------EKP-L 50
           M   T   +R   A+      + YT  +V +      ++       +         KP L
Sbjct: 21  MEGLTGYVFRNALAKDFPGADVYYTPFLVVNQHHTFKRRERRDVDPRNQIGLSATGKPRL 80

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+  +D    +   + + D GY E+NLN GCPS  V     G  ++ +   +      
Sbjct: 81  VPQLMASDPDLFLWGCQYLSDLGYEEVNLNAGCPSPTVTAKGKGCGMLEDTLKLNRFFDR 140

Query: 111 MCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSP 165
           + + L    IPV +  +  +  +  A  + +L++      +  + IHAR  +A   G+  
Sbjct: 141 VFEGLERQRIPVRISVKTRLGMED-AGEMEDLMRVYTMYPIARLMIHARVGRAAYSGMPD 199

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---------PSVDGVMIG 216
           +D              ++K N  L +  NG +       KIL            +G+M+G
Sbjct: 200 QD---------SFCKALEKNN--LPVSYNGDILTPEDGEKILVRAEGHDLQKHFNGLMLG 248

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           R   ++ A+   V         G  P      ++F  ++          + ++  +++++
Sbjct: 249 RGVLRDPALFRKVR--------GGPPADRAELENFVGELFEGYAQAMDGYGNALLRMKEL 300

Query: 277 TRHMIGLF 284
             ++   F
Sbjct: 301 WSYLAAHF 308


>gi|212546591|ref|XP_002153449.1| tRNA dihydrouridine synthase (Smm1), putative [Penicillium
           marneffei ATCC 18224]
 gi|210064969|gb|EEA19064.1| tRNA dihydrouridine synthase (Smm1), putative [Penicillium
           marneffei ATCC 18224]
          Length = 446

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 48/190 (25%), Positives = 84/190 (44%), Gaps = 17/190 (8%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             ++  L  QIG A     V+AAK+V       I++N GCP      G  GA L+  PD 
Sbjct: 103 ENEKGKLIFQIGTASPELAVQAAKVVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDK 161

Query: 104 VGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +   + A+ + +  P    ++VK R+  D +        LV  +  +G+ G+ IH R   
Sbjct: 162 LVSILEALVREVGTPYKIGISVKIRLFSDPEETKA----LVTRLVATGITGLTIHCRTTP 217

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
           ++        ++      ++  + +E   +   +NG +    QAL+++    VDG MI  
Sbjct: 218 MRPRERAIREQL-----SMIATVCREAG-VACVMNGDVTSRDQALELMKEYNVDGAMIAT 271

Query: 218 AAYKNSAMLT 227
           +A  NS+   
Sbjct: 272 SAEANSSCFR 281


>gi|170572085|ref|XP_001891977.1| dihydrouridine synthase domain containing protein [Brugia malayi]
 gi|158603180|gb|EDP39210.1| dihydrouridine synthase domain containing protein [Brugia malayi]
          Length = 437

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 49/246 (19%), Positives = 92/246 (37%), Gaps = 34/246 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--------RGDKKNILGFST--QEKPL 50
           MV       R  A       L+YTE IV   +L          +   +L      +++  
Sbjct: 16  MVRAGRTPLRTLALQY-GADLVYTEEIVDQKLLDILGTTDYTCEDDVVLRICNRVEKQKC 74

Query: 51  ALQI---GGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLNPDIVG 105
            LQI          +    +++ + G +   I++N+GCP      G  GA L+ NP+   
Sbjct: 75  VLQIAKMFSCREQMMQNERQMLLENGNDVAAIDINMGCPKPFSIAGGMGAALLGNPERAK 134

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +       +IP++ K R+              VK +++ G++ I +H R+        
Sbjct: 135 EIVQTCVSVSTIPISCKIRVL----DKQEDTLEFVKMLERCGISAIGVHGRR-------- 182

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALKILPS--VDGVMIGRAAY 220
           +  R+      + + EI +    + +  N   G ++     +K         VMI R A 
Sbjct: 183 RSERQSNMNRLNEIREITR-VVSVPVIANGFSGSIKKYEDIIKFWEQSXASSVMIARKAL 241

Query: 221 KNSAML 226
            N ++ 
Sbjct: 242 SNPSIF 247


>gi|238923624|ref|YP_002937140.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Eubacterium rectale ATCC 33656]
 gi|238875299|gb|ACR75006.1| putative protein involved in tRNA-dihydrouridine synthesis
           [Eubacterium rectale ATCC 33656]
          Length = 312

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 57/268 (21%), Positives = 114/268 (42%), Gaps = 20/268 (7%)

Query: 22  LYTEMI-VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
            YT  I  A  +    K++I   +     L  Q       ++++  + +  +GY+EIN+N
Sbjct: 30  YYTPFIPAAKRMNAKIKRDIDPVNNDGITLIPQAMSIVADEVIDLHRQLVPYGYDEINVN 89

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCPS  V     G+ ++  PD++   +  +      PV++K R+G +D         L+
Sbjct: 90  LGCPSGTVVSKKRGSGILAYPDMLDSFLDELYTKADFPVSIKTRVGFNDD---ELWHRLI 146

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLED 199
           +   K  ++ + +H R            +  P +D D    ++K NPD   +  NG + D
Sbjct: 147 EIYSKYPISELTVHPRVQKDFY------KNTPRMD-DFALAMQKINPDKTTLCYNGDITD 199

Query: 200 ---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               +      P +D +MIGR  + N A++  +       ++          K++  +I 
Sbjct: 200 TNSFNALTDCFPDIDEIMIGRGLFANPALIAELK-----GISMDKAELRERLKNWHDEIL 254

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +      +    +  ++++I  +M GLF
Sbjct: 255 SGYLSIFSGEKDAIFRMKEIWAYMHGLF 282


>gi|322501518|emb|CBZ36597.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 660

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 51/412 (12%), Positives = 106/412 (25%), Gaps = 140/412 (33%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQE---------- 47
           MVD ++  +R   R      + YT M+ A     G       +     +E          
Sbjct: 120 MVDQSELPFRMLCRQY-GATVAYTPMLHAKCFAEGAVYRSHFLSVCPPEEVKAAMEASLA 178

Query: 48  ----------------------------------KPLALQIGGADISKLVEAAKIVED-- 71
                                             +P  +Q  G D   ++ AA+      
Sbjct: 179 SPPIAAGGHGSGSSMRGGVGAGSENAVADTALVDRPCIVQFCGNDADTVLRAARFAVLGE 238

Query: 72  ----------------------------------------FGYNEINLNVGCPSARVHEG 91
                                                   +  + ++LN+GCP      G
Sbjct: 239 QAAAAEQTSGSGGASVAPVYPVHVRVNGLSSSEKAPEHLLYQCDAVDLNLGCPQGIARRG 298

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN------------- 138
            +G+ LM + +++   +  +   L +PVT K R+         A                
Sbjct: 299 HYGSFLMEDWELIHTIVHTLHVELEVPVTAKIRVFDHPGHVEAAGDKRECATNCSSAACQ 358

Query: 139 ---------------------------LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                                        + I+ +G   + IH R   +KG      ++ 
Sbjct: 359 ESDAVCAAADTSRESMKEVFDEALTILYARMIRDAGAQVLCIHGRTREMKG------QQT 412

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
              + +++  ++      + +  NG +      +  L     +G M       +  + + 
Sbjct: 413 GLANMELIRRVRDALGGTIPVISNGNVRTYDDVIDHLQETRCEGHMCAEPLLWDPKLFSN 472

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQQITRH 279
             +      T  +   TR+       +    +  Y          L ++  H
Sbjct: 473 PSQPVMPGRTHGADKATRLSALHTALVYMQWVRHYPVDIGFVKAHLFKMCFH 524


>gi|320165665|gb|EFW42564.1| tRNA dihydrouridine synthase Dus2 [Capsaspora owczarzaki ATCC
           30864]
          Length = 503

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 90/234 (38%), Gaps = 38/234 (16%)

Query: 18  NNALLYTE------MIVAD----------AILRGDKKNILGFSTQEKP-LALQIGGADIS 60
              L+Y+E      MI A             ++ D   I      E+  L  Q+G AD +
Sbjct: 10  GADLVYSEEIIDHRMIRAKRTYNPHLHSVDFVQPDGTVIFRTCPAERGKLVFQMGTADPA 69

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IP 118
           + V  A++V       +++N+GCP +   +G  GA L+ +PD +   + A+  A+   + 
Sbjct: 70  RAVAVARLVM-HDVLAVDVNMGCPKSYSTDGGMGAALLKHPDKIHAILTALVAAVGEHVH 128

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+             L K I+ +GV+ + +H R    +   P     +  +    
Sbjct: 129 VTCKIRVL----ATVEETVALAKMIESTGVSALAVHCRLTHERPREPGHPDMLKPIV--- 181

Query: 179 VYEIKKENPDLFIGLNG---GLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
                 +   + +  NG    +       A +       VM+ RAA  N ++  
Sbjct: 182 ------DALSIPVIANGGSLDIVSHDDIEAFRQRTGCASVMVARAAQNNPSVFR 229


>gi|213023307|ref|ZP_03337754.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 213

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 45/196 (22%), Positives = 81/196 (41%), Gaps = 20/196 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+   +PVTVK R+G D          +  +++++G + + +H R             +
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK-------AQGYR 196

Query: 171 IPNLDYDIVYEIKKEN 186
             ++D+  + EI++  
Sbjct: 197 AEHIDWQAIGEIRQRL 212


>gi|310790767|gb|EFQ26300.1| dihydrouridine synthase [Glomerella graminicola M1.001]
          Length = 427

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 58/239 (24%), Positives = 101/239 (42%), Gaps = 38/239 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD    V+AA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 113 LIFQIGTADPDLAVQAARLVAG-DVAGIDVNAGCPKPFSISGGMGAALLKTPDKLCAILE 171

Query: 110 AMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+   +     I ++VK R+             LV+ +  +G+ G+ IH R   ++    
Sbjct: 172 ALVANIMPEFEIGISVKIRLL----DTPEQTEALVRKLCATGITGLTIHCRTTPMRPRER 227

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               ++      +V E+  E   +   +NG +E    A+ ++    VDG MI  AA  NS
Sbjct: 228 AIREQL-----RMVAEVCHEAG-VACIMNGDVESRDHAVDLIKEYGVDGAMIATAAEANS 281

Query: 224 AMLTT-VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           +   + VD   ++                W++I+A+   YA    +  G     T++++
Sbjct: 282 SCFRSKVDGGLAS----------------WQEIAATYVKYALEVDNKYGN----TKYLL 320


>gi|326482381|gb|EGE06391.1| tRNA-dihydrouridine synthase [Trichophyton equinum CBS 127.97]
          Length = 419

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 102/246 (41%), Gaps = 38/246 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 108 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 166

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 167 ALVREVGQPWQIGISVKIRLLKDPRDT----ERLVTALCATGITGLTVHCRTTPMRPREA 222

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    +   +NG ++    AL+++    VDG MI  +A  N 
Sbjct: 223 AIRDQLP-----MIASICRSAG-VACLMNGDVKSRDHALELMSQYDVDGAMIATSAESNF 276

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +   +  +                    WR+++      A    +  G     T++++ +
Sbjct: 277 SCFRSAAD---------------GGCVSWRELAHEYVAVAMECENKWGN----TKYLLNI 317

Query: 284 FHGFPN 289
           F   P 
Sbjct: 318 F--LPG 321


>gi|254514890|ref|ZP_05126951.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR5-3]
 gi|219677133|gb|EED33498.1| tRNA-dihydrouridine synthase C [gamma proteobacterium NOR5-3]
          Length = 315

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 65/305 (21%), Positives = 118/305 (38%), Gaps = 32/305 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-MIVADAIL-----RGDKKNIL--GFSTQEKPLAL 52
           M    D   R     L       TE M V   +L           +   G ++   P+ L
Sbjct: 1   MEGVIDHTMRELLTRLGGVDRCVTEFMRVTRELLPARVFHRICPELAQGGRTSSGAPVFL 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G D + + E A    + G   I+LN GCP+  V+    G+ ++  P+ V   +AA  
Sbjct: 61  QILGGDATLVAENAARAAELGGLGIDLNFGCPAKTVNRSDGGSIILREPERVHAIVAAAR 120

Query: 113 KA--LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +A  +S+P++VK R+G +D+       ++V  I  +  + + IHAR         + +  
Sbjct: 121 RAVPVSVPLSVKIRLGFEDRDR---FLDIVSGIDAAKPSELVIHART--------RADGY 169

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLT 227
            P   +D +  + +   DL +  NG +    D   A         +M+GR       +  
Sbjct: 170 RPPAYWDQIA-LARSVTDLPLVANGEIWGVGDAQLARAK-SGTPDLMLGRGVLCRPDLPR 227

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            V       L  ++     +       ++ ++  Y AR+      +  I + +  L H +
Sbjct: 228 LVRAA-DLGLEQNALSWDDIRALLLTYLAVTLDTYDARY-----AVNPIKQWLGYLRHYY 281

Query: 288 PNSRR 292
           P +  
Sbjct: 282 PQAAA 286


>gi|302502698|ref|XP_003013310.1| hypothetical protein ARB_00495 [Arthroderma benhamiae CBS 112371]
 gi|291176873|gb|EFE32670.1| hypothetical protein ARB_00495 [Arthroderma benhamiae CBS 112371]
          Length = 476

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 102/246 (41%), Gaps = 38/246 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 160 LVFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILE 218

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 219 ALVREVGQPWQIGISVKIRLLKDPKDT----ERLVTALCATGITGLTVHCRTTPMRPREA 274

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    +   +NG ++    AL+++    VDG MI  +A  N 
Sbjct: 275 AIRDQLP-----MIASICRSAG-VACLMNGDVKSRDHALELMSQYDVDGAMIATSAESNF 328

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
           +   +  +                    WR+++      A    +  G     T++++ +
Sbjct: 329 SCFRSAAD---------------GGCVSWRELAHEYVAVAMECENKWGN----TKYLLNI 369

Query: 284 FHGFPN 289
           F   P 
Sbjct: 370 F--LPG 373


>gi|88801417|ref|ZP_01116945.1| hypothetical protein PI23P_02122 [Polaribacter irgensii 23-P]
 gi|88782075|gb|EAR13252.1| hypothetical protein PI23P_02122 [Polaribacter irgensii 23-P]
          Length = 317

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 54/272 (19%), Positives = 105/272 (38%), Gaps = 39/272 (14%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTE-------MIVADAILRGDKKNILGFSTQEKPLALQI 54
            +TD  +R  F          Y+        M+    I    +K++L  +  E  +  QI
Sbjct: 12  GFTDYKFRNAFNHFFGGIDTFYSPYIRLNGKMV----IKNSYQKDLLLENNSELEVIPQI 67

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
              D  + +  +K V   GY E+N N+GCP   V +   G+ L+ + + +   +  +   
Sbjct: 68  ITNDAEEFLFVSKYVRALGYKELNWNLGCPYPMVTKRGMGSGLISDAEKINSILHKVHNE 127

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD--NRK 170
             I V++K R+G +       +  ++  +    +  I IHAR  K + KG +  +   + 
Sbjct: 128 SDILVSMKMRMGYE---NPEEILGVLPILDTYPLKNIAIHARIGKQLYKGGTDLEAFQKC 184

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDM---SQALKILPSVDGVMIGRAAYKNSAMLT 227
           + N  + + Y             NG +  +    +  +  PS+D  MIGR    +  + +
Sbjct: 185 LDNSKHKMYY-------------NGDITSVVAFHKLQERFPSIDHWMIGRGLIGDPFLPS 231

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            +        T     +  V ++F  +I    
Sbjct: 232 MIKA----DTTEYPKERFDVFREFHDRIYQEY 259


>gi|291525684|emb|CBK91271.1| tRNA-dihydrouridine synthase [Eubacterium rectale DSM 17629]
          Length = 312

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 57/268 (21%), Positives = 114/268 (42%), Gaps = 20/268 (7%)

Query: 22  LYTEMI-VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
            YT  I  A  +    K++I   +     L  Q       ++++  + +  +GY+EIN+N
Sbjct: 30  YYTPFIPAAKRMNAKIKRDIDPVNNDGITLIPQAMSIVADEVIDLHRQLVPYGYDEINVN 89

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCPS  V     G+ ++  PD++   +  +      PV++K R+G +D         L+
Sbjct: 90  LGCPSGTVVSKKRGSGILAYPDMLDSFLDELYTKADFPVSIKTRVGFNDD---ELWPRLI 146

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLED 199
           +   K  ++ + +H R            +  P +D D    ++K NPD   +  NG + D
Sbjct: 147 EIYSKYPISELIVHPRVQKDFY------KNTPRMD-DFALAMQKINPDKTTLCYNGDITD 199

Query: 200 MSQALK---ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
            +         P +D +MIGR  + N A++  +       ++          K++  +I 
Sbjct: 200 TNSFKALTDCFPDIDEIMIGRGLFANPALIAELK-----GISMDKAELRERLKNWHDEIL 254

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +      +    +  ++++I  +M GLF
Sbjct: 255 SGYLTIFSGEKDAIFRMKEIWAYMHGLF 282


>gi|145230842|ref|XP_001389685.1| tRNA-dihydrouridine synthase 3 [Aspergillus niger CBS 513.88]
 gi|187471046|sp|A2QAU6|DUS3_ASPNC RecName: Full=tRNA-dihydrouridine synthase 3
 gi|134055808|emb|CAK37330.1| unnamed protein product [Aspergillus niger]
          Length = 748

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 49/284 (17%), Positives = 83/284 (29%), Gaps = 61/284 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK--------------- 48
           +  +R     L      Y+EM ++  +++G+K    ++     E                
Sbjct: 349 NMPFRRLCVEL-GAQFTYSEMAMSLPLIQGNKSEWALMRAHESEMLPPTMLPGADIVQGY 407

Query: 49  ------PLALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI      +  +A + +         I+LN GCP   V +   G+ L+ +
Sbjct: 408 DNSKDMKFGAQIAANKPWQAFKATEALAKVTPNLRVIDLNCGCPIDLVFKDGAGSALLEH 467

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           P  +   I  M      IP+TVK R+G  D  P      L + +   G            
Sbjct: 468 PSKLEKIIRGMNTVSDQIPITVKIRMGTKDNNPNA--LKLTERLLLGGYETSLLHHDGAA 525

Query: 150 ---GIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDL 189
               I +H R    +     D   I                  D + E           +
Sbjct: 526 GAAAITLHGRSRQQRYTRQADWEYISECAALIKRLNEKTDAVTDTIREPDARTQPNGGKV 585

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +   NG           +    VD VM+GR       +   +  
Sbjct: 586 YFLGNGDCYSHVDYDNHINNAGVDAVMLGRGPLIKPWLFEEIQA 629


>gi|310790042|gb|EFQ25575.1| dihydrouridine synthase [Glomerella graminicola M1.001]
          Length = 767

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 52/283 (18%), Positives = 90/283 (31%), Gaps = 58/283 (20%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEKP-------------- 49
           +  +R     L    L Y+EM +   +++G  +   ++     E                
Sbjct: 368 NLPFRRLCVDL-GAQLTYSEMALGMPLVQGVKNDWALMKAHESEISPPKVNQVSSNIVQG 426

Query: 50  --------LALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLML 99
                      QI G+     V+A  ++  +  +   I+LN GCP   V +   G+ L+ 
Sbjct: 427 YDNSRDLKFGAQISGSQAWHCVKAVDLLNRYVPHLRLIDLNCGCPIDMVFKAGGGSALLE 486

Query: 100 NPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVAL---------RNLVKSIKKSGVN 149
               +   +  M      IP+TVK R GV    P             R     +   G  
Sbjct: 487 AHGKLERMVRGMNTVSGEIPITVKLRTGVRQNRPTATTILGKLAFGSRENRDRLGAPGCA 546

Query: 150 GIWIHARKAILKGLSPKDNRKIPNL---------DYDIVYEIKKEN----------PDLF 190
            I +H R    +     D   I            + D + +  +E             +F
Sbjct: 547 AITLHGRSREQRYTKKADWGYIAECAAMIKSYNEEKDKITDTAREPDESTLPNAKDGRMF 606

Query: 191 IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
              NG      +  + +    VD VMIGR A     +   +++
Sbjct: 607 FLGNGDCYSHVEYYEHIEKAKVDTVMIGRGALVKPWLFEEIEK 649


>gi|253744195|gb|EET00435.1| tRNA dihydrouridine synthase, putative [Giardia intestinalis ATCC
           50581]
          Length = 459

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 89/237 (37%), Gaps = 31/237 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK------NILGFSTQEKPLALQI 54
           MVD ++  YR   R      L +T M   + ++   K        +    + ++PL LQ+
Sbjct: 24  MVDGSELPYRLLTRRYGVE-LAWTPMYNTNNLVTSSKAMNQLVAELKYGGSIDRPLVLQL 82

Query: 55  GGADISKLVEA----AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            G + S    A     ++     ++ + LN+GCP A    G +GA LM +  +  + +  
Sbjct: 83  SGNNPSNFEIAYNTLIQMGAGHCFDVVELNMGCPQAVALRGKYGAYLMGHLSLAEEILKI 142

Query: 111 MCKALSI-----PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +    ++      V VK R+             +   +  +GV  + +H R  + +  S 
Sbjct: 143 LVAVTTLSGLGHKVAVKTRL----DTSVADTVAMCLRLCSTGVAMLTLHGRTKVQRTGS- 197

Query: 166 KDNRKIPNLDYDIVYEI----KKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIG 216
                +   D+  +  +    +   P +    NGG+ ++    ++       G M  
Sbjct: 198 ----AVGPPDWQALASVFKDLRAAYPQMVFFANGGVWNIETHERLCTFTGCHGTMSA 250


>gi|226321186|ref|ZP_03796724.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           29805]
 gi|226233406|gb|EEH32149.1| putative histidine phosphokinase/phophatase [Borrelia burgdorferi
           29805]
          Length = 188

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 40/176 (22%), Positives = 81/176 (46%), Gaps = 15/176 (8%)

Query: 1   MVDWTDRHYRFFARLLTNN----ALLYTEMIVADAILRGDKKNI----LGFSTQEKPLAL 52
           M D TD  +R    L+ +      + +TE I    IL G K+++    L  +   +PL  
Sbjct: 17  MEDVTDTVFRNLIHLIGSAEGEPHIYFTEFISTKGILNGSKQSVQHIFLKPNELNRPLIA 76

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           QI G    +   A +I+   G+  I++N+GCP +++ +    + L+ N  +  + I A  
Sbjct: 77  QIWGNVPEQFYRAIEILGGMGFWGIDINMGCPKSKIIKKGVCSALINNKSLAKEIILASK 136

Query: 113 KAL---SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +A    ++P++VK R G         + + +  +    ++ + ++ R A+ +   P
Sbjct: 137 EACARFNLPLSVKTRHGF----SYPEVDDWLGFLLGLEIDMLTVYPRLAVNQSKGP 188


>gi|328851782|gb|EGG00933.1| hypothetical protein MELLADRAFT_39468 [Melampsora larici-populina
           98AG31]
          Length = 224

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 97/238 (40%), Gaps = 35/238 (14%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILR---------GDKKNILGFSTQEK---- 48
           VD +D  +R          ++YT+MI AD  L           D K        E+    
Sbjct: 5   VDQSDLPFRILVAR-HGATMVYTQMIWADRFLSDPQYHDFHLNDVKAWCKRKDIEQDLTK 63

Query: 49  -PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            PL +Q+GG D+ +++  AK  E +  + I+LN+GCP     +  +GA L+   +     
Sbjct: 64  IPLIVQLGGNDVERVLRTAKCFEPW-CDGIDLNMGCPQTHALQNGYGASLLFRKNH---- 118

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                +A+SI ++         +   +   NLV   +++G + I +H R           
Sbjct: 119 ----DQAISIGISTSSLSYKCKEKAHIW--NLVLLSRQAGASWITLHPR------FISCR 166

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            R+  +     V E+K+    + +  NGG+   S   K L     DG+M+G     N 
Sbjct: 167 RRRKGSPFLRFVKELKQAV-KIPVISNGGVRSYSDFEKNLNETGADGLMVGEPLLTNP 223


>gi|331211843|ref|XP_003307191.1| up-regulated in lung cancer 8 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309297594|gb|EFP74185.1| up-regulated in lung cancer 8 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 464

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 91/243 (37%), Gaps = 24/243 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG----DKKNILGFSTQEKPLALQIGG 56
           MV       R  A       L++   IV  AI+      D      F      L  QIG 
Sbjct: 129 MVRIGTLPTRLLALEY-GADLVWGPEIVDKAIIGSTRVVDADRRSDFRKSR--LIYQIGS 185

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA------- 109
           A+    ++AA+ V +   + I+LN GCP     +G  GA L+  PD +            
Sbjct: 186 ANKELALQAAQTVAN-DVSGIDLNCGCPKDFSLKGGMGAALLKEPDKLCGVRFSHPINSN 244

Query: 110 --AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              +    + P++VK R+    +       +LVK I  +GV+ + +H R   ++   P  
Sbjct: 245 SLEIQNLPTHPISVKIRLLPSQEDT----LSLVKKICDTGVSCLTVHCRTQPMRSTEPAL 300

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAM 225
             ++  +  D V  I+     L +  NG           K L  V  VMI R A  N + 
Sbjct: 301 LHRLREI-VDFVNGIRTSENPLPVVANGDCFSAQDLPKFKELTGVSRVMIARGAESNVSC 359

Query: 226 LTT 228
              
Sbjct: 360 FRQ 362


>gi|159469612|ref|XP_001692957.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158277759|gb|EDP03526.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 283

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 93/228 (40%), Gaps = 36/228 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG-------------------DKKNIL 41
           MV    +  R  A       ++Y+E +VA  ++                       + + 
Sbjct: 12  MVRVGMQPMRLLAASY-GADIVYSEELVAQRVIASTRVVNEELQSIDFLDRGGEHGRVMF 70

Query: 42  GFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
             + +E+P L  Q+G AD    ++AA++V      E+ LN+GCP A   +G  GA L+  
Sbjct: 71  RTTAEERPRLVFQLGAADAVLALQAAQVVAG-DVAEVGLNMGCPKAFSLQGGMGAALLRK 129

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           P+I  D +  + + L+IPV+ K R+   DQ        L + +   G+N + +H R    
Sbjct: 130 PEIAEDIMKTLHRNLNIPVSCKIRLLDTDQDTV----ELARRLAACGINALAVHGRTT-- 183

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKE-NPD-LFIGLNGGLEDMSQALKI 206
                   R      +D +  +     PD + +  NG +     A ++
Sbjct: 184 ------QQRPRDPAHWDPIRLVVDALAPDGVPVVANGDVFTWEDAQRV 225


>gi|308161253|gb|EFO63708.1| Embryo-related protein [Giardia lamblia P15]
          Length = 406

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 93/230 (40%), Gaps = 30/230 (13%)

Query: 23  YTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE---- 76
           +T+M  ADA+L        +L  +   + + LQ+ G +      AA+++ D         
Sbjct: 86  FTQMYTADALLHNSLLRDVVLSTAASGEKVILQLCGNNPFSFRTAAELLYDSPIASQLIA 145

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           +++N+GCP++      +G  +  N  +V   I+        PVT K R     +     +
Sbjct: 146 LDINLGCPASCASSRGYGFYVTQNWPLVHRIISETSSTRLFPVTCKIRPLNSIEKTVDYM 205

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY---------------- 180
             LV     SG +GI IH R    +G   +  +        +V+                
Sbjct: 206 LLLV----MSGASGITIHMRHTTRQGKHAQSVKPAYLEFEKLVHTFRQKLDTLFNSLDRS 261

Query: 181 EIKKENPD--LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           EI +E       I LNGG+++  +A  +L +   DGVM+G    KN   L
Sbjct: 262 EIAREKSHLYPVIILNGGIKNRQEADHLLTTYPADGVMLGVGLLKNPTCL 311


>gi|146095124|ref|XP_001467487.1| dihydrouridine synthase (Dus) [Leishmania infantum JPCM5]
 gi|134071852|emb|CAM70545.1| putative dihydrouridine synthase (Dus) [Leishmania infantum JPCM5]
          Length = 660

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 51/412 (12%), Positives = 106/412 (25%), Gaps = 140/412 (33%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQE---------- 47
           MVD ++  +R   R      + YT M+ A     G       +     +E          
Sbjct: 120 MVDQSELPFRMLCRQY-GATVAYTPMLHAKCFAEGAVYRSHFLSVCPPEEVKAAMEASLA 178

Query: 48  ----------------------------------KPLALQIGGADISKLVEAAKIVED-- 71
                                             +P  +Q  G D   ++ AA+      
Sbjct: 179 SPPIAAGGHGGGSSMRGGVGAGSENAVADTALVDRPCIVQFCGNDADTVLRAARFAVLGE 238

Query: 72  ----------------------------------------FGYNEINLNVGCPSARVHEG 91
                                                   +  + ++LN+GCP      G
Sbjct: 239 QAAAAEQTSGSGGASVAPVYPVHVRVNGLSSSEKAPEHLLYQCDAVDLNLGCPQGIARRG 298

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN------------- 138
            +G+ LM + +++   +  +   L +PVT K R+         A                
Sbjct: 299 HYGSFLMEDWELIHTIVHTLHVELEVPVTAKIRVFDHPGHVEAAGDKRECATNCSSAACQ 358

Query: 139 ---------------------------LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
                                        + I+ +G   + IH R   +KG      ++ 
Sbjct: 359 ESDAVCAAADTSREPMKEAFDEALTILYARMIRDAGAQVLCIHGRTREMKG------QQT 412

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
              + +++  ++      + +  NG +      +  L     +G M       +  + + 
Sbjct: 413 GLANMELIRRVRDALGGTIPVISNGNVRTYDDVIDHLQETRCEGHMCAEPLLWDPKLFSN 472

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGKLQQITRH 279
             +      T  +   TR+       +    +  Y          L ++  H
Sbjct: 473 PSQPVMPGRTHGADKATRLSALHTALVYMQWVRHYPVDIGFVKAHLFKMCFH 524


>gi|322701013|gb|EFY92764.1| tRNA dihydrouridine synthase (Smm1), putative [Metarhizium acridum
           CQMa 102]
          Length = 413

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 58/210 (27%), Positives = 90/210 (42%), Gaps = 20/210 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + VEAA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 104 LIFQIGTADPDRAVEAARLVAA-DVAGIDVNAGCPKPFSTSGGMGAALLRTPDKLVAILE 162

Query: 110 AMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +     I ++VK RI             LV+ +  +G+ G+ +H R   ++   P
Sbjct: 163 ALVKNITPEFDIGISVKIRIL----ETPAETEALVRRLVATGITGLTVHCRTTPMR---P 215

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++      L   +V  I  E   +   +NG +E+  Q LK+      DG MI  AA KN 
Sbjct: 216 RERAIRDQLR--MVANICHEAG-VACIMNGDVENRDQGLKLAEKYGADGAMIAVAAEKNP 272

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +   +        L G  P+  +  K    
Sbjct: 273 SCFRS---EADGGLLGWEPVVEQYIKYAME 299


>gi|320593462|gb|EFX05871.1| tRNA dihydrouridine synthase [Grosmannia clavigera kw1407]
          Length = 752

 Score =  122 bits (306), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 53/279 (18%), Positives = 86/279 (30%), Gaps = 56/279 (20%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN---ILGFSTQEKP------------- 49
           +  +R     L   A  Y+EM +   +L G       +   +T+  P             
Sbjct: 353 NLPFRRLCVELGCEA-TYSEMALGLDLLTGKPSEWALLKAHATEAVPPRVDSVRSAQTAG 411

Query: 50  --------LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLML 99
                      QI        ++A + +     +   +++N GCP   + +   G+ L+ 
Sbjct: 412 YDNGRDLRFGAQIAANQPWMAIKATEALSRLVPHLRLVDMNCGCPIEMLFKTGGGSGLLE 471

Query: 100 NPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAV--ALRNLV-------KSIKKSGVN 149
             + +   I  M      +P+T K R+GV D  P     +  L          +   G  
Sbjct: 472 AHNKLERMIRGMNAVSGEVPITAKLRVGVRDGSPTAHKVIERLAFGGVETRGRLGAPGCA 531

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDY-------------DIVYEIKKEN----PDLFIG 192
            I +H R    +   P D R I                  D V E           +F  
Sbjct: 532 AITLHGRTRNQRYKKPADWRYIAECAALVRSYNESRDKITDTVREPDDRTLPPGGRIFFL 591

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            NG      Q    +    VD VMIGR A     +   +
Sbjct: 592 GNGDCFSHEQYRAQIDQADVDTVMIGRGALVKPWIFEEI 630


>gi|326475386|gb|EGD99395.1| tRNA dihydrouridine synthase [Trichophyton tonsurans CBS 112818]
          Length = 419

 Score =  122 bits (306), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 101/245 (41%), Gaps = 38/245 (15%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             Q+G A     VEAAK++ D   + I++N GCP      G  GA L+  PD +   + A
Sbjct: 109 VFQLGTASPELAVEAAKVIAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDKLVSILEA 167

Query: 111 MCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +  P    ++VK R+  D +        LV ++  +G+ G+ +H R   ++     
Sbjct: 168 LVREVGQPWQIGISVKIRLLKDPRDT----ERLVTALCATGITGLTVHCRTTPMRPREAA 223

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              ++P     ++  I +    +   +NG ++    AL+++    VDG MI  +A  N +
Sbjct: 224 IRDQLP-----MIASICRSAG-VACLMNGDVKSRDHALELMSQYDVDGAMIATSAESNFS 277

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
              +  +                    WR+++      A    +  G     T++++ +F
Sbjct: 278 CFRSAAD---------------GGCVSWRELAHEYVAVAMECENKWGN----TKYLLNIF 318

Query: 285 HGFPN 289
              P 
Sbjct: 319 --LPG 321


>gi|242020724|ref|XP_002430802.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
 gi|212515999|gb|EEB18064.1| tRNA-dihydrouridine synthase, putative [Pediculus humanus corporis]
          Length = 622

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 44/286 (15%), Positives = 107/286 (37%), Gaps = 32/286 (11%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNIL--GFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +  +E +VA++IL+      L       E+   +Q+ G +   + 
Sbjct: 287 NLPFRRICKEF-GADVTCSETVVANSILQSQPFEWLLTKRHETEELFGIQLFGNNPFIMT 345

Query: 64  EAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              +++E+    + I++ +G P+  +         +    +V   +  + +  S+P+TV 
Sbjct: 346 RCGQLLEEKTNVDFIDICIGSPNDTMVRPRGTTSQVRREKVVETIVRCLSRVSSLPLTVT 405

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R+G  D          + + K   ++ + +  R           NR+   +D+  V ++
Sbjct: 406 TRLG--DYSDEKISNKFLPNYKSCEISLLTVQGR-----------NRETKQMDWKYVNDL 452

Query: 183 KKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            ++   + +     +   +  L I    P++ GV++ R A     + + + E     ++ 
Sbjct: 453 AQKVSPVKVYGLSDVFSYTDYLDIQENYPNLSGVLLSRGALVKPWIFSELKEQRDWDISS 512

Query: 240 SSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI--GL 283
                         +I     +Y   H  S  K  ++TR  +   L
Sbjct: 513 GERF----------EIIKKFVNYGLEHWGSDTKGVELTRRFLLDWL 548


>gi|301510952|ref|ZP_07236189.1| TIM-barrel protein, nifR3 family protein [Acinetobacter baumannii
           AB058]
          Length = 119

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 32/104 (30%), Positives = 53/104 (50%), Gaps = 3/104 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TDR +R   +         +EM+ AD  LR  KK++    F  +  P++ QI G+D
Sbjct: 17  MAGVTDRPFRTLCKYF-GAGHAVSEMMTADKTLRMTKKSLYRANFDGELAPISAQIAGSD 75

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +L EAA+     G   +++N+GCP+ +V     G+ L+ + D
Sbjct: 76  PEQLAEAARYQVANGAQIVDINMGCPAKKVCNKLAGSALLQDED 119


>gi|225374618|ref|ZP_03751839.1| hypothetical protein ROSEINA2194_00234 [Roseburia inulinivorans DSM
           16841]
 gi|225213543|gb|EEG95897.1| hypothetical protein ROSEINA2194_00234 [Roseburia inulinivorans DSM
           16841]
          Length = 326

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/291 (18%), Positives = 107/291 (36%), Gaps = 26/291 (8%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           M   T   YR  + +   +    +T  I    +    KK+I     Q   +  QI     
Sbjct: 8   MEGLTGYIYRNAYQKYFHDIDRYFTPFITNKKLDFKVKKDIDPEHNQGMEVVPQILTNQP 67

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
              +     ++ +GY+E+NLN+GCPS  V   + GA  +  PD +   +  +  A    +
Sbjct: 68  DDFISIVNQLKQYGYDEVNLNLGCPSGTVVAKNRGAGFLAVPDELDSFLDKIFNACDCKI 127

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G D         NL+   +K  ++ + +H R                       
Sbjct: 128 SIKTRVGKD---SPDEWENLLAIYEKYPLSELIVHPRIQKDFYKYTPRMET--------- 175

Query: 180 YEIKKENPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTT---VDEYF 233
           Y+   E+    +  NG +       +  +  P  + VM+GR   ++  ++     V+  F
Sbjct: 176 YQYAAEHSRHSLCFNGDIHSVGAYGRLRQTFPETEKVMLGRGILQDPGLVGELRMVEAQF 235

Query: 234 SNPLTGSS-------PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
           +   TG+         +  +  + F   I        +   ++  K++++ 
Sbjct: 236 AAKDTGTPVGNKKCNVVDKQTLRAFHDDICDGYKGVMSGDRNTLFKMKELW 286


>gi|322707013|gb|EFY98592.1| tRNA dihydrouridine synthase (Smm1), putative [Metarhizium
           anisopliae ARSEF 23]
          Length = 457

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 55/210 (26%), Positives = 88/210 (41%), Gaps = 20/210 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG AD  + VEAA++V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 148 LIFQIGTADPDRAVEAARLVAA-DVAGIDVNAGCPKPFSTSGGMGAALLRTPDKLVAILE 206

Query: 110 AMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ K +     I ++VK RI             LV+ +  +G+ G+ +H R   ++    
Sbjct: 207 ALVKNITPEFDIGISVKIRIL----ETPAETEALVRRLVATGITGLTVHCRTTPMRPRER 262

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               ++      +V  I  E   +   +NG +E+  Q +K+      DG MI  AA KN 
Sbjct: 263 AIRDQL-----RMVANICHEAG-IACIMNGDVENRDQGIKLAGEYGADGAMIAVAAEKNP 316

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +   +        L G  P+  +  K    
Sbjct: 317 SCFRS---EADGGLLGWEPVVEQYIKYAME 343


>gi|295110086|emb|CBL24039.1| tRNA-U20a,U20b-dihydrouridine synthase [Ruminococcus obeum A2-162]
          Length = 316

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 54/290 (18%), Positives = 104/290 (35%), Gaps = 27/290 (9%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGA 57
              T+  YR             +   I A   L    +       +         QI   
Sbjct: 9   EGITNHIYRKALHECFGGFDKYFIPFIRAKQNLNFSGREKKDIDPENNHGMYAVPQILTR 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +    +  A  +   GY EINLN+GCPS  V     GA  +   D +   +  +     +
Sbjct: 69  NADDFLRTASQLAGLGYREINLNLGCPSKTVVTKGCGAGFLDRTDELERFLNHIFANTDL 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K R+G+DD   A    +L++   +  +  + +H R            + +PNL+  
Sbjct: 129 KISIKTRLGMDD---AEEFEDLLEIYNRFPLEELIVHPRVQKDFY------KNVPNLEAF 179

Query: 178 IVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                K +NP  +   NG +   ED ++  +  PSVD  M+GR      ++   +     
Sbjct: 180 EYAVQKSKNPLCY---NGDIFSAEDFAKVQERFPSVDCFMMGRGVLALPSLAKEIR---- 232

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
               G         + F   +  +     +   +   K++++  ++  +F
Sbjct: 233 ----GGKAADKEEIRKFHDIVYHTYCQEVSGDRNVLFKMKELWFYLAPMF 278


>gi|219116258|ref|XP_002178924.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409691|gb|EEC49622.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 497

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 91/336 (27%), Positives = 131/336 (38%), Gaps = 72/336 (21%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-------------RGDKKNILGFSTQE 47
           M  +T    R   R L+ NA L+TEM   + +L                 +N    S+Q 
Sbjct: 42  MQCYTHAPLRQLYRTLSANATLWTEMEKVEDLLATGSKGLERRFGRYWTNRNTHASSSQP 101

Query: 48  KPLALQIGGADISKLVEAAKIV-------EDFGYNEINLNVGCPSARVHEGS---FGACL 97
           + L LQIGG    KL E    +       + F + ++NLN GCP   +  G    +GA L
Sbjct: 102 ENLVLQIGGNQPDKLRECLLRLSAQSQDQDAFPFTQVNLNCGCP--GIEAGGATTYGASL 159

Query: 98  MLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQI------------------------ 131
           M  PD  G  +  M   L     V++KCRIGV D                          
Sbjct: 160 MKQPDYTGTLLQTMRDVLPSTTKVSLKCRIGVVDTPADLSLRTEATRSGGDAVHDTTTVA 219

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
              AL   V   + +GV+ + +HAR A+L GLSP  NR +P+LDY +V  I  + PDL +
Sbjct: 220 SYQALHRYVSIARDAGVSHVILHARVAVLTGLSPSKNRIVPSLDYRMVERIATDFPDLRV 279

Query: 192 GLNGGLEDMSQALK-----------------ILPS---VDGVMIGRAAYKNSAMLTTVDE 231
            LNGG+ ++    +                 +LP    V   M GR   +    L  V +
Sbjct: 280 TLNGGIRNLGDLQRLRRFTSSPTTKTTCTPPVLPENSLVASHMAGRWMLRRPLDLAAVQD 339

Query: 232 YFSNPLTGSSPIKT-RVDKDFWRKISASMTDYAARH 266
           YF    +     K  +       +      DY  + 
Sbjct: 340 YFDAEASDEGDGKPGKHIGAVAAQALERYVDYVTKE 375


>gi|163815550|ref|ZP_02206923.1| hypothetical protein COPEUT_01715 [Coprococcus eutactus ATCC 27759]
 gi|158449187|gb|EDP26182.1| hypothetical protein COPEUT_01715 [Coprococcus eutactus ATCC 27759]
          Length = 322

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/284 (18%), Positives = 106/284 (37%), Gaps = 27/284 (9%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T   YR    +        +   I       +   + +++L  + Q   +  Q+  
Sbjct: 13  MEGITGYIYRNAHHKYFGGVDKYFMPFIAPAKGRPLRNRELRDVLPENNQGINVVPQLLT 72

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 V+AAK ++  GY E+N+N+GCPS  V     GA L+ + + + + +  +  A  
Sbjct: 73  NSGEGFVKAAKFLKKLGYGEVNINLGCPSKTVVTKYKGAGLLYDTERLDNFLYEVFAAGV 132

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V++K RIG D    +V   +++   KK  V+ + IH R       +  +         
Sbjct: 133 MDVSIKTRIGRD---SSVEFEDIIDIYKKYPVSELIIHPRVQTDFYKNTPNM-------- 181

Query: 177 DIVYEIKKENPDL-FIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++  E          +  NG +    D  + +   P +  VMIGR    +  +   +   
Sbjct: 182 EVFAEGVAAYGRTDTVCYNGDINSVADYERFIGNYPDIMKVMIGRGMIADPCLAERIK-- 239

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                  ++  +T     F+        +Y    +  G  + ++
Sbjct: 240 ------STATGRTYDWNRFFTFHDELYRNYCESDVGRGNTMFKM 277


>gi|255010234|ref|ZP_05282360.1| nifR3 family TIM-barrel protein [Bacteroides fragilis 3_1_12]
 gi|313148028|ref|ZP_07810221.1| dihydrouridine synthase [Bacteroides fragilis 3_1_12]
 gi|313136795|gb|EFR54155.1| dihydrouridine synthase [Bacteroides fragilis 3_1_12]
          Length = 311

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 96/235 (40%), Gaps = 18/235 (7%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A +     + +T  +  D       D ++IL  + +   L  Q+  ++ 
Sbjct: 14  GYTEAAYRNAHAAVFGGIDVYHTPFVRVDRGEFRHKDVRDILPENNRVARLIPQLIASEA 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K      +  + GY EI++N+GCP   + +   G+ ++  PD V   +    +   I  
Sbjct: 74  DKTERMIALFIEQGYREIDINLGCPFPMLAKRQCGSGMLPYPDKVEALLKQTEQFPDIRF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +     ++   L+  +  + +  I +H R  I +     D        +   
Sbjct: 134 SVKMRLGWEKPDECLS---LIPLLNAAPLTEITLHPRLGIQQYKGEVDMEG-----FTSF 185

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDE 231
           YE  +      +  NG +  ++   +I    P++ GVMIGR    N A+     E
Sbjct: 186 YEACRH----PVVYNGDILTIADIHRITDRFPNLAGVMIGRGLLTNPALGWEYKE 236


>gi|145344190|ref|XP_001416620.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576846|gb|ABO94913.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 345

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 92/248 (37%), Gaps = 36/248 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--------------DKKNILGF--- 43
           MV  +    R  A       L+Y E +V    +                D K  L F   
Sbjct: 20  MVRISTLATRLLAHEY-GADLVYGEELVDKRFMHCRRILNKELGSVDFIDAKGTLTFRTV 78

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             + + +  Q+G +  +  +++A++V       I++N+GCP      G  GA L+  P++
Sbjct: 79  PEERERVVFQVGTSSAASALKSAELVA-RDVAAIDVNMGCPKHFSTSGGMGARLLSQPEL 137

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           V D +  + + L     VT K R+   ++  A     L K I+  GV+   +H R     
Sbjct: 138 VRDILTTLRRNLPSTTHVTCKIRLLESERETA----ELAKMIESCGVSAFAVHGRYIP-- 191

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAA 219
                  R      ++++  +  E  D  +  NG +E       ++        M  R A
Sbjct: 192 ------QRPREPAHWNLIKNVV-EAVDCPVIANGDVECYEDFARIRAQTGAASAMCARGA 244

Query: 220 YKNSAMLT 227
             N ++  
Sbjct: 245 QWNLSIFR 252


>gi|156844300|ref|XP_001645213.1| hypothetical protein Kpol_1060p9 [Vanderwaltozyma polyspora DSM
           70294]
 gi|156115872|gb|EDO17355.1| hypothetical protein Kpol_1060p9 [Vanderwaltozyma polyspora DSM
           70294]
          Length = 383

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 70/333 (21%), Positives = 125/333 (37%), Gaps = 74/333 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFS------------- 44
           MV   +   R  A L     LL+T  I+   ++   R + KN+                 
Sbjct: 13  MVRAGELPTRLLA-LQHGADLLWTPEIIDKKLIQCTREENKNLDTVDFIIPSKTDNKPST 71

Query: 45  --------TQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGA 95
                    ++  L  Q+G +  +  VEAA KIV D   + I++N GCP         GA
Sbjct: 72  LVFRTFPKNEQGKLIFQMGTSSPTLAVEAALKIVND--VDGIDINAGCPKHFSIHSGMGA 129

Query: 96  CLMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            L+  PDI+   +  +   +    + P++VK RI  D +        LV+ +  +G++ +
Sbjct: 130 ALLKTPDILCSILENLVSKVGKPYNKPISVKIRILDDKETTVA----LVERLCTTGISNL 185

Query: 152 WIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
            +H R       +P  NR+ P  DY   + EI ++N ++ + +NG +++     ++   +
Sbjct: 186 TVHCRT------TPMRNREAPIRDYIPSIKEICEKN-NVSLIMNGAIKNKVHFKELREEL 238

Query: 211 D-----GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
                 G MI   A  N  + +       NPL              W  +       A  
Sbjct: 239 GLSKDIGGMIAECAETNPTVFSQ------NPL-------------MWYDVCKQYIKIANE 279

Query: 266 HLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
             +  G     T++M+      P        ++
Sbjct: 280 FENIIGN----TKYMLN--RIIPGKSEFYQYIS 306


>gi|291528191|emb|CBK93777.1| tRNA-dihydrouridine synthase [Eubacterium rectale M104/1]
          Length = 312

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 114/268 (42%), Gaps = 20/268 (7%)

Query: 22  LYTEMI-VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
            YT  I  A  +    K++I   +     L  Q       ++++  + +  +GY+EIN+N
Sbjct: 30  YYTPFIPAAKRMNAKIKRDIDPVNNDGITLIPQAMSIVADEVIDLHRQLVPYGYDEINVN 89

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCPS  V     G+ ++  PD++   +  +      PV++K R+G +D         L+
Sbjct: 90  LGCPSGTVVSKKRGSGILAYPDMLDSFLDELYTKADFPVSIKTRVGFNDD---ELWPKLI 146

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLED 199
           +   K  ++ + +H R            +  P +D D    ++K NPD   +  NG + D
Sbjct: 147 EIYSKYPISELTVHPRVQKDFY------KNTPRMD-DFALAMQKINPDKTTLCYNGDITD 199

Query: 200 ---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               +      P +D +MIGR  + N A++  +       ++          +++  +I 
Sbjct: 200 TNSFNALTDCFPDIDEIMIGRGLFANPALIAELK-----GISMDKAELRERLRNWHDEIL 254

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLF 284
           +      +    +  ++++I  +M G+F
Sbjct: 255 SGYLSIFSGEKDAIFRMKEIWAYMHGMF 282


>gi|218512468|ref|ZP_03509308.1| tRNA-dihydrouridine synthase protein [Rhizobium etli 8C-3]
          Length = 204

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 71/186 (38%), Gaps = 25/186 (13%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A  KA+ IPVT+K R+G D+   ++   ++ +  + +G+  + IH R  +       
Sbjct: 5   LIEATVKAVDIPVTLKMRLGWDE--NSINAPDIARRAEAAGIQLVTIHGRTRM------- 55

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                   D+D +  + ++   + +  NG +E    A +IL     D VMIGR       
Sbjct: 56  -QFYDGRADWDAIRAV-RDVISIPLIANGDVETAEDAQEILRRSGADAVMIGRGCQGRPW 113

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
                    +  L G++  +     D   +    M D+          ++   +H+    
Sbjct: 114 H--------AGVLAGAAEPQREDIADIAVEHYRMMLDFYGE----AVAIRHARKHLGWYL 161

Query: 285 HGFPNS 290
             F  +
Sbjct: 162 ERFAPA 167


>gi|303286323|ref|XP_003062451.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
 gi|226455968|gb|EEH53270.1| dihydrouridine synthase [Micromonas pusilla CCMP1545]
          Length = 346

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 45/219 (20%), Positives = 87/219 (39%), Gaps = 15/219 (6%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVED 71
           ++ + N+A    E +       G +  I     +E+  L LQ+G  D ++ ++ A +   
Sbjct: 50  SKRVENHAFGTVEFVNTKENSSGFRDVIFQTIPEERGRLVLQLGTGDATRALKCALLAAK 109

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
              + +++N+GCP         G+ L+  P+ V D +  + + L   V V C+I + +  
Sbjct: 110 -DISAVDINMGCPLKFSTSSGAGSALLKKPEQVRDIMTTLRRNLPSEVHVTCKIRLLETT 168

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                  L + I+  GV+   +HAR            R      +D++  +  E+    +
Sbjct: 169 --EKTIELARVIEACGVSAFGVHAR--------YVSQRPRQPAHWDLMKHVV-ESVSCPV 217

Query: 192 GLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTT 228
             NG +       +I         M GRAA  N ++   
Sbjct: 218 IANGDVFKHEDFERIKSETGAASAMCGRAALWNLSVFRE 256


>gi|159110381|ref|XP_001705451.1| Dihydrouridine synthase, putative [Giardia lamblia ATCC 50803]
 gi|157433536|gb|EDO77777.1| Dihydrouridine synthase, putative [Giardia lamblia ATCC 50803]
          Length = 555

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 47/253 (18%), Positives = 91/253 (35%), Gaps = 33/253 (13%)

Query: 8   HYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEA 65
            +R    +     +   EM+ A  IL GD + +  +     EK   +Q+ G     + E 
Sbjct: 188 PFRRLC-IHYGCEITLCEMVFARDILHGDAQELRKIKRHPDEKCFGIQLAGRGQELM-EI 245

Query: 66  AKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KALSIPVTV 121
              +      + I+LN  CP     +   GA L  N   +   +  M    +   +PV +
Sbjct: 246 VNFISQCCSCDFIDLNAACPQDIATKKCCGAALAANLKKLVSSVDCMVRGGEHYGVPVFL 305

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY----- 176
           K R G  D        ++ ++++ SG+ G+ +H R A  +     +   + ++ +     
Sbjct: 306 KIRAG--DLRGDWTGDSVAQALRLSGLYGLSVHLRTAKQRYSKLANWDYLVSMRHALDNC 363

Query: 177 ------DIVYEIKKENPD-----------LFIGLNGGLEDM-SQALKILPSVDGVMIGRA 218
                 D+  ++K +                +G NG + D          +VD  +I R 
Sbjct: 364 EESTAPDLEPQLKHDISSSTTNRPIIRTPPLLGGNGDIFDYTDLHRDDHSTVDYYLIARG 423

Query: 219 AYKNSAMLTTVDE 231
           A     +   + E
Sbjct: 424 ALVKPWIFQEIKE 436


>gi|154299041|ref|XP_001549941.1| hypothetical protein BC1G_11833 [Botryotinia fuckeliana B05.10]
 gi|150857536|gb|EDN32728.1| hypothetical protein BC1G_11833 [Botryotinia fuckeliana B05.10]
          Length = 434

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 87/188 (46%), Gaps = 17/188 (9%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + K L  QIG +D  + V+ A+IV       I++N GCP      G  GA L+  PD + 
Sbjct: 108 EGKKLIFQIGTSDPERAVQCARIVAA-DVAGIDVNAGCPKPFSTSGGMGAALLQTPDKLC 166

Query: 106 DCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ + +     I ++VK R+       A     LV+ +  +G+ G+ IH R   ++
Sbjct: 167 AILEALVREIVPEFEIGISVKIRLL----ETAEKTEALVRKLCATGITGLTIHCRTTPMR 222

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
                   ++      ++ +I +E+  +   +NG +E+  QALK+      +G MI  AA
Sbjct: 223 PRERAIREQLK-----MIADICRESG-VACLMNGDVENRDQALKLAEEFGTNGGMIAVAA 276

Query: 220 YKNSAMLT 227
             NS+   
Sbjct: 277 EANSSCFR 284


>gi|229825556|ref|ZP_04451625.1| hypothetical protein GCWU000182_00917 [Abiotrophia defectiva ATCC
           49176]
 gi|229790119|gb|EEP26233.1| hypothetical protein GCWU000182_00917 [Abiotrophia defectiva ATCC
           49176]
          Length = 323

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 68/329 (20%), Positives = 115/329 (34%), Gaps = 54/329 (16%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVAD---AILRGDKKNILGFSTQEKPLALQIGG 56
           M   T R +R  F +        YT  I       + + D K +   + +   +  QI  
Sbjct: 11  MEGITGRIFRKTFNKYFKGVNDYYTPFITPKEKRGLDKKDIKELAPENNEGITIIPQILS 70

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM---CK 113
                   AA+ +   GY E+NLN+GCPS  V     G+  + + D +   +  +     
Sbjct: 71  NSAEAFNLAAEKLMRLGYKEVNLNLGCPSGTVVNKGRGSGALKDLDSLEKLLTLIYSKSA 130

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKI 171
              + ++VK RIG +    A    N++   KK  V  + IH   R    KG   K++  +
Sbjct: 131 NTGLKISVKTRIGYE---KAEEFENILSLYKKFPVEKLIIHPRSRTEFYKGEVHKESFAL 187

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTT 228
              +Y  +    +      +  NG L  ++      +  P +  +MIGR   ++  ++  
Sbjct: 188 AVDEYLKIGAADR------LCFNGELNTVADIKNLNEEFPDISRIMIGRGLLRHPFLIEG 241

Query: 229 V----------------DEYFSNPLT--GSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
           V                DE F    T    SP      K+ W  I  S  D         
Sbjct: 242 VLEKESEDRKVRLKNYLDELFYTYFTEFNGSPAAVLKMKELWYYIKESFRDCED------ 295

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHILTV 299
             ++ I +          N+   R  + V
Sbjct: 296 -YIKDIRK--------AKNAAEYRAAVNV 315


>gi|50290121|ref|XP_447492.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49526802|emb|CAG60429.1| unnamed protein product [Candida glabrata]
          Length = 371

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 103/253 (40%), Gaps = 40/253 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------ILGFST- 45
           MV   +   R  A       L+++  I+   +++  +                +L F T 
Sbjct: 13  MVRAGELPTRLMALKY-GAGLVWSPEIIDKKLIQTQRVENSSLSSVDYVMPSGVLVFRTV 71

Query: 46  ---QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   L  QIG AD +   EAA  V     + I+LN GCP         G+ L+  P+
Sbjct: 72  PSLERGKLIFQIGSADPALAKEAALKVIQ-DVDGIDLNCGCPKHFSIHAGMGSALLKKPE 130

Query: 103 IVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            +   +  + + +      P++ K R+  D+     +   LVK I  +G+  + +H R  
Sbjct: 131 KLCSILKELVEHVGTPHGKPISCKIRLLEDE----ASTLELVKMICDTGIRNLTVHCRT- 185

Query: 159 ILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVM 214
                +P  NR+ P  DY D ++ + K+   + + +NG +    +  ++    P + G M
Sbjct: 186 -----TPMRNRETPIRDYIDSIFSVCKKAG-VSLLINGAIRHREEFEQLFSYNPEIGG-M 238

Query: 215 IGRAAYKNSAMLT 227
           I  AA  N  + +
Sbjct: 239 IAEAAESNPTVFS 251


>gi|150016954|ref|YP_001309208.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
 gi|149903419|gb|ABR34252.1| dihydrouridine synthase, DuS [Clostridium beijerinckii NCIMB 8052]
          Length = 318

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 44/289 (15%), Positives = 104/289 (35%), Gaps = 27/289 (9%)

Query: 22  LYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
            +   I      +    +  ++L    +   +  QI   +    ++    +  FG NE+N
Sbjct: 30  YFMPFISPTKNKSFTSRELNDVLPEHNEGINVIPQILTNNSEYFIDTVNQLGKFGNNEVN 89

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN+GCPS  V     G+  +     + + +  +    S  +++K RIG D          
Sbjct: 90  LNLGCPSGTVVAKHKGSGFLAQRKQLDEFLEDIFSNASTKISIKTRIGKD---SPDEFYE 146

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L++   K  +  + IH R       +  +     +                 +  NG + 
Sbjct: 147 LIEIFNKYPLEELIIHPRIQTDFYKNKPNMEVFKDAL---------ALSKNPVCYNGDIF 197

Query: 199 DMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
           ++       +  P ++ VM+GR    N  ++  +          +  +   + K F  K+
Sbjct: 198 NIEDYKKLSEAYPKLETVMLGRGLIANPGLIEEIKT--------NRVMDKELMKSFHDKV 249

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLF-HGFPNSRRCRHILTVEAGA 303
                +  +   +   K++++  +MI +F +    +++ R   +++   
Sbjct: 250 CTGYEEVLSGDRNVLFKMKELWFYMIHMFSNSDKYAKKIRKTNSLQEYK 298


>gi|308159933|gb|EFO62447.1| Dihydrouridine synthase, putative [Giardia lamblia P15]
          Length = 556

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 50/287 (17%), Positives = 99/287 (34%), Gaps = 40/287 (13%)

Query: 8   HYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEA 65
            +R    +     +   EM+ A  IL GD + +  +     EK   +Q+ G     + E 
Sbjct: 188 PFRRLC-IHYGCEITLCEMVFARDILHGDAQELRKIKRHPDEKCFGIQLAGRGQELM-EI 245

Query: 66  AKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KALSIPVTV 121
              +      + ++LN  CP     +   GA L  N   + + +  M    +   IPV +
Sbjct: 246 VNFISKCCSCDFVDLNAACPQDIATKKCCGAALAANLKKLVNSVDCMVRGGEHYGIPVFL 305

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY----- 176
           K R G  D        ++  +++ SG+ G+ +H R A  +     +     ++ +     
Sbjct: 306 KIRAG--DLHGNWTGSSVAHALRLSGLYGLSVHLRTAKQRYSKLANWDYSASMRHALDSC 363

Query: 177 -------DIVYEIKKENPD-----------LFIGLNGGLEDM-SQALKILPSVDGVMIGR 217
                  D+  ++K +                +G NG + D          +VD  +I R
Sbjct: 364 EENTAKPDLEPQLKYDVGSSTTVTPSTRTPPLLGGNGDIFDYTDLYRDDHSTVDYYLIAR 423

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
            A     +   + E           + ++   D  R  ++   +Y  
Sbjct: 424 GALVKPWIFQEIKE------GRRIDMSSQSRLDMLRLFASFCLEYYG 464


>gi|332879624|ref|ZP_08447319.1| dihydrouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
 gi|332682590|gb|EGJ55492.1| dihydrouridine synthase [Capnocytophaga sp. oral taxon 329 str.
           F0087]
          Length = 313

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 58/319 (18%), Positives = 113/319 (35%), Gaps = 45/319 (14%)

Query: 1   MV---DWTDRHYR-FFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQI 54
           M      T+  YR  F +      + YT  I      + R D +++   + +   L  QI
Sbjct: 8   MAPLQGLTEAPYRNAFEKHFGGVDVYYTPFIRWEHGGLRRKDVRDLHPDANKVGHLVPQI 67

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
             A   +  +    V  +GY E++LN+GC    + +   G  L+  P+ V   +  + + 
Sbjct: 68  IAASAEEAEQILAQVVPYGYQEVDLNMGCAFPMLVKKGKGCGLLPEPERVRGLLQVVERY 127

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I  +VK R+G +    A     L+  + ++ ++ + +HAR            +     
Sbjct: 128 PDISFSVKMRLGYE---NAAECMELLSVLNETRLSRVVVHARTG--------RQQYKGEC 176

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTT--- 228
           D +      +E     +  NG +  +    ++      ++GVM+GR       +      
Sbjct: 177 DREAFLRFARECRH-PVVYNGDVTTVESLSELQQGMPFLEGVMMGRGLLAAPWVAIEYHE 235

Query: 229 --------------------VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
                               +D Y      G   + T++ K FW  I         + +H
Sbjct: 236 GTAWSMERRMSSLRALHADLLDHYVQTLEGGEKQLLTKM-KAFWEYIYPEGDRKCRKKIH 294

Query: 269 SGGKLQQITRHMIGLFHGF 287
              K+   T+ +  L  G+
Sbjct: 295 KAQKMADYTQAVFQLLSGY 313


>gi|210615986|ref|ZP_03290886.1| hypothetical protein CLONEX_03105 [Clostridium nexile DSM 1787]
 gi|210149991|gb|EEA81000.1| hypothetical protein CLONEX_03105 [Clostridium nexile DSM 1787]
          Length = 316

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 61/292 (20%), Positives = 102/292 (34%), Gaps = 27/292 (9%)

Query: 2   VDWTDRHYR-FFARLLTNNALLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQIGGA 57
              T   YR  +          +T  IV          + K IL    Q   +  QI   
Sbjct: 9   EGLTTYVYRNVYHHFFHPMDKYFTPFIVPHPNRGFKPKELKEILPQHNQGLCVVPQILTN 68

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +    +  A+   ++GY EINLN+GCPS  V     G+  +  PD +   +  + +    
Sbjct: 69  NAEDFIRTAQEFREYGYEEINLNLGCPSGTVTAKKKGSGFLGYPDELERFLYEIFERTES 128

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            +++K RIGV+          L+    K  +  + IH R       +  +          
Sbjct: 129 KISIKTRIGVE---HPEEFERLLNIYNKFEMEELIIHPRVRADFYKNKPNMEVFGQA--- 182

Query: 178 IVYEIKKENPDLFIGLNGG--LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            V E K       +  NG   ++       K  P V+ VM+GR    N  +L  + E   
Sbjct: 183 -VKESKNR-----LCYNGDLFIKSHFEAFEKEYPQVERVMLGRGVMVNPGLLNLICE--- 233

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                   +   V + F  +      +  +       K++++   MI LF G
Sbjct: 234 -----GKSLDKEVLRAFQDEFYRKNQEVLSGDRAVLFKMKELWFFMIHLFEG 280


>gi|296807698|ref|XP_002844234.1| tRNA-dihydrouridine synthase 2 [Arthroderma otae CBS 113480]
 gi|238843717|gb|EEQ33379.1| tRNA-dihydrouridine synthase 2 [Arthroderma otae CBS 113480]
          Length = 425

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 54/246 (21%), Positives = 99/246 (40%), Gaps = 38/246 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     V+AA++V D   + I++N GCP      G  GA L+  PD +   + 
Sbjct: 115 LVFQLGTASPELAVQAARVVAD-DVSGIDVNAGCPKPFSTLGGMGAALLQTPDRLVSILE 173

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +  P    ++VK RI  D +        LV ++  +G+ G+ +H R   ++    
Sbjct: 174 ALVREVGQPWQIGISVKIRILKDPE----QTERLVTALCATGITGLTVHCRTTPMRPREA 229

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P     ++  I +    +   +NG ++    AL ++    VDG MI  +A  N 
Sbjct: 230 AIRDQLP-----MIASICRSAG-VACLMNGDVKSRDHALALMSQYDVDGAMIATSAESN- 282

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
              +         L              WR ++      A    +  G     T++++ +
Sbjct: 283 --FSCFRSAADGGLAS------------WRDLAHEYISTAMECENKWGN----TKYLLNI 324

Query: 284 FHGFPN 289
           F   P 
Sbjct: 325 F--LPG 328


>gi|325067270|ref|ZP_08125943.1| dihydrouridine synthase [Actinomyces oris K20]
          Length = 180

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 39/173 (22%), Positives = 71/173 (41%), Gaps = 39/173 (22%)

Query: 1   MVDWTDRHYRFFAR-------------------------LLTNNALLYTEMIVADAILRG 35
           M   T+  +R   R                         LL    L  TEM+   A++  
Sbjct: 7   MAGVTNASFRRLCREMAEAALPESLRPSHPGPLPTPDGGLLAPAGLYVTEMVTTRALVER 66

Query: 36  DKKN--ILGFSTQEKPLALQIGGADISKLVEAAKI-VEDFGYNEINLNVGCPSARVHEGS 92
           +++   ++     E+  ++Q+ G D + +  A +I VE+   + I+LN GCP  +V    
Sbjct: 67  NERTLAMVRTDPAERVRSIQLYGVDPATVGAAVRILVEEDLADHIDLNFGCPVPKVTRKG 126

Query: 93  FGACLMLNPDIVGDC-----------IAAMCKALSIPVTVKCRIGVDDQIPAV 134
            GA L    D++              + A+ +A  +PVT+K R+G+D++    
Sbjct: 127 GGAALPWKRDLLAAILTEAVRASEAAVRAVGRARQVPVTMKMRLGIDEEHETF 179


>gi|190344922|gb|EDK36711.2| hypothetical protein PGUG_00809 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 362

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 97/252 (38%), Gaps = 35/252 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----------------GDKKNILGFS 44
           MV   +   R  A       L+++  IV   I++                 + K +    
Sbjct: 13  MVRSGELPTRLMALRY-GADLVWSPEIVDKKIIQCKRVENVKLATTDFIDSNNKVVFRTH 71

Query: 45  T--QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   L  QIG A+    VEAAK+V     + I+LN GCP         GA L+ NPD
Sbjct: 72  PASERGRLIFQIGSANPELAVEAAKVVA-RDVDGIDLNCGCPKNFSTHSGMGAELLTNPD 130

Query: 103 IVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           ++   +  + + +     IP++VK R+   D         L+  I K+GV  + +H R  
Sbjct: 131 VLVSILKNLVEKIGNVYRIPISVKIRLL--DATDPEPSIKLIDRICKTGVANLTLHCRTK 188

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---GVMI 215
            ++   P     +P     I+  +   N      LNG + +  +  ++        G MI
Sbjct: 189 PMRNRQPPIRTFLP----QIIETVHSNNVS--FILNGAIRNRQEFYELQARYGKQIGAMI 242

Query: 216 GRAAYKNSAMLT 227
             +A  N  + +
Sbjct: 243 AESAEANPTVFS 254


>gi|83766214|dbj|BAE56357.1| unnamed protein product [Aspergillus oryzae]
          Length = 444

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 41/179 (22%), Positives = 75/179 (41%), Gaps = 9/179 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A     V+AAK+V       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LIFQLGTASPELAVQAAKVVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVSILE 163

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ + +  P  +   + +           LV  + K+G+ G+ +H R   ++        
Sbjct: 164 ALVREIGEPYQIGISVKIRILEKPEITEALVSRLVKTGITGLTVHCRTPAMRPRERAIRE 223

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           ++      ++ +I  +   +   +NG +    Q L ++    VDG MI  +A  N +  
Sbjct: 224 QL-----RMIRDICHDAG-VACLMNGDVTSRDQGLALMEEFGVDGAMIATSAEANPSCF 276


>gi|164655383|ref|XP_001728821.1| hypothetical protein MGL_3988 [Malassezia globosa CBS 7966]
 gi|159102707|gb|EDP41607.1| hypothetical protein MGL_3988 [Malassezia globosa CBS 7966]
          Length = 395

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 88/241 (36%), Gaps = 25/241 (10%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFSTQEKP-L 50
              R  +      +L++   +V  AI+               R   K +      E+P L
Sbjct: 55  LPCRLLSLEY-GASLVWGPEVVDRAIMETERDVDPTTGVVEFRKGDKPVFSTHPIERPYL 113

Query: 51  ALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
             Q+G A      EA +IV        ++LN GCP      G  G+ L+  PD++ D I 
Sbjct: 114 IYQLGSATPEFAAEAVRIVTQHDDVAGVDLNCGCPKPFSTLGGMGSNLLSTPDLLCDIIK 173

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           AM +A    + V+ K R+    +     +  +V++     +  + IH R   ++      
Sbjct: 174 AMRRAAPPHVSVSCKIRLLPTQEETFSLVEKIVRARA---IRVLTIHCRTKPMRPREAAL 230

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAM 225
             +   +   +    K+   D+ +  NG    ++    L+ L      M+ R    N + 
Sbjct: 231 LERFRAVAEHVAKIAKETEQDVTVVCNGDCFSVADIPHLRELTGASSFMMARGPEANMSC 290

Query: 226 L 226
            
Sbjct: 291 F 291


>gi|213615509|ref|ZP_03371335.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
          Length = 210

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 40/194 (20%), Positives = 76/194 (39%), Gaps = 29/194 (14%)

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
           +    GA L+ +P+++     AM  A+   +PVTVK R+G D          +  +++++
Sbjct: 2   NGSGGGATLLTDPELIYQGAKAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQA 58

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + + +H R             +  ++D+  + EI++    + +  NG + D   A   
Sbjct: 59  GASELVVHGRTK-------AQGYRAEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQAC 110

Query: 207 L--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +     D VMIGR A  N   L+ V +Y                +  W ++   +  Y  
Sbjct: 111 MATSGCDAVMIGRGAL-NIPNLSRVVKYNE-------------PRMPWPEVVTLLQKYTR 156

Query: 265 RHLHSGGKLQQITR 278
                   L  + R
Sbjct: 157 LEKQGDTGLYHVAR 170


>gi|321259143|ref|XP_003194292.1| hypothetical protein CGB_E3650W [Cryptococcus gattii WM276]
 gi|317460763|gb|ADV22505.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 493

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 96/238 (40%), Gaps = 30/238 (12%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFSTQEKP-L 50
              R  + L     L+++  +V  AI+                  +  I      EKP L
Sbjct: 124 LPMRLLS-LYYGAGLVWSPEVVDKAIIGAERSVDPVTGVITYHKGQGPIFSTHPAEKPFL 182

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG ++    V+AA+ V+      I+LN GCP         GA L+  P+++ D + A
Sbjct: 183 IFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLSTPELLLDILRA 241

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  ++ +P++ K R+             L   I ++G+  + +H R   ++        +
Sbjct: 242 LLDSIPLPISCKIRLLPTQPSTLY----LASRIIRTGIRNLTVHCRTRQMRPGERALWER 297

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML 226
           + +     + ++ K    + +  NG  E  S   +I      D VM+ R+A +N ++ 
Sbjct: 298 LGS-----IVDLGKRRG-ISVICNGDGEGWSNWERIKNETGADSVMLARSAERNPSVF 349


>gi|225570267|ref|ZP_03779292.1| hypothetical protein CLOHYLEM_06363 [Clostridium hylemonae DSM
           15053]
 gi|225161062|gb|EEG73681.1| hypothetical protein CLOHYLEM_06363 [Clostridium hylemonae DSM
           15053]
          Length = 319

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 94/252 (37%), Gaps = 23/252 (9%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +IL    +   +  Q+        +  A  ++++GY E+NLN+GCPS  V     G+
Sbjct: 47  EKNDILPEHNRGMKVVPQLLTNKADDFILTAGKLKEYGYREVNLNLGCPSRTVVSKYRGS 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  P+ +   +  + +     ++VK R G D          L++   K  +  + IH 
Sbjct: 107 GFLARPEELDRFLYEVFEKTETDISVKTRTGRD---SPQEFVRLMEIYNKYPLKELIIHP 163

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDG 212
           R       +  D           V+          +  NG +   ED+        +VD 
Sbjct: 164 RTQQDFYKNTPDLS---------VFAQALSVSRCPVCYNGDIFTTEDLKVFRARFANVDK 214

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           VM+GR    N  ++   ++         + I     + F   +     +  +       K
Sbjct: 215 VMLGRGLLVNPMLIEMAED--------GTAIDMERIRKFHDMVYGGYREVLSGDKVILFK 266

Query: 273 LQQITRHMIGLF 284
           ++++  +MI LF
Sbjct: 267 MKELWSYMIHLF 278


>gi|58268108|ref|XP_571210.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57227444|gb|AAW43903.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 491

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 96/238 (40%), Gaps = 30/238 (12%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFSTQEKP-L 50
              R  + L     L+++  +V  AI+                  +  I      EKP L
Sbjct: 121 LPMRLLS-LYYGAGLVWSPEVVDRAIIGAERSVDPVTGVITYHKGQGPIFSTHPAEKPFL 179

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG ++    V+AA+ V+      I+LN GCP         GA L+  P+++ D + A
Sbjct: 180 IFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLSTPELLLDILRA 238

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  ++ +P++ K R+             L   I ++GV  + +H R   ++        +
Sbjct: 239 LLDSIPLPISCKIRLLPTQPSTLY----LASRILRTGVRNLTVHCRTRQMRPGERALWER 294

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           + +     + E+ K    + +  NG  E  S   +I      D VM+ R+A +N ++ 
Sbjct: 295 LSS-----IVELGKRRG-ISVICNGDGEGWSNWDRIRNETGADSVMLARSAERNPSVF 346


>gi|258564268|ref|XP_002582879.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
 gi|237908386|gb|EEP82787.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
          Length = 431

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 85/188 (45%), Gaps = 17/188 (9%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +   L  Q+G A  S  VEAAKIV     + I++N GCP      G  GA L+  PD + 
Sbjct: 102 ERGKLVFQLGTATPSLAVEAAKIVAA-DVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLV 160

Query: 106 DCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ + +  P    ++VK RI  + +        LV  + K+G+ G+ +H R   ++
Sbjct: 161 SILEALVEEVGKPYEIGISVKIRILAEPERTES----LVTRLCKTGITGLTVHCRTTPMR 216

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                   ++P     ++  I ++   +   +NG +    +A+ ++    VDG MI  +A
Sbjct: 217 PREAAIREQLP-----MIASICRKAG-VACVMNGDVTSRDEAMTLIREYGVDGAMIATSA 270

Query: 220 YKNSAMLT 227
             N +   
Sbjct: 271 ESNFSCFR 278


>gi|134112079|ref|XP_775575.1| hypothetical protein CNBE2890 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50258234|gb|EAL20928.1| hypothetical protein CNBE2890 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 491

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 96/238 (40%), Gaps = 30/238 (12%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFSTQEKP-L 50
              R  + L     L+++  +V  AI+                  +  I      EKP L
Sbjct: 121 LPMRLLS-LYYGAGLVWSPEVVDRAIIGAERSVDPATGVITYHKGQGPIFSTHPAEKPFL 179

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG ++    V+AA+ V+      I+LN GCP         GA L+  P+++ D + A
Sbjct: 180 IFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLSTPELLLDILRA 238

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  ++ +P++ K R+             L   I ++GV  + +H R   ++        +
Sbjct: 239 LLDSIPLPISCKIRLLPTQPSTLY----LASRILRTGVRNLTVHCRTRQMRPGERALWER 294

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
           + +     + E+ K    + +  NG  E  S   +I      D VM+ R+A +N ++ 
Sbjct: 295 LSS-----IVELGKRRG-ISVICNGDGEGWSNWDRIRNETGADSVMLARSAERNPSVF 346


>gi|207727951|ref|YP_002256345.1| trna-dihydrouridine synthase c (partial sequence c terminus)
           protein [Ralstonia solanacearum MolK2]
 gi|206591194|emb|CAQ56806.1| probable trna-dihydrouridine synthase c (partial sequence c
           terminus) protein [Ralstonia solanacearum MolK2]
          Length = 190

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 19/140 (13%), Positives = 47/140 (33%), Gaps = 8/140 (5%)

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
               + +      +Y+ +  +K  +  + +  NG +   ++A ++L     D +MIGRAA
Sbjct: 5   HWKTRADLYHGEAEYETIAAVK-ASVRIPVVANGDIATPAKAKQVLDVTGADAIMIGRAA 63

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
                +   ++ +        +P    +       +      Y          ++   +H
Sbjct: 64  QGRPWLFREIEHFLQTGTLLPAPEVEEIRGIMNTHLEEHYAFY-----GEYTGVRTARKH 118

Query: 280 MIGLFHGFPNSRRCRHILTV 299
           +     G   +   RH +  
Sbjct: 119 IAWYTRGLAGANLFRHRMNT 138


>gi|119603805|gb|EAW83399.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_a [Homo
           sapiens]
          Length = 237

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/199 (25%), Positives = 85/199 (42%), Gaps = 32/199 (16%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVK 141
           S       +GACL+  P++V D +  +   +  P   V++K RI  D +       +L +
Sbjct: 38  SKWAMAEGYGACLINKPELVQDMVKQVRNQVETPGFSVSIKIRIHDDLKRTV----DLCQ 93

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             + +GV+ I +H R A  +            + YD +  I KEN  + +  NG +  + 
Sbjct: 94  KAEATGVSWITVHGRTAEERHQ---------PVHYDSIK-IIKENMSIPVIANGDIRSLK 143

Query: 202 QALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
           +A  +  +   DGVM+ R    N AM    +E         +P+K   D   W  I+  +
Sbjct: 144 EAENVWRITGTDGVMVARGLLANPAMFAGYEE---------TPLKCIWD---WVDIALEL 191

Query: 260 -TDYAARHLHSGGKLQQIT 277
            T Y   H H    +++IT
Sbjct: 192 GTPYMCFHQHLMYMMEKIT 210


>gi|149239919|ref|XP_001525835.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
 gi|146449958|gb|EDK44214.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL
           YB-4239]
          Length = 504

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 104/253 (41%), Gaps = 30/253 (11%)

Query: 34  RGDKKNILGFSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
                 +     +E   L  Q+G +     VEAA  V +   + I+LN GCP +    G 
Sbjct: 77  HNQDNVVFRKHPEETGKLIFQLGTSTPELAVEAALRVIE-DVDGIDLNCGCPKSFSTHGG 135

Query: 93  FGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            GA L+  PDI+   + A+ + +      P++ K R+  + +   +    L++ I ++G+
Sbjct: 136 MGAELLKTPDILCSILRALVEKVGNPNKKPISCKIRLLPNFEASKL----LIEQICQTGI 191

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN------GGLEDMSQ 202
             + IH R  I++         +P L   I+     E+  + + LN      G L  + +
Sbjct: 192 RNLTIHCRTPIMRNRQDPFWNYLPKLI-PII-----ESHGISVILNGNFQGRGDLTSLQE 245

Query: 203 ALKILPSVDGVMIGRAAYKNSAML---TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
           AL   P++  +MI   A  N ++     T     +     ++P   +   +   ++    
Sbjct: 246 ALGN-PNL-SIMIAEGAEANPSIFINTNTNTNNSNTHSVANTPSLPKTQAEIINEVVELG 303

Query: 260 TDYAARHLHSGGK 272
             Y   +L+SG K
Sbjct: 304 KKY---YLYSGTK 313


>gi|209880479|ref|XP_002141679.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
 gi|209557285|gb|EEA07330.1| dihydrouridine synthase family protein [Cryptosporidium muris RN66]
          Length = 330

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 101/252 (40%), Gaps = 39/252 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--------------RGDKKNILGFST- 45
           MV++T+  +R    L     +++TE I+   IL                D +N + FST 
Sbjct: 12  MVNFTNLPFRLTC-LDYGADIVFTEEIMDFNILKTNRIFNEKSGIYEYTDDRNSVIFSTN 70

Query: 46  --QEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             +   +  QIG       ++A + I+ DF     ++N+GCP         G+ L+L P+
Sbjct: 71  QNENGKVIFQIGTFCSVNALKACEHIINDFCA--FDINMGCPKLYNIRRGMGSALLLKPE 128

Query: 103 IVGDCIAAMCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           I  D +  + + L    +T K R+  D +       + ++      ++GI +HAR     
Sbjct: 129 IAEDILKCLNRNLPKCSITCKIRLLDDFKKT----LDFIRLCSNCNISGITVHART---- 180

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS----VDGVMIG 216
              PK+   +    +DI   IK E    + +  NG     S            VD  M+ 
Sbjct: 181 ---PKEKYDVFP-HWDIFPLIKSELSSCIPVIANGDFSSASLINSFESKFPNAVDSFMLS 236

Query: 217 RAAYKNSAMLTT 228
           R+A  + ++   
Sbjct: 237 RSARHDPSIFLQ 248


>gi|323456305|gb|EGB12172.1| hypothetical protein AURANDRAFT_36241 [Aureococcus anophagefferens]
          Length = 367

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 102/238 (42%), Gaps = 15/238 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----KNILGFSTQEKPLALQIGG 56
           M  +T+ H  F  R L  +  L+TEM  A  +L  D       ++     + P  LQ+GG
Sbjct: 25  MQTYTNAHLNFLLRRLAPDVTLWTEMEKAADVLACDDAALASRLVAGGADDAPPVLQLGG 84

Query: 57  ADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            D   L  A         +  E+N+N GCP+       +GA LM +       + A+  A
Sbjct: 85  DDPRALAAATTRACRLRTDLREVNINAGCPAIASGGADYGATLMRDAAATRRLVEAVRDA 144

Query: 115 L--SIPVTVKCRIGVDDQIP------AVALRNLVKSIKKSGV-NGIWIHARKAILKGLSP 165
              S  V++KCR+GV +            L   V     SG  + + +H R AIL GL+P
Sbjct: 145 APPSCAVSLKCRVGVRETWSDEAPARYDELHAFVAETSSSGCLDHVVVHCRLAILAGLAP 204

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS 223
             NR  P L  D    + ++ P L +  NGG+     +      +DGVM GRA  +  
Sbjct: 205 GANRCRPPLHPDFARRLARDFPALRVTRNGGIGSFGDSDARDDGLDGVMAGRAVLRRP 262


>gi|171058809|ref|YP_001791158.1| dihydrouridine synthase DuS [Leptothrix cholodnii SP-6]
 gi|170776254|gb|ACB34393.1| dihydrouridine synthase DuS [Leptothrix cholodnii SP-6]
          Length = 339

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 93/242 (38%), Gaps = 26/242 (10%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGF---------STQEKPLA 51
           M    D   R     +       +E I     L  + +  L           +    P+ 
Sbjct: 1   MEGLLDAPLRDILTRVGGVDRCVSEFIRVTGTLLPE-RVFLRIVPELEHGCRTPSGVPVR 59

Query: 52  LQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
            Q+ G+D + L + A  +   G   ++LN GCP+  V+    GA L+  P  +   +AA+
Sbjct: 60  PQLMGSDAACLADNAARLAQMGAEGVDLNFGCPAQVVNRHGGGAALLREPQRLAAIVAAV 119

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+   +PV+ K R+G D    AV   +  +++   G   + +HAR         K   
Sbjct: 120 RRAVPAHLPVSAKMRLGYDHDEHAV---DCAQALVDGGAAELVVHART--------KAQG 168

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
             P   +  V E++   P      NG + +   AL+       D +M+GR    +  +  
Sbjct: 169 YRPPAWWAKVAEVRAAVPVPV-VANGEIWNADDALRCRRESGCDDLMLGRGMVADPGLAL 227

Query: 228 TV 229
            +
Sbjct: 228 AI 229


>gi|153813385|ref|ZP_01966053.1| hypothetical protein RUMOBE_03804 [Ruminococcus obeum ATCC 29174]
 gi|149830562|gb|EDM85653.1| hypothetical protein RUMOBE_03804 [Ruminococcus obeum ATCC 29174]
          Length = 316

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 93/252 (36%), Gaps = 23/252 (9%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+I   +        QI   +    +  A  ++++GY E+NLN+GCPS  V     GA
Sbjct: 47  EKKDISPENNSGMYAVPQILTRNADDFLRTANQLKEYGYQEVNLNLGCPSKTVVTKGCGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  P+ +   +  +     + ++VK R+G++D   A     L++   +  +  + IH 
Sbjct: 107 GFLARPEELEQFLDRIFSKTDMKISVKTRLGMED---AEEFPRLMEIYNRFPMEELIIHP 163

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDG 212
           R       +  +                       +  NG +       +I    P V+ 
Sbjct: 164 RVQKDFYNNTPNLEAFGEAL---------AISKNPVCYNGDIFSTDDFKRIQSQFPDVEC 214

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
            M+GR    + ++   +         G         + F   +  +  +  +   +   K
Sbjct: 215 FMMGRGVLADPSLAREIR--------GGKAADQSDIRRFHDLLYHTYREEVSGDRNVLFK 266

Query: 273 LQQITRHMIGLF 284
           +++I  ++  +F
Sbjct: 267 MKEIWFYLAPMF 278


>gi|145616686|ref|XP_363722.2| hypothetical protein MGG_01648 [Magnaporthe oryzae 70-15]
 gi|145023291|gb|EDK06730.1| hypothetical protein MGG_01648 [Magnaporthe oryzae 70-15]
          Length = 428

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/212 (24%), Positives = 93/212 (43%), Gaps = 17/212 (8%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + K L  Q+G  D  +   AA  +       I+LN GCP      G  GA L+ +PD + 
Sbjct: 98  EGKRLIFQLGSGDPER-AVAAARLVANDVAGIDLNAGCPKPFSTTGGMGAALLRDPDRLV 156

Query: 106 DCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ + +     I ++VK R+       A     LV+ + K+G+  + +H R   ++
Sbjct: 157 AILEALVREVAPAAEIGISVKIRLL----ETAAETEALVRRLVKTGITALTVHCRTTPMR 212

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P++      L   +V ++ +E   +   +NG ++D  + +++      DG MI RAA
Sbjct: 213 ---PRERAIRGQLR--MVADVCREAG-VACLMNGDVKDRDEGVRLAAEYGTDGAMIARAA 266

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
            +N +      +    P T + P+  R   D 
Sbjct: 267 EENPSCFRAGADGGLAPWTETVPLFMRFCLDM 298


>gi|53711476|ref|YP_097468.1| nifR3 family TIM-barrel protein [Bacteroides fragilis YCH46]
 gi|253564462|ref|ZP_04841919.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_2_5]
 gi|52214341|dbj|BAD46934.1| putative nifR3 family TIM-barrel enzyme [Bacteroides fragilis
           YCH46]
 gi|251948238|gb|EES88520.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_2_5]
 gi|301161208|emb|CBW20746.1| conserved hypothetical protein [Bacteroides fragilis 638R]
          Length = 310

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 96/235 (40%), Gaps = 18/235 (7%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A +     + +T  +  D       D ++IL  + +   L  Q+  +++
Sbjct: 13  GYTEAAYRNAHAAVFGGVDVYHTPFVRIDRGEFRHKDVRDILPENNRVPHLIPQLIASEM 72

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K      +  + GY E+++N+GCP   + +   G+ ++ +PD V   +  + +   +  
Sbjct: 73  DKTERIIALFIEQGYREMDINLGCPFPMLAKRQCGSGMLPHPDKVETLLKQIEQYPDVSF 132

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +     + L  L+ +   +    I +H R  I +      N +     Y+  
Sbjct: 133 SVKMRLGWEKPDECLTLLPLLNAAPLT---EIIVHPRLGIQQYKGEV-NMEGFTAFYEAC 188

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                      +  NG    +ED+    +  P + GVMIGR    N A+     E
Sbjct: 189 RH--------PVIYNGDILTIEDIRCITEKFPKLTGVMIGRGLLANPALGWEYKE 235


>gi|70944501|ref|XP_742175.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56521005|emb|CAH88154.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 251

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/207 (26%), Positives = 93/207 (44%), Gaps = 34/207 (16%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R GVDD      L++ ++++   G     IH+RKA LKGL PK NR +P L+Y+ V
Sbjct: 1   SVKIRTGVDDLDSFSFLKSFIETVSSVGCEHFIIHSRKAWLKGLDPKQNRSVPPLEYNKV 60

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--------------VD-------------- 211
           +++ K  P+L   LNGG++ + Q + +L                 D              
Sbjct: 61  FDLCKLYPNLKFTLNGGIKSIEQGVALLNGYVPINKTTGNHNKYTDNNYIKVEDYDINPL 120

Query: 212 -GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
            GVMIGRA   N  +L   D+   N  T ++    R   + ++      + +     +S 
Sbjct: 121 YGVMIGRACMDNITVLAKTDKLVYNHDTLATAYSRRTVLEAYKSYLEQNSSF-----YSL 175

Query: 271 GKLQQITRHMIGLFHGFPNSRRCRHIL 297
               ++ + ++G+  G P  R  R+ +
Sbjct: 176 VNAFELLKPILGVLKGMPGHRLFRNKI 202


>gi|281356662|ref|ZP_06243153.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
 gi|281316789|gb|EFB00812.1| dihydrouridine synthase DuS [Victivallis vadensis ATCC BAA-548]
          Length = 288

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 41/195 (21%), Positives = 83/195 (42%), Gaps = 18/195 (9%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           F     P+ +Q+ G     +  AA    + G   INLN GCPS +V  G  G   + +  
Sbjct: 42  FLESGLPVTVQLMGNRPEVIAAAAARFMELGAAGINLNFGCPSRQVTSGGAGGGALRDLA 101

Query: 103 IVGDCIAAMCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGV-NGIWIHARK--A 158
            +   +  + KA+   P++VK R G +       ++ ++ ++ ++G  +  ++H R    
Sbjct: 102 GMVTTVETVKKAIPASPLSVKLRTGWE---SPDEMQRILPALAETGCVSAFFLHFRTVRE 158

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
             + +S ++ R    L         +    + + LNG ++    A ++L      GVM  
Sbjct: 159 QYRPVSGREERFEAGL---------RLAAPVPVVLNGDIDSPDDASELLERTGAAGVMCA 209

Query: 217 RAAYKNSAMLTTVDE 231
           R   ++  +L  + +
Sbjct: 210 RGWLRDPLLLNRIRQ 224


>gi|50557204|ref|XP_506010.1| YALI0F29205p [Yarrowia lipolytica]
 gi|49651880|emb|CAG78822.1| YALI0F29205p [Yarrowia lipolytica]
          Length = 394

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 43/186 (23%), Positives = 74/186 (39%), Gaps = 9/186 (4%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             +   +  Q+G A+    V A K+V       I+LN GCP         GA L+  PD 
Sbjct: 80  EAERDKIIFQVGSANPEIAVAACKMVAK-DVAGIDLNCGCPKHFSMHAGMGAALLKTPDK 138

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   + A+ K +  P  V   + +           LV  + ++GV  + IH R   ++  
Sbjct: 139 LVAILEALVKEVGEPFNVSISVKIRLLETEEKTLELVDRLAQTGVKNLTIHCRTTPMRPR 198

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
            P     +       V E+  ++  +   +NG +E   +   +     +DG MI RAA  
Sbjct: 199 EPVIRDTLAK-----VAEVCHKHG-ITCLVNGDVEGRHELADLQEKYGIDGAMIARAAEA 252

Query: 222 NSAMLT 227
           N++   
Sbjct: 253 NASCFR 258


>gi|89891167|ref|ZP_01202674.1| conserved hypothetical protein [Flavobacteria bacterium BBFL7]
 gi|89516479|gb|EAS19139.1| conserved hypothetical protein [Flavobacteria bacterium BBFL7]
          Length = 316

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 92/264 (34%), Gaps = 23/264 (8%)

Query: 3   DWTDRHYRFF-ARLLTNNALLYTEMI--VADAILRGDKKNILGFSTQEKP-LALQIGGAD 58
            +T+  +R    +        Y   I       +    +  L       P L  Q+    
Sbjct: 12  GFTEFRFRNAQHKYFGGIDTYYAPYIRFNNKPDISAKYQRDLQLENNHVPDLIPQVMTNS 71

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + + A K +   GY E+N N+GCP   V +   G+ L+  P  +   +  +     + 
Sbjct: 72  ADEFITAVKYIRSLGYKELNWNLGCPYPMVTKKGMGSGLICEPSKIDAILDRVHNETDVI 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V++K R+G    +    + +    ++K  +  I IHAR          D +         
Sbjct: 132 VSMKMRMGY---LEPTEILDTFPILEKYPIKSIAIHARIGKQLYKGGVDLQS-------- 180

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++   +     +  NG +  ++   K+    P++D  M+GR    +  + + +      
Sbjct: 181 -FQRCLDTSKTKLYYNGDITTVAGFRKMQEQFPTIDHWMLGRGLIADPFLPSMIKA--DT 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASM 259
            +      +  + ++F   I    
Sbjct: 238 EIYPE--NRWEIFREFHDAIYQEY 259


>gi|313204382|ref|YP_004043039.1| dihydrouridine synthase dus [Paludibacter propionicigenes WB4]
 gi|312443698|gb|ADQ80054.1| dihydrouridine synthase DuS [Paludibacter propionicigenes WB4]
          Length = 312

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 62/324 (19%), Positives = 121/324 (37%), Gaps = 30/324 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVADA--ILR-GDKKNILGFSTQEKPLALQIGGAD 58
             TD  +R  +   + +    +T  +        R     ++L      +    Q  G D
Sbjct: 10  GLTDWIFRESYTEHIGHFDKTFTPFVRVQGGDFYRPSQCNDLLPERNIFQKPVPQFLGRD 69

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +      ++    GY E+N+N+GCP   V     GA L+ +   V   +  +     + 
Sbjct: 70  AASFKVFEELCIAQGYTEVNINMGCPFPIVTGKQMGAGLLQHSADVDRLLEGVFSNSDLK 129

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V+VKCR+G   Q  A     L+       +  I IH R    +     D      +D  +
Sbjct: 130 VSVKCRLG---QQSADEFAPLIPVFNAYPLEEIIIHPRVGKQQYKGEVD------IDAFV 180

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            Y+ + ++P  F   NG +    D+ +  ++ P V   M+GR   +N  +L+ +      
Sbjct: 181 HYQSQLQHPVCF---NGDIVTPADVERIRQLAPQVSRFMLGRGVLRNPFLLSELR----- 232

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
               +   K  + + F + +        +  LH   +L+++  +    F G    +  + 
Sbjct: 233 GEELTLGQKAEMLRGFHQSVIELCKQKYSGDLHFLKRLEEMWEYQADAFEG--GRKIYKQ 290

Query: 296 ILTVEAGASTATHH-IIETAFNLM 318
              V+   + A +  ++  A N M
Sbjct: 291 ---VKKSKNLAQYEAVVFQAINEM 311


>gi|303242447|ref|ZP_07328929.1| dihydrouridine synthase DuS [Acetivibrio cellulolyticus CD2]
 gi|302590032|gb|EFL59798.1| dihydrouridine synthase DuS [Acetivibrio cellulolyticus CD2]
          Length = 313

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 65/277 (23%), Positives = 114/277 (41%), Gaps = 24/277 (8%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDK---KNIL-GFSTQEKPLALQIGGADISKLVEAAK 67
           FAR   N    YT  I +  + + +    K+IL  ++     L  Q+ G D ++    A 
Sbjct: 20  FARHFGNIDAYYTPFISSSEVDKVNNLLLKDILPEYNDPAVKLVPQLLGNDGAQFKAFAC 79

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            + D GY+EIN N+GCP   V +   G+ ++ +PD++   +   C   S  VTVK R+G 
Sbjct: 80  AISDIGYHEINWNIGCPYPTVTKKKKGSGILQHPDMIKKVLDTACSDSSYTVTVKMRLGW 139

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D     + + +    +    + G+ IHAR  I       D       +++ +    K   
Sbjct: 140 DKLEEGMRVMD---VLNDYPLGGVIIHARTGIQMYEGHVDLE-----EFETLAASCKH-- 189

Query: 188 DLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
              +  NG +      L+I   LP +   M+GR A  +  + T +        T S   K
Sbjct: 190 --EVTYNGDIFTHDDFLRISSRLPFIKNFMLGRGALSDPFLPTVIK-----GQTVSDANK 242

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             + ++F  +I        +   H   K+++   +M 
Sbjct: 243 ISIVREFHNEIFNYYKCKLSGDKHLCDKMKEFWYYMH 279


>gi|265764875|ref|ZP_06093150.1| nifR3 family TIM-barrel protein [Bacteroides sp. 2_1_16]
 gi|263254259|gb|EEZ25693.1| nifR3 family TIM-barrel protein [Bacteroides sp. 2_1_16]
          Length = 310

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 96/235 (40%), Gaps = 18/235 (7%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A +     + +T  +  D       D ++IL  + +   L  Q+  +++
Sbjct: 13  GYTEAAYRNAHAAVFGGVDVYHTPFVRIDRGEFRHKDVRDILPENNRVPHLIPQLIASEM 72

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K      +  + GY E+++N+GCP   + +   G+ ++ +PD V   +  + +   +  
Sbjct: 73  DKTERIIALFIEQGYREMDINLGCPFPMLAKRQCGSGMLPHPDKVETLLKQIEQYPGVSF 132

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +     + L  L+ +   +    I +H R  I +      N +     Y+  
Sbjct: 133 SVKMRLGWEKPDECLTLLPLLNAAPLT---EIIVHPRLGIQQYKGEV-NMEGFTAFYEAC 188

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                      +  NG    +ED+    +  P + GVMIGR    N A+     E
Sbjct: 189 RH--------PVIYNGDILTIEDIRCITEKFPKLTGVMIGRGLLANPALGWEYKE 235


>gi|293371535|ref|ZP_06617953.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CMC 3f]
 gi|292633483|gb|EFF52048.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CMC 3f]
          Length = 314

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 53/277 (19%), Positives = 102/277 (36%), Gaps = 25/277 (9%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   A         YT  +  +  +    D + I   + Q   L  Q+     
Sbjct: 14  GYTDVIYRNAHAACFGGIDTYYTPFVRLEKGSFHHRDIRGIEPGNNQVSHLIPQLIAPST 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K  +   +  + GY E ++N+GCP   + +   G+ ++  P+ V + +  + K   I  
Sbjct: 74  EKAEKILSLFIEKGYKEADINMGCPFPILTKRHNGSGILPYPEEVKELLNLVLKYPEISF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G ++        +L   I    +  + +H R    +     +        +   
Sbjct: 134 SIKMRLGWENPD---ECLHLAPIINDLPLRQVTMHPRLGKQQYKGEVNLEG-----FSAF 185

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            E+ K      +  NG +   ED+ +  K  P++ G+MIGR    N A+     E     
Sbjct: 186 QEVCKH----PLIYNGDIHSLEDIQRIQKQFPALAGIMIGRGLLANPALALEYKE----- 236

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
                     + + F    ++  T YA +      +L
Sbjct: 237 --NRILTADEMREKFHSMHTSVYTQYAEQLEGGDEQL 271


>gi|241952298|ref|XP_002418871.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
 gi|223642210|emb|CAX44177.1| tRNA-dihydrouridine synthase, putative [Candida dubliniensis CD36]
          Length = 451

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 61/261 (23%), Positives = 103/261 (39%), Gaps = 45/261 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---------------------DKKN 39
           MV   +   R  +       LL+T  +V   IL+                      DKK 
Sbjct: 13  MVRSGELPIRLLSLKY-GCDLLWTPELVDKKILQSTRIINQELNTIDYIVSNHQQSDKKT 71

Query: 40  IL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           ++      +   L LQ+G +D    VEAA  V D   + I+LN GCP         GA L
Sbjct: 72  VIFRKHPDETGKLILQLGSSDPQLAVEAANKVID-DVDGIDLNCGCPKNFSTHSGMGAEL 130

Query: 98  MLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +  PD +   +  + + + IP    ++ K R+           +NL++ I ++G++ + I
Sbjct: 131 LKTPDKLCCILINLVEKIGIPKKKSISCKIRLF----NNYYQSKNLIEKILQTGISNLTI 186

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG------GLEDMSQALKIL 207
           H R  I++         +P L   I+     EN  + + +NG       L+++  AL   
Sbjct: 187 HCRTPIMRNRQDPIWNFLPKLI-PII-----ENSQVNLIINGNMQNVNDLKNLQMALNDN 240

Query: 208 PSVDGVMIGRAAYKNSAMLTT 228
                +MI  AA  N ++   
Sbjct: 241 EKKLSIMIAEAAEANPSIFNQ 261


>gi|257440871|ref|ZP_05616626.1| dihydrouridine synthase family protein [Faecalibacterium
           prausnitzii A2-165]
 gi|257196651|gb|EEU94935.1| dihydrouridine synthase family protein [Faecalibacterium
           prausnitzii A2-165]
          Length = 313

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 50/298 (16%), Positives = 100/298 (33%), Gaps = 34/298 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNA----LLYTEMIV---ADAILRGDKKNILGFSTQEKPLALQ 53
           M   TDR +R   +            Y   +       +++     +   +     +  Q
Sbjct: 8   MEGLTDRIWRQAHQRWFGAPEAPVRYYAPFLSPPENRVLIKKKMAELEPAANPGVQVIPQ 67

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   D          +   GY E+NLN GCPS  V     G+ ++ +P  +   + A+  
Sbjct: 68  LLAKDGELAAWMIGELRRMGYTEVNLNFGCPSGTVTAKGKGSGMLRDPQKLDAFLDAVFS 127

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKI 171
                V+VK R+GV     A     ++    K  +  + IH R  K + +G + ++    
Sbjct: 128 QAGGSVSVKTRLGV---ARAEEFGEILDVYNKYPLCELTIHPRVMKQLYRGQADREAFAA 184

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTT 228
                              +  NG +  +     +    P + G+M+GR    + A+L  
Sbjct: 185 YLPACTA-----------PVCYNGDVTTVDDLRALEAAFPELSGIMVGRGLIADPALLRK 233

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                     G         + +  ++    T+       +  +++    ++I LF G
Sbjct: 234 A--------VGGPAASREELRGYHDELYHGYTEAFGMASCAVSRMKAHWFYLIHLFDG 283


>gi|256840560|ref|ZP_05546068.1| dihydrouridine synthase [Parabacteroides sp. D13]
 gi|298377610|ref|ZP_06987562.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 3_1_19]
 gi|256737832|gb|EEU51158.1| dihydrouridine synthase [Parabacteroides sp. D13]
 gi|298265629|gb|EFI07290.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 3_1_19]
          Length = 310

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 99/269 (36%), Gaps = 25/269 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR    R+       YT  +  +       D K+I     ++  +  Q+  +  
Sbjct: 11  GYTDSVYREAHTRVFGGVDTYYTPFVRIEKGGFRNKDLKDIACDRNRQVHVVPQLIASTP 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +     ++ ++ GY E ++N+GCP         G+ L+   +     +  + +   I  
Sbjct: 71  DEFRPIVRLFQENGYKEADINLGCPFPMQVRAHRGSGLLRYKEEAESLLRTIEEFPDISF 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    +  L      + K  +  I +H R  I +            +D+D  
Sbjct: 131 SVKMRLGWECTDESFVLL---SLLNKLPLKHITLHPRLGIQQ--------YKGAIDWDGF 179

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                E  +L +  NG    LED+    +  P + G+M+GR    +  + T         
Sbjct: 180 SRFYDEC-ELPLYYNGDLVGLEDIRGIKERFPGLAGIMLGRGLLASPWLATEF------- 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           ++G                 + M +YAAR
Sbjct: 232 VSGQVLTVNERRDKLVMFHESLMDEYAAR 260


>gi|238916319|ref|YP_002929836.1| tRNA-dihydrouridine synthase C [Eubacterium eligens ATCC 27750]
 gi|238871679|gb|ACR71389.1| tRNA-dihydrouridine synthase C [Eubacterium eligens ATCC 27750]
          Length = 333

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 113/291 (38%), Gaps = 26/291 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNAL---LYTEMIV---ADAILRGDKKNILGFSTQEKPLALQI 54
           M   TD  YR               +T  I    ++  L  + ++I     ++    +Q+
Sbjct: 4   MEGLTDFTYRNAYEKTFGKGRITKYFTPFISPNKSENFLAREIRDIDRGHNKDTYTVVQV 63

Query: 55  GGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              +    +  AK++ E +GY+EINLN GCPS  V     G+ ++ + + +   +  + +
Sbjct: 64  MTNEAKDFIWTAKMLYEKYGYSEINLNAGCPSGTVVSKDKGSGMLRDTEKLDRFLDEVFE 123

Query: 114 AL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                 +I V+VK RIGV+D         +++      +  + +H R         ++  
Sbjct: 124 DAFIRENIKVSVKTRIGVEDDDS---FPQIMEVYNSYPLEELIVHPRVRTDYY---RNEL 177

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ---ALKILPSVDGVMIGRAAYKNSAML 226
            +    Y +      +N    + LNG +          ++ P VD  M+GR    +  ++
Sbjct: 178 HLDAFRYAV------DNSRNKLVLNGDIFTRKNFLEMKEMFPEVDTFMLGRGLIADPGLI 231

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
             + +     +        ++ K+    + A+ T       H+  +++++ 
Sbjct: 232 NVLTDDNPQAMVRDLNADKKLMKELHDLVYAARTAIMPGDTHAIHRMKEMW 282


>gi|227872442|ref|ZP_03990784.1| dihydrouridine synthase, DuS [Oribacterium sinus F0268]
 gi|227841702|gb|EEJ51990.1| dihydrouridine synthase, DuS [Oribacterium sinus F0268]
          Length = 323

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 60/330 (18%), Positives = 106/330 (32%), Gaps = 32/330 (9%)

Query: 4   WTDRHYRFFAR-LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP---LALQIGGADI 59
            T    R   R L       ++  I ++       +     + +      L  QI G   
Sbjct: 11  ITGYPLRNAHRALFPETDAYFSPFISSNEEGHYTGRIERDCAVENNNGLVLIPQIMGNRP 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC---KALS 116
             +    K +E  GY E NLN+GCPS  V     G+ ++  P ++ D    +    K   
Sbjct: 71  EFVHATMKYMESLGYQECNLNLGCPSGTVVAKGKGSGMLRIPLLLEDFFQELFSLLKDSK 130

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           + V++K RIG++          L         + I +H R                 ++ 
Sbjct: 131 MRVSIKTRIGLNTDG---EWEELFAVFNHFPFSEIIVHPRTQK--------QYYSGRVNL 179

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL---KILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
                I K    L +  NG +E     L   +  P + G+M GR    N A+        
Sbjct: 180 HCFQNICK-YSKLPLVYNGDVETREDILFLQEQFPEIQGIMCGRGLLSNPALFREAR--- 235

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH-GFPNSRR 292
                G   ++    K+F R +  +         +   K ++   +    +  G    + 
Sbjct: 236 -----GGKALQEGEFKEFLRLVEENFAKEIQGERNILAKYKEFWSYFAKSYQGGEKGLKE 290

Query: 293 CRHILTVEAGASTATHHIIETAFNLMIESL 322
            R    + A    A +     +   + E L
Sbjct: 291 VRKAKNL-AEYKAAKYRFFAESHFQVREGL 319


>gi|67525019|ref|XP_660571.1| hypothetical protein AN2967.2 [Aspergillus nidulans FGSC A4]
 gi|40744362|gb|EAA63538.1| hypothetical protein AN2967.2 [Aspergillus nidulans FGSC A4]
 gi|259486087|tpe|CBF83649.1| TPA: tRNA dihydrouridine synthase (Smm1), putative (AFU_orthologue;
           AFUA_3G08390) [Aspergillus nidulans FGSC A4]
          Length = 437

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 61/283 (21%), Positives = 108/283 (38%), Gaps = 40/283 (14%)

Query: 23  YTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +T M  ++++ + D K      L  + ++  L  Q+G A+    V+A K+V     N I+
Sbjct: 72  FTRM-PSNSVNKDDAKESVIYRLDPAREKGKLIFQMGTANPELAVQAGKLVAA-DVNGID 129

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N GCP      G  GA L+  PD +   + A+ K +  P  +   + +          +
Sbjct: 130 VNSGCPKPFSTSGGMGAALLRTPDKLVSILEALVKEVGEPYQIGISVKIRLLETPELTES 189

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
           LV  + ++G+ G+ IH R   +        R       D +  I     N  +   +NG 
Sbjct: 190 LVSRLVRTGITGLTIHCRTTPM--------RPRERAIRDQLRMIVSTCHNAGVACIMNGD 241

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           +    +AL ++     DG MI  AA  NS+         S    G +P         WR+
Sbjct: 242 VTSRDEALALMQEYGADGAMIATAAEANSSCFR------SEADGGLAP---------WRE 286

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-RRCRHI 296
           +            +  G     T+++I +    P   +  R  
Sbjct: 287 VVHEYVKLCIECENRFGN----TKYLINML--IPGKDKEFREA 323


>gi|115384898|ref|XP_001208996.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
 gi|114196688|gb|EAU38388.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
          Length = 441

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 77/180 (42%), Gaps = 9/180 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A     V+AAKIV       I++N GCP      G  GA L+  PD +   + 
Sbjct: 105 LIFQIGTASPELAVQAAKIVAG-DVAGIDVNSGCPKPFSTSGGMGAALLRTPDKLVAILE 163

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ + +  P  +   + +          +LV  + K+G+ G+ +H R   ++   P++  
Sbjct: 164 ALVREVGTPYQIGISVKIRILETPELTESLVSRLVKTGITGLTVHCRTTPMR---PRERA 220

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
               L   +V  +   N  +   +NG +     AL ++    VDG MI  +A  N +   
Sbjct: 221 IRDQLR--MVANVC-HNAGVACVMNGDVTSRDDALALMQEYGVDGAMIATSAESNFSCFR 277


>gi|241649968|ref|XP_002411233.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215503863|gb|EEC13357.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 326

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 94/279 (33%), Gaps = 68/279 (24%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM +A  +L+G +    +L     E    +Q+ GA   ++ 
Sbjct: 37  NLPFRRICKEF-GADVTCGEMAMASNLLQGQQSEWALLKRHASEDLFGVQVCGAHADQMT 95

Query: 64  EAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             A+++ E    + +++N+GCP   V++   G+ LM     + + +  M   + +P+T+K
Sbjct: 96  RCAQLLTEKCSVDFVDINMGCPIDFVYKKGAGSGLMGRAKKLSEIVFGMSSVMDVPLTLK 155

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R                     +G+                  + R+I    + ++ ++
Sbjct: 156 MR---------------------AGIQ-----------------EGRQIA---HQVIQDL 174

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           K+                  AL        V   R A     +   + E     ++ S  
Sbjct: 175 KR-------------WTDRVALITRLIASAVCSSRGALIKPWIFMEIKEQRHWDISSSER 221

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           +          +I    T Y   H  S  +  + TR  +
Sbjct: 222 L----------EILKKYTGYGLDHWGSDTEGVERTRRFL 250


>gi|114615414|ref|XP_001164035.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 1 [Pan
           troglodytes]
 gi|114615416|ref|XP_001164118.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 2 [Pan
           troglodytes]
 gi|114615418|ref|XP_001164161.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 3 [Pan
           troglodytes]
 gi|114615420|ref|XP_001164233.1| PREDICTED: similar to dihydrouridine synthase 4-like isoform 4 [Pan
           troglodytes]
 gi|84627517|gb|AAI11775.1| DUS4L protein [Homo sapiens]
 gi|119603806|gb|EAW83400.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
 gi|119603809|gb|EAW83403.1| dihydrouridine synthase 4-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
 gi|194386236|dbj|BAG59682.1| unnamed protein product [Homo sapiens]
          Length = 196

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 49/192 (25%), Positives = 84/192 (43%), Gaps = 32/192 (16%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            +GACL+  P++V D +  +   +  P   V++K RI  D +       +L +  + +GV
Sbjct: 4   GYGACLINKPELVQDMVKQVRNQVETPGFSVSIKIRIHDDLKRTV----DLCQKAEATGV 59

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-- 206
           + I +H R A  +            + YD +  I KEN  + +  NG +  + +A  +  
Sbjct: 60  SWITVHGRTAEERHQ---------PVHYDSIK-IIKENMSIPVIANGDIRSLKEAENVWR 109

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM-TDYAAR 265
           +   DGVM+ R    N AM    +E         +P+K   D   W  I+  + T Y   
Sbjct: 110 ITGTDGVMVARGLLANPAMFAGYEE---------TPLKCIWD---WVDIALELGTPYMCF 157

Query: 266 HLHSGGKLQQIT 277
           H H    +++IT
Sbjct: 158 HQHLMYMMEKIT 169


>gi|146422997|ref|XP_001487432.1| hypothetical protein PGUG_00809 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 362

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 96/251 (38%), Gaps = 35/251 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR----------------GDKKNILGFS 44
           MV   +   R  A       L+++  IV   I++                 + K +    
Sbjct: 13  MVRSGELPTRLMALRY-GADLVWSPEIVDKKIIQCKRVENVKLATTDFIDSNNKVVFRTH 71

Query: 45  T--QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
              +   L  QIG A+    VEAAK+V     + I+LN GCP         GA L+ NPD
Sbjct: 72  PASERGRLIFQIGSANPELAVEAAKVVA-RDVDGIDLNCGCPKNFSTHSGMGAELLTNPD 130

Query: 103 IVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           ++   +  + + +     IP++VK R+   D         L+  I K+GV  + +H R  
Sbjct: 131 VLVLILKNLVEKIGNVYRIPISVKIRLL--DATDPEPSIKLIDRICKTGVANLTLHCRTK 188

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---GVMI 215
            ++   P     +P     I+  +   N      LNG + +  +  ++        G MI
Sbjct: 189 PMRNRQPPIRTFLP----QIIETVHSNNVS--FILNGAIRNRQEFYELQARYGKQIGAMI 242

Query: 216 GRAAYKNSAML 226
             +A  N  + 
Sbjct: 243 AESAEANPTVF 253


>gi|60679746|ref|YP_209890.1| hypothetical protein BF0150 [Bacteroides fragilis NCTC 9343]
 gi|60491180|emb|CAH05928.1| conserved hypothetical protein [Bacteroides fragilis NCTC 9343]
          Length = 310

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 95/235 (40%), Gaps = 18/235 (7%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A +     + +T  +  D       D ++IL  + +   L  Q+  +++
Sbjct: 13  GYTEAAYRNAHAAVFGGVDVYHTPFVRIDRGEFRHKDVRDILPENNRVPHLIPQLIASEM 72

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K      +  + GY E+++N+GCP   + +   G+ ++ +PD V   +  + +   +  
Sbjct: 73  DKTERIIALFIEQGYREMDINLGCPFPMLAKRQCGSGMLPHPDKVETLLKQIEQYPDVSF 132

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G       + L  L+ +   +    I +H R  I +      N +     Y+  
Sbjct: 133 SVKMRLGWKKPDECLTLLPLLNAAPLT---EIIVHPRLGIQQYKGEV-NMEGFTAFYEAC 188

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                      +  NG    +ED+    +  P + GVMIGR    N A+     E
Sbjct: 189 RH--------PVIYNGDILTIEDIRCITEKFPKLTGVMIGRGLLANPALGWEYKE 235


>gi|255710875|ref|XP_002551721.1| KLTH0A06028p [Lachancea thermotolerans]
 gi|238933098|emb|CAR21279.1| KLTH0A06028p [Lachancea thermotolerans]
          Length = 397

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 106/263 (40%), Gaps = 47/263 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFST--------- 45
           MV   +   R  A       L+++  I+   +++  +      K I   +          
Sbjct: 13  MVRAGELPTRLLALKY-GADLVWSPEIIDKKLIQCKRQVNDKLKTIDFVAPSSNDNKPPC 71

Query: 46  ---------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
                    +   L  Q+G +  S  VEAA +V     + I++N GCP         GA 
Sbjct: 72  VVFRTFPDAERGRLIFQMGTSTPSLAVEAAMVVIK-DVDGIDVNAGCPKHFSIHSGMGAA 130

Query: 97  LMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  P+ +   ++++ + +      P++VK RI            NLVK +  +G++ + 
Sbjct: 131 LLKTPETLCSILSSLVEKVGRPHEKPISVKIRIL----DSEELTLNLVKKLCGTGISNLT 186

Query: 153 IHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
           +H R       +P  NR+ P  +Y   +Y+I + N ++ + +NG ++ +    ++   +D
Sbjct: 187 VHCRT------TPMRNRQAPIRNYVPSIYKICQAN-NVSLIMNGAIQSLEHFRQLRKQMD 239

Query: 212 -----GVMIGRAAYKNSAMLTTV 229
                G M+   A  N  + +  
Sbjct: 240 LPETIGGMMADCAEANPTVFSEA 262


>gi|331002215|ref|ZP_08325734.1| hypothetical protein HMPREF0491_00596 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411309|gb|EGG90725.1| hypothetical protein HMPREF0491_00596 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 311

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 111/287 (38%), Gaps = 29/287 (10%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVA---DAILRGDKKNILGFSTQEKPLALQIGG 56
           M   T+  +R  + +        +T  I         + +   +     + + L  Q+  
Sbjct: 8   MEGVTNYVFRKVYIKHFKGVDKFFTPFITPHMKKGFSKSELMELNREYNKGQYLVPQVLL 67

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL- 115
            +  + ++    ++  GY+E N+N+GCPSA V     G+  + + D +     A+ +   
Sbjct: 68  NNAEEFLKLTDEIKQMGYSEFNINLGCPSATVTSKKRGSGFLQDIDSLDKFFYAIFEKRK 127

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +I +++K RIG  D         L+K  KK   N I IH R   L+    K+N  +P   
Sbjct: 128 NIKISIKTRIGFCD---YDEWDELLKVYKKYDFNEIIIHPR---LRSDFYKNNVYLP-AF 180

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-----VDGVMIGRAAYKNSAMLTTVD 230
            D    +     +  +  NG +  ++  +K+  +      DG+M+GR   +N  +  ++ 
Sbjct: 181 LDAGGRL-----NTKLIYNGDINTLNDYIKLKENLKNNIADGIMVGRGLVRNPLLAESIK 235

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                  + +         DF   I            ++  KL++I 
Sbjct: 236 -------SDNKIFDLSKTIDFVNDIRDEYLSLDFGERNTLFKLKEIW 275


>gi|262381181|ref|ZP_06074319.1| dihydrouridine synthase [Bacteroides sp. 2_1_33B]
 gi|262296358|gb|EEY84288.1| dihydrouridine synthase [Bacteroides sp. 2_1_33B]
          Length = 310

 Score =  116 bits (290), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 99/269 (36%), Gaps = 25/269 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR    R+       YT  +  +       D K+I     ++  +  Q+  +  
Sbjct: 11  GYTDSVYREAHTRVFGGVDTYYTPFVRIEKGGFRNKDLKDIACDRNRQVHVVPQLIASTP 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +     ++ ++ GY E ++N+GCP         G+ L+   +     +  + +   I  
Sbjct: 71  DEFRSIVRLFQENGYREADINLGCPFPMQVRAHRGSGLLRYKEEAESLLRTIEEFPDISF 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    +  L      + K  +  I +H R  I +            +D+D  
Sbjct: 131 SVKMRLGWECADESFVLL---SLLNKLPLKHITLHPRLGIQQ--------YKGAIDWDGF 179

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
               +E   L +  NG    LED+    +  P + G+M+GR    +  + T         
Sbjct: 180 SRFYEEC-KLPLYYNGDLVGLEDIRGIKERFPGLAGLMLGRGLLASPWLATEF------- 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           ++G                 + M +YAAR
Sbjct: 232 VSGQVLTVNERRDKLVMFHESLMDEYAAR 260


>gi|150007185|ref|YP_001301928.1| dihydrouridine synthase [Parabacteroides distasonis ATCC 8503]
 gi|255015200|ref|ZP_05287326.1| dihydrouridine synthase [Bacteroides sp. 2_1_7]
 gi|149935609|gb|ABR42306.1| putative nifR3 family TIM-barrel enzyme with dihydrouridine
           synthase domain [Parabacteroides distasonis ATCC 8503]
          Length = 310

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 51/269 (18%), Positives = 99/269 (36%), Gaps = 25/269 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR    R+       YT  +  +       D K+I     ++  +  Q+  +  
Sbjct: 11  GYTDSVYREAHTRVFGGVDTYYTPFVRIEKGGFRNKDLKDIACDRNRQVHVVPQLIASTP 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +     ++ ++ GY E ++N+GCP         G+ L+   +     +  + +   I  
Sbjct: 71  DEFRPIVRLFQENGYKEADINLGCPFPMQVRAHRGSGLLRYKEEAESLLRTIEEFPDISF 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +    +  L      + K  +  I +H R  I +            +D+D  
Sbjct: 131 SMKMRLGWECTDESFVLL---SLLNKLPLKHITLHPRLGIQQ--------YKGAIDWDGF 179

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                E  +L +  NG    LED+    +  P + G+M+GR    +  + T         
Sbjct: 180 SRFYDEC-ELPLYYNGDLVGLEDIRGIKERFPGLAGIMLGRGLLASPWLATEF------- 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           ++G                 + M +YAAR
Sbjct: 232 VSGQVLTVNERRDKLVMFHESLMDEYAAR 260


>gi|218259777|ref|ZP_03475366.1| hypothetical protein PRABACTJOHN_01025 [Parabacteroides johnsonii
           DSM 18315]
 gi|218224905|gb|EEC97555.1| hypothetical protein PRABACTJOHN_01025 [Parabacteroides johnsonii
           DSM 18315]
          Length = 320

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 84/232 (36%), Gaps = 18/232 (7%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   AR+       YT  +    D     + +++   +     L  Q+  A  
Sbjct: 14  GYTDWVYREAHARVFGGVDTYYTPFVRLEKDGFRNKELRDLAPEANASASLVPQMIAASP 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +    A +  + GY   ++N+GCP         GA ++  PD V   +  + +   I  
Sbjct: 74  EEFRRIAGLFRESGYRRADINLGCPFPMQARQHRGAGILPYPDEVKVLLETIFEFPEIQF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G D    A AL   +  +    +  + +H R    +     D        YD  
Sbjct: 134 SVKLRLGWDSPEEAQALLPFLNRL---PLTHLTLHPRIGTQQYKGKTDLSAFSRF-YDSC 189

Query: 180 YEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
                    L +  NG +    D+       P + G+MIGR    +  + T 
Sbjct: 190 --------TLPLFYNGDIRTLPDIRSLTGRFPRLKGIMIGRGLLSSPWLATE 233


>gi|253748358|gb|EET02530.1| Dihydrouridine synthase, putative [Giardia intestinalis ATCC 50581]
          Length = 553

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 89/250 (35%), Gaps = 29/250 (11%)

Query: 8   HYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEA 65
            +R    +     +   EM+ A  IL GD + +  +     EK   +Q+ G     +   
Sbjct: 188 PFRRLC-IHYGCEITLCEMVFARDILHGDAQELRKIKRHPDEKCFGIQLAGRGQDLMEII 246

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK---ALSIPVTVK 122
             I +    + ++LN  CP     +   GA L  N   +   +  M +      +P+ +K
Sbjct: 247 NFIAQCCSCDFVDLNAACPQDIATKKCCGAALASNLKKLVSSVDCMVRGGSHYGLPIFLK 306

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI----------- 171
            R G  D        ++ ++++ S + G+ +HAR A  +     +   +           
Sbjct: 307 IRAG--DMYGNWTGDSVAQALRLSRLYGLSVHARTAKQRYSKMANWDYLASMRQTLEDHE 364

Query: 172 -PNLDYDIVYEIKKENP-------DLF-IGLNGGLEDM-SQALKILPSVDGVMIGRAAYK 221
                 ++  ++K+          D   +G NG + D          +VD  +I R A  
Sbjct: 365 EGAAKSEVEPQLKQGIALDSTTTHDPPLLGGNGDIFDYTDLYRDDHSTVDYYLIARGALV 424

Query: 222 NSAMLTTVDE 231
              +   + E
Sbjct: 425 KPWIFQEIKE 434


>gi|213052349|ref|ZP_03345227.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
          Length = 200

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 42/176 (23%), Positives = 72/176 (40%), Gaps = 13/176 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P+++     AM 
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPELIYQGAKAMR 146

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+   +PVTVK R+G D          +  +++++G + + +H R       +  
Sbjct: 147 AAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTKAQGYRAEH 199


>gi|301311149|ref|ZP_07217077.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 20_3]
 gi|300830723|gb|EFK61365.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 20_3]
          Length = 310

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/269 (18%), Positives = 98/269 (36%), Gaps = 25/269 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR    R+       YT  +  +       D K+I     ++  +  Q+  +  
Sbjct: 11  GYTDSVYREAHTRVFGGVDTYYTPFVRIEKGGFRNKDLKDIACDRNRQVHVVPQLIASTP 70

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +     ++ ++ GY E ++N+GCP         G+ L+   +     +  + +   I  
Sbjct: 71  DEFRPIVRLFQENGYKEADINLGCPFPMQVRAHRGSGLLRYKEEAESLLRTIEEFPDISF 130

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    +  L      + K  +  I +H R  I +            +D+D  
Sbjct: 131 SVKMRLGWECTDESFVLL---SLLNKLPLKHITLHPRLGIQQ--------YKGAIDWDGF 179

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                E  +  +  NG    LED+    +  P + G+M+GR    +  + T         
Sbjct: 180 SRFYDEC-EFPLYYNGDLVGLEDIRGIKERFPGLAGIMLGRGLLASPWLATEF------- 231

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           ++G                 + M +YAAR
Sbjct: 232 VSGQVLTVNERRDKLVMFHESLMDEYAAR 260


>gi|154482706|ref|ZP_02025154.1| hypothetical protein EUBVEN_00382 [Eubacterium ventriosum ATCC
           27560]
 gi|149736482|gb|EDM52368.1| hypothetical protein EUBVEN_00382 [Eubacterium ventriosum ATCC
           27560]
          Length = 326

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 46/281 (16%), Positives = 96/281 (34%), Gaps = 41/281 (14%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQ----EKPLALQIGGADISKLVEAAKIVEDFGYNE- 76
            Y   I      R   K I     +       L  QI        ++AA  + + GY++ 
Sbjct: 30  YYAPFISPSINDRLKGKEIRDLLPENNNKGINLVPQILANRADYFIKAANQLIELGYDKE 89

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC--------KALSIPVTVKCRIGVD 128
           INLN GCPS  V   + GA  + + + +                +  ++ ++VK RIG+ 
Sbjct: 90  INLNAGCPSGTVVSKNKGAGFLKDTEAMDRFFDETFNWLEKKNSEGHNLSISVKTRIGMY 149

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +        N+++   K  ++ + +H R          +                 EN  
Sbjct: 150 EPD---EFENILEVYNKYPISQLIVHPRTREQLYKGTPNMEAFKYAL---------ENSK 197

Query: 189 LFIGLNGGLEDMSQALKILPSVD--------GVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             +  NG +  +    +I+  ++         +MIGR    N  ++  +         G 
Sbjct: 198 NPVCYNGDINTVENYHRIIEKINDDSEMKIGSIMIGRGLIGNPNLVNEIK--------GG 249

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
             +  ++ + +  ++            H   K++++  +M 
Sbjct: 250 KKLTKKMLEVYHDRLYNDFEKIMKADKHLLFKMKEMWTYMS 290


>gi|270610579|ref|ZP_06221673.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae HK1212]
 gi|270318070|gb|EFA29330.1| tRNA-dihydrouridine synthase B [Haemophilus influenzae HK1212]
          Length = 162

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 27/157 (17%), Positives = 55/157 (35%), Gaps = 16/157 (10%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           ++    + K  ++ G+  + +H R         +        +YD +  +K+    + + 
Sbjct: 8   SLNCVQIGKIAEQCGIQALTVHGRT--------RACLFEGEAEYDNIKAVKQAI-AIPVI 58

Query: 193 LNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            NG ++   +A  +L     D +MIGRAA  N  +   V+    +      P        
Sbjct: 59  ANGDIDSARKAKFVLDYTGADAIMIGRAALGNPWLFQAVENLIEHNSISQMPSLKEKCGQ 118

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
             R I      Y  +    G ++    +H+     G 
Sbjct: 119 ILRHIQELHQFYGEQ---KGYRI--ARKHVAWYLQGI 150


>gi|123494891|ref|XP_001326617.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121909534|gb|EAY14394.1| hypothetical protein TVAG_255860 [Trichomonas vaginalis G3]
          Length = 313

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 102/247 (41%), Gaps = 37/247 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-----------------RGDKKNILGF 43
           MV  +   +R          L+++  +V  AI+                  G  + I   
Sbjct: 18  MVRGSSLSFRLACLEY-GADLVFSPGLVDLAIIGSTMEKDDNNISLIKVENGHNRRIFHT 76

Query: 44  STQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           + +E+  L +Q+   D    ++AA +  +F  + I++N GCP +       G+ + L  +
Sbjct: 77  TAEERGKLIIQLITVDGPNAIKAADMCTEF-ASGIDINCGCPESFACHRGGGSKMQL--E 133

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
              D +  +     +P++VK R+    +          K++  +G   I +H R A  K 
Sbjct: 134 SAVDVVKTLKMNSPLPISVKMRV----KDTVEESLQFAKAMVDAGAVAITVHGRLAADK- 188

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
                  +  ++DY+ + EI  +N +     NGG+ + + A ++      D +MI  AA 
Sbjct: 189 -------RHGSVDYEHMKEIF-DNINCAKIGNGGICNKADAAEMRVKTGCDSIMIATAAL 240

Query: 221 KNSAMLT 227
           KN ++ +
Sbjct: 241 KNPSVFS 247


>gi|254669917|emb|CBA04472.1| tRNA-dihydrouridine synthase B [Neisseria meningitidis alpha153]
          Length = 207

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 30/210 (14%), Positives = 67/210 (31%), Gaps = 21/210 (10%)

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           M +A  +P     +           L  + K  +  G+  + +H R         +    
Sbjct: 1   MRQAYPLP----SKPVWGWHDDHQNLPVIAKIAEDCGIAALAVHGRT--------RTQMY 48

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
                Y+++ E K    ++ + +NG +    +A  +L   + DG+MIGR A         
Sbjct: 49  KGEARYELIAETKCRL-NIPVWVNGDITSPQKAQAVLKQTAADGIMIGRGAQGRPWFFRD 107

Query: 229 VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
           +  Y  + +   +             I A    Y          ++   +H+       P
Sbjct: 108 LKHYAEHGVLPPALSLAECAAAILNHIRAIHAFY-----GDSAGVRIARKHIGWYIDEMP 162

Query: 289 NSRRCRHILTVEAGASTATHHIIETAFNLM 318
           +  + R  +     ++ A +  +      +
Sbjct: 163 DGEQTRREIN-RLDSAAAQYDTLAGYLERL 191


>gi|9187612|emb|CAB96955.1| hypothetical protein, similar to (AF091072.1) predicted protein
           [Homo sapiens]
          Length = 465

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 34/164 (20%), Positives = 67/164 (40%), Gaps = 6/164 (3%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 300 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHQCEDIFGVQLEGAFPDTMT 358

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           + A+++      + +++NVGCP   V++   G  LM         +  M + L +P+TVK
Sbjct: 359 KCAELLSRTVEVDFVDINVGCPIDLVYKKGGGCALMNRSTKFQQIVRGMNQVLDVPLTVK 418

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            R GV +++       L+  ++  GV  + +        G   +
Sbjct: 419 IRTGVQERVNLA--HRLLPELRDWGVALVTVGLGTPRALGPRGR 460


>gi|238883846|gb|EEQ47484.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 433

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 107/262 (40%), Gaps = 46/262 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---------------------DKKN 39
           MV   +   R  +       LL+T  +V   IL+                      DKK 
Sbjct: 13  MVRSGELPIRLLSLRY-GCDLLWTPELVDKKILQSTRIINQELNTIDYIVSNHQQSDKKT 71

Query: 40  IL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           ++      +   L LQ+G +D    V+AA+ V D   + I+LN GCP         GA L
Sbjct: 72  VIFRKHPDETGRLILQLGSSDPQLAVDAARKVID-DVDGIDLNCGCPKNFSTHSGMGAEL 130

Query: 98  MLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +  PD +   +  + + + IP    ++ K R+           +NL++ I ++G++ + I
Sbjct: 131 LKTPDKLCSILINLVEKIGIPNKKSISCKIRLF----NNYDQSKNLIEKILQTGISNLTI 186

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD-- 211
           H R  I++         +P L    +  I+    +L I  NG +++++    +  +++  
Sbjct: 187 HCRTPIMRNRQDPVWNFLPKL----IPIIQTAGVNLVI--NGNMQNVADLKNLQSALNDN 240

Query: 212 -----GVMIGRAAYKNSAMLTT 228
                 +MI  AA  N ++ + 
Sbjct: 241 GGGKLSIMIAEAAEANPSVFSH 262


>gi|313217157|emb|CBY38320.1| unnamed protein product [Oikopleura dioica]
          Length = 163

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 35/162 (21%), Positives = 72/162 (44%), Gaps = 11/162 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI--LGFSTQEKPLALQIGGAD 58
           MV ++   +R   R   N  + ++ M+++D+ +         L  + ++ PL +Q     
Sbjct: 1   MVRYSRLPFRALCRKF-NVDVCFSPMLISDSFINSASARDADLRSNAEDGPLVVQFAANK 59

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                + A+++       I+LN GCP   V+  ++G  LM  P+++ D +    +A+   
Sbjct: 60  GEDFAKVAQMLYGH-CEGIDLNCGCPQRWVNALNYGDILMKQPELLADIVLQARRAIPDS 118

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
              ++VK R+  D          + + I+K+G   + IH R 
Sbjct: 119 EFSISVKTRVFDDLH----TTIEMARRIEKAGATMLSIHGRT 156


>gi|114663254|ref|XP_001166802.1| PREDICTED: dihydrouridine synthase 2-like, SMM1 homolog isoform 5
           [Pan troglodytes]
          Length = 477

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 94/253 (37%), Gaps = 62/253 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEK------ 48
           MV       R  A L     ++Y E      MI    ++      +   +  ++      
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVFRTC 77

Query: 49  -----PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
                 +  Q+G +D  + +  A++VE+     I++N+GCP     +             
Sbjct: 78  EREQNRVVFQMGTSDAERALAVARLVEN-DVAGIDVNMGCPKQYSTK------------- 123

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               ++ + K    PVT K RI    +       +LVK I+++G+  I +H RK      
Sbjct: 124 ---ILSTLVKGTHRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK------ 170

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGV 213
             ++ R    +  +++  I  +   + +  NG           +ED  QA     +   V
Sbjct: 171 --REERPQHPVSCEVIKAIA-DTLSIPVIANGGSHDHIQQYSDIEDFRQA----TAASSV 223

Query: 214 MIGRAAYKNSAML 226
           M+ RAA  N ++ 
Sbjct: 224 MVARAAMWNPSIF 236


>gi|58268106|ref|XP_571209.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|57227443|gb|AAW43902.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 496

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 95/243 (39%), Gaps = 35/243 (14%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAIL---------------RGDKKNILGFSTQEKP-L 50
              R  + L     L+++  +V  AI+                  +  I      EKP L
Sbjct: 121 LPMRLLS-LYYGAGLVWSPEVVDRAIIGAERSVDPVTGVITYHKGQGPIFSTHPAEKPFL 179

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QIG ++    V+AA+ V+      I+LN GCP         GA L+  P+++ D + A
Sbjct: 180 IFQIGSSNPELAVKAAQTVQQ-DVAGIDLNCGCPKPFSTHAGMGAALLSTPELLLDILRA 238

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  ++ +P++ K R+             L   I ++GV  + +H R   ++        +
Sbjct: 239 LLDSIPLPISCKIRLLPTQPSTLY----LASRILRTGVRNLTVHCRTRQMRPGERALWER 294

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-------ILPSVDGVMIGRAAYKNS 223
           + +     + E+ K    + +  NG  E  S   +            D VM+ R+A +N 
Sbjct: 295 LSS-----IVELGKRRG-ISVICNGDGEGWSNWDRIRNETGMCASCADSVMLARSAERNP 348

Query: 224 AML 226
           ++ 
Sbjct: 349 SVF 351


>gi|320181530|gb|EFW56448.1| tRNA dihydrouridine synthase B [Shigella boydii ATCC 9905]
          Length = 109

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 30/104 (28%), Positives = 58/104 (55%), Gaps = 2/104 (1%)

Query: 26  MIVADAILRGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ ++  +    K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+GC
Sbjct: 1   MMSSNPQVWESDKSRLRMVHIDEPGIRTVQIAGSDPKEMADAARINVESGAQIIDINMGC 60

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           P+ +V+    G+ L+  PD+V   +  +  A+ +PVT+K R G 
Sbjct: 61  PAKKVNRKLAGSALLQYPDVVKSILTEVVNAVDVPVTLKIRTGW 104


>gi|56807747|ref|ZP_00365610.1| COG0042: tRNA-dihydrouridine synthase [Streptococcus pyogenes M49
           591]
          Length = 191

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 74/211 (35%), Gaps = 23/211 (10%)

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     IP+TVK R G  D   AV       + + +GV+ + +H R         ++  
Sbjct: 1   EVTSVXDIPLTVKMRTGWADSSLAVEN---ALAAESAGVSALAMHGRT--------REQM 49

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
                D++ +  + K    +    NG +  +  A  ++    VD VMIGRAA  N  + T
Sbjct: 50  YTGTCDHETLARVSKAITKIPFIGNGDVRSVQDAKFMIEEIGVDAVMIGRAAMNNPYLFT 109

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGF 287
            ++ +F         +      D  +     + +     +     +++          G 
Sbjct: 110 QINHFFETGQELPD-LPFAKKLDIAKDHLKRLINLKGETIA----VREFRGLAPHYLRGT 164

Query: 288 PNSRRCRHILTVEAGASTATHHIIETAFNLM 318
             + + R  ++     +      +E  F  +
Sbjct: 165 AGAAKVRGAVSRAETLAE-----VEAIFETV 190


>gi|149038073|gb|EDL92433.1| dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)
           (predicted), isoform CRA_b [Rattus norvegicus]
          Length = 380

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 41/156 (26%), Positives = 68/156 (43%), Gaps = 27/156 (17%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G  GA L+ +PD +   ++ + K    PVT K RI    +       NLV
Sbjct: 1   MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDT----LNLV 56

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----- 195
           K I+++G++ I +H R         +D R    +  +++  I  E   + +  NG     
Sbjct: 57  KRIERTGISAIAVHGRN--------RDERPQHPVSCEVIRAIA-ETLSIPVIANGGSHDH 107

Query: 196 -----GLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
                 +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 108 IQQHLDIEDFRQA----TAASSVMVARAAMWNPSIF 139


>gi|71747358|ref|XP_822734.1| tRNA-dihydrouridine synthase 2 [Trypanosoma brucei TREU927]
 gi|70832402|gb|EAN77906.1| tRNA-dihydrouridine synthase 2, putative [Trypanosoma brucei]
          Length = 435

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 63/346 (18%), Positives = 120/346 (34%), Gaps = 71/346 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-------------------------G 35
           MV      +R F        ++++E +VA  ++R                          
Sbjct: 13  MVRVGTVGFRVFC-AAQGADIVFSEEVVASKLIRCKREVRTYTGCPCSMVEFVSYEPYKN 71

Query: 36  DKKNILGFST----------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
             K  + F+T          +  P+ LQ+G A+ +    AA +  D   + I++N+GCP 
Sbjct: 72  KFKRSIAFATVARGGCNSQGEGAPVVLQLGVAEPAIGARAALLCVD-DVDGIDVNMGCPK 130

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAV 134
               +   GA LM +P      + A+ +A++           +P++ K R+       A 
Sbjct: 131 KFSVDNGMGAALMRDPARAAAILVAVDEAVNSPEKVVARRRRVPISFKTRLLDTADATAQ 190

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIG 192
            L ++++ +    V+ I +HAR       SP    +        + +++  K    +   
Sbjct: 191 MLLSVMEGVGPDRVHAITLHARTPDQLPDSPPHYERAAA----TISQLRSHKLFSKVCFV 246

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKT---- 245
           LNG +       +       D  MI R A  + ++ + V  E   +P     P       
Sbjct: 247 LNGSISSRGDGRRKAAQFGFDAAMIARHAMLDMSVFSKVSSEPREDPGDDREPCTDFMAT 306

Query: 246 --------RVDKDFWRKISASMTDYAARHLHSGGKLQQIT--RHMI 281
                    + +   R      T Y     H    +  IT  +H++
Sbjct: 307 PMACASWMELYRGLLRHHVIYRTPYVYTKYHLTRSVPNITALKHLM 352


>gi|296820214|ref|XP_002849907.1| tRNA-dihydrouridine synthase 1 [Arthroderma otae CBS 113480]
 gi|238837461|gb|EEQ27123.1| tRNA-dihydrouridine synthase 1 [Arthroderma otae CBS 113480]
          Length = 573

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 72/203 (35%), Gaps = 36/203 (17%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
            +DA +   +  + G    ++PL +Q    +  +L+ AA+ VE                 
Sbjct: 145 SSDAAVTATEPYLDGNPKYDRPLIVQFCANNPDELLRAARHVE----------------- 187

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
                +      +PD++   I  +   LSIPVT K RI               K I  +G
Sbjct: 188 ----GYCDA--EDPDLIYKLINKLHAELSIPVTAKFRIL----ETKEKTLEYAKMILSAG 237

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI 206
            + + +H R+   KG            +++ +  ++    P+  I  NG + +       
Sbjct: 238 ASILSVHGRRREQKG------HNTGVANWEYIRYLRDNLPPETVIFANGNILNHGDIRDC 291

Query: 207 L--PSVDGVMIGRAAYKNSAMLT 227
           L     DGVM       +  + +
Sbjct: 292 LESTGADGVMSAEGNLSDPTIFS 314


>gi|50310669|ref|XP_455356.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644492|emb|CAG98064.1| KLLA0F06094p [Kluyveromyces lactis]
          Length = 359

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 57/275 (20%), Positives = 102/275 (37%), Gaps = 53/275 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK------KNILGFST--------- 45
           MV   +   R  A L     L+++  I+   +++  +      K +              
Sbjct: 13  MVRAGELPTRLLA-LKHGADLVWSPEIIDKKLIQCQRQVNDTLKTVDFIIPAKREGTEPG 71

Query: 46  ---------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
                    +   L  QIG +  S  VEAA  V +     I++N GCP         GA 
Sbjct: 72  VVFRTVPEVEHGKLIFQIGTSTPSLAVEAALKVIE-DVAGIDVNAGCPKHFSIHSGMGAA 130

Query: 97  LMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  PD +   +  + + +      P++VK RI  D++        LV+ +  +G+  + 
Sbjct: 131 LLQTPDKLCSILIELVEKVGKIYGKPISVKIRILKDEEDT----LTLVEKLCATGITNLT 186

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-----L 207
           +H R   ++         IP      +YEI + N  + + +NG + D     ++     L
Sbjct: 187 VHCRTTPMRNRESPIRAYIPK-----IYEICERN-KVSLIMNGAIRDKEHFEQLRSDLNL 240

Query: 208 PSVDGVMIGRAAYKNSAMLTT--------VDEYFS 234
           P   G M+   A +N  + +         V EY  
Sbjct: 241 PKTIGGMMADCAERNPTVFSESPLPWFKAVKEYLD 275


>gi|148679393|gb|EDL11340.1| mCG20459, isoform CRA_a [Mus musculus]
          Length = 380

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 41/156 (26%), Positives = 68/156 (43%), Gaps = 27/156 (17%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G  GA L+ +PD +   ++ + K    PVT K RI    +       NLV
Sbjct: 1   MGCPKEYSTKGGMGAALLSDPDKIEKILSTLVKGTHRPVTCKIRILPSLEDT----LNLV 56

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----- 195
           K I+++G++ I +H R         +D R    +  +++  I  E   + +  NG     
Sbjct: 57  KRIERTGISAIAVHGRN--------RDERPQHPVSCEVIRAIA-ETLSIPVIANGGSHDH 107

Query: 196 -----GLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
                 +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 108 IQQHVDIEDFRQA----TAASSVMVARAAMWNPSIF 139


>gi|330974611|gb|EGH74677.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 178

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 43/169 (25%), Positives = 74/169 (43%), Gaps = 13/169 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL--RGDKKNILGFS-----TQEKPLAL 52
           M    D   R     +       TE I V++ ++      K    F          PL L
Sbjct: 8   MEGLVDDILRNVLTKVGGIDWCVTEFIRVSERLMPAHYFYKYASEFHNGAKTDAGTPLRL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   L E A    + G   ++LN GCP+  V+    GA L+  P+++   ++ + 
Sbjct: 68  QLLGSDPVCLAENAAFACELGAPVLDLNFGCPAKTVNRSRGGAVLLKEPELLHTIVSQVR 127

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +A+   IPVT K R+G ++   A+   +  +++   G   I +HAR  +
Sbjct: 128 RAVPKDIPVTAKMRLGYENTDLAL---DCARALADGGAEQIVVHARTKV 173


>gi|261332512|emb|CBH15507.1| tRNA-dihydrouridine synthase 2, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 435

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 63/346 (18%), Positives = 121/346 (34%), Gaps = 71/346 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILR-------------------------G 35
           MV      +R F        ++++E +VA  ++R                          
Sbjct: 13  MVRVGTVGFRVFC-AAQGADIVFSEEVVASKLIRCKREVRTYAGCPCSMVEFVSYEPYKN 71

Query: 36  DKKNILGFST----------QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
             K  + F+T          +  P+ LQ+G A+ +    AA +  D   + I++N+GCP 
Sbjct: 72  KFKRSIAFATVARGGCNSQGEGAPVVLQLGVAEPAIGARAALLCVD-DVDGIDVNMGCPK 130

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAV 134
               +   GA LM +P      + A+ +A++           +P++ K R+       A 
Sbjct: 131 KFSVDNGMGAALMRDPARAAAILVAVDEAVNSPEKVVARRRRVPISFKTRLLDTADATAQ 190

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIG 192
            L ++++ +    V+ I +HAR       SP    ++       + +++  K    +   
Sbjct: 191 MLLSVMEGVGPDRVHAITLHARTPDQLPDSPPHYERVAA----TISQLRSHKLFSKVCFV 246

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKT---- 245
           LNG +       +       D  MI R A  + ++ + V  E   +P     P       
Sbjct: 247 LNGSISSRGDGRRKAAQFGFDAAMIARHAMLDMSVFSKVSSEPREDPGDDRGPCTDFMAT 306

Query: 246 --------RVDKDFWRKISASMTDYAARHLHSGGKLQQIT--RHMI 281
                    + +   R      T Y     H    +  IT  +H++
Sbjct: 307 PMACASWMELYRGLLRHHVIYRTPYVYTKYHLTRSVPNITALKHLM 352


>gi|116192117|ref|XP_001221871.1| hypothetical protein CHGG_05776 [Chaetomium globosum CBS 148.51]
 gi|88181689|gb|EAQ89157.1| hypothetical protein CHGG_05776 [Chaetomium globosum CBS 148.51]
          Length = 464

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 56/310 (18%), Positives = 94/310 (30%), Gaps = 90/310 (29%)

Query: 1   MVDWTDRHYRFFARLLTNNA-----LLYTEMIVADAILRGDKKNILGFSTQ--------- 46
           MVD ++  +R  +R     +     L Y+ M  A       K     F            
Sbjct: 43  MVDQSEFAWRMLSRSFLPESEQSGLLAYSPMFHARLFSESQKYRDQHFQPTKPDCDKLYL 102

Query: 47  ------EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
                 ++P  +Q    D   L+ AAKI   +  + ++LN+GCP     +G +G+ L  +
Sbjct: 103 DGNPAIDRPFFVQFCANDPQALLNAAKIAAPY-CDAVDLNLGCPQGIAKKGHYGSFLQED 161

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D++   I  + + L IPVT K RI         A     +++ +   + +   A     
Sbjct: 162 QDLIHQLIKILHENLDIPVTAKIRIL----ETKEATLKYAQNVLRPTASILTCLAA---- 213

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
                                                             DG+M      
Sbjct: 214 -----------------------------------------------TGADGIMSAEGNL 226

Query: 221 KNSAMLTTVDEYFSNPLTGSSPI---KTRVDKDFWR--KISASMTDYAAR-HLHSGGKLQ 274
            N           + P  G  P    + +  K  WR  ++     D   + H  +G +  
Sbjct: 227 SNPGFFA------APPPAGQEPRGYWRGKDGKGGWRVDEVFRRYLDIMHKGHPAAGPRRP 280

Query: 275 Q--ITRHMIG 282
           Q    RH  G
Sbjct: 281 QKTARRHHQG 290


>gi|330914420|ref|XP_003296632.1| hypothetical protein PTT_06777 [Pyrenophora teres f. teres 0-1]
 gi|311331132|gb|EFQ95267.1| hypothetical protein PTT_06777 [Pyrenophora teres f. teres 0-1]
          Length = 698

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 83/254 (32%), Gaps = 40/254 (15%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-------------- 49
           +  YR          + ++EM +   +++GDK    ++     E                
Sbjct: 337 NMPYRRLCVDF-GCQVTWSEMAMGMPLIQGDKGEWPLMKAHESEISPPKFLGKNTVVQGY 395

Query: 50  -------LALQIGGADISKLVEAAKIVEDFGY--NEINLNVGCPSARVHEGSFGACLMLN 100
                     QI         +  +++ ++      I+LN GCP   V E   G+ L+ +
Sbjct: 396 DNSKDLKFGAQIAANKPWLATKTVEVLTEYCPKLRAIDLNCGCPINLVCEKGSGSALLDS 455

Query: 101 PDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
              +   +  M      +P+TVK R+G  D  P      L+K +   G      H     
Sbjct: 456 EAKLEHILRGMSYVSKEVPITVKIRMGTKDNHPTAQ--KLIKRLVLGG------HEAVES 507

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            KG S       P  + D           ++   NG           L    VD VM+GR
Sbjct: 508 GKGTSGT-GPTSPTAEAD--PRDLANGGHVYFVGNGDCYSHEDYYNNLANAGVDTVMVGR 564

Query: 218 AAYKNSAMLTTVDE 231
            A     +   +++
Sbjct: 565 GALIKPWLFEEIEK 578


>gi|68482812|ref|XP_714632.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|68483004|ref|XP_714536.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436113|gb|EAK95481.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
 gi|46436216|gb|EAK95582.1| potential tRNA dihydrouridine synthase [Candida albicans SC5314]
          Length = 433

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 107/262 (40%), Gaps = 46/262 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG---------------------DKKN 39
           MV   +   R  +       LL+T  +V   IL+                      DKK 
Sbjct: 13  MVRSGELPIRLLSLRY-GCDLLWTPELVDKKILQSTRIINQELNTIDYIVSNHQQSDKKT 71

Query: 40  IL--GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           ++      +   L LQ+G +D    V+AA+ V D   + I+LN GCP         GA L
Sbjct: 72  VIFRKHPVETGRLILQLGSSDPQLAVDAARKVID-DVDGIDLNCGCPKNFSTHSGMGAEL 130

Query: 98  MLNPDIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           +  PD +   +  + + + IP    ++ K R+           +NL++ I ++G++ + I
Sbjct: 131 LKTPDKLCSILINLVEKIGIPNKKSISCKIRLF----NNYDQSKNLIEKILQTGISNLTI 186

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD-- 211
           H R  I++         +P L    +  I+    +L I  NG +++++    +  +++  
Sbjct: 187 HCRTPIMRNRQDPVWNFLPKL----IPIIQTAGVNLVI--NGNMQNVADLKNLQSALNDN 240

Query: 212 -----GVMIGRAAYKNSAMLTT 228
                 +MI  AA  N ++ + 
Sbjct: 241 GGGKLSIMIAEAAEANPSVFSH 262


>gi|154314901|ref|XP_001556774.1| hypothetical protein BC1G_04792 [Botryotinia fuckeliana B05.10]
 gi|150848330|gb|EDN23523.1| hypothetical protein BC1G_04792 [Botryotinia fuckeliana B05.10]
          Length = 278

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 70/186 (37%), Gaps = 19/186 (10%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           S    P   Q G     ++  +  ++  +  N +++N GCP +     S GA LM   ++
Sbjct: 31  SPTSGPTIAQFGVCSPLEISRSTTLLAPY-VNGVDINCGCPQSWACACSIGAALMHKREL 89

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V + +     AL        R G + +       + + +++ +GV+ I IH R       
Sbjct: 90  VAEMVKEAKSALK-------RDGFEGKKTVRETIDFINTVQDAGVDFITIHGRMRSTPSS 142

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
            P +   I         ++   +  +    NG +  +S A        V GVM  R   +
Sbjct: 143 HPVNLEAI---------KLLTTHTTVPTLSNGDIFTLSDAFHHTSHTGVSGVMSARGLLE 193

Query: 222 NSAMLT 227
           N A+  
Sbjct: 194 NPALFA 199


>gi|315305585|ref|ZP_07875289.1| tRNA-dihydrouridine synthase B [Listeria ivanovii FSL F6-596]
 gi|313626046|gb|EFR95474.1| tRNA-dihydrouridine synthase B [Listeria ivanovii FSL F6-596]
          Length = 147

 Score =  112 bits (282), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 41/149 (27%), Positives = 72/149 (48%), Gaps = 12/149 (8%)

Query: 62  LVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V D +AA+  A+  PVT
Sbjct: 1   LVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKVYDMVAAVVDAVDKPVT 60

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK RIG D++        L      +    +    R  + +G          + ++D++ 
Sbjct: 61  VKMRIGWDEEHVFAIENALAAERAGAAAVAMHGRTRVQMYEG----------SANWDVLR 110

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS 209
           ++K+E   +    NG +     A +IL  
Sbjct: 111 DVKREL-KIPFMANGDVRTPEDAKRILEH 138


>gi|85116943|ref|XP_965143.1| hypothetical protein NCU00950 [Neurospora crassa OR74A]
 gi|28926947|gb|EAA35907.1| hypothetical protein NCU00950 [Neurospora crassa OR74A]
 gi|38567022|emb|CAE76320.1| related to tRNA dihydrouridine synthase [Neurospora crassa]
          Length = 475

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 46/184 (25%), Positives = 82/184 (44%), Gaps = 17/184 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
              QIG +D ++ VE AK+V     + I++N GCP         GA L+  P+ +   + 
Sbjct: 123 HIFQIGTSDPARAVECAKLVAA-DVSGIDVNAGCPKPFSTHAGMGAALLRTPEKLVSILE 181

Query: 110 AMCK----ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+      A  I ++VK R+             LV+ +  +G+ G+ IH R   ++   P
Sbjct: 182 ALVAEIKPAFDIGISVKIRLL----ETPAETEALVRRLCATGITGLTIHCRTTPMR---P 234

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++      L   ++ ++  E   +   +NG +E+   AL+++     DG MI   A KN 
Sbjct: 235 RERAIRGQLR--MIADVCHEFG-VACLVNGDVENRDHALELMAEYGTDGAMIATCAEKNG 291

Query: 224 AMLT 227
           +   
Sbjct: 292 SCFR 295


>gi|150865372|ref|XP_001384560.2| hypothetical protein PICST_72127 [Scheffersomyces stipitis CBS
           6054]
 gi|149386628|gb|ABN66531.2| predicted protein [Scheffersomyces stipitis CBS 6054]
          Length = 390

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 109/259 (42%), Gaps = 45/259 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--------------------RGDKKNI 40
           MV   +   R  +       L+++  IV   ++                     G K   
Sbjct: 13  MVRSGELPNRIMSLKY-GADLVWSPEIVDRKLIQTRRVVNEEIKTVDYVVDSPHGAKLVF 71

Query: 41  LGFSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
             F   E   L LQ+G +D    V+AA+ V     + I+LN GCP +       GA L+ 
Sbjct: 72  RTFPELEAGKLILQLGSSDPDLAVQAAEKVIK-DVDGIDLNCGCPKSFSTHSGMGAALLS 130

Query: 100 NPDIVGDCIAAMCKALSI----PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            P+++   +  + + + I    P++ K R+  D +    A R+LV  I ++G+  + IH 
Sbjct: 131 TPELLCSVLRDLVQKVGIPNQKPISCKIRLLDDLE----ATRSLVDQICETGIANLTIHC 186

Query: 156 RKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSV 210
           R+  ++      NR+ P   Y  +I+  +  ++  + + +NG L+   D+     +  + 
Sbjct: 187 RQRAMR------NRQEPIWHYLSEIIPRV--QSKGISVVINGNLQSKADLCSLQDLFNNK 238

Query: 211 D-GVMIGRAAYKNSAMLTT 228
           D G MI  AA  N ++ + 
Sbjct: 239 DIGGMIAEAAEANPSVFSD 257


>gi|330995636|ref|ZP_08319534.1| dihydrouridine synthase [Paraprevotella xylaniphila YIT 11841]
 gi|329574695|gb|EGG56256.1| dihydrouridine synthase [Paraprevotella xylaniphila YIT 11841]
          Length = 313

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 59/319 (18%), Positives = 114/319 (35%), Gaps = 45/319 (14%)

Query: 1   MV---DWTDRHYR-FFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQI 54
           M      T+  YR  F +      + YT  I      + R D +++   + +   L  QI
Sbjct: 8   MAPLQGLTEAPYRNAFEKHFGGVDVYYTPFIRWEHGGLRRKDVRDLHPDANKVGHLVPQI 67

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
             A   +       V  +GY E++LN+GC    + +   G  L+  P+ V   +  + + 
Sbjct: 68  IAASAEEAELILDQVVSYGYQEVDLNMGCAFPMLVKKGKGCGLLPEPERVRGLLQVVERY 127

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I  +VK R+G +    A     L+  + ++ ++ + +HAR            +     
Sbjct: 128 PDISFSVKMRLGYE---NAAECMELLPVLNETRLSRVVVHARTG--------RQQYKGVC 176

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTT--- 228
           D +      +E     +  NG +  +    ++   +P ++GVM+GR       +      
Sbjct: 177 DREAFLRFARECRH-PVVYNGDVTTVEFLSELQRGMPFLEGVMMGRGLLAAPWVAIEYHE 235

Query: 229 --------------------VDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
                               +D Y      G   + T++ K FW  I         + +H
Sbjct: 236 GAAWSMERRMSSLRALHADLLDHYVQTLEGGEKQLLTKM-KAFWEYIYPEGDRKCRKKIH 294

Query: 269 SGGKLQQITRHMIGLFHGF 287
              K+   T+ +  L  G+
Sbjct: 295 KVQKVADYTQAVFQLLSGY 313


>gi|325281268|ref|YP_004253810.1| dihydrouridine synthase DuS [Odoribacter splanchnicus DSM 20712]
 gi|324313077|gb|ADY33630.1| dihydrouridine synthase DuS [Odoribacter splanchnicus DSM 20712]
          Length = 313

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 61/305 (20%), Positives = 119/305 (39%), Gaps = 27/305 (8%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TDR YR  FA       + YT  I  +  A+ + D ++I   +     L  QI     
Sbjct: 15  GYTDRIYRNAFAHYFGGVEVYYTPFIRVEKGALRKRDLRDIEPETNTVADLIPQILPGSA 74

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +       V + GY +I++N+GCP   +     GA ++L P  V + +A + +   I  
Sbjct: 75  DEFRLLTDAVGEKGYRQIDINLGCPFPMIAGKHKGAGMLLYPAQVAEVLAPIAEYPEIQF 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G ++    + L  L+ +++   ++ I +HAR    +     D        +   
Sbjct: 135 SLKMRLGWENASECMVLVELLNTLR---LSRIALHARTGKQQYKGHPDLEA-----FQGF 186

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           YE+ +      +  NG +E +S   +IL     + GV IGR    +  +       F   
Sbjct: 187 YELCQH----PLYYNGDIESLSDIRQILTRFPLLKGVFIGRGLLSSPLLAKE----FKGN 238

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI-----GLFHGFPNSR 291
            T     +  +   F  ++ ++ +           K++ +  + +      L      S 
Sbjct: 239 ETFLPEQRMSIYFAFHEELFSAYSQVLQGETQLLVKMKTLWEYFLPETDRKLLKRIKKST 298

Query: 292 RCRHI 296
           R +  
Sbjct: 299 RLQQY 303


>gi|319900465|ref|YP_004160193.1| tRNA-U20a,U20b-dihydrouridine synthase [Bacteroides helcogenes P
           36-108]
 gi|319415496|gb|ADV42607.1| tRNA-U20a,U20b-dihydrouridine synthase [Bacteroides helcogenes P
           36-108]
          Length = 323

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 60/320 (18%), Positives = 124/320 (38%), Gaps = 32/320 (10%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR    R+       Y+  +  +   I R D ++IL  +  +  L  Q+  ++ 
Sbjct: 21  GYTDAVYRRAHVRIFGGIETYYSPFVRIEHGEIRRKDIRDILPENNPDLHLIPQLIASEA 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            K      +  + GY E ++N+GCP   + +   GA ++  P+ V   +   + K  +I 
Sbjct: 81  DKAERITALFTEKGYQEADINLGCPFPMLAKRHNGAGMLPYPEEVKALLTDTVKKHPNIS 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G D+    +A   L+    +  ++ I +H R    +     D +      Y+ 
Sbjct: 141 FSVKLRLGWDNPEECLA---LLPIFNELPLSHIILHPRLGRQQYKGEIDLKGF-EAFYNG 196

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             +         +  NG L   ED+    +  P + G++IGR    + A+     EY   
Sbjct: 197 CSK--------PLLYNGDLNTPEDIHSIARRFPQLAGIVIGRGLLASPAL---ALEYLQG 245

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS-RRCR 294
               S  +  +V +      ++         +    K++    +++      P + ++ R
Sbjct: 246 KPLSSDEMARKVSRLHAEVFNSYKEQLQGGDIQLLMKMKSFWEYLL------PGADKKAR 299

Query: 295 ---HILTVEAGASTATHHII 311
              H  +  A    A  +++
Sbjct: 300 KTIHKTSKLANYQAAVSNLL 319


>gi|237724433|ref|ZP_04554914.1| nifR3 family TIM-barrel protein [Bacteroides sp. D4]
 gi|229437302|gb|EEO47379.1| nifR3 family TIM-barrel protein [Bacteroides dorei 5_1_36/D4]
          Length = 305

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 53/294 (18%), Positives = 106/294 (36%), Gaps = 28/294 (9%)

Query: 3   DWTDRHYRFFARL-LTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  +R F           YT  +  +       D ++I   +     +  Q+  +  
Sbjct: 10  GFTEAPWRNFHEEVFGGIDAYYTPFVRIERGGFRNRDVRDIAPENNTVSHVVPQLIASTP 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L   A +  + GY E + N+GCP   V     G+ ++  P  V   +  +     +  
Sbjct: 70  VELERLAALFTEKGYKEADFNMGCPFPLVARKHKGSGILPYPAEVEALLKELTHYPELSF 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    A   R L+  +  + +  I +H R    +        ++    +   
Sbjct: 130 SVKMRLGWE---SADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-----EVDLAAFTAF 181

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           YE         +  NG    +ED+ +  +  P ++GVM+GR    N A+      Y +  
Sbjct: 182 YEECAH----PLVYNGDLLTVEDIRKVEEKFPCLEGVMLGRGLLANPALAWE---YVNGT 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                 +  +V     + + A +  Y   HL    +L    +         P++
Sbjct: 235 SFSPDKLHEKV-----KALHARLLQYYEAHLQGEAQLLSKMKPYWEYL--LPDA 281


>gi|325288142|ref|YP_004263932.1| dihydrouridine synthase DuS [Cellulophaga lytica DSM 7489]
 gi|324323596|gb|ADY31061.1| dihydrouridine synthase DuS [Cellulophaga lytica DSM 7489]
          Length = 315

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 51/266 (19%), Positives = 99/266 (37%), Gaps = 23/266 (8%)

Query: 3   DWTDRHYRFFA-RLLTNNALLYTEMI--VADAILRGDKKNILGFSTQEK-PLALQIGGAD 58
            +TD ++R    +        Y   I      +++G  +  L         L  Q+  AD
Sbjct: 12  GFTDYNFRNAHQKFFGGIDTYYAPYIRFNKKMVIKGSYQRDLNPEVNTSLDLIPQVMTAD 71

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
             + + A K ++  GY E+N N+GCP   V     G+ L+ NP+ +   +        + 
Sbjct: 72  ADQFIFAIKYIQSLGYKELNWNLGCPYPMVTNSGMGSGLICNPEKIDHILDRAHSETDVT 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V++K R+G ++      +      + K  +  I IHAR          D +      +  
Sbjct: 132 VSMKMRLGYENSN---EILESFSVLDKYPLKSIAIHARLGKQLYKGGVDLQG-----FQK 183

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSAMLTTVDEYFSN 235
             ++ K      +  NG +  ++Q  K+      +   MIGR    +  + + +     N
Sbjct: 184 CVDVAKHT----LYYNGDITTVAQFKKMKEQFPSIQHFMIGRGLIADPFLPSMIK----N 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTD 261
             T     + ++ K+F   I     +
Sbjct: 236 NSTEYPKGRWQIFKEFHDTIYHQYDE 261


>gi|289621262|emb|CBI52045.1| unnamed protein product [Sordaria macrospora]
          Length = 456

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 80/184 (43%), Gaps = 17/184 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
              QIG +D S+ VE AK+V     + I++N GCP         GA L+  PD +   + 
Sbjct: 118 HIFQIGTSDPSRAVECAKLVAA-DVSGIDVNAGCPKPFSTHAGMGAALLRTPDKLVSILE 176

Query: 110 AMCK----ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+      A  I ++VK R+             LV+ +  +G+ G+ IH R   ++   P
Sbjct: 177 ALVAEIKPAFDIGISVKIRLL----ETPAETETLVRRLCAAGITGLTIHCRTTPMR---P 229

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++      L   ++ ++  E   +   +NG +E     L+++     DG MI   A KN 
Sbjct: 230 RERAIRGQLR--MIADVCHEYG-VACVVNGDVEGRDHGLELMAEYGTDGAMIATCAEKNG 286

Query: 224 AMLT 227
           +   
Sbjct: 287 SCFR 290


>gi|296500911|ref|YP_003662611.1| Nif3 family protein [Bacillus thuringiensis BMB171]
 gi|296321963|gb|ADH04891.1| Nif3 family protein [Bacillus thuringiensis BMB171]
          Length = 155

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 25/129 (19%), Positives = 49/129 (37%), Gaps = 8/129 (6%)

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
                 D+DI+ ++K+ + ++ +  NG +     A ++L    VDGVMIGRAA  +  M+
Sbjct: 1   MYEGKADWDIIKQVKQ-SVNIPVIGNGDVATPQDAKRMLDEIGVDGVMIGRAALGDPWMI 59

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
               +Y         P            +     D      +    ++++ +H      G
Sbjct: 60  YRTVKYLETGELMPEPTVREKI-----DVCMLHLDRLIDLKNESVAVREMRKHAAWYLKG 114

Query: 287 FPNSRRCRH 295
              +   R+
Sbjct: 115 VRGNASVRN 123


>gi|71013186|ref|XP_758561.1| hypothetical protein UM02414.1 [Ustilago maydis 521]
 gi|46098219|gb|EAK83452.1| hypothetical protein UM02414.1 [Ustilago maydis 521]
          Length = 477

 Score =  111 bits (278), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 74/203 (36%), Gaps = 26/203 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q   +      +A++++  F  + ++LN GCP    +E   G+ L+  P+ V D + 
Sbjct: 169 LVAQFASSKPEPFADASELIGRF-VDGVDLNCGCPQPWAYEELLGSYLLRQPETVRDMVR 227

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A+   +     V+VK RI  D ++    +RN +     +G + + IH R        P +
Sbjct: 228 AVKARMGSDFCVSVKIRIDPDLRLTDALVRNALH----AGASILQIHGRTRWQSSSEPVN 283

Query: 168 NRKIPNL-----------DYDIVYEIKKENPD------LFIGLNGGLEDMSQAL--KILP 208
              I               +           D      +    NG +  +  A+  +   
Sbjct: 284 LDGIKFAVDAANACGFRTSWGSKGGAAARFADGGSGGLVPCVANGDVWTLDDAIHYRQTT 343

Query: 209 SVDGVMIGRAAYKNSAMLTTVDE 231
              G M  R    N A+ +  ++
Sbjct: 344 GCRGAMSARGLLANPALFSGYNQ 366



 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE 47
          MV ++   +R        + +  T MI+A    R +      FST +
Sbjct: 47 MVRYSKLAFRTLVSRYETH-ITTTPMILAKEFSRTEAARNSEFSTNQ 92


>gi|212692604|ref|ZP_03300732.1| hypothetical protein BACDOR_02101 [Bacteroides dorei DSM 17855]
 gi|237709084|ref|ZP_04539565.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|265752608|ref|ZP_06088177.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_1_33FAA]
 gi|212664889|gb|EEB25461.1| hypothetical protein BACDOR_02101 [Bacteroides dorei DSM 17855]
 gi|229456780|gb|EEO62501.1| conserved hypothetical protein [Bacteroides sp. 9_1_42FAA]
 gi|263235794|gb|EEZ21289.1| nifR3 family TIM-barrel protein [Bacteroides sp. 3_1_33FAA]
          Length = 305

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 53/294 (18%), Positives = 106/294 (36%), Gaps = 28/294 (9%)

Query: 3   DWTDRHYRFFARL-LTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  +R F           YT  +  +       D ++I   +     +  Q+  +  
Sbjct: 10  GFTEAPWRNFHEEVFGGIDAYYTPFVRIERGGFRNRDVRDIAPENNTVSHVVPQLIASTP 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +L   A +  + GY E + N+GCP   V     G+ ++  P  V   +  +     +  
Sbjct: 70  VELERLAALFTEKGYKEADFNMGCPFPLVARKHKGSGILPYPAEVEALLKELTHYPELSF 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    A   R L+  +  + +  I +H R    +        ++    +   
Sbjct: 130 SVKMRLGWE---SADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-----EVDLAAFTAF 181

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           YE         +  NG    +ED+ +  +  P ++GVM+GR    N A+      Y +  
Sbjct: 182 YEECAH----PLVYNGDLLTVEDIRKVEEKFPCLEGVMLGRGLLANPALAWE---YVNGI 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
                 +  +V     + + A +  Y   HL    +L    +         P++
Sbjct: 235 SFSPDKLHEKV-----KALHARLLQYYEAHLQGEAQLLSKMKPYWEYL--LPDA 281


>gi|255944963|ref|XP_002563249.1| Pc20g07240 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211587984|emb|CAP86053.1| Pc20g07240 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 463

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 106/280 (37%), Gaps = 37/280 (13%)

Query: 23  YTEMIVADAILRGDKKN--ILGFST--QEKPLALQIGGADISKLVEAAKIVEDFGYNEIN 78
           +T M           K   I       ++  L  QIG A+   L   A  V     + I+
Sbjct: 84  FTRMPSNGGRPNKPTKESIIYRIDPAREKGRLIYQIGTANPE-LAVQAARVVAADVSGID 142

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LN GCP      G  GA L+  PD++   + A+ K +  P  +   + +           
Sbjct: 143 LNSGCPKPFSTSGGMGAALLRTPDLLVSILEALVKEVGQPFQIGISVKIRILSKPEETEA 202

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           LV  + K+G+ G+ +H R   ++        ++P     +V  I  E   +   +NG + 
Sbjct: 203 LVSRLVKTGITGLTVHCRTTPMRPRERAIRDQLP-----MVARICHEAG-VACLMNGDVT 256

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
              + L ++    VDG MI  +A  NS+         +    G++P         WR++ 
Sbjct: 257 SRDEGLALMAEYGVDGAMIATSAETNSSCFR------AKEDGGAAP---------WREVV 301

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLF-----HGFPNSR 291
               +Y    + S  +L   T++++ +        F  ++
Sbjct: 302 ---YEYLCFCMESENRLGN-TKYLLNILIPGKDKEFKGAK 337


>gi|260944248|ref|XP_002616422.1| hypothetical protein CLUG_03663 [Clavispora lusitaniae ATCC 42720]
 gi|238850071|gb|EEQ39535.1| hypothetical protein CLUG_03663 [Clavispora lusitaniae ATCC 42720]
          Length = 393

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 101/259 (38%), Gaps = 43/259 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL-------------------RGDKKNIL 41
           MV   +   R  A       L+++  I+   I                    +   KN L
Sbjct: 32  MVRSGELPTRLMALKF-GADLVWSPEIIDKKIRTCSRVENKELETIDFIETGKNGSKNSL 90

Query: 42  GFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
            F T    +E  L  Q+G AD    VE A  V     + I+LN GCP         GA L
Sbjct: 91  IFRTNRKYEEGKLIFQLGSADPDIAVEGALKVIQ-DVDGIDLNCGCPKPFSTHAGMGAAL 149

Query: 98  MLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           + NPD++   +  + + +      P++ K R+   D   A     L+  +  +G+  + +
Sbjct: 150 LSNPDLLCSILENLVEKVGKPYRKPISAKIRLL--DSKSAEPSLALIDRLCSTGITNLTV 207

Query: 154 HARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQAL--KILPSV 210
           H R   ++      NR+ P  DY   +Y++  +   + + +NG      +A   K     
Sbjct: 208 HCRTREMR------NRESPVRDYVSQIYDLTNKRG-VSLVINGAFRCRKEAEQFKQFMGN 260

Query: 211 D--GVMIGRAAYKNSAMLT 227
           D  G+M+  AA  N ++ +
Sbjct: 261 DQIGIMMAEAAESNPSVFS 279


>gi|254581674|ref|XP_002496822.1| ZYRO0D08932p [Zygosaccharomyces rouxii]
 gi|238939714|emb|CAR27889.1| ZYRO0D08932p [Zygosaccharomyces rouxii]
          Length = 373

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 97/254 (38%), Gaps = 40/254 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFST------------- 45
           MV   +   R  A +     L++   I+   +++        LG                
Sbjct: 13  MVRAGELPTRILA-IRNGADLVWGPEIIDKKLIQCKRHVNEKLGCVDYLVDGTTSPVFRT 71

Query: 46  ----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
               ++  +  QIG +  S  ++AA  V     + I++N GCP         GA L+  P
Sbjct: 72  CPQIEKGKIVFQIGTSTPSLAIQAALTVIQ-DVDGIDINAGCPKHFSIHSGMGAALLRTP 130

Query: 102 DIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D + + +  + + +  P    ++VK R+  + +        L+  + ++G++ + +H R 
Sbjct: 131 DKLCEILCELVEKVGRPYGKTISVKIRLLDNREDT----LQLINRLCQTGISHLTVHCRT 186

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDG 212
             ++         I       +YE+ + N    I  NGG++  S   +I     LP   G
Sbjct: 187 TPMRNREQPIRGYIKE-----IYEVCQTNGVTLII-NGGIKSRSHFQEIQRDLELPKEIG 240

Query: 213 VMIGRAAYKNSAML 226
            M+   A +N  + 
Sbjct: 241 GMMADCAEQNPTVF 254


>gi|254566505|ref|XP_002490363.1| Dihydrouridine synthase, member of a family of dihydrouridine
           synthases [Pichia pastoris GS115]
 gi|238030159|emb|CAY68082.1| Dihydrouridine synthase, member of a family of dihydrouridine
           synthases [Pichia pastoris GS115]
 gi|328350757|emb|CCA37157.1| tRNA-dihydrouridine synthase 2 [Pichia pastoris CBS 7435]
          Length = 366

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 69/334 (20%), Positives = 126/334 (37%), Gaps = 76/334 (22%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILG---------------- 42
           MV   +   R  A L     L++    +   IL+ ++     LG                
Sbjct: 13  MVRVGELPTRLLA-LKHGADLVWGPETIDKKILQCERVENRKLGTIDFLSQGGSTKVPGV 71

Query: 43  -------FSTQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
                  +   EK  L  Q+G A+    V AAKIV +   + I++N GCP         G
Sbjct: 72  TNLVFRVYPPAEKGKLIFQMGTANPELAVRAAKIVVN-DVSGIDVNAGCPKHFSIHSGMG 130

Query: 95  ACLMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           A L+  P ++ + +  +   +      P++VK R+  ++Q        LV+ + K+G++ 
Sbjct: 131 AALLSTPALLEEILTRLVTEVGRPNGKPISVKIRVLENEQKT----LELVERLVKTGISN 186

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
           + +H R   ++      NR+ P  DY + + +  + N  + + +NGG++D +  + I   
Sbjct: 187 LTVHCRTKNMR------NREAPIRDYLEGILDHCRSN-KVSLVINGGIKDRNDFIAIQEK 239

Query: 209 -SVD-GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
             +D G M+   A  N      V            P+        WR++     ++A R 
Sbjct: 240 YGMDVGAMVASEAELNPTCFRKV------------PLP-------WREVCKEFLEFADRF 280

Query: 267 LHSGGKLQQITRHMIGLFHG--FPNSRRCRHILT 298
            +  G  +           G   P     R  L+
Sbjct: 281 ANWKGNSK--------YCLGRIVPGGDPIRRDLS 306


>gi|317474612|ref|ZP_07933886.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
 gi|316909293|gb|EFV30973.1| dihydrouridine synthase [Bacteroides eggerthii 1_2_48FAA]
          Length = 318

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 95/237 (40%), Gaps = 20/237 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEK-PLALQIGGAD 58
            +TD  YR   AR+       Y+  +  +   I R D ++I   + +E   L  Q+  + 
Sbjct: 15  GYTDAVYRLAHARIFGGIDTYYSPFVRVEHGEIRRKDARDISSKNNREGIHLIPQLIASQ 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
             KL +   +  +  Y E ++N+GCP   + +   GA ++  PD V D + A  +    I
Sbjct: 75  PDKLEQIITLFIENNYQEADINLGCPFPMLAKRHNGAGMLPYPDEVKDLLTAAIEKYPQI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             +VK R+G +    A     L+       +  I +H R    +     D        ++
Sbjct: 135 HFSVKLRLGWE---NAEECLALLPLFNALPLTHIILHPRLGKQQYKGEVDLSG-----FE 186

Query: 178 IVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
             Y   ++     +  NG    +ED+    +  P + GV+IGR    N A+     +
Sbjct: 187 AFYNGCEK----PLLYNGDLHTVEDIQTITEHFPKLAGVVIGRGLLANPALAWEYRQ 239


>gi|153807233|ref|ZP_01959901.1| hypothetical protein BACCAC_01511 [Bacteroides caccae ATCC 43185]
 gi|149130353|gb|EDM21563.1| hypothetical protein BACCAC_01511 [Bacteroides caccae ATCC 43185]
          Length = 314

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 56/277 (20%), Positives = 99/277 (35%), Gaps = 25/277 (9%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A         YT  +    D     D + I   S Q   L  Q+    I
Sbjct: 14  GYTEAFYRNAHAACFGGIDSYYTPFVRLEKDGFRNKDVREIAPESNQVPHLVPQLIATSI 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K      +  + GY E ++N+GCP   + +   G+ ++  PD V   +    K   I  
Sbjct: 74  EKAETILSLFIEKGYKEADINLGCPFPLLAKRHNGSGILPYPDEVKTLLGLTLKYPQISF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G ++         L   +    +  I +H R    +     D        +D  
Sbjct: 134 SVKMRLGWENPD---ECLQLAPILNDLPLRHITMHPRLGKQQYKGSVDLNG-----FDAF 185

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + +      +  NG +   +D+ +  +  P++ GVMIGR    N A+     E     
Sbjct: 186 LNVCQH----PLIYNGDINCPDDVHRIRQQFPALAGVMIGRGLLANPALALEYKE----- 236

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
               +     + +      ++    YAA+     G+L
Sbjct: 237 --NRTLTPDEMKEKLHIMHTSVYNQYAAQLEGGDGQL 271


>gi|6324342|ref|NP_014412.1| Smm1p [Saccharomyces cerevisiae S288c]
 gi|1730664|sp|P53720|DUS2_YEAST RecName: Full=tRNA-dihydrouridine synthase 2; AltName: Full=Protein
           SMM1
 gi|1302496|emb|CAA96293.1| SMM1 [Saccharomyces cerevisiae]
 gi|1616627|emb|CAA62924.1| SMM1 protein [Saccharomyces cerevisiae]
 gi|151944543|gb|EDN62821.1| tRNA dihydrouridine synthase [Saccharomyces cerevisiae YJM789]
 gi|190408986|gb|EDV12251.1| tRNA-dihydrouridine synthase 2 [Saccharomyces cerevisiae RM11-1a]
 gi|207341587|gb|EDZ69599.1| YNR015Wp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|285814662|tpg|DAA10556.1| TPA: Smm1p [Saccharomyces cerevisiae S288c]
          Length = 384

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 104/260 (40%), Gaps = 47/260 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------I 40
           MV   +   R  A L     L+++  I+   +++  +K                      
Sbjct: 13  MVRAGELPTRLMA-LAHGADLVWSPEIIDKKLIQCVRKENTALQTVDYVVPSKVQTRPET 71

Query: 41  LGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           L F T    +   L  QIG A  +   +AA  V +   + I++N GCP         G+ 
Sbjct: 72  LVFRTYPKLESSKLIFQIGSASPALATQAALKVIN-DVSGIDINAGCPKHFSIHSGMGSA 130

Query: 97  LMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  PD +   +  + K +    S P++VK R+    Q        LVK +  +G+  + 
Sbjct: 131 LLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLDTKQDT----LQLVKRLCATGITNLT 186

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALK----IL 207
           +H RK  ++      NR+ P  DY   +YEI + N ++ + +NG + D S          
Sbjct: 187 VHCRKTEMR------NREQPITDYIAEIYEICQAN-NVSLIVNGAIRDRSHFHDLQANHW 239

Query: 208 PSVD-GVMIGRAAYKNSAML 226
            + + G MI   A ++  + 
Sbjct: 240 KNTNIGGMIAECAERDPTVF 259


>gi|256273339|gb|EEU08277.1| Smm1p [Saccharomyces cerevisiae JAY291]
          Length = 384

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 104/260 (40%), Gaps = 47/260 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------I 40
           MV   +   R  A L     L+++  I+   +++  +K                      
Sbjct: 13  MVRAGELPTRLMA-LAHGADLVWSPEIIDKKLIQCIRKENTALQTVDYVVPSKVQTRPET 71

Query: 41  LGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           L F T    +   L  QIG A  +   +AA  V +   + I++N GCP         G+ 
Sbjct: 72  LVFRTYPKLESSKLIFQIGSASPALATQAALKVIN-DVSGIDINAGCPKHFSIHSGMGSA 130

Query: 97  LMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  PD +   +  + K +    S P++VK R+    Q        LVK +  +G+  + 
Sbjct: 131 LLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLDTKQDT----LQLVKRLCATGITNLT 186

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALK----IL 207
           +H RK  ++      NR+ P  DY   +YEI + N ++ + +NG + D S          
Sbjct: 187 VHCRKTEMR------NREQPITDYIAEIYEICQAN-NVSLIVNGAIRDRSHFHDLQANHW 239

Query: 208 PSVD-GVMIGRAAYKNSAML 226
            + + G MI   A ++  + 
Sbjct: 240 KNTNIGGMIAECAERDPTVF 259


>gi|154490205|ref|ZP_02030466.1| hypothetical protein PARMER_00437 [Parabacteroides merdae ATCC
           43184]
 gi|154089097|gb|EDN88141.1| hypothetical protein PARMER_00437 [Parabacteroides merdae ATCC
           43184]
          Length = 320

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 90/248 (36%), Gaps = 20/248 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   A++       YT  +  +       + ++++  +     L  Q+  A  
Sbjct: 14  GYTDSVYREAHAQIFGGVETYYTPFVRLEKTGFRNKELRDLVPEANTSASLVPQMIAASP 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            +    A +  + GY   ++N+GCP         GA ++  PD V   +  + +   I  
Sbjct: 74  EEFRRIAGLFRESGYRRADINLGCPFPMQARQHRGAGILPYPDEVKVLLETIFEFPEIQF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G D    A AL   +  +    +  + +H R    +     D        YD  
Sbjct: 134 SVKLRLGWDSPEEAQALLPFLNGL---PLTHLTLHPRIGTQQYKGKTDLSAFSRF-YDSC 189

Query: 180 YEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                    L +  NG +    D+       P + G+MIGR    +  + T        P
Sbjct: 190 --------TLPLFYNGDIRTLPDIRSLTGRFPRLKGIMIGRGLLSSPWLATEYIS--DTP 239

Query: 237 LTGSSPIK 244
           LT    I+
Sbjct: 240 LTAQEKIE 247


>gi|189465014|ref|ZP_03013799.1| hypothetical protein BACINT_01358 [Bacteroides intestinalis DSM
           17393]
 gi|189437288|gb|EDV06273.1| hypothetical protein BACINT_01358 [Bacteroides intestinalis DSM
           17393]
          Length = 313

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 51/269 (18%), Positives = 104/269 (38%), Gaps = 23/269 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   AR+       YT  +  +   I + D + I   + +   L  Q+   D+
Sbjct: 14  GYTEAIYRQAHARIFGGIESYYTPFVRVEHGEIRKKDMREITLENNRGVQLIPQLIAPDV 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            K+ +   +  + GY  +++N+GCP   + +   G+ ++  P+ V + + AA+     + 
Sbjct: 74  DKMEQIIALFIEKGYKNVDINLGCPFPLLAKRHNGSGMLPYPEEVRELLTAAIKNHPDLQ 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G +    A     L+  + +  +  I +H R    +     D +      ++ 
Sbjct: 134 FSVKMRLGWE---NAEECLALLPLLNELPLTHIIMHPRLGKQQYKGEVDLKG-----FET 185

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            Y   +      +  NG    +ED+    +  P + G+MIGR    N A+       +  
Sbjct: 186 FYNECRH----PLMYNGDLLTIEDIQAIRERFPQLAGIMIGRGLLANPALALE----YQQ 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAA 264
               S        + F   + A   +   
Sbjct: 238 GHPLSEKDMQERLRLFHADVFAQYGNLLE 266


>gi|259148964|emb|CAY82208.1| Smm1p [Saccharomyces cerevisiae EC1118]
          Length = 384

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 104/260 (40%), Gaps = 47/260 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------I 40
           MV   +   R  A L     L+++  I+   +++  +K                      
Sbjct: 13  MVRAGELPTRLMA-LAHGADLVWSPEIIDKKLIQCIRKENTALQTVDYVVPSKVQTRPET 71

Query: 41  LGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           L F T    +   L  QIG A  +   +AA  V +   + I++N GCP         G+ 
Sbjct: 72  LVFRTYPKLESSKLIFQIGSASPALATQAALKVIN-DVSGIDINAGCPKHFSIHSGMGSA 130

Query: 97  LMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  PD +   +  + K +    S P++VK R+    Q        LVK +  +G+  + 
Sbjct: 131 LLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLNTKQDT----LQLVKRLCATGITNLT 186

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALK----IL 207
           +H RK  ++      NR+ P  DY   +YEI + N ++ + +NG + D S          
Sbjct: 187 VHCRKTEMR------NREQPITDYIAEIYEICQAN-NVSLIVNGAIRDRSHFHDLQANHW 239

Query: 208 PSVD-GVMIGRAAYKNSAML 226
            + + G MI   A ++  + 
Sbjct: 240 KNTNIGGMIAECAERDPTVF 259


>gi|323331765|gb|EGA73178.1| Smm1p [Saccharomyces cerevisiae AWRI796]
          Length = 372

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 104/260 (40%), Gaps = 47/260 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------I 40
           MV   +   R  A L     L+++  I+   +++  +K                      
Sbjct: 1   MVRAGELPTRLMA-LAHGADLVWSPEIIDKKLIQCVRKENTALQTVDYVVPSKVQTRPET 59

Query: 41  LGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           L F T    +   L  QIG A  +   +AA  V +   + I++N GCP         G+ 
Sbjct: 60  LVFRTYPKLESSKLIFQIGSASPALATQAALKVIN-DVSGIDINAGCPKHFSIHSGMGSA 118

Query: 97  LMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  PD +   +  + K +    S P++VK R+    Q        L+K +  +G+  + 
Sbjct: 119 LLRTPDTLCLILKELVKNVGNPHSKPISVKIRLLDTKQDT----LQLIKRLCATGITNLT 174

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALK----IL 207
           +H RK  ++      NR+ P  DY   +YEI + N ++ + +NG + D S          
Sbjct: 175 VHCRKTEMR------NREQPITDYIAEIYEICQAN-NVSLIVNGAIRDRSHFHDLQANHW 227

Query: 208 PSVD-GVMIGRAAYKNSAML 226
            + + G MI   A ++  + 
Sbjct: 228 KNTNIGGMIAECAERDPTVF 247


>gi|47192407|emb|CAF87237.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 142

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 36/129 (27%), Positives = 64/129 (49%), Gaps = 7/129 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
           MV ++   +R   R  +   + +T MIVA   ++  K     F+T   ++PL +Q    +
Sbjct: 16  MVRYSKLAFRSLVRKYS-CDVCFTPMIVASDFIQSTKARDSEFTTNQHDRPLIVQFAADN 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
              L +AA +V  F  + +++N GCP        +GACL+  P++V D +A +   +  P
Sbjct: 75  AQTLADAACVVAPFS-DGVDINCGCPQRWAMSAGYGACLINKPELVKDMVARVRNQVGNP 133

Query: 119 ---VTVKCR 124
              V++K R
Sbjct: 134 NYTVSIKIR 142


>gi|186703885|emb|CAQ43570.1| tRNA-dihydrouridine synthase 2 [Zygosaccharomyces rouxii]
          Length = 373

 Score =  110 bits (275), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 97/254 (38%), Gaps = 40/254 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFST------------- 45
           MV   +   R  A +     L++   I+   +++        LG                
Sbjct: 13  MVRAGELPTRILA-IRNGADLVWGPEIIDKKLIQCKRHVNEKLGCVDYLVDGTTSPVFRT 71

Query: 46  ----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
               ++  +  QIG +  S  ++AA  V     + I++N GCP         GA L+  P
Sbjct: 72  CPQIEKGKIVFQIGTSTPSLAIQAALTVIQ-DVDGIDINAGCPKHFSIHSGMGAALLRTP 130

Query: 102 DIVGDCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           D + + +  + + +  P    ++VK R+  + +        L+  + ++G++ + +H R 
Sbjct: 131 DKLCEILCELVEKVGRPYGKTISVKIRLLDNREDT----LQLINRLCQNGISHLTVHCRT 186

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-----LPSVDG 212
             ++         I       +YE+ + N    I  NGG++  S   +I     LP   G
Sbjct: 187 TPMRNREQPIRGYIKE-----IYEVCQTNGVTLII-NGGIKSRSHFQEIQRDLELPKEIG 240

Query: 213 VMIGRAAYKNSAML 226
            M+   A +N  + 
Sbjct: 241 GMMADCAEQNPTVF 254


>gi|213421321|ref|ZP_03354387.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 197

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 71/183 (38%), Gaps = 29/183 (15%)

Query: 100 NPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +P+++     AM  A+   +PVTVK R+G D          +  +++++G + + +H R 
Sbjct: 1   DPELIYQGAKAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRT 57

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMI 215
                       +  ++D+  + EI++    + +  NG + D   A   +     D VMI
Sbjct: 58  K-------AQGYRAEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMI 109

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           GR A  N   L+ V +Y                +  W ++   +  Y          L  
Sbjct: 110 GRGAL-NIPNLSRVVKYNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYH 155

Query: 276 ITR 278
           + R
Sbjct: 156 VAR 158


>gi|116182068|ref|XP_001220883.1| hypothetical protein CHGG_01662 [Chaetomium globosum CBS 148.51]
 gi|88185959|gb|EAQ93427.1| hypothetical protein CHGG_01662 [Chaetomium globosum CBS 148.51]
          Length = 641

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 40/210 (19%), Positives = 72/210 (34%), Gaps = 31/210 (14%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
           QI        V+A + +     +   ++LN GCP   V +   G+ L+ +   +   I  
Sbjct: 312 QIAANAPWVAVKATEALSQLLPHLRLVDLNCGCPVDAVFKSGSGSALLDSHSKLERMIRG 371

Query: 111 MCKALS-IPVTVKCRIGVDD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           M      +P+T K R+G  D         +  A+   +L   I   G   + +H R  + 
Sbjct: 372 MNAVSGEVPITAKIRMGSRDGKLTAQKLVERLALGSEDLRDMIGAPGCAAVTLHGRTRLQ 431

Query: 161 KGLSPKDNRKIPNLD-------------YDIVYEIKKEN----PDLFIGLNGGLEDMSQA 203
           +     D   I                  D + E  +        ++   NG      + 
Sbjct: 432 RYTKAADWGYIAECAALIKQFNEKSNDLADTIREADENTLPNGGKMYFLGNGDCYSHVEY 491

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
              + +  VD VMIGR A     +   +++
Sbjct: 492 FDHVDNAKVDSVMIGRGALVKPWVFEEIEK 521


>gi|316965778|gb|EFV50452.1| dihydrouridine synthase (Dus) superfamily [Trichinella spiralis]
          Length = 787

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 81/177 (45%), Gaps = 16/177 (9%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALS 116
           +    V+AA+IV     + ++LN GCP  +  + + G+ L+ N   + + I     + L 
Sbjct: 50  NCDDFVKAAEIVY-TQCDGVDLNCGCPKRKTLDANCGSALLDNASHLAELIKQSRLRILD 108

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
              ++  +I + + +      +L + ++ +G+  I +H R    +            +D 
Sbjct: 109 SKFSISVKIRIYENLKDTV--DLCQKLQSAGITFINVHGRTVEQRH---------EPVDV 157

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V+++ K++  + +  NG +  +S          V+GVM+ RA  +N A+ T  D+
Sbjct: 158 E-VFKVIKDSLQIPVVANGDVRSLSDVHYYHQHAGVEGVMVARALLENPALFTGADK 213


>gi|164659486|ref|XP_001730867.1| hypothetical protein MGL_1866 [Malassezia globosa CBS 7966]
 gi|159104765|gb|EDP43653.1| hypothetical protein MGL_1866 [Malassezia globosa CBS 7966]
          Length = 212

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 41/174 (23%), Positives = 75/174 (43%), Gaps = 24/174 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILG--------------FS 44
           MV  +D  +R  A         +T+M   + IL  +   +  L                +
Sbjct: 21  MVGQSDLAFRLTAVQY-GATATWTQMYHTEDILYHNETYEKALRALEMGSAARENCDIVT 79

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-- 102
            +  P  +Q+ G D  + V+AA+       + I+LN+GCP AR  +G +G  L+   +  
Sbjct: 80  GERAPQIVQLAGDDPEQFVQAARRFLPI-ADAIDLNLGCPQARARDGHYGGYLLKRREWP 138

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           ++   + A+CK+  +P+T K R+             L + +  +G + I +HAR
Sbjct: 139 LLERIVQALCKSCDVPITTKIRLCDTASDTY----ELGQRLALAGSSVITLHAR 188


>gi|160884027|ref|ZP_02065030.1| hypothetical protein BACOVA_02001 [Bacteroides ovatus ATCC 8483]
 gi|156110757|gb|EDO12502.1| hypothetical protein BACOVA_02001 [Bacteroides ovatus ATCC 8483]
          Length = 314

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 47/279 (16%), Positives = 101/279 (36%), Gaps = 18/279 (6%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A         YT  +  +       D + I   + Q   L  Q+     
Sbjct: 14  GYTEVFYRNAHAACFGGIDTYYTPFVRLEKGGFRHRDVRGIDPGNNQVAHLIPQLIAPSF 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K  +   +  + GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  
Sbjct: 74  EKAEKILSLFIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQTLLSLITEYPQISF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +D         L   I +  +  + +H R    +     D +      ++  
Sbjct: 134 SIKMRLGWED---PEECLKLAPIINELPLRQVVMHPRLGKQQYKGEVDLKA-----FEAF 185

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
               K      +  NG +   ED+ +  +  P + G+MIGR    N A+     +  +  
Sbjct: 186 QNACKH----PLIYNGDINSVEDIHRIQEQFPGLAGIMIGRGLLANPALALEYRQNRALE 241

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
                     + K  + + +  +     + L+      +
Sbjct: 242 FDEMREKLQSMHKCVYNQYAEQLEGGDEQLLNKMKTFWE 280


>gi|260172570|ref|ZP_05758982.1| dihydrouridine synthase [Bacteroides sp. D2]
 gi|315920863|ref|ZP_07917103.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313694738|gb|EFS31573.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 314

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 47/279 (16%), Positives = 100/279 (35%), Gaps = 18/279 (6%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A         YT  +          D + I   + Q   L  Q+     
Sbjct: 14  GYTEVFYRNAHAACFGGIDTYYTPFVRFEKGGFRHRDVRGIDPGNNQVAHLIPQLIAPSF 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K  +   +  + GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  
Sbjct: 74  EKAEKILSLFIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQALLSLITEYPQISF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +D         L   I +  +  + +H R    +     D +      ++  
Sbjct: 134 SIKMRLGWED---PEECLKLAPIINELPLRQVVMHPRLGKQQYKGEVDLKA-----FEAF 185

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
               K      +  NG +   ED+ +  +  P + G+MIGR    N A+     +  +  
Sbjct: 186 QNACKH----PLIYNGDINSVEDIHRIQEQFPGLAGIMIGRGLLANPALALEYRQNRALE 241

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
                     + K  + + +  +     + L+      +
Sbjct: 242 FDEMREKLQSMHKCVYNQYAEQLEGGDEQLLNKMKTFWE 280


>gi|313611217|gb|EFR86015.1| probable tRNA-dihydrouridine synthase 1 [Listeria monocytogenes FSL
           F2-208]
          Length = 123

 Score =  109 bits (272), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 34/107 (31%), Positives = 55/107 (51%), Gaps = 4/107 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ V
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNKV 123


>gi|237716774|ref|ZP_04547255.1| dihydrouridine synthase [Bacteroides sp. D1]
 gi|237720529|ref|ZP_04551010.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|262405549|ref|ZP_06082099.1| dihydrouridine synthase [Bacteroides sp. 2_1_22]
 gi|294644573|ref|ZP_06722327.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CC 2a]
 gi|294809605|ref|ZP_06768298.1| dihydrouridine synthase (Dus) [Bacteroides xylanisolvens SD CC 1b]
 gi|229442757|gb|EEO48548.1| dihydrouridine synthase [Bacteroides sp. D1]
 gi|229450280|gb|EEO56071.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|262356424|gb|EEZ05514.1| dihydrouridine synthase [Bacteroides sp. 2_1_22]
 gi|292640126|gb|EFF58390.1| dihydrouridine synthase (Dus) [Bacteroides ovatus SD CC 2a]
 gi|294443217|gb|EFG11991.1| dihydrouridine synthase (Dus) [Bacteroides xylanisolvens SD CC 1b]
          Length = 315

 Score =  109 bits (272), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 48/280 (17%), Positives = 103/280 (36%), Gaps = 19/280 (6%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   A         YT  +  +       D + I   + Q   L  Q+     
Sbjct: 14  GYTDVIYRNAHAACFGGIDTYYTPFVRLEKGGFRHRDVRGIEPGNNQVPHLIPQLIAPSF 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-AMCKALSIP 118
            K  +   ++ + GY E+++N+GCP   + +   G+ ++  P+ V   ++  + +   I 
Sbjct: 74  EKAEKILSLLIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQALLSWLITEYPQIS 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            ++K R+G +D         L   I +  +  + +H R    +     D +      ++ 
Sbjct: 134 FSIKMRLGWED---PEECLKLAPIINELPLRQVVMHPRLGKQQYKGEVDLKA-----FEA 185

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
              + K      +  NG +   ED+ +  +  P + G+MIGR    N A+     +  + 
Sbjct: 186 FQGVCKH----PLIYNGDINSVEDIHRIQEQFPGLAGMMIGRGLLANPALALEYRQNRAL 241

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
                      + K  + + +  +     + L+      +
Sbjct: 242 EFDEMREKLQSMHKCVYNQYAEQLEGGDEQLLNKMKTFWE 281


>gi|18043390|gb|AAH19480.1| Dus1l protein [Mus musculus]
          Length = 365

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 67/192 (34%), Gaps = 29/192 (15%)

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G +GA L    D++   I    + LS+PVT K R+  +            + ++K+G
Sbjct: 3   AKRGHYGAFLQEEWDLLQRMILLAHERLSVPVTCKIRVFPEIDKTV----RYAQMLEKAG 58

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              + +H R    KG             ++ +  ++K    + +  NG ++ +    + +
Sbjct: 59  CQLLTVHGRTKEQKG------PMAGTASWEHIKAVRKAVG-IPVFANGNIQCLQDVERCI 111

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD--YA 263
               V GVM       N A+             G SP    + +++   +        Y 
Sbjct: 112 QDTGVQGVMSAEGNLHNPALF-----------EGRSPAVWELAEEYLDIVRQHPCPLSYV 160

Query: 264 ARHLHSGGKLQQ 275
             HL    KL  
Sbjct: 161 RAHL---FKLWH 169


>gi|308810258|ref|XP_003082438.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
 gi|116060906|emb|CAL57384.1| tRNA-dihydrouridine synthase (ISS) [Ostreococcus tauri]
          Length = 295

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 32/151 (21%), Positives = 60/151 (39%), Gaps = 15/151 (9%)

Query: 99  LNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             P+ +   +  +   +   P+TVK R+G++   PA     + + ++ +G   I +H R 
Sbjct: 16  KKPEQLERLVNGIVSGIDGAPLTVKIRLGIESSSPAT---KIAERLENAGAAAIIVHGRT 72

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMI 215
                   K+ R   + DYD++ +I  E   + +  NG +     A + L      G+M+
Sbjct: 73  --------KEQRYTKSADYDVIRQIVSER-AIPVIGNGDVLTWYDAQQRLDYSGCAGIMV 123

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           GR A     +     E      T    +  R
Sbjct: 124 GRGALIKPWIFKEFREKKEWEPTAEDRVGRR 154


>gi|218131773|ref|ZP_03460577.1| hypothetical protein BACEGG_03394 [Bacteroides eggerthii DSM 20697]
 gi|217986076|gb|EEC52415.1| hypothetical protein BACEGG_03394 [Bacteroides eggerthii DSM 20697]
          Length = 318

 Score =  108 bits (271), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 95/237 (40%), Gaps = 20/237 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEK-PLALQIGGAD 58
            +TD  YR   AR+       Y+  +  +   I R D ++I   + +E   L  Q+  + 
Sbjct: 15  GYTDAVYRLAHARIFGGIDTYYSPFVRVEHGEIRRKDARDISSKNNREGIHLIPQLIASQ 74

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-I 117
             KL +   +  +  Y E ++N+GCP   + +   GA ++  PD V D + A  +    I
Sbjct: 75  PDKLEQIITLFIENNYQEADINLGCPFPMLAKRHNGAGMLPYPDEVKDLLTAAIEKYPQI 134

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             +VK R+G +    A     L+       +  I +H R    +     D        ++
Sbjct: 135 HFSVKLRLGWE---NAEECLALLPLFNALPLTHIILHPRLGKQQYKGEVDLSG-----FE 186

Query: 178 IVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
             Y   ++     +  NG    +ED+    +  P + GV+IGR    N A+     +
Sbjct: 187 AFYNGCEK----PLLYNGDLHTVEDIQTITERFPKLAGVVIGRGLLANPALAWEYRQ 239


>gi|298387098|ref|ZP_06996652.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 1_1_14]
 gi|298260248|gb|EFI03118.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 1_1_14]
          Length = 314

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 93/242 (38%), Gaps = 32/242 (13%)

Query: 3   DWTDRHYRFFA-RLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
            +T+  YR             YT  +    + +G+ +   + G   +   +   I     
Sbjct: 14  GYTEAIYRNAHDAFFGGVDTYYTPFV---RLEKGNFRRRDVRGIEPENNGVTHLI----P 66

Query: 60  SKLVEAAKIVE-------DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +  +A+  E       + GY E+++N+GCP   + +   G+ ++  P+ V   ++ + 
Sbjct: 67  QLIASSAEKAEVILSLFIEKGYQEVDINLGCPFPLLAKRHNGSGILPYPEEVKALLSIVT 126

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +   I  +VK R+G +     +A   L   +    +  I +H R          D +   
Sbjct: 127 RYPQISFSVKMRLGWEQPDECLA---LAPILNDLPLRQITMHPRLGKQGYKGEVDLQ--- 180

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
                 V+   +E   L +  NG +   ED+ +     PS+ G+MIGR    N A+    
Sbjct: 181 ------VFSAFREVCRLPLVYNGDIHNLEDIQRISAQFPSLAGIMIGRGLLANPALALEY 234

Query: 230 DE 231
            E
Sbjct: 235 KE 236


>gi|268598864|ref|ZP_06133031.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae MS11]
 gi|268582995|gb|EEZ47671.1| tRNA-dihydrouridine synthase C [Neisseria gonorrhoeae MS11]
          Length = 196

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 75/177 (42%), Gaps = 14/177 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI------VADAILRGDKKNILGFST--QEKPLAL 52
           M    D   R     +       +E +       + +I       I   +      P  +
Sbjct: 20  MRGLVDDVMRDLLTRIGGYDECVSEFVRITHTVHSRSIWLKYVPEIANGNKTFSGTPCTV 79

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D   +   A     FG ++I+LN GCP+  V++   GA L+  P+++   +  + 
Sbjct: 80  QLLGSDADNMAANALEAVRFGADKIDLNFGCPAPTVNKHKGGAILLKEPELIFHIVKTLR 139

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             L   IP+T K R+G +D+ PA+       +I + G  G+ +HAR    +G  P+ 
Sbjct: 140 GRLPAHIPLTGKMRLGYEDKSPAL---ECACAIAEGGACGLTVHART-KAEGYEPRR 192


>gi|330892748|gb|EGH25409.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. mori str.
           301020]
          Length = 109

 Score =  107 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 40/82 (48%), Positives = 57/82 (69%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           M+DWTD H R+F R L+ +ALLYTEM+   A+L GD++  L     E PLALQ+GG+  +
Sbjct: 28  MMDWTDHHCRYFMRKLSKHALLYTEMVTTGALLHGDRERFLRHDETEHPLALQLGGSTAA 87

Query: 61  KLVEAAKIVEDFGYNEINLNVG 82
            L   +++ E+ GY+E+NLNVG
Sbjct: 88  DLAACSRLAEEAGYDEVNLNVG 109


>gi|29348735|ref|NP_812238.1| dihydrouridine synthase [Bacteroides thetaiotaomicron VPI-5482]
 gi|253568922|ref|ZP_04846332.1| dihydrouridine synthase [Bacteroides sp. 1_1_6]
 gi|29340641|gb|AAO78432.1| putative nifR3 family TIM-barrel enzyme with dihydrouridine
           synthase domain [Bacteroides thetaiotaomicron VPI-5482]
 gi|251840941|gb|EES69022.1| dihydrouridine synthase [Bacteroides sp. 1_1_6]
          Length = 314

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 93/242 (38%), Gaps = 32/242 (13%)

Query: 3   DWTDRHYRFFA-RLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
            +T+  YR             YT  +    + +G+ +   + G   +   +   I     
Sbjct: 14  GYTEAIYRNAHDAFFGGVDTYYTPFV---RLEKGNFRRRDVRGIEPENNGVPHLI----P 66

Query: 60  SKLVEAAKIVE-------DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +  +A+  E       + GY E+++N+GCP   + +   G+ ++  P+ V   ++ + 
Sbjct: 67  QLIASSAEKAEVILSLFIEKGYQEVDINLGCPFPLLAKRHNGSGILPYPEEVKALLSIVT 126

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +   I  +VK R+G +     +A   L   +    +  I +H R          D +   
Sbjct: 127 RYPQISFSVKMRLGWEQPDECLA---LAPILNDLPLRQITMHPRLGKQGYKGEVDLQG-- 181

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
              +    E+ +    L +  NG +   ED+ +     PS+ G+MIGR    N A+    
Sbjct: 182 ---FSAFREVCQ----LPLVYNGDIHNLEDIQRISTQFPSLAGIMIGRGLLANPALALEY 234

Query: 230 DE 231
            E
Sbjct: 235 KE 236


>gi|12835061|dbj|BAB23138.1| unnamed protein product [Mus musculus]
          Length = 365

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 66/192 (34%), Gaps = 29/192 (15%)

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
              G +GA L    D++   I    + LS+PVT K R+  +            + ++K+G
Sbjct: 3   AKRGHYGAFLQEEWDLLQRMILLAHERLSVPVTCKIRVFPEIDKTV----RYAQMLEKAG 58

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              + +H R    KG             ++ +  ++K    + +  NG ++ +    + +
Sbjct: 59  CQLLTVHGRTKEQKG------PMAGTASWEHIKAVRKAVG-IPVFANGNIQCLQDVERCI 111

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD--YA 263
               V GVM       N A+               SP    + +++   +        Y 
Sbjct: 112 QDTGVQGVMSAEGNLHNPALFDD-----------RSPAVWELAEEYLDIVRQHPCPLSYV 160

Query: 264 ARHLHSGGKLQQ 275
             HL    KL  
Sbjct: 161 RAHL---FKLWH 169


>gi|294895585|ref|XP_002775215.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
 gi|239881269|gb|EER07031.1| tRNA-dihydrouridine synthase, putative [Perkinsus marinus ATCC
           50983]
          Length = 125

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 50/122 (40%), Positives = 75/122 (61%), Gaps = 6/122 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK-----KNILGFSTQEKPLALQIG 55
           MVD +DR +R F RLL++   ++TEM+V  A++  +      + ++GF+  E P+  Q+G
Sbjct: 1   MVDVSDRDFRMFMRLLSSKCEVWTEMLVDQALVHNEDIPRQLEKVIGFTEAEHPIVCQLG 60

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVGDCIAAMCKA 114
           G D SKL  AA+I    GY+E+NLNVGCPS+RV      G  LM  P++V DC+  +   
Sbjct: 61  GHDPSKLAAAARIAHRRGYDEVNLNVGCPSSRVAGHGLMGVALMKTPELVRDCLRTLDDE 120

Query: 115 LS 116
           +S
Sbjct: 121 VS 122


>gi|255023090|ref|ZP_05295076.1| hypothetical protein LmonocyFSL_05790 [Listeria monocytogenes FSL
           J1-208]
          Length = 122

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 33/106 (31%), Positives = 54/106 (50%), Gaps = 4/106 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18  MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDI 103
              LVEAAK V +    + I++N+GCP  ++ +   GA  +L+P+ 
Sbjct: 77  KETLVEAAKFVAENTTADIIDINMGCPVNKIIKCEAGAKWLLDPNK 122


>gi|169623807|ref|XP_001805310.1| hypothetical protein SNOG_15147 [Phaeosphaeria nodorum SN15]
 gi|111056252|gb|EAT77372.1| hypothetical protein SNOG_15147 [Phaeosphaeria nodorum SN15]
          Length = 442

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 40/180 (22%), Positives = 77/180 (42%), Gaps = 9/180 (5%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+G A+   L   A  +       I++N GCP      G  GA L+  PD++ + + 
Sbjct: 107 LIYQMGTANPE-LAVKAAKMVAADVAGIDVNSGCPKPFSTAGGMGAALLKTPDLLCNILT 165

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           ++ + +  P  +   + +           LV  + K+G+ G+ +H R   ++        
Sbjct: 166 SLVEEVGKPYEIGISVKIRILDTPEETAALVSRLVKTGITGLTVHCRTTPMRPRERAIRH 225

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           ++      ++  I +E   +   +NG +   ++ALK++    VDG MI   A KN +   
Sbjct: 226 QLK-----MIGNICREAG-VACVMNGDVTSRTEALKLMEEFNVDGAMIATEAEKNPSCFR 279


>gi|296088965|emb|CBI38530.3| unnamed protein product [Vitis vinifera]
          Length = 160

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 34/153 (22%), Positives = 69/153 (45%), Gaps = 14/153 (9%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +G ++  + + AA+IV       +++N+GCP +    G  GA L+  P+++ D +  + +
Sbjct: 1   MGTSNAERALTAAQIVCK-DVAAVDINMGCPKSFSISGGMGAALLTRPELIHDILTILKR 59

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L IPVT K R+    Q        L + I+K+GV  + +H R+          +R    
Sbjct: 60  NLDIPVTCKIRLLKSSQETV----ELAQQIEKTGVAALAVHGRRI--------ADRPRDP 107

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
             ++ + ++      + +  NG +       +I
Sbjct: 108 AKWNEIADVVAAL-SIPVIANGDVFGYDDFQRI 139


>gi|116181790|ref|XP_001220744.1| hypothetical protein CHGG_01523 [Chaetomium globosum CBS 148.51]
 gi|88185820|gb|EAQ93288.1| hypothetical protein CHGG_01523 [Chaetomium globosum CBS 148.51]
          Length = 655

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 41/161 (25%), Positives = 72/161 (44%), Gaps = 16/161 (9%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK----ALSIPVTVKCRIGVD 128
               I++N GCP      G  GA L+  P+ +   + A+ +    A  + V+VK R+   
Sbjct: 156 DVAGIDVNAGCPKPFSVSGGMGAALLRTPEKLAGILEALVRDITPAYGLGVSVKIRLL-- 213

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
               A     LV+ + ++G+ G+ +H R   ++   P++      L   +V E+  E   
Sbjct: 214 --ETAAETEALVRRLVRTGITGLTVHCRTTPMR---PRERAIRGQLR--MVREVCHEAG- 265

Query: 189 LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           +   +NG +E   QA  ++    VDG MI  AA +N +   
Sbjct: 266 VACLMNGDVESRDQADALVEEFGVDGAMIATAAERNPSCFR 306


>gi|224536765|ref|ZP_03677304.1| hypothetical protein BACCELL_01641 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521623|gb|EEF90728.1| hypothetical protein BACCELL_01641 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 313

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 105/269 (39%), Gaps = 23/269 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   AR+       YT  +  +   I + D + I   + +   L  Q+   D+
Sbjct: 14  GYTEAIYRQAHARIFGGVESYYTPFVRVEHGEIRKKDMREITLENNRGVQLIPQLIAPDV 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            K+     +  + GY  +++N+GCP   + +   G+ ++  P+ V + + AA+     + 
Sbjct: 74  DKMELIIALFIEKGYKNVDINLGCPFPLLAKRHNGSGMLPYPEEVRELLTAAIKNHPDLQ 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G ++   ++AL  L+  +  +    I +H R    +     D +      ++ 
Sbjct: 134 FSVKMRLGWENPEESLALLPLLNELPLT---HIIMHPRLGKQQYKGEVDLKG-----FEA 185

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            Y          +  NG    +ED+    +  P + G+MIGR    N A+       +  
Sbjct: 186 FYNECSH----PLIYNGDLLTVEDIQTISERFPRLAGIMIGRGLLANPALALE----YQQ 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAA 264
               S        + F   + A   +   
Sbjct: 238 GHPLSEKDMQERLRLFHADVFAQYGNLLE 266


>gi|220672921|emb|CAX13644.1| novel protein similar to H.sapiens DUS3L, dihydrouridine synthase
           3-like (S. cerevisiae) (DUS3L, zgc:63779) [Danio rerio]
          Length = 224

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 37/166 (22%), Positives = 64/166 (38%), Gaps = 21/166 (12%)

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            L +P+TVK R GV  Q  +     L+  +KK GV+ I +H R         ++ R    
Sbjct: 1   VLDVPLTVKIRTGV--QQNSNIAHKLIPEMKKWGVSLITLHGRS--------REQRYTKL 50

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY 232
            D+D +    +    + +  NG +     A+K     V G+M+ R A     + T + E 
Sbjct: 51  ADWDYINTCAQLAAPVPLFGNGDILSYEDAMKARETGVSGIMVARGALIKPWLFTEIKET 110

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
               ++ +  +           I    T +   H  S  +  + TR
Sbjct: 111 RHWDISSTERL----------DILRDFTHFGLEHWGSDTQGVEKTR 146


>gi|300123558|emb|CBK24830.2| unnamed protein product [Blastocystis hominis]
          Length = 263

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 35/149 (23%), Positives = 60/149 (40%), Gaps = 9/149 (6%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G  G+ L+  PDI    +  + K+ S+PV+ K R+      P     N +
Sbjct: 1   MGCPKQFSVQGHMGSALLKTPDIACSIVQGLSKSTSLPVSCKIRLL---DGPIENTINFM 57

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           K +  SG + I +H R    +   P      P     ++  +K   P + +  NG +   
Sbjct: 58  KRLVDSGASAITLHLRYTDDRPRVPCHKEFFPT----VLEAMKAYAPSVPVCYNGDIFSF 113

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAMLT 227
                +       G+MIGR A  +  +  
Sbjct: 114 EDVCSLRKKFPTTGLMIGRGAILDMGVFR 142


>gi|147674360|ref|YP_001216574.1| tRNA-dihydrouridine synthase C [Vibrio cholerae O395]
 gi|146316243|gb|ABQ20782.1| tRNA-dihydrouridine synthase C [Vibrio cholerae O395]
          Length = 158

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 36/151 (23%), Positives = 63/151 (41%), Gaps = 10/151 (6%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNI---LGF---STQEKPLAL 52
           M    D   R     + +     TE +    +L  D     +   L     +    P+ +
Sbjct: 8   MEGVLDHLMRDMLTQINDYDFCVTEFVRVVNLLLPDHVFYRLCPELRHGSKTPSGVPVKV 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G D   + E A    + G   I+LN GCP+  V++   GA L+ +P+++   + A  
Sbjct: 68  QLLGQDPHWMAENAIRAAELGAYGIDLNFGCPAKMVNQSKGGAALLQHPELIYQVVKACR 127

Query: 113 KALS--IPVTVKCRIGVDDQIPAVALRNLVK 141
            A+   IPV+ K R+G +D      + + V 
Sbjct: 128 DAVPAHIPVSAKIRLGWEDPEDCFEIVDAVA 158


>gi|299146981|ref|ZP_07040048.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 3_1_23]
 gi|298514866|gb|EFI38748.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. 3_1_23]
          Length = 314

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 47/279 (16%), Positives = 101/279 (36%), Gaps = 18/279 (6%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A         YT  +  +       D + I   + Q   L  Q+     
Sbjct: 14  GYTEVFYRNAHAACFGGIDTYYTPFVRLEKGGFRHRDVRGIEPGNNQVAHLIPQLIAPSF 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K  +   +  + GY E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  
Sbjct: 74  EKAEKILSLFIEKGYKEVDINIGCPFPMLAKRHNGSGILPYPEEVQALLSLITEYPQISF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +D         L   I +  +  + +H R    +     D +      ++  
Sbjct: 134 SIKMRLGWED---PEECLKLAPIINELPLRQVVMHPRLGKQQYKGEVDLKA-----FEAF 185

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
               K      +  NG +   ED+ +  +  P + G+MIGR    N A+     +  +  
Sbjct: 186 QNACKH----PLIYNGDINSVEDIHRIQEQFPGLAGMMIGRGLLANPALALEYRQNRALE 241

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
                     + K  + + +  +     + L+      +
Sbjct: 242 FDEMREKLQSMHKCVYNQYAEQLEGGDEQLLNKMKTFWE 280


>gi|164657526|ref|XP_001729889.1| hypothetical protein MGL_2875 [Malassezia globosa CBS 7966]
 gi|159103783|gb|EDP42675.1| hypothetical protein MGL_2875 [Malassezia globosa CBS 7966]
          Length = 308

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 79/249 (31%), Gaps = 43/249 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  Q+  +  S L +AA++V  +  + I+LN GCP    +E   G+ L+  P++V D I 
Sbjct: 45  LVCQLAASHSSPLADAAELVSPY-VDGIDLNCGCPQPWAYEERVGSYLLEEPELVADMIR 103

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK------ 161
            +   L     V+VK RI  D +     +RN +     +G + I IH R           
Sbjct: 104 TVKGRLGDAYCVSVKIRIDPDLRRTDTLVRNALH----AGASFITIHGRTRHESSGSDPV 159

Query: 162 ---------------GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-- 204
                          GL         +  +    E           +NG +     A+  
Sbjct: 160 HLDAVQFAVDCARTCGLQTARGTSPGDA-WTW-AEDGGAGGFAPCVVNGDIWSNEDAMAW 217

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +      G M  R    N A+             G         + F           + 
Sbjct: 218 RAHTGARGAMSARGLLANPALFA-----------GEPHTPREAVRRFVDYAMKWSLPTSL 266

Query: 265 RHLHSGGKL 273
            H H    L
Sbjct: 267 LHRHLAYML 275


>gi|322490625|emb|CBZ25887.1| dihydrouridine synthase domain protein-like protein [Leishmania
           mexicana MHOM/GT/2001/U1103]
          Length = 440

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 59/329 (17%), Positives = 112/329 (34%), Gaps = 67/329 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP----------- 49
           MV      +R          +++TE +VA A L   ++ ++ + T + P           
Sbjct: 17  MVRVCSPGFRALCG-AHGADIVFTEEVVA-AKLAMCQREVVHYPTVDTPMAEYVSYDPFK 74

Query: 50  -------------------------------LALQIGGADISKLVEAAKIVEDFGYNEIN 78
                                          + LQ+G AD  +   AA +V     + I+
Sbjct: 75  NTYKRTVVLSTPVLPGITDGGRKAERIAAPRIVLQLGVADPVR-GAAAALVCSNDIDGID 133

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------------IPVTVKCRIG 126
           +N+GCP        FGA LM  P++ G  + A+  A++            I V++K R+ 
Sbjct: 134 INMGCPKKFSVHNGFGAALMKRPEVGGAIVRAVHDAVNSDSNVDARGGKRIAVSLKTRLK 193

Query: 127 VDDQIPAVALRNLVKSIKKSGV----NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
              +     LR ++ + + +      + I IHAR    +  S +        +   +   
Sbjct: 194 DTAEATVGMLRAMLTAAQHTPANPALHAITIHARTPEQR--SEQAPLYDRAAEVVRICRA 251

Query: 183 KKENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                 + + LNG +       A   L   D  MI RAA +++     +     +     
Sbjct: 252 NAAFEGICLVLNGSVLSRQDGEAKCALYGFDAAMIARAALEDARCFHRICSELPDSSVAH 311

Query: 241 --SPIKTRVDKDFWRKISASMTDYAARHL 267
                     +++   I   +  Y+ R+ 
Sbjct: 312 DGEAQSREDAEEYAMAIMKELFFYSVRYR 340


>gi|323335734|gb|EGA77015.1| Smm1p [Saccharomyces cerevisiae Vin13]
          Length = 361

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 83/187 (44%), Gaps = 22/187 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L  QIG A  +   +AA  V +   + I++N GCP         G+ L+  PD +   + 
Sbjct: 62  LIFQIGSASPALATQAALKVIN-DVSGIDINAGCPKHFSIHSGMGSALLRTPDTLCLILK 120

Query: 110 AMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            + K +    S P++VK R+    Q        LVK +  +G+  + +H RK  ++    
Sbjct: 121 ELVKNVGNPHSKPISVKIRLLNTKQDT----LQLVKRLCATGITNLTVHCRKTEMR---- 172

Query: 166 KDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALK----ILPSVD-GVMIGRAA 219
             NR+ P  DY   +YEI + N ++ + +NG + D S           + + G MI   A
Sbjct: 173 --NREQPITDYIAEIYEICQAN-NVSLIVNGAIRDRSHFHDLQANHWKNTNIGGMIAECA 229

Query: 220 YKNSAML 226
            ++  + 
Sbjct: 230 ERDPTVF 236


>gi|218674773|ref|ZP_03524442.1| tRNA-dihydrouridine synthase A [Rhizobium etli GR56]
          Length = 88

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 42/75 (56%), Positives = 57/75 (76%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
          M+DWTDRH R+F R ++  ALLYTEM+VADAI+ G ++ +LG    E PLALQ+GG+D +
Sbjct: 13 MIDWTDRHCRYFHRQISRQALLYTEMVVADAIIHGPRERLLGHDVAEHPLALQLGGSDPA 72

Query: 61 KLVEAAKIVEDFGYN 75
          KL EA +I E +GY+
Sbjct: 73 KLAEAVRIAEPYGYD 87


>gi|86130500|ref|ZP_01049100.1| dihydrouridine synthase [Dokdonia donghaensis MED134]
 gi|85819175|gb|EAQ40334.1| dihydrouridine synthase [Dokdonia donghaensis MED134]
          Length = 315

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 43/217 (19%), Positives = 87/217 (40%), Gaps = 27/217 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+  AD    +   K ++  GY E+N N+GCP   V +   G+ L+ N + +   + 
Sbjct: 63  VIPQVMTADPDDFIFVIKYIQSLGYKELNWNLGCPYPMVTKSGMGSGLICNTEKIDHILD 122

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD 167
                  + +++K R+G +       + N    ++K  +  + IHAR  K + KG    +
Sbjct: 123 RAHTETDVTISMKMRLGYE---SPEEIINSFPILEKYPLKSVAIHARLGKQLYKGGVDLE 179

Query: 168 --NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKN 222
              + I    + + Y             NG +  ++Q  K+    PS++  MIGR    +
Sbjct: 180 GFQKCIDTAKHKLYY-------------NGDITTVAQFRKMRARFPSIEHFMIGRGLIAD 226

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
             + + +        T     +  + ++F  +I    
Sbjct: 227 PFLPSMIKA----DTTAYPENRWAIFREFHDEIYTQY 259


>gi|332297694|ref|YP_004439616.1| dihydrouridine synthase DuS [Treponema brennaborense DSM 12168]
 gi|332180797|gb|AEE16485.1| dihydrouridine synthase DuS [Treponema brennaborense DSM 12168]
          Length = 345

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 97/260 (37%), Gaps = 36/260 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK--KNILGFSTQEKPLALQIGGAD 58
           M   T    R            +TEMI A  +L G    K  L    +   +  Q+ GA 
Sbjct: 8   MATLTHEALRRSVFGFGGCDEYFTEMIQAGTLLTGGPFEKYYLHTGPEPDKIVWQLTGAK 67

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP-DIVGDCIAAMCKALS- 116
              L  AA++V   G   +++N+GC +  + +   G   ML P       +  + +A+  
Sbjct: 68  ADALARAAELVAGVGGVGVDVNMGCCAPEIVKSGAGIAWMLKPYAETAAMLEGVRRAVEN 127

Query: 117 ----------------------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
                                 +  +VK R+G D+        + +  +  +GV  I +H
Sbjct: 128 AKPAANRPAEENAKPAANRRAALRFSVKIRLG-DEDFTDDRFFSFIDMLVGTGVRQITLH 186

Query: 155 ARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP---SV 210
            R    +  +P     +  L DY     +     D+ + LNG + D + A K      +V
Sbjct: 187 PRTRKERYRTPPRLEYVRKLCDY-----LNARGSDVKVVLNGAVCDAASARKAYEIAPAV 241

Query: 211 DGVMIGRAAYKNSAMLTTVD 230
           DG+MI RAA +   +   + 
Sbjct: 242 DGIMIARAAIRKPWVFAEIK 261


>gi|295086114|emb|CBK67637.1| tRNA-U20a,U20b-dihydrouridine synthase [Bacteroides xylanisolvens
           XB1A]
          Length = 315

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 50/283 (17%), Positives = 104/283 (36%), Gaps = 25/283 (8%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   A         YT  +  +       D + I   + Q   L  Q+     
Sbjct: 14  GYTDVFYRNAHAACFGGIDTYYTPFVRLEKGGFRHRDVRGIEPGNNQVPHLIPQLIAPSF 73

Query: 60  SKLVEAAKIV---EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKAL 115
               +A KI+    + GY E+++N+GCP   + +   G+ ++  P+ V   ++  + +  
Sbjct: 74  D---KADKILSLFIEKGYKEVDINMGCPFPMLAKRHNGSGILPYPEEVQALLSLLITEYP 130

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            I  ++K R+G +D         L   I +  +  + +H R    +     D +      
Sbjct: 131 QISFSIKMRLGWEDPK---ECLKLAPIINELPLRQVVMHPRLGKQQYKGEVDLKA----- 182

Query: 176 YDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++    + K      +  NG +   ED+    +  P + G+MIGR    N A+     + 
Sbjct: 183 FEAFQGVCKH----PLIYNGDINSVEDIHHIQEQFPGLAGMMIGRGLLANPALALEYRQN 238

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
            +  L         + +  + + +  +     + L+      +
Sbjct: 239 RTLELDEIREKLQSMHRCVYNQYAEQLEGGDEQLLNKMKTFWE 281


>gi|198274061|ref|ZP_03206593.1| hypothetical protein BACPLE_00198 [Bacteroides plebeius DSM 17135]
 gi|198273139|gb|EDY97408.1| hypothetical protein BACPLE_00198 [Bacteroides plebeius DSM 17135]
          Length = 327

 Score =  104 bits (261), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/224 (22%), Positives = 92/224 (41%), Gaps = 22/224 (9%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMI-VADAILRGDKKNILGFSTQEKPL---ALQIGGA 57
            +T+  +R   A+ L      YT  + +    +R   K+    S +E  +     Q+  +
Sbjct: 30  GFTEVAWRNAHAQCLGGVDAYYTPFVRLEKGEIRN--KDRRDVSPEENTVSRLVPQVIAS 87

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +L      +   GY EI++N+GCP   +     GA ++ +P+ V   +  M     +
Sbjct: 88  EPEELKVLTDFLASQGYREIDVNMGCPFPLIVRRGKGAGILSSPEKVEALLETMKVFPEV 147

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             +VK R+G  D   A   + LV  + +S V  + +H R    +     D R+     Y+
Sbjct: 148 RFSVKMRLGGQD---AEEWKALVPLLNRSCVTQVTLHPRIGKQQYKGTVD-RETFRAFYE 203

Query: 178 IVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRA 218
                        +  NG    + D+ + L+  P + GVM+GR 
Sbjct: 204 ACER--------PLVYNGDLLTVADIREVLEAFPRLKGVMLGRG 239


>gi|221120394|ref|XP_002167268.1| PREDICTED: similar to GH10224 [Hydra magnipapillata]
          Length = 136

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 29/109 (26%), Positives = 47/109 (43%), Gaps = 4/109 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
           MV+ ++  +R   R      L YT M  A   +  +K       T   ++PL  Q    D
Sbjct: 26  MVEQSELAFRSLCREY-GAQLCYTPMWHAALFVNNEKYRKAAIETAFHDRPLLFQFCAND 84

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
                EA  + E +  + ++LN+GCP      G +G+ LM   D+V + 
Sbjct: 85  PQIFAEACALAEPY-CDGVDLNLGCPQVIAARGHYGSYLMEELDLVEEI 132


>gi|255690639|ref|ZP_05414314.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides finegoldii DSM 17565]
 gi|260623662|gb|EEX46533.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides finegoldii DSM 17565]
          Length = 313

 Score =  104 bits (259), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 51/277 (18%), Positives = 100/277 (36%), Gaps = 25/277 (9%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A +       YT  +  +  +    D + I   +     L  Q+     
Sbjct: 13  GYTEAFYRNAHAAVFGGIDTYYTPFVRIEKESFRNKDIREIDFANNHVPHLVPQLIAPSA 72

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K      +  + GY E ++N+GCP   + +   G+ ++  P+ V   +  + K   I  
Sbjct: 73  EKAETILSLFIEKGYGEADINLGCPFPILAKRHNGSGILPYPEEVKTLLGIVVKYPQIRF 132

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G ++    +A   +   +    +  + +H R    +     D        +   
Sbjct: 133 SVKMRLGWENPEECLA---IAPLLNDLPLRQVTMHPRLGKQQYKGDVDLEG-----FAAF 184

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             + K      +  NG +   ED+ +  +  P + GVMIGR    N A+     E     
Sbjct: 185 QSVCKH----PLIYNGDIKRREDILRIQEQFPMLAGVMIGRGLLANPALALEYKE----- 235

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
               +     +        ++  + YAA+     G+L
Sbjct: 236 --NRTLSADEMRNKLHSMHTSVYSQYAAQLEGGEGQL 270


>gi|45184895|ref|NP_982613.1| AAR072Cp [Ashbya gossypii ATCC 10895]
 gi|44980504|gb|AAS50437.1| AAR072Cp [Ashbya gossypii ATCC 10895]
          Length = 384

 Score =  104 bits (259), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 101/261 (38%), Gaps = 47/261 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK---------KNILGFSTQEKP-- 49
           MV   +   R  A L     L++   I+   +++  +           +L  +   KP  
Sbjct: 13  MVRAGELPTRLLA-LRHGADLVWGPEIIDKKLVQCQRVPNDELQTVDYVLPSTHAGKPPV 71

Query: 50  -------------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
                        +  Q+G A  +  V AA  V       I++N GCP         GA 
Sbjct: 72  VVFRTAPALEGGRVIFQLGTASPTLAVRAANTVIG-DVAGIDVNAGCPKHFSIHAGMGAA 130

Query: 97  LMLNPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L+  PD +   + A+   +    S P++VK R+  D      A  +LV+ +  +G++ + 
Sbjct: 131 LLRTPDTLCGILRALVDEVGRPHSKPISVKIRLLDDL----AATLDLVEKLCATGISNLT 186

Query: 153 IHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD 211
           +H R       +P  NR+ P   Y   ++E+ +    + + +NG LE      ++   + 
Sbjct: 187 VHCRT------TPMRNREAPIRSYLASIFELCQA-SKVSLIMNGALEGRKHFEEVRAELK 239

Query: 212 -----GVMIGRAAYKNSAMLT 227
                G MI  AA  N  + +
Sbjct: 240 LPTDVGGMIAEAAEANPTVFS 260


>gi|194765699|ref|XP_001964964.1| GF22896 [Drosophila ananassae]
 gi|190617574|gb|EDV33098.1| GF22896 [Drosophila ananassae]
          Length = 148

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 54/109 (49%), Gaps = 4/109 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R    + L YT M  A+        +K+ L     ++PL +Q  G D
Sbjct: 35  MVDQSELAWRMLCRRYGAH-LCYTPMYHANLFATDPKYRKDALQTCAGDRPLVIQFCGND 93

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
             ++++AA   +D   + +++N+GCP A    G +G+ L    +++ + 
Sbjct: 94  AQQILDAALAAQDH-CDAVDINLGCPQAIAKRGHYGSFLQDEWELLTEI 141


>gi|329954094|ref|ZP_08295189.1| dihydrouridine synthase [Bacteroides clarus YIT 12056]
 gi|328528071|gb|EGF55051.1| dihydrouridine synthase [Bacteroides clarus YIT 12056]
          Length = 316

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 56/277 (20%), Positives = 105/277 (37%), Gaps = 27/277 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   AR+       Y+  +  +   I R D ++I   + +   L  Q+  +  
Sbjct: 14  GYTDAAYRQAHARIFGGIDTYYSPFVRVEHGEIRRKDARDIHPENNRNIHLIPQLIASCP 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IP 118
           +KL +   ++ +  Y E ++N+GCP   + +   GA ++  P+ V D + A  +    I 
Sbjct: 74  NKLEQIMSLLTEHNYQEADINLGCPFPMLAKRHNGAGMLPYPEEVKDLLTAAIEQYPQIR 133

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G ++    +AL      +    +  I +H R    +     D        YD 
Sbjct: 134 FSVKLRLGWENASECIALL---PLLNALPLAHIILHPRLGKQQYKGEVDLNGF-EAFYDG 189

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             +         +  NG    +ED+    +  P + G++IGR    N A+     +    
Sbjct: 190 CDK--------PLLYNGDLHTIEDIQIITERFPKLAGLVIGRGLLANPALAWEYRQ---- 237

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
              G     + +     +  +A    Y    L  G  
Sbjct: 238 ---GRKLSPSEMAAKVKQLHTAVYNSY-EEQLQGGEM 270


>gi|294777363|ref|ZP_06742814.1| dihydrouridine synthase (Dus) [Bacteroides vulgatus PC510]
 gi|294448431|gb|EFG16980.1| dihydrouridine synthase (Dus) [Bacteroides vulgatus PC510]
          Length = 305

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 48/285 (16%), Positives = 103/285 (36%), Gaps = 22/285 (7%)

Query: 3   DWTDRHYRFFARL-LTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  +R   +         YT  +  +       D + I   +     L  Q+  +  
Sbjct: 10  GFTEAPWRNLHQEVFGGIDAYYTPFVRMEKGEFRNKDVREIASENNTVSRLIPQLIASTP 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L   A +  + GY E ++N+GCP   +     G+ ++  P  V   +  +     +  
Sbjct: 70  AELERLAGLFIEKGYKEADINMGCPFPLMTGKHKGSGILPYPAEVEALLKELVHYPELGF 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    A   R L+  +  + +  I +H R    +        ++    +   
Sbjct: 130 SVKMRLGWE---CADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-----EVDLAAFTAF 181

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           YE         +  NG    +ED+ +  +  P ++GVM+GR    N A+       ++N 
Sbjct: 182 YEECAH----PLVYNGDLLTVEDIRKVDEEFPRLEGVMLGRGLLANPALAWE----YANG 233

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
              S        K    ++      +         K++    +++
Sbjct: 234 TVFSPDELYEKVKALHARLLQYYEAHLQGEAQLLSKMKPYWEYLL 278


>gi|320593632|gb|EFX06041.1| tRNA dihydrouridine synthase [Grosmannia clavigera kw1407]
          Length = 441

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/214 (21%), Positives = 91/214 (42%), Gaps = 20/214 (9%)

Query: 23  YTEMIVADAILRGDKKNILGF---STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           ++ M  + +     K+++L     + +   L  Q+G  +     EAA  +       I++
Sbjct: 82  WSRMPSSFSPHTTPKESVLYRIDPAHEGARLVFQMGTCNPDT-AEAAARLVAADVAGIDI 140

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK----ALSIPVTVKCRIGVDDQIPAVA 135
           N GCP     +G  GA L+  PD++   +  +      A  I ++VK R+  D    A  
Sbjct: 141 NAGCPKPFSTDGGMGAALLKTPDLLCAILERLVATITPAFGIGISVKIRLLAD----AAE 196

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            + LV+ +  +G+ G+ +H R   ++        ++      +V +  +    +   +NG
Sbjct: 197 TKTLVRRLVATGITGLTVHCRTRNMRPRERAIRDQL-----RMVADECRAAG-VACLMNG 250

Query: 196 GLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
            +    QAL ++    VDG MI  AA +N +   
Sbjct: 251 DVTSRDQALSLMAEYGVDGAMIATAAERNPSCFR 284


>gi|149372757|ref|ZP_01891778.1| hypothetical protein SCB49_12379 [unidentified eubacterium SCB49]
 gi|149354454|gb|EDM43019.1| hypothetical protein SCB49_12379 [unidentified eubacterium SCB49]
          Length = 317

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 48/264 (18%), Positives = 93/264 (35%), Gaps = 23/264 (8%)

Query: 3   DWTDRHYRFFA-RLLTNNALLYTEMI--VADAILRGDKKNILGFSTQEK-PLALQIGGAD 58
            +TD  +R    +        Y   I      I++G  +  L         L  Q+  AD
Sbjct: 12  GFTDATFRNAQQKYFGGIDTFYAPYIRFNRKMIIKGSYQRDLNPEVNTSLNLIPQVMTAD 71

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               +   K ++  GY E+N N+GCP   V +   G+ L+ N   +   +        + 
Sbjct: 72  ADHFIFVIKYIQSLGYKELNWNLGCPYPMVTKSGMGSGLICNTTQIDHILDRAHSETDVT 131

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           +++K R+G +    +  +    K + K  +  I IHAR          D        +  
Sbjct: 132 ISMKMRLGYE---SSSEIVESFKILDKYPIKNIAIHARLGKQLYKGGVDLEA-----FQK 183

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             ++ K      +  NG +  ++Q   +    PS++  MIGR    +  + + +      
Sbjct: 184 CIDVAKHT----LYYNGDITSVAQFKAMQERFPSIEHFMIGRGLIADPFLPSMIKA---- 235

Query: 236 PLTGSSPIKTRVDKDFWRKISASM 259
                   +  + ++F   I    
Sbjct: 236 DTNQYPENRWEIFREFHDTIYQQY 259


>gi|150003817|ref|YP_001298561.1| nifR3 family TIM-barrel protein [Bacteroides vulgatus ATCC 8482]
 gi|149932241|gb|ABR38939.1| putative nifR3 family TIM-barrel enzyme [Bacteroides vulgatus ATCC
           8482]
          Length = 305

 Score =  103 bits (258), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/294 (17%), Positives = 105/294 (35%), Gaps = 28/294 (9%)

Query: 3   DWTDRHYRFFARL-LTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  +R   +         YT  +  +       D + I   +     L  Q+  +  
Sbjct: 10  GFTEAPWRNLHQEVFGGIDAYYTPFVRMEKGEFRNKDVREIASENNTVSRLIPQLIASTP 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L   A +  + GY E ++N+GCP   +     G+ ++  P  V   +  +     +  
Sbjct: 70  AELERLAGLFIEKGYKEADINMGCPFPLMTGKHKGSGILPYPAEVEALLKELVHYPELGF 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    A   R L+  +  + +  I +H R    +        ++    +   
Sbjct: 130 SVKMRLGWE---CADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-----EVDLAAFTAF 181

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           YE         +  NG    +ED+ +  +  P ++GVM+GR    N A+        +  
Sbjct: 182 YEECAH----PLVYNGDLLTVEDIRKVDEEFPRLEGVMLGRGLLANPAL--------AWE 229

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
               +        +  + + A +  Y   HL    +L    +         P++
Sbjct: 230 YANGTVFSPDELHEKVKALHARLLQYYEAHLQGEAQLLSKMKPYWEYL--LPDA 281


>gi|298480434|ref|ZP_06998631.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. D22]
 gi|298273255|gb|EFI14819.1| nifR3 family TIM-barrel enzyme with dihydrouridine synthase domain
           protein [Bacteroides sp. D22]
          Length = 314

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 46/279 (16%), Positives = 100/279 (35%), Gaps = 18/279 (6%)

Query: 3   DWTDRHYR-FFARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  YR   A         YT  +  +       D + I   + Q   L  Q+     
Sbjct: 14  GYTEVFYRNAHAACFGGIDTYYTPFVRLEKGGFRHRDVRGIEPGNNQVAHLIPQLIAPSF 73

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            K  +   +  +  Y E+++N+GCP   + +   G+ ++  P+ V   ++ + +   I  
Sbjct: 74  EKAEKILSLFIEKEYKEVDINIGCPFPMLAKRHNGSGILPYPEEVQALLSLITEYPQISF 133

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++K R+G +D         L   I +  +  + +H R    +     D +      ++  
Sbjct: 134 SIKMRLGWED---PEECLKLAPIINELPLRQVVMHPRLGKQQYKGEVDLKA-----FEAF 185

Query: 180 YEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
               K      +  NG +   ED+ +  +  P + G+MIGR    N A+     +  +  
Sbjct: 186 QNACKH----PLIYNGDINSVEDIHRIQEQFPGLAGMMIGRGLLANPALALEYRQNRALE 241

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
                     + K  + + +  +     + L+      +
Sbjct: 242 FDEMREKLQSMHKCVYNQYAEQLEGGDEQLLNKMKTFWE 280


>gi|296231401|ref|XP_002761128.1| PREDICTED: tRNA-dihydrouridine synthase 2-like isoform 3
           [Callithrix jacchus]
          Length = 458

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 85/242 (35%), Gaps = 59/242 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEKPLALQI 54
           MV       R  A L     ++Y E      MI    ++      +   +  ++ +    
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVF--- 74

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
                           +   N +   +G           GA L+ +PD +   ++ + K 
Sbjct: 75  -------------RTCEREQNRVVFQMG---------GMGAALLSDPDKIEKILSTLVKG 112

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
              PVT K RI    +       +LVK I+++G+  I +H RK        ++ R    +
Sbjct: 113 THRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK--------REERPQHPV 160

Query: 175 DYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGVMIGRAAYKNSA 224
             +++  I  +   + +  NG           +ED  QA     +   VM+ RAA  N +
Sbjct: 161 SCEVIKAIA-DTLSIPVIANGGSHDHIQRYSDIEDFRQA----TAASSVMVARAAMWNPS 215

Query: 225 ML 226
           + 
Sbjct: 216 IF 217


>gi|254880956|ref|ZP_05253666.1| nifR3 family TIM-barrel protein [Bacteroides sp. 4_3_47FAA]
 gi|319639964|ref|ZP_07994691.1| nifR3 family TIM-barrel enzyme [Bacteroides sp. 3_1_40A]
 gi|254833749|gb|EET14058.1| nifR3 family TIM-barrel protein [Bacteroides sp. 4_3_47FAA]
 gi|317388242|gb|EFV69094.1| nifR3 family TIM-barrel enzyme [Bacteroides sp. 3_1_40A]
          Length = 305

 Score =  102 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 52/294 (17%), Positives = 108/294 (36%), Gaps = 28/294 (9%)

Query: 3   DWTDRHYRFFARL-LTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +T+  +R   +         YT  +  +       D + I   +     L  Q+  +  
Sbjct: 10  GFTESPWRNLHQEVFGGIDAYYTPFVRMEKGEFRNKDVREIASGNNTVSRLIPQLIASTP 69

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
           ++L   A +  + GY E ++N+GCP   +     G+ ++  P  V   +  +     +  
Sbjct: 70  AELERLAGLFIEKGYKEADINMGCPFPLMTGKHKGSGILPYPAEVEALLKELVHYPELGF 129

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R+G +    A   R L+  +  + +  I +H R    +        ++    +   
Sbjct: 130 SVKMRLGWE---CADEWRPLLPLLNAAPLRRIVLHPRIGKQQYKG-----EVDLAAFTAF 181

Query: 180 YEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           YE         +  NG    +ED+ +  +  P ++GVM+GR    N A+      Y +  
Sbjct: 182 YEECAH----PLVYNGDLLTVEDIRKVDEEFPRLEGVMLGRGLLANPALAWE---YANGA 234

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
           +     +  +V     + + A +  Y   HL    +L    +         P++
Sbjct: 235 VFSPDELHEKV-----KALHARLLQYYEAHLQGEVQLLSKMKPYWEYL--LPDA 281


>gi|213420477|ref|ZP_03353543.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 79

 Score =  102 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 39/78 (50%), Positives = 56/78 (71%)

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
              IHARKA L GLSPK+NR+IP LDY  VY++K++ P L + +NGG++ + +A + L  
Sbjct: 1   MFIIHARKAWLSGLSPKENREIPPLDYPRVYQLKRDFPHLTMSINGGIKSLEEAKEHLRH 60

Query: 210 VDGVMIGRAAYKNSAMLT 227
           +DGVM+GR AY+N  +L 
Sbjct: 61  MDGVMVGREAYQNPGILA 78


>gi|329960701|ref|ZP_08299044.1| dihydrouridine synthase [Bacteroides fluxus YIT 12057]
 gi|328532574|gb|EGF59368.1| dihydrouridine synthase [Bacteroides fluxus YIT 12057]
          Length = 316

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 52/289 (17%), Positives = 106/289 (36%), Gaps = 28/289 (9%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-----EKPLALQIGG 56
            +TD  YR   AR+       Y+  +    I  G+ +       +        L  Q+  
Sbjct: 15  GYTDAVYRRAHARIFGGIETYYSPFV---RIEHGEIRRRDVRDAEPGANPGLHLIPQLIA 71

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-KAL 115
            ++ K      +  + GY E+++N+GCP   + +   GA ++  P+ V   ++ +  K  
Sbjct: 72  PEVDKAERIISLFIEKGYREVDINLGCPFPVLAKRHNGAGMLPYPEEVRTLLSTITGKHP 131

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            I  +VK R+G +    ++A   L+    +  ++ I +H R    +     D        
Sbjct: 132 DIRFSVKLRLGWERPEESLA---LLPLFNELPLSHIILHPRLGKQQYKGETDPEGF-KAF 187

Query: 176 YDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           Y+   +         +  NG    +ED+       P + G++IGR    N A+     EY
Sbjct: 188 YEGCNK--------PLFYNGDLLTVEDIRSVTTRFPRLAGLVIGRGLLANPAL---ALEY 236

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                  +  +  +V +       +         L    K++    +++
Sbjct: 237 RQGEPLSADEMARKVSRLHTEVYESYREQLQGGELQLLMKMKSFWEYLL 285


>gi|302409896|ref|XP_003002782.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
 gi|261358815|gb|EEY21243.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
          Length = 466

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 52/266 (19%), Positives = 86/266 (32%), Gaps = 57/266 (21%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGD--KKNILGFSTQE-------KPLAL---- 52
           +  +R  A  L    L Y+EM +   +++G      +L     E        P+      
Sbjct: 100 NLPFRRLAVEL-GAELTYSEMAMGLPLIQGTKADWTLLKAHESELVPPKAGGPIVQGYDN 158

Query: 53  --------QIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSARVHEGSFGACLMLNPD 102
                   QI        V+AA+ ++ F  +   I+LN GCP   + +   G+ L+    
Sbjct: 159 AKDIKFGAQISANQPWVAVKAAECLKRFVPHLRVIDLNCGCPIDMLFKAGGGSALLEAHG 218

Query: 103 IVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAVA---------LRNLVKSIKKSGVNGIW 152
            +   +  M      IPVTVK R GV +  P             R   + +   G   I 
Sbjct: 219 KLERMVRGMNTVSGEIPVTVKIRTGVRNNRPTATSIINKLAFGAREHRERLGAPGCAAIT 278

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV-- 210
           +H R         ++ R     D+  V E            N   +D        P    
Sbjct: 279 LHGRS--------REQRYTRRADWSYVAECAALIKS----YN-DTKDADTDTIREPDAST 325

Query: 211 -----DGVMIGRAAYKNSAMLTTVDE 231
                DG M       N+ +   +++
Sbjct: 326 LPNSKDGKMY---FLGNAWLFEEIEK 348


>gi|119177354|ref|XP_001240465.1| hypothetical protein CIMG_07628 [Coccidioides immitis RS]
          Length = 453

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 42/188 (22%), Positives = 82/188 (43%), Gaps = 17/188 (9%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +   L  Q+G A+   L   A  V     + I++N GCP      G  GA L+  PD + 
Sbjct: 102 ERGKLIFQLGTANP-SLAVEAAKVVAADVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLV 160

Query: 106 DCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ + +  P    ++VK R+  + +        LV  + ++G+ G+ +H R   ++
Sbjct: 161 SILEALVEEIGKPYEIGISVKIRLLAEPERTEA----LVTRVCRTGITGLTVHCRTTPMR 216

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                   ++P     ++  I ++   +   +NG +    +A+K++    VDG MI  +A
Sbjct: 217 PREAAIREQLP-----MIASICRKAG-VACLMNGDVRSRDEAMKLIREYGVDGAMIATSA 270

Query: 220 YKNSAMLT 227
             N +   
Sbjct: 271 ESNFSCFR 278


>gi|324504592|gb|ADY41982.1| tRNA-dihydrouridine synthase 2-like protein [Ascaris suum]
          Length = 454

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 95/233 (40%), Gaps = 38/233 (16%)

Query: 18  NNALLYTEMIVADAIL--RGDKKNILGF--------------STQEKP-LALQIGGADIS 60
              L+YTE IV   +L  R    ++L                + +E+    LQ+G  +  
Sbjct: 49  GADLVYTEEIVDQRLLNSRRIVNDVLHTVDYVIEEDVVLRVATERERNKCVLQVGTNNGD 108

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++   AK V D     I++N+GCP      G  GA L+  PD + + + ++    S+PV+
Sbjct: 109 RIAAVAKKVHDDIAA-IDVNMGCPKPFSLTGGMGAALLTQPDKIKEILTSLVSVSSVPVS 167

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+             LV+ I+K GV  + +H R+        +D R+      + + 
Sbjct: 168 CKIRVL----DKLEDTLALVRLIEKCGVAAVGVHGRR--------RDERQGDANRVNEIR 215

Query: 181 EIKKENPDLFIGLNG------GLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
           E+ +    + +  NG        +D+ Q  K       +M+ R A  N ++  
Sbjct: 216 EVVRAL-SIPVIANGASGMVKEFKDVEQFRKE-SEASSIMLARRALSNPSIFR 266


>gi|254168949|ref|ZP_04875788.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|197622055|gb|EDY34631.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
          Length = 299

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 45/207 (21%), Positives = 90/207 (43%), Gaps = 12/207 (5%)

Query: 36  DKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           + K+ +  + +   P+   I G++  +    AK +ED+G + + LN+ CP A+     +G
Sbjct: 78  NYKDEIKIAKEGGVPIIGSIFGSNAEEFSYLAKKMEDYGADAVELNLSCPHAK----GYG 133

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS---IKKSGVNGI 151
             +  + D+V + I ++ +A+ IPV  K     ++ +          +   I       I
Sbjct: 134 MEVGTDLDLVEEIINSVKRAVKIPVWAKLTPNTNNIVEIAKAAENADAFVLINTLKAMAI 193

Query: 152 WIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            I A++ +LK        + I  +    VYE+ +E     IG+ GG+E+   A++ ++  
Sbjct: 194 DIDAKRPVLKNVFGGLSGKAIKPIGVRAVYEVYREVEKPIIGV-GGIENGRDAIEYMMAG 252

Query: 210 VDGVMIGRAAYKN-SAMLTTVDEYFSN 235
              V IG A Y     +   + +    
Sbjct: 253 ASAVEIGTALYTRGIEVFKEIAKEIEE 279


>gi|303316025|ref|XP_003068017.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
 gi|240107693|gb|EER25872.1| Dihydrouridine synthase family protein [Coccidioides posadasii C735
           delta SOWgp]
          Length = 453

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 42/188 (22%), Positives = 82/188 (43%), Gaps = 17/188 (9%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +   L  Q+G A+   L   A  V     + I++N GCP      G  GA L+  PD + 
Sbjct: 102 ERGKLIFQLGTANP-SLAVEAAKVVAADVSGIDVNSGCPKPFSTSGGMGAALLQTPDRLV 160

Query: 106 DCIAAMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ + +  P    ++VK R+  + +        LV  + ++G+ G+ +H R   ++
Sbjct: 161 SILEALVEEIGKPYEIGISVKIRLLAEPERTEA----LVTRLCRTGITGLTVHCRTTPMR 216

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                   ++P     ++  I ++   +   +NG +    +A+K++    VDG MI  +A
Sbjct: 217 PREAAIREQLP-----MIASICRKAG-VACLMNGDVRSRDEAMKLIREYGVDGAMIATSA 270

Query: 220 YKNSAMLT 227
             N +   
Sbjct: 271 ESNFSCFR 278


>gi|254166940|ref|ZP_04873794.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|289596507|ref|YP_003483203.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|197624550|gb|EDY37111.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
 gi|289534294|gb|ADD08641.1| dihydroorotate dehydrogenase family protein [Aciduliprofundum
           boonei T469]
          Length = 299

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/207 (21%), Positives = 90/207 (43%), Gaps = 12/207 (5%)

Query: 36  DKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           + K+ +  + +   P+   I G++  +    AK +ED+G + + LN+ CP A+     +G
Sbjct: 78  NYKDEIKIAKEGGVPIIGSIFGSNPEEFSYLAKKMEDYGADAVELNLSCPHAK----GYG 133

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS---IKKSGVNGI 151
             +  + ++V + I ++ +A+ IPV  K     ++ +          +   I       I
Sbjct: 134 MEVGTDLELVEEIINSVKRAVKIPVWAKLTPNTNNIVEIAKAAENADAFVLINTLKAMAI 193

Query: 152 WIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            I A++ +LK        + I  +    VYE+ +E     IG+ GG+E+   A++ I+  
Sbjct: 194 DIDAKRPVLKNVFGGLSGKAIKPIGVRAVYEVYREIEKPIIGV-GGIENGRDAIEYIMAG 252

Query: 210 VDGVMIGRAAYKN-SAMLTTVDEYFSN 235
              V IG A Y     +   + +    
Sbjct: 253 ASAVEIGTALYTRGIEVFKEIAKEIEE 279


>gi|270294956|ref|ZP_06201157.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270274203|gb|EFA20064.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 322

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 90/236 (38%), Gaps = 19/236 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   AR+       Y+  +  +   I R D ++I      +  L  Q+   D 
Sbjct: 21  GYTDAVYRRAHARIFGGIETYYSPFVRMEHGEIRRKDARDIEPDHNPDLHLIPQLIAPDT 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            KL     +  + GY E ++N+GCP   +     G+ ++  P+ V   +  A+ +   I 
Sbjct: 81  DKLEHIMSLFIEKGYRETDINLGCPFPMLARRHNGSGMLPYPEEVKALLSEAIDRHPDIR 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G +    A     L+    +  +  I +H R    +            +D + 
Sbjct: 141 FSVKLRLGWE---QAEECLALLPLFNELPLAHIILHPRLGKQQ--------YKGEVDLEG 189

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                KE     +  NG L    D+       P + G++IGR    N A+     +
Sbjct: 190 FEAFYKECTH-PLFYNGDLHTANDIRSITTRFPRLAGIVIGRGLLANPALALEYKQ 244


>gi|167957490|ref|ZP_02544564.1| tRNA-dihydrouridine synthase [candidate division TM7 single-cell
           isolate TM7c]
          Length = 278

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 37/170 (21%), Positives = 69/170 (40%), Gaps = 12/170 (7%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            + + A       ++ I++N+GCP+    +   GA L+  PD V     A  K   +PV+
Sbjct: 1   DMEQFAAHCAKLDFDGIDINMGCPAKSAIKSG-GAALIRRPD-VAVAAIAAAKTAGLPVS 58

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R+G          R  + +I +  +  + IH R        P           DI+ 
Sbjct: 59  VKTRLGY---TYVDEWREWLTTILQQDIVNLTIHLRTKKEMSKVPAHYELTD----DIIK 111

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYKNSAMLT 227
              +  P   + +NG + + +   ++    P ++G+MIGR  + +     
Sbjct: 112 LRDEIAPQTLLTINGDIRNRAHGEELFATHPGLNGLMIGRGVFSDPFCFR 161


>gi|294788397|ref|ZP_06753640.1| dihydrouridine synthase (Dus) [Simonsiella muelleri ATCC 29453]
 gi|294483828|gb|EFG31512.1| dihydrouridine synthase (Dus) [Simonsiella muelleri ATCC 29453]
          Length = 175

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 49/92 (53%), Gaps = 3/92 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILG--FSTQEKPLALQIGGAD 58
           M   TD  +R  A+         +EM+ +D  L+  +K++     + +   +A+QI G++
Sbjct: 22  MAGITDNPFRQIAKQF-GADWTVSEMLSSDPTLQQTRKSLQRRNHTGESGVIAVQIAGSN 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
             +L +AA++  + G   I++N+GCP+ +V  
Sbjct: 81  PHELAKAAQLNYENGAQVIDINMGCPAKKVCN 112


>gi|82777377|ref|YP_403726.1| putative regulator protein [Shigella dysenteriae Sd197]
 gi|81241525|gb|ABB62235.1| putative regulator protein [Shigella dysenteriae Sd197]
          Length = 191

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 73/193 (37%), Gaps = 32/193 (16%)

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M +A+   +PV+VK R+G D          +  +++++G   + +H R            
Sbjct: 1   MREAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QG 50

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            +  ++D+  + EI+++  ++ +  NG + D   A + +     D VMIGR A  N   L
Sbjct: 51  YRAEHIDWQAIGEIRQQL-NIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGAL-NIPNL 108

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGL 283
           + V +Y                +  W ++ A +  Y          L  + R    +  L
Sbjct: 109 SRVVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYL 155

Query: 284 FHGFPNSRRCRHI 296
              +  +      
Sbjct: 156 RKEYDEATELFQH 168


>gi|160888611|ref|ZP_02069614.1| hypothetical protein BACUNI_01028 [Bacteroides uniformis ATCC 8492]
 gi|317477952|ref|ZP_07937135.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
 gi|156861925|gb|EDO55356.1| hypothetical protein BACUNI_01028 [Bacteroides uniformis ATCC 8492]
 gi|316905866|gb|EFV27637.1| dihydrouridine synthase [Bacteroides sp. 4_1_36]
          Length = 322

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 90/236 (38%), Gaps = 19/236 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   AR+       Y+  +  +   I R D ++I   +  +  L  Q+   D 
Sbjct: 21  GYTDAVYRRAHARIFGGIETYYSPFVRMEHGEIRRKDARDIEPDNNPDLHLIPQLIAPDA 80

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIP 118
            KL     +  + GY E ++N+GCP   +     G  ++  P+ V   +  A+ +   I 
Sbjct: 81  DKLEHIMSLFIEKGYQEADINLGCPFPMLARRHNGCGMLPYPEEVKALLSEAIDRHPDIR 140

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G +    A     L+    +  +  I +H R    +            +D + 
Sbjct: 141 FSVKLRLGWE---QAEECLALLPLFNELPLAHIILHPRLGKQQ--------YKGEVDLEG 189

Query: 179 VYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                KE     +  NG L    D+       P + G++IGR    N A+     +
Sbjct: 190 FEAFYKECTH-PLFYNGDLHTANDIRSITTRFPRLAGIVIGRGLLANPALALEYKQ 244


>gi|254173214|ref|ZP_04879887.1| dihydroorotate dehydrogenase [Thermococcus sp. AM4]
 gi|214032623|gb|EEB73452.1| dihydroorotate dehydrogenase [Thermococcus sp. AM4]
          Length = 300

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/225 (21%), Positives = 81/225 (36%), Gaps = 17/225 (7%)

Query: 27  IVADAILRGDKKNILGFSTQ---EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     K  L        + PL + I G    +    A+ + D   +   LN+ C
Sbjct: 68  INAMGLPNPGWKGFLEMVEGYTFDFPLIVSIFGGTPEEFAFLAQKLSDV-ADAFELNLSC 126

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRN 138
           P A+     +G  +   P+ V + + A+  A   PV  K    +DD          A  +
Sbjct: 127 PHAK----GYGMEIGQKPENVYEVVKAVKDATDKPVIAKLTPNIDDITKLGLAAEKAGAD 182

Query: 139 LVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I I+ARK IL           +  +    VY++ K   ++ +   GG+
Sbjct: 183 AVSAINTLKAVAIDIYARKPILSNRVGGYSGPGVKPVALRAVYDLAKAL-EVPVIGIGGI 241

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGS 240
                A++ +L     + IG A       +   + E     L G 
Sbjct: 242 TTWQDAVEFLLAGASALQIGTAVSLRGWKVFREIKEGIEAYLEGE 286


>gi|332097473|gb|EGJ02453.1| dihydrouridine synthase family protein [Shigella boydii 3594-74]
          Length = 191

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 72/193 (37%), Gaps = 32/193 (16%)

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           M +A+   +PV+VK R+G D          +  +++++G   + +H R            
Sbjct: 1   MREAVPAHLPVSVKVRLGWDSGEKKF---EIADAVQQAGATELVVHGRTKE-------QG 50

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            +  ++D+  + EI++   ++ +  NG + D   A + +     D VMIGR A  N   L
Sbjct: 51  YRAEHIDWQAIGEIRQRL-NIPVIANGEIWDWQSAQQCMAISGCDSVMIGRGAL-NIPNL 108

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGL 283
           + V +Y                +  W ++ A +  Y          L  + R    +  L
Sbjct: 109 SRVVKYNE-------------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYL 155

Query: 284 FHGFPNSRRCRHI 296
              +  +      
Sbjct: 156 RKEYDEATELFQH 168


>gi|194383804|dbj|BAG59260.1| unnamed protein product [Homo sapiens]
          Length = 458

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 84/242 (34%), Gaps = 59/242 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVADAILRGDKKNILGFSTQEKPLALQI 54
           MV       R  A L     ++Y E      MI    ++      +   +  ++ +    
Sbjct: 19  MVRVGTLPMRLLA-LDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDDRVVF--- 74

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
                           +   N +   +G           GA L+ + D +   ++ + K 
Sbjct: 75  -------------RTCEREQNRVVFQMG---------GMGAALLSDSDKIEKILSTLVKG 112

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
              PVT K RI    +       +LVK I+++G+  I +H RK        ++ R    +
Sbjct: 113 TRRPVTCKIRILPSLEDT----LSLVKRIERTGIAAIAVHGRK--------REERPQHPV 160

Query: 175 DYDIVYEIKKENPDLFIGLNG----------GLEDMSQALKILPSVDGVMIGRAAYKNSA 224
             +++  I  +   + +  NG           +ED  QA     +   VM+ RAA  N +
Sbjct: 161 SCEVIKAIA-DTLSIPVIANGGSHDHIQQYSDIEDFRQA----TAASSVMVARAAMWNPS 215

Query: 225 ML 226
           + 
Sbjct: 216 IF 217


>gi|70930687|ref|XP_737208.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56512402|emb|CAH78878.1| conserved hypothetical protein [Plasmodium chabaudi chabaudi]
          Length = 141

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 32/111 (28%), Positives = 55/111 (49%), Gaps = 4/111 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++  +R   R   N  L +T M  +   +   K          Q+KPL +Q  G D
Sbjct: 32  MVDLSELPFRLLCRNY-NCDLAFTPMFHSKNFVEHSKYRTGYFKTCDQDKPLIVQFCGND 90

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
            S +++A   ++D   N +++N+GCP     +G++GA L+   D V + I+
Sbjct: 91  PSIILKAIDYIKDE-VNGVDINLGCPQQIAKKGNYGAFLLHKHDEVVNLIS 140


>gi|207342565|gb|EDZ70296.1| YML080Wp-like protein [Saccharomyces cerevisiae AWRI1631]
          Length = 135

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 32/100 (32%), Positives = 51/100 (51%), Gaps = 7/100 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI-----LRGDKKNILGFSTQEKPLALQIG 55
           MVD ++  +R  +R      L YT M+ A         R D  + L  S+ ++PL +Q  
Sbjct: 36  MVDQSELAWRILSRRY-GATLAYTPMLHAKLFATSKKYREDNWSSLDGSSVDRPLVVQFC 94

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
             D   L+ AAK+VED   + ++LN+GCP     +G +G+
Sbjct: 95  ANDPEYLLAAAKLVED-KCDAVDLNLGCPQGIAKKGHYGS 133


>gi|167764072|ref|ZP_02436199.1| hypothetical protein BACSTE_02455 [Bacteroides stercoris ATCC
           43183]
 gi|167698188|gb|EDS14767.1| hypothetical protein BACSTE_02455 [Bacteroides stercoris ATCC
           43183]
          Length = 317

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 91/236 (38%), Gaps = 19/236 (8%)

Query: 3   DWTDRHYRF-FARLLTNNALLYTEMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADI 59
            +TD  YR   A +       Y+  +  +   I R D ++I   + +   L  Q+     
Sbjct: 15  GYTDAAYRQAHACIFGGIDTYYSPFVRVEHGEIRRKDIRDINPENNRNIHLIPQLIAPQP 74

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IP 118
           S L +   +  +  Y E ++N+GCP   + +   GA ++  P+ + + + A  +    I 
Sbjct: 75  STLEQIVSLFIEHNYQEADINLGCPFPMLAKRHNGAGMLPYPEEIKELLTAATEKYPQIR 134

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            +VK R+G +    A     L+  +    ++ I +H R    +     D        Y  
Sbjct: 135 FSVKLRLGWE---NANECLALLPLLNTLPLSHIILHPRLGKQQYKGEVDLNGF-EAFYHG 190

Query: 179 VYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
             +         +  NG    +ED+    +  P + GV+IGR    N A+     +
Sbjct: 191 CDK--------PLLYNGDLHTIEDIQTVTERFPRLAGVVIGRGLLANPALAWEYQQ 238


>gi|322705649|gb|EFY97233.1| Dihydrouridine synthase [Metarhizium anisopliae ARSEF 23]
          Length = 339

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 80/257 (31%), Gaps = 45/257 (17%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----EKPLALQIGGADISKL 62
             +R          L +T MI+A    R +       +      + P  LQ G     +L
Sbjct: 7   LAFRQTVHQY-GTDLCWTPMILAKEFNRSEFARDSDLTISTTAAQPPTILQFGANTPLEL 65

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK--------- 113
             A+ +   F  + ++LN GCP +     + GA LM    +V D +    +         
Sbjct: 66  ARASSLAAPF-VSGVDLNCGCPQSWACAETLGAALMDQRALVRDMVTETRQRLRQDGWAV 124

Query: 114 --------ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
                   A    V+VK R+  D +     L  ++   +   V+ + IH R       +P
Sbjct: 125 AKENDMESARGRSVSVKIRVHDDLRKTVDFLDTVIGHPQFRNVDWVTIHPRTRHTPSTTP 184

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE---------------DMSQALKILPSV 210
                +  L       +        + L+G +                D S        +
Sbjct: 185 IFAEALEMLTQRYAATL-------PLLLSGDVFDLSALPIRSTRPPDPDPSTPRPSTTHL 237

Query: 211 DGVMIGRAAYKNSAMLT 227
            G M  R    N A+  
Sbjct: 238 SGFMSARGLLANPALFA 254


>gi|183230428|ref|XP_648510.2| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
 gi|169802927|gb|EAL43123.2| dihydrouridine synthase (Dus) family protein [Entamoeba histolytica
           HM-1:IMSS]
          Length = 366

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 106/247 (42%), Gaps = 43/247 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-----------AILRGDKKN--ILGFSTQE 47
           MV      YR  A L    + ++TE +V+             I++   KN  +L    ++
Sbjct: 32  MVGICTISYRSMA-LDAGASAVFTEELVSKRLCECKRVENSGIIQYIHKNDVMLTLKPEQ 90

Query: 48  KP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +    LQ+G  D+   V+   ++++     I++N+GC      +G  G  L+ N D +  
Sbjct: 91  QSKTILQLGTFDVESSVKCVSLIQE--VCGIDINLGCGMWFSTKGEMGQALVDNRDKLEK 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+   LS P++ K R+    Q         ++ +   G++ I +H R          
Sbjct: 149 IVKALV-GLSKPISAKIRL----QQTHEETLEFIQWLYSLGISIISLHGR---------- 193

Query: 167 DNRKIPNLDYDIVYEIKKENPDLF--IGLNGGL---EDMSQALKILPSVDGVMIGRAA-- 219
            ++++  +D D   E++K   D    + LNG +   ED+++ L    +V GVMIGR +  
Sbjct: 194 HHKELYGVDCDW-AELEKLVKDCPYDLILNGDICKQEDITKLLSFGKNVRGVMIGRGSGI 252

Query: 220 ---YKNS 223
                N 
Sbjct: 253 HLGLFNP 259


>gi|171696070|ref|XP_001912959.1| hypothetical protein [Podospora anserina S mat+]
 gi|170948277|emb|CAP60441.1| unnamed protein product [Podospora anserina S mat+]
          Length = 516

 Score =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 48/193 (24%), Positives = 82/193 (42%), Gaps = 17/193 (8%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L  + ++  L  QIG +D  +   AA  +       I++N GCP      G  GA L+ 
Sbjct: 191 RLDPTREKGKLVFQIGTSDPDR-ALAAARLVAGDVAGIDVNAGCPKPFSTSGGMGAALLQ 249

Query: 100 NPDIVGDCIAAMCKAL----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            PD +   +  + + +     I V+VK R+             LV+ +  +G+ G+ IH 
Sbjct: 250 TPDKLVAILENLTRHIIPEFGIGVSVKIRLL----ETPEKTEALVRRLVGTGITGLTIHC 305

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R   ++   P++      L   ++  I +E   +   +NG + D     K++    VDG 
Sbjct: 306 RTTPMR---PRERAIRGQLR--MIGYICREAG-VACVVNGDVADRRDGYKLMEEFRVDGA 359

Query: 214 MIGRAAYKNSAML 226
           MI  AA KN  + 
Sbjct: 360 MIATAAEKNPNVF 372


>gi|16081529|ref|NP_393883.1| dihydroorotate dehydrogenase 1B [Thermoplasma acidophilum DSM 1728]
 gi|13878694|sp|Q9HL35|PYRD_THEAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|10639575|emb|CAC11547.1| DIHYDROOROTATE DEHYDROGENASE B related protein [Thermoplasma
           acidophilum]
          Length = 300

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 78/186 (41%), Gaps = 22/186 (11%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
             KP+   +  +D    V   + ++++G + + LN+ CP    H   FG  +  +PD+V 
Sbjct: 91  SGKPVIGSVFASDAESFVNLGRKMQEYGCDAVELNLSCP----HVKGFGLEVGSDPDLVE 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---------IHAR 156
           D +  M   +S+PV  K    V D      +  + K+ +K+    +          I AR
Sbjct: 147 DIVNEMKSKISVPVFAKLSPNVSD------IIEIAKAAEKADAYVLINTVKAMKIDIRAR 200

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
             +L           I  +    VYE+KKE     IG+ GG+     A++ I+     V 
Sbjct: 201 MPVLTNAYGGLSGPAIKPVGVRYVYEVKKETGKDIIGV-GGITTYEDAVEYIMAGASAVQ 259

Query: 215 IGRAAY 220
           IG A Y
Sbjct: 260 IGTALY 265


>gi|195999940|ref|XP_002109838.1| hypothetical protein TRIADDRAFT_53129 [Trichoplax adhaerens]
 gi|190587962|gb|EDV28004.1| hypothetical protein TRIADDRAFT_53129 [Trichoplax adhaerens]
          Length = 519

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/215 (20%), Positives = 91/215 (42%), Gaps = 22/215 (10%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST----QEKPLALQIGGADISK 61
           D  +R   R   N  L YT ++ A+ IL         F      Q++PL +Q+   D ++
Sbjct: 37  DLAFRLLCR-HHNVQLFYTPLLKAEEILNDWDSYKYHFLNANNFQDRPLIVQLCSRDPNR 95

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +++AA+ V+    + I+L +   S    +      +  +  ++   I+ +   L++PV  
Sbjct: 96  MLQAAERVDSL-CDAIDLTLH--SETNAKTILNQAVGKDFQLLQRMISLLRDNLNMPVAC 152

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K +I  D    +  L    K ++ +G   + I        G   K+ R   + D++IV  
Sbjct: 153 KIKIAADKDSSS--LIKYAKRLESAGCQLLSI--------GCRHKEPRFRLD-DWNIVKA 201

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
           +K ++  + +     +  +++A   L      G+M
Sbjct: 202 VK-DSVVIPVFACSDISTLAEADLCLEYTGAQGIM 235


>gi|167540353|ref|XP_001741843.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165893431|gb|EDR21688.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 355

 Score = 99.1 bits (246), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 108/247 (43%), Gaps = 43/247 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-----------AILRGDKKN--ILGFSTQE 47
           MV      YR  A L    + ++TE +V+             +++   KN  +L    ++
Sbjct: 21  MVGICTVSYRTMA-LDAGASAVFTEELVSKRLCECKRVENSGLIQYIHKNDVMLTLKPEQ 79

Query: 48  KP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +    LQ+G  D+   ++   ++++     I++N+GC      +G  G  L+ N D +  
Sbjct: 80  QSKTILQLGTFDVESSIKCVSLIKE--VCGIDINLGCGMWFSTKGEMGQALVSNRDKLEK 137

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+ K L  P++ K R+    Q         ++ +   G++ I +H R          
Sbjct: 138 IVKALVK-LGKPISAKIRL----QQTHEETLEFIQWLYSLGISIISLHGR---------- 182

Query: 167 DNRKIPNLDYDIVYEIKKENPDLF--IGLNGGL---EDMSQALKILPSVDGVMIGRAA-- 219
            ++++  +D D V E++K   D    + LNG +   ED+++ L    +V GVMIGRA+  
Sbjct: 183 HHKELYGVDCDWV-ELEKVVKDCPYDLILNGDICKQEDITKLLSFGKNVRGVMIGRASGI 241

Query: 220 ---YKNS 223
                N 
Sbjct: 242 HLGLFNP 248


>gi|240102413|ref|YP_002958722.1| dihydroorotate dehydrogenase 1B [Thermococcus gammatolerans EJ3]
 gi|239909967|gb|ACS32858.1| Dihydroorotase dehydrogenase (pyrD) [Thermococcus gammatolerans
           EJ3]
          Length = 300

 Score = 99.1 bits (246), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 47/216 (21%), Positives = 81/216 (37%), Gaps = 17/216 (7%)

Query: 27  IVADAILRGDKKNILGFSTQ---EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     K  L        + PL + I G    +    A+ + D   +   LN+ C
Sbjct: 68  INAMGLPNPGWKGFLEMVEGYTFDFPLIVSIFGGTPEEFAFLAEKLSDV-ADAFELNLSC 126

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRN 138
           P A+     +G  +  NP+ V + + A+  A   PV  K    +DD          A  +
Sbjct: 127 PHAK----GYGMEIGQNPENVYEVVKAVKDATDRPVIAKLTPNIDDITKLGLAAEKAGAD 182

Query: 139 LVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I I+AR+ IL           +  +    VY++ K   D+ +   GG+
Sbjct: 183 AVSAINTLKAIAIDIYARRPILSNRVGGYSGPGVKPVALRAVYDLAK-VLDIPVIGIGGI 241

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDE 231
                A++ +L     + IG A       +   ++E
Sbjct: 242 TTWQDAVEFLLAGASALQIGTAVSLRGWKVFREINE 277


>gi|225717964|gb|ACO14828.1| tRNA-dihydrouridine synthase 4-like [Caligus clemensi]
          Length = 192

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 32/137 (23%), Positives = 61/137 (44%), Gaps = 7/137 (5%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ---EKPLALQIGGA 57
           MV ++   +R    L     + ++ MI+AD+ +   +     F+T    ++PL +Q    
Sbjct: 20  MVRYSKLPFRRLI-LSYGADVAFSPMILADSFVSSPEARFNEFTTDPLRDRPLIVQFASK 78

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-- 115
            +   V AA++V       ++L+ GCP         GA L+  P+ + D + +       
Sbjct: 79  SVDDFVSAAQLVAPH-AEGVDLDCGCPQGWAIREGIGAALLQRPEFISDVVRSTKNRTQH 137

Query: 116 SIPVTVKCRIGVDDQIP 132
           S+ V+VK R+  D +  
Sbjct: 138 SLSVSVKIRLQKDHRRT 154


>gi|325960157|ref|YP_004291623.1| TiM-barrel protein [Methanobacterium sp. AL-21]
 gi|325331589|gb|ADZ10651.1| TIM-barrel protein [Methanobacterium sp. AL-21]
          Length = 238

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 38/148 (25%), Positives = 69/148 (46%), Gaps = 17/148 (11%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + + +N  C  A + +  +G  LM  PD + + +    +  S  V+VK R  V+     
Sbjct: 96  VDVVEINAHCRQAELVKSGYGQALMNYPDELYNLVHGTVEGCSKQVSVKIRANVEG---- 151

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           V    ++++I+ +G + I + A K               + DYD +  +K+ N D F+  
Sbjct: 152 VNYLKVLEAIENAGAHYIHVDAMKPGY-----------DSADYDFITWVKR-NTDSFVIG 199

Query: 194 NGGLEDMSQALKIL-PSVDGVMIGRAAY 220
           N  ++D++ A K+L    DG+ I RAA 
Sbjct: 200 NNSIKDIASARKMLSSGADGISIARAAI 227


>gi|261416953|ref|YP_003250636.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261373409|gb|ACX76154.1| dihydrouridine synthase DuS [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302325599|gb|ADL24800.1| conserved hypothetical protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 330

 Score = 98.7 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 78/210 (37%), Gaps = 21/210 (10%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
             QI    + +    A  +   GY EI+ N+GCP         GA ++ +   V + +  
Sbjct: 73  IPQIIANSVDEFKILADALIAKGYTEIDFNMGCPFPMQVNRHRGAGILNDKQTVQEIMDE 132

Query: 111 MCK------ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           + K         +  +VK R+G D    A A   ++  + ++ ++ I +H R    +   
Sbjct: 133 IRKISNANGTAPVKFSVKMRLGQDTPDEAFA---ILPILNEAPLSQITLHPRLGKQQYKG 189

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI---LPSVDGVMIGRAAYK 221
             D +      ++  YE  +      +  NG +  +SQ  ++    P + GVMIGR    
Sbjct: 190 TIDFKS-----FEKFYEECRH----PLVYNGDITSVSQICEMERRYPKLAGVMIGRGMLA 240

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
             +M     E              ++ +  
Sbjct: 241 RPSMAADYKELRDINCADPQDFLRKLFQMH 270


>gi|332293467|ref|YP_004432076.1| dihydrouridine synthase DuS [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171553|gb|AEE20808.1| dihydrouridine synthase DuS [Krokinobacter diaphorus 4H-3-7-5]
          Length = 318

 Score = 98.7 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/215 (20%), Positives = 82/215 (38%), Gaps = 23/215 (10%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q+  A   + +   K +E  GY E+N N+GCP   V +   G+ L+ N + +   + 
Sbjct: 63  VIPQVMTASADEFMFVIKYIESLGYTELNWNLGCPYPMVTKSGMGSGLICNTEKINHILD 122

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKD 167
                 S+ +++K R+G   + P   L +  K + K  +  + IHAR  K + KG    +
Sbjct: 123 RAHSESSVTISMKMRLGY--ESPNEILESF-KVLDKYPLKNVAIHARLGKQLYKGGVDLE 179

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAAYKNSA 224
                   +    ++ K      +  NG +  + Q  K+      +   MIGR    +  
Sbjct: 180 G-------FQKCIDVAKHT----LYYNGDITSVEQFRKMRERFPSIKHFMIGRGLIADPF 228

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
           + + +        T     +    + F   I    
Sbjct: 229 LPSMIKA----DTTEYPANRWETFRAFHDTIYEQY 259


>gi|295398020|ref|ZP_06808076.1| dihydroorotate oxidase [Aerococcus viridans ATCC 11563]
 gi|294973778|gb|EFG49549.1| dihydroorotate oxidase [Aerococcus viridans ATCC 11563]
          Length = 307

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/201 (19%), Positives = 82/201 (40%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +   VEA + + +      I LN+ CP+ ++    FG     +P++  
Sbjct: 93  DVPIIQSVAGSTVEDYVEATRALSQPENVKAIELNISCPNVKLGGLQFGT----DPEVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
           D    +  A  +PV VK    V D      +  + K+++ +G + I +            
Sbjct: 149 DLTKQVKAATDLPVYVKLTPNVTD------ITAIAKAVEAAGADAIVMINTITGQTFDLE 202

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            R+ +L G         +  +   +V ++ +   D+ I   GG+E +   L++ +     
Sbjct: 203 TRQPVLGGITGGLSGSSVKYVALRMVRQVAQ-VVDIPIIGVGGIESIDDVLEMIIAGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V +G A Y N  +   + E  
Sbjct: 262 VQVGSANYANPMICKEIIEGL 282


>gi|15679224|ref|NP_276341.1| dihydroorotate dehydrogenase 1B [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|3914506|sp|O27281|PYRD_METTH RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|2622323|gb|AAB85702.1| dihydroorotate oxidase [Methanothermobacter thermautotrophicus str.
           Delta H]
          Length = 303

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/213 (20%), Positives = 83/213 (38%), Gaps = 26/213 (12%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            +  L    +E PL   + GA   +   AA  VE++  + I LNV CP A       GA 
Sbjct: 82  FREELKLVDEEVPLIASVYGASPEEFASAAASVEEY-ADMIELNVSCPHAMA---GCGAS 137

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--- 153
           +  +P++    ++A+  A+ +P++ K    V D      +  +  S +++G + + +   
Sbjct: 138 IGQDPELTFRVVSAVKDAVDVPISTKLTPNVTD------IVEIAGSAEEAGSDALTLINS 191

Query: 154 ----------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                      AR  +           I  +    VY++ + + D+ I   GG+ D   A
Sbjct: 192 LGPGMKIDIKTARPILSNAFGGMSGPAIKPVAVRCVYDVYR-SVDIPIMGVGGVRDFQDA 250

Query: 204 LKIL-PSVDGVMIGRAAYKN-SAMLTTVDEYFS 234
           ++ L      V +G A   +   +   +     
Sbjct: 251 VEFLFAGARAVQVGTAIMYDGPEVFMKICRGLE 283


>gi|57642195|ref|YP_184673.1| dihydroorotate dehydrogenase 1B [Thermococcus kodakarensis KOD1]
 gi|73913697|sp|Q5JHR7|PYRD_PYRKO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|57160519|dbj|BAD86449.1| dihydroorotate dehydrogenase [Thermococcus kodakarensis KOD1]
          Length = 302

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 46/222 (20%), Positives = 81/222 (36%), Gaps = 17/222 (7%)

Query: 27  IVADAILRGDKKNILGFSTQ---EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     K  L        + PL + I G    +    A+ + +   +   LN+ C
Sbjct: 70  INAMGLPNPGWKGFLEMVEGYSFDFPLIVSIFGGTPEEFAFLAEKLSEV-ADAFELNLSC 128

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRN 138
           P A+     +G  +   P+ V   + A+  A   PV  K    +DD          A  +
Sbjct: 129 PHAK----GYGMEIGQKPENVYAVVKAVKDATDKPVIAKLTPNIDDITKLGLAAENAGAD 184

Query: 139 LVKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I I+ARK IL   +       +  +    VY++ +   D+ +   GG+
Sbjct: 185 AVSAINTLKAIAIDIYARKPILSNKVGGYSGPGVKPVALRAVYDLAR-TLDIPVIGIGGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPL 237
                A++ +L     + IG A       +   ++E     L
Sbjct: 244 TTWQDAVEFLLAGASALQIGTAVSLRGWKVFREINEGIERYL 285


>gi|325069036|ref|ZP_08127709.1| TIM-barrel protein, nifR3 family [Actinomyces oris K20]
          Length = 192

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 25/124 (20%), Positives = 49/124 (39%), Gaps = 8/124 (6%)

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +  +K E  DL +  NG +     A++++     DGV++GR       +   +    
Sbjct: 1   WEEIARLK-EATDLPVLGNGDIWLGDDAVRMMEATGCDGVVVGRGCQGRPWLFADIVSAM 59

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRC 293
                 SSP +TR D D   ++        A  +     ++ + +H+     G+P     
Sbjct: 60  H-----SSPARTRPDLDSVIEVIRRHGRMLADEMGEDRGVRDLRKHVGWYLKGYPVGGAA 114

Query: 294 RHIL 297
           R  L
Sbjct: 115 RADL 118


>gi|71408629|ref|XP_806706.1| tRNA-dihydrouridine synthase 2 [Trypanosoma cruzi strain CL Brener]
 gi|70870530|gb|EAN84855.1| tRNA-dihydrouridine synthase 2, putative [Trypanosoma cruzi]
          Length = 430

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 61/342 (17%), Positives = 121/342 (35%), Gaps = 67/342 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----------------------- 37
           MV   +  +R F        +++TE +VA  + R  +                       
Sbjct: 13  MVRVGNVGFRVFC-AAQGADVVFTEEVVAAKLARCHREVRVHNDAAGPMIEFVAYELFKN 71

Query: 38  ------------KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
                       +++   S +  P+ LQ+G +D +  V AA +  +   + I++N+GCP 
Sbjct: 72  QYKRSVVFTTPARDMTSRSGEGAPVVLQLGVSDAAVGVAAALLCCE-DVDGIDVNMGCPK 130

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAV 134
               +   GA LM +       + A+  AL+           +P++ K R+    +  A 
Sbjct: 131 KFSVDNGMGAALMRDTSKAASILFALDDALNAPDKLAARGRRVPLSFKTRLLETAEATAD 190

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIG 192
            L ++++ +  + VN I +HAR             +      + V  ++      ++   
Sbjct: 191 MLISIMEKVGANRVNAITLHARTVNQVAEDSPHYDRAA----EAVRRLRSHPLFKEMCFV 246

Query: 193 LNGGLEDMSQ-ALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKT 245
           LNG +      A+K+     D VMI R A  + ++ +                  +P+ +
Sbjct: 247 LNGSVRSRDDGAVKMAQFGFDAVMIARHAMWDMSVFSRHVSSAGRRSSLSSEDAEAPLAS 306

Query: 246 RVDKDFWRKISASMTDYA------ARHLHSGGKLQQITRHMI 281
               D +R +  +   Y         HL          RH++
Sbjct: 307 TSWMDLYRALLRTHAKYCTPFTYVKYHLTRSIPCIPALRHLM 348


>gi|257075749|ref|ZP_05570110.1| dihydroorotate dehydrogenase 1B [Ferroplasma acidarmanus fer1]
          Length = 298

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 48/199 (24%), Positives = 85/199 (42%), Gaps = 16/199 (8%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           ++  +    + I   ++  KP+   I G    +    A+ ++ +G + + LN+ CP    
Sbjct: 72  SNPGIENYGQEIKIATSSGKPVIGSIFGQTPEEFAMLAEKMQAYGASAVELNLSCP---- 127

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN------LVKS 142
           H   +G  +  +P++V   ++A+   ++IPV  K      D +             L+ +
Sbjct: 128 HVKGYGTEIGSDPELVSAIVSAVKSRINIPVYAKLSPNTSDMLGQAIAAGKADGYVLINT 187

Query: 143 IKKSGVNGIWIHA-RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           IK   ++     A    I  GLS K    I  +    VYE+KKE     IG+ GG+ +  
Sbjct: 188 IKAMKIDINTGKAVLSNIYGGLSGK---SIKPVGIRYVYEVKKETGKTIIGV-GGINNFE 243

Query: 202 QALK-ILPSVDGVMIGRAA 219
            AL+ I+     V IG A 
Sbjct: 244 DALEYIMAGASAVQIGSAI 262


>gi|283768233|ref|ZP_06341146.1| conserved domain protein [Bulleidia extructa W1219]
 gi|283105110|gb|EFC06481.1| conserved domain protein [Bulleidia extructa W1219]
          Length = 111

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 45/89 (50%), Gaps = 4/89 (4%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              ++  YR   R  +   L+ +EMI   A+    +K   +     +E P++LQ+ G+D 
Sbjct: 22  AGISNPVYRSLMRQ-SGAGLVVSEMISDKALHYKSEKTFKMCETVEEEHPVSLQLFGSDP 80

Query: 60  SKLVEAAKIVEDF-GYNEINLNVGCPSAR 87
             + EAA+ + +    + I++N+GCP  +
Sbjct: 81  DTMAEAAEYLNEHSNCDVIDINMGCPVQK 109


>gi|68491772|ref|XP_710328.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
 gi|68491789|ref|XP_710320.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
 gi|46431504|gb|EAK91057.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
 gi|46431513|gb|EAK91065.1| possible tRNA dihydrouridine synthase fragment [Candida albicans
           SC5314]
          Length = 487

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 42/184 (22%), Positives = 78/184 (42%), Gaps = 18/184 (9%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
           +  YR   + L    + Y+EM ++  +++G      +      E P   +QI  +     
Sbjct: 313 NLPYRRLMKTL-GADVTYSEMALSVPLIQGHNPEWALPKAHVSEYPGFGVQIASSKHWAA 371

Query: 63  VEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPV 119
            +AA+ +       +E+NLN GCP   +++   G+ L+  P  +   ++ M   +  IPV
Sbjct: 372 AKAAEAIYRNTTHVSELNLNCGCPIDLLYKQGQGSALLDQPSKLLRILSGMNASSGDIPV 431

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           TVK R G+ +        NLV  + + G    I +H R         +  R     D++ 
Sbjct: 432 TVKIRTGIKEGKNTAV--NLVSRVLEEGNAAAITLHGRS--------RQQRYSKEADWNY 481

Query: 179 VYEI 182
           + E+
Sbjct: 482 IAEV 485


>gi|167381618|ref|XP_001735786.1| tRNA-dihydrouridine synthase [Entamoeba dispar SAW760]
 gi|165902070|gb|EDR27991.1| tRNA-dihydrouridine synthase, putative [Entamoeba dispar SAW760]
          Length = 366

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 107/247 (43%), Gaps = 43/247 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-----------AILRGDKKN--ILGFSTQE 47
           MV      YR  A L      ++TE +V+             +++   KN  +L    ++
Sbjct: 32  MVGICTVSYRTMA-LDAGANAVFTEELVSKRLCECKRVENSGLIQYIHKNDVMLTLKPEQ 90

Query: 48  KP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +    LQ+G  D+   ++   ++++     I++N+GC      +G  G  L+ N D +  
Sbjct: 91  QSKTILQLGTFDVESSIKCVSLIKE--VCGIDINLGCGMWFSTKGEMGQALVSNRDKLEK 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+ K L  P++ K R+    Q         ++ +   G++ I +H R          
Sbjct: 149 IVKALVK-LGKPISAKIRL----QQTHEETLEFIQWLYSLGISIISLHGR---------- 193

Query: 167 DNRKIPNLDYDIVYEIKKENPDLF--IGLNGGL---EDMSQALKILPSVDGVMIGRAA-- 219
            ++++  +D D V E++K   D    + LNG +   ED+++ L    +V GVMIGRA+  
Sbjct: 194 HHKELYGVDCDWV-ELEKVVKDCPYDLILNGDICKQEDITKLLSFGKNVRGVMIGRASGI 252

Query: 220 ---YKNS 223
                N 
Sbjct: 253 HLGLFNP 259


>gi|71404581|ref|XP_804984.1| dihydrouridine synthase [Trypanosoma cruzi strain CL Brener]
 gi|70868213|gb|EAN83133.1| dihydrouridine synthase, putative [Trypanosoma cruzi]
          Length = 430

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 60/342 (17%), Positives = 121/342 (35%), Gaps = 67/342 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----------------------- 37
           MV   +  +R F        +++TE IVA  + R  +                       
Sbjct: 13  MVRVGNVGFRVFC-AAQGADVVFTEEIVAAKLARCHREVRVHNDAAGPMIEFVAYELFKN 71

Query: 38  ------------KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
                       +++   S +  P+ LQ+G +D +  V AA +  +   + I++N+GCP 
Sbjct: 72  QYKRSVVFTTPARDMANQSGEGAPVVLQLGVSDAAVGVAAALLCCE-DVDGIDVNMGCPK 130

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAV 134
               +   GA LM +       + A+  AL+           +P++ K R+    +  A 
Sbjct: 131 KFSVDNGMGAALMRDTSKAASILFALDDALNAPDKLAARGRRVPLSFKIRLLETAEATAD 190

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIG 192
            L ++++ +  + V+ I +HAR             +      + V  ++      ++   
Sbjct: 191 MLISIMEKVGANRVHAITLHARTVNQVAEDSPHYDRAA----EAVRRLRSHPLFKEMCFV 246

Query: 193 LNGGLEDMSQ-ALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKT 245
           LNG +      A+K+     D +MI R A  + ++ +                  +P+ +
Sbjct: 247 LNGSVRSRDDGAVKMAQFGFDAIMIARHAMWDMSVFSRHVSSAGGRSSLTSEDAEAPLAS 306

Query: 246 RVDKDFWRKISASMTDYA------ARHLHSGGKLQQITRHMI 281
               D +R +  +   Y         HL          RH++
Sbjct: 307 TSWMDLYRSLLRTHAKYCTPFTYVKYHLTRSIPCIPALRHLM 348


>gi|15668835|ref|NP_247638.1| dihydroorotate dehydrogenase 1B [Methanocaldococcus jannaschii DSM
           2661]
 gi|2500041|sp|Q58070|PYRD_METJA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|1591367|gb|AAB98649.1| dihydroorotase dehydrogenase (pyrD) [Methanocaldococcus jannaschii
           DSM 2661]
          Length = 306

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 56/210 (26%), Positives = 89/210 (42%), Gaps = 33/210 (15%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D  L   +K     +  +  +   I G D  +  E AK +E +  + I LN+ CP A+  
Sbjct: 81  DEYLEEIEKVRDELNRMDVRIIGSIYGKDEEEFAEVAKKMERY-VDIIELNISCPHAK-- 137

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              +GA +  NPD+  D   A+ KA+ IPV  K    V D      +  + +++  +GV+
Sbjct: 138 --GYGATIGQNPDLSYDVCKAVKKAVKIPVFAKLTPNVTD------IIEIAQAVVDAGVD 189

Query: 150 -----------GIWIHARKAIL----KGLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGL 193
                       I I A+K IL     GLS K  + I   + +D+      EN D+ I  
Sbjct: 190 GLVAINTVRGMAIDIRAKKPILANKFGGLSGKAIKSIGIKVVWDLY-----ENFDVPIIG 244

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
            GG+     A++ ++     V IG   Y  
Sbjct: 245 VGGIMSGEDAIEYMMAGASAVQIGSGVYYR 274


>gi|312137365|ref|YP_004004702.1| dihydroorotate oxidase b, catalytic subunit [Methanothermus
           fervidus DSM 2088]
 gi|311225084|gb|ADP77940.1| dihydroorotate oxidase B, catalytic subunit [Methanothermus
           fervidus DSM 2088]
          Length = 301

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 44/196 (22%), Positives = 76/196 (38%), Gaps = 26/196 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I G+   +  E +K V D   + I +NV CP A      +G+ +  +P +  + +
Sbjct: 92  PIIASIAGSSPKEFAEVSKEVSDL-VDMIEINVSCPHA---GEGYGSFIGQDPKLTYEVV 147

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHAR 156
            A+ KA+++PV+VK    V D      +  +  + KK G + +             I   
Sbjct: 148 KAVKKAVNLPVSVKLTANVAD------IVEIAINAKKGGCDALTLINSVGPGMKIDIKTA 201

Query: 157 KAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K +L           I  +    VYEI  EN ++ I   GG+      ++ L      V 
Sbjct: 202 KPVLSNRFGGLSGPAIKPIAIRCVYEIY-ENMEIPIIGVGGITTYKDVIEFLYAGARAVQ 260

Query: 215 IGRAAYKN-SAMLTTV 229
           IG         +   +
Sbjct: 261 IGTGILYKGVNIFQDI 276


>gi|167520832|ref|XP_001744755.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163777086|gb|EDQ90704.1| predicted protein [Monosiga brevicollis MX1]
          Length = 267

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 40/210 (19%), Positives = 75/210 (35%), Gaps = 15/210 (7%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-EKPLALQIGGADIS 60
           V  +D  +R         A  ++ M+ A   +       L   TQ  + + +Q    +  
Sbjct: 38  VGGSDLAFRTMCYERGVVA-AFSPMLYARHAVENPNYLNLNLDTQPAENVIVQFCANNGD 96

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
               A   V       ++LN+   S R   G +G  L+ NP  +   + A   A  +P+T
Sbjct: 97  FFARAIDKV-RLRCRGVDLNLSWTSKRAERGGYGEYLLKNPTQLESVVRAGV-ATQVPIT 154

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K R+    Q          + ++  GV+ + I  R       S + + +    +++ + 
Sbjct: 155 CKLRL----QASVAETIATAQRLEAWGVSLLTIEGRT------SAQLDSRRGIANWEDIA 204

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPSV 210
           +I+     + I  NG L    Q    L   
Sbjct: 205 QIRAAVG-IPILYNGDLVVREQIEACLAYT 233


>gi|322701572|gb|EFY93321.1| Dihydrouridine synthase [Metarhizium acridum CQMa 102]
          Length = 354

 Score = 96.8 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 46/272 (16%), Positives = 84/272 (30%), Gaps = 60/272 (22%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ----EKPLALQIGGADISKL 62
             +R          L +T MI+A    R +       +      + P  LQ G  +  +L
Sbjct: 7   LAFRQTVHQY-GTDLCWTPMILAKEFNRSEFARDSDLTISTTAAQPPTILQFGANNPLEL 65

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK--------- 113
             A+ +   F  + ++LN GCP +     + GA LM    +V D +    +         
Sbjct: 66  ARASSLAAPF-VSGVDLNCGCPQSWACAETLGAALMDQRALVRDMVTETRQRLRQDGWAV 124

Query: 114 --------ALSIPVTVKCRIGVDDQIPAVA-----LRNLVKSIKKSG----VNGIWIHAR 156
                   A    V+VK R+  D +    A       + ++++        V+ + IH R
Sbjct: 125 AAESDMESASGRSVSVKIRVHDDLRPANAAETQRKTIDFLETVIGHPQFRNVDWVTIHPR 184

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM---------------- 200
                  +P     +  L       +        + L+G + D+                
Sbjct: 185 TRHTPSTTPIFTEALEILTQRYAATL-------PLLLSGDVFDLSALPIRSTKPLDLSTL 237

Query: 201 -----SQALKILPSVDGVMIGRAAYKNSAMLT 227
                +        + G M  R    N A+  
Sbjct: 238 TVKDEATPRPSTTHLSGFMSARGLLANPALFA 269


>gi|48477247|ref|YP_022953.1| dihydroorotate dehydrogenase 1B [Picrophilus torridus DSM 9790]
 gi|48429895|gb|AAT42760.1| dihydroorotate dehydrogenase [Picrophilus torridus DSM 9790]
          Length = 297

 Score = 96.4 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 76/189 (40%), Gaps = 11/189 (5%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
              +   I G         AK +ED+G   + LN+ CP  +     FG  +  +  +V  
Sbjct: 89  GSNVIGSIFGTGPEDFSYLAKRMEDYGAIAVELNLSCPHVK----GFGLEVGSDSGLVES 144

Query: 107 CIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKG- 162
            ++ +   ++IPV  K      D   +  A    + +  I       I I+AR  +L   
Sbjct: 145 IVSEVKSKVNIPVFAKLSPNTHDILEEARAAEKADALVLINTLKAMKIDINARMPVLSNI 204

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                 R I  +    VYE+ +E     IG+ GG+E+   A++ I+     V IG   Y+
Sbjct: 205 YGGLSGRSIKPVGIRYVYEVSRELKIPVIGV-GGIENYEDAIEYIMAGASAVEIGTGIYR 263

Query: 222 N-SAMLTTV 229
           +   + + +
Sbjct: 264 HGKKIFSEI 272


>gi|322828000|gb|EFZ31960.1| dihydrouridine synthase, putative [Trypanosoma cruzi]
          Length = 430

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 58/342 (16%), Positives = 121/342 (35%), Gaps = 67/342 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDK----------------------- 37
           MV   +  +R F        +++TE +VA  + R  +                       
Sbjct: 13  MVRVGNVGFRVFC-AAQGADVVFTEEVVAAKLARCHREVRVHNDAAGPMIEFVAYELFKN 71

Query: 38  ------------KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
                       +++   S +  P+ LQ+G +D +  V AA +  +   + I++N+GCP 
Sbjct: 72  QYKRSVVFTTPARDMANQSGEGAPVVLQLGVSDAAVGVAAALLCCE-DVDGIDVNMGCPK 130

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----------IPVTVKCRIGVDDQIPAV 134
               +   GA LM +       + ++  AL+           +P++ K R+    +  A 
Sbjct: 131 KFSVDNGMGAALMRDTSKAASILFSLDDALNSPDKLAARGRRVPLSFKIRLLETAEATAD 190

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIG 192
            L ++++ +  + V+ I +HAR             +      + V  ++      ++   
Sbjct: 191 MLISIMEKVGANRVHAITLHARTVNQVAEDSPHYDRAA----EAVRRLRSHPLFKEMCFV 246

Query: 193 LNGGLEDMSQ-ALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKT 245
           LNG +      A+K+     D +MI R A  + ++ +                  +P+ +
Sbjct: 247 LNGSVRSRDDGAVKMAQFGFDAIMIARHAMWDMSVFSRHVSSAGGRSSLSSEDAEAPLAS 306

Query: 246 RVDKDFWRKISASMTDYA------ARHLHSGGKLQQITRHMI 281
               D +R +  +   Y         HL          RH++
Sbjct: 307 TSWMDLYRSLLRTHAKYCTPFTYVKYHLTRSIPCIPALRHLM 348


>gi|312796562|ref|YP_004029484.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
 gi|312168337|emb|CBW75340.1| NIFR3-like protein [Burkholderia rhizoxinica HKI 454]
          Length = 150

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 34/116 (29%), Positives = 52/116 (44%), Gaps = 9/116 (7%)

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           A + L  VDGVMIGR AY N  +L  VD  F  P   +             ++  +M +Y
Sbjct: 28  AHEHLHHVDGVMIGREAYHNPFLLADVDRRFYEPSALAR---------TRGEVEQAMIEY 78

Query: 263 AARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
                  G  +  +TRHM+GL+   P +R  R +L+     +T    I + A  ++
Sbjct: 79  IGAEQARGTYIGAVTRHMLGLYRDQPGARGWRRVLSDHRKLATGDSRIFDEARAML 134


>gi|196250796|ref|ZP_03149483.1| transcriptional regulator involved in nitrogen regulation,
           NifR3/Smm1 family [Geobacillus sp. G11MC16]
 gi|196209746|gb|EDY04518.1| transcriptional regulator involved in nitrogen regulation,
           NifR3/Smm1 family [Geobacillus sp. G11MC16]
          Length = 111

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 24/111 (21%), Positives = 42/111 (37%), Gaps = 8/111 (7%)

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
                 D++I+ ++K E  ++ +  NG ++    A ++L    VDGVMIGRAA  N  M+
Sbjct: 1   MYEGKADWNIIKQVK-EAVNIPVIGNGDVKTPQDAKRMLEETGVDGVMIGRAALGNPWMI 59

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                Y         P  T         +     D           ++++ 
Sbjct: 60  YRTVHYLETGELIPEPTPTEKI-----DVCLLHLDRLIALKGEYIAVKEMR 105


>gi|153814602|ref|ZP_01967270.1| hypothetical protein RUMTOR_00816 [Ruminococcus torques ATCC 27756]
 gi|145848096|gb|EDK25014.1| hypothetical protein RUMTOR_00816 [Ruminococcus torques ATCC 27756]
          Length = 211

 Score = 96.0 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 37/138 (26%), Positives = 56/138 (40%), Gaps = 3/138 (2%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +KK+IL    +      QI        V+ AK +E +GY EINLNVGCPS  V     GA
Sbjct: 47  EKKDILPEHNKGMHAVPQILTNCAEDFVQTAKKLEQYGYKEINLNVGCPSKTVVTKGRGA 106

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +  P+ +   +  + +   I ++VK RIG            L+    K  +  + IH 
Sbjct: 107 GFLAFPERLDLFLEEVFQNCPIDISVKTRIG---TESGEEFPKLMDIYNKYPIKELIIHP 163

Query: 156 RKAILKGLSPKDNRKIPN 173
           R         +    +  
Sbjct: 164 RTQKDFYKIFRIWMCLKK 181


>gi|302406498|ref|XP_003001085.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
 gi|261360343|gb|EEY22771.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
          Length = 325

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 60/148 (40%), Gaps = 15/148 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P     +G +GA L  + D+V   +  + + LSIPVT K RI         A      ++
Sbjct: 56  PQGIARKGHYGAFLQEDQDLVFRLVNTLHRNLSIPVTAKIRIL----DTREATLAYALNV 111

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLE---D 199
            ++G + + +H R+   KG            D+  +  ++ +  P+  +  NG +    D
Sbjct: 112 LRAGASILTVHGRRREQKG------HLTGLADWSTIRWLRDQLPPETVLFANGNILEHGD 165

Query: 200 MSQALKILPSVDGVMIGRAAYKNSAMLT 227
           +++ L+     D VM       +  +  
Sbjct: 166 LAKCLEA-TGADAVMSAEGNLSDPGLFA 192


>gi|294496112|ref|YP_003542605.1| dihydroorotate oxidase B, catalytic subunit [Methanohalophilus
           mahii DSM 5219]
 gi|292667111|gb|ADE36960.1| dihydroorotate oxidase B, catalytic subunit [Methanohalophilus
           mahii DSM 5219]
          Length = 299

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 46/204 (22%), Positives = 83/204 (40%), Gaps = 24/204 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   I G D ++  E A  +     +   LNV CP A      +GA +  +PD+V +
Sbjct: 88  DAPLIASIFGGDAAEFTEVANGLLSSKPDCFELNVSCPHAE----GYGASVGTDPDLVHE 143

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
             A++  A+ +PV VK    V D         + ++ + +G +            I IH+
Sbjct: 144 ITASVVDAVDVPVWVKLTPNVTDITS------IGRAAESAGASAVVAINTVRGMAIDIHS 197

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
              IL           +  +    VY++  E  D+ +   GG+     A+++ L     V
Sbjct: 198 GYPILGNRFGGLSGPAVKPVAVKCVYDLY-EALDIPVIGVGGITCPQDAIEMILAGASAV 256

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPL 237
            IG A + ++ +  T+ +     L
Sbjct: 257 EIGSAVHDDTQIFETISKGIDTYL 280


>gi|289192997|ref|YP_003458938.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus sp.
           FS406-22]
 gi|288939447|gb|ADC70202.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus sp.
           FS406-22]
          Length = 302

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 50/206 (24%), Positives = 86/206 (41%), Gaps = 25/206 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D  L   KK     +  +  +   + G +  +  E AK +E +  + I LN+ CP A+  
Sbjct: 77  DEYLEEIKKVRDELNRMDVKIIGSVYGKNEEEFAEVAKRMEKY-VDIIELNISCPHAK-- 133

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              +GA +  NPD+      A+ KA+ +PV  K    V D      +  + +++  +GV+
Sbjct: 134 --GYGATIGQNPDLSYSVCKAVKKAVKVPVFAKLTPNVTD------IVEIAQAVVDAGVD 185

Query: 150 -----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                       I I A+K IL         R I  +   +V+++  EN D+ I   GG+
Sbjct: 186 GLVAINTVRGMAIDIKAKKPILGNKFGGLSGRAIKPIGIKVVWDLY-ENFDVPIIGVGGI 244

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKN 222
                A++ ++     V IG   Y  
Sbjct: 245 MSGEDAIEYMMAGASAVQIGSGVYYR 270


>gi|316968258|gb|EFV52559.1| dihydrouridine synthase (Dus) superfamily [Trichinella spiralis]
          Length = 355

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 36/128 (28%), Positives = 58/128 (45%), Gaps = 8/128 (6%)

Query: 26  MIVADAILRGD--KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           M+ A   L  +  +K       +++PL  Q    +   L  AA +V +   + I++N+GC
Sbjct: 1   MLHAGNFLTDELYRKTHFTTCPEDRPLIAQFCANEPETLFNAASLVANQ-CDAIDINLGC 59

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P      G +GA L  + D+V   I + C+ L IPVT K RI  + +          + I
Sbjct: 60  PQTIARRGKYGAYLQDDWDLVSSLIKSACR-LPIPVTCKIRIFPEVRRTV----EYAQMI 114

Query: 144 KKSGVNGI 151
           + SG   I
Sbjct: 115 QASGCTEI 122


>gi|303243957|ref|ZP_07330296.1| dihydroorotate dehydrogenase family protein [Methanothermococcus
           okinawensis IH1]
 gi|302485609|gb|EFL48534.1| dihydroorotate dehydrogenase family protein [Methanothermococcus
           okinawensis IH1]
          Length = 304

 Score = 94.9 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 48/198 (24%), Positives = 79/198 (39%), Gaps = 26/198 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  L   I G D  +  E A+I+E +    I LN+ CP A    G +GA +  NPD+   
Sbjct: 94  DTKLIGSIYGKDQKEFSEVAEIIEPY-VELIELNISCPHA---GGGYGAQIGQNPDLSYK 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IH 154
            ++A+  A++IPV  K    V D      ++ + K++ ++G +GI             I 
Sbjct: 150 VVSAVKDAVNIPVIAKLTPNVVD------IKEIAKTVVEAGADGITAINTLGPGMVIDIE 203

Query: 155 ARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDG 212
            +K IL           I  +    VY+I     D+ I   GG+         +L     
Sbjct: 204 TQKPILGNRFGGMSGPAIKPIAIKNVYDIY-SVVDVPIIGVGGITTGYDVIEFMLAGAQA 262

Query: 213 VMIGRAAYKNSA-MLTTV 229
           V +G   Y     +   +
Sbjct: 263 VQVGTGIYYRGYDIFNKI 280


>gi|221127160|ref|XP_002167936.1| PREDICTED: similar to predicted protein, partial [Hydra
           magnipapillata]
          Length = 156

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 37/142 (26%), Positives = 59/142 (41%), Gaps = 19/142 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MI-----------VADAILRGDKKNILGF 43
           MV      +R  A       ++YTE      MI             D +L          
Sbjct: 14  MVRIGTLPFRLLALRY-GADIVYTEEIIDYKMIECKRIENKLLDTTDFLLADGTVVFRTC 72

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             ++  L  Q+G  +  + +  A+++E    + I++N+GCP     +G  GA L+  PD 
Sbjct: 73  KEEKGKLVFQMGTNNAERALSVAQMLEK-DIDGIDINMGCPKEFSVKGGMGAALLTQPDK 131

Query: 104 VGDCIAAMCKALSIPVTVKCRI 125
           V   +  + + LSIPVT K RI
Sbjct: 132 VKQILTGLVQNLSIPVTCKIRI 153


>gi|76156838|gb|AAX27956.2| SJCHGC08364 protein [Schistosoma japonicum]
          Length = 170

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 35/141 (24%), Positives = 61/141 (43%), Gaps = 17/141 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI----------------VADAILRGDKKNILGFS 44
           MV  +    R        + ++  E+I                  D IL          +
Sbjct: 31  MVRVSTHPMRLLCLEYGADYVISEELIDQRVIRSSRIANDELNTVDFILPDGSVTFRTSA 90

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            ++  + +Q+G ++    ++AAK++E+     I++N+GCP A   +G  GA L+  PD V
Sbjct: 91  EEKNRVIVQLGTSNPETALKAAKVLEN-DVMAIDVNMGCPKAYSVKGGMGAALLTKPDTV 149

Query: 105 GDCIAAMCKALSIPVTVKCRI 125
            + +  +   L IPVT K RI
Sbjct: 150 KEILTTLTTNLRIPVTCKMRI 170


>gi|198427128|ref|XP_002120497.1| PREDICTED: similar to tRNA-dihydrouridine synthase 2-like (hDUS2)
           (Up-regulated in lung cancer) (URLC8) [Ciona
           intestinalis]
          Length = 482

 Score = 94.1 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 93/246 (37%), Gaps = 33/246 (13%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEK---PLALQIGGA 57
           MV       R  A L     ++Y+E I+    +R  +   +   T E       L I  +
Sbjct: 67  MVRIGRLPTRLLA-LKYGADIVYSEEIIDHRFIRCKRYVNVKIDTTESRKWNYKLYIFAS 125

Query: 58  DISKLVEAAKIVEDFGYNEINLNVG-------CPSAR----VHEGSFGACLMLNPDIVGD 106
             +   + +  ++  G  +  L+         C   +    +  G  GA L+  P+ V +
Sbjct: 126 VPNLHGKHSLPLDALGTIDFILDTDSRPLFRTCKHEKEKVVLQLGGMGAALITQPENVKE 185

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +  +   LSIPVT K RI  +          LV+ I+ +GV  + +H R         K
Sbjct: 186 ILTTLVNGLSIPVTCKIRILPEIDKT----LELVRIIESTGVAALAVHGR--------YK 233

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-----LKILPSVDGVMIGRAAYK 221
             R    +  D++  I  E   + +  NGG  +++        +   +   VM+ R+A  
Sbjct: 234 HERPRHPVHCDVIKAI-TETVKIPVIANGGSSNIACYDDIEKFRASTNASSVMLARSAQW 292

Query: 222 NSAMLT 227
           N ++  
Sbjct: 293 NCSVFR 298


>gi|304315343|ref|YP_003850490.1| dihydroorotate dehydrogenase [Methanothermobacter marburgensis str.
           Marburg]
 gi|302588802|gb|ADL59177.1| predicted dihydroorotate dehydrogenase [Methanothermobacter
           marburgensis str. Marburg]
          Length = 302

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 44/213 (20%), Positives = 79/213 (37%), Gaps = 26/213 (12%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            K  L     + PL   I G+   +    A  VED+  + I LNV CP A       GA 
Sbjct: 79  FKEELRGVDDDVPLIASIYGSSPEEFARVAASVEDY-VDMIELNVSCPHAMA---GCGAS 134

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---- 152
           +  +  +    ++A+  A+ +PV+ K    V D      +  + KS + +G + +     
Sbjct: 135 IGQDAGLTFRVVSAVKDAVGVPVSTKLTPNVTD------IVEIAKSAEDAGSDALTLINS 188

Query: 153 --------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                   I   K +L           I  +    VY++ + + ++ I   GG+ D   A
Sbjct: 189 LGPGMKIDIKTAKPVLSNAFGGMSGPAIKPVAVRCVYDVYR-SVEIPIIGAGGVRDFRDA 247

Query: 204 LKIL-PSVDGVMIGRAAYKN-SAMLTTVDEYFS 234
           ++ L      V +G A   +   +   +     
Sbjct: 248 VEFLFAGAVAVQVGTAIMYDGPEIFMGICRGLE 280


>gi|13542001|ref|NP_111689.1| dihydroorotate dehydrogenase 1B [Thermoplasma volcanium GSS1]
 gi|30173362|sp|Q979G6|PYRD_THEVO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|14325433|dbj|BAB60337.1| dihydroorotate oxidase [Thermoplasma volcanium GSS1]
          Length = 301

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 44/194 (22%), Positives = 80/194 (41%), Gaps = 11/194 (5%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +P+   +   +  +  + +  +E++G + I LN+ CP  +     FG  +  +PD+V D 
Sbjct: 93  RPIIGSVFAYNAEEFTKLSVKMEEYGVDAIELNLSCPHVK----GFGLEVGSDPDLVEDI 148

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS---IKKSGVNGIWIHARKAILKGL- 163
           +  +   + +PV  K    V + I          +   I       I I++R  +L  L 
Sbjct: 149 VNEIKSKVKVPVFAKLSPNVSNIIEIAKAAEKADAYVLINTVKAMAIDIYSRSPVLSNLY 208

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
                  I  +    VYE+KKE     IG+ GG+ +   A++ I+     V IG A YK 
Sbjct: 209 GGLSGPAIKPVGIRYVYEVKKETGKEIIGV-GGISNYKDAIEYIMAGASAVQIGTALYKY 267

Query: 223 -SAMLTTVDEYFSN 235
              +   ++     
Sbjct: 268 GKGIFREMEWQLRT 281


>gi|194390922|dbj|BAG60579.1| unnamed protein product [Homo sapiens]
          Length = 336

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 28/174 (16%), Positives = 61/174 (35%), Gaps = 24/174 (13%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           +   +    + LS+PVT K R+  +            + ++K+G   + +H R    KG 
Sbjct: 2   IAKRVLLAHEKLSVPVTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG- 56

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                       ++ +  ++K    + +  NG ++ +    + L    V GVM       
Sbjct: 57  -----PLSGAASWEHIKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLH 110

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
           N A+             G SP    + +++   +   +       L    +L++
Sbjct: 111 NPALF-----------EGRSPAVWELAEEYLDIVREHLFKLWHHTLQVHQELRE 153


>gi|161485673|ref|NP_633769.2| dihydroorotate dehydrogenase 1B [Methanosarcina mazei Go1]
          Length = 301

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 73/198 (36%), Gaps = 22/198 (11%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
              + P+   I G   S+  E A+ +     +   LNV CP A      +GA +  NP +
Sbjct: 87  ENSDAPVIASIFGGTPSEFAEVAEGLLPAKPDAFELNVSCPHAE----GYGAAIGSNPCL 142

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI 159
           V    AA+   +++PV VK    V D      +  +  + +  G + +     +      
Sbjct: 143 VEAVTAAVKDVVNVPVWVKLTPNVAD------ITCIGNAAESGGADAVVAINTVKGMAID 196

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKI-LPSVD 211
           ++   P    +   L    V  +  +         ++ +   GG+     A+++ +    
Sbjct: 197 IESGYPVLGNRSGGLSGKAVKPVAVKCVYDLFTALEIPVIGVGGVSSWEDAVEMIMAGAA 256

Query: 212 GVMIGRAAYKNSAMLTTV 229
            V +G A Y    + + +
Sbjct: 257 AVQVGSAVYDRVGIFSEI 274


>gi|288871174|ref|ZP_06116619.2| dihydrouridine synthase family protein [Clostridium hathewayi DSM
           13479]
 gi|288864521|gb|EFC96819.1| dihydrouridine synthase family protein [Clostridium hathewayi DSM
           13479]
          Length = 192

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 45/204 (22%), Positives = 74/204 (36%), Gaps = 16/204 (7%)

Query: 1   MVDWTDRHYR-FFARLLTNNALLYTEMIVADAILR---GDKKNILGFSTQEKPLALQIGG 56
           M   T   YR     L  +  L  T  +  +   R    ++ +IL    +   L  QI  
Sbjct: 1   MEGITGYVYRNAHHALFPHVDLYVTPFLQPNQNHRFSSRERNDILPEHNKGITLIPQILT 60

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                 +  A  +E  GY+E+NLN+GCPS  V     GA  +   + +   +  +C  + 
Sbjct: 61  NRAEDFIWMAGELEALGYDEVNLNLGCPSGTVVSKYKGAGFLAKKEELDAFLDEVCSGIR 120

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           I ++VK R+G+           L++   K  +  + IH R       +  D         
Sbjct: 121 IRLSVKTRLGM---ASPDEFEELLEIYNKYPLKELIIHPRVRSDFYKNTPDRAAFCRA-- 175

Query: 177 DIVYEIKKENPDLFIGLNGGLEDM 200
             V   K E     +  NG +   
Sbjct: 176 --VKASKNE-----VWYNGDIFTA 192


>gi|241171154|ref|XP_002410603.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
 gi|215494872|gb|EEC04513.1| tRNA-dihydrouridine synthase, putative [Ixodes scapularis]
          Length = 214

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 38/190 (20%), Positives = 76/190 (40%), Gaps = 30/190 (15%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            +GA L+ +P++V D +      LS P   V+VK RI  D +       ++ + ++ + V
Sbjct: 4   GYGAHLLSDPELVRDMVHQTRNRLSDPGFTVSVKIRICEDMRKTV----DMCQKLEAARV 59

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + + +H R         KD R  P ++ + +  +K +   + +  NG +  + +A ++  
Sbjct: 60  SFVTVHGRT--------KDQRSEP-VNLEAIKNVK-DALRIPVVANGDVTSLREADRVYR 109

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
               +GVM  R   +N AM    +                  +D+    +      A  H
Sbjct: 110 ATGTNGVMAARGLLENPAMFQGTEH-----------TPASCVRDWLWLSTQLGCPLAQFH 158

Query: 267 LHSGGKLQQI 276
            H    L+ +
Sbjct: 159 HHLMFMLEHV 168


>gi|30173323|sp|Q8PW56|PYRD_METMA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|20906259|gb|AAM31441.1| Dihydroorotate dehydrogenase [Methanosarcina mazei Go1]
          Length = 314

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 73/198 (36%), Gaps = 22/198 (11%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
              + P+   I G   S+  E A+ +     +   LNV CP A      +GA +  NP +
Sbjct: 100 ENSDAPVIASIFGGTPSEFAEVAEGLLPAKPDAFELNVSCPHAE----GYGAAIGSNPCL 155

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI 159
           V    AA+   +++PV VK    V D      +  +  + +  G + +     +      
Sbjct: 156 VEAVTAAVKDVVNVPVWVKLTPNVAD------ITCIGNAAESGGADAVVAINTVKGMAID 209

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKI-LPSVD 211
           ++   P    +   L    V  +  +         ++ +   GG+     A+++ +    
Sbjct: 210 IESGYPVLGNRSGGLSGKAVKPVAVKCVYDLFTALEIPVIGVGGVSSWEDAVEMIMAGAA 269

Query: 212 GVMIGRAAYKNSAMLTTV 229
            V +G A Y    + + +
Sbjct: 270 AVQVGSAVYDRVGIFSEI 287


>gi|14520860|ref|NP_126335.1| dihydroorotate dehydrogenase 1B [Pyrococcus abyssi GE5]
 gi|9297056|sp|Q9V0Y6|PYRD_PYRAB RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|5458077|emb|CAB49566.1| pyrD dihydroorotase dehydrogenase [Pyrococcus abyssi GE5]
          Length = 303

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 85/231 (36%), Gaps = 29/231 (12%)

Query: 27  IVADAILRGDKKNILGFSTQEK---PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     +  L    +EK   P+ + I G    +    A+ + +   +   LN+ C
Sbjct: 70  INAMGLPNPGWEAFLEEFRKEKFDFPVIVSIFGGTPEEFAFLAEKLGEV-ADAFELNLSC 128

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P A+     +G  +   P+ V + + A+      PV  K    V D      +R L  + 
Sbjct: 129 PHAK----GYGMEIGQKPENVYEVVKAVKDVTDKPVIAKLTPNVSD------IRELGLAA 178

Query: 144 KKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           +K+G +            I I+A++ IL           +  +    VY++     D+ +
Sbjct: 179 EKAGADGVSAINTVKAIAIDIYAKRPILSNKFGGYSGPGVKPIALRAVYDLASSL-DIPV 237

Query: 192 GLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGS 240
              GG+     A++ +L     + IG A Y     +   + E  S  L   
Sbjct: 238 IGIGGITTWQDAVEFLLAGASALQIGTAVYLRGFSVFREIAEGISRYLKEE 288


>gi|258617180|ref|ZP_05714950.1| dihydrouridine synthase family protein [Enterococcus faecium DO]
          Length = 203

 Score = 93.0 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 47/213 (22%), Positives = 76/213 (35%), Gaps = 26/213 (12%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               I A  KA  +PV+VK RIG  +      +   +  +    +  + +H R       
Sbjct: 2   AAQLIEA-AKAGGLPVSVKTRIGYTEMS---EMEEWISHLLHQDIANLSVHLRTRKEMSK 57

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
                  IP     I+    +  P   I +NG + D     ++     VDG+MIGR  +K
Sbjct: 58  VDAHWEVIPK----IIALRDQIAPQTLITINGDIPDRQTGEELAEKYGVDGIMIGRGIFK 113

Query: 222 NSAML-TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
           N         E+    L G   ++  +   +   I  S+T      LH   K+       
Sbjct: 114 NPYAFEKDPREHTEKELIGLLRLQLDLQDHYSEIIPRSIT-----GLHRFFKI------- 161

Query: 281 IGLFHGFPNSRRCRHILTVEAGASTATHHIIET 313
                GFP +   R  L +   ++     I+ET
Sbjct: 162 --YIKGFPGANDLRVQL-MNTKSTDEVREILET 191


>gi|91773205|ref|YP_565897.1| dihydroorotate dehydrogenase 1B [Methanococcoides burtonii DSM
           6242]
 gi|91712220|gb|ABE52147.1| Dihydroorotate dehydrogenase, catalytic subunit [Methanococcoides
           burtonii DSM 6242]
          Length = 300

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 77/199 (38%), Gaps = 22/199 (11%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            S  + P+   I G +    V+ A+ + D       LNV CP A      +GA +  +  
Sbjct: 85  RSGTDVPVIASIFGGNAEDFVKVAEGLADSEPAAFELNVSCPHAE----GYGATIGTDTC 140

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKA 158
           +V    AA+C A+ +PV VK    V D      ++ + K+ +  G + +     +     
Sbjct: 141 MVESITAAVCDAVDVPVWVKLTPNVTD------IKAIGKAAQNGGADAVVAINTLRGMAI 194

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKK-------ENPDLFIGLNGGLEDMSQALK-ILPSV 210
            +    P    +   L    V  +         E  D+ +   GG+     A++ ++   
Sbjct: 195 DINSGYPILGNRFGGLSGPAVKPVAIKCVYDLYEALDIPVIGVGGVSTWEDAVEMMMAGA 254

Query: 211 DGVMIGRAAYKNSAMLTTV 229
             V IG A +++  + + +
Sbjct: 255 SAVQIGSAVHESVDIFSDI 273


>gi|4959881|gb|AAD34541.1| NifR3 homolog X2 [Sterkiella histriomuscorum]
          Length = 116

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 26/125 (20%), Positives = 58/125 (46%), Gaps = 12/125 (9%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G +G+ L+   +++   +  + + L +PVT K R   +++        L + I++ G   
Sbjct: 1   GKYGSFLLEKTELIRSLVTTLAQNLKVPVTCKVRCLPNEEDT----LKLARMIEECGAAL 56

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
           + +H R    K       ++    +++I+ +IK+    + +  NGG+      +K L  +
Sbjct: 57  LVVHGRTREHK------KQQTGPANWEIIRKIKQSL-RIPVIANGGMATYEDCMKCLEYL 109

Query: 211 DGVMI 215
            GVM+
Sbjct: 110 -GVMV 113


>gi|324543886|gb|ADY49671.1| tRNA-dihydrouridine synthase 1 [Ascaris suum]
          Length = 107

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 29/104 (27%), Positives = 50/104 (48%), Gaps = 13/104 (12%)

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG DD+   + +    K  +K+G + I +H R    +         +   ++DI+  +
Sbjct: 1   MRIGWDDE--HINVIENAKLAEKAGASAIIVHGRTTKQQ--------YMGEANWDIIKAV 50

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           K E  ++ +  NG ++   +A  +L    VDG+MIGRAA  N  
Sbjct: 51  K-EAVNIPVIGNGDIDSPIKAKAMLDYSGVDGIMIGRAAMGNPW 93


>gi|258615864|ref|ZP_05713634.1| dihydrouridine synthase family protein [Enterococcus faecium DO]
          Length = 116

 Score = 92.6 bits (229), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 4/98 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN----ILGFSTQEKPLALQIGG 56
           M D TD  +R   +      + +TE   +D+    D K+     L F+  E+P+   I G
Sbjct: 19  MEDVTDVVFRHVVKHAAAPDVFFTEFTNSDSFCHPDGKDSVRGRLTFTEDEQPMVAHIWG 78

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
                  E +  + + G+  I++N+GCP   V E   G
Sbjct: 79  DKPEFFREMSIAMAEMGFQGIDINMGCPVPNVAERGKG 116


>gi|14591298|ref|NP_143376.1| dihydroorotate dehydrogenase 1B [Pyrococcus horikoshii OT3]
 gi|9297037|sp|O59185|PYRD_PYRHO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|3257941|dbj|BAA30624.1| 303aa long hypothetical dihydroorotate dehydrogenase [Pyrococcus
           horikoshii OT3]
          Length = 303

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 43/204 (21%), Positives = 76/204 (37%), Gaps = 16/204 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEK---PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     +  L     E+   P+ + I G    +    A+ +E    +   LN+ C
Sbjct: 70  INAMGLPNPGWEAFLNEFIDERFDFPVIVSIFGGTPEEFAFLAEKLEPV-ADAFELNLSC 128

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL---- 139
           P A+     +G  +  +P  V + + A+      PV  K    V+D              
Sbjct: 129 PHAK----GYGMEIGQDPKNVYEVVKAVKDVTDKPVIAKLTPNVNDITKLGLAAERGGAD 184

Query: 140 -VKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I I+A++ IL   +       I  +    VY++ K   D+ +   GG+
Sbjct: 185 GVSAINTVKAIAIDIYAKRPILSNKVGGYSGPGIKPIALRAVYDLAK-VLDIPVIGIGGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAY 220
                A++ +L     + IG A Y
Sbjct: 244 TSWRDAVEFLLAGASALQIGTAVY 267


>gi|15673328|ref|NP_267502.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. lactis
           Il1403]
 gi|18202791|sp|Q9CFW8|PYRDB_LACLA RecName: Full=Dihydroorotate dehydrogenase B, catalytic subunit;
           AltName: Full=DHOdehase B; Short=DHOD B; Short=DHODase
           B; AltName: Full=Dihydroorotate oxidase B
 gi|12724328|gb|AAK05444.1|AE006366_13 dihydroorotate dehydrogenase B [Lactococcus lactis subsp. lactis
           Il1403]
 gi|326406882|gb|ADZ63953.1| dihydroorotate dehydrogenase catalytic subunit [Lactococcus lactis
           subsp. lactis CV56]
          Length = 311

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 87/223 (39%), Gaps = 31/223 (13%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGC 83
           E+I+A+ +        L  +  + P+   + G++    V   AKI +      I LN+ C
Sbjct: 82  EVIMAEKLPW------LNENFPDLPIIANVAGSEEDDYVAVCAKIGDAPNVKVIELNISC 135

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P    +    G     +PD+    + A      +P+ VK    V D +P      + K++
Sbjct: 136 P----NVKHGGQAFGTDPDVAAALVKACKAVSKVPLYVKLSPNVTDIVP------IAKAV 185

Query: 144 KKSGVNGIWI-----------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           + +G +G+ +             RK +L           I  +   +++++ +   D+ I
Sbjct: 186 EAAGADGLTMINTLMGVRFDLKTRKPVLANITGGLSGPAIKPVALKLIHQVAQ-VVDIPI 244

Query: 192 GLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              GG+E     L++ +     V +G A + +  +   + E  
Sbjct: 245 IGMGGVESAQDVLEMYMAGASAVAVGTANFADPFVCPKIIEKL 287


>gi|313623241|gb|EFR93489.1| dihydroorotate dehydrogenase [Listeria innocua FSL J1-023]
          Length = 304

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  ++I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCSRIAESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKSVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKAI-LKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK +   G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPVIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|315282837|ref|ZP_07871156.1| dihydroorotate dehydrogenase [Listeria marthii FSL S4-120]
 gi|313613507|gb|EFR87332.1| dihydroorotate dehydrogenase [Listeria marthii FSL S4-120]
          Length = 304

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKSVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKAI-LKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK +   G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPVIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|146103428|ref|XP_001469559.1| dihydrouridine synthase domain protein-like protein [Leishmania
           infantum]
 gi|134073929|emb|CAM72668.1| dihydrouridine synthase domain protein-like protein [Leishmania
           infantum JPCM5]
 gi|322503403|emb|CBZ38488.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 439

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 65/335 (19%), Positives = 116/335 (34%), Gaps = 79/335 (23%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQI------ 54
           MV      +R          +++TE +VA A L   ++ ++ + T + P+A  +      
Sbjct: 17  MVRVCSPGFRALCG-AHGADVVFTEEVVA-AKLATCQREVVHYPTVDTPMAEYVSYDPFK 74

Query: 55  -------------------GGADISKLVEAAKIVEDFGY-----------------NEIN 78
                              GG    ++  A +IV   G                  + I+
Sbjct: 75  NTYKRTVVLSTPVLPDITCGGHKAERIA-APRIVLQLGVADPARGAAAALVCSNDIDGID 133

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----------IPVTVKCRIGVD 128
           +N+GCP        FGA LM  P++ G  + A+  A++            V +  +  + 
Sbjct: 134 INMGCPKKFSVHNGFGAALMKRPEVGGAIVRAVHDAVNSDSNVEARGGKRVAMSLKTRLQ 193

Query: 129 DQIPAVA--LRNLVKSIKKSG----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           D   A    LR ++ + + +     ++ I IHAR          D R      YD   E+
Sbjct: 194 DTAEATVGMLRAILAAAQHTPTNPILHAITIHARTP--------DQRSEQAPLYDRAAEV 245

Query: 183 KK------ENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAML--TTVDEY 232
            +          + + LNG +       A   L   D  MI RAA +++        +  
Sbjct: 246 VRTCRADAAFEGICLVLNGSVLSRQDGEAKCALYGFDAAMIARAALEDARCFHRKGSELR 305

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
           FS+    S    T   + +   I   +  Y+ R+ 
Sbjct: 306 FSSAAHDSEAQSTEDAEVYAMAIMKELFFYSVRYR 340


>gi|281491891|ref|YP_003353871.1| dihydroorotate dehydrogenase catalytic subunit [Lactococcus lactis
           subsp. lactis KF147]
 gi|281375602|gb|ADA65108.1| Dihydroorotate dehydrogenase, catalytic subunit [Lactococcus lactis
           subsp. lactis KF147]
          Length = 311

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 87/223 (39%), Gaps = 31/223 (13%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGC 83
           E+I+A+ +        L  +  + P+   + G++    V   AKI +      I LN+ C
Sbjct: 82  EVIMAEKLPW------LNENFPDLPIIANVAGSEEDDYVAVCAKIGDAPNVKAIELNISC 135

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P    +    G     +PD+    + A      +P+ VK    V D +P      + K++
Sbjct: 136 P----NVKHGGQAFGTDPDVAAALVKACKAVSKVPLYVKLSPNVTDIVP------IAKAV 185

Query: 144 KKSGVNGIWI-----------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           + +G +G+ +             RK +L           I  +   +++++ +   D+ I
Sbjct: 186 EAAGADGLTMINTLMGVRFDLKTRKPVLANITGGLSGPAIKPVALKLIHQVAQ-VVDIPI 244

Query: 192 GLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              GG+E     L++ +     V +G A + +  +   + E  
Sbjct: 245 IGMGGVESAQDVLEMYMAGASAVAVGTANFADPFVCPKIIEKL 287


>gi|226224436|ref|YP_002758543.1| dihydroorotase dehydrogenase [Listeria monocytogenes Clip81459]
 gi|254933305|ref|ZP_05266664.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes HPB2262]
 gi|259547529|sp|C1KWD2|PYRD_LISMC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|225876898|emb|CAS05607.1| Putative dihydroorotase dehydrogenase [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|293584865|gb|EFF96897.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes HPB2262]
 gi|328473555|gb|EGF44392.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 220]
 gi|332312274|gb|EGJ25369.1| Dihydroorotate dehydrogenase [Listeria monocytogenes str. Scott A]
          Length = 304

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 43/219 (19%), Positives = 86/219 (39%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +PD+      A+    ++PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPDVAHRLTKAVKNVATVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +E  
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-REVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|218509228|ref|ZP_03507106.1| tRNA-dihydrouridine synthase protein [Rhizobium etli Brasil 5]
          Length = 117

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQIGGADI 59
           M   TD  +R  A       L+ TEM+ +  ++    ++         +P  +Q+ G + 
Sbjct: 34  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAESWSRLKAAGFRPHMVQLAGREA 92

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP 84
             + EAAKI  D G + I++N+GCP
Sbjct: 93  HWMAEAAKIAADHGADIIDINMGCP 117


>gi|16803873|ref|NP_465358.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes EGD-e]
 gi|224500064|ref|ZP_03668413.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes Finland
           1988]
 gi|224501366|ref|ZP_03669673.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL R2-561]
 gi|254831566|ref|ZP_05236221.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 10403S]
 gi|284802279|ref|YP_003414144.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 08-5578]
 gi|284995421|ref|YP_003417189.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 08-5923]
 gi|30173346|sp|Q8Y667|PYRD_LISMO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|16411287|emb|CAC99911.1| pyrD [Listeria monocytogenes EGD-e]
 gi|284057841|gb|ADB68782.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 08-5578]
 gi|284060888|gb|ADB71827.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes 08-5923]
          Length = 304

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 42/219 (19%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKNVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|212224413|ref|YP_002307649.1| dihydroorotate dehydrogenase 1B [Thermococcus onnurineus NA1]
 gi|212009370|gb|ACJ16752.1| dihydroorotate dehydrogenase [Thermococcus onnurineus NA1]
          Length = 300

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 44/216 (20%), Positives = 79/216 (36%), Gaps = 17/216 (7%)

Query: 27  IVADAILRGDKKNILGFSTQ---EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     K  L        + PL + I G    +    A+ + +   N   LN+ C
Sbjct: 68  INAMGLPNPGWKGFLEMVEGYTFDFPLIVSIFGGTPEEFAFLAEKLSEV-ANAFELNLSC 126

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRN 138
           P A+     +G  +   P++V + + A+      PV  K    +DD          A  +
Sbjct: 127 PHAK----GYGMEIGQRPEMVYEVVKAVKDVTDKPVIAKLTPNIDDITKLGLAAEKAGAD 182

Query: 139 LVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I ++AR+ IL           +  +    VY++ K   ++ +   GG+
Sbjct: 183 AVAAINTLKAIAIDVYARRPILSNRVGGYSGPGVKPVALRAVYDLAKAL-NIPVIGIGGI 241

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDE 231
                AL+  L     + IG A       +   ++E
Sbjct: 242 TTWRDALEFFLAGARALQIGTAVALRGWKVFREINE 277


>gi|256810615|ref|YP_003127984.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           fervens AG86]
 gi|256793815|gb|ACV24484.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           fervens AG86]
          Length = 302

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 47/190 (24%), Positives = 83/190 (43%), Gaps = 33/190 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G +  +  E AK +E +  + I LN+ CP A+     +GA +  NP++      
Sbjct: 97  IIGSVYGKNEEEFAEVAKRMEKY-VDIIELNISCPHAK----GYGATIGQNPELSYSVCK 151

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
           A+ K++ +PV  K    V D      +  + +++  +GV+            I I A+K 
Sbjct: 152 AVKKSVKVPVFAKLTPNVTD------IIEIAQAVVDAGVDGLVAINTVRGMAIDIKAKKP 205

Query: 159 IL----KGLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           IL     GLS K  + I   + +D+      EN D+ I   GG+ +   A++ ++     
Sbjct: 206 ILGNKFGGLSGKAIKPIGIKVVWDLY-----ENFDVPIIGVGGIMNGEDAIEYMMAGASA 260

Query: 213 VMIGRAAYKN 222
           V IG   Y  
Sbjct: 261 VQIGSGVYYR 270


>gi|46908065|ref|YP_014454.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47093070|ref|ZP_00230848.1| dihydroorotate dehydrogenase [Listeria monocytogenes str. 4b H7858]
 gi|254826125|ref|ZP_05231126.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J1-194]
 gi|254852739|ref|ZP_05242087.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL R2-503]
 gi|254994290|ref|ZP_05276480.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J2-064]
 gi|255522430|ref|ZP_05389667.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J1-175]
 gi|300763854|ref|ZP_07073851.1| dihydroorotate dehydrogenase [Listeria monocytogenes FSL N1-017]
 gi|67460857|sp|Q71YI3|PYRD_LISMF RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|46881335|gb|AAT04631.1| dihydroorotate dehydrogenase [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47018571|gb|EAL09326.1| dihydroorotate dehydrogenase [Listeria monocytogenes str. 4b H7858]
 gi|258606063|gb|EEW18671.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL R2-503]
 gi|293595365|gb|EFG03126.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J1-194]
 gi|300515590|gb|EFK42640.1| dihydroorotate dehydrogenase [Listeria monocytogenes FSL N1-017]
          Length = 304

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 43/219 (19%), Positives = 86/219 (39%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +PD+      A+    ++PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPDVAHRLTKAVKNVATVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +E  
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-REVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|47096554|ref|ZP_00234144.1| dihydroorotate dehydrogenase [Listeria monocytogenes str. 1/2a
           F6854]
 gi|254899470|ref|ZP_05259394.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes J0161]
 gi|254912391|ref|ZP_05262403.1| dihydroorotate dehydrogenase [Listeria monocytogenes J2818]
 gi|254936718|ref|ZP_05268415.1| dihydroorotate dehydrogenase [Listeria monocytogenes F6900]
 gi|47015086|gb|EAL06029.1| dihydroorotate dehydrogenase [Listeria monocytogenes str. 1/2a
           F6854]
 gi|258609315|gb|EEW21923.1| dihydroorotate dehydrogenase [Listeria monocytogenes F6900]
 gi|293590373|gb|EFF98707.1| dihydroorotate dehydrogenase [Listeria monocytogenes J2818]
          Length = 304

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/193 (20%), Positives = 77/193 (39%), Gaps = 25/193 (12%)

Query: 47  EKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + GA     V+  A+I E      I LN+ CP    +    G     +P++  
Sbjct: 93  ETPIIANVAGATEDDYVQVCARIGESKAVKAIELNISCP----NVKHGGIAFGTDPEVAH 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
               A+    S+PV VK    V D      + ++ ++I+ +G +G+ +            
Sbjct: 149 RLTKAVKNVASVPVYVKLSPNVAD------IVSIAQAIEAAGADGLTMINTLLGMRIDLK 202

Query: 155 ARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
            RK  I  G        I  +   +++++ +   ++ I   GG++ +   L+ L    D 
Sbjct: 203 TRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVSNIPIIGMGGVQTVDDVLEFLIAGADA 261

Query: 213 VMIGRAAYKNSAM 225
           V +G   + +  +
Sbjct: 262 VAVGTMNFTDPFI 274


>gi|154345488|ref|XP_001568681.1| dihydrouridine synthase domain protein-like protein [Leishmania
           braziliensis MHOM/BR/75/M2904]
 gi|134066023|emb|CAM43808.1| dihydrouridine synthase domain protein-like protein [Leishmania
           braziliensis MHOM/BR/75/M2904]
          Length = 440

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 82/222 (36%), Gaps = 26/222 (11%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----------- 116
           +V     + I++N+GCP     +  FGA LM  P++ G  + A+  A++           
Sbjct: 123 LVCSDDIDGIDVNMGCPKKFSVQNGFGAALMKRPEVGGAIVRAVHDAVNSNASVEARGGR 182

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG----VNGIWIHARKAILKGLSPKDNRKI 171
            + V++K R+    +     LR ++ +   +     ++ I +HAR    +     +   +
Sbjct: 183 RVAVSLKTRLKETTEDTVEMLRAMLTAAHHTPTSPVLHAITVHARTPNQRS----EQAPL 238

Query: 172 PNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAMLT 227
            +   ++V   +       +   LNG +       A   L   DG MI RAA +++    
Sbjct: 239 YSRAAEVVRTCRSDTAFEGICFVLNGSILSRQDGEAKCALYGFDGAMIARAALEDARCFH 298

Query: 228 TVDEYFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAARHL 267
                                  K++   I   +  Y+ R+ 
Sbjct: 299 REGRELPTSSAADEGEAQLAEDAKEYAMSIMKELFFYSVRYR 340


>gi|254482153|ref|ZP_05095394.1| Dihydroorotate dehydrogenase family protein [marine gamma
           proteobacterium HTCC2148]
 gi|214037478|gb|EEB78144.1| Dihydroorotate dehydrogenase family protein [marine gamma
           proteobacterium HTCC2148]
          Length = 552

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/175 (21%), Positives = 65/175 (37%), Gaps = 23/175 (13%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +++ L   I G  I + VE AKI+     + + LN+ CP A+     +G  +  +PD+V
Sbjct: 104 PEDRFLLTSIFGGSIDEFVEVAKILAPVS-DGLELNLSCPHAK----GYGMAMGQDPDMV 158

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-----------WI 153
            + +AA+   + IPV  K      D         + ++ +  G +G              
Sbjct: 159 REIVAAVKAVVDIPVIPKLTPNTPDITV------IARAAEAGGADGFCAINTVGPGYTSA 212

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           H    +  G      + I  +    V E+  E  DL I   GG+           
Sbjct: 213 HGHPVLSNGAGGMSGKGILPIGLKCVKEVA-EVSDLPIIGCGGVSSADDVRAFFD 266


>gi|306829318|ref|ZP_07462508.1| dihydroorotate dehydrogenase B [Streptococcus mitis ATCC 6249]
 gi|304428404|gb|EFM31494.1| dihydroorotate dehydrogenase B [Streptococcus mitis ATCC 6249]
          Length = 328

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 80/199 (40%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 115 PIIANVAGFSKQEYAAVSRGISKAANVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 172

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 173 VKAAVEASDVPVYVKLTPSVTD------VVTIAKAAEDAGASGLTMINTLVGMRFDLKTR 226

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 227 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 285

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E+ 
Sbjct: 286 VGTANFTNPYACPDIIEHL 304


>gi|46108752|ref|XP_381434.1| hypothetical protein FG01258.1 [Gibberella zeae PH-1]
          Length = 362

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 47/264 (17%), Positives = 84/264 (31%), Gaps = 56/264 (21%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS----TQEKPLALQIGG 56
           MV +    +R        + L ++ MI+A    R        +S     ++ P  +Q G 
Sbjct: 32  MVRYGKLAFRQTVHKYGVD-LCWSPMILAKEFNRSSFARDSDWSFSTEPKQPPTIVQFGA 90

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
               +L  A+ +V       ++LN GCP +     + GA LM + ++V D +    + L+
Sbjct: 91  NVPLELARASALVAP-SSQGVDLNCGCPQSWACAETLGAALMNHRELVRDMVVETRQRLA 149

Query: 117 IPVT-VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
                V     +D                   ++ + IH R       +P     +  L 
Sbjct: 150 SDGWGVGLEKDIDSPKGRSNRL----------IDWLTIHPRTRSTPSTTPIRTEALEILT 199

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMS----------------QALKIL------------ 207
                  +K +  L I L+G + D+S                  +  L            
Sbjct: 200 -------EKYSKILPILLSGDVFDLSTLPFQPTITTNNDTPLPCIDKLVLNDTNSAVNMP 252

Query: 208 ----PSVDGVMIGRAAYKNSAMLT 227
                 + G M  R    N A+  
Sbjct: 253 RPSNTHLSGFMSARGLLANPAICA 276


>gi|315612974|ref|ZP_07887885.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis ATCC 49296]
 gi|315315084|gb|EFU63125.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis ATCC 49296]
          Length = 328

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 80/199 (40%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 115 PIIANVAGFSKQEYAAVSRGISKATNVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 172

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 173 VKAAVEASDVPVYVKLTPSVTD------VVTIAKAAEDAGASGLTMINTLVGMRFDLKTR 226

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 227 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 285

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E+ 
Sbjct: 286 VGTANFTNPYACPDIIEHL 304


>gi|20089472|ref|NP_615547.1| dihydroorotate dehydrogenase 1B [Methanosarcina acetivorans C2A]
 gi|30173337|sp|Q8TT55|PYRD_METAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|19914377|gb|AAM04027.1| dihydroorotate oxidase [Methanosarcina acetivorans C2A]
          Length = 311

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/194 (20%), Positives = 76/194 (39%), Gaps = 24/194 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I G   S+  E A+ +     + + LNV CP A      +GA +  NP +V    
Sbjct: 102 PVIASIFGGAPSEFAEVAEGLLPAKPDALELNVSCPHAE----GYGAAVGSNPCLVEAVT 157

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARK 157
           AA+   +++PV VK    V D      +  +  + +  G +            I I +  
Sbjct: 158 AAVKDVVNVPVWVKLTPNVAD------ITCIGNAAESGGADAVVAINTVKGMAIDIESGY 211

Query: 158 AILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L   S     + +  +    VY++     ++ +   GG+     A++ ++     V +
Sbjct: 212 PVLGNRSGGLSGKAVKPVAVKCVYDLYTAL-EIPVIGVGGVSSWEDAVELMMAGAAAVQV 270

Query: 216 GRAAYKNSAMLTTV 229
           G A Y    + + +
Sbjct: 271 GSAVYDRVDIFSEI 284


>gi|331266573|ref|YP_004326203.1| dihydroorotate dehydrogenase [Streptococcus oralis Uo5]
 gi|326683245|emb|CBZ00863.1| dihydroorotate dehydrogenase [Streptococcus oralis Uo5]
          Length = 312

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 80/199 (40%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 99  PIIANVAGFSKQEYAAVSRGISKAANVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 157 VKAAVEASDVPVYVKLTPSVTD------VVTIAKAAEDAGASGLTMINTLVGMRFDLKTR 210

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 211 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E+ 
Sbjct: 270 VGTANFTNPYACPDIIEHL 288


>gi|323452132|gb|EGB08007.1| hypothetical protein AURANDRAFT_5440 [Aureococcus anophagefferens]
          Length = 200

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 56/154 (36%), Gaps = 13/154 (8%)

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV--DDQIPAVALRNL 139
           GCP         G+ L+ +P  +   +  +C+A  +PV+VK R+     +    +     
Sbjct: 1   GCPIYEATRRGLGSALLRSPRKLARLVGGICEASPVPVSVKLRLSPAGPNDANYLDHVAA 60

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           ++ + + G   + +H R A  +   P D   I                 + +  NG +  
Sbjct: 61  LRDLGEEGPAFLTLHGRTATQRYGKPADWAAIEAA--------AGAAGAVPLVGNGDVLT 112

Query: 200 ---MSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
               +      P+  G+M+GR A     +   + 
Sbjct: 113 HYEAAARRAAAPAAAGLMVGRGALVTPWLFDEIR 146


>gi|300811424|ref|ZP_07091919.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300497582|gb|EFK32609.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 309

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 40/195 (20%), Positives = 79/195 (40%), Gaps = 24/195 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     + P+   +GG  +   VE AKI+     + + LN+ CP   V EG     ++  
Sbjct: 91  LREKHPDLPILASVGGESVEDYVEVAKILAAAKPDALELNLSCP--NVSEGGMTFGIV-- 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P++V      + + + +PV VK    V       ++  + ++ ++ G +G+         
Sbjct: 147 PEMVEKITRLVKEKVDLPVYVKLTPNV------TSIVEIAQAAERGGADGLTLINTLLGL 200

Query: 153 ---IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
              +  R+ +L         + +  +   +V ++K+    L I   GG+     A + IL
Sbjct: 201 HLDLKTRRPVLGNDFGGLSGQAVKPVAVRMVAQVKQAT-SLPIIGVGGINSPEDAAEFIL 259

Query: 208 PSVDGVMIGRAAYKN 222
                V IG  A+ +
Sbjct: 260 AGASAVQIGSMAFHD 274


>gi|297619716|ref|YP_003707821.1| dihydroorotate dehydrogenase family protein [Methanococcus voltae
           A3]
 gi|297378693|gb|ADI36848.1| dihydroorotate dehydrogenase family protein [Methanococcus voltae
           A3]
          Length = 319

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 41/213 (19%), Positives = 82/213 (38%), Gaps = 36/213 (16%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
               +  +   I G +  +  E A+ + D+  + I LN+ CP A    G +G+ +  + +
Sbjct: 105 MHELDVKIIGSIYGKNEKEFAEVAEKIVDY-VDLIELNISCPHA---GGGYGSSIGQDCN 160

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---------- 152
           +    ++++     +PV  K    V D      ++ +  S++ +G +GI           
Sbjct: 161 LSHKVVSSVKNLSDVPVVAKLTPNVTD------IKEIAVSVEDAGADGITAINTLGPGMV 214

Query: 153 --IHARKA----ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK- 205
             I A+K     I  G+S K  + I   +   +Y       D+ I   GG+     A++ 
Sbjct: 215 IDIDAKKPILGNIYGGMSGKAVKPIAIKNVYDIY----SAVDIPIIGVGGITTGRDAIEF 270

Query: 206 ILPSVDGVMIGRAAYKNSA-MLT----TVDEYF 233
           ++     V +G   Y     +       + EY 
Sbjct: 271 MMAGASAVQVGTGVYYRGYDIFNKINDEIKEYL 303


>gi|296109015|ref|YP_003615964.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           infernus ME]
 gi|295433829|gb|ADG13000.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           infernus ME]
          Length = 302

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 82/210 (39%), Gaps = 30/210 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
                   +   I G D  +  E AK +ED+  + I LN+ CP A+     +GA +  +P
Sbjct: 89  RIEKMGVRIIGSIYGKDEDEFREVAKKIEDY-VDIIELNISCPHAK----GYGATIGQDP 143

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARK 157
           ++      A+ + + +PV  K    V +      +  + +++  + V+G      +   K
Sbjct: 144 ELSYKVCKAVKEEVKVPVFAKLTPNVSN------ILEIAEALVDAKVDGFVAINTVRGMK 197

Query: 158 AILKGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
             +K   P           + I  +   IVY++  EN D  I   GG+     A++ ++ 
Sbjct: 198 IDIKAKRPILSNKFGGLSGKAIKPIGVKIVYDLY-ENFDKPIIGVGGIFTGEDAIEYMMA 256

Query: 209 SVDGVMIGRAAYKNSA-----MLTTVDEYF 233
               V +G A Y         +   + E+ 
Sbjct: 257 GASAVQVGSAVYFRGYDVFKKICDEIKEFL 286


>gi|323450369|gb|EGB06251.1| hypothetical protein AURANDRAFT_72033 [Aureococcus anophagefferens]
          Length = 2222

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 89/234 (38%), Gaps = 19/234 (8%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
           MVD ++R +R  AR      L Y+ M+VA A+     +   +     +++PL +Q+GG+ 
Sbjct: 22  MVDQSERAFRAVARR-HGVGLCYSPMLVASALGDASYRAAYLDAPDARDRPLFVQVGGSG 80

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            + +  AA++    G + +++N+GCP +    G +G       D V    A         
Sbjct: 81  EAFVAAAARVARAGGCDAVDVNLGCPQSCARRGGYG-AFTDEDDAVALVAAVAAAVKPTR 139

Query: 119 VTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           VT K R   +   P      A       +  +G + + +HAR    KG    D   +  +
Sbjct: 140 VTCKIRAVPERDAPLVPDRAATARYAARLAAAGASCVAVHARTREAKGRGAADWAVVAAV 199

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              +   +           NG +     A  ++       VM   A   +  + 
Sbjct: 200 VAAVDVPV---------IGNGDVRTRRDADALIAETGCAAVMSAEALLADPRLF 244


>gi|289435176|ref|YP_003465048.1| hypothetical protein lse_1813 [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|289171420|emb|CBH27964.1| pyrD [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 304

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 42/219 (19%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          + P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFDTPIIANVAGATEEDYVKVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKAVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIESAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V IG   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAIGTMNFTDPFI 274


>gi|34581031|ref|ZP_00142511.1| nifR3-like protein [Rickettsia sibirica 246]
 gi|28262416|gb|EAA25920.1| nifR3-like protein [Rickettsia sibirica 246]
          Length = 119

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 4/94 (4%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL---RGDKKNILGFSTQEKPLALQIGGA 57
           M   TD  +R   +      L+ +EMI + A++   R   K             +Q+ G 
Sbjct: 18  MSGVTDLEFRRLVKRF-GAGLVVSEMIASRAMIVESRQSLKKSAIMRDDATSDCVQLAGC 76

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           + + + EAAK+ E      I+LN GCP+ +V  G
Sbjct: 77  EPNVIAEAAKMNEGVRAKIIDLNFGCPAKKVVGG 110


>gi|163790400|ref|ZP_02184831.1| dihydroorotate dehydrogenase [Carnobacterium sp. AT7]
 gi|159874304|gb|EDP68377.1| dihydroorotate dehydrogenase [Carnobacterium sp. AT7]
          Length = 309

 Score = 89.9 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 41/201 (20%), Positives = 80/201 (39%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G  I +  E  K +        + +NV CP    +    G     +P++V 
Sbjct: 93  DTPVIASVAGTTIEEYCEVTKRLCQSPTVRALEINVSCP----NVKEGGLTFGASPELVY 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
           D   A+    ++P+ +K    V D      +  + ++ +K+G +GI +            
Sbjct: 149 DITKAVKAVATVPIYIKLTPNVTD------IVAIAQAAEKAGADGISMINTVLGMSINLE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
           +RK +L   +       I  +   +VY++ +      IG+ GG+  +   L++ L     
Sbjct: 203 SRKPVLANKTGGLSGAAIKPIAIRMVYQVARAVSIPIIGM-GGISTVDDVLEMFLAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V IG A Y N  +   + E  
Sbjct: 262 VAIGTANYANPMICKELIEAL 282


>gi|217964014|ref|YP_002349692.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b) [Listeria
           monocytogenes HCC23]
 gi|254829171|ref|ZP_05233858.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL N3-165]
 gi|254788891|sp|B8DDR9|PYRD_LISMH RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|217333284|gb|ACK39078.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b) [Listeria
           monocytogenes HCC23]
 gi|258601581|gb|EEW14906.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL N3-165]
 gi|307571415|emb|CAR84594.1| pyrD [Listeria monocytogenes L99]
 gi|313608125|gb|EFR84182.1| dihydroorotate dehydrogenase [Listeria monocytogenes FSL F2-208]
          Length = 304

 Score = 89.9 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    ++PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKNVATVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|16801013|ref|NP_471281.1| dihydroorotate dehydrogenase 1B [Listeria innocua Clip11262]
 gi|30173354|sp|Q92AH5|PYRD_LISIN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|16414448|emb|CAC97177.1| pyrD [Listeria innocua Clip11262]
 gi|313618279|gb|EFR90336.1| dihydroorotate dehydrogenase [Listeria innocua FSL S4-378]
          Length = 304

 Score = 89.5 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 84/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  ++I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCSRIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D I       +
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKSVASVPVYVKLSPNVADIIS------I 176

Query: 140 VKSIKKSGVNGIWI-----------HARKAI-LKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK +   G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPVIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|94987154|ref|YP_595087.1| dihydroorotate dehydrogenase [Lawsonia intracellularis PHE/MN1-00]
 gi|94731403|emb|CAJ54766.1| Dihydroorotate dehydrogenase [Lawsonia intracellularis PHE/MN1-00]
          Length = 314

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 44/212 (20%), Positives = 79/212 (37%), Gaps = 26/212 (12%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           +K +     +E P+   +    + +  E  A +  + G   + +NV CP   V  G    
Sbjct: 92  QKKLPRLPWKETPVIANLYATSVEEFSELTAILAAEEGVAALEVNVSCP--NVKSGGTFF 149

Query: 96  CLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-- 152
               +P +      A+CK A S PV VK    V D      +  + K+++ +G + I   
Sbjct: 150 G--QDPSLAAKVTEAVCKNAGSKPVMVKLSPNVTD------ITIIAKAVESAGADAISCI 201

Query: 153 ---------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
                    I  RK++L  +        I  +    V+E+ K   ++ +   GG+     
Sbjct: 202 NTLTGMAVDIRKRKSLLSTVIGGLSGPGIKPIALRCVWEVCKAV-NIPVIGIGGITSARD 260

Query: 203 ALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            L+ IL     V IG   +    +   + E  
Sbjct: 261 VLEFILVGAHAVQIGTMNFIQPDIAFRIAEAL 292


>gi|293365211|ref|ZP_06611928.1| dihydroorotate dehydrogenase B [Streptococcus oralis ATCC 35037]
 gi|291316661|gb|EFE57097.1| dihydroorotate dehydrogenase B [Streptococcus oralis ATCC 35037]
          Length = 328

 Score = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 79/199 (39%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 115 PIIANVAGFSKQEYAAVSQGISKATNVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 172

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 173 VKAAVEASDVPVYVKLTPSVTD------VVTIAKAAEDAGASGLTMINTLVGMRFDLKTR 226

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 227 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 285

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E  
Sbjct: 286 VGTANFTNPYACPDIIENL 304


>gi|73668988|ref|YP_305003.1| dihydroorotate dehydrogenase 1B [Methanosarcina barkeri str.
           Fusaro]
 gi|72396150|gb|AAZ70423.1| dihydroorotate oxidase B, catalytic subunit [Methanosarcina barkeri
           str. Fusaro]
          Length = 301

 Score = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 75/198 (37%), Gaps = 24/198 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
               P+   I G   ++  E A+ +     +   LNV CP A      +GA +  NP +V
Sbjct: 88  DSGVPVIASIFGGSPAEFKEVAEGLLPAKPDAFELNVSCPHAE----GYGAAVGSNPCLV 143

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
               AA+   +S+PV VK    V D      +  +  + +  G +            I I
Sbjct: 144 EAITAAVKNIVSVPVWVKLTPNVSD------ITCIGNAAEAGGADAVVAINTLKGMAIDI 197

Query: 154 HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
            +   +L   S     + +  +    VY++     ++ +   GG+     A++ ++    
Sbjct: 198 ESGYPVLGNRSGGLSGKAVKPVAVKCVYDLYTAL-EIPVIGVGGVSSWQDAVEMMMAGAA 256

Query: 212 GVMIGRAAYKNSAMLTTV 229
            V +G A Y    + + +
Sbjct: 257 AVQVGSAVYDRLDVFSEI 274


>gi|154315260|ref|XP_001556953.1| hypothetical protein BC1G_04669 [Botryotinia fuckeliana B05.10]
 gi|150847632|gb|EDN22825.1| hypothetical protein BC1G_04669 [Botryotinia fuckeliana B05.10]
          Length = 1174

 Score = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 68/181 (37%), Gaps = 36/181 (19%)

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + I  + K L +PVT K RI            +  K +  +G + + +H R   +KG  
Sbjct: 782 QELINTLHKELDVPVTAKIRIL----DTREKTLDYAKMVISAGASILTVHGRTREMKG-- 835

Query: 165 PKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGL---EDMSQALKILPSVDGVMIGRAAY 220
                K    +++++  +++  P  + + +NG +   ED+   LK     DGVM      
Sbjct: 836 ----HKTGLANWEMLRFLRESLPKEVVLFVNGNILAREDIDDCLKA-TGADGVMSAEGNL 890

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM 280
            +  + +             +P      +++WR +   M          G ++  + R  
Sbjct: 891 YDPTIFSD------------APAPGEEGREYWRSLDGKMG---------GWRMDAVLRRY 929

Query: 281 I 281
           +
Sbjct: 930 L 930


>gi|310790879|gb|EFQ26412.1| dihydrouridine synthase [Glomerella graminicola M1.001]
          Length = 344

 Score = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 46/314 (14%), Positives = 94/314 (29%), Gaps = 78/314 (24%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA 66
             +R          L +T MI++    R                ++Q G +   +L  ++
Sbjct: 4   LAFRQTVHEY-GTDLCWTPMILSKEFNRNKFAR----------DSVQFGSSSPLELARSS 52

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL----------- 115
            +   +  N ++LN GCP +     + GA LM   ++V + + +  + L           
Sbjct: 53  SLAAPY-VNGVDLNCGCPQSWACAETLGAALMEKRELVREMVVSTRQRLASDGWHVGKER 111

Query: 116 ------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                    ++VK R+  D +     +  ++ + +   ++ + IH R        P +  
Sbjct: 112 DIDSPKGRSISVKIRVHNDLRRTMDFIDTVIGNPQDRNIDFLTIHPRTRHTASSIPINTE 171

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLED------------------MSQALKILPSVD 211
            +  L       ++K   +L I L+G +                               D
Sbjct: 172 SLGIL-------LEKYGDNLPILLSGDVFSMATLPLSTVSRAAPQPSEPKTINGHNGYTD 224

Query: 212 ---------GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                    G+M  R    N A+             G         + F R +  +    
Sbjct: 225 FTPSGTKLAGLMSARGILANPALYA-----------GHESCPWEAVESFMRHVVRAPMPV 273

Query: 263 AARHLHSGGKLQQI 276
                H    L ++
Sbjct: 274 KLVQHH----LHEM 283


>gi|307703749|ref|ZP_07640690.1| dihydroorotate dehydrogenase family protein [Streptococcus oralis
           ATCC 35037]
 gi|307622584|gb|EFO01580.1| dihydroorotate dehydrogenase family protein [Streptococcus oralis
           ATCC 35037]
          Length = 312

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 79/199 (39%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 99  PIIANVAGFSKQEYAAVSQGISKATNVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 157 VKAAVEASDVPVYVKLTPSVTD------VVTIAKAAEDAGASGLTMINTLVGMRFDLKTR 210

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 211 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E  
Sbjct: 270 VGTANFTNPYACPDIIENL 288


>gi|307701802|ref|ZP_07638816.1| dihydrouridine synthase (Dus) [Mobiluncus mulieris FB024-16]
 gi|307613060|gb|EFN92315.1| dihydrouridine synthase (Dus) [Mobiluncus mulieris FB024-16]
          Length = 292

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 36/154 (23%), Positives = 67/154 (43%), Gaps = 16/154 (10%)

Query: 19  NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YN 75
             +   EM+ A A+  G  ++  ++     +   ++Q+ G     L  AA  +   G  +
Sbjct: 121 EGMFVGEMVTAKALRMGSARSWVMVKSGPLQAVKSIQLYGVVGEDLAWAAGELVRRGLAD 180

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVKCR 124
            I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK R
Sbjct: 181 HIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVKIR 240

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            G+D +       ++ +  + +GV  + +HAR  
Sbjct: 241 SGIDAEHR--IFLDVARVAEDNGVAAVTLHARTT 272


>gi|315303744|ref|ZP_07874251.1| dihydroorotate dehydrogenase [Listeria ivanovii FSL F6-596]
 gi|313627886|gb|EFR96512.1| dihydroorotate dehydrogenase [Listeria ivanovii FSL F6-596]
          Length = 304

 Score = 89.1 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          + P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFDTPIIANVAGATEEDYVKVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKAVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIESAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|313632742|gb|EFR99711.1| dihydroorotate dehydrogenase [Listeria seeligeri FSL N1-067]
          Length = 304

 Score = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          + P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFDTPIIANVAGATEEDYVKVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKAVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIESAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|290893038|ref|ZP_06556027.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J2-071]
 gi|290557398|gb|EFD90923.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes FSL J2-071]
          Length = 304

 Score = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVQVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    ++PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKNVATVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAIS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|85117655|ref|XP_965295.1| hypothetical protein NCU03195 [Neurospora crassa OR74A]
 gi|28927102|gb|EAA36059.1| conserved hypothetical protein [Neurospora crassa OR74A]
          Length = 341

 Score = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 78/235 (33%), Gaps = 61/235 (25%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  +Q G  D  +L  A+ +V  +    ++LN GCP +     + GA LM   ++V D +
Sbjct: 33  PTVVQFGANDPQELARASTLVAPY-AGGVDLNCGCPQSWACAETLGAALMEKRELVRDMV 91

Query: 109 AAMCKA-------------LSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
               +              +  P    V+VK R+  D +     +  ++   +   ++ +
Sbjct: 92  IETREYLRRDGWGVGKERDVDNPKGRSVSVKIRVHKDLRKTMDFITTVLGPSQDRHIDWL 151

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGL------------- 197
            IH R         +       ++ + +  +     D + I L+G +             
Sbjct: 152 TIHPRT--------RQTPSSTPINVEALEILTSTFGDKVPILLSGDVFTLNSLPFTSPLL 203

Query: 198 ---------------------EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                                +     L  LP + G+M  RA   N A+    D 
Sbjct: 204 DPANTPTLTSKSITTDNVEKKKTPQSPLLNLPKLSGLMSARAILANPALYAGYDA 258


>gi|116512185|ref|YP_809401.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. cremoris
           SK11]
 gi|116107839|gb|ABJ72979.1| dihydroorotate oxidase B, catalytic subunit [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 311

 Score = 88.7 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 48/255 (18%), Positives = 102/255 (40%), Gaps = 43/255 (16%)

Query: 1   MVDWTDRHYRFF---ARLL-TNNALLYT--------EMIVADAILRGDKKNILGFSTQEK 48
           MV  T  H RF     R+  T + +L +        E+I+++ +        L  +  E 
Sbjct: 46  MVKATTLHPRFGNPTTRVAETASGMLNSIGLQNPGLEVIMSEKLPW------LNENFPEL 99

Query: 49  PLALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G++    +   AKI +      I LN+ CP    +    G    ++P++  D 
Sbjct: 100 PIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCP----NVKHGGQAFGIDPEVAADL 155

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A      +P+ VK    V D +P      + K+++ +G +G+ +             R
Sbjct: 156 VKACKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGLTMINTLMGVRFDLKTR 209

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           + IL           I  +   +++++ ++  D+ I   GG+ +    L++ +     V 
Sbjct: 210 QPILANITGGLSGPAIKPVALKLIHQV-EQVVDIPIIGMGGVANAQDVLEMYMAGASAVA 268

Query: 215 IGRAAYKNSAMLTTV 229
           +G A + +  +   +
Sbjct: 269 VGTANFADPFVCPKI 283


>gi|306825429|ref|ZP_07458769.1| dihydroorotate dehydrogenase B [Streptococcus sp. oral taxon 071
           str. 73H25AP]
 gi|304432367|gb|EFM35343.1| dihydroorotate dehydrogenase B [Streptococcus sp. oral taxon 071
           str. 73H25AP]
          Length = 319

 Score = 88.7 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 79/199 (39%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 106 PIIANVAGFSKQEYAAVSQGISKAANVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 163

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 164 VKAAVEASDVPVYVKLTPSVTD------VVTIAKAAEDAGASGLTMINTLVGMRFDLKTR 217

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 218 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 276

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E  
Sbjct: 277 VGTANFTNPYACPDIIENL 295


>gi|322374500|ref|ZP_08049014.1| dihydroorotate dehydrogenase B [Streptococcus sp. C300]
 gi|321280000|gb|EFX57039.1| dihydroorotate dehydrogenase B [Streptococcus sp. C300]
          Length = 330

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 79/199 (39%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  +PD+  + 
Sbjct: 117 PIIANVAGFSKQEYAAVSRGISKAANVKAIELNISCP--NVDHGNHGLLIGQDPDLAYEV 174

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  +A  +PV VK    V D +       + K+ + +G +G+ +             R
Sbjct: 175 VKAAVEASDVPVYVKLTPSVTDVVS------IAKAAEDAGASGLTMINTLVGMRFDLKTR 228

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +    L I   GG++    AL++ L     + 
Sbjct: 229 KPILANGTGGMSGPAVFPVALKLIRQVAQTTG-LPIIGMGGVDSAEAALEMYLAGASAIG 287

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E+ 
Sbjct: 288 VGTANFTNPYACPDIIEHL 306


>gi|313637312|gb|EFS02803.1| dihydroorotate dehydrogenase [Listeria seeligeri FSL S4-171]
          Length = 304

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          + P+   + GA     V+  A+I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFDTPIIANVAGATEEDYVKVCARIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKAVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIESAGADGLTMINTLLGMRIDLKTRKPIIANGTGGFSGPAIKPVAIRMIHQV-RAVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|220928070|ref|YP_002504979.1| dihydroorotate dehydrogenase [Clostridium cellulolyticum H10]
 gi|219998398|gb|ACL74999.1| dihydroorotate dehydrogenase family protein [Clostridium
           cellulolyticum H10]
          Length = 307

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/220 (19%), Positives = 86/220 (39%), Gaps = 29/220 (13%)

Query: 33  LRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +    K+ L F    +  +   I G  I +  E A+I+   G + I +NV CP    +  
Sbjct: 81  VESFIKDDLPFLKNHKTKIIANIAGNTIEEYCEMAEILASSGVDAIEMNVSCP----NVK 136

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-- 149
           +        P  + +  +A+ K    P+ VK    V D      +R++  + + +G +  
Sbjct: 137 AGCLAFGTTPKGIEEITSAVKKYCKQPLIVKLTPNVSD------IRSIAVAAEGAGADCI 190

Query: 150 ---------GIWIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
                     I I+ +K IL           +  +   +VYE    +  + +   GG+  
Sbjct: 191 SLINTILGLAIDINKKKPILANNFGGLSGPAVKPIALRMVYE-AAHSVKIPVIGMGGISS 249

Query: 200 MSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
              A++ IL     +M+G A + N      +++ +++Y  
Sbjct: 250 WEDAIEFILAGASAIMVGTANFVNPIVPIEIISGIEKYLQ 289


>gi|119589551|gb|EAW69145.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_d [Homo
           sapiens]
          Length = 239

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 23/127 (18%), Positives = 41/127 (32%), Gaps = 11/127 (8%)

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVM 214
           R         ++ R     D+  + E  +    + +  NG +     A   +   V G+M
Sbjct: 48  RLLPQLHGRSREQRYTKLADWQYIEECVQAASPMPLFGNGDILSFEDANRAMQTGVTGIM 107

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           I R A     + T + E     ++ S              I    T+Y   H  S  +  
Sbjct: 108 IARGALLKPWLFTEIKEQRHWDISSSE----------RLDILRDFTNYGLEHWGSDTQGV 157

Query: 275 QITRHMI 281
           + TR  +
Sbjct: 158 EKTRRFL 164


>gi|270292932|ref|ZP_06199143.1| dihydroorotate dehydrogenase B [Streptococcus sp. M143]
 gi|270278911|gb|EFA24757.1| dihydroorotate dehydrogenase B [Streptococcus sp. M143]
          Length = 330

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 42/207 (20%), Positives = 80/207 (38%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L       P+   + G    +    ++ I +      I LN+ CP   V  G+ G  +  
Sbjct: 109 LEREYSTLPIIANVAGFSKQEYAAVSRGISKAANVKAIELNISCP--NVDHGNHGLLIGQ 166

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           +PD+  + + A  +A  +PV VK    V D      +  + K+ + +G +G+ +      
Sbjct: 167 DPDLAYEVVKAAVEASDVPVYVKLTPSVTD------IVTVAKAAEDAGASGLTMINTLVG 220

Query: 154 -----HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
                  RK IL  G        +  +   ++ ++ +   DL I   GG++    AL++ 
Sbjct: 221 MRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMY 279

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L     + +G A + N      + E  
Sbjct: 280 LAGASAIGVGTANFTNPYACPDIIENL 306


>gi|147921507|ref|YP_684678.1| dihydroorotate dehydrogenase 1B [uncultured methanogenic archaeon
           RC-I]
 gi|121690641|sp|Q0W8E1|PYRD_UNCMA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|110620074|emb|CAJ35352.1| dihydroorotate dehydrogenase [uncultured methanogenic archaeon
           RC-I]
          Length = 301

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 48/220 (21%), Positives = 82/220 (37%), Gaps = 14/220 (6%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
               P+   I GA   +    A  +   G +   LNV CP A+     +G     +P++V
Sbjct: 89  ESGVPVIASIFGATPEEFTAVANGL--PGADAYELNVSCPHAK----GYGMQCGTDPELV 142

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRNLVKSIKKSGVNGIWIHARKAI 159
                A+  A+ +PV VK    V D  P          + V +I       I I+    I
Sbjct: 143 RSITKAVKAAVKVPVWVKLTPNVTDIRPIGLAAQEGGADAVVAINTLKAMAIDINTGWPI 202

Query: 160 LKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGR 217
           L   S       +  +    VY++  E  D+ +   GG+ + + A++ ++     V IG 
Sbjct: 203 LGNRSGGLSGPAVKPVAIKCVYDLY-EVLDIPVIGVGGVSNWADAIEFMMAGACAVEIGS 261

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           A Y++     +V    SN L   +     +     R +  
Sbjct: 262 AVYEDIGTFASVSMGISNYLDRKNMKLDEIIGLAHRVVKQ 301


>gi|116873268|ref|YP_850049.1| dihydroorotate dehydrogenase 1B [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|123461213|sp|A0AJT8|PYRD_LISW6 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116742146|emb|CAK21270.1| dihydroorotate dehydrogenase [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 304

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/219 (19%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +++L          E P+   + GA     VE  ++I E      I L
Sbjct: 67  MLNAIGLQNPGLEHVLAHELPFLEQFETPIIANVAGATEDDYVEVCSRIGESKAVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 127 NISCP----NVKHGGIAFGTDPEVAHRLTKAVKSVASVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RSVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 274


>gi|325685769|gb|EGD27843.1| dihydroorotate oxidase [Lactobacillus delbrueckii subsp. lactis DSM
           20072]
          Length = 309

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 79/195 (40%), Gaps = 24/195 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     + P+   +GG  +   VE A+I+     + + LN+ CP   V EG     ++  
Sbjct: 91  LREKHPDLPILASVGGESVEDYVEVAEILAAAKPDALELNLSCP--NVSEGGMTFGIV-- 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P++V      + + + +PV VK    V       ++  + ++ ++ G +G+         
Sbjct: 147 PEMVEKITRLVKEKVDLPVYVKLTPNV------TSIVEIAQAAERGGADGLTLINTLLGL 200

Query: 153 ---IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
              +  R+ +L         + +  +   +V ++++    L I   GG+     A + IL
Sbjct: 201 HLDLKTRRPVLGNDFGGLSGQAVKPVAVRMVAQVRQAT-SLPIIGVGGINSPEDAAEFIL 259

Query: 208 PSVDGVMIGRAAYKN 222
                V IG  A+ +
Sbjct: 260 AGASAVQIGSMAFHD 274


>gi|159904860|ref|YP_001548522.1| dihydroorotate dehydrogenase 1B [Methanococcus maripaludis C6]
 gi|159886353|gb|ABX01290.1| dihydroorotate dehydrogenase family protein [Methanococcus
           maripaludis C6]
          Length = 304

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 40/203 (19%), Positives = 82/203 (40%), Gaps = 30/203 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G + S+  +AA+I+ ++  + + LN+ CP A    G +G+ +  +P +  + ++
Sbjct: 97  IIGSIYGKNDSEFQKAAEIIGNY-VDVLELNISCPHA---GGGYGSSIGQDPGLCKNVVS 152

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARK 157
           A+     IPV  K    V D      ++ +  ++  +G +GI             I +  
Sbjct: 153 AVKDVSDIPVIAKLTPNVTD------IKEIANAVVNAGADGIVAINTLGPGMVIDIESGV 206

Query: 158 AILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            IL         + I  +    VY+I     D+ +   GG+     A++ ++     V +
Sbjct: 207 PILGNRVGGMSGKAIKPIAVKNVYDICSAV-DVPVIGVGGITTGDDAIEFMMAGASAVQV 265

Query: 216 GRAAYKNSA-ML----TTVDEYF 233
           G   Y     +       ++EY 
Sbjct: 266 GTGVYYRGYDIFQKINNEIEEYL 288


>gi|269976453|ref|ZP_06183438.1| tRNA-dihydrouridine synthase B [Mobiluncus mulieris 28-1]
 gi|269935254|gb|EEZ91803.1| tRNA-dihydrouridine synthase B [Mobiluncus mulieris 28-1]
          Length = 292

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 36/154 (23%), Positives = 68/154 (44%), Gaps = 16/154 (10%)

Query: 19  NALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YN 75
             +   EM+ A A+  G  ++  ++   + +   ++Q+ G     L  AA  +   G  +
Sbjct: 121 EGMFVGEMVTAKALRMGSARSWVMVKSGSLQAVKSIQLYGVVGEDLAWAAGELVRRGLAD 180

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC-----------KALSIPVTVKCR 124
            I+LN GCP  +V     G+ L       G+ +AA+            ++  +PVTVK R
Sbjct: 181 HIDLNFGCPVPKVTRKGGGSALPWKTAYFGEVVAAVVAATRVASEDSGRSFPVPVTVKIR 240

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            G+D +       ++ +  + +GV  + +HAR  
Sbjct: 241 SGIDAEHR--IFLDVARVAEDNGVAAVTLHARTT 272


>gi|308798905|ref|XP_003074232.1| MGC53781 protein (ISS) [Ostreococcus tauri]
 gi|116000404|emb|CAL50084.1| MGC53781 protein (ISS) [Ostreococcus tauri]
          Length = 555

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 58/187 (31%), Gaps = 26/187 (13%)

Query: 99  LNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
              +     + A   AL S  +T K RI   D   +     L   +   G   + +H R 
Sbjct: 301 RETEKYEKVLRAASAALTSTSLTFKTRIAYTD--SSRVAHTLSPKVAGWGAAAMTLHGRT 358

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVM 214
                   +  R     D++ +  + KE   + +  NG +    D    +     VD  M
Sbjct: 359 --------RAQRYRSVADWEYIK-LTKEVSSVPLIGNGDVYMQSDYYTHMAEHS-VDTCM 408

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           + R A     + T + E     ++ S              I  S   +   H     +  
Sbjct: 409 LARGALIKPWLFTEIKERRDWDISSSERF----------DILKSFVSHGLEHWGCDSRGV 458

Query: 275 QITRHMI 281
           + TR  +
Sbjct: 459 ENTRKYL 465


>gi|221103885|ref|XP_002170616.1| PREDICTED: similar to dihydrouridine synthase 1-like, partial
           [Hydra magnipapillata]
          Length = 153

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 32/163 (19%), Positives = 57/163 (34%), Gaps = 26/163 (15%)

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
              C  ++ P+T K R+               K ++++G   + +H R+   KG      
Sbjct: 1   KTACARITKPITCKIRVY----ESIEKTVTYAKRLERAGAKILTVHGRRRDQKG------ 50

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            K     +D +  +K EN  + +  NG ++ +   +K L    VDG+M    A  N A+ 
Sbjct: 51  PKTGLASWDHIKAVK-ENVQIPVFANGNIQYLRDVIKCLEYTKVDGIMSAEGALCNPAIF 109

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD--YAARHL 267
           +           G  P    +   +            Y   HL
Sbjct: 110 S-----------GRQPPAWEMADSYLAYAEKYTPPVGYIRGHL 141


>gi|157692234|ref|YP_001486696.1| dihydroorotate dehydrogenase 1B [Bacillus pumilus SAFR-032]
 gi|167011966|sp|A8FD19|PYRD_BACP2 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|157680992|gb|ABV62136.1| dihydroorotate oxidase [Bacillus pumilus SAFR-032]
          Length = 310

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 89/229 (38%), Gaps = 27/229 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +   VE A+ + +    + + LN+ CP    +  + G     +P +  
Sbjct: 91  DTPIIANVAGSQVDDYVEVAEQISQAKNVHALELNISCP----NVKTGGIAFGTDPQMAA 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
               A+    S+PV VK    V        +  + ++I+ +G +G+ +            
Sbjct: 147 ALTKAVKDVSSVPVYVKLSPNV------ANIVEIAQAIESAGADGLTMINTLIGMRLDLK 200

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             +  +           I  +   +V+E+ +      IG+ GG+++    L+ +L     
Sbjct: 201 TGKPILANKTGGLSGPAIKPVAVRMVHEVSQAVSIPIIGM-GGVQNAEDVLEFLLAGASA 259

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLT--GSSPIKTRVDKDFWRKISASM 259
           V +G A + N  +   + E   N L   G S ++  + + +  +  A  
Sbjct: 260 VAVGTANFVNPFICPEIIEELPNVLAAYGYSSVEECIGRSWKHEALAHH 308


>gi|328553552|gb|AEB24044.1| dihydroorotate dehydrogenase 1B [Bacillus amyloliquefaciens TA208]
          Length = 311

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 86/227 (37%), Gaps = 30/227 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +     +++L          + P+   + G+ +    E A+ +      + + L
Sbjct: 65  MLNAIGLQNPGLEHVLKHELPWLEQFDTPIIANVAGSQVEDYKEVAEHISKAPNVHALEL 124

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +  + G     +P +  D I A+ +  ++PV VK    V        +  +
Sbjct: 125 NISCP----NVKTGGIAFGTDPAMAADLIKAVKEVSAVPVYVKLSPNV------ANITEI 174

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K+I+ +G +G+ +              R  +           I  +   +VYE+ +   
Sbjct: 175 AKAIEAAGADGLTMINTLVGMRLDLKTGRPILANKTGGLSGPAIKPVAIRMVYEVSQAV- 233

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + I   GG++    AL+ +L     V +G A + N  +   + E  
Sbjct: 234 QIPIIGMGGVQTAEDALEFLLAGASAVAVGTANFVNPFVCPEIIEQL 280


>gi|289617969|emb|CBI55546.1| unnamed protein product [Sordaria macrospora]
          Length = 336

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/295 (16%), Positives = 97/295 (32%), Gaps = 71/295 (24%)

Query: 26  MIVADAILRGDKKNI--LGFSTQEK--PLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           MI+A    R        L  ST     P  +Q G     +L  A+ +V  +    ++LN 
Sbjct: 1   MILAKEFNRNRFARDSDLTISTNGHQPPTVVQFGANVPQELARASTLVAPY-AGGVDLNC 59

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-----------------SIPVTVKCR 124
           GCP +     + GA LM   ++V D +    + L                    V+VK R
Sbjct: 60  GCPQSWACAETLGAALMEKRELVRDMVVETREYLRRDGWGVGKEKDIDNPKGRSVSVKIR 119

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +  D +     +  ++   +   ++ + IH R         +       ++ + +  +  
Sbjct: 120 VHKDLRKTMDFITTVLGPSQDRHIDWLTIHPRT--------RQTPSSTPINVEALEILTS 171

Query: 185 ENPD-LFIGLNGGLED----------------------------------MSQALKILPS 209
              D + I L+G +                                     +Q +  +P 
Sbjct: 172 TFGDQVPILLSGDVFTLNSLPFTSPLLDPANTPTFTSKSISTDNVEKKKQPNQPVLNIPK 231

Query: 210 VDGVMIGRAAYKNSAMLTTVD----EYFSNPLT--GSSPIKTRVDKDFWRKISAS 258
           + G+M  RA   N A+    D    E     ++    +P+  ++ +    ++ A 
Sbjct: 232 LSGLMSARAILANPALYAGYDACPWEALETFMSHLARAPLPFKLVQHHLSEMCAP 286


>gi|315231294|ref|YP_004071730.1| dihydroorotate dehydrogenase [Thermococcus barophilus MP]
 gi|315184322|gb|ADT84507.1| dihydroorotate dehydrogenase [Thermococcus barophilus MP]
          Length = 299

 Score = 87.6 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/202 (22%), Positives = 78/202 (38%), Gaps = 16/202 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEK---PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     +        EK   P+ + I G D  +    A+ + +   +   LN+ C
Sbjct: 66  INAMGLPNPGWEAFYKEFKNEKFDFPVIVSIFGKDEREFAFLAEKLSEV-ADAFELNLSC 124

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRN 138
           P A+     +G  +  NP++V   + A+      PV  K    +DD          A  +
Sbjct: 125 PHAK----GYGMEIGQNPEMVYKVVKAVKDTTDKPVIAKLTPNIDDITKIGLAAERAEAD 180

Query: 139 LVKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I I+AR+ IL   +       I  +    VY++ K   D+ I   GG+
Sbjct: 181 AVSAINTVKAVAIDIYARRPILSNKVGGYSGPGIKPIALRAVYDLAK-VLDIDIIGVGGI 239

Query: 198 EDMSQALK-ILPSVDGVMIGRA 218
                A++ ++     + IG A
Sbjct: 240 TTWQDAVEFLMAGAKALQIGTA 261


>gi|323339843|ref|ZP_08080112.1| dihydroorotate oxidase [Lactobacillus ruminis ATCC 25644]
 gi|323092716|gb|EFZ35319.1| dihydroorotate oxidase [Lactobacillus ruminis ATCC 25644]
          Length = 311

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 42/191 (21%), Positives = 80/191 (41%), Gaps = 25/191 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG+     VE A  +   GY + + LN+ CP   V +G         P++    
Sbjct: 97  PIIGSVGGSSEEDYVEVASRLSQSGYVDALELNISCP--NVKKGGMAFG--TVPEVAKKL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + KA S+PV VK    V D      +  + K++++ G +G+ +             R
Sbjct: 153 TEEVKKASSVPVYVKLSPNVTD------VCAIAKAVEEGGADGLTMINTLLGMHIDLKTR 206

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K++L  L+       +  +   ++Y++     DL I   GG+E     +++ L     V 
Sbjct: 207 KSVLGNLTGGFSGHGVLPVAIRMIYQVA-HVCDLPIIGVGGIERPEDIIEMYLAGASAVQ 265

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 266 VGSAHFDDPLI 276


>gi|222151024|ref|YP_002560178.1| dihydroorotate dehydrogenase [Macrococcus caseolyticus JCSC5402]
 gi|222120147|dbj|BAH17482.1| dihydroorotate dehydrogenase [Macrococcus caseolyticus JCSC5402]
          Length = 305

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 92/247 (37%), Gaps = 38/247 (15%)

Query: 14  RLLTNNALLYTE----MIVA--------DAILRGDKKNILGFSTQEKPLALQIGGADISK 61
           R   N      E    MI A        D I++ + K +  F   E P+   + G+ +  
Sbjct: 50  RRFGNPTPRVAETSSGMINAIGLQNPGVDHIIQHELKWLEQF---ETPIIANVAGSKVED 106

Query: 62  LVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            VE A+ + +      + LN+ CP    +    G     +PD   +    +    S+PV 
Sbjct: 107 YVEVAEKISNAPNVCALELNISCP----NVKEGGIQFGTDPDTAKELTRKVKAVSSVPVY 162

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKS--GVNGI-WIHARKAILKGLSPK--------DNR 169
           VK    V        + ++ K++ +   G+  I  +   +   K  +P            
Sbjct: 163 VKLSPNV------TNIVDMAKAVAEYADGITMINTLVGLRVNEKTGTPIISNIIGGLSGP 216

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTT 228
            +  +   +VYE+++  P++ I   GG+ +    +  +    D V +G A ++N  +   
Sbjct: 217 AVKPVAMRMVYEVRRALPNIPIIAMGGVTEAQDVIDYISVGADAVAVGTANFQNPTVCKD 276

Query: 229 VDEYFSN 235
           + +    
Sbjct: 277 IIDALPG 283


>gi|157876542|ref|XP_001686617.1| dihydrouridine synthase domain protein-like protein [Leishmania
           major]
 gi|68129692|emb|CAJ08998.1| dihydrouridine synthase domain protein-like protein [Leishmania
           major strain Friedlin]
          Length = 455

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 41/223 (18%), Positives = 84/223 (37%), Gaps = 28/223 (12%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----------- 116
           +V     + I++N+GCP        FGA LM  P++ G  + A+  A++           
Sbjct: 138 LVCSNDIDGIDINMGCPKKFSVHNGFGAALMKRPEVGGAIVRAVHGAVNSDSNVEARGGK 197

Query: 117 -IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV----NGIWIHARKAILKGLSPKDNRKI 171
            + V++K R+    +     LR ++ + + +      + I IHAR    +     +   +
Sbjct: 198 RVAVSLKTRLQDTAEATVGMLRAILAASQHTPANPVLHAITIHARTPDQR----PEQAPL 253

Query: 172 PNLDYDIVYEIKKEN---PDLFIGLNGGLEDMSQ--ALKILPSVDGVMIGRAAYKNSAML 226
            +   ++V   + +       ++ LNG +       A       D  MI RAA +++   
Sbjct: 254 YDRAAEVVRACRADAAFEGICWV-LNGSVLSRQDGEAKCARYGFDAAMIARAALEDARCF 312

Query: 227 TTVDEYF--SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
                    S+         T   +++   I   +  Y+ R+ 
Sbjct: 313 HRKGSELPASSAAHDGEAQSTEDAEEYAMAIMKELFFYSVRYR 355


>gi|325126167|gb|ADY85497.1| Dihydroorotate dehydrogenase B, catalytic unit [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 309

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 39/195 (20%), Positives = 78/195 (40%), Gaps = 24/195 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     + P+   +GG  +   VE A+I+     + + LN+ CP   V EG     ++  
Sbjct: 91  LREKHPDLPILASVGGESVEDYVEVAEILAAAKPDALELNLSCP--NVSEGGMTFGIV-- 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P++V      + + + +PV VK    V       ++  + ++ +  G +G+         
Sbjct: 147 PEMVEKITRLVKEKVDLPVYVKLTPNV------TSIVEIAQAAEGGGADGLTLINTLLVL 200

Query: 153 ---IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
              +  R+ +L         + +  +   +V ++K+    L I   GG+     A + IL
Sbjct: 201 HLDLKTRRPVLGNDFGGLYGQAVKPVAVRMVAQVKQAT-SLPIIGVGGINSPEDAAEFIL 259

Query: 208 PSVDGVMIGRAAYKN 222
                V IG  A+ +
Sbjct: 260 AGASAVQIGSMAFYD 274


>gi|119476356|ref|ZP_01616707.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding protein
           [marine gamma proteobacterium HTCC2143]
 gi|119450220|gb|EAW31455.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding protein
           [marine gamma proteobacterium HTCC2143]
          Length = 541

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 38/165 (23%), Positives = 69/165 (41%), Gaps = 11/165 (6%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +++ L + I G ++ + V+ AKI+  F  + + LN+ CP A+     +G  +  +PD+V
Sbjct: 91  PEDRFLLISIFGGNVDEYVQVAKIMAPF-ADGLELNLSCPHAK----GYGMAMGQDPDLV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----HARKAI 159
            +  AA+  A++IPV  K    V +     A      +    GVN +       H +  +
Sbjct: 146 REITAAVKAAVTIPVIPKLTPNVPNIGEIAAAAVAGGADAICGVNTVGPGQYNSHGQAVL 205

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
             G+     + +  +    V EI     D  I   GG+       
Sbjct: 206 SNGMGGMSGKGVLPIALKCVDEISNAV-DCPIIACGGISSADNVR 249


>gi|305663799|ref|YP_003860087.1| dihydroorotate oxidase B, catalytic subunit [Ignisphaera aggregans
           DSM 17230]
 gi|304378368|gb|ADM28207.1| dihydroorotate oxidase B, catalytic subunit [Ignisphaera aggregans
           DSM 17230]
          Length = 301

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 47/196 (23%), Positives = 86/196 (43%), Gaps = 17/196 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + IGG+   + +E A + ++FG N I LN+ CP A+     +G  +  +P  V   +
Sbjct: 94  PIIISIGGSSEREFIEVASLADEFGANGIELNLSCPHAK----GYGIEIGADPSSVYSIV 149

Query: 109 AAMCKALSIPVTVK---CRIGVDDQIPAVA----LRNLVKSIKKSGVNGIWIHA-RKAIL 160
             +   + IP+  K   C   V+  I A++       L+ ++K   ++   +      I 
Sbjct: 150 KEVSSVVKIPIIAKLGLCDRVVESSIKALSGGARALTLINTVKAMAIDVYTMKPILSNIF 209

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            GLS      I  +   IVYE+ +E  +  I   GG++    A +  L     V IG A 
Sbjct: 210 GGLS---GPPIHPIAVRIVYEVYRET-EADIIGCGGVDSWESAAEFFLAGAKAVQIGTAI 265

Query: 220 YKNSAMLTTVDEYFSN 235
           Y++  ++  + +    
Sbjct: 266 YRDENIVNNIVQGLQQ 281


>gi|168333707|ref|ZP_02691960.1| dihydroorotate dehydrogenase family protein [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 302

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 76/224 (33%), Gaps = 33/224 (14%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           E I ++  L                + + + G  I    +  + + +   + + +N+ CP
Sbjct: 79  EFISSELPLLSKFNT---------NVIVNVAGRTIEDYCKVVEKLNETTVDMLEINISCP 129

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              V  G  G     +  +      A+    + P+ +K    V D      +  + K+++
Sbjct: 130 --NVKCGGIGFG--TDAKLAASVTKAVRHISTKPLIIKLTPNVTD------ITEIAKAVE 179

Query: 145 KSGVNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
             G + I            +H    ILK          I  +   +VY++++    L I 
Sbjct: 180 AEGADCISLINTLLGMKIDVHKFSPILKNKVGGLSGPAIKPIAVRMVYQVRRAV-ALPII 238

Query: 193 LNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             GG+      A  +L   D V IG A   N  +   +   F+ 
Sbjct: 239 GLGGIATGEDVAEFLLAGADLVSIGTACLHNPLIFLDIKRTFTE 282


>gi|13096500|pdb|1EP1|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase B
 gi|13096502|pdb|1EP2|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase B Complexed With Orotate
 gi|13096504|pdb|1EP3|A Chain A, Crystal Structure Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase B. Data Collected Under Cryogenic
           Conditions
          Length = 311

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 78/197 (39%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++    +   AKI +      I LN+ CP    +    G     +P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCP----NVKHGGQAFGTDPEVAA 153

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
             + A      +P+ VK    V D +P      + K+++ +G +G+ +            
Sbjct: 154 ALVKACKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGLTMINTLMGVRFDLK 207

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            R+ IL           I  +   +++++ ++  D+ I   GG+ +    L++ +     
Sbjct: 208 TRQPILANITGGLSGPAIKPVALKLIHQVAQDV-DIPIIGMGGVANAQDVLEMYMAGASA 266

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +   +
Sbjct: 267 VAVGTANFADPFVCPKI 283


>gi|308173516|ref|YP_003920221.1| dihydroorotate dehydrogenase catalytic subunit [Bacillus
           amyloliquefaciens DSM 7]
 gi|307606380|emb|CBI42751.1| dihydroorotate dehydrogenase (catalytic subunit) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328911656|gb|AEB63252.1| dihydroorotate dehydrogenase (catalytic subunit) [Bacillus
           amyloliquefaciens LL3]
          Length = 311

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 85/227 (37%), Gaps = 30/227 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +     +++L          + P+   + G+ +    E A+ +      + + L
Sbjct: 65  MLNAIGLQNPGLEHVLKHELPWLEQFDTPIIANVAGSQVEDYKEVAEHISKAPNVHALEL 124

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +  + G     +P +  D   A+ +  ++PV VK    V        +  +
Sbjct: 125 NISCP----NVKTGGIAFGTDPAMAADLTKAVKEVSAVPVYVKLSPNV------ANITEI 174

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K+I+ +G +G+ +              R  +           I  +   +VYE+ +   
Sbjct: 175 AKAIEAAGADGLTMINTLVGMRLDLKTGRPILANKTGGLSGPAIKPVAIRMVYEVSQAV- 233

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + I   GG++    AL+ +L     V +G A + N  +   + E  
Sbjct: 234 QIPIIGMGGVQTAEDALEFLLAGASAVAVGTANFVNPFVCPEIIEQL 280


>gi|194014711|ref|ZP_03053328.1| dihydroorotate dehydrogenase [Bacillus pumilus ATCC 7061]
 gi|194013737|gb|EDW23302.1| dihydroorotate dehydrogenase [Bacillus pumilus ATCC 7061]
          Length = 310

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 88/229 (38%), Gaps = 27/229 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +   VE AK + +    + + LN+ CP    +  + G     +P +  
Sbjct: 91  DTPIIANVAGSQVDDYVEVAKQISQAKNVHALELNISCP----NVKTGGIAFGTDPHMAA 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
               A+    S+PV VK    V        +  + ++I+ +G +G+ +            
Sbjct: 147 ALTKAVKDVSSVPVYVKLSPNV------ANIVEIAQAIEYAGADGLTMINTLIGMRLDLK 200

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             +  +           +  +   +V+E+ +      IG+ GG+++    L+ +L     
Sbjct: 201 TGKPILANKTGGLSGPAVKPVAVRMVHEVSQAVSIPIIGM-GGVQNAEDVLEFLLAGASA 259

Query: 213 VMIGRAAYKNSAMLTTVDEYFSN--PLTGSSPIKTRVDKDFWRKISASM 259
           V +G A + N  +   + E   N     G S ++  + + +  +  A  
Sbjct: 260 VAVGTANFVNPFICPEIIEELPNVLEAYGYSSVEECIGRSWKHEALAHH 308


>gi|154685970|ref|YP_001421131.1| dihydroorotate dehydrogenase 1B [Bacillus amyloliquefaciens FZB42]
 gi|166234202|sp|A7Z4H4|PYRD_BACA2 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|154351821|gb|ABS73900.1| PyrD [Bacillus amyloliquefaciens FZB42]
          Length = 311

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 39/227 (17%), Positives = 86/227 (37%), Gaps = 30/227 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINL 79
           M+ A  +     +++L          + P+   + G+ +    E A+ + +    + + L
Sbjct: 65  MLNAIGLQNPGLEHVLNHELPWLEQFDTPIIANVAGSQVDDYKEVAEHISQAPNVHALEL 124

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +  + G     +P +  +   A+ +  ++PV VK    V        +  +
Sbjct: 125 NISCP----NVKTGGIAFGTDPVMAAELTKAVKEVSAVPVYVKLSPNV------ANITEI 174

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K+I+ +G +G+ +              R  +           I  +   +VYE+ +   
Sbjct: 175 AKAIEAAGADGLTMINTLIGMRLDLKTGRPILANKTGGLSGPAIKPVAIRMVYEVSQAV- 233

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            + I   GG++    AL+ +L     V +G A + N  +   + E  
Sbjct: 234 HIPIIGMGGVQTAEDALEFLLAGASAVAVGTANFVNPFVCPEIIEQL 280


>gi|125623937|ref|YP_001032420.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|146345500|sp|P54322|PYRDB_LACLM RecName: Full=Dihydroorotate dehydrogenase B, catalytic subunit;
           AltName: Full=DHOdehase B; Short=DHOD B; Short=DHODase
           B; AltName: Full=Dihydroorotate oxidase B
 gi|124492745|emb|CAL97700.1| PyrDB protein [Lactococcus lactis subsp. cremoris MG1363]
 gi|300070711|gb|ADJ60111.1| dihydroorotate dehydrogenase 1B [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 311

 Score = 86.0 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 77/197 (39%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++    +   AKI +      I LN+ CP    +    G     +P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDAANVKAIELNISCP----NVKHGGQAFGTDPEVAA 153

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
             + A      +P+ VK    V D +P      + K+++ +G +G+ +            
Sbjct: 154 ALVKACKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGLTMINTLMGVRFDLK 207

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            R+ IL           I  +   +++++ +   D+ I   GG+ +    L++ +     
Sbjct: 208 TRQPILANITGGLSGPAIKPVALKLIHQVAQ-VVDIPIIGMGGVANAQDVLEMYMAGASA 266

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +   +
Sbjct: 267 VAVGTANFADPFVCPKI 283


>gi|150403356|ref|YP_001330650.1| dihydroorotate dehydrogenase 1B [Methanococcus maripaludis C7]
 gi|150034386|gb|ABR66499.1| dihydroorotate dehydrogenase family protein [Methanococcus
           maripaludis C7]
          Length = 304

 Score = 86.0 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 81/203 (39%), Gaps = 26/203 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G +  +  +AA+I+     + + LN+ CP A    G +G+ +  +P +  + ++
Sbjct: 97  IIGSIYGKNDVEFQKAAEIIVPH-VDVLELNISCPHA---GGGYGSSIGQDPCLCKNVVS 152

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARK 157
           A+     IPV  K    V D      ++ +  ++  +G +GI             I +  
Sbjct: 153 AVKDVSDIPVIAKLTPNVTD------IKEIANAVVNAGADGIVAINTLGPGMVIDIESGV 206

Query: 158 AILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            IL   +     + I  +    VY+I     D+ +   GG+   + A++ ++     V +
Sbjct: 207 PILGNKVGGMSGKAIKPIAVKNVYDIFSAV-DVPVIGVGGVTTGADAIEFMMAGASAVQV 265

Query: 216 GRAAYKNSA-MLTTVDEYFSNPL 237
           G   Y     +   ++E     L
Sbjct: 266 GTGVYYRGYDIFQKINEEIEEYL 288


>gi|330508198|ref|YP_004384626.1| dihydroorotate dehydrogenase, catalytic subunit [Methanosaeta
           concilii GP-6]
 gi|328929006|gb|AEB68808.1| dihydroorotate dehydrogenase, catalytic subunit [Methanosaeta
           concilii GP-6]
          Length = 299

 Score = 86.0 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 39/218 (17%), Positives = 76/218 (34%), Gaps = 27/218 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I  +   +  + ++   +   + + LN+ CP A      +G+ L   PD+V    
Sbjct: 94  PVIASIFASSAEEFAQISR---NLDADALELNLSCPHAE----KYGSELGRYPDLVESVT 146

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARK 157
            A+  A S+PV VK      D      +  L  + ++ G +            I I    
Sbjct: 147 GAVKAASSVPVWVKLTPNTAD------ILELGLAAQRGGADAVVAINTLKAMAIDIETGY 200

Query: 158 AILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMI 215
            IL         R I  +    VY++     ++ +   GG+     A+++ +     + +
Sbjct: 201 PILGNRFGGLSGRAIKPVAVRAVYDLASRL-EIPVIGVGGISSWEDAVEMIMAGASAIQV 259

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           G A  +   +   +    S  L   S     +     R
Sbjct: 260 GTALLQGYGIFEEIASGLSAYLERKSITLDELCGMAGR 297


>gi|116514463|ref|YP_813369.1| dihydroorotate dehydrogenase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116093778|gb|ABJ58931.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 309

 Score = 86.0 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 38/189 (20%), Positives = 75/189 (39%), Gaps = 24/189 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     + P+   +GG  +   VE A+I+     + + LN+ CP   V EG     ++  
Sbjct: 91  LREKHPDLPILASVGGESVEDYVEVAEILAAAKPDALELNLSCP--NVSEGGMTFGIV-- 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P++V      + + + +PV VK    V       ++  + ++ +  G +G+         
Sbjct: 147 PEMVEKITRLVKEKVDLPVYVKLTPNV------TSIVEIAQAAEGGGADGLTLINTLLVL 200

Query: 153 ---IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
              +  R+ +L         + +  +   +V ++K+    L I   GG+     A + IL
Sbjct: 201 HLDLKTRRPVLGNDFGGLYGQAVKPVAVRMVAQVKQAT-SLPIIGVGGINSPEDAAEFIL 259

Query: 208 PSVDGVMIG 216
                V IG
Sbjct: 260 AGASAVQIG 268


>gi|307244502|ref|ZP_07526609.1| dihydroorotate dehydrogenase 1B [Peptostreptococcus stomatis DSM
           17678]
 gi|306492120|gb|EFM64166.1| dihydroorotate dehydrogenase 1B [Peptostreptococcus stomatis DSM
           17678]
          Length = 300

 Score = 86.0 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 93/235 (39%), Gaps = 33/235 (14%)

Query: 17  TNNALLYTE----MIVADAI----LRGDKKNILG-FSTQEKPLALQIGGADISKLVEAAK 67
            N  +   E    M+ +  +    ++G     L  FS  +    + +GG      VE A+
Sbjct: 54  GNEGMRVHETPSGMMNSVGLENPGVQGFIDRELDDFSKIDTCRIVNLGGGCEDDYVEGAR 113

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +++D  ++ + LN+ CP    +    G    +  ++  + + ++ KA   P+ VK     
Sbjct: 114 LLDDKDFDIVELNISCP----NVKHGGMAFGIKSEVAREVVRSVRKATKKPLIVKLSPNA 169

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKGL-SPKDNRKIPNLD 175
           +D      +  + K  ++ G +GI            IH R+ +   + +      I  + 
Sbjct: 170 ED------IVEMAKVCQEEGADGISLVNTFKAMAIDIHKRRPVFNNVTAGLSGPAIKPIA 223

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTV 229
             +VYE+ +      +G+ GG+      ++ I+     + IG A + N  +   +
Sbjct: 224 LRMVYEVCQAVTIPVVGM-GGIMTAEDVIEFIMAGATCIQIGTANFTNPRIGQDI 277


>gi|301801807|emb|CBW34518.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae INV200]
          Length = 312

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASDVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLSGASAIGVGTANFTNPYACPDIIENL 288


>gi|133778319|gb|AAH23942.1| Dus3l protein [Mus musculus]
          Length = 274

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 24/127 (18%), Positives = 43/127 (33%), Gaps = 12/127 (9%)

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVM 214
               L G S ++ R     D+  + +  K    + +  NG +     A   +   V G+M
Sbjct: 84  PHPQLHGRS-REQRYTRLADWPYIEQCAKVASPMPLFGNGDILSFEDANCAMQTGVAGIM 142

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
           + R A     + T + E     ++ S  +           I    T Y   H  S  +  
Sbjct: 143 VARGALLKPWLFTEIKEQRHWDISSSERL----------DILRDFTHYGLEHWGSDTQGV 192

Query: 275 QITRHMI 281
           + TR  +
Sbjct: 193 ERTRRFL 199


>gi|296331130|ref|ZP_06873604.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674285|ref|YP_003865957.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151774|gb|EFG92649.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412529|gb|ADM37648.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 311

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 36/201 (17%), Positives = 78/201 (38%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +   VE A+ +      + + LN+ CP    +  + G     NP++  
Sbjct: 91  DTPIIANVAGSQVEDYVEVAEHISKAPNVHALELNISCP----NVKTGGIAFGTNPEMAA 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           D   A+ +   +PV VK    V        +  +  +I+++G +G+ +            
Sbjct: 147 DLTKAVKEVSDVPVYVKLSPNV------ANITEIASAIEEAGADGLTMINTLIGMRLDLK 200

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             +  +           +  +   +VYE+ +   ++ I   GG++    AL+ +L     
Sbjct: 201 SGKPILANKTGGLSGPAVKPVAIRMVYEVSQAV-NIPIIGMGGVQTAEDALEFLLAGASA 259

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V +G A + N      + E  
Sbjct: 260 VAVGTANFVNPFACPDIIEQL 280


>gi|322391869|ref|ZP_08065334.1| dihydroorotate dehydrogenase B [Streptococcus peroris ATCC 700780]
 gi|321145349|gb|EFX40745.1| dihydroorotate dehydrogenase B [Streptococcus peroris ATCC 700780]
          Length = 327

 Score = 85.6 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 36/176 (20%), Positives = 70/176 (39%), Gaps = 22/176 (12%)

Query: 71  DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
                 I LN+ CP   V  G+ G  +  +PD+  D + A  +A  +PV VK    V D 
Sbjct: 138 ANNVKAIELNISCP--NVDHGNHGLLIGQDPDLAFDVVKAAVEASDVPVYVKLTPSVTD- 194

Query: 131 IPAVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDI 178
                +  + K+ + +G +G+ +             RK IL  G        +  +   +
Sbjct: 195 -----IVTIAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKL 249

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + ++ + + +L I   GG++     +++ L     + +G A + N      + E  
Sbjct: 250 IRQVAQ-STNLPIIGMGGVDSAEAVIEMYLAGASAIGVGTANFTNPYACPDIIENL 304


>gi|313124210|ref|YP_004034469.1| dihydroorotate oxidase b, catalytic subunit [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
 gi|312280773|gb|ADQ61492.1| Dihydroorotate oxidase B, catalytic subunit [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
          Length = 309

 Score = 85.6 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 78/195 (40%), Gaps = 24/195 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     + P+   +GG  +   VE A+I+     + + LN+ CP   V EG     ++  
Sbjct: 91  LREKHPDLPILASVGGESVEDYVEVAEILAAAKPDALELNLSCP--NVSEGGMTFGIV-- 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P++V      + + + +PV VK    V       ++  + ++ ++ G +G+         
Sbjct: 147 PEMVEKITRLVKEKVDLPVYVKLTPNV------TSIVEIAQAAERGGADGLTLINTLLGL 200

Query: 153 ---IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-ALKIL 207
              +  R+ +L         + +  +   +V ++ ++   L I   GG+      A  IL
Sbjct: 201 HLDLKTRRPVLGNDFGGLSGQAVKPVAIRMVAQV-RQTTSLPIIGVGGINSPEDTAEFIL 259

Query: 208 PSVDGVMIGRAAYKN 222
                V IG  A+ +
Sbjct: 260 AGASAVQIGSMAFHD 274


>gi|289167808|ref|YP_003446077.1| dihydroorotate dehydrogenase [Streptococcus mitis B6]
 gi|288907375|emb|CBJ22212.1| dihydroorotate dehydrogenase [Streptococcus mitis B6]
          Length = 312

 Score = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 39/176 (22%), Positives = 70/176 (39%), Gaps = 22/176 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASDVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFNLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E   N
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENLPN 290


>gi|291484106|dbj|BAI85181.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. natto
           BEST195]
          Length = 311

 Score = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 86/218 (39%), Gaps = 28/218 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARV 88
           D++L  +   +  F T   P+   + G+ +   VE A+ +      + + LN+ CP    
Sbjct: 77  DSVLHNELPWLEQFDT---PIIANVAGSQVEDYVEVAEHISKAPNVHALELNISCP---- 129

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +  + G     NP++  D   A+ +  ++PV VK    V        +  +  +I+++G 
Sbjct: 130 NVKTGGIAFGTNPEMAADLTKAVKEVSNVPVYVKLSPNV------ANITEIALAIEEAGA 183

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  +           +  +   +VYE+ +   ++ I   GG
Sbjct: 184 DGLTMINTLIGMRLDLKTGKPILANKTGGLSGPAVKPVAIRMVYEVSQ-VVNIPIIGMGG 242

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++    AL+ +L     V +G A + N      + E  
Sbjct: 243 VQTAEDALEFLLAGASAVAVGTANFVNPFACPEIIEQL 280


>gi|319789140|ref|YP_004150773.1| dihydroorotate dehydrogenase family protein [Thermovibrio
           ammonificans HB-1]
 gi|317113642|gb|ADU96132.1| dihydroorotate dehydrogenase family protein [Thermovibrio
           ammonificans HB-1]
          Length = 301

 Score = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 45/201 (22%), Positives = 74/201 (36%), Gaps = 27/201 (13%)

Query: 50  LALQIGGADISK--LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +   I G+ + +   V AA    D G + + LNV CP   V +G  G    ++P      
Sbjct: 94  VIANIYGSTVEEYRAVAAALKGVD-GVDAVELNVSCP--NVKKG--GLAFGVDPVEAARV 148

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
             A+      PV VK    V D +       + K+++ +G + I            I  R
Sbjct: 149 TEAVKSVCDKPVIVKLSPNVTDPV------EIAKAVESAGADAISAINTLLGMAIDIRKR 202

Query: 157 KAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K  LK          I  +   IVY++ K    + +   GG+     A++  L     V 
Sbjct: 203 KPRLKNRFGGLSGPAIKPVAVRIVYQVSKAV-SVPVIGIGGITTWEDAVEFFLAGASAVQ 261

Query: 215 IGRAAYKNSAMLTTVDEYFSN 235
           +G A + N   +  +     N
Sbjct: 262 VGTANFFNPKAVEEIVAGIEN 282


>gi|15615097|ref|NP_243400.1| dihydroorotate dehydrogenase [Bacillus halodurans C-125]
 gi|20139769|sp|Q9K9W1|PYRD_BACHD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|10175154|dbj|BAB06253.1| dihydroorotate dehydrogenase [Bacillus halodurans C-125]
          Length = 305

 Score = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 84/210 (40%), Gaps = 25/210 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGAC 96
             +   +  + P+   I G+ ++  VE A+ +      + + LN+ CP    +    G  
Sbjct: 84  NELARLADVDVPIVANIAGSTVNDYVEVAEAISRVDNVHALELNISCP----NVKEGGIA 139

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--- 153
               PD+       + +  ++PV VK    V D      +  + ++++++G +G+ +   
Sbjct: 140 FGTVPDVAAQLTQEVKRVSTVPVYVKLSPNVSD------IVEMAQAVERAGADGLSMINT 193

Query: 154 --------HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                     R  IL  G        I  +   ++Y++ +      IG+ GG++     L
Sbjct: 194 LLGMRLDLKRRTPILANGTGGLSGPAIKPVAIRMIYQVSQAVSIPIIGM-GGIQSADDVL 252

Query: 205 K-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           + +L   D V +G A + +  +  T+ +  
Sbjct: 253 EFMLAGADAVAVGTANFTDPYVCPTIIDEL 282


>gi|134046225|ref|YP_001097710.1| dihydroorotate dehydrogenase 1B [Methanococcus maripaludis C5]
 gi|132663850|gb|ABO35496.1| dihydroorotate oxidase B, catalytic subunit [Methanococcus
           maripaludis C5]
          Length = 304

 Score = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 40/203 (19%), Positives = 84/203 (41%), Gaps = 30/203 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G + S+  +AA+I+ ++  + + LN+ CP A    G +G+ +  +P +  + ++
Sbjct: 97  IIGSIYGKNDSEFQKAAEIIGNY-VDVLELNISCPHA---GGGYGSSIGQDPCLCKNVVS 152

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARK 157
           A+     IPV  K    V D      ++ +  ++  +G +GI             I +  
Sbjct: 153 AVNDVSDIPVIAKLTPNVTD------IKEIANAVINAGADGIVAINTLGPGMVIDIESGV 206

Query: 158 AILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            IL   +     + I  +    VY+I     D+ +   GG+   + A++ ++     V +
Sbjct: 207 PILGNKVGGMSGKAIKPIAVKNVYDICSAV-DVPVIGVGGITTGADAIEFMMAGASAVQV 265

Query: 216 GRAAYKNSA-ML----TTVDEYF 233
           G   Y     +       ++EY 
Sbjct: 266 GTGVYYRGYDIFQKINNEIEEYL 288


>gi|307706462|ref|ZP_07643271.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis SK321]
 gi|307618172|gb|EFN97330.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis SK321]
          Length = 312

 Score = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASDVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVLPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|307704694|ref|ZP_07641593.1| dihydroorotate dehydrogenase [Streptococcus mitis SK597]
 gi|307621741|gb|EFO00779.1| dihydroorotate dehydrogenase [Streptococcus mitis SK597]
          Length = 312

 Score = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASDVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|116753763|ref|YP_842881.1| dihydroorotate dehydrogenase 1B [Methanosaeta thermophila PT]
 gi|116665214|gb|ABK14241.1| dihydroorotate oxidase B, catalytic subunit [Methanosaeta
           thermophila PT]
          Length = 304

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/189 (20%), Positives = 70/189 (37%), Gaps = 25/189 (13%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
               P+   I G+   +  E   I      +   LN+ CP A    G +G  +  +P  V
Sbjct: 90  EGGVPVVASIFGSCPEEFAE---IASALDVDGFELNLSCPHA----GGYGMEIGCDPANV 142

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAIL 160
            +   A+ +A+++PV VK    V D      +R L  + ++ G N +     + A    +
Sbjct: 143 EEITRAVRRAVNVPVWVKLTPNVTD------IRVLGIAAQRGGANAVVAINTLKAMAIDV 196

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKI-LPSVDG 212
           +   P     I  L    +  +            ++ +   GG+     A+++ +    G
Sbjct: 197 ESGYPILGNVIGGLSGPAIKPVALRCVYELSGVLEIPVIGVGGVSCWQDAVEMIMAGAAG 256

Query: 213 VMIGRAAYK 221
           V IG A   
Sbjct: 257 VQIGTALMG 265


>gi|261207811|ref|ZP_05922496.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium TC 6]
 gi|289566263|ref|ZP_06446695.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium D344SRF]
 gi|294616602|ref|ZP_06696378.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1636]
 gi|294617882|ref|ZP_06697491.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1679]
 gi|260078194|gb|EEW65900.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium TC 6]
 gi|289161970|gb|EFD09838.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium D344SRF]
 gi|291590552|gb|EFF22285.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1636]
 gi|291595827|gb|EFF27111.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1679]
          Length = 310

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/194 (22%), Positives = 75/194 (38%), Gaps = 25/194 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   + GA     VE  +KI E      I LN+ CP    +    G     +PD+ 
Sbjct: 95  NELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCP----NVKHGGIAFGTDPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +           
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDL 204

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             RK IL           I  +   +++++      L I   GG++ +   L++ +    
Sbjct: 205 KTRKPILANQTGGLSGPAIKPVAIRLIHQVA-SISSLPIIGMGGVQTVDDVLEMFMAGAS 263

Query: 212 GVMIGRAAYKNSAM 225
            V IG A + +  +
Sbjct: 264 AVAIGTANFTDPYI 277


>gi|293553495|ref|ZP_06674123.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1039]
 gi|291602372|gb|EFF32596.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1039]
          Length = 310

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/194 (22%), Positives = 75/194 (38%), Gaps = 25/194 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   + GA     VE  +KI E      I LN+ CP    +    G     +PD+ 
Sbjct: 95  NELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCP----NVKHGGIAFGTDPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +           
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDL 204

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             RK IL           I  +   +++++      L I   GG++ +   L++ +    
Sbjct: 205 KTRKPILANQTGGLSGPAIKPVAIRLIHQVA-SISSLPIIGMGGVQTVDDVLEMFMAGAS 263

Query: 212 GVMIGRAAYKNSAM 225
            V IG A + +  +
Sbjct: 264 AVAIGTANFTDPYI 277


>gi|229918570|ref|YP_002887216.1| dihydroorotate dehydrogenase family protein [Exiguobacterium sp.
           AT1b]
 gi|229469999|gb|ACQ71771.1| dihydroorotate dehydrogenase family protein [Exiguobacterium sp.
           AT1b]
          Length = 308

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 84/218 (38%), Gaps = 28/218 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV 88
           DAI+      +  F T+   +   + G+   + VE A+ +  D     I LN+ CP    
Sbjct: 78  DAIIEEKLPFLSTFDTE---IIANVAGSTPDEYVEVARRISADPTIKAIELNISCP---- 130

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P +  +    +  A S PV VK    V       ++ ++ ++++ +G 
Sbjct: 131 NVKCGGMQFGTDPVMAAELTRLVKAASSKPVYVKLSPNV------TSITDMARAVEAAGA 184

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              R  +   +       I  +   +VYE+ +   ++ I   GG
Sbjct: 185 DGLTMINTLVGMRIDIETGRPILANRIGGLSGPAIKPVAVRMVYEVAQAV-NIPIIAMGG 243

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +   L+ I      V +G A ++N  +   + E  
Sbjct: 244 VRTVDDVLEFIYAGASAVAVGTANFENPYVCQEIIEAL 281


>gi|227551412|ref|ZP_03981461.1| dihydroorotate oxidase [Enterococcus faecium TX1330]
 gi|257887479|ref|ZP_05667132.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,141,733]
 gi|257895974|ref|ZP_05675627.1| dihydroorotate dehydrogenase [Enterococcus faecium Com12]
 gi|293377432|ref|ZP_06623634.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium PC4.1]
 gi|293570484|ref|ZP_06681539.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E980]
 gi|227179421|gb|EEI60393.1| dihydroorotate oxidase [Enterococcus faecium TX1330]
 gi|257823533|gb|EEV50465.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,141,733]
 gi|257832539|gb|EEV58960.1| dihydroorotate dehydrogenase [Enterococcus faecium Com12]
 gi|291609430|gb|EFF38697.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E980]
 gi|292643950|gb|EFF62058.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium PC4.1]
          Length = 310

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/194 (22%), Positives = 76/194 (39%), Gaps = 25/194 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   + GA     VE  +KI E      I LN+ CP    +    G     +PD+ 
Sbjct: 95  NELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCP----NVKHGGIAFGTDPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +           
Sbjct: 151 FQLTQAVKKVASVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDL 204

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             RK IL           I  +   +++++     +L I   GG++ +   L++ +    
Sbjct: 205 KTRKPILANQTGGLSGPAIKPVAIRLIHQVA-SISNLPIIGMGGVQTVDDVLEMFMAGAS 263

Query: 212 GVMIGRAAYKNSAM 225
            V IG A + +  +
Sbjct: 264 AVAIGTANFTDPYI 277


>gi|167948845|ref|ZP_02535919.1| tRNA-dihydrouridine synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 109

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/87 (43%), Positives = 56/87 (64%), Gaps = 1/87 (1%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEG 91
               ++  L F   E P+A+Q+GG++ +      + + E  GY+E+NLNVGCPS RV  G
Sbjct: 13  CTAMQERFLEFDVSEHPVAIQLGGSNPAGACRGRRGLAETAGYDEVNLNVGCPSDRVQNG 72

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIP 118
             GACLM +P++V DC+ AM +A+SIP
Sbjct: 73  MIGACLMAHPELVADCVRAMKEAVSIP 99


>gi|104774368|ref|YP_619348.1| dihydroorotate dehydrogenase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423449|emb|CAI98330.1| Dihydroorotate dehydrogenase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
          Length = 309

 Score = 85.3 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 37/189 (19%), Positives = 75/189 (39%), Gaps = 24/189 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     + P+   +GG  +   VE A+I+     + + LN+ CP   V EG     ++  
Sbjct: 91  LREKHPDLPILASVGGESVEDYVEVAEILAAAKPDALELNLSCP--NVSEGGMTFGIV-- 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P+++      + + + +PV VK    V       ++  + ++ +  G +G+         
Sbjct: 147 PEMLEKITRLVKEKVDLPVYVKLTPNV------TSIVEIAQAAEGGGADGLTLINTLLVL 200

Query: 153 ---IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
              +  R+ +L         + +  +   +V ++K+    L I   GG+     A + IL
Sbjct: 201 HLDLKTRRPVLGNDFGGLYGQAVKPVAVRMVAQVKQAT-SLPIIGVGGINSPEDAAEFIL 259

Query: 208 PSVDGVMIG 216
                V IG
Sbjct: 260 AGASAVQIG 268


>gi|257898603|ref|ZP_05678256.1| dihydroorotate dehydrogenase [Enterococcus faecium Com15]
 gi|257836515|gb|EEV61589.1| dihydroorotate dehydrogenase [Enterococcus faecium Com15]
          Length = 310

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/194 (22%), Positives = 76/194 (39%), Gaps = 25/194 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   + GA     VE  +KI E      I LN+ CP    +    G     +PD+ 
Sbjct: 95  NELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCP----NVKHGGIAFGTDPDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +           
Sbjct: 151 FQLTQAVKKVASVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDL 204

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             RK IL           I  +   +++++     +L I   GG++ +   L++ +    
Sbjct: 205 KTRKPILANQTGGLSGPAIKPVAIRLIHQVA-SISNLPIIGMGGVQTVDDVLEMFMAGAS 263

Query: 212 GVMIGRAAYKNSAM 225
            V IG A + +  +
Sbjct: 264 AVAIGTANFTDPYI 277


>gi|51246867|ref|YP_066751.1| dihydroorotate dehydrogenase, catalytic subunit [Desulfotalea
           psychrophila LSv54]
 gi|50877904|emb|CAG37744.1| probable dihydroorotate dehydrogenase, catalytic subunit
           [Desulfotalea psychrophila LSv54]
          Length = 309

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/205 (20%), Positives = 80/205 (39%), Gaps = 25/205 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            Q  P  + I G  + +  + A+ +    G   I +N+ CP   V +G        NP++
Sbjct: 97  EQGLPAVVNILGDSLEEYRDIAQKLRGVKGIAAIEVNISCP--NVKKGGVAFG--TNPEM 152

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIW 152
                  +  A  +PV VK    V D      +  + ++++  G +           GI 
Sbjct: 153 AARVTRTVKDAADVPVMVKLSPNVTD------ITEIARAVEAGGADSLSMINTLIGMGID 206

Query: 153 IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           I  R+  L   +       I  +   +VY++ K    + I   GG+  +   ++ +L   
Sbjct: 207 IKTRRPSLANIIGGLSGPAIKPVALRMVYQVAK-VVSVPIIGIGGISSLEDVIEFLLAGA 265

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSN 235
             V IG A + + A+ + + E  ++
Sbjct: 266 SAVQIGTANFVDPAISSDLVEQLAD 290


>gi|321315319|ref|YP_004207606.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis BSn5]
 gi|320021593|gb|ADV96579.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis BSn5]
          Length = 311

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 85/218 (38%), Gaps = 28/218 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARV 88
           D++L  +   +  F T   P+   + G+ +   VE A+ +      + + LN+ CP    
Sbjct: 77  DSVLHHELPWLEQFDT---PIIANVAGSQVDDYVEVAEHISKAPNVHALELNISCP---- 129

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +  + G     NP++  D   A+ +   +PV VK    V        +  +  +I+++G 
Sbjct: 130 NVKTGGIAFGTNPEMAADLTKAVKEVSDVPVYVKLSPNV------ANITEIALAIEEAGA 183

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  +           +  +   +VYE+ +   ++ I   GG
Sbjct: 184 DGLTMINTLIGMRLDLKTGKPILANKTGGLSGPAVKPVAIRMVYEVSQAV-NIPIIGMGG 242

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++    AL+ +L     V +G A + N      + E  
Sbjct: 243 VQTAEDALEFLLAGASAVAVGTANFVNPFACLEIIEQL 280


>gi|170289867|ref|YP_001736683.1| dihydroorotate dehydrogenase family protein [Candidatus Korarchaeum
           cryptofilum OPF8]
 gi|170173947|gb|ACB07000.1| dihydroorotate dehydrogenase family protein [Candidatus Korarchaeum
           cryptofilum OPF8]
          Length = 275

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 76/199 (38%), Gaps = 21/199 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E P+    GG    ++   A  ++D G + + LN  CP    H    G  +   P+++ +
Sbjct: 68  EIPVIGSAGGNTPEEVAYVAGRLQDCGVDAVELNASCP----HVRGHGLEVGSTPELMRE 123

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            ++ + + + IP+ VK    V D     +    +  + + +I       I + A   +L 
Sbjct: 124 LVSEVRRNVKIPIIVKLSPMVPDIASLGRSAFESGADALNAINTVRAMYIDVEAMTPVLS 183

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
               GLS    R I       V  + +      +   GG+E    A++ +L     V IG
Sbjct: 184 NKFGGLSGPAIRPI------AVRCVYELAGICDVIGTGGVETWRDAVEMMLAGAKAVGIG 237

Query: 217 RAAYKN-SAMLTTVDEYFS 234
            A Y+    +   ++    
Sbjct: 238 TAIYRRGLEVFEEINRGLE 256


>gi|218887233|ref|YP_002436554.1| dihydroorotate dehydrogenase [Desulfovibrio vulgaris str. 'Miyazaki
           F']
 gi|218758187|gb|ACL09086.1| dihydroorotate dehydrogenase family protein [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 308

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/219 (19%), Positives = 82/219 (37%), Gaps = 27/219 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARV 88
           D +    +  +     +E P+   +   D  +  E AA +  + G   + +N+ CP   V
Sbjct: 80  DGVDYFVRTTLPKLPWREVPIVANLYACDPGEFGELAAVLAAEEGVAALEVNISCP--NV 137

Query: 89  HEGSFGACLMLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
            EG        +P        A+  +A S PV VK    V D      + ++ ++++ +G
Sbjct: 138 KEGGVIFG--QDPRQAAKVTEAVKMRAGSKPVIVKLSPNVTD------IAHMARAVEDAG 189

Query: 148 VN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            +           G+ I+ RK +L   +       I  +    V++  K    + +   G
Sbjct: 190 ADVLSCINTLTGMGVDINTRKPLLANVVGGLSGPAIKPVALRCVWQAAKAV-SIPVIGIG 248

Query: 196 GLEDMSQALK-ILPSVDGVMIGRAAYKNS-AMLTTVDEY 232
           G+      L+ +L     V +G A +     +   VD+ 
Sbjct: 249 GITSAEDVLEFLLVGAHAVQVGTANFIRPDFVFRLVDDL 287


>gi|163816502|ref|ZP_02207866.1| hypothetical protein COPEUT_02691 [Coprococcus eutactus ATCC 27759]
 gi|158448202|gb|EDP25197.1| hypothetical protein COPEUT_02691 [Coprococcus eutactus ATCC 27759]
          Length = 304

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/214 (17%), Positives = 79/214 (36%), Gaps = 28/214 (13%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           ++IL     +  + + + G      V+  + + D   + + +NV CP    +    G   
Sbjct: 87  RDILFLRDYDTKIIVNVCGKSKEDYVDCVEKLGDCDVDLLEINVSCP----NVKEGGIAF 142

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG------- 150
              PD + D   A+  A   P+ +K    V D      +  + ++ +  G +        
Sbjct: 143 GQQPDALYDITKAVKAAAKQPIIMKLSPNVTD------ITEMARAAEAGGADAVSLINTL 196

Query: 151 ----IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               I ++ R  A+    +      I  +   +VY++      L I   GG+     AL+
Sbjct: 197 TGMKIDVNRRTFAVANKTAGVSGPAIHPIAVRMVYQVANAI-KLPIIGMGGVATTEDALE 255

Query: 206 I-LPSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + +     V +G A + N      ++  ++EY  
Sbjct: 256 MIMVGASAVAVGTANFHNPYATVEIIKGIEEYMK 289


>gi|45358002|ref|NP_987559.1| dihydroorotate dehydrogenase 1B [Methanococcus maripaludis S2]
 gi|44920759|emb|CAF29995.1| Dihydroorotate oxidase [Methanococcus maripaludis S2]
          Length = 304

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 83/203 (40%), Gaps = 30/203 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G + S+  +AA+I+ ++  + + LN+ CP A    G +G+ +  +P +  + ++
Sbjct: 97  IIGSIYGKNDSEFQKAAEIIGNY-VDVLELNISCPHA---GGGYGSSIGQDPYLCKNVVS 152

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARK 157
           A+     IPV  K    V D      ++ +  ++  +G +GI             I +  
Sbjct: 153 AVKDVSDIPVIAKLTPNVTD------IKEIANAVVNAGADGIVAINTLGPGMVIDIESGV 206

Query: 158 AILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            IL         + +  +    VY+I     D+ +   GG+   + A++ ++     V +
Sbjct: 207 PILGNRVGGMSGKAVKPIAVKNVYDICSAV-DVPVIGVGGITTGADAIEFMMAGASAVQV 265

Query: 216 GRAAYKNSA-ML----TTVDEYF 233
           G   Y     +       ++EY 
Sbjct: 266 GTGVYYRGYDIFQKINNEIEEYL 288


>gi|225854468|ref|YP_002735980.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae JJA]
 gi|225723113|gb|ACO18966.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae JJA]
          Length = 312

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|310780263|ref|YP_003968595.1| dihydroorotate oxidase B, catalytic subunit [Ilyobacter polytropus
           DSM 2926]
 gi|309749586|gb|ADO84247.1| dihydroorotate oxidase B, catalytic subunit [Ilyobacter polytropus
           DSM 2926]
          Length = 306

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 39/200 (19%), Positives = 78/200 (39%), Gaps = 25/200 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G  I + VE AK VE       I LN+ CP    +    G      P++ G  
Sbjct: 96  PIITNINGRTIEEYVEIAKRVESIEAVKAIELNISCP----NVKDGGMAFGARPEVAGAV 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
             A+ +  + PV VK    V D      +  + K ++++G +            I I  +
Sbjct: 152 TKAVKEVTTKPVIVKLSPNVTD------IVAIAKIVEENGADAVALINTLLGMSIDIKKK 205

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L           +  +   ++Y++ +      +G+ GG+  ++ A++ ++     + 
Sbjct: 206 KPVLGNIFGGLSGPAVKPVALRMIYQVSQAVKIPVLGM-GGISSVNDAIEFLMAGASAIS 264

Query: 215 IGRAAYKNSAMLTTVDEYFS 234
           +G   + N  +   + E   
Sbjct: 265 LGTGIFMNPILPLEIKEGLE 284


>gi|148992901|ref|ZP_01822520.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae SP9-BS68]
 gi|168490217|ref|ZP_02714416.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae SP195]
 gi|169833969|ref|YP_001694409.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           Hungary19A-6]
 gi|194398689|ref|YP_002037599.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae G54]
 gi|225856622|ref|YP_002738133.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae P1031]
 gi|225858757|ref|YP_002740267.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae 70585]
 gi|147928353|gb|EDK79369.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae SP9-BS68]
 gi|168996471|gb|ACA37083.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae Hungary19A-6]
 gi|183571422|gb|EDT91950.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae SP195]
 gi|194358356|gb|ACF56804.1| dihydroorotate dehydrogenase B [Streptococcus pneumoniae G54]
 gi|225721785|gb|ACO17639.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae 70585]
 gi|225725581|gb|ACO21433.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae P1031]
 gi|301794102|emb|CBW36508.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae INV104]
 gi|332073297|gb|EGI83776.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA17570]
 gi|332204967|gb|EGJ19032.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA47901]
          Length = 312

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|149010390|ref|ZP_01831761.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP19-BS75]
 gi|147764871|gb|EDK71800.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP19-BS75]
          Length = 312

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|298503026|ref|YP_003724966.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae TCH8431/19A]
 gi|298238621|gb|ADI69752.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae TCH8431/19A]
          Length = 328

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 140 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 194

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 195 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 251

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 252 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 304


>gi|195392594|ref|XP_002054942.1| GJ19062 [Drosophila virilis]
 gi|194149452|gb|EDW65143.1| GJ19062 [Drosophila virilis]
          Length = 137

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/136 (27%), Positives = 57/136 (41%), Gaps = 13/136 (9%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP     +G  GA L+ +P      +  +   L IPVT K RI  D          LV
Sbjct: 1   MGCPKEFSIKGGMGAALLADPAKAAHILRTLSSQLDIPVTCKIRILPDLLDT----IRLV 56

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           + +  +G+  I IHAR         +D R       D+++ +     D+ I  NGG  DM
Sbjct: 57  QQLAVTGIAAIGIHART--------RDERPQHRPHPDVLHAVASAV-DIPIIANGGSRDM 107

Query: 201 SQALKILPSVDGVMIG 216
               +    V  V++G
Sbjct: 108 HTFARFGIWVTTVVVG 123


>gi|325295664|ref|YP_004282178.1| dihydroorotate dehydrogenase family protein [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325066112|gb|ADY74119.1| dihydroorotate dehydrogenase family protein [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 303

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/202 (20%), Positives = 79/202 (39%), Gaps = 25/202 (12%)

Query: 50  LALQIGGADISK-LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   I G+ I + +  A ++    G + + LN+ CP   V +G  G    ++P       
Sbjct: 95  VIANIYGSTIEEYMAVAKELKGAPGVDAVELNISCP--NVKKG--GLAFGVDPVEAAKLT 150

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARK 157
            A+ K+   PV VK    V D      +  + KS++ +G +            I I+ RK
Sbjct: 151 EAVKKSTDKPVIVKLSPNVTD------IVEIAKSVESAGADALSAINTLLGMAIDIYKRK 204

Query: 158 AILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
             +K          I  +   +VY++ K    + +   GG+     A++  L     + +
Sbjct: 205 PRIKNKFGGLSGPAIKPVAVRMVYQVSKAVK-IPVIGIGGISTWEDAVEFFLAGASAIQV 263

Query: 216 GRAAYKNSAMLTTVDEYFSNPL 237
           G A + N   +  + +   + L
Sbjct: 264 GTANFFNPKAVEEIVKGLEDYL 285


>gi|307708598|ref|ZP_07645062.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis NCTC 12261]
 gi|307615347|gb|EFN94556.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           mitis NCTC 12261]
          Length = 312

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  NPD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQNPDLAYDVVKAAVEASDVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|325663471|ref|ZP_08151881.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331087003|ref|ZP_08336078.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 9_1_43BFAA]
 gi|325470370|gb|EGC73601.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330409453|gb|EGG88896.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 9_1_43BFAA]
          Length = 300

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/202 (16%), Positives = 71/202 (35%), Gaps = 24/202 (11%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            +  + + + G       E  + +     + + +N+ CP    +    G     NP    
Sbjct: 91  HDTKIIVNVCGRSKEDYCEVVERLASEDVDMLEINISCP----NVKEGGIAFGQNPKAAE 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIH 154
           +  +A+ K    PV +K    V D      +  + K+++  G +            I +H
Sbjct: 147 EITSAVKKYAKQPVIMKLSPNVTD------ITEMAKAVEAGGADAVSLINTLTGMKIDVH 200

Query: 155 ARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R  A+           I  +   +VY++     ++ I   GG+     A++ IL     
Sbjct: 201 RRAFALANKTGGVSGPAIKPIAVRMVYQVANAV-NIPIIGMGGIATAEDAIEFILAGASA 259

Query: 213 VMIGRAAYKNSAMLTTVDEYFS 234
           V +G A + N  +   + +   
Sbjct: 260 VSVGTANFINPGVTAEIVDGIE 281


>gi|257884643|ref|ZP_05664296.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,501]
 gi|257820481|gb|EEV47629.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,501]
          Length = 310

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 43/194 (22%), Positives = 75/194 (38%), Gaps = 25/194 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   + GA     VE  +KI E      I LN+ CP    +    G     +P++ 
Sbjct: 95  NELPIIANVAGACEEDYVEVCSKISEAPNVKAIELNISCP----NVKHGGIAFGTDPEVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +           
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDL 204

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             RK IL           I  +   +++++      L I   GG++ +   L++ +    
Sbjct: 205 KTRKPILANQTGGLSGPAIKPVAIRLIHQVA-SISSLPIIGMGGVQTVDDVLEMFMAGAS 263

Query: 212 GVMIGRAAYKNSAM 225
            V IG A + +  +
Sbjct: 264 AVAIGTANFTDPYI 277


>gi|15900841|ref|NP_345445.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae TIGR4]
 gi|148988405|ref|ZP_01819852.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP6-BS73]
 gi|168485916|ref|ZP_02710424.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC1087-00]
 gi|168494393|ref|ZP_02718536.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC3059-06]
 gi|221231727|ref|YP_002510879.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae ATCC 700669]
 gi|237650887|ref|ZP_04525139.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae CCRI
           1974]
 gi|237821895|ref|ZP_04597740.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298229842|ref|ZP_06963523.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298254541|ref|ZP_06978127.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|303259876|ref|ZP_07345851.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP-BS293]
 gi|303262290|ref|ZP_07348234.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP14-BS292]
 gi|303264712|ref|ZP_07350630.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS397]
 gi|303267241|ref|ZP_07353106.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS457]
 gi|303269527|ref|ZP_07355292.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS458]
 gi|14972438|gb|AAK75085.1| dihydroorotate dehydrogenase B [Streptococcus pneumoniae TIGR4]
 gi|147926086|gb|EDK77160.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP6-BS73]
 gi|183571069|gb|EDT91597.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC1087-00]
 gi|183575702|gb|EDT96230.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674187|emb|CAR68715.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae ATCC 700669]
 gi|302636613|gb|EFL67104.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP14-BS292]
 gi|302639081|gb|EFL69541.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP-BS293]
 gi|302640963|gb|EFL71345.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS458]
 gi|302643250|gb|EFL73532.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS457]
 gi|302645799|gb|EFL76028.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS397]
 gi|332076238|gb|EGI86704.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA41301]
          Length = 312

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|168491053|ref|ZP_02715196.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183574652|gb|EDT95180.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae CDC0288-04]
          Length = 312

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|330938357|gb|EGH41985.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 121

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 5/89 (5%)

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              DG++IGRAA     +   ++ +     T  +P  + V++     ++A    Y     
Sbjct: 3   TGADGLLIGRAAQGRPWIFREIEHFLRTGETLPAPQSSEVERILLEHLAALHVFY----- 57

Query: 268 HSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
                ++   +H+       P +R  R  
Sbjct: 58  GDVMGVRIARKHVSWYLATLPGAREFRAH 86


>gi|182683910|ref|YP_001835657.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae CGSP14]
 gi|182629244|gb|ACB90192.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae CGSP14]
          Length = 330

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 142 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 196

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 197 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 253

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 254 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 306


>gi|111658035|ref|ZP_01408737.1| hypothetical protein SpneT_02000768 [Streptococcus pneumoniae
           TIGR4]
          Length = 319

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 131 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 185

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 186 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 242

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 243 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 295


>gi|309800244|ref|ZP_07694421.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           infantis SK1302]
 gi|308116126|gb|EFO53625.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           infantis SK1302]
          Length = 312

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 68/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V  G+ G  +  +P++  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHGNHGLLIGQDPELAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK  I  G        +  +   ++ 
Sbjct: 179 ---IVTIAKAAEDAGASGLTMINTLVGMRFDLKTRKPIIANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +    L I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTKLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|148543364|ref|YP_001270734.1| dihydroorotate dehydrogenase 1B [Lactobacillus reuteri DSM 20016]
 gi|184152774|ref|YP_001841115.1| dihydroorotate dehydrogenase 1B [Lactobacillus reuteri JCM 1112]
 gi|227364438|ref|ZP_03848528.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           MM2-3]
 gi|325683637|ref|ZP_08163153.1| dihydroorotate oxidase [Lactobacillus reuteri MM4-1A]
 gi|189038428|sp|A5VHS3|PYRD_LACRD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|229470318|sp|B2G5A3|PYRD_LACRJ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|148530398|gb|ABQ82397.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           DSM 20016]
 gi|183224118|dbj|BAG24635.1| dihydroorotate dehydrogenase [Lactobacillus reuteri JCM 1112]
 gi|227070531|gb|EEI08864.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           MM2-3]
 gi|324977987|gb|EGC14938.1| dihydroorotate oxidase [Lactobacillus reuteri MM4-1A]
          Length = 308

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/198 (20%), Positives = 79/198 (39%), Gaps = 26/198 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L  +  + P+     G    + V+   +     G   I LNV CP    +    G  +  
Sbjct: 92  LRKNYPQLPIIASAAGFSEDEYVKVVSEFANTAGVKAIELNVSCP----NVKHGGMAMGT 147

Query: 100 NPDIVGDCIAAMCKA-LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
           +P+++   +  + KA L IP+ VK    V + +P      L ++ ++ G NG+ +     
Sbjct: 148 DPEVLQRLVKQVVKAALGIPIYVKLTPNVTNIVP------LAQAAEQGGANGLTMINTLT 201

Query: 154 -------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK- 205
                    R A+           I  L   +++++ ++   L I   GG+E     L+ 
Sbjct: 202 GLSIDLKTRRPALANVTGGLSGPAIKPLALRMIHQV-RQVSSLPIIGVGGIESAEDVLEF 260

Query: 206 ILPSVDGVMIGRAAYKNS 223
           ++   + V IG A++ + 
Sbjct: 261 MMAGANAVQIGAASFHDP 278


>gi|323706443|ref|ZP_08118005.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323534228|gb|EGB24017.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 301

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/221 (21%), Positives = 86/221 (38%), Gaps = 31/221 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA ++ +   +  F+T+   +   I G  I + V  A+ +   G + + +NV CP   V 
Sbjct: 78  DAFIKDELPFLNRFNTK---VIANIAGETIEEFVLLAQKLNIDGVDALEINVSCP--NVK 132

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           EG     +  +P+ V +    + +  +  V VK    V D           K+ +  G +
Sbjct: 133 EGGMSFGI--DPNSVHEITKKVKEVSNKTVIVKLTPNVTDIKIY------AKAAEDGGAD 184

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            I+ R+ + K   +      I  +    VYE K+      IG+ GG+
Sbjct: 185 AISLINTVTGMAIDINTRRPVFKNVFAGLSGPAIKPIALKNVYEAKRAVSIPVIGM-GGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYF 233
                AL+ ++     V IG   + N A    +L  + +Y 
Sbjct: 244 SSAEDALEFMITGATAVAIGTYNFINPAGSIDILEGIKKYM 284


>gi|227543831|ref|ZP_03973880.1| dihydroorotate oxidase [Lactobacillus reuteri CF48-3A]
 gi|300908899|ref|ZP_07126362.1| dihydroorotate oxidase [Lactobacillus reuteri SD2112]
 gi|112943111|gb|ABI26297.1| dihydroorotate dehydrogenase [Lactobacillus reuteri]
 gi|227186208|gb|EEI66279.1| dihydroorotate oxidase [Lactobacillus reuteri CF48-3A]
 gi|300894306|gb|EFK87664.1| dihydroorotate oxidase [Lactobacillus reuteri SD2112]
          Length = 308

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/198 (20%), Positives = 79/198 (39%), Gaps = 26/198 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L  +  + P+     G    + V+   +     G   I LNV CP    +    G  +  
Sbjct: 92  LRKNYPQLPIIASAAGFSEDEYVKVVSEFANTAGVKAIELNVSCP----NVKHGGMAMGT 147

Query: 100 NPDIVGDCIAAMCKA-LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
           +P+++   +  + KA L IP+ VK    V + +P      L ++ ++ G NG+ +     
Sbjct: 148 DPEVLQRLVKQVVKAALGIPIYVKLTPNVTNIVP------LAQAAEEGGANGLTMINTLT 201

Query: 154 -------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK- 205
                    R A+           I  L   +++++ ++   L I   GG+E     L+ 
Sbjct: 202 GLSIDLKTRRPALANVTGGLSGPAIKPLALRMIHQV-RQVSSLPIIGVGGIESAEDVLEF 260

Query: 206 ILPSVDGVMIGRAAYKNS 223
           ++   + V IG A++ + 
Sbjct: 261 MMAGANAVQIGAASFHDP 278


>gi|148984706|ref|ZP_01817974.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP3-BS71]
 gi|147923097|gb|EDK74212.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP3-BS71]
 gi|301799940|emb|CBW32523.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae OXC141]
          Length = 312

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/170 (22%), Positives = 69/170 (40%), Gaps = 22/170 (12%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D      +
Sbjct: 128 IELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD------I 179

Query: 137 RNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKK 184
             + K+ + +G +G+ +             RK IL  G        +  +   ++ ++ +
Sbjct: 180 VTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIRQVAQ 239

Query: 185 ENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 240 -TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|116492120|ref|YP_803855.1| dihydroorotate dehydrogenase 1B [Pediococcus pentosaceus ATCC
           25745]
 gi|122266416|sp|Q03HA9|PYRD_PEDPA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116102270|gb|ABJ67413.1| dihydroorotate oxidase B, catalytic subunit [Pediococcus
           pentosaceus ATCC 25745]
          Length = 304

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/208 (20%), Positives = 83/208 (39%), Gaps = 26/208 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L  +  + P+   I G++    VE AK +        I +N+ CP   V +G  G     
Sbjct: 89  LAENYPDLPIVGSIAGSNPDDYVEVAKRMATAPNVKFIEVNISCP--NVAKG--GLAFGT 144

Query: 100 NPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
           +P +V D    +   + + PV +K   GV + +P      +  + ++ G +G+ +     
Sbjct: 145 DPVVVEDMTRRIKAVVPNKPVFMKLTPGVTEIVP------IALAAERGGADGLVMINTLM 198

Query: 154 ------HARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK- 205
                   RK  L  G      + I  +   +++++ +E  +L I   GG+     AL+ 
Sbjct: 199 GMEIDLETRKPRLSNGTGGLSGKAIHPIAVRMIHQV-REVTNLPIIGVGGVFSAKDALEL 257

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++     V +G A Y N      + +  
Sbjct: 258 MVAGAGAVQVGSANYGNPHACHDIIQGL 285


>gi|270290829|ref|ZP_06197053.1| dihydroorotate dehydrogenase [Pediococcus acidilactici 7_4]
 gi|270280889|gb|EFA26723.1| dihydroorotate dehydrogenase [Pediococcus acidilactici 7_4]
          Length = 303

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 44/189 (23%), Positives = 74/189 (39%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    + V  A ++        I +NV CP   V +G         P +V + 
Sbjct: 97  PIVGSVAGNIFEEYVTVAHRMASAPNVKLIEVNVSCP--NVKKGGIAFG--TEPQMVREL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+   +  PV VK    V       A+  LV + +  G +G+ +           H R
Sbjct: 153 TQAIKAQVDCPVLVKLTPAV------TAIEPLVLAAEAGGADGLVMINTLMGMEIDLHTR 206

Query: 157 KAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K  L  G      + I  L   +V++  ++  DL I   GG+   + AL+ ++     + 
Sbjct: 207 KPHLSNGTGGLSGKAIHPLAVRMVHQ-ARQVTDLPIIGVGGVFTPADALELMVAGAQAIQ 265

Query: 215 IGRAAYKNS 223
           IG A+Y N 
Sbjct: 266 IGSASYGNP 274


>gi|153824276|ref|ZP_01976943.1| conserved hypothetical protein [Vibrio cholerae B33]
 gi|126518202|gb|EAZ75427.1| conserved hypothetical protein [Vibrio cholerae B33]
          Length = 206

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 71/198 (35%), Gaps = 26/198 (13%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   + A   A+   IPV+ K R+G +D         +V ++ ++  + + +HAR     
Sbjct: 2   IYQVVKACRDAVPAHIPVSAKIRLGWEDPEDCF---EIVDAVAQAKADELTVHARTK--- 55

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
                   K   + +  + +I+++   + +  NG + + +     +    VD +M+ R A
Sbjct: 56  ----AGGYKASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCRGA 110

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
             N   L  V ++    +     +           +    T +  R         +I + 
Sbjct: 111 L-NVPNLGNVVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIKQW 159

Query: 280 MIGLFHGFPNSRRCRHIL 297
              L H +P +      L
Sbjct: 160 FAYLRHAYPQANELFGEL 177


>gi|194467523|ref|ZP_03073510.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
 gi|194454559|gb|EDX43456.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
          Length = 308

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 40/198 (20%), Positives = 79/198 (39%), Gaps = 26/198 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L  +  + P+     G    + V+   +     G   I LNV CP    +    G  +  
Sbjct: 92  LRKNYPQLPIIASAAGFSEDEYVKVVSEFANTAGVKAIELNVSCP----NVKHGGMAMGT 147

Query: 100 NPDIVGDCIAAMCKA-LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
           +P+++   +  + KA L IP+ VK    V + +P      L ++ ++ G NG+ +     
Sbjct: 148 DPEVLQRLVKQVVKAALGIPIYVKLTPNVTNIVP------LAQAAEQGGANGLTMINTLT 201

Query: 154 -------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK- 205
                    R A+           I  L   +++++ ++   L I   GG+E     L+ 
Sbjct: 202 GLSIDLKTRRPALANVTGGLSGPAIKPLALRMIHQV-RQVSSLPIIGVGGIESAEDVLEF 260

Query: 206 ILPSVDGVMIGRAAYKNS 223
           ++   + V IG A++ + 
Sbjct: 261 MMAGANAVQIGAASFHDP 278


>gi|304386349|ref|ZP_07368682.1| dihydroorotate oxidase [Pediococcus acidilactici DSM 20284]
 gi|304327706|gb|EFL94933.1| dihydroorotate oxidase [Pediococcus acidilactici DSM 20284]
          Length = 303

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 74/189 (39%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+   + V  A ++        I +NV CP    +    G      P +V + 
Sbjct: 97  PIVGSVAGSTFEEYVTVAHRMASAPNVKLIEVNVSCP----NVKEGGIAFGTEPQMVREL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+   +  PV VK    V       A+  LV + +  G +G+ +           H R
Sbjct: 153 TQAIKAQVDCPVLVKLTPAV------TAIEPLVLAAEAGGADGLVMINTLMGMEIDLHTR 206

Query: 157 KAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K  L  G      + I  L   +V++  ++  DL I   GG+   + AL+ ++     + 
Sbjct: 207 KPHLSNGTGGLSGKAIHPLAVRMVHQ-ARQVTDLPIIGVGGVFTPADALELMVAGAQAIQ 265

Query: 215 IGRAAYKNS 223
           IG A+Y N 
Sbjct: 266 IGSASYGNP 274


>gi|511017|emb|CAA52280.1| dihydroorotate dehydrogenase B [Lactococcus lactis subsp. cremoris
           MG1363]
          Length = 311

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 78/197 (39%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   + G++    +   AKI +      I LN+ CP    +    G     +P++  
Sbjct: 98  ELPIIANVAGSEEADYVAVCAKIGDRANVKAIELNISCP----NVKHGGQAFGTDPEVAA 153

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
             + A      +P+ VK    V D +P      + K+++ +G +G+ +            
Sbjct: 154 ALVKACKAVSKVPLYVKLSPNVTDIVP------IAKAVEAAGADGLTMINTLMGVRFDLK 207

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            R+ IL           I  +   +++++ ++  D+ I   GG+ +    L++ +     
Sbjct: 208 TRQPILANITGGLSGPAIKPVALKLIHQVAQDV-DIPIIGMGGVANAQVVLEMYMAGASR 266

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +   +
Sbjct: 267 VAVGTANFADPFVCPKI 283


>gi|331236666|ref|XP_003330991.1| PP35 [Puccinia graminis f. sp. tritici CRL 75-36-700-3]
 gi|309309981|gb|EFP86572.1| PP35 [Puccinia graminis f. sp. tritici CRL 75-36-700-3]
          Length = 228

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 29/163 (17%), Positives = 57/163 (34%), Gaps = 40/163 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS 60
           MV ++   +R        + + +T MI+     R                          
Sbjct: 42  MVRYSKLPFRQLVSEYETH-ITFTPMILHRVAKRKGISRY-------------------- 80

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA--AMCKALSIP 118
                         + I++N GCP     +   G+ L+  PD+V + +    +      P
Sbjct: 81  -------------VDGIDINCGCPQQWACKEGIGSALLRKPDLVRELVRFIKVSCGQDFP 127

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           V++K RI  D +  +     L+K+  ++ V+ I +H  +  L 
Sbjct: 128 VSIKIRIDDDLRNTS----QLIKTAIQANVSMITVHGIQRFLS 166


>gi|20089578|ref|NP_615653.1| hypothetical protein MA0693 [Methanosarcina acetivorans C2A]
 gi|19914494|gb|AAM04133.1| hypothetical protein (multi-domain) [Methanosarcina acetivorans
           C2A]
          Length = 379

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 46/208 (22%), Positives = 86/208 (41%), Gaps = 24/208 (11%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           E I  + +     K  +        +A+ +    +  L+EAAKIV++ G   + LN  C 
Sbjct: 68  EFISDEPM--ELIKKEIRAVNSGSVVAVNVRSTTLEPLIEAAKIVKEEGA-ILELNAHCK 124

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              + E   G  L+ +   +   I A+ +   + ++VK R  V + I       L + I 
Sbjct: 125 QPEMLEAGIGEALLRDLPRLSAWIKAIKE-TGVVLSVKVRANVINDI------ELARLID 177

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K+G + I +    A+L+G            D D +    ++   LF+  N  + D + A 
Sbjct: 178 KAGADIIHV---DAMLEGFG---------ADLDAIVN-YRDATRLFLIGNNSVTDFATAK 224

Query: 205 KILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            +     D V + R A +N  +++ + E
Sbjct: 225 DMFSRGADMVSVARGAMENPELISQLVE 252


>gi|295094684|emb|CBK83775.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Coprococcus sp. ART55/1]
          Length = 304

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 75/205 (36%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      VE  + + D   + + +NV CP    +    G      PD + D
Sbjct: 96  DTKIIVNVCGKSKEDYVECVEKLGDCDVDLLEINVSCP----NVKEGGIAFGQQPDALYD 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              A+  A   P+ +K    V D      +  + ++ +  G +            I ++ 
Sbjct: 152 ITKAVKAAAKQPIIMKLSPNVTD------ITEMARAAEAGGADAVSLINTLTGMKIDVNR 205

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           R  A+    +      I  +   +VY++      L I   GG+     AL++ +     V
Sbjct: 206 RTFAVANKTAGVSGPAIHPIAVRMVYQVANAI-KLPIIGMGGVATTEDALEMIMVGASAV 264

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            +G A + N      ++  ++EY  
Sbjct: 265 AVGTANFHNPYATVEIIKGIEEYMK 289


>gi|212639627|ref|YP_002316147.1| dihydroorotate dehydrogenase 1B [Anoxybacillus flavithermus WK1]
 gi|226724728|sp|B7GFA1|PYRD_ANOFW RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|212561107|gb|ACJ34162.1| Dihydroorotate dehydrogenase (catalytic subunit) [Anoxybacillus
           flavithermus WK1]
          Length = 312

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 76/201 (37%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ + + VE AK +      + + LN+ CP   V +G         P++  
Sbjct: 93  DVPIIANVAGSTVEEYVEVAKRISKAPNVHALELNISCP--NVKKGGIAFG--TVPEVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +   A+ +   +PV VK    V        +  + K+I+++G +G+ +            
Sbjct: 149 ELTRAVKEVSDVPVYVKLSPNV------TNIVAMAKAIEQAGADGLTMINTLVGMRIDVK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             +  +  G        I  +   ++YE+ +    L I   GG++     ++        
Sbjct: 203 TGKPILANGTGGLSGPAIKPIAIRMIYEVSQAV-SLPIIGMGGIQSAEDVIEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V IG A + +  +   +    
Sbjct: 262 VAIGTANFIDPYVCPNIIAEL 282


>gi|149019555|ref|ZP_01834874.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP23-BS72]
 gi|147930930|gb|EDK81910.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP23-BS72]
          Length = 312

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 67/165 (40%), Gaps = 22/165 (13%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA 224
           ++ +   DL I   GG++    AL++ L     + +G A + N  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPY 279


>gi|261403127|ref|YP_003247351.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           vulcanius M7]
 gi|261370120|gb|ACX72869.1| dihydroorotate dehydrogenase family protein [Methanocaldococcus
           vulcanius M7]
          Length = 302

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 49/190 (25%), Positives = 83/190 (43%), Gaps = 33/190 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G D  + ++ AK +E F  + I LN+ CP A+     +GA +  NP++  +  A
Sbjct: 97  VIGSIYGKDEKEFMDVAKKIESF-VDAIELNISCPHAK----GYGATIGQNPEMSYNVCA 151

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKA 158
           A+   + IPV  K    V D      +  +  ++ ++GV+G           I I A+K 
Sbjct: 152 AVKDVVKIPVFAKLTPNVSD------IVEIAGAVVEAGVDGLVAINTVRGMVIDIKAKKP 205

Query: 159 ILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           IL     GLS K  + +     +D+      EN D+ I   GG+     A++ ++     
Sbjct: 206 ILSNKFGGLSGKAIKPVGIKAVWDLY-----ENFDVPIIGVGGIMSGEDAIEYMMAGASA 260

Query: 213 VMIGRAAYKN 222
           V +G   Y  
Sbjct: 261 VQVGSGVYYR 270


>gi|21227953|ref|NP_633875.1| hypothetical protein MM_1851 [Methanosarcina mazei Go1]
 gi|20906376|gb|AAM31547.1| hypothetical protein MM_1851 [Methanosarcina mazei Go1]
          Length = 372

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 45/208 (21%), Positives = 88/208 (42%), Gaps = 24/208 (11%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           E I  + +     K  +        +A+ +   ++  L+EAAK+V++ G   + LN  C 
Sbjct: 61  EFISDEPL--ELIKQEIRAVNSGSAVAVNVRSTNLEPLIEAAKLVKEEGA-ILELNAHCK 117

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              + E   G  L+ +   +   I A+ +   + ++VK R  V + +       L + I 
Sbjct: 118 QPEMLESGIGEALLHDLPRLSAWIKAIKE-TGVVLSVKVRANVVNDV------ELARLID 170

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K+G + I +    A+L+G            D D +    ++   LF+  N  + D + A 
Sbjct: 171 KAGADIIHV---DAMLEGFG---------ADLDAISN-YRDATRLFLIGNNSITDFAAAK 217

Query: 205 KILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           ++     D V + R A +NS ++  + E
Sbjct: 218 EMFSRGADMVSVARGAMENSDLIKELVE 245


>gi|16078618|ref|NP_389437.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309428|ref|ZP_03591275.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313753|ref|ZP_03595558.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318677|ref|ZP_03599971.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322949|ref|ZP_03604243.1| dihydroorotate dehydrogenase 1B [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|131720|sp|P25996|PYRD_BACSU RecName: Full=Dihydroorotate dehydrogenase, catalytic subunit;
           AltName: Full=DHOdehase; Short=DHOD; Short=DHODase;
           AltName: Full=Dihydroorotate oxidase
 gi|143392|gb|AAA21272.1| dihydroorotase dehydrogenase [Bacillus subtilis]
 gi|2633927|emb|CAB13428.1| dihydroorotate dehydrogenase (catalytic subunit) [Bacillus subtilis
           subsp. subtilis str. 168]
          Length = 311

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 85/218 (38%), Gaps = 28/218 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARV 88
           D++L  +   +  F T   P+   + G+ +   VE A+ +      + + LN+ CP    
Sbjct: 77  DSVLHHELPWLEQFDT---PIIANVAGSQVDDYVEVAEHISKAPNVHALELNISCP---- 129

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +  + G     NP++  D   A+ +   +PV VK    V        +  +  +I+++G 
Sbjct: 130 NVKTGGIAFGTNPEMAADLTKAVKEVSDVPVYVKLSPNV------ANITEIALAIEEAGA 183

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  +           +  +   +VYE+ +   ++ I   GG
Sbjct: 184 DGLTMINTLIGMRLDLKTGKPILANKTGGLSGPAVKPVAIRMVYEVSQ-MVNIPIIGMGG 242

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++    AL+ +L     V +G A + N      + E  
Sbjct: 243 VQTAEDALEFLLAGASAVAVGTANFVNPFACPEIIEQL 280


>gi|116517057|ref|YP_816334.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae D39]
 gi|161410749|ref|NP_358460.2| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae R6]
 gi|116077633|gb|ABJ55353.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus
           pneumoniae D39]
          Length = 312

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSTEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|38196995|gb|AAH03659.2| DUS1L protein [Homo sapiens]
          Length = 299

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 53/161 (32%), Gaps = 29/161 (18%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           VT K R+  +            + ++K+G   + +H R    KG             ++ 
Sbjct: 13  VTCKIRVFPEIDKTV----RYAQMLEKAGCQLLTVHGRTKEQKG------PLSGAASWEH 62

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  ++K    + +  NG ++ +    + L    V GVM       N A+           
Sbjct: 63  IKAVRKAV-AIPVFANGNIQCLQDVERCLRDTGVQGVMSAEGNLHNPALF---------- 111

Query: 237 LTGSSPIKTRVDKDFWRKISASMTD--YAARHLHSGGKLQQ 275
             G SP    + +++   +        Y   HL    KL  
Sbjct: 112 -EGRSPAVWELAEEYLDIVREHPCPLSYVRAHL---FKLWH 148


>gi|149006359|ref|ZP_01830071.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP18-BS74]
 gi|225861149|ref|YP_002742658.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|307127485|ref|YP_003879516.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae 670-6B]
 gi|147762136|gb|EDK69098.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP18-BS74]
 gi|225728081|gb|ACO23932.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|306484547|gb|ADM91416.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae 670-6B]
 gi|327389242|gb|EGE87587.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA04375]
 gi|332075580|gb|EGI86048.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA17545]
 gi|332201430|gb|EGJ15500.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA47368]
          Length = 312

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSTEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|303254431|ref|ZP_07340537.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae BS455]
 gi|302598598|gb|EFL65638.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae BS455]
          Length = 312

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVVQ-TTDLPIIGMGGVDSAEAALEMYLAEASAIGVGTANFTNPYACPDIIENL 288


>gi|297583972|ref|YP_003699752.1| dihydroorotate dehydrogenase family protein [Bacillus
           selenitireducens MLS10]
 gi|297142429|gb|ADH99186.1| dihydroorotate dehydrogenase family protein [Bacillus
           selenitireducens MLS10]
          Length = 311

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 87/205 (42%), Gaps = 25/205 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+ + I G  +   VE ++ V   G  + + LN+ CP+ ++    FG+    +P +  
Sbjct: 93  DIPVLVNIAGNAVEDYVETSRKVAASGKASALELNISCPNVKIGGMQFGS----DPAVAR 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILK 161
           +   A+ + + IP+ VK    V D      +  + K+++  G +G+     +      ++
Sbjct: 149 ELTRAVKEVIDIPLYVKLSPNVTD------IVAMAKAVEAGGADGLSMINTLVGMTIDVQ 202

Query: 162 GLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
              P             I  +   ++Y++ +E     IG+ GG++ +   ++ ++     
Sbjct: 203 TGQPVLANKRGGLSGPAIKPVAIRMIYDVSQEVSIPIIGM-GGVQTVDDIIEFMMAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPL 237
           V +G A ++N  +   + +     L
Sbjct: 262 VAVGTANFQNPMICPELIDGLETRL 286


>gi|218883785|ref|YP_002428167.1| dihydroorotate dehydrogenase 1B [Desulfurococcus kamchatkensis
           1221n]
 gi|218765401|gb|ACL10800.1| Dihydroorotate dehydrogenase, PyrD [Desulfurococcus kamchatkensis
           1221n]
          Length = 302

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 44/187 (23%), Positives = 74/187 (39%), Gaps = 9/187 (4%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           KPL L IGG+ + + V+ A++  + G + + LN+ CP A      +G  L  +P +V   
Sbjct: 95  KPLILSIGGSSVEEFVKLAELASEAGVDAVELNLSCPHAE----GYGLELGSDPMLVYRI 150

Query: 108 IAAMCKALSIPVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG- 162
           +       S+PV  K     R+         A    +  I       I ++  K +L   
Sbjct: 151 VKDAVSVASLPVIAKLGLTDRVIESAGKALEAGVKALTLINTVKAMSIDVYTLKPVLSNK 210

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
                   I  +   +VY++ +E     IG+ G    M  A  IL     V +G A   N
Sbjct: 211 YGGLSGPPIHPIAVRVVYDVYREYRAEIIGVGGVSSWMDVAELILAGARAVQVGTALIWN 270

Query: 223 SAMLTTV 229
             ++  +
Sbjct: 271 ENIVDEI 277


>gi|15458470|gb|AAK99670.1| Dihydroorotate dehydrogenase [Streptococcus pneumoniae R6]
          Length = 330

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 142 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 196

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 197 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 253

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 254 QVAQ-TTDLPIIGMGGVDSTEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 306


>gi|298674196|ref|YP_003725946.1| dihydroorotate dehydrogenase family protein [Methanohalobium
           evestigatum Z-7303]
 gi|298287184|gb|ADI73150.1| dihydroorotate dehydrogenase family protein [Methanohalobium
           evestigatum Z-7303]
          Length = 302

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 86/232 (37%), Gaps = 33/232 (14%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           YTE +    I                P+   I   D    V+ A+ +     +   LNV 
Sbjct: 76  YTEFV--QEIENAKNNTS-------TPIIASIFAGDTEGFVKVAEELSSANPDGFELNVS 126

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP A      +GA +  +  +V +  A++C  + +PV VK    V        + ++ K+
Sbjct: 127 CPHAE----GYGATIGCDSCLVEEITASVCDVIDVPVWVKLTPNV------TNIVDIGKA 176

Query: 143 IKKSGVNG-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLF 190
            ++ G +            I I+    IL         R I  +    VY++   + D+ 
Sbjct: 177 AERGGADAVVSINTVRGMSIDINTGYPILGNRYGGLSGRAIRPIAVKCVYDLY-ASLDIP 235

Query: 191 IGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +   GG+     A+++ +     V +G A  ++  +  ++     + L+ + 
Sbjct: 236 VVGVGGVSCWQDAVEMIMAGASAVQVGSAVSQSMDVFKSISSGIEDYLSANE 287


>gi|299143799|ref|ZP_07036879.1| dihydroorotate oxidase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
 gi|298518284|gb|EFI42023.1| dihydroorotate oxidase [Peptoniphilus sp. oral taxon 386 str.
           F0131]
          Length = 299

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 43/211 (20%), Positives = 86/211 (40%), Gaps = 25/211 (11%)

Query: 33  LRGDKKNILG-FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +    +NILG  +T E  + + +GG  + + VEAAKI+ D+ +  I LN+ CP    +  
Sbjct: 78  IHYFAENILGKMNTLETNVIVNLGGNTVEEYVEAAKILNDYEFFAIELNISCP----NVK 133

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             G    +  D       A+ KA    + VK      D      +    K+++K+G +GI
Sbjct: 134 HGGMAFGIEADSAALVTEAVKKATRHRLIVKLSPNARD------IVESAKAVEKAGADGI 187

Query: 152 WIH------------ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +              +       +      I  +   + +++ K N  + +   GG+ +
Sbjct: 188 SLVNTFLAMAIDAKTGKAVFNNTYAGLSGPAIKPIALRMTHQVCK-NVSIPVIAMGGITN 246

Query: 200 MSQALK-ILPSVDGVMIGRAAYKNSAMLTTV 229
              A++ I+     + +G A + N  ++  +
Sbjct: 247 GMDAIEFIMAGASAIQVGTANFMNPNVILDI 277


>gi|326203552|ref|ZP_08193416.1| dihydroorotate dehydrogenase family protein [Clostridium
           papyrosolvens DSM 2782]
 gi|325986372|gb|EGD47204.1| dihydroorotate dehydrogenase family protein [Clostridium
           papyrosolvens DSM 2782]
          Length = 307

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/203 (19%), Positives = 81/203 (39%), Gaps = 28/203 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G  I +  E A+I+ D   + I +NV CP    +  +       +P  + +  +
Sbjct: 99  IIANIAGNTIEEYCEMAEILGDSQVDAIEMNVSCP----NVKAGCLAFGTSPKGIEEITS 154

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
           A+ K    P+ VK    V D      ++++  + + +G +            I I+ +K 
Sbjct: 155 AVKKYCKQPLIVKLTPNVSD------IKSIAMAAEGAGADCISLINTILGLAIDINKKKP 208

Query: 159 IL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           IL           +  +   +VYE    +  + +   GG+     A++ IL     VM+G
Sbjct: 209 ILANNFGGLSGPAVKPIALRMVYE-AAHSVKIPVIGMGGISSWEDAVEFILVGASAVMVG 267

Query: 217 RAAYKNSA----MLTTVDEYFSN 235
            A + N      ++  +++Y  +
Sbjct: 268 TANFVNPTIPIEIVNGIEKYLEH 290


>gi|317486114|ref|ZP_07944961.1| dihydroorotate dehydrogenase [Bilophila wadsworthia 3_1_6]
 gi|316922637|gb|EFV43876.1| dihydroorotate dehydrogenase [Bilophila wadsworthia 3_1_6]
          Length = 314

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 77/218 (35%), Gaps = 31/218 (14%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     ++ L          E P+   +     ++  E A  +  + G   + +
Sbjct: 77  MLNAVGLQNDGVESFLKNKLPRLPWHETPVIANLYATSPAEFAELAGILAAEEGIAGLEV 136

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRN 138
           N+ CP   V  G        +P +  +   A+ K A ++PV VK    V D      +  
Sbjct: 137 NISCP--NVKNGGVLFG--QDPALAAEVTQAVKKHAGNLPVIVKLSPNVTD------ITA 186

Query: 139 LVKSIKKSGVNGIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKEN 186
           + K+ +++G + I            +  RK +L   +       +  +    V+++    
Sbjct: 187 IAKAAEQAGADAISCINTITGMGVDVKTRKPLLANVVGGLSGPAVKPVALRCVWQVCNAV 246

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
             + +   GG+      L+ IL     V IG   +   
Sbjct: 247 -KIPVIGIGGITCAQDVLEFILVGAHAVEIGTMNFVRP 283


>gi|56964096|ref|YP_175827.1| dihydroorotate dehydrogenase catalytic subunit [Bacillus clausii
           KSM-K16]
 gi|81822095|sp|Q5WFJ4|PYRD_BACSK RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|56910339|dbj|BAD64866.1| dihydroorotate dehydrogenase catalytic subunit [Bacillus clausii
           KSM-K16]
          Length = 304

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 36/215 (16%), Positives = 86/215 (40%), Gaps = 29/215 (13%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           + +  F   + P+   I G+ +   +E AA++ +    + I LN+ CP    +    G  
Sbjct: 84  QELPRFDDYDVPILANIAGSTMDDYIEVAAELSQQRNVSAIELNISCP----NVKQGGIA 139

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--- 153
               P+I  +    +    ++PV VK    V D      +  + K+I+K+G +G+ +   
Sbjct: 140 FGTVPEIAAELTKEVKAVSAVPVYVKLSPNVAD------IVAIAKAIEKAGADGLAMINT 193

Query: 154 --------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                     R+ +L           I  +   +++++ ++  D+ I   GG++     +
Sbjct: 194 LLGMRIDAKTRRPVLANQYGGLSGAAIKPVALRMIHQVSQQV-DIPIIGMGGIQTAEDVI 252

Query: 205 K-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + +L     + +G A + +      ++  +  +  
Sbjct: 253 EFLLAGASCIAVGTANFTDPYTCPNIIRDLPHWLD 287


>gi|312136545|ref|YP_004003882.1| tim-barrel protein [Methanothermus fervidus DSM 2088]
 gi|311224264|gb|ADP77120.1| TIM-barrel protein [Methanothermus fervidus DSM 2088]
          Length = 238

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 33/145 (22%), Positives = 54/145 (37%), Gaps = 16/145 (11%)

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            +N  C    + E   G  L+ + D + + +  + K    PV+VK R  V    P V  R
Sbjct: 99  EINAHCRQKEIIELGCGQALLYDLDFLEEYVTEVVKKAHKPVSVKFRANV----PGVDER 154

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +   +   G + I   A K                 D + V ++     + F+  N  +
Sbjct: 155 EVASLLDDIGCDYIHFDAMKP-----------GADCADLNSVKKVSSAIKNAFLIGNNSI 203

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYK 221
            D+  A  +L    DG+ I RAA  
Sbjct: 204 RDIKSARNMLKSGADGISIARAALG 228


>gi|322376458|ref|ZP_08050951.1| dihydroorotate dehydrogenase B [Streptococcus sp. M334]
 gi|321282265|gb|EFX59272.1| dihydroorotate dehydrogenase B [Streptococcus sp. M334]
          Length = 330

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 77/199 (38%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    +  +   G    I LN+ CP   V   + G  +  +PD+  D 
Sbjct: 117 PIIANVAGFSKQEYAAVSHGISKAGNVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDV 174

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           + A  ++  +PV VK    V D      +  + K+ + +G +G+ +             R
Sbjct: 175 VKAAVESSGVPVYVKLTPSVTD------IVTVAKAAEDAGASGLTMINTLVGMRFDLKTR 228

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL  G        +  +   ++ ++ +   DL I   GG++    AL++ L     + 
Sbjct: 229 KPILANGTGGMSGPAVFPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIG 287

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N      + E  
Sbjct: 288 VGTANFTNPYACPDIIENL 306


>gi|307709145|ref|ZP_07645604.1| dihydroorotate dehydrogenase [Streptococcus mitis SK564]
 gi|307620091|gb|EFN99208.1| dihydroorotate dehydrogenase [Streptococcus mitis SK564]
          Length = 312

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 68/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +   PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQGPDLAYDVVKAAVEASDVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLSGASAIGVGTANFTNPYACPDIIENL 288


>gi|125973464|ref|YP_001037374.1| dihydroorotate oxidase B, catalytic subunit [Clostridium
           thermocellum ATCC 27405]
 gi|256005360|ref|ZP_05430325.1| dihydroorotate dehydrogenase family protein [Clostridium
           thermocellum DSM 2360]
 gi|281417665|ref|ZP_06248685.1| dihydroorotate dehydrogenase family protein [Clostridium
           thermocellum JW20]
 gi|125713689|gb|ABN52181.1| dihydroorotate oxidase B, catalytic subunit [Clostridium
           thermocellum ATCC 27405]
 gi|255990679|gb|EEU00796.1| dihydroorotate dehydrogenase family protein [Clostridium
           thermocellum DSM 2360]
 gi|281409067|gb|EFB39325.1| dihydroorotate dehydrogenase family protein [Clostridium
           thermocellum JW20]
 gi|316940299|gb|ADU74333.1| dihydroorotate dehydrogenase family protein [Clostridium
           thermocellum DSM 1313]
          Length = 307

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 87/225 (38%), Gaps = 25/225 (11%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
            A +  +   +  ++T+   +   I G  I    + A+++ D   + I LNV CP   V 
Sbjct: 83  RAFIENEIPFLRKYNTK---IIANIAGNTIEDYCKMAELLSDADIDAIELNVSCP--NVK 137

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD--------QIPAVALRNLVK 141
           +G        +P  + +  + + K    P+ VK    V D        +       +L+ 
Sbjct: 138 KG--CVAFGNSPAGISEITSKVKKYCKKPLIVKLTPNVTDIKEIAVAAEAAGADALSLIN 195

Query: 142 SIKKSGVNGIWIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +I    ++   IH ++ IL   +       +  +   +VYE+      + +   GG+   
Sbjct: 196 TILGMAID---IHRKRPILANNVGGLSGPAVKPIAVRMVYEVC-SVVKIPVIGMGGISSG 251

Query: 201 SQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNPLTGS 240
             A++ +L     VM+G A + N A    ++  +  Y      GS
Sbjct: 252 EDAVEFMLAGASAVMVGTANFINPAACIDVVEGIKNYLKMYNHGS 296


>gi|257416234|ref|ZP_05593228.1| pyrimidine biosynthesis D protein [Enterococcus faecalis AR01/DG]
 gi|257158062|gb|EEU88022.1| pyrimidine biosynthesis D protein [Enterococcus faecalis ARO1/DG]
          Length = 312

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +PDI    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSHLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|284161538|ref|YP_003400161.1| dihydroorotate dehydrogenase [Archaeoglobus profundus DSM 5631]
 gi|284011535|gb|ADB57488.1| dihydroorotate dehydrogenase family protein [Archaeoglobus
           profundus DSM 5631]
          Length = 294

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 43/196 (21%), Positives = 76/196 (38%), Gaps = 21/196 (10%)

Query: 35  GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
            +    L       PL +   G++  +  E  KI +        LN+ CP A+      G
Sbjct: 76  KEFARELKMFNGACPLIVSFFGSNPEEFAELVKIFDFANA--FELNLSCPHAK----GLG 129

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----- 149
             +  + D+V + I A+ +    PV  K    +D     V L  + +S K  G+      
Sbjct: 130 LEIGRDFDLVYEIIRAVKRNTDKPVFAKVSANLD----YVELAKVCESAKADGIVAINTV 185

Query: 150 ---GIWIHARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               I I +++ IL  +S     + I  +    V++I +E   + +   GG+ +    ++
Sbjct: 186 RGMAIDIVSKRPILSNVSGGVSGKAIKPIALKCVWDIYEEV-SIPVIGCGGISNWKDVVE 244

Query: 206 -ILPSVDGVMIGRAAY 220
             L     V IG A Y
Sbjct: 245 FALAGARAVQIGSAFY 260


>gi|148998601|ref|ZP_01826041.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP11-BS70]
 gi|168575626|ref|ZP_02721562.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae MLV-016]
 gi|307067621|ref|YP_003876587.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae AP200]
 gi|147755599|gb|EDK62646.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP11-BS70]
 gi|183578496|gb|EDT99024.1| dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate
           oxidase b) (dhodehase b) (dhodase b) (dhod b)
           [Streptococcus pneumoniae MLV-016]
 gi|306409158|gb|ADM84585.1| Dihydroorotate dehydrogenase [Streptococcus pneumoniae AP200]
 gi|332202819|gb|EGJ16888.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           pneumoniae GA41317]
          Length = 312

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 124 NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 178

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 179 ---IVTVAKAAEYAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 235

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++ +   DL I   GG++    AL++ L     + +G A + N      + E  
Sbjct: 236 QVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYACPDIIENL 288


>gi|293376323|ref|ZP_06622561.1| dihydroorotate dehydrogenase 1B [Turicibacter sanguinis PC909]
 gi|325845267|ref|ZP_08168571.1| dihydroorotate oxidase, catalytic subunit [Turicibacter sp. HGF1]
 gi|292645071|gb|EFF63143.1| dihydroorotate dehydrogenase 1B [Turicibacter sanguinis PC909]
 gi|325488708|gb|EGC91113.1| dihydroorotate oxidase, catalytic subunit [Turicibacter sp. HGF1]
          Length = 303

 Score = 82.6 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 74/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  + + V  AK I +      + +N+ CP    +    G     +  +  + 
Sbjct: 95  PIIANVAGKTLEEYVTVAKKICQAPNVAALEINISCP----NVKEGGIAFGTDAKVAAEL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
             A+ +  ++PV +K    V        +  + K+++ +G +GI +              
Sbjct: 151 TKAIKEVSTVPVYIKLSPNV------TNVVEIAKAVEAAGADGITMINTLLGMRFDMKTG 204

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           +  +  G        I  +   +++++ K N ++ I   GG+E     L+        V 
Sbjct: 205 KPILANGTGGLSGPAIKPVALRMIHDVYK-NVNIPIIGMGGIETAEDVLEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N  +   + E  
Sbjct: 264 VGTANFINPYVCVDIIEQL 282


>gi|258645191|ref|ZP_05732660.1| dihydroorotate oxidase [Dialister invisus DSM 15470]
 gi|260402540|gb|EEW96087.1| dihydroorotate oxidase [Dialister invisus DSM 15470]
          Length = 303

 Score = 82.6 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 79/201 (39%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   I G +  +    AK +   G +   +N+ CP    +    G     +P +  +
Sbjct: 94  DVPVICNIVGKNPEEYGMVAKALSVEGVDAFEVNISCP----NVKCGGIAFGSDPHMAAE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ +   +PV +K    V D      + ++ ++++ +G +            I +  
Sbjct: 150 VTRAVKRNTDLPVIMKLSPNVTD------IVSIARAVEDAGADAVSLINTLLGLAIDVKT 203

Query: 156 RKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ IL  ++       I  +   +V+++      + +   GG+   + A++ ++   D V
Sbjct: 204 RRPILGNVTGGLSGPAIKPVALRMVWQVA-HAVHIPVCGMGGIMTGTDAVEFMMAGADTV 262

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G A+  +   +  + +   
Sbjct: 263 QVGTASLASPYAIPKITDELR 283


>gi|328957538|ref|YP_004374924.1| dihydroorotate dehydrogenase 1B [Carnobacterium sp. 17-4]
 gi|328673862|gb|AEB29908.1| dihydroorotate dehydrogenase 1B [Carnobacterium sp. 17-4]
          Length = 309

 Score = 82.6 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 36/201 (17%), Positives = 76/201 (37%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G  + + +E  K +        + +NV CP    +    G      P+ V 
Sbjct: 93  DTPVIASVAGTTVEEYIEVTKKLCQSPTVRALEINVSCP----NVKEGGLTFGSKPESVY 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           D   A+    ++P+ +K    V        +  + ++ +K G +GI            + 
Sbjct: 149 DITRAVKTVSTVPIYIKLTPNV------TNIVEIAQAAEKGGADGISMINTLLGMSIDVE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            ++ IL   +       +  +   +VY++ +      IG+ GG+  +   L++ +     
Sbjct: 203 TKRPILANKTGGLSGPAVKPIAIRMVYQVSRAVSIPIIGM-GGISTVDDVLEMFMAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V IG A Y N  +   + E  
Sbjct: 262 VAIGTANYANPMICKELIEAL 282


>gi|295425253|ref|ZP_06817956.1| dihydroorotate oxidase [Lactobacillus amylolyticus DSM 11664]
 gi|295065029|gb|EFG55934.1| dihydroorotate oxidase [Lactobacillus amylolyticus DSM 11664]
          Length = 318

 Score = 82.6 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 44/197 (22%), Positives = 79/197 (40%), Gaps = 29/197 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG D +  VE A+ +   G  N + +NV CP   V  G       ++PD++ 
Sbjct: 107 ELPIMASVGGDDEAGYVEVARKLSASGLVNTLEINVSCP--NVARGGMSFG--VHPDVIE 162

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
           D    +   ++IP+ VK    V D      +  + K+ +  G +GI +            
Sbjct: 163 DLTKKIKDVVNIPIYVKLTPNVTD------IVEIAKAAQAGGADGISMINTVLGMEIDLK 216

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           +RK +L   +       I  +   ++ ++ +   DL I   GG+E     ++  L     
Sbjct: 217 SRKPVLGHNMGGFSGHAIKPIAIRMIAQVHQAV-DLPIIGMGGIETAEDVVEFFLAGASA 275

Query: 213 VMIGRA----AYKNSAM 225
           V +G A    A     +
Sbjct: 276 VAVGTAHFHDALACPHI 292


>gi|325958065|ref|YP_004289531.1| dihydroorotate dehydrogenase family protein [Methanobacterium sp.
           AL-21]
 gi|325329497|gb|ADZ08559.1| dihydroorotate dehydrogenase family protein [Methanobacterium sp.
           AL-21]
          Length = 300

 Score = 82.6 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 38/182 (20%), Positives = 73/182 (40%), Gaps = 25/182 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P    I GA+  +  + A  +++   + I LNV CP A    G  GA +  +P +    +
Sbjct: 90  PAIASIYGANPDEFSKIATHIQE-DVDAIELNVSCPHAM---GGCGAAIGQDPLLTSSIV 145

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHAR 156
           +A+ +++++P+ VK    V D      +  +  S + +G + +             I   
Sbjct: 146 SAVKESVNVPILVKLTPNVTD------IVEVAVSAQDAGADALTLINSLGPGMKIDITTG 199

Query: 157 KAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K IL           I  +    VY++  +  ++ +   GG+ +    L+ I      V 
Sbjct: 200 KPILSNRFGGMSGPAIKPVAVRCVYDVF-DAVEIPVVGVGGIRNYEDVLEFIYAGATCVQ 258

Query: 215 IG 216
           IG
Sbjct: 259 IG 260


>gi|315420425|gb|ADU15859.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacterium
           saccharolyticum]
          Length = 301

 Score = 82.6 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 46/221 (20%), Positives = 85/221 (38%), Gaps = 31/221 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA ++ +   +  F+T+   +   I G  I + V  A+ +   G + + +NV CP    +
Sbjct: 78  DAFIKDELPFLNRFNTK---VIANIAGETIEEFVSLAQKLNIDGVDALEINVSCP----N 130

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G    ++P+ V      + +A +  V VK    V D           K+ +  G +
Sbjct: 131 VKEGGMSFGVDPNSVYAITKKVKQASNKTVIVKLTPNVTDIKIY------AKAAEDGGAD 184

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            I+ R+ + K   +      I  +    VYE K+      IG+ GG+
Sbjct: 185 AISLINTVTGMAIDINTRRPVFKNVFAGLSGPAIKPIALKNVYEAKRAVSIPVIGM-GGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYF 233
                AL+ ++     V +G   + N A    +L  + +Y 
Sbjct: 244 SSAEDALEFMIAGATAVAVGTYNFINPAGSIDILEGIKKYM 284


>gi|154500487|ref|ZP_02038525.1| hypothetical protein BACCAP_04159 [Bacteroides capillosus ATCC
           29799]
 gi|150270718|gb|EDM98014.1| hypothetical protein BACCAP_04159 [Bacteroides capillosus ATCC
           29799]
          Length = 340

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 33/207 (15%), Positives = 72/207 (34%), Gaps = 25/207 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA +  +   +     +   +   I G          + +   G + I +N+ CP+ +  
Sbjct: 116 DAFIEHELPRLKDIDIR---IIANISGNTPEDYGVMCEKLSAAGVDMIEVNISCPNVKAG 172

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             ++G      P++  +      K  ++PV VK    V D      +  + ++++ +G +
Sbjct: 173 GLAYGT----RPELAAEVTEEAKKHSTVPVMVKLSPNVTD------ITEIARAVEGAGAD 222

Query: 150 GI----WIHARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I     I   +  LK   P             +  +   +V+E+        +G+ G  
Sbjct: 223 AISLINTIRGMRIDLKTRRPILKMNTGGLSGPAVFPVAVRMVWEVANAVKVPVLGMGGVS 282

Query: 198 EDMSQALKILPSVDGVMIGRAAYKNSA 224
                A  +L     V +G A + +  
Sbjct: 283 NGRDAAEMMLAGATAVSVGAACFADPY 309


>gi|312901881|ref|ZP_07761146.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0470]
 gi|311291074|gb|EFQ69630.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0470]
          Length = 311

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +PDI    
Sbjct: 97  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 153 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMVNTLLGMRIDLKTR 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 207 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 265

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 266 VGTANFTDPYI 276


>gi|88602443|ref|YP_502621.1| dihydroorotate dehydrogenase 1B [Methanospirillum hungatei JF-1]
 gi|88187905|gb|ABD40902.1| dihydroorotate oxidase B, catalytic subunit [Methanospirillum
           hungatei JF-1]
          Length = 295

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 43/204 (21%), Positives = 75/204 (36%), Gaps = 26/204 (12%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
              P+ + I G +  +  E A    +       LNV CP A      FGA +  NPD+V 
Sbjct: 91  DGDPVIVSIFGGNPEEFHEVAGWFAE-KAQAFELNVSCPHAA----GFGAQIGTNPDVVK 145

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WI 153
            C  A+ K    PV VK    V D      +  + ++ ++ G + I              
Sbjct: 146 ACTEAV-KVWKKPVWVKLTPNVTD------ITAIGRAAEEGGADAIVAINTVRAMRISTG 198

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             R  +         + +  +    VYE+ +    + I   GG+      ++++    +G
Sbjct: 199 LKRPVLGNKYGGLSGKAVFPIAVRCVYELYEAC-SIPIIGCGGVSCAEDVIEMMMAGAEG 257

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNP 236
           V IG A  ++  +   + E    P
Sbjct: 258 VEIGSAVVQDPEIFRHICEELYAP 281


>gi|261219466|ref|ZP_05933747.1| nifR3 family TIM-barrel protein [Brucella ceti M13/05/1]
 gi|261321962|ref|ZP_05961159.1| nifR3 family TIM-barrel protein [Brucella ceti M644/93/1]
 gi|260924555|gb|EEX91123.1| nifR3 family TIM-barrel protein [Brucella ceti M13/05/1]
 gi|261294652|gb|EEX98148.1| nifR3 family TIM-barrel protein [Brucella ceti M644/93/1]
          Length = 162

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 45/137 (32%), Gaps = 21/137 (15%)

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
            + +H R         +        D+D ++ + ++   + +  NG +   + A +IL  
Sbjct: 1   MVTVHGRT--------RCQFYEGTADWDAIHAV-RDAVRIPLVANGDVSSRADAEEILRR 51

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
              D VM+GRA+Y    +   +           S    R        I     D    H 
Sbjct: 52  SGADAVMVGRASYGQPWLAGAI---------AGSDFAPRDANGILDYIIRHYED-MLDHY 101

Query: 268 HSGGKLQQITRHMIGLF 284
            S   ++   +H+    
Sbjct: 102 GSKIGIRHARKHLGWYM 118


>gi|119503735|ref|ZP_01625817.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding protein
           [marine gamma proteobacterium HTCC2080]
 gi|119460243|gb|EAW41336.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding protein
           [marine gamma proteobacterium HTCC2080]
          Length = 551

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 35/169 (20%), Positives = 66/169 (39%), Gaps = 23/169 (13%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +++ L + I G  + + V  AKI+E    +   LN+ CP A      +G  +  +P IV
Sbjct: 91  PEDRFLLVSIFGGSVEEFVAVAKILEPV-ADGFELNLSCPHA----SGYGMAMGQDPKIV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
            + IAA+ + +S PV  K    V        +  + ++   +G +G+             
Sbjct: 146 HEIIAAVKQVVSKPVIPKLTPNV------TNIAEIGQAALDAGADGLCAINTVGPGYTES 199

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           H    +  G+     + +       + E+ +   D  I   GGL   + 
Sbjct: 200 HGEAVLSNGVGGMSGKGVLPTALKCIREL-RAITDKPIIGCGGLSSAAD 247


>gi|239906263|ref|YP_002953003.1| dihydroorotate dehydrogenase [Desulfovibrio magneticus RS-1]
 gi|259547508|sp|C4XPD6|PYRD_DESMR RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|239796128|dbj|BAH75117.1| dihydroorotate dehydrogenase [Desulfovibrio magneticus RS-1]
          Length = 306

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 80/228 (35%), Gaps = 31/228 (13%)

Query: 26  MIVADAILRGDKKNILG-----FSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     +  L         +E P+   +   D  +  E A  +  + G   + +
Sbjct: 68  MLNAIGLQNCGVEKFLRDKLPRLPWRETPIIANLYACDADEFAELAGVLSAEEGVAALEV 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRN 138
           N+ CP    +  + G     +P + G    A+ K A   PV VK    V D      + +
Sbjct: 128 NISCP----NVKAGGIAFGQDPCMAGKLAEAVKKRAGDKPVWVKLSPNVTD------IVS 177

Query: 139 LVKSIKKSGVNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKEN 186
           + ++    G + +            I +RK  L  +        I  +    V+++ +  
Sbjct: 178 IARAAVLGGADALTCINTLTGMSVDIRSRKPRLANVIGGLSGPAIKPVALRAVWQVCQAV 237

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
               IG+ GG+      L+ IL     V IG A +    M   + E  
Sbjct: 238 SAPVIGV-GGISSAEDVLEFILVGAHAVQIGTANFMRPDMAFRIAERL 284


>gi|322387775|ref|ZP_08061384.1| dihydroorotate dehydrogenase B [Streptococcus infantis ATCC 700779]
 gi|321141642|gb|EFX37138.1| dihydroorotate dehydrogenase B [Streptococcus infantis ATCC 700779]
          Length = 327

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/165 (21%), Positives = 67/165 (40%), Gaps = 22/165 (13%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V  G+ G  +  +PD+    + A   A S+PV VK    V D   
Sbjct: 140 NVKAIELNISCP--NVDHGNHGLLIGQDPDLAYVVVKAAVGASSVPVYVKLTPSVTD--- 194

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVY 180
              +  + K+++ +G +G+ +             RK  I  G        +  +   ++ 
Sbjct: 195 ---IVTIAKAVEDAGASGLTMINTLVGMRFDLKTRKPIIANGTGGMSGPAVFPVALKLIR 251

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA 224
           ++ +   +L I   GG++    A+++ L     + +G A + N  
Sbjct: 252 QVAQ-TTNLPIIGMGGVDSAEAAIEMYLAGASAIGVGTANFTNPY 295


>gi|69247606|ref|ZP_00604417.1| Dihydroorotate dehydrogenase 1 [Enterococcus faecium DO]
 gi|257878234|ref|ZP_05657887.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,230,933]
 gi|257880986|ref|ZP_05660639.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,502]
 gi|257889568|ref|ZP_05669221.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,410]
 gi|257892492|ref|ZP_05672145.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,408]
 gi|258616256|ref|ZP_05714026.1| dihydroorotate dehydrogenase [Enterococcus faecium DO]
 gi|260559784|ref|ZP_05831963.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium C68]
 gi|293559356|ref|ZP_06675898.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1162]
 gi|293569854|ref|ZP_06680941.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1071]
 gi|294621722|ref|ZP_06700886.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium U0317]
 gi|314939733|ref|ZP_07846955.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133a04]
 gi|314941766|ref|ZP_07848643.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133C]
 gi|314948311|ref|ZP_07851703.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0082]
 gi|314952399|ref|ZP_07855406.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133A]
 gi|314991982|ref|ZP_07857435.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133B]
 gi|314995720|ref|ZP_07860810.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133a01]
 gi|68194774|gb|EAN09252.1| Dihydroorotate dehydrogenase 1 [Enterococcus faecium DO]
 gi|257812462|gb|EEV41220.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,230,933]
 gi|257816644|gb|EEV43972.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,502]
 gi|257825928|gb|EEV52554.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,410]
 gi|257828871|gb|EEV55478.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,408]
 gi|260074008|gb|EEW62331.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium C68]
 gi|291587602|gb|EFF19479.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1071]
 gi|291598731|gb|EFF29784.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium U0317]
 gi|291606720|gb|EFF36112.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecium E1162]
 gi|313590111|gb|EFR68956.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133a01]
 gi|313593417|gb|EFR72262.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133B]
 gi|313595516|gb|EFR74361.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133A]
 gi|313599444|gb|EFR78287.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133C]
 gi|313640962|gb|EFS05542.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0133a04]
 gi|313645292|gb|EFS09872.1| dihydroorotate dehydrogenase 1B [Enterococcus faecium TX0082]
          Length = 310

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/194 (22%), Positives = 74/194 (38%), Gaps = 25/194 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   + GA     VE  +KI E      I LN+ CP    +    G     + D+ 
Sbjct: 95  NELPIIANVAGACEEDYVEVCSKIGEAPNVKAIELNISCP----NVKHGGIAFGTDSDVA 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+ K  S+PV VK    V D +P      + ++I+  G +G  +           
Sbjct: 151 FQLTQAVKKVSSVPVYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDL 204

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             RK IL           I  +   +++++      L I   GG++ +   L++ +    
Sbjct: 205 KTRKPILANQTGGLSGPAIKPVAIRLIHQVA-SISSLPIIGMGGVQTVDDVLEMFMAGAS 263

Query: 212 GVMIGRAAYKNSAM 225
            V IG A + +  +
Sbjct: 264 AVAIGTANFTDPYI 277


>gi|229545674|ref|ZP_04434399.1| dihydroorotate oxidase [Enterococcus faecalis TX1322]
 gi|256619207|ref|ZP_05476053.1| pyrimidine biosynthesis D [Enterococcus faecalis ATCC 4200]
 gi|256853269|ref|ZP_05558639.1| pyrimidine biosynthesis D [Enterococcus faecalis T8]
 gi|300861014|ref|ZP_07107101.1| dihydroorotate oxidase, catalytic subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|307275825|ref|ZP_07556964.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX2134]
 gi|307291848|ref|ZP_07571719.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0411]
 gi|229309242|gb|EEN75229.1| dihydroorotate oxidase [Enterococcus faecalis TX1322]
 gi|256598734|gb|EEU17910.1| pyrimidine biosynthesis D [Enterococcus faecalis ATCC 4200]
 gi|256711728|gb|EEU26766.1| pyrimidine biosynthesis D [Enterococcus faecalis T8]
 gi|295113095|emb|CBL31732.1| dihydroorotate oxidase B, catalytic subunit [Enterococcus sp. 7L76]
 gi|300850053|gb|EFK77803.1| dihydroorotate oxidase, catalytic subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|306497114|gb|EFM66660.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0411]
 gi|306507517|gb|EFM76648.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX2134]
 gi|315029553|gb|EFT41485.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX4000]
 gi|315032026|gb|EFT43958.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0017]
 gi|315144953|gb|EFT88969.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX2141]
          Length = 312

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +PDI    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|225017618|ref|ZP_03706810.1| hypothetical protein CLOSTMETH_01547 [Clostridium methylpentosum
           DSM 5476]
 gi|224949583|gb|EEG30792.1| hypothetical protein CLOSTMETH_01547 [Clostridium methylpentosum
           DSM 5476]
          Length = 303

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 72/192 (37%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           T+   +   I G+      E A+ +++   + I LN+ CP    +    GA    + D  
Sbjct: 91  TRGTTIVANIAGSTAEDCAEVARRLDETDVHMIELNISCP----NVKHGGAAFGTSCDCA 146

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
                A+  A   P+ VK    V       ++ ++ K+++ +G + + +           
Sbjct: 147 AQVTKAVRAATKKPLMVKLSPNV------TSITDIAKAVEDAGADALSLINTLLGMRIDI 200

Query: 154 -HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
              R  + + +       +  +   +V+++        +G+ GG+     A++ ++    
Sbjct: 201 RTGRPILKQNVGGLSGPAVFPIAVRMVWQVANAVEIPVVGM-GGITRWQDAVEMMMAGAS 259

Query: 212 GVMIGRAAYKNS 223
              +G A + + 
Sbjct: 260 AFQVGAALFSDP 271


>gi|257085041|ref|ZP_05579402.1| pyrimidine biosynthesis D protein [Enterococcus faecalis Fly1]
 gi|256993071|gb|EEU80373.1| pyrimidine biosynthesis D protein [Enterococcus faecalis Fly1]
          Length = 312

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +PDI    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|312111739|ref|YP_003990055.1| dihydroorotate dehydrogenase [Geobacillus sp. Y4.1MC1]
 gi|311216840|gb|ADP75444.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y4.1MC1]
          Length = 313

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 77/201 (38%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+ + + VE AK +        + LN+ CP   V +G      +  P+I  
Sbjct: 93  DVPVIANIAGSTMEEYVEVAKHISKAPNVCALELNISCP--NVKKGGIAFGTI--PEIAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           +    + +   +PV VK    V D      +  + K+I+ +G +G+            + 
Sbjct: 149 ELTKLVKEVSEVPVYVKLSPNVTD------IVEIAKAIEAAGADGLTMINTILGMRIDVK 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             + +L   +       I  +   ++YE+ +      IG+ GG++     ++        
Sbjct: 203 TAEPVLANRTGGLSGPAIKPIAIRMIYEVSQAVSIPIIGM-GGIQSAEDVIEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V IG A + +  +   +    
Sbjct: 262 VAIGTANFIDPFVCPNIIAEL 282


>gi|288561102|ref|YP_003424588.1| tRNA-dihydrouridine synthase DusA2 [Methanobrevibacter ruminantium
           M1]
 gi|288543812|gb|ADC47696.1| tRNA-dihydrouridine synthase DusA2 [Methanobrevibacter ruminantium
           M1]
          Length = 237

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/172 (24%), Positives = 75/172 (43%), Gaps = 21/172 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           ++  + G+    L++ +KI      + I +N  C    +     G  ++L PD+  D I 
Sbjct: 73  VSANLRGSTPDPLIKISKI---EKLDIIEINCHCRQEELVAVGCGQSMLLRPDL-EDYIR 128

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + K     V++K R  V+          + K  +  GV+ + I A K            
Sbjct: 129 EVVKKSESKVSMKMRANVEGVDN----LEIAKLAEDCGVDYLHIDAMK-----------M 173

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
            + + D+ ++ EI  EN ++FI  N  +  +SQA K+L    +G+ I RAA 
Sbjct: 174 GVRDADFYLIKEIA-ENTNIFIIGNNSINSISQAEKMLNAGANGISIARAAI 224


>gi|163941624|ref|YP_001646508.1| dihydroorotate dehydrogenase 1B [Bacillus weihenstephanensis KBAB4]
 gi|226710746|sp|A9VTC4|PYRD_BACWK RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|163863821|gb|ABY44880.1| dihydroorotate dehydrogenase family protein [Bacillus
           weihenstephanensis KBAB4]
          Length = 309

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 87/242 (35%), Gaps = 34/242 (14%)

Query: 15  LLTNNALLYTE----MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEA 65
              N      E    M+ A  +    L     + L F  Q + P+   + G+     V  
Sbjct: 52  RYGNPTPRVAETPGGMLNAIGLQNPGLEKVMNSELPFLEQFDLPIIANVAGSQAEDYVAV 111

Query: 66  AKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AK +      + + LN+ CP    +  + G     NP+I  D    + +   +PV VK  
Sbjct: 112 AKAISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADLTKRVKEVSEVPVYVKLS 167

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DNRKIP 172
             V        +  + K+I+ +G +G+ +              K IL   +       I 
Sbjct: 168 PNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTAKPILANRTGGLSGPAIK 221

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
            +   +V+E+ +   ++ I   GG+E     ++        V +G A + +  +  T+ E
Sbjct: 222 PVALRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVAVGTANFIDPFVCPTIIE 280

Query: 232 YF 233
             
Sbjct: 281 EL 282


>gi|302874436|ref|YP_003843069.1| dihydroorotate dehydrogenase family protein [Clostridium
           cellulovorans 743B]
 gi|307690958|ref|ZP_07633404.1| dihydroorotate dehydrogenase 1B [Clostridium cellulovorans 743B]
 gi|302577293|gb|ADL51305.1| dihydroorotate dehydrogenase family protein [Clostridium
           cellulovorans 743B]
          Length = 298

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 81/215 (37%), Gaps = 28/215 (13%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K +    T +  +   +GG  I   V  A +++    + + LN+ CP   V EG     +
Sbjct: 82  KELPKMKTYDTVVLANLGGGTIEDYVTGAAMLDATDIDILELNISCP--NVKEGGMAFGI 139

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-------- 149
               D+ G  +  + K  S P+ VK     +D      + ++     ++G +        
Sbjct: 140 --KADVAGQVVKEVRKVTSKPLMVKLSPNAED------IVDMAVKCVEAGADSLSLVNTF 191

Query: 150 ---GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               + I  RK + K   +      I  +   +VYE+ +      +G+ GG+     AL+
Sbjct: 192 KAMAVDIRTRKPMFKNITAGLSGPAIKPIALRMVYEVCRAVEVPVVGM-GGIVSAQDALE 250

Query: 206 -ILPSVDGVMIGRAAYKNSAM----LTTVDEYFSN 235
            I+     V IG   +    +    +  ++EY   
Sbjct: 251 FIMCGAKAVQIGTGNFIKPTLALDVIAGIEEYLKE 285


>gi|315162369|gb|EFU06386.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0645]
          Length = 312

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSHLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|161528898|ref|YP_001582724.1| dihydroorotate dehydrogenase family protein [Nitrosopumilus
           maritimus SCM1]
 gi|160340199|gb|ABX13286.1| dihydroorotate dehydrogenase family protein [Nitrosopumilus
           maritimus SCM1]
          Length = 303

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/202 (18%), Positives = 77/202 (38%), Gaps = 29/202 (14%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDI 103
            Q+ P+ + + G+      +  K  E+       LN+ CP  A+V     G  +  +P++
Sbjct: 90  NQDVPIIVSLVGSIPEDFEKMIKQFENCKVTAYELNLSCPHVAKV-----GLEVGDDPEL 144

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
           V   +  +  + ++PV  K        +      N V +  +SG++ I            
Sbjct: 145 VKKIVTTVKNSTNVPVIAKV------GLGTTHYLNTVGTAIESGIDAITAINTVRSMAID 198

Query: 153 IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           +  ++ IL           I  +    VYEI  +  D+ I   GG+     A++  L   
Sbjct: 199 VETQRPILSNKFGGLSGTPIKPIALRCVYEISSKY-DIPIIGCGGISTWEDAVEFFLAGA 257

Query: 211 DGVMIGRAAYKNSAM--LTTVD 230
             V +G +A  ++ +     ++
Sbjct: 258 SSVQLG-SAIGDNWIDVFNEIN 278


>gi|229168625|ref|ZP_04296347.1| Dihydroorotate dehydrogenase [Bacillus cereus AH621]
 gi|228614781|gb|EEK71884.1| Dihydroorotate dehydrogenase [Bacillus cereus AH621]
          Length = 306

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 87/242 (35%), Gaps = 34/242 (14%)

Query: 15  LLTNNALLYTE----MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEA 65
              N      E    M+ A  +    L     + L F  Q + P+   + G+     V  
Sbjct: 49  RYGNPTPRVAETPGGMLNAIGLQNPGLEKVMNSELPFLEQFDLPIIANVAGSQAEDYVAV 108

Query: 66  AKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AK +      + + LN+ CP    +  + G     NP+I  D    + +   +PV VK  
Sbjct: 109 AKAISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADLTKQVKEVSEVPVYVKLS 164

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DNRKIP 172
             V        +  + K+I+ +G +G+ +              K IL   +       I 
Sbjct: 165 PNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTAKPILANRTGGLSGPAIK 218

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
            +   +V+E+ +   ++ I   GG+E     ++        V +G A + +  +  T+ E
Sbjct: 219 PVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVAVGTANFIDPFVCPTIIE 277

Query: 232 YF 233
             
Sbjct: 278 EL 279


>gi|85713368|ref|ZP_01044378.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
 gi|85692806|gb|EAQ30794.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
          Length = 60

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/59 (52%), Positives = 44/59 (74%), Gaps = 1/59 (1%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
          M+DWTDRH R+F RLL+ N LLYT+M+   AI+ G  ++ L ++ +E P+ALQ+GGAD 
Sbjct: 1  MLDWTDRHCRYFHRLLSPNTLLYTDMVTTGAIIYGQ-QDFLAYNDEEHPVALQLGGADP 58


>gi|229013069|ref|ZP_04170234.1| Dihydroorotate dehydrogenase [Bacillus mycoides DSM 2048]
 gi|229134694|ref|ZP_04263503.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-ST196]
 gi|228648740|gb|EEL04766.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-ST196]
 gi|228748323|gb|EEL98183.1| Dihydroorotate dehydrogenase [Bacillus mycoides DSM 2048]
          Length = 306

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 87/242 (35%), Gaps = 34/242 (14%)

Query: 15  LLTNNALLYTE----MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEA 65
              N      E    M+ A  +    L     + L F  Q + P+   + G+     V  
Sbjct: 49  RYGNPTPRVAETPGGMLNAIGLQNPGLEKVMNSELPFLEQFDLPIIANVAGSQAEDYVAV 108

Query: 66  AKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AK +      + + LN+ CP    +  + G     NP+I  D    + +   +PV VK  
Sbjct: 109 AKAISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADLTKRVKEVSEVPVYVKLS 164

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DNRKIP 172
             V        +  + K+I+ +G +G+ +              K IL   +       I 
Sbjct: 165 PNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTAKPILANRTGGLSGPAIK 218

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
            +   +V+E+ +   ++ I   GG+E     ++        V +G A + +  +  T+ E
Sbjct: 219 PVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVAVGTANFIDPFVCPTIIE 277

Query: 232 YF 233
             
Sbjct: 278 EL 279


>gi|315038743|ref|YP_004032311.1| dihydroorotate dehydrogenase 1B [Lactobacillus amylovorus GRL 1112]
 gi|325957179|ref|YP_004292591.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus 30SC]
 gi|312276876|gb|ADQ59516.1| dihydroorotate dehydrogenase 1B [Lactobacillus amylovorus GRL 1112]
 gi|325333744|gb|ADZ07652.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus 30SC]
 gi|327183884|gb|AEA32331.1| dihydroorotate dehydrogenase 1B [Lactobacillus amylovorus GRL 1118]
          Length = 307

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/188 (21%), Positives = 78/188 (41%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG      VE AK + D G  N + +NV CP   V  G       ++PD+V + 
Sbjct: 98  PIMASVGGDSEDDYVEVAKKLSDSGLVNALEINVSCP--NVDRGGMSFG--VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              +   +++P+ VK    V D      +  + K+ +K G +G           I +  R
Sbjct: 154 TQKIKNVVNVPIYVKLTPNVTD------VVTIAKAAEKGGADGLSMINTLLGMDIDVKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L   +       +  +   ++ ++ + + +L I   GG+      +K +L     V 
Sbjct: 208 KPVLGHNMGGLSGEAVKPVALRMIAQVHQ-SVNLPIIGMGGISSAEDVVKFMLAGASAVA 266

Query: 215 IGRAAYKN 222
           +G A + +
Sbjct: 267 VGTAHFHD 274


>gi|229061490|ref|ZP_04198834.1| Dihydroorotate dehydrogenase [Bacillus cereus AH603]
 gi|228717724|gb|EEL69374.1| Dihydroorotate dehydrogenase [Bacillus cereus AH603]
          Length = 300

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 87/242 (35%), Gaps = 34/242 (14%)

Query: 15  LLTNNALLYTE----MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEA 65
              N      E    M+ A  +    L     + L F  Q + P+   + G+     V  
Sbjct: 49  RYGNPTPRVAETPGGMLNAIGLQNPGLEKVMNSELPFLEQFDLPIIANVAGSQAEDYVAV 108

Query: 66  AKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AK +      + + LN+ CP    +  + G     NP+I  D    + +   +PV VK  
Sbjct: 109 AKAISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADLTKRVKEVSEVPVYVKLS 164

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DNRKIP 172
             V        +  + K+I+ +G +G+ +              K IL   +       I 
Sbjct: 165 PNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTAKPILANRTGGLSGPAIK 218

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
            +   +V+E+ +   ++ I   GG+E     ++        V +G A + +  +  T+ E
Sbjct: 219 PVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVAVGTANFIDPFVCPTIIE 277

Query: 232 YF 233
             
Sbjct: 278 EL 279


>gi|227530640|ref|ZP_03960689.1| dihydroorotate dehydrogenase 1B [Lactobacillus vaginalis ATCC
           49540]
 gi|227349421|gb|EEJ39712.1| dihydroorotate dehydrogenase 1B [Lactobacillus vaginalis ATCC
           49540]
          Length = 305

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/220 (18%), Positives = 79/220 (35%), Gaps = 30/220 (13%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLM 98
            L     + PL   IGGA +   V   + +   G  + + LN+ CP    +    G    
Sbjct: 91  HLKHQYPDLPLVASIGGASVEDYVMVTERLAATGLVDALELNISCP----NVKHGGMAFG 146

Query: 99  LNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---- 153
            +P +      A+  A   +PV VK    V D      +  + ++++  G +G+ +    
Sbjct: 147 TDPQVAEKLTKAVKAASGDVPVYVKLTPNVTD------IVEIAQAVEAGGADGLSMINTL 200

Query: 154 -------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                    RK +L   +       I  L   ++Y++     ++ I   GG+      ++
Sbjct: 201 LGMKINLKTRKPVLGNIMGGLSGTAIKPLAIRMIYQV-SHAVNIPIIGEGGISSAEDVIE 259

Query: 206 -ILPSVDGVMIGRA----AYKNSAMLTTVDEYFSNPLTGS 240
             L     V +G A    A     ++  + +  +    GS
Sbjct: 260 FFLAGASAVQVGSAHFHDALAMPHIIEQLPQAMARVGIGS 299


>gi|210608869|ref|ZP_03288033.1| hypothetical protein CLONEX_00212 [Clostridium nexile DSM 1787]
 gi|210152855|gb|EEA83861.1| hypothetical protein CLONEX_00212 [Clostridium nexile DSM 1787]
          Length = 300

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 70/196 (35%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + + D G + + +N+ CP    +    G     N     +
Sbjct: 92  DTKIIVNVCGKSTEDYCEVVERLADEGVDMLEINISCP----NVKEGGIAFGQNAKAAEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              A+ K    PV +K    V D      +  + K+++  G + I            I+ 
Sbjct: 148 ITKAVKKYAKQPVIMKLSPNVTD------IAEMAKAVEAGGADAISLINTLTGMKIDINR 201

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           RK +L           I  +   +VY+       + I   GG+     A+++ L     V
Sbjct: 202 RKFVLANKTGGVSGPAIHPIAVRMVYQ-AFHAVKVPIIGMGGIASAEDAIEMILAGASAV 260

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A + N ++   +
Sbjct: 261 SVGTANFHNPSVTMEI 276


>gi|255972650|ref|ZP_05423236.1| pyrimidine biosynthesis D [Enterococcus faecalis T1]
 gi|256762643|ref|ZP_05503223.1| pyrimidine biosynthesis D [Enterococcus faecalis T3]
 gi|255963668|gb|EET96144.1| pyrimidine biosynthesis D [Enterococcus faecalis T1]
 gi|256683894|gb|EEU23589.1| pyrimidine biosynthesis D [Enterococcus faecalis T3]
 gi|315150766|gb|EFT94782.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0012]
          Length = 311

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 97  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 153 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 207 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 265

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 266 VGTANFTDPYI 276


>gi|228987029|ref|ZP_04147154.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229019087|ref|ZP_04175922.1| Dihydroorotate dehydrogenase [Bacillus cereus AH1273]
 gi|229025331|ref|ZP_04181749.1| Dihydroorotate dehydrogenase [Bacillus cereus AH1272]
 gi|229092930|ref|ZP_04224063.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-42]
 gi|229123398|ref|ZP_04252602.1| Dihydroorotate dehydrogenase [Bacillus cereus 95/8201]
 gi|229157463|ref|ZP_04285540.1| Dihydroorotate dehydrogenase [Bacillus cereus ATCC 4342]
 gi|229174550|ref|ZP_04302081.1| Dihydroorotate dehydrogenase [Bacillus cereus MM3]
 gi|228608919|gb|EEK66210.1| Dihydroorotate dehydrogenase [Bacillus cereus MM3]
 gi|228625913|gb|EEK82663.1| Dihydroorotate dehydrogenase [Bacillus cereus ATCC 4342]
 gi|228660174|gb|EEL15810.1| Dihydroorotate dehydrogenase [Bacillus cereus 95/8201]
 gi|228690434|gb|EEL44218.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-42]
 gi|228735916|gb|EEL86493.1| Dihydroorotate dehydrogenase [Bacillus cereus AH1272]
 gi|228742187|gb|EEL92352.1| Dihydroorotate dehydrogenase [Bacillus cereus AH1273]
 gi|228772623|gb|EEM21064.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 306

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 87/242 (35%), Gaps = 34/242 (14%)

Query: 15  LLTNNALLYTE----MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEA 65
              N      E    M+ A  +    L     + L F  Q + P+   + G+     V  
Sbjct: 49  RYGNPTPRVAETPGGMLNAIGLQNPGLEKVMNSELPFLEQFDLPIIANVAGSQAEDYVAV 108

Query: 66  AKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AK +      + + LN+ CP    +  + G     NP+I  D    + +   +PV VK  
Sbjct: 109 AKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADLTKRVKEVSEVPVYVKLS 164

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DNRKIP 172
             V        +  + K+I+ +G +G+ +              K IL   +       I 
Sbjct: 165 PNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTAKPILANRTGGLSGPAIK 218

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
            +   +V+E+ +   ++ I   GG+E     ++        V +G A + +  +  T+ E
Sbjct: 219 PVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVAVGTANFIDPFVCPTIIE 277

Query: 232 YF 233
             
Sbjct: 278 EL 279


>gi|255975702|ref|ZP_05426288.1| pyrimidine biosynthesis D [Enterococcus faecalis T2]
 gi|256959123|ref|ZP_05563294.1| pyrimidine biosynthesis D protein [Enterococcus faecalis DS5]
 gi|255968574|gb|EET99196.1| pyrimidine biosynthesis D [Enterococcus faecalis T2]
 gi|256949619|gb|EEU66251.1| pyrimidine biosynthesis D protein [Enterococcus faecalis DS5]
 gi|315037126|gb|EFT49058.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0027]
          Length = 311

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 97  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 153 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 207 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 265

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 266 VGTANFTDPYI 276


>gi|169350948|ref|ZP_02867886.1| hypothetical protein CLOSPI_01725 [Clostridium spiroforme DSM 1552]
 gi|169292010|gb|EDS74143.1| hypothetical protein CLOSPI_01725 [Clostridium spiroforme DSM 1552]
          Length = 305

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/199 (19%), Positives = 73/199 (36%), Gaps = 25/199 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   IGG+     VE AK + +      + LN+ CP   VH G        NP++  D  
Sbjct: 97  VIANIGGSAPEDYVETAKRLSNHDMVGALELNISCP--NVHSGGIQFG--TNPEMAADLT 152

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HAR 156
             + +   +PV VK    V D      +  + K ++++G +GI +              +
Sbjct: 153 RRVKEVSKVPVYVKLSPNVTD------IVAMAKVVEEAGADGITMINTLVGMRFDFKTGK 206

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMI 215
             I           I  +   +VY++ +      IG+ GG++     ++++      V I
Sbjct: 207 PIIANKTGGYSGPAIFPVALRMVYQVSQAVKIPVIGM-GGIQSARDVIEMMSAGASAVAI 265

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           G     +      + E   
Sbjct: 266 GCQNLIDPYACKKIIEDLE 284


>gi|182417147|ref|ZP_02948520.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           butyricum 5521]
 gi|237668928|ref|ZP_04528912.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182378989|gb|EDT76495.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           butyricum 5521]
 gi|237657276|gb|EEP54832.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 298

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/201 (18%), Positives = 73/201 (36%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
              +   IGG  I   V A   + +   + I LN+ CP    +    G    +  D+  D
Sbjct: 91  GTNVIANIGGGCIEDYVAAVTKINEADVDMIELNISCP----NVKHGGMAFGIKSDVAYD 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            +  +   +  P+ VK     +D      + ++    +K+G +            I I+ 
Sbjct: 147 VVKEIKSIVKKPLMVKLSPNAED------IVDMAVKCEKAGADSISLINTLKGMAIDIYK 200

Query: 156 RKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +   +S       +  +   +VYE+ K   D+ +   GG+     A++ ++     V
Sbjct: 201 RKPVFNNISAGLSGPAVKPVALRMVYEVSKAI-DIPVIGLGGISTGKDAIEFMMAGASAV 259

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            IG   + N      + E   
Sbjct: 260 QIGTINFINPMAGKEIIEEME 280


>gi|34581029|ref|ZP_00142509.1| nifR3-like protein [Rickettsia sibirica 246]
 gi|28262414|gb|EAA25918.1| nifR3-like protein [Rickettsia sibirica 246]
          Length = 108

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 6/108 (5%)

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+GR AY    +++ +D Y       S+P              A +  Y          +
Sbjct: 1   MVGRGAYGKPWLISQIDHYLKTGEEKSAPSIAEQLDIVTEHYEAILDYY-----GESVGV 55

Query: 274 QQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
               +H+     G PNS   R  + +      A    I   +  ++E+
Sbjct: 56  PIARKHIGWYSSGLPNSAEFRGAVNL-MNDPLAVKEKIAEFYTSVMET 102


>gi|315172446|gb|EFU16463.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX1346]
          Length = 312

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGTAFGTDPEVAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|302414912|ref|XP_003005288.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
 gi|261356357|gb|EEY18785.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
          Length = 343

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 49/273 (17%), Positives = 81/273 (29%), Gaps = 45/273 (16%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P  LQ G     ++  ++ +   +  N  +LN GCP +     + GA LM   ++V D +
Sbjct: 31  PTVLQWGANKPEEIARSSLLAAPY-VNGFDLNCGCPQSWACAETLGAALMEKRELVRDMV 89

Query: 109 AAMCKAL-----------------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
               +AL                    V+VK R+  D +     +  ++       V+ +
Sbjct: 90  IETRQALERDGWGVGKEKDIENPQGRSVSVKIRVHKDLRKTIDFIETVIGDQHNRHVDWL 149

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEI-----------------KKENPDLFIGLN 194
            IH R       +P     +  L       +                     P   I  N
Sbjct: 150 TIHPRTRSTPSSTPIFGDSLAILIEKYGARLPVLLSGDVFSLSSLPLSPLLAPQPTIVTN 209

Query: 195 GGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLT-------TVDEYFSNPLTGSSPIKTR 246
           G  E  + +       + G+M  R    N A+            E F   LT +      
Sbjct: 210 GESEPALPRFRPSTTKLAGLMSARGILANPALYAGHESCPWQAVEAFLRHLTRAPLHLKL 269

Query: 247 VDKDFWRKISASMTDYAARHLHSGGK--LQQIT 277
           V           M       L  G +  L  +T
Sbjct: 270 VLHHLGEMCGPGMGPDKNALLTKGERAQLNAMT 302


>gi|229549866|ref|ZP_04438591.1| dihydroorotate oxidase [Enterococcus faecalis ATCC 29200]
 gi|257090028|ref|ZP_05584389.1| pyrimidine biosynthesis D protein [Enterococcus faecalis CH188]
 gi|257419439|ref|ZP_05596433.1| pyrimidine biosynthesis D protein [Enterococcus faecalis T11]
 gi|312903462|ref|ZP_07762642.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0635]
 gi|312951644|ref|ZP_07770539.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0102]
 gi|818705|gb|AAA67066.1| pyrimidine biosynthesis D [Enterococcus faecalis OG1RF]
 gi|229305135|gb|EEN71131.1| dihydroorotate oxidase [Enterococcus faecalis ATCC 29200]
 gi|256998840|gb|EEU85360.1| pyrimidine biosynthesis D protein [Enterococcus faecalis CH188]
 gi|257161267|gb|EEU91227.1| pyrimidine biosynthesis D protein [Enterococcus faecalis T11]
 gi|310630361|gb|EFQ13644.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0102]
 gi|310633338|gb|EFQ16621.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0635]
 gi|315152335|gb|EFT96351.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0031]
 gi|315168888|gb|EFU12905.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX1341]
 gi|315169605|gb|EFU13622.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX1342]
 gi|315577842|gb|EFU90033.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0630]
 gi|323480873|gb|ADX80312.1| dihydroorotate dehydrogenase B, catalytic subunit [Enterococcus
           faecalis 62]
 gi|327535278|gb|AEA94112.1| dihydroorotate oxidase [Enterococcus faecalis OG1RF]
 gi|1585613|prf||2201400A pyrD gene
          Length = 312

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|325681279|ref|ZP_08160809.1| dihydroorotate dehydrogenase 1B [Ruminococcus albus 8]
 gi|324107201|gb|EGC01487.1| dihydroorotate dehydrogenase 1B [Ruminococcus albus 8]
          Length = 303

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 87/236 (36%), Gaps = 33/236 (13%)

Query: 11  FFARLLTNNALLYTE----MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISK 61
              R   N A    E    M+ +  +  G     L +      T++  +   I G+ I +
Sbjct: 48  TLHRREGNPAPRVAETPSGMLNSVGLQNGGVDKFLSYELPNLVTKDTRIIANIAGSTIEE 107

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             E A  ++    + I LN+ CP    +    GA    +  I G    A+      PV V
Sbjct: 108 CAELAAKLKGSAVDMIELNISCP----NVKQGGAAFGTDCTIAGQVTKAVKDNSDKPVMV 163

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK-GLSPKDNR 169
           K    V       ++ ++ KS++ +G +            I I+  + +L+  +      
Sbjct: 164 KLSPNV------TSITDIAKSVEANGADAVSLINTLLGMRIDINTGRPVLRNNVGGLSGP 217

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
            +  +   +V+++     ++ +   GG+     A++ ++     V +G A + +  
Sbjct: 218 AVFPVAVRMVWQVANAV-NIPVCGMGGVSTWEDAIEIMMAGASLVQVGAAIFADPY 272


>gi|288553131|ref|YP_003425066.1| dihydroorotate dehydrogenase family protein [Bacillus pseudofirmus
           OF4]
 gi|288544291|gb|ADC48174.1| dihydroorotate dehydrogenase family protein [Bacillus pseudofirmus
           OF4]
          Length = 314

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/214 (19%), Positives = 87/214 (40%), Gaps = 25/214 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGAC 96
           K +   S  + P+   + GA +   VE A+ +        + LN+ CP    +    G  
Sbjct: 89  KELPRLSQYDVPIIANVAGAQMEDYVEVARELSQSPTVAALELNISCP----NVKQGGIA 144

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--- 153
               P++  +  AA+ +  + PV VK    V D      +  + K+++ +G +G+ +   
Sbjct: 145 FGTVPEVAAELTAAVKQVSTKPVYVKLSPNVSD------IVEMAKAVEAAGADGLSMINT 198

Query: 154 --------HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                    +RK IL  G        I  +   +++++ +      IG+ GG++ +   +
Sbjct: 199 LLGMRIDLKSRKPILANGAGGLSGPAIKPVAIRMIHQVSQAVSIPIIGM-GGVQAVDDVI 257

Query: 205 K-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + +L     V IG A + +  +   + +   + L
Sbjct: 258 EMMLAGASAVAIGTANFVDPYICPNIIKELPDKL 291


>gi|295399742|ref|ZP_06809723.1| dihydroorotate dehydrogenase family protein [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978145|gb|EFG53742.1| dihydroorotate dehydrogenase family protein [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 313

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 77/201 (38%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+ + + VE AK +        + LN+ CP   V +G      +  P+I  
Sbjct: 93  DVPVIANIAGSTMEEYVEVAKHISKAPNVCALELNISCP--NVKKGGIAFGTI--PEIAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           +    + +   +PV VK    V D      +  + K+I+ +G +G+            + 
Sbjct: 149 ELTKLVKEISEVPVYVKLSPNVTD------IVEIAKAIEAAGADGLTMINTILGMRIDVK 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             + +L   +       I  +   ++YE+ +      IG+ GG++     ++        
Sbjct: 203 TAEPVLANRTGGLSGPAIKPIAIRMIYEVSQAVSIPIIGM-GGIQSAEDVIEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V IG A + +  +   +    
Sbjct: 262 VAIGTANFIDPFVCPNIIAEL 282


>gi|29376266|ref|NP_815420.1| dihydroorotate dehydrogenase [Enterococcus faecalis V583]
 gi|227518903|ref|ZP_03948952.1| dihydroorotate dehydrogenase [Enterococcus faecalis TX0104]
 gi|227553519|ref|ZP_03983568.1| dihydroorotate dehydrogenase [Enterococcus faecalis HH22]
 gi|256961783|ref|ZP_05565954.1| pyrimidine biosynthesis D protein [Enterococcus faecalis Merz96]
 gi|257082409|ref|ZP_05576770.1| pyrimidine biosynthesis D protein [Enterococcus faecalis E1Sol]
 gi|257087000|ref|ZP_05581361.1| pyrimidine biosynthesis D protein [Enterococcus faecalis D6]
 gi|257422469|ref|ZP_05599459.1| dihydroorotate dehydrogenase B [Enterococcus faecalis X98]
 gi|293383489|ref|ZP_06629402.1| dihydroorotate oxidase [Enterococcus faecalis R712]
 gi|293388856|ref|ZP_06633342.1| dihydroorotate oxidase [Enterococcus faecalis S613]
 gi|307277920|ref|ZP_07559004.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0860]
 gi|307289252|ref|ZP_07569208.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0109]
 gi|312907682|ref|ZP_07766673.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis DAPTO 512]
 gi|312910300|ref|ZP_07769147.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis DAPTO 516]
 gi|30179832|sp|Q47741|PYRDB_ENTFA RecName: Full=Dihydroorotate dehydrogenase B, catalytic subunit;
           AltName: Full=DHOdehase B; Short=DHOD B; Short=DHODase
           B; AltName: Full=Dihydroorotate oxidase B
 gi|29343729|gb|AAO81490.1| dihydroorotate dehydrogenase [Enterococcus faecalis V583]
 gi|227073592|gb|EEI11555.1| dihydroorotate dehydrogenase [Enterococcus faecalis TX0104]
 gi|227177346|gb|EEI58318.1| dihydroorotate dehydrogenase [Enterococcus faecalis HH22]
 gi|256952279|gb|EEU68911.1| pyrimidine biosynthesis D protein [Enterococcus faecalis Merz96]
 gi|256990439|gb|EEU77741.1| pyrimidine biosynthesis D protein [Enterococcus faecalis E1Sol]
 gi|256995030|gb|EEU82332.1| pyrimidine biosynthesis D protein [Enterococcus faecalis D6]
 gi|257164293|gb|EEU94253.1| dihydroorotate dehydrogenase B [Enterococcus faecalis X98]
 gi|291079280|gb|EFE16644.1| dihydroorotate oxidase [Enterococcus faecalis R712]
 gi|291081781|gb|EFE18744.1| dihydroorotate oxidase [Enterococcus faecalis S613]
 gi|306499961|gb|EFM69322.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0109]
 gi|306505317|gb|EFM74503.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0860]
 gi|310626710|gb|EFQ09993.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis DAPTO 512]
 gi|311289573|gb|EFQ68129.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis DAPTO 516]
 gi|315027870|gb|EFT39802.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX2137]
 gi|315156136|gb|EFU00153.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0043]
 gi|315163866|gb|EFU07883.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX1302]
 gi|315576076|gb|EFU88267.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0309B]
 gi|315580651|gb|EFU92842.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0309A]
          Length = 312

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|324991091|gb|EGC23025.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK353]
          Length = 312

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEVTKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLRSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|227892690|ref|ZP_04010495.1| dihydroorotate dehydrogenase 1B [Lactobacillus ultunensis DSM
           16047]
 gi|227865467|gb|EEJ72888.1| dihydroorotate dehydrogenase 1B [Lactobacillus ultunensis DSM
           16047]
          Length = 307

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 43/188 (22%), Positives = 79/188 (42%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG      VE AK + +    N + +NV CP   V  G       ++PD+V + 
Sbjct: 98  PIMASVGGDSEDDYVEVAKKLSNSKLVNALEINVSCP--NVARGGMSFG--VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
              + K ++IP+ VK    V D         + ++ +K G +GI            +  R
Sbjct: 154 TRNIKKVVNIPIYVKLTPNVTDITV------IARAAEKGGADGISMINTVLGMEIDVKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K IL   +       I  +   ++ ++++   DL I   GG+E     ++ +L   + V 
Sbjct: 208 KPILGHNMGGLSGEAIKPIAIRMISQVRQAT-DLPIIGMGGIESAQDVVEFMLAGANAVA 266

Query: 215 IGRAAYKN 222
           +G A + +
Sbjct: 267 VGTAHFHD 274


>gi|319947135|ref|ZP_08021369.1| dihydroorotate dehydrogenase B [Streptococcus australis ATCC
           700641]
 gi|319747183|gb|EFV99442.1| dihydroorotate dehydrogenase B [Streptococcus australis ATCC
           700641]
          Length = 312

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 77/198 (38%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPELPIIANVAGFSNEEYATVSGKISQAPNVKAIELNISCP--NVDHGNNGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  D + A  +A S+PV VK    V D      +  + K+ + +G +G+ +      
Sbjct: 149 VPELAYDAVKAAVEASSVPVYVKLTPSVAD------ITQVAKAAEDAGASGLTMINTLVG 202

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                   +  I  G        I  +   ++ ++ + +  L I   GG++    A++++
Sbjct: 203 MRFDLKTGKPIIANGTGGMSGPAIFPVALKLIRQVAQ-STKLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFTDPY 279


>gi|223984197|ref|ZP_03634345.1| hypothetical protein HOLDEFILI_01638 [Holdemania filiformis DSM
           12042]
 gi|223963812|gb|EEF68176.1| hypothetical protein HOLDEFILI_01638 [Holdemania filiformis DSM
           12042]
          Length = 305

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/200 (19%), Positives = 71/200 (35%), Gaps = 25/200 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           K +   + G    + VE AK ++      I  +N+ CP    +    G    ++PD   +
Sbjct: 96  KKVVANVSGFSKEEYVECAKKMDAQDIVGILEVNISCP----NVHGGGMSFGVSPDAAAE 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
              A+    + PV +K    V D      +  + K+ + +G +GI +             
Sbjct: 152 ITRAVKAVTTKPVYIKLSPNVTD------IVAIAKACEDAGADGISMINTLLGARFDLRT 205

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
            R  I   +       I  +   +VY++  E   L I   GG+      ++++      V
Sbjct: 206 GRPIIANVMGGFSGPAIKPVALRMVYQVY-EAVKLPIIGIGGIASAEDVIEMMYAGATAV 264

Query: 214 MIGRAAYKNSAMLTTVDEYF 233
            IG    +N      + E  
Sbjct: 265 EIGAENLRNPYACKEIIERL 284


>gi|317131027|ref|YP_004090341.1| dihydroorotate dehydrogenase family protein [Ethanoligenens
           harbinense YUAN-3]
 gi|315469006|gb|ADU25610.1| dihydroorotate dehydrogenase family protein [Ethanoligenens
           harbinense YUAN-3]
          Length = 307

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 77/205 (37%), Gaps = 24/205 (11%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q   L   I G         A  ++    + + LN+ CP+ +    +FG       +   
Sbjct: 96  QGTRLISNIAGDAPEDYAALAARLDGEPVDMLELNISCPNVKTGGMAFGV----TCEGAA 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIH 154
           +   A+  A   P+ VK    V D      + ++ ++++ +G +            I I 
Sbjct: 152 EVTRAVRAATKKPLCVKLSPNVTD------IASIAQAVEDAGADALSLINTLLGMRIDIR 205

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            R+ IL   +       +  +    V+++ K      IG+ GG+     A+++ L     
Sbjct: 206 TRRPILSNNVGGLSGPAVFPVALRCVWQVAKAVRIPVIGM-GGIATWEDAVQMFLAGASA 264

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPL 237
           V +G A + +   +  + +  ++ L
Sbjct: 265 VQVGTATFTDPYAMLAIRDGLADYL 289


>gi|325111064|ref|YP_004272132.1| dihydroorotate oxidase B, catalytic subunit [Planctomyces
           brasiliensis DSM 5305]
 gi|324971332|gb|ADY62110.1| dihydroorotate oxidase B, catalytic subunit [Planctomyces
           brasiliensis DSM 5305]
          Length = 345

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 68/177 (38%), Gaps = 25/177 (14%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I LN+ CP       S G     NP+     + A  +A  +P+  K    + + IP    
Sbjct: 151 IELNISCP-----NVSGGVDFGTNPESTEKVVRAAREACDLPIIAKLTPNITNIIPV--- 202

Query: 137 RNLVKSIKKSGVNGIWI-----------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKK 184
               ++ K  G + + +             RK +L   L       I  L   IV+++++
Sbjct: 203 ---AEAAKAGGADAVSLVNTFQGMAVNWKTRKPVLGNVLGGLSGPAIKPLALRIVHQVRR 259

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
              D+ I   GG+  +   ++ L      V IG A++ N  +   + +  S+ LT  
Sbjct: 260 AV-DIPIIGVGGISSIDDVMEFLVTGASAVQIGTASFYNPGLSGQLKQQLSDILTAE 315


>gi|304316989|ref|YP_003852134.1| dihydroorotate dehydrogenase [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778491|gb|ADL69050.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 301

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 47/222 (21%), Positives = 85/222 (38%), Gaps = 31/222 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D  LR +   +  F T+   + + I G  I + V  A+ ++  G + + LNV CP    +
Sbjct: 78  DGFLRDELPFLKKFDTK---VIVNIAGETIEEFVTMAQKLDIDGVHALELNVSCP----N 130

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G    +NP+ + +    +    +  V VK    V D           K+ +  G +
Sbjct: 131 VKEGGMAFGVNPNSIYEITKRVKGVTNKIVIVKLTPNVADIKIY------AKAAEDGGAD 184

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +            I++RK I K   +      +  +    VYE KK      IG+ GG+
Sbjct: 185 AVSLINTITGMAVDINSRKPIFKNIFAGLSGPAVKPIALKYVYEAKKAVSIPVIGM-GGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
                A++ ++     V IG   + N      +L  + +Y +
Sbjct: 244 SSAEDAIEFMIVGATAVAIGTYNFINPTCTMDILEDIKKYMN 285


>gi|237737212|ref|ZP_04567693.1| dihydroorotate oxidase B [Fusobacterium mortiferum ATCC 9817]
 gi|229421074|gb|EEO36121.1| dihydroorotate oxidase B [Fusobacterium mortiferum ATCC 9817]
          Length = 305

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/201 (20%), Positives = 77/201 (38%), Gaps = 25/201 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             +   I G  + + VE AK V+       + LN+ CP    +    G     NP++   
Sbjct: 96  TNIIANINGKTVEEYVEIAKRVDKIPEIAVVELNISCP----NVKDGGMAFGANPEVAAR 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
               + K  S P+ VK    V D      + ++ K ++++G +            I I  
Sbjct: 152 VTREVRKVTSKPLVVKLSPNVTD------IASIAKIVEENGADAVSLINTLLGMVIDIRT 205

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           +K +L           +  +   +VY++ K   ++ I   GG+  +  AL+ I+     +
Sbjct: 206 KKPVLGNTFGGFSGPAVKPVAVRMVYQVYKAV-NIPIIGMGGIASVEDALEFIMAGASMI 264

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            IG A + N  +   + E   
Sbjct: 265 SIGSAIFSNPMLAVEIAEGLQ 285


>gi|288561242|ref|YP_003424728.1| dihydroorotate dehydrogenase PyrD [Methanobrevibacter ruminantium
           M1]
 gi|288543952|gb|ADC47836.1| dihydroorotate dehydrogenase PyrD [Methanobrevibacter ruminantium
           M1]
          Length = 278

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 72/196 (36%), Gaps = 26/196 (13%)

Query: 51  ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              I GA   +    A  +E    + I +N+ CP A      +GA +  NPD+  + ++A
Sbjct: 94  IASIYGATPDEFSYVAGKIESL-VDMIEMNISCPHAM---EGYGASIGQNPDLTREFVSA 149

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------------IHARK 157
           +   +S+PV  K    V        +  +  + ++ G +G+              I    
Sbjct: 150 VKDTVSVPVLAKLTPNV------TNISEIAIAAEEGGADGLTLINSLGPGMKIDIITGNP 203

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
            +           I  +    VY+   E  D+ I   GG+ + +  ++ L      V IG
Sbjct: 204 ILANKFGGMSGPAIKPIAVRCVYD-AYEATDIPIVGVGGIRNYTDVVEFLYAGASAVQIG 262

Query: 217 RAA-YKNSAMLTTVDE 231
            +  Y+   +   + +
Sbjct: 263 TSIMYEGPEIFGRIRK 278


>gi|222445341|ref|ZP_03607856.1| hypothetical protein METSMIALI_00969 [Methanobrevibacter smithii
           DSM 2375]
 gi|261350098|ref|ZP_05975515.1| dihydroorotate oxidase [Methanobrevibacter smithii DSM 2374]
 gi|222434906|gb|EEE42071.1| hypothetical protein METSMIALI_00969 [Methanobrevibacter smithii
           DSM 2375]
 gi|288860884|gb|EFC93182.1| dihydroorotate oxidase [Methanobrevibacter smithii DSM 2374]
          Length = 303

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/202 (17%), Positives = 74/202 (36%), Gaps = 25/202 (12%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           ++      K+ +     +       I GA   +  +    +ED+  + I LN+ CP A  
Sbjct: 72  SNPGAENFKEELKRIDRKGNVSIASIYGATPEEFSKLVLEIEDY-VDMIELNISCPHAM- 129

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
               +GA +  + ++    ++A   + + PV  K    V D      +  +  + + +G 
Sbjct: 130 --EGYGASIGQDANLTHKIVSAAKDSANKPVIAKLTPNVTD------IVEIAVAAQDAGA 181

Query: 149 NGIWI-------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +G+ +              AR  +         + I  +    VY +  +N D+ I   G
Sbjct: 182 DGLTLINSLGPGMKINIDVARPVLSNKFGGMSGKAIKPIALRNVYTVY-DNVDIPIIGVG 240

Query: 196 GLEDMSQALKIL-PSVDGVMIG 216
           G+ +    ++ L      V IG
Sbjct: 241 GISNFEDVVEFLFAGARAVQIG 262


>gi|326389920|ref|ZP_08211483.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993980|gb|EGD52409.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 302

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 42/201 (20%), Positives = 73/201 (36%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G  I +    AK ++  G + I +NV CP   V +G     +  NP+ + +   
Sbjct: 95  VIANIAGETIEEFAYMAKKLDIDGVDGIEINVSCP--NVKKGGMAFGI--NPEDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
            + K     V VK    V D           K+ +  G +            I I  R  
Sbjct: 151 EVKKVTQKTVIVKLTPNVTDIGV------CAKAAEDGGADAVSLINTIAGMAINIDTRTP 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K + +      I  +   +VYE  +      IG+ GG+     AL+ ++     V IG
Sbjct: 205 VFKNVIAGLSGPAIKPIALRMVYEAARAVKIPVIGM-GGISSFKDALEFMIAGAKAVAIG 263

Query: 217 RAAYKNSA----MLTTVDEYF 233
              + N      ++  + +Y 
Sbjct: 264 TCNFVNPYCTVEVIEGIKQYM 284


>gi|148643104|ref|YP_001273617.1| dihydroorotate dehydrogenase 1B [Methanobrevibacter smithii ATCC
           35061]
 gi|148552121|gb|ABQ87249.1| dihydroorotate dehydrogenase, PyrD [Methanobrevibacter smithii ATCC
           35061]
          Length = 303

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 34/202 (16%), Positives = 73/202 (36%), Gaps = 25/202 (12%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           ++      K+ +     +       I GA   +  +    +ED+  + I LN+ CP A  
Sbjct: 72  SNPGAENFKEELKRIDRKGNVSIASIYGATPEEFSKLVLEIEDY-VDMIELNISCPHAM- 129

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
               +GA +  + ++    ++A   + + PV  K    V D      +  +  + + +G 
Sbjct: 130 --EGYGASIGQDANLTHKIVSAAKDSANKPVIAKLTPNVTD------IVEIAVAAQDAGA 181

Query: 149 NGIWI-------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           + + +              AR  +         + I  +    VY +  +N D+ I   G
Sbjct: 182 DALTLINSLGPGMKINIDVARPVLSNKFGGMSGKAIKPIALRNVYTVY-DNVDIPIIGVG 240

Query: 196 GLEDMSQALK-ILPSVDGVMIG 216
           G+ +    ++ +      V IG
Sbjct: 241 GISNFEDVVEFLFAGARAVQIG 262


>gi|303249003|ref|ZP_07335248.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           fructosovorans JJ]
 gi|302489589|gb|EFL49529.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           fructosovorans JJ]
          Length = 306

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 40/202 (19%), Positives = 69/202 (34%), Gaps = 26/202 (12%)

Query: 47  EKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +   D  +  E A  + +  G   + +N+ CP    +  + G     NP + G
Sbjct: 94  ETPIIANLYACDADEFAELAGVLADAEGVAALEVNISCP----NVKAGGIAFGQNPSMAG 149

Query: 106 DCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------I 153
               A+ K A   PV VK    V D      +  + ++    G + +            I
Sbjct: 150 KLAEAVKKRARDKPVWVKLSPNVTD------IVEIARAAVLGGADALTCINTLTGMSVDI 203

Query: 154 HARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK  L  +        I  +    V+++ +      +   GG+      L+ IL    
Sbjct: 204 RTRKPRLANVIGGLSGPAIKPVALRCVWQVCRAVSA-PVIAVGGVSSAEDVLEFILAGAH 262

Query: 212 GVMIGRAAYKNSAMLTTVDEYF 233
            V IG A +    M   + E  
Sbjct: 263 AVQIGTANFMRPDMAFRIAERL 284


>gi|297544806|ref|YP_003677108.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296842581|gb|ADH61097.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 302

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 43/187 (22%), Positives = 70/187 (37%), Gaps = 24/187 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I +    AK ++  G + I +NV CP   V +G     +  NPD + +   
Sbjct: 95  VIVNIAGETIEEFAYMAKKLDIDGVDGIEINVSCP--NVKKGGMAFGI--NPDDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
            + K     V VK    V D           K+ +  G +            I I  RK 
Sbjct: 151 EVKKVTQKTVIVKLTPNVTDIGV------CAKAAEDGGADAVSLINTIAGMAIDIDTRKP 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K + +      I  +   +VYE  +      IG+ GG+     AL+ ++     V IG
Sbjct: 205 VFKNVIAGLSGPAIKPIALRMVYEAVRAVKIPVIGM-GGISSFKDALEFMIAGAKAVAIG 263

Query: 217 RAAYKNS 223
              + N 
Sbjct: 264 TCNFVNP 270


>gi|229111354|ref|ZP_04240907.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock1-15]
 gi|228672130|gb|EEL27421.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock1-15]
          Length = 306

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|148381185|ref|YP_001255726.1| dihydroorotate oxidase [Clostridium botulinum A str. ATCC 3502]
 gi|153931789|ref|YP_001385560.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum A str. ATCC
           19397]
 gi|153936654|ref|YP_001388966.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum A str. Hall]
 gi|148290669|emb|CAL84798.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           botulinum A str. ATCC 3502]
 gi|152927833|gb|ABS33333.1| dihydroorotate oxidase [Clostridium botulinum A str. ATCC 19397]
 gi|152932568|gb|ABS38067.1| dihydroorotate oxidase [Clostridium botulinum A str. Hall]
          Length = 298

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 71/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + K
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEIVKEVKK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQKPLMVKLSPNAED------IVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+   + +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPIALRMVYEVCKQV-KIPVIGIGGICNYEDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|116627763|ref|YP_820382.1| dihydroorotate dehydrogenase 1B [Streptococcus thermophilus LMD-9]
 gi|116101040|gb|ABJ66186.1| dihydroorotate oxidase B, catalytic subunit [Streptococcus
           thermophilus LMD-9]
          Length = 315

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 92  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 149

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 150 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 203

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 204 TRYDLATRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 262

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 263 IAGASAIGVGTANFADPY 280


>gi|291562467|emb|CBL41283.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [butyrate-producing bacterium SS3/4]
          Length = 300

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 69/191 (36%), Gaps = 24/191 (12%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            +  + + + G   S  V+  + + D   + + +N+ CP    +    G     +P    
Sbjct: 91  HDTKIIVNVCGKSESDYVDVVERLADADVDMLEINISCP----NVKEGGIAFGQDPKCAE 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIH 154
               A+ K    PV +K    V D      +  + ++++  G +            I I+
Sbjct: 147 QITKAVKKVAKQPVIMKLSPNVTD------IAEMARAVEAGGADVVSLINTITGMKIDIN 200

Query: 155 ARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R  A+           I  +   +VY++        IG+ GG+     AL+ IL     
Sbjct: 201 KRTFALANKTGGMSGPAIKPVAVRMVYQVANAVKIPVIGM-GGIMTAEDALEFILAGATA 259

Query: 213 VMIGRAAYKNS 223
           V IG A + N 
Sbjct: 260 VSIGTANFINP 270


>gi|138894681|ref|YP_001125134.1| dihydroorotate dehydrogenase 1B [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247703|ref|ZP_03146405.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           G11MC16]
 gi|166199352|sp|A4IM35|PYRD_GEOTN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|134266194|gb|ABO66389.1| Dihydroorotate dehydrogenase [Geobacillus thermodenitrificans
           NG80-2]
 gi|196212487|gb|EDY07244.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           G11MC16]
          Length = 313

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 80/197 (40%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+ + + VE AA I +    + + LN+ CP   V +G         P++  
Sbjct: 93  DVPIIANIAGSTMEEYVEVAAAISKAPNVHALELNISCP--NVKKGGIAFG--TVPEVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    + +  ++PV VK    V D      +  + K+I+++G +G+ +            
Sbjct: 149 ELTRLVKEVSAVPVYVKLSPNVTD------IVAMAKAIEQAGADGLTMINTLVGMRIDVK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             R  +  G        +  +   ++YE+ +      IG+ GG++     L+        
Sbjct: 203 TGRPILANGTGGLSGPAVKPIAVRMIYEVSQAVSIPIIGM-GGVQTAEDVLEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +  T+
Sbjct: 262 VAVGTANFIDPFVCPTI 278


>gi|256964981|ref|ZP_05569152.1| pyrimidine biosynthesis D protein [Enterococcus faecalis HIP11704]
 gi|307273076|ref|ZP_07554322.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0855]
 gi|256955477|gb|EEU72109.1| pyrimidine biosynthesis D protein [Enterococcus faecalis HIP11704]
 gi|306510061|gb|EFM79085.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0855]
          Length = 312

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 98  PIIANVAGACEDDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|312862833|ref|ZP_07723073.1| dihydroorotate oxidase, catalytic subunit [Streptococcus
           vestibularis F0396]
 gi|311101693|gb|EFQ59896.1| dihydroorotate oxidase, catalytic subunit [Streptococcus
           vestibularis F0396]
          Length = 318

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 80/233 (34%), Gaps = 28/233 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 95  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 152

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 153 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 206

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 207 TRYDLATRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 265

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSN-----PLTGSSPIKTRVDKDFWRK 254
                 + +G A + +      + +          +T    ++  V  D  +K
Sbjct: 266 IAGASAIGVGTANFADPYACPKIIDRLPEVMDKYGITTLEDLREEVRTDLLKK 318


>gi|55820990|ref|YP_139432.1| dihydroorotate dehydrogenase 1B [Streptococcus thermophilus LMG
           18311]
 gi|55736975|gb|AAV60617.1| dihydroorotate dehydrogenase B [Streptococcus thermophilus LMG
           18311]
          Length = 315

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 92  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 149

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 150 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 203

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 204 TRYDLVTRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 262

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 263 IAGASAIGVGTANFADPY 280


>gi|323351511|ref|ZP_08087165.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis VMC66]
 gi|322121997|gb|EFX93723.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis VMC66]
          Length = 312

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 74/199 (37%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    A+ + +      I LN+ CP   V  G+ G  +   P++  + 
Sbjct: 99  PIIANVAGFSNQEYATVAEKISQASNVKAIELNISCP--NVDHGNAGLLIGQVPELAYEA 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A  +   +PV VK    V D      +  + K+++ +G  G  +            +R
Sbjct: 157 TKAAVETSVVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVGMRFDLRSR 210

Query: 157 KA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K  I  G        +  +   ++ ++ +    L I   GG++    AL++       + 
Sbjct: 211 KPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMFIAGASAIG 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + N     T+ E  
Sbjct: 270 VGTANFTNPYACPTIIENL 288


>gi|229180160|ref|ZP_04307504.1| Dihydroorotate dehydrogenase [Bacillus cereus 172560W]
 gi|228603369|gb|EEK60846.1| Dihydroorotate dehydrogenase [Bacillus cereus 172560W]
          Length = 306

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|228902389|ref|ZP_04066544.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis IBL 4222]
 gi|228909711|ref|ZP_04073534.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis IBL 200]
 gi|228922637|ref|ZP_04085937.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228966837|ref|ZP_04127881.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|229047569|ref|ZP_04193159.1| Dihydroorotate dehydrogenase [Bacillus cereus AH676]
 gi|229071384|ref|ZP_04204606.1| Dihydroorotate dehydrogenase [Bacillus cereus F65185]
 gi|229081137|ref|ZP_04213647.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock4-2]
 gi|229129162|ref|ZP_04258135.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-Cer4]
 gi|229146456|ref|ZP_04274827.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-ST24]
 gi|229152082|ref|ZP_04280277.1| Dihydroorotate dehydrogenase [Bacillus cereus m1550]
 gi|229192054|ref|ZP_04319023.1| Dihydroorotate dehydrogenase [Bacillus cereus ATCC 10876]
 gi|228591380|gb|EEK49230.1| Dihydroorotate dehydrogenase [Bacillus cereus ATCC 10876]
 gi|228631431|gb|EEK88065.1| Dihydroorotate dehydrogenase [Bacillus cereus m1550]
 gi|228637089|gb|EEK93548.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-ST24]
 gi|228654399|gb|EEL10264.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-Cer4]
 gi|228702181|gb|EEL54657.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock4-2]
 gi|228711675|gb|EEL63628.1| Dihydroorotate dehydrogenase [Bacillus cereus F65185]
 gi|228723816|gb|EEL75171.1| Dihydroorotate dehydrogenase [Bacillus cereus AH676]
 gi|228792936|gb|EEM40494.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228837066|gb|EEM82407.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228850000|gb|EEM94831.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis IBL 200]
 gi|228857246|gb|EEN01751.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis IBL 4222]
          Length = 306

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|228477418|ref|ZP_04062054.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           salivarius SK126]
 gi|228250853|gb|EEK10041.1| dihydroorotate dehydrogenase B, catalytic subunit [Streptococcus
           salivarius SK126]
          Length = 318

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 95  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 152

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 153 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 206

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 207 TRYDLATRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 265

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 266 IAGASAIGVGTANFADPY 283


>gi|47569512|ref|ZP_00240192.1| dihydroorotate dehydrogenase [Bacillus cereus G9241]
 gi|206971012|ref|ZP_03231963.1| dihydroorotate oxidase [Bacillus cereus AH1134]
 gi|47553841|gb|EAL12212.1| dihydroorotate dehydrogenase [Bacillus cereus G9241]
 gi|206733784|gb|EDZ50955.1| dihydroorotate oxidase [Bacillus cereus AH1134]
          Length = 309

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFIDPFVCPTIIEEL 282


>gi|30021973|ref|NP_833604.1| dihydroorotate dehydrogenase 1B [Bacillus cereus ATCC 14579]
 gi|75763138|ref|ZP_00742911.1| Dihydroorotate dehydrogenase, catalytic subunit [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|218899038|ref|YP_002447449.1| dihydroorotate oxidase [Bacillus cereus G9842]
 gi|296504379|ref|YP_003666079.1| dihydroorotate dehydrogenase 1B [Bacillus thuringiensis BMB171]
 gi|81837316|sp|Q819S5|PYRD_BACCR RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|226724730|sp|B7IUP4|PYRD_BACC2 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|29897529|gb|AAP10805.1| Dihydroorotate dehydrogenase, catalytic subunit [Bacillus cereus
           ATCC 14579]
 gi|74489375|gb|EAO52818.1| Dihydroorotate dehydrogenase, catalytic subunit [Bacillus
           thuringiensis serovar israelensis ATCC 35646]
 gi|218541213|gb|ACK93607.1| dihydroorotate oxidase [Bacillus cereus G9842]
 gi|296325431|gb|ADH08359.1| dihydroorotate dehydrogenase 1B [Bacillus thuringiensis BMB171]
          Length = 309

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFIDPFVCPTIIEEL 282


>gi|55822912|ref|YP_141353.1| dihydroorotate dehydrogenase 1B [Streptococcus thermophilus
           CNRZ1066]
 gi|55738897|gb|AAV62538.1| dihydroorotate dehydrogenase B [Streptococcus thermophilus
           CNRZ1066]
          Length = 315

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 92  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 149

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 150 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 203

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 204 TRYDLVTRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 262

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 263 IAGASAIGVGTANFADPY 280


>gi|322372986|ref|ZP_08047522.1| dihydroorotate dehydrogenase B [Streptococcus sp. C150]
 gi|321278028|gb|EFX55097.1| dihydroorotate dehydrogenase B [Streptococcus sp. C150]
          Length = 318

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 95  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 152

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 153 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 206

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 207 TRYDLATRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 265

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 266 IAGASAIGVGTANFADPY 283


>gi|228916522|ref|ZP_04080088.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228928933|ref|ZP_04091965.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935200|ref|ZP_04098026.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228940973|ref|ZP_04103531.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947604|ref|ZP_04109894.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228973904|ref|ZP_04134479.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980493|ref|ZP_04140803.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis Bt407]
 gi|229031516|ref|ZP_04187516.1| Dihydroorotate dehydrogenase [Bacillus cereus AH1271]
 gi|229104447|ref|ZP_04235115.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-28]
 gi|229140533|ref|ZP_04269088.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-ST26]
 gi|229162820|ref|ZP_04290777.1| Dihydroorotate dehydrogenase [Bacillus cereus R309803]
 gi|229186125|ref|ZP_04313294.1| Dihydroorotate dehydrogenase [Bacillus cereus BGSC 6E1]
 gi|229197996|ref|ZP_04324710.1| Dihydroorotate dehydrogenase [Bacillus cereus m1293]
 gi|228585475|gb|EEK43579.1| Dihydroorotate dehydrogenase [Bacillus cereus m1293]
 gi|228597301|gb|EEK54952.1| Dihydroorotate dehydrogenase [Bacillus cereus BGSC 6E1]
 gi|228620702|gb|EEK77571.1| Dihydroorotate dehydrogenase [Bacillus cereus R309803]
 gi|228643094|gb|EEK99370.1| Dihydroorotate dehydrogenase [Bacillus cereus BDRD-ST26]
 gi|228678969|gb|EEL33178.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-28]
 gi|228729805|gb|EEL80785.1| Dihydroorotate dehydrogenase [Bacillus cereus AH1271]
 gi|228779313|gb|EEM27570.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis Bt407]
 gi|228785770|gb|EEM33774.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228812124|gb|EEM58455.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818652|gb|EEM64719.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824365|gb|EEM70171.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830740|gb|EEM76345.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228843101|gb|EEM88183.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 306

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|30263887|ref|NP_846264.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. Ames]
 gi|42782977|ref|NP_980224.1| dihydroorotate dehydrogenase 1B [Bacillus cereus ATCC 10987]
 gi|47529316|ref|YP_020665.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49186734|ref|YP_029986.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. Sterne]
 gi|49478431|ref|YP_037946.1| dihydroorotate dehydrogenase 1B [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141602|ref|YP_085225.1| dihydroorotate dehydrogenase 1B [Bacillus cereus E33L]
 gi|65321212|ref|ZP_00394171.1| COG0167: Dihydroorotate dehydrogenase [Bacillus anthracis str.
           A2012]
 gi|165872320|ref|ZP_02216957.1| dihydroorotate oxidase [Bacillus anthracis str. A0488]
 gi|167636449|ref|ZP_02394748.1| dihydroorotate oxidase [Bacillus anthracis str. A0442]
 gi|167641152|ref|ZP_02399407.1| dihydroorotate oxidase [Bacillus anthracis str. A0193]
 gi|170688834|ref|ZP_02880037.1| dihydroorotate oxidase [Bacillus anthracis str. A0465]
 gi|170708788|ref|ZP_02899224.1| dihydroorotate oxidase [Bacillus anthracis str. A0389]
 gi|177654911|ref|ZP_02936628.1| dihydroorotate oxidase [Bacillus anthracis str. A0174]
 gi|190566008|ref|ZP_03018927.1| dihydroorotate oxidase [Bacillus anthracis Tsiankovskii-I]
 gi|196035815|ref|ZP_03103217.1| dihydroorotate oxidase [Bacillus cereus W]
 gi|196047428|ref|ZP_03114640.1| dihydroorotate oxidase [Bacillus cereus 03BB108]
 gi|206976741|ref|ZP_03237645.1| dihydroorotate oxidase [Bacillus cereus H3081.97]
 gi|217961305|ref|YP_002339873.1| dihydroorotate dehydrogenase 1B [Bacillus cereus AH187]
 gi|218905014|ref|YP_002452848.1| dihydroorotate oxidase [Bacillus cereus AH820]
 gi|222097330|ref|YP_002531387.1| dihydroorotate dehydrogenase 1b [Bacillus cereus Q1]
 gi|225865866|ref|YP_002751244.1| dihydroorotate oxidase [Bacillus cereus 03BB102]
 gi|227813207|ref|YP_002813216.1| dihydroorotate oxidase [Bacillus anthracis str. CDC 684]
 gi|229600629|ref|YP_002868120.1| dihydroorotate oxidase [Bacillus anthracis str. A0248]
 gi|254683406|ref|ZP_05147266.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str.
           CNEVA-9066]
 gi|254721417|ref|ZP_05183206.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. A1055]
 gi|254735924|ref|ZP_05193630.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739828|ref|ZP_05197521.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. Kruger B]
 gi|254751018|ref|ZP_05203057.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. Vollum]
 gi|254756683|ref|ZP_05208712.1| dihydroorotate dehydrogenase 1B [Bacillus anthracis str. Australia
           94]
 gi|301055375|ref|YP_003793586.1| dihydroorotate dehydrogenase [Bacillus anthracis CI]
 gi|81824211|sp|Q636E2|PYRD_BACCZ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|81828223|sp|Q6HET0|PYRD_BACHK RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|81830988|sp|Q732I5|PYRD_BACC1 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|81837833|sp|Q81WF4|PYRD_BACAN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|226724729|sp|B7JJX1|PYRD_BACC0 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|226724732|sp|B7HLL8|PYRD_BACC7 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|254788875|sp|C3P654|PYRD_BACAA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|254788876|sp|C3L742|PYRD_BACAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|254788877|sp|C1EPP8|PYRD_BACC3 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|254788878|sp|B9IVW1|PYRD_BACCQ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|30258531|gb|AAP27750.1| dihydroorotate oxidase [Bacillus anthracis str. Ames]
 gi|42738904|gb|AAS42832.1| dihydroorotate dehydrogenase [Bacillus cereus ATCC 10987]
 gi|47504464|gb|AAT33140.1| dihydroorotate oxidase [Bacillus anthracis str. 'Ames Ancestor']
 gi|49180661|gb|AAT56037.1| dihydroorotate dehydrogenase [Bacillus anthracis str. Sterne]
 gi|49329987|gb|AAT60633.1| dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51975071|gb|AAU16621.1| dihydroorotate dehydrogenase [Bacillus cereus E33L]
 gi|164711996|gb|EDR17536.1| dihydroorotate oxidase [Bacillus anthracis str. A0488]
 gi|167510932|gb|EDR86323.1| dihydroorotate oxidase [Bacillus anthracis str. A0193]
 gi|167528191|gb|EDR90978.1| dihydroorotate oxidase [Bacillus anthracis str. A0442]
 gi|170126273|gb|EDS95164.1| dihydroorotate oxidase [Bacillus anthracis str. A0389]
 gi|170667189|gb|EDT17949.1| dihydroorotate oxidase [Bacillus anthracis str. A0465]
 gi|172080422|gb|EDT65509.1| dihydroorotate oxidase [Bacillus anthracis str. A0174]
 gi|190562927|gb|EDV16893.1| dihydroorotate oxidase [Bacillus anthracis Tsiankovskii-I]
 gi|195991464|gb|EDX55430.1| dihydroorotate oxidase [Bacillus cereus W]
 gi|196021736|gb|EDX60431.1| dihydroorotate oxidase [Bacillus cereus 03BB108]
 gi|206745051|gb|EDZ56454.1| dihydroorotate oxidase [Bacillus cereus H3081.97]
 gi|217066673|gb|ACJ80923.1| dihydroorotate oxidase [Bacillus cereus AH187]
 gi|218538865|gb|ACK91263.1| dihydroorotate oxidase [Bacillus cereus AH820]
 gi|221241388|gb|ACM14098.1| dihydroorotate dehydrogenase [Bacillus cereus Q1]
 gi|225789315|gb|ACO29532.1| dihydroorotate oxidase [Bacillus cereus 03BB102]
 gi|227004879|gb|ACP14622.1| dihydroorotate oxidase [Bacillus anthracis str. CDC 684]
 gi|229265037|gb|ACQ46674.1| dihydroorotate oxidase [Bacillus anthracis str. A0248]
 gi|300377544|gb|ADK06448.1| dihydroorotate dehydrogenase [Bacillus cereus biovar anthracis str.
           CI]
 gi|324327783|gb|ADY23043.1| dihydroorotate dehydrogenase 1B [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941654|gb|AEA17550.1| dihydroorotate dehydrogenase 1B [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 309

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFIDPFVCPTIIEEL 282


>gi|196038772|ref|ZP_03106080.1| dihydroorotate oxidase [Bacillus cereus NVH0597-99]
 gi|196030495|gb|EDX69094.1| dihydroorotate oxidase [Bacillus cereus NVH0597-99]
          Length = 309

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFIDPFVCPTIIEEL 282


>gi|78486289|ref|YP_392214.1| dihydroorotate dehydrogenase family protein [Thiomicrospira
           crunogena XCL-2]
 gi|78364575|gb|ABB42540.1| dihydroorotate oxidase B, catalytic subunit [Thiomicrospira
           crunogena XCL-2]
          Length = 297

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 82/218 (37%), Gaps = 28/218 (12%)

Query: 34  RGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
               K+ L      +    + + G+ I +  E  ++ +      I +N+ CP   V +G 
Sbjct: 63  HAVIKDYLPKLDLSQSQFIINVSGSSIEEYAEVVRLFDQTDLPAIEVNISCP--NVKKGG 120

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-- 150
                  +PD+    + A     S P+ VK      D      +    + +  +G +   
Sbjct: 121 AAFG--NDPDMAAKVVEACRANTSKPLIVKLSPNQTD------IAEGARRVIDAGADMLS 172

Query: 151 ---------IWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                    I IH+ +  L     GLS    + +  L    VY++ K++ ++ I   GG+
Sbjct: 173 AINTLMGMQIDIHSARPTLGNNQGGLSGPAIKPVALLKVHQVYQVAKQH-NVPIIGLGGI 231

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                A++ +L     V +G A  K+  ++  +++   
Sbjct: 232 ASADDAIEFLLAGASMVAVGTAMAKDPLLVKKINQGIE 269


>gi|312278317|gb|ADQ62974.1| Dihydroorotate dehydrogenase B [Streptococcus thermophilus ND03]
          Length = 315

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 92  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 149

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 150 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 203

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 204 TRYDLATRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 262

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 263 IAGASAIGVGTANFADPY 280


>gi|228954161|ref|ZP_04116189.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228805481|gb|EEM52072.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 306

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 74/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL           I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANCTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|171779810|ref|ZP_02920766.1| hypothetical protein STRINF_01648 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281912|gb|EDT47346.1| hypothetical protein STRINF_01648 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 314

 Score = 79.9 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/228 (16%), Positives = 82/228 (35%), Gaps = 23/228 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    ++ +        I LN+ CP   V  G+ G  +  
Sbjct: 91  LAEHFPELPIIANVAGFSNDEYAYVSEKISKAPNVKAIELNISCP--NVDHGNHGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +   +PV VK    V D      +  + K+++++G  G  +      
Sbjct: 149 VPELAYAAVKASVENSDVPVYVKLTPSVTD------ITTVAKAVEEAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ + + DL I   GG++    A++++
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-SSDLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
                 + +G A + +      + +     +   S       +   R+
Sbjct: 262 IAGASAIGVGTANFADPYACPNIIDRLPEVMDQYSITDLETLRREVRQ 309


>gi|317057514|ref|YP_004105981.1| dihydroorotate dehydrogenase family protein [Ruminococcus albus 7]
 gi|315449783|gb|ADU23347.1| dihydroorotate dehydrogenase family protein [Ruminococcus albus 7]
          Length = 303

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 88/236 (37%), Gaps = 33/236 (13%)

Query: 11  FFARLLTNNALLYTE----MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISK 61
              R   N A    E    M+ +  +  G     L +      T++  +   I G+ I +
Sbjct: 48  TLHRREGNPAPRVAETPSGMLNSVGLQNGGVDKFLSYELPNLVTKDTRIIANIAGSTIEE 107

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             E A  ++    + I LN+ CP    +    GA    + +I G    A+      PV V
Sbjct: 108 CAELAAKLKGSDIDMIELNISCP----NVKQGGAAFGTDCNIAGAVTKAVKDNSDKPVMV 163

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK-GLSPKDNR 169
           K    V       ++ ++ KS++ +G +            I I+  + ILK  +      
Sbjct: 164 KLSPNV------TSIVDIAKSVEANGADAVSLINTLLGMRIDINTGRPILKNNVGGLSGP 217

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
            +  +   +V+++     ++ +   GG+     A++ ++     V +G A + +  
Sbjct: 218 AVFPVAVRMVWQVANAV-NIPVCGMGGVSTWEDAVEIMMAGASLVQVGAAIFNDPF 272


>gi|319649633|ref|ZP_08003789.1| dihydroorotate dehydrogenase [Bacillus sp. 2_A_57_CT2]
 gi|317398795|gb|EFV79477.1| dihydroorotate dehydrogenase [Bacillus sp. 2_A_57_CT2]
          Length = 313

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 80/211 (37%), Gaps = 25/211 (11%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGA 95
            + +L     + P+   + G+     V  AK + +    + + LN+ CP+ +    +FG 
Sbjct: 83  NEELLWLEQYDVPIIANVAGSQEEDYVAVAKRISESPNVHALELNISCPNVKTGGIAFGT 142

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-- 153
                P+I  +    + +   +PV VK    V        +  + K+++  G +G+ +  
Sbjct: 143 I----PEIAKNLTKKVKEVSEVPVYVKLSPNV------TNIVEMAKAVEDGGADGLTMIN 192

Query: 154 --HARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                +  LK  SP             I  +   ++YE+ ++   L I   GG+E     
Sbjct: 193 TLVGMRIDLKTGSPVLANRTGGLSGPAIKPVALRMIYEVSQQV-SLPIIGMGGIESAEDV 251

Query: 204 LKIL-PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++        V +G A + +  +   + +  
Sbjct: 252 IEYFYAGASAVAVGTANFVDPFVCPKIIDRL 282


>gi|322516826|ref|ZP_08069727.1| dihydroorotate dehydrogenase B [Streptococcus vestibularis ATCC
           49124]
 gi|322124624|gb|EFX96092.1| dihydroorotate dehydrogenase B [Streptococcus vestibularis ATCC
           49124]
          Length = 318

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 70/198 (35%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +  E + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 95  LQEHYPELPIIANVAGFSNEEYAEVSHKISKASNVKAIELNISCP--NVDHGNNGLLIGQ 152

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A      +PV VK    V D           K+++ +G  G  +      
Sbjct: 153 VPELAYAAVKASVSHSDVPVYVKLTPSVADITSV------AKAVEDAGATGFTMINTLVG 206

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++     DL I   GG++    A+++ 
Sbjct: 207 TRYDLATRKPIIANGQGGMSGPAVFPVALKLIRQVA-LASDLPIIGMGGVDSAEAAIEMF 265

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 266 IAGASAIGVGTANFADPY 283


>gi|218235763|ref|YP_002368684.1| dihydroorotate dehydrogenase 1B [Bacillus cereus B4264]
 gi|226724731|sp|B7H6M0|PYRD_BACC4 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|218163720|gb|ACK63712.1| dihydroorotate oxidase [Bacillus cereus B4264]
          Length = 309

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIETAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFIDPFVCPTIIEEL 282


>gi|152976245|ref|YP_001375762.1| dihydroorotate dehydrogenase 1B [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|189038416|sp|A7GRK9|PYRD_BACCN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|152024997|gb|ABS22767.1| dihydroorotate dehydrogenase family protein [Bacillus cytotoxicus
           NVH 391-98]
          Length = 309

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 39/199 (19%), Positives = 76/199 (38%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+ +   V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQVEDYVAVAKKISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------TNIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   D+ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQ-VVDIPIIGMGGIESAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFVDPLVCPTIIEEL 282


>gi|300856728|ref|YP_003781712.1| dihydroorotate dehydrogenase [Clostridium ljungdahlii DSM 13528]
 gi|300436843|gb|ADK16610.1| dihydroorotate dehydrogenase [Clostridium ljungdahlii DSM 13528]
          Length = 296

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 73/196 (37%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   IGG+ I   VE+ + +     + I LN+ CP   V  G     +     +  +
Sbjct: 89  DTVVIANIGGSTIDDYVESVEKLSSSDVDIIELNISCP--NVKSGGMAFGI--KSKVAYE 144

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++A+ K    P+ VK     +D      + ++      +G +            I I  
Sbjct: 145 IVSAVRKVCKKPLMVKLSPNAED------IVDMAYKCCDAGADSLSLVNTFKAMAIDIKN 198

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RKA+     S      I  +   +VYE+ K    + +   GG+     A++ I+     +
Sbjct: 199 RKAVFDNITSGLSGPAIKPIALRMVYEVSKAV-KVPVVGIGGIVSFQDAIEFIMAGAYAI 257

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A +    +   +
Sbjct: 258 QVGTANFIKPDICLDI 273


>gi|268608526|ref|ZP_06142253.1| dihydroorotate dehydrogenase 1B [Ruminococcus flavefaciens FD-1]
          Length = 303

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 81/198 (40%), Gaps = 28/198 (14%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           I GA   +  E A  ++D   + I LN+ CP+ +    +FG       D+  +    + +
Sbjct: 100 IAGATPEECAEVAAKLDDTDVHMIELNISCPNVKQGGAAFGTSC----DMAAEVTRKVRE 155

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILK- 161
           A   P+ VK    V       ++ ++ KS++ +G +            I I+  + IL+ 
Sbjct: 156 ATKKPLVVKLSPNV------TSITDIAKSVEAAGADAVSLINTLLGMRIDINTGRPILRN 209

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
            +       +  +   +V+++        IG+ GG+     A++ ++     V +G A +
Sbjct: 210 NVGGMSGPAVFPIAVRMVWQVANAVNIPVIGM-GGVSSGRDAIELMMAGASAVQVGAAIF 268

Query: 221 KNSA----MLTTVDEYFS 234
            +      ++  ++E+  
Sbjct: 269 TDPYAPVKIIDEMNEFLD 286


>gi|224007839|ref|XP_002292879.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971741|gb|EED90075.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 389

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 60/335 (17%), Positives = 111/335 (33%), Gaps = 89/335 (26%)

Query: 10  RFFARLLTNNALLYTEMIVADAIL--RGDKKNI-----------LGFSTQEK-------- 48
           R  AR      L Y+ M+    ++      K +           +      +        
Sbjct: 2   RMLARK-HGAILCYSPMLRDRDVIAAHQHWKTLSTEDRLDIWKDVKIDGAGRTNSMNETG 60

Query: 49  -------------PLALQIGGADISKLVEAA-KIVEDFGYNE-------INLNVGCPSAR 87
                         L +Q+ G+  + L  A   ++E F  N        I+LN+GCP   
Sbjct: 61  YLMLHDTCRDDTCNLVVQLSGSTPNNLHNATTALLEMFTNNNDGTLPVGIDLNLGCPQKC 120

Query: 88  VHEGSFGACLM-LNPDIVGDCIAAMCKAL----------SIP-VTVKCRIGVDDQIPAVA 135
             +  FGA L+  N +   +CIA+M  A+          S P ++ K R+          
Sbjct: 121 AEDEGFGAFLVERNAEGAVECIASMRLAIVEFCQKNLISSKPMLSAKIRLL----DSVED 176

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD---LFIG 192
                + ++ +G++ I IH R    K             D++   ++         L + 
Sbjct: 177 TIAFARKLRNAGIDYIAIHCRNREAKHD--------GAADWEAGAKLVSSLSVGDALPVI 228

Query: 193 LNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           +NGG+   + A  +    +  GVM+     +N                 +  I T  + +
Sbjct: 229 VNGGISCYTDAEFVTKQTNCHGVMVATGYLQN---------------HRNYAITTEGECN 273

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
               +++   DYA R  +       I +H   +F 
Sbjct: 274 SAVNVASEYLDYAER--YPPPSYLYIQKHFRWIFR 306


>gi|23098948|ref|NP_692414.1| dihydroorotase dehydrogenase [Oceanobacillus iheyensis HTE831]
 gi|30173248|sp|Q8CWG1|PYRD_OCEIH RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|22777176|dbj|BAC13449.1| dihydroorotase dehydrogenase (catalytic subunit, dihydroorotate
           oxidase) (EC 1.3.3.1) [Oceanobacillus iheyensis HTE831]
          Length = 304

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 79/203 (38%), Gaps = 27/203 (13%)

Query: 42  GFSTQEKPLALQIGGADISK--LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
             +  +  +   I G+ I +   V AA   +    + + LN+ CP    +    G     
Sbjct: 87  RLAKYDTSIIANIAGSSIEEYEFV-AASFNQTTDVDALELNISCP----NVKEGGIQFGT 141

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHA 155
           +P +       + KA + PV VK    V +      +  + K+++++G +G+     +  
Sbjct: 142 DPFMAKKVTEVVKKASNKPVYVKLSPNVHN------IVEMAKAVEEAGADGLSMINTLTG 195

Query: 156 RKAILKGLSP--------KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            K  L    P             I  +   ++YE++++     IG+ GG+      L+ L
Sbjct: 196 MKIHLPSRKPLIANKTGGLSGPAIKPVAIRMIYEVRQQVSIPIIGM-GGITSAEDVLEYL 254

Query: 208 -PSVDGVMIGRAAYKNSAMLTTV 229
               D V +G A ++N  +   +
Sbjct: 255 IAGADAVAVGTANFQNPFVCVDI 277


>gi|332361139|gb|EGJ38943.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK1056]
          Length = 312

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|327460288|gb|EGF06625.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK1057]
          Length = 312

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|237746522|ref|ZP_04577002.1| oxidoreductase iron-sulfur protein [Oxalobacter formigenes HOxBLS]
 gi|229377873|gb|EEO27964.1| oxidoreductase iron-sulfur protein [Oxalobacter formigenes HOxBLS]
          Length = 415

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 40/197 (20%), Positives = 77/197 (39%), Gaps = 16/197 (8%)

Query: 25  EMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           EMI    + +  +    L     +K +   I G+D  +    A+ V D G + I  N  C
Sbjct: 77  EMISDKPLDVNLENMRRLKREFPDKVMIASIMGSDDDEWRTLAQKVTDTGADIIECNFSC 136

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVALRNLVK- 141
           P   +   + G+ +  +P++V     A+C+A  +PV  K    +   ++PA+A  N    
Sbjct: 137 PQ--MTSSAMGSDVGQSPELVARYTEAVCRATHLPVLAKMTPNIGHMELPAIAAVNAGAK 194

Query: 142 -SIKKSGVNGIW-----IHARKAILKGL---SPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
                + +  I        +   ++ G    S      I  +    + ++K+  E   + 
Sbjct: 195 GIAAINTIKAITRIDTECLSPMPVVNGKSSISGYSGPAIKPIALRFIAQMKQHPELRHIP 254

Query: 191 IGLNGGLEDMSQALKIL 207
           +   GG+     AL+ L
Sbjct: 255 VSGIGGIVTWKDALEFL 271


>gi|330883229|gb|EGH17378.1| tRNA-dihydrouridine synthase B [Pseudomonas syringae pv. glycinea
           str. race 4]
          Length = 117

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
            DG++IGRAA     +   ++ +        +P  + V++     ++A    Y       
Sbjct: 1   ADGLLIGRAAQGRPWIFREIEHFLRTGEKLPAPQSSEVERILLEHLAALHVFY-----GD 55

Query: 270 GGKLQQITRHMIGLFHGFPNSRRCRHI 296
              ++   +H+       P +R  R  
Sbjct: 56  VMGVRIARKHVSWYLATLPGAREFRAH 82


>gi|145613924|ref|XP_363331.2| hypothetical protein MGG_01257 [Magnaporthe oryzae 70-15]
 gi|145020935|gb|EDK05064.1| hypothetical protein MGG_01257 [Magnaporthe oryzae 70-15]
          Length = 313

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 82/260 (31%), Gaps = 39/260 (15%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
            +      + P  +Q G     +L  A+ +V  F    ++LN GCP +     + GA LM
Sbjct: 31  TLATTPQPQPPTIVQFGANVPVELARASSLVAPF-VAGVDLNCGCPQSWACAETLGAALM 89

Query: 99  LNPDIVGDCIAAMCK-------ALSIP----------VTVKCRIGVDDQIPAVALRNLVK 141
              ++V D +            A+ +           V+VK R+  D +     +  ++ 
Sbjct: 90  ERRELVRDMVVETRSRLASDGWAVGLERDKNDPKGRSVSVKIRVHKDLRKTMDFIDTVIG 149

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
                 ++ + IH R        P +   +  L            P+             
Sbjct: 150 DPNARNIDFLTIHPRTRATPSREPINVESLSILVESPASAGAAGAPN------------D 197

Query: 202 QALKILPSVDGVMIGRAAYKNSAMLTT--------VDEYFSNPLTGSSPIKTRVDKDFWR 253
            +   +P + G+M  R    N ++           V+ + +       P K  V      
Sbjct: 198 TSRPAIPKLRGLMSARGLLANPSLFAGTQRCSWDVVEHFLNRAAQAPLPFKL-VTHHLTE 256

Query: 254 KISASMTDYAARHLHSGGKL 273
             +  M    A  L+   ++
Sbjct: 257 MTAPGMGPDKASLLNKRERI 276


>gi|311068075|ref|YP_003972998.1| dihydroorotate dehydrogenase 1B [Bacillus atrophaeus 1942]
 gi|310868592|gb|ADP32067.1| dihydroorotate dehydrogenase 1B [Bacillus atrophaeus 1942]
          Length = 311

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 75/197 (38%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ +   VE A+ +      N + LN+ CP    +  + G     NP +  
Sbjct: 91  DTPIIANVAGSQVEDYVEVAEQISKAPNVNALELNISCP----NVKTGGIAFGTNPAMAA 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +   A+ K   +PV VK    V        +  +  +I+++G +G+ +            
Sbjct: 147 ELTKAVKKVSQVPVYVKLSPNV------ANIAEIAVAIEEAGADGLTMINTLIGMRLDLK 200

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             +  +           +  +   +VYE+ +   ++ I   GG++    A + +L     
Sbjct: 201 TGQPILANKTGGLSGPAVKPVAIRMVYEVSQAV-NIPIIGMGGVQTAEDAFEFLLAGASA 259

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + N      +
Sbjct: 260 VAVGTANFVNPFACPEI 276


>gi|118479105|ref|YP_896256.1| dihydroorotate dehydrogenase 1B [Bacillus thuringiensis str. Al
           Hakam]
 gi|166234203|sp|A0RHQ6|PYRD_BACAH RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|118418330|gb|ABK86749.1| dihydroorotate oxidase B, catalytic subunit [Bacillus thuringiensis
           str. Al Hakam]
          Length = 309

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 74/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 95  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I  +G +G+ +              
Sbjct: 151 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIANAGADGLTMINTLLGMRLDLKTA 204

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 205 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFIDPFVCPTIIEEL 282


>gi|229075642|ref|ZP_04208624.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock4-18]
 gi|229098355|ref|ZP_04229301.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-29]
 gi|228685060|gb|EEL38992.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-29]
 gi|228707418|gb|EEL59609.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock4-18]
          Length = 306

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           + IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 QPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIESAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|283853402|ref|ZP_06370648.1| dihydroorotate dehydrogenase family protein [Desulfovibrio sp.
           FW1012B]
 gi|283571215|gb|EFC19229.1| dihydroorotate dehydrogenase family protein [Desulfovibrio sp.
           FW1012B]
          Length = 308

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 69/207 (33%), Gaps = 26/207 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
                  P+   +   D  +  E A  + +  G   + +N+ CP    +  + G     +
Sbjct: 89  RLPHAATPIIANLYACDADEFAELAGVLSKAEGVAALEVNISCP----NVKAGGIAFGQD 144

Query: 101 PDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
           P + G    A+ K A   PV VK    V D      +  + ++    G + +        
Sbjct: 145 PAMAGRLTEAVKKRAGDKPVWVKLSPNVTD------IVAIARAAVLGGADALTCINTLTG 198

Query: 153 ----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
               I  RK  L  G+       I  +    V+++ +      +   GG+      L+ +
Sbjct: 199 MSVDIRTRKPRLANGIGGLSGPAIKPVALRCVWQVCRAVSA-PVIAVGGISSAEDVLEFM 257

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L     V IG A +    M   + E  
Sbjct: 258 LVGAHAVQIGTANFMRPDMAFRIAERL 284


>gi|257079155|ref|ZP_05573516.1| pyrimidine biosynthesis D protein [Enterococcus faecalis JH1]
 gi|294779372|ref|ZP_06744773.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis PC1.1]
 gi|307269525|ref|ZP_07550864.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX4248]
 gi|256987185|gb|EEU74487.1| pyrimidine biosynthesis D protein [Enterococcus faecalis JH1]
 gi|294453501|gb|EFG21902.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis PC1.1]
 gi|306514145|gb|EFM82721.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX4248]
          Length = 311

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 71/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +    KI +      I LN+ CP    +    G     +PDI    
Sbjct: 97  PIIANVAGACEEDYVAVCTKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 153 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 207 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 265

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 266 VGTANFTDPYI 276


>gi|289423365|ref|ZP_06425173.1| dihydroorotate dehydrogenase, catalytic subunit [Peptostreptococcus
           anaerobius 653-L]
 gi|289156296|gb|EFD04953.1| dihydroorotate dehydrogenase, catalytic subunit [Peptostreptococcus
           anaerobius 653-L]
          Length = 300

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 91/236 (38%), Gaps = 21/236 (8%)

Query: 15  LLTNNALLYTE----MIVADAILRGD-----KKNILGFSTQEKPLALQIGGADISKLVEA 65
              N  +   E    M+ +  +         +K +  FS  +    + +GG  +   V+ 
Sbjct: 52  RPGNEGMRVHETPSGMMNSVGLENPGVEGFIEKELDNFSKLDLCRIVNLGGGCLEDYVKG 111

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+++E   ++ I LN+ CP   V  G     +    ++  + + A+ KA + P+ VK   
Sbjct: 112 AELLEGKDFDMIELNISCP--NVKHGGMAYGI--KSEVAREVVRAVKKATTKPLMVKLSP 167

Query: 126 GVDDQIPAVALR-----NLVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIV 179
             +D +           + +  +       I I  +K +   + +      I  +   +V
Sbjct: 168 NAEDIVAMAIACQEEGADAISLVNTFKAMAIDIRNKKPVFNNVTAGLSGPAIKPIALRMV 227

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           YE+ K      +G+ GG+ D +  ++ I+     V +G A + N  +   +    +
Sbjct: 228 YEVAKAVTIPVVGM-GGIMDANDVIEFIMAGATCVQVGTANFVNPRIGQDIIRDLN 282


>gi|332366827|gb|EGJ44568.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK1059]
          Length = 312

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 76/207 (36%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                   +  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLTTCKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|168183553|ref|ZP_02618217.1| dihydroorotate oxidase [Clostridium botulinum Bf]
 gi|237796692|ref|YP_002864244.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum Ba4 str.
           657]
 gi|182673288|gb|EDT85249.1| dihydroorotate oxidase [Clostridium botulinum Bf]
 gi|229263231|gb|ACQ54264.1| dihydroorotate oxidase [Clostridium botulinum Ba4 str. 657]
          Length = 298

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 71/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + K
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEIVKEVKK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQKPLMVKLSPNAED------IVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+   + +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPIALRMVYEVCKQV-KIPVIGIGGICNYKDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|329571891|gb|EGG53569.1| dihydroorotate oxidase, catalytic subunit [Enterococcus faecalis
           TX1467]
          Length = 311

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 71/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +    KI +      I LN+ CP    +    G     +PDI    
Sbjct: 97  PIIANVAGACEEDYVAVCTKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 153 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 207 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 265

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 266 VGTANFTDPYI 276


>gi|312864800|ref|ZP_07725031.1| dihydroorotate oxidase, catalytic subunit [Streptococcus downei
           F0415]
 gi|311099927|gb|EFQ58140.1| dihydroorotate oxidase, catalytic subunit [Streptococcus downei
           F0415]
          Length = 312

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 37/198 (18%), Positives = 73/198 (36%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LQKHYPDLPIIANVAGFSNEEYASVAGKISQAPNVEAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++      A  +A  +PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYAATKAAVEASQVPVYVKLTPSVAD------ISQIAKAVEDAGATGFTMINTLVG 202

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                   +  I  G        +  +   ++ ++ + N  L I   GG++    AL+++
Sbjct: 203 MRFNLQSRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-NSKLPIIGMGGVDSAEAALEMM 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFTDPF 279


>gi|325687521|gb|EGD29542.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK72]
          Length = 312

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 77/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHFPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|160893866|ref|ZP_02074649.1| hypothetical protein CLOL250_01420 [Clostridium sp. L2-50]
 gi|156864518|gb|EDO57949.1| hypothetical protein CLOL250_01420 [Clostridium sp. L2-50]
          Length = 303

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 72/217 (33%), Gaps = 29/217 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +        +          +  + + + G      ++  + + D   + + +N
Sbjct: 69  MMNAIGLQNPGIDTFIKRDLPFLAKYDTKVIVNVCGKSKEDYIDVVERLADTDIDMLEMN 128

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP    +    G      P+ + D   A+ K    PV +K    V D      +  + 
Sbjct: 129 VSCP----NVKEGGIAFGQKPEALYDITQAVKKVAKQPVIMKLSPNVTD------ITEMA 178

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           ++ +  G + + +                A+    +      I  +   +VY++      
Sbjct: 179 RAAEAGGADALSLINTLTGMKIDVKRRTFAVKNKTAGVSGPAIHPIAVRMVYQVANAV-K 237

Query: 189 LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA 224
           L I   GG+     AL++ +     + +G A + N  
Sbjct: 238 LPIIGMGGIATTEDALEMIMAGASAIAVGTANFNNPY 274


>gi|315147409|gb|EFT91425.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX4244]
          Length = 312

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 71/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +    KI +      I LN+ CP    +    G     +PDI    
Sbjct: 98  PIIANVAGACEEDYVAVCTKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPDIAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 267 VGTANFTDPYI 277


>gi|239826551|ref|YP_002949175.1| dihydroorotate dehydrogenase 1B [Geobacillus sp. WCH70]
 gi|259547522|sp|C5D8Q2|PYRD_GEOSW RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|239806844|gb|ACS23909.1| dihydroorotate dehydrogenase family protein [Geobacillus sp. WCH70]
          Length = 313

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 76/201 (37%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ + + VE AK +      + + LN+ CP   V +G         P+I  
Sbjct: 93  DVPIIANVAGSTMEEYVEVAKHISKAPNVHALELNISCP--NVKKGGIAFG--TVPEIAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           +    + +   +PV VK    V        +  + K+I+ +G +G+            + 
Sbjct: 149 ELTKLVKEVSEVPVYVKLSPNV------TNIVEMAKAIEAAGADGLTMINTLLGMRIDVK 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             K IL   +       I  +   ++YE+ +      IG+ GG++     ++        
Sbjct: 203 TAKPILANRTGGLSGPAIKPIAIRMIYEVSQAVSIPIIGM-GGIQSAEDVIEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V IG A + +  +   +    
Sbjct: 262 VAIGTANFIDPFVCPNIIAEL 282


>gi|262282838|ref|ZP_06060605.1| dihydroorotate dehydrogenase B [Streptococcus sp. 2_1_36FAA]
 gi|262261090|gb|EEY79789.1| dihydroorotate dehydrogenase B [Streptococcus sp. 2_1_36FAA]
          Length = 312

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 75/207 (36%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L       P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPGLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A      +PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDTSDVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|167756536|ref|ZP_02428663.1| hypothetical protein CLORAM_02073 [Clostridium ramosum DSM 1402]
 gi|237733134|ref|ZP_04563615.1| dihydroorotate dehydrogenase 1B [Mollicutes bacterium D7]
 gi|167702711|gb|EDS17290.1| hypothetical protein CLORAM_02073 [Clostridium ramosum DSM 1402]
 gi|229383816|gb|EEO33907.1| dihydroorotate dehydrogenase 1B [Coprobacillus sp. D7]
          Length = 305

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 73/199 (36%), Gaps = 25/199 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   IGG+     VE AK +        + LN+ CP   VH G        NP++  D  
Sbjct: 97  VIANIGGSAPDDYVETAKRISTHDMVGALELNISCP--NVHSGGIQFG--TNPEMAADLT 152

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HAR 156
             + +   +PV VK    V D      +  + K+++ +G +GI +              +
Sbjct: 153 RRVKEVSKVPVYVKLSPNVTD------IVAMAKAVEAAGADGITMINTLVGMRFDFKTGK 206

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMI 215
             I           I  +   +VY++ +      IG+ GG+++    ++++      V I
Sbjct: 207 PIIANKTGGYSGPAIFPVALRMVYQVSQAVKIPVIGM-GGIQNARDVIEMMSAGASAVAI 265

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           G     +  +   +     
Sbjct: 266 GCQNLIDPYVCEKIINDLE 284


>gi|125718062|ref|YP_001035195.1| dihydroorotate dehydrogenase 1B [Streptococcus sanguinis SK36]
 gi|125497979|gb|ABN44645.1| Dihydroorotate dehydrogenase B, putative [Streptococcus sanguinis
           SK36]
 gi|325694442|gb|EGD36351.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK150]
          Length = 312

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQASNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A  +  ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVETSAVPVYVKLTPSVAD------ITQVAKAVEDAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFNLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIENL 288


>gi|229086449|ref|ZP_04218621.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-44]
 gi|228696766|gb|EEL49579.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock3-44]
          Length = 300

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP++  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEVAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSGVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIESAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFVDPFVCPTIIEEL 279


>gi|157150915|ref|YP_001450539.1| dihydroorotate dehydrogenase 1B [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075709|gb|ABV10392.1| dihydroorotate dehydrogenase B [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 312

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 81/228 (35%), Gaps = 23/228 (10%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYSDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A     ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDTSAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
                 + +G A + +     T+ E     +           +   R+
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDLPKAMDKYGIESLETLRKEVRE 309


>gi|85713392|ref|ZP_01044397.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
 gi|85692787|gb|EAQ30780.1| Predicted tRNA-dihydrouridine synthase [Idiomarina baltica OS145]
          Length = 97

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 10/99 (10%)

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             +LT ++  +++  T  S             ++  M  Y  +H+ +GG+   + RHM+G
Sbjct: 1   PWLLTELETLYTSNPTSIS----------RESVARQMIPYIQQHIAAGGRAWHVVRHMLG 50

Query: 283 LFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
           LF G P  ++ R  L+++         +IE A     +S
Sbjct: 51  LFQGQPGGKKWRQFLSIKGPRLNDAEALIEGAIEFRTDS 89


>gi|56419689|ref|YP_147007.1| dihydroorotate dehydrogenase 1B [Geobacillus kaustophilus HTA426]
 gi|81819759|sp|Q5L0U1|PYRD_GEOKA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|56379531|dbj|BAD75439.1| dihydroorotate dehydrogenase, catalytic subunit (dihydroorotate
           oxidase) [Geobacillus kaustophilus HTA426]
          Length = 313

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 80/197 (40%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+ + + VE A+ + +    + + LN+ CP   V +G         PD+  
Sbjct: 93  DVPIIANIAGSTVEEYVEVAEAISQAPNVHALELNISCP--NVKKGGIAFG--TVPDVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    + +  ++PV VK    V D      +  + K+I+++G +G+ +            
Sbjct: 149 ELTRLVKQVSAVPVYVKLSPNVTD------IVAMAKAIEQAGADGLTMINTLVGMRIDVK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             R  +  G        +  +   ++YE+ +      IG+ GG++     L+        
Sbjct: 203 TGRPILANGTGGLSGPAVKPIAIRMIYEVSQAVSIPIIGM-GGIQTAEDVLEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +  T+
Sbjct: 262 VAVGTANFVDPFVCPTI 278


>gi|289808099|ref|ZP_06538728.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. AG3]
          Length = 62

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 30/57 (52%), Positives = 41/57 (71%), Gaps = 1/57 (1%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGA 57
          M+DWTDRH R+F RLL+   LLYTEM+   AI+ G   + L +S +E P+ALQ+GG+
Sbjct: 7  MLDWTDRHCRYFLRLLSRQTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVALQLGGS 62


>gi|296133331|ref|YP_003640578.1| dihydroorotate dehydrogenase family protein [Thermincola sp. JR]
 gi|296031909|gb|ADG82677.1| dihydroorotate dehydrogenase family protein [Thermincola potens JR]
          Length = 305

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 82/222 (36%), Gaps = 35/222 (15%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGS 92
               K +      + P+ + I G  +    E AK +    G   + +N+ CP   V +G 
Sbjct: 82  HFISKALPYLKEYDTPVVVNIAGNTLEDYAELAKRLTAANGVAALEVNISCP--NVKKGG 139

Query: 93  ---FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
                 C M       + I  + +  ++PV  K    V        +  + + + ++G +
Sbjct: 140 MVFGTDCFM-----AAEVIRTVKQHTTLPVIAKLSPNV------TNIVEIAQGVAEAGAD 188

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +            IH RK +L   +       I  +   I++++ +   +L I   GG+
Sbjct: 189 ALALINTLLGMAIDIHTRKPVLGNTVGGLSGPAIRPVAVRIIWQVAQAV-NLPILGMGGI 247

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
                A++ IL     V +G A + N      +L  +++Y  
Sbjct: 248 MSGEDAIEFILAGATAVAVGTANFVNPRATMDVLEGIEQYME 289


>gi|302853480|ref|XP_002958255.1| hypothetical protein VOLCADRAFT_69189 [Volvox carteri f.
           nagariensis]
 gi|300256443|gb|EFJ40709.1| hypothetical protein VOLCADRAFT_69189 [Volvox carteri f.
           nagariensis]
          Length = 252

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 80/234 (34%), Gaps = 57/234 (24%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--------------------I 40
           MV       R          ++Y+E +V   ++   ++                     +
Sbjct: 12  MVRVGTYPMRLLTAGY-GADIVYSEELVDKRVIASVRRVNEALGTVDFLDKGGEQGGRLM 70

Query: 41  LGFSTQEKP-LALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLM 98
              S  E+P L  Q+G A+    + A  +V  D G   +++N+GCP     +G  GA L+
Sbjct: 71  FRTSASERPRLVFQLGTAEAVGALRAVSVVAGDVGA--LDVNMGCPKQFSLQGGMGAALL 128

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             P++                     +G+DD    V    L + +   GV+ I +H R  
Sbjct: 129 RKPEVAE-------------------VGLDDPRDTV---ELARRLGACGVSAIAVHGRTT 166

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSV 210
                     R     ++  +  +    E+  + +  NG +   S A ++    
Sbjct: 167 --------QQRPRDPANWAHIRLVVDALESTRVPVIANGDIMSYSDAQRVRQET 212


>gi|78355103|ref|YP_386552.1| dihydroorotate oxidase B, catalytic subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78217508|gb|ABB36857.1| dihydroorotate oxidase B, catalytic subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 308

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 66/202 (32%), Gaps = 25/202 (12%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           QE P+   +   D  +  E A  +  + G   I +N+ CP   V EG        +    
Sbjct: 95  QETPVIANLYACDPDEFAELAGILAAEEGIAAIEVNISCP--NVSEGGILFG--QDARQA 150

Query: 105 GDCIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI 159
                A+ +     PV VK    V D      +  + ++++ SG + +     +      
Sbjct: 151 ARVTGAVKRRSGTKPVIVKLSPNVTD------IAEIARAVEDSGADMLSCINTLSGMAVD 204

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIK-------KENPDLFIGLNGGLEDMSQALK-ILPSVD 211
           ++   P     I  L    +  +          +  + +   GG       L+ +L    
Sbjct: 205 IRSRKPLLANVIGGLSGPAIKPVALRCVWQAARSVSIPVIGIGGATTAEDILEFMLVGAH 264

Query: 212 GVMIGRAAYKNSAM-LTTVDEY 232
            V IG A +         VDE 
Sbjct: 265 AVQIGTANFMRPDCAFRLVDEL 286


>gi|332097417|gb|EGJ02397.1| tRNA-dihydrouridine synthase C [Shigella boydii 3594-74]
          Length = 113

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 26/113 (23%), Positives = 44/113 (38%), Gaps = 8/113 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +     +     + +
Sbjct: 1   MEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRV 60

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           Q+ G     L E A    + G   ++LN GCPS  V+    GA L+ +P+++ 
Sbjct: 61  QLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIY 113


>gi|327469974|gb|EGF15438.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK330]
          Length = 312

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 74/199 (37%), Gaps = 23/199 (11%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G ++      A KI +      I LN+ CP   V  G+ G  +   P++  + 
Sbjct: 99  PIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQVPELAYEA 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
             A   A ++PV VK    V D      +  + K+++ +G  G  +              
Sbjct: 157 TKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVGMRFDLKSR 210

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           +  I  G        +  +   ++ ++ +    L I   GG++    AL++       V 
Sbjct: 211 QPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMFIAGASAVG 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +     T+ E  
Sbjct: 270 VGTANFTDPYACPTIIEDL 288


>gi|168179114|ref|ZP_02613778.1| dihydroorotate oxidase [Clostridium botulinum NCTC 2916]
 gi|226950664|ref|YP_002805755.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum A2 str.
           Kyoto]
 gi|182670100|gb|EDT82076.1| dihydroorotate oxidase [Clostridium botulinum NCTC 2916]
 gi|226843259|gb|ACO85925.1| dihydroorotate oxidase [Clostridium botulinum A2 str. Kyoto]
          Length = 298

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 71/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + K
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEIVKEVKK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQKPLMVKLSPNAED------IVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+   + +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPIALRMVYEVCKQV-KIPVIGIGGICNYKDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|320104613|ref|YP_004180204.1| dihydroorotate oxidase B, catalytic subunit [Isosphaera pallida
           ATCC 43644]
 gi|319751895|gb|ADV63655.1| dihydroorotate oxidase B, catalytic subunit [Isosphaera pallida
           ATCC 43644]
          Length = 348

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 76/224 (33%), Gaps = 25/224 (11%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARV 88
           D I    + ++         + + + G    +  E A ++  + G   + LN+ CP    
Sbjct: 115 DGIDHFLEHHLPYLRGLGTAIVVNVAGESPEQFAELAGRVGSEPGVAAVELNLSCP---- 170

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              S G  L + P  V   +A        P+  K    V D +P      L ++    G 
Sbjct: 171 -NVSHGLDLGIEPATVQRVVARCRAVCETPLWAKLTPNVTDIVP------LARAAWDGGA 223

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + + +              R  +           I  +   +V+E+ +  P L I   GG
Sbjct: 224 DAVTLINTLKGLAVDWRRRRPILANDFGGLSGPAIKPVALRMVWEVHRALPSLPIVGVGG 283

Query: 197 LEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +  +  AL+ L      V +G A +       T+ +  S  L G
Sbjct: 284 ILTLDDALEFLVAGASAVQVGTATFFQPDAALTIRQALSAALAG 327


>gi|282163851|ref|YP_003356236.1| hypothetical protein MCP_1181 [Methanocella paludicola SANAE]
 gi|282156165|dbj|BAI61253.1| conserved hypothetical protein [Methanocella paludicola SANAE]
          Length = 376

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 34/214 (15%), Positives = 83/214 (38%), Gaps = 28/214 (13%)

Query: 25  EMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E I  D  A +      +   + +   + + +        + AA++ + +G   + +N  
Sbjct: 66  EFISDDIFAFIES---ELRKVTGKGVVIGINVRATTPEPFLRAAELAKKYGA-ILEINAH 121

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           C    +   + G  ++ +   +   ++ + K   + +++K R G  D +       L + 
Sbjct: 122 CRQEEMAALNVGEAMLKDRIALARLVSDIKK-TGVVLSLKMRSGAVDDVK------LARI 174

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++K+G++ + + A      G+   +   I  L         +++  LFI  N  + +   
Sbjct: 175 LEKAGLDILHVDAM-----GMRGTNLNAIKKL---------RDSTTLFIIGNNSVNNYET 220

Query: 203 ALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           A  +     D V + RAA  N  ++  +  Y  +
Sbjct: 221 AQAMYSAGSDMVSVARAAMANPKLIKGIVSYIED 254


>gi|18977911|ref|NP_579268.1| dihydroorotate dehydrogenase 1B [Pyrococcus furiosus DSM 3638]
 gi|30173338|sp|Q8U0P6|PYRD_PYRFU RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|18893677|gb|AAL81663.1| dihydroorotate dehydrogenase (dihydroorotate oxidase) (dhodehase)
           [Pyrococcus furiosus DSM 3638]
          Length = 300

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/216 (21%), Positives = 80/216 (37%), Gaps = 17/216 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEK---PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           I A  +     K  L    +E    P+ + I G +  +    A+ +E  G +   LN+ C
Sbjct: 67  INAMGLPNPGWKAFLEEFEKESFDFPVIVSIFGGNPEEFAFLAEKLERVG-DAFELNLSC 125

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRN 138
           P A+     +G  +  +P+ V   + A+      PV  K      D          A  +
Sbjct: 126 PHAK----GYGLEIGQDPENVYRVVKAVKDVTDKPVIAKLTPNTSDITKLGLAAEKAEAD 181

Query: 139 LVKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            V +I       I I+A++ IL           I  +    VY++  +  D+ I   GG+
Sbjct: 182 GVSAINTLKAIAIDIYAKRPILSNKFGGYSGPGIKPIALRAVYDLASKL-DIPIIGIGGI 240

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA-MLTTVDE 231
                A++ +L     V IG A Y     +   + E
Sbjct: 241 TTWQDAVEFLLAGASAVQIGTAVYLKGFSVFREIAE 276


>gi|315221729|ref|ZP_07863645.1| dihydroorotate dehydrogenase 1B [Streptococcus anginosus F0211]
 gi|315189216|gb|EFU22915.1| dihydroorotate dehydrogenase 1B [Streptococcus anginosus F0211]
          Length = 313

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/190 (20%), Positives = 76/190 (40%), Gaps = 23/190 (12%)

Query: 49  PLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    A KI +      I LN+ CP   V  G+ G  +   PD+  + 
Sbjct: 99  PIIANVAGFSNEEYAFVAGKISQAPNVKAIELNISCP--NVDHGNGGLLIGQVPDLAYNA 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A  +A S+PV VK    V D      +  + K+++ +G  G  +            +R
Sbjct: 157 TKAAVEASSVPVYVKLTPSVAD------ITEISKAVEAAGATGFTMINTLVGMRFDLKSR 210

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K+IL  G        +  +   ++ ++ + +  L I   GG++    A+++       + 
Sbjct: 211 KSILANGTGGMSGPAVFPVALKLIRQVAQ-SSSLPIIGMGGVDSAEAAIEMFIAGASAIG 269

Query: 215 IGRAAYKNSA 224
           +G A + +  
Sbjct: 270 VGTANFTDPH 279


>gi|229117380|ref|ZP_04246757.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock1-3]
 gi|228666080|gb|EEL21545.1| Dihydroorotate dehydrogenase [Bacillus cereus Rock1-3]
          Length = 306

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G     NP+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTNPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           + IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 QPILANRTGGLSGPVIKPVAIRMVHEVSQAV-NIPIIGMGGIESAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|312867748|ref|ZP_07727954.1| dihydroorotate oxidase, catalytic subunit [Streptococcus
           parasanguinis F0405]
 gi|311096811|gb|EFQ55049.1| dihydroorotate oxidase, catalytic subunit [Streptococcus
           parasanguinis F0405]
          Length = 312

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    ++ + +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPELPIIANVAGFSNEEYATVSRKISQAPNVKAIELNISCP--NVDHGNNGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +A S+PV VK    V D      +  + K+ + +G  G+ +      
Sbjct: 149 VPELAYAAVKAAVEASSVPVYVKLTPSVAD------ITQVAKAAEDAGATGLTMINTLVG 202

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                   +  I  G        +  +   ++ ++ + +  L I   GG++    A++++
Sbjct: 203 MRFDLKTGKPIIANGTGGMSGPAVFPVALKLIRQVAQ-STKLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|226227385|ref|YP_002761491.1| dihydroorotate dehydrogenase [Gemmatimonas aurantiaca T-27]
 gi|226090576|dbj|BAH39021.1| dihydroorotate dehydrogenase [Gemmatimonas aurantiaca T-27]
          Length = 327

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 80/234 (34%), Gaps = 34/234 (14%)

Query: 15  LLTNNALLYTE----MIVADAI-------LRGDKKNILGFSTQEKPLALQIGGADISKLV 63
              N AL  +E    M+ A  +       +R D    L        + + + G  I    
Sbjct: 70  RPGNPALRVSEFAGGMMNAIGLANPGLESVRRDYLPWLPAHHPGTRVFVNVVGNSIEDFA 129

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
              + ++D  G +   LNV CP+ +     FGA    +P  +   ++A   A   P+ VK
Sbjct: 130 TVVRGLDDVPGVDAFELNVSCPNVKAGGLEFGA----DPQALHALVSAARGATKRPIFVK 185

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKGLSPKDNRK 170
               +       A+ +  +    +G  G+ +              R  +  G        
Sbjct: 186 LSPTL-----GAAIADTARVAVDAGATGLTLVNTMPGTVIDTDRRRPKLSFGSGGVSGPA 240

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS 223
           +  +     + + +  P + +   GG+     AL+ L      V +G AA ++ 
Sbjct: 241 LLPVGLLATWRVSRALPTVPLIGLGGISTGDDALQYLMAGASLVGVGTAALRDP 294


>gi|73669116|ref|YP_305131.1| hypothetical protein Mbar_A1605 [Methanosarcina barkeri str.
           Fusaro]
 gi|72396278|gb|AAZ70551.1| conserved hypothetical protein [Methanosarcina barkeri str. Fusaro]
          Length = 379

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 46/208 (22%), Positives = 85/208 (40%), Gaps = 24/208 (11%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           E I  + +     K  +   T    +A+ +    +  L+EAAKIV++ G   + LN  C 
Sbjct: 68  EFISDEPM--EFMKKEIRAVTSGSAVAVNVRSTTLEPLIEAAKIVKEEGA-ILELNAHCR 124

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              + E   G  L+ +   +   I A+ +   + ++VK R  V + I       L + I 
Sbjct: 125 QPEMLEAGLGEALLHDLPKLSAWIRAIKE-TGVVLSVKVRANVVNDI------ELARLID 177

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K+G + I +    A ++G            D D +    ++   LF+  N  ++D   A 
Sbjct: 178 KAGADIIHV---DAEMEGFG---------ADLDAILN-YRDATRLFLIGNNSVKDFEAAK 224

Query: 205 KILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           ++     D V   R   +NS ++  + E
Sbjct: 225 EMFTRGADMVSAARGVLENSGLIQELVE 252


>gi|160931529|ref|ZP_02078924.1| hypothetical protein CLOLEP_00361 [Clostridium leptum DSM 753]
 gi|156869400|gb|EDO62772.1| hypothetical protein CLOLEP_00361 [Clostridium leptum DSM 753]
          Length = 303

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 32/206 (15%), Positives = 72/206 (34%), Gaps = 24/206 (11%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            QE  +   I G    +  + A+ + +   + I +N+ CP    +    G     +   V
Sbjct: 91  EQETVVIANIAGNTPEEYAQMAEKLSESSVDMIEMNISCP----NVKHGGVQFGTSCQSV 146

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWI 153
           G     +      P+ VK    V D      +  + ++ +  G +            I I
Sbjct: 147 GAITREVRAHCKKPLMVKLSPNVSD------IAEIARAAESEGADALSLINTLTGMRIDI 200

Query: 154 HARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
           + R+ I++          +  +   +V++         +G+ GG+     A++ +L    
Sbjct: 201 NTRRPIIRNNTGGLSGPAVFPVAVRMVWQTAGAVKIPVVGM-GGISTWRDAVEMMLAGAS 259

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPL 237
            + +G A + +      + E  +  L
Sbjct: 260 AIQVGTALFSDPYAPLKIKEGLNRYL 285


>gi|332360819|gb|EGJ38625.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK49]
          Length = 312

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQIAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQMAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|156937022|ref|YP_001434818.1| dihydroorotate dehydrogenase 1B [Ignicoccus hospitalis KIN4/I]
 gi|156566006|gb|ABU81411.1| dihydroorotate oxidase B, catalytic subunit [Ignicoccus hospitalis
           KIN4/I]
          Length = 302

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/180 (22%), Positives = 68/180 (37%), Gaps = 23/180 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + I G D  +  EAA    D G + + LN+ CP A+      G  L ++ + V   +
Sbjct: 95  PVVVSIAGKDEREFAEAAWASVDAGASALELNLSCPHAK----GLGLELGMDINAVRKVV 150

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARK 157
            A+   +++PV  K             L +   +   +G +G           I I   +
Sbjct: 151 EAVATTVNVPVFAKL-------GLVDKLVDTASAALDAGASGLVLINTIRAMVIDIDVME 203

Query: 158 AILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            +L   +     R I  +    VYE+ KE     +G+ G  E       +L     V IG
Sbjct: 204 PVLTNKVGGLSGRAIHPIAVRAVYEVYKELKAPIVGVGGVYEWRDAVELVLAGASAVQIG 263


>gi|167040447|ref|YP_001663432.1| dihydroorotate dehydrogenase 1B [Thermoanaerobacter sp. X514]
 gi|300914498|ref|ZP_07131814.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter sp.
           X561]
 gi|307724266|ref|YP_003904017.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter sp.
           X513]
 gi|229485591|sp|B0K2E5|PYRD_THEPX RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|166854687|gb|ABY93096.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter sp.
           X514]
 gi|300889433|gb|EFK84579.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter sp.
           X561]
 gi|307581327|gb|ADN54726.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter sp.
           X513]
          Length = 302

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/201 (20%), Positives = 74/201 (36%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I +    AK ++  G + I +NV CP   V +G     +  NP+ + +   
Sbjct: 95  VIVNIAGETIEEFAYMAKKLDIDGVDGIEINVSCP--NVKKGGMAFGI--NPEDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
            + K     V VK    V D           K+ +  G +            I I  R  
Sbjct: 151 EVKKVTQKTVIVKLTPNVGDIGV------CAKAAEDGGADAVSLINTIAGMAINIDTRTP 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K + +      I  +   +VYE  +      IG+ GG+     AL+ ++     V IG
Sbjct: 205 VFKNVIAGLSGPAIKPIALRMVYEAARAVKIPVIGM-GGISSFKDALEFMIAGAKAVAIG 263

Query: 217 RAAYKNSA----MLTTVDEYF 233
              + N      ++  + +Y 
Sbjct: 264 TCNFVNPNCTIEVIEGIKQYM 284


>gi|167037753|ref|YP_001665331.1| dihydroorotate dehydrogenase 1B [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320116167|ref|YP_004186326.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|229485590|sp|B0KA32|PYRD_THEP3 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|166856587|gb|ABY94995.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319929258|gb|ADV79943.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 302

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/201 (20%), Positives = 74/201 (36%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I +    AK ++  G + I +NV CP   V +G     +  NP+ + +   
Sbjct: 95  VIVNIAGETIEEFAYMAKKLDIDGVDGIEINVSCP--NVKKGGMAFGI--NPEDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
            + K     V VK    V D           K+ +  G +            I I  R  
Sbjct: 151 EVKKVTQKTVIVKLTPNVGDIGV------CAKAAEDGGADAVSLINTIAGMAINIDTRTP 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K + +      I  +   +VYE  +      IG+ GG+     AL+ ++     V IG
Sbjct: 205 VFKNVIAGLSGPAIKPIALRMVYEAARAVKIPVIGM-GGISSFKDALEFMIAGAKAVAIG 263

Query: 217 RAAYKNSA----MLTTVDEYF 233
              + N      ++  + +Y 
Sbjct: 264 TCNFVNPNCTIEVIEGIKQYM 284


>gi|297530687|ref|YP_003671962.1| dihydroorotate dehydrogenase [Geobacillus sp. C56-T3]
 gi|297253939|gb|ADI27385.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           C56-T3]
          Length = 313

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 78/197 (39%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+   + VE A+ +      + + LN+ CP   V +G         PD+  
Sbjct: 93  DVPIIANIAGSTAEEYVEVAEAISKAPNVHALELNISCP--NVKKGGIAFG--TVPDVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    + +  ++PV VK    V D      +  + K+I+++G +G+ +            
Sbjct: 149 ELTRLVKEVSAVPVYVKLSPNVTD------IVAMAKAIEQAGADGLTMINTLVGMRIDVR 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             R  +  G        +  +   ++YE+ +      IG+ GG++     L+        
Sbjct: 203 TGRPILANGTGGLSGPAVKPIAIRMIYEVSQAVSIPIIGM-GGIQTAEDVLEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +  T+
Sbjct: 262 VAVGTANFVDPFVCPTI 278


>gi|150400165|ref|YP_001323932.1| dihydroorotate dehydrogenase 1B [Methanococcus vannielii SB]
 gi|150012868|gb|ABR55320.1| dihydroorotate dehydrogenase family protein [Methanococcus
           vannielii SB]
          Length = 304

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 36/201 (17%), Positives = 80/201 (39%), Gaps = 26/201 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G + ++  + A+ +     + + LN+ CP A    G +G+ +  +  +  + ++
Sbjct: 97  IIGSIYGKNETEFQKVAENLIPH-VDVLELNISCPHA---GGGYGSSIGQDKCLSKNVVS 152

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARK 157
           A+     IPV VK    V D      ++ +  S+  +G +GI             I ++K
Sbjct: 153 AVKSVSDIPVIVKLTPNVTD------IKEISNSVVNAGADGIVAINTLGPGMVIDIESKK 206

Query: 158 AILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L         + I  +    VY+I     ++ +   GG+     A++ ++    GV +
Sbjct: 207 PVLANKFGGMSGKAIKPIAVKNVYDIC-STVEVPVIGVGGITTGYDAIEFMMAGASGVQV 265

Query: 216 GRAAYKNSA-MLTTVDEYFSN 235
           G   Y     +   +++    
Sbjct: 266 GTGVYYRGYDIFQKINQEIEE 286


>gi|332360286|gb|EGJ38099.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK355]
          Length = 312

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/207 (19%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L       P+   + G ++        KI +    N I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPNLPIIANVAGFSNHEYATVTGKISQAPNVNAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G +G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGASGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 V +G A + +     T+ E  
Sbjct: 262 IAGASAVGVGTANFTDPYACPTIIENL 288


>gi|84490203|ref|YP_448435.1| dihydroorotate dehydrogenase 1B [Methanosphaera stadtmanae DSM
           3091]
 gi|84373522|gb|ABC57792.1| PyrD [Methanosphaera stadtmanae DSM 3091]
          Length = 306

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 77/203 (37%), Gaps = 25/203 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+   I G       + A   +D+  +   LNV CP A+     FG+ +  NP++  D 
Sbjct: 93  TPVIASIYGDSEEVFSDVANQTKDY-VDAFELNVSCPHAK---CGFGSNIGENPELTHDI 148

Query: 108 IAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----HARKAILK 161
           ++++   +  +P+ VK    V D      +  + K+ + +G + + +        +   K
Sbjct: 149 VSSVKDNIKDVPIIVKLTPNVTD------ITEIAKAAEDAGADALTLINSVGPGLRIDYK 202

Query: 162 GLSPKDNRKIPNLDYDIVYEIK-------KENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
              P  N     +   ++  I         E  D+ +   GG+     AL+ L      +
Sbjct: 203 TARPILNNVFGGIAGPMIKPIALKCVYKTYETVDIPLFGVGGIRTYKDALEFLYAGASLL 262

Query: 214 MIGRAA-YKNSAMLTTVDEYFSN 235
            IG +  Y+   +   +    SN
Sbjct: 263 QIGTSIMYEGPEIFKNITHDLSN 285


>gi|320100761|ref|YP_004176353.1| dihydroorotate oxidase B, catalytic subunit [Desulfurococcus
           mucosus DSM 2162]
 gi|319753113|gb|ADV64871.1| dihydroorotate oxidase B, catalytic subunit [Desulfurococcus
           mucosus DSM 2162]
          Length = 299

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/194 (23%), Positives = 75/194 (38%), Gaps = 9/194 (4%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            KPL L IGG  I + V+ A+   + G + + LN+ CP AR     +G  L  +P +V  
Sbjct: 91  GKPLVLSIGGGGIDEFVKLAEAASEAGVDAVELNLSCPHAR----GYGLELGGDPALVYT 146

Query: 107 CIAAMCKALSIPVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +       S PV  K     RI              +  I       I +++RK +L  
Sbjct: 147 IVKNTVSVSSAPVVAKLGLSDRIMESAGKALEGGAKALTLINTVKAMAIDVYSRKPVLSN 206

Query: 163 LSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
                    I  +   +VY++ +E     IG+ G    +  A  IL     + +G A   
Sbjct: 207 KHGGLSGPPIHPIAVRVVYDVYREYRAEVIGVGGVSSWIDAAELILAGARAIQVGTAVLF 266

Query: 222 NSAMLTTVDEYFSN 235
           N  ++  +++    
Sbjct: 267 NEKVVEEINKGLRE 280


>gi|261419343|ref|YP_003253025.1| dihydroorotate dehydrogenase 1B [Geobacillus sp. Y412MC61]
 gi|319766159|ref|YP_004131660.1| dihydroorotate dehydrogenase [Geobacillus sp. Y412MC52]
 gi|261375800|gb|ACX78543.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y412MC61]
 gi|317111025|gb|ADU93517.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y412MC52]
          Length = 313

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 79/197 (40%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+ + + VE A+ +      + + LN+ CP   V +G         PD+  
Sbjct: 93  DVPIIANIAGSTVEEYVEVAEAISKAPNVHALELNISCP--NVKKGGIAFG--TVPDVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    + +  ++PV VK    V D      +  + K+I+++G +G+ +            
Sbjct: 149 ELTRLVKEVSAVPVYVKLSPNVTD------IVAMAKAIEQAGADGLTMINTLVGMRIDVK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             R  +  G        +  +   ++YE+ +      IG+ GG++     L+        
Sbjct: 203 TGRPILANGTGGLSGPAVKPIAIRMIYEVSQAVSIPIIGM-GGIQTAEDVLEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +  T+
Sbjct: 262 VAVGTANFVDPFVCPTI 278


>gi|256752471|ref|ZP_05493329.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256748673|gb|EEU61719.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 302

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/201 (20%), Positives = 74/201 (36%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I +    AK ++  G + I +NV CP   V +G     +  NP+ + +   
Sbjct: 95  VIVNIAGETIEEFAYMAKKLDIDGVDGIEINVSCP--NVKKGGMAFGI--NPEDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
            + K     V VK    V D           K+ +  G +            I I  R  
Sbjct: 151 EVKKVTQKTVIVKLTPNVGDIGV------CAKAAEDGGADAVSLINTIAGMAINIDTRTP 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K + +      I  +   +VYE  +      IG+ GG+     AL+ ++     V IG
Sbjct: 205 VFKNVIAGLSGPAIKPIALRMVYEAARAVKIPVIGM-GGISSFKDALEFMIAGAKAVAIG 263

Query: 217 RAAYKNSA----MLTTVDEYF 233
              + N      ++  + +Y 
Sbjct: 264 TCNFVNPNCTIEVIEGIKQYM 284


>gi|169345727|ref|ZP_02865686.1| dihydroorotate oxidase [Clostridium perfringens C str. JGS1495]
 gi|169297127|gb|EDS79243.1| dihydroorotate oxidase [Clostridium perfringens C str. JGS1495]
          Length = 299

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 69/192 (35%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK          A  + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSP------NAENICNMAYRCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAS 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|302871820|ref|YP_003840456.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574679|gb|ADL42470.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 300

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 46/221 (20%), Positives = 86/221 (38%), Gaps = 28/221 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +A +  +   +  F T+   +   I G    + ++ AKIV     + I +N+ CP    +
Sbjct: 78  EAFVNDELPFLRKFDTK---IIANINGFSKEEFMDLAKIVSPL-VDMIEVNLSCP----N 129

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G     +P+ V +    + K  + PV VK    V D      +  L  + +K+G +
Sbjct: 130 VKEGGMVFGKDPNKVYEITKEVKKVSACPVIVKLTPNVTD------ITQLAVAAEKAGAD 183

Query: 150 GIW-----------IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            I  RK ++K ++       I  +   +VYE  K+   + I   GG+
Sbjct: 184 AISLINTISAMAIDIETRKPLIKMVTGGLSGPAIKPIAVRMVYECFKKV-KIPIIGMGGI 242

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            +   A++ I+     + IG   + N   +  + E     L
Sbjct: 243 MNHKDAIEFIIAGATAIQIGTVNFINPNAVYEIKEGIEAYL 283


>gi|164687049|ref|ZP_02211077.1| hypothetical protein CLOBAR_00675 [Clostridium bartlettii DSM
           16795]
 gi|164603934|gb|EDQ97399.1| hypothetical protein CLOBAR_00675 [Clostridium bartlettii DSM
           16795]
          Length = 300

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/224 (17%), Positives = 86/224 (38%), Gaps = 29/224 (12%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           MI +  +    + G  +  L F  + +      IGG  +   ++  +++ D   + I LN
Sbjct: 67  MINSVGLENPGVEGFIEKELPFFEKLDLVRIANIGGGCLEDYIKGVELLNDKDIDIIELN 126

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP+ +    +FG       ++  + +  +      P+ +K     +D      +  + 
Sbjct: 127 ISCPNVKAGGMAFGI----KSEVAREVVREVRAVCKKPLVIKLSPNAED------IVEMA 176

Query: 141 KSIKKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPD 188
           K  ++ G +            I I  RK + +   +      I  +   +V+E+ K N  
Sbjct: 177 KVCEEEGADGVSLVNTFKALAIDIKNRKPVFENVYAGLSGPAIKPIALRMVHEVCK-NVS 235

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + +   GG+     A++ I+     V IG A + N  +   + E
Sbjct: 236 IPVFGMGGITTAEDAIEFIMAGATCVQIGTANFMNPRVGLEIIE 279


>gi|331003517|ref|ZP_08327014.1| dihydroorotate dehydrogenase [Lachnospiraceae oral taxon 107 str.
           F0167]
 gi|330412358|gb|EGG91749.1| dihydroorotate dehydrogenase [Lachnospiraceae oral taxon 107 str.
           F0167]
          Length = 301

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/232 (17%), Positives = 82/232 (35%), Gaps = 33/232 (14%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +        +         ++  + + + G  IS  VE  + + D   +   +N
Sbjct: 67  MLNAIGLQNPGVDTFIERDLKFLKEKDTKIIVNVCGRSISDYVETVERLSDEDVDMFEIN 126

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +    G     N D V +  + +      P+ +K    V D      +  + 
Sbjct: 127 ISCP----NVSHGGIAFGTNVDSVKEITSQIKAHSKKPIIMKLSPNVTD------ITEIA 176

Query: 141 KSIKKSGVNGI----WIHARK--------AILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K  + +G + +     I   K        AI           I  +   +VY++      
Sbjct: 177 KGAEAAGADALSLINTITGMKIDINKRCFAIANKTGGMSGPAIKPIALRMVYQVANAV-K 235

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS--AML--TTVDEYFSN 235
           L I   GG+     A++ +L   + V +G A + N   ++L    +++Y  N
Sbjct: 236 LPIIGMGGISTPEDAIEFLLAGANMVSVGTANFINPNASILVAEGIEKYLDN 287


>gi|168186095|ref|ZP_02620730.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           botulinum C str. Eklund]
 gi|169296114|gb|EDS78247.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           botulinum C str. Eklund]
          Length = 298

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 73/189 (38%), Gaps = 24/189 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   +   + + +   + I LN+ CP   V  G     +    D+  D ++ + +
Sbjct: 98  LGGGSVEDYLRGIEKLNNADVDIIELNISCP--NVKSGGMAFGI--KSDVAYDVVSKVRE 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK          A  + ++ +   K+G +GI            I+ RK +   
Sbjct: 154 ICKKPLVVKLSP------NAENIIDMAEKCCKAGADGISLVNTFKAMAIDINKRKPVFNN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +V+E+ K N D+ +   GG+     A++ I+     V IG A +
Sbjct: 208 VYAGFSGPAIKPIALRMVHEVCK-NVDVPVIGMGGIASAEDAIEFIMAGATAVQIGTANF 266

Query: 221 KNSAMLTTV 229
               +   +
Sbjct: 267 IKPNIALDI 275


>gi|323489519|ref|ZP_08094746.1| dihydroorotate dehydrogenase 1B [Planococcus donghaensis MPA1U2]
 gi|323396650|gb|EGA89469.1| dihydroorotate dehydrogenase 1B [Planococcus donghaensis MPA1U2]
          Length = 304

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 74/197 (37%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G      VE AK +        + +N+ CP   V +G        +P++  
Sbjct: 93  DVPIIANVAGTTTEDYVEVAKKISQSPNVQALEINISCP--NVKQGGITFG--TDPNVAR 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +   A+ +  ++PV +K    V        + ++ K++++ G +GI +            
Sbjct: 149 ELTRAVKEVSAVPVYIKLSPNV------TNIVSIAKAVEEGGADGITMINTLLGMRMDTK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDG 212
             R  I           I  +   +VYE+ +    L I   GG+ ++   +  L      
Sbjct: 203 TGRPIIANITGGLSGPAIKPVALRMVYEVSQHT-KLPIIGMGGVTNVDDVIDFLSAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + N  +   +
Sbjct: 262 VAVGTANFVNPFVCPEI 278


>gi|307267033|ref|ZP_07548548.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306917958|gb|EFN48217.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 302

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/201 (20%), Positives = 74/201 (36%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I +    AK ++  G + I +NV CP   V +G     +  NP+ + +   
Sbjct: 95  VIVNIAGETIEEFAYMAKKLDIDGVDGIEINVSCP--NVKKGGMAFGI--NPEDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
            + K     V VK    V D           K+ +  G +            I I  R  
Sbjct: 151 EVKKVTQKTVIVKLTPNVTDIGV------CAKAAEDGGADAVSLINTIAGMAINIDTRTP 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K + +      I  +   +V+E  +      IG+ GG+     AL+ ++     V IG
Sbjct: 205 VFKNVIAGLSGPAIKPIALRMVHEAARAVKIPVIGM-GGISSFKDALEFMIAGAKAVAIG 263

Query: 217 RAAYKNSA----MLTTVDEYF 233
              + N      ++  + +Y 
Sbjct: 264 TCNFVNPNCTIEVIEGIKQYM 284


>gi|110799177|ref|YP_695828.1| dihydroorotate dehydrogenase 1B [Clostridium perfringens ATCC
           13124]
 gi|110673824|gb|ABG82811.1| dihydroorotate oxidase [Clostridium perfringens ATCC 13124]
          Length = 299

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 69/192 (35%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK          A  + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSP------NAENICNMAYRCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAS 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|168205417|ref|ZP_02631422.1| dihydroorotate oxidase [Clostridium perfringens E str. JGS1987]
 gi|170663041|gb|EDT15724.1| dihydroorotate oxidase [Clostridium perfringens E str. JGS1987]
          Length = 299

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 69/192 (35%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK          A  + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSP------NAENICNMAYKCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAS 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|198434443|ref|XP_002130803.1| PREDICTED: similar to Dihydropyrimidine dehydrogenase [Ciona
           intestinalis]
          Length = 1030

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 84/237 (35%), Gaps = 34/237 (14%)

Query: 25  EMIVADAILRGDKK-NILGFSTQEKPLALQIGG----ADISKLVEAAKIVEDFGYNEINL 79
           E+I         +    L     EK +   I       D ++L   AK+ ED G + + L
Sbjct: 615 ELISEKTCTYWCRSVTELKRDFPEKIVIASIMCAFNRNDWTEL---AKMSEDAGADALEL 671

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     +P +V +    +  A+ IP   K    V        +  +
Sbjct: 672 NLSCPHGM-GERGMGLACGQDPKLVIEICKWVRAAVKIPFFAKLTPNV------TNIVTI 724

Query: 140 VKSIKKSGVNGIWIHARKAILKGLS---------PKDNR---------KIPNLDYDIVYE 181
            ++ K  G +G+      + L GL           K +R          I  +    V  
Sbjct: 725 AEAAKDGGADGVTATNTVSGLMGLRGDSTAWPAIGKQHRTTYGGVSGNAIRPIALKAVSA 784

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           I +  P   +   GG++     L+ L +   V+   +A +N    T +D+Y S   T
Sbjct: 785 ISRAFPGFPVLATGGIDSAEAGLQYLHAGASVLQVCSAVQNQD-FTLIDDYLSGLKT 840


>gi|18310160|ref|NP_562094.1| dihydroorotate dehydrogenase 1B [Clostridium perfringens str. 13]
 gi|18144839|dbj|BAB80884.1| dihydroorotate oxidase [Clostridium perfringens str. 13]
          Length = 299

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 69/192 (35%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK          A  + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSP------NAENICNMAYRCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAS 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|168214665|ref|ZP_02640290.1| dihydroorotate oxidase [Clostridium perfringens CPE str. F4969]
 gi|170713859|gb|EDT26041.1| dihydroorotate oxidase [Clostridium perfringens CPE str. F4969]
          Length = 299

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/190 (17%), Positives = 69/190 (36%), Gaps = 24/190 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
              +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+  +
Sbjct: 91  GTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVAYE 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++ + K    P+ VK          A  + N+     ++G +            I I  
Sbjct: 147 VVSKVRKICDKPLMVKLSP------NAENICNMAYRCAEAGADSISLINTLKGMAIDIKN 200

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++     +
Sbjct: 201 RKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGASAI 259

Query: 214 MIGRAAYKNS 223
            IG   + N 
Sbjct: 260 QIGTINFVNP 269


>gi|212703974|ref|ZP_03312102.1| hypothetical protein DESPIG_02027 [Desulfovibrio piger ATCC 29098]
 gi|212672677|gb|EEB33160.1| hypothetical protein DESPIG_02027 [Desulfovibrio piger ATCC 29098]
          Length = 313

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/228 (18%), Positives = 82/228 (35%), Gaps = 31/228 (13%)

Query: 26  MIVADAI----LRGDKKNILGFSTQEK-PLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +    +    K  L     ++ P+   +     ++  E AA++ E+ G   + +
Sbjct: 75  MLNAVGLQNDGVEAFCKEKLPRLPWQQLPVIANLYATSPAEFGELAARLNEEEGVAALEV 134

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           NV CP   V  G        +P +      A   A  + P+ +K    V D      +  
Sbjct: 135 NVSCP--NVKSGGILFG--QDPKLAAAVTRAARDAAPNKPLIIKLSPNVTD------IAL 184

Query: 139 LVKSIKKSGVNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKEN 186
           + +S++ +G + I            +  RK  L  +        I  +    V+++ K  
Sbjct: 185 MARSVQDAGADMISCINTLSGMAVDVARRKPRLANVIGGLSGPAIKPVALRCVWQVCKAV 244

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
            D+ +   GG+      L+ IL     V IG A + +      + +  
Sbjct: 245 -DIPVIGLGGICSAEDVLEFILVGAHAVQIGTANFISPDRAFEIVKEL 291


>gi|156543632|ref|XP_001604620.1| PREDICTED: similar to dihydropyrimidine dehydrogenase [Nasonia
           vitripennis]
          Length = 1025

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/207 (21%), Positives = 69/207 (33%), Gaps = 33/207 (15%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L     EK +   I       D ++L + A   E  G   + L
Sbjct: 611 ELISEKTAAYWCKGITELKRDFPEKVVIASIMCTYNKADWTELAQMA---EATGCEALEL 667

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     +P++V +    +  A+ IP  VK    + D    VAL   
Sbjct: 668 NLSCPHGM-GEKGMGLACGQDPELVRNIARWVRAAVKIPFFVKLTPNITD---VVALAKA 723

Query: 140 VKSIKKSGVNGI------------------WIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
               +  GV+ I                     A+     G+S    R I       + +
Sbjct: 724 AYEGQADGVSAINTVQGLMSVKADGTPWPAVGSAKATTYGGVSGNATRPIA---LRAISK 780

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP 208
           + K  P   I   GG++    +L+ L 
Sbjct: 781 VAKALPGFPILGIGGVDSAEVSLQFLQ 807


>gi|323457319|gb|EGB13185.1| hypothetical protein AURANDRAFT_19510 [Aureococcus anophagefferens]
          Length = 217

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/175 (25%), Positives = 69/175 (39%), Gaps = 17/175 (9%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI-LGFST--QEKPLALQIGGAD 58
           V +++  +R   R L       T MI A       +      FS    ++PL  Q+GG+D
Sbjct: 46  VGYSEPAFRVLCRTL-GAQCCSTPMIDAAGYAASPRYRAEYAFSGGAADRPLTAQLGGSD 104

Query: 59  ISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            + L  AA +V   G  + + LN+GCP     +   GA LM +P     CI AM  AL  
Sbjct: 105 PAALARAAALVAATGHCDAVELNMGCPQRCAKKTGSGAFLMEDPARAVACIKAMRAALDA 164

Query: 118 ----------PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
                      V    +I   D +          +++++G   + +H R     G
Sbjct: 165 HNAGRPAGAPKVACVVKIRCFDDVARTLAL--AAALERAGAEMLTVHGRTRHAGG 217


>gi|206889947|ref|YP_002248386.1| dihydroorotate dehydrogenase, catalytic subunit
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|229485592|sp|B5YJH1|PYRD_THEYD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|206741885|gb|ACI20942.1| dihydroorotate dehydrogenase, catalytic subunit
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 303

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 90/225 (40%), Gaps = 22/225 (9%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVED-FGYNEINL 79
           MI +  +    L   KK  L F  +    + +   G ++ + +E AK++++  G + + +
Sbjct: 67  MINSIGLQNIGLEAFKKEKLPFLKKFNTNIIVNFFGENLDEYIEVAKLLDETEGVHALEM 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----QIPAV 134
           NV CP+        G      P+++ + I  +   +  P+ VK    V +     +I   
Sbjct: 127 NVSCPNKTSEWRKMGL----EPELLREAIKRVRLHIKKPLIVKLAPQVTEIALMARICEE 182

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGL 193
              + V  I       I I  RK+++  L+       I  +    V+E+ +      IG+
Sbjct: 183 EGADAVSLINTIPAMVIDIKTRKSMIGTLTGGLSGPAIRPVALRAVWEVAQAVKIPVIGV 242

Query: 194 NGGLEDMSQALKIL-PSVDGVMIGRAAYKNS----AMLTTVDEYF 233
            GG+     AL+ L      + +G A + N      ++  + ++ 
Sbjct: 243 -GGIVSAEDALQFLIAGAKAIQVGTANFINPIATVEIIEGIKQFL 286


>gi|121534315|ref|ZP_01666139.1| dihydroorotate dehydrogenase family protein [Thermosinus
           carboxydivorans Nor1]
 gi|121307085|gb|EAX48003.1| dihydroorotate dehydrogenase family protein [Thermosinus
           carboxydivorans Nor1]
          Length = 306

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 77/188 (40%), Gaps = 24/188 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + I G  I +  E A+ + + G   + +N+ CP    +    G     +PD     +
Sbjct: 99  PVIVNISGGTIEEYGELARRLANSGIAGLEVNISCP----NVKQGGMIFGTDPDSAAAVV 154

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
           + + K  ++PV  K    V D      +  + ++++ +G + I            +H+ +
Sbjct: 155 SEVKKYATVPVIAKLSPNVTD------IVAMAQAVESAGADAISLINTLLGMAIDVHSWR 208

Query: 158 AILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L   +       +  +   +V+++ K      IG+ GG+     A++ +L     V +
Sbjct: 209 PVLGNIVGGLSGPAVKPIAVRMVWQVAKAVKVPVIGM-GGIMTAEDAVEFLLAGASAVAV 267

Query: 216 GRAAYKNS 223
           G A + N 
Sbjct: 268 GTANFINP 275


>gi|15895908|ref|NP_349257.1| dihydroorotate dehydrogenase 1B [Clostridium acetobutylicum ATCC
           824]
 gi|15025678|gb|AAK80597.1|AE007762_7 Dihydroorotate dehydrogenase [Clostridium acetobutylicum ATCC 824]
 gi|325510060|gb|ADZ21696.1| dihydroorotate dehydrogenase 1B [Clostridium acetobutylicum EA
           2018]
          Length = 298

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 80/205 (39%), Gaps = 24/205 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K +      +    + +GG+     +   +++E+   + I LN+ CP    +    G   
Sbjct: 82  KELPKMKKIDTVCIVNLGGSCEDDYLRGMELLENTDADMIELNISCP----NVKHGGMAF 137

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            +  ++  + ++ + K  + P+ VK     +D      + ++    +++G + I      
Sbjct: 138 GIKSEVAYNVVSQVRKVCTKPLMVKLSPNAED------IVDMAVKCEEAGADAISLVNTF 191

Query: 153 ------IHARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 I  +K I   +S     R I  +   +VYE+ K      +G+ GG+     A++
Sbjct: 192 KGMAIDIKKKKPIFDNISAGLSGRAIKPIALRMVYEVCKNVSVPVVGM-GGIYTAEDAIE 250

Query: 206 -ILPSVDGVMIGRAAYKNSAMLTTV 229
            I+     V +G A +    +   +
Sbjct: 251 FIMAGAFAVQVGTANFIKPDICIDI 275


>gi|325261797|ref|ZP_08128535.1| dihydroorotate oxidase [Clostridium sp. D5]
 gi|324033251|gb|EGB94528.1| dihydroorotate oxidase [Clostridium sp. D5]
          Length = 300

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 32/205 (15%), Positives = 70/205 (34%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    +  E  + + D   + + +N+ CP    +    G     NP  V +
Sbjct: 92  DTKIIVNVCGKTTEEYCEVVERLADEPVDLLEINISCP----NVKEGGIAFGQNPKAVEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               + +    PV +K    V D      +    K+ +  G + + +             
Sbjct: 148 ITREVKRRAKQPVIMKLSPNVTD------ITETAKAAEAGGADVLSLINTLTGMKIDIHR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++        IG+ GG+     A++ IL     V
Sbjct: 202 QAFALANKTGGVSGPAVKPIAVRMVYQVANAVKVPVIGM-GGITTYEDAVEFILAGATAV 260

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            +G A + N      ++  ++ Y  
Sbjct: 261 SVGTANFFNPTATVEIVEGIERYME 285


>gi|227904296|ref|ZP_04022101.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus ATCC
           4796]
 gi|227867944|gb|EEJ75365.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus ATCC
           4796]
          Length = 307

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/184 (21%), Positives = 75/184 (40%), Gaps = 25/184 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG   S  VE AK + D    N + +NV CP   V +G       ++PD+V + 
Sbjct: 98  PIMASVGGDSESDYVEVAKKLSDSDLVNALEINVSCP--NVAQGGMSFG--VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
              +   + +P+ VK    V D      +  + ++ +K G +GI            +  R
Sbjct: 154 TKKIKDVVDVPIYVKLTPNVTD------IVAIAQAAEKGGADGISMINTVLGMDIDVQTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + +L   +       +  +   ++ ++ + N  L I   GG+      +K +L     V 
Sbjct: 208 RPVLGHNVGGLSGEAVKPIAIRMISQVYQ-NVTLPIIGMGGISSAEDVIKFMLAGASAVA 266

Query: 215 IGRA 218
           +G A
Sbjct: 267 VGTA 270


>gi|58337655|ref|YP_194240.1| dihydroorotate dehydrogenase 1B [Lactobacillus acidophilus NCFM]
 gi|81311432|sp|Q5FJB5|PYRD_LACAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|58254972|gb|AAV43209.1| dihydroorotate dehydrogenase B, catalytic unit [Lactobacillus
           acidophilus NCFM]
          Length = 307

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/184 (21%), Positives = 75/184 (40%), Gaps = 25/184 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG   S  VE AK + D    N + +NV CP   V +G       ++PD+V + 
Sbjct: 98  PIMASVGGDSESDYVEVAKKLSDSDLVNALEINVSCP--NVAQGGMSFG--VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
              +   + +P+ VK    V D      +  + ++ +K G +GI            +  R
Sbjct: 154 TKKIKDVVDVPIYVKLTPNVTD------IVAIAQAAEKGGADGISMINTVLGMDIDVQTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + +L   +       +  +   ++ ++ + N  L I   GG+      +K +L     V 
Sbjct: 208 RPVLGHNVGGLSGEAVKPIAIRMISQVYQ-NVTLPIIGMGGISSAEDVIKFMLAGASAVA 266

Query: 215 IGRA 218
           +G A
Sbjct: 267 VGTA 270


>gi|302337951|ref|YP_003803157.1| dihydroorotate dehydrogenase [Spirochaeta smaragdinae DSM 11293]
 gi|301635136|gb|ADK80563.1| dihydroorotate dehydrogenase family protein [Spirochaeta
           smaragdinae DSM 11293]
          Length = 597

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 96/250 (38%), Gaps = 36/250 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           L + + G+   + V   ++ E F    + + LN  CP A      +G  + ++P++V   
Sbjct: 121 LNVSLSGSSPEEFV---RLAEGFSPVADTLELNFSCPHA---APGYGMSIGVDPELVERY 174

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
           + A+ +   +P+  K     +D      +  + ++  ++G +G+              H+
Sbjct: 175 VKAIREVTDLPLLPKLTPNTED------IGAVAEAAMRAGADGLVAVNTFGPELYIEKHS 228

Query: 156 RKAILK----GLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-S 209
            K IL     G   K  R I     + V  I+++   D  I   GG+ED +  + +    
Sbjct: 229 GKPILMNIHGGKGGKSGRWIHREAVEKVRSIREQVGADPLIIGMGGVEDATGVIAMREAG 288

Query: 210 VDGVMIGRA-AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            D V IG A A           E  +         +T V +    ++      Y  R   
Sbjct: 289 ADVVGIGSAFAMVRPEDWEGWFEELAPSDGAEKNGRTAVPRIEKPQMV--YRPYRIRSAR 346

Query: 269 SG-GKLQQIT 277
           SG G L++IT
Sbjct: 347 SGIGGLRRIT 356


>gi|299821735|ref|ZP_07053623.1| dihydroorotate oxidase [Listeria grayi DSM 20601]
 gi|299817400|gb|EFI84636.1| dihydroorotate oxidase [Listeria grayi DSM 20601]
          Length = 300

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 85/219 (38%), Gaps = 30/219 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +     ++++          + P+   + G  +   V+  A++ +      I L
Sbjct: 67  MLNAIGLQNPGLEHVMAHELPFLEQYDTPIIANVAGTTVDDYVKVCARVGDSKVVKAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP   V +G        +P I  D   A+     +PV VK    V D      + ++
Sbjct: 127 NISCP--NVKKGGITFG--TDPHIAHDLTKAVKAVAKVPVYVKLSPNVAD------IVSI 176

Query: 140 VKSIKKSGVNGIWI-----------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK IL           I  +   +++++ +E  
Sbjct: 177 AQAIEAAGADGLTMINTLLGMRIDLKTRKPILANQTGGLSGPAIKPVAIRMIHQV-REVS 235

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   +    +
Sbjct: 236 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTEPYI 274


>gi|32489914|emb|CAE05107.1| OSJNBa0009K15.27 [Oryza sativa Japonica Group]
 gi|39546255|emb|CAD39832.3| OSJNBa0079F16.3 [Oryza sativa Japonica Group]
          Length = 481

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/157 (21%), Positives = 62/157 (39%), Gaps = 7/157 (4%)

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA-M 225
                +L Y+  + + ++ PD+   LNGG+  + Q    I      VM+GRAAY N   M
Sbjct: 285 YMYPTSLGYEYYFALLRDFPDVQFTLNGGITTIDQVTASIRQGAHRVMVGRAAYNNPWNM 344

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFH 285
           L  VD       T  S  + ++ + +     + M  Y      S   ++Q+ + ++ LFH
Sbjct: 345 LGHVDSEVYGMPTRRS-SRRQILESYQVYGDSIMGQYGP----SRPNVRQLVKPLLNLFH 399

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
             P +   +                +E   + +  S+
Sbjct: 400 SEPGNGLWKRKADSTLRHCKTLESFLEETLDAIPNSV 436


>gi|167749376|ref|ZP_02421503.1| hypothetical protein EUBSIR_00328 [Eubacterium siraeum DSM 15702]
 gi|167657657|gb|EDS01787.1| hypothetical protein EUBSIR_00328 [Eubacterium siraeum DSM 15702]
 gi|291556258|emb|CBL33375.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium siraeum
           V10Sc8a]
          Length = 306

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 72/196 (36%), Gaps = 24/196 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
              TQ+  +   I GA I   +  A+ ++    + I LN+ CP    +    GA   +  
Sbjct: 91  RLRTQDTVVIANIAGAVIDDYIAVAEKLDATDVDMIELNISCP----NVKQGGATWGVTC 146

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------G 150
           +       A+  A   PV VK    V        +  + K+++  G +            
Sbjct: 147 EGAASVTRAVRNATKKPVIVKLTPNV------TNITEIAKAVEAEGADSVSLINTLLGMR 200

Query: 151 IWIHARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I I  R+ IL   +       +  +   +V+++        IG+ GG+     A++ ++ 
Sbjct: 201 IDIRTRRPILHNNVGGLSGPAVFPVAVRMVWQVANAVKIPVIGM-GGIATAEDAIEMMMA 259

Query: 209 SVDGVMIGRAAYKNSA 224
               V +G A + +  
Sbjct: 260 GASAVQMGTAIFNDPY 275


>gi|182626654|ref|ZP_02954398.1| dihydroorotate oxidase [Clostridium perfringens D str. JGS1721]
 gi|177908048|gb|EDT70627.1| dihydroorotate oxidase [Clostridium perfringens D str. JGS1721]
          Length = 299

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 70/192 (36%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK          A  + N+  S  ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSP------NAENICNMAYSCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAS 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|330832838|ref|YP_004401663.1| dihydroorotate dehydrogenase 1B [Streptococcus suis ST3]
 gi|329307061|gb|AEB81477.1| dihydroorotate dehydrogenase 1B [Streptococcus suis ST3]
          Length = 313

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 92/249 (36%), Gaps = 39/249 (15%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE----MIVADAI-------LRGDKKNILGFSTQEKP 49
           M+  T RH R       N      E    M+ A  +       +  +K   L     + P
Sbjct: 44  MIKATTRHPR-----YGNATPRVAETPAGMLNAIGLQNPGVDVVLSEKLPWLEQHFPDLP 98

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   + G    +    + KI +      I LN+ CP   V  G+ G  +   P++    +
Sbjct: 99  IIANVAGFSNEEYAYVSGKISKAPNVKAIELNISCP--NVDHGNNGLLIGQVPELAYQAV 156

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARK 157
            A  +A S+PV VK    V D         L K+ + +G  G+ +             R+
Sbjct: 157 KAAVEASSVPVYVKLTPSVADITL------LAKAAEDAGATGLTMINTLVGMRFNLKTRQ 210

Query: 158 AIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMI 215
            IL  G        +  +   ++ ++ +   DL I   GG++   +A++++      V +
Sbjct: 211 PILANGTGGMSGPAVFPVALKLIRQVAQ-VTDLPIIGMGGVDTADKAIEMMVAGASAVGV 269

Query: 216 GRAAYKNSA 224
           G A + +  
Sbjct: 270 GTANFTDPF 278


>gi|308181400|ref|YP_003925528.1| dihydroorotate dehydrogenase 1B [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|308046891|gb|ADN99434.1| dihydroorotate dehydrogenase 1B [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 305

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 77/200 (38%), Gaps = 19/200 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + GA   + V  A K+        + +N+ CP    +    G     
Sbjct: 89  LATHYPDLPIIGSVAGASFDEYVAVARKMASAPNVKLLEINISCP----NVDHGGLAFGT 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP--------AVALRNLVKSIKKSGVNGI 151
           +P  V     A+  A+  PV +K    V D +P          A   ++ ++   G++  
Sbjct: 145 DPATVRALTKAIVAAVDKPVFMKLTPNVTDIVPIALAAEAGGAAGLTMINTLTGMGID-- 202

Query: 152 WIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            +  R+ IL  G      + I  L   +++++++    L I   GG+   +  L+  L  
Sbjct: 203 -LATRQPILAHGTGGLSGKAIHPLAVRMIHDVRQHT-KLPIIGVGGVFTPADVLEFYLAG 260

Query: 210 VDGVMIGRAAYKNSAMLTTV 229
            + V +G A Y +    T +
Sbjct: 261 ANAVQVGAATYGHPTACTDI 280


>gi|303240751|ref|ZP_07327264.1| dihydroorotate dehydrogenase family protein [Acetivibrio
           cellulolyticus CD2]
 gi|302591639|gb|EFL61374.1| dihydroorotate dehydrogenase family protein [Acetivibrio
           cellulolyticus CD2]
          Length = 307

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/191 (20%), Positives = 69/191 (36%), Gaps = 24/191 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   I G  +    E A I+     + + LNV CP   V +G            + +
Sbjct: 97  DTAIIANIAGNTLEDYCEMADILSVEDIDAVELNVSCP--NVKKG--CMSFGNTTAGITE 152

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
               + K    P+ VK    V D      ++ +  + +  G + I            IH 
Sbjct: 153 ITREVRKHCKKPLIVKLTPNVTD------VKEIALAAEAEGADAISLINTLYGMAIDIHR 206

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ IL           +  +   +VYE+        IG+ GG+     A++ +L     V
Sbjct: 207 RRPILANNFGGLSGPAVKPVAVRMVYEVSNTVKIPVIGM-GGITTGDDAVEFMLAGARAV 265

Query: 214 MIGRAAYKNSA 224
           M+G A + N A
Sbjct: 266 MVGTANFVNPA 276


>gi|284048650|ref|YP_003398989.1| dihydroorotate dehydrogenase family protein [Acidaminococcus
           fermentans DSM 20731]
 gi|283952871|gb|ADB47674.1| dihydroorotate dehydrogenase family protein [Acidaminococcus
           fermentans DSM 20731]
          Length = 312

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 75/195 (38%), Gaps = 24/195 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+ + I G         A++++  G + I LN+ CP   V +G  G     +    G+ 
Sbjct: 101 TPVIVNIDGDSAEDYGTLAEMLDVDGVDAIELNISCP--NVAQG--GLAFGTDCHAAGEV 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
           + A       PV  K    V D      +  + ++++ +G + I +              
Sbjct: 157 VKAAKAHTHKPVITKLSPNVTD------ITEIARAVEAAGTDAISLINTLVGMKIDIWKQ 210

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           R  +   +       +  +   +VY++ +      IG+ GG+     A++ IL     V 
Sbjct: 211 RPVLGNTVGGLSGPAVHPVAVRMVYQVAQAVKVPLIGM-GGISSWQDAVEFILAGATAVA 269

Query: 215 IGRAAYKNSAMLTTV 229
           +G  ++ + ++  T+
Sbjct: 270 VGTCSFTDPSLAETI 284


>gi|213419249|ref|ZP_03352315.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
 gi|213861619|ref|ZP_03386089.1| tRNA-dihydrouridine synthase A [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
          Length = 52

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            L  ITRHM+GLF G P +R+ R  L+  A  + A   ++E A  L+ + 
Sbjct: 2   YLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADAAVLEQALKLIADK 51


>gi|294500994|ref|YP_003564694.1| dihydroorotate dehydrogenase, catalytic subunit [Bacillus
           megaterium QM B1551]
 gi|294350931|gb|ADE71260.1| dihydroorotate dehydrogenase, catalytic subunit [Bacillus
           megaterium QM B1551]
          Length = 313

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/206 (19%), Positives = 82/206 (39%), Gaps = 25/206 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + GA I + V  AK +        + LN+ CP    +    G    ++P I  
Sbjct: 93  DVPIIANVAGASIEEYVHVAKEISTVSNVKALELNISCP----NVKEGGIAFGVDPVIAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
               A+    ++PV VK    V +      + ++  +++++G +G+ +            
Sbjct: 149 RLTKAVKDVSNVPVYVKLSPNVSN------IVDMAMAVEEAGADGLTMINTLLGMRLDLK 202

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             + +L  G        I  +   +VYE+ ++  ++ I   GG+     AL+ L      
Sbjct: 203 TAQPVLANGTGGLSGPSIKPVAIRMVYEVSQKV-NIPIIGMGGVTTAEDALEFLYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLT 238
           V +G A + +  +  T+ +     LT
Sbjct: 262 VAVGTANFVDPYVCPTIIDELPRLLT 287


>gi|328946242|gb|EGG40386.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK1087]
          Length = 312

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 77/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHFPDLPIIANVAGFSNQEYSTVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A   A ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVDASAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|95931325|ref|ZP_01314040.1| dihydroorotate dehydrogenase family protein [Desulfuromonas
           acetoxidans DSM 684]
 gi|95132626|gb|EAT14310.1| dihydroorotate dehydrogenase family protein [Desulfuromonas
           acetoxidans DSM 684]
          Length = 307

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/220 (18%), Positives = 84/220 (38%), Gaps = 28/220 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           DA +R     +   +T   P+ +   G  + + +E A+ + D    + + LN+ CP    
Sbjct: 83  DAFIRDKVPYLQTLNT---PVIVNFFGNQLHEYIEVAEKLSDIEAVDAVELNISCP---- 135

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G      P    + ++ + + L+ P+ VK    V D         + +++++SG 
Sbjct: 136 NVKQGGIVFGTEPCAAAEVVSGVREKLNKPLIVKLTPNVTDITV------MARAVEESGA 189

Query: 149 NGI---------WIHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + I          +   K  L    G        I  +   +VY++ +      IG+ GG
Sbjct: 190 DVISCVNTLTGMAVDIEKQCLHLANGTGGLSGPAIKPVALRMVYQVVRAVSVPVIGI-GG 248

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     AL+ +L     V +G A   N   ++ + +    
Sbjct: 249 IMTAKDALEFLLVGATAVQVGTANLVNPGAMSEIVDGIEQ 288


>gi|168217866|ref|ZP_02643491.1| dihydroorotate oxidase [Clostridium perfringens NCTC 8239]
 gi|182380129|gb|EDT77608.1| dihydroorotate oxidase [Clostridium perfringens NCTC 8239]
          Length = 299

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 70/192 (36%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGI--KSDVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK     +D      + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSPNAED------ICNMAYRCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAK 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|120601123|ref|YP_965523.1| dihydroorotate dehydrogenase family protein [Desulfovibrio vulgaris
           DP4]
 gi|120561352|gb|ABM27096.1| dihydroorotate oxidase B, catalytic subunit [Desulfovibrio vulgaris
           DP4]
          Length = 307

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/221 (18%), Positives = 78/221 (35%), Gaps = 27/221 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARV 88
           D +     + +     +E P+   I   D  +  E AA +  + G   + +N+ CP   V
Sbjct: 79  DGVECFINEKLPRLPWRELPVIANIYACDPGEFGELAAVLAAEEGVAALEVNISCP--NV 136

Query: 89  HEGSFGACLMLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
            EG        +         A+  +A + PV VK    V D      +  + ++++ +G
Sbjct: 137 KEGGILFG--QDARQAARVTEAVKMRAGAKPVIVKLSPNVTD------IVTMARAVEDAG 188

Query: 148 VNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            + +            I  R+ +L  +        I  +    V+++ +    + +   G
Sbjct: 189 ADMLSCINTLSGMGVDIRTRRPLLANVIGGLSGPAIKPVALRCVWQVSRAV-SIPVIGIG 247

Query: 196 GLEDMSQALK-ILPSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           G+      L+ IL     V +G A +         VDE   
Sbjct: 248 GIASAEDVLEFILVGAHAVQVGTANFMRPDFAFRLVDELNE 288


>gi|259501327|ref|ZP_05744229.1| dihydroorotate oxidase [Lactobacillus iners DSM 13335]
 gi|302190949|ref|ZP_07267203.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners AB-1]
 gi|309806011|ref|ZP_07700037.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|312873761|ref|ZP_07733806.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           2052A-d]
 gi|259167297|gb|EEW51792.1| dihydroorotate oxidase [Lactobacillus iners DSM 13335]
 gi|308167614|gb|EFO69767.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|311090759|gb|EFQ49158.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           2052A-d]
          Length = 306

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 45/205 (21%), Positives = 84/205 (40%), Gaps = 29/205 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL   +GG+ IS  +  AK + D G  N + +NV CP    +  + G  L  +P +V   
Sbjct: 98  PLIASVGGSQISDYITIAKKLSDSGLLNALEINVSCP----NVAAGGMHLGTDPVVVEKL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
            + + K ++IPV +K    V        +  + ++ ++ G +           GI I   
Sbjct: 154 TSEIKKVVNIPVYIKLTPNV------TNIVEIAQAAERGGADGLSMINTLLGLGIDIKTH 207

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           KA L  G        I  +   +V ++ +    L I   GG+E     ++ +L     V 
Sbjct: 208 KATLGNGFGGWSGSAIKPVAVRMVAQVHQAV-KLPIIGMGGIETAEDIVEFMLAGASAVA 266

Query: 215 IGRAAYKN----SAMLTTVDEYFSN 235
           +G A +K+      ++  ++   + 
Sbjct: 267 VGTAHFKDGLAIPHLVADLETLLNE 291


>gi|306833357|ref|ZP_07466484.1| dihydroorotate dehydrogenase B [Streptococcus bovis ATCC 700338]
 gi|304424127|gb|EFM27266.1| dihydroorotate dehydrogenase B [Streptococcus bovis ATCC 700338]
          Length = 314

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 76/198 (38%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    ++ + +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPELPIIANVAGFSNDEYAYVSEKISKASNVKAIELNISCP--NVDHGNHGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +   +PV VK    V D      +  + K+++++G  G  +      
Sbjct: 149 VPELAYAAVKASVEHSDVPVYVKLTPSVAD------ITTVAKAVEEAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ + + DL I   GG++    A++++
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-STDLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFADPY 279


>gi|282164223|ref|YP_003356608.1| dihydroorotate dehydrogenase [Methanocella paludicola SANAE]
 gi|282156537|dbj|BAI61625.1| dihydroorotate dehydrogenase [Methanocella paludicola SANAE]
          Length = 315

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 86/240 (35%), Gaps = 18/240 (7%)

Query: 27  IVADAILRGDKKNILGFST----QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           I A  +     K  L           P+   I GA  ++ +E AK +   G +   LNV 
Sbjct: 76  INAMGLPNPSYKEFLPELETAKDSGVPVIASIFGATEAEFIEVAKGL--PGASAYELNVS 133

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL-----R 137
           CP AR     +G  +  +P +V     A+   ++ PV VK    V D             
Sbjct: 134 CPHAR----GYGMQVGTDPALVKAIAHAVKGTVNAPVWVKLTPNVTDITSIGRAAQEGGA 189

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + V +I       I I +   IL  +        I  +    VY++     D+ +   GG
Sbjct: 190 DAVVAINTLKAIAIDIDSGYPILGNIQGGLSGPAIKPVAVRCVYDLYSAL-DIPVIGAGG 248

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
           +   + A++ I+     V IG A Y +  +   V    S+ L   +     +     R +
Sbjct: 249 VSSWADAVEFIMAGAAAVEIGSAVYDDIGVFAAVSMGLSDYLDRKNMTLKDLTGMAHRMV 308


>gi|28379199|ref|NP_786091.1| dihydroorotate dehydrogenase 1B [Lactobacillus plantarum WCFS1]
 gi|254557331|ref|YP_003063748.1| dihydroorotate dehydrogenase 1B [Lactobacillus plantarum JDM1]
 gi|29337222|sp|P77887|PYRD_LACPL RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|28272037|emb|CAD64942.1| dihydroorotate oxidase [Lactobacillus plantarum WCFS1]
 gi|44885276|emb|CAA91006.2| dihydroorotate dehydrogenase [Lactobacillus plantarum]
 gi|254046258|gb|ACT63051.1| dihydroorotate dehydrogenase 1B [Lactobacillus plantarum JDM1]
          Length = 305

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 77/200 (38%), Gaps = 19/200 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + GA   + V  A K+        + +N+ CP    +    G     
Sbjct: 89  LATHYPDLPIIGSVAGASFDEYVAVARKMASAPNVKLLEINISCP----NVDHGGLAFGT 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP--------AVALRNLVKSIKKSGVNGI 151
           +P  V     A+  A+  PV +K    V D +P          A   ++ ++   G++  
Sbjct: 145 DPATVTALTKAIVAAVDKPVFMKLTPNVTDIVPIALAAEAGGAAGLTMINTLTGMGID-- 202

Query: 152 WIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            +  R+ IL  G      + I  L   +++++++    L I   GG+   +  L+  L  
Sbjct: 203 -LATRQPILAHGTGGLSGKAIHPLAVRMIHDVRQHT-KLPIIGVGGVFTPADVLEFYLAG 260

Query: 210 VDGVMIGRAAYKNSAMLTTV 229
            + V +G A Y +    T +
Sbjct: 261 ANAVQVGAATYGHPTACTDI 280


>gi|329667277|gb|AEB93225.1| dihydroorotate dehydrogenase [Lactobacillus johnsonii DPC 6026]
          Length = 307

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 45/196 (22%), Positives = 85/196 (43%), Gaps = 25/196 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   +GG D +  +E AK + D G  N + +NV CP   V++G       +
Sbjct: 90  LRNEYPDLPIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCP--NVNQGGMSFG--V 145

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG--------- 150
           +PD+V +    +   + IP+ VK    V D      +  + K+ +  G +G         
Sbjct: 146 HPDVVEELTKKIKSVVKIPIYVKLTPNVTD------ITQIAKAAENGGADGLSLINTLLG 199

Query: 151 --IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I +  RK +L   +       +  +   +V+++ +E+  L I   GG+      ++ I
Sbjct: 200 MEIDVETRKPVLGHNIGGLSGEAVKPIAIRMVHQV-RESTTLPIIGMGGISSAKDVIEFI 258

Query: 207 LPSVDGVMIGRAAYKN 222
           L   + V +G A +K+
Sbjct: 259 LAGANAVAVGTAHFKD 274


>gi|327474448|gb|EGF19854.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK408]
          Length = 312

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/199 (19%), Positives = 77/199 (38%), Gaps = 23/199 (11%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G ++      A KI +      I LN+ CP   V  G+ G  +   P++  + 
Sbjct: 99  PIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQVPELAYEA 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A  ++ S+PV VK    V D      + ++ K+++ +G  G  +            +R
Sbjct: 157 TKAAVESSSVPVYVKLTPSVAD------ITHVAKAVEDAGAAGFTMINTLVGMRFDLKSR 210

Query: 157 KA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K  I  G        +  +    + ++ +    L I   GG++    AL++       + 
Sbjct: 211 KPIIANGTGGMSGPAVFPVALKQIRQVAQA-SKLPIIGMGGVDSAEAALEMFIAGASAIG 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +     T+ E  
Sbjct: 270 VGTANFTDPYACPTIIEDL 288


>gi|110803925|ref|YP_698519.1| dihydroorotate dehydrogenase 1B [Clostridium perfringens SM101]
 gi|110684426|gb|ABG87796.1| dihydroorotate oxidase [Clostridium perfringens SM101]
          Length = 299

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 70/192 (36%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGI--KSDVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK     +D      + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSPNAED------ICNMAYRCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             RK +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRKPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAK 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|168209705|ref|ZP_02635330.1| dihydroorotate oxidase [Clostridium perfringens B str. ATCC 3626]
 gi|170712183|gb|EDT24365.1| dihydroorotate oxidase [Clostridium perfringens B str. ATCC 3626]
          Length = 299

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 33/192 (17%), Positives = 68/192 (35%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
                +   +GGA I    +A  ++     + I LN+ CP   V  G     +    D+ 
Sbjct: 89  ELGTNIIANVGGATIEDYEKAVSLLNKEKIDMIELNISCP--NVKSGGMAFGIQS--DVA 144

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWI 153
            + ++ + K    P+ VK          A  + N+     ++G +            I I
Sbjct: 145 YEVVSKVRKICDKPLMVKLSP------NAENICNMAYKCAEAGADSISLINTLKGMAIDI 198

Query: 154 HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
             R  +     +      +  +   +V+E+ K   D+ +   GG+     A++ ++    
Sbjct: 199 KNRNPVFNNVYAGLSGPAVKPIALRMVHEVAK-TVDIPVIGLGGISTAEDAIEFMMAGAS 257

Query: 212 GVMIGRAAYKNS 223
            + IG   + N 
Sbjct: 258 AIQIGTINFVNP 269


>gi|46581716|ref|YP_012524.1| dihydroorotate dehydrogenase [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|46451139|gb|AAS97784.1| dihydroorotate dehydrogenase [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|311235352|gb|ADP88206.1| dihydroorotate dehydrogenase family protein [Desulfovibrio vulgaris
           RCH1]
          Length = 307

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/221 (18%), Positives = 78/221 (35%), Gaps = 27/221 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARV 88
           D +     + +     +E P+   I   D  K  E AA +  + G   + +N+ CP   V
Sbjct: 79  DGVECFINEKLPRLPWRELPVIANIYACDPGKFGELAAVLAAEEGVAALEVNISCP--NV 136

Query: 89  HEGSFGACLMLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
            EG        +         A+  +A + PV VK    V D      +  + ++++ +G
Sbjct: 137 KEGGILFG--QDARQAARVTEAVKMRAGAKPVIVKLSPNVTD------IVTMARAVEDAG 188

Query: 148 VNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            + +            I  R+ +L  +        I  +    V+++ +    + +   G
Sbjct: 189 ADMLSCINTLSGMGVDIRTRRPLLANVIGGLSGPAIKPVALRCVWQVSRAV-SIPVIGIG 247

Query: 196 GLEDMSQALK-ILPSVDGVMIGRAAYKNSAM-LTTVDEYFS 234
           G+      L+ IL     V +G A +         VDE   
Sbjct: 248 GIASAEDVLEFILVGAHAVQVGTANFMRPDFAFRLVDELNE 288


>gi|218134202|ref|ZP_03463006.1| hypothetical protein BACPEC_02092 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991577|gb|EEC57583.1| hypothetical protein BACPEC_02092 [Bacteroides pectinophilus ATCC
           43243]
          Length = 300

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 32/190 (16%), Positives = 66/190 (34%), Gaps = 24/190 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      VE  + + D   + + +N+ CP    +    G       +   +
Sbjct: 92  DTKIIVNVCGRSKEDYVEVVERLADEPVDMLEINISCP----NVKEGGIAFGQKAEAAYE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              A+      PV +K    V D      +  + ++++  G +            I I+ 
Sbjct: 148 ITKAVKAVAKQPVIMKLSPNVTD------ITEMARAVEAGGADVVSLINTLTGMKIDINR 201

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R  A+           I  +   +VY++      + I   GG+     AL+ I+     V
Sbjct: 202 RTFAVANKTGGLSGPAIRPVAVRMVYQVSNAV-KIPIIGMGGITCADDALEFIMAGATAV 260

Query: 214 MIGRAAYKNS 223
            +G A + N 
Sbjct: 261 SVGTANFHNP 270


>gi|295101476|emb|CBK99021.1| dihydroorotate oxidase B, catalytic subunit [Faecalibacterium
           prausnitzii L2-6]
          Length = 305

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 80/198 (40%), Gaps = 32/198 (16%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG    + VE A ++ + G + + LN+ CP+ +V   ++G       +  G+ +  +  
Sbjct: 104 LGGHSEEEYVEGAAMLSESGVDIVELNISCPNVKVGGMAYGV----KAEAAGEVVRMVRD 159

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK- 161
           A   P+ VK          A  +  + K+++ +G + I            +  R+ +   
Sbjct: 160 ACKKPLMVKLSPQ------AENIPEMCKAVEAAGADAISLTNTFQACAIDLEKRRPVFDN 213

Query: 162 ---GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
              GLS    R I   + +  V  +     ++ +   GG+     AL+ I+     V +G
Sbjct: 214 IFAGLSGPAVRPIALRMVWQAVGAV-----NIPVVGLGGIATGRDALEFIMAGATAVQVG 268

Query: 217 RAAYKNSAMLTTVDEYFS 234
            A + N   + T+ E  +
Sbjct: 269 AANFANPRAMETIAEEMA 286


>gi|295111359|emb|CBL28109.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Synergistetes bacterium SGP1]
          Length = 313

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/211 (18%), Positives = 78/211 (36%), Gaps = 20/211 (9%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGAC 96
           + +  +     P+ L + G       EA +IV  D     + LN+ CP         G  
Sbjct: 90  QELPRYDGIGAPVVLSLSGNRKEHYREALEIVANDPRIAAVELNLSCP-----NIGTGLA 144

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGI 151
               PD++ + + A  +A  +P+ VK    V D     ++      + V          I
Sbjct: 145 FSSTPDVLRETLKAAREATRLPIFVKLAPNVTDIRVSARVSEEEGADAVTIANTWRAMLI 204

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKI-LP 208
            +  R  +L  +S       P +    ++ +   +    + I  +GG+     A++  L 
Sbjct: 205 DVETRSPVLSNVSG--GMSGPAVKPQTLFLVWQARAATAIPIIASGGIARWQDAVEYFLA 262

Query: 209 SVDGVMIGRAAYKNSA----MLTTVDEYFSN 235
               V +G A ++N A    ++  +D Y + 
Sbjct: 263 GASMVQVGSANFQNPAAMVQIVDGIDRYLAE 293


>gi|325978141|ref|YP_004287857.1| dihydroorotate dehydrogenase 1B [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|325178069|emb|CBZ48113.1| dihydroorotate dehydrogenase 1B [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 314

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 75/198 (37%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    ++ +        I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPELPIIANVAGFSNDEYAYVSEKISKAPNVKAIELNISCP--NVDHGNHGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +   +PV VK    V D      +  + K+++++G  G  +      
Sbjct: 149 VPELAYAAVKASVEHSDVPVYVKLTPSVAD------ITTVAKAVEEAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ + + DL I   GG++    A++++
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-STDLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFADPY 279


>gi|320166820|gb|EFW43719.1| dihydropyrimidine dehydrogenase [Capsaspora owczarzaki ATCC 30864]
          Length = 1056

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 65/189 (34%), Gaps = 32/189 (16%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L        +   I  + +    +E AK+ E  G + + LN+ CP     E   G     
Sbjct: 663 LKRDHPAHVVIASIMCSFNREDWIELAKMAEASGADALELNLSCPHGM-GERGMGLACGQ 721

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
           +P++V +    +  A+ +P   K    V        + ++ ++ K+ G  G+        
Sbjct: 722 DPELVRNICKWVRSAIKVPFFAKLTPNV------TNIVDIARAAKEGGATGVTATNTVSG 775

Query: 153 --------------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
                          + ++    G+S    R I       V  I +  P   I   GG++
Sbjct: 776 LMHLKGDATAWPGVGNDKRTTYGGVSGNAIRPIA---LKAVSAISRNFPGFPILATGGID 832

Query: 199 DMSQALKIL 207
               AL+ L
Sbjct: 833 SADAALQFL 841


>gi|228960102|ref|ZP_04121766.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228799618|gb|EEM46571.1| Dihydroorotate dehydrogenase [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 306

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 73/199 (36%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +        + LN+ CP    +  + G     N +I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVYALELNISCP----NVKTGGIAFGTNTEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIETAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFIDPFVCPTIIEEL 279


>gi|295706343|ref|YP_003599418.1| dihydroorotate dehydrogenase, catalytic subunit [Bacillus
           megaterium DSM 319]
 gi|294804002|gb|ADF41068.1| dihydroorotate dehydrogenase, catalytic subunit [Bacillus
           megaterium DSM 319]
          Length = 313

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 38/201 (18%), Positives = 80/201 (39%), Gaps = 25/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + GA I + V  AK +        + LN+ CP    +    G    ++P I  
Sbjct: 93  DVPIIANVAGASIEEYVHVAKEISTVSNVKALELNISCP----NVKEGGIAFGVDPVIAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
               A+    ++PV VK    V +      + ++  +++++G +G+ +            
Sbjct: 149 RLTKAVKDVSNVPVYVKLSPNVSN------IVDMAMAVEEAGADGLTMINTLLGMRLDLK 202

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             + +L  G        I  +   +VYE+ ++  ++ I   GG+     AL+ L      
Sbjct: 203 TAQPVLANGTGGLSGPSIKPVAIRMVYEVSQKV-NIPIIGMGGVTTAEDALEFLYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYF 233
           V +G A + +  +  T+ +  
Sbjct: 262 VAVGTANFVDPYVCPTIIDEL 282


>gi|300361819|ref|ZP_07057996.1| dihydroorotate oxidase [Lactobacillus gasseri JV-V03]
 gi|300354438|gb|EFJ70309.1| dihydroorotate oxidase [Lactobacillus gasseri JV-V03]
          Length = 307

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 83/188 (44%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG D +  VE A+ + D G  N + +NV CP   V++G       ++PD+V   
Sbjct: 98  PIMASVGGEDEAGYVEVAQKLSDSGLVNALEINVSCP--NVNQGGMSFG--VHPDVVESL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              +    ++P+ VK    V D      +  + K+ +K G +G           I I  R
Sbjct: 154 TKKIKAVTNVPIYVKLTPNVTD------IIQIAKAAEKGGADGLSLINTLLGMDIDIKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L   +       +  +   +V+++ +++  L I   GG+      +K +L   + V 
Sbjct: 208 KPVLGHNVGGLSGEAVKPVALRMVHQV-RQSTSLPIIGMGGISSAQDVIKFMLAGANAVA 266

Query: 215 IGRAAYKN 222
           +G A +K+
Sbjct: 267 VGTAHFKD 274


>gi|116629731|ref|YP_814903.1| dihydroorotate dehydrogenase 1B [Lactobacillus gasseri ATCC 33323]
 gi|116095313|gb|ABJ60465.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus gasseri
           ATCC 33323]
          Length = 311

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 50/207 (24%), Positives = 91/207 (43%), Gaps = 26/207 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARV 88
           DA++    K  L  S  + P+   +GG D +  VE AK + D G  N + +NV CP   V
Sbjct: 84  DAVIEDKLKP-LRQSYPDLPIMASVGGEDEAGYVEVAKKLSDSGLVNALEINVSCP--NV 140

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           ++G       ++PD+V      +    ++P+ VK    V D      +  + K+ +K G 
Sbjct: 141 NQGGMSFG--VHPDVVESLTKKIKAVTNVPIYVKLTPNVTD------ITQISKAAEKGGA 192

Query: 149 NG-----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G           I I  RK +L   +       +  +   +V+++ +++  L I   GG
Sbjct: 193 DGLSLINTLLGMDIDIKTRKPVLGHNIGGLSGEAVKPVALRMVHQV-RQSTSLPIIGMGG 251

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKN 222
           +      +K +L   + V +G A +K+
Sbjct: 252 ISSAQDVIKFMLAGANAVAVGTAHFKD 278


>gi|238853381|ref|ZP_04643760.1| dihydroorotate dehydrogenase B, catalytic subunit [Lactobacillus
           gasseri 202-4]
 gi|282851814|ref|ZP_06261177.1| dihydroorotate dehydrogenase 1B [Lactobacillus gasseri 224-1]
 gi|238833953|gb|EEQ26211.1| dihydroorotate dehydrogenase B, catalytic subunit [Lactobacillus
           gasseri 202-4]
 gi|282557056|gb|EFB62655.1| dihydroorotate dehydrogenase 1B [Lactobacillus gasseri 224-1]
          Length = 307

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 50/207 (24%), Positives = 91/207 (43%), Gaps = 26/207 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARV 88
           DA++    K  L  S  + P+   +GG D +  VE AK + D G  N + +NV CP   V
Sbjct: 80  DAVIEDKLKP-LRQSYPDLPIMASVGGEDEAGYVEVAKKLSDSGLVNALEINVSCP--NV 136

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           ++G       ++PD+V      +    ++P+ VK    V D      +  + K+ +K G 
Sbjct: 137 NQGGMSFG--VHPDVVESLTKKIKAVTNVPIYVKLTPNVTD------ITQISKAAEKGGA 188

Query: 149 NG-----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G           I I  RK +L   +       +  +   +V+++ +++  L I   GG
Sbjct: 189 DGLSLINTLLGMDIDIKTRKPVLGHNIGGLSGEAVKPVALRMVHQV-RQSTSLPIIGMGG 247

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKN 222
           +      +K +L   + V +G A +K+
Sbjct: 248 ISSAQDVIKFMLAGANAVAVGTAHFKD 274


>gi|315640848|ref|ZP_07895947.1| dihydroorotate oxidase [Enterococcus italicus DSM 15952]
 gi|315483387|gb|EFU73884.1| dihydroorotate oxidase [Enterococcus italicus DSM 15952]
          Length = 310

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 81/209 (38%), Gaps = 25/209 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L  S  + P+   + G+ + + V   + I +      I LN+ CP    +    G     
Sbjct: 90  LASSHPDLPIIANVAGSTLDEYVAVCQSISQAPNVQAIELNISCP----NVKQGGIAFGT 145

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           +PD+  +   A+    ++P+ VK    V D      + ++  +++K+G +G+ +      
Sbjct: 146 DPDVAYELTKAVKSVSAVPIYVKLSPNVTD------IVSIALAVEKAGADGLTMINTLLG 199

Query: 154 -----HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
                  R  IL           I  +   ++ ++ +   DL I   GG+  +   L++ 
Sbjct: 200 MRIDLKTRLPILANQTGGLSGPAIKPVAIRMIRQVSQ-VCDLPIIGMGGVGTVDDVLEMF 258

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     V +G A + +  +   + E   N
Sbjct: 259 MAGASAVAVGTANFTDPWICQKLIEQLPN 287


>gi|225027672|ref|ZP_03716864.1| hypothetical protein EUBHAL_01931 [Eubacterium hallii DSM 3353]
 gi|224954986|gb|EEG36195.1| hypothetical protein EUBHAL_01931 [Eubacterium hallii DSM 3353]
          Length = 300

 Score = 77.2 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 38/192 (19%), Positives = 70/192 (36%), Gaps = 24/192 (12%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +   + + + G   S  VE  + + D   + + +NV CP    +    G     NPD +
Sbjct: 90  EKGASIIVNVCGRSTSDYVEVVERLADEPVDLLEINVSCP----NVKEGGIAFGQNPDAL 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWI 153
            +   A+      P+ +K    V D      +  + K+ +  G +            I I
Sbjct: 146 YEITKAIKAKAKQPIVMKLSPNVTD------ITEMAKAAEAGGCDALSLINTITGMKIDI 199

Query: 154 HARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
           H RK +L           I  +   +VY++      L I   GG+     A++ ++    
Sbjct: 200 HRRKFVLANKTGGMSGPAIKPVAVRMVYQV-SHACKLPIIGMGGILTGEDAIEMMMAGAT 258

Query: 212 GVMIGRAAYKNS 223
            V +G A + N 
Sbjct: 259 MVSVGTANFHNP 270


>gi|118575750|ref|YP_875493.1| dihydroorotate dehydrogenase [Cenarchaeum symbiosum A]
 gi|118194271|gb|ABK77189.1| dihydroorotate dehydrogenase [Cenarchaeum symbiosum A]
          Length = 281

 Score = 77.2 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 42/195 (21%), Positives = 79/195 (40%), Gaps = 15/195 (7%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDI 103
            Q  P  + + G+  ++ V   K   D G     +N+ CP  A+V     G  +  +P +
Sbjct: 71  GQGLPAVVSLVGSAPAEFVSMIKEFRD-GAAAFEINLSCPHVAKV-----GLEVGDDPGL 124

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSGVNGIWIHARKA 158
           VG+ ++A  +A  +PV  K  +G    I        A  + + +I       I + A+K 
Sbjct: 125 VGEIVSAAKRAADVPVFAKVGLGSTHYIKTAGAAAEAGADAITAINTVRAMSIDVEAKKP 184

Query: 159 ILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           +L  G        I  +    V+E+  +  D+ +   GG+     A++ +L     V +G
Sbjct: 185 VLSNGFGGLSGPPIRPIAVRCVWELASKY-DVPVIGCGGVSSWEDAIEMMLAGACAVQVG 243

Query: 217 RAAYKNSAMLTTVDE 231
            AA     +   ++ 
Sbjct: 244 SAAGGRIGIFGEINA 258


>gi|331092149|ref|ZP_08340979.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401921|gb|EGG81495.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 300

 Score = 77.2 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 68/202 (33%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + +     + + +N+ CP    +    G     NP    +
Sbjct: 92  DTKIIVNVCGRTTEDYCEVVERLSHEDVDMLEINISCP----NVKEGGIAFGQNPKSAEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
               + K    PV +K    V D      +  + K+++  G +            I +H 
Sbjct: 148 ITKEIKKYAKQPVIMKLSPNVTD------ITEMAKAVEAGGADAVSLINTLTGMKIDVHK 201

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R  A+           I  +   +VY+       L I   GG+     A++ IL     V
Sbjct: 202 RTFALANKTGGVSGPAIKPIAVRMVYQTANAI-KLPIIAMGGIATAEDAIEFILAGATAV 260

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A + N ++   + E    
Sbjct: 261 AVGTANFINPSVTMEIAEGIEQ 282


>gi|119720067|ref|YP_920562.1| dihydroorotate dehydrogenase family protein [Thermofilum pendens
           Hrk 5]
 gi|119525187|gb|ABL78559.1| dihydroorotate oxidase B, catalytic subunit [Thermofilum pendens
           Hrk 5]
          Length = 299

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 90/209 (43%), Gaps = 31/209 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   IG +   + +  A+ +E  G++ + LN  CP  +      GA LM +PD V   +
Sbjct: 95  PVIASIGASTPDEALRIAEALE--GFDALELNASCPHVK----GLGADLMSDPDAVYGIV 148

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
           +A+ K+    V +K     D          + +    +GV+G             ++ARK
Sbjct: 149 SAL-KSSGYRVFLKLSPHGD-------YLAVARKAYSAGVDGFTAINTAKAMVIDVYARK 200

Query: 158 AILKGLSPKDN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L G+    + R I  +   +VYE+ +E P++ +   GG+E   +A++ IL     V +
Sbjct: 201 PVLGGVVGGLSGRAIHPIAVRVVYELHREFPEVPVIGTGGVEGWVEAVELILAGASAVGV 260

Query: 216 G----RAAYKNSAMLTTVDEYFSNPLTGS 240
           G    R       +L  ++ Y  +    S
Sbjct: 261 GTALKRGFEVIGEILGGIERYLRDEGFPS 289


>gi|20807966|ref|NP_623137.1| dihydroorotate dehydrogenase 1B [Thermoanaerobacter tengcongensis
           MB4]
 gi|30173328|sp|Q8R9R7|PYRD_THETN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|20516538|gb|AAM24741.1| Dihydroorotate dehydrogenase [Thermoanaerobacter tengcongensis MB4]
          Length = 301

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 44/204 (21%), Positives = 78/204 (38%), Gaps = 28/204 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+ + I G  + + V  A+ ++  G   I +NV CP   V +G       +NPD + D
Sbjct: 92  DVPVIVNIAGETVEEFVYMAEKLDIEGIEGIEINVSCP--NVKKGGMAFG--VNPDDIFD 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               + KA S  V VK    V D      ++   K+ +K G + I +             
Sbjct: 148 ITRKVRKATSKTVIVKLTPNVTD------IKVCAKAAEKGGADAISLINTVAGMAVDIDK 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
            R      +       I  +   +VYE+        IG+ GG+ +   AL+ L      +
Sbjct: 202 RRPVFENVIGGLSGPAIKPIALKMVYEVVTVVSIPVIGM-GGIMNYKDALEFLIVGARAI 260

Query: 214 MIGRAAYKNSA----MLTTVDEYF 233
            +G   + N      ++  + +Y 
Sbjct: 261 AVGTCNFVNPYCTVEIIDGIKKYM 284


>gi|302023808|ref|ZP_07249019.1| dihydroorotate dehydrogenase 1B [Streptococcus suis 05HAS68]
          Length = 261

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 40/198 (20%), Positives = 77/198 (38%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 35  LEQHFPDLPIIANVAGFSNEEYAYVSGKISKAPNVKAIELNISCP--NVDHGNNGLLIGQ 92

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +A S+PV VK    V D         L K+ + +G  G+ +      
Sbjct: 93  VPELAYQAVKAAVEASSVPVYVKLTPSVADITL------LAKAAEDAGATGLTMINTLVG 146

Query: 154 -----HARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  R+ IL  G        +  +   ++ ++ +   DL I   GG++   +A++++
Sbjct: 147 MRFNLKTRQPILANGTGGMSGPAVFPVALKLIRQVAQ-VTDLPIIGMGGVDTADKAIEMM 205

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 V +G A + +  
Sbjct: 206 VAGASAVGVGTANFTDPF 223


>gi|298372408|ref|ZP_06982398.1| dihydroorotate oxidase [Bacteroidetes oral taxon 274 str. F0058]
 gi|298275312|gb|EFI16863.1| dihydroorotate oxidase [Bacteroidetes oral taxon 274 str. F0058]
          Length = 302

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 83/230 (36%), Gaps = 31/230 (13%)

Query: 26  MIVADAILRGDKKNILGFSTQE------KPLALQIGGADISKLVEAAK-IVEDFGYNEIN 78
           M+ A  +     + ++G    E      KP+   + G  + + VE A+ + E      I 
Sbjct: 66  MLNAVGLQNPGVEAVVGHELPELAKIYRKPIIANVCGFSLEEYVEVARRMCETDNVGWIE 125

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           LNV CP    +    G     +     +  +A+    S PV VK    V D      +  
Sbjct: 126 LNVSCP----NVKHGGMSFGTDAGCAAEVTSAVKAVCSKPVIVKLSPNVTD------IVA 175

Query: 139 LVKSIKKSGVNGI----WIHARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKEN 186
           + ++ +++G +G+     +   +  L+   P             +  +   +VY++ K  
Sbjct: 176 IAQACQEAGADGLCLINTLLGMRLDLQKRRPILANITGGFSGDAVFPVALRMVYQVAK-V 234

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             + I   GG+      ++ ++     V +G A   N      + E   N
Sbjct: 235 CRIPIVGCGGISTARDVVEMMMAGASAVEVGTANLINPYACRDIIEDLPN 284


>gi|228992619|ref|ZP_04152545.1| Dihydroorotate dehydrogenase [Bacillus pseudomycoides DSM 12442]
 gi|228998665|ref|ZP_04158252.1| Dihydroorotate dehydrogenase [Bacillus mycoides Rock3-17]
 gi|229006167|ref|ZP_04163853.1| Dihydroorotate dehydrogenase [Bacillus mycoides Rock1-4]
 gi|228755008|gb|EEM04367.1| Dihydroorotate dehydrogenase [Bacillus mycoides Rock1-4]
 gi|228761133|gb|EEM10092.1| Dihydroorotate dehydrogenase [Bacillus mycoides Rock3-17]
 gi|228766951|gb|EEM15588.1| Dihydroorotate dehydrogenase [Bacillus pseudomycoides DSM 12442]
          Length = 300

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 74/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V  AK +      + + LN+ CP    +  + G      P+I  D 
Sbjct: 92  PIIANVAGSQAEDYVAVAKEISKAPNVHALELNISCP----NVKTGGIAFGTVPEIAADL 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + +   +PV VK    V        +  + K+I+ +G +G+ +              
Sbjct: 148 TKRVKEVSEVPVYVKLSPNV------ANIVEIAKAIENAGADGLTMINTLLGMRLDLKTA 201

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K IL   +       I  +   +V+E+ +   ++ I   GG+E     ++        V 
Sbjct: 202 KPILANRTGGLSGPAIKPVAIRMVHEVSQAV-NIPIIGMGGIESAEDVIEFFYAGASAVA 260

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 261 VGTANFVDPFVCPTIIEEL 279


>gi|114049527|emb|CAJ75873.1| PyrD protein [Lactobacillus plantarum subsp. plantarum]
          Length = 305

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 76/200 (38%), Gaps = 19/200 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + GA   + V  A K+        + +N+ CP    +    G     
Sbjct: 89  LATHYPDLPIIGSVAGASFDEYVAVARKMASAPNVKLLEINISCP----NVDHGGLAFGT 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP--------AVALRNLVKSIKKSGVNGI 151
           +P  V     A+  A+  PV +K    V D +P          A   ++ ++   G++  
Sbjct: 145 DPATVTALTKAIVAAVDKPVFMKLTPNVTDIVPIALAAEAGGAAGLTMINTLTGMGID-- 202

Query: 152 WIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            +  R+ IL  G      + I  L   +++++++    L I   GG+      L+  L  
Sbjct: 203 -LATRQPILAHGTGGLSGKAIHPLAVRMIHDVRQHT-KLPIIGVGGVFTPVDVLEFCLAG 260

Query: 210 VDGVMIGRAAYKNSAMLTTV 229
            + V +G A Y +    T +
Sbjct: 261 ANAVQVGAATYGHPTACTDI 280


>gi|227890081|ref|ZP_04007886.1| dihydroorotate dehydrogenase 1B [Lactobacillus johnsonii ATCC
           33200]
 gi|227849525|gb|EEJ59611.1| dihydroorotate dehydrogenase 1B [Lactobacillus johnsonii ATCC
           33200]
          Length = 307

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 83/188 (44%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG D +  +E AK + D G  N + +NV CP   V++G       ++PD+V + 
Sbjct: 98  PIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCP--NVNQGGMSFG--VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              +   + IP+ VK    V D      +  + K+ +  G +G           I +  R
Sbjct: 154 TKKIKSVVKIPIYVKLTPNVTD------ITQIAKAAENGGADGLSLINTLLGMEIDVETR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L   +       +  +   +V+++ +E+  L I   GG+      ++ IL   + V 
Sbjct: 208 KPVLGHNIGGLSGEAVKPIAIRMVHQV-RESTTLPIIGMGGISSAKDVIEFILAGANAVA 266

Query: 215 IGRAAYKN 222
           +G A +K+
Sbjct: 267 VGTAHFKD 274


>gi|219852340|ref|YP_002466772.1| dihydroorotate dehydrogenase 1B [Methanosphaerula palustris E1-9c]
 gi|219546599|gb|ACL17049.1| dihydroorotate dehydrogenase family protein [Methanosphaerula
           palustris E1-9c]
          Length = 295

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 70/204 (34%), Gaps = 15/204 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            +P+   I G    +    A        +   LN+ CP A      +GA L  +P +V +
Sbjct: 92  GEPVIASIFGGSPEEFKTVAGWFAG-KVSGFELNLSCPHAE----GYGAALGSDPSLVEE 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRN-----LVKSIKKSGVNGIWIHARKAIL- 160
           C  A+    ++P  VK    V D               + +I       I    R+ +L 
Sbjct: 147 CTRAVASY-NLPTWVKLTPNVTDITIYGRAAERGGATALVAINTVKAMRISPELRRPVLG 205

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            G        I  +    VYE+ +    + I   GG+      L+ ++     V IG A 
Sbjct: 206 HGYGGLSGNAILPIAVRCVYELYEAC-SIPIIGCGGISSARDVLEMMMAGATAVEIGSAV 264

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPI 243
             +  +  +++     P  G  P 
Sbjct: 265 LSDQQIFRSIERELYAP-DGEDPT 287


>gi|320546620|ref|ZP_08040932.1| dihydroorotate dehydrogenase B [Streptococcus equinus ATCC 9812]
 gi|320448675|gb|EFW89406.1| dihydroorotate dehydrogenase B [Streptococcus equinus ATCC 9812]
          Length = 315

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 75/198 (37%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    ++ +        I LN+ CP   V  G+ G  +  
Sbjct: 92  LAEHFPELPIIANVAGFSNDEYAYVSEKISKAPNVKAIELNISCP--NVDHGNHGLLIGQ 149

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +   +PV VK    V D      +  + K+++++G  G  +      
Sbjct: 150 VPELAYAAVKASVENSEVPVYVKLTPSVAD------ITTVAKAVEEAGATGFTMINTLVG 203

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ + + DL I   GG++    AL+++
Sbjct: 204 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-SSDLPIIGMGGVDSAEAALEMM 262

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 263 IAGASAIGVGTANFADPY 280


>gi|291531442|emb|CBK97027.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium siraeum
           70/3]
          Length = 306

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/196 (18%), Positives = 71/196 (36%), Gaps = 24/196 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
               Q+  +   I GA I   +  A+ ++    + I LN+ CP    +    GA   +  
Sbjct: 91  RLRKQDTVVIANIAGAVIDDYIAVAEKLDATDVDMIELNISCP----NVKQGGATWGVTC 146

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------G 150
           +       A+  A   PV VK    V        +  + K+++  G +            
Sbjct: 147 EGAASVTRAVRNATKKPVIVKLTPNV------TNITEIAKAVEAEGADSVSLINTLLGMR 200

Query: 151 IWIHARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I I  R+ IL   +       +  +   +V+++        IG+ GG+     A++ ++ 
Sbjct: 201 IDIRTRRPILHNNVGGLSGPAVFPVAVRMVWQVANAVKIPVIGM-GGIATAEDAIEMMMA 259

Query: 209 SVDGVMIGRAAYKNSA 224
               V +G A + +  
Sbjct: 260 GASAVQMGTAIFNDPY 275


>gi|225621504|ref|YP_002722763.1| dihydroorotate dehydrogenase FMN-binding domain-containing protein
           [Brachyspira hyodysenteriae WA1]
 gi|254788879|sp|C0QYH6|PYRD_BRAHW RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|225216325|gb|ACN85059.1| dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain
           protein [Brachyspira hyodysenteriae WA1]
          Length = 303

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 46/207 (22%), Positives = 83/207 (40%), Gaps = 30/207 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ L I GA I + V+ A+I  +    + + LN+ CP    +  + G     + +    
Sbjct: 93  TPIILNINGATIDEYVKVAEIANEIERVDFVELNISCP----NVKNGGMAFGASCESAES 148

Query: 107 CIAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIH 154
              A+ K LS  P+ VK    V D      + ++ K+++ +G +            I   
Sbjct: 149 TTKAVKKVLSKKPLIVKLSPNVTD------IASIAKAVEDAGADSVSLVNTFLSMKIDTK 202

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           I  +   +VY++ K      +G+ GG+ + + AL+ IL     
Sbjct: 203 TRKPLLGNIFGGLSGACIRPIAVRMVYQVYKAVKIPIVGM-GGITNYNDALEFILAGASL 261

Query: 213 VMIGRAAYKNS----AMLTTVDEYFSN 235
           V IG   + N      ++  +D Y   
Sbjct: 262 VSIGAGIFSNPILPIEVINGIDNYLKE 288


>gi|150391898|ref|YP_001321947.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           metalliredigens QYMF]
 gi|189038413|sp|A6TVS0|PYRD_ALKMQ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|149951760|gb|ABR50288.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           metalliredigens QYMF]
          Length = 302

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 75/187 (40%), Gaps = 24/187 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I    E  K + D   + + LN+ CP    +  + G C   +P +V +   
Sbjct: 98  IIVNIAGRTIEDYCEVVKKLGDADVDLLELNISCP----NVKAGGVCFGTDPFMVEEVTK 153

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
           A+ K    P+ VK    V D +P      + K+    G +GI            IH RK 
Sbjct: 154 AVKKVAKQPLIVKLTPNVTDIVP------IAKAAVAGGADGISLINTLLGMAIDIHKRKP 207

Query: 159 ILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           IL   +       I  +   +VY++     D+ I   GG+     A++ IL    GV +G
Sbjct: 208 ILANVMGGFSGPAIKPVALRMVYQVANAV-DVPIIGMGGIMTGEDAVEFILAGASGVAVG 266

Query: 217 RAAYKNS 223
            A + N 
Sbjct: 267 TANFINP 273


>gi|311029958|ref|ZP_07708048.1| dihydroorotate dehydrogenase 1B [Bacillus sp. m3-13]
          Length = 313

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/199 (18%), Positives = 77/199 (38%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+ I   V+ AK I      + + LN+ CP    +  + G     +P +  + 
Sbjct: 95  PIIANVAGSLIEDYVKVAKEISAAPNVHALELNISCP----NVKTGGIAFGTDPAVAFEV 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
             A+ +   +PV VK    V        +  +  +I+++G +G+ +              
Sbjct: 151 TKAVKEVAEVPVYVKLSPNV------ANISEIAVAIEQAGADGLTMINTLLGMRIDLKTG 204

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           R  +           I  +   +++E+ ++     IG+ GG++     L+ L      V 
Sbjct: 205 RPVLANSTGGLSGPAIKPVAIRMIHEVSQKVSIPIIGM-GGVQSAEDVLEYLFAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +  +  T+ E  
Sbjct: 264 VGTANFVDPFICPTIIEEL 282


>gi|115976525|ref|XP_001177822.1| PREDICTED: similar to Dihydropyrimidine dehydrogenase
           [Strongylocentrotus purpuratus]
          Length = 1025

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 43/223 (19%), Positives = 74/223 (33%), Gaps = 40/223 (17%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L     ++ +   I  +    D +KL   AK+ E+ G + + L
Sbjct: 611 ELISEKTAAYWCKIVTELKRDFPDRIVIASIMCSFNKDDWTKL---AKMSEEAGADALEL 667

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     +P++V +    +  A+ IP   K    V        + ++
Sbjct: 668 NLSCPHGM-GEKGMGLACGQDPELVLNICRWVRAAVKIPFFAKLTPNV------TNILDI 720

Query: 140 VKSIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDI 178
            ++ K+   +G+                         +K    G+S    R I       
Sbjct: 721 ARAAKEGNADGVTATNTVSGLMGLKASSNAWPAVGKQKKTTYGGVSGNAIRPIA---LKA 777

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
           V  I    P   I   GG++    AL+ L      V +  A  
Sbjct: 778 VSVIANNLPGFPILATGGIDSAESALQFLHAGASAVQVCSAIQ 820


>gi|115736135|ref|XP_001197282.1| PREDICTED: similar to Dihydropyrimidine dehydrogenase, partial
           [Strongylocentrotus purpuratus]
          Length = 873

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 43/223 (19%), Positives = 74/223 (33%), Gaps = 40/223 (17%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L     ++ +   I  +    D +KL   AK+ E+ G + + L
Sbjct: 611 ELISEKTAAYWCKIVTELKRDFPDRIVIASIMCSFNKDDWTKL---AKMSEEAGADALEL 667

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     +P++V +    +  A+ IP   K    V        + ++
Sbjct: 668 NLSCPHGM-GEKGMGLACGQDPELVLNICRWVRAAVKIPFFAKLTPNV------TNILDI 720

Query: 140 VKSIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDI 178
            ++ K+   +G+                         +K    G+S    R I       
Sbjct: 721 ARAAKEGNADGVTATNTVSGLMGLKASSNAWPAVGKQKKTTYGGVSGNAIRPIA---LKA 777

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
           V  I    P   I   GG++    AL+ L      V +  A  
Sbjct: 778 VSVIANNLPGFPILATGGIDSAESALQFLHAGASAVQVCSAIQ 820


>gi|115627904|ref|XP_781238.2| PREDICTED: similar to MGC81821 protein [Strongylocentrotus
           purpuratus]
 gi|115937279|ref|XP_001194175.1| PREDICTED: similar to MGC81821 protein [Strongylocentrotus
           purpuratus]
          Length = 900

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 43/223 (19%), Positives = 74/223 (33%), Gaps = 40/223 (17%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L     ++ +   I  +    D +KL   AK+ E+ G + + L
Sbjct: 611 ELISEKTAAYWCKIVTELKRDFPDRIVIASIMCSFNKDDWTKL---AKMSEEAGADALEL 667

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     +P++V +    +  A+ IP   K    V        + ++
Sbjct: 668 NLSCPHGM-GEKGMGLACGQDPELVLNICRWVRAAVKIPFFAKLTPNV------TNILDI 720

Query: 140 VKSIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDI 178
            ++ K+   +G+                         +K    G+S    R I       
Sbjct: 721 ARAAKEGNADGVTATNTVSGLMGLKASSNAWPAVGKQKKTTYGGVSGNAIRPIA---LKA 777

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
           V  I    P   I   GG++    AL+ L      V +  A  
Sbjct: 778 VSVIANNLPGFPILATGGIDSAESALQFLHAGASAVQVCSAIQ 820


>gi|27768991|gb|AAH42543.1| Dpyd protein [Mus musculus]
          Length = 879

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 69/207 (33%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  L   I         + E +K+ E  G + + LN+
Sbjct: 465 ELISEKTAAYWCHSVTELKADFPDNILIASIMCSYNKSDWM-ELSKMAEASGADALELNL 523

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ +P   K    V D      + ++ +
Sbjct: 524 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVRVPFFAKLTPNVTD------IVSIAR 576

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         R+    G+S    R I       V 
Sbjct: 577 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGIGRRTTYGGVSGTAIRPIA---LRAVT 633

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 634 AIARALPGFPILATGGIDSAESGLQFL 660


>gi|25140985|ref|NP_740748.1| dihydropyrimidine dehydrogenase [NADP+] [Mus musculus]
 gi|81878130|sp|Q8CHR6|DPYD_MOUSE RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|24980778|gb|AAH39699.1| Dihydropyrimidine dehydrogenase [Mus musculus]
 gi|148680406|gb|EDL12353.1| dihydropyrimidine dehydrogenase [Mus musculus]
          Length = 1025

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 69/207 (33%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  L   I         + E +K+ E  G + + LN+
Sbjct: 611 ELISEKTAAYWCHSVTELKADFPDNILIASIMCSYNKSDWM-ELSKMAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ +P   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVRVPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         R+    G+S    R I       V 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGIGRRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 780 AIARALPGFPILATGGIDSAESGLQFL 806


>gi|227499711|ref|ZP_03929811.1| dihydroorotate oxidase [Anaerococcus tetradius ATCC 35098]
 gi|227218178|gb|EEI83441.1| dihydroorotate oxidase [Anaerococcus tetradius ATCC 35098]
          Length = 299

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 63/180 (35%), Gaps = 29/180 (16%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   V  A+I++    + I LN+ CP    +    G     +P      I  +  
Sbjct: 99  LGGHSVDDYVRGAEIIDSTSSDMIELNISCP----NVKEGGMAFGTDPSKACQVIKKVRS 154

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKG 162
               P+ VK    V +      + +  K  +  G +            I I  RK +   
Sbjct: 155 KTKKPLIVKLSPNVSN------IGDFAKIAQDQGADVISLINTINAMAIDIRQRKPVFAN 208

Query: 163 L-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
             +      +  +   +VYE+ K   DL I   GG+     A++       +M G  A +
Sbjct: 209 KTAGLSGPAVKPIAVRMVYEVSKAV-DLPIIGMGGIMTYEDAIEF------IMAGAWAIQ 261


>gi|169836870|ref|ZP_02870058.1| hypothetical protein cdivTM_07144 [candidate division TM7
           single-cell isolate TM7a]
          Length = 79

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           ST E P+  QI G + + +   A    + G++ I++N+GCP+    +   GA L+ NP++
Sbjct: 1   STDEDPIVAQIWGGNPNDMQNLASYCRELGFHGIDINMGCPAKSAIKSG-GAALIRNPEL 59

Query: 104 VGDCIAAMCKALSIPVTVK 122
             + I A  KA ++PV+VK
Sbjct: 60  AIESIKA-AKAANLPVSVK 77


>gi|89098719|ref|ZP_01171601.1| dihydroorotate dehydrogenase [Bacillus sp. NRRL B-14911]
 gi|89086681|gb|EAR65800.1| dihydroorotate dehydrogenase [Bacillus sp. NRRL B-14911]
          Length = 313

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 88/253 (34%), Gaps = 35/253 (13%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVH 89
            +     + +      + P+   I G+     +E A+ + +      + LN+ CP+ +  
Sbjct: 77  GLDHVLMEELPRLEQYDVPIIANIAGSTEEDYIEVARELSKASNVKALELNISCPNVKTG 136

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             +FG      P+I       +  A ++PV VK    V        +  + K++++ G +
Sbjct: 137 GIAFGTI----PEIAKSLTKKVKAASAVPVYVKLSPNV------TNIVEMAKAVEEGGAD 186

Query: 150 GIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           G+ +              R  +           I  +   ++YE+ ++  DL I   GG+
Sbjct: 187 GLTMINTLLGMRMDLNTGRPILANRTGGLSGPSIKPVALRMIYEVSQQV-DLPIIGMGGV 245

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           E     ++        V +G A + +  +   + +               ++K  +  IS
Sbjct: 246 ETAEDVIEFFYAGASAVAVGTANFVDPFVCPNIIDKL----------PELLEKLGFEHIS 295

Query: 257 ASMTDYAARHLHS 269
                   +H  S
Sbjct: 296 ECTGRSWGKHEES 308


>gi|90415938|ref|ZP_01223871.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding [marine
           gamma proteobacterium HTCC2207]
 gi|90332312|gb|EAS47509.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding [marine
           gamma proteobacterium HTCC2207]
          Length = 546

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/166 (22%), Positives = 66/166 (39%), Gaps = 11/166 (6%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +++ L + I G  + + VE AKI+     + + LN+ CP A+     +G  +  +P++V
Sbjct: 91  PEDRFLLVSIFGGSLEEFVEVAKIMAPV-ADGLELNLSCPHAK----GYGMAMGQDPEMV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
               AA+   + IPV  K      +     Q  A    + + +I   G      H    +
Sbjct: 146 RAITAAVKAVVDIPVIPKLTPNTPNIGEIAQAAAAGGADGICAINTVGPGFTASHGHPVL 205

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
             G      + +  +    V EI +E  DL I   GG    +   +
Sbjct: 206 SNGAGGMSGKGVLPIALKCVREI-REVTDLPIIGCGGASSAADTRE 250


>gi|296876594|ref|ZP_06900644.1| dihydroorotate dehydrogenase 1B [Streptococcus parasanguinis ATCC
           15912]
 gi|296432413|gb|EFH18210.1| dihydroorotate dehydrogenase 1B [Streptococcus parasanguinis ATCC
           15912]
          Length = 312

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPDLPIIANVAGFSNEEYATVSGKISQAPNVKAIELNISCP--NVDHGNNGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +A S+PV VK    V D      +  + K+ + +G  G+ +      
Sbjct: 149 VPELAYAAVKAAVEASSVPVYVKLTPSVAD------ITQVAKAAEDAGATGLTMINTLVG 202

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                   +  I  G        +  +   ++ ++ + +  L I   GG++    A++++
Sbjct: 203 MRFDLKTGKPIIANGTGGMSGPAVFPVALKLIRQVAQ-STKLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|213583993|ref|ZP_03365819.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 137

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 28/111 (25%), Positives = 44/111 (39%), Gaps = 8/111 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P++
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDPEL 137


>gi|315158222|gb|EFU02239.1| dihydroorotate dehydrogenase 1B [Enterococcus faecalis TX0312]
          Length = 312

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 71/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +   AKI +      I LN+ CP    +    G     +P++    
Sbjct: 98  PIIANVAGACEEDYVAVCAKIGQAPNVKAIELNISCP----NVKHGGIAFGTDPEVAFQL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K  S+P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 154 TQAVKKVASVPIYVKLSPNVTDIVP------IAQAIEAGGADGFSMINTLLGMRIDLKTR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++      L I   GG++ +   L++ +     V 
Sbjct: 208 KPILANQTGGLSGPAIKPVAIRLIRQVA-SVSQLPIIGMGGVQTVDDVLEMFMAGASAVG 266

Query: 215 IGRAAYKNSAM 225
            G A + +  +
Sbjct: 267 GGTANFTDPYI 277


>gi|298674504|ref|YP_003726254.1| methanogenesis marker protein 9 [Methanohalobium evestigatum
           Z-7303]
 gi|298287492|gb|ADI73458.1| methanogenesis marker protein 9 [Methanohalobium evestigatum
           Z-7303]
          Length = 381

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 40/208 (19%), Positives = 81/208 (38%), Gaps = 23/208 (11%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
           E I  + +     K  +        +A+ +  A    L+EAA+I ++     + L+  C 
Sbjct: 68  EFITDNPL--QFLKEEINNVDTGSVVAVNVRSATPEPLIEAAQIAKESDA-ILELDAHCR 124

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              +     G  LM +   + D I  + +   + ++VK R  V D +       L + I+
Sbjct: 125 QEEMVNIGVGEALMHDTSRLADWIQKIKE-TGVVLSVKIRANVVDDV------ELSRQIE 177

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +G + + I    A L+G +  D + I  +         +++  + +  N  + + S A 
Sbjct: 178 SAGADILHI---DATLEGKNTADLKAIRKI---------RDSVRMTLIGNNSITEFSDAK 225

Query: 205 KILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            I     D V + R    N  ++  + E
Sbjct: 226 DIFSRGADLVSVSRGVMDNPYLIDELVE 253


>gi|313905227|ref|ZP_07838595.1| dihydrouridine synthase DuS [Eubacterium cellulosolvens 6]
 gi|313469980|gb|EFR65314.1| dihydrouridine synthase DuS [Eubacterium cellulosolvens 6]
          Length = 288

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 74/224 (33%), Gaps = 32/224 (14%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---------SIPVTVKCRI 125
              NLN GCP+  V     GA L+ N   +   +  + + +          + V+VK R 
Sbjct: 46  QNFNLNTGCPAPTVVTRHKGAGLLENLVELEMLLDEIFEGIEKIRTGSGREMRVSVKTRT 105

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G+     A AL +     ++   + I IH R         ++         ++   +   
Sbjct: 106 GIRSHEEAEALMD---VFERYPFSEIIIHPRV--------REEYYKGQAHPEVFAALAGR 154

Query: 186 NPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                +  NG L       +     P V   M GR    + A++  +         G   
Sbjct: 155 CGK-KLCYNGDLYTAGIWQERKAQFPEVTDWMFGRGFVTDPALVRQIQ--------GGKK 205

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
           ++     +F  +I     +      ++  +L ++  +    F G
Sbjct: 206 LEAAELLEFHDRILDGYLEMGTEDRNAMFRLFELWTYWRFHFQG 249


>gi|312622390|ref|YP_004024003.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202857|gb|ADQ46184.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 300

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/201 (20%), Positives = 75/201 (37%), Gaps = 25/201 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G    + VE  KI+     + I +N+ CP    +    G     +P+ V +   
Sbjct: 95  IIANINGFTKEEFVELTKILGSL-VDMIEVNLSCP----NVKEGGMAFGKDPEKVYEITK 149

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
           ++    S P+ VK    V D      +  L  + +K+G + I            I  RK 
Sbjct: 150 SVKDVASCPIIVKLTPNVTD------ITQLAIAAEKAGADAISLINTVSAMAIDIETRKP 203

Query: 159 ILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           ++K ++       I  +   +VYE  K+   + I   GG+ +   A++        + IG
Sbjct: 204 LIKMVTGGLSGPAIKPIAVRMVYECFKKV-RIPIVGMGGIMNYKDAIEFFIAGATAIQIG 262

Query: 217 RAAYKNSAMLTTVDEYFSNPL 237
              + N   +  + E     L
Sbjct: 263 TVNFINPKAVCEIKEGIEAYL 283


>gi|325689641|gb|EGD31645.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK115]
          Length = 312

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 78/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++      A  +  ++PV VK    V D      +  + K+++ +G +G  +      
Sbjct: 149 VPELAYGATKAAVETSAVPVYVKLTPSVAD------VTQVAKAVEDAGADGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|28386052|gb|AAH44730.1| Dpyd protein [Mus musculus]
          Length = 512

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 69/207 (33%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  L   I         + E +K+ E  G + + LN+
Sbjct: 98  ELISEKTAAYWCHSVTELKADFPDNILIASIMCSYNKSDWM-ELSKMAEASGADALELNL 156

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ +P   K    V D      + ++ +
Sbjct: 157 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVRVPFFAKLTPNVTD------IVSIAR 209

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         R+    G+S    R I       V 
Sbjct: 210 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGIGRRTTYGGVSGTAIRPIA---LRAVT 266

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 267 AIARALPGFPILATGGIDSAESGLQFL 293


>gi|327542500|gb|EGF28976.1| dihydroorotate dehydrogenase family protein [Rhodopirellula baltica
           WH47]
          Length = 305

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/218 (17%), Positives = 80/218 (36%), Gaps = 30/218 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV 88
           DA L      + G      P+ + + G  +    E A+ V +  G + I LN+ CP    
Sbjct: 83  DAFLEHHLPYLAGL---GTPIIVSVAGRTVEDFTELARRVGQCDGVSAIELNLSCP---- 135

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              S G     N +   + +A+   A  +P+  K    V        + ++ +     G 
Sbjct: 136 -NVSGGIDFGTNAESCREVVASARNACDVPILAKLTPNVTR------IADIAQGAADGGA 188

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + + +              R  +  G+       I  +    V+++++   D+ I   GG
Sbjct: 189 DAVCLINTVLGMAVDWKKRRPILGNGMGGLSGPAIKPIALRCVHQVRQAV-DIPIIGIGG 247

Query: 197 LEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEY 232
           + ++   ++ L      V IG A Y +  + +  +D+ 
Sbjct: 248 VANIDDVMQFLVTGASAVQIGTANYYDPTVSMRLIDQL 285


>gi|218283814|ref|ZP_03489728.1| hypothetical protein EUBIFOR_02322 [Eubacterium biforme DSM 3989]
 gi|218215574|gb|EEC89112.1| hypothetical protein EUBIFOR_02322 [Eubacterium biforme DSM 3989]
          Length = 302

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 80/218 (36%), Gaps = 28/218 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARV 88
           D+I+  +   +  + T+   +   + GA     VE  K + D        LN+ CP    
Sbjct: 78  DSIIENELPFLAQYDTE---IMANVAGACEEDYVEVIKKLNDQPVIKAYELNISCP---- 130

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G  L   P++         +A + PV VK    V D      +  + K+++++G 
Sbjct: 131 NVKHGGIGLGTKPELAAHVTKICKEAATKPVYVKLSPNVTD------IVEIAKAVEEAGA 184

Query: 149 NGI----WIHARKAILKGLSP--------KDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +GI     +   +  LK   P             I  +   +VY++ +   ++ I   GG
Sbjct: 185 DGIVLINTLMGMRINLKTGKPLLANVTGGLSGPAIKPVALRMVYQVAQAV-NIPIIGVGG 243

Query: 197 LEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +      L+ L      V +G   + +  +   + E  
Sbjct: 244 ITCAEDVLEFLNAGASAVEVGAQNFVDPYVCPKIIEDL 281


>gi|328950916|ref|YP_004368251.1| dihydroorotate dehydrogenase family protein [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451240|gb|AEB12141.1| dihydroorotate dehydrogenase family protein [Marinithermus
           hydrothermalis DSM 14884]
          Length = 299

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/224 (18%), Positives = 82/224 (36%), Gaps = 35/224 (15%)

Query: 23  YTE----MIVA-----DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
            TE    M+ A       + R  +  +     Q   + + + G    +    A+ V  F 
Sbjct: 60  VTETPGGMLNAIGLENKGVERYVQDELPWLREQGARVIVNVFGDTPEEFAYVAERVSPF- 118

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + + LN+ CP    +    G     +P    + + A+  A   PV VK         P 
Sbjct: 119 AHLLELNLSCP----NVHGAGLPFAHDPQAAAEVVRAVKDATDRPVIVKL-------SPN 167

Query: 134 VALRNLVKSIKKSGVNG-----------IWIHARKAILKGLSPK-DNRKIPNLDYDIVYE 181
             +  + ++ + +GV+G           I +  R+ +L   +       +  +   +VYE
Sbjct: 168 APILPVAEACEAAGVDGFSLINTLLGMRIDLETRRPVLGHKTGGLSGPAVKPVAVRLVYE 227

Query: 182 IKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
           + +      +G+ GG+  +  AL+  L     V +G A + +  
Sbjct: 228 LYRHTDKPILGM-GGIRTVEDALEFALAGARMVAVGTATFSDPF 270


>gi|325696570|gb|EGD38460.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK160]
          Length = 312

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 77/207 (37%), Gaps = 23/207 (11%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI        I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISLATNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++  +   A  +  ++PV VK    + D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYEATKAAVETSAVPVYVKLTPSIAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSADAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 + +G A + +     T+ E  
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIEDL 288


>gi|153939958|ref|YP_001392587.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum F str.
           Langeland]
 gi|152935854|gb|ABS41352.1| dihydroorotate oxidase [Clostridium botulinum F str. Langeland]
 gi|295320572|gb|ADG00950.1| dihydroorotate oxidase [Clostridium botulinum F str. 230613]
          Length = 298

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 72/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + +
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEVVKEVKE 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQKPLMVKLSPNAED------IVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+  ++ +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPIALRMVYEVCKQV-EIPVIGIGGICNYKDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|319939237|ref|ZP_08013600.1| dihydroorotate oxidase B [Streptococcus anginosus 1_2_62CV]
 gi|319811633|gb|EFW07909.1| dihydroorotate oxidase B [Streptococcus anginosus 1_2_62CV]
          Length = 313

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 36/199 (18%), Positives = 72/199 (36%), Gaps = 23/199 (11%)

Query: 49  PLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G    +    A KI +      I LN+ CP   V  G+ G  +   PD+  + 
Sbjct: 99  PIIANVAGFSNEEYAFVAGKISQAPNVKAIELNISCP--NVDHGNGGLLIGQVPDLAYEA 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A      +PV VK    V D      +  +  +++ +G  G  +            +R
Sbjct: 157 AKAAVDVSEVPVYVKLTPSVAD------ITQIAIAVEAAGATGFTMINTLVGMRFDLKSR 210

Query: 157 KA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K  I  G        +  +   ++ ++ + +  L I   GG++    A+++       + 
Sbjct: 211 KPIIANGTGGMSGPAVFPVALKLIRQVAQ-SSSLPIIGMGGVDSAEAAIEMFIAGASAIG 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A + +      + E  
Sbjct: 270 VGTANFTDPYACPNIIENL 288


>gi|307354065|ref|YP_003895116.1| dihydroorotate dehydrogenase family protein [Methanoplanus
           petrolearius DSM 11571]
 gi|307157298|gb|ADN36678.1| dihydroorotate dehydrogenase family protein [Methanoplanus
           petrolearius DSM 11571]
          Length = 296

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 44/198 (22%), Positives = 73/198 (36%), Gaps = 14/198 (7%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + KP+   I GA+  +  E A    D       LNV CP A      +GA +  +PD+V 
Sbjct: 92  KGKPVIASIFGANPEEFAEVASWFMD-SAAGFELNVSCPHAE----GYGAQIGSDPDLVY 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           +C  A+ K    PV VK    V            A  + + +I       I    RK +L
Sbjct: 147 ECTRAVSK-TGKPVWVKLTPNVTSIADCGAAAERAGASALVAINTVRAMRISTDLRKPML 205

Query: 161 KGLSPKDNR-KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRA 218
              S   +   I  +    V+++ +   D+ I   GG+      ++ ++     V IG A
Sbjct: 206 GNGSGGLSGDAIFPIAVKCVWDLYEAC-DIPIVGCGGVSSADNVIEMMMAGASAVEIGSA 264

Query: 219 AYKNSAMLTTVDEYFSNP 236
                 +   +     + 
Sbjct: 265 VLNGVDIFEKISGELYSG 282


>gi|154505058|ref|ZP_02041796.1| hypothetical protein RUMGNA_02568 [Ruminococcus gnavus ATCC 29149]
 gi|153794537|gb|EDN76957.1| hypothetical protein RUMGNA_02568 [Ruminococcus gnavus ATCC 29149]
          Length = 300

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 32/196 (16%), Positives = 68/196 (34%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + + +   + + +N+ CP    +    G     NP    +
Sbjct: 92  DTKIIVNVCGRSTEDYCEVVERLANEDVDMLEINISCP----NVKEGGIAFGQNPKAAEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
              A+ K    PV +K    V       ++  + K+++  G + I +             
Sbjct: 148 ITRAVKKYAKQPVIMKLSPNV------TSISEMAKAVEAGGADAISLINTLTGMKIDINR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
              A+           I  +   +VYE      ++ I   GG+E    A+++L      V
Sbjct: 202 KTFALANKTGGVSGPAIHPIAVRMVYEAANAV-NVPIIGMGGIETAEDAIEMLLVGASAV 260

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A + N  +   +
Sbjct: 261 SVGTANFYNPNVTMEI 276


>gi|32475529|ref|NP_868523.1| dihydroorotate dehydrogenase [Rhodopirellula baltica SH 1]
 gi|32446071|emb|CAD75900.1| dihydroorotate dehydrogenase [Rhodopirellula baltica SH 1]
          Length = 305

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 39/218 (17%), Positives = 80/218 (36%), Gaps = 30/218 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV 88
           DA L      + G      P+ + + G  +    E A+ V +  G + I LN+ CP    
Sbjct: 83  DAFLEHHLPYLAGL---GTPIIVSVAGRTVEDFTELARRVGQCDGVSAIELNLSCP---- 135

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              S G     N +   + +A+   A  +P+  K    V        + ++ +     G 
Sbjct: 136 -NVSGGIDFGTNAESCREVVASARNACDVPILAKLTPNVTR------IADIAQGAADGGA 188

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + + +              R  +  G+       I  +    V+++++   D+ I   GG
Sbjct: 189 DAVCLINTVLGMAVDWKKRRPILGNGMGGLSGPAIKPIALRCVHQVRQAV-DIPIIGIGG 247

Query: 197 LEDMSQALKIL-PSVDGVMIGRAAYKNSAM-LTTVDEY 232
           + ++   ++ L      V IG A Y +  + +  +D+ 
Sbjct: 248 VANIDDVMQFLVTGASAVQIGTANYYDPTVSMRLIDQL 285


>gi|326925020|ref|XP_003208720.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+]-like [Meleagris
            gallopavo]
          Length = 1214

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 33/159 (20%), Positives = 57/159 (35%), Gaps = 25/159 (15%)

Query: 67   KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
            K+ E  G + + LN+ CP     E   G     +P++V +    + +A+ IP   K    
Sbjct: 881  KMAEAAGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPN 939

Query: 127  VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------------SPKDN 168
            V D      + N+  + ++ G +G+      + L GL                       
Sbjct: 940  VTD------IVNIAMAAQEGGADGVTATNTVSGLMGLKADGTPWPAVGAGLRTTYGGVSG 993

Query: 169  RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              I  +    V  I +  P   I   GG++    AL+ L
Sbjct: 994  NAIRPIALRAVSAIARALPGFPILATGGIDSAESALQFL 1032


>gi|254479717|ref|ZP_05093007.1| dihydroorotate dehydrogenase family protein [Carboxydibrachium
           pacificum DSM 12653]
 gi|214034346|gb|EEB75130.1| dihydroorotate dehydrogenase family protein [Carboxydibrachium
           pacificum DSM 12653]
          Length = 263

 Score = 76.0 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 48/221 (21%), Positives = 84/221 (38%), Gaps = 31/221 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA +  +   + GF     P+ + I G  + + V  A+ ++  G   I +NV CP   V 
Sbjct: 40  DAFIERELPFLKGFD---VPVIVNIAGETVEEFVYMAEKLDIEGIEGIEINVSCP--NVK 94

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           +G       +NPD + D    + KA S  V VK    V D      ++   K+ +K G +
Sbjct: 95  KGGMAFG--VNPDDIFDITRKVRKATSKTVIVKLTPNVTD------IKVCAKAAEKGGAD 146

Query: 150 GIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I +              R      +       I  +   +VYE+        IG+ GG+
Sbjct: 147 AISLINTVAGMAVDIDKRRPVFENVIGGLSGPAIKPIALKMVYEVVTVVSIPVIGM-GGI 205

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSA----MLTTVDEYF 233
            +   AL+ L      + +G   + N      ++  + +Y 
Sbjct: 206 MNYKDALEFLIVGARAIAVGTCNFVNPYCTVEIIDGIKKYM 246


>gi|52080156|ref|YP_078947.1| dihydroorotate dehydrogenase 1B [Bacillus licheniformis ATCC 14580]
 gi|52003367|gb|AAU23309.1| dihydroorotate dehydrogenase (catalytic subunit) [Bacillus
           licheniformis ATCC 14580]
          Length = 311

 Score = 76.0 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 78/192 (40%), Gaps = 25/192 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ I   VE A+ +      + + LN+ CP    +  + G      P++ G
Sbjct: 91  DTPIIANVAGSQIEDYVEVAEEISKAPNVHALELNISCP----NVKTGGIAFGTQPEMAG 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +   A+ +  S+PV VK    V        + ++  +I+++G +G+ +            
Sbjct: 147 ELTKAVKEVASVPVYVKLSPNV------ANITDIALAIEEAGADGLTMINTLIGMRLDLK 200

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             +  +           +  +   +V+E+ ++     IG+ GG++     L+ +L     
Sbjct: 201 TGKPILANKTGGLSGPAVKPVAIRMVHEVSQKVSIPIIGM-GGVQSAEDVLEFLLAGASA 259

Query: 213 VMIGRAAYKNSA 224
           V +G A + N  
Sbjct: 260 VAVGTANFVNPF 271


>gi|170758255|ref|YP_001788556.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169405244|gb|ACA53655.1| dihydroorotate oxidase [Clostridium botulinum A3 str. Loch Maree]
          Length = 298

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 71/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + +
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEVVKEVKE 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK          A  + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQKPLMVKLSP------NAEYIVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+  ++ +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPIALRMVYEVCKQV-EIPVIGIGGICNYKDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|124027158|ref|YP_001012478.1| dihydroorotate dehydrogenase 1B [Hyperthermus butylicus DSM 5456]
 gi|123977852|gb|ABM80133.1| Dihydroorotate dehydrogenase [Hyperthermus butylicus DSM 5456]
          Length = 302

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 67/180 (37%), Gaps = 11/180 (6%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + I G+   +    A   E+ G + I +N+ CP A+      G      P +V   +
Sbjct: 94  PVVVSIAGSSEDEFSRLASAAEEAGADAIEVNLSCPHAKGMGREIGI----EPRLVYSVV 149

Query: 109 AAMCKALSIPVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL- 163
           +A      IPV  K     R+         A    V  I       I ++A K +L  L 
Sbjct: 150 SATASVTRIPVIAKLGYVDRLVEAVGKALEAGARAVTLINTLPAMMIDVYAMKPVLGNLV 209

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
                  I  +    +YE+ +E     IG  GG+ED   A + +L     V +G A    
Sbjct: 210 GGLSGPAIHPVAVRAIYEVYREYRIDIIGA-GGVEDWRTAAELVLAGARAVQVGTALVTR 268


>gi|322385154|ref|ZP_08058801.1| dihydroorotate dehydrogenase B [Streptococcus cristatus ATCC 51100]
 gi|321270778|gb|EFX53691.1| dihydroorotate dehydrogenase B [Streptococcus cristatus ATCC 51100]
          Length = 312

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 72/198 (36%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    + KI +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPDLPIIANVAGFSNEEYAYVSGKISQAPNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
             D+  + + A   A  +PV VK    V D      +  + K+ + +G +G+ +      
Sbjct: 149 VTDLAYEAVKAAVAASQVPVYVKLTPSVAD------ITQVAKAAEDAGASGLTMINTLVG 202

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                   R  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKTKRPIIANGTGGMSGPAVFPVALKLIRQVAQ-FTKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFTDPY 279


>gi|291515965|emb|CBK65175.1| dihydroorotate oxidase B, catalytic subunit [Alistipes shahii WAL
           8301]
          Length = 303

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 84/234 (35%), Gaps = 35/234 (14%)

Query: 26  MIVA--------DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNE 76
           MI A        DA++R +   +  F    KP+   I G  + +     + ++       
Sbjct: 67  MINAVGLQNPGIDAVIREELPRLKTFF--RKPVIANISGFSVEEYAYCCERIDRQEQVGL 124

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I +NV CP+ R    SFG C    PD   +   A+    + PV +K    V D      +
Sbjct: 125 IEVNVSCPNVRHGGMSFGTC----PDAAAEVTRAVKAVTTKPVFIKLSPNVTD------I 174

Query: 137 RNLVKSIKKSGVNGI------------WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
             + ++ +++G +GI                R  I   +       +  +   +VY++ +
Sbjct: 175 VAIARACEEAGADGICLINTLLGMRIDIARRRPVIANTMGGFSGAAVFPVALRMVYQVAR 234

Query: 185 ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
               + +   GG+      ++ ++     V +G A   N      + E     +
Sbjct: 235 AC-RIPVMGCGGVTTARDVIEMMMAGASAVQVGAANLVNPYASKEIVEALPGEM 287


>gi|206901164|ref|YP_002251281.1| dihydroorotate dehydrogenase [Dictyoglomus thermophilum H-6-12]
 gi|206740267|gb|ACI19325.1| dihydroorotate dehydrogenase [Dictyoglomus thermophilum H-6-12]
          Length = 306

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/207 (20%), Positives = 79/207 (38%), Gaps = 32/207 (15%)

Query: 40  ILGFSTQEKP--------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +  F  +E P        + + I G    +  E A+ +     + + LN+ CP   V  G
Sbjct: 78  LQKFLEEEMPFLERLSTNVIVSIAGEKKEEYYEIARNLRGCKISGVELNLSCP--NVEGG 135

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
                +  + ++V +    + K +  PV VK      D      +  +VK++K +G   +
Sbjct: 136 GMLFGI--DKEMVKEITKKVVKEIGKPVWVKLTPQAKD------IVEIVKAVKDAGGEAV 187

Query: 152 WIH-----------ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +             RK + K   +      +  L    V+E+ +EN  L I   GG+  
Sbjct: 188 VLFNTFLGLAIDWKKRKPVFKRIFAGYSGPAVKPLVLRYVWEVYEENL-LPIVGCGGIVS 246

Query: 200 MSQALK-ILPSVDGVMIGRAAYKNSAM 225
            S  L+ I      V IG A +++  +
Sbjct: 247 FSDVLEYIFAGASLVQIGSANFRDPWI 273


>gi|167766247|ref|ZP_02438300.1| hypothetical protein CLOSS21_00750 [Clostridium sp. SS2/1]
 gi|317497599|ref|ZP_07955917.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167712074|gb|EDS22653.1| hypothetical protein CLOSS21_00750 [Clostridium sp. SS2/1]
 gi|291559871|emb|CBL38671.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [butyrate-producing bacterium SSC/2]
 gi|316895158|gb|EFV17322.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 300

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 67/188 (35%), Gaps = 24/188 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + + G      +E  + + D   + + +NV CP    +    G     +P  + D   
Sbjct: 95  IIVNVCGKSEKDYLEVVERLADQPVDLLEINVSCP----NVKEGGIAFGQDPKALYDITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKA 158
           A+      P+ +K    V D      +  + K+   +G +            I I  R  
Sbjct: 151 AVKAKAKQPIIMKLSPNVTD------ITEMAKAAVDAGSDALSLINTLTGMKIDIERRDF 204

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           +L           I  +   +VY++     D+ I   GG+     AL+ I+     V +G
Sbjct: 205 VLANKTGGMSGPAIKPVAVRMVYQVANAV-DVPIIGMGGISTAEDALEFIMAGATAVSVG 263

Query: 217 RAAYKNSA 224
            A + N A
Sbjct: 264 TANFINPA 271


>gi|332221979|ref|XP_003260142.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+] isoform 1
           [Nomascus leucogenys]
          Length = 1025

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 68/204 (33%), Gaps = 29/204 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E AK  ED G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELAKKSEDSGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIWIHARKAILKGL------------------SPKDNRKIPNLDYDIVYEIK 183
           + K+ G +G+      + L GL                         I  +    V  I 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKSDGTPWPAVGIAKRTTYGGVSGTAIRPIALRAVTSIA 782

Query: 184 KENPDLFIGLNGGLEDMSQALKIL 207
           +  P   I   GG++     L+ L
Sbjct: 783 RALPGFPILATGGIDSAESGLQFL 806


>gi|313906445|ref|ZP_07839781.1| dihydroorotate dehydrogenase family protein [Eubacterium
           cellulosolvens 6]
 gi|313468712|gb|EFR64078.1| dihydroorotate dehydrogenase family protein [Eubacterium
           cellulosolvens 6]
          Length = 304

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 32/190 (16%), Positives = 70/190 (36%), Gaps = 24/190 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +E    + D   + + +N+ CP    +    G     +P +   
Sbjct: 96  DTKIIVNVCGHSEEEYLEVVDRLADEPVDMLEINISCP----NVKEGGIAFGTDPKVAEQ 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              A+      PV +K    V D      +  + ++++  G + I            ++ 
Sbjct: 152 ITKAVKTHAKQPVIMKLSPNVTD------ITEMARAVEAGGADVISLINTLTGMKIDVNR 205

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           +  +   +VY++ +      IG+ GG+     AL+ IL     V
Sbjct: 206 RKFVLANKTGGMSGPAVKPIAVRMVYQVAQAVKVPIIGM-GGIATAEDALEFILAGATAV 264

Query: 214 MIGRAAYKNS 223
            +G A + + 
Sbjct: 265 SVGTANFIDP 274


>gi|109011616|ref|XP_001106007.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+] [Macaca mulatta]
          Length = 1025

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 68/204 (33%), Gaps = 29/204 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E AK  ED G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELAKKSEDSGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIWIHARKAILKGL------------------SPKDNRKIPNLDYDIVYEIK 183
           + K+ G +G+      + L GL                         I  +    V  I 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKSDGTPWPAVGIAKRTTYGGVSGTAIRPIALRAVTSIA 782

Query: 184 KENPDLFIGLNGGLEDMSQALKIL 207
           +  P   I   GG++     L+ L
Sbjct: 783 RALPGFPILATGGIDSAESGLQFL 806


>gi|77918900|ref|YP_356715.1| putative oxidoreductase [Pelobacter carbinolicus DSM 2380]
 gi|77544983|gb|ABA88545.1| dihydroorotate oxidase B, catalytic subunit [Pelobacter
           carbinolicus DSM 2380]
          Length = 314

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 73/190 (38%), Gaps = 25/190 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+     G  + +  E A+ + D      + LN+ CP   V +G        +P    +
Sbjct: 104 TPVIANFFGNSLEEYGEVARRLSDLSEVAAVELNISCP--NVKKGGIVFG--TDPQAAAE 159

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
            +  + + LS P+ VK    V D         + ++++++G + I            +H 
Sbjct: 160 VVTLVRRHLSKPLIVKLTPNVTDITV------MARAVEEAGADAICCINTLTGMAVDVHR 213

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
           R+  I  G        I  +   +VY++ +   ++ +   GG+     AL+ L      V
Sbjct: 214 RQLRIANGTGGLSGPAIRPVAVRMVYQVVQAV-NVPVIGVGGITCAEDALEFLIVGARAV 272

Query: 214 MIGRAAYKNS 223
            +G A + + 
Sbjct: 273 QVGTANFVDP 282


>gi|134299542|ref|YP_001113038.1| dihydroorotate dehydrogenase 1B [Desulfotomaculum reducens MI-1]
 gi|189038438|sp|A4J560|PYRD_DESRM RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|134052242|gb|ABO50213.1| dihydroorotate oxidase B, catalytic subunit [Desulfotomaculum
           reducens MI-1]
          Length = 304

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 77/202 (38%), Gaps = 25/202 (12%)

Query: 47  EKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + I G    +  + AA++ E  G   + +N+ CP   V +G        +     
Sbjct: 94  QTNVIVNISGNTAEEYGQLAARLDEADGIAALEVNISCP--NVKKGGMAFG--GDFRTAA 149

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           +    +  + ++PV VK    V D      +  + ++++ +G +            I + 
Sbjct: 150 EVTKVVKNSTALPVIVKLSPNVTD------IAEIARAVEGAGADGLSVINTLLGMAIDVR 203

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L   +       +  +    V+++ K    + I   GG+ + + AL+ IL     
Sbjct: 204 KRKPVLGNTMGGLSGPAVKPVALRAVWQVYKAV-HIPIIGMGGIMNATDALEFILAGAQA 262

Query: 213 VMIGRAAYKNSAMLTTVDEYFS 234
           V +G A + N      + +   
Sbjct: 263 VSVGTANFVNPYATKEIIQGME 284


>gi|309388710|gb|ADO76590.1| dihydroorotate oxidase B, catalytic subunit [Halanaerobium
           praevalens DSM 2228]
          Length = 411

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 39/211 (18%), Positives = 78/211 (36%), Gaps = 23/211 (10%)

Query: 25  EMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    +         L      K +   I G +  +  E A++V + G + I  N  C
Sbjct: 78  EQISDKPLAENLATIKKLKQDYPHKIIIASIMGENEKEWAELAEMVTEAGADLIECNFSC 137

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------P 132
           P   +  G+ G+ +  NP++V    AA+ +   +PV  K    + +              
Sbjct: 138 PQ--MTSGAMGSDVGQNPELVKKYSAAVSQVTDLPVIAKMTPNIGNMEIPAIAAVNGGAD 195

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
           A++  N +KS+ +  ++      +      +S    + +  +    + E+K+  +  D+ 
Sbjct: 196 ALSAINTIKSLTEIDLDDFTPMPKVNGKSSISGYSGKAVKPIALRFIAELKQHPQLKDVP 255

Query: 191 IGLNGGLEDMSQA-------LKILPSVDGVM 214
           +   GG+E    A        + L     VM
Sbjct: 256 LSGMGGIETWEDAAEFLALGCRNLQMTTSVM 286


>gi|283795658|ref|ZP_06344811.1| dihydroorotate oxidase [Clostridium sp. M62/1]
 gi|291077330|gb|EFE14694.1| dihydroorotate oxidase [Clostridium sp. M62/1]
          Length = 300

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 76/230 (33%), Gaps = 35/230 (15%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQI--------GGADISKLVEAAKIVEDFGYNEI 77
           MI A  +     +    F+ ++ P   Q          G      ++  + + D   + +
Sbjct: 66  MINAVGLQNPGFQ---VFAERDIPYLKQFDTKIIVNVCGKTTEDYIDVVEKLSDQPVDML 122

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            +N+ CP    +    G     +P  V      + +    PV +K    V D        
Sbjct: 123 EINISCP----NVKEGGIAFGQDPKAVEAITREVKRHAKQPVIMKLSPNVTDITV----- 173

Query: 138 NLVKSIKKSGVNG-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            + K+ +  G +            I IH R  A+           I  +   +VY++   
Sbjct: 174 -MAKAAEAGGADVLSLINTITGMKIDIHRRTFAVANKTGGLSGPAIKPVAVRMVYQVANA 232

Query: 186 NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                IG+ GG+     A++ ++     V +G A + N  +   + +   
Sbjct: 233 VSLPVIGM-GGIMCADDAIEFMMAGATAVAVGTANFHNPYVTEEIVKGIE 281


>gi|149177305|ref|ZP_01855910.1| dihydroorotate dehydrogenase [Planctomyces maris DSM 8797]
 gi|148843830|gb|EDL58188.1| dihydroorotate dehydrogenase [Planctomyces maris DSM 8797]
          Length = 317

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/218 (16%), Positives = 78/218 (35%), Gaps = 27/218 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGA 95
           K +   S+ E  L + I G  I ++   A  ++ +      + LN+ CP+     G    
Sbjct: 95  KQLNYLSSLETALIVNIAGRSIDEMAVMASRLDQYSDQITALELNISCPN---VSGGVDY 151

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-- 153
                P++    +  + ++  +P+  K    V       ++  + ++    G + + +  
Sbjct: 152 G--TRPEMTEKMLKQVTESCQLPIIAKLTPNV------TSVVEIAQAASAGGADAVSLIN 203

Query: 154 ---------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                      RK IL G         I  +   +V ++ +   D+ I   GG+ ++   
Sbjct: 204 TVQGTAIDWRRRKPILGGIFGGLSGPAIKPVALRVVCQVARAV-DVPIIGVGGIANIDDV 262

Query: 204 LK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           ++ I+     V IG A + N  +   +       L   
Sbjct: 263 MEFIVAGASAVQIGTANFYNPGLAAQLVSELEGILVSE 300


>gi|194211086|ref|XP_001490668.2| PREDICTED: dihydropyrimidine dehydrogenase [Equus caballus]
          Length = 1080

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 66/204 (32%), Gaps = 29/204 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E AK  E  G + + LN+
Sbjct: 666 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELAKQAEASGADALELNL 724

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ +P   K    V D      + ++ +
Sbjct: 725 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVRVPFFAKLTPNVTD------IVSIAR 777

Query: 142 SIKKSGVNGIW------------IHARKAILKGLSPK------DNRKIPNLDYDIVYEIK 183
           + K+ G +G+                      G+  +          I  +    V  I 
Sbjct: 778 AAKEGGADGVTATNTVSGLMELKADGTPWPAVGIGKRTTYGGVSGTAIRPIALRAVTSIA 837

Query: 184 KENPDLFIGLNGGLEDMSQALKIL 207
           +  P   I   GG++     L+ L
Sbjct: 838 RALPGFPILATGGIDSAESGLQFL 861


>gi|302925557|ref|XP_003054119.1| hypothetical protein NECHADRAFT_74526 [Nectria haematococca mpVI
           77-13-4]
 gi|256735060|gb|EEU48406.1| hypothetical protein NECHADRAFT_74526 [Nectria haematococca mpVI
           77-13-4]
          Length = 165

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 42/113 (37%), Gaps = 6/113 (5%)

Query: 7   RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP----LALQIGGADISKL 62
             +R          L +T M++A    R         +   KP      +Q G     +L
Sbjct: 34  LAFRQTVHKY-GVDLCWTPMVLAKEFNRNSFARDSDLTISSKPNQPATIVQFGANVPLEL 92

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
             A+ +V       ++LN GCP +       GA LM + ++V D +    + L
Sbjct: 93  ARASALVAP-DVQGVDLNCGCPQSWACAEKLGAALMNHRELVRDMVVETRQRL 144


>gi|52785533|ref|YP_091362.1| dihydroorotate dehydrogenase 1B [Bacillus licheniformis ATCC 14580]
 gi|319646065|ref|ZP_08000295.1| PyrD protein [Bacillus sp. BT1B_CT2]
 gi|52348035|gb|AAU40669.1| PyrD [Bacillus licheniformis ATCC 14580]
 gi|317391815|gb|EFV72612.1| PyrD protein [Bacillus sp. BT1B_CT2]
          Length = 312

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 78/192 (40%), Gaps = 25/192 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+ I   VE A+ +      + + LN+ CP    +  + G      P++ G
Sbjct: 92  DTPIIANVAGSQIEDYVEVAEEISKAPNVHALELNISCP----NVKTGGIAFGTQPEMAG 147

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +   A+ +  S+PV VK    V        + ++  +I+++G +G+ +            
Sbjct: 148 ELTKAVKEVASVPVYVKLSPNV------ANITDIALAIEEAGADGLTMINTLIGMRLDLK 201

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             +  +           +  +   +V+E+ ++     IG+ GG++     L+ +L     
Sbjct: 202 TGKPILANKTGGLSGPAVKPVAIRMVHEVSQKVSIPIIGM-GGVQSAEDVLEFLLAGASA 260

Query: 213 VMIGRAAYKNSA 224
           V +G A + N  
Sbjct: 261 VAVGTANFVNPF 272


>gi|217967954|ref|YP_002353460.1| dihydroorotate dehydrogenase family protein [Dictyoglomus turgidum
           DSM 6724]
 gi|217337053|gb|ACK42846.1| dihydroorotate dehydrogenase family protein [Dictyoglomus turgidum
           DSM 6724]
          Length = 306

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 84/222 (37%), Gaps = 36/222 (16%)

Query: 40  ILGFSTQEKP--------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +  F  +E P        + + I G    +  E A+++ +   + I +N+ CP   V  G
Sbjct: 78  LDKFLEEEIPFLEKLNTNVIVSIAGEKKEEYYEIARVLRECKISGIEINLSCP--NVEGG 135

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
                +  + ++V +    +   +  PV VK      D      +  + K+++ +G   +
Sbjct: 136 GMLFGI--DSEMVKEITKNVVNIVDKPVWVKLTPQAKD------IIGVAKAVRSAGGEAV 187

Query: 152 WIH-----------ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +             R+ + K   +      I  +    V+E+ +EN  L I   GG+ +
Sbjct: 188 VVFNTFLGLAIDWKKREPVFKRIFAGYSGPAIKPIVLRYVWELYEEN-ILPIVGCGGIVN 246

Query: 200 MSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNP 236
            +  L+ I      V IG A +++      ++  V  YF   
Sbjct: 247 FTDVLEYIFAGASLVQIGSANFRDPWIGEKIVKEVQNYFKEE 288


>gi|313889165|ref|ZP_07822821.1| dihydroorotate oxidase, catalytic subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844905|gb|EFR32310.1| dihydroorotate oxidase, catalytic subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 301

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 80/211 (37%), Gaps = 28/211 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
             +     + + +GG  I + +E+A+I+ D+ +  I LN+ CP   V EG     +  + 
Sbjct: 89  DMNKLGTEVFVNLGGNTIEEYIESAEILNDYDFAAIELNISCP--NVKEGGMAFGM--DK 144

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-------- 153
           D     +  + K  +  V VK      D      +  + K+++  G  G+ +        
Sbjct: 145 DSAAKVVREVMKVTNKKVFVKLSPNAGD------IVGIAKAVEAEGATGLSLINTILGMA 198

Query: 154 ----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
                         +      +  +   I++++ K N D+ I   GG+ +    L+ ++ 
Sbjct: 199 IDLDREEIPFDNTYAGLSGPAVKPIALRILHQVAK-NVDIPIIGMGGISNYRDVLEFLMA 257

Query: 209 SVDGVMIGRAAYKNSA----MLTTVDEYFSN 235
               V +G   + N      ++T ++ Y   
Sbjct: 258 GATAVEVGTYNFMNPNGGAEIITDLERYLEE 288


>gi|153955965|ref|YP_001396730.1| PyrD2 [Clostridium kluyveri DSM 555]
 gi|219856307|ref|YP_002473429.1| hypothetical protein CKR_2964 [Clostridium kluyveri NBRC 12016]
 gi|146348823|gb|EDK35359.1| PyrD2 [Clostridium kluyveri DSM 555]
 gi|219570031|dbj|BAH08015.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 296

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 78/204 (38%), Gaps = 28/204 (13%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG    + ++  + + D   + I LN+ CP   V  G     +    ++ G  + ++ +
Sbjct: 96  LGGNTEEEYIKGVEKLNDSIVDIIELNISCP--NVKSGGMAFGI--KSEVAGKVVDSVKR 151

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++  +  ++G + +            I  RKA+   
Sbjct: 152 VCRKPLMVKLSPNAED------IVDMAYTCCQAGADALSLVNTFKAMAVDIENRKAVFDN 205

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K   D+ +   GG+     AL+ I+     + +G A +
Sbjct: 206 ITAGLSGPAIKPIALRMVYEVSK-VVDIPVVGIGGICSWQDALEFIMAGASAIQVGTANF 264

Query: 221 KNS----AMLTTVDEYFSNPLTGS 240
                   ++  ++EY       S
Sbjct: 265 IKPDICLDIIKGIEEYMEKEKIKS 288


>gi|323698344|ref|ZP_08110256.1| dihydroorotate dehydrogenase family protein [Desulfovibrio sp.
           ND132]
 gi|323458276|gb|EGB14141.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           desulfuricans ND132]
          Length = 305

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/217 (17%), Positives = 75/217 (34%), Gaps = 27/217 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVH 89
            +     K +     +E  +   +   D ++  E AA +  + G   + +NV CP    +
Sbjct: 76  GVEHFVTKALPNLPWREVAVIANLYACDAAEFGELAAVLAGEEGVAALEVNVSCP----N 131

Query: 90  EGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
               G     +P  +     A+ K A + PV VK    V D      +    ++ +  G 
Sbjct: 132 VKEGGVAFGQDPAQITRVTEAVKKNAGNKPVMVKLSPNVTD------ITTCARAAEAGGA 185

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + + +            + R  I   ++      I  +    V+++     D+ +   GG
Sbjct: 186 DSLSLINTLSGMAVDIRNRRPRIANVIAGLSGPAIKPVALRCVHQVV-HAVDIPVVGIGG 244

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAM-LTTVDE 231
           +     AL+ +L     V +G A +          DE
Sbjct: 245 ISSAEDALEFLLVGAQAVQVGTANFLRPDFAFGLADE 281


>gi|306831239|ref|ZP_07464399.1| dihydroorotate dehydrogenase B [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|304426475|gb|EFM29587.1| dihydroorotate dehydrogenase B [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
          Length = 314

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 75/198 (37%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    ++ +        I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPDLPIIANVAGFSNDEYAYVSEKISKAPNVKAIELNISCP--NVDHGNHGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +   +PV VK    V D      +  + K+++++G  G  +      
Sbjct: 149 VPELAYAAVKASVEHSDVPVYVKLTPSVAD------ITTVAKAVEEAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ + + DL I   GG++    A++++
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-STDLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFADPY 279


>gi|268319399|ref|YP_003293055.1| hypothetical protein FI9785_918 [Lactobacillus johnsonii FI9785]
 gi|262397774|emb|CAX66788.1| pyrD [Lactobacillus johnsonii FI9785]
          Length = 307

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 45/188 (23%), Positives = 81/188 (43%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG D +  +E AK + D G  N + +NV CP+      SFG      PD+V + 
Sbjct: 98  PIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCPNVNQGGMSFGVY----PDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              +   + IP+ VK    V D      +  + K+ +  G +G           I +  R
Sbjct: 154 TKKIKSVVKIPIYVKLTPNVTD------ITQIAKAAENGGADGLSLINTLLGMEIDVETR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L   +       +  +   +V+++ +E+  L I   GG+      ++ IL   + V 
Sbjct: 208 KPVLGHNIGGLSGEAVKPIAIRMVHQV-RESTTLPIIGMGGISSAKDVIEFILAGANAVA 266

Query: 215 IGRAAYKN 222
           +G A +K+
Sbjct: 267 VGTAHFKD 274


>gi|328949335|ref|YP_004366672.1| dihydroorotate dehydrogenase family protein [Treponema
           succinifaciens DSM 2489]
 gi|328449659|gb|AEB15375.1| dihydroorotate dehydrogenase family protein [Treponema
           succinifaciens DSM 2489]
          Length = 591

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 36/218 (16%), Positives = 81/218 (37%), Gaps = 24/218 (11%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
            ++ +   +L   T        + G D+   ++ A++++      I LN+ CP    +  
Sbjct: 363 FIQNELPEMLKLDTV---SIANLAGHDLDSYIKGAELLDKTPVPAIELNISCP----NVK 415

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA--------VALRNLVKSI 143
           + G    +NP+    C++A+ KA S P+ VK      D +              +L+ +I
Sbjct: 416 AGGMAWGINPEAAFTCVSAVRKATSKPLIVKLSPNAPDLVSVALACIKAGANALSLINTI 475

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD------LFIGLNGGL 197
           +   ++      R       +      +  +   +VY++ K          + +   GG+
Sbjct: 476 QAVAID--IESGRPVFDNIKAGLCGPAVKPIALRMVYDVVKAVNSLPKEQQIPVIGLGGI 533

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                A++ I+     + +G A + N   +  + E   
Sbjct: 534 SKWQDAVEFIMAGASAIQVGTATFSNPKTMIEIIEGLK 571


>gi|47086253|ref|NP_998058.1| dihydropyrimidine dehydrogenase [NADP+] [Danio rerio]
 gi|82185925|sp|Q6NYG8|DPYD_DANRE RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|42793999|gb|AAH66602.1| Dihydropyrimidine dehydrogenase [Danio rerio]
          Length = 1022

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 55/163 (33%), Gaps = 31/163 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+ ++   + + LN+ CP     E   G     +P++V +    + KA SIP   K   
Sbjct: 654 AKMAQESQADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRKATSIPFFAKLTP 712

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLS 164
            V        + ++  +  + G +G+                          +    G+S
Sbjct: 713 NV------TNIVDIATAAYEGGADGVTATNTVSGLMALKADATPWPGIGRGARTTYGGVS 766

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               R I       V  I +  P   I   GG++     L+ L
Sbjct: 767 GNAIRPIA---LRAVSAIARALPGFPILATGGIDSAESGLQFL 806


>gi|289450712|ref|YP_003475036.1| dihydroorotate oxidase catalytic subunit [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289185259|gb|ADC91684.1| dihydroorotate oxidase, catalytic subunit [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 316

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 39/195 (20%), Positives = 72/195 (36%), Gaps = 25/195 (12%)

Query: 49  PLALQIGGADI-SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL + I G      L  AA++ E  G   + +N+ CP    +    G     +P +V   
Sbjct: 106 PLLVNIAGNSESEYLQVAAEMSECPGVGALEVNISCP----NVKQGGITFGQDPAMVERL 161

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
            + +      PV +K    V D         L K+ +  G +G+            +   
Sbjct: 162 TSKIKTVSKCPVYMKLSPNVTDITV------LAKAAEAGGADGLSLINTLLGMRLDLKTG 215

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           K +L  G        I  +   ++Y++ +      IG+ GG+     AL+++      V 
Sbjct: 216 KPVLANGTGGLSGPAIKPVAVRMIYQVYRAVKIPLIGM-GGVMTAEDALEMMYAGAGAVA 274

Query: 215 IGRAAYKNSAMLTTV 229
           +G A + N  +   +
Sbjct: 275 VGTANFVNPFVCPEI 289


>gi|312127562|ref|YP_003992436.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311777581|gb|ADQ07067.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 300

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 82/221 (37%), Gaps = 28/221 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +A +  +   + GF T+   +   I G    + VE  +I+     + I +N+ CP    +
Sbjct: 78  EAFINDELPFLKGFDTK---IIANINGFTKEEFVELTRILTSL-VDMIEVNLSCP----N 129

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G     +P  V +   ++    S P+ VK    V D      +  L  + + +G +
Sbjct: 130 VKEGGMVFGKDPKKVYEITKSVKNVASCPIIVKLTPNVTD------ITQLAIAAEDAGAD 183

Query: 150 GIW-----------IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            I  RK ++K ++       I  +   +VYE  K+   + I   GG+
Sbjct: 184 AISLINTVSAMAIDIETRKPLIKMVTGGLSGPAIKPIAVRMVYECFKKV-RIPIIGMGGI 242

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            +   A++        + IG   + N   +  + E     L
Sbjct: 243 MNYKDAIEFFIAGATAIQIGTVNFINPKAVCEIKEGIEAYL 283


>gi|118094317|ref|XP_426639.2| PREDICTED: similar to dihydropyrimidine dehydrogenase [Gallus
           gallus]
          Length = 1178

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 56/159 (35%), Gaps = 25/159 (15%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K+ E  G + + LN+ CP     E   G     +P++V +    + +A+ IP   K    
Sbjct: 808 KMAEAAGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPN 866

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------------SPKDN 168
           V D      + N+  + ++ G +G+      + L GL                       
Sbjct: 867 VTD------IVNIAVAAQEGGADGVTATNTVSGLMGLKADGTPWPAVGAGLRTTYGGVSG 920

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             I  +    V  I +  P   I   GG++     L+ L
Sbjct: 921 NAIRPIALRAVSAIARALPGFPILATGGIDSAESGLQFL 959


>gi|295108552|emb|CBL22505.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Ruminococcus obeum A2-162]
          Length = 301

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 68/201 (33%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + + D   + + +NV CP    +    G     +P  +  
Sbjct: 93  DTKIIVNVCGKSTEDYCEVVERLADEPVDLLEINVSCP----NVKEGGIAFGQDPHALEA 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
               + K    P+ +K    V D      +  + K+ +  G +            I I+ 
Sbjct: 149 ITKEVKKYAKQPIIMKLSPNVTD------ITEMAKAAEAGGADILSLINTLTGMKIDIYR 202

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R  A+           +  +   +VY++ +    L I   GG+     AL+ I+     V
Sbjct: 203 RTFALANKTGGMSGPAVKPVAVRMVYQVAQAV-KLPIIGMGGIATAEDALEFIMAGATAV 261

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G A + N      + E   
Sbjct: 262 SVGTANFFNPYATVEIAEGIE 282


>gi|170755388|ref|YP_001782875.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum B1 str.
           Okra]
 gi|169120600|gb|ACA44436.1| dihydroorotate oxidase [Clostridium botulinum B1 str. Okra]
          Length = 298

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 72/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + +
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEVVKEVKE 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQKPLMVKLSPNAED------IVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+  ++ +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPMALRMVYEVCKQV-EIPVIGIGGICNYKDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|296127420|ref|YP_003634672.1| dihydroorotate dehydrogenase family protein [Brachyspira murdochii
           DSM 12563]
 gi|296019236|gb|ADG72473.1| dihydroorotate dehydrogenase family protein [Brachyspira murdochii
           DSM 12563]
          Length = 303

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/206 (21%), Positives = 82/206 (39%), Gaps = 30/206 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ L I GAD  + V+ A+I  +    + + LN+ CP    +  + G     + +     
Sbjct: 94  PIILNINGADTDEYVKVAEIANEIERVDFVELNISCP----NVKNGGMAFGASCESAESI 149

Query: 108 IAAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
             A+ K L+  P+ VK    V D      + ++ KS++ +G +            I    
Sbjct: 150 TKAVKKVLNKKPLIVKLSPNVTD------IASIAKSVEYAGADSVSLVNTFLAMKIDTKT 203

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           +K +L           I  +   +VY++ K      +G+ GG+   + AL+ I+     V
Sbjct: 204 KKPLLGNIFGGLSGSCIRPIAVRMVYQVYKAVKVPIVGM-GGISSYNDALEFIIAGASLV 262

Query: 214 MIGRAAYKNSAM----LTTVDEYFSN 235
            IG   + N  +    +  +D Y   
Sbjct: 263 SIGAGIFSNPTLPIEVINGIDNYLKE 288


>gi|311110625|ref|ZP_07712022.1| dihydroorotate oxidase [Lactobacillus gasseri MV-22]
 gi|311065779|gb|EFQ46119.1| dihydroorotate oxidase [Lactobacillus gasseri MV-22]
          Length = 307

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/207 (23%), Positives = 91/207 (43%), Gaps = 26/207 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARV 88
           DA++    K  L  S  + P+   +GG D +  VE AK + D G  N + +NV CP   V
Sbjct: 80  DAVIEDKLKP-LRQSYPDLPIMASVGGEDEAGYVEVAKKLSDSGLVNALEINVSCP--NV 136

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           ++G       ++PD+V      +    ++P+ +K    V D      +  + K+ +K G 
Sbjct: 137 NQGGMSFG--VHPDVVESLTKKIKAVTNVPIYLKLTPNVTD------ITQISKAAEKGGA 188

Query: 149 NG-----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G           I I  RK +L   +       +  +   +V+++ +++  L I   GG
Sbjct: 189 DGLSLINTLLGMDIDIKTRKPVLGHNIGGLSGEAVKPVALRMVHQV-RQSTSLPIIGMGG 247

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKN 222
           +      +K +L   + V +G A +K+
Sbjct: 248 ISSAQDVIKFMLAGANAVAVGTAHFKD 274


>gi|300768578|ref|ZP_07078477.1| dihydroorotate oxidase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300493885|gb|EFK29054.1| dihydroorotate oxidase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 305

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 76/200 (38%), Gaps = 19/200 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + GA   + V  A K+        + +N+ CP    +    G     
Sbjct: 89  LATHYPDLPIIGSVAGASFDEYVAVARKMASAPNVKLLEINISCP----NVDHGGLAFGT 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP--------AVALRNLVKSIKKSGVNGI 151
           +P  V     A+  A+  PV +K    V D +P          A   ++ ++   G++  
Sbjct: 145 DPATVTALTKAIVAAVDKPVFMKLTPNVTDIVPIALAAEAGGAAGLTMINTLTGMGID-- 202

Query: 152 WIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            +  R+ IL  G      + I  L   +++++++    L I   GG+      L+  L  
Sbjct: 203 -LATRQPILAHGTGGLSGKAIHPLAVRMIHDVRQHT-KLPIIGVGGVFTPVDVLEFYLAG 260

Query: 210 VDGVMIGRAAYKNSAMLTTV 229
            + V +G A Y +    T +
Sbjct: 261 ANAVQVGAATYGHPTACTDI 280


>gi|301758641|ref|XP_002915175.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+]-like [Ailuropoda
           melanoleuca]
          Length = 1026

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 70/207 (33%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA--DISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I  +      + E +K+ E  G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYSKNDWM-ELSKMAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         ++    G+S    R I       V 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGFGKRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 780 SIARALPGFPILATGGIDSAESGLQFL 806


>gi|281349697|gb|EFB25281.1| hypothetical protein PANDA_003122 [Ailuropoda melanoleuca]
          Length = 1009

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 70/207 (33%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA--DISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I  +      + E +K+ E  G + + LN+
Sbjct: 598 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYSKNDWM-ELSKMAEASGADALELNL 656

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 657 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 709

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         ++    G+S    R I       V 
Sbjct: 710 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGFGKRTTYGGVSGTAIRPIA---LRAVT 766

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 767 SIARALPGFPILATGGIDSAESGLQFL 793


>gi|167752767|ref|ZP_02424894.1| hypothetical protein ALIPUT_01028 [Alistipes putredinis DSM 17216]
 gi|167659836|gb|EDS03966.1| hypothetical protein ALIPUT_01028 [Alistipes putredinis DSM 17216]
          Length = 310

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 76/203 (37%), Gaps = 31/203 (15%)

Query: 48  KPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           KP+   I G  + +     + ++ +     I +NV CP    +    G     +P+   +
Sbjct: 102 KPVIANISGFSVEEYAYCCERIDKEEQVGLIEVNVSCP----NVRHGGMSFGTSPEAAAE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              A+    + PV +K    V D      +  + ++ +++G +GI            +  
Sbjct: 158 VTRAVKAVTTKPVYIKLSPNVTD------IVAIARACEEAGADGICLINTMLGMRIDVKC 211

Query: 156 RKA----ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           RK     ++ G S      I  +   +VY++ +    + +   GG+E     ++ ++   
Sbjct: 212 RKPIIANVMGGFSGA---AIFPVAVRMVYQVARAC-RIPVMGCGGVETAHDVIEMMMAGA 267

Query: 211 DGVMIGRAAYKNSAMLTTVDEYF 233
             V +G A  +N      + E  
Sbjct: 268 TAVQVGAANLRNPYACKEIVEAL 290


>gi|1172785|sp|P46539|PYRD_BACCL RecName: Full=Dihydroorotate dehydrogenase, catalytic subunit;
           AltName: Full=DHOdehase; Short=DHOD; Short=DHODase;
           AltName: Full=Dihydroorotate oxidase
 gi|312445|emb|CAA51741.1| dihydroorotate oxidase [Bacillus caldolyticus]
          Length = 313

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 78/197 (39%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I G+ + + VE A+ +      + + LN+ CP   V +G         PD+  
Sbjct: 93  DVPIIANIAGSTVEEYVEVAEAISKAPNVHALELNISCP--NVKKGGIAFG--TVPDVAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    + +  ++PV V     V D      +  + K+I+++G +G+ +            
Sbjct: 149 ELTRLVKEVAAVPVYVNVSPNVTD------IVAMAKAIEQAGADGLTMINTLVGMRIDVK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             R  +  G        +  +   ++YE+ +      IG+ GG++     L+        
Sbjct: 203 TGRPILANGTGGLSGPAVKPIAIRMIYEVSQAVSIPIIGM-GGIQTAEDVLEFFYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V +G A + +  +  T+
Sbjct: 262 VAVGTANFVDPFVCPTI 278


>gi|295695968|ref|YP_003589206.1| dihydroorotate dehydrogenase family protein [Bacillus tusciae DSM
           2912]
 gi|295411570|gb|ADG06062.1| dihydroorotate dehydrogenase family protein [Bacillus tusciae DSM
           2912]
          Length = 309

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 75/189 (39%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + + G+ + + VE A+ +        + LN+ CP+ R     FG     +PD+  + 
Sbjct: 97  PVIVNVAGSVVEEYVETARRLSGSRDVAALELNISCPNVRCGGMHFGT----DPDMAAEV 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
            AA+     +PV VK    V D      +  L ++++++G +G+ +              
Sbjct: 153 TAAVKAVSRVPVFVKLSPNVTD------IVALAQAVERAGADGLSMINTLVGMRIDIERR 206

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           R  +           I  +   ++YE+ +    + I   GG+     A++  +     V 
Sbjct: 207 RPILANFFGGLSGPAIKPVALRMIYEVSR-VVRIPIIGMGGITSGEDAVEFFMAGASAVA 265

Query: 215 IGRAAYKNS 223
           +G A +   
Sbjct: 266 VGTANFIKP 274


>gi|301608531|ref|XP_002933845.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+] [Xenopus
           (Silurana) tropicalis]
          Length = 898

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 55/163 (33%), Gaps = 31/163 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A + E  G + + LN+ CP     E   G     +P++V +    + +A+ IP   K   
Sbjct: 527 ALMAEASGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVKIPFFAKLTP 585

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLS 164
            V D      +  +  + ++ G +G+                          +    G+S
Sbjct: 586 NVTD------VVKIAMAAQEGGADGVTATNTVSGLMGLKADATPWPAVGRGSRTTYGGVS 639

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               R I       V  I +  P   I   GG++     L+ L
Sbjct: 640 GNAIRPIA---LRAVSAIARALPGFPILATGGIDSAESGLQFL 679


>gi|313891606|ref|ZP_07825213.1| dihydroorotate oxidase, catalytic subunit [Dialister
           microaerophilus UPII 345-E]
 gi|313119884|gb|EFR43069.1| dihydroorotate oxidase, catalytic subunit [Dialister
           microaerophilus UPII 345-E]
          Length = 301

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 78/206 (37%), Gaps = 25/206 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   I G    +  + A+ +   G + + +N+ CP+ +      G     NP    +
Sbjct: 92  DVPVIANIFGKTKEEYGKVARALTVEGVSALEVNISCPNIK----EGGVAFGTNPLSAAE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
               + ++  +PV +K    V D      +  + K+++ +G + I            +  
Sbjct: 148 ITKEVKRSTHLPVIMKLSPNVTD------IAAIAKAVENAGADAISLINTLLGISIDLRT 201

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
           R+ IL           I  +   +V++++    ++ I   GG+     A +      D V
Sbjct: 202 RRPILGNITGGLSGPAIKPVALRMVWQVRNAV-NIPICGMGGIMTGKDAAEFFIAGADIV 260

Query: 214 MIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +G A   N  A++   DE  +   +
Sbjct: 261 QVGTANLINPDAIMRITDELNAWGDS 286


>gi|291541385|emb|CBL14495.1| dihydroorotate oxidase B, catalytic subunit [Ruminococcus bromii
           L2-63]
          Length = 303

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/188 (17%), Positives = 66/188 (35%), Gaps = 24/188 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G         A+ + +   + I LN+ CP+ +     FG       + VG   A
Sbjct: 96  IIANIAGNTPEDYCAMAEKLSETDVDMIELNISCPNVKSGGVQFGTSC----ESVGAITA 151

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARK 157
           A+ K    P+ VK    V D      + ++ +S + +G + I +              R 
Sbjct: 152 AVKKYCKKPLIVKLSPNVTD------IASIAQSAEANGADAISMINTLTGMRIDINSRRP 205

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
            I           I  +   +V+++      + I   GG+     A++ ++     + IG
Sbjct: 206 IIRNNTGGMSGPAIFPVAVRMVWQVANAV-KIPIIGMGGISSWQDAIEMMMAGATALQIG 264

Query: 217 RAAYKNSA 224
              + +  
Sbjct: 265 TVLFTDPY 272


>gi|323650140|gb|ADX97156.1| dihydropyrimidine dehydrogenase [NADP+] [Perca flavescens]
          Length = 619

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/160 (21%), Positives = 56/160 (35%), Gaps = 25/160 (15%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+ E+ G + + LN+ CP     E   G     +P +V +    +  A+SIP   K   
Sbjct: 250 AKMAEESGADALELNLSCPHGM-GERGMGLACGQDPVLVRNICRWVRAAISIPFFAKLTP 308

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------------SPKD 167
            V        + ++ K+  + G +G+      + L GL                      
Sbjct: 309 NV------TNIVDIAKAAHEGGADGVTATNTVSGLMGLKADGSPWPSVGTDKRTTYGGVS 362

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              I  +    V  I K  P   I   GG++     L+ L
Sbjct: 363 GNAIRPIALRAVSAIAKAIPGFPILATGGIDSAESGLQFL 402


>gi|187776845|ref|ZP_02993318.1| hypothetical protein CLOSPO_00384 [Clostridium sporogenes ATCC
           15579]
 gi|187775504|gb|EDU39306.1| hypothetical protein CLOSPO_00384 [Clostridium sporogenes ATCC
           15579]
          Length = 298

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 73/195 (37%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + +
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEVVKKVKE 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G N I            I  +  + + 
Sbjct: 154 ICQKPLIVKLSPNAED------IVDMAIKCEKAGANAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 L-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           + +      I  +   +VYE+ K+   + +   GG+ +    ++ I+     V IG A +
Sbjct: 208 VTAGLSGPCIKPIALRMVYEVCKQV-KIPVIGIGGICNYKDVIEFIMAGATAVQIGTANF 266

Query: 221 KNSAMLTTVDEYFSN 235
            +      + E   N
Sbjct: 267 MHPYSALDIIEELEN 281


>gi|122891156|emb|CAM14145.1| dihydropyrimidine dehydrogenase [Danio rerio]
 gi|148725195|emb|CAN88518.1| dihydropyrimidine dehydrogenase [Danio rerio]
          Length = 738

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 55/163 (33%), Gaps = 31/163 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+ ++   + + LN+ CP     E   G     +P++V +    + KA SIP   K   
Sbjct: 370 AKMAQESQADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRKATSIPFFAKLTP 428

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLS 164
            V        + ++  +  + G +G+                          +    G+S
Sbjct: 429 NV------TNIVDIATAAYEGGADGVTATNTVSGLMALKADATPWPGIGRGARTTYGGVS 482

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               R I       V  I +  P   I   GG++     L+ L
Sbjct: 483 GNAIRPIA---LRAVSAIARALPGFPILATGGIDSAESGLQFL 522


>gi|324992836|gb|EGC24756.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK405]
 gi|324994524|gb|EGC26437.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK678]
 gi|327462143|gb|EGF08470.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK1]
 gi|327489824|gb|EGF21614.1| dihydroorotate dehydrogenase B [Streptococcus sanguinis SK1058]
          Length = 312

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 81/228 (35%), Gaps = 23/228 (10%)

Query: 41  LGFSTQEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G ++      A KI        I LN+ CP   V  G+ G  +  
Sbjct: 91  LEKHYPDLPIIANVAGFSNQEYATVAGKISLATNVKAIELNISCP--NVDHGNAGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++      A  +  ++PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 149 VPELAYGATKAAVETSAVPVYVKLTPSVAD------ITQVAKAVEDAGAAGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                 +RK  I  G        +  +   ++ ++ +    L I   GG++    AL++ 
Sbjct: 203 MRFDLKSRKPIIANGTGGMSGPAVFPVALKLIRQVAQA-SKLPIIGMGGVDSAEAALEMF 261

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
                 + +G A + +     T+ E   + +           +   R+
Sbjct: 262 IAGASAIGVGTANFTDPYACPTIIENLPDLMDKYGIESLETLRKEVRE 309


>gi|288905168|ref|YP_003430390.1| dihydroorotate dehydrogenase B [Streptococcus gallolyticus UCN34]
 gi|288731894|emb|CBI13459.1| dihydroorotate dehydrogenase B [Streptococcus gallolyticus UCN34]
          Length = 314

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 74/198 (37%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   + G    +    ++ +        I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPELPIIANVAGFSNDEYAYVSEKISKAPNVKAIELNISCP--NVDHGNHGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +   +PV VK    V D      +  + K+++++G  G  +      
Sbjct: 149 VPELAYAAVKASVEYSDVPVYVKLTPSVAD------ITTVAKAVEEAGATGFTMINTLVG 202

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  RK  I  G        +  +   ++ ++ +   DL I   GG++    A++++
Sbjct: 203 MRFDLKTRKPIIANGTGGMSGPAVFPVALKLIRQVAQ-GTDLPIIGMGGVDSAEAAIEMM 261

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 262 IAGASAIGVGTANFADPY 279


>gi|118442862|ref|YP_878883.1| dihydroorotate dehydrogenase 1B [Clostridium novyi NT]
 gi|118133318|gb|ABK60362.1| dihydroorotate dehydrogenase [Clostridium novyi NT]
          Length = 310

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/213 (17%), Positives = 80/213 (37%), Gaps = 27/213 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +A ++     +    T    +   +GG  +   +   + + +   + I LN+ CP   V 
Sbjct: 89  EAFIKDKLPKMRKLDTA---IFANLGGGSVEDYLRGIEKLNNTDVDIIELNISCP--NVK 143

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G     +    ++  D ++ + +    P+ VK          A  + ++ +   K+G +
Sbjct: 144 SGGMAFGI--KSNVAYDVVSKVREICKKPLVVKLSP------NAENIIDMAEKCCKAGAD 195

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           GI            I+ RK +     +      I  +   +V+E+ K N D+ +   GG+
Sbjct: 196 GISLVNTFKAMAIDINKRKPVFNNVYAGLSGPAIKPIALRMVHEVCK-NVDVPVIGMGGI 254

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTV 229
                A++ I+     V IG A +    +   +
Sbjct: 255 VSSEDAIEFIMAGATAVQIGTANFIKPNIALDI 287


>gi|257437805|ref|ZP_05613560.1| dihydroorotate oxidase [Faecalibacterium prausnitzii A2-165]
 gi|257199728|gb|EEU98012.1| dihydroorotate oxidase [Faecalibacterium prausnitzii A2-165]
          Length = 308

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 74/187 (39%), Gaps = 32/187 (17%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG    + VE A ++ +   + + LN+ CP+ +V   ++G       +  G+ +  +  
Sbjct: 104 LGGHSEEEYVEGAALLSESAVDIVELNISCPNVKVGGMAYGV----KAEAAGEVVRMVRA 159

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK- 161
           A   P+ VK          A  +  + K+++ +G + I            +  RK +   
Sbjct: 160 ACKKPLMVKLSPQ------AENIPEMCKAVEAAGADAISLTNTFQACAIDLEKRKPVFNN 213

Query: 162 ---GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
              GLS    R I   + +  V  +     ++ +   GG+     AL+ I+     V +G
Sbjct: 214 IFAGLSGPAVRPIALRMVWQAVGAV-----NIPVVGLGGIATGRDALEFIMAGATAVQVG 268

Query: 217 RAAYKNS 223
            A + N 
Sbjct: 269 AANFANP 275


>gi|257469422|ref|ZP_05633514.1| dihydroorotate dehydrogenase 1B [Fusobacterium ulcerans ATCC 49185]
 gi|317063668|ref|ZP_07928153.1| dihydroorotate oxidase B [Fusobacterium ulcerans ATCC 49185]
 gi|313689344|gb|EFS26179.1| dihydroorotate oxidase B [Fusobacterium ulcerans ATCC 49185]
          Length = 305

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/208 (19%), Positives = 78/208 (37%), Gaps = 25/208 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           +  +     +   I G  + + +E AK VE     + I LN+ CP    +    G     
Sbjct: 89  MKEAGITTNIIANINGKTVEEYIEIAKRVEQIKEVDIIELNISCP----NVKDGGMAFGA 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG--------- 150
           NP++ G     + K  + P+ VK    V D      +  + K ++++G +          
Sbjct: 145 NPEVAGRVTREVRKVTTKPLVVKLSPNVTD------IAYIAKVVEENGADAVSLINTLLG 198

Query: 151 --IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I +  +K +L           +  +   +VY++ K   ++ I   GG+     AL+ I
Sbjct: 199 MVIDLKTKKPLLGNTFGGFSGPAVKPVALRMVYQVYKAV-NIPIVGMGGISSTEDALEFI 257

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +     V +G   + N  +   V E   
Sbjct: 258 MAGASMVSLGTGIFFNPVLPVEVAEGLQ 285


>gi|322807550|emb|CBZ05125.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           botulinum H04402 065]
          Length = 298

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 72/195 (36%), Gaps = 24/195 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  I   +E  + +     + I LN+ CP    +    G    +  +I  + +  + +
Sbjct: 98  VGGGCIEDYIEVIEKLNKTDVDMIELNISCP----NVKHGGMAFGIKSEIAYEVVKEVKE 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
               P+ VK     +D      + ++    +K+G + I            I  +  + + 
Sbjct: 154 ICQRPLMVKLSPNAED------IVDMAIKCEKAGADAISLVNTFKAMAIDIKRKTPVFEN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +VYE+ K+  ++ +   GG+ +    ++ I+     V IG   +
Sbjct: 208 ITAGLSGPCIKPIALRMVYEVCKQV-EIPVIGIGGICNYKDVIEFIMAGATAVQIGTTNF 266

Query: 221 KNSAMLTTVDEYFSN 235
            N      + E   N
Sbjct: 267 MNPYSAVDIIEDLEN 281


>gi|289578531|ref|YP_003477158.1| dihydroorotate dehydrogenase [Thermoanaerobacter italicus Ab9]
 gi|289528244|gb|ADD02596.1| dihydroorotate dehydrogenase family protein [Thermoanaerobacter
           italicus Ab9]
          Length = 302

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/201 (19%), Positives = 76/201 (37%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + I G  I +    AK ++  G + I +NV CP   V +G     +  NP+ + +   
Sbjct: 95  VIVNIAGETIEEFAYMAKKLDIDGVDGIEVNVSCP--NVKKGGMAFGI--NPEDIFNITK 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            + K     V VK    V D           K+ ++ G + +            I  RK 
Sbjct: 151 EVKKVTQKTVIVKLTPNVGDIGV------CAKAAEEGGADAVSLINTIAGMAVDIDTRKP 204

Query: 159 ILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           + K  ++      +  +   +VYE  K      IG+ GG+     A++ ++     + IG
Sbjct: 205 VFKNIIAGLSGPAVKPIALRMVYEAAKSVKIPVIGM-GGICSYQDAIEFMIAGAKAMAIG 263

Query: 217 RAAYKNSA----MLTTVDEYF 233
              + N      ++  + +Y 
Sbjct: 264 TCNFVNPYCTVEVIEGIKQYM 284


>gi|158321215|ref|YP_001513722.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           oremlandii OhILAs]
 gi|189038414|sp|A8MIU4|PYRD_ALKOO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|158141414|gb|ABW19726.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           oremlandii OhILAs]
          Length = 302

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/223 (21%), Positives = 89/223 (39%), Gaps = 31/223 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +A ++ D + +  + T+   + + I G  ++   +  + + D   + I LN+ CP+ +  
Sbjct: 81  EAFIKDDIQFLRQYDTK---IIVNIAGRTVADYCKVTEKLGDADIDLIELNISCPNVKAG 137

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             +FG     NP +V +   A+ K    P+ VK    V D      +  + K+    G +
Sbjct: 138 GVNFGT----NPAMVEEVTKAVKKVARQPLIVKLTPNVTD------IVEIAKAAVAGGAD 187

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            IH RK IL   +       I  +   +VY++      + I   GG+
Sbjct: 188 AISLINTLLGMAIDIHGRKPILANVVGGLSGPAIKPVALRMVYQVANAV-QVPIIGMGGI 246

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFSN 235
                A+  +L    GV +G A + N      +L  +++Y   
Sbjct: 247 ATGEDAIAFMLAGATGVAVGTANFMNPRATMEVLEGIEDYMDQ 289


>gi|222529371|ref|YP_002573253.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           bescii DSM 6725]
 gi|254788873|sp|B9MS26|PYRD_ANATD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|222456218|gb|ACM60480.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 300

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 74/204 (36%), Gaps = 25/204 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   I G    + VE  KI+     + I +N+ CP    +    G     +P  V +
Sbjct: 92  DTKIIANINGFSKEEFVELTKILTSL-VDMIEVNLSCP----NVKEGGMVFGKDPKKVYE 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              ++    S P+ VK    V D      +  L  + + +G + I            I  
Sbjct: 147 ITKSVKDVASCPIIVKLTPNVTD------ITQLAVAAENAGADAISLINTVSAMAIDIET 200

Query: 156 RKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
           RK ++K ++       I  +   +VYE  K+   + I   GG+ +   A++        +
Sbjct: 201 RKPLIKMVTGGLSGPAIKPIAVRMVYECFKKV-RIPIIGMGGIMNYKDAIEFFIAGATAI 259

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPL 237
            IG   + N   +  + E     L
Sbjct: 260 QIGTVNFINPKAVCEIKEGIEAYL 283


>gi|225376607|ref|ZP_03753828.1| hypothetical protein ROSEINA2194_02249 [Roseburia inulinivorans DSM
           16841]
 gi|225211490|gb|EEG93844.1| hypothetical protein ROSEINA2194_02249 [Roseburia inulinivorans DSM
           16841]
          Length = 301

 Score = 74.9 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 31/205 (15%), Positives = 74/205 (36%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +E  + + D   + + +N+ CP    +    G     +P  V  
Sbjct: 92  DTKIMVNVCGHSTEEYIEVVERLRDQPVDLLEINISCP----NVKEGGIAFGQDPKAVEA 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               M K  + PV +K    V D      +  + ++ +  G +G+ +             
Sbjct: 148 ITKEMKKHAAQPVIMKLSPNVTD------ITEMARAAEAGGADGLSLINTITGMKIDINR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
            +  +           I  +   +VY+  +      +G+ GG+ +   A+++ L     V
Sbjct: 202 QKFVLANKTGGMSGPAIHPVAVRMVYQTAQAVSIPIVGM-GGIMNAEDAIEMILAGATAV 260

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            +G A + N      ++  + +Y  
Sbjct: 261 SVGTANFTNPHVTEEIVAGIRDYME 285


>gi|42519206|ref|NP_965136.1| dihydroorotate dehydrogenase 1B [Lactobacillus johnsonii NCC 533]
 gi|81832219|sp|Q74J29|PYRD_LACJO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|41583494|gb|AAS09102.1| dihydroorotate dehydrogenase [Lactobacillus johnsonii NCC 533]
          Length = 307

 Score = 74.9 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 83/188 (44%), Gaps = 25/188 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GG D +  +E AK + D G  N + +NV CP   V++G       ++PD+V + 
Sbjct: 98  PIMASVGGEDEAGYLEVAKKLSDSGLVNALEINVSCP--NVNQGGMSFG--VHPDVVEEL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              +   + IP+ VK    V D      +  + K+ +  G +G           I +  R
Sbjct: 154 TKKIKSLVKIPIYVKLTPNVTD------ITQIAKAAENGGADGLSLINTLLGMEIDVETR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L   +       +  +   +V+++ +E+  L I   GG+      ++ IL   + V 
Sbjct: 208 KPVLGHNIGGLSGEAVKPIAIRMVHQV-RESTTLPIIGMGGISSAKDVIEFILAGANAVA 266

Query: 215 IGRAAYKN 222
           +G A +K+
Sbjct: 267 VGTAHFKD 274


>gi|323483963|ref|ZP_08089336.1| hypothetical protein HMPREF9474_01085 [Clostridium symbiosum
           WAL-14163]
 gi|323693440|ref|ZP_08107651.1| dihydroorotate dehydrogenase 1B [Clostridium symbiosum WAL-14673]
 gi|323402679|gb|EGA95004.1| hypothetical protein HMPREF9474_01085 [Clostridium symbiosum
           WAL-14163]
 gi|323502495|gb|EGB18346.1| dihydroorotate dehydrogenase 1B [Clostridium symbiosum WAL-14673]
          Length = 301

 Score = 74.9 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 38/231 (16%), Positives = 78/231 (33%), Gaps = 33/231 (14%)

Query: 26  MIVADAILRGDKKNILGFSTQ-----EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           MI A  +     +             +  + + + G      ++  + + D   + + +N
Sbjct: 67  MINAIGLQNPGYEVFAKRDIPYLKQFDTKIIVNVCGKTTEDYIDVVEKLSDEPVDMLEIN 126

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +    G     +P  V      + K    PV +K    V D         + 
Sbjct: 127 ISCP----NVKEGGIAFGQDPKAVEAITREVKKYAKQPVIMKLSPNVTDITV------MA 176

Query: 141 KSIKKSGVNG-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           ++ +  G +            I IH R  A+           I  +   +VY++      
Sbjct: 177 RAAEAGGADVLSLINTLTGMKIDIHKRTFAVANRTGGLSGPAIKPVAVRMVYQVANAV-K 235

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           L I   GG+ +   A++ IL     V +G A + N      ++  +++Y +
Sbjct: 236 LPIIGMGGIMNADDAIEFILAGATAVSVGTANFHNPYATVEIVKGIEDYMA 286


>gi|302385998|ref|YP_003821820.1| dihydroorotate dehydrogenase family protein [Clostridium
           saccharolyticum WM1]
 gi|302196626|gb|ADL04197.1| dihydroorotate dehydrogenase family protein [Clostridium
           saccharolyticum WM1]
          Length = 300

 Score = 74.9 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 78/228 (34%), Gaps = 29/228 (12%)

Query: 26  MIVADAILRGDK----KNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           MI A  +         K  L F  Q +  + + + G    + +E  + + D   + + +N
Sbjct: 66  MINAIGLQNPGMEVFIKRDLPFLKQYDTKIIVNVCGKTAEEYIEVVERLADEPVDMLEIN 125

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +    G     +P  V      + K    PV +K    V D      +  + 
Sbjct: 126 ISCP----NVKEGGIAFGQDPKAVEAITREVKKYAKQPVIMKLSPNVTD------IGEMA 175

Query: 141 KSIKKSGVNG-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K+ +  G +            I I+ R  A+           I  +   +VY+       
Sbjct: 176 KAAEAGGADVLSLINTLTGMKIDINRRTFAVANKTGGLSGPAIKPIAVRMVYQAANAV-K 234

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           L I   GG+ +   A++ +L     V +G A ++N      +     +
Sbjct: 235 LPIIGMGGIMNAEDAVEFLLAGATAVSVGTANFRNPYAAEEIVRGIED 282


>gi|317472264|ref|ZP_07931592.1| dihydroorotate dehydrogenase [Anaerostipes sp. 3_2_56FAA]
 gi|316900221|gb|EFV22207.1| dihydroorotate dehydrogenase [Anaerostipes sp. 3_2_56FAA]
          Length = 418

 Score = 74.9 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/195 (20%), Positives = 69/195 (35%), Gaps = 16/195 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           EMI    +    +    L      K +   I G++  +    AK V + G + I  N  C
Sbjct: 79  EMISDKPLEDNLEYMRRLKQDYPTKVIVASIMGSNEEEWEILAKKVTEAGVDMIECNFSC 138

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------P 132
           P   +   + G+ +  NPD+V      +  A  +PV  K    + +              
Sbjct: 139 PQ--MTSSAMGSDVGQNPDLVRRYCEVVSGATHLPVIAKMTPNIGNMEIPAIAAMEGGAK 196

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N VK+I    V  +           +S      +  +    + ++K+  E  D+ 
Sbjct: 197 GIAAINTVKAITNIDVENMTAMPVVNGKSSISGYSGAAVKPIALRFITQMKQHPELKDVP 256

Query: 191 IGLNGGLEDMSQALK 205
           I   GG+E    AL 
Sbjct: 257 ITGIGGIETWKDALD 271


>gi|323140640|ref|ZP_08075564.1| dihydroorotate oxidase, catalytic subunit [Phascolarctobacterium
           sp. YIT 12067]
 gi|322414904|gb|EFY05699.1| dihydroorotate oxidase, catalytic subunit [Phascolarctobacterium
           sp. YIT 12067]
          Length = 321

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/224 (15%), Positives = 76/224 (33%), Gaps = 29/224 (12%)

Query: 26  MIVADAILRGDKKNILGFSTQE-----KPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+    +     +  L  +  E      P+ + I G    +    AK ++  G + + +N
Sbjct: 73  MLNCIGLENPGSEYFLEHTLPELKKYNVPVIVNIYGHTPEEYGAVAKKLDVDGVDAVEIN 132

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +    G      P+   + + A+       V  K    V D +       + 
Sbjct: 133 ISCP----NVKEGGIVFGTVPEAAAEVVRAVKANTGKMVIAKLSPNVTDIVV------MA 182

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K+++ +G + I +              R  +           +  +   +VY++ +    
Sbjct: 183 KAVEAAGADAISMINTLLGTKIDIERQRPVLGNVTGGLSGPAVRPVAVRLVYQVAQAV-H 241

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + I   GG+     A++ +L     V +G A +    +  T+  
Sbjct: 242 IPIIGMGGIMCAEDAIEFMLAGASAVAVGTANFVQPDIAETIAH 285


>gi|167748210|ref|ZP_02420337.1| hypothetical protein ANACAC_02954 [Anaerostipes caccae DSM 14662]
 gi|167652202|gb|EDR96331.1| hypothetical protein ANACAC_02954 [Anaerostipes caccae DSM 14662]
          Length = 431

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/195 (20%), Positives = 69/195 (35%), Gaps = 16/195 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           EMI    +    +    L      K +   I G++  +    AK V + G + I  N  C
Sbjct: 92  EMISDKPLEDNLEYMRRLKQDYPTKVIVASIMGSNEEEWEILAKKVTEAGVDMIECNFSC 151

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------P 132
           P   +   + G+ +  NPD+V      +  A  +PV  K    + +              
Sbjct: 152 PQ--MTSSAMGSDVGQNPDLVRRYCEVVSGATHLPVIAKMTPNIGNMEIPAIAAMEGGAK 209

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N VK+I    V  +           +S      +  +    + ++K+  E  D+ 
Sbjct: 210 GIAAINTVKAITNIDVENMTAMPVVNGKSSISGYSGAAVKPIALRFITQMKQHPELKDVP 269

Query: 191 IGLNGGLEDMSQALK 205
           I   GG+E    AL 
Sbjct: 270 ITGIGGIETWKDALD 284


>gi|158321476|ref|YP_001513983.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           oremlandii OhILAs]
 gi|158141675|gb|ABW19987.1| dihydroorotate dehydrogenase family protein [Alkaliphilus
           oremlandii OhILAs]
          Length = 372

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 35/179 (19%), Positives = 64/179 (35%), Gaps = 30/179 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G   S++   A+ VE FG + + L V CP      G     ++  P  + +   
Sbjct: 93  VIANILGHTSSEIAYIAQKVEQFGADAVELGVSCPH-----GEGLEGVISEPSKLYEFTK 147

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARK 157
           A+   + IPV VK           V +  L ++ +K+G + I             I   +
Sbjct: 148 AVVDRIKIPVMVKL------SSNTVNVVKLARAAEKAGASAISGIDTVRSIAGVDIEKGR 201

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            +L          I  +    +  I +    + I   GG+ +    L+ +      M+G
Sbjct: 202 VLLPTFGGYSGDAIRPIGLAAIASIAQAT-SIPICGIGGITNYEHILEYM------MLG 253


>gi|146296941|ref|YP_001180712.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|229485542|sp|A4XKT6|PYRD_CALS8 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|145410517|gb|ABP67521.1| dihydroorotate oxidase B, catalytic subunit [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 300

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/201 (19%), Positives = 75/201 (37%), Gaps = 25/201 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G    + VE  K++     + I +N+ CP    +    G     +P+ V +   
Sbjct: 95  IIANINGFTKEEFVELTKVLSSL-VDMIEVNLSCP----NVKEGGMVFGKDPEKVYEITK 149

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
           ++    S P+ VK    V D      +  L  + +K+G + I            I  RK 
Sbjct: 150 SVKDVASCPIIVKLTPNVTD------IAQLAIAAEKAGADAISLINTVSAMAIDIETRKP 203

Query: 159 ILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           ++K ++       I  +   +VYE  K+   + I   GG+ +   A++        + IG
Sbjct: 204 LIKMVTGGLSGPAIKPIAVRMVYECFKKV-RIPIVGMGGIMNYKDAIEFFIAGATAIQIG 262

Query: 217 RAAYKNSAMLTTVDEYFSNPL 237
              + N   +  + E     L
Sbjct: 263 TVNFINPKAVCEIKEGIEAYL 283


>gi|312793566|ref|YP_004026489.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312180706|gb|ADQ40876.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 300

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/221 (19%), Positives = 83/221 (37%), Gaps = 28/221 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +A +  +   + GF T+   +   I G    + VE  KI+     + I +N+ CP    +
Sbjct: 78  EAFVNEELPFLKGFDTK---VIANINGFAKEEFVELTKILTSL-VDMIEVNLSCP----N 129

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G     +P+ V +   ++    S P+ VK    V D      +  L  + + +G +
Sbjct: 130 VKEGGMVFGKDPEKVYEITKSVKDVASCPIIVKLTPNVTD------IIQLAIAAENAGAD 183

Query: 150 GIW-----------IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            I  RK ++K ++       I  +   +VYE  K+   + I   GG+
Sbjct: 184 AISLINTVSAMAIDIETRKPLIKMVTGGLSGPAIKPIAVRMVYECFKKV-RIPIIGMGGI 242

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            +   A++        + IG   + N   +  + E     L
Sbjct: 243 MNYKDAIEFFIAGATAIQIGTVNFINPKAVCEIKEGIEAYL 283


>gi|319892197|ref|YP_004149072.1| Dihydroorotate dehydrogenase, catalytic subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317161893|gb|ADV05436.1| Dihydroorotate dehydrogenase, catalytic subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323464702|gb|ADX76855.1| dihydroorotate dehydrogenase [Staphylococcus pseudintermedius ED99]
          Length = 306

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 31/208 (14%), Positives = 74/208 (35%), Gaps = 15/208 (7%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVH 89
            +       +   +  + P+   + G+     V  A+ +        + LN+ CP+ +  
Sbjct: 77  GVHHIIDHELKALAQHDVPIIANVAGSMEEDYVYVAEHISKAPNVKALELNISCPNVKEG 136

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL-------RNLVKS 142
              FG     +P I  +    +     +PV VK    V + +              ++ +
Sbjct: 137 GMQFGV----DPTIASELTRKVKAVSEVPVYVKLSPNVTNIVEMAEAIAQYADGLTMINT 192

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           +    ++      +  I           I  +   +V++++K  PD+ I   GG+++   
Sbjct: 193 LVGMRIDART--GKPIIYNVTGGLSGPAIKPVALRMVHDVRKALPDIPIIAMGGVQNAQD 250

Query: 203 ALKILP-SVDGVMIGRAAYKNSAMLTTV 229
            +  +    D V +G A ++N  +   +
Sbjct: 251 VIDYVSVGADAVAVGTANFQNPMVCKEI 278


>gi|260821394|ref|XP_002606018.1| hypothetical protein BRAFLDRAFT_129513 [Branchiostoma floridae]
 gi|229291355|gb|EEN62028.1| hypothetical protein BRAFLDRAFT_129513 [Branchiostoma floridae]
          Length = 1044

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/206 (17%), Positives = 66/206 (32%), Gaps = 33/206 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L     +K +   I  +    D  +L + A+     G + + L
Sbjct: 616 ELISEKTAAYWCQTVTELKRDFPDKIVIASIMCSYNKDDWIELAQMAEKA---GSDALEL 672

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     +P++V +    +  A+ IP   K    + D         +
Sbjct: 673 NLSCPHGM-GERGMGLACGQDPELVRNICRWVRSAIKIPFFAKMTPNITDVTV------I 725

Query: 140 VKSIKKSGVNGIWI------------HARKAILKG------LSPKDNRKIPNLDYDIVYE 181
            ++ K+   +G+              +AR     G              I  +    V  
Sbjct: 726 AQAAKEGMADGVTATNTVSGLMGLKSNARAWPAVGQEMRTTYGGVSGNAIRPIALRAVSA 785

Query: 182 IKKENPDLFIGLNGGLEDMSQALKIL 207
           I +  P   I   GG++     L+ L
Sbjct: 786 IARALPGFPILATGGIDSAEAGLQFL 811


>gi|255028807|ref|ZP_05300758.1| dihydroorotate dehydrogenase 1B [Listeria monocytogenes LO28]
          Length = 178

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 29/159 (18%), Positives = 63/159 (39%), Gaps = 24/159 (15%)

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P++      A+    S+PV VK    V D      + ++
Sbjct: 1   NISCP----NVKHGGIAFGTDPEVAHRLTKAVKNVASVPVYVKLSPNVAD------IVSI 50

Query: 140 VKSIKKSGVNGIWI-----------HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            ++I+ +G +G+ +             RK  I  G        I  +   +++++ +   
Sbjct: 51  AQAIEAAGADGLTMINTLLGMRIDLKTRKPIIANGTGGLSGPAIKPVAIRMIHQV-RAVS 109

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++ I   GG++ +   L+ L    D V +G   + +  +
Sbjct: 110 NIPIIGMGGVQTVDDVLEFLIAGADAVAVGTMNFTDPFI 148


>gi|225570767|ref|ZP_03779790.1| hypothetical protein CLOHYLEM_06870 [Clostridium hylemonae DSM
           15053]
 gi|225160229|gb|EEG72848.1| hypothetical protein CLOHYLEM_06870 [Clostridium hylemonae DSM
           15053]
          Length = 300

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 38/208 (18%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D   R D   +  F T+   + + + G       E  + + +   + + +N+ CP    +
Sbjct: 78  DLFCRRDIPFLKQFDTK---IIVNVCGRTTEDYCEVVERLAEEDVDMLEINISCP----N 130

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G     NP  V +  A + K    PV +K    V D      +    ++ +  G +
Sbjct: 131 VKEGGIAFGQNPKAVEEITAEVKKRAKQPVIMKLSPNVTD------ITETARAAEAGGAD 184

Query: 150 G-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                       I IH R  A+           +  +   +VY+       L I   GG+
Sbjct: 185 VLSLINTLTGMKIDIHRRTFALANKTGGLSGPAVKPVAVRMVYQAANAV-KLPIIGMGGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA 224
                A++ +L     V +G A + + +
Sbjct: 244 ATAEDAIEFLLAGASAVSVGTANFYDPS 271


>gi|315301144|ref|ZP_07872421.1| probable tRNA-dihydrouridine synthase 1 [Listeria ivanovii FSL
          F6-596]
 gi|313630489|gb|EFR98345.1| probable tRNA-dihydrouridine synthase 1 [Listeria ivanovii FSL
          F6-596]
          Length = 87

 Score = 74.9 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
          M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18 MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59 ISKLVEAAKIV 69
             LVEAAK V
Sbjct: 77 KETLVEAAKFV 87


>gi|24379647|ref|NP_721602.1| dihydroorotate dehydrogenase 1B [Streptococcus mutans UA159]
 gi|24377601|gb|AAN58908.1|AE014959_2 putative dihydroorotate dehydrogenase B [Streptococcus mutans
           UA159]
          Length = 309

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 76/198 (38%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    ++ + +      I LN+ CP   V  G+ G  +  
Sbjct: 90  LAEHYPDLPIIANVAGFSNEEYAYVSEKISQAPNVKAIELNISCP--NVDHGNHGLLIGQ 147

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +A  +PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 148 VPELTYAAVKAAVEASQVPVYVKLTPSVAD------ITTVAKAVEAAGATGFTMINTLVG 201

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  +K  I  G        +  +   +++++ + +  L I   GG++    AL+++
Sbjct: 202 MRFDLKTKKPIIANGTGGMSGPAVFPVALKLIHQVAQ-SSQLPIIGMGGVDSAEAALEMM 260

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 261 IAGASAIAVGTANFTDPF 278


>gi|323702039|ref|ZP_08113707.1| dihydroorotate dehydrogenase family protein [Desulfotomaculum
           nigrificans DSM 574]
 gi|323532921|gb|EGB22792.1| dihydroorotate dehydrogenase family protein [Desulfotomaculum
           nigrificans DSM 574]
          Length = 304

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 79/209 (37%), Gaps = 29/209 (13%)

Query: 43  FSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           F+  +  + + I G  +      AAK+    G   + +N+ CP   V +G        +P
Sbjct: 90  FAGLKTRVIVNIAGNTVDDYARLAAKLDGVPGVAGLEVNISCP--NVKKGGMAFG--SDP 145

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------G 150
               +   A+  A  +PV VK    V D         + +++  +G +            
Sbjct: 146 AAAAEVTKAVKNATGLPVIVKLSPNVTDITV------IARAVADAGADALSLINTLLGMA 199

Query: 151 IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I +  RK +L   +       +  +    V+++ +    L I   GG+     AL+ IL 
Sbjct: 200 IDVRRRKPMLGNIMGGLSGPAVKPVAVRAVWQVYQ-TVKLPIIGMGGIVTAQDALEFILA 258

Query: 209 SVDGVMIGRAAYKNSA----MLTTVDEYF 233
               V +G A + N+     +L  +++Y 
Sbjct: 259 GASAVAVGTANFINATATLEVLAGIEQYL 287


>gi|309803608|ref|ZP_07697700.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|309805602|ref|ZP_07699645.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|312870729|ref|ZP_07730836.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           3008A-a]
 gi|312872879|ref|ZP_07732941.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           2062A-h1]
 gi|312875152|ref|ZP_07735165.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           2053A-b]
 gi|315653078|ref|ZP_07906006.1| dihydroorotate oxidase [Lactobacillus iners ATCC 55195]
 gi|329919621|ref|ZP_08276610.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners SPIN 1401G]
 gi|308164356|gb|EFO66611.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|308165103|gb|EFO67343.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|311089259|gb|EFQ47690.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           2053A-b]
 gi|311091613|gb|EFQ49995.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           2062A-h1]
 gi|311093741|gb|EFQ52078.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus iners LEAF
           3008A-a]
 gi|315489613|gb|EFU79247.1| dihydroorotate oxidase [Lactobacillus iners ATCC 55195]
 gi|328937426|gb|EGG33848.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners SPIN 1401G]
          Length = 306

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 84/205 (40%), Gaps = 29/205 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL   +GG+ IS  +  +K + D G  N + +NV CP    +  + G  L  +P +V   
Sbjct: 98  PLIASVGGSQISDYITISKKLSDSGLLNALEINVSCP----NVAAGGMHLGTDPVVVEKL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
            + + K ++IPV +K    V        +  + ++ ++ G +           GI I   
Sbjct: 154 TSEIKKVVNIPVYIKLTPNV------TNIVEIAQAAERGGADGLSMINTLLGLGIDIKTH 207

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           KA L  G        I  +   +V ++ +    L I   GG+E     ++ +L     V 
Sbjct: 208 KATLGNGFGGWSGSAIKPVAVRMVAQVHQAV-KLPIIGMGGIETAEDIVEFMLAGASAVA 266

Query: 215 IGRAAYKN----SAMLTTVDEYFSN 235
           +G A +K+      ++  ++   + 
Sbjct: 267 VGTAHFKDGLAIPHLVADLETLLNE 291


>gi|290580356|ref|YP_003484748.1| putative dihydroorotate dehydrogenase B [Streptococcus mutans
           NN2025]
 gi|254997255|dbj|BAH87856.1| putative dihydroorotate dehydrogenase B [Streptococcus mutans
           NN2025]
          Length = 309

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 76/198 (38%), Gaps = 23/198 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    ++ + +      I LN+ CP   V  G+ G  +  
Sbjct: 90  LAEHYPDLPIIANVAGFSNEEYAYVSEKISQAPNVKAIELNISCP--NVDHGNHGLLIGQ 147

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
            P++    + A  +A  +PV VK    V D      +  + K+++ +G  G  +      
Sbjct: 148 VPELTYAAVKAAVEASQVPVYVKLTPSVAD------ITTVAKAVEAAGATGFTMINTLVG 201

Query: 154 -----HARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  +K  I  G        +  +   +++++ + +  L I   GG++    AL+++
Sbjct: 202 MRFDLKTKKPIIANGTGGMSGPAVFPVALKLIHQVAQ-SSQLPIIGMGGVDSAEAALEMM 260

Query: 208 -PSVDGVMIGRAAYKNSA 224
                 + +G A + +  
Sbjct: 261 IAGASAIAVGTANFTDPF 278


>gi|29170609|gb|AAO66291.1| dihydropyrimidine dehydrogenase [Brevibacillus agri]
          Length = 425

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 68/177 (38%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE  G + + LN GCP     E   G+ +  +PD++   +  + +    PV VK 
Sbjct: 116 EIVKKVEAIGVDGLELNFGCPHGMA-ERGMGSAVGQHPDLIRQQVEWVKEVAQTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-------- 175
              + D      +R   ++    G + I +      L G+       IP++D        
Sbjct: 175 TPNITD------IRFTARAASAGGADAISMINTINSLMGVDLDKWLPIPHVDGKGAHGGY 228

Query: 176 ---------YDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                     ++V E  ++    + I   GG+ +   A++ +L    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARDPFVGVPISGIGGISNWRDAVEFLLMGATGVQVCTAAMH 285


>gi|153813263|ref|ZP_01965931.1| hypothetical protein RUMOBE_03680 [Ruminococcus obeum ATCC 29174]
 gi|149830676|gb|EDM85767.1| hypothetical protein RUMOBE_03680 [Ruminococcus obeum ATCC 29174]
          Length = 301

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 68/201 (33%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + + D   + + +NV CP    +    G     NP  +  
Sbjct: 93  DTKIIVNVCGKSTEDYCEVVEKLADEPVDLLEINVSCP----NVKEGGIAFGQNPHALEA 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               + K    P+ +K    V D      +  + ++ +  G + + +             
Sbjct: 149 ITKEVKKYAKQPIIMKLSPNVTD------ITEMARAAEAGGADILSLINTLTGMKIDIYR 202

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++ +    L I   GG+     AL+ I+     V
Sbjct: 203 KTFALANKTGGMSGPAVKPVAVRMVYQVAQAV-KLPIIGMGGIATAEDALEFIMAGATAV 261

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G A + N    T + +  +
Sbjct: 262 SVGTANFFNPYATTEIVDGLA 282


>gi|160880418|ref|YP_001559386.1| dihydroorotate dehydrogenase family protein [Clostridium
           phytofermentans ISDg]
 gi|229485557|sp|A9KKR5|PYRD_CLOPH RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|160429084|gb|ABX42647.1| dihydroorotate dehydrogenase family protein [Clostridium
           phytofermentans ISDg]
          Length = 300

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/191 (16%), Positives = 70/191 (36%), Gaps = 24/191 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G  + + VE  + + +   + + LN+ CP    +          +P ++  
Sbjct: 92  DTKVIVNVCGKSVKEYVEVVERLSEEAVDLLELNISCP----NVKEGCIAFGQDPKMIAM 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            +  + +    PV VK    V D      +  + K+ +  G + + +            H
Sbjct: 148 IMDEIKRHAKQPVIVKLSPNVTD------ITEMAKAAEAGGADALSLINTLTGMKIDINH 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              AI           +  +   +VY++      L I   GG+++   AL+ I+     V
Sbjct: 202 RAFAIANKTGGMSGPAVKPIAVRMVYQVANAV-KLPIIGMGGIQNAEDALEFIMAGATVV 260

Query: 214 MIGRAAYKNSA 224
            +G A + N  
Sbjct: 261 AVGTANFINPY 271


>gi|73960011|ref|XP_537061.2| PREDICTED: similar to Dihydropyrimidine dehydrogenase [NADP+]
           precursor (DPD) (DHPDHase) (Dihydrouracil dehydrogenase)
           (Dihydrothymine dehydrogenase) [Canis familiaris]
          Length = 1074

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 68/204 (33%), Gaps = 29/204 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA--DISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L        +   I  +      + E +K+ E  G + + LN+
Sbjct: 659 ELISEKTAAYWCQSVTELKADFPGNIVIASIMCSYSKNDWM-ELSKMAEASGADALELNL 717

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 718 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 770

Query: 142 SIKKSGVNGIWIHARKAILKGL------------------SPKDNRKIPNLDYDIVYEIK 183
           + K+ G +G+      + L GL                         I  +    V  I 
Sbjct: 771 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGIEKRTTYGGVSGTAIRPIALRAVTSIA 830

Query: 184 KENPDLFIGLNGGLEDMSQALKIL 207
           +  P   I   GG++     L+ L
Sbjct: 831 RALPGFPILATGGIDSAESGLQFL 854


>gi|295091342|emb|CBK77449.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Clostridium cf. saccharolyticum K10]
          Length = 300

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 78/235 (33%), Gaps = 39/235 (16%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQI--------GGADISKLVEAAKIVEDFGYNEI 77
           MI A  +     +    F+ ++ P   Q          G      ++  + + D   + +
Sbjct: 66  MINAVGLQNPGFQ---VFAERDIPYLKQFDTKIIVNVCGRTTEDYIDVVEKLSDQPVDML 122

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            +N+ CP    +    G     +P  V      + +    PV +K    V D        
Sbjct: 123 EINISCP----NVKEGGIAFGQDPKAVEAITREVKRHAKQPVIMKLSPNVTDITV----- 173

Query: 138 NLVKSIKKSGVNG-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            + K+ +  G +            I IH R  A+           I  +   +VY++   
Sbjct: 174 -MAKAAEAGGADVLSLINTITGMKIDIHRRTFAVANKTGGLSGPAIKPVAVRMVYQVANA 232

Query: 186 NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSN 235
                IG+ GG+     A++ ++     V +G A + N      ++  ++ Y   
Sbjct: 233 VSLPVIGM-GGIMCADDAIEFMMAGATAVAVGTANFHNPYATEEIVKGIEAYMRQ 286


>gi|118776473|gb|ABL14244.1| dihydroprimidine dehydrogenase [Bacillus fordii]
          Length = 426

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 68/177 (38%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K V+D G +   LN+GCP     E   G+ +  +PD+V        +A  +PV  K 
Sbjct: 116 EIVKRVQDVGVDGFELNLGCPHGMS-ERGMGSAVGQHPDLVEKTTLYAKEASEVPVITKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNG-------------IWIHA-RKAILKGLSPKDNR 169
              + D      +    ++ ++ G +              IWIH  R  ++ GL      
Sbjct: 175 TPNITD------ITATARAAQRGGADAISMINTINSLMESIWIHGIRSRMINGLGAHGGY 228

Query: 170 KIP---NLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
             P    +  +++ E  ++    + I   GG+      ++ +L    GV I  AA  
Sbjct: 229 SGPAVKPIALNMIGECARQKDITIPISGIGGVSTWQDTVEFMLMGAGGVQICTAAMH 285


>gi|253583846|ref|ZP_04861044.1| dihydroorotate oxidase B [Fusobacterium varium ATCC 27725]
 gi|251834418|gb|EES62981.1| dihydroorotate oxidase B [Fusobacterium varium ATCC 27725]
          Length = 305

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/208 (19%), Positives = 78/208 (37%), Gaps = 25/208 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           +  +     +   I G  + + +E AK VE     + I LN+ CP    +    G     
Sbjct: 89  MKEAGITTNIIANINGKTVEEYIEIAKRVEKIKEVDIIELNISCP----NVKDGGMAFGA 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           NP++ G     + K  + P+ VK    V D      +  + K ++++G +          
Sbjct: 145 NPEVAGRVTREVRKVTTKPLVVKLSPNVTD------IAYIAKVVEENGADAVSLINTLLG 198

Query: 150 -GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I +  +K +L           +  +   +VY++ K   ++ I   GG+     AL+ I
Sbjct: 199 MAIDLKTKKPLLGNTFGGFSGPAVKPVALRMVYQVYKAV-NIPIVGMGGISSTEDALEFI 257

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +     V +G   + N  +   V E   
Sbjct: 258 MAGASMVSLGTGIFFNPVLPVEVAEGLQ 285


>gi|291244574|ref|XP_002742170.1| PREDICTED: dihydropyrimidine dehydrogenase-like [Saccoglossus
           kowalevskii]
          Length = 1025

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 58/313 (18%), Positives = 101/313 (32%), Gaps = 45/313 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L    ++K +   I  +    D +KL   AK+ ED G + + L
Sbjct: 610 ELISEKTAAYWCQTVTELKADFKDKIIISSIMCSYNKEDWTKL---AKMAEDSGADALEL 666

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP     E   G     + ++V +    +  A+ IP   K    V D +       +
Sbjct: 667 NLSCPHGM-GERGMGLACGQDAELVRNICRWVRAAVKIPFFAKLTPNVTDIVV------I 719

Query: 140 VKSIKKSGVNGIW------------------IHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            K+  +   +G+                       K  L          I  +    V  
Sbjct: 720 AKAAYEGKADGVTATNTVSGLMGLKSNGTAWPAVGKEKLTTYGGVSGNAIRPIALRAVSA 779

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           I +  P   I   GG++     L+ L      + +G A        T +++Y +   T  
Sbjct: 780 IGRALPGFPILATGGIDSADAGLQFLQSGASLLQVGSAVQNQ--DFTVIEDYITGLKTLM 837

Query: 241 SPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVE 300
                    D+  +   ++     + +    KL +I    IG   G PN    R      
Sbjct: 838 YLKSIDELSDWDGQSPPTLRHQLGKPV---PKLNEI----IG--KGIPNFGPYREKRAEI 888

Query: 301 AGASTATHHIIET 313
             A+ AT  ++  
Sbjct: 889 VAANKATIDLLAE 901


>gi|312135188|ref|YP_004002526.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           owensensis OL]
 gi|311775239|gb|ADQ04726.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           owensensis OL]
          Length = 300

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 77/204 (37%), Gaps = 25/204 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   I G    + VE  KI+     + I +N+ CP    +    G     +P+ V +
Sbjct: 92  DTKIIANINGFAKEEFVELTKILTSL-VDMIEVNLSCP----NVKEGGMVFGKDPEKVYE 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              ++    S P+ VK    V D      +  L  + +K+G + I            I  
Sbjct: 147 ITNSVKNVASCPIIVKLTPNVTD------ITQLAVAAEKAGADAISLINTISAMAIDIET 200

Query: 156 RKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
           RK +++ ++       I  +   +VYE  K+   + I   GG+ +   A++        +
Sbjct: 201 RKPLIQMVTGGLSGPAIKPIAVRMVYECFKKV-RIPIIGMGGIMNYKDAIEFFIAGATAI 259

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPL 237
            IG   + N   +  + E   + L
Sbjct: 260 QIGTVNFINPKAVYEIKEGIEDYL 283


>gi|124485418|ref|YP_001030034.1| dihydroorotate dehydrogenase 1B [Methanocorpusculum labreanum Z]
 gi|124362959|gb|ABN06767.1| dihydroorotate oxidase B, catalytic subunit [Methanocorpusculum
           labreanum Z]
          Length = 294

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 38/196 (19%), Positives = 73/196 (37%), Gaps = 15/196 (7%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + +P+ + I G    +    A    D       LN+ CP A      +GA + +NP +V 
Sbjct: 91  KGEPVVVSIFGGTPEEFGTVASWFPD--AAAFELNLSCPHAE----GYGASIGVNPRVVR 144

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           +C   + K  + PV VK    V D     +       + + ++       I    R+ +L
Sbjct: 145 ECTE-IVKTYNKPVWVKLTPNVTDIKIIGKAAEEGGADAIVAVNTVKAMRISTELRRPVL 203

Query: 161 KG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRA 218
                    + I  +    VY++  +  D+ I   GG+      L+ ++     V IG A
Sbjct: 204 GNVFGGLSGQAIFPIAVRSVYDLY-DAVDIPIIGCGGISSADNVLEMMMAGASAVEIGSA 262

Query: 219 AYKNSAMLTTVDEYFS 234
            + +  + + +     
Sbjct: 263 IHDSVNIFSEIAADLY 278


>gi|84490187|ref|YP_448419.1| hypothetical protein Msp_1405 [Methanosphaera stadtmanae DSM 3091]
 gi|84373506|gb|ABC57776.1| conserved hypothetical protein [Methanosphaera stadtmanae DSM 3091]
          Length = 242

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 31/173 (17%), Positives = 65/173 (37%), Gaps = 23/173 (13%)

Query: 50  LALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +++ + G          ++V  +   + + +N  C    V +   G  L+ +   +   +
Sbjct: 82  ISVNLRGIKPESF----RVVKNNKNIDILEINAHCRQEAVVKAGAGEGLLKDKKRLSQVL 137

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +     + V+VK R  V      V    + K I+   ++ I + A            N
Sbjct: 138 DEVSSY-DMDVSVKIRANVCG----VDTLEITKLIESYNIDYIHLDA-----------TN 181

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
             I   DY+I+ E+   N ++ +  N  +      +K++    D V + RAA 
Sbjct: 182 PGIMEADYEIIEEVSN-NTEIHLIGNNSVTTHDDYMKMINSGADSVSVARAAL 233


>gi|294495549|ref|YP_003542042.1| methanogenesis marker protein 9 [Methanohalophilus mahii DSM 5219]
 gi|292666548|gb|ADE36397.1| methanogenesis marker protein 9 [Methanohalophilus mahii DSM 5219]
          Length = 375

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 52/268 (19%), Positives = 98/268 (36%), Gaps = 50/268 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY-------TEMIVADA--ILRGDKKNILGFSTQE---- 47
           M   TD  +         +A L         E   A A  ++   +K  +     E    
Sbjct: 24  MAGITDSSF---VNSYGKSAALVIIGGYNLDERTNAAACELIERGRKEFVSQEPIEYITK 80

Query: 48  --------KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
                     + + +  ++I  L+E A IV D G   + L+  C    + E   G  LM 
Sbjct: 81  EINAVDFDGVVGINLRSSEIKPLIEMAGIVRDAGA-VMELDAHCRQPEMKEAGVGEALME 139

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +   + + I  + +   + ++VK R  V D I       L K+I+ +G + I + A K  
Sbjct: 140 DLPRLTEWIRQIKE-TGVVLSVKIRANVVDDI------KLAKAIENAGADIIHVDAMK-- 190

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
                     +    D D +  I ++   +F+  N  ++    A ++     D V +GR 
Sbjct: 191 ----------EGAGADLDAIRRI-RDATRIFLIGNNSVQSFDDAKEMFSRGGDMVSVGRQ 239

Query: 219 AYKNS----AMLTTVDEYFSNPLTGSSP 242
           A  +     +++  V E+       ++P
Sbjct: 240 AMDSPQLVDSLVEAVSEFQETTGWYNAP 267


>gi|47522904|ref|NP_999209.1| dihydropyrimidine dehydrogenase [NADP+] precursor [Sus scrofa]
 gi|2498311|sp|Q28943|DPYD_PIG RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil
           dehydrogenase; Flags: Precursor
 gi|558307|gb|AAA57475.1| dihydropyrimidine dehydrogenase [Sus scrofa]
          Length = 1025

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 68/207 (32%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E ++  E  G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELSRKAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         ++    G+S    R I       V 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 780 TIARALPGFPILATGGIDSAESGLQFL 806


>gi|13399647|pdb|1H7W|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
 gi|13399648|pdb|1H7W|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
 gi|13399649|pdb|1H7W|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
 gi|13399650|pdb|1H7W|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
 gi|20663633|pdb|1GT8|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And Uracil-4-Acetic Acid
 gi|20663634|pdb|1GT8|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And Uracil-4-Acetic Acid
 gi|20663635|pdb|1GT8|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And Uracil-4-Acetic Acid
 gi|20663636|pdb|1GT8|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And Uracil-4-Acetic Acid
 gi|20663641|pdb|1GTE|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
           Complex With 5-Iodouracil
 gi|20663642|pdb|1GTE|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
           Complex With 5-Iodouracil
 gi|20663643|pdb|1GTE|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
           Complex With 5-Iodouracil
 gi|20663644|pdb|1GTE|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
           Complex With 5-Iodouracil
 gi|20663675|pdb|1GTH|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And 5-Iodouracil
 gi|20663676|pdb|1GTH|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And 5-Iodouracil
 gi|20663677|pdb|1GTH|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And 5-Iodouracil
 gi|20663678|pdb|1GTH|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex With Nadph And 5-Iodouracil
          Length = 1025

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 68/207 (32%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E ++  E  G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELSRKAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         ++    G+S    R I       V 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 780 TIARALPGFPILATGGIDSAESGLQFL 806


>gi|325570246|ref|ZP_08146112.1| dihydroorotate oxidase [Enterococcus casseliflavus ATCC 12755]
 gi|325156729|gb|EGC68903.1| dihydroorotate oxidase [Enterococcus casseliflavus ATCC 12755]
          Length = 307

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/195 (20%), Positives = 74/195 (37%), Gaps = 25/195 (12%)

Query: 45  TQEKPLALQIGGADISK-LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             E P+   + G+ +   ++   +I +      I LN+ CP    +    G     +P +
Sbjct: 92  HPELPIIANVAGSTVEDYVLVCQEISQAENVKAIELNISCP----NVKHGGITFGTDPAV 147

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
            G    A+ K   +P+ VK    V D +P      + K+I+  G +G  +          
Sbjct: 148 AGALTEAVKKVSQVPIYVKLSPNVTDIVP------IAKAIEAGGADGFTMINTLLGMRID 201

Query: 154 -HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSV 210
              RK IL           I  +   ++ ++ +    L I   GG+  +   L++ L  V
Sbjct: 202 LKTRKPILANQTGGLSGPSIKPVAIRLIKQVAQ-VSQLPIIGMGGVMSVDDVLEMYLAGV 260

Query: 211 DGVMIGRAAYKNSAM 225
             V +G A + +  +
Sbjct: 261 SAVAVGTANFTDPYI 275


>gi|160944597|ref|ZP_02091824.1| hypothetical protein FAEPRAM212_02110 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443781|gb|EDP20785.1| hypothetical protein FAEPRAM212_02110 [Faecalibacterium prausnitzii
           M21/2]
          Length = 308

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 74/187 (39%), Gaps = 32/187 (17%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG    + VE A ++ +   + + LN+ CP+ +V   ++G       +  G+ +  +  
Sbjct: 104 LGGHSEEEYVEGAAMLSESAVDIVELNISCPNVKVGGMAYGV----KAEAAGEVVRMVRA 159

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK- 161
           A   P+ VK          A  +  + K+++ +G + I            +  R+ +   
Sbjct: 160 ACKKPLMVKLSPQ------AENIPEMCKAVEAAGADAISLTNTFQACAIDLEKRRPVFNN 213

Query: 162 ---GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
              GLS    R I   + +  V  +     ++ +   GG+     AL+ I+     V +G
Sbjct: 214 IFAGLSGPAVRPIALRMVWQAVGAV-----NIPVVGLGGIATGRDALEFIMAGATAVQVG 268

Query: 217 RAAYKNS 223
            A + N 
Sbjct: 269 AANFANP 275


>gi|332686641|ref|YP_004456415.1| dihydroorotate dehydrogenase, catalytic subunit [Melissococcus
           plutonius ATCC 35311]
 gi|332370650|dbj|BAK21606.1| dihydroorotate dehydrogenase, catalytic subunit [Melissococcus
           plutonius ATCC 35311]
          Length = 308

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 75/199 (37%), Gaps = 25/199 (12%)

Query: 49  PLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + GA     +E  +KI +    + I LN+ CP    +    G     +P++    
Sbjct: 96  PIIANVAGACEEDYIEVCSKISQVKNVHAIELNISCP----NVKHGGIAFGTDPEVAFQL 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
              + K   +P+ VK    V D +P      + K+I+  G +G+ +             R
Sbjct: 152 TQVVKKVSQVPIYVKLSPNVTDIVP------IAKAIEAGGADGLSMINTLLGMRIDLKTR 205

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + +L           I  +   ++ ++     +L I   GG++ +   L+  +     V 
Sbjct: 206 QPVLANQTGGLSGAAIKPVAIRLIRQVA-AITNLPIIGMGGIQSVEDILEFFMAGASAVA 264

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           IG A + +  +   + E  
Sbjct: 265 IGTANFTDPYICPRLIEEL 283


>gi|302344296|ref|YP_003808825.1| dihydroorotate dehydrogenase family protein [Desulfarculus baarsii
           DSM 2075]
 gi|301640909|gb|ADK86231.1| dihydroorotate dehydrogenase family protein [Desulfarculus baarsii
           DSM 2075]
          Length = 307

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/201 (20%), Positives = 81/201 (40%), Gaps = 16/201 (7%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           + Q+ P A+ + G  I + V+ A+ ++   G   + LNV CP+ +    +FG     NP 
Sbjct: 93  AGQDTPAAVNLYGESIDEFVQLAQRLDGLAGVAALELNVSCPNVKAGGMAFGT----NPQ 148

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA--------VALRNLVKSIKKSGVNGIWIH 154
            V    AA+ +  S+P+ VK    V D +               L+ ++    ++     
Sbjct: 149 AVAQVTAAVRRVTSLPLWVKLTPNVTDPVAVAGAAMEAGADALCLINTLLGMAIDARRRA 208

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R A + G        I  +   +V+++ +  P   I   GG+     A + +L     V
Sbjct: 209 PRLANVVG--GLSGPAIKPVGLRMVWQVARALPGAPIIGLGGICCGEDAAEYLLAGASAV 266

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G A++ +      V +  +
Sbjct: 267 QVGTASFADPTACARVADELA 287


>gi|291398457|ref|XP_002715523.1| PREDICTED: dihydropyrimidine dehydrogenase [Oryctolagus cuniculus]
          Length = 1029

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/169 (18%), Positives = 58/169 (34%), Gaps = 26/169 (15%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + E ++  E  G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 650 NKSDWM-ELSRKAEASGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 707

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           +P   K    V D I       + ++ K+ G +G+      + L GL             
Sbjct: 708 VPFFAKLTPNVTDIIS------IARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGIG 761

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 762 KRTTYGGVSGTAIRPIALRAVTAIARALPGFPILATGGIDSAESGLQFL 810


>gi|327401692|ref|YP_004342531.1| dihydroorotate dehydrogenase family protein [Archaeoglobus
           veneficus SNP6]
 gi|327317200|gb|AEA47816.1| dihydroorotate dehydrogenase family protein [Archaeoglobus
           veneficus SNP6]
          Length = 313

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/208 (19%), Positives = 81/208 (38%), Gaps = 31/208 (14%)

Query: 29  ADAILRGDKKNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDF--GYNEINLNVGCPS 85
           +   +R   + +  F  + + PL + +  +   +       +       +   LN+ CP 
Sbjct: 87  SSPGVRAFAEELEKFRAEGRSPLVVSLFASTSEEFAS----LTPHFPMADAFELNLSCPH 142

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
           A     + G+    +P++V + +A + ++   PV  K    V D      +  + K+ ++
Sbjct: 143 AENVGMAVGS----DPELVKEIVAEVKRSTEKPVFAKLSPNVLD------VVEIGKAAEE 192

Query: 146 SGVNG-----------IWIHARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            GV+            I I +RK  L  +S       I  +    V+++ KE  D+ +  
Sbjct: 193 GGVDAVVAVNTVKGMSIDIVSRKPKLSNISGGVSGEAIKPIALKCVWDLYKEL-DVPVIG 251

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAY 220
            GG+      ++ IL     V IG A +
Sbjct: 252 VGGITTWKDVVEFILAGATAVQIGSALF 279


>gi|300814247|ref|ZP_07094523.1| dihydroorotate dehydrogenase 1B [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300511671|gb|EFK38895.1| dihydroorotate dehydrogenase 1B [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 300

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 73/194 (37%), Gaps = 24/194 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  + + VE A+I+ED  +N + LNV CP   V +G     L   P  + + +  + K
Sbjct: 100 LGGNTLDEYVEGAEILEDLDFNFLELNVSCP--NVSKGGMAFGLEAGP--LFEVVKNVRK 155

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILK 161
                + VK      D      +  + ++ +++G +G+ +              +     
Sbjct: 156 VTKKKLIVKLSPNARD------MVEVARACQEAGADGVSLINTILGMAIDFDKRKNVFNN 209

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
             +      +  +   +V++I +   D+ I   GG+      L+ L      V +G   +
Sbjct: 210 DYAGLSGPCVKPIALRMVHQISRAI-DIPIVAMGGVTSYKDVLEFLMVGASAVEVGTYNF 268

Query: 221 KNSAMLTTVDEYFS 234
            N      + E   
Sbjct: 269 MNPYGPKEIIEDLE 282


>gi|124298016|gb|AAI31779.1| Dihydropyrimidine dehydrogenase [Homo sapiens]
          Length = 1025

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 38/169 (22%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NGI      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGITATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|296489272|gb|DAA31385.1| dihydropyrimidine dehydrogenase [Bos taurus]
          Length = 1025

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 69/209 (33%), Gaps = 35/209 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E ++  E  G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNRNDWM-ELSRKAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVRIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G NG+                         ++    G+S    R I       V 
Sbjct: 723 AAKEGGANGVTATNTVSGLMGLKADGTPWPAVGREKRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS 209
            I +  P+  I   GG++     L+ L  
Sbjct: 780 TIARALPEFPILATGGIDSAESGLQFLHG 808


>gi|27806651|ref|NP_776466.1| dihydropyrimidine dehydrogenase [NADP+] [Bos taurus]
 gi|2498309|sp|Q28007|DPYD_BOVIN RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|677951|gb|AAB40985.1| dihydropyrimidine dehydrogenase [Bos taurus]
          Length = 1025

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 69/209 (33%), Gaps = 35/209 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E ++  E  G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNRNDWM-ELSRKAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVRIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G NG+                         ++    G+S    R I       V 
Sbjct: 723 AAKEGGANGVTATNTVSGLMGLKADGTPWPAVGREKRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILPS 209
            I +  P+  I   GG++     L+ L  
Sbjct: 780 TIARALPEFPILATGGIDSAESGLQFLHG 808


>gi|238916477|ref|YP_002929994.1| dihydroorotate oxidase [Eubacterium eligens ATCC 27750]
 gi|238871837|gb|ACR71547.1| dihydroorotate oxidase [Eubacterium eligens ATCC 27750]
          Length = 303

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 80/231 (34%), Gaps = 33/231 (14%)

Query: 26  MIVADAILRGDKKNILGFSTQ-----EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +        +          +  + + + G   +  V+A + + +   + + +N
Sbjct: 69  MMNAIGLQNPGLDTFVKRDIPFLKQYDTKIIVNVCGKSEADYVDAVEKLGEQPVDLLEIN 128

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +    G      P        A+ K    PV +K    V D      +  + 
Sbjct: 129 ISCP----NVKEGGIAFGQVPSSAEAITKAVKKVAKQPVIMKLSPNVTD------ITEMA 178

Query: 141 KSIKKSGVNG-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K+++  G +            I ++ R  A+    +      I  +   +VY++     +
Sbjct: 179 KAVEAGGADAVSLINTLTGMKIDVNRRTFAVANKTAGVSGPAIHPIAVRMVYQVANAI-N 237

Query: 189 LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           L I   GG+     AL++ +     V +G A + +      ++  + EY  
Sbjct: 238 LPIIGMGGIRTAEDALEMIMVGASAVAVGTANFNDPYTTIKVIDGIREYME 288


>gi|205373300|ref|ZP_03226104.1| dihydroorotate dehydrogenase 1B [Bacillus coahuilensis m4-4]
          Length = 312

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 84/224 (37%), Gaps = 28/224 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARV 88
           + ++  + + +  F     P+   + G+     V+ AK +      N + LN+ CP+ + 
Sbjct: 79  EGVIESELERLKQFD---VPIIANVAGSVTEDYVQVAKEMSTVSNVNALELNISCPNVKT 135

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              +FG      P++  +   A+ +  S+PV VK    V D      +  + K++++ G 
Sbjct: 136 GGIAFGTI----PEVAMELTKAVKEVSSVPVYVKLSPNVSD------IVAMAKAVEQGGA 185

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +GI +                 +           I  +   ++YE+ +   DL I   GG
Sbjct: 186 DGITMINTLIGMTLDEKTGLPILANKTGGLSGPAIKPVALRMIYEVAQHV-DLPIIGMGG 244

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           ++     +  +      V +G A + +  +  T+       L  
Sbjct: 245 IQSAQDVIDFISVGASAVAVGTANFIDPFVCPTIIHDLPEKLDA 288


>gi|238926950|ref|ZP_04658710.1| dihydroorotate oxidase [Selenomonas flueggei ATCC 43531]
 gi|238885184|gb|EEQ48822.1| dihydroorotate oxidase [Selenomonas flueggei ATCC 43531]
          Length = 314

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 31/202 (15%), Positives = 72/202 (35%), Gaps = 24/202 (11%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            + +         + + I G+ + +  E A  +   G   + +N+ CP   V EG     
Sbjct: 92  HETLPRIQDYGMNVIVNISGSSVEEYAEVADRLNVPGVAALEVNISCP--NVREGGIVFG 149

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG------ 150
              +P    + + A+    + PV  K    V       ++  +  +++ +G +       
Sbjct: 150 --TDPRAAAEVVRAVRAKSNHPVMAKLSPNV------TSITEMALAVEDAGADAVSLINT 201

Query: 151 -----IWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                I IH  + +L   +       +  +   +V+E+      + +   GG+     A+
Sbjct: 202 LVGMQIDIHRWQPVLGNRTGGLSGPAVKPIAVRMVWEVA-HVVHIPVIGMGGIASWQDAV 260

Query: 205 K-ILPSVDGVMIGRAAYKNSAM 225
           +  L     V +G A + +  +
Sbjct: 261 EFFLAGASAVAVGTANFADPKI 282


>gi|329122077|ref|ZP_08250685.1| dihydroorotate oxidase [Dialister micraerophilus DSM 19965]
 gi|327466884|gb|EGF12400.1| dihydroorotate oxidase [Dialister micraerophilus DSM 19965]
          Length = 301

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 35/206 (16%), Positives = 77/206 (37%), Gaps = 25/206 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   I G    +  + A+ +   G + + +N+ CP+ +      G     NP    +
Sbjct: 92  DVPVIANIFGKTKEEYGKVARALTVEGVSALEVNISCPNIK----EGGVAFGTNPLSAAE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
               + +   +PV +K    V D      +  + K+++ +G + I            +  
Sbjct: 148 ITKEVKRNTHLPVIMKLSPNVTD------IAAIAKAVENAGADAISLINTLLGISIDLRT 201

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
           R+ +L           I  +   +V++++    ++ I   GG+     A +      D V
Sbjct: 202 RRPVLGNITGGLSGPAIKPVALRMVWQVRNAV-NIPICGMGGIMTGKDAAEFFIAGSDIV 260

Query: 214 MIGRAAYKNS-AMLTTVDEYFSNPLT 238
            +G A   N  A++   DE  +   +
Sbjct: 261 QVGTANLINPDAIMRITDELNAWGDS 286


>gi|260438028|ref|ZP_05791844.1| dihydroorotate oxidase [Butyrivibrio crossotus DSM 2876]
 gi|292809507|gb|EFF68712.1| dihydroorotate oxidase [Butyrivibrio crossotus DSM 2876]
          Length = 300

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 63/190 (33%), Gaps = 24/190 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      VE  + +     + + +N+ CP    +    G     N   +  
Sbjct: 92  DTKIIVNVCGKSERDYVEVVERLAGEPVDMLEINISCP----NVKEGGIAFGQNAANIEH 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARK----- 157
              A+      PV +K    V D      +  + K+ +  G + +     I   K     
Sbjct: 148 ITKAIKNVAKQPVIMKLSPNVTD------ITEMAKAAEAGGADVLSLINTITGMKIDINR 201

Query: 158 ---AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++      + I   GG+     AL+ IL     V
Sbjct: 202 QTFAVANKTGGLSGPAVKPVAVRMVYQVANAV-KIPIIGMGGIATAEDALEFILAGATAV 260

Query: 214 MIGRAAYKNS 223
            IG A + N 
Sbjct: 261 SIGTANFHNP 270


>gi|224077972|ref|XP_002305469.1| predicted protein [Populus trichocarpa]
 gi|222848433|gb|EEE85980.1| predicted protein [Populus trichocarpa]
          Length = 224

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 65/208 (31%), Gaps = 50/208 (24%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           +GCP   V     G+ L+  P  +   I A           + +  VD          L+
Sbjct: 1   MGCPIDIVVSKGAGSSLLTKPMRMKSIIEAASG------YFEGKNRVDS---------LI 45

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLED 199
             I       + IH R                  D+D +Y+  ++ P+ L +  NG +  
Sbjct: 46  ADIGNWEAGAVTIHGRSC--------QQHYSNLADWDYIYQCARKAPEYLQVFGNGDVFS 97

Query: 200 MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
                K   ++D               T + E     ++     +  + KD+ R      
Sbjct: 98  RVDWNKH--TLD--------------FTEIKEQRRWDISSGE--RLNILKDYVRS----- 134

Query: 260 TDYAARHLHSGGKLQQITRHMIGLFHGF 287
                 H  S  K  + TRH +  + G+
Sbjct: 135 ---GLEHWGSDTKGVETTRHFLLEWLGY 159


>gi|187933348|ref|YP_001886765.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum B str.
           Eklund 17B]
 gi|187721501|gb|ACD22722.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           botulinum B str. Eklund 17B]
          Length = 298

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 78/227 (34%), Gaps = 29/227 (12%)

Query: 26  MIVADAI----LRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +    + G  KN L         +   +GG       EA + + D   N I LN
Sbjct: 65  MMNSVGLQNPGIEGFIKNELPKMQKLNTNILANVGGGCFEDYAEAIEKLNDTEVNMIELN 124

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP+ +    ++G        +  + +  + K    P+ VK          A  +  + 
Sbjct: 125 ISCPNVKCGGMAYGI----KSQVAYEFVKEIKKICKKPLMVKLSP------NAENIVEMA 174

Query: 141 KSIKKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPD 188
              +++G +            I  + RK I     +      +  +   +V+E+ K    
Sbjct: 175 AKCEEAGADSLSLINTLKGLAIDPYKRKPIFNNVYAGLSGPAVKPVALRMVHEVSKAVSI 234

Query: 189 LFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             IGL GG+ + +     ++     V IG   + N      + E   
Sbjct: 235 PVIGL-GGISNGIDAIEFMMAGARAVQIGTVNFVNPMAGKEIIEEME 280


>gi|301299460|ref|ZP_07205736.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852942|gb|EFK80550.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 314

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/213 (20%), Positives = 86/213 (40%), Gaps = 29/213 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   +GGA     VE A  +   G  N + LN+ CP   VHEG        
Sbjct: 92  LREKYPELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCP--NVHEGGMAFG--T 147

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
            P++       + +  ++PV VK    V D      +  + K++++ G +GI        
Sbjct: 148 VPEVAERLTKKVKEVSTVPVYVKLSPNVTD------IVAIAKAVERGGADGISMINTVLG 201

Query: 153 ----IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
               + + K +L   +     + +  +   ++Y++ + N DL I   GG+E +   L++ 
Sbjct: 202 MHIDVASGKPVLGNIMGGLSGKAVKAIAIRMIYQVAQ-NTDLPIIGMGGVETVDDVLEMY 260

Query: 207 LPSVDGVMIGRAAYKN----SAMLTTVDEYFSN 235
           +     V +G A + +      ++  + +    
Sbjct: 261 MAGASAVAVGTAHFHDSMICPHLIEELPKRMEE 293


>gi|218778655|ref|YP_002429973.1| dihydroorotate dehydrogenase family protein [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760039|gb|ACL02505.1| dihydroorotate dehydrogenase family protein [Desulfatibacillum
           alkenivorans AK-01]
          Length = 306

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 79/203 (38%), Gaps = 29/203 (14%)

Query: 49  PLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL L I G    +    AA+I        I +N+ CP    +  + G    ++P +    
Sbjct: 98  PLVLNIYGKTSEEYERLAARIDNVEDVAGIEVNISCP----NVSAGGIAFGVDPMMAARL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
           +  +      PV VK    V D      +  + ++++ +G + I            + AR
Sbjct: 154 VGKVRARTRKPVIVKLSPNVTD------VTAIARAVEDAGADAISLINTLTGMAIDLDAR 207

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + +L           I  +   +V+++ K    + +   GG+ +   AL+ ++     + 
Sbjct: 208 RPVLANITGGLSGPAIKPVALRMVWQVAK-VVKVPVIGIGGIMNARDALEFLMAGASAIQ 266

Query: 215 IGRAAYKNSA----MLTTVDEYF 233
           +G A + + A    +L  ++ YF
Sbjct: 267 VGTANFVDPASPVKILEGIEAYF 289


>gi|149025817|gb|EDL82060.1| rCG28563 [Rattus norvegicus]
          Length = 557

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 68/204 (33%), Gaps = 29/204 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  L   I         + E +K+ E  G + + LN+
Sbjct: 143 ELISEKTAAYWCHSVTELKADFPDNILIASIMCSYNKNDWM-ELSKMAEASGADALELNL 201

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +++ +P   K    V D      + ++ +
Sbjct: 202 SCPHGM-GERGMGLACGQDPELVRNICRWVRQSVRVPFFAKLTPNVTD------IVSIAR 254

Query: 142 SIKKSGVNGIWIHARKAILKGL------------------SPKDNRKIPNLDYDIVYEIK 183
           + K+ G +G+      + L GL                         I  +    V  I 
Sbjct: 255 AAKEGGADGVTATNTVSGLMGLKADGSPWPSVGSGKRTTYGGVSGTAIRPIALRAVTAIA 314

Query: 184 KENPDLFIGLNGGLEDMSQALKIL 207
           +  P   I   GG++     L+ L
Sbjct: 315 RALPGFPILATGGIDSAESGLQFL 338


>gi|126649697|ref|ZP_01721933.1| dihydroorotate dehydrogenase [Bacillus sp. B14905]
 gi|126593416|gb|EAZ87361.1| dihydroorotate dehydrogenase [Bacillus sp. B14905]
          Length = 303

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 81/238 (34%), Gaps = 38/238 (15%)

Query: 26  MIVADAI----LRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINL 79
           M+ A  +    +       L F    + P+   + G +    VE A+ +        + L
Sbjct: 67  MLNAIGLQNPGIEKVMNEELKFLEGYDVPIIANVAGTETEDYVEVARRISAAPNVQALEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P    + + A+    ++PV VK    V        + ++
Sbjct: 127 NISCP----NVKCGGIQFGTDPTTARELVKAVKAVSTVPVYVKLSPNV------TNIVDI 176

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
             +++  G +GI +              +  I  G        +  +   +VYE+ K   
Sbjct: 177 ALAVEAGGADGITMINTLVGMRLDERTGKPVIANGTGGLSGPAVKPVAIRMVYEVYKAV- 235

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           ++ I   GG+ +    +  +      V +G A +        VD +    +    P K
Sbjct: 236 NIPIIGMGGVTEAQDVIDFMSAGASAVAVGTANF--------VDHFVCPNIIDELPAK 285


>gi|323700196|ref|ZP_08112108.1| dihydroorotate dehydrogenase family protein [Desulfovibrio sp.
           ND132]
 gi|323460128|gb|EGB15993.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           desulfuricans ND132]
          Length = 300

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/207 (19%), Positives = 77/207 (37%), Gaps = 27/207 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA  + D   + GF T+   +A+ I G  I + VE A+ +     + + LN+ CP    +
Sbjct: 78  DAFCQDDIPFLRGFDTK---IAVNIAGRTIDEYVEVAERLASADVDLLELNISCP----N 130

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G    ++P +      A+      P+ VK    V D      +  + ++++  G +
Sbjct: 131 VKEGGVAFGVDPAMAEAVTRAVKAVAGQPLIVKLSPNVTD------IAAIARAVEAGGAD 184

Query: 150 G-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                       I +H R  +L           I  +   +VY++ +    L I   GG+
Sbjct: 185 AVSLINTLLGARIDVHRRAFVLSTKQGGLSGPAIKPVAVRMVYQVARAV-HLPIIGMGGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNS 223
                A + ++     V +G A     
Sbjct: 244 MTGEDAAEFLMAGATAVAVGTANLFKP 270


>gi|224543225|ref|ZP_03683764.1| hypothetical protein CATMIT_02425 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523858|gb|EEF92963.1| hypothetical protein CATMIT_02425 [Catenibacterium mitsuokai DSM
           15897]
          Length = 306

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/200 (19%), Positives = 80/200 (40%), Gaps = 25/200 (12%)

Query: 54  IGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           IGG+ I   V+ AAK+ ++     + LN+ CP   VH G        +P +  +   A+ 
Sbjct: 101 IGGSCIDDYVQTAAKLTKEDCIGALELNISCP--NVHAGGMAIG--TDPAMAAEVTRAVK 156

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAIL 160
             ++ P+ VK    V D      +  + K+++++G +GI +              +  I 
Sbjct: 157 AVITKPLYVKLSPNVTD------IVAIAKAVEEAGADGISMINTLVGMRFDIRSGKPIIA 210

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAA 219
                     I  +   +VY++ +      IG+ GG+     A++++      V +G A 
Sbjct: 211 NKTGGYSGPAIFPVALRMVYQVSQAVNIPVIGM-GGISTGRDAIEMMIAGASAVQVGCAN 269

Query: 220 YKNSAMLTTVDEYFSNPLTG 239
             +      + +  ++ L  
Sbjct: 270 LVDPYACPRIIQEMNDELDA 289


>gi|220936434|ref|YP_002515333.1| dihydroorotate dehydrogenase 1 [Thioalkalivibrio sp. HL-EbGR7]
 gi|219997744|gb|ACL74346.1| dihydroorotate dehydrogenase 1 [Thioalkalivibrio sp. HL-EbGR7]
          Length = 321

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 76/212 (35%), Gaps = 27/212 (12%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            E      + G+ I + +   +  +D   + I +N+ CP    +    G     +PD+  
Sbjct: 101 DETRFIANVSGSTIEEYIAVTRRFDDSPVDAIEINISCP----NVKEGGVAFGNDPDMSA 156

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
             + A  +    P+  K      D      +    +   ++G +   +            
Sbjct: 157 RVVEACRQVTQKPLITKLSPNQTD------IAENARRCIEAGTDAFAVINTLMGMAIDAE 210

Query: 155 ARKAI----LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
           +R+A+      GLS    + I  L    VY++ + +  + I   GG+   S AL+ L   
Sbjct: 211 SREAVIGNNQGGLSGPAIKPIALLKVHQVYQVARPHG-VPIIGQGGVTSPSDALEFLIAG 269

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
              V +G A + +  +   +++   + L    
Sbjct: 270 ASAVGVGTALFYDPLICKKINQGIRDYLDRHD 301


>gi|291544812|emb|CBL17921.1| dihydroorotate oxidase B, catalytic subunit [Ruminococcus sp.
           18P13]
          Length = 303

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/225 (17%), Positives = 86/225 (38%), Gaps = 28/225 (12%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K +     ++  +   I G+ + + V  A+ +E    + I LN+ CP+ +    +FGA  
Sbjct: 84  KELPYLMQKDTVILANIAGSTVKECVTIAQQLEQTDVHMIELNISCPNVKQGGMAFGASC 143

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG------- 150
                       A+ KA + P+ VK    V        +  + K+ + +G +        
Sbjct: 144 AG----AESITRAVRKATTKPLVVKLSPNV------TNIAEIAKATETAGADALSLINTL 193

Query: 151 ----IWIHARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               I I +R+ ILK  +       I  +   +V++       + I   GG+     A++
Sbjct: 194 LGMRIDIRSRRPILKNNMGGMSGAAIFPIAVRMVWQCANAV-RIPIIGMGGVTTGKDAIE 252

Query: 206 -ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNPLTGSSPIKT 245
            ++     V +G A + +      ++  ++++       ++   T
Sbjct: 253 LMMAGASAVQVGAAIFTDPYAPIRIIREMNQWLDENHIATARELT 297


>gi|154150653|ref|YP_001404271.1| dihydroorotate dehydrogenase 1B [Candidatus Methanoregula boonei
           6A8]
 gi|153999205|gb|ABS55628.1| dihydroorotate dehydrogenase family protein [Methanoregula boonei
           6A8]
          Length = 296

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 43/201 (21%), Positives = 73/201 (36%), Gaps = 27/201 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           KP+ + I G D  +  E A   +      + LN+ CP A      +GA + +NPD+V  C
Sbjct: 93  KPVIVSIFGGDPEEFAEVAGWFKGM-AAGLELNLSCPHAE----GYGASIGVNPDLVEKC 147

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHA 155
             A+   L +P  VK    V D      +  + K+ ++ G + I                
Sbjct: 148 TRAV-STLGMPTWVKLTPNVTD------ITAIGKAAERGGASAIVAVNTVKAMRISTALR 200

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           R  +           I  +    VYE+ +    L I   GG+      ++ ++     V 
Sbjct: 201 RPVLGNRYGGLSGEAIFPVAVRCVYELYEAC-SLPIIGCGGISSADNVIEMMMAGACAVE 259

Query: 215 IGRAAY-KNSAMLTTVDEYFS 234
           IG A    +  +  T+     
Sbjct: 260 IGSAVQKHDITVFETIKNDLY 280


>gi|320527188|ref|ZP_08028374.1| dihydroorotate dehydrogenase 1B [Solobacterium moorei F0204]
 gi|320132379|gb|EFW24923.1| dihydroorotate dehydrogenase 1B [Solobacterium moorei F0204]
          Length = 306

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/200 (19%), Positives = 74/200 (37%), Gaps = 25/200 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           KP+   I G  + + V  A+ ++       I +N+ CP    +    G     N + V +
Sbjct: 96  KPVIANISGFSVEEYVTLAREMDQVDNVGIIEVNISCP----NVDHGGLAFGTNANNVRE 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
               + +  + PV +K    V D      ++ + ++ ++ G +GI            I+ 
Sbjct: 152 LTKKIKEVTTKPVYMKLSPNVTD------IKEIARAAQEGGADGISLINTLMGMRIDINR 205

Query: 156 RKAI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +            I  +   +VYE+  E  +L I   GG+      ++ ++     V
Sbjct: 206 RKPVIANKKGGFSGPAIFPVALRMVYEVY-EVTNLPIIGIGGISSAEDVIEMMMAGATAV 264

Query: 214 MIGRAAYKNSAMLTTVDEYF 233
            IG A   N      + E  
Sbjct: 265 QIGAANLINPMACKEIIEEL 284


>gi|134046259|ref|YP_001097744.1| putative TIM-barrel protein [Methanococcus maripaludis C5]
 gi|132663884|gb|ABO35530.1| putative TIM-barrel protein [Methanococcus maripaludis C5]
          Length = 256

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/151 (21%), Positives = 63/151 (41%), Gaps = 16/151 (10%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQI 131
             + + LN  C    + + + G  L+ N   + D +  + +  L IP+ +K R      +
Sbjct: 111 NADILELNCHCRQQEITDLNLGQNLLKNEAKLTDFLKNIRELNLKIPIFLKLRANF---L 167

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
            A  L  L+K I++   +GI I          +P+ N      D + + +I++  P+  I
Sbjct: 168 TAEELIELLKKIREY-FDGIHIDC-------FNPRKNY----ADLEYLKKIRESFPEKII 215

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
             N  +  +  A ++L   D V + R    N
Sbjct: 216 IGNNSVNSVESAKEMLKYADFVSVARCVLAN 246


>gi|13591940|ref|NP_112289.1| dihydropyrimidine dehydrogenase [NADP+] [Rattus norvegicus]
 gi|81861573|sp|O89000|DPYD_RAT RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|3628593|dbj|BAA33218.1| dihydropyrimidine dehydrogenase [Rattus norvegicus]
          Length = 1025

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 68/204 (33%), Gaps = 29/204 (14%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  L   I         + E +K+ E  G + + LN+
Sbjct: 611 ELISEKTAAYWCHSVTELKADFPDNILIASIMCSYNKNDWM-ELSKMAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P++V +    + +++ +P   K    V D      + ++ +
Sbjct: 670 SCPHGM-GERGMGLACGQDPELVRNICRWVRQSVRVPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIWIHARKAILKGL------------------SPKDNRKIPNLDYDIVYEIK 183
           + K+ G +G+      + L GL                         I  +    V  I 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKADGSPWPSVGSGKRTTYGGVSGTTIRPIALRAVTAIA 782

Query: 184 KENPDLFIGLNGGLEDMSQALKIL 207
           +  P   I   GG++     L+ L
Sbjct: 783 RALPGFPILATGGIDSAESGLQFL 806


>gi|282882167|ref|ZP_06290806.1| dihydroorotate oxidase [Peptoniphilus lacrimalis 315-B]
 gi|281297932|gb|EFA90389.1| dihydroorotate oxidase [Peptoniphilus lacrimalis 315-B]
          Length = 300

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 73/194 (37%), Gaps = 24/194 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  + + VE A+I+ED  +N + LNV CP   V +G     L   P  + + +  + K
Sbjct: 100 LGGNTLDEYVEGAEILEDLDFNFLELNVSCP--NVSKGGMAFGLEAGP--LFEVVKNVRK 155

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILK 161
                + VK      D      +  + ++ +++G +G+ +              +     
Sbjct: 156 VTKKKLIVKLSPNARD------MVEVARACQEAGADGVSLINTILGMAIDFDKRKNVFNN 209

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
             +      +  +   +V++I +   D+ I   GG+      L+ L      V +G   +
Sbjct: 210 DYAGLSGPCVKPIALRMVHQISRAI-DIPIVAMGGVTSYKDVLEFLMVGASAVEVGTYNF 268

Query: 221 KNSAMLTTVDEYFS 234
            N      + E   
Sbjct: 269 MNPYGPKEIIEDLE 282


>gi|291459995|ref|ZP_06599385.1| dihydroorotate oxidase [Oribacterium sp. oral taxon 078 str. F0262]
 gi|291417336|gb|EFE91055.1| dihydroorotate oxidase [Oribacterium sp. oral taxon 078 str. F0262]
          Length = 303

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 81/231 (35%), Gaps = 37/231 (16%)

Query: 26  MIVADAILRGDKKNILGFSTQE------KPLALQIGGADISKLVEAAKIVEDF----GYN 75
           M+ +  +     +N++     E      KP+   I G     + E  ++ E+        
Sbjct: 67  MLNSVGLQNPGLRNVIEHELPELSEFFHKPVIANISG---FSIAEYIELAEEMDQVKNVG 123

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            + LNV CP    +    G     + D V      + KA   PV VK    V D      
Sbjct: 124 ILELNVSCP----NVRGGGLAFGTDADNVYTLCCGVKKATKKPVYVKLSPNVTD------ 173

Query: 136 LRNLVKSIKKSGVNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIK 183
           + ++ K+ +K G +GI            I  R+ +LK          I  +   +VY+++
Sbjct: 174 IVSIAKACEKGGADGISLINTLLGLRIDIQRRRTVLKNRMGGLSGPAIFPVALRMVYQVR 233

Query: 184 KENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           +      IG+ GG+      ++ ++     V IG        +   +    
Sbjct: 234 RAVKIPLIGM-GGISSAEDVIEMMMAGASAVQIGAMNLTEPLICQRIIREL 283


>gi|300214100|gb|ADJ78516.1| Dihydroorotate dehydrogenase [Lactobacillus salivarius CECT 5713]
          Length = 314

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/213 (20%), Positives = 86/213 (40%), Gaps = 29/213 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   +GGA     VE A  +   G  N + LN+ CP   VHEG        
Sbjct: 92  LREKYPELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCP--NVHEGGMAFG--T 147

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
            P++       + +  ++PV VK    V D      +  + K++++ G +GI        
Sbjct: 148 VPEVAERLTKKVKEVSTVPVYVKLSPNVTD------IVAIAKAVERGGADGISMINTVLG 201

Query: 153 ----IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
               + + K +L   +     + +  +   ++Y++ + N DL I   GG+E +   L++ 
Sbjct: 202 MHIDVASGKPVLGNIMGGLSGKAVKAIAIRMIYQVAQ-NTDLPIIGMGGVETVDDVLEMY 260

Query: 207 LPSVDGVMIGRAAYKN----SAMLTTVDEYFSN 235
           +     V +G A + +      ++  + +    
Sbjct: 261 MAGASAVAVGTAHFHDSMICPHLIEELPKRMEE 293


>gi|295104394|emb|CBL01938.1| dihydroorotate oxidase B, catalytic subunit [Faecalibacterium
           prausnitzii SL3/3]
          Length = 308

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 75/187 (40%), Gaps = 32/187 (17%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG    + VE A ++ +   + + LN+ CP+ +V   ++G       +  G+ +  +  
Sbjct: 104 LGGHSEEEYVEGAAMLSESAVDIVELNISCPNVKVGGMAYGV----KAEAAGEVVRMVRA 159

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK- 161
           A   P+ VK          A ++  + K+++ +G + I            +  R+ +   
Sbjct: 160 ACKKPLMVKLSPQ------AESIPEMCKAVEAAGADAISLTNTFQACAIDLEKRRPVFNN 213

Query: 162 ---GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
              GLS    R I   + +  V  +     ++ +   GG+     AL+ I+     V +G
Sbjct: 214 IFAGLSGPAVRPIALRMVWQAVGAV-----NIPVVGLGGIATGRDALEFIMAGATAVQVG 268

Query: 217 RAAYKNS 223
            A + N 
Sbjct: 269 AANFANP 275


>gi|213423731|ref|ZP_03356711.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 135

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 42/109 (38%), Gaps = 8/109 (7%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           Q+ G     L E A      G   ++LN GCPS  V+    GA L+ +P
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDLNCGCPSKVVNGSGGGATLLTDP 135


>gi|294786896|ref|ZP_06752150.1| dihydroorotate oxidase [Parascardovia denticolens F0305]
 gi|294485729|gb|EFG33363.1| dihydroorotate oxidase [Parascardovia denticolens F0305]
          Length = 353

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 28/187 (14%), Positives = 66/187 (35%), Gaps = 23/187 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       +  + + D   + + +NV CP    +  + G  +  +P  +   + 
Sbjct: 142 VVTNVAGHSNDDYCQVVEKLADSPADMLEINVSCP----NVSAGGMAVGSDPAALEVLMK 197

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARK 157
            +      P+ VK    + D      +  + ++   +G + + +              R 
Sbjct: 198 RLRPLADKPLIVKLTPNITD------ITTVARAAVDNGADALSLINTFVGMRIDIRTGRP 251

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
            I           I  +   +VY++++  P + +   GG+     AL+ L    + V +G
Sbjct: 252 IIANVTGGVSGPAIHPMALAMVYKVRQALPHIPLIGIGGIATAEDALEFLYAGANAVEVG 311

Query: 217 RAAYKNS 223
            AA  + 
Sbjct: 312 SAALIDP 318


>gi|270308537|ref|YP_003330595.1| dihydroorotate dehydrogenase [Dehalococcoides sp. VS]
 gi|270154429|gb|ACZ62267.1| dihydroorotate dehydrogenase [Dehalococcoides sp. VS]
          Length = 417

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 70/189 (37%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + I    I    E A+ ++   G + I +N+ CP    +          +P+     
Sbjct: 209 PVIVNIAAESIEDYAELARRLDKVPGVSGIEVNISCP----NVKCGCIEFGSSPESAARV 264

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
             A+  A ++P+ +K            ++  L +++  +G + I            I  R
Sbjct: 265 TDAVRNATTLPLIIKLTP------NTSSIIELARAVADAGADAISLINTLRGMRIDIKKR 318

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + IL           I  +   +VY++     ++ +   GG+ +   AL+ I+     + 
Sbjct: 319 RPILGNHTGGLSGPAIKPVAVSMVYQVSGAV-NVPVIGGGGIMNAEDALEFIMAGATAIQ 377

Query: 215 IGRAAYKNS 223
           IG A   N 
Sbjct: 378 IGTANLVNP 386


>gi|226325469|ref|ZP_03800987.1| hypothetical protein COPCOM_03274 [Coprococcus comes ATCC 27758]
 gi|225206212|gb|EEG88566.1| hypothetical protein COPCOM_03274 [Coprococcus comes ATCC 27758]
          Length = 300

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 70/196 (35%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +E  + + D   + + +N+ CP    +  +       +   V +
Sbjct: 92  DTKIIVNVCGHAPEEYLEVVERLADEPIDMMEINISCP----NVNAGFLAFGQDAKHVEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               + K    P+ +K    V D      +  + K+ +  G + + +             
Sbjct: 148 LTGQIKKIAKQPIIMKLTPNVTD------ITEIAKAAEAGGADAVSLINTLTGMKIDINR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++ +   ++ I   GG+     A++ +L     V
Sbjct: 202 KTFAVANKTGGVSGPIVKPIAVRMVYQVAQAV-NIPIIGMGGISCAEDAIEFLLAGASAV 260

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A + N A+   V
Sbjct: 261 SVGTANFHNPAVTMEV 276


>gi|325849658|ref|ZP_08170861.1| hypothetical protein HMPREF9246_1705 [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325479999|gb|EGC83077.1| hypothetical protein HMPREF9246_1705 [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 109

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 5/94 (5%)

Query: 2   VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADI 59
              +D  +R  +         +TEM+  +A+   +KK   +L  S  EK   +Q+ G+  
Sbjct: 16  AGVSDVGFRLISEKY-GADKTFTEMVSVNALYYDNKKTNDLLFISENEKNCNIQLFGSKP 74

Query: 60  SKLVEAAKIVEDF--GYNEINLNVGCPSARVHEG 91
             + +  K   ++     EI+ N+GCP A++ + 
Sbjct: 75  EVIEKVIKDKINYIDRSKEISFNMGCPVAKITKK 108


>gi|150401339|ref|YP_001325105.1| dihydroorotate dehydrogenase 1B [Methanococcus aeolicus Nankai-3]
 gi|150014042|gb|ABR56493.1| dihydroorotate dehydrogenase family protein [Methanococcus aeolicus
           Nankai-3]
          Length = 305

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/202 (22%), Positives = 79/202 (39%), Gaps = 27/202 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G D ++  + A+ +  F  + I LN+ CP A    G +GA +  NPD+    ++
Sbjct: 97  IIGSIYGKDSNEFSKVAETISPF-VDVIELNISCPHA---GGFYGAQIGQNPDLSHSVVS 152

Query: 110 AMCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHAR 156
           A+   ++  PV  K    V D      ++ + KS++ +G +GI             I  +
Sbjct: 153 AVKDCVNKQPVMAKLTPNVAD------IKEIAKSVEDAGADGIVAINTLGPGMVIDIETK 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVM 214
           K IL         + I  +    VY+I     +L I   GG+   +     +L     V 
Sbjct: 207 KPILGNKFGGMSGKAIKPIAIKNVYDIYSAV-ELPIIGVGGITMGLDAIEFMLAGASAVQ 265

Query: 215 IGRAAYKNSA-MLTTVDEYFSN 235
           +G   Y     +   + E    
Sbjct: 266 VGTGVYYRGYDIFDKICEEMEQ 287


>gi|325913770|ref|ZP_08176131.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners UPII 60-B]
 gi|325476970|gb|EGC80121.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners UPII 60-B]
          Length = 306

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 85/205 (41%), Gaps = 29/205 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL   +GG+ IS  +  +K + D G  N + +NV CP    +  + G  L  +P +V   
Sbjct: 98  PLIASVGGSQISDYITISKKLSDSGLLNALEINVSCP----NVAAGGMHLGTDPVVVEKL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
            + + K ++IPV +K    V        +  + ++ ++ G +           GI I   
Sbjct: 154 TSEIKKVVNIPVYIKLTPNV------TNIVEIAQAAERGGADGLSMINTLLGLGIDIKTH 207

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           KA L  G        I  +   +V ++ +    L I   GG+E  +  ++ +L     V 
Sbjct: 208 KATLGNGFGGWSGSAIKPVAVRMVAQVHQAV-KLPIIGMGGIETAADIVEFMLAGASAVA 266

Query: 215 IGRAAYKN----SAMLTTVDEYFSN 235
           +G A +K+      ++  ++   + 
Sbjct: 267 VGTAHFKDGLAIPHLVADLETLLNE 291


>gi|188590495|ref|YP_001921441.1| dihydropyrimidine dehydrogenase [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500776|gb|ACD53912.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E3 str. Alaska E43]
          Length = 412

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 41/198 (20%), Positives = 70/198 (35%), Gaps = 22/198 (11%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLN 80
           E I    + +  D    L  +   K +   I G +      L   AK+V + G + I  N
Sbjct: 79  EQISDHPLQQNLDDLRRLKENYPTKIVVASIMGENEKEWEDL---AKLVTEAGADMIECN 135

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI--------- 131
             CP    HE         NP++V     A  +  ++P+  K    + D           
Sbjct: 136 FSCPQMTSHEMGSDVG--QNPELVKKYCEATRRGTNLPILAKMTPNIGDMSVPAIASMEG 193

Query: 132 --PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENP 187
               +A  N +KSI    +N +           +S    + +  +    +YE+ K  +  
Sbjct: 194 GATGLATINTIKSITGIDINSMTAKPVVNAKSSVSGYSGKAVKPIALRFIYELAKNEKLK 253

Query: 188 DLFIGLNGGLEDMSQALK 205
            + I   GG+E    AL+
Sbjct: 254 GVPISGIGGIETWEDALE 271


>gi|251777769|ref|ZP_04820689.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
 gi|243082084|gb|EES47974.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
          Length = 412

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 41/198 (20%), Positives = 70/198 (35%), Gaps = 22/198 (11%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLN 80
           E I    + +  D    L  +   K +   I G +      L   AK+V + G + I  N
Sbjct: 79  EQISDHPLQQNLDDLRRLKENYPTKIVVASIMGENEKEWEDL---AKLVTEAGADMIECN 135

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI--------- 131
             CP    HE         NP++V     A  +  ++P+  K    + D           
Sbjct: 136 FSCPQMTSHEMGSDVG--QNPELVKKYCEATRRGTNLPILAKMTPNIGDMSVPAIASMEG 193

Query: 132 --PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENP 187
               +A  N +KSI    +N +           +S    + +  +    +YE+ K  +  
Sbjct: 194 GATGLATINTIKSITGIDINSMTAKPVVNAKSSVSGYSGKAVKPIALRFIYELAKNEKLK 253

Query: 188 DLFIGLNGGLEDMSQALK 205
            + I   GG+E    AL+
Sbjct: 254 GVPISGIGGIETWEDALE 271


>gi|90961176|ref|YP_535092.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius UCC118]
 gi|90820370|gb|ABD99009.1| Dihydroorotate dehydrogenase [Lactobacillus salivarius UCC118]
          Length = 314

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/213 (20%), Positives = 86/213 (40%), Gaps = 29/213 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   +GGA     VE A  +   G  N + LN+ CP   VHEG        
Sbjct: 92  LREKYPELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCP--NVHEGGMAFG--T 147

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
            P++       + +  ++PV VK    V D      +  + K++++ G +GI        
Sbjct: 148 VPEVAERLTKKVKEVSTVPVYVKLSPNVTD------IVAIAKAVERGGADGISMINTVLG 201

Query: 153 ----IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
               + + K +L   +     + +  +   ++Y++ + N DL I   GG+E +   L++ 
Sbjct: 202 MHIDVASGKPVLGNIMGGLSGKAVKAIAIRMIYQVAQ-NTDLPIIGMGGVETVDDVLEMY 260

Query: 207 LPSVDGVMIGRAAYKN----SAMLTTVDEYFSN 235
           +     V +G A + +      ++  + +    
Sbjct: 261 MAGASAVAVGTAHFHDSMICPHLIEELPKRMEE 293


>gi|266620439|ref|ZP_06113374.1| dihydroorotate oxidase [Clostridium hathewayi DSM 13479]
 gi|288867964|gb|EFD00263.1| dihydroorotate oxidase [Clostridium hathewayi DSM 13479]
          Length = 238

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 65/202 (32%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      VE  + + D   + + +N+ CP    +    G     +P  V  
Sbjct: 30  DTKIIVNVCGRTTEDYVEVVERLGDEPVDMLEINISCP----NVKEGGIAFGQDPKAVEA 85

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               + K    PV +K    V D         + K+ +  G + I +             
Sbjct: 86  ITREVKKHAKQPVIMKLSPNVTDITV------MAKAAEAGGADVISLINTLTGMKIDINR 139

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY+       + I   GG+ +   AL+ IL     V
Sbjct: 140 RTFAVANKTGGLSGPAVKPVAVRMVYQAANAV-KIPIIGMGGIMNAEDALEFILAGATAV 198

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A + N      V     N
Sbjct: 199 SVGTANFHNPYATAEVVSGIEN 220


>gi|148706256|gb|EDL38203.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_c [Mus
           musculus]
          Length = 429

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 307 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMT 365

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEG 91
           + A+++      + +++NVGCP   V++ 
Sbjct: 366 KCAELLNRTIDVDFVDINVGCPIDLVYKK 394


>gi|187935649|ref|YP_001886506.1| dihydropyrimidine dehydrogenase [Clostridium botulinum B str.
           Eklund 17B]
 gi|187723802|gb|ACD25023.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           B str. Eklund 17B]
          Length = 412

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 41/198 (20%), Positives = 70/198 (35%), Gaps = 22/198 (11%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLN 80
           E I    + +  D    L  +   K +   I G +      L   AK+V + G + I  N
Sbjct: 79  EQISDHPLQQNLDDLRRLKENYPTKIVVASIMGENEKEWEDL---AKLVTEAGADMIECN 135

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI--------- 131
             CP    HE         NP++V     A  +  ++P+  K    + D           
Sbjct: 136 FSCPQMTSHEMGSDVG--QNPELVKKYCEATRRGTNLPILAKMTPNIGDMSVPAIASMEG 193

Query: 132 --PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENP 187
               +A  N +KSI    +N +           +S    + +  +    +YE+ K  +  
Sbjct: 194 GATGLATINTIKSITGIDINSMTAKPVVNAKSSVSGYSGKAVKPIALRFIYELAKNEKLK 253

Query: 188 DLFIGLNGGLEDMSQALK 205
            + I   GG+E    AL+
Sbjct: 254 GVPISGIGGIETWEDALE 271


>gi|30851162|gb|AAH52481.1| Dus3l protein [Mus musculus]
          Length = 426

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLV 63
           +  +R   +      +   EM V   +L+G      +L     E    +Q+ GA    + 
Sbjct: 304 NLPFRRICKRF-GADVTCGEMAVCTNLLQGQMSEWALLKRHPCEDIFGVQLEGAFPDTMT 362

Query: 64  EAAKIVEDF-GYNEINLNVGCPSARVHEG 91
           + A+++      + +++NVGCP   V++ 
Sbjct: 363 KCAELLNRTIDVDFVDINVGCPIDLVYKK 391


>gi|315226530|ref|ZP_07868318.1| dihydroorotate dehydrogenase [Parascardovia denticolens DSM 10105]
 gi|315120662|gb|EFT83794.1| dihydroorotate dehydrogenase [Parascardovia denticolens DSM 10105]
          Length = 357

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 28/187 (14%), Positives = 66/187 (35%), Gaps = 23/187 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       +  + + D   + + +NV CP    +  + G  +  +P  +   + 
Sbjct: 146 VVTNVAGHSNDDYCQVVEKLADSPADMLEINVSCP----NVSAGGMAVGSDPAALEVLMK 201

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARK 157
            +      P+ VK    + D      +  + ++   +G + + +              R 
Sbjct: 202 RLRPLADKPLIVKLTPNITD------ITTVARAAVDNGADALSLINTFVGMRIDIRTGRP 255

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
            I           I  +   +VY++++  P + +   GG+     AL+ L    + V +G
Sbjct: 256 IIANVTGGVSGPAIHPMALAMVYKVRQALPHIPLIGIGGIATAEDALEFLYAGANAVEVG 315

Query: 217 RAAYKNS 223
            AA  + 
Sbjct: 316 SAALIDP 322


>gi|251778858|ref|ZP_04821778.1| dihydroorotate oxidase [Clostridium botulinum E1 str. 'BoNT E
           Beluga']
 gi|243083173|gb|EES49063.1| dihydroorotate oxidase [Clostridium botulinum E1 str. 'BoNT E
           Beluga']
          Length = 298

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 39/227 (17%), Positives = 78/227 (34%), Gaps = 29/227 (12%)

Query: 26  MIVADAI----LRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +    + G  KN L         +   +GG       EA + + D   + I LN
Sbjct: 65  MMNSVGLQNPGIEGFIKNELPEMQKLNTNILANVGGGCFEDYAEAIEKLNDTEVDMIELN 124

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP+ +    ++G        +  + +  + K    P+ VK          A  +  + 
Sbjct: 125 ISCPNVKCGGMAYGI----KSQVAYEFVKEIKKICQKPLMVKLSP------NAENIVEMA 174

Query: 141 KSIKKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPD 188
              +++G +            I  + RK I     +      +  +   +V+E+ K    
Sbjct: 175 AKCEEAGADSLSLINTLKGLAIDPYKRKPIFNNVYAGLSGPAVKPVALRMVHEVSKAVSI 234

Query: 189 LFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             IGL GG+ + +     ++     V IG   + N      + E   
Sbjct: 235 PVIGL-GGISNGIDAIEFMMAGARAVQIGTINFVNPMAGKEIIEEME 280


>gi|298529500|ref|ZP_07016903.1| dihydroorotate dehydrogenase family protein [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298510936|gb|EFI34839.1| dihydroorotate dehydrogenase family protein [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 304

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/203 (19%), Positives = 77/203 (37%), Gaps = 27/203 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   +      + VE A I+ D      + +N+ CP    +    G     +P+  
Sbjct: 91  DETPVVANLYAQGAEEFVELAAILGDAPRVGALEVNISCP----NVRCGGVQFGQDPEAA 146

Query: 105 GDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
                 + +A    P+ +K    V D      +R + ++++ +G + I            
Sbjct: 147 ASVTREVRRASPDKPLIIKLSPNVTD------IRVIARAVRDAGADVISLINTLGGMAVD 200

Query: 153 IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           IH+RK  L   +       +  +   +VYE+  E  D+ +   GG+ +    L+ I+   
Sbjct: 201 IHSRKPRLANIVGGLSGPAVKPVALKMVYEVCSEV-DIPVIGLGGICNARDVLEFIMVGA 259

Query: 211 DGVMIGRAAYKNSA-MLTTVDEY 232
             V +G A +     +   VDE 
Sbjct: 260 HAVQVGTANFMRPDLIFDLVDEL 282


>gi|332809597|ref|XP_513583.3| PREDICTED: dihydropyrimidine dehydrogenase [NADP+] isoform 3 [Pan
           troglodytes]
          Length = 1025

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDATPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|300870690|ref|YP_003785561.1| dihydroorotate dehydrogenase [Brachyspira pilosicoli 95/1000]
 gi|300688389|gb|ADK31060.1| dihydroorotate dehydrogenase, DHOD class 1B FMN binding domain
           protein [Brachyspira pilosicoli 95/1000]
          Length = 304

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 42/207 (20%), Positives = 81/207 (39%), Gaps = 30/207 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ L I G+ + + V+ A+I  +    + I LN+ CP    +  + G     + +    
Sbjct: 94  TPIILNINGSTLEEYVKVAEIANEIDRVDFIELNISCP----NVKNGGMAFGASCESAEK 149

Query: 107 CIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIH 154
               + K L   P+ VK    V D      + ++ KS++ +G +            I I 
Sbjct: 150 TTKEVKKVLTKKPLIVKLSPNVTD------IVSIAKSVEYAGADSVSLVNTFLAMKIDIK 203

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            +K +L           I  +   +VY++ K      +G+ GG++    AL+ I+     
Sbjct: 204 TKKPLLGNTFGGLSGAAIMPIALRMVYQVYKAVKIPIVGM-GGIQKYEDALEFIMAGASV 262

Query: 213 VMIGRAAYKNSA----MLTTVDEYFSN 235
           V IG   + N      ++  ++ Y   
Sbjct: 263 VSIGSGIFSNPTLPIEIIKQINNYLEE 289


>gi|291546923|emb|CBL20031.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Ruminococcus sp. SR1/5]
          Length = 301

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 34/205 (16%), Positives = 69/205 (33%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + + +   + + +NV CP    +    G     NP  + +
Sbjct: 93  DTKIIVNVCGKSAKDYCEVVERLGNEPVDMLEINVSCP----NVKEGGIAFGQNPKALEE 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
               + K    PV +K    V D      +  + K+ +  G +            I I+ 
Sbjct: 149 ITKEVKKYAKQPVIMKLSPNVTD------ITEMAKAAEAGGADVLSLINTLTGMKIDINR 202

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R  A+           +  +   +VY++      L I   GG+     AL+ I+     V
Sbjct: 203 RTFALANKTGGMSGPAVKPVAVRMVYQVANAV-SLPIIGMGGIATAEDALEFIMAGATAV 261

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            +G A + N      +   +  +  
Sbjct: 262 SVGTANFFNPYATVEIADGIQAFLE 286


>gi|158255870|dbj|BAF83906.1| unnamed protein product [Homo sapiens]
          Length = 1025

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|55663515|emb|CAH70570.1| dihydropyrimidine dehydrogenase [Homo sapiens]
 gi|55962906|emb|CAI15125.1| dihydropyrimidine dehydrogenase [Homo sapiens]
          Length = 1025

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|124297137|gb|AAI31778.1| Dihydropyrimidine dehydrogenase [Homo sapiens]
          Length = 1025

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|119943098|ref|NP_000101.2| dihydropyrimidine dehydrogenase [NADP+] isoform 1 [Homo sapiens]
 gi|160332325|sp|Q12882|DPYD_HUMAN RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil
           dehydrogenase; Flags: Precursor
 gi|693912|gb|AAB51366.1| dihydropyrimidine dehydrogenase [Homo sapiens]
 gi|6729338|dbj|BAA89789.1| dihydropyrimidine dehydrogenase [Homo sapiens]
 gi|119593409|gb|EAW73003.1| dihydropyrimidine dehydrogenase, isoform CRA_b [Homo sapiens]
          Length = 1025

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|558305|gb|AAA57474.1| dihydropyrimidine dehydrogenase [Homo sapiens]
          Length = 1025

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/169 (21%), Positives = 62/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V  I +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAESGLQFL 806


>gi|332637262|ref|ZP_08416125.1| dihydroorotate dehydrogenase B, catalytic subunit [Weissella
           cibaria KACC 11862]
          Length = 319

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/190 (19%), Positives = 77/190 (40%), Gaps = 25/190 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLML 99
           L  +  + P+ + + G  + +    AK+ +   Y   + LN+ CP   V +G       +
Sbjct: 91  LATALPDLPVMISVAGETVLEYQTLAKVFDRIDYIKALELNLSCP--NVDKGGMEFG--V 146

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
           +P+   + +AA+ +    P+  K    V D  P      + K++  +G +G+        
Sbjct: 147 DPETAAEVVAAVREVTDKPLYAKLSPNVTDIKP------IAKAVADAGADGLVLINTVVG 200

Query: 153 ----IHARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
               +  R+  + +G        I  +   +++E      D+ I   GG++ +  AL+ +
Sbjct: 201 MSLDLATRQPRLYRGTGGMSGAAIHPIAVRMIWE-AASVVDIPIIGVGGVDSIDAALELM 259

Query: 207 LPSVDGVMIG 216
           L     V IG
Sbjct: 260 LAGASAVQIG 269


>gi|167761648|ref|ZP_02433775.1| hypothetical protein CLOSCI_04060 [Clostridium scindens ATCC 35704]
 gi|167660791|gb|EDS04921.1| hypothetical protein CLOSCI_04060 [Clostridium scindens ATCC 35704]
          Length = 300

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 43/208 (20%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D   R D   +  F T+   + + + G       E  + + D   + + +N+ CP    +
Sbjct: 78  DVFCRRDIPFLKQFDTR---IIVNVCGRTTEDYCEVVERLADEAVDMLEINISCP----N 130

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G     NP  V    A + K    PV +K    V D      +    K+ +  G +
Sbjct: 131 VKEGGIAFGQNPKAVETITAEVKKRARQPVIMKLSPNVTD------ITETAKAAEAGGAD 184

Query: 150 G-----------IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                       I IH R  A+           I  +   +VY++      L I   GG+
Sbjct: 185 VLSLINTLTGMKIDIHKRAFALANRTGGLSGPAIKPIAVRMVYQVGNAV-KLPIIGMGGI 243

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSA 224
                A++ +L     V +G A + N A
Sbjct: 244 ATAEDAIEFLLAGATAVSVGTANFFNPA 271


>gi|257051848|ref|YP_003129681.1| dihydropyrimidine dehydrogenase [Halorhabdus utahensis DSM 12940]
 gi|256690611|gb|ACV10948.1| dihydropyrimidine dehydrogenase [Halorhabdus utahensis DSM 12940]
          Length = 262

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/188 (21%), Positives = 64/188 (34%), Gaps = 26/188 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L   A+   D G     LN  C    + E   G  L+  PD +   +     A +  V
Sbjct: 97  EPLERIAESCADHGAIC-ELNAHCRQDEMCETGAGEALLAEPDRLAKQVETAADAGAT-V 154

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +VK R  +D     V L  + + I+ +G + + + A  +                   +V
Sbjct: 155 SVKVRTEIDG----VDLLAVARRIEAAGADAVHVDAMDSE-----------------GVV 193

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            EI     DLF+  N G+ D     + L    D V +GR +    A+L  V         
Sbjct: 194 AEIV-AATDLFVIANNGVRDRETVREYLACGADAVSVGRPS-DRPAVLKRVRNATEGWFE 251

Query: 239 GSSPIKTR 246
            +      
Sbjct: 252 SAETATRE 259


>gi|327441128|dbj|BAK17493.1| dihydroorotate dehydrogenase [Solibacillus silvestris StLB046]
          Length = 303

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 86/238 (36%), Gaps = 38/238 (15%)

Query: 26  MIVADAILRGDKKNILG-----FSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINL 79
           M+ A  +     + ++G       + + P+   + G +++  VE A +I +      + L
Sbjct: 67  MLNAIGLQNPGIEKVMGEELKFLESYDVPVIANVAGTEVADYVEVADRISKASNVKALEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P+      AA+    S+PV VK    V        + ++
Sbjct: 127 NISCP----NVKCGGIQFGTDPETARQLTAAVKAVSSVPVYVKLSPNV------TNIVDI 176

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K+++  G +GI +              +  I  G        I  +   +VY++ K   
Sbjct: 177 AKAVEAGGADGITMINTLVGMRLDERTGKPVIANGTGGLSGPAIKPVAIRMVYDVYKAV- 235

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           ++ I   GG+      +  +      V +G A +        VD +    +    P+ 
Sbjct: 236 NIPIIGMGGVTCAQDVIDFMSAGASAVAVGTANF--------VDHFVCPTIIEELPVL 285


>gi|51892398|ref|YP_075089.1| dihydroorotate dehydrogenase catalytic subunit [Symbiobacterium
           thermophilum IAM 14863]
 gi|51856087|dbj|BAD40245.1| dihydroorotate dehydrogenase catalytic subunit [Symbiobacterium
           thermophilum IAM 14863]
          Length = 306

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 38/216 (17%), Positives = 78/216 (36%), Gaps = 29/216 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +      + L         Q   + + I G  + + V  A+ +E  G   + LN
Sbjct: 71  MLNAIGLQNPGVDHFLTVDWPWLQEQGATVIVNIVGRTVEEYVAVARRLEGTGVAAVELN 130

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +    G      P       AA+ KA ++P+ VK    V D      +  + 
Sbjct: 131 ISCP----NVKEGGMAFGTTPGSAAAVTAAVRKATTLPLIVKLSPNVAD------VVAIA 180

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           ++++ +G +G+ +              R  +           I  +   +V+++      
Sbjct: 181 RAVEDAGADGLSVINTLQGMSIDIRRGRPHLGNVFGGLSGPAIKPVALRMVWQVAGAVKV 240

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
             IG+ GG+     A + ++     V +G A + + 
Sbjct: 241 PVIGV-GGIMSGEDAAEFLMAGASAVQVGTACFIDP 275


>gi|296121038|ref|YP_003628816.1| dihydroorotate dehydrogenase [Planctomyces limnophilus DSM 3776]
 gi|296013378|gb|ADG66617.1| dihydroorotate dehydrogenase family protein [Planctomyces
           limnophilus DSM 3776]
          Length = 333

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 39/190 (20%), Positives = 71/190 (37%), Gaps = 18/190 (9%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           L + I G      V  A+ +++F     + LN+ CP+     G        NP +  + +
Sbjct: 119 LIVNIAGKSTDDFVVMARRLDEFNAIQALELNISCPN---VSGGVDYG--TNPTMTAEVV 173

Query: 109 AAMCKALSIPVTVKCRIGVDD--------QIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           AA+ +A S P+  K    V                  +LV + +   V+      R    
Sbjct: 174 AAVRQATSKPIIAKLTPNVTSVVEIARAAASAGADALSLVNTFQGFAVDWKTGEPRLGNG 233

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAA 219
             L       I  L   IV+++ +   D  I   GG++ +   L+ L      V +G A 
Sbjct: 234 --LGGLSGPAIKPLALRIVWQVAQAV-DCPIIGVGGIQSLDDVLEFLVCGATAVQVGTAN 290

Query: 220 YKNSAMLTTV 229
           + N ++ + +
Sbjct: 291 FYNPSLSSQL 300


>gi|308273129|emb|CBX29732.1| Dihydroorotate dehydrogenase [uncultured Desulfobacterium sp.]
          Length = 305

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 38/190 (20%), Positives = 71/190 (37%), Gaps = 25/190 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P  + I G  I +    A++++D    + I +N+ CP   V +G       +NP     
Sbjct: 96  TPTIVNIYGTSIDEYSLLAEMIDDIEEISGIEVNISCP--NVEKGGVAFG--VNPKAAYK 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
              A+ K  S P+ VK    V D      +  +  S   +G + + +             
Sbjct: 152 VTKAVRKKTSKPLMVKLSPNVTD------ITEIALSAADAGADSLSLINTITGMSIDIKT 205

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           I  +   +V+++ K+  D+ +   GG+     A++ I+     V
Sbjct: 206 RRSRLANITGGLSGPAIKPIALRMVWQVAKKV-DIPVVGVGGIFTADDAIEFIIAGATAV 264

Query: 214 MIGRAAYKNS 223
            IG A + N 
Sbjct: 265 QIGTANFINP 274


>gi|326692766|ref|ZP_08229771.1| dihydroorotate dehydrogenase [Leuconostoc argentinum KCTC 3773]
          Length = 309

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 38/184 (20%), Positives = 72/184 (39%), Gaps = 25/184 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   I G  + +  + AK++   G+   I +N+ CP   V  G       ++     
Sbjct: 96  ELPVMASIAGESVQEYRDLAKLLSTTGHITAIEVNLSCP--NVDRGGMAFG--VDAQAAA 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           + I A+     +P+  K    V D  P      + K+++ +G +GI            ++
Sbjct: 152 EVITAVKSVTDLPIYAKLSPNVTDIKP------IAKAVEAAGADGIVLINTVVGMRFDLN 205

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
            R   L +G        I  +    VYE+ +    + +   GG+  +  AL++L      
Sbjct: 206 TRAPQLARGTGGMSGAAIHPIAVRFVYEVAQ-TVAIPVIGVGGIRTVDDALEMLMAGASA 264

Query: 213 VMIG 216
           V +G
Sbjct: 265 VQVG 268


>gi|150015891|ref|YP_001308145.1| dihydroorotate dehydrogenase 1B [Clostridium beijerinckii NCIMB
           8052]
 gi|149902356|gb|ABR33189.1| dihydroorotate dehydrogenase family protein [Clostridium
           beijerinckii NCIMB 8052]
          Length = 298

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 33/218 (15%), Positives = 75/218 (34%), Gaps = 27/218 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA +  +   +  +      +   IGG  +     A   ++    + I LN+ CP    +
Sbjct: 77  DAFIENELAKMRKY---GTNVIANIGGGCLEDYEAAVSKIDSSNVDMIELNISCP----N 129

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G    +   +  D +  +      P+ VK     +D      + ++    +++G +
Sbjct: 130 VKHGGMAFGIKSKVAYDVVREIKAMTKKPLMVKLSPNAED------IVDMAVKCQEAGAD 183

Query: 150 -----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                       I ++ R+ +     +      +  +   +VYE+ K   D+ +   GG+
Sbjct: 184 SISLINTLKGMAIDVYKRRPVFNNITAGLSGPAVKPIALRMVYEVAKAV-DIPVIGLGGI 242

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                A++ ++     V IG   + N      + E   
Sbjct: 243 SSGKDAVEFMMAGASAVQIGTINFVNPMAGKEIVEEME 280


>gi|260589140|ref|ZP_05855053.1| dihydroorotate oxidase [Blautia hansenii DSM 20583]
 gi|331082556|ref|ZP_08331681.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 6_1_63FAA]
 gi|260540560|gb|EEX21129.1| dihydroorotate oxidase [Blautia hansenii DSM 20583]
 gi|330400534|gb|EGG80164.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 300

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 77/218 (35%), Gaps = 23/218 (10%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQI--------GGADISKLVEAAKIVEDFG 73
           +++ M+ A  +     +    F  ++ P   Q          G    + +   + + D  
Sbjct: 62  IHSGMMNAIGLQNPGME---VFCERDLPYLQQFDTKVIVNVCGHAPEEYLAVVERLADEP 118

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + + +N+ CP    +  +       +P  V +  A + K    PV +K    V D    
Sbjct: 119 ADMLEINISCP----NVNANFLAFGQDPKHVEELTAQIKKIAKQPVIMKLTPNVTDIAEI 174

Query: 134 VAL-----RNLVKSIKKSGVNGIWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                    + V  I       I I+ R  A+           +  +   +VY++ +   
Sbjct: 175 ARAAEAGGADAVSLINTLTGMKIDINRRTFALANKTGGVSGPCVKPIAVRMVYQVAQAV- 233

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
           ++ I   GG+++   AL+ I+     V IG A + N  
Sbjct: 234 NIPIIGMGGIQNAEDALEFIMAGATAVSIGTANFTNPY 271


>gi|224057361|ref|XP_002188844.1| PREDICTED: dihydropyrimidine dehydrogenase [Taeniopygia guttata]
          Length = 1162

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 60/171 (35%), Gaps = 34/171 (19%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D ++L + A++    G + + LN+ CP     E   G     +P++V +    + +A+ I
Sbjct: 786 DWTELSKMAQVA---GADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVHI 841

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHAR 156
           P   K    V D      +  +  + ++ G +G+                          
Sbjct: 842 PFFAKLTPNVTD------IVKIAMAAQEGGADGVTATNTVSGLMGLKADSTPWPAVGRGL 895

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +    G+S    R I       V  I +  P   I   GG++     L+ L
Sbjct: 896 RTTYGGMSGNAIRPIA---LRAVSAIARALPGFPILATGGIDSAEAGLQFL 943


>gi|302380560|ref|ZP_07269025.1| dihydroorotate dehydrogenase 1B [Finegoldia magna ACS-171-V-Col3]
 gi|302311503|gb|EFK93519.1| dihydroorotate dehydrogenase 1B [Finegoldia magna ACS-171-V-Col3]
          Length = 298

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/197 (21%), Positives = 81/197 (41%), Gaps = 24/197 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           IGG+DI   +EA +++       I LN+ CP   V EG     +    DI  + ++ + K
Sbjct: 98  IGGSDIKSYIEAVELISSTDIKIIELNISCP--NVKEGGMAFGI--KCDIAQNVVSEVRK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
                + VK     +D      +  + K+ + SG + I            I+ RKA+   
Sbjct: 154 HTDKILMVKLSPNAND------IVEMAKTCEDSGADAISLVNTFNALAVDINKRKAVFDN 207

Query: 163 L-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           + +      I  +   +  ++ K N  + +   GG+++   AL+ I+     V +G A +
Sbjct: 208 MTAGLSGPCIKPIALRMCRDVCK-NVKIPVCGMGGIQNYKDALEFIMVGCHLVQVGTANF 266

Query: 221 KNSAMLTTVDEYFSNPL 237
            N  ++  +     N L
Sbjct: 267 VNPNVMVEIANGMENYL 283


>gi|153813810|ref|ZP_01966478.1| hypothetical protein RUMTOR_00016 [Ruminococcus torques ATCC 27756]
 gi|317501954|ref|ZP_07960138.1| dihydroorotate dehydrogenase 1B [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331088230|ref|ZP_08337149.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 3_1_46FAA]
 gi|145848206|gb|EDK25124.1| hypothetical protein RUMTOR_00016 [Ruminococcus torques ATCC 27756]
 gi|316896634|gb|EFV18721.1| dihydroorotate dehydrogenase 1B [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330408474|gb|EGG87940.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 300

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 70/192 (36%), Gaps = 24/192 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G       E  + + +   + + +N+ CP    +    G     NP+   +
Sbjct: 92  DTKIIVNVCGRSTEDYCEVVERLANEDVDMLEINISCP----NVKEGGIAFGQNPNAAEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              A+ K    P+ +K    V       ++  + K+++  G +            I ++ 
Sbjct: 148 ITKAVKKYAKQPIIMKLSPNV------TSISEMAKAVEAGGADAVSLINTLTGMKIDVNK 201

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           +  +L           I  +   +VYE         IG+ GG+     A+++ L     V
Sbjct: 202 KAFVLANKTGGVSGPAIHPIAVRMVYEAANVVSVPVIGM-GGIASAEDAIEMILAGASAV 260

Query: 214 MIGRAAYKNSAM 225
            +G A + + A+
Sbjct: 261 SVGTANFFDPAV 272


>gi|323455788|gb|EGB11656.1| hypothetical protein AURANDRAFT_20791 [Aureococcus anophagefferens]
          Length = 132

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 29/107 (27%), Positives = 43/107 (40%), Gaps = 10/107 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVAD-----AILRGDKKNILGFSTQEKPLALQIG 55
           MVD +   +R  AR      L +T MI A         RG           + PL  Q  
Sbjct: 27  MVDQSGLAFRLLARKY-GAELAFTPMIHAGVSQCPQRGRGYLARHFQTGDGDWPLVAQFA 85

Query: 56  GADISKLVEAAKIVEDFGYNE----INLNVGCPSARVHEGSFGACLM 98
           GAD  ++  +   V +         ++LN+GCP     +G +GA L+
Sbjct: 86  GADEDEVSRSVARVLERDPTNNVVALDLNLGCPQQIARKGRYGAFLL 132


>gi|307727004|ref|YP_003910217.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1003]
 gi|307587529|gb|ADN60926.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1003]
          Length = 325

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 37/272 (13%), Positives = 98/272 (36%), Gaps = 31/272 (11%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           T+N +L +  I +  +       +  ++  E P+ + +          A + +       
Sbjct: 61  TSNGMLNSIGIPSRGLDYYLAHVLPAYTRFETPVVVSVSADTAVDFASACEQLSLPEVAA 120

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I  N+ CP+      +FG     +P      + A+ +    P+ VK          A  +
Sbjct: 121 IEANISCPNLEADGMAFGM----DPQTTWQVVDAVRRRTRHPLWVKLTP------NAGNI 170

Query: 137 RNLVKSIKKSGVNG-----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKK 184
             + K+ + +G +            I +  R+  L   +       I  +   +V++  +
Sbjct: 171 AQVAKAAEDAGADAVVMGNTVLGMSIDVRTRRPSLGNVMGGLSGPSIKPIALRLVHQCYR 230

Query: 185 ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF-----SNPLT 238
               + +   GG+++   A++ +L     V +G A++++  ++  + +          + 
Sbjct: 231 AI-SIPVIGCGGIQNAEDAVEFMLAGASAVQVGTASFRDPGVMQKIIDGLGRYCVEEGIE 289

Query: 239 GSSPIKTRVDKDFWRKISASMTDYAARHLHSG 270
             + +  +V+ D   ++S     +    +  G
Sbjct: 290 SLASLVGKVELDA--QLSERWARFCMDRIEEG 319


>gi|114566805|ref|YP_753959.1| hypothetical protein Swol_1279 [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|122318174|sp|Q0AXG6|PYRD_SYNWW RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|114337740|gb|ABI68588.1| dihydroorotate oxidase B, catalytic subunit [Syntrophomonas wolfei
           subsp. wolfei str. Goettingen]
          Length = 302

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 45/198 (22%), Positives = 76/198 (38%), Gaps = 17/198 (8%)

Query: 50  LALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   I G  I +    A +++   G   I LN+ CP    +    G     +P+ V   +
Sbjct: 95  VIANIAGNSIEEYALMASLLQGQEGIAGIELNISCP----NVKQGGIQFGTDPETVRQVV 150

Query: 109 AAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKG- 162
           AA+ K  S+PV  K    V D        A    + +  I   G   I I+ +K +L   
Sbjct: 151 AAVKKETSLPVIPKLSPNVTDIVAIALAAADGGADALSMINTLGGMAININLKKPVLGNI 210

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                   I  +   ++Y++ +E  DL I   GG+ +   AL+  +     V IG   + 
Sbjct: 211 FGGLSGPAIKPVALKMIYQVYREV-DLPILGGGGIVNHIDALEFFMAGATAVSIGTGNFV 269

Query: 222 NSA----MLTTVDEYFSN 235
           N      +L  + +Y   
Sbjct: 270 NPCLALELLEGIKKYMQE 287


>gi|300173173|ref|YP_003772339.1| dihydroorotate dehydrogenase [Leuconostoc gasicomitatum LMG 18811]
 gi|299887552|emb|CBL91520.1| Dihydroorotate dehydrogenase [Leuconostoc gasicomitatum LMG 18811]
          Length = 308

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/223 (19%), Positives = 91/223 (40%), Gaps = 25/223 (11%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            + P+ + I G  + + VE A+ +   G+   I +N+ CP   V  G       ++    
Sbjct: 97  DDMPVMVSIAGETVQEYVELARRLTHSGFVTAIEVNLSCP--NVDRGGMAFG--VDAQTA 152

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
            + IAA+ +A  +P+  K    V D  P      +VK+++ +G +GI +           
Sbjct: 153 SEVIAALRQATHLPLYAKLSPNVTDIKP------IVKALETAGADGIVLINTVMGMSFDL 206

Query: 154 -HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
              +  + +G+     + I  +    VYE   +  ++ I   GG+  ++ AL+ ++    
Sbjct: 207 AKRQARLARGIGGMSGKSIHPIAVRFVYE-AAQTVNIPIIGVGGIASVADALELMMAGAS 265

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
            + +G A  +    +  + +  +  L        R   + +RK
Sbjct: 266 AIQVGGALTQKPEAMLEIIDAMTEALDKYEFTDVRAVTNTFRK 308


>gi|312868958|ref|ZP_07729138.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus oris
           PB013-T2-3]
 gi|311095522|gb|EFQ53786.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus oris
           PB013-T2-3]
          Length = 308

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/211 (18%), Positives = 85/211 (40%), Gaps = 31/211 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGG---ADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           DA++R      L     + P+     G   A+   +VE  ++      + I LNV CP  
Sbjct: 82  DAVVREKLP-WLHRHYPDLPVIASAAGFSTAEYETVVE--QLAAAPTVSAIELNVSCP-- 136

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
             +    G  +  +P ++ D    +  +A   P+ VK    V D +P      L ++ ++
Sbjct: 137 --NVKHGGLAMGTDPAVLEDLTRKVVRRAKGKPIYVKLTPNVTDIVP------LAQAAER 188

Query: 146 SGVNGIWI-----------HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGL 193
            G NG+ +             R+ +L  ++       +  +   +++++ +    L I  
Sbjct: 189 GGANGLTMVNTLTGLSINLRTRRPVLANVTGGLSGPALKPMALRMIHQV-RAVSSLPIIG 247

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
            GG+E     L+ ++   + V +G A++ + 
Sbjct: 248 VGGIESAEDVLEFMMAGANAVEVGAASFHDP 278


>gi|313895495|ref|ZP_07829051.1| dihydroorotate oxidase, catalytic subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|312975621|gb|EFR41080.1| dihydroorotate oxidase, catalytic subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
          Length = 309

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 29/201 (14%), Positives = 70/201 (34%), Gaps = 24/201 (11%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
                   + + I G  +      A+ +       + +N+ CP    +    G     +P
Sbjct: 94  RIRHYGMNVIVNISGGSVEDYAAVAERLNVPDVAALEINISCP----NVKEGGIVFGTDP 149

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------- 152
                 + A+ + +  PV  K    V       ++  + ++++ +G + I          
Sbjct: 150 HAAASVVRAVRRTVQKPVIAKLSPNV------TSITEMARAVEAAGADMISLINTLIGMR 203

Query: 153 --IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
             I   K +L   +       +  +   +VY++ +    + I   GG+     A++  L 
Sbjct: 204 IDIETGKPVLGNRTGGLSGPAVKPVAVRMVYDVARAV-RVPIIGMGGIASWEDAVEFFLA 262

Query: 209 SVDGVMIGRAAYKNSAMLTTV 229
               V +G A + + A++  +
Sbjct: 263 GASAVAVGTANFTDPAIMMKI 283


>gi|303233810|ref|ZP_07320464.1| dihydroorotate dehydrogenase 1B [Finegoldia magna BVS033A4]
 gi|302495244|gb|EFL54996.1| dihydroorotate dehydrogenase 1B [Finegoldia magna BVS033A4]
          Length = 298

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/197 (21%), Positives = 80/197 (40%), Gaps = 24/197 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           IGG+DI   +EA +++       I LN+ CP   V EG     +    DI  + ++ + K
Sbjct: 98  IGGSDIKSYIEAVELISSTDIKIIELNISCP--NVKEGGMAFGI--KCDIAQNVVSEVRK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
                + VK     +D      +  + K+ + SG + I            I+ RKA+   
Sbjct: 154 HTDKILMVKLSPNAND------IVEMAKTCEDSGADAISLVNTFNALAVDINKRKAVFDN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +  ++ K N  + +   GG+++   AL+ I+     V +G A +
Sbjct: 208 ITAGLSGPCIKPIALRMCRDVCK-NVKIPVCGMGGIQNYKDALEFIMVGCHLVQVGTANF 266

Query: 221 KNSAMLTTVDEYFSNPL 237
            N  ++  +     N L
Sbjct: 267 VNPNVMVEIANGMENYL 283


>gi|210620559|ref|ZP_03292107.1| hypothetical protein CLOHIR_00050 [Clostridium hiranonis DSM 13275]
 gi|210155273|gb|EEA86279.1| hypothetical protein CLOHIR_00050 [Clostridium hiranonis DSM 13275]
          Length = 300

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 32/189 (16%), Positives = 77/189 (40%), Gaps = 12/189 (6%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   V+  +++ D   + + LN+ CP+ +    +FG       ++  + +  + K
Sbjct: 100 VGGGCLEDYVKGVELLNDQDIDMVELNISCPNVKAGGMAFGI----KNEVAREVVREVRK 155

Query: 114 ALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL-SPKD 167
               P+ VK     +D     ++      + V  +       I I  RK + + + +   
Sbjct: 156 VCKHPLVVKLSPNAEDIVGMAKVCEEEGADGVSLVNTFKALAIDIKRRKPVFENVTAGLS 215

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAML 226
              I  +   +VYE+ K   ++ +   GG+      ++ I+     V +G A + +  + 
Sbjct: 216 GPAIKPIALRMVYEVSKAV-NIPVIGIGGISTAEDVIEFIMAGATVVQVGTANFMDPEIG 274

Query: 227 TTVDEYFSN 235
           T + +  ++
Sbjct: 275 TKIIKDLND 283


>gi|169824422|ref|YP_001692033.1| dihydroorotate dehydrogenase [Finegoldia magna ATCC 29328]
 gi|167831227|dbj|BAG08143.1| dihydroorotate dehydrogenase [Finegoldia magna ATCC 29328]
          Length = 298

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/197 (21%), Positives = 80/197 (40%), Gaps = 24/197 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           IGG+DI   +EA +++       I LN+ CP   V EG     +    DI  + ++ + K
Sbjct: 98  IGGSDIKSYIEAVELISSTDIKIIELNISCP--NVKEGGMAFGI--KCDIAQNVVSEVRK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
                + VK     +D      +  + K+ + SG + I            I+ RKA+   
Sbjct: 154 HTDKILMVKLSPNAND------IVEMAKTCEDSGADAISLVNTFNALAIDINKRKAVFDN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +  ++ K N  + +   GG+++   AL+ I+     V +G A +
Sbjct: 208 ITAGLSGPCIKPIALRMCRDVCK-NVKIPVCGMGGIQNYKDALEFIMVGCHLVQVGTANF 266

Query: 221 KNSAMLTTVDEYFSNPL 237
            N  ++  +     N L
Sbjct: 267 VNPNVMVEIANGMENYL 283


>gi|227891887|ref|ZP_04009692.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius ATCC
           11741]
 gi|227866350|gb|EEJ73771.1| dihydroorotate dehydrogenase 1B [Lactobacillus salivarius ATCC
           11741]
          Length = 319

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 44/213 (20%), Positives = 86/213 (40%), Gaps = 29/213 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L     E P+   +GGA     VE A  +   G  N + LN+ CP   VHEG        
Sbjct: 97  LREKYPELPIIGSVGGATEDDYVEVATKLSQSGMVNALELNISCP--NVHEGGMAFG--T 152

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
            P++       + +  ++PV VK    V D      +  + K++++ G +GI        
Sbjct: 153 VPEVAERLTKKVKEVSTVPVYVKLSPNVTD------IVAIAKAVERGGADGISMINTVLG 206

Query: 153 ----IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
               + + K +L   +     + +  +   ++Y++ + N DL I   GG+E +   L++ 
Sbjct: 207 MHIDVASGKPVLGNIMGGLSGKAVKAIAIRMIYQVSQ-NTDLPIIGMGGVETVDDVLEMY 265

Query: 207 LPSVDGVMIGRAAYKN----SAMLTTVDEYFSN 235
           +     V +G A + +      ++  + +    
Sbjct: 266 MAGASAVAVGTAHFHDSMICPHLIEELPKRMEE 298


>gi|57233863|ref|YP_182083.1| dihydroorotate dehydrogenase 1B [Dehalococcoides ethenogenes 195]
 gi|57224311|gb|AAW39368.1| dihydroorotate dehydrogenase [Dehalococcoides ethenogenes 195]
          Length = 310

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 70/189 (37%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + I    I    E A+ ++   G + I +N+ CP    +          +P+     
Sbjct: 102 PVIVNIAAESIEDYAELARRLDKVPGVSGIEVNISCP----NVKCGCIEFGSSPESAARV 157

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
             A+  A ++P+ +K            ++  L +++  +G + I            I  R
Sbjct: 158 TDAVRNATTLPLIIKLTP------NTSSITELARAVADAGADAISLINTLRGMRIDIKKR 211

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + IL           I  +   +VY++     ++ +   GG+ +   AL+ I+     V 
Sbjct: 212 RPILGNHTGGLSGPAIKPVAVSMVYQVSGAV-NVPVIGGGGIMNAEDALEFIMAGATAVQ 270

Query: 215 IGRAAYKNS 223
           IG A   N 
Sbjct: 271 IGTANLVNP 279


>gi|227484853|ref|ZP_03915169.1| dihydroorotate oxidase [Anaerococcus lactolyticus ATCC 51172]
 gi|227237213|gb|EEI87228.1| dihydroorotate oxidase [Anaerococcus lactolyticus ATCC 51172]
          Length = 299

 Score = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 70/198 (35%), Gaps = 24/198 (12%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
              +  ++     +  +   +GG      ++ AK ++    + I LN+ CP    +    
Sbjct: 79  HFIENELVFMRKYDTVVIANLGGHSYDDYIQGAKKLDKADIDMIELNISCP----NLKEG 134

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW- 152
           G     +P    + I+ +      P+ VK    V        +    K  ++ G + +  
Sbjct: 135 GMAFGTDPHKAREVISLVRAETKHPLIVKLSPNVTH------IGEFAKIAEECGADAVSL 188

Query: 153 ----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
                     I  RK +     +      I  +   + YE+ K   D+ +   GG+ ++ 
Sbjct: 189 VNTFNAMAVDIRKRKFVFNNKTAGLSGPAIKPIAIRMTYEVAKAV-DIPVIAMGGIMNVE 247

Query: 202 QALK-ILPSVDGVMIGRA 218
             L+ ++   + V +G A
Sbjct: 248 DCLEFMMVGANAVQVGTA 265


>gi|301615800|ref|XP_002937358.1| PREDICTED: hypothetical protein LOC100487204 [Xenopus (Silurana)
           tropicalis]
          Length = 1161

 Score = 72.5 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 21/106 (19%), Positives = 46/106 (43%), Gaps = 13/106 (12%)

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           + LS+PVT K R+  + +          K ++K+G   + +H R    KG          
Sbjct: 607 QKLSVPVTCKIRVFPEIEKTV----EYAKMLEKAGCQLLTVHGRTKEQKG------PLTG 656

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
              ++ +  ++    ++ +  NG ++ ++ A + +   +V GVM  
Sbjct: 657 IASWEHIKAVRNAV-NIPVFANGNIQYLNDAERCMRETAVQGVMSA 701


>gi|91201891|emb|CAJ74951.1| similar to dihydroorotate oxidase (dihydroorotate dehydrogenase B)
           catalytic subunit [Candidatus Kuenenia stuttgartiensis]
          Length = 306

 Score = 72.5 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 71/196 (36%), Gaps = 30/196 (15%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---LN 100
           +    P+   I G      +E A+ +   G++ I + + CP         G  L+     
Sbjct: 91  NEIGVPVIASIIGTCTDDFIEVAEGLSASGFSAIEIPLSCPHTP------GFGLLSGQGT 144

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P    +   A+ +  ++P+ VK    V +         + K+ + +G NGI         
Sbjct: 145 PKATYEITYAVRRKTNVPIFVKISPNVPEITS------IAKAAEDAGANGITAVNSMGPG 198

Query: 153 ----IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
               I ++K +L   +       +  +    VY++ +    + I   GG+     A++ +
Sbjct: 199 MVINIESKKPVLGFKVGGVTGDALRPIAVRCVYDVYQAV-KIPIIGVGGISTGRHAIEMM 257

Query: 207 LPSVDGVMIGRAAYKN 222
           +     V IG   Y  
Sbjct: 258 MAGASAVGIGTGVYTR 273


>gi|293400957|ref|ZP_06645102.1| dihydroorotate oxidase [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305983|gb|EFE47227.1| dihydroorotate oxidase [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 302

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 81/246 (32%), Gaps = 40/246 (16%)

Query: 14  RLLTNNALLYTE----MIVADAILRGDKKNILGFSTQEKPLALQI--------GGADISK 61
           +   N      E    M+ A  +       I+    +E P   Q          GA   +
Sbjct: 50  KRFGNPTPRVAETPSGMLNAIGLQNPGVDVIM---EKELPWLAQFDTEIIANVAGASEEE 106

Query: 62  LVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
            VE  + +          LN+ CP    +    G  L   P++          A + PV 
Sbjct: 107 YVEVIEKLNATDVVKAYELNISCP----NVKHGGIGLGTTPELAAKVTKMAKAAANKPVY 162

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DN 168
           VK    V        +  + K+++++G +G+ +           H  K IL  ++     
Sbjct: 163 VKLSPNV------TNIVEIAKAVEEAGADGLVMINTMMGMRLDLHTGKPILANVTGGLSG 216

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLT 227
             I  +   +VY++ +   ++ I   GG+      L+ L      V +G   + +     
Sbjct: 217 PAIKPVAIRMVYQVAQAV-NIPIIGVGGITRAEDVLEFLYAGASAVEVGMQNFIDPYCCV 275

Query: 228 TVDEYF 233
            + E  
Sbjct: 276 KIIEEL 281


>gi|237748005|ref|ZP_04578485.1| oxidoreductase iron-sulfur protein [Oxalobacter formigenes OXCC13]
 gi|229379367|gb|EEO29458.1| oxidoreductase iron-sulfur protein [Oxalobacter formigenes OXCC13]
          Length = 415

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 75/203 (36%), Gaps = 16/203 (7%)

Query: 19  NALLYTEMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
                 EMI    + +       L      K +   I G++  +    A+ V D G + I
Sbjct: 71  AGFKNMEMISDKPLEVNLKNMARLKREYPHKVMIASIMGSNDDEWRTLAQKVTDIGADII 130

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVAL 136
             N  CP   +   + G+ +  +P++V     A+C+A  +PV  K    +   +IPA+A 
Sbjct: 131 ECNFSCPQ--MTSSTMGSDVGQSPELVAQYTEAVCRATRLPVLAKMTPNIGHMEIPAIAA 188

Query: 137 RNLVK--SIKKSGVNGIW-----IHARKAILKGL---SPKDNRKIPNLDYDIVYEIKK-- 184
            +         + V  I        +   ++ G    S      I  +    + ++K+  
Sbjct: 189 IHAGAKGIAAINTVKAITNLDLECLSPMPVVNGKSSISGYSGPAIKPIALRFIAQMKQHP 248

Query: 185 ENPDLFIGLNGGLEDMSQALKIL 207
           +  D+ +   GG+      L+ L
Sbjct: 249 QLKDIPVSGIGGIVTWQDVLEFL 271


>gi|313625404|gb|EFR95177.1| probable tRNA-dihydrouridine synthase 1 [Listeria innocua FSL
           J1-023]
          Length = 125

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 22/125 (17%), Positives = 38/125 (30%), Gaps = 8/125 (6%)

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
               A +IL     DGVMIGRAA  N  M+    ++         P      +     ++
Sbjct: 1   TPEDAKRILEHTGADGVMIGRAALGNPWMIYRTVKFLETGELLPEPEPREKMETAMLHLN 60

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
                           +++  +H      G   S R + +   +A   +    I+     
Sbjct: 61  R-----LVELKGENIAVREFRQHAAYYLKGARGSTRAK-VAANQATKQSEMEAILNEFVL 114

Query: 317 LMIES 321
              E 
Sbjct: 115 QYEEK 119


>gi|194769374|ref|XP_001966779.1| GF19101 [Drosophila ananassae]
 gi|190618300|gb|EDV33824.1| GF19101 [Drosophila ananassae]
          Length = 1034

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 65/180 (36%), Gaps = 34/180 (18%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +      AD ++L   AK   + G + + LN+ CP     E   G     +P++V     
Sbjct: 636 IMCSFNEADWTEL---AKRAAESGADALELNLSCPHGM-GERGMGLACGQDPELVEQISR 691

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG------------------- 150
            + +A+++P  +K    + D      +  + ++ K+ G +G                   
Sbjct: 692 WVRRAVTLPFFIKLTPNITD------IVAIAEAAKRGGADGGSAINTVQGLMSLKADATA 745

Query: 151 --IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
                  ++    G+S    R    +    + +I +  P   I   GG++    AL+ + 
Sbjct: 746 WPAIGKEQRTTYGGVSGNATR---PMALKAISDIARRVPGFPILGIGGIDSGEVALQFIQ 802


>gi|269797631|ref|YP_003311531.1| dihydroorotate dehydrogenase [Veillonella parvula DSM 2008]
 gi|269094260|gb|ACZ24251.1| dihydroorotate dehydrogenase family protein [Veillonella parvula
           DSM 2008]
          Length = 316

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 79/215 (36%), Gaps = 24/215 (11%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
              +K +      + PL   +    + +    A+ +   G   + +NV CP+      +F
Sbjct: 93  HFVRKILPDLEKYDVPLLANMSAGTVEEFAWMAETLSVDGIAGLEVNVSCPNVECEGMAF 152

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---- 149
           G     +P +V     A+ K    PV VK    V D      +  + K+++  G N    
Sbjct: 153 GI----DPKVVEQVTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGNGVSL 202

Query: 150 -------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
                   I IH RK +L           +  +   +V+++ K    + I   GG+   +
Sbjct: 203 INTLLGMAIDIHRRKPVLGNIYGGLSGPAVKPVALRMVHQVYKGVT-IPIIGLGGIMTGT 261

Query: 202 QALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            A++ ++     V +G A   +   ++ +    S 
Sbjct: 262 DAIEFMMAGAQAVQVGTATMVDPTAISRIAREMSE 296


>gi|323466236|gb|ADX69923.1| Dihydroorotate dehydrogenase 1B [Lactobacillus helveticus H10]
          Length = 307

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 39/194 (20%), Positives = 76/194 (39%), Gaps = 25/194 (12%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACL 97
             L     + P+   +GG      VE AK +   G  N + +NV CP   V +G      
Sbjct: 88  TKLRHQYPDLPIMASVGGDSEDDYVEVAKKLSASGLVNALEINVSCP--NVAQGGMSFG- 144

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            ++  +V +    +  A+++P+ VK    V D      +  + K+ +  G +GI      
Sbjct: 145 -VHAGVVEELTKKIKTAVALPIYVKLTPNVTD------IVEIAKAAESGGADGISMINTL 197

Query: 153 ------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 I  RK +L   +       +  +   ++ ++++    L I   GG+      ++
Sbjct: 198 LGMRIDIKTRKPLLGHNMGGLSGEAVKPIAIRMISQVRQATT-LPIIGMGGINSAQDVIE 256

Query: 206 -ILPSVDGVMIGRA 218
            +L   + V +G A
Sbjct: 257 FMLAGANAVAVGTA 270


>gi|255658275|ref|ZP_05403684.1| dihydroorotate oxidase [Mitsuokella multacida DSM 20544]
 gi|260849588|gb|EEX69595.1| dihydroorotate oxidase [Mitsuokella multacida DSM 20544]
          Length = 316

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 34/208 (16%), Positives = 73/208 (35%), Gaps = 24/208 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            +    K+ +         + + I G+      + A +++  G   I LNV CP    + 
Sbjct: 79  GVEHFLKETLPRIQQYGMNVIVNISGSTAEDYGKLAGLLDVPGVAAIELNVSCP----NV 134

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
              G     +P+     + A       PV +K    V D      +  + K+++ +G + 
Sbjct: 135 KEGGIVFGTDPEAASAVVRAAKAHTKKPVILKLSPNVTD------IVAMAKAVEAAGADA 188

Query: 151 -----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
                      I IH  + +L           +  +   +V+++ +    + I   GG+ 
Sbjct: 189 VSLINTLLGMEIDIHRFRPVLGNITGGLSGPCVKPVAVRMVWQVAQAV-HIPIIGMGGIA 247

Query: 199 DMSQALK-ILPSVDGVMIGRAAYKNSAM 225
               A++  L     V +G A + +  +
Sbjct: 248 SAEDAVEFFLAGASAVAVGTANFTDPEI 275


>gi|327270715|ref|XP_003220134.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+]-like [Anolis
           carolinensis]
          Length = 1036

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 31/162 (19%), Positives = 56/162 (34%), Gaps = 31/162 (19%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K+ E  G + + LN+ CP     E   G     +P++V +    + +A+ IP   K    
Sbjct: 666 KMAEASGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPN 724

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLSP 165
           V D      + ++ ++ ++ G +G+                          K    G+S 
Sbjct: 725 VTD------IVSIARASQEGGADGVTATNTVSGLMGLRADGIPWPAVGRGDKTTYGGVSG 778

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              R I       V  I    P   +   GG++     L+ L
Sbjct: 779 NAIRPIA---LRAVSAIAHALPGFPVLATGGIDSAESGLQFL 817


>gi|312875936|ref|ZP_07735926.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311797417|gb|EFR13756.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 300

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 82/221 (37%), Gaps = 28/221 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           +A +  +   + GF T+   +   I G    + VE  KI+     + I +N+ CP    +
Sbjct: 78  EAFINEELSFLKGFDTK---IIANINGFAKEEFVELTKILTSL-VDMIEVNLSCP----N 129

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G     +P+ V +   ++    S P+ VK    V D      +  L  + + +G +
Sbjct: 130 VKEGGMVFGKDPEKVYEITKSVKDVASCPIIVKLTPNVTD------ITQLAVAAENAGAD 183

Query: 150 GIW-----------IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            I            I  RK ++K ++       I  +   +V E  K+   + I   GG+
Sbjct: 184 AISLINTVSAMAIDIETRKPLIKMVTGGLSGPAIKPIAVRMVLECFKKV-RIPIIGMGGI 242

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            +   A++        + IG   + N   +  + E     L
Sbjct: 243 MNYKDAIEFFIAGATAIQIGTVNFINPKAVCEIKEGIEAYL 283


>gi|303231602|ref|ZP_07318326.1| dihydroorotate dehydrogenase 1B [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302513719|gb|EFL55737.1| dihydroorotate dehydrogenase 1B [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 316

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 75/202 (37%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   +    + +    A+ +   G   + +NV CP+        G    ++P +V  
Sbjct: 106 DVPLLANMSAGTVEEFAWMAETLSVDGIAGLEVNVSCPNVE----CEGMAFGVDPKVVEQ 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ K    PV VK    V D      +  + K+++  G N            I IH 
Sbjct: 162 VTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGNGVSLINTLLGMAIDIHR 215

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           +  +   +V+++ K    + I   GG+   + A++ ++     V
Sbjct: 216 RKPLLGNIYGGLSGPAVKPVALRMVHQVYKGVT-IPIIGLGGIMSGTDAIEFMMAGAQAV 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A   +   ++ +     +
Sbjct: 275 QVGTATMVDPTAISRIAREMGD 296


>gi|170760141|ref|YP_001788137.1| dihydropyrimidine dehydrogenase [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169407130|gb|ACA55541.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           A3 str. Loch Maree]
          Length = 411

 Score = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 65/180 (36%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +   K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ + 
Sbjct: 93  RKLKENYPNKVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSG 147
            NP +V     A+ +   IP+  K    + D               +A  N +K I    
Sbjct: 151 QNPQLVKKYCEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVD 210

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
           ++    +        +S    + +  +    + ++   +   D+ I   GG+E    A +
Sbjct: 211 LDKFIGYPIVNGKSSISGYSGKAVKPIALRFIQQLVTDERLKDVPISGIGGIETWEDAAE 270


>gi|167574586|ref|ZP_02367460.1| dihydroorotate dehydrogenase family protein [Burkholderia
           oklahomensis C6786]
          Length = 319

 Score = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 33/237 (13%), Positives = 84/237 (35%), Gaps = 24/237 (10%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             N +L +  I +  I    +  +  ++    P+   +     ++   A + +       
Sbjct: 54  AGNGMLNSIGIPSHGIDYYLEHVLPAYTGCGTPVVASVSADTAAEFARACEALSLPEVAA 113

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I  N+ CP+      +FG     +       + A+ +    P+ VK          A  +
Sbjct: 114 IEANISCPNLEADGMAFGM----DAGATRQVVDAVRRRTRHPLWVKLTP------NAGNV 163

Query: 137 RNLVKSIKKSGVNG-----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKK 184
             + K+ + +G +            I +  R+  L   +       I  +   +V++  +
Sbjct: 164 AKIAKAAEDAGADAVVMGNTVLGMSIDVRTRRPSLGNVMGGLSGPSIKPIALRLVHQCHR 223

Query: 185 ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
               + +   GG++    A++ +L     V +G A++++  ++ T+ +      T  
Sbjct: 224 AI-SIPVIGCGGIQSADDAIEFLLAGASAVQVGTASFRDPGVMRTIVDGLERFCTDE 279


>gi|325911919|ref|ZP_08174322.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners UPII 143-D]
 gi|325476221|gb|EGC79384.1| dihydroorotate dehydrogenase 1B [Lactobacillus iners UPII 143-D]
          Length = 306

 Score = 72.2 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 43/205 (20%), Positives = 85/205 (41%), Gaps = 29/205 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL   +GG+ IS  +  +K + D G  N + +NV CP    +  + G  L  +P +V   
Sbjct: 98  PLIASVGGSQISDYITISKKLSDSGLLNALEINVSCP----NVAAGGMHLGTDPVVVEKL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
            + + K ++IP+ +K    V        +  + ++ ++ G +           GI I   
Sbjct: 154 TSEIKKVVNIPIYIKLTPNV------TNIVEIAQAAERGGADGLSMINTLLGLGIDIKTH 207

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           KA L  G        I  +   +V ++ +    L I   GG+E  +  ++ +L     V 
Sbjct: 208 KATLGNGFGGWSGSAIKPVAVRMVAQVHQAV-KLPIIGMGGIETAADIVEFMLAGASAVA 266

Query: 215 IGRAAYKN----SAMLTTVDEYFSN 235
           +G A +K+      ++  ++   + 
Sbjct: 267 VGTAHFKDGLAIPHLVADLETLLNE 291


>gi|94967420|ref|YP_589468.1| dihydroorotate oxidase B, catalytic subunit [Candidatus Koribacter
           versatilis Ellin345]
 gi|94549470|gb|ABF39394.1| dihydroorotate oxidase B, catalytic subunit [Candidatus Koribacter
           versatilis Ellin345]
          Length = 321

 Score = 72.2 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 68/189 (35%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G       E  +I+ D  G     LNV CP    +    G     +P ++ + 
Sbjct: 112 PVFCNVYGTCNEDYEETIRILNDGEGITAYELNVSCP----NTQHGGMTFGADPTLLAEV 167

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
           +    KA + P+ VK    V       ++  + K  + +G + I            +  R
Sbjct: 168 VTVAKKAATRPLIVKLSPNV------TSIPQMAKIAQDAGADAISLVNTFVGMAIDVETR 221

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K  +   ++      I  +   +VYE  K    + +   GG+      ++ +L     V 
Sbjct: 222 KPRISNIVAGLSGPAIKPIALRMVYEAAK-TVTIPVIGIGGISTAEDIVEFMLAGATAVE 280

Query: 215 IGRAAYKNS 223
           +G A + + 
Sbjct: 281 VGTANFWDP 289


>gi|257869383|ref|ZP_05649036.1| dihydroorotate dehydrogenase [Enterococcus gallinarum EG2]
 gi|257803547|gb|EEV32369.1| dihydroorotate dehydrogenase [Enterococcus gallinarum EG2]
          Length = 306

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 69/191 (36%), Gaps = 25/191 (13%)

Query: 49  PLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+     V    KI +      I LNV CP    +    G     +P +  + 
Sbjct: 96  PIIANVAGSTQEDYVTVCQKISQAPNVKAIELNVSCP----NVKHGGITFGTDPQVAKEL 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+     +P+ VK    V D +P      + K+I+  G +G  +             R
Sbjct: 152 TQAVKAVSQVPIYVKLSPNVTDIVP------IAKAIEAGGADGFTMINTLLGMRIDLKTR 205

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           + IL           I  +   ++ ++ +    L I   GG+  +   L++ L     V 
Sbjct: 206 RPILANQTGGLSGPAIKPVAIRLIKQVAQ-VSSLPIIGMGGVMTVDDVLEMYLAGASAVA 264

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 265 VGTANFTDPYI 275


>gi|332800372|ref|YP_004461871.1| dihydroorotate dehydrogenase family protein [Tepidanaerobacter sp.
           Re1]
 gi|332698107|gb|AEE92564.1| dihydroorotate dehydrogenase family protein [Tepidanaerobacter sp.
           Re1]
          Length = 305

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 77/204 (37%), Gaps = 29/204 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G  +    + AK +    G   + +N+ CP   V +G  G      P+   + 
Sbjct: 98  PVIANIDGDTVEDYHKIAKKLSSLEGLAALEVNISCP--NVEKG--GLAFGQEPESAFEV 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
           I A+ +A  +P+  K    V        ++ + ++   +G +            I I  +
Sbjct: 154 IKAVREATRLPIIAKLSPNVTH------IQKIAEAAVSAGADAVSLINTLLGMAIDIDTQ 207

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + I  +  +      +  +   +V+E+  E  D+ +   GG+     A++ IL     V 
Sbjct: 208 QPIFSRKFAGLSGPAVKPVALRMVWEVC-EAVDVPVIGMGGITTWQDAVEFILAGASAVA 266

Query: 215 IGRAAYKNSA----MLTTVDEYFS 234
           IG A + N      ++  +  Y  
Sbjct: 267 IGTANFVNPTAPLEIIEGIKAYLD 290


>gi|291333815|gb|ADD93498.1| dihydroorotate dehydrogenase/oxidoreductase FAD binding protein
           [uncultured marine bacterium MedDCM-OCT-S04-C13]
          Length = 546

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/166 (21%), Positives = 64/166 (38%), Gaps = 11/166 (6%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +++ L + I G  + + VE AKI+     N + LN+ CP A+     +G  +  +P++V
Sbjct: 91  PEDRFLLVSIFGGSVEEFVEVAKIMAPV-ANGLELNLSCPHAK----GYGMAMGQDPELV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            +  AA+   + IPV  K      +        A    + + +I   G      H    +
Sbjct: 146 REVTAAVKAVVEIPVIPKLTPNTPNIAEIALAAAAGGADALCAINTVGPGYTSSHGHAVL 205

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
             G      + +  +    V EI     +L I   GG    +   +
Sbjct: 206 SNGAGGMSGKGVLPIALKCVSEI-SAVTELPIIGCGGASSAADIRE 250


>gi|188587355|ref|YP_001918900.1| dihydroorotate oxidase B, catalytic subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|259547533|sp|B2A2U4|PYRD_NATTJ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|179352042|gb|ACB86312.1| dihydroorotate oxidase B, catalytic subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 303

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/201 (18%), Positives = 79/201 (39%), Gaps = 32/201 (15%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS--FGACLMLNPDIVGDCIAAMC 112
           GG D   +    K+    G   + +N+ CP   + EG   +G     +P++    ++ + 
Sbjct: 102 GGNDEEYVEITQKLNNCQGIAGLEVNISCP--NIREGGLVYGV----DPELTYRLVSKVR 155

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILK 161
           ++ S PV VK    V D      +  + K+ +++G +            I I  ++ +  
Sbjct: 156 QSTSFPVIVKLSPNVTD------ITEIAKACERAGADGLSLINTVAGMAIDIDQKEPVFD 209

Query: 162 GLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            +S       I  +    VY++ +   DL +   GG+ +   A++ IL     V +G   
Sbjct: 210 NISAGLSGPAIKPIALKAVYQVSQAV-DLPVMGMGGIYNYQDAIEFILAGATSVALGTVN 268

Query: 220 YKNS----AMLTTVDEYFSNP 236
           +       +++  +D Y    
Sbjct: 269 FAEPTAAKSIIQGIDNYLERE 289


>gi|126311394|ref|XP_001381838.1| PREDICTED: similar to dihydropyrimidine dehydrogenase [Monodelphis
           domestica]
          Length = 1047

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 71/207 (34%), Gaps = 33/207 (15%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG----ADISKLVEAAKIVEDFGYNEINL 79
           E+I    A         L     +  L   +       D ++L   +K+ E  G + + L
Sbjct: 633 ELISEKTAAYWCQCVTELKADFPDNILIASLMCTYNKNDWTEL---SKMAEAAGADALEL 689

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ C S  + E   G     +PD+V +    + +A+ IP   K    + D      + ++
Sbjct: 690 NLSC-SHGMGERGMGLACGQDPDMVRNICRWIRQAVRIPFFAKLTPNITD------IVSI 742

Query: 140 VKSIKKSGVNGIW------------IHARKAILKGLSPK------DNRKIPNLDYDIVYE 181
            ++ ++ G +G+                      GL  K          +  +    V  
Sbjct: 743 ARAAQEGGADGVTATNTVLGLMGLKADGTPWPAIGLGKKTTYGSISGTAVRPIALRAVAA 802

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP 208
           I ++ P   I   GG++     L+ L 
Sbjct: 803 IARDLPGFPILATGGIDSAESGLQFLQ 829


>gi|310829702|ref|YP_003962059.1| hypothetical protein ELI_4154 [Eubacterium limosum KIST612]
 gi|308741436|gb|ADO39096.1| hypothetical protein ELI_4154 [Eubacterium limosum KIST612]
          Length = 302

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/216 (17%), Positives = 79/216 (36%), Gaps = 40/216 (18%)

Query: 26  MIVA--------DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
           MI +        DA +  +  ++ G  T      + +GG D +  +EA + +       +
Sbjct: 68  MINSIGLENPGVDAFIENEWPHLKGIDTV---TVVNVGGKDEASYLEAIERINAINAQLV 124

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            LN+ CP+ +    ++G       ++  D    +      PV VK    V++      + 
Sbjct: 125 ELNISCPNVKAGGMAYGI----KAEMAADITRKVVAVSKAPVMVKLSPNVEN------IA 174

Query: 138 NLVKSIKKSGVNGI----WIHARKAILK--------GLSPKDNRKIPNLDYDIVYEIKKE 185
            +  + ++SG  GI     I A     K          +      +  +   + +++ K 
Sbjct: 175 EIALACEESGACGISLINTIQAMAVDYKKKKIVFDNTYAGLSGPAVKPIALRMTHQVCKA 234

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
             D+ +   GG+     AL+       +M+G A  +
Sbjct: 235 V-DVPVMAMGGISTWEDALEF------IMVGAACVQ 263


>gi|262068145|ref|ZP_06027757.1| dihydroorotate oxidase [Fusobacterium periodonticum ATCC 33693]
 gi|291378124|gb|EFE85642.1| dihydroorotate oxidase [Fusobacterium periodonticum ATCC 33693]
          Length = 304

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 80/222 (36%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIEDYVYVADKISKSQNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +PD+  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPDVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANITGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDNLESAL 287


>gi|188590377|ref|YP_001921723.1| dihydroorotate dehydrogenase 1B [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500658|gb|ACD53794.1| dihydroorotate dehydrogenase [Clostridium botulinum E3 str. Alaska
           E43]
          Length = 298

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/227 (17%), Positives = 77/227 (33%), Gaps = 29/227 (12%)

Query: 26  MIVADAI----LRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +    + G  KN L         +   +GG       EA + +     N I LN
Sbjct: 65  MMNSVGLQNPGIEGFIKNELPKMQELNTNILANVGGGCFEDYAEAIEKLNHTEVNMIELN 124

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP+ +    ++G        +  + +  + K    P+ VK          A  +  + 
Sbjct: 125 ISCPNVKCGGMAYGI----KSQVAYEFVKEIKKICKKPLMVKLSP------NAENIVEMA 174

Query: 141 KSIKKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPD 188
              +++G +            I  + RK I     +      +  +   +V+E+ K    
Sbjct: 175 AKCEEAGADSLSLINTLKGLAIDPYKRKPIFNNVYAGLSGPAVKPVALRMVHEVSKAVSI 234

Query: 189 LFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             IGL GG+ + +     ++     V IG   + N      + E   
Sbjct: 235 PVIGL-GGISNGIDAIEFMMAGARAVQIGTINFVNPMAGKEIIEEME 280


>gi|330996952|ref|ZP_08320817.1| dihydroorotate dehydrogenase 1B [Paraprevotella xylaniphila YIT
           11841]
 gi|329572026|gb|EGG53697.1| dihydroorotate dehydrogenase 1B [Paraprevotella xylaniphila YIT
           11841]
          Length = 303

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/205 (19%), Positives = 78/205 (38%), Gaps = 29/205 (14%)

Query: 48  KPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+      E AA+I E      I LN+ CP    +    G    +  +    
Sbjct: 94  TNMIVNVSGSCCEDYAECAARINELERIPAIELNISCP----NVKQGGMAFGVTAEGASA 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+ KA    + VK    V        + ++ +S++ +G +            I I  
Sbjct: 150 VVKAVRKAYDKTLIVKLSPNV------TNVADIARSVEDAGADAVSLINTLMGMAIDIEK 203

Query: 156 RKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ K      +GL GG+ +   A++ +L     +
Sbjct: 204 RRPVLSIATGGLSGPAVKPVALRMVWQVAKAVKIPVVGL-GGIMNARDAIEFLLAGASAI 262

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            IG A + + A    +   +DEY  
Sbjct: 263 EIGTANFIDPAVTVKVARGIDEYLE 287


>gi|154483491|ref|ZP_02025939.1| hypothetical protein EUBVEN_01195 [Eubacterium ventriosum ATCC
           27560]
 gi|149735743|gb|EDM51629.1| hypothetical protein EUBVEN_01195 [Eubacterium ventriosum ATCC
           27560]
          Length = 300

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 66/190 (34%), Gaps = 24/190 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      ++  + +     + + +N+ CP    +    G     +P  V  
Sbjct: 92  DTNIIVNVCGRTTEDYIDVVEKLGHEKVDMLEINISCP----NVKHGGIAFGQDPKAVEA 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
              A+      PV +K    V D      +  + K+ +  G + + +             
Sbjct: 148 ITKAVKAVAKQPVIMKLSPNVTD------ITEMAKAAEAGGADALSLINTLTGMQIDVER 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            +  +           I  +   +VY++        IG+ GG+ + S A++ IL     V
Sbjct: 202 QKFVLANKTGGLSGPAIKPVAVRMVYQVANAVKVPIIGM-GGIANASDAMEFILAGATAV 260

Query: 214 MIGRAAYKNS 223
            +G A + N 
Sbjct: 261 SVGTANFNNP 270


>gi|325479548|gb|EGC82644.1| dihydroorotate dehydrogenase 1B [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 299

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 75/204 (36%), Gaps = 28/204 (13%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   ++ A+I++    + I LN+ CP    +    G     +P    + I  +  
Sbjct: 99  LGGHCVDDYIKGAEILDQTTSDMIELNISCP----NVKEGGMAFGTDPSKAREVIRKVRS 154

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHA--------RKAILK 161
             + P+ VK    V        +    K  +  G + I     I+A        +     
Sbjct: 155 KTNKPLIVKLSPNVGS------IVEFAKIAEDEGADSISLINTINALAVDIKSKKTIFAN 208

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      +  +   +VYE+     D+ +   GG+ +   AL+ I+     + +G A +
Sbjct: 209 KTAGLSGPCVKPIALRMVYEVSNAV-DIPVIGMGGIMNYEDALEFIMAGATAIQVGTANF 267

Query: 221 KN----SAMLTTVDEYFSNPLTGS 240
            +      +++ +++Y       S
Sbjct: 268 IDYKSMENIISGIEKYMKEENISS 291


>gi|301058592|ref|ZP_07199597.1| dihydroorotate oxidase, catalytic subunit [delta proteobacterium
           NaphS2]
 gi|300447324|gb|EFK11084.1| dihydroorotate oxidase, catalytic subunit [delta proteobacterium
           NaphS2]
          Length = 305

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/178 (19%), Positives = 70/178 (39%), Gaps = 28/178 (15%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           G   + +N+ CP   V +G        +PD+       + +    PV VK    V D   
Sbjct: 122 GVAALEVNISCP--NVEQGGMAFG--TDPDMAARVTERVLRETDKPVIVKLSPNVTD--- 174

Query: 133 AVALRNLVKSIKKSGVNGIW-----------IHARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +R + ++++K+G + I            I  R + L  G        I  +   +V 
Sbjct: 175 ---IRVIARAVEKAGAHAISLINTLTGMTIDIEKRTSKLANGSGGLSGPAIRPVALHMVR 231

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA----MLTTVDEYF 233
           ++ +    L +   GG+ +   AL+ L    D V +G A + N      +++ ++++ 
Sbjct: 232 QVVQ-TVRLPVIGIGGIREARDALEFLIAGADAVQVGTANFVNPGASLDIISGIEKFL 288


>gi|187778598|ref|ZP_02995071.1| hypothetical protein CLOSPO_02193 [Clostridium sporogenes ATCC
           15579]
 gi|187772223|gb|EDU36025.1| hypothetical protein CLOSPO_02193 [Clostridium sporogenes ATCC
           15579]
          Length = 411

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 63/171 (36%), Gaps = 15/171 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G +  +  E A++V + G + I  N  CP   +   + G+ +  NP +V   
Sbjct: 102 KVLVASIMGQNEKEWEELARLVTEVGADIIECNFSCPQ--MTSSAMGSDVGQNPQLVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
             A+ +   IP+  K    + D               +A  N +K I    ++    +  
Sbjct: 160 CEAVRRGTDIPILAKMTPNIGDMSVPAIASMEGGATGIATINTIKCITGVDLDKFIGYPI 219

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
                 +S    + +  +    + ++   +   D+ I   GG+E    A +
Sbjct: 220 VNGKSSISGYSGKAVKPIALRFIQQLVTDERLKDIPISGIGGIETWEDAAE 270


>gi|315301146|ref|ZP_07872422.1| probable tRNA-dihydrouridine synthase 1 [Listeria ivanovii FSL
           F6-596]
 gi|313630483|gb|EFR98340.1| probable tRNA-dihydrouridine synthase 1 [Listeria ivanovii FSL
           F6-596]
          Length = 122

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 22/117 (18%), Positives = 35/117 (29%), Gaps = 8/117 (6%)

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
           D  + L+     DGVMIGRAA  N  M+    +Y         P      +     ++  
Sbjct: 1   DAKRILEH-TGADGVMIGRAALGNPWMIYRTVKYLETGELLPEPEPREKMQTAMLHLNR- 58

Query: 259 MTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
                         +++  +H      G   S   R  +        A   +I   F
Sbjct: 59  ----LVELKGENIAVREFRQHAAYYLKGARGS--TRAKVAANQATKQAEMELILNEF 109


>gi|66354366|gb|AAY44826.1| suppressor-of-rudimentary dihydropyrimidine dehydrogenase mutant
           [Drosophila melanogaster]
          Length = 1031

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  + +     E A   E  G + + LN+ CP     E   G     
Sbjct: 623 LKRDFPEKIVIASIMCSFNEEDWTELAIKAEQSGADALELNLSCPHGM-GERGMGLACGQ 681

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK------- 144
           +P++V      + KA+ +P  +K    + D +   A            + +++       
Sbjct: 682 DPELVEQISRWVRKAVKLPFFIKLTPNITDIVSIAAAAKRGGADGGSAINTVQGLMGLKA 741

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            S         ++    G+S    R    +    + +I    P   I   GG++    AL
Sbjct: 742 DSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFPILGIGGIDSGEVAL 798

Query: 205 K 205
           +
Sbjct: 799 Q 799


>gi|18858217|ref|NP_572538.1| suppressor of rudimentary, isoform B [Drosophila melanogaster]
 gi|24640763|ref|NP_727320.1| suppressor of rudimentary, isoform C [Drosophila melanogaster]
 gi|10728539|gb|AAF46461.2| suppressor of rudimentary, isoform B [Drosophila melanogaster]
 gi|22831986|gb|AAN09247.1| suppressor of rudimentary, isoform C [Drosophila melanogaster]
 gi|24850449|gb|AAN64918.1| dihydropyrimidine dehydrogenase [Drosophila melanogaster]
 gi|189181839|gb|ACD81696.1| GH13260p [Drosophila melanogaster]
          Length = 1031

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  + +     E A   E  G + + LN+ CP     E   G     
Sbjct: 623 LKRDFPEKIVIASIMCSFNEEDWTELAIKAEQSGADALELNLSCPHGM-GERGMGLACGQ 681

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK------- 144
           +P++V      + KA+ +P  +K    + D +   A            + +++       
Sbjct: 682 DPELVEQISRWVRKAVKLPFFIKLTPNITDIVSIAAAAKRGGADGGSAINTVQGLMGLKA 741

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            S         ++    G+S    R    +    + +I    P   I   GG++    AL
Sbjct: 742 DSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFPILGIGGIDSGEVAL 798

Query: 205 K 205
           +
Sbjct: 799 Q 799


>gi|220931785|ref|YP_002508693.1| dihydroorotate oxidase B, catalytic subunit [Halothermothrix orenii
           H 168]
 gi|219993095|gb|ACL69698.1| dihydroorotate oxidase B, catalytic subunit [Halothermothrix orenii
           H 168]
          Length = 304

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/203 (16%), Positives = 73/203 (35%), Gaps = 29/203 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + I G  +      A  +  +   + + +NV CP    +    G     + ++V   
Sbjct: 97  PVIVNISGHAVEDFARLADKLAPYSEISALEVNVSCP----NLAGGGMAFGTDSELVYRV 152

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
              + +     V VK    V D      +  + ++ + +G +            I +  +
Sbjct: 153 TKKVKENYPGSVIVKLSPNVTD------IVEIARAAESAGADVLSLINTLLGMAIDVEKQ 206

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L           I  +   +VY++ ++  ++ I   GG+     AL+ IL     V 
Sbjct: 207 KPVLGNIFGGLSGPAIKPVALRMVYQVAQQV-EIPIIGMGGIMSGKDALEFILAGASAVA 265

Query: 215 IGRAAYKNS----AMLTTVDEYF 233
           +G A   +      +L  + +Y 
Sbjct: 266 VGTANLVDPLAGQKVLREIHDYL 288


>gi|294793332|ref|ZP_06758477.1| dihydroorotate oxidase [Veillonella sp. 6_1_27]
 gi|294455763|gb|EFG24128.1| dihydroorotate oxidase [Veillonella sp. 6_1_27]
          Length = 316

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/202 (19%), Positives = 75/202 (37%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   +    I +    A+ +   G   + +NV CP+        G    ++P +V  
Sbjct: 106 DVPLLANMSAGTIDEFAWMAETLSVDGIAGLEVNVSCPNVE----CEGMAFGVDPKVVES 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ K    PV VK    V D      +  + K+++  G N            I IH 
Sbjct: 162 VTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGNGVSLINTLLGMAIDIHR 215

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           +  +   +V+++ K    + I   GG+   + A++ ++     V
Sbjct: 216 RKPVLGNTYGGLSGPAVKPVALRMVHQVYKGVT-IPIIGLGGIMTGTDAIEFMMAGAQAV 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A   +   ++ +    S 
Sbjct: 275 QVGTATMVDPTAISRIAREMSE 296


>gi|291517823|emb|CBK73044.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Butyrivibrio fibrisolvens 16/4]
          Length = 302

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/232 (16%), Positives = 83/232 (35%), Gaps = 35/232 (15%)

Query: 26  MIVADAI----LRGDKKNILGFSTQEKP--LALQIGGADISKLVEAA-KIVEDFGYNEIN 78
           M+ A  +    +    +  L F  Q K   + + + G    + +E   ++  +   + + 
Sbjct: 66  MLNAIGLQNPGVEVFCERDLKFLEQYKNTKVIVNVCGHSAEEYIEVVERLANESRVDMLE 125

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+ CP    +    G      P  V +    +      P+ +K    V D      ++ 
Sbjct: 126 INISCP----NVKEGGIAFGQAPKAVEEITRLVKSHAKQPIVMKLSPNVTD------IKV 175

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDN------------RKIPNLDYDIVYEIKKEN 186
           + K+ +  G + I +      +K    + N              +  +   +VYE     
Sbjct: 176 MAKAAEAGGADAISLINTLTGMKIDVERQNFVLANKTGGMSGPAVHPIAVRMVYECANSV 235

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYF 233
               IG+ GG+     A++ +L     V +G A + N      +L+ +++Y 
Sbjct: 236 SIPIIGM-GGITTWEDAIEMMLAGATAVSVGTANFFNPTATMDILSGIEDYM 286


>gi|237740189|ref|ZP_04570670.1| dihydroorotate dehydrogenase [Fusobacterium sp. 2_1_31]
 gi|229422206|gb|EEO37253.1| dihydroorotate dehydrogenase [Fusobacterium sp. 2_1_31]
          Length = 304

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 80/222 (36%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +      + P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKL---EAYDVPIIANVAGSDIEDYVYVADKISKAPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +PD+  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPDVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDNLESAL 287


>gi|313158558|gb|EFR57952.1| dihydroorotate oxidase, catalytic subunit [Alistipes sp. HGB5]
          Length = 319

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/200 (17%), Positives = 74/200 (37%), Gaps = 25/200 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           KP+   I G  I +     + ++ +     I +NV CP    +    G     +P+   +
Sbjct: 111 KPVIANISGFSIEEYAYCCERIDREEQVGIIEVNVSCP----NVRHGGMSFGTSPECAAE 166

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              A+    + PV +K    V D      + ++ ++ +++G +GI            +  
Sbjct: 167 VTRAVKTVTTKPVYIKLSPNVTD------IVSIARACEEAGADGICLINTLLGMRIDVRC 220

Query: 156 RKAI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RKA+    +       +  +   +VY++ K    + +   GG+      ++ ++     V
Sbjct: 221 RKAVIANTMGGFSGAAVFPVAVRMVYQVAKAC-SVPVMGCGGVTTARDVIEMMMAGATAV 279

Query: 214 MIGRAAYKNSAMLTTVDEYF 233
            +G A   N      + E  
Sbjct: 280 QVGAANLVNPYASKEIVEAL 299


>gi|253681153|ref|ZP_04861956.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           D str. 1873]
 gi|253563002|gb|EES92448.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           D str. 1873]
          Length = 298

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 74/201 (36%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   +GG  I   +   + +     + I LN+ CP    +    G    +  ++  D
Sbjct: 91  DTVIFANLGGGSIEDYLMGVEKLNKVDVDIIELNISCP----NVKHGGMAFGIKSEVAYD 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
            ++ +      P+ VK          A  + ++ +S  K+G +GI            I  
Sbjct: 147 VVSKVRNICKKPLIVKLSP------NAENIVDMAESCCKAGADGISLVNTFKGMAIDIKQ 200

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK++     +      I  +   +V+E+ K N D+ +   GG+     A++ I+     +
Sbjct: 201 RKSVFNNIYAGLSGPAIKPIALRMVHEVCK-NIDVPVIGMGGIVSAEDAIEFIMAGATAI 259

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G   +    +   + E   
Sbjct: 260 QVGTGNFMKPNISLDIIEGIE 280


>gi|160938652|ref|ZP_02086004.1| hypothetical protein CLOBOL_03547 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438351|gb|EDP16110.1| hypothetical protein CLOBOL_03547 [Clostridium bolteae ATCC
           BAA-613]
          Length = 300

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 68/191 (35%), Gaps = 24/191 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + ++  + + D   + + +N+ CP    +    G     +P  V  
Sbjct: 92  DTKIVVNVCGKTTEEYIDVVERLGDQPVDMLEINISCP----NVKEGGIAFGQDPKAVEA 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
               +      P+ +K    V D         + ++ +  G + I            IH 
Sbjct: 148 ITREVKAHARQPIIMKLSPNVTDITV------MARAAEAGGADAISLINTLTGMKIDIHK 201

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R  A+           +  +   +VY++ +      IG+ GG+ +   AL+ IL     V
Sbjct: 202 RAFALANRTGGLSGPAVKPVAVRMVYQVAQAVKVPIIGM-GGIRNADDALEFILAGATAV 260

Query: 214 MIGRAAYKNSA 224
            IG A + N  
Sbjct: 261 AIGTANFHNPY 271


>gi|153855912|ref|ZP_01996874.1| hypothetical protein DORLON_02899 [Dorea longicatena DSM 13814]
 gi|149751815|gb|EDM61746.1| hypothetical protein DORLON_02899 [Dorea longicatena DSM 13814]
          Length = 300

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/205 (14%), Positives = 73/205 (35%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +   + + D   + + +N+ CP    +  +       +   V +
Sbjct: 92  DTKIIVNVCGHAPEEYLAVVERLADEPIDMMEINISCP----NVNAGFLAFGQDAKHVEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
             A + K    P+ +K    V D      +  + K+ +  G +            I I+ 
Sbjct: 148 LTAQIKKIAKQPIIMKLTPNVTD------ITEIAKAAEAGGADALSLINTLTGMKIDINR 201

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           R  A+           +  +   +VY+  +   ++ I   GG+     A+++ L     V
Sbjct: 202 RTFAVANKTGGVSGPVVHPIAVRMVYQTAQAV-NIPIIGMGGIATPEDAIEMILAGASAV 260

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            +G A + N      ++  ++ Y  
Sbjct: 261 SVGTANFYNPNATIEIIDGIEAYMK 285


>gi|238019709|ref|ZP_04600135.1| hypothetical protein VEIDISOL_01584 [Veillonella dispar ATCC 17748]
 gi|237863750|gb|EEP65040.1| hypothetical protein VEIDISOL_01584 [Veillonella dispar ATCC 17748]
          Length = 317

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 76/202 (37%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   +    I +    A+ +   G   + +NV CP+        G    ++P +V  
Sbjct: 106 DVPLLANMSAGTIDEFAWMAETLSVDGIAGLEVNVSCPNVE----CEGMAFGVDPKVVEQ 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ K    PV VK    V D      +  + K+++  G +            I IH 
Sbjct: 162 VTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGDGVSLINTILGMAIDIHR 215

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           +  +   +V+++ K   ++ I   GG+   + A++ ++     V
Sbjct: 216 RKPVLGNIYGGLSGPAVKPVALRMVHQVYK-GVNIPIMGLGGIMTGTDAIEFMMAGAQAV 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A   +   ++ +     +
Sbjct: 275 QVGTATMVDPTAISRIAREMGD 296


>gi|16182390|gb|AAL13488.1| GH01650p [Drosophila melanogaster]
          Length = 864

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  + +     E A   E  G + + LN+ CP     E   G     
Sbjct: 456 LKRDFPEKIVIASIMCSFNEEDWTELAIKAEQSGADALELNLSCPHGM-GERGMGLACGQ 514

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK------- 144
           +P++V      + KA+ +P  +K    + D +   A            + +++       
Sbjct: 515 DPELVEQISRWVRKAVKLPFFIKLTPNITDIVSIAAAAKRGGADGGSAINTVQGLMGLKA 574

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            S         ++    G+S    R    +    + +I    P   I   GG++    AL
Sbjct: 575 DSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFPILGIGGIDSGEVAL 631

Query: 205 K 205
           +
Sbjct: 632 Q 632


>gi|20094042|ref|NP_613889.1| hypothetical protein MK0604 [Methanopyrus kandleri AV19]
 gi|19887019|gb|AAM01819.1| tRNA-dihydrouridine synthase [Methanopyrus kandleri AV19]
          Length = 244

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 70/194 (36%), Gaps = 23/194 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L     E P+A+ +  AD  +  E +  + D   + + +N  C    +     G  L+ +
Sbjct: 57  LSRVDVEIPVAVNVRFADPREAGELSGELADL-VDVVEINAHCRQPEIVRAGAGEALLED 115

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
              + + + A+ +   + V+VK R       P  A  + +++++ S V+ + + A K   
Sbjct: 116 RTRLIEIVEAVAEH-DVYVSVKLR------GPHPAFEDALEALRDSSVDVLHVDAMKP-- 166

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
                          Y++ Y        + +  N  +       ++       V +GR  
Sbjct: 167 -----------GEPTYELEYVRAAARVGVPVIGNNSVRTPEDVDRMFEAGASAVSVGRPI 215

Query: 220 Y-KNSAMLTTVDEY 232
              +  +L  +  Y
Sbjct: 216 LEGDWDVLERLVRY 229


>gi|297588400|ref|ZP_06947043.1| dihydroorotate oxidase [Finegoldia magna ATCC 53516]
 gi|297573773|gb|EFH92494.1| dihydroorotate oxidase [Finegoldia magna ATCC 53516]
          Length = 298

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/197 (20%), Positives = 78/197 (39%), Gaps = 24/197 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           IGG+DI   +EA +++       I LN+ CP   V EG     +    D+    ++ + K
Sbjct: 98  IGGSDIKSYIEAVELISSTDIKIIELNISCP--NVKEGGMAFGI--KCDVAQKVVSEVRK 153

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG 162
                + VK     +D      +  + K+ + SG + +            I+ RK +   
Sbjct: 154 HTDKVLMVKLSPNAND------IVEMAKTCEDSGADALSLVNTFNALAVDINKRKPVFDN 207

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      I  +   +  ++ K N  + +   GG+++   AL+ I+     V +G A +
Sbjct: 208 ITAGLSGPCIKPIALRMCRDVCK-NVKIPVCGMGGIQNYKDALEFIMVGCHLVQVGTANF 266

Query: 221 KNSAMLTTVDEYFSNPL 237
            N  ++  +     N L
Sbjct: 267 VNPNVMVEIANGMENYL 283


>gi|257875733|ref|ZP_05655386.1| dihydroorotate dehydrogenase [Enterococcus casseliflavus EC20]
 gi|257809899|gb|EEV38719.1| dihydroorotate dehydrogenase [Enterococcus casseliflavus EC20]
          Length = 307

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGGADISK-LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+ +   ++   +I +      I LN+ CP    +    G     +P + G  
Sbjct: 96  PIIANVAGSTVEDYVLVCQEISQAENVKAIELNISCP----NVKHGGITFGTDPAVAGAL 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K   +P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 152 TEAVKKVSQVPIYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDLKTR 205

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++ +    L I   GG+  +   L++ L     V 
Sbjct: 206 KPILANQTGGLSGPSIKPVAIRLIKQVAQ-VSQLPIIGMGGVMSVDDVLEMYLAGASAVA 264

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 265 VGTANFTDPYI 275


>gi|332878351|ref|ZP_08446075.1| dihydroorotate dehydrogenase 1B [Capnocytophaga sp. oral taxon 329
           str. F0087]
 gi|332683676|gb|EGJ56549.1| dihydroorotate dehydrogenase 1B [Capnocytophaga sp. oral taxon 329
           str. F0087]
          Length = 303

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 78/205 (38%), Gaps = 29/205 (14%)

Query: 48  KPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+      E AA+I E      I LN+ CP    +    G    +  +    
Sbjct: 94  TNMIVNVSGSCCEDYAECAARINELERIPAIELNISCP----NVKQGGMAFGVTAEGASA 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+ KA    + VK    V        + ++ +S++ +G +            I I  
Sbjct: 150 VVKAVRKAYDKTLIVKLSPNV------TNVADIARSVEDAGADSVSLINTLMGMAIDIEK 203

Query: 156 RKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ +      +GL GG+ +   A++ +L     +
Sbjct: 204 RRPVLSIATGGLSGPAVKPVALRMVWQVAQAVKIPVVGL-GGIMNARDAIEFLLAGASAI 262

Query: 214 MIGRAAYKNSA----MLTTVDEYFS 234
            IG A + + A    +   +DEY  
Sbjct: 263 EIGTANFIDPAVTVKVARGIDEYLE 287


>gi|303230218|ref|ZP_07316986.1| dihydroorotate dehydrogenase 1B [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302515144|gb|EFL57118.1| dihydroorotate dehydrogenase 1B [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 316

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 75/202 (37%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   +    + +    A+ +   G   + +NV CP+        G    ++P +V  
Sbjct: 106 DVPLLANMSAGTVEEFAWMAETLSVDGIAGLEVNVSCPNVE----CEGMAFGVDPKVVEQ 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ K    PV VK    V D      +  + K+++  G N            I IH 
Sbjct: 162 VTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGNGVSLINTLLGMAIDIHR 215

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           +  +   +V+++ K    + I   GG+   + A++ ++     V
Sbjct: 216 RKPLLGNIYGGLSGPAVKPVALRMVHQVYKGIT-IPIIGLGGIMSGTDAIEFMMAGAQAV 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A   +   ++ +     +
Sbjct: 275 QVGTATMVDPTAISRIAREMGD 296


>gi|1561730|gb|AAC47288.1| Dreg-3 protein [Drosophila melanogaster]
          Length = 626

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 64/180 (35%), Gaps = 19/180 (10%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  + +     E A   E  G + + LN+ CP     E   G     
Sbjct: 219 LKRDFPEKIVIASIMCSFNEEDWTELAIKAEQSGADALELNLSCPHGM-GERGMGLACGQ 277

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-------LRNLVKSIK-------K 145
           +P++V      + KA+ +P  +K    + D +   A       +R+ + +++        
Sbjct: 278 DPELVEQISRWVRKAVKLPFFIKLTPNITDIVSIAAAAKREEPMRSAINTVQGLMGLKAD 337

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           S         ++    G+S    R    +    + +I    P   I   GG++    AL+
Sbjct: 338 STAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFPILGIGGIDSGEVALQ 394


>gi|292493436|ref|YP_003528875.1| dihydroorotate dehydrogenase [Nitrosococcus halophilus Nc4]
 gi|291582031|gb|ADE16488.1| dihydroorotate dehydrogenase family protein [Nitrosococcus
           halophilus Nc4]
          Length = 331

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/206 (17%), Positives = 75/206 (36%), Gaps = 29/206 (14%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L F+  E      + G+ + + VE  +  +D   + I +N+ CP    +    G     +
Sbjct: 104 LDFT--ETRYIANVSGSTVEEYVEVTRGFDDSPIDAIEINISCP----NVKEGGVAFGND 157

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           PD+    + A  K    P+  K            ++    +   ++G +           
Sbjct: 158 PDMSARVVEACRKVTHKPLITKLSP------NQTSIEENARRCIEAGTDAFAVINTLMGM 211

Query: 153 ---IHARKA----ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
              I  R      I  G+S    + I  L    VY++ +++  + I   GG+     AL+
Sbjct: 212 AIDIEQRTPLLGNIQGGVSGPAIKPIALLKVRQVYQVCRQHG-IPIIGQGGVASSEDALE 270

Query: 206 IL-PSVDGVMIGRAAYKNSAMLTTVD 230
            L      V +G A + +  + + ++
Sbjct: 271 FLIAGATTVGVGTALFYDPLLCSKIN 296


>gi|253579490|ref|ZP_04856759.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848991|gb|EES76952.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 300

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 73/199 (36%), Gaps = 30/199 (15%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +   + + D   + + +N+ CP    +  +       +   V +
Sbjct: 92  DTKIIVNVCGHAPEEYLAVVERLADQPIDMMEINISCP----NVNAGFLAFGQDAHHVEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             A + K    PV +K    V D      +  + K  +  G + + +      L G+   
Sbjct: 148 LTAQIKKIAKQPVIMKLTPNVTD------ITEIAKGAEAGGADAVSL---INTLTGMKID 198

Query: 167 DNRK---------------IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
            NRK               +  +   +VY++ +   ++ I   GG+     A++ IL   
Sbjct: 199 INRKTFALANKTGGVSGPIVKPIAVRMVYQVAQAV-NIPIIGMGGISCAEDAIEFILAGA 257

Query: 211 DGVMIGRAAYKNSAMLTTV 229
             V +G A + N A+   V
Sbjct: 258 SAVSVGTANFHNPAVTLEV 276


>gi|225390348|ref|ZP_03760072.1| hypothetical protein CLOSTASPAR_04101 [Clostridium asparagiforme
           DSM 15981]
 gi|225043592|gb|EEG53838.1| hypothetical protein CLOSTASPAR_04101 [Clostridium asparagiforme
           DSM 15981]
          Length = 309

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/191 (16%), Positives = 67/191 (35%), Gaps = 24/191 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      ++  + + D   + + +N+ CP    +    G     +P  V  
Sbjct: 101 DTKIVVNVCGKTTEDYIDVVERLGDQPVDLLEINISCP----NVKEGGIAFGQDPKAVEA 156

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
              A+      P+ +K    V D         + ++ ++ G + I +             
Sbjct: 157 ITKAVKAHAKQPIIMKLSPNVTDITV------MARAAEEGGADAISLINTLTGMKIDVNR 210

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           I  +   +VY++ +      IG+ GG+ +   AL+ IL     V
Sbjct: 211 RTFALANRTGGLSGPAIKPVAVRMVYQVAQTVRVPVIGM-GGICNAEDALEFILAGAAAV 269

Query: 214 MIGRAAYKNSA 224
            IG A + N  
Sbjct: 270 AIGTANFHNPY 280


>gi|225849961|ref|YP_002730195.1| dihydroorotate dehydrogenase 1B [Persephonella marina EX-H1]
 gi|225646103|gb|ACO04289.1| dihydroorotate dehydrogenase, catalytic subunit (dihydroorotate
           oxidase) (dhodehase) (dhodase) (dhod) [Persephonella
           marina EX-H1]
          Length = 320

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 86/225 (38%), Gaps = 42/225 (18%)

Query: 26  MIVADAI----LRGDKKNILG-FSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINL 79
           M+ +  +    +    KNIL      +  +   + G D  + ++ A+++    G + + L
Sbjct: 76  MLNSIGLQNPGVEYFIKNILPQLREYDTVIVANVFGEDEDEYLKVAEVLNKADGVDLLEL 135

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           NV CP   V +G  G     +P+ + + +  + + +  P+ VK    + D      + + 
Sbjct: 136 NVSCP--NVKKG--GIAFGSDPETLFNLVYRLKQVMEKPLLVKLSPNITD------ILDT 185

Query: 140 VKSIKKSGVNGI------------------WIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
             +  ++G +G+                   I  R   L G +      I  +   ++Y+
Sbjct: 186 ATASVEAGADGLVLINTLLGMAIDIDKEEPIIGMRTGGLSGPA------ILPVAVRMIYQ 239

Query: 182 IKKENP-DLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA 224
           + ++    + I   GG+     AL+  L     V IG A + +  
Sbjct: 240 VYEKYGSSVPIIGVGGITTAQDALQHILAGAVSVQIGTANFYDPY 284


>gi|149182332|ref|ZP_01860810.1| dihydroorotate dehydrogenase [Bacillus sp. SG-1]
 gi|148849951|gb|EDL64123.1| dihydroorotate dehydrogenase [Bacillus sp. SG-1]
          Length = 313

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 30/193 (15%), Positives = 71/193 (36%), Gaps = 25/193 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+     V+ A+ +      + + LN+ CP    +  + G      P+I  
Sbjct: 93  DVPIIANVAGSQTEDYVQVAETISTAPNVSALELNISCP----NVKTGGIAFGTVPEIAK 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    +    S+PV VK    V        +  + K+++  G +G+ +            
Sbjct: 149 ELTKKVKAVSSVPVYVKLSPNV------ANIVEMAKAVEDGGADGLTMINTLIGMRIDTK 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
             +  I           I  +   ++YE+ +   ++ I   GG++ +   ++        
Sbjct: 203 TGKPVIANVTGGLSGPAIKPVSIRMIYEVSQRV-NIPIIGMGGIQTVDDIIEYFYAGASA 261

Query: 213 VMIGRAAYKNSAM 225
           V +G A + +  +
Sbjct: 262 VAVGTANFVDPFI 274


>gi|324501269|gb|ADY40567.1| Dihydropyrimidine dehydrogenase [NADP+] [Ascaris suum]
          Length = 1059

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/163 (21%), Positives = 52/163 (31%), Gaps = 31/163 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A   E  G + + LN+ CP     E   G     +P++V      +  A+ IP   K   
Sbjct: 676 ASRAEAAGADALELNLSCPHGM-GERGMGLACGQDPNMVRSICQWVRSAVEIPFFAKMTP 734

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLS 164
            V D      +R + K+ K    +G+                         R+    G+S
Sbjct: 735 NVTD------IRTIAKAAKDGNADGVTATNTVSGLMSLKEDGSAWPSVGVERRTTYGGVS 788

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               R I       V  I    P   I   GG+E     L+ L
Sbjct: 789 GSAIRPIA---LRAVSAIANALPGFPILATGGIESAETGLQFL 828


>gi|257866100|ref|ZP_05645753.1| dihydroorotate dehydrogenase [Enterococcus casseliflavus EC30]
 gi|257872431|ref|ZP_05652084.1| dihydroorotate dehydrogenase [Enterococcus casseliflavus EC10]
 gi|257800034|gb|EEV29086.1| dihydroorotate dehydrogenase [Enterococcus casseliflavus EC30]
 gi|257806595|gb|EEV35417.1| dihydroorotate dehydrogenase [Enterococcus casseliflavus EC10]
          Length = 307

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 49  PLALQIGGADISK-LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G+ +   ++   +I +      I LN+ CP    +    G     +P + G  
Sbjct: 96  PIIANVAGSTVEDYVLVCQEISQAENVKAIELNISCP----NVKHGGITFGTDPAVAGAL 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
             A+ K   +P+ VK    V D +P      + ++I+  G +G  +             R
Sbjct: 152 TEAVKKVSQVPIYVKLSPNVTDIVP------IAQAIEAGGADGFTMINTLLGMRIDLKTR 205

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVM 214
           K IL           I  +   ++ ++ +    L I   GG+  +   L++ L     V 
Sbjct: 206 KPILANQTGGLSGPSIKPVAIRLIKQVAQ-VSQLPIIGMGGVMSVDDVLEMYLAGASAVA 264

Query: 215 IGRAAYKNSAM 225
           +G A + +  +
Sbjct: 265 VGTANFTDPYI 275


>gi|226950228|ref|YP_002805319.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           A2 str. Kyoto]
 gi|226840903|gb|ACO83569.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           A2 str. Kyoto]
          Length = 411

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 65/180 (36%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +   K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ + 
Sbjct: 93  RKLKENYPNKVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSG 147
            NP +V     A+ +   IP+  K    + D               +A  N +K I    
Sbjct: 151 QNPQLVKKYCEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVD 210

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
           ++    +        +S    + +  +    + ++   +   ++ I   GG+E    A +
Sbjct: 211 LDKFIGYPIVNGKSSISGYSGKAVKPIALRFIQQLVTDERLKNVPISGIGGIETWEDAAE 270


>gi|34762315|ref|ZP_00143319.1| Dihydroorotate dehydrogenase [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|27888037|gb|EAA25100.1| Dihydroorotate dehydrogenase [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
          Length = 304

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 79/222 (35%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIDDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVAKNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKSIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V IG A + +  +   + +     L
Sbjct: 246 VMDEWDVIDFISAGASAVAIGTANFTDPFVCPKIIDNLETAL 287


>gi|213585423|ref|ZP_03367249.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 99

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 45/107 (42%), Gaps = 13/107 (12%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +     AM  A+   +PVTVK R+G D          +  +++++G + + +H R     
Sbjct: 1   IYQGAKAMRAAVPSHLPVTVKVRLGWDSGDRKF---EIADAVQQAGASELVVHGRTK--- 54

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
                   +  ++D+  + EI++    + +  NG + D   A   + 
Sbjct: 55  ----AQGYRAEHIDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMA 96


>gi|240143893|ref|ZP_04742494.1| dihydroorotate oxidase [Roseburia intestinalis L1-82]
 gi|257204085|gb|EEV02370.1| dihydroorotate oxidase [Roseburia intestinalis L1-82]
 gi|291535019|emb|CBL08131.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Roseburia intestinalis M50/1]
 gi|291539583|emb|CBL12694.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Roseburia intestinalis XB6B4]
          Length = 302

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 76/205 (37%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G   S+ +E    + D   + + +N+ CP    +    G     NP +V D
Sbjct: 92  DTRIVVNVCGHTTSEYIEVVDRLADQPVDLLEINISCP----NVKEGGIAFGQNPKMVED 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
               +      PV +K    V D      +  + ++ +  G +G           I IH 
Sbjct: 148 ITREIKAHAKQPVIMKLSPNVTD------ITEMARAAEAGGADGLSLINTLTGMKIDIHR 201

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           R  A+           +  +   +VY+  +   ++ I   GG+ +   A+++ L     V
Sbjct: 202 RTFALANRTGGMSGPAVHPVAVRMVYQTAQAV-NIPIVGMGGIMNADDAIEMILAGATAV 260

Query: 214 MIGRAAYKNS----AMLTTVDEYFS 234
            +G A + N      ++  + +Y  
Sbjct: 261 SVGTANFTNPQVTMEIVDGIRDYME 285


>gi|168184462|ref|ZP_02619126.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           Bf]
 gi|237796254|ref|YP_002863806.1| dihydropyrimidine dehydrogenase [Clostridium botulinum Ba4 str.
           657]
 gi|182672460|gb|EDT84421.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           Bf]
 gi|229261448|gb|ACQ52481.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           Ba4 str. 657]
          Length = 411

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 66/180 (36%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +   K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ + 
Sbjct: 93  RKLKENYPNKVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSG 147
            NP +V     A+ +   IP+  K    + D               +A  N +K I    
Sbjct: 151 QNPQLVKKYCEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVD 210

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
           ++    +        +S    + +  +    + ++   ++  ++ I   GG+E    A +
Sbjct: 211 LDKFIGYPIVNGKSSISGYSGKAVKPIALRFIQQLVTDEKLKNVPISGIGGIETWEDAAE 270


>gi|158521506|ref|YP_001529376.1| dihydroorotate dehydrogenase family protein [Desulfococcus
           oleovorans Hxd3]
 gi|158510332|gb|ABW67299.1| dihydroorotate dehydrogenase family protein [Desulfococcus
           oleovorans Hxd3]
          Length = 303

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 75/210 (35%), Gaps = 29/210 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P  + I G  +      A+ ++       + +N+ CP+ +    +FG     +P    + 
Sbjct: 95  PCFVNIYGQTVEDYAGLAERLDGLNAIAGLEVNISCPNVKAGGMAFGV----DPASAAEV 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
           + A+       + VK    V D      +  + +S++ +G +            + IH R
Sbjct: 151 VRAVRAKTGKHLMVKLSPNVSD------ITAIAQSVENAGADSISLINTLAGMAVDIHTR 204

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           +  L           I  +   +V+E  +      +G+ GG+     AL+ L      V 
Sbjct: 205 RPKLANIFGGLSGPAIKPVALKMVWETARRVKVPVVGM-GGIMTAEDALEFLIAGATAVQ 263

Query: 215 IGRAAYKNSA----MLTTVDEYFSNPLTGS 240
           +G A + N      +L  +D +       +
Sbjct: 264 VGTANFLNPGVTMEILDGIDAFLDANHIPA 293


>gi|329766414|ref|ZP_08257959.1| dihydroorotate dehydrogenase family protein [Candidatus
           Nitrosoarchaeum limnia SFB1]
 gi|329137105|gb|EGG41396.1| dihydroorotate dehydrogenase family protein [Candidatus
           Nitrosoarchaeum limnia SFB1]
          Length = 303

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/199 (18%), Positives = 77/199 (38%), Gaps = 29/199 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDC 107
           P+ + + G+            ++       LN+ CP  A+V     G  +  +P++V   
Sbjct: 94  PIIVSLVGSIAEDFEMMVSQFKNCKVTAYELNLSCPHVAKV-----GLEVGDDPELVKKI 148

Query: 108 IAAMCKALSIPVTVK-----------CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           ++ +  + ++PV  K            +  +D  I A+   N V+++       I +  +
Sbjct: 149 VSTVKNSTAVPVIAKVGLGTTHYLNTVKTAIDSGIDAITAINTVRAM------AIDVETQ 202

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + IL           I  +    VYEI  +  D+ I   GG+     A++ IL     + 
Sbjct: 203 RPILSNKFGGLSGTPIKPIALRCVYEISSKY-DIPIIGCGGISTWEDAIEFILGGASAIQ 261

Query: 215 IGRAAYKNSAM--LTTVDE 231
           +G +A  +  +     +++
Sbjct: 262 LG-SAIGDRWLNVFNDIND 279


>gi|167588533|ref|ZP_02380921.1| dihydroorotate dehydrogenase family protein [Burkholderia ubonensis
           Bu]
          Length = 319

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 81/232 (34%), Gaps = 24/232 (10%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             + +L +  I +  I    +  +  ++    P+   +          A + +       
Sbjct: 54  AGDGMLNSIGIPSRGIDDYVEHVLPAYTGHGTPVVASVSADTADAFASACEALSRPDVAA 113

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I  N+ CP+      +FG     +       + A+ +    P+ VK          A  +
Sbjct: 114 IEANISCPNLEADGMAFGM----DAATTRQVVDAIRRRTGHPLWVKLTP------NAGNI 163

Query: 137 RNLVKSIKKSGVNG-----------IWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKK 184
             + K+ + +G +            I +  R+  L   +       I  +   +V++  +
Sbjct: 164 ATIAKAAEDAGADAVVMGNTVLGMSIDVRTRRPSLGNVMGGLSGPSIKPIALRLVHQCYR 223

Query: 185 ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
               + +   GG+   + A++ +L     V +G A++++  ++ T+ +    
Sbjct: 224 AV-SIPVIGCGGIRSAADAVEFLLAGASAVQVGTASFRDPGVMRTIIDGLEQ 274


>gi|291549071|emb|CBL25333.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Ruminococcus torques L2-14]
          Length = 300

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 27/196 (13%), Positives = 69/196 (35%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +   + + D   + + +N+ CP    +  +       +   V  
Sbjct: 92  DTKIIVNVCGHAPEEYLAVVERLADEPIDMMEINISCP----NVNAGFLAFGQDAHNVEK 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
             A + K    P+ +K    V D      +  + ++ +  G + + +             
Sbjct: 148 LTAQIKKIAKQPIIMKLTPNVTD------ITEIARAAEAGGADAVSLINTLTGMKIDINR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++ +   ++ I   GG+     A++ +L     V
Sbjct: 202 KTFAVANKTGGVSGPIVKPVAVRMVYQVAQAV-NIPIIGMGGISCAEDAIEFLLAGASAV 260

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A + N A+   V
Sbjct: 261 SVGTANFHNPAVTLEV 276


>gi|195479863|ref|XP_002101056.1| GE17405 [Drosophila yakuba]
 gi|194188580|gb|EDX02164.1| GE17405 [Drosophila yakuba]
          Length = 1031

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 63/191 (32%), Gaps = 34/191 (17%)

Query: 41  LGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           L     EK +   I     +     E A   E  G + + LN+ CP     E   G    
Sbjct: 623 LKRDFPEKIVIASIMCSFNEADW-TELAIKAEQSGADALELNLSCPHGM-GERGMGLACG 680

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-------- 150
            +P++V      + KA+ +P  +K    + D      + ++  + ++ G +G        
Sbjct: 681 QDPELVEQISRWVRKAVKLPFFIKLTPNITD------IVSIAAAAQRGGADGGSAINTVQ 734

Query: 151 -------------IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                             ++    G+S    R    +    + +I    P   I   GG+
Sbjct: 735 GLMGLKADSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFPILGIGGI 791

Query: 198 EDMSQALKILP 208
           +    AL+ + 
Sbjct: 792 DSGEVALQFIQ 802


>gi|147899974|ref|NP_001087488.1| dihydropyrimidine dehydrogenase [Xenopus laevis]
 gi|51258279|gb|AAH80003.1| MGC81821 protein [Xenopus laevis]
          Length = 940

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 31/158 (19%), Positives = 54/158 (34%), Gaps = 25/158 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           + E  G N + LN+ CP     E   G     +P++V +    + +A+ IP   K    V
Sbjct: 656 MAEASGANALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVKIPFFAKLTPNV 714

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------------SPKDNR 169
            D      +  +  + ++ G +G+      + L GL                        
Sbjct: 715 TD------VVKIAMAAQEGGADGVTATNTVSGLMGLKADATPWPAVGSGSRTTYGGVSGN 768

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            I  +    V  I +  P   I   GG++     L+ L
Sbjct: 769 AIRPIALRAVSAIARALPGFPILATGGIDSAESGLQFL 806


>gi|299535897|ref|ZP_07049217.1| dihydroorotate dehydrogenase 1B [Lysinibacillus fusiformis ZC1]
 gi|298728649|gb|EFI69204.1| dihydroorotate dehydrogenase 1B [Lysinibacillus fusiformis ZC1]
          Length = 303

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 73/210 (34%), Gaps = 33/210 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G + +  VE A+ +        + LN+ CP    +    G     +P    + 
Sbjct: 95  PIIANVAGTETADYVEVARRISTASNVKALELNISCP----NVKCGGIQFGTDPATAREL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
           + A+     +PV VK    V        + ++  +++  G +GI +              
Sbjct: 151 VKAVKAVSEVPVYVKLSPNV------TNIVDIALAVEAGGADGITMINTLVGMRLDERTG 204

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVM 214
           +  I  G        +  +   +VYE+ K   ++ I   GG+ +    +  +      V 
Sbjct: 205 KPVIANGTGGLSGPAVKPVAIRMVYEVYKAV-NIPIIGMGGVTEAQDVIDFMSAGASAVA 263

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           +G A +        VD +    +    P K
Sbjct: 264 VGTANF--------VDHFVCPNIIEELPAK 285


>gi|58376848|ref|XP_309214.2| AGAP001021-PA [Anopheles gambiae str. PEST]
 gi|55245087|gb|EAA04946.2| AGAP001021-PA [Anopheles gambiae str. PEST]
          Length = 1039

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 34/170 (20%), Positives = 59/170 (34%), Gaps = 26/170 (15%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           ++   + E A   E  G + + LN+ CP     E   G     +P++V +    +  A+ 
Sbjct: 644 SEPDWI-ELASRAEAAGADMLELNLSCPHGM-GESGMGLACGQDPELVYNISRWVRGAVR 701

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------------WIHARKA 158
           IP  VK    + D    V++    K  +  GV+ I                      R+ 
Sbjct: 702 IPFFVKLTPNITD---IVSIAQAAKRGQADGVSAINTVQGLMSLRADGSPWPAVGADRRT 758

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
              G+S    R         +  I  + P   I   GG++    AL+ + 
Sbjct: 759 TYGGVSGNATRPQAM---RAISLIANKLPGFPICGIGGIDSAEVALQFIQ 805


>gi|167567553|ref|ZP_02360469.1| dihydroorotate dehydrogenase family protein [Burkholderia
           oklahomensis EO147]
          Length = 319

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 84/237 (35%), Gaps = 24/237 (10%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             N +L +  I +  I    +  +  ++    P+   +     ++   A + +       
Sbjct: 54  AGNGMLNSIGIPSHGIDYYLEHVLPAYTGYGTPVVASVSADTAAEFARACEALSLPEVAA 113

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I  N+ CP+      +FG     +       + A+ +    P+ VK          A  +
Sbjct: 114 IEANISCPNLEADGMAFGM----DAGATRQVVDAVRRRTRHPLWVKLTP------NAGNV 163

Query: 137 RNLVKSIKKSGVNGIWI-----------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKK 184
             + K+ + +G + + +             R+  L   +       I  +   +V++  +
Sbjct: 164 AKIAKAAEDAGADAVVMGNTVLGMSIDARTRRPSLGNVMGGLSGPSIKPIALRLVHQCHR 223

Query: 185 ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
               + +   GG++    A++ +L     V +G A++++  ++ T+ +      T  
Sbjct: 224 AI-SIPVIGCGGIQSADDAIEFLLAGASAVQVGTASFRDPGVMRTIVDGLERFCTDE 279


>gi|257388622|ref|YP_003178395.1| hypothetical protein Hmuk_2582 [Halomicrobium mukohataei DSM 12286]
 gi|257170929|gb|ACV48688.1| conserved hypothetical protein [Halomicrobium mukohataei DSM 12286]
          Length = 256

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 89/244 (36%), Gaps = 40/244 (16%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV-- 63
           D   R  AR +       TE + +D +     +  L  + +E P+     G ++      
Sbjct: 46  DDATRRAARSMVERDR--TEFLPSDPL--AFVQRQLR-AMEELPIR---AGVNVRSAALA 97

Query: 64  ---EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              +AA   +D     + +N  C  A + E   G  L+  P+ +   + A   A    V+
Sbjct: 98  PIEDAAGRCQDHDA-ILEINAHCRQAEMCEAGAGQALLDRPEKLCRQVEAAT-ATGATVS 155

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  VD     V L  L   ++++G + + + A  +                   +V 
Sbjct: 156 VKVRAEVDG----VELPTLAAKLERAGADAVHVDAMDSE-----------------HVVG 194

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY-FSNPLT 238
           EI      LF+  N  + D   A +      D V +GRA+  +  +L  V         T
Sbjct: 195 EIADATG-LFVIANNEVRDAESAHEYFRYGADAVSVGRAS-DDPDVLAAVRRATHEWFQT 252

Query: 239 GSSP 242
           G+ P
Sbjct: 253 GAKP 256


>gi|328865277|gb|EGG13663.1| dihydropyrimidine dehydrogenase [Dictyostelium fasciculatum]
          Length = 1016

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/200 (18%), Positives = 65/200 (32%), Gaps = 28/200 (14%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           ++       K++  L     EK +   I  G +     + A + E  G + + LN+ CP 
Sbjct: 615 SEKTCHYWCKSVTELKRDFPEKVVIASIMCGFNKEDWQQLAVMAEASGADMLELNLSCPH 674

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
               E   G     NP++V      + +A+ IP   K    V        ++ +  +   
Sbjct: 675 GM-GERGMGLACGQNPELVLHICKWVREAIKIPFFAKLTPNV------TEVKEIALAAYN 727

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIP------------------NLDYDIVYEIKKENP 187
            G  G+      + L GL    N                       +    V  I++  P
Sbjct: 728 GGATGVTAINTVSGLMGLKGDSNAWPAVGSEKRTTYGGVSGNATRPMALRAVSSIRRALP 787

Query: 188 DLFIGLNGGLEDMSQALKIL 207
           D  I   GG +     ++ L
Sbjct: 788 DYPIMATGGADSADTCIQFL 807


>gi|297517944|ref|ZP_06936330.1| tRNA-dihydrouridine synthase A [Escherichia coli OP50]
          Length = 77

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 27/51 (52%), Positives = 36/51 (70%), Gaps = 1/51 (1%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLA 51
          M+DWTDRH R+F RLL+ N LLYTEM+   AI+ G   + L +S +E P+A
Sbjct: 27 MLDWTDRHCRYFLRLLSRNTLLYTEMVTTGAIIHGKG-DYLAYSEEEHPVA 76


>gi|241754001|ref|XP_002401173.1| dihydropyrimidine dehydrogenase, putative [Ixodes scapularis]
 gi|215508370|gb|EEC17824.1| dihydropyrimidine dehydrogenase, putative [Ixodes scapularis]
          Length = 833

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 65/204 (31%), Gaps = 27/204 (13%)

Query: 25  EMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I     A   G    +         +A  +   D     E A++ E  G + + LN+ 
Sbjct: 410 ELISEKTAAYWCGSISELKRDFPDHVVIASIMCTFDEKDWTELAQMAETAGADALELNLS 469

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G     +P++V +    + KA+ IP   K    V        + ++ K+
Sbjct: 470 CPHGM-GERGMGLACGQDPNLVRNICLWVRKAVKIPFFAKLTPNV------TNVVDIAKA 522

Query: 143 IKKSGVNGIWIHARKAILKGL------------------SPKDNRKIPNLDYDIVYEIKK 184
             +   +G+      + L GL                         I  +    V  I +
Sbjct: 523 AYEGKADGVTAVNTVSGLMGLKYNSDPWPGVGAQKRTTYGGMSGNAIRPIALRAVSAIAR 582

Query: 185 ENPDLFIGLNGGLEDMSQALKILP 208
             P   I   GG++      + L 
Sbjct: 583 ALPGFPILATGGIDSAEAGFQFLQ 606


>gi|224370034|ref|YP_002604198.1| PyrD [Desulfobacterium autotrophicum HRM2]
 gi|223692751|gb|ACN16034.1| PyrD [Desulfobacterium autotrophicum HRM2]
          Length = 302

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 32/204 (15%), Positives = 76/204 (37%), Gaps = 29/204 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G    +  + A I+++  G   + +N+ CP    +  + GA   ++P+   + 
Sbjct: 94  PVFANIYGKTAEEYAQLAAIIDNLPGITGVEVNISCP----NVSAGGAAFGVDPEAALEV 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
           +  + ++ S  V VK    V D      +  +  ++++ G +            I     
Sbjct: 150 VQGVRQSTSKHVMVKLSPNVTD------ITTIALAVERGGADSISLINTLTGLAIDAETA 203

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
             +L           I  +   +V+++ K    + +   GG+     AL+ I+     V 
Sbjct: 204 SPMLANITGGLSGPAIKPVALRMVWQVAK-VVKVPVIGIGGIMTAKDALEFIIAGATAVQ 262

Query: 215 IGRAAYKNSA----MLTTVDEYFS 234
           +G A   +      ++  + ++  
Sbjct: 263 VGTATLADPDAPLRIVKGIRQFMQ 286


>gi|160914210|ref|ZP_02076431.1| hypothetical protein EUBDOL_00218 [Eubacterium dolichum DSM 3991]
 gi|158433837|gb|EDP12126.1| hypothetical protein EUBDOL_00218 [Eubacterium dolichum DSM 3991]
          Length = 302

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 38/208 (18%), Positives = 72/208 (34%), Gaps = 28/208 (13%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLM 98
           +  F T+   +   + GA   + +E  K + D        LN+ CP    +    G  L 
Sbjct: 88  LAQFDTE---IIANVAGASEDEYIEVIKKLNDNAVVKAYELNISCP----NVKHGGIGLG 140

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIH 154
            +P +         +A   PV VK    V        +  + K+++++G +GI     + 
Sbjct: 141 TDPKLAAHITKLAKEAAEKPVYVKLSPNV------TNIVEIAKAVEEAGADGIVLINTLM 194

Query: 155 ARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
             +  LK   P             +  +   +VY++  E   + I   GG+      L+ 
Sbjct: 195 GMRLDLKTGKPILANKTGGLSGPCVKPIAIRMVYQVY-EAVKIPIIGVGGITCAEDVLEF 253

Query: 207 L-PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L      V +G   + +      + E  
Sbjct: 254 LYAGAQAVEVGAQNFVDPYCCQKIIEDL 281


>gi|195565891|ref|XP_002106529.1| GD16077 [Drosophila simulans]
 gi|194203907|gb|EDX17483.1| GD16077 [Drosophila simulans]
          Length = 1031

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  + +     E A   E  G + + LN+ CP     E   G     
Sbjct: 623 LKRDFPEKIVIASIMCSFNEDDWTELAIKAEQSGADALELNLSCPHGM-GERGMGLACGQ 681

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK------- 144
           +P++V      + KA+ +P  +K    + D +   A            + +++       
Sbjct: 682 DPELVEQISRWVRKAVKLPFFIKLTPNITDIVSIAAAAKRGGADGGSAINTVQGLMGLKA 741

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            S         ++    G+S    R    +    + +I    P   I   GG++    AL
Sbjct: 742 DSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFPILGIGGIDSGEVAL 798

Query: 205 K 205
           +
Sbjct: 799 Q 799


>gi|83590953|ref|YP_430962.1| dihydroorotate oxidase B, catalytic subunit [Moorella thermoacetica
           ATCC 39073]
 gi|83573867|gb|ABC20419.1| dihydroorotate oxidase B, catalytic subunit [Moorella thermoacetica
           ATCC 39073]
          Length = 352

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/222 (19%), Positives = 79/222 (35%), Gaps = 32/222 (14%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHE 90
            LR     +  F+    PL + I G  + +  E AA++    G   + +N+ CP   V E
Sbjct: 130 FLREKLPYLRRFTP---PLIVNIAGRTVEEYGELAARLSAAEGIAALEVNISCP--NVRE 184

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G         P++     A +     +PV VK    V D         L ++++ +G + 
Sbjct: 185 GGIVFG--TVPEMAARVTATVKGQTHLPVIVKLTPNVTDITV------LARAVEDAGADA 236

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +              R A+   +       I  +    V+ + +      IG+ GG+ 
Sbjct: 237 LSLINTLQGMAIDLETRRPALANIVGGLSGPAIKPVALCAVWRVARAVKIPVIGM-GGIV 295

Query: 199 DMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFSN 235
               AL+ +L     V +G A   N      ++  +  Y   
Sbjct: 296 TARDALEFLLAGARAVAVGTAGLVNPRAIIEVIDGIKAYLQE 337


>gi|139439778|ref|ZP_01773169.1| Hypothetical protein COLAER_02200 [Collinsella aerofaciens ATCC
           25986]
 gi|133774928|gb|EBA38748.1| Hypothetical protein COLAER_02200 [Collinsella aerofaciens ATCC
           25986]
          Length = 302

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 76/219 (34%), Gaps = 28/219 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARV 88
           A  R     +   S     +  Q+ G  + + V A ++  +         +NV CP+   
Sbjct: 77  AFARESGPWLEQLSKDGCQVICQVAGHSVDEFVRALEMYVELCPWAAGYEINVSCPNIAA 136

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
                GA +   P+     +AA  K    P+ VK           V +  + K+++ +G 
Sbjct: 137 ----GGAAMGSTPEGASSVMAACRKVTDKPLFVKM--------APVNVAEIAKALEAAGA 184

Query: 149 N-----------GIWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +            I +H RK  + K           ++   +V+E+ +   D+ I   GG
Sbjct: 185 DGLSVINSIQGMAIDVHTRKSRVAKPKGGLSGPLCHHIAVRMVWEVAQAV-DIPINGVGG 243

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +     A + IL     V +G A + +      +     
Sbjct: 244 VMTGEDAAEFILAGATCVSVGMANFVDPCASLKIAHELE 282


>gi|291523201|emb|CBK81494.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Coprococcus catus GD/7]
          Length = 301

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/202 (16%), Positives = 67/202 (33%), Gaps = 26/202 (12%)

Query: 38  KNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGA 95
           K  L F  + +  + + + G    + ++  + + D    + + +N+ CP    +    G 
Sbjct: 82  KRDLPFLEKYDTKVIVNVCGHSTEEYLDVVERLADEPRVDMLEINISCP----NVKEGGI 137

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI---- 151
               +P  V     A+      P+ +K    V D         + K+ +  G + +    
Sbjct: 138 AFGQDPKAVEAITKAVKAKAKQPIIMKLSPNVTDITV------MAKAAEAGGADCLSLIN 191

Query: 152 --------WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                         AI           +  +   +VY++      + I   GG+     A
Sbjct: 192 TLTGMKIDIERQTFAIANKTGGLSGPAVKPVAVRMVYQVANAV-KIPIIGMGGICTAEDA 250

Query: 204 LK-ILPSVDGVMIGRAAYKNSA 224
           ++ IL     V IG A + N  
Sbjct: 251 MEFILAGATAVSIGTANFTNPY 272


>gi|302391680|ref|YP_003827500.1| dihydroorotate oxidase B, catalytic subunit [Acetohalobium
           arabaticum DSM 5501]
 gi|302203757|gb|ADL12435.1| dihydroorotate oxidase B, catalytic subunit [Acetohalobium
           arabaticum DSM 5501]
          Length = 305

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 79/195 (40%), Gaps = 30/195 (15%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  +L E  K+ +  G   + +N+ CP   V +G  G      P +    + A+ +   +
Sbjct: 109 EYQELAE--KLSQPEGIAALEVNISCP--NVKKG--GLAFGTEPKMAAGVVKAVTENTDL 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKGL-SP 165
           PV  K    V D      +  + ++++++G + I            I  ++ IL      
Sbjct: 163 PVITKLSPNVTD------ITEIAQAVEEAGSDIISLINTLVGMKIDIDTQEPILANTIGG 216

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
                I  +   +VY++ +   DL +   GG+ +   A++ +L     V +G A + N  
Sbjct: 217 LSGPAIRPVAVKMVYQVAQAV-DLPLIGMGGIMNSRDAVEFLLAGASAVSVGTANFSNPG 275

Query: 225 ----MLTTVDEYFSN 235
               ++  ++EY S 
Sbjct: 276 VTMEIIDGIEEYLSE 290


>gi|254518509|ref|ZP_05130565.1| dihydroorotate dehydrogenase 1B [Clostridium sp. 7_2_43FAA]
 gi|226912258|gb|EEH97459.1| dihydroorotate dehydrogenase 1B [Clostridium sp. 7_2_43FAA]
          Length = 299

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/216 (18%), Positives = 78/216 (36%), Gaps = 29/216 (13%)

Query: 26  MIVA-----DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +       I R  K+ +         +   +GG  I    EA + + D   + I LN
Sbjct: 65  MMNSVGLQNPGIDRFIKEELPKMKELGTNIIANVGGGCIEDYEEAIQKLRDTDIDMIELN 124

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP   V  G     +    ++  + ++ + K    P+ VK     +D      +  + 
Sbjct: 125 ISCP--NVKSGGMAFGI--KSNVAYEVVSKIKKISDKPLMVKLSPNAED------IVRMA 174

Query: 141 KSIKKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPD 188
            S +++G +            I  + RK I     +      +  +   +V+E+ K    
Sbjct: 175 VSCEEAGADSISLINTLKGFAIDPYKRKPIFNNIYAGLSGPAVKPIALRMVHEVSKAVSI 234

Query: 189 LFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNS 223
             IGL GG+ + +     ++     + IG   + N 
Sbjct: 235 PVIGL-GGISNGIDAIEFMMAGATAIQIGTVNFINP 269


>gi|313894665|ref|ZP_07828228.1| dihydroorotate oxidase, catalytic subunit [Veillonella sp. oral
           taxon 158 str. F0412]
 gi|313440855|gb|EFR59284.1| dihydroorotate oxidase, catalytic subunit [Veillonella sp. oral
           taxon 158 str. F0412]
          Length = 316

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 76/202 (37%), Gaps = 24/202 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   +    I +    A+ +   G   + +NV CP+        G    ++P +V  
Sbjct: 106 DVPLLANMSAGTIEEFAWMAETLSVDGIAGLEVNVSCPNVE----CEGMAFGVDPKVVEQ 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ K    PV VK    V D      +  + K+++  G +            I IH 
Sbjct: 162 VTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGDGVSLINTILGMAIDIHR 215

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ K   ++ I   GG+   + A++ ++     V
Sbjct: 216 RQPVLGNIYGGLSGPAVKPVALRMVHQVYK-GVNIPIMGLGGIMTGTDAIEFMMAGAQAV 274

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A   +   ++ +    S 
Sbjct: 275 QVGVATMVDPTAISRIAREMSE 296


>gi|320528989|ref|ZP_08030081.1| dihydroorotate dehydrogenase 1B [Selenomonas artemidis F0399]
 gi|320138619|gb|EFW30509.1| dihydroorotate dehydrogenase 1B [Selenomonas artemidis F0399]
          Length = 309

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/201 (14%), Positives = 69/201 (34%), Gaps = 24/201 (11%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
                   + + I G  +      A+ +       + +N+ CP    +    G     +P
Sbjct: 94  RIRHYGMNVIVNISGGSVEDYAAVAERLNVPDVAALEINISCP----NVKEGGIVFGTDP 149

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------- 152
                 + A+ +    PV  K    V       ++  + ++++ +G + I          
Sbjct: 150 HAAASVVRAVRRTAQKPVIAKLSPNV------TSITEMARAVEAAGADMISLINTLIGMR 203

Query: 153 --IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
             I   K +L   +       +  +   +VY++ +    + I   GG+     A++  L 
Sbjct: 204 IDIETGKPVLGNRTGGLSGPAVKPVAVRMVYDVARAV-RVPIIGMGGIASWEDAVEFFLA 262

Query: 209 SVDGVMIGRAAYKNSAMLTTV 229
               V +G A + + A++  +
Sbjct: 263 GASAVAVGTANFTDPAIMMKI 283


>gi|256810451|ref|YP_003127820.1| TIM-barrel protein [Methanocaldococcus fervens AG86]
 gi|256793651|gb|ACV24320.1| TIM-barrel protein [Methanocaldococcus fervens AG86]
          Length = 254

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/153 (18%), Positives = 58/153 (37%), Gaps = 16/153 (10%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +V     + I LN  C    +     G  LM N +++ + +  M   ++ PV +K R+  
Sbjct: 105 LVIAKHADIIELNCHCRQQEITSLGIGQELMKNKNLLKEFLYKMR-GINKPVFLKIRLNY 163

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                 +   N V+       +G+ +        G         P  D + +  + +E  
Sbjct: 164 IPIEELINNLNYVRDYF----DGLHV---DCFYPGK--------PYADLNSLKILAEEFK 208

Query: 188 DLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           D  I  N  ++ + +A ++L   D + + RA  
Sbjct: 209 DKIIIGNNSVDSLEKAKEMLKYADFISVARAVL 241


>gi|294782717|ref|ZP_06748043.1| dihydroorotate oxidase [Fusobacterium sp. 1_1_41FAA]
 gi|294481358|gb|EFG29133.1| dihydroorotate oxidase [Fusobacterium sp. 1_1_41FAA]
          Length = 304

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/222 (17%), Positives = 78/222 (35%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARV 88
           D I+    K +      + P+   + G+DI   V  A  +        + LN+ CP    
Sbjct: 80  DEIISNQLKKL---EAYDVPIIANVAGSDIEDYVYVADKISKVPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +PD+  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPDVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDNLESAL 287


>gi|269121264|ref|YP_003309441.1| dihydroorotate dehydrogenase [Sebaldella termitidis ATCC 33386]
 gi|268615142|gb|ACZ09510.1| dihydroorotate dehydrogenase family protein [Sebaldella termitidis
           ATCC 33386]
          Length = 322

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 72/204 (35%), Gaps = 25/204 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G  + + +E A+  E       I LN+ CP    +    G     NPD+    
Sbjct: 101 PVIANINGKILEEYIEIAERAEAIDVIKAIELNISCP----NVKDGGMAFGANPDMAAKV 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              + +    P+ VK    V D      +  + K ++  G +            I I+ +
Sbjct: 157 TREVRRVTKKPLIVKLSPNVTD------IAGIAKLVEAEGADALSLINTLLGMSIDINKK 210

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L           +  +   +VY++        +G+ GG+     AL+  +     + 
Sbjct: 211 KPLLGNIFGGLSGPAVKPVALRMVYQVSNAVSIPLLGM-GGISTAEDALEFFMAGASAIS 269

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLT 238
           +G   ++N      + +   N  T
Sbjct: 270 VGTGFFQNPLAAVEIKQGLINYCT 293


>gi|168179227|ref|ZP_02613891.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           NCTC 2916]
 gi|182669884|gb|EDT81860.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           NCTC 2916]
          Length = 411

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 65/180 (36%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +   K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ + 
Sbjct: 93  RKLKENYPNKVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSG 147
            NP +V     A+ +   IP+  K    + D               +A  N +K I    
Sbjct: 151 QNPQLVKKYCEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVD 210

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
           ++    +        +S    + +  +    + ++   +   ++ I   GG+E    A +
Sbjct: 211 LDKFIGYPIVNGKSSISGYSGKAVKPIALRFIQQLVTDERLRNVPISGIGGIETWEDAAE 270


>gi|315652441|ref|ZP_07905429.1| dihydroorotate oxidase [Eubacterium saburreum DSM 3986]
 gi|315485340|gb|EFU75734.1| dihydroorotate oxidase [Eubacterium saburreum DSM 3986]
          Length = 301

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 76/206 (36%), Gaps = 28/206 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           ++  + + + G  IS  +E  + +     + + +N+ CP    +    G     N D V 
Sbjct: 92  KDTKIIVNVCGRSISDYIETVERLSHEAVDMLEINISCP----NVSHGGITFGTNVDSVR 147

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARK---- 157
           D  + +      PV +K    V D      +  + K+ + +G + +     +   K    
Sbjct: 148 DITSQVKVHSKKPVIMKLSPNVTD------ITEIAKAAEDAGADALSLINTVTGMKIDIN 201

Query: 158 ----AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
               AI           I  +   +VY++        IG+ GG+     A++ +L     
Sbjct: 202 KRCFAIANKTGGMSGPAIKPVALRMVYQVANAVKIPVIGM-GGIVTADDAIEFLLAGATM 260

Query: 213 VMIGRAAYKNSA----MLTTVDEYFS 234
           V +G A + N      ++  +++Y  
Sbjct: 261 VSVGTANFFNPDASIMVVDGIEKYLE 286


>gi|150403324|ref|YP_001330618.1| putative TIM-barrel protein [Methanococcus maripaludis C7]
 gi|150034354|gb|ABR66467.1| putative TIM-barrel protein [Methanococcus maripaludis C7]
          Length = 254

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/151 (20%), Positives = 59/151 (39%), Gaps = 16/151 (10%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQI 131
             + + LN  C    + +   G  L+ N   + D +  + K  L IP+ +K R      +
Sbjct: 111 NADILELNCHCRQPEITDLELGQNLLKNESKLIDFLKNIRKLNLEIPIFLKLRANF---L 167

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
            A  L  L+  +++   +GI I          +P  N      D + + +I++  P+  I
Sbjct: 168 TAEELIELLDKVREY-FDGIHIDC-------FNPGKNY----ADLEYLKKIRESFPEKII 215

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
             N  +  +  A ++L   D   + R    N
Sbjct: 216 IGNNSVNSIETAKEMLEYADFASVARCVLSN 246


>gi|320032373|gb|EFW14326.1| tRNA dihydrouridine synthase [Coccidioides posadasii str. Silveira]
          Length = 310

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 20/98 (20%), Positives = 42/98 (42%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I++N GCP      G  GA L+  PD +   + A+ + +  P  +   + +         
Sbjct: 140 IDVNSGCPKPFSTSGGMGAALLQTPDRLVSILEALVEEIGKPYEIGISVKIRLLAEPERT 199

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             LV  + ++G+ G+ +H R   ++        ++P +
Sbjct: 200 EALVTRLCRTGITGLTVHCRTTPMRPREAAIREQLPMI 237


>gi|2829825|sp|P96192|DUSC_AZOVI RecName: Full=tRNA-dihydrouridine synthase C
 gi|1850794|emb|CAA72146.1| Yoh1 protein [Azotobacter vinelandii]
          Length = 309

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 79/243 (32%), Gaps = 31/243 (12%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAILRGDKKNILG-------FSTQEKPLAL 52
           M    D   R     +       TE + V D +L   +   L         +    P+ L
Sbjct: 8   MEGLVDELLRDLLTRVGGIDWCVTEFVRVCDRLLPVAQFEKLAPELRHGWRTRAGTPMHL 67

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           Q+ G+D + L E A +  + G   I+LN GCP+          C               C
Sbjct: 68  QLLGSDPACLAENAALAAELGAPAIDLNFGCPAKTSTARGADGC--------CSTSRNCC 119

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNL------VKSIKKSGVNGIWIHARKAILKGLSPK 166
              S      CR    D+  A  +R         +++ + GV  + +HAR  +       
Sbjct: 120 MPSSARCAGPCRRCAGDRQDAPGVRPARGRPGVRRALVEGGVAHLVVHARTKVEGYR--- 176

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
                P   ++ +  + +E   + +  N          + +  V+ VM+G        + 
Sbjct: 177 -----PPASWEWLARV-REAVAVPVYANRKSGRRRIGCREISGVEDVMLGCGLVSRPDLA 230

Query: 227 TTV 229
             +
Sbjct: 231 RQI 233


>gi|306820698|ref|ZP_07454326.1| dihydroorotate oxidase [Eubacterium yurii subsp. margaretiae ATCC
           43715]
 gi|304551308|gb|EFM39271.1| dihydroorotate oxidase [Eubacterium yurii subsp. margaretiae ATCC
           43715]
          Length = 303

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/202 (21%), Positives = 76/202 (37%), Gaps = 29/202 (14%)

Query: 48  KPLALQIGGADISKLVEAAK---IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           K +   I G  I + VE AK   +VE+ G   I +NV CP   VH G       ++   V
Sbjct: 95  KKIIANISGFSIEEYVECAKKMDVVENVG--IIEVNVSCP--NVHNGGMAYG--VSAQSV 148

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAIL 160
            +   A+      PV +K    V D      +  + K+ + SG +G+     +   +  +
Sbjct: 149 SEVTKAVKDVSKKPVYIKLSPNVTD------IVEIAKTCESSGADGLSLINTLLGMRIDI 202

Query: 161 KGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVD 211
           +  +P             I  +   +VY++        IG+ GG+      ++++     
Sbjct: 203 RKKAPVIANKMGGFSGPAIFPVALRMVYQVANAVKIPVIGM-GGVSRAQDVIEMMMAGAS 261

Query: 212 GVMIGRAAYKNSAMLTTVDEYF 233
            V +G A   N      + E  
Sbjct: 262 AVQVGSANLVNPFACKEIIEEL 283


>gi|255528042|ref|ZP_05394877.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296188156|ref|ZP_06856548.1| dihydropyrimidine dehydrogenase [Clostridium carboxidivorans P7]
 gi|255508256|gb|EET84661.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296047282|gb|EFG86724.1| dihydropyrimidine dehydrogenase [Clostridium carboxidivorans P7]
          Length = 412

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 75/195 (38%), Gaps = 16/195 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           EMI    +    ++  +L  +   K L   I G +  +  + AK V + G + I  N  C
Sbjct: 78  EMIAEHPLDFNLEQMRLLKKNYPNKVLIASIMGENEEEWTKLAKSVTEVGADIIECNFSC 137

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------P 132
           P   +   + G+ +  NP +V    AA+ K   +P+  K    + +              
Sbjct: 138 PQ--MTSSAMGSDVGQNPALVKKYSAAVRKGTHLPIIAKMTPNIGNMEMPAIGAIEGGAT 195

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLF 190
            ++  N +K I    ++ +           +S    + I  +    + ++ KE    ++ 
Sbjct: 196 GISAINTIKCITGMDLDKLVGLPIVNGKSSISGYSGKAIKPIALRFIAQLAKEPKLKNVP 255

Query: 191 IGLNGGLEDMSQALK 205
           I   GG+E+   AL+
Sbjct: 256 ISGIGGIENWEDALE 270


>gi|197100733|ref|NP_001126169.1| dihydropyrimidine dehydrogenase [NADP+] [Pongo abelii]
 gi|75041534|sp|Q5R895|DPYD_PONAB RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|55730588|emb|CAH92015.1| hypothetical protein [Pongo abelii]
          Length = 1025

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/169 (21%), Positives = 61/169 (36%), Gaps = 28/169 (16%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
            D ++L   AK  ED G + + LN+ CP     E   G     +P++V +    + +A+ 
Sbjct: 648 NDWTEL---AKKSEDSGADALELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQ 703

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL------------- 163
           IP   K    V D      + ++ ++ K+ G NG+      + L GL             
Sbjct: 704 IPFFAKLTPNVTD------IVSIARAAKEGGANGVTATNTVSGLMGLKSDGTPWPAVGIA 757

Query: 164 -----SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       I  +    V    +  P   I   GG++     L+ L
Sbjct: 758 KRTTYGGVSGTAIRPIALRAVTSTARALPGFPILATGGIDSAESGLQFL 806


>gi|197301626|ref|ZP_03166699.1| hypothetical protein RUMLAC_00353 [Ruminococcus lactaris ATCC
           29176]
 gi|197299356|gb|EDY33883.1| hypothetical protein RUMLAC_00353 [Ruminococcus lactaris ATCC
           29176]
          Length = 300

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 26/192 (13%), Positives = 69/192 (35%), Gaps = 24/192 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +E  + + D   + + +N+ CP    +  +       +   V +
Sbjct: 92  DTKIIVNVCGHAPEEYLEVVERLADEPIDMMEINISCP----NVNAGFLAFGQDAKHVEE 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
               + K    P+ +K    V D      +  + K+ +  G + + +             
Sbjct: 148 LTGQIKKIAKQPIIMKLTPNVTD------ITEIAKATEAGGADAVSLINTLTGMKIDINR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++ +   ++ I   GG+     A++ +L     V
Sbjct: 202 KTFAVANKTGGVSGPIVKPIAVRMVYQVAQAV-NIPIIGMGGISCAEDAIEFLLAGASAV 260

Query: 214 MIGRAAYKNSAM 225
            +G A + + A+
Sbjct: 261 SVGTANFHDPAV 272


>gi|195393212|ref|XP_002055248.1| GJ18897 [Drosophila virilis]
 gi|194149758|gb|EDW65449.1| GJ18897 [Drosophila virilis]
          Length = 1031

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/190 (21%), Positives = 67/190 (35%), Gaps = 32/190 (16%)

Query: 41  LGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  G + +   E A   E  G + + LN+ CP     E   G     
Sbjct: 624 LKRDFPEKIIIASIMCGYNEADWTELAIKAEKSGADALELNLSCPHGM-GESGMGLACGQ 682

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG--------- 150
            P +V D    + KA+ +P  +K    + D      + ++ ++ ++ G +G         
Sbjct: 683 EPKLVEDISRWVRKAVKVPFFIKLTPNITD------IVSIAQAAQRGGADGGSAINTVQG 736

Query: 151 ------------IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
                            ++    G+S    R I       V EI K+ P   I   GG++
Sbjct: 737 LMSLKADATAWPAVGKEQRTTYGGVSGNATRPIA---LRAVSEIAKKLPGFAILGIGGID 793

Query: 199 DMSQALKILP 208
               AL+ L 
Sbjct: 794 SGEVALQFLQ 803


>gi|304436898|ref|ZP_07396862.1| dihydroorotate oxidase [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304370097|gb|EFM23758.1| dihydroorotate oxidase [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 310

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/202 (16%), Positives = 73/202 (36%), Gaps = 24/202 (11%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            + +   +     + + I G+ +      A  +   G   + +N+ CP   V EG     
Sbjct: 92  HETLPRIADYGMNVIVNISGSSVEDYAALAARLNVTGVAALEVNISCP--NVREGGIVFG 149

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---- 152
              +P    + + A+C   + PV  K    V       ++  +  +++ +G + I     
Sbjct: 150 --TDPRAAAEVVRAVCAESTHPVIAKLSPNV------TSITEMALAVEDAGADAISLINT 201

Query: 153 -------IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                  IH  + +L   +       +  +   +V+E+        IG+ GG+     A+
Sbjct: 202 LIGMQIDIHRWQPVLGNRTGGLSGPAVKPVAVRMVWEVAHAVRVPVIGM-GGIASWQDAV 260

Query: 205 K-ILPSVDGVMIGRAAYKNSAM 225
           +  L     V +G A + +  +
Sbjct: 261 EFFLAGASAVAVGTANFADPEI 282


>gi|187936058|gb|ACD37553.1| dihydrogenpyrimidine dehydrogenase [Adineta vaga]
          Length = 968

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 71/224 (31%), Gaps = 28/224 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           A      K +         +A  +   D     E AK+ E  G + + LN+ CP     E
Sbjct: 628 AYWLQCIKELKNDFPDRIIIASIMCSFDEQDWTELAKVTEAAGADALELNLSCPHGM-GE 686

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
              G       D+V +    +  A+ IP   K    +        + ++ ++ K+ G +G
Sbjct: 687 KGMGLACGQKADLVLNICKWVRAAVKIPFFAKMTPNI------TNIVDIARAAKEGGADG 740

Query: 151 IWI-----------HARKAILKGLSPKDNRK-------IPNLDYDIVYEIKKENPDLFIG 192
           +             H   A       K+          I  +    V  I +  P   I 
Sbjct: 741 VTATNTVSGLMSIRHDTTAWPSVGKSKNTTYGGVSGNAIRPIALRAVSAIGRALPGFPIL 800

Query: 193 LNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             GG++     ++ L      + +  A        T +D+Y + 
Sbjct: 801 ATGGIDSADAGIQFLYAGASALQVCSAVQNQ--DFTLIDDYITG 842


>gi|319937447|ref|ZP_08011852.1| dihydroorotate dehydrogenase 1B [Coprobacillus sp. 29_1]
 gi|319807287|gb|EFW03896.1| dihydroorotate dehydrogenase 1B [Coprobacillus sp. 29_1]
          Length = 305

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/189 (20%), Positives = 72/189 (38%), Gaps = 25/189 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   IGG+ I   VE AK +        + LN+ CP   VH G        NP++  +  
Sbjct: 97  VIANIGGSAIDDYVETAKRLSAHDKVGALELNISCP--NVHCGGIQFG--TNPEMAAEVT 152

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HAR 156
            A+    S PV VK    V D      +  +  +++++G +GI +              +
Sbjct: 153 RAVKAVSSKPVYVKLSPNVTD------IVAMALAVEEAGADGITMINTMIGMRFDLKTGK 206

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMI 215
             I           I  +   +VY++ +      IG+ GG+     A++++    + V +
Sbjct: 207 PVIANKTGGYSGPAIFPVALRMVYQVSQAVSIPIIGM-GGISSGKDAIEMMIAGANAVAV 265

Query: 216 GRAAYKNSA 224
           G     +  
Sbjct: 266 GCQNLVDPY 274


>gi|289191633|ref|YP_003457574.1| TIM-barrel protein [Methanocaldococcus sp. FS406-22]
 gi|288938083|gb|ADC68838.1| TIM-barrel protein [Methanocaldococcus sp. FS406-22]
          Length = 258

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 30/160 (18%), Positives = 61/160 (38%), Gaps = 17/160 (10%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + I LN  C    +     G  LM N +++ + +  M + L+ P+ +K R+        
Sbjct: 113 ADVIELNCHCRQKEITSLGIGQELMKNKNLLKEFLTKMKE-LNKPIFLKIRLNYIPLKEL 171

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   N V+       +G+ +        G         P  D + +  + +E  D  I  
Sbjct: 172 IDNLNYVRDYF----DGLHV---DCFYPGK--------PYADLNSLKTLAEEFSDKVIIG 216

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAY-KNSAMLTTVDEY 232
           N  ++ + +A ++L   D V + R     N   +  ++E 
Sbjct: 217 NNSIDSLEKAKEMLRYSDFVSVARTVLKGNVKWIKELNER 256


>gi|297620172|ref|YP_003708277.1| TIM-barrel protein [Methanococcus voltae A3]
 gi|297379149|gb|ADI37304.1| TIM-barrel protein [Methanococcus voltae A3]
          Length = 281

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/169 (20%), Positives = 61/169 (36%), Gaps = 35/169 (20%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACL-----MLNPDIVGDCIAA--MCKAL-------SI 117
              + I  N  C    +     G  L     M N   +   I    + + +       SI
Sbjct: 121 ENCDIIEFNCHCRQPEITNLGLGQELITKKGMKNLCNILKFIKDTNIIRNINITDSDNSI 180

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGV----NGIWIHARKAILKGLSPKDNRKIPN 173
           PV +K R         ++   L+K+ +++ +    +GI I          +P  N     
Sbjct: 181 PVFIKIRA------NYISSEELIKNFEENSIMDYIDGIHIDC-------FNPGHNY---- 223

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
            D D + +I+   PD+ I  N  ++ +  A K+L   D V + R    N
Sbjct: 224 ADLDYLKDIRIAFPDIIIIGNNSVKSVEDAKKMLKYCDFVSVARCVLSN 272


>gi|332652653|ref|ZP_08418398.1| dihydroorotate oxidase [Ruminococcaceae bacterium D16]
 gi|332517799|gb|EGJ47402.1| dihydroorotate oxidase [Ruminococcaceae bacterium D16]
          Length = 327

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 73/213 (34%), Gaps = 25/213 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I G    +     + + + G + I +N+ CP+ +    ++G      P++  +   
Sbjct: 119 VIANISGNTPEEYGIMCEKLSEAGVDMIEVNISCPNVKAGGLAYGT----RPELAAEVTQ 174

Query: 110 AMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARK 157
                A  +PV VK    V D      +  + ++++  G +            I ++  +
Sbjct: 175 VAKAHAGKVPVMVKLSPNVTD------ITEIARAVEDGGADAVSLINTLRGMRIDVNTHR 228

Query: 158 AILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            ILK          +  +   +V+E+ +      +G+ G       A  +L     V +G
Sbjct: 229 PILKMNTGGMSGPAVLPVAVRMVWEVAQAVKIPILGMGGVSRGEDAAQLMLAGATAVAVG 288

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
            A + +      +          S     RV +
Sbjct: 289 TAMFADP--FAPIKVRDELADIASRQGLERVAQ 319


>gi|187251139|ref|YP_001875621.1| dihydroorotate dehydrogenase [Elusimicrobium minutum Pei191]
 gi|186971299|gb|ACC98284.1| Dihydroorotate dehydrogenase [Elusimicrobium minutum Pei191]
          Length = 303

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/224 (16%), Positives = 79/224 (35%), Gaps = 27/224 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARV 88
             +    +  +      +      I G ++      AK + +    + I +N+ CP   V
Sbjct: 74  KGLEYFIENTLPFLKNFDTRTVASIAGNNVEDYTTLAKRLNECKEVHAIEVNMSCP--NV 131

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
             G        +     + ++A+ K  + P+  K    V D         + K+I+++G 
Sbjct: 132 VHGQNKGLFSQDEKTTFEIMSAVRKNTNKPIFGKISPMVADITV------IAKAIERAGG 185

Query: 149 NGIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + +            +  R+ +L           +  +   +V+++ K      IG+ GG
Sbjct: 186 DAVALINTIPAMGVDLKTRRPLLGNITGGLSGPAVKPVALKLVWDVYKAVKIPVIGM-GG 244

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTT----VDEYFSN 235
           +     AL+ IL     V +G   + N  +       +++YF  
Sbjct: 245 IMCAQDALEFILCGATAVQVGTGNFVNPKLTEETALGIEKYFKE 288


>gi|281356661|ref|ZP_06243152.1| dihydroorotate dehydrogenase family protein [Victivallis vadensis
           ATCC BAA-548]
 gi|281316788|gb|EFB00811.1| dihydroorotate dehydrogenase family protein [Victivallis vadensis
           ATCC BAA-548]
          Length = 306

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 27/174 (15%), Positives = 66/174 (37%), Gaps = 25/174 (14%)

Query: 65  AAKI-VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           AA++  E  G   + +N+ CP    +  + G     +P +  + ++ + +A ++P+  K 
Sbjct: 114 AARLDAERDGITALEINISCP----NVKAGGVAFGTDPVLAAEVVSTVRRATTLPLITKL 169

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHARKAILKGLSPKDNRKI 171
              V        +    ++++ +G + +                R  I           +
Sbjct: 170 SPNV------TNIAEFARAVEAAGSDMVSLINTITAMAIDIETRRPKIANRTGGFSGPAL 223

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
             +   +VY++ +      IG+ GG+     A++ +L     V +G A + +  
Sbjct: 224 KPIAVRMVYDVARAVKIPVIGM-GGIMTGEDAVEFLLAGASAVAVGTANFVDPY 276


>gi|313635109|gb|EFS01450.1| probable tRNA-dihydrouridine synthase 1 [Listeria seeligeri FSL
          N1-067]
 gi|313639781|gb|EFS04525.1| probable tRNA-dihydrouridine synthase 1 [Listeria seeligeri FSL
          S4-171]
          Length = 84

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGAD 58
          M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL+LQI G +
Sbjct: 18 MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPLSLQIFGGE 76

Query: 59 ISKLVEAA 66
             LVEAA
Sbjct: 77 KETLVEAA 84


>gi|78223048|ref|YP_384795.1| dihydroorotate dehydrogenase 1B [Geobacter metallireducens GS-15]
 gi|123571803|sp|Q39UK4|PYRD_GEOMG RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|78194303|gb|ABB32070.1| dihydroorotate oxidase B, catalytic subunit [Geobacter
           metallireducens GS-15]
          Length = 305

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 75/198 (37%), Gaps = 17/198 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P  +   G  + +  E A+ ++       + +N+ CP    +    G      P     
Sbjct: 96  TPAIVNFFGNTVEEYAELAERLDKIPEVAGMEINISCP----NVKHGGIVFGTEPKAAYS 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            + A+ +A   PV VK    V D        A A  + +  I       I + +R+ IL 
Sbjct: 152 VVKAVREATIKPVIVKLSPNVTDIVEMAWACADAEADALSLINTLTGMAIDLKSRRPILA 211

Query: 162 GLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            ++       +  +   +V+++ K    + +   GG+   + AL+ +L     V +G A 
Sbjct: 212 NVTGGLSGPAVKPVALRMVWQVAKAV-KIPVIGIGGIMSGTDALEFMLAGATAVQVGTAN 270

Query: 220 YKNSA----MLTTVDEYF 233
           + + A    +   +++Y 
Sbjct: 271 FLDPAASERIAAEMEQYL 288


>gi|300856746|ref|YP_003781730.1| dihydropyrimidine dehydrogenase [Clostridium ljungdahlii DSM 13528]
 gi|300436861|gb|ADK16628.1| dihydropyrimidine dehydrogenase [Clostridium ljungdahlii DSM 13528]
          Length = 408

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/197 (19%), Positives = 77/197 (39%), Gaps = 16/197 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    +    +  + L    ++K +   I G +  +  + A++V   G + I  N  C
Sbjct: 76  EQISEHPLEYNLECISKLKREFKDKVIVASIMGENEQQWTKLAELVTKAGADIIECNFSC 135

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC-----------RIGVDDQIP 132
           P   + E S G+ +  NP++V     A+ +  S+PV  K               +     
Sbjct: 136 PQ--MAEESMGSDVGQNPELVEKYCKAVRRGTSLPVLAKMTPNIGNMVIPAEASIHGGAD 193

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N VKSI +  ++    +        +S    + I  +    + ++ K  +  ++ 
Sbjct: 194 GIAAINTVKSITRVDLDKFSPYPIINGKSAVSGYSGKAIKPIALRFISDLAKSEKLKEIP 253

Query: 191 IGLNGGLEDMSQALKIL 207
           I   GG+E    A++ L
Sbjct: 254 ISGIGGIETWEDAVEFL 270


>gi|253682030|ref|ZP_04862827.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           D str. 1873]
 gi|253561742|gb|EES91194.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           D str. 1873]
          Length = 411

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 69/180 (38%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +   K L   I G + S+  + AK+V + G + I  N  CP    H+        
Sbjct: 93  RRLKENYPSKVLVASIMGQNESEWTKLAKLVTEIGADIIECNFSCPQMTSHDMGSDVG-- 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIG-----------VDDQIPAVALRNLVKSIKKSG 147
            NP++V     A+ K  ++P+  K               ++     +A  N +K I    
Sbjct: 151 QNPELVKKYCQAVRKGTNLPILAKMTPNIGNMTIPAIASIEGGATGIATINTIKCISGID 210

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
           ++ +           +S    + +  +    +YE+K  K+  ++ +   GG+E    A++
Sbjct: 211 LDNMVGLPVINGKSSVSGYSGKAVKPIALRFIYELKTNKKLKEIPLSGIGGIETWEDAVE 270


>gi|332157745|ref|YP_004423024.1| dihydroorotate dehydrogenase 1B [Pyrococcus sp. NA2]
 gi|331033208|gb|AEC51020.1| dihydroorotate dehydrogenase 1B [Pyrococcus sp. NA2]
          Length = 299

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/199 (19%), Positives = 76/199 (38%), Gaps = 14/199 (7%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E P+ + + G +  +     + +++   +   LN+ CP A+     +G  +  +P+ V  
Sbjct: 89  EFPVIVSVFGGNPDEFAFLVERLDEV-ADAFELNLSCPHAK----GYGMEIGQDPENVYR 143

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRNLVKSIKKSGVNGIWIHARKAILK 161
            +    +    P+  K     +D +        A  + V +I       I I+A++ IL 
Sbjct: 144 IVKVTKEITDKPIIAKLTPNTNDIVKLGLAAERAEADAVSAINTVKAIAIDIYAKRPILS 203

Query: 162 G-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
             +       I  +    VY++ K   D+ I   GG+     A++  L     V IG A 
Sbjct: 204 NKVGGYSGPGIKPIALRAVYDLAKSL-DIPIIGIGGITSWEDAVEFFLAGASAVQIGTAV 262

Query: 220 YKN-SAMLTTVDEYFSNPL 237
           Y    ++   +     N L
Sbjct: 263 YLKGLSVFKEIANGLENYL 281


>gi|255528107|ref|ZP_05394937.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296184868|ref|ZP_06853279.1| dihydroorotate dehydrogenase 1B [Clostridium carboxidivorans P7]
 gi|255508203|gb|EET84613.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296050650|gb|EFG90073.1| dihydroorotate dehydrogenase 1B [Clostridium carboxidivorans P7]
          Length = 297

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/213 (16%), Positives = 82/213 (38%), Gaps = 27/213 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           D  ++ + +N+  F T    +   +GGA I   ++  + +     + + LN+ CP   V 
Sbjct: 76  DHFIQYELENMKKFDTA---IIANLGGAAIEDYIKGVEKLNSTDIDILELNISCP--NVK 130

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
            G     +     +  + ++ + K    P+ VK     +D      + ++     ++G +
Sbjct: 131 SGGMAFGI--KSKVAFEVVSEVKKICKKPLMVKLSPNAED------IIDMAYRCCEAGAD 182

Query: 150 -----------GIWIHARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                       I I+ R+ +   +S       I  +   +VYE+ K   ++ +   GG+
Sbjct: 183 SISLVNTFKGMAIDINKREPVFNNISAGLSGPAIKPIALRMVYEVSKAV-NVPVIGLGGI 241

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTV 229
                A++ I+     + +G A +    +   +
Sbjct: 242 SSWKDAIEFIMAGATAIQVGTANFIKPDICLDI 274


>gi|237743993|ref|ZP_04574474.1| dihydroorotate dehydrogenase [Fusobacterium sp. 7_1]
 gi|229433024|gb|EEO43236.1| dihydroorotate dehydrogenase [Fusobacterium sp. 7_1]
          Length = 305

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 79/222 (35%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIDDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVAKNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +     L
Sbjct: 246 VMDEWDVVDFISAGASAVAVGTANFTDPFVCPKIIDNLETAL 287


>gi|161508237|ref|YP_001577727.1| dihydroorotate dehydrogenase 1B [Lactobacillus helveticus DPC 4571]
 gi|172048331|sp|A8YVZ9|PYRD_LACH4 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|160349226|gb|ABX27900.1| Dihydroorotate dehydrogenase [Lactobacillus helveticus DPC 4571]
          Length = 307

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/192 (20%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACL 97
             L     + P+   +GG      VE AK +   G  N + +NV CP   V +G      
Sbjct: 88  TKLRHQYPDLPIMASVGGDSEDDYVEVAKKLSASGLVNALEINVSCP--NVAQGGMSFG- 144

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            ++  +V +    +  A+++P+ VK    V D      +  + K+ +  G +GI      
Sbjct: 145 -VHAGVVEELTKKIKMAVALPIYVKLTPNVTD------IVEIAKAAESGGADGISMINTL 197

Query: 153 ------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 I  RK +L   +       +  +   ++ ++ ++   L I   GG+      ++
Sbjct: 198 LGMRIDIKTRKPLLGHNMGGLSGEAVKPIAIRMISQV-RQVTQLPIIGMGGISTAQDVIE 256

Query: 206 -ILPSVDGVMIG 216
            IL   + V +G
Sbjct: 257 FILAGANAVAVG 268


>gi|296110380|ref|YP_003620761.1| dihydroorotate dehydrogenase, catalytic subunit
           (dihydroorotateoxidase) [Leuconostoc kimchii IMSNU
           11154]
 gi|295831911|gb|ADG39792.1| dihydroorotate dehydrogenase, catalytic subunit
           (dihydroorotateoxidase) [Leuconostoc kimchii IMSNU
           11154]
          Length = 306

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 92/227 (40%), Gaps = 29/227 (12%)

Query: 29  ADAILRGDKKNIL----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGC 83
           A+  +    K+ L           P+ + I G  + + V  A+++ +  Y   I +N+ C
Sbjct: 75  ANPGIHNVLKDFLPAIKAKYGNALPVMVSIAGETVDEYVALAQLLTNTAYLTAIEVNLSC 134

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P   V  G       ++ +   + I ++ K  ++P+  K    V D      +R + K++
Sbjct: 135 P--NVDRGGMAFG--VSAEAASEVITSVKKVTNLPIYAKLSPNVTD------IRPIAKAV 184

Query: 144 KKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           + +G +GI +              +  + +G      + +  +   +VYE   +   + I
Sbjct: 185 EVAGASGIVLINTVTGMSFDLQKRQPKLARGTGGLSGKAVHPIAVRLVYE-AAQTVSIPI 243

Query: 192 GLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              GG+E +  AL+ ++     V +G A   N+ +++ + +     L
Sbjct: 244 IGVGGIEAVDDALEFMMAGASAVQVGAALAYNTHVMSDIIKALPGAL 290


>gi|170754614|ref|YP_001782424.1| dihydropyrimidine dehydrogenase [Clostridium botulinum B1 str.
           Okra]
 gi|169119826|gb|ACA43662.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           B1 str. Okra]
          Length = 411

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 62/171 (36%), Gaps = 15/171 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ +  NP +V   
Sbjct: 102 KVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVGQNPQLVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
             A+ +   IP+  K    + D               +A  N +K I    ++    +  
Sbjct: 160 CEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVDLDKFIGYPI 219

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
                 +S    + +  +    + ++   +    + I   GG+E    A +
Sbjct: 220 VNGKSSISGYSGKAVKPIALRFIQQLVTDERLKSVPISGIGGIETWEDAAE 270


>gi|194890619|ref|XP_001977354.1| GG18994 [Drosophila erecta]
 gi|190649003|gb|EDV46281.1| GG18994 [Drosophila erecta]
          Length = 1033

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 34/181 (18%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 41  LGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  G +     E A   E  G + + LN+ CP     E   G     
Sbjct: 623 LKRDFPEKIVIASIMCGFNEDDWTELATKAEQSGADALELNLSCPHGM-GERGMGMACGQ 681

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK------- 144
           +P +V      + KA+ +P+ +K    + D +   A            + +++       
Sbjct: 682 DPQLVEQISRWVRKAVKLPIFIKLTPNITDIVSIAAAAKRGGADGGSAINTVQGLMGLKA 741

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            S         ++    G+S    R    +    + +I    P   I   GG++    AL
Sbjct: 742 DSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRLPGFPILGIGGIDSGEVAL 798

Query: 205 K 205
           +
Sbjct: 799 Q 799


>gi|297617027|ref|YP_003702186.1| dihydroorotate dehydrogenase [Syntrophothermus lipocalidus DSM
           12680]
 gi|297144864|gb|ADI01621.1| dihydroorotate dehydrogenase family protein [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 312

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 40/202 (19%), Positives = 77/202 (38%), Gaps = 25/202 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  +      A I++   G   + +N+ CP    +    G     +P ++ + +
Sbjct: 104 VIVNIAGNQVEDYARLAAILDRQPGIAGLEVNISCP----NVKQGGLQFGTDPIMIDEVV 159

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HAR 156
            A+ ++  +P+ VK    V D      +  + K+   +G N I +              R
Sbjct: 160 RAVRESTRLPLIVKLSPNVTD------IVAMAKAAVNAGANAISLINTLLGMAIDVEKRR 213

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            A+           I  +   +VY++ KE  D+ I   GG+ + S AL+ IL     V I
Sbjct: 214 PALGNIFGGLSGPAIKPIAVRMVYQVAKEV-DVPILGMGGIMNYSDALEFILAGATAVSI 272

Query: 216 GRAAYKNSAMLTTVDEYFSNPL 237
           G   + +  +   +       L
Sbjct: 273 GTGNFVDPGISRRIIGDLEQYL 294


>gi|325288862|ref|YP_004265043.1| dihydroorotate oxidase B, catalytic subunit [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964263|gb|ADY55042.1| dihydroorotate oxidase B, catalytic subunit [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 304

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/179 (19%), Positives = 70/179 (39%), Gaps = 26/179 (14%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  A +     G   + +N+ CP+ +      G     +P    + IAA+ K   +
Sbjct: 109 DYMMMASAFQK--GCGIAALEVNISCPNIK----HGGMAFGTDPRSAEEVIAAVRKNTGL 162

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKAILKG-LSP 165
           P+  K    V       ++ ++ K+++  G +            I IHA+K +L   +  
Sbjct: 163 PLIAKLSPNV------TSIADMAKAVESGGADAVSLINTLLGMSIDIHAQKPLLANKVGG 216

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
                +  +   +VY++  E   + I   GG+     A++ +L     V IG A + + 
Sbjct: 217 LSGPAVRPVAVRMVYQVF-EAVKIPIIGMGGIMTWQDAVEFMLAGASAVSIGTANFTDP 274


>gi|326790917|ref|YP_004308738.1| dihydroorotate dehydrogenase [Clostridium lentocellum DSM 5427]
 gi|326541681|gb|ADZ83540.1| dihydroorotate dehydrogenase family protein [Clostridium
           lentocellum DSM 5427]
          Length = 315

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 87/216 (40%), Gaps = 29/216 (13%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           MI A  +    +    ++ L F+ + +  +   + G  I++     + + +   + + +N
Sbjct: 80  MINAVGLQNPGVDYYIEHELPFARKFDTKIIANVAGHSITEYCSVVERLNETDVDMLEVN 139

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP   V EG  G     + D+       + +  + P+ +K    V D      + ++ 
Sbjct: 140 ISCP--NVKEGGIGFG--TSCDMASKVTREVKRLTTKPIIIKLTPNVTD------IASIA 189

Query: 141 KSIKKSGVNG-----------IWIHARKAI-LKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +S++  G +            I +H ++ +    +       +  +   +VY++++   +
Sbjct: 190 QSVEAEGADAVSLINTLLGMKIDVHRKRPVIANKMGGFSGPAVKPVAVRMVYQVRRAV-N 248

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
           + I   GG+      ++ ++   D + +G AA+ N 
Sbjct: 249 IPIIGLGGIMTGEDVVEFLMAGADAISVGTAAFANP 284


>gi|291526028|emb|CBK91615.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Eubacterium rectale DSM 17629]
 gi|291527237|emb|CBK92823.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Eubacterium rectale M104/1]
          Length = 302

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 31/190 (16%), Positives = 72/190 (37%), Gaps = 24/190 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G  + + ++  K + D   + + +N+ CP    +    G     +P  V  
Sbjct: 93  DTRIVVNVCGHSLDEYLDVVKRLADEPIDMMEINISCP----NVKEGGIAFGTDPKGVET 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
             + + K    PV +K    V       ++ ++ ++ +  G +            I I+ 
Sbjct: 149 ITSEIKKYAKQPVIMKLSPNV------TSIADIARAAEAGGADAVSLINTITGMKIDINR 202

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
           R  +L           +  +   +VYE      ++ I   GG+ + + A+++ L     V
Sbjct: 203 RSFVLANKTGGMSGPAVHPVAVRMVYE-TAHAVNIPIIGMGGITNAADAIEMILAGATAV 261

Query: 214 MIGRAAYKNS 223
            +G A + N 
Sbjct: 262 SVGTANFVNP 271


>gi|255691904|ref|ZP_05415579.1| dihydroorotate oxidase [Bacteroides finegoldii DSM 17565]
 gi|260622457|gb|EEX45328.1| dihydroorotate oxidase [Bacteroides finegoldii DSM 17565]
          Length = 303

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 77/198 (38%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                E  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIETNMIVNVSGSTIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+  A    + VK    V D      +  + ++ ++SG +           
Sbjct: 144 AKGASEVVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL           +  +   +V+++ K   ++ +   GG+ D   A++ +L
Sbjct: 198 AIDAERRRPILSTITGGMSGAAVKPIALRMVWQVAK-VVNIPVIGLGGIMDWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGASAIQIGTANFIDPAV 274


>gi|312978330|ref|ZP_07790073.1| dihydroorotate oxidase [Lactobacillus crispatus CTV-05]
 gi|310894849|gb|EFQ43920.1| dihydroorotate oxidase [Lactobacillus crispatus CTV-05]
          Length = 307

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 37/190 (19%), Positives = 78/190 (41%), Gaps = 25/190 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG   +  VE A+ + + G  N + +NV CP   V +G       ++ D+V 
Sbjct: 96  ELPIVASVGGDSEADYVEVAQKLSNSGLVNALEINVSCP--NVAQGGMSFG--VHADVVE 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    +   ++IP+ VK    V D         + K+ +K G +G+ +            
Sbjct: 152 ELTRKIKAVVNIPIYVKLTPNVTDITV------IAKAAEKGGADGLSMINTLLGMRIDVK 205

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             R  +   +       +  +   ++ ++ ++   L I   GG+      ++ +L   + 
Sbjct: 206 KRRPLLGHNMGGLSGEAVKPIAIRMISQV-RQITSLPIIGMGGIASAEDVVEFMLAGANA 264

Query: 213 VMIGRAAYKN 222
           V +G A +K+
Sbjct: 265 VAVGTAHFKD 274


>gi|15668316|ref|NP_247112.1| hypothetical protein MJ_0144 [Methanocaldococcus jannaschii DSM
           2661]
 gi|2495829|sp|Q57608|Y144_METJA RecName: Full=Uncharacterized protein MJ0144
 gi|1590906|gb|AAB98127.1| conserved hypothetical protein [Methanocaldococcus jannaschii DSM
           2661]
          Length = 258

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 30/159 (18%), Positives = 61/159 (38%), Gaps = 17/159 (10%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + I LN  C    +     G  LM N +++ + +  M + L+ P+ +K R+        
Sbjct: 113 ADIIELNCHCRQPEITSLGIGQELMKNKNLLKEFLTKMKE-LNKPIFLKIRLNCIPLKEL 171

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +   N V+       +G+ +        G         P  D D +  + +E  D  I  
Sbjct: 172 IDNLNYVRDYF----DGLHV---DCFYPGK--------PYADMDSLKILAEEFNDKIIIG 216

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAY-KNSAMLTTVDE 231
           N  ++ + +A ++L   D V + R     N   +  +++
Sbjct: 217 NNSIDSIEKAKEMLKYSDFVSVARTILKGNVEWIKELNK 255


>gi|28211971|ref|NP_782915.1| dihydroorotate dehydrogenase 1B [Clostridium tetani E88]
 gi|28204414|gb|AAO36852.1| dihydroorotate dehydrogenase [Clostridium tetani E88]
          Length = 304

 Score = 69.8 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/217 (16%), Positives = 79/217 (36%), Gaps = 16/217 (7%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     + +   +  +  +   +GG  I   + A   +     + I LN+ CP   V E
Sbjct: 81  GIDYFINRELKKMNKIDTNIIANVGGGSIEDYLGAIDKLNKTDIDLIELNISCP--NVKE 138

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKK 145
           G     +     +  D ++ + K    P+ VK     +D +             +  +  
Sbjct: 139 GGMAFGI--KSKVAYDVVSRVKKICKKPLIVKLSPNAEDIVDMAVKCCEGGAEAISLVNT 196

Query: 146 SGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                + I +RK++     +      I  +   +VYE+ K N ++ +   GG+ +   A+
Sbjct: 197 FKAMAVDIKSRKSVFNNITAGLSGVAIKPIALRMVYEVCK-NVNVPVIGLGGINNWQDAI 255

Query: 205 K-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNP 236
           + I+     + +G A + N      ++  ++ Y    
Sbjct: 256 EFIMVGATAIQVGTANFINPYSSIKIVHGIESYMKKE 292


>gi|331269853|ref|YP_004396345.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           BKT015925]
 gi|329126403|gb|AEB76348.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           BKT015925]
          Length = 411

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 66/180 (36%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L      K L   I G + S+    A++V + G + I  N  CP    H+        
Sbjct: 93  RKLKEDYPSKVLVASIMGQNESEWTRLAELVTEIGADIIECNFSCPQMTSHDMGSDVG-- 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIG-----------VDDQIPAVALRNLVKSIKKSG 147
            NP++V     A+ K   +P+  K               ++     +A  N +K I    
Sbjct: 151 QNPELVKKYCQAVRKGTHLPILAKMTPNIGNMTIPAIASIEGGATGIATINTIKCISGIN 210

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
           ++ +           +S    + +  +    ++E+K  +E  ++ +   GG+E    A++
Sbjct: 211 LDNMVGLPVINGKSSISGYSGKAVKPIALRFIHELKTNEELKNIPVSGIGGIETWEDAVE 270


>gi|224476308|ref|YP_002633914.1| dihydroorotate dehydrogenase, catalytic subunit [Staphylococcus
           carnosus subsp. carnosus TM300]
 gi|254788902|sp|B9DPN4|PYRD_STACT RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|222420915|emb|CAL27729.1| dihydroorotate dehydrogenase, catalytic subunit [Staphylococcus
           carnosus subsp. carnosus TM300]
          Length = 305

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 84/244 (34%), Gaps = 35/244 (14%)

Query: 15  LLTNNALLYTE----MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEA 65
              N      E    MI A  +    +    ++ L    Q + P+   + G+     V  
Sbjct: 52  RYGNETPRVAETDSGMINAIGLQNPGVHHIIEHELKKLEQFDVPIIANVAGSVEEDYVYV 111

Query: 66  AKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           A+ +        + LN+ CP    +    G    ++P +  +    +     +PV VK  
Sbjct: 112 AEHISKAPNVKALELNISCP----NVKEGGMQFGVDPQVAAELTRKVKAVSEVPVYVKLS 167

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIP 172
             V        +  + K+I +   +G+ +              +  I   +       I 
Sbjct: 168 PNV------TNIVEMAKAIAEY-ADGLTMINTLVGLRIDGKSGKPIIANTIGGLSGPAIK 220

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            +   +VYE++K   D+ I   GG+++    +  +    + V +G A ++N  +   + +
Sbjct: 221 PVALRMVYEVRKAI-DIPIIAMGGVQNAQDVIDYISVGANAVAVGTANFQNPMVCKEIID 279

Query: 232 YFSN 235
               
Sbjct: 280 ELPT 283


>gi|332297006|ref|YP_004438928.1| dihydroorotate dehydrogenase family protein [Treponema
           brennaborense DSM 12168]
 gi|332180109|gb|AEE15797.1| dihydroorotate dehydrogenase family protein [Treponema
           brennaborense DSM 12168]
          Length = 588

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/202 (18%), Positives = 73/202 (36%), Gaps = 30/202 (14%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           + G+ I   V+ A+++       I LN+ CP   V  G     L  +P    D  AA+ K
Sbjct: 377 LSGSSIETYVKGAQLLAGTDVPMIELNISCP--NVKAGGMAFGL--DPCSAADVTAAVRK 432

Query: 114 ALS-IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHARKAIL 160
           A    P+ VK      D      +  +  +++ +G + I               AR    
Sbjct: 433 AAPRTPLIVKLSPNAPD------VVAVAHAVRTAGADAISLINTVQAIAIDIEKARPVFA 486

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKK------ENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              +      +  L   +VY++ +      +   + +   GG+     A++ I+     V
Sbjct: 487 NVRAGLSGPAVKPLALRLVYDLVQSMNRLPQRERIPVIGLGGIATWQDAVEFIMAGASAV 546

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A + +   +  + E   N
Sbjct: 547 QVGTATFADPLCMKHIIEGIGN 568


>gi|153940176|ref|YP_001392096.1| dihydropyrimidine dehydrogenase [Clostridium botulinum F str.
           Langeland]
 gi|152936072|gb|ABS41570.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           F str. Langeland]
 gi|295320101|gb|ADG00479.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           F str. 230613]
          Length = 411

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 63/171 (36%), Gaps = 15/171 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ +  NP +V   
Sbjct: 102 KVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVGQNPQLVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
             A+ +   IP+  K    + D               +A  N +K I    ++    +  
Sbjct: 160 CEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVDLDKFIGYPI 219

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALK 205
                 +S    + +  +    + ++   +   ++ I   GG+E    A +
Sbjct: 220 VNGKSSISGYSGKAVKPIALRFIQQLVTDERLKNVPISGIGGIETWEDAAE 270


>gi|227878925|ref|ZP_03996828.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus JV-V01]
 gi|256843503|ref|ZP_05548991.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus 125-2-CHN]
 gi|256849737|ref|ZP_05555168.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-1A-US]
 gi|262046689|ref|ZP_06019650.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-3A-US]
 gi|293380101|ref|ZP_06626190.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus 214-1]
 gi|227861471|gb|EEJ69087.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus JV-V01]
 gi|256614923|gb|EEU20124.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus 125-2-CHN]
 gi|256713226|gb|EEU28216.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-1A-US]
 gi|260573138|gb|EEX29697.1| dihydroorotate dehydrogenase B [Lactobacillus crispatus MV-3A-US]
 gi|290923314|gb|EFE00228.1| dihydroorotate dehydrogenase 1B [Lactobacillus crispatus 214-1]
          Length = 307

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 37/190 (19%), Positives = 78/190 (41%), Gaps = 25/190 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG   +  VE A+ + + G  N + +NV CP   V +G       ++ D+V 
Sbjct: 96  ELPIVASVGGDSEADYVEVAQKLSNSGLVNALEINVSCP--NVAQGGMSFG--VHADVVE 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    +   ++IP+ VK    V D         + K+ +K G +G+ +            
Sbjct: 152 ELTRKIKAVVNIPIYVKLTPNVTDITV------IAKAAEKGGADGLSMINTLLGMRIDVK 205

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             R  +   +       +  +   ++ ++ ++   L I   GG+      ++ +L   + 
Sbjct: 206 KRRPLLGHNMGGLSGEAVKPIAIRMISQV-RQITSLPIIGMGGIASAEDVVEFMLAGANA 264

Query: 213 VMIGRAAYKN 222
           V +G A +K+
Sbjct: 265 VAVGTAHFKD 274


>gi|168236356|ref|ZP_02661414.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|197290436|gb|EDY29791.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
          Length = 411

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|281208037|gb|EFA82215.1| dihydropyrimidine dehydrogenase [Polysphondylium pallidum PN500]
          Length = 1012

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 66/209 (31%), Gaps = 34/209 (16%)

Query: 29  ADAILRGDKK--NILGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           ++       K    L      K +   I  G +     E AK+ E  G + + LN+ CP 
Sbjct: 613 SEKTCHYWCKAVTELKRDFPSKVVIASIMCGFNKEDWQELAKMAEASGADALELNLSCPH 672

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
               E   G     NPD+V      + +A+ IP   K    V        ++ +  +   
Sbjct: 673 GM-GERGMGLACGQNPDLVLHICKWVREAIKIPFFAKLTPNV------TEVKEIALAAYN 725

Query: 146 SGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            G  G+                         ++    G+S    R    +    V  I++
Sbjct: 726 GGATGVTAINTVSGLMSLKGDASPWPAIGKEKRTTYGGVSGNATR---PMALRAVSSIRR 782

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGV 213
             PD  I   GG +     ++ L    GV
Sbjct: 783 TLPDFPIMATGGADSADTCIQFLHCGAGV 811


>gi|289433033|ref|YP_003462906.1| dihydroorotate dehydrogenase [Dehalococcoides sp. GT]
 gi|288946753|gb|ADC74450.1| dihydroorotate dehydrogenase family protein [Dehalococcoides sp.
           GT]
          Length = 324

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 70/191 (36%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+ + I    I    E A+ ++   G + I +N+ CP    +          +P+   
Sbjct: 114 DVPVIVNIAAESIEDYAELARRLDKVPGVSGIEVNISCP----NVKCGCIEFGSSPESAA 169

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
                +  A ++P+ VK            ++  L K++  +G + I            I 
Sbjct: 170 RVTDVVRNATTLPLIVKLTP------NTSSITELAKAVADAGADAISLINTLRGMRIDIK 223

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L           I  +   +VY++     ++ +   GG+ +   AL+ ++     
Sbjct: 224 KRRPVLGNHTGGLSGPAIKPVAISMVYQVAGAV-NVPVIGGGGIMNAEDALEFLMAGATA 282

Query: 213 VMIGRAAYKNS 223
           + IG A   N 
Sbjct: 283 IQIGTANLVNP 293


>gi|260101461|ref|ZP_05751698.1| dihydroorotate oxidase [Lactobacillus helveticus DSM 20075]
 gi|260084735|gb|EEW68855.1| dihydroorotate oxidase [Lactobacillus helveticus DSM 20075]
          Length = 307

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/192 (20%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACL 97
             L     + P+   +GG      VE AK +   G  N + +NV CP   V +G      
Sbjct: 88  TKLRHQYLDLPIMASVGGDSEDDYVEVAKKLSASGLVNALEINVSCP--NVAQGGMSFG- 144

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            ++  +V +    +  A+++P+ VK    V D      +  + K+ +  G +GI      
Sbjct: 145 -VHAGVVEELTKKIKMAVALPIYVKLTPNVTD------IVEIAKAAESGGADGISMINTL 197

Query: 153 ------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 I  RK +L   +       +  +   ++ ++ ++   L I   GG+      ++
Sbjct: 198 LGMRIDIKTRKPLLGHNMGGLSGEAVKPIAIRMISQV-RQVTQLPIIGMGGISTAQDVIE 256

Query: 206 -ILPSVDGVMIG 216
            IL   + V +G
Sbjct: 257 FILAGANAVAVG 268


>gi|257784614|ref|YP_003179831.1| dihydroorotate dehydrogenase family protein [Atopobium parvulum DSM
           20469]
 gi|257473121|gb|ACV51240.1| dihydroorotate dehydrogenase family protein [Atopobium parvulum DSM
           20469]
          Length = 308

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/215 (17%), Positives = 77/215 (35%), Gaps = 28/215 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSAR 87
           D  +      +     +   + +Q+    + ++++  + +E+   +   I LNV CP+  
Sbjct: 82  DDFIAHTDDYMKDLEDRGTRVIMQMAAHSVQEMIDVVERLEELNPHISAIELNVSCPNLE 141

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
                 G  L   P+   + + A+     +P+ VK           V +  + K+ +  G
Sbjct: 142 ----KGGRPLGGTPEQATEIMKAVRPLTKLPILVKM--------APVNVAEIGKAFEAEG 189

Query: 148 VNGIW-----------IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            +G+            +H RK+ L K           N    +V+E  +    + I   G
Sbjct: 190 ADGLTLINSIPGMSINVHTRKSRLSKPTGGLSGPLCHNAAVRMVWECAQAV-SIPICGVG 248

Query: 196 GLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTV 229
           G+E    A + IL     V +G A   +      +
Sbjct: 249 GVETGEDAAEFILAGATAVSVGSANLYDPMCAPRI 283


>gi|167630181|ref|YP_001680680.1| dihydroorotate dehydrogenase, catalytic subunit [Heliobacterium
           modesticaldum Ice1]
 gi|226724739|sp|B0TGQ8|PYRD_HELMI RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|167592921|gb|ABZ84669.1| dihydroorotate dehydrogenase, catalytic subunit [Heliobacterium
           modesticaldum Ice1]
          Length = 309

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 77/204 (37%), Gaps = 29/204 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+ + + G  +      A I+++  G   + +N+ CP   V EG      +  P    
Sbjct: 95  DTPVIVNVSGNSVEDYGRLASILDEADGVAALEVNISCP--NVKEGGIQFGTL--PASAA 150

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
               A+ +    PV VK    V D      +  + +++  +G + +            I 
Sbjct: 151 AVTRAVRENTQKPVIVKLSPNVTD------ITEMARAVVDAGADALALINTLLGMDIDIC 204

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L           I  +   ++Y++ +    + I   GG+ +   A+  +L     
Sbjct: 205 TRRPVLANIFGGLSGPAIKPVALRMIYQVYRAV-HVPILGMGGIMNSQDAIAFMLAGATA 263

Query: 213 VMIGRAAYKNS----AMLTTVDEY 232
           + +G A + N      +L  ++EY
Sbjct: 264 IAVGTANFTNPRATMDILEGIEEY 287


>gi|194736993|ref|YP_002115276.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|194712495|gb|ACF91716.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. CVM19633]
          Length = 411

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|322807129|emb|CBZ04703.1| dihydropyrimidine dehydrogenase [NADP+] [Clostridium botulinum
           H04402 065]
          Length = 411

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 62/171 (36%), Gaps = 15/171 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ +  NP +V   
Sbjct: 102 KVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVGQNPQLVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
             A+ +   IP+  K    + D               +A  N +K I    ++    +  
Sbjct: 160 CEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVDLDKFIGYPI 219

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALK 205
                 +S    + +  +    + ++  +     + I   GG+E    A +
Sbjct: 220 VNGKSSISGYSGKAVKPIALRFIQQLVTDGRLKSVPISGIGGIETWEDAAE 270


>gi|328465360|gb|EGF36609.1| dihydroorotate dehydrogenase 1B [Lactobacillus helveticus MTCC
           5463]
          Length = 306

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/192 (20%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACL 97
             L     + P+   +GG      VE AK +   G  N + +NV CP   V +G      
Sbjct: 88  TKLRHQYLDLPIMASVGGDSEDDYVEVAKKLSASGLVNALEINVSCP--NVAQGGMSFG- 144

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            ++  +V +    +  A+++P+ VK    V D      +  + K+ +  G +GI      
Sbjct: 145 -VHAGVVEELTKKIKMAVALPIYVKLTPNVTD------IVEIAKAAESGGADGISMINTL 197

Query: 153 ------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 I  RK +L   +       +  +   ++ ++ ++   L I   GG+      ++
Sbjct: 198 LGMRIDIKTRKPLLGHNMGGLSGEAVKPIAIRMISQV-RQVTQLPIIGMGGISTAQDVIE 256

Query: 206 -ILPSVDGVMIG 216
            IL   + V +G
Sbjct: 257 FILAGANAVAVG 268


>gi|148380778|ref|YP_001255319.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           A str. ATCC 3502]
 gi|153931280|ref|YP_001385063.1| dihydropyrimidine dehydrogenase [Clostridium botulinum A str. ATCC
           19397]
 gi|153934691|ref|YP_001388532.1| dihydropyrimidine dehydrogenase [Clostridium botulinum A str. Hall]
 gi|148290262|emb|CAL84382.1| putative iron-sulfur oxidoreductase [Clostridium botulinum A str.
           ATCC 3502]
 gi|152927324|gb|ABS32824.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           A str. ATCC 19397]
 gi|152930605|gb|ABS36104.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           A str. Hall]
          Length = 411

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 62/171 (36%), Gaps = 15/171 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G +  +  E AK+V + G + I  N  CP   +   + G+ +  NP +V   
Sbjct: 102 KVLVASIMGQNEKEWEELAKLVTEVGADIIECNFSCPQ--MTSSAMGSDVGQNPQLVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
             A+ +   IP+  K    + D               +A  N +K I    ++    +  
Sbjct: 160 CEAVRRGTDIPILAKMTPNIGDMSVPAIASIEGGATGIATINTIKCITGVDLDKFIGYPI 219

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALK 205
                 +S    + +  +    + ++  +     + I   GG+E    A +
Sbjct: 220 VNGKSSISGYSGKAVKPIALRFIQQLVTDGRLKSVPISGIGGIETWEDAAE 270


>gi|160902130|ref|YP_001567711.1| dihydroorotate dehydrogenase family protein [Petrotoga mobilis
           SJ95]
 gi|259547538|sp|A9BJH4|PYRD_PETMO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|160359774|gb|ABX31388.1| dihydroorotate dehydrogenase family protein [Petrotoga mobilis
           SJ95]
          Length = 300

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 78/204 (38%), Gaps = 16/204 (7%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           ++Q+  +   + G  I + V + + +     + I LN+ CP    +    G       +I
Sbjct: 90  NSQDTVIIANVSGNTIDEYVISVEKLNQTDIDMIELNISCP----NVKEGGISFGTKAEI 145

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             + +  + K    P+ VK     ++     +    A  + +  +       I I  +KA
Sbjct: 146 ASNVVTQVRKVCQKPLIVKLSPSAENIVEMAESCVEAGADALSLVNTFPALAIDISKKKA 205

Query: 159 ILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           I     +      I  +   +VYE+ K   D+ I   GG+ D   A++ I+     V +G
Sbjct: 206 IFDNITAGLSGPCIKPIALRMVYEVSKAV-DVPIIGIGGIMDYRDAIEYIMAGAWAVQVG 264

Query: 217 RAAYKNSA----MLTTVDEYFSNP 236
            A + N      ++  ++EY    
Sbjct: 265 TANFINPNACAEIIEGIEEYLQKE 288


>gi|73749056|ref|YP_308295.1| dihydroorotate dehydrogenase 1B [Dehalococcoides sp. CBDB1]
 gi|73660772|emb|CAI83379.1| dihydroorotate dehydrogenase [Dehalococcoides sp. CBDB1]
          Length = 310

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 70/191 (36%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+ + I    I    E A+ ++   G + I +N+ CP    +          +P+   
Sbjct: 100 DVPVIVNIAAESIEDYAELARRLDKVPGVSGIEVNISCP----NVKCGCIEFGSSPESAA 155

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
                +  A ++P+ VK            ++  L K++  +G + I            I 
Sbjct: 156 RVTDVVRNATTLPLIVKLTP------NTSSITELAKAVADAGADAISLINTLRGMRIDIK 209

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L           I  +   +VY++     ++ +   GG+ +   AL+ ++     
Sbjct: 210 KRRPVLGNHTGGLSGPAIKPVAISMVYQVAGAV-NVPVIGGGGIMNAEDALEFLMAGATA 268

Query: 213 VMIGRAAYKNS 223
           + IG A   N 
Sbjct: 269 IQIGTANLVNP 279


>gi|330983303|gb|EGH81406.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 67

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 256 SASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAF 315
             SM  Y A H+ SGG +  +TRHM+GL  GFP +RR R +L+V+   +     +++ A 
Sbjct: 2   LESMRPYIAAHIASGGNMHHVTRHMLGLGLGFPGARRFRQLLSVDIHKAENPMLLLDQAA 61

Query: 316 NLM 318
             +
Sbjct: 62  AFL 64


>gi|332701407|ref|ZP_08421495.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332551556|gb|EGJ48600.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 306

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 45/221 (20%), Positives = 75/221 (33%), Gaps = 37/221 (16%)

Query: 26  MIVADAI----LRGDKKNILGFST-QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  I    +    ++ L F   +E  +   +   D  +  E AA +    G   + +
Sbjct: 69  MLNAIGIQNIGVEAFLRDKLPFLPWRETAVIANLYACDAHEFGELAAVLASVEGMTALEV 128

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALRN 138
           NV CP    +    G     NP  +      +   A S PV VK    V D      + +
Sbjct: 129 NVSCP----NVKEGGVAFGQNPGQIRAVTEEVKRNAGSKPVIVKLSPNVTD------IAD 178

Query: 139 LVKSIKKSGVNGIW-----------IHARKA----ILKGLSPKDNRKIPNLDYDIVYEIK 183
             ++    G + +            I  RK     +  GLS      I  +    V+++ 
Sbjct: 179 AARAAVDGGADMLSCINTLMGMAVDIRTRKPRLANVYGGLS---GPAIKPVALRCVHQVC 235

Query: 184 KENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
           +      IG+ GG+      L  IL     V +G A +   
Sbjct: 236 RAVSVPVIGV-GGIASAEDILDFILVGAHAVQVGTANFMRP 275


>gi|258515562|ref|YP_003191784.1| dihydroorotate dehydrogenase 1B [Desulfotomaculum acetoxidans DSM
           771]
 gi|257779267|gb|ACV63161.1| dihydroorotate dehydrogenase family protein [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 305

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 41/202 (20%), Positives = 80/202 (39%), Gaps = 29/202 (14%)

Query: 49  PLALQIGGADISKL-VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + I G  +    + A K+    G   + +N+ CP   V +G        +P+   + 
Sbjct: 96  PVIVNISGDTVEDYGLLAGKLDSASGVAGLEVNISCP--NVKKGGLQFG--SDPESAAEV 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
           +  +  +  +PV VK    V       ++ +L  S+ ++G +            I I AR
Sbjct: 152 VRVIKSSTGLPVIVKLSPNV------TSITDLAVSVAEAGADALSLINTILGMAIDIKAR 205

Query: 157 KAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + +L   +       +  +    V+++ K    L I   GG+     A++ IL     V 
Sbjct: 206 RPVLGNIMGGLSGPAVRPVAVRCVWQVYKAV-KLPIIGMGGIVSAEDAIEFILAGASAVA 264

Query: 215 IGRAAYKNS----AMLTTVDEY 232
           +G A + N      +L  ++EY
Sbjct: 265 VGTANFVNPRATVEILEGIEEY 286


>gi|147669822|ref|YP_001214640.1| dihydroorotate dehydrogenase 1B [Dehalococcoides sp. BAV1]
 gi|146270770|gb|ABQ17762.1| dihydroorotate oxidase B, catalytic subunit [Dehalococcoides sp.
           BAV1]
          Length = 324

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 70/191 (36%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+ + I    I    E A+ ++   G + I +N+ CP    +          +P+   
Sbjct: 114 DVPVIVNIAAESIEDYAELARRLDKVPGVSGIEVNISCP----NVKCGCIEFGSSPESAA 169

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
                +  A ++P+ VK            ++  L K++  +G + I            I 
Sbjct: 170 KVTDVVRNATTLPLIVKLTP------NTSSITELAKAVADAGADAISLINTLRGMRIDIK 223

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L           I  +   +VY++     ++ +   GG+ +   AL+ ++     
Sbjct: 224 KRRPVLGNHTGGLSGPAIKPVAISMVYQVAGAV-NVPVIGGGGIMNAEDALEFLMAGATA 282

Query: 213 VMIGRAAYKNS 223
           + IG A   N 
Sbjct: 283 IQIGTANLVNP 293


>gi|322661451|gb|EFY57675.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
          Length = 366

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|322615214|gb|EFY12136.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322617805|gb|EFY14701.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624602|gb|EFY21433.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626948|gb|EFY23744.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322634134|gb|EFY30870.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322635675|gb|EFY32385.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640190|gb|EFY36854.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646387|gb|EFY42899.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649354|gb|EFY45790.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322656475|gb|EFY52764.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322665661|gb|EFY61845.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322667185|gb|EFY63352.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322671191|gb|EFY67319.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675169|gb|EFY71246.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322680777|gb|EFY76812.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686952|gb|EFY82929.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323192716|gb|EFZ77943.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323198852|gb|EFZ83951.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323205138|gb|EFZ90116.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323208181|gb|EFZ93125.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323213535|gb|EFZ98326.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215794|gb|EGA00537.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323221293|gb|EGA05716.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223841|gb|EGA08144.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231240|gb|EGA15355.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323233674|gb|EGA17766.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323237744|gb|EGA21804.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245727|gb|EGA29721.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323246535|gb|EGA30514.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2009159199]
 gi|323253020|gb|EGA36853.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008282]
 gi|323254772|gb|EGA38575.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008283]
 gi|323259528|gb|EGA43163.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323268311|gb|EGA51786.1| dihydropyrimidine dehydrogenase subunit B [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008285]
          Length = 411

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|260886389|ref|ZP_05897652.1| dihydroorotate oxidase [Selenomonas sputigena ATCC 35185]
 gi|330838844|ref|YP_004413424.1| dihydroorotate dehydrogenase family protein [Selenomonas sputigena
           ATCC 35185]
 gi|260863910|gb|EEX78410.1| dihydroorotate oxidase [Selenomonas sputigena ATCC 35185]
 gi|329746608|gb|AEB99964.1| dihydroorotate dehydrogenase family protein [Selenomonas sputigena
           ATCC 35185]
          Length = 304

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 33/183 (18%), Positives = 66/183 (36%), Gaps = 24/183 (13%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           I      +  E A++++  G + I +N+ CP    +    G     +P         + K
Sbjct: 102 ISAGTAEEYGEMAQMLDVEGVDGIEVNISCP----NVKEGGIVFGTDPVQAARVTQEVKK 157

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKG 162
               PV VK    V D      +  + ++++++G +            I +  R+ +L  
Sbjct: 158 HTKKPVIVKLSPNVTD------IPQMARAVEEAGADAVSLINTLTGMAIDVEKRQPLLGN 211

Query: 163 -LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAY 220
                    +  +   +VY+  +      IG+ GG++     A  +L     V IG   +
Sbjct: 212 ITGGLSGPAVKPIALRMVYQAAQAVSIPVIGM-GGIQTGEDVAAFLLVGASAVEIGAENF 270

Query: 221 KNS 223
            N 
Sbjct: 271 ANP 273


>gi|224583312|ref|YP_002637110.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|224467839|gb|ACN45669.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
          Length = 411

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITSIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|104774746|ref|YP_619726.1| dihydroorotate dehydrogenase 1B [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|122983869|sp|Q1G864|PYRD_LACDA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|103423827|emb|CAI98852.1| Dihydroorotate dehydrogenase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325126585|gb|ADY85915.1| Dihydroorotate dehydrogenase B, catalytic unit [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 307

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/192 (19%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACL 97
             L     + P+   +GG      VE AK +   G  N + +NV CP   V +G      
Sbjct: 88  TKLRHQYLDLPIMASVGGDSEDDYVEVAKKLSASGLVNALEINVSCP--NVAQGGMSFG- 144

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            ++  +V +    +  A+++P+ VK    V D      +  + K+ +  G +GI      
Sbjct: 145 -VHAGVVEELTKKIKMAVALPIYVKLTPNVTD------IVEIAKAAESGGADGISMINTV 197

Query: 153 ------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 +  RK +L   +       +  +   ++ ++ ++   L I   GG+      ++
Sbjct: 198 LGMRIDVKTRKPLLGHNMGGLSGEAVKPIAIRMISQV-RQVTQLPIIGMGGISTAQDVIE 256

Query: 206 -ILPSVDGVMIG 216
            IL   + V +G
Sbjct: 257 FILAGANAVAVG 268


>gi|16765517|ref|NP_461132.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|62180774|ref|YP_217191.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|161613121|ref|YP_001587086.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167991114|ref|ZP_02572213.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|168229542|ref|ZP_02654600.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CDC 191]
 gi|168259472|ref|ZP_02681445.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|168466133|ref|ZP_02700003.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|168818103|ref|ZP_02830103.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Weltevreden str. HI_N05-537]
 gi|194470352|ref|ZP_03076336.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|197248087|ref|YP_002147158.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|198241985|ref|YP_002216271.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|205353322|ref|YP_002227123.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207857621|ref|YP_002244272.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|238912629|ref|ZP_04656466.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|16420724|gb|AAL21091.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|62128407|gb|AAX66110.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Choleraesuis str. SC-B67]
 gi|161362485|gb|ABX66253.1| hypothetical protein SPAB_00829 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194456716|gb|EDX45555.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|195631189|gb|EDX49749.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|197211790|gb|ACH49187.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Agona str. SL483]
 gi|197936501|gb|ACH73834.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|205273103|emb|CAR38058.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205330434|gb|EDZ17198.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205335946|gb|EDZ22710.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Kentucky str. CDC 191]
 gi|205345012|gb|EDZ31776.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Weltevreden str. HI_N05-537]
 gi|205351177|gb|EDZ37808.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|206709424|emb|CAR33765.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|261247401|emb|CBG25226.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267994252|gb|ACY89137.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158748|emb|CBW18260.1| putative oxidoreductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312913177|dbj|BAJ37151.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320086627|emb|CBY96398.1| Dihydropyrimidine dehydrogenase [NADP+] DHPDHase; DPD;
           Dihydrouracil dehydrogenase; Dihydrothymine
           dehydrogenase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
 gi|321224841|gb|EFX49904.1| Dihydropyrimidine [Salmonella enterica subsp. enterica serovar
           Typhimurium str. TN061786]
 gi|322715249|gb|EFZ06820.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130514|gb|ADX17944.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|326624022|gb|EGE30367.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326628411|gb|EGE34754.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
 gi|332989121|gb|AEF08104.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 411

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|168242273|ref|ZP_02667205.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL486]
 gi|194448536|ref|YP_002046240.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|197261723|ref|ZP_03161797.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|200387718|ref|ZP_03214330.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|194406840|gb|ACF67059.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL476]
 gi|197239978|gb|EDY22598.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|199604816|gb|EDZ03361.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|205338639|gb|EDZ25403.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL486]
          Length = 411

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|259502016|ref|ZP_05744918.1| dihydroorotate oxidase [Lactobacillus antri DSM 16041]
 gi|259170017|gb|EEW54512.1| dihydroorotate oxidase [Lactobacillus antri DSM 16041]
          Length = 308

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 74/184 (40%), Gaps = 27/184 (14%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-C 112
              A+   +VE  ++      N I LNV CP    +    G  +  +P ++      +  
Sbjct: 108 FSTAEYETVVE--QLAAAPTVNAIELNVSCP----NVKHGGLAMGTDPAVLEGLTRKVVR 161

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILK 161
           +A   P+ VK    V D +P      L ++ ++ G NG+ +             R+ +L 
Sbjct: 162 RAKGKPIYVKLTPNVTDIVP------LAQAAERGGANGLTMINTLTGLSIDLRTRRPVLA 215

Query: 162 GLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            ++       +  +   +++++ +    L I   GG+E     L+ ++   + V +G A+
Sbjct: 216 NVTGGLSGPALKPMALRMIHQV-RAVSSLPIIGVGGIETAEDVLEFMMAGANAVEVGAAS 274

Query: 220 YKNS 223
           + + 
Sbjct: 275 FHDP 278


>gi|642230|emb|CAA58832.1| putative nitrogen fixation regulatory protein-3 homologue
           [Entamoeba histolytica]
          Length = 165

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 33/166 (19%), Positives = 68/166 (40%), Gaps = 21/166 (12%)

Query: 17  TNNALLYTEMIVAD-----------AILRGDKKN--ILGFSTQEKP-LALQIGGADISKL 62
              + ++TE +V+             I++   KN  +L    +++    LQ+G  D+   
Sbjct: 5   AGASAVFTEELVSKRLCECKRVENSGIIQYIHKNDVMLTLKPEQQSKTILQLGTFDVESS 64

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           V+   ++++     I++N+GC      +G  G  L+ N D +   + A+   LS P++ K
Sbjct: 65  VKCVSLIQE--VCGIDINLGCGMWFSTKGEMGQALVDNRDKLEKIVKALV-GLSKPISAK 121

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            R+    Q         ++ +   G++ I +H R          D 
Sbjct: 122 IRL----QQTHEETLEFIQWLYSLGISIISLHGRHHKELYGVDCDW 163


>gi|213021477|ref|ZP_03335924.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 132

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 22/107 (20%), Positives = 38/107 (35%), Gaps = 17/107 (15%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
           +D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ V +
Sbjct: 1   IDWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSRVVK 58

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           Y                +  W ++   +  Y          L  + R
Sbjct: 59  YNE-------------PRMPWPEVVTLLQKYTRLEKQGDTGLYHVAR 92


>gi|167551143|ref|ZP_02344898.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA29]
 gi|205324061|gb|EDZ11900.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA29]
          Length = 411

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIAMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|33333732|gb|AAQ11981.1| dihydropyrimidine dehydrogenase [Dictyostelium discoideum]
          Length = 1009

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 37/200 (18%), Positives = 64/200 (32%), Gaps = 28/200 (14%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           ++       K I  L     ++ +   I  G +     + AK+ E  G + I LN+ CP 
Sbjct: 612 SEKTCHYWCKAIGELKRDFPDRIVIASIMCGFNKEDWTQLAKMAEASGADGIELNLSCPH 671

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
               E   G     + ++V      +  A  +P   K    V        ++ + K+   
Sbjct: 672 GM-GEKGMGLACGQDTELVFHICQWVRAATRLPFFAKLTPNV------TEIKEIAKAAHD 724

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIP------------------NLDYDIVYEIKKENP 187
            G +G+      + L GL    N                       +    V  I+K  P
Sbjct: 725 GGADGVTAINTVSGLMGLKGDSNAWPAIGDEKRTTYGGVSGNATRPIALRAVSSIRKSLP 784

Query: 188 DLFIGLNGGLEDMSQALKIL 207
           D  I   GG +     ++ L
Sbjct: 785 DYPIMATGGADSADATIQFL 804


>gi|66828195|ref|XP_647452.1| dihydropyrimidine dehydrogenase [Dictyostelium discoideum AX4]
 gi|74859332|sp|Q55FT1|DPYD_DICDI RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|60475501|gb|EAL73436.1| dihydropyrimidine dehydrogenase [Dictyostelium discoideum AX4]
          Length = 1009

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 37/200 (18%), Positives = 64/200 (32%), Gaps = 28/200 (14%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           ++       K I  L     ++ +   I  G +     + AK+ E  G + I LN+ CP 
Sbjct: 612 SEKTCHYWCKAIGELKRDFPDRIVIASIMCGFNKEDWTQLAKMAEASGADGIELNLSCPH 671

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
               E   G     + ++V      +  A  +P   K    V        ++ + K+   
Sbjct: 672 GM-GEKGMGLACGQDTELVFHICQWVRAATRLPFFAKLTPNV------TEIKEIAKAAHD 724

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIP------------------NLDYDIVYEIKKENP 187
            G +G+      + L GL    N                       +    V  I+K  P
Sbjct: 725 GGADGVTAINTVSGLMGLKGDSNAWPAIGDEKRTTYGGVSGNATRPIALRAVSSIRKSLP 784

Query: 188 DLFIGLNGGLEDMSQALKIL 207
           D  I   GG +     ++ L
Sbjct: 785 DYPIMATGGADSADATIQFL 804


>gi|294795151|ref|ZP_06760285.1| dihydroorotate oxidase [Veillonella sp. 3_1_44]
 gi|294453943|gb|EFG22318.1| dihydroorotate oxidase [Veillonella sp. 3_1_44]
          Length = 316

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/196 (19%), Positives = 74/196 (37%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   +    I +    A+ +   G   + +NV CP+        G    ++P +V  
Sbjct: 106 DVPLLANMSAGTIDEFTWMAETLSVDGIAGLEVNVSCPNVE----CEGMAFGVDPKVVES 161

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
              A+ K    PV VK    V D      +  + K+++  G N            I IH 
Sbjct: 162 VTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGNGVSLINTLLGMAIDIHR 215

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           +  +   +V+++ K    + I   GG+   + A++ ++     V
Sbjct: 216 RKPVLGNTYGGLSGPAVKPVALRMVHQVYKGVT-IPIIGLGGIMTGTDAIEFMMAGAQAV 274

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A   +   ++ +
Sbjct: 275 QVGTATMVDPTAISRI 290


>gi|194500464|gb|ACF75488.1| dihydrogenpyrimidine dehydrogenase [Adineta vaga]
          Length = 835

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 63/198 (31%), Gaps = 31/198 (15%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           A      K +         +A  +   D     E AK+ E  G + + LN+ CP     E
Sbjct: 628 AYWLQCIKELKNDFPDRIIIASIMCSFDEQDWTELAKVTEAAGADALELNLSCPHGM-GE 686

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
              G       D+V +    +  A+ IP   K    +        + ++ ++ K+ G +G
Sbjct: 687 KGMGLACGQKADLVLNICKWVRAAVKIPFFAKMTPNI------TNIVDIARAAKEGGADG 740

Query: 151 IW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           +                        ++     G+S    R I       V  I +  P  
Sbjct: 741 VTATNTVSGLMSIRHDTTAWPSVGKSQNTTYGGVSGNAIRPIA---LRAVSAIGRALPGF 797

Query: 190 FIGLNGGLEDMSQALKIL 207
            I   GG++     ++ L
Sbjct: 798 PILATGGIDSADAGIQFL 815


>gi|194446223|ref|YP_002041458.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194404886|gb|ACF65108.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Newport str. SL254]
          Length = 411

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|254304287|ref|ZP_04971645.1| dihydroorotate oxidase [Fusobacterium nucleatum subsp. polymorphum
           ATCC 10953]
 gi|148324479|gb|EDK89729.1| dihydroorotate oxidase [Fusobacterium nucleatum subsp. polymorphum
           ATCC 10953]
          Length = 305

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 80/222 (36%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIEDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKTVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDNLESAL 287


>gi|241889334|ref|ZP_04776635.1| dihydroorotate dehydrogenase [Gemella haemolysans ATCC 10379]
 gi|241863877|gb|EER68258.1| dihydroorotate dehydrogenase [Gemella haemolysans ATCC 10379]
          Length = 304

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 81/231 (35%), Gaps = 30/231 (12%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +    +    +  L    + + P+   + G++I   V  A+ +      + + L
Sbjct: 68  MLNAIGLQNPGVHEIMETKLKELEKYDVPIIANVAGSEIDDYVYVAEHISKAPNVHALEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P+   +    + +  S+PV VK    V        +  +
Sbjct: 128 NISCP----NVKHGGIQFGTDPETAKNLTRKVKEVSSVPVYVKLSPNV------TNIVAM 177

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K++++ G +GI +              +  I           I  +   +VY++ +   
Sbjct: 178 AKAVEEGGADGITMINTLVGVRLDKKTGKPIIANVTGGLSGPAIKPVAIRMVYQVSQAV- 236

Query: 188 DLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           ++ I   GG+ D       I      V +G A + +      + +     L
Sbjct: 237 NIPIIGMGGIMDEWDVIDFISAGASAVAVGTANFADPYACPKIIDKLEAAL 287


>gi|261404276|ref|YP_003240517.1| dihydroorotate dehydrogenase family protein [Paenibacillus sp.
           Y412MC10]
 gi|261280739|gb|ACX62710.1| dihydroorotate dehydrogenase family protein [Paenibacillus sp.
           Y412MC10]
          Length = 310

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 75/201 (37%), Gaps = 34/201 (16%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVED----------FGYNEINLNVGCPSARV 88
            +   ++    + + +GG  + +  E A+++ +             + I LN+ CP+ + 
Sbjct: 85  ELSDMTSHGTAVIVNLGGGTVREYAEGAELLTEASSKLRSAGKRAVDMIELNISCPNIK- 143

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
                G    +  +   + + A+  A ++P+ VK   G  D      LR + +  +  G 
Sbjct: 144 ---EGGLAFGIENEQAREVVRAVRNATTLPLLVKLSPGAKD------LREMARMCEAEGA 194

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              R    +  +      I  +   +V+++ + +  + +   GG
Sbjct: 195 DGLSLINTIQAMAIDIRERRSVFDRAYAGLSGPAIKPIALRMVHQVAR-SVSIPVVGIGG 253

Query: 197 LEDMSQALK-ILPSVDGVMIG 216
           +      L+ I+     V IG
Sbjct: 254 ICSAEDILEFIMAGAAAVQIG 274


>gi|116514881|ref|YP_813787.1| dihydroorotate dehydrogenase 1B [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|122274387|sp|Q047M3|PYRD_LACDB RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116094196|gb|ABJ59349.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 307

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 38/192 (19%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACL 97
             L     + P+   +GG      VE AK +   G  N + +NV CP   V +G      
Sbjct: 88  TKLRHQYIDLPIMASVGGDSEDDYVEVAKKLSASGLVNALEINVSCP--NVAQGGMSFG- 144

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
            ++  +V +    +  A+++P+ VK    V D      +  + K+ +  G +GI      
Sbjct: 145 -VHAGVVEELTKKIKMAVALPIYVKLTPNVTD------IVEIAKAAESGGADGISMINTV 197

Query: 153 ------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 +  RK +L   +       +  +   ++ ++ ++   L I   GG+      ++
Sbjct: 198 LGMRIDVKTRKPLLGHNMGGLSGEAVKPIAIRMISQV-RQVTQLPIIGMGGISTAQDVIE 256

Query: 206 -ILPSVDGVMIG 216
            IL   + V +G
Sbjct: 257 FILAGANAVAVG 268


>gi|222445269|ref|ZP_03607784.1| hypothetical protein METSMIALI_00897 [Methanobrevibacter smithii
           DSM 2375]
 gi|222434834|gb|EEE41999.1| hypothetical protein METSMIALI_00897 [Methanobrevibacter smithii
           DSM 2375]
          Length = 236

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 31/147 (21%), Positives = 56/147 (38%), Gaps = 18/147 (12%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
           + + +N  C    +     G  ++   D+       +    S  V+VK R  VD      
Sbjct: 96  DIVEINCHCRQDEILAIGCGQNMLKRDDLAEYI-GDVVDNASCEVSVKIRANVDGTDT-- 152

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               + K I+ +G + + I A K             I + DYD++ +I   N ++ +  N
Sbjct: 153 --LKIAKLIENTGADYLHIDAMKV-----------GIFDADYDLLAKIC-SNTNIKVIGN 198

Query: 195 GGLEDMSQALKIL-PSVDGVMIGRAAY 220
             ++   +  K+L   V G  I RA  
Sbjct: 199 NSIDSEQKIEKMLKTGVFGFSIARAVI 225


>gi|156369958|ref|XP_001628240.1| predicted protein [Nematostella vectensis]
 gi|156215211|gb|EDO36177.1| predicted protein [Nematostella vectensis]
          Length = 1081

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 32/163 (19%), Positives = 57/163 (34%), Gaps = 31/163 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+ E  G + + LN+ CP     E   G     + ++V +    +  A++IP   K   
Sbjct: 654 AKMAEAAGADALELNLSCPHGM-GERGMGLACGQDAELVRNICRWVRAAITIPFFAKLTP 712

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLS 164
            V D +       + ++ K+   +G+                         ++    G+S
Sbjct: 713 NVTDIVV------IARAAKEGNADGVTATNTVSGLMGLKGTSEAWPAIGREKRTTYGGMS 766

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               R I       V  I +  P   I   GG++    AL+ L
Sbjct: 767 GNAIRPIA---LRAVSAIGRALPGFPILATGGIDSADAALQFL 806


>gi|310657591|ref|YP_003935312.1| pyrd [Clostridium sticklandii DSM 519]
 gi|308824369|emb|CBH20407.1| PyrD [Clostridium sticklandii]
          Length = 311

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 41/223 (18%), Positives = 78/223 (34%), Gaps = 38/223 (17%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG--------------YNEINLNVGCP 84
            +   S  +      +GG+ +   +E AK++E+                 + + LN+ CP
Sbjct: 82  ELQQMSNIDTVKIANLGGSTLETYIEGAKLIEEHNKKVKANASTLLHTAVDLVELNISCP 141

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              V EG     +    +     +  + K LS+P+ VK          A  + N+ K+ +
Sbjct: 142 --NVKEGGIAFGITC--EGAEKVVREVRKVLSVPMAVKLSP------NAENIVNVAKTCE 191

Query: 145 KSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
             G +GI +              R       +      I  +   +V E+ K      IG
Sbjct: 192 YEGADGISLINTFSALKIDIKKRRPVFDNVYAGLSGPAIKPIALKMVREVSKAVKVPVIG 251

Query: 193 LNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + GG+     A++ I+     +  G A++ N      + E   
Sbjct: 252 M-GGITTAEDAIEFIMAGAHLIQFGTASFINPYAGKDIVEGIE 293


>gi|239627206|ref|ZP_04670237.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239517352|gb|EEQ57218.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 300

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 35/191 (18%), Positives = 66/191 (34%), Gaps = 24/191 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G      ++  + + D   + + +N+ CP    +    G     +P  V  
Sbjct: 92  DTRIIVNVCGRTTEDYIDVVERLGDEPVDMLEINISCP----NVKEGGIAFGQDPKAVEA 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
              A+      P+ +K    V D         + K+ +  G + I            IH 
Sbjct: 148 ITKAVKAHAKQPIIMKLSPNVTDITV------MAKAAQAGGTDAISLINTLTGMKIDIHK 201

Query: 156 RK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R  A+           I  +   +VY+  +    + I   GG+ +   AL+ IL     V
Sbjct: 202 RAFALANKTGGLSGPAIKPVALRMVYQTAQAV-QVPIIGMGGIMNGEDALEFILAGASAV 260

Query: 214 MIGRAAYKNSA 224
            IG A + N  
Sbjct: 261 AIGTANFHNPY 271


>gi|56412899|ref|YP_149974.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197361830|ref|YP_002141466.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|56127156|gb|AAV76662.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|197093306|emb|CAR58754.1| putative dihydropyrimidine dehydrogenase [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
          Length = 411

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSRKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|329769958|ref|ZP_08261356.1| dihydroorotate dehydrogenase [Gemella sanguinis M325]
 gi|328837562|gb|EGF87188.1| dihydroorotate dehydrogenase [Gemella sanguinis M325]
          Length = 304

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 36/218 (16%), Positives = 79/218 (36%), Gaps = 30/218 (13%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +    +    +  L    + + P+   + G++I   V  A+ +        + L
Sbjct: 68  MLNAIGLQNPGVHEIMETKLKELEKYDVPIIANVAGSEIDDYVYVAEHISKAPNVCALEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P+   +    + +  S+PV VK    V D      + ++
Sbjct: 128 NISCP----NVKHGGIQFGTDPETAKNLTKKVKEVSSVPVYVKLSPNVTD------IVSM 177

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K++++ G +GI +              +  I           +  +   +VY++ +   
Sbjct: 178 AKAVEEGGADGITMINTLVGVRLDRKTGKPIIANVTGGLSGPAVKPVAIRMVYQVSQAV- 236

Query: 188 DLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSA 224
           ++ I   GG+ D       I      V +G A + +  
Sbjct: 237 NIPIIGMGGVMDEWDVIDFISAGASAVAVGTANFADPY 274


>gi|118581041|ref|YP_902291.1| dihydroorotate dehydrogenase 1B [Pelobacter propionicus DSM 2379]
 gi|189038441|sp|A1ASB3|PYRD_PELPD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|118503751|gb|ABL00234.1| dihydroorotate oxidase B, catalytic subunit [Pelobacter propionicus
           DSM 2379]
          Length = 304

 Score = 69.5 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 74/201 (36%), Gaps = 25/201 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P  +   G+   +  E A  +++      + +N+ CP    +    G     +P   G 
Sbjct: 95  TPAIVNFFGSTPEEYAELAGRLDEIPQVAGLEVNISCP----NVKQGGIVFGTDPACAGQ 150

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            +AA  +A   P+ VK    V D +       + ++   +G +            I + +
Sbjct: 151 VVAACRRATKKPLIVKLSPNVTDVVV------MAQACADAGADALSLINTLTGMAIDLKS 204

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK +L           I  +   +V+++ +    + +   GG+   + AL+ IL     V
Sbjct: 205 RKPVLANITGGLSGPAIKPVALRMVWQVSRAV-QVPLIGIGGITSATDALEFILAGASAV 263

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G A++   +    + +   
Sbjct: 264 QVGTASFITPSASQEIAQGME 284


>gi|294785966|ref|ZP_06751253.1| dihydroorotate oxidase [Fusobacterium sp. 3_1_27]
 gi|294486303|gb|EFG33666.1| dihydroorotate oxidase [Fusobacterium sp. 3_1_27]
          Length = 304

 Score = 69.1 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 80/222 (36%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIMANVAGSDIEDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLIGIVLDRKTGKPIIANITGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDNLESAL 287


>gi|312383321|gb|EFR28456.1| hypothetical protein AND_03577 [Anopheles darlingi]
          Length = 1672

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 58/162 (35%), Gaps = 27/162 (16%)

Query: 66   AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            A+  E  G + + LN+ CP     E   G     +P++V +    + +A+ IP  VK   
Sbjct: 1286 ARRAETAGADMLELNLSCPHGM-GESGMGLACGQDPELVYNISVWVRRAVRIPFFVKLTP 1344

Query: 126  GVDDQIPAVALRNLVKSIKKSGVNGIW-------------------IHARKAILKGLSPK 166
             + D    VA+    +  +  GV+ I                    IH R     G+S  
Sbjct: 1345 NITD---IVAIAQAAQRGQADGVSAINTVQGLMSLRTDGTPWPAVGIHKRTT-YGGVSGN 1400

Query: 167  DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
              R         V  I  + P   I   GG++    AL+ + 
Sbjct: 1401 ATR---PQALRAVSLIGNKLPGFPICGIGGIDSADVALQFIQ 1439


>gi|327399332|ref|YP_004340201.1| dihydroorotate dehydrogenase family protein [Hippea maritima DSM
           10411]
 gi|327181961|gb|AEA34142.1| dihydroorotate dehydrogenase family protein [Hippea maritima DSM
           10411]
          Length = 307

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/221 (19%), Positives = 93/221 (42%), Gaps = 29/221 (13%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGS 92
           R  ++ +   +     +   I G ++++ VE A+ ++ +   + I +NV CP    +  +
Sbjct: 83  RFIEEKLPKMADLNTHIIANIYGTEVAEFVEIAEKLDKEKLVSAIEVNVSCP----NVSA 138

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-- 150
            GA    +PD+V    +++ K    PV VK    V+D      +  + ++ +  G +   
Sbjct: 139 GGALFGKDPDMVFVLTSSIKKVTKKPVIVKLTPNVED------IAFIAQAAQSGGADAVS 192

Query: 151 ---------IWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
                    I    +K +L   +       I  +   +VYE  K+   + I   GG+ + 
Sbjct: 193 LINTITGMVIDTKTKKPVLANKTGGLSGPAIYPVGVRMVYETYKKI-KIPIVGVGGIYNA 251

Query: 201 SQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNP 236
             AL+ I+     + +G A + + +    ++  ++E+ +N 
Sbjct: 252 DVALQYIMAGASLIQVGTANFIDPSITVDIIKGIEEFLANE 292


>gi|288817736|ref|YP_003432083.1| dihydroorotate dehydrogenase [Hydrogenobacter thermophilus TK-6]
 gi|288787135|dbj|BAI68882.1| dihydroorotate dehydrogenase [Hydrogenobacter thermophilus TK-6]
 gi|308751335|gb|ADO44818.1| dihydroorotate dehydrogenase family protein [Hydrogenobacter
           thermophilus TK-6]
          Length = 325

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 46/218 (21%), Positives = 76/218 (34%), Gaps = 30/218 (13%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVED-FGYNEINL 79
           M+ +  +    + G  K I     + +      I G    + VE    +ED        L
Sbjct: 75  MLNSIGLQNPGVEGFLKKIYPHIEKIDTHFIANIFGETEEEYVEVCMALEDARKIVAYEL 134

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           NV CP   V +G        +  ++G  + ++   +  PV VK          A  +   
Sbjct: 135 NVSCP--NVKKGGMLFG--HDAVVLGRLVESVKAKVKKPVLVKLSP------NAGNVVEF 184

Query: 140 VKSIKKSGVNGI----WIHARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKENP 187
            K    +G +G+     +   K  +K   P             I  +   +V+E+  E  
Sbjct: 185 AKVCADAGADGLVLINTLLGMKIDVKAQKPDLSTFTGGLSGPAILPIAVRMVWEVFSELG 244

Query: 188 D-LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNS 223
           D L I   GG+ D   AL+  L     V IG A + + 
Sbjct: 245 DKLPIIGVGGIHDTDSALEHILAGASAVQIGTANFSDP 282


>gi|189425363|ref|YP_001952540.1| dihydroorotate dehydrogenase [Geobacter lovleyi SZ]
 gi|229485559|sp|B3E4T4|PYRD_GEOLS RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|189421622|gb|ACD96020.1| dihydroorotate dehydrogenase family protein [Geobacter lovleyi SZ]
          Length = 304

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 67/202 (33%), Gaps = 25/202 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P      G    +  E A  ++       + +N+ CP    +    G     +P     
Sbjct: 95  TPAIANFFGYTPDEYAELASRLDAIPEVAALEVNISCP----NVKQGGIVFGTDPGCAAS 150

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            +AA   A    + VK    V D      +  + ++ + +G + + +             
Sbjct: 151 VVAACRAATQKTLIVKLSPNVTD------IVEMAQACEGAGADALSVINTLTGMAIDLER 204

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           I  +   +V+++ +    + +   GG+   + AL+ IL     V
Sbjct: 205 RRPVLANVTGGLSGPAIKPVALRMVWQVARAV-KVPVIGIGGIMSATDALEFILAGATAV 263

Query: 214 MIGRAAYKNSAMLTTVDEYFSN 235
            +G A++ N A    + E    
Sbjct: 264 QVGTASFVNPAAAQEIAEGMEQ 285


>gi|329767645|ref|ZP_08259165.1| dihydroorotate dehydrogenase [Gemella haemolysans M341]
 gi|328839072|gb|EGF88658.1| dihydroorotate dehydrogenase [Gemella haemolysans M341]
          Length = 304

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/218 (16%), Positives = 79/218 (36%), Gaps = 30/218 (13%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +    +    +  L    + + P+   + G++I   V  A+ +      + + L
Sbjct: 68  MLNAIGLQNPGVHEILETKLKELEKYDVPIIANVAGSEIDDYVYVAEHISKAPNVHALEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P+   +    + +  S+PV VK    V D      +  +
Sbjct: 128 NISCP----NVKHGGIQFGTDPETAKNLTRKVKEVSSVPVYVKLSPNVTD------IVAM 177

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K++++ G +GI +              +  I           +  +   +VY++ +   
Sbjct: 178 AKAVEEGGADGITMINTLVGVRLDKKTGKPIIANVTGGLSGPAVKPVAIRMVYQVSQAV- 236

Query: 188 DLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSA 224
           ++ I   GG+ D       I      V +G A + +  
Sbjct: 237 NIPIIGMGGIMDEWDVIDFISAGASAVAVGTANFADPY 274


>gi|220905462|ref|YP_002480774.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219869761|gb|ACL50096.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 308

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 70/193 (36%), Gaps = 26/193 (13%)

Query: 46  QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           QE  +   I  +   +    AA++ ++ G   + +NV CP   V EG        +P ++
Sbjct: 95  QETAVIANIYASSAEEFGRLAARLNDEEGVAALEVNVSCP--NVREGGVAFG--QDPGMI 150

Query: 105 GDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI 159
               + +   A    + VK    V D         + ++ + +G + I     +      
Sbjct: 151 AQVTSIVRHAAPGKHIMVKLSPNVTDITV------MARAAEDAGADSISCINTLLGMAVD 204

Query: 160 LKGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           L+   P             I  +    V+++ +      IG+ GG+  +   L+ IL   
Sbjct: 205 LQTRRPSLANVVGGLSGPAIKPVALRCVWQVARAVKIPVIGV-GGISCVEDVLEFILAGA 263

Query: 211 DGVMIGRAAYKNS 223
             V IG A++   
Sbjct: 264 HAVQIGTASFMRP 276


>gi|13399651|pdb|1H7X|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex Of A Mutant Enzyme (C671a), Nadph And 5-
           Fluorouracil
 gi|13399652|pdb|1H7X|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex Of A Mutant Enzyme (C671a), Nadph And 5-
           Fluorouracil
 gi|13399653|pdb|1H7X|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex Of A Mutant Enzyme (C671a), Nadph And 5-
           Fluorouracil
 gi|13399654|pdb|1H7X|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
           Complex Of A Mutant Enzyme (C671a), Nadph And 5-
           Fluorouracil
          Length = 1025

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 67/207 (32%), Gaps = 35/207 (16%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E ++  E  G + + LN+
Sbjct: 611 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELSRKAEASGADALELNL 669

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
             P     E   G     +P++V +    + +A+ IP   K    V D      + ++ +
Sbjct: 670 SAPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTD------IVSIAR 722

Query: 142 SIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVY 180
           + K+ G +G+                         ++    G+S    R I       V 
Sbjct: 723 AAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIA---LRAVT 779

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
            I +  P   I   GG++     L+ L
Sbjct: 780 TIARALPGFPILATGGIDSAESGLQFL 806


>gi|256846776|ref|ZP_05552231.1| dihydroorotate dehydrogenase [Fusobacterium sp. 3_1_36A2]
 gi|256717742|gb|EEU31300.1| dihydroorotate dehydrogenase [Fusobacterium sp. 3_1_36A2]
          Length = 304

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 78/219 (35%), Gaps = 28/219 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIDDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVAKNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGLAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + D       I      V IG A + +  +   + +   
Sbjct: 246 VMDEWDVIDFISAGASAVAIGTANFTDPFVCPKIIDSLE 284


>gi|256545206|ref|ZP_05472571.1| dihydroorotate oxidase [Anaerococcus vaginalis ATCC 51170]
 gi|256399033|gb|EEU12645.1| dihydroorotate oxidase [Anaerococcus vaginalis ATCC 51170]
          Length = 299

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 74/199 (37%), Gaps = 24/199 (12%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I    K+ +    T++      +GG  +   V+ A++++      I LN+ CP    + 
Sbjct: 76  GIEYFIKEELPFLETKDAVTIANLGGHSVEDYVKGAQMLDKTSVPIIELNISCP----NV 131

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN- 149
              G     NP    + I  + KA    + VK    V D      ++  VK  + SG + 
Sbjct: 132 KEGGMAFGTNPKKACEVIEKVRKATKKVLMVKLSPNVGD------IKEFVKIAENSGADC 185

Query: 150 ----------GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
                      I +  +KA+ +   +      I  +   +VYE      +L I   GG+ 
Sbjct: 186 ISLVNTFNALAIDVDNKKAVFENKTAGLSGPCIKPIALRMVYE-ASNATNLPIIGMGGIS 244

Query: 199 DMSQALK-ILPSVDGVMIG 216
           +    L+ I+     V +G
Sbjct: 245 NYRDCLEFIMAGASAVQVG 263


>gi|323344178|ref|ZP_08084404.1| dihydroorotate oxidase [Prevotella oralis ATCC 33269]
 gi|323094907|gb|EFZ37482.1| dihydroorotate oxidase [Prevotella oralis ATCC 33269]
          Length = 303

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 69/191 (36%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A  ++       I LN+ CP   V +G     +  +     
Sbjct: 93  DTHIIVNVSGNSPDDYAECAARIDALSNIPAIELNISCP--NVKDGGMAFGVTCSG--AA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      +  + ++ +  G +            I I 
Sbjct: 149 SVVKAVRQRYHKTLIVKLSPNVTD------ITEIARACEAEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+++L  G        I  +   +V+++ K      IGL GG+     A++ ++     
Sbjct: 203 KRRSLLSIGTGGLSGPAIKPVALRMVWQVAKAVKIPVIGL-GGICTAQDAIEFLMAGATA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFIDP 272


>gi|148244175|ref|YP_001218869.1| dihydroorotase dehydrogenase [Candidatus Vesicomyosocius okutanii
           HA]
 gi|146326002|dbj|BAF61145.1| dihydroorotate dehydrogenase [Candidatus Vesicomyosocius okutanii
           HA]
          Length = 325

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 87/252 (34%), Gaps = 36/252 (14%)

Query: 11  FFARLLTNNALLYTE----MIVADAILRGD-----KKNILGFSTQEKPLALQIGGADISK 61
              R L N     TE    MI A  +          K +      E    + I G+   +
Sbjct: 51  TLKRCLGNIPHRVTETPSGMINAIGLQNPGSDVVINKILPKLDKTETNFIINISGSSFEE 110

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
             E  K  ++   + I +N+ CP   + +G        +P++    +    +  + P+  
Sbjct: 111 YGEITKRFDNTDIHAIEINISCP--NIKKGGVTFG--NDPNMSYRVVEICRRNTTKPIIT 166

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAI----LKGLSPK 166
           K      D   +       +    +G +G+            I  +K I      G+S  
Sbjct: 167 KLSPNQTDIAFS------AQRCIDAGTDGLAVINTLMGMAINITTKKPIIGNNQGGVSGP 220

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAM 225
             + I  L    VY++ K   ++ I   GG+   + A++ I+     + IG A + +  +
Sbjct: 221 AIKPIALLKVYQVYQVSKHY-NIPIIGQGGITTANDAIEFIIAGASAIGIGTALFYDPLV 279

Query: 226 LTTVDEYFSNPL 237
              ++   S  L
Sbjct: 280 CHKINHGISEYL 291


>gi|256027393|ref|ZP_05441227.1| dihydroorotate dehydrogenase 1B [Fusobacterium sp. D11]
 gi|289765357|ref|ZP_06524735.1| dihydroorotate dehydrogenase 1B [Fusobacterium sp. D11]
 gi|289716912|gb|EFD80924.1| dihydroorotate dehydrogenase 1B [Fusobacterium sp. D11]
          Length = 305

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 80/222 (36%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIEDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVETGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDIIDFISAGASAVAVGTANFTDPFVCPKIIDNLESTL 287


>gi|237740835|ref|ZP_04571316.1| dihydroorotate dehydrogenase [Fusobacterium sp. 4_1_13]
 gi|229431132|gb|EEO41344.1| dihydroorotate dehydrogenase [Fusobacterium sp. 4_1_13]
          Length = 304

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 39/219 (17%), Positives = 78/219 (35%), Gaps = 28/219 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIEDYVYVADKISKSPNVRALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVEAGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANITGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + D       I      V +G A + +  +   + +   
Sbjct: 246 VMDEWDVVDFISAGASAVAVGTANFTDPYVCPKIIDNLE 284


>gi|126178746|ref|YP_001046711.1| dihydroorotate dehydrogenase 1B [Methanoculleus marisnigri JR1]
 gi|125861540|gb|ABN56729.1| dihydroorotate oxidase B, catalytic subunit [Methanoculleus
           marisnigri JR1]
          Length = 295

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 69/201 (34%), Gaps = 26/201 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            +P+ + I G    +    A        + + LN+ CP A      +GA +  +P +V +
Sbjct: 92  GEPVIVSIFGGTPEEFRTVAGWFAG-TASGLELNLSCPHAE----GYGAAIGSDPALVEE 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIH 154
           C  A+   L +P  VK    V D      +  +  + ++ G + I               
Sbjct: 147 CTRAVAS-LGVPTWVKLTPNVAD------IAEIGAAAERGGADAIVAVNTVKAMRISTAL 199

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +         + I  +    VY++ +    + I   GG+      ++ ++     V
Sbjct: 200 RRPVLGNRFGGLSGKAIFPVAVRCVYDLYEAC-SIPIVGCGGVSTADNVVEMMMAGASAV 258

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            IG A      +   + +   
Sbjct: 259 EIGSAVIDEIGIFAAIADDLY 279


>gi|89895603|ref|YP_519090.1| hypothetical protein DSY2857 [Desulfitobacterium hafniense Y51]
 gi|89335051|dbj|BAE84646.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 314

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 67/179 (37%), Gaps = 26/179 (14%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  A +     G + + +N+ CP    +    G     +PD   + IA + +   +
Sbjct: 119 DYETMASALQ--SSSGIHALEVNISCP----NVKHGGMHFGTHPDSAEEVIALVKRKTDL 172

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG-LSP 165
           PV  K    V D      +  + K++++ G + I            I  R+ +L   +  
Sbjct: 173 PVIAKLSPNVTD------IVAMAKAVERGGADIISMINTLLGMSIDIEKRQPLLANKMGG 226

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
                I  +   +V+++ +    + I   GG+     A++ +L     V IG   + N 
Sbjct: 227 LSGPAIRPVAVRMVWQVAQAV-KVPIIGMGGILTWQDAVEFMLAGAKAVSIGTGNFVNP 284


>gi|330795628|ref|XP_003285874.1| dihydropyrimidine dehydrogenase [Dictyostelium purpureum]
 gi|325084179|gb|EGC37613.1| dihydropyrimidine dehydrogenase [Dictyostelium purpureum]
          Length = 944

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/172 (19%), Positives = 57/172 (33%), Gaps = 25/172 (14%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           + G +     E AK  E  G + + LN+ CP     E   G     + ++V      +  
Sbjct: 575 MCGFNKEDWTELAKKAEASGADGLELNLSCPHGM-GEKGMGLACGQDTELVFHICQWVRA 633

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP- 172
           A+ IP   K    V        ++++ K+    G +G+      + L GL    N     
Sbjct: 634 AVKIPFFAKLTPNV------TEIKDIAKAAHDGGADGVTAINTVSGLMGLKGDSNAWPAI 687

Query: 173 -----------------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                             +    V  I+K  PD  I   GG +     ++ L
Sbjct: 688 GDEKRTTYGGVSGNATRPMALRAVSSIRKTLPDYPIMATGGCDSADATIQFL 739


>gi|11498351|ref|NP_069579.1| dihydroorotase dehydrogenase (pyrD) [Archaeoglobus fulgidus DSM
           4304]
 gi|3914509|sp|O29513|PYRD_ARCFU RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|2649866|gb|AAB90494.1| dihydroorotase dehydrogenase (pyrD) [Archaeoglobus fulgidus DSM
           4304]
          Length = 299

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/217 (20%), Positives = 80/217 (36%), Gaps = 33/217 (15%)

Query: 35  GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-----NEINLNVGCPSARVH 89
            D    L   T E PL + + G  + +  +   +V+ F       +   LN+ CP  +  
Sbjct: 78  KDFAEELKDYTNEAPLLISLYGHSVEEFSD---LVDTFDSALPYLHGYELNLSCPHVK-- 132

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G  + ++ ++    +  +      PV  K     D          L K ++ +GV+
Sbjct: 133 --GAGLDIGMDLELSAAIVEELKGKTKNPVFAKLSAMHD-------YLKLAKVLEDAGVD 183

Query: 150 GIWIH-----------ARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           GI I            + K +L  LS       I  +    VY++ KE  ++ I   GG+
Sbjct: 184 GITISNTLRGMKIDIMSGKPVLSNLSGGVSGPAIKPIALKCVYDLYKEI-EVPIVGCGGI 242

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
                 L+ I+     V IG A Y +  +  ++ E  
Sbjct: 243 TSFEDVLEFIMAGARAVQIGSAVYYSRRIFYSLKESL 279


>gi|291085135|ref|ZP_06352165.2| dihydroorotate dehydrogenase family protein [Citrobacter youngae
           ATCC 29220]
 gi|291072078|gb|EFE10187.1| dihydroorotate dehydrogenase family protein [Citrobacter youngae
           ATCC 29220]
          Length = 380

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 62  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 119

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 120 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 173

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 174 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 233

Query: 200 MSQALKIL 207
              A + L
Sbjct: 234 WEDAAEFL 241


>gi|149028166|gb|EDL83604.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_a
           [Rattus norvegicus]
          Length = 174

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 31/97 (31%), Gaps = 11/97 (11%)

Query: 186 NPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
            P      NG +     A   +   V G+M+ R A     + T + E     ++ S  + 
Sbjct: 13  RPHCVSSGNGDILSFEDANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSERL- 71

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                     I    T Y   H  S  +  + TR  +
Sbjct: 72  ---------DILRDFTHYGLEHWGSDTQGVERTRRFL 99


>gi|28210641|ref|NP_781585.1| dihydroorotate dehydrogenase 1B [Clostridium tetani E88]
 gi|28203079|gb|AAO35522.1| dihydroorotate dehydrogenase [Clostridium tetani E88]
          Length = 301

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 75/185 (40%), Gaps = 24/185 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   ++A +++     + + LN+ CP+ +    +FG       D   + +  + +
Sbjct: 100 LGGHSMDDYLQAVELLNKEKIDLLELNISCPNVKQGGMNFGV----KTDFAREVVRKIRE 155

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAIL-K 161
                + VK     +D      +  + K  ++ G NGI            I+ RK++   
Sbjct: 156 VCKHKLVVKLSPNAED------IVGIAKVCEEEGANGISLVNTFLGLAIDINKRKSVFNN 209

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           G +      I  +   +V ++ KE     +GL GG+     A++ I+     V +G A++
Sbjct: 210 GYAGLSGPAIKPIALRMVNQVAKELTIPVMGL-GGISTWQDAIEFIMAGATTVQVGTASF 268

Query: 221 KNSAM 225
               +
Sbjct: 269 MKPDI 273


>gi|47211504|emb|CAF94123.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1103

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 58/168 (34%), Gaps = 35/168 (20%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGAC-----LMLNPDIVGDCIAAMCKALSIPVT 120
           AK+ ED G + + LN+ CP      G   AC        +P +V +    +  A+SIP  
Sbjct: 727 AKMAEDSGADALELNLSCPHGMGERGMGLACDVIYVFDQDPVLVRNICRWVRAAVSIPFF 786

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAI 159
            K    V        + ++ K+  + G NG+                         ++  
Sbjct: 787 AKLTPNV------TNIVDIAKAAHEGGANGVTATNTVSGMMGLKADGAPWPSVGKGKRTT 840

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             G+S    R I       V  I +  P   I   GG++     L+ L
Sbjct: 841 YGGVSGNAIRPIA---LRAVSAIARAIPGFPILATGGIDSADTGLQFL 885


>gi|291287331|ref|YP_003504147.1| dihydroorotate dehydrogenase family protein [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290884491|gb|ADD68191.1| dihydroorotate dehydrogenase family protein [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 304

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 83/208 (39%), Gaps = 25/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + +   G  + + VE AKI+++   + + +N+ CP+ +      G     +P +  +
Sbjct: 94  DTKVIVNFWGKTLDEYVEVAKILDEADVDMLEMNISCPNIK----EGGIAFGTDPKMTFE 149

Query: 107 CIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
             + + K L + P+ VK    V D      ++   K+ + +G + I            IH
Sbjct: 150 VTSRVKKVLKNKPLMVKLSPNVTD------IKVFAKACEDAGADAISAINTLLGMAVNIH 203

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK  +  ++       I  +   +V+E  K    + +   GG+ +    ++  L     
Sbjct: 204 TRKPYISNVTGGLSGPAIKPVAVRMVHETFK-TVKIPVMGIGGISNWQDIVEFALVGASA 262

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + +G   + +  +   + +   + LT +
Sbjct: 263 MQVGTVNFVDPQIPLKIIDELESYLTAN 290


>gi|304383021|ref|ZP_07365498.1| dihydroorotate oxidase [Prevotella marshii DSM 16973]
 gi|304335842|gb|EFM02095.1| dihydroorotate oxidase [Prevotella marshii DSM 16973]
          Length = 303

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 70/196 (35%), Gaps = 25/196 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+      E A  +++      I LN+ CP   V +G     +  +
Sbjct: 88  RIKDIDTNMIVNVSGSSPETYAECAARIDELDRIPAIELNISCP--NVSDGGMAFGVTCS 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                  +AA+ K     + VK    V D      +  + +  +  G +           
Sbjct: 146 G--AASVVAAVRKVYHKTLIVKLSPNVTD------IAQIARVCEDEGADCVSLINTLMGM 197

Query: 150 GIWIHARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I I  R+++L  G        I  +   +V+++ +      IG+ GG+     A++  +
Sbjct: 198 AIDIERRRSLLSIGTGGLSGPAIKPVALRMVWQVARAVSIPVIGM-GGISTAHDAVEFFM 256

Query: 208 PSVDGVMIGRAAYKNS 223
                V IG A + + 
Sbjct: 257 AGASAVQIGAANFIDP 272


>gi|195355035|ref|XP_002043999.1| GM13670 [Drosophila sechellia]
 gi|194129244|gb|EDW51287.1| GM13670 [Drosophila sechellia]
          Length = 922

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 41  LGFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  + +     E A   E  G + + LN+ CP     E   G     
Sbjct: 623 LKRDFPEKIVIASIMCSFNEDDWTELAIKAEQSGADALELNLSCPHGM-GERGMGLACGQ 681

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK------- 144
           +P++V      + KA+ +P  +K    + D +   A            + +++       
Sbjct: 682 DPELVEQISRWVRKAVKLPFFIKLTPNITDIVSIAAAAKRGGADGGSAINTVQGLMGLKA 741

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            S         ++    G+S    R    +    + +I    P   I   GG++    AL
Sbjct: 742 DSTAWPAIGKEQRTTYGGVSGNATR---PMALKAISDIANRVPGFLILGIGGIDSGEVAL 798

Query: 205 K 205
           +
Sbjct: 799 Q 799


>gi|282850078|ref|ZP_06259460.1| dihydroorotate dehydrogenase 1B [Veillonella parvula ATCC 17745]
 gi|282580267|gb|EFB85668.1| dihydroorotate dehydrogenase 1B [Veillonella parvula ATCC 17745]
          Length = 316

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/215 (17%), Positives = 77/215 (35%), Gaps = 24/215 (11%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
              +K +      + PL   +    I +    A+ +   G   + +NV CP+        
Sbjct: 93  HFVRKILPDLEKYDVPLLANMSAGTIDEFAWMAETLSVDGIAGLEVNVSCPNVE----CE 148

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---- 149
           G    ++  +V     A+ K    PV VK    V D      +  + K+++  G N    
Sbjct: 149 GMAFGVDSKVVEAVTKAVRKVTDKPVIVKLSPNVTD------IVEIAKAVEAGGGNGVSL 202

Query: 150 -------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
                   I IH RK +L           +  +   +++++ K    + I   GG+   +
Sbjct: 203 INTLLGMAIDIHRRKPVLGNIYGGLSGPAVKPVALRMIHQVYKGVT-IPIIGLGGIMTGT 261

Query: 202 QALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            A++ ++     V +G A   +   ++ +    S 
Sbjct: 262 DAIEFMMAGAQAVQVGTATMVDPTAISRIAREMSE 296


>gi|257066278|ref|YP_003152534.1| dihydroorotate dehydrogenase family protein [Anaerococcus prevotii
           DSM 20548]
 gi|256798158|gb|ACV28813.1| dihydroorotate dehydrogenase family protein [Anaerococcus prevotii
           DSM 20548]
          Length = 299

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 59/182 (32%), Gaps = 24/182 (13%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   V+ A I++      I LN+ CP    +    G      P    + I  +  
Sbjct: 99  LGGHSVEDYVKGADILDKTSVPMIELNISCP----NVKEGGMAFGTEPKKACEVIKKVRN 154

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILK 161
               P+ VK    V        + +  K  +  G + I +              R     
Sbjct: 155 VTKKPLIVKLSPNVGS------IGDFAKIAEDEGADAISLINTINAMAIDIRRKRPVFEN 208

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
             +      +  +   + YE      ++ +   GG+     A++ I+     + +G A +
Sbjct: 209 KTAGLSGPCVKPIAVRMTYE-AASVVNIPVIGMGGIMTYEDAIEFIMAGASAIQVGTANF 267

Query: 221 KN 222
            +
Sbjct: 268 ID 269


>gi|149028169|gb|EDL83607.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_d
           [Rattus norvegicus]
          Length = 159

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 32/94 (34%), Gaps = 11/94 (11%)

Query: 189 LFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           + +  NG +     A   +   V G+M+ R A     + T + E     ++ S  +    
Sbjct: 1   MPLFGNGDILSFEDANCAMQTGVAGIMVARGALLKPWLFTEIKEQRHWDISSSERL---- 56

Query: 248 DKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
                  I    T Y   H  S  +  + TR  +
Sbjct: 57  ------DILRDFTHYGLEHWGSDTQGVERTRRFL 84


>gi|282880245|ref|ZP_06288962.1| dihydroorotate dehydrogenase 1B [Prevotella timonensis CRIS 5C-B1]
 gi|281305905|gb|EFA97948.1| dihydroorotate dehydrogenase 1B [Prevotella timonensis CRIS 5C-B1]
          Length = 303

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 69/199 (34%), Gaps = 25/199 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G         A  +++      I LN+ CP+ +    +FG           
Sbjct: 93  DTHMLVNVSGNTPDDYAACAARIDELDKIPAIELNISCPNVKAGGMAFGVTCAG----AA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +A    + VK    V        + ++  + +  G +            I I 
Sbjct: 149 SVVKAVRQAYHKTLIVKLSPNV------TNIADIAMACEAEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           +  +   +V+++ K      IGL GG+     A+  ++     
Sbjct: 203 RRKPVLSIATGGLSGPAVKPVALRMVWQVAKAVKIPVIGL-GGISSAEDAIAFMMAGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDE 231
           + IG A + +  +   V +
Sbjct: 262 IQIGTANFVDPTITLQVRD 280


>gi|195058500|ref|XP_001995454.1| GH17755 [Drosophila grimshawi]
 gi|193896240|gb|EDV95106.1| GH17755 [Drosophila grimshawi]
          Length = 1033

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 64/187 (34%), Gaps = 26/187 (13%)

Query: 41  LGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           L     EK +   I  +    D ++L       E  G + + LN+ CP     E   G  
Sbjct: 624 LKRDFPEKIIIASIMCSYNEADWTELAT---KAEASGADALELNLSCPHGM-GESGMGLA 679

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL--------VKSIK---- 144
               P +V D    + KA+ +P  +K    + D +       L        + +++    
Sbjct: 680 CGQEPKLVMDISRWVRKAVKVPFFIKLTPNITDIVSIARAAQLGGADGGSAINTVQGLMS 739

Query: 145 ---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
               +         ++    G+S    R    +    V EI K+ P   I   GG++   
Sbjct: 740 LKADATAWPAIGKEQRTTYGGVSGNATR---PMALRAVSEIAKKLPGFAILGIGGIDSGE 796

Query: 202 QALKILP 208
            AL+ L 
Sbjct: 797 VALQFLQ 803


>gi|204929087|ref|ZP_03220230.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
 gi|204321631|gb|EDZ06830.1| dihydroorotate dehydrogenase family protein [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
          Length = 411

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLQMHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|188996111|ref|YP_001930362.1| dihydroorotate dehydrogenase family protein [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|226710791|sp|B2V726|PYRD_SULSY RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|188931178|gb|ACD65808.1| dihydroorotate dehydrogenase family protein [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 311

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 73/192 (38%), Gaps = 25/192 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  +   + G D  + +  A+ ++   G + + LNV CP   V +G        +P+++ 
Sbjct: 93  DTKIFANVFGEDEDEYLAVAERLDKADGVHGLELNVSCP--NVKKGGIAFG--TDPEVLY 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + +  M K    P+ VK    V +      + +   +   +G +            I + 
Sbjct: 149 NLVYKMKKITKKPLLVKLSPNVSN------ILDTADACVSAGADGLVLINTLLGVAIDVE 202

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKI-LPSVD 211
             K IL           +  +   +++++ ++    + I   GG+ +   AL+  L    
Sbjct: 203 REKPILSTITGGLSGPAMLPIAVRMIWQVYQKYGSRIPIIGVGGISNYKDALQHILAGAS 262

Query: 212 GVMIGRAAYKNS 223
            + +G A + + 
Sbjct: 263 AIQVGTANFYDP 274


>gi|331270316|ref|YP_004396808.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           BKT015925]
 gi|329126866|gb|AEB76811.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           BKT015925]
          Length = 298

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/213 (17%), Positives = 77/213 (36%), Gaps = 27/213 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA ++     +    T    +   +GG  I   +   + +     + I LN+ CP    +
Sbjct: 77  DAFIKDKLPEMKKLDTA---IFANLGGGSIEDYLMGIEKLNKTDVDIIELNISCP----N 129

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G    +  ++  D ++ +       + VK     +D      +  + K+   +G +
Sbjct: 130 VKHGGMAFGIKSEVAYDVVSKVKSICKKTLIVKLSPNAED------IVEMAKACCTAGAD 183

Query: 150 GIW-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           GI            I+ RK +     +      I  +   +V+E+ K N D+ +   GG+
Sbjct: 184 GISLVNTFKAMAIDINKRKPVFDNVYAGLSGAAIKPIALRMVHEVCK-NVDVPVIGMGGI 242

Query: 198 EDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTV 229
                A++ I+     V IG A +    +   +
Sbjct: 243 VSARDAIEFIMAGATAVQIGTANFMKPNIALDI 275


>gi|297792133|ref|XP_002863951.1| hypothetical protein ARALYDRAFT_917859 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297309786|gb|EFH40210.1| hypothetical protein ARALYDRAFT_917859 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 758

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 27/124 (21%), Positives = 55/124 (44%), Gaps = 20/124 (16%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE------------- 47
           MV      +R  A       + Y E I+   +++ +++  + + T E             
Sbjct: 12  MVRVGTLSFRMLAAEY-GADITYGEEIIDHKLVKCERRINVAYGTTEFVEKGTDNVVFST 70

Query: 48  -----KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
                  +  Q+G +D  + ++AA+IV +     +++N+GCP A   +G  GA L+  P+
Sbjct: 71  CKEERNRVVFQMGTSDAVRALKAAEIVCN-DVATVDINMGCPKAFSIQGGMGAALLSKPE 129

Query: 103 IVGD 106
           ++ D
Sbjct: 130 LIHD 133


>gi|189426035|ref|YP_001953212.1| dihydrouridine synthase, DuS [Geobacter lovleyi SZ]
 gi|189422294|gb|ACD96692.1| dihydrouridine synthase, DuS [Geobacter lovleyi SZ]
          Length = 219

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/207 (13%), Positives = 66/207 (31%), Gaps = 29/207 (14%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P +  + I    +A+   V+ +    +        + +L+   +  GV+ + +H R  +
Sbjct: 22  QPILANETILLAVQAI---VSARLINILIGYSDPQQIFSLLPLFESGGVDFLVLHPRTVL 78

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
                          D+ I   + +E   L +  NG +  +   L++L      G+M+GR
Sbjct: 79  --------QEYKGLADHGITTRVVQETG-LPVIANGDVRTVEDGLRVLEQTKAAGLMLGR 129

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ--- 274
            A  +  +   +      P       +  + + +   +               GK++   
Sbjct: 130 GAIADPLLFQRLRA--GRPDQPERAARAAMLRHYLAGLLERYQGIFCGEQQILGKVKSVF 187

Query: 275 ------QITRHMIGLFHGFPNSRRCRH 295
                    + +     G   +R  R 
Sbjct: 188 ATMDDPDFAKQI----KGLKKARTIRQ 210


>gi|228471334|ref|ZP_04056135.1| dihydroorotate dehydrogenase [Porphyromonas uenonis 60-3]
 gi|228306835|gb|EEK15948.1| dihydroorotate dehydrogenase [Porphyromonas uenonis 60-3]
          Length = 304

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 79/208 (37%), Gaps = 25/208 (12%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           S  +  + + + G+ I   V  A+ + D      I LN+ CP    +    G    +N +
Sbjct: 91  SHYDTEVLVNVSGSTIDDYVACAERLNDHPKVRAIELNISCP----NVKEGGMSFGVNCE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GI 151
              + ++A+ KA    + VK    V D      +  + ++ +++G +            I
Sbjct: 147 SAHEVVSAVRKAYKGHLMVKLSPNVTD------ITAIARAAEEAGADSLSLINTLLGMAI 200

Query: 152 WIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
            +  RK  L           +  +   +V+++ +      IGL GG+  +   ++ +L  
Sbjct: 201 DVKTRKPKLSTITGGLSGPAVKPIAVRMVWQVSQAVSIPVIGL-GGIASVEDVVEFLLAG 259

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              V +G   +    + + +    SN L
Sbjct: 260 ATAVQVGTYNFVEPDIASKLVHGLSNYL 287


>gi|295693236|ref|YP_003601846.1| dihydroorotate dehydrogenase [Lactobacillus crispatus ST1]
 gi|295031342|emb|CBL50821.1| Dihydroorotate dehydrogenase [Lactobacillus crispatus ST1]
          Length = 307

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 78/190 (41%), Gaps = 25/190 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E P+   +GG   +  VE A+ + + G  N + +NV CP   V +G       ++ D+V 
Sbjct: 96  ELPIVASVGGDSEADYVEVAQKLSNSGLVNALEINVSCP--NVAQGGMSFG--VHADVVE 151

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    +   ++IP+ VK    V D         + K+ +K G +G+ +            
Sbjct: 152 ELTRKIKAVVNIPIYVKLTPNVTDITV------IAKAAEKGGADGLSMINTLLGMRIDVK 205

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             R  +   +       +  +   ++ ++ ++   L I   GG+      ++ +L   + 
Sbjct: 206 KRRPLLGHNMGGLSGEAVKPIAIRMISQV-RQITSLPIIGMGGIASAEDVVEFMLAGANA 264

Query: 213 VMIGRAAYKN 222
           + +G A +K+
Sbjct: 265 IAVGTAHFKD 274


>gi|157125488|ref|XP_001654354.1| dihydropyrimidine dehydrogenase [Aedes aegypti]
 gi|108873619|gb|EAT37844.1| dihydropyrimidine dehydrogenase [Aedes aegypti]
          Length = 1056

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 58/173 (33%), Gaps = 25/173 (14%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   +     E AK  E  G + + LN+ CP     E   G     +P +V +    +  
Sbjct: 661 MCTYNEEDWTELAKRAEAAGADMLELNLSCPHGM-GESGMGLACGQDPKLVYNISLWVRA 719

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------------WIHA 155
           A+ IP  VK    + D    VA+    +  K  GV+ I                      
Sbjct: 720 AVKIPFFVKLTPNITD---IVAIAQAAQRGKADGVSAINTVQGLMSIKADTTPWPAVGVD 776

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           ++    G+S    R         +  I  + P   I   GG++    AL+ + 
Sbjct: 777 KRTTYGGVSGNATRPQA---LRAISLIGNKMPGFPICGIGGIDSADVALQFIQ 826


>gi|157103945|ref|XP_001648193.1| dihydropyrimidine dehydrogenase [Aedes aegypti]
 gi|108869301|gb|EAT33526.1| dihydropyrimidine dehydrogenase [Aedes aegypti]
          Length = 1037

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 58/173 (33%), Gaps = 25/173 (14%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +   +     E AK  E  G + + LN+ CP     E   G     +P +V +    +  
Sbjct: 642 MCTYNEEDWTELAKRAEAAGADMLELNLSCPHGM-GESGMGLACGQDPKLVYNISLWVRA 700

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------------WIHA 155
           A+ IP  VK    + D    VA+    +  K  GV+ I                      
Sbjct: 701 AVKIPFFVKLTPNITD---IVAIAQAAQRGKADGVSAINTVQGLMSIKADTTPWPAVGVD 757

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           ++    G+S    R         +  I  + P   I   GG++    AL+ + 
Sbjct: 758 KRTTYGGVSGNATRPQA---LRAISLIGNKMPGFPICGIGGIDSADVALQFIQ 807


>gi|116494937|ref|YP_806671.1| dihydroorotate dehydrogenase 1B [Lactobacillus casei ATCC 334]
 gi|227535063|ref|ZP_03965112.1| dihydroorotate dehydrogenase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|122263645|sp|Q038Z3|PYRD_LACC3 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116105087|gb|ABJ70229.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus casei
           ATCC 334]
 gi|227187278|gb|EEI67345.1| dihydroorotate dehydrogenase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
          Length = 291

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 73/186 (39%), Gaps = 25/186 (13%)

Query: 49  PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G D+++    AK +        + +N+ CP    +    G     +P++    
Sbjct: 94  PIIASIAGVDVAEYAAVAKKLSAAPNVKALEVNISCP----NVKQGGMAFGTDPEVAAAV 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKG 162
             A+  A S+P+ VK    V D      +  + K+++++G +G+      +  R  I  G
Sbjct: 150 TRAVKAASSVPIFVKLTPNVTD------ITAIAKAVEQAGADGLSLINTFVGMRLDIATG 203

Query: 163 LSPKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
               DN            +   +VY++        IG+ GG+     A ++L      + 
Sbjct: 204 KPLLDNVTGGVSGPALLPMALHMVYQVAHAVRVPLIGM-GGISSGHDAAEMLAAGATALA 262

Query: 215 IGRAAY 220
           +G A Y
Sbjct: 263 VGSANY 268


>gi|256847339|ref|ZP_05552785.1| dihydroorotate dehydrogenase [Lactobacillus coleohominis 101-4-CHN]
 gi|256716003|gb|EEU30978.1| dihydroorotate dehydrogenase [Lactobacillus coleohominis 101-4-CHN]
          Length = 308

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/173 (23%), Positives = 66/173 (38%), Gaps = 25/173 (14%)

Query: 49  PLALQIGGAD-ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +GGA     +  A K+      + + LNV CP   V  G       ++P  V   
Sbjct: 99  PILGSVGGASLTEYVTVATKLAASGLVDALELNVSCP--NVAHGGMSFG--VDPHAVEKI 154

Query: 108 IAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
             A+   A ++PV VK    V D      +  + K+ +  G +G           I I  
Sbjct: 155 TRAVKDVAGTVPVYVKLTPNVTD------IVEIAKAAEAGGADGLSLINTVLGLHIDIET 208

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           RK +L  G+       I  L   +VY++      L I   GG+E  +  ++  
Sbjct: 209 RKPVLGNGMGGYSGTAIKPLAVRMVYQVA-HATKLPIIGQGGIETAADVVEFF 260


>gi|239631463|ref|ZP_04674494.1| dihydroorotate oxidase B [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|239525928|gb|EEQ64929.1| dihydroorotate oxidase B [Lactobacillus paracasei subsp. paracasei
           8700:2]
          Length = 291

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 73/186 (39%), Gaps = 25/186 (13%)

Query: 49  PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G D+++    AK +        + +N+ CP    +    G     +P++    
Sbjct: 94  PIIASIAGVDVAEYAAVAKKLSAAPNVKALEVNISCP----NVKQGGMAFGTDPEVAAAV 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKG 162
             A+  A S+P+ VK    V D      +  + ++++++G +G+      +  R  I  G
Sbjct: 150 TRAVKAASSVPIFVKLTPNVTD------ITAIAEAVEQAGADGLSLINTFVGMRLDIATG 203

Query: 163 LSPKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
               DN            +   +VY++        IG+ GG+     A ++L      + 
Sbjct: 204 KPLLDNVTGGVSGPALLPMALHMVYQVAHAVRVPLIGM-GGISSGHDAAEMLAAGATALA 262

Query: 215 IGRAAY 220
           +G A Y
Sbjct: 263 VGSANY 268


>gi|301066500|ref|YP_003788523.1| dihydroorotate dehydrogenase [Lactobacillus casei str. Zhang]
 gi|300438907|gb|ADK18673.1| Dihydroorotate dehydrogenase [Lactobacillus casei str. Zhang]
          Length = 290

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 74/186 (39%), Gaps = 25/186 (13%)

Query: 49  PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G D+++    AK +        + +N+ CP    +    G     +P++    
Sbjct: 94  PIIASIAGVDVAEYAAVAKKLSAAPNVKALEVNISCP----NVKQGGMAFGTDPEVAAAV 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKG 162
             A+  A S+P+ VK    V D      +  + ++++++G +G+      +  R  I  G
Sbjct: 150 TRAVKAASSVPIFVKLTPNVTD------ITAIAEAVEQAGADGLSLINTFVGMRLDIATG 203

Query: 163 LSPKDN-------RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
               DN         +  +   +VY++        IG+ GG+     A ++L      + 
Sbjct: 204 KPLLDNVTGGVSGPAVLPMALHMVYQVAHAVRVPLIGM-GGISSGHDAAEMLAAGATALA 262

Query: 215 IGRAAY 220
           +G A Y
Sbjct: 263 VGSANY 268


>gi|300112982|ref|YP_003759557.1| dihydroorotate dehydrogenase family protein [Nitrosococcus watsonii
           C-113]
 gi|299538919|gb|ADJ27236.1| dihydroorotate dehydrogenase family protein [Nitrosococcus watsonii
           C-113]
          Length = 331

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/201 (17%), Positives = 69/201 (34%), Gaps = 27/201 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            E      + G+ I + V   +  +D   + I +N+ CP    +    G     +PD+  
Sbjct: 107 SETYYIANVSGSTIEEYVAVTRRFDDSPIDAIEINISCP----NVKEGGVAFGNDPDMSA 162

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
             +    K    P+  K            ++    +   ++G +              I 
Sbjct: 163 RVVEVCRKVTRKPLITKLSP------NQTSIEENARRCIEAGTDAFAVINTLMGMAIDIE 216

Query: 155 ARKA----ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
            R      I  GLS    + I  L    VY++ +E+  + I   GG+     AL+ L   
Sbjct: 217 QRTPLLGNIQGGLSGPAIKPIALLKVRQVYQVCREHG-IPIIGQGGVASGKDALEFLIAG 275

Query: 210 VDGVMIGRAAYKNSAMLTTVD 230
              V +G A + +  +   ++
Sbjct: 276 ATTVGVGTALFYDPLLCAKIN 296


>gi|166032784|ref|ZP_02235613.1| hypothetical protein DORFOR_02499 [Dorea formicigenerans ATCC
           27755]
 gi|166027141|gb|EDR45898.1| hypothetical protein DORFOR_02499 [Dorea formicigenerans ATCC
           27755]
          Length = 300

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 30/196 (15%), Positives = 66/196 (33%), Gaps = 24/196 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    +     + + D   + + +N+ CP    +  +       +   V  
Sbjct: 92  DTKIIVNVCGHAPEEYFRVVERLADEPIDMMEINISCP----NVNAGFLAFGQDAKNVEK 147

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
             A + K    P+ +K    V D      +  + K+ +  G + I +             
Sbjct: 148 LTADIKKIAKQPIIMKLTPNVTD------ITEIAKAAEAGGADAISLINTLTGMKIDINR 201

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY+      ++ I   GG+     A++ IL     V
Sbjct: 202 KTFALANKTGGVSGPIVKPVAVRMVYQ-AAHAVNIPIIGMGGIASAEDAIEFILAGASAV 260

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A + N A+   V
Sbjct: 261 SVGTANFHNPAVTMEV 276


>gi|146230653|gb|ABQ12723.1| BaiH [Clostridium hiranonis DSM 13275]
          Length = 661

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/199 (22%), Positives = 75/199 (37%), Gaps = 24/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCI 108
           +  +AA+ VE+ G   I L   C            P        +G CL      V + I
Sbjct: 149 QFGQAARRVEEAGCGGIGL--HCAHAYMLPGSFLSPLRNKRMDEYGGCLDNRARFVIEMI 206

Query: 109 AAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAI--LKG 162
             + + +S    +  RI  D++         +  L     ++GVN   +        L+ 
Sbjct: 207 EEVRRNVSPDFPIMLRISGDERMIGGNSLEDMLYLAPKFVEAGVNMFEVSGGTQYEGLEH 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + P  N+ I  ++     EIKK   D+ +   G + D+  A +I+    VDGV IGR   
Sbjct: 267 IIPSQNKSIG-VNVHEASEIKK-VVDVPVYAVGKINDIRYAAEIVERGLVDGVSIGRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTG 239
            +  +     E   + +T 
Sbjct: 325 ADPDLCNKAKENLFDEITP 343


>gi|257466502|ref|ZP_05630813.1| dihydroorotate dehydrogenase 1B [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917659|ref|ZP_07913899.1| dihydroorotate dehydrogenase [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313691534|gb|EFS28369.1| dihydroorotate dehydrogenase [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 306

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 79/209 (37%), Gaps = 25/209 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L        L + I G  +   +E AK V++      + LN+ CP    +    G     
Sbjct: 89  LRKEGITTNLIVNINGKTMEDYIEIAKRVDNIDEIAIVELNISCP----NVKDGGMAFGA 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           NP++ G     + K    P+ VK    V D      +  + K ++++G +          
Sbjct: 145 NPEVAGAVTREVRKVTKKPLVVKLSPNVTD------IAKIAKIVEENGADAVSLINTVLG 198

Query: 150 -GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I +  +K +L           +  +   ++Y++  E   + I   GG+ + + AL+ +
Sbjct: 199 MAIDVKTKKPVLGNTFGGMSGGAVKPIALRMIYQVY-EAVKIPIVGMGGILNGTDALEFL 257

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     + IG   + N  +   +++   +
Sbjct: 258 MAGASILSIGTGFFINPMVSLEIEKTLRD 286


>gi|191638447|ref|YP_001987613.1| dihydroorotate dehydrogenase 1B [Lactobacillus casei BL23]
 gi|190712749|emb|CAQ66755.1| Dihydroorotate dehydrogenase (Dihydroorotate oxidase) (DHOdehase)
           (DHODase) (DHOD) [Lactobacillus casei BL23]
 gi|327382479|gb|AEA53955.1| Dihydroorotate dehydrogenase family protein [Lactobacillus casei
           LC2W]
 gi|327385677|gb|AEA57151.1| Dihydroorotate dehydrogenase family protein [Lactobacillus casei
           BD-II]
          Length = 291

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 73/186 (39%), Gaps = 25/186 (13%)

Query: 49  PLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G D+++    AK +        + +N+ CP    +    G     +P++    
Sbjct: 94  PIIASIAGVDVAEYAAVAKKLSAAPNVKALEVNISCP----NVKQGGMAFGTDPEVAAAV 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKG 162
             A+  A S+P+ VK    V D      +  + ++++++G +G+      +  R  I  G
Sbjct: 150 TRAVKAASSVPIFVKLTPNVTD------ITAIAEAVEQAGADGLSLINTFVGMRLDIATG 203

Query: 163 LSPKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
               DN            +   +VY++        IG+ GG+     A ++L      + 
Sbjct: 204 KPLLDNVTGGVSGPALLPMALHMVYQVAHAVRVPLIGM-GGISSGHDAAEMLAAGATALA 262

Query: 215 IGRAAY 220
           +G A Y
Sbjct: 263 VGSANY 268


>gi|281412393|ref|YP_003346472.1| dihydroorotate dehydrogenase family protein [Thermotoga
           naphthophila RKU-10]
 gi|281373496|gb|ADA67058.1| dihydroorotate dehydrogenase family protein [Thermotoga
           naphthophila RKU-10]
          Length = 270

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/195 (20%), Positives = 77/195 (39%), Gaps = 20/195 (10%)

Query: 49  PLALQIGGADISKLVEAA---KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           P+   +GG    + +E A   K V D  +  +  N  CP    +    G  ++ N +   
Sbjct: 81  PMIASLGGDSFEEYLEVAHAFKKVADR-FYAVEFNFSCP----NVKEGGLSIVKNVEEWE 135

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG--- 162
             +A + K L         +     I  + + +  + + K+G +GI +      L     
Sbjct: 136 KLLATLRKELP-----DTFLIAKVGIEGIFVEDAAEFVMKAGWDGITLVNTVRGLHFEKD 190

Query: 163 ---LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
              L       +  +    VYE+KK  P LF+  +GG+  +  A + L    D + +G A
Sbjct: 191 TMILGGLSGPLLKPIALRTVYEVKKRFPKLFVIASGGVYSVKDAEEFLKVGADVIGVGSA 250

Query: 219 AYKNSAMLTTVDEYF 233
            +K+  ++  + +Y 
Sbjct: 251 LFKDPGVVEEIGKYL 265


>gi|269127220|ref|YP_003300590.1| dihydroorotate dehydrogenase family protein [Thermomonospora
           curvata DSM 43183]
 gi|268312178|gb|ACY98552.1| dihydroorotate dehydrogenase family protein [Thermomonospora
           curvata DSM 43183]
          Length = 336

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 78/218 (35%), Gaps = 26/218 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGAC 96
           +++   + +E P+ + + G  + +  E A+ V+       + +N+  P+       FG  
Sbjct: 84  RDMPWLTEREVPVIVSVAGHSVEEYAEVARRVQIAPALAAVEINLAAPNLEDRGRMFG-- 141

Query: 97  LMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI- 153
               P    D + A+       +PV  K    V D      L  +  +   +G +G+ + 
Sbjct: 142 --RLPGPAADVVRAVRSVTRRDVPVLAKLAPDVSD------LVTIALACVDAGADGLSLI 193

Query: 154 ----------HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
                     H  +  L G+S       I  +    VYE+    P   I   GG+     
Sbjct: 194 NTMAGLAIDPHTMRPALAGVSGGLSGPAIRPVALRCVYEVHAALPTTPIIGIGGVSSGLD 253

Query: 203 ALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           AL+ IL     V +G A + +      +     + L+ 
Sbjct: 254 ALEFILAGASAVAVGTALFHDPVAPPRIVRELEDALSA 291


>gi|148643032|ref|YP_001273545.1| tRNA-dihydrouridine synthase [Methanobrevibacter smithii ATCC
           35061]
 gi|261350172|ref|ZP_05975589.1| putative TIM-barrel protein [Methanobrevibacter smithii DSM 2374]
 gi|148552049|gb|ABQ87177.1| tRNA-dihydrouridine synthase [Methanobrevibacter smithii ATCC
           35061]
 gi|288860958|gb|EFC93256.1| putative TIM-barrel protein [Methanobrevibacter smithii DSM 2374]
          Length = 236

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 31/147 (21%), Positives = 57/147 (38%), Gaps = 18/147 (12%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
           + + +N  C    +     G  ++   D+       +    S  V+VK R  VD     +
Sbjct: 96  DIVEINCHCRQDEILAIGCGQNMLKRDDLAEYI-GDVVDNASCEVSVKIRANVDG----I 150

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               + K I+ +G + + I A K             I + DYD++ +I   N ++ +  N
Sbjct: 151 DTLKIAKLIENTGADYLHIDAMKV-----------GIFDADYDLLAKIC-SNTNIKVIGN 198

Query: 195 GGLEDMSQALKIL-PSVDGVMIGRAAY 220
             ++   +  K+L   V G  I RA  
Sbjct: 199 NSIDSEQKIEKMLKTGVFGFSIARAVI 225


>gi|167768313|ref|ZP_02440366.1| hypothetical protein CLOSS21_02869 [Clostridium sp. SS2/1]
 gi|317497756|ref|ZP_07956069.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167709837|gb|EDS20416.1| hypothetical protein CLOSS21_02869 [Clostridium sp. SS2/1]
 gi|291560289|emb|CBL39089.1| dihydroorotate oxidase B, catalytic subunit [butyrate-producing
           bacterium SSC/2]
 gi|316894945|gb|EFV17114.1| dihydroorotate dehydrogenase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 418

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 70/195 (35%), Gaps = 16/195 (8%)

Query: 25  EMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    + +  +    L      K +   I G++  +    AK V + G + I  N  C
Sbjct: 79  EQISDKPLEVNLEYMRRLKQDYPNKVIVASIMGSNDEEWTTLAKAVTEAGVDMIECNFSC 138

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA---------- 133
           P   +   + G+ +  NP++V      +  A  +PV  K    + +              
Sbjct: 139 PQ--MTSHAMGSDVGQNPELVKHYCEVVTAATHLPVIAKMTPNIGNMEIPAIASMEGGAA 196

Query: 134 -VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N VK+I    +  I           +S      +  +    + ++K+  +  ++ 
Sbjct: 197 GIAAINTVKAITNIDIENITAMPVVNGKSSISGYSGAAVKPIALRFITQMKQHPDLVNVP 256

Query: 191 IGLNGGLEDMSQALK 205
           I   GG+E    AL+
Sbjct: 257 ITGVGGIETWRDALE 271


>gi|229827416|ref|ZP_04453485.1| hypothetical protein GCWU000182_02804 [Abiotrophia defectiva ATCC
           49176]
 gi|229788354|gb|EEP24468.1| hypothetical protein GCWU000182_02804 [Abiotrophia defectiva ATCC
           49176]
          Length = 302

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 81/215 (37%), Gaps = 29/215 (13%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGAC 96
           +++      +  +   + G    + VE  K +        + +N+ CP+ +    +FG  
Sbjct: 84  RDLEKLRGIDTVVMANVCGHTTEEYVEVVKRLAGSEVVKLLEINISCPNVKAGGITFGT- 142

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG------ 150
              NPD   +   A+ K    PV +K    V D      +  L ++ +  G +G      
Sbjct: 143 ---NPDAAFEVTKAIKKYAKQPVIMKLTPNVTD------ITELARACEAGGADGLSLINT 193

Query: 151 -----IWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
                I IH RK A+           +  +   +VY++ K    L I   GG+     A+
Sbjct: 194 LTGMKIDIHKRKFALANKTGGLSGPAVKPVAVRMVYQVSKAV-KLPIIGMGGIMTGEDAV 252

Query: 205 K-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + ++     V +G A + N      ++  + EY +
Sbjct: 253 EFLMAGATAVSVGTANFNNPTASIEVVKGIKEYMA 287


>gi|210620592|ref|ZP_03292140.1| hypothetical protein CLOHIR_00083 [Clostridium hiranonis DSM 13275]
 gi|210155306|gb|EEA86312.1| hypothetical protein CLOHIR_00083 [Clostridium hiranonis DSM 13275]
          Length = 661

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/199 (22%), Positives = 75/199 (37%), Gaps = 24/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCI 108
           +  +AA+ VE+ G   I L   C            P        +G CL      V + I
Sbjct: 149 QFGQAARRVEEAGCGGIGL--HCAHAYMLPGSFLSPLRNKRMDEYGGCLDNRARFVIEMI 206

Query: 109 AAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAI--LKG 162
             + + +S    +  RI  D++         +  L     ++GVN   +        L+ 
Sbjct: 207 EEVRRNVSPDFPIMLRISGDERMIGGNSLEDMLYLAPKFVEAGVNMFEVSGGTQYEGLEH 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + P  N+ I  ++     EIKK   D+ +   G + D+  A +I+    VDGV IGR   
Sbjct: 267 IIPSQNKSIG-VNVHEASEIKK-VVDVPVYAVGKINDIRYAAEIVERGLVDGVSIGRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTG 239
            +  +     E   + +T 
Sbjct: 325 ADPDLCNKAKENLFDEITP 343


>gi|260497940|ref|ZP_05816057.1| dihydroorotate oxidase [Fusobacterium sp. 3_1_33]
 gi|260196501|gb|EEW94031.1| dihydroorotate oxidase [Fusobacterium sp. 3_1_33]
          Length = 305

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 80/222 (36%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIDDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVETGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + D       I      V +G A + +  +   + +   + L
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDNLESTL 287


>gi|289423327|ref|ZP_06425135.1| dihydroorotate oxidase [Peptostreptococcus anaerobius 653-L]
 gi|289156258|gb|EFD04915.1| dihydroorotate oxidase [Peptostreptococcus anaerobius 653-L]
          Length = 417

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/197 (20%), Positives = 76/197 (38%), Gaps = 16/197 (8%)

Query: 25  EMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    + +  +  + L      K LA+ I G+   +    AK V + G + I  N  C
Sbjct: 79  EQISDKPLEKNLEYISRLKKDFPTKVLAVSIMGSTEEEWSILAKKVTEAGADLIECNFSC 138

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------P 132
           P   +   + G+ +  NP++V     A+ ++  +PV  K    + +              
Sbjct: 139 PQ--MTSHAMGSDVGQNPELVEKYTRAVVESTHLPVIAKMTPNIGNMEIPAMAAMKGGAK 196

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N +K+I    V  +           +S      +  +    + ++K+  E  D+ 
Sbjct: 197 GIAAINTIKAITNIDVENMTAMPVVNAKSSISGYSGAAVKPIALRFITQMKQHEELKDVP 256

Query: 191 IGLNGGLEDMSQALKIL 207
           I   GG+E  S AL+ L
Sbjct: 257 ITGMGGIETWSDALEFL 273


>gi|260583541|ref|ZP_05851289.1| dihydroorotate oxidase [Granulicatella elegans ATCC 700633]
 gi|260158167|gb|EEW93235.1| dihydroorotate oxidase [Granulicatella elegans ATCC 700633]
          Length = 304

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 79/229 (34%), Gaps = 30/229 (13%)

Query: 26  MIVADAI----LRGDKKNILG-FSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +    +    +  L      + P+   + G++I   V  A+ +      + + L
Sbjct: 68  MLNAIGLQNPGVHEIMETKLKALEKYDVPIIANVAGSEIEDYVYVAEHISKAPNVHALEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P +       +  A S+PV VK    V D      + ++
Sbjct: 128 NISCP----NVKHGGIQFGTDPCVARTLTEKVKAASSVPVYVKLSPNVTD------IVSM 177

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K++++ G +GI +              +  I           I  +   +VY + +   
Sbjct: 178 AKAVEEGGADGITMINTLVGIRLDRKTGKPIIANVTGGLSGPAIKPVAIRMVYLVSQAV- 236

Query: 188 DLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + I   GG+ D       I      V +G A + +  +   + +    
Sbjct: 237 QIPIIGMGGIMDEWDVIDFISAGASAVAVGTANFTDPYVCPKIIDRLEG 285


>gi|255009392|ref|ZP_05281518.1| dihydroorotate dehydrogenase 1B [Bacteroides fragilis 3_1_12]
 gi|313147150|ref|ZP_07809343.1| dihydroorotate dehydrogenase [Bacteroides fragilis 3_1_12]
 gi|313135917|gb|EFR53277.1| dihydroorotate dehydrogenase [Bacteroides fragilis 3_1_12]
          Length = 303

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 81/211 (38%), Gaps = 29/211 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP    +    G    + 
Sbjct: 88  RIKDIQTHMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCP----NVKQGGMAFGVT 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
              V + + A+  A    + VK    V D      +  + ++ + +G +           
Sbjct: 144 TKGVSEVVQAVRSAYKKTLIVKLSPNVTD------IAEMARAAEANGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL  +        +  +   +V+++ K   ++ +   GG+ +   A++ +L
Sbjct: 198 AIDAERRRPILSTVTGGMSGAAVKPIALRMVWQVAKAV-NIPVIGLGGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM----LTTVDEYFS 234
                V IG A + + A+    +  +++Y  
Sbjct: 257 AGASAVQIGTANFIDPAITIKVIDGINDYLE 287


>gi|221130349|ref|XP_002163778.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 1023

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 67/204 (32%), Gaps = 33/204 (16%)

Query: 25  EMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I   + A        ++     +  +A  + G +     E AK+ E  G   + LN+ 
Sbjct: 610 ELISEKSAAYWCKSISELVKDFPNQILIASIMCGYNQEDWTELAKMSEVAGAPALELNLS 669

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G     N ++V +    +  A+ IP   K    V D      +  +  +
Sbjct: 670 CPHGM-GEKGMGLACGQNAELVYNICKWVRAAVKIPFFAKLTPNVTD------IVEIALA 722

Query: 143 IKKSGVNGIW--------IH-------------ARKAILKGLSPKDNRKIPNLDYDIVYE 181
            K  G +G+         +H              ++    G+S    R I       V  
Sbjct: 723 AKNGGADGVTATNTVSGLMHLKSNAVPWPAVGQEKRTTYGGVSGNSIRPIA---LRAVSA 779

Query: 182 IKKENPDLFIGLNGGLEDMSQALK 205
           I    P   I   GG++     L+
Sbjct: 780 IASALPGFPILATGGIDSAEVGLQ 803


>gi|309776346|ref|ZP_07671334.1| dihydroorotate oxidase [Erysipelotrichaceae bacterium 3_1_53]
 gi|308915942|gb|EFP61694.1| dihydroorotate oxidase [Erysipelotrichaceae bacterium 3_1_53]
          Length = 302

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 72/191 (37%), Gaps = 28/191 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLM 98
           +  F T+   +   + GA   + VE  + +          LN+ CP    +    G  L 
Sbjct: 88  LAQFDTE---IIANVAGASEEEYVEVIEKLNSSDVVKAYELNISCP----NVKHGGIGLG 140

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
            +P +         +A + PV VK    V D      +  + K+++++G +G+ +     
Sbjct: 141 TDPALAARVTRMAKEAATKPVYVKLSPNVTD------IVAIAKAVEEAGADGLVLINTMM 194

Query: 154 ------HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 H+ K IL  ++       I  +   +VY++ +    + I   GG+      L+ 
Sbjct: 195 GMRLDYHSAKPILANVTGGLSGPAIKPVAIRMVYQVAQAV-SIPIIGVGGITRAEDVLEF 253

Query: 207 L-PSVDGVMIG 216
           L      V +G
Sbjct: 254 LYAGASAVEVG 264


>gi|313887133|ref|ZP_07820829.1| dihydroorotate oxidase, catalytic subunit [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|312923362|gb|EFR34175.1| dihydroorotate oxidase, catalytic subunit [Porphyromonas
           asaccharolytica PR426713P-I]
          Length = 304

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 71/189 (37%), Gaps = 25/189 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLN 100
             S  +  + + + G+ I   V  A+ + D      I LN+ CP    +    G    +N
Sbjct: 89  EISHYDTEILVNVSGSTIEDYVACAERLNDHPKVRAIELNISCP----NVKEGGMSFGVN 144

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
            +   + I+A+ KA    + VK    V D      +  +  + +++G +           
Sbjct: 145 CESAYEVISAVRKAYKGHLMVKLSPNVTD------ITAIACAAEEAGADSLSLINTLLGM 198

Query: 150 GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I +  RK  L           +  +   +V+++ +      IGL GG+  +   ++ +L
Sbjct: 199 AIDVKTRKPKLSTITGGLSGPAVKPIAVRMVWQVAQAVSIPVIGL-GGIATIEDVIEFLL 257

Query: 208 PSVDGVMIG 216
                V +G
Sbjct: 258 AGATAVQVG 266


>gi|332300485|ref|YP_004442406.1| dihydroorotate dehydrogenase family protein [Porphyromonas
           asaccharolytica DSM 20707]
 gi|332177548|gb|AEE13238.1| dihydroorotate dehydrogenase family protein [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 304

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 71/189 (37%), Gaps = 25/189 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLN 100
             S  +  + + + G+ I   V  A+ + D      I LN+ CP    +    G    +N
Sbjct: 89  EISHYDTEILVNVSGSTIEDYVACAERLNDHPKVRAIELNISCP----NVKEGGMSFGVN 144

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
            +   + I+A+ KA    + VK    V D      +  +  + +++G +           
Sbjct: 145 CESAYEVISAVRKAYKGHLMVKLSPNVTD------ITAIACAAEEAGADSLSLINTLLGM 198

Query: 150 GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I +  RK  L           +  +   +V+++ +      IGL GG+  +   ++ +L
Sbjct: 199 AIDVKTRKPKLSTITGGLSGPAVKPIAVRMVWQVAQAVSIPVIGL-GGIATIEDVIEFLL 257

Query: 208 PSVDGVMIG 216
                V +G
Sbjct: 258 AGATAVQVG 266


>gi|169335517|ref|ZP_02862710.1| hypothetical protein ANASTE_01931 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258255|gb|EDS72221.1| hypothetical protein ANASTE_01931 [Anaerofustis stercorihominis DSM
           17244]
          Length = 300

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/216 (17%), Positives = 84/216 (38%), Gaps = 24/216 (11%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           K++   +     + +  G       +E  +++     + I LN+ CP   V EG    C+
Sbjct: 84  KDLPYMNKLGTRVIVNYGAHSTEDFLEGIELLNKEELDFIELNISCP--NVKEGGMAFCM 141

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-------- 149
             +     D   A+ +    P+ VK          A ++  + K+++ +G +        
Sbjct: 142 --DNKSAYDITKAVKEKSVHPIIVKLSP------NAPSIVEVAKAVESAGADAVSLTNTF 193

Query: 150 ---GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               I I+ +K +     +      I  +   +V+++ KE  ++ I   GG+ +   AL+
Sbjct: 194 LAMAIDINKKKPVFDNVYAGLSGSAIKPIALRMVHQVAKEI-EIPILSYGGVSNYMDALE 252

Query: 206 -ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            I+     V +G A + +  ++  + +     L  +
Sbjct: 253 FIMAGSTLVGVGSAIFADPTVMIDIKKDLEEYLIRN 288


>gi|295400793|ref|ZP_06810769.1| dihydroorotate dehydrogenase family protein [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111355|ref|YP_003989671.1| dihydroorotate dehydrogenase [Geobacillus sp. Y4.1MC1]
 gi|294977056|gb|EFG52658.1| dihydroorotate dehydrogenase family protein [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216456|gb|ADP75060.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y4.1MC1]
          Length = 422

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/178 (21%), Positives = 72/178 (40%), Gaps = 15/178 (8%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L  +   K + + I G++  + +  AK V + G + + LN  CP   +   + GA +  N
Sbjct: 96  LKKNYPNKVIGVSIMGSNEEEWITLAKAVTEAGADILELNFSCPQ--MTSHAMGADVGQN 153

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALR----------NLVKSIKKSGVN 149
           P++V     A+ +   +PV  K    +   + PA+A            N +KSI    ++
Sbjct: 154 PELVRKYCKAVVENTHLPVVAKMTPNITRMEEPAIAAAQGGAHGISAINTIKSITNIDLD 213

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALK 205
            +           +S    + I  +    + E+   KE   + +   GG+E    AL+
Sbjct: 214 ILTGRPVVNGKSSISGYSGKAIKPIALRFIAELAKCKELKSVQLSGIGGIETWQDALE 271


>gi|213646116|ref|ZP_03376169.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
          Length = 335

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++VE+ G + I  N  CP   +   + G+ + 
Sbjct: 17  RRLKQDYPDKVLIASIMGENEQQWQELARLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 74

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  S+P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 75  QSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------MCEVALAAKRGGADGIATINTVK 128

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 129 SITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRFIQQLRMHPELRDFPISGIGGIET 188

Query: 200 MSQALKIL 207
              A + L
Sbjct: 189 WEDAAEFL 196


>gi|242017470|ref|XP_002429211.1| Dihydropyrimidine dehydrogenase, putative [Pediculus humanus
           corporis]
 gi|212514100|gb|EEB16473.1| Dihydropyrimidine dehydrogenase, putative [Pediculus humanus
           corporis]
          Length = 1015

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 36/160 (22%), Positives = 54/160 (33%), Gaps = 25/160 (15%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K  E+ G + + LN+ CP     E   G     +P++V +    +  A+ IP  VK    
Sbjct: 651 KKAEESGADALELNLSCPHGM-GERGMGLACGQDPELVQNISEWVRSAIKIPFFVKLTPN 709

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGI------------------WIHARKAILKGLSPKDN 168
           V D    V +       K +GV+ I                     A +    G S    
Sbjct: 710 VTD---IVEIARAAYEGKANGVSAINTVSGLMGVKVNATPWPSVGVALRTTYGGTSGNAI 766

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           R    +    V  I K  P   I   GG++     L+ L 
Sbjct: 767 R---PMGLKAVSAISKALPGFPILGMGGIDSAEAGLQFLQ 803


>gi|283856189|ref|YP_161855.2| dihydroorotate dehydrogenase [Zymomonas mobilis subsp. mobilis ZM4]
 gi|283775185|gb|AAV88744.2| dihydroorotate dehydrogenase [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 355

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 73/198 (36%), Gaps = 29/198 (14%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML-NPDIVGDCIAAMCKA 114
           G        AA++V + G   +  N+ CP+  V+       L+  +  +V   + A+  A
Sbjct: 168 GKIEEDYALAARMVAETGAPVLEANLSCPNEGVNS------LLCFDAPLVQKIVEAIKAA 221

Query: 115 L-SIPVTVKCRIGVDDQIPAVALRNLVKSIKK--SGVNGI-WIHARKAILKGLS------ 164
           +   P+ +K     D+      L +LV  +    SG + I  + AR    KG +      
Sbjct: 222 VPDRPLLIKTAYFKDN----AKLADLVSRVGHLVSGFSTINTLSARPLDEKGQAALSPSR 277

Query: 165 PKDNRKIPNLDY---DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           P+       + +   ++V  +     +++ D  I   GG+         +    + VM  
Sbjct: 278 PEGGVCGDAIRWAGLEMVQRLAAFREEKSLDYAIVGVGGVNKPEHYKAYIEAGANAVMTA 337

Query: 217 RAAYKNSAMLTTVDEYFS 234
             +  N  +     ++ +
Sbjct: 338 TGSMWNPHLAEETKKFLA 355


>gi|126651249|ref|ZP_01723459.1| dihydropyrimidine dehydrogenase [Bacillus sp. B14905]
 gi|126592087|gb|EAZ86153.1| dihydropyrimidine dehydrogenase [Bacillus sp. B14905]
          Length = 427

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 64/177 (36%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +A   PV VK 
Sbjct: 123 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEAARTPVIVKL 181

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++ K+ G + I +      L G+       +P           
Sbjct: 182 TPNITDITVT------AEAAKRGGADAISMINTINSLAGVDLDTWNTVPHVAGKGAHGGY 235

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +   A + IL    GV +  AA  
Sbjct: 236 CGPAVKPIALNMVAECARNPLVNVPISGIGGISNWQDAAEFILMGATGVQVCTAAMH 292


>gi|317496523|ref|ZP_07954872.1| dihydroorotate dehydrogenase [Gemella moribillum M424]
 gi|316913326|gb|EFV34823.1| dihydroorotate dehydrogenase [Gemella moribillum M424]
          Length = 304

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 81/231 (35%), Gaps = 30/231 (12%)

Query: 26  MIVADAI----LRGDKKNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +    +    +  L    + + P+   + G++I   V  A+ +        + L
Sbjct: 68  MLNAIGLQNPGVHEIMETKLKELEKYDVPIIANVAGSEIDDYVYVAEHISKSPNVYALEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +    G     +P+   +    +    S+PV VK    V D      +  +
Sbjct: 128 NISCP----NVKHGGIQFGTDPETAKNLTQKVKAVSSVPVYVKLSPNVTD------IVAM 177

Query: 140 VKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            K++++ G +GI +              +  I           +  +   +VY++ +   
Sbjct: 178 AKAVEEGGADGITMINTLVGVRLDRKTGKPIIANVTGGLSGPAVKPVAIRMVYQVSQAV- 236

Query: 188 DLFIGLNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           ++ I   GG+ D       I      V +G A + +      + +   + L
Sbjct: 237 NIPIIGMGGIMDEWDVIDFISAGASAVAVGTANFTDPYACPKIIDKLESAL 287


>gi|296328094|ref|ZP_06870627.1| dihydroorotate oxidase [Fusobacterium nucleatum subsp. nucleatum
           ATCC 23726]
 gi|296154765|gb|EFG95549.1| dihydroorotate oxidase [Fusobacterium nucleatum subsp. nucleatum
           ATCC 23726]
          Length = 304

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/219 (17%), Positives = 78/219 (35%), Gaps = 28/219 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIEDYVYVADKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVETGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + D       I      V +G A + +  +   + +   
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDSLE 284


>gi|253700442|ref|YP_003021631.1| dihydroorotate dehydrogenase 1B [Geobacter sp. M21]
 gi|259547519|sp|C6E6N2|PYRD_GEOSM RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|251775292|gb|ACT17873.1| dihydroorotate dehydrogenase family protein [Geobacter sp. M21]
          Length = 305

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 78/206 (37%), Gaps = 29/206 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ + + G  + +  E A  ++   G   I +N+ CP    +    G     +P    +
Sbjct: 96  TPVIVNLYGNTLEEYGEVAARLDGLAGVAGIEVNISCP----NVKQGGIVFGTDPGAAQE 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            +  + K  S P+ VK    V D +       + K+   +G + + +             
Sbjct: 152 VVRLVKKNTSKPMIVKLSPNVTDVVV------MAKACADAGADALSLINTLTGMAIDLER 205

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           I  +   +V+++ K    L +   GG+ +   AL+ +L     V
Sbjct: 206 RRPVLANVTGGLSGPAIKPVALRMVWQVGKAV-KLPLIGIGGIMNGRDALEFMLAGATAV 264

Query: 214 MIGRAAYKNSA----MLTTVDEYFSN 235
            +G A++ + +    +   +++Y ++
Sbjct: 265 QVGTASFLDPSAAQRIAREMEQYLAD 290


>gi|229541173|ref|ZP_04430233.1| dihydroorotate dehydrogenase family protein [Bacillus coagulans
           36D1]
 gi|229325593|gb|EEN91268.1| dihydroorotate dehydrogenase family protein [Bacillus coagulans
           36D1]
          Length = 396

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 72/191 (37%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   + G+     V  + ++ +    + + LN+ CP    +  S G     +P++  
Sbjct: 183 DVPIIANVAGSTFEDYVYVSTRLSKAPNVHALELNISCP----NVKSGGIAFGTDPEMAF 238

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           +    +     +PV VK    V D      +  + K+ +  G +G+ +            
Sbjct: 239 ELTRQVKAVSEVPVYVKLSPNVTD------IVAIAKAAEAGGADGLTMINTLLGMKIDLK 292

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDG 212
            AR  +           +  +   ++YE+ +E  D+ I   GG+     A++ L      
Sbjct: 293 TARPLLANETGGLSGPAVKPVAVRMIYEVSREV-DIPIIGMGGIMTAEDAVEFLYAGASA 351

Query: 213 VMIGRAAYKNS 223
           V +G A + + 
Sbjct: 352 VAVGTANFIDP 362


>gi|317505376|ref|ZP_07963302.1| dihydroorotate oxidase [Prevotella salivae DSM 15606]
 gi|315663504|gb|EFV03245.1| dihydroorotate oxidase [Prevotella salivae DSM 15606]
          Length = 301

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 74/208 (35%), Gaps = 25/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A+I++       I LN+ CP   V EG     +    +   
Sbjct: 93  DTNMIVNVSGNSAETYAECAQIIDTLEAIPAIELNISCP--NVKEGGMAFGVTC--EGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIH 154
             + A+       + VK    V D      + ++ ++ +  G +            I I 
Sbjct: 149 SIVKAVRAVYHKTLIVKLSPNVTD------IASIARACEAEGADAVSLINTLMGMAIDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L   +       +  +   +VY++        IGL GG+     A++ ++     
Sbjct: 203 KRQPLLSIRTGGLSGPAVKPVALRMVYDVAHAVKIPVIGL-GGISSTEDAIEFLMCGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + IG A + +  +   V +  +  L   
Sbjct: 262 IEIGTANFVDPTITKKVKDGLNTWLDAH 289


>gi|295100181|emb|CBK89270.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium
           cylindroides T2-87]
          Length = 302

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 73/208 (35%), Gaps = 28/208 (13%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLM 98
           +  F T+   +   + GA     V+  + + D        LN+ CP    +    G  L 
Sbjct: 88  LAQFDTE---IIANVAGATEEDYVKVIEALNDSEVIKAYELNISCP----NVKHGGIGLG 140

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIH 154
             P++          A   PV VK    V D      +  + K+++++G +G+     + 
Sbjct: 141 TKPELAAHVTKLAKAAAKKPVYVKLSPNVTD------IVEIAKAVEEAGADGLVLINTLM 194

Query: 155 ARKAILKGLSP--------KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
             +  LK   P             I  +   +VY++ +   ++ I   GG+      L+ 
Sbjct: 195 GMRIDLKTGKPLLANITGGLSGPAIKPVAIRMVYQVAQAV-NIPIIGVGGITSAEDVLEF 253

Query: 207 L-PSVDGVMIGRAAYKNSAMLTTVDEYF 233
           L      V +G   + +  +   + E  
Sbjct: 254 LNAGASAVEVGAQNFVDPYVCPKIIEDL 281


>gi|210633950|ref|ZP_03297921.1| hypothetical protein COLSTE_01838 [Collinsella stercoris DSM 13279]
 gi|210158994|gb|EEA89965.1| hypothetical protein COLSTE_01838 [Collinsella stercoris DSM 13279]
          Length = 302

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 71/205 (34%), Gaps = 30/205 (14%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCP 84
           + A A   G    +   + +   +  Q+ G    + V A ++ ++         +NV CP
Sbjct: 75  VSAFAANYGPW--LADLTDKGTQVICQVAGHSTEEYVRALEMFDELCPWAAGFEINVSCP 132

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              +  G         P+   + + A  K    P+ VK           V +  + ++++
Sbjct: 133 --NIAAGGAACG--STPEGAAEVMRACRKVCDRPLFVKM--------APVRIPEIARALE 180

Query: 145 KSGVNGIW-----------IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
             G +G+            +H R++ L K            +   +V+E      D+ + 
Sbjct: 181 AEGADGLTVINSIPGMAIDVHTRRSKLSKPTGGLSGPLCHPIAVRMVWEAANAV-DIPVC 239

Query: 193 LNGGLEDMSQALK-ILPSVDGVMIG 216
             GG+     A + IL     V +G
Sbjct: 240 GVGGVMTGEDAAEFILAGACCVSVG 264


>gi|320536156|ref|ZP_08036206.1| dihydroorotate dehydrogenase 1B [Treponema phagedenis F0421]
 gi|320146992|gb|EFW38558.1| dihydroorotate dehydrogenase 1B [Treponema phagedenis F0421]
          Length = 298

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 80/204 (39%), Gaps = 28/204 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   +GG+ I   V++  ++E+     I LN+ CP   V EG     +    +     ++
Sbjct: 94  IIANVGGSKIEDYVQSVTLLENTSIRIIELNISCP--NVKEGGMAFGI--KCETAYQVVS 149

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKA 158
           A+ KA    + VK          A  +R +  S  ++G +            I I  RK 
Sbjct: 150 AVRKATRKKLMVKLSP------NAENIRAMAASCVEAGADMLSLVNTFNALAIDIKKRKP 203

Query: 159 ILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           +     +      I  +   +V E  KE     IGL GG+ +   A++ I+     V +G
Sbjct: 204 VFNNITAGLSGPCIKPIALRMVREAAKEVDVTVIGL-GGIMNWQDAIEFIMAGAAAVQVG 262

Query: 217 RAAYKNSA----MLTTVDEYFSNP 236
            A + +      ++  ++++  + 
Sbjct: 263 TANFTDPTVMLKIIRGIEQFMHDE 286


>gi|198471457|ref|XP_001355634.2| GA15293 [Drosophila pseudoobscura pseudoobscura]
 gi|198145925|gb|EAL32693.2| GA15293 [Drosophila pseudoobscura pseudoobscura]
          Length = 1027

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 61/188 (32%), Gaps = 28/188 (14%)

Query: 41  LGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           L     EK +   I     +     E +   E  G + + LN+ CP     E   G    
Sbjct: 621 LKRDFPEKIVIASIMCSFNEADW-TELSIKAEASGADALELNLSCPHGM-GERGMGLACG 678

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------- 151
             PD+V      +  A+ +P  +K    + D     A+    K     G + I       
Sbjct: 679 QIPDMVEQISRWVRNAVKLPFFIKLTPNITD---ITAIAKAAKLGGADGCSAINTVQGLM 735

Query: 152 -----------WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
                          ++    G+S    R    +    + EI K+ PD  I   GG++  
Sbjct: 736 GLKADATAWPAVGEEKRTTYGGVSGNATR---PMALRAISEIAKKIPDFPILGIGGIDSG 792

Query: 201 SQALKILP 208
             AL+ L 
Sbjct: 793 EVALQFLQ 800


>gi|149917812|ref|ZP_01906307.1| Dihydroorotate dehydrogenase 1 [Plesiocystis pacifica SIR-1]
 gi|149821332|gb|EDM80734.1| Dihydroorotate dehydrogenase 1 [Plesiocystis pacifica SIR-1]
          Length = 334

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/212 (17%), Positives = 74/212 (34%), Gaps = 31/212 (14%)

Query: 26  MIVADAILRGDKKNILG-----FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN-- 78
           MI +  +     +  L       +  +  + +   G D    V+ AK + + G   I+  
Sbjct: 81  MINSIGLENVGCEAFLTEKLPFLADLDVSVWVNFFGTDFETYVDCAKTLSEGGEGRIDVL 140

Query: 79  -LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            +N+ CP+ +      G      P++      A  +A  +P+ VK    V D      + 
Sbjct: 141 EMNISCPNIK----KGGIEFGTVPEVAHRLTKACVEASEVPIVVKLTPNVSD------IV 190

Query: 138 NLVKSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
            + +++K++G  G+ +              R  I           I  +   +V+++ K 
Sbjct: 191 AMAQAVKEAGAIGVSLINTITAMAIDVRSRRSRIATTYGGLSGPAIKPVALRMVHQVAKA 250

Query: 186 NPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
            P   I   GG+      L+        V +G
Sbjct: 251 LPGFPICGMGGILTGEDVLEYFIAGAHCVQLG 282


>gi|256422463|ref|YP_003123116.1| dihydropyrimidine dehydrogenase [Chitinophaga pinensis DSM 2588]
 gi|256037371|gb|ACU60915.1| dihydroorotate dehydrogenase family protein [Chitinophaga pinensis
           DSM 2588]
          Length = 422

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 51/276 (18%), Positives = 95/276 (34%), Gaps = 39/276 (14%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +     +    +        +   +   +     E  K VED G + + LN G
Sbjct: 75  ELISDRPLDINLKEIAECVRLFPDRAMIVSLMADNNRESWHELIKKVEDTGAHGLELNFG 134

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP---------- 132
           CP     E   GA +  +P+I G  +A + +  SIPV  K    V   +P          
Sbjct: 135 CPHGM-TERGMGAAVGQDPEIAGRVVAWVMEVASIPVITKLTPNVHSVVPTGRASVLAGC 193

Query: 133 -AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDL 189
            A++L N ++S+    ++    +                +  +   ++  I ++     +
Sbjct: 194 HALSLINTIQSVTGVNLDTFVPNPNVGGQSTFGGYCGPAVKPIALKMLTTISQDPVTSRV 253

Query: 190 FIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK-------------NSAM----LTTVDE 231
            I   GG+     A + +L     V +  AA +             N+ M      T+D+
Sbjct: 254 PISGIGGISTWKDAAEFMLLGATTVQVCTAAMRYGFRIIEDLCDGLNNWMDEKGFRTIDD 313

Query: 232 YFSNPLTGSSPIKTRVDK-DFWRKISASMTDYAARH 266
           +       S P  T  ++ D    I A++      H
Sbjct: 314 FIG----RSVPTLTSWEELDINYHIVANINQEKCIH 345


>gi|163783751|ref|ZP_02178737.1| dihydroorotase dehydrogenase [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880997|gb|EDP74515.1| dihydroorotate dehydrogenase [Hydrogenivirga sp. 128-5-R1-1]
          Length = 311

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 74/218 (33%), Gaps = 30/218 (13%)

Query: 26  MIVADAILRGDKKNILG-----FSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINL 79
           M+ +  +     +  L          +    + + G    + VE  K +E         L
Sbjct: 68  MLNSIGLQNPGVEKFLKELYPEIEKIDTHFIVNVFGETEEEYVEVCKALESADKVVAYEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           NV CP   V +G        +P ++G+ +  + K +  P+ VK    V D      +   
Sbjct: 128 NVSCP--NVKKGGIAFG--HDPQVLGNLVENIKKNIKKPLLVKLSPNVTD------VTEF 177

Query: 140 VKSIKKSGVNGIW-----------IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENP 187
            K    SG +G+            IH  +  L   +       I  +   +V++  ++  
Sbjct: 178 AKVCIDSGADGLVLINTLLGMRINIHKERPELSTKTGGLSGPAIFPIAVRMVWQTFEKFG 237

Query: 188 D-LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNS 223
             + I   GG+     AL+        V IG A + + 
Sbjct: 238 HRIPIIGVGGITTHEDALEHVYAGASAVQIGTANFYDP 275


>gi|255524401|ref|ZP_05391358.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296187521|ref|ZP_06855916.1| dihydropyrimidine dehydrogenase [Clostridium carboxidivorans P7]
 gi|255511958|gb|EET88241.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296048043|gb|EFG87482.1| dihydropyrimidine dehydrogenase [Clostridium carboxidivorans P7]
          Length = 412

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 48/215 (22%), Positives = 94/215 (43%), Gaps = 30/215 (13%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E +   ++ +   D K  L  +   K L   I G++  +  + A++V + G + I  N  
Sbjct: 78  EQVSEHSLEQNLADMKK-LKENYPNKVLVASIMGSNEEEWTKLAQLVTEIGADIIECNFS 136

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVALRN--- 138
           CP   +   + G+ +  NP++V    AA+ +   +PV  K    + + ++PA+A      
Sbjct: 137 CPQ--MTSHAMGSDVGQNPELVKKYSAAVRRGTHLPVLAKMTPNIGNMEVPAIASIEGGA 194

Query: 139 ----LVKSIKK-SGVN-----GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--N 186
                + +IK  +GV+     G+ I   K+ + G S K    +  +    + ++ KE   
Sbjct: 195 TGIAAINTIKCITGVDLDKKVGLPIVNGKSSISGYSGK---AVKPIALRFINQLAKEPKL 251

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
            ++ I   GG+E    AL+       +M+G A  +
Sbjct: 252 KNVPISGIGGIETWEDALEF------IMLGAANLQ 280


>gi|257452645|ref|ZP_05617944.1| dihydroorotate dehydrogenase 1B [Fusobacterium sp. 3_1_5R]
 gi|317059184|ref|ZP_07923669.1| dihydroorotate dehydrogenase [Fusobacterium sp. 3_1_5R]
 gi|313684860|gb|EFS21695.1| dihydroorotate dehydrogenase [Fusobacterium sp. 3_1_5R]
          Length = 306

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 78/209 (37%), Gaps = 25/209 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLML 99
           L        L + I G  +   +E AK V+       + LN+ CP    +    G     
Sbjct: 89  LRKEGITTNLIVNINGKTMEDYIEIAKRVDKIDEIAIVELNISCP----NVKDGGMAFGA 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           NP++ G     + K    P+ VK    V D      +  + K ++++G +          
Sbjct: 145 NPEVAGAVTREVRKVTKKPLVVKLSPNVTD------IAKIAKIVEENGADAVSLINTVLG 198

Query: 150 -GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I +  +K +L           +  +   ++Y++  E   + I   GG+ + + AL+ +
Sbjct: 199 MAIDVKTKKPVLGNTFGGMSGGAVKPIALRMIYQVY-EAVKIPIVGMGGILNGTDALEFL 257

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     + IG   + N  +   +++   +
Sbjct: 258 MAGASILSIGTGFFINPMVSLEIEKTLRD 286


>gi|309702460|emb|CBJ01786.1| putative oxidoreductase, 4Fe-4S binding subunit [Escherichia coli
           ETEC H10407]
          Length = 411

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + ++ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAERGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|261403570|ref|YP_003247794.1| TIM-barrel protein [Methanocaldococcus vulcanius M7]
 gi|261370563|gb|ACX73312.1| TIM-barrel protein [Methanocaldococcus vulcanius M7]
          Length = 259

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 25/152 (16%), Positives = 52/152 (34%), Gaps = 16/152 (10%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           V     + + +N  C    +     G  LM +   +   +  +  +L++P+ +K R+   
Sbjct: 110 VIAKHADIVEVNCHCRQREITSLGLGQELMRDVKRLERFLEEI-GSLNVPIFLKIRLNYI 168

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
                +   ++VK       +            G         P  D   +  +     D
Sbjct: 169 PIDKLIKNLDVVK-------DYFTGLHVDCFYPGK--------PYADLSSLKILSDHFKD 213

Query: 189 LFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
             I  N  ++ + +AL++L   D V + RA  
Sbjct: 214 KVIIGNNSVDSLEKALEMLKYADFVSVARAVL 245


>gi|221116321|ref|XP_002159340.1| PREDICTED: similar to tRNA-dihydrouridine synthase 4-like [Hydra
          magnipapillata]
          Length = 87

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
          MV ++ + +R   R   N  L YT MI+AD+ ++  +     F+T   ++PL +Q    +
Sbjct: 16 MVRYSKQPFRHLVRRY-NCDLAYTPMIMADSFIKSIEARDSDFTTNKDDRPLIVQFAANN 74

Query: 59 ISKLVEAAKIV 69
             L  AA+I+
Sbjct: 75 AEDLALAAEII 85


>gi|197118778|ref|YP_002139205.1| dihydroorotate dehydrogenase 1B [Geobacter bemidjiensis Bem]
 gi|226710763|sp|B5EFU4|PYRD_GEOBB RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|197088138|gb|ACH39409.1| dihydroorotate dehydrogenase [Geobacter bemidjiensis Bem]
          Length = 305

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/204 (16%), Positives = 76/204 (37%), Gaps = 29/204 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ + + G  + +  E A  ++   G   I +N+ CP    +    G     +P    +
Sbjct: 96  TPVIVNLYGNTLEEYGEVAARLDGLSGVAGIEVNISCP----NVKQGGIVFGTDPGAAQE 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            +  + K  + P+ VK    V D +       + K+   +G + + +             
Sbjct: 152 VVRLVKKNTTKPMIVKLSPNVTDVVL------MAKACADAGADALSLINTLTGMAIDLER 205

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           I  +   +V+++ K    L +   GG+ +   AL+ +L     V
Sbjct: 206 RRPVLANVTGGLSGPAIKPVALRMVWQVAKAV-KLPLIGIGGIMNGRDALEFMLAGATAV 264

Query: 214 MIGRAAYKNSA----MLTTVDEYF 233
            +G A++ + +    +   +++Y 
Sbjct: 265 QVGTASFLDPSAAQRIAREMEQYL 288


>gi|23465365|ref|NP_695968.1| dihydroorotate dehydrogenase [Bifidobacterium longum NCC2705]
 gi|189439392|ref|YP_001954473.1| dihydroorotate dehydrogenase [Bifidobacterium longum DJO10A]
 gi|239622113|ref|ZP_04665144.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|312132796|ref|YP_004000135.1| pyrd1 [Bifidobacterium longum subsp. longum BBMN68]
 gi|317483153|ref|ZP_07942150.1| dihydroorotate dehydrogenase [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689131|ref|YP_004208865.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691014|ref|YP_004220584.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp. longum
           JCM 1217]
 gi|23326009|gb|AAN24604.1| dihydroorotate dehydrogenase [Bifidobacterium longum NCC2705]
 gi|189427827|gb|ACD97975.1| Dihydroorotate dehydrogenase [Bifidobacterium longum DJO10A]
 gi|239515304|gb|EEQ55171.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|311773760|gb|ADQ03248.1| PyrD1 [Bifidobacterium longum subsp. longum BBMN68]
 gi|316915407|gb|EFV36832.1| dihydroorotate dehydrogenase [Bifidobacterium sp. 12_1_47BFAA]
 gi|320455870|dbj|BAJ66492.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp. longum
           JCM 1217]
 gi|320460467|dbj|BAJ71087.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 323

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/206 (14%), Positives = 68/206 (33%), Gaps = 23/206 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     +++         +   + G          + + D   + + +NV CP    + 
Sbjct: 97  GIDHYLAEDLPKLKAAGAFVISNVAGHCDDDYAAVVEKLADSDADMLEINVSCP----NV 152

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G  +  +P  + + +  +      P+ VK    V D           ++  + G + 
Sbjct: 153 SAGGMSVGTDPVALANLMDRLRPMTDKPMIVKLTPNVTDITVP------ARAAVEHGADA 206

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +              +  I           +  +    VY ++   P++ I   GG++
Sbjct: 207 LSMINTLKGMRINIRTGKPIIANVTGGVSGPAVLPVGLAAVYRVRTALPEIPIIGLGGID 266

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNS 223
              +AL+ L    + V +G AA  + 
Sbjct: 267 SGEKALEYLYAGANAVEVGAAALFDP 292


>gi|322389443|ref|ZP_08062995.1| dihydroorotate dehydrogenase B [Streptococcus parasanguinis ATCC
           903]
 gi|321143821|gb|EFX39247.1| dihydroorotate dehydrogenase B [Streptococcus parasanguinis ATCC
           903]
          Length = 312

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 32/203 (15%), Positives = 73/203 (35%), Gaps = 15/203 (7%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G    +    ++ + +      I LN+ CP   V  G+ G  +  
Sbjct: 91  LAQHYPDLPIIANVAGFSNEEYATVSRKISQAPNVTAIELNISCP--NVDHGNNGLLIGQ 148

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL--------RNLVKSIKKSGVNGI 151
            P++    + A  +A S+PV VK    V D                 ++ ++     +  
Sbjct: 149 VPELAYAAVKAAVEASSVPVYVKLTPSVADITQVAKAAEDAGAAGLTMINTLVGMRFDLK 208

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
               +  I  G        +  +   ++ ++ + +  L I   GG++    A++++    
Sbjct: 209 T--GKPIIANGTGGMSGPAVFPVALKLIRQVAQ-STKLPIIGMGGVDSAEAAIEMMIAGA 265

Query: 211 DGVMIGRAAYKNSAMLTTVDEYF 233
             + +G A + +     T+ E  
Sbjct: 266 SAIGVGTANFTDPYACPTIIEDL 288


>gi|219670025|ref|YP_002460460.1| dihydroorotate dehydrogenase [Desulfitobacterium hafniense DCB-2]
 gi|219540285|gb|ACL22024.1| dihydroorotate dehydrogenase family protein [Desulfitobacterium
           hafniense DCB-2]
          Length = 314

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 67/179 (37%), Gaps = 26/179 (14%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +  A +     G + + +N+ CP    +    G     +PD   + IA +     +
Sbjct: 119 DYETMASALQ--SGSGIHALEVNISCP----NVKHGGMHFGTHPDSAEEVIALVRGKTDL 172

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG-LSP 165
           PV  K    V D      +  + K++++ G + I            I  R+ +L   +  
Sbjct: 173 PVIAKLSPNVTD------IVAMAKAVERGGADIISMINTLLGMSIDIEKRQPLLANKMGG 226

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
                I  +   +V+++ +      IG+ GG+     A++ +L     V IG   + N 
Sbjct: 227 LSGPAIRPVAVRMVWQVAQAVKVPIIGM-GGILTWQDAVEFMLAGAKAVSIGTGNFVNP 284


>gi|322419287|ref|YP_004198510.1| dihydroorotate dehydrogenase family protein [Geobacter sp. M18]
 gi|320125674|gb|ADW13234.1| dihydroorotate dehydrogenase family protein [Geobacter sp. M18]
          Length = 305

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/206 (16%), Positives = 77/206 (37%), Gaps = 29/206 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+   + G  + +  E A  ++   G   I +N+ CP    +    G     +P    +
Sbjct: 96  TPVIANLYGNTLEEYGEVASRLDGLPGVAGIEVNISCP----NVKQGGIVFGTDPGAARE 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            ++ + K  S P+ +K    V D +       + K+   +G + + +             
Sbjct: 152 VVSLVRKNTSKPLILKLSPNVTDVVL------MAKACADAGADALSLINTLTGMAIDLER 205

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           I  +   +V+++ +    L +   GG+ +   AL+ +L     V
Sbjct: 206 RRPVLANVTGGLSGPAIKPVALRMVWQVARAV-KLPLIGIGGIMNGRDALEFMLAGATAV 264

Query: 214 MIGRAAYKNSA----MLTTVDEYFSN 235
            +G A++ + +    +   ++EY + 
Sbjct: 265 QVGTASFLDPSAAQRIAREMEEYLAE 290


>gi|116623492|ref|YP_825648.1| dihydroorotate oxidase B, catalytic subunit [Candidatus Solibacter
           usitatus Ellin6076]
 gi|123124756|sp|Q01YA2|PYRD_SOLUE RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116226654|gb|ABJ85363.1| dihydroorotate oxidase B, catalytic subunit [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 304

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 41/217 (18%), Positives = 74/217 (34%), Gaps = 30/217 (13%)

Query: 26  MIVADAI----LRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           MI +  +    +R      L   +     +   + G      VE  +++ D  G     L
Sbjct: 68  MINSVGLQNIGVRAFVAEKLPALAGLRTAVFANVFGYCTEDYVEVVRVLNDHAGLAGYEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           NV CP    +    G     +P ++ + + A  +  + P+ VK    V       A+  L
Sbjct: 128 NVSCP----NTAHGGIYFSNDPVLLAEVVTAAKRVATRPLIVKLSPNVS------AIEPL 177

Query: 140 VKSIKKSGVNGIWIH------------ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
            +  ++SG + + +              R  I  G        I  +    VY+  +   
Sbjct: 178 ARVAEESGADALSLVNTVISLAIDARTRRPRIGAGFGGLSGPAIKPIALRFVYQAARAVR 237

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS 223
              IGL GG+     A + L      V +G A + + 
Sbjct: 238 IPVIGL-GGIATGEDAAEFLIAGASAVEVGTATFWDP 273


>gi|317152924|ref|YP_004120972.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316943175|gb|ADU62226.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 305

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 63/191 (32%), Gaps = 24/191 (12%)

Query: 47  EKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E  +   +   D ++  E A  +  + G   + +NV CP    +    G     +P  + 
Sbjct: 92  EVAIIANLYACDAAEFGELAGMLAAEEGIAALEVNVSCP----NVREGGIAFGQDPAQIA 147

Query: 106 DCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAIL 160
               A+ K A + PV VK    V D           ++ +  G + +     +      +
Sbjct: 148 RVTEAVKKRAGNKPVMVKLSPNVTDITV------CARAAEDGGADCLSLINTLSGMAVDI 201

Query: 161 KGLSPKDNRKIPNLDYDIVYEIK-------KENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           +   P+    I  L    +  +             + +   GG+     AL+ IL     
Sbjct: 202 RKRQPRIANVIAGLSGPAIKPVALRCVHQAVRAVSIPVVGIGGIASAEDALEFILVGAHA 261

Query: 213 VMIGRAAYKNS 223
           V +G A +   
Sbjct: 262 VQVGTANFLRP 272


>gi|46191197|ref|ZP_00206704.1| COG0167: Dihydroorotate dehydrogenase [Bifidobacterium longum
           DJO10A]
 gi|227547174|ref|ZP_03977223.1| dihydroorotate oxidase [Bifidobacterium longum subsp. infantis ATCC
           55813]
 gi|227212294|gb|EEI80190.1| dihydroorotate oxidase [Bifidobacterium longum subsp. infantis ATCC
           55813]
          Length = 328

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 29/206 (14%), Positives = 68/206 (33%), Gaps = 23/206 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     +++         +   + G          + + D   + + +NV CP    + 
Sbjct: 102 GIDHYLAEDLPKLKAAGAFVISNVAGHCDDDYAAVVEKLADSDADMLEINVSCP----NV 157

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G  +  +P  + + +  +      P+ VK    V D           ++  + G + 
Sbjct: 158 SAGGMSVGTDPVALANLMDRLRPMTDKPMIVKLTPNVTDITVP------ARAAVEHGADA 211

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +              +  I           +  +    VY ++   P++ I   GG++
Sbjct: 212 LSMINTLKGMRINIRTGKPIIANVTGGVSGPAVLPVGLAAVYRVRTALPEIPIIGLGGID 271

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNS 223
              +AL+ L    + V +G AA  + 
Sbjct: 272 SGEKALEYLYAGANAVEVGAAALFDP 297


>gi|291516929|emb|CBK70545.1| dihydroorotate oxidase B, catalytic subunit [Bifidobacterium longum
           subsp. longum F8]
          Length = 328

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 29/206 (14%), Positives = 68/206 (33%), Gaps = 23/206 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     +++         +   + G          + + D   + + +NV CP    + 
Sbjct: 102 GIDHYLAEDLPKLKAAGAFVISNVAGHCDDDYAAVVEKLADSDADMLEINVSCP----NV 157

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G  +  +P  + + +  +      P+ VK    V D           ++  + G + 
Sbjct: 158 SAGGMSVGTDPVALANLMDRLRPMTDKPMIVKLTPNVTDITVP------ARAAVEHGADA 211

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +              +  I           +  +    VY ++   P++ I   GG++
Sbjct: 212 LSMINTLKGMRINIRTGKPIIANVTGGVSGPAVLPVGLAAVYRVRTALPEIPIIGLGGID 271

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNS 223
              +AL+ L    + V +G AA  + 
Sbjct: 272 SGEKALEYLYAGANAVEVGAAALFDP 297


>gi|308511285|ref|XP_003117825.1| CRE-DPYD-1 protein [Caenorhabditis remanei]
 gi|308238471|gb|EFO82423.1| CRE-DPYD-1 protein [Caenorhabditis remanei]
          Length = 1074

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 65/204 (31%), Gaps = 35/204 (17%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I   +          L      K +   I          VE A   E+ G + + LN+
Sbjct: 640 ELISEKSTEYWLQCIRELKRDHPTKIVVASIMCTYNKADW-VELATQSEEAGADILELNL 698

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P+IV +    +   + IP   K    + D      +R + +
Sbjct: 699 SCPHGM-GEKGMGLACGQSPEIVKEICRWVRACVKIPFFPKMTPNITD------VREIAR 751

Query: 142 SIKKSGVNGIW--------IH-------------ARKAILKGLSPKDNRKIPNLDYDIVY 180
           + +  G +G+         +H             A++    G+S    R I       V 
Sbjct: 752 AARDGGASGVTATNTVSSLMHMKADGNAWPAIGGAKRTTYGGMSGSAIRPIAM---KAVS 808

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL 204
            I  E     I   GG+E     L
Sbjct: 809 SIANELDGFPIMATGGIESAETGL 832


>gi|227824460|ref|ZP_03989292.1| dihydroorotate dehydrogenase [Acidaminococcus sp. D21]
 gi|226904959|gb|EEH90877.1| dihydroorotate dehydrogenase [Acidaminococcus sp. D21]
          Length = 308

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 78/198 (39%), Gaps = 24/198 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + I G   ++  E A +++  G + + LN+ CP   V +G  G     +      
Sbjct: 97  DTKVIVNIDGDSAAEYGELAAMLDVDGVDALELNISCP--NVAQG--GLAFGTSCSAAAQ 152

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
            + A  K    P+  K    V D      +  + ++++ +G + I            I  
Sbjct: 153 VVEAAKKRTHKPIITKLSPNVTD------ITEIARAVEAAGTDMISLINTLVGMKIDIQT 206

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           +K +L   +       +  +   +VY++ +      IG+ GG+   + A++  L     +
Sbjct: 207 QKPVLGNIMGGLSGPAVRPVAVRMVYQVAQAVKVPLIGM-GGITCAADAIEFFLAGASAI 265

Query: 214 MIGRAAYKNSAMLTTVDE 231
            +G A + N  +  T+ +
Sbjct: 266 AVGTANFDNPRLAETISQ 283


>gi|195446906|ref|XP_002070975.1| GK25544 [Drosophila willistoni]
 gi|194167060|gb|EDW81961.1| GK25544 [Drosophila willistoni]
          Length = 1033

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 63/187 (33%), Gaps = 26/187 (13%)

Query: 41  LGFSTQEKPLALQIGGA----DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           L     EK +   I  +    D  +L   A++ E  G + + LN+ CP     E   G  
Sbjct: 621 LKKDFPEKIIIASIMCSYNEADWKEL---AQLAEKSGADALELNLSCPHGM-GERGMGLA 676

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIK---- 144
              +P +V      + + +++P  +K    + +                  + +++    
Sbjct: 677 CGQDPKLVEQISRWVREVITVPFFIKLTPNITNIWTIAEAAQRGGASGGSAINTVQGLMS 736

Query: 145 ---KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
               +         ++    G+S    R    +    + +I K  P   I   GG++   
Sbjct: 737 LKADATAWPAIGQEKRTTYGGVSGNATR---PMALHAISDIAKRLPGFPILGIGGIDSGE 793

Query: 202 QALKILP 208
            AL+ + 
Sbjct: 794 VALQFIQ 800


>gi|195130537|ref|XP_002009708.1| GI15089 [Drosophila mojavensis]
 gi|193908158|gb|EDW07025.1| GI15089 [Drosophila mojavensis]
          Length = 1035

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/191 (20%), Positives = 66/191 (34%), Gaps = 33/191 (17%)

Query: 41  LGFSTQEKPLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     EK +   I  G + +   E A   E  G + + LN+ CP     E   G     
Sbjct: 624 LKRDFPEKIIIASIMCGYNEADWTELATRAEQSGADALELNLSCPHGM-GESGMGLACGQ 682

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG--------- 150
            P +V D    + KA+ IP  +K    + D      + ++ K+  + G NG         
Sbjct: 683 EPRLVEDISRWVRKAVKIPFFIKLTPNITD------IVSIAKAAHRGGANGGSAINTVQG 736

Query: 151 ------------IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGL 197
                            ++    G+S    R    +    + EI +  P D  I   GG+
Sbjct: 737 LMSLKADGTAWPAIGKEQRTTYGGVSGNATR---PMALRAISEIARALPKDFVILGIGGI 793

Query: 198 EDMSQALKILP 208
           +    AL+ + 
Sbjct: 794 DSGEVALQFIQ 804


>gi|118602066|ref|YP_903281.1| dihydroorotate oxidase B, catalytic subunit [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567005|gb|ABL01810.1| dihydroorotate oxidase B, catalytic subunit [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 312

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/201 (19%), Positives = 74/201 (36%), Gaps = 27/201 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E    + I G+ I +  E  K  ++   + I +N+ CP   V EG        +PDI   
Sbjct: 96  ETHFIINISGSSIEEYGEITKRFDNTNIDAIEINISCP--NVREGGVTFG--NDPDISYR 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HA 155
            +    K  S P+  K      D           +    +G + + +             
Sbjct: 152 VVDICRKNTSKPIITKLSPNQTDIALN------AQRCIDAGTDALAVINTLMGMSIDTKT 205

Query: 156 RKAI----LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           +K I      GLS    + I  L    VY++ K   ++ I   GG+   + A++ I+   
Sbjct: 206 KKPIIGNNQGGLSGPAIKPIALLKVHQVYQVSKHY-NVPIIGQGGITTANDAIEFIIAGA 264

Query: 211 DGVMIGRAAYKNSAMLTTVDE 231
             + IG A + +  +   +++
Sbjct: 265 ATIGIGTALFYDPLVCHKIND 285


>gi|115680274|ref|XP_001190439.1| PREDICTED: similar to tRNA-dihydrouridine synthase
           [Strongylocentrotus purpuratus]
 gi|115717831|ref|XP_001201154.1| PREDICTED: similar to tRNA-dihydrouridine synthase
           [Strongylocentrotus purpuratus]
          Length = 499

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 30/127 (23%), Positives = 47/127 (37%), Gaps = 25/127 (19%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE-----MIVADAILRGDKKNILG------------- 42
           MV       R  A     + +   E     M+      R     +LG             
Sbjct: 47  MVRIGTLPTRLLALEYGADIVYCQELIDFKMLT----CRRHVNRVLGTVDYISKDDVVIF 102

Query: 43  --FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
              S +   L  Q+G AD  + +  AK+VE    + I++N+GCP     +G  GA L+  
Sbjct: 103 RTCSKETDRLVFQMGTADAQRALRVAKMVEK-DVSGIDINMGCPKDFSLKGGMGAALLQK 161

Query: 101 PDIVGDC 107
           PD + + 
Sbjct: 162 PDTIKEI 168



 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 6/33 (18%), Positives = 13/33 (39%), Gaps = 2/33 (6%)

Query: 197 LEDMSQALK--ILPSVDGVMIGRAAYKNSAMLT 227
           ++  +   +   +     VMI R A  N ++  
Sbjct: 177 IKSYADIERFREMTGASSVMIAREAQWNPSIFR 209


>gi|258539663|ref|YP_003174162.1| dihydroorotate dehydrogenase 1B [Lactobacillus rhamnosus Lc 705]
 gi|257151339|emb|CAR90311.1| Dihydroorotate dehydrogenase [Lactobacillus rhamnosus Lc 705]
          Length = 290

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/194 (20%), Positives = 73/194 (37%), Gaps = 25/194 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   I GAD+++    AK +        + +N+ CP   V +G        
Sbjct: 86  LASHYPDLPIIASIAGADVAEYTAVAKKLSAAPNVKALEVNISCP--NVDQGGMAFG--T 141

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IH 154
           +P +      A+ +A S+P+ VK    V D      +  + K+++ +G +GI      + 
Sbjct: 142 DPSVAAAVTKAVKEASSVPIFVKLTPNVTD------ITTIAKAVEAAGADGISLINTFVG 195

Query: 155 ARKAILKG-------LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            R  I  G               +  +   +VY++      + I   GG+       ++L
Sbjct: 196 MRLDIQTGEPILTNVTGGVSGPALFPMALHMVYQVA-HTVHIPIIGMGGVSSGHDVAEML 254

Query: 208 -PSVDGVMIGRAAY 220
                 V IG A Y
Sbjct: 255 AAGAKAVAIGSANY 268


>gi|303325894|ref|ZP_07356337.1| dihydroorotate oxidase [Desulfovibrio sp. 3_1_syn3]
 gi|302863810|gb|EFL86741.1| dihydroorotate oxidase [Desulfovibrio sp. 3_1_syn3]
          Length = 308

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/218 (19%), Positives = 81/218 (37%), Gaps = 31/218 (14%)

Query: 26  MIVADAI----LRGDKKNILGFST-QEKPLALQIGGADISKLVE-AAKIVEDFGYNEINL 79
           M+ A  +    +    ++ L     +E P+   +     ++  E AA++  + G   + +
Sbjct: 70  MLNAVGLQNDGVEVFCRDKLPHLPWRETPIIANMYATSPTEFGELAARLDGEEGVAALEV 129

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRN 138
           NV CP   V EG        +P +     AA+ K A    V VK    V D      +  
Sbjct: 130 NVSCP--NVKEGGVLFG--QDPKLAAAVTAAVRKGAPHKHVMVKLSPNVTD------IAL 179

Query: 139 LVKSIKKSGVN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKEN 186
           + +S++ +G +            + +  R+  L   +       I  +    V++  +  
Sbjct: 180 MARSVEDAGADSVSCINTLLGMAVDLRTRRPSLANVVGGLSGPAIKPVALRCVWQAAQAV 239

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
               +G+ GG+     AL+ IL     V +G A +   
Sbjct: 240 KIPVVGM-GGIVSAEDALEFILVGAAAVQVGTANFMRP 276


>gi|42526494|ref|NP_971592.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding [Treponema
           denticola ATCC 35405]
 gi|41816687|gb|AAS11473.1| dihydroorotate dehydrogenase/oxidoreductase, FAD-binding [Treponema
           denticola ATCC 35405]
          Length = 591

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/208 (20%), Positives = 77/208 (37%), Gaps = 38/208 (18%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR   K        +  L + +  ++    +   K  E+   +   LN  CP A      
Sbjct: 100 LRSSWKT-------DSILNVSLSASNPEDFISLLKGFEEL-ADCFELNFSCPHA---SAG 148

Query: 93  FGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           FGA +  +P I  + +  + KAL    +P+ VK    V+D      +  +  ++ ++G +
Sbjct: 149 FGASIGCDPAIAAEYVKIIKKALPDCAVPIFVKLTPNVED------IGAIASAVIEAGAD 202

Query: 150 GIW------------IHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENP-DLFIG 192
           GI              H+ K IL+    G        +     + + +I+K    ++ I 
Sbjct: 203 GITAINTVGPKVYIEPHSGKPILQNKLGGKGGMSGAWVFPRALECIGQIRKAVGEEIPII 262

Query: 193 LNGGLED-MSQALKILPSVDGVMIGRAA 219
             GG+      A  +    D + IG A 
Sbjct: 263 GMGGVMTGAQAAELVRAGADIIGIGSAC 290


>gi|19703766|ref|NP_603328.1| dihydroorotate dehydrogenase 1B [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|30173330|sp|Q8RG85|PYRD_FUSNN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|19713904|gb|AAL94627.1| Dihydroorotate dehydrogenase [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 304

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 39/219 (17%), Positives = 78/219 (35%), Gaps = 28/219 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           D I+    K +  +     P+   + G+DI   V  A KI +      + LN+ CP    
Sbjct: 80  DEIISNQLKKLEKYD---VPIIANVAGSDIEDYVYVANKISKSPNVKALELNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P++  +    +    S+PV VK    V D      +  + K+++  G 
Sbjct: 133 NVKHGGIQFGTDPNVARNLTEKVKAVSSVPVYVKLSPNVTD------IVAMAKAVETGGA 186

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  I           I  +   +VY++ +   ++ I   GG
Sbjct: 187 DGLTMINTLVGIVLDRKTGKPIIANTTGGLSGPAIRPVAIRMVYQVAQAV-NIPIIGMGG 245

Query: 197 LED-MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + D       I      V +G A + +  +   + +   
Sbjct: 246 VMDEWDVIDFISAGASAVAVGTANFTDPFVCPKIIDSLE 284


>gi|163783896|ref|ZP_02178871.1| dihydroorotase dehydrogenase [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880840|gb|EDP74369.1| dihydroorotate dehydrogenase [Hydrogenivirga sp. 128-5-R1-1]
          Length = 318

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 83/219 (37%), Gaps = 30/219 (13%)

Query: 26  MIVADAI----LRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINL 79
           M+ +  +    +    KNIL      +  +   + G D  + ++  + ++   G + + L
Sbjct: 76  MLNSIGLQNPGVEYFSKNILPKLRKYDTIIIANVFGEDEEEYLKVGEFLDKTEGVHALEL 135

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRN 138
           NV CP   V +G        +PD + + +  + +  S P+ VK    V D    A A   
Sbjct: 136 NVSCP--NVKKGGIAFG--SDPDTLYNLVYKLKQITSKPLLVKLSPNVTDITQTAQACVE 191

Query: 139 -------LVKSIKKSGVNG----IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                  L+ ++    ++       +  +   L G +      I  +   ++Y++ ++  
Sbjct: 192 AKTDGLVLINTLLGMAIDVNKEQPILATKTGGLSGPA------ILPVAVRMIYQVFEKYG 245

Query: 188 D-LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA 224
             + I   GG+     AL+  L     V IG A + +  
Sbjct: 246 SAVPIIGVGGITTAEDALQHFLAGAVAVQIGTANFYDPY 284


>gi|225574383|ref|ZP_03782993.1| hypothetical protein RUMHYD_02452 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038385|gb|EEG48631.1| hypothetical protein RUMHYD_02452 [Blautia hydrogenotrophica DSM
           10507]
          Length = 301

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 28/205 (13%), Positives = 71/205 (34%), Gaps = 28/205 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G    + +   + + +   + + +N+ CP    +  +        P  V  
Sbjct: 93  DTKIVVNVCGHAPEEYLRVVERLAEEKIDLMEINISCP----NVNANFLAFGQEPACVEQ 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
             A + K    P+ +K    V D      +  + ++ +  G + + +             
Sbjct: 149 LTAQIKKIARQPIIMKLTPNVTD------ITEVARAAEAGGADAVSLINTLTGMKIDVQR 202

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              A+           +  +   +VY++ +   ++ I   GG+     AL+ IL     V
Sbjct: 203 RTFALANKTGGMSGPAVKPVAVRMVYQVAQAV-EIPIIGMGGIVTAEDALEFILAGASAV 261

Query: 214 MIGRAAYKNS----AMLTTVDEYFS 234
            +G A +        ++  ++EY  
Sbjct: 262 SVGTANFFRPEATLEVVRGIEEYME 286


>gi|241761402|ref|ZP_04759490.1| dihydroorotate dehydrogenase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
 gi|241374309|gb|EER63806.1| dihydroorotate dehydrogenase [Zymomonas mobilis subsp. mobilis ATCC
           10988]
          Length = 355

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 73/198 (36%), Gaps = 29/198 (14%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML-NPDIVGDCIAAMCKA 114
           G        AA++V + G   +  N+ CP+  V+       L+  +  +V   + A+  A
Sbjct: 168 GKIEEDYALAARMVAETGAPVLEANLSCPNEGVNS------LLCFDASLVQKIVEAIKAA 221

Query: 115 L-SIPVTVKCRIGVDDQIPAVALRNLVKSIKK--SGVNGI-WIHARKAILKGLS------ 164
           +   P+ +K     D+      L +LV  +    SG + I  + AR    KG +      
Sbjct: 222 VPDRPLLIKTAYFKDN----AKLADLVSRVGHLVSGFSTINTLSARPLDEKGQAALSPSR 277

Query: 165 PKDNRKIPNLDY---DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           P+       + +   ++V  +     +++ D  I   GG+         +    + VM  
Sbjct: 278 PEGGVCGDAIRWAGLEMVQRLAAFREEKSLDYAIVGVGGVNKPEHYKAYIEAGANAVMTA 337

Query: 217 RAAYKNSAMLTTVDEYFS 234
             +  N  +     ++ +
Sbjct: 338 TGSMWNPHLAEETKKFLA 355


>gi|94266829|ref|ZP_01290491.1| Dihydroorotate dehydrogenase 1 [delta proteobacterium MLMS-1]
 gi|93452504|gb|EAT03098.1| Dihydroorotate dehydrogenase 1 [delta proteobacterium MLMS-1]
          Length = 327

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 77/208 (37%), Gaps = 27/208 (12%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  + +  E A+ ++   G   I +N+ CP    +    G     +P +     
Sbjct: 120 VVVNILGNSVEEYRELAQRLDGVAGIGAIEVNISCP----NVKEGGVAFGTDPRMAARVT 175

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLS 164
            A+ +A  +P+ +K    V D      +  + ++  + G + +     +      L+   
Sbjct: 176 QAVREASGLPLIIKLSPNVSD------IATMARAAAEHGADAVSLINTLLGMAIDLESRR 229

Query: 165 PKDNRKIPNLDYDIVYEI-------KKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           PK    +  L    +  +          +  + +   GG+ + + AL+ I+     + +G
Sbjct: 230 PKLANVVGGLSGPAIKPVALRMVWQAAGSVKIPVIGIGGIMNATDALEFIVAGASAIQVG 289

Query: 217 RAAYKNS----AMLTTVDEYFSNPLTGS 240
            A          ++  + +Y ++   GS
Sbjct: 290 TANLIRPRATAEIINGIQDYLTSRQMGS 317


>gi|15679034|ref|NP_276151.1| hypothetical protein MTH1016 [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|2622118|gb|AAB85512.1| conserved protein [Methanothermobacter thermautotrophicus str.
           Delta H]
          Length = 242

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/164 (19%), Positives = 60/164 (36%), Gaps = 19/164 (11%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  ++VE + I      + + +N  C    + E   G  ++++P+ + D  A +      
Sbjct: 81  EPERIVEISSI---ESVDVVEINAHCRQPEITEIGAGQSMLMDPEFLEDFTAEVTGKARS 137

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+VK R  V               +   GV+ I + A K                 D +
Sbjct: 138 EVSVKIRGNVPGADTVGV----AGVLADLGVDYIHLDAMKP-----------GEDRADLE 182

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
           +V  + +   D  +  N  + D+  A  +L    D V + RAA 
Sbjct: 183 LVSLVSEVKGDSILIGNNSVRDIESARAMLAAGADAVSVARAAI 226


>gi|328955618|ref|YP_004372951.1| dihydroorotate oxidase B, catalytic subunit [Coriobacterium
           glomerans PW2]
 gi|328455942|gb|AEB07136.1| dihydroorotate oxidase B, catalytic subunit [Coriobacterium
           glomerans PW2]
          Length = 307

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/222 (14%), Positives = 74/222 (33%), Gaps = 32/222 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCPSAR 87
              +      +   + +   +  Q+ G   ++ V A ++  +         LNV CP   
Sbjct: 81  RGFVEQSGTYLERLAGKGTQIICQVAGHSTAEYVSALELFCELCPWAAGFELNVSCP--N 138

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
           V EG         P+   + + A  +    P+ VK           V +  + ++++ +G
Sbjct: 139 VAEGGIACG--STPEAAAEVVRACRRVCDRPLLVKM--------APVRVDEIARAVEDAG 188

Query: 148 VNGIWIHA------------RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            + + I              R  + +         +  +   +V+E  +    + I   G
Sbjct: 189 ADALTIINSIPGMSIDIETHRSRLSRPTGGLSGPLLHPIAVRMVWEAFRAV-RIPIIGVG 247

Query: 196 GLED-MSQALKILPSVDGVMIGRAAYKNSA----MLTTVDEY 232
           G+      A  IL     V +G A+  +      +L  ++ +
Sbjct: 248 GIMTGADAAEFILAGATSVAVGMASLVDPGASLRILAELEAW 289


>gi|289547875|ref|YP_003472863.1| dihydroorotate dehydrogenase [Thermocrinis albus DSM 14484]
 gi|289181492|gb|ADC88736.1| dihydroorotate dehydrogenase family protein [Thermocrinis albus DSM
           14484]
          Length = 310

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/212 (17%), Positives = 73/212 (34%), Gaps = 29/212 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLN 100
                +    + + G    + +E    +ED        LNV CP   V +G        +
Sbjct: 88  RIEKIDTHFIVNVFGETEEEYLEVCLALEDRPKIVAYELNVSCP--NVKKGGMLFG--HD 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHAR 156
             ++   +  +   +  PV VK    V D      +R   +   +SG +G+     +   
Sbjct: 144 TKVLSRLVERVKAKVRKPVLVKLSPNVGD------IRTFARVCVESGADGLVAINTLVGM 197

Query: 157 KAILKGLSPK--------DNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI- 206
           K  ++   P             I  +   IV+E+ +E    + +   GG+ D   AL+  
Sbjct: 198 KIDVRSGKPDLSTFVGGLSGPAILPIAVRIVWEVFQEVRGSVPVIGVGGIYDTDSALQHI 257

Query: 207 LPSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           L     V +G A + +      ++  +  Y  
Sbjct: 258 LAGASAVQVGTANFFDPKCPLRIIEGIKSYME 289


>gi|299141936|ref|ZP_07035071.1| dihydroorotate oxidase [Prevotella oris C735]
 gi|298576787|gb|EFI48658.1| dihydroorotate oxidase [Prevotella oris C735]
          Length = 301

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 74/208 (35%), Gaps = 25/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G         A+ +++      I LN+ CP   V EG     +    +   
Sbjct: 93  DTNMIVNVSGNSAESYAACAQRIDELNRIPAIELNISCP--NVKEGGMAFGVTC--EGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
             + A+  A    + VK    V D      +  + ++ +  G + +            I 
Sbjct: 149 SIVKAVRAAYHKTLIVKLSPNVTD------IAAIARACEAEGADAVSLINTLMGMAVDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L   +       +  +   +VY++        +GL GG+  +  A++ ++     
Sbjct: 203 KRQPLLSIRTGGLSGPAVKPVALRMVYDVAHAVKIPVVGL-GGISSVEDAIEFLMCGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + IG A + +  +   V +  +  L   
Sbjct: 262 IEIGTANFVDPTITKKVKDGMNTWLDAH 289


>gi|187733441|ref|YP_001879524.1| dihydropyrimidine dehydrogenase [Shigella boydii CDC 3083-94]
 gi|187430433|gb|ACD09707.1| dihydroorotate dehydrogenase family protein [Shigella boydii CDC
           3083-94]
          Length = 411

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|170682869|ref|YP_001744341.1| dihydropyrimidine dehydrogenase [Escherichia coli SMS-3-5]
 gi|170520587|gb|ACB18765.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           SMS-3-5]
          Length = 411

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|71984108|ref|NP_508927.2| DihydroPYrimidine Dehydrogenase family member (dpyd-1)
           [Caenorhabditis elegans]
 gi|97536128|sp|Q18164|DPYD_CAEEL RecName: Full=Dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|62630064|gb|AAK39195.2| Dihydropyrimidine dehydrogenase protein 1, partially confirmed by
           transcript evidence [Caenorhabditis elegans]
          Length = 1059

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 64/204 (31%), Gaps = 35/204 (17%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I   +          L      K +   I         +  A K  E+ G + + LN+
Sbjct: 625 ELISEKSCEYWLQCIRELKRDHPTKIVIASIMCVYNKADWIELATK-SEEAGADILELNL 683

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            CP     E   G     +P+IV +    +   + IP   K    + D      +R + +
Sbjct: 684 SCPHGM-GEKGMGLACGQSPEIVKEICRWVRACVKIPFFPKMTPNITD------VREIAR 736

Query: 142 SIKKSGVNGIW--------IH-------------ARKAILKGLSPKDNRKIPNLDYDIVY 180
           + +  G +G+         +H              ++    G+S    R I       V 
Sbjct: 737 AARDGGASGVTATNTVSSLMHMKADGNAWPAIGSTKRTTYGGMSGSAIRPIAM---KAVS 793

Query: 181 EIKKENPDLFIGLNGGLEDMSQAL 204
            I  E     I   GG+E     L
Sbjct: 794 SIANELDGFPIMATGGIESAETGL 817


>gi|301024363|ref|ZP_07188052.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 196-1]
 gi|299880460|gb|EFI88671.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 196-1]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|218705675|ref|YP_002413194.1| dihydropyrimidine dehydrogenase [Escherichia coli UMN026]
 gi|293405615|ref|ZP_06649607.1| yeiA protein [Escherichia coli FVEC1412]
 gi|298381296|ref|ZP_06990895.1| yeiA protein [Escherichia coli FVEC1302]
 gi|300897797|ref|ZP_07116190.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 198-1]
 gi|331663649|ref|ZP_08364559.1| putative oxidoreductase [Escherichia coli TA143]
 gi|218432772|emb|CAR13666.1| putative oxidoreductase subunit [Escherichia coli UMN026]
 gi|291427823|gb|EFF00850.1| yeiA protein [Escherichia coli FVEC1412]
 gi|298278738|gb|EFI20252.1| yeiA protein [Escherichia coli FVEC1302]
 gi|300358512|gb|EFJ74382.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 198-1]
 gi|331059448|gb|EGI31425.1| putative oxidoreductase [Escherichia coli TA143]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|293410506|ref|ZP_06654082.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291470974|gb|EFF13458.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|218700619|ref|YP_002408248.1| dihydropyrimidine dehydrogenase [Escherichia coli IAI39]
 gi|300935069|ref|ZP_07150100.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 21-1]
 gi|218370605|emb|CAR18412.1| putative oxidoreductase subunit [Escherichia coli IAI39]
 gi|300459650|gb|EFK23143.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 21-1]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|296454107|ref|YP_003661250.1| dihydroorotate dehydrogenase family protein [Bifidobacterium longum
           subsp. longum JDM301]
 gi|296183538|gb|ADH00420.1| dihydroorotate dehydrogenase family protein [Bifidobacterium longum
           subsp. longum JDM301]
          Length = 323

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 28/206 (13%), Positives = 68/206 (33%), Gaps = 23/206 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     +++         +   + G          + + D   + + +NV CP    + 
Sbjct: 97  GIDHYLAEDLPKLKAAGAFVISNVAGHCDDDYAAVVEKLADSDADMLEINVSCP----NV 152

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G  +  +P  + + +  +      P+ VK    + D           ++  + G + 
Sbjct: 153 SAGGMSVGTDPVALANLMDRLRPMTDKPMIVKLTPNITDITVP------ARAAVEHGADA 206

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +              +  I           +  +    VY ++   P++ I   GG++
Sbjct: 207 LSMINTLKGMRINIRTGQPIIANVTGGVSGPAVLPVGLAAVYRVRTALPEIPIIGLGGID 266

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNS 223
              +AL+ L    + V +G AA  + 
Sbjct: 267 SGEKALEYLYAGANAVEVGAAALFDP 292


>gi|331647798|ref|ZP_08348890.1| putative oxidoreductase [Escherichia coli M605]
 gi|281179239|dbj|BAI55569.1| putative dihydropyrimidine dehydrogenase [Escherichia coli SE15]
 gi|330911980|gb|EGH40490.1| hypothetical protein ECAA86_02352 [Escherichia coli AA86]
 gi|331043522|gb|EGI15660.1| putative oxidoreductase [Escherichia coli M605]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|241895143|ref|ZP_04782439.1| dihydroorotate dehydrogenase B, catalytic subunit [Weissella
           paramesenteroides ATCC 33313]
 gi|241871639|gb|EER75390.1| dihydroorotate dehydrogenase B, catalytic subunit [Weissella
           paramesenteroides ATCC 33313]
          Length = 323

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/182 (19%), Positives = 70/182 (38%), Gaps = 25/182 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P  L I GA + + V+ AKI++     N I LN+ CP   V EG     +  +   +   
Sbjct: 99  PKMLSISGATVDEFVQLAKIIDKLPAINAIELNLSCP--NVDEGGCAFGVTESG--IHSV 154

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------------A 155
           ++A+    +  +  K    V D  P      L  + + +G +G+ +              
Sbjct: 155 VSAVRAVTTKAIYAKLSPNVTDIKP------LAVTAENAGADGLTMVNTLVGMSLDLQSR 208

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
              + +G        +  L  ++++E       + I   GG+  +  AL+ ++     V 
Sbjct: 209 SARLYRGKGGLSGEALHPLAVELIWE-AASAVHIPIIGVGGVSSIDDALELMMAGASAVQ 267

Query: 215 IG 216
           +G
Sbjct: 268 VG 269


>gi|221104913|ref|XP_002170640.1| PREDICTED: similar to predicted protein, partial [Hydra
           magnipapillata]
          Length = 611

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 65/204 (31%), Gaps = 33/204 (16%)

Query: 25  EMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I   + A        ++     +  +A  + G +     E AK+ E  G   + LN+ 
Sbjct: 198 ELISEKSAAYWCKSISELVKDFPNQVLIASIMCGYNQEDWTELAKMSEAAGAPALELNLS 257

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G       + V +    +  A+ IP   K    V D      +  +  +
Sbjct: 258 CPHGM-DEKGMGLACGQKAEFVYNICKWVRAAVKIPFFAKLTPNVTD------IVEIALA 310

Query: 143 IKKSGVNGIW--------IH-------------ARKAILKGLSPKDNRKIPNLDYDIVYE 181
            K  G +G+         +H              ++    G+S    R I       V  
Sbjct: 311 AKNGGADGVTATNTVSGLMHLKSNAVPWPAVGQEKRTTYGGVSGNSIRPIA---LRAVSA 367

Query: 182 IKKENPDLFIGLNGGLEDMSQALK 205
           I    P   I   GG++     L+
Sbjct: 368 IASALPGFPILATGGIDSAEVGLQ 391


>gi|89108964|ref|AP_002744.1| predicted oxidoreductase [Escherichia coli str. K-12 substr. W3110]
 gi|90111398|ref|NP_416652.4| Dihydropyrimidine dehydrogenase, NADH-dependent, subunit B
           [Escherichia coli str. K-12 substr. MG1655]
 gi|157161627|ref|YP_001458945.1| dihydropyrimidine dehydrogenase [Escherichia coli HS]
 gi|161367574|ref|NP_288730.2| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 EDL933]
 gi|161986503|ref|YP_311088.2| dihydropyrimidine dehydrogenase [Shigella sonnei Ss046]
 gi|162139776|ref|NP_311066.2| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 str.
           Sakai]
 gi|168750527|ref|ZP_02775549.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4113]
 gi|168757729|ref|ZP_02782736.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4401]
 gi|168763803|ref|ZP_02788810.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4501]
 gi|168767760|ref|ZP_02792767.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4486]
 gi|168773142|ref|ZP_02798149.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4196]
 gi|168779990|ref|ZP_02804997.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4076]
 gi|168788957|ref|ZP_02813964.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC869]
 gi|168801164|ref|ZP_02826171.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC508]
 gi|170081770|ref|YP_001731090.1| oxidoreductase [Escherichia coli str. K-12 substr. DH10B]
 gi|188496096|ref|ZP_03003366.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           53638]
 gi|193062277|ref|ZP_03043372.1| dihydroorotate dehydrogenase family protein [Escherichia coli E22]
 gi|193071085|ref|ZP_03052011.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           E110019]
 gi|194427185|ref|ZP_03059736.1| dihydroorotate dehydrogenase family protein [Escherichia coli B171]
 gi|194436016|ref|ZP_03068118.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           101-1]
 gi|195935523|ref|ZP_03080905.1| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807187|ref|ZP_03249524.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4206]
 gi|208814189|ref|ZP_03255518.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4045]
 gi|208819511|ref|ZP_03259831.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396337|ref|YP_002271556.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4115]
 gi|217327385|ref|ZP_03443468.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. TW14588]
 gi|238901329|ref|YP_002927125.1| putative oxidoreductase [Escherichia coli BW2952]
 gi|253772926|ref|YP_003035757.1| dihydropyrimidine dehydrogenase [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162161|ref|YP_003045269.1| dihydropyrimidine dehydrogenase [Escherichia coli B str. REL606]
 gi|254794046|ref|YP_003078883.1| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 str.
           TW14359]
 gi|256022169|ref|ZP_05436034.1| dihydropyrimidine dehydrogenase [Escherichia sp. 4_1_40B]
 gi|260844753|ref|YP_003222531.1| putative oxidoreductase [Escherichia coli O103:H2 str. 12009]
 gi|261223394|ref|ZP_05937675.1| predicted oxidoreductase [Escherichia coli O157:H7 str. FRIK2000]
 gi|261259056|ref|ZP_05951589.1| putative oxidoreductase [Escherichia coli O157:H7 str. FRIK966]
 gi|291283401|ref|YP_003500219.1| putative oxidoreductase [Escherichia coli O55:H7 str. CB9615]
 gi|297517340|ref|ZP_06935726.1| dihydropyrimidine dehydrogenase [Escherichia coli OP50]
 gi|300930376|ref|ZP_07145785.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 187-1]
 gi|300950094|ref|ZP_07164041.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 116-1]
 gi|300955831|ref|ZP_07168172.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 175-1]
 gi|301644164|ref|ZP_07244172.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 146-1]
 gi|307138806|ref|ZP_07498162.1| dihydropyrimidine dehydrogenase [Escherichia coli H736]
 gi|312973604|ref|ZP_07787776.1| uncharacterized protein yeiA [Escherichia coli 1827-70]
 gi|331642772|ref|ZP_08343907.1| putative oxidoreductase [Escherichia coli H736]
 gi|331683824|ref|ZP_08384420.1| putative oxidoreductase [Escherichia coli H299]
 gi|3183568|sp|P25889|YEIA_ECOLI RecName: Full=Uncharacterized protein yeiA
 gi|85675261|dbj|BAE76624.1| predicted oxidoreductase [Escherichia coli str. K12 substr. W3110]
 gi|87082059|gb|AAC75208.2| Dihydropyrimidine dehydrogenase, NADH-dependent, subunit B
           [Escherichia coli str. K-12 substr. MG1655]
 gi|157067307|gb|ABV06562.1| dihydroorotate dehydrogenase family protein [Escherichia coli HS]
 gi|169889605|gb|ACB03312.1| predicted oxidoreductase [Escherichia coli str. K-12 substr. DH10B]
 gi|187771295|gb|EDU35139.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4196]
 gi|188015281|gb|EDU53403.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4113]
 gi|188491295|gb|EDU66398.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           53638]
 gi|189001874|gb|EDU70860.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4076]
 gi|189355322|gb|EDU73741.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4401]
 gi|189362895|gb|EDU81314.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4486]
 gi|189366084|gb|EDU84500.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4501]
 gi|189371361|gb|EDU89777.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC869]
 gi|189376637|gb|EDU95053.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC508]
 gi|192931943|gb|EDV84542.1| dihydroorotate dehydrogenase family protein [Escherichia coli E22]
 gi|192955608|gb|EDV86085.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           E110019]
 gi|194414806|gb|EDX31077.1| dihydroorotate dehydrogenase family protein [Escherichia coli B171]
 gi|194424744|gb|EDX40729.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           101-1]
 gi|208726988|gb|EDZ76589.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4206]
 gi|208735466|gb|EDZ84153.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4045]
 gi|208739634|gb|EDZ87316.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4042]
 gi|209157737|gb|ACI35170.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. EC4115]
 gi|217319752|gb|EEC28177.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           O157:H7 str. TW14588]
 gi|238862745|gb|ACR64743.1| predicted oxidoreductase [Escherichia coli BW2952]
 gi|242377789|emb|CAQ32552.1| NADH-dependent dihydropyrimidine dehydrogenase subunit, subunit of
           NAD-dependent dihydropyrimidine dehydrogenase
           [Escherichia coli BL21(DE3)]
 gi|253323970|gb|ACT28572.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974062|gb|ACT39733.1| dihydropyrimidine dehydrogenase [Escherichia coli B str. REL606]
 gi|253978230|gb|ACT43900.1| dihydropyrimidine dehydrogenase [Escherichia coli BL21(DE3)]
 gi|254593446|gb|ACT72807.1| predicted oxidoreductase [Escherichia coli O157:H7 str. TW14359]
 gi|257759900|dbj|BAI31397.1| predicted oxidoreductase [Escherichia coli O103:H2 str. 12009]
 gi|260448759|gb|ACX39181.1| dihydroorotate dehydrogenase family protein [Escherichia coli DH1]
 gi|290763274|gb|ADD57235.1| putative oxidoreductase [Escherichia coli O55:H7 str. CB9615]
 gi|300317298|gb|EFJ67082.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 175-1]
 gi|300450584|gb|EFK14204.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 116-1]
 gi|300461698|gb|EFK25191.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 187-1]
 gi|301077462|gb|EFK92268.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 146-1]
 gi|310332199|gb|EFP99434.1| uncharacterized protein yeiA [Escherichia coli 1827-70]
 gi|315136780|dbj|BAJ43939.1| putative oxidoreductase [Escherichia coli DH1]
 gi|320192230|gb|EFW66875.1| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 str.
           EC1212]
 gi|320641218|gb|EFX10696.1| dihydropyrimidine dehydrogenase subunit B [Escherichia coli O157:H7
           str. G5101]
 gi|320646606|gb|EFX15517.1| dihydropyrimidine dehydrogenase subunit B [Escherichia coli O157:H-
           str. 493-89]
 gi|320651861|gb|EFX20236.1| dihydropyrimidine dehydrogenase subunit B [Escherichia coli O157:H-
           str. H 2687]
 gi|320657585|gb|EFX25383.1| dihydropyrimidine dehydrogenase subunit B [Escherichia coli O55:H7
           str. 3256-97 TW 07815]
 gi|320663191|gb|EFX30500.1| dihydropyrimidine dehydrogenase subunit B [Escherichia coli O55:H7
           str. USDA 5905]
 gi|320667942|gb|EFX34845.1| dihydropyrimidine dehydrogenase subunit B [Escherichia coli O157:H7
           str. LSU-61]
 gi|323161774|gb|EFZ47655.1| hypothetical protein ECE128010_2020 [Escherichia coli E128010]
 gi|323168713|gb|EFZ54393.1| hypothetical protein SS53G_1042 [Shigella sonnei 53G]
 gi|323936761|gb|EGB33046.1| dihydroorotate dehydrogenase [Escherichia coli E1520]
 gi|323940784|gb|EGB36972.1| dihydroorotate dehydrogenase [Escherichia coli E482]
 gi|323961611|gb|EGB57217.1| dihydroorotate dehydrogenase [Escherichia coli H489]
 gi|323972971|gb|EGB68168.1| dihydroorotate dehydrogenase [Escherichia coli TA007]
 gi|324118013|gb|EGC11912.1| dihydroorotate dehydrogenase [Escherichia coli E1167]
 gi|326339497|gb|EGD63308.1| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 str.
           1125]
 gi|326343958|gb|EGD67719.1| dihydropyrimidine dehydrogenase [Escherichia coli O157:H7 str.
           1044]
 gi|331039570|gb|EGI11790.1| putative oxidoreductase [Escherichia coli H736]
 gi|331078776|gb|EGI49978.1| putative oxidoreductase [Escherichia coli H299]
 gi|332343925|gb|AEE57259.1| conserved hypothetical protein [Escherichia coli UMNK88]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|307172628|gb|EFN63987.1| Dihydropyrimidine dehydrogenase [NADP+] [Camponotus floridanus]
          Length = 383

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/154 (22%), Positives = 57/154 (37%), Gaps = 13/154 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK  E  G + + LN+ CP     E   G     +P++V +    + +A+ IP  VK   
Sbjct: 13  AKKAEAAGSDGLELNLSCPHGM-GESGMGLACGQDPELVRNISRWVREAVKIPFFVKLTP 71

Query: 126 GVDD-----QIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGL------SPKDNRKIPN 173
            + D     +       + V +I   SG+ G++  A      GL                
Sbjct: 72  NITDILSIAKAAYEGKADGVTAINTVSGLMGLYADATPWPAVGLNKLTTYGGVSGNATRP 131

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               I+  + K  P   I   GG++    AL+ L
Sbjct: 132 QALRIISTVSKHLPGFPILGAGGVDSADVALQFL 165


>gi|333001282|gb|EGK20850.1| hypothetical protein SFVA6_3000 [Shigella flexneri VA-6]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVKKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|323171798|gb|EFZ57442.1| hypothetical protein ECLT68_3438 [Escherichia coli LT-68]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|284165172|ref|YP_003403451.1| tRNA-dihydrouridine synthase-like protein [Haloterrigena turkmenica
           DSM 5511]
 gi|284014827|gb|ADB60778.1| tRNA-dihydrouridine synthase-like protein [Haloterrigena turkmenica
           DSM 5511]
          Length = 250

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 81/237 (34%), Gaps = 29/237 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           R  AR L       TE +  D I   D + +          A  +  A    + +AA++ 
Sbjct: 42  RAAARELVARDR--TEFLPDDPIAFID-RQLAALEDVPIQPAFNVRSATPDPIPDAARVC 98

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            D     + +N  C    +     G  L+ + + + D +          V VK R     
Sbjct: 99  RDRDA-FLEINAHCRQDELCAAGCGETLLRDRERLCDYVRRAAD-TGATVGVKVRA---- 152

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           ++P V L  L  +I+ +G + + + A                   D + +        DL
Sbjct: 153 EVPGVDLPALAAAIETAGADYLHVDAM------------------DSESIVREIAAATDL 194

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           F+  N G+ D +   + +    D V +GR +  N  +L  V E     L    P   
Sbjct: 195 FVVANNGVRDDATVREYVDYGADAVSVGRPS-DNPVVLERVREAVDRHLALEEPPSR 250


>gi|212696129|ref|ZP_03304257.1| hypothetical protein ANHYDRO_00665 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676758|gb|EEB36365.1| hypothetical protein ANHYDRO_00665 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 299

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/176 (20%), Positives = 66/176 (37%), Gaps = 24/176 (13%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   V+  ++++      I LN+ CP    +    G     +P    + I  + K
Sbjct: 99  LGGHSVEDYVKGCELLDKTSVPIIELNISCP----NVKEGGMAFGTDPMKACEVIEKVRK 154

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKG 162
                + VK    V D      ++  VK  + SG +            I +  +KA+ + 
Sbjct: 155 TTKKVLMVKLSPNVGD------IKEFVKIAENSGADCISLVNTFNAMAIDVDNKKAVFEN 208

Query: 163 L-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
             +      I  +   +VYE  K      IG+ GG+ +    L+ I+     V +G
Sbjct: 209 KTAGLSGPCIKPIALRMVYEASKATSLPVIGM-GGISNYKDCLEFIMAGASAVQVG 263


>gi|215487368|ref|YP_002329799.1| dihydropyrimidine dehydrogenase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|312967440|ref|ZP_07781655.1| uncharacterized protein yeiA [Escherichia coli 2362-75]
 gi|215265440|emb|CAS09841.1| predicted oxidoreductase [Escherichia coli O127:H6 str. E2348/69]
 gi|312287637|gb|EFR15542.1| uncharacterized protein yeiA [Escherichia coli 2362-75]
 gi|320196016|gb|EFW70640.1| dihydropyrimidine dehydrogenase [Escherichia coli WV_060327]
          Length = 411

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRAHPELHDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|260753316|ref|YP_003226209.1| dihydroorotate dehydrogenase [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|258552679|gb|ACV75625.1| dihydroorotate dehydrogenase [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
          Length = 355

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 73/198 (36%), Gaps = 29/198 (14%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML-NPDIVGDCIAAMCKA 114
           G        AA++V + G   +  N+ CP+  V+       L+  +  +V   + A+  A
Sbjct: 168 GKIEEDYALAARMVAETGAPVLEANLSCPNEGVNS------LLCFDAPLVQKIVEAIKVA 221

Query: 115 L-SIPVTVKCRIGVDDQIPAVALRNLVKSIKK--SGVNGI-WIHARKAILKGLS------ 164
           +   P+ +K     D+      L +LV  +    SG + I  + AR    KG +      
Sbjct: 222 VPDRPLLIKTAYFKDN----AKLADLVSRVGHLVSGFSTINTLSARPLDEKGQAALSPSR 277

Query: 165 PKDNRKIPNLDY---DIVYEIK----KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           P+       + +   ++V  +     +++ D  I   GG+         +    + VM  
Sbjct: 278 PEGGVCGDAIRWAGLEMVQRLAAFREEKSLDYAIVGVGGVNKPEHYKAYIEAGANAVMTA 337

Query: 217 RAAYKNSAMLTTVDEYFS 234
             +  N  +     ++ +
Sbjct: 338 TGSMWNPHLAEETKKFLA 355


>gi|323188128|gb|EFZ73423.1| hypothetical protein ECRN5871_3885 [Escherichia coli RN587/1]
          Length = 411

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|170019536|ref|YP_001724490.1| dihydropyrimidine dehydrogenase [Escherichia coli ATCC 8739]
 gi|169754464|gb|ACA77163.1| dihydroorotate dehydrogenase family protein [Escherichia coli ATCC
           8739]
          Length = 411

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEVGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|91092056|ref|XP_970271.1| PREDICTED: similar to dihydropyrimidine dehydrogenase [Tribolium
           castaneum]
 gi|270004691|gb|EFA01139.1| hypothetical protein TcasGA2_TC010364 [Tribolium castaneum]
          Length = 1016

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 27/160 (16%), Positives = 51/160 (31%), Gaps = 25/160 (15%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K+ ED G + + LN+ CP     E   G      P++V      +   + IP  +K    
Sbjct: 646 KMAEDAGADALELNLSCPHGM-GESGMGLACGQKPELVKGISQWVRATVKIPFFIKLTPN 704

Query: 127 VDDQIPAVALRNLVKSIKKSGVN------------GIWIHARKAILKGLSPKDNR----- 169
           +        + ++  +  + G +            G+  +       GL  +        
Sbjct: 705 I------TNIVDIATAAYEGGADGVAAINTVSGLMGLSANGSPWPAVGLDKRTTYGGVSG 758

Query: 170 -KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
                +    V  +    P   I   GG++    AL+ L 
Sbjct: 759 NATRPMGLRAVSAVANALPGFAIMGIGGIDSADVALQYLQ 798


>gi|110642356|ref|YP_670086.1| dihydropyrimidine dehydrogenase [Escherichia coli 536]
 gi|117624348|ref|YP_853261.1| dihydropyrimidine dehydrogenase [Escherichia coli APEC O1]
 gi|161486180|ref|NP_754568.2| dihydropyrimidine dehydrogenase [Escherichia coli CFT073]
 gi|191170189|ref|ZP_03031743.1| dihydroorotate dehydrogenase family protein [Escherichia coli F11]
 gi|218559065|ref|YP_002391978.1| dihydropyrimidine dehydrogenase [Escherichia coli S88]
 gi|227887202|ref|ZP_04005007.1| dihydropyrimidine dehydrogenase [Escherichia coli 83972]
 gi|300981478|ref|ZP_07175559.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 200-1]
 gi|300982861|ref|ZP_07176325.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 45-1]
 gi|301048883|ref|ZP_07195876.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 185-1]
 gi|306814738|ref|ZP_07448900.1| dihydropyrimidine dehydrogenase [Escherichia coli NC101]
 gi|331658226|ref|ZP_08359188.1| putative oxidoreductase [Escherichia coli TA206]
 gi|110343948|gb|ABG70185.1| putative dihydropyrimidine dehydrogenase [Escherichia coli 536]
 gi|115513472|gb|ABJ01547.1| putative dihydropyrimidine dehydrogenase [Escherichia coli APEC O1]
 gi|190909705|gb|EDV69290.1| dihydroorotate dehydrogenase family protein [Escherichia coli F11]
 gi|218365834|emb|CAR03575.1| putative oxidoreductase subunit [Escherichia coli S88]
 gi|227835552|gb|EEJ46018.1| dihydropyrimidine dehydrogenase [Escherichia coli 83972]
 gi|294490821|gb|ADE89577.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           IHE3034]
 gi|300299259|gb|EFJ55644.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 185-1]
 gi|300307551|gb|EFJ62071.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 200-1]
 gi|300408661|gb|EFJ92199.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 45-1]
 gi|305852132|gb|EFM52584.1| dihydropyrimidine dehydrogenase [Escherichia coli NC101]
 gi|307554216|gb|ADN46991.1| dihydroorotate dehydrogenase family protein [Escherichia coli ABU
           83972]
 gi|307626312|gb|ADN70616.1| dihydropyrimidine dehydrogenase [Escherichia coli UM146]
 gi|315285782|gb|EFU45222.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 110-3]
 gi|315294488|gb|EFU53836.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 153-1]
 gi|315297989|gb|EFU57259.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 16-3]
 gi|323951943|gb|EGB47817.1| dihydroorotate dehydrogenase [Escherichia coli H252]
 gi|323955912|gb|EGB51665.1| dihydroorotate dehydrogenase [Escherichia coli H263]
 gi|323968071|gb|EGB63481.1| dihydroorotate dehydrogenase [Escherichia coli M863]
 gi|324013972|gb|EGB83191.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 60-1]
 gi|324114437|gb|EGC08406.1| dihydroorotate dehydrogenase [Escherichia fergusonii B253]
 gi|327252385|gb|EGE64044.1| hypothetical protein ECSTEC7V_2552 [Escherichia coli STEC_7v]
 gi|331056474|gb|EGI28483.1| putative oxidoreductase [Escherichia coli TA206]
          Length = 411

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|172057950|ref|YP_001814410.1| dihydroorotate dehydrogenase family protein [Exiguobacterium
           sibiricum 255-15]
 gi|259547517|sp|B1YIR7|PYRD_EXIS2 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|171990471|gb|ACB61393.1| dihydroorotate dehydrogenase family protein [Exiguobacterium
           sibiricum 255-15]
          Length = 309

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 75/197 (38%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  +   + G+   +  +  + +  D     I LN+ CP+ +     FG     +P +  
Sbjct: 93  DTEIIANVAGSTPEEYEDVTRRISRDPVVKAIELNISCPNVKSGGLQFGT----DPQMAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAIL 160
           +    +      PV VK    V       ++  + ++++++G +G+      +  R  + 
Sbjct: 149 ELTRRVKAVSEKPVYVKLSPNV------TSIVEMAQAVEQAGADGLTMINTLVGMRIDVR 202

Query: 161 KGLSPKDNR-------KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDG 212
            G     NR        I  +   +++++ +    + I   GG+ ++   L++       
Sbjct: 203 TGQPILANRIGGLSGPAIKPVAVRMIHDVAQ-VVTIPIIGMGGVMEVDDVLEMIYAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           V IG A + N  +   +
Sbjct: 262 VAIGTANFVNPFICQEL 278


>gi|320173376|gb|EFW48577.1| dihydropyrimidine dehydrogenase [Shigella dysenteriae CDC 74-1112]
          Length = 304

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|12516464|gb|AAG57285.1|AE005446_13 putative oxidoreductase [Escherichia coli O157:H7 str. EDL933]
 gi|13362508|dbj|BAB36462.1| putative oxidoreductase [Escherichia coli O157:H7 str. Sakai]
 gi|73856146|gb|AAZ88853.1| putative oxidoreductase [Shigella sonnei Ss046]
 gi|209766278|gb|ACI81451.1| putative oxidoreductase [Escherichia coli]
 gi|209766280|gb|ACI81452.1| putative oxidoreductase [Escherichia coli]
 gi|209766282|gb|ACI81453.1| putative oxidoreductase [Escherichia coli]
 gi|209766286|gb|ACI81455.1| putative oxidoreductase [Escherichia coli]
          Length = 413

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 95  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 152

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 153 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 206

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 207 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 266

Query: 200 MSQALKIL 207
              A + L
Sbjct: 267 WEDAAEFL 274


>gi|317132141|ref|YP_004091455.1| dihydroorotate dehydrogenase family protein [Ethanoligenens
           harbinense YUAN-3]
 gi|315470120|gb|ADU26724.1| dihydroorotate dehydrogenase family protein [Ethanoligenens
           harbinense YUAN-3]
          Length = 401

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 73/197 (37%), Gaps = 16/197 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    +    D    L  +  +K L   I G    +  + A++ E  G + +  N  C
Sbjct: 77  EQISDHPLEENMDVLRRLKQAYPQKVLVASIMGETEEEWTKLARLAEQVGVDMLECNFSC 136

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA---------- 133
           P   + + + G+ +  + ++V     A+ K   +PV  K    + +  P           
Sbjct: 137 PQ--MTKSTMGSDVGQSKELVETYCRAVRKGTKLPVLAKMTPNIGNMEPVAIAAMRGGAD 194

Query: 134 -VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N +KSI +  V     +        +S      +  +    ++++ K  +  ++ 
Sbjct: 195 GIAAINTIKSITRLDVEHFSAYPDVDGQSSVSGYSGEAVRPIALRFIHDLAKHPQLQNVP 254

Query: 191 IGLNGGLEDMSQALKIL 207
           I   GG+E    AL+  
Sbjct: 255 ISGIGGIETWRDALEFF 271


>gi|194431438|ref|ZP_03063730.1| dihydroorotate dehydrogenase family protein [Shigella dysenteriae
           1012]
 gi|194420263|gb|EDX36340.1| dihydroorotate dehydrogenase family protein [Shigella dysenteriae
           1012]
 gi|332092632|gb|EGI97703.1| hypothetical protein SD15574_2140 [Shigella dysenteriae 155-74]
          Length = 411

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|297569958|ref|YP_003691302.1| dihydroorotate dehydrogenase family protein [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925873|gb|ADH86683.1| dihydroorotate dehydrogenase family protein [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 308

 Score = 66.8 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/203 (17%), Positives = 80/203 (39%), Gaps = 29/203 (14%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  + +  + A+ ++   G   + +N+ CP    +    G     +P +     
Sbjct: 101 VVVNILGNTVDEYAQLARRLDGIEGVTALEVNISCP----NVKEGGVAFGTDPLMASAVT 156

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLS 164
           AA+ +A  +P+ +K    V D      ++ + +S+ +SG + +     +      L G  
Sbjct: 157 AAVRRASKLPLIIKLSPNVTD------IQLMARSVAESGADAVSLINTLLGMAIDLAGRR 210

Query: 165 PK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
           P+            I  +   +V++  +      IG+ GG+     AL+ I+     V +
Sbjct: 211 PRLANVVGGLSGPAIKPVALRMVWQAAQAVKIPVIGI-GGIMTAEDALEFIVAGAHAVQV 269

Query: 216 GRAAYKNSA----MLTTVDEYFS 234
           G A + N      ++  +  Y +
Sbjct: 270 GTANFVNPGATEEIVEGIAAYLA 292


>gi|193792430|gb|ACF20989.1| BaiH [Clostridium hylemonae DSM 15053]
          Length = 672

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/199 (21%), Positives = 74/199 (37%), Gaps = 24/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG------------SFGACLMLNPDIVGDCI 108
           +   AA+ V++ G   I+L   C  A +  G             +G CL      + + I
Sbjct: 160 QFGAAARRVQEAGCGGISL--HCAHAYMQPGTFLSPLRNKRMDEYGGCLDNRARFILEVI 217

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI--LKG 162
             + K +S    V  RI  D++            L    + +GV+ + +        L+ 
Sbjct: 218 EEVRKNVSADFPVFLRISGDERAEGGNSLEDMLYLAPKFEAAGVDLLEVSGGTQYEGLEY 277

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
             P   ++I    Y+   EIKK    + +   G + D+  A  I+    VDGV +GR   
Sbjct: 278 TIPSQGKRIGMNIYEA-AEIKK-VVGIPVYAVGKINDIRYAADIVERGIVDGVAVGRPLL 335

Query: 221 KNSAMLTTVDEYFSNPLTG 239
            +  +     E   + +T 
Sbjct: 336 ADPDLCKKAKENRFDDITP 354


>gi|229829319|ref|ZP_04455388.1| hypothetical protein GCWU000342_01406 [Shuttleworthia satelles DSM
           14600]
 gi|229792482|gb|EEP28596.1| hypothetical protein GCWU000342_01406 [Shuttleworthia satelles DSM
           14600]
          Length = 305

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 29/201 (14%), Positives = 73/201 (36%), Gaps = 25/201 (12%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCPSARVHEGSFGA 95
           ++++      +  + + + G    + +   + + +    + + +N+ CP    +    G 
Sbjct: 82  QRDLAFLDAFDTRVVVNVCGHTEEEYLRVVETLADQKRVDLLEINISCP----NVREGGM 137

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-- 153
               +P +V    +++ K  + P+ +K    V       ++ ++ ++ +  G + I +  
Sbjct: 138 AFGTDPAMVEYITSSVKKRAAQPIIIKLTPNV------TSIADVARAAEAGGADVISLIN 191

Query: 154 ----------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                     H   A+           I  +   +VYE  +    + I   GG+     A
Sbjct: 192 TITGMKIDVGHRTFALANKTGGMSGPAIHPIAVRMVYEAAQAV-KIPIIGMGGIASAEDA 250

Query: 204 LKI-LPSVDGVMIGRAAYKNS 223
           L++ L     V IG A +   
Sbjct: 251 LEMILAGATAVAIGTANFYRP 271


>gi|309788035|ref|ZP_07682644.1| uncharacterized protein yeiA [Shigella dysenteriae 1617]
 gi|308924169|gb|EFP69667.1| uncharacterized protein yeiA [Shigella dysenteriae 1617]
          Length = 411

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 75/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K  + + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTLNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|293415430|ref|ZP_06658073.1| yeiA protein [Escherichia coli B185]
 gi|291433078|gb|EFF06057.1| yeiA protein [Escherichia coli B185]
          Length = 411

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|224537012|ref|ZP_03677551.1| hypothetical protein BACCELL_01888 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224521379|gb|EEF90484.1| hypothetical protein BACCELL_01888 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 494

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 33/198 (16%), Positives = 65/198 (32%), Gaps = 26/198 (13%)

Query: 39  NILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
             L     EK +   I G   D   ++  A++ E+ G + I  N  CP   + +   G+ 
Sbjct: 190 RRLKERYPEKVIIASIMGRNCDEWTVL--ARMAEEAGADLIECNFSCPQ--MAKQGLGSD 245

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKK 145
           +  + D++     A  K   +P+  K    + +              ++A  N VKSI +
Sbjct: 246 IGQDQDLIALYTRATRKGSRLPIIAKMTPNIGNMELPAMTAIANGANSLAAINTVKSITR 305

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP--DLFIGLNGGLEDMSQA 203
                   +        +     + +  +    + ++    P   + +   GG+     A
Sbjct: 306 INTENFSSYPDIGGQSAVGGYSGQAVKPIALRFIRDLASYPPLKGIPLFGIGGITTWQDA 365

Query: 204 LK-------ILPSVDGVM 214
           L         L     VM
Sbjct: 366 LDFILLGCTALQVCTSVM 383


>gi|315615386|gb|EFU96018.1| uncharacterized protein yeiA [Escherichia coli 3431]
          Length = 399

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 81  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 138

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 139 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 192

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 193 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 252

Query: 200 MSQALKIL 207
              A + L
Sbjct: 253 WEDAAEFL 260


>gi|289207238|ref|YP_003459304.1| dihydroorotate dehydrogenase [Thioalkalivibrio sp. K90mix]
 gi|288942869|gb|ADC70568.1| dihydroorotate dehydrogenase family protein [Thioalkalivibrio sp.
           K90mix]
          Length = 330

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 72/200 (36%), Gaps = 27/200 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +E      + G+ I + +E  +  +D   + I +N+ CP    +    G     +P++  
Sbjct: 100 EETRFFANVSGSTIEEYIEVTRRFDDSPIDAIEINISCP----NVKEGGVAFGNDPEMSA 155

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
             + A     S P+  K      D      +    +    +G +G             + 
Sbjct: 156 RVVEACRSVTSKPLITKLSPNQTD------IAENGRRCIDAGTDGFAVINTLMGMAVDVE 209

Query: 155 ARKAI----LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
            R+A+      GLS    + I  L    VY++   + ++ I   GG+ +   AL+ L   
Sbjct: 210 NRRAVIGNNQGGLSGPAIKPIALLKVQQVYQVAAPH-NVPIIGQGGVMNARDALEFLIAG 268

Query: 210 VDGVMIGRAAYKNSAMLTTV 229
              V +G   + +   L  +
Sbjct: 269 ASTVGVGTGLFYDPLCLPKI 288


>gi|213692321|ref|YP_002322907.1| dihydroorotate dehydrogenase family protein [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|213523782|gb|ACJ52529.1| dihydroorotate dehydrogenase family protein [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|320458454|dbj|BAJ69075.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 323

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 29/206 (14%), Positives = 68/206 (33%), Gaps = 23/206 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     +++         +   + G          + + D   + + +NV CP    + 
Sbjct: 97  GIDHYLAEDLPKLKAAGAFVISNVAGHCDDDYAAVVEKLADSDADMLEINVSCP----NV 152

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G  +  +P  + + +  +      P+ VK    V D           ++  + G + 
Sbjct: 153 SAGGMSVGTDPVALANLMDRLRPMTDKPMIVKLTPNVTDITVP------ARAAVEHGADA 206

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +              +  I           +  +    VY ++   P++ I   GG++
Sbjct: 207 LSMINTLKGMRINIRTGQPIIANVTGGISGPAVLPVGLAAVYRVRTALPEIPIIGLGGID 266

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNS 223
              +AL+ L    + V +G AA  + 
Sbjct: 267 SGEKALEYLYAGANAVEVGAAALFDP 292


>gi|91211433|ref|YP_541419.1| dihydropyrimidine dehydrogenase [Escherichia coli UTI89]
 gi|237704612|ref|ZP_04535093.1| dihydropyrimidine dehydrogenase [Escherichia sp. 3_2_53FAA]
 gi|26108933|gb|AAN81136.1|AE016763_95 Hypothetical protein yeiA [Escherichia coli CFT073]
 gi|91073007|gb|ABE07888.1| hypothetical protein YeiA [Escherichia coli UTI89]
 gi|226900978|gb|EEH87237.1| dihydropyrimidine dehydrogenase [Escherichia sp. 3_2_53FAA]
          Length = 413

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 95  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 152

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 153 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 206

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 207 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 266

Query: 200 MSQALKIL 207
              A + L
Sbjct: 267 WEDAAEFL 274


>gi|313837183|gb|EFS74897.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL037PA2]
 gi|314927797|gb|EFS91628.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL044PA1]
 gi|314971955|gb|EFT16053.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL037PA3]
 gi|328907261|gb|EGG27027.1| dihydroorotate dehydrogenase 1B [Propionibacterium sp. P08]
          Length = 307

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 32/197 (16%), Positives = 70/197 (35%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTGDYVRVCEVISTAPNVAALEINISCP--NVKRGGMTFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
           N  +  D   A+  A S+PV VK    V D      +  + +++  +G +G+        
Sbjct: 145 NATVAHDLTQAVVSAASVPVYVKLSPNVTD------ITEIARAVTDAGADGLTLINTLTG 198

Query: 153 ----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
               +  R  +L           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINVARRAPVLANATGGLSGPAVLPIAVRMIDAVTRAV-DIPVIGMGGVTTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|292656600|ref|YP_003536497.1| dihydropyrimidine dehydrogenase [Haloferax volcanii DS2]
 gi|291370175|gb|ADE02402.1| dihydropyrimidine dehydrogenase [Haloferax volcanii DS2]
          Length = 263

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 77/229 (33%), Gaps = 27/229 (11%)

Query: 24  TEMIVADA--ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           +E +  D    +     ++  F  +++ +A+ +       +   A +  D G   + +N 
Sbjct: 54  SEFLADDPVGFVAAQLDSLDEFGGEDRFVAVNVRATSPDPIRAVAAVCADRGA-GVEINA 112

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            C    +     G  L+ + D +   +AA  +     V  K R  +D     V   NL  
Sbjct: 113 HCRQDELCAVGCGETLLRDSDRLAAYVAAAAE-SGASVGAKVRAEIDG----VDHPNLAA 167

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           ++  +G + + + A  +                            PDLF+  N G+    
Sbjct: 168 TLADAGADWLHVDAMDSEAVIADVAA-----------------AAPDLFLVANNGVRGRE 210

Query: 202 QALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
            A + L    D V +GR +  N  +L  V     +   G        D+
Sbjct: 211 TATEYLDYGADAVSVGRPS-DNPRVLRRVRTAVDDWFAGREDAAESGDE 258


>gi|2415547|emb|CAA04299.1| NifR3-like protein [Campylobacter jejuni]
          Length = 81

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 16/95 (16%)

Query: 189 LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           + +  NG + +   A ++      DG+MIGRA+  N  +   +                 
Sbjct: 1   IPVIANGDI-NAQNAKEVYKITKCDGLMIGRASVGNPWIFYEIK------------SGKS 47

Query: 247 VDKDFWRKISASMTDYAARHLHSGGKLQQITRHMI 281
           V +   ++I  +  D   +H +    +    +H+ 
Sbjct: 48  VYEKLKKEIILTHFDEMIKH-YKDQGVSIFRKHLH 81


>gi|198274664|ref|ZP_03207196.1| hypothetical protein BACPLE_00820 [Bacteroides plebeius DSM 17135]
 gi|198272111|gb|EDY96380.1| hypothetical protein BACPLE_00820 [Bacteroides plebeius DSM 17135]
          Length = 303

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 76/192 (39%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +    E A I+ +      I LN+ CP   V +G     +  +     +
Sbjct: 94  TNMIVNVSGSQVEDYAETASIINELENIPAIELNISCP--NVKQGGMAFGVTAHG--AAE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++A+ K     + VK    V D      +  + ++++ +G +            I    
Sbjct: 150 VVSAVRKVYKKTLIVKLSPNVTD------ITEIARAVEGAGADSVSLINTLLGMAIDAEK 203

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L     +
Sbjct: 204 RRPILSTVTGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMNWKDAVEFLLAGATAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAI 274


>gi|332028865|gb|EGI68891.1| Dihydropyrimidine dehydrogenase [Acromyrmex echinatior]
          Length = 1019

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 59/163 (36%), Gaps = 31/163 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK  E  G + + LN+ CP     E   G     +P++V +    + +A+ IP  VK   
Sbjct: 649 AKKAETAGSDGLELNLSCPHGM-GESGMGLACGQDPELVRNICRWVREAVKIPFFVKLTP 707

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW----------IHA-----------RKAILKGLS 164
            + D      + ++ K+  +   +G+           +HA           +     G+S
Sbjct: 708 NITD------ILSIAKAAYEGKADGVTAINTISGLMGLHADATPWPAVGLNKSTTYGGVS 761

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               R         +  I +  P   I   GG++    AL+ L
Sbjct: 762 GNATRPQA---LKAISIISRHLPGFPILGTGGVDSADVALQFL 801


>gi|313679855|ref|YP_004057594.1| dihydroorotate oxidase b, catalytic subunit [Oceanithermus
           profundus DSM 14977]
 gi|313152570|gb|ADR36421.1| dihydroorotate oxidase B, catalytic subunit [Oceanithermus
           profundus DSM 14977]
          Length = 301

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 75/203 (36%), Gaps = 30/203 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + + + G + +     A+ V  +  + I +N+ CP   VH G        +P+   + + 
Sbjct: 96  VIVNVFGDEAADFAHVARKVSPY-ADLIEVNLSCP--NVHGGRLPFA--HDPEAAAEVVR 150

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            +  A   PV  K         P   L  + + ++ +GV+G             +  R+ 
Sbjct: 151 RVKDATDRPVLAKL-------SPNGPLLPVAEVLEAAGVDGFSLINTLLGMRMDLERRRP 203

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           +L           +  +   +VYE+ +      +G+ GG+     AL+  L     V +G
Sbjct: 204 VLGNRQGGLSGPAVKPVAVRLVYELYRHTDRPILGM-GGIASAEDALEFALAGARLVAVG 262

Query: 217 RAAYKNSA----MLTTVDEYFSN 235
            A + +      +   ++ +F  
Sbjct: 263 TATFADPYAPLKIARGLEAFFQG 285


>gi|313897774|ref|ZP_07831315.1| dihydroorotate oxidase, catalytic subunit [Clostridium sp. HGF2]
 gi|312957309|gb|EFR38936.1| dihydroorotate oxidase, catalytic subunit [Clostridium sp. HGF2]
          Length = 302

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 35/191 (18%), Positives = 70/191 (36%), Gaps = 28/191 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
           +  F T+   +   + GA   + VE   K+ +        LN+ CP    +    G  L 
Sbjct: 88  LAQFDTE---IIANVAGASEEEYVEVITKLNKSEVVKAYELNISCP----NVKHGGIGLG 140

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------ 152
            +P +         +A   PV VK    V        +  + K+++++G +G+       
Sbjct: 141 TDPKLAASVTRMAKEAAEKPVYVKLSPNV------TNIVEIAKAVEEAGADGLVLINTLM 194

Query: 153 -----IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                +H  K +L  ++       I  +   +V+++     ++ I   GG+      L+ 
Sbjct: 195 GMRMDLHTGKPLLANVTGGLSGPAIKPVAVCMVHQVASAV-NIPIIGVGGITRAEDVLEF 253

Query: 207 L-PSVDGVMIG 216
           L      V +G
Sbjct: 254 LYAGASAVEVG 264


>gi|221272036|sp|A8XKG6|DPYD_CAEBR RecName: Full=Probable dihydropyrimidine dehydrogenase [NADP+];
           Short=DHPDHase; Short=DPD; AltName: Full=Dihydrothymine
           dehydrogenase; AltName: Full=Dihydrouracil dehydrogenase
 gi|309359452|emb|CAP33140.2| CBR-DPYD-1 protein [Caenorhabditis briggsae AF16]
          Length = 1053

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 64/209 (30%), Gaps = 45/209 (21%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGG----ADISKLV---EAAKIVEDFGYNE 76
           E+I   +          L      K +   I       D  +L    EAA      G + 
Sbjct: 635 ELISEKSCEYWLQCIRELKRDHPTKIVVASIMCVYNKEDWIELATKSEAA------GADI 688

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           + LN+ CP     E   G     +P+IV +    +   + IP   K    + D      +
Sbjct: 689 LELNLSCPHGM-GEKGMGLACGQSPEIVKEICRWVRACVKIPFFPKMTPNITD------V 741

Query: 137 RNLVKSIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLD 175
           R + ++ +  G +G+                       + ++    G+S    R I    
Sbjct: 742 REIARAARDGGASGVTATNTVSSLMHMKADGNAWPAIGNTKRTTYGGMSGSAIRPIAM-- 799

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
              V  I  E     I   GG+E     L
Sbjct: 800 -KAVSSIANELDGFPIMATGGIESAETGL 827


>gi|268579437|ref|XP_002644701.1| C. briggsae CBR-DPYD-1 protein [Caenorhabditis briggsae]
          Length = 1032

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 64/209 (30%), Gaps = 45/209 (21%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGG----ADISKLV---EAAKIVEDFGYNE 76
           E+I   +          L      K +   I       D  +L    EAA      G + 
Sbjct: 625 ELISEKSCEYWLQCIRELKRDHPTKIVVASIMCVYNKEDWIELATKSEAA------GADI 678

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           + LN+ CP     E   G     +P+IV +    +   + IP   K    + D      +
Sbjct: 679 LELNLSCPHGM-GEKGMGLACGQSPEIVKEICRWVRACVKIPFFPKMTPNITD------V 731

Query: 137 RNLVKSIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLD 175
           R + ++ +  G +G+                       + ++    G+S    R I    
Sbjct: 732 REIARAARDGGASGVTATNTVSSLMHMKADGNAWPAIGNTKRTTYGGMSGSAIRPIAM-- 789

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
              V  I  E     I   GG+E     L
Sbjct: 790 -KAVSSIANELDGFPIMATGGIESAETGL 817


>gi|329959981|ref|ZP_08298477.1| dihydroorotate dehydrogenase 1B [Bacteroides fluxus YIT 12057]
 gi|328533115|gb|EGF59884.1| dihydroorotate dehydrogenase 1B [Bacteroides fluxus YIT 12057]
          Length = 303

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 70/196 (35%), Gaps = 25/196 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I    E A I+ +      I LN+ CP   V +G     +   
Sbjct: 88  RIKDVQTNMIVNVSGSAIEDYAETAAIINELDKIPAIELNISCP--NVKQGGMAFGVTAK 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+       + VK    V D      +  + ++ +  G +           
Sbjct: 146 G--AEEVVKAVRSVYKKTLIVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL  +        +  +   +V+++ K      IGL GG+ D   A++ +L
Sbjct: 198 AIDAERRRPILSTVTGGMSGAAVKPIALRMVWQVAKAVKIPVIGL-GGIMDWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNS 223
                + IG A + + 
Sbjct: 257 AGASAIQIGTANFIDP 272


>gi|167772620|ref|ZP_02444673.1| hypothetical protein ANACOL_04001 [Anaerotruncus colihominis DSM
           17241]
 gi|167665098|gb|EDS09228.1| hypothetical protein ANACOL_04001 [Anaerotruncus colihominis DSM
           17241]
          Length = 371

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 44/218 (20%), Positives = 79/218 (36%), Gaps = 36/218 (16%)

Query: 14  RLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG 73
           RL  +   L+  M+ +   L   ++ I     ++  L   + GA  S+    AK VE  G
Sbjct: 57  RLYQHGGSLFNTMLYSTIDLEQWEQEIKRIDKRDSILICSVWGATESETAYIAKKVERLG 116

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + I L++  P        FG     + + +G  + A+ +A+ +PV VK          A
Sbjct: 117 ADAIELSISAPIGT-RSTRFG----RSQEQIGGYVRAVVEAVDLPVMVKL------SYDA 165

Query: 134 VALRNLVKSIKKSGVNGI-------------WIHARK--AILKGLSPKDNRKIPNLDYDI 178
            A    V +++++G   I               H         G S  + R +       
Sbjct: 166 SANVAFVHAVEQAGAQAISAIDSLKGLAGVDIEHGMPLMPTCGGYSGANLRPVALATTAT 225

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
           + ++ +      I   GG+E     L+       VM+G
Sbjct: 226 LAQLTR----CEICGIGGIESYEHVLEY------VMLG 253


>gi|299538616|ref|ZP_07051899.1| dihydropyrimidine dehydrogenase [Lysinibacillus fusiformis ZC1]
 gi|298726203|gb|EFI66795.1| dihydropyrimidine dehydrogenase [Lysinibacillus fusiformis ZC1]
          Length = 420

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +A   PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEAARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       +P           
Sbjct: 175 TPNITDITVT------AEAATRGGADAVSMINTINSLAGVDLDSWNTVPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +   A + IL    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARNPLVNVPISGIGGISNWQDAAEFILMGATGVQVCTAAMH 285


>gi|146320868|ref|YP_001200579.1| dihydroorotate dehydrogenase 1B [Streptococcus suis 98HAH33]
 gi|253751780|ref|YP_003024921.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus suis
           SC84]
 gi|253753604|ref|YP_003026745.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus suis
           P1/7]
 gi|253755515|ref|YP_003028655.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus suis
           BM407]
 gi|145691674|gb|ABP92179.1| putative dihydroorotate dehydrogenase B [Streptococcus suis
           98HAH33]
 gi|251816069|emb|CAZ51689.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus suis
           SC84]
 gi|251817979|emb|CAZ55761.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus suis
           BM407]
 gi|251819850|emb|CAR45844.1| dihydroorotate dehydrogenase, catalytic subunit [Streptococcus suis
           P1/7]
 gi|292558348|gb|ADE31349.1| putative dihydroorotate dehydrogenase B [Streptococcus suis GZ1]
 gi|319758129|gb|ADV70071.1| dihydroorotate dehydrogenase 1B [Streptococcus suis JS14]
          Length = 313

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 27/243 (11%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE----MIVADAILRGDKKNIL-------GFSTQEKP 49
           M+  T RH R       N      E    M+ A  +     + +L            + P
Sbjct: 44  MIKATTRHPR-----YGNATPRVAETPAGMLNAIGLQNPGVEAVLSEKLPWLEQHFPDLP 98

Query: 50  LALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           +   + G    +    + KI +      I LN+ CP   V  G+ G  +   P++    +
Sbjct: 99  IIANVAGFSNEEYAYVSGKISKAPNVKAIELNISCP--NVDHGNNGLLIGQVPELAYQAV 156

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAIL-KG 162
            A  +A S+PV VK    V D            +   + +N +      +  R+ IL  G
Sbjct: 157 KAAVEASSVPVYVKLTPSVADITLLAKAAEAAGATGLTMINTLVGMRFNLKTRQPILANG 216

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYK 221
                   +  +   ++ ++ +   DL I   GG++   +A++++      + +G A + 
Sbjct: 217 TGGMSGPAVFPVALKLIRQVAQ-MTDLPIIGMGGVDTADKAIEMMVAGASAIGVGTANFT 275

Query: 222 NSA 224
           +  
Sbjct: 276 DPF 278


>gi|307311274|ref|ZP_07590918.1| dihydroorotate dehydrogenase family protein [Escherichia coli W]
 gi|306908780|gb|EFN39277.1| dihydroorotate dehydrogenase family protein [Escherichia coli W]
 gi|315061456|gb|ADT75783.1| dihydropyrimidine dehydrogenase, NADH-dependent, subunit B
           [Escherichia coli W]
 gi|323377963|gb|ADX50231.1| dihydroorotate dehydrogenase family protein [Escherichia coli KO11]
          Length = 411

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|148264205|ref|YP_001230911.1| dihydroorotate dehydrogenase 1B [Geobacter uraniireducens Rf4]
 gi|189038422|sp|A5G3H0|PYRD_GEOUR RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|146397705|gb|ABQ26338.1| dihydroorotate oxidase B, catalytic subunit [Geobacter
           uraniireducens Rf4]
          Length = 305

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/204 (13%), Positives = 74/204 (36%), Gaps = 25/204 (12%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ + + G  + +  E A+ ++       + +N+ CP    +    G     +P+   +
Sbjct: 96  TPVIVNLYGNTLEEYGELAEKLDKLPEVAGLEVNISCP----NVKQGGIVFGTDPNAAYE 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            ++ + ++   P+ VK    V        +  +  +   +G + + +             
Sbjct: 152 VVSLVRESTIKPLIVKLSPNV------TNVVEMANACVDAGADALSLINTLTGMAIDLQK 205

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           I  +   +V+++ +    + +   GG+   + AL+ +L     V
Sbjct: 206 RRPILANMTGGLSGPAIKPVALRMVWQVAQAV-KVPVIGIGGIMTATDALEFMLAGATAV 264

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPL 237
            +G A + + +   T+ E     L
Sbjct: 265 QVGTANFLDPSAAQTIAEGMETYL 288


>gi|195168436|ref|XP_002025037.1| GL26798 [Drosophila persimilis]
 gi|194108482|gb|EDW30525.1| GL26798 [Drosophila persimilis]
          Length = 393

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 33/159 (20%), Positives = 53/159 (33%), Gaps = 25/159 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
             E  G + + LN+ CP     E   G      PD+V      +  A+ +P  +K    +
Sbjct: 15  KAEASGADALELNLSCPHGM-GERGMGLACGQIPDMVEQISRWVRNAVKLPFFIKLTPNI 73

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI------------------WIHARKAILKGLSPKDNR 169
            D     A+    K     G + I                      ++    G+S    R
Sbjct: 74  TD---ITAIAKAAKLGGADGCSAINTVQGLMGLKADATAWPAVGEEKRTTYGGVSGNATR 130

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
               +    + EI K+ PD  I   GG++    AL+ L 
Sbjct: 131 ---PMALRAISEIAKKIPDFPILGIGGIDSGEVALQFLQ 166


>gi|308178912|ref|YP_003918318.1| dihydroorotate oxidase catalytic subunit [Arthrobacter arilaitensis
           Re117]
 gi|307746375|emb|CBT77347.1| putative dihydroorotate oxidase catalytic subunit [Arthrobacter
           arilaitensis Re117]
          Length = 329

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 68/197 (34%), Gaps = 24/197 (12%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
               + + IGG    +    A+ +     +   +NV CP+        G  +  +PD V 
Sbjct: 111 SGTRVVVSIGGLFTQEYFTVAEELGQEDVDAFEVNVSCPNLE----HDGLPIGTSPDRVF 166

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH----------- 154
           + I  + K    P+ VK    V+       +  + K+ + +G   + +            
Sbjct: 167 EVIQGIRKHTDHPLFVKLTPTVNS------IGEIAKAAEDAGATAVTVANSFSGLAIDAP 220

Query: 155 ARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDG 212
            RK++L  G        +  L   +V +  +    + +   GG+      A  ++     
Sbjct: 221 RRKSVLGSGAGGYTGPAVKPLALKLVRDAAQAVT-IPVIGCGGITTSRDVAEFMIAGATA 279

Query: 213 VMIGRAAYKNSAMLTTV 229
           + +G A +     +  +
Sbjct: 280 IQVGTATFTRPTAMGEI 296


>gi|281426104|ref|ZP_06257017.1| dihydroorotate oxidase [Prevotella oris F0302]
 gi|281399680|gb|EFB30511.1| dihydroorotate oxidase [Prevotella oris F0302]
          Length = 301

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 73/208 (35%), Gaps = 25/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G         A+ +++      I LN+ CP   V EG     +    +   
Sbjct: 93  DTNMIVNVSGNSAESYAACAQRIDELDRIPAIELNISCP--NVKEGGMAFGVTC--EGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
             + A+       + VK    V D      +  + ++ +  G + +            I 
Sbjct: 149 SIVKAVRAVYHKTLIVKLSPNVTD------IAAIARACEAEGADAVSLINTLMGMAVDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L   +       +  +   +VY++        +GL GG+     A++ ++     
Sbjct: 203 KRQPLLSIRTGGLSGPAVKPVALRMVYDVAHAVKIPVVGL-GGISSAEDAIEFLMCGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + IG A + + A+   V +  +  L   
Sbjct: 262 IEIGTANFVDPAITKKVKDGINTWLDAH 289


>gi|222033908|emb|CAP76649.1| Uncharacterized protein yeiA [Escherichia coli LF82]
 gi|312946768|gb|ADR27595.1| dihydropyrimidine dehydrogenase [Escherichia coli O83:H1 str. NRG
           857C]
 gi|324006546|gb|EGB75765.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 57-2]
          Length = 411

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELHDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|209919605|ref|YP_002293689.1| dihydropyrimidine dehydrogenase [Escherichia coli SE11]
 gi|256017685|ref|ZP_05431550.1| dihydropyrimidine dehydrogenase [Shigella sp. D9]
 gi|260856120|ref|YP_003230011.1| putative oxidoreductase [Escherichia coli O26:H11 str. 11368]
 gi|260868849|ref|YP_003235251.1| putative oxidoreductase [Escherichia coli O111:H- str. 11128]
 gi|300822593|ref|ZP_07102731.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 119-7]
 gi|300902204|ref|ZP_07120204.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 84-1]
 gi|301306535|ref|ZP_07212599.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 124-1]
 gi|309793025|ref|ZP_07687453.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 145-7]
 gi|331668846|ref|ZP_08369694.1| putative oxidoreductase [Escherichia coli TA271]
 gi|331678095|ref|ZP_08378770.1| putative oxidoreductase [Escherichia coli H591]
 gi|209912864|dbj|BAG77938.1| putative dihydropyrimidine dehydrogenase [Escherichia coli SE11]
 gi|257754769|dbj|BAI26271.1| predicted oxidoreductase [Escherichia coli O26:H11 str. 11368]
 gi|257765205|dbj|BAI36700.1| predicted oxidoreductase [Escherichia coli O111:H- str. 11128]
 gi|300405723|gb|EFJ89261.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 84-1]
 gi|300524793|gb|EFK45862.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 119-7]
 gi|300838236|gb|EFK65996.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 124-1]
 gi|308123311|gb|EFO60573.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 145-7]
 gi|315255341|gb|EFU35309.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 85-1]
 gi|323152183|gb|EFZ38473.1| hypothetical protein ECEPECA14_5793 [Escherichia coli EPECa14]
 gi|323176957|gb|EFZ62547.1| hypothetical protein ECOK1180_4323 [Escherichia coli 1180]
 gi|323944963|gb|EGB41028.1| dihydroorotate dehydrogenase [Escherichia coli H120]
 gi|324020615|gb|EGB89834.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 117-3]
 gi|331064040|gb|EGI35951.1| putative oxidoreductase [Escherichia coli TA271]
 gi|331074555|gb|EGI45875.1| putative oxidoreductase [Escherichia coli H591]
          Length = 411

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|323184230|gb|EFZ69607.1| hypothetical protein ECOK1357_2501 [Escherichia coli 1357]
          Length = 411

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|289824092|ref|ZP_06543689.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
          Length = 100

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 16/103 (15%), Positives = 26/103 (25%), Gaps = 6/103 (5%)

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           MIGRAA     +   +  Y              V +     +      Y       G ++
Sbjct: 1   MIGRAAQGRPWIFREIQHYLDTGELLPPLPLAEVKRLLCTHVRELHDFYGQ---AKGYRI 57

Query: 274 QQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFN 316
               +H+           + R        AS      +E  F 
Sbjct: 58  --ARKHVSWYLQEHAPDDQFRRTFNAIEDASE-QLEALEAYFE 97


>gi|332278699|ref|ZP_08391112.1| dihydropyrimidine dehydrogenase [Shigella sp. D9]
 gi|332101051|gb|EGJ04397.1| dihydropyrimidine dehydrogenase [Shigella sp. D9]
          Length = 413

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 95  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 152

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 153 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 206

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 207 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 266

Query: 200 MSQALKIL 207
              A + L
Sbjct: 267 WEDAAEFL 274


>gi|242279625|ref|YP_002991754.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           salexigens DSM 2638]
 gi|259547492|sp|C6BW12|PYRD_DESAD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|242122519|gb|ACS80215.1| dihydroorotate dehydrogenase family protein [Desulfovibrio
           salexigens DSM 2638]
          Length = 305

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 34/190 (17%), Positives = 62/190 (32%), Gaps = 26/190 (13%)

Query: 49  PLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   +   D  +  E A  +  + G   + +NV CP    +    G     +P  +   
Sbjct: 94  PVLANLYATDAEEFGELAGVLAGEEGVAALEVNVSCP----NVKEGGIAFGQDPKQITKV 149

Query: 108 IAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHA 155
             A+ K A + P+ +K    V D           K+ +  G + +            I  
Sbjct: 150 AEAVKKNAGNKPIIIKLSPNVTDITV------CAKAAEDGGADALSLINTLSGMAVDIER 203

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R   L  +        +  +    VY+         +GL GG+     A + +L     V
Sbjct: 204 RTPRLANVIGGLSGPAVKPVALRCVYQTVNAVKIPVMGL-GGITTAEDAAEFLLVGAKAV 262

Query: 214 MIGRAAYKNS 223
            IG   + + 
Sbjct: 263 QIGTGNFLSP 272


>gi|225570535|ref|ZP_03779560.1| hypothetical protein CLOHYLEM_06637 [Clostridium hylemonae DSM
           15053]
 gi|225160732|gb|EEG73351.1| hypothetical protein CLOHYLEM_06637 [Clostridium hylemonae DSM
           15053]
          Length = 672

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 42/199 (21%), Positives = 76/199 (38%), Gaps = 24/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGS------------FGACLMLNPDIVGDCI 108
           +   AA+ V++ G   I+L   C  A +  G+            +G CL      + + I
Sbjct: 160 QFGAAARRVQEAGCGGISL--HCAHAYMLPGAFLSPLRNKRMDEYGGCLDNRARFILEVI 217

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI--LKG 162
             + K +S    V  RI  D++            L    + +GV+ + +        L+ 
Sbjct: 218 EEVRKNVSADFPVFLRISGDERAEGGNSLEDMLYLAPKFEAAGVDLLEVSGGTQYEGLEY 277

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + P   ++I    Y+   EIKK    + +   G + D+  A  I+    VDGV +GR   
Sbjct: 278 IIPSQGKRIGMNIYEA-AEIKK-VVGIPVYAVGKINDIRYAADIVERGIVDGVAVGRPLL 335

Query: 221 KNSAMLTTVDEYFSNPLTG 239
            +  +     E   + +T 
Sbjct: 336 ADPDLCKKAKENRFDDITP 354


>gi|169827564|ref|YP_001697722.1| dihydropyrimidine dehydrogenase [Lysinibacillus sphaericus C3-41]
 gi|168992052|gb|ACA39592.1| dihydropyrimidine dehydrogenase [Lysinibacillus sphaericus C3-41]
          Length = 420

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +A   PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEAARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       +P           
Sbjct: 175 TPNITDITVT------AEAATRGGADAVSMINTINSLAGVDLDTWNTVPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +   A + IL    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARNPLVNVPISGIGGISNWQDAAEFILMGATGVQVCTAAMH 285


>gi|307201146|gb|EFN81057.1| Dihydropyrimidine dehydrogenase [NADP+] [Harpegnathos saltator]
          Length = 962

 Score = 65.6 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 69/188 (36%), Gaps = 21/188 (11%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+  E  G + + LN+ CP     E   G     + ++V +    + +A+ IP  VK   
Sbjct: 616 ARKAEVAGSDALELNLSCPHGM-GESGMGLACGQDSELVRNISRWVREAIKIPFFVKLTP 674

Query: 126 GVD--------------DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +               D + A+     +  ++ +G+    + ++     G+S    R  
Sbjct: 675 NITDIVSIAKAAYEGKADGVSAINTVQGLMGLRSTGIPWPAVDSKFTTYGGVSGNATRPQ 734

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVD 230
                  V  I K+ P   I   GG++    AL+ L      + IG A        T +D
Sbjct: 735 A---LRAVSTISKQLPGFSILGIGGIDSADVALQFLHCGASVIQIGSAIQNQ--DFTLID 789

Query: 231 EYFSNPLT 238
           +Y +   T
Sbjct: 790 DYVTGLKT 797


>gi|160946725|ref|ZP_02093928.1| hypothetical protein PEPMIC_00683 [Parvimonas micra ATCC 33270]
 gi|158447109|gb|EDP24104.1| hypothetical protein PEPMIC_00683 [Parvimonas micra ATCC 33270]
          Length = 298

 Score = 65.6 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 77/201 (38%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   IGG+ +   +++ +++       I LN+ CP   V  G     +    DI   
Sbjct: 91  DTQILANIGGSQLEDYLKSVELINKTNIKIIELNISCP--NVKSGGMAFGI--KCDIAEG 146

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            +  + +     + VK          A  ++ + K+  ++G +            I I+ 
Sbjct: 147 IVRKVRENTDKVLMVKLSP------NAENIKEMAKTCVEAGADCLSLVNTFNALAIDIYN 200

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RKA+   + +      I  +   +V ++     D+ I   GG+ +   A++ I+     +
Sbjct: 201 RKAVFDNVTAGLSGACIKPIALRMVRDVA-SVVDVPIIGMGGIMNWQDAIEFIMAGSTAI 259

Query: 214 MIGRAAYKNSAMLTTVDEYFS 234
            +G A + N  ++  + E   
Sbjct: 260 QVGTANFINPRVMIDIIEGME 280


>gi|251798657|ref|YP_003013388.1| dihydropyrimidine dehydrogenase [Paenibacillus sp. JDR-2]
 gi|247546283|gb|ACT03302.1| dihydroorotate dehydrogenase family protein [Paenibacillus sp.
           JDR-2]
          Length = 434

 Score = 65.6 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE  G + + LN GCP     E   G+     PD+V        +A   PV VK 
Sbjct: 116 EIVKKVEAVGVDGLELNFGCPHGMA-ERGMGSASGQQPDLVEAQTMWAKEAAKTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    K+  + G + I +      L G+       IP           
Sbjct: 175 TPNITD------ITATAKAAVRGGADAISLINTINSLAGVDLDTWNTIPHVGGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKK-ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +   A++ +L    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARNAQVNVPISGIGGVSNWRDAVEFMLMGATGVQVCTAAMH 285


>gi|15643101|ref|NP_228144.1| dihydroorotate dehydrogenase [Thermotoga maritima MSB8]
 gi|148269723|ref|YP_001244183.1| dihydroorotate dehydrogenase family protein [Thermotoga petrophila
           RKU-1]
 gi|9297058|sp|Q9WYG8|PYRD_THEMA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|166215966|sp|A5IK84|PYRD_THEP1 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|4980834|gb|AAD35420.1|AE001714_11 dihydroorotate dehydrogenase [Thermotoga maritima MSB8]
 gi|147735267|gb|ABQ46607.1| dihydroorotate oxidase B, catalytic subunit [Thermotoga petrophila
           RKU-1]
          Length = 270

 Score = 65.6 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 77/195 (39%), Gaps = 20/195 (10%)

Query: 49  PLALQIGGADISKLVEAA---KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           P+   +GG    + +E A   K V D  +  +  N  CP    +    G  ++ N +   
Sbjct: 81  PMIASLGGDSFEEYLEVARVFKKVADR-FYAVEFNFSCP----NVKEGGLSIVKNAEEWK 135

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG--- 162
             +  + K L         +     +  + + +  + + K+G +GI +      L     
Sbjct: 136 KLLNTLRKELP-----DSFLIAKVGVEGIFVEDAAEFVMKTGWDGITLVNTVRGLHFEKD 190

Query: 163 ---LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
              L       +  +    VYE+KK  P+LF+  +GG+  +  A + L    D + +G A
Sbjct: 191 TMILGGLSGPVLKPIALRAVYEVKKRFPELFVIASGGVYSVKDAEEFLKVGADVIGVGSA 250

Query: 219 AYKNSAMLTTVDEYF 233
            +K+  ++  + +Y 
Sbjct: 251 LFKDPGVVEEIGKYL 265


>gi|313114928|ref|ZP_07800425.1| dihydroorotate dehydrogenase 1B [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622750|gb|EFQ06208.1| dihydroorotate dehydrogenase 1B [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 308

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/168 (19%), Positives = 66/168 (39%), Gaps = 31/168 (18%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG    + VE A ++ D   + + LN+ CP+ +V   ++G       +  G+ +  +  
Sbjct: 104 LGGHSEEEYVEGAAMLSDSAVDIVELNISCPNVKVGGMAYGV----KAEAAGEVVRMVRA 159

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILK- 161
           A   P+ VK          A  +  + K+++ +G + I            +  R+ +   
Sbjct: 160 ACKKPLMVKLSPQ------AENIPEMCKAVEAAGADAISLTNTFQACAIDLEKRRPVFNN 213

Query: 162 ---GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
              GLS    R I   + +  V  +     ++ +   GG+     AL+
Sbjct: 214 IFAGLSGPAVRPIALRMVWQAVGAV-----NIPVVGLGGIATGRDALE 256


>gi|296160829|ref|ZP_06843642.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           Ch1-1]
 gi|295888921|gb|EFG68726.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           Ch1-1]
          Length = 312

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/197 (16%), Positives = 65/197 (32%), Gaps = 18/197 (9%)

Query: 49  PLALQIGGADISKL-VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL   I    +      AAK+        I  NV CP+ +    +FG     +     D 
Sbjct: 93  PLIASISADSVDDFGALAAKLAVPEIAA-IEANVSCPNLKADGKAFGM----DAQATHDV 147

Query: 108 IAAMCKALSIPVTVKCRIG--------VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + AM +   +PV  K               +        +  ++    ++      + A 
Sbjct: 148 VRAMRERSGLPVWAKMTPNAGNVVEVAKAAEEAGAEAIVMGNAMLAMAIDTETFRPKVAN 207

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRA 218
           L G      R    +   + Y+  +    + +   GG+   S A++ +L     V +G  
Sbjct: 208 LMGGIT--GRATKPVLLRMAYQCAQAV-KIPVIGCGGIASASDAIEYLLAGCTAVQVGTE 264

Query: 219 AYKNSAMLTTVDEYFSN 235
            + N  ++  + +  + 
Sbjct: 265 NFVNPGVMPAIIDELNG 281


>gi|325473434|gb|EGC76629.1| dihydroorotate dehydrogenase/oxidoreductase [Treponema denticola
           F0402]
          Length = 592

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 42/208 (20%), Positives = 76/208 (36%), Gaps = 38/208 (18%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           LR   K        +  L + +  ++    +   K  E+   +   LN  CP A      
Sbjct: 100 LRSSWKT-------DSILNISLSASNPEDFISLLKGFEEL-ADCFELNFSCPHA---SAG 148

Query: 93  FGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           FGA +  +P I    +  + KAL    +P+ VK    V+D      +  +  ++ ++G +
Sbjct: 149 FGASIGCDPAIASGYVKTIKKALPDCTVPIFVKLTPNVED------IGAIAAAVIEAGAD 202

Query: 150 GIW------------IHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIG 192
           GI              H+ K IL+    G        +     + + +I+K   + + I 
Sbjct: 203 GITAINTVGPKVYIEPHSGKPILQNKLGGKGGMSGAWVFPRALECIGQIRKAVGEGIPII 262

Query: 193 LNGGLED-MSQALKILPSVDGVMIGRAA 219
             GG+      A  +    D + IG A 
Sbjct: 263 GMGGVMTGAQAAELVRAGADIIGIGSAC 290


>gi|157364774|ref|YP_001471541.1| dihydroorotate dehydrogenase family protein [Thermotoga lettingae
           TMO]
 gi|157315378|gb|ABV34477.1| dihydroorotate dehydrogenase family protein [Thermotoga lettingae
           TMO]
          Length = 276

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 83/196 (42%), Gaps = 23/196 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDF--GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +     G D+ ++++ AK ++ F   +  I  N+ CP   V +G  G  L+ +   + + 
Sbjct: 88  VIASFSGDDVDQMLQIAKKIKPFEKKFIAIEFNLSCP--NVSKGGLG--LLSDIHGLDNL 143

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK- 166
           + ++ + L+  +  K        I  + +    + +KK G  G+ +      L  +  K 
Sbjct: 144 LLSIRRELNGFLIAKI------GIEGIFVEAAAEILKKCGWQGLSLINTIRSLYIIGKKI 197

Query: 167 -----DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRA 218
                    +  +    VYE+K    DL++   GG+   ED    +K     D V IG A
Sbjct: 198 IKGGLSGPVLKPVALRAVYEVKNRVSDLYVIGGGGIMNEEDADDFIK--AGADAVSIGTA 255

Query: 219 AYKNSAMLTTVDEYFS 234
            +K+  +++ + ++ S
Sbjct: 256 IFKDPKIVSKIAKHIS 271


>gi|157158894|ref|YP_001463498.1| dihydropyrimidine dehydrogenase [Escherichia coli E24377A]
 gi|191165356|ref|ZP_03027198.1| dihydroorotate dehydrogenase family protein [Escherichia coli B7A]
 gi|218554712|ref|YP_002387625.1| dihydropyrimidine dehydrogenase [Escherichia coli IAI1]
 gi|300819162|ref|ZP_07099364.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 107-1]
 gi|300926249|ref|ZP_07142052.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 182-1]
 gi|301328626|ref|ZP_07221687.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 78-1]
 gi|331653576|ref|ZP_08354577.1| putative oxidoreductase [Escherichia coli M718]
 gi|157080924|gb|ABV20632.1| dihydroorotate dehydrogenase family protein [Escherichia coli
           E24377A]
 gi|190904519|gb|EDV64226.1| dihydroorotate dehydrogenase family protein [Escherichia coli B7A]
 gi|218361480|emb|CAQ99069.1| putative oxidoreductase subunit [Escherichia coli IAI1]
 gi|300417678|gb|EFK00989.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 182-1]
 gi|300528315|gb|EFK49377.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 107-1]
 gi|300845018|gb|EFK72778.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 78-1]
 gi|320199742|gb|EFW74331.1| dihydropyrimidine dehydrogenase [Escherichia coli EC4100B]
 gi|331048425|gb|EGI20501.1| putative oxidoreductase [Escherichia coli M718]
          Length = 411

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELCDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|333016869|gb|EGK36193.1| hypothetical protein SFK227_2748 [Shigella flexneri K-227]
          Length = 367

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 49  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 106

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 107 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 160

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 161 SITNIDLNQKIGMPIVNGKSSISGYSGKVVKPIALRFIQQMRTHPELRDFPISGIGGIET 220

Query: 200 MSQALKIL 207
              A + L
Sbjct: 221 WEDAAEFL 228


>gi|333002866|gb|EGK22422.1| hypothetical protein SFK272_2909 [Shigella flexneri K-272]
          Length = 380

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 62  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 119

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 120 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 173

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 174 SITNIDLNQKIGMPIVNGKSSISGYSGKVVKPIALRFIQQMRTHPELRDFPISGIGGIET 233

Query: 200 MSQALKIL 207
              A + L
Sbjct: 234 WEDAAEFL 241


>gi|55376990|ref|YP_134840.1| dihydropyrimidine dehydrogenase [Haloarcula marismortui ATCC 43049]
 gi|55229715|gb|AAV45134.1| dihydropyrimidine dehydrogenase [Haloarcula marismortui ATCC 43049]
          Length = 248

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/170 (21%), Positives = 62/170 (36%), Gaps = 26/170 (15%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA + +      I +N  C    +     G  L+  PD +   + A        V+VK 
Sbjct: 93  RAAAVCQRHDA-IIEINAHCRQDEMCAAGAGESLLREPDRLAAFVEAAAS-TGATVSVKG 150

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R  +D     V+L  + ++I+ +G +   + A                   D + V    
Sbjct: 151 RAELDG----VSLPAVAQAIEDAGGDVFHVDAM------------------DSESVIADV 188

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
            +  DLF+  N G+   +   + L    D V +GRA+      L TV E 
Sbjct: 189 ADATDLFVVANNGVRGTATTREYLSYGADAVSVGRAS-DKPETLDTVREA 237


>gi|291456747|ref|ZP_06596137.1| dihydroorotate oxidase [Bifidobacterium breve DSM 20213]
 gi|291382024|gb|EFE89542.1| dihydroorotate oxidase [Bifidobacterium breve DSM 20213]
          Length = 328

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/206 (15%), Positives = 68/206 (33%), Gaps = 23/206 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            I     +++         +   + G       E  + + D   + + +NV CP    + 
Sbjct: 102 GIDHYLAEDLPKLKAAGAFVISNVAGHCDDDYAEVVEKLADSDADMLEINVSCP----NV 157

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G  +  +P  + + +  +      P+ VK    V D           ++  + G + 
Sbjct: 158 SAGGMSVGADPVALANLMDRLRPLTDKPMIVKLTPNVTDITVP------ARAAVEHGADA 211

Query: 151 IWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +            +    I           +  +    VY  +   PD+ I   GG++
Sbjct: 212 LSMINTLKGMRINIRNGEPIIANVTGGVSGPAVLPIGLAAVYHTRTVLPDIPIIGLGGID 271

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNS 223
              +AL+ L    + V +G AA  + 
Sbjct: 272 SGEKALEYLYAGANAVEVGAAALFDP 297


>gi|94264825|ref|ZP_01288601.1| Dihydroorotate dehydrogenase 1 [delta proteobacterium MLMS-1]
 gi|93454706|gb|EAT04967.1| Dihydroorotate dehydrogenase 1 [delta proteobacterium MLMS-1]
          Length = 327

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 80/209 (38%), Gaps = 29/209 (13%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  + +  E A+ ++   G   + +N+ CP    +    G     +P +     
Sbjct: 120 VVVNILGNSVEEYRELAQRLDGVAGLGALEVNISCP----NVKEGGVAFGTDPRMAARVT 175

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLS 164
            A+ +A  +P+ +K    V D      +  + ++  + G + +     +      L+   
Sbjct: 176 QAVREASGLPLIIKLSPNVSD------IATMARAAAEHGADAVSLINTLLGMAIDLENRR 229

Query: 165 PK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
           PK            I  +   +V+++   +  + +   GG+ + + AL+ I+     + +
Sbjct: 230 PKLTNVVGGLSGPAIKPVALRMVWQVAG-SVKIPVIGIGGIMNATDALEFIVAGASAIQV 288

Query: 216 GRAAYKNS----AMLTTVDEYFSNPLTGS 240
           G A          ++  + +Y ++   GS
Sbjct: 289 GTANLIRPRATAEIINGIQDYLTSRQMGS 317


>gi|320120535|gb|EFE28865.2| dihydroorotate oxidase [Filifactor alocis ATCC 35896]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 42/178 (23%), Positives = 70/178 (39%), Gaps = 28/178 (15%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV 134
           + I LN+ CP+ +    +FG   M   D          K  SIP+ VK          A 
Sbjct: 124 DIIELNISCPNVKAGGMAFG---MNACD-AEYITKEAKKITSIPLVVKLSP------NAH 173

Query: 135 ALRNLVKSIKKSGVNG-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEI 182
            L  + ++++ +G +G           I IH RKA+   + +      I  +   +V E+
Sbjct: 174 HLVEVAQAVESAGADGLSLVNTFNALEIDIHRRKAVFDNVTAGLSGPAIRPIALRMVREV 233

Query: 183 KKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSN 235
            K      IG+ GG+E     +K I+     V  G A++ N      ++  V+ Y   
Sbjct: 234 SKAVSIPVIGM-GGVETWEDVIKFIMAGAHLVQFGTASFINPMAGLELVEGVERYMEE 290


>gi|167763096|ref|ZP_02435223.1| hypothetical protein BACSTE_01463 [Bacteroides stercoris ATCC
           43183]
 gi|167699436|gb|EDS16015.1| hypothetical protein BACSTE_01463 [Bacteroides stercoris ATCC
           43183]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 70/192 (36%), Gaps = 28/192 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  AA I E      I LN+ CP   V +G     +        + + A+       +
Sbjct: 107 DYMETAAIINELVNIPAIELNISCP--NVKQGGMAFGVTAKG--AEEVVKAVRSVYKKTL 162

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKGL-SPKD 167
            VK    V D      +  + ++ +  G +            +    R+ IL  +     
Sbjct: 163 IVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGMAVDAERRRPILSTVTGGMS 216

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAM- 225
              +  +   +V+++ K      IGL GG+ +   A++ +L     + IG A + + A+ 
Sbjct: 217 GAAVKPIALRMVWQVAKAVKIPVIGL-GGIMNWKDAVEFMLAGASAIQIGTANFIDPAIT 275

Query: 226 ---LTTVDEYFS 234
                 +D+Y +
Sbjct: 276 VKVAEGIDDYLN 287


>gi|209766284|gb|ACI81454.1| putative oxidoreductase [Escherichia coli]
          Length = 413

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 73/188 (38%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 95  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 152

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V      + +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 153 QSPELVEKYCRTVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 206

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 207 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 266

Query: 200 MSQALKIL 207
              A + L
Sbjct: 267 WEDAAEFL 274


>gi|26554241|ref|NP_758175.1| dihydroorotate dehydrogenase 1B [Mycoplasma penetrans HF-2]
 gi|81846193|sp|Q8EUY2|PYRD_MYCPE RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|26454250|dbj|BAC44579.1| dihydroorotate dehydrogenase [Mycoplasma penetrans HF-2]
          Length = 306

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/222 (16%), Positives = 83/222 (37%), Gaps = 28/222 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV 88
           D I+  + K +  +     P+   + G DI   V  AK + +      + LN+ CP    
Sbjct: 82  DHIINHELKELEKYD---VPIIANVAGDDIDDYVYVAKRISQAKNVVALELNISCP---- 134

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +  + G     + ++  +    + K  S PV VK    V D      +  + K+I+++  
Sbjct: 135 NVKNGGIQFGTDCNVAYNLTKKVKKVSSKPVYVKLSPNVSD------IVGMAKAIEEAKA 188

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              +  +           I  +   ++Y++ +   ++ I   GG
Sbjct: 189 DGLSLINTLIGMALDPKSGKPILANKTGGLSGPAIKPVAIRMIYQVSQAV-NIPIIGMGG 247

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + ++   +  +      V IG A + N  +   + +   + L
Sbjct: 248 ISNVQDVIDFISAGASAVAIGTANFINPYICVEIIDQLESKL 289


>gi|160889580|ref|ZP_02070583.1| hypothetical protein BACUNI_02006 [Bacteroides uniformis ATCC 8492]
 gi|317480071|ref|ZP_07939182.1| dihydroorotate dehydrogenase [Bacteroides sp. 4_1_36]
 gi|156861097|gb|EDO54528.1| hypothetical protein BACUNI_02006 [Bacteroides uniformis ATCC 8492]
 gi|316903748|gb|EFV25591.1| dihydroorotate dehydrogenase [Bacteroides sp. 4_1_36]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 72/198 (36%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I    E A I+ +      I LN+ CP   V +G     +   
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYAETAAIINELDKIPAIELNISCP--NVKQGGMAFGVTAK 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+       + VK    V D      +  + ++ +  G +           
Sbjct: 146 G--AEEVVKAVRSVYKKTLIVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERRRPILSTVTGGMSGAAVKPIALRMVWQVAKAVKIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGASAIQIGTANFIDPAV 274


>gi|222055868|ref|YP_002538230.1| dihydroorotate dehydrogenase family protein [Geobacter sp. FRC-32]
 gi|254788889|sp|B9M211|PYRD_GEOSF RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|221565157|gb|ACM21129.1| dihydroorotate dehydrogenase family protein [Geobacter sp. FRC-32]
          Length = 305

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/206 (13%), Positives = 78/206 (37%), Gaps = 29/206 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+ + + G  + +  E A+ ++       + +N+ CP    +    G     +P+   
Sbjct: 95  DTPVIVNLYGNTLEEYGELAEKLDRLPEVAGLEVNISCP----NVKQGGIVFGTDPNAAA 150

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           + +  + ++ S P+ +K    V D      +  +  +   +G + + +            
Sbjct: 151 EVVGLVRRSTSKPLIIKLSPNVTD------VVRMADACVNAGADALSLINTLTGMAIDLQ 204

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             R  +           I  +   +V+++ +    + I   GG+   + AL+ +L     
Sbjct: 205 KRRPILANITGGLSGPAIKPVALRMVWQVSQAM-AVPIIGIGGIMSATDALEFMLAGATA 263

Query: 213 VMIGRAAYKNSA----MLTTVDEYFS 234
           V +G A + + +    +   +++Y +
Sbjct: 264 VQVGTANFLDPSAAQTIAAGIEDYLA 289


>gi|218695758|ref|YP_002403425.1| dihydropyrimidine dehydrogenase [Escherichia coli 55989]
 gi|218352490|emb|CAU98267.1| putative oxidoreductase subunit [Escherichia coli 55989]
          Length = 401

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 83  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 140

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 141 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 194

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 195 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 254

Query: 200 MSQALKIL 207
              A + L
Sbjct: 255 WEDAAEFL 262


>gi|53713691|ref|YP_099683.1| dihydroorotate dehydrogenase 1B [Bacteroides fragilis YCH46]
 gi|60681963|ref|YP_212107.1| dihydroorotate dehydrogenase 1B [Bacteroides fragilis NCTC 9343]
 gi|253565639|ref|ZP_04843094.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_2_5]
 gi|81314972|sp|Q5LCI2|PYRD_BACFN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|81824996|sp|Q64TN0|PYRD_BACFR RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|52216556|dbj|BAD49149.1| dihydroorotate dehydrogenase [Bacteroides fragilis YCH46]
 gi|60493397|emb|CAH08183.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Bacteroides fragilis NCTC 9343]
 gi|251945918|gb|EES86325.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_2_5]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 81/211 (38%), Gaps = 29/211 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP    +    G    + 
Sbjct: 88  RIKDIQTHMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCP----NVKQGGMAFGVT 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
              V + + A+  A    + VK    V D      +  + ++ + +G +           
Sbjct: 144 TKGVSEVVQAVRSAYKKTLIVKLSPNVTD------IAEMARAAEANGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    ++ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERKRPILSTVTGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM----LTTVDEYFS 234
                + IG A + + A+    +  +++Y  
Sbjct: 257 AGASAIQIGTANFIDPAITIKVIDGINDYLE 287


>gi|301021088|ref|ZP_07185129.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 69-1]
 gi|331673675|ref|ZP_08374438.1| putative oxidoreductase [Escherichia coli TA280]
 gi|300398269|gb|EFJ81807.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 69-1]
 gi|331068948|gb|EGI40340.1| putative oxidoreductase [Escherichia coli TA280]
          Length = 411

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 73/191 (38%), Gaps = 33/191 (17%)

Query: 39  NILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
             L     +K L   I G +      L   A++V++ G + I  N  CP   +   + G+
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEDL---ARMVQEAGADMIECNFSCPQ--MTSHAMGS 147

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIH 154
            +  +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+
Sbjct: 148 DVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAIN 201

Query: 155 ARKAIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
             K+I                   +S    + +  +    + +++   E  D  I   GG
Sbjct: 202 TVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGG 261

Query: 197 LEDMSQALKIL 207
           +E    A + L
Sbjct: 262 IETWEDAAEFL 272


>gi|126179673|ref|YP_001047638.1| hypothetical protein Memar_1729 [Methanoculleus marisnigri JR1]
 gi|125862467|gb|ABN57656.1| conserved hypothetical protein [Methanoculleus marisnigri JR1]
          Length = 378

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 77/210 (36%), Gaps = 33/210 (15%)

Query: 30  DAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP 84
              L  D    LG         +  + + + G+  +   E A+  ED    EI+    C 
Sbjct: 68  KEFLYDDPLEALGREIDALKESDVVMGINLRGSTPASYAEVARAFEDAVVYEID--AHCR 125

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              + E   G  L+ NP  + + I A+ KA  + V+VK R GV           L +++ 
Sbjct: 126 QPAMLEAGCGEHLLRNPAKLAEIIRAL-KAEDVTVSVKIRAGVAADDAV-----LARTVW 179

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           K+G + + +                   +  ++ V +I+  +P L +  N  +    +A+
Sbjct: 180 KAGADILHVDLM----------------DFGHNKVRQIRNASP-LTLIANNSITTFDKAM 222

Query: 205 KILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
                  D V + R    ++  L  +D   
Sbjct: 223 DAFSHGADLVSLAR--QSDTWTLAGLDAAI 250


>gi|270296702|ref|ZP_06202901.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270272689|gb|EFA18552.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 72/198 (36%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I    E A I+ +      I LN+ CP   V +G     +   
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYAETAAIINELDKIPAIELNISCP--NVKQGGMAFGVTAK 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+       + VK    V D      +  + ++ +  G +           
Sbjct: 146 G--AEEVVKAVRSVYKKTLIVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERRRPILSTVTGGMSGAAVKPIALRMVWQVAKAVKIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGASAIQIGTANFIDPAV 274


>gi|323977659|gb|EGB72745.1| dihydroorotate dehydrogenase [Escherichia coli TW10509]
          Length = 411

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 73/191 (38%), Gaps = 33/191 (17%)

Query: 39  NILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
             L     +K L   I G +      L   A++V++ G + I  N  CP   +   + G+
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEDL---ARLVQEAGADMIECNFSCPQ--MTSHAMGS 147

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIH 154
            +  +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+
Sbjct: 148 DVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAIN 201

Query: 155 ARKAIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
             K+I                   +S    + +  +    + +++   E  D  I   GG
Sbjct: 202 TVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGG 261

Query: 197 LEDMSQALKIL 207
           +E    A + L
Sbjct: 262 IETWEDAAEFL 272


>gi|213161136|ref|ZP_03346846.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
          Length = 115

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 4/69 (5%)

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEY 232
           D+  + EI++    + +  NG + D   A   +     D VMIGR A  N   L+ V +Y
Sbjct: 1   DWQAIGEIRQRLT-IPVIANGEIWDWQSAQACMATSGCDAVMIGRGAL-NIPNLSRVVKY 58

Query: 233 FSNPLTGSS 241
               +    
Sbjct: 59  NEPRMPWPE 67


>gi|304315151|ref|YP_003850298.1| FMN-binding protein [Methanothermobacter marburgensis str. Marburg]
 gi|302588610|gb|ADL58985.1| predicted FMN-binding protein [Methanothermobacter marburgensis
           str. Marburg]
          Length = 242

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 55/148 (37%), Gaps = 16/148 (10%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
            + + +N  C    +     G  ++ +PD + D  + + K  +  V+VK R  V    P 
Sbjct: 94  VDIVEINAHCRQPEITSLGAGQAMLHDPDFLKDFTSEVVKGANAEVSVKIRGNV----PG 149

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           V   ++   +   GV  I + A K                 D ++V E+ +   +  +  
Sbjct: 150 VDTADIAGMLDDLGVGYIHLDAMKP-----------GEDRADLELVSEVSQSLRNAVMIG 198

Query: 194 NGGLEDMS-QALKILPSVDGVMIGRAAY 220
           N  + D    A  +    D V I RAA 
Sbjct: 199 NNSVRDPESAAAMLAAGADAVSIARAAI 226


>gi|295084201|emb|CBK65724.1| dihydroorotate oxidase B, catalytic subunit [Bacteroides
           xylanisolvens XB1A]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 76/198 (38%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------- 153
                + + A+  A    + VK    V D      +  + ++ ++SG + + +       
Sbjct: 144 AKGASEVVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 154 -----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
                  R  +           +  +   +V+++ K   ++ +   GG+ D   A++ +L
Sbjct: 198 AIDAERKRPILSTITGGMSGAAVKPIALRMVWQVAK-VVNIPVIGLGGIMDWRDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGATAIQIGTANFIDPAV 274


>gi|299145624|ref|ZP_07038692.1| dihydroorotate oxidase [Bacteroides sp. 3_1_23]
 gi|298516115|gb|EFI39996.1| dihydroorotate oxidase [Bacteroides sp. 3_1_23]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 76/198 (38%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------- 153
                + + A+  A    + VK    V D      +  + ++ ++SG + + +       
Sbjct: 144 AKGASEVVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 154 -----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
                  R  +           +  +   +V+++ K      IGL GG+ D   A++ +L
Sbjct: 198 AIDAERKRPILSTITGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMDWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGATAIQIGTANFIDPAV 274


>gi|119468602|ref|ZP_01611654.1| putative NADH-dependent flavin oxidoreductase [Alteromonadales
           bacterium TW-7]
 gi|119447658|gb|EAW28924.1| putative NADH-dependent flavin oxidoreductase [Alteromonadales
           bacterium TW-7]
          Length = 364

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 59/179 (32%), Gaps = 20/179 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK  ++ G + I L             P +   +  +G  L     IV +   A+
Sbjct: 159 DFASAAKRADELGLDLIELHGAHGYLLHQFLSPISNKRDDEYGGNLTNRMRIVLEVFKAV 218

Query: 112 CKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                ++ PV ++      V+          L K++ + G + I +        GLSP  
Sbjct: 219 RAEFSVNKPVGIRISATDWVEGGWDLEQSIALAKALDELGCDFIHVSTA-----GLSPLQ 273

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              +            K+  ++ +   G + +  QA  IL     D V + R    N  
Sbjct: 274 QIPVEPCFQVPFATAIKQAVNMPVIAVGLITEAQQAENILSEHKADAVALARGILYNPH 332


>gi|15605646|ref|NP_213021.1| dihydroorotase dehydrogenase [Aquifex aeolicus VF5]
 gi|3914513|sp|O66461|PYRD_AQUAE RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|2982802|gb|AAC06426.1| dihydroorotase dehydrogenase [Aquifex aeolicus VF5]
          Length = 306

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 70/194 (36%), Gaps = 29/194 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEI---NLNVGCPSARVHEGSFGACLMLNPDI 103
           +      + G    + VE    +ED   ++I    LNV CP   V +G        +P I
Sbjct: 92  DTHFIANVFGETEEEYVEVCMALED--ADKIVAYELNVSCP--NVKKGGILFG--HDPVI 145

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
           +G+ +  +   +  P+ VK    V D      +    K   ++G +G+ +          
Sbjct: 146 LGNLVDRIKAKIKKPLLVKLSPNVTD------VTEFAKVCIENGADGLVLINTLMGMKIN 199

Query: 154 --HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKI-LPS 209
               +  +           I  +   ++Y++ ++  D + I   GG+     A++  +  
Sbjct: 200 IWKRKPDLATKTGGLSGPAILPIAVRMIYQVYEKFGDRIPIIGVGGITTWEDAMEHVMAG 259

Query: 210 VDGVMIGRAAYKNS 223
              V +G A +   
Sbjct: 260 ASAVQVGTANFYEP 273


>gi|160884625|ref|ZP_02065628.1| hypothetical protein BACOVA_02614 [Bacteroides ovatus ATCC 8483]
 gi|237717567|ref|ZP_04548048.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_2_4]
 gi|293371584|ref|ZP_06617999.1| dihydroorotate dehydrogenase 1B [Bacteroides ovatus SD CMC 3f]
 gi|156110364|gb|EDO12109.1| hypothetical protein BACOVA_02614 [Bacteroides ovatus ATCC 8483]
 gi|229453153|gb|EEO58944.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_2_4]
 gi|292633447|gb|EFF52015.1| dihydroorotate dehydrogenase 1B [Bacteroides ovatus SD CMC 3f]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 76/198 (38%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------- 153
                + + A+  A    + VK    V D      +  + ++ ++SG + + +       
Sbjct: 144 AKGASEVVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 154 -----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
                  R  +           +  +   +V+++ K      IGL GG+ D   A++ +L
Sbjct: 198 AIDAERKRPILSTITGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMDWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGATAIQIGTANFIDPAV 274


>gi|260654638|ref|ZP_05860128.1| dihydroorotate oxidase [Jonquetella anthropi E3_33 E1]
 gi|260630654|gb|EEX48848.1| dihydroorotate oxidase [Jonquetella anthropi E3_33 E1]
          Length = 317

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 75/195 (38%), Gaps = 25/195 (12%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +D+ ++++A + V     + + LNV CP    +         ++P +    +  + +  S
Sbjct: 109 SDLERILDAMEPVAP-SVDCVELNVSCP----NVDQGCMSWGVDPALTAQAVQQVRRRWS 163

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHARKAILKGLS 164
            P+ VK      D         + K+ + +G + +             + AR A  + ++
Sbjct: 164 GPLWVKLTPQAPDP------CAVAKAAQDAGASALVVANTWLGAAIDTVKARPAFDRVVA 217

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS 223
                 I  L   +V+++     D+ +   GG+     A+ +L      V +G A + + 
Sbjct: 218 GLSGPAIFPLALRMVWQVCGAV-DIPVVGCGGVASADSAVAMLMAGAAAVEVGMALFSDF 276

Query: 224 AMLTTVDEYFSNPLT 238
           ++L  +       ++
Sbjct: 277 SVLERIARGLEEEVS 291


>gi|332981993|ref|YP_004463434.1| dihydroorotate oxidase B, catalytic subunit [Mahella australiensis
           50-1 BON]
 gi|332699671|gb|AEE96612.1| dihydroorotate oxidase B, catalytic subunit [Mahella australiensis
           50-1 BON]
          Length = 304

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/204 (15%), Positives = 74/204 (36%), Gaps = 28/204 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  +   + G    +   AA  ++    + + LN+ CP    +    G      P+ V D
Sbjct: 95  DTVVIANLAGNSRDEYCVAANKLDKADIDMLELNISCP----NVKEGGLSFGATPESVYD 150

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HA 155
               +      P+ VK    V        ++++  + + +G + + +           H 
Sbjct: 151 ITKQVRNYCHHPLVVKLSPNVGS------IKDVASAAQDAGADALSLINTLLGMAIDPHT 204

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ IL           I  +   +V++   +  D+ +   GG+ + + A++ +L     V
Sbjct: 205 RRPILGNITGGLSGPAIKPVALYMVWQ-AAQTVDIPVIGMGGIMNGNDAIEFMLAGAVAV 263

Query: 214 MIGRAAYKNSA----MLTTVDEYF 233
            +G A          ++  +++Y 
Sbjct: 264 QVGTANLVEPMATVRIIDDIEQYM 287


>gi|218131105|ref|ZP_03459909.1| hypothetical protein BACEGG_02710 [Bacteroides eggerthii DSM 20697]
 gi|317477012|ref|ZP_07936254.1| dihydroorotate dehydrogenase [Bacteroides eggerthii 1_2_48FAA]
 gi|217986809|gb|EEC53142.1| hypothetical protein BACEGG_02710 [Bacteroides eggerthii DSM 20697]
 gi|316906805|gb|EFV28517.1| dihydroorotate dehydrogenase [Bacteroides eggerthii 1_2_48FAA]
          Length = 303

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 76/205 (37%), Gaps = 29/205 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ I   V+ A+I+ D      I LN+ CP   V +G     +        +
Sbjct: 94  TNMIVNVSGSAIEDYVKTAEIINDLVNIPAIELNISCP--NVKQGGMAFGVTAKG--AEE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            + A+       + VK    V D      +  + ++ +  G + + +             
Sbjct: 150 VVKAVRSVYKKTLIVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGMAVDAER 203

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
            R  +           +  +   +V+++ K      IGL GG+ +   A++ +L     +
Sbjct: 204 KRPILSTVTGGMSGAAVKPIALRMVWQVAKAVKIPVIGL-GGIMNWKDAVEFMLAGASAI 262

Query: 214 MIGRAAYKNSAM----LTTVDEYFS 234
            IG A + + A+       +D+Y +
Sbjct: 263 QIGTANFIDPAITVKVAEGIDDYLN 287


>gi|170288398|ref|YP_001738636.1| dihydroorotate dehydrogenase family protein [Thermotoga sp. RQ2]
 gi|170175901|gb|ACB08953.1| dihydroorotate dehydrogenase family protein [Thermotoga sp. RQ2]
          Length = 270

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/195 (22%), Positives = 76/195 (38%), Gaps = 20/195 (10%)

Query: 49  PLALQIGGADISKLVEAA---KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           P+   +GG    + +E A   K V D  +  +  N  CP    +    G  ++ N +   
Sbjct: 81  PMIASLGGDSFEEYLEVARVFKKVADR-FYAVEFNFSCP----NVKEGGLSIVKNAEEWK 135

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG------VNGIWIHARKAI 159
             +  + K L  P +        + I        V   +  G      V G+       I
Sbjct: 136 KLLNTLRKEL--PDSFLIAKVGVEGIFVEDAAEFVMKAEWDGITLVNTVRGLHFEKDTMI 193

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
           L GLS      +  +    VYE+KK  P+LF+  +GG+  +  A + L    D + +G A
Sbjct: 194 LGGLS---GPVLKPIALRAVYEVKKRFPELFVIASGGVYSVKDAEEFLKVGADVIGVGSA 250

Query: 219 AYKNSAMLTTVDEYF 233
            +K+  ++  + +Y 
Sbjct: 251 LFKDPGVVEEIGKYL 265


>gi|268323690|emb|CBH37278.1| dihydroorotate dehydrogenase electron transfer
           subunit/dihydroorotate dehydrogenase [uncultured
           archaeon]
          Length = 589

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 60/177 (33%), Gaps = 34/177 (19%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL L I G ++ +  E AKI   +  + +  N  CP       S    +   P ++  
Sbjct: 377 DVPLILSIFGKNVEECREVAKIATKYPIDMLEFNASCPH------SDFVAVENQPKLLRS 430

Query: 107 CIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------- 152
            I  +   +   P+ VK    V D         L  +++K+G + I              
Sbjct: 431 IIKEIRAIVHPKPIAVKISPNVGDP------AGLAMTLEKAGADAITAINTVIARPVDNR 484

Query: 153 ----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               I        G S KD         +IV+ + KE   + I   GG+      + 
Sbjct: 485 LDTHILGNPTGYGGKSGKDLTVGGK---EIVFNLYKEL-KIPIIAVGGIFSAKDVID 537


>gi|270261325|ref|ZP_06189598.1| hypothetical protein SOD_a05550 [Serratia odorifera 4Rx13]
 gi|270044809|gb|EFA17900.1| hypothetical protein SOD_a05550 [Serratia odorifera 4Rx13]
          Length = 365

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 47/219 (21%), Positives = 75/219 (34%), Gaps = 33/219 (15%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADIS----KLVEAAKIVEDFGYNEINL---- 79
            A    +    + L FS  + P A  +   DI     + VEAAK  +  G+  I L    
Sbjct: 122 AARGGWQTQSASTLPFSPHDAPPAA-MSLNDIERLKAQFVEAAKRADRLGFELIELHGAH 180

Query: 80  -----NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC------KALSIPVTVK--CRIG 126
                    P A      +G  L     ++ +    +       KAL + ++       G
Sbjct: 181 GYLLHQFLSPLANQRNDQYGGSLQNRMRLLLEIFNEVRAVFPAEKALGVRISASDWVEGG 240

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
            D+Q        L K++K+ G + I + +      GLSP+    +         EI K  
Sbjct: 241 WDEQQSVT----LAKALKELGCDYIHVSSG-----GLSPQQKIPVGPSYQVPFAEIIKRE 291

Query: 187 PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             L     G + +  QA  I+     D V + R    N 
Sbjct: 292 SGLPTIAVGLITEPEQAEAIVSTGQADMVALARGILYNP 330


>gi|237713197|ref|ZP_04543678.1| dihydroorotate dehydrogenase [Bacteroides sp. D1]
 gi|262406664|ref|ZP_06083213.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_1_22]
 gi|294643458|ref|ZP_06721272.1| dihydroorotate dehydrogenase 1B [Bacteroides ovatus SD CC 2a]
 gi|294808129|ref|ZP_06766898.1| dihydroorotate dehydrogenase 1B [Bacteroides xylanisolvens SD CC
           1b]
 gi|298484009|ref|ZP_07002178.1| dihydroorotate oxidase [Bacteroides sp. D22]
 gi|229446664|gb|EEO52455.1| dihydroorotate dehydrogenase [Bacteroides sp. D1]
 gi|262355367|gb|EEZ04458.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_1_22]
 gi|292641206|gb|EFF59410.1| dihydroorotate dehydrogenase 1B [Bacteroides ovatus SD CC 2a]
 gi|294444672|gb|EFG13370.1| dihydroorotate dehydrogenase 1B [Bacteroides xylanisolvens SD CC
           1b]
 gi|298269790|gb|EFI11382.1| dihydroorotate oxidase [Bacteroides sp. D22]
          Length = 303

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 76/198 (38%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------- 153
                + + A+  A    + VK    V D      +  + ++ ++SG + + +       
Sbjct: 144 AKGASEVVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 154 -----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
                  R  +           +  +   +V+++ K      IGL GG+ D   A++ +L
Sbjct: 198 AIDAERKRPILSTITGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMDWRDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGATAIQIGTANFIDPAV 274


>gi|329954854|ref|ZP_08295871.1| dihydroorotate dehydrogenase 1B [Bacteroides clarus YIT 12056]
 gi|328526958|gb|EGF53969.1| dihydroorotate dehydrogenase 1B [Bacteroides clarus YIT 12056]
          Length = 303

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 70/192 (36%), Gaps = 28/192 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             +  AA I E      I LN+ CP   V +G     +        + + A+       +
Sbjct: 107 DYMETAAIINELVNIPAIELNISCP--NVKQGGMAFGVTAKG--AEEVVKAVRSVYKKTL 162

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKGL-SPKD 167
            VK    V D      +  + ++ +  G +            +    R+ IL  +     
Sbjct: 163 IVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGMAVDAERRRPILSTVTGGMS 216

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAM- 225
              +  +   +V+++ K      IGL GG+ +   A++ +L     + IG A + + A+ 
Sbjct: 217 GAAVKPIALRMVWQVAKAVKIPVIGL-GGIMNWKDAVEFMLAGASAIQIGTANFIDPAIT 275

Query: 226 ---LTTVDEYFS 234
                 +D+Y +
Sbjct: 276 VKVAEGIDDYLN 287


>gi|325497960|gb|EGC95819.1| dihydropyrimidine dehydrogenase [Escherichia fergusonii ECD227]
          Length = 411

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 73/191 (38%), Gaps = 33/191 (17%)

Query: 39  NILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
             L     +K L   I G +      L   A++V++ G + I  N  CP   +   + G+
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEDL---ARLVQEAGADMIECNFSCPQ--MTSHAMGS 147

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIH 154
            +  +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+
Sbjct: 148 DVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAIN 201

Query: 155 ARKAIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
             K+I                   +S    + +  +    + +++   E  D  I   GG
Sbjct: 202 TVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGG 261

Query: 197 LEDMSQALKIL 207
           +E    A + L
Sbjct: 262 IETWEDAAEFL 272


>gi|218549560|ref|YP_002383351.1| dihydropyrimidine dehydrogenase [Escherichia fergusonii ATCC 35469]
 gi|218357101|emb|CAQ89734.1| putative oxidoreductase subunit [Escherichia fergusonii ATCC 35469]
          Length = 411

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 73/191 (38%), Gaps = 33/191 (17%)

Query: 39  NILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
             L     +K L   I G +      L   A++V++ G + I  N  CP   +   + G+
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEDL---ARLVQEAGADMIECNFSCPQ--MTSHAMGS 147

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIH 154
            +  +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+
Sbjct: 148 DVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAIN 201

Query: 155 ARKAIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
             K+I                   +S    + +  +    + +++   E  D  I   GG
Sbjct: 202 TVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGG 261

Query: 197 LEDMSQALKIL 207
           +E    A + L
Sbjct: 262 IETWEDAAEFL 272


>gi|311278870|ref|YP_003941101.1| dihydroorotate dehydrogenase family protein [Enterobacter cloacae
           SCF1]
 gi|308748065|gb|ADO47817.1| dihydroorotate dehydrogenase family protein [Enterobacter cloacae
           SCF1]
          Length = 411

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 70/188 (37%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +  L   I G +  +  E A +VE+ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKQDYPDNVLIASIMGENEQQWQELAHLVEEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI       
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 154 ---------HARKAILKGL---SPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
                         I+ G    S    + +  +    V +++   E  D  I   GG+E+
Sbjct: 205 SITNIDLNQKTGMPIVNGKSSISGYSGKAVKPIALRFVQQLRTHPELKDFPISGIGGIEN 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|293446497|ref|ZP_06662919.1| yeiA protein [Escherichia coli B088]
 gi|291323327|gb|EFE62755.1| yeiA protein [Escherichia coli B088]
          Length = 335

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 74/188 (39%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 17  RQLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 74

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 75  QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 128

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 129 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 188

Query: 200 MSQALKIL 207
              A + L
Sbjct: 189 WEDAAEFL 196


>gi|224025863|ref|ZP_03644229.1| hypothetical protein BACCOPRO_02605 [Bacteroides coprophilus DSM
           18228]
 gi|224019099|gb|EEF77097.1| hypothetical protein BACCOPRO_02605 [Bacteroides coprophilus DSM
           18228]
          Length = 303

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +    E A I+ +  +   I LN+ CP   V +G     +        +
Sbjct: 94  TNMIVNVSGSQVEDYAETASIINELDHIPAIELNISCP--NVKQGGMAFGVTAKG--AAE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++A+ K     + VK    V D      +  + ++ + +G +            I    
Sbjct: 150 VVSAVRKVYHKTLIVKLSPNVTD------ITEIARAAEGAGADSVSLINTLLGMAIDAEK 203

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L     +
Sbjct: 204 RKPILSTVTGGMSGAAVKPIALRMVWQVAKAVQIPVIGL-GGIMNWKDAVEFLLAGASAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAV 274


>gi|57652424|ref|YP_184965.1| hypothetical protein SACOL0059 [Staphylococcus aureus subsp. aureus
           COL]
 gi|87160657|ref|YP_492800.1| hypothetical protein SAUSA300_0082 [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88193852|ref|YP_498637.1| hypothetical protein SAOUHSC_00031 [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|151220237|ref|YP_001331060.1| hypothetical protein NWMN_0025 [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|258452227|ref|ZP_05700241.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282927919|ref|ZP_06335529.1| conserved hypothetical protein [Staphylococcus aureus A9765]
 gi|284023090|ref|ZP_06377488.1| hypothetical protein Saura13_00744 [Staphylococcus aureus subsp.
           aureus 132]
 gi|294850435|ref|ZP_06791166.1| hypothetical protein SKAG_02525 [Staphylococcus aureus A9754]
 gi|6332752|dbj|BAA86634.1| hypothetical protein [Staphylococcus aureus]
 gi|57286610|gb|AAW38704.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           COL]
 gi|87126631|gb|ABD21145.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87201410|gb|ABD29220.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           NCTC 8325]
 gi|150373037|dbj|BAF66297.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|257860064|gb|EEV82898.1| conserved hypothetical protein [Staphylococcus aureus A5948]
 gi|282592009|gb|EFB97039.1| conserved hypothetical protein [Staphylococcus aureus A9765]
 gi|294822705|gb|EFG39143.1| hypothetical protein SKAG_02525 [Staphylococcus aureus A9754]
 gi|315196073|gb|EFU26432.1| hypothetical protein CGSSa01_08689 [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|329731736|gb|EGG68096.1| hypothetical protein SA21189_1189 [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 150

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 21/156 (13%), Positives = 52/156 (33%), Gaps = 20/156 (12%)

Query: 173 NLDYDIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           +  ++++  IK    +  P+  + +N  + D    L++     +DG+MIGR  + N    
Sbjct: 5   DAHWELIEAIKNLRDEIAPNTLLTINDDIPDRKTGLELAEKYGIDGIMIGRGIFHNPFTF 64

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                            +    K+    +   ++ +         + + + R       G
Sbjct: 65  -------------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRG 111

Query: 287 FPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              +   RH L +   +      +++     M E +
Sbjct: 112 IRGASELRHQL-MNTQSIAEVRALLDEFEAQMDEDV 146


>gi|222099309|ref|YP_002533877.1| Dihydroorotate dehydrogenase [Thermotoga neapolitana DSM 4359]
 gi|221571699|gb|ACM22511.1| Dihydroorotate dehydrogenase [Thermotoga neapolitana DSM 4359]
          Length = 270

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/195 (22%), Positives = 76/195 (38%), Gaps = 20/195 (10%)

Query: 49  PLALQIGGADISKLVEAA---KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           P+   +GG    + +E A   K V D  +  +  N  CP    +    G  ++ N +   
Sbjct: 81  PMIASLGGDSFEEYLEVARVFKKVADR-FYAVEFNFSCP----NVKEGGLSIVKNAEEWK 135

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG------VNGIWIHARKAI 159
             +  + K L  P +        + I        V   +  G      V G+       I
Sbjct: 136 KLLNTLRKEL--PDSFLIAKVGVEGIFVEDAAEFVMKAEWDGITLVNTVRGLHFEKDTMI 193

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
           L GLS      +  +    VYE+KK  P+LF+  +GG+  +  A + L    D + +G A
Sbjct: 194 LGGLS---GPVLKPIALRAVYEVKKRFPELFVIASGGVYSVKDAEEFLKVGADVIGVGSA 250

Query: 219 AYKNSAMLTTVDEYF 233
            +K+  ++  + +Y 
Sbjct: 251 LFKDPGVVEEIGKYL 265


>gi|332093238|gb|EGI98298.1| hypothetical protein SB521682_0944 [Shigella boydii 5216-82]
          Length = 411

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 73/188 (38%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++   + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEADADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|189461362|ref|ZP_03010147.1| hypothetical protein BACCOP_02017 [Bacteroides coprocola DSM 17136]
 gi|189431891|gb|EDV00876.1| hypothetical protein BACCOP_02017 [Bacteroides coprocola DSM 17136]
          Length = 303

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 75/192 (39%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +    E A I+ +      I LN+ CP   V +G     +  +     +
Sbjct: 94  TNMIVNVSGSQVEDYAETASIINELDNIPAIELNISCP--NVKQGGMAFGVTAHG--AAE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++A+ K     + VK    V D      +  + ++ + +G +            I    
Sbjct: 150 VVSAVRKVYHKTLIVKLSPNVTD------ITEIARAAEGAGADSVSLINTLLGMAIDAEK 203

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK IL  +        +  +   +V+++ K      +GL GG+ +   A++ +L     +
Sbjct: 204 RKPILSTVTGGMSGAAVKPIALRMVWQVAKAVKTPVVGL-GGIMNWKDAVEFLLAGATAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAI 274


>gi|117926701|ref|YP_867318.1| dihydroorotate oxidase B, catalytic subunit [Magnetococcus sp.
           MC-1]
 gi|117610457|gb|ABK45912.1| dihydroorotate oxidase B, catalytic subunit [Magnetococcus sp.
           MC-1]
          Length = 312

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/208 (16%), Positives = 76/208 (36%), Gaps = 27/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + PL   I G+   +  E A+I +      I +N+ CP    +    G     +PD+   
Sbjct: 99  DTPLIANISGSTTEQYGEIARIFDQSPVAAIEINISCP----NVKEGGIAFGSDPDMAAA 154

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HA 155
            +  + +A + P+  K    V D      +  + K   ++G + + +             
Sbjct: 155 VVEEVRRATTKPIITKLSPNVTD------ITTVAKRAIEAGSDALSVINTLMGMAIDLKK 208

Query: 156 RKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
           R+ +L     GLS    + +  L     Y++ +++  + I   GG+      L+  L   
Sbjct: 209 RRPVLGNLQGGLSGPAVKPVALLKVWQTYQLARQH-QIPIIGQGGIASADDVLEFFLVGA 267

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               +  + +K+  +   + +     + 
Sbjct: 268 SATGLCTSLFKDPLLPMRIAQALHQGVA 295


>gi|329928261|ref|ZP_08282161.1| dihydroorotate dehydrogenase 1B [Paenibacillus sp. HGF5]
 gi|328937940|gb|EGG34342.1| dihydroorotate dehydrogenase 1B [Paenibacillus sp. HGF5]
          Length = 310

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 75/201 (37%), Gaps = 34/201 (16%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVED----------FGYNEINLNVGCPSARV 88
            +   ++    + + +GG  + +  E A+++ +             + I LN+ CP+ + 
Sbjct: 85  ELSDMASHGTAVIVNLGGGTVREYAEGAELLTEASRKLRSAGKRAVDMIELNISCPNIK- 143

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
                G    +  +     + A+  A ++P+ VK   G  D      L+ + +  +  G 
Sbjct: 144 ---EGGLAFGIENEQARAVVRAVRNATTLPLLVKLSPGAKD------LKEMARMCEAEGA 194

Query: 149 N-----------GIWIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +            I I  R ++  +  +      I  +   +V+++ + +  + +   GG
Sbjct: 195 DGLSLINTIQAMAIDIRERCSVFDRAYAGLSGPAIKPIALRMVHQVAR-SVSIPVVGIGG 253

Query: 197 LEDMSQALK-ILPSVDGVMIG 216
           +      L+ I+     V IG
Sbjct: 254 ICSAEDVLEFIMAGAAAVQIG 274


>gi|320139483|gb|EFW31354.1| conserved domain protein [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320142115|gb|EFW33935.1| conserved domain protein [Staphylococcus aureus subsp. aureus
           MRSA177]
          Length = 150

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 21/156 (13%), Positives = 52/156 (33%), Gaps = 20/156 (12%)

Query: 173 NLDYDIVYEIK----KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           +  ++++  IK    +  P+  + +N  + D    L++     +DG+MIGR  + N    
Sbjct: 5   DAHWELIEAIKNLRDEIAPNTLLTINDDIPDRKTGLELAEKYGIDGIMIGRGIFHNPFTF 64

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                            +    K+    +   ++ +         + + + R       G
Sbjct: 65  -------------EKEPREHTSKELLDLLRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRG 111

Query: 287 FPNSRRCRHILTVEAGASTATHHIIETAFNLMIESL 322
              +   RH L +   +      +++     M E +
Sbjct: 112 IRGASELRHQL-MNTQSIAEARALLDEFEAQMDEDV 146


>gi|146318664|ref|YP_001198376.1| dihydroorotate dehydrogenase B [Streptococcus suis 05ZYH33]
 gi|145689470|gb|ABP89976.1| putative dihydroorotate dehydrogenase B [Streptococcus suis
           05ZYH33]
          Length = 244

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 78/203 (38%), Gaps = 13/203 (6%)

Query: 32  ILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARV 88
           + R   K +  L     + P+   + G    +    + KI +      I LN+ CP   V
Sbjct: 10  LRRSYPKKLPWLEQHFPDLPIIANVAGFSNEEYAYVSGKISKAPNVKAIELNISCP--NV 67

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
             G+ G  +   P++    + A  +A S+PV VK    V D            +   + +
Sbjct: 68  DHGNNGLLIGQVPELAYQAVKAAVEASSVPVYVKLTPSVADITLLAKAAEAAGATGLTMI 127

Query: 149 NGIW-----IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           N +      +  R+ IL  G        +  +   ++ ++ +   DL I   GG++   +
Sbjct: 128 NTLVGMRFNLKTRQPILANGTGGMSGPAVFPVALKLIRQVAQ-MTDLPIIGMGGVDTADK 186

Query: 203 ALKIL-PSVDGVMIGRAAYKNSA 224
           A++++      + +G A + +  
Sbjct: 187 AIEMMVAGASAIGVGTANFTDPF 209


>gi|291543218|emb|CBL16327.1| dihydroorotate oxidase B, catalytic subunit [Ruminococcus sp.
           18P13]
          Length = 486

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/183 (19%), Positives = 73/183 (39%), Gaps = 15/183 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +  EK +   I G + ++  E A+  E  G + I  N  CP   +     G+ + 
Sbjct: 179 RRLKEAFPEKVIVSSIMGRNEAEWTELARRSEQAGADIIECNFSCPQ--MCGNGLGSDVG 236

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGV-DDQIPAVALRN-------LVKSIKK-SGVN 149
            +P++V    AA+ K   +P+  K    +   ++PA+A           + ++K  +GV+
Sbjct: 237 QDPELVRAYTAAVRKGTRLPILAKMTPNLAHMELPAIAAVEAGADGLAAINTVKSITGVD 296

Query: 150 GIWIHARKAI--LKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALK 205
              + +   +     +S    + +  +    +Y++        + I   GG+E    A +
Sbjct: 297 LDSMASLPQVDGRSAVSGYSGKAVKPIALRFIYDMASCDRLKGVPISGMGGIETWQDAAE 356

Query: 206 ILP 208
            L 
Sbjct: 357 FLA 359


>gi|218690296|ref|YP_002398508.1| dihydropyrimidine dehydrogenase [Escherichia coli ED1a]
 gi|218427860|emb|CAR08626.1| putative oxidoreductase subunit [Escherichia coli ED1a]
          Length = 411

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 73/188 (38%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P++V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
                + L
Sbjct: 265 WEDTAEFL 272


>gi|313203220|ref|YP_004041877.1| dihydroorotate oxidase b, catalytic subunit [Paludibacter
           propionicigenes WB4]
 gi|312442536|gb|ADQ78892.1| dihydroorotate oxidase B, catalytic subunit [Paludibacter
           propionicigenes WB4]
          Length = 303

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 77/209 (36%), Gaps = 28/209 (13%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSAR 87
           AD  +      I    T    + + + G+ I   VE A+++        I LN+ CP+ +
Sbjct: 78  ADYFINHIYPTIKDIDTN---IIVNVSGSTIEDYVETAEMLNSLEKIPAIELNISCPNVK 134

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
               +FG   +         +  + +A    + VK    V D      +  +  +++  G
Sbjct: 135 EGGMAFGTSCLS----AAQVVKEVRRAYKNELIVKLSPNVTD------ISEIALAVEAEG 184

Query: 148 VN-----------GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            +            I    RK IL           +  +   +V+++ +      IGL G
Sbjct: 185 ADSVSLINTLLGMAINAEKRKPILSTITGGLSGPAVKPIALRMVWQVAQAVKIPVIGL-G 243

Query: 196 GLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
           G+ + + A++ +L     + IG A + + 
Sbjct: 244 GIMNAADAIEFMLAGASAIQIGTANFIDP 272


>gi|84502295|ref|ZP_01000443.1| probable dihydroorotate dehydrogenase, catalytic subunit
           [Oceanicola batsensis HTCC2597]
 gi|84389655|gb|EAQ02374.1| probable dihydroorotate dehydrogenase, catalytic subunit
           [Oceanicola batsensis HTCC2597]
          Length = 314

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/186 (17%), Positives = 64/186 (34%), Gaps = 22/186 (11%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
           F     P+   I    +    + A  + D     I  N+ CP+ R H  +FG     +P 
Sbjct: 87  FDKFGPPVIASISADTVEDFGKLAGYITDPRIAAIEANISCPNLRAHGRAFGM----DPV 142

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKA 158
                I AM    ++P+  K    V D      +  + + ++ +G + +     I     
Sbjct: 143 ASAQVITAMKANTTLPIWAKLTPNVGD------IAEMARCVEGAGADAVITANAILGMAI 196

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEI-------KKENPDLFIGLNGGLEDMSQALK-ILPSV 210
             + ++P+    +  L    V  +         E   + +   GG+      ++ +L   
Sbjct: 197 DAETMTPRLGNVVGGLTGPAVKPVILRMVNQCAEAVKIPVIGCGGIATGEDVVEYMLAGA 256

Query: 211 DGVMIG 216
             V IG
Sbjct: 257 SAVQIG 262


>gi|153955017|ref|YP_001395782.1| dihydropyrimidine dehydrogenase [Clostridium kluyveri DSM 555]
 gi|219855458|ref|YP_002472580.1| hypothetical protein CKR_2115 [Clostridium kluyveri NBRC 12016]
 gi|146347875|gb|EDK34411.1| PyrD1 [Clostridium kluyveri DSM 555]
 gi|219569182|dbj|BAH07166.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 401

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 70/197 (35%), Gaps = 16/197 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    +    +    L     +K L   I G    +  + A++V   G + I  N  C
Sbjct: 76  EQISDHPLEENLEHMRKLKQKYPQKVLVASIMGETEEEWTKLAEMVTQIGADIIECNFSC 135

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----------P 132
           P   +           +P++V +   A+ K  S+P+  K    + D              
Sbjct: 136 PQMSLQSMGADVG--QSPELVENYCRAVRKGTSLPILAKMTPNLSDMTIPAAASIRGGAD 193

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            +A  N +KSI +  +N    +        +S    + I  +    + ++ K  +   + 
Sbjct: 194 GIAAINTIKSITRVDLNKFSPYPIIGGKSSVSGYSGKAIKPIALRFIQDLAKSPKLKGIP 253

Query: 191 IGLNGGLEDMSQALKIL 207
           I   GG+E+    L+ +
Sbjct: 254 ISGMGGIENWEDVLEFM 270


>gi|288962204|ref|YP_003452499.1| dihydropyrimidine dehydrogenase (NADP+) [Azospirillum sp. B510]
 gi|288914470|dbj|BAI75955.1| dihydropyrimidine dehydrogenase (NADP+) [Azospirillum sp. B510]
          Length = 427

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 67/180 (37%), Gaps = 21/180 (11%)

Query: 61  KLVEAA-----KIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            + EAA     + V + G  + + LN+GCP     E   G+ +   P++V      +  A
Sbjct: 110 TMTEAAWAGLARRVAETGAADGLELNLGCPHGM-CERGMGSAIGQVPEMVEQVTRWVKNA 168

Query: 115 LSIPVTVKCRIGVDDQIPAVALRN--------LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +++PV VK    + + + +             L+ ++       +   A   ++ G    
Sbjct: 169 VNLPVIVKLTPNITNILWSAEAAKRGGADAISLINTVNSIVAVDLDAMAPTPVVDGKGSH 228

Query: 167 DNR---KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                  +  +  ++V EI +  +   L +   GG+     A + L      V +  AA 
Sbjct: 229 GGYCGPAVKPIALNMVAEIARNPDTSGLPVSGIGGITTWRDAAEFLALGATNVQVCTAAM 288


>gi|110760297|ref|XP_393690.3| PREDICTED: dihydropyrimidine dehydrogenase [NADP+]-like isoform 1
           [Apis mellifera]
          Length = 1024

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/156 (21%), Positives = 51/156 (32%), Gaps = 19/156 (12%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +  E  G + + LN+ CP     E   G     +P +V +    + +A+ IP  VK    
Sbjct: 653 QKAERAGADALELNLSCPHGM-GESGMGLACGQDPVLVRNISRWIREAVKIPFFVKLTPN 711

Query: 127 VDD-----QIPAVALRNLVKSI----------KKSGVNGIWIHARKAILKGLSPKDNRKI 171
           + D     +       N V +I            +         +     G+S    R  
Sbjct: 712 ITDIVSIAKAAYEGHANGVSAINTVQSLMGLHADATPWPAVGIKKATTYGGMSGNATRPQ 771

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                  V  I K  P   I   GG+E    AL+ L
Sbjct: 772 A---LRAVSAISKALPGFPILGIGGIESADVALQFL 804


>gi|288799988|ref|ZP_06405447.1| dihydroorotate oxidase [Prevotella sp. oral taxon 299 str. F0039]
 gi|288333236|gb|EFC71715.1| dihydroorotate oxidase [Prevotella sp. oral taxon 299 str. F0039]
          Length = 301

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/172 (19%), Positives = 67/172 (38%), Gaps = 24/172 (13%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           AA+I E      I LN+ CP+ +    +FG   +         + A+ +  +  + VK  
Sbjct: 112 AARINELENIPAIELNISCPNVKAGGMAFGVTALG----AASVVKAVREVYNKTLIVKLS 167

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILK-GLSPKDNRKIP 172
             V       ++ ++ K+ +  G +            I I  RK IL           + 
Sbjct: 168 PNV------TSVVDIAKACEAEGADSVSLINTLMGMAIDIEKRKPILSIATGGLSGPAVK 221

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
            +   +V+++ K      IGL GG+   + A++ ++     + IG A + + 
Sbjct: 222 PVALRMVWQVAKAVKIPVIGL-GGISSATDAIEFLMAGATAIQIGTANFLDP 272


>gi|257791414|ref|YP_003182020.1| dihydroorotate dehydrogenase family protein [Eggerthella lenta DSM
           2243]
 gi|257475311|gb|ACV55631.1| dihydroorotate dehydrogenase family protein [Eggerthella lenta DSM
           2243]
          Length = 356

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 74/194 (38%), Gaps = 24/194 (12%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +   + + + G    + V+  + +ED   +   +N+ CP+      + G C     D 
Sbjct: 144 AERGATVIVNVSGHSFDEYVQVIEALEDVPVDAYEVNISCPNVDAGGMTIGTC----TDS 199

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
           V   ++    A   P+ VK    V D      +  + ++   +G + + +          
Sbjct: 200 VEAVVSRCRAATKRPLIVKLTPNVTD------VTEIARAAVSAGADALSLINTLLGMAID 253

Query: 154 --HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
               R  + +G+       +  +   +V+E+ +   D+ +   GG+   + A++ +L   
Sbjct: 254 AERRRPQLARGVGGLSGPAVKPVALRMVWEVHQAV-DVPLLGMGGISCATDAVEFMLAGA 312

Query: 211 DGVMIGRAAYKNSA 224
             V +G A + N  
Sbjct: 313 TAVAVGTANFVNPH 326


>gi|170017350|ref|YP_001728269.1| dihydroorotate dehydrogenase B, catalytic subunit [Leuconostoc
           citreum KM20]
 gi|169804207|gb|ACA82825.1| Dihydroorotate dehydrogenase B, catalytic subunit [Leuconostoc
           citreum KM20]
          Length = 306

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/217 (21%), Positives = 81/217 (37%), Gaps = 41/217 (18%)

Query: 25  EMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE----IN 78
           E +VAD +  +    K +        P+   + G     + E   + E     +    I 
Sbjct: 80  EAVVADILPAIHEKYKTL--------PVLASVAG---ETVGEYVALTERLTATKQVTAIE 128

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
            N+ CP   V  G     +    +   + I AM  A ++P+  K    V D  P      
Sbjct: 129 ANLSCP--NVDRGGMAFGVTA--ESAAEVIHAMRAATTLPIYAKMSPNVTDIKP------ 178

Query: 139 LVKSIKKSGVNGIW-----------IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +VK+++ +G +GI            ++ R+A L +G        +  +    VYE  +  
Sbjct: 179 IVKAVETAGADGIVLINTVVGMSLDLNTRQARLARGTGGMSGTSVHPIAVRFVYETAQTV 238

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKN 222
               IG+ GG+  +   L+ ++     V IG A   N
Sbjct: 239 SIPVIGV-GGVSTVDDVLELMMAGASAVQIGTALAGN 274


>gi|29346302|ref|NP_809805.1| dihydroorotate dehydrogenase 1B [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253568278|ref|ZP_04845689.1| dihydroorotate dehydrogenase [Bacteroides sp. 1_1_6]
 gi|81842272|sp|Q8A9C3|PYRD_BACTN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|29338197|gb|AAO75999.1| dihydroorotate dehydrogenase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251842351|gb|EES70431.1| dihydroorotate dehydrogenase [Bacteroides sp. 1_1_6]
          Length = 303

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 78/198 (39%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+  A    + VK    V D      +  + ++ ++SG +           
Sbjct: 144 AKGASEVVKAVRAAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    ++ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERKRPILSTVTGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGASAIQIGTANFIDPAV 274


>gi|325831358|ref|ZP_08164612.1| dihydroorotate dehydrogenase 1B [Eggerthella sp. HGA1]
 gi|325486612|gb|EGC89060.1| dihydroorotate dehydrogenase 1B [Eggerthella sp. HGA1]
          Length = 357

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 74/194 (38%), Gaps = 24/194 (12%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +   + + + G    + V+  + +ED   +   +N+ CP+      + G C     D 
Sbjct: 145 AERGATVIVNVSGHSFDEYVQVIEALEDVPVDAYEVNISCPNVDAGGMTIGTC----TDS 200

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
           V   ++    A   P+ VK    V D      +  + ++   +G + + +          
Sbjct: 201 VEAVVSRCRAATKRPLIVKLTPNVTD------VTEIARAAVSAGADALSLINTLLGMAID 254

Query: 154 --HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
               R  + +G+       +  +   +V+E+ +   D+ +   GG+   + A++ +L   
Sbjct: 255 AERRRPQLARGVGGLSGPAVKPVALRMVWEVHQAV-DVPLLGMGGISCATDAVEFMLAGA 313

Query: 211 DGVMIGRAAYKNSA 224
             V +G A + N  
Sbjct: 314 TAVAVGTANFVNPH 327


>gi|124485929|ref|YP_001030545.1| hypothetical protein Mlab_1109 [Methanocorpusculum labreanum Z]
 gi|124363470|gb|ABN07278.1| metal-binding transcription factor-like protein [Methanocorpusculum
           labreanum Z]
          Length = 367

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 65/168 (38%), Gaps = 29/168 (17%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + GA     V AAK    FG + I  ++  C    + +   G  L+ NP+ +   ++A+ 
Sbjct: 94  LRGATPEAFVSAAKR---FGPSVIYEIDAHCRQQPMIDAGCGEYLLHNPEKLCAIVSALA 150

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + V+VK R GV D       R L + + K+G + + +                   
Sbjct: 151 AE-GMTVSVKTRAGVVDD------RQLARMLWKAGASILHVDLMDT-------------- 189

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
              +  + +I+   P + I  N G+    + +       D V + R+A
Sbjct: 190 --GHTKIRQIRNSCPLI-IIANNGVSSPDKMMDYFAHGADLVSVARSA 234


>gi|56419957|ref|YP_147275.1| dihydropyrimidine dehydrogenase [Geobacillus kaustophilus HTA426]
 gi|56379799|dbj|BAD75707.1| dihydropyrimidine dehydrogenase [Geobacillus kaustophilus HTA426]
          Length = 429

 Score = 64.5 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 62/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +    PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVERQTYWVKEVARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    ++  + G + I +      L G+       IP           
Sbjct: 175 TPNITD------ITATAEAAAQGGADAISLINTINSLMGVDLDTWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +     + I   GG+ +   A++ +L    GV +  A   
Sbjct: 229 CGPAVKPIALNMVAECARHPRIRIPISGIGGISNWRDAVEFMLMGATGVQVCTAVMH 285


>gi|89097591|ref|ZP_01170480.1| dihydropyrimidine dehydrogenase [Bacillus sp. NRRL B-14911]
 gi|89087887|gb|EAR66999.1| dihydropyrimidine dehydrogenase [Bacillus sp. NRRL B-14911]
          Length = 429

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE+ G + + LN GCP     E   G+     P++V        +A   PV VK 
Sbjct: 116 EIVKRVEEIGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWAKEAARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    ++  K G + + +      L G+       IP           
Sbjct: 175 TPNITD------ITATAEAAVKGGADAVSMINTINSLAGVDLDTWNTIPHVGGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +     + I   GG+ +   A++ +L    GV I  AA  
Sbjct: 229 CGPAVKPIALNMVAECARNPAISVPISGMGGISNWQNAVEFMLMGASGVQICTAAMH 285


>gi|261419625|ref|YP_003253307.1| dihydropyrimidine dehydrogenase [Geobacillus sp. Y412MC61]
 gi|319766442|ref|YP_004131943.1| dihydroorotate dehydrogenase [Geobacillus sp. Y412MC52]
 gi|261376082|gb|ACX78825.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y412MC61]
 gi|317111308|gb|ADU93800.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y412MC52]
          Length = 429

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 62/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +    PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVERQTYWVKEVARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    ++  + G + I +      L G+       IP           
Sbjct: 175 TPNITD------ITATAEAAAQGGADAISLINTINSLMGVDLDTWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +     + I   GG+ +   A++ +L    GV +  A   
Sbjct: 229 CGPAVKPIALNMVAECARHPRIRIPISGIGGISNWRDAVEFMLMGATGVQVCTAVMH 285


>gi|114778351|ref|ZP_01453198.1| Dihydroorotate dehydrogenase 1 [Mariprofundus ferrooxydans PV-1]
 gi|114551314|gb|EAU53871.1| Dihydroorotate dehydrogenase 1 [Mariprofundus ferrooxydans PV-1]
          Length = 318

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 31/210 (14%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +E        G    +  E A+I +D     I +N+ CP   V EG        NP + 
Sbjct: 101 HKETQFWANANGTSPEEYAEVARIFDDSPVTAIEINISCP--NVKEGGVHFG--NNPVMA 156

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------I 153
              + AM      P+  K      D      +    + + ++G +G+            I
Sbjct: 157 ARVVEAMRPMTKKPLITKLSPNTAD------IAETARMVIEAGTDGLSVINTLVGMAVDI 210

Query: 154 HARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
             R  ++     GLS    + +          +  ++ ++ I   GG+     A++  + 
Sbjct: 211 EQRSPVIANISGGLSGPAIKPVALWKIHQTRAVAAKH-NIPILGQGGITSAKDAIEFAIV 269

Query: 209 SVDGVMIGRAAYKNS----AMLTTVDEYFS 234
             D + +G   + +      +L  + +Y  
Sbjct: 270 GSDAIGLGTGLFYDPLLCHKLLEEMRDYLR 299


>gi|301310152|ref|ZP_07216091.1| dihydroorotate dehydrogenase family protein [Bacteroides sp. 20_3]
 gi|300831726|gb|EFK62357.1| dihydroorotate dehydrogenase family protein [Bacteroides sp. 20_3]
          Length = 497

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/208 (17%), Positives = 70/208 (33%), Gaps = 24/208 (11%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           ++A +  +   +  L     +K +   I G    +    A+     G + I  N  CP  
Sbjct: 185 SEASVEENFDTLYRLKQRYPDKLIISSIMGRTDDEWTRLAQYSTQAGADIIECNFSCPQ- 243

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VA 135
            + +   G+ +  NP++V    AA  +   +P+  K    +    P            +A
Sbjct: 244 -MTQEGMGSDVGQNPELVRRFTAATRRGTHLPILAKMTPNIGQMTPVALAAHEGGATGIA 302

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGL 193
             N +K I +     +        L  +S    + +  +    ++E+  +     + I  
Sbjct: 303 AINTIKCITRIDEKALTARPVVCGLSSVSGYSGKAVRPIALRFIHELASDPSAGKMPISG 362

Query: 194 NGGLEDMSQALKI-------LPSVDGVM 214
            GG+E    AL         L     VM
Sbjct: 363 IGGIETWRDALDFLLLGCTNLQICTAVM 390


>gi|189465638|ref|ZP_03014423.1| hypothetical protein BACINT_01998 [Bacteroides intestinalis DSM
           17393]
 gi|189437912|gb|EDV06897.1| hypothetical protein BACINT_01998 [Bacteroides intestinalis DSM
           17393]
          Length = 303

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 75/198 (37%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                E  + + + G+ I   V+ A+ + +      I LN+ CP   V +G     +   
Sbjct: 88  RIKDIETNMIVNVSGSAIEDYVKTAEAINELDKIPAIELNISCP--NVKQGGMAFGVTAK 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+  A    + VK    V       ++  + ++++  G +           
Sbjct: 146 G--AEEVVKAVRAAYKKTLIVKLSPNV------TSIAEIARAVENGGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL  +        +  +   +V+++ +      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERRRPILSTVTGGMSGAAVKPIALRMVWQVAQAVKIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGASAIQIGTANFIDPAV 274


>gi|224539982|ref|ZP_03680521.1| hypothetical protein BACCELL_04894 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224518408|gb|EEF87513.1| hypothetical protein BACCELL_04894 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 303

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 75/198 (37%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                E  + + + G+ I   V+ A+ + +      I LN+ CP   V +G     +   
Sbjct: 88  RIKDIETNMIVNVSGSAIEDYVKTAEAINELDKIPAIELNISCP--NVKQGGMAFGVTAK 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+  A    + VK    V       ++  + ++++  G +           
Sbjct: 146 G--AEEVVKAVRAAYKKTLIVKLSPNV------TSIAEIARAVENGGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    R+ IL  +        +  +   +V+++ +      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERRRPILSTVTGGMSGAAVKPIALRMVWQVAQAVKIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGASAIQIGTANFIDPAV 274


>gi|332830619|gb|EGK03230.1| dihydroorotate dehydrogenase [Dysgonomonas gadei ATCC BAA-286]
          Length = 303

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/206 (18%), Positives = 78/206 (37%), Gaps = 29/206 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+ I   VE  + + D      I LN+ CP+ +    +FG C     D   
Sbjct: 93  DTNVIVNVSGSTIEDYVECTEKLVDLDKIPAIELNISCPNVKEGGMAFGVC----ADSAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           D   A+ K     + VK    V D      +  + ++++  G +            I I+
Sbjct: 149 DVTRAVRKVWDKTLIVKLSPNVTD------VTEIARAVEAEGADSVSLINTLLGMAIDIN 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L  ++       +  +   +V++         IG+ GG+     A++ IL     
Sbjct: 203 KRRPVLSTVTGGLSGPCVKPVALRMVWQTYNAVKIPVIGM-GGISCWQDAIEFILAGSSA 261

Query: 213 VMIGRAAYKNSAM----LTTVDEYFS 234
           + IG   + +  +    +  + EY  
Sbjct: 262 IQIGTHNFIDPTISVKVVDGIKEYLD 287


>gi|159904891|ref|YP_001548553.1| TIM-barrel protein [Methanococcus maripaludis C6]
 gi|159886384|gb|ABX01321.1| TIM-barrel protein [Methanococcus maripaludis C6]
          Length = 260

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/155 (20%), Positives = 61/155 (39%), Gaps = 22/155 (14%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMCK-ALSIPVTVKCRIGVDD 129
             + + LN  C    + +   G  L+   N   + D + ++ +  L IPV +K R     
Sbjct: 111 NADILELNCHCRQTEITDLEIGQNLLKLENESKLFDFLKSIHELNLEIPVFLKLRANF-- 168

Query: 130 QIPAVALRNLVKSIKKSGV--NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
               + +  L++ + K  V  +GI I          +P +N      D + + +I++  P
Sbjct: 169 ----LTVEELIELLNKVRVYFDGIHIDC-------FNPGNNY----ADLEYLKKIRQNFP 213

Query: 188 DLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           +  I  N  +  +  A ++L   D   + R    N
Sbjct: 214 EKIIIGNNSVNSVETAKEMLEYADFASVARCVLAN 248


>gi|266625622|ref|ZP_06118557.1| dihydrouridine synthase family protein [Clostridium hathewayi DSM
           13479]
 gi|288862473|gb|EFC94771.1| dihydrouridine synthase family protein [Clostridium hathewayi DSM
           13479]
          Length = 182

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 22/156 (14%), Positives = 46/156 (29%), Gaps = 20/156 (12%)

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                  L++   K  +  + IH R       +  D           V   K E     +
Sbjct: 2   SPDEFEELLEIYNKYPLKELIIHPRVRSDFYKNTPDRAAFCRA----VKASKNE-----V 52

Query: 192 GLNGGLEDMSQALKILPSV---DGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
             NG +       +    V   D +M+GR    N  +   +      P            
Sbjct: 53  WYNGDIFTAGDWKEFHAGVPEVDCIMMGRGLLANPGLAGEIKG-LGGP-------DKEWI 104

Query: 249 KDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           ++F   +     +  +   +   K+++   +++ LF
Sbjct: 105 REFHDMVYQGYRETISGDRNVLFKMKEFWFYLLFLF 140


>gi|300918787|ref|ZP_07135356.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 115-1]
 gi|300414030|gb|EFJ97340.1| dihydropyrimidine dehydrogenase [Escherichia coli MS 115-1]
          Length = 411

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 73/188 (38%), Gaps = 27/188 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G +  +  E A++V++ G + I  N  CP   +   + G+ + 
Sbjct: 93  RRLKEDYPDKVLIASIMGENEQQWEELARLVQEAGADMIECNFSCPQ--MTSHAMGSDVG 150

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARK 157
            +P +V     A+ +  ++P+  K    + D      +  +  + K+ G +GI  I+  K
Sbjct: 151 QSPVLVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGADGIAAINTVK 204

Query: 158 AIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLED 199
           +I                   +S    + +  +    + +++   E  D  I   GG+E 
Sbjct: 205 SITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDFPISGIGGIET 264

Query: 200 MSQALKIL 207
              A + L
Sbjct: 265 WEDAAEFL 272


>gi|170741202|ref|YP_001769857.1| dihydroorotate dehydrogenase family protein [Methylobacterium sp.
           4-46]
 gi|168195476|gb|ACA17423.1| dihydroorotate dehydrogenase family protein [Methylobacterium sp.
           4-46]
          Length = 320

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/222 (15%), Positives = 73/222 (32%), Gaps = 26/222 (11%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPS 85
           I +  +    +K +   +  + PL + I           AA++    G   I  N+ CP 
Sbjct: 76  IPSKGVTHFVEKTMPHDAAYDAPLIVSISAPTPEGFARLAAELTIP-GVAGIEANISCP- 133

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
             + E      +    D        +  A  +P+ VK             +  + ++ ++
Sbjct: 134 -NIEEDGRAFAM--RADSTAAVTRQLRAATDLPLWVKLTP------NTAEMPEVARAAQE 184

Query: 146 SGVNGI----WIHARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKENPDLFIGL 193
           +G + +     I +    L+   P             +  +    VY   K    + +  
Sbjct: 185 AGADAVVVANTIPSMAIDLRTFKPCLGNIMGGLSGPAVKPIVLRHVYLCAKAVT-IPVIG 243

Query: 194 NGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            GG+     A + +L     V +G A +   A +TT+ +   
Sbjct: 244 CGGIGTAEDAAEYMLAGAAAVQVGTATFLQPAAMTTIIDGLE 285


>gi|255654268|ref|ZP_05399677.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-23m63]
 gi|296452557|ref|ZP_06894253.1| dihydroorotate oxidase [Clostridium difficile NAP08]
 gi|296881031|ref|ZP_06904975.1| dihydroorotate oxidase [Clostridium difficile NAP07]
 gi|296258605|gb|EFH05504.1| dihydroorotate oxidase [Clostridium difficile NAP08]
 gi|296427965|gb|EFH13868.1| dihydroorotate oxidase [Clostridium difficile NAP07]
          Length = 300

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/256 (15%), Positives = 97/256 (37%), Gaps = 37/256 (14%)

Query: 11  FFARLLTNNALLYTE----MIVADAI----LRGDKKNILGF-STQEKPLALQIGGADISK 61
              +   NN +   E    M+ +  +    ++G   N L F S  +      +GG  +  
Sbjct: 48  TLNKKPGNNGMRVHETPSGMMNSVGLENPGVQGFIDNELPFFSKLDLVRIANVGGGTLED 107

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            +   +++ D   + I LN+ CP+ +    +FG       ++  + +  +     +P+ +
Sbjct: 108 YLLGVQMLNDKPIDIIELNISCPNVKAGGMAFGI----KNEVAREVVREVRNITKLPLVI 163

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKGLSPKDNR 169
           K     +D      +  + K  ++ G +G+ +            + R       +     
Sbjct: 164 KLSPNAED------IVEMAKVCEEEGADGVSLVNTFKAMAIDIKNRRPVFENVYAGLSGP 217

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS----A 224
            I  +   +V+E+ K N ++ +   GG+   + A++ I+     + +G A + N      
Sbjct: 218 AIKPIALRMVHEVCK-NVNIPVMGMGGITKATDAIEFIMAGATCIQVGTANFMNPRIGIE 276

Query: 225 MLTTVDEYFSNPLTGS 240
           ++  ++E+       S
Sbjct: 277 IIDGINEFMDREGIKS 292


>gi|295402305|ref|ZP_06812261.1| dihydroorotate dehydrogenase family protein [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294975698|gb|EFG51320.1| dihydroorotate dehydrogenase family protein [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 427

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 61/177 (34%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +    PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEVARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    ++  + G + I +      L G+       IP           
Sbjct: 175 TPNITD------ITATAEAAVQGGADAISMINTINSLMGVDLDTWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +     + I   GG+     A++ +L    GV +  A   
Sbjct: 229 CGPAVKPIALNMVAECARHPRIHVPISGIGGISSWKDAVEFMLMGATGVQVCTAVMH 285


>gi|281420774|ref|ZP_06251773.1| dihydroorotate oxidase [Prevotella copri DSM 18205]
 gi|281405066|gb|EFB35746.1| dihydroorotate oxidase [Prevotella copri DSM 18205]
          Length = 302

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/203 (15%), Positives = 76/203 (37%), Gaps = 33/203 (16%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A  + +      I LN+ CP   V +G     +    +   
Sbjct: 93  DTNMIVNVSGHSPESYAECAARINELDKIPAIELNISCP--NVKDGGMAFGVTC--EGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ K     + VK    V       ++ ++ ++++  G +            + I 
Sbjct: 149 SVVKAVRKVYKKTLIVKLSPNV------TSIADIARAVEAEGADSVSLINTLMGMAVDIE 202

Query: 155 ARKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
            R+ +L     GLS    + +   + +D+ + +     ++ +   GG+     A++ ++ 
Sbjct: 203 KRQPLLSIRTGGLSGPCVKPVALRMVWDVAHAV-----NIPVVGLGGISSAKDAIEFLMC 257

Query: 209 SVDGVMIGRAAYKNSAMLTTVDE 231
               + IG A + + A+   V +
Sbjct: 258 GATAIEIGTANFIDPAVTKKVKD 280


>gi|313905393|ref|ZP_07838758.1| dihydroorotate dehydrogenase family protein [Eubacterium
           cellulosolvens 6]
 gi|313469716|gb|EFR65053.1| dihydroorotate dehydrogenase family protein [Eubacterium
           cellulosolvens 6]
          Length = 520

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 67/201 (33%), Gaps = 28/201 (13%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I   ++         L      K +   I G    +  + A + E+ G + I  N  C
Sbjct: 195 EQISDHSLEENLAFFRQLKKDYPTKIIIASIMGRTEEEWTKLAALCEEAGADMIECNFSC 254

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P   +     G  + +N ++V     A+ K   +PV  K    +        +    K+ 
Sbjct: 255 PQ--MVGEGLGCEVGINNELVETYTRAVRKGTKLPVLAKMTPNI------TKMEEPAKAA 306

Query: 144 KKSGVNGI-----------------WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK-- 184
            + G +GI                       A    +S    + +  +    ++++KK  
Sbjct: 307 LRGGADGIAAINTIKSIMNVNFETYATAPSVAGRSSVSGYSGKAVKPIALRFIHDLKKDP 366

Query: 185 ENPDLFIGLNGGLEDMSQALK 205
           E  D+ +   GG+E    A +
Sbjct: 367 ELKDVPVSGMGGIETWKDAAE 387


>gi|147678141|ref|YP_001212356.1| dihydroorotate dehydrogenase 1B [Pelotomaculum thermopropionicum
           SI]
 gi|146274238|dbj|BAF59987.1| dihydroorotate dehydrogenase [Pelotomaculum thermopropionicum SI]
          Length = 307

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/212 (17%), Positives = 80/212 (37%), Gaps = 29/212 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLN 100
           G +  + P+ + I G  + +    A  ++       I +N+ CP   V +G        +
Sbjct: 91  GLAGYDLPVIVNIAGETVEEYALLAGRLDRVQAVAGIEVNISCP--NVKKGGMQFG--SD 146

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           P +  +   A+  +   PV VK    V       ++  + + + ++G + +         
Sbjct: 147 PAMAAEVTRAVRASTGKPVIVKLSPNV------TSIVAVARKVAEAGADALSMINTLLGM 200

Query: 153 ---IHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
              I  R+ +L  ++       +  +    V+E+ +E  DL I   GG+     A++ IL
Sbjct: 201 AVDIRKRRPLLGNVTGGLSGPAVRPVAVRAVWEVYREV-DLPIIGMGGITCAGDAIEFIL 259

Query: 208 PSVDGVMIGRAAYKNS----AMLTTVDEYFSN 235
                V +G A + N      +   ++ Y   
Sbjct: 260 AGATAVAVGTANFVNPRATVEIAEGIERYLEE 291


>gi|150016815|ref|YP_001309069.1| dihydropyrimidine dehydrogenase [Clostridium beijerinckii NCIMB
           8052]
 gi|149903280|gb|ABR34113.1| dihydroorotate dehydrogenase family protein [Clostridium
           beijerinckii NCIMB 8052]
          Length = 517

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 67/195 (34%), Gaps = 22/195 (11%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            L      K +   I G +  +  + AK++ + G + I  N  CP   +     G+ +  
Sbjct: 210 RLKKDYPSKIIVASIMGQNEEEWTKLAKLMTEAGADIIECNFSCPH--MTSKGVGSDVGQ 267

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGV-----------DDQIPAVALRNLVKSIKKSGV 148
           NPD+V     A  K  ++P+  K    +           +     +A  N +KSI    +
Sbjct: 268 NPDLVALYTKATRKGTNLPILAKMTPNIGNVEIPAMAAMEAGATGIAAINTIKSIMNLNL 327

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQA--- 203
                         +     + +  +    ++++K  +E  D  I   GG+E    A   
Sbjct: 328 ENFESEPNVEGKTSVGGYSGKAVKPIALRFIHDMKACEELKDAPISGMGGIETWKDAAEF 387

Query: 204 ----LKILPSVDGVM 214
                + L     VM
Sbjct: 388 MALGCENLQITTSVM 402


>gi|260175033|ref|ZP_05761445.1| dihydroorotate dehydrogenase 1B [Bacteroides sp. D2]
 gi|315923264|ref|ZP_07919504.1| dihydroorotate dehydrogenase [Bacteroides sp. D2]
 gi|313697139|gb|EFS33974.1| dihydroorotate dehydrogenase [Bacteroides sp. D2]
          Length = 303

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 76/198 (38%), Gaps = 25/198 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG      
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS---- 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------- 153
                + + A+  A    + VK    V D      +  + ++ ++SG + + +       
Sbjct: 144 AKGASEVVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGM 197

Query: 154 -----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
                  R  +           +  +   +V+++ K   ++ +   GG+ D   A++ +L
Sbjct: 198 AIDAERKRPILSTITGGMSGAAVKPIALRMVWQVAK-VINIPVIGLGGIMDWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM 225
                + IG A + + A+
Sbjct: 257 AGATAIQIGTANFIDPAV 274


>gi|257463213|ref|ZP_05627612.1| dihydroorotate dehydrogenase 1B [Fusobacterium sp. D12]
          Length = 306

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 81/209 (38%), Gaps = 25/209 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLML 99
           L        L   I G  + + +E AK V++      I LN+ CP    +    G     
Sbjct: 89  LRREGVTTSLIANINGKTMEEYMEIAKRVDNIEEVAMIELNISCP----NVKDGGMAFGA 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           NP++ G     + K    P+ VK    V D      +  + K ++++G +          
Sbjct: 145 NPEVAGAVTREVRKITKKPLIVKLSPNVTD------IAMIAKIVEENGADAVSLINTVLG 198

Query: 150 -GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I + ++K +L           +  +   ++Y++ +      +G+ GG+ + + AL+ +
Sbjct: 199 MAIDVKSKKPLLGNVFGGMSGGAVKPIALRMIYQVYEAVTIPIVGM-GGILNGTDALEFL 257

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     + IG   + N  +   V++   +
Sbjct: 258 MAGASLLSIGTGFFINPMVSVEVEKTLRD 286


>gi|312111477|ref|YP_003989793.1| dihydroorotate dehydrogenase [Geobacillus sp. Y4.1MC1]
 gi|311216578|gb|ADP75182.1| dihydroorotate dehydrogenase family protein [Geobacillus sp.
           Y4.1MC1]
          Length = 427

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 61/177 (34%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +    PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEVARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    ++  + G + I +      L G+       IP           
Sbjct: 175 TPNITD------ITATAEAAVQGGADAISMINTINSLMGVDLDTWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +     + I   GG+     A++ +L    GV +  A   
Sbjct: 229 CGPAVKPIALNMVAECARHPRIHVPISGIGGISSWKDAVEFMLMGATGVQVCTAVMH 285


>gi|315644726|ref|ZP_07897856.1| dihydroorotate dehydrogenase family protein [Paenibacillus vortex
           V453]
 gi|315279876|gb|EFU43176.1| dihydroorotate dehydrogenase family protein [Paenibacillus vortex
           V453]
          Length = 310

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/174 (17%), Positives = 67/174 (38%), Gaps = 27/174 (15%)

Query: 59  ISKLVEAAKIVEDFG---YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
              L EA+  ++  G    + I LN+ CP+ +      G    +  +   + + A+ +A 
Sbjct: 112 AELLTEASLKLQAAGKRAIDMIELNISCPNIK----EGGLAFGVENEQAQEVVRAVRRAT 167

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKGL 163
           ++P+ VK   G  D      L+ + +  +  G +G+ +              R    +  
Sbjct: 168 ALPLLVKLSPGARD------LKEMARMCEAEGADGLSLINTIQAMAIDIRERRSVFDRAY 221

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           +      I  +   +V+++ +      +G+ GG+      L+ I+     V IG
Sbjct: 222 AGLSGPAIKPIALRMVHQVARSVSIPLVGI-GGISCAEDILEFIMAGAAAVQIG 274


>gi|47207088|emb|CAF94223.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 176

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 33/135 (24%), Positives = 53/135 (39%), Gaps = 23/135 (17%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTE------MIVAD----------AILRGDKKNILGFS 44
           MV       R  A L     ++Y E      M                +  D++ +    
Sbjct: 17  MVRVGTLPMRLLA-LDYGADIVYCEELIDIKMAQCHRVVNEVLDTVDFVAPDERVMFRTC 75

Query: 45  TQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            +EK  +  Q+G AD  + +  A++VE      I++N+GCP     +G  GA L+ +PD 
Sbjct: 76  EKEKNKVVFQMGTADPDRALTVAQLVE-RDVAAIDVNMGCPKEYSTKGGMGAALLSDPDR 134

Query: 104 VGDCIAAMCKALSIP 118
               I A+   L  P
Sbjct: 135 ----IEAVSDPLRQP 145


>gi|229552253|ref|ZP_04440978.1| dihydroorotate oxidase [Lactobacillus rhamnosus LMS2-1]
 gi|229314389|gb|EEN80362.1| dihydroorotate oxidase [Lactobacillus rhamnosus LMS2-1]
          Length = 266

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/181 (19%), Positives = 68/181 (37%), Gaps = 24/181 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   I GAD+++    AK +        + +N+ CP   V +G        
Sbjct: 86  LASHYPDLPIIASIAGADVAEYTAVAKKLSAAPNVKALEVNISCP--NVDQGGMAFG--T 141

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IH 154
           +P +      A+ +A S+P+ VK    V D      +  + K+++ +G +GI      + 
Sbjct: 142 DPSVAAAVTKAVKEASSVPIFVKLTPNVTD------ITTIAKAVEAAGADGISLINTFVG 195

Query: 155 ARKAILKG-------LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            R  I  G               +  +   +VY++      + I   GG+       ++L
Sbjct: 196 MRLDIQTGEPILTNVTGGVSGPALFPMALHMVYQVA-HTVHIPIIGMGGVSSGHDVAEML 254

Query: 208 P 208
            
Sbjct: 255 A 255


>gi|153806308|ref|ZP_01958976.1| hypothetical protein BACCAC_00567 [Bacteroides caccae ATCC 43185]
 gi|149130985|gb|EDM22191.1| hypothetical protein BACCAC_00567 [Bacteroides caccae ATCC 43185]
          Length = 303

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 77/192 (40%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ I   V+ A+I+ +      I LN+ CP+ +    +FG           +
Sbjct: 94  TNMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCPNVKQGGMAFGVS----AKGASE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+  A    + VK    V D      +  + ++ ++SG +            I    
Sbjct: 150 VVKAVRSAYKKTLIVKLSPNVTD------ITEIARAAEESGADSVSLINTLLGMAIDAER 203

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           ++ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L     +
Sbjct: 204 KRPILSTVTGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMNWKDAVEFMLAGASAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAV 274


>gi|199598365|ref|ZP_03211784.1| Dihydroorotate dehydrogenase [Lactobacillus rhamnosus HN001]
 gi|199590684|gb|EDY98771.1| Dihydroorotate dehydrogenase [Lactobacillus rhamnosus HN001]
          Length = 290

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 69/180 (38%), Gaps = 24/180 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   I GAD+++    AK +        + +N+ CP   V +G        
Sbjct: 86  LASHYPDLPIIASIAGADVAEYAAVAKKLSAAPNVKALEVNISCP--NVDQGGMAFG--T 141

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
           +P +      A+  A S+P+ VK    V D      +  + K+++ +G +GI        
Sbjct: 142 DPSVAAAVTQAVKAASSVPIFVKLTPNVTD------ITTIAKAVEAAGADGISLINTFVG 195

Query: 153 ----IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               I   + IL  +        +  +   +VY++      + I   GG+     A ++L
Sbjct: 196 MRLDIETGEPILTNVTGGVSGPALFPMALQMVYQVA-HAVHISIIGMGGVSSGHDAAEML 254


>gi|317060801|ref|ZP_07925286.1| dihydroorotate dehydrogenase [Fusobacterium sp. D12]
 gi|313686477|gb|EFS23312.1| dihydroorotate dehydrogenase [Fusobacterium sp. D12]
          Length = 303

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 81/209 (38%), Gaps = 25/209 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLML 99
           L        L   I G  + + +E AK V++      I LN+ CP    +    G     
Sbjct: 86  LRREGVTTSLIANINGKTMEEYMEIAKRVDNIEEVAMIELNISCP----NVKDGGMAFGA 141

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           NP++ G     + K    P+ VK    V D      +  + K ++++G +          
Sbjct: 142 NPEVAGAVTREVRKITKKPLIVKLSPNVTD------IAMIAKIVEENGADAVSLINTVLG 195

Query: 150 -GIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I + ++K +L           +  +   ++Y++ +      +G+ GG+ + + AL+ +
Sbjct: 196 MAIDVKSKKPLLGNVFGGMSGGAVKPIALRMIYQVYEAVTIPIVGM-GGILNGTDALEFL 254

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +     + IG   + N  +   V++   +
Sbjct: 255 MAGASLLSIGTGFFINPMVSVEVEKTLRD 283


>gi|301163402|emb|CBW22952.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Bacteroides fragilis 638R]
          Length = 303

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 80/211 (37%), Gaps = 29/211 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP    +    G    + 
Sbjct: 88  RIKDIQTHMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCP----NVKQGGMAFGVT 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
              V + + A   A    + VK    V D      +  + ++ + +G +           
Sbjct: 144 TKGVSEVVQAARSAYKKTLIVKLSPNVTD------IAEMARAAEANGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    ++ IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L
Sbjct: 198 AIDAERKRPILSTVTGGMSGAAVKPIALRMVWQVAKAVNIPVIGL-GGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSAM----LTTVDEYFS 234
                + IG A + + A+    +  +++Y  
Sbjct: 257 AGASAIQIGTANFIDPAITIKVIDGINDYLE 287


>gi|258508450|ref|YP_003171201.1| dihydroorotate dehydrogenase 1B [Lactobacillus rhamnosus GG]
 gi|257148377|emb|CAR87350.1| Dihydroorotate dehydrogenase [Lactobacillus rhamnosus GG]
 gi|259649763|dbj|BAI41925.1| dihydroorotate dehydrogenase [Lactobacillus rhamnosus GG]
          Length = 290

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 69/180 (38%), Gaps = 24/180 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   I GAD+++    AK +        + +N+ CP   V +G        
Sbjct: 86  LASHYPDLPIIASIAGADVAEYAAVAKKLSAAPNVKALEVNISCP--NVDQGGMAFG--T 141

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------- 152
           +P +      A+  A S+P+ VK    V D      +  + K+++ +G +GI        
Sbjct: 142 DPSVAAAVTQAVKAASSVPIFVKLTPNVTD------ITTIAKAVEAAGADGISLINTFVG 195

Query: 153 ----IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               I   + IL  +        +  +   +VY++      + I   GG+     A ++L
Sbjct: 196 MRLDIETGEPILTNVTGGVSGPALFPMALQMVYQVA-HAVHISIIGMGGVSSGHDAAEML 254


>gi|238924828|ref|YP_002938344.1| dihydroorotate dehydrogenase, catalytic subunit [Eubacterium
           rectale ATCC 33656]
 gi|238876503|gb|ACR76210.1| dihydroorotate dehydrogenase, catalytic subunit [Eubacterium
           rectale ATCC 33656]
          Length = 302

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 66/184 (35%), Gaps = 12/184 (6%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + + + G  + + ++  K + D   + + +N+ CP    +    G     +P  V  
Sbjct: 93  DTRIVVNVCGHSLDEYLDVVKRLADEPIDMMEINISCP----NVKEGGIAFGTDPKGVET 148

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVAL-----RNLVKSIKKSGVNGIWIHARKAILK 161
             + + K    PV +K    V               + V  I       I I+ R  +L 
Sbjct: 149 ITSEIKKYAKQPVIMKLSPNVTSIAEIARAAEAGGADAVSLINTITGMKIDINRRSFVLA 208

Query: 162 GL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA 219
                     +  +   +VYE      ++ I   GG+ + + A+++ L     V +G A 
Sbjct: 209 NKTGGMSGPAVHPVAVRMVYE-TAHAVNIPIIGMGGITNAADAIEMILAGATAVSVGTAN 267

Query: 220 YKNS 223
           + N 
Sbjct: 268 FVNP 271


>gi|297623162|ref|YP_003704596.1| dihydroorotate dehydrogenase family protein [Truepera radiovictrix
           DSM 17093]
 gi|297164342|gb|ADI14053.1| dihydroorotate dehydrogenase family protein [Truepera radiovictrix
           DSM 17093]
          Length = 451

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 77/232 (33%), Gaps = 28/232 (12%)

Query: 10  RFFARLLTNNALL---YTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVE 64
           R+       N L      E+I    +     +   +         +   +  +D     +
Sbjct: 57  RYGGWEYGGNKLAAINNIELISDRPLEVNLREIAEVKRLFPDRAVIVSAMFESDPQVWAD 116

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC- 123
           A + +ED G + I LN GCP     E   G+ +   P+        +    S+PV VK  
Sbjct: 117 AVRRIEDTGADAIELNYGCPHGMS-ERGMGSAVGQVPEYCSMITEWVTSVASVPVIVKLT 175

Query: 124 ----------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
                     R  ++ +  A++L N + S+    ++   +        G        +  
Sbjct: 176 PNITDIKAPARAAIEGRAAALSLINTINSVIGVDLDAFTLKPNVGGKGGHGGYAGPAVKP 235

Query: 174 LDYDIVYEIKK--ENPD--LFIGLNGGLEDMSQALKI-------LPSVDGVM 214
           +   ++ E+ +  E  D  + I   GG++    A +        L     VM
Sbjct: 236 IALSMLSEVMQLPETRDFRIPISGMGGIQTWRDAAEFLLLGATSLQVCTAVM 287


>gi|149002514|ref|ZP_01827448.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP14-BS69]
 gi|147759451|gb|EDK66443.1| dihydroorotate dehydrogenase 1B [Streptococcus pneumoniae
           SP14-BS69]
          Length = 210

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/136 (22%), Positives = 54/136 (39%), Gaps = 21/136 (15%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
               I LN+ CP   V   + G  +  +PD+  D + A  +A  +PV VK    V D   
Sbjct: 80  NVKAIELNISCP--NVDHCNHGLLIGQDPDLAYDVVKAAVEASEVPVYVKLTPSVTD--- 134

Query: 133 AVALRNLVKSIKKSGVNGIWI-----------HARKAIL-KGLSPKDNRKIPNLDYDIVY 180
              +  + K+ + +G +G+ +             RK IL  G        +  +   ++ 
Sbjct: 135 ---IVTVAKAAEDAGASGLTMINTLVGMRFDLKTRKPILANGTGGMSGPAVFPVALKLIR 191

Query: 181 EIKKENPDLFIGLNGG 196
           ++ +   DL I   GG
Sbjct: 192 QVAQ-TTDLPIIGMGG 206


>gi|229815184|ref|ZP_04445520.1| hypothetical protein COLINT_02230 [Collinsella intestinalis DSM
           13280]
 gi|229809194|gb|EEP44960.1| hypothetical protein COLINT_02230 [Collinsella intestinalis DSM
           13280]
          Length = 307

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 63/192 (32%), Gaps = 28/192 (14%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSARVHEGSFGACL 97
           +   + +   +  Q+ G    + V A ++  +         +NV CP   +  G      
Sbjct: 91  LADLTAKGTQVICQVAGHSTEEYVRALEMFVELCPWAAGYEINVSCP--NIAAGGAACG- 147

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---- 153
              P+   + + A  K    P+ VK           V +  + ++++  G +G+ +    
Sbjct: 148 -STPEGASEVMRACRKVTDKPLFVKM--------APVRIPEIARALEAEGADGLTVINSI 198

Query: 154 --------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                     R  + K            +   +V+E      D+ I   GG+     A +
Sbjct: 199 PGMSIDVRTRRSRLSKPTGGLSGPLCHPIAVRMVWEAANAV-DIPICGVGGVMTGEDAAE 257

Query: 206 -ILPSVDGVMIG 216
            IL     V +G
Sbjct: 258 FILAGACCVSVG 269


>gi|265764015|ref|ZP_06092583.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_1_16]
 gi|263256623|gb|EEZ27969.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_1_16]
          Length = 303

 Score = 63.3 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/211 (15%), Positives = 80/211 (37%), Gaps = 29/211 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A+I+ +      I LN+ CP    +    G    + 
Sbjct: 88  RIKDIQTHMIVNVSGSAIEDYVKTAEIINELDKIPAIELNISCP----NVKQGGMAFGVT 143

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
              V + + A+  A    + VK    V D      +  + ++ + +G +           
Sbjct: 144 TKGVSEVVQAVRSAYKKTLIVKLSPNVTD------IAEMARAAEANGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I    ++ IL  +        +  +   +V+++ K   ++ +   GG+ +   A++ +L
Sbjct: 198 AIDAERKRPILSTVTGGMSGAAVKPIALRMVWQVAKAV-NIPVIGLGGIMNWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
                + IG A + +      ++  +++Y  
Sbjct: 257 AGASAIQIGTANFIDPTVTIKVIDGINDYLE 287


>gi|325279436|ref|YP_004251978.1| dihydroorotate dehydrogenase family protein [Odoribacter
           splanchnicus DSM 20712]
 gi|324311245|gb|ADY31798.1| dihydroorotate dehydrogenase family protein [Odoribacter
           splanchnicus DSM 20712]
          Length = 301

 Score = 63.3 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 77/207 (37%), Gaps = 29/207 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E  + + + G+ I+   E A+ +    +   I LN+ CP    +    G     +     
Sbjct: 93  ETNILVNVSGSTITDYAETAEKINALDHIPAIELNISCP----NVKEGGMAFGTSCASAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + + A+ +     + VK    V        ++ +  +++  G +            I   
Sbjct: 149 EVVKAVRRVYKKHLMVKLSPNV------TNIQEIALAVESEGADSVSLINTLLGMAIDAK 202

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           +  +   +V+++ K      +GL GG+   + A++ +L     
Sbjct: 203 KRKPVLSTITGGLSGACVKPIALRMVWQVAKAVKIPVVGL-GGIMCATDAIEFLLAGASA 261

Query: 213 VMIGRAAYKNSA----MLTTVDEYFSN 235
           V IG A + + A    ++  +++Y   
Sbjct: 262 VQIGTANFIDPAITVKIIEGINDYLDE 288


>gi|262377507|ref|ZP_06070729.1| NADH:flavin oxidoreductase [Acinetobacter lwoffii SH145]
 gi|262307563|gb|EEY88704.1| NADH:flavin oxidoreductase [Acinetobacter lwoffii SH145]
          Length = 369

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 69/195 (35%), Gaps = 24/195 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              E+AK   + G++ I L+            P +   +  +G  L     +  + + AM
Sbjct: 160 DFAESAKRAVEAGFDLIELHAAHGYLLHQFMSPLSNKRDDQYGGSLENRMRLTLEVLQAM 219

Query: 112 CKAL--SIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             A+    P+ V+      +   D     +   L K+++ +G   I I +      GL  
Sbjct: 220 KAAVPDGYPIGVRISASDWMDQPDSWTIDSSIELSKALEAAGAAYIHISSA-----GLHA 274

Query: 166 KDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           K N  +   +Y +   +  K+  ++ +   G + +  QA  IL     D + + RA   +
Sbjct: 275 KQNIDVKP-NYQVPFADAIKKVVNIPVIAVGLITEAKQAEDILQKGQADAIALARAILYD 333

Query: 223 SAMLTTVDEYFSNPL 237
                         +
Sbjct: 334 PHWPWHAAAALEEKI 348


>gi|212550935|ref|YP_002309252.1| dihydroorotate dehydrogenase 1B [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|229485539|sp|B6YRL9|PYRD_AZOPC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|212549173|dbj|BAG83841.1| dihydroorotate dehydrogenase [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
          Length = 302

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 75/197 (38%), Gaps = 25/197 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E  + + I G+ I   V  A+ + +      I LN+ CP+ +      G     N     
Sbjct: 93  ETNIMVNISGSTIEDCVSCAEKINELDKIPAIELNISCPNMK----QGGMAFGTNCSNAS 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + + A+ K     + VK    V D      +  + K+++ +G +            I I 
Sbjct: 149 EIVNAVRKVYHKILIVKLSPNVTD------ITEIAKAVEIAGADAVSLINTLIGMAIDIK 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            +K IL  ++       I  +   +VY+  K    + I   GG+ +   A++ IL     
Sbjct: 203 IKKPILSTVTGGLSGPCIKPIALRMVYQTYK-IVKIPIIGLGGISNSDDAIEFILAGASA 261

Query: 213 VMIGRAAYKNSAMLTTV 229
           + +G   + +  + T +
Sbjct: 262 IQVGTYNFIDPTISTKI 278


>gi|77166274|ref|YP_344799.1| dihydroorotate dehydrogenase 1 [Nitrosococcus oceani ATCC 19707]
 gi|254435794|ref|ZP_05049301.1| dihydroorotate dehydrogenase family protein [Nitrosococcus oceani
           AFC27]
 gi|76884588|gb|ABA59269.1| dihydroorotate oxidase B, catalytic subunit [Nitrosococcus oceani
           ATCC 19707]
 gi|207088905|gb|EDZ66177.1| dihydroorotate dehydrogenase family protein [Nitrosococcus oceani
           AFC27]
          Length = 331

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 67/204 (32%), Gaps = 27/204 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            E      + G+ I +     +  ++   + I +N+ CP    +    G     +P +  
Sbjct: 107 SETRYIANVSGSTIEEYTAVTRRFDNSPIDAIEINISCP----NVKEGGVAFGNDPHMSA 162

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
             + A  K    P+  K            ++    +   ++G +G             I 
Sbjct: 163 RVVEACRKVTRKPLITKLSP------NQTSIEENARRCIEAGTDGFAVINTLMGMAIDIE 216

Query: 155 ARKA----ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
            R      I  GLS    + I  L    VY+  + +  + I   GG+     AL+ L   
Sbjct: 217 QRTPLLGNIQGGLSGPAIKPIALLKVRQVYQACRAHG-IPIIGQGGVASGKDALEFLIAG 275

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYF 233
              V +G A + +  +   ++   
Sbjct: 276 ATTVGVGTALFYDPLLCAKINAEI 299


>gi|95931414|ref|ZP_01314122.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfuromonas acetoxidans
           DSM 684]
 gi|95132532|gb|EAT14223.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfuromonas acetoxidans
           DSM 684]
          Length = 342

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 66/189 (34%), Gaps = 16/189 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAA 110
               +AA   ++ GY+ I L+       C    P     +  +G  L     IV + + A
Sbjct: 145 ELFADAAVRAQNAGYDIIELHAAHGYLLCEFLSPLTNQRQDRYGGSLENRCRIVLETVKA 204

Query: 111 MCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + + + IP+ V+      +++         L K ++K GV  + I A             
Sbjct: 205 IKEKVDIPLMVRISADEWMENGWKVEDSIYLSKELEKIGVAAMHISAGGNHEVVDHLPAF 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
             +   DY    +  K+   + +   G +    Q   IL +   D V  GR   ++   +
Sbjct: 265 EPLYQCDY---AQKIKQAVSIPVIAVGLITTPQQGEGILKNGMCDFVAYGRELLRSPNFV 321

Query: 227 TTVDEYFSN 235
               + F  
Sbjct: 322 FQAAKLFEE 330


>gi|330974595|gb|EGH74661.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 143

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 44/132 (33%), Gaps = 13/132 (9%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
              ++ +  I +E   + +  NG +  +    +         +MIGR       +   + 
Sbjct: 1   PAHWEWIARI-QEVVKVPVVANGEIWTVEDWRRCREICGARDIMIGRGLVARPDLARQIV 59

Query: 231 EYFSNPL--TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFP 288
                      +      + + FW+     MT      + + G+L+Q    ++ L   +P
Sbjct: 60  AAQKGEEVVPMTWDALQPMLRVFWQDCLVKMT-----LIQAPGRLKQW---LVLLTKSYP 111

Query: 289 NSRRCRHILTVE 300
            +    + L  E
Sbjct: 112 EATLMFNRLRRE 123


>gi|298376819|ref|ZP_06986774.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           3_1_19]
 gi|298266697|gb|EFI08355.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           3_1_19]
          Length = 497

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 57/169 (33%), Gaps = 22/169 (13%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+     G + I  N  CP   + +   G+ +  +P++V    AA  +   +P+  K   
Sbjct: 224 AQYSMQAGADIIECNFSCPQ--MTQEGMGSDVGQSPELVRRFTAATRRGTHLPILAKMTP 281

Query: 126 GVDDQIPA-----------VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            +    P            +A  N +K I +            + L  +S    R +  +
Sbjct: 282 NIGQMTPVALAAHEGGATGIAAINTIKCITRIDEKAFTARPVVSGLSSVSGYSGRAVRPI 341

Query: 175 DYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKI-------LPSVDGVM 214
               ++E+  +     + I   GG+E    AL         L     VM
Sbjct: 342 ALRFIHELASDPSAGKMPISGIGGIETWRDALDFLLLGCTNLQICTAVM 390


>gi|227873450|ref|ZP_03991704.1| dihydroorotate oxidase [Oribacterium sinus F0268]
 gi|227840705|gb|EEJ51081.1| dihydroorotate oxidase [Oribacterium sinus F0268]
          Length = 314

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 33/198 (16%), Positives = 65/198 (32%), Gaps = 21/198 (10%)

Query: 48  KPLALQIGGADISKL---VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           KPL   I G    +     E    VE+ G   + +N+ CP   VH G        +   V
Sbjct: 106 KPLVANISGFSFEEFSILAEEMDKVENVG--LLEVNISCP--NVHNGGMAFG--TDAKNV 159

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIKKSGVNGIWIHAR 156
            +    + +    PV +K    V D                 L+ ++    ++      R
Sbjct: 160 AEVCKRVKEKTKKPVYMKLSPNVTDITEMAKAAEAAGADGISLINTLLGMRID--IKRRR 217

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
             +   +       +  +   +VY+++K    + I   GG+      ++ ++     V I
Sbjct: 218 PVLANKVGGYSGPAVFPIALRMVYQVRKAV-QIPIIGMGGIASAEDVIEMMMAGASAVEI 276

Query: 216 GRAAYKNSAMLTTVDEYF 233
           G     +  +   + E  
Sbjct: 277 GAENLVHPYVCRDILENL 294


>gi|317129271|ref|YP_004095553.1| dihydroorotate dehydrogenase [Bacillus cellulosilyticus DSM 2522]
 gi|315474219|gb|ADU30822.1| dihydroorotate dehydrogenase family protein [Bacillus
           cellulosilyticus DSM 2522]
          Length = 308

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 82/218 (37%), Gaps = 30/218 (13%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +      ++L          + P+ + I G  +   +E  K +      N I L
Sbjct: 67  MLNAIGLQNPGLAHVLEHELPWLEQYDTPIVVNIAGYQVEDYMEVTKAISKVKNVNAIEL 126

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP   V EG        +     +    +     +PV VK    V D      +  +
Sbjct: 127 NISCP--NVKEGGITFG--TDASTAANLTEKVKAVSQVPVYVKLSPNVTD------IVEI 176

Query: 140 VKSIKKSGVNGI----WIHARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKENP 187
            K+++++G +G+     +   +  LK   P             I  +   +++++ ++  
Sbjct: 177 AKAVEQAGADGLSMINTLLGMRIDLKTGQPILANKTGGLSGAAIKPVAIRMIHDVSQQVS 236

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
              IG+ GG+ ++   L+ ++     V +G A + +  
Sbjct: 237 IPIIGM-GGIYEVDDILEFMMAGASAVAVGTANFIDPF 273


>gi|282859335|ref|ZP_06268446.1| dihydroorotate dehydrogenase 1B [Prevotella bivia JCVIHMP010]
 gi|282587881|gb|EFB93075.1| dihydroorotate dehydrogenase 1B [Prevotella bivia JCVIHMP010]
          Length = 302

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 32/192 (16%), Positives = 65/192 (33%), Gaps = 27/192 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +    + + G       EAA  + +      I LN+ CP   V EG     +        
Sbjct: 93  DTNFIVNVSGDSPETYAEAAAKINELDKIPAIELNISCP--NVKEGGMSFGVTC--AGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
             + A+    +  + VK    V D      +  + +  +  G + + +            
Sbjct: 149 SVVKAVRVHYNKTLIVKLSPNVTD------IAAIARVCEDEGADSVSLINTLMGMAIDIE 202

Query: 154 -HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
            H  K  ++         +  +   +VY++ K      IGL GG+     A++ ++    
Sbjct: 203 RHRPKLSIR-TGGLSGPAVKPVALRMVYDVAKAVKIPVIGL-GGISTAEDAIEFLMAGAS 260

Query: 212 GVMIGRAAYKNS 223
            + IG A + + 
Sbjct: 261 AIQIGTANFVDP 272


>gi|15921375|ref|NP_377044.1| dihydropyrimidine dehydrogenase [Sulfolobus tokodaii str. 7]
 gi|15622161|dbj|BAB66153.1| 350aa long hypothetical dihydroorotate dehydrogenase [Sulfolobus
           tokodaii str. 7]
          Length = 350

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 47/211 (22%), Positives = 80/211 (37%), Gaps = 32/211 (15%)

Query: 25  EMIVADAILRGDKKNILGFSTQEK--PLALQI-GGADISKLVEAAKIVEDFGYNEINLNV 81
           E+I  D +   DK   +  S   K  P+ + I GG D S+ +  A+  ED G + + LN 
Sbjct: 76  ELITEDPLEVWDKYLRVIKSEIGKSAPIIVSIMGGPDYSEWIRLARWAEDRGADMLELNF 135

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP     E   GA +  + D+V +    +  ++ IPV  K    + D      +R   K
Sbjct: 136 GCPHGE-PEKRTGAFIGQHADLVQEYTKEVVSSVGIPVIAKLTPNITD------IRETAK 188

Query: 142 SIKKSGVNGIWI--------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKK--E 185
           + + +G   +                      + G S       P +    +  + K   
Sbjct: 189 AAENAGAKAVTAINTVNGVIAVDIERAQPLPDINGYSGYGGISGPAVKPIGLAAVSKIYT 248

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
           +  L I   GG+ D   A++       +M+G
Sbjct: 249 STSLQISGVGGIFDWRDAVEY------IMMG 273


>gi|260912560|ref|ZP_05919092.1| dihydroorotate oxidase [Prevotella sp. oral taxon 472 str. F0295]
 gi|260633325|gb|EEX51483.1| dihydroorotate oxidase [Prevotella sp. oral taxon 472 str. F0295]
          Length = 302

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/191 (15%), Positives = 67/191 (35%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A  V+       I LN+ CP    +    G           
Sbjct: 93  DTRMIVNVSGNTPEDYAECAARVDALENIPAIELNISCP----NVKEGGMAFGTTCAGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      +  + ++++  G +            I I 
Sbjct: 149 SVVRAVRERYRKTLIVKLSPNVTD------VTEIARAVEAEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+++L           +  +   +V+++ K    + I   GG+ + + A++ ++     
Sbjct: 203 RRQSVLSINTGGLSGPAVKPVALRMVWQVAKAV-KIPIIGLGGICNATDAIEFMMAGASA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFLDP 272


>gi|295695972|ref|YP_003589210.1| dihydroorotate dehydrogenase family protein [Bacillus tusciae DSM
           2912]
 gi|295411574|gb|ADG06066.1| dihydroorotate dehydrogenase family protein [Bacillus tusciae DSM
           2912]
          Length = 318

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 74/206 (35%), Gaps = 28/206 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            PL + I G         A  +   G   I +N+ CP+  V  G +   +    D     
Sbjct: 94  TPLVVSISGESPEGYARLAHRLTVPGVQAIEVNISCPNLEV--GGWSPAM--EADGTYRT 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HAR 156
           I A+ +A  + +  K      D +         ++ +++G + + +           H +
Sbjct: 150 IRAVREATDLSIWAKLTPNTGDMVSV------ARAAQEAGADALVVANTLIGMAIDPHTK 203

Query: 157 KAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  L  ++       +  +   +VY+I   +  + I   GG+  +   L+ +L     V 
Sbjct: 204 RPKLGNVTGGLSGPAVKPIILRMVYQIY-PHVSIPIIGCGGISRVDDVLEYLLAGARAVQ 262

Query: 215 IGRAAYKNS----AMLTTVDEYFSNP 236
           +G   + N      ++  ++EY    
Sbjct: 263 VGTYNFVNPRGMTEIIRDLEEYVERE 288


>gi|193213171|ref|YP_001999124.1| dihydroorotate dehydrogenase family protein [Chlorobaculum parvum
           NCIB 8327]
 gi|193086648|gb|ACF11924.1| dihydroorotate dehydrogenase family protein [Chlorobaculum parvum
           NCIB 8327]
          Length = 313

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 38/216 (17%), Positives = 78/216 (36%), Gaps = 37/216 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
              + + I G  I    +  + ++   G     LN+ CP    +       + ++PD   
Sbjct: 103 GTQVIVNIAGKSIDDYCQVVERLDQVEGIAAYELNLSCP----NVKGECMIMGVSPDATR 158

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + ++ + K     + VK    V       ++  +  + ++SG +            I   
Sbjct: 159 EIVSTLRKLTDRHLMVKLTPNV------TSISAIALAAEESGADSVSLINTVVGMAIDYR 212

Query: 155 ARKAILK----GLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
            RK +LK    GLS    + I     +++   +K     + I   GG+   + A++ +L 
Sbjct: 213 TRKPLLKNVTGGLSGPAIKPIALAKVWEVSNAVK-----IPIVGMGGIASFADAMEFLLA 267

Query: 209 SVDGVMIGRAAYKNSA----MLTTVDEYFSNPLTGS 240
               + IG   +        +   +D +FS P   S
Sbjct: 268 GASAIQIGTMNFVYPDIGEKIAIEIDNFFSQPDAPS 303


>gi|85859164|ref|YP_461366.1| dihydroorotate dehydrogenase, catalytic subunit [Syntrophus
           aciditrophicus SB]
 gi|85722255|gb|ABC77198.1| dihydroorotate dehydrogenase, catalytic subunit [Syntrophus
           aciditrophicus SB]
          Length = 330

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 35/223 (15%), Positives = 83/223 (37%), Gaps = 32/223 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV 88
            A +      +  F+T    +   I G  + +  + A+I+    G   + +N+ CP   V
Sbjct: 105 RAFVEQKLPFLKDFTTA---VIANIFGETLDEYEKVAEILTAAGGVAALEVNISCP--NV 159

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
            +G        +P++  +    + ++ ++PV +K    V D      +  + +S++ +G 
Sbjct: 160 KKGGIAFG--ADPEMAAEVTGRVKQSTNLPVIMKLSPNVTD------ISAIAESVEAAGA 211

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + + +              +  +           +  +   +V+++        IGL GG
Sbjct: 212 DAVSLINTLTGMSVDVERRKPHLYNMTGGLSGPAVKPVALRMVWQVASRVQIPVIGL-GG 270

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNS----AMLTTVDEYFS 234
           +   + AL+ L      V +G A + +      +L  +  Y  
Sbjct: 271 IMTANDALEFLIVGAKAVQVGTANFVDPRATMKILDGMTHYLR 313


>gi|325297793|ref|YP_004257710.1| dihydroorotate dehydrogenase family protein [Bacteroides
           salanitronis DSM 18170]
 gi|324317346|gb|ADY35237.1| dihydroorotate dehydrogenase family protein [Bacteroides
           salanitronis DSM 18170]
          Length = 303

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 81/205 (39%), Gaps = 29/205 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ I    E A I++   +   I LN+ CP   V +G     +  +     +
Sbjct: 94  TNMIVNVSGSQIEDYAETASIIDGLEHIPAIELNISCP--NVKQGGMAFGVTAHG--ASE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++A+ K     + VK    V D      +  + ++++ +G +            I    
Sbjct: 150 VVSAVRKVYHKTLIVKLSPNVTD------ITEIARAVESAGADSVSLINTLLGMAIDAEK 203

Query: 156 RKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           RK IL  +        +  +   +V+++ K      IGL GG+ +   A++ +L     V
Sbjct: 204 RKPILSTVTGGMSGAAVKPIALRMVWQVAKTVKIPVIGL-GGIMNARDAIEFLLAGATAV 262

Query: 214 MIGRAAYKNSAM----LTTVDEYFS 234
            IG A + + A+       ++EY  
Sbjct: 263 QIGTANFIDPAITVKVAEGINEYLD 287


>gi|150007812|ref|YP_001302555.1| dihydropyrimidine dehydrogenase [Parabacteroides distasonis ATCC
           8503]
 gi|149936236|gb|ABR42933.1| oxidoreductase iron-sulfur protein [Parabacteroides distasonis ATCC
           8503]
          Length = 497

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 70/208 (33%), Gaps = 24/208 (11%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           ++A +  +   +  L     +K +   I G    +    A+     G + I  N  CP  
Sbjct: 185 SEASVEENFDTLYRLKQRYPDKLIISSIMGRTDDEWTRLAQYSTQAGADIIECNFSCPQ- 243

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VA 135
            + +   G+ +  +P++V    AA  +   +P+  K    +    P            +A
Sbjct: 244 -MTQEGMGSDVGQSPELVRRFTAATRRGTHLPILAKMTPNIGQMTPVALAAHEGGATGIA 302

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGL 193
             N +K I +     +        L  +S    + +  +    ++E+  +     + I  
Sbjct: 303 AINTIKCITRIDEKALTARPVVCGLSSVSGYSGKAVRPIALRFIHELASDPSAGKMPISG 362

Query: 194 NGGLEDMSQALKI-------LPSVDGVM 214
            GG+E    AL         L     VM
Sbjct: 363 IGGIETWRDALDFLLLGCTNLQICTAVM 390


>gi|294673298|ref|YP_003573914.1| dihydroorotate oxidase, catalytic subunit [Prevotella ruminicola
           23]
 gi|294473654|gb|ADE83043.1| dihydroorotate oxidase, catalytic subunit [Prevotella ruminicola
           23]
          Length = 301

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 33/193 (17%), Positives = 70/193 (36%), Gaps = 25/193 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+      E A  ++       I LN+ CP   V +G     +        
Sbjct: 93  DTNMIVNVSGSSPEDYAECAARIDALENIPAIELNISCP--NVKDGGMAFGVTC--AGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      +  + ++++  G +            I I 
Sbjct: 149 SVVKAVRQRYHKTLIVKLSPNVTD------IAEIARAVEAEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           +  +   +V+++ K      IGL GG+     A++ ++     
Sbjct: 203 KRKTLLSINTGGLSGPCVKPVALRMVWQVAKAVKIPVIGL-GGISCAKDAIEFLMAGATA 261

Query: 213 VMIGRAAYKNSAM 225
           + IG A + + A+
Sbjct: 262 IEIGTANFLDPAV 274


>gi|317490556|ref|ZP_07949032.1| dihydroorotate dehydrogenase [Eggerthella sp. 1_3_56FAA]
 gi|316910336|gb|EFV31969.1| dihydroorotate dehydrogenase [Eggerthella sp. 1_3_56FAA]
          Length = 301

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 73/194 (37%), Gaps = 24/194 (12%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +   + + + G    + V+  + +ED   +   +N+ CP+      + G C     D 
Sbjct: 89  AERGATVIVNVSGHSFDEYVQVIEALEDAPVDAYEVNISCPNVDAGGMTIGTC----TDS 144

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
           V   ++    A   P+ VK    V D      +  + ++   +G + + +          
Sbjct: 145 VEAVVSRCRAATKRPLIVKLTPNVTD------VTEIARAAVSAGADALSLINTLLGMAID 198

Query: 154 --HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
               R  + +G+       +  +   +V+E+ +   D+ +   GG+     A++ +L   
Sbjct: 199 AERRRPQLARGVGGLSGPAVKPVALRMVWEVHQAV-DVPLLGMGGISCAIDAVEFMLAGA 257

Query: 211 DGVMIGRAAYKNSA 224
             V +G A + N  
Sbjct: 258 TAVAVGTANFVNPH 271


>gi|262381679|ref|ZP_06074817.1| oxidoreductase iron-sulfur protein [Bacteroides sp. 2_1_33B]
 gi|262296856|gb|EEY84786.1| oxidoreductase iron-sulfur protein [Bacteroides sp. 2_1_33B]
          Length = 497

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 70/208 (33%), Gaps = 24/208 (11%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           ++A +  +   +  L     +K +   I G    +    A+     G + I  N  CP  
Sbjct: 185 SEASVEENFDTLYRLKQRYPDKLIISSIMGRTDDEWTRLAQYSTQAGADIIECNFSCPQ- 243

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VA 135
            + +   G+ +  +P++V    AA  +   +P+  K    +    P            +A
Sbjct: 244 -MTQEGMGSDVGQSPELVRRFTAATRRGTHLPILAKMTPNIGQMTPVALAAHEGGATGIA 302

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGL 193
             N +K I +     +        L  +S    + +  +    ++E+  +     + I  
Sbjct: 303 AINTIKCITRIDEKALTARPVVCGLSSVSGYSGKAVRPIALRFIHELASDPSAGKMPISG 362

Query: 194 NGGLEDMSQALKI-------LPSVDGVM 214
            GG+E    AL         L     VM
Sbjct: 363 IGGIETWRDALDFLLLGCTNLQICTAVM 390


>gi|302345691|ref|YP_003814044.1| dihydroorotate dehydrogenase 1B [Prevotella melaninogenica ATCC
           25845]
 gi|302149734|gb|ADK95996.1| dihydroorotate dehydrogenase 1B [Prevotella melaninogenica ATCC
           25845]
          Length = 302

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 29/191 (15%), Positives = 68/191 (35%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A+ ++   G   I +N+ CP   V EG     +  +     
Sbjct: 93  DTNMIVNVSGNSPETYAETAEKLDALEGIPAIEVNISCP--NVKEGGMLFGVTCSG--AA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      + ++ ++ +  G +            I I 
Sbjct: 149 SIVKAVRQHYHKTMIVKLSPNVTD------IASIARACEDEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+  L   +       +  +   +V ++ K    + +   GG+     A++ ++     
Sbjct: 203 RRRPKLSIRTGGLSGPAVKPVAVRMVNDVAKAV-KIPVIGLGGISTAEDAIEFLMAGATA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFLDP 272


>gi|290996101|ref|XP_002680621.1| dihydroorotate dehydrogenase family protein [Naegleria gruberi]
 gi|284094242|gb|EFC47877.1| dihydroorotate dehydrogenase family protein [Naegleria gruberi]
          Length = 1038

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 31/161 (19%), Positives = 51/161 (31%), Gaps = 31/161 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A   E  G + I LN+ CP     E   G    ++P +V +    +     IP   K   
Sbjct: 655 ATKAEQAGADMIELNLSCPHGM-GEKGLGLACGMDPYLVLNICKWVRAVTKIPFFAKLTP 713

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW---------------------IHARKAILKGLS 164
            V D      +  +  + +  G +G+                         ++    G+S
Sbjct: 714 NVTD------VLQIATAARDGGADGVTATNTVSGLMTLKPDATAWPAVGANKRTTYGGVS 767

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
               R I       V ++ K  P   I   GG +    AL+
Sbjct: 768 GNAIRPIAM---KAVSKVAKNIPGYPILATGGCDSADVALQ 805


>gi|325289503|ref|YP_004265684.1| dihydroorotate oxidase B, catalytic subunit [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964904|gb|ADY55683.1| dihydroorotate oxidase B, catalytic subunit [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 502

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 69/195 (35%), Gaps = 16/195 (8%)

Query: 25  EMIVADAILRG-DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E I    +    +  + L      K +   I G D  +    A+ V + G + I  N  C
Sbjct: 179 EQISDHTLEENLEFMSRLKRDFPHKVVVASILGQDEEEWTFLARKVTEAGVDIIECNFSC 238

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV-----------DDQIP 132
           P   +     G+ +  +P++V    AA  K   +P+  K    +           ++   
Sbjct: 239 PH--MTGEGLGSDVGQSPELVALYTAATRKGTDLPILAKMTPNIGNMEIPAIAAMENGAT 296

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLF 190
            +A  N +KSI    ++      R      +     + +  +    ++++KK     +  
Sbjct: 297 GIAAINTIKSIMNINLDDFVSEPRVDGKSCVGGYSGKTVKPIALRFIHDMKKHPKLKECP 356

Query: 191 IGLNGGLEDMSQALK 205
           I   GG+E    A +
Sbjct: 357 ISGMGGIETWRDAAE 371


>gi|296108975|ref|YP_003615924.1| TIM-barrel protein [Methanocaldococcus infernus ME]
 gi|295433789|gb|ADG12960.1| TIM-barrel protein [Methanocaldococcus infernus ME]
          Length = 241

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 29/156 (18%), Positives = 59/156 (37%), Gaps = 17/156 (10%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           KI+ +   + I LN  C    + E   G  L+ N  ++   +  +   L  P+ +K R+ 
Sbjct: 95  KIISEH-ADIIELNCHCRQREITELGIGQELLRNVKLLSSFLEKLYS-LDKPLFLKIRLN 152

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
             +    +   +LV+       +G+ +        G    D   +          I++  
Sbjct: 153 YIETEELIKNLSLVREYF----DGLHV---DCFYPGKDYPDIEGL--------KRIRESF 197

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
            D  I  N  +  + +A ++L   + + + RA  KN
Sbjct: 198 EDKTIIGNNSITSLERAKEMLKYSNLISVARAVLKN 233


>gi|194376574|dbj|BAG57433.1| unnamed protein product [Homo sapiens]
          Length = 109

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 15/93 (16%)

Query: 188 DLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
            + +  NG +  + +A  +  +   DGVM+ R    N AM    +E         +P+K 
Sbjct: 2   SIPVIANGDIRSLKEAENVWRITGTDGVMVARGLLANPAMFAGYEE---------TPLKC 52

Query: 246 RVDKDFWRKISASM-TDYAARHLHSGGKLQQIT 277
             D   W  I+  + T Y   H H    +++IT
Sbjct: 53  IWD---WVDIALELGTPYMCFHQHLMYMMEKIT 82


>gi|154705703|gb|ABS84237.1| putative dihydropyrimidine dehydrogenase [Delftia sp. I24]
          Length = 439

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 61/167 (36%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ +        +   +PV VK    +
Sbjct: 123 MVEDTGADGLELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTQWCKQYSRLPVIVKLTPNI 181

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + S+    ++ + +H                +  +  
Sbjct: 182 TDVRFPARAAKAGGADAVSLINTINSLMGVNLDTLVMHPSTDGQGSHGGYCGPAVKPIAQ 241

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 242 NMVAEIARDPQTAGLPISGIGGITTWKDAAEYIALGCGNVQVCTAAM 288


>gi|160898303|ref|YP_001563885.1| dihydropyrimidine dehydrogenase [Delftia acidovorans SPH-1]
 gi|160363887|gb|ABX35500.1| dihydroorotate dehydrogenase family protein [Delftia acidovorans
           SPH-1]
          Length = 439

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 61/167 (36%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ +        +   +PV VK    +
Sbjct: 123 MVEDTGADGLELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTQWCKQYSRLPVIVKLTPNI 181

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + S+    ++ + +H                +  +  
Sbjct: 182 TDVRFPARAAKAGGADAVSLINTINSLMGVNLDTLVMHPSTDGQGSHGGYCGPAVKPIAQ 241

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 242 NMVAEIARDPQTAGLPISGIGGITTWKDAAEYIALGCGNVQVCTAAM 288


>gi|163758230|ref|ZP_02165318.1| NADH:flavin oxidoreductase/NADH oxidase [Hoeflea phototrophica
           DFL-43]
 gi|162284519|gb|EDQ34802.1| NADH:flavin oxidoreductase/NADH oxidase [Hoeflea phototrophica
           DFL-43]
          Length = 371

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 66/209 (31%), Gaps = 24/209 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
              V AA+     G+  I +++           P +     ++G  L   M  P  V D 
Sbjct: 158 EDFVRAAERAVRLGFCGIEVHMAHGYLLHQFLSPLSNQRNDAYGGTLENRMRFPLEVFDA 217

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I A   A  IPV ++      V+      +   L  ++K+ G   I +        G+SP
Sbjct: 218 IRAAV-APHIPVWIRVSATDWVEGGWDLESTLALCAAVKERGCAAIHVSTG-----GVSP 271

Query: 166 KDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           K    +           IK E   L     G + D  QA  I+     D + + R    +
Sbjct: 272 KQKIPVGPGFQVPFATRIKAETG-LPTIAVGLITDPQQADAIVQNGEADAIALARGILYD 330

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
                         ++          ++F
Sbjct: 331 PHWPWHAAAALGAKVSAPKQYWRSAPREF 359


>gi|256840078|ref|ZP_05545587.1| oxidoreductase iron-sulfur protein [Parabacteroides sp. D13]
 gi|256739008|gb|EEU52333.1| oxidoreductase iron-sulfur protein [Parabacteroides sp. D13]
          Length = 497

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 70/208 (33%), Gaps = 24/208 (11%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           ++A +  +   +  L     +K +   I G    +    A+     G + I  N  CP  
Sbjct: 185 SEASVEENFDTLYRLKQRYPDKLIISSIMGRTDDEWTRLAQYSTQAGADIIECNFSCPQ- 243

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VA 135
            + +   G+ +  +P++V    AA  +   +P+  K    +    P            +A
Sbjct: 244 -MTQEGMGSDVGQSPELVRRFTAATRRGTHLPILAKMTPNIGQMTPVALAAHEGGATGIA 302

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGL 193
             N +K I +     +        L  +S    + +  +    ++E+  +     + I  
Sbjct: 303 AINTIKCITRIDEKALTARPVVCGLSSVSGYSGKAVRPIALRFIHELASDPSAGKMPISG 362

Query: 194 NGGLEDMSQALKI-------LPSVDGVM 214
            GG+E    AL         L     VM
Sbjct: 363 IGGIETWRDALDFLLLGCTNLQICTAVM 390


>gi|255013479|ref|ZP_05285605.1| dihydropyrimidine dehydrogenase [Bacteroides sp. 2_1_7]
          Length = 452

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 70/208 (33%), Gaps = 24/208 (11%)

Query: 29  ADAILRGDKKNI--LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           ++A +  +   +  L     +K +   I G    +    A+     G + I  N  CP  
Sbjct: 140 SEASVEENFDTLYRLKQRYPDKLIISSIMGRTDDEWTRLAQYSTQAGADIIECNFSCPQ- 198

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VA 135
            + +   G+ +  +P++V    AA  +   +P+  K    +    P            +A
Sbjct: 199 -MTQEGMGSDVGQSPELVRRFTAATRRGTHLPILAKMTPNIGQMTPVALAAHEGGATGIA 257

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGL 193
             N +K I +     +        L  +S    + +  +    ++E+  +     + I  
Sbjct: 258 AINTIKCITRIDEKALTARPVVCGLSSVSGYSGKAVRPIALRFIHELASDPSAGKMPISG 317

Query: 194 NGGLEDMSQALKI-------LPSVDGVM 214
            GG+E    AL         L     VM
Sbjct: 318 IGGIETWRDALDFLLLGCTNLQICTAVM 345


>gi|304439889|ref|ZP_07399783.1| dihydroorotate oxidase [Peptoniphilus duerdenii ATCC BAA-1640]
 gi|304371628|gb|EFM25240.1| dihydroorotate oxidase [Peptoniphilus duerdenii ATCC BAA-1640]
          Length = 299

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 37/224 (16%), Positives = 81/224 (36%), Gaps = 29/224 (12%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADI-SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +    K+ L   T   P      G++   + +++A+I+ D+ ++ I LN+ CP   V EG
Sbjct: 78  IHEFVKHELKDMTNLGPRIFVNLGSNTLDEYLKSAEILNDYEFDFIELNISCP--NVKEG 135

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
                +    +        + +     + VK          A  +     ++++ G +GI
Sbjct: 136 GMAFGI--KCESSEMITRKIKEISKHKIVVKLSP------NAENIVENALAVEEGGADGI 187

Query: 152 W-----------IHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
                       +  RK +     +      I  +   +V+++     D+ +   GG+  
Sbjct: 188 SLVNTFLGMAIDLEKRKPVFDNVYAGLSGPAIKPIALRMVHQVA-HAVDIPVMAIGGVAG 246

Query: 200 MSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNPLT 238
               L+ I+     V +G   + N      +L  +++Y     T
Sbjct: 247 YRDVLEFIMAGAKLVQVGTYNFMNPYGVKEILEDLEKYLEKNNT 290


>gi|288932438|ref|YP_003436498.1| TIM-barrel protein [Ferroglobus placidus DSM 10642]
 gi|288894686|gb|ADC66223.1| TIM-barrel protein [Ferroglobus placidus DSM 10642]
          Length = 236

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 69/175 (39%), Gaps = 27/175 (15%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI E++    + +N  C      E   G  L+ N + + + +    K     V+VK R 
Sbjct: 83  AKICEEYDV-LLEINAHCRQPEFMEIGAGQSLLFNQEKLLNIVEKCSKYCD--VSVKIRG 139

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G++    +++ +           +   +H    I  G            DY+++ EI   
Sbjct: 140 GLNLDYSSLSEKLF--------SSAFILHVDAMIPGGG----------ADYNLIKEI-SA 180

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV--DEYFSNPL 237
             +  +  N  ++D++ A K++      V + RA  KN  +   +  D+  S P+
Sbjct: 181 FGN--VIGNNSVKDINTARKMIESGAKLVSLARAVIKNERIFDELLEDDILSLPI 233


>gi|256830609|ref|YP_003159337.1| dihydroorotate dehydrogenase family protein [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579785|gb|ACU90921.1| dihydroorotate dehydrogenase family protein [Desulfomicrobium
           baculatum DSM 4028]
          Length = 302

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 78/226 (34%), Gaps = 31/226 (13%)

Query: 26  MIVADAI----LRGDKKNILGFSTQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLN 80
           M+ A  +    +    K  L +      L   +         E AA    +     + +N
Sbjct: 66  MLNAIGLQNVGVEKFLKEKLPYIPAGATLIANLYAQTPEDFGELAAIFSGEDKIAALEVN 125

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNL 139
           + CP   V EG        +P +    + A+ K A S PV VK    V D      +R +
Sbjct: 126 ISCP--NVREGGVQFG--QDPHMASAVVGAVKKRAGSKPVIVKLSPNVTD------VRVI 175

Query: 140 VKSIKKSGVNGIW-----------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENP 187
            ++   +G + +            I  RK+ L  +        I  +   +V+++ +   
Sbjct: 176 ARAAVDAGADMLSLINTLSGMAVDIRTRKSRLANVVGGLSGPAIKPVALRMVHQVVQSVN 235

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAM-LTTVDE 231
              IG+ GG+      L+ IL     V +G   +         V+E
Sbjct: 236 VPVIGM-GGIVSAEDVLEFILVGAHAVQVGTYNFMRPDNAFRLVEE 280


>gi|296115914|ref|ZP_06834537.1| dihydroorotate dehydrogenase family protein [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295977486|gb|EFG84241.1| dihydroorotate dehydrogenase family protein [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 311

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 70/196 (35%), Gaps = 18/196 (9%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            + +  ++    PL + I   D +     A+ V   G + I  N+ CP+      +F   
Sbjct: 81  NRTLPHYTQWGTPLIVSISAPDAAGFATLARAVSIAGVDAIEANISCPNIEADGKAFAM- 139

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD--------QIPAVALRNLVKSIKKSGV 148
                +     +AA+  A  +P+ VK      D        +        +  +I    +
Sbjct: 140 ---EANATTKVVAALRAATDLPLWVKLTPNCHDMSVIARAAEAAGADAVVVANTILGMSI 196

Query: 149 NGIWIHARKA-ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
           +      R   ++ GLS      I  +     Y+  + +  + +   GG+     A++ +
Sbjct: 197 DTRTFRPRLGNVMGGLSGA---AIKPIILRQTYQCAR-SVAIPVIGCGGITTADDAVEYM 252

Query: 207 LPSVDGVMIGRAAYKN 222
           L     V +G A++ N
Sbjct: 253 LAGAVAVQVGTASFIN 268


>gi|70729914|ref|YP_259653.1| dihydropyrimidine dehydrogenase [Pseudomonas fluorescens Pf-5]
 gi|68344213|gb|AAY91819.1| dihydroorotate dehydrogenase family protein [Pseudomonas
           fluorescens Pf-5]
          Length = 424

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEQVTRWCKTYCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    +  +  H                +  +  
Sbjct: 181 TDIRMAARAAHRGGADAVSLINTINSITSVDLERMVAHPMVGSQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 241 NMVAEIARDPQTRGLPICGIGGIGSWRDAAEFVALGCGAVQVCTAAM 287


>gi|146304708|ref|YP_001192024.1| dihydroorotate oxidase B, catalytic subunit [Metallosphaera sedula
           DSM 5348]
 gi|145702958|gb|ABP96100.1| dihydroorotate oxidase B, catalytic subunit [Metallosphaera sedula
           DSM 5348]
          Length = 290

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 72/187 (38%), Gaps = 35/187 (18%)

Query: 46  QEKPLALQIG----GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           + KP+  ++     G+   ++V+ A +  D     I +NV  P    +  S+GA +    
Sbjct: 80  ELKPVGCKLFVSVGGSSKDEIVKTASLANDL-AEIIEINVSSP----NRRSYGADMAQQ- 133

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------- 152
             V + +  +    + PV VK         P   +++L     + G +G+          
Sbjct: 134 --VKEIVKDVKGVTTKPVFVKL-------GPWDNVQDLAGKALEGGADGLTLINTLKGMK 184

Query: 153 ---IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
              I A+  +  G      R I  L   +++++ KE     I   GG+     AL+++  
Sbjct: 185 VDVISAKPILSYGTGGISGRCIHPLAVRVIHDVYKEY-SPEIIGIGGVFSAEDALELMEV 243

Query: 209 --SVDGV 213
              V GV
Sbjct: 244 GAKVVGV 250


>gi|253747688|gb|EET02265.1| tRNA-dihydrouridine synthase, putative [Giardia intestinalis ATCC
           50581]
          Length = 431

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 37/226 (16%), Positives = 76/226 (33%), Gaps = 42/226 (18%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-IVGDC 107
           PL +Q+   +   +     ++  +    I+LN+GC +     G  G  LM   + ++   
Sbjct: 97  PLVVQLTVNENDDIDRICSLLAPWCV-GIDLNLGCGAQFAVSGGRGQRLMNKAEGVIARF 155

Query: 108 IAA---MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA-ILKGL 163
           + A   +  A    ++   +  +            ++   + GV+ I IH RK    +G 
Sbjct: 156 LKALDHIESAGGRHISFSIKQRL--LGSTEETVEKIRVFYELGVSCIAIHMRKKGEERGS 213

Query: 164 SPKDNRKIPNL---DYDIVYEI-KKENPDLF--------IGLNGGLEDMSQA-------L 204
           +  D     ++    Y  ++ +  + N  LF        I  NG L              
Sbjct: 214 TQADWNAFFHVLAKFYTWLWTVSCQRNLQLFEDTLRTFQIVANGDLFTREAIANFFALSE 273

Query: 205 KILPSV---------------DGVMIGRAAYKNSAMLTTVDEYFSN 235
           + L  +                 VM+ R A  +  + + ++E    
Sbjct: 274 QHLSQLPVEIRPYLTTRYGRWTPVMLARGAISDLTLFSFINEQRET 319


>gi|294501167|ref|YP_003564867.1| dihydroorotate dehydrogenase [Bacillus megaterium QM B1551]
 gi|294351104|gb|ADE71433.1| dihydroorotate dehydrogenase [Bacillus megaterium QM B1551]
          Length = 426

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   GA     PD+V        +    PV VK 
Sbjct: 116 EIVKKVEDVGVDGLELNFGCPHGMA-ERGMGAASGQVPDLVEKQTHWAKEVAQTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       IP           
Sbjct: 175 TPNITDITVT------AEAAVRGGADAVSMINTINSLAGVDIHSWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +  +A++ +L    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARSPFINVPISGMGGVSNWQEAVEFMLMGATGVQVCTAAMH 285


>gi|258592887|emb|CBE69196.1| Dihydroorotate dehydrogenase (Dihydroorotate oxidase) (DHOdehase)
           (DHODase) (DHOD) [NC10 bacterium 'Dutch sediment']
          Length = 315

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 76/199 (38%), Gaps = 22/199 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + I G  I   VE AK + D  G +   LN+ CP   V +G    C   N  +    
Sbjct: 96  PVIVNIAGESIEDYVELAKRLSDHEGISGFELNISCP--NVADGLIFGC---NAALAHQL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDD--------QIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +A + +A  +P+  K    V D                +L+ ++    ++      +   
Sbjct: 151 VAKVRQATPLPLIPKLSPNVTDAVEIARALADAGADALSLINTLIGMAIDVRTRRPKLGN 210

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRA 218
           + G        I  +   +V+E+ +      IG+ GG+     AL+ L      V +G A
Sbjct: 211 VTG--GLSGPAIRPVAVRMVWEVARAVKLPLIGM-GGIMTADDALEFLIAGATAVAVGTA 267

Query: 219 AYKNSA----MLTTVDEYF 233
            + + +    ++  ++ Y 
Sbjct: 268 NFTSPSSTERVIDGIEAYL 286


>gi|76801658|ref|YP_326666.1| hypothetical protein NP2026A [Natronomonas pharaonis DSM 2160]
 gi|76557523|emb|CAI49104.1| conserved hypothetical protein [Natronomonas pharaonis DSM 2160]
          Length = 255

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 25/172 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           +VEAA +  D     + LN  C  + +     G  L+ + D + + + A        V+V
Sbjct: 91  IVEAAAVCADRDA-IVELNAHCRQSEMCAAGAGESLLKDDDRLCEQVRAAAD-TGATVSV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R  VD     V L  L  ++  +G + + + A  +                   +V  
Sbjct: 149 KVRTEVDG----VDLPALAAALSAAGASVLHVDAMDSE-----------------HVVGA 187

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           + +  P+ F+  N G+ D     + L    D V +GR +  + A+L  V   
Sbjct: 188 VTEAAPNAFVVANNGVRDRKTTREYLDYGADAVSVGRPS-DDPALLARVRRA 238


>gi|117165070|emb|CAJ88623.1| putative hihydroorotate dehydrogenase [Streptomyces ambofaciens
           ATCC 23877]
          Length = 297

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 68/206 (33%), Gaps = 30/206 (14%)

Query: 24  TEMIVADAILR----GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
           T M+ +    R         +  F+    P+   +      +L E A +V   G   + L
Sbjct: 63  TGMLNSTTYSRRPVGDWCAMLRRFADDGLPVIASVHAESPDELAELADLVGQAGSPALEL 122

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
            + C        + G  L   P+ V     A+ +   +P +VK   G         LR  
Sbjct: 123 GISC-------LNEGGGLDDTPERVAAYTDAVRRRTPVPFSVKLAAG-------ERLRER 168

Query: 140 VKSIKKSGVNGIWI-----------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           V++    G + I +              +  L G        I  L    ++ +++    
Sbjct: 169 VEAALACGADAITLSDTVAGLAVDADTGEVRLGGAFGYSGAGIKPLVLAEIFGLRRAGLT 228

Query: 189 LFIGLNGGLEDMSQALKILP-SVDGV 213
           + +  +GG+E+     + L    D V
Sbjct: 229 VPVMASGGVENGRDVAEYLSVGADAV 254


>gi|15898696|ref|NP_343301.1| NADH oxidase [Sulfolobus solfataricus P2]
 gi|284175397|ref|ZP_06389366.1| NADH oxidase [Sulfolobus solfataricus 98/2]
 gi|13815163|gb|AAK42091.1| NADH oxidase [Sulfolobus solfataricus P2]
 gi|261603188|gb|ACX92791.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus solfataricus
           98/2]
          Length = 555

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 52/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           V + +  + + + I V ++  +   D   +    +  + K ++K+G++ I +   R   L
Sbjct: 195 VEEILKGIREKVRITVGIRISVTEFDNGGLTPEIVAEIGKRLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   ++   L+     ++ ++   + I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYYKRTSFLEE---AKVVRDTVKIPIFLVGSIITPQDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|332796815|ref|YP_004458315.1| dihydroorotate dehydrogenase family protein [Acidianus hospitalis
           W1]
 gi|332694550|gb|AEE94017.1| dihydroorotate dehydrogenase family protein [Acidianus hospitalis
           W1]
          Length = 290

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/171 (20%), Positives = 64/171 (37%), Gaps = 28/171 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L + IGG D  ++V +A+I E+   + I +N   P    +   +G  +     IV + + 
Sbjct: 88  LFVSIGGNDAKQIVNSAEIAEN-KADIIEINASSP----NRKGYGESI---SSIVHEIVK 139

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            +   +  PV VK         P      +     ++G +GI                K 
Sbjct: 140 EVKSHVKKPVFVKI-------GPWDNALEIAGKALEAGADGITAVNTLKGLMIDTEEFKP 192

Query: 159 ILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           +L  G      + I  L   I+ ++ +E  +  I   GG+    + L +L 
Sbjct: 193 VLSYGTGGISGKCIYPLALRIIKDLYREY-EPDIIGIGGVFSFREVLGMLS 242


>gi|154492155|ref|ZP_02031781.1| hypothetical protein PARMER_01787 [Parabacteroides merdae ATCC
           43184]
 gi|154087380|gb|EDN86425.1| hypothetical protein PARMER_01787 [Parabacteroides merdae ATCC
           43184]
          Length = 303

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/184 (16%), Positives = 66/184 (35%), Gaps = 25/184 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+ +   VE A+ + D      I LN+ CP    +    G    +      
Sbjct: 93  DTNMIVNVSGSSVETYVECAEKIADLDNIPAIELNISCP----NVKQGGMAFGVTTCGAS 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + + A+ K     + VK    V D      +  + ++++  G +            I   
Sbjct: 149 EVVKAVRKVYPKTLIVKLSPNVTD------ITEIARAVEAEGADSVSLINTMLGMAIDAE 202

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           +  +   +V++  K    + I   GG+ +   A++ +L     
Sbjct: 203 KRKPVLSTITGGLSGPCVKPVALRMVWQTYKAV-KIPIIGLGGISNWKDAVEFMLAGATA 261

Query: 213 VMIG 216
           + IG
Sbjct: 262 IQIG 265


>gi|311031550|ref|ZP_07709640.1| dihydropyrimidine dehydrogenase [Bacillus sp. m3-13]
          Length = 428

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/178 (22%), Positives = 64/178 (35%), Gaps = 28/178 (15%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE  G + + LN GCP     E   G+     PD+V        +A + PV VK 
Sbjct: 116 EIVKKVEAVGVDGLELNFGCPHGMA-ERGMGSASGQVPDLVEKQTYWAKEAANTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       IP           
Sbjct: 175 TPNITDITVT------AEAAVRGGADAVSMINTINSLAGVDLDSWNTIPHVGGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  + NP +   I   GG+ +   A++ +L    GV I  AA  
Sbjct: 229 CGPAVKPIALNMVGECAR-NPRINVPISGMGGVSNWQNAVEFMLMGATGVQICTAAMH 285


>gi|221194760|ref|ZP_03567817.1| dihydroorotate dehydrogenase, catalytic subunit [Atopobium rimae
           ATCC 49626]
 gi|221185664|gb|EEE18054.1| dihydroorotate dehydrogenase, catalytic subunit [Atopobium rimae
           ATCC 49626]
          Length = 308

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 78/209 (37%), Gaps = 28/209 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE--INLNVGCPSAR 87
           DA +      +     +   + +Q+    + ++V+  +  E+   +   + LN+ CP   
Sbjct: 82  DAFVDHVGSYMDELENRGTRVIMQMAAHSVQEMVDVVERTEELAPHISALELNISCP--- 138

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
            +    G  L   P    + + A+    ++P+ VK           V +  + ++++  G
Sbjct: 139 -NLARGGTPLGATPRQAAEVMRAVRPLTTLPLLVKM--------APVNVAEIGRALEAEG 189

Query: 148 VNGIW-----------IHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            NG+            +H R++ L K           N+   +V+E  +    + I   G
Sbjct: 190 ANGLTLINSLSGMSIDVHTRRSRLSKPTGGMSGPLCHNVAVRMVWECAQAV-RIPICGVG 248

Query: 196 GLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
           G+E    A + IL     V +G A   + 
Sbjct: 249 GVETGEDAAEFILAGATAVSVGSANLYDP 277


>gi|167032777|ref|YP_001668008.1| dihydroorotate dehydrogenase family protein [Pseudomonas putida
           GB-1]
 gi|166859265|gb|ABY97672.1| dihydroorotate dehydrogenase family protein [Pseudomonas putida
           GB-1]
          Length = 311

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 70/191 (36%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + PL + I         E AA++ +  G   I  N+ CP+   H  SFG       +   
Sbjct: 91  DSPLIVSISAPTAQGFAELAARLSDVPGVAGIEANISCPNLEAHGQSFGM----QAESTR 146

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           + +A M +A S+P+ VK          A  +  +  + + SG + + +            
Sbjct: 147 NVVALMRQATSLPLWVKLTP------NAGEVVPVALAAQDSGADAVVVGNTLLGLSIDIE 200

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             R  +   +       I  L   + Y+  +   ++ I   GG+     AL+ I      
Sbjct: 201 RGRARLGNFMGGISGAAIRPLMVRLTYQCAQAL-EIPIIGCGGISTADDALEFIYAGASA 259

Query: 213 VMIGRAAYKNS 223
           V +G A + + 
Sbjct: 260 VQVGTATFLHP 270


>gi|154173753|ref|YP_001407677.1| NADH oxidase [Campylobacter curvus 525.92]
 gi|112803570|gb|EAU00914.1| NADH oxidase [Campylobacter curvus 525.92]
          Length = 343

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 58/177 (32%), Gaps = 16/177 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA   ++ GY  I L+            P     E  +G        ++ + + A
Sbjct: 146 EAFVSAAVRAQEAGYEIIELHAAHGYLLNEFLSPGINKREDGYGGSFENRTRLLKEILLA 205

Query: 111 MCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A S+PV ++      V           L K +++ G   I + A             
Sbjct: 206 VKQATSVPVGIRISADSWVAGDWDVADSVRLAKQLEELGAAFIHVSAGGLFESVDDAPKF 265

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
             +    Y    +  KE  ++ +   G +   S+   +L     D V  GR   +N 
Sbjct: 266 APLYQAGY---AKAVKEAVNIPVIAVGLITRASEGEALLLGGACDLVAYGRELLRNP 319


>gi|225848522|ref|YP_002728685.1| dihydroorotate dehydrogenase 1B [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225643391|gb|ACN98441.1| dihydroorotate dehydrogenase, catalytic subunit (dihydroorotate
           oxidase) (dhodehase) (dhodase) (dhod)
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 313

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 69/193 (35%), Gaps = 25/193 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  +   + G D  + +  A+ ++   G + + LNV CP   V +G        +P ++ 
Sbjct: 95  DTRIFANVFGEDEEEYLAVAERLDRADGVDGLELNVSCP--NVKKGGIAFG--SDPQVLY 150

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           D +  + K    P+ VK    V        + +   +   +  +            I + 
Sbjct: 151 DLVYKLKKITKKPLLVKLSPNV------TNILDTADACVSANADGLVLINTLLGVAIDVE 204

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             K IL           I  +   +++++  K    + I   GG+ +   AL+  L    
Sbjct: 205 REKPILSTITGGLSGPAILPIAVRMIWQVYAKYGSKVAIIGVGGISNTQDALQHILAGAV 264

Query: 212 GVMIGRAAYKNSA 224
            + +G A + +  
Sbjct: 265 AIQVGTANFYDPY 277


>gi|317128027|ref|YP_004094309.1| dihydroorotate dehydrogenase [Bacillus cellulosilyticus DSM 2522]
 gi|315472975|gb|ADU29578.1| dihydroorotate dehydrogenase family protein [Bacillus
           cellulosilyticus DSM 2522]
          Length = 422

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   G+     P++V      + +  + PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEVATTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       IP           
Sbjct: 175 TPNITDITVT------AEAAVRGGADAVSMINTINSLAGVDIDTWNTIPNVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +    ++ +L    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARNPLVNVPISGIGGISNWKDTVEYLLMGATGVQVCTAAMH 285


>gi|313611214|gb|EFR86013.1| probable tRNA-dihydrouridine synthase 1 [Listeria monocytogenes FSL
           F2-208]
          Length = 106

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 18/110 (16%), Positives = 33/110 (30%), Gaps = 6/110 (5%)

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           GVMIGRAA  N  M+    ++         P      +     ++               
Sbjct: 1   GVMIGRAALGNPWMIYRTVKFLETGELLLEPEPREKMQTAMLHLNR-----LVELKGENI 55

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIES 321
            +++  +H      G   S R + +   +A   +    I+        E 
Sbjct: 56  AVREFRQHAAYYLKGARGSTRAK-VAANQATKQSEMESILNEFVLQYEEK 104


>gi|254973846|ref|ZP_05270318.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-66c26]
 gi|255091231|ref|ZP_05320709.1| dihydroorotate dehydrogenase 1B [Clostridium difficile CIP 107932]
 gi|255099349|ref|ZP_05328326.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-63q42]
 gi|255305182|ref|ZP_05349354.1| dihydroorotate dehydrogenase 1B [Clostridium difficile ATCC 43255]
 gi|255312890|ref|ZP_05354473.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-76w55]
 gi|255515649|ref|ZP_05383325.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-97b34]
 gi|255648743|ref|ZP_05395645.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-37x79]
 gi|306518861|ref|ZP_07405208.1| dihydroorotate dehydrogenase 1B [Clostridium difficile QCD-32g58]
          Length = 300

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/186 (15%), Positives = 74/186 (39%), Gaps = 16/186 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            +++ D   + I LN+ CP+ +    +FG       ++  + +  +     +P+ +K   
Sbjct: 112 VQMLNDKPIDIIELNISCPNVKAGGMAFGI----KNEVAREVVREVRNITKLPLVIKLSP 167

Query: 126 GVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIV 179
             +D     ++      + V  +       I I  R+ + +   +      I  +   +V
Sbjct: 168 NAEDIVGMAKVCEEEGADGVSLVNTFKAMAIDIKNRRPVFENVYAGLSGPAIKPIALRMV 227

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
           +E+ K N ++ +   GG+   + A++ I+     + +G A + N      ++  ++E+  
Sbjct: 228 HEVCK-NVNIPVMGMGGITKATDAIEFIMAGATCIQVGTANFMNPRIGIEIIDGINEFMD 286

Query: 235 NPLTGS 240
                S
Sbjct: 287 REGIKS 292


>gi|66819071|ref|XP_643195.1| dihydroorotate oxidase [Dictyostelium discoideum AX4]
 gi|166231961|sp|P07670|PYRD_DICDI RecName: Full=Dihydroorotate dehydrogenase; Short=DHOD;
           Short=DHODase; Short=DHOdehase; AltName:
           Full=Dihydroorotate oxidase
 gi|60471284|gb|EAL69246.1| dihydroorotate oxidase [Dictyostelium discoideum AX4]
          Length = 370

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 61/187 (32%), Gaps = 30/187 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---I 117
             V+  +I  D G   + +N  CP   V  G        NPD V +  + + K LS   I
Sbjct: 181 DFVDTVRIACDAGAKMVEVNYSCP--NVVTGEGQIY--HNPDAVYEISSTLVKELSSKNI 236

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGL 163
           P+ +K  +  D +     +  L +  +++GV                I         +  
Sbjct: 237 PLIIKVGVMDDLEK----MERLFQQAERAGVAAIAGINTLSMKVTDKITGEPSLGASRLT 292

Query: 164 SPKDNRKIPNLDYDIVYE----IKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRA 218
           S      I +   D V      IKK+N  L +   GG+         L    D  M    
Sbjct: 293 SGVCGAPIRSAALDWVSTASSIIKKQNSKLKLLGCGGIVKPEHFDDFLNSGADIAMSATG 352

Query: 219 AYKNSAM 225
              +  +
Sbjct: 353 LMWDPYI 359


>gi|295706514|ref|YP_003599589.1| dihydroorotate dehydrogenase [Bacillus megaterium DSM 319]
 gi|294804173|gb|ADF41239.1| dihydroorotate dehydrogenase [Bacillus megaterium DSM 319]
          Length = 426

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   GA     PD+V        +    PV VK 
Sbjct: 116 EIVKKVEDVGVDGLELNFGCPHGMA-ERGMGAASGQVPDLVEKQTYWAKEVAQTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       IP           
Sbjct: 175 TPNITDITVT------AEAAVRGGADAVSMINTINSLAGVDIHSWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +  +A++ +L    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARSPFINVPISGMGGVSNWQEAVEFMLMGATGVQVCTAAMH 285


>gi|28210533|ref|NP_781477.1| dihydropyrimidine dehydrogenase [Clostridium tetani E88]
 gi|28202970|gb|AAO35414.1| oxidoreductase iron-sulfur protein [Clostridium tetani E88]
          Length = 411

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/185 (21%), Positives = 72/185 (38%), Gaps = 27/185 (14%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K L   I G +  +  E AK+V + G + I  N  CP   +  G+ G+ +  +P++V   
Sbjct: 102 KVLIASIMGENEKEWTELAKMVTEAGADIIECNYSCPQ--MASGAMGSDVGQSPELVKKY 159

Query: 108 IAAMCKALSIPVTVKCRIGV-DDQIPAVALRN--LVKSIKKSGVNGIW-----------I 153
             A  K   +P+  K    +   +IPA+A            + +  I            I
Sbjct: 160 SRATRKGSKLPILAKMTPNIGHMEIPAIASIEGGATGIAAINTIKCITGINLDNQISLPI 219

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILPSVD 211
              K+ + G S K    I  +    + ++ +  +   + I   GG+E    AL+      
Sbjct: 220 VNGKSSISGYSGK---AIKPIALRFIAQMSQNEKLKGVPISGIGGIETWEDALEF----- 271

Query: 212 GVMIG 216
            +M+G
Sbjct: 272 -IMLG 275


>gi|219851341|ref|YP_002465773.1| methanogenesis marker protein 9 [Methanosphaerula palustris E1-9c]
 gi|219545600|gb|ACL16050.1| methanogenesis marker protein 9 [Methanosphaerula palustris E1-9c]
          Length = 372

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 60/168 (35%), Gaps = 28/168 (16%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + G+         +I E FG   I  ++  C    + E   G  L+ +PD +   I A+ 
Sbjct: 98  LRGSTPEAF---TRIAEAFGTRVIYEVDAHCRQPEMMEAGAGQYLLEHPDKLDAIIRALK 154

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
            A  + V+VK R GV           L K + K+G + + +                   
Sbjct: 155 SAGVV-VSVKIRAGVVLDDRV-----LAKRLWKAGADILHVDLM---------------- 192

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
           +  Y  + +I+   P + I  N  +    +   +     D V + R A
Sbjct: 193 DYGYSKLRQIRNSCPLMLI-ANNSITSFDRMRDMFTHGADLVSLARQA 239


>gi|20094001|ref|NP_613848.1| dihydroorotate dehydrogenase [Methanopyrus kandleri AV19]
 gi|19886969|gb|AAM01778.1| Dihydroorotate dehydrogenase [Methanopyrus kandleri AV19]
          Length = 318

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 66/188 (35%), Gaps = 15/188 (7%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
               + P+   +           A+       + + LNV CP A      +GA L  +P+
Sbjct: 89  RDEFDVPVYASVAADGPEGFKRLAR-AFSGVADGLELNVSCPHA---GKGYGAELGSDPE 144

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI-------PAVALRNLVKSIKKSGVNG-IWIH 154
            V +   A  +A   PV+VK    VD +           A    + ++   G    I + 
Sbjct: 145 AVAEITEAAVRAFDGPVSVKLTPNVDRETLLEVAAAAIDAGAEALTAVNTLGPGLRIDLR 204

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL-PSVD 211
               +L  G+       +  +   +V ++  E   ++ I   GG+ +    ++ L     
Sbjct: 205 TASPVLGAGVGGLSGPALKPIALRVVADLALEFGEEVEIIGVGGIRNGEDVVEFLFAGAK 264

Query: 212 GVMIGRAA 219
            V +  AA
Sbjct: 265 AVQVATAA 272


>gi|126697759|ref|YP_001086656.1| dihydroorotate dehydrogenase 1B [Clostridium difficile 630]
 gi|123067175|sp|Q18CS6|PYRD_CLOD6 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|115249196|emb|CAJ67008.1| Dihydroorotate dehydrogenase catalytic subunit [Clostridium
           difficile]
          Length = 300

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/186 (15%), Positives = 74/186 (39%), Gaps = 16/186 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            +++ D   + I LN+ CP+ +    +FG       ++  + +  +     +P+ +K   
Sbjct: 112 VQMLNDKPIDIIELNISCPNVKAGGMAFGI----KNEVAREVVREVRNITKLPLVIKLSP 167

Query: 126 GVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIV 179
             +D     ++      + V  +       I I  R+ + +   +      I  +   +V
Sbjct: 168 NAEDIVGMAKVCEEEGADGVSLVNTFKAMAIDIKNRRPVFENVYAGLSGPAIKPIALRMV 227

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
           +E+ K N ++ +   GG+   + A++ I+     + +G A + N      ++  ++E+  
Sbjct: 228 HEVCK-NVNIPVMGMGGITKATDAIEFIMAGATCIQVGTANFINPRIGIEIIDGINEFMD 286

Query: 235 NPLTGS 240
                S
Sbjct: 287 REGIKS 292


>gi|170702554|ref|ZP_02893430.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           IOP40-10]
 gi|170132542|gb|EDT00994.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           IOP40-10]
          Length = 325

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/229 (14%), Positives = 80/229 (34%), Gaps = 18/229 (7%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             + +L +  I +  I    +  +  ++    P+   +          A + +       
Sbjct: 61  AGDGMLNSIGIPSRGIDDYLEHVLPAYTGHGTPVVASVSADTADAFARACEALSRPDVAA 120

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI---GVDDQIPA 133
           I  N+ CP+      +FG     +  +    + A+      P+ VK       +     A
Sbjct: 121 IEANISCPNLEADGMAFGM----DAGMTRQVVDAIRTRTGHPLWVKLTPNAGNIAKIAQA 176

Query: 134 VALRNLVKSIKKSGVNGIWIHARKA------ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                    +  + V G+ I  R        ++ GLS      I  +   +V++  +   
Sbjct: 177 AQDAGADAIVMGNTVLGMSIDVRTRRPSLGNVMGGLS---GPSIKPIALRLVHQCYRAV- 232

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +   GG+   + A++ +L     V +G A++++  ++ T+ +    
Sbjct: 233 SIPVIGCGGIRSAADAIEFLLAGASAVQVGTASFRDPGVMRTIIDGLEQ 281


>gi|150020172|ref|YP_001305526.1| dihydroorotate dehydrogenase family protein [Thermosipho
           melanesiensis BI429]
 gi|149792693|gb|ABR30141.1| dihydroorotate dehydrogenase family protein [Thermosipho
           melanesiensis BI429]
          Length = 271

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 80/193 (41%), Gaps = 16/193 (8%)

Query: 51  ALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
            L +GG    + ++ A+I+  +   +  I  N  CP   V +G  G  ++ +     + +
Sbjct: 84  ILSLGGDSKEEYIKVAEIISPYAKYFEAIEFNFSCP--NVKKG--GLSIITDKSDWEEIL 139

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS-----GVNGIWIHARKAILKGL 163
             + K L     +  ++ ++     ++ + + K+          V G+     K I  G+
Sbjct: 140 KRVRKILPNTFLI-AKLSIEGHFVEISSQTVAKNAWDGLTLINCVRGLMFEDGKIITGGI 198

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           S      +  +    +YE++K   D++I  +GG+     A + L    + + IG A +K+
Sbjct: 199 S---GPLLKPISLRAIYEVRKRLRDIYIIASGGIYSKEDAKEFLNIGANAISIGSALFKD 255

Query: 223 SAMLTTVDEYFSN 235
             ++  + +Y   
Sbjct: 256 PQIVEEIGKYLKG 268


>gi|288802707|ref|ZP_06408145.1| dihydroorotate oxidase [Prevotella melaninogenica D18]
 gi|288334857|gb|EFC73294.1| dihydroorotate oxidase [Prevotella melaninogenica D18]
          Length = 302

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/190 (14%), Positives = 66/190 (34%), Gaps = 25/190 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A+ ++   G   I +N+ CP   V EG     +  +     
Sbjct: 93  DTNMIVNVSGNSPESYAETAEKLDALEGIPAIEVNISCP--NVKEGGMSFGVTCSG--AA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WI 153
             + A+ +     + VK    V D      + ++ ++ +  G + +              
Sbjct: 149 SIVKAVRQHYHKTMIVKLSPNVTD------VASIARACEDEGADSVSLINTLMGMAIDIE 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           H R  +           +  +   +V ++ K    + I   GG+     A++ ++     
Sbjct: 203 HRRPKLSIRTGGLSGPAVKPVAVRMVNDVAKAV-KIPIIGLGGISTAEDAIEFLMAGATA 261

Query: 213 VMIGRAAYKN 222
           + IG A + +
Sbjct: 262 IQIGTANFID 271


>gi|85704751|ref|ZP_01035852.1| dihydropyrimidine dehydrogenase [Roseovarius sp. 217]
 gi|85670569|gb|EAQ25429.1| dihydropyrimidine dehydrogenase [Roseovarius sp. 217]
          Length = 434

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 75/218 (34%), Gaps = 29/218 (13%)

Query: 25  EMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKL-VEAAKIVEDFGYNEINLNVG 82
           E+I    + +   +   +     ++ L   +          E  + VED G + + LN G
Sbjct: 79  ELITDRPLEVNLKEMRRVKRDWPDRALIASLMVPVNEDAWREILQRVEDTGCDGVELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G+ +   P+ VG       K  ++PV VK    + D      +R   ++
Sbjct: 139 CPHGMS-ERGMGSAVGQVPEYVGQVAYWCKKHSNLPVIVKLTPNITD------IRKPAQA 191

Query: 143 IKKSGVNG--------------IWIHARKAILKGLSPKDNR---KIPNLDYDIVYEIKK- 184
            K+ G +               + + A +  + G           +  +  ++V EI + 
Sbjct: 192 AKEGGADAVSLINTINSITSVDLDLFAPEPTIDGQGAHGGYCGPAVKPIALNMVAEIARD 251

Query: 185 -ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                L I   GG+     A + +      V +  AA 
Sbjct: 252 PATAGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|56965540|ref|YP_177274.1| dihydropyrimidine dehydrogenase [Bacillus clausii KSM-K16]
 gi|56911786|dbj|BAD66313.1| dihydropyrimidine dehydrogenase [Bacillus clausii KSM-K16]
          Length = 419

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE  G + + LN GCP     E   G+     P +V      + +    PV VK 
Sbjct: 116 EIVKRVEAVGVDGLELNFGCPHGMA-ERGMGSASGQVPALVEQQTVWVKEVARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-------- 175
              + D      +    ++  + G + I +      L G+     + IPN+D        
Sbjct: 175 TPNITD------ITATAEAAAQGGADAISLINTINSLAGVDIDTWQTIPNVDGLGTHGGY 228

Query: 176 ---------YDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                      ++ +  +  N ++ I   GG+     A++ +L     V +  AA  
Sbjct: 229 CGPAVKPIALHMLGDCARHPNVNIPISGIGGIATWQDAVQFLLMGASNVQVCTAAMH 285


>gi|225175222|ref|ZP_03729218.1| dihydroorotate dehydrogenase family protein [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169398|gb|EEG78196.1| dihydroorotate dehydrogenase family protein [Dethiobacter
           alkaliphilus AHT 1]
          Length = 316

 Score = 61.8 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/193 (16%), Positives = 72/193 (37%), Gaps = 28/193 (14%)

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           +N+ CP+ +    +FG     +P +V   +  +       + +K    V D      +  
Sbjct: 125 INISCPNVKAGGMAFGT----DPAVVSALVKELRSLTDKTLIIKLSPNVTD------IAG 174

Query: 139 LVKSIKKSGVNGIWI-----------HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKEN 186
           + K+ ++ G + + +           H ++ +L  L+       +  +   +V+++  E 
Sbjct: 175 IAKAAEEGGADALSLINTLLGMAIDTHTKRPVLANLTGGLSGPAVKPVALRMVWQV-TEA 233

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTT----VDEYFSNPLTGSS 241
            ++ +   GG+     A++ +L     V IG A + N  +       +  Y       S 
Sbjct: 234 VNIPVIGMGGISSAQDAVEFLLAGATAVAIGAANFVNPTVCPETVQGIHRYLEEEGYSSV 293

Query: 242 PIKTRVDKDFWRK 254
                + K  W+K
Sbjct: 294 QEIVGLAKKEWQK 306


>gi|172064965|ref|YP_001815677.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           MC40-6]
 gi|171997207|gb|ACB68124.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           MC40-6]
          Length = 325

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/229 (14%), Positives = 80/229 (34%), Gaps = 18/229 (7%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             + +L +  I +  I    +  +  ++    P+   +          A + +       
Sbjct: 61  AGDGMLNSIGIPSRGIDDYLEHVLPAYTGHGTPVVASVSADTADAFARACEALSRPDVAA 120

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI---GVDDQIPA 133
           I  N+ CP+      +FG     +  +    + A+      P+ VK       +     A
Sbjct: 121 IEANISCPNLEADGMAFGM----DAGMTRQVVDAIRTRTGHPLWVKLTPNAGNIAKIAQA 176

Query: 134 VALRNLVKSIKKSGVNGIWIHARKA------ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                    +  + V G+ I  R        ++ GLS      I  +   +V++  +   
Sbjct: 177 AQDAGADAIVMGNTVLGMSIDVRTRRPSLGNVMGGLS---GPSIKPIALRLVHQCYRAV- 232

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +   GG+   + A++ +L     V +G A++++  ++ T+ +    
Sbjct: 233 SIPVIGCGGIRSAADAIEFLLAGASAVQVGTASFRDPGVMRTIIDGLEQ 281


>gi|260681965|ref|YP_003213250.1| dihydroorotate dehydrogenase 1B [Clostridium difficile CD196]
 gi|260685563|ref|YP_003216696.1| dihydroorotate dehydrogenase 1B [Clostridium difficile R20291]
 gi|260208128|emb|CBA60408.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile CD196]
 gi|260211579|emb|CBE01784.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile R20291]
          Length = 282

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/186 (15%), Positives = 74/186 (39%), Gaps = 16/186 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            +++ D   + I LN+ CP+ +    +FG       ++  + +  +     +P+ +K   
Sbjct: 94  VQMLNDKPIDIIELNISCPNVKAGGMAFGI----KNEVAREVVREVRNITKLPLVIKLSP 149

Query: 126 GVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIV 179
             +D     ++      + V  +       I I  R+ + +   +      I  +   +V
Sbjct: 150 NAEDIVGMAKVCEEEGADGVSLVNTFKAMAIDIKNRRPVFENVYAGLSGPAIKPIALRMV 209

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
           +E+ K N ++ +   GG+   + A++ I+     + +G A + N      ++  ++E+  
Sbjct: 210 HEVCK-NVNIPVMGMGGITKATDAIEFIMAGATCIQVGTANFMNPRIGIEIIDGINEFMD 268

Query: 235 NPLTGS 240
                S
Sbjct: 269 REGIKS 274


>gi|115360646|ref|YP_777783.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           AMMD]
 gi|115285974|gb|ABI91449.1| dihydroorotate oxidase B, catalytic subunit [Burkholderia ambifaria
           AMMD]
          Length = 325

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/229 (14%), Positives = 80/229 (34%), Gaps = 18/229 (7%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
             + +L +  I +  I    +  +  ++    P+   +          A + +       
Sbjct: 61  AGDGMLNSIGIPSRGIDDYLEHVLPAYTGHGTPVVASVSADTADAFARACEALSRPDVAA 120

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI---GVDDQIPA 133
           I  N+ CP+      +FG     +  +    + A+      P+ VK       +     A
Sbjct: 121 IEANISCPNLEADGMAFGM----DAGMTRQVVDAIRTRTGHPLWVKLTPNAGNIAKIAQA 176

Query: 134 VALRNLVKSIKKSGVNGIWIHARKA------ILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                    +  + V G+ I  R        ++ GLS      I  +   +V++  +   
Sbjct: 177 AQDAGADAIVMGNTVLGMSIDVRTRRPSLGNVMGGLS---GPSIKPIALRLVHQCYRAV- 232

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            + +   GG+   + A++ +L     V +G A++++  ++ T+ +    
Sbjct: 233 SIPVIGCGGIRSAADAIEFLLAGASAVQVGTASFRDPGVMRTIIDGLEQ 281


>gi|114769062|ref|ZP_01446688.1| dihydropyrimidine dehydrogenase [alpha proteobacterium HTCC2255]
 gi|114549979|gb|EAU52860.1| dihydropyrimidine dehydrogenase [alpha proteobacterium HTCC2255]
          Length = 434

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/209 (21%), Positives = 75/209 (35%), Gaps = 17/209 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ V        K  S PV VK    +
Sbjct: 124 LVEETGADGIELNFGCPHGMA-ERGMGSAVGQVPEYVEMVTGWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  +                +  +  
Sbjct: 183 SDIRKPAAAAQAGGADAVSLINTISSIISVDLDVMAPNPTIDGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++V EI +  E  +L I   GG+     A + ++     V +  AA         V E  
Sbjct: 243 NMVAEIARNPETANLPISGIGGITSWRDAAEYMVLGCGNVQVCTAAMT--YGFKIVQEMI 300

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           S              ++F R+   ++TD+
Sbjct: 301 SGLSQWMDEKGYESTEEFVRQAVPNVTDW 329


>gi|183598677|ref|ZP_02960170.1| hypothetical protein PROSTU_02085 [Providencia stuartii ATCC 25827]
 gi|188020864|gb|EDU58904.1| hypothetical protein PROSTU_02085 [Providencia stuartii ATCC 25827]
          Length = 364

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 84/240 (35%), Gaps = 40/240 (16%)

Query: 5   TDRHYRFFARLLTNNALLYTEM-----IVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
           TD  +      L   +L   E      + A  +  G        S QE     Q      
Sbjct: 110 TDLPW------LGGQSLSKQEQNGWETVSASNLPFGHSHPPRELSKQEIHDIQQ------ 157

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V+AAK  E  G++ I ++            P A   +  +G        ++ D   A
Sbjct: 158 -QFVDAAKRAEYAGFDVIEIHAAHGYLLHQFLSPIANQRQDEYGGNFKNRSRLLIDVFRA 216

Query: 111 MCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A++  + V  RI   D +           L + ++  G + I + +      GLS +
Sbjct: 217 VRDAVNPNIAVGVRISATDWVSGGWGVPESIELTEQLEALGCDYIHVSSG-----GLSSE 271

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               I   +Y + + +   E+  + +   G + + +QA  I+     D V IGR    N 
Sbjct: 272 QQIPISP-NYQVPLAQAIHEHTMMPVIAVGLITEPNQAEAIIATGQADFVSIGRGILFNP 330


>gi|289580296|ref|YP_003478762.1| dihydropyrimidine dehydrogenase [Natrialba magadii ATCC 43099]
 gi|289529849|gb|ADD04200.1| dihydropyrimidine dehydrogenase [Natrialba magadii ATCC 43099]
          Length = 246

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 79/226 (34%), Gaps = 31/226 (13%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI--SKLVEAAK 67
           R  AR L       TE +  D +   D + +     +  P+   +         + + A+
Sbjct: 42  RAAARELVARDR--TEFLPDDPLTFVD-RQLQALEPESTPIQPAVNVRSATREPIRDVAQ 98

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +  +     + +N  C    +     G  L+ + D +   +       S  V VK R   
Sbjct: 99  VCHEHDA-LLEINAHCRQDELCAVGCGETLLADTDRLAGYVETAAS-TSAAVGVKVRA-- 154

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
             ++P V L  L   ++ +G + + + A                      ++ EI  +  
Sbjct: 155 --EVPGVELPVLAGVLESAGASFVHVDAMDTE-----------------SVIAEIA-DAT 194

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           DLF+  N G+ D     + +    D V +GR +  N  +L  V + 
Sbjct: 195 DLFVIANNGVRDEETVREYVEYGADAVSVGRPS-DNPVVLERVHDA 239


>gi|262381738|ref|ZP_06074876.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_1_33B]
 gi|301310210|ref|ZP_07216149.1| dihydroorotate oxidase [Bacteroides sp. 20_3]
 gi|262296915|gb|EEY84845.1| dihydroorotate dehydrogenase [Bacteroides sp. 2_1_33B]
 gi|300831784|gb|EFK62415.1| dihydroorotate oxidase [Bacteroides sp. 20_3]
          Length = 305

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/188 (18%), Positives = 70/188 (37%), Gaps = 33/188 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+ +   VE A+ + +      I LN+ CP    +    G    +     G
Sbjct: 93  DTNMIVNVSGSSVETYVECAEKIAELDRIPAIELNISCP----NVKQGGMAFGVTTCGAG 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + + A+ +     + VK    V D      +  + K+++  G +            I   
Sbjct: 149 EVVKAVRRVYPKTLIVKLSPNVTD------ITEIAKAVEAEGADSVSLINTMLGMAIDAE 202

Query: 155 ARKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
            RK IL     GLS    + +   + +   + +K     + I   GG+ +   A++ +L 
Sbjct: 203 KRKPILSTITGGLSGPCVKPVALRMVWQTYHAVK-----IPIIGLGGISNWKDAVEFMLA 257

Query: 209 SVDGVMIG 216
               + IG
Sbjct: 258 GASAIQIG 265


>gi|303243890|ref|ZP_07330230.1| TIM-barrel protein [Methanothermococcus okinawensis IH1]
 gi|302485826|gb|EFL48750.1| TIM-barrel protein [Methanothermococcus okinawensis IH1]
          Length = 269

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/150 (20%), Positives = 50/150 (33%), Gaps = 19/150 (12%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPD--IVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            + + LN  C    + + S G  L+   +  I+   +  +   ++IPV +K R       
Sbjct: 115 ADILELNCHCRQPEITQLSIGQELLKKENNIILKKFLEKIKLNINIPVFLKVRANFVPVN 174

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLF 190
             +   N V+                    GL     N      D D + EI+    D  
Sbjct: 175 ELINNLNNVR----------------PYFNGLHIDCFNPGKNYPDLDYLKEIRYNFKDKI 218

Query: 191 IGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           I  N  +  +  A K+L   D V + R   
Sbjct: 219 IIGNNSINSIEDAEKMLKYCDFVSVARCVL 248


>gi|288928535|ref|ZP_06422382.1| dihydroorotate oxidase [Prevotella sp. oral taxon 317 str. F0108]
 gi|288331369|gb|EFC69953.1| dihydroorotate oxidase [Prevotella sp. oral taxon 317 str. F0108]
          Length = 302

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/191 (16%), Positives = 67/191 (35%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A  ++       I LN+ CP    +    G           
Sbjct: 93  DTRMIVNVSGNTPEDYAECATRIDALENIPAIELNISCP----NVKEGGMAFGTTCAGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+       + VK    V D      +  + ++++  G +            I I 
Sbjct: 149 SVVRAVRARYGKTLIVKLSPNVTD------VTEIARAVEAEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+++L           +  +   +V+++ K      IGL GG+ + + A++ I+     
Sbjct: 203 RRQSVLSINTGGLSGPAVKPVALRMVWQVAKAVKIPVIGL-GGICNATDAIEFIMAGASA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFLDP 272


>gi|319902125|ref|YP_004161853.1| dihydroorotate oxidase B, catalytic subunit [Bacteroides helcogenes
           P 36-108]
 gi|319417156|gb|ADV44267.1| dihydroorotate oxidase B, catalytic subunit [Bacteroides helcogenes
           P 36-108]
          Length = 303

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 71/196 (36%), Gaps = 25/196 (12%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLN 100
                +  + + + G+ I   V+ A I+ +      I LN+ CP   V +G     +   
Sbjct: 88  RIKDIQTNMIVNVSGSAIEDYVKTAAIINELDKIPAIELNISCP--NVKQGGMAFGVTAK 145

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN----------- 149
                + + A+       + VK    V D      +  + ++ +  G +           
Sbjct: 146 G--AEEVVKAVRSVYKKTLIVKLSPNVTD------ITEIARAAENGGADSVSLINTLLGM 197

Query: 150 GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
            I   +R+ IL  +        +  +   +V+++ K      IGL GG+     A++ +L
Sbjct: 198 AIDAESRRPILSTVTGGMSGAAVKPIALRMVWQVAKAVKIPVIGL-GGIMGWKDAVEFML 256

Query: 208 PSVDGVMIGRAAYKNS 223
                + IG A + + 
Sbjct: 257 AGASAIQIGTANFIDP 272


>gi|219670538|ref|YP_002460973.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfitobacterium
           hafniense DCB-2]
 gi|219540798|gb|ACL22537.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfitobacterium
           hafniense DCB-2]
          Length = 682

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 61/180 (33%), Gaps = 17/180 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              +AA   +  G++ + +  G          P+       +G  L        + +AA+
Sbjct: 147 TFAQAAVRTQKAGFDGVEILAGTGYLISEFLSPATNKRTDEYGGDLPNRMRFALEIMAAI 206

Query: 112 CKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + +    PV V+      +         R   K++  +GV+ I +       + L P+ 
Sbjct: 207 RQGVGPDFPVVVRIAGHDFIPGGHTNKEARTFAKALAAAGVDAINVTGG--WHETLVPQI 264

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
              +P   +  +    K+  DL +  +  +     A  IL S   D V   R    +  +
Sbjct: 265 TMNVPPAAFRYLVRGIKQAVDLPVFASNRITTPELARDILTSGDADLVGFARPILADPNL 324


>gi|256372463|ref|YP_003110287.1| dihydroorotate dehydrogenase family protein [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256009047|gb|ACU54614.1| dihydroorotate dehydrogenase family protein [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 309

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 77/228 (33%), Gaps = 25/228 (10%)

Query: 26  MIVA-----DAILRGDKKNILGFSTQEKPLALQIGGADI----SKLVEAAKIVEDFGYNE 76
           M+ +       I R   +     +    P+AL + G         +  AA+I     Y  
Sbjct: 67  MVNSVGLAGPGIDRWLAETWPSLADARIPVALSVWGRQPRDYGETVRRAARIAPSLVY-- 124

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I LN+ CP+       F      +P+     + A+   ++ P+ VK     D  +     
Sbjct: 125 IELNLSCPNLEADRALFA----HDPNATARVVGAVRDEVATPILVKLSANTDRIVDVAHA 180

Query: 137 RNLVKSIKKSGVNGIWI----HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFI 191
                +     +N ++       R+A+          R +  +    V +++   P + I
Sbjct: 181 AVAAGADGLVAINTLFAQWYDDGREALGTARGGGLSGRAVQPIALRAVADLRAALPTVPI 240

Query: 192 GLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS----AMLTTVDEYFS 234
              GG+       + +    D V IG A + +      +L  ++   +
Sbjct: 241 IGVGGVATADDVERFVRAGADAVQIGTALFVDPRRPVLVLAEIERRLA 288


>gi|149201032|ref|ZP_01878007.1| dihydropyrimidine dehydrogenase [Roseovarius sp. TM1035]
 gi|149145365|gb|EDM33391.1| dihydropyrimidine dehydrogenase [Roseovarius sp. TM1035]
          Length = 434

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 74/218 (33%), Gaps = 29/218 (13%)

Query: 25  EMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKL-VEAAKIVEDFGYNEINLNVG 82
           E+I    + +  ++   +     ++ L   +          E    VED G + + LN G
Sbjct: 79  ELITDRPLEVNLEEMRRVKRDWPDRALIASLMVPVNEDAWREILHRVEDTGCDGVELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G+ +   P+ VG       K  ++PV VK    + D      +R   ++
Sbjct: 139 CPHGMS-ERGMGSAVGQVPEYVGQVAHWCKKHSNLPVIVKLTPNITD------IRKPAQA 191

Query: 143 IKKSGVNG--------------IWIHARKAILKGLSPKDNR---KIPNLDYDIVYEIKK- 184
            K  G +               + + A +  + G           +  +  ++V EI + 
Sbjct: 192 AKDGGADAVSLINTINSITSVDLDLFAPEPTIDGRGAHGGYCGPAVKPIALNMVAEIARD 251

Query: 185 -ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                L I   GG+     A + +      V +  AA 
Sbjct: 252 PATAGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|312868661|ref|ZP_07728854.1| dihydropyrimidine dehydrogenase [Lactobacillus oris PB013-T2-3]
 gi|311095775|gb|EFQ54026.1| dihydropyrimidine dehydrogenase [Lactobacillus oris PB013-T2-3]
          Length = 431

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/180 (21%), Positives = 63/180 (35%), Gaps = 15/180 (8%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L     +K L   I G       + AK+V   G + I LN  CP   +   + G+ + 
Sbjct: 95  RRLKEEYPDKVLIASIMGETPQDWTDLAKLVTAAGADMIELNFSCPQ--MTSHTMGSDVG 152

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----------NLVKSIKKSG 147
            NP++     AA+ K   +PV  K    +   IP V              N VKSI    
Sbjct: 153 TNPELCKTNCAAVKKGTDLPVLAKMTPNITTMIPVVKACLAGGADGVSSINTVKSITDVD 212

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP--DLFIGLNGGLEDMSQALK 205
           ++             +S    + +  +    + +I+       L +   GG+E    A +
Sbjct: 213 LDNKVALPNINGKSAVSGLSGKSVKPIALRFLQQIRSAAGLEQLPVSGIGGIETWEDAAE 272


>gi|45357969|ref|NP_987526.1| putative TIM-barrel protein [Methanococcus maripaludis S2]
 gi|44920726|emb|CAF29962.1| Putative TIM-barrel protein [Methanococcus maripaludis S2]
          Length = 256

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/153 (18%), Positives = 57/153 (37%), Gaps = 18/153 (11%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLML--NPDIVGDCIAAMCK-ALSIPVTVKCRIGVDD 129
             + + LN  C    +   + G  L+   N   + + +  + K  L IP+ +K R     
Sbjct: 111 NADILELNCHCRQPEITYLNLGQNLLKFENESKLINFLENIQKLNLEIPIFLKLRANF-- 168

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
            + A  L   +  ++    +GI I              N    + D + + +I++  P+ 
Sbjct: 169 -LKAEELIKSLDKVRGY-FDGIHIDC-----------FNPGKNHADLEYLKKIRENFPEK 215

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
            I  N  +  +  A ++L   D V + R    N
Sbjct: 216 IIIGNNSVNSVESAKEMLEYADFVSVARCVLSN 248


>gi|171687271|ref|XP_001908576.1| hypothetical protein [Podospora anserina S mat+]
 gi|170943597|emb|CAP69249.1| unnamed protein product [Podospora anserina S mat+]
          Length = 88

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 6/89 (6%)

Query: 7  RHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS----TQEKPLALQIGGADISKL 62
            +R          L +T MI+A    R        F+      + P  +Q G     +L
Sbjct: 2  LAFRQTVHHY-GTDLCWTPMILAKEFNRNKFARDSDFTISTAGPQPPTIVQFGANVPQEL 60

Query: 63 VEAAKIVEDFGYNEINLNVGCPSARVHEG 91
            A+ +V  F  + ++LN GCP +     
Sbjct: 61 ARASSLVVPF-ASGVDLNCGCPQSWACSS 88


>gi|315646652|ref|ZP_07899769.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus vortex V453]
 gi|315277978|gb|EFU41299.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus vortex V453]
          Length = 340

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 73/208 (35%), Gaps = 18/208 (8%)

Query: 54  IGGADISKLVEA----AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           + GA++ +L+ A    A+   + G++ + +             P        +G  L L 
Sbjct: 133 LSGAEVEELIRAFREGARRAVEAGFDTVEIHGAHGYLIHQFHSPLTNQRSDEYGQDLPLF 192

Query: 101 PDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            + V + +  +  + + I + V  +  VD          + K  + +GV+   I +    
Sbjct: 193 GERVVEAVKEVLPEGMPIIMRVSAKEYVDGGYDVQHCAEICKRYRDAGVDIFHISSGGEG 252

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             G S       P    D+  E K+    + +   G L+D + A +++     D V IGR
Sbjct: 253 PVG-SNGGPEAKPGYQVDLAAEFKQ-LLKVPVIAVGLLDDYNAAQEVILSGKADLVAIGR 310

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
              ++        +          P + 
Sbjct: 311 GMLRDPYWAVHAAKALDGGQKVPKPYER 338


>gi|158605003|gb|ABW74812.1| oxidoreductase, FAD/FMN-binding [Campylobacter concisus 13826]
          Length = 340

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 65/194 (33%), Gaps = 17/194 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VEAA   +  GY  + ++           C  A      +G        ++ + +  + 
Sbjct: 145 FVEAAIRAKSAGYEAVEIHAAHGYLINQFLCTGANKRSDEYGGTFENRIRLLLEILREIK 204

Query: 113 KALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
              +I V V+      +           L + ++ +G + I + A     K  S      
Sbjct: 205 ARANITVGVRISASSWLKGDWDVEESVKLARELENNGADFIHVSAGGVYAKVDSAPKFTP 264

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM-LT 227
           +    Y    +  K   ++ +   G +   S+   +L     DGV +GR   +N     +
Sbjct: 265 LYQAGY---AKAVKNAVNIPVFAVGLITKASECEALLLGDVCDGVALGRELLRNPYFAFS 321

Query: 228 TVDEYFSNPLTGSS 241
            + E+  N    ++
Sbjct: 322 AMKEFGENDKIENA 335


>gi|88706120|ref|ZP_01103827.1| Dihydroorotate dehydrogenase [Congregibacter litoralis KT71]
 gi|88699514|gb|EAQ96626.1| Dihydroorotate dehydrogenase [Congregibacter litoralis KT71]
          Length = 541

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/177 (22%), Positives = 70/177 (39%), Gaps = 14/177 (7%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
             ++ L   I G  + + VE A+++     + + LN+ CP A      +G  +  +P +V
Sbjct: 91  PDDRFLLTSIFGGSVEEFVEVARLLAPHS-DGLELNLSCPHA----SGYGMAMGQDPVVV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK-----SIKKSGVNGIWIHARKAI 159
            + +AA+  A+ IPV  K      D                 +I   G      H    +
Sbjct: 146 AEIVAAVKAAVDIPVIPKLTPNTPDIGAIAKAAADAGADGFCAINTVGPGYTSSHGEPVL 205

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGV 213
             G+     + +  +    + EI +E  DL I   GG     D+ +A+K   +V GV
Sbjct: 206 SNGVGGMSGKGVLPIALKCIREI-REVSDLPIVGCGGFSSAADVDEAMKAGANVVGV 261


>gi|255279980|ref|ZP_05344535.1| dihydroorotate oxidase [Bryantella formatexigens DSM 14469]
 gi|255269753|gb|EET62958.1| dihydroorotate oxidase [Bryantella formatexigens DSM 14469]
          Length = 301

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 69/185 (37%), Gaps = 24/185 (12%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           +GG  +   +   + +     + + LN+ CP+ +    +FG       ++  + +  +  
Sbjct: 101 LGGHSLDGYLRGMEKLNQVDLDILELNISCPNVKSGGMNFGT----KTEVAREIVRKIRA 156

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLSPKDN- 168
           A    + VK     +D      + +L +  ++ G +G+            LK   P  N 
Sbjct: 157 ACRHKLVVKLSPNAED------IVSLAQMCEEEGADGVSLVNTFLGMAIDLKKKQPVFNN 210

Query: 169 -------RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
                    I  +   +V+++ K      +GL GG+     A++ I+     V +G A +
Sbjct: 211 VYAGLSGPAIKPIALRMVHQVSKAVSIPVMGL-GGITTWEDAIEFIMAGAAVVQVGTATF 269

Query: 221 KNSAM 225
               +
Sbjct: 270 MKPDI 274


>gi|313232715|emb|CBY19385.1| unnamed protein product [Oikopleura dioica]
          Length = 1278

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/213 (14%), Positives = 67/213 (31%), Gaps = 33/213 (15%)

Query: 25   EMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
            E+I   +        + +     ++  ++  +   +     E A      G + + LN+ 
Sbjct: 859  ELISEKSAEYWYRSIRELKDDFPEKIVISSIMASYNKEDWQELAIGSCKAGADMLELNLS 918

Query: 83   CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
            CP     E   G     N D+V +    + +  ++P   K    + D      +  + ++
Sbjct: 919  CPHGM-GERGMGLACGQNTDMVYNISKWVKEVTTVPFFPKMTPNITD------ITTIAQA 971

Query: 143  IKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVYE 181
             K  G +G+                         +K    G++    R I       V  
Sbjct: 972  AKDGGADGVTATNTVSGLMQIKGDGTPWPGVGSEKKTTYGGVAGNAIRPIAM---KAVSA 1028

Query: 182  IKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
            I +  P   I   GG++    +++   +    M
Sbjct: 1029 IARAIPGFPILATGGIDSADVSMQYFNAGASAM 1061


>gi|313213832|emb|CBY40684.1| unnamed protein product [Oikopleura dioica]
          Length = 711

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/213 (14%), Positives = 67/213 (31%), Gaps = 33/213 (15%)

Query: 25  EMIV--ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I   +        + +     ++  ++  +   +     E A      G + + LN+ 
Sbjct: 292 ELISEKSAEYWYRSIRELKDDFPEKIVISSIMASYNKEDWQELAIGSCKAGADMLELNLS 351

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G     N D+V +    + +  ++P   K    + D      +  + ++
Sbjct: 352 CPHGM-GERGMGLACGQNTDMVYNISKWVKEVTTVPFFPKMTPNITD------ITTIAQA 404

Query: 143 IKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            K  G +G+                         +K    G++    R I       V  
Sbjct: 405 AKDGGADGVTATNTVSGLMQIKGDGTPWPGVGSEKKTTYGGVAGNAIRPIAM---KAVSA 461

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
           I +  P   I   GG++    +++   +    M
Sbjct: 462 IARAIPGFPILATGGIDSADVSMQYFNAGASAM 494


>gi|195953617|ref|YP_002121907.1| dihydroorotate dehydrogenase 1B [Hydrogenobaculum sp. Y04AAS1]
 gi|195933229|gb|ACG57929.1| dihydroorotate dehydrogenase family protein [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 310

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 65/192 (33%), Gaps = 25/192 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +      + G    + +E  +I+ED    +   LNV CP   V +G        +P ++ 
Sbjct: 93  DTHFIANVFGETEEEYIEVIRILEDVPKISAYELNVSCP--NVKKGGVVFG--QDPVVLR 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
             I  +      P+ VK    V D      +    K   ++  +GI +            
Sbjct: 149 SLIEKIKSFAKKPLLVKLSPNVTD------ITEFAKICIEAKADGIVLINTLIGMKIDIY 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKI-LPSVD 211
           + R  +           I  +   ++++  ++    + I   GG+     AL+  L    
Sbjct: 203 NERPFLATKTGGLSGPAILPIAVRMIWQTYEKYGKAIPIIGVGGISTYVDALEHILAGAS 262

Query: 212 GVMIGRAAYKNS 223
            V IG A +   
Sbjct: 263 AVQIGTANFYKP 274


>gi|89896119|ref|YP_519606.1| hypothetical protein DSY3373 [Desulfitobacterium hafniense Y51]
 gi|89335567|dbj|BAE85162.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 682

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 61/180 (33%), Gaps = 17/180 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              +AA   +  G++ + +  G          P+       +G  L        + +AA+
Sbjct: 147 TFAQAAVRTQKAGFDGVEILAGTGYLISEFLSPATNKRTDEYGGDLPNRMRFALEIMAAI 206

Query: 112 CKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + +    PV V+      +         R   K++  +GV+ I +       + L P+ 
Sbjct: 207 RQGVGPDFPVVVRIAGHDFIPGGHTNKEARTFAKALAAAGVDAINVTGG--WHETLVPQI 264

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
              +P   +  +    K+  DL +  +  +     A  IL S   D V   R    +  +
Sbjct: 265 TMNVPPAAFRYLVRGIKQAVDLPVFASNRITTPELARDILTSGDADLVGFARPILADPNL 324


>gi|218262058|ref|ZP_03476665.1| hypothetical protein PRABACTJOHN_02337 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223617|gb|EEC96267.1| hypothetical protein PRABACTJOHN_02337 [Parabacteroides johnsonii
           DSM 18315]
          Length = 303

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/184 (16%), Positives = 66/184 (35%), Gaps = 25/184 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+ +   VE A+ + D      I LN+ CP    +    G    +      
Sbjct: 93  DTNMIVNVSGSSVETYVECAEKIADLDKILAIELNISCP----NVKQGGMAFGVTTCGAS 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + + A+ K     + VK    V D      +  + ++++  G +            I   
Sbjct: 149 EVVKAVRKVYPKTLIVKLSPNVTD------ITEIARAVEAEGADSVSLINTMLGMAIDAE 202

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           +  +   +V++  K    + I   GG+ +   A++ +L     
Sbjct: 203 KRKPVLSTITGGLSGPCVKPVALRMVWQTYKAV-KIPIIGLGGISNWKDAVEFMLAGATA 261

Query: 213 VMIG 216
           + IG
Sbjct: 262 IQIG 265


>gi|262091721|gb|ACY25311.1| dihydroorotate dehydrogenase subfamily 1 family protein [uncultured
           actinobacterium]
          Length = 324

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/205 (14%), Positives = 72/205 (35%), Gaps = 27/205 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYN--EINLNVGCP----SARVHEGSFGACLMLNPDI 103
           +   I G  I     AA ++ +   +   I +N+ CP    S++      G     + D+
Sbjct: 101 IVASIWGFSIDDYRSAASLLSEVSTDLAAIEINLSCPNIGSSSKAANTPHGIF-AHDEDL 159

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
             + +  +C    +P+  K     D       + ++  ++ K+G   + +          
Sbjct: 160 SAEIVR-VCSVAKVPLWAKLSPNTDR------VVDVAAAVSKAGCQAVTLINTALGLAID 212

Query: 154 --HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
                 A+  G        I  +    +++++   P L I   GG+ +   A++ ++   
Sbjct: 213 VETGLPALGNGGGGLSGSGIHPIAVRTIFDVRTRLPRLPIIGVGGIANGEDAIEMMMAGA 272

Query: 211 DGVMIGRAAYKNSAMLTTVDEYFSN 235
             + +G A + +      +D     
Sbjct: 273 SCIQVGTATFADPRAAMRIDREMRQ 297


>gi|317472478|ref|ZP_07931800.1| dihydroorotate dehydrogenase [Anaerostipes sp. 3_2_56FAA]
 gi|316900051|gb|EFV22043.1| dihydroorotate dehydrogenase [Anaerostipes sp. 3_2_56FAA]
          Length = 300

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 59/175 (33%), Gaps = 12/175 (6%)

Query: 38  KNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           K  L F  +    + + + G      +E  + + D   + + +NV CP    +    G  
Sbjct: 82  KRDLPFLKEAGATVIVNVCGKTTEDYLEVVERLSDQPADLLEINVSCP----NVKEGGIA 137

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKKSGVNGI 151
              +P  + +   A+      P+ +K    V D             + +  I       I
Sbjct: 138 FGQDPKALYEITKAVKAKAKQPIIMKLSPNVTDIKEMAKAAEAAGSDALSLINTLTGMKI 197

Query: 152 WIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            I  R  +L   +       I  +   +VYE+        IG+ GG+     AL+
Sbjct: 198 DIEKRDFLLANKTGGLSGPAIKPVAVRMVYEVCSTVKIPVIGM-GGILTAEDALE 251


>gi|310644713|ref|YP_003949472.1| dihydroorotate dehydrogenase 1b [Paenibacillus polymyxa SC2]
 gi|309249664|gb|ADO59231.1| dihydroorotate dehydrogenase 1B [Paenibacillus polymyxa SC2]
          Length = 310

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/209 (13%), Positives = 79/209 (37%), Gaps = 37/209 (17%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF----------GYNEINLN 80
           A L+ +  ++  ++T    +   +GG+++ + V+A  ++ +           G + + LN
Sbjct: 80  AFLKDELDDMTRWNTA---VIANVGGSNLEEYVQAVAMITENAQKRRTMNRRGVDMLELN 136

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP+ +     FG       ++  + +  +    ++P+ VK          A  +  + 
Sbjct: 137 ISCPNVKQGGMQFGI----QTEVAREVVRQVRNVTALPLVVKLSP------NAENITQMA 186

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
              ++ G +G+ +              R       +      I  +   +V+++ +    
Sbjct: 187 VMCEEEGADGVSLINTFSAMKIDIRRRRSVFANTYAGLSGPAIKPIALRMVHQVAQAVSI 246

Query: 189 LFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
             IG+ GG+  +   ++  +     + +G
Sbjct: 247 PVIGM-GGISSVEDIIEFTMAGAAAIQVG 274


>gi|167748040|ref|ZP_02420167.1| hypothetical protein ANACAC_02778 [Anaerostipes caccae DSM 14662]
 gi|167652558|gb|EDR96687.1| hypothetical protein ANACAC_02778 [Anaerostipes caccae DSM 14662]
          Length = 300

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 59/175 (33%), Gaps = 12/175 (6%)

Query: 38  KNILGFSTQ-EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           K  L F  +    + + + G      +E  + + D   + + +NV CP    +    G  
Sbjct: 82  KRDLPFLKEAGATVIVNVCGKTTEDYLEVVERLSDQPADLLEINVSCP----NVKEGGIA 137

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKKSGVNGI 151
              +P  + +   A+      P+ +K    V D             + +  I       I
Sbjct: 138 FGQDPKALYEITKAVKAKAKQPIIMKLSPNVTDIKEMAKAAEAAGSDALSLINTLTGMKI 197

Query: 152 WIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            I  R  +L   +       I  +   +VYE+        IG+ GG+     AL+
Sbjct: 198 DIEKRDFLLANKTGGLSGPAIKPVAVRMVYEVCSTVKIPVIGM-GGILTAEDALE 251


>gi|150020029|ref|YP_001305383.1| dihydroorotate dehydrogenase family protein [Thermosipho
           melanesiensis BI429]
 gi|149792550|gb|ABR29998.1| dihydroorotate dehydrogenase family protein [Thermosipho
           melanesiensis BI429]
          Length = 360

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/125 (21%), Positives = 48/125 (38%), Gaps = 10/125 (8%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDD--QIPAVALRNLVK---SIKKSGVNG-IW 152
            + + + + + A+ K  + P+ +K    + D  +     L N      +I   G    I 
Sbjct: 129 KDYNTIANIVKAIRKNTNKPIFMKLSPHIPDPVEFTKTILENGANGIVAINSWGPTMKID 188

Query: 153 IHARKAI---LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I  RK +    KG        I  +   IV  I+   PD+ I   GG++     ++ +L 
Sbjct: 189 IKNRKTLIGNEKGQVWLSGPVIKPIALSIVKTIRDAFPDITIIGVGGIKSAEDVIEFLLS 248

Query: 209 SVDGV 213
             D V
Sbjct: 249 GADAV 253


>gi|261880302|ref|ZP_06006729.1| dihydroorotate oxidase [Prevotella bergensis DSM 17361]
 gi|270332991|gb|EFA43777.1| dihydroorotate oxidase [Prevotella bergensis DSM 17361]
          Length = 301

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 72/201 (35%), Gaps = 33/201 (16%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G  +      A  ++       I LN+ CP   V EG     +    +    
Sbjct: 94  TNIIVNVSGHSLDSYAACAAKIDALDKIPAIELNISCP--NVKEGGMAFGVTC--EGAAS 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+ K     + VK    V D      +  + ++ +  G +            I I  
Sbjct: 150 VVRAVRKVYHKTLIVKLSPNVTD------VAEIARACEAEGADSVSLINTLMGMAIDIER 203

Query: 156 RKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
           RK  L     GLS    + +   + +D+ + +K     + +   GG+ +   A++ ++  
Sbjct: 204 RKPKLSIRTGGLSGPAVKPVAVRMVWDVSHAVK-----IPVIGLGGIMNAEDAIEFMMAG 258

Query: 210 VDGVMIGRAAYKNSAMLTTVD 230
              + IG A + + ++   V 
Sbjct: 259 ATAIQIGTANFIDPSVTLRVK 279


>gi|225851829|ref|YP_002732062.1| dihydropyrimidine dehydrogenase [Brucella melitensis ATCC 23457]
 gi|256264655|ref|ZP_05467187.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 2 str.
           63/9]
 gi|225640194|gb|ACO00108.1| dihydroorotate dehydrogenase family protein [Brucella melitensis
           ATCC 23457]
 gi|263095024|gb|EEZ18732.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 2 str.
           63/9]
 gi|326408324|gb|ADZ65389.1| dihydropyrimidine dehydrogenase [Brucella melitensis M28]
 gi|326538039|gb|ADZ86254.1| dihydroorotate dehydrogenase family protein [Brucella melitensis
           M5-90]
          Length = 436

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              A++L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDALSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWQDAAEFIALGCGTVQVCTAAM 289


>gi|187924666|ref|YP_001896308.1| dihydropyrimidine dehydrogenase [Burkholderia phytofirmans PsJN]
 gi|187715860|gb|ACD17084.1| dihydroorotate dehydrogenase family protein [Burkholderia
           phytofirmans PsJN]
          Length = 444

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTRLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRTGSRAAYKGGADGVSLINTINSIVAVDLDAMSPLPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKEN--PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDVETPNLPISGIGGITTWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|312886520|ref|ZP_07746128.1| dihydropyrimidine dehydrogenase (NADP+) ;dihydrouracil
           dehydrogenase (NAD+) ;dihydroorotate oxidase B,
           catalytic subunit [Mucilaginibacter paludis DSM 18603]
 gi|311300923|gb|EFQ77984.1| dihydropyrimidine dehydrogenase (NADP+) ;dihydrouracil
           dehydrogenase (NAD+) ;dihydroorotate oxidase B,
           catalytic subunit [Mucilaginibacter paludis DSM 18603]
          Length = 422

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 70/212 (33%), Gaps = 23/212 (10%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +     + K +L        +   +         E  K V+D G + + LN G
Sbjct: 75  ELISDRPLAINLTEIKEVLKEFPDRAMVVSLMADNTRESWHELIKQVQDTGAHGLELNFG 134

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----------QI 131
           CP     E   GA +  +P+I    +  + +   IPV  K    V               
Sbjct: 135 CPHGM-TERGMGAAVGQDPEIARMVVEWVMEVAQIPVITKLTPNVHSVVPTGLASVLGGT 193

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDL 189
            A++L N ++S+    ++ +  +                +  +   ++  I +      +
Sbjct: 194 NALSLINTIQSVTGIDLDTLIPNPNVGGKSAFGGYCGPAVKPIALKMLTTISQNEITRRV 253

Query: 190 FIGLNGGLEDMSQALK-ILPS------VDGVM 214
            +   GG+     A++ +L           VM
Sbjct: 254 PVSGIGGISTWKDAVEFMLLGASNVQVCTAVM 285


>gi|239831126|ref|ZP_04679455.1| dihydroorotate dehydrogenase family protein [Ochrobactrum
           intermedium LMG 3301]
 gi|239823393|gb|EEQ94961.1| dihydroorotate dehydrogenase family protein [Ochrobactrum
           intermedium LMG 3301]
          Length = 436

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 59/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ V   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVAMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARGAHAAGTDAVSLINTINSIVSVDLDSMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDPETRGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|227823015|ref|YP_002826987.1| dihydropyrimidine dehydrogenase [Sinorhizobium fredii NGR234]
 gi|227342016|gb|ACP26234.1| dihydropyrimidine dehydrogenase [Sinorhizobium fredii NGR234]
          Length = 437

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/209 (20%), Positives = 69/209 (33%), Gaps = 17/209 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDVRKPARAAKAGGTDAVSLINTINSITSVNLDTFSPEPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++V EI +  E   L I   GG+     A + L      V +  AA         V E  
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFLTLGAGNVQVCTAAMT--YGFKIVQEMI 300

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           S           R   D   +   ++TD+
Sbjct: 301 SGLSDWMDAKGHRTLDDICGRAVPNVTDW 329


>gi|17987922|ref|NP_540556.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 1 str.
           16M]
 gi|256044012|ref|ZP_05446923.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256112806|ref|ZP_05453727.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 3 str.
           Ether]
 gi|260563371|ref|ZP_05833857.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 1 str.
           16M]
 gi|265990421|ref|ZP_06102978.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265994249|ref|ZP_06106806.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 3 str.
           Ether]
 gi|17983659|gb|AAL52820.1| dihydropyrimidine dehydrogenase (nadp+) [Brucella melitensis bv. 1
           str. 16M]
 gi|260153387|gb|EEW88479.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 1 str.
           16M]
 gi|262765362|gb|EEZ11151.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 3 str.
           Ether]
 gi|263001205|gb|EEZ13780.1| dihydropyrimidine dehydrogenase [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 436

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              A++L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDALSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWQDAAEFIALGCGTVQVCTAAM 289


>gi|150005813|ref|YP_001300557.1| dihydroorotate dehydrogenase 1B [Bacteroides vulgatus ATCC 8482]
 gi|237725410|ref|ZP_04555891.1| dihydroorotate dehydrogenase [Bacteroides sp. D4]
 gi|229485540|sp|A6L5H1|PYRD_BACV8 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|149934237|gb|ABR40935.1| dihydroorotate dehydrogenase [Bacteroides vulgatus ATCC 8482]
 gi|229436097|gb|EEO46174.1| dihydroorotate dehydrogenase [Bacteroides dorei 5_1_36/D4]
          Length = 303

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 74/192 (38%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   V+ A+I+ D  +   I LN+ CP+ +    +FG           +
Sbjct: 94  TNMIVNVSGSAVEDYVKTAEIINDLDHIPAIELNISCPNVKQGGMAFGVS----ACGCSE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+       + VK    V D      +  + ++ + SG +            +    
Sbjct: 150 VVKAVRNVYKKTLIVKLSPNVTD------ITEIARAAEASGADSVSLINTLLGMAVDAEK 203

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ K   ++ +   GG+     A++ +L     +
Sbjct: 204 RRPVLSTITGGMSGAAVKPIALRMVWQVAKAV-NIPVIGLGGIMGWKDAVEFMLAGATAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAI 274


>gi|149915521|ref|ZP_01904047.1| dihydroorotate dehydrogenase family protein [Roseobacter sp.
           AzwK-3b]
 gi|149810413|gb|EDM70256.1| dihydroorotate dehydrogenase family protein [Roseobacter sp.
           AzwK-3b]
          Length = 434

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 57/168 (33%), Gaps = 15/168 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + V + G + + LN GCP     E   G+ +   P+ V        K   +PV VK    
Sbjct: 123 ERVIETGCDGVELNFGCPHGMS-ERGMGSAVGQVPEYVQQVTEWCKKHSDLPVIVKLTPN 181

Query: 127 V-----------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           +           D    AV+L N + SI    ++                     +  + 
Sbjct: 182 IADIRKPAQAAKDGGADAVSLINTINSITSVDLDLFSPEPMIDGQGAHGGYCGPAVKPIA 241

Query: 176 YDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 242 LNMVAEIARDPNLRGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|294674486|ref|YP_003575102.1| dihydroorotate oxidase [Prevotella ruminicola 23]
 gi|294472971|gb|ADE82360.1| dihydroorotate oxidase [Prevotella ruminicola 23]
          Length = 398

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 72/195 (36%), Gaps = 21/195 (10%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
             L  +   K +   I G    + +E AK+ E+ G + I LN  CP  R+     G+ + 
Sbjct: 91  RRLKQNYPTKVVIASIMGQFEEEWIELAKLAEEAGCDAIELNFSCPQMRLA--GMGSDIG 148

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI--WIHAR 156
            +P++V    + + +++ IPV  K    +              +   S +N I     ++
Sbjct: 149 QDPELVNFYTSYVKRSVKIPVIPKMTPNITQMTRPAMGAYFAGADAISAINTIKSVTMSK 208

Query: 157 KAILKG---LSPKDNRKIPNLDYDIVYEIKKENPD-------LFIGLNGGLEDMSQA--- 203
           +A + G   LS    + +  +    + E+  +          + +   GG+E    A   
Sbjct: 209 EAEVSGKQTLSGYSGQAVKPIALRFILEMSMDPVINGTHGRAIELSGIGGIETWRDAVDF 268

Query: 204 ----LKILPSVDGVM 214
                + +     VM
Sbjct: 269 IQLGCRNVQVCTAVM 283


>gi|170767624|ref|ZP_02902077.1| dihydroorotate dehydrogenase family protein [Escherichia albertii
           TW07627]
 gi|170123958|gb|EDS92889.1| dihydroorotate dehydrogenase family protein [Escherichia albertii
           TW07627]
          Length = 411

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 72/191 (37%), Gaps = 33/191 (17%)

Query: 39  NILGFSTQEKPLALQIGGAD---ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
             L     +K L   I G +      L   A++V++ G + I  N  CP   +   + G+
Sbjct: 93  RRLKQDYPDKVLIASIMGENEQQWEDL---ARLVQEAGADMIECNFSCPQ--MTSHAMGS 147

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIH 154
            +  +P +V     A+ +  ++P+  K    + D      + ++  + K  G +GI  I+
Sbjct: 148 DVGQSPVLVEKYCRAVKRGSTLPMLAKMTPNIGD------MCDVALAAKHGGADGIAAIN 201

Query: 155 ARKAIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
             K+I                   +S    + +  +    + +++   E  D  I   GG
Sbjct: 202 TVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELHDFPISGIGG 261

Query: 197 LEDMSQALKIL 207
           +E    A + L
Sbjct: 262 IETWEDAAEFL 272


>gi|78042999|ref|YP_360329.1| dihydroorotate dehydrogenase catalytic subunit [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|123576126|sp|Q3AC05|PYRD_CARHZ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|77995114|gb|ABB14013.1| dihydroorotate dehydrogenase, catalytic subunit [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 307

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 80/238 (33%), Gaps = 34/238 (14%)

Query: 26  MIVADAIL-----RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINL 79
           MI +  +         +K +         L L I G  + +    A+  + F     + L
Sbjct: 66  MINSIGLANPGWDYFCEKILPQIKDLNDILILNIAGESVEEFQYLAREAQRFDEIKALEL 125

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           NV CP   V +G        + + +   ++++ K  S  + VK    V D          
Sbjct: 126 NVSCP--NVSKGGIAFG--TDLEALKQIVSSVRKIYSKTLIVKLTPNVTDITVY------ 175

Query: 140 VKSIKKSGVNGIW-----------IHARKAILKGLS-PKDNRKIPNLDYDIVYEIKKENP 187
            K+ + +G + +            + ++K IL           I  +   +VY+  K   
Sbjct: 176 AKAAENAGADALTLINTFTGMVIDVKSKKPILGNKHGGVSGPAIRPMAVKMVYDCFKAV- 234

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNPLTGS 240
            + I   GG++    AL+  L     + +G   +        ++  + EY       S
Sbjct: 235 SIPIIGVGGIDSKEAALEFFLAGATAIQVGSQNFVEPGFMPRLIRELGEYLQEENIES 292


>gi|325268929|ref|ZP_08135552.1| dihydroorotate oxidase [Prevotella multiformis DSM 16608]
 gi|324988741|gb|EGC20701.1| dihydroorotate oxidase [Prevotella multiformis DSM 16608]
          Length = 302

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/191 (15%), Positives = 63/191 (32%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A ++    G   I +N+ CP   V EG     +        
Sbjct: 93  DTNMIVNVSGDSPESYAETAGRLDVLDGIPAIEVNISCP--NVKEGGMAFGVTC--AGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WI 153
             + A+       + VK    V D      +  + ++ +  G + +              
Sbjct: 149 SIVKAVRARYHKTLIVKLSPNVTD------IAGIARACEDEGADSVSLINTLMGMAIDIE 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           H R  +           +  +   +V ++ +      IGL GG+     A++ ++     
Sbjct: 203 HRRPKLSIRTGGLSGPAVKPVAVRMVNDVARAVKIPVIGL-GGISTAEDAIEFLMAGATA 261

Query: 213 VMIGRAAYKNS 223
           V IG A + + 
Sbjct: 262 VQIGTANFLDP 272


>gi|256840020|ref|ZP_05545529.1| dihydroorotate dehydrogenase [Parabacteroides sp. D13]
 gi|256738950|gb|EEU52275.1| dihydroorotate dehydrogenase [Parabacteroides sp. D13]
          Length = 305

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 69/187 (36%), Gaps = 33/187 (17%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   VE A+ + +      I LN+ CP    +    G    +     G+
Sbjct: 94  TNMIVNVSGSSVETYVECAEKIAELDRIPAIELNISCP----NVKQGGMAFGVTTCGAGE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+ +     + VK    V D      +  + K+++  G +            I    
Sbjct: 150 VVKAVRRVYPKTLIVKLSPNVTD------ITEIAKAVEAEGADSVSLINTMLGMAIDAEK 203

Query: 156 RKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
           RK IL     GLS    + +   + +   + +K     + I   GG+ +   A++ +L  
Sbjct: 204 RKPILSTITGGLSGPCVKPVALRMVWQTYHAVK-----IPIIGLGGISNWKDAVEFMLAG 258

Query: 210 VDGVMIG 216
              + IG
Sbjct: 259 ASAIQIG 265


>gi|296158460|ref|ZP_06841291.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           Ch1-1]
 gi|295891404|gb|EFG71191.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           Ch1-1]
          Length = 444

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRLGSRAAYKGGADGVSLINTINSIVAVDLDAMSPLPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKEN--PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDVETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|227827060|ref|YP_002828839.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           M.14.25]
 gi|229584228|ref|YP_002842729.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           M.16.27]
 gi|227458855|gb|ACP37541.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           M.14.25]
 gi|228019277|gb|ACP54684.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           M.16.27]
          Length = 555

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 53/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           V + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 VEEILKGIKEKAKITVGIRISVTEFDNEGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   +++  L+     ++ ++  ++ I L G +     A+K+    D V++GR   
Sbjct: 255 GSSMPYYYKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKMREVADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|308071463|ref|YP_003873068.1| dihydroorotate dehydrogenase [Paenibacillus polymyxa E681]
 gi|305860742|gb|ADM72530.1| Dihydroorotate dehydrogenase (Dihydroorotate oxidase)
           [Paenibacillus polymyxa E681]
          Length = 310

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/201 (12%), Positives = 72/201 (35%), Gaps = 34/201 (16%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDF----------GYNEINLNVGCPSARV 88
            +   +     +   +GG+++ + V+A  ++ +           G + + LN+ CP+ + 
Sbjct: 85  ELDDMTQWNTAVIANVGGSNLEEYVQAVAMITENAQKRRTMNRRGVDMLELNISCPNVKQ 144

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
               FG       ++  + +  +    ++P+ VK          A  +  +    ++ G 
Sbjct: 145 GGMQFGI----QTEVAREVVRQVRNVTALPLVVKLSP------NAENITQMAVMCEEEGA 194

Query: 149 NGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +G+ +              R       +      I  +   +V+++ +      IG+ GG
Sbjct: 195 DGVSLINTFSAMKIDIRRRRSVFANMYAGLSGPAIKPIALRMVHQVAQAVSIPVIGM-GG 253

Query: 197 LEDMSQALK-ILPSVDGVMIG 216
           +  +   ++  +     + +G
Sbjct: 254 ISSVEDIIEFTMAGAAAIQVG 274


>gi|303236480|ref|ZP_07323067.1| dihydroorotate dehydrogenase 1B [Prevotella disiens FB035-09AN]
 gi|302483331|gb|EFL46339.1| dihydroorotate dehydrogenase 1B [Prevotella disiens FB035-09AN]
          Length = 302

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 70/195 (35%), Gaps = 33/195 (16%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       EAA+ +        I LN+ CP   V EG     +  +     
Sbjct: 93  DTNIIVNVSGNSPDTYAEAAERLNGLEHVPAIELNISCP--NVKEGGMSFGVTCSG--AA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
             +  + K  +  + VK    V D      + ++ ++ +  G + + +            
Sbjct: 149 SVVREVRKRYNKTLIVKLSPNVTD------IASIARTCEAEGADAVSLINTLMGMSIDIE 202

Query: 154 ---HARKAILKGLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
              H       GLS    + +   + YD+ + +K     + +   GG+   + A++ ++ 
Sbjct: 203 KRAHRLSIRTGGLSGPAVKPVAVRMVYDVAHAVK-----IPVIGLGGISTAADAIEFLMA 257

Query: 209 SVDGVMIGRAAYKNS 223
               + IG A + + 
Sbjct: 258 GATAIQIGTANFVDP 272


>gi|322434826|ref|YP_004217038.1| dihydroorotate dehydrogenase family protein [Acidobacterium sp.
           MP5ACTX9]
 gi|321162553|gb|ADW68258.1| dihydroorotate dehydrogenase family protein [Acidobacterium sp.
           MP5ACTX9]
          Length = 317

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 76/208 (36%), Gaps = 27/208 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARV 88
            A + G    +   +     +   + G  +   +E  +++ D  G +   LN  CP    
Sbjct: 92  KAFVEGKMPRLREIA--GAVVIANVFGFTVEDCLEVIRVLNDAPGISLYELNASCP---- 145

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +    G     +P ++G+ +    K  + PV VK    V       ++  + ++   +G 
Sbjct: 146 NTAHGGMVFGTDPTLLGNLVGKCAKLAARPVVVKLSPNV------TSIALMARTAAGAGA 199

Query: 149 NGIWIH------------ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            G+ +              R  I    +      I  +   +VYE  +    + I   GG
Sbjct: 200 QGLSLVNTFLSMAIDPETRRPRIANVTAGLSGPGIKPIAVRMVYEAAQAV-RIPILGMGG 258

Query: 197 LEDMSQALK-ILPSVDGVMIGRAAYKNS 223
           + + S A++ +L     V +G A+Y + 
Sbjct: 259 ILNASDAVEFMLAGATAVQVGTASYADP 286


>gi|296273120|ref|YP_003655751.1| NADH:flavin oxidoreductase/NADH oxidase [Arcobacter nitrofigilis
           DSM 7299]
 gi|296097294|gb|ADG93244.1| NADH:flavin oxidoreductase/NADH oxidase [Arcobacter nitrofigilis
           DSM 7299]
          Length = 342

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/196 (18%), Positives = 75/196 (38%), Gaps = 17/196 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA   ++  Y+ I L+       C    P + + +  +G  L     ++ +    
Sbjct: 145 ELFVNAALRAKEADYDAIELHGAHGYFLCEFLSPLSNLRDDIYGGSLENRCRLLLEAAKE 204

Query: 111 MCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + + + +P  V +     +++         L K ++K GV+ I + +     K   P + 
Sbjct: 205 IKEKVDLPLIVRISADEWMNEGWNIEDSIYLSKELEKVGVDSIHVSSGGNQEKPNKPIEL 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-AM 225
           + +   D+    EIK+E  ++ +   G +    +  K+L     D V  GR   ++    
Sbjct: 265 KPMYQADFA--KEIKEEV-NIPVIAVGLITTAQEGEKLLEEKYCDFVAYGRELLRSPNFA 321

Query: 226 LTTVDEYFSNPLTGSS 241
               +E+    L  SS
Sbjct: 322 FLAANEFNKKELINSS 337


>gi|288554818|ref|YP_003426753.1| dihydropyrimidine dehydrogenase subunit B [Bacillus pseudofirmus
           OF4]
 gi|288545978|gb|ADC49861.1| dihydropyrimidine dehydrogenase [Bacillus pseudofirmus OF4]
          Length = 428

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 63/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   GA     P++V        +    PV VK 
Sbjct: 116 EIVKRVEDVGVDGLELNFGCPHGMA-ERGMGAASGQVPELVEKQTYWAKEVAQTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       +P           
Sbjct: 175 TPNITDITVT------AEAAVQGGADAVSMINTINSLAGVDIDSWNTVPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +  + ++ I   GG+ +   A++ +L    GV +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARNPHVNVPISGMGGVSNWENAVEFMLMGATGVQVCTAAMH 285


>gi|238619219|ref|YP_002914044.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           M.16.4]
 gi|238380288|gb|ACR41376.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           M.16.4]
          Length = 554

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 53/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           V + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 VEEILKGIKEKAKITVGIRISVTEFDNEGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   +++  L+     ++ ++  ++ I L G +     A+K+    D V++GR   
Sbjct: 255 GSSMPYYYKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKMREVADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|212693181|ref|ZP_03301309.1| hypothetical protein BACDOR_02688 [Bacteroides dorei DSM 17855]
 gi|237709921|ref|ZP_04540402.1| dihydroorotate dehydrogenase [Bacteroides sp. 9_1_42FAA]
 gi|265753574|ref|ZP_06088929.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_1_33FAA]
 gi|212664286|gb|EEB24858.1| hypothetical protein BACDOR_02688 [Bacteroides dorei DSM 17855]
 gi|229456014|gb|EEO61735.1| dihydroorotate dehydrogenase [Bacteroides sp. 9_1_42FAA]
 gi|263235288|gb|EEZ20812.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_1_33FAA]
          Length = 303

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 73/192 (38%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   V+ A+I+ D      I LN+ CP+ +    +FG           +
Sbjct: 94  TNMIVNVSGSAVEDYVKTAEIINDLDNIPAIELNISCPNVKQGGMAFGVS----ACGCSE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+       + VK    V D      +  + ++ + SG +            +    
Sbjct: 150 VVKAVRNVYKKTLIVKLSPNVTD------ITEIARAAEASGADSVSLINTLLGMAVDAEK 203

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ K   ++ +   GG+     A++ +L     +
Sbjct: 204 RRPVLSTITGGMSGAAVKPIALRMVWQVAKAV-NIPVIGLGGIMGWKDAVEFMLAGATAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAI 274


>gi|312111347|ref|YP_003989663.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y4.1MC1]
 gi|311216448|gb|ADP75052.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y4.1MC1]
          Length = 640

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 65/187 (34%), Gaps = 20/187 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA   +  GY+ + ++ G          P +      +G  LM       + I  + 
Sbjct: 148 FGDAALRAKKAGYDAVEIHGGHGYLINQFLSPFSNKRTDEYGGTLMNRARFAVEIIENVR 207

Query: 113 KALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +     +  R      V+  +     + + + ++++G + I  H    + K +     
Sbjct: 208 KKVGKHFPILFRISTVEFVEGGLTIEDTKVIARMLEQAGADAI--HCSTGVYKTMMYVIQ 265

Query: 169 RKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                  + +    EIKK    + +   G + D   A  +L     D + +GRAA  +  
Sbjct: 266 PAAVPHGFSVSFAAEIKK-VVSIPVIAVGRINDPLIAESVLLSDKADLISMGRAALADPE 324

Query: 225 MLTTVDE 231
           +     E
Sbjct: 325 LPNKAKE 331


>gi|325971826|ref|YP_004248017.1| dihydroorotate dehydrogenase [Spirochaeta sp. Buddy]
 gi|324027064|gb|ADY13823.1| dihydroorotate dehydrogenase family protein [Spirochaeta sp. Buddy]
          Length = 577

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 83/231 (35%), Gaps = 43/231 (18%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L + +    I   +   K   D   + + LN  CP A V    +GA +  +  I  + + 
Sbjct: 105 LNVSLSANSIEDFITLVK-AFDEVADLVELNFSCPHASV---GYGASIGCDQAIAAEYVR 160

Query: 110 AMCKALSI---PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI--------WIHARKA 158
           A+ +A S    P+ VK    V+D      + ++ K++  SG +G+         +H    
Sbjct: 161 AIKEATSCCKAPLFVKLTPNVED------IGSIAKAVMDSGADGLVAINTVGPIVHLDPV 214

Query: 159 --------ILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDM-SQALKILP 208
                    L G      ++I +     V  I+    D + +   GG+      AL +  
Sbjct: 215 SGMPILQNKLGGKGGCSGKQIFSAALHAVTAIRHACGDAIPLIAMGGVSTGDEVALLVQA 274

Query: 209 SVDGVMIGRAAYKNSAMLTTVDE-----YFSNPLTGSSPIKTRVDKDFWRK 254
             D V IG A       L TVD+     Y     T +  +   V+    R 
Sbjct: 275 GADAVGIGSA-------LGTVDQQDWPSYLYAVKTEAEALLRNVETSRVRH 318


>gi|269796615|ref|YP_003316070.1| NADH:flavin oxidoreductase [Sanguibacter keddieii DSM 10542]
 gi|269098800|gb|ACZ23236.1| NADH:flavin oxidoreductase [Sanguibacter keddieii DSM 10542]
          Length = 359

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 28/198 (14%), Positives = 68/198 (34%), Gaps = 21/198 (10%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
                +AA    + G++ + ++            P +      +G  L     ++ +   
Sbjct: 157 PGAFADAAVRAHEAGFDVVEIHAAHGYLLHQFLSPLSNRRTDGYGGSLEARSRLLVEVTD 216

Query: 110 AMCKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+        P+ V+      + D +    +  + K + + GV+ + +        G +P
Sbjct: 217 AVRAEWPADKPLFVRVSATDWLPDGLSVDDVAQVSKVLGEHGVDLVDVSTG-----GNAP 271

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 P        +++     + +   G + + +QA ++L   S D VM+GR A ++ 
Sbjct: 272 AQIPVGPGYQVPAARDVRGVAG-IPVSAVGLITEPAQAEQVLADGSADAVMLGREALRDP 330

Query: 224 AMLTTVDEYFSNPLTGSS 241
                       P+  + 
Sbjct: 331 HWPLRAAHELGVPVEDAR 348


>gi|222480744|ref|YP_002566981.1| hypothetical protein Hlac_2335 [Halorubrum lacusprofundi ATCC
           49239]
 gi|222453646|gb|ACM57911.1| conserved hypothetical protein [Halorubrum lacusprofundi ATCC
           49239]
          Length = 276

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 87/242 (35%), Gaps = 19/242 (7%)

Query: 6   DRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA 65
           D   R  AR L       +E + AD +   D + +   S       + +  A +  + EA
Sbjct: 45  DPASRAAARDLVARDR--SEFLPADPLAWID-RELDQLSEAPIRPGVNVRSATVEPVREA 101

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A +  +       +N  C  + +     G  L+ + D + + +AA+ +  +   +VK R 
Sbjct: 102 AAVCAERDAVC-EVNAHCRQSELRAVGCGESLLRDIDRLAEYVAAVAETGATT-SVKVRA 159

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
               ++P V L  +  ++  +G + + + A           D         +        
Sbjct: 160 ----EVPGVDLVAVTDAVADAGADWLHVDAMD----SEGIVDELTAGRATDET----GSP 207

Query: 186 NPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             DL +  N G+      A       D V +GR + +  A L+ + +  S    G  P +
Sbjct: 208 RDDLTVIANNGVRGRETVAEYAAYGADAVSVGRPS-ERPASLSRIADAVSAWREGELPEE 266

Query: 245 TR 246
           + 
Sbjct: 267 SE 268


>gi|210621738|ref|ZP_03292787.1| hypothetical protein CLOHIR_00732 [Clostridium hiranonis DSM 13275]
 gi|210154620|gb|EEA85626.1| hypothetical protein CLOHIR_00732 [Clostridium hiranonis DSM 13275]
          Length = 643

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 39/188 (20%), Positives = 73/188 (38%), Gaps = 31/188 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----PSARVHEGS------FGACLMLNPDIVGDCI 108
               EAA+   + GY+ I     C     P + +  G       +G  L        +CI
Sbjct: 142 DSFGEAARRSVEAGYDCI--GFHCGHNYLPHSFLTAGMNNRDDEYGGSLENRAKFPLECI 199

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGL 163
            A+ K +   +P+ ++     D     + + +++K     K++GV+ + I     I  GL
Sbjct: 200 RAIRKNIPNDMPLIMRVDAHDDYFKNGLTIDDIIKFCLMAKEAGVDALDISRGNMITPGL 259

Query: 164 SPKDNRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMI 215
                 ++P +D       +    IKKE   + I + G +     A +I+     D V++
Sbjct: 260 K----YEVPPIDIPNGFNVENAARIKKETGMVTIAV-GRINTPKLADEIIADGKADMVVV 314

Query: 216 GRAAYKNS 223
           GR    + 
Sbjct: 315 GRGQLADP 322


>gi|326392336|ref|ZP_08213765.1| dihydrouridine synthase DuS [Thermoanaerobacter ethanolicus JW
          200]
 gi|325991619|gb|EGD50182.1| dihydrouridine synthase DuS [Thermoanaerobacter ethanolicus JW
          200]
          Length = 52

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG--DKKNILGFSTQEK 48
          M   TD+ +R   + +    L YTEM+ A  +  G  + K +     +EK
Sbjct: 1  MAGVTDKPFRVICQEM-GCGLAYTEMVSAKGLYYGSENTKVLTDIDEEEK 49


>gi|315926023|ref|ZP_07922226.1| dihydroorotate oxidase [Pseudoramibacter alactolyticus ATCC 23263]
 gi|315620693|gb|EFV00671.1| dihydroorotate oxidase [Pseudoramibacter alactolyticus ATCC 23263]
          Length = 303

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 74/196 (37%), Gaps = 26/196 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
           DA +  +  ++   S  +    + +GG+D +  + A + + D     I LN+ CP    +
Sbjct: 80  DAFIVNEWPHL---SALDTVTVVNVGGSDEASYLAAIEKLNDLPVALIELNISCP----N 132

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL--------RNLVK 141
               G    ++PD  G        A + P+ VK      D +              +L+ 
Sbjct: 133 VKCGGMAFGMDPDQAGRITEKAAAASTHPIMVKLTPNAPDIVAVARACEAAGAAGLSLIN 192

Query: 142 SIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +I+   V+   + A+K +     +      +  +   I +++      + +   GG+ D 
Sbjct: 193 TIQAMAVD---VDAKKIVFDNIYAGLSGPAVKPIALRITHQVVNAV-RIPVMAMGGIADW 248

Query: 201 SQALKILPSVDGVMIG 216
             AL+       +M+G
Sbjct: 249 RDALEF------IMVG 258


>gi|321459596|gb|EFX70648.1| hypothetical protein DAPPUDRAFT_202177 [Daphnia pulex]
          Length = 1040

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 28/153 (18%), Positives = 51/153 (33%), Gaps = 31/153 (20%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           + LN+ CP     E   G     +P++V +    +  A++IP   K    V       ++
Sbjct: 669 LELNLSCPHGM-GERGMGLACGQDPELVRNICRWVRAAVTIPFFAKLTPNV------TSI 721

Query: 137 RNLVKSIKKSGVNGIW---------------------IHARKAILKGLSPKDNRKIPNLD 175
             + ++  +   +G+                         +K    G+S    R I    
Sbjct: 722 VAIARAAYEGQADGVTATNTVSGLMGVRSDGSAWPSIGKEQKTTYGGMSGNAIRPIA--- 778

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
              V  I +  P   I   GG++    AL+ L 
Sbjct: 779 LKAVSAIARALPGFPILATGGIDSADAALQFLQ 811


>gi|91784371|ref|YP_559577.1| dihydropyrimidine dehydrogenase [Burkholderia xenovorans LB400]
 gi|91688325|gb|ABE31525.1| dihydropyrimidine dehydrogenase (NADP+) / dihydroorotate oxidase B,
           catalytic subunit [Burkholderia xenovorans LB400]
          Length = 444

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRLGSRAAYKGGADGVSLINTINSIVAVDLDAMSPLPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDAETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|78059775|ref|YP_366350.1| dihydropyrimidine dehydrogenase [Burkholderia sp. 383]
 gi|77964325|gb|ABB05706.1| dihydroorotate oxidase B, catalytic subunit / dihydrouracil
           dehydrogenase (NAD+) / dihydropyrimidine dehydrogenase
           (NADP+) [Burkholderia sp. 383]
          Length = 438

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDHMAPMPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|261367609|ref|ZP_05980492.1| dihydroorotate oxidase [Subdoligranulum variabile DSM 15176]
 gi|282570397|gb|EFB75932.1| dihydroorotate oxidase [Subdoligranulum variabile DSM 15176]
          Length = 302

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 76/210 (36%), Gaps = 32/210 (15%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            +       +         +   +GG  I + VE  + +   G + + LN+ CP    + 
Sbjct: 77  GVQHFIDHELPAMRRCGTTVWANLGGHTIEENVEGVEKLCAAGIDVLELNISCP----NV 132

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
              G    +      + + A+ K  ++P+ VK          A ++  + K+++ +G +G
Sbjct: 133 KQGGLAFGIRAQDASEVVGAVRKVCTVPLVVKLSPQ------AESIPEMCKAVEAAGADG 186

Query: 151 IW-----------IHARKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLN 194
           I            +  R+ +      GLS    R I   + +  V  +      + +   
Sbjct: 187 ISLCNTFQACAIDLEKRRPVFNNTFAGLSGPAVRPIALRMVWQAVGAV-----SIPVVGL 241

Query: 195 GGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
           GG+     AL+ I+     V +G A + + 
Sbjct: 242 GGILTGRDALEFIMAGAAAVQVGTANFLDP 271


>gi|110634405|ref|YP_674613.1| dihydropyrimidine dehydrogenase [Mesorhizobium sp. BNC1]
 gi|110285389|gb|ABG63448.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) [Chelativorans sp. BNC1]
          Length = 437

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+   + I LN GCP     E   G+ +   P+ V   +    +   +PV  K    +
Sbjct: 124 LVEETEADGIELNFGCPHGMS-ERGMGSAVGQVPEYVEMVVRWCKQHTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPARAAHAGGTDAVSLINTINSITAVDLDSFAPEPTIDSKGTHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + L      V +  AA 
Sbjct: 243 NMVAEIARDPETRGLPISGIGGITTWRDAAEFLALGAGTVQVCTAAM 289


>gi|332534189|ref|ZP_08410036.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332036355|gb|EGI72825.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 364

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 65/199 (32%), Gaps = 28/199 (14%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AAK  ++ G + I L             P +   + ++G  L     ++ D   A+
Sbjct: 159 DFVSAAKRADELGLDLIELHGAHGYLLHQFLSPLSNKRDDNYGGSLENRMRLLLDVFKAV 218

Query: 112 C------KALSIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
                  KA+ + ++       G D +   V    L K++ + G + I +        GL
Sbjct: 219 REVFPSNKAVGVRISATDWVEGGWDLEQSIV----LSKALDELGCDFIHVSTA-----GL 269

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
           SP+    +            KE   + +   G +    QA  I+     DGV + R    
Sbjct: 270 SPEQQIPVKPNFQVPFATAIKEAVKMPVIAVGLITQAQQAEDIISEQQADGVALARGILY 329

Query: 222 NSAMLTTVDEYFSNPLTGS 240
           N              +T  
Sbjct: 330 NPHWPWHAAAELGATVTAP 348


>gi|259502930|ref|ZP_05745832.1| dihydroorotate dehydrogenase [Lactobacillus antri DSM 16041]
 gi|259169123|gb|EEW53618.1| dihydroorotate dehydrogenase [Lactobacillus antri DSM 16041]
          Length = 431

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 42/193 (21%), Positives = 69/193 (35%), Gaps = 35/193 (18%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           D    L      K L   I G       + AK+V   G + I LN  CP   +   + G+
Sbjct: 92  DAMRRLKKEYPNKVLIASIMGETPQDWTDLAKLVTAAGADMIELNFSCPQ--MTSHTMGS 149

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--- 152
            +  NP++     AA+ +  ++PV  K    +   IP       VK+    G +GI    
Sbjct: 150 DVGTNPELCKSNCAAVKRGTNLPVLAKMTPNITTMIPV------VKACLAGGADGISSIN 203

Query: 153 ------------------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP--DLFIG 192
                             I+ + A+  GLS K    +  +    + +I+       L + 
Sbjct: 204 TVKSITDVDLDNKVALPNINGKSAV-SGLSGK---SVKPIALRFLQQIRSAAGLEQLPVS 259

Query: 193 LNGGLEDMSQALK 205
             GG+E    A +
Sbjct: 260 GIGGIETWEDAAE 272


>gi|168184782|ref|ZP_02619446.1| putative dihydroorotate dehydrogenase [Clostridium botulinum Bf]
 gi|229587300|ref|YP_002860338.1| putative hihydroorotate dehydrogenase [Clostridium botulinum Ba4
           str. 657]
 gi|182672196|gb|EDT84157.1| putative dihydroorotate dehydrogenase [Clostridium botulinum Bf]
 gi|229260286|gb|ACQ51323.1| putative hihydroorotate dehydrogenase [Clostridium botulinum Ba4
           str. 657]
          Length = 298

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 65/162 (40%), Gaps = 14/162 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I      +LV  A  +E+ G   + L + CP+                + + D  
Sbjct: 99  PVIPSIVADTKDELVNLALQMEEVGCKALELGISCPNEIGIN-----------EKIYDFT 147

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPA-VALRNLVKSIKKSG-VNGIWIHA-RKAILKGLSP 165
            A+C+ +S+PV+VK    V  +     A+    KS+  S  +  I ++      L     
Sbjct: 148 RAVCREVSVPVSVKLTSEVKVEEKVRKAMCAGAKSVSISDSIPAIVVNTDGTLPLGVRCG 207

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                I  +    +Y +KK N D+ +   GG+E+ +  L+ L
Sbjct: 208 YSGPAIKPIVQKNIYYLKKNNADVEVIGIGGIENANDVLEYL 249


>gi|260591482|ref|ZP_05856940.1| dihydroorotate oxidase [Prevotella veroralis F0319]
 gi|260536513|gb|EEX19130.1| dihydroorotate oxidase [Prevotella veroralis F0319]
          Length = 302

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 66/191 (34%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A  +++      I +N+ CP    +    G    ++     
Sbjct: 93  DTNMIVNVSGNSPESYAETAARLDELDAIPAIEVNISCP----NVREGGMAFGVSCSGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      + ++ ++ +  G +            I I 
Sbjct: 149 TVVKAVRQHYHKTMIVKLSPNVTD------IASIARACEDEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R + L   +       I  +   +V ++ K    + +   GG+     A++ ++     
Sbjct: 203 RRCSKLSIRTGGLSGPAIKPVAVRMVNDVAKAV-KIPVIGLGGISTAEDAIEFLMAGATA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFIDP 272


>gi|254304256|ref|ZP_04971614.1| FMN reductase [Fusobacterium nucleatum subsp. polymorphum ATCC
           10953]
 gi|148324448|gb|EDK89698.1| FMN reductase [Fusobacterium nucleatum subsp. polymorphum ATCC
           10953]
          Length = 311

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 76/185 (41%), Gaps = 20/185 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL--------NVGCPSARVHEG---SFGACLMLNPDIVGDCI 108
              +++AK  ++ G + I L        N+   S+ +      ++G  L+   ++V + I
Sbjct: 133 DYFIKSAKFCQEAGLDGIELHGAHTYFFNML--SSEISNKREDNYGGNLIERLNLVKEII 190

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+         +  R+G  + I         K+++K GV+ + + +     + L   D 
Sbjct: 191 EAIKSFSKDDFIISYRMGWTENINTDI--ETAKALEKLGVDILHVSSGIPEDRKLKLPDE 248

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AM 225
            +  +  Y  + ++KK      I +N  ++ +S+  K++     D V  GR    +   +
Sbjct: 249 FEYNDFVYTGI-QVKKNVNIPVIVVN-DIKTLSRGNKLIEDGDCDFVAYGRPFLSDPNFI 306

Query: 226 LTTVD 230
           + ++ 
Sbjct: 307 IHSIK 311


>gi|190893106|ref|YP_001979648.1| dihydropyrimidine dehydrogenase [Rhizobium etli CIAT 652]
 gi|190698385|gb|ACE92470.1| dihydropyrimidine dehydrogenase protein [Rhizobium etli CIAT 652]
          Length = 437

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 59/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 TDIRRPARAAKAGGTDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + L      V +  AA 
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFLALGAGNVQVCTAAM 289


>gi|148559324|ref|YP_001258321.1| dihydropyrimidine dehydrogenase [Brucella ovis ATCC 25840]
 gi|148370581|gb|ABQ60560.1| dihydroorotate dehydrogenase family protein [Brucella ovis ATCC
           25840]
          Length = 436

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 59/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-EHGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   G +     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGDITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|294790856|ref|ZP_06756014.1| dihydroorotate oxidase [Scardovia inopinata F0304]
 gi|294458753|gb|EFG27106.1| dihydroorotate oxidase [Scardovia inopinata F0304]
          Length = 335

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/212 (14%), Positives = 72/212 (33%), Gaps = 27/212 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       +  + + D   + + +NV CP   V  G        +P  +   + 
Sbjct: 126 VVTNVAGHSDEDYCQVVEKLADSPADMLEINVSCP--NVSSGGMAVG--SDPHALERLMK 181

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARK 157
            +      P+ +K    + D      +  + ++ + +G + + +              + 
Sbjct: 182 KLRPLTDKPMIIKLTPNITD------MTEVARAAEANGADALSMINTFVGMRINTQTGKP 235

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
            I           I  +    VY +++  P + I   GG+  +  AL+ L    + V +G
Sbjct: 236 IIANITGGVSGPAIHPMALAFVYRVRQALPKIPIIGIGGIATVDDALEFLYAGANAVEVG 295

Query: 217 RAAYKNS----AMLTTVDEYFSNPLTGSSPIK 244
            AA  +      +   +D+   +    +  +K
Sbjct: 296 SAALIDPTAPLHIARQLDQELDSRPELAELLK 327


>gi|167760745|ref|ZP_02432872.1| hypothetical protein CLOSCI_03130 [Clostridium scindens ATCC 35704]
 gi|167661632|gb|EDS05762.1| hypothetical protein CLOSCI_03130 [Clostridium scindens ATCC 35704]
          Length = 661

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 39/199 (19%), Positives = 73/199 (36%), Gaps = 24/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCI 108
           +  +AA+  E+ G   I+L   C            P        +G  L      V + I
Sbjct: 149 QFGQAARRAEEAGCGAISL--HCAHAYMLPGSFLSPLRNKRMDEYGGSLDNRARFVIEMI 206

Query: 109 AAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAI--LKG 162
               + +S+   +  RI  D++         +  L    + +GV+ + I        L+ 
Sbjct: 207 EEARRNVSLDFPIFLRISGDERMVGGNSLEDMLYLAPKFEAAGVSMLEISGGTQYEGLEH 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + P  N+      Y+   EIKK    + +   G + D+  A +I+    VDGV +GR   
Sbjct: 267 IIPCQNKSRGVNVYEA-SEIKK-VVGIPVYAVGKINDIRYAAEIVERGLVDGVAMGRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTG 239
            +  +     +   + +T 
Sbjct: 325 ADPDLCKKAVKGQFDEITP 343


>gi|146275842|ref|YP_001166002.1| NADH:flavin oxidoreductase/NADH oxidase [Novosphingobium
           aromaticivorans DSM 12444]
 gi|145322533|gb|ABP64476.1| NADH:flavin oxidoreductase/NADH oxidase [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 711

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 33/183 (18%), Positives = 67/183 (36%), Gaps = 20/183 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  + A+  ++ G++ I ++ G          P        +G  L     +  + IAA+
Sbjct: 172 QFAQGARRAKEAGFDGIEIHGGHGYLLSSFTSPYTNTRTDKYGGSLENRLRLTLEVIAAI 231

Query: 112 CKALSI--PVTVKC---RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL--S 164
              +    PV +K     +G    I     +   K ++ +GV+ I I +      G   S
Sbjct: 232 RAEVGRDYPVWIKLDSREVGKPGGITLDMAKEAAKLVEAAGVDAITITSYHDTSVGKLHS 291

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE--DMSQALKILPSVDGVMIGRAAYKN 222
             +   + N +     EI+K    + +  +G +E      A+      D V +GR    +
Sbjct: 292 ESNIPHLENWNLPATAEIRK-VVSIPVIGSGRIEVDSAESAIAK-GETDFVAMGRKLLAD 349

Query: 223 SAM 225
             +
Sbjct: 350 PHL 352


>gi|294785227|ref|ZP_06750515.1| NADH oxidase [Fusobacterium sp. 3_1_27]
 gi|294486941|gb|EFG34303.1| NADH oxidase [Fusobacterium sp. 3_1_27]
          Length = 311

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 76/185 (41%), Gaps = 20/185 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL--------NVGCPSARVHEG---SFGACLMLNPDIVGDCI 108
              +++AK  ++ G + I L        N+   S+ +      ++G  L+   ++V + I
Sbjct: 133 DCFIKSAKFCQEAGLDGIELHGAHTYFFNML--SSEISNKREDNYGGNLIERLNLVKEII 190

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+         +  R+G  + I         K+++K GV+ + + +     + L   D 
Sbjct: 191 EAIKSFSKDDFIISYRMGWTENINTDI--ETAKALEKLGVDILHVSSGIPEDRKLKLPDE 248

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AM 225
            +  +  Y  + ++KK      I +N  ++ +S+  K++     D V  GR    +   +
Sbjct: 249 FEYNDFVYTGI-QVKKNVNIPVIVVN-DIKTLSRGNKLIEDGDCDFVAYGRPFLSDPNFI 306

Query: 226 LTTVD 230
           + ++ 
Sbjct: 307 IHSIK 311


>gi|237744667|ref|ZP_04575148.1| NADH oxidase [Fusobacterium sp. 7_1]
 gi|229431896|gb|EEO42108.1| NADH oxidase [Fusobacterium sp. 7_1]
          Length = 316

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 76/185 (41%), Gaps = 20/185 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL--------NVGCPSARVHEG---SFGACLMLNPDIVGDCI 108
              +++AK  ++ G + I L        N+   S+ +      ++G  L+   ++V + I
Sbjct: 138 DCFIKSAKFCQEAGLDGIELHGAHTYFFNML--SSEISNKREDNYGGNLIERLNLVKEII 195

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+         +  R+G  + I         K+++K GV+ + + +     + L   D 
Sbjct: 196 EAIKSFSKDDFIISYRMGWTENINTDI--ETAKALEKLGVDILHVSSGIPEDRKLKLPDE 253

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AM 225
            +  +  Y  + ++KK      I +N  ++ +S+  K++     D V  GR    +   +
Sbjct: 254 FEYNDFVYTGI-QVKKNVNIPVIVVN-DIKTLSRGNKLIEDGDCDFVAYGRPFLSDPNFI 311

Query: 226 LTTVD 230
           + ++ 
Sbjct: 312 IHSIK 316


>gi|254882007|ref|ZP_05254717.1| dihydroorotate dehydrogenase [Bacteroides sp. 4_3_47FAA]
 gi|319640986|ref|ZP_07995693.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_1_40A]
 gi|254834800|gb|EET15109.1| dihydroorotate dehydrogenase [Bacteroides sp. 4_3_47FAA]
 gi|317387364|gb|EFV68236.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_1_40A]
          Length = 303

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/192 (15%), Positives = 73/192 (38%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   V+ A+I+ D  +   I LN+ CP+ +    +FG           +
Sbjct: 94  TNMIVNVSGSAVEDYVKTAEIINDLDHIPAIELNISCPNVKQGGMAFGVS----ACGCSE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+       + VK    V D      +  + ++ + SG +            +    
Sbjct: 150 VVKAVRNVYKKTLIVKLSPNVTD------ITEIARAAEASGADSVSLINTLLGMAVDAEK 203

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ K   ++ +   GG+     A++ +L     +
Sbjct: 204 RRPVLSTITGGMSGAAVKPIALRMVWQVAKAV-NIPVIGLGGIMGWKDAVEFMLAGATAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + +  +
Sbjct: 263 QIGTANFIDPTI 274


>gi|238789959|ref|ZP_04633738.1| NADH flavin oxidoreductase [Yersinia frederiksenii ATCC 33641]
 gi|238721907|gb|EEQ13568.1| NADH flavin oxidoreductase [Yersinia frederiksenii ATCC 33641]
          Length = 362

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 75/203 (36%), Gaps = 24/203 (11%)

Query: 39  NILGFSTQEKPLALQIGGADISK--LVEAAKIVEDFGYNEINLNVG---------CPSAR 87
           + L F  +  P AL +   D  K   V AAK   + G+  I ++            P A 
Sbjct: 133 SALPFGERHPPQALSLERIDEIKSAFVAAAKRAVESGFELIEVHAAHGYLLHQFLSPLAN 192

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSI 143
             + ++G  L     +V +  + +  A+   + V  RI   D +           L K +
Sbjct: 193 QRDDNYGGSLENRLRLVLEIFSEIRAAIDKKIAVGVRISATDWVNGGWDTEQSIVLAKQL 252

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQ 202
           +  G + I + +      GLSP+    +   +Y + + +  +E     +   G + +  Q
Sbjct: 253 EILGCDYIHVSSG-----GLSPEQQIPVSP-NYQVPLAQKVREAVKTPVMAVGLITEPEQ 306

Query: 203 ALKILP--SVDGVMIGRAAYKNS 223
           A  I+     D + + R    + 
Sbjct: 307 AEAIIATGQADFIALARGILYDP 329


>gi|258647816|ref|ZP_05735285.1| dihydroorotate oxidase [Prevotella tannerae ATCC 51259]
 gi|260851634|gb|EEX71503.1| dihydroorotate oxidase [Prevotella tannerae ATCC 51259]
          Length = 303

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 26/189 (13%), Positives = 60/189 (31%), Gaps = 17/189 (8%)

Query: 56  GADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G+        A  V +      I LN+ CP    +    G     +       +  + + 
Sbjct: 102 GSSPEDYAACAARVNELEDIPGIELNISCP----NVKDGGMAFGTSAKCAAAVVKEVRRH 157

Query: 115 LSIPVTVKCRIGVDDQIPAVAL--------RNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
               + VK    V D                +L+ ++    ++      + +I  G    
Sbjct: 158 YDKLLVVKLSPNVTDIAEIAKAAEAEGADGLSLINTLMGMAIDVETRRPKLSIATG--GL 215

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAM 225
               I  +   +V+++ +      IGL GG+      ++ ++     V +G A + + ++
Sbjct: 216 SGPAIKPVALRMVWQVARVVKIPVIGL-GGIMTAQDVVEFLMAGATAVQVGTANFIDPSI 274

Query: 226 LTTVDEYFS 234
              +     
Sbjct: 275 TMRIAADLE 283


>gi|297571587|ref|YP_003697361.1| dihydroorotate dehydrogenase [Arcanobacterium haemolyticum DSM
           20595]
 gi|296931934|gb|ADH92742.1| dihydroorotate dehydrogenase family protein [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 307

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 31/208 (14%), Positives = 74/208 (35%), Gaps = 33/208 (15%)

Query: 48  KPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           KP+   + G  I++    A  ++       + +NV CP   VH+G        +P+   +
Sbjct: 95  KPVMANVAGFSIAEYKHVAATLDAVENVGWLEINVSCP--NVHDGGKTFA--DSPESAAE 150

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKG 162
             A +    S PV +K          +  +  + ++ + +G + +         +  L+ 
Sbjct: 151 VCAEIKSVTSKPVIMKLSP------NSSRVVEIAQACEVAGADALSLINTFVGMRLNLRT 204

Query: 163 LSPKDNRKIP------------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
            +P    +               L +D+ + +     ++ I   GG++  +  L+++   
Sbjct: 205 GAPILANRTGGVSGPGVFPMAIRLIWDVSHAV-----NIPIIGIGGVQSAADVLEMMHAG 259

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              V +G A   +     T+       +
Sbjct: 260 ATAVQVGTANLIDPYACHTIIRDLPGEM 287


>gi|255013537|ref|ZP_05285663.1| dihydroorotate dehydrogenase 1B [Bacteroides sp. 2_1_7]
          Length = 305

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 69/187 (36%), Gaps = 33/187 (17%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   VE A+ + +      I LN+ CP    +    G    +     G+
Sbjct: 94  TNMIVNVSGSSVETYVECAEKIAELDRIPAIELNISCP----NVKQGGMAFGVTTCGAGE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+ +     + VK    V D      +  + K+++  G +            I    
Sbjct: 150 VVKAVRRVYPKTLIVKLSPNVTD------ITEIAKAVEAEGADSVSLINTMLGMAIDAEK 203

Query: 156 RKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
           RK IL     GLS    + +   + +   + +K     + I   GG+ +   A++ +L  
Sbjct: 204 RKPILSTITGGLSGPCVKPVALRMVWQTYHAVK-----IPIIGLGGISNWKDAVEFMLAG 258

Query: 210 VDGVMIG 216
              + IG
Sbjct: 259 ATAIQIG 265


>gi|148544533|ref|YP_001271903.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri DSM 20016]
 gi|184153896|ref|YP_001842237.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri JCM 1112]
 gi|227363039|ref|ZP_03847176.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri MM2-3]
 gi|325682854|ref|ZP_08162370.1| dihydroorotate dehydrogenase [Lactobacillus reuteri MM4-1A]
 gi|148531567|gb|ABQ83566.1| dihydroorotate oxidase B, catalytic subunit [Lactobacillus reuteri
           DSM 20016]
 gi|183225240|dbj|BAG25757.1| putative oxidoreductase [Lactobacillus reuteri JCM 1112]
 gi|227071923|gb|EEI10209.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri MM2-3]
 gi|324977204|gb|EGC14155.1| dihydroorotate dehydrogenase [Lactobacillus reuteri MM4-1A]
          Length = 432

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 62/159 (38%), Gaps = 27/159 (16%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+V + G + I LN  CP   +   + G+ +  NP++      A+ +  S+PV  K   
Sbjct: 122 AKLVTETGADMIELNFSCPQ--MTSHTMGSDVGTNPELCKKNCEAVKRGTSLPVLAKMTP 179

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAIL----------------KGLSPKDN 168
            +   +P       VK+  + G +G   I+  K+I+                  +S    
Sbjct: 180 NITTMVPV------VKACLEGGADGFSAINTVKSIVDVDLKKKVGLPNIDGKSSVSGLSG 233

Query: 169 RKIPNLDYDIVYEIKKENP--DLFIGLNGGLEDMSQALK 205
           + +  +    + +++       L I   GG+E    A +
Sbjct: 234 KAVKPIALRFLQQLRSAAGLEQLPISGIGGIETWEDAAE 272


>gi|254688596|ref|ZP_05151850.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 6 str. 870]
 gi|260754066|ref|ZP_05866414.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 6 str. 870]
 gi|260674174|gb|EEX60995.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 6 str. 870]
          Length = 436

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|222086790|ref|YP_002545324.1| dihydroorotate oxidase protein [Agrobacterium radiobacter K84]
 gi|221724238|gb|ACM27394.1| dihydroorotate oxidase protein [Agrobacterium radiobacter K84]
          Length = 437

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 70/209 (33%), Gaps = 17/209 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 TDVRMPARAAKAGGTDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++V EI ++     L I   GG+     A + L      V +  AA         V E  
Sbjct: 243 NMVAEIARDPQTQGLPISGIGGITTWRDAAEFLALGAGNVQVCTAAMT--YGFKIVQEMI 300

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           +           R   D   +   +++D+
Sbjct: 301 TGLSDWMDEKGHRTLDDIIARAVPNVSDW 329


>gi|194466721|ref|ZP_03072708.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
 gi|227543869|ref|ZP_03973918.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           CF48-3A]
 gi|300909615|ref|ZP_07127076.1| dihydroorotate dehydrogenase [Lactobacillus reuteri SD2112]
 gi|157805448|gb|ABV80266.1| dihydropyrimidine dehydrogenase [Lactobacillus reuteri]
 gi|194453757|gb|EDX42654.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           100-23]
 gi|227186130|gb|EEI66201.1| dihydroorotate dehydrogenase family protein [Lactobacillus reuteri
           CF48-3A]
 gi|300893480|gb|EFK86839.1| dihydroorotate dehydrogenase [Lactobacillus reuteri SD2112]
          Length = 432

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 62/159 (38%), Gaps = 27/159 (16%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+V + G + I LN  CP   +   + G+ +  NP++      A+ +  S+PV  K   
Sbjct: 122 AKLVTEAGADMIELNFSCPQ--MTSHTMGSDVGTNPELCKKNCEAVKRGTSLPVLAKMTP 179

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAIL----------------KGLSPKDN 168
            +   +P       VK+  + G +G   I+  K+I+                  +S    
Sbjct: 180 NITTMVPV------VKACLEGGADGFSAINTVKSIVDVDLKKKVGLPNIDGKSSVSGLSG 233

Query: 169 RKIPNLDYDIVYEIKKENP--DLFIGLNGGLEDMSQALK 205
           + +  +    + +++       L I   GG+E    A +
Sbjct: 234 KAVKPIALRFLQQLRSAAGLEQLPISGIGGIETWEDAAE 272


>gi|254701102|ref|ZP_05162930.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 5 str. 513]
 gi|261751635|ref|ZP_05995344.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 5 str. 513]
 gi|261741388|gb|EEY29314.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 5 str. 513]
          Length = 436

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|124514846|gb|EAY56357.1| Dihydroorotate dehydrogenase [Leptospirillum rubarum]
          Length = 368

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 65/203 (32%), Gaps = 22/203 (10%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               V  A + ++ G   + +N  CP    +       L  NPD  G+ +  + K L   
Sbjct: 170 AQDFVYTAHLAKETGAKILEVNFSCP----NVKGKEGQLYQNPDASGEILKRIRKELGRD 225

Query: 119 VTVKCRIGVDDQIPAVA--------LRNLVKSIKKSGVNGIWIHARKAIL---KGLSPKD 167
             +  +IG  D    +           + + +I       I    + A+    +  S   
Sbjct: 226 FHLIMKIGFSDNPEHLDRLVEATSPYLDAISAINTVTGTIINPEGKPALPGPGRERSGLC 285

Query: 168 NRKIPNLDYDIVY----EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
              I NL    +      +++  P L +   GG   +           D VM    A  +
Sbjct: 286 GSGIKNLSLKTIRGLKQALRRRAPQLSLIGVGGFNTVEDYPDFREAGADIVMSATGAMWD 345

Query: 223 SAMLTTVDE--YFSNPLTGSSPI 243
             +   V +  +  + L   SP+
Sbjct: 346 PFLAYHVKQRTFVQDTLPSDSPV 368


>gi|160871705|ref|ZP_02061837.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Rickettsiella grylli]
 gi|159120504|gb|EDP45842.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Rickettsiella grylli]
          Length = 355

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/189 (19%), Positives = 63/189 (33%), Gaps = 26/189 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPV 119
             + AA + ++ G + I LN  CP   + +      L  N D V      + K +  IP+
Sbjct: 173 DFMTAALMAKEAGADIIELNFSCP--NLMKSDEP--LYRNMDCVSQITTRVVKCVGDIPL 228

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKGLSPKD 167
            +K     + + P      L+ S  ++GV GI              H      +  S   
Sbjct: 229 LLKIGFIHEHEFP----LKLLISAARAGVRGISAINSISMRVLNQNHRPAFGKRIYSGIS 284

Query: 168 NRKIPNLDYDIVYEI----KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
              I  L    V ++    +KE  +L I   GG+       +      D V+       N
Sbjct: 285 GYPIRRLALQSVKKLTQINQKEKLNLTIVGMGGITVAEHFDEFFDRGADAVLSATGVMWN 344

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 345 PYLAMQFHQ 353


>gi|306844922|ref|ZP_07477504.1| dihydroorotate dehydrogenase family protein [Brucella sp. BO1]
 gi|306274751|gb|EFM56535.1| dihydroorotate dehydrogenase family protein [Brucella sp. BO1]
          Length = 436

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|150007754|ref|YP_001302497.1| dihydroorotate dehydrogenase 1B [Parabacteroides distasonis ATCC
           8503]
 gi|298375699|ref|ZP_06985656.1| dihydroorotate oxidase [Bacteroides sp. 3_1_19]
 gi|166199373|sp|A6LB11|PYRD_PARD8 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|149936178|gb|ABR42875.1| dihydroorotate dehydrogenase [Parabacteroides distasonis ATCC 8503]
 gi|298268199|gb|EFI09855.1| dihydroorotate oxidase [Bacteroides sp. 3_1_19]
          Length = 305

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 69/187 (36%), Gaps = 33/187 (17%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   VE A+ + +      I LN+ CP    +    G    +     G+
Sbjct: 94  TNMIVNVSGSSVETYVECAEKIAELDRIPAIELNISCP----NVKQGGMAFGVTTCGAGE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+ +     + VK    V D      +  + K+++  G +            I    
Sbjct: 150 VVKAVRRVYPKILIVKLSPNVTD------ITEIAKAVEAEGADSVSLINTMLGMAIDAEK 203

Query: 156 RKAILK----GLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
           RK IL     GLS    + +   + +   + +K     + I   GG+ +   A++ +L  
Sbjct: 204 RKPILSTITGGLSGPCVKPVALRMVWQTYHAVK-----IPIIGLGGISNWKDAVEFMLAG 258

Query: 210 VDGVMIG 216
              + IG
Sbjct: 259 ASAIQIG 265


>gi|153955191|ref|YP_001395956.1| enoate reductase [Clostridium kluyveri DSM 555]
 gi|219855623|ref|YP_002472745.1| hypothetical protein CKR_2280 [Clostridium kluyveri NBRC 12016]
 gi|146348049|gb|EDK34585.1| Predicted enoate reductase [Clostridium kluyveri DSM 555]
 gi|219569347|dbj|BAH07331.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 704

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 33/203 (16%), Positives = 69/203 (33%), Gaps = 31/203 (15%)

Query: 43  FSTQE-KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGS 92
           F+T+E   L  Q         ++AAK  +  G + + L+ G          P   +    
Sbjct: 187 FTTEEIHNLIGQ--------FIKAAKRAQQSGADGVELHAGHGYLLNQFLSPYTNIRSDE 238

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----------LVKS 142
           +G        I+ + I  + +  S    +  R+ VD+    +              + KS
Sbjct: 239 YGGSFENRLRIMKELIEGIHRECSADFPISVRLTVDEFYEKIDYPEQGLHLNDGVEIAKS 298

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++  G + I +    +  + +  +     P     +   +K +   + +   G +    Q
Sbjct: 299 LEAYGADAINVTTGNSDTQFMITEPISFQPGWRKYLSKAVK-DAVHIPVISVGVIRTPEQ 357

Query: 203 ALKILPSVDGVMIG--RAAYKNS 223
           A ++L   D   IG  R    + 
Sbjct: 358 AEQLLLEGDQDFIGLARPLLADP 380


>gi|163842566|ref|YP_001626970.1| dihydropyrimidine dehydrogenase [Brucella suis ATCC 23445]
 gi|163673289|gb|ABY37400.1| dihydroorotate dehydrogenase family protein [Brucella suis ATCC
           23445]
          Length = 436

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|225626809|ref|ZP_03784848.1| dihydroorotate dehydrogenase family protein [Brucella ceti str.
           Cudo]
 gi|254707974|ref|ZP_05169802.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis M163/99/10]
 gi|254709446|ref|ZP_05171257.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis B2/94]
 gi|256030940|ref|ZP_05444554.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis M292/94/1]
 gi|260168075|ref|ZP_05754886.1| dihydropyrimidine dehydrogenase [Brucella sp. F5/99]
 gi|261315465|ref|ZP_05954662.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis M163/99/10]
 gi|261316968|ref|ZP_05956165.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis B2/94]
 gi|261757524|ref|ZP_06001233.1| dihydropyrimidine dehydrogenase [Brucella sp. F5/99]
 gi|265988004|ref|ZP_06100561.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis M292/94/1]
 gi|225618466|gb|EEH15509.1| dihydroorotate dehydrogenase family protein [Brucella ceti str.
           Cudo]
 gi|261296191|gb|EEX99687.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis B2/94]
 gi|261304491|gb|EEY07988.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis M163/99/10]
 gi|261737508|gb|EEY25504.1| dihydropyrimidine dehydrogenase [Brucella sp. F5/99]
 gi|264660201|gb|EEZ30462.1| dihydropyrimidine dehydrogenase [Brucella pinnipedialis M292/94/1]
          Length = 436

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|300728133|ref|ZP_07061504.1| dihydroorotate oxidase [Prevotella bryantii B14]
 gi|299774559|gb|EFI71180.1| dihydroorotate oxidase [Prevotella bryantii B14]
          Length = 302

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 28/208 (13%), Positives = 74/208 (35%), Gaps = 25/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+        A+ ++   G   I +N+ CP    +  + G     +     
Sbjct: 93  DTNMIVNVSGSSPENYAACAEKLDALDGIPAIEVNISCP----NVKNGGMAFGTSVRGAS 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      +  + ++ +  G +            + I 
Sbjct: 149 SIVKAVREVYHKTMIVKLSPNVTD------IAEIARACESEGADSVSLINTLMGMAVDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L   +       +  +   +VY++      + +   GG+     A++ ++     
Sbjct: 203 KRKPLLSIRTGGLSGPAVKPVALRMVYDVA-HAVKIPVVGLGGICTAQDAIEFLMCGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + +G A + + A+   + +  S+ L   
Sbjct: 262 IEVGTANFLDPAVTKKIKDGISDWLDAH 289


>gi|256368743|ref|YP_003106249.1| dihydropyrimidine dehydrogenase [Brucella microti CCM 4915]
 gi|255998901|gb|ACU47300.1| dihydropyrimidine dehydrogenase [Brucella microti CCM 4915]
          Length = 436

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|23501189|ref|NP_697316.1| dihydropyrimidine dehydrogenase [Brucella suis 1330]
 gi|161618261|ref|YP_001592148.1| dihydropyrimidine dehydrogenase [Brucella canis ATCC 23365]
 gi|254703651|ref|ZP_05165479.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 3 str. 686]
 gi|260567096|ref|ZP_05837566.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 4 str. 40]
 gi|261754289|ref|ZP_05997998.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 3 str. 686]
 gi|23347067|gb|AAN29231.1| dihydroorotate dehydrogenase family protein [Brucella suis 1330]
 gi|161335072|gb|ABX61377.1| dihydroorotate dehydrogenase family protein [Brucella canis ATCC
           23365]
 gi|260156614|gb|EEW91694.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 4 str. 40]
 gi|261744042|gb|EEY31968.1| dihydropyrimidine dehydrogenase [Brucella suis bv. 3 str. 686]
          Length = 436

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|62289276|ref|YP_221069.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 1 str. 9-941]
 gi|82699207|ref|YP_413781.1| dihydropyrimidine dehydrogenase [Brucella melitensis biovar Abortus
           2308]
 gi|189023530|ref|YP_001934298.1| dihydropyrimidine dehydrogenase [Brucella abortus S19]
 gi|237814768|ref|ZP_04593766.1| dihydroorotate dehydrogenase family protein [Brucella abortus str.
           2308 A]
 gi|254696719|ref|ZP_05158547.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254729629|ref|ZP_05188207.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 4 str. 292]
 gi|256060433|ref|ZP_05450604.1| dihydropyrimidine dehydrogenase [Brucella neotomae 5K33]
 gi|256256844|ref|ZP_05462380.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 9 str. C68]
 gi|260545967|ref|ZP_05821708.1| dihydropyrimidine dehydrogenase [Brucella abortus NCTC 8038]
 gi|260757288|ref|ZP_05869636.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 4 str. 292]
 gi|260761110|ref|ZP_05873453.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260883093|ref|ZP_05894707.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 9 str. C68]
 gi|261324422|ref|ZP_05963619.1| dihydropyrimidine dehydrogenase [Brucella neotomae 5K33]
 gi|297247693|ref|ZP_06931411.1| dihydropyrimidine dehydrogenase (NADP+) [Brucella abortus bv. 5
           str. B3196]
 gi|62195408|gb|AAX73708.1| dihydroorotate dehydrogenase family protein [Brucella abortus bv. 1
           str. 9-941]
 gi|82615308|emb|CAJ10269.1| Legume lectin, beta domain:Dihydroorotate dehydrogenase:4Fe-4S
           ferredoxin, iron-sulfur binding domain:FMN/related
           compound-bi [Brucella melitensis biovar Abortus 2308]
 gi|189019102|gb|ACD71824.1| dihydropyrimidine dehydrogenase [Brucella abortus S19]
 gi|237789605|gb|EEP63815.1| dihydroorotate dehydrogenase family protein [Brucella abortus str.
           2308 A]
 gi|260097374|gb|EEW81249.1| dihydropyrimidine dehydrogenase [Brucella abortus NCTC 8038]
 gi|260667606|gb|EEX54546.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 4 str. 292]
 gi|260671542|gb|EEX58363.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260872621|gb|EEX79690.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 9 str. C68]
 gi|261300402|gb|EEY03899.1| dihydropyrimidine dehydrogenase [Brucella neotomae 5K33]
 gi|297174862|gb|EFH34209.1| dihydropyrimidine dehydrogenase (NADP+) [Brucella abortus bv. 5
           str. B3196]
          Length = 436

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|226312824|ref|YP_002772718.1| dihydropyrimidine dehydrogenase [Brevibacillus brevis NBRC 100599]
 gi|226095772|dbj|BAH44214.1| conserved hypothetical protein [Brevibacillus brevis NBRC 100599]
          Length = 425

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/112 (24%), Positives = 46/112 (41%), Gaps = 7/112 (6%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE  G + + LN GCP     E   G+ +  +PD++   +  + +    PV VK 
Sbjct: 116 EIVKKVEAIGVDGLELNFGCPHGMA-ERGMGSAVGQHPDLIRQQVEWVKEVAQTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
              + D      +R   ++    G + I +      L G+       IP++D
Sbjct: 175 TPNITD------IRFTARAASLGGADAISMINTINSLMGVDLDKWLPIPHVD 220


>gi|294776465|ref|ZP_06741940.1| dihydroorotate dehydrogenase 1B [Bacteroides vulgatus PC510]
 gi|294449662|gb|EFG18187.1| dihydroorotate dehydrogenase 1B [Bacteroides vulgatus PC510]
          Length = 303

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 74/192 (38%), Gaps = 25/192 (13%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             + + + G+ +   V+ A+I+ D  +   I LN+ CP+ +    +FG           +
Sbjct: 94  TNMIVNVSGSAVEDYVKTAEIINDLDHIPAIELNISCPNVKQGGMAFGVS----ACGCSE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            + A+       + VK    V D      +  + ++ + SG +            +    
Sbjct: 150 VVKAVRNVYKKTLIVKLSPNVTD------ITEIARAAETSGADSVSLINTLLGMAVDAEK 203

Query: 156 RKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
           R+ +L           +  +   +V+++ K   ++ +   GG+     A++ +L     +
Sbjct: 204 RRPVLSTITGGMSGAAVKPIALRMVWQVAK-VVNIPVIGLGGIMGWKDAVEFMLAGATAI 262

Query: 214 MIGRAAYKNSAM 225
            IG A + + A+
Sbjct: 263 QIGTANFIDPAI 274


>gi|254713135|ref|ZP_05174946.1| dihydropyrimidine dehydrogenase [Brucella ceti M644/93/1]
 gi|254716511|ref|ZP_05178322.1| dihydropyrimidine dehydrogenase [Brucella ceti M13/05/1]
 gi|261218305|ref|ZP_05932586.1| dihydropyrimidine dehydrogenase [Brucella ceti M13/05/1]
 gi|261320846|ref|ZP_05960043.1| dihydropyrimidine dehydrogenase [Brucella ceti M644/93/1]
 gi|260923394|gb|EEX89962.1| dihydropyrimidine dehydrogenase [Brucella ceti M13/05/1]
 gi|261293536|gb|EEX97032.1| dihydropyrimidine dehydrogenase [Brucella ceti M644/93/1]
          Length = 436

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|253576687|ref|ZP_04854014.1| dihydroorotate dehydrogenase 1B [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251843897|gb|EES71918.1| dihydroorotate dehydrogenase 1B [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 310

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 35/237 (14%), Positives = 80/237 (33%), Gaps = 41/237 (17%)

Query: 11  FFARLLTNNALLYTE----MIVADAILRGDKKNILGFSTQEKPLALQI--------GGAD 58
                  N  +   E    M+ +  +        L    +E P   Q+        GG  
Sbjct: 48  TLHPKAGNEGVRVAETASGMLNSVGLENPGIYAFLR---EECPRWEQLDLVRIVNLGGNT 104

Query: 59  ISKLVEAAKIVEDFGY----------NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           I + VE A+++++             + I LN+ CP+ +    ++G       +I    +
Sbjct: 105 IEEYVEGARLIDEDAAWRRREGRTAVDMIELNISCPNVKAGGMAYGI----KTEIARQVV 160

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIKKSGVNGIWIHARKAIL 160
             +  A ++P+ VK     +D +    +          L+ +     ++      R    
Sbjct: 161 REVRAATTLPLIVKLSPNAEDIVGMAVMCQEEQADGVSLINTFSAMKID--ITKRRSVFD 218

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
              +      I  +   +V+++ +      +G+ GG+      ++ I+     V +G
Sbjct: 219 NLYAGLSGPAIKPIALRMVHQVCQAVTLPVMGM-GGISCAEDVVEFIMAGAAVVQVG 274


>gi|147918836|ref|YP_687438.1| hypothetical protein RRC405 [uncultured methanogenic archaeon RC-I]
 gi|110622834|emb|CAJ38112.1| conserved hypothetical protein [uncultured methanogenic archaeon
           RC-I]
          Length = 376

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 83/211 (39%), Gaps = 28/211 (13%)

Query: 25  EMIVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E I    +  + GD K     S +   + + +  A +  L+ AAK+ + +G   + LN  
Sbjct: 66  EFITDRPLELIEGDLK---KVSGKGVAIGINVRAASLEPLIAAAKLAKKYGA-ILELNAH 121

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           C    +     G  ++ +   +   I  + K   + +++K R G+ D++P      L++ 
Sbjct: 122 CRQEEMAAIGVGEVMLKDRIGLSKTIVELKK-TGVVLSLKMRAGIVDEVP------LLRL 174

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++K+G++ + I        G    +   +  L         ++   LFI  N  +     
Sbjct: 175 LEKAGLDIVHIDTM-----GTRGPNVNVLKKL---------RDGTGLFIIGNNSINGYES 220

Query: 203 ALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           A        D + + R   +N  ++ ++  Y
Sbjct: 221 AQAAYSAGCDMISLARPVLENPKIIKSLVTY 251


>gi|302888248|ref|XP_003043011.1| hypothetical protein NECHADRAFT_37088 [Nectria haematococca mpVI
           77-13-4]
 gi|256723925|gb|EEU37298.1| hypothetical protein NECHADRAFT_37088 [Nectria haematococca mpVI
           77-13-4]
          Length = 411

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 71/201 (35%), Gaps = 31/201 (15%)

Query: 54  IGGADISKL----VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLN 100
           + G ++ +L     +AA+     G++ + ++            P +     ++G      
Sbjct: 181 LTGEEVEELKTAYAQAAQRAVKAGFDVLEIHAAHGYLLHQFLSPVSNRRTDAYGGNFENR 240

Query: 101 PDIVGDCIAAMCKALS--IPVTV------------KCRIGVDDQIPAVALRNLVKSIKKS 146
             ++ + +  +   +   +P+ V            K +    +         L   +   
Sbjct: 241 TRLLLEIVERIRAVIPETMPLFVRISATDWFEFDEKLKQEFPESWTVDQSGKLASLLADR 300

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALK 205
           GV+ + + +     K  S    R  P     +   IKK   D + +   GG++  + A +
Sbjct: 301 GVDLVDVSSGGIHAK--SAIAIRPGPGYQVHLAQAIKKAVGDKILVSAVGGIKTGTLAEE 358

Query: 206 ILP-SVDGVMIGRAAYKNSAM 225
           +L   +D VM GR   +N  +
Sbjct: 359 VLQSGIDVVMAGRWFQQNPGL 379


>gi|15893489|ref|NP_346838.1| NADH-dependent flavine oxidoreductase [Clostridium acetobutylicum
           ATCC 824]
 gi|15023028|gb|AAK78178.1|AE007533_2 NADH-dependent flavine oxidoreductase [Clostridium acetobutylicum
           ATCC 824]
 gi|325507606|gb|ADZ19242.1| NADH-dependent flavine oxidoreductase [Clostridium acetobutylicum
           EA 2018]
          Length = 351

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 70/179 (39%), Gaps = 17/179 (9%)

Query: 64  EAAKIVEDFGYNEINLNVGCP--------SARVHEGSFGACLMLNPDI-VGDCIAAMCKA 114
           EAA+   + GY+ I L+ GC         + RV++ +       NP+  V + +  + K 
Sbjct: 146 EAARRAYEAGYDGIELH-GCHGYLICQFLNKRVNKRNDEYG--KNPENFVIEILEGIRKV 202

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
                 V  R+G  +      +    K  ++ G++ + +    +  + ++  ++ K  N 
Sbjct: 203 TPKEFIVGIRLGGFEPAIEDGIH-YAKIFEQQGIDFLDVSYGFSNGQEINVGEDYKYSNA 261

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            Y     IKKE   + +    G+     A  IL   +VD V I R A  N        E
Sbjct: 262 VYAA-ERIKKEV-SVPVFAVDGINSGDMAEAILNETNVDLVDIARGALINPNWANDARE 318


>gi|302348765|ref|YP_003816403.1| Dihydroorotate dehydrogenase [Acidilobus saccharovorans 345-15]
 gi|302329177|gb|ADL19372.1| Dihydroorotate dehydrogenase [Acidilobus saccharovorans 345-15]
          Length = 301

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 39/202 (19%), Positives = 79/202 (39%), Gaps = 15/202 (7%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARV 88
           A+  + G + ++   +    P+ + + G+      + A + E+ G   + LN+ CP   V
Sbjct: 73  ANPGIEGLRDHMRALAGLGIPIIVSVAGSLPEDFAKVAAVAEEAGAAAVELNLSCPH--V 130

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN-------LVK 141
            +      +  +P +    ++A+   + IPV  K  I       A A          L+ 
Sbjct: 131 EKMGLDIGM--DPVMSRKVVSAVASTVKIPVIAKLGISDKMVETAEASLEAGAKGLTLIN 188

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           +++   ++   +  R A+  G+       I  +    VYE+ +E     I   GG+E   
Sbjct: 189 TVRAMRIDVYSL--RPALGHGIGGLSGPAIHPIAVRAVYEVYREL-RPDIFGAGGVERWE 245

Query: 202 QALK-ILPSVDGVMIGRAAYKN 222
            A++ IL     V +G    + 
Sbjct: 246 DAVELILAGAKAVQVGSGLVRR 267


>gi|315123259|ref|YP_004065265.1| putative NADH-dependent flavin oxidoreductase [Pseudoalteromonas
           sp. SM9913]
 gi|315017019|gb|ADT70356.1| putative NADH-dependent flavin oxidoreductase [Pseudoalteromonas
           sp. SM9913]
          Length = 364

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 60/179 (33%), Gaps = 20/179 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AAK  ++ G + I +             P A   +  +G  L     ++ D   A+
Sbjct: 159 DFVNAAKRADELGLDLIEIHGAHGYLLHQFLSPLANKRDDQYGGSLENRMRLLLDVFKAV 218

Query: 112 CKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A      + V +     VD          L K++   G + I +        GLSP+ 
Sbjct: 219 RTAFPSNKAVGVRISATDWVDGGWDLPQSIELAKALDALGCDFIHVSTA-----GLSPEQ 273

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
           +  +            K+  ++ +   G + +  QA  I+     DGV + R    N  
Sbjct: 274 DIPVVKNFQVPFATAIKQVVNMPVIAVGLITEAQQAESIISDERADGVALARGILYNPH 332


>gi|149183199|ref|ZP_01861646.1| dihydropyrimidine dehydrogenase [Bacillus sp. SG-1]
 gi|148849095|gb|EDL63298.1| dihydropyrimidine dehydrogenase [Bacillus sp. SG-1]
          Length = 428

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 61/177 (34%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VE  G + + LN GCP     E   GA     P++V        +    PV VK 
Sbjct: 116 EIVKKVEAVGVDGLELNFGCPHGMA-ERGMGAASGQVPELVEKQTYWAKEVAKTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + + +      L G+       IP           
Sbjct: 175 TPNITDITVT------AEAAVQGGADAVSMINTINSLAGVDLDSWNTIPHVAGKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+ +   A++ IL    GV +  AA  
Sbjct: 229 CGPAVKPISLNMVAECARNPRVNVPISGMGGVSNWQDAVEFILMGASGVQVCTAAMH 285


>gi|254250832|ref|ZP_04944151.1| Dihydroorotate dehydrogenase 1 [Burkholderia cenocepacia PC184]
 gi|124879966|gb|EAY67322.1| Dihydroorotate dehydrogenase 1 [Burkholderia cenocepacia PC184]
          Length = 508

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 193 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 251

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 252 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 311

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E PDL I   GG+     A + ++     V +  AA  
Sbjct: 312 NMVAEIARDPETPDLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 359


>gi|315185323|gb|EFU19098.1| dihydroorotate oxidase B, catalytic subunit [Spirochaeta
           thermophila DSM 6578]
          Length = 303

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/206 (16%), Positives = 70/206 (33%), Gaps = 29/206 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G+D  +  E    +E         +N+ CP   V +G         P  V   
Sbjct: 94  PVIGNIAGSDPEEYAEVISFLEAHTDLWGYEINISCP--NVKKGGITIG--TEPTTVERL 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHAR 156
              +      P+ VK    V D      +  + ++ +  G +            I IH +
Sbjct: 150 TRTLRDLTPKPLIVKLTPNVTD------ITEIARAAEAGGADALSCINTVVGMAIDIHKK 203

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           + ++ +  +      I  +    VY ++       IG+ G +E    A++ +L     + 
Sbjct: 204 RPVIPQKTAGLSGPAIKPIGLAAVYRVRTSVRIPIIGIGGIME-PEDAIEYLLAGASAIQ 262

Query: 215 IGRAAYKNSA----MLTTVDEYFSNP 236
           +G A + +      +L  +  Y    
Sbjct: 263 VGTALFVDPHTPDRILKGIKSYMEQE 288


>gi|170696015|ref|ZP_02887153.1| dihydroorotate dehydrogenase family protein [Burkholderia graminis
           C4D1M]
 gi|170139095|gb|EDT07285.1| dihydroorotate dehydrogenase family protein [Burkholderia graminis
           C4D1M]
          Length = 442

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ +      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 TDIRVGSRAAYKGGADGVSLINTINSIVAVDLDAMSPLPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDTETPNLPISGIGGISTWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|317051703|ref|YP_004112819.1| dihydroorotate dehydrogenase family protein [Desulfurispirillum
           indicum S5]
 gi|316946787|gb|ADU66263.1| dihydroorotate dehydrogenase family protein [Desulfurispirillum
           indicum S5]
          Length = 299

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 83/232 (35%), Gaps = 33/232 (14%)

Query: 26  MIVADAI----LRGDKKNIL-GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +    +R   +  L         +     G  + + VE AK +   G   + +N
Sbjct: 65  MLNAIGLQNIGVRSFVEEKLPRLREIGASVIANFYGNTVEEYVECAKALSVEGIQALEMN 124

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           + CP    +  S G     +  +    + A+  A   P+ VK    V D      +R   
Sbjct: 125 ISCP----NVKSGGIAFGSDVSMTAAVVQAVRAATEKPLIVKLSPNVAD------IRPFA 174

Query: 141 KSIKKSGVN-----------GIWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPD 188
           ++   +G +            I +  RK  +  L+       I  +   +VY++     D
Sbjct: 175 ETAVAAGADSLSLINTLIGMAIDVETRKPRIGNLTGGLSGPAIKPVGVRMVYQVCG-VTD 233

Query: 189 LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSA----MLTTVDEYFSN 235
           + +   GG+ +   AL+  L     V +G   + +      +L  ++ YFS 
Sbjct: 234 VPVIGMGGIMNYRDALEYFLAGASAVQVGTVNFTDPCASLKILEDLERYFSE 285


>gi|307944819|ref|ZP_07660157.1| dihydropyrimidine dehydrogenase [NADP+] [Roseibium sp. TrichSKD4]
 gi|307772033|gb|EFO31256.1| dihydropyrimidine dehydrogenase [NADP+] [Roseibium sp. TrichSKD4]
          Length = 437

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 59/168 (35%), Gaps = 15/168 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K VED G + + LN GCP     E   G+ +   P+ +        +   +PV VK    
Sbjct: 122 KKVEDTGADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWCKQHTRMPVIVKLTPN 180

Query: 127 VDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           + D              AV+L N + SI    ++ +                   +  + 
Sbjct: 181 ITDIRKPAQAAHAGGADAVSLINTINSIVGVDLDAMAPSPTIDGKGAHGGYCGPAVKPIA 240

Query: 176 YDIVYEIKKENP--DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 241 LNMVAEIARDPTTHGLPISGIGGVTTWRDAAEFMALGAGSVQVCTAAM 288


>gi|255088383|ref|XP_002506114.1| predicted protein [Micromonas sp. RCC299]
 gi|226521385|gb|ACO67372.1| predicted protein [Micromonas sp. RCC299]
          Length = 434

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 61/175 (34%), Gaps = 23/175 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE  +  E+ G +   +N  CP     E   GA +  +  ++ +    + +  ++PV  K
Sbjct: 179 VEVVRRCEEVGVDAFEINFSCPHGM-PERKMGAAMGQDCTVLDEVCGWVKEVATVPVWAK 237

Query: 123 CRIGVDDQIPAVALR---------NLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDN 168
               + D      +           +   +   GVN   +     +       G S K  
Sbjct: 238 MTPNITDITEPANVCLEKGMDGIAAINTIMSIMGVNLDTLAPEPCVEGHSTPGGYSYKAV 297

Query: 169 RKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALK-------ILPSVDGVMI 215
           R I       + + IKKE PD  +   GG++    A +        +    GVMI
Sbjct: 298 RPIALAKCMAIAQMIKKEFPDRTLSGIGGIDTGGHAAEFILLGSDTVQVCTGVMI 352


>gi|169831461|ref|YP_001717443.1| dihydroorotate dehydrogenase family protein [Candidatus
           Desulforudis audaxviator MP104C]
 gi|229485558|sp|B1I4M6|PYRD_DESAP RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|169638305|gb|ACA59811.1| dihydroorotate dehydrogenase family protein [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 307

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 72/205 (35%), Gaps = 22/205 (10%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARV 88
           +A++R     +  F     P+ + I G  + +    A  ++   G   + +N+ CP    
Sbjct: 80  EALVRDILPRLARFD---VPVIVSIAGETVDEYARLAGRLDGVPGIAALEVNISCP---- 132

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD--------QIPAVALRNLV 140
           +  + G      P +    +  + +   +PV  K    V D                +L+
Sbjct: 133 NVKAGGIAFGTEPAMTAAVVRQVRENTRLPVIAKLSPNVTDIRTIALAAAGAGADALSLI 192

Query: 141 KSIKKSGVNGIWIHARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++       I +  R+ +L           +  +    V+++ +      IG+ GG+  
Sbjct: 193 NTLSAM---VIDVERRRPLLGNVFGGLSGPAVRPVAVRAVWQVYQAVELPLIGM-GGIMT 248

Query: 200 MSQALK-ILPSVDGVMIGRAAYKNS 223
              AL+ IL     V +G A   N 
Sbjct: 249 ARDALEFILAGARAVAVGTANLVNP 273


>gi|332885164|gb|EGK05415.1| dihydroorotate dehydrogenase [Dysgonomonas mossii DSM 22836]
          Length = 303

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/206 (16%), Positives = 76/206 (36%), Gaps = 29/206 (14%)

Query: 47  EKPLALQIGGADISKLVEAA-KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G+ I   VE + K+V       I LN+ CP    +    G     +     
Sbjct: 93  DTNIIVNVSGSTIEDYVECSQKLVALEKIPAIELNISCP----NVKEGGMAFGTSACSAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           D   A+ +  +  + VK    V D      +  + K+++  G + +            I+
Sbjct: 149 DVTKAVREVWNKTLIVKLSPNVTD------ITEIAKAVEGEGADAVSLINTLLGMAVDIN 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L  ++       +  +   +V++         IG+ GG+     A++ IL     
Sbjct: 203 KRRPVLSTVTGGLSGPCVKPIALRMVWQTYNAVKIPVIGM-GGISSWQDAIEFILAGSSA 261

Query: 213 VMIGRAAYKNSAM----LTTVDEYFS 234
           + IG   + +  +    +  + EY  
Sbjct: 262 IQIGTHNFIDPTISVKVVDGIKEYLD 287


>gi|229541980|ref|ZP_04431040.1| dihydroorotate dehydrogenase family protein [Bacillus coagulans
           36D1]
 gi|229326400|gb|EEN92075.1| dihydroorotate dehydrogenase family protein [Bacillus coagulans
           36D1]
          Length = 426

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 61/178 (34%), Gaps = 28/178 (15%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K VED G + + LN GCP     E   GA     P +V      + +A   PV VK 
Sbjct: 116 EIVKRVEDAGVDGLELNFGCPHGMA-ERGMGAASGQVPQLVEQQTYWVKEAAKTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D            +  + G + + +      L G+     + +P           
Sbjct: 175 TPNITDITATAF------AAVQGGADAVSMINTINSLMGVDLDTWQTVPHVAGLGTHGGY 228

Query: 173 ------NLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +   +V E  ++ PD+ + +   GG+     A + +L     V +  A   
Sbjct: 229 CGPAVKPIALSMVAECARD-PDIPVPISGIGGIATWKDAAEFMLMGASNVQVCTAVMH 285


>gi|225874521|ref|YP_002755980.1| dihydroorotate dehydrogenase, catalytic subunit [Acidobacterium
           capsulatum ATCC 51196]
 gi|225793537|gb|ACO33627.1| dihydroorotate dehydrogenase, catalytic subunit [Acidobacterium
           capsulatum ATCC 51196]
          Length = 305

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 63/182 (34%), Gaps = 24/182 (13%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K+ E  G     +N  CP    +    G     +   + + +A        PV VK    
Sbjct: 113 KLNEAEGIAAYEINASCP----NTKHGGMAFGADHGALAELVAHCRHYSRRPVIVKLSPN 168

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG-LSPKDNRKIPNL 174
           V       ++  + +  + SG + I            +  R+  ++          I  +
Sbjct: 169 V------TSIAAMARCAESSGADAISLVNTFVSLAIDVETRQPRIRNITGGLSGPAIKPI 222

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYF 233
              +V+E  +      IG+ GG+     A++ +L     V +G A+Y +   +  +    
Sbjct: 223 AVRMVWEAAQAVKIPVIGM-GGIATAEDAVEFLLAGATAVQVGTASYADPRAIENISHSL 281

Query: 234 SN 235
           ++
Sbjct: 282 AH 283


>gi|170735207|ref|YP_001774321.1| dihydroorotate dehydrogenase family protein [Burkholderia
           cenocepacia MC0-3]
 gi|169821245|gb|ACA95826.1| dihydroorotate dehydrogenase family protein [Burkholderia
           cenocepacia MC0-3]
          Length = 437

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|62871418|gb|AAY18593.1| putative dihydropyrimidinase dehydrogenase [Bacillus sp. TS-23]
          Length = 349

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 62/177 (35%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K V+D G +   LN GCP     E   G+     P++V      + +    PV VK 
Sbjct: 38  EIVKRVQDVGVDGFELNFGCPHGMA-ERGMGSASGQVPELVEKQTYWVKEVAEKPVIVKL 96

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D      +    ++  + G + I +      L G+       IP           
Sbjct: 97  TPNITD------ITATAEAAVQGGADAISMINTINSLMGVDLDTWHTIPHVAGKGAHGGY 150

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    ++ I   GG+    +A++ +L    GV +  A   
Sbjct: 151 CGPAVKPIALNMVAECARHPRINVPISGMGGVSSWKEAVEFMLMGATGVQVCTAVMH 207


>gi|197295563|ref|YP_002154104.1| dihydropyrimidine dehydrogenase [Burkholderia cenocepacia J2315]
 gi|195945042|emb|CAR57667.1| putative dihydroorotate dehydrogenase family protein [Burkholderia
           cenocepacia J2315]
          Length = 438

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|320352428|ref|YP_004193767.1| dihydroorotate oxidase B, catalytic subunit [Desulfobulbus
           propionicus DSM 2032]
 gi|320120930|gb|ADW16476.1| dihydroorotate oxidase B, catalytic subunit [Desulfobulbus
           propionicus DSM 2032]
          Length = 313

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 66/179 (36%), Gaps = 26/179 (14%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           G + + +N+ CP   V +G         P++     AA+ +  ++PV VK    V D   
Sbjct: 128 GIDALEVNISCP--NVKKGGVAFG--TVPEMAAAVTAAVKRVTTLPVIVKLSPNVTD--- 180

Query: 133 AVALRNLVKSIKKSGVNGI----WIHARKAILKGLSPKDNRKIPNLDYDIVYEI------ 182
              +  + +++   G + +     +       +   PK    I  L    V  +      
Sbjct: 181 ---IVAMARAVADGGADALSLINTLIGMAIDARTRRPKLANVIGGLSGPAVKPVALRMVW 237

Query: 183 -KKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSN 235
               +  + +   GG+     A++ +L     V +G A + N A    +L  ++ Y  +
Sbjct: 238 QVTSSVSIPVIGIGGIGTPEDAIEFLLAGASAVQVGTANFYNPAAVSQILAGIETYLRD 296


>gi|322711799|gb|EFZ03372.1| FMN binding oxidoreductase, putative [Metarhizium anisopliae ARSEF
           23]
          Length = 410

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 26/147 (17%), Positives = 53/147 (36%), Gaps = 13/147 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGV 148
           ++G        IV + I A+ KA+     V  ++   D      L   V+ ++    +G+
Sbjct: 208 AYGGSPKKRARIVVEIIEAVRKAVPKEFCVGIKLNSVDHQSQTELEECVEQLEVIVAAGI 267

Query: 149 NGIWI----HARKAILKGLS--PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDM 200
           + + I    +    ++ G +  P   R      +  +  + I+     + + + GG    
Sbjct: 268 DFLEISGGTYENPEMMIGKANPPVSERTAAREAFFIEFAHAIRDRFKGVPLMVTGGFRSR 327

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAM 225
                 +     D V IGR A  N  +
Sbjct: 328 QGMEAAIKDGGCDLVGIGRPAILNPFL 354


>gi|219565286|dbj|BAH04179.1| b-type dihydroorotate dehydrogenase [Bifidobacterium bifidum]
          Length = 315

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 85/247 (34%), Gaps = 29/247 (11%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +      + L             +   + G    +  E    + D   + + +N
Sbjct: 79  MVNSVGLQNPGVDHYLVDELPKLKDLGATVITNVAGHSDDEYAEVVAKLADSRADMLEIN 138

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V+ G        +P+ +   I  + K  S P+ VK    V D      +  + 
Sbjct: 139 VSCP--NVNHGGMSVG--TDPEALHRLIDRLRKITSKPMIVKLSPNVTD------ITAIA 188

Query: 141 KSIKKSGVNG-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPD 188
           ++   +G +            I I   + IL           I  +    V+ +++  PD
Sbjct: 189 RAAVDAGADALSLINTLVGMRIDIRTGEPILSNRTGGVSGPAIFPIALSYVWRVRQALPD 248

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           + I   GG++   +AL+ L    + V +G AA  +      V     + L     +  ++
Sbjct: 249 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALYDPTAPLRVARELDDLLDSRPELAAKL 308

Query: 248 DK-DFWR 253
              + WR
Sbjct: 309 AAGETWR 315


>gi|107023146|ref|YP_621473.1| dihydropyrimidine dehydrogenase [Burkholderia cenocepacia AU 1054]
 gi|116686614|ref|YP_839861.1| dihydropyrimidine dehydrogenase [Burkholderia cenocepacia HI2424]
 gi|105893335|gb|ABF76500.1| dihydroorotate oxidase B, catalytic subunit [Burkholderia
           cenocepacia AU 1054]
 gi|116652329|gb|ABK12968.1| dihydropyrimidine dehydrogenase (NADP+) [Burkholderia cenocepacia
           HI2424]
          Length = 437

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|259503299|ref|ZP_05746201.1| 2-enoate reductase [Lactobacillus antri DSM 16041]
 gi|259168754|gb|EEW53249.1| 2-enoate reductase [Lactobacillus antri DSM 16041]
          Length = 707

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 66/184 (35%), Gaps = 22/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+AA+  +  G + + L+ G          P + + +  +G  +     I+ + I  +
Sbjct: 198 QFVDAAERAQKAGADGVELHAGHGYLLNQFTSPYSNLRKDGYGGPIENRVRIIAEIIQGI 257

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----------LVKSIKKSGVNGIWIHARKAILK 161
            K       +  R+ VD+    +              L K +++ G + + +    A  +
Sbjct: 258 KKRCGSDFPISVRLTVDEFYEKIGYPQMGITLPEGVRLAKEVERVGADALNVTIATADTQ 317

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV-DGVMIGRAA 219
            L  +     P     +V  IK E   + I   G +   +QA  IL     D + + R  
Sbjct: 318 VLISEPVSYEPGWRQYLVKAIK-EAVSIPIIAVGVIRTPNQAEAILRSGTQDFIGLARPM 376

Query: 220 YKNS 223
             + 
Sbjct: 377 LADP 380


>gi|327192567|gb|EGE59517.1| dihydropyrimidine dehydrogenase protein [Rhizobium etli CNPAF512]
          Length = 437

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 32/153 (20%), Positives = 55/153 (35%), Gaps = 14/153 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 TDIRRPARAAKAGGSDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           ++V EI +  E   L I   GG+     A + L
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFL 275


>gi|153007710|ref|YP_001368925.1| dihydropyrimidine dehydrogenase [Ochrobactrum anthropi ATCC 49188]
 gi|151559598|gb|ABS13096.1| dihydroorotate dehydrogenase family protein [Ochrobactrum anthropi
           ATCC 49188]
          Length = 436

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARGAKENGTDAVSLINTINSIVSVDLDSMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|83944378|ref|ZP_00956833.1| dihydropyrimidine dehydrogenase [Sulfitobacter sp. EE-36]
 gi|83953420|ref|ZP_00962142.1| dihydropyrimidine dehydrogenase [Sulfitobacter sp. NAS-14.1]
 gi|83842388|gb|EAP81556.1| dihydropyrimidine dehydrogenase [Sulfitobacter sp. NAS-14.1]
 gi|83844922|gb|EAP82804.1| dihydropyrimidine dehydrogenase [Sulfitobacter sp. EE-36]
          Length = 434

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 33/166 (19%), Positives = 60/166 (36%), Gaps = 15/166 (9%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VE+ G + I LN GCP     E   G+ +   P+ +        +   +PV VK    + 
Sbjct: 125 VEETGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIEMVTRWCKQYTRMPVIVKLTPNIT 183

Query: 129 DQIPAVALRN--------LVKSIKKSGVNGIWIHARKAILKGLSPKDNR---KIPNLDYD 177
           + +               L+ +I       + + A + ++ G           +  +  +
Sbjct: 184 NVLYPAEAAKRGGADAVSLINTINSITSVDLDLFAPEPMIDGKGTHGGYCGPAVKPIALN 243

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +V EI +  E  D+ I   GG+     A + L      V +  AA 
Sbjct: 244 MVAEIARNPETADMPISGIGGVTTWRDAAEFLALGAGNVQVCTAAM 289


>gi|295400801|ref|ZP_06810777.1| NADPH dehydrogenase [Geobacillus thermoglucosidasius C56-YS93]
 gi|294977064|gb|EFG52666.1| NADPH dehydrogenase [Geobacillus thermoglucosidasius C56-YS93]
          Length = 399

 Score = 59.1 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 65/187 (34%), Gaps = 20/187 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA   +  GY+ + ++ G          P +      +G  LM       + I  + 
Sbjct: 148 FGDAALRAKKAGYDAVEIHGGHGYLINQFLSPFSNKRTDEYGGTLMNRARFAVEIIENVR 207

Query: 113 KALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +     +  R      V+  +     + + + ++++G + I  H    + K +     
Sbjct: 208 KKVGKHFPILFRISTVEFVEGGLTIEDTKVIARMLEQAGADAI--HCSTGVYKTMMYVIQ 265

Query: 169 RKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                  + +    EIKK    + +   G + D   A  +L     D + +GRAA  +  
Sbjct: 266 PAAVPHGFSVSFAAEIKK-VVSIPVIAVGRINDPLIAESVLLSDKADLISMGRAALADPE 324

Query: 225 MLTTVDE 231
           +     E
Sbjct: 325 LPNKAKE 331


>gi|218780363|ref|YP_002431681.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218761747|gb|ACL04213.1| Predicted NADH:flavin oxidoreductase/NADH oxidase
           [Desulfatibacillum alkenivorans AK-01]
          Length = 666

 Score = 59.1 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/199 (18%), Positives = 74/199 (37%), Gaps = 20/199 (10%)

Query: 45  TQEKPLALQIGGAD--ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSF 93
           T+E P AL + G    I    E+A+ V+  GY+ + +  G          P     +  +
Sbjct: 127 TRETPEALTLEGIKQTIVDFAESAERVKKCGYDAVEVLSGTGYLISEFLSPVTNARDDEY 186

Query: 94  GACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSI-KKSGV 148
           G           + + A+ + +    PV V+      ++    A  L    + + ++ GV
Sbjct: 187 GGSFENRIRFGVEIMKAIREKVGPDYPVMVRLDNNDFMEGGQRADELTEYARILAEECGV 246

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + + +       +   P+    +P   Y  + +  K+  D+ +  +  +     A +I+ 
Sbjct: 247 DALCVKGN--WHEARVPQMTTNVPRGTYAYLAKNVKDVVDVPVIASHRIHSPEVARQIIR 304

Query: 208 -PSVDGVMIGRAAYKNSAM 225
               D V  GRA   +  M
Sbjct: 305 DGFCDMVAFGRALIADPYM 323


>gi|195438144|ref|XP_002066997.1| GK24771 [Drosophila willistoni]
 gi|194163082|gb|EDW77983.1| GK24771 [Drosophila willistoni]
          Length = 1045

 Score = 59.1 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/155 (24%), Positives = 58/155 (37%), Gaps = 17/155 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE A +  + G + + LN+ CP+    +G     L  +P IV D    +  A+ IP  VK
Sbjct: 669 VELATLAANCGSDALELNLSCPNGMAEKG-----LGQDPKIVADICRWVRGAIKIPFYVK 723

Query: 123 C-----------RIGVDDQIPAVALRNLVKSIKKSGVNG-IWIHARKAILKGLSPKDNRK 170
                       +  VD +   V   N V S+     +G  W       L          
Sbjct: 724 LTPNVTDIVEIAKAAVDGKANGVTAINTVSSLMDLRADGTPWPAVGAEQLTSYGGLSGSV 783

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           I  L    +  I K+  ++ I   GG+E    AL+
Sbjct: 784 IRPLALRAISAIAKKLQNIAILGTGGVESGETALQ 818


>gi|86358877|ref|YP_470769.1| dihydropyrimidine dehydrogenase [Rhizobium etli CFN 42]
 gi|86282979|gb|ABC92042.1| probable dihydroorotate oxidase protein [Rhizobium etli CFN 42]
          Length = 437

 Score = 59.1 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/153 (20%), Positives = 55/153 (35%), Gaps = 14/153 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 TDIRRPARAAKAGGTDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           ++V EI +  E   L I   GG+     A + L
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFL 275


>gi|149055088|gb|EDM06905.1| PP3111 protein, isoform CRA_a [Rattus norvegicus]
          Length = 298

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 15/107 (14%), Positives = 28/107 (26%), Gaps = 13/107 (12%)

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT 228
                ++ +  ++K    + +  NG +  +    + +    V GVM       N A+   
Sbjct: 2   AGTASWEHIKAVRKAVG-IPVFANGNIRCLQDVERCIQDTGVQGVMSAEGNLHNPALFEG 60

Query: 229 --------VDEYFSNPLTGSSPIKTRVDKDF--WRKISASMTDYAAR 265
                    DEY         P+       F  W             
Sbjct: 61  RSPAVWELADEYLDIVRQHPCPLSYVRAHLFKLWHHTLQVHQQLREE 107


>gi|222149525|ref|YP_002550482.1| dihydropyrimidine dehydrogenase [Agrobacterium vitis S4]
 gi|221736507|gb|ACM37470.1| dihydroorotate dihydrogenase protein [Agrobacterium vitis S4]
          Length = 437

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/212 (19%), Positives = 74/212 (34%), Gaps = 17/212 (8%)

Query: 25  EMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVG 82
           E+I    + +   +  ++  +  ++ L   I      +   A   +VE+ G + I LN G
Sbjct: 79  ELITDRPLQVNLQEMKMVKMNWPDRALIASIMVPCEEEEWRAILPLVEETGADGIELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----------QI 131
           CP     E   GA +   P+ +   +    +   +PV  K    + D             
Sbjct: 139 CPHGMS-ERGMGAAVGQVPEYIEMVVRWCKQYSRMPVITKLTPNITDIRKPARAAKAGGT 197

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDL 189
            AV+L N + SI    ++    +                +  +  ++V EI +  E   L
Sbjct: 198 DAVSLINTINSIVSVDLDSFAPNPSVGGKGSHGGYCGPAVKPIALNMVAEIARDPETYGL 257

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            I   GG+     A + L      V +  AA 
Sbjct: 258 PISGIGGITTWRDAAEFLALGAGNVQVCTAAM 289


>gi|330820854|ref|YP_004349716.1| dihydroorotate dehydrogenase family protein [Burkholderia gladioli
           BSR3]
 gi|327372849|gb|AEA64204.1| dihydroorotate dehydrogenase family protein [Burkholderia gladioli
           BSR3]
          Length = 439

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 59/168 (35%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC---- 123
            +ED G + + LN GCP     E   GA +   P+ V      + +   +P  VK     
Sbjct: 122 RIEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMITRWVKEGTKLPCLVKLTPNI 180

Query: 124 -------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                  R         V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAWKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPQTPNLPISGIGGISTWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|315924015|ref|ZP_07920242.1| dihydroorotate dehydrogenase [Pseudoramibacter alactolyticus ATCC
           23263]
 gi|315622641|gb|EFV02595.1| dihydroorotate dehydrogenase [Pseudoramibacter alactolyticus ATCC
           23263]
          Length = 418

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 66/182 (36%), Gaps = 21/182 (11%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G+   +    A+  E  G + I  N  CP   +   + G+ +  NPD+V   
Sbjct: 103 KVIVSSIMGSTDEEWAFLARESEKAGADLIECNFSCPQ--MTSSTMGSDVGQNPDLVKHY 160

Query: 108 IAAMCKALSIPVTVKC-----------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
              +  A  +PV  K            R  ++     +A  N VK+I    ++ +     
Sbjct: 161 CEVVSAATCLPVIAKMTPNIGNMEIPARAAIEGGAKGIAAINTVKAITNLDIDKMVGMPI 220

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENP--DLFIGLNGGLEDMSQALKILPSVDGVM 214
                 +S      +  +    + ++K +    D+ +   GG+E     L+ L      M
Sbjct: 221 VNGKSAVSGYSGAAVKPIALRFISDLKHDPVLKDVPLTGVGGIETWRDCLEFL------M 274

Query: 215 IG 216
           +G
Sbjct: 275 LG 276


>gi|224283050|ref|ZP_03646372.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum NCIMB 41171]
 gi|313140202|ref|ZP_07802395.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum NCIMB 41171]
 gi|313132712|gb|EFR50329.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum NCIMB 41171]
          Length = 320

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 85/247 (34%), Gaps = 29/247 (11%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +      + L             +   + G    +  E    + D   + + +N
Sbjct: 84  MVNSVGLQNPGVDHYLVDELPKLKDLGATVITNVAGHSDDEYAEVVAKLADSRADMLEIN 143

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V+ G        +P+ +   I  + K  S P+ VK    V D      +  + 
Sbjct: 144 VSCP--NVNHGGMSVG--TDPEALHRLIDRLRKITSKPMIVKLSPNVTD------ITTIA 193

Query: 141 KSIKKSGVNG-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPD 188
           ++   +G +            I I   + IL           I  +    V+ +++  PD
Sbjct: 194 RAAVDAGADALSLINTLVGMRIDIRTGEPILSNRTGGVSGPAIFPIALSYVWRVRQALPD 253

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           + I   GG++   +AL+ L    + V +G AA  +      V     + L     +  ++
Sbjct: 254 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALYDPTAPLRVARELDDLLDSRPELAAKL 313

Query: 248 DK-DFWR 253
              + WR
Sbjct: 314 AAGETWR 320


>gi|182677648|ref|YP_001831794.1| NADH:flavin oxidoreductase/NADH oxidase [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633531|gb|ACB94305.1| NADH:flavin oxidoreductase/NADH oxidase [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 367

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 62/198 (31%), Gaps = 22/198 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
               EAAK     G + + ++            P +      +G  L   M  P  V D 
Sbjct: 160 EAFAEAAKRAGRLGIDLVQIHAAHGYLLHQFLSPISNQRTDDYGGSLENRMRFPLEVFDA 219

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A   A   PV+V+      V+            K+++  G + I + +      GL+ 
Sbjct: 220 VRAAFPA-GRPVSVRVSGTDWVEGGWEVEQTIAFAKALEARGCDAIHVSSG-----GLAA 273

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           +    I       +    K    + +   G +    QA  I+ +   D + + RA   N 
Sbjct: 274 EQKIPIGPSYQVPLARAVKAAVKIPVVAVGLITGYEQAEAIVSTGDADLIALARAILYNP 333

Query: 224 AMLTTVDEYFSNPLTGSS 241
                   YF   +    
Sbjct: 334 RWPWHAAAYFGAHVKAPP 351


>gi|91772280|ref|YP_564972.1| hypothetical protein Mbur_0212 [Methanococcoides burtonii DSM 6242]
 gi|91711295|gb|ABE51222.1| Hypothetical protein Mbur_0212 [Methanococcoides burtonii DSM 6242]
          Length = 429

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 44/243 (18%)

Query: 1   MVDWTDRHYRFFARLLTNNALLY---------TEMIVADAILRGDKKNI----LGFSTQE 47
           M   TD  +   ++   N  L           T    A  + RG ++ +    L F   E
Sbjct: 74  MAGITDSVF--ASKNAKNAGLAVIGGYNLDEETNAAAAKLVERGRQEFLSDAPLEFFETE 131

Query: 48  KP-------LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
                    +   +    +  L++AA IV+D G   + L+  C    +     G  LM +
Sbjct: 132 VNAVDTGGAVGFNVRAVSLEPLLKAATIVKDAG-GILELDAHCRQEEMVSIGVGEALMKD 190

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
              + + I  + +   + ++VK R  V D I       L +SI+ +G + + + A K   
Sbjct: 191 LPRLNEWIKKIKE-TGVVLSVKVRANVVDDI------ALARSIENAGADILHVDAMK--- 240

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
                    +    D   +  I +++  L +  N  + D+  A  +     D + + R  
Sbjct: 241 ---------EGAGADLRAILRI-RDSTRLLLIGNNSIMDIMDARDMFSKGADMISVSRVV 290

Query: 220 YKN 222
            ++
Sbjct: 291 LED 293


>gi|416702|sp|P32370|BAIH_EUBSP RecName: Full=NADH-dependent flavin oxidoreductase
 gi|543631|pir||C36912 probable oxidoreductase (EC 1.-.-.-), bile acid-inducible -
           Eubacterium sp
 gi|1381570|gb|AAC45417.1| NADH:flavin oxidoreductase [Clostridium scindens]
          Length = 661

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/199 (19%), Positives = 72/199 (36%), Gaps = 24/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCI 108
           +  +AA+  E+ G   I+L   C            P        +G  L      V + I
Sbjct: 149 QFGQAARRAEEAGCGAISL--HCAHAYMLPGSFLSPLRNKRMDEYGGSLDNRARFVIEMI 206

Query: 109 AAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAI--LKG 162
               + +S    +  RI  D++         +  L    + +GV+ + +        L+ 
Sbjct: 207 EEARRNVSPDFPIFLRISGDERMVGGNSLEDMLYLAPKFEAAGVSMLEVSGGTQYEGLEH 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           + P  N+      Y+   EIKK    + +   G + D+  A +I+    VDGV +GR   
Sbjct: 267 IIPCQNKSRGVNVYEA-SEIKK-VVGIPVYAVGKINDIRYAAEIVERGLVDGVAMGRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTG 239
            +  +     E   + +T 
Sbjct: 325 ADPDLCKKAVEGQFDEITP 343


>gi|257063897|ref|YP_003143569.1| dihydroorotate oxidase B, catalytic subunit [Slackia
           heliotrinireducens DSM 20476]
 gi|256791550|gb|ACV22220.1| dihydroorotate oxidase B, catalytic subunit [Slackia
           heliotrinireducens DSM 20476]
          Length = 306

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/195 (17%), Positives = 72/195 (36%), Gaps = 25/195 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P  + + G  + + V   + +E  G  +   +N+ CP    +  + G     +   V   
Sbjct: 98  PAIVNVSGHSLEEYVAVVEALEADGQADAYEINISCP----NVDAGGLTFGTHVPSVEAV 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHAR 156
           + A   A   P+ VK    V D      +  + ++ + SG +            I +  R
Sbjct: 154 VGACRAATKRPMIVKLTPNVTD------ITEIARAAEASGADALSMINTLLGMAIDVRTR 207

Query: 157 KAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K +L + +       +  +   +V++       + I   GG+     A++ +L     + 
Sbjct: 208 KPVLSRVVGGLSGPAVKPVALRMVWQCHNAV-SIPILGMGGIMTGEDAIEFMLAGATAIA 266

Query: 215 IGRAAYKNSAMLTTV 229
           +G A + N   +T V
Sbjct: 267 VGTANFVNPTAVTDV 281


>gi|254718477|ref|ZP_05180288.1| dihydropyrimidine dehydrogenase [Brucella sp. 83/13]
 gi|265983446|ref|ZP_06096181.1| dihydropyrimidine dehydrogenase [Brucella sp. 83/13]
 gi|306838284|ref|ZP_07471130.1| dihydroorotate dehydrogenase family protein [Brucella sp. NF 2653]
 gi|264662038|gb|EEZ32299.1| dihydropyrimidine dehydrogenase [Brucella sp. 83/13]
 gi|306406575|gb|EFM62808.1| dihydroorotate dehydrogenase family protein [Brucella sp. NF 2653]
          Length = 436

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGVTTWRDAAEFIALGCGTVQVCTAAM 289


>gi|186476292|ref|YP_001857762.1| dihydropyrimidine dehydrogenase [Burkholderia phymatum STM815]
 gi|184192751|gb|ACC70716.1| dihydroorotate dehydrogenase family protein [Burkholderia phymatum
           STM815]
          Length = 436

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 59/168 (35%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC---- 123
           +VED G + + LN GCP     E   G+ +   P+ V      + +   +P  VK     
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGSAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 124 -------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                  R         V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAWKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPGLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|310287419|ref|YP_003938677.1| dihydroorotate dehydrogenase, catalytic subunit [Bifidobacterium
           bifidum S17]
 gi|309251355|gb|ADO53103.1| Dihydroorotate dehydrogenase, catalytic subunit [Bifidobacterium
           bifidum S17]
          Length = 320

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 85/247 (34%), Gaps = 29/247 (11%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +      + L             +   + G    +  E    + D   + + +N
Sbjct: 84  MVNSVGLQNPGVDHYLVDELPKLKDLGATVITNVAGHSDDEYAEVVAKLADSRADMLEIN 143

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V+ G        +P+ +   I  + K  S P+ VK    V D      +  + 
Sbjct: 144 VSCP--NVNHGGMSVG--TDPEALHRLIDRLRKITSKPMIVKLSPNVTD------ITTIA 193

Query: 141 KSIKKSGVNG-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPD 188
           ++   +G +            I I   + IL           I  +    V+ +++  PD
Sbjct: 194 RAAVDAGADALSLINTLVGMRIDIRTGEPILSNRTGGVSGPAIFPIALSYVWRVRQALPD 253

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           + I   GG++   +AL+ L    + V +G AA  +      V     + L     +  ++
Sbjct: 254 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALYDPTAPLRVARELDDLLDSRPELAAKL 313

Query: 248 DK-DFWR 253
              + WR
Sbjct: 314 AAGETWR 320


>gi|311064331|ref|YP_003971056.1| dihydroorotate dehydrogenase, catalytic subunit pyrD
           [Bifidobacterium bifidum PRL2010]
 gi|310866650|gb|ADP36019.1| pyrD Dihydroorotate dehydrogenase, catalytic subunit
           [Bifidobacterium bifidum PRL2010]
          Length = 317

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 85/247 (34%), Gaps = 29/247 (11%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ +  +      + L             +   + G    +  E    + D   + + +N
Sbjct: 81  MVNSVGLQNPGVDHYLVDELPKLKDLGATVITNVAGHSDDEYAEVVAKLADSRADMLEIN 140

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V+ G        +P+ +   I  + K  S P+ VK    V D      +  + 
Sbjct: 141 VSCP--NVNHGGMSVG--TDPEALHRLIDRLRKITSKPMIVKLSPNVTD------ITTIA 190

Query: 141 KSIKKSGVNG-----------IWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPD 188
           ++   +G +            I I   + IL           I  +    V+ +++  PD
Sbjct: 191 RAAVDAGADALSLINTLVGMRIDIRTGEPILSNRTGGVSGPAIFPIALSYVWRVRQALPD 250

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           + I   GG++   +AL+ L    + V +G AA  +      V     + L     +  ++
Sbjct: 251 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALYDPTAPLRVARELDDLLDSRPELAAKL 310

Query: 248 DK-DFWR 253
              + WR
Sbjct: 311 AAGETWR 317


>gi|254475131|ref|ZP_05088517.1| dihydroorotate dehydrogenase family protein [Ruegeria sp. R11]
 gi|214029374|gb|EEB70209.1| dihydroorotate dehydrogenase family protein [Ruegeria sp. R11]
          Length = 434

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/209 (21%), Positives = 69/209 (33%), Gaps = 17/209 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   G+ +   P+ +        K  S PV VK    +
Sbjct: 124 RVEATGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIQMVTEWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRHPARAAKAGGADAVSLINTINSIVSVDLDAMAPEPTIGDKGTHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
           ++V EI +  +   L I   GG+     A + +      V +  AA         V E  
Sbjct: 243 NMVAEIARCPQTHGLPISAIGGVTTWRDAAEFMTMGAGNVQVCTAAMT--YGFNVVKEMI 300

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           S           +   DF  K   ++TD+
Sbjct: 301 SGLNQWMDDKGYKTLDDFVGKAVPNVTDW 329


>gi|333030676|ref|ZP_08458737.1| dihydroorotate dehydrogenase family protein [Bacteroides coprosuis
           DSM 18011]
 gi|332741273|gb|EGJ71755.1| dihydroorotate dehydrogenase family protein [Bacteroides coprosuis
           DSM 18011]
          Length = 305

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 75/197 (38%), Gaps = 29/197 (14%)

Query: 56  GADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G+ I + V+ A+I++       I LN+ CP    +    G    ++P      + A+ + 
Sbjct: 104 GSTIEEYVKTAEIIDKLDNIPAIELNISCP----NVKEGGMAFGVSPIQAAAVVKAVREV 159

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------GIWIHA--RKAILKG- 162
               + VK    V D      +  + K  + +G +         G+ IHA  R+ +L   
Sbjct: 160 YHKTLIVKLSPNVTD------IAEIAKVAEDNGADGVSLINTVLGMAIHAEKRRPVLSTI 213

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                   +  +   +V+++      + I   GG+ D + A++ +L     + +G   + 
Sbjct: 214 TGGLSGPCVKPIALRMVWQVANAV-KIPIIGMGGIMDATDAIEFLLAGASAIQVGTVNFV 272

Query: 222 NS----AMLTTVDEYFS 234
                  +L  + +Y  
Sbjct: 273 EPTATIDILNGIKDYMH 289


>gi|241205971|ref|YP_002977067.1| dihydropyrimidine dehydrogenase [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859861|gb|ACS57528.1| dihydroorotate dehydrogenase family protein [Rhizobium
           leguminosarum bv. trifolii WSM1325]
          Length = 437

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/153 (20%), Positives = 55/153 (35%), Gaps = 14/153 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 SDIRRPARAAKAGGTDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           ++V EI +  E   L I   GG+     A + L
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFL 275


>gi|116253448|ref|YP_769286.1| dihydropyrimidine dehydrogenase [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258096|emb|CAK09197.1| putative dihydropyrimidine dehydrogenase [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 437

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/153 (20%), Positives = 55/153 (35%), Gaps = 14/153 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 TDVRRPARAAKAGGTDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           ++V EI +  E   L I   GG+     A + L
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFL 275


>gi|170701515|ref|ZP_02892467.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           IOP40-10]
 gi|170133572|gb|EDT01948.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           IOP40-10]
          Length = 435

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|303232357|ref|ZP_07319050.1| putative dihydroorotate oxidase, catalytic subunit [Atopobium
           vaginae PB189-T1-4]
 gi|302481541|gb|EFL44608.1| putative dihydroorotate oxidase, catalytic subunit [Atopobium
           vaginae PB189-T1-4]
          Length = 357

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 65/201 (32%), Gaps = 28/201 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +  Q+ G  I +   A    E+     +   +N+ CP    +    G  +   P    + 
Sbjct: 151 VICQVAGHAIDEYKAALLYFEEHAPFASGFEINISCP----NIACGGVAMGATPQGAAEI 206

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HA- 155
           + A+    + P+ +K          A  +  + K+ +  G + + +           H  
Sbjct: 207 VRALRPCTTRPLLIKM--------GAQRIAEIAKACESEGADALTLINSIPGMAINTHTY 258

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVM 214
           +  I +         I  +   +V+E      D+ I   GG+      A  +L     V 
Sbjct: 259 KSKISRPTGGMSGPAIHPIAVRMVWEAHNAV-DIPICGVGGVTCGEDVAEFMLAGATAVS 317

Query: 215 IGRAAYKNSAMLTTVDEYFSN 235
           +G A   + +    +   F  
Sbjct: 318 VGLANLYDPSSAHRILHEFKQ 338


>gi|291457058|ref|ZP_06596448.1| dihydroorotate oxidase family protein [Bifidobacterium breve DSM
           20213]
 gi|291380893|gb|EFE88411.1| dihydroorotate oxidase family protein [Bifidobacterium breve DSM
           20213]
          Length = 387

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/233 (15%), Positives = 72/233 (30%), Gaps = 41/233 (17%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINL 79
           +  + + D +  +  +   + L     G+ +  +            A+++++ G   + +
Sbjct: 161 SPDVWQPDMRAAIAAAGLGQVLVPSFQGSRVEGMSEEEYIADHATTARLIKETGAKLMVM 220

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N  CP            L  NP +VG    A+ + +  IP+ VK      D    + +R+
Sbjct: 221 NTSCP-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDDLELMVRS 275

Query: 139 LV----------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            V                K +   G   +    R       S      I     D+V  +
Sbjct: 276 TVGHGTVQGFSTINTISAKLVDADGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARL 330

Query: 183 K----KENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVD 230
                K   D  I   GG+   +          D VM    A  ++ +   + 
Sbjct: 331 AAIREKLGLDFEINGVGGVVSPADYQAYRNAGADSVMSATGAMWDAELARKIK 383


>gi|302405092|ref|XP_003000383.1| NADPH dehydrogenase [Verticillium albo-atrum VaMs.102]
 gi|261361040|gb|EEY23468.1| NADPH dehydrogenase [Verticillium albo-atrum VaMs.102]
          Length = 414

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 64/190 (33%), Gaps = 29/190 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
             E A+I  + G+  + ++       +               +G           + I A
Sbjct: 169 FAETARISAEAGFQGVQVHGA--HGYLVAQFLSAKTNTRTDEYGGSPAKRARFAVEIIDA 226

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGI----------WIHARK 157
           +   +     V  ++   D      L + V+ +K   ++GV+ I           ++   
Sbjct: 227 IRAVVPKEFCVGIKLNSVDHQSEAELGDCVEQLKLITQAGVDFIEVSGGTYEDPTMNLGP 286

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMI 215
           + ++G S +  +       D    I+ + PD+ + + GG          +     D V I
Sbjct: 287 SAVEGKSER-TKAREAFFLDFAAAIRDQFPDVPLVVTGGFRTRQGMESAVREGGCDAVGI 345

Query: 216 GRAAYKNSAM 225
           GR A  N ++
Sbjct: 346 GRPAVLNPSL 355


>gi|229578773|ref|YP_002837171.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           Y.G.57.14]
 gi|228009487|gb|ACP45249.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           Y.G.57.14]
          Length = 555

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/133 (15%), Positives = 52/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           + + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 IEEILKGIKEKAKITVGIRISVTEFDNDGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   +++  L+     ++ ++  ++ I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYYKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|171741443|ref|ZP_02917250.1| hypothetical protein BIFDEN_00526 [Bifidobacterium dentium ATCC
           27678]
 gi|283455214|ref|YP_003359778.1| pyr Dd [Bifidobacterium dentium Bd1]
 gi|171277057|gb|EDT44718.1| hypothetical protein BIFDEN_00526 [Bifidobacterium dentium ATCC
           27678]
 gi|283101848|gb|ADB08954.1| pyr Dihydroorotate dehydrogenase [Bifidobacterium dentium Bd1]
          Length = 375

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/223 (16%), Positives = 69/223 (30%), Gaps = 31/223 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D K  +  +   + L     G+ +  +         V  A++V + G   + +N  C
Sbjct: 154 WQPDMKKAIEAAGSGQLLVPSFQGSRVDGMDQDDYIADHVTTARLVCETGAGLMEMNTSC 213

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVK- 141
           P            L  +P +VG    A+   +   P+ VK     +D    + ++     
Sbjct: 214 P-----NEGHNRLLCHDPHLVGRITEAVKNEIGDRPLVVKLAYIPNDADLEIMVKETAAH 268

Query: 142 -------SIKKSGVNGIWIHARKAIL---KGLSPKDNRKIPNLDYDIVYEIK----KENP 187
                  +I       +  H  +A+    +  S      I     D+V  +     K   
Sbjct: 269 GTVQGFSTINTISAKLVDAHGNQALPGAGRDRSGVCGNAIRGAGLDMVGRLHAIREKLGL 328

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           D  I   GG+              + VM    A  N+ +   +
Sbjct: 329 DFTIVGVGGVVRPEDYRAYREAGANAVMSATGAMWNANLARDI 371


>gi|325859998|ref|ZP_08173125.1| dihydroorotate dehydrogenase 1B [Prevotella denticola CRIS 18C-A]
 gi|327313705|ref|YP_004329142.1| dihydroorotate dehydrogenase 1B [Prevotella denticola F0289]
 gi|325482524|gb|EGC85530.1| dihydroorotate dehydrogenase 1B [Prevotella denticola CRIS 18C-A]
 gi|326944747|gb|AEA20632.1| dihydroorotate dehydrogenase 1B [Prevotella denticola F0289]
          Length = 301

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/191 (14%), Positives = 64/191 (33%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A+ ++       I +N+ CP   V EG     +  +     
Sbjct: 93  DTNMIVNVSGDSPESYAETAERLDALDSIPAIEVNISCP--NVKEGGMSFGVTCSG--AA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +     + VK    V D      +  +  + +  G +            I I 
Sbjct: 149 SIVKAVRQHYHKTMIVKLSPNVTD------IAGIACACEDEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R   L   +       +  +   +V ++ K    + +   GG+     A++ ++     
Sbjct: 203 RRCPKLSIRTGGLSGPAVKPVAVRMVNDVAKAV-KIPVIGLGGISTAEDAIEFLMAGATA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFIDP 272


>gi|288930461|ref|YP_003434521.1| dihydroorotate dehydrogenase [Ferroglobus placidus DSM 10642]
 gi|288892709|gb|ADC64246.1| dihydroorotate dehydrogenase family protein [Ferroglobus placidus
           DSM 10642]
          Length = 297

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/193 (22%), Positives = 79/193 (40%), Gaps = 36/193 (18%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL + + G+   +    AK+   F   +   LN+ CP    H   +G  +  +PD+V + 
Sbjct: 94  PLIVSVFGSSPEEF---AKVTSHFPFASAFELNLSCP----HSEKYGLTVGSDPDLVKEI 146

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHAR 156
           +  + KA + PV  K    VD       +  + K+ ++ G +GI            I  +
Sbjct: 147 VKKVKKATNKPVFAKVSANVD-------VVEVGKAAEEGGADGIVAINTVKGMRIDIFTK 199

Query: 157 KAILKGLS-PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           K IL  +S       I  +    V+++ +E  ++ I  +GG+      ++ +L     V 
Sbjct: 200 KPILSNISGGVSGSAIKPIAIKCVWDLYEEL-EIPIIGSGGVTTWRDVVEFMLAGASAVE 258

Query: 215 IG-------RAAY 220
           +G       RA Y
Sbjct: 259 VGSVMYYSLRAIY 271


>gi|34540801|ref|NP_905280.1| dihydroorotate dehydrogenase 1B [Porphyromonas gingivalis W83]
 gi|81833781|sp|Q7MVJ6|PYRD_PORGI RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|34397115|gb|AAQ66179.1| dihydroorotate dehydrogenase [Porphyromonas gingivalis W83]
          Length = 307

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/197 (14%), Positives = 73/197 (37%), Gaps = 29/197 (14%)

Query: 56  GADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G+ +    E ++I+ +  +   I LN+ CP+ +    ++G       +     + A+ +A
Sbjct: 103 GSTLDDYAETSRIINELEHIRAIELNISCPNVKQGGMAYGV----TCEGAASVVKAVRRA 158

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKG 162
               + VK    V D      +  + ++++  G + I +              R  +   
Sbjct: 159 YDKTLIVKLSPNVTD------ITEIARAVESEGADAISMVNTFLGMAIDAEKRRPILSTT 212

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                   I  +   +V++  K    + I   GG+   + A++ +L     V +G   + 
Sbjct: 213 TGGLSGPCIKPIALRMVWQTAK-VVQVPIIGMGGIASAADAIEFLLAGATAVQVGCYNFV 271

Query: 222 NS----AMLTTVDEYFS 234
           +      ++  +++Y  
Sbjct: 272 DPAAASYIVDGIEDYLR 288


>gi|255323505|ref|ZP_05364636.1| NADH oxidase [Campylobacter showae RM3277]
 gi|255299542|gb|EET78828.1| NADH oxidase [Campylobacter showae RM3277]
          Length = 341

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 57/181 (31%), Gaps = 17/181 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+AA   +  GY  I ++            P   + +  +G         + + ++ + 
Sbjct: 145 FVQAAIRAQSAGYAAIEIHAAHGYLISEFLSPGINLRDDEYGGSFENRTRFLKEILSEIK 204

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+ IP  V +     V           L + ++  G   I + A     +  S      
Sbjct: 205 AAVKIPAGVRISADSWVKGDWSLEDSVRLARELEALGAAFIHVSAGGLFERTDSAPAFTP 264

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           +    Y    +  K+   + +   G +   S+   +L S   D V  GR   +N      
Sbjct: 265 LYQASY---AKAVKQAVSIPVIAVGLITKASEGEALLLSGVCDAVAYGRELLRNP-NFAQ 320

Query: 229 V 229
            
Sbjct: 321 A 321


>gi|171320519|ref|ZP_02909546.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           MEX-5]
 gi|171094239|gb|EDT39319.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           MEX-5]
          Length = 435

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|168702720|ref|ZP_02734997.1| dihydroorotate dehydrogenase [Gemmata obscuriglobus UQM 2246]
          Length = 304

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/213 (18%), Positives = 66/213 (30%), Gaps = 21/213 (9%)

Query: 26  MIVADAILRGDKKNILGFS-----TQEKPLALQIGGADISKLVEAAKIVED--FGYNEIN 78
           M+ A  +     ++ L        T    +   I G    + V  A  V     G   + 
Sbjct: 67  MLNAIGLDNDGLEHFLTHHLPYLKTLPTAIVGNIAGKSEDEFVAMAARVHQSRDGLAALE 126

Query: 79  LNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALR 137
           LN+ CP       + G     +P++    I     A   +P+  K    V D        
Sbjct: 127 LNLSCP-----NVAGGTDFATDPELTKRIIRRCRDACPDLPLIAKLTPNVTDITLIARAA 181

Query: 138 NLVKSIKKSGVNGIWI-----HARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFI 191
               +   S VN           RK IL  ++       I  L    V+ I +    + +
Sbjct: 182 ADGGADAVSAVNTFVGMAVDWRRRKPILGNVTGGLSGPAIKPLALRAVWRIAQ-LKAVPV 240

Query: 192 GLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS 223
              GG+  +   +  L      V IG A + + 
Sbjct: 241 IAVGGIASLDDVMDFLVVGASAVQIGTANFYDP 273


>gi|115360706|ref|YP_777843.1| dihydropyrimidine dehydrogenase [Burkholderia ambifaria AMMD]
 gi|115286034|gb|ABI91509.1| dihydroorotate oxidase B, catalytic subunit / dihydrouracil
           dehydrogenase (NAD+) / dihydropyrimidine dehydrogenase
           (NADP+) [Burkholderia ambifaria AMMD]
          Length = 435

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|301063684|ref|ZP_07204196.1| NADH oxidase domain protein [delta proteobacterium NaphS2]
 gi|300442221|gb|EFK06474.1| NADH oxidase domain protein [delta proteobacterium NaphS2]
          Length = 379

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/157 (17%), Positives = 62/157 (39%), Gaps = 9/157 (5%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--PVTVK--CRIGVDDQIPAVALRNL 139
           P+    +  +G  +     I  + + A+ KA+ +  P+ +K  C   +D+ +        
Sbjct: 177 PAYNQRKDEYGGSIQNRVRIHCEILQAVRKAVGLEYPLFIKMNCADFIDNGLDIEDSLQA 236

Query: 140 VKSIKKSGVNGIWIHA---RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            +   + GVN I +     R   L    P  N K     +    +  K   ++ + L GG
Sbjct: 237 ARIFNEMGVNAIEVSGGIIRTGKLAPSRPGINSKEKEAYFKEYAKKIKAAVNIPVILVGG 296

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           ++ +  A+ I+     D + + RA  +   ++   ++
Sbjct: 297 IKTLDTAINIIDEEIADYISMSRALIREPDLINRWEK 333


>gi|308161635|gb|EFO64073.1| Hypothetical protein GLP15_3459 [Giardia lamblia P15]
          Length = 462

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/231 (16%), Positives = 73/231 (31%), Gaps = 60/231 (25%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDC 107
           PL +Q+   +   +     I+  +    I+LN+GC +     G  G  LM    ++V   
Sbjct: 97  PLVVQLTVNEHDDINRICNILAPWCV-GIDLNLGCGAQFAISGGRGQRLMDKAEEVVIRF 155

Query: 108 IAAMCK-----ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + A+ +        I  ++K R+    +     +R         GVN I +H R+     
Sbjct: 156 LKALQQIENSGGRRISFSIKQRLLSSIEETIDKMRTFYNL----GVNCIAVHMRRK---- 207

Query: 163 LSPKDNRKIPNLDYDIVYEIKK--------------------ENPDLFIGLNGGLEDMSQ 202
               + R   + D+   +++                            +  NG L     
Sbjct: 208 ---GEERSCTHADWSSFFQVLSGLYTWLWTTFCQGNLQFFEDALRTFHVVANGDLFSRET 264

Query: 203 ALK------------------ILPSVDG----VMIGRAAYKNSAMLTTVDE 231
            L+                   L +  G    VM+ R A  +  + + + E
Sbjct: 265 ILEFFALSEQYFSQLPIEIQPYLSNRYGRLTPVMLARGAISDLTLFSFIIE 315


>gi|172065004|ref|YP_001815716.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           MC40-6]
 gi|171997246|gb|ACB68163.1| dihydroorotate dehydrogenase family protein [Burkholderia ambifaria
           MC40-6]
          Length = 435

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISSWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|150397561|ref|YP_001328028.1| dihydropyrimidine dehydrogenase [Sinorhizobium medicae WSM419]
 gi|150029076|gb|ABR61193.1| dihydroorotate dehydrogenase family protein [Sinorhizobium medicae
           WSM419]
          Length = 437

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPARAARAGGTDAVSLINTINSITGVNLDTFSPEPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDTETHGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|323526708|ref|YP_004228861.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1001]
 gi|323383710|gb|ADX55801.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1001]
          Length = 442

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   G+ +   P+ +      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKEGTRLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 TDIRLGSRAAYKGGADGVSLINTINSIVAVDLDAMSPLPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDEQTPNLPISGIGGISTWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|120609661|ref|YP_969339.1| dihydropyrimidine dehydrogenase [Acidovorax citrulli AAC00-1]
 gi|120588125|gb|ABM31565.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) [Acidovorax citrulli AAC00-1]
          Length = 442

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 75/238 (31%), Gaps = 50/238 (21%)

Query: 4   WTDRHY-------RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
            TDR         R   R   + A++ + M+     +    K IL               
Sbjct: 80  ITDRPLAVNLEEIRRVKRTWPDRAMIVSIMV---PCVEESWKRILP-------------- 122

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                      +VED G + I LN GCP     E   GA +   P+ +            
Sbjct: 123 -----------MVEDTGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTQWCKHYTH 170

Query: 117 IPVTVKCRIGVDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +PV VK    + D              AV+L N + SI    ++ + +            
Sbjct: 171 LPVIVKLTPNITDVRQPARAARAGGADAVSLINTINSIMGVDLDRMAMSPNTGGQGSHGG 230

Query: 166 KDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 231 YCGPAVKPIALNMVAEIARDEQTAGLPISGIGGVSTWRDAAEFIALGCGTVQVCTAAM 288


>gi|307729120|ref|YP_003906344.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1003]
 gi|307583655|gb|ADN57053.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1003]
          Length = 440

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 62/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   G+ +   P+ +      + + L +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKEGLRLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 TDIRLGSRAAYKGGADGVSLINTINSIVAVDLDAMSPLPMVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDEQTPNLPISGIGGISTWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|229037740|ref|ZP_04189575.1| Dihydroorotate dehydrogenase 1 [Bacillus cereus AH1271]
 gi|228727594|gb|EEL78735.1| Dihydroorotate dehydrogenase 1 [Bacillus cereus AH1271]
          Length = 416

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 64/177 (36%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K V+D G +   LN GCP     E   G+     PD+V      + +   +PV VK 
Sbjct: 116 EIVKRVQDVGVDGFELNFGCPHGMA-ERGMGSASGQVPDLVEKQTYWVKEVAEVPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-------- 175
              + D      +     +  K G + + +      L G++      IP++D        
Sbjct: 175 TPNITD------ITETAYAAVKGGADAVSMINTINSLMGVNIDTWNPIPHVDGKGAHGGY 228

Query: 176 ---------YDIVYEIKKEN-PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                     ++V E  +    ++ I   GG+ +    ++ IL     V +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARHPEINVPISGMGGISNWRDTVEFILMGSTSVQVCTAAMH 285


>gi|227515720|ref|ZP_03945769.1| dihydroorotate oxidase [Lactobacillus fermentum ATCC 14931]
 gi|227085920|gb|EEI21232.1| dihydroorotate oxidase [Lactobacillus fermentum ATCC 14931]
          Length = 305

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 67/173 (38%), Gaps = 25/173 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   IGG+  +  V  A+ +   G  + + LNV CP    +    G     +  ++   
Sbjct: 99  PVVGSIGGSTETDYVLVAEKLAKSGLVSALELNVSCP----NVAHGGMAFGTDAKVLESL 154

Query: 108 IAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              + + +  +P+ VK    V D      +  + +  +  G +G           I I  
Sbjct: 155 TNQVKRVVGDVPLYVKLTPNVTD------ITEVARGAEAGGADGLSLINTVLGLHIDIRT 208

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + +L  G+      ++  L   +VY++ +    L I   GG+E  +  L+ +
Sbjct: 209 GQPVLGNGMGGYSGTEVKPLAVRMVYQVARAT-KLPIIGMGGIETAADVLEFM 260


>gi|163736157|ref|ZP_02143576.1| dihydroorotate dehydrogenase family protein [Phaeobacter
           gallaeciensis BS107]
 gi|161390027|gb|EDQ14377.1| dihydroorotate dehydrogenase family protein [Phaeobacter
           gallaeciensis BS107]
          Length = 434

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   G+ +   P+ +        K  S PV VK    +
Sbjct: 124 RVEATGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIQMVTEWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRQPARAAKAGGADAVSLINTINSIVSVNLDAMAPEPTIGDKGTHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  +   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARCPQTHGLPISAIGGVTTWRDAAEFMTMGAGNVQVCTAAM 289


>gi|261406269|ref|YP_003242510.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp.
           Y412MC10]
 gi|261282732|gb|ACX64703.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp.
           Y412MC10]
          Length = 340

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 70/199 (35%), Gaps = 18/199 (9%)

Query: 54  IGGADISKLVEA----AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +  A++  L++A    A+   + G++ + +             P        +G  L L 
Sbjct: 133 LSTAEVEDLIQAFREGARRAVEAGFDTVEIHGAHGYLIHQFHSPLTNQRSDEYGQDLPLF 192

Query: 101 PDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            + V   +  +  + + I + V  +  VD          + K  + +GV+   I +    
Sbjct: 193 GERVVQAVKEVLPEGMPIIMRVSAKEYVDGGYDVEYCAEICKRYRDAGVDIFHISSGGEG 252

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           + G S       P    D+  E K+    + +   G L+D + A +++     D V IGR
Sbjct: 253 VVG-SNGGPEAKPGYQVDLAAEFKQ-LLKVPVIAVGLLDDYNVAQEVVLSGKADMVAIGR 310

Query: 218 AAYKNSAMLTTVDEYFSNP 236
              ++        +     
Sbjct: 311 GMLRDPYWAVHAAKALDEE 329


>gi|229582479|ref|YP_002840878.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           Y.N.15.51]
 gi|228013195|gb|ACP48956.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           Y.N.15.51]
          Length = 555

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/133 (15%), Positives = 52/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           + + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 IEEILKGIKEKAKITVGIRISVTEFDNDGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   +++  L+     ++ ++  ++ I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYYKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|308233696|ref|ZP_07664433.1| dihydroorotate dehydrogenase family protein [Atopobium vaginae DSM
           15829]
 gi|328943993|ref|ZP_08241458.1| dihydroorotate oxidase [Atopobium vaginae DSM 15829]
 gi|327491962|gb|EGF23736.1| dihydroorotate oxidase [Atopobium vaginae DSM 15829]
          Length = 309

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/199 (14%), Positives = 64/199 (32%), Gaps = 28/199 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +  Q+ G  I + V A ++ E+         +N+ CP    +    GA +   P    + 
Sbjct: 103 VICQVAGHSIDEYVAALEVFEEKASFAAGFEINISCP----NIACGGAAMGSTPQGAAEI 158

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHA 155
           +  +      P+ VK           V +  + ++++  G + +                
Sbjct: 159 MRRLRPLTKRPLLVKM--------GPVNIPEIARALESEGADALSLINSIPGMAIDTTTY 210

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGVM 214
           +  + +         I  +   +V+E  K    + +   GG+   +  A  IL     V 
Sbjct: 211 KSKLSRPTGGFSGPAIHPIAVRMVWEAHKAV-KIPLCGIGGITTGLEAAEFILAGATAVS 269

Query: 215 IGRAAYKNSAMLTTVDEYF 233
           +G A   +      +    
Sbjct: 270 VGLANLYDPMSAPRILHEL 288


>gi|327438819|dbj|BAK15184.1| dihydroorotate dehydrogenase [Solibacillus silvestris StLB046]
          Length = 427

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 60/177 (33%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K V+D G +   LN GCP     E   GA     P++V        +   +PV VK 
Sbjct: 116 EIVKRVQDVGVDGFELNFGCPHGMA-ERGMGAASGQVPELVEKQTYWAKEYAEVPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP----------- 172
              + D           ++  + G + I +      L G+       IP           
Sbjct: 175 TPNITDITVT------AEAAVRGGADAISMINTINSLAGVDLNSWNTIPHVGNKGAHGGY 228

Query: 173 ------NLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                  +  ++V E  +    +L I   GG+ +   A + IL     V +  AA  
Sbjct: 229 CGPAVKPIALNMVGECARSPYINLPISGIGGISNWQDAAEFILMGSTSVQVCTAAMH 285


>gi|294340642|emb|CAZ89034.1| putative NADPH dehydrogenase [Thiomonas sp. 3As]
          Length = 371

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/191 (20%), Positives = 63/191 (32%), Gaps = 26/191 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVGDC 107
            V+AA+     G   + L   C           P +   +  +G  L   M  P  V D 
Sbjct: 160 FVQAARHAAGLGLQAVEL--HCAHGYLLHQFLSPLSNQRDDGYGGSLIQRMRYPLEVFDA 217

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A   A SIP+ V+      V+            +++K  G + I + +      GLSP
Sbjct: 218 VRAALPA-SIPLGVRVSATDWVEGGWDLEQTLAFAQALKARGCDWIDVSSG-----GLSP 271

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           K    I       + +  +E   L     G + +  QA  I+     D V + RA   N 
Sbjct: 272 KQQIPIGPGYQVPLAQAVREATGLPTMAVGLITEAQQAEAIVAEGRADLVALARALLWNP 331

Query: 224 AMLTTVDEYFS 234
                      
Sbjct: 332 HWPWQAAAALG 342


>gi|260663069|ref|ZP_05863962.1| dihydroorotate dehydrogenase [Lactobacillus fermentum 28-3-CHN]
 gi|260552690|gb|EEX25690.1| dihydroorotate dehydrogenase [Lactobacillus fermentum 28-3-CHN]
          Length = 305

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 66/173 (38%), Gaps = 25/173 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   IGG+  +  V  A+ +   G  + + LNV CP    +    G     +  ++   
Sbjct: 99  PVVGSIGGSTETDYVLVAEKLAKSGLVSALELNVSCP----NVAHGGMAFGTDAKVLESL 154

Query: 108 IAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              + + +  +P+ VK    V D      +  + +  +  G +G           I I  
Sbjct: 155 TNQVKRVVGDVPLYVKLTPNVTD------ITEVARGAEAGGADGLSLINTVLGLHIDIRT 208

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + +L  G+       +  L   +VY++ +    L I   GG+E  +  L+ +
Sbjct: 209 GQPVLGNGMGGYSGTAVKPLAVRMVYQVARAT-KLPIIGMGGIETAADVLEFM 260


>gi|229162093|ref|ZP_04290066.1| Dihydroorotate dehydrogenase 1 [Bacillus cereus R309803]
 gi|228621415|gb|EEK78268.1| Dihydroorotate dehydrogenase 1 [Bacillus cereus R309803]
          Length = 416

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 64/177 (36%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  K V+D G +   LN GCP     E   G+     PD+V      + +   +PV VK 
Sbjct: 116 EIVKRVQDVGVDGFELNFGCPHGMA-ERGMGSASGQVPDLVEKQTYWVKEVAEVPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-------- 175
              + D      +     +  + G + + +      L G++      IP++D        
Sbjct: 175 TPNITD------ITETAYAAVQGGADAVSMINTINSLMGVNIDTWNPIPHVDGKGAHGGY 228

Query: 176 ---------YDIVYEIKKEN-PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
                     ++V E  +    ++ I   GG+ +    ++ IL     V +  AA  
Sbjct: 229 CGPAVKPIALNMVAECARHPEINVPISGMGGISNWRDTVEFILMGSTSVQVCTAAMH 285


>gi|206603965|gb|EDZ40445.1| Dihydroorotate dehydrogenase [Leptospirillum sp. Group II '5-way
           CG']
          Length = 368

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 61/199 (30%), Gaps = 20/199 (10%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
               V  A + ++ G   + +N  CP    +       L  NPD  G+ +  + K L   
Sbjct: 170 AQDFVYTAHLAKETGAKILEVNFSCP----NVKGKEGQLYQNPDASGEILKRIRKDLGRD 225

Query: 119 VTVKCRIGVDDQIPAVA--------LRNLVKSIKKSGVNGIWIHARKAIL---KGLSPKD 167
             +  +IG  D    +           + + +I       I    + A+    +  S   
Sbjct: 226 FHLIMKIGFSDNPEHLDRLVEATSPYLDAISAINTVTGTIINPEGKPALPGPGRERSGLC 285

Query: 168 NRKIPNLDYDIVY----EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
              I NL    +      +++  P L +   GG   +           D VM    A  +
Sbjct: 286 GSGIKNLSLKTIRGLRQALRRRAPQLSLIGVGGFNTVEDYPDFREAGADIVMSATGAMWD 345

Query: 223 SAMLTTVDEYFSNPLTGSS 241
             +   V +      T  S
Sbjct: 346 PFLAYHVKQRTFVQDTLPS 364


>gi|184155677|ref|YP_001844017.1| dihydroorotate dehydrogenase 1B [Lactobacillus fermentum IFO 3956]
 gi|183227021|dbj|BAG27537.1| dihydroorotate dehydrogenase [Lactobacillus fermentum IFO 3956]
          Length = 305

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 66/173 (38%), Gaps = 25/173 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   IGG+  +  V  A+ +   G  + + LNV CP    +    G     +  ++   
Sbjct: 99  PVVGSIGGSTETDYVLVAEKLAKSGLVSALELNVSCP----NVAHGGMAFGTDAKVLESL 154

Query: 108 IAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              + + +  +P+ VK    V D      +  + +  +  G +G           I I  
Sbjct: 155 TNQVKRVVGDVPLYVKLTPNVTD------ITEVARGAEAGGADGLSLINTVLGLHIDIRT 208

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + +L  G+       +  L   +VY++ +    L I   GG+E  +  L+ +
Sbjct: 209 GQPVLGNGMGGYSGTAVKPLAVRMVYQVARAT-KLPIIGMGGIETAADVLEFM 260


>gi|242237505|ref|YP_002985686.1| dihydropyrimidine dehydrogenase [Dickeya dadantii Ech703]
 gi|242129562|gb|ACS83864.1| dihydroorotate dehydrogenase family protein [Dickeya dadantii
           Ech703]
          Length = 437

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/169 (21%), Positives = 62/169 (36%), Gaps = 23/169 (13%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ +        +  S+PV VK    +
Sbjct: 123 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIERVTRWCKQYCSLPVIVKLTPNI 181

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + S+    ++ + +                 +  +  
Sbjct: 182 TDIRYPARAAKRGGADAVSLINTINSVMGVDLDQMLMTPHTGGKGSHGGYCGPAVKPIAL 241

Query: 177 DIVYEIKKENPD---LFIGLNGGLEDMSQALK-------ILPSVDGVMI 215
           ++V EI ++ PD   L I   GG+     A +        +     VM+
Sbjct: 242 NMVSEIARD-PDTFGLPISGIGGISTWRDAAEFIALGCGTVQVCTAVMV 289


>gi|299783385|gb|ADJ41383.1| Dihydroorotate dehydrogenase [Lactobacillus fermentum CECT 5716]
          Length = 305

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 66/173 (38%), Gaps = 25/173 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   IGG+  +  V  A+ +   G  + + LNV CP    +    G     +  ++   
Sbjct: 99  PVVGSIGGSTETDYVLVAEKLAKSGLVSALELNVSCP----NVAHGGMAFGTDAKVLESL 154

Query: 108 IAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHA 155
              + + +  +P+ VK    V D      +  + +  +  G +G           I I  
Sbjct: 155 TNQVKRVVGDVPLYVKLTPNVTD------ITEVARGAEAGGADGLSLINTVLGLHIDIRT 208

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + +L  G+       +  L   +VY++ +    L I   GG+E  +  L+ +
Sbjct: 209 GQPVLGNGMGGYSGTAVKPLAVRMVYQVARAT-KLPIIGMGGIETAADVLEFM 260


>gi|320106189|ref|YP_004181779.1| dihydroorotate dehydrogenase family protein [Terriglobus saanensis
           SP1PR4]
 gi|319924710|gb|ADV81785.1| dihydroorotate dehydrogenase family protein [Terriglobus saanensis
           SP1PR4]
          Length = 309

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 62/170 (36%), Gaps = 24/170 (14%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K+ E  G     LN  CP    +    G     +P ++ +    +      P+ VK    
Sbjct: 120 KLNEAEGIAIYELNASCP----NTRHGGMVFGTDPGLLEELTQRVKAVSRRPLMVKLSPN 175

Query: 127 VDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKGL-SPKDNRKIPNL 174
           V       ++  +  + ++ G +            I I  RK  +K + +      I  +
Sbjct: 176 V------TSIGGMALAAERGGADAVSLVNTFVSMAIDIETRKPRIKNVTAGLSGPAIKPI 229

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNS 223
              +V+E  +      +G+ GG+     A++ +L     V +G A+Y + 
Sbjct: 230 AVRMVWEAARAVKIPVVGM-GGVLRAEDAVEFLLAGATAVQVGTASYADP 278


>gi|326201043|ref|ZP_08190915.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium papyrosolvens
           DSM 2782]
 gi|325988611|gb|EGD49435.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium papyrosolvens
           DSM 2782]
          Length = 329

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 64/176 (36%), Gaps = 20/176 (11%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AAK V+D G++ + +             P +      +G  ++    I    I A+ 
Sbjct: 149 FANAAKRVKDAGFDGVEIHSAHGYLLSQFLSPISNKRSDEYGGNVLNRIKIHLQVIDAVK 208

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+    TV  R+G  D +             +  +K+GV  + I            K+ 
Sbjct: 209 KAVGEDFTVFLRLGAADYMEGGTTIEDSSIAAREFQKAGVAALDISGGFCGYSKPDAKEQ 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                  + +   IK++   + + L GG+ +   A ++L     D + +GR    +
Sbjct: 269 GYF----WPLTKAIKEQV-SIPVILTGGITEPEVAEQLLTDGKADLIGVGRIILND 319


>gi|238590723|ref|XP_002392406.1| hypothetical protein MPER_08020 [Moniliophthora perniciosa FA553]
 gi|215458389|gb|EEB93336.1| hypothetical protein MPER_08020 [Moniliophthora perniciosa FA553]
          Length = 121

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 16/80 (20%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ-------------E 47
           MVD ++  +R  +R      L+YT MI A   +  D ++    +               +
Sbjct: 36  MVDQSELAWRRLSRRY-GAQLIYTPMINAK--MWSDPRHHAYRTAAFDIASGEEGDPSID 92

Query: 48  KPLALQIGGADISKLVEAAK 67
           +PL +Q    D  KL+E+AK
Sbjct: 93  RPLIIQFCANDPDKLLESAK 112


>gi|319935413|ref|ZP_08009850.1| hypothetical protein HMPREF9488_00681 [Coprobacillus sp. 29_1]
 gi|319809629|gb|EFW06042.1| hypothetical protein HMPREF9488_00681 [Coprobacillus sp. 29_1]
          Length = 640

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 67/186 (36%), Gaps = 24/186 (12%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
                + A   +++G++ + L+ G          P        +G C      I    + 
Sbjct: 134 ADAFAKGAVDAKEYGFDMVMLHFGHGWLPTQFLSPHYNKRTDGYGGCFENRVKIPIQIVE 193

Query: 110 AMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAIL 160
            + +A+    P+ ++      ++D  P   +   ++ I+   ++ + I        KA+ 
Sbjct: 194 RVRQAVGPDYPLDMRISGFEYIEDGTPIDEIIRFIQLIEDK-IDMVHISCGLEREIKAMT 252

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           K  S        N+ +    +  KE   + + + G +    +A +IL     D V+IGR 
Sbjct: 253 KMSSTPYFDHKINVQWS---QKVKEYVHIPVAVVGAIMTPEEAEEILANHQADAVVIGRQ 309

Query: 219 AYKNSA 224
              +  
Sbjct: 310 IIADPF 315


>gi|15898816|ref|NP_343421.1| NADH oxidase [Sulfolobus solfataricus P2]
 gi|13815305|gb|AAK42211.1| NADH oxidase [Sulfolobus solfataricus P2]
          Length = 555

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/133 (15%), Positives = 52/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           + + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 IEEILKGIKEKAKITVGIRISVTEFDNEGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   +++  L+     ++ ++  ++ I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYYKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|323476783|gb|ADX82021.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           HVE10/4]
          Length = 555

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/133 (15%), Positives = 53/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           + + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 IEEILKGIKEKAKITVGIRISVTEFDNEGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P  ++++  L+     ++ ++  ++ I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYHKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|72079118|ref|XP_787723.1| PREDICTED: similar to Dus1l protein [Strongylocentrotus purpuratus]
 gi|115942363|ref|XP_001193114.1| PREDICTED: similar to Dus1l protein [Strongylocentrotus purpuratus]
          Length = 291

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 28/88 (31%), Gaps = 10/88 (11%)

Query: 184 KENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTT--------VDEYF 233
           K    + +  NG ++ +    + +    VDGVM       N A+            DEY 
Sbjct: 2   KAAVKIPVFANGNIQSLQDVHRCMEETGVDGVMTAEGNLHNPALFEGTHPKVWDITDEYI 61

Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTD 261
               T  +P+       F     + M  
Sbjct: 62  DLVKTYPTPLSAVRAHLFKILHHSLMVH 89


>gi|323474144|gb|ADX84750.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           REY15A]
          Length = 555

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/133 (15%), Positives = 53/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           + + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 IEEILKGIKEKAKITVGIRISVTEFDNEGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P  ++++  L+     ++ ++  ++ I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYHKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|227829821|ref|YP_002831600.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           L.S.2.15]
 gi|284997100|ref|YP_003418867.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           L.D.8.5]
 gi|227456268|gb|ACP34955.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           L.S.2.15]
 gi|284444995|gb|ADB86497.1| NADH:flavin oxidoreductase/NADH oxidase [Sulfolobus islandicus
           L.D.8.5]
          Length = 555

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/133 (15%), Positives = 52/133 (39%), Gaps = 6/133 (4%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWI-HARKAIL 160
           + + +  + +   I V ++  +   D        +  + K ++K+G++ I +   R   L
Sbjct: 195 IEEILKGIKEKAKITVGIRISVTEFDNEGLTPEIVAEIGKKLEKAGIDYIHLSAGRDGPL 254

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               P   +++  L+     ++ ++  ++ I L G +     A+K     D V++GR   
Sbjct: 255 GSSMPYYYKRLAFLEE---AKVVRDAVNIPIFLVGSVITPVDAIKAREIADVVVLGRQLL 311

Query: 221 KNSAMLTTVDEYF 233
            +   L       
Sbjct: 312 ADPYWLEKAKRDL 324


>gi|163741314|ref|ZP_02148706.1| dihydropyrimidine dehydrogenase [Phaeobacter gallaeciensis 2.10]
 gi|161385667|gb|EDQ10044.1| dihydropyrimidine dehydrogenase [Phaeobacter gallaeciensis 2.10]
          Length = 434

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   G+ +   P+ +        K  S PV VK    +
Sbjct: 124 RVEATGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIQMVTEWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRHPARAAKAGGADAVSLINTINSIVSVNLDAMAPEPTIGDKGTHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  +   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARCPQTHGLPISAIGGVTTWRDAAEFMTMGAGNVQVCTAAM 289


>gi|227546994|ref|ZP_03977043.1| possible dihydroorotate oxidase [Bifidobacterium longum subsp.
           infantis ATCC 55813]
 gi|227212526|gb|EEI80415.1| possible dihydroorotate oxidase [Bifidobacterium longum subsp.
           infantis ATCC 55813]
          Length = 375

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 75/234 (32%), Gaps = 41/234 (17%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINL 79
           +  + + D +  +  +   + L     G+ +  +            A++V++ G   + +
Sbjct: 150 SPDVWQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVM 209

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N  CP            L  NP +VG    A+ + +  IP+ VK      D    + +R+
Sbjct: 210 NTSCP-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDALELMVRS 264

Query: 139 LV----------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            V                K +  +G   +    R       S      I     D+V  +
Sbjct: 265 TVGHGTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARL 319

Query: 183 K--KENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
              +E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 320 AAIREKLGLDFAINGVGGVVSPADYQAYRDAGADSVMSATGAMWDAELAHKIKA 373


>gi|118430958|ref|NP_147090.2| dihydroorotate dehydrogenase 1B [Aeropyrum pernix K1]
 gi|150421637|sp|Q9YFI6|PYRD_AERPE RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|116062284|dbj|BAA79175.2| probable dihydroorotate dehydrogenase [Aeropyrum pernix K1]
          Length = 306

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 48/209 (22%), Positives = 82/209 (39%), Gaps = 30/209 (14%)

Query: 40  ILGFSTQEK--PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           +L  + +E   P+   I G    + VE A  +E+ G + + LN+ CP    H    G  L
Sbjct: 87  MLAQTVEEASIPVIASIAGGAPGEWVEMASTLEEAGVSAVELNLSCP----HFAGGGLEL 142

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----- 152
             +P  V   ++A+   L IPV  K          +  L +      ++G  G+      
Sbjct: 143 GQDPAAVASVVSAVASTLRIPVIAKL-------GYSDRLVDAASKALEAGARGLTLINSM 195

Query: 153 ------IHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                 ++A+K +L         + I  +    VYE+  E     I   GG+E    A++
Sbjct: 196 RAMKIDVYAKKPVLGNRVGGLSGKPIHPIAVRAVYEVYGETRA-DIFAAGGVESWEDAVE 254

Query: 206 -ILPSVDGVMIGRAAYKN--SAMLTTVDE 231
             L     V +G AA+      +L ++ E
Sbjct: 255 FYLAGAKAVQVG-AAFITIGPHVLRSIVE 282


>gi|160879659|ref|YP_001558627.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           phytofermentans ISDg]
 gi|160428325|gb|ABX41888.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           phytofermentans ISDg]
          Length = 645

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 69/198 (34%), Gaps = 27/198 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK   + GY+ I  + G          P        +G  L      + +CI A+ 
Sbjct: 147 FGEAAKRAVEAGYDTIEFHAGHNYTPHSFLSPYFNRRTDEYGGSLPNRARFLIECIEAIR 206

Query: 113 KAL--SIPVTVKCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           + +   +P+ ++     D          +    K  K SGV+ + +          +   
Sbjct: 207 QNIPEDMPLFMRLDAHDDYLEGGLTIEEVIEFCKMAKASGVDVLDVSRGN----FSTAAI 262

Query: 168 NRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             ++P +D       +    I+KE   + + + G + D  QA  IL     D V+IGRA 
Sbjct: 263 KYEVPPIDLPRGFNVENAARIRKETGMITVAV-GRINDPLQAETILTDDKADMVVIGRAQ 321

Query: 220 YKNSAMLTTVDEYFSNPL 237
             +        E     +
Sbjct: 322 LADPEFCNKAKEGREGSI 339


>gi|325273455|ref|ZP_08139703.1| dihydropyrimidine dehydrogenase subunit B [Pseudomonas sp. TJI-51]
 gi|324101411|gb|EGB99009.1| dihydropyrimidine dehydrogenase subunit B [Pseudomonas sp. TJI-51]
          Length = 424

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/159 (22%), Positives = 57/159 (35%), Gaps = 17/159 (10%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V        +  S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKQHCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE-----NPDLFIGLNGGLEDMSQALKILPSV 210
           ++V EI ++      P   IG  G   D ++ + +    
Sbjct: 241 NMVAEIARDPATHGLPICGIGGIGNWRDAAEFMALGSGA 279


>gi|152986422|ref|YP_001345936.1| dihydropyrimidine dehydrogenase [Pseudomonas aeruginosa PA7]
 gi|150961580|gb|ABR83605.1| probable oxidoreductase [Pseudomonas aeruginosa PA7]
          Length = 424

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 61/173 (35%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCSLPVIVKLTPNI 180

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI-------------LKGLSPKDNRK 170
            D      +R   ++ ++ G + +     I++  ++                        
Sbjct: 181 TD------IRQSARAAQRGGADAVSLINTINSITSVDLERMVALPVVGTQSTHGGYCGSA 234

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 235 VKPIALNMVAEIARDPQTRGLPICGIGGIGSWRDAAEFVALGCGAVQVCTAAM 287


>gi|288924786|ref|ZP_06418723.1| dihydroorotate oxidase [Prevotella buccae D17]
 gi|315607802|ref|ZP_07882795.1| dihydroorotate oxidase [Prevotella buccae ATCC 33574]
 gi|288338573|gb|EFC76922.1| dihydroorotate oxidase [Prevotella buccae D17]
 gi|315250271|gb|EFU30267.1| dihydroorotate oxidase [Prevotella buccae ATCC 33574]
          Length = 301

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/208 (14%), Positives = 73/208 (35%), Gaps = 25/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G         A+ ++       I +N+ CP   V +G     +    +   
Sbjct: 93  DTNMIVNVSGHSADSYAACAEKIDSLERIPAIEVNISCP--NVKDGGMAFGVTC--EGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+       + VK    V D      +  + ++ +  G +            + I 
Sbjct: 149 SVVKAVRAKYHKTMIVKLSPNVTD------VAEIARACEAEGADSVSLINTLMGMAVDIE 202

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            R+ +L   +       +  +   +VY++        +GL GG+     A++ ++     
Sbjct: 203 KRQPMLSIRTGGLSGPAVKPVALRMVYDVYHAVKIPVVGL-GGISSARDAIEFMMCGATA 261

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + IG A + + A+   V +  ++ L   
Sbjct: 262 IEIGTANFIDPAITKKVKDGINDWLDAH 289


>gi|134057155|emb|CAK48758.1| unnamed protein product [Aspergillus niger]
          Length = 415

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/216 (17%), Positives = 76/216 (35%), Gaps = 31/216 (14%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              EAAK     G++ I +             P +      +G        ++ +   A+
Sbjct: 194 DFGEAAKRAVRAGFDAIEVHSAHGYLLHQFLSPVSNHRTDRYGGSFENRIRVLLEVCDAI 253

Query: 112 CKALS--IPVTVKC------------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             A+   +P+ V+             +    +         L   +   GV+ I + +  
Sbjct: 254 RDAIPDTMPLLVRISATDWFEFDEGLKKEFPESWTVEQSVRLAPILADHGVDLIDVSSG- 312

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMI 215
             +   S    R  P     + +E+K+   D L +   GG++    A +++   +D V+ 
Sbjct: 313 -GVHSKSAIAIRPGPAYQVHLAHEVKQAVGDRLLVTAVGGIKTGKLAEEVVQSGIDAVLA 371

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           GR   +N  ++      F+N L     + T++D  F
Sbjct: 372 GRWFQQNPGLVR----AFANELGVKVRMATQIDWSF 403


>gi|260892282|ref|YP_003238379.1| dihydroorotate dehydrogenase family protein [Ammonifex degensii
           KC4]
 gi|260864423|gb|ACX51529.1| dihydroorotate dehydrogenase family protein [Ammonifex degensii
           KC4]
          Length = 308

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/206 (16%), Positives = 68/206 (33%), Gaps = 27/206 (13%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G  + + VE A  + + G   + LN+ CP+ +      G     +P +      
Sbjct: 100 VIGSVAGETVEEYVEVACRLAEAGVAALELNLSCPNVKA-----GTLFGHDPLLAAQVTR 154

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
           A+ +AL    P  VK  +  +D         + ++  ++G  G+ +              
Sbjct: 155 AVREALGDDFPFLVKLGVVGND------FLAVARAAVEAGATGLSLINTLPGLAVDVKRR 208

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  +  G        I  +    V+   +E   + I   GG+  +   L  +L     V 
Sbjct: 209 KLLLGHGTGGLSGPAIKPVALWAVWRAHREL-QVPIIGMGGVVSVEDVLAFLLCGARAVA 267

Query: 215 IGRAAYKNSAMLTTVDEYFSNPLTGS 240
           +G        +   + E     L   
Sbjct: 268 VGSGTLAFPRLAWELVEGLEQALAKE 293


>gi|332707883|ref|ZP_08427898.1| tRNA-dihydrouridine synthase [Lyngbya majuscula 3L]
 gi|332353349|gb|EGJ32874.1| tRNA-dihydrouridine synthase [Lyngbya majuscula 3L]
          Length = 52

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/39 (56%), Positives = 31/39 (79%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN 39
          M+DWTDRH R F R+L+  ALL+TEM++ADA++ GD+  
Sbjct: 14 MMDWTDRHCRAFHRVLSKRALLWTEMVIADAVIHGDRDR 52


>gi|15966201|ref|NP_386554.1| dihydropyrimidine dehydrogenase [Sinorhizobium meliloti 1021]
 gi|307308552|ref|ZP_07588254.1| dihydroorotate dehydrogenase family protein [Sinorhizobium meliloti
           BL225C]
 gi|307317330|ref|ZP_07596770.1| dihydroorotate dehydrogenase family protein [Sinorhizobium meliloti
           AK83]
 gi|15075471|emb|CAC47027.1| Dihydropyrimidine dehydrogenase [Sinorhizobium meliloti 1021]
 gi|306896919|gb|EFN27665.1| dihydroorotate dehydrogenase family protein [Sinorhizobium meliloti
           AK83]
 gi|306900952|gb|EFN31561.1| dihydroorotate dehydrogenase family protein [Sinorhizobium meliloti
           BL225C]
          Length = 437

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPARAAKAGGTDAVSLINTINSITGVNLDTFSPEPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDPETYGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|317500819|ref|ZP_07959032.1| hypothetical protein HMPREF1026_00975 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|316897786|gb|EFV19844.1| hypothetical protein HMPREF1026_00975 [Lachnospiraceae bacterium
           8_1_57FAA]
          Length = 641

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 65/195 (33%), Gaps = 20/195 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +A+K  ++ G++ I L   C            P        +G  L+    ++ + + A
Sbjct: 147 AKASKNAKEAGFDGIEL--HCAHAYMLLGSFLSPLRNKRTDEYGGSLLNRARLLFEVLDA 204

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A      +  R+   ++ P          L+  ++K GV+   I       +     
Sbjct: 205 IKEACGEDFPIVLRMSGSERDPQGNTLEDMKRLIPYLEKHGVDCFEISGGTQYERCNKII 264

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                            KE     +   G + D   A  +L    VDGV++GRA   +  
Sbjct: 265 PCHGEEEFTNLKEARAIKEITTKPVITVGKILDAQLAEDVLEANEVDGVVLGRALLADPD 324

Query: 225 MLTTVDEYFSNPLTG 239
            +   +E   + +  
Sbjct: 325 FVEKAEEKRYDEIAP 339


>gi|13471617|ref|NP_103183.1| dihydropyrimidine dehydrogenase [Mesorhizobium loti MAFF303099]
 gi|14022359|dbj|BAB48969.1| probable oxidoreductase [Mesorhizobium loti MAFF303099]
          Length = 437

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPARAAHAGGTDAVSLINTINSITGVDLDSFAPMPTIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + L      V +  AA 
Sbjct: 243 NMVAEIARDPETRGLPISGIGGITTWRDAAEFLALGAGNVQVCTAAM 289


>gi|329922336|ref|ZP_08278013.1| NADPH dehydrogenase [Paenibacillus sp. HGF5]
 gi|328942199|gb|EGG38470.1| NADPH dehydrogenase [Paenibacillus sp. HGF5]
          Length = 340

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 70/199 (35%), Gaps = 18/199 (9%)

Query: 54  IGGADISKLVEA----AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +  A++  L++A    A+   + G++ + +             P        +G  L L 
Sbjct: 133 LSTAEVEDLIQAFREGARRAVEAGFDTVEIHGAHGYLIHQFHSPLTNQRSDEYGQDLPLF 192

Query: 101 PDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            + V   +  +  + + I + V  +  VD          + K  + +GV+   I +    
Sbjct: 193 GERVVQAVKEVLPEGMPIIMRVSAKEYVDGGYDVQYCAEICKRYRDAGVDIFHISSGGEG 252

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           + G S       P    D+  E K+    + +   G L+D + A +++     D V IGR
Sbjct: 253 VVG-SNGGPEAKPGYQVDLAAEFKQ-LLKVPVIAVGLLDDYNVAQEVVLSGKADMVAIGR 310

Query: 218 AAYKNSAMLTTVDEYFSNP 236
              ++        +     
Sbjct: 311 GMLRDPYWAVHAAKALDEE 329


>gi|39943624|ref|XP_361349.1| hypothetical protein MGG_03823 [Magnaporthe oryzae 70-15]
 gi|145014510|gb|EDJ99078.1| hypothetical protein MGG_03823 [Magnaporthe oryzae 70-15]
          Length = 418

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/187 (13%), Positives = 62/187 (33%), Gaps = 19/187 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
                 A+ +E  G++ I L+       +               +G  L     ++ +  
Sbjct: 175 EGFAHTAEYLEKAGFDGIELHAA--HGYLLAQFLSETTNQRTDEYGGSLENRMRLILEVT 232

Query: 109 AAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A + +  S    +  +       +          L ++++ +G++ +          G +
Sbjct: 233 AEVRRRTSKNFILGIKINSVEFQEKGFKPEEAVQLCEALEAAGMDFVETSGGTYESFGFA 292

Query: 165 PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
            +        +Y  +    I+K    + +   GG + +   +  L  VDG+ IGRAA   
Sbjct: 293 HRKESSRKRENYFIEFAEVIRKAVKHMVVYTTGGFKTVGAMVDALQGVDGIGIGRAAGSE 352

Query: 223 SAMLTTV 229
             +   +
Sbjct: 353 PDLAKDI 359


>gi|86137294|ref|ZP_01055871.1| dihydropyrimidine dehydrogenase [Roseobacter sp. MED193]
 gi|85825629|gb|EAQ45827.1| dihydropyrimidine dehydrogenase [Roseobacter sp. MED193]
          Length = 434

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/167 (23%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   GA +   P+ +        K  S PV VK    +
Sbjct: 124 KVEATGADGIELNFGCPHGMA-ERGMGAAVGQVPEYIQMVTEWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRFPARAAKAGGGDAVSLINTINSIVSVDLDQMAPEPTVGGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E  DL I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARCPETHDLPISAIGGVTTWKDAAEFMALGAGNVQVCTAAM 289


>gi|322691954|ref|YP_004221524.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp. longum
           JCM 1217]
 gi|320456810|dbj|BAJ67432.1| putative dihydroorotate dehydrogenase [Bifidobacterium longum
           subsp. longum JCM 1217]
          Length = 371

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 73/234 (31%), Gaps = 41/234 (17%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINL 79
           +  + + D +  +  +   + L     G+ +  +            A++V++ G   + +
Sbjct: 146 SPDVWQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVM 205

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N  CP            L  NP +VG    A+ + +  IP+ VK      D    + +R+
Sbjct: 206 NTSCP-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDGDLELMVRS 260

Query: 139 LV----------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            V                K +  +G   +    R       S      I     D+V  +
Sbjct: 261 TVGHGTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARL 315

Query: 183 K----KENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
                K   D  I   GG+   +          D VM    A  ++ +   +  
Sbjct: 316 AAIREKLGLDFKINGVGGVVSPADYQAYRNAGADSVMSATGAMWDAELAHKIKA 369


>gi|217076624|ref|YP_002334340.1| dihydroorotate dehydrogenase [Thermosipho africanus TCF52B]
 gi|217036477|gb|ACJ74999.1| dihydroorotate dehydrogenase [Thermosipho africanus TCF52B]
          Length = 272

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/207 (20%), Positives = 85/207 (41%), Gaps = 34/207 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           +E    L +GG    + ++ A+ +  +   +  I  N  CP   V +G  G  ++ + + 
Sbjct: 80  KETKTILSLGGDSKDEYIKIAEKIAPYAKKFEAIEFNFSCP--NVKKG--GLSILSDINE 135

Query: 104 VGDCIAAMCK---------ALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
             + +  + K          LSI    V V  +   +     + L N V+        G+
Sbjct: 136 WQEILENVRKILPDSFLIAKLSIEGNFVEVLSKKVKEFGWNGLTLINCVR--------GL 187

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILP 208
            I   K ++ GLS      +  +    +YE++K   D++I  +GG+   +D+   L  L 
Sbjct: 188 LIKDGKIVMGGLS---GPILKPIALRAIYEVRKVLKDIYIIASGGIYTKKDVDDFL--LV 242

Query: 209 SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             + + IG A +K+  ++  + +Y   
Sbjct: 243 GANAISIGSALFKDPQVVEELGKYLKG 269


>gi|229818416|ref|ZP_04448697.1| hypothetical protein BIFANG_03723 [Bifidobacterium angulatum DSM
           20098]
 gi|229784286|gb|EEP20400.1| hypothetical protein BIFANG_03723 [Bifidobacterium angulatum DSM
           20098]
          Length = 377

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 69/228 (30%), Gaps = 31/228 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D K  +  +   + L     G+ +  +         V  A +V + G   + +N  C
Sbjct: 155 WQPDMKKAIAEAGDGQLLVPSFQGSRVDGMDRKAYIADHVTTAHLVAETGAGLMEMNTSC 214

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P            L  +P +VGD   A+   +   P+ VK     +D      ++  V  
Sbjct: 215 P-----NEGHNRLLCHDPHLVGDITEAVKNEIGDRPLIVKLAYIPNDADLETMVKETVGR 269

Query: 143 IKKSGVNGI-WIHARKAILKG----------LSPKDNRKIPNLDYDIVYEIK----KENP 187
               G + I  I AR     G           S      I     D+V  +     K   
Sbjct: 270 GAVQGFSTINTISARLVDANGNQALPGAGRDRSGVCGNAIRGAGLDMVGRLSAIREKLGV 329

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D  I   GG+              + VM    A  ++ +   + +   
Sbjct: 330 DFAIVGVGGVIRPDDYKAYRAAGANAVMSATGAMWDANLAREIKKTLR 377


>gi|145500820|ref|XP_001436393.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124403532|emb|CAK68996.1| unnamed protein product [Paramecium tetraurelia]
          Length = 997

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/166 (19%), Positives = 53/166 (31%), Gaps = 27/166 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +  Q    D  +L    K   +  ++ + LN+ CP     E   G     NP IV D   
Sbjct: 650 IMCQHIEQDWRELTRKCK--NEGQFDMLELNLSCPHGM-TELGMGRACGENPAIVKDICQ 706

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +   + IPV VK      D        ++ ++ K+ G   + +      L    P    
Sbjct: 707 WVTSEIDIPVIVKITPNYPDS------ADIAQAAKEGGAKAVTLTNTFPTLMDPDPLGTP 760

Query: 170 KIP------------------NLDYDIVYEIKKENPDLFIGLNGGL 197
                                 +      E+ K  PD+ I  +GG+
Sbjct: 761 WPAVGEENNVTYGGGCGSMLRPIALRKTSEVAKAIPDIAIFGSGGI 806


>gi|134290941|ref|YP_001114710.1| dihydropyrimidine dehydrogenase [Burkholderia vietnamiensis G4]
 gi|134134130|gb|ABO58455.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) / dihydroorotate oxidase B,
           catalytic subunit [Burkholderia vietnamiensis G4]
          Length = 435

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPQTPNLPISGIGGISSWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|296454958|ref|YP_003662102.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp. longum
           JDM301]
 gi|296184390|gb|ADH01272.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp. longum
           JDM301]
          Length = 375

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 75/234 (32%), Gaps = 41/234 (17%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINL 79
           +  + + D +  +  +   + L     G+ +  +            A++V++ G   + +
Sbjct: 150 SPDVWQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVM 209

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N  CP            L  NP +VG    A+ + +  IP+ VK      D    + +R+
Sbjct: 210 NTSCP-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDALELMVRS 264

Query: 139 LV----------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            V                K +  +G   +    R       S      I     D+V  +
Sbjct: 265 TVGHGTVQGFSTINTISAKLVDANGNQALPGAGRD-----HSGVCGNAIRGAGLDMVARL 319

Query: 183 K--KENPDLFIGLN--GGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
              +E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 320 AAIREKLGLDFAINGVGGVVSPADYQAYRNAGADSVMSATGAMWDAELAHKIKA 373


>gi|23335996|ref|ZP_00121226.1| COG0167: Dihydroorotate dehydrogenase [Bifidobacterium longum
           DJO10A]
 gi|189440460|ref|YP_001955541.1| dihydroorotate dehydrogenase [Bifidobacterium longum DJO10A]
 gi|189428895|gb|ACD99043.1| Dihydroorotate dehydrogenase [Bifidobacterium longum DJO10A]
          Length = 371

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 74/230 (32%), Gaps = 41/230 (17%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +            A++V++ G   + +N  C
Sbjct: 150 WQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVMNTSC 209

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV-- 140
           P            L  NP +VG    A+ + +  IP+ VK      D +  + +R+ V  
Sbjct: 210 P-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDVLELMVRSTVGH 264

Query: 141 --------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--K 184
                         K +  +G   +    R       S      I     D+V  +   +
Sbjct: 265 GTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARLAAIR 319

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 320 EKLGLDFAINGVGGVVSPADYQAYRDAGADSVMSATGAMWDAELAHKIKA 369


>gi|154249158|ref|YP_001409983.1| dihydroorotate dehydrogenase family protein [Fervidobacterium
           nodosum Rt17-B1]
 gi|154153094|gb|ABS60326.1| dihydroorotate dehydrogenase family protein [Fervidobacterium
           nodosum Rt17-B1]
          Length = 276

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 29/196 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEI--NLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+ L +GG    + +   KI++ +    I    N  CP    +    G  +M +     +
Sbjct: 94  PVILSLGGDFFEEYLSITKIIKPYTSKFIAVEYNFSCP----NVKRGGLSIMSDIGEWKN 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------HAR 156
            +  +   +         +     I    +      +K +G +G+ +             
Sbjct: 150 LLKEIRTEVP-----DVFLIAKLGIEGGFVEENAAIVKDTGWDGVTVINTIRGLMFNDEG 204

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDMSQALKILPSVDGV 213
           + IL GLS  +   +  +    VYE++K   D+FI  +GG+   ED+   LK+    D V
Sbjct: 205 EMILGGLSGPN---LLPIALRAVYEVRKRLSDIFIIASGGVYKREDVELFLKL--GADAV 259

Query: 214 MIGRAAYKNSAMLTTV 229
            +G A +KN  +L  +
Sbjct: 260 SVGSALFKNEKVLNEL 275


>gi|209883298|ref|YP_002287155.1| FAD/FMN-binding oxidoreductase [Oligotropha carboxidovorans OM5]
 gi|209871494|gb|ACI91290.1| FAD/FMN-binding oxidoreductase [Oligotropha carboxidovorans OM5]
          Length = 366

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/205 (19%), Positives = 65/205 (31%), Gaps = 27/205 (13%)

Query: 39  NILGFSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSA 86
           + L F T + P   L  Q       + V AA+     G+  I L             P +
Sbjct: 134 SALPFETSDHPPLALDAQGLSRVRDEFVRAARRAATLGFEGIELHGAHGYLLHQFLSPLS 193

Query: 87  RVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIGV--DDQIPAVALRNLVK 141
                ++G  L   M  P  + D + A       PV ++       D      +     K
Sbjct: 194 NTRTDAYGGSLENRMRFPLEIYDAVRAAY-PQDKPVWIRVSATDWADGGWDLESSIAFAK 252

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDM 200
            +K  G   I + +      GL+P    K+      +    I+ E  ++     G +   
Sbjct: 253 ELKARGCPAIHVSSG-----GLTPAQQIKVGPGYQVEFAARIRAEA-EIPTIAVGLITGA 306

Query: 201 SQALKIL--PSVDGVMIGRAAYKNS 223
            QA  IL     D + + R    + 
Sbjct: 307 QQAEDILVKGQADAIALARGILYDP 331


>gi|229591377|ref|YP_002873496.1| dihydropyrimidine dehydrogenase [Pseudomonas fluorescens SBW25]
 gi|229363243|emb|CAY50336.1| putative dihydropyrimidine dehydrogenase [Pseudomonas fluorescens
           SBW25]
          Length = 424

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 RVEATGCDGIELNFGCPHGM-PERGMGAAVGQVPEYVEQVTRWCKTYCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    +  +                   +  +  
Sbjct: 181 TDIRVAARAAYRGGADAVSLINTINSITSVDLERMVALPMVGTQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+ +   A + +      V +  AA 
Sbjct: 241 NMVAEIARDPQTQGLPICGIGGIGNWRDAAEFVALGCGAVQVCTAAM 287


>gi|332185015|ref|ZP_08386764.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Sphingomonas sp. S17]
 gi|332014739|gb|EGI56795.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Sphingomonas sp. S17]
          Length = 375

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 54/176 (30%), Gaps = 14/176 (7%)

Query: 93  FGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSG 147
           +G  L   M  P  V D + A   A   PVTV+      V+              ++  G
Sbjct: 200 YGGDLANRMRFPLEVFDAVRAAFPA-DKPVTVRVSGTDWVEGGWTVDETAIFASELETRG 258

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              I + +      GL P+    +       + ++ K+   + +   G + D  QA  IL
Sbjct: 259 CAAIHVSSG-----GLDPRQKIPVGPSYQVPLAKVVKQAVSMPVIAVGLITDPHQAESIL 313

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
                D + I R    +                 + P   R +     +I   M  
Sbjct: 314 QDGDADAIAIARGVLWDPRWPWHAAAAL-GASVDAPPQHLRSEPHEAGRILKEMGP 368


>gi|322382721|ref|ZP_08056573.1| dihydroorotate dehydrogenase 1B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321153330|gb|EFX45766.1| dihydroorotate dehydrogenase 1B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 292

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/152 (19%), Positives = 60/152 (39%), Gaps = 12/152 (7%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            G + I LN+ CP   V EG     +    +I  + +  + +A  +P+ VK      D +
Sbjct: 110 RGISMIELNISCP--NVKEGGMAFGI--ETEIAREVVREVRQATGLPLAVKLSPNARDIV 165

Query: 132 PAVALR-----NLVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKE 185
               +      + V  +       I I  ++++   L +      I  +   +V+++ + 
Sbjct: 166 SMAVMCEEEGADAVSLVNTFTGMKIDIQKKQSVFTNLYAGLSGPAIKPIALRMVHQVARH 225

Query: 186 NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
                IG+ GG+     A++ I+     V IG
Sbjct: 226 VNIPVIGM-GGISSAEDAVEFIMAGASIVQIG 256


>gi|167461798|ref|ZP_02326887.1| dihydroorotate dehydrogenase 1B [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 307

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/152 (19%), Positives = 60/152 (39%), Gaps = 12/152 (7%)

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            G + I LN+ CP   V EG     +    +I  + +  + +A  +P+ VK      D +
Sbjct: 125 RGISMIELNISCP--NVKEGGMAFGI--ETEIAREVVREVRQATGLPLAVKLSPNARDIV 180

Query: 132 PAVALR-----NLVKSIKKSGVNGIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKE 185
               +      + V  +       I I  ++++   L +      I  +   +V+++ + 
Sbjct: 181 SMAVMCEEEGADAVSLVNTFTGMKIDIQKKQSVFTNLYAGLSGPAIKPIALRMVHQVARH 240

Query: 186 NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
                IG+ GG+     A++ I+     V IG
Sbjct: 241 VNIPVIGM-GGISSAEDAVEFIMAGASIVQIG 271


>gi|104782302|ref|YP_608800.1| dihydropyrimidine dehydrogenase [Pseudomonas entomophila L48]
 gi|95111289|emb|CAK16009.1| putative dihydroorotate dehydrogenase, FMN-linked, 4Fe-4S
           ferredoxin-type protein [Pseudomonas entomophila L48]
          Length = 424

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/151 (23%), Positives = 54/151 (35%), Gaps = 14/151 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK 205
           ++V EI +  E   L I   GG+     A +
Sbjct: 241 NMVAEIARDPETRGLPICGIGGIGTWRDAAE 271


>gi|221202549|ref|ZP_03575578.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans CGD2M]
 gi|221207748|ref|ZP_03580755.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans CGD2]
 gi|221172245|gb|EEE04685.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans CGD2]
 gi|221177586|gb|EEE10004.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans CGD2M]
          Length = 435

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPIPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISTWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|23465827|ref|NP_696430.1| hypothetical protein BL1265 [Bifidobacterium longum NCC2705]
 gi|23326523|gb|AAN25066.1| hypothetical protein with similarity to dihydroorotate
           dehydrogenase [Bifidobacterium longum NCC2705]
          Length = 371

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 73/230 (31%), Gaps = 41/230 (17%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +            A++V++ G   + +N  C
Sbjct: 150 WQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVMNTSC 209

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV-- 140
           P            L  NP +VG    A+ + +  IP+ VK      D    + +R+ V  
Sbjct: 210 P-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDGDLELMVRSTVGH 264

Query: 141 --------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--K 184
                         K +  +G   +    R       S      I     D+V  +   +
Sbjct: 265 GTVQGFSTINTISAKLVDANGNQALPGAGRD-----HSGVCGNAIRGAGLDMVARLAAIR 319

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 320 EKLGLDFAINGVGGVVSPADYQAYRDAGADSVMSATGAMWDAELAHKIKA 369


>gi|331003589|ref|ZP_08327086.1| hypothetical protein HMPREF0491_01948 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412430|gb|EGG91821.1| hypothetical protein HMPREF0491_01948 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 420

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 68/207 (32%), Gaps = 24/207 (11%)

Query: 25  EMIVADA--ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           EM       +  G  K +      +  ++  +G +D       AK  E  G + I  N  
Sbjct: 79  EMTSDKPNEVNFGFIKQLKKDFPNKVIVSSIMGASDDEW-AILAKESEKAGADMIECNFS 137

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC-----------RIGVDDQI 131
           CP   +   + G+ +  NPD+V            +P+  K            R  ++   
Sbjct: 138 CPQ--MTSSTMGSDVGQNPDLVKHYCEVASSNTKLPIIAKMTPNLGNMEIPARAALEGGA 195

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDL 189
             +A  N VKSI    +N             +S      +  +    + ++  +     +
Sbjct: 196 KGIAAINTVKSITNLDINLRTGMPVVNGKSAISGYSGAAVKPIALRFISDLMHDPVVSKV 255

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIG 216
            I   GG+E     L+ L      M+G
Sbjct: 256 PITGMGGIETWRDCLEFL------MLG 276


>gi|223038910|ref|ZP_03609202.1| NADH oxidase [Campylobacter rectus RM3267]
 gi|222879883|gb|EEF14972.1| NADH oxidase [Campylobacter rectus RM3267]
          Length = 341

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 55/181 (30%), Gaps = 17/181 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V AA   +  GY  I ++            P   + +  +G         + + ++ + 
Sbjct: 145 FVRAAIRAQCAGYAAIEIHAAHGYLISEFLSPGVNLRDDEYGGSSENRTRFLKEILSEIK 204

Query: 113 KALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
            A+ IPV V+      V           L K ++  G   I +       +  S      
Sbjct: 205 TAVQIPVGVRISAQSWVKGDWSLDDSVQLAKKLEALGAAFIHVSTGGFFERTDSAPTVAP 264

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           +    Y    +  K+   + +   G +   S+   +L     D V  GR   +N      
Sbjct: 265 LYQASY---AKAVKQAVGIPVIAVGLITKASEGEALLLGSVCDAVAYGRELLRNP-NFAQ 320

Query: 229 V 229
            
Sbjct: 321 A 321


>gi|212716772|ref|ZP_03324900.1| hypothetical protein BIFCAT_01709 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660476|gb|EEB21051.1| hypothetical protein BIFCAT_01709 [Bifidobacterium catenulatum DSM
           16992]
          Length = 377

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 70/228 (30%), Gaps = 31/228 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +         V  A +V + G   + +N  C
Sbjct: 155 WQPDMQKAIAAAGDGQLLVPSFQGSRVEGMDREAYIADHVTTAHLVAETGAGLMEMNTSC 214

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P            L  +P +VG+   A+   +   P+ VK     +D    + ++  V  
Sbjct: 215 P-----NEGHNRLLCHDPHLVGEITEAVKNEIGDRPLIVKLAYIPNDTDLEIMVKETVGH 269

Query: 143 IKKSGVNGI-WIHARKAILKG----------LSPKDNRKIPNLDYDIVYEIK----KENP 187
               G + I  I A+     G           S      I     D+V  +     K   
Sbjct: 270 GAVQGFSTINTISAKLVDANGNQALPGAGRDRSGVCGNAIRGAGLDMVGRLSAIREKLGL 329

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D  I   GG+              + VM    A  ++ +   + E   
Sbjct: 330 DFAIVGVGGVIRPEDYKAYREAGANAVMSATGAMWDANLAREIKETLR 377


>gi|46127399|ref|XP_388253.1| hypothetical protein FG08077.1 [Gibberella zeae PH-1]
          Length = 413

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/219 (17%), Positives = 77/219 (35%), Gaps = 37/219 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             + AAK     G++ I ++            P +      +G        +V + I  +
Sbjct: 192 DFLAAAKRAIRAGFDVIEIHAAHGYLLHQFLSPVSNQRTDEYGGSFENRIRVVLEIIDLI 251

Query: 112 CKALS--IPVTVKC------------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
              +    P+ V+             +    +         L + + K GV+ + + +  
Sbjct: 252 RGEIPETTPILVRVSATDWFEYDAQFKDEFPESWTVEQTCKLAQILPKHGVDLVDVSSG- 310

Query: 158 AILKGLSPKDNRKI---PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDG 212
               G+ PK    I   P    D+  ++KK   D + +   GG++    A ++L   +D 
Sbjct: 311 ----GIHPKSAIAIKAGPAYQVDLAKQVKKAVGDSVLVSAVGGIKTGHLAEEVLQSGIDV 366

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           V  GR   +N  ++      F+N L     +  ++D  F
Sbjct: 367 VRAGRWFQQNPGLVR----AFANELGVEVKMANQIDWSF 401


>gi|84686032|ref|ZP_01013928.1| Dihydroorotate dehydrogenase [Maritimibacter alkaliphilus HTCC2654]
 gi|84666125|gb|EAQ12599.1| Dihydroorotate dehydrogenase [Rhodobacterales bacterium HTCC2654]
          Length = 338

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/154 (18%), Positives = 55/154 (35%), Gaps = 14/154 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + + LN GCP     E   G+ +   P+ VG     + K   +P  VK    +
Sbjct: 20  RVGETGADGVELNFGCPHGMA-ERGMGSAVGQVPEYVGQITQWVKKHSDLPCIVKLTPNI 78

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV++ N + SI    ++ +        L          +  +  
Sbjct: 79  TDIRQPALAAKQGGADAVSMINTINSITSVNLDAMCPEPMIDGLGTHGGYCGPAVKPIAM 138

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP 208
           ++V E+ +  +   + I   GG+     A + + 
Sbjct: 139 NMVAEVARWEKTAGIPISAIGGISTWRDAAEFMA 172


>gi|312133782|ref|YP_004001121.1| pyrd3 [Bifidobacterium longum subsp. longum BBMN68]
 gi|291516554|emb|CBK70170.1| Dihydroorotate dehydrogenase [Bifidobacterium longum subsp. longum
           F8]
 gi|311773064|gb|ADQ02552.1| PyrD3 [Bifidobacterium longum subsp. longum BBMN68]
          Length = 375

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 73/230 (31%), Gaps = 41/230 (17%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +            A++V++ G   + +N  C
Sbjct: 154 WQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVMNTSC 213

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV-- 140
           P            L  NP +VG    A+ + +  IP+ VK      D    + +R+ V  
Sbjct: 214 P-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDALELMVRSTVGH 268

Query: 141 --------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--K 184
                         K +  +G   +    R       S      I     D+V  +   +
Sbjct: 269 GTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARLAAIR 323

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 324 EKLGLDFAINGVGGVVSPADYQAYRDAGADSVMSATGAMWDAELAHKIKA 373


>gi|317482975|ref|ZP_07941979.1| dihydroorotate dehydrogenase [Bifidobacterium sp. 12_1_47BFAA]
 gi|316915582|gb|EFV37000.1| dihydroorotate dehydrogenase [Bifidobacterium sp. 12_1_47BFAA]
          Length = 375

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 73/230 (31%), Gaps = 41/230 (17%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +            A++V++ G   + +N  C
Sbjct: 154 WQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVMNTSC 213

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV-- 140
           P            L  NP +VG    A+ + +  IP+ VK      D    + +R+ V  
Sbjct: 214 P-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDALELMVRSTVGH 268

Query: 141 --------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--K 184
                         K +  +G   +    R       S      I     D+V  +   +
Sbjct: 269 GTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARLAAIR 323

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 324 EKLGLDFAINGVGGVVSPADYQAYRDAGADSVMSATGAMWDAELAHKIKA 373


>gi|237735617|ref|ZP_04566098.1| NADH:flavin oxidoreductase [Mollicutes bacterium D7]
 gi|229381362|gb|EEO31453.1| NADH:flavin oxidoreductase [Coprobacillus sp. D7]
          Length = 646

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 63/184 (34%), Gaps = 22/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCIA 109
               AAK  ++ G++ I L   C          S  V++   ++G CL     IV +   
Sbjct: 149 DFGSAAKRAKEAGFDGIEL--HCAHGYLLAEFLSPFVNKRVDNYGGCLQNRVRIVAEIYL 206

Query: 110 AMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            M K +    P+ V+      V           L    ++ G +GI I        G   
Sbjct: 207 EMRKQVGDDFPIIVRLSGNEYVHGGRTEAETYELCTIFEELGFDGIHISNGSYASPGNRA 266

Query: 166 --KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYK 221
                     L+ +I  ++KK      I  N  + D   A  L  +   D + +GR +  
Sbjct: 267 VIAPMFTEHALNMEISAQVKKLVDLPVIVTNR-INDPQMADTLINMDKADFIGMGRGSLT 325

Query: 222 NSAM 225
           +  +
Sbjct: 326 DPDL 329


>gi|161522384|ref|YP_001585313.1| dihydropyrimidine dehydrogenase [Burkholderia multivorans ATCC
           17616]
 gi|189348740|ref|YP_001941936.1| dihydropyrimidine dehydrogenase [Burkholderia multivorans ATCC
           17616]
 gi|160345937|gb|ABX19021.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans ATCC 17616]
 gi|189338878|dbj|BAG47946.1| dihydroorotate oxidase [Burkholderia multivorans ATCC 17616]
          Length = 435

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPIPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISTWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|15595636|ref|NP_249130.1| dihydropyrimidine dehydrogenase [Pseudomonas aeruginosa PAO1]
 gi|9946297|gb|AAG03828.1|AE004481_4 probable oxidoreductase [Pseudomonas aeruginosa PAO1]
          Length = 425

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 60/173 (34%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 123 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKAHCSLPVIVKLTPNI 181

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI-------------LKGLSPKDNRK 170
            D      +R   ++  + G + +     I++  ++                        
Sbjct: 182 TD------IRQSARAAHRGGADAVSLINTINSITSVDLERMVALPVVGTQSTHGGYCGSA 235

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 236 VKPIALNMVAEIARDPQTRGLPICGIGGIGSWRDAAEFVALGCGAVQVCTAAM 288


>gi|85712439|ref|ZP_01043488.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Idiomarina baltica OS145]
 gi|85693717|gb|EAQ31666.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Idiomarina baltica OS145]
          Length = 676

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/177 (14%), Positives = 58/177 (32%), Gaps = 17/177 (9%)

Query: 64  EAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
             AK+ +  GY+ + +            CP        +G        +    +  + + 
Sbjct: 151 RCAKLAQKAGYDGVEIMGSEGYLINQFLCPRTNKRTDEWGGDFNGRSRLALAIVNRVREQ 210

Query: 115 LSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +     +  R+     V+D      +  L ++++K+GV    I+      +   P     
Sbjct: 211 VGKDFIIIFRLSMLDLVEDGHTLDEVIELGQALEKAGVT--IINTGIGWHEARVPTIVTS 268

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
           +P   +  + E  K++  + +     +     A  IL     D V + R    +  +
Sbjct: 269 VPRGAFAWITERVKQSLSVPVVAVNRINTPEIAEHILSSGQADMVSMARPLLADPEL 325


>gi|108804312|ref|YP_644249.1| dihydroorotate oxidase B, catalytic subunit [Rubrobacter
           xylanophilus DSM 9941]
 gi|108765555|gb|ABG04437.1| dihydroorotate oxidase B, catalytic subunit [Rubrobacter
           xylanophilus DSM 9941]
          Length = 304

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/219 (17%), Positives = 69/219 (31%), Gaps = 12/219 (5%)

Query: 26  MIVADAILRGDKKNILGF---STQEKPLALQIGGADISKLVE-AAKIVEDFGYNEINLNV 81
           M+ +  +     +  L          P+ + + G  + +      ++  D     I LN+
Sbjct: 66  MVNSIGLQNPGVEEFLRALGAWEVGVPVFVSVAGETVEEFALLCGRVAADGRAAAIELNL 125

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKC-RIGVDDQIPAVALRNL 139
            CP   V  G    C    P  V + +AA  +A   +P+  K    GV     A      
Sbjct: 126 SCP--NVERGGQVFC--AGPSAVEEVVAACRRAAPDVPLLAKLALEGVVQNALAAEAAGA 181

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
                 + V  + + AR   +          I  L    VY++        +G  G    
Sbjct: 182 DGLTVMNTVPALAVDARARRVLLRGGLSGPAIKPLALRAVYDVASAAEIPVVGCGGVCSG 241

Query: 200 MSQALKILPSVDGVMIGR-AAYKNSA-MLTTVDEYFSNP 236
              A  +L     V +G     ++ A +L   + Y    
Sbjct: 242 ADVAEFMLAGARAVQVGSAGFVRDPAEILAEFERYLREE 280


>gi|290975626|ref|XP_002670543.1| predicted protein [Naegleria gruberi]
 gi|284084103|gb|EFC37799.1| predicted protein [Naegleria gruberi]
          Length = 365

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/200 (19%), Positives = 70/200 (35%), Gaps = 23/200 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             +EAAK     G++ I ++            P + +    +G        ++   +  +
Sbjct: 163 DFIEAAKRAVKAGFDVIEIHGAHGYLIHSFMSPVSNLRTDMYGGSFENRTRLLLQIVDGV 222

Query: 112 CKALS--IP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              +   +P  V + C   +++   +     + + +K  GV+ I          G  P  
Sbjct: 223 RGVIPEEMPLFVRLSCEDYMEEGWTSDDTVKVSQILKDHGVDLIDCSTG-----GTKPIQ 277

Query: 168 NRK--IPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           N    +    Y + Y +  KE  D+  G  G LED   A K++     D V+IGRA   +
Sbjct: 278 NVHGLVVEPGYQVKYSVAIKEKVDILTGAVGKLEDPILANKVIEEKKADLVLIGRAMMGD 337

Query: 223 SAMLTTVDEYFSNPLTGSSP 242
                   +       G  P
Sbjct: 338 PYWALRAAKTLGYANAGIPP 357


>gi|254466887|ref|ZP_05080298.1| dihydroorotate dehydrogenase family protein [Rhodobacterales
           bacterium Y4I]
 gi|206687795|gb|EDZ48277.1| dihydroorotate dehydrogenase family protein [Rhodobacterales
           bacterium Y4I]
          Length = 434

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/166 (21%), Positives = 57/166 (34%), Gaps = 15/166 (9%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VE  G + I LN GCP     E   G+ +   P+ +        K  S PV VK    + 
Sbjct: 125 VEATGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIQMVTEWCKKYYSKPVIVKLTPNIT 183

Query: 129 D-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           D              AV+L N + SI    ++ +                   +  +  +
Sbjct: 184 DIRHPARAAHAGNADAVSLINTINSITSVNLDSMAPEPTIGGKGTHGGYCGPAVKPIALN 243

Query: 178 IVYEIKKEN--PDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 244 MVAEIARDAQTRGLPISAIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|126462585|ref|YP_001043699.1| dihydropyrimidine dehydrogenase [Rhodobacter sphaeroides ATCC
           17029]
 gi|221639626|ref|YP_002525888.1| dihydropyrimidine dehydrogenase [Rhodobacter sphaeroides KD131]
 gi|126104249|gb|ABN76927.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) [Rhodobacter sphaeroides ATCC
           17029]
 gi|221160407|gb|ACM01387.1| Dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase [Rhodobacter sphaeroides KD131]
          Length = 434

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 73/218 (33%), Gaps = 29/218 (13%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +     + K++         +   +   D          VED G + + LN G
Sbjct: 79  ELITDRPLEVNLREIKSVKRDYPDRALVVSLMVPCDEESWKAILAHVEDTGADGVELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G+ +   P+ +      + +   +P  VK    V D      +R   ++
Sbjct: 139 CPHGMA-ERGMGSAVGQVPEYIEMVTRWVKQHSRMPCIVKLTPNVTD------IRKPAEA 191

Query: 143 IKKSGVNGIWI--------------HARKAILKGLSPKDNR---KIPNLDYDIVYEIKK- 184
            ++ G + + +               A    + G           +  +  ++V EI + 
Sbjct: 192 ARRGGADAVSLINTINSITGVDIDSFAPMPTIDGKGTHGGYCGPAVKPIALNMVAEIARN 251

Query: 185 -ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
            E   L I   GG+     A++ +L     V +  AA 
Sbjct: 252 PETHGLPISGIGGVTTWRDAVEFMLLGAGNVQVCTAAM 289


>gi|220928537|ref|YP_002505446.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium cellulolyticum
           H10]
 gi|219998865|gb|ACL75466.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium cellulolyticum
           H10]
          Length = 329

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 67/180 (37%), Gaps = 28/180 (15%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA+ V+  G++ + +             P +      +G  ++    I    I A+ 
Sbjct: 149 FANAAERVKKAGFDGVEIHSAHGYLLSQFFSPISNKRSDEYGGNVLSRIKIHLQIINAVK 208

Query: 113 KALSIPVTVKCRIGVDD--------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           KA+    TV  R+G  D        +   +A        +K+GV+ + I           
Sbjct: 209 KAVGEDFTVFLRLGASDYMEGGITIEDSLIATGEF----EKAGVSALDISGGFCGYIKPD 264

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            K+        + +   IK E+  + + L GG+ D   A ++L     D + +GR+  K+
Sbjct: 265 AKEQGYF----WPLTKAIK-EHVSIPVILTGGITDAESAEQLLAGGKADLIGVGRSILKD 319


>gi|110668901|ref|YP_658712.1| tRNA-dihydrouridine synthase [Haloquadratum walsbyi DSM 16790]
 gi|109626648|emb|CAJ53115.1| tRNA-dihydrouridine synthase [Haloquadratum walsbyi DSM 16790]
          Length = 258

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/161 (19%), Positives = 57/161 (35%), Gaps = 25/161 (15%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-IVGDCIAAMCKALSI 117
              +  A +    +    + +N  C    +     G  L+ + +  + + I A     ++
Sbjct: 88  PEPVRVAGRHCAKYNA-ILEINAHCRQDEMCTVGAGETLLQDNESQLRELIKAGRAGGAM 146

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+VK R G+D     V L  + ++I  +G   I + A    +                 
Sbjct: 147 -VSVKVRAGIDG----VDLTAIARTIADAGGEIIHVDAMDTEVS---------------- 185

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
            + +I    P+LFI  N G+       +      D V IGR
Sbjct: 186 -IKQIATAAPELFIIANNGVRGHESVREYYGYGADAVSIGR 225


>gi|20808970|ref|NP_624141.1| NADH:flavin oxidoreductase [Thermoanaerobacter tengcongensis MB4]
 gi|20517635|gb|AAM25745.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Thermoanaerobacter tengcongensis MB4]
          Length = 640

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/181 (19%), Positives = 62/181 (34%), Gaps = 26/181 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V+AA      G + + +  G          P A   +  +G           + +  +  
Sbjct: 147 VDAAIRAYKAGADFLEIQFGHGYLIHQFLSPHANKRQDEYGGSFENRIRFGIEILEEIRS 206

Query: 114 AL-SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWI------HARKAILKGLS 164
            L   PV V+      V+D         LVK ++  GV  I +       A    ++ L 
Sbjct: 207 ELPGFPVIVRISAEEFVEDGWKLEDTIKLVKILEGKGVAAIDVSLGTMCEAAPITMQTLG 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            K       L +D   +IK+E  ++ +   G +     A +IL     D V +GR    +
Sbjct: 267 TKKG-----LSWDYAEKIKREV-NIPVIAVGRINSPDIAEEILSKGKADLVALGRPLVAD 320

Query: 223 S 223
            
Sbjct: 321 P 321


>gi|84499399|ref|ZP_00997687.1| putative FMN oxidoreductase [Oceanicola batsensis HTCC2597]
 gi|84392543|gb|EAQ04754.1| putative FMN oxidoreductase [Oceanicola batsensis HTCC2597]
          Length = 382

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/217 (17%), Positives = 76/217 (35%), Gaps = 16/217 (7%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V  A+   + G++ + +++           P A   E ++G  L        + + A
Sbjct: 163 EAFVTGAQRALEAGFDMVEIHMAHGYLLQSFLTPLANRREDAYGGSLENRMRYPLEVVRA 222

Query: 111 MCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  AL   +P+  +      +D          L K++K++GV+ +   +   +L G +  
Sbjct: 223 VRAALPDDVPLFTRISATDWIDGGWEPGDSVALAKALKQAGVDVVDCSSGGNMLHG-ATN 281

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
            N            ++ +E   +     G +     A ++L     D + IGR +  N  
Sbjct: 282 SNLARGPAYQAQFAKLLREETGIMTQAVGLIRTPDLAEQLLQEGQADLIAIGRQSLFNPY 341

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
                 E    P   + P         W++  ASM +
Sbjct: 342 WAHHAAERLGVPDWEAWPAPYAWWLSRWKRGLASMDE 378


>gi|254486347|ref|ZP_05099552.1| dihydroorotate dehydrogenase family protein [Roseobacter sp.
           GAI101]
 gi|214043216|gb|EEB83854.1| dihydroorotate dehydrogenase family protein [Roseobacter sp.
           GAI101]
          Length = 425

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/173 (17%), Positives = 60/173 (34%), Gaps = 33/173 (19%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + + LN GCP     E   GA +   P+ +      +  +  +PV VK    +
Sbjct: 115 LVEETGADGVELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWVKASTRMPVIVKLTPNI 173

Query: 128 DDQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNR---K 170
            D      +R   ++  + G +               + + A +  + G           
Sbjct: 174 AD------IRKPAEAALRGGADAVSLINTINSITSVDLDLFAPEPTIDGKGAHGGYCGPA 227

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKIL-------PSVDGVM 214
           +  +  ++V EI ++     + I   GG+     A + +            VM
Sbjct: 228 VKPIALNMVAEIARDPGLSQVPISGIGGVTTWRDAAEFMALGAGNVQVCTAVM 280


>gi|147676602|ref|YP_001210817.1| hypothetical protein PTH_0267 [Pelotomaculum thermopropionicum SI]
 gi|146272699|dbj|BAF58448.1| hypothetical protein [Pelotomaculum thermopropionicum SI]
          Length = 641

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/139 (17%), Positives = 51/139 (36%), Gaps = 7/139 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSI--PVTVKC--RIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L+       + I ++ +      PVT++      V D       R   + ++++G 
Sbjct: 189 YGGDLLGRMRFPVEIIRSIRRHAGRDYPVTIRIAGDERVSDGRTIEETRVAARLLEEAGY 248

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +                  P L+ +   +IKK    + +   G + D   A  IL 
Sbjct: 249 DALHVTTATTATMHYIAPPYYLPPALNVEYAEKIKK-CVSIPVITTGCIYDPHFAESILA 307

Query: 209 S--VDGVMIGRAAYKNSAM 225
               D V +GRA+  +  +
Sbjct: 308 EGRADLVGMGRASIADPEL 326


>gi|77463755|ref|YP_353259.1| dihydropyrimidine dehydrogenase [Rhodobacter sphaeroides 2.4.1]
 gi|77388173|gb|ABA79358.1| dihydroorotate oxidase B, catalytic subunit / dihydropyrimidine
           dehydrogenase (NADP+) / dihydrouracil dehydrogenase
           (NAD+) [Rhodobacter sphaeroides 2.4.1]
          Length = 434

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 73/218 (33%), Gaps = 29/218 (13%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +     + K++         +   +   D          VED G + + LN G
Sbjct: 79  ELITDRPLEVNLREIKSVKRDYPDRALVVSLMVPCDEESWKAILAHVEDTGADGVELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G+ +   P+ +      + +   +P  VK    V D      +R   ++
Sbjct: 139 CPHGMA-ERGMGSAVGQVPEYIEMVTRWVKQHSQMPCIVKLTPNVTD------IRKPAEA 191

Query: 143 IKKSGVNGIWI--------------HARKAILKGLSPKDNR---KIPNLDYDIVYEIKK- 184
            ++ G + + +               A    + G           +  +  ++V EI + 
Sbjct: 192 ARRGGADAVSLINTINSITGVDIDSFAPMPTIDGKGTHGGYCGPAVKPIALNMVAEIARN 251

Query: 185 -ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
            E   L I   GG+     A++ +L     V +  AA 
Sbjct: 252 PETHGLPISGIGGVTTWRDAVEFMLLGAGNVQVCTAAM 289


>gi|297170976|gb|ADI21991.1| dihydroorotate dehydrogenase [uncultured myxobacterium
           HF0200_01L06]
          Length = 328

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 67/186 (36%), Gaps = 11/186 (5%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             E  +   + G +IS+    A+ + E+     I +N  CP  +     FG     +P +
Sbjct: 112 DDEVTIVASVFGHEISEYAAVARRLSEEPRIAAIEVNASCPHVKSGGMEFG----QDPGV 167

Query: 104 VGDCIAAMCKALSIPVTVK-----CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +   + A+  A S PV VK      RI    ++      + V  I       + I  R+ 
Sbjct: 168 LASLVGAVRAASSRPVLVKLSPNVTRIVEMAKVCQEEGADAVSLINTVQALDVDIENRRP 227

Query: 159 ILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           +L   L       I  +   +V+++ +       G+ G          +L     V +G 
Sbjct: 228 LLSNVLGGLSGPAIRPIALRMVWQVSQALSIPICGIGGIGTAEDAVKFLLCGASAVQVGT 287

Query: 218 AAYKNS 223
           A Y N 
Sbjct: 288 ANYLNP 293


>gi|313125876|ref|YP_004036146.1| tRNA-dihydrouridine synthase [Halogeometricum borinquense DSM
           11551]
 gi|312292241|gb|ADQ66701.1| tRNA-dihydrouridine synthase [Halogeometricum borinquense DSM
           11551]
          Length = 257

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 66/187 (35%), Gaps = 27/187 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA+I  D     + +N  C    +     G  L+ + D + + +AA     +  V+VK 
Sbjct: 94  RAARICADRNA-ILEVNAHCRQDELCAVGCGETLLRDTDRLCEYVAAAADEGAT-VSVKV 151

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R     +I  V+L      +  +G + + + A  +                  +++ ++ 
Sbjct: 152 RA----EIEGVSLETTADRVADAGASILHVDAMDSE-----------------EVIADVS 190

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                LF+  N  +   +   + L    D V +GR +  +  +L  V     +     + 
Sbjct: 191 D--SSLFVVANNEVRGEASVREYLGYGADAVSVGRPS-TDPRVLRRVRAAVDDWFDDETG 247

Query: 243 IKTRVDK 249
               + +
Sbjct: 248 ASGEISE 254


>gi|268591476|ref|ZP_06125697.1| anthraniloyl-CoA monooxygenase [Providencia rettgeri DSM 1131]
 gi|291313130|gb|EFE53583.1| anthraniloyl-CoA monooxygenase [Providencia rettgeri DSM 1131]
          Length = 765

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/200 (17%), Positives = 67/200 (33%), Gaps = 22/200 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AAK  E  G++ + L  G          P       ++G  L          I+A
Sbjct: 560 DQFVAAAKRAETAGFDWLELQAGHGYLLSSFISPLTNQRTDNYGGALENRLRFPLAIISA 619

Query: 111 MCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKD 167
           + +  S P++V+      VD          + +++K++G + I       +  +      
Sbjct: 620 VRQVWSKPLSVRISSTDWVDGGTTVDDAVEIGRAMKQAGADMIDCSSGEVSPQQQPVYGR 679

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-A 224
             + P  D      I+ E   + +   G + D  Q   I+ +   D   + R    +   
Sbjct: 680 MYQTPMAD-----RIRNEAG-IPVIAVGAITDADQVNSIIAAGRADLCALSRPLLSDPAW 733

Query: 225 MLTTVDEYFSNPLTGSSPIK 244
           +L     Y        +P +
Sbjct: 734 VLHECARY-GWETRWPAPYE 752


>gi|325525301|gb|EGD03152.1| dihydropyrimidine dehydrogenase subunit B [Burkholderia sp. TJI49]
          Length = 438

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 62/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDHMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+ +   A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISNWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|306823723|ref|ZP_07457097.1| possible dihydroorotate oxidase [Bifidobacterium dentium ATCC
           27679]
 gi|309801864|ref|ZP_07695981.1| dihydroorotate oxidase [Bifidobacterium dentium JCVIHMP022]
 gi|304552721|gb|EFM40634.1| possible dihydroorotate oxidase [Bifidobacterium dentium ATCC
           27679]
 gi|308221516|gb|EFO77811.1| dihydroorotate oxidase [Bifidobacterium dentium JCVIHMP022]
          Length = 375

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/223 (17%), Positives = 68/223 (30%), Gaps = 31/223 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D K  +  +   + L     G+ +  +         V  A++V + G   + +N  C
Sbjct: 154 WQPDMKKAIEAAGSGQLLVPSFQGSRVDGMDQDDYIADHVTTARLVCETGAGLMEMNTSC 213

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P            L  +P +VG    A+   +   P+ VK     +D    + ++     
Sbjct: 214 P-----NEGHNRLLCHDPHLVGRITEAVKNEIGDRPLVVKLAYIPNDADLEIMVKETAAH 268

Query: 143 IKKSGVNGI-WIHARKAILKG----------LSPKDNRKIPNLDYDIVYEIK----KENP 187
               G + I  I A+     G           S      I     D+V  +     K   
Sbjct: 269 GTVQGFSTINTISAKLVDANGNQALPGVGRDRSGVCGNAIRGAGLDMVGRLHAIREKLGL 328

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           D  I   GG+              + VM    A  N+ +   +
Sbjct: 329 DFTIVGVGGVVRPEDYRAYREAGANAVMSATGAMWNANLARDI 371


>gi|15920268|ref|NP_375937.1| oxidoreductase [Sulfolobus tokodaii str. 7]
 gi|15621050|dbj|BAB65046.1| 546aa long hypothetical oxidoreductase [Sulfolobus tokodaii str. 7]
          Length = 546

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/191 (18%), Positives = 65/191 (34%), Gaps = 30/191 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---------LNPDI------- 103
              V+A++  E  G++ I L                 L+            D        
Sbjct: 141 MDFVKASERAEKSGFDGIEL-----------HGAHGYLIAQFLSPATNKREDKYKDGVIF 189

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILKG 162
           + + +  + + +SIPV    RI V +  P      LV  I K   N + +IH        
Sbjct: 190 LEELLKEIRRVVSIPVG--MRISVTEFDPQGLTPELVAKIVKRVENLLDYIHLSAGRDGP 247

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           L    +       Y    ++ ++  +L + L G +  +  A K+L   D V++GR    +
Sbjct: 248 LGGSSSFYYKRPSYVDEAKVVRKVTNLPLLLVGSVSTVEDAEKVLEVADAVVLGRQILAD 307

Query: 223 SAMLTTVDEYF 233
              +  V    
Sbjct: 308 PDWVIKVKNNL 318


>gi|322690021|ref|YP_004209755.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis 157F]
 gi|320461357|dbj|BAJ71977.1| putative dihydroorotate dehydrogenase [Bifidobacterium longum
           subsp. infantis 157F]
          Length = 371

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 73/230 (31%), Gaps = 41/230 (17%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +            A++V++ G   + +N  C
Sbjct: 150 WQPDMRVAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVMNTSC 209

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV-- 140
           P            L  NP +VG    A+ + +  IP+ VK      D    + +R+ V  
Sbjct: 210 P-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDALELMVRSTVGH 264

Query: 141 --------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--K 184
                         K +  +G   +    R       S      I     D+V  +   +
Sbjct: 265 GTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARLAAIR 319

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           E   L   +N  GG+   +          D VM    A  ++ +   +  
Sbjct: 320 EKLGLDFAINGVGGVVSPADYQAYRDAGADSVMSATGAMWDAELAHKIKA 369


>gi|307595349|ref|YP_003901666.1| NADH:flavin oxidoreductase/NADH oxidase [Vulcanisaeta distributa
           DSM 14429]
 gi|307550550|gb|ADN50615.1| NADH:flavin oxidoreductase/NADH oxidase [Vulcanisaeta distributa
           DSM 14429]
          Length = 555

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/172 (16%), Positives = 65/172 (37%), Gaps = 14/172 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI-------VGDCIAAMCK 113
             V+AA   E  G++ I L+       +        +    D        + + +  +  
Sbjct: 145 DFVKAAIRAERSGFDGIELHGA--HGYLIAQFLSPAVNRRSDRYRDGVIFLEELLKEVRS 202

Query: 114 ALSIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +SIP+ ++  +   D        +  ++K ++   ++ + + A +    G S     K 
Sbjct: 203 VVSIPIGLRISVTEFDNEGLTPEMVAKIIKRVEGL-LDYVHLSAGRDGPLGSSMPFYYKR 261

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS 223
           P+   +   ++ +    L + L G +     A+K+L   D V+IGR    + 
Sbjct: 262 PSFIDE--AKVVRSTTKLPLFLVGSISTPEDAVKVLEVADAVVIGRQLLADP 311


>gi|332558611|ref|ZP_08412933.1| dihydropyrimidine dehydrogenase subunit B [Rhodobacter sphaeroides
           WS8N]
 gi|332276323|gb|EGJ21638.1| dihydropyrimidine dehydrogenase subunit B [Rhodobacter sphaeroides
           WS8N]
          Length = 434

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 73/218 (33%), Gaps = 29/218 (13%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +     + K++         +   +   D          VED G + + LN G
Sbjct: 79  ELITDRPLEVNLREIKSVKRDYPDRALVVSLMVPCDEESWKAILAHVEDTGADGVELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
           CP     E   G+ +   P+ +      + +   +P  VK    V D      +R   ++
Sbjct: 139 CPHGMA-ERGMGSAVGQVPEYIEMVTRWVKQHSRMPCIVKLTPNVTD------IRKPAEA 191

Query: 143 IKKSGVNGIWI--------------HARKAILKGLSPKDNR---KIPNLDYDIVYEIKK- 184
            ++ G + + +               A    + G           +  +  ++V EI + 
Sbjct: 192 ARRGGADAVSLINTINSITGVDIDSFAPMPTIDGKGTHGGYCGPAVKPIALNMVAEIARN 251

Query: 185 -ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
            E   L I   GG+     A++ +L     V +  AA 
Sbjct: 252 PETHGLPISGIGGVTTWRDAVEFMLLGAGNVQVCTAAM 289


>gi|300691785|ref|YP_003752780.1| dihydroorotate dehydrogenase, FMN-linked, 4Fe-4S ferredoxin-type
           protein [Ralstonia solanacearum PSI07]
 gi|299078845|emb|CBJ51506.1| putative dihydroorotate dehydrogenase, FMN-linked, 4Fe-4S
           ferredoxin-type protein [Ralstonia solanacearum PSI07]
          Length = 435

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 59/168 (35%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   G+ +   P+ V      +     +P  VK    +
Sbjct: 122 MVEDTGADAVELNFGCPHGMS-ERGMGSAVGQVPEYVEMVTRWVKAGTRLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 TDIRLGSRAAYKGGADGVSLINTINSIVAVDLDQMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKEN--PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P L I   GG+     A + ++     V +  AA  
Sbjct: 241 NMVAEIARDAQTPGLPISGIGGISTWRDAAEFMVLGAGSVQVCTAAMH 288


>gi|221215696|ref|ZP_03588657.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans CGD1]
 gi|221164398|gb|EED96883.1| dihydroorotate dehydrogenase family protein [Burkholderia
           multivorans CGD1]
          Length = 435

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPIPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI +  E P+L I   GG+     A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPETPNLPISGIGGISTWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|308210755|dbj|BAJ22678.1| daidzein reductase [Lactococcus garvieae]
 gi|322229362|dbj|BAJ72750.1| daidzein reductase [Lactococcus garvieae]
          Length = 644

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 61/181 (33%), Gaps = 23/181 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAM 111
              + A   +  G+  ++++  C         P        +G  L      + + I  +
Sbjct: 151 YFGDCALRAQTAGFEIVDVHAACGVLLSNFLSPRNNTRNDMYGGSLHNRARFLLEVIRDI 210

Query: 112 CKAL-SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGLS 164
            K   ++P+ ++        D I       + K  + +G + I I    HA      GL 
Sbjct: 211 KKKCPNLPLAIRLSGIDFEPDGITIEETCEVAKMCEAAGADAINITWGSHAEVINAAGLL 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            K        ++    ++ K+   +   L GG+       K+L     D + IG+ A  +
Sbjct: 271 SKHG-----ANHVEAAKMIKDAVSIPTMLCGGIYSPEIGEKLLEDGVCDFIGIGKPALAD 325

Query: 223 S 223
            
Sbjct: 326 P 326


>gi|88799395|ref|ZP_01114973.1| dihydropyrimidine dehydrogenase [Reinekea sp. MED297]
 gi|88777934|gb|EAR09131.1| dihydropyrimidine dehydrogenase [Reinekea sp. MED297]
          Length = 424

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 61/175 (34%), Gaps = 27/175 (15%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            K VE  G + + LN GCP     E   GA +   P+ V        +   +PV VK   
Sbjct: 120 VKEVEKTGADGLELNFGCPHGM-PERGMGAAVGQVPEYVEQVTRWCKQYSKLPVIVKLTP 178

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWI--------------HARKAILKGLSPKDNR-- 169
            + D   +       ++  + G + + +                 + I+ G S       
Sbjct: 179 NITDIRYS------ARAANRGGADAVSLINTINSITGIDLDQMTARPIVDGKSTHGGYCG 232

Query: 170 -KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
             +  +  ++V EI +  E   L I   GG+ +   A + +      V +  AA 
Sbjct: 233 PAVKPIALNMVSEIARDPETQRLPISGIGGISNWRDAAEFISLGAGCVQVCTAAM 287


>gi|299139109|ref|ZP_07032285.1| dihydroorotate oxidase [Acidobacterium sp. MP5ACTX8]
 gi|298598789|gb|EFI54951.1| dihydroorotate oxidase [Acidobacterium sp. MP5ACTX8]
          Length = 355

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 59/195 (30%), Gaps = 36/195 (18%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML-NPDIVGDCIAAMCKAL-SIP 118
                A+++E+ G   I +N+ CP          A L+  +     + +  +   L S+P
Sbjct: 171 DFALGARLLEETGVKIIEVNLSCP------NEGTAELLCFDVQRSREVVETIKNELGSVP 224

Query: 119 VTVKCRIGVDDQIPAVALRNL--------------VKSIKKSGVNGIWIHARKAILKGLS 164
           + VK     D+      ++ L               + + K+G   +    R       S
Sbjct: 225 LVVKLAYFADNARLETLIKELGPIVDGIAAINTISAEIVDKAGNQALPGEGRL-----RS 279

Query: 165 PKDNRKIPNLDYDIVYEIKKEN-------PDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
                 I     D+   +             + +G  G   D  +  K     D VM   
Sbjct: 280 GVCGHSIKWAGVDMAGRLAGLREKLGLKYEIVGVGGAGSAADYDEYRK--AGADVVMSAT 337

Query: 218 AAYKNSAMLTTVDEY 232
           AA  N  +   +   
Sbjct: 338 AAMWNPLLAQEIKRA 352


>gi|209550605|ref|YP_002282522.1| dihydropyrimidine dehydrogenase [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536361|gb|ACI56296.1| dihydroorotate dehydrogenase family protein [Rhizobium
           leguminosarum bv. trifolii WSM2304]
          Length = 437

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 55/153 (35%), Gaps = 14/153 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + + LN GCP     E   G+ +   P+ +   +    +   +P+  K    +
Sbjct: 124 LVEETGADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPIITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++    +                +  +  
Sbjct: 183 TDVRRPARAAKAGGTDAVSLINTINSIVSVDLDNFAPNPTVGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           ++V EI +  E   L I   GG+     A + L
Sbjct: 243 NMVAEIARDPETYGLPISGIGGITTWRDAAEFL 275


>gi|167590078|ref|ZP_02382466.1| dihydroorotate dehydrogenase family protein [Burkholderia ubonensis
           Bu]
          Length = 435

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   GA +   P+ V      + +   +P  VK    +
Sbjct: 122 LVEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKEGTKLPCLVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D               V+L N + SI    ++ +                   +  +  
Sbjct: 181 SDIRMGSRAAYKGGADGVSLINTINSIVAVDLDQMAPIPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           ++V EI ++   P+L I   GG+     A + I+     V +  AA  
Sbjct: 241 NMVAEIARDPQTPNLPISGIGGISTWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|328874309|gb|EGG22675.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium fasciculatum]
          Length = 578

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/183 (16%), Positives = 63/183 (34%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
            K V+AAK  E  G++ I ++       +               +G  L      + + +
Sbjct: 368 DKFVDAAKRAEQAGFDVIEIHAA--HGYLISEFLSGTSNKRTDDYGGSLENRSRFLYEIV 425

Query: 109 AAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGL 163
             + K       + ++    +  +          L K +K+ GV+ +          + +
Sbjct: 426 RKIRKVYDGVLFVRISCSEWVQEEGAFTPEDSIPLAKKLKELGVDLLDCSSGGNNPRQHV 485

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
             K   ++P  D      +KK  P+      G +E   +A ++L     D VM+ R   +
Sbjct: 486 VAKPLYQVPFADL-----VKKNVPNFLTAAVGLIETAEEAEQVLQQQSADLVMLARPFLR 540

Query: 222 NSA 224
           +  
Sbjct: 541 DPF 543


>gi|39996854|ref|NP_952805.1| dihydroorotate dehydrogenase 1B [Geobacter sulfurreducens PCA]
 gi|81832035|sp|Q74CB9|PYRD_GEOSL RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|39983742|gb|AAR35132.1| dihydroorotate dehydrogenase [Geobacter sulfurreducens PCA]
 gi|298505868|gb|ADI84591.1| dihydroorotate dehydrogenase [Geobacter sulfurreducens KN400]
          Length = 305

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 74/199 (37%), Gaps = 15/199 (7%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ +   G  + +  E A+ ++       + +N+ CP    +    G     +P     
Sbjct: 96  TPVIVNFFGNTLEEYAELAERLDLIPEVAAVEINISCP----NVKHGGIVFGTDPKAAYS 151

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRNLVKSIKKSGVNGIWIHARKAILK 161
            + A+ +A   PV VK    V D +      A A  + +  I       I +  R+ IL 
Sbjct: 152 VVKAVREATIKPVIVKLSPNVTDIVEMAWACADAEADALSLINTLTGMAIDLDKRRPILA 211

Query: 162 GLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
            ++       +  +   +V+++ +      IG+ G +  +     +L     V +G A +
Sbjct: 212 NVTGGLSGPAVKPIALRMVWQVARAVKIPVIGIGGIMTGIDALEFMLAGATAVQVGTANF 271

Query: 221 KNSA----MLTTVDEYFSN 235
            +      +   ++ Y ++
Sbjct: 272 LDPGAAGRIAAEMERYLAD 290


>gi|186476273|ref|YP_001857743.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phymatum
           STM815]
 gi|184192732|gb|ACC70697.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phymatum
           STM815]
          Length = 686

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/176 (12%), Positives = 56/176 (31%), Gaps = 17/176 (9%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              A++ +  GY+ + +            CP       ++G  L     +  + + A+  
Sbjct: 145 ARCARLAQRAGYDGVEIMGSEGYLLNQFLCPRTNRRNDAYGGTLDNRMRLAREIVEAVRA 204

Query: 114 ALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A      V  R+ + D             + ++++ +GV     +      +   P    
Sbjct: 205 ACGERFIVVYRLSLIDLVEGGNTWDETVQVARALEAAGVTMF--NTGIGWHEARVPTIVT 262

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNS 223
            +P   +  +    K    + + ++  +     A ++L    G  V + R    + 
Sbjct: 263 SVPRAAFAPLTARLKTVVKVPVIVSNRINTPEVAEELLAQGAGDLVSMARPLLADP 318


>gi|89067347|ref|ZP_01154860.1| dihydropyrimidine dehydrogenase [Oceanicola granulosus HTCC2516]
 gi|89046916|gb|EAR52970.1| dihydropyrimidine dehydrogenase [Oceanicola granulosus HTCC2516]
          Length = 434

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 55/167 (32%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   G+ +   P+ +   +    +    PV VK    +
Sbjct: 124 RVAETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYYDRPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPATAAKNGGADAVSLINTINSITGVDLDNFAPMPTIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARNPETRGLPISGIGGITTWRDAAEFMALGCGNVQVCTAAM 289


>gi|260881619|ref|ZP_05404854.2| oxidoreductase, FAD/FMN-binding [Mitsuokella multacida DSM 20544]
 gi|260847994|gb|EEX68001.1| oxidoreductase, FAD/FMN-binding [Mitsuokella multacida DSM 20544]
          Length = 349

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 65/184 (35%), Gaps = 20/184 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +   AA+  +  GY+ + +             P     E ++G  +     I  + I A
Sbjct: 167 EQFARAAERAKTAGYDGVEIHSAHAYLLNQFYSPLTNHREDNYGGNIDNRLRIHREVIRA 226

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+     +  R+G  D     ++        K +  +G++ + I            +
Sbjct: 227 VRDAVGKEFIISLRLGGCDYSEGGSVIEDSVYASKVLADAGIDMLNITGGMCRY----TR 282

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                P    D+   IKK    + + L GG++ +  A  +L   + D + +GR   KN  
Sbjct: 283 KGHNEPGYFQDMSSAIKKAV-SIPVMLTGGVKTLEDAETLLKNEAADLIGVGREIMKNPY 341

Query: 225 MLTT 228
            L  
Sbjct: 342 WLNE 345


>gi|254452317|ref|ZP_05065754.1| dihydroorotate dehydrogenase family protein [Octadecabacter
           antarcticus 238]
 gi|198266723|gb|EDY90993.1| dihydroorotate dehydrogenase family protein [Octadecabacter
           antarcticus 238]
          Length = 434

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + I LN GCP     E   G+ +   P+ +        +  S PV VK    +
Sbjct: 124 LVEDTGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIEMVTRWCKQYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPAAAAMRGGADAVSLINTINSITSVNLDSMSPEPSIDGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEISRFEETKGLPISGIGGVTTWRDAAEFITLGCGNVQVCTAAM 289


>gi|260434049|ref|ZP_05788020.1| dihydroorotate dehydrogenase family protein [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260417877|gb|EEX11136.1| dihydroorotate dehydrogenase family protein [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 434

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   G+ +   PD +        K    PV VK    +
Sbjct: 124 RVAETGADGIELNFGCPHGMS-ERGMGSAVGQVPDYIEMVTRWCKKYYDRPVIVKLTPNI 182

Query: 128 DD-QIPAVALRN-------LVKSIKKSGVNGIWIHARKAILKGLSPKDNR---KIPNLDY 176
            D + PA A RN       L+ +I       +   + +  + G           +  +  
Sbjct: 183 TDIRKPAAAARNGGADAVSLINTINSITSVNLDTFSPEPSIDGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +      L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARAEATQGLPISGIGGVTTWRDAAEFMALGCGTVQVCTAAM 289


>gi|126741278|ref|ZP_01756957.1| dihydropyrimidine dehydrogenase [Roseobacter sp. SK209-2-6]
 gi|126717683|gb|EBA14406.1| dihydropyrimidine dehydrogenase [Roseobacter sp. SK209-2-6]
          Length = 404

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 86/254 (33%), Gaps = 19/254 (7%)

Query: 25  EMIVADAILRGDKK-NILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVG 82
           E+I   ++    ++   +     ++ + + I      +  +A    VE  G + I LN G
Sbjct: 79  ELITDRSLETNLEEITRVKKDYPDRAVIVSIMVPCEEEAWKAILPKVEATGADGIELNFG 138

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----------QI 131
           CP     E   G+ +   P+ +        K  S PV VK    + D             
Sbjct: 139 CPHGMA-ERGMGSAVGQVPEYIQMVTEWCKKYYSKPVIVKLTPNITDVRFPARAAKAGGG 197

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDL 189
            AV+L N + SI    ++ +                   +  +  ++V EI +  +   L
Sbjct: 198 DAVSLINTINSIVSVDLDSMAPEPTVGGKGTHGGYCGPAVKPIALNMVAEIARCPQTHGL 257

Query: 190 FIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
            I   GG+     A + ++     V +  AA         V E  S              
Sbjct: 258 PISAIGGVTTWKDAAEFMVMGAGNVQVCTAAMT--YGFNVVKEMISGLSNWMDEKGYTST 315

Query: 249 KDFWRKISASMTDY 262
           +DF  +   ++TD+
Sbjct: 316 QDFIGQAVPNVTDW 329


>gi|254478193|ref|ZP_05091575.1| oxidoreductase, FAD/FMN-binding family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214035922|gb|EEB76614.1| oxidoreductase, FAD/FMN-binding family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 640

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/181 (19%), Positives = 62/181 (34%), Gaps = 26/181 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V+AA      G + + +  G          P     +  +G           + +  +  
Sbjct: 147 VDAAIRAYKAGADFLEIQFGHGYLIHQFLSPHTNKRQDEYGGSFENRIRFGIEILEEIRS 206

Query: 114 AL-SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWI------HARKAILKGLS 164
            L   PV V+      V+D         LVK +++ GV  I +       A    ++ L 
Sbjct: 207 ELPGFPVIVRISAEEFVEDGWKLEDTIKLVKILEEKGVAAIDVSLGTMCEAAPITMQTLG 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            K       L +D   +IK+E  ++ +   G +     A +IL     D V +GR    +
Sbjct: 267 TKKG-----LSWDYAEKIKREV-NIPVIAVGRINSPDIAEEILSKGKADLVALGRPLVAD 320

Query: 223 S 223
            
Sbjct: 321 P 321


>gi|306842448|ref|ZP_07475099.1| dihydroorotate dehydrogenase family protein [Brucella sp. BO2]
 gi|306287304|gb|EFM58784.1| dihydroorotate dehydrogenase family protein [Brucella sp. BO2]
          Length = 436

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 61/167 (36%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPMPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +  S   V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIGGITTWRDAAEFIALSCGTVQVCTAAM 289


>gi|167757303|ref|ZP_02429430.1| hypothetical protein CLORAM_02853 [Clostridium ramosum DSM 1402]
 gi|167703478|gb|EDS18057.1| hypothetical protein CLORAM_02853 [Clostridium ramosum DSM 1402]
          Length = 646

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 63/184 (34%), Gaps = 22/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCIA 109
               AAK  ++ G++ I L   C          S  V++   ++G CL     IV +   
Sbjct: 149 DFGSAAKRAKEAGFDGIEL--HCAHGYLLAEFLSPFVNKRVDNYGGCLQNRVRIVAEIYL 206

Query: 110 AMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            M K +    P+ V+      V           L    ++ G +GI I        G   
Sbjct: 207 EMRKQVGDDFPIIVRLSGNEYVHGGRTEAETYELCMIFEELGFDGIHISNGSYASPGNRA 266

Query: 166 --KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILPSVDGVMIGRAAYK 221
                     L+ +I  ++KK      I  N  + D   A  L  +   D + +GR +  
Sbjct: 267 VIAPMFTEHALNMEISAQVKKLVDLPVIVTNR-INDPQMADTLINMDKADFIGMGRGSLT 325

Query: 222 NSAM 225
           +  +
Sbjct: 326 DPDL 329


>gi|163735778|ref|ZP_02143207.1| dihydropyrimidine dehydrogenase [Roseobacter litoralis Och 149]
 gi|161390864|gb|EDQ15204.1| dihydropyrimidine dehydrogenase [Roseobacter litoralis Och 149]
          Length = 434

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   GA +   P+ +        +  S PV VK    +
Sbjct: 124 KVEATGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 183 TDVRKPAAAAKRGGADAVSLINTINSIVSVDLDTMSPHPSIDGKGTHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E   + I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARDAETRGMPISGIGGVTTWRDAAEYITMGCGNVQVCTAAM 289


>gi|21674415|ref|NP_662480.1| dihydroorotate dehydrogenase [Chlorobium tepidum TLS]
 gi|21647598|gb|AAM72822.1| dihydroorotate dehydrogenase [Chlorobium tepidum TLS]
          Length = 305

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 36/216 (16%), Positives = 81/216 (37%), Gaps = 37/216 (17%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + I G  I    +  + ++   G     LN+ CP    +       + ++PD   
Sbjct: 95  DTQVIVNIAGKSIDDYCQVVERLDTVEGIAAYELNLSCP----NVKGECMIMGVSPDATR 150

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------H 154
           + ++ + K     + VK    V       ++  +  + +++G + + +            
Sbjct: 151 EIVSTLRKQTRRHLMVKLTPNV------TSISAIALAAEEAGADSVSLINTVVGMAVDYR 204

Query: 155 ARKAILK----GLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
            RK +LK    GLS    + I     +++   +K     + I   GG+   S A++ +L 
Sbjct: 205 KRKPLLKNVTGGLSGPAIKPIALAKVWEVSKAVK-----IPIVGMGGIASFSDAMEFLLV 259

Query: 209 SVDGVMIGRAAYKNSA----MLTTVDEYFSNPLTGS 240
               + IG   +        +   +D++FS P   +
Sbjct: 260 GASAIQIGTMNFVYPDIGEKIAVAIDKFFSQPDAPA 295


>gi|119025200|ref|YP_909045.1| hypothetical protein BAD_0182 [Bifidobacterium adolescentis ATCC
           15703]
 gi|118764784|dbj|BAF38963.1| hypothetical protein [Bifidobacterium adolescentis ATCC 15703]
          Length = 380

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 69/228 (30%), Gaps = 31/228 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D K  +  +   + L     G+ +  +         V  A +V + G   + +N  C
Sbjct: 158 WQPDMKKAIAAAGDGQLLVPSFQGSRVDGMDRKAYIADHVTTAHLVTETGAGLMEMNTSC 217

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P            L  +P +VG+   A+   +   P+ VK     +D      +R  V  
Sbjct: 218 P-----NEGHNRLLCHDPHLVGEITEAVKNEIGDRPLIVKLAYIPNDTDLETMVRETVGH 272

Query: 143 IKKSGVNGI-WIHARKAILKG----------LSPKDNRKIPNLDYDIVYEIK----KENP 187
               G + I  I AR     G           S      I     D+V  +     K   
Sbjct: 273 GTVQGFSTINTISARLVDANGNQALPGAGRDRSGVCGNAIRGAGLDMVGRLAAIREKLGF 332

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D  I   GG+              + VM    A  ++ +   + E   
Sbjct: 333 DFAIVGVGGVIRPDDYKAYREAGANAVMSATGAMWDANLAREIKETLR 380


>gi|149919740|ref|ZP_01908217.1| dihydroorotate dehydrogenase family protein [Plesiocystis pacifica
           SIR-1]
 gi|149819347|gb|EDM78778.1| dihydroorotate dehydrogenase family protein [Plesiocystis pacifica
           SIR-1]
          Length = 366

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 29/150 (19%), Positives = 53/150 (35%), Gaps = 18/150 (12%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  + V+  G +   +N+ CP   + E   GA +  +P+IV + +  + +  +IPV  K 
Sbjct: 122 EMVERVQATGVDAFEMNLSCPHG-LPERRMGAAMGGDPEIVREVVGWVKEVSTIPVWAKM 180

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHARKAILKGLSP--KDNR 169
              V D     A      +    G++ I             +     +    +P      
Sbjct: 181 TPNVGD---VTASPKAAVAAGADGISAINTILSVIGVDLDTLKPMPTVEGYTTPGGYSGM 237

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
               +    V EI +  P+  I   GG+  
Sbjct: 238 AARPIALRHVMEIARALPETTISGMGGIYS 267


>gi|301775699|ref|XP_002923270.1| PREDICTED: tRNA-dihydrouridine synthase 2-like [Ailuropoda
           melanoleuca]
          Length = 287

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 53/180 (29%), Gaps = 56/180 (31%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
            GA L+ +PD +    A   KA  I                        +I  +G     
Sbjct: 1   MGAALLSDPDKIEKARATRNKAPPIK----------------------AAIICAGCC--- 35

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG----------GLEDMSQ 202
                 +      ++ R    +  + +  I  E   + +  NG           +ED  Q
Sbjct: 36  ------VSSSTVKREERPQHPVSCEAIKAIA-ETLSIPVIANGGSHDHIQKYLDIEDFRQ 88

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
           A     +   VM+ RAA  N ++             G  P++  V + + R        Y
Sbjct: 89  A----TAASSVMVARAAMWNPSIFLK---------EGLRPLE-EVMQKYIRYAVQYENHY 134


>gi|256158986|ref|ZP_05456823.1| dihydropyrimidine dehydrogenase [Brucella ceti M490/95/1]
 gi|256254344|ref|ZP_05459880.1| dihydropyrimidine dehydrogenase [Brucella ceti B1/94]
 gi|261221504|ref|ZP_05935785.1| dihydropyrimidine dehydrogenase [Brucella ceti B1/94]
 gi|265997467|ref|ZP_06110024.1| dihydropyrimidine dehydrogenase [Brucella ceti M490/95/1]
 gi|260920088|gb|EEX86741.1| dihydropyrimidine dehydrogenase [Brucella ceti B1/94]
 gi|262551935|gb|EEZ07925.1| dihydropyrimidine dehydrogenase [Brucella ceti M490/95/1]
          Length = 436

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLSISGIGGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|239620911|ref|ZP_04663942.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis CCUG 52486]
 gi|239516172|gb|EEQ56039.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis CCUG 52486]
          Length = 375

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 72/234 (30%), Gaps = 41/234 (17%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINL 79
           +  + + D +  +  +   + L     G+ +  +            A++V+  G   + +
Sbjct: 150 SPDVWQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKQTGAKLMVM 209

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRN 138
           N  CP            L  NP +VG    A+ + +  IP+ VK      D    + +R+
Sbjct: 210 NTSCP-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDGDLELMVRS 264

Query: 139 LV----------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            V                K +  +G   +    R       S      I     D+V  +
Sbjct: 265 TVGHGTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARL 319

Query: 183 K----KENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
                K   D  I   GG+   +          D VM    A  ++ +   +  
Sbjct: 320 AAIREKLGLDFKINGVGGVVSPADYQAYRNAGADSVMSATGAMWDAELAHKIKA 373


>gi|107099425|ref|ZP_01363343.1| hypothetical protein PaerPA_01000437 [Pseudomonas aeruginosa PACS2]
 gi|313111935|ref|ZP_07797724.1| putative dihydroorotate dehydrogenase [Pseudomonas aeruginosa
           39016]
 gi|310884226|gb|EFQ42820.1| putative dihydroorotate dehydrogenase [Pseudomonas aeruginosa
           39016]
          Length = 424

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 60/173 (34%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCSLPVIVKLTPNI 180

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI-------------LKGLSPKDNRK 170
            D      +R   ++  + G + +     I++  ++                        
Sbjct: 181 TD------IRQSARAAHRGGADAVSLINTINSITSVDLERMVALPVVGTQSTHGGYCGSA 234

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 235 VKPIALNMVAEIARDPQTRGLPICGIGGIGSWRDAAEFVALGCGAVQVCTAAM 287


>gi|119589549|gb|EAW69143.1| dihydrouridine synthase 3-like (S. cerevisiae), isoform CRA_b [Homo
           sapiens]
          Length = 192

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 12/80 (15%)

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           +   V G+MI R A     + T + E     ++ S  +           I    T+Y   
Sbjct: 1   MQTGVTGIMIARGALLKPWLFTEIKEQRHWDISSSERL----------DILRDFTNYGLE 50

Query: 266 HLHSGGKLQQITRHMI--GL 283
           H  S  +  + TR  +   L
Sbjct: 51  HWGSDTQGVEKTRRFLLEWL 70


>gi|167756686|ref|ZP_02428813.1| hypothetical protein CLORAM_02224 [Clostridium ramosum DSM 1402]
 gi|167702861|gb|EDS17440.1| hypothetical protein CLORAM_02224 [Clostridium ramosum DSM 1402]
          Length = 643

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 67/176 (38%), Gaps = 15/176 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +   +A I ++ G++ I ++            P        +G           + + ++
Sbjct: 150 EFANSAIIAKNAGFDAIEIHGHAGYLVDQFMSPVWNKRTDEYGGSAENRMRFATEIVQSI 209

Query: 112 CKALSIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+ +PV  +        +         L++ ++K+GV+ + I A     +        
Sbjct: 210 KQAVDLPVIFRIALDHLFVEGRTLDESMELIEILEKAGVDALDIDAG-CYERIDYIFPTA 268

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            + +   D V +  +++ ++ I +N G      AL+++ S   D VM GR    + 
Sbjct: 269 YLGDACMDYVCKEARKHVNIPI-MNAGNHTPESALRLIESKDADFVMFGRQFIADP 323


>gi|319779830|ref|YP_004139306.1| NADH:flavin oxidoreductase/NADH oxidase [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317165718|gb|ADV09256.1| NADH:flavin oxidoreductase/NADH oxidase [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 681

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 79/247 (31%), Gaps = 32/247 (12%)

Query: 61  KLVEAAKIVEDFGYNEINL--------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               AA   +  G++ I +            P     +  +G  L     +  D +  + 
Sbjct: 128 DFAAAAVRCKKGGFDGIEILSHSHLLGQFLSPLINFRQDDYGGSLENRLRLTFDVLNGVR 187

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+     +  RI  +D     +       + + +++ G+         A    L     
Sbjct: 188 DAVGDEFIIGLRITGNDFLKGGLSREDCIEIAQRLEQCGLVDFLNVLAGAPYDDLGLAQW 247

Query: 169 RK---IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIG--RAAYK 221
                 P   +  V +  +E   L I   GG+ D++ A   L   DG+  M+G  RA   
Sbjct: 248 MPPMGTPAARFLGVAKDIREAVSLPIFYAGGIADIATARHALR--DGIVDMVGMTRAHIA 305

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK----LQQIT 277
           +  +++ +             I+T V  ++         D       + G+      +  
Sbjct: 306 DPYLVSKLQ------TGQEDRIRTCVGMNYCADRVNQGKDALCGQNAATGRERFFPHRFR 359

Query: 278 RH-MIGL 283
           RH + GL
Sbjct: 360 RHEIAGL 366


>gi|89055203|ref|YP_510654.1| dihydropyrimidine dehydrogenase [Jannaschia sp. CCS1]
 gi|88864752|gb|ABD55629.1| dihydroorotate oxidase B, catalytic subunit / dihydrouracil
           dehydrogenase (NAD+) / dihydropyrimidine dehydrogenase
           (NADP+) [Jannaschia sp. CCS1]
          Length = 434

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + I LN GCP     E   GA +   P+ +        +  S PV VK    +
Sbjct: 124 LVEDTGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDITKPAAAAKRGGADAVSLINTINSITSVNLDTMSPEPSIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARSPETHGLPISGIGGVTTWRDAAEFMTLGAGNVQVCTAAM 289


>gi|217076475|ref|YP_002334191.1| dihydroorotate dehydrogenase family protein [Thermosipho africanus
           TCF52B]
 gi|217036328|gb|ACJ74850.1| dihydroorotate dehydrogenase family protein [Thermosipho africanus
           TCF52B]
          Length = 360

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/125 (20%), Positives = 47/125 (37%), Gaps = 10/125 (8%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKKSGVNG-IW 152
            + + + + +  + K    P+ +K    + D +    +      N + +I   G    I 
Sbjct: 129 KDYNTIAEIVKTIRKNTKKPIFMKISPHIPDPVEFTKVAIGNGANGIVAINSLGPTMKID 188

Query: 153 IHARKAI---LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I  RK +    KG        I  L   IV  ++   PD+ I   GG++     ++ +L 
Sbjct: 189 IKNRKVLIGNEKGQVWLSGPAIKPLALAIVKMLRDAFPDITIIGVGGIKSADDVIEFLLA 248

Query: 209 SVDGV 213
             D V
Sbjct: 249 GADAV 253


>gi|159043912|ref|YP_001532706.1| dihydropyrimidine dehydrogenase [Dinoroseobacter shibae DFL 12]
 gi|157911672|gb|ABV93105.1| dihydroorotate dehydrogenase family protein [Dinoroseobacter shibae
           DFL 12]
          Length = 432

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + + LN GCP     E   G+ +   P+ +        +   +PV VK    +
Sbjct: 123 LVEETGADAVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVARWCKQHTRMPVIVKLTPNI 181

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 182 TDIRYPARAAHAGGADAVSLINTISSITSVNLDSFSPEPSIDGKGSHGGYCGPAVKPIAL 241

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   + I   GG+     A + L      V +  AA 
Sbjct: 242 NMVAEIARDAETAGMPISGIGGVTTWRDAAEFLALGAGNVQVCTAAM 288


>gi|326789659|ref|YP_004307480.1| dihydroorotate dehydrogenase [Clostridium lentocellum DSM 5427]
 gi|326540423|gb|ADZ82282.1| dihydroorotate dehydrogenase family protein [Clostridium
           lentocellum DSM 5427]
          Length = 494

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 63/187 (33%), Gaps = 22/187 (11%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G +  +    A+IV + G + I  N  CP   +     G+ +  NP +V   
Sbjct: 199 KVIVASIMGTNEEEWTYLARIVTEAGADIIECNFSCPH--MATDGLGSDVGQNPFLVATY 256

Query: 108 IAAMCKALSIPVTVKCRIGV-DDQIPAVALRNL----------VKSIKKSGVNGIWIHAR 156
             A  K   +P+  K    +   +IPA+A              +KSI    +       +
Sbjct: 257 TKATRKGTHLPILAKMTPNLGHMEIPALAAMEAGATGIAAINTIKSIMNVDLESFCSGPK 316

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQA-------LKIL 207
                 +     + +  +    +YE+K         I   GG+E    A        + L
Sbjct: 317 VRGKTSVGGYSGKAVKPIALRFIYEMKSHEGLRKTPISGMGGIETWKDAAEFLALGCENL 376

Query: 208 PSVDGVM 214
                VM
Sbjct: 377 QVTTAVM 383


>gi|162453678|ref|YP_001616045.1| putative NADH-dependent flavin oxidoreductase [Sorangium cellulosum
           'So ce 56']
 gi|161164260|emb|CAN95565.1| putative NADH-dependent flavin oxidoreductase [Sorangium cellulosum
           'So ce 56']
          Length = 362

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 60/182 (32%), Gaps = 19/182 (10%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSGV 148
           G        ++ + + A+  A+     V  R+  +D   A          L + + + G 
Sbjct: 189 GGAWENRARLLRETLRAVRAAVPASFVVGVRLSPEDWGQAKGLDLDENLTLARWLAEDGA 248

Query: 149 NGIWIHARKAILKGLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + +  H         S K     P  L  + V         L + + GG+   ++A  +L
Sbjct: 249 DFL--HLSLWDSSKPSQKRGDTHPLPLFREAVG------VSLPLVVAGGVWTRAEAEALL 300

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
                GV +GRAA  N        +  ++P            + + R +S +   Y  R 
Sbjct: 301 DKGATGVALGRAAITNP----DWPQRIADPAWQPRRPPLTRAELYERGVSETFAGYLRRW 356

Query: 267 LH 268
             
Sbjct: 357 KG 358


>gi|116054170|ref|YP_788613.1| dihydropyrimidine dehydrogenase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|254237329|ref|ZP_04930652.1| hypothetical protein PACG_03400 [Pseudomonas aeruginosa C3719]
 gi|254243537|ref|ZP_04936859.1| hypothetical protein PA2G_04355 [Pseudomonas aeruginosa 2192]
 gi|115589391|gb|ABJ15406.1| putative dihydroorotate dehydrogenase [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|126169260|gb|EAZ54771.1| hypothetical protein PACG_03400 [Pseudomonas aeruginosa C3719]
 gi|126196915|gb|EAZ60978.1| hypothetical protein PA2G_04355 [Pseudomonas aeruginosa 2192]
          Length = 425

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 60/173 (34%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 123 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCSLPVIVKLTPNI 181

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI-------------LKGLSPKDNRK 170
            D      +R   ++  + G + +     I++  ++                        
Sbjct: 182 TD------IRQSARAAHRGGADAVSLINTINSITSVDLERMVALPVVGTQSTHGGYCGSA 235

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 236 VKPIALNMVAEIARDPQTRGLPICGIGGIGSWRDAAEFVALGCGAVQVCTAAM 288


>gi|259417001|ref|ZP_05740921.1| dihydroorotate dehydrogenase family protein [Silicibacter sp.
           TrichCH4B]
 gi|259348440|gb|EEW60217.1| dihydroorotate dehydrogenase family protein [Silicibacter sp.
           TrichCH4B]
          Length = 434

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 56/167 (33%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   G+ +   P+ +        +    PV VK    +
Sbjct: 124 RVAETGCDGIELNFGCPHGMA-ERGMGSAVGQVPEYIQMVTEWCKQYYDKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRHPARAAHAGNADAVSLINTINSITSVNLDAMSPEPMIGGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDPQTAGLPISAIGGVTTWRDAAEFIALGAGNVQVCTAAM 289


>gi|313898757|ref|ZP_07832291.1| putative NADH oxidase [Clostridium sp. HGF2]
 gi|312956339|gb|EFR37973.1| putative NADH oxidase [Clostridium sp. HGF2]
          Length = 642

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/191 (15%), Positives = 68/191 (35%), Gaps = 28/191 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            + +   +  G++ I L   C            P       ++G  L     ++ + I A
Sbjct: 149 AQTSLQAKQAGFDGIEL--HCAHAYMLLGSFLSPMRNKRCDAYGGSLDHRARLLFEVIDA 206

Query: 111 MCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKG---- 162
           + +A      +  RI  D++         +  LV  +   GV+   +       +     
Sbjct: 207 IKEACGRDFPIVLRISGDEKDAQGNTVEDMCYLVPKLIAHGVDAFEVSGGTQYERPNKII 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
            S  ++  +       + E+      + + + G + D + A++++    VDGV+ GRA  
Sbjct: 267 PSHGEHEGVNVAQAARIREV----SSVPVLVVGKVLDPAMAMELVDQKAVDGVVFGRALL 322

Query: 221 KNSAMLTTVDE 231
            +  ++    E
Sbjct: 323 ADPYLVNKAAE 333


>gi|547573|emb|CAA79376.1| unnamed protein product [Saccharomyces cerevisiae]
          Length = 106

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 14/94 (14%), Positives = 28/94 (29%), Gaps = 14/94 (14%)

Query: 189 LFIGLNGGLEDMSQALKILPS---VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           +    NG + +     + L     +D VM+ R A     +   V+       T +  +  
Sbjct: 1   IQFVGNGDVNNFEDWYRYLNGNENIDSVMVARGALIKPWIFEEVESQQYLDKTSTERL-- 58

Query: 246 RVDKDFWRKISASMTDYAARHLHSGG-KLQQITR 278
                    I      ++  H  +    + Q  R
Sbjct: 59  --------DILRDYAQFSMEHWGTDEYGISQCRR 84


>gi|218889181|ref|YP_002438045.1| dihydropyrimidine dehydrogenase [Pseudomonas aeruginosa LESB58]
 gi|218769404|emb|CAW25164.1| probable oxidoreductase [Pseudomonas aeruginosa LESB58]
          Length = 425

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 60/173 (34%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 123 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCSLPVIVKLTPNI 181

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI-------------LKGLSPKDNRK 170
            D      +R   ++  + G + +     I++  ++                        
Sbjct: 182 TD------IRQSARAAHRGGADAVSLINTINSITSVDLERMVALPVVGTQSTHGGYCGSA 235

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 236 VKPIALNMVAEIARDPQTRGLPICGIGGIGSWRDAAEFVALGCGAVQVCTAAM 288


>gi|300716196|ref|YP_003740999.1| NADH-dependent flavin oxidoreductase [Erwinia billingiae Eb661]
 gi|299062032|emb|CAX59148.1| Putative NADH-dependent flavin oxidoreductase [Erwinia billingiae
           Eb661]
          Length = 364

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/138 (19%), Positives = 49/138 (35%), Gaps = 13/138 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           +G  L     +  +    + +A   + PV V+      V+          L ++++  G 
Sbjct: 199 YGGSLENRMRLTLEIFREVRRAFPANKPVGVRISATDWVEGGWDVEQSIALSQALEAEGC 258

Query: 149 NGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             I + +      GLSP    K+ PN        IKK    + +   G + +  QA  +L
Sbjct: 259 AYIHVSSG-----GLSPAQQIKVGPNYQVPFAAAIKKAVT-IPVIAVGMITEPEQAEAVL 312

Query: 208 --PSVDGVMIGRAAYKNS 223
                D V + R    + 
Sbjct: 313 VEQQADMVALARGMLYDP 330


>gi|11497864|ref|NP_069086.1| NADH-dependent flavin oxidoreductase [Archaeoglobus fulgidus DSM
           4304]
 gi|2650386|gb|AAB90979.1| NADH-dependent flavin oxidoreductase [Archaeoglobus fulgidus DSM
           4304]
          Length = 378

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/186 (17%), Positives = 62/186 (33%), Gaps = 27/186 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V+AA   E  G++ + L+            P     +  +G        I+ D    
Sbjct: 164 EAFVKAALRAEKAGFDAVQLHAAHGYLLSEFISPHVNRRKDEYG---QERAKILLDIFDG 220

Query: 111 MCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWI---------HARKAI 159
           + +   IPV +K      V   +       + K +  +G   I +         H R  +
Sbjct: 221 IRQRSRIPVMIKMNACDFVPGGLEIDEAVRIAKLLDDAGFEAIEVSGGMYESIYHNRYNV 280

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
           +     K          +  + IK E   + +   GG++    A ++L  VD V + R  
Sbjct: 281 VSQKVAKSGEAYFR---EYAFRIK-EAVSIPVMAVGGIKSRQTAEELLKKVDFVSMSRPL 336

Query: 220 YKNSAM 225
            ++  +
Sbjct: 337 IRDPYL 342


>gi|302761068|ref|XP_002963956.1| hypothetical protein SELMODRAFT_80950 [Selaginella moellendorffii]
 gi|302769089|ref|XP_002967964.1| hypothetical protein SELMODRAFT_88846 [Selaginella moellendorffii]
 gi|300164702|gb|EFJ31311.1| hypothetical protein SELMODRAFT_88846 [Selaginella moellendorffii]
 gi|300167685|gb|EFJ34289.1| hypothetical protein SELMODRAFT_80950 [Selaginella moellendorffii]
          Length = 411

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 44/288 (15%), Positives = 92/288 (31%), Gaps = 48/288 (16%)

Query: 25  EMIVADAILRGDKK-NILGFSTQEKPLALQI---GGADISKLVEAAKIVEDFGYNEINLN 80
           E+I          +   L     ++ L   I      D  +  E  + VE  G + + +N
Sbjct: 115 ELISDRPFETMLAELRRLKQEYPDRILIGSIMEEYDKDAWE--EIIERVEATGVDALEIN 172

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
             CP     E   GA +  + D++G+  + +    ++PV  K    V D      +    
Sbjct: 173 FSCPHGM-PERKMGAAVGKDCDLLGEVCSWINAKATVPVWAKMTPNVTD------ITQPA 225

Query: 141 KSIKKSGVNGI---------------WIHARKAIL-----KGLSPKDNRKIPNLDYDIVY 180
           ++  ++G  G+                +     +       G S +  R I       + 
Sbjct: 226 RTAIEAGCEGLSAINTITSIMGINLDTLRPEPCVEGYSTPGGYSSRAVRPIALAKVMAIA 285

Query: 181 E-IKKENPD--LFIGLNGGLEDMSQALK-------ILPSVDGVMIGRAAYKNSAMLTTVD 230
           + +K E PD  + +   GG+E    A +        +    GVM+    Y    ++  + 
Sbjct: 286 QMLKSEYPDRNISLSGIGGVESGDNAAEFILLGANTVQVCTGVMM----YGYP-LVKRLC 340

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
           +     +   +       +    +   + TD   R   +    +   +
Sbjct: 341 KELQAFMAKHNFTSLDDFRGTSLQYMTTHTDLVQRQQEAIRSRRAARK 388


>gi|163758602|ref|ZP_02165689.1| putative dihydropyrimidine dehydrogenase [Hoeflea phototrophica
           DFL-43]
 gi|162283892|gb|EDQ34176.1| putative dihydropyrimidine dehydrogenase [Hoeflea phototrophica
           DFL-43]
          Length = 436

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VED G + I LN GCP     E   G+ +   P+ +        +   +PV VK    +
Sbjct: 124 RVEDTGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIQMVAEWCKQYCRLPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRYPARAAKAGGADAVSLINTISSIVSVDLDNFAPMPTIDGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG++    A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETRGLPISGIGGVQTWRDAAEFIALGCGTVQVCTAAM 289


>gi|313498079|gb|ADR59445.1| Dihydropyrimidine dehydrogenase [Pseudomonas putida BIRD-1]
          Length = 424

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 39/167 (23%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTYCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+ +   A + +      V +  AA 
Sbjct: 241 NMVAEIARDPETRGLPICGIGGIGNWRDAAEFMALGSGAVQVCTAAM 287


>gi|90418415|ref|ZP_01226327.1| dihydroorotate dehydrogenase [Aurantimonas manganoxydans SI85-9A1]
 gi|90338087|gb|EAS51738.1| dihydroorotate dehydrogenase [Aurantimonas manganoxydans SI85-9A1]
          Length = 447

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 30/173 (17%), Positives = 61/173 (35%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + + LN GCP     E   GA +   P+ +        +   +PV VK    +
Sbjct: 123 LVEETGADGVELNFGCPHGMS-ERGMGAAVGQVPEYIEMVARWCKQHSKLPVIVKLTPNI 181

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWI--------------HARKAILKGLSPKDNR---K 170
            D      +R   ++ ++ G + + +               A    + G           
Sbjct: 182 TD------IRFPARAARRGGADAVSLINTISSIVSIDLDNFAPTPTIDGKGSHGGYCGPA 235

Query: 171 IPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++   +   +   GG+     A + +      V +  AA 
Sbjct: 236 VKPIALNMVAEIARDPETIGMPMSGIGGITTWRDAAEFIALGCGTVQVCTAAM 288


>gi|213693173|ref|YP_002323759.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|213524634|gb|ACJ53381.1| dihydroorotate dehydrogenase [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|320459354|dbj|BAJ69975.1| putative dihydroorotate dehydrogenase [Bifidobacterium longum
           subsp. infantis ATCC 15697]
          Length = 371

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 71/230 (30%), Gaps = 41/230 (17%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +            A++V++ G   + +N  C
Sbjct: 150 WQPDMRAAIEAAGPGQVLVPSFQGSRVEGMSEEEYIADHATTARLVKETGAKLMVMNTSC 209

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLV-- 140
           P            L  NP +VG    A+ + +  IP+ VK      D    + +R+ V  
Sbjct: 210 P-----NEGHNRLLCHNPLLVGRITEAVKQEIGDIPLMVKLAYIPSDDALELMVRSTVGH 264

Query: 141 --------------KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--- 183
                         K +  +G   +    R       S      I     D+V  +    
Sbjct: 265 GTVQGFSTINTISAKLVDANGNQALPGAGRD-----RSGVCGNAIRGAGLDMVARLAAIR 319

Query: 184 -KENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
            K   D  I   GG+   +          D VM    A  ++ +   +  
Sbjct: 320 EKLGLDFKINGVGGVVSPADYQAYRNAGADSVMSATGAMWDAELAHKIKA 369


>gi|302335773|ref|YP_003800980.1| dihydroorotate dehydrogenase family protein [Olsenella uli DSM
           7084]
 gi|301319613|gb|ADK68100.1| dihydroorotate dehydrogenase family protein [Olsenella uli DSM
           7084]
          Length = 307

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 67/198 (33%), Gaps = 10/198 (5%)

Query: 32  ILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVH 89
            +R D + + G   +   +  Q+ G  + +   A ++ +D     + + LN+ CP   V 
Sbjct: 83  FVRQDGEYLQGLRERGCQVICQVVGHSVEECTRAVELYDDLAPFASGLELNISCP--NVS 140

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK-SGV 148
            G         P    + + A+     +PV VK       +           ++   + +
Sbjct: 141 RGGAALG--ATPAAAAEVMRAVRPHTKLPVIVKMAPHDVGETARALEAEGADALSLINTI 198

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALK- 205
            G+ I  R    +          P + +  V  + +      + +   GG+     A + 
Sbjct: 199 PGMAIDVRTRRSRLSRATAGISGPVVHHMAVRMVWEAYHAVRIPLCGIGGVTTGEDAAEF 258

Query: 206 ILPSVDGVMIGRAAYKNS 223
           IL     V +G A   + 
Sbjct: 259 ILAGATAVSVGTANLCDP 276


>gi|309812833|ref|ZP_07706570.1| oxidoreductase, FAD/FMN-binding [Dermacoccus sp. Ellin185]
 gi|308433201|gb|EFP57096.1| oxidoreductase, FAD/FMN-binding [Dermacoccus sp. Ellin185]
          Length = 364

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 79/233 (33%), Gaps = 24/233 (10%)

Query: 39  NILGFSTQEKPLALQIGGAD--ISKLVEAAKIVEDFGYNEINLNVG---------CPSAR 87
           + + F     P A+ +   D  +   V+AA+  ++ G++ + L+            P++ 
Sbjct: 136 SAVAFDGYATPRAMTLADIDDVVDAFVDAARRADEAGFDVVELHAAHGYLLHEFLSPASN 195

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV--DDQIPAVALRNLVKSI 143
           + +  +G        ++      +  A     P+ V+       +          L + +
Sbjct: 196 LRDDEYGGSFENRARLLLRIATEVRAAWPEAKPLFVRVSATDWAETGWNIDETVRLAREL 255

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           K  GV+ +          G  P D    PN       EI++   D+  G  G + + +QA
Sbjct: 256 KSVGVDLVDTSTG-----GNVPADIPVGPNYQVRFASEIRRGA-DIATGAVGLITEPAQA 309

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
             IL     D V+IGRA  +                   +P   +  +  W  
Sbjct: 310 EAILTEGDADVVLIGRAGLREPYWPLRAAAEL-GLTWRETPYPAQYTRGAWEH 361


>gi|310794203|gb|EFQ29664.1| NADH:flavin oxidoreductase/NADH oxidase [Glomerella graminicola
           M1.001]
          Length = 409

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/189 (15%), Positives = 70/189 (37%), Gaps = 28/189 (14%)

Query: 62  LVEAAKIVEDFGYNEINLN----------VGCPSARVHEG--SFGACLMLNPDIVGDCIA 109
             + AK+  D G+  I ++          +   S ++++   ++G        IV + I 
Sbjct: 170 FAQTAKLASDAGFAGIEIHGAHGYLLAQFM---SDKINKRTDAYGGSPAARVRIVVEIIR 226

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK---AILKGL 163
           A+ + +     V  +    D      L   ++ +K   ++GV+ + +        ++   
Sbjct: 227 AIREVVPKTFCVGIKFNSVDHQAQAELDACIEQLKLITEAGVDFLEVSGGSYEDPVMFSN 286

Query: 164 S---PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
           +    K +R      +  +    I+++ PD+ + + GG          L     D + + 
Sbjct: 287 NDNEKKSDRTKAREAFFLEFARVIRRDFPDVPLMVTGGFRSRQGMEAALTNNGCDLIGLA 346

Query: 217 RAAYKNSAM 225
           R A  N A+
Sbjct: 347 RPAVLNPAL 355


>gi|254520393|ref|ZP_05132449.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium sp. 7_2_43FAA]
 gi|226914142|gb|EEH99343.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium sp. 7_2_43FAA]
          Length = 646

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 74/184 (40%), Gaps = 27/184 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAAMC 112
             +AAK   + GY+ +  + G    P + + +        +G  L      + +CI ++ 
Sbjct: 148 FGDAAKRAVEAGYDTVEFHAGHNYTPHSFLSKAFNKRMDEYGGSLENRARFLLECIKSIR 207

Query: 113 KAL--SIPVTVKCRIGVD---DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           + +   +P+ ++     D   D +    +    K  K++GV+ + +          S   
Sbjct: 208 ENIPEDMPLFMRIDAHDDCVEDGLTIEEVIQFCKWAKEAGVDVLDVSRGN----FSSAAV 263

Query: 168 NRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
             ++P +D       +    IKKE   + + + G + D  QA +I+     D V++GRA 
Sbjct: 264 KYEVPPVDVPRGFNVENAARIKKETGMITVAV-GRINDPEQADEIIRSGKADMVVMGRAQ 322

Query: 220 YKNS 223
             + 
Sbjct: 323 LADP 326


>gi|99081341|ref|YP_613495.1| dihydropyrimidine dehydrogenase [Ruegeria sp. TM1040]
 gi|99037621|gb|ABF64233.1| dihydropyrimidine dehydrogenase (NADP+) / dihydrouracil
           dehydrogenase (NAD+) / dihydroorotate oxidase B,
           catalytic subunit [Ruegeria sp. TM1040]
          Length = 434

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 56/167 (33%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   G+ +   P+ +        +    PV VK    +
Sbjct: 124 RVAETGCDGIELNFGCPHGMA-ERGMGSAVGQVPEYIQMVTEWCKQYYDKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRHPARAAKAGNADAVSLINTINSITSVNLDAMSPEPMIGGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEISRDPQTAGLPISAIGGVTTWRDAAEFIALGAGNVQVCTAAM 289


>gi|146303200|ref|YP_001190516.1| NADH:flavin oxidoreductase/NADH oxidase [Metallosphaera sedula DSM
           5348]
 gi|145701450|gb|ABP94592.1| NADH:flavin oxidoreductase/NADH oxidase [Metallosphaera sedula DSM
           5348]
          Length = 556

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/187 (18%), Positives = 66/187 (35%), Gaps = 37/187 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---------LNPDI------- 103
               +A++  E  G++ I L                 L+            D        
Sbjct: 155 DDFAKASERAERAGFDGIEL-----------HGAHGYLIAQFLSPATNKRTDRYSDGVIF 203

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIH---ARKAI 159
           + + I  +   +SIPV    RI V +         LV K + +   +  ++H    R   
Sbjct: 204 LEELIKEVRSRVSIPVG--LRISVTEFDDEGLTPELVSKIVSRVETHLDYVHLSAGRDGP 261

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
           L    P   ++   L+Y    E+++  P + + L G +  +  A ++L   D V++GR  
Sbjct: 262 LGSSMPIYWKRPAFLEYA--KEMRR--PRIPLLLVGSVITLKDAEEVLEVADAVVLGRQL 317

Query: 220 YKNSAML 226
             +   L
Sbjct: 318 LADPDWL 324


>gi|255264310|ref|ZP_05343652.1| dihydroorotate dehydrogenase family protein [Thalassiobium sp.
           R2A62]
 gi|255106645|gb|EET49319.1| dihydroorotate dehydrogenase family protein [Thalassiobium sp.
           R2A62]
          Length = 434

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 56/167 (33%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + I LN GCP     E   GA +   P+ +        +  S PV VK    +
Sbjct: 124 LVEDTGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYSKPVIVKLTPNI 182

Query: 128 DDQIPAVALRN--------LVKSIKKSGVNGIWIHARKAILKGLSPKDNR---KIPNLDY 176
            D     A           L+ +I       +   + +  + G           +  +  
Sbjct: 183 TDVRKPAAAAKRGGADAVSLINTINSITSVNLDSMSPEPSIDGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E     I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARNSETQGFPISGIGGVTTWRDAAEFITLGCGNVQVCTAAM 289


>gi|188989728|ref|YP_001901738.1| NADPH dehydrogenase [Xanthomonas campestris pv. campestris str.
           B100]
 gi|167731488|emb|CAP49663.1| NADPH dehydrogenase [Xanthomonas campestris pv. campestris]
          Length = 376

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 37/198 (18%), Positives = 61/198 (30%), Gaps = 22/198 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AAK  E  G   I L+            P +     ++G  L     +      A
Sbjct: 169 EAFVTAAKRAERLGLQLIELHAAHGYLMHQFLSPLSNQRSDAYGGSLDNRMRLTLRIFDA 228

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S    I V +     VD          L K++   G + I + +      GL P+
Sbjct: 229 VRAAVSDQMAIGVRISATDWVDGGWDLPQSIALSKALDARGAHYIHVSSG-----GLDPR 283

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
               +    Y I   E  +   D  +   G + +  QA  IL     D + + R    + 
Sbjct: 284 QQIPV-QASYQIPFAEAIRAQVDTPVIGVGLITEPQQAEAILRDGQADAIALARGILYDP 342

Query: 224 AMLTTVDEYFSNPLTGSS 241
                        +T + 
Sbjct: 343 RWPWHAAAALGASVTPAP 360


>gi|312961803|ref|ZP_07776301.1| dihydroorotate dehydrogenase 1 [Pseudomonas fluorescens WH6]
 gi|311284062|gb|EFQ62645.1| dihydroorotate dehydrogenase 1 [Pseudomonas fluorescens WH6]
          Length = 424

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +V+  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVQATGCDGIELNFGCPHGM-PERGMGAAVGQVPEYVEQVTRWCKTYCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    +  +                   +  +  
Sbjct: 181 TDIRVAARAAYRGGADAVSLINTINSITSVDLERMVALPTVGTQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI ++     L I   GG+ +   A + +      V +  AA 
Sbjct: 241 NMVAEIARDPQTQGLPICGIGGIGNWRDAAEFVALGCGAVQVCTAAM 287


>gi|332852283|ref|ZP_08434088.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013150]
 gi|332870506|ref|ZP_08439270.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013113]
 gi|332729413|gb|EGJ60753.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013150]
 gi|332732243|gb|EGJ63511.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013113]
          Length = 368

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 64/180 (35%), Gaps = 23/180 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
                AK   + G+  I ++            P A      +G  L     +  + + A+
Sbjct: 160 DFAATAKRAVEAGFELIEVHAAHGYLLHQFLSPIANQRTDEYGGSLENRMRMTLEVLQAI 219

Query: 112 CKAL--SIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             A+    PV V+      +  ++Q    +   L K++++ G   I + +      GL  
Sbjct: 220 KLAVPEGYPVGVRLSATDWMDGNEQWDIESTVGLSKALEQLGAAYIHVSSG-----GLHE 274

Query: 166 KDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
             N  I    Y +   E  K++  + +   G + D   A +IL    D + + RA   + 
Sbjct: 275 HQNITIG-AGYQVPFAEQVKKHVAIPVIAVGLITDPQHAEQILENQADAIGLARAMLYDP 333


>gi|326791074|ref|YP_004308895.1| 2,4-dienoyl-CoA reductase (NADPH) [Clostridium lentocellum DSM
           5427]
 gi|326541838|gb|ADZ83697.1| 2,4-dienoyl-CoA reductase (NADPH) [Clostridium lentocellum DSM
           5427]
          Length = 644

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 38/194 (19%), Positives = 67/194 (34%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AAK   + GY+ I  + G          P        +G  L      + +CI A
Sbjct: 144 HAFGTAAKRAVEAGYDTIEFHAGHNYTPHSFLSPYFNRRNDEYGGSLENRARFLIECIKA 203

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSP 165
           +   +   +P+ ++     D     + +       K  K++GV+ + +          S 
Sbjct: 204 IRSNIPEDMPLFMRIDAHDDYLENGLTIEEVIAFCKMAKEAGVDVLDVSRGN----FSSK 259

Query: 166 KDNRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
               ++P++D       +    IKKE   L I + G +    QA  I+     D V+IGR
Sbjct: 260 ALKYEVPSIDLPRGFNVENAARIKKETGMLTIAV-GRINTPEQADIIIGNNQADMVVIGR 318

Query: 218 AAYKNSAMLTTVDE 231
               +        E
Sbjct: 319 GQLADPDFCNKAKE 332


>gi|291558287|emb|CBL35404.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium siraeum
           V10Sc8a]
          Length = 494

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 61/177 (34%), Gaps = 16/177 (9%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G    +    A++ E+ G + I  N  CP    H          NP++V   
Sbjct: 193 KIIVSSIMGESEDEWTALARLSEEAGVDMIECNFSCPQMTSHSMGSDVG--TNPELVAKY 250

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
            AA+ +   +PV  K    + +               +A  N VKSI    ++       
Sbjct: 251 TAAVRRGTKLPVLAKMTPNITNMEIPAIAAVNAGADGIAAINTVKSITNVDLDSFVPAPD 310

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSV 210
                 +     + +  +    + ++K+     ++ I   GG+E     L+ IL   
Sbjct: 311 INGKSAVGGYSGKAVKPIALRFISDMKRNETLENVEISGMGGIETWRDGLEFILMGC 367


>gi|331089705|ref|ZP_08338602.1| hypothetical protein HMPREF1025_02185 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330404286|gb|EGG83832.1| hypothetical protein HMPREF1025_02185 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 641

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 64/195 (32%), Gaps = 20/195 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +A+K  ++ G++ I L   C            P        +G  L+    ++ + + A
Sbjct: 147 AKASKNAKEAGFDGIEL--HCAHAYMLLGSFLSPLRNKRTDEYGGSLLNRARLLFEVLDA 204

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +       +  R+   ++ P          L+  ++K GV+   I       +     
Sbjct: 205 IKETCGEDFPIVLRMSGSERDPQGNTLEDMKRLIPYLEKHGVDCFEISGGTQYERCNKII 264

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                            KE     +   G + D   A  +L    VDGV++GRA   +  
Sbjct: 265 PCHGEEEFTNLKEARAIKEITTKPVITVGKILDAQLAEDVLEANEVDGVVLGRALLADPD 324

Query: 225 MLTTVDEYFSNPLTG 239
            +   +E   + +  
Sbjct: 325 FVEKAEEKRYDEIAP 339


>gi|254479411|ref|ZP_05092743.1| oxidoreductase, FAD/FMN-binding family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214034656|gb|EEB75398.1| oxidoreductase, FAD/FMN-binding family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 606

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 29/141 (20%), Positives = 48/141 (34%), Gaps = 12/141 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGV 148
           +G  L        + +  +  AL    TV CRI  DD               K ++K+G 
Sbjct: 161 YGGSLEGRARFAVEILKEIKDALP-DFTVICRINGDDFTDGGFNIKESIEFAKILEKNGA 219

Query: 149 NGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQAL 204
           + I + +         +SP      P L      +IK+      I  N  G + D  + L
Sbjct: 220 SAIDVSSGVSSTSEYHISPMGIEDRPLL--PFTKKIKESISIPVIAANKLGDVYDWERIL 277

Query: 205 KILPSVDGVMIGRAAYKNSAM 225
           +     D + I R    +  +
Sbjct: 278 EERI-ADFIGIARGLIGDPDL 297


>gi|227497843|ref|ZP_03928028.1| NADPH dehydrogenase [Actinomyces urogenitalis DSM 15434]
 gi|226832727|gb|EEH65110.1| NADPH dehydrogenase [Actinomyces urogenitalis DSM 15434]
          Length = 377

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 65/216 (30%), Gaps = 28/216 (12%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA+   + GY+ + L             P +     ++G        +  + +AA+
Sbjct: 167 DFASAARRAVEAGYDLVELHGAHGYLIHQFLSPLSNHRTDAYGGSPEGRRRLALEAVAAV 226

Query: 112 CKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+     V  R+   D     + +     L   +   G + + I        G  P  
Sbjct: 227 REAVGPDTVVGIRLSATDWAEGGLTSADTAELAHQLVAQGADVLHIST-----SGNVPAR 281

Query: 168 NRKIPNLDYDIVYEIKKEN--------PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
               P        E+K+           +  +   G +E+  QA ++L     D V +GR
Sbjct: 282 FPIGPGYQVRFAAEVKQAVAGMTTPGGGEPVVIAVGLIENGPQAEQVLITGQADAVAVGR 341

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            A ++                  +       +  WR
Sbjct: 342 YALRDPYAPLRWAHELGVTEWDKAGFPLPYWRGTWR 377


>gi|48477445|ref|YP_023151.1| NADH oxidoreductase [Picrophilus torridus DSM 9790]
 gi|48430093|gb|AAT42958.1| NADH oxidoreductase [Picrophilus torridus DSM 9790]
          Length = 542

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 81/224 (36%), Gaps = 29/224 (12%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQ---EKPLAL--QIGGAD----ISKLVEAAKIVEDF 72
           ++T+++ A      D    + F+     E P     ++   D        + AA++    
Sbjct: 97  IFTQLVHAGGKANPDYNKRMIFAPSSLNEYPFLRPDEMTVNDIESVEEDFLRAARLAYRA 156

Query: 73  GYNEINLNVGCP---------SARVHEGS--FGACLMLNPDIVGDCIAAMCKALSIPVTV 121
            ++ I ++             S  +++ +  +G  L  N  I  + I  +   L  PV +
Sbjct: 157 NFDGIEIHGA--HGYLIQEFISKDLNKRNDRYGGSLENNVRIANEIIDMIRAELDFPVGI 214

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           +  +  D+           + IK +         R A     +P    +      + +Y+
Sbjct: 215 RLSLYEDEGYGPDYGIKAARLIKNADYVHFS-AGRSAPPGSSAPFYYER------NHIYK 267

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             +E  D    + G + D++ A  +L   D V+ GRAA  +  +
Sbjct: 268 RIRERIDKKTMVVGSVIDINDARTVLEGSDLVVFGRAALADPFL 311


>gi|237733974|ref|ZP_04564455.1| NADH:flavin oxidoreductase [Mollicutes bacterium D7]
 gi|229383055|gb|EEO33146.1| NADH:flavin oxidoreductase [Coprobacillus sp. D7]
          Length = 649

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 66/176 (37%), Gaps = 15/176 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +   +A I ++ G++ I ++            P        +G           + + ++
Sbjct: 156 EFANSAIIAKNAGFDAIEIHGHAGYLVDQFMSPVWNKRTDEYGGSAENRMRFATEIVQSI 215

Query: 112 CKALSIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +A+ +PV  +        +         L++ ++K+GV+ + I A     +        
Sbjct: 216 KQAVDLPVIFRIALDHLFAEGRTLDESMELIEILEKAGVDALDIDAG-CYERIDYIFPTA 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            + +   D V    +++ ++ I +N G      AL+++ S   D VM GR    + 
Sbjct: 275 YLGDACMDYVCSEARKHVNIPI-MNAGNHTPESALRLIESKDADFVMFGRQFIADP 329


>gi|163796768|ref|ZP_02190726.1| dihydropyrimidine dehydrogenase [alpha proteobacterium BAL199]
 gi|159178022|gb|EDP62569.1| dihydropyrimidine dehydrogenase [alpha proteobacterium BAL199]
          Length = 435

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 59/168 (35%), Gaps = 15/168 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K V+D G + + LN GCP     E   G+ +   P+ +      +  +  +PV VK    
Sbjct: 122 KQVDDTGADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKASTRMPVIVKLTPN 180

Query: 127 VDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           + D              AV+L N V SI    ++                     +  + 
Sbjct: 181 ITDIRYPARAAHKGGADAVSLINTVSSITSVNLDTFSPEPSIDGKGSHGGYCGPAVKPIA 240

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            ++V +I +  E   L I   GG+     A + +      V +  AA 
Sbjct: 241 LNMVADIARDAETRGLPISGIGGITTWRDAAEFMALGAGNVQVCTAAM 288


>gi|154486575|ref|ZP_02027982.1| hypothetical protein BIFADO_00392 [Bifidobacterium adolescentis
           L2-32]
 gi|154084438|gb|EDN83483.1| hypothetical protein BIFADO_00392 [Bifidobacterium adolescentis
           L2-32]
          Length = 380

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 69/228 (30%), Gaps = 31/228 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D K  +  +   + L     G+ +  +         V  A +V + G   + +N  C
Sbjct: 158 WQPDMKKAIAAAGDGQLLVPSFQGSRVDGMDRKAYIADHVTTAHLVTETGAGLMEMNTSC 217

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P            L  +P +VG+   A+   +   P+ VK     +D      +R  V  
Sbjct: 218 P-----NEGHNRLLCHDPHLVGEITEAVKNEIGDRPLIVKLAYIPNDTDLETMVRETVGH 272

Query: 143 IKKSGVNGI-WIHARKAILKG----------LSPKDNRKIPNLDYDIVYEIK----KENP 187
               G + I  I AR     G           S      I     D+V  +     K   
Sbjct: 273 GTVQGFSTINTISARLVDANGNQALPGAGRDRSGVCGNAIRGAGLDMVGRLAAIREKLGL 332

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D  I   GG+              + VM    A  ++ +   + E   
Sbjct: 333 DFAIVGVGGVIRPDDYKAYREAGANVVMSATGAMWDANLAREIKETLR 380


>gi|268589924|ref|ZP_06124145.1| xenobiotic reductase A [Providencia rettgeri DSM 1131]
 gi|291314638|gb|EFE55091.1| xenobiotic reductase A [Providencia rettgeri DSM 1131]
          Length = 363

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 67/179 (37%), Gaps = 22/179 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + +EAA   E  G++ I ++            P + + +  +G C      ++ +    M
Sbjct: 158 QFIEAAIRAEKAGFDVIEIHAAHGYILHEFLSPVSNLRQDEYGGCFKNRTRLLINIFHEM 217

Query: 112 CKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+S  V +  RI   D             L + ++  G + I + +      GLS + 
Sbjct: 218 REAISPNVAIGVRISATDWLESGWSVPESIELTELLEDLGCDYIHVSSG-----GLSTEQ 272

Query: 168 NRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +   +Y + + +   EN  + +   G + +  QA  I+     D V IGR      
Sbjct: 273 QIPLSP-NYQVPLAQAIHENTMMPVIAVGLITEPLQAEAIVATHQADFVAIGRGILFEP 330


>gi|331225781|ref|XP_003325561.1| hypothetical protein PGTG_07394 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
 gi|309304551|gb|EFP81142.1| hypothetical protein PGTG_07394 [Puccinia graminis f. sp. tritici
           CRL 75-36-700-3]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
           L  Q GG D   +  AA +++ +  + I++N GCP    ++   G+ L+   
Sbjct: 255 LVAQFGGHDPFYMGHAAALIKKY-VDGIDINCGCPQQWAYKEGIGSALLRKW 305


>gi|296386938|ref|ZP_06876437.1| dihydropyrimidine dehydrogenase [Pseudomonas aeruginosa PAb1]
          Length = 424

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 61/173 (35%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCSLPVIVKLTPNI 180

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI----WIHARKAI-------------LKGLSPKDNRK 170
            D      +R   ++  + G + +     I++  ++                        
Sbjct: 181 TD------IRQSARAAHRGGADAVSLINTINSITSVDLERMVALPVVGTQSTHGGYCGSA 234

Query: 171 IPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +  +  ++V EI ++     L I   GG+ +   A + +      V +  AA 
Sbjct: 235 VKPIALNMVAEIARDPQTRGLPICGIGGIGNWRDAAEFVALGCGAVQVCTAAM 287


>gi|70927134|ref|XP_735999.1| hypothetical protein [Plasmodium chabaudi chabaudi]
 gi|56510160|emb|CAH86847.1| hypothetical protein PC302189.00.0 [Plasmodium chabaudi chabaudi]
          Length = 152

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           GVMIGRA   N  +L   D+   N  T ++    R   + ++      + +     +S  
Sbjct: 23  GVMIGRACMDNITVLAKTDKLVYNHDTLATAYSRRTVLEAYKSYLEQNSSF-----YSLV 77

Query: 272 KLQQITRHMIGLFHGFPNSRRCRHIL 297
              ++ + ++G+  G P  R  R+ +
Sbjct: 78  NAFELLKPILGVLKGMPGHRLFRNKI 103


>gi|322370313|ref|ZP_08044872.1| dihydropyrimidine dehydrogenase [Haladaptatus paucihalophilus
           DX253]
 gi|320550021|gb|EFW91676.1| dihydropyrimidine dehydrogenase [Haladaptatus paucihalophilus
           DX253]
          Length = 247

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/165 (19%), Positives = 56/165 (33%), Gaps = 25/165 (15%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           V +     + LN  C    +     G  L+   D + + + A  +     V+VK R    
Sbjct: 97  VCERHGAILELNAHCRQEEMCAVGAGQSLLRTTDRLREQVHAAAE-TGATVSVKVRT--- 152

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
            ++P V L  +V+     G   + + A                   D + V     +  D
Sbjct: 153 -EVPGVDLPKVVRQAVDGGAEIVHLDAM------------------DSEHVVRDVADATD 193

Query: 189 LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
            F+  N G+ D     + L    D V +GR +  +  +L  V   
Sbjct: 194 CFLVANNGVRDEETVAEYLDYGADAVSVGRPS-DDPEVLARVRRA 237


>gi|167750622|ref|ZP_02422749.1| hypothetical protein EUBSIR_01599 [Eubacterium siraeum DSM 15702]
 gi|167656301|gb|EDS00431.1| hypothetical protein EUBSIR_01599 [Eubacterium siraeum DSM 15702]
          Length = 432

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 61/177 (34%), Gaps = 16/177 (9%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G    +    A++ E+ G + I  N  CP    H          NP++V   
Sbjct: 131 KIIVSSIMGESEDEWTALARLSEEAGVDMIECNFSCPQMTSHSMGSDVG--TNPELVAKY 188

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI-----------PAVALRNLVKSIKKSGVNGIWIHAR 156
            AA+ +   +PV  K    + +               +A  N VKSI    ++       
Sbjct: 189 TAAVKRGTKLPVLAKMTPNITNMEIPAIAAVNAGADGIAAINTVKSITNVDLDSFVPTPN 248

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSV 210
                 +     + +  +    + ++K+     ++ I   GG+E     L+ IL   
Sbjct: 249 INGKSAVGGYSGKAVKPIALRFISDMKRNETLENVEISGMGGIETWRDGLEFILMGC 305


>gi|221126279|ref|XP_002164598.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 1399

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/151 (23%), Positives = 51/151 (33%), Gaps = 14/151 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VED G + I LN GCP     E   GA +   P+ +            +PV VK    +
Sbjct: 631 RVEDTGADAIELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTEWCKHYSKLPVIVKLTPNI 689

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI       + +                 +  +  
Sbjct: 690 TDIRKPAQAAKRGGADAVSLINTINSIMGVDPYTLTMSPSTGGKGSHGGYCGPAVKPIAL 749

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK 205
           ++V EI +  E   L I   GG+     AL 
Sbjct: 750 NMVAEIARDPETAGLPISGIGGIGTWRDALD 780


>gi|83951608|ref|ZP_00960340.1| dihydroorotate dehydrogenase family protein [Roseovarius
           nubinhibens ISM]
 gi|83836614|gb|EAP75911.1| dihydroorotate dehydrogenase family protein [Roseovarius
           nubinhibens ISM]
          Length = 434

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/174 (19%), Positives = 61/174 (35%), Gaps = 27/174 (15%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + V   G + + LN GCP     E   G+ +   P+ VG           +PV VK    
Sbjct: 123 EAVAGTGCDGVELNFGCPHGMS-ERGMGSAVGQVPEYVGQVAEWCKTYTDLPVIVKLTPN 181

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWI--------------HARKAILKGLSPKDNR--- 169
           + D      +R   ++ K+SG + + +               + +  + GL         
Sbjct: 182 ITD------IRKPAQAAKQSGADAVSLINTINSITSVNLDSFSPEPSVDGLGAHGGYCGP 235

Query: 170 KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +  +  ++V EI +      L I   GG+     A + +      V +  AA 
Sbjct: 236 AVKPIALNMVAEIARDPATAGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 289


>gi|254283225|ref|ZP_04958193.1| dihydroorotate dehydrogenase [gamma proteobacterium NOR51-B]
 gi|219679428|gb|EED35777.1| dihydroorotate dehydrogenase [gamma proteobacterium NOR51-B]
          Length = 549

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 72/184 (39%), Gaps = 24/184 (13%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            +++ L + I G  + + V  A ++     + + LN+ CP A+     +G  +  +PD+V
Sbjct: 91  PEDRFLLVSIFGGSVEEFVAVATLLAPV-ADGLELNLSCPHAK----GYGMAMGQDPDMV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
            + +AA+  A++IPV  K      D      +  + ++   +G + +             
Sbjct: 146 AEVVAAVKAAVAIPVVPKLTPNASD------IAAIGRAAVDAGADALCAINTVGPGLTSS 199

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDG 212
           H    +   +     + +  +    + E+ +   ++ I   GGL         +    D 
Sbjct: 200 HGHPVLSNEVGGMSGKGVLPIALKCIREL-RAVTEVPIIGCGGLSTAEDCRAAMTAGADI 258

Query: 213 VMIG 216
           V IG
Sbjct: 259 VGIG 262


>gi|25029433|ref|NP_739487.1| putative NADH-dependent flavin oxidoreductase [Corynebacterium
           efficiens YS-314]
 gi|259508384|ref|ZP_05751284.1| xenobiotic reductase A [Corynebacterium efficiens YS-314]
 gi|23494722|dbj|BAC19687.1| putative NADH-dependent flavin oxidoreductase [Corynebacterium
           efficiens YS-314]
 gi|259164054|gb|EEW48608.1| xenobiotic reductase A [Corynebacterium efficiens YS-314]
          Length = 383

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 73/212 (34%), Gaps = 24/212 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                A++   + G++ I +             P A      +G        ++ + + A
Sbjct: 175 EDFAAASRRAVEAGFDSIEIHGAHGYLLHQFLTPLANKRTDDYGGSFDNRTRLIREVVTA 234

Query: 111 MCKALS--IPVTVKCRIG--VDDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +   +   +P+ V+      +DD+    A     LV+ +K  GV+ + I        G +
Sbjct: 235 VRATIPEEMPLVVRLSATDWIDDEPSWDADQTVRLVEILKGLGVDAVDISTG-----GAA 289

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           P      P    D    +K+E   +     G + + +QA ++L     D + +GRA  ++
Sbjct: 290 PARIPVGPGYQVDFAARVKREVG-IPTSAVGLITEPAQAQELLDDGLADIISLGRAVLRD 348

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
            +           P     P      +  W +
Sbjct: 349 PSWPLRAAHELGLP-NEEIPYPASYWRGVWPE 379


>gi|218782673|ref|YP_002433991.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218764057|gb|ACL06523.1| Predicted NADH:flavin oxidoreductase/NADH oxidase
           [Desulfatibacillum alkenivorans AK-01]
          Length = 668

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC----- 83
           A AI R   K +   +  +    +Q+         +AAK V+D  Y+ + + + C     
Sbjct: 125 ASAITREVPKEM---TIDDIKNTIQLY-------ADAAKRVKDAHYDVVEI-LACTGYLI 173

Query: 84  -----PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAV 134
                P     +  +G           + I A+ KA+     V  RI  +D         
Sbjct: 174 NQFLSPVTNHRKDEYGGSFENRTRFGREVIEAVRKAVGDDYIVGLRISGNDFMPGGHTNE 233

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
              +     +K+GV+ + +       +   P+    +P+  Y  +    KE  ++ +  +
Sbjct: 234 ESSDFAVIAEKAGVDYVNVTGG--WHETNIPQLTSNVPSGAYVYLARGVKEKVNVPVIAS 291

Query: 195 GGLEDMSQALKIL--PSVDGVMI--GRAAYKNSAMLTTVDEYFSNPLTG 239
             + D   A K L   + D  MI  GR    +  +   V E     +  
Sbjct: 292 NRMGDPDVAEKALRSGACD--MICWGRPMLADPELPNKVKEGREWEIIP 338


>gi|160915850|ref|ZP_02078058.1| hypothetical protein EUBDOL_01872 [Eubacterium dolichum DSM 3991]
 gi|158432326|gb|EDP10615.1| hypothetical protein EUBDOL_01872 [Eubacterium dolichum DSM 3991]
          Length = 641

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 68/198 (34%), Gaps = 26/198 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCIAA 110
           V+A+   +  G++ I L   C            P       ++G  L+    ++ + I  
Sbjct: 147 VKASLDAQRAGFDGIEL--HCAHAYMLLGSFLSPLRNKRTDAYGGSLLNRARLLFEVIDG 204

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A      +  R+   ++ P          L+  ++K GV+   I       +    K
Sbjct: 205 IKEACGKDFPIILRMSGSEKDPQGNTLEDMKRLIPYLEKHGVDCFEISGGTQYER--CNK 262

Query: 167 DNRKIPNLDY---DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
                   ++   +    IK       I + G + D   A  +L    VDGV+IGRA   
Sbjct: 263 IIPCHGEAEFTNLEEAKAIKSVATKPVITV-GKILDARLAEDVLDAGEVDGVVIGRALLA 321

Query: 222 NSAMLTTVDEYFSNPLTG 239
               +   +E   + +  
Sbjct: 322 EPDFVKKAEEARYDEIAP 339


>gi|294341780|emb|CAZ90209.1| Dihydropyrimidine dehydrogenase [Thiomonas sp. 3As]
          Length = 438

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 59/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VED G + I LN GCP     E   GA +   P+ +    A   +   +PV VK    +
Sbjct: 124 RVEDTGCDGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTAWCKRYSRLPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI       + +                 +  +  
Sbjct: 183 TDVRQPARAARAGGADAVSLINTINSIIGVDPATLTMTPSTGGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V +I ++     L I   GG+ +   AL  +      V +  AA 
Sbjct: 243 NMVADIARDPKTAGLPISGIGGIGNWRDALDFIALGAGSVQVCTAAM 289


>gi|330796921|ref|XP_003286512.1| dihydroorotate oxidase [Dictyostelium purpureum]
 gi|325083493|gb|EGC36944.1| dihydroorotate oxidase [Dictyostelium purpureum]
          Length = 368

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 61/187 (32%), Gaps = 30/187 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SI 117
             ++  +I  D G   + +N  CP   V  G        NPD V +  + + K L   +I
Sbjct: 182 DFIDTVRIAVDAGSKIVEVNYSCP--NVVTGEGQIY--HNPDAVYEISSTLVKELAPKNI 237

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------------IHARKAILKGL 163
           P+ +K  +  D       +  L +  + +GV  I                       +  
Sbjct: 238 PLIIKVGVMEDLDK----MAKLFQQAENAGVAAIAGINTLSMKVTDKVSGEPSLGESRLT 293

Query: 164 SPKDNRKIPNLDYDIVYE----IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
           S      I +   D V      IKK+N +L +   GG+       + L    D  M    
Sbjct: 294 SGVCGAPIRSAALDWVSTASSIIKKQNNNLKLLGCGGIVKPEHFDQFLDAGADIAMSATG 353

Query: 219 AYKNSAM 225
              +  +
Sbjct: 354 LMWDPYI 360


>gi|254510639|ref|ZP_05122706.1| dihydropyrimidine dehydrogenase [NADP+] [Rhodobacteraceae bacterium
           KLH11]
 gi|221534350|gb|EEE37338.1| dihydropyrimidine dehydrogenase [NADP+] [Rhodobacteraceae bacterium
           KLH11]
          Length = 434

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   G+ +   P+ +        +    PV VK    +
Sbjct: 124 RVAETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWCKQYYDRPVIVKLTPNI 182

Query: 128 DD-QIPAVALRN-------LVKSIKKSGVNGIWIHARKAILKGLSPKDNR---KIPNLDY 176
            D + PA A RN       L+ +I       +   + +  + G           +  +  
Sbjct: 183 TDIRKPAAAARNGGADAVSLINTINSITSVNLDTFSPEPSIDGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +      L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARAEATHGLPISGIGGVTTWRDAAEFISLGCGTVQVCTAAM 289


>gi|324513342|gb|ADY45486.1| tRNA-dihydrouridine synthase 2-like protein [Ascaris suum]
          Length = 158

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/135 (24%), Positives = 50/135 (37%), Gaps = 19/135 (14%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAIL--RGDKKNILGF--------------S 44
           MV       R  A       L+YTE IV   +L  R    ++L                +
Sbjct: 22  MVRAGRTPLRLLALEY-GADLVYTEEIVDQRLLNSRRIVNDVLHTVDYVIEEDVVLRVAT 80

Query: 45  TQEKP-LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            +E+    LQ+G  +  ++   AK V D     I++N+GCP      G  GA L+  PD 
Sbjct: 81  ERERNKCVLQVGTNNGDRIAAVAKKVHDDIAA-IDVNMGCPKLFSLTGGMGAALLTQPDK 139

Query: 104 VGDCIAAMCKALSIP 118
           + +           P
Sbjct: 140 IKEMHQRFRNRKRTP 154


>gi|209544343|ref|YP_002276572.1| dihydropyrimidine dehydrogenase [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209532020|gb|ACI51957.1| dihydroorotate dehydrogenase family protein [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 426

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC---- 123
           +VED G + I LN GCP     E + G+ +   PD V      + +   +P  VK     
Sbjct: 122 LVEDTGADGIELNFGCPHGMS-ERNMGSAVGQVPDYVEMVTRWVKQNTRMPTIVKLTPNI 180

Query: 124 -------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                  R  +     AV+L N ++S+    ++ +        L          +  +  
Sbjct: 181 TNILVPARAALRGGADAVSLINTIQSVVAVDLDAMAPMPVVDGLGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYK 221
            +V EI +  +   L I   GG+     A + L      V +  AA  
Sbjct: 241 RMVGEIARSPDMSGLPISGIGGISTWRDAAEFLVMGATNVQVCTAAMH 288


>gi|326315758|ref|YP_004233430.1| dihydroorotate dehydrogenase family protein [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323372594|gb|ADX44863.1| dihydroorotate dehydrogenase family protein [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 449

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 74/238 (31%), Gaps = 50/238 (21%)

Query: 4   WTDRHY-------RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
            TDR         R   R   + A++ + M+     +    K IL               
Sbjct: 80  ITDRPLAVNLEEIRRVKRAWPDRAMIVSIMV---PCVEESWKRILP-------------- 122

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                      +VED G + I LN GCP     E   GA +   P+ +            
Sbjct: 123 -----------MVEDTGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTQWCKHYTH 170

Query: 117 IPVTVKCRIGVDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +PV VK    + D              AV+L N + SI    +  + +            
Sbjct: 171 LPVIVKLTPNITDVRQPARAARAGGADAVSLINTINSIMGVDLERMAMSPHTGGWGSHGG 230

Query: 166 KDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                +  +  ++V EI ++     L I   GG+     A + +      V +  AA 
Sbjct: 231 YCGPAVKPIALNMVAEIARDAQTAGLPISGIGGVSTWRDAAEFIALGCGTVQVCTAAM 288


>gi|162147298|ref|YP_001601759.1| dihydropyrimidine dehydrogenase [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161785875|emb|CAP55446.1| Dihydroorotate dehydrogenase [Gluconacetobacter diazotrophicus PAl
           5]
          Length = 426

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 61/168 (36%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC---- 123
           +VED G + I LN GCP     E + G+ +   PD V      + +   +P  VK     
Sbjct: 122 LVEDTGADGIELNFGCPHGMS-ERNMGSAVGQVPDYVEMVTRWVKQNTRMPTIVKLTPNI 180

Query: 124 -------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                  R  +     AV+L N ++S+    ++ +        L          +  +  
Sbjct: 181 TNILVPARAALRGGADAVSLINTIQSVVAVDLDAMAPMPVVDGLGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYK 221
            +V EI +  +   L I   GG+     A + L      V +  AA  
Sbjct: 241 RMVGEIARSPDMSGLPISGIGGISTWRDAAEFLVMGATNVQVCTAAMH 288


>gi|163744663|ref|ZP_02152023.1| dihydropyrimidine dehydrogenase [Oceanibulbus indolifex HEL-45]
 gi|161381481|gb|EDQ05890.1| dihydropyrimidine dehydrogenase [Oceanibulbus indolifex HEL-45]
          Length = 437

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/166 (19%), Positives = 58/166 (34%), Gaps = 15/166 (9%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VE+ G + I LN GCP     E   G+ +   P+ +            +PV VK    + 
Sbjct: 125 VEETGADGIELNFGCPHGMA-ERGMGSAVGQVPEYIEMVTRWCKMYTRMPVIVKLTPNIT 183

Query: 129 DQIPAVALRN--------LVKSIKKSGVNGIWIHARKAILKGLSPKDNR---KIPNLDYD 177
           + +               L+ +I       + + + + ++ G           +  +  +
Sbjct: 184 NVLYPAEAAKRGGADAVSLINTINSITSVDLDLFSPEPMIDGKGTHGGYCGPAVKPIALN 243

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +V EI +  E   L I   GG+     A + L      V +  AA 
Sbjct: 244 MVAEIARNPETHGLPISGIGGVTTWRDAAEFLALGAGNVQVCTAAM 289


>gi|20807468|ref|NP_622639.1| NADH:flavin oxidoreductase [Thermoanaerobacter tengcongensis MB4]
 gi|20515995|gb|AAM24243.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Thermoanaerobacter tengcongensis MB4]
          Length = 606

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/141 (20%), Positives = 48/141 (34%), Gaps = 12/141 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGV 148
           +G  L        + +  +  AL    TV CRI  DD               K ++K+G 
Sbjct: 161 YGGSLEGRVRFAVEILKEIKDALP-DFTVICRINGDDFTDGGFNIKESIEFAKILEKNGA 219

Query: 149 NGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQAL 204
           + I + +         +SP      P L      +IK+      I  N  G + D  + L
Sbjct: 220 SAIDVSSGVSSTSEYHISPMGIEDRPLL--PFTKKIKESISIPVIAANKLGDVYDWERIL 277

Query: 205 KILPSVDGVMIGRAAYKNSAM 225
           +     D + I R    +  +
Sbjct: 278 EERI-ADFIGIARGLIGDPDL 297


>gi|309774908|ref|ZP_07669927.1| NADH-dependent flavin oxidoreductase [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308917305|gb|EFP63026.1| NADH-dependent flavin oxidoreductase [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 642

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/216 (14%), Positives = 77/216 (35%), Gaps = 35/216 (16%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC------------PSARVHEGSF 93
           +E P  +++          A+   +  G++ I L   C            P       ++
Sbjct: 139 EELPHIIELYAN-------ASLQAKQAGFDGIEL--HCAHAYMLLGSFLSPMRNKRCDAY 189

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVN 149
           G  L     ++ + I A+  A      +  R+  D++         +  LV  + + G++
Sbjct: 190 GGSLDNRARLLFEVIDAIKAACGKDFPIILRMSGDEKDAQGNTVEDMCYLVPKLIEHGID 249

Query: 150 GIWIHARKAILKG----LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
              I       +      S  ++  +   + + +  +      + + + G + D   A+ 
Sbjct: 250 AFEISGGTQYERPNKIIPSHGEHEGVNVAEAEKIRRV----SSVPVIVVGKILDPCMAMD 305

Query: 206 ILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           ++    VDG++ GRA   ++A++    E   + +  
Sbjct: 306 LVDKGTVDGIVFGRALLADAALVKKAHEERFDEIAP 341


>gi|385923|gb|AAB26630.1| orf1 5'of atwA [Methanothermobacter thermautotrophicus]
          Length = 138

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/137 (19%), Positives = 48/137 (35%), Gaps = 16/137 (11%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
              + E   G  ++++P+ + D  A +       V+VK R  V               + 
Sbjct: 1   QPEITEIGAGQSMLMDPEFLEDFTAEVTGKARSEVSVKIRGNVPGADTVGV----AGVLA 56

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
             GV+ I + A K                 D ++V  + +   D  +  N  + D+  A 
Sbjct: 57  DLGVDYIHLDAMKP-----------GEDRADLELVSLVSEVKGDSILIGNNSVRDIESAR 105

Query: 205 KIL-PSVDGVMIGRAAY 220
            +L    D V + RAA 
Sbjct: 106 AMLAAGADAVSVARAAI 122


>gi|71281629|ref|YP_270636.1| oxidoreductase, FAD/FMN-binding [Colwellia psychrerythraea 34H]
 gi|71147369|gb|AAZ27842.1| oxidoreductase, FAD/FMN-binding [Colwellia psychrerythraea 34H]
          Length = 399

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 66/186 (35%), Gaps = 16/186 (8%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
                +AA I +D G+  + ++ G          P     +  +G C+     I+ + I 
Sbjct: 148 PDMYAKAAIIAQDTGFTGVQIHAGHGFLLSQFLSPLFNRRKDRYGGCIEDRSQIIVEIIE 207

Query: 110 AMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            +   +     +  ++   DQ    +       +V+ + K+ ++ I +          S 
Sbjct: 208 KIRLTVGRTFPIGIKMNSSDQLEGGLSQEDALEVVRILDKTSIDLIELSGGSYFPGAKSS 267

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            D+        D   +  +   ++ + + GG +   QA  +L   +VD V +GRA     
Sbjct: 268 SDSASGGPYFVDFAIK-ARSVTNIPLVVTGGFKTREQATNVLSSDTVDFVGLGRALILKP 326

Query: 224 AMLTTV 229
            +    
Sbjct: 327 DLPKEW 332


>gi|145220191|ref|YP_001130900.1| dihydroorotate oxidase B, catalytic subunit [Prosthecochloris
           vibrioformis DSM 265]
 gi|145206355|gb|ABP37398.1| dihydroorotate oxidase B, catalytic subunit [Chlorobium
           phaeovibrioides DSM 265]
          Length = 310

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/235 (14%), Positives = 77/235 (32%), Gaps = 26/235 (11%)

Query: 26  MIVADAILRGDKKNILG-----FSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +     +  +        T +  + + I G  I   +E    ++   G +   +
Sbjct: 73  MVNAIGLANVGIERFIADKVPFLRTLDTSIIVNIAGRSIDDYLEVVSRLDAVPGLDAYEI 132

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL--- 136
           N+ CP    +       + ++PD   + +  +    S  + +K    V            
Sbjct: 133 NLSCP----NVKGECMIMGVSPDATREIVTELRAITSRHLMIKLTPNVTSISSIALAAEA 188

Query: 137 -----RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                 +L+ ++    V+  W   R  +           I  +    V+E+        +
Sbjct: 189 AGADSLSLINTVVGMAVD--WKKRRPLLTNVTGGLSGPAIKPIALAKVWEVYNAVSIPVV 246

Query: 192 GLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM----LTTVDEYFSNPLTGSS 241
           G+ GG+     A++ L      + IG   +    +       ++++FS P   + 
Sbjct: 247 GM-GGIASFDDAMEFLVTGASAIQIGTMNFVQPDIGEKVAAAIEKFFSTPGAPTP 300


>gi|315637020|ref|ZP_07892244.1| NADPH dehydrogenase [Arcobacter butzleri JV22]
 gi|315478850|gb|EFU69559.1| NADPH dehydrogenase [Arcobacter butzleri JV22]
          Length = 343

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/196 (15%), Positives = 67/196 (34%), Gaps = 17/196 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAA 110
              +  A   ++  Y+ I L+       C    P +      +G  L     +V +    
Sbjct: 145 ELFINTAFRAKEADYDAIELHAAHGYLLCEFLSPISNNRIDIYGGTLENRCRLVLEIAKD 204

Query: 111 MCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + + + +P  V +     + +         L K ++K GV+ I + +   I    +    
Sbjct: 205 IKQKVDLPLIVRISADEWMKNGWNIEDSIYLSKELEKLGVDAIHVSSGGNIENPDNAPKI 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-AM 225
             +    +    +  KEN ++ +   G +    +   +L +   D V  GR   +N   +
Sbjct: 265 EPLYQASW---AKKIKENINIPVIAVGLIITPKEGEYLLENKFCDFVAYGRELLRNPNFV 321

Query: 226 LTTVDEYFSNPLTGSS 241
               +E+       SS
Sbjct: 322 FNAANEFKEKEKIDSS 337


>gi|260464286|ref|ZP_05812478.1| dihydroorotate dehydrogenase family protein [Mesorhizobium
           opportunistum WSM2075]
 gi|259029910|gb|EEW31194.1| dihydroorotate dehydrogenase family protein [Mesorhizobium
           opportunistum WSM2075]
          Length = 437

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+   + I LN GCP     E   GA +   P+ +   +    +   +PV  K    +
Sbjct: 124 VVEETEADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVVRWCKQNTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDVRKPARAALAGGTDAVSLINTINSITGVDLDSFAPQPIIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDTETRGLPISGIGGITTWRDAAEFMALGAGNVQVCTAAM 289


>gi|242218572|ref|XP_002475075.1| predicted protein [Postia placenta Mad-698-R]
 gi|220725754|gb|EED79728.1| predicted protein [Postia placenta Mad-698-R]
          Length = 409

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 64/194 (32%), Gaps = 34/194 (17%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+AA      G + +++         N   P +      +G        +  + + A+ 
Sbjct: 198 FVDAAARAVKAGVDVVDVHGAHGYLLHNFMSPVSNRRTDKYGGSFENRIHLTLEVVDAVR 257

Query: 113 KA--LSIPVTVKC------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA----RKAIL 160
                 +P+  +           +         NL + +   GV+ I + +    R+  +
Sbjct: 258 AVIPTDMPLMFRVSATDWLEEFDEPSWQLEDTVNLAEILADHGVDLIDVSSGGTDRRQKI 317

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           K ++P                +KK   D + +   GG++D   A  +L    VD V++GR
Sbjct: 318 KFIAPAYQAHFAEA-------VKKRVGDRMLVAGVGGIKDGHIAQHVLQEQGVDMVLVGR 370

Query: 218 AAYKN---SAMLTT 228
              K+         
Sbjct: 371 QFLKDHQSVWTFAQ 384


>gi|319782785|ref|YP_004142261.1| dihydroorotate dehydrogenase [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317168673|gb|ADV12211.1| dihydroorotate dehydrogenase family protein [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 437

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+   + I LN GCP     E   GA +   P+ +   +    +   +PV  K    +
Sbjct: 124 VVEETEADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVVRWCKQNTRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDVRKPARAAHAGGTDAVSLINTINSITGVDLDSFAPQPTIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDPETQGLPISGIGGITTWRDAAEFMALGAGNVQVCTAAM 289


>gi|312898426|ref|ZP_07757816.1| dihydroorotate dehydrogenase 1B [Megasphaera micronuciformis F0359]
 gi|310620345|gb|EFQ03915.1| dihydroorotate dehydrogenase 1B [Megasphaera micronuciformis F0359]
          Length = 304

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/160 (17%), Positives = 57/160 (35%), Gaps = 23/160 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
               E A  ++  G + + +N+ CP    +    G     +P        ++ K    PV
Sbjct: 108 EDYGELAARLDVAGIDAVEVNISCP----NVKEGGIVFGTDPKAAAAVTESVRKHTKKPV 163

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKAILKG-LSPKD 167
            VK    V D         + K+++ +G + +            I AR+ +L        
Sbjct: 164 IVKLSPNVTDITV------MAKAVEAAGADAVSLINTLTGMAVDIDARRPLLGNITGGLS 217

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              +  +   +V++  K      +GL GG+     A++ +
Sbjct: 218 GPAVKPVALRMVWQTAKAVSIPVLGL-GGISSWKDAVEFM 256


>gi|301062062|ref|ZP_07202764.1| putative NADH oxidase [delta proteobacterium NaphS2]
 gi|300443828|gb|EFK07891.1| putative NADH oxidase [delta proteobacterium NaphS2]
          Length = 667

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/179 (13%), Positives = 57/179 (31%), Gaps = 17/179 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            K  EAA      G++ + +             P   + +  +G           + IA 
Sbjct: 146 DKFAEAAVRARTAGFDAVEILGSAGYLISQFLSPITNLRKDEYGGSFENRMRFGLETIAK 205

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+    PV ++      ++     +  R    + +K+GV+   +       +   P+
Sbjct: 206 VRNAVGSDYPVLLRIAGNDFMEGSNTNLEARQFAAAAEKAGVDLFDVTGG--WHETRVPQ 263

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
               +P   Y  +    +      +  +  + D   A ++L     D V + R    + 
Sbjct: 264 LTMGVPRKAYVYLARGIRSAVSAPVISSNRINDPETAEQVLRSDGADLVTMARGLLADP 322


>gi|307729144|ref|YP_003906368.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1003]
 gi|307583679|gb|ADN57077.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1003]
          Length = 682

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/186 (11%), Positives = 56/186 (30%), Gaps = 21/186 (11%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              A++ +  GY+ + +            CP        +G  +     +  + +  +  
Sbjct: 145 ARCARLAQRAGYDGVEIMGSEGYLLNQFLCPRTNRRTDRYGGSIQNRMRLAREIVERVRA 204

Query: 114 ALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                  V  R+ + D             + ++++ +GV     +      +   P    
Sbjct: 205 VCGERFIVVYRLSLIDLVEGGNTWEETVQVARALEAAGVTLF--NTGIGWHEARIPTIVT 262

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG----VMIGRAAYKNSAM 225
            +P   +  +    K   ++ + ++  +     A  +L   DG    V + R    +   
Sbjct: 263 SVPRAAFAALSARLKAAVNVPVIVSNRINTPEVAEALL--ADGAGDLVSMARPLLADPDF 320

Query: 226 LTTVDE 231
           +    E
Sbjct: 321 VRKTAE 326


>gi|322369621|ref|ZP_08044185.1| NADH-dependent flavin oxidoreductase [Haladaptatus paucihalophilus
           DX253]
 gi|320550791|gb|EFW92441.1| NADH-dependent flavin oxidoreductase [Haladaptatus paucihalophilus
           DX253]
          Length = 363

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/205 (19%), Positives = 71/205 (34%), Gaps = 23/205 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+   D G+    ++            P     E  +G  L     IV +   A
Sbjct: 160 DDFAAAAERSLDAGFEIAEVHAAHGYLLHEFLSPVTNDREDEYGGSLENRTRIVREVTEA 219

Query: 111 MCKAL--SIPVTVKCR-IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           +        PV V+        +  +  + +   L   +   G + I + A      GL 
Sbjct: 220 VRDVWPDDKPVFVRISATDWLPERESWTIEDSVHLADRLGDIGADLIDVSAG-----GLH 274

Query: 165 PKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           P      P  +Y +   E  +E+ D+ +G  GG+ + +QA  ++ +   D  +IGR   +
Sbjct: 275 PDQRIPNPGPNYQVPFAERIREDTDVPVGAVGGITEPAQADALIRNGRADLAIIGREHLR 334

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTR 246
           +        E      +   PI+ R
Sbjct: 335 DPYFTLHAAEELDAEDSVEWPIQYR 359


>gi|167769964|ref|ZP_02442017.1| hypothetical protein ANACOL_01305 [Anaerotruncus colihominis DSM
           17241]
 gi|167667798|gb|EDS11928.1| hypothetical protein ANACOL_01305 [Anaerotruncus colihominis DSM
           17241]
          Length = 371

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/180 (20%), Positives = 67/180 (37%), Gaps = 24/180 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
            L   I  +  S++   A+  E  G + + L++  P   + E      + L P+ + + +
Sbjct: 92  HLICSIRASSPSEIAYIAQRTERLGADALQLDLYAPMDSMIE-----DIHLQPEKLYEFV 146

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAV---------ALRNLVKSIKKSGVNGIWIHARKAI 159
            A   A+SIPV  +    +    P +         A+  +      SGV+          
Sbjct: 147 HAAASAVSIPVMTRLPYNLAASAPHLHAVERAGLRAICAIESLRALSGVDLETQTTLMPT 206

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
             G + +  R I       + ++     DL I   GG+ED    L+       +M+G AA
Sbjct: 207 YGGYTGRHIRPISLAATATLAQL----TDLPICGVGGVEDYRSILEF------IMLGAAA 256


>gi|297526229|ref|YP_003668253.1| dihydroorotate dehydrogenase family protein [Staphylothermus
           hellenicus DSM 12710]
 gi|297255145|gb|ADI31354.1| dihydroorotate dehydrogenase family protein [Staphylothermus
           hellenicus DSM 12710]
          Length = 301

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 45/207 (21%), Positives = 69/207 (33%), Gaps = 20/207 (9%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
                  P  + IGG D  +    A+   D     + LN+ CP    H   FG       
Sbjct: 86  EIHRYGLPAIVSIGGRDPGEFQVLAEKALDAKPEALELNLSCP----HTPGFGVDAAATD 141

Query: 102 DIVGDCIAAMCKALSIPVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             +      +    SIPV  K     RI  + +I      + V  I       I ++  K
Sbjct: 142 KALKHIALNVSSISSIPVWGKLGFSRRIVRESEILLSNGVDAVVLINTLPGMFIDVYVGK 201

Query: 158 AIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L  G        I  +    VY++ +E     IG+ GG+ D    ++ +L     V I
Sbjct: 202 PVLTHGYGGLSGPAIHPVAVYSVYKVYEELGAEIIGV-GGVVDWKTCVELLLAGAKAVQI 260

Query: 216 GRA-------AYKNSAMLTTVDEYFSN 235
           G            N  +L  V +Y   
Sbjct: 261 GTGFYMVGYDIVHN--ILDGVKKYMEE 285


>gi|207111068|ref|ZP_03245230.1| transcriptional regulator, putative [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 67

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L  S  E     QI G+  S + EA + +      N I+ N GCP+ +V     G+ L+ 
Sbjct: 1   LEKSPLEDHFMAQISGSKESVVKEAVEKINALEHVNGIDFNCGCPAPKVANHGNGSGLLK 60

Query: 100 NPDIVGD 106
           + + +  
Sbjct: 61  DLNHLVK 67


>gi|169836869|ref|ZP_02870057.1| tRNA-dihydrouridine synthase [candidate division TM7 single-cell
           isolate TM7a]
          Length = 88

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKEN----PDLFIGLNGGLEDMSQALKIL---PSVDGVM 214
            L  K         ++++ EI K      P   + +NG +++ +   +I+   P V+G+M
Sbjct: 6   HLRTKKEMSKVPAHFELIDEIVKLRNEISPQTLLTINGDIKNRAHGEEIVKNHPGVNGIM 65

Query: 215 IGRAAYKNSAMLT 227
           IGR  + +     
Sbjct: 66  IGRGIFTDPFCFR 78


>gi|290963062|ref|YP_003494244.1| bifunctional hydroxylase/oxidoreductase [Streptomyces scabiei
           87.22]
 gi|260652588|emb|CBG75721.1| putative bifunctional hydroxylase/oxidoreductase [Streptomyces
           scabiei 87.22]
          Length = 791

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/200 (16%), Positives = 63/200 (31%), Gaps = 17/200 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA+   + G++ I ++            P A     ++G  L        +   A+
Sbjct: 549 DFARAARRGVEAGFDLIEVHAAHGYLLSSFLSPVANRRADAYGGPLENRLRFPLEVFDAV 608

Query: 112 CKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+  S+PVTV+      + D        ++ ++  + G   I + A   + +   P  
Sbjct: 609 RRAVPSSVPVTVRISATDWMPDGNTGDDAVDIARAFIEHGAAAIDVSAG-QVAQDEQPAY 667

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS-A 224
            R       D++         + +   G +        IL     D   +GR    N   
Sbjct: 668 GRSYQTPFADLIRHKVAGPAGVPVIAVGAISSYDDVNSILLAGRADLCALGRTHLYNPQW 727

Query: 225 MLTTVDEYFSNPLTGSSPIK 244
            L    E          P++
Sbjct: 728 TLQAAAEQEYRGPGARWPVQ 747


>gi|170721018|ref|YP_001748706.1| dihydropyrimidine dehydrogenase [Pseudomonas putida W619]
 gi|169759021|gb|ACA72337.1| dihydroorotate dehydrogenase family protein [Pseudomonas putida
           W619]
          Length = 424

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/159 (21%), Positives = 56/159 (35%), Gaps = 17/159 (10%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           ++PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTHCALPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE-----NPDLFIGLNGGLEDMSQALKILPSV 210
           ++V EI ++      P   IG  G   D ++ + +    
Sbjct: 241 NMVAEIARDPQTRGLPICGIGGIGNWRDAAEFIALGSGA 279


>gi|317471237|ref|ZP_07930602.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
 gi|316901284|gb|EFV23233.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
          Length = 356

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/177 (22%), Positives = 71/177 (40%), Gaps = 23/177 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPS--------ARVHEG--SFGACLMLNPDIVG-DCI 108
            + V+AA      GY+ + L+ GC S        +RV++    +G      P+    + +
Sbjct: 144 DQFVKAAVRAYQAGYDGVELH-GCHSYLMCEFFNSRVNKRTDEYGQY----PERFAVEIL 198

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKD 167
             + +A+     V  R+G  +   A  +R+  K +++ G++ + I +      +  +PKD
Sbjct: 199 EKIKEAVPKEFIVGIRLGAFEPALADGIRH-AKLLEEHGIDFLDISYGFSGEDEPGAPKD 257

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
                 +      EIKK        +N  + D   A  IL    VD   IGR    N
Sbjct: 258 FPYKDVIH--AAGEIKKHVSVPVFAVN-SITDARMAEDILERTGVDMADIGRGVLVN 311


>gi|56696653|ref|YP_167014.1| dihydropyrimidine dehydrogenase [Ruegeria pomeroyi DSS-3]
 gi|56678390|gb|AAV95056.1| dihydroorotate dehydrogenase family protein [Ruegeria pomeroyi
           DSS-3]
          Length = 434

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 53/167 (31%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   GA +   P+ +             PV VK    +
Sbjct: 124 RVAETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKTYYDKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRYPARAARNGGADAVSLINTISSITSVNLDNFSPEPSIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +      L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEISRDPATQGLPISGIGGVTTWRDAAEFMSLGCGTVQVCTAAM 289


>gi|189218638|ref|YP_001939279.1| dihydroorotate dehydrogenase fused to Fe-S-cluster domain
           [Methylacidiphilum infernorum V4]
 gi|189185496|gb|ACD82681.1| Dihydroorotate dehydrogenase fused to Fe-S-cluster domain
           [Methylacidiphilum infernorum V4]
          Length = 387

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/172 (19%), Positives = 62/172 (36%), Gaps = 23/172 (13%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ +E  G + I LN GCP     E   G+ +  +P    +  + + +  S+P+ VK   
Sbjct: 67  AQKIEGSGADGIELNFGCPHGM-PERGTGSKIGQDPARCAEVTSWVRRVTSLPLIVKLTP 125

Query: 126 GVDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
            V D              A++L N ++SI    ++   +    A     S      I  +
Sbjct: 126 NVTDISCIARAAIAGGASALSLINTLESILGVDIDTFEVLPSIAGKSSHSGYSGEAIKPI 185

Query: 175 DYDIVYEIKK----ENPDLFIGLNGGLEDMSQALKI-------LPSVDGVMI 215
             ++  ++      +   L I   GG+      ++        L     VM+
Sbjct: 186 ALNLTAKVASMEEVQKKGLAISAMGGISSWRDGVEFLLLGATSLQLCTSVML 237


>gi|330810232|ref|YP_004354694.1| dihydropyrimidine dehydrogenase [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327378340|gb|AEA69690.1| putative dihydropyrimidine dehydrogenase [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 424

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/151 (22%), Positives = 53/151 (35%), Gaps = 14/151 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEQVTRWCKTYCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 181 TDIRVAARAAHRGGADAVSLINTINSITSVDLDRMVALPSVGSQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK 205
           ++V EI ++     L I   GG+     A +
Sbjct: 241 NMVAEIARDPQTQGLPICGIGGIGSWRDAAE 271


>gi|260221587|emb|CBA30301.1| Uncharacterized protein yeiA [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 435

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/151 (23%), Positives = 51/151 (33%), Gaps = 14/151 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VED G + I LN GCP     E   GA +   P+ +            +PV VK    +
Sbjct: 124 RVEDTGADAIELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTEWCKHYSKLPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI       + +                 +  +  
Sbjct: 183 TDIRKPAQAAKRGGADAVSLINTINSIMGVDPYTLTMSPSTGGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALK 205
           ++V EI +  E   L I   GG+     AL 
Sbjct: 243 NMVAEIARDPETAGLPISGIGGIGTWRDALD 273


>gi|229585060|ref|YP_002843562.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           M.16.27]
 gi|238619962|ref|YP_002914788.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           M.16.4]
 gi|228020110|gb|ACP55517.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           M.16.27]
 gi|238381032|gb|ACR42120.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           M.16.4]
          Length = 290

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 28/172 (16%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL + +GGA I+++ E  K++E      I +NV  P    +   +G  L     ++GD +
Sbjct: 87  PLIVSVGGASINEIKEVVKVIE-SKAKIIEINVSSP----NRKGYGESL---STLIGDIV 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
             +     +PV VK         P   +  L     + G +G             I   K
Sbjct: 139 ENVKSVTRLPVFVKL-------GPWDNVVELAGRALEKGADGFTLINTIRGLIVDIETFK 191

Query: 158 AI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I   G      R +  +   I+ ++ +E   + I   GG+ D +  + +L 
Sbjct: 192 PILYYGTGGVSGRCLYPVALRIIRDVYEEYG-VDIIGVGGVYDWTDVIGMLA 242


>gi|227827789|ref|YP_002829569.1| dihydroorotate dehydrogenase [Sulfolobus islandicus M.14.25]
 gi|227459585|gb|ACP38271.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           M.14.25]
 gi|323474857|gb|ADX85463.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           REY15A]
 gi|323477598|gb|ADX82836.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           HVE10/4]
          Length = 290

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 28/172 (16%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL + +GGA I+++ E  K++E      I +NV  P    +   +G  L     ++GD +
Sbjct: 87  PLIVSVGGASINEIKEVVKVIE-SKAKIIEINVSSP----NRKGYGESL---STLIGDIV 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
             +     +PV VK         P   +  L     + G +G             I   K
Sbjct: 139 ENVKSVTRLPVFVKL-------GPWDNVVELAGRALEKGADGFTLINTIRGLIVDIETFK 191

Query: 158 AI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I   G      R +  +   I+ ++ +E   + I   GG+ D +  + +L 
Sbjct: 192 PILYYGTGGVSGRCLYPVALRIIRDVYEEYG-VDIIGVGGVYDWTDVIGMLA 242


>gi|227830499|ref|YP_002832279.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           L.S.2.15]
 gi|229579312|ref|YP_002837710.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           Y.G.57.14]
 gi|284997994|ref|YP_003419761.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           L.D.8.5]
 gi|227456947|gb|ACP35634.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           L.S.2.15]
 gi|228010026|gb|ACP45788.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           Y.G.57.14]
 gi|284445889|gb|ADB87391.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           L.D.8.5]
          Length = 290

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 28/172 (16%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL + +GGA I+++ E  K++E      I +NV  P    +   +G  L     ++GD +
Sbjct: 87  PLIVSVGGASINEIKEVVKVIE-SKAKIIEINVSSP----NRKGYGESL---STLIGDIV 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
             +     +PV VK         P   +  L     + G +G             I   K
Sbjct: 139 ENVKSVTRLPVFVKL-------GPWDNVVELAGRALEKGADGFTLINTIRGLIVDIETFK 191

Query: 158 AI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I   G      R +  +   I+ ++ +E   + I   GG+ D +  + +L 
Sbjct: 192 PILYYGTGGVSGRCLYPVALRIIRDVYEEYG-VDIIGVGGVYDWTDVIGMLA 242


>gi|229581928|ref|YP_002840327.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           Y.N.15.51]
 gi|228012644|gb|ACP48405.1| dihydroorotate dehydrogenase family protein [Sulfolobus islandicus
           Y.N.15.51]
          Length = 290

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 66/172 (38%), Gaps = 28/172 (16%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL + +GGA I+++ E  K++E      I +NV  P    +   +G  L     ++GD +
Sbjct: 87  PLIVSVGGASINEIKEVVKVIE-SKAKIIEINVSSP----NRKGYGESL---STLIGDIV 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
             +     +PV VK         P   +  L     + G +G             I   K
Sbjct: 139 ENVKSVTRLPVFVKL-------GPWDNVVELAGRALEKGADGFTLINTIRGLIVDIETFK 191

Query: 158 AI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I   G      R +  +   I+ ++ +E   + I   GG+ D +  + +L 
Sbjct: 192 PILYYGTGGVSGRCLYPVALRIIRDVYEEYG-VDIIGVGGVYDWTDVIGMLA 242


>gi|219683869|ref|YP_002470252.1| dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis AD011]
 gi|219621519|gb|ACL29676.1| dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis AD011]
          Length = 324

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 76/218 (34%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       +    + D   + + +NV CP   V  G        +P  +   + 
Sbjct: 117 VVSNVAGHCDDDYAQVVAKLADSDADMLEINVSCP--NVTHGGMSVG--TDPMALSRLME 172

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKGLS 164
            +      P+ VK    V D      +  + K+  +SG + +      +  R  I  G  
Sbjct: 173 RLRPMTDKPMIVKLTPNVTD------ITAIAKAAVESGADALSMINTLVGMRINIKTGEP 226

Query: 165 PKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
              NR           +    V+ ++   PD+ I   GG++   +AL+ L    + V +G
Sbjct: 227 IIANRTGGVSGPAVFPVGLACVWRVRTALPDVPIIGIGGIDSGEKALEYLYAGANAVEVG 286

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA  +      V     + L     +  ++ K D WR
Sbjct: 287 GAALYDPTAPIRVARELDDLLDSRPQLAHKLVKGDTWR 324


>gi|190572328|ref|YP_001970173.1| putative NADH/FMN oxidoreductase [Stenotrophomonas maltophilia
           K279a]
 gi|190010250|emb|CAQ43858.1| putative NADH/FMN oxidoreductase [Stenotrophomonas maltophilia
           K279a]
          Length = 366

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 45/138 (32%), Gaps = 11/138 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSG 147
            +G  L     ++ +   A+  A+S  V V  RI     VD     V    L + +   G
Sbjct: 199 GYGGSLPNRLRLLVEVFDAVRAAVSDKVAVGVRISASDWVDGGWDLVQSEALAQVLDARG 258

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            N + + +      GL  +    +            K    + +   G + +  QA  IL
Sbjct: 259 CNFLHVSSG-----GLDERQKITVGPGYQVPFAAAIKAKVRMPVIAVGMITEPEQAESIL 313

Query: 208 --PSVDGVMIGRAAYKNS 223
                D V + R    + 
Sbjct: 314 RHRHADAVALARGILYDP 331


>gi|254693078|ref|ZP_05154906.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 3 str. Tulya]
 gi|261213313|ref|ZP_05927594.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 3 str. Tulya]
 gi|260914920|gb|EEX81781.1| dihydropyrimidine dehydrogenase [Brucella abortus bv. 3 str. Tulya]
          Length = 436

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 59/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   GA +   P+ VG  +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYVGMVVKWCKQYSRMPVITKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRKPARAAFANGTDAVSLINTINSIVSVDLDTMSPVPSIDGRGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I    G+     A + +      V +  AA 
Sbjct: 243 NMVAEIARDAETAGLPISGIVGITTWRDAAEFIALGCGTVQVCTAAM 289


>gi|84503342|ref|ZP_01001411.1| dihydropyrimidine dehydrogenase [Oceanicola batsensis HTCC2597]
 gi|84388252|gb|EAQ01203.1| dihydropyrimidine dehydrogenase [Oceanicola batsensis HTCC2597]
          Length = 434

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 57/173 (32%), Gaps = 27/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   G+ +   P+ +        K    PV VK    +
Sbjct: 124 RVAETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIQMVTEWCKKYYDRPVIVKLTPNI 182

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI--------WIH------ARKAILKGLSPKDNR---K 170
            D      +R   ++ +  G + +          H      A +  + G           
Sbjct: 183 TD------IRKPAEAARAGGADAVSLINTINSITHVDLDLMAPEPTIDGKGSHGGYCGPA 236

Query: 171 IPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           +  +   +V EI +      L I   GG+     A + ++     V +  AA 
Sbjct: 237 VKPIALSMVSEIARNQATHGLPISGIGGVTTWRDAAEFMVLGCGNVQVCTAAM 289


>gi|225351214|ref|ZP_03742237.1| hypothetical protein BIFPSEUDO_02804 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225158670|gb|EEG71912.1| hypothetical protein BIFPSEUDO_02804 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 392

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/227 (16%), Positives = 69/227 (30%), Gaps = 31/227 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +         V  A +V + G   + +N  C
Sbjct: 171 WQPDMQKAIAAAGDGQLLVPSFQGSRVEGMDREAYIADHVTTAHLVAETGAGLMEMNTSC 230

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKS 142
           P            L  +P +VG+   A+   +   P+ VK     +D    + ++     
Sbjct: 231 P-----NEGHNRLLCHDPHLVGEITEAVKNEIGDRPLIVKLAYIPNDADLEIMVKETAGH 285

Query: 143 IKKSGVNGI-WIHARKAILKG----------LSPKDNRKIPNLDYDIVYEI----KKENP 187
               G + I  I A+     G           S      I     D+V  +    +K   
Sbjct: 286 GAVQGFSTINTISAKLVDANGNQALPGAGRDRSGVCGNAIRGAGLDMVGRLNAIREKLGL 345

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
           D  I   GG+              + VM    A  N+ +   +    
Sbjct: 346 DFAIVGVGGVIRPEDYKAYREAGANAVMSATGAMWNARLAQDIKAAL 392


>gi|148547035|ref|YP_001267137.1| dihydropyrimidine dehydrogenase [Pseudomonas putida F1]
 gi|148511093|gb|ABQ77953.1| dihydropyrimidine dehydrogenase (NADP+) / dihydrouracil
           dehydrogenase (NAD+) [Pseudomonas putida F1]
          Length = 424

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           ++PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTYCALPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+ +   A + +      V +  AA 
Sbjct: 241 NMVAEIARDPETRGLPICGIGGIGNWRDAAEFMALGSGAVQVCTAAM 287


>gi|26990740|ref|NP_746165.1| dihydropyrimidine dehydrogenase [Pseudomonas putida KT2440]
 gi|24985736|gb|AAN69629.1|AE016596_7 dihydroorotate dehydrogenase family protein [Pseudomonas putida
           KT2440]
          Length = 424

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           ++PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTYCALPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+ +   A + +      V +  AA 
Sbjct: 241 NMVAEIARDPETRGLPICGIGGIGNWRDAAEFMALGSGAVQVCTAAM 287


>gi|300087200|ref|YP_003757722.1| dihydroorotate dehydrogenase family protein [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299526933|gb|ADJ25401.1| dihydroorotate dehydrogenase family protein [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 334

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/188 (19%), Positives = 65/188 (34%), Gaps = 23/188 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + I G         A+ +    G   + +N+ CP+ +     FGA     P+     
Sbjct: 127 PVIVNIAGDSAEDYASIARRLNGVPGIAALEVNISCPNVKAGCLEFGA----TPESAATV 182

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGL 163
            AA+  A S+PV VK      D      +  L + +  +G + I     +      ++  
Sbjct: 183 TAAVRNATSLPVIVKLTPNTGD------IAALARGVASAGADAISLINTLRGMAIDIRKR 236

Query: 164 SPKDNRKIPNLDYDIVYEIK-------KENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            P        L    +  +            D+ I   GG+     AL+ I+     V +
Sbjct: 237 RPVLANVTGGLSGPAIKPVALAMVWQTAAAVDIPIIGGGGITSAEDALEFIMAGARAVEV 296

Query: 216 GRAAYKNS 223
           G AA  + 
Sbjct: 297 GTAALVDP 304


>gi|291533297|emb|CBL06410.1| dihydroorotate dehydrogenase (subfamily 1) family protein
           [Megamonas hypermegale ART12/1]
          Length = 192

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/147 (17%), Positives = 56/147 (38%), Gaps = 23/147 (15%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           G + + +N+ CP    +    G     +P        A+       V VK    V D   
Sbjct: 9   GVDAVEVNISCP----NVKEGGIVFGTDPKAAAAVTHAVKTHTKKTVIVKLSPNVTD--- 61

Query: 133 AVALRNLVKSIKKSGVNGIW-----------IHARKAILKGLSPK-DNRKIPNLDYDIVY 180
              +  + K+++++G + I            I+ RK +L  ++       +  +   +V+
Sbjct: 62  ---IVQMAKAVEEAGADAISMINTLTGMAIDINTRKPLLGNITGGLSGPAVKPVALRMVW 118

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL 207
           ++ K   ++ I   GG+     A++ L
Sbjct: 119 QVAKAV-NIPIIGMGGIASAEDAIEFL 144


>gi|254522061|ref|ZP_05134116.1| xenobiotic reductase A [Stenotrophomonas sp. SKA14]
 gi|219719652|gb|EED38177.1| xenobiotic reductase A [Stenotrophomonas sp. SKA14]
          Length = 366

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/138 (18%), Positives = 45/138 (32%), Gaps = 11/138 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSG 147
            +G  L     ++ +   A+  A+S  V V  R+     VD     V    L + +   G
Sbjct: 199 GYGGSLPNRLRLLVEVFDAVRAAVSDKVAVGVRLSASDWVDGGWDLVQSEALAQVLDARG 258

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            N + + +      GL  +    +            K    + +   G + +  QA  IL
Sbjct: 259 CNFLHVSSG-----GLDERQKITVGPGYQVPFAAAIKAKVRMPVIAVGMITEPEQAESIL 313

Query: 208 --PSVDGVMIGRAAYKNS 223
                D V + R    + 
Sbjct: 314 RHRHADAVALARGILYDP 331


>gi|167746419|ref|ZP_02418546.1| hypothetical protein ANACAC_01129 [Anaerostipes caccae DSM 14662]
 gi|167653379|gb|EDR97508.1| hypothetical protein ANACAC_01129 [Anaerostipes caccae DSM 14662]
          Length = 356

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/177 (22%), Positives = 71/177 (40%), Gaps = 23/177 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPS--------ARVHEG--SFGACLMLNPDIVG-DCI 108
            + V+AA      GY+ + L+ GC S        +RV++    +G      P+    + +
Sbjct: 144 DQFVKAAVRAYQAGYDGVELH-GCHSYLMCEFFNSRVNKRTDEYGQY----PERFAVEIL 198

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKD 167
             + +A+     V  R+G  +   A  +R+  K +++ G++ + I +      +  +PKD
Sbjct: 199 ERIKEAVPKEFIVGIRLGAFEPALADGIRH-AKLLEEHGIDFLDISYGFSGEDEPGAPKD 257

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
                 +      EIKK        +N  + D   A  IL    VD   IGR    N
Sbjct: 258 FPYKDVIH--AAGEIKKHVSVPVFAVN-SITDARMAEDILERTGVDMADIGRGVLVN 311


>gi|110680292|ref|YP_683299.1| dihydropyrimidine dehydrogenase [Roseobacter denitrificans OCh 114]
 gi|109456408|gb|ABG32613.1| dihydroorotate dehydrogenase family protein, putative [Roseobacter
           denitrificans OCh 114]
          Length = 434

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   GA +   P+ +        +  S PV VK    +
Sbjct: 124 RVEATGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  +                +  +  
Sbjct: 183 TDIRKPAAAAKRGGADAVSLINTINSIVSVDLDTMSPYPSIDGKGTHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARDPETHGLPISGIGGVTTWRDAAEYITMGCGNVQVCTAAM 289


>gi|325955675|ref|YP_004239335.1| NADPH dehydrogenase [Weeksella virosa DSM 16922]
 gi|323438293|gb|ADX68757.1| NADPH dehydrogenase [Weeksella virosa DSM 16922]
          Length = 357

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 62/195 (31%), Gaps = 21/195 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              +AA+   + GY  I ++            P        +G         + + + A+
Sbjct: 159 YFTDAARRAVEAGYEIIEIHAAHGYLIHQFLSPLVNFRSDEYGGSFENRIRFLLEILEAV 218

Query: 112 CKALSIP---VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            K LS     V +      +          L K + + GV  I       +  G +  + 
Sbjct: 219 KKELSTQSLWVRISATDWAEGGWDLHQSIELAKILPEYGVEVID------VSSGGAVHEQ 272

Query: 169 RKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
           +     +Y +   E  K++  +     G +++  QA  IL     D VM+GR   +N   
Sbjct: 273 KIKVEKNYQVPFAEAIKKSTSILTACVGLIDEAEQAEDILQENKADIVMMGRELLRNPYF 332

Query: 226 LTTVDEYFSNPLTGS 240
                +     +   
Sbjct: 333 PIQAADILGATVDWP 347


>gi|15897526|ref|NP_342131.1| dihydroorotate dehydrogenase (dihydroorotate oxidase) (DHOdehase)
           (pyrD) [Sulfolobus solfataricus P2]
 gi|284174846|ref|ZP_06388815.1| dihydroorotate dehydrogenase (dihydroorotate oxidase) (DHOdehase)
           (pyrD) [Sulfolobus solfataricus 98/2]
 gi|9910612|sp|Q9UX04|PYRD_SULSO RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|6015863|emb|CAB57690.1| dihydroorotate dehydrogenase (dihydroorotate oxidase) (dhodehase)
           [Sulfolobus solfataricus P2]
 gi|13813777|gb|AAK40921.1| Dihydroorotate dehydrogenase (dihydroorotate oxidase) (DHOdehase)
           (pyrD) [Sulfolobus solfataricus P2]
 gi|261602288|gb|ACX91891.1| dihydroorotate dehydrogenase family protein [Sulfolobus
           solfataricus 98/2]
          Length = 290

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/172 (20%), Positives = 68/172 (39%), Gaps = 28/172 (16%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL + +GG+ I+++ E  ++V+      I +NV  P    +   +G  L     ++GD I
Sbjct: 87  PLIVSVGGSSINEIKEVVEVVQ-SKAKIIEINVSSP----NRKGYGESL---SKLIGDII 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
            ++     +PV VK         P   +  L     + G +G+            +   K
Sbjct: 139 ESVKSVTKLPVFVKL-------GPWDNVIELAGKALEKGADGLTLINTIKGLIIDVETFK 191

Query: 158 AI-LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I   G      R +  +   I+ ++ +E   + I   GG+ D +  + +L 
Sbjct: 192 PILYYGTGGVSGRCLYPIALRIIKDVYEEYG-VDIIGVGGVYDWTDVIGMLA 242


>gi|117956088|gb|ABK58633.1| putative NADH-dependent flavin oxidoreductase [Azoarcus anaerobius]
          Length = 371

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/213 (15%), Positives = 67/213 (31%), Gaps = 23/213 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           VE+ K     GY+ I ++ G          P A      +G  L        +   AM +
Sbjct: 161 VESVKRALRIGYDLIEMHAGHGYLTHQFLSPLANQRTDEYGGSLQNRMRFALETFEAMRE 220

Query: 114 ALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                  +  R+   D +             + ++K G + I + +      GL P    
Sbjct: 221 VWPKDKPMGARVSASDWVEGGWTVDETVAFARELRKLGCDYIDVSSG-----GLHPAQAV 275

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN---SA 224
            +    +  + +  +   D+ + + G + D   A KI+     D V +GR A  +     
Sbjct: 276 PLAPAYHAEIAQRIRNEADIKVMVVGLIADPHVATKIVESGQADFVCMGRGAMWDPRFPW 335

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
                    +     S+P   ++    +     
Sbjct: 336 HAAETFGAEAQYPARSTPCLPKLRPQLFPNHQE 368


>gi|326382618|ref|ZP_08204309.1| NADH:flavin oxidoreductase [Gordonia neofelifaecis NRRL B-59395]
 gi|326198737|gb|EGD55920.1| NADH:flavin oxidoreductase [Gordonia neofelifaecis NRRL B-59395]
          Length = 669

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/140 (16%), Positives = 50/140 (35%), Gaps = 13/140 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV----DDQIPAVALRNLVKSIKKSGV 148
           +G        I+ + +  + + +     +  R+ V     D I       L + +++ GV
Sbjct: 219 YGGSFENRARILLEIVDEIRQRVPWDFPLSVRLSVVDYEPDGITIDETVRLARLLQEHGV 278

Query: 149 NGIWIHARKAILKGLSPKDN---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           + I        L           R +    ++ +    ++  D+ +  +G L     A +
Sbjct: 279 DVIHASGGHHALMEWEVSPWFMPRALHKWGWEQI----RDAVDIPVIASGSLVSPEVAEE 334

Query: 206 ILPS--VDGVMIGRAAYKNS 223
           IL +   D V +GRA   + 
Sbjct: 335 ILAADSADFVSLGRAMLADP 354


>gi|163732644|ref|ZP_02140089.1| oxidoreductase, putative [Roseobacter litoralis Och 149]
 gi|161394004|gb|EDQ18328.1| oxidoreductase, putative [Roseobacter litoralis Och 149]
          Length = 377

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 82/229 (35%), Gaps = 24/229 (10%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDC 107
                +AA + +  G+  + ++ G     +              S+G  +     I+ + 
Sbjct: 117 PQVYAQAAMLAQKAGFGGVLIHAG--HGFLLSQFLSPLFNHRTDSYGGTIGARFRIIREV 174

Query: 108 IAAMCKALSI--PVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           ++A+ +A+    PV ++      ++  +       +V+ +  + V+ I I          
Sbjct: 175 LSAVRQAVGAAYPVGIRINATDKLEGGLTHHDALEVVRLLDDTSVDLIDISGGTYFPGAA 234

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           S  D        +    +  K    + I L+GG E   QALK L   + D V +GRA   
Sbjct: 235 SSSDELATSGPYFTDFGKKAKTVTSVPIILSGGFETRDQALKTLEDSAADAVSLGRAMVL 294

Query: 222 NSAMLTTVDEYFSNPLTGS---SPIKTRVDKDFWRKISASMTDYAARHL 267
           N A+                  SP +  V   +  +++A   D  A HL
Sbjct: 295 NPAIANAWQSAAGGDPAFPRFVSPPRGGVTAWYSMRLTALGED--AEHL 341


>gi|153816256|ref|ZP_01968924.1| hypothetical protein RUMTOR_02505 [Ruminococcus torques ATCC 27756]
 gi|145846439|gb|EDK23357.1| hypothetical protein RUMTOR_02505 [Ruminococcus torques ATCC 27756]
          Length = 651

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/231 (14%), Positives = 78/231 (33%), Gaps = 32/231 (13%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-------- 82
           + +R D   +     +       +      K  ++A   +++G++ + L+ G        
Sbjct: 118 SFVRNDGTEVRAMDEK-------MMDEIADKFAKSACDAKEYGFDGVLLHFGHGWLPAQF 170

Query: 83  -CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP----AVALR 137
             P     +  +G             +  + +A+     +  RI  ++ I        + 
Sbjct: 171 LSPYFNKRKDEYGGSFENRIKFPMMIVDRVRQAVGRDYMLDMRISGEEHIEGGMEIDEVA 230

Query: 138 NLVKSIKKSGVNGIWIHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
             +K I+   ++ + I     I       +SP      P+     + ++ KE   + + +
Sbjct: 231 EFIKRIEDK-IDMVHISCGVEIDNRTKIYMSPTA--YAPHKINAKMAKLVKEKVKIPVAV 287

Query: 194 NGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            GG+    +A +IL     D V+IGR    +      V + +        P
Sbjct: 288 VGGIMTPEEAEEILEDGCADAVVIGRQLIADPWW---VKKAWEGRSEDIVP 335


>gi|227326833|ref|ZP_03830857.1| putative NADH-dependent flavin oxidoreductase [Pectobacterium
           carotovorum subsp. carotovorum WPP14]
          Length = 364

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 63/180 (35%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V++AK  +  G++ I ++            P        +G  L     +V +   A
Sbjct: 157 DSFVDSAKRADRLGFDLIEIHAAHGYLLHQFLSPLTNQRTDGYGGSLQNRMRLVVEIYRA 216

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         + V +    GV+          L K++ + G + I + +      GLSP 
Sbjct: 217 IRDVFPEHKAVGVRISATDGVEGGWDLEQSVQLSKALHELGCDFIHVSSG-----GLSPL 271

Query: 167 DN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 PN       +IK+E     I + G + +  QA  I+     D + + RA   + 
Sbjct: 272 QQIHPAPNYQVPYAQQIKQEVGITTIAV-GLITEPEQAEAIVATGEADAIGLARAILFDP 330


>gi|193214451|ref|YP_001995650.1| dihydroorotate dehydrogenase family protein [Chloroherpeton
           thalassium ATCC 35110]
 gi|193087928|gb|ACF13203.1| dihydroorotate dehydrogenase family protein [Chloroherpeton
           thalassium ATCC 35110]
          Length = 311

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/203 (13%), Positives = 67/203 (33%), Gaps = 27/203 (13%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + + G  I    E  K + +  G +   +N+ CP    +         ++     +  
Sbjct: 102 VVVNVVGGSIEDYCEVIKTLNEVEGIDGYEINLSCP----NVKGECIIFGVDAHATHEIT 157

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLS 164
           +A+ +     + +K    V       ++ ++  + +K+G + I     +       +   
Sbjct: 158 SALREITDRHLMIKLTPNV------TSIGSIAMAAEKAGADSISLINTLVGMAVDYRTKK 211

Query: 165 PKDNRKIPNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           P        L    +  +          + ++ I   GG+ D   A++        V IG
Sbjct: 212 PLLRNVTGGLSGPAIKPVAVAKVWEASKSVNIPIIGMGGIADFEDAMEFFVVGASAVQIG 271

Query: 217 RAAYKNSA----MLTTVDEYFSN 235
              +        +   ++EYF N
Sbjct: 272 TMNFVYPNISSKIARRIEEYFRN 294


>gi|307267556|ref|ZP_07549033.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306917423|gb|EFN47720.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 641

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 61/177 (34%), Gaps = 17/177 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V AA    + G + + +  G          P     E  +G           + +A + K
Sbjct: 147 VRAAVRAYEAGADALEIQFGHGYLIHQFLSPYTNKREDEYGGSFENRIRFGMEILAEIKK 206

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + +   +  RI  D+ +P          L K+++  GV  I +    +   G       
Sbjct: 207 EIGVDFPIIVRISADELVPGGWTLEDAIRLAKALEDKGVAAIDVSLGSSCESGAITLQTL 266

Query: 170 KI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                L ++   +IK++  ++ +   G +     A +IL     D V +GR    + 
Sbjct: 267 GTQKGLAWEFASKIKEQV-NIPVIAVGRINTPELAEEILVSGKADLVALGRPLVADP 322


>gi|294678050|ref|YP_003578665.1| dihydropyrimidine dehydrogenase [Rhodobacter capsulatus SB 1003]
 gi|294476870|gb|ADE86258.1| dihydropyrimidine dehydrogenase (NADP(+)) [Rhodobacter capsulatus
           SB 1003]
          Length = 433

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/173 (18%), Positives = 57/173 (32%), Gaps = 33/173 (19%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE+   + + LN GCP     E   GA +   PD V      + +   +P  VK    +
Sbjct: 124 RVEETEADGVELNFGCPHGMA-ERGMGAAVGQVPDYVEMVTRWVKQHSRMPCIVKLTPNI 182

Query: 128 DDQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNR---K 170
            D      +R   ++ K+ G +               + + A +  + G           
Sbjct: 183 SD------IRKPAEAAKRGGADAVSLINTINSITSVDLDLFAPQPTIDGFGTHGGYCGPA 236

Query: 171 IPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL-------PSVDGVM 214
           +  +  ++V EI +      L I   GG+     A + +            VM
Sbjct: 237 VKPIALNMVAEIARNPATRGLPISGIGGVTTWRDAAEFMALGAHNVQVCTAVM 289


>gi|183601596|ref|ZP_02962966.1| dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|241190905|ref|YP_002968299.1| Dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|241196311|ref|YP_002969866.1| Dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|183219202|gb|EDT89843.1| dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|240249297|gb|ACS46237.1| Dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|240250865|gb|ACS47804.1| Dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|295793894|gb|ADG33429.1| Dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis V9]
          Length = 327

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 76/218 (34%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       +    + D   + + +NV CP   V  G        +P  +   + 
Sbjct: 120 VVSNVAGHCDDDYAQVVAKLADSDADMLEINVSCP--NVTHGGMSVG--TDPMALSRLME 175

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKGLS 164
            +      P+ VK    V D      +  + K+  +SG + +      +  R  I  G  
Sbjct: 176 RLRPMTDKPMIVKLTPNVTD------ITAIAKAAVESGADALSMINTLVGMRINIKTGEP 229

Query: 165 PKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
              NR           +    V+ ++   PD+ I   GG++   +AL+ L    + V +G
Sbjct: 230 IIANRTGGVSGPAVFPVGLACVWRVRTALPDVPIIGIGGIDSGEKALEYLYAGANAVEVG 289

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA  +      V     + L     +  ++ K D WR
Sbjct: 290 GAALYDPTAPIRVARELDDLLDSRPQLAHKLVKGDTWR 327


>gi|149180123|ref|ZP_01858628.1| putative NADH-dependent flavin oxidoreductase [Bacillus sp. SG-1]
 gi|148852315|gb|EDL66460.1| putative NADH-dependent flavin oxidoreductase [Bacillus sp. SG-1]
          Length = 404

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/182 (23%), Positives = 73/182 (40%), Gaps = 32/182 (17%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            VEAAK  ++ G++ I ++    +  V +             +G  L     +    I A
Sbjct: 181 FVEAAKNAKEAGFDGIEIHGA--NGYVLDQFLTDYTNQREDQYGGSLENRLRLPIQVIKA 238

Query: 111 MCKAL--SIPVTVKCRI-GVDDQIPAVALRN-----LVKSIKKSGVNGIWIHARKAILKG 162
           + +A+    PV ++     V+D     A        +   I+++G++ I I    A    
Sbjct: 239 VREAVGADYPVGIRLSQTKVNDSDHKWAGGESDAEVIFSKIEEAGIDYIHIAEPDAA--- 295

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
            +P  +   P+L      E+ K+  D  +  NG L D + A  +L     D V IG+AA 
Sbjct: 296 -APAFSDNGPSLV-----ELVKKYTDTVVIANGSLGDPNAAEALLKDGKADIVTIGKAAL 349

Query: 221 KN 222
            N
Sbjct: 350 AN 351


>gi|121611067|ref|YP_998874.1| dihydropyrimidine dehydrogenase [Verminephrobacter eiseniae EF01-2]
 gi|121555707|gb|ABM59856.1| dihydroorotate dehydrogenase family protein [Verminephrobacter
           eiseniae EF01-2]
          Length = 436

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 75/238 (31%), Gaps = 50/238 (21%)

Query: 4   WTDRHY-------RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
            TDR         R   R     AL+ + M+  + +     KNIL               
Sbjct: 80  ITDRPLHTNLAEIRRVKRRWPGRALIVSLMVACEEL---RWKNILA-------------- 122

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                       VED G + + LN GCP     E   GA +   P+ +    A       
Sbjct: 123 -----------QVEDTGADGVELNFGCPHGMS-ERGMGAAVGQVPEYITLVTAWCKHYSR 170

Query: 117 IPVTVKCRIGVDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +PV VK    + D              AV+L N + S+    +  + +            
Sbjct: 171 LPVIVKLTPNITDVRQAARAARAGGADAVSLINTINSVMGVDLERMQMIPSTDGWGSHGG 230

Query: 166 KDNRKIPNLDYDIVYEIKKENP--DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                +  +   +V EI ++ P   L +   GG+     A + +      V +  AA 
Sbjct: 231 YCGPAVLPIALHMVAEIARDAPTAGLPLSGIGGIGTWRDAAQFIALGCSTVQVCTAAM 288


>gi|157737306|ref|YP_001489989.1| NADH:flavin oxidoreductase/NADH oxidase [Arcobacter butzleri
           RM4018]
 gi|157699160|gb|ABV67320.1| NADH:flavin oxidoreductase/NADH oxidase [Arcobacter butzleri
           RM4018]
          Length = 341

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 75/198 (37%), Gaps = 21/198 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNV--GC-------PSARVHEGSFGACLMLNPDIVGDCIAA 110
              ++AA   ++  Y+ I ++   GC       P        +G  L     ++ +    
Sbjct: 143 ELFLKAAFRAKEADYDFIEVHSTHGCLLNQFLSPLTNNRIDIYGGTLENRCRLILEIANE 202

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +++P+    RIG D+ +           L K ++K GV+ I + +   + +  +  
Sbjct: 203 IKQKVNLPLI--LRIGADEWMKNGWNIEDSIYLSKELEKVGVDCIDVSSGGNLEEPDNAP 260

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS- 223
               +    +    +  KEN ++ +   G +    +   +L +   D V  GR   +NS 
Sbjct: 261 KIEPLYQASW---AKKIKENVNIPVIAVGLITTPKEGEYLLENKFCDFVAYGRELLRNSN 317

Query: 224 AMLTTVDEYFSNPLTGSS 241
            +    +E+       SS
Sbjct: 318 FVFNAANEFKEKEKIDSS 335


>gi|300710769|ref|YP_003736583.1| dihydropyrimidine dehydrogenase [Halalkalicoccus jeotgali B3]
 gi|299124452|gb|ADJ14791.1| dihydropyrimidine dehydrogenase [Halalkalicoccus jeotgali B3]
          Length = 245

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 63/179 (35%), Gaps = 25/179 (13%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
            AA  +         +N  C  A +     G  L+ + D + + + A  +     V+VK 
Sbjct: 89  RAAGEICRRHDAICEINAHCRQAELRRVGCGETLLADTDRLCEQVRAAAE-TGARVSVKV 147

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R     ++P V L    ++++++G   I + A                   D + V    
Sbjct: 148 RA----EVPGVDLVETARAVERAGAGIIHVDAM------------------DSEPVVLAV 185

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            E  +L +  N G+       +      D V +GR +  +  +LT V E      +  +
Sbjct: 186 CEASELSVIANNGVRGRESVAEYAEYGADAVSVGRPS-DDPRVLTRVREAVDELASREA 243


>gi|254503835|ref|ZP_05115986.1| dihydroorotate dehydrogenase family protein [Labrenzia alexandrii
           DFL-11]
 gi|222439906|gb|EEE46585.1| dihydroorotate dehydrogenase family protein [Labrenzia alexandrii
           DFL-11]
          Length = 437

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 58/168 (34%), Gaps = 15/168 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K VED   + + LN GCP     E   G+ +   P+ +      + K   +P  VK    
Sbjct: 122 KAVEDTEADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKKHSRMPCIVKLTPN 180

Query: 127 VDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           + D              AV+L N + SI    ++ +                   +  + 
Sbjct: 181 ITDIRKPAQAAKAGGADAVSLINTINSIVGVDLDAMSPAPMVDGKGAHGGYCGPAVKPIA 240

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 241 LNMVAEIARDPETHGLPISGIGGVTTWRDAAEFMALGAGSVQVCTAAM 288


>gi|329895415|ref|ZP_08270996.1| NADH:flavin oxidoreductase/NADH oxidase [gamma proteobacterium
           IMCC3088]
 gi|328922298|gb|EGG29644.1| NADH:flavin oxidoreductase/NADH oxidase [gamma proteobacterium
           IMCC3088]
          Length = 708

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 65/182 (35%), Gaps = 18/182 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  + AK     G + + ++ G          P        +G        ++ + +AA+
Sbjct: 170 QFADGAKRAIAAGCDAVEVHGGHGYILSSFLSPKTNQRTDQYGGSDENRARLICEVVAAV 229

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNL---VKSIKKSGVNGIWIHARKAILKGL--S 164
            +A+    PV VK       +   + + +     + I+ +G + I + A     +G   S
Sbjct: 230 REAVGPDFPVIVKIDSREVGKEGGITVEHAKVTARLIEAAGADAITVSAYHDGGQGKMHS 289

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNS 223
             +     N + +    IK     + +  +G +E D+          D +M+GR    + 
Sbjct: 290 ASNIPHEENANVEAAKAIK-AIVSIPVITSGRIELDVGDQAIGRGEYDYLMMGRKLLADP 348

Query: 224 AM 225
            +
Sbjct: 349 DL 350


>gi|289668083|ref|ZP_06489158.1| putative NADH flavin oxidoreductase [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 365

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 70/224 (31%), Gaps = 26/224 (11%)

Query: 47  EKPLALQI--GGADI--SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSF 93
           E+P+   +   G D      V +AK  E  G   I L+            P +     ++
Sbjct: 141 EQPVPQALDEAGIDAVVDAFVASAKRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAY 200

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVN 149
           G  L     +      A+  A+S  + +  RI   D             L K++   G +
Sbjct: 201 GGSLENRMRLTLRIFDAVRAAVSEKIAIGVRISATDWVQGGWDVQQSIALSKALDARGAH 260

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I + +      GL P+    +    Y I   +  +      +   G + + +QA  IL 
Sbjct: 261 YIHVSSG-----GLDPRQQIPL-QAGYQIPFAQEIRAAVSTPVIGVGLITEPAQAEAILQ 314

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
               D + + R    +              +T +        +D
Sbjct: 315 EGQADAIALARGILYDPRWPWHAAAALGASVTPAPQYLRCEPRD 358


>gi|289664443|ref|ZP_06486024.1| putative NADH flavin oxidoreductase [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 372

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 70/224 (31%), Gaps = 26/224 (11%)

Query: 47  EKPLALQI--GGADI--SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSF 93
           E+P+   +   G D      V +AK  E  G   I L+            P +     ++
Sbjct: 148 EQPVPQALDEAGIDAVVDAFVASAKRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAY 207

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVN 149
           G  L     +      A+  A+S  + +  RI   D             L K++   G +
Sbjct: 208 GGSLENRMRLTLRIFDAVRAAVSEKIAIGVRISATDWVQGGWDVQQSIALSKALDARGAH 267

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I + +      GL P+    +    Y I   +  +      +   G + + +QA  IL 
Sbjct: 268 YIHVSSG-----GLDPRQQIPL-QAGYQIPFAQEIRAAVSTPVIGVGLITEPAQAEAILQ 321

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
               D + + R    +              +T +        +D
Sbjct: 322 EGQADAIALARGILYDPRWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|312144423|ref|YP_003995869.1| dihydroorotate dehydrogenase family protein [Halanaerobium sp.
           'sapolanicus']
 gi|311905074|gb|ADQ15515.1| dihydroorotate dehydrogenase family protein [Halanaerobium sp.
           'sapolanicus']
          Length = 363

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 81/235 (34%), Gaps = 48/235 (20%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQIG-------GADISKLVEAAKIVEDFGY 74
           L++EM        G  K +     +E P+  ++G       G    ++ E A+ VE F  
Sbjct: 71  LWSEM--------GPDKWL----NEEYPVIKELGLPVIVGLGYSAEEISELARKVEPF-A 117

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD----DQ 130
           + + L+                L  +P  V + + A  KA+ +PV VK    +D     +
Sbjct: 118 DALELSTH-------------YLGSDPSPVIESVKAAKKAVDLPVLVKLSPQIDIAKFAK 164

Query: 131 IPAVALRNLVKSIKKSG----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
               A  + +  I   G    ++     A      G        I  L    V+E  K  
Sbjct: 165 AAQKAGADGLVLINSFGPTLDIDLESGRALMGSENGYGWLSGDAIFPLALRAVFEAVKAV 224

Query: 187 PDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKN-SA----MLTTVDEYFSN 235
            ++ I   GG+     A+K+ +   + V +   A  N       +   +D Y   
Sbjct: 225 -EIPIIAVGGISRGEDAVKMIMAGAEAVQVCTTAILNGPTVYSKIAREIDRYLEE 278


>gi|251773195|gb|EES53747.1| dihydroorotate dehydrogenase [Leptospirillum ferrodiazotrophum]
          Length = 364

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/183 (16%), Positives = 54/183 (29%), Gaps = 20/183 (10%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
                 AAK+  + G   I +N  CP+ +  EG        +P   G     +   +   
Sbjct: 171 AENFTRAAKMAVEAGAMAIEMNFSCPNVKGTEGQIF----QDPSAAGSIAQKVRAGIGTN 226

Query: 119 VTVKCRIGVDDQIPAV--------ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD--- 167
           V +  ++G      A            + + +I       I    R A+      K    
Sbjct: 227 VPLIAKVGYIGSAQAAGELVSAIGPFVDAIAAINTLSATIINPEGRPALPGPGREKSGVC 286

Query: 168 NRKIPNLDYDIVYEIKKEN--PDLFI--GLNGGLEDMSQA-LKILPSVDGVMIGRAAYKN 222
              I      +V  + +E     L +     GGL  +    L +    D  M    A  +
Sbjct: 287 GNGIRTAALGVVSRLSQEVRARKLPVALVAVGGLMTVEDIDLALSSGADFAMSATGAMWD 346

Query: 223 SAM 225
             +
Sbjct: 347 PFL 349


>gi|194363989|ref|YP_002026599.1| NADH:flavin oxidoreductase/NADH oxidase [Stenotrophomonas
           maltophilia R551-3]
 gi|194346793|gb|ACF49916.1| NADH:flavin oxidoreductase/NADH oxidase [Stenotrophomonas
           maltophilia R551-3]
          Length = 366

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 45/138 (32%), Gaps = 11/138 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSG 147
            +G  L     ++ +   A+  A+S  V V  RI     VD     V    L + +   G
Sbjct: 199 GYGGSLPNRLRLLVEVFDAVRAAVSDKVAVGVRISASDWVDGGWDLVQSEALAQVMDARG 258

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            N + + +      GL  +    +            K    + +   G + +  QA  IL
Sbjct: 259 CNFLHVSSG-----GLDERQKITVGPGYQVPFAAAIKAKVRMPVIAVGMITEPEQAESIL 313

Query: 208 --PSVDGVMIGRAAYKNS 223
                D V + R    + 
Sbjct: 314 RHRHADAVALARGILYDP 331


>gi|126727112|ref|ZP_01742949.1| dihydropyrimidine dehydrogenase [Rhodobacterales bacterium
           HTCC2150]
 gi|126703540|gb|EBA02636.1| dihydropyrimidine dehydrogenase [Rhodobacterales bacterium
           HTCC2150]
          Length = 434

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 54/167 (32%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I LN GCP     E   GA +   P+ +        K  S PV VK    +
Sbjct: 124 KVEATGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRAPAEAAKRGGADAVSLINTINSIVSVDLDAMCPEPSIDGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +        I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARAPATAGFPISGIGGVTTWRDAAEYITLGCGNVQVCTAAM 289


>gi|83312553|ref|YP_422817.1| 2,4-dienoyl-CoA reductase [Magnetospirillum magneticum AMB-1]
 gi|82947394|dbj|BAE52258.1| 2,4-dienoyl-CoA reductase [Magnetospirillum magneticum AMB-1]
          Length = 666

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 73/232 (31%), Gaps = 40/232 (17%)

Query: 23  YTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y+ M  IVA + +R    +       +  +   I         E A++    GY+ + + 
Sbjct: 108 YSRMKDIVAPSAIRAPINSQAPRELSDAEIVQTIA-----DYAECARLAVLAGYDGVEV- 161

Query: 81  VGCPSARVHEGSF-----------------GACLMLNPDIVGDCIAAMCKALS----IPV 119
                  +    +                 G  L      + + + A+  AL     + V
Sbjct: 162 -------MASEGYLINEFLALRTNKRTDRWGGDLHGRMRFLVEIVRAVRAALGEAAMMSV 214

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            +     V+D + A  +  + ++I+  G + I  ++     +   P     +P   +   
Sbjct: 215 RLSMVDLVEDGLAAEEVVAVARAIEAEGCDLI--NSGIGWHEARVPTIAHTVPQGAWSWA 272

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               K    + +  +  ++    A  ++     D V + R    + A    V
Sbjct: 273 TARVKAAVGIPVAASNRIKTPDLAESLIAEGQCDLVSMARPLLADPAFAAKV 324


>gi|187924640|ref|YP_001896282.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
 gi|187715834|gb|ACD17058.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
          Length = 701

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/218 (13%), Positives = 67/218 (30%), Gaps = 26/218 (11%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINL- 79
           Y   +V+ + ++             KP AL I G    +      A++ +  GY+ I + 
Sbjct: 129 YQPFVVSASAIKSPISKF-------KPRALSIAGIAKTVRDYARCARLAQRAGYDGIEIM 181

Query: 80  --------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-- 129
                      CP       ++G  +     +  + +  +         V  RI + D  
Sbjct: 182 GSEGYLLNQFLCPRTNHRADAYGGSIENRMRLAREIVERVRAVCGERFIVVYRISLIDLV 241

Query: 130 --QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                      + ++++ +GV     +      +   P     +P   +  +    K   
Sbjct: 242 EGGNTWDETVQVAQALEAAGVTMF--NTGIGWHEARVPTIVTSVPRAAFAELSARLKAAV 299

Query: 188 DLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNS 223
            + + ++  +     A  +L    G  V + R    + 
Sbjct: 300 KVPVIVSNRINTPEVAEALLAQGAGDLVSMARPLLADP 337


>gi|323692181|ref|ZP_08106424.1| hypothetical protein HMPREF9475_01287 [Clostridium symbiosum
           WAL-14673]
 gi|323503755|gb|EGB19574.1| hypothetical protein HMPREF9475_01287 [Clostridium symbiosum
           WAL-14673]
          Length = 641

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/145 (12%), Positives = 50/145 (34%), Gaps = 9/145 (6%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP------AVALRNLVKSIKKS 146
           +G   +    +  D ++++ +A      V CRI   ++IP            +   ++ +
Sbjct: 170 YGVDYLGRSKLYRDIVSSIKQACGREFPVICRISSSERIPGRQGRGIEETVKIAPLLEAA 229

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + I +     + +             +   +  +K+    + +   G +     A ++
Sbjct: 230 GADAIHVSIGMPLSEQYISAPMDVPDAFNRGEIACVKRAV-RIPVIAVGRINSPELAEEL 288

Query: 207 L--PSVDGVMIGRAAYKNSAMLTTV 229
           L   + D   +GR    +   +  +
Sbjct: 289 LRDGTADFTAVGRGLLADPDFVNKI 313


>gi|146277498|ref|YP_001167657.1| dihydropyrimidine dehydrogenase [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555739|gb|ABP70352.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) [Rhodobacter sphaeroides ATCC
           17025]
          Length = 434

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 59/173 (34%), Gaps = 33/173 (19%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            +ED G + + LN GCP     E   G+ +   P+ +      +     +P  VK    V
Sbjct: 124 RIEDTGADGVELNFGCPHGMA-ERGMGSAVGQVPEYIEMVTRWVKTHSRMPCIVKLTPNV 182

Query: 128 DDQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNR---K 170
            D      +R   ++ K+ G +               I   A   ++ G           
Sbjct: 183 TD------IRKPAEAAKRGGADAVSLINTINSITGVDIDAFAPMPMIDGKGTHGGYCGPA 236

Query: 171 IPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALK-ILPS------VDGVM 214
           +  +  ++V EI +  E   L I   GG+     A++ +L           VM
Sbjct: 237 VKPIALNMVAEIARNPETHGLPISGIGGVTTWRDAVEFMLLGAGNVQVCTAVM 289


>gi|291531974|emb|CBK97559.1| dihydroorotate oxidase B, catalytic subunit [Eubacterium siraeum
           70/3]
          Length = 494

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 68/187 (36%), Gaps = 22/187 (11%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G    +    A++ E+ G + I  N  CP    H          NP++V   
Sbjct: 193 KIIVSSIMGESEDEWTALARLSEEAGVDMIECNFSCPQMTSHSMGSDVG--TNPELVTKY 250

Query: 108 IAAMCKALSIPVTVKCRIGVDD-QIPAVALRN-------LVKSIKKSGVNGIWIHARKAI 159
            AA+ +   +PV  K    + + +IPA+A  N        + ++K      +        
Sbjct: 251 TAAVRRGTKLPVLAKMTPNITNMEIPAIAAVNAGADGIAAINTVKSITNVDLDSFVPTPD 310

Query: 160 LKGLS---PKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSV--- 210
           + G S       + +  +    + ++K+     ++ I   GG+E     L+ IL      
Sbjct: 311 INGKSAVGGYSGKAVKPIALRFISDMKRNETLENVEISGMGGIETWRDGLEFILMGCTNL 370

Query: 211 ---DGVM 214
                VM
Sbjct: 371 QVTTSVM 377


>gi|39934385|ref|NP_946661.1| putative NADH:flavin oxidoreductase [Rhodopseudomonas palustris
           CGA009]
 gi|39648234|emb|CAE26753.1| putative NADH:flavin oxidoreductase [Rhodopseudomonas palustris
           CGA009]
          Length = 371

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 61/179 (34%), Gaps = 24/179 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
             ++A+     G + + L+            P +   E  +G  L   M  P  V + + 
Sbjct: 162 FAQSARRAARLGVDAVQLHAAHGYLLHQFFSPISNKREDEYGGSLENRMRFPLEVFEGVR 221

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIH-ARKAILKGLSPK 166
           A       PVTV+      +D            ++++  G + + +       L+ +S  
Sbjct: 222 AAF-PTDRPVTVRISGADWIDGGATIDDAVAFAQALEARGCSALNVSSGGIDPLQRISDG 280

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            N ++P           K+   + +   G + D  QA  I+ +   D V + R    + 
Sbjct: 281 PNYQVPFA------RAVKQAVSIPVVAVGLITDYEQAEAIIATGDADLVALARGILYDP 333


>gi|70608009|ref|YP_256879.1| flavin oxidoreductase/NADH oxidase [Sulfolobus acidocaldarius DSM
           639]
 gi|68568657|gb|AAY81586.1| flavin oxidoreductase/NADH oxidase [Sulfolobus acidocaldarius DSM
           639]
          Length = 550

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 57/190 (30%), Gaps = 32/190 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM---------LNPDI------- 103
              V+AA+  E  G++ I L                 L+            D        
Sbjct: 141 DDFVKAAERAEKSGFDGIEL-----------HGAHGYLIAQFLSPATNKREDEYRDGVKF 189

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I  + + +SIPV ++      D   +    +  + K ++           R   L 
Sbjct: 190 LEEIIKEVKRVVSIPVGLRISATEFDPQGLNPETVGKIAKRVENLLDYLHLSAGRDGPLG 249

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
           G S            +    I+ +     +   G +  +  A K+L   D  ++ R    
Sbjct: 250 GSSS--FYYKEPSYLEEAKVIRNQFGKTLLVA-GSILTVDDAEKVLEFADAAVLARQILA 306

Query: 222 NSAMLTTVDE 231
           +   L  V +
Sbjct: 307 DPDWLIKVKD 316


>gi|307945999|ref|ZP_07661334.1| NADH:flavin oxidoreductase/nadh oxidase [Roseibium sp. TrichSKD4]
 gi|307769663|gb|EFO28889.1| NADH:flavin oxidoreductase/nadh oxidase [Roseibium sp. TrichSKD4]
          Length = 333

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/191 (17%), Positives = 65/191 (34%), Gaps = 30/191 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+  E  G++ + +   C +  + +             +G  L     +  + I  
Sbjct: 118 FVDAARRAERAGFDGVEI--HCANGYLLDQFLTADTNTRDDRYGGSLDNRLRLTVEIIHK 175

Query: 111 MCKALSIPVTVKCR--IGVDDQIPAVALRNLVKS------IKKSGVNGIWIHARKAILKG 162
           +  A         R      ++        L  +      +  +G + I + + K   K 
Sbjct: 176 VKAATGAEFLTGVRLSQAKANRQKYFWPNGLADAETIFSGVANAGADFIHLASEKGGYKV 235

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
            S          D + +    KE   L +  NGGL D+  A +++     D + IG+ A 
Sbjct: 236 HSYTQ-------DGENLTAFAKELTGLPVIANGGLHDIDLANEVISSEQADFISIGKTAM 288

Query: 221 KNSAMLTTVDE 231
            N  +   V E
Sbjct: 289 LNPDLPNRVAE 299


>gi|295677003|ref|YP_003605527.1| 2,4-dienoyl-CoA reductase (NADPH) [Burkholderia sp. CCGE1002]
 gi|295436846|gb|ADG16016.1| 2,4-dienoyl-CoA reductase (NADPH) [Burkholderia sp. CCGE1002]
          Length = 680

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/193 (12%), Positives = 62/193 (32%), Gaps = 19/193 (9%)

Query: 48  KPLALQIGGAD--ISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGAC 96
           KP AL + G D  +      A++ +  GY+ + +            CP        +G  
Sbjct: 128 KPRALTLAGIDRTVRDYARCARLAQRAGYDGVEIMGSEGYLLNQFLCPRTNRRTDRYGGS 187

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIW 152
           +     +  + +  +         V  R+ + D             + ++++ +GV    
Sbjct: 188 IENRMRLACEIVERVRAECGERFIVVYRLSLIDLVEGGNTWEETVQVAQALEAAGVTIF- 246

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SV 210
            +      +   P     +P   +  +    K + ++ +  +  +     A  ++   + 
Sbjct: 247 -NTGIGWHEARVPTIVTSVPRAAFASLTARLKASVNVPVIASNRINTPEVAEALIADGAA 305

Query: 211 DGVMIGRAAYKNS 223
           D V + R    + 
Sbjct: 306 DLVSMARPLLADP 318


>gi|167034636|ref|YP_001669867.1| dihydropyrimidine dehydrogenase [Pseudomonas putida GB-1]
 gi|166861124|gb|ABY99531.1| dihydroorotate dehydrogenase family protein [Pseudomonas putida
           GB-1]
          Length = 424

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           ++PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEMVTRWCKTYCALPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +  H                +  +  
Sbjct: 181 TDIRQSARAAHRGGADAVSLINTINSITSVDLDRMVAHPIVGDQSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  +   L I   GG+ +   A + +      V +  AA 
Sbjct: 241 NMVAEIARDPDTRGLPICGIGGIGNWRDAAEFMALGSGAVQVCTAAM 287


>gi|81428568|ref|YP_395568.1| dihydroorotate oxidase, catalytic subunit [Lactobacillus sakei
           subsp. sakei 23K]
 gi|123564263|sp|Q38X22|PYRD_LACSS RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|78610210|emb|CAI55259.1| Dihydroorotate oxidase, catalytic subunit [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 307

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/201 (15%), Positives = 66/201 (32%), Gaps = 17/201 (8%)

Query: 49  PLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   + G  +   +    +I +    + I LN+ CP    +    G     +P+     
Sbjct: 98  PIIANVAGNTEADYVAVCERISQAPNVHAIELNISCP----NVAHGGLEFGTSPEAAATL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIKKSGVNGIWIHARKAI 159
             A      +PV VK    V D  P              L+ ++    ++        A 
Sbjct: 154 TKACVAVSQVPVYVKLSPNVTDIRPIAKAVEAAGAAGFSLINTLVGMRIDPKTRQPILAN 213

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRA 218
             G        I  +   +V+++ +   +L I   GG+     AL+ +    + + +G A
Sbjct: 214 QTG--GLSGLAIKPVAIRLVHQV-RSISNLPIIGMGGVATAGDALELMAAGANAIAVGTA 270

Query: 219 AYKNSAMLTTVDEYFSNPLTG 239
            +        + +   + L  
Sbjct: 271 NFSEPFACPNIIKALPDELAK 291


>gi|299132889|ref|ZP_07026084.1| NADH:flavin oxidoreductase/NADH oxidase [Afipia sp. 1NLS2]
 gi|298593026|gb|EFI53226.1| NADH:flavin oxidoreductase/NADH oxidase [Afipia sp. 1NLS2]
          Length = 366

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/188 (20%), Positives = 60/188 (31%), Gaps = 23/188 (12%)

Query: 39  NILGFSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSA 86
           + L F+  E P   L  Q         V AAK   + G++ I ++            P +
Sbjct: 134 SALPFAAGENPPTALDAQGLARVRDDFVRAAKRAAELGFDGIEIHAAHGYLLHQFLSPLS 193

Query: 87  RVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIGV--DDQIPAVALRNLVK 141
                 +G  L   M  P  + D + A   A   PV V+       D            K
Sbjct: 194 NARTDQYGGSLENRMRFPLEIYDAVRAAFPA-DKPVWVRLSATDWADGGWDVDGSIAFAK 252

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +K  G   I + +      GL+P    K+         E  +    +     G + +  
Sbjct: 253 QLKARGCPVIHVSSG-----GLTPSQQIKLGPGYQVAFSERIRAEAGIPTIAVGLITEPK 307

Query: 202 QALKILPS 209
           QA +IL  
Sbjct: 308 QAEEILTK 315


>gi|2065442|emb|CAA73354.1| dihydroorotate oxidase [Sulfolobus acidocaldarius]
          Length = 265

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 83/240 (34%), Gaps = 55/240 (22%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L + IGG+++++ ++A   + D     I LNV  P    +   FG     N   V + + 
Sbjct: 63  LIISIGGSNVNEYIDAVSKINDI-PVMIELNVSSP----NRRGFGES---NLTYVEEIVK 114

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAIL-------- 160
            +   +  PV VK         P   +  +      +G +G+  I+  K +L        
Sbjct: 115 NVKSIVKKPVFVKL-------GPWDNIVEIAGRALSAGADGLTLINTLKGMLIDVEDFKP 167

Query: 161 ---KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               G      + I  L   +++++ KE  +  I   GG+ D   A++++          
Sbjct: 168 ILSYGTGGISGKCIHALAVRVIHDVFKEY-EPEIIGVGGVFDWRDAIELIS--------- 217

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                              L G   +      D  R+I   +  Y       G K+++I 
Sbjct: 218 ---------------VGAKLVGLGTVLVEKGFDVIREIREGIGTYLEE---KGLKVEEIR 259


>gi|330836989|ref|YP_004411630.1| dihydroorotate dehydrogenase family protein [Spirochaeta coccoides
           DSM 17374]
 gi|329748892|gb|AEC02248.1| dihydroorotate dehydrogenase family protein [Spirochaeta coccoides
           DSM 17374]
          Length = 598

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 76/201 (37%), Gaps = 34/201 (16%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
           + +    +    L + +  ++    +   K   D   + I LN  CP A      +G+ +
Sbjct: 104 RELRKRHSLRAYLLVSLSASNPDDFITLVK-AFDGVCDGIELNFSCPHA---SSGYGSSI 159

Query: 98  MLNPDIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--- 152
             +P I    + A+ +  ++  P+ +K    V+D      +  + +S+ ++G +G+    
Sbjct: 160 GCDPHIASSYVRAIRENTALIHPLFIKLTPNVED------IGIVARSVMEAGADGLTAIN 213

Query: 153 -----IHA----RKAILK----GLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGL- 197
                +H        IL+    G      + +     + V EI++     + +   GG  
Sbjct: 214 TVGPWMHTDPVSGTPILQNALGGKGGASGKWVRARALECVREIRQAVGQHVPLIGMGGAT 273

Query: 198 --EDMSQALKILPSVDGVMIG 216
              D++  ++     D V +G
Sbjct: 274 YGTDVAAFIE--AGADAVGLG 292


>gi|323486672|ref|ZP_08091993.1| hypothetical protein HMPREF9474_03744 [Clostridium symbiosum
           WAL-14163]
 gi|323400053|gb|EGA92430.1| hypothetical protein HMPREF9474_03744 [Clostridium symbiosum
           WAL-14163]
          Length = 641

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 18/145 (12%), Positives = 49/145 (33%), Gaps = 9/145 (6%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP------AVALRNLVKSIKKS 146
           +G   +    +  D ++++ +A      V CRI   + IP            +   ++ +
Sbjct: 170 YGVDYLGRSKLYRDIVSSIKQACGREFPVICRISSSEGIPGGQGRGIEETVKIAPLLEAA 229

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + I +     + +             +   +  +K+    + +   G +     A ++
Sbjct: 230 GADAIHVSIGMPLSEQYISAPMDVPDAFNRGEIACVKRAV-RIPVIAVGRINSPELAEEL 288

Query: 207 L--PSVDGVMIGRAAYKNSAMLTTV 229
           L   + D   +GR    +   +  +
Sbjct: 289 LRDGTADFTAVGRGLLADPDFVNKI 313


>gi|229496602|ref|ZP_04390316.1| dihydroorotate dehydrogenase [Porphyromonas endodontalis ATCC
           35406]
 gi|229316499|gb|EEN82418.1| dihydroorotate dehydrogenase [Porphyromonas endodontalis ATCC
           35406]
          Length = 307

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/184 (15%), Positives = 68/184 (36%), Gaps = 25/184 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G++I   V  + ++    +   I LN+ CP   V EG     +        
Sbjct: 97  DTQVLVNVSGSNIEDYVNTSALIATLDHIPAIELNISCP--NVKEGGMAFGVTAKG--AY 152

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
           + ++A+       + VK    V D      +  +  +++ +G + I +            
Sbjct: 153 EVVSAVRAVYPKHLMVKLSPNVTD------ITEIAGAVEDAGADSISLINTILGMAIDAE 206

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
             R  +           +  +   +V+++ K+   + I   GG+   S A++ +L     
Sbjct: 207 KQRPILSTITGGLSGPCVKPIALRMVWQVAKKV-HIPIIGMGGIASTSDAIEFLLAGASA 265

Query: 213 VMIG 216
           + +G
Sbjct: 266 IQVG 269


>gi|332974936|gb|EGK11849.1| anthraniloyl-CoA monooxygenase [Desmospora sp. 8437]
          Length = 340

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 58/208 (27%), Gaps = 35/208 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML---------------NPDIV 104
               +AA+     G + + +                 L+                 PD  
Sbjct: 144 ELFGQAAERAVQAGVDTLEI-----------HGAHGYLIHQFISRISNRRTDEYGEPDRF 192

Query: 105 G-DCIAAMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             D I A+ K +  S+P+ ++       D            K  +  GV+   + +    
Sbjct: 193 ASDVIRAVRKRIPESMPLMMRISAVEYADGGYTLEETVERCKKFRDLGVDVFDVSSGGES 252

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             G S +     P         I+KE   + +   G L+D   A  ++     D V +GR
Sbjct: 253 PTGPS-RVLAAAPGYQVPFAAAIRKEVG-VPVVAVGNLDDPKVAEMVVRNGQADAVAVGR 310

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
              +N                   P + 
Sbjct: 311 GMLRNPYWANEAALALGQENILPRPYRP 338


>gi|56460849|ref|YP_156130.1| NADH:flavin oxidoreductase [Idiomarina loihiensis L2TR]
 gi|56179859|gb|AAV82581.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Idiomarina
           loihiensis L2TR]
          Length = 649

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 59/177 (33%), Gaps = 19/177 (10%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              AK+ +  GY+ + +            CP     +  +G           + + A+  
Sbjct: 123 ARGAKLAQKAGYDGVEIMGSEGYLINQFLCPRTNKRDDKWGGSFENRMRFPLEIVKAVRA 182

Query: 114 ALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     I   +     V+D      +  L K ++++GV    I+      +   P    
Sbjct: 183 AVGEKSIIIFRLSMLDLVEDGHQLDEVLQLGKLLEQAGVT--IINTGIGWHEARVPTIVT 240

Query: 170 KIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +P   +  + E +++E     + +N  +     A  IL     D V + R    + 
Sbjct: 241 SVPRGAFSWITERVRRELSVPVVAVNR-INTPEIAEHILESNQADMVSMARPLLADP 296


>gi|325661505|ref|ZP_08150130.1| hypothetical protein HMPREF0490_00864 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472221|gb|EGC75434.1| hypothetical protein HMPREF0490_00864 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 658

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 66/179 (36%), Gaps = 17/179 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG----------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
           +  EAA  V+  G + + ++             P       ++G  +     +  + I  
Sbjct: 148 QFGEAAFRVKQAGGDGVEIHAAHAHGLLGGFLSPLYNKRTDAYGGDIHGRLRLTLEVIEE 207

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K       +  RI  D+        N    + K ++K+GV+ I +     I++G S  
Sbjct: 208 VRKMCGKDFIIDVRISGDEYTDGGQNLNDAVYVAKQLEKAGVDFIHVSGGTTIMRGSSIP 267

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                P   +  V E  K+   + +   G + +   A +++ +   D  MIGRA   + 
Sbjct: 268 A-PGTPMGSHSKVGEEIKKQVSIPVATVGRITEPWFAEELIANGKADICMIGRANLCDP 325


>gi|255307083|ref|ZP_05351254.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile ATCC 43255]
          Length = 361

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/124 (21%), Positives = 50/124 (40%), Gaps = 22/124 (17%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IH 154
            I    + ++IPV VK    +D+      + +  K ++++G + I             I 
Sbjct: 131 MIKDAKERVNIPVIVKLPPMIDE------IGDFAKKLEEAGADAITACDSVGPAFRIDIE 184

Query: 155 ARKAIL--KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             + +L   G+       I  +    +YEIKK+  ++ I   GG      AL++ +   D
Sbjct: 185 TGQPLLGGNGIGYLSGETIKPITLQRIYEIKKQV-NIPIIGLGGCVSGDDALEMIMAGAD 243

Query: 212 GVMI 215
            V I
Sbjct: 244 FVGI 247


>gi|254461883|ref|ZP_05075299.1| dihydroorotate dehydrogenase family protein [Rhodobacterales
           bacterium HTCC2083]
 gi|206678472|gb|EDZ42959.1| dihydroorotate dehydrogenase family protein [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 434

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/167 (21%), Positives = 57/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + I LN GCP     E   GA +   P+ +        +  S PV VK    +
Sbjct: 124 LVEDTGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRKPAAAARAGGADAVSLINTINSITSVNLDSMSPEPSIDGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +      + I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARAEATAGMPISGIGGVTTWRDAAEFMALGCGNVQVCTAAM 289


>gi|311063656|ref|YP_003970381.1| dihydroorotate dehydrogenase Pyr [Bifidobacterium bifidum PRL2010]
 gi|310865975|gb|ADP35344.1| Pyr Dihydroorotate dehydrogenase [Bifidobacterium bifidum PRL2010]
          Length = 383

 Score = 54.1 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 70/242 (28%), Gaps = 50/242 (20%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +         V  A++V + G + + +N  C
Sbjct: 147 WQPDMRRAIAAAGPGQVLLPSFQGSRVEGMSGDDYIADHVATARLVCETGADLMEMNTSC 206

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKC---------------RIGV 127
           P            L  +P +VG    A+   +   P+ VK                R  +
Sbjct: 207 P-----NEGHNRLLCHDPHLVGRITEAVKGEIGDRPLIVKLAYIPPTEVEGGWGPDRRVI 261

Query: 128 DDQIPAVALRNL----------------VKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           DD    + +R                   + +  +G   +    R     G+     R  
Sbjct: 262 DDAALELMVRQTAARGTVQAFSTINTISARLVDANGGQALPGKGRDR--SGVCGSAIRGA 319

Query: 172 PNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTV 229
                  +  I++    D  I   GG+              D VM    A  ++ +   +
Sbjct: 320 GLDMVSRLAAIRERLGLDYAIIGVGGVVAPEDYRAYRAAGADAVMSATGAMWDAELARKI 379

Query: 230 DE 231
             
Sbjct: 380 KA 381


>gi|307719447|ref|YP_003874979.1| oxidoreductase [Spirochaeta thermophila DSM 6192]
 gi|306533172|gb|ADN02706.1| putative oxidoreductase [Spirochaeta thermophila DSM 6192]
          Length = 326

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 61/177 (34%), Gaps = 26/177 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   +  +      EAA  +E+ G + + LNV  P       +         + + D +
Sbjct: 99  PVIASLNCSSREWWAEAASRIEEAGADALELNVA-PFP----SNDAESSQEVEERIYDIV 153

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH-----------ARK 157
                A+S+P+ VK            +L +L+  I+  G  G+ +             R+
Sbjct: 154 RTARSAVSVPIAVKVGPYF------TSLGHLLARIEALGAGGVVLFNRFYQVDIAPSTRR 207

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
            +        +     L +  +   ++   +L I  + G+   +  A  +L     V
Sbjct: 208 LVSGHRLSDPHEFSHTLRWTALEAPRR---NLDIVASCGIHSGLDIAKAVLAGASAV 261


>gi|153816297|ref|ZP_01968965.1| hypothetical protein RUMTOR_02548 [Ruminococcus torques ATCC 27756]
 gi|145846350|gb|EDK23268.1| hypothetical protein RUMTOR_02548 [Ruminococcus torques ATCC 27756]
          Length = 638

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/195 (14%), Positives = 63/195 (32%), Gaps = 20/195 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGC------------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +A+K  ++ G++ I L   C            P        +G  L+    ++ + + A
Sbjct: 144 AKASKNAKEAGFDGIEL--HCAHAYMLLGSFLSPLRNKRTDEYGGSLLNRARLLFEVLDA 201

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +       +  R+   ++ P          L+  ++K GV+   I       +     
Sbjct: 202 IKETCGEDFPIVLRMSGSERDPQGNTLEDMKRLIPYLEKHGVDCFEISGGTQYERCNKII 261

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                            K      +   G + D   A  ++    VDGV++GRA   +  
Sbjct: 262 PCHGEEEFTNLKEARAIKAITAKPVITVGKILDAQLAEDVIETNEVDGVVLGRALLADPD 321

Query: 225 MLTTVDEYFSNPLTG 239
            +   +E   + +  
Sbjct: 322 FVEKAEEKRYDEIAP 336


>gi|224282311|ref|ZP_03645633.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum NCIMB 41171]
 gi|310286759|ref|YP_003938017.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum S17]
 gi|313139458|ref|ZP_07801651.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum NCIMB 41171]
 gi|309250695|gb|ADO52443.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum S17]
 gi|313131968|gb|EFR49585.1| dihydroorotate dehydrogenase [Bifidobacterium bifidum NCIMB 41171]
          Length = 383

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 70/242 (28%), Gaps = 50/242 (20%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKL---------VEAAKIVEDFGYNEINLNVGC 83
            + D +  +  +   + L     G+ +  +         V  A++V + G + + +N  C
Sbjct: 147 WQPDMRRAIAAAGPGQVLLPSFQGSRVEGMSGDDYIADHVATARLVCETGADLMEMNTSC 206

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKC---------------RIGV 127
           P            L  +P +VG    A+   +   P+ VK                R  +
Sbjct: 207 P-----NEGHNRLLCHDPHLVGRITEAVKGEIGDRPLIVKLAYIPPTEVEGGWGPDRRVI 261

Query: 128 DDQIPAVALRNL----------------VKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           DD    + +R                   + +  +G   +    R     G+     R  
Sbjct: 262 DDAALELMVRQTAARGTVQAFSTINTISARLVDANGGQALPGKGRDR--SGVCGSAIRGA 319

Query: 172 PNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTV 229
                  +  I++    D  I   GG+              D VM    A  ++ +   +
Sbjct: 320 GLDMVSRLAAIRERLGLDYAIIGVGGVVAPEDYRAYRAAGADAVMSATGAMWDAELARKI 379

Query: 230 DE 231
             
Sbjct: 380 KA 381


>gi|110678338|ref|YP_681345.1| oxidoreductase, putative [Roseobacter denitrificans OCh 114]
 gi|109454454|gb|ABG30659.1| oxidoreductase, putative [Roseobacter denitrificans OCh 114]
          Length = 400

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 68/184 (36%), Gaps = 19/184 (10%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDC 107
                +AA + +  G+  + ++ G     +              S+G  +     I+ + 
Sbjct: 142 PHAYAQAAMLAQSAGFGGVLIHAG--HGFLLSQFLSPLFNHRTDSYGGSISGRFRIIREV 199

Query: 108 IAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           ++A+ +A+     V  RI   D++          ++V+ +  + V+ I I          
Sbjct: 200 LSAVRQAVGAAYPVGIRINATDKLAGGLTHHDALDVVRLLDDTSVDLIDISGGTYFPGAA 259

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           S  D        +    +  K    + I L+GG E   QALK L     D + +GRA   
Sbjct: 260 SSSDELATSGPYFSEFGKKAKSVTSVPIVLSGGFETRDQALKALQGGAADAISLGRAMVL 319

Query: 222 NSAM 225
           N A+
Sbjct: 320 NPAI 323


>gi|70607328|ref|YP_256198.1| dihydroorotate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
 gi|9297106|sp|O08358|PYRD_SULAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|21038935|emb|CAD31980.1| DHOdehase catalytic subunit [Sulfolobus acidocaldarius]
 gi|68567976|gb|AAY80905.1| dihydroorotate dehydrogenase [Sulfolobus acidocaldarius DSM 639]
          Length = 291

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 83/240 (34%), Gaps = 55/240 (22%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L + IGG+++++ ++A   + D     I LNV  P    +   FG     N   V + + 
Sbjct: 89  LIISIGGSNVNEYIDAVSKINDI-PVMIELNVSSP----NRRGFGES---NLTYVEEIVK 140

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-IHARKAIL-------- 160
            +   +  PV VK         P   +  +      +G +G+  I+  K +L        
Sbjct: 141 NVKSIVKKPVFVKL-------GPWDNIVEIAGRALSAGADGLTLINTLKGMLIDVEDFKP 193

Query: 161 ---KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               G      + I  L   +++++ KE  +  I   GG+ D   A++++          
Sbjct: 194 ILSYGTGGISGKCIHALAVRVIHDVFKEY-EPEIIGVGGVFDWRDAIELIS--------- 243

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
                              L G   +      D  R+I   +  Y       G K+++I 
Sbjct: 244 ---------------VGAKLVGLGTVLVEKGFDVIREIREGIGTYLEE---KGLKVEEIR 285


>gi|312144085|ref|YP_003995531.1| dihydroorotate dehydrogenase family protein [Halanaerobium sp.
           'sapolanicus']
 gi|311904736|gb|ADQ15177.1| dihydroorotate dehydrogenase family protein [Halanaerobium sp.
           'sapolanicus']
          Length = 311

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 67/198 (33%), Gaps = 17/198 (8%)

Query: 49  PLALQIGGADISKL-VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G       V A K+        + +N+ CP+ +      G     +P+ V   
Sbjct: 104 PIFANISGYSTEDFLVLADKLNNRPEIAGLEVNLSCPNIK----GGGMIFGTDPEKVYQI 159

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAV-----ALRNLVKSIKKSGVNGIWIHARKAIL-K 161
              + +  S  + VK    + D          A  + V  I       I I  RK +L  
Sbjct: 160 SKKIREIYSGYIIVKLTPNITDITLTALAAQNAGADAVAMINTLSAMKIDIDKRKPLLAN 219

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
                    +  +   ++Y+  K+  ++ I   GG+      L+ IL     V IG    
Sbjct: 220 TFGGLSGPAVKPVALKMIYQSYKKL-EIPIIGLGGVSSGEDVLEFILAGATAVGIGTINM 278

Query: 221 KNSA----MLTTVDEYFS 234
              A    ++  ++ Y S
Sbjct: 279 LEPAAALRIIEEIESYLS 296


>gi|289178647|gb|ADC85893.1| Dihydroorotate dehydrogenase [Bifidobacterium animalis subsp.
           lactis BB-12]
          Length = 368

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 76/218 (34%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       +    + D   + + +NV CP   V  G        +P  +   + 
Sbjct: 161 VVSNVAGHCDDDYAQVVAKLADSDADMLEINVSCP--NVTHGGMSVG--TDPMALSRLME 216

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKGLS 164
            +      P+ VK    V D      +  + K+  +SG + +      +  R  I  G  
Sbjct: 217 RLRPMTDKPMIVKLTPNVTD------ITAIAKAAVESGADALSMINTLVGMRINIKTGEP 270

Query: 165 PKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
              NR           +    V+ ++   PD+ I   GG++   +AL+ L    + V +G
Sbjct: 271 IIANRTGGVSGPAVFPVGLACVWRVRTALPDVPIIGIGGIDSGEKALEYLYAGANAVEVG 330

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA  +      V     + L     +  ++ K D WR
Sbjct: 331 GAALYDPTAPIRVARELDDLLDSRPQLAHKLVKGDTWR 368


>gi|282599750|ref|ZP_05971732.2| xenobiotic reductase A [Providencia rustigianii DSM 4541]
 gi|282567678|gb|EFB73213.1| xenobiotic reductase A [Providencia rustigianii DSM 4541]
          Length = 321

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 37/179 (20%), Positives = 69/179 (38%), Gaps = 22/179 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+AAK  E  G++ I ++            P++ + +  +G        ++ +    +
Sbjct: 116 QFVDAAKRAEQAGFDVIEIHAAHGYLLHSFLSPNSNLRQDEYGGSFANRSRLLVETFKEI 175

Query: 112 CKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+S  + V  RI   D I           L + +++ G + I + +      GLS K 
Sbjct: 176 REAVSPEIAVGVRISATDWIEGGWDLTESIELTQILEELGSSYIHVSSG-----GLSDKQ 230

Query: 168 NRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              + PN    +  EI  +   L +   G + +  QA  IL     D + IGR      
Sbjct: 231 QIPVGPNYQVPLAQEIHNQT-QLPVIAVGLITEPLQAEAILATGQADFIAIGRGILYEP 288


>gi|149913378|ref|ZP_01901911.1| NADH:flavin oxidoreductase/NADH oxidase [Roseobacter sp. AzwK-3b]
 gi|149812498|gb|EDM72327.1| NADH:flavin oxidoreductase/NADH oxidase [Roseobacter sp. AzwK-3b]
          Length = 371

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 56/179 (31%), Gaps = 22/179 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
               +A      G+  I +++           P A      +G  L   M  P  V D I
Sbjct: 159 DFAASACRAVALGFRGIEVHMAHGYLLHQFLSPIANERLDDYGGSLENRMRFPLEVFDAI 218

Query: 109 AAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A      IPV V+      V           L   +K+ G   I + +      G+SPK
Sbjct: 219 KAAI-PDDIPVWVRVSATDWVPGGWDIEDTVALAHRMKERGCAAIHVSSG-----GVSPK 272

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               + +     +    KE   L     G + D + A  IL     D + + R    + 
Sbjct: 273 QQIPLSDGYQVPLAARVKEAVGLPTIAVGLITDPAHAEAILEKGEADAIALARGMLYDP 331


>gi|118592955|ref|ZP_01550343.1| dihydropyrimidine dehydrogenase [Stappia aggregata IAM 12614]
 gi|118434489|gb|EAV41142.1| dihydropyrimidine dehydrogenase [Stappia aggregata IAM 12614]
          Length = 437

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/174 (17%), Positives = 58/174 (33%), Gaps = 27/174 (15%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K VE+   + + LN GCP     E   G+ +   P+ +      + +   +P  VK    
Sbjct: 122 KKVEETEADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKQHSRMPCIVKLTPN 180

Query: 127 VDDQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNR--- 169
           + D      +R   ++ K  G +               + I +    + G          
Sbjct: 181 ITD------VRKPAQAAKAGGADAVSLINTINSIMGVDLDIMSPSPSVDGKGAHGGYCGP 234

Query: 170 KIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +  +  ++V EI +      L I   GG+     A + +      V +  AA 
Sbjct: 235 AVKPIALNMVAEIARDPATHGLPISGIGGVTTWRDAAEFMALGAGSVQVCTAAM 288


>gi|169769925|ref|XP_001819432.1| NADH-dependent flavin oxidoreductase [Aspergillus oryzae RIB40]
 gi|238487746|ref|XP_002375111.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus flavus
           NRRL3357]
 gi|83767291|dbj|BAE57430.1| unnamed protein product [Aspergillus oryzae]
 gi|220699990|gb|EED56329.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus flavus
           NRRL3357]
          Length = 421

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/204 (14%), Positives = 69/204 (33%), Gaps = 29/204 (14%)

Query: 65  AAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           A K     G + + + N           P+       +G        +  +      +A+
Sbjct: 204 AVKRAVKAGADFVEIHNAHGYLLMSFLSPAVNKRTDEYGGSFENRIRLSMEIAKLTREAV 263

Query: 116 --SIPVTVKCR--------IGVDDQIPAVALRNLVKSIKKSG-VNGIWIH-ARKAILKGL 163
               PV ++             +    +       +++ +SG ++ I I        + +
Sbjct: 264 PEDKPVFLRVSATDWLEESRPSEPSWKSEDTVKFAQALAESGYIDLIDISSGGTHQAQHI 323

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
             K   + P         +K+   D L +G  G ++    A  +L    +D VM+GR   
Sbjct: 324 HAKPGFQAPFAV-----AVKRAVGDKLKVGSVGMIDSAQLANSLLEKEGLDFVMVGRGFQ 378

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIK 244
           KN  ++    +  +  ++ ++ I+
Sbjct: 379 KNPGLVWAWADDLNVEISMANQIR 402


>gi|326431283|gb|EGD76853.1| hypothetical protein PTSG_08201 [Salpingoeca sp. ATCC 50818]
          Length = 699

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/220 (17%), Positives = 68/220 (30%), Gaps = 35/220 (15%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIV 69
                    L ++  + A  ++  D      +     + PL           +       
Sbjct: 1   MCSKPYGVQLAFSPRLYAKHLVNEDLYREQHMVTCDDDLPLV---------TMA-----A 46

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
                  ++L     S R   G +GACL+   D+VGD + A  +        K   GV  
Sbjct: 47  PTCKALCLDLTWN--SKRAINGQYGACLLQQRDLVGDMLTAATQQGH-----KVFAGVRV 99

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +  LV+ ++KSG  GI +  R                  ++D+V  IK     L
Sbjct: 100 TDETQDVEGLVRMVEKSGCVGIVVDTRTTE---------ETAAICNWDVVARIK-ALTAL 149

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
            +  +  L   ++    L     D V+          + +
Sbjct: 150 PVLAHASLNSPNEIQPFLKHTGADAVVATTELLFQPTLFS 189


>gi|152967718|ref|YP_001363502.1| NADH:flavin oxidoreductase/NADH oxidase [Kineococcus radiotolerans
           SRS30216]
 gi|151362235|gb|ABS05238.1| NADH:flavin oxidoreductase/NADH oxidase [Kineococcus radiotolerans
           SRS30216]
          Length = 379

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/199 (14%), Positives = 64/199 (32%), Gaps = 22/199 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA+  E  G++ + L+            P +      +G  L     ++ + + A+ 
Sbjct: 162 FADAARRAETAGFDVVELHAAHGYLLHQFLSPLSNHRTDGYGGDLAGRSRLLLEVLDAVR 221

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                  PV V+      V+          L + +   G + +      A   G  P+  
Sbjct: 222 AVWPRDKPVLVRLSTSDWVEGGWDVAESVELTRELAARGADLV-----DASSGGNDPRQR 276

Query: 169 RKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
             +           I++E   + +   G + + +QA ++L     D V + R    +   
Sbjct: 277 IPVGPGYQVPAAARIRRETG-VPVAAVGLILEPAQAEQVLVSGDADAVFLARPLLADPRW 335

Query: 226 LTTVDEYFSNPLTGSSPIK 244
                +    P   + P +
Sbjct: 336 PQRAAQALHAPEAVAWPPQ 354


>gi|296450521|ref|ZP_06892276.1| conserved hypothetical protein [Clostridium difficile NAP08]
 gi|296879355|ref|ZP_06903350.1| conserved hypothetical protein [Clostridium difficile NAP07]
 gi|296260648|gb|EFH07488.1| conserved hypothetical protein [Clostridium difficile NAP08]
 gi|296429898|gb|EFH15750.1| conserved hypothetical protein [Clostridium difficile NAP07]
          Length = 377

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/124 (20%), Positives = 50/124 (40%), Gaps = 22/124 (17%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IH 154
            +    + ++IPV VK    +D+      + +  K ++++G + I             I 
Sbjct: 147 MLKDAKERVNIPVIVKLPPMIDE------IGDFAKKLEEAGADAITACDSVGPAFRIDIE 200

Query: 155 ARKAIL--KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             + +L   G+       I  +    +YEIKK+  ++ I   GG      AL++ +   D
Sbjct: 201 TGQPLLGGNGIGYLSGETIKPITLQRIYEIKKQV-NIPIIGLGGCVSGDDALEMIMAGAD 259

Query: 212 GVMI 215
            V I
Sbjct: 260 FVGI 263


>gi|254439390|ref|ZP_05052884.1| dihydroorotate dehydrogenase family protein [Octadecabacter
           antarcticus 307]
 gi|198254836|gb|EDY79150.1| dihydroorotate dehydrogenase family protein [Octadecabacter
           antarcticus 307]
          Length = 434

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/154 (22%), Positives = 54/154 (35%), Gaps = 14/154 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + I LN GCP     E   GA +   P+ +        K  S PV VK    +
Sbjct: 124 LVEDTGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKKYYSKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRQPAAAARRGGADAVSLINTINSITSVNLDSMSPEPSIDGKGTHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP 208
            +V EI +  E   + I   GG+     A + + 
Sbjct: 243 SMVSEIARFEETKGMPISGIGGVTTWRDAAEFIT 276


>gi|331084913|ref|ZP_08334001.1| hypothetical protein HMPREF0987_00304 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330411007|gb|EGG90429.1| hypothetical protein HMPREF0987_00304 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 648

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 66/179 (36%), Gaps = 17/179 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG----------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
           +  EAA  V+  G + + ++             P       ++G  +     +  + I  
Sbjct: 148 QFGEAAFRVKQAGGDGVEIHAAHAHGLLGGFLSPLYNKRTDAYGGDIHGRLRLTLEVIEE 207

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K       +  RI  D+        N    + K ++K+GV+ I +     I++G S  
Sbjct: 208 VRKMCGKDFIIDVRISGDEYTDGGQNLNDAVYVAKQLEKAGVDFIHVSGGTTIMRGSSIP 267

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                P   +  V E  K+   + +   G + +   A +++ +   D  MIGRA   + 
Sbjct: 268 A-PGTPMGSHSKVGEEIKKQVSIPVATVGRITEPWFAEELIANGKADICMIGRANLCDP 325


>gi|209515499|ref|ZP_03264364.1| dihydroorotate dehydrogenase family protein [Burkholderia sp. H160]
 gi|209503966|gb|EEA03957.1| dihydroorotate dehydrogenase family protein [Burkholderia sp. H160]
          Length = 426

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 59/173 (34%), Gaps = 27/173 (15%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VED G + + LN GCP     E   GA +   P+ +      + +   +P  VK    V 
Sbjct: 123 VEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWVKEGTRLPCLVKLTPNVT 181

Query: 129 DQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNRKIPNL 174
           D      +R+  ++  K G +G              + + A    + G         P  
Sbjct: 182 D------IRHGARAAMKGGADGVSLINTINSIVGVDLDVMAPLPTVDGKGTHGGYCGPAA 235

Query: 175 DYDIVYEIKKENPDL-----FIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
               ++ + +   D       I   GG+ D   A + I+     V +  AA  
Sbjct: 236 KPIALHMVAEIARDPQTHGLPISGIGGISDWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|169836627|ref|ZP_02869815.1| tRNA-dihydrouridine synthase A [candidate division TM7 single-cell
           isolate TM7a]
          Length = 43

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/43 (32%), Positives = 24/43 (55%)

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           GG++ + +  + L  VD VM+GR  Y N  +LT   +Y+ +  
Sbjct: 1   GGIKTVEEIDEHLKHVDSVMLGREIYDNPMILTEFGKYYGSEE 43


>gi|160946850|ref|ZP_02094053.1| hypothetical protein PEPMIC_00811 [Parvimonas micra ATCC 33270]
 gi|158447234|gb|EDP24229.1| hypothetical protein PEPMIC_00811 [Parvimonas micra ATCC 33270]
          Length = 339

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 42/198 (21%), Positives = 78/198 (39%), Gaps = 25/198 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIA 109
             + + K+V+  G++ + +   C           P +      +G  L      +GD + 
Sbjct: 144 DFINSVKLVKQAGFDFVEI--HCAHGYLINQFLSPLSNQRNDEYGGSLEKRYKFLGDILK 201

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ K + I V ++      D+    +L +++K +K +  +G+  ++  +   G+ PK   
Sbjct: 202 AI-KNIDIDVHIRVSANEYDEKGN-SLEDIIKILKLAKDDGVVFNSISS--GGVVPKSPL 257

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMI--GRAAYKNSAM 225
             P    ++  EIKK    L +   G LED      +L   + D  MI  GR   KN   
Sbjct: 258 VYPGYQAELSREIKKA--GLTVSAVGLLEDYGLCEYLLQSDACD--MIYQGRTLLKNPNW 313

Query: 226 LTTVDEYFSNPLTGSSPI 243
           +     YF        P+
Sbjct: 314 VYGAGAYFDEGKEIEYPL 331


>gi|315126528|ref|YP_004068531.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas sp. SM9913]
 gi|315015042|gb|ADT68380.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas sp. SM9913]
          Length = 657

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 58/182 (31%), Gaps = 17/182 (9%)

Query: 61  KLVEAAKIVEDFGYNEIN--------LN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               +A + E  GY+ +         +N    P     +  FG  L     +  + + A+
Sbjct: 143 DFAHSAYLAEKAGYDGVEVMGSEGYLINEFMAPHTNKRDDEFGGSLENRMRLAVEIVKAV 202

Query: 112 CKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              +S    +  R+ V D IP       +     +++K+GV+    +      +   P  
Sbjct: 203 RAKVSDKFLIIFRLSVIDLIPNGSTPEEVTQQAIALEKAGVDIF--NTGIGWHEARVPTI 260

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
              +P   +    +  K+   + +     +     A  IL     D + + R    +   
Sbjct: 261 ASMVPPGAFKEASKRLKDVISVPVIAVNRINTPEIANDILTAGEADLISMARPLLADPEF 320

Query: 226 LT 227
             
Sbjct: 321 FN 322


>gi|322433905|ref|YP_004216117.1| dihydroorotate dehydrogenase family protein [Acidobacterium sp.
           MP5ACTX9]
 gi|321161632|gb|ADW67337.1| dihydroorotate dehydrogenase family protein [Acidobacterium sp.
           MP5ACTX9]
          Length = 489

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 59/177 (33%), Gaps = 26/177 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           +     ED G + + LN GCP     E   G+ +   P+        + +    PV VK 
Sbjct: 116 DMVAQAEDAGADGLELNFGCPHGMS-ERGMGSAVGQVPEYAEQITYWVKERARTPVIVKL 174

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIW--------------IHARKAILKGLSPKDNR 169
              + D      +R   ++ K+ G + +                   + ++ G S     
Sbjct: 175 TPNISD------IRMPARAAKRGGADALSAINTINSITGIDLDTFEPRPMVDGKSSHGGY 228

Query: 170 KIPNLDYDIVYEIKKENPD----LFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
             P +    +  +++   D    L +   GG+     A + IL     V +  AA  
Sbjct: 229 CGPAVKPIALNMVQQIMADKDAMLPLSGIGGIGTWKDAAEFILLGCGNVQVCTAAMH 285


>gi|310780671|ref|YP_003969002.1| NADH:flavin oxidoreductase/NADH oxidase [Ilyobacter polytropus DSM
           2926]
 gi|309749994|gb|ADO84654.1| NADH:flavin oxidoreductase/NADH oxidase [Ilyobacter polytropus DSM
           2926]
          Length = 361

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 66/189 (34%), Gaps = 19/189 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA+  +D G++ I ++            P     +  +G  L      + +   AM 
Sbjct: 146 FGQAARRSKDAGFDGIEIHAAHTYLINQFLSPYYNQRKDEYGGSLENRMRFLVEIYNAMR 205

Query: 113 KALS--IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
                  P+ VK       D  +     R + K +++ G+N I     IH +   L G  
Sbjct: 206 NETDSDYPILVKLTASDFFDGGLTFEETRRISKKMEEIGINAIEVSGNIHGKGESLIGHE 265

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG--RAAYKN 222
            +  +      +    EI  E   + +   GG++    A KIL S +  M G  R     
Sbjct: 266 FEGYKIQDEAYFGRFAEIISEELKIPVITVGGIKTYETADKILNSSNISMFGLSRPLLTE 325

Query: 223 SAMLTTVDE 231
             ++    +
Sbjct: 326 PNLIKRWKD 334


>gi|78189739|ref|YP_380077.1| dihydroorotate dehydrogenase 1 [Chlorobium chlorochromatii CaD3]
 gi|78171938|gb|ABB29034.1| dihydroorotate oxidase B, catalytic subunit [Chlorobium
           chlorochromatii CaD3]
          Length = 313

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/211 (13%), Positives = 75/211 (35%), Gaps = 25/211 (11%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  I    E    ++   G +   +N+ CP    +       + ++ ++  + +
Sbjct: 105 VIVNIAGRSIDDYCEVVSRLDGVEGLDGYEINLSCP----NVKGECMIMGVSSEMTYEIV 160

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARK 157
           +A+       + +K    V       ++  +  + +K+G + + +             RK
Sbjct: 161 SALRSITPRHLMIKLTPNV------TSISTIALAAEKAGADSLSLINTVVGMAVNYKTRK 214

Query: 158 AILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +LK ++       I  +    V+E+ +      +G+ GG+     A++ +L     + I
Sbjct: 215 PLLKNVTGGLSGPAIKPIALAKVWEVYQAVSIPIVGM-GGIASFEDAMEFLLVGARAIQI 273

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           G   +    +   +           + +  R
Sbjct: 274 GTMNFVYPDISEKIAVALEAHFAAPNAMPLR 304


>gi|192289918|ref|YP_001990523.1| NADH:flavin oxidoreductase/NADH oxidase [Rhodopseudomonas palustris
           TIE-1]
 gi|192283667|gb|ACF00048.1| NADH:flavin oxidoreductase/NADH oxidase [Rhodopseudomonas palustris
           TIE-1]
          Length = 371

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 58/179 (32%), Gaps = 24/179 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
             ++A+     G + + L+            P +   E  +G  L   M  P  V + + 
Sbjct: 162 FAQSARRAARLGVDAVQLHAAHGYLLHQFFSPISNKREDEYGGSLEKRMRFPLEVFEGVR 221

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PVTV+      +D            ++++  G + +       +  G     
Sbjct: 222 AAF-PTDRPVTVRISGADWIDGGATIDDAVAFAQALEARGCSAL------NVSSGGIDPL 274

Query: 168 NRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            R     +Y +      K+   + +   G + D  QA  I+ +   D V + R    + 
Sbjct: 275 QRITDGPNYQVPFARAVKQAVSIPVVAVGLITDYEQAEAIIATGDADLVALARGILYDP 333


>gi|307267435|ref|ZP_07548924.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306917541|gb|EFN47826.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 667

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 70/206 (33%), Gaps = 43/206 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
           K  EAA I +  G++ + ++       VHEG                 +G  LM      
Sbjct: 159 KFAEAAVIAKMSGFDGVEIHA------VHEGYLLDQFTIALFNKRTDKYGGDLMGRLRFP 212

Query: 105 GDCIAAMCKAL--SIPVTVK---------CRIGVDDQIPAVAL-------RNLVKSIKKS 146
            + + A+ KA     PV+++          R G   +     L           K ++++
Sbjct: 213 IEIVQAIKKACGDDFPVSLRYSVKSYIKGIRQGGLAEEEFTELGRDIDEGLEAAKILEEA 272

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G +     A        +     +   L   +  ++KK   ++ + + G +ED   A   
Sbjct: 273 GYDAFNADAGTYDSWYWNHPPMYQKKGLYLPLTKKLKK-VVNVPVLVAGRMEDPELASSA 331

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVD 230
           L     D ++IGR    +  +   + 
Sbjct: 332 LEEGKADAIVIGRGLLADPQLPNKIK 357


>gi|297544436|ref|YP_003676738.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296842211|gb|ADH60727.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 684

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 68/210 (32%), Gaps = 33/210 (15%)

Query: 40  ILGFSTQEKP---LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG----- 91
           +   + + KP      QI G  +   VEAA   E  G++ + L+                
Sbjct: 175 LAMHNPKYKPSDFTKQQIQGF-VQDFVEAAIRAEKSGFDAVELHFA--HGWFVNQFLSPD 231

Query: 92  ------SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVK 141
                  +G           D +  + KAL   +TV CRI   D        +      K
Sbjct: 232 TNKRTDEYGGNFEGRTKFAIDILRGVKKALP-EMTVICRINGSDFTDGGFTIDESVRFAK 290

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KENPDLFIGLN---GG 196
            ++  G + + I      +   S      +   D  ++  +K  KEN  + +      G 
Sbjct: 291 LLEGYGADALDISGG---VSSTSEYHISPMGIEDRPLIGVVKRIKENVTIPVIAVDKLGS 347

Query: 197 LEDMSQALKILPS-VDGVMIGRAAYKNSAM 225
           + D  + L+      D + I R    +  +
Sbjct: 348 VYDWEKILE--DGIADFIGIARGFIGDPDL 375


>gi|150018145|ref|YP_001310399.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
 gi|149904610|gb|ABR35443.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
          Length = 351

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/189 (20%), Positives = 72/189 (38%), Gaps = 24/189 (12%)

Query: 64  EAAKIVEDFGYNEINLNVGCP--------SARVHEG--SFGACLMLNPDI-VGDCIAAMC 112
           EA +   + GY+ + L+ GC         +  V++    +G     NP+  V + +  + 
Sbjct: 146 EAVRRAYEAGYDGVELH-GCHGYLISQFLNKNVNKRTDEYGT----NPERFVLEILEGIR 200

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           K       +  R+G   +       +  K + KSG++ + I       + ++   + K  
Sbjct: 201 KVTPEEFVIGIRLGGF-EPSIEDGVSYAKILDKSGIDFLDISYGFFNEQEINISKDYKYS 259

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVD 230
           N  Y    +IK+E       +NG +     A +IL   +VD V IG+    N       +
Sbjct: 260 NAVYAA-EKIKQEVSIPVFAVNG-INSAEIAEEILNETNVDIVDIGKGILINPNW---AN 314

Query: 231 EYFSNPLTG 239
                  TG
Sbjct: 315 HAMDGKDTG 323


>gi|298693354|gb|ADI96576.1| hypothetical protein SAOV_0034 [Staphylococcus aureus subsp. aureus
           ED133]
          Length = 190

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/128 (14%), Positives = 39/128 (30%), Gaps = 16/128 (12%)

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           + D    L++     +DGVMIGR  + N                     +    K+    
Sbjct: 73  IPDRKTGLELAEKYGIDGVMIGRGIFHNPFAF-------------EKEPREHTSKELLDL 119

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
           +   ++ +         + + + R       G   +   RH L +   +      +++  
Sbjct: 120 LRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGASELRHQL-MNTQSIAEARALLDEF 178

Query: 315 FNLMIESL 322
              M E L
Sbjct: 179 EAQMDEDL 186


>gi|254975666|ref|ZP_05272138.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-66c26]
 gi|255314794|ref|ZP_05356377.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-76w55]
 gi|255517469|ref|ZP_05385145.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-97b34]
 gi|255650579|ref|ZP_05397481.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-37x79]
 gi|255656048|ref|ZP_05401457.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-23m63]
 gi|260683677|ref|YP_003214962.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile CD196]
 gi|260687337|ref|YP_003218471.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile R20291]
 gi|306520522|ref|ZP_07406869.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-32g58]
 gi|260209840|emb|CBA63725.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile CD196]
 gi|260213354|emb|CBE04953.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile R20291]
          Length = 361

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/124 (20%), Positives = 50/124 (40%), Gaps = 22/124 (17%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IH 154
            +    + ++IPV VK    +D+      + +  K ++++G + I             I 
Sbjct: 131 MLKDAKERVNIPVIVKLPPMIDE------IGDFAKKLEEAGADAITACDSVGPAFRIDIE 184

Query: 155 ARKAIL--KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             + +L   G+       I  +    +YEIKK+  ++ I   GG      AL++ +   D
Sbjct: 185 TGQPLLGGNGIGYLSGETIKPITLQRIYEIKKQV-NIPIIGLGGCVSGDDALEMIMAGAD 243

Query: 212 GVMI 215
            V I
Sbjct: 244 FVGI 247


>gi|126699694|ref|YP_001088591.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile 630]
 gi|255101208|ref|ZP_05330185.1| dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile QCD-63q42]
 gi|115251131|emb|CAJ68962.1| Dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile]
          Length = 361

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/124 (20%), Positives = 50/124 (40%), Gaps = 22/124 (17%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IH 154
            +    + ++IPV VK    +D+      + +  K ++++G + I             I 
Sbjct: 131 MLKDAKERVNIPVIVKLPPMIDE------IGDFAKKLEEAGADAITACDSVGPAFRIDIE 184

Query: 155 ARKAIL--KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
             + +L   G+       I  +    +YEIKK+  ++ I   GG      AL++ +   D
Sbjct: 185 TGQPLLGGNGIGYLSGETIKPITLQRIYEIKKQV-NIPIIGLGGCVSGDDALEMIMAGAD 243

Query: 212 GVMI 215
            V I
Sbjct: 244 FVGI 247


>gi|261337393|ref|ZP_05965277.1| dihydroorotate oxidase [Bifidobacterium gallicum DSM 20093]
 gi|270277777|gb|EFA23631.1| dihydroorotate oxidase [Bifidobacterium gallicum DSM 20093]
          Length = 328

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 72/187 (38%), Gaps = 23/187 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G    +  E    + D   + + +NV CP    +  + G  +  +P  +   I 
Sbjct: 121 VVTNVAGHSDDEYAEVVAKLADCDADMLEINVSCP----NVSAGGISVGTDPVALSRLIT 176

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IWIHARKA 158
            + K    P+ VK    V D         + ++  +SG +            I I+  + 
Sbjct: 177 RLRKLTDKPMIVKLTPNVTDITL------IARAAVESGADALSMINTLLGMRIDINTGEP 230

Query: 159 ILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           I++ ++       +  +    V+ ++   PD+ I   GG++   +AL+ L    + V +G
Sbjct: 231 IIEHVTGGLSGPAVFPVGLACVWRVRSVLPDVPIIGIGGIDSGEKALEYLYAGANAVEVG 290

Query: 217 RAAYKNS 223
            AA  + 
Sbjct: 291 GAALLDP 297


>gi|167036567|ref|YP_001664145.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|320114995|ref|YP_004185154.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
 gi|166855401|gb|ABY93809.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|319928086|gb|ADV78771.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter brockii
           subsp. finnii Ako-1]
          Length = 641

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 59/177 (33%), Gaps = 17/177 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V+AA    + G + + +  G          P     E  +G           + +  + K
Sbjct: 147 VKAAVRAYEAGADALEIQFGHGYLIHQFLSPHTNKREDEYGGSFENRIRFGMEILDEIKK 206

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +  RI  D+ +P          L K ++  GV  I +    +   G       
Sbjct: 207 EIGADFPIIVRISADEFVPGGWALEDAIRLAKILEDKGVAAIDVSLGSSCESGAITLQTL 266

Query: 170 KI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                L ++   +IKK+  ++ +   G +     A +IL     D V +GR    + 
Sbjct: 267 GTQKGLAWEFASKIKKQV-NIPVIAVGRINTPELAEEILVSGKADLVALGRPLVADP 322


>gi|317051581|ref|YP_004112697.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfurispirillum indicum
           S5]
 gi|316946665|gb|ADU66141.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfurispirillum indicum
           S5]
          Length = 995

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/179 (15%), Positives = 66/179 (36%), Gaps = 17/179 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A  + + G++ + +  G          P     +  +G  L        + + A+ 
Sbjct: 476 FASSAARIREAGFDAVEILAGTGYLISEFLSPLTNQRQDEYGGSLENRMRFGLEVVRAVK 535

Query: 113 KALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +A      V  R+  +D +P       L+    +++  GV+ I ++      +   P+  
Sbjct: 536 EATGNAYPVMVRLNGNDFMPGGIGRRDLQTFALALEAVGVDAICVNVG--WHEAQVPQII 593

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
            K+P   +  +    +    + +  +  + D + A ++L     D V +GRA   +  +
Sbjct: 594 TKVPRGAFAYLAREIRTLVGIPVIASHRINDPATARRLLGQGMCDMVAMGRALIADPWL 652


>gi|261822079|ref|YP_003260185.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium wasabiae
           WPP163]
 gi|261606092|gb|ACX88578.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium wasabiae
           WPP163]
          Length = 364

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 65/198 (32%), Gaps = 22/198 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V++AK  +  G++ I ++            P       ++G  L     +V +   A
Sbjct: 157 ESFVDSAKRADRLGFDLIEIHAAHGYLLHQFLSPLTNQRTDNYGGSLQNRMRLVIEIYRA 216

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         + V +    GV+          L K++ + G + I + +      GLSP 
Sbjct: 217 VRDVFPAHKAVGVRISATDGVEGGWDLEQSVQLSKALHELGCDFIHVSSG-----GLSPL 271

Query: 167 DN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 PN        IK+E     I + G + +  QA  I+     D + + RA   + 
Sbjct: 272 QQIHPAPNYQVPYAQRIKQEVGITTIAV-GLITEPEQAEAIVATGEADAIGLARAILFDP 330

Query: 224 AMLTTVDEYFSNPLTGSS 241
                        ++   
Sbjct: 331 RWPWHAAARLGAQISAPP 348


>gi|118377270|ref|XP_001021815.1| Dihydroorotate dehydrogenase family protein [Tetrahymena
           thermophila]
 gi|89303582|gb|EAS01570.1| Dihydroorotate dehydrogenase family protein [Tetrahymena
           thermophila SB210]
          Length = 1080

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 30/157 (19%), Positives = 54/157 (34%), Gaps = 25/157 (15%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           V+D  ++ I LN+ CP    +E   G     +PDIV D  + +     IP+ VK      
Sbjct: 742 VKDAPFDMIELNLSCPHGM-NEKGMGRACGEDPDIVRDITSWVTSQTKIPIIVKITP--- 797

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWI----------HARKAILKGLSPKDNRKIPNLDYDI 178
                     L K+  + G   + +          +       G+  + N         I
Sbjct: 798 ---NYGQAEILAKAAYEGGAKAVTLTNTMPGLVDPYPDGESFNGVGVEKNVAPGGSTGSI 854

Query: 179 VY--------EIKKENPDLFIGLNGGLEDMSQALKIL 207
           +         ++ K  P++ I  +GG+      +  L
Sbjct: 855 LRPFAMRKCVDVAKFVPEIDIFASGGIISGDHGINYL 891


>gi|126731572|ref|ZP_01747378.1| dihydropyrimidine dehydrogenase [Sagittula stellata E-37]
 gi|126708108|gb|EBA07168.1| dihydropyrimidine dehydrogenase [Sagittula stellata E-37]
          Length = 434

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 59/167 (35%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + I LN GCP     E   GA +   P+ +             PV VK    +
Sbjct: 124 RVAETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKMYYDKPVIVKLTPNI 182

Query: 128 DD-QIPAVALRN-------LVKSIKKSGVNGIWIHARKAILKGLSPKDNR---KIPNLDY 176
            D + PA A RN       L+ +I       +   A +  + G           +  +  
Sbjct: 183 TDIRKPAAAARNGGADAVSLINTINSITSVDLDSFAPEPTIDGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
            +V EI ++     L I   GG+     A + ++     V +  AA 
Sbjct: 243 SMVSEIARDPQTHGLPISGIGGVTTWRDAAEFMVLGCGNVQVCTAAM 289


>gi|296157006|ref|ZP_06839843.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
 gi|295892892|gb|EFG72673.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
          Length = 365

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/183 (16%), Positives = 64/183 (34%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AAK   D G+  + L+       + +            ++G  L      + + +
Sbjct: 158 EDFVAAAKRARDAGFEWLELHFA--HGYLGQSFFSTHSNQRDDAYGGSLENRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           AA+ K     +P+T +         D+   V    L K+ K+ G++ + +      +   
Sbjct: 216 AAVRKVWPEHLPLTARFGVIEYDGRDEETLVESIELAKNFKREGLDMLSV-----SVGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
           +PK            + +  +    + +    G++    A   +    +D VM+GRA   
Sbjct: 271 TPKAAIPWAPAFLAPIAQRVRREAGIPVSSAWGIDTPELADGAVKSEQLDLVMVGRAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|330992501|ref|ZP_08316449.1| hypothetical protein SXCC_02408 [Gluconacetobacter sp. SXCC-1]
 gi|329760700|gb|EGG77196.1| hypothetical protein SXCC_02408 [Gluconacetobacter sp. SXCC-1]
          Length = 424

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 60/168 (35%), Gaps = 15/168 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC---- 123
           IVE+ G + I LN GCP     E + GA +   P+ V        +   +PV VK     
Sbjct: 122 IVEETGADGIELNFGCPHGMS-ERNMGAAVGQVPEYVEMVTRWCKQNTRMPVIVKLTPNI 180

Query: 124 -------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
                  R  +     AV+L N ++S+    ++ +                   +  +  
Sbjct: 181 TNILMPARAALRGGADAVSLINTIQSVIGVDLDLMAPMPTVDGKGTHGGYCGPAVKPIAL 240

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYK 221
            ++ +I +  E   L I   GG+     A + L      + +  AA  
Sbjct: 241 RMIGDIARDPELARLPISGIGGIGSWRDAAEFLAMGASTLQVCTAAMH 288


>gi|301048874|ref|ZP_07195868.1| conserved domain protein [Escherichia coli MS 185-1]
 gi|300299329|gb|EFJ55714.1| conserved domain protein [Escherichia coli MS 185-1]
          Length = 131

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 41/123 (33%), Gaps = 20/123 (16%)

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           + EI++   ++ +  +G +     A + +     D VMIGR A  N   L+ V +Y    
Sbjct: 1   IGEIRQRL-NISVIAHGEIWGWQSAQQCMAISGCDAVMIGRGAL-NIPNLSRVVKYNE-- 56

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR---HMIGLFHGFPNSRRC 293
                       +  W ++ A +  Y          L  + R    +  L   +  +   
Sbjct: 57  -----------PRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATEL 105

Query: 294 RHI 296
              
Sbjct: 106 FQH 108


>gi|282863060|ref|ZP_06272120.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces sp. ACTE]
 gi|282562042|gb|EFB67584.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces sp. ACTE]
          Length = 368

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 58/165 (35%), Gaps = 20/165 (12%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN-----------LV 140
           ++G        +  + + A+       + +  RI   D +   A  +           L 
Sbjct: 205 AYGGSFENRTRLALEVVDAVRAVWPDELPLFFRISATDWLSENAEDDREGWTGDDTVRLA 264

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLED 199
           + ++  GV+ + +        GL+P+ +  + PN        ++ E  DL +   G + D
Sbjct: 265 RELRAHGVDLLDVSTG-----GLAPRASIPVGPNYQVPFAARVRTET-DLPVAAVGLITD 318

Query: 200 MSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             QA KIL     D V++GR   ++              +    P
Sbjct: 319 PVQAEKILTEGEADAVLLGRELLRDPYFARNAARALGGDVAIPEP 363


>gi|271500116|ref|YP_003333141.1| NADH:flavin oxidoreductase/NADH oxidase [Dickeya dadantii Ech586]
 gi|270343671|gb|ACZ76436.1| NADH:flavin oxidoreductase/NADH oxidase [Dickeya dadantii Ech586]
          Length = 364

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 73/205 (35%), Gaps = 27/205 (13%)

Query: 39  NILGFSTQEKPLAL----QIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPS 85
           + L +S ++ P       QI    I     +AK  +  G++ I ++            P 
Sbjct: 133 SALPYSPEDTPPVAMSHDQIK-NLIDAFAASAKRADRLGFDLIEIHAAHGYLLHQFLSPL 191

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVK 141
           +   +  +G  L     ++ +   A+ +       + V +     V+          L  
Sbjct: 192 SNQRDDEYGGSLPNRMRLLREVYMAVREVFPPHKAVGVRISATDAVEGGWDLTQSIELGH 251

Query: 142 SIKKSGVNGIWIH-ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            +++ G + I +     + L+ + P  N ++P        +I++E   L     G + + 
Sbjct: 252 MLRQLGCDYIHVSSGGLSPLQHIQPAPNYQVPFAQ-----KIRQETG-LVTIAVGLITEP 305

Query: 201 SQALKIL--PSVDGVMIGRAAYKNS 223
            QA  IL     D V + RA   N 
Sbjct: 306 EQAEAILATEEADAVALARAMLFNP 330


>gi|227111662|ref|ZP_03825318.1| putative NADH-dependent flavin oxidoreductase [Pectobacterium
           carotovorum subsp. brasiliensis PBR1692]
          Length = 364

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 62/180 (34%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V++AK  +  G++ I ++            P        +G  L     +V +   A
Sbjct: 157 DSFVDSAKRADRLGFDLIEIHAAHGYLLHQFLSPLTNQRTDGYGGSLQNRMRLVIEIYRA 216

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         + V +    GV+          L K++ + G + I + +      GLSP 
Sbjct: 217 IRDVFPEHKAVGVRISATDGVEGGWDLEQSVQLSKALHELGCDFIHVSSG-----GLSPL 271

Query: 167 DN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 PN        IK+E     I + G + +  QA  I+     D + + RA   + 
Sbjct: 272 QQIHPAPNYQVPYAQRIKQEVGITTIAV-GLITEPEQAEAIVATGEADAIGLARAILFDP 330


>gi|330834188|ref|YP_004408916.1| dihydroorotate oxidase B, catalytic subunit [Metallosphaera cuprina
           Ar-4]
 gi|329566327|gb|AEB94432.1| dihydroorotate oxidase B, catalytic subunit [Metallosphaera cuprina
           Ar-4]
          Length = 290

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 64/171 (37%), Gaps = 28/171 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L + +GG+   ++V+ +   E      I +N+  P+ R       +        V + + 
Sbjct: 88  LFVSVGGSSKEEIVKVSHEAERL-ATIIEINLSSPNRRSFGADMAS-------QVKEIVK 139

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            +  +++ PV VK         P   +  L       G +G+            + +RK 
Sbjct: 140 DVRGSVTKPVFVKL-------GPWDNVLELAGKALDGGADGLTLINTLKGMRIDVESRKP 192

Query: 159 ILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           +L  G      + I  L   I++++ KE     I   GG+  +  A++ L 
Sbjct: 193 LLSYGTGGISGKCIHPLAVRIIHDVFKEY-STEIIGVGGVFTLYDAIEFLE 242


>gi|21229785|ref|NP_635702.1| FMN oxidoreductase [Xanthomonas campestris pv. campestris str. ATCC
           33913]
 gi|66766662|ref|YP_241424.1| FMN oxidoreductase [Xanthomonas campestris pv. campestris str.
           8004]
 gi|21111279|gb|AAM39626.1| FMN oxidoreductase [Xanthomonas campestris pv. campestris str. ATCC
           33913]
 gi|66571994|gb|AAY47404.1| FMN oxidoreductase [Xanthomonas campestris pv. campestris str.
           8004]
          Length = 365

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 60/198 (30%), Gaps = 22/198 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AAK  E      I L+            P +     ++G  L     +      A
Sbjct: 158 EAFVTAAKRAERLELQLIELHAAHGYLMHQFLSPLSNQRSDAYGGSLDNRMRLTLRIFDA 217

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S    I V +     VD          L K++   G + I + +      GL P+
Sbjct: 218 VRAAVSDQMAIGVRISATDWVDGGWDLPQSIALSKALDARGAHYIHVSSG-----GLDPR 272

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
               +    Y I   E  +   D  +   G + +  QA  IL     D + + R    + 
Sbjct: 273 QQIPV-QASYQIPFAEAIRAQVDTPVIGVGLITEPQQAEAILRDGQADAIALARGILYDP 331

Query: 224 AMLTTVDEYFSNPLTGSS 241
                        +T + 
Sbjct: 332 RWPWHAAAALGASVTPAP 349


>gi|193217047|ref|YP_002000289.1| NADH-dependent flavin oxidoreductase [Mycoplasma arthritidis
           158L3-1]
 gi|193002370|gb|ACF07585.1| NADH-dependent flavin oxidoreductase [Mycoplasma arthritidis
           158L3-1]
          Length = 367

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 42/271 (15%), Positives = 83/271 (30%), Gaps = 57/271 (21%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           + A AI    K +    S +E  +   I     S    A K     G++ + L       
Sbjct: 119 VSASAIAATRKDSEQPRSLEENEIHDII-----SDFANATKRAIAAGFDGVEL------- 166

Query: 87  RVHEGSFGACLML----------------NPDIVGDCIAAMCKALSIPVTVKCRI----- 125
                     L+                 +       I A+  A+ I V  + +      
Sbjct: 167 ----HGANTYLLQQFFSPHSNRRLDSWGGDRQKRFSFIKAVVDAV-IKVVQETKPNNFLV 221

Query: 126 -----GVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS-PKDNRKIPNLDY 176
                  + + P ++L +   LV+ +    ++ + I  R    K ++    N+ I    Y
Sbjct: 222 GYRFSPEEIENPGISLEDTLFLVRQLANEKLDYLHISLRNFEQKSINLDYQNKTILAYIY 281

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY---- 232
           + + +       + +   G +       K L + D V IGRA   N    + + E     
Sbjct: 282 ETIAK------KIPLIGVGNIWTNQDINKALENCDLVAIGRATIINPNYASLILENKSNS 335

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
             + ++        +    W  + + M D  
Sbjct: 336 LKHEVSKQECEALNICGGLWDYVVSLMGDKI 366


>gi|84579231|dbj|BAE73049.1| hypothetical protein [Macaca fascicularis]
          Length = 468

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 22/107 (20%), Positives = 37/107 (34%), Gaps = 5/107 (4%)

Query: 25  EMIVAD-AILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    A         L     +  +   I         + E AK  ED G + + LN+
Sbjct: 364 ELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM-ELAKKSEDSGADALELNL 422

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            CP     E   G     +P++V +    + +A+ IP   +      
Sbjct: 423 SCPHGM-GERGMGLACGQDPELVRNICRWVRQAVQIPFFCQADPKCH 468


>gi|260801022|ref|XP_002595395.1| hypothetical protein BRAFLDRAFT_69225 [Branchiostoma floridae]
 gi|229280641|gb|EEN51407.1| hypothetical protein BRAFLDRAFT_69225 [Branchiostoma floridae]
          Length = 358

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 41/132 (31%), Gaps = 15/132 (11%)

Query: 185 ENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           ++  + +  NG + ++    + +     DG+M       N A+     E  + P+   + 
Sbjct: 1   DSVKIPVFANGNILNLQSVERCMKETGTDGIMTAEGNLHNPALF----EGKNPPVWEMAD 56

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG------FPNSRRCRHI 296
              ++ ++   ++SA          HS      +      L  G         S   +  
Sbjct: 57  EYLQLVRENPCQLSAVRGHLFKLWHHSLQIHTDMR---TALAQGKTFESLVEVSEEMKRR 113

Query: 297 LTVEAGASTATH 308
              EA    A  
Sbjct: 114 CQEEASKPGADQ 125


>gi|311114636|ref|YP_003985857.1| dihydroorotate oxidase [Gardnerella vaginalis ATCC 14019]
 gi|310946130|gb|ADP38834.1| dihydroorotate oxidase [Gardnerella vaginalis ATCC 14019]
          Length = 331

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/231 (17%), Positives = 79/231 (34%), Gaps = 32/231 (13%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +      + L             +   + G       +  + + D   + + +N
Sbjct: 95  MVNAVGLQNPGVDHYLVDELPKLKKLGALVITNVAGHSDDDYAQVVEKLADSSADMLEIN 154

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V  G        +P  +   I  +      P+ VK    V D      + ++ 
Sbjct: 155 VSCP--NVTHGGMSVG--TDPVALHRLIKRLRAMTDKPMIVKMTPNVTD------IVSIC 204

Query: 141 KSIKKSGVNGIW-----IHARKAILKGLSPKDNR-------KIPNLDYDIVYEIKKENPD 188
           K+   +G + +      +  R  I  G     NR        I  +    V+ +++  PD
Sbjct: 205 KAAVDAGADALSMINTLVGLRIDIRTGEPIIANRTGGVSGPAIFPIGLGFVWRVRQAMPD 264

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + I   GG++   +AL+ L    + V +G AA  +      +   +D+   
Sbjct: 265 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALVDPTAPIRIARELDDLLD 315


>gi|27375286|ref|NP_766815.1| oxidoreductase [Bradyrhizobium japonicum USDA 110]
 gi|27348422|dbj|BAC45440.1| bll0175 [Bradyrhizobium japonicum USDA 110]
          Length = 370

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/181 (20%), Positives = 59/181 (32%), Gaps = 24/181 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDC 107
              VEAAK  E  G + I L             P +      +G  L   M  P  V D 
Sbjct: 157 EAFVEAAKRAERIGIDAIELHGAHGYLLHQFLSPISNRRTDEYGGSLQNRMRFPLEVYDA 216

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A+      P+ ++      V+             ++K  G++ I      A   G+SP
Sbjct: 217 VRAVFPH-DKPIGMRVSSTDWVEGGWDLAQTIEFASALKARGIDWI-----DASSGGVSP 270

Query: 166 KDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                +           I++E   L     G + D   A +I+     D V +GR    +
Sbjct: 271 LQKIPLGPGYQVHFADAIRRETG-LPTIAVGMISDAKHAEEIVASGKADMVALGRGMLYD 329

Query: 223 S 223
            
Sbjct: 330 P 330


>gi|78045886|ref|YP_362061.1| putative NADH flavin oxidoreductase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|78034316|emb|CAJ21961.1| putative NADH flavin oxidoreductase [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
          Length = 372

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 64/207 (30%), Gaps = 22/207 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +AK  E  G   I L+            P +     ++G  L     +      A
Sbjct: 165 DAFVASAKRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMRLTLRIFDA 224

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + V  RI   D             L +++   G + I + +      GL P+
Sbjct: 225 VRAAVSEKIAVGVRISATDWVQGGWDVQQSIALSQALDARGAHYIHVSSG-----GLDPR 279

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +    Y I   +  +   +  +   G + + +QA  IL     D + + R    + 
Sbjct: 280 QQIPL-QAGYQIPFAQEIRAQVNTPVIGVGLITEPAQAEAILQEGQADAIALARGILYDP 338

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                        +T +        +D
Sbjct: 339 RWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|7253|emb|CAA26674.1| unnamed protein product [Dictyostelium discoideum]
          Length = 369

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 58/175 (33%), Gaps = 30/175 (17%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDD 129
           G   + +N  CP   V  G        NPD V +  + + K LS   IP+ +K  +  D 
Sbjct: 192 GAKMVEVNYSCP--NVVTGEGQIY--HNPDAVYEISSTLVKELSSKNIPLIIKVGVMDDL 247

Query: 130 QIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNRKIPNLD 175
           +     +  L++  +++GV                I         +  S      I +  
Sbjct: 248 EK----MEGLLQQAERAGVAAIAGINTLSMKVTDKITGEPSLGPSRLTSGVCGAPIRSAA 303

Query: 176 YDIVYE----IKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
            D V      IKK+N  L +   GG++        L    D  M       +  +
Sbjct: 304 LDWVSTASSIIKKQNSKLKLLGCGGIDKPEHFDDFLNSGADIAMSAIGLMWDPYI 358


>gi|158421738|ref|YP_001523030.1| NADH flavin oxidoreductase [Azorhizobium caulinodans ORS 571]
 gi|158328627|dbj|BAF86112.1| NADH flavin oxidoreductase [Azorhizobium caulinodans ORS 571]
          Length = 367

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/166 (21%), Positives = 58/166 (34%), Gaps = 13/166 (7%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTV 121
           EA +I    GY  +      P +     ++G  L        +   A+  AL  S+PV V
Sbjct: 176 EAVEIHAAHGY--LLHQFLSPLSNARTDAYGGSLENRMRFPLEVFEAVRAALPDSVPVIV 233

Query: 122 KCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +      VD            +++K  G + I + +      GLSP     +       +
Sbjct: 234 RVSGTDWVDGGWDIEGTIAFAQALKARGADAIHVSSG-----GLSPLQQIPVEPGYQVPL 288

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +  KE   L     G + +  QA  +L     D + I R A  + 
Sbjct: 289 AKAVKEATGLPTIAVGLITEPKQAEAVLAAGEADAIGIARGALYDP 334


>gi|147674229|ref|YP_001216573.1| hypothetical protein VC0395_A0623 [Vibrio cholerae O395]
 gi|146316112|gb|ABQ20651.1| conserved hypothetical protein [Vibrio cholerae O395]
          Length = 157

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/140 (13%), Positives = 46/140 (32%), Gaps = 14/140 (10%)

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           +   +     K   + +  + +I+++   + +  NG + + +     +    VD +M+ R
Sbjct: 1   MHARTKAGGYKASEIKWHYIDQIRQKC-SIPLIANGEVWNYADGQACIQTTGVDSLMVCR 59

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            A  N   L  V ++    +     +           +    T +  R         +I 
Sbjct: 60  GAL-NVPNLGNVVKHNHAAMPWHEVV----------DLLLRYTQFEVRGDKGKYYPNRIK 108

Query: 278 RHMIGLFHGFPNSRRCRHIL 297
           +    L H +P +      L
Sbjct: 109 QWFAYLRHAYPQANELFGEL 128


>gi|117928503|ref|YP_873054.1| dihydroorotate oxidase B, catalytic subunit [Acidothermus
           cellulolyticus 11B]
 gi|117648966|gb|ABK53068.1| dihydroorotate oxidase B, catalytic subunit [Acidothermus
           cellulolyticus 11B]
          Length = 351

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 28/174 (16%), Positives = 62/174 (35%), Gaps = 17/174 (9%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAV 134
           + +N+ CP   V +         +P      +AA+ +A    +PV  K    V D +   
Sbjct: 147 LEVNISCP--NVEDRGQVFA--CDPRAASAVLAAVREAADPAVPVFAKLSPDVTDIVAVA 202

Query: 135 AL--------RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
                      +L+ ++    ++   +    + + G        I  +    V+++    
Sbjct: 203 TACVAAGADGLSLINTLLGLVIDTETLRPALSGVTG--GLSGPAIRPVAVRCVWQVHAAL 260

Query: 187 PDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           PD+ I   GG+     AL+ +L     V +G   + + +    + +  +  L  
Sbjct: 261 PDVPIIGMGGIRSGLDALQFLLAGACAVSVGTEIFHDPSAPARIRDELAEALAA 314


>gi|326382788|ref|ZP_08204478.1| NADH:flavin oxidoreductase/NADH oxidase [Gordonia neofelifaecis
           NRRL B-59395]
 gi|326198378|gb|EGD55562.1| NADH:flavin oxidoreductase/NADH oxidase [Gordonia neofelifaecis
           NRRL B-59395]
          Length = 686

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 61/186 (32%), Gaps = 17/186 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDI 103
           QI    I     AAK+    GY+ I +  G         CP        +G         
Sbjct: 143 QIIWHVIRSFGSAAKLARQAGYDAIEIMGGEGYLINQFLCPHTNDRTDKWGGSTENRQRF 202

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
           + + I  + K +     +  R  V D +      +    L +  ++ GV+ I  +     
Sbjct: 203 LVEIIKDIRKKVPRDFPIILRQSVADFVKNGQTFDEIALLAQKAEELGVDAI--NTDIGW 260

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +   P     +P   +    E  +E  D+ +  +  +     A +IL    VD V + R
Sbjct: 261 HEAQVPTIVTSVPRGAFVKFTERLREVVDIPLIASNRINTPEFAEEILDRGKVDAVSMAR 320

Query: 218 AAYKNS 223
               + 
Sbjct: 321 PLLADP 326


>gi|115399038|ref|XP_001215108.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
 gi|114191991|gb|EAU33691.1| conserved hypothetical protein [Aspergillus terreus NIH2624]
          Length = 425

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/206 (15%), Positives = 73/206 (35%), Gaps = 29/206 (14%)

Query: 63  VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A K     G + + + N           P+  +    +G        +  +      +
Sbjct: 204 VAAVKRAVKAGADFVEIHNAHGYLLMSFLSPAVNLRTDEYGGSFENRIRLSMEVAKLTRE 263

Query: 114 AL--SIPVTVKCR--------IGVDDQIPAVALRNLVKSIKKSG-VNGIWIH-ARKAILK 161
           A+   +PV ++          +               +++ +SG ++ + +        +
Sbjct: 264 AVPKDMPVFLRVSATDWLEESMPDQPSWRVEDTVRFAQALAESGNIDLLDVSSGGTHAAQ 323

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
            +  K   + P         +KK   D L +G  G ++    A  +L    +D V++GR 
Sbjct: 324 HIHAKPGFQAPFA-----IAVKKAVGDKLAVGTVGMIDSAHMANSLLEKDGLDMVLVGRG 378

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIK 244
             KN +++ T  E  +  L+ ++ I+
Sbjct: 379 FQKNPSLVWTWAEELNLELSMANQIR 404


>gi|194333396|ref|YP_002015256.1| dihydroorotate dehydrogenase family protein [Prosthecochloris
           aestuarii DSM 271]
 gi|194311214|gb|ACF45609.1| dihydroorotate dehydrogenase family protein [Prosthecochloris
           aestuarii DSM 271]
          Length = 309

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 82/235 (34%), Gaps = 30/235 (12%)

Query: 26  MIVADAI----LRGDKKNILGF-STQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINL 79
           M+ A  +    L       L F    +  + + + G  I   V+  + ++++ G +   +
Sbjct: 72  MVNAIGLANVGLERFVAEKLPFLQNLDTAVIVNVAGKSIDDYVQVVQRIDEYDGIDGYEI 131

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +       + ++     + I+ +    +  + VK    V       ++  +
Sbjct: 132 NLSCP----NVKGECMIMGVSSTATFEIISKLRSITNRHLMVKLTPNV------TSISAI 181

Query: 140 VKSIKKSGVNGIWI-----------HARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENP 187
             + +++G + + +             RK +L           I  +    V+E+     
Sbjct: 182 ALAAEEAGADSVSLINTLVGMAVDHKTRKPLLTNITGGLSGPAIKPVALAKVWEVYNAV- 240

Query: 188 DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           ++ I   GG+ ++  A++ L      + IG   +    +  T+ +      +   
Sbjct: 241 NIPIVGMGGISNVEDAMEFLVTGARAIQIGTMNFVYPDIGQTIADKLEEYFSSPE 295


>gi|126734202|ref|ZP_01749949.1| dihydroorotate dehydrogenase family protein, putative [Roseobacter
           sp. CCS2]
 gi|126717068|gb|EBA13932.1| dihydroorotate dehydrogenase family protein, putative [Roseobacter
           sp. CCS2]
          Length = 434

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 54/167 (32%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V   G + I LN GCP     E   GA +   P+ +        +    PV VK    +
Sbjct: 124 RVAATGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYDKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDVRKPAAAAMRGGADAVSLINTINSITSVNLDTMSPEPSIDGKGSHGGYCGPAVKPIAM 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            +V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 SMVSEIARNPETHGLPISGIGGVTTWRDAAEFISLGCGNVQVCTAAM 289


>gi|260429222|ref|ZP_05783199.1| dihydroorotate dehydrogenase family protein [Citreicella sp. SE45]
 gi|260419845|gb|EEX13098.1| dihydroorotate dehydrogenase family protein [Citreicella sp. SE45]
          Length = 434

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/167 (20%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VED G + + LN GCP     E   G+ +   P+ +      + +   +P  VK    +
Sbjct: 124 LVEDTGADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKQYTRMPCIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPAMAAHAGGADAVSLINTINSITSVDLDLFAPEPTIDGKGAHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVAEIARSPEMRGLPISGIGGVTTWKDAAEFMALGAGNVQVCTAAM 289


>gi|307610153|emb|CBW99699.1| hypothetical protein LPW_14671 [Legionella pneumophila 130b]
          Length = 870

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 44/277 (15%), Positives = 82/277 (29%), Gaps = 65/277 (23%)

Query: 54  IGGADISKLVEAAKIV----------EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             G + +KL E  K+           E      I +N+ CP+A V     G  L   PD 
Sbjct: 509 FYGENGNKLEEITKLAILMLKRMVPKEFHHKIRIGINMCCPAASVENIGSGFGLRNKPDF 568

Query: 104 VGDCIAAMCKA-LSIPVTVKCRIGVDDQ--------------IPAVALRNLVKSIKKSGV 148
           +   + A+     ++ V  K  +   +               I  V    L + + K+  
Sbjct: 569 IERIVKAIKDTDSNLKVEFKTLMLSHEDSYGDSNQTSGSTKNISEVQNERLTRIVSKTKA 628

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KEN-----PDLFIGLNGGLE--- 198
           + +       + +G          +    I+ E K  KE        +    N  +    
Sbjct: 629 DRL-------VYQGKPRNIEAYSGDAVSSIIREAKTPKEFQFGYSGMVATITNHDIHQLG 681

Query: 199 ---------DMSQALKILPSVDG-------VMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                     +   L+ +    G       VM+GR    ++ +L     Y S+       
Sbjct: 682 YKVVGEPHYSVQSILEKIKKQLGEVPIEFEVMLGRVLLGSAWVLQG--RYASDAEILLHT 739

Query: 243 IKTRVDKDFWRKISASMTDYAAR--HLHSGGKLQQIT 277
           +     +  W   +  M  Y      +     ++ IT
Sbjct: 740 LLQAAIEQEW---AEGMGRYGVDIYQIQILYNIRHIT 773


>gi|310642311|ref|YP_003947069.1| NADH-dependent flavin oxidoreductase-like protein [Paenibacillus
           polymyxa SC2]
 gi|309247261|gb|ADO56828.1| NADH-dependent flavin oxidoreductase-like protein [Paenibacillus
           polymyxa SC2]
          Length = 340

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 48/309 (15%), Positives = 95/309 (30%), Gaps = 81/309 (26%)

Query: 5   TDRHYR-FFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKP-------------- 49
           TD HY  + +R +    L+  EM       R   +++  +S +  P              
Sbjct: 37  TDWHYVHYVSRAVGGTGLIIVEMTAVHPDGRITDRDLGIWSDEHNPAYRKIVEEVHKYGA 96

Query: 50  -LALQIGGA-----------------------DISKLVEA------------AKIVEDFG 73
            +A+Q+G A                       D   L  A            A+   + G
Sbjct: 97  KIAIQLGHAGRKAEDAETPVGPSSIPFSERFKDPHTLTRAEVKELVQAYKEGARRAVEAG 156

Query: 74  YNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG-DCIAAMCKAL--SIPVTV 121
           ++ + +             P     E  +G     +  + G + I A+ + L   +PV +
Sbjct: 157 FDTVEIHGAHGYLIHQFHSPLTNTREDEYG----QDLSLFGVEVIRAVKEVLPADMPVLM 212

Query: 122 KC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGLSPKDNRKIPNLD 175
           +   +  V D      +  + +  + +GV+   I            G S +   ++    
Sbjct: 213 RISAKEYVQDGYDVEYIAAIGERYRDAGVDIFHISSGGEGPIGSSGGPSARAGYQVDLAH 272

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYF 233
                   +E  ++ +   G L+D   A +++     D V IGRA  ++           
Sbjct: 273 ------TIREKLNVPVIAVGLLDDYEDARRVVQQNEADLVAIGRAMLRDPYWALHASRAL 326

Query: 234 SNPLTGSSP 242
                   P
Sbjct: 327 KVQADIPEP 335


>gi|77459665|ref|YP_349172.1| dihydropyrimidine dehydrogenase [Pseudomonas fluorescens Pf0-1]
 gi|77383668|gb|ABA75181.1| dihydropyrimidine dehydrogenase (NADP+) / dihydroorotate oxidase B,
           catalytic subunit [Pseudomonas fluorescens Pf0-1]
          Length = 424

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 34/151 (22%), Positives = 52/151 (34%), Gaps = 14/151 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE  G + I LN GCP     E   GA +   P+ V           S+PV VK    +
Sbjct: 122 LVEATGADGIELNFGCPHGM-PERGMGAAVGQVPEYVEQVTRWCKTYCSLPVIVKLTPNI 180

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    +  +                   +  +  
Sbjct: 181 TDIRVAARAAHRGGADAVSLINTINSITSVDLEHMVALPTVGSKSTHGGYCGSAVKPIAL 240

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALK 205
           ++V EI ++     L I   GG+     A +
Sbjct: 241 NMVAEIARDPQTQGLPICGIGGIGSWRDAAE 271


>gi|332755186|gb|EGJ85550.1| hypothetical protein SFK671_2726 [Shigella flexneri K-671]
          Length = 289

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 59/154 (38%), Gaps = 27/154 (17%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           G + I  N  CP   +   + G+ +  +P++V     A+ +  ++P+  K    + D   
Sbjct: 5   GADMIECNFSCPQ--MTSHAMGSDVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD--- 59

Query: 133 AVALRNLVKSIKKSGVNGI-WIHARKAIL----------------KGLSPKDNRKIPNLD 175
              +  +  + K+ G +GI  I+  K+I                   +S    + +  + 
Sbjct: 60  ---MCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIA 116

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
              + +++   E  D  I   GG+E    A + L
Sbjct: 117 LRFIQQMRTHPELRDFPISGIGGIETWEDAAEFL 150


>gi|50120713|ref|YP_049880.1| putative NADH-dependent flavin oxidoreductase [Pectobacterium
           atrosepticum SCRI1043]
 gi|49611239|emb|CAG74685.1| putative NADH-dependent flavin oxidoreductase [Pectobacterium
           atrosepticum SCRI1043]
          Length = 364

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 64/180 (35%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V++AK  +  G++ I ++            P       S+G  L     +V +   A
Sbjct: 157 DSFVDSAKRADSLGFDLIEIHAAHGYLLHQFLSPLTNQRTDSYGGSLQNRMHLVVEIYRA 216

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +       + V +    GV+          L K++ + G + I + +      GLSP 
Sbjct: 217 VREVFPAHKAVGVRISATDGVEGGWDLEQSVQLSKALHELGCDFIHVSSG-----GLSPL 271

Query: 167 DN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 PN        IK+E     I + G + +  QA  I+     D + + RA   + 
Sbjct: 272 QQIHPAPNYQVPYAQRIKQEVGITTIAV-GLITEPEQAEAIVATGEADAIGLARAILFDP 330


>gi|302532930|ref|ZP_07285272.1| oxidoreductase [Streptomyces sp. C]
 gi|302441825|gb|EFL13641.1| oxidoreductase [Streptomyces sp. C]
          Length = 356

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/157 (14%), Positives = 52/157 (33%), Gaps = 14/157 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG---VDDQIPAVALRNLVKSIKKSG 147
           +G        +  + + A+ +     +P+  +        ++   A     L + +++ G
Sbjct: 200 YGGSFENRTRLAVEVVDAVREVWPEELPLFFRISATDWLEENGWTADETVRLARLLQEHG 259

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           V+ + +        GL+P     +           +K E   L +   G + +  QA K+
Sbjct: 260 VDLLDVSTG-----GLAPHVRIPVGPGYQVPFAARVKAETT-LPVAAVGLITEPEQAEKV 313

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           L     D V++GR   ++              +    
Sbjct: 314 LANGEADAVLLGRELLRDPYWARRAAAELGAEIPTPD 350


>gi|281208313|gb|EFA82491.1| dihydroorotate oxidase [Polysphondylium pallidum PN500]
          Length = 371

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 36/187 (19%), Positives = 59/187 (31%), Gaps = 30/187 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SI 117
             ++ A I  D G   I +N  CP   V  G        NPD V     A+   L    +
Sbjct: 185 DFLDVANIALDAGAKVIEVNYSCP--NVCTGEGQIY--NNPDEVYKISKALVDILQPKGV 240

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI--------------WIHARKAILKGL 163
           P+ +K  +  D ++    +  L +  +++GV  I                       +  
Sbjct: 241 PLIIKVGVMEDREL----MTKLFRRAEEAGVAAIAGINTMSMKITDSKTGAPSLGENRLT 296

Query: 164 SPKDNRKIPNLDYDIV---YEIKKEN-PDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
           S      I +   D V     I  +N  +L +   GG+         L   VD  M    
Sbjct: 297 SGVCGAPIRSAALDWVRNARSIVNDNKLNLKLLGCGGVVLPEHFDDFLEQGVDIAMSATG 356

Query: 219 AYKNSAM 225
              +  +
Sbjct: 357 LMWDPYI 363


>gi|315186134|gb|EFU19896.1| dihydroorotate oxidase [Spirochaeta thermophila DSM 6578]
          Length = 326

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 61/177 (34%), Gaps = 26/177 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   +  +      EAA  +E+ G + + LNV  P       +         + + D +
Sbjct: 99  PVIASLNCSSREWWAEAASRIEEAGADALELNVA-PFP----SNDAESSQEAEERIYDIV 153

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH-----------ARK 157
                A+S+P+ VK            +L +L+  I+  G  G+ +             R+
Sbjct: 154 RTARSAVSVPIAVKVGPYF------TSLGHLLARIEALGAGGVVLFNRFYQVDIDPSRRR 207

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
            +        +     L +  +   ++   +L I  + G+   +  A  +L     V
Sbjct: 208 LVSGHRLSDPHEFSHTLRWTALEAPRR---NLDIAASCGIHSGLDIAKAVLAGASAV 261


>gi|258517347|ref|YP_003193569.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257781052|gb|ACV64946.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 647

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/191 (16%), Positives = 62/191 (32%), Gaps = 23/191 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA  +++ G + I +N G          P        +G  L        + +  
Sbjct: 147 EGFVNAAWRLKNSGLDGIEINAGQFSLLRQFLSPLTNYRSDDYGGSLENRVRFCREVLQE 206

Query: 111 MCKALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSG-VNGIWIHARKAILKGLS 164
           + +A      +  R+  D+  P         R++ + + K G V+   +         ++
Sbjct: 207 VRRATGSDFLIGLRLCGDEYAPWGGLNPEDCRDIARHLCKGGLVDWFTVETGSIYSLHMT 266

Query: 165 PKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG---RAAY 220
               R     DY      +  E  D+ +   G +  +  A K+L    GV +    RA  
Sbjct: 267 SASMR--HPEDYAAQPACLIAEAVDIPVCATGSIVSVKLAEKLLNE--GVQLAEMTRALI 322

Query: 221 KNSAMLTTVDE 231
            +  +     E
Sbjct: 323 ADPDLPARAKE 333


>gi|77360353|ref|YP_339928.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875264|emb|CAI86485.1| 2,4-dienoyl-CoA reductase [NADPH] [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 657

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 61/189 (32%), Gaps = 17/189 (8%)

Query: 61  KLVEAAKIVEDFGYNEIN--------LN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               +A + E  GY+ +         +N    P        FG  L     +  + + A+
Sbjct: 143 DFAHSAYMAEKAGYDGVEVMGSEGYLINEFMAPHTNKRNDEFGGSLENRMRLAVEIVKAV 202

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKS----IKKSGVNGIWIHARKAILKGLSPKD 167
              +S    +  R+ V D IP  +    V      ++K+GV+    +      +   P  
Sbjct: 203 RAKVSEQFLIIFRLSVMDLIPNGSTPEEVTIQALELEKAGVDIF--NTGIGWHEARIPTI 260

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
              +P   +    +  K+   + +     +     A +IL +   D + + R    +   
Sbjct: 261 ASMVPPGAFKEASKRLKDVIKVPVIAVNRINTPEIANEILNAGDADLISMARPLLADPEF 320

Query: 226 LTTVDEYFS 234
               +   S
Sbjct: 321 FNKYNNQLS 329


>gi|298252672|ref|ZP_06976466.1| dihydroorotate dehydrogenase [Gardnerella vaginalis 5-1]
 gi|297533036|gb|EFH71920.1| dihydroorotate dehydrogenase [Gardnerella vaginalis 5-1]
          Length = 338

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 76/231 (32%), Gaps = 32/231 (13%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +      + L        +    +   + G       +  + + D   + + +N
Sbjct: 102 MVNAVGLQNPGVDHYLVDELPKLKSMGALVITNVAGHSDDDYAQVVEKLADSAADMLEIN 161

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V  G        +P  +   I  +      P+ VK    V D      + ++ 
Sbjct: 162 VSCP--NVTHGGMSVG--TDPVALHRLIKRLRAMTDKPMIVKMTPNVTD------IVSIC 211

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K+   +G + + +                 I           I  +    V+ +++  PD
Sbjct: 212 KAAVDAGADALSMINTLVGLRIDIRTGEPIIANRTGGVSGPAIFPIGLGFVWRVRQAMPD 271

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + I   GG++   +AL+ L    + V +G AA  +      +   +D+   
Sbjct: 272 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALVDPTAPIRIARELDDLLD 322


>gi|149923408|ref|ZP_01911813.1| NADH:flavin oxidoreductase/NADH oxidase [Plesiocystis pacifica
           SIR-1]
 gi|149815715|gb|EDM75241.1| NADH:flavin oxidoreductase/NADH oxidase [Plesiocystis pacifica
           SIR-1]
          Length = 400

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/218 (14%), Positives = 70/218 (32%), Gaps = 47/218 (21%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
                 AA +  D G++ I L++G          P        +G  L     +  + + 
Sbjct: 149 PETFARAAGLALDAGFDAIELHLGHGYLLSQFLSPRTNKRRDDYGGSLQNRLRLPVEVLR 208

Query: 110 AMCKAL-----SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWI------HAR 156
           A+  A+       P+  K   R  +   +       + + +++ G + + +      H+ 
Sbjct: 209 AVRAAVEARRPGTPIVCKTNLRDDLRGGLELDEAVEIARVLEREGADALVLSGGFVSHSA 268

Query: 157 KAILKGLSPKDN--------------RKIPNLDYDI----------VYEIKKENPDLFIG 192
             +L+G  P  +              R +     +           +    +   D+ + 
Sbjct: 269 FYLLRGDRPLKDMIAVESDPKQRLALRLLGPAVIEAHPFEELFFLPLARQVRAAVDMPLC 328

Query: 193 LNGGLED-MSQALKILPSVDGVMIGRAAYKNSAMLTTV 229
           L GG+    +    +    + V +GRA  +N   +  V
Sbjct: 329 LLGGVVSGANMEQAMAEGFELVAVGRALLENPNFVRDV 366


>gi|15790440|ref|NP_280264.1| hypothetical protein VNG1431C [Halobacterium sp. NRC-1]
 gi|10580932|gb|AAG19744.1| conserved hypothetical protein [Halobacterium sp. NRC-1]
          Length = 223

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 55/157 (35%), Gaps = 25/157 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L + A +        + +N  C    + +   G  L+ +   + + + A     +  V+V
Sbjct: 71  LRDVAAVCAAHDA-ILEVNAHCRQDELCDAGAGETLLRDTSRLCEQVRAASDEGAA-VSV 128

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV      V L  L ++I+++G   I + A                   D   V  
Sbjct: 129 KVRAGVQG----VHLPVLAQAIERAGAAAIHVDAM------------------DSRRVVR 166

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
              +   LF+  N G+       + L    D V +GR
Sbjct: 167 DVADATALFVVANNGVRTRDDVFEYLSYGADAVSVGR 203


>gi|218782533|ref|YP_002433851.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218763917|gb|ACL06383.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
          Length = 373

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/200 (15%), Positives = 71/200 (35%), Gaps = 20/200 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
            K  EAA   +  G++ + L              S  V+     +G  L        + +
Sbjct: 143 DKFAEAAVRAKKAGFDVVELHGATGYLLSQFI--SPWVNRRTDEYGGSLDNRMRFGLEVL 200

Query: 109 AAMCKAL-SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +  A+  +PV  +      + + +  V      ++++K+G   + +         +  
Sbjct: 201 KKVRDAVGDMPVGFRFMAHEWLPEGLELVDSLPYARALEKAGAAYLSVSGGSWESFMVPE 260

Query: 166 KDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
              + I      D+   +KKE  ++ +   G +++ + A +IL     D + + R  + +
Sbjct: 261 VLIKSIQPCYMVDLAAAVKKEV-EIPVIAAGRIQEGAVAERILLEGKADLIGLARPLWAD 319

Query: 223 SAMLTTVDEYFSNPLTGSSP 242
              L  V     + +   SP
Sbjct: 320 PGWLEKVRHDREDEIIPCSP 339


>gi|169236176|ref|YP_001689376.1| hypothetical protein OE3058F [Halobacterium salinarum R1]
 gi|167727242|emb|CAP14028.1| conserved hypothetical protein [Halobacterium salinarum R1]
          Length = 243

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 55/157 (35%), Gaps = 25/157 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L + A +        + +N  C    + +   G  L+ +   + + + A     +  V+V
Sbjct: 91  LRDVAAVCAAHDA-ILEVNAHCRQDELCDAGAGETLLRDTSRLCEQVRAASDEGAA-VSV 148

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K R GV      V L  L ++I+++G   I + A                   D   V  
Sbjct: 149 KVRAGVQG----VHLPVLAQAIERAGAAAIHVDAM------------------DSRRVVR 186

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
              +   LF+  N G+       + L    D V +GR
Sbjct: 187 DVADATALFVVANNGVRTRDDVFEYLSYGADAVSVGR 223


>gi|297243395|ref|ZP_06927328.1| dihydroorotate dehydrogenase [Gardnerella vaginalis AMD]
 gi|296888642|gb|EFH27381.1| dihydroorotate dehydrogenase [Gardnerella vaginalis AMD]
          Length = 341

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 77/231 (33%), Gaps = 32/231 (13%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +      + L        +    +   + G       +  + + D   + + +N
Sbjct: 105 MVNAVGLQNPGVDHYLVDELPKLKSMGALIITNVAGHSDDDYAQVVEKLADSAADMLEIN 164

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V  G        +P  +   I  +    S P+ VK    V D      + ++ 
Sbjct: 165 VSCP--NVTHGGMSVG--TDPVALHRLIKRLRAMTSKPMIVKMTPNVTD------IVSIC 214

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K+   +G + + +                 I           I  +    V+ +++  PD
Sbjct: 215 KAAVDAGADALSMINTLVGLRIDIRTGEPIIANRTGGVSGPAIFPIGLGFVWRVRQAMPD 274

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + I   GG++   +AL+ L    + V +G AA  +      +   +D+   
Sbjct: 275 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALVDPTAPIRIARELDDLLD 325


>gi|323456942|gb|EGB12808.1| hypothetical protein AURANDRAFT_19007 [Aureococcus anophagefferens]
          Length = 154

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 18/37 (48%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           ++LN+GCP         G+ LM +P      + AM +
Sbjct: 118 VDLNMGCPKPFSAGNGMGSALMRDPARAASIVKAMRR 154


>gi|319791794|ref|YP_004153434.1| NADH:flavin oxidoreductase/NADH oxidase [Variovorax paradoxus EPS]
 gi|315594257|gb|ADU35323.1| NADH:flavin oxidoreductase/NADH oxidase [Variovorax paradoxus EPS]
          Length = 348

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 35/178 (19%), Positives = 60/178 (33%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            V+AA+     G + + ++            P A   +  +G  L   M  P  V D + 
Sbjct: 137 FVDAARRAARLGLDGLEIHAAHGYLLHQFLSPLANHRDDEYGGSLENRMRFPLEVFDAVR 196

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
               A   PV V+      V D           K+++  G   I + +      G+SPK 
Sbjct: 197 EAFPA-DRPVWVRVSAIDWVPDGWDLEGTVAFAKALEARGCAAIHVSSG-----GVSPKQ 250

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +         E  K    + +   G + +  QA +I+     D V + RA   + 
Sbjct: 251 AIALGAGYQVPFAERVKSEVGMPVIAVGLITEPRQAEEIIAKGQADAVSLARAILYDP 308


>gi|11498067|ref|NP_069291.1| NADH oxidase (noxB-1) [Archaeoglobus fulgidus DSM 4304]
 gi|2650172|gb|AAB90780.1| NADH oxidase (noxB-1) [Archaeoglobus fulgidus DSM 4304]
          Length = 632

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/187 (14%), Positives = 61/187 (32%), Gaps = 17/187 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA   +  G++ + L             P+       +G  L        + I  
Sbjct: 142 EEFADAAVRAKKAGFDAVELIGSAGYLISQFFSPATNKRTDEYGGSLENRTRFAVEIIQK 201

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +    S PV ++      ++       ++ + K ++ +GV  + I+      +   P 
Sbjct: 202 IKEKCGESYPVMIRIPGDEFIEGGNTVREMKQIAKILEDAGV--VAINVMAGWHESRKPL 259

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG--RAAYKNSA 224
               +P   +  +    K    + +  +  + D   A KIL      M+   RA   +  
Sbjct: 260 TTMLVPRGGFAYLAAEIKSAVSVPVIASHRINDPIVAEKILQEGKADMVAMLRALIADPE 319

Query: 225 MLTTVDE 231
           +     E
Sbjct: 320 LPKKAKE 326


>gi|297566516|ref|YP_003685488.1| dihydroorotate dehydrogenase family protein [Meiothermus silvanus
           DSM 9946]
 gi|296850965|gb|ADH63980.1| dihydroorotate dehydrogenase family protein [Meiothermus silvanus
           DSM 9946]
          Length = 461

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/214 (14%), Positives = 66/214 (30%), Gaps = 25/214 (11%)

Query: 25  EMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +     + +++         +   +  +      +    +ED G + I LN G
Sbjct: 75  ELISDRPLEVNLREIRDVKRHWPDRAVIVSAMVESTPEAWRDIVLKIEDTGADGIELNYG 134

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----------QI 131
           CP     E   G+ +   P+        +     IPV VK    + +             
Sbjct: 135 CPHGMS-ERGMGSAVGQVPEYCEQITRWVTSVAKIPVIVKLTPNITNISYPAKAAVAGGA 193

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK----ENP 187
            A++L N + SI    ++ + +        G        +  +   ++ ++         
Sbjct: 194 QAISLINTINSIIGVNLDTLELVPNIGGKGGHGGYAGPAVKPIALHLLSQVATTPEVSGS 253

Query: 188 DLFIGLNGGLEDMSQALKI-------LPSVDGVM 214
            + I   GG+     A +        L     VM
Sbjct: 254 GIPISGMGGISTWRDAAEFLLLGATSLQVCTAVM 287


>gi|290791243|gb|EFD94902.1| hypothetical protein GL50803_7390 [Giardia lamblia ATCC 50803]
          Length = 462

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/227 (16%), Positives = 71/227 (31%), Gaps = 52/227 (22%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV-GDC 107
           PL +Q+   +   + +   I+  +    I+LN+GC +     G  G  L+   + V    
Sbjct: 97  PLVVQLTVNEYDDVDKICSILAPWCV-GIDLNLGCGAQFAVSGGRGQRLVDKAENVIARF 155

Query: 108 IAAMCKALS-----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK----- 157
           + A+ +        I  ++K R+    +     +    K     GVN I +H R+     
Sbjct: 156 LKALQQIEDSGGRRISFSIKQRLLGSVEETVNKMCAFYKL----GVNCIAVHMRRKGEER 211

Query: 158 -----------AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                       +L GL           D  +  +  +      +  NG L         
Sbjct: 212 GCTHADWGSFFQVLSGLYTWFWTVFCQGDLQLFEDALRTF---HVVANGDLFSRETITDF 268

Query: 207 L---------------PSVDG-------VMIGRAAYKNSAMLTTVDE 231
                           P +         VM+ R A  + ++ + + E
Sbjct: 269 FSLSEQYFSQLPTDIQPYLSSRYGRLTPVMLARGAISDLSLFSFILE 315


>gi|119477667|ref|ZP_01617817.1| hypothetical protein GP2143_09400 [marine gamma proteobacterium
           HTCC2143]
 gi|119449170|gb|EAW30410.1| hypothetical protein GP2143_09400 [marine gamma proteobacterium
           HTCC2143]
          Length = 357

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 71/209 (33%), Gaps = 24/209 (11%)

Query: 25  EMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           E+I    +   D       G ST+E     Q+        + AA+  E  G+  + L+  
Sbjct: 111 ELINDRPVCPSDHSETGSRGLSTKE---VEQLA----EDFITAAQRAEAAGFEGVELHGA 163

Query: 83  -----C----PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIP 132
                C    P+       +G  L     I+ D IA + +  S    +  R+  +   + 
Sbjct: 164 HGYILCQFLSPTINQRSDQYGGSLENRSRILMDIIAGIRERCSPDFVLGVRLSPERFDVK 223

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
              +  L + +  +G   I             P +             E+ +    L   
Sbjct: 224 LAEILELSQQLMSAG--SIDFLDMSLWNVFKEPAEEEFQGRSLASYFTELDRGATKLGFA 281

Query: 193 LNGGLEDMSQALKILP-SVDGVMIGRAAY 220
             G +   ++A + L  +VD VM+GRAA 
Sbjct: 282 --GSIRTPAEAQQCLDLNVDFVMLGRAAI 308


>gi|295681146|ref|YP_003609720.1| dihydroorotate dehydrogenase [Burkholderia sp. CCGE1002]
 gi|295441041|gb|ADG20209.1| dihydroorotate dehydrogenase family protein [Burkholderia sp.
           CCGE1002]
          Length = 426

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 58/173 (33%), Gaps = 27/173 (15%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VED G + + LN GCP     E   GA +   P+ +      + +   +P  VK    V 
Sbjct: 123 VEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWVKEGTRLPCLVKLTPNVT 181

Query: 129 DQIPAVALRNLVKSIKKSGVNG--------------IWIHARKAILKGLSPKDNRKIPNL 174
           D      +R+  ++    G +G              + + A    + G         P  
Sbjct: 182 D------IRHGARAAMNGGADGVSLINTINSIVGVDLDLMAPLPTVDGKGTHGGYCGPAA 235

Query: 175 DYDIVYEIKKENPDL-----FIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
               ++ + +   D       I   GG+ D   A + I+     V +  AA  
Sbjct: 236 KPIALHMVAEIARDPQTHGLPISGIGGISDWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|226327820|ref|ZP_03803338.1| hypothetical protein PROPEN_01697 [Proteus penneri ATCC 35198]
 gi|225203524|gb|EEG85878.1| hypothetical protein PROPEN_01697 [Proteus penneri ATCC 35198]
          Length = 363

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 38/178 (21%), Positives = 65/178 (36%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+AA+  E  G++ I ++            P +      +G        ++ D   A+ 
Sbjct: 159 FVDAARRAESAGFDVIEIHGAHGYLLHEFLSPLSNHRTDQYGGDFNNRSRLLVDIFVAVK 218

Query: 113 KALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+S  V V  RI   D         +   L + +++ G + I + +      GLS K  
Sbjct: 219 NAVSDNVCVGIRISATDWVEGGWDLESTIALTQHLEELGCHYIHVSSG-----GLSEKQE 273

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            K+ PN        I  E   L +   G + +  QA  IL     D + +GR    + 
Sbjct: 274 IKLGPNYQVPFAQAIYNET-QLPVITVGLITEPEQAEAILLTEQADFIALGRGILYDP 330


>gi|126465503|ref|YP_001040612.1| dihydroorotate oxidase B, catalytic subunit [Staphylothermus
           marinus F1]
 gi|126014326|gb|ABN69704.1| dihydroorotate oxidase B, catalytic subunit [Staphylothermus
           marinus F1]
          Length = 301

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 43/206 (20%), Positives = 74/206 (35%), Gaps = 18/206 (8%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
                  P  + IGG D  +    A+   D     + LN+ CP    H   FG   +   
Sbjct: 86  EIHKYGLPAIVSIGGRDPREFQILAEKALDARPEALELNLSCP----HTPGFGVDTVATD 141

Query: 102 DIVGDCIAAMCKALSIPVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +++      +    +IPV  K     RI  + +I      + V  I       I ++  K
Sbjct: 142 EVLKHVALNVSSVSNIPVWGKLGFSRRIIRESEILLNNGVDAVVLINTLPGMFIDVYVGK 201

Query: 158 AIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L  G        I  +    VY++ +E     IG+ GG+ D   +++ +L     + I
Sbjct: 202 PVLTHGFGGLSGPAIHPVAVYSVYKVYEELGAEIIGV-GGVIDWKTSVELLLAGAKAIQI 260

Query: 216 GRAAYK------NSAMLTTVDEYFSN 235
           G   Y       N  +L  + +Y   
Sbjct: 261 GTGFYMVGYNIVN-NILDGIKKYMEE 285


>gi|299137065|ref|ZP_07030248.1| dihydroorotate dehydrogenase family protein [Acidobacterium sp.
           MP5ACTX8]
 gi|298601580|gb|EFI57735.1| dihydroorotate dehydrogenase family protein [Acidobacterium sp.
           MP5ACTX8]
          Length = 471

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 59/176 (33%), Gaps = 28/176 (15%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            +  ED G + + LN GCP     E   G+ +   P+        + +    PV VK   
Sbjct: 118 VQRAEDAGADGLELNFGCPHGMS-ERGMGSAVGQVPEYCEQITGWVKEKARTPVIVKLTP 176

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI---------------WIHARKAILKGLSPKDNRK 170
            + D      +R   ++ K+ G + +                +  R  ++ G S      
Sbjct: 177 NISD------IRIPARAAKRGGADALSAINTINSITSIDLDTLEPR-PMVDGKSSHGGYC 229

Query: 171 IPNLDYDIVYEIKKENPDL----FIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
            P +    +  +++   D      +   GG+     A + IL     V +  AA  
Sbjct: 230 GPAVKPIALNMVQQVMSDPDAALPMSGIGGIGTWQDAAEFILLGSGTVQVCTAAMH 285


>gi|326390295|ref|ZP_08211855.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993740|gb|EGD52172.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 667

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 70/206 (33%), Gaps = 43/206 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
           K  EAA I +  G++ + ++       VHEG                 +G  LM      
Sbjct: 159 KFAEAAVIAKMSGFDGVEIHA------VHEGYLLDQFTIALFNKRTDKYGGDLMGRLRFP 212

Query: 105 GDCIAAMCKAL--SIPVTVK---------CRIGVDDQIPAVAL-------RNLVKSIKKS 146
            + + A+ KA     PV+++          R G   +     L           K ++++
Sbjct: 213 IEIVQAIKKACGDDFPVSLRYSVKSYIKGIRQGGLAEEEFTELGRDIDEGLEAAKILEEA 272

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G +     A        +     +   L   +  ++KK   ++ + + G +ED   A   
Sbjct: 273 GYDAFNADAGTYDSWYWNHPPMYQKKGLYLPLTEKLKK-VVNVPVLVAGRMEDPELASSA 331

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVD 230
           L     D ++IGR    +  +   + 
Sbjct: 332 LEEGKADAIVIGRGLLADPQLPNKIK 357


>gi|115373492|ref|ZP_01460789.1| dihydropyrimidine dehydrogenase (NADP+) [Stigmatella aurantiaca
           DW4/3-1]
 gi|310825270|ref|YP_003957628.1| dihydropyrimidine dehydrogenase [Stigmatella aurantiaca DW4/3-1]
 gi|115369498|gb|EAU68436.1| dihydropyrimidine dehydrogenase (NADP+) [Stigmatella aurantiaca
           DW4/3-1]
 gi|309398342|gb|ADO75801.1| Dihydropyrimidine dehydrogenase [Stigmatella aurantiaca DW4/3-1]
          Length = 462

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 38/214 (17%), Positives = 75/214 (35%), Gaps = 20/214 (9%)

Query: 25  EMIVADAILRGDKKNIL---GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    +   + + +L       +   +A  +         E  +  ED G + + LN 
Sbjct: 75  ELITDRPL-EVNFREMLEVKKRFPKHTLVASLMVETKEEW-REIIQRSEDAGADLLELNF 132

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----------Q 130
           GCP     E   G+ +   P ++ +      +   +PV VK    V D            
Sbjct: 133 GCPHGM-CERGMGSAVGAEPKVLEEIARWAVEFARVPVIVKLTPNVGDILEPGEAAVRAG 191

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPD 188
           +PA++L N VKSI    ++ +    R              +  +   ++ ++ +  +   
Sbjct: 192 VPALSLINTVKSIMGVDLDRMVPLPRVGDASTNGGYCGPAVKPIALHLLSQLARHPQCGR 251

Query: 189 LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYK 221
           L I   GG+ +   A + +      V +  A   
Sbjct: 252 LAISGIGGISNWRDAAEFIALGATSVQVCTAVMH 285


>gi|328542363|ref|YP_004302472.1| dihydroorotate dehydrogenase family protein [polymorphum gilvum
           SL003B-26A1]
 gi|326412110|gb|ADZ69173.1| Dihydroorotate dehydrogenase family protein [Polymorphum gilvum
           SL003B-26A1]
          Length = 434

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 58/168 (34%), Gaps = 15/168 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K VED   + + LN GCP     E   G+ +   P+ +        +   +PV VK    
Sbjct: 120 KQVEDTEADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWCKQHTRMPVIVKLTPN 178

Query: 127 VDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
           + D              AV+L N + SI    ++ +                   +  + 
Sbjct: 179 ITDIRKPARAARAGGADAVSLINTINSIVSVDLDRMCPSPTIDGKGAHGGYCGPAVKPIA 238

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 239 LNMVAEIARDPETAGLPISGIGGVTTWRDAAEFMALGAGNVQVCTAAM 286


>gi|283783383|ref|YP_003374137.1| dihydroorotate dehydrogenase 1B [Gardnerella vaginalis 409-05]
 gi|283442061|gb|ADB14527.1| dihydroorotate dehydrogenase 1B [Gardnerella vaginalis 409-05]
          Length = 333

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 75/231 (32%), Gaps = 32/231 (13%)

Query: 26  MIVADAILRGDKKNIL-----GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           M+ A  +      + L             +   + G       +  + + D   + + +N
Sbjct: 97  MVNAVGLQNPGVDHYLVDELPKLKKMGALVITNVAGHSDDDYAQVVEKLADSAADMLEIN 156

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
           V CP   V  G        +P  +   I  +      P+ VK    V D      + ++ 
Sbjct: 157 VSCP--NVTHGGMSVG--TDPVALHRLIKRLRAMTDKPMIVKMTPNVTD------IVSIC 206

Query: 141 KSIKKSGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           K+   +G + + +                 I           I  +    V+ +++  PD
Sbjct: 207 KAAVDAGADALSMINTLVGLRIDIRTGEPIIANRTGGVSGPAIFPIGLGFVWRVRQAMPD 266

Query: 189 LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA----MLTTVDEYFS 234
           + I   GG++   +AL+ L    + V +G AA  +      +   +D+   
Sbjct: 267 IPIIGIGGIDSGEKALEYLYAGANAVEVGAAALVDPTAPIRIARELDDLLD 317


>gi|307353152|ref|YP_003894203.1| methanogenesis marker protein 9 [Methanoplanus petrolearius DSM
           11571]
 gi|307156385|gb|ADN35765.1| methanogenesis marker protein 9 [Methanoplanus petrolearius DSM
           11571]
          Length = 380

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 71/197 (36%), Gaps = 33/197 (16%)

Query: 25  EMIVAD--AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNV 81
           E I  D  A L+ + + + G        A+ + G+     V    I  + G   I  ++ 
Sbjct: 70  EFISTDPAATLKAEIEKLAGTD---VIPAINLRGSSPESFVS---IAHELGDGVIYEIDA 123

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            C    +     G   + N + +   ++A+ K+  + V+VK R GV +         L +
Sbjct: 124 HCRQPAMISAGCGEYYLQNTEKLAMVVSAL-KSTGVTVSVKIRAGVVEDDS-----ELAR 177

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            + K+G + + +     +  G S              + +I+   P L +  N  +    
Sbjct: 178 LLWKAGADILHV---DLMDFGSSK-------------IKQIRNSCP-LLLIANNSVNTFD 220

Query: 202 QALKILP-SVDGVMIGR 217
           +   +     D V + R
Sbjct: 221 RMKDLFAHGADMVSLAR 237


>gi|258575089|ref|XP_002541726.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
 gi|237901992|gb|EEP76393.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
          Length = 424

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 66/203 (32%), Gaps = 36/203 (17%)

Query: 57  ADISKLVEA----AKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDI 103
           ADI +  EA     +     G++ I + N           P +      +G        +
Sbjct: 193 ADIEEFKEAWGAAVRRAVKAGFDYIEIHNAHGYLLYSFLSPVSNNRTDEYGGSFENRIRL 252

Query: 104 VGDCIAAMCKAL--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
             + I    + +   +P+ ++          R  +        +R     ++K GV+ + 
Sbjct: 253 TLEIIDISRQNMPEDMPLFLRVSASDWLEESRPDLPSWKSEDTVRFAQAVVEKGGVDFLD 312

Query: 153 IHARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-- 208
           I +      G  P     +           +KK   D + +G  G + D  QA  +L   
Sbjct: 313 ISSG-----GNHPDQRITLGPAFQAHFAIAVKKAVKDRIAVGTVGSITDGKQANDLLERE 367

Query: 209 SVDGVMIGRAAYKNS---AMLTT 228
            +D V++GR   KN         
Sbjct: 368 GLDAVLVGRLFQKNPAVVWKFAE 390


>gi|148257287|ref|YP_001241872.1| dihydropyrimidine dehydrogenase [Bradyrhizobium sp. BTAi1]
 gi|146409460|gb|ABQ37966.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) [Bradyrhizobium sp. BTAi1]
          Length = 441

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 70/206 (33%), Gaps = 30/206 (14%)

Query: 25  EMIVADAILRGDKK-NILGFSTQEKPLALQIG--GADISKLVEAAKIVEDFGYNEINLNV 81
           E+I    +    ++   +     ++ + + +     + +      K VE  G + + LN 
Sbjct: 78  ELITDRPLEVNLQEITQVKRDWPDRAVVVSLMVPCQEPNWTA-IIKRVEQTGADGVELNF 136

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           GCP     E   GA +   P+ +         A  +PV VK    V   +P        +
Sbjct: 137 GCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKAATRMPVIVKLTPNVASILPP------AE 189

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD-----------------YDIVYEIKK 184
           + K+ G + + +      L G+        P++D                  ++V  I +
Sbjct: 190 AAKRGGADAVSLINTVNALMGVDIDQMAPWPHIDGYGTHGGMCGSVVKPIALNMVSAIAR 249

Query: 185 --ENPDLFIGLNGGLEDMSQALKILP 208
                 L I   GG+E    A + + 
Sbjct: 250 HPATQGLPISGIGGIEKWRDAAEFMA 275


>gi|332535710|ref|ZP_08411462.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332034885|gb|EGI71414.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 653

 Score = 52.1 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 58/182 (31%), Gaps = 17/182 (9%)

Query: 61  KLVEAAKIVEDFGYNEIN--------LN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               +A + E  GY+ +         +N    P     +  FG  L     +  + + A+
Sbjct: 139 DFAYSAYMAEKAGYDGVEVMGSEGYLINEFMAPHTNKRDDEFGGSLENRMRLALEIVKAV 198

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKS----IKKSGVNGIWIHARKAILKGLSPKD 167
              +S    +  R+ V D IP  +    V      ++K+GV+    +      +   P  
Sbjct: 199 RAKVSEKFLIIFRLSVIDLIPNGSTPEEVVIQATELEKAGVDIF--NTGIGWHEARVPTI 256

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
              +P   +    +  K+   + +     +     A  IL     D + + R    +   
Sbjct: 257 ASMVPPGAFKEASKRLKDVVSVPVIAVNRINTPEIANDILNAGEADLISMARPLLADPEF 316

Query: 226 LT 227
             
Sbjct: 317 FN 318


>gi|309389728|gb|ADO77608.1| dihydroorotate oxidase B, catalytic subunit [Halanaerobium
           praevalens DSM 2228]
          Length = 321

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/197 (17%), Positives = 61/197 (30%), Gaps = 17/197 (8%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G   +  +  A  +E       I +N+ CP+ +      G      P+ V   
Sbjct: 114 PILANISGYSQADFLTLASKLEKRKELAGIEVNLSCPNIK----GGGMVFGTAPEKVYQI 169

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVAL-----RNLVKSIKKSGVNGIWIHARKAIL-K 161
              + +  S  + VK    + D             + V  I       I I  +K +L  
Sbjct: 170 TKKVREIYSGYIIVKLTPNITDITETALAAEKGGADAVAMINTLSAMKIDIDQQKPVLAN 229

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMIGRAAY 220
                    +  +   +VY+  K+   + I   GG+         +L     V IG    
Sbjct: 230 TFGGLSGPAVKPVAVKMVYQSYKKL-SIPILGLGGVSSGRDVIEFMLAGAAAVEIGTINM 288

Query: 221 KNSA----MLTTVDEYF 233
                   ++  + EY 
Sbjct: 289 IEPTAGLRIIAEIKEYL 305


>gi|150018356|ref|YP_001310610.1| NADPH dehydrogenase NamA [Clostridium beijerinckii NCIMB 8052]
 gi|149904821|gb|ABR35654.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
          Length = 338

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 66/175 (37%), Gaps = 16/175 (9%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK  +  G++ I +             P + + +  +G  +      + + + A+ 
Sbjct: 144 FKEAAKRADKAGFDAIEIHGAHGYLIHQFLSPLSNLRKDEYGGDIKNRIRFLKEILEAVK 203

Query: 113 KALSIPVTVKCRIG-VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
           +       +  R+   D +   + L ++++ I +       +H       GL P +    
Sbjct: 204 EVWPKEKAILLRVSAYDYKEGGITLNDMIEIINEIKEYIDIVHLST---GGLIPVEINAY 260

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           P    +    I KE  ++     G + D++ A +I+ +   D V +GR   +N  
Sbjct: 261 PGYQVNY-SSIIKEKCNIPTIAVGLITDINMAEEIISNGRADLVAVGRELLRNPY 314


>gi|293396595|ref|ZP_06640871.1| xenobiotic reductase A [Serratia odorifera DSM 4582]
 gi|291420859|gb|EFE94112.1| xenobiotic reductase A [Serratia odorifera DSM 4582]
          Length = 365

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 68/203 (33%), Gaps = 32/203 (15%)

Query: 43  FSTQEKPLALQI--GGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG 91
               E P A+ +        + V AAK  +  G+  I L             P A     
Sbjct: 138 HPHDEAPQAMSLERIATLKRQFVAAAKRADRLGFELIELHGAHGYLLHQFLSPLANQRTD 197

Query: 92  SFGACLMLNPDIVGDCIAAMC------KALSIPVTVK--CRIGVDDQIPAVALRNLVKSI 143
            +G  L     ++ +  + +       KA+ + ++       G D+Q   +    L K +
Sbjct: 198 QYGGSLQNRMRLLLEIFSEVRAVFPANKAVGVRISASDWVEGGWDEQQSVI----LAKEL 253

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           K+ G + I + +      GLS +    +           IK+E   +     G + +  Q
Sbjct: 254 KELGCDYIHVSSG-----GLSAQQKIPVGPGYQVPFAATIKREVG-MPTIAVGLITEPEQ 307

Query: 203 ALKILP--SVDGVMIGRAAYKNS 223
           A  I+     D V + R    N 
Sbjct: 308 AETIIASGQADMVALARGILYNP 330


>gi|242223402|ref|XP_002477331.1| predicted protein [Postia placenta Mad-698-R]
 gi|220723179|gb|EED77471.1| predicted protein [Postia placenta Mad-698-R]
          Length = 412

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/211 (15%), Positives = 61/211 (28%), Gaps = 38/211 (18%)

Query: 62  LVEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+AAK     G++ I + N           P++      +G        +  + + A+ 
Sbjct: 196 FVDAAKRALRAGFDVIEIHNAHGYLLHEFVSPASNKRTDEYGGSFENRVRLSLEVVDAVR 255

Query: 113 KAL--SIPVTVKCRIGV--------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
             +   +P+ ++             +    A         + + GV+ + +        G
Sbjct: 256 AVIPPDMPLFLRISATDWLEKSLANEPSWTAQDTVRFADLLAEHGVDLLDVSTG-----G 310

Query: 163 LSPKDNRKIPNLDYDIVYE-IKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           L P    +          E +KK +   + I   G + D   A  +L     D V + R 
Sbjct: 311 LHPAQKIEGGPAYQARFAEMVKKAHGHRILIAAVGAISDGKTAQGVLDKNQADVVFVARQ 370

Query: 219 AYKNS---AMLTT-------VDEYFSNPLTG 239
             KN                V         G
Sbjct: 371 FQKNPGSVWQFAEELGVVTTVAHQIEWGFAG 401


>gi|162454677|ref|YP_001617044.1| dihydropyrimidine dehydrogenase [Sorangium cellulosum 'So ce 56']
 gi|161165259|emb|CAN96564.1| Dihydropyrimidine dehydrogenase [Sorangium cellulosum 'So ce 56']
          Length = 462

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 67/212 (31%), Gaps = 16/212 (7%)

Query: 25  EMIVADAI-LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC 83
           E+I    + +   +   +        L   +      +  E  +  ED G + + LN GC
Sbjct: 75  ELITDRPLDVNLKEMREIKRRYPGHALIASLMVETKDEWREIIRKAEDTGADGLELNFGC 134

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA---------- 133
           P     E   G+ +   P ++ +      +  + PV VK    V D +            
Sbjct: 135 PHGM-CERGMGSAVGNEPAVLQEIARWAVEFATTPVIVKLTPNVGDILEPGEAVLRSGAH 193

Query: 134 -VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLF 190
            V+L N VKS+    +  +    R              +  +   ++ ++ +      L 
Sbjct: 194 GVSLINTVKSLMGVDLERMVPLPRVGGASTNGGYCGPAVKPIALHLLSQLARHPGVGRLP 253

Query: 191 IGLNGGLE-DMSQALKILPSVDGVMIGRAAYK 221
           I   GG+      A  I      V +  A   
Sbjct: 254 ISGIGGISNSRDAAEFIALGATSVQVCTAVMH 285


>gi|209516626|ref|ZP_03265479.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. H160]
 gi|209502901|gb|EEA02904.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. H160]
          Length = 680

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/218 (12%), Positives = 67/218 (30%), Gaps = 26/218 (11%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGAD--ISKLVEAAKIVEDFGYNEINL- 79
           Y   +V+ + L+             KP AL + G D  +      A++ +  GY+ + + 
Sbjct: 110 YQPFVVSASALKSPISKF-------KPRALTLAGIDRTVRDYARCARLAQRAGYDGVEIM 162

Query: 80  --------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-- 129
                      CP        +G  +     +  + +  +         V  R+ + D  
Sbjct: 163 GSEGYLLNQFLCPRTNRRTDRYGGSIENRMRLAREIVERVRAECGERFIVVYRLSLIDLV 222

Query: 130 --QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                      + ++++ +GV     +      +   P     +P   +  +    K   
Sbjct: 223 EGGNTWEETVQVAQALEAAGVTIF--NTGIGWHEARVPTIVTSVPRAAFASLSARLKTAV 280

Query: 188 DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            + +  +  +     A  ++   S D V + R    + 
Sbjct: 281 KVPVIASNRINTPEMAETLIADGSADLVSMARPLLADP 318


>gi|114766788|ref|ZP_01445722.1| dihydropyrimidine dehydrogenase [Pelagibaca bermudensis HTCC2601]
 gi|114540982|gb|EAU44040.1| dihydropyrimidine dehydrogenase [Roseovarius sp. HTCC2601]
          Length = 434

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 58/167 (34%), Gaps = 15/167 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + + LN GCP     E   G+ +   P+ +      + +   +P  VK    +
Sbjct: 124 LVEETGADGVELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTRWVKQYTRMPCIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++                     +  +  
Sbjct: 183 TDIRKPAMAAHAGGADAVSLINTINSITSVDLDLFAPEPTIDGKGAHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           ++V EI +  E   L I   GG+     A + +      V +  AA 
Sbjct: 243 NMVSEIARSPEMRGLPISGIGGVTTWKDAAEFMALGAGNVQVCTAAM 289


>gi|260575576|ref|ZP_05843574.1| dihydroorotate dehydrogenase family protein [Rhodobacter sp. SW2]
 gi|259022219|gb|EEW25517.1| dihydroorotate dehydrogenase family protein [Rhodobacter sp. SW2]
          Length = 432

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 58/173 (33%), Gaps = 33/173 (19%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            +ED   + + LN GCP     E   G+ +   P+ +      + +   +P  VK    +
Sbjct: 124 RIEDTEADGVELNFGCPHGMA-ERGMGSAVGQVPEYIEMVTRWVKQHSRMPCIVKLTPNI 182

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWI--------------HARKAILKGLSPKDNR---K 170
            D      +R   ++ K+ G + + +               A + ++ G           
Sbjct: 183 SD------IRKPAEAAKRGGADAVSLINTINSITSVNLDDFAPEPMIDGKGTHGGYCGPA 236

Query: 171 IPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL-------PSVDGVM 214
           +  +  ++V EI +      L I   GG+     A + +            VM
Sbjct: 237 VKPIALNMVAEIARHPATRGLPISGIGGVSTWRDAAEFMALGAGNVQVCTAVM 289


>gi|121606904|ref|YP_984233.1| dihydropyrimidine dehydrogenase [Polaromonas naphthalenivorans CJ2]
 gi|120595873|gb|ABM39312.1| dihydrouracil dehydrogenase (NAD+) / dihydropyrimidine
           dehydrogenase (NADP+) [Polaromonas naphthalenivorans
           CJ2]
          Length = 435

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/176 (21%), Positives = 59/176 (33%), Gaps = 20/176 (11%)

Query: 64  EAA-----KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
           EAA       VED G + + LN GCP     E   G+ +   P+ +            +P
Sbjct: 115 EAAWKSILARVEDTGADGLELNFGCPHGMS-ERGMGSAVGQVPEYIEMVTQWCKHYSRLP 173

Query: 119 VTVKCRIGVDD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           V VK    + D              AV+L N + SI       + +              
Sbjct: 174 VIVKLTPNITDIRIPARAARRGGADAVSLINTINSIMGVDPYSLTMLPSTGGKGSHGGYC 233

Query: 168 NRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
              +  +  ++V EI ++     L I   GG+     AL  +      V +  AA 
Sbjct: 234 GPAVKPIALNMVAEIARDPQTAGLPISGIGGVGSWRDALDYIALGAGTVQVCTAAM 289


>gi|288561420|ref|YP_003424906.1| NADH:flavin oxidoreductase/NADH oxidase family protein
           [Methanobrevibacter ruminantium M1]
 gi|288544130|gb|ADC48014.1| NADH:flavin oxidoreductase/NADH oxidase family protein
           [Methanobrevibacter ruminantium M1]
          Length = 316

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 66/176 (37%), Gaps = 20/176 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VEAA   +  G++ + ++            P        +G  L     +  + I  + 
Sbjct: 128 FVEAAVRSQKSGFDGVEIHAAHEYLLNQFYSPYTNKRTDEYGGSLENRMRLHNEIIREIR 187

Query: 113 KALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +A+     I +       ++       +   VKS  +SGV+ I I       +    ++ 
Sbjct: 188 EAVGDDYIIAIRFGAYDYLEGGSKMEDIPAAVKSFVESGVDMIDISGGLCRYQNPYSREP 247

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               +L      +I KE+ D+ + L GG++    A +++     D + IGRA   +
Sbjct: 248 GYFKDL-----SKIAKESCDIPVILTGGVKKAKDAERLINEGYCDLIGIGRALLMD 298


>gi|223938296|ref|ZP_03630191.1| dihydroorotate dehydrogenase family protein [bacterium Ellin514]
 gi|223893010|gb|EEF59476.1| dihydroorotate dehydrogenase family protein [bacterium Ellin514]
          Length = 374

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/173 (22%), Positives = 66/173 (38%), Gaps = 23/173 (13%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  +  +D G +   LN  CP   + E   GA +  +PD++ +    +  A   PV  K 
Sbjct: 119 EIVERCQDAGVDAFELNFSCPHG-LPERKMGAAMGQDPDVLKEVCGWVKSAAKKPVWAKM 177

Query: 124 RI---GVDDQIPAVAL-----RNLVKSIKK-SGVNGIWIHARKAILKGLSP--KDNRKIP 172
                 ++D   A  L      + + +I+  +GVN   +     +    +P     + + 
Sbjct: 178 TPNVTHIEDPSRAALLGGATGLSAINTIRSVTGVNLDTLRPEPTVEGYTTPGGYSCKAVK 237

Query: 173 NLDYDIVYE----IKKENPDLFIGLNGGLEDM-SQALKILPS------VDGVM 214
            +   +V E    I+KE P   +   GG+E     A  IL          GVM
Sbjct: 238 PIALRMVMEIAQMIRKEFPGRSLSGLGGIESGNDAAQFILLGSDTVQVCTGVM 290


>gi|325927346|ref|ZP_08188599.1| NADH:flavin oxidoreductase [Xanthomonas perforans 91-118]
 gi|325928594|ref|ZP_08189779.1| NADH:flavin oxidoreductase [Xanthomonas perforans 91-118]
 gi|325541027|gb|EGD12584.1| NADH:flavin oxidoreductase [Xanthomonas perforans 91-118]
 gi|325542269|gb|EGD13758.1| NADH:flavin oxidoreductase [Xanthomonas perforans 91-118]
          Length = 372

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 64/207 (30%), Gaps = 22/207 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +AK  E  G   I L+            P +     ++G  L     +      A
Sbjct: 165 DAFVASAKRAERQGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMRLTLRIFDA 224

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + V  RI   D             L +++   G + I + +      GL P+
Sbjct: 225 VRAAVSEKIAVGVRISATDWVQGGWDVQQSIALSQALDARGAHYIHVSSG-----GLDPR 279

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +    Y I   +  +   +  +   G + + +QA  IL     D + + R    + 
Sbjct: 280 QQIPL-QAGYQIPFAQEIRAQVNTPVIGVGLITEPAQAEAILQEGQADAIALARGILYDP 338

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                        +T +        +D
Sbjct: 339 RWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|156337820|ref|XP_001619894.1| hypothetical protein NEMVEDRAFT_v1g223715 [Nematostella vectensis]
 gi|156203911|gb|EDO27794.1| predicted protein [Nematostella vectensis]
          Length = 137

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           + + IP+TVK R G+ D+        LV +++  G + + IH R         ++ R   
Sbjct: 55  QVIDIPLTVKIRAGIHDKKYTWNAHKLVGNLRDWGTDMVTIHGRS--------REQRYTK 106

Query: 173 NLDYDIVY 180
           + D+D + 
Sbjct: 107 SADWDYIK 114


>gi|253573711|ref|ZP_04851054.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp. oral
           taxon 786 str. D14]
 gi|251847239|gb|EES75244.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp. oral
           taxon 786 str. D14]
          Length = 336

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 71/194 (36%), Gaps = 19/194 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               + A+  ++ G++ I ++            P     E  +G        ++ + I A
Sbjct: 143 EGFRDGARRAKEAGFDVIEIHGAHGYLLNEFLSPVTNHREDEYGGNADNRYRLLSEVIEA 202

Query: 111 MCKALSIPVTVKCRIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +    S P+ V+      D          N  + +K  GV+ I   +      GL P   
Sbjct: 203 VNSVWSGPLFVRISANEYDPQGNSLEQYINYARRMKAQGVDLIDCSSG-----GLVPAQI 257

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           +  P    ++  +I+++  ++  G  G + D S A +IL +   D V++GR   +N    
Sbjct: 258 QTFPGYQVNLAEQIRRQA-EVATGAVGLITDPSHAEEILGNGRADLVLLGRELLRNPYWA 316

Query: 227 TTVDEYFSNPLTGS 240
               +  +  L   
Sbjct: 317 YEAAKALNTTLERP 330


>gi|254386967|ref|ZP_05002248.1| oxidoreductase [Streptomyces sp. Mg1]
 gi|194345793|gb|EDX26759.1| oxidoreductase [Streptomyces sp. Mg1]
          Length = 360

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/159 (17%), Positives = 50/159 (31%), Gaps = 14/159 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-----IPAVALRNLVKSIKKS 146
           ++G           + + A+       + +  RI   D        A     L   + + 
Sbjct: 203 AYGGSFENRTRFALEVVDAVRAVWPQELPLFFRISATDWLEGAGWTADETVRLAGLLLEH 262

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           GV+ + +        GL+P     +           +K E   L +   G + D  QA K
Sbjct: 263 GVDLLDVSTG-----GLAPGVRIPVGPGYQVPFAARVKAETG-LPVAAVGLITDPEQAEK 316

Query: 206 ILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           IL     D V++GR   ++              +   SP
Sbjct: 317 ILADGEADAVLLGRELLRDPYWARRAAAELGGEVRQPSP 355


>gi|239626191|ref|ZP_04669222.1| NADH oxidase [Clostridiales bacterium 1_7_47_FAA]
 gi|239520421|gb|EEQ60287.1| NADH oxidase [Clostridiales bacterium 1_7_47FAA]
          Length = 641

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/181 (13%), Positives = 59/181 (32%), Gaps = 16/181 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K  +AA      G++ + L             P +      +G  L        + + A
Sbjct: 146 EKFADAALRARKAGFDAVELHGAHGYLIAQFLSPFSNRRVDEYGGTLENRARFAVETVKA 205

Query: 111 MCKALSI--PV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +      PV   +     +D  +     + + + ++++G + I            +  
Sbjct: 206 VKERAGWDYPVLLRISATEFIDQGMNVEQAKAICRLVEQAGADAINCSQSGPATFYNTVP 265

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                     ++  EI+K    + +   G +     A +++     D V +GRA+  +  
Sbjct: 266 SFYVQSGAFVELADEIRK-VVGIPVATVGRINSPQLAEEVILSGKADLVAMGRASVADPY 324

Query: 225 M 225
           +
Sbjct: 325 L 325


>gi|226310019|ref|YP_002769913.1| NADPH dehydrogenase [Brevibacillus brevis NBRC 100599]
 gi|226092967|dbj|BAH41409.1| NADPH dehydrogenase [Brevibacillus brevis NBRC 100599]
          Length = 342

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 79/235 (33%), Gaps = 29/235 (12%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL-------- 79
            A A   G  K     +T+E     Q+      K  ++A+   + G++ I +        
Sbjct: 119 SAIAFPGGRYKTPRALTTEE---VKQMV----VKFQDSARRAVEAGFDTIEIHGAHGYLV 171

Query: 80  -NVGCPSARVHEGSFGACLMLNPDIVG-DCIAAMCKAL--SIPVTVKCR--IGVDDQIPA 133
                P     +  +G     +  + G + I A+ + +   +P+ ++      VD     
Sbjct: 172 HQFHSPLTNQRDDEYG----RDKALFGVEIIQAIKEVIPADMPLIMRVSAVEYVDGGYGL 227

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                L +  K++GV+   I +      G + +     P     +   IK+   D+ +  
Sbjct: 228 DYSTELCRRYKEAGVDIFHISSGGEGPIGSAGRPGVH-PGYQVPLARAIKQAL-DVPVIA 285

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
            G L+D   A   + +   D V +GR   ++           S          +R
Sbjct: 286 VGNLDDPQVAEASIGNGDTDLVAVGRGMLRDPYWALHAIHELSADELQPPKQYSR 340


>gi|327400805|ref|YP_004341644.1| TIM-barrel protein [Archaeoglobus veneficus SNP6]
 gi|327316313|gb|AEA46929.1| TIM-barrel protein [Archaeoglobus veneficus SNP6]
          Length = 247

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 51/164 (31%), Gaps = 25/164 (15%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE A IV  +G   I +N  C      E   G  LM +P  +   +  +  A      VK
Sbjct: 92  VEVADIVRRYG-GIIEINAHCRQPEFIEAKCGQWLMEHPKELASVVREVSDAALT--GVK 148

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R                +   K+G   + + A                   D+ +V  I
Sbjct: 149 LR-------NGAKCVEAARLAFKAGAAYVHVDAMIP------------GGLCDFRLVERI 189

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
            +    + IG N  +  +  A K+      V   RA  K+    
Sbjct: 190 SR--LGITIGNN-SVNSLEMAEKMAKVAHLVSAARAILKDPHFF 230


>gi|52082002|ref|YP_080793.1| putative NADH-dependent flavin oxidoreductase YqiG [Bacillus
           licheniformis ATCC 14580]
 gi|52787389|ref|YP_093218.1| YqiG [Bacillus licheniformis ATCC 14580]
 gi|52005213|gb|AAU25155.1| putative NADH-dependent flavin oxidoreductase YqiG [Bacillus
           licheniformis ATCC 14580]
 gi|52349891|gb|AAU42525.1| YqiG [Bacillus licheniformis ATCC 14580]
          Length = 364

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/218 (14%), Positives = 67/218 (30%), Gaps = 27/218 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDC 107
               + A+   + G++ + +             P        +G  L   M  P  + + 
Sbjct: 144 HSFGQTARRAIEAGFDGVEIHGANGFLIHQFFSPYYNRRNDGWGGTLEKRMRFPLQIIEE 203

Query: 108 IAAMCKALSIP---VTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           I  +  +   P   +  K      +   I      + V  +++ G++ + +     +   
Sbjct: 204 IRRVADSCHKPSFIIGYKFSPEEPETPGITMDETLSFVNVLREQGLDYLHV---SLVDFR 260

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYK 221
             P+          +++ E  ++   L +   G +     AL+ L    D + IGR    
Sbjct: 261 SLPRRGADRSRARMELIKEAVQDR--LPLIGAGQVHTPEDALQALETGADLIGIGRGLLM 318

Query: 222 NSAMLTTVDE----YFSNPLTGSSPIKTRVDKDFWRKI 255
           +   L  V           L+     K  +   FW  I
Sbjct: 319 DPEWLQKVRAGKEDDIQTTLSRHDQRKLAIPDAFWESI 356


>gi|46119162|ref|XP_384931.1| hypothetical protein FG04755.1 [Gibberella zeae PH-1]
          Length = 411

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/193 (19%), Positives = 68/193 (35%), Gaps = 30/193 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINL------------NVGCPSARVHEGSFGACLMLNPDIVGDC 107
            + V+ A +  D G++ I L            N   P        +G        IV D 
Sbjct: 167 ERFVKTAVLASDAGFDGIELHGAHGYLLSQFLN---PKTNHRTDEYGGSAAARAKIVVDI 223

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK------- 157
           I A+ KA+    TV  +    D   + AL   ++ ++    +G++ + I           
Sbjct: 224 IKAIRKAVPRSFTVGIKFNSVDHQSSQALEECIEQLRLITDAGIDFLEISGGSYEDPPGV 283

Query: 158 --AILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDG 212
                   + K++ K     + D    I+ + P L + + GG          L   S+D 
Sbjct: 284 VDPDKVTAAKKESTKAREAFFLDFAIAIRDQFPGLPLLVTGGFRSRKVIQDALASGSLDL 343

Query: 213 VMIGRAAYKNSAM 225
           V + R A  + ++
Sbjct: 344 VGLARPAMLDPSV 356


>gi|332799737|ref|YP_004461236.1| 2,4-dienoyl-CoA reductase [Tepidanaerobacter sp. Re1]
 gi|332697472|gb|AEE91929.1| 2,4-dienoyl-CoA reductase (NADPH) [Tepidanaerobacter sp. Re1]
          Length = 646

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 66/179 (36%), Gaps = 19/179 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAM 111
              +AA   +  G++ I ++            P        +G           + + A+
Sbjct: 152 DFAQAASFAQKAGFDAIEIHGHAGYLIDQFLSPIWNKRTDEYGGSAENRARFAVEIVQAV 211

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARK-AILKGLSPK 166
              +   + +  RI +D + P          L++ ++K+GV+   + A     +  + P 
Sbjct: 212 RNTVGSDMPILFRIALDHRFPGGRTLEDSMPLLEILEKAGVDAFDVDAGAYETMDYIFPT 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               + +     V +  +++ ++ +  N G      AL+++ S   D VM GR A  + 
Sbjct: 272 A--YVGDACMAYVCKEARKHVNVPLI-NAGNHSPETALELVNSGDCDFVMFGRQAIADP 327


>gi|88601964|ref|YP_502142.1| hypothetical protein Mhun_0667 [Methanospirillum hungatei JF-1]
 gi|88187426|gb|ABD40423.1| conserved hypothetical protein [Methanospirillum hungatei JF-1]
          Length = 367

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/152 (18%), Positives = 64/152 (42%), Gaps = 25/152 (16%)

Query: 68  IVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + ++ G + I  ++  C    + +   G  L+ +P+++   + A+  A  + V+VK R G
Sbjct: 106 LAQELGNSVIYEIDAHCRQQPMIDARSGEFLLHHPEVLISYVQALKIA-GVLVSVKIRAG 164

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +     A     L + + K+G + + I                   + D+  + +I+  +
Sbjct: 165 I-----AADDVELSRLLWKAGADILHIDLM----------------DFDHTHLKKIRDTS 203

Query: 187 PDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
           P +FI  N G+    +A ++     D + + R
Sbjct: 204 P-IFIIANNGITTFEKAKEMFAHGADMISLAR 234


>gi|302888451|ref|XP_003043112.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256724027|gb|EEU37399.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 411

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/190 (20%), Positives = 66/190 (34%), Gaps = 26/190 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V+ A +V D G++ I L             P        +G        IV D I A
Sbjct: 167 DRFVKTAVLVADAGFDGIELHGAHGYLLSQFLSPKTNQRTDEYGGSAGARAKIVVDIIKA 226

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARKAILKGLSPKD 167
           + KA+    TV  +    D   + AL   ++ ++    +G++ + I       + +   D
Sbjct: 227 IRKAVPPSFTVGIKFNSVDHQSSQALEECLEQLRLITDAGIDFLEISGGT-YEEPIGIID 285

Query: 168 NRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVM 214
             KIP               D    I+ + P L + + GG          L   S+D V 
Sbjct: 286 PDKIPAAKRESTKAREAFFLDFAKAIRGQFPGLPLLVTGGFRSRKVIEDALASGSLDMVG 345

Query: 215 IGRAAYKNSA 224
           I R    + +
Sbjct: 346 IARPGVLDPS 355


>gi|255524903|ref|ZP_05391851.1| nitrogen regulation protein [Clostridium carboxidivorans P7]
 gi|255511381|gb|EET87673.1| nitrogen regulation protein [Clostridium carboxidivorans P7]
          Length = 79

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 2  VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLAL 52
            +T   +R     L    L YTEM+  +A+   DK    +L  + +EK  + 
Sbjct: 23 AGYTCYPFRILCSEL-GAGLCYTEMVNCNALKYKDKATQKLLFTTPEEKIKSC 74


>gi|323526684|ref|YP_004228837.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1001]
 gi|323383686|gb|ADX55777.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1001]
          Length = 682

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/220 (13%), Positives = 70/220 (31%), Gaps = 30/220 (13%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGAD--ISKLVEAAKIVEDFGYNEINL- 79
           Y   +V+ + L+             +P AL I G +  +      A++ +  GY+ + + 
Sbjct: 110 YQPFVVSASALKSPISKF-------RPRALSIAGIEKTVRDYARCARLAQRAGYDGVEIM 162

Query: 80  --------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-- 129
                      CP        +G  +     I  + +  + +A      V  R+ + D  
Sbjct: 163 GSEGYLLNQFLCPRTNRRTDRYGGSIENRMRIAREIVERVREACGERFIVVYRLSLIDLV 222

Query: 130 --QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                      + ++++ +GV     +      +   P     +P   +  +        
Sbjct: 223 EGGNTWDETVQVARALEAAGVTIF--NTGIGWHEARVPTIVTSVPRAAFAGLSARLTAAV 280

Query: 188 DLFIGLNGGLEDMSQALKILPSVDG----VMIGRAAYKNS 223
           ++ + ++  +     A  +L   DG    V + R    + 
Sbjct: 281 NVPVIVSNRINTPEVAEALL--ADGAGHLVSMARPLLADP 318


>gi|119386194|ref|YP_917249.1| dihydroorotate dehydrogenase [Paracoccus denitrificans PD1222]
 gi|119376789|gb|ABL71553.1| dihydroorotate oxidase B, catalytic subunit [Paracoccus
           denitrificans PD1222]
          Length = 359

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 60/178 (33%), Gaps = 22/178 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-SARVHEGSFGACLMLNPDIVGDCI 108
           L   +  A I   V  A+ VED G      N+G P +++  +G+    L  +P  V + +
Sbjct: 116 LVASVVMAGIEDAVRRARAVEDAGLRVFEFNIGTPYASQAAKGAVSTEL--SPARVAELV 173

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +  A+SIPV VK          +  +  LV +   +G +   I  R   L        
Sbjct: 174 GQVTSAVSIPVWVKL------SGQSERVPELVAAATGAGADSAVIAGRALGLVPDLETMQ 227

Query: 169 RKIP-------------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
             +                 +  +   +       IG+NG       A  +L     V
Sbjct: 228 PMLGTSCGIGGYWNLPLTCHWLAMTRARLGAGRALIGINGACSGRDVARMMLAGASAV 285


>gi|322693224|gb|EFY85092.1| FMN binding oxidoreductase, putative [Metarhizium acridum CQMa 102]
          Length = 409

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 53/147 (36%), Gaps = 13/147 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGV 148
           ++G        IV + + A+ KA+     V  ++   D      L   V+ ++    +G+
Sbjct: 208 AYGGSPKKRARIVIEILEAVRKAVPKDFCVGIKLNSVDHQSQKELEECVEQLEVIVAAGI 267

Query: 149 NGIWI----HARKAILKGLS--PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDM 200
           + + I    +    ++ G +  P   R      +  +  + I+     + + + GG    
Sbjct: 268 DFLEISGGTYENPEMMVGRANPPVSERTAAREAFFIEFAHAIRDRFEGVPLMVTGGFRSR 327

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAM 225
                 +     D V IGR +  N  +
Sbjct: 328 QGMEAAIKDGGCDLVGIGRPSILNPLL 354


>gi|84514681|ref|ZP_01002045.1| dihydropyrimidine dehydrogenase [Loktanella vestfoldensis SKA53]
 gi|84511732|gb|EAQ08185.1| dihydropyrimidine dehydrogenase [Loktanella vestfoldensis SKA53]
          Length = 434

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/154 (20%), Positives = 52/154 (33%), Gaps = 14/154 (9%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V++ G + I LN GCP     E   GA +   P+ +        +    PV VK    +
Sbjct: 124 RVQETGADGIELNFGCPHGMS-ERGMGAAVGQVPEYIEMVTRWCKQYYDKPVIVKLTPNI 182

Query: 128 DD-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            D              AV+L N + SI    ++ +                   +  +  
Sbjct: 183 TDIRQPAAAAMRGGADAVSLINTINSITSVNLDTMSPEPSIDGKGSHGGYCGPAVKPIAL 242

Query: 177 DIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP 208
            +V EI +  E   L I   GG+     A + + 
Sbjct: 243 SMVSEIARHPETRGLAISGIGGVTTWRDAAEYIS 276


>gi|312602354|ref|YP_004022199.1| dihydropyrimidine dehydrogenase [NADP+] subunit beta [Burkholderia
           rhizoxinica HKI 454]
 gi|312169668|emb|CBW76680.1| Dihydropyrimidine dehydrogenase [NADP+] beta subunit (EC 1.3.1.2)
           [Burkholderia rhizoxinica HKI 454]
          Length = 425

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 60/167 (35%), Gaps = 15/167 (8%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
           VED G + + LN GCP     E   GA +   P+ V      + +A  +P  VK    + 
Sbjct: 123 VEDTGADAVELNFGCPHGMS-ERGMGAAVGQVPEYVEMVTRWVKQASRLPCLVKLTPNIT 181

Query: 129 D-----------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           D               V+L N + SI    +  +                   +  +  +
Sbjct: 182 DIRLGSRAAYAGGADGVSLINTINSIVAVDLEQMAPMPTVDGKGTHGGYCGPAVKPIALN 241

Query: 178 IVYEIKKE--NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           +V EI ++   P L I   GG+ +   A + I+     V +  AA  
Sbjct: 242 MVAEIARDPNTPGLPISGMGGISNWRDAAEFIVLGAGSVQVCTAAMH 288


>gi|292670825|ref|ZP_06604251.1| dihydroorotate oxidase [Selenomonas noxia ATCC 43541]
 gi|292647446|gb|EFF65418.1| dihydroorotate oxidase [Selenomonas noxia ATCC 43541]
          Length = 316

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 68/201 (33%), Gaps = 32/201 (15%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
                   + + I G+ +      A  +       + +N+ CP    +    G     +P
Sbjct: 98  RIRNYGMNVIVNISGSSVDDYAHIAARLNGSDIAALEINISCP----NVKEGGIVFGTDP 153

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------- 152
                 + A+C   + PV  K    V       ++  +  +++ +G N I          
Sbjct: 154 HAAAAVVRAVCVQTNKPVIAKLSPNV------TSITEMALAVENAGANIISLINTLVGMQ 207

Query: 153 --IHARKAIL----KGLSPKDNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
             I  R+ +L     GLS    + I   + ++  + +      + +   GG+     A++
Sbjct: 208 IDIDRRRPVLGNCTGGLSGPAVKPIALRMVWETAHAV-----HIPVIGMGGIASWQDAVE 262

Query: 206 -ILPSVDGVMIGRAAYKNSAM 225
             L     + +G A + +  +
Sbjct: 263 FFLAGASAIAVGTANFIDPNI 283


>gi|71066076|ref|YP_264803.1| putative NADH-dependent flavin oxidoreductase [Psychrobacter
           arcticus 273-4]
 gi|71039061|gb|AAZ19369.1| putative NADH-dependent flavin oxidoreductase [Psychrobacter
           arcticus 273-4]
          Length = 363

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 60/177 (33%), Gaps = 22/177 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            VEA+K  ++ G++ I ++    +  + +             +G        ++     A
Sbjct: 159 FVEASKNAKEAGFDGIEIHGA--NGYILDQFLTDYTNKRTDEYGGSTENRVRLLEKVSRA 216

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + +A+    TV  RI                  K + +  I+    +A L  +   D   
Sbjct: 217 VREAVGQDYTVGIRISQGKVNDYD--HKWANKEKDAEI--IFGQLAQAGLDYIHVTDFEA 272

Query: 171 IPNLDYD---IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                 D       + K+   L +  NG L D  +A +I+     D + + R A  N
Sbjct: 273 WQPAFGDEGPTFAALAKKYGKLPVIANGSLHDPEKAKEIVEKGGADIITLARGALSN 329


>gi|158321339|ref|YP_001513846.1| NADH:flavin oxidoreductase/NADH oxidase [Alkaliphilus oremlandii
           OhILAs]
 gi|158141538|gb|ABW19850.1| NADH:flavin oxidoreductase/NADH oxidase [Alkaliphilus oremlandii
           OhILAs]
          Length = 645

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 68/181 (37%), Gaps = 21/181 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AAK   + G++ I  + G          P+       +G  L        +CI  + 
Sbjct: 147 FGAAAKRAVEAGFDCIEFHAGHNYMPHAFLSPAFNKRTDEYGGSLENRARFSIECIKEIR 206

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
             +   +P+ ++     D     + + ++++  K + V G+ +    +     S     +
Sbjct: 207 NNIPEDMPLFMRVVAQDDYLENGLTIEDIIEFCKLAKVAGVDV-LNVSRGNFSSAAIKYE 265

Query: 171 IPNLDYDI------VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           +P +D            IK+E   + I + G + D +QA +I+     D V+IGR    +
Sbjct: 266 VPPVDLPKGFNVANAERIKRETGMITIAV-GRINDPAQADEIIGSGKADMVVIGRGQLAD 324

Query: 223 S 223
            
Sbjct: 325 P 325


>gi|298486831|ref|ZP_07004887.1| NADH:flavin oxidoreductase [Pseudomonas savastanoi pv. savastanoi
           NCPPB 3335]
 gi|298158698|gb|EFH99762.1| NADH:flavin oxidoreductase [Pseudomonas savastanoi pv. savastanoi
           NCPPB 3335]
          Length = 365

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 52/135 (38%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  D IA + K A   PV V+   G  +              ++  ++  +GV+ I
Sbjct: 209 QRLRLTLDVIAEVKKVAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFGALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A                D  ++   ++  PD+ +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAW--------QPAFAQGDASLIKLARRYAPDVALIANGGLHDPEKAEQVLREGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|289679894|ref|ZP_06500784.1| tRNA-dihydrouridine synthase C [Pseudomonas syringae pv. syringae
           FF5]
          Length = 64

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 97  LMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           ++  P+++   ++ + +A+   IPVT K R+G ++   A+   +  +++   G   I +H
Sbjct: 1   MLKEPELLHSIVSQVRRAVPQHIPVTAKMRLGYENTDGAL---DCARALADGGAEQIVVH 57

Query: 155 ARKAI 159
           AR  +
Sbjct: 58  ARTKV 62


>gi|289625721|ref|ZP_06458675.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289646330|ref|ZP_06477673.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|330869659|gb|EGH04368.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           aesculi str. 0893_23]
          Length = 365

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 52/135 (38%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  D IA + K A   PV V+   G  +              ++  ++  +GV+ I
Sbjct: 209 QRLRLTLDVIAEVKKVAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFGALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A                D  ++   ++  PD+ +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAW--------QPAFAQGDASLIKLARRYAPDVALIANGGLHDPEKAEQVLREGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|119472415|ref|ZP_01614533.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Alteromonadales
           bacterium TW-7]
 gi|119444937|gb|EAW26235.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Alteromonadales
           bacterium TW-7]
          Length = 653

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 58/182 (31%), Gaps = 17/182 (9%)

Query: 61  KLVEAAKIVEDFGYNEIN--------LN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               +A + E  GY+ +         +N    P     E  FG  L     +  + + A+
Sbjct: 139 DFAHSAYMAEKAGYDGVEVMGSEGYLINEFMAPHTNKREDEFGGSLENRMRLALEIVKAV 198

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKS----IKKSGVNGIWIHARKAILKGLSPKD 167
              +S    +  R+ V D IP  +  + V      ++K+GV+    +      +   P  
Sbjct: 199 RAKVSDKFLIIFRLSVMDLIPDGSTPDEVVIQATELEKAGVDIF--NTGIGWHEARVPTI 256

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
              +P   +    +  K    + +     +     A  IL     D + + R    +   
Sbjct: 257 ASMVPPGAFKEASKRLKSVVSVPVIAVNRINTPDIANDILNAGEADLISMARPLLADPEF 316

Query: 226 LT 227
             
Sbjct: 317 FN 318


>gi|253688897|ref|YP_003018087.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251755475|gb|ACT13551.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 364

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 62/180 (34%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +AK  +  G++ I ++            P       ++G  L     +V +   A
Sbjct: 157 DSFVSSAKRADRLGFDLIEIHAAHGYLLHQFLSPLTNQRTDNYGGSLQNRIRLVVEIYRA 216

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         + V +    GV+          L +++ + G + I + +      GLSP 
Sbjct: 217 VRDVFPAHKAVGVRISATDGVEGGWDLEQSVQLSQALHELGCDFIHVSSG-----GLSPL 271

Query: 167 DN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 PN        IK+E     I + G + +  QA  I+     D + + RA   + 
Sbjct: 272 QQIHPAPNYQVPYAQRIKQEVGITTIAV-GLITEPEQAEAIVATGEADAIGLARAILFDP 330


>gi|189485746|ref|YP_001956687.1| dihydroorotate dehydrogenase catalytic subunit [uncultured Termite
           group 1 bacterium phylotype Rs-D17]
 gi|229485593|sp|B1GYY3|PYRD_UNCTG RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|170287705|dbj|BAG14226.1| dihydroorotate dehydrogenase catalytic subunit [uncultured Termite
           group 1 bacterium phylotype Rs-D17]
          Length = 306

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/164 (19%), Positives = 59/164 (35%), Gaps = 30/164 (18%)

Query: 49  PLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCP--SARVHEGSFGACLMLNPDIVG 105
           P+ + + G  + + VE  KI+    G + I LN+ CP    ++           +  ++ 
Sbjct: 96  PVIVSVAGVAVGEYVEIVKILSSQNGVSAIELNLSCPNLKKKIVCH--------DLPLMR 147

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
           D I  + K   +PV  K    V D      +  L  + + +G +G+            I 
Sbjct: 148 DVIRGVKKVSRVPVIAKLSPLVTD------ISELALTAQNAGADGVTLTNTYPAMAVDIR 201

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
             K  L           I  +    VY+  ++   + I   GG+
Sbjct: 202 TFKPKLSTVKGGMSGACIKPMSVRCVYDAYQDI-KIPIIGCGGI 244


>gi|322688600|ref|YP_004208334.1| oxidoreductase [Bifidobacterium longum subsp. infantis 157F]
 gi|320459936|dbj|BAJ70556.1| putative oxidoreductase [Bifidobacterium longum subsp. infantis
           157F]
          Length = 454

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 295 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 354

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 355 DVMDVSTGGIM----SGVSIPVKPNYQVPFAEQVKSKA-DIPVTAVGLITKPKQAAKILA 409

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 410 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 441


>gi|257455713|ref|ZP_05620942.1| 2,4-dienoyl-coa reductase [Enhydrobacter aerosaccus SK60]
 gi|257446996|gb|EEV22010.1| 2,4-dienoyl-coa reductase [Enhydrobacter aerosaccus SK60]
          Length = 701

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/191 (15%), Positives = 63/191 (32%), Gaps = 35/191 (18%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPDIVG 105
            + AK+ +  GY+ + +        +    +                 G  L        
Sbjct: 156 AKTAKLAQMAGYDGVEI--------MGSEGYLLNQFLSNHVNQRTDQWGGSLENRMRFAL 207

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + I A+ +A+     +  R+     V D      +  + K+I+K+GV    I+      +
Sbjct: 208 EVIKAVREAVGEAFIITFRLSMIDLVPDGNTMDEVITIAKAIEKAGVT--IINTGIGWHE 265

Query: 162 GLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   + D++ E+K+      I  N  +     A ++L     D V + R 
Sbjct: 266 ARVPTIVTSVPRAAFADVIAEVKRHVTIPVIAANR-VNMPETAEQLLADNQADLVQMARP 324

Query: 219 AYKNSAMLTTV 229
              +   +   
Sbjct: 325 FLADPDWVAKA 335


>gi|157837422|gb|ABV82775.1| unknown [Chromohalobacter sp. HS2]
          Length = 366

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 59/178 (33%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +AK  E  G+  I L+            P +   +  +G  L     IV +   A+ 
Sbjct: 162 FVASAKRAERLGFELIELHAAHGYLLHEFLSPLSNQRDDEYGGSLENRMRIVLEIFDAVR 221

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                  PV ++      V+          L +++   G + I          GL P+  
Sbjct: 222 AVFPDDKPVGIRISGSDWVEGGWDLEQSVELARALDARGCSFIDCSGG-----GLDPRQT 276

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
             + PN        +K+E   + +   G + +  QA  I+     D V + R    + 
Sbjct: 277 LNVGPNYQVPFARRMKQEV-AMPVIAVGLITEPEQAEGIVFGGEADAVALARGMLFDP 333


>gi|326772223|ref|ZP_08231508.1| oxidoreductase, FAD/FMN-binding [Actinomyces viscosus C505]
 gi|326638356|gb|EGE39257.1| oxidoreductase, FAD/FMN-binding [Actinomyces viscosus C505]
          Length = 368

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/155 (14%), Positives = 57/155 (36%), Gaps = 13/155 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
             + A+ +A+     +  R+   D     +         + + ++GV+ + I +      
Sbjct: 218 QVVRAVREAIGPETVLDIRLSASDWAEGGVTGEETAAFSRELVEAGVDVLHISSG----- 272

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           G  P +    P     +  ++++     D+ +   G +E+ +QA + L     D + +GR
Sbjct: 273 GNVPAEVPVGPGYQLTLAQQVRRAVAGSDVPVVGVGLIEEAAQAEQALISGQADAIAVGR 332

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           AA ++  +               +P   +  +  W
Sbjct: 333 AALRDPYLPLRWAADLGVRSWEEAPWPIQYWRGTW 367


>gi|258543222|ref|YP_003188655.1| dihydropyrimidine dehydrogenase [Acetobacter pasteurianus IFO
           3283-01]
 gi|256634300|dbj|BAI00276.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-01]
 gi|256637360|dbj|BAI03329.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-03]
 gi|256640412|dbj|BAI06374.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-07]
 gi|256643469|dbj|BAI09424.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-22]
 gi|256646524|dbj|BAI12472.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-26]
 gi|256649577|dbj|BAI15518.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-32]
 gi|256652563|dbj|BAI18497.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO
           3283-01-42C]
 gi|256655621|dbj|BAI21548.1| dihydroorotate dehydrogenase [Acetobacter pasteurianus IFO 3283-12]
          Length = 422

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/160 (20%), Positives = 57/160 (35%), Gaps = 26/160 (16%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           IVE+ G + I LN GCP     E + GA +   P+ V        +   +PV VK    +
Sbjct: 122 IVEETGADGIELNFGCPHGMS-ERNMGAAVGQVPEYVEMVTRWCKQNTRMPVIVKLTPNI 180

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWI--------------HARKAILKGLSPKDNR---K 170
            + +          + K+ G +G+ +               A   I+ G           
Sbjct: 181 TNILMP------AHAAKRGGADGVSLINTIQSVIGVDLDAMAPMPIVGGKGTHGGYCGPA 234

Query: 171 IPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP 208
           +  +   ++ EI +  E   + I   GG+     A + L 
Sbjct: 235 VKPIALRMIGEIARDPEMAGMPISGIGGIGTWRDAAEFLA 274


>gi|119383472|ref|YP_914528.1| NADH:flavin oxidoreductase/NADH oxidase [Paracoccus denitrificans
           PD1222]
 gi|119373239|gb|ABL68832.1| NADH:flavin oxidoreductase/NADH oxidase [Paracoccus denitrificans
           PD1222]
          Length = 367

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA+     G + I ++            P +   E  +G  L        +   A+ 
Sbjct: 162 FAEAARRAVRLGIDAIQIHAAHGYLLHQFLSPLSNRREDEYGGSLENRMRFPLEVFEAVR 221

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+    PVTV+      V+            ++++  G   I + +      GL  +  
Sbjct: 222 DAVPQGYPVTVRISGTDWVEGGWDIAGSIAFSQALEARGCAAIHVSSG-----GLDRRQQ 276

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
             +       +    K+   + +   G + +  QA  I+ + D  MI   R    + 
Sbjct: 277 IPVGPNYQVPLARAVKQAVGIPVIAVGLITEPEQAEAIVATGDADMIALARTVLYDP 333


>gi|262393687|ref|YP_003285541.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio sp. Ex25]
 gi|262337281|gb|ACY51076.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio sp. Ex25]
          Length = 670

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 199 EIVKAVRKAVGDKFIIIFRLSMLDLVEQGSTFEDVIELAKALEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARVPTIATQVPRGAFTWVTEKVKPHVSVPIITCNRINTPDEAERILSSGHADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|46191121|ref|ZP_00120567.2| COG1902: NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Bifidobacterium longum DJO10A]
 gi|189439840|ref|YP_001954921.1| NADH/flavin oxidoreductase [Bifidobacterium longum DJO10A]
 gi|312133243|ref|YP_004000582.1| nema [Bifidobacterium longum subsp. longum BBMN68]
 gi|317482591|ref|ZP_07941606.1| NADH:flavin oxidoreductase/NADH oxidase [Bifidobacterium sp.
           12_1_47BFAA]
 gi|189428275|gb|ACD98423.1| NADH/flavin oxidoreductase [Bifidobacterium longum DJO10A]
 gi|311772446|gb|ADQ01934.1| NemA [Bifidobacterium longum subsp. longum BBMN68]
 gi|316916013|gb|EFV37420.1| NADH:flavin oxidoreductase/NADH oxidase [Bifidobacterium sp.
           12_1_47BFAA]
          Length = 457

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 298 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 357

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 358 DVMDVSTGGIM----SGVSIPVKPNYQVPFSEQVKAKA-DIPVTAVGLITKPKQAAKILA 412

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 413 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 444


>gi|87121946|ref|ZP_01077831.1| oxidoreductase, FAD/FMN-binding [Marinomonas sp. MED121]
 gi|86162744|gb|EAQ64024.1| oxidoreductase, FAD/FMN-binding [Marinomonas sp. MED121]
          Length = 402

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 77/205 (37%), Gaps = 20/205 (9%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
            +   +AA I ++ G+  + ++ G          P   + +  +G  +     I+   I 
Sbjct: 145 PASYAKAASIAKEVGFTGVQIHAGHGFLLSQFLSPLFNLRDDKYGGSIENRCRIILAIID 204

Query: 110 AMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+  A+    P+ +K      ++  +        ++ + K+ V+ I I A        S 
Sbjct: 205 AVRLAIGPHFPIGIKINASDLLEGGLTEDDALAHIRLLDKTSVDLIEISAGTYFPGAKSS 264

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            DN     + Y    +  K    + + + GG++ +S A  +L   S D V + RA   N 
Sbjct: 265 SDNLSKG-VYYKSFAKRAKNLTSIPLMVTGGVKSLSDACSLLQDKSADLVGLARAMVLNP 323

Query: 224 AM----LTTVDEYFSNPLTGSSPIK 244
            +        ++  S P   S P +
Sbjct: 324 DLANDWFAGTNQTLSFPRFDSPPAE 348


>gi|332978609|gb|EGK15313.1| old Yellow enzyme family NADH:flavin oxidoreductase [Psychrobacter
           sp. 1501(2011)]
          Length = 654

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/181 (14%), Positives = 58/181 (32%), Gaps = 19/181 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG------C-PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            K+   A   +  G + ++++        C P        FG  L          + AM 
Sbjct: 144 DKMCACALRAQQAGVDVVSIHGDRLVGALCSPIMNTRSDEFGGSLENRTRFALRLVQAMR 203

Query: 113 KAL-------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +        +PV    R      I    +    + ++++GV+ + +            
Sbjct: 204 ATVPEMVIEYKLPVITPERGKGGVSIDEAPI--FAQWLEQAGVDMLHVAQANHTGNMADT 261

Query: 166 KDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                + P   +  +    K+   + +  +G + D + +  +L     D + IGRA   +
Sbjct: 262 IPPMGVQPYCFFADITASVKQVVSIPVSTSGRIIDPAMSEVLLNEGKADMIGIGRALLAD 321

Query: 223 S 223
            
Sbjct: 322 P 322


>gi|307719735|ref|YP_003875267.1| dihydroorotate dehydrogenase [Spirochaeta thermophila DSM 6192]
 gi|306533460|gb|ADN02994.1| dihydroorotate dehydrogenase [Spirochaeta thermophila DSM 6192]
          Length = 303

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/202 (16%), Positives = 67/202 (33%), Gaps = 21/202 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I G+D  +  E    +E         +N+ CP   V +G        +P  V   
Sbjct: 94  PVIGNIAGSDPEEYAEVVSFLEAHTDLWGYEINISCP--NVKKGGITIG--TDPTTVERL 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPA--------VALRNLVKSIKKSGVNGIWIHARKAI 159
              +    + P+ VK    V D                + + ++    ++      R  I
Sbjct: 150 TRTLRDLTTKPLIVKLTPNVTDIAEIARAAEAGGADALSCINTVVGMAID--IRKKRPVI 207

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRA 218
            +  +      I  +    VY ++       IG+ G +E    A++ +L     V +G A
Sbjct: 208 PQKTAGLSGPAIKPIGVAAVYRVRTAVRIPIIGIGGIME-PEDAIEYLLAGATAVQVGTA 266

Query: 219 AYKNS----AMLTTVDEYFSNP 236
            + +      +L  +  Y +  
Sbjct: 267 LFVDPRTPSRILKGITSYMAQE 288


>gi|296208611|ref|XP_002751145.1| PREDICTED: dihydropyrimidine dehydrogenase [NADP+] [Callithrix
           jacchus]
          Length = 974

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 45/126 (35%), Gaps = 24/126 (19%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +P++V +    + +A+ IP   K    V D      + ++ ++ K+ G +G+      + 
Sbjct: 636 DPELVRNICRWVRQAVRIPFFAKLTPNVTD------IVSIARAAKEGGADGVTATNTVSG 689

Query: 160 LKGL------------------SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           L GL                         I  +    V  I +  P   I   GG++   
Sbjct: 690 LMGLKSDGTPWPAVGIAKRTTYGGVSGTAIRPIALRAVTSIARALPGFPILATGGIDSAE 749

Query: 202 QALKIL 207
            AL+ L
Sbjct: 750 SALQFL 755


>gi|291517302|emb|CBK70918.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Bifidobacterium longum subsp. longum F8]
          Length = 454

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 295 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 354

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 355 DVMDVSTGGIM----SGVSIPVKPNYQVPFSEQVKAKA-DIPVTAVGLITKPKQAAKILA 409

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 410 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 441


>gi|269104389|ref|ZP_06157085.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Photobacterium damselae subsp. damselae CIP
           102761]
 gi|268161029|gb|EEZ39526.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Photobacterium damselae subsp. damselae CIP
           102761]
          Length = 673

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/221 (16%), Positives = 73/221 (33%), Gaps = 43/221 (19%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-------------- 91
           + + LA Q     I+K  E+A I +  GY+ + ++       VHEG              
Sbjct: 143 EHRELATQEVKHFIAKFAESAAIAQKAGYDGVEIHA------VHEGYLLDQFSLSFFNQR 196

Query: 92  --SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV------------DDQIPAVALR 137
              +G           + + A+         V  R  V             ++      R
Sbjct: 197 TDEYGGSFENRYRFAVEIVKAIKSVCGERFPVSLRYSVKSNMKGYGQGILPEEDAVEVGR 256

Query: 138 NL------VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
           +L       K ++ +G + + + A        +   N   P +       +  E  D+ +
Sbjct: 257 DLEEGLRAAKYLQDAGYDALNVDAGTYDSWYWNHPANYFKPGMYQPYCKAV-SEVVDIPV 315

Query: 192 GLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVD 230
            + G +ED   A K +     DG+ +GR    +  ++  + 
Sbjct: 316 LMAGRMEDPDLAAKAVQEGVADGISMGRPLLADPDVVNKIR 356


>gi|78187450|ref|YP_375493.1| dihydroorotate dehydrogenase 1 [Chlorobium luteolum DSM 273]
 gi|78167352|gb|ABB24450.1| dihydroorotate oxidase B, catalytic subunit [Chlorobium luteolum
           DSM 273]
          Length = 331

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/199 (14%), Positives = 67/199 (33%), Gaps = 25/199 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  I +  E    ++   G +   +N+ CP    +       + ++PD   + +
Sbjct: 123 IVVNIAGRSIDEYAEVVSRLDAVPGLDGYEINLSCP----NVKGECMIMGVSPDATREIV 178

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARK 157
             +       + +K    V       ++  +  + +K+G +            I    R+
Sbjct: 179 TELRSITGRHLMIKLTPNV------TSISAIAIAAEKAGADSVSLINTLVGMAIDWKKRR 232

Query: 158 AILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMI 215
            +LK ++       I  +    V+E+      + I   GG+     A++ L      V I
Sbjct: 233 PLLKNVTGGLSGPAIKPVALAKVWEVNNAV-SIPIVGMGGIASFDDAMEFLVAGAGAVQI 291

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           G   +    +   +     
Sbjct: 292 GTMNFVQPDIGEKIATAME 310


>gi|322690586|ref|YP_004220156.1| oxidoreductase [Bifidobacterium longum subsp. longum JCM 1217]
 gi|320455442|dbj|BAJ66064.1| putative oxidoreductase [Bifidobacterium longum subsp. longum JCM
           1217]
          Length = 457

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 298 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 357

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 358 DVMDVSTGGIM----SGVSIPVKPNYQVPFSEQVKAKA-DIPVTAVGLITKPKQAAKILA 412

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 413 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 444


>gi|260548868|ref|ZP_05823090.1| xenobiotic reductase A [Acinetobacter sp. RUH2624]
 gi|260408036|gb|EEX01507.1| xenobiotic reductase A [Acinetobacter sp. RUH2624]
          Length = 369

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 56/149 (37%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--PVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPAGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVSIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D   A +IL     D + + RA   + 
Sbjct: 306 ITDPQHAEQILENQQADAIGLARAMLYDP 334


>gi|91779381|ref|YP_554589.1| NADH-flavin oxidoreductase/NADH oxidase family protein
           [Burkholderia xenovorans LB400]
 gi|91692041|gb|ABE35239.1| NADH-flavin oxidoreductase / NADH oxidase familyprotein
           [Burkholderia xenovorans LB400]
          Length = 365

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/183 (17%), Positives = 65/183 (35%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AAK   D G+  + L+       + +            ++G  L      + + +
Sbjct: 158 EDFVAAAKRARDAGFEWLELHFA--HGYLGQSFFSTHSNQRDDAYGGSLENRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           AA+ K     +P+T +         D+   V    L K+ K+ G++ + +    ++    
Sbjct: 216 AAVRKVWPEHLPLTARFGVIEYDGRDEQTLVESIELAKNFKREGLDMLSV----SVGFST 271

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
                   P     I   +++E   + +    G++    A   +    +D VM+GRA   
Sbjct: 272 PTAAIPWAPAFLAPIAQRVRREAG-IPVSSAWGIDTPELADGAVKSEQLDLVMVGRAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|315274620|ref|ZP_07869479.1| probable tRNA-dihydrouridine synthase 1 [Listeria marthii FSL
          S4-120]
 gi|313615750|gb|EFR89019.1| probable tRNA-dihydrouridine synthase 1 [Listeria marthii FSL
          S4-120]
 gi|313625411|gb|EFR95182.1| probable tRNA-dihydrouridine synthase 1 [Listeria innocua FSL
          J1-023]
          Length = 68

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 3/52 (5%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPL 50
          M   ++  +R   +      L+  EMI    I   + K   +L    +EKPL
Sbjct: 18 MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEKPL 68


>gi|15921769|ref|NP_377438.1| dihydroorotate dehydrogenase [Sulfolobus tokodaii str. 7]
 gi|15622556|dbj|BAB66547.1| 261aa long hypothetical dihydroorotate dehydrogenase [Sulfolobus
           tokodaii str. 7]
          Length = 261

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 70/182 (38%), Gaps = 29/182 (15%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM 98
            +   +  E  L + +GG+ I +++E  K V D G   I LN+  P    +   +G  L 
Sbjct: 49  ELKKINEMECKLIVSVGGSSIDEIIEVIKKV-DRG-EIIELNLSSP----NRKGYGESLA 102

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIH 154
                V + +  +    + PV VK         P   +  +      +G +G+     + 
Sbjct: 103 SY---VYEVVKNVKGVTNKPVFVKL-------GPWDNIIEIAGRAISAGADGLSLINTVK 152

Query: 155 A--------RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                    +K +  G      + I  L   I++++ KE  ++ I   GG+     A+++
Sbjct: 153 GMVIDVETFKKVMHYGTGGISGKCIHPLAVRIIHDVYKEY-NVDIIGMGGVFSGIDAIEL 211

Query: 207 LP 208
           + 
Sbjct: 212 MS 213


>gi|317472578|ref|ZP_07931897.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
 gi|316899987|gb|EFV21982.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
          Length = 655

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/194 (19%), Positives = 72/194 (37%), Gaps = 20/194 (10%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EAA++ ++ G++ + ++            P     +  FG  L          + A+ KA
Sbjct: 164 EAARLCKETGFDMVQVHAAHGWLFSQFLSPVMNQRKDEFGGSLENRARFFLMAVDAVRKA 223

Query: 115 LSIPVTVKCRIGVDD-QIPAVALRNLVKSIK--KSGVNGIWI----HARKAILKGLSPKD 167
           +     ++ RI  DD     + L + VK  +     V+ I +    H    +     P  
Sbjct: 224 VGPHFPIEARISGDDFTDNGLGLEDCVKVAQMIDDKVDLINVSCGNHEDPDMFCRTHPSA 283

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                 ++  +  +IKK   +  +   G L D +Q   I+     D V +GRA+  +  +
Sbjct: 284 FYPRG-VNVYLAAQIKKHV-NTPVACVGSLNDPAQMEDIIAAGQADAVELGRASLADPYL 341

Query: 226 LTTVDEYFSNPLTG 239
                E  +  +T 
Sbjct: 342 PKKAYEGRAEDITP 355


>gi|304395927|ref|ZP_07377809.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. aB]
 gi|304356296|gb|EFM20661.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. aB]
          Length = 366

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/178 (15%), Positives = 57/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VE+A+     G   I ++            P +      +G  L        +   A+ 
Sbjct: 159 FVESARRAVRLGIQLIEVHAAHGYLLHQFLSPLSNQRSDEYGGSLENRLRFPLEVFKAVR 218

Query: 113 KALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +A+   +PV V+      V+            + ++      I + +      GLS K  
Sbjct: 219 EAVPAAVPVGVRISATDWVEGGWEIEQSIAFSRELEALNCAYIHVSSG-----GLSEKQK 273

Query: 169 RKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
             +   +Y +      +E   + +   G + +  QA  +L     D V + R    + 
Sbjct: 274 ISVGP-NYQVPFARDIREQVSIPVIAVGLITEPQQAEDLLQQGEADLVALARGILYDP 330


>gi|258404157|ref|YP_003196899.1| dihydroorotate dehydrogenase family protein [Desulfohalobium
           retbaense DSM 5692]
 gi|257796384|gb|ACV67321.1| dihydroorotate dehydrogenase family protein [Desulfohalobium
           retbaense DSM 5692]
          Length = 304

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/200 (18%), Positives = 71/200 (35%), Gaps = 27/200 (13%)

Query: 48  KPLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
            P+ + +    + +  E   ++    G   + +N+ CP   V EG        +P +   
Sbjct: 93  TPVIVNLYAQAVEEFAELTDRLATAKGVAGLEVNISCP--NVREGGVQFG--QDPVLAAR 148

Query: 107 CIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
              A+ K A ++PV VK    V D         + +++   G + I            IH
Sbjct: 149 VTEAVKKRAGALPVMVKLSPNVTDVTV------MARAVADGGADCISCINTLTGMAVDIH 202

Query: 155 ARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
           +R+  L  +        I  +   +V+++ +          GG+      L+ +L     
Sbjct: 203 SRRPCLANVVGGLSGPAIKPVALRMVHQVVRAVDVPV-VGLGGISSAEDVLEFLLVGAHA 261

Query: 213 VMIGRAAYKNSAM-LTTVDE 231
           V +G A +         VDE
Sbjct: 262 VQLGTANFVRPDTAFKLVDE 281


>gi|229817541|ref|ZP_04447823.1| hypothetical protein BIFANG_02804 [Bifidobacterium angulatum DSM
           20098]
 gi|229785330|gb|EEP21444.1| hypothetical protein BIFANG_02804 [Bifidobacterium angulatum DSM
           20098]
          Length = 319

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 64/187 (34%), Gaps = 23/187 (12%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       E    + D   + + +NV CP   V  G        +P  +   + 
Sbjct: 112 VIANVAGHCDEDYCEVVAKLADCDADMLEINVSCP--NVTHGGMSVG--TDPVALSKLMD 167

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----HARKAILKGLS 164
            +      P+ VK    V        + +  ++  + G + + +       R  I  G  
Sbjct: 168 KLRPMTDKPMIVKLTPNV------TNITDPARAAVEHGADALSMINTLLGMRLNIKTGEP 221

Query: 165 PKDNRKIP-------NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
              NR           +    VY ++   P++ I   GG++   +AL+ L    + V +G
Sbjct: 222 IIANRTGGVSGPAVLPVGIAAVYRVRTALPEVPIIGIGGIDTGEKALEYLYAGANAVEVG 281

Query: 217 RAAYKNS 223
            AA  + 
Sbjct: 282 AAALFDP 288


>gi|331011002|gb|EGH91058.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 370

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/140 (20%), Positives = 54/140 (38%), Gaps = 16/140 (11%)

Query: 94  GACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKS 146
           G  +     +  D IA + K A   PV V+   G  +              ++  ++  +
Sbjct: 204 GGDVQQRLRLTLDVIAEVKKMAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFGALADA 263

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ I +   +A                D  +V   ++  PD+ +  NGGL D  +A ++
Sbjct: 264 GVDYIHVTEHEAW--------QPAFAQGDASLVKLARRYAPDVALIANGGLHDPEKADQV 315

Query: 207 L-PSVDGVMIGRAAYKNSAM 225
           L    D + +G+ A  N  +
Sbjct: 316 LHQGADIIAVGKGALANPDL 335


>gi|307564674|ref|ZP_07627204.1| dihydroorotate dehydrogenase 1B [Prevotella amnii CRIS 21A-A]
 gi|307346602|gb|EFN91909.1| dihydroorotate dehydrogenase 1B [Prevotella amnii CRIS 21A-A]
          Length = 302

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 67/198 (33%), Gaps = 29/198 (14%)

Query: 56  GADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G+      EA+K + +    + I LN+ CP   V EG     +  +           C  
Sbjct: 102 GSSPETYAEASKKINELKQISAIELNISCP--NVKEGGMAFGVTCSGAAAVVKAVRAC-- 157

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHARKAILKGL 163
               + VK    V D      + ++  + +  G +            I I  R   L   
Sbjct: 158 YDKTLIVKLSPNVTD------IASIALACEDEGADGLSLINTLMGMAIDIERRCPKLSIR 211

Query: 164 SPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYK 221
           +       I  +   +VY++ K    + I   GG+     A++  +     + IG A + 
Sbjct: 212 TGGLSGPAIKPVALRMVYDVAKAV-KIPIIGLGGISTAEDAIEFFMAGATAIQIGTANFV 270

Query: 222 NSA----MLTTVDEYFSN 235
           +      +   ++E+  N
Sbjct: 271 DPMVSIKVCKGINEWLDN 288


>gi|302391251|ref|YP_003827071.1| dihydroorotate dehydrogenase family protein [Acetohalobium
           arabaticum DSM 5501]
 gi|302203328|gb|ADL12006.1| dihydroorotate dehydrogenase family protein [Acetohalobium
           arabaticum DSM 5501]
          Length = 409

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/183 (18%), Positives = 63/183 (34%), Gaps = 19/183 (10%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
               +  L   I G  +    + A+ +E  G + + LN GCP  R  +   G  L  +P+
Sbjct: 101 CHEHDVRLIGSISGTTMESWQDLAQRIEATGIDMLELNFGCPHPRDLDYKSGQVLGSSPE 160

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI---------WI 153
              +   A+ + + IPV +K      + +  V +   V     +GV  I           
Sbjct: 161 AAAEVTEAVVEVVDIPVFIKVTP---EAVSPVEVTKRVTEAGAAGVTAINRYPALDIDIE 217

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
             R  +    +      +  +    + +I KE        NG +      +K       +
Sbjct: 218 DGRPLLHSTYAGVGGPWMRPITLKWLSKISKEVGAPISATNG-ISTWKDIVKC------I 270

Query: 214 MIG 216
           M+G
Sbjct: 271 MVG 273


>gi|167749023|ref|ZP_02421150.1| hypothetical protein ANACAC_03804 [Anaerostipes caccae DSM 14662]
 gi|167651645|gb|EDR95774.1| hypothetical protein ANACAC_03804 [Anaerostipes caccae DSM 14662]
          Length = 655

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/194 (19%), Positives = 72/194 (37%), Gaps = 20/194 (10%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EAA++ ++ G++ + ++            P     +  FG  L          + A+ KA
Sbjct: 164 EAARLCKETGFDMVQVHAAHGWLFSQFLSPVMNQRKDEFGGSLENRARFFLMAVDAVRKA 223

Query: 115 LSIPVTVKCRIGVDD-QIPAVALRNLVKSIK--KSGVNGIWI----HARKAILKGLSPKD 167
           +     ++ RI  DD     + L + VK  +     V+ I +    H    +     P  
Sbjct: 224 VGPHFPIEARISGDDFTDNGLGLEDCVKVAQMIDDKVDLINVSCGNHEDPDMFCRTHPSA 283

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                 ++  +  +IKK   +  +   G L D +Q   I+     D V +GRA+  +  +
Sbjct: 284 FYPRG-VNVYLAAQIKKHV-NTPVACVGSLNDPAQMEDIIAAGQADAVELGRASLADPYL 341

Query: 226 LTTVDEYFSNPLTG 239
                E  +  +T 
Sbjct: 342 PKKAYEGRAEDITP 355


>gi|126700799|ref|YP_001089696.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile 630]
 gi|254976768|ref|ZP_05273240.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-66c26]
 gi|255094153|ref|ZP_05323631.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile CIP 107932]
 gi|255102322|ref|ZP_05331299.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-63q42]
 gi|255308215|ref|ZP_05352386.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile ATCC 43255]
 gi|255315904|ref|ZP_05357487.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-76w55]
 gi|255518564|ref|ZP_05386240.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-97b34]
 gi|255651684|ref|ZP_05398586.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-37x79]
 gi|260684718|ref|YP_003216003.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile CD196]
 gi|260688376|ref|YP_003219510.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile R20291]
 gi|306521483|ref|ZP_07407830.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-32g58]
 gi|115252236|emb|CAJ70076.1| Dihydroorotate dehydrogenase, catalytic subunit [Clostridium
           difficile]
 gi|260210881|emb|CBA66039.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile CD196]
 gi|260214393|emb|CBE06800.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile R20291]
          Length = 369

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 78/235 (33%), Gaps = 38/235 (16%)

Query: 17  TNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE 76
           TN+  L TE+       +  ++          P+ + + G    ++ E A +V+ +  + 
Sbjct: 62  TNSGFLNTELWSELPKEQWIEEEYKKVKETGLPVIVSM-GYSAEQIAEVAPLVKPY-ADA 119

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           + L+                +  +   + + + A    L +PV +K     D Q      
Sbjct: 120 VELSTH-------------YVGTDVAPIVNALKAAKAVLDVPVFMKMSPHTDIQT----- 161

Query: 137 RNLVKSIKKSGVN------------GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
             + K+++++G +             I ++    I+   +         +    +  I +
Sbjct: 162 --IAKAVEEAGADGLVMINSFGPCMAIDVNTGYPIMGSKAGYGWLSGAPIRPLAIRCIYE 219

Query: 185 E--NPDLFIGLNGGLEDM-SQALKILPSVDGVMIG-RAAYKNSAMLTTVDEYFSN 235
                ++ I   GG+      A  ++     V +   A  K  ++   + +  + 
Sbjct: 220 ASQVVNIPIIGVGGITCGKDVAEMMMAGASAVQVCTEAILKGPSIYGKIAKELNE 274


>gi|237755631|ref|ZP_04584244.1| dihydroorotate dehydrogenase, catalytic subunit
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692195|gb|EEP61190.1| dihydroorotate dehydrogenase, catalytic subunit
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 209

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/118 (16%), Positives = 48/118 (40%), Gaps = 11/118 (9%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGA 95
            + +      +  +   + G D  + +  A+ ++   G + + LNV CP   V +G    
Sbjct: 83  NETLPKLKEYDTKIFANVFGEDEDEYLAVAERLDKADGVHGLELNVSCP--NVKKGGIAF 140

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
               +P+++ + +  M K    P+ VK    V +      + +   +   +G +G+ +
Sbjct: 141 G--TDPEVLYNLVYKMKKITKKPLLVKLSPNVSN------ILDTADACVSAGADGLVL 190


>gi|115629997|ref|XP_001202224.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
 gi|115642346|ref|XP_001193327.1| PREDICTED: hypothetical protein, partial [Strongylocentrotus
           purpuratus]
          Length = 41

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 9/40 (22%), Positives = 13/40 (32%), Gaps = 2/40 (5%)

Query: 194 NGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           NG +         +      G MI R A     + T + E
Sbjct: 1   NGDILSFEDSNFFREQSGATGQMIARGALIKPWIFTEIKE 40


>gi|171677272|ref|XP_001903587.1| hypothetical protein [Podospora anserina S mat+]
 gi|170936704|emb|CAP61362.1| unnamed protein product [Podospora anserina S mat+]
          Length = 416

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/204 (14%), Positives = 64/204 (31%), Gaps = 26/204 (12%)

Query: 63  VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A K     G + + + N           P A      +G        +  +      +
Sbjct: 194 VAAVKRAMAAGADFVEIHNAHGYLLSSFLSPHANRRTDGYGGSFENRIRLSLEIAKLTRE 253

Query: 114 AL--SIPVTVKC-------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+  + PV ++            ++   A       +++   G   +          G+ 
Sbjct: 254 AVGENTPVLLRVSATDWVEETLPEESWTAEDTVKFAQALAAQGCVDLI----DISSGGVH 309

Query: 165 PKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
           P                 +KK   D + +   G + +  QA K+L    +D  ++GR   
Sbjct: 310 PAQKIVSGPAFQAPFAVAVKKAVGDKMLVATVGSITNGRQANKLLEEDGLDVALVGRGFQ 369

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIK 244
           K+  +  T  ++    +  +S I+
Sbjct: 370 KDPGLTWTFAQHVDTEIAMASQIR 393


>gi|213029592|ref|ZP_03344039.1| dihydropyrimidine dehydrogenase [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 191

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 57/151 (37%), Gaps = 27/151 (17%)

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I  N  CP   +   + G+ +  +P++V     A+ +  S+P+  K    + D      
Sbjct: 1   MIECNFSCPQ--MTSHAMGSDVGQSPELVEKYCRAVKRGSSLPMLAKMTPNIGD------ 52

Query: 136 LRNLVKSIKKSGVNGI-WIHARKAIL----------------KGLSPKDNRKIPNLDYDI 178
           +  +  + K+ G +GI  I+  K+I                   +S    + +  +    
Sbjct: 53  MCEVALAAKRGGADGIATINTVKSITNIDLNRKIGMPVVNGKSSISGYSGKAVKPIALRF 112

Query: 179 VYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           + +++   E  D  I   GG+E    A + L
Sbjct: 113 IQQLRMHPELRDFPISGIGGIETWEDAAEFL 143


>gi|297627229|ref|YP_003688992.1| NADH-dependent flavin oxidoreductase [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922994|emb|CBL57576.1| NADH-dependent flavin oxidoreductase [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 370

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/176 (21%), Positives = 60/176 (34%), Gaps = 25/176 (14%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVK------CRIGVDDQIPAVALRNLVKSIK 144
           +G  L     ++ + + A+        P+ ++         G+D +  A  +  LV    
Sbjct: 208 YGGDLPGRSRLMREIVDAVRSVWPATKPLGLRLSATDWTERGLDLETAAAVMHELV---A 264

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQ 202
             G+N I + +      GL+       P     +   IK    D    +   G + D +Q
Sbjct: 265 DHGLNWIDVSSG-----GLNGGPIPMGPGYQVSLATAIKDALVDTDAVVSSVGMITDATQ 319

Query: 203 ALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           A  IL     D V IGRAA +N             PL  +      V   FWR   
Sbjct: 320 AETILATDQADAVSIGRAALRNPHWAAQAAVELGVPLEDNP-----VADQFWRAYL 370


>gi|91223669|ref|ZP_01258934.1| 2,4-dienoyl-CoA reductase [Vibrio alginolyticus 12G01]
 gi|269965993|ref|ZP_06180085.1| 2,4-dienoyl-CoA reductase [Vibrio alginolyticus 40B]
 gi|91191755|gb|EAS78019.1| 2,4-dienoyl-CoA reductase [Vibrio alginolyticus 12G01]
 gi|269829389|gb|EEZ83631.1| 2,4-dienoyl-CoA reductase [Vibrio alginolyticus 40B]
          Length = 670

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 199 EIVKAVRKAVGDKFIIIFRLSMLDLVEQGSTFEDVIELAKALEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIITCNRINTPDEAERILSSGHADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|257068439|ref|YP_003154694.1| NADH:flavin oxidoreductase [Brachybacterium faecium DSM 4810]
 gi|256559257|gb|ACU85104.1| NADH:flavin oxidoreductase [Brachybacterium faecium DSM 4810]
          Length = 368

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 27/175 (15%), Positives = 60/175 (34%), Gaps = 21/175 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V+AA+  E  G++ + L+            P        +G        +  +  AA+
Sbjct: 170 DFVDAARRAEAAGFDAVELHFAHGYLVHEFLSPLVNTRTDGYGGDGPGRRRLAIEIAAAV 229

Query: 112 CKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +      P+ V+      +D          L + ++  GV+ + +    A++  ++   
Sbjct: 230 REQWPAERPLLVRLSATDWIDGGWDIEQSVELARELEAVGVDALHVSTGGAVIADIAVGP 289

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
             ++            ++   + +   G + D   A  +L     D V +GRAA 
Sbjct: 290 EYQVGFA------RTLRDAVAMPVAAVGLITDPHGAQAVLDRGDADFVAVGRAAL 338


>gi|332967690|gb|EGK06799.1| oxidoreductase [Desmospora sp. 8437]
          Length = 203

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/140 (17%), Positives = 49/140 (35%), Gaps = 9/140 (6%)

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
           V   ++G        ++ +   A+ +A+    T+  RI                  + + 
Sbjct: 35  VQMNTYGGSTENRVRLLVEVSKAIREAVGKDFTIGIRISQAKVNDYT--HKWAGKEQDAE 92

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNL---DYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           +  I+    +A L  +   +              +  + K+  ++ +  NG LED   A 
Sbjct: 93  I--IFSQLGQAGLDYIHVTEYEAWKPAFDTSEASLASLAKKYGNIPVIANGHLEDPESAR 150

Query: 205 KILP--SVDGVMIGRAAYKN 222
           KI+     D V +G+ A  N
Sbjct: 151 KIIENGEADVVTLGKGALAN 170


>gi|91784348|ref|YP_559554.1| 2,4-dienoyl-CoA reductase [Burkholderia xenovorans LB400]
 gi|91688302|gb|ABE31502.1| 2,4-dienoyl-CoA reductase [Burkholderia xenovorans LB400]
          Length = 681

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/218 (12%), Positives = 68/218 (31%), Gaps = 26/218 (11%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGG--ADISKLVEAAKIVEDFGYNEINL- 79
           Y   +V+ + L+             KP AL I G    +      A++ +  GY+ + + 
Sbjct: 110 YQPFVVSASALKSPISKF-------KPRALSIAGIAKTVRDYARCARLAQRAGYDGVEIM 162

Query: 80  --------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-- 129
                      CP       ++G  +     +  + +  +         V  RI + D  
Sbjct: 163 GSEGYLLNQFLCPRTNRRTDAYGGSIENRMRLAREIVERVRAECGERFIVMYRISLIDLV 222

Query: 130 --QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
                      + ++++ +GV     +      +   P     +P   +  +    +   
Sbjct: 223 EGGNTWDETVQVARALEAAGVTMF--NTGIGWHEARVPTIVTSVPRAAFAALSARLRAAV 280

Query: 188 DLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNS 223
            + + ++  +     A ++L    G  V + R    + 
Sbjct: 281 KVPVIVSNRINTPDVAEELLAQGAGDLVSMARPLLADP 318


>gi|330835529|ref|YP_004410257.1| NADH:flavin oxidoreductase/NADH oxidase [Metallosphaera cuprina
           Ar-4]
 gi|329567668|gb|AEB95773.1| NADH:flavin oxidoreductase/NADH oxidase [Metallosphaera cuprina
           Ar-4]
          Length = 543

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/175 (16%), Positives = 60/175 (34%), Gaps = 16/175 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI-------VGDCIAAMCK 113
             V+A +  E  G++ I ++       +             D        + D +  +  
Sbjct: 143 DFVKAGERAERAGFDGIEIHGA--HGYLVAQFLSPATNRREDRYKDGVLFLEDLLKEIRS 200

Query: 114 ALSIPVT--VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +SIPV   V      D  +    +  ++  ++           R   L    P    K 
Sbjct: 201 RVSIPVGLRVSVTEFDDTGLNPELVSKIISRVESQLDYVHLSAGRDGPLGASMPIYWSKP 260

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS-AM 225
             L+Y     +++  P + + L G +  + +A ++L   D V++GR    +   +
Sbjct: 261 AFLEYA--RHVRR--PKVPMMLAGSVTTLDEAEQVLELADAVVLGRQLLADPEWL 311


>gi|325067451|ref|ZP_08126124.1| putative NADH-dependent flavin oxidoreductase [Actinomyces oris
           K20]
          Length = 368

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/155 (15%), Positives = 57/155 (36%), Gaps = 13/155 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+   D     +         + + ++GV+ + I +      
Sbjct: 218 EVVRAVREAIGSQTVLDIRLSASDWAEGGVTGEETAAFSRELVEAGVDVLHISSG----- 272

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           G  P      P     +  ++K+     D+ +   G +E+ +QA + L     D + +GR
Sbjct: 273 GNVPTAVPVGPGYQLPLAEQVKRAVAGSDVPVVGVGLIEEAAQAEQALISGQADAIAVGR 332

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
           AA ++  +               +P   +  +  W
Sbjct: 333 AALRDPYLPLRWAADLGVRSWEEAPWPIQYWRGTW 367


>gi|296452037|ref|ZP_06893750.1| possible dihydroorotate oxidase [Clostridium difficile NAP08]
 gi|296879567|ref|ZP_06903548.1| possible dihydroorotate oxidase [Clostridium difficile NAP07]
 gi|296259110|gb|EFH05992.1| possible dihydroorotate oxidase [Clostridium difficile NAP08]
 gi|296429449|gb|EFH15315.1| possible dihydroorotate oxidase [Clostridium difficile NAP07]
          Length = 369

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/203 (12%), Positives = 68/203 (33%), Gaps = 38/203 (18%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + + G    ++ E A +V+ +  + + L+                +  +   + + +
Sbjct: 94  PVIVSM-GYSAEQIAEVAPLVKPY-ADAVELSTH-------------YVGTDVAPIVNAL 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN------------GIWIHAR 156
            A    L +PV +K     D Q        + K+++++G +             I ++  
Sbjct: 139 KAAKAVLDVPVFMKMSPHTDIQT-------IAKAVEEAGADGLVMINSFGPCMAIDVNTG 191

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDM-SQALKILPSVDGV 213
             I+   +         +    +  I +     ++ I   GG+      A  ++     V
Sbjct: 192 YPIMGSKAGYGWLSGAPIRPLAIRCIYEASQVVNIPIIGVGGITCGKDVAEMMMAGASAV 251

Query: 214 MIG-RAAYKNSAMLTTVDEYFSN 235
            +   A  K  ++   + +  + 
Sbjct: 252 QVCTEAILKGPSIYGKIAKELNE 274


>gi|54297359|ref|YP_123728.1| hypothetical protein lpp1404 [Legionella pneumophila str. Paris]
 gi|53751144|emb|CAH12555.1| hypothetical protein lpp1404 [Legionella pneumophila str. Paris]
          Length = 870

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 47/270 (17%), Positives = 82/270 (30%), Gaps = 51/270 (18%)

Query: 54  IGGADISKLVEAAKIV----------EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
             G D +KL E  K+           E      I +N+ CP+A V     G  L   PD 
Sbjct: 509 FYGGDGNKLEEITKLAILMLKRMVPKEFHHKIRIGINMCCPAASVENIGSGFGLRNKPDF 568

Query: 104 VGDCIAAMCKA-LSIPVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +   + A+  A  ++ V  K  +        D          +  I+   +  I    + 
Sbjct: 569 IERIVKAIKDADSNLKVEFKTLMLSHEDGYGDGDQISGNTKNISEIQNERLTRIVYKTKA 628

Query: 158 AILKGLSPKDNRKIPNLD--YDIVYEIK--KEN-----PDLFIGLNGGLE---------- 198
             L       N +  N+D    I+ E+   KE        +    N  +           
Sbjct: 629 NRLVYQGKPRNIETYNVDTVSCIIREVNTPKEFQFGYSGMVATITNHDINQLGYKVVGEP 688

Query: 199 --DMSQALKILPSVDG-------VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
              +   L+ +    G       VM+GR    ++ +L     Y S+       +     +
Sbjct: 689 HYSVQSILEKIKKQLGEVPTEFEVMLGRVLLGSAWVLQG--RYASDAEILLHTLLQAAIE 746

Query: 250 DFWRKISASMTDYAAR--HLHSGGKLQQIT 277
             W   +  M  Y      +     ++ IT
Sbjct: 747 QEW---ARGMGRYGIDIYQIQVLYNIRHIT 773


>gi|317509175|ref|ZP_07966799.1| NADH:flavin oxidoreductase/NADH oxidase [Segniliparus rugosus ATCC
           BAA-974]
 gi|316252532|gb|EFV11978.1| NADH:flavin oxidoreductase/NADH oxidase [Segniliparus rugosus ATCC
           BAA-974]
          Length = 370

 Score = 51.0 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/210 (14%), Positives = 65/210 (30%), Gaps = 22/210 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V AA+  ++ G++ + ++            P +      +G        ++ D + A+ 
Sbjct: 164 FVAAARRADEAGFDVVEIHGAHGYLIHEFLSPLSNQRNDEYGGDFTGRTKLLLDTVDAVR 223

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                  P+ V+       +          L   + + G++ I + +      G    D 
Sbjct: 224 AVWPEGKPLFVRLSGTDWTEGGWDVEQTARLSAILAERGIDLIDVSSG-----GNVLADI 278

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              P+    +   +K     L +   G + +  QA  IL     D V I RAA +     
Sbjct: 279 PVGPSYQVPLATHVKTHAG-LPVAAVGLITEPEQAEAILANEEADAVFIARAALREPTWP 337

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
                         +P   +  +  W  + 
Sbjct: 338 LRAAATL-GVKWRDAPYPAQYTRGKWDDVI 366


>gi|189425084|ref|YP_001952261.1| dihydroorotate dehydrogenase [Geobacter lovleyi SZ]
 gi|189421343|gb|ACD95741.1| dihydroorotate dehydrogenase family protein [Geobacter lovleyi SZ]
          Length = 398

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/161 (20%), Positives = 59/161 (36%), Gaps = 27/161 (16%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM--CKALSIPVTVKC 123
           A   +D G + + LN  CP     E   GA +  NPD        +  CK ++IPV  K 
Sbjct: 120 ALGCQDAGADLLELNFSCPHGY-PERGRGAAIGQNPDYAAQITRWVTDCKEITIPVIPKL 178

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK------------- 170
              V        ++N+ + +  +G +G           G   +  R              
Sbjct: 179 TAAV------ANIQNIAEELALAGAHGFCAINTIPSFFGFDLRTLRPKPDIGGKTSYGGY 232

Query: 171 ----IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               I  +    V E+ + +P L +  +GG+ +   A++ +
Sbjct: 233 SGPGIKPIALRAVSELCQ-SPGLPVMASGGIANGFDAVEFM 272


>gi|289578157|ref|YP_003476784.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           italicus Ab9]
 gi|289527870|gb|ADD02222.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           italicus Ab9]
          Length = 667

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 34/183 (18%), Positives = 58/183 (31%), Gaps = 25/183 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            VEAA   E  G++ + L+                       +G           D +  
Sbjct: 182 FVEAAIRAEKSGFDAVELHFA--HGWFVNQFLSPDTNKRTDEYGGNFEGRTKFAIDILRG 239

Query: 111 MCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + KAL   +TV CRI     +D            K ++  G + + I      +   S  
Sbjct: 240 VKKALP-EMTVICRINGSDFIDGGFTIDESVRFAKLLEGYGADALDISGG---VSSTSEY 295

Query: 167 DNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               +   D  ++  +K  KEN  + +     L  +    KIL     D + I R    +
Sbjct: 296 HISPMGIEDRPLIGVVKRIKENVTIPVIAVDKLGSVYDWGKILEDGIADFIGIARGFIGD 355

Query: 223 SAM 225
             +
Sbjct: 356 PDL 358


>gi|291279608|ref|YP_003496443.1| dihydroorotate oxidase [Deferribacter desulfuricans SSM1]
 gi|290754310|dbj|BAI80687.1| dihydroorotate oxidase [Deferribacter desulfuricans SSM1]
          Length = 306

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/106 (19%), Positives = 46/106 (43%), Gaps = 11/106 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + +   G  I + VE AKI++    + + +N+ CP+ +      G     +  +   
Sbjct: 95  DTRIIVNFWGKTIEEYVEVAKILDSVDIDMLEINISCPNIK----EGGIAFGTDHKMTEK 150

Query: 107 CIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            ++++ K + + P+ VK    V D      ++   K  + SG + I
Sbjct: 151 VVSSVKKNIKNKPLIVKLSPNVTD------IKLFAKICEDSGADAI 190


>gi|297584520|ref|YP_003700300.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus selenitireducens
           MLS10]
 gi|297142977|gb|ADH99734.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus selenitireducens
           MLS10]
          Length = 339

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/196 (15%), Positives = 63/196 (32%), Gaps = 19/196 (9%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA      G++ I L             P +      +G  L     ++ +   A+ 
Sbjct: 146 FQQAAIRANQAGFDVIELHGAHGYLINQFLSPLSNKRTDQYGGTLENRFRLLKEITEAVQ 205

Query: 113 KALSIPVTVKCRIG-VDDQIPAVALRNLVKS-IKKSGVNGIWIHARKAILKGLSPKDNRK 170
                P+ V+  +     +       + + + +K+ GV+ I   +   +   +      +
Sbjct: 206 DVWDGPLFVRLSLNEYHPEGNQDNDFDFLATELKRLGVDLIDCSSGGVVRTPIDVYPGYQ 265

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           IP      + E  K    +  G  G +     A +I+ +   D V +GR   +N      
Sbjct: 266 IP------LAERLKAATGIRTGAVGLITTAETADEIIRNDRADLVFLGRELLRNPYWPLF 319

Query: 229 VDEYFSNPLTGSSPIK 244
             E     +    P +
Sbjct: 320 AAETLKAEIEPPKPYR 335


>gi|163792744|ref|ZP_02186721.1| putative FMN oxidoreductase [alpha proteobacterium BAL199]
 gi|159182449|gb|EDP66958.1| putative FMN oxidoreductase [alpha proteobacterium BAL199]
          Length = 387

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 72/210 (34%), Gaps = 19/210 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFG---ACLMLNPDIVGDCIA 109
             +AA+   + G++ + +++           P +      +G   A  M  P  V + + 
Sbjct: 167 FADAAERAGEAGFDIVEIHMAHGYLLQSFLSPLSNKRSDGYGGDRAGRMRFPLEVAEAVR 226

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A+      P+ V+      +DD         L   +K  G++ I   +     KG +  +
Sbjct: 227 AVWPK-DKPLFVRISSVDGIDDGWEMDDSVALAHELKAGGIDVIDCSSGGNSPKGATNAN 285

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-A 224
             + P         IK+E   +     G + +   A  IL     D + +GR A  +   
Sbjct: 286 LTRGPGYQVPFAERIKREVG-IQTMAVGLIREPELAEMILQDGRADLIAVGRQALVDPFW 344

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
            L     +  +P     P +     + W K
Sbjct: 345 ALHAAQHFDIDPDFEKWPHQYAWWLEKWDK 374


>gi|169851586|ref|XP_001832482.1| NADH:flavin oxidoreductase/NADH oxidase [Coprinopsis cinerea
           okayama7#130]
 gi|116506336|gb|EAU89231.1| NADH:flavin oxidoreductase/NADH oxidase [Coprinopsis cinerea
           okayama7#130]
          Length = 429

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/204 (16%), Positives = 69/204 (33%), Gaps = 28/204 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             AAK     G++ I ++            P +      +G        ++ + + A+  
Sbjct: 202 ASAAKRAVQAGFDVIEIHSAHGYLLHEFLSPVSNKRTDEYGGSFENRTRLLVEVVDAVRA 261

Query: 114 ALS--IPVTVKCR--------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            +   +P+ V+          +  +    +     L   +   GV+ + + +      G 
Sbjct: 262 VIPETMPLFVRVSGTEWLEEVLPEEPSWRSEDTVRLAGILADHGVDLLDVSSG-----GN 316

Query: 164 SPKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            P+   K            +K+     LF+   GGL D + A  IL     D + +GR  
Sbjct: 317 DPRQKIKSGTAYQAPFAGAVKQALGSKLFVSAVGGLYDGNVAQGILDKGWADAIFVGRMF 376

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPI 243
            KN  ++  + +     +T +  I
Sbjct: 377 QKNPGVVWAMADDLDVDITAAKQI 400


>gi|156975313|ref|YP_001446220.1| hypothetical protein VIBHAR_03043 [Vibrio harveyi ATCC BAA-1116]
 gi|156526907|gb|ABU71993.1| hypothetical protein VIBHAR_03043 [Vibrio harveyi ATCC BAA-1116]
          Length = 670

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 199 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKALEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIITCNRINTPDEAERILSSGHADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|310644645|ref|YP_003949404.1| NADH-dependent flavin oxidoreductase-like protein [Paenibacillus
           polymyxa SC2]
 gi|309249596|gb|ADO59163.1| NADH-dependent flavin oxidoreductase-like protein [Paenibacillus
           polymyxa SC2]
          Length = 342

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 63/179 (35%), Gaps = 21/179 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           K  +AA+     G + I L             P     +  +G  L        + I A+
Sbjct: 146 KFADAARRAVQAGVDTIELHGAHGYLIHQFHSPVTNKRDDEYGKDL---SRFGVEVIQAV 202

Query: 112 CKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            K +   +P+ ++      VD          L ++ + +GV+ I + +      G     
Sbjct: 203 RKEMPAGMPLILRISAVEYVDGGYDVDHAIELSRAYQAAGVDVIHVSSGGEGPAGARKPG 262

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNSA 224
           N     + +       +E  ++ +   G L+D + A  ++ + D   V +GR   ++  
Sbjct: 263 NYPGYQVPF---ARQIREALNIPVIAVGVLDDPALAQSVIGNEDADLVAVGRGLLRDPY 318


>gi|288575023|ref|ZP_06393380.1| dihydroorotate dehydrogenase family protein [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570764|gb|EFC92321.1| dihydroorotate dehydrogenase family protein [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 304

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/207 (15%), Positives = 72/207 (34%), Gaps = 30/207 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVED--FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+   +   D   L    + + +     + I LNV CP   V +G       ++P +   
Sbjct: 95  PIIANVSMEDERGLALIVERLVEVADCVDAIELNVSCP--NVDKG--CMSWGVSPVLTSQ 150

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIHA 155
            ++ + K    P+ VK      D           ++ + SG +            I + +
Sbjct: 151 AVSMVQKIWKGPLWVKMTPQAPDPEGV------ARAAEDSGADALVVANTWLGMAIDVDS 204

Query: 156 RKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
           RKA+  + ++      +  +   +V+++      + +   GG+         I+     V
Sbjct: 205 RKAVFDRVVAGFSGPAVFPMALRLVWQVSSAV-SIPVIGCGGVSSGRDLLSMIMAGATAV 263

Query: 214 MIGRAAYKNS----AMLTTVDEYFSNP 236
            +G   +++      +L  V  Y +  
Sbjct: 264 ELGTGMFRDIRLPENILREVKAYMTKE 290


>gi|51891678|ref|YP_074369.1| putative xenobiotic reductase [Symbiobacterium thermophilum IAM
           14863]
 gi|51855367|dbj|BAD39525.1| putative xenobiotic reductase [Symbiobacterium thermophilum IAM
           14863]
          Length = 349

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/158 (17%), Positives = 54/158 (34%), Gaps = 14/158 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           +G  L+    ++     A+ +A     PV V+      V+          L + +K  GV
Sbjct: 190 YGGPLVNRARLLRRVFEAVREAFPADRPVWVRISATDWVEGGWDIAESVELARMMKAWGV 249

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVY--EIKKENPDLFIGLNGGLEDMSQALKI 206
           + + +        G SP          Y + +   I++E   +  G  G +    QA  +
Sbjct: 250 DLVDVSTG-----GNSPLQRIPSIGPGYQVAFAERIRREAG-IATGAVGLITTPEQADSV 303

Query: 207 L--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           +     D  ++GR   +N            + +T   P
Sbjct: 304 VRTGQADVALLGRELLRNPYFPLAAAHRLGHEVTWPEP 341


>gi|326391558|ref|ZP_08213089.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325992388|gb|EGD50849.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 641

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 59/177 (33%), Gaps = 17/177 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V+AA    + G + + +  G          P     E   G           + +  + K
Sbjct: 147 VKAAVRAYEAGADALEIQFGHGYLIHQFLSPHTNKREDEHGGSFENRIRFGMEILDEIKK 206

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +  RI  D+ +P          L K+++  GV  I +    +   G       
Sbjct: 207 EIGADFPIIVRISADEFVPGGWTLEDAIRLAKALEDKGVAAIDVSLGSSCESGAITLQTL 266

Query: 170 KI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                L ++   +IK++  ++ +   G +     A +IL     D V +GR    + 
Sbjct: 267 GTQKGLAWEFASKIKEQV-NIPVIAVGRINTPELAEEILVSGKADLVALGRPLVADP 322


>gi|163794670|ref|ZP_02188640.1| putative NADH-dependent flavin oxidoreductase [alpha
           proteobacterium BAL199]
 gi|159179943|gb|EDP64468.1| putative NADH-dependent flavin oxidoreductase [alpha
           proteobacterium BAL199]
          Length = 369

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 59/177 (33%), Gaps = 14/177 (7%)

Query: 84  PSARVHEGSFGACL---MLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNL 139
           P + V    +G  +   M  P  V D   A+  +A  + V V     +DD +    +   
Sbjct: 189 PLSNVRNDRYGGSIEGRMQFPLEVFDACRAVWPEAKPVGVRVSATDWIDDGLSVDEVVEF 248

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLE 198
            K++K+ G + I + +      G  P     +           +K+E   + +   G + 
Sbjct: 249 CKALKERGCDFIDVSSG-----GNHPGQKITLGPGYQVPFAERVKREVG-IPVMAVGLIT 302

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +  QA  I+     D V + R    N               T   P   R   D WR
Sbjct: 303 EPVQAENIVASGQADFVALARGVMDNPRWAWHAARAL-GAQTDYPPQYARCKPDTWR 358


>gi|153833864|ref|ZP_01986531.1| 2,4-dienoyl-coa reductase (nadph) [Vibrio harveyi HY01]
 gi|148869806|gb|EDL68780.1| 2,4-dienoyl-coa reductase (nadph) [Vibrio harveyi HY01]
          Length = 670

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 199 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKALEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIITCNRINTPDEAEQILSSGHADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|282877565|ref|ZP_06286380.1| dihydroorotate dehydrogenase 1B [Prevotella buccalis ATCC 35310]
 gi|281300137|gb|EFA92491.1| dihydroorotate dehydrogenase 1B [Prevotella buccalis ATCC 35310]
          Length = 303

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/191 (16%), Positives = 66/191 (34%), Gaps = 25/191 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + + G       E A  ++       I LN+ CP   V EG     +        
Sbjct: 93  DTHMIVNVSGNTPDDYAECAARIDALDKIPAIELNISCP--NVKEGGMAFGVTC--AGAA 148

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
             + A+ +A    + VK    V D      +  + ++ +  G +            I I 
Sbjct: 149 AVVKAVRRAYHKTLIVKLSPNVTD------VAEIARACEAEGADSVSLINTLMGMAIDIE 202

Query: 155 ARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +L           +  +   +V+++ K   ++ +   GG+     A++  +     
Sbjct: 203 RRKPVLSIATGGLSGPAVKPVALRMVWQVAKAV-NIPVIGLGGISTAKDAIEFFMAGATA 261

Query: 213 VMIGRAAYKNS 223
           + IG A + + 
Sbjct: 262 IQIGTANFVDP 272


>gi|85711446|ref|ZP_01042504.1| Xenobiotic reductase A [Idiomarina baltica OS145]
 gi|85694598|gb|EAQ32538.1| Xenobiotic reductase A [Idiomarina baltica OS145]
          Length = 362

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 57/177 (32%), Gaps = 15/177 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AA+   D G+  + L+            P A      +G         + + + A+
Sbjct: 159 DFVAAAERARDLGFEWLELHFAHGYLGQSFFSPHANQRTDEYGGSFENRARFLVETVRAV 218

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                 + P+T +  +   D      L+  ++  +     G+        +   +P  N 
Sbjct: 219 KAVWPDNFPLTARFGVIEFDGNDEEQLQESIELTELLKAEGLDF--LNVSISFSTPHANI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                    + E  +   D+ +    G++    A   +    +D VM+GRA   N  
Sbjct: 277 PWGPGFMAPIAERIRNAADIPVASAWGIDLPQLAEHTVAQGQLDLVMVGRAHLSNPH 333


>gi|154150959|ref|YP_001404577.1| hypothetical protein Mboo_1416 [Candidatus Methanoregula boonei
           6A8]
 gi|153999511|gb|ABS55934.1| conserved hypothetical protein [Methanoregula boonei 6A8]
          Length = 379

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/168 (16%), Positives = 60/168 (35%), Gaps = 32/168 (19%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + G+  +     A   E FG   +  ++  C  A +     G   + N   +   + A+ 
Sbjct: 99  LRGSSPAAFTAVA---EAFGNAVVYEIDAHCRQAPMVAAGAGEYYLKNTGTLVAVVKALK 155

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +   + V+VK R GV         R LV+++ ++G + + I                   
Sbjct: 156 EK-GVTVSVKIRAGVSGDD-----RALVRTLWQAGADILHIDLMD--------------- 194

Query: 173 NLDYDIVYEIKKENPDLF--IGLNGGLEDMSQALKILP-SVDGVMIGR 217
               + + ++++        I  N G+    +  ++L    D V + R
Sbjct: 195 ----EGIAKLRQIRNTCPLMIIANNGITSFDRMREMLSHGADLVSLAR 238


>gi|222480523|ref|YP_002566760.1| NADH:flavin oxidoreductase/NADH oxidase [Halorubrum lacusprofundi
           ATCC 49239]
 gi|222453425|gb|ACM57690.1| NADH:flavin oxidoreductase/NADH oxidase [Halorubrum lacusprofundi
           ATCC 49239]
          Length = 370

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 53/166 (31%), Gaps = 14/166 (8%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI----GVDDQIPAVALR 137
           P     + ++G        ++ + + A+ +      PV V+          D        
Sbjct: 201 PVTNDRDDAYGGSFENRTRLLREVVEAVREVWPDDQPVFVRISATDWLPDRDSWDVDDSV 260

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY-EIKKENPDLFIGLNGG 196
            L   + ++G + I +        G+ P          Y + Y E  +E  D+ +   GG
Sbjct: 261 RLAPLLAEAGADLIDVSGG-----GIHPDQQLPGAGPGYQVPYAEAIREGTDVPVAAVGG 315

Query: 197 LEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           + + + A  ++     D V +GR   ++              +   
Sbjct: 316 ITEPTHADALVRNERADLVALGREMLRHPYWPLEAAHELGADVAWP 361


>gi|320459099|dbj|BAJ69720.1| putative oxidoreductase [Bifidobacterium longum subsp. infantis
           ATCC 15697]
          Length = 460

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 301 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQSIALSKVLKEHGV 360

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 361 DVMDVSTGGIM----SGVSIPVKPNYQVPFAEQVKSKA-DIPVTAVGLITKPKQAAKILA 415

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 416 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 447


>gi|261337611|ref|ZP_05965495.1| xenobiotic reductase A [Bifidobacterium gallicum DSM 20093]
 gi|270278036|gb|EFA23890.1| xenobiotic reductase A [Bifidobacterium gallicum DSM 20093]
          Length = 409

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 78/242 (32%), Gaps = 28/242 (11%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC--- 83
           +   AI  GD++     +  E             +  +AA  V   G++ I L+      
Sbjct: 179 VAPSAIAYGDQRTPRELTVDEIHEIQH-------RFRDAAWRVMTAGFDAIELHAAHGYL 231

Query: 84  ------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP--VTVKCRIGVDDQIPA 133
                 P   + E  +G  L     ++ + +  +   +   +P  V V      +     
Sbjct: 232 LSEFLDPLTNLREDEYGGSLRNRMRMLLETVDEVRGVIRDDMPLLVRVSATDWAEGGWDL 291

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                L + +K  GV+ I +        GL P     +  L      +  +   ++    
Sbjct: 292 EQTIELARELKDHGVDLIDVSTG-----GLVPHVTVPVKPLYQVRFADEVRRGANIPTTA 346

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
            G +    +A KI+     D V IGRAA ++             P+   +P      +  
Sbjct: 347 VGLITKPKEAAKIVKGYEADAVEIGRAALRDPYWPLRAYAKLGVPVDK-TPYPPAYVRGA 405

Query: 252 WR 253
           +R
Sbjct: 406 YR 407


>gi|255657128|ref|ZP_05402537.1| putative dihydroorotate dehydrogenase, catalytic subunit
           [Clostridium difficile QCD-23m63]
          Length = 318

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/203 (12%), Positives = 68/203 (33%), Gaps = 38/203 (18%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+ + + G    ++ E A +V+ +  + + L+                +  +   + + +
Sbjct: 94  PVIVSM-GYSAEQIAEVAPLVKPY-ADAVELSTH-------------YVGTDVAPIVNAL 138

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN------------GIWIHAR 156
            A    L +PV +K     D Q        + K+++++G +             I ++  
Sbjct: 139 KAAKAVLDVPVFMKMSPHTDIQT-------IAKAVEEAGADGLVMINSFGPCMAIDVNTG 191

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDM-SQALKILPSVDGV 213
             I+   +         +    +  I +     ++ I   GG+      A  ++     V
Sbjct: 192 YPIMGSKAGYGWLSGAPIRPLAIRCIYEASQVVNIPIIGVGGITCGKDVAEMMMAGASAV 251

Query: 214 MIG-RAAYKNSAMLTTVDEYFSN 235
            +   A  K  ++   + +  + 
Sbjct: 252 QVCTEAILKGPSIYGKIAKELNE 274


>gi|42526380|ref|NP_971478.1| oxidoreductase, FAD/FMN-binding [Treponema denticola ATCC 35405]
 gi|41816492|gb|AAS11359.1| oxidoreductase, FAD/FMN-binding [Treponema denticola ATCC 35405]
          Length = 335

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 71/192 (36%), Gaps = 23/192 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCP-SARVHEGSFGACLMLNPDIVGDCIAA 110
             V+AA+  ++ G + + +             P   +  +   G+ +     +  + I A
Sbjct: 150 DFVQAARRAKEAGLDGVEIHSAHGYLLNQFFSPIMNKRTDKYNGSSIEGRTRLHIEIIEA 209

Query: 111 MCKALSIPVTVKCRIGVDDQIPA-VALRNLVKSI---KKSGVNGIWIHARKAILKGLSPK 166
           + K   +   +  R+G  D I    +L + V++    KK+GV+ + I        G    
Sbjct: 210 IRKMTGLDFLIAVRLGACDYISGGSSLEDSVEACLLFKKAGVDLLDISG------GFCGY 263

Query: 167 DNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            N ++    +   + +  KE     + L GG+     A KIL     D + +GRA   +S
Sbjct: 264 TNPELEEEGWFSRITQAVKEKVGAPVILTGGIVSPEAAEKILQEEKADLIGVGRALLNDS 323

Query: 224 AMLTTVDEYFSN 235
                  +    
Sbjct: 324 DWPKKAKQKLEG 335


>gi|212709540|ref|ZP_03317668.1| hypothetical protein PROVALCAL_00582 [Providencia alcalifaciens DSM
           30120]
 gi|212687878|gb|EEB47406.1| hypothetical protein PROVALCAL_00582 [Providencia alcalifaciens DSM
           30120]
          Length = 363

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 65/179 (36%), Gaps = 22/179 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V++AK  E  G+  I ++            P A   +  +G         + D    +
Sbjct: 158 QFVDSAKRAEQAGFELIEIHAAHGYLLHEFLSPIANQRQDEYGGSFANRTRFLVDVFREI 217

Query: 112 CKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A+S  + V  RI   D             L + +++ G + I + +      GLS K 
Sbjct: 218 RAAVSPHIAVGIRISATDWVEGGWDLPQSIKLTEILEEFGCDYIHVSSG-----GLSDKQ 272

Query: 168 NRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +   +Y + + +   E+ D+ +   G + +  QA  I+     D + IGR      
Sbjct: 273 QIPVSP-NYQVPLAQAIHEHTDMPVIAVGLITEPHQAEAIIATGQADFIAIGRGILYEP 330


>gi|291297830|ref|YP_003509108.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
 gi|290567050|gb|ADD40015.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
          Length = 752

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 62/180 (34%), Gaps = 17/180 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
            +  ++A+   + G++ + L   C    +  G            +G  L        + +
Sbjct: 544 DQFADSARRAREAGFDLLEL--HCAHGYLLSGFISPLTNRRTDEYGGDLANRLRFPLEVL 601

Query: 109 AAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           AA+ +     +TV+       +D I       + ++   +GV+GI +   + +++     
Sbjct: 602 AAIREVWDGALTVRISATDWCEDGITGADSVEIARAFAAAGVDGIDVSTGQVVVEEKPAY 661

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS-VDGVMIGRAAYKNSA 224
                      I + ++ E P L +   G +     A   IL    D   +GR    +  
Sbjct: 662 GRSYQTPYADRIRHALRAEFPRLAVIAVGAISSADDANSIILAGRADLCALGRVHLYDPH 721


>gi|226505722|ref|NP_001142101.1| hypothetical protein LOC100274265 [Zea mays]
 gi|194707116|gb|ACF87642.1| unknown [Zea mays]
 gi|223947605|gb|ACN27886.1| unknown [Zea mays]
          Length = 415

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/190 (19%), Positives = 72/190 (37%), Gaps = 29/190 (15%)

Query: 54  IGGADISKLVEAA-----KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + G+ + +  +AA     + VE+ G + + +N  CP     E   GA +  + D++ +  
Sbjct: 146 LIGSIMEEYNKAAWHELIERVEESGVDALEINFSCPHGM-PERKMGAAVGQDCDLLEEVC 204

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVAL-----RNLVKSIKK----SGVNGIWIHARKAI 159
             + +  ++PV  K    + D      +        V +I       G+N   +     +
Sbjct: 205 GWINEKATVPVWAKMTPNITDITQPARISLKSGCEGVSAINTIMSVMGINLKTLRPEPCV 264

Query: 160 LKGLSP--KDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLEDMSQALK-ILPSVD 211
               +P     R +  +    V +I +   + F     +   GG+E  + A + IL   D
Sbjct: 265 EGYSTPGGYSARAVHPIALAKVMQIARMMKEEFADGQSLSAIGGVETGNDAAEFILLGAD 324

Query: 212 ------GVMI 215
                 GVMI
Sbjct: 325 TVQVCTGVMI 334


>gi|116750996|ref|YP_847683.1| NADH:flavin oxidoreductase/NADH oxidase [Syntrophobacter
           fumaroxidans MPOB]
 gi|116700060|gb|ABK19248.1| NADH:flavin oxidoreductase/NADH oxidase [Syntrophobacter
           fumaroxidans MPOB]
          Length = 642

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 64/185 (34%), Gaps = 20/185 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC----------PSARVHEGSFGACLMLNPDIVGDCIAAM 111
            VEAA    D G++ I L+  C          P       ++G  L     ++ + +  +
Sbjct: 149 FVEAAVRARDCGFDAIELHA-CHDYWLNFFLSPHFNHRRDAYGGSLENRSRLLREIVRDI 207

Query: 112 CKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL-SPK 166
             A+     + V +     V+D +       +   ++K GV+ +         +   SP 
Sbjct: 208 RSAVGDSMILGVRLSMEEFVEDGLTLSETLQVGTWLEKLGVDYLSASGGIGKTQHRMSPP 267

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                 +L Y  + E  K +  + +   G L+      K +     D   +GR+   +  
Sbjct: 268 MEVPRGSLLY--LAEALKRSVSVPVIGVGRLDRPEVFRKAVEEGCADIAGVGRSLIADPE 325

Query: 225 MLTTV 229
            +  V
Sbjct: 326 YVAKV 330


>gi|323704860|ref|ZP_08116437.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535786|gb|EGB25560.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 602

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/187 (13%), Positives = 60/187 (32%), Gaps = 20/187 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AAK  ++ G++ + L+            P+       +G           + +  +
Sbjct: 120 DFVNAAKRAKEAGFDAVELHFAHGWFVNQFLSPNVNTRNDEYGGNFYGRARFALEILKRV 179

Query: 112 CKAL-SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGLSPK 166
              + +I V  +       D          L + +++ G + I + +         +SP 
Sbjct: 180 KSEVPNIAVICRINGSDYTDGGFDIEESVKLSRLLEEHGADAINVSSGVGSTSEYHISPM 239

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
                P +DY    +I+       I  +  G  +D    ++     D + I R    +  
Sbjct: 240 GIDDKPIIDYA--KKIRDSVSIPVIAADKLGDADDWEAIVRD-GYADFIGIARGLIGDPD 296

Query: 225 -MLTTVD 230
            +   ++
Sbjct: 297 CIFKYIN 303


>gi|166364399|ref|YP_001656672.1| nitrogen regulation protein NifR3-like protein [Microcystis
          aeruginosa NIES-843]
 gi|166086772|dbj|BAG01480.1| nitrogen regulation protein NifR3 homolog [Microcystis aeruginosa
          NIES-843]
          Length = 81

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 3  DWTDRHYRFFARLLTNNALLYTEMIVADAILR 34
            TD  +R   R    +++LYTEM+ A  I R
Sbjct: 36 GVTDLVFRCLVRRFAPDSMLYTEMVNATEISR 67


>gi|239623417|ref|ZP_04666448.1| NADH:flavin oxidoreductase [Clostridiales bacterium 1_7_47_FAA]
 gi|239522383|gb|EEQ62249.1| NADH:flavin oxidoreductase [Clostridiales bacterium 1_7_47FAA]
          Length = 625

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/127 (15%), Positives = 42/127 (33%), Gaps = 7/127 (5%)

Query: 105 GDCIAAMCKALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
              I A+  A     PV  +      V+          + + ++ +G + I +       
Sbjct: 181 AQIIKAIKSACGSGFPVVFRISGTEMVEGGRTVQETGEIARILEAAGADAIHVSIGMPES 240

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
            G            + +    IKK      I +N  + D+  A++++     D V + RA
Sbjct: 241 GGYISATMDVEDCFNVENAAVIKKYVSIPVIAVNR-IVDIKDAVEVVEQGKADMVSMARA 299

Query: 219 AYKNSAM 225
              +  +
Sbjct: 300 QLADPEL 306


>gi|227356050|ref|ZP_03840441.1| NADPH dehydrogenase [Proteus mirabilis ATCC 29906]
 gi|227163827|gb|EEI48735.1| NADPH dehydrogenase [Proteus mirabilis ATCC 29906]
          Length = 363

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 40/178 (22%), Positives = 64/178 (35%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VEAAK  E  G + I ++            P +      +G        ++ D   A+ 
Sbjct: 159 FVEAAKRAESAGIDVIEIHGAHGYLLHEFLSPLSNHRTDQYGGDFNNRSRLLIDVFTAVK 218

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+S  + V  RI   D +           L + ++  G + I + +      GLS K  
Sbjct: 219 KAVSDKMCVGVRISATDWVEGGWDLESSIALTQHLEDLGCHYIHVSSG-----GLSDKQA 273

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            K+ PN        I  E   L +   G + +  QA  IL     D + +GR    + 
Sbjct: 274 IKLGPNYQVPFAQAIYNET-QLPVIAVGLITEPEQAEAILLTEQADFIALGRGILYDP 330


>gi|197285553|ref|YP_002151425.1| NADH-dependent flavin oxidoreductase [Proteus mirabilis HI4320]
 gi|194683040|emb|CAR43531.1| putative NADH-dependent flavin oxidoreductase [Proteus mirabilis
           HI4320]
          Length = 363

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 40/178 (22%), Positives = 64/178 (35%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VEAAK  E  G + I ++            P +      +G        ++ D   A+ 
Sbjct: 159 FVEAAKRAESAGIDVIEIHGAHGYLLHEFLSPLSNHRTDQYGGDFNNRSRLLIDVFTAVK 218

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+S  + V  RI   D +           L + ++  G + I + +      GLS K  
Sbjct: 219 KAVSDKMCVGVRISATDWVEGGWDLESSIALTQHLEDLGCHYIHVSSG-----GLSDKQA 273

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            K+ PN        I  E   L +   G + +  QA  IL     D + +GR    + 
Sbjct: 274 IKLGPNYQVPFAQAIYNET-QLPVIAVGLITEPEQAEAILLTEQADFIALGRGILYDP 330


>gi|332093489|gb|EGI98547.1| hypothetical protein SB359474_2529 [Shigella boydii 3594-74]
          Length = 289

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 58/154 (37%), Gaps = 27/154 (17%)

Query: 73  GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
           G + I  N  CP   +   + G+ +  +P +V     A+ +  ++P+  K    + D   
Sbjct: 5   GADMIECNFSCPQ--MTSHAMGSDVGQSPVLVEKYCRAVKRGSTLPMLAKMTPNIGD--- 59

Query: 133 AVALRNLVKSIKKSGVNGI-WIHARKAIL----------------KGLSPKDNRKIPNLD 175
              +  +  + K+ G +GI  I+  K+I                   +S    + +  + 
Sbjct: 60  ---MCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIA 116

Query: 176 YDIVYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
              + +++   E  D  I   GG+E    A + L
Sbjct: 117 LRFIQQMRTHPELRDFPISGIGGIETWEDAAEFL 150


>gi|313898863|ref|ZP_07832397.1| putative NADH oxidase [Clostridium sp. HGF2]
 gi|312956445|gb|EFR38079.1| putative NADH oxidase [Clostridium sp. HGF2]
          Length = 642

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 42/220 (19%), Positives = 79/220 (35%), Gaps = 40/220 (18%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC--- 83
           + +D  + G     +   T E+ +A             AAK     GY+ +     C   
Sbjct: 118 VASDLHVHGHTIPAVDVETIEEVVAC---------FGAAAKRAVKAGYDCVE--FHCGHN 166

Query: 84  --------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPA 133
                   P+    E ++G           DCI A+ +++   +P+ ++     D     
Sbjct: 167 YLPHSFLSPAFNHREDAYGGTFEKRCKFPLDCIRAIRQSIPRDMPLLMRLDAQDDYLENG 226

Query: 134 VALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD------YDIVYEIKK 184
           + + +     +  K++GV+ + I     I  GL      ++P +D       D    I++
Sbjct: 227 LTIEDVIAFCRLAKEAGVDVLDISRGNMITAGLK----YEVPPIDIPKGFNVDNCARIRR 282

Query: 185 ENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           E   L     G +     A +IL     D V++GRA   +
Sbjct: 283 ETGML-CIAVGRINTPQLAEEILEQNKADMVVMGRAQLAD 321


>gi|23465782|ref|NP_696385.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium longum
           NCC2705]
 gi|23326472|gb|AAN25021.1| probable NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium
           longum NCC2705]
          Length = 371

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 212 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 271

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 272 DVMDVSTGGIM----SGVSIPVKPNYQVPFSEQVKAKA-DIPVTAVGLITKPKQAAKILA 326

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 327 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 358


>gi|83951329|ref|ZP_00960061.1| hypothetical protein ISM_12240 [Roseovarius nubinhibens ISM]
 gi|83836335|gb|EAP75632.1| hypothetical protein ISM_12240 [Roseovarius nubinhibens ISM]
          Length = 677

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 63/188 (33%), Gaps = 17/188 (9%)

Query: 61  KLVEAAKIVEDFGYNEINL--------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           +   AA+  +  G++ I L            P     +  +G  L     +    I A+ 
Sbjct: 149 QFAAAARRCQQGGFDGIELLSHSHLLGQFLSPLVNQRDDDYGGSLENRLRLTLQVIEAVR 208

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +A+   + +  R+  D+     + A     + + I  +G          A    L     
Sbjct: 209 EAVGPDMILGMRVTGDELTAGGLTADDCVTIAQQISATGAVDFLNILAGAPYDDLGLAGW 268

Query: 169 ---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                +P   +  V    +   DL I   GG+ D++ A   +    VD + + RA   + 
Sbjct: 269 VPPMGLPAAAHLSVASRIRRAVDLPIFHAGGIADIATARHAVAEGHVDLIGMTRAHMADP 328

Query: 224 AMLTTVDE 231
            ++  +  
Sbjct: 329 YLVAKLAR 336


>gi|160879803|ref|YP_001558771.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           phytofermentans ISDg]
 gi|160428469|gb|ABX42032.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           phytofermentans ISDg]
          Length = 354

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 48/127 (37%), Gaps = 6/127 (4%)

Query: 99  LNPDIVG-DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             P++   + I  + K       +  R+G  +     A+    +  ++SGV+ + I    
Sbjct: 188 QKPELFALEIIREIRKQTPSDFIIGMRLGGFEPTLEDAIA-YARIFEESGVDFLDI--SY 244

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
             ++  +P   +  P  D     +  KE   + +    G+     A KIL    VD V I
Sbjct: 245 GFVQESTPVVPKDYPFKDIIYAAQKIKEAVSIPVFAVNGINSPELADKILEQTKVDMVDI 304

Query: 216 GRAAYKN 222
           GR    N
Sbjct: 305 GRGTLVN 311


>gi|255536210|ref|YP_003096581.1| NADH:flavin oxidoreductase/NADH oxidase [Flavobacteriaceae
           bacterium 3519-10]
 gi|255342406|gb|ACU08519.1| NADH:flavin oxidoreductase/NADH oxidase [Flavobacteriaceae
           bacterium 3519-10]
          Length = 348

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 38/185 (20%), Positives = 65/185 (35%), Gaps = 32/185 (17%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA+   D G++ I ++            P + V    +G         + + I A+ 
Sbjct: 152 FKEAAQRALDAGFDVIEIHAAHGYLIHQFLSPLSNVRTDEYGGSFENRSRFIIEIIDAVN 211

Query: 113 ----KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------IHARKAILKG 162
               +   + V +       D         L K +K+ GV+ I       IH  K  L  
Sbjct: 212 GLLDENHPLFVRISGTEYAKDGWNIKDSVELAKVLKEKGVDLIDVSSGGNIHGAKISLF- 270

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAY 220
               D  ++P         IKKE+  +  G  G ++   QA +IL     D + + R   
Sbjct: 271 ----DGYQVPLA-----ASIKKESG-IATGAVGLIKTAKQAEEILQNEQADLIFVAREIL 320

Query: 221 KNSAM 225
           +N  +
Sbjct: 321 RNPYL 325


>gi|159485198|ref|XP_001700634.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158272158|gb|EDO97963.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 364

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/89 (29%), Positives = 36/89 (40%), Gaps = 20/89 (22%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V  +CR+GVD+      L   V                    KGLSP  NR +P L +  
Sbjct: 74  VGSRCRLGVDECDSYAQLHEFV--------------------KGLSPHQNRTVPPLRHQW 113

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + + ++ P L   LNGGL+    A   L
Sbjct: 114 AWALARDFPHLQFSLNGGLQTCHDARAAL 142



 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 209 SVDGVMIGRAAYKNSA-MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASM 259
            ++GVMIGR AY +    L   D       + ++P +    K +   +   +
Sbjct: 245 GLEGVMIGRGAYNDPWGCLADADRCLWGDDSNAAPNRRCGSKRWKAAVDEVL 296


>gi|300914108|ref|ZP_07131424.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X561]
 gi|307724656|ref|YP_003904407.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X513]
 gi|300889043|gb|EFK84189.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X561]
 gi|307581717|gb|ADN55116.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X513]
          Length = 667

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 58/185 (31%), Gaps = 29/185 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            VEAA   E  G++ + L+                       +G           D +  
Sbjct: 182 FVEAAIRAEKSGFDAVELHFA--HGWFVNQFLSPDTNKRTDEYGGNFEGRTKFALDILRE 239

Query: 111 MCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K +   +TV CRI      D            K ++  G + + I +    +   S  
Sbjct: 240 VKKTIP-EMTVICRINGSDFTDRGFTIEESVRFAKLLEYHGADALDISSG---VSSTSEY 295

Query: 167 DNRKIPNLDYDIVYEIK--KENPDLFIGLN---GGLEDMSQALKILPS-VDGVMIGRAAY 220
               +   D  ++  +K  KEN  + +      G + D  + L+      D + I R   
Sbjct: 296 HISPMGIGDKPLIGIVKRIKENVTIPVIAIDKLGSVYDWEKVLE--DGIADFIGIARGFI 353

Query: 221 KNSAM 225
            +  +
Sbjct: 354 GDPDL 358


>gi|271964315|ref|YP_003338511.1| dihydroorotate dehydrogenase [Streptosporangium roseum DSM 43021]
 gi|270507490|gb|ACZ85768.1| dihydroorotate dehydrogenase family protein [Streptosporangium
           roseum DSM 43021]
          Length = 324

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/199 (15%), Positives = 66/199 (33%), Gaps = 29/199 (14%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           GG        A ++ +  G + + +N+ CP   + +         +     + +A++   
Sbjct: 103 GGTVAEYTALARRLTDAPGVSAVEVNLSCP--NIEDRGRVFA--RDGAASAEVVASVRSV 158

Query: 115 L--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------------WIHARKAIL 160
           +   +PV  K    V D +         ++    G + +                R ++ 
Sbjct: 159 MRYDVPVVAKLSPDVMDVVSV------ARACVDGGADALSMINNPLGMSIDTEAMRPSLA 212

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
                     I  L    V+++    P + I   GG+     A + IL     V +G A 
Sbjct: 213 AVTGGLSGPAIRPLAVRCVWQVHAALPSVPIIGMGGVLTGRDAFELILAGACVVAVGTAL 272

Query: 220 YKNSA----MLTTVDEYFS 234
           + +      +L  ++E  +
Sbjct: 273 FHDPYACLRILRELEELLA 291


>gi|282900037|ref|ZP_06307996.1| hypothetical protein CRC_01430 [Cylindrospermopsis raciborskii
           CS-505]
 gi|281195069|gb|EFA70007.1| hypothetical protein CRC_01430 [Cylindrospermopsis raciborskii
           CS-505]
          Length = 231

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/157 (19%), Positives = 53/157 (33%), Gaps = 30/157 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A  V + G + I ++         +   G       + + D I  + + +  PV      
Sbjct: 88  ALAVAEAGADIIAIDA-----TQRKRPGG-------EKLVDIIRGIHQQIGKPVMADVDT 135

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
                          K    SG + +   +       K L P     + +    IV  +K
Sbjct: 136 FTS-----------AKLAIDSGADIVGTTLFGYTEETKNLIPPGWELLKH----IVENLK 180

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
            E+PD+ +   GG+    +A K L    D V++G A 
Sbjct: 181 VEHPDILVICEGGISSPEEAKKALELGADAVVVGTAI 217


>gi|261346602|ref|ZP_05974246.1| anthraniloyl-CoA monooxygenase [Providencia rustigianii DSM 4541]
 gi|282565307|gb|EFB70842.1| anthraniloyl-CoA monooxygenase [Providencia rustigianii DSM 4541]
          Length = 771

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 67/201 (33%), Gaps = 21/201 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AAK  +  G++ + L  G          P        FG  L          ++A
Sbjct: 563 DQFVAAAKRADQAGFDWLELQAGHGYLLSSFISPLTNQRTDGFGGSLENRLRFPLAVVSA 622

Query: 111 MCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K      P++V+      V+          + K++ ++G + I   + +     +SP 
Sbjct: 623 VRKVWPEGKPLSVRISATDWVEGGTTVDEAVLIGKALHQAGADIIDCSSGE-----VSPL 677

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS- 223
                  +    + +  +    + +   G + D  Q   I+ S   D   + R    +  
Sbjct: 678 QQPVYGRMYQTPIADRIRNEGSVPVIAVGAITDADQVNSIIASGRADLCALSRPLLADPA 737

Query: 224 AMLTTVDEYFSNPLTGSSPIK 244
            +L     +  N +   +P +
Sbjct: 738 WLLHECARFGWNTVNWPAPYE 758


>gi|222629260|gb|EEE61392.1| hypothetical protein OsJ_15567 [Oryza sativa Japonica Group]
          Length = 209

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/102 (14%), Positives = 32/102 (31%), Gaps = 7/102 (6%)

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAML----TTVDEY 232
           + ++      + +  NG + +     +I        VM+ R A  N+++      T  E 
Sbjct: 100 IADVVSAL-SIPVIANGDVFEYEDFKRIKDATGAASVMVARGAMWNASIFCPKGKTPWED 158

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
                   S +     K   + I   +  Y+      G  + 
Sbjct: 159 VKREYVRKSILWDNDLKSTKQTIKEMIMHYSCLEFPEGKGVN 200


>gi|227833316|ref|YP_002835023.1| Fmn oxidoreductase protein [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184300|ref|ZP_06043721.1| Fmn oxidoreductase protein [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454332|gb|ACP33085.1| Fmn oxidoreductase protein [Corynebacterium aurimucosum ATCC
           700975]
          Length = 342

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 29/185 (15%), Positives = 64/185 (34%), Gaps = 16/185 (8%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA+   D G + + +             PS+   E ++G        +V + + A+
Sbjct: 134 EFRQAARNAIDAGMDGVEIHGANGYLLHQFLSPSSNHREDAYGGSPQNRYRLVEEILRAV 193

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            + +     +  R+     I  +   +    +   G     I      L  +S       
Sbjct: 194 AEEIGAD-RLALRLSPQHNIQGIEETDAADVLATYGGLLRAIE--DLGLAYVSFLHAEPT 250

Query: 172 PNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
             L  ++   + + N    + LN   G +   ++A +++   D V +GR A  N  ++  
Sbjct: 251 GELITEL-STLARANGRTRVILNSGFGQVTQCAEARELVQHGDAVAVGRLAISNPDLVRR 309

Query: 229 VDEYF 233
             E  
Sbjct: 310 WQEQL 314


>gi|309776087|ref|ZP_07671078.1| NADH oxidase [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916038|gb|EFP61787.1| NADH oxidase [Erysipelotrichaceae bacterium 3_1_53]
          Length = 648

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 73/189 (38%), Gaps = 17/189 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG----------CPSARVHEGSFGACL 97
           +P+ ++     I +  EAA  V+  G + + ++             P        +G  +
Sbjct: 135 RPVTIEELHMIIKQFGEAAFRVKQAGGDGVEIHAAHAHGLLGGFLTPLYNKRCDEYGGDI 194

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLV---KSIKKSGVNGIWI 153
                +  + IA + K       +  RI  D+     + L ++V   K ++++GV+ + +
Sbjct: 195 NGRLKLTLEVIAEVRKMCGDDFIIDVRISGDEYSDGGLNLDDMVYVSKQLERAGVDMLHV 254

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
                I +G +       P     +  EIKK    + +   G + +   A +++ +   D
Sbjct: 255 SGGTTIKRGSAIPAAGTKPGAHAHLSQEIKKHV-SIPVATVGRITEPWIADELIANGKAD 313

Query: 212 GVMIGRAAY 220
             MIGRA  
Sbjct: 314 MCMIGRANL 322


>gi|307131551|ref|YP_003883567.1| FMN oxidoreductase [Dickeya dadantii 3937]
 gi|306529080|gb|ADM99010.1| FMN oxidoreductase [Dickeya dadantii 3937]
          Length = 390

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/205 (16%), Positives = 70/205 (34%), Gaps = 27/205 (13%)

Query: 39  NILGFSTQEKPLAL----QIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPS 85
           + L +   + P       QI    I     +A+  +  G++ I ++            P 
Sbjct: 158 SALPYHPDDTPPVAMSHDQIK-NLIDAFAASARRADRLGFDLIEIHAAHGYLLHQFLSPL 216

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVK 141
               +  +G  L     ++ +   A+ +       + V +     V+          L  
Sbjct: 217 TNQRDDEYGGSLTNRMRLLREIYMAVREVFPPHKAVGVRISATDAVEGGWDLAQSVELGH 276

Query: 142 SIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            +++ G + I +     + L+ + P  N ++P        +I++E   L     G + + 
Sbjct: 277 VLRQLGCDYIHVSSGGLSPLQQIHPAPNYQVPFAQ-----KIRQETG-LVTIAVGLITEP 330

Query: 201 SQALKIL--PSVDGVMIGRAAYKNS 223
            QA  IL     D + + RA   N 
Sbjct: 331 EQAEAILATEEADAIALARAMLFNP 355


>gi|326526047|dbj|BAJ93200.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 417

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 34/190 (17%), Positives = 72/190 (37%), Gaps = 29/190 (15%)

Query: 54  IGGADISKLVEAA-----KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + G+ + +  +AA     + VE+ G + + +N  CP     E   GA +  +  ++ +  
Sbjct: 148 LIGSIMEEYNKAAWHELIERVEESGVDALEINFSCPHGM-PERKMGAAVGQDCALLEEVS 206

Query: 109 AAMCKALSIPVTVKCRIGVDD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + +  ++PV  K    + D         +  +  +  +   +   G++   +     +
Sbjct: 207 GWINEKATVPVWSKMTPNITDITQPSRIALKSGSEGIAAINTIMSVMGIDLKTLRPEPCV 266

Query: 160 L-----KGLSPKDNRKIPNLDYDIVYE-IKKENPD-LFIGLNGGLEDMSQALK-ILPSVD 211
                  G S +    I       +   IK+E P+   +   GG+E  + A + IL   D
Sbjct: 267 EGYSTPGGYSARAVHPIALAKVMQIARLIKEEFPEGRSLSAIGGVETGNDAAEFILLGAD 326

Query: 212 ------GVMI 215
                 GVM+
Sbjct: 327 TVQVCTGVMM 336


>gi|266621058|ref|ZP_06113993.1| dihydroorotate oxidase [Clostridium hathewayi DSM 13479]
 gi|288867298|gb|EFC99596.1| dihydroorotate oxidase [Clostridium hathewayi DSM 13479]
          Length = 307

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 65/201 (32%), Gaps = 26/201 (12%)

Query: 38  KNILGFSTQEK-PLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGA 95
           K IL     E  PL + +   D  ++ E A  +E       I +N+ CP         G 
Sbjct: 86  KEILPHLPCETTPLIIDMKAVDKYQMEELAASIEQMDRIMGIEINLNCPY------GPGT 139

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--- 152
               NPD + D +A +  A      +  ++   D    + +  +  + ++ G + I    
Sbjct: 140 PYWKNPDELKDLVARVRAAAPHK-WLIAKVPGGD----IPVEEISVACQEGGADAITSYS 194

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKEN--PDLFIGLNGGLEDMSQA 203
                 I  R    +                + +   ++     D+ +   GG+      
Sbjct: 195 SLNGSCIDIRTGTYRCGGGGSGGFSGPAFKPVGILMCRRAATAVDIPVIGIGGISCAEDV 254

Query: 204 LK-ILPSVDGVMIGRAAYKNS 223
           ++ I+     V +G A     
Sbjct: 255 IEYIMAGAYAVQVGSANLSRP 275


>gi|169794829|ref|YP_001712622.1| putative FMN oxidoreductase [Acinetobacter baumannii AYE]
 gi|213157844|ref|YP_002320642.1| NADPH dehydrogenase [Acinetobacter baumannii AB0057]
 gi|215482376|ref|YP_002324558.1| xenobiotic reductase A [Acinetobacter baumannii AB307-0294]
 gi|301345449|ref|ZP_07226190.1| xenobiotic reductase A [Acinetobacter baumannii AB056]
 gi|301510333|ref|ZP_07235570.1| xenobiotic reductase A [Acinetobacter baumannii AB058]
 gi|301595030|ref|ZP_07240038.1| xenobiotic reductase A [Acinetobacter baumannii AB059]
 gi|169147756|emb|CAM85619.1| putative FMN oxidoreductase [Acinetobacter baumannii AYE]
 gi|213057004|gb|ACJ41906.1| NADPH dehydrogenase [Acinetobacter baumannii AB0057]
 gi|213985758|gb|ACJ56057.1| xenobiotic reductase A [Acinetobacter baumannii AB307-0294]
          Length = 368

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 29/148 (19%), Positives = 56/148 (37%), Gaps = 14/148 (9%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 305

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNS 223
           + D   A +IL    D + + RA   + 
Sbjct: 306 ITDPQHAEQILENQADAIGLARAMLYDP 333


>gi|21241095|ref|NP_640677.1| FMN oxidoreductase [Xanthomonas axonopodis pv. citri str. 306]
 gi|21106393|gb|AAM35213.1| FMN oxidoreductase [Xanthomonas axonopodis pv. citri str. 306]
          Length = 365

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/207 (15%), Positives = 63/207 (30%), Gaps = 22/207 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +A   E  G   I L+            P +     ++G  L     +      A
Sbjct: 158 DAFVASATRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMRLTLRIFDA 217

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + V  RI   D             L +++   G + I + +      GL P+
Sbjct: 218 VRAAVSEKIAVGVRISATDWVEGGWDVQQSIALSQALDARGAHYIHVSSG-----GLDPR 272

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +    Y I   +  +   +  +   G + + +QA  IL     D + + R    + 
Sbjct: 273 QQIPL-QAGYQIPFAQEIRAQVNTPVIGVGLITEPAQAEAILQEGQADAIALARGILYDP 331

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                        +T +        +D
Sbjct: 332 RWPWHAAAALGASVTPAPQYLRCEPRD 358


>gi|226938983|ref|YP_002794054.1| FadH [Laribacter hongkongensis HLHK9]
 gi|226713907|gb|ACO73045.1| FadH [Laribacter hongkongensis HLHK9]
          Length = 717

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/179 (13%), Positives = 56/179 (31%), Gaps = 19/179 (10%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
                A + +  GY+ + +            C         +G           + + A+
Sbjct: 188 DFARCAALAQQAGYDGVEVMGSEGYLINQFLCSRTNQRTDEWGGPFANRMRFAVETVKAV 247

Query: 112 CKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A+     +  R+     VD+      +  L ++I+ +G   I  +      +   P  
Sbjct: 248 RAAVGTGFIIIYRLSMLDLVDEGSSWDEVVTLARAIEAAGATLI--NTGIGWHEARIPTI 305

Query: 168 NRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +P   +  V  ++  +     I  N  + D + A ++L     D V + R    + 
Sbjct: 306 ATSVPRAGFAWVTKKLMGQVGIPLITTNR-INDPAVAERVLAEGCADMVSMARPLLADP 363


>gi|167040019|ref|YP_001663004.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X514]
 gi|166854259|gb|ABY92668.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X514]
          Length = 612

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 58/185 (31%), Gaps = 29/185 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            VEAA   E  G++ + L+                       +G           D +  
Sbjct: 127 FVEAAIRAEKSGFDAVELHFA--HGWFVNQFLSPDTNKRTDEYGGNFEGRTKFALDILRE 184

Query: 111 MCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K +   +TV CRI      D            K ++  G + + I +    +   S  
Sbjct: 185 VKKTIP-EMTVICRINGSDFTDRGFTIEESVRFAKLLEYHGADALDISSG---VSSTSEY 240

Query: 167 DNRKIPNLDYDIVYEIK--KENPDLFIGLN---GGLEDMSQALKILPS-VDGVMIGRAAY 220
               +   D  ++  +K  KEN  + +      G + D  + L+      D + I R   
Sbjct: 241 HISPMGIGDKPLIGIVKRIKENVTIPVIAIDKLGSVYDWEKVLE--DGIADFIGIARGFI 298

Query: 221 KNSAM 225
            +  +
Sbjct: 299 GDPDL 303


>gi|308049661|ref|YP_003913227.1| 2,4-dienoyl-CoA reductase [Ferrimonas balearica DSM 9799]
 gi|307631851|gb|ADN76153.1| 2,4-dienoyl-CoA reductase [Ferrimonas balearica DSM 9799]
          Length = 674

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/175 (14%), Positives = 56/175 (32%), Gaps = 17/175 (9%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
              A++ +  GY+ + L            C      +  +G  L        + + A+ +
Sbjct: 147 ARCARLAQKAGYDGVELMGSEGYLLNQFLCRRTNERQDQYGGALENRARFPLEMVRAVRE 206

Query: 114 ALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+     VD       +  L K ++++GV    I+      +   P    
Sbjct: 207 AVGPDFIIIFRLSMLDLVDGGNDWEEVVQLAKWLEEAGVT--IINTGIGWHEARIPTIAT 264

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            +P   +  + E  +    + +     +     A  IL     D V + R    +
Sbjct: 265 SVPRAAFSFITERLRSEVKVPLVATNRINTPDVAESILASGQADMVSMARPLLAD 319


>gi|46202075|ref|ZP_00053819.2| COG1902: NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Magnetospirillum magnetotacticum MS-1]
          Length = 676

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/226 (13%), Positives = 73/226 (32%), Gaps = 24/226 (10%)

Query: 23  YTEM--IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y+ M  IVA + +R    +       +  +   +           A++    GY+ + + 
Sbjct: 118 YSRMKDIVAPSAIRAPINSATPRELTDAEIVQTVA-----DYANCARLALLAGYDGVEVM 172

Query: 81  VG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGV 127
                       P        +G  L      + + + A+ +AL     + V +     V
Sbjct: 173 ASEGYLINEFLAPRTNKRTDRWGGDLHGRMRFLVEIVRAVRQALGEAKMMSVRLSMVDLV 232

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           +D + A  +  + ++I+  G + I  ++     +   P     +P   +       K   
Sbjct: 233 EDGLSADEVVAVAQAIEIEGCDLI--NSGIGWHEARVPTIAHTVPQGVWSWATARVKAAV 290

Query: 188 DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            + +  +  ++    A  ++     D V + R    + A    V  
Sbjct: 291 KIPVAASNRIKTPDLAESLIAEGQCDLVSMARPLLADPAFAAKVAR 336


>gi|301064160|ref|ZP_07204607.1| putative NADH oxidase [delta proteobacterium NaphS2]
 gi|300441780|gb|EFK06098.1| putative NADH oxidase [delta proteobacterium NaphS2]
          Length = 638

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 29/150 (19%), Positives = 55/150 (36%), Gaps = 7/150 (4%)

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSI 143
           + + ++G  +        + +  + K +    P++ K      V D +       ++K +
Sbjct: 182 IRQDAYGGDIQGRTRFAREIVREVRKRVGDAYPISFKISAMEFVKDGLNVEESITILKIL 241

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
            K GV+ I + A          +          +  Y IKKE  ++ I   G + D   A
Sbjct: 242 VKEGVDVIQVSAGNDATPEWISQPTFMEKACLTEFAYAIKKEM-NVPIMSVGRINDPQLA 300

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            +I+     D V +GR    + AM     E
Sbjct: 301 EEIIKTGKADLVCMGRGLLADPAMPNKARE 330


>gi|222151913|ref|YP_002561073.1| NADH-dependent flavin oxidoreductase homolog [Macrococcus
           caseolyticus JCSC5402]
 gi|222121042|dbj|BAH18377.1| NADH-dependent flavin oxidoreductase homolog [Macrococcus
           caseolyticus JCSC5402]
          Length = 346

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 61/173 (35%), Gaps = 15/173 (8%)

Query: 64  EAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL-MLNPDIVGDCIAAMCK 113
           E+A+   + G++ I +             PS       +G  L +   +++    + M +
Sbjct: 153 ESARRAVEAGFDAIEVHGAHGYLIHQFHSPSINKRTDEYGKDLSLFGCEVIQAVKSVMPE 212

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            + +   +  R  +D         ++ ++ + +GV+   I        G     N     
Sbjct: 213 GMPLIFRISAREYMDGGYDLEHALHIAEAYQAAGVDVFHISTGGEAPAGKEKPGNYPGYQ 272

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           + +       KE  ++ +   G L+    A  +L +  +D V IGR    +  
Sbjct: 273 VPF---ARAFKERFNIPVIAVGMLDSAETAEMVLNNDDIDLVAIGRGMLNDPY 322


>gi|121710278|ref|XP_001272755.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           clavatus NRRL 1]
 gi|119400905|gb|EAW11329.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           clavatus NRRL 1]
          Length = 421

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 34/224 (15%), Positives = 69/224 (30%), Gaps = 33/224 (14%)

Query: 49  PLALQIGGADISKL----VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGA 95
           P+  Q+   DI  L    V A K     G + I + N           P+       +G 
Sbjct: 184 PVPQQMTKQDIEDLKVAWVAAVKRAVKAGADFIEIHNGHGYLLMSFLSPAVNTRTDEYGG 243

Query: 96  CLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--------IGVDDQIPAVALRNLVKSIKK 145
                  +  +        +  ++P+ ++                           ++  
Sbjct: 244 SFENRIRLSMEIAQLTRDNVPENMPIFLRVSATDWLEESQPNQPSWQVQDTVRFATALAD 303

Query: 146 SGVNGIWIHARKAILKGLSPKDNR--KIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQ 202
           SG   +       +  G +         P         +KK   D L +   G +++   
Sbjct: 304 SGAVDVI-----DVSSGGTHAAQHIHARPAFQAPFAIAVKKAVGDKLAVATVGMIDNAHL 358

Query: 203 ALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           A  +L    +D V+IGR   KN  ++    E  +  ++ ++ I+
Sbjct: 359 ANSLLEEDGLDLVLIGRGFLKNPGLVWAFAEQLNLEISMANQIR 402


>gi|11498861|ref|NP_070090.1| NADH oxidase (noxB-2) [Archaeoglobus fulgidus DSM 4304]
 gi|2649317|gb|AAB89981.1| NADH oxidase (noxB-2) [Archaeoglobus fulgidus DSM 4304]
          Length = 632

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/187 (14%), Positives = 61/187 (32%), Gaps = 17/187 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA   +  G++ + L             P+       +G  L        + I  
Sbjct: 142 EEFADAAVRAKKAGFDAVELIGSAGYLISQFFSPATNKRTDEYGGSLENRTRFAVEIIQK 201

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +    S PV ++      ++       ++ + K ++ +GV  + I+      +   P 
Sbjct: 202 IKEKCGESYPVMIRIPGDEFIEGGNTVREMKQIAKILEDAGV--VAINVMAGWHESRKPL 259

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG--RAAYKNSA 224
               +P   +  +    K    + +  +  + D   A KIL      M+   RA   +  
Sbjct: 260 TTMLVPRGGFAYLAAEIKSAVSVSVIASHRINDPIVAEKILQEGKADMVAMLRALIADPE 319

Query: 225 MLTTVDE 231
           +     E
Sbjct: 320 LPKKAKE 326


>gi|319647866|ref|ZP_08002084.1| YqiG protein [Bacillus sp. BT1B_CT2]
 gi|317390207|gb|EFV71016.1| YqiG protein [Bacillus sp. BT1B_CT2]
          Length = 364

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 32/218 (14%), Positives = 68/218 (31%), Gaps = 27/218 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDC 107
               + A+   + G++ + +             P       S+G  L   M  P  + + 
Sbjct: 144 HSFGQTARRAIEAGFDGVEIHGANGFLIHQFFSPYYNRRNDSWGGTLEKRMRFPLQIIEE 203

Query: 108 IAAMCKALSIP---VTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           I  +  +   P   +  K      +   I      + V  +++ G++ + +     +   
Sbjct: 204 IRRVADSCHKPSFIIGYKFSPEEPETPGITMDETLSFVNVLREQGLDYLHV---SLVDFR 260

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYK 221
             P+          +++ E  ++   L +   G +     AL+ L    D + IGR    
Sbjct: 261 SLPRRGADRSRARMELIKEAVQDR--LPLIGAGQVHTPEDALQALETGADLIGIGRGLLM 318

Query: 222 NSAMLTTVDE----YFSNPLTGSSPIKTRVDKDFWRKI 255
           +   L  V           L+     K  +   FW  I
Sbjct: 319 DPEWLQKVRAGKEDDIQTTLSRHDQRKLAIPDAFWESI 356


>gi|269962122|ref|ZP_06176476.1| 2,4-dienoyl-CoA reductase [Vibrio harveyi 1DA3]
 gi|269833206|gb|EEZ87311.1| 2,4-dienoyl-CoA reductase [Vibrio harveyi 1DA3]
          Length = 670

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/132 (17%), Positives = 50/132 (37%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K++++SGV    I+      +
Sbjct: 199 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKALEESGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIITCNRINTPDEAERILSSGHADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|294934773|ref|XP_002781232.1| hypothetical protein Pmar_PMAR005076 [Perkinsus marinus ATCC 50983]
 gi|239891570|gb|EER13027.1| hypothetical protein Pmar_PMAR005076 [Perkinsus marinus ATCC 50983]
          Length = 114

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 25/36 (69%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGD 36
           MVD +DR +R F RLL++   ++TEM+V  A++  +
Sbjct: 71  MVDVSDRDFRMFMRLLSSKCEVWTEMLVDQALVHNE 106


>gi|315647803|ref|ZP_07900904.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus vortex V453]
 gi|315276449|gb|EFU39792.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus vortex V453]
          Length = 345

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 67/208 (32%), Gaps = 26/208 (12%)

Query: 54  IGGADISKLVE----AAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +   ++ ++VE    A +     G++ I L             P     +  +G  L   
Sbjct: 133 LSTEEVQQMVEKFRLAVRRAVKAGFDAIELHGAHGYLIHQFHSPLTNQRKDEYGQDLTK- 191

Query: 101 PDIVGDCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                + I A    +   +P+ ++   R  V             K  + +GV+   I   
Sbjct: 192 --FGKEVIQAAKSEMPEDMPLIMRISAREYVTGGYGIQESIAFAKEYQAAGVDMFHI--- 246

Query: 157 KAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGV 213
            A  +G    + R   ++ Y + +    KE   + +   G L++ + A  ++     D V
Sbjct: 247 SAGGEGPIAAEGRPGTHVAYQVPLARQIKEALQVPVIAVGRLDEPALANAVVGNEEADLV 306

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +GR   +N                  +
Sbjct: 307 AVGRGMLRNPYWALEAAAVLQKETAIPT 334


>gi|94495320|ref|ZP_01301901.1| putative NADH:flavin oxidoreductase [Sphingomonas sp. SKA58]
 gi|94425586|gb|EAT10606.1| putative NADH:flavin oxidoreductase [Sphingomonas sp. SKA58]
          Length = 370

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 30/163 (18%), Positives = 52/163 (31%), Gaps = 20/163 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
               +AA+     G   + ++            P +      +G  L   M  P  V D 
Sbjct: 160 EAFADAARRAGRLGIEAVQIHAAHGYLLHEFLSPISNRRGDEYGGSLDNRMRFPLEVFDA 219

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +     A   PVTV+      V+    A       + +K+ G   I +        GL P
Sbjct: 220 VRESFPA-DRPVTVRVSGTDWVEGGWTAEETARFAQELKRRGCAAIHVSGG-----GLDP 273

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           +    +       +    K+   + +   G + D  QA +IL 
Sbjct: 274 RQQIPVGPGYQVPLARTVKDAVAMPVIAVGLITDPHQAERILE 316


>gi|294011963|ref|YP_003545423.1| putative oxidoreductase [Sphingobium japonicum UT26S]
 gi|292675293|dbj|BAI96811.1| putative oxidoreductase [Sphingobium japonicum UT26S]
          Length = 367

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/132 (20%), Positives = 48/132 (36%), Gaps = 17/132 (12%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRI-------GVDDQIPAVALRNLV-KSIKKSGVNGIWIH 154
           ++ +   A+   +   V V  RI              A     ++  S+ ++G + I + 
Sbjct: 213 LILETFKAVRAKVGAKVPVGVRISQGKVNDYHHKWADAERDAEIIFGSLAEAGADFIHVT 272

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
             +A     +P+    +           K+  P   I  NGGL ++ QA+  L    D V
Sbjct: 273 EFEAWKPAFAPEGPSLMRLA--------KRYAPKAAIFANGGLHNIEQAVAALDDGADIV 324

Query: 214 MIGRAAYKNSAM 225
            I R A  N  +
Sbjct: 325 TIARGALANPDL 336


>gi|157692491|ref|YP_001486953.1| NADH-dependent flavin dehydrogenase [Bacillus pumilus SAFR-032]
 gi|157681249|gb|ABV62393.1| NADH-dependent flavin dehydrogenase [Bacillus pumilus SAFR-032]
          Length = 344

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/145 (17%), Positives = 51/145 (35%), Gaps = 12/145 (8%)

Query: 106 DCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A  + +   +P+ ++   +  VD          L  +  ++G     I    +  +
Sbjct: 197 EILKAAKEEIPDDMPLIMRISAKEYVDGGYNIQDAIELANAYHQAGAEIFDI---TSGGE 253

Query: 162 GLSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGR 217
           G  P  NR   +  Y +    EIKK   ++ +   G L+D   A  +  +   D V +GR
Sbjct: 254 GQIPAMNRPGTHAAYQVPLAREIKKAL-NVPVIAVGRLDDPILANAVVGMEDADLVAVGR 312

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSP 242
              +N        +          P
Sbjct: 313 GMLRNPYWAMEAAKQLKKSTDELVP 337


>gi|193078270|gb|ABO13234.2| putative FMN oxidoreductase [Acinetobacter baumannii ATCC 17978]
          Length = 369

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 56/149 (37%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D   A +IL     D + + RA   + 
Sbjct: 306 ITDPQHAEQILENQQADAIGLARAMLYDP 334


>gi|126642852|ref|YP_001085836.1| putative FMN oxidoreductase [Acinetobacter baumannii ATCC 17978]
          Length = 346

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 56/149 (37%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 169 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 228

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 229 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 282

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D   A +IL     D + + RA   + 
Sbjct: 283 ITDPQHAEQILENQQADAIGLARAMLYDP 311


>gi|187919110|ref|YP_001888141.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
 gi|187717548|gb|ACD18771.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
          Length = 365

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 30/183 (16%), Positives = 64/183 (34%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AAK   D G+  + L+       + +            ++G  L      + + +
Sbjct: 158 EDFVAAAKRALDAGFEWLELHFA--HGYLGQSFFSTHSNQRDDAYGGSLENRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           AA+ K     +P+T +         D+   V    L K+ K+ G++ + +      +   
Sbjct: 216 AAVRKVWPEHLPLTARFGVIEYDGRDEETLVESIELAKNFKREGLDMLSV-----SVGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           +P             + E  +    + +    G++    A + +    +D VM+GRA   
Sbjct: 271 TPTAAIPWAPAFLAPIAERVRREAGIPVSSAWGIDTPELADRSVKDGQLDLVMVGRAHLA 330

Query: 222 NSA 224
           +  
Sbjct: 331 DPH 333


>gi|239501758|ref|ZP_04661068.1| NADH:flavin oxidoreductase [Acinetobacter baumannii AB900]
          Length = 369

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 56/149 (37%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D   A +IL     D + + RA   + 
Sbjct: 306 ITDPQHAEQILENQQADAIGLARAMLYDP 334


>gi|213970373|ref|ZP_03398502.1| NADH:flavin oxidoreductase / NADH oxidase family [Pseudomonas
           syringae pv. tomato T1]
 gi|301381156|ref|ZP_07229574.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Pseudomonas syringae pv. tomato Max13]
 gi|302063122|ref|ZP_07254663.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Pseudomonas syringae pv. tomato K40]
 gi|302132569|ref|ZP_07258559.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Pseudomonas syringae pv. tomato NCPPB 1108]
 gi|213924844|gb|EEB58410.1| NADH:flavin oxidoreductase / NADH oxidase family [Pseudomonas
           syringae pv. tomato T1]
          Length = 365

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 51/135 (37%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  D IA + KA    PV V+   G  +              ++  ++  +GV+ I
Sbjct: 209 QRLRLTLDVIAEVKKAAGQAPVGVRISQGKVNDFQHKWAGGERDAEIIFGALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            I   +A                +  +V   ++  PD+ +  NGGL D  +A ++     
Sbjct: 269 HITEHQAW--------QPAFAQGEASLVRLARRYAPDVALIANGGLHDPEKAAQVFRDGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|284164807|ref|YP_003403086.1| NADH:flavin oxidoreductase/NADH oxidase [Haloterrigena turkmenica
           DSM 5511]
 gi|284014462|gb|ADB60413.1| NADH:flavin oxidoreductase/NADH oxidase [Haloterrigena turkmenica
           DSM 5511]
          Length = 368

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 29/166 (17%), Positives = 56/166 (33%), Gaps = 21/166 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC--------RIGVDDQIPAVALRNLVKS 142
           +G        +V + + A+ +      PV V+         R   D        R     
Sbjct: 208 YGGSFENRTRLVREVVEAVREVWPDDKPVFVRISGTDWLDDRESWDIDQSVRLAREFADL 267

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
               GV+ + + +      GL P             + E  +E  D+ +G  GG+ + +Q
Sbjct: 268 ----GVDLVDVSSG-----GLHPDQRVPGGPNFQVPLAEAVREGSDVAVGAVGGVTEPAQ 318

Query: 203 ALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           A  I+ +   D V++GR   ++            +      P++ R
Sbjct: 319 ADAIVRNGRADLVLVGRQFLRDPYFGLRAAGELEDDAAPHWPVQYR 364


>gi|118471340|ref|YP_887288.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium smegmatis
           str. MC2 155]
 gi|118172627|gb|ABK73523.1| NADH:flavin oxidoreductase/nadh oxidase [Mycobacterium smegmatis
           str. MC2 155]
          Length = 377

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/142 (17%), Positives = 47/142 (33%), Gaps = 7/142 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +G  +     +     AA+  A+     V  R+                  + + V    
Sbjct: 201 YGGTVAHRIRLAAQISAAVRTAVGADFLVGVRLSQ--TKVNDFEYRWPGGAQDAEVIFTA 258

Query: 153 IHARKAILKGLSPKDNRKIPNLDYD---IVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
           + A       ++ +    I     D    +  + ++   L +  NGG+ D +QA  +L  
Sbjct: 259 LAATGIDYLHIASEGRDFIDGARLDDGRTITALARQVTGLPVIANGGMHDTTQAAGVLDG 318

Query: 210 --VDGVMIGRAAYKNSAMLTTV 229
              D + IGR A  N  +   V
Sbjct: 319 GHADVLSIGRGALANPDLPQRV 340


>gi|171742991|ref|ZP_02918798.1| hypothetical protein BIFDEN_02116 [Bifidobacterium dentium ATCC
           27678]
 gi|283455993|ref|YP_003360557.1| dihydroorotate dehydrogenase [Bifidobacterium dentium Bd1]
 gi|306822800|ref|ZP_07456176.1| dihydroorotate oxidase [Bifidobacterium dentium ATCC 27679]
 gi|309801311|ref|ZP_07695440.1| dihydroorotate oxidase, catalytic subunit [Bifidobacterium dentium
           JCVIHMP022]
 gi|171278605|gb|EDT46266.1| hypothetical protein BIFDEN_02116 [Bifidobacterium dentium ATCC
           27678]
 gi|283102627|gb|ADB09733.1| Dihydroorotate dehydrogenase [Bifidobacterium dentium Bd1]
 gi|304553432|gb|EFM41343.1| dihydroorotate oxidase [Bifidobacterium dentium ATCC 27679]
 gi|308222200|gb|EFO78483.1| dihydroorotate oxidase, catalytic subunit [Bifidobacterium dentium
           JCVIHMP022]
          Length = 317

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/219 (16%), Positives = 74/219 (33%), Gaps = 24/219 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
            +   + G       E    + D   + + +NV CP    +  + G  +  +P  +   I
Sbjct: 109 NVIANVAGHCDDDYAEVVAKLNDSPADMLEINVSCP----NVSAGGMSVGTDPVALSRLI 164

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARK 157
             + K     + VK    V D           ++  +SG + +            I   +
Sbjct: 165 TRLRKITDKKMIVKLTPNVTDITVP------ARAAVESGADALSLINTLLGMRINIRTGE 218

Query: 158 AILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMI 215
            I+  +        +  +    V+ ++   P++ I   GG++   +AL+ L    + V +
Sbjct: 219 PIITHVTGGVSGPAVLPVGLAAVWRVRTALPEVPIIGIGGIDSGEKALEYLYAGANAVEV 278

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
           G AA         V       L     +  ++ K + WR
Sbjct: 279 GAAALFEPTAPLRVARELDALLDARPELADKLAKGETWR 317


>gi|325914429|ref|ZP_08176776.1| NADH:flavin oxidoreductase [Xanthomonas vesicatoria ATCC 35937]
 gi|325539437|gb|EGD11086.1| NADH:flavin oxidoreductase [Xanthomonas vesicatoria ATCC 35937]
          Length = 376

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/174 (17%), Positives = 55/174 (31%), Gaps = 13/174 (7%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNL 139
           P +     ++G  L     +      A+  A+S  + V  RI     VD          L
Sbjct: 202 PLSNQRSDAYGGSLENRMRLTLRIFDAVRAAVSERIAVGVRISATDWVDGGWDLEQSIAL 261

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLE 198
            K++   G + I + +      GL P+    +    Y I   +  K      +   G + 
Sbjct: 262 SKALDARGAHYIHVSSG-----GLDPRQQIAV-QAGYQIPFAQQIKAQVATPVIGVGLIT 315

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           + +QA  IL     D + + R    +              +T +        +D
Sbjct: 316 EPAQAEAILQDGQADAIALARGILYDPRWPWHAAAALGASVTPAPQYLRCEPRD 369


>gi|238025209|ref|YP_002909441.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia glumae BGR1]
 gi|237879874|gb|ACR32206.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia glumae BGR1]
          Length = 370

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 55/148 (37%), Gaps = 12/148 (8%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALR---N 138
           P A   +  +G         + + +AA+ +     +P+T +  +   D   A  L    N
Sbjct: 191 PHANQRDDDYGGSWTKRGRFLNETLAAVREVWPERLPLTARFGVIEYDGNDAATLDASIN 250

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L    K+ G++ + +      +   +P  N          +    K+   L +    G++
Sbjct: 251 LAGDFKRGGLDLLSV-----SIGFSTPAANIPWGPAFLAPIAARVKQETGLPVASAWGID 305

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSA 224
           D   A + +    +D VM+GRA   N  
Sbjct: 306 DPVIANRTVADAQLDLVMVGRAHLANPH 333


>gi|254429598|ref|ZP_05043305.1| oxidoreductase, FAD/FMN-binding family [Alcanivorax sp. DG881]
 gi|196195767|gb|EDX90726.1| oxidoreductase, FAD/FMN-binding family [Alcanivorax sp. DG881]
          Length = 672

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 57/180 (31%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL-----------NVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
                A + +  GY+ + +              C + R  +  +G           + + 
Sbjct: 146 DFAHTAWLAKKAGYDGVEIMGSEGYLINQFTASCTNKR--KDKYGGSAENRRRFPVEIVR 203

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSP 165
            + K       V  RI V D +P  A R     L K ++ +G + +  ++     +   P
Sbjct: 204 EVRKRCGDDFIVMFRISVVDLVPDGATREEVLALAKEVEAAGASLL--NSGIGWHEARVP 261

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                +P   +       K+   + +  +  + D   A  IL     D V + R    + 
Sbjct: 262 TIVTSVPRAAFVEATRQVKDVVSIPVVASNRINDPDVAEAILVAGQADAVSMARPLLADP 321


>gi|52841679|ref|YP_095478.1| hypothetical protein lpg1449 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52628790|gb|AAU27531.1| hypothetical protein lpg1449 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 870

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 75/237 (31%), Gaps = 41/237 (17%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSIPVTVKCRI------GVDD 129
           I +N+ CP+A V     G  L   PD +   + A+  A  ++ V  K  +        D 
Sbjct: 542 IGINMCCPAASVENIGSGFGLRNKPDFIERIVKAIKDADSNLKVEFKTLMLSHEDGYGDG 601

Query: 130 QIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRKIPNLDYDIVYEIK--KEN 186
              +   +N+ +   +     ++   A + + +G          +    I+ E+   KE 
Sbjct: 602 DQISGNTKNISEIQNECLTRIVYKTKANRLVYQGKPRNIETYNVDAVSCIIREVNTPKEF 661

Query: 187 -----PDLFIGLNGGLE------------DMSQALKILPSVDG-------VMIGRAAYKN 222
                  +    N  +              +   L+ +    G       VM+GR    +
Sbjct: 662 QFGYSGMVATITNHDINQLGYKVVGEPHYSVQSILEKIKKQLGEVPIEFEVMLGRVLLGS 721

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR--HLHSGGKLQQIT 277
           + +L     Y S+       +     +  W   +  M  Y      +     ++ IT
Sbjct: 722 AWVLQG--RYASDAEILLHTLFQAAIEQEW---ARGMGRYGIDIYQIQVLYNIRHIT 773


>gi|289449538|ref|YP_003475871.1| putative NADPH dehydrogenase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
 gi|289184085|gb|ADC90510.1| putative NADPH dehydrogenase [Clostridiales genomosp. BVAB3 str.
           UPII9-5]
          Length = 313

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/193 (15%), Positives = 66/193 (34%), Gaps = 27/193 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIA 109
           + V AA  V+  G++ + +   C           P     E  +G  +     +  + + 
Sbjct: 128 EFVAAALRVKTAGFDGVEI--HCAHGYLLNQFYSPRKNHREDEYGGDVAGRLRLTCEILT 185

Query: 110 AMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            + +A+     + V        ++      +    K + ++G + I I      L G   
Sbjct: 186 EVRRAVGADYLVAVRFGAVDYRENGSLLTEVAPAAKLLVQAGADLIDISGG---LTGFMR 242

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           +D   +    +    +  K    + + L GG+     A  +L +   D + +GR   +N 
Sbjct: 243 RDC--VTPGWFKAEAQAAKIGGGVSVLLTGGITSRETAEDLLAAGVCDLIGVGRPLLQNP 300

Query: 224 AMLTTVDEYFSNP 236
            +   +D    N 
Sbjct: 301 GV---IDALLGND 310


>gi|150015451|ref|YP_001307705.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
 gi|149901916|gb|ABR32749.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
          Length = 346

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 66/193 (34%), Gaps = 21/193 (10%)

Query: 65  AAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AAK   + GY+ I +             P        +G  L      + + + A+ +  
Sbjct: 148 AAKRCIEIGYDIIEIHGAHGYLINQFLSPLTNKRTDEYGGNLENRARFLKEVVKAVREVW 207

Query: 116 --SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
               P+ ++      +++      L  ++  +K+ G++ I + +      G++P      
Sbjct: 208 TKEKPIILRISAEDYLNEGNHPEDLAKIINLVKEEGIDIINVSSG-----GVAPTPVPIK 262

Query: 172 PNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
               Y I   EI KEN  L +   G +     A +I+ +   D + +GR   +       
Sbjct: 263 VYEGYQIKFAEIIKENTGLPVIAGGLIISPYMAEEIIQNDRADMIFLGRILLRKPYWPLE 322

Query: 229 VDEYFSNPLTGSS 241
            D      +    
Sbjct: 323 ADSKLDGEVKWPE 335


>gi|213692922|ref|YP_002323508.1| NADH:flavin oxidoreductase/NADH oxidase [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|213524383|gb|ACJ53130.1| NADH:flavin oxidoreductase/NADH oxidase [Bifidobacterium longum
           subsp. infantis ATCC 15697]
          Length = 371

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 54/152 (35%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A+   V V  RI   D             L K +K+ GV
Sbjct: 212 YGGDLTGRSRFLVEVVDAVRGAVPEGVPVLVRISATDWAAGGWDLDQSIALSKVLKEHGV 271

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 272 DVMDVSTGGIM----SGVSIPVKPNYQVPFAEQVKSKA-DIPVTAVGLITKPKQAAKILA 326

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 327 HGEADAVEIGRAALRDPYWPLRAANKLGIPST 358


>gi|148265580|ref|YP_001232286.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter uraniireducens
           Rf4]
 gi|146399080|gb|ABQ27713.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter uraniireducens
           Rf4]
          Length = 653

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 64/187 (34%), Gaps = 17/187 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              ++A  V + G++ I L  G          P        +G  L          IAA+
Sbjct: 147 YFAKSAIHVREGGFDGIELQFGHSSLARQFLSPLTNFRNDEYGGSLENRMRAPLKFIAAV 206

Query: 112 CKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            KA+    T+  R+  D+ IP       ++ +    + SG+    +    A    L   +
Sbjct: 207 RKAVGNDFTLGIRMCADEMIPGGLDLAQVQEICARFEASGLIDF-MDLSIATFYNLYLVE 265

Query: 168 NRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG--RAAYKNSA 224
                 L Y I +    +E   L +   G + D   A K+L +    MIG  R    +  
Sbjct: 266 GSMHTPLGYTIPLAAGIRERIKLPVFCTGRINDPVMAEKVLANGQADMIGMCRGLICDPF 325

Query: 225 MLTTVDE 231
           +     E
Sbjct: 326 LPKKAQE 332


>gi|184159396|ref|YP_001847735.1| NADH:flavin oxidoreductase [Acinetobacter baumannii ACICU]
 gi|183210990|gb|ACC58388.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family [Acinetobacter
           baumannii ACICU]
 gi|322509308|gb|ADX04762.1| Putative FMN oxidoreductase [Acinetobacter baumannii 1656-2]
 gi|323519335|gb|ADX93716.1| NADH:flavin oxidoreductase [Acinetobacter baumannii TCDC-AB0715]
          Length = 369

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 57/149 (38%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D  QA +IL     D + + RA   + 
Sbjct: 306 ITDPQQAEQILENQQADAIGLARAMLYDP 334


>gi|126664202|ref|ZP_01735194.1| hypothetical protein FBBAL38_12070 [Flavobacteria bacterium BAL38]
 gi|126623734|gb|EAZ94430.1| hypothetical protein FBBAL38_12070 [Flavobacteria bacterium BAL38]
          Length = 766

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 77/236 (32%), Gaps = 32/236 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
           + V+AAK  ++ G++ I L             P   + +  FG  +   +  P  V   I
Sbjct: 541 QFVQAAKNADEAGFDMIELQAHHGFLLASFLSPLTNIRKDEFGGSIENRLKYPLEVFKAI 600

Query: 109 AAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +      P++V+       ++ I    +  +  + K +G + I +     +  G  P 
Sbjct: 601 REVF-PTDKPISVRISATDWSENGISEQEVTTIATAFKAAGADIINVSTGNTVA-GQKPL 658

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA---AYKNS 223
             R       D V    +    +     G ++D+ Q   IL +      GRA   A    
Sbjct: 659 TGRMWQTPFSDAV----RNTVHIPTITAGYIQDIDQINTILLN------GRADLVALGRP 708

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
            +L   D  F          +     + ++   + +    A        +++  + 
Sbjct: 709 LLL---DANFVRNAQAYEQFQANDIPNPYKMGVSHLYPLKASEKKQVEGMKKSLKP 761


>gi|302886531|ref|XP_003042155.1| hypothetical protein NECHADRAFT_69841 [Nectria haematococca mpVI
           77-13-4]
 gi|256723064|gb|EEU36442.1| hypothetical protein NECHADRAFT_69841 [Nectria haematococca mpVI
           77-13-4]
          Length = 429

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 70/191 (36%), Gaps = 24/191 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+ +E  G++ I L             P        +G  L     IV +  + 
Sbjct: 175 EGFAHAAEYLEKAGFDGIELHGAHGYLIAQFLSPRTNKRTDEYGGNLENRSRIVFEIASE 234

Query: 111 MCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAI 159
           + K +S    +  +        + I     +NL  +++ +  + I I          K +
Sbjct: 235 IRKRVSPKFILGIKINSVEYQPEGITLDDAKNLSIALENAHFDFIEISGGNYEKLAFKHV 294

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
            +    ++N  +   + +I+  +K E     +   GG +     +  L ++DGV +GRAA
Sbjct: 295 KEENRKRENYFLTQAE-EIIKSLKGETR---VFSTGGFKTTEGLVNSLATLDGVGLGRAA 350

Query: 220 YKNSAMLTTVD 230
            ++  +   + 
Sbjct: 351 CQDPGLPNAIK 361


>gi|220904914|ref|YP_002480226.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219869213|gb|ACL49548.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 365

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 38/195 (19%), Positives = 68/195 (34%), Gaps = 25/195 (12%)

Query: 49  PLALQIGGADISK----LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGA 95
           P+   +  ADI +     V AA+  +  GY  + L+            P +   E  +G 
Sbjct: 142 PVPSALSTADIDRLTASFVTAAQRAQRAGYKAVELHAAHGYLLHEFLSPLSNKREDEYGG 201

Query: 96  CLMLNPDIVGDCIAAMCKALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGI 151
            L           AA+ KAL   IPV ++                  L + ++K+G   I
Sbjct: 202 SLENRMRFPLQVFAAVRKALPSVIPVGMRVSGTDFTPGGWDVQECAVLAQRLEKAGGAFI 261

Query: 152 WIHARKAILKGLSPKD-NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA--LKILP 208
            +        GL+P+   R  P     +   +K+    + +   G + +   A  + +  
Sbjct: 262 HVSGG-----GLTPEQKIRLAPGYQVHLAQAVKQAVDSMPVIAVGLITEPELAAGIIVTG 316

Query: 209 SVDGVMIGRAAYKNS 223
             D V +GR    + 
Sbjct: 317 QADMVAVGRGMMYDP 331


>gi|313900697|ref|ZP_07834190.1| putative NADH oxidase [Clostridium sp. HGF2]
 gi|312954759|gb|EFR36434.1| putative NADH oxidase [Clostridium sp. HGF2]
          Length = 648

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/179 (15%), Positives = 65/179 (36%), Gaps = 17/179 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG----------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
           +  EAA  V+  G + + ++             P        +G  +     +  + +  
Sbjct: 148 QFGEAALRVKQAGGDGVEIHAAHAHGLLGGFLTPLYNKRCDEYGGDINGRLKLTLEVVEE 207

Query: 111 MCKALSIPVTVKCRIGVDD-QIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPK 166
           +         +  RI  D+     + L +++   K ++  G + + +     I +G +  
Sbjct: 208 VRSVCGPDFIIDVRISGDEYSDGGLNLDDMIYVSKQLETHGADMLHVSGGTTIKRGSAIP 267

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                P +   +  EIKK   ++ +   G + +   A +++ +   D  MIGRA   + 
Sbjct: 268 AAGTKPGVHAHLSQEIKKHV-NIPVATVGRITEPWIADELIANGKADICMIGRANLCDP 325


>gi|260557196|ref|ZP_05829412.1| NADH:flavin oxidoreductase [Acinetobacter baumannii ATCC 19606]
 gi|260409302|gb|EEX02604.1| NADH:flavin oxidoreductase [Acinetobacter baumannii ATCC 19606]
          Length = 369

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 57/149 (38%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D  QA +IL     D + + RA   + 
Sbjct: 306 ITDPQQAEQILENQQADAIGLARAMLYDP 334


>gi|167760350|ref|ZP_02432477.1| hypothetical protein CLOSCI_02724 [Clostridium scindens ATCC 35704]
 gi|167662023|gb|EDS06153.1| hypothetical protein CLOSCI_02724 [Clostridium scindens ATCC 35704]
          Length = 648

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 71/192 (36%), Gaps = 17/192 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG----------CPSARVHEGSFGACL 97
           +P+ ++     I +  EAA  V+  G + + ++             P        +G  +
Sbjct: 135 RPVTVEELHTIIRQFGEAALRVKKAGADGVEIHAAHAHGLLGGFLSPLYNKRTDEYGGDI 194

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLV---KSIKKSGVNGIWI 153
                +  + +A + K       +  RI  D+     + L + +   K ++K+GV+ + +
Sbjct: 195 NGRLRLTLEVVAEVRKMCGPEFIIDVRISGDEYSDGGLNLNDAIYVSKQLEKTGVDMLHV 254

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
                I +G S             +  EIKK    + +   G + +   A +++ +   D
Sbjct: 255 SGGTTIKRGSSIPAPGTKMGSHSALSAEIKKHV-SIPVATVGRITEPWLAEELIANDKAD 313

Query: 212 GVMIGRAAYKNS 223
             MIGRA     
Sbjct: 314 ICMIGRANLCEP 325


>gi|313672971|ref|YP_004051082.1| dihydroorotate oxidase b, catalytic subunit [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939727|gb|ADR18919.1| dihydroorotate oxidase B, catalytic subunit [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 304

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 77/204 (37%), Gaps = 23/204 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           +  + +   G  + + +E A+++++   + + +N+ CP+ +      G     +P +  +
Sbjct: 94  DTKIIVNFWGKMLEEYIEVARVLDEEDVDMLEMNISCPNIK----EGGIAFGTDPKMTYE 149

Query: 107 CIAAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IH 154
            +    K + + P+ VK    V        ++   K  +++G + I            I+
Sbjct: 150 VVYNCKKVMKNKPLVVKLSPNV------TNIKVFGKVAEEAGADAISAINTLLGMAININ 203

Query: 155 ARKAILKG-LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
            RK  L           I  +   +VYE+ K      IG+ G +         L     V
Sbjct: 204 TRKPFLSNITGGLSGPAIKPVAIRMVYELYKTIKIPIIGIGGIMSYRDVIEFYLAGASAV 263

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPL 237
            +G A + +  +   + +  +N L
Sbjct: 264 QVGTANFVDPEIPIKIIDELNNYL 287


>gi|58583969|ref|YP_202985.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84625752|ref|YP_453124.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzae MAFF 311018]
 gi|58428563|gb|AAW77600.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84369692|dbj|BAE70850.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzae MAFF 311018]
          Length = 372

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 67/208 (32%), Gaps = 24/208 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +A+  E  G   I L+            P +     ++G  L     +      A
Sbjct: 165 DAFVASAQRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMRLTLRIFDA 224

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + +  RI   D             L +++   G + I + +      GL P+
Sbjct: 225 VRAAVSEKIAIGVRISATDWVEGGWDVQQSIALSQALDARGAHYIHVSSG-----GLDPR 279

Query: 167 DNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
               +    Y I    EI+ +     IG+ G + + +QA  I+     D + + R    +
Sbjct: 280 QQIPL-QAGYQIPFAQEIRAQVSRPVIGV-GLITEPAQAEAIVQEGQADAIALARGILYD 337

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                         +T +        +D
Sbjct: 338 PRWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|34581030|ref|ZP_00142510.1| nifR3-like protein [Rickettsia sibirica 246]
 gi|28262415|gb|EAA25919.1| nifR3-like protein [Rickettsia sibirica 246]
          Length = 79

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           M +  +      A  +A+ +PVTVK R+G DD         L K  + SGV  
Sbjct: 1   MRDEQLAAKIFEATVEAVKLPVTVKMRMGWDDNTKNA--PTLAKIAESSGVQM 51


>gi|56420867|ref|YP_148185.1| NADPH dehydrogenase NamA [Geobacillus kaustophilus HTA426]
 gi|68052472|sp|Q5KXG9|NAMA_GEOKA RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|292659591|pdb|3GR7|A Chain A, Structure Of Oye From Geobacillus Kaustophilus, Hexagonal
           Crystal Form
 gi|292659592|pdb|3GR7|B Chain B, Structure Of Oye From Geobacillus Kaustophilus, Hexagonal
           Crystal Form
 gi|292659593|pdb|3GR8|A Chain A, Structure Of Oye From Geobacillus Kaustophilus,
           Orthorhombic Crystal Form
 gi|292659594|pdb|3GR8|B Chain B, Structure Of Oye From Geobacillus Kaustophilus,
           Orthorhombic Crystal Form
 gi|56380709|dbj|BAD76617.1| NADH-dependent flavin oxidoreductase [Geobacillus kaustophilus
           HTA426]
          Length = 340

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 76/193 (39%), Gaps = 23/193 (11%)

Query: 49  PLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEGSFGA 95
           P   ++  ADI + V+A    A+  ++ G++ I ++            P +   +  +G 
Sbjct: 129 PTPKEMTKADIEETVQAFQNGARRAKEAGFDVIEIHAAHGYLINEFLSPLSNRRQDEYGG 188

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                   +G+ I A+ +    P+ V+        D + A       K +K+ GV+ + +
Sbjct: 189 SPENRYRFLGEVIDAVREVWDGPLFVRISASDYHPDGLTAKDYVPYAKRMKEQGVDLVDV 248

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
            +   +   ++     ++P        E+ +   D+  G  G +    QA +IL +   D
Sbjct: 249 SSGAIVPARMNVYPGYQVPFA------ELIRREADIPTGAVGLITSGWQAEEILQNGRAD 302

Query: 212 GVMIGRAAYKNSA 224
            V +GR   +N  
Sbjct: 303 LVFLGRELLRNPY 315


>gi|308071403|ref|YP_003873008.1| NADH-dependent flavin oxidoreductase yqjM [Paenibacillus polymyxa
           E681]
 gi|305860682|gb|ADM72470.1| Probable NADH-dependent flavin oxidoreductase yqjM [Paenibacillus
           polymyxa E681]
          Length = 342

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 61/179 (34%), Gaps = 21/179 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           K  +AA+     G + I L             P     +  +G  L        + I A+
Sbjct: 146 KFADAARRAVQAGVDTIELHGAHGYLIHQFHSPVTNKRDDVYGQEL---SRFGVEVIQAV 202

Query: 112 CKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            K +   +P+ ++      VD          L ++ + +GV+ I +        G     
Sbjct: 203 RKQMPAGMPLILRISAVEYVDGGYDVDHAIELSRAYQAAGVDVIHVSTGGEGPAGARKPG 262

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNSA 224
           N     + +       +E  ++ +   G L+D + A  ++ + D   V + R   ++  
Sbjct: 263 NYPGYQVPF---ARQIREALNIPVIAVGALDDPALAQSVIGNEDADLVAVARGLLRDPY 318


>gi|302672141|ref|YP_003832101.1| dihydroorotate dehydrogenase PyrD [Butyrivibrio proteoclasticus
           B316]
 gi|302396614|gb|ADL35519.1| dihydroorotate dehydrogenase PyrD [Butyrivibrio proteoclasticus
           B316]
          Length = 301

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 35/183 (19%), Positives = 66/183 (36%), Gaps = 15/183 (8%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARV 88
           D  +  D K +  + T+   + + + G  +   +E  + + ++   + + +NV CP    
Sbjct: 78  DVFVERDLKFLEDYDTK---VIVNVCGKSVEDYLEVVERLGDESRVDMLEINVSCP---- 130

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +          N D + D  + + K    PV +K    V              +   S +
Sbjct: 131 NVKEGAIAFGQNKDALYDITSRIKKVAKQPVIMKLSPNVTSIAEMARAAEAAGADAISLI 190

Query: 149 NGIW-----IHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           N I      IH RK A+           I  +   +VYE         IG+ GG+ +   
Sbjct: 191 NTITGMKIDIHKRKFALANKTGGMSGPAIKPVAVRMVYEASHAVKIPVIGM-GGIANGDD 249

Query: 203 ALK 205
           A++
Sbjct: 250 AIE 252


>gi|302186705|ref|ZP_07263378.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           syringae 642]
          Length = 365

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 51/135 (37%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  + IAA+ K A   PV V+   G  +              ++  ++  +GV+ I
Sbjct: 209 QRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFAALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A     +      +            +  PD+ +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAWQPAFAQSKATLVELAH--------RYAPDIALIANGGLHDPEKADQVLRQGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|242398432|ref|YP_002993856.1| Dihydroorotate dehydrogenase family protein [Thermococcus sibiricus
           MM 739]
 gi|242264825|gb|ACS89507.1| Dihydroorotate dehydrogenase family protein [Thermococcus sibiricus
           MM 739]
          Length = 309

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 58/178 (32%), Gaps = 29/178 (16%)

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP+ +            +  +    +  + K    P+  K    V D      +  +
Sbjct: 128 NLSCPNVKGKRRWA-----EDAKLTEKVVKIVRKLTGKPIIAKLAPDVTD------IVEI 176

Query: 140 VKSIKKSGVNGIWI-----HARKAILKGLSPKDNRKIPNLDYDIVYEIK-------KENP 187
            K+   +G +G+ I       R  +  GL P    K   L    V  I        +E  
Sbjct: 177 AKTAVDAGADGLTIGNGAQAMRIDVETGL-PILKLKTGGLGGPAVKPITLAKVFKTREAL 235

Query: 188 DLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA----MLTTVDEYFSNPLTGS 240
           D+ I   GG+ +   A++  +     + +G A   +      ++  +  +       S
Sbjct: 236 DVPIIGIGGIMNWQDAIEYAMAGASLLGLGTAVMVDPEAPVRIIEGIKAFLERKKIES 293


>gi|218281540|ref|ZP_03487969.1| hypothetical protein EUBIFOR_00534 [Eubacterium biforme DSM 3989]
 gi|218217329|gb|EEC90867.1| hypothetical protein EUBIFOR_00534 [Eubacterium biforme DSM 3989]
          Length = 667

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 30/220 (13%), Positives = 68/220 (30%), Gaps = 26/220 (11%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------CP 84
           A L  D ++ +  ++ E     Q+     + + + A+  +  G + I ++        C 
Sbjct: 151 AKLHHDMQHFVTEASVE-----QLTAIK-NSIAQCARKAQKAGIDAIEIHGDRLLGSLCS 204

Query: 85  SARVHEG-SFGACLMLNPDIVGDCIAAMCKALS----------IPVTVKCRIGVDDQIPA 133
           +   H   ++G  L        + + A+ +A            I V     +     +  
Sbjct: 205 TVLNHRTDNYGGSLENRTRYALEVLQAIKEAAPSMMVEYKLPIITVNPDGSLRGKGGLLE 264

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY-EIKKENPDLFIG 192
                  K +  +G++ I +                     ++ +   E  K      + 
Sbjct: 265 DEAVEFAKMLDAAGIDMIQVAQANHTGNMGDTIPPMGAVPYNWTLGACEKVKAVVSCPVA 324

Query: 193 LNGGLEDMSQALKILPSVDGVMI--GRAAYKNSAMLTTVD 230
             G +  +    KIL      MI  GR+   +  +   V+
Sbjct: 325 TVGRVVSVEAGEKILEDGTADMIGYGRSLLTDPDIANKVE 364


>gi|297171975|gb|ADI22960.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [uncultured
           nuHF2 cluster bacterium HF0500_39O04]
          Length = 759

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 28/199 (14%), Positives = 60/199 (30%), Gaps = 22/199 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V A ++ E+  ++ I +++           P + V    +G  L+       + + A
Sbjct: 532 DSFVRAGRMAEEAEFDMIEIHMAHGYLLSSFISPVSNVRRDEYGGELVNRLKFPVEILKA 591

Query: 111 MCKALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +         + CRI   D + +          + K + ++G + I +   +   +    
Sbjct: 592 VRSVWPNSKPISCRISATDWLDSGGLTGEDAVEVAKLLYENGCDIIDVSTGQTTPQAKPI 651

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                  +L   +  E K           G +    Q   I+ +   D V + R    + 
Sbjct: 652 YGRMFQTHLSEQVRLEAKG-----PTIAVGNITSADQVNTIVAAGRADLVALARPHLTDP 706

Query: 224 AM-LTTVDEYFSNPLTGSS 241
              L     Y   P     
Sbjct: 707 HFTLKAAAHYGYTPQFWPE 725


>gi|149923761|ref|ZP_01912154.1| 2,4-dienoyl-CoA reductase [Plesiocystis pacifica SIR-1]
 gi|149815390|gb|EDM74931.1| 2,4-dienoyl-CoA reductase [Plesiocystis pacifica SIR-1]
          Length = 688

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 31/235 (13%), Positives = 74/235 (31%), Gaps = 25/235 (10%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV 69
           R   ++L      Y+ + VA + ++         +  E+ +   I          AA++ 
Sbjct: 113 RIAMQILHTGRYAYSPLAVAPSAIQSPISPFKPRALSERGVRSTIA-----DFARAARLA 167

Query: 70  EDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           ++ GY+ + +                   +  +G           + +     A+     
Sbjct: 168 KEAGYDGVEIMGSEGYLINQFIARHTNHRKDGWGGSYANRIRFALEIVRQTRDAVGEDFI 227

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     + D      +  L K ++++G +   I+      +   P     +P   +
Sbjct: 228 IIYRLSMLDLIPDGSTWDEVVELAKKVEEAGAS--IINTGIGWHEARVPTIGTMVPRGAF 285

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             V  ++  E     +  N  +     A +IL     D V + R    +   +L 
Sbjct: 286 TWVTKKLMGEVSLPLVTSNR-INMPETAERILADGHADMVSMARPLLADPEWVLK 339


>gi|110834566|ref|YP_693425.1| 2,4-dienoyl-CoA reductase [Alcanivorax borkumensis SK2]
 gi|110647677|emb|CAL17153.1| 2,4-dienoyl-CoA reductase [NADPH] [Alcanivorax borkumensis SK2]
          Length = 672

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 28/178 (15%), Positives = 54/178 (30%), Gaps = 17/178 (9%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
                A + +  GY+ + +             P        +G           + +  +
Sbjct: 146 DFAHTALLAKKAGYDGVEIMGSEGYLINQFTAPCTNKRTDKYGGSAENRRRFPVEIVREV 205

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            K       V  RI V D +P  A R     L K ++ +G + +  ++     +   P  
Sbjct: 206 RKQCGDDFIVMFRISVVDLVPDGATREEVLALAKEVEAAGASLL--NSGIGWHEARVPTI 263

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
              +P   +       KE   + +  +  + D   A  IL     D V + R    + 
Sbjct: 264 VTSVPRAAFVEATRQVKEVVSIPVVASNRINDPDVAEAILVAGQADAVSMARPLLADP 321


>gi|77917687|ref|YP_355502.1| NADH:flavin oxidoreductase [Pelobacter carbinolicus DSM 2380]
 gi|77543770|gb|ABA87332.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Pelobacter
           carbinolicus DSM 2380]
          Length = 377

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 21/148 (14%), Positives = 57/148 (38%), Gaps = 11/148 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  +     +V + + A+ KA+    PV +K      V+  +    +  + + ++++G+
Sbjct: 186 YGGPVENRAKLVLEVLQAVRKAVGPDYPVLIKLNSEDFVEGGVTVEDMLKVAERLQQAGI 245

Query: 149 NGIWIHARKAILKG-----LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           + + +        G        + +     + Y    E+ K+   + + L GG+     A
Sbjct: 246 DAVEMSGGTIYASGDMSSLRPGRLDTPDTEVFYRKAAELFKQRLTVPLILVGGILSYEVA 305

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTV 229
             +L     D + + R+  +   ++   
Sbjct: 306 ETLLTEGTADFIALCRSLIREPDLIRRW 333


>gi|189499584|ref|YP_001959054.1| dihydroorotate dehydrogenase family protein [Chlorobium
           phaeobacteroides BS1]
 gi|189495025|gb|ACE03573.1| dihydroorotate dehydrogenase family protein [Chlorobium
           phaeobacteroides BS1]
          Length = 314

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/212 (14%), Positives = 76/212 (35%), Gaps = 29/212 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           +  + + I G  I       + +E     +   +N+ CP    +       + ++     
Sbjct: 103 DTGVIVNIAGKSIDDYCTVIERLESSEDISAYEINLSCP----NVKGECMIMGVSSTATF 158

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-----------GIWIH 154
           + I+ +       + VK    V       ++  +  + + +G +            I   
Sbjct: 159 EIISKLRTLTERHLMVKLTPNV------TSISAIAIAAEDAGADSVSLINTLVGMAIDYK 212

Query: 155 ARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
            RK +LK ++       I  +    V+E+        +G+ GG+     A++ +L     
Sbjct: 213 TRKPLLKNVTGGLSGPAIKPVALAKVWEVYNAVKIPVVGM-GGISSFKDAMEFLLAGASA 271

Query: 213 VMIGRAAYKNSAM----LTTVDEYFSNPLTGS 240
           + IG   + +  +       ++E+F++P+  S
Sbjct: 272 IQIGTMNFVDPDIGETVANAIEEFFADPVNPS 303


>gi|91203012|emb|CAJ72651.1| similar to NADH oxidase [Candidatus Kuenenia stuttgartiensis]
          Length = 659

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/181 (14%), Positives = 66/181 (36%), Gaps = 9/181 (4%)

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAIL 160
            + +  + K +     V CRI  D+           + + K ++++G + I + +     
Sbjct: 220 REIVEEIRKKVPADYPVICRISADEYTETGLKLEESKEIAKILERAGASAIHV-SACNYA 278

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
                     +    +  + E  K   ++ +   G ++D + A ++L     D +++GR+
Sbjct: 279 SAFFNIPCYYLEEGCFIHLAEGIKAIVNIPVLSVGRIQDPAMAEEVLKENKADLIVLGRS 338

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
              +      V E   + +         ++    +K+  ++  Y  +       LQQ T+
Sbjct: 339 LIADPCWPNKVKEGNLDDIQVCLSCNRCIESISDKKLICTVNPYIGK--DERFHLQQTTK 396

Query: 279 H 279
            
Sbjct: 397 P 397


>gi|26989212|ref|NP_744637.1| xenobiotic reductase, putative [Pseudomonas putida KT2440]
 gi|24984054|gb|AAN68101.1|AE016442_2 xenobiotic reductase, putative [Pseudomonas putida KT2440]
          Length = 366

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 64/181 (35%), Gaps = 21/181 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA+     G+  + L+              +      +G  +      + + ++A
Sbjct: 158 EEFVMAARRALSAGFEWLELHFAHGYLGQSFLSAHSNRRSDGYGGNVENRRRFLIETMSA 217

Query: 111 MCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +     +P+TV+  +   D      L     L++ +K +G + + +     I     P
Sbjct: 218 VREVWPEHLPLTVRLGVIEYDNQDEQTLLEAIALIRQLKNAGADLVNVSTGFNI-----P 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
             +          + E  +    + +    G+E  + A +++     D VM+GRA   + 
Sbjct: 273 NTDTPWAPAFLAPIAERIRHEAGIPVAAAWGIESPALADRLVRDGQADLVMVGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|325923744|ref|ZP_08185362.1| NADH:flavin oxidoreductase [Xanthomonas gardneri ATCC 19865]
 gi|325545782|gb|EGD17018.1| NADH:flavin oxidoreductase [Xanthomonas gardneri ATCC 19865]
          Length = 376

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/198 (16%), Positives = 62/198 (31%), Gaps = 22/198 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +A+  E  G   I L+            P +     ++G  L     +      A
Sbjct: 169 DAFVASAQRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMRLTLGIFDA 228

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + +  RI   D             L K++   G + I + +      GL P+
Sbjct: 229 VRAAVSDKIAIGVRISATDWVEGGWDLAQSIALSKALDARGAHYIHVSSG-----GLDPR 283

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +    Y I   +  K   D  +   G + + +QA  I+     D + + R    + 
Sbjct: 284 QQIPV-QAGYQIPFAQQIKAQVDTPVIGVGLITEPTQAEAIVQDGQADAIALARGILYDP 342

Query: 224 AMLTTVDEYFSNPLTGSS 241
                        +T + 
Sbjct: 343 RWPWHAAAALGASVTPAP 360


>gi|153952981|ref|YP_001393746.1| NADH oxidase [Clostridium kluyveri DSM 555]
 gi|146345862|gb|EDK32398.1| Predicted NADH oxidase [Clostridium kluyveri DSM 555]
          Length = 328

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 64/177 (36%), Gaps = 20/177 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  EAA  V++ G++ + +             P     +  +G  +     I  D +  +
Sbjct: 148 EFKEAALRVKNAGFDGVEIHSAHGYLLNQFLSPITNKRQDEYGGDITGRIKIHRDIVKNV 207

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+     +  R+G  D +             + ++K+GV+ + I             +
Sbjct: 208 REAVGESFPIFMRLGASDYMDGGLTIEDSKLAAQQLEKTGVDVLDISGGLCRYTIPGVNE 267

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                 L   I     KE   + + + GG+     A +IL     D + +GRA YK+
Sbjct: 268 EGYFTPLSKAI-----KEVVSIPVIVTGGIIHAKTADEILSRGEADLIGVGRAIYKD 319


>gi|195940569|ref|ZP_03085951.1| oxidoreductase, FAD/FMN-binding protein [Escherichia coli O157:H7
           str. EC4024]
          Length = 364

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 35/146 (23%), Positives = 52/146 (35%), Gaps = 17/146 (11%)

Query: 94  GACLMLNPDIVGDCIAAMC------KALSIPVT-VKCRIGVDDQIPAVA-LRNLVKSIKK 145
           G  L     I  + I A+       K L + V+  K            A    +   +  
Sbjct: 202 GGSLENRLAITLEVIRAVRNKIGADKVLGVRVSQGKVNDFHHKWKEGEAGAMTIFGLLAD 261

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +GV+ I +   K+ L            N    +V   ++  P+  I  NGGL+D   A K
Sbjct: 262 AGVDYIHVTEYKSWL--------PAFENGGKSLVQIAREAAPETVIIANGGLDDCETAEK 313

Query: 206 ILP-SVDGVMIGRAAYKNSAMLTTVD 230
           +L    D V IG+AA  N      V 
Sbjct: 314 LLDMGADFVSIGKAALANPDWPRKVR 339


>gi|325473325|gb|EGC76520.1| oxidoreductase [Treponema denticola F0402]
          Length = 335

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 70/192 (36%), Gaps = 23/192 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCP-SARVHEGSFGACLMLNPDIVGDCIAA 110
             V+AA+  ++ G + + +             P   +  +   G+ +     +  + I A
Sbjct: 150 DFVQAARRAKEAGLDGVEIHSAHGYLLNQFFSPIMNKRTDKYNGSSIEGRTKLHIEIIEA 209

Query: 111 MCKALSIPVTVKCRIGVDDQIPA-VALRNLVKSI---KKSGVNGIWIHARKAILKGLSPK 166
           + K       +  R+G  D I    +L + V++    KK+GV+ + I        G    
Sbjct: 210 IRKITGPDFLIAVRLGACDYISGGSSLEDSVEACLLFKKAGVDLLDISG------GFCGY 263

Query: 167 DNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            N ++    +   + +  KE     + L GG+     A KIL     D + +GRA   +S
Sbjct: 264 TNPELEEEGWFSRITQAVKEKVGAPVILTGGIVSPEAAEKILQEEKADLIGVGRALLNDS 323

Query: 224 AMLTTVDEYFSN 235
                  +    
Sbjct: 324 DWPKKAKQKLEG 335


>gi|302389697|ref|YP_003825518.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosediminibacter
           oceani DSM 16646]
 gi|302200325|gb|ADL07895.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosediminibacter
           oceani DSM 16646]
          Length = 646

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/188 (12%), Positives = 62/188 (32%), Gaps = 16/188 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +AA+  ++ G++ I +             P +      +G           + +  
Sbjct: 149 EAFGQAARRAKEAGFDAIEIHGAHGYLINQFLSPYSNKRTDEYGGTFENRMRFPLEVVKR 208

Query: 111 MCKAL--SIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +    P+   +     V   +     +   + + ++G+N + +         +  +
Sbjct: 209 VREEVGADFPIIYRISAEEYVTGGLTIEDTKVFARKLVEAGINALHVSGGVYESSAMIIQ 268

Query: 167 DNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                     +    IKK  N  + +   G ++D   A +++     D V +GRA   + 
Sbjct: 269 PAAISQGCFVENAAAIKKAINGKVPVIAVGRIKDPVMAEQVIQEGKADLVSMGRALLADP 328

Query: 224 AMLTTVDE 231
            +   V E
Sbjct: 329 ELPKKVSE 336


>gi|239623117|ref|ZP_04666148.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridiales bacterium
           1_7_47_FAA]
 gi|239522484|gb|EEQ62350.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridiales bacterium
           1_7_47FAA]
          Length = 325

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 58/180 (32%), Gaps = 23/180 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC----------P--SARVHEGSFGACLMLNPDIVGDCIA 109
              AA    + G++ + +   C          P  + R      G        +  D + 
Sbjct: 142 FASAAVRAREAGFDGVQIKA-CHVYLLSQFYSPLTNHRTRGKYTGNSFEGRIRLTLDVLR 200

Query: 110 AMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           ++  A+     V  R  V D  PA           + I++ G + + +       +   P
Sbjct: 201 SVRDAVGRDYPVSVRFPVQDYDPAGSSLEEGVRAARLIQEWGASFLDLSGG-PKYRYFHP 259

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                    D      + ++   + + + GG+ + S A ++L     D   + RA  KN 
Sbjct: 260 FIQSPGWFGDD---AAVIRQAVRIPVMVTGGITEYSHAEQLLNDHKADLTGVCRAVLKNP 316



 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 6/67 (8%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            G+ + + V AA++++++G + ++L+ G P  R     +    + +P   GD  A + +A
Sbjct: 224 AGSSLEEGVRAARLIQEWGASFLDLSGG-PKYR-----YFHPFIQSPGWFGDDAAVIRQA 277

Query: 115 LSIPVTV 121
           + IPV V
Sbjct: 278 VRIPVMV 284


>gi|327393892|dbj|BAK11314.1| NADPH dehydrogenase NamA [Pantoea ananatis AJ13355]
          Length = 366

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 81/233 (34%), Gaps = 36/233 (15%)

Query: 39  NILGFSTQEK-PLALQIGGADISK----LVEAAKIVEDFGYNEINLNVG---------CP 84
           + L FS  E  PL +Q   +D+ +     V  AK     G   I ++            P
Sbjct: 133 SALSFSDGEHLPLEMQ--ASDLERVKNAFVATAKRAVRLGIELIEVHAAHGYLLHQFLSP 190

Query: 85  SARVHEGSFGACL---MLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALR 137
            +      +G  L   M  P    +   A+ +A+   IPV V+      V+         
Sbjct: 191 LSNKRSDEYGGSLENRMRYP---LEVFHAVREAVPAEIPVGVRISASDWVEGGWDVGQSI 247

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGG 196
              K ++      I + +      GLS +   K+ PN       +I+++   + +   G 
Sbjct: 248 AFSKQLESLNCAYIHVSSG-----GLSEQQQIKVGPNYQVPFARDIRQQIG-IPVIAVGL 301

Query: 197 LEDMSQALKIL--PSVDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIKTR 246
           + +  QA +IL     D V + R    N         E+ +N       +++ 
Sbjct: 302 ITEPQQAEEILQQEEADLVALARGMLYNPRWPWHAAAEFNANVKAPPQYLRSE 354


>gi|115448547|ref|NP_001048053.1| Os02g0736400 [Oryza sativa Japonica Group]
 gi|46390439|dbj|BAD15901.1| putative dihydropyrimidine dehydrogenase [Oryza sativa Japonica
           Group]
 gi|70906540|gb|AAZ14951.1| putative dihydroorotate dehydrogenase [Oryza sativa Japonica Group]
 gi|113537584|dbj|BAF09967.1| Os02g0736400 [Oryza sativa Japonica Group]
 gi|218191531|gb|EEC73958.1| hypothetical protein OsI_08851 [Oryza sativa Indica Group]
 gi|222623634|gb|EEE57766.1| hypothetical protein OsJ_08303 [Oryza sativa Japonica Group]
          Length = 414

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 72/190 (37%), Gaps = 29/190 (15%)

Query: 54  IGGADISKLVEAA-----KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + G+ + +  +AA     + VE+ G + + +N  CP     E   GA +  + D++ +  
Sbjct: 145 LIGSIMEEYNKAAWHELIERVEESGVDALEINFSCPHGM-PERKMGAAVGQDCDLLEEVC 203

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVAL-----RNLVKSIKK----SGVNGIWIHARKAI 159
             + +  ++PV  K    + D      +        V +I       G+N   +     +
Sbjct: 204 GWINEKATVPVWAKMTPNITDITKPARISLKSGCEGVSAINTIMSVMGINLKTLRPEPCV 263

Query: 160 LKGLSP--KDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLEDMSQALK-ILPSVD 211
               +P     R +  +    V +I +   + F     +   GG+E  + A + IL   D
Sbjct: 264 EGYSTPGGYSARAVHPIALAKVMQIARMMKEEFADGQSLSAIGGVETGNDAAEFILLGAD 323

Query: 212 ------GVMI 215
                 GVM+
Sbjct: 324 TVQVCTGVMM 333


>gi|417339|sp|P32382|NADO_THEBR RecName: Full=NADH oxidase
 gi|48123|emb|CAA47660.1| NADH oxidase [Thermoanaerobacter brockii]
          Length = 651

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/150 (17%), Positives = 52/150 (34%), Gaps = 4/150 (2%)

Query: 91  GSFGACLMLNP-DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           G      M  P +I+     A+ +   I         V+        + + K ++++GV+
Sbjct: 193 GGSFERRMRFPLEIIRRIKEAVGEDYPISFRFSADEFVEGGNTLEEGKQIAKMLEEAGVH 252

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + + A          + +R        +  EIKK   ++ +   G + +   A KI+  
Sbjct: 253 VLHVSAGIYESMPTLLEPSRFEQGWRVYLAEEIKK-VVNIPVITVGVIREPEFAEKIIAE 311

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              D V +GR    +        E   N +
Sbjct: 312 GRADFVAVGRGLIADPEWPKKAKEGRQNEI 341


>gi|219853638|ref|YP_002470760.1| hypothetical protein CKR_0295 [Clostridium kluyveri NBRC 12016]
 gi|219567362|dbj|BAH05346.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 335

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 64/177 (36%), Gaps = 20/177 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  EAA  V++ G++ + +             P     +  +G  +     I  D +  +
Sbjct: 155 EFKEAALRVKNAGFDGVEIHSAHGYLLNQFLSPITNKRQDEYGGDITGRIKIHRDIVKNV 214

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+     +  R+G  D +             + ++K+GV+ + I             +
Sbjct: 215 REAVGESFPIFMRLGASDYMDGGLTIEDSKLAAQQLEKTGVDVLDISGGLCRYTIPGVNE 274

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                 L   I     KE   + + + GG+     A +IL     D + +GRA YK+
Sbjct: 275 EGYFTPLSKAI-----KEVVSIPVIVTGGIIHAKTADEILSRGEADLIGVGRAIYKD 326


>gi|307266457|ref|ZP_07547992.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306918498|gb|EFN48737.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 651

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/150 (17%), Positives = 52/150 (34%), Gaps = 4/150 (2%)

Query: 91  GSFGACLMLNP-DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           G      M  P +I+     A+ +   I         V+        + + K ++++GV+
Sbjct: 193 GGSFERRMRFPLEIIRRIKEAVGEDYPISFRFSADEFVEGGNTLEEGKQIAKMLEEAGVH 252

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + + A          + +R        +  EIKK   ++ +   G + +   A KI+  
Sbjct: 253 VLHVSAGIYESMPTLLEPSRFEQGWRVYLAEEIKK-VVNIPVITVGVIREPEFAEKIIAE 311

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              D V +GR    +        E   N +
Sbjct: 312 GRADFVAVGRGLIADPEWPKKAKEGRQNEI 341


>gi|74317595|ref|YP_315335.1| putative NADH-dependent flavin oxidoreductase [Thiobacillus
           denitrificans ATCC 25259]
 gi|74057090|gb|AAZ97530.1| putative NADH-dependent flavin oxidoreductase [Thiobacillus
           denitrificans ATCC 25259]
          Length = 370

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 64/180 (35%), Gaps = 24/180 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
           + V AA+  E  G++ I L+            P + V +  +G  L   M  P  V D +
Sbjct: 159 EFVTAAQRAERLGFDVIELHAAHGYLLHEFLSPLSNVRDDRYGGSLENRMRFPLEVFDAM 218

Query: 109 AAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A   A  +P+ V+      V+            +++++ G   I + +      GLSP 
Sbjct: 219 RAALHA-DVPLGVRISATDWVEGGWDIAQSLAFAEALRRRGCAFIDVSSG-----GLSPA 272

Query: 167 DNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +          +I+ E   +     G + D  QA  I+     D V + R    + 
Sbjct: 273 QQIPVAPGYQLPFAAQIRGETG-MPTMAVGLITDPHQAENIVAGGHADLVALARGMLYDP 331


>gi|50955452|ref|YP_062740.1| NADH-dependent flavin oxidoreductase [Leifsonia xyli subsp. xyli
           str. CTCB07]
 gi|50951934|gb|AAT89635.1| NADH-dependent flavin oxidoreductase [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 361

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 50/164 (30%), Gaps = 19/164 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG------VDDQIPAVALRNLVKSIK 144
           +G  L     ++   +A +   +   +PV V+           D+Q  A          +
Sbjct: 202 YGGSLENRARLLLRIVAEVRTEVGGDVPVFVRFSGSDWTPGGWDEQQTATV----AGWAQ 257

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           ++G +   I +         P               E  + + ++ +   G +    QA 
Sbjct: 258 EAGADFFDISSGGIQTGVRIPLQPGYQVPF-----AEHVRRSAEVEVSAVGLITTPRQAA 312

Query: 205 KILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
            I+ +   D VM+ R   ++             P+    P   R
Sbjct: 313 DIVENGSADAVMLARELLRDPHFPLRAAHELGVPIGYWPPQYLR 356


>gi|189219398|ref|YP_001940039.1| dihydroorotate dehydrogenase [Methylacidiphilum infernorum V4]
 gi|189186256|gb|ACD83441.1| Dihydroorotate dehydrogenase [Methylacidiphilum infernorum V4]
          Length = 314

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 78/218 (35%), Gaps = 34/218 (15%)

Query: 23  YTEM-IVADAILRGDKKNILGFSTQEK-----PLALQIGGADISKLVEAAKIVEDFGYNE 76
           Y+E  + ++ +L    ++ L F  + K     P+   + G         AK +E+ G + 
Sbjct: 51  YSEFPMSSEYLLTS--ESYLDFIREAKRKARIPIIASLNGRSPGWWCRYAKQIEEAGADG 108

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL 136
           I LN+  P          +  M   +     +  + K + IP+ VK             +
Sbjct: 109 IELNIY-PFPLDINQPSDSIEMDTLE----IVRLVRKEIQIPLGVKIYPY------YTNV 157

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP-----------NLDYDIVYEIKKE 185
            N+ +  + +GVNG+ +  R   L+     +N +I             L    +  +   
Sbjct: 158 GNMAQRFQAAGVNGLALFNR--FLQPDIDVENFEIKRGIQLGTSRDNRLALSWIAFLYNR 215

Query: 186 NPDLFIGLNGGL-EDMSQALKILPSVDGVMIGRAAYKN 222
              L +   GG+ E +     IL     VM+  A  + 
Sbjct: 216 L-KLDLAATGGVMEAVDAIRLILAGASVVMVCSAILEK 252


>gi|72383938|ref|YP_293292.1| 2,4-dienoyl-CoA reductase [Ralstonia eutropha JMP134]
 gi|72123281|gb|AAZ65435.1| 2,4-dienoyl-CoA reductase [Ralstonia eutropha JMP134]
          Length = 676

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/179 (12%), Positives = 54/179 (30%), Gaps = 17/179 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                 A++  + GY+ + +             P        FG           + + A
Sbjct: 143 EDFANTAELAWEGGYDGVEIMGSEGYLINQFTAPFTNQRTDEFGGSFEARIRFPLEVLKA 202

Query: 111 MCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +     V  RI     ++  +    +  L + ++ +G +   I+      +   P 
Sbjct: 203 IRRRVVDRFLVVYRISAVDLIEGGMTGAEVAELARRVEANGAD--IINTGVGWHESAVPT 260

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +P   +    E  K   D+ +  +  +     A  +L     D V + R    + 
Sbjct: 261 IAASVPRSAWAYAIENVKRAVDIPVIASNRINTPDGAEALLSSGCADMVSMARPLLADP 319


>gi|227546396|ref|ZP_03976445.1| NADPH dehydrogenase [Bifidobacterium longum subsp. infantis ATCC
           55813]
 gi|227213377|gb|EEI81249.1| NADPH dehydrogenase [Bifidobacterium longum subsp. infantis ATCC
           55813]
          Length = 457

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 53/152 (34%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+  A    V V  RI   D             L K +K+ GV
Sbjct: 298 YGGDLTGRSRFLVEVVDAVRGAAPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 357

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 358 DVMDVSTGGIM----SGVSIPVKPNYQVPFAEQVKSKA-DIPVTAVGLITKPKQAAKILA 412

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 413 RGEADAVEIGRAALRDPYWPLRAANKLGIPST 444


>gi|194292968|ref|YP_002008875.1| NADH:flavin oxidoreductase [Cupriavidus taiwanensis LMG 19424]
 gi|193226872|emb|CAQ72823.1| putative NADH:flavin oxidoreductase [Cupriavidus taiwanensis LMG
           19424]
          Length = 376

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 60/177 (33%), Gaps = 20/177 (11%)

Query: 62  LVEAAKIVEDFGYNEINL------------NVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
             +AA++  + G++ + +            N         + ++G  +     ++ + I 
Sbjct: 163 FAQAARLARETGFDGVEIHGANGYLLDQFLNGH---TNQRQDAWGGGIAQRMRLLLETIR 219

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+  A+   V V  R  +             +  + +      I A       ++  +  
Sbjct: 220 AVRAAVGRDVIVGVR--ISQAKVNDFTYQWPEGTEGAAAVFAGIAASGVDYLHVTEHEAW 277

Query: 170 KIPNL--DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           +      D  +V   ++  P L I  NG L +  +A  +L      V +GR A  N 
Sbjct: 278 QPAFAGGDASLVQHARRAAPGLAIVANGSLAEPVRAAGMLEQGATLVALGRGALANP 334


>gi|91793065|ref|YP_562716.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella denitrificans
           OS217]
 gi|91715067|gb|ABE54993.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella denitrificans
           OS217]
          Length = 369

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/190 (16%), Positives = 62/190 (32%), Gaps = 22/190 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V +AK     G + I L             P +   + S+G  L     ++ +  +AM
Sbjct: 159 DFVASAKRAVSLGLDAIELHGAHGYLLHQFLSPLSNHRDDSYGGSLENRMRLMLEVFSAM 218

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              +   + +  RI   D +           L K++++ G + +       +  G     
Sbjct: 219 RAVVPATMALGVRISATDWVEGGWTLEQSIVLAKALQQLGCDFLH------VSSGGLSSQ 272

Query: 168 NRKIPNLDYDIVY-EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                   Y + + E  K    + +   G + + +QA  I+ +   D V + R    N  
Sbjct: 273 QVIPIEAGYQVSFSEAIKAQVSMPVIAVGLITEATQAEAIINTHAADAVALARGILYNPH 332

Query: 225 MLTTVDEYFS 234
            +    E   
Sbjct: 333 WVWHAAEQLK 342


>gi|330821569|ref|YP_004350431.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia gladioli
           BSR3]
 gi|327373564|gb|AEA64919.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia gladioli
           BSR3]
          Length = 368

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/148 (16%), Positives = 53/148 (35%), Gaps = 12/148 (8%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALR---N 138
           P A      +G         + + +A +  A   ++P+T +  +   D   A  L     
Sbjct: 191 PHANQRSDEYGGDWTRRSRFLLETLADVRAAWPENLPLTARFGVIEYDGDDAATLDASIR 250

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L   +K+ G++ + +      +   +P             +    K+   L +    G++
Sbjct: 251 LAGDLKRGGLDMLSV-----SVGFSTPDAQIPWGPGFLAPIAAQVKQATGLPVASAWGID 305

Query: 199 DMSQALKILPS--VDGVMIGRAAYKNSA 224
           D   A + +    +D VM+GRA   +  
Sbjct: 306 DPKVANRTVEQGQLDLVMVGRAHLADPH 333


>gi|300727885|ref|ZP_07061264.1| dihydropyrimidine dehydrogenase [Prevotella bryantii B14]
 gi|299774869|gb|EFI71482.1| dihydropyrimidine dehydrogenase [Prevotella bryantii B14]
          Length = 508

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/174 (16%), Positives = 59/174 (33%), Gaps = 15/174 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           K +   I G +  +    A+  E+ G + I  N  CP   +     G  +  +  ++   
Sbjct: 205 KVIVASIMGQNEEEWTTLARKCEEAGADVIECNFSCP--NMENDKLGITIGQDATLIERF 262

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPA-----------VALRNLVKSIKKSGVNGIWIHAR 156
             A     ++P+  K    + D +P            +A  N + SI    +  +     
Sbjct: 263 TRATRLGTNLPILAKMTPNITDMVPMAIAAKRGGADGIAAINTINSITGVDLESLVAKPE 322

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGLEDMSQALKILP 208
                 +     + +  +    + ++   +E  D+ I   GG+E    A+  L 
Sbjct: 323 VHGYSMVGGYSGQAVKPIALRFISDLGHSEELADMHISGMGGIESWIDAVDFLA 376


>gi|282856739|ref|ZP_06266003.1| dihydroorotate dehydrogenase, catalytic subunit (dihydroorotate
           oxidase) (dhodehase) (dhodase) (dhod) [Pyramidobacter
           piscolens W5455]
 gi|282585435|gb|EFB90739.1| dihydroorotate dehydrogenase, catalytic subunit (dihydroorotate
           oxidase) (dhodehase) (dhodase) (dhod) [Pyramidobacter
           piscolens W5455]
          Length = 309

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/200 (15%), Positives = 57/200 (28%), Gaps = 26/200 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+ L +       L      + +     + + LNV CP    +         ++P +   
Sbjct: 99  PVMLNVCMQSAEDLAYMMDRIAEAKDLVDGVELNVSCP----NTDHGCMSWGVDPALTAQ 154

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALR------------NLVKSIKKSGVNGIWIH 154
                 +    P+ VK      D                      +     +        
Sbjct: 155 ATEMARRRWDGPLWVKLTPQAPDVAAVAKAAESAGASAVVAANTWLGMAVDTARGVPVFS 214

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGV 213
            R A L G  P        L +D    +K     + +   GG++    AL + +     V
Sbjct: 215 RRVAGLSG--PAVFPLALRLVWDAAGAVK-----IPVIGCGGVDGPDSALAMIMAGASAV 267

Query: 214 MIGRAAYKNSAMLTTVDEYF 233
            +G A + +  +L  V E  
Sbjct: 268 EVGAALFSDFEVLENVHEGL 287


>gi|317159408|ref|XP_001827289.2| NADH oxidase [Aspergillus oryzae RIB40]
          Length = 412

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 75/197 (38%), Gaps = 19/197 (9%)

Query: 85  SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALRNLVK 141
           S R ++   ++G  +     ++ +   A+ + ++   TV  +I  V+ Q     L   V+
Sbjct: 188 SPRTNKRQDNYGGSIKNRMKLISEIRKAISERVAETFTVGIKINTVEFQESTFNLEETVQ 247

Query: 142 SI---KKSGVNGIWIHARKAILKGLSPKDNRKIPN-----LDYDIVYEIKKENPDLFIGL 193
                +K   + + +         +  K    IP      L+Y  +Y  K E   +++  
Sbjct: 248 LCIEFEKMRFDFVELSGGTYEDWTIGRKQVASIPQHEGFFLEYGRIYSEKMERTKVYVT- 306

Query: 194 NGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            GG   +   ++ +  VDG+ + R   +   + +      S  +  + PIK   D     
Sbjct: 307 -GGYRSVKGMIRAVQEVDGIGLARPLCQEPHLCS---HILSGSVETAPPIKIDTDNFHLT 362

Query: 254 KISASMTDYAARHLHSG 270
            ++A M     +HL  G
Sbjct: 363 SVAALMQM---QHLGKG 376


>gi|296445257|ref|ZP_06887216.1| NADH:flavin oxidoreductase/NADH oxidase [Methylosinus trichosporium
           OB3b]
 gi|296257212|gb|EFH04280.1| NADH:flavin oxidoreductase/NADH oxidase [Methylosinus trichosporium
           OB3b]
          Length = 368

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/130 (19%), Positives = 43/130 (33%), Gaps = 10/130 (7%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
           M  P  V D + +   A   PV+V+      V+            K++   G + I + +
Sbjct: 210 MRFPLEVFDAVRSAFPA-DKPVSVRVSGTDWVEGGWTIDETVAFAKALAARGCDAIHVSS 268

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM- 214
                 GL P     +       +    K   D+ +   G +    QA  I+ + D  M 
Sbjct: 269 G-----GLHPAQAIPVGPSYQVPLARAVKSAVDIPVIAVGLITGFEQAEAIVATGDADMI 323

Query: 215 -IGRAAYKNS 223
            I R    + 
Sbjct: 324 AIARTILYDP 333


>gi|296453614|ref|YP_003660757.1| NADH:flavin oxidoreductase/NADH oxidase [Bifidobacterium longum
           subsp. longum JDM301]
 gi|296183045|gb|ADG99926.1| NADH:flavin oxidoreductase/NADH oxidase [Bifidobacterium longum
           subsp. longum JDM301]
          Length = 457

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/152 (21%), Positives = 53/152 (34%), Gaps = 11/152 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+   +   V V  RI   D             L K +K+ GV
Sbjct: 298 YGGDLTGRSRFLVEVVDAVRGVVPEGVPVLVRISATDWAAGGWDLDQTIALSKVLKEHGV 357

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +     +    S       PN       ++K +  D+ +   G +    QA KIL 
Sbjct: 358 DVMDVSTGGIM----SGVSIPVKPNYQVPFAEQVKSKA-DIPVTAVGLITKPKQAAKILA 412

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
               D V IGRAA ++             P T
Sbjct: 413 RGEADAVEIGRAALRDPYWPLRAANKLGIPST 444


>gi|317157401|ref|XP_001826449.2| FMN binding oxidoreductase [Aspergillus oryzae RIB40]
          Length = 418

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 70/182 (38%), Gaps = 26/182 (14%)

Query: 61  KLVEAAKIVEDFGYNEINL------------NVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           K V+ A+++ D G++ + L            N   P   +   ++G  L      V D I
Sbjct: 172 KFVDTARLMADSGFSGVELHGAHGYLIDQFLN---PKTNLRTDAYGGTLEKRAKFVLDII 228

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS--IKKSGVNGIWIHAR----KAILKG 162
             + KA+     V  ++   D   +     + +   + ++G++ + +        +++ G
Sbjct: 229 TEIRKAVPSKFCVGIKLNSADHSSSTFEETMAQIGLLVEAGIDFLEVSGGSYEDPSMMGG 288

Query: 163 LSPKDNRKIPNLDYDIVY---EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
             P+ + +    +   +    E +K  PDL   L GG    + A   +     D + IGR
Sbjct: 289 TQPQKSARTAAREAFFIEFATEARKRYPDLVFMLTGGFRSRTGAESAIKENACDLIGIGR 348

Query: 218 AA 219
            A
Sbjct: 349 PA 350


>gi|284991554|ref|YP_003410108.1| dihydroorotate oxidase [Geodermatophilus obscurus DSM 43160]
 gi|284064799|gb|ADB75737.1| dihydroorotate oxidase [Geodermatophilus obscurus DSM 43160]
          Length = 385

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/196 (15%), Positives = 61/196 (31%), Gaps = 15/196 (7%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--DCIAAMCKALSI 117
                 A++ ++ G + + LN+ CP+      + G    L  D       +  + +AL  
Sbjct: 185 DDFAATARLAQEAGASVVELNLSCPNTLSTSTAAGVKPPLCLDAGATVAVVEGVRRALDD 244

Query: 118 PVTVKCRIGVDDQIPAVAL-RNLVKSIKK-SGVNGIWIHARK---------AILKGLSPK 166
              +  ++   D     AL   L   +   +G+N +    R+           L GLS  
Sbjct: 245 RTGLVAKLSWLDGARLEALVPRLAPLVDGIAGINTLQSRVRRSDGEPTFPGRELAGLSGA 304

Query: 167 DNRKIPNLDYDIVYEIKKENPDLF-IGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA 224
             R         +  ++      F +   GG+ D +    +     D V     A+    
Sbjct: 305 AVRDSALDFTRRLVALRDAGGRHFDVLAMGGVTDPASFAALFALGADAVQSASGAFAAPF 364

Query: 225 MLTTVDEYFSNPLTGS 240
           +           L  +
Sbjct: 365 LARDCVAALGETLPRA 380


>gi|261417832|ref|YP_003251514.1| NADPH dehydrogenase NamA [Geobacillus sp. Y412MC61]
 gi|319767356|ref|YP_004132857.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y412MC52]
 gi|261374289|gb|ACX77032.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y412MC61]
 gi|317112222|gb|ADU94714.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y412MC52]
          Length = 340

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 75/193 (38%), Gaps = 23/193 (11%)

Query: 49  PLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEGSFGA 95
           P   ++  ADI + V+A    A+  ++ G++ I ++            P +   +  +G 
Sbjct: 129 PTPKEMTKADIEETVQAFQNGARRAKEAGFDVIEIHAAHGYLINEFLSPLSNRRQDEYGG 188

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                   + D I A+ +    P+ V+        D + A       K +K+ GV+ + +
Sbjct: 189 SPENRYRFLSDVIDAVREVWDGPLFVRISASDYHPDGLTAKDYVPYAKRMKEQGVDLVDV 248

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
            +   +   ++     ++P        E+ +   D+  G  G +    QA +IL +   D
Sbjct: 249 SSGAVVPARMNVYPGYQVPFA------ELIRREADIPTGAVGLITSGWQAEEILQNGRAD 302

Query: 212 GVMIGRAAYKNSA 224
            V +GR   +N  
Sbjct: 303 LVFLGRELLRNPY 315


>gi|67522851|ref|XP_659486.1| hypothetical protein AN1882.2 [Aspergillus nidulans FGSC A4]
 gi|40745891|gb|EAA65047.1| hypothetical protein AN1882.2 [Aspergillus nidulans FGSC A4]
 gi|259487236|tpe|CBF85749.1| TPA: NADH-dependent flavin oxidoreductase, putative
           (AFU_orthologue; AFUA_2G04320) [Aspergillus nidulans
           FGSC A4]
          Length = 421

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 70/211 (33%), Gaps = 36/211 (17%)

Query: 49  PLALQIGGADISKL----VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGA 95
           P+  Q+   DI  L    V A K     G + I + N           P+       +G 
Sbjct: 184 PVRKQMTRDDIENLKTAWVAAVKRAVRAGADFIEIHNAHGYLLMSFLSPAVNTRTDEYGG 243

Query: 96  CLMLNPDIVGDCIAAMCKALS--IPVTVKCR-----IGVDDQIPAVALRN---LVKSIKK 145
                  +  +      +A+   +PV ++             +P+  L +     K++ +
Sbjct: 244 SFENRIRLSMEIAKLTREAVPDHLPVFLRVSATDWLEESRPDLPSWRLEDTVKFAKALAE 303

Query: 146 SG-VNGIWIH-ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQ 202
           SG ++ + +        + +  K   + P         +KK   D L +G  G ++    
Sbjct: 304 SGYIDVLDVSSGGTHADQHIHAKPGFQAPFA-----AAVKKAVGDKLLVGTVGMIDSAHL 358

Query: 203 ALKILP--SVDGVMIGRAAYKNS---AMLTT 228
           A  +L    +D  ++GR   KN         
Sbjct: 359 ANSLLEKEGLDLTLVGRGFQKNPGLVWAFAE 389


>gi|311109809|ref|YP_003982660.1| NADH:flavin oxidoreductase/NADH oxidase family protein 2
           [Achromobacter xylosoxidans A8]
 gi|310764498|gb|ADP19945.1| NADH:flavin oxidoreductase/NADH oxidase family protein 2
           [Achromobacter xylosoxidans A8]
          Length = 376

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 37/153 (24%), Positives = 56/153 (36%), Gaps = 18/153 (11%)

Query: 84  PSARVHEGSFGACL---MLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRN 138
           P   + +  +G  L   M  P  V    AA+  AL   IP++V+    VD       L +
Sbjct: 193 PVTNLRQDQYGGSLENRMRFPLQVA---AAVRDALPSDIPLSVRI-SAVDGIEGGWQLAD 248

Query: 139 ---LVKSIKKSGVNGIWIHAR---KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                + +K  GV+ +   +         G  P   ++ P         +K+E   +   
Sbjct: 249 SIVFSRELKALGVDLVDCSSGGIQAPATAGQGPLAVKRGPGFQVPFAQTVKQEAG-IATI 307

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
             G + D  QA  IL     D V IGR A  N 
Sbjct: 308 AVGLIVDPEQAEAILAENKADLVAIGREALHNP 340


>gi|163782576|ref|ZP_02177573.1| oxidoreductase, FAD/FMN-binding protein [Hydrogenivirga sp.
           128-5-R1-1]
 gi|159882149|gb|EDP75656.1| oxidoreductase, FAD/FMN-binding protein [Hydrogenivirga sp.
           128-5-R1-1]
          Length = 351

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 65/182 (35%), Gaps = 22/182 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               EA K   + G++ I ++            P     +  +G        ++ + +  
Sbjct: 154 ESYREAVKRATEAGFDLIEIHAAHGYLLHEFLSPVTNRRKDEYGGSFENRVRLLLEVVRI 213

Query: 111 MCKAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSP 165
             + L  S P++V+      V           L K +K  GV+ I     R A  +  S 
Sbjct: 214 AREELPESTPLSVRISAVDYVKGGWSLEESVELAKLLKAEGVDLIDCSSGRIAQEESFSE 273

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P  +      I++E   +     G ++   QA +IL +   D V +GR   ++ 
Sbjct: 274 YPGHQVPFAE-----RIRREAG-VKTIAVGMIKTYEQAEEILSNGRADLVAVGREFLRDP 327

Query: 224 AM 225
            +
Sbjct: 328 YL 329


>gi|242062600|ref|XP_002452589.1| hypothetical protein SORBIDRAFT_04g028610 [Sorghum bicolor]
 gi|241932420|gb|EES05565.1| hypothetical protein SORBIDRAFT_04g028610 [Sorghum bicolor]
          Length = 420

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 72/190 (37%), Gaps = 29/190 (15%)

Query: 54  IGGADISKLVEAA-----KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + G+ + +  +AA     + VE+ G + + +N  CP     E   GA +  + D++ +  
Sbjct: 151 LIGSIMEEYNKAAWHELIERVEESGVDALEINFSCPHGM-PERKMGAAVGQDCDLLEEVC 209

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVAL-----RNLVKSIKK----SGVNGIWIHARKAI 159
             + +  ++PV  K    + D      +        V +I       G+N   +     +
Sbjct: 210 GWINEKATVPVWAKMTPNITDITQPARISLKSGCEGVSAINTIMSVMGINLKTLRPEPCV 269

Query: 160 LKGLSP--KDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLEDMSQALK-ILPSVD 211
               +P     R +  +    V +I +   + F     +   GG+E  + A + IL   D
Sbjct: 270 EGYSTPGGYSARAVHPIALAKVMQIARMMKEEFADGQSLSAIGGVETGNDAAEFILLGAD 329

Query: 212 ------GVMI 215
                 GVM+
Sbjct: 330 TVQVCTGVMM 339


>gi|56964206|ref|YP_175937.1| NADH-dependent flavin oxidoreductase [Bacillus clausii KSM-K16]
 gi|56910449|dbj|BAD64976.1| NADH-dependent flavin oxidoreductase [Bacillus clausii KSM-K16]
          Length = 340

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/200 (16%), Positives = 65/200 (32%), Gaps = 28/200 (14%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG-DCIAA 110
               AA+   + G++ I L             P        +G     +  +   + I A
Sbjct: 144 TFKAAARRAVEAGFDAIELHGAHGYLIHQFLSPYTNTRTDRYG----KDRTLFAKEVIRA 199

Query: 111 MCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +  S+P+ ++      VD            + +K  GV+   + +      G  P 
Sbjct: 200 VKSVIPDSMPLLMRISATEYVDGGYDIEEAIRFSQILKDEGVDVFDVSSG-----GEGPI 254

Query: 167 DNRKIP--NLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
            +R +P  +  Y   + +  K+   + +   G LE+   A  ++     D V +GR    
Sbjct: 255 GSRGLPGSHAGYQTPLAKQIKQALSVPVIAVGRLENPVLANAVIGNEEADLVAVGRGLLA 314

Query: 222 NSAMLTTVDEYFSNPLTGSS 241
           N             P+   +
Sbjct: 315 NPYWALGAASELQLPVEAPT 334


>gi|152985826|ref|YP_001350854.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa PA7]
 gi|150960984|gb|ABR83009.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa PA7]
          Length = 681

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 69/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + ++            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPIKSPISWFTPRELTERGIRRTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     + S+G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDSWGGPLENRMRLALEIVRGIRRIVGERFILSYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWEEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAEALLAEGKADLVSMARPLLADP 328


>gi|328875380|gb|EGG23745.1| dihydroorotate oxidase [Dictyostelium fasciculatum]
          Length = 369

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/187 (14%), Positives = 54/187 (28%), Gaps = 30/187 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SI 117
            +V+ A+I  + G   + +N  CP   V  G        NPD V +   A+   L   +I
Sbjct: 182 DMVDVARIAVEAGSKVVEVNYSCP--NVVTGEGQIY--NNPDQVYEISKALVSELQPHNI 237

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPK 166
           P+ +K  +  D       +  L+    ++GV  I                +  L      
Sbjct: 238 PLVIKVGVLEDKNK----MEKLMLQAHRAGVTAIAGINTMSMKVIDRDTNEPALGPGRLS 293

Query: 167 DNRKIPNLDYDIVYEIKKENPDL-------FIGLNGGLEDMSQALKIL-PSVDGVMIGRA 218
                  +    +  I +    +        +   GG+         L    +       
Sbjct: 294 SGVCGAPIRQTAIDWISQARQVIDQHKLPLQLIGCGGIVQPQHFDDFLNAGANFCTSATG 353

Query: 219 AYKNSAM 225
              +  +
Sbjct: 354 LMWDPYL 360


>gi|297529500|ref|YP_003670775.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. C56-T3]
 gi|297252752|gb|ADI26198.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. C56-T3]
          Length = 340

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 74/193 (38%), Gaps = 23/193 (11%)

Query: 49  PLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEGSFGA 95
           P   ++  ADI + V+A    A+  ++ G++ I ++            P +   +  +G 
Sbjct: 129 PTPKEMTKADIEETVQAFQNGARRAKEAGFDVIEIHAAHGYLINEFLSPLSNRRQDEYGG 188

Query: 96  CLMLNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                   +GD I A+ +    P  V +       D +         K +K+ GV+ + +
Sbjct: 189 SPENRYRFLGDVIDAVREVWDGPLFVRISASDYHPDGLTTKDYVPYAKRMKEQGVDLVDV 248

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
            +   +   ++     ++P        E+ +   D+  G  G +    QA +IL +   D
Sbjct: 249 SSGAIVPARMNVYPGYQVPFA------ELIRREADIPTGAVGLITSGWQAEEILQNGRAD 302

Query: 212 GVMIGRAAYKNSA 224
            V +GR   +N  
Sbjct: 303 LVFLGRELLRNPY 315


>gi|308069270|ref|YP_003870875.1| NADH-dependent flavin oxidoreductase yqjM [Paenibacillus polymyxa
           E681]
 gi|305858549|gb|ADM70337.1| Probable NADH-dependent flavin oxidoreductase yqjM [Paenibacillus
           polymyxa E681]
          Length = 361

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/210 (15%), Positives = 74/210 (35%), Gaps = 28/210 (13%)

Query: 54  IGGADISKLVEA----AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +  A++ +LV+A    A+   + G++ + +             P     E  +G     +
Sbjct: 154 LKTAEVRELVQAYKEGARRAVEAGFDTVEIHGAHGYLIHQFHSPLTNTREDEYG----QD 209

Query: 101 PDIVG-DCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             + G + I A+ + L   +PV ++   +  V+D      +  + +  + +G +   I +
Sbjct: 210 LSLFGVEVIHAVKEVLPADMPVLMRISAKEYVEDGYNVEYITGVGERYRDAGADIFHISS 269

Query: 156 RKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDG 212
                               Y + +    +E  ++ +   G L+D   A +++     D 
Sbjct: 270 GGEG---PIGSGGGPSARAGYQVELAHTIREKLNVPVIAVGLLDDYEDARRVVQQKEADL 326

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           V IGRA  ++              +    P
Sbjct: 327 VAIGRAMLRDPYWALHASRELKVQVDIPEP 356


>gi|119480069|ref|XP_001260063.1| NADH-dependent flavin oxidoreductase, putative [Neosartorya
           fischeri NRRL 181]
 gi|119408217|gb|EAW18166.1| NADH-dependent flavin oxidoreductase, putative [Neosartorya
           fischeri NRRL 181]
          Length = 421

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/227 (14%), Positives = 74/227 (32%), Gaps = 31/227 (13%)

Query: 45  TQEKPLALQIGGADISKL----VEAAKIVEDFGYNEINL-NVGC--------PSARVHEG 91
           T + P+  ++   DI  L    V A K     G + I + N           P+      
Sbjct: 180 TDKNPVPKEMTKQDIEDLKTAWVAAVKRAVKAGADFIEIHNAHGYLLMSFLSPAVNTRTD 239

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--------IGVDDQIPAVALRNLVK 141
            +G        +  +      + +   +PV ++                   V      K
Sbjct: 240 EYGGSFENRIRLSLEIAKLTRENVPKDMPVFLRVSATDWLEEVQPHKPSWRGVDTVRFAK 299

Query: 142 SIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLED 199
            + ++G V+ + + +        S +     P         +K    D L +   G ++ 
Sbjct: 300 ILAETGYVDVLDVSSGGT----HSEQHIHAKPGFQAPFAIAVKNAVGDKLAVASVGMIDS 355

Query: 200 MSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
              A  +L    +D V++GR   KN  ++    +  +  ++ ++ I+
Sbjct: 356 AHMANSLLEKDGLDLVLVGRGFQKNPGLVWAWADELNVEISMANQIR 402


>gi|67464349|pdb|1Z41|A Chain A, Crystal Structure Of Oxidized Yqjm From Bacillus Subtilis
 gi|67464350|pdb|1Z41|B Chain B, Crystal Structure Of Oxidized Yqjm From Bacillus Subtilis
 gi|67464351|pdb|1Z42|A Chain A, Crystal Structure Of Oxidized Yqjm From Bacillus Subtilis
           Complexed With P-Hydroxybenzaldehyde
 gi|67464352|pdb|1Z42|B Chain B, Crystal Structure Of Oxidized Yqjm From Bacillus Subtilis
           Complexed With P-Hydroxybenzaldehyde
 gi|67464355|pdb|1Z44|A Chain A, Crystal Structure Of Oxidized Yqjm From Bacillus Subtilis
           Complexed With P-Nitrophenol
 gi|67464356|pdb|1Z44|B Chain B, Crystal Structure Of Oxidized Yqjm From Bacillus Subtilis
           Complexed With P-Nitrophenol
 gi|67464357|pdb|1Z48|A Chain A, Crystal Structure Of Reduced Yqjm From Bacillus Subtilis
 gi|67464358|pdb|1Z48|B Chain B, Crystal Structure Of Reduced Yqjm From Bacillus Subtilis
          Length = 338

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 64/193 (33%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA   ++ G++ I ++            P +      +G         + + I  +
Sbjct: 145 EFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEV 204

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P  V V      D  +         K  K+ GV+ I   +   +       D  
Sbjct: 205 KQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWXKEQGVDLIDCSSGALV-----HADIN 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P        +I+++  D   G  G + D S A +IL +   D + IGR   ++     
Sbjct: 260 VFPGYQVSFAEKIREQA-DXATGAVGXITDGSXAEEILQNGRADLIFIGRELLRDPFFAR 318

Query: 228 TVDEYFSNPLTGS 240
           T  +  +  +   
Sbjct: 319 TAAKQLNTEIPAP 331


>gi|85711408|ref|ZP_01042467.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Idiomarina baltica OS145]
 gi|85694909|gb|EAQ32848.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Idiomarina baltica OS145]
          Length = 370

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/143 (19%), Positives = 54/143 (37%), Gaps = 21/143 (14%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCR------IGVDDQIPAVA--LRNLVKSIKK 145
           G  +      V   + A   A+     V  R         D Q P     +  +VK +K+
Sbjct: 199 GGGMAKRLKFVEMVVKAAKSAVDDDFIVGIRVGQITVTDPDYQWPEGEDGMIRIVKGLKE 258

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE--DMSQA 203
           +GV+ I  H     +     KD         + + E+ ++  D+ + +NGG++  +    
Sbjct: 259 AGVDYI--HTTDTSVDRKPFKDGSN------NTLAEVVQDFSDIPVIVNGGIDESNYEHI 310

Query: 204 LKILPSVDGVM-IGRAAYKNSAM 225
                +  G++ IG+ A  N  +
Sbjct: 311 AAHYEN--GLLAIGKKALANPDL 331


>gi|290967744|ref|ZP_06559299.1| dihydroorotate dehydrogenase 1B [Megasphaera genomosp. type_1 str.
           28L]
 gi|290782260|gb|EFD94833.1| dihydroorotate dehydrogenase 1B [Megasphaera genomosp. type_1 str.
           28L]
          Length = 304

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/199 (14%), Positives = 71/199 (35%), Gaps = 24/199 (12%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           PL + +  + + +    A+ ++  G   + +N+ CP    +    G     +P       
Sbjct: 97  PLIVNMSASTVEEYGRLAEQLDVPGVAAVEVNISCP----NVKEGGIVFGTDPQAAAAVT 152

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HAR 156
           AA+      PV +K    V D      + ++ ++++ +G + + +            H R
Sbjct: 153 AAVKAHTKKPVIMKLSPNVTD------IVSMAEAVEAAGADAVSLINTLTGMAIDIQHKR 206

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
             +           I  +   +V+++ K+     +G+ GG+      ++ +L     V +
Sbjct: 207 PLLGNITGGLSGPAIKPIALRMVWQVAKQIRIPVLGM-GGICCWQDVVEFMLAGASVVAV 265

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           G   +     L  +     
Sbjct: 266 GAYNFLQPTALADIAAGLE 284


>gi|251799040|ref|YP_003013771.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp. JDR-2]
 gi|247546666|gb|ACT03685.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp. JDR-2]
          Length = 343

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/221 (15%), Positives = 72/221 (32%), Gaps = 32/221 (14%)

Query: 54  IGGADISKLVE----AAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +   +  ++VE    A +     G + I +             P        +G     +
Sbjct: 133 LTTEEAEQMVEKFRLAVRRAVQAGVDTIEIHGAHGYLIHQFVSPLTNKRADKYG----QD 188

Query: 101 PDIV-GDCIAAMCKALS--IPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
             +   + I A    +   +P+ ++   R   +            K  K++GV+   I  
Sbjct: 189 RTLFGKEVIKAAKSEMPAHMPLFMRISAREYAEGGYGINESIAFAKEFKEAGVDVFHI-- 246

Query: 156 RKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG-- 212
             A  +G      R   +  Y + +    +E  D+ +   G L+D + A  ++ + D   
Sbjct: 247 -SAGGEGQIAAAGRPGTHAGYQVPLARAIREALDIPVIAVGRLDDPALANSVIGNEDADL 305

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           V +GR   +N              +     +  + D+ F R
Sbjct: 306 VAVGRGMLRNPYWALEAASVLHKEIE----VPRQYDRGFAR 342


>gi|72161890|ref|YP_289547.1| NADH:flavin oxidoreductase [Thermobifida fusca YX]
 gi|71915622|gb|AAZ55524.1| NADH:flavin oxidoreductases, Old Yellow enzyme family [Thermobifida
           fusca YX]
          Length = 656

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/155 (14%), Positives = 59/155 (38%), Gaps = 8/155 (5%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV----DDQIPAVALRNL 139
           P++   +  +G  L      + + I A+   +    T+  R+ +    D    A    ++
Sbjct: 189 PASNHRDDEYGGDLAGRMRFLLEIIDAIRAEVGPDFTLGVRMNLYEALDGGYDAAEGVDI 248

Query: 140 VKSIKKSG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
            K+++ +G ++ + +            + +   P    D+  ++ +    L +   G + 
Sbjct: 249 AKALEATGKIDYLSVVVGDNWGAPSYIQPHYYQPAQWADLAAQVTRAV-SLPVIYTGRVT 307

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           D   A K++     D V + RA   +  ++T   +
Sbjct: 308 DPHTAEKVIAQGQADLVGMARAIITDPEIITKTAQ 342


>gi|330950452|gb|EGH50712.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae Cit
           7]
          Length = 370

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/135 (18%), Positives = 52/135 (38%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRN------LVKSIKKSGVNGI 151
               +  + IAA+ K A   PV V+   G  +        +      +  ++  +GV+ I
Sbjct: 209 QRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQHKWAGDESDAEIIFDALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A     +  +   +           ++  P + +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAWQPAFAQGEASLVELA--------RRYAPGVALIANGGLHDPQKADQVLRQGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|313651254|gb|EFS15652.1| uncharacterized protein yeiA [Shigella flexneri 2a str. 2457T]
 gi|332756236|gb|EGJ86587.1| hypothetical protein SF274771_2646 [Shigella flexneri 2747-71]
 gi|332765954|gb|EGJ96164.1| dihydroorotate dehydrogenase family protein [Shigella flexneri
           2930-71]
 gi|333001825|gb|EGK21391.1| hypothetical protein SFK218_3124 [Shigella flexneri K-218]
 gi|333016664|gb|EGK35993.1| hypothetical protein SFK304_2940 [Shigella flexneri K-304]
          Length = 282

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/151 (17%), Positives = 57/151 (37%), Gaps = 27/151 (17%)

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I  N  CP   +   + G+ +  +P++V     A+ +  ++P+  K    + D      
Sbjct: 1   MIECNFSCPQ--MTSHAMGSDVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------ 52

Query: 136 LRNLVKSIKKSGVNGI-WIHARKAIL----------------KGLSPKDNRKIPNLDYDI 178
           +  +  + K+ G +GI  I+  K+I                   +S    + +  +    
Sbjct: 53  MCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRF 112

Query: 179 VYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           + +++   E  D  I   GG+E    A + L
Sbjct: 113 IQQMRTHPELRDFPISGIGGIETWEDAAEFL 143


>gi|291617457|ref|YP_003520199.1| NamA [Pantoea ananatis LMG 20103]
 gi|291152487|gb|ADD77071.1| NamA [Pantoea ananatis LMG 20103]
          Length = 386

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 80/233 (34%), Gaps = 36/233 (15%)

Query: 39  NILGFSTQEK-PLALQIGGADISK----LVEAAKIVEDFGYNEINLNVG---------CP 84
           + L FS  E  PL +Q   +D+ +     V  AK     G   I ++            P
Sbjct: 153 SALSFSDGEHLPLEMQ--ASDLERVKNAFVATAKRAVRLGIELIEVHAAHGYLLHQFLSP 210

Query: 85  SARVHEGSFGACL---MLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALR 137
            +      +G  L   M  P    +   A+ +A+   IPV V+      V+         
Sbjct: 211 LSNKRSDEYGGSLENRMRYP---LEVFHAVREAVPAEIPVGVRISASDWVEGGWDVGQSI 267

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGG 196
              K ++      I + +      GLS +   K+ PN       +I+++   + +   G 
Sbjct: 268 AFSKQLESLNCAYIHVSSG-----GLSEQQQIKVGPNYQVPFARDIRQQIG-IPVIAVGL 321

Query: 197 LEDMSQALKIL--PSVDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIKTR 246
           + +  QA  IL     D V + R    N         E+ +N       +++ 
Sbjct: 322 ITEPQQAEDILQQEEADLVALARGMLYNPRWPWHAAAEFNANVKAPPQYLRSE 374


>gi|85706547|ref|ZP_01037640.1| 2,4-dienoyl-CoA reductase [Roseovarius sp. 217]
 gi|85668959|gb|EAQ23827.1| 2,4-dienoyl-CoA reductase [Roseovarius sp. 217]
          Length = 677

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 44/132 (33%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +       +  RI   D I    PA  +  L + I+ +G +   ++      +
Sbjct: 203 EIVRAVRERCGPDFLIIYRISAADLIEGGAPADEIAALARKIEAAGAD--ILNTGIGWHE 260

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P     +P   +       K    + +  +  +   + A  IL S D  MI   R  
Sbjct: 261 ARVPTIAYPVPRGAWRKAAANIKAAVSIPVVASNRINTPAMAEDILSSGDADMISMARPF 320

Query: 220 YKNSAMLTTVDE 231
             +   +    E
Sbjct: 321 LADPHFVKKARE 332


>gi|160903178|ref|YP_001568759.1| dihydroorotate dehydrogenase family protein [Petrotoga mobilis
           SJ95]
 gi|160360822|gb|ABX32436.1| dihydroorotate dehydrogenase family protein [Petrotoga mobilis
           SJ95]
          Length = 363

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/161 (18%), Positives = 60/161 (37%), Gaps = 29/161 (18%)

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG----- 150
            L  +P  + + I A  +   +PV VK    VD       +    K  + +G +G     
Sbjct: 126 YLGNDPTPMINSIRAAKETTDLPVMVKLSPQVD-------IPKFAKEAENAGADGLVLIN 178

Query: 151 -------IWIHARKAIL---KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
                  I + + K +L    G      + I  L    V+E  + + ++ +   GG+   
Sbjct: 179 SFGPTLDIDLESGKPLLGSENGFGWLSGQAIFPLALRSVFEAVR-SVNIPVVGVGGINTG 237

Query: 201 SQALKI-LPSVDGVMIGRAAYKN-SAML----TTVDEYFSN 235
            +A+K+ +     V +  AA  N   +       +++Y  +
Sbjct: 238 KEAIKMIMAGAQAVQVCTAAILNGPQIYKKITNEIEKYLDD 278


>gi|28870255|ref|NP_792874.1| NADH:flavin oxidoreductase / NADH oxidase family [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|28853502|gb|AAO56569.1| NADH:flavin oxidoreductase / NADH oxidase family [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 365

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 50/135 (37%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGI 151
               +  D IA + KA    PV V+   G  +               +  ++  +GV+ I
Sbjct: 209 QRLRLTLDVIAEVKKAAGQAPVGVRISQGKVNDFQHKWAGGERDAEVIFGALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            I   +A                +  +V   ++  PD+ +  NGGL D  +A ++     
Sbjct: 269 HITEHQAW--------QPAFAQGEASLVRLARRYAPDVALIANGGLHDPEKAAQVFRDGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|168015012|ref|XP_001760045.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162688795|gb|EDQ75170.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 386

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 79/236 (33%), Gaps = 46/236 (19%)

Query: 4   WTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV 63
            +DR +           +L  EM     +       IL  S  E+         D  +  
Sbjct: 92  ISDRPF---------ETML-AEM---KQLKEEYPDRILIASIMEE------YNRDAWE-- 130

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  + VE+ G +   +N  CP     E   G  +  +  ++ +    +    +IPV  K 
Sbjct: 131 EIIERVEETGVDAFEVNFSCPHGM-PERKMGMAMGQDCSVLDEVCGWINAKATIPVWAKM 189

Query: 124 RIGVDD--QIPAVALRNLVKSIKK-------SGVNGIWIHARKAIL-----KGLSPKDNR 169
              + D  Q   VAL    + +          G+N   +     +       G S K  R
Sbjct: 190 TPNITDITQPARVALNAGCEGVAAINTITSVMGINLDTLRPEPCVEGYSTPGGYSSKAVR 249

Query: 170 KIPNLDYDIVYE-IKKENP--DLFIGLNGGLEDMSQALK-ILPSVD------GVMI 215
            I       + + +K E P  +  +   GG+E    A + IL   D      GVM+
Sbjct: 250 PIALAKVMSIAQMMKAEFPGQNKSLSGIGGIETGDHAAEFILLGADTVQVCTGVML 305


>gi|313620971|gb|EFR92119.1| probable tRNA-dihydrouridine synthase 1 [Listeria innocua FSL
          S4-378]
          Length = 71

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEK 48
          M   ++  +R   +      L+  EMI    I   + K   +L    +EK
Sbjct: 18 MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTLDMLYIDEKEK 66


>gi|107103912|ref|ZP_01367830.1| hypothetical protein PaerPA_01004983 [Pseudomonas aeruginosa PACS2]
          Length = 681

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 68/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + L+            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPLKSPISWFTPRELSERGIRKTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     +  +G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDQWGGPLENRMRLALEIVRGIRRIVGQRFILCYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWDEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAESLLATDKADLVSMARPLLADP 328


>gi|238490974|ref|XP_002376724.1| NADH oxidase, putative [Aspergillus flavus NRRL3357]
 gi|220697137|gb|EED53478.1| NADH oxidase, putative [Aspergillus flavus NRRL3357]
          Length = 413

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 39/214 (18%), Positives = 72/214 (33%), Gaps = 31/214 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            EAAK      ++ I ++            P +      +G        I+ +    +  
Sbjct: 194 AEAAKRAVRANFDAIEIHAAHGYLLHQFLSPVSNRRTDKYGGSFENRVRILLEICEEVRA 253

Query: 114 ALS--IPVTVKCRI----GVDDQIPAVALR--------NLVKSIKKSGVNGIWIHARKAI 159
            +   +P+ V+         DD +               L   +   GV+ + + +    
Sbjct: 254 VIPTAMPLLVRISATDWFEFDDNLTKEFPESWTVAQSIRLALLLADRGVDLVDVSSGGIH 313

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
            K  S    R  P        EIKK     L I   GG++  + A +++   +D V  GR
Sbjct: 314 AK--SAIAIRSGPGYQVHFAQEIKKAVGEKLLISAVGGIKTGALAEEVVQSGIDAVQAGR 371

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
              +N  ++      F+N L     + T++D  F
Sbjct: 372 WFQQNPGLVR----AFANELGVKVRMATQIDWSF 401


>gi|302874369|ref|YP_003843002.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium cellulovorans
           743B]
 gi|307691032|ref|ZP_07633478.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium cellulovorans
           743B]
 gi|302577226|gb|ADL51238.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium cellulovorans
           743B]
          Length = 332

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/215 (16%), Positives = 76/215 (35%), Gaps = 33/215 (15%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL------- 79
           + A AI+    +  +     ++ +   I         +AAK V+D G++ + +       
Sbjct: 120 VSASAIIHPSMRFEVPRELSKEEIKEII-----KNFKDAAKRVKDAGFDGVEIHSAHGYL 174

Query: 80  --NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-------- 129
                 P        +G  ++    I  + I A+ + +     V  R+G  D        
Sbjct: 175 LNQFYSPLTNKRTDDYGGDVLGRIRIHLEIIKAVKEVVGEEFPVLLRLGSSDYREDGTTI 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           +   +A+       +K+G++ + +            +       L      E  KE   +
Sbjct: 235 EDSKIAVLEF----EKAGIDILDVSGGFCGYMAPGREGQGYFSEL-----TEAIKEVISI 285

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            + L GG+ ++  A  ++     D V +GRA  ++
Sbjct: 286 PVILTGGITEVEAAENLIATGKTDLVGVGRAMLQD 320


>gi|254244287|ref|ZP_04937609.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa 2192]
 gi|126197665|gb|EAZ61728.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa 2192]
          Length = 681

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 68/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + L+            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPLKSPISWFTPRELSERGIRKTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     +  +G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDQWGGPLENRMRLALEIVRGIRRIVGQRFILCYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWDEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAESLLATDKADLVSMARPLLADP 328


>gi|114563676|ref|YP_751189.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella frigidimarina
           NCIMB 400]
 gi|114334969|gb|ABI72351.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella frigidimarina
           NCIMB 400]
          Length = 397

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 70/186 (37%), Gaps = 16/186 (8%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
                ++A + +D G+  + ++ G          P     +  +G  +     I+ + IA
Sbjct: 144 PDMYAKSAMLAKDVGFTGVQIHAGHGFLLSQFLSPLFNHRQDQYGGSIEARCRIIVEIIA 203

Query: 110 AMCKAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            +  A+  S P+ +K      ++  +        ++ + ++ ++ I I          S 
Sbjct: 204 KVRSAVGDSFPIGIKINSTDQLEGGLTQEDALAAIRILDQTSLDLIEISGGSYFPGAKSS 263

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            D+        +     K+   ++ I + GG +  +QALK++   +VD V + RA     
Sbjct: 264 SDSSTKGPYFAEFAATAKR-LSNVPIAVTGGFKTYAQALKVIESGAVDFVGLARALVITP 322

Query: 224 AMLTTV 229
            +    
Sbjct: 323 ELAKDW 328


>gi|325289344|ref|YP_004265525.1| 2,4-dienoyl-CoA reductase (NADPH) [Syntrophobotulus glycolicus DSM
           8271]
 gi|324964745|gb|ADY55524.1| 2,4-dienoyl-CoA reductase (NADPH) [Syntrophobotulus glycolicus DSM
           8271]
          Length = 707

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/183 (14%), Positives = 61/183 (33%), Gaps = 16/183 (8%)

Query: 64  EAAKIVEDFGYNEINLN------VGC---PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EAA+  ++ G++ + ++      + C     +      +G  L        + I A+  A
Sbjct: 216 EAARRAKEAGFDAVEIHGAHGYLIDCFLNAYSNTRTDEYGGDLERRARFGREVIRAVRAA 275

Query: 115 L--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +    PV ++   R      I         +  +  G++ + I          +      
Sbjct: 276 VGADFPVLMRMSARENYPGGITLEEGIKAARLYEAEGIDALDISQGCYGAMPYTVPPYYL 335

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
              ++     +IK  N  + + + G +     A +IL     D + +GR    +   +  
Sbjct: 336 PERVNVYNASQIK-MNVQIPVIVAGKIYTPDIAEEILQNGEADFISLGRILLTDPDFVRK 394

Query: 229 VDE 231
             E
Sbjct: 395 TQE 397


>gi|15600007|ref|NP_253501.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa PAO1]
 gi|9951081|gb|AAG08199.1|AE004894_5 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa PAO1]
          Length = 681

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 68/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + L+            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPLKSPISWFTPRELSERGIRKTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     +  +G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDQWGGPLENRMRLALEIVRGIRRIVGQRFILCYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWDEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAESLLATDKADLVSMARPLLADP 328


>gi|323488959|ref|ZP_08094196.1| NADPH dehydrogenase NamA [Planococcus donghaensis MPA1U2]
 gi|323397351|gb|EGA90160.1| NADPH dehydrogenase NamA [Planococcus donghaensis MPA1U2]
          Length = 338

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 78/224 (34%), Gaps = 24/224 (10%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINL---------NVGCPS 85
           + L F    K L  ++   DI + +EA    A   +  G++ I L             P 
Sbjct: 119 SALAFDDSYK-LPKEMSSQDIEETIEAFQLGAIRAKKAGFDVIELHGAHGYLLNQFLSPL 177

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ--IPAVALRNLVKSI 143
                  +G        ++G  I A+ +    P+ V+       +  + A     + + +
Sbjct: 178 TNQRTDEYGGSAENRYRLLGKVIDAVNEVWDGPLFVRISAHDYSEGGMTADQYVEMCQWM 237

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           K+ GV+ + + +   +     P      P         IKKE P +  G  G +     A
Sbjct: 238 KQQGVDLVDVSSGAVV-----PARIPVFPGYQVPFAETIKKETP-IATGAVGLITSPLHA 291

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
            +IL +   D V + R   ++     T  +  +  +T   P K 
Sbjct: 292 EEILQNDRADMVFLARELLRDPYWAYTAAKELNAEITAPEPYKR 335


>gi|116784451|gb|ABK23347.1| unknown [Picea sitchensis]
          Length = 368

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/173 (17%), Positives = 62/173 (35%), Gaps = 25/173 (14%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + VE+ G + + +N  CP     E   GA +  +  ++ +    + +  ++PV  K    
Sbjct: 116 ERVEETGVDALEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWVNEKATVPVWAKMTPN 174

Query: 127 VDD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDNRKIP 172
           V D         +  +  +  +   +   G+N   +     +       G S K    I 
Sbjct: 175 VTDIAEPARVALRSGSEGIAAINTIMSVMGINLDTLRPEPCVEGYSTPGGYSSKAVHPIA 234

Query: 173 NLDYDIVYE-IKKENPDLF--IGLNGGLEDMSQALK-------ILPSVDGVMI 215
                 + + +K E PD    +   GG+E+   A +        +    GVM+
Sbjct: 235 LAKVMSIAQMMKSEFPDPALSLSGIGGVENGGHAAEFILLGANTVQVCTGVMM 287


>gi|218893908|ref|YP_002442777.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa LESB58]
 gi|218774136|emb|CAW29953.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa LESB58]
          Length = 681

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 68/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + L+            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPLKSPISWFTPRELSERGIRKTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     +  +G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDQWGGPLENRMRLALEIVRGIRRIVGQRFILCYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWDEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAESLLATDKADLVSMARPLLADP 328


>gi|319785683|ref|YP_004145158.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317464195|gb|ADV25927.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 373

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 55/179 (30%), Gaps = 20/179 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V+AA+     G + + ++            P +      +G  L     ++     A
Sbjct: 167 EAFVDAARRAARIGLDLVEIHAAHGYLLHQFLSPLSNQRTDEYGGSLENRLRLLLRVFDA 226

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  AL   V+V  RI   D             L + +   G + I + +      GL P+
Sbjct: 227 VRAALPEHVSVGVRISATDWVEGGWDLEQSIALARELDARGCHFIHVSSG-----GLDPR 281

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               I            +E   + +   G +    QA  I+     D V + R    + 
Sbjct: 282 QQIAIGPGYQVPFAAAIREQVRMPVIAVGLITGARQAEAIVADGQADAVALARGILYDP 340


>gi|167754669|ref|ZP_02426796.1| hypothetical protein CLORAM_00172 [Clostridium ramosum DSM 1402]
 gi|167705501|gb|EDS20080.1| hypothetical protein CLORAM_00172 [Clostridium ramosum DSM 1402]
          Length = 637

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 32/147 (21%), Positives = 59/147 (40%), Gaps = 11/147 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L        +CIAA+   +    P+ VK      V+          + K ++ +G+
Sbjct: 186 YGGSLENRMRFTLECIAAIRTNVGPDFPILVKFTPVHKVEGFRQIDEGIAMAKILEDAGI 245

Query: 149 NGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
             + +     +A  K +S   N +   LD  +V  IK EN  L +   G L D  +A ++
Sbjct: 246 EALHVDVGCYEAWYKAISTVYNEEGHQLD--VVKAIK-ENVSLPVLGQGKLFDPKKAQEV 302

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +    +D V++G     +      V +
Sbjct: 303 VAQGVLDYVVLGHQMLADPHWANKVKQ 329


>gi|290992522|ref|XP_002678883.1| predicted protein [Naegleria gruberi]
 gi|284092497|gb|EFC46139.1| predicted protein [Naegleria gruberi]
          Length = 362

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 62/180 (34%), Gaps = 19/180 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AAK     G++ I ++            P++   +  FG        I+ + ++ 
Sbjct: 163 EDFVAAAKRAVLAGFDVIEIHAAHGYMINSFLSPTSNKRKDKFGGSFENRIRILTEIVSR 222

Query: 111 MCKALS--IP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +   +P  V + C   V D         L + +K  GV+ I   +     + LS  
Sbjct: 223 VRSCIPETMPLFVRISCDEYVSDGWDIEDSVRLAEILKDLGVDIIDCSSGGNSSRLLSQA 282

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                P         +++    + +   G + +  QA +IL     D V IGR    +  
Sbjct: 283 -LMAFPMYQVKYAERVRQ---VMPVAAVGKITEPVQANQILTEGKADLVFIGRKDLGDPY 338


>gi|78223407|ref|YP_385154.1| 2,4-dienoyl-CoA reductase [Geobacter metallireducens GS-15]
 gi|78194662|gb|ABB32429.1| 2,4-dienoyl-CoA reductase [Geobacter metallireducens GS-15]
          Length = 688

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/219 (15%), Positives = 67/219 (30%), Gaps = 22/219 (10%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           +G           + + AM  A+    P+ V+  +   V D             ++K+G 
Sbjct: 191 YGGDPQRRMAFGIETVRAMRNAVGEDFPLFVRHGVVDAVPDGASLAEGVAFAVELEKAGA 250

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +      + G               +   +K+      IG+ G ++    A  IL 
Sbjct: 251 DVLNVSLATPPICGGYVPTGADPVATHVHLAEAVKRAVGIPVIGV-GRIKTPDVAESILA 309

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
              VD V IGR  + +        E     +          ++    +      +YAA  
Sbjct: 310 QGKVDLVAIGRQLFADPHWPLKAAEGRIAEIVPCIDCHECYERATAGEGVECTVNYAAGR 369

Query: 267 LHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGAST 305
                  ++I           P  R+ R +L V  G + 
Sbjct: 370 EDE----RRIR----------PAERK-RRVLVVGGGPAG 393


>gi|73670765|ref|YP_306780.1| NADH-dependent flavine oxidoreductase [Methanosarcina barkeri str.
           Fusaro]
 gi|72397927|gb|AAZ72200.1| NADH-dependent flavine oxidoreductase [Methanosarcina barkeri str.
           Fusaro]
          Length = 325

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 30/179 (16%), Positives = 59/179 (32%), Gaps = 15/179 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + +AA    + G+N +  +       C     S       +G  ++    ++   +  + 
Sbjct: 121 MKQAAIRACEIGFNGVEFHFAYGFTLCKFLDASYNRRTDKYGGDVLYRARVLTQILPEIR 180

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
                   V  R+G         +    K+ +K+G++ + I           P D     
Sbjct: 181 NNTPKNFIVSVRMGEYLPESKDGI-EAAKAFEKAGIDLLHISFGMQPPANTVP-DGFICS 238

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
            + Y     IKKE     I +N  +    Q   ++ +  VD V +GR    +      V
Sbjct: 239 PITYSGCK-IKKEVKIPVIAVN-EIRTEEQVRFLIENDYVDLVAVGRGMLADPEFANHV 295


>gi|254515606|ref|ZP_05127666.1| dihydroorotate dehydrogenase [gamma proteobacterium NOR5-3]
 gi|219675328|gb|EED31694.1| dihydroorotate dehydrogenase [gamma proteobacterium NOR5-3]
          Length = 541

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 38/178 (21%), Positives = 67/178 (37%), Gaps = 12/178 (6%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
             ++ L   I G  + + VE AK++  F  + + LN+ CP A      +G  +  +P +V
Sbjct: 91  PADRFLLTSIFGGSVEEFVEVAKLLAPFS-DGLELNLSCPHA----SGYGMAMGQDPVVV 145

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK-----SIKKSGVNGIWIHARKAI 159
            + +AA+  A+ +PV  K      D                 +I   G      H    +
Sbjct: 146 AEIVAAVKAAVDVPVIPKLTPNTPDIGAIAKAAAGAGADGFCAINTVGPGYTSSHGEPVL 205

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
             G+     + +  +    + EI +E  DL I   GG    S   +      D + +G
Sbjct: 206 SNGVGGMSGKGVLPIALKCIREI-REVSDLPIVGCGGFSSASDVDEAFKAGADVIGVG 262


>gi|110597034|ref|ZP_01385323.1| dihydroorotate dehydrogenase family protein [Chlorobium
           ferrooxidans DSM 13031]
 gi|110341225|gb|EAT59690.1| dihydroorotate dehydrogenase family protein [Chlorobium
           ferrooxidans DSM 13031]
          Length = 314

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/244 (14%), Positives = 80/244 (32%), Gaps = 38/244 (15%)

Query: 26  MIVADAILRGDKKNILG-----FSTQEKPLALQIGGADISKLVEAAKIVED-FGYNEINL 79
           MI A  +     +  +        T +  + + I G  I +  E    ++   G +   +
Sbjct: 77  MINAIGLANVGIERFIEEKVPFLRTLDTAVIVNIAGRSIDEYGEVVSKLDRVDGLDGYEI 136

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL 139
           N+ CP    +       + ++ +   + ++ + K     + +K    V           +
Sbjct: 137 NLSCP----NVKGECMIMGVSRNATFEIVSELRKITHRHLMIKLTPNVTSISS------I 186

Query: 140 VKSIKKSGVNGIWI-----------HARKAILK----GLSPKDNRKIPNLD-YDIVYEIK 183
             + +++G + + +             RK +LK    GLS    + I     +++   +K
Sbjct: 187 ALAAEEAGADSVSLINTVVGMAVDYKTRKPLLKNITGGLSGPAIKPIALAKVWEVYNAVK 246

Query: 184 KENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                + +   GG+     A++ L      V IG   +    +   V        +    
Sbjct: 247 -----IPVVGMGGIAGFEDAMEFLVTGARAVQIGTMNFVYPDISEKVAVAIEQHFSAPGA 301

Query: 243 IKTR 246
           I  R
Sbjct: 302 IPIR 305


>gi|296391644|ref|ZP_06881119.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa PAb1]
          Length = 681

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 68/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + L+            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPLKSPISWFTPRELSERGIRKTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     +  +G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDQWGGPLENRMRLALEIVRGIRRIVGERFILCYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWDEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAESLLAAGKADLVSMARPLLADP 328


>gi|116052961|ref|YP_793279.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|115588182|gb|ABJ14197.1| 2,4-dienoyl-CoA reductase FadH2 [Pseudomonas aeruginosa UCBPP-PA14]
          Length = 681

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/216 (11%), Positives = 68/216 (31%), Gaps = 22/216 (10%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL--- 79
           Y  M V+ + L+            E+ +   I        V  A++ +   Y+ + +   
Sbjct: 120 YHPMAVSASPLKSPISWFTPRELSERGIRKTI-----RAFVRCARLAKAAAYDGVEVMGS 174

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---- 129
                    CP     +  +G  L     +  + +  + + +     +  R+ + D    
Sbjct: 175 EGYLLNQFLCPRTNRRDDQWGGPLENRMRLALEIVRGIRRIVGERFILCYRLSLLDLVEG 234

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                 +R +  +++++G+  +  +      +   P     +P   +  V    +    +
Sbjct: 235 GNTWDEVRRIALALEEAGITLL--NTGIGWHESRVPTIVTSVPRAAFAEVSARLRHELKV 292

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +  +  +     A  +L     D V + R    + 
Sbjct: 293 PVIASNRINTPEVAESLLAAGKADLVSMARPLLADP 328


>gi|148263658|ref|YP_001230364.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter uraniireducens
           Rf4]
 gi|146397158|gb|ABQ25791.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter uraniireducens
           Rf4]
          Length = 667

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/179 (15%), Positives = 67/179 (37%), Gaps = 17/179 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPS------ARVHEGS---FGACLMLNPDIVGDCIAAMC 112
             +AA  V+  G++ + +  G         + V       +G  L        + + A+ 
Sbjct: 147 FAQAALRVKTAGFDAVEILAGTGYLISEFLSEVTNKRIDDYGGSLENRMRFGLEVLRAVR 206

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +++     +  R+  +D          L+   + +  +G + I ++      + L P+  
Sbjct: 207 ESVGPAFPLVVRMNGNDFMKGGTGRRELQEFARCLVAAGTDAICVNVG--WHEALVPQIV 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
            K+P   +  +    KE   + +  +  + D + A  ++     D V +GRA   + A+
Sbjct: 265 TKVPRGVFAYLARGVKEAVHVPVIASHRINDPAVARDLIADGMCDMVAMGRALIADPAL 323


>gi|16082491|ref|NP_393640.1| NADH:flavin oxidoreductase [Thermoplasma acidophilum DSM 1728]
          Length = 548

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 76/213 (35%), Gaps = 26/213 (12%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLV----EAAKIVEDFGYNEINLNVGCP 84
           A AI   ++  I    T   P   ++  +DI  ++    +AA I E  G++ I ++    
Sbjct: 107 AKAIGAINEYKIAPSKTNFDPSVREMDASDIEDVISAYRKAANIAERSGFDGIEIHGA-- 164

Query: 85  SARVHEG-----------SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
              + +             +G           + I A+   + IPV ++  +  D++   
Sbjct: 165 HGYLVDEFLSPWWNKRTDRYGGSFENRIRFAQEVIDAVRSEVDIPVGIRISLYEDEEDGY 224

Query: 134 --VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                  + +SI+   ++ + + A      G S   +   P+    I  +++       I
Sbjct: 225 SPDYGMKIAESIRN--IDYVHVSAGNNEPPGSS--ASFYSPHAH--IFQKLRGSTGKTLI 278

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
              G +        +L + D V +GRA   +  
Sbjct: 279 VA-GSITAREDVDLVLSAADFVAVGRAMLADPY 310


>gi|83775193|dbj|BAE65316.1| unnamed protein product [Aspergillus oryzae]
          Length = 246

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 69/170 (40%), Gaps = 14/170 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
           K V+ A+++ D G++ + L+    +      ++G  L      V D I  + KA+     
Sbjct: 12  KFVDTARLMADSGFSGVELHG---AHGYLIDAYGGTLEKRAKFVLDIITEIRKAVPSKFC 68

Query: 121 VKCRIGVDDQIPAVALRNLVKS--IKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNL 174
           V  ++   D   +     + +   + ++G++ + +        +++ G  P+ + +    
Sbjct: 69  VGIKLNSADHSSSTFEETMAQIGLLVEAGIDFLEVSGGSYEDPSMMGGTQPQKSARTAAR 128

Query: 175 DYDIVY---EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           +   +    E +K  PDL   L GG    + A   +     D + IGR A
Sbjct: 129 EAFFIEFATEARKRYPDLVFMLTGGFRSRTGAESAIKENACDLIGIGRPA 178


>gi|281357935|ref|ZP_06244420.1| NADH:flavin oxidoreductase/NADH oxidase [Victivallis vadensis ATCC
           BAA-548]
 gi|281315593|gb|EFA99621.1| NADH:flavin oxidoreductase/NADH oxidase [Victivallis vadensis ATCC
           BAA-548]
          Length = 360

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 23/186 (12%), Positives = 57/186 (30%), Gaps = 15/186 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA    + G++ + ++            P        +G  L     ++ + +++
Sbjct: 143 DLFTSAAVRAHEAGFDAVEVHAAHGYLLSQFLSPVYNKRTDRYGGELANRARLLYEIVSS 202

Query: 111 MCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+    P+ VK       D    A    ++ + +++ GV+ I +       +     
Sbjct: 203 IRNAVGGDFPILVKINSDDFADGGFTAAECGSVCEELQERGVDAIELSGGIPASRPGFGS 262

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                    Y  +    +   D+ + L GG          L     D + + R   +   
Sbjct: 263 LRNAGEPPYYREIARKIRNRIDIPVILVGGFTRFETCNAALHDGCADLIALSRPLIREPE 322

Query: 225 MLTTVD 230
           ++    
Sbjct: 323 LIERWR 328


>gi|218670690|ref|ZP_03520361.1| dihydropyrimidine dehydrogenase [Rhizobium etli GR56]
          Length = 214

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
           +VE+ G + I LN GCP     E   G+ +   P+ +   +    +   +PV  K    +
Sbjct: 124 LVEETGADGIELNFGCPHGMS-ERGMGSAVGQVPEYIEMVVRWCKQYTRMPVITKLTPNI 182

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWI 153
            D      +R   ++ K  G + + +
Sbjct: 183 TD------IRRPARAAKAGGTDAVSL 202


>gi|83776037|dbj|BAE66156.1| unnamed protein product [Aspergillus oryzae]
          Length = 409

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/188 (18%), Positives = 72/188 (38%), Gaps = 17/188 (9%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALRNLVKSI---KKSG 147
           ++G  +     ++ +   A+ + ++   TV  +I  V+ Q     L   V+     +K  
Sbjct: 194 NYGGSIKNRMKLISEIRKAISERVAETFTVGIKINTVEFQESTFNLEETVQLCIEFEKMR 253

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-----LDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
            + + +         +  K    IP      L+Y  +Y  K E   +++   GG   +  
Sbjct: 254 FDFVELSGGTYEDWTIGRKQVASIPQHEGFFLEYGRIYSEKMERTKVYVT--GGYRSVKG 311

Query: 203 ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
            ++ +  VDG+ + R   +   + + +    S  +  + PIK   D      ++A M   
Sbjct: 312 MIRAVQEVDGIGLARPLCQEPHLCSHI---LSGSVETAPPIKIDTDNFHLTSVAALMQM- 367

Query: 263 AARHLHSG 270
             +HL  G
Sbjct: 368 --QHLGKG 373


>gi|91200420|emb|CAJ73467.1| similar to 2,4-dieonyl-CoA reductase, FMN-linked [Candidatus
           Kuenenia stuttgartiensis]
          Length = 682

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/139 (17%), Positives = 54/139 (38%), Gaps = 8/139 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L        + + A+ +      PV  +      V+D I       +   ++K+G 
Sbjct: 199 YGGSLENRARFAKELVIAIKEEAGGDYPVIFRLSGEDFVEDGIRINDSVEIAGILEKAGA 258

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           +   +       +   P  +  IP + Y +  E  K + ++ +  +  + D+S A +IL 
Sbjct: 259 DAFNVSPG--WHESRIPIMSMVIPRMTYVLFSEKIKAHVNVPVISSVRINDLSLAEEILD 316

Query: 209 S--VDGVMIGRAAYKNSAM 225
           +   D V +GR    +  +
Sbjct: 317 NDRADAVSVGRPLIADPEL 335


>gi|325569378|ref|ZP_08145534.1| Oye family NADH-dependent flavin oxidoreductase [Enterococcus
           casseliflavus ATCC 12755]
 gi|325157378|gb|EGC69539.1| Oye family NADH-dependent flavin oxidoreductase [Enterococcus
           casseliflavus ATCC 12755]
          Length = 370

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 32/229 (13%), Positives = 70/229 (30%), Gaps = 28/229 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A +     G++ + L             P +      +G  L      +   +  
Sbjct: 147 ENFKKATERAIKAGFDGVELHGANTYLIQQFFSPHSNRRSDEWGGSLENRYRFIEKLVDE 206

Query: 111 MCKALS----IPVTVKCRIGVDD-QIPAVALRN---LVKSIKKSGVNGIWIHARKAILKG 162
           + + +         V  R   ++ + P +   +   LV  + + G++ + I       K 
Sbjct: 207 VLETVDQSGVKEFIVGYRFSPEEFEEPGIRFEDTLFLVDQLAEKGLDYLHISLADYTRKS 266

Query: 163 LSPKDNRK-IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
           +S     K I    Y+ + +       + +   G +     A  +L   D V +GRA   
Sbjct: 267 ISKAYQEKSILAYVYEKIAQ------RVPLIGVGDVRTSKDAAGLLEHADFVAVGRALLI 320

Query: 222 NSA----MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
           +      +L   DE     ++     +  +    W  +   M D     
Sbjct: 321 DPHWGQKVLDGQDELIRTTVSTYEREELVLQNGVWGFMENMMPDRLNEE 369


>gi|10639307|emb|CAC11309.1| NADH oxidase related protein [Thermoplasma acidophilum]
          Length = 536

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 76/213 (35%), Gaps = 26/213 (12%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLV----EAAKIVEDFGYNEINLNVGCP 84
           A AI   ++  I    T   P   ++  +DI  ++    +AA I E  G++ I ++    
Sbjct: 95  AKAIGAINEYKIAPSKTNFDPSVREMDASDIEDVISAYRKAANIAERSGFDGIEIHGA-- 152

Query: 85  SARVHEG-----------SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
              + +             +G           + I A+   + IPV ++  +  D++   
Sbjct: 153 HGYLVDEFLSPWWNKRTDRYGGSFENRIRFAQEVIDAVRSEVDIPVGIRISLYEDEEDGY 212

Query: 134 --VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                  + +SI+   ++ + + A      G S   +   P+    I  +++       I
Sbjct: 213 SPDYGMKIAESIRN--IDYVHVSAGNNEPPGSS--ASFYSPHAH--IFQKLRGSTGKTLI 266

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
              G +        +L + D V +GRA   +  
Sbjct: 267 VA-GSITAREDVDLVLSAADFVAVGRAMLADPY 298


>gi|238586743|ref|XP_002391263.1| hypothetical protein MPER_09331 [Moniliophthora perniciosa FA553]
 gi|215455695|gb|EEB92193.1| hypothetical protein MPER_09331 [Moniliophthora perniciosa FA553]
          Length = 190

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/159 (19%), Positives = 59/159 (37%), Gaps = 27/159 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      P+        G   M +P ++ + +     A++IPV  K
Sbjct: 6   AEQARIAEEAGACAVMALERVPAD--IRAQGGVARMSDPKLIKEIV----DAVTIPVMAK 59

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            RIG   +          + ++  G++ I         + L+P D     N  +  V  +
Sbjct: 60  VRIGHFVE---------AQILQSLGIDYID------ESEVLTPADEEHHINKHFXKVPFV 104

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                 +     GG+   + A  ++    DGV +G   +
Sbjct: 105 C-----VVNFAAGGIATPADAALMMQLGCDGVFVGSGIF 138


>gi|153955074|ref|YP_001395839.1| NADH oxidase [Clostridium kluyveri DSM 555]
 gi|219855513|ref|YP_002472635.1| hypothetical protein CKR_2170 [Clostridium kluyveri NBRC 12016]
 gi|146347932|gb|EDK34468.1| Predicted NADH oxidase [Clostridium kluyveri DSM 555]
 gi|219569237|dbj|BAH07221.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 349

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 36/209 (17%), Positives = 75/209 (35%), Gaps = 28/209 (13%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP--- 84
            +D I R      +     E     Q         V AA   E  G++ +  +       
Sbjct: 120 SSDYIHRNISARAMTKH--ELHSIQQ-------DFVNAALRAEKAGFDGVEFHGAHSYLM 170

Query: 85  ----SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
               S ++++    +G  L        + +  + + +     V  R+G ++     ++ N
Sbjct: 171 TQFFSTKINKRVDEYGGSLDNRLRFTMEILQGVKQKVGASFVVGIRMGCNESDLETSI-N 229

Query: 139 LVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNG 195
           + K  + SG++ I +        +K   PKD       ++ +    K KE  ++ +    
Sbjct: 230 MAKKFEASGMDYIHVSTGYDNTPIKEEVPKDF----PCNWIVYGAAKIKEQVNIPVIAVN 285

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKN 222
            ++   QA  ++ +   D V IGRA   +
Sbjct: 286 SIKTKEQANYLIDNNLADFVAIGRAQLAD 314


>gi|16079439|ref|NP_390263.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. subtilis str.
           168]
 gi|221310301|ref|ZP_03592148.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. subtilis str.
           168]
 gi|221314625|ref|ZP_03596430.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. subtilis str.
           NCIB 3610]
 gi|221319548|ref|ZP_03600842.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. subtilis str.
           JH642]
 gi|221323824|ref|ZP_03605118.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. subtilis str.
           SMY]
 gi|321311860|ref|YP_004204147.1| NADPH dehydrogenase NamA [Bacillus subtilis BSn5]
 gi|1731075|sp|P54550|NAMA_BACSU RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|1303964|dbj|BAA12619.1| YqjM [Bacillus subtilis]
 gi|2634817|emb|CAB14314.1| NADPH-dependent flavin oxidoreductase [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291484816|dbj|BAI85891.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. natto BEST195]
 gi|320018134|gb|ADV93120.1| NADPH dehydrogenase NamA [Bacillus subtilis BSn5]
          Length = 338

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 66/193 (34%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA   ++ G++ I ++            P +      +G         + + I  +
Sbjct: 145 EFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEV 204

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P  V V      D  +         K +K+ GV+ I   +   +       D  
Sbjct: 205 KQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALV-----HADIN 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P        +I+++  D+  G  G + D S A +IL +   D + IGR   ++     
Sbjct: 260 VFPGYQVSFAEKIREQA-DMATGAVGMITDGSMAEEILQNGRADLIFIGRELLRDPFFAR 318

Query: 228 TVDEYFSNPLTGS 240
           T  +  +  +   
Sbjct: 319 TAAKQLNTEIPAP 331


>gi|308178394|ref|YP_003917800.1| flavin oxidoreductase [Arthrobacter arilaitensis Re117]
 gi|307745857|emb|CBT76829.1| putative flavin oxidoreductase [Arthrobacter arilaitensis Re117]
          Length = 369

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/197 (17%), Positives = 67/197 (34%), Gaps = 25/197 (12%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC- 112
            + AK  +  G++ + ++            P +      +G         + + I A+  
Sbjct: 173 AQGAKRADAAGFDLVQIHAAHGYLVHQFLSPLSNKRTDEYGGSFENRTRYLREIIEAVAA 232

Query: 113 -----KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                KAL I  + +    V++         L K +   GV    + +      G+    
Sbjct: 233 VWPENKALGIRFSGE--DWVEEGWVIADTIQLAKELYGFGVRHFDLSSA-----GIGKFY 285

Query: 168 NRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
               P     +   +K+  P D F+   G + + +QA +I+     DGV IGRAA  +  
Sbjct: 286 GPSGPGYQVPLAQAVKEALPEDAFVTAVGVITEPAQAGQIVGTGQADGVCIGRAALGDPQ 345

Query: 225 MLTTVDEYFSNPLTGSS 241
                 +     +   +
Sbjct: 346 WPNRAAQALGAEMAAPA 362


>gi|302549575|ref|ZP_07301917.1| oxidoreductase [Streptomyces viridochromogenes DSM 40736]
 gi|302467193|gb|EFL30286.1| oxidoreductase [Streptomyces viridochromogenes DSM 40736]
          Length = 359

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 56/178 (31%), Gaps = 13/178 (7%)

Query: 67  KIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC 123
           +I E  G +   +N    P +     ++G           + + A+ +      P+  + 
Sbjct: 176 EIAEIHGAHGYLINEFLSPHSNHRTDAYGGSYENRTRFALEVVDAVRQVWPQDKPLFFRI 235

Query: 124 RIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
                  +D   A         +K  GV+ + +          S       P        
Sbjct: 236 SATDWLEEDGWSADDTVRFAADLKAHGVDLLDVSTG----GNASGVRIPTGPGYQVPFAA 291

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +K+E   L +   G + ++ QA KIL     D V++GR   +N +            
Sbjct: 292 RVKRETT-LPVAAVGLITEVEQAEKILANGEADAVLLGRELLRNPSWARLAARELGGE 348


>gi|56808851|ref|ZP_00366563.1| COG0042: tRNA-dihydrouridine synthase [Streptococcus pyogenes M49
          591]
          Length = 82

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFS 44
          M   T+  +R  A+      L+  EMI    +L  ++K +    
Sbjct: 24 MAGVTNSAFRTIAKEF-GAGLVVMEMISEKGLLYNNEKTLHMLH 66


>gi|330901544|gb|EGH32963.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           japonica str. M301072PT]
          Length = 370

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 52/135 (38%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  + IAA+ K A   PV V+   G  +              ++  ++  +GV+ I
Sbjct: 209 QRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFAALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A     +      +           ++  PD+ +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAWQPAFAQGQASLVELA--------RRYAPDVTLIANGGLHDPQKADQVLRAGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|23097483|ref|NP_690949.1| NADH-dependent flavin oxidoreductase [Oceanobacillus iheyensis
           HTE831]
 gi|22775706|dbj|BAC11984.1| NADH-dependent flavin oxidoreductase [Oceanobacillus iheyensis
           HTE831]
          Length = 343

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 76/211 (36%), Gaps = 29/211 (13%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG-DCIAA 110
           +  +AAK   + G++ I +             P     E  +G     +  + G + I A
Sbjct: 144 QFQDAAKRAVEAGFDTIEIHGAHGYLIHQFHSPLINKREDRYG----EDLSLFGVEVIQA 199

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +   +P+ ++                 ++ K  +++GV+   I +      G    
Sbjct: 200 IKEVIPEDMPLLMRISAMEYMDEGYDLNHSVDIAKKYQEAGVDVFHISSGGEGPPGKRKP 259

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNS- 223
            N     + +       ++  ++ I   G LE    A   L + D   + IGR   K+  
Sbjct: 260 ANHPGYQIRF---ARTFRQELNVPIIAVGVLEHPKVAEAALGNEDADLIAIGRGMLKDPY 316

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
             +  ++E     +TG +    + ++ F RK
Sbjct: 317 WAIHAIEE-----ITGIAVPPKQYERAFPRK 342


>gi|285016987|ref|YP_003374698.1| nadh:flavin oxidoreductase [Xanthomonas albilineans GPE PC73]
 gi|283472205|emb|CBA14712.1| putative nadh:flavin oxidoreductase protein [Xanthomonas
           albilineans]
          Length = 365

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 25/146 (17%), Positives = 52/146 (35%), Gaps = 11/146 (7%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNL 139
           P + + E ++G  L     ++    AA+  A+S  + V  RI   D             L
Sbjct: 191 PLSNLREDAYGGSLDNRMRLLLRVHAAVRAAVSSTIAVGVRISATDWVEGGWDVAQSMVL 250

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++++  G + + + +      GL  +    +       + E      D+ +   G + +
Sbjct: 251 AQALQAQGCDYLHVSSG-----GLDRRQRIPVAPGYQVPLAETLHRAVDMPVIAVGLITE 305

Query: 200 MSQALKILPS--VDGVMIGRAAYKNS 223
             QA  IL     D + + R    + 
Sbjct: 306 PQQAEAILAEGRADAIALARGILYDP 331


>gi|157364729|ref|YP_001471496.1| dihydroorotate dehydrogenase [Thermotoga lettingae TMO]
 gi|157315333|gb|ABV34432.1| dihydroorotate dehydrogenase [Thermotoga lettingae TMO]
          Length = 386

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/160 (16%), Positives = 59/160 (36%), Gaps = 23/160 (14%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A++ E  G   + LNV CP   +             + +      +  ++ IP+ VK  +
Sbjct: 120 ARMAEGAGAPALELNVSCPHGSISFRGGDV-----EEKILSVAKIVRDSVKIPLIVKLPM 174

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI--------PNLDYD 177
            +   +       + K +++SG++G+ +  R   L     K+   +            ++
Sbjct: 175 QLSSPLS------MAKMLERSGIDGVVMFNRLTGLDINLEKERPVLHEGYAGHGGPWAFN 228

Query: 178 IV-YEIKKENPD--LFIGLNGGLEDMSQALK-ILPSVDGV 213
            V   I   +P   + +  +GG+      +K I    + V
Sbjct: 229 YVLRWIAASSPHLNISVAASGGVGSGEDIIKYIYAGANAV 268


>gi|299139852|ref|ZP_07033024.1| NADH:flavin oxidoreductase/NADH oxidase [Acidobacterium sp.
           MP5ACTX8]
 gi|298598206|gb|EFI54372.1| NADH:flavin oxidoreductase/NADH oxidase [Acidobacterium sp.
           MP5ACTX8]
          Length = 384

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 54/168 (32%), Gaps = 11/168 (6%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           +G  L        + I A+       +PV V+  +   V+  +         K +K  G+
Sbjct: 206 YGGSLANRARFPLEIIRAVRANFPEELPVWVRLSVTDWVEGGLTVEDAIEFAKLVKSEGI 265

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + I + +      G  P+    +         E  +    +  G  G + D +QA +I+ 
Sbjct: 266 DLIDVSSG-----GNDPRQQIPVGPGYQVAFAERVRREVGIATGAVGMITDPAQADQIIR 320

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
               D V++ R   ++        +    P       +        R+
Sbjct: 321 TGQADLVLLARELLRDPYWPIHAADALQRPAIWPKQYERAALGKVERR 368


>gi|254560142|ref|YP_003067237.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacterium
           extorquens DM4]
 gi|254267420|emb|CAX23259.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacterium
           extorquens DM4]
          Length = 336

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 54/147 (36%), Gaps = 17/147 (11%)

Query: 94  GACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQI------PAVALRNLVKSIKK 145
           G  +     +V     A+   +  S+PV V+   G  +               +  ++ +
Sbjct: 173 GGDMRRRTMLVRAVFDAVRATVPASVPVGVRISQGKVNDFGHKWAGREQDAEAIFGTLAE 232

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G + + +   K          +         +V   ++  P + +  NGG++D ++A +
Sbjct: 233 AGASYLHVTEHKVWEPAFEGGRD--------SLVALARRYAPHVTLIANGGVQDAARAQE 284

Query: 206 IL-PSVDGVMIGRAAYKNSAMLTTVDE 231
           ++    D V +G+AA  N      V  
Sbjct: 285 VMAAGADIVALGKAALANPDFPNRVRA 311


>gi|149179144|ref|ZP_01857713.1| hypothetical protein PM8797T_17554 [Planctomyces maris DSM 8797]
 gi|148842004|gb|EDL56398.1| hypothetical protein PM8797T_17554 [Planctomyces maris DSM 8797]
          Length = 354

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/197 (14%), Positives = 57/197 (28%), Gaps = 31/197 (15%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-- 116
                  AK   + G + +  N  CP   V        L   P+     +A+  KA+S  
Sbjct: 165 ADDYARCAKWAIESGADCVETNFSCP--NVCTRDG--QLYQQPE-AAALVASRVKAVSGT 219

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIK--------------KSGVNGIWIHARKAILKG 162
           +P  +K             L+ ++                    G        R     G
Sbjct: 220 VPYLIKIGHLSQKAEAHAFLQAVLPFAAGIVMTNSVATTVVDDQGTPLFSGEQR-----G 274

Query: 163 LSPKDNRKIP----NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGR 217
           +     R+       L  +++ E+  + P   +   GG+   S     L    +   +  
Sbjct: 275 ICGAATRQASLNQLRLFTELIAELPADQPRPDLISCGGIGSASDVRTFLAAGANATHLAT 334

Query: 218 AAYKNSAMLTTVDEYFS 234
           AA  +  +   + +  +
Sbjct: 335 AAMCDPLIACQIRKELA 351


>gi|309774909|ref|ZP_07669928.1| NADH oxidase [Erysipelotrichaceae bacterium 3_1_53]
 gi|308917306|gb|EFP63027.1| NADH oxidase [Erysipelotrichaceae bacterium 3_1_53]
          Length = 642

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 38/185 (20%), Positives = 71/185 (38%), Gaps = 31/185 (16%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIAA 110
              AAK   + GY+ +     C           P+    E ++G           DCI A
Sbjct: 144 FGAAAKRAVEAGYDCVE--FHCGHNYLPHSFLSPAFNHREDAYGGTFEKRCKFPLDCIRA 201

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGLSP 165
           + + +   +P+ ++     D     + + ++++     K++GV+ + I     I  GL  
Sbjct: 202 IRENIPQDMPLLMRLDAQDDYLENGLTIEDVIRYCKLAKEAGVDVLDISRGNMITAGLK- 260

Query: 166 KDNRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
               ++P +D       D   +I+KE   L     G +     A +IL     D V++GR
Sbjct: 261 ---YEVPPIDIPKGFNVDNCAKIRKETGML-CIAVGRINTPFLAEEILEQDKADLVVMGR 316

Query: 218 AAYKN 222
           A   +
Sbjct: 317 AQLAD 321


>gi|260772424|ref|ZP_05881340.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio metschnikovii CIP 69.14]
 gi|260611563|gb|EEX36766.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio metschnikovii CIP 69.14]
          Length = 643

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 19/207 (9%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHE 90
           I  F+  E  +  QI    I     +A++ +  GY+ + +            C    V  
Sbjct: 99  IAKFTPSEMSVR-QIR-NTIQAFAHSAELAQLAGYDGVEIMGSEGYLINQFICKRTNVRY 156

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKS 146
             +G           + + A+ +A+     +  R+     V++      +  L K ++K+
Sbjct: 157 DDWGGSYENRMRFPLEVVRAIREAVGKEFIIIFRLSMLDLVEEGSTFEEVLQLAKGLEKA 216

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV    I+      +   P    ++P   +  V E  K +  + +     +    QA KI
Sbjct: 217 GVT--IINTGIGWHEARIPTIATQVPRAAFSWVTEKIKSHLTVPVVTCNRINTPEQAEKI 274

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDE 231
           L     D V + R    +   +   ++
Sbjct: 275 LASGQADMVSMARPFLADPDFVRKAEQ 301


>gi|167757294|ref|ZP_02429421.1| hypothetical protein CLORAM_02844 [Clostridium ramosum DSM 1402]
 gi|167703469|gb|EDS18048.1| hypothetical protein CLORAM_02844 [Clostridium ramosum DSM 1402]
          Length = 660

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 51/144 (35%), Gaps = 7/144 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGV 148
           +G  +     ++ + IA + K       +  RI  DD             + K ++ + V
Sbjct: 203 YGGDITHRIRLLLEVIANVRKKCGRDFAIIVRISGDDYEAGGQSLHEGCYIAKRLEAAQV 262

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I +     I +G S            D   EIKK   ++ +   G L +     ++L 
Sbjct: 263 DMIHVSGGTTIHRGSSIAPPGTPQASHIDSAREIKK-CVNIPVSTVGRLNEPWILEEVLE 321

Query: 209 S--VDGVMIGRAAYKNSAMLTTVD 230
               D  M+GR+   +   +  + 
Sbjct: 322 RDLADVCMVGRSLLCDPDFVNKIK 345


>gi|242239013|ref|YP_002987194.1| NADH:flavin oxidoreductase/NADH oxidase [Dickeya dadantii Ech703]
 gi|242131070|gb|ACS85372.1| NADH:flavin oxidoreductase/NADH oxidase [Dickeya dadantii Ech703]
          Length = 365

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 63/180 (35%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                +A+  +  G++ I L+            P     +  +G  L      + +   A
Sbjct: 157 DAFAASARRADRLGFDLIELHAAHGYLLHQFLSPLTNQRDDEYGGSLQNRMRFLREVYTA 216

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +       I V +    GV+          L   +++   + I + +      GLSP+
Sbjct: 217 VREVFPRHKAIGVRISATDGVEGGWDLAQSLELAHLLRQLDCDFIHVSSG-----GLSPR 271

Query: 167 DNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               + PN       EI+++     I + G + +  QA  I+ +   D V + RA   + 
Sbjct: 272 QQLTVYPNYQVPYAREIRRQTGITTIAV-GLITEPEQAEAIVATGDADAVALARAILFDP 330


>gi|28898925|ref|NP_798530.1| 2,4-dienoyl-CoA reductase [Vibrio parahaemolyticus RIMD 2210633]
 gi|28807144|dbj|BAC60414.1| 2,4-dienoyl-CoA reductase [Vibrio parahaemolyticus RIMD 2210633]
          Length = 667

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 48/132 (36%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K ++ +GV    I+      +
Sbjct: 196 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKGLEDAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 254 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPDEAERILASGQADMVSMARPF 313

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 314 LADPYFVAKAEQ 325


>gi|84502424|ref|ZP_01000560.1| probable oxidoreductase [Oceanicola batsensis HTCC2597]
 gi|84389236|gb|EAQ02033.1| probable oxidoreductase [Oceanicola batsensis HTCC2597]
          Length = 396

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 58/177 (32%), Gaps = 19/177 (10%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+AA+  +  G++ + +             P       ++G  L      V +   AM 
Sbjct: 161 FVDAARRADRAGFDLVEIHGAHGYLLHQFLSPVTNHRTDAYGGSLENRMRFVLEIAQAMR 220

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                   +  R+   D  P    ++    L K++K  GV+ + + A          K  
Sbjct: 221 AVWPREKALGFRMNSTDWHPEGLTQDDADTLAKALKAIGVDYVVMSAGNLA---PGCKIP 277

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM--IGRAAYKNS 223
              P    +    +K       + + G +     A +I+ S D  M  IGR    N 
Sbjct: 278 PAAPGHQVEYARRVKAATGMTTMAV-GLIATADLAERIIESGDADMVAIGRGMLDNP 333


>gi|153838578|ref|ZP_01991245.1| 2,4-dienoyl-coa reductase (nadph) [Vibrio parahaemolyticus AQ3810]
 gi|149748043|gb|EDM58902.1| 2,4-dienoyl-coa reductase (nadph) [Vibrio parahaemolyticus AQ3810]
          Length = 670

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 48/132 (36%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K ++ +GV    I+      +
Sbjct: 199 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKGLEDAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPDEAERILASGQADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|294627530|ref|ZP_06706113.1| NADH flavin oxidoreductase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292598161|gb|EFF42315.1| NADH flavin oxidoreductase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 372

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/207 (14%), Positives = 61/207 (29%), Gaps = 22/207 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                +A   E  G   I L+            P +     ++G  L     +      A
Sbjct: 165 DAFAASATRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMLLTLRIFDA 224

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + V  RI   D             L +++   G + I + +      GL P+
Sbjct: 225 VRAAVSEKIAVGVRISATDWVEGGWDVQQGIALSQALDARGAHYIHVSSG-----GLDPR 279

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +    Y I   +  +      +   G + + +QA  I+     D + + R    + 
Sbjct: 280 QQIPL-QAGYQIPFAQEIRAQVSTPVIGVGLITEPAQAEAIVQEGQADAIALARGILYDP 338

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                        +T +        +D
Sbjct: 339 RWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|148272506|ref|YP_001222067.1| putative oxidoreductase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830436|emb|CAN01371.1| putative oxidoreductase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
          Length = 359

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/191 (14%), Positives = 60/191 (31%), Gaps = 22/191 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+   D G++ + ++            P +   +  FG  L     ++   I A
Sbjct: 158 DDFAAAARRSVDAGFDVLEIHAAHGYLMHQFLSPLSNHRDDEFGGSLENRARLLLQVIDA 217

Query: 111 MCKAL-SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP- 165
           +   +  +P+ V+        D          +     + G +   I           P 
Sbjct: 218 VRAEVPDVPLLVRFSATDWAGDAGWDEQQTATVAGWAAEHGADFFDISTGGNTTGVTIPV 277

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P  +Y       KE+  + +   G + + +QA  ++     D VM+GR   ++ 
Sbjct: 278 APGYQVPFAEY------VKEHAKVALNAVGLITEPAQAEAVVAEGRADAVMLGREMLRDP 331

Query: 224 AMLTTVDEYFS 234
                      
Sbjct: 332 HFALRAAHELG 342


>gi|328474534|gb|EGF45339.1| 2,4-dienoyl-CoA reductase [Vibrio parahaemolyticus 10329]
          Length = 670

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 48/132 (36%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K ++ +GV    I+      +
Sbjct: 199 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKGLEDAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPDEAERILASGQADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|308094699|ref|ZP_05891231.2| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio parahaemolyticus AN-5034]
 gi|308095282|ref|ZP_05904698.2| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio parahaemolyticus
           Peru-466]
 gi|308125647|ref|ZP_05776431.2| oxidoreductase, FAD/FMN-binding family [Vibrio parahaemolyticus
           K5030]
 gi|308088799|gb|EFO38494.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio parahaemolyticus
           Peru-466]
 gi|308094300|gb|EFO43995.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio parahaemolyticus AN-5034]
 gi|308115071|gb|EFO52611.1| oxidoreductase, FAD/FMN-binding family [Vibrio parahaemolyticus
           K5030]
          Length = 671

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 48/132 (36%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K ++ +GV    I+      +
Sbjct: 200 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIELAKGLEDAGVT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 258 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPDEAERILASGQADMVSMARPF 317

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 318 LADPYFVAKAEQ 329


>gi|257865574|ref|ZP_05645227.1| NADH:flavin oxidoreductase/NADH oxidase [Enterococcus casseliflavus
           EC30]
 gi|257871911|ref|ZP_05651564.1| NADH:flavin oxidoreductase/NADH oxidase [Enterococcus casseliflavus
           EC10]
 gi|257799508|gb|EEV28560.1| NADH:flavin oxidoreductase/NADH oxidase [Enterococcus casseliflavus
           EC30]
 gi|257806075|gb|EEV34897.1| NADH:flavin oxidoreductase/NADH oxidase [Enterococcus casseliflavus
           EC10]
          Length = 370

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 34/228 (14%), Positives = 69/228 (30%), Gaps = 26/228 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A +     G++ + L             P +      +G  L      +   +  
Sbjct: 147 ENFKKATERAIKAGFDGVELHGANTYLIQQFFSPHSNRRSDEWGGSLENRYRFIEKLVDE 206

Query: 111 MCKALS----IPVTVKCRIGVDD-QIPAVALRN---LVKSIKKSGVNGIWIHARKAILKG 162
           + + +         V  R   ++ + P +   +   LV  + + G++ + I       K 
Sbjct: 207 VLETVDQSGVKEFIVGYRFSPEEFEEPGIRFEDTLFLVDQLAEKGLDYLHISLADYTRKS 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           +S     K        VYE  K    + +   G +     A  +L   D V +GRA   +
Sbjct: 267 ISKSYQEKSMLA---YVYE--KIAQRVPLIGVGDVRTSKDAAGLLEHADFVAVGRALLID 321

Query: 223 SA----MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
                 +L   DE     ++     +  +    W  +   M D     
Sbjct: 322 PHWGQKVLDGQDELIRTTVSPYEREELVLQNGVWGFMENMMPDRLNEE 369


>gi|50083932|ref|YP_045442.1| putative FMN oxidoreductase [Acinetobacter sp. ADP1]
 gi|49529908|emb|CAG67620.1| putative FMN oxidoreductase [Acinetobacter sp. ADP1]
          Length = 370

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 27/180 (15%), Positives = 64/180 (35%), Gaps = 23/180 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               +A    + G+  I ++            P + + +  +G        +  + + A+
Sbjct: 160 DFAASAVRAVEAGFKLIEIHAAHGYLLHQFLSPLSNLRDDEYGGSFENRIRMTLEVLQAV 219

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKKSGVNGIWIH-ARKAILKGLSP 165
              +     V  RI   D +P  +        L +++++ G   I +      +++ +  
Sbjct: 220 KAVVPEGFPVGVRISATDWMPTQSWDIESSVGLSQALEQLGAAYIHVSSGGLHVMQDIKV 279

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N ++P        +IK+ N  + +   G + +  QA  IL     D + + RA   + 
Sbjct: 280 GANYQVPFA-----AQIKQ-NVSIPVIAVGLITEPDQAEAILQNDEADAIALARAMQYDP 333


>gi|82749804|ref|YP_415545.1| hypothetical protein SAB0027c [Staphylococcus aureus RF122]
 gi|82655335|emb|CAI79715.1| conserved hypothetical protein [Staphylococcus aureus RF122]
          Length = 159

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 38/128 (29%), Gaps = 16/128 (12%)

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
           + D    L++     +DGVMI R  + N                     +    K+    
Sbjct: 42  IPDRKTGLELAEKYGIDGVMIDRGIFHNPFAF-------------EKEPREHTSKELLDL 88

Query: 255 ISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAGASTATHHIIETA 314
           +   ++ +         + + + R       G   +   RH L +   +      +++  
Sbjct: 89  LRLHLSLFNKYEKDEIRQFKSLRRFFKIYVRGIRGASELRHQL-MNTQSIAEARALLDEF 147

Query: 315 FNLMIESL 322
              M E +
Sbjct: 148 EAQMDEDI 155


>gi|108758350|ref|YP_631586.1| FAD/FMN-binding oxidoreductase [Myxococcus xanthus DK 1622]
 gi|108462230|gb|ABF87415.1| oxidoreductase, FAD/FMN-binding [Myxococcus xanthus DK 1622]
          Length = 361

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/178 (15%), Positives = 60/178 (33%), Gaps = 27/178 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
              AA+   + G++ + L+       +               +G  L     ++ + + A
Sbjct: 146 FANAARRCAEAGFDAVELHGA--HGYLFSQFLSTVFNRRQDRWGGSLENRWRLLQETVRA 203

Query: 111 MCKALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +A    + +  R+  +D   A          + + + + GV+ + +   KA    L  
Sbjct: 204 VRRAAP-SLVLAVRLSPEDARQARGLDLDESLEVARMLTREGVDILHLSLWKAAHNTLKR 262

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
            D    P     +  +       + +   G +    +A   L    D V +GRAA  N
Sbjct: 263 PDQHATP-----LFRQAVGTGVRIVVA--GEVRTREEAEAQLARGADAVAVGRAAIAN 313


>gi|91225755|ref|ZP_01260784.1| putative NADH-dependent flavin oxidoreductase [Vibrio alginolyticus
           12G01]
 gi|91189644|gb|EAS75919.1| putative NADH-dependent flavin oxidoreductase [Vibrio alginolyticus
           12G01]
          Length = 341

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 71/218 (32%), Gaps = 23/218 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              A+K  +D G++ + ++            P     E  +G  L      + +  +   
Sbjct: 120 FALASKRAQDAGFDGVEIHAAHTYLINQFLSPYYNRREDEYGDGLENRMRFLLEIYSETR 179

Query: 113 KALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGLS 164
           K +    P+ VK       D  +     R + K +++ GV+ I +    H +   L G +
Sbjct: 180 KLVGSEFPILVKLTATEFFDGGLTFDETRVVCKKLEEVGVDAIIVSGNVHGKANELVGQT 239

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAAY 220
                      +     +  ++  + +   GGL D+    KI  + D     V   R   
Sbjct: 240 FDGYTLQEEGYFHEYGHVISQDVSIPVITVGGLSDIDAIEKIAENTDIQFFAV--SRPLL 297

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
               ++    E    P+      K R  +  +  +  +
Sbjct: 298 AEPQLIKRWKEGNRAPVDCERCSKCRTKRGNFCVVYKN 335


>gi|295681408|ref|YP_003609982.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1002]
 gi|295441303|gb|ADG20471.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1002]
          Length = 366

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 28/155 (18%), Positives = 47/155 (30%), Gaps = 13/155 (8%)

Query: 93  FGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSG 147
           +G  L   M  P  V + +         PVT++      VD           V +++  G
Sbjct: 202 YGGSLENRMRFPLEVFEAVREAFSH-DRPVTMRVSATDWVDGGWSLQDAIAFVHALEARG 260

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
              I + +      G +P     I            K+   L +   G + D  QA  IL
Sbjct: 261 CAAINVSSG-----GSNPAAQIPIGPGYQVPFARAVKQATTLPVVAVGLITDFEQAESIL 315

Query: 208 PS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +   D + + R    N         +F   +   
Sbjct: 316 STGDADLIALARTVLFNPRWPWHAAAHFGTQVRAP 350


>gi|317484343|ref|ZP_07943264.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
 gi|316924421|gb|EFV45586.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
          Length = 628

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 61/188 (32%), Gaps = 16/188 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V+AA+   + G++ + +             P   + E ++G           + + A
Sbjct: 133 EAYVQAARRAVEAGFDAVEIHGAHGYLINQFMSPLTNLREDAYGGSFENRMRFPLEVLRA 192

Query: 111 MCKAL--SIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K +    P+  +      +   I       + K +  +GV+ + +             
Sbjct: 193 VRKQVGPDFPILFRYSMEEFMPGGIDMEQAVRIAKVMADNGVDMLNVSIGIGESVEYIIP 252

Query: 167 DNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                   + D    IK+     + + + G + +   A  I+     D V +GRA   + 
Sbjct: 253 PASVPDGWNADRAAAIKRAVGSRIPVAVVGRICNRKTAENIIASGKADLVAMGRALLADP 312

Query: 224 AMLTTVDE 231
            +   + E
Sbjct: 313 FLPAKLAE 320


>gi|291301855|ref|YP_003513133.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
 gi|290571075|gb|ADD44040.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
          Length = 683

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/179 (12%), Positives = 57/179 (31%), Gaps = 17/179 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V  AK+    GY+ + +                   + ++G        +  + +  
Sbjct: 144 DAFVRCAKLARRAGYDGVEIMGSEGYFINQFLARRTNDRDDAWGGDHKRRMRLPVEIVGR 203

Query: 111 MCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A+     V  R      V+D      +  L ++++ +G + +   A     +   P 
Sbjct: 204 VREAVGDDFLVIYRTSMLELVEDGQTFDEIVELAQAVEGAGASILS--AGIGWHEAKIPT 261

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               +P   +    +  + +  + I  +  +     A ++L     D V + R    + 
Sbjct: 262 IITSVPRAAFAWAAKRLRPHVGIPIVASNRINTPELAERLLAEGVCDLVSMARPLLADP 320


>gi|300933965|ref|ZP_07149221.1| 2,4-dienoyl-CoA reductase [Corynebacterium resistens DSM 45100]
          Length = 746

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 50/150 (33%), Gaps = 20/150 (13%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + I A+  A+     +  RI V D          +  L   ++ +GV+     +     +
Sbjct: 226 EIIKAIRAAVPEDFVIDYRISVLDLVEGGQTQEEILQLATQLEAAGVDLFS--SGIGWHE 283

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS---------VDG 212
              P     +P   +    ++ +++ ++ +  +  + D   A K+L            DG
Sbjct: 284 AQVPTIVTSVPRGAFAWATKVLRDHVNVPVVASNRINDPEVAEKVLTGGWDEGDGTPADG 343

Query: 213 -----VMIGRAAYKNSAMLTTVDEYFSNPL 237
                V + R    +  ++       +  +
Sbjct: 344 PQADLVSMARPLLADPELVNRAARGLAKEI 373


>gi|322420708|ref|YP_004199931.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter sp. M18]
 gi|320127095|gb|ADW14655.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter sp. M18]
          Length = 653

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 62/186 (33%), Gaps = 17/186 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             ++A    + G++ I L  G          P        +G  L          I+A+ 
Sbjct: 148 FAKSAIHAREGGFDGIELQFGHSSLARQFLSPLTNFRTDEYGGSLENRMRAPLKFISAVR 207

Query: 113 KALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +A+    T+  R+  D+ IP       ++ +    + SG+         A    L   + 
Sbjct: 208 RAVGNDFTLGIRMCADEMIPGGLDLAQVQEICARFEASGLIDFN-DLSIATFYNLYLVEG 266

Query: 169 RKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG--RAAYKNSAM 225
                L Y I +    +E   + +   G + D   A K+L +    MIG  R    +  +
Sbjct: 267 SMHTPLGYTIPLAAGVRERVKIPVFCTGRINDPVMAEKVLANGQADMIGMCRGLICDPFL 326

Query: 226 LTTVDE 231
                E
Sbjct: 327 PKKAQE 332


>gi|329577258|gb|EGG58722.1| hypothetical protein HMPREF9520_00912 [Enterococcus faecalis
          TX1467]
          Length = 79

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN--ILGFSTQEKPLALQIG 55
          M   ++  +R   +      L+  EMI    I   +KK   +L    +E PL+ +  
Sbjct: 18 MAGISNAAFRVTVKEF-GAGLVVCEMISDKGIKLRNKKTLEMLYIDEREYPLSYKFL 73


>gi|157372917|ref|YP_001480906.1| NADH:flavin oxidoreductase/NADH oxidase [Serratia proteamaculans
           568]
 gi|157324681|gb|ABV43778.1| NADH:flavin oxidoreductase/NADH oxidase [Serratia proteamaculans
           568]
          Length = 587

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/143 (15%), Positives = 53/143 (37%), Gaps = 7/143 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L      + + +  +   +    PV V+   +  V   +     R +VK +++ G+
Sbjct: 135 YGGSLRDRMRFLEEIVKDVRSKVGADFPVLVRLSTKEFVPGGLSLAETRVIVKRMEELGI 194

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + I       +    +  +  ++ N  +  + E  K+   + +   G + D   A   L 
Sbjct: 195 DAINCSQGI-VTVSNNIVEPFQVGNAPFVDIAEEIKKIVSIPVITTGRINDADLAETTLL 253

Query: 208 -PSVDGVMIGRAAYKNSAMLTTV 229
               D + + RA+  +  +   V
Sbjct: 254 AGKSDFIGMARASLADPDLPKKV 276


>gi|289422477|ref|ZP_06424320.1| NADH oxidase [Peptostreptococcus anaerobius 653-L]
 gi|289157049|gb|EFD05671.1| NADH oxidase [Peptostreptococcus anaerobius 653-L]
          Length = 329

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/140 (17%), Positives = 51/140 (36%), Gaps = 13/140 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI-GVDDQIPAVALRNLVKS---IKKSGV 148
           +G  L     I  + I AM +AL     +  R+   D       L + +++    +++G+
Sbjct: 190 YGGSLENRIRIHLEIIKAMRQALGQDYPLALRLGACDYTDGGNNLEDAIRASKAFEEAGI 249

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + I     I       +     ++ Y I     K N  + + L GG+  +  A  ++ 
Sbjct: 250 DLLDISGGYYIFNNPYSTEEGYFKDVTYAI-----KSNVSIPVILTGGIHSVDTADYLIE 304

Query: 209 SVDGVMIGRAAYKNSAMLTT 228
           +    MIG        +   
Sbjct: 305 NKYADMIG---VGRP-IFKD 320


>gi|163850542|ref|YP_001638585.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacterium
           extorquens PA1]
 gi|163662147|gb|ABY29514.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacterium
           extorquens PA1]
          Length = 366

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/135 (18%), Positives = 53/135 (39%), Gaps = 16/135 (11%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPA------VALRNLVKSIKKSGVNGIWIHARK 157
           V D + A  +A  +PV V+   G  +               +  ++ ++G + + +   K
Sbjct: 216 VFDAVRATVRA-GVPVGVRISQGKVNDFGHKWAGGEQDAEAIFGTLAEAGASYLHVTEHK 274

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
                     +         +V   ++  PD+ +  NGG++D ++A +++    D V +G
Sbjct: 275 VWEPAFEGGRD--------SLVALARRYAPDVTLIANGGVQDAARAQEVMAAGADIVALG 326

Query: 217 RAAYKNSAMLTTVDE 231
           +AA  N      V  
Sbjct: 327 KAALANPDFPNRVRA 341


>gi|331653568|ref|ZP_08354569.1| tRNA-dihydrouridine synthase C [Escherichia coli M718]
 gi|331048417|gb|EGI20493.1| tRNA-dihydrouridine synthase C [Escherichia coli M718]
          Length = 36

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 2/34 (5%)

Query: 192 GLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
             NG + D   A + +     D VMIGR A    
Sbjct: 2   IANGEIWDWQSAQQCIAISGCDAVMIGRGALNIP 35


>gi|294102580|ref|YP_003554438.1| dihydroorotate dehydrogenase family protein [Aminobacterium
           colombiense DSM 12261]
 gi|293617560|gb|ADE57714.1| dihydroorotate dehydrogenase family protein [Aminobacterium
           colombiense DSM 12261]
          Length = 311

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 68/208 (32%), Gaps = 30/208 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
             P  + +    I +  E  K + +       + LN+ CP    +    G    ++P+  
Sbjct: 95  GMPFFVNVVMESIEETQETLKALAEHDDIIKGVELNISCP----NVDGDGMAWGVSPEST 150

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH---------- 154
              +AA        + VK      D            + + SG +G+ +           
Sbjct: 151 AQAVAASRSVWQGSLLVKLTPQCHDPYGV------ALAAEASGADGLVVANTWLGMAIDI 204

Query: 155 --ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVD 211
              R    +  +      +  L   +V+++  E   L +   GG+     AL + L    
Sbjct: 205 NQCRPVFNRTFAGFSGPAVFPLALRLVWQVC-EATSLPVIGCGGVSTWQDALSMILAGAS 263

Query: 212 GVMIGRAAYKNSAMLTTV----DEYFSN 235
            V +G A + +S M  ++    D Y   
Sbjct: 264 AVELGTAMFVHSDMPRSICKGLDAYLEG 291


>gi|218779010|ref|YP_002430328.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760394|gb|ACL02860.1| Predicted NADH:flavin oxidoreductase/NADH oxidase
           [Desulfatibacillum alkenivorans AK-01]
          Length = 415

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 25/226 (11%), Positives = 67/226 (29%), Gaps = 56/226 (24%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
               V +A+I E  G++ + ++ G          P     +  +G   +    ++ +   
Sbjct: 148 AEDYVRSAEICEQAGFDGVQIHAGHGYLINQFLTPYTNRRDDQYGGSFVKRLRLLLEIYW 207

Query: 110 AMCKALSIPVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------ 153
            + +  ++ V +K      +     +    L  + + +++ G++ + +            
Sbjct: 208 GIRERTNLTVIMKINGADYLPGRQGLSTAQLVEVARILQEEGLDALEVTVGHYESGFPMI 267

Query: 154 ------HARKAILKGLSP----------------------KDNRKIPNLDYDIVYEIKKE 185
                   +  + +G+ P                               +     E KK+
Sbjct: 268 RGNFGPFFKGLMEEGIGPQLPWFRRFGITCFRHPLAYIFDHIWPAQEGFNLHYAREFKKK 327

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
                I + GG        + +     D V +GRA   +  +   +
Sbjct: 328 LSIPVICV-GGFLTREHMEQAIDGGACDAVSVGRAMIADPYLFRNI 372


>gi|161520867|ref|YP_001584294.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia multivorans
           ATCC 17616]
 gi|189352950|ref|YP_001948577.1| NADPH2 dehydrogenase [Burkholderia multivorans ATCC 17616]
 gi|160344917|gb|ABX18002.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia multivorans
           ATCC 17616]
 gi|189336972|dbj|BAG46041.1| NADPH2 dehydrogenase [Burkholderia multivorans ATCC 17616]
          Length = 369

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 65/180 (36%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AAK   D G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAAKRARDIGFEWLELHFAHGYLGQSFFSVHSNRRTDEYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            K     +P+TV+  +   D      L     L + +K+ G++ + +      +   +P 
Sbjct: 219 RKVWPEHLPLTVRFGVIEYDGRDEETLAESIALTQRLKQEGLDMLSV-----SVGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPVAERVRREAGLPVSSAWGIDTPQLANRVVADEQLDLVMVGRAHLADPH 333


>gi|326566736|gb|EGE16875.1| NADPH dehydrogenase [Moraxella catarrhalis 103P14B1]
 gi|326571453|gb|EGE21468.1| NADPH dehydrogenase [Moraxella catarrhalis BC7]
 gi|326575264|gb|EGE25192.1| NADPH dehydrogenase [Moraxella catarrhalis CO72]
 gi|326577482|gb|EGE27362.1| NADPH dehydrogenase [Moraxella catarrhalis O35E]
          Length = 353

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 75/218 (34%), Gaps = 23/218 (10%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           +   AI  G+    L ++ Q      Q+   +I  LV+A     K   + G++ I L+  
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRQLSIDEIKALVQAFADSVKRAVNAGFDAIELHAA 172

Query: 83  --------C-PSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIP 132
                   C P +      +G   +L  + V   + A M   + + V +  +   ++   
Sbjct: 173 HGYLIHQFCAPKSNQRSDEYGQDRLLFGEQVIHAVRAVMPDEMPLIVRISAQEYGENGFD 232

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           +     + K    +G +   +      +     K           +  ++K       + 
Sbjct: 233 SDYGVEIAKRFSSAGADVFHVSGGGDGVL-CEGKHPEFYAGYQVALARKVKYATGK-PVI 290

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             G L+D + A  +L     D V IGR   ++   +L 
Sbjct: 291 AVGMLDDPAVADHVLGVGDADLVAIGRGLLRDPYWVLN 328


>gi|119026353|ref|YP_910198.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium
           adolescentis ATCC 15703]
 gi|118765937|dbj|BAF40116.1| probable NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 373

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 58/168 (34%), Gaps = 14/168 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G        ++ + + A+   +   +PV V+                  L K +K  GV
Sbjct: 213 YGGSFDNRVRMLVEVVDAIRSVVPDTMPVLVRVSATDWAAGGWDLDQTVELAKILKAHGV 272

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + I +        GL P     +   DY +   E  +    +     G +    QA KIL
Sbjct: 273 DLIDVSTG-----GLIPDVTIPVKP-DYQVPFAEQVRSRAGIPTTAVGLITKPKQAKKIL 326

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
              + D V IGRAA ++             P+   +P +    +  +R
Sbjct: 327 KSGAADAVEIGRAALRDPYWPLRAAHKLDVPV-EEAPYQPPYLRGAFR 373


>gi|210631812|ref|ZP_03297054.1| hypothetical protein COLSTE_00943 [Collinsella stercoris DSM 13279]
 gi|210159932|gb|EEA90903.1| hypothetical protein COLSTE_00943 [Collinsella stercoris DSM 13279]
          Length = 639

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 37/192 (19%), Positives = 72/192 (37%), Gaps = 31/192 (16%)

Query: 64  EAAKIVEDFGYNEINLNVGC-----PSARVHEG------SFGACLMLNPDIVGDCIAAMC 112
           +AA    + GY+ I     C     P + +  G       +G  L         CI A+ 
Sbjct: 145 KAAARCVEAGYDCIE--FHCAHNYLPHSFLSAGLNHRDDEWGGSLENRAKFPLACIRAIR 202

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           + +   +P+ ++     D     + + +     K  +++GV+ + +     +    +  +
Sbjct: 203 ENIPEDMPLFMRIGAFDDCLENGMTIEDTIEFCKMAREAGVDVLDVSRGNIV----TAAN 258

Query: 168 NRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             ++P +D       D    I++E     IG+ G +     A KIL    VD V++GRA 
Sbjct: 259 ALEVPPIDLKPGFNIDNAVRIRRETGMPTIGV-GRINTPELAEKILEDDQVDLVVMGRAQ 317

Query: 220 YKNSAMLTTVDE 231
             +        E
Sbjct: 318 LADPEFCNKARE 329


>gi|154488245|ref|ZP_02029362.1| hypothetical protein BIFADO_01819 [Bifidobacterium adolescentis
           L2-32]
 gi|154083396|gb|EDN82441.1| hypothetical protein BIFADO_01819 [Bifidobacterium adolescentis
           L2-32]
          Length = 375

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 58/168 (34%), Gaps = 14/168 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G        ++ + + A+   +   +PV V+                  L K +K  GV
Sbjct: 215 YGGSFDNRVRMLVEVVDAIRSVVPDTMPVLVRVSATDWAAGGWDLDQTVELAKILKAHGV 274

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + I +        GL P     +   DY +   E  +    +     G +    QA KIL
Sbjct: 275 DLIDVSTG-----GLIPDVTIPVKP-DYQVPFAEQVRSRAGIPTTAVGLITKPKQAKKIL 328

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
              + D V IGRAA ++             P+   +P +    +  +R
Sbjct: 329 KSGAADAVEIGRAALRDPYWPLRAAHKLDVPV-EEAPYQPPYLRGAFR 375


>gi|289522184|ref|ZP_06439038.1| NADH oxidase [Anaerobaculum hydrogeniformans ATCC BAA-1850]
 gi|289504020|gb|EFD25184.1| NADH oxidase [Anaerobaculum hydrogeniformans ATCC BAA-1850]
          Length = 648

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/129 (14%), Positives = 47/129 (36%), Gaps = 17/129 (13%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWI-----HAR 156
           + I  + ++L     +  R   DD +      +    + K ++ +GVN + +        
Sbjct: 206 EIIKGIRQSLGPNFPICFRFNADDFVEDGITLDEAKIIAKILEDAGVNVLSVSVGIYETM 265

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
             +L+    ++  ++         E  K+  ++ +   G + +   A  ++     D V 
Sbjct: 266 PKLLEPFHFEEGWRV------YTAEAIKKVVNIPVITVGVIRNPEFAETVIAEGKADFVA 319

Query: 215 IGRAAYKNS 223
           IGR    + 
Sbjct: 320 IGRGLIADP 328


>gi|237733542|ref|ZP_04564023.1| NADH:flavin oxidoreductase [Mollicutes bacterium D7]
 gi|229383375|gb|EEO33466.1| NADH:flavin oxidoreductase [Coprobacillus sp. D7]
          Length = 625

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 32/147 (21%), Positives = 59/147 (40%), Gaps = 11/147 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L        +CIAA+   +    P+ VK      V+          + K ++ +G+
Sbjct: 174 YGGSLENRMRFTLECIAAIRTNVGPDFPILVKFTPVHKVEGFRQIDEGIAMAKILEGAGI 233

Query: 149 NGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
             + +     +A  K +S   N +   LD  +V  IK EN  L +   G L D  +A ++
Sbjct: 234 EALHVDVGCYEAWYKAISTVYNEEGHQLD--VVKAIK-ENVSLPVLGQGKLFDPKKAQEV 290

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +    +D V++G     +      V +
Sbjct: 291 VAQGVLDYVVLGHQMLADPHWANKVKQ 317


>gi|296112795|ref|YP_003626733.1| NADPH dehydrogenase [Moraxella catarrhalis RH4]
 gi|295920489|gb|ADG60840.1| NADPH dehydrogenase [Moraxella catarrhalis RH4]
          Length = 353

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 38/222 (17%), Positives = 76/222 (34%), Gaps = 31/222 (13%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           +   AI  G+    L ++ Q      Q+   +I  LV+A     K   + G++ I L+  
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRQLSIDEIKALVQAFADSVKRAVNAGFDAIELHAA 172

Query: 83  --------C-PSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIP 132
                   C P +      +G   +L  + V   + A M   + + V +  +   ++   
Sbjct: 173 HGYLIHQFCAPKSNQRSDEYGQDRLLFGEQVIHAVRAVMPDEMPLIVRISAQEYGENGFD 232

Query: 133 AVALRNLVKSIKKSGVNGIWIHAR----KAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +     + K    +G +   +           K        ++P        ++K     
Sbjct: 233 SDYGVEIAKRFSTAGADVFHVSGGGDGVLCEGKHPQFYAGYQVPLA-----RKVKHATGK 287

Query: 189 LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             +   G L+D + A  +L     D V IGR   ++   +L 
Sbjct: 288 -PVIAVGMLDDPAVADHVLGMGDADLVAIGRGLLRDPYWVLN 328


>gi|291296268|ref|YP_003507666.1| dihydroorotate dehydrogenase family protein [Meiothermus ruber DSM
           1279]
 gi|290471227|gb|ADD28646.1| dihydroorotate dehydrogenase family protein [Meiothermus ruber DSM
           1279]
          Length = 461

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 6/123 (4%)

Query: 10  RFFARLLTNNALL---YTEMIVADAILRG--DKKNILGFSTQEKPLALQIGGADISKLVE 64
           R+ A       +L     E+I    +     + +++         +   +  +      +
Sbjct: 57  RYGAWHYGGQKMLAINNVELISDRPLEVNLREIRDVKRHWPDRAVIVSAMVESTPEAWRD 116

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
               +ED G + I LN GCP     E   G+ +   P+        +     IPV VK  
Sbjct: 117 IILKIEDTGADGIELNYGCPHGMS-ERGMGSAVGQVPEYCQQITQWVMDVAKIPVIVKLT 175

Query: 125 IGV 127
             V
Sbjct: 176 PNV 178


>gi|116750276|ref|YP_846963.1| dihydroorotate dehydrogenase family protein [Syntrophobacter
           fumaroxidans MPOB]
 gi|116699340|gb|ABK18528.1| dihydroorotate oxidase B, catalytic subunit [Syntrophobacter
           fumaroxidans MPOB]
          Length = 302

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/203 (15%), Positives = 71/203 (34%), Gaps = 29/203 (14%)

Query: 50  LALQIGGADISKLV-EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  + +    A+K+  + G   + +N+ CP    +    G     +P      +
Sbjct: 78  VIVNIFGNTVDEYAGLASKLDGEDGVAALEINISCP----NVKQGGMVFGTDPATAAAVV 133

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLS 164
            A+    ++P+  K    V        +  + ++   +G + I     + A    +    
Sbjct: 134 GAVRARTALPLITKLTPNVTR------IGEIARAAVDAGTDAISCINTVAAMAVDIFSRR 187

Query: 165 PK--------DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
           PK            +  +     YE+ +      +   GG+   + AL+ +L     V +
Sbjct: 188 PKLANVFGGLSGPAVKPIALRCTYEVLQAV-KCPVIGVGGIGTATDALEFMLLGARAVQV 246

Query: 216 GRAAYKNSA----MLTTVDEYFS 234
           G A + N      +L  ++ +  
Sbjct: 247 GTANFVNPGVSVEILEGIERFLR 269


>gi|317035794|ref|XP_001396977.2| hypothetical protein ANI_1_1472134 [Aspergillus niger CBS 513.88]
          Length = 262

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 68/195 (34%), Gaps = 25/195 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V  +++    G+  + L+            P+A +    +G        I+ D I A
Sbjct: 11  DQFVYTSRLASQTGFQGVELHAAHGYLLSQFLSPTANLRTDQYGGSPAGRVKIIVDIIHA 70

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK---AILKGLS 164
           + KA+     V  ++   D     AL+  V+ +K   ++GV+ + I         +   S
Sbjct: 71  IRKAVPATFCVGIKLNSVDHQSESALKACVEQLKLIVEAGVDFVEISGGSYEDPQMMSSS 130

Query: 165 PKDNRKIPNLD--------YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
             + +   +           +    I+ + P   + + GG    +   K L     D + 
Sbjct: 131 ASNKQPEKSARTVAREAFFLEFASAIRAQFPGTPLMVTGGFRTRTGMEKALIDKDCDMIG 190

Query: 215 IGRAAYKNSAMLTTV 229
           IGR A     +   +
Sbjct: 191 IGRPAVLKPTLPNDI 205


>gi|27366398|ref|NP_761926.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio vulnificus CMCP6]
 gi|27362599|gb|AAO11453.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio vulnificus CMCP6]
          Length = 670

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 50/135 (37%), Gaps = 8/135 (5%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
             + + A+ KA+     +  R+ + D +   +       L K+++ +GV    I+     
Sbjct: 197 AVEIVKAVRKAVGSDFIIIFRLSMLDLVEQGSTFEDVIMLAKALEDAGVT--IINTGIGW 254

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +   P    ++P   +  V E  K +  + I     +    +A +IL     D V + R
Sbjct: 255 HEARVPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPEEAERILASGQADMVSMAR 314

Query: 218 AAYKNSAMLTTVDEY 232
               +   +   ++ 
Sbjct: 315 PFLADPHFIAKAEQA 329


>gi|310794172|gb|EFQ29633.1| NADH:flavin oxidoreductase/NADH oxidase [Glomerella graminicola
           M1.001]
          Length = 433

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 26/215 (12%), Positives = 66/215 (30%), Gaps = 29/215 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL-NVGC--------PSARVHEGS 92
                 K + +Q      +   +A +     G++ I + N           P +      
Sbjct: 189 EHHASPKEMTIQDIDEFKAAFADAVRRALKAGFDAIEIHNAHGYLLHEFLSPVSNKRTDK 248

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--------IGVDDQIPAVALRNLVKS 142
           +G        +  + +      +   +P+ ++            + +         L   
Sbjct: 249 YGGSWENRVRLTLEMVEQTRAIIPEDMPLFLRISATDWLEEQKDMPESWTGDDTVRLAPL 308

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDM 200
           + + GV+ + +        G   + +  +          ++K+     + +   G +E+ 
Sbjct: 309 LAERGVDLLDVSTG-----GNHERQHPHVAPAYQAPFAVKVKQAVGSKMAVSSVGAIENA 363

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAM-LTTVDEY 232
             A  +L    +D V +GR   KN  +  +  DE 
Sbjct: 364 KLANDLLEKDGLDFVFVGRGFQKNPGLVFSWADEL 398


>gi|167758355|ref|ZP_02430482.1| hypothetical protein CLOSCI_00695 [Clostridium scindens ATCC 35704]
 gi|167664252|gb|EDS08382.1| hypothetical protein CLOSCI_00695 [Clostridium scindens ATCC 35704]
          Length = 641

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 31/183 (16%), Positives = 59/183 (32%), Gaps = 26/183 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHE--------------GSFGACLMLNPDIVGDCI 108
            EAA+   + G + + +++      +                G      M  P +    +
Sbjct: 150 AEAARRAMEGGADAVEIHMA--HGYLVSSFMSPRTNKRVDEFGGNFENRMRFPRL---IV 204

Query: 109 AAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+ KA+   V +  RI   D++           +   +++ GV  + +     I     
Sbjct: 205 EAVKKAVGDKVAIIARINSADEVLGGLDVHDSAAIAAYLEECGVQALHVSRAVHIKDEYM 264

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                       D+V EIKK      I + G   +   A  ++     D V  GR +  +
Sbjct: 265 WAPTTIHGGFSADLVSEIKKAVSIPVITV-GRFTEPQYAELLVKEGRADLVAFGRQSLAD 323

Query: 223 SAM 225
             M
Sbjct: 324 PHM 326


>gi|320156921|ref|YP_004189300.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio vulnificus MO6-24/O]
 gi|319932233|gb|ADV87097.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio vulnificus MO6-24/O]
          Length = 670

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 50/135 (37%), Gaps = 8/135 (5%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
             + + A+ KA+     +  R+ + D +   +       L K+++ +GV    I+     
Sbjct: 197 AVEIVKAVRKAVGSDFIIIFRLSMLDLVEQGSTFEDVIMLAKALEDAGVT--IINTGIGW 254

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +   P    ++P   +  V E  K +  + I     +    +A +IL     D V + R
Sbjct: 255 HEARVPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPEEAERILASGQADMVSMAR 314

Query: 218 AAYKNSAMLTTVDEY 232
               +   +   ++ 
Sbjct: 315 PFLADPHFIAKAEQA 329


>gi|212696400|ref|ZP_03304528.1| hypothetical protein ANHYDRO_00937 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676678|gb|EEB36285.1| hypothetical protein ANHYDRO_00937 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 220

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 10/100 (10%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           + G  I   +  A ++ D+  + I LN+ CP   V  G       +  +I GD +  + +
Sbjct: 102 LSGHSIDDYIRGADLLNDYKIDFIELNISCP--NVKNGGMNFG--VKAEIAGDLVKKVRR 157

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                   K ++ +     A  + +L K  +  G +G+ +
Sbjct: 158 V------CKHKLIIKLSPNAENIVDLGKVCEDEGADGLSL 191


>gi|90579231|ref|ZP_01235041.1| putative 2,4-dienoyl-CoA reductase [Vibrio angustum S14]
 gi|90440064|gb|EAS65245.1| putative 2,4-dienoyl-CoA reductase [Vibrio angustum S14]
          Length = 670

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 31/225 (13%), Positives = 72/225 (32%), Gaps = 24/225 (10%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
           LL       +   V+ + +R        F+  E      +   +      +A++  + GY
Sbjct: 105 LLHAGRYAMSPFAVSASAIRSPIS---KFTPSEMSERQILKTINA--FANSAELAREAGY 159

Query: 75  NEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           + + L            C  + +    +G           + + A+   +     +  R+
Sbjct: 160 DGVELMGSEGYLINQFICQRSNLRYDDWGGSYENRIRFPLEIVKAVRARVGRDFIIIFRL 219

Query: 126 G----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-Y 180
                V+       +  L K+++++GV    ++      +   P    ++P   +  V  
Sbjct: 220 SMLDLVEQGSTHEEVVMLAKALEQAGVT--ILNTGIGWHEARVPTIATQVPRAAFAWVTE 277

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +K+E     +  N  +     A  IL     D V + R    + 
Sbjct: 278 RLKQEVSIPLVTCNR-INTPQVAEDILSSGQADMVSMARPFLADP 321


>gi|326569348|gb|EGE19408.1| NADPH dehydrogenase [Moraxella catarrhalis BC8]
 gi|326576649|gb|EGE26556.1| NADPH dehydrogenase [Moraxella catarrhalis 101P30B1]
          Length = 353

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 36/218 (16%), Positives = 74/218 (33%), Gaps = 23/218 (10%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           +   AI  G+    L ++ Q      Q+   +I  LV+A     K   + G++ I L+  
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRQLSIDEIKALVQAFADSVKRAVNAGFDAIELHAA 172

Query: 83  --------C-PSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIP 132
                   C P +      +G   +L  + V   + A M   + + V +  +   ++   
Sbjct: 173 HGYLIHQFCAPKSNQRSDEYGQDRLLFGEQVIHAVRAVMPDEMPLIVRISAQEYGENGFD 232

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           +     + K    +G +   +      +                 +  ++K       + 
Sbjct: 233 SDYGVEIAKRFSTAGADVFHVSGGGDGVLCEGKHPQFYAG-YQVALARKVKHATGK-PVI 290

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             G L+D + A  +L     D V IGR   ++   +L 
Sbjct: 291 AVGMLDDPAVADHVLGVGDADLVAIGRGLLRDPYWVLN 328


>gi|37679337|ref|NP_933946.1| 2,4-dienoyl-CoA reductase [Vibrio vulnificus YJ016]
 gi|37198080|dbj|BAC93917.1| 2,4-dienoyl-CoA reductase [Vibrio vulnificus YJ016]
          Length = 670

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 50/135 (37%), Gaps = 8/135 (5%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
             + + A+ KA+     +  R+ + D +   +       L K+++ +GV    I+     
Sbjct: 197 AVEIVKAVRKAVGSDFIIIFRLSMLDLVEQGSTFEDVIMLAKALEDAGVT--IINTGIGW 254

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +   P    ++P   +  V E  K +  + I     +    +A +IL     D V + R
Sbjct: 255 HEARVPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPEEAERILASGQADMVSMAR 314

Query: 218 AAYKNSAMLTTVDEY 232
               +   +   ++ 
Sbjct: 315 PFLADPHFIAKAEQA 329


>gi|308273888|emb|CBX30488.1| hypothetical protein N47_K27280 [uncultured Desulfobacterium sp.]
          Length = 343

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 36/76 (47%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+   +    +   ++ AK+ ++ G + + + + CP   +    +      NP IV + 
Sbjct: 43  TPVIASLMAISVEGYIKGAKMFQEAGADAVEILLACPLPFLLPHPYVGGASFNPAIVEEV 102

Query: 108 IAAMCKALSIPVTVKC 123
            + + KA++IP+ VK 
Sbjct: 103 CSEVRKAVTIPLGVKM 118


>gi|308271717|emb|CBX28325.1| hypothetical protein N47_G36490 [uncultured Desulfobacterium sp.]
          Length = 406

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 36/76 (47%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
            P+   +    +   ++ AK+ ++ G + + + + CP   +    +      NP IV + 
Sbjct: 106 TPVIASLMAISVEGYIKGAKMFQEAGADAVEILLACPLPFLLPHPYVGGASFNPAIVEEV 165

Query: 108 IAAMCKALSIPVTVKC 123
            + + KA++IP+ VK 
Sbjct: 166 CSEVRKAVTIPLGVKM 181


>gi|257438878|ref|ZP_05614633.1| NADH:flavin oxidoreductase [Faecalibacterium prausnitzii A2-165]
 gi|257198693|gb|EEU96977.1| NADH:flavin oxidoreductase [Faecalibacterium prausnitzii A2-165]
          Length = 641

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 26/215 (12%), Positives = 70/215 (32%), Gaps = 18/215 (8%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------C 83
           D + +    +++ F+ +   ++ ++  A I K+   A   +  G + I ++        C
Sbjct: 118 DEMRQRLHHDMMFFTDE---VSEEMLMAIIDKMCACAVRAQKAGVDVIQIHGDRLNGCLC 174

Query: 84  PSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL-----SIPVTVKCRIGVDDQIPAVALR 137
            +   H        + N       +  A+ KA+        +++         I      
Sbjct: 175 STRMNHRTDKFGGSLENRVRFARMLTRAIRKAVPGMIIDYKLSIVTPQRGKGGIDEADAV 234

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
              + + + GV+   +                 +    + + +    K+  ++ +   G 
Sbjct: 235 QFAQWLVEDGVDMFHVAQANHTGNMADTIPPMGVQPYGFFVRIAGDIKKAVNVPVSAVGR 294

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           + D   A +++ S   D V +GR    +      +
Sbjct: 295 IVDAEMAERVIESGMADMVAVGRPLLADPDWGAKI 329


>gi|332829468|gb|EGK02117.1| hypothetical protein HMPREF9455_01751 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 370

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 39/178 (21%), Positives = 56/178 (31%), Gaps = 18/178 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  EAA+   + G+N I L             P     E  +G  L      V +   A
Sbjct: 158 HQFAEAARRAVEIGFNAIELHGAHGYLIHQFLSPITNKREDEYGGSLENRIRFVLEVFDA 217

Query: 111 MCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A      V  RI   D I           L + + + G   I  H     L G   K
Sbjct: 218 VTLATPKGFPVCIRISATDWIENGWDLAQSIELARQLDERGCGYI--HVSTGGLDGELQK 275

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
            +   P         IKKE     IG+ G +    QA   +     D + +GR    +
Sbjct: 276 LSALYPGYQLPFAEAIKKEVKMPVIGV-GLITQSQQAENAIKESKADLIAVGRGMLYD 332


>gi|330969986|gb|EGH70052.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 365

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 51/135 (37%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGI 151
               +  + IAA+ K A   PV V+   G  +               +  ++  +GV+ I
Sbjct: 209 QRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQHKWAGGEGDAEVIFAALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A     +      +           ++  PD+ +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAWQPAFTQGQASLVELA--------RRYAPDVALIANGGLHDPQKADQVLRQGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|317127895|ref|YP_004094177.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus cellulosilyticus
           DSM 2522]
 gi|315472843|gb|ADU29446.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus cellulosilyticus
           DSM 2522]
          Length = 649

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/183 (18%), Positives = 62/183 (33%), Gaps = 26/183 (14%)

Query: 61  KLVEAAKIVEDFGYNEINL------------NVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           K V AA   ++ G + + L            N   P   +    +G         + + I
Sbjct: 150 KFVTAAIRCKEAGVDGVELHGAHGYLISQFLN---PHTNLRTDMYGGSFANRMRFLEEII 206

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAILKGLS 164
             + +      PV V+  +   D+         N+ + ++K GV+ I  HA       + 
Sbjct: 207 IGIKEQCGNDYPVIVRLSVDEFDEDGIDVALSKNISRYLEKIGVDAI--HASAGNYNSME 264

Query: 165 PKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
                 +    + +    EIKKE  ++ +   G + +      IL     D V IGR   
Sbjct: 265 KVIESPLYEQGWRVYLAEEIKKEV-NIPVITVGSIREPKYVESILAEGKADFVAIGRGHI 323

Query: 221 KNS 223
            + 
Sbjct: 324 ADP 326


>gi|251778577|ref|ZP_04821497.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
 gi|243082892|gb|EES48782.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
          Length = 362

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/148 (14%), Positives = 48/148 (32%), Gaps = 23/148 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN------------GI 151
           + D + A   AL  PV +K     D       ++ + K+++++G +             I
Sbjct: 134 IVDAMKAAKAALDCPVFMKMSPHTD-------IQKIAKALEEAGADGLVMINSVGPCMAI 186

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKIL-P 208
            I     I+   +         +    +  I        + I   GG+     A ++L  
Sbjct: 187 DIETGYPIMGSQTGYGWLSGSAVKPVAIRNIYDASKVIKIPIIGVGGITSGKDAAEMLMA 246

Query: 209 SVDGVMIG-RAAYKNSAMLTTVDEYFSN 235
               V +   A  K   +   + +  ++
Sbjct: 247 GAQSVQVCTEAILKGPTVYGKIAKELND 274


>gi|290977597|ref|XP_002671524.1| predicted protein [Naegleria gruberi]
 gi|284085093|gb|EFC38780.1| predicted protein [Naegleria gruberi]
          Length = 374

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 32/197 (16%), Positives = 65/197 (32%), Gaps = 30/197 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
           + V+AAK     G++ I ++       +               +G C       + + + 
Sbjct: 168 QFVDAAKRAIKAGFDLIEIHGA--HGYLISSFLSQTSNKRSDEYGGCFENRIRFLVELVE 225

Query: 110 AMCKALS--IPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWI-----HARKAI 159
            +   +   +P+ V+        D+         L K ++K GV+ +       +A   +
Sbjct: 226 RIRANIPSEMPLFVRISADEYVGDEGWTMKDTTELAKILQKCGVDLLDCSSGGNNANAKL 285

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           L   S     ++P  +      +KK    L  G  G ++D   A  ++     D V+IGR
Sbjct: 286 LSPTSIVQGYQVPFSE-----GVKKSVDGLATGAVGKIKDAQFANDLIKDQKADLVLIGR 340

Query: 218 AAYKNSAMLTTVDEYFS 234
               +            
Sbjct: 341 QELNDPYWPIRAAHELE 357


>gi|218780735|ref|YP_002432053.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218762119|gb|ACL04585.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
          Length = 666

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 66/180 (36%), Gaps = 17/180 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPS------ARVHEGS---FGACLMLNPDIVGDCIAAM 111
               AA    + GYN + +  G         ++V       +G           +   A+
Sbjct: 146 DFASAALRGVEAGYNGVEILAGTGYLISEFLSKVTNQRSDEYGGAFENRMRFGLEVARAV 205

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A+     +  RI  ++ +P    R+      + + + GV+G+ ++      +   P+ 
Sbjct: 206 KAAVGPDYPLMFRINGNEFMPGGLRRDQLILFARRLVEQGVDGLCVNVG--WHEARVPQI 263

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
             ++P   +  +    KE+ D+ +  +  + D   A  +L     D V +GRA   +  +
Sbjct: 264 LAEVPRGAFAYLSRGIKESVDVPVIASHRINDPETARNMLSDSMCDMVAMGRALIADPYL 323


>gi|125975470|ref|YP_001039380.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           ATCC 27405]
 gi|281419496|ref|ZP_06250510.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           JW20]
 gi|125715695|gb|ABN54187.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           ATCC 27405]
 gi|281406902|gb|EFB37166.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           JW20]
          Length = 645

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 60/172 (34%), Gaps = 7/172 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L      + +CI +    +    P  V +    G            + K +K+ G+
Sbjct: 194 YGGSLENRMRFLLECIESARNNVGSDFPMIVGLALDHGFPGGRELDETIEIAKRLKQIGI 253

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +         L          +  D   +++++   + +  +G + D   A K++ 
Sbjct: 254 DTLHLRRGSYDNMNLLIPTEYMEDAVSVDYAAKVREQAG-IQVISDGNISDPVLANKLME 312

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
              +D V +GRA   +   +  V       +         +++ F+ + +A 
Sbjct: 313 ENKLDFVGLGRALLADPEWVNKVRADKKEDIVPCVRCMQCINRIFFGQYAAC 364


>gi|227485154|ref|ZP_03915470.1| conserved hypothetical protein [Anaerococcus lactolyticus ATCC
           51172]
 gi|227236864|gb|EEI86879.1| conserved hypothetical protein [Anaerococcus lactolyticus ATCC
           51172]
          Length = 44

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 284 FHGFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
           FHG P  R  R +L+  A    A   ++E A  +
Sbjct: 1   FHGQPGGRAFRQVLSEGAHRLGADWTLVEQALAV 34


>gi|148556192|ref|YP_001263774.1| NADH:flavin oxidoreductase/NADH oxidase [Sphingomonas wittichii
           RW1]
 gi|148501382|gb|ABQ69636.1| NADH:flavin oxidoreductase/NADH oxidase [Sphingomonas wittichii
           RW1]
          Length = 413

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 74/217 (34%), Gaps = 46/217 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA++  + G++ + L++G          P +     ++G           + +AA
Sbjct: 148 DEFVAAARLAVEAGFDAVELHMGHGYLLNQFISPLSNKRRDAYGGNAGKRVRFPAEVLAA 207

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARK--------- 157
           + +A+   + V  +I + D     A         ++++ +G + + +   +         
Sbjct: 208 VKRAVGDRIAVLAKINLYDGAKGGATVEDGIVTARALEAAGADMLVLSGGRNIESSYVMF 267

Query: 158 ----------------------AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
                                  +LK  +PK  R       D    ++       +G  G
Sbjct: 268 SSPLPYDDLAKMQGGWLAKLQFKLLKMATPKTVRFSELYFLDAARRVRAAVG-CRLGYLG 326

Query: 196 GLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
           G+  +  A + L    D V++ RA   + A++     
Sbjct: 327 GVLSLPAAEQALNEGFDAVVMARALVHDPALVAKWRA 363


>gi|332876236|ref|ZP_08444011.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6014059]
 gi|332735508|gb|EGJ66560.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6014059]
          Length = 369

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 56/149 (37%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR----IGVDDQIPAVALR 137
           P A      +G  L     +  + + A+  A+    PV V+      +  ++Q    +  
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWMDGNEQWDIESTV 251

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   I + +      GL    N  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYIHVSSG-----GLHEHQNITIG-AGYQVPFAEQVKKHVAIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + D  QA +IL     D + + RA     
Sbjct: 306 ITDPQQAEQILENQQADAIGLARAMLYAP 334


>gi|251794548|ref|YP_003009279.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp. JDR-2]
 gi|247542174|gb|ACS99192.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp. JDR-2]
          Length = 346

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 57/176 (32%), Gaps = 33/176 (18%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSIK 144
           +G  L+       + + A  +A+    P+ ++     + +           L   ++ + 
Sbjct: 171 YGGSLLARTRFAEEVVRACREAVGPDFPIVLRISQWKEREYTVKLAYNPEELEQFLQPLV 230

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG------------ 192
            +GV+      R+      +  D           V  I  + P + +G            
Sbjct: 231 DAGVDIFHCSTRRYWEPEFAGSDLNLAG-----WVKRITGK-PTITVGSVGLDSDFMTFF 284

Query: 193 ------LNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                  N G++ + Q L+     D V IGRA   + A  + + E     L   +P
Sbjct: 285 TEGKSSANTGIDGLVQKLEK-DECDLVAIGRALLVDPAWASKIREGKLTELVPFTP 339


>gi|104780442|ref|YP_606940.1| oxidireductase [Pseudomonas entomophila L48]
 gi|95109429|emb|CAK14130.1| putative oxidireductase [Pseudomonas entomophila L48]
          Length = 368

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 30/191 (15%), Positives = 61/191 (31%), Gaps = 20/191 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V A +     G+  + ++            P +      +G+C      +      A
Sbjct: 157 DAFVAATERALKAGFKVVEIHAAHGYLLHQFLSPLSNQRRDDYGSCFENRIRLTLQVTEA 216

Query: 111 MCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + KA    +PV V+      V+D         L + ++  GV+ I + +      G S  
Sbjct: 217 VRKAWPEDLPVFVRVSATDWVEDGWNPDETVELARRLRGLGVDLIDVSSG-----GTSVN 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                         E  ++  ++  G  G + + +QA  IL     D + + R   ++  
Sbjct: 272 AEIPTGPGYQTRFAERVRKESEIATGTVGMITEPAQAEHILRTGQADVIFLARELLRDPY 331

Query: 225 MLTTVDEYFSN 235
                D+    
Sbjct: 332 WPLHADDDLGG 342


>gi|119193881|ref|XP_001247544.1| hypothetical protein CIMG_01315 [Coccidioides immitis RS]
          Length = 424

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 65/203 (32%), Gaps = 36/203 (17%)

Query: 57  ADISKLVEA----AKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDI 103
           ADI +  EA     +     G + I + N           P +      +G        +
Sbjct: 193 ADIEEFKEAWGAAVRRAVKAGVDYIEIHNAHGYLLYSFLSPVSNNRTDEYGGSFENRMRL 252

Query: 104 VGDCIAAMCKAL--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
             + +    K +  ++P+ ++          R  +        +R      +K GV+ + 
Sbjct: 253 TLEIVDISRKNMPENMPLFLRVSATDWLEESRPDLPSWKLEDTVRFAQVLAEKGGVDFLD 312

Query: 153 IHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-- 208
           I +      G       KI           +KK   D + +G  G + +  QA  +L   
Sbjct: 313 ISSA-----GNHTDQKIKIGPGFQAPFAIAVKKAVGDRIAVGTVGSITNGKQANDLLENE 367

Query: 209 SVDGVMIGRAAYKNS---AMLTT 228
            +D V++GR   KN         
Sbjct: 368 GLDAVLVGRLFQKNPAVVWAFAE 390


>gi|324528660|gb|ADY48937.1| tRNA-dihydrouridine synthase 3 [Ascaris suum]
          Length = 90

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 2/41 (4%)

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +       K L    ++GVMI R A     + T + E   
Sbjct: 16  DILSYHDYYKRLEEYPINGVMIARGALIKPWIFTEIKERRE 56


>gi|116626688|ref|YP_828844.1| dihydropyrimidine dehydrogenase [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116229850|gb|ABJ88559.1| dihydropyrimidine dehydrogenase (NADP+) / dihydrouracil
           dehydrogenase (NAD+) / dihydroorotate oxidase B,
           catalytic subunit [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 446

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 42/227 (18%), Positives = 73/227 (32%), Gaps = 30/227 (13%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
            K  ED G + + LN GCP     E   GA +   PD        + +    PV VK   
Sbjct: 118 VKRSEDAGADGLELNFGCPHGMS-ERGMGAAVGQVPDYSCMITEWVKEVARTPVLVKLTP 176

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIW--------------IHARKAILKGLSPKDNRKI 171
            + D      +R + ++ K+   + +                   +  + G +       
Sbjct: 177 NITD------IRAVARAAKRGRADALSAINTINSITGIDLDTFTPRPNVGGKTSHGGYCG 230

Query: 172 PNLDYDIVYEIKKENPDLFIGL-----NGGLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           P +    ++ +++   D  +GL      G       A  IL     V +  AA       
Sbjct: 231 PAVKPIALHLVQQIASDPAVGLPISGIGGIGGWREAAEFILLGCGTVQVCTAAMH--YGF 288

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
             V++              R  +DF       +TD+  +HL    K+
Sbjct: 289 RIVEDMIDGLSNWMDEKGFRTIEDFRGLSVPRVTDW--KHLDLNYKI 333


>gi|317146647|ref|XP_001821546.2| NADH oxidase [Aspergillus oryzae RIB40]
          Length = 456

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 60/172 (34%), Gaps = 29/172 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            +AAK     G + I ++            P +     S+G        ++ + I ++ K
Sbjct: 221 AKAAKRAVQAGADVIEIHAAHGYLIHQFLSPVSNHRTDSYGGSFENRTRLLLEIIESVRK 280

Query: 114 AL--SIPVTVKCRI----------GVDDQIPAVALRNLVKSIKKSGVNGIWI-----HAR 156
            +   +P+ ++                          L K + ++GV+ + +     H  
Sbjct: 281 EMPAGMPLFLRVSSTEWLESTEIGTKYGTWTVEDTIRLAKLLPEAGVDLLDVSSGGNHPM 340

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + +   L+     KI      I  E+K+   +L IG  G + +  QA  ++ 
Sbjct: 341 QTVNSFLTKDYQTKIAA---RIRKELKQSGVNLLIGAVGMITEAEQARDLVE 389


>gi|83769409|dbj|BAE59544.1| unnamed protein product [Aspergillus oryzae]
          Length = 478

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 60/172 (34%), Gaps = 29/172 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            +AAK     G + I ++            P +     S+G        ++ + I ++ K
Sbjct: 221 AKAAKRAVQAGADVIEIHAAHGYLIHQFLSPVSNHRTDSYGGSFENRTRLLLEIIESVRK 280

Query: 114 AL--SIPVTVKCRI----------GVDDQIPAVALRNLVKSIKKSGVNGIWI-----HAR 156
            +   +P+ ++                          L K + ++GV+ + +     H  
Sbjct: 281 EMPAGMPLFLRVSSTEWLESTEIGTKYGTWTVEDTIRLAKLLPEAGVDLLDVSSGGNHPM 340

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + +   L+     KI      I  E+K+   +L IG  G + +  QA  ++ 
Sbjct: 341 QTVNSFLTKDYQTKIAA---RIRKELKQSGVNLLIGAVGMITEAEQARDLVE 389


>gi|303311719|ref|XP_003065871.1| oxidoreductase, FAD/FMN-binding family protein [Coccidioides
           posadasii C735 delta SOWgp]
 gi|240105533|gb|EER23726.1| oxidoreductase, FAD/FMN-binding family protein [Coccidioides
           posadasii C735 delta SOWgp]
          Length = 424

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 65/203 (32%), Gaps = 36/203 (17%)

Query: 57  ADISKLVEA----AKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDI 103
           ADI +  EA     +     G + I + N           P +      +G        +
Sbjct: 193 ADIEEFKEAWGAAVRRAVKAGVDYIEIHNAHGYLLYSFLSPVSNNRTDEYGGSFENRMRL 252

Query: 104 VGDCIAAMCKAL--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
             + +    K +  ++P+ ++          R  +        +R      +K GV+ + 
Sbjct: 253 TLEIVDISRKNMPENMPLFLRVSATDWLEESRPDLPSWKLEDTVRFAQVLAEKGGVDFLD 312

Query: 153 IHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-- 208
           I +      G       KI           +KK   D + +G  G + +  QA  +L   
Sbjct: 313 ISSG-----GNHTDQKIKIGPGFQAPFAIAVKKAVGDRIAVGTVGSITNGKQANDLLENE 367

Query: 209 SVDGVMIGRAAYKNS---AMLTT 228
            +D V++GR   KN         
Sbjct: 368 GLDAVLVGRLFQKNPAVVWAFAE 390


>gi|326564416|gb|EGE14644.1| NADPH dehydrogenase [Moraxella catarrhalis 12P80B1]
 gi|326567502|gb|EGE17617.1| NADPH dehydrogenase [Moraxella catarrhalis BC1]
          Length = 353

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 75/218 (34%), Gaps = 23/218 (10%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           +   AI  G+    L ++ Q      Q+   +I  LV+A     K   + G++ I L+  
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRQLSIDEIKALVQAFADSVKRAVNAGFDAIELHAA 172

Query: 83  --------C-PSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIP 132
                   C P +      +G   +L  + V   + A M   + + V +  +   ++   
Sbjct: 173 HGYLIHQFCAPKSNQRSDEYGQDRLLFGEQVIHAVRAVMPDEMPLIVRISAQEYGENGFD 232

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           +     + K    +G +   +      +     K           +  ++K       + 
Sbjct: 233 SDYGVEIAKRFSTAGADVFHVSGGGDGVL-CEGKHPEFYAGYQVALARKVKHATGK-PVI 290

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             G L+D + A  +L     D V IGR   ++   +L 
Sbjct: 291 AVGMLDDPAVADHVLGVGDADLVAIGRGLLRDPYWVLN 328


>gi|66046168|ref|YP_236009.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           syringae B728a]
 gi|63256875|gb|AAY37971.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           syringae B728a]
          Length = 365

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 51/135 (37%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGI 151
               +  + IAA+ K A   PV V+   G  +               +  ++  +GV+ I
Sbjct: 209 QRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQHKWAGGEGDAEVIFAALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A     +      +           ++  PD+ +  NGGL D  +A ++L    
Sbjct: 269 HVTEHEAWQPAFTQGQASLVELA--------RRYAPDVALIANGGLHDPQKADQVLRQGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|71282132|ref|YP_269165.1| 2,4-dienoyl-CoA reductase [Colwellia psychrerythraea 34H]
 gi|71147872|gb|AAZ28345.1| 2,4-dienoyl-CoA reductase [Colwellia psychrerythraea 34H]
          Length = 674

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/136 (14%), Positives = 45/136 (33%), Gaps = 9/136 (6%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVN 149
           G           D +  + +A+     +  R+ + D               ++I+K+G  
Sbjct: 188 GGAFENRIKFGVDVVRRIREAVGEKFIIIFRLSMMDLVEGGSTFEEAVQFGQAIEKAGAT 247

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
              I+      +   P    K+P   +  V    KE+ ++ +  +  +     A  +L +
Sbjct: 248 --IINTGIGWHEARIPTIQTKVPRAAFTWVTAKYKEHFNIPVITSNRINTPEVAEAVLQN 305

Query: 210 VDGVMIGRAAYKNSAM 225
            D  MI   +     +
Sbjct: 306 GDADMI---SMARPFL 318


>gi|238493801|ref|XP_002378137.1| FMN binding oxidoreductase, putative [Aspergillus flavus NRRL3357]
 gi|220696631|gb|EED52973.1| FMN binding oxidoreductase, putative [Aspergillus flavus NRRL3357]
          Length = 393

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 69/182 (37%), Gaps = 26/182 (14%)

Query: 61  KLVEAAKIVEDFGYNEINL------------NVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           K V+ A+++ D G++ + L            N   P   +    +G  L      V D I
Sbjct: 147 KFVDTARLMADSGFSGVELHGAHGYLIDQFLN---PKTNLRTDVYGGTLEKRAKFVLDII 203

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS--IKKSGVNGIWIHAR----KAILKG 162
             + KA+     V  ++   D   +     + +   + ++G++ + +        +++ G
Sbjct: 204 TEIRKAVPSKFCVGIKLNSADHSSSTFEETMAQIGLLVEAGIDFLEVSGGSYEDPSMMGG 263

Query: 163 LSPKDNRKIPNLDYDIVY---EIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
             P+ + +    +   +    E +K  PDL   L GG    + A   +     D + IGR
Sbjct: 264 TQPQKSARTAAREAFFIEFATEARKRYPDLVFMLTGGFRSRTGAESAIKENACDLIGIGR 323

Query: 218 AA 219
            A
Sbjct: 324 PA 325


>gi|328774098|gb|EGF84135.1| hypothetical protein BATDEDRAFT_29250 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 405

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/148 (16%), Positives = 48/148 (32%), Gaps = 6/148 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G        ++ +    + K      PV V+  C    +    +     L K++   GV
Sbjct: 238 YGGSFENRSRLLIEVCQEVRKHWPEGKPVFVRLSCSDWAEGGWTSDDTVQLAKTLVNFGV 297

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I   +   +        +      +      I K    +  G+ GG+ D   A  IL 
Sbjct: 298 DLIDCSSGGNVPHASVSPLHSHDAGWNVPFSEAIAKNASGMHTGVVGGISDPHHAESILQ 357

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFS 234
               D +++GR   +N   +    +   
Sbjct: 358 EGKADLILLGRELLRNPIWVGQAAQALG 385


>gi|223983048|ref|ZP_03633251.1| hypothetical protein HOLDEFILI_00531 [Holdemania filiformis DSM
           12042]
 gi|223964985|gb|EEF69294.1| hypothetical protein HOLDEFILI_00531 [Holdemania filiformis DSM
           12042]
          Length = 546

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 76/218 (34%), Gaps = 26/218 (11%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-----C- 83
           D  ++     I       K + +Q     I  L +  K  +DFG++ I L+ G     C 
Sbjct: 109 DGTVQMPSDGICYTGEMGKAMTVQQMEDQIRDLADNCKKAKDFGFSMIMLHFGHDSQCCQ 168

Query: 84  ---PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRI--GVDDQIPAVAL 136
              P       S+G  L        + + A+ +A+    P+ ++      V +      +
Sbjct: 169 FLSPVWNRRTDSYGGSLDNRIRFAREALIAVRQAVGPRYPIMMRISRQLMVPESYSEDDM 228

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN---------LDYDIVYEIKKENP 187
              +K ++   V+ + + A      G        +            +      +K+E  
Sbjct: 229 LYFLKQVEDL-VDIVNVSAGMDCYGGTVEHYEANVHTHTTVFEPQYYNAAFARRVKQEC- 286

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            + + L GG+ D +   +++     D VM+GR    + 
Sbjct: 287 RVKVALVGGITDPAVCEQLIAEGSTDLVMLGRQLVADP 324


>gi|322833672|ref|YP_004213699.1| NADH:flavin oxidoreductase/NADH oxidase [Rahnella sp. Y9602]
 gi|321168873|gb|ADW74572.1| NADH:flavin oxidoreductase/NADH oxidase [Rahnella sp. Y9602]
          Length = 365

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/138 (16%), Positives = 48/138 (34%), Gaps = 13/138 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           +G  L     ++ +    +  A     P+ V+      V+          L K++ + G 
Sbjct: 199 YGGSLENRMRLLLEIFGEIRAAFPAEKPIGVRISATDWVEGGWDLEQSIELAKALDELGC 258

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + I + +      GLSP     +   +Y +   +  K    + +   G + +  QA  I+
Sbjct: 259 SYIHVSSG-----GLSPHQKITVGP-NYQVPFADGIKRYVKMPVIAVGLITEPEQAEAII 312

Query: 208 --PSVDGVMIGRAAYKNS 223
                D + + R    N 
Sbjct: 313 GTGQADMIALARGILYNP 330


>gi|330974530|gb|EGH74596.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 679

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVRRVREAVGAQFIIIFRLSMLDLVEGGSSWEEIVELAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|330892039|gb|EGH24700.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           mori str. 301020]
          Length = 370

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 28/140 (20%), Positives = 52/140 (37%), Gaps = 16/140 (11%)

Query: 94  GACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKS 146
           G  +     +  D IA + K A   PV V+   G  +              ++  ++  +
Sbjct: 204 GGDVQQRLRLTLDVIAEVKKMAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFGALADA 263

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ I +   +A                   +V   ++  P + +  NGGL D  +A K+
Sbjct: 264 GVDYIHVTEHEAW--------QPAFAQGKASLVELARRYAPGVALIANGGLHDPEKADKV 315

Query: 207 L-PSVDGVMIGRAAYKNSAM 225
           L    D + +G+ A  N  +
Sbjct: 316 LHQGADIIAVGKGALANPDL 335


>gi|221133876|ref|ZP_03560181.1| NADH:flavin oxidoreductase/NADH oxidase [Glaciecola sp. HTCC2999]
          Length = 679

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 25/176 (14%), Positives = 57/176 (32%), Gaps = 17/176 (9%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            + A+  +  GY+ + +            C      +  FG  L     +  + +     
Sbjct: 153 AKCAQYAQSAGYDGVEIMGSEGYLINQFFCERTNFRDDEFGGSLENRARLAVETVKQTRL 212

Query: 114 ALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+ + D      P   +  L K+I+ +G   I  +      +   P    
Sbjct: 213 AVGSDFIIIYRLSMLDLVEGGAPWEEVVYLAKAIEAAGATLI--NTGIGWHEARVPTIAT 270

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +P   +  + +  KE+ ++ +     +     A  +L     D V + R    + 
Sbjct: 271 SVPRAAFTWITQRMKEHVNVPLITTNRINTPEVAESVLAQGHADMVSMARPFLADP 326


>gi|37527773|ref|NP_931118.1| hypothetical protein plu3917 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787209|emb|CAE16289.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 289

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 61/180 (33%), Gaps = 27/180 (15%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
           +  F  ++ P+ + I       L   A  +       + L + C                
Sbjct: 88  LREFKEEQLPVIVSIHAESPEALASLAVRISAVTDAPLELGISC--------LHADDFTE 139

Query: 100 N-PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----- 153
           + P+ V +    + +  + P  VK  +G         L   V++  + G + I +     
Sbjct: 140 DTPERVFNYTKVVKERTNTPFAVKLSLG-------DNLYGRVQAAVEGGADAITLSDTIS 192

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                    +A+L G+       I  +    +Y ++K    + I  +GG++D +   + L
Sbjct: 193 GIAFDTANGEALLNGVCGYSGPGIKPMVLAAIYNLRKRGVTIPILGSGGVQDGNDVHEYL 252


>gi|218529251|ref|YP_002420067.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacterium
           chloromethanicum CM4]
 gi|218521554|gb|ACK82139.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacterium
           chloromethanicum CM4]
          Length = 366

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/135 (17%), Positives = 53/135 (39%), Gaps = 16/135 (11%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQI------PAVALRNLVKSIKKSGVNGIWIHARK 157
           V D + A  +A  +PV V+   G  +               +  ++ ++G + + +   K
Sbjct: 216 VFDAVRATVRA-GVPVGVRISQGKVNDFGHKWAGREQDAEAIFGTLAEAGASYLHVTEHK 274

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
                     +         +V   ++  P + +  NGG++D+++A +++    D V +G
Sbjct: 275 VWEPAFEGGRD--------SLVALARRYAPHVTLIANGGVQDVARAQEVMAAGADIVALG 326

Query: 217 RAAYKNSAMLTTVDE 231
           +AA  N      V  
Sbjct: 327 KAALANPDFPNRVRA 341


>gi|83815963|ref|YP_446480.1| dihydroorotate oxidase [Salinibacter ruber DSM 13855]
 gi|83757357|gb|ABC45470.1| dihydroorotate oxidase [Salinibacter ruber DSM 13855]
          Length = 366

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 79/222 (35%), Gaps = 39/222 (17%)

Query: 43  FSTQEKPLALQIG-GADISKLVEAAKIVEDF---------GYNEINLNVGCPSARVHEGS 92
            S + +PL + +    D   + EAA  +EDF           + + LNV CP     +G 
Sbjct: 133 RSDRARPLGINLAKTHDPDIMGEAA--LEDFRTSFRQLVGQADYVTLNVSCP--NTPDGG 188

Query: 93  FGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKS 146
                  +P  +   + A+        L++PV VK    + D++     L  ++      
Sbjct: 189 TF----EDPAALDALLGAITAEQKAPGLAVPVLVKLSPPLSDRVLFDTRLEEILAVAADH 244

Query: 147 GVNGIWIHARKAILKGLSPKDNR---------KIPNLDYDIVYEI----KKENPDLFIGL 193
            ++G       +  KG+    +R           P L+      +    +  + ++ I  
Sbjct: 245 DIDGFIATNTASDRKGVETSADRLDEIGAGGLSGPPLEARATRLVQYLYRATDGEIPIIG 304

Query: 194 NGGLEDMSQAL-KILPSVDGVMIGRAA-YKNSAMLTTVDEYF 233
            GG+ D   A  KI      V +  A  Y+   ++  + E  
Sbjct: 305 VGGVHDAESAYTKIRAGASLVQLYTALVYEGPGLVRRIKEGL 346


>gi|188994769|ref|YP_001929021.1| putative dihydroorotate dehydrogenase [Porphyromonas gingivalis
           ATCC 33277]
 gi|188594449|dbj|BAG33424.1| putative dihydroorotate dehydrogenase [Porphyromonas gingivalis
           ATCC 33277]
          Length = 232

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 42/99 (42%), Gaps = 11/99 (11%)

Query: 56  GADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G+ +    E ++I+ +  +   I LN+ CP+ +    ++G       +     + A+ +A
Sbjct: 85  GSTLDDYAETSRIINELEHIRAIELNISCPNVKQGGMAYGV----TCEGAASVVKAVRRA 140

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
               + VK    V D      +  + ++++  G + I +
Sbjct: 141 YDKTLIVKLSPNVTD------ITEIARAVESEGADAISM 173


>gi|166713953|ref|ZP_02245160.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 369

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 53/166 (31%), Gaps = 13/166 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSG 147
           ++G  L     +      A+  A+S  + +  RI   D             L +++   G
Sbjct: 203 AYGGSLENRMRLTLRIFDAVRAAVSEKIAIGVRISATDWVEGGWDVQQSIALSQALDARG 262

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKI 206
            + I + +      GL P+    +    Y I   +  + +    +   G + + +QA  I
Sbjct: 263 AHYIHVSSG-----GLDPRQQIPL-QAGYQIPFAQEIRAHVRTPVIGVGLITEPAQAEAI 316

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           +     D + + R    +              +T +        +D
Sbjct: 317 VQEGQADAIALARGILYDPRWPWHAAAALGASVTPAPQYLRCEPRD 362


>gi|66044920|ref|YP_234761.1| NADH:flavin oxidoreductase/NADH oxidase:FAD-dependent pyridine
           nucleotide-disulphide oxidoreductase [Pseudomonas
           syringae pv. syringae B728a]
 gi|63255627|gb|AAY36723.1| NADH:flavin oxidoreductase/NADH oxidase:FAD-dependent pyridine
           nucleotide-disulphide oxidoreductase [Pseudomonas
           syringae pv. syringae B728a]
          Length = 679

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVRRVREAVGAQFIIIFRLSMLDLVEGGSSWEEIVELAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|119356429|ref|YP_911073.1| dihydroorotate oxidase B, catalytic subunit [Chlorobium
           phaeobacteroides DSM 266]
 gi|119353778|gb|ABL64649.1| dihydroorotate oxidase B, catalytic subunit [Chlorobium
           phaeobacteroides DSM 266]
          Length = 314

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 25/190 (13%), Positives = 68/190 (35%), Gaps = 25/190 (13%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G  I +  E    ++D  G     +N+ CP    +       + ++     + +
Sbjct: 106 IIVNIAGRSIDEYAEVIARLDDVEGIGGYEINLSCP----NVKGECMIMGVSRSATHEIV 161

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARK 157
           + + K  +  + +K    V           +  + +++G + + +             RK
Sbjct: 162 SVLRKITNRHLMIKLTPNVTSISS------IALAAEEAGADSVSLINTLVGMAVNYKTRK 215

Query: 158 AILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMI 215
            +L+ ++       I  +    V+E+     ++ +   GG+     A++ +L     + I
Sbjct: 216 PLLRNVTGGLSGPAIKPIALAKVWEVFNAV-NIPVVGMGGITGFEDAMEFLLVGATAIQI 274

Query: 216 GRAAYKNSAM 225
           G   +    +
Sbjct: 275 GTMNFVYPDI 284


>gi|328880787|emb|CCA54026.1| 2,4-dienoyl-CoA reductase [Streptomyces venezuelae ATCC 10712]
          Length = 361

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/159 (13%), Positives = 51/159 (32%), Gaps = 12/159 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV---DDQIPAVALRNLVKSIKKS 146
           ++G        +  + + A+       +PV  +        +    A         +++ 
Sbjct: 203 AYGGSFENRTRLALEVVDAVRAVWPEELPVFFRVSATDWLAERGWTADETVRFAALLREH 262

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ + + +         P +    P         +K E   L +   G + +  QA KI
Sbjct: 263 GVDLLDVSSG----GNGGPAEIPVGPGYQVPFAARVKAETG-LPVAAVGLITESDQAEKI 317

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           +     D V++GR   ++++               + P 
Sbjct: 318 VANGEADAVLLGRELLRDASWARRAARDLGATTHPAPPP 356


>gi|253991099|ref|YP_003042455.1| 2,4-dienoyl-coa reductase [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782549|emb|CAQ85713.1| 2,4-dienoyl-coa reductase [nadph] (2,4-dienoyl coenzyme a
           reductase) [Photorhabdus asymbiotica]
          Length = 673

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 23/181 (12%), Positives = 57/181 (31%), Gaps = 35/181 (19%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPDI 103
                A++ +  GY+ + +        +    +                 G        +
Sbjct: 144 DFAHCAQLAQQAGYDGVEI--------MGSEGYLINQFLTARTNHRQDKWGGSFENRMRL 195

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+ +A      +  R+     V++      +  L  +I+++G +   I+     
Sbjct: 196 AVEIVKAVRQATGKEFILIYRLSMLDLVEEGSNWQEIEQLAVAIEQAGAS--IINTGIGW 253

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
            +   P     +P   +  V  ++  +     I  N  + D   A ++L     D V + 
Sbjct: 254 HEARIPTIATMVPRAGFSWVTRKLMGKVSIPLITTNR-INDPQIAEQVLAQGCADMVSMA 312

Query: 217 R 217
           R
Sbjct: 313 R 313


>gi|119356597|ref|YP_911241.1| NADH:flavin oxidoreductase/NADH oxidase [Chlorobium
           phaeobacteroides DSM 266]
 gi|119353946|gb|ABL64817.1| NADH:flavin oxidoreductase/NADH oxidase [Chlorobium
           phaeobacteroides DSM 266]
          Length = 646

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 21/144 (14%), Positives = 47/144 (32%), Gaps = 18/144 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSG 147
           +G         + + ++ +         +  R+ VD+              +   ++ +G
Sbjct: 187 YGNSFENRMRFLLEIVSGIRNRCGKNFPIGVRLSVDEFLGQYGNDLATSCRIASELELAG 246

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYD------IVYEIKKENPDLFIGLNGGLEDMS 201
           ++ + I          SP+ N  I    ++      +  EIKK    + +     ++D  
Sbjct: 247 IDFLDISCTIP----DSPEINACIEPGTFEQGWKKYMAAEIKK-FVKIPLIAVANIKDPD 301

Query: 202 QALKILPS--VDGVMIGRAAYKNS 223
            A  IL     D V + R    + 
Sbjct: 302 IAEAILEENCCDLVGVARGHLADP 325


>gi|281205080|gb|EFA79273.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Polysphondylium pallidum PN500]
          Length = 411

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 58/177 (32%), Gaps = 19/177 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+AA   E  G++ + ++            P++      +G   +    ++ D + A+ 
Sbjct: 215 FVDAAIRCEKAGFDAVEIHGAHGYLIDSFLSPTSNKRTDQYGGSFLGRIKLLLDIVKAVR 274

Query: 113 KALSI--PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                   V + C   V D         L + + +  V+ +   +      G S      
Sbjct: 275 AVWKKLLLVRISCEEWVADGWHLDDSIALARHLHELDVDILDCSSG-----GNSHNQKIA 329

Query: 171 IPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              L        IKK  P L     G +    +A+ ++     D VM+ R   ++  
Sbjct: 330 FGPLYQVPFAEGIKKAIPGLITSAVGLINTPEEAMSVIDEQRADIVMMARPFLRDPF 386


>gi|159128974|gb|EDP54088.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           fumigatus A1163]
          Length = 421

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 33/223 (14%), Positives = 71/223 (31%), Gaps = 31/223 (13%)

Query: 49  PLALQIGGADISKL----VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGA 95
           P+  ++   DI  L    V A K     G + I + N           P+       +G 
Sbjct: 184 PVPKEMTKQDIEDLKTAWVAAVKRAVKAGADFIEIHNAHGYLLMSFLSPAVNTRTDEYGG 243

Query: 96  CLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--------IGVDDQIPAVALRNLVKSIKK 145
                  +  +      + +   +PV ++                   V      K + +
Sbjct: 244 SFENRIRLSLEIAKLTRENVPKDMPVFLRVSATDWLEEVQPNKPSWRGVDTVRFAKILAE 303

Query: 146 SG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQA 203
           +G V+ + + +        S +     P         +K    D L +   G +     A
Sbjct: 304 TGYVDVLDVSSGGT----HSEQHIHAKPGFQAPFAIAVKNAVGDKLAVASVGMIASAHLA 359

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             +L    +D V++GR   KN  ++    +  +  ++ ++ I+
Sbjct: 360 NSLLEKDGLDLVLVGRGFQKNPGLVWAWADELNVEISMANQIR 402


>gi|78486307|ref|YP_392232.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Thiomicrospira crunogena XCL-2]
 gi|91206953|sp|Q31E65|HIS4_THICR RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|78364593|gb|ABB42558.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Thiomicrospira
           crunogena XCL-2]
          Length = 246

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 29/157 (18%), Positives = 58/157 (36%), Gaps = 15/157 (9%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
            V+ R G+ D    V   ++V   ++    G   + +       +G           ++ 
Sbjct: 14  CVRLRQGLMD-DATVFSGDIVAMAERWVNQGARRLHMVDLNGAFEG---------KPVNG 63

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D VY++++  PDL I + GG+ D+      L   V   +IG  A  N   +    + F  
Sbjct: 64  DAVYQVREAFPDLPIQIGGGIRDLETIEAYLKAGVSYCIIGTKAVHNPEFVAEACKAFPG 123

Query: 236 PL-TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            +  G    +  V  + W +++        +   + G
Sbjct: 124 HIMVGLDAKEGMVAINGWAEVTDHNVIDLGKQFENDG 160


>gi|107104500|ref|ZP_01368418.1| hypothetical protein PaerPA_01005577 [Pseudomonas aeruginosa PACS2]
 gi|218894502|ref|YP_002443372.1| putative FMN oxidoreductase [Pseudomonas aeruginosa LESB58]
 gi|254237917|ref|ZP_04931240.1| hypothetical protein PACG_04020 [Pseudomonas aeruginosa C3719]
 gi|254242949|ref|ZP_04936271.1| hypothetical protein PA2G_03736 [Pseudomonas aeruginosa 2192]
 gi|126169848|gb|EAZ55359.1| hypothetical protein PACG_04020 [Pseudomonas aeruginosa C3719]
 gi|126196327|gb|EAZ60390.1| hypothetical protein PA2G_03736 [Pseudomonas aeruginosa 2192]
 gi|218774731|emb|CAW30548.1| probable FMN oxidoreductase [Pseudomonas aeruginosa LESB58]
          Length = 686

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 67/188 (35%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ + K    +G+               +  +  
Sbjct: 213 EVGEDFCVGMRICGDEFHPDGLSHEDMKQIAKYYSDTGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE  D+ +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMTFPPEPFLHLAAGIKEVVDVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|330952721|gb|EGH52981.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae Cit
           7]
          Length = 679

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 45/127 (35%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVRRVREAVGAHFIIIFRLSMLDLVEGGSSWEEIVELAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + + ++ +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVNIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|302392732|ref|YP_003828552.1| ferredoxin-dependent glutamate synthase [Acetohalobium arabaticum
           DSM 5501]
 gi|302204809|gb|ADL13487.1| ferredoxin-dependent glutamate synthase [Acetohalobium arabaticum
           DSM 5501]
          Length = 471

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 60/181 (33%), Gaps = 25/181 (13%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           M  P    + +  +     +PV +K             L   ++   K+GV+ + I   +
Sbjct: 232 MKQPSDFFEIVQQLRDEYGVPVGLKF-------CATHYLEQELEIAVKAGVDYVVIDGAE 284

Query: 158 AILKGLSPKDNRKIP-NLDYDIVYEIK-------KENPDLFIGLNGGLEDMSQALKILP- 208
           A   G        +     Y +   +K       K+     +  +GGL      LK L  
Sbjct: 285 AGTHGGPTTLQDDVGLPTLYALSRAVKFLEEKGVKDRVS--VIASGGLTTPGHFLKALAL 342

Query: 209 SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
             D V IG     + A++  +    S  L    P +  +    +++      + AA HL 
Sbjct: 343 GADAVYIG-----SIALMALLQTQMSKALPQEPPPQIPLYLGKFKEDLD--VEEAAEHLA 395

Query: 269 S 269
            
Sbjct: 396 K 396


>gi|116053545|ref|YP_793872.1| putative FMN oxidoreductase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|313111671|ref|ZP_07797465.1| DgcA, Dimethylglycine catabolism [Pseudomonas aeruginosa 39016]
 gi|115588766|gb|ABJ14781.1| putative oxidoreductase, FMN-binding [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|310883967|gb|EFQ42561.1| DgcA, Dimethylglycine catabolism [Pseudomonas aeruginosa 39016]
          Length = 686

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 67/188 (35%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ + K    +G+               +  +  
Sbjct: 213 EVGEDFCVGMRICGDEFHPDGLSHEDMKQIAKYYSDTGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE  D+ +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMTFPPEPFLHLAAGIKEVVDVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|188585649|ref|YP_001917194.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350336|gb|ACB84606.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 645

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 46/137 (33%), Gaps = 8/137 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGV 148
           +G        +V +   AM   +  + P+ ++     D +          +VK ++K G+
Sbjct: 192 YGGSFENRMRLVTEIYQAMRDEVGPNFPILIRMAADHDFEGGRTVEESIEIVKYLEKLGM 251

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           +   I       K               D    IKKE       LN G      A++ + 
Sbjct: 252 DAFDIDLGCYEQKQWIVPSIYTGLGCMADAAAAIKKEVNVPV--LNSGTHTPETAVETIE 309

Query: 209 S--VDGVMIGRAAYKNS 223
           +   D +M+GR    + 
Sbjct: 310 NEKADFIMLGRPLIADP 326


>gi|290580909|ref|YP_003485301.1| putative dihydroorotate dehydrogenase dihydroorotate oxidase
           [Streptococcus mutans NN2025]
 gi|254997808|dbj|BAH88409.1| putative dihydroorotate dehydrogenase dihydroorotate oxidase
           [Streptococcus mutans NN2025]
          Length = 330

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 43/220 (19%), Positives = 72/220 (32%), Gaps = 20/220 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEG 91
              D    L      K   L + G    +     K+VE   Y   + LN+ CP   V   
Sbjct: 99  YYLDYVTELQKQPDSKNHFLSLVGMSPEETHTILKMVEASKYQGLVELNLSCP--NVPGK 156

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIK 144
              A    + +     ++ +    + P+ +K     D      A A+ N      V  I 
Sbjct: 157 PQIAY---DFETTDQILSEVFTYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLTFVNCIN 213

Query: 145 KSGVNGIWIHARKAILK---GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDM 200
             G NG+ I     ++K   G        +       V+   K+ NP + I   GG++  
Sbjct: 214 SIG-NGLVIEDETVVIKPKNGFGGIGGDYVKPTALANVHAFYKRLNPSIQIIGTGGVKTG 272

Query: 201 SQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSNPLT 238
             A +  L     V IG A   +   +   + +     +T
Sbjct: 273 RDAFEHILCGASMVQIGTALHQEGPQIFKRITKELKAIMT 312


>gi|229816152|ref|ZP_04446463.1| hypothetical protein COLINT_03199 [Collinsella intestinalis DSM
           13280]
 gi|229808278|gb|EEP44069.1| hypothetical protein COLINT_03199 [Collinsella intestinalis DSM
           13280]
          Length = 649

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 67/176 (38%), Gaps = 17/176 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG----------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
           +  +AA  ++  G + + ++             P        +G  L      + + IA 
Sbjct: 150 QFGDAAVRMQKAGVDGVEVHAAHAHGMLGGFLSPQYNKRTDEYGGSLDARMRFLLEVIAE 209

Query: 111 MCKALSIPVTVKCRIGVDD-QIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPK 166
           + +       +  RI  D+     + L +++   + ++K+GV+ I +     I +G +  
Sbjct: 210 IRERCGKDFIIDVRISGDEYTDGGLTLNDMIYVSRRLEKAGVDMIHVSGGTTIKRGSAIP 269

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
                     D+  EIKK    + +   G + +   A +++   + D  M+GRA  
Sbjct: 270 AAGTKQASHADLSREIKKHVT-IPVATVGRINEAWIAEELIEDGAADICMMGRANL 324


>gi|188574702|ref|YP_001911631.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzae PXO99A]
 gi|188519154|gb|ACD57099.1| FMN oxidoreductase [Xanthomonas oryzae pv. oryzae PXO99A]
          Length = 372

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 34/208 (16%), Positives = 66/208 (31%), Gaps = 24/208 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V +A+  E  G   I L+            P +     ++G  L     +       
Sbjct: 165 DAFVASAQRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSLENRMRLTLRIFDV 224

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + +  RI   D             L +++   G + I + +      GL P+
Sbjct: 225 VRAAVSEKIAIGVRISATDWVEGGWDVQQSIALSQALDARGAHYIHVSSG-----GLDPR 279

Query: 167 DNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
               +    Y I    EI+ +     IG+ G + + +QA  I+     D + + R    +
Sbjct: 280 QQIPL-QAGYQIPFAQEIRAQVSRPVIGV-GLITEPAQAEAIVQEGQADAIALARGILYD 337

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                         +T +        +D
Sbjct: 338 PRWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|24379073|ref|NP_721028.1| dihydroorotate dehydrogenase 1A [Streptococcus mutans UA159]
 gi|24376971|gb|AAN58334.1|AE014903_10 putative dihydroorotate dehydrogenase; dihydroorotate oxidase
           [Streptococcus mutans UA159]
          Length = 311

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 43/220 (19%), Positives = 72/220 (32%), Gaps = 20/220 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEG 91
              D    L      K   L + G    +     K+VE   Y   + LN+ CP   V   
Sbjct: 80  YYLDYVTELQKQPDSKNHFLSLVGMSPEETHTILKMVEASKYQGLVELNLSCP--NVPGK 137

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIK 144
              A    + +     ++ +    + P+ +K     D      A A+ N      V  I 
Sbjct: 138 PQIAY---DFETTDQILSEVFTYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLTFVNCIN 194

Query: 145 KSGVNGIWIHARKAILK---GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDM 200
             G NG+ I     ++K   G        +       V+   K+ NP + I   GG++  
Sbjct: 195 SIG-NGLVIEDETVVIKPKNGFGGIGGDYVKPTALANVHAFYKRLNPSIQIIGTGGVKTG 253

Query: 201 SQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSNPLT 238
             A +  L     V IG A   +   +   + +     +T
Sbjct: 254 RDAFEHILCGASMVQIGTALHQEGPQIFKRITKELKAIMT 293


>gi|15600591|ref|NP_254085.1| DgcA, Dimethylglycine catabolism [Pseudomonas aeruginosa PAO1]
 gi|9951723|gb|AAG08783.1|AE004952_5 DgcA, Dimethylglycine catabolism [Pseudomonas aeruginosa PAO1]
          Length = 686

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 67/188 (35%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ + K    +G+               +  +  
Sbjct: 213 EVGEDFCVGMRICGDEFHPDGLSHEDMKQIAKYYSDTGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE  D+ +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMTFPPEPFLHLAAGIKEVVDVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|152988218|ref|YP_001351496.1| putative FMN oxidoreductase [Pseudomonas aeruginosa PA7]
 gi|150963376|gb|ABR85401.1| probable FMN oxidoreductase [Pseudomonas aeruginosa PA7]
          Length = 686

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 67/188 (35%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ + K    +G+               +  +  
Sbjct: 213 EVGEDFCVGMRICGDEFHPDGLSHEDMKQIAKYYSDTGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE  D+ +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMTFPPEPFLHLAAGIKEVVDVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|330901119|gb|EGH32538.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           japonica str. M301072PT]
          Length = 679

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVRRVREAVGAQFIIIFRLSMLDLVEGGSSWEEIVELAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|296392258|ref|ZP_06881733.1| putative FMN oxidoreductase [Pseudomonas aeruginosa PAb1]
          Length = 686

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 67/188 (35%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ + K    +G+               +  +  
Sbjct: 213 EVGEDFCVGMRICGDEFHPDGLSHEDMKQIAKYYSDTGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE  D+ +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMTFPPEPFLHLAAGIKEVVDVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|126739086|ref|ZP_01754780.1| oxidoreductase, FAD/FMN-binding protein [Roseobacter sp. SK209-2-6]
 gi|126719703|gb|EBA16411.1| oxidoreductase, FAD/FMN-binding protein [Roseobacter sp. SK209-2-6]
          Length = 422

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 38/286 (13%), Positives = 82/286 (28%), Gaps = 29/286 (10%)

Query: 8   HYRFFARLLTNNAL-LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGA------DIS 60
            +R  AR  + N   L+ ++  A A+         G S  E P       +         
Sbjct: 112 AFRQLARQGSTNGAQLWLQLGHAGALAHLPISKPKGPSEIEFPDFRSEAMSLAEIQAVPD 171

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
              + A    + G+  + ++       +              ++G  +     ++ + + 
Sbjct: 172 CFAKTALRAAELGFGGVQIHAA--HGFLLSQFLSPLFNHRTDAYGGSIEARMRLLIETVE 229

Query: 110 AMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            +   +     +  ++   DQ+           +V  ++  GV+ + I          S 
Sbjct: 230 TVRALVPSDFVMAVKLNATDQLDGGLAEEDSLKVVAELEGRGVDLLDISGGTYFPGASSS 289

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNS 223
            +   I     D      +    + +   GG +   +A       +VD V + R    + 
Sbjct: 290 SERASIGPYFVDFARA-ARHITSIPLMATGGFKRQEEAEAAVHSGTVDAVGLARGFVLDP 348

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHS 269
           ++  T     S PL              W   +  MTD        
Sbjct: 349 SLPATWQTDKSAPLFPRFATLPPGGMTAW--FTMRMTDLGEEREGQ 392


>gi|149188175|ref|ZP_01866470.1| 2,4-dienoyl-CoA reductase [Vibrio shilonii AK1]
 gi|148838163|gb|EDL55105.1| 2,4-dienoyl-CoA reductase [Vibrio shilonii AK1]
          Length = 667

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 24/184 (13%), Positives = 64/184 (34%), Gaps = 17/184 (9%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             +A + ++ GY+ + +            C    V    +G        +  + + A+  
Sbjct: 144 ANSASLAQEAGYDGVEIMGSEGYFINQFICKRTNVRYDEWGGSYENRIRLPLEIVKAVRA 203

Query: 114 ALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+     V+       +  L ++++++GV    I+      +   P    
Sbjct: 204 AVGKEFIIIFRLSMLDLVEQGSTFEEVVQLGQALEQAGVT--IINTGIGWHEAKVPTIAT 261

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           ++P   +  V E  +   ++ +     +    +A +IL     D V + R    +   + 
Sbjct: 262 QVPRGAFTWVTEKIRPYLNVPVITTNRINTPEEAERILSSGHADMVSMARPFLADPNFIA 321

Query: 228 TVDE 231
             ++
Sbjct: 322 KAEQ 325


>gi|70989429|ref|XP_749564.1| NADH-dependent flavin oxidoreductase [Aspergillus fumigatus Af293]
 gi|66847195|gb|EAL87526.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           fumigatus Af293]
          Length = 421

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 33/223 (14%), Positives = 71/223 (31%), Gaps = 31/223 (13%)

Query: 49  PLALQIGGADISKL----VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGA 95
           P+  ++   DI  L    V A K     G + I + N           P+       +G 
Sbjct: 184 PVPKEMTKQDIEDLKTAWVAAVKRAVKAGADFIEIHNAHGYLLMSFLSPAVNTRTDEYGG 243

Query: 96  CLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--------IGVDDQIPAVALRNLVKSIKK 145
                  +  +      + +   +PV ++                   V      K + +
Sbjct: 244 SFENRIRLSLEIAKLTRENVPKDMPVFLRVSATDWLEEVQPNKPSWRGVDTVRFAKILAE 303

Query: 146 SG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQA 203
           +G V+ + + +        S +     P         +K    D L +   G +     A
Sbjct: 304 TGYVDVLDVSSGGT----HSEQHIHAKPGFQAPFAIAVKNAVGDKLAVASVGMIASAHLA 359

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             +L    +D V++GR   KN  ++    +  +  ++ ++ I+
Sbjct: 360 NSLLEKDGLDLVLVGRGFQKNPGLVWAWADELNVEISMANQIR 402


>gi|168058192|ref|XP_001781094.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162667491|gb|EDQ54120.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 386

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 37/176 (21%), Positives = 63/176 (35%), Gaps = 25/176 (14%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E  + VE+ G +   +N  CP     E   G  +  +  ++ +    +    +IPV  K 
Sbjct: 131 EIIERVEEAGVDAFEINFSCPHGM-PERKMGMAMGQDCSVLEEVCGWINAKATIPVWAKM 189

Query: 124 RIGVDD--QIPAVALRNLVKSIKK-------SGVNGIWIHARKAIL-----KGLSPKDNR 169
              + D  Q    ALR+  + +          G+N   +     +       G S K  R
Sbjct: 190 TPNITDITQPARTALRSGCEGVAAINTIMSVMGINLDTLRPEPCVEGYSTPGGYSCKAVR 249

Query: 170 KIPNLDYDIVYE-IKKENP--DLFIGLNGGLEDMSQALK-------ILPSVDGVMI 215
            I       + + +K E P  D  +   GG+E  S A +        +    GVM+
Sbjct: 250 PIALAKVMSIAQMMKTEFPGQDRSLSGIGGVESGSHAAEFILLGASTVQVCTGVML 305


>gi|118475694|ref|YP_891794.1| NADPH dehydrogenase [Campylobacter fetus subsp. fetus 82-40]
 gi|261886428|ref|ZP_06010467.1| NADPH dehydrogenase [Campylobacter fetus subsp. venerealis str.
           Azul-94]
 gi|118414920|gb|ABK83340.1| NADPH dehydrogenase [Campylobacter fetus subsp. fetus 82-40]
          Length = 338

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 33/174 (18%), Positives = 57/174 (32%), Gaps = 14/174 (8%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           K  EAA   +D  Y+ I +             P     E  FG  L      +   I  +
Sbjct: 144 KFKEAAIRAKDSDYDLIEIHGAHGYLINQFLSPLTNKREDEFGGNLENRMRFLNLIIEEL 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
              +   V +      D       ++ + K  ++ G + I + A   +    +P    KI
Sbjct: 204 KDIIPFGVRLSADEWEDGGNTTEDIKIVAKKCEELGASYISVSAGGVVE---NPTHMPKI 260

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
             L      +  KE  ++ +   G +    Q   +L +   D V  GR   +N 
Sbjct: 261 KPLYQAQYAKDIKEVINIPVIAAGLITTKEQGEYLLDNGFCDLVAYGRELLRNP 314


>gi|294508415|ref|YP_003572473.1| dihydroorotate dehydrogenase [Salinibacter ruber M8]
 gi|294344744|emb|CBH25522.1| Dihydroorotate dehydrogenase [Salinibacter ruber M8]
          Length = 398

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 79/222 (35%), Gaps = 39/222 (17%)

Query: 43  FSTQEKPLALQIG-GADISKLVEAAKIVEDF---------GYNEINLNVGCPSARVHEGS 92
            S + +PL + +    D   + EAA  +EDF           + + LNV CP     +G 
Sbjct: 165 RSDRARPLGINLAKTHDPDIMGEAA--LEDFRTSFRQLVGQADYVTLNVSCP--NTPDGG 220

Query: 93  FGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKS 146
                  +P  +   + A+        L++PV VK    + D++     L  ++      
Sbjct: 221 TF----EDPAALDALLGAITAEQKAPGLAVPVLVKLSPPLSDRVLFDTRLEEILAVAADH 276

Query: 147 GVNGIWIHARKAILKGLSPKDNR---------KIPNLDYDIVYEI----KKENPDLFIGL 193
            ++G       +  KG+    +R           P L+      +    +  + ++ I  
Sbjct: 277 DIDGFIATNTASDRKGVETSADRLDEIGAGGLSGPPLEARATRLVQYLYRATDGEIPIIG 336

Query: 194 NGGLEDMSQAL-KILPSVDGVMIGRAA-YKNSAMLTTVDEYF 233
            GG+ D   A  KI      V +  A  Y+   ++  + E  
Sbjct: 337 VGGVHDAESAYTKIRAGASLVQLYTALVYEGPGLVRRIKEGL 378


>gi|225414595|ref|ZP_03761784.1| hypothetical protein CLOSTASPAR_05819 [Clostridium asparagiforme
           DSM 15981]
 gi|225041881|gb|EEG52127.1| hypothetical protein CLOSTASPAR_05819 [Clostridium asparagiforme
           DSM 15981]
          Length = 634

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 21/140 (15%), Positives = 48/140 (34%), Gaps = 10/140 (7%)

Query: 106 DCIAAMCKALSI--PVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+        PV  +      V+          ++K ++++G++ + +       +
Sbjct: 184 EIVRAIKAICGTEYPVVFRISGDEMVERGRKLPETIEIIKLLEEAGIDAVHVSIGMPESE 243

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
                        +      +K+E   + +   G +  M QA +IL     D   IGRA 
Sbjct: 244 EYMCAPMDIPDGFNTSAAEAVKREV-KIPVITVGRITTMEQAEEILEQGKADLTAIGRAQ 302

Query: 220 YKNSAMLTTVDEYFSNPLTG 239
             +  +   V++Y       
Sbjct: 303 LADPGL---VNKYMGGDPAP 319


>gi|167948798|ref|ZP_02535872.1| Dihydrouridine synthase TIM-barrel protein nifR3 [Endoriftia
           persephone 'Hot96_1+Hot96_2']
          Length = 66

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 72  FGYNEINLNVGCPSARVHEGS-FGACLMLNPDIVG-DCIAAMCKALSIPVTVK 122
                +++N+GCP+ +V +GS  G+ L+ +  + G         A+ IPVT++
Sbjct: 4   MAPRVVDINMGCPAKKVCQGSRAGSALLRDSALAGQRFFKQWVDAVDIPVTLE 56


>gi|239994058|ref|ZP_04714582.1| NADPH2 dehydrogenase [Alteromonas macleodii ATCC 27126]
          Length = 368

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 50/141 (35%), Gaps = 19/141 (13%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKK 145
              G  L+       + ++A+      ++P+TV+        DD+        LVK  K+
Sbjct: 205 QGRGRFLL-------ETLSAVRAVWPENLPLTVRFGVIEYDGDDEQTLSESIELVKQFKE 257

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            G + + +      +   +P  N          + +  ++   + +    G++    A  
Sbjct: 258 IGTDFVSV-----SVGFNTPDANIPWGPAFLAPIAKKVRDEAGIPVATAWGVDTPELAND 312

Query: 206 ILP--SVDGVMIGRAAYKNSA 224
            +    +D VM+GR    N  
Sbjct: 313 TIENQQLDVVMVGRMHLTNPH 333


>gi|239624920|ref|ZP_04667951.1| dihydroorotate dehydrogenase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521306|gb|EEQ61172.1| dihydroorotate dehydrogenase [Clostridiales bacterium 1_7_47FAA]
          Length = 362

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/139 (19%), Positives = 45/139 (32%), Gaps = 23/139 (16%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI------- 151
            + D VG  +  +      P+ VK    + D +          + + +G +G+       
Sbjct: 129 KDFDEVGHIVKTIRSMTDKPLWVKMNANIPDPVG------FAGACRDNGADGVVAITSLG 182

Query: 152 ------WIHARKA--ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
                   H R    I  G        I  L    V  IK+  P L +  +GG       
Sbjct: 183 PNMVIDIEHRRPLIGIPGGYVWTSGPAIKPLALACVNMIKEAYPGLSVIASGGCAKAEDV 242

Query: 204 LK-ILPSVDGV-MIGRAAY 220
           ++ +L   D V M+  A  
Sbjct: 243 IEFLLAGADAVQMLSEAML 261


>gi|320162232|ref|YP_004175457.1| dihydroorotate dehydrogenase family protein [Anaerolinea
           thermophila UNI-1]
 gi|319996086|dbj|BAJ64857.1| dihydroorotate dehydrogenase family protein [Anaerolinea
           thermophila UNI-1]
          Length = 335

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 26/116 (22%), Positives = 45/116 (38%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--- 105
           P+   + G      VE A+ +E+ G + + LN+               +  + DI     
Sbjct: 104 PIIGSLNGVSAGGWVEYARKIEEAGADALELNM-------------YYIPTDTDITAQEL 150

Query: 106 -----DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                D ++ +C  +SIPV VK            AL NL + +  +G  G+ +  R
Sbjct: 151 EQNYVDLVSEVCSRVSIPVAVKLSPFF------TALPNLARRLAGAGAKGLVLFNR 200


>gi|320039781|gb|EFW21715.1| NADH:flavin oxidoreductase [Coccidioides posadasii str. Silveira]
          Length = 424

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 64/203 (31%), Gaps = 36/203 (17%)

Query: 57  ADISKLVEA----AKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDI 103
           ADI +  EA     +     G + I + N           P +      +G        +
Sbjct: 193 ADIEEFKEAWGAAVRRAVKAGVDYIEIHNAHGYLLYSFLSPVSNNRTDEYGGSFENRMRL 252

Query: 104 VGDCIAAMCKALS--IPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
             + +    K +   +P+ ++          R  +        +R      +K GV+ + 
Sbjct: 253 TLEIVDISRKNMPEHMPLFLRVSATDWLEESRPDLPSWKLEDTVRFAQVLAEKGGVDFLD 312

Query: 153 IHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-- 208
           I +      G       KI           +KK   D + +G  G + +  QA  +L   
Sbjct: 313 ISSG-----GNHTDQKIKIGPGFQAPFAIAVKKAVGDRIAVGTVGSITNGKQANDLLENE 367

Query: 209 SVDGVMIGRAAYKNS---AMLTT 228
            +D V++GR   KN         
Sbjct: 368 GLDAVLVGRLFQKNPAVVWAFAE 390


>gi|237808255|ref|YP_002892695.1| NADH:flavin oxidoreductase/NADH oxidase [Tolumonas auensis DSM
           9187]
 gi|237500516|gb|ACQ93109.1| NADH:flavin oxidoreductase/NADH oxidase [Tolumonas auensis DSM
           9187]
          Length = 366

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 69/192 (35%), Gaps = 25/192 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AA+   D G+  + L+       + +             +G         + + +A
Sbjct: 161 DFVNAARRARDAGFEWLELHFA--HGYLAQSFFSVHANQRTDQYGGDFAGRSRFLLETLA 218

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L+K  + +G++ + +      +   +
Sbjct: 219 AVREVWPENLPLTARFGVIEYDGRDEETLAESIELIKLFRNNGLDMVNV-----SVGFST 273

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P       +     V +  ++  +L +  + G++D   A K +    +D VMIGRA   N
Sbjct: 274 PNATIPWGSAFLAPVAQRVRQEANLPVASSWGIDDPVVANKTVADGQLDLVMIGRAHLAN 333

Query: 223 SAMLTTVDEYFS 234
                   +   
Sbjct: 334 PNWPYQAAQALK 345


>gi|188587173|ref|YP_001918718.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351860|gb|ACB86130.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 652

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 23/147 (15%), Positives = 56/147 (38%), Gaps = 16/147 (10%)

Query: 100 NPDIV-GDCIAAMCKALSIPVTVKCRIGVDDQ---------IPAVALRNLVKSIKKSGVN 149
           + D+   + + A+ +       V  R+  D+          I     +   + ++  GV+
Sbjct: 195 DRDLFPVEIVKAIKEKCGQDFPVMYRLCADESLGDELINGGITLEDAKKTAEKLENVGVD 254

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLD---YDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
              +      +  L    +  +   +    D+  EIKK   ++ +   GG+E    A ++
Sbjct: 255 AFDVTGGSDDVIHLYVPSSYVLEENEGCFIDLAAEIKK-TVNVPVMSGGGVESPDAAEQL 313

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDE 231
           L    VD + +GR    +   ++ +++
Sbjct: 314 LESGQVDMIFMGRQLIADPEWVSKIEK 340


>gi|254253951|ref|ZP_04947268.1| NADH flavin oxidoreductase [Burkholderia dolosa AUO158]
 gi|124898596|gb|EAY70439.1| NADH flavin oxidoreductase [Burkholderia dolosa AUO158]
          Length = 369

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 31/182 (17%), Positives = 63/182 (34%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AAK   D G+  + L+       + +             +G         + D +A
Sbjct: 159 DFVAAAKRARDLGFEWLELHFA--HGYLAQSFFSVHSNRRDDEYGGSAENRGRFLVDTLA 216

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ K     +P+T +  +   D      L     L K +K+ G++ + +      +   +
Sbjct: 217 AVRKVWPEHLPLTARLGVIEYDGRDEETLAESIELTKRMKQEGLDMLSV-----SVGFST 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P             + E  +    L +    G++    A +++    +D VM+GRA   +
Sbjct: 272 PDAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVAEQQLDLVMVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|307266956|ref|ZP_07548473.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306918005|gb|EFN48262.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 605

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 24/143 (16%), Positives = 46/143 (32%), Gaps = 16/143 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGV 148
           +G           D +  + K +   +TV CRI      D+           K ++  G 
Sbjct: 161 YGGNFEGRTKFALDILREVKKTIP-EMTVICRINGSDFTDEGFTIEESARFAKLLEYHGA 219

Query: 149 NGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQA 203
           + + I           +SP      P +    + +  KEN  + +      G + D  + 
Sbjct: 220 DALDISGGVSSTSEYHISPMGIEDKPLIG---IAKRIKENVTIPVIAVDKLGSVYDWEKI 276

Query: 204 LKILPS-VDGVMIGRAAYKNSAM 225
           L+      D + I R    +  +
Sbjct: 277 LE--EGIADFIGIARGLIGDPDL 297


>gi|297585489|ref|YP_003701269.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus selenitireducens
           MLS10]
 gi|297143946|gb|ADI00704.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus selenitireducens
           MLS10]
          Length = 642

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 25/182 (13%), Positives = 65/182 (35%), Gaps = 17/182 (9%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
                AK  ++ G++ + +             P     +  +G        +  +   A+
Sbjct: 147 DFANGAKNAKEAGFHAVEIMGSEGYLINQFISPVTNQRDDDWGGSFEKRIRLPIEVTKAV 206

Query: 112 CKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+    PV  +      ++          L K+++++G + + +       +   P  
Sbjct: 207 REAVGPDYPVIFRMSGLDLIEGSTTDEETLELAKALEEAGADVLNV--GIGWHESRVPTI 264

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
           + K+P + +  V E   +   + +  +  + D   A KI+    V  V + R    + A+
Sbjct: 265 SMKVPRMQFVPVAERIADAVGVPVVASNRINDPRDAAKIIANSKVALVSMARPFLADPAI 324

Query: 226 LT 227
           ++
Sbjct: 325 VS 326


>gi|237735625|ref|ZP_04566106.1| conserved hypothetical protein [Mollicutes bacterium D7]
 gi|229381370|gb|EEO31461.1| conserved hypothetical protein [Coprobacillus sp. D7]
          Length = 649

 Score = 46.3 bits (109), Expect = 0.007,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 51/144 (35%), Gaps = 7/144 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGV 148
           +G  +     ++ + IA + K       +  RI  DD             + K ++ + V
Sbjct: 192 YGGDITHRIRLLLEVIANVRKKCGRGFAIIVRISGDDYEAGGQSLHEGCYIAKRLEAAQV 251

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I +     I +G S            D   EIKK   ++ +   G L +     ++L 
Sbjct: 252 DMIHVSGGTTIHRGSSIAPPGTPQASHIDSAREIKKCI-NIPVSTVGRLNEPWILEEVLE 310

Query: 209 S--VDGVMIGRAAYKNSAMLTTVD 230
               D  M+GR+   +   +  + 
Sbjct: 311 RDLADVCMVGRSLLCDPDFVNKIK 334


>gi|284048171|ref|YP_003398510.1| NADH:flavin oxidoreductase/NADH oxidase [Acidaminococcus fermentans
           DSM 20731]
 gi|283952392|gb|ADB47195.1| NADH:flavin oxidoreductase/NADH oxidase [Acidaminococcus fermentans
           DSM 20731]
          Length = 336

 Score = 46.3 bits (109), Expect = 0.007,   Method: Composition-based stats.
 Identities = 28/142 (19%), Positives = 54/142 (38%), Gaps = 11/142 (7%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVN 149
           G+ L      + + I A+  +L     V  R+     ++       L   V+ ++++G++
Sbjct: 197 GSTLEGRTRFLVEVIQAVRSSLPRDFVVTLRLGGGDYMEGGSRPEELPQAVEYLQQAGLD 256

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
           GI +     I       +      L         KE   + + L GG+    QA + L  
Sbjct: 257 GISLSGGLCIFFRPGHPEAGYFAEL-----SRAAKETARIPVLLTGGITTGEQAEQFLAT 311

Query: 209 -SVDGVMIGRAAYKNSAMLTTV 229
              D + +GRAA K+  +   +
Sbjct: 312 GQADLIGLGRAALKDHQVFRKI 333


>gi|281210745|gb|EFA84911.1| CCCH-type Zn finger-containing protein [Polysphondylium pallidum
           PN500]
          Length = 153

 Score = 46.3 bits (109), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/74 (17%), Positives = 22/74 (29%), Gaps = 12/74 (16%)

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            +M+ R A     + T + E     ++ S  +           +      Y   H  S  
Sbjct: 16  ALMVARGALIKPWIFTEIKEKRDCDISASERL----------DLVKQFAHYGLDHWGSDQ 65

Query: 272 KLQQITRHMI--GL 283
                TRH +   L
Sbjct: 66  LGVDNTRHFLLNWL 79


>gi|260900720|ref|ZP_05909115.1| oxidoreductase, FAD/FMN-binding family [Vibrio parahaemolyticus
           AQ4037]
 gi|308109735|gb|EFO47275.1| oxidoreductase, FAD/FMN-binding family [Vibrio parahaemolyticus
           AQ4037]
          Length = 670

 Score = 46.3 bits (109), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 48/132 (36%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA+     +  R+     V+       +  L K ++ +GV    I+      +
Sbjct: 199 EIVKAVRKAVGEKFIIIFRLSMLDLVEQGSTFEDVIALAKGLEDAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIVTCNRINTPDEAERILASGQADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 317 LADPYFVAKAEQ 328


>gi|163855468|ref|YP_001629766.1| NADH-dependent flavin oxidoreductase [Bordetella petrii DSM 12804]
 gi|163259196|emb|CAP41496.1| NADH-dependent flavin oxidoreductase [Bordetella petrii]
          Length = 374

 Score = 46.3 bits (109), Expect = 0.007,   Method: Composition-based stats.
 Identities = 41/184 (22%), Positives = 63/184 (34%), Gaps = 27/184 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
             +A       GY  + ++            P     +  +G  L   M  P  V    A
Sbjct: 162 FRDATVRAVSAGYRFVEIHAAHGYLLHSFLSPVTNKRQDEYGGSLENRMRFPLQVA---A 218

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHAR---KAILK 161
           A+  AL   IPV+V+    VD       L +     + +K  GV+ I   +         
Sbjct: 219 AVRDALPSDIPVSVRI-SAVDGIEGGWQLSDSILFSRELKALGVDLIDCSSGGIQAPATA 277

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           G  P+  ++ P         +K+E   +     G + D  QA  IL     D V +GR A
Sbjct: 278 GQGPQAVKRGPGFQVPFAQAVKQEAG-IGTIAVGLIVDPEQAEAILVGDKADLVAVGREA 336

Query: 220 YKNS 223
             N 
Sbjct: 337 LLNP 340


>gi|37231562|gb|AAH58431.1| Dus2l protein [Mus musculus]
          Length = 289

 Score = 46.3 bits (109), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 14/52 (26%)

Query: 185 ENPDLFIGLNG----------GLEDMSQALKILPSVDGVMIGRAAYKNSAML 226
           E   + +  NG           +ED  QA     +   VM+ RAA  N ++ 
Sbjct: 1   ETLSIPVIANGGSHDHIQQHVDIEDFRQA----TAASSVMVARAAMWNPSIF 48


>gi|123406266|ref|XP_001302760.1| Dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
 gi|123470791|ref|XP_001318599.1| Dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
 gi|121884080|gb|EAX89830.1| Dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
 gi|121901362|gb|EAY06376.1| Dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
          Length = 811

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 18/99 (18%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSF-----------GACLMLNPDIVGDCIAAMCKA 114
            K V   G + + LN+ CP   VH               G  L  +P  V      + +A
Sbjct: 481 VKNVIAAGADALELNLSCP-NEVHGEGGCKGGFDTENKIGMALGTHPISVKRISQYVKEA 539

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
            ++P  VK    + D I      ++ ++  + G +G+ +
Sbjct: 540 TTVPFFVKLTPNITDPI------DIAQAALEGGADGVAM 572


>gi|332981009|ref|YP_004462450.1| dihydroorotate oxidase [Mahella australiensis 50-1 BON]
 gi|332698687|gb|AEE95628.1| dihydroorotate oxidase [Mahella australiensis 50-1 BON]
          Length = 385

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 35/172 (20%), Positives = 57/172 (33%), Gaps = 32/172 (18%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI---AAMCKALSIPVTVK 122
           A +++  G   + LNV CP   +             D+  + I     +   + IPV VK
Sbjct: 122 AALMQQAGAPALELNVSCPHGSIVFRGG-------TDVASEIIRVTELVLNEIDIPVIVK 174

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----------KAILKGLSPKDNRKI 171
               +       A   + K+++ +G  G+ +  R             IL G         
Sbjct: 175 LSPQL------TAPLQIAKAVEDAGAKGVVMFNRLTGLDIDIDVESPILHG--GYAGHGG 226

Query: 172 PNLDYDIVYEIKKENPDLF--IGLNGGLEDMSQALK-ILPSVDGVMIGRAAY 220
           P   Y  +  I +  P L   I  +GG       +K IL     V +  A  
Sbjct: 227 PWAIYYALRWISEAYPQLHVDISASGGAVTADDVVKYILAGAKTVQVCTAIM 278


>gi|77919787|ref|YP_357602.1| NADH oxidase [Pelobacter carbinolicus DSM 2380]
 gi|77545870|gb|ABA89432.1| NADH oxidase [Pelobacter carbinolicus DSM 2380]
          Length = 637

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 27/180 (15%), Positives = 58/180 (32%), Gaps = 16/180 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +AA+     G++ I +             P     +  +G CL        + + A
Sbjct: 143 DCFKKAAERAIKAGFDAIEIHGAHGYLIAQFMSPYTNKRDDIYGGCLENRMRFPVEILKA 202

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNL----VKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         +  R  +++ +P      L     K + ++G++ +   A  A     +  
Sbjct: 203 IRSVAGPDFPILFRYSINEYVPNGVTPELAKDMAKIMVENGIDALHFSAGLAESNQYTIP 262

Query: 167 DNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                   + D    IK+     + + + G + +   A  IL     D V +GR    + 
Sbjct: 263 SGALGRGWNADGAEAIKEAIGSKVPVSVAGRINNRETAEAILASGKADLVSMGRGLLADP 322


>gi|239618433|ref|YP_002941755.1| dihydroorotate dehydrogenase family protein [Kosmotoga olearia TBF
           19.5.1]
 gi|239507264|gb|ACR80751.1| dihydroorotate dehydrogenase family protein [Kosmotoga olearia TBF
           19.5.1]
          Length = 361

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 19/129 (14%), Positives = 42/129 (32%), Gaps = 21/129 (16%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           +P+++   I  + K    PV +K    V +         + K+++++G +GI        
Sbjct: 130 DPELMKHLIRTVKKHTDKPVFLKFDPSVPEPEV------MAKAVEEAGGDGIVAINSLGP 183

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALK 205
                   + + L           P +    +  +K+        I   GG+      + 
Sbjct: 184 GYPLYRELKSSPLGSTHGFGWISGPVIKPIALAMVKRVASSCNLPIIGVGGISSADDVID 243

Query: 206 -ILPSVDGV 213
            I+     V
Sbjct: 244 FIMAGASAV 252


>gi|256004241|ref|ZP_05429224.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           DSM 2360]
 gi|255991831|gb|EEU01930.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           DSM 2360]
 gi|316939592|gb|ADU73626.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium thermocellum
           DSM 1313]
          Length = 645

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 60/172 (34%), Gaps = 7/172 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L      + +CI +    +    P  V +    G            + K +K+ G+
Sbjct: 194 YGGSLENRMRFLLECIESARNNVGSDFPMIVGLALDHGFPGGRELDETIEIAKRLKQIGI 253

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +         L          +  D   +++++   + +  +G + D   A K++ 
Sbjct: 254 DTLHLRRGSYDNMNLLIPTEYMEDAVSVDYAAKVREQAG-IQVISDGNISDPVLANKLVE 312

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
              +D V +GRA   +   +  V       +         +++ F+ + +A 
Sbjct: 313 ENKLDFVGLGRALLADPEWVNKVRADKKEDIVPCVRCMQCINRIFFGQYAAC 364


>gi|15838333|ref|NP_299021.1| NAD(P)H-dependent 2-cyclohexen-1-one reductase [Xylella fastidiosa
           9a5c]
 gi|9106800|gb|AAF84541.1|AE003996_10 NAD(P)H-dependent 2-cyclohexen-1-one reductase [Xylella fastidiosa
           9a5c]
          Length = 368

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 61/184 (33%), Gaps = 21/184 (11%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P++      +G         V + + A+ +A+  P  V  RI  +         +    +
Sbjct: 195 PASNQRTDQYGGSPENRARFVVELVQAVAEAVG-PGRVGLRISPEHNYQETFEPDRSDVL 253

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL---EDM 200
              G   +    R   L  LS         L  ++      +     +  N G      +
Sbjct: 254 ATYGA--LLDALRPLGLAYLSVLHQEPTGALVEELARRFAGK-----VAANSGFATFTSL 306

Query: 201 SQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            +A +I+  P +D V++GRAA  N  ++               P+       F+   +A 
Sbjct: 307 EEAEQIVAAPFIDAVVVGRAALANPDLIERWK--------SEQPLTEPRYDLFYTHDAAG 358

Query: 259 MTDY 262
            TDY
Sbjct: 359 YTDY 362


>gi|163840203|ref|YP_001624608.1| NADH-dependent flavin oxidoreductase [Renibacterium salmoninarum
           ATCC 33209]
 gi|162953679|gb|ABY23194.1| NADH-dependent flavin oxidoreductase [Renibacterium salmoninarum
           ATCC 33209]
          Length = 365

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 31/203 (15%), Positives = 65/203 (32%), Gaps = 20/203 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             ++A+     G++ I ++            P     E  +G        +  + + A+ 
Sbjct: 165 FADSARRAVQIGFDVIEIHAAHGYLLHQFLSPLVNTREDKWGGSEERRFRLTLEVVEAVR 224

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +  S+P+ ++          + A A+  L    K  GV+ I + +   + +   P   
Sbjct: 225 AVMPESMPLLLRVSASDWFPSGLDADAVSRLAVLAKARGVDLIDVSSGGIVAEAKIPVGP 284

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
                    I  E       + +   G + D  QA  +L     D V++ RAA +N    
Sbjct: 285 GYQTAFAQQIRREAA-----IPVASVGLITDAFQADHLLRTEQADAVLVARAALRNPHWW 339

Query: 227 TTVDEYFSNPLTGSSPIKTRVDK 249
                     L  +   +    +
Sbjct: 340 QQAAHDLGIVLPWAPQYERATPR 362


>gi|46137869|ref|XP_390626.1| hypothetical protein FG10450.1 [Gibberella zeae PH-1]
          Length = 409

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 26/187 (13%), Positives = 62/187 (33%), Gaps = 25/187 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCIAA 110
             + A I  + G++ + ++             S + ++    +G        I+ D   A
Sbjct: 171 FAKTACIASESGFDGVEIHAA--HGYLLSQFLSEKSNKRTDQYGGSPAARAKIIVDVCKA 228

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKS---IKKSGVNGIWIHARKA----ILKGL 163
           +  A      V  +    D      L   ++    I + G++ + +         +  G 
Sbjct: 229 IRAATPATFCVGLKFNSADHQSPKELEECLEQMTLIAEVGLDFLEVSGGSWENPTMFTGT 288

Query: 164 SPKDNRKIPNLD---YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
             K +      +    +   E++ + P+  + + GG    +   + L     D + +GR 
Sbjct: 289 GEKKSASTAARESFFLEFAREMRAKLPNTPLMVTGGFRTRAGMEEALSEGACDLIGLGRP 348

Query: 219 AYKNSAM 225
           A  N  +
Sbjct: 349 AIVNPFL 355


>gi|297625388|ref|YP_003687151.1| dihydroorotate dehydrogenase [Propionibacterium freudenreichii
           subsp. shermanii CIRM-BIA1]
 gi|296921153|emb|CBL55700.1| Dihydroorotate dehydrogenase [Propionibacterium freudenreichii
           subsp. shermanii CIRM-BIA1]
          Length = 385

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 69/183 (37%), Gaps = 32/183 (17%)

Query: 47  EKPLALQIGGADI-SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           E PL   + GA   +   E A+ ++D G + I LN+      +  G          D   
Sbjct: 153 EIPLIGSLNGASGGTWTAE-ARRMQDAGASAIELNI-----YLVPGDTSITGREVEDRHV 206

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------- 156
           + + A+   ++IPV VK                +  S+  +G +G+ +  R         
Sbjct: 207 EILRAVKDVVNIPVAVKLSPYFSS------FGEVATSLCDAGADGLVMFNRFLQPDIDVN 260

Query: 157 -KAILKGL---SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
            + ++ G    SP+  R        +  ++K       + ++GG+E     +K +L   D
Sbjct: 261 KREVVSGFELSSPEIGRLPRTWAAVLSGKVKSS-----LAVSGGVETRDDIVKGLLAGAD 315

Query: 212 GVM 214
            VM
Sbjct: 316 VVM 318


>gi|320012280|gb|ADW07130.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces flavogriseus
           ATCC 33331]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 28/164 (17%), Positives = 53/164 (32%), Gaps = 20/164 (12%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---------LV 140
           ++G        +  + + A+       +P+  +          A   R          L 
Sbjct: 203 AYGGSFENRVRLALEVVDAVRAVWPEELPLFFRISATDWLTENADDPREGWTGDDTVRLA 262

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLED 199
           + +   GV+ + +        GL+PK    + P         ++KE   L +   G + D
Sbjct: 263 RELLAHGVDLLDVSTG-----GLAPKARIPVEPGYQVPFAERVRKETG-LPVAAVGLITD 316

Query: 200 MSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             QA KIL   S D V++GR   ++              +    
Sbjct: 317 PVQAEKILADGSADAVLLGRELLRDPYFARNAARALGGDVRAPE 360


>gi|269968094|ref|ZP_06182131.1| putative NADH-dependent flavin oxidoreductase [Vibrio alginolyticus
           40B]
 gi|269827340|gb|EEZ81637.1| putative NADH-dependent flavin oxidoreductase [Vibrio alginolyticus
           40B]
          Length = 356

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 71/218 (32%), Gaps = 23/218 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              A+K  +D G++ + ++            P     E  +G  L      + +  +   
Sbjct: 135 FALASKRAQDAGFDGVEIHAAHTYLINQFLSPYYNRREDEYGGDLENRMRFLLEIYSETR 194

Query: 113 KALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
           K +    P+ VK       D  +     R + K +++ GV+ I     IH +   L G +
Sbjct: 195 KLVGSEFPILVKLTATEFFDGGLTFDETRVVCKKLEEVGVDAIVVSGNIHGKANELVGQT 254

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAAY 220
                      +     +  ++  + +   GGL D+    KI  + D     V   R   
Sbjct: 255 FDGYTLQEEGYFHEYGHVISQDVSIPVITVGGLSDIDAIEKIAENTDIQFFAV--SRPLL 312

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
               ++    E    P+      K R  +  +  +  +
Sbjct: 313 AEPQLIKRWKEGNRAPVDCERCSKCRTKRGNFCVVYKN 350


>gi|326571994|gb|EGE21997.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis BC7]
 gi|326572213|gb|EGE22208.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis BC8]
          Length = 716

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 60/176 (34%), Gaps = 23/176 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
                 AK+ +  GY+ + +              SAR ++   S+G  L        + +
Sbjct: 171 DDYAHTAKLAKKAGYDGVEIMGSEGYLINQFL--SARTNKRTDSYGGSLENRMRFAIEVV 228

Query: 109 AAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+ KA  I   +  R      V+D      +  L K+++ +GV+   I+      +   
Sbjct: 229 RAVRKAAGINFIITFRLSMIELVEDGATMQDVITLAKALELAGVS--IINTGIGWHEARI 286

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           P     +P   +      +K       I  N  +     A +IL     D V + R
Sbjct: 287 PTIVTSVPRAAFTRYTAAVKHAVSIPVIAANR-INMPQTAEEILSSGQADLVQMAR 341


>gi|238756201|ref|ZP_04617519.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia ruckeri ATCC 29473]
 gi|238705558|gb|EEP97957.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia ruckeri ATCC 29473]
          Length = 673

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 27/195 (13%), Positives = 60/195 (30%), Gaps = 35/195 (17%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPDI 103
                AK+ +  GY+ + +        +    +                 G C       
Sbjct: 144 DFAHCAKLAQQAGYDGVEI--------MGSEGYLINQFLAARTNQRTDEWGGCFENRMRF 195

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+ +A      +  R+     V++      +  L  +I+++G   I  +     
Sbjct: 196 AVEIVRAVRQAAGTEFILIYRLSMLDLVEEGSDWQEIEQLALAIEQAGATLI--NTGIGW 253

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
            +   P     +P   +  V  ++  +     I  N  + D   A ++L     D V + 
Sbjct: 254 HEARIPTIATMVPRAGFSWVTRKLMGKVTIPLITTNR-INDPEVAEQVLADGCADMVSMA 312

Query: 217 RAAYKNSAMLTTVDE 231
           R    + A +    E
Sbjct: 313 RPFLADPAFVQKAAE 327


>gi|330987280|gb|EGH85383.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 370

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 50/136 (36%), Gaps = 8/136 (5%)

Query: 94  GACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           G  ++    +  + IAA+ K A   PV V+   G  +              + + V    
Sbjct: 204 GGEVVQRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQ----HKWAGGGRDAEVIFAT 259

Query: 153 IHARKAILKGLSPKDNRKIPNL--DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
           +         ++  +  +         +V   ++  P + +  NGGL D  +A ++L   
Sbjct: 260 LAGAGVDYIHVTEHEAWQPAFAQGKASLVELARRYAPGVALIANGGLHDPEKADQVLHQG 319

Query: 210 VDGVMIGRAAYKNSAM 225
            D + +G+ A  N  +
Sbjct: 320 ADIIAVGKGALANPDL 335


>gi|330506626|ref|YP_004383054.1| NADH oxidase [Methanosaeta concilii GP-6]
 gi|328927434|gb|AEB67236.1| NADH oxidase [Methanosaeta concilii GP-6]
          Length = 647

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/144 (16%), Positives = 51/144 (35%), Gaps = 18/144 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSG 147
           +G  L      + D I  + +       +  R+ V++              + + +K++G
Sbjct: 189 YGGSLENRMRFLLDIIRGIREQCGGDFPIGVRLSVEEFLGKEGNDLEESCRICEVLKEAG 248

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYD------IVYEIKKENPDLFIGLNGGLEDMS 201
           V+ I +          SP+    I    Y+      +  EIKK   ++ I     +++  
Sbjct: 249 VDFIDVSCTIP----GSPEVCACIEPGTYEQGWKRYMAAEIKKHV-NIPIIAVCNIKEPD 303

Query: 202 QALKIL--PSVDGVMIGRAAYKNS 223
            A +IL     D + + R    + 
Sbjct: 304 VAEEILVEGCCDFIGVARGHLADP 327


>gi|218961595|ref|YP_001741370.1| dihydroorotate dehydrogenase, catalytic subunit (Dihydroorotate
           oxidase) (DHOdehase) (DHODase) (DHOD) [Candidatus
           Cloacamonas acidaminovorans]
 gi|167730252|emb|CAO81164.1| dihydroorotate dehydrogenase, catalytic subunit (Dihydroorotate
           oxidase) (DHOdehase) (DHODase) (DHOD) [Candidatus
           Cloacamonas acidaminovorans]
          Length = 305

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 70/189 (37%), Gaps = 25/189 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL +   G+ + + V+  + +E   G +   +NV CP+      + G    ++PD+V   
Sbjct: 98  PLIVSFSGSSLKEFVQMLECLEKQEGISGYEVNVSCPNVE----NEGIAFGIDPDVVNKL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HA 155
            A +       + VK    V D      +  + K+ ++ G   I +            + 
Sbjct: 154 CALLSPLTERELIVKLSPNVTD------IAVIAKAAEEGGATAISLINTIWGMAIDYRNG 207

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           +  I KG+       I  L   + Y   +    + +   GG+ +   AL+        + 
Sbjct: 208 KSRIKKGIGGYSGIGIKPLALALTYRAAQAV-KIPVIAMGGIYNWQDALEFFWAGASMIA 266

Query: 215 IGRAAYKNS 223
           +G A + + 
Sbjct: 267 LGTANFIDP 275


>gi|304409907|ref|ZP_07391526.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS183]
 gi|307302386|ref|ZP_07582144.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica BA175]
 gi|304351316|gb|EFM15715.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS183]
 gi|306914424|gb|EFN44845.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica BA175]
          Length = 364

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 63/180 (35%), Gaps = 24/180 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +A+  E  G + I ++            P +      +G  L     ++     A+ 
Sbjct: 160 FVSSAQRAERLGLDAIEIHAAHGYLLHQFLSPLSNQRTNKYGGSLENRLSLLLAVFDAIK 219

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +S  + +  RI   D +           L K+++  G + I +        GLSP   
Sbjct: 220 AVISPKMALGVRISATDWVEGGWDLAQSLVLAKALESRGCDFIHVSTG-----GLSPLQQ 274

Query: 169 RKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             IP  ++  V   E  K   ++ +   G + D ++A  IL     D + + R    +  
Sbjct: 275 --IPVAEHFQVPFAEAIKAEVNIPVIAVGLITDANKAETILAQGQADAIALARTMLYDPH 332


>gi|266622857|ref|ZP_06115792.1| NADH-dependent flavin oxidoreductase [Clostridium hathewayi DSM
           13479]
 gi|288865387|gb|EFC97685.1| NADH-dependent flavin oxidoreductase [Clostridium hathewayi DSM
           13479]
          Length = 646

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 32/216 (14%), Positives = 71/216 (32%), Gaps = 29/216 (13%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC--- 83
           + +   L    +     + +E P  +Q           A       G++ I L   C   
Sbjct: 119 VASSVYLNSMAQRTRAVTLEEIPGIIQKYAKGAYDARRA-------GFDGIEL--HCAHA 169

Query: 84  ---------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIP 132
                    P        +G  L     ++ + + A+ +A     PV ++      D+  
Sbjct: 170 YMLLGSFLSPMRNKRTDRYGGSLDNRARLLCEVLDAIREACGPDFPVILRMSGSERDEQG 229

Query: 133 A--VALRNLVKSIKKSGVNGIWIHARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENPDL 189
                ++ LV  +++ GV    I       +       + ++  ++      + +     
Sbjct: 230 NTLEDMKYLVPVLERHGVAAFEISGGTQYERCNKIIPCHGEVQGVNVPEAEALHEAASVP 289

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            I + G + +   A  ++    VDGV++GRA   + 
Sbjct: 290 VIVV-GKINEPRFAGYLVDSGKVDGVVLGRALIADP 324


>gi|188585401|ref|YP_001916946.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350088|gb|ACB84358.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 330

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 30/178 (16%), Positives = 59/178 (33%), Gaps = 20/178 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+  ++ G++ + +             P        +G  +     I  + I A
Sbjct: 146 EAFSNAARRTKEAGFDGVEIHSAHGYLLNQFYSPLTNKRTDKYGGDVHKRIRIHLEVIEA 205

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K +     +  R+G  D               +  +K+GV+ + I    +        
Sbjct: 206 VKKEVGEDFPILLRLGASDYQEGGTTIEDSKIAAREFEKAGVDILDISGGHSGYMVNGLD 265

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
                  L      E  KE   + + L GG+ +   A K+L     D + +GRA  ++
Sbjct: 266 GQGFFAPL-----TEAIKEVVSIPVILTGGITEPEAAEKLLIEGKADLIGVGRAILED 318


>gi|302530333|ref|ZP_07282675.1| oxidoreductase [Streptomyces sp. AA4]
 gi|302439228|gb|EFL11044.1| oxidoreductase [Streptomyces sp. AA4]
          Length = 363

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 65/183 (35%), Gaps = 22/183 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
                A ++ E  GY  + ++            P +      +G      M  P  V   
Sbjct: 168 EDFAHATRMAELAGYQAVEIHASHGYLLHQFLSPLSNRRTDQYGGSAQNRMRFPLRVARA 227

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL-KGLS 164
           +         PV V+      V+  I         K +   G++ + + +   +  +G  
Sbjct: 228 VREAFPE-DKPVFVRITATDWVEGSIALDDAAEFAKELAAVGIDLLDVTSGVLVRDRGAR 286

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P +   +   + +    +K E+  L +   G + D++ A +I+     D V++GR+  ++
Sbjct: 287 PPNQEGV---NVEFAAALK-ESSGLAVAPVGQITDLAAAGQIIRWGKADAVLMGRSLLRD 342

Query: 223 SAM 225
             +
Sbjct: 343 PYL 345


>gi|327328666|gb|EGE70426.1| xenobiotic reductase A [Propionibacterium acnes HL103PA1]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 AQFRGAWR 366


>gi|324556519|gb|ADY49812.1| tRNA-dihydrouridine synthase 2-like protein [Ascaris suum]
          Length = 96

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           G  +  ++   AK V D     I++N+GCP      G  GA L+  PD + + 
Sbjct: 13  GTNNGDRIAAVAKKVHDDIAA-IDVNMGCPKLFSLTGGMGAALLTQPDKIKEV 64


>gi|169773045|ref|XP_001820991.1| NADH oxidase [Aspergillus oryzae RIB40]
 gi|83768852|dbj|BAE58989.1| unnamed protein product [Aspergillus oryzae]
          Length = 413

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 38/214 (17%), Positives = 71/214 (33%), Gaps = 31/214 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            EAAK      ++ I ++            P +      +G        I+ +    +  
Sbjct: 194 AEAAKRAVRANFDAIEIHAAHGYLLHQFLSPVSNRRTDKYGGSFENRVRILLEICEEVRA 253

Query: 114 ALS--IPVTVKCRI----GVDDQIPAVALR--------NLVKSIKKSGVNGIWIHARKAI 159
            +   +P+ V+         DD +               L   +   GV+ + + +    
Sbjct: 254 VIPTAMPLLVRISATDWFEFDDNLTKEFPESWTVAQSIRLALLLADRGVDLVDVSSGGIH 313

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
            K  S    R           EIKK     L I   GG++  + A +++   +D V  GR
Sbjct: 314 AK--SAIAIRSGQGYQVHFAQEIKKAVGEKLLISAVGGIKTGALAEEVVQSGIDAVQAGR 371

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
              +N  ++      F+N L     + T++D  F
Sbjct: 372 WFQQNPGLVR----AFANELGVKVRMATQIDWSF 401


>gi|319653572|ref|ZP_08007671.1| NADH-dependent flavin oxidoreductase [Bacillus sp. 2_A_57_CT2]
 gi|317394771|gb|EFV75510.1| NADH-dependent flavin oxidoreductase [Bacillus sp. 2_A_57_CT2]
          Length = 373

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 40/217 (18%), Positives = 68/217 (31%), Gaps = 27/217 (12%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDCI- 108
             E  +     GY+ + +             P +   E  FG  L   M  P  V D + 
Sbjct: 152 FGETTRRAIQAGYDGVEIHGANGYLIQQFFSPHSNRREDRFGGSLEKRMTFPLAVVDAVQ 211

Query: 109 AAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+ +    P  V  R       +  I       LV  +   G++ + +       K   
Sbjct: 212 EAVKEHAKEPFIVGYRFSPEEPTEPGITMEDTLQLVDVLSDKGLDYLHVSLMDFWSKPRR 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNS 223
             D     +    I + ++K N  L +   G +    +A+K L   V  V +GR      
Sbjct: 272 GAD-----DAKPRIQHLLEKMNNRLPLIGVGSIHTPDEAVKALETGVAMVALGRELIMEP 326

Query: 224 AMLTTVDE----YFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  V E      +  L+     K  +    W+ I 
Sbjct: 327 DWVQKVQEGKESEIATTLSKKDQEKLVIPDPLWQAIV 363


>gi|315092249|gb|EFT64225.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL110PA4]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|313813768|gb|EFS51482.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL025PA1]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|299534167|ref|ZP_07047518.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           S44]
 gi|298717814|gb|EFI58820.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           S44]
          Length = 671

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 21/184 (11%), Positives = 56/184 (30%), Gaps = 17/184 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V  A +  + GY+ + +  G          P        +G             +  +  
Sbjct: 147 VRCACLAREAGYDGVEVMGGEGYLINQFLAPLTNFRTDEWGGDAAGRSRFALRIVQGIRA 206

Query: 114 ALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+ + D +        + +L + ++ +GV+    +      +   P    
Sbjct: 207 AVPENFVISFRLSLMDLVEHGSHWKEVLDLARQLEAAGVDLF--NTSVGWHEARIPTIAM 264

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
            +P   +    E  ++   + +  +  +     A  ++     D V + R    + A + 
Sbjct: 265 MVPRAAFSWAAEQLRQAVSVPVAASNRINTPEVADDLIAQGHADMVAMARPFLADPAFVR 324

Query: 228 TVDE 231
               
Sbjct: 325 KAQA 328


>gi|282854883|ref|ZP_06264217.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes J139]
 gi|282582029|gb|EFB87412.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes J139]
 gi|314981609|gb|EFT25702.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL110PA3]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|315104688|gb|EFT76664.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL050PA2]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|183231113|ref|XP_656317.2| dihydropyrimidine dehydrogenase [Entamoeba histolytica HM-1:IMSS]
 gi|169802613|gb|EAL50934.2| dihydropyrimidine dehydrogenase, putative [Entamoeba histolytica
           HM-1:IMSS]
          Length = 901

 Score = 46.0 bits (108), Expect = 0.009,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 64/177 (36%), Gaps = 29/177 (16%)

Query: 66  AKIVEDFGYNEINLNVGCP--------SARVHEGSF------GACLMLNPDIVGDCIAAM 111
           AK+ E+ G + + LN  CP        +    EG F         + ++P  +  C   +
Sbjct: 554 AKLSEEAGADALELNFSCPNECHGNDGNEGGCEGGFKSHNAMAMAIGVSPAAIERCTRYV 613

Query: 112 CKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKK----SGVNGIWIHARKAILKGL-- 163
            +++ IPV  K    V   +++ A A+R     +       G++ I +        G+  
Sbjct: 614 VESVHIPVYPKLTPNVGNIEELAAAAMRGGASGVSTINTVFGISEITLSGHPWPQVGVER 673

Query: 164 ----SPKDNRKIPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALK-ILPSVDGV 213
                      +  +    + ++ + N ++   +   GG+     A++ I      V
Sbjct: 674 NTISGGLSGDLVRPIAIRQIAQVLRHNENVRGHLLGIGGVRSAETAMQLIYTGASVV 730


>gi|314959468|gb|EFT03570.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL002PA1]
          Length = 366

 Score = 46.0 bits (108), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|221210160|ref|ZP_03583141.1| xenobiotic reductase A [Burkholderia multivorans CGD1]
 gi|221170848|gb|EEE03314.1| xenobiotic reductase A [Burkholderia multivorans CGD1]
          Length = 369

 Score = 46.0 bits (108), Expect = 0.009,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 64/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AAK   D G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAAKRARDIGFEWLELHFAHGYLGQSFFSVHSNRRTDEYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            K     +P+T +  +   D      L     L + +K+ G++ + +      +   +P 
Sbjct: 219 RKVWPEHLPLTARFGVIEYDGRDEETLAESIALTQRLKQEGLDMLSV-----SVGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPVAERVRREAGLPVSSAWGIDTPQLANRVVADEQLDLVMVGRAHLADPH 333


>gi|196248794|ref|ZP_03147494.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. G11MC16]
 gi|196211670|gb|EDY06429.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. G11MC16]
          Length = 340

 Score = 46.0 bits (108), Expect = 0.009,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 77/197 (39%), Gaps = 23/197 (11%)

Query: 45  TQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEG 91
            +  P   ++  ADI + V+A    A+  +  G++ I ++            P +   + 
Sbjct: 125 NESSPTPKEMTKADIEETVQAFQDGARRAKKAGFDVIEIHAAHGYLINEFLSPLSNRRQD 184

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVN 149
            +G         +G+ I A+ +    P+ V+        D +        VK +K+ GV+
Sbjct: 185 EYGGSPENRYRFLGEVIDAVREVWDGPLFVRISASDYHPDGLTVKDYVPYVKRMKEQGVD 244

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + + +   +   +      ++P  ++     I++E   +  G  G +    QA ++L +
Sbjct: 245 LVDVSSGAVVPARIDVYPGYQVPFAEF-----IRREAG-IPTGAVGLITSGWQAEEVLHN 298

Query: 210 --VDGVMIGRAAYKNSA 224
              D V +GR   +N  
Sbjct: 299 GRADLVFLGRELLRNPY 315


>gi|134300260|ref|YP_001113756.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum reducens
           MI-1]
 gi|134052960|gb|ABO50931.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum reducens
           MI-1]
          Length = 668

 Score = 46.0 bits (108), Expect = 0.009,   Method: Composition-based stats.
 Identities = 23/139 (16%), Positives = 49/139 (35%), Gaps = 8/139 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L        + +AA+ +A+     I V V     +         +   ++++KSGV
Sbjct: 185 YGGDLQARMTFGLEVVAAVREAVGSDYPIIVRVAGNDFMPGSHTNTEAQVFCQAMEKSGV 244

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           N I +       +   P+    +P   Y  +    K+   + +     +     A  IL 
Sbjct: 245 NAINVTGG--WHETQVPQITMNVPPGAYAYLAYGIKQAVSIPVIACNRINTPDLAEAILQ 302

Query: 209 S--VDGVMIGRAAYKNSAM 225
               D + + R+   +  +
Sbjct: 303 EGKADFIGMARSLMADPEL 321


>gi|315079178|gb|EFT51181.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL053PA2]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|314974992|gb|EFT19087.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL053PA1]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|186471055|ref|YP_001862373.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phymatum
           STM815]
 gi|184197364|gb|ACC75327.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phymatum
           STM815]
          Length = 373

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 48/132 (36%), Gaps = 17/132 (12%)

Query: 103 IVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGIWIH 154
           ++ D + A+   +   +PV ++   G  +   +      A   ++  ++  +G++ + + 
Sbjct: 213 LLVDVVEAVRLGIGDAVPVGIRISQGKVNDFGSRWSGGEADAEVIFGTLADAGIDFLHVT 272

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGV 213
             +A         +  +            +  P + +  NGGL    +    L    + V
Sbjct: 273 EFEAWQPAFEGTHDSLVTLAH--------RYAPAVTVIANGGLHTAERINHALASGANLV 324

Query: 214 MIGRAAYKNSAM 225
            +GR A  N  +
Sbjct: 325 TVGRGALANPDL 336


>gi|313810601|gb|EFS48315.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL083PA1]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|289426077|ref|ZP_06427824.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes SK187]
 gi|289153620|gb|EFD02334.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes SK187]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|262281150|ref|ZP_06058932.1| NADPH dehydrogenase [Acinetobacter calcoaceticus RUH2202]
 gi|262257381|gb|EEY76117.1| NADPH dehydrogenase [Acinetobacter calcoaceticus RUH2202]
          Length = 369

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 26/149 (17%), Positives = 56/149 (37%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----- 138
           P A      +G  L     +  + + A+  A+     V  R+   D +  V   +     
Sbjct: 192 PIANQRTDEYGGSLENRMRMALEVLQAIKLAVPAGYPVGVRLSATDWLDGVEHWDIESTV 251

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   + + +      GL    + +I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYVHVSSG-----GLHEHQSIQIG-AGYQVPFAEQVKKHVSIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + +   A++IL     D + + RA   + 
Sbjct: 306 ITEPEHAVQILENQQADAIGLARAMLYDP 334


>gi|134082503|emb|CAK97309.1| unnamed protein product [Aspergillus niger]
          Length = 417

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 68/195 (34%), Gaps = 25/195 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V  +++    G+  + L+            P+A +    +G        I+ D I A
Sbjct: 166 DQFVYTSRLASQTGFQGVELHAAHGYLLSQFLSPTANLRTDQYGGSPAGRVKIIVDIIHA 225

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK---KSGVNGIWIHARK---AILKGLS 164
           + KA+     V  ++   D     AL+  V+ +K   ++GV+ + I         +   S
Sbjct: 226 IRKAVPATFCVGIKLNSVDHQSESALKACVEQLKLIVEAGVDFVEISGGSYEDPQMMSSS 285

Query: 165 PKDNRKIPNLD--------YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVM 214
             + +   +           +    I+ + P   + + GG    +   K L     D + 
Sbjct: 286 ASNKQPEKSARTVAREAFFLEFASAIRAQFPGTPLMVTGGFRTRTGMEKALIDKDCDMIG 345

Query: 215 IGRAAYKNSAMLTTV 229
           IGR A     +   +
Sbjct: 346 IGRPAVLKPTLPNDI 360


>gi|170782426|ref|YP_001710759.1| putative oxidoreductase [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169156995|emb|CAQ02164.1| putative oxidoreductase [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 359

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 29/191 (15%), Positives = 59/191 (30%), Gaps = 22/191 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+   D G++ + L+            P +   +  FG  L     ++   I A
Sbjct: 158 DDFAAAARRSVDAGFDVLELHAAHGYLLHQFLSPLSNHRDDEFGGSLENRARLLLQVIDA 217

Query: 111 MCKAL-SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP- 165
           +   +   P+ V+        D          +     + G +   I           P 
Sbjct: 218 VRAEVPDAPLLVRFSATDWAGDAGWDEQQTATVAAWAAEHGADFFDISTGGNTTGVTIPV 277

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
               ++P  +Y       KE+  + +   G + + +QA  ++     D VM+GR   ++ 
Sbjct: 278 APGYQVPFAEY------VKEHAKVALNAVGLITEPAQAEAVVAEGRADAVMLGREMLRDP 331

Query: 224 AMLTTVDEYFS 234
                      
Sbjct: 332 HFALRAAHELG 342


>gi|325662307|ref|ZP_08150916.1| hypothetical protein HMPREF0490_01655 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471309|gb|EGC74532.1| hypothetical protein HMPREF0490_01655 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 641

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 61/178 (34%), Gaps = 15/178 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLN----VGCPSARVHEG---SFGACLMLNPDIVGDCIAAMCK 113
           K+ E AK  +  G + I ++    VG  S+ +       +G  L        + + A+ K
Sbjct: 145 KMCECAKRAQAAGIDAIQVHGDRLVGALSSTILNHRTDKYGGSLENRTRFAIELVTALRK 204

Query: 114 AL-----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           A+        + V         + A       K ++++GV+ + +               
Sbjct: 205 AVPDMIIDYKLAVVTPQRGKGGVIAEEAVIFAKWLEEAGVDMLHVAQANHTGNMADTIPP 264

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             + P   +  +    KE  ++ +   G +   + A  IL     D + +GR    + 
Sbjct: 265 MGVQPYAFFADIAGKVKEQVNIPVSTVGRIVSPALAESILESGKADIIGLGRPLLADP 322


>gi|302036455|ref|YP_003796777.1| dihydroorotate dehydrogenase [Candidatus Nitrospira defluvii]
 gi|300604519|emb|CBK40851.1| Dihydroorotate dehydrogenase [Candidatus Nitrospira defluvii]
          Length = 308

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 70/220 (31%), Gaps = 47/220 (21%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
            Y EMI            +  F    KP+   I G      +  A+ +     + I +N+
Sbjct: 79  AYAEMI----------PELTRF---GKPVIASIAGLCEDDFLTMARAINQARPDLIEVNL 125

Query: 82  GCP----SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
            CP      ++           +P      +  +   +++P+ VK     D    AV   
Sbjct: 126 SCPNIPGKPQIA---------YDPVDSERLLKRVRPLITVPMGVKLPPYFDPAHHAV--- 173

Query: 138 NLVKSIKKSGVNGI-----WIHARKAILKGLSP--KDNRKIPNLDYDIVYEIKKENP--- 187
            + + I++ GV+ +       +      K  +P  K       L   ++  +   N    
Sbjct: 174 -MAEVIRRCGVDYLNLINSVGNGLVVDPKHETPVIKPKGGFGGLGGSLIKPVALANVRAF 232

Query: 188 ------DLFIGLNGG-LEDMSQALKILPSVDGVMIGRAAY 220
                  + I   GG ++ +     +L     V +G A  
Sbjct: 233 WKLLEGRIPIIGTGGVVQGVDAFEHVLCGASAVQVGTALV 272


>gi|90407650|ref|ZP_01215830.1| imidazole glycerol phosphate synthase subunit HisF [Psychromonas
           sp. CNPT3]
 gi|90311241|gb|EAS39346.1| imidazole glycerol phosphate synthase subunit HisF [Psychromonas
           sp. CNPT3]
          Length = 257

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 11/111 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D      +  L K   + G + +  +   A ++G           +D   V  + +
Sbjct: 21  VQFRDHKVVGDIVQLAKRYAEQGADELVFYDISASVEGRV---------VDKSWVSRVAQ 71

Query: 185 ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
              D+   + GG++ +  A +IL    D + I   A  N  ++  + E F 
Sbjct: 72  -VIDIPFCVAGGIKSIEDAQQILKFGADKISINSPALSNPNLINQLSERFG 121


>gi|83721130|ref|YP_443834.1| FAD/FMN-binding oxidoreductase [Burkholderia thailandensis E264]
 gi|167582872|ref|ZP_02375746.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           TXDOH]
 gi|167621013|ref|ZP_02389644.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           Bt4]
 gi|83654955|gb|ABC39018.1| oxidoreductase, FAD/FMN-binding [Burkholderia thailandensis E264]
          Length = 370

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 59/180 (32%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
              VE+AK     G + I ++            P A     ++G  L   M  P  V D 
Sbjct: 157 CAFVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRTDAYGGSLENRMRFPLEVFDA 216

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A       PV V+      V             + +K+ G + I + +      G+SP
Sbjct: 217 VRAAF-PDDRPVGVRVSATDWVTGGWELDDTIAFARELKRRGCDWIDVSSG-----GVSP 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                +         +  K   DL     G + D   A +++ +   D V + RA   + 
Sbjct: 271 LQKIPLSPGYQVPFAQAIKRAVDLPTIAVGLISDPEHANRVIEAGDADFVAMARAMLYDP 330


>gi|159903506|ref|YP_001550850.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Prochlorococcus
           marinus str. MIT 9211]
 gi|226700344|sp|A9BAN4|HIS4_PROM4 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|159888682|gb|ABX08896.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Prochlorococcus marinus str. MIT 9211]
          Length = 255

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 11/91 (12%)

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  G + + I    A  +G S  D         D++ +I K    + I + GG+    +A
Sbjct: 40  EDMGASRLHIVDLDAARQGFSSND---------DVIKQIAKSL-SIPIQIGGGIRTSKRA 89

Query: 204 LKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
            ++L   +D V+IG AA ++  ++  +   F
Sbjct: 90  KELLDYGIDRVIIGTAALEDPRLVEDLASAF 120



 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 65/185 (35%), Gaps = 33/185 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AK + D+G + + +              G   + +P +V D  +A  K + + +  K   
Sbjct: 89  AKELLDYGIDRVII--------------GTAALEDPRLVEDLASAFPKKIVLGIDAKEGK 134

Query: 123 -CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
               G  +Q   V   +L+K    + +  I        +      +   + +L    V +
Sbjct: 135 VATRGWIEQSD-VRTEDLIKQFSNAKIAAII----STDISTDGTLEGPNLKSL--TSVAK 187

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP----SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           +        +  +GG+  ++  + +       V GV++GRA Y N   L    +   N  
Sbjct: 188 VSNA----PVIASGGIGSLADLISLTTLEKAGVTGVIVGRALYDNKFSLEEAIKVLLNID 243

Query: 238 TGSSP 242
               P
Sbjct: 244 LQDQP 248


>gi|288870932|ref|ZP_06115793.2| NADH oxidase [Clostridium hathewayi DSM 13479]
 gi|288865388|gb|EFC97686.1| NADH oxidase [Clostridium hathewayi DSM 13479]
          Length = 655

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 67/192 (34%), Gaps = 31/192 (16%)

Query: 64  EAAKIVEDFGYNEINLNVGC-----PSARVHEG------SFGACLMLNPDIVGDCIAAMC 112
            AA    + GY+ I     C     P + +  G       +G           +CI A+ 
Sbjct: 158 HAAARCVEAGYDCIE--FHCAHNYLPHSFLSGGLNHRTDEYGGSFENRSRFPLECIRAIR 215

Query: 113 KAL--SIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            A+   +P+ ++     D     +    +        ++GV+ + +     I  G     
Sbjct: 216 SAIPGDMPLFMRIDAHDDYLPGGLTIEEVIEFCCIAGENGVDVLDVSRGNIITAGSV--- 272

Query: 168 NRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             ++P +D       +    I++E   + I + G +    QA +IL     D +++GRA 
Sbjct: 273 -YEVPPIDIPRGFNVENAARIRRETKMVTIAV-GRINTAEQAEEILEADKADLIVMGRAQ 330

Query: 220 YKNSAMLTTVDE 231
             +        E
Sbjct: 331 LADPEFCNKAKE 342


>gi|320184421|gb|EFW59230.1| dihydropyrimidine dehydrogenase [Shigella flexneri CDC 796-83]
          Length = 282

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 27/151 (17%), Positives = 56/151 (37%), Gaps = 27/151 (17%)

Query: 76  EINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            I  N  CP   +   + G+ +  +P +V     A+ +  ++P+  K    + D      
Sbjct: 1   MIECNFSCPQ--MTSHAMGSDVGQSPVLVEKYCRAVKRGSTLPMLAKMTPNIGD------ 52

Query: 136 LRNLVKSIKKSGVNGIW-IHARKAIL----------------KGLSPKDNRKIPNLDYDI 178
           +  +  + K+ G +GI  I+  K+I                   +S    + +  +    
Sbjct: 53  MCEVALAAKRGGADGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRF 112

Query: 179 VYEIKK--ENPDLFIGLNGGLEDMSQALKIL 207
           + +++   E  D  I   GG+E    A + L
Sbjct: 113 IQQMRTHPELRDFPISGIGGIETWEDAAEFL 143


>gi|326564620|gb|EGE14840.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis 12P80B1]
          Length = 716

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 60/176 (34%), Gaps = 23/176 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
                 AK+ +  GY+ + +              SAR ++   S+G  L        + +
Sbjct: 171 DDYAHTAKLAKKAGYDGVEIMGSEGYLINQFL--SARTNKRTDSYGGSLENRMRFAIEVV 228

Query: 109 AAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+ +A  I   +  R      V+D      +  L K+++ +GV+   I+      +   
Sbjct: 229 RAVREAAGINFIITFRLSMIELVEDGATMQDVITLAKALELAGVS--IINTGIGWHEARI 286

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           P     +P   +      +K       I  N  +     A +IL     D V + R
Sbjct: 287 PTIVTSVPRAAFTRYTAAVKHAVSIPVIAANR-INMPQTAEEILSSGQADLVQMAR 341


>gi|328906503|gb|EGG26278.1| oxidoreductase, FAD/FMN-binding [Propionibacterium sp. P08]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 50/151 (33%), Gaps = 13/151 (8%)

Query: 109 AAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+  AL   +P+  +  +    DD         L +     GV+ +      A   G S
Sbjct: 223 EAVRGALPDDMPLLARLSVTDWRDDGWTVEDSIELSRRFASVGVDLV-----DASSGGNS 277

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                  P    D+   ++ E   +     G +     A ++L     D +M+GRAA ++
Sbjct: 278 SAPIPVAPGYQADLAARVRAEA-SIPTSTVGMIWTSELAEELLTRGCADAIMVGRAALRD 336

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +            P   +     R  +  WR
Sbjct: 337 TNWPLRAAHELGVPNEDAPWHPARF-RGAWR 366


>gi|294667829|ref|ZP_06733039.1| NADH flavin oxidoreductase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292602455|gb|EFF45896.1| NADH flavin oxidoreductase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 372

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 30/207 (14%), Positives = 60/207 (28%), Gaps = 22/207 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                +A   E  G   I L+            P +     ++G        +      A
Sbjct: 165 DAFAASATRAERLGLELIELHAAHGYLMHQFLSPLSNQRSDAYGGSPENRMRLTLRIFDA 224

Query: 111 MCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+S  + V  RI   D             L +++   G + I + +      GL P+
Sbjct: 225 VRAAVSEKIAVGVRISATDWVEGGWDVQQSIALSQALDARGAHYIHVSSG-----GLDPR 279

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +    Y I   +  +      +   G + + +QA  I+     D + + R    + 
Sbjct: 280 QQIPL-QAGYQIPFAQEIRAQVSTPVIGVGLITEPAQAEAIVQEGQADAIALARGILYDP 338

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
                        +T +        +D
Sbjct: 339 RWPWHAAAALGASVTPAPQYLRCEPRD 365


>gi|289427998|ref|ZP_06429702.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes J165]
 gi|295131634|ref|YP_003582297.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           SK137]
 gi|289158881|gb|EFD07081.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes J165]
 gi|291376038|gb|ADD99892.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           SK137]
 gi|313763762|gb|EFS35126.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL013PA1]
 gi|313771778|gb|EFS37744.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL074PA1]
 gi|313793691|gb|EFS41722.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL110PA1]
 gi|313803002|gb|EFS44210.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL110PA2]
 gi|313808412|gb|EFS46879.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL087PA2]
 gi|313816920|gb|EFS54634.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL059PA1]
 gi|313818167|gb|EFS55881.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL046PA2]
 gi|313821025|gb|EFS58739.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL036PA1]
 gi|313823903|gb|EFS61617.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL036PA2]
 gi|313827157|gb|EFS64871.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL063PA1]
 gi|313829722|gb|EFS67436.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL063PA2]
 gi|313831642|gb|EFS69356.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL007PA1]
 gi|313834796|gb|EFS72510.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL056PA1]
 gi|313839370|gb|EFS77084.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL086PA1]
 gi|314916479|gb|EFS80310.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL005PA4]
 gi|314918858|gb|EFS82689.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL050PA1]
 gi|314921067|gb|EFS84898.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL050PA3]
 gi|314927050|gb|EFS90881.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL036PA3]
 gi|314956586|gb|EFT00838.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL027PA1]
 gi|314961870|gb|EFT05971.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL002PA2]
 gi|314964860|gb|EFT08960.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL082PA1]
 gi|314968635|gb|EFT12733.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL037PA1]
 gi|314977912|gb|EFT22006.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL045PA1]
 gi|314979599|gb|EFT23693.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL072PA2]
 gi|314984680|gb|EFT28772.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL005PA1]
 gi|314988334|gb|EFT32425.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL005PA2]
 gi|314990424|gb|EFT34515.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL005PA3]
 gi|315082357|gb|EFT54333.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL078PA1]
 gi|315083813|gb|EFT55789.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL027PA2]
 gi|315087310|gb|EFT59286.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL002PA3]
 gi|315089728|gb|EFT61704.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL072PA1]
 gi|315095603|gb|EFT67579.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL038PA1]
 gi|315100237|gb|EFT72213.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL059PA2]
 gi|315102561|gb|EFT74537.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL046PA1]
 gi|315109521|gb|EFT81497.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL030PA2]
 gi|327326609|gb|EGE68397.1| oxidoreductase, FAD/FMN-binding family protein [Propionibacterium
           acnes HL096PA3]
 gi|327332873|gb|EGE74605.1| oxidoreductase, FAD/FMN-binding family protein [Propionibacterium
           acnes HL096PA2]
 gi|327335272|gb|EGE76982.1| oxidoreductase, FAD/FMN-binding family protein [Propionibacterium
           acnes HL097PA1]
 gi|327447700|gb|EGE94354.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL043PA2]
 gi|327448575|gb|EGE95229.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL043PA1]
 gi|327449572|gb|EGE96226.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL013PA2]
 gi|327455886|gb|EGF02541.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL087PA3]
 gi|327456022|gb|EGF02677.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL092PA1]
 gi|327458038|gb|EGF04693.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL083PA2]
 gi|328757200|gb|EGF70816.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL087PA1]
 gi|328757391|gb|EGF71007.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL020PA1]
 gi|328757581|gb|EGF71197.1| oxidoreductase, FAD/FMN-binding protein [Propionibacterium acnes
           HL025PA2]
 gi|328761998|gb|EGF75504.1| oxidoreductase, FAD/FMN-binding family protein [Propionibacterium
           acnes HL099PA1]
 gi|332676498|gb|AEE73314.1| NADPH dehydrogenase [Propionibacterium acnes 266]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|150401246|ref|YP_001325012.1| putative TIM-barrel protein [Methanococcus aeolicus Nankai-3]
 gi|150013949|gb|ABR56400.1| putative TIM-barrel protein [Methanococcus aeolicus Nankai-3]
          Length = 306

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 29/164 (17%), Positives = 54/164 (32%), Gaps = 31/164 (18%)

Query: 75  NEINLNVGCPSARVHEGSFGACLMLNPDIV-----GDCIAAMCKALS-----------IP 118
           +   LN  C    + +   G  L+   +          I  +   LS            P
Sbjct: 141 DIFELNCHCRQKEITDLGIGQELLKKENNRILKNNLKIINKINNELSGQLNGQLHGSSTP 200

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           + +K R      I +  L N + ++K    +G+ I           P  N      D D 
Sbjct: 201 IFLKIRANF---ISSNELINNLNNVKDY-FDGLHIDC-------FYPNKNC----ADLDY 245

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           + +++    D  I  N  +  ++ A  +L   D V + R   ++
Sbjct: 246 LMDLRNNFKDKIIIGNNSVNSINDAKNMLKYCDFVSVARCILRD 289


>gi|50843556|ref|YP_056783.1| NADH:flavin oxidoreductase [Propionibacterium acnes KPA171202]
 gi|50841158|gb|AAT83825.1| NADH:flavin oxidoreductase [Propionibacterium acnes KPA171202]
 gi|314924362|gb|EFS88193.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL001PA1]
 gi|314965887|gb|EFT09986.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL082PA2]
 gi|315094821|gb|EFT66797.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL060PA1]
 gi|315107750|gb|EFT79726.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL030PA1]
          Length = 366

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+GRAA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGRAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|331016470|gb|EGH96526.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Pseudomonas syringae pv. lachrymans str. M302278PT]
          Length = 365

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 25/135 (18%), Positives = 49/135 (36%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCKALS-IPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGI 151
               +  D IA + KA    PV V+   G  +               +  ++  + V+ I
Sbjct: 209 QRLRLTLDVIAEVKKAAGQAPVGVRISQGKVNDFQHKWAGGERDAEVIFGALADARVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A                +  +V   ++  PD+ +  NGGL D  +A ++     
Sbjct: 269 HVTEHQAW--------QPAFAQGEASLVRLARRYAPDVALIANGGLHDPEKAAQVFRDGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|163740787|ref|ZP_02148180.1| hypothetical protein RG210_13141 [Phaeobacter gallaeciensis 2.10]
 gi|161385778|gb|EDQ10154.1| hypothetical protein RG210_13141 [Phaeobacter gallaeciensis 2.10]
          Length = 764

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 33/209 (15%), Positives = 69/209 (33%), Gaps = 24/209 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
           + V AA++ E  G++ I L+            P + +   ++G  L   +  P  V + +
Sbjct: 550 EFVAAAQMAERAGFDMIELHAAHGYLISSFISPKSNIRTDAYGGALANRLRYPLEVFEAM 609

Query: 109 AAMCKALSIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A+      P++V+        D+ +       + ++   +G + I + A +   +   P
Sbjct: 610 RAVW-PTDKPMSVRISANDWVGDEGVTPEEAVEIARAFTAAGADIIDVSAGQTSTE-AQP 667

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R       D +         +     G + +   A  IL +   D V +GR    + 
Sbjct: 668 VYGRMFQTPFSDRIRNDA----GIATMAVGNIYEADHANSILMAGRADLVCVGRPHLADP 723

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
              L               P     D+ +
Sbjct: 724 YWTLHEASRIGDRHADWPLPYLAGRDQAW 752


>gi|307546050|ref|YP_003898529.1| NADH:flavin oxidoreductase/NADH oxidase [Halomonas elongata DSM
           2581]
 gi|307218074|emb|CBV43344.1| NADH:flavin oxidoreductase/NADH oxidase [Halomonas elongata DSM
           2581]
          Length = 690

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 35/219 (15%), Positives = 76/219 (34%), Gaps = 28/219 (12%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------- 82
           + + R   K I     +E    +      I    +AA+  ++ G + + L+         
Sbjct: 130 EPVHRSTCKTI----EEEDIWRI------IDDFAQAARRAKEGGLDGVELSAVHQHLMDQ 179

Query: 83  CPSARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD----DQIPAVAL 136
             S RV++    +G           + + A+ + +     V  RI  D    D +    +
Sbjct: 180 FWSPRVNKRTDQWGGSFENRMRFGMEVLKAVREEVGDDFVVGMRICGDEFHPDGLSHDDM 239

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NRKIPNLDYDIVYEIKKENPDLFIGL 193
           + +      +G    +           +  +   N   P   +  +    KE  ++ +  
Sbjct: 240 KQIAAYYDATGQVDFFGVVGSGCDTHDTLANVIPNMSYPPEPFLHLAAGIKEVVNVPVIH 299

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVD 230
              ++D +QA +IL    VD V + RA   +  ++T + 
Sbjct: 300 AQNIKDPNQANRILEGGHVDLVGMTRAHIADPHLITKIK 338


>gi|44151609|gb|AAS46742.1| putative NADH:flavin oxidoreductase 1 [Pleurotus djamor]
          Length = 395

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 68/210 (32%), Gaps = 40/210 (19%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL-------------NVGCPSARVHE 90
           + +E   A      +    VEA +  E+ G++ I +             N+      V  
Sbjct: 174 TPKEMDEAHLTYVENA--FVEAIERCEEVGFDFIEIHSAHGYLFHSFLSNLS----NVRT 227

Query: 91  GSFGACLMLNPDIV-GDCIAAMCKALSIPVTVKC---------RIGVDDQIPAVALRN-- 138
            S+G   + N        I +  +A S P+ V+              D       +    
Sbjct: 228 DSYGGQPLENRLRFPLRVIKSCREAWSKPLFVRISASDWAEGPEKADDGTWKQWGIEQSK 287

Query: 139 -LVKSIKKSGVNGIWI-HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            L   + K GV+ +          + +      ++P  +      +KK  P L +G  G 
Sbjct: 288 VLAGELVKIGVDLVDCSSGGNWAQQKIPFSHGYQVPFAE-----SLKKAYPSLNVGAVGL 342

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           + D  +A   L     D +++ R   +N  
Sbjct: 343 ISDPEKAEGYLQEGKADIILLARELLRNPH 372


>gi|326563707|gb|EGE13958.1| NADPH dehydrogenase [Moraxella catarrhalis 46P47B1]
          Length = 353

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 35/222 (15%), Positives = 76/222 (34%), Gaps = 31/222 (13%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           +   AI  G+    L ++ Q      Q+   +I  LV+A     K   + G++ I L+  
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRQLSIDEIKALVQAFADSVKRAVNAGFDAIELHAA 172

Query: 83  --------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGV--D 128
                   C P +      +G     +  + G+ +    +A+    +P+ ++       +
Sbjct: 173 HGYLIHQFCAPKSNQRSDEYG----QDRLLFGEQVIKAVRAVMPDEMPLIMRISAQEYGE 228

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   +     + K    +G +   +      +     K           +  ++K     
Sbjct: 229 NGFDSDYGVEIAKRFSTAGADVFHVSGGGDGVL-CEGKHPEFYAGYQVPMARKVKHATGK 287

Query: 189 LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             +   G L+D + A  +L     D V IGR   ++   +L 
Sbjct: 288 -PVIAVGMLDDPAVADHVLGVGDADLVAIGRGLLRDPYWVLN 328


>gi|312882481|ref|ZP_07742222.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309369881|gb|EFP97392.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 667

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 66/193 (34%), Gaps = 23/193 (11%)

Query: 57  ADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG-- 105
             I    ++A +  + GY+ + +            C   +     +        + +   
Sbjct: 138 NTIDAFAKSASLAVEAGYDGVEVMGSEGYLLNQFIC---KRTNNRYDEWGGCYENRIRFP 194

Query: 106 -DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            + + A+ KA      +  R+     V++      +  L K ++K+GV    I+      
Sbjct: 195 LEVVRAIRKAAGKKFIIIFRLSMLDLVEEGSTFDEVVMLAKELEKAGVT--IINTGIGWH 252

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
           +   P    ++P   +  V E  + + ++ I     +    +A KIL     D V + R 
Sbjct: 253 EARVPTIATQVPRGAFTWVTEKVRPHINVPIVTCNRINTPEEAEKILSGGHADMVSMARP 312

Query: 219 AYKNSAMLTTVDE 231
              +   +   ++
Sbjct: 313 FLADPHFVNKAEQ 325


>gi|226313644|ref|YP_002773538.1| 2,4-dienoyl-CoA reductase [NADPH] [Brevibacillus brevis NBRC
           100599]
 gi|226096592|dbj|BAH45034.1| putative 2,4-dienoyl-CoA reductase [NADPH] [Brevibacillus brevis
           NBRC 100599]
          Length = 667

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 25/179 (13%), Positives = 60/179 (33%), Gaps = 17/179 (9%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             + A   +  G++ + +             P     E  +G   +       +    + 
Sbjct: 148 FADGAVRAKKAGFDAVEIMGSEGYLINQFLSPVTNKREDEWGGDFLRRARFGIEVAKRVR 207

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +A+ +   +  R+     + D           K ++++GV+ + +       +   P   
Sbjct: 208 QAVGLDYPIIYRMSGLDLMPDSTTMEETLQFAKMLEEAGVDALNV--GIGWHESQVPTIG 265

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
             +P   Y  V +  K+  ++ +  +  + DM QA  IL     D V + R    +  +
Sbjct: 266 MMVPRGAYVWVAQQVKQIVNIPVIASNRINDMRQAETILYEEYSDMVSMARPFLADPYI 324


>gi|15229529|ref|NP_188408.1| dihydroorotate dehydrogenase family protein / dihydroorotate
           oxidase family protein [Arabidopsis thaliana]
 gi|9294485|dbj|BAB02704.1| senescencs-related protein; dihydroorotate dehydrogenase-like
           protein [Arabidopsis thaliana]
 gi|14334712|gb|AAK59534.1| putative dehydrogenase [Arabidopsis thaliana]
 gi|16323430|gb|AAL15209.1| putative dehydrogenase [Arabidopsis thaliana]
 gi|24850451|gb|AAN64919.1| putative dehydrogenase [Arabidopsis thaliana]
 gi|332642489|gb|AEE76010.1| pyrimidine 1 [Arabidopsis thaliana]
          Length = 426

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 31/171 (18%), Positives = 57/171 (33%), Gaps = 24/171 (14%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 176 RVEQTGVDALEINFSCPHGM-PERRMGAAVGQDCALLDEVCGWINAKATVPVWAKMTPNI 234

Query: 128 DD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDNRKIPN 173
            D         +     +  +   +   G++   +     +       G S K  R I  
Sbjct: 235 TDITEPARVSLKSGCEGIAAINTIMSVMGIDMKTLRPEPCVEGYSTPGGYSYKAVRPIAL 294

Query: 174 LDYDIVYE-IKKENP-DLFIGLNGGLED-MSQALKILPS------VDGVMI 215
                + + +K E   D  +   GG+E     A  IL          GVM+
Sbjct: 295 AKVMNIAKMMKSEFSEDRSLSGIGGVETGYDAAEFILLGSNTVQVCTGVMM 345


>gi|312171000|emb|CBX79259.1| hypothetical protein, similar to dihydroorotate oxidase [Erwinia
           amylovora ATCC BAA-2158]
          Length = 294

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 66/196 (33%), Gaps = 35/196 (17%)

Query: 35  GDKKNILG-FSTQEKPLALQIGGADISK---LVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            +  ++LG F  Q+ P+   +      +   LV A + + D           CP      
Sbjct: 82  DNWLDLLGQFHQQQLPIIASVHAPSPGETGLLVAAIRHISD-----------CPLELGIS 130

Query: 91  GSFGACLMLN-PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
                    + P+ V     A+ +      +VK  +G         L   V++  + G +
Sbjct: 131 CLHADDFTEDNPERVYAYADAVRQQTDAKFSVKLSLGQ-------YLHERVQAACEGGAS 183

Query: 150 GIWI-----------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
            I +              KA+L G+       I  L    + E+++    + I  +GG++
Sbjct: 184 AITLSDTIPGIAFDLVEGKAVLGGVCGYSGPGIKPLVLAAICELRQRGVSVPIMGSGGVQ 243

Query: 199 D-MSQALKILPSVDGV 213
             +     +L   + V
Sbjct: 244 SGLDVHEYMLAGAETV 259


>gi|289676630|ref|ZP_06497520.1| NADH:flavin oxidoreductase/NADH oxidase:FAD-dependent pyridine
           nucleotide-disulphide oxidoreductase [Pseudomonas
           syringae pv. syringae FF5]
          Length = 285

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 133 LAVEIVRRVREAVGAQFIIIFRLSMLDLVEGGSSWEEIVELAKAVEQAGATLI--NTGIG 190

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 191 WHEARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 250

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 251 RPFLADP 257


>gi|257485826|ref|ZP_05639867.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 121

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           ++  +GV+ I +   +A                D  +V   ++  PD+ +  NGGL D  
Sbjct: 10  ALADAGVDYIHVTEHEAW--------QPAFAQGDASLVKLARRYAPDVALIANGGLHDPE 61

Query: 202 QALKIL-PSVDGVMIGRAAYKNSAM 225
           +A ++L    D + +G+ A  N  +
Sbjct: 62  KADQVLHQGADIIAVGKGALANPDL 86


>gi|317123395|ref|YP_004097507.1| dihydroorotate oxidase A [Intrasporangium calvum DSM 43043]
 gi|315587483|gb|ADU46780.1| dihydroorotate oxidase A [Intrasporangium calvum DSM 43043]
          Length = 342

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 23/129 (17%), Positives = 55/129 (42%), Gaps = 19/129 (14%)

Query: 94  GACLMLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           G   + +   + + + A+  +A   P+ VK    + D+    A+  +++     GV+G+ 
Sbjct: 187 GLRGLQDRAALDELVGALAAEAQGTPLLVKIAPDLTDE----AIGEVLQVCADHGVSGL- 241

Query: 153 IHARKAILKGLSPKDNRKIPNLD-------------YDIVYEIKKENPDLFIGLNGGLED 199
           I     + +G     +R + +++              ++V  I +E P+L +   GG+  
Sbjct: 242 IATNTTVSRGGVAAADRPVADVETGGLSGRPLTARAREVVAFIHREAPELPVIGVGGISS 301

Query: 200 MSQALKILP 208
           +  A ++L 
Sbjct: 302 VDDAHRMLD 310


>gi|309808959|ref|ZP_07702835.1| putative dihydroorotate dehydrogenase 1B [Lactobacillus iners
           LactinV 01V1-a]
 gi|308167806|gb|EFO69948.1| putative dihydroorotate dehydrogenase 1B [Lactobacillus iners
           LactinV 01V1-a]
          Length = 186

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 46/98 (46%), Gaps = 11/98 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL   +GG+ IS  +  AK + D G  N + +NV CP    +  + G  L  +P +V   
Sbjct: 98  PLIASVGGSQISDYITIAKKLSDSGLLNALEINVSCP----NVAAGGMHLGTDPVVVEKL 153

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            + + K ++IP+ +K    V        +  + ++ ++
Sbjct: 154 TSEIKKVVNIPIYIKLTPNV------TNIVEIAQAAER 185


>gi|239996726|ref|ZP_04717250.1| 2,4-dienoyl-CoA reductase [Alteromonas macleodii ATCC 27126]
          Length = 692

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 26/177 (14%), Positives = 58/177 (32%), Gaps = 20/177 (11%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V+ A + +  GY+ + +            C         +G  L     +  + +  + +
Sbjct: 166 VKCAALAQQAGYDGVEIMGSEGYLINQFFCERTNHRNDEWGGSLENRARLAIEIVKGVRE 225

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +  R+ + D +   A  +    L K I+K+G   I  +      +   P  + 
Sbjct: 226 KVGTNFIIIYRLSMLDLVEGGAKWDEVVYLAKEIEKAGATLI--NTGIGWHEARVPTIST 283

Query: 170 KIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
            +P   +  +   +KKE     I  N  +     A  +L      M+   +     +
Sbjct: 284 SVPRAAFTWITERMKKEVSIPLITTNR-INTPEVAESVLAQGHADMV---SMARPFL 336


>gi|218514795|ref|ZP_03511635.1| tRNA-dihydrouridine synthase protein [Rhizobium etli 8C-3]
          Length = 54

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN 39
          M   TD  +R  A       L+ TEM+ +  ++    ++
Sbjct: 5  MSGVTDMPFRELAWRF-GAGLVVTEMVASRELVNDTAES 42


>gi|221196528|ref|ZP_03569575.1| xenobiotic reductase A [Burkholderia multivorans CGD2M]
 gi|221203197|ref|ZP_03576216.1| xenobiotic reductase A [Burkholderia multivorans CGD2]
 gi|221177131|gb|EEE09559.1| xenobiotic reductase A [Burkholderia multivorans CGD2]
 gi|221183082|gb|EEE15482.1| xenobiotic reductase A [Burkholderia multivorans CGD2M]
          Length = 369

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 64/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AA+   D G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAARRARDIGFEWLELHFAHGYLGQSFFSVHSNRRTDEYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            K     +P+T +  +   D      L     L + +K+ G++ + +      +   +P 
Sbjct: 219 RKVWPEHLPLTARFGVIEYDGRDEETLAESIALTERLKQEGLDMLSV-----SVGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPVAERVRREAGLPVSSAWGIDTPQLANRVVADEQLDLVMVGRAHLADPH 333


>gi|167386568|ref|XP_001737815.1| dihydropyrimidine dehydrogenase [Entamoeba dispar SAW760]
 gi|165899267|gb|EDR25906.1| dihydropyrimidine dehydrogenase, putative [Entamoeba dispar SAW760]
          Length = 901

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 64/177 (36%), Gaps = 29/177 (16%)

Query: 66  AKIVEDFGYNEINLNVGCP--------SARVHEGSF------GACLMLNPDIVGDCIAAM 111
           AK+ E+ G + + LN  CP        +    EG F         + ++P  +  C   +
Sbjct: 554 AKLSEEAGADALELNFSCPNECHGNDGNEGGCEGGFKSHNAMAMAIGVSPAAIERCTRYV 613

Query: 112 CKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKK----SGVNGIWIHARKAILKGL-- 163
            +++ IPV  K    V   +++ A A+R     +       G++ I +        G+  
Sbjct: 614 VESVHIPVYPKLTPNVGNIEELAAAAMRGGASGVSTINTVFGISEITLSGHPWPQVGVER 673

Query: 164 ----SPKDNRKIPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALK-ILPSVDGV 213
                      +  +    + ++ + N ++   +   GG+     A++ I      V
Sbjct: 674 NTISGGLSGDLVRPIAIRQIAQVLRHNENVRGHLLGIGGVRSAETAMQLIYTGASVV 730


>gi|326561042|gb|EGE11407.1| NADPH dehydrogenase [Moraxella catarrhalis 7169]
          Length = 353

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 35/222 (15%), Positives = 76/222 (34%), Gaps = 31/222 (13%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           +   AI  G+    L ++ Q      Q+   +I  LV+A     K   + G++ I L+  
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRQLSIDEIKALVQAFADSVKRAVNAGFDAIELHAA 172

Query: 83  --------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIGV--D 128
                   C P +      +G     +  + G+ +    +A+    +P+ ++       +
Sbjct: 173 HGYLIHQFCAPKSNQRSDEYG----QDRLLFGEQVIKAVRAVMPDEMPLIMRISAQEYGE 228

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +   +     + K    +G +   +      +     K           +  ++K     
Sbjct: 229 NGFDSDYGVEIAKRFSTAGADVFHVSGGGDGVL-CEGKHPEFYAGYQVPMARKVKHATGK 287

Query: 189 LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             +   G L+D + A  +L     D V IGR   ++   +L 
Sbjct: 288 -PVIAVGMLDDPAVADHVLGVGDADLVAIGRGLLRDPYWVLN 328


>gi|168213014|ref|ZP_02638639.1| NADH oxidase [Clostridium perfringens CPE str. F4969]
 gi|170715366|gb|EDT27548.1| NADH oxidase [Clostridium perfringens CPE str. F4969]
          Length = 640

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 70/188 (37%), Gaps = 19/188 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG------CPSARVHEG--SFGACLMLNPDIVGDCIAAMC 112
           K+   A   E  G + I ++        C S  +++    +G  L        + + A+ 
Sbjct: 145 KMCNCAIRAEKAGVDIIQIHGDRLVGSLC-STILNKRTDKYGGTLENRTRFALEFVRALK 203

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           KA+ ++ +  K  +   ++       +      K ++++GV+ + +              
Sbjct: 204 KAVPNMTIDYKFSVVTPERGKGGVNLDEAPIFAKWLEEAGVDMLHVAQANHTGNMADTIP 263

Query: 168 NRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +    +  DI  +IKK + ++ +   G + +   A  IL     D + IGR    ++
Sbjct: 264 PMGVQPYGFFVDIAAQIKK-SVNIPVSTVGRIFNPKMAESILESDKADIIGIGRILLADA 322

Query: 224 AMLTTVDE 231
             +  + E
Sbjct: 323 DWVNKIIE 330


>gi|149926417|ref|ZP_01914678.1| 2,4-dienoyl-CoA reductase [Limnobacter sp. MED105]
 gi|149824780|gb|EDM83994.1| 2,4-dienoyl-CoA reductase [Limnobacter sp. MED105]
          Length = 678

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 26/180 (14%), Positives = 62/180 (34%), Gaps = 23/180 (12%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCIAA 110
              +AKI ++ GY+ + +            C   R +     +G  +     +  + +  
Sbjct: 146 FARSAKIAQEAGYDGVEVMGSEGYFLNQFIC--KRTNHRTDRWGGSVENRARLSVEIVRR 203

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +     +  R  + D +      +    + K I+K+G   I  +      +   P 
Sbjct: 204 IRETVGEKFIIIYRHSLLDLVEGGNTWDEVSYIAKEIEKAGATMI--NTGIGWHEARVPT 261

Query: 167 DNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +P   + ++   ++KE     I  N  +     A ++L   + D V + R    + 
Sbjct: 262 IVTSVPRAAFAELTARLRKEIKIPVIASNR-INKPDVAEQLLADGACDMVSMARPLLADP 320


>gi|108805059|ref|YP_644996.1| NADH:flavin oxidoreductase/NADH oxidase [Rubrobacter xylanophilus
           DSM 9941]
 gi|108766302|gb|ABG05184.1| NADH:flavin oxidoreductase/NADH oxidase [Rubrobacter xylanophilus
           DSM 9941]
          Length = 664

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 62/191 (32%), Gaps = 31/191 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               EAA  +E  G++ I +             P        +G  L        + I A
Sbjct: 156 EAFAEAAARLERCGWDGIEITSLGGHLIEQFWSPVINKRTDRYGGDLAGRMRFSVEVIEA 215

Query: 111 MCKALSIPVTVKCRIGVDDQIPAV-----ALRNLVKSIKK---------SGVNGIWIHAR 156
           + +A+S    V  R+  D +   +      +  +   +           SG  G    A+
Sbjct: 216 VAEAVSDDFIVGFRMTGDPKTDVIGLTPEDMLEIATRLDDLGRIDLFNISGGTGATYEAQ 275

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
            A + G +       P      +    KE+  + +   G + D  QA + + +   D V 
Sbjct: 276 AATVPGDTYARGCYCP------LARRMKEHLSVPVLAAGRILDPEQAEEAIAAGDCDLVA 329

Query: 215 IGRAAYKNSAM 225
           + RA   +  +
Sbjct: 330 MTRAIIADPDL 340


>gi|325274209|ref|ZP_08140330.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas sp. TJI-51]
 gi|324100643|gb|EGB98368.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas sp. TJI-51]
          Length = 678

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 29/223 (13%), Positives = 65/223 (29%), Gaps = 22/223 (9%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++            E+ +  QI        V  A + +  GY+
Sbjct: 106 LHAGRYAYSPRQVAPSAIQAPINPFKPKELDEQGIEKQIA-----DFVNCAVLAQRAGYD 160

Query: 76  EINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS----IPVTVK 122
            + +                      +G        +  + ++ +  A+     I   + 
Sbjct: 161 GVEIMGSEGYFINQFLAAHTNQRTDRWGGSYENRMRLAVEIVSRVRAAVGPNFIIIFRLS 220

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
               V+       +  L K+I+++G   I  +      +   P    K+P   +  V   
Sbjct: 221 MLDLVEGGSDWAEIEQLAKAIEQAGATLI--NTGIGWHEARIPTIATKVPRAAFSKVTAK 278

Query: 183 KKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
            +    + +     +     A  +L   D  M+   R    + 
Sbjct: 279 LRGVVSIPLITTNRINTPEVAEAVLAEGDADMVSMARPFLADP 321


>gi|169344549|ref|ZP_02865517.1| NADH oxidase [Clostridium perfringens C str. JGS1495]
 gi|169297310|gb|EDS79420.1| NADH oxidase [Clostridium perfringens C str. JGS1495]
          Length = 640

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 70/188 (37%), Gaps = 19/188 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG------CPSARVHEG--SFGACLMLNPDIVGDCIAAMC 112
           K+   A   E  G + I ++        C S  +++    +G  L        + + A+ 
Sbjct: 145 KMCNCAIRAEKAGVDIIQIHGDRLVGSLC-STILNKRTDKYGGTLENRTRFALEFVRALK 203

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           KA+ ++ +  K  +   ++       +      K ++++GV+ + +              
Sbjct: 204 KAVPNMTIDYKFSVVTPERGKGGVNLDEAPIFAKWLEEAGVDMLHVAQANHTGNMADTIP 263

Query: 168 NRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +    +  DI  +IKK + ++ +   G + +   A  IL     D + IGR    ++
Sbjct: 264 PMGVQPYGFFVDIAAQIKK-SVNIPVSTVGRIFNPKMAESILESDKADIIGIGRILLADA 322

Query: 224 AMLTTVDE 231
             +  + E
Sbjct: 323 DWVNKIIE 330


>gi|167767158|ref|ZP_02439211.1| hypothetical protein CLOSS21_01677 [Clostridium sp. SS2/1]
 gi|167711133|gb|EDS21712.1| hypothetical protein CLOSS21_01677 [Clostridium sp. SS2/1]
          Length = 331

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 24/177 (13%), Positives = 60/177 (33%), Gaps = 18/177 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLN---------VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  + A+  ++ G++ + ++            P +      +G  +        + I  
Sbjct: 152 EQFRDCARRAKEAGFDAVEVHGAHGYLIGAFASPFSNKRSDEYGGTIRNRARFAMEIIEN 211

Query: 111 MCKALSI--PV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +      PV   +     V   +     + L + ++++G + I  H  + +       
Sbjct: 212 IKEKCGKDYPVLYRMSAVEYVPGGLEIEESKILARLVEEAGADCI--HCSQGVYASTHVI 269

Query: 167 DNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
               + P   Y       K+  D+ +   G + D+  A  +L     D V + RA+ 
Sbjct: 270 IPPSVVPRAAYVENAAEIKKVVDIPVIAVGRINDVEIAESVLQADKADLVTMARASL 326


>gi|118471664|ref|YP_889370.1| 2,4-dienoyl-CoA reductase [Mycobacterium smegmatis str. MC2 155]
 gi|118172951|gb|ABK73847.1| 2,4-dienoyl-coA reductase [Mycobacterium smegmatis str. MC2 155]
          Length = 671

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 25/187 (13%), Positives = 59/187 (31%), Gaps = 17/187 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V  A +  + GY+ + +             P       S+G           + +  
Sbjct: 142 EDFVRCALLAHEAGYDGVEIMGSEGYLINQFLAPRTNRRTDSWGGSAANRRRFPVEIVRR 201

Query: 111 MCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A+     V  R+     V+D      +  L   ++++G   I  ++     +   P 
Sbjct: 202 VREAVGPDFIVCYRMSMADYVEDGQSWDEIVCLATEVEEAGATLI--NSGFGWHEARVPT 259

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
               +PN  +  +     EN  + +  +  +     A +IL    V  + + R    +  
Sbjct: 260 IVTSVPNSAFVDISSAVAENVRIPVIASNRINMPQAAEQILAETGVQLISMARPLLSDPD 319

Query: 225 MLTTVDE 231
            +   + 
Sbjct: 320 WVRKAEA 326


>gi|328706442|ref|XP_001944849.2| PREDICTED: dihydropyrimidine dehydrogenase [NADP+]-like
            [Acyrthosiphon pisum]
          Length = 1297

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 71/239 (29%), Gaps = 51/239 (21%)

Query: 16   LTNNALLYTEMIVAD-AILRGDKKNILGFSTQEKPLALQIGG----ADISKLVEAAKIVE 70
            +  NA L  E+I    A         L     +  L   I       D + L   A++  
Sbjct: 782  VARNAFLNIELISEKTAAYWLRSIRELKRDFPQHILIASIMCAYIENDWTSL---ARLAC 838

Query: 71   DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA-----AMCKALS------IPV 119
            D G + + LN+ CP     E   G     +P +V +        A+  A        +PV
Sbjct: 839  DAGADALELNLSCPHGM-GESGMGLACGQDPVLVENISRWVKRVAVRPASDGGTPTAVPV 897

Query: 120  TVKCRIGVDDQIPAVALR---------NLVKSIKKSGVNGIWIH-ARKAILKGLSPKD-- 167
             VK    V D +                 V ++   G   +  +  R     G +  +  
Sbjct: 898  FVKITPNVTDVVAVARAAVRLGGADGVTAVNTVSALGPLDVTGNGGRPWPGVGRTTAETP 957

Query: 168  --------NRKIPNLDYDIVYEIKKEN-----------PDLFIGLNGGLEDMSQALKIL 207
                       +  +    V  + +             P + I   GG++  +  L+ L
Sbjct: 958  RTTYGGMSGTAVRPMGLRAVSALSRALGPDATAGGDGGPPVQIMATGGVDSAAATLQYL 1016


>gi|314928748|gb|EFS92579.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL044PA1]
          Length = 341

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 50/151 (33%), Gaps = 13/151 (8%)

Query: 109 AAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+  AL   +P+  +  +    DD         L +     GV+ +      A   G S
Sbjct: 198 EAVRGALPDDMPLLARLSVTDWRDDGWTVEDSIELSRRFASVGVDLV-----DASSGGNS 252

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                  P    D+   ++ E   +     G +     A ++L     D +M+GRAA ++
Sbjct: 253 SAPIPVAPGYQADLAARVRAEA-SIPTSTVGMIWTSELAEELLTRGCADAIMVGRAALRD 311

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +            P   +     R  +  WR
Sbjct: 312 TNWPLRAAHELGVPNEDAPWHPARF-RGAWR 341


>gi|188586961|ref|YP_001918506.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351648|gb|ACB85918.1| NADH:flavin oxidoreductase/NADH oxidase [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 331

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 23/177 (12%), Positives = 61/177 (34%), Gaps = 20/177 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             ++A +   + G++ + +             P     +  +G        +  +  + +
Sbjct: 147 DFIKATERAMEAGFDGVEIHGAHGFLLNQFNSPLTNFRQDKYGGSRKNRARLSLEVASDL 206

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            + +   + +      D     + + +   + K + ++GV+ I +       +G +    
Sbjct: 207 KEVVGNKLLLYRLGATDGYDKGLTMPDAIWIAKELVRNGVDIIDVSGGHGGYRGHTRSQG 266

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             +P     I  EIK+      +   GG+     A +++    +D V +GRA     
Sbjct: 267 YFVP-----IAVEIKQNLTQPVMVA-GGISSPQYANEVIEEEGLDFVGVGRALLSRP 317


>gi|116619815|ref|YP_821971.1| NADH:flavin oxidoreductase/NADH oxidase [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116222977|gb|ABJ81686.1| NADH:flavin oxidoreductase/NADH oxidase [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 378

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 28/197 (14%), Positives = 61/197 (30%), Gaps = 22/197 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG--------C-PSARVHEGSFGACLMLNPDIVGDCIAA 110
               +AA+     G++ + ++          C P +      +G  L+       +   A
Sbjct: 181 EAFAKAARRALQAGFDVVEIHGAHGYLIHEFCSPLSNQRTDQYGGSLVNRIRFALEVTEA 240

Query: 111 MCKA--LSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +       +PV   +     V+          L +++K  GV+ I   +      G S  
Sbjct: 241 VRSVWPAGLPVLYRISATDWVEGGWSPDDSVELARALKARGVDLIDCSSG-----GNSTA 295

Query: 167 DNRK-IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                +P        +I++E  ++     G +    QA  I+     D V++ R   ++ 
Sbjct: 296 QKIPLVPGYQVPYAEKIRREA-EIPTAAVGMITTAEQAEGIVSEGKADLVLLAREFLRDP 354

Query: 224 AMLTTVDEYFSNPLTGS 240
                         +  
Sbjct: 355 YFPLHAAAELGEKPSPP 371


>gi|323495029|ref|ZP_08100118.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio brasiliensis LMG 20546]
 gi|323310686|gb|EGA63861.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio brasiliensis LMG 20546]
          Length = 670

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 32/200 (16%), Positives = 66/200 (33%), Gaps = 19/200 (9%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHE 90
           I  F+  E     QI    I    ++A +  + GY+ + +            C       
Sbjct: 126 IARFAPSEMSTR-QIN-NTIEAFAKSAALAVEAGYDGVEVMGSEGYLLNQFICKRTNTRY 183

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKS 146
             +G           + + A+ KA      +  R+     V++      +  L + ++K+
Sbjct: 184 DEWGGSYQNRIRFPLEVVKAIRKAAGNEFIIIFRLSMLDLVEEGSTFEEVVELAQELEKA 243

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV    I+      +   P    ++P   +  V E  + + ++ I     +    +A  I
Sbjct: 244 GVT--IINTGIGWHEARIPTIATQVPRGAFTWVTEKVRPHVNVPIVTCNRINTPEEAESI 301

Query: 207 LP--SVDGVMIGRAAYKNSA 224
           L     D V + R    +  
Sbjct: 302 LASGHADMVSMARPFLADPH 321


>gi|296118717|ref|ZP_06837293.1| N-ethylmaleimide reductase [Corynebacterium ammoniagenes DSM 20306]
 gi|295968206|gb|EFG81455.1| N-ethylmaleimide reductase [Corynebacterium ammoniagenes DSM 20306]
          Length = 383

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 31/186 (16%), Positives = 66/186 (35%), Gaps = 20/186 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               ++A+   D G + I ++            PS+ V E  +G        +  + I A
Sbjct: 169 EDFRQSARRAVDAGLDGIEIHSANGYLLHEFLAPSSNVREDQYGGNPAHRARLTAEVIRA 228

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + + +        RI     +  +   +  ++I  +    ++ H     L  +S   N  
Sbjct: 229 VAEEIGED-RTAVRISPQHHVQGIDESDTQETI--ATYQALFAHISDLKLAYVSVLVNEP 285

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGG------LEDMSQALKILPSVDGVMIGRAAYKNSA 224
              +  ++   I++E+    + LN G      L+D    +  L   D  +IGR    N  
Sbjct: 286 EGEVATEVRRLIQQEHG-WPLLLNSGFAVISQLDDAQYWVDEL-GADAAVIGRMLIANPD 343

Query: 225 MLTTVD 230
           ++   +
Sbjct: 344 LVERWE 349


>gi|332141816|ref|YP_004427554.1| 2,4-dienoyl-CoA reductase [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327551838|gb|AEA98556.1| 2,4-dienoyl-CoA reductase [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 680

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 45/132 (34%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D          +  L K I+K+G     I+      +
Sbjct: 205 EVVRRVREAVGKHFIIIYRLSMLDLVEGGSTYEEVVQLGKEIEKAGAT--IINTGIGWHE 262

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    +E   + +  +  +     A ++L   D  M+   R  
Sbjct: 263 ARIPTIATKVPRAAFTWVTAKFREALSIPVITSNRINTPEVAEEVLSRGDADMVSMARPF 322

Query: 220 YKNSAMLTTVDE 231
             +   +    +
Sbjct: 323 LADPDFVRKAQQ 334


>gi|168207548|ref|ZP_02633553.1| NADH oxidase [Clostridium perfringens E str. JGS1987]
 gi|170661114|gb|EDT13797.1| NADH oxidase [Clostridium perfringens E str. JGS1987]
          Length = 640

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 70/188 (37%), Gaps = 19/188 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG------CPSARVHEG--SFGACLMLNPDIVGDCIAAMC 112
           K+   A   E  G + I ++        C S  +++    +G  L        + + A+ 
Sbjct: 145 KMCNCAIRAEKAGVDIIQIHGDRLVGSLC-STILNKRTDKYGGTLENRTRFALEFVRALK 203

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           KA+ ++ +  K  +   ++       +      K ++++GV+ + +              
Sbjct: 204 KAVPNMTIDYKFSVVTPERGKGGVNLDEASIFAKWLEEAGVDMLHVAQANHTGNMADTIP 263

Query: 168 NRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +    +  DI  +IKK + ++ +   G + +   A  IL     D + IGR    ++
Sbjct: 264 PMGVQPYGFFVDIAAQIKK-SVNIPVSTVGRIFNPKMAESILESDKADIIGIGRILLADA 322

Query: 224 AMLTTVDE 231
             +  + E
Sbjct: 323 DWVNKIIE 330


>gi|150017584|ref|YP_001309838.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
 gi|149904049|gb|ABR34882.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
          Length = 647

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 21/127 (16%), Positives = 55/127 (43%), Gaps = 10/127 (7%)

Query: 106 DCIAAMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK-AIL 160
           + ++++  A+   +P+  +       +         +LVK ++++GV+ I I A     +
Sbjct: 204 EIVSSIRNAVGPDMPILFRMSLDHRFEGGRTIEDSMHLVKLLEEAGVDAIDIDAGSSEAI 263

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           + + P     + +   + + E  ++  +L I  +G       A++++   + D VM GR 
Sbjct: 264 EYVFPPS--YLGDACMEYLCEPTRKAVNLPILNSGN-HTPETAVRLIESGNADLVMFGRP 320

Query: 219 AYKNSAM 225
              +  +
Sbjct: 321 LIADPEL 327


>gi|293611031|ref|ZP_06693330.1| NADH:flavin oxidoreductase [Acinetobacter sp. SH024]
 gi|292826683|gb|EFF85049.1| NADH:flavin oxidoreductase [Acinetobacter sp. SH024]
          Length = 383

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 55/149 (36%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----- 138
           P A      +G  L     +  + + A+  A+     V  R+   D + ++   +     
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWLESIEHWDVESTV 251

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   + + +      GL    +  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYVHVSSG-----GLHEHQSITIG-AGYQVPFAEQVKKHVSIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + +   A +IL     D + + RA   + 
Sbjct: 306 ITEPEHAEQILENQQADAIGLARAMLYDP 334


>gi|302414270|ref|XP_003004967.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
 gi|261356036|gb|EEY18464.1| tRNA-dihydrouridine synthase [Verticillium albo-atrum VaMs.102]
          Length = 244

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
           + +   L  Q+G AD    V+AA++V       I++N GCP         G  
Sbjct: 107 AKEAGRLIFQVGTADPDLAVQAARLVAG-DVAGIDVNAGCPKPFSTHSGMGRA 158


>gi|187935492|ref|YP_001884833.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           B str. Eklund 17B]
 gi|187723645|gb|ACD24866.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           B str. Eklund 17B]
          Length = 362

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 25/141 (17%), Positives = 46/141 (32%), Gaps = 9/141 (6%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN-----LVKSIKKSGVNGIWIHARKA 158
           + D + A   AL  PV +K     D Q  A AL +     LV          I +     
Sbjct: 134 IVDAMKAAKAALDCPVFMKMSPHTDIQKIAKALEDAGADGLVMINSVGPCMAIDVETGYP 193

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKIL-PSVDGVMI 215
           I+   +        ++    +  I        + I   GG+     A ++L      V +
Sbjct: 194 IMGSQTGYGWLSGSSVKPVAIRNIYDASKVIKIPIIGVGGVTCGRDAAEMLMAGAQSVQV 253

Query: 216 G-RAAYKNSAMLTTVDEYFSN 235
              A  K  ++   + +  ++
Sbjct: 254 CTEAILKGPSIYGKIAKELND 274


>gi|221068341|ref|ZP_03544446.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           KF-1]
 gi|220713364|gb|EED68732.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           KF-1]
          Length = 671

 Score = 45.6 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 22/184 (11%), Positives = 55/184 (29%), Gaps = 17/184 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V  A +  + GY+ + +  G          P        +G             +  +  
Sbjct: 147 VRCACLAREAGYDGVEVMGGEGYLINQFLAPLTNFRTDEWGGDATGRSRFALRIVQGIRA 206

Query: 114 ALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+ + D +        + +L + ++ +GV+    +      +   P    
Sbjct: 207 AVPENFVISFRLSLMDLVEHGSHWKEVLDLARQLQAAGVDLF--NTSVGWHEARIPTIAM 264

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
            +P   +    E  K    + +  +  +     A  ++     D V + R    + A + 
Sbjct: 265 MVPRAAFSWAAEQLKHAVSVPVAASNRINTPEVADDLIAQGHADMVAMARPFLADPAFVR 324

Query: 228 TVDE 231
               
Sbjct: 325 KAQA 328


>gi|313836283|gb|EFS73997.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL037PA2]
          Length = 341

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 50/151 (33%), Gaps = 13/151 (8%)

Query: 109 AAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+  AL   +P+  +  +    DD         L +     GV+ +      A   G S
Sbjct: 198 EAVRGALPDDMPLLARLSVTDWRDDGWTVEDSIELSRRFASVGVDLV-----DASSGGNS 252

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                  P    D+   ++ E   +     G +     A ++L     D +M+GRAA ++
Sbjct: 253 SAPIPVAPGYQADLAARVRAEA-SIPTSTVGMIWTSELAEELLTRGCADAIMVGRAALRD 311

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +            P   +     R  +  WR
Sbjct: 312 TNWPLRAAHELGVPNEDAPWHPARF-RGAWR 341


>gi|302834385|ref|XP_002948755.1| hypothetical protein VOLCADRAFT_80405 [Volvox carteri f.
           nagariensis]
 gi|300265946|gb|EFJ50135.1| hypothetical protein VOLCADRAFT_80405 [Volvox carteri f.
           nagariensis]
          Length = 396

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 32/173 (18%), Positives = 58/173 (33%), Gaps = 26/173 (15%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
             E+   +   +N  CP   + E   G  +  +P+++G+    +  A + PV  K    V
Sbjct: 144 RCEEINVDAFEINFSCPHG-LPERRMGMAMGQDPEVLGEVCGWINAAATKPVWAKMTPNV 202

Query: 128 DDQIPAVAL-----RNLVKSIKK----SGVNGIWIHARKAILKGLSP--KDNRKIPNLDY 176
            D     A+        V +I       GVN   +    ++    +P     + +  +  
Sbjct: 203 TDIAYPAAVALAAGCEGVAAINTISCIMGVNLDTLRPEPSVEGYTTPGGYSWKAVKPIAL 262

Query: 177 DIVYEIKKENPDLF------IGLNGGLEDMSQALK--------ILPSVDGVMI 215
                I K     F      +   GG+E  + A +        +     GVMI
Sbjct: 263 AKCTAIAKTIQRDFAGEGKSLSGIGGVETGADAAEFILLGSDTVQQVCTGVMI 315


>gi|238881218|gb|EEQ44856.1| conserved hypothetical protein [Candida albicans WO-1]
          Length = 432

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 69/199 (34%), Gaps = 28/199 (14%)

Query: 61  KLVEAAKIVED---------FGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               AA+   +          G +   +N    P +      +G         + + I +
Sbjct: 204 DFGAAARRAVEISGFDAVEIHGAHGYLINEFYSPISNKRADEYGGSFENRTRFLKEVIDS 263

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHA-----RKAI 159
           +  ++   +PV ++     +   P          L   + + G+  + + +     R+  
Sbjct: 264 VKSSIPNDVPVFLRISAAENSPDPEAWTIEDSKKLADILVEKGIALVDVSSGGNDYRQPP 323

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE-DMSQALKILPS--VDGVMI 215
             G+S K+ R+   +   +   IK+   D L +   GGLE D     K L     D  +I
Sbjct: 324 RSGIS-KELRE--PIHVPLSRAIKQHVGDKLLVSCVGGLEKDPELLNKYLEEGTFDLALI 380

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           GR   +N  ++    + F 
Sbjct: 381 GRGFLRNPGLVWEFADKFG 399


>gi|297563737|ref|YP_003682711.1| NADH:flavin oxidoreductase/NADH oxidase [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
 gi|296848185|gb|ADH70205.1| NADH:flavin oxidoreductase/NADH oxidase [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
          Length = 669

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 25/179 (13%), Positives = 55/179 (30%), Gaps = 17/179 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA++    GY+ + +              +    E  +G           + +  
Sbjct: 143 EDFVRAAELARLAGYDGVEIMGSEGYLINQFVARATNRREDDWGGSFENRMRFPVEIVRR 202

Query: 111 MCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +     V  R+ + D +P       +  L K+++++G     I+      +   P 
Sbjct: 203 VRERVGADFIVVYRLSMLDLVPGGSTFDEVVRLAKAVEEAGAT--IINTGIGWHEARIPT 260

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
               +P   Y  V    +    + +     +     A  IL   D  M+   R    + 
Sbjct: 261 IATSVPRGAYSWVTRRLRGRVSVPLVAVNRINTPEVAEAILAGGDADMVSLARPFLADP 319


>gi|77359841|ref|YP_339416.1| electron acceptor reductase/NADH oxidase, FAD binding, iron-sulfur
           cluster binding site [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874752|emb|CAI85973.1| putative electron acceptor reductase/NADH oxidase, FAD binding,
           iron-sulfur cluster binding site [Pseudoalteromonas
           haloplanktis TAC125]
          Length = 706

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 32/174 (18%), Positives = 71/174 (40%), Gaps = 26/174 (14%)

Query: 73  GYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           G++ I L+     + +  G            +G  +     ++ + IAA+ + +  + P+
Sbjct: 185 GFDAIELHSA--HSYILAGFLSSYYNKRDDEYGGSIENRARLLLEVIAAIRERVGQNFPL 242

Query: 120 TVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGL----SPKDNRKIP 172
            V+      +    + L + +   K ++++GVN + I A   +  G     +P  ++   
Sbjct: 243 WVRLDAHELNTPGGITLEDCIAVSKMVEQAGVNAVSISAYATLTTGSAFTAAPLVHKPAG 302

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAM 225
            LD+     +KKE   + +   G LE D++ A       D + +GR    +  +
Sbjct: 303 FLDWA--AAVKKEV-SIPVIAVGRLEPDIADAAIASGKCDFIAMGRKLLADPEL 353


>gi|292486930|ref|YP_003529800.1| dihydroorotate oxidase-like protein [Erwinia amylovora CFBP1430]
 gi|292900676|ref|YP_003540045.1| dihydroorotate dehydrogenase [Erwinia amylovora ATCC 49946]
 gi|291200524|emb|CBJ47653.1| putative dihydroorotate dehydrogenase [Erwinia amylovora ATCC
           49946]
 gi|291552347|emb|CBA19392.1| hypothetical protein, similar to dihydroorotate oxidase [Erwinia
           amylovora CFBP1430]
          Length = 294

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 66/196 (33%), Gaps = 35/196 (17%)

Query: 35  GDKKNILG-FSTQEKPLALQIGGADISK---LVEAAKIVEDFGYNEINLNVGCPSARVHE 90
            +  ++LG F  Q+ P+   +      +   LV A + + D           CP      
Sbjct: 82  DNWLDLLGQFHQQQLPIIASVHAPSPGETGLLVAAIRHISD-----------CPLELGIS 130

Query: 91  GSFGACLMLN-PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
                    + P+ V     A+ +      +VK  +G         L   V++  + G +
Sbjct: 131 CLHADDFTEDNPERVYAYANAVRQQTDAKFSVKLSLGQ-------YLHERVQAACEGGAS 183

Query: 150 GIWI-----------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
            I +              KA+L G+       I  L    + E+++    + I  +GG++
Sbjct: 184 AITLSDTIPGIAFDLVEGKAVLGGVCGYSGPGIKPLVLAAICELRQRGVSVPIMGSGGVQ 243

Query: 199 DMSQALK-ILPSVDGV 213
                 + +L   + V
Sbjct: 244 SGQDVHEYMLAGAETV 259


>gi|138895903|ref|YP_001126356.1| NADPH dehydrogenase NamA [Geobacillus thermodenitrificans NG80-2]
 gi|167012459|sp|A4IQK7|NAMA_GEOTN RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|134267416|gb|ABO67611.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Geobacillus thermodenitrificans NG80-2]
          Length = 340

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 77/197 (39%), Gaps = 23/197 (11%)

Query: 45  TQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEG 91
            +  P   ++  ADI K V+A    A+  +  G++ I ++            P +   + 
Sbjct: 125 NESSPTPKEMTKADIEKTVQAFQDGARRAKKAGFDVIEIHAAHGYLINEFLSPLSNRRQD 184

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVN 149
            +G         +G+ I A+ +    P+ V+        D +        VK +K+ GV+
Sbjct: 185 EYGGSPENRYHFLGEVIDAVREVWDGPLFVRISASDYHPDGLTVKDYVPYVKRMKEQGVD 244

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            + + +   +   +      ++P  ++     I++E   +  G  G +    QA ++L +
Sbjct: 245 LVDVSSGAVVPARIDVYPGYQVPFAEF-----IRREAG-IPTGAVGLITSGWQAEEVLHN 298

Query: 210 --VDGVMIGRAAYKNSA 224
              D V +GR   +N  
Sbjct: 299 GRADLVFLGRELLRNPY 315


>gi|314971215|gb|EFT15313.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL037PA3]
          Length = 341

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 50/151 (33%), Gaps = 13/151 (8%)

Query: 109 AAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+  AL   +P+  +  +    DD         L +     GV+ +      A   G S
Sbjct: 198 EAVRGALPDDMPLLARLSVTDWRDDGWTVEDSIELSRRFASVGVDLV-----DASSGGNS 252

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                  P    D+   ++ E   +     G +     A ++L     D +M+GRAA ++
Sbjct: 253 SAPIPVAPGYQADLAARVRAEA-SIPTSTVGMIWTSELAEELLTRGCADAIMVGRAALRD 311

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +            P   +     R  +  WR
Sbjct: 312 TNWPLRAAHELGVPNEDAPWHPARF-RGAWR 341


>gi|313674811|ref|YP_004052807.1| 2,4-dienoyl-CoA reductase [Marivirga tractuosa DSM 4126]
 gi|312941509|gb|ADR20699.1| 2,4-dienoyl-CoA reductase [Marivirga tractuosa DSM 4126]
          Length = 674

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 23/128 (17%), Positives = 48/128 (37%), Gaps = 8/128 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   A+ +A+     +  R+ + D IP       +  L K ++K+GV    I+      +
Sbjct: 200 EIAKAIREAVGKEFIIIFRLSMLDLIPNGSTWEEVVQLAKELEKAGVT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P     +P   +  V E  K+  ++ +     +     A +IL     D V + R  
Sbjct: 258 ARVPTIVTSVPRAAFTWVTERMKKEVNIPLITTNRINMPETAEEILSSGQADMVSMARPF 317

Query: 220 YKNSAMLT 227
             +  ++ 
Sbjct: 318 LADPEIIN 325


>gi|255522549|ref|ZP_05389786.1| hypothetical protein LmonocFSL_15284 [Listeria monocytogenes FSL
          J1-175]
          Length = 56

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 1/40 (2%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNI 40
          M   ++  +R   +      L+  EMI    I   + K +
Sbjct: 18 MAGISNSAFRLTVKEF-GAGLVCCEMISDKGIAYRNAKTL 56


>gi|322696553|gb|EFY88343.1| NADH oxidase [Metarhizium acridum CQMa 102]
          Length = 387

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 59/184 (32%), Gaps = 27/184 (14%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG 105
                     AA+ +   GY+ I L             P+       +G  LM    I+ 
Sbjct: 170 FANVTEGFAHAAEYLHRAGYDGIELHGAHGYLLAQFLSPTTNKRTDKYGGSLMNRARIIF 229

Query: 106 DCIAAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   A+   +     V  +       D         +L  ++++SG + + +        
Sbjct: 230 EINDAIRARVPKSFIVSIKLNSVEFQDGGFSTHDCTDLCAALEESGFDFVELSGGTYEAG 289

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFI-GLN-------GGLEDMSQALKILPSVDGV 213
           G   +         + +      E  D+ + GLN       GG    S  +K L +V GV
Sbjct: 290 GFYHRKESTKKREAFFL------EFADIIVPGLNKTKVYVTGGFRTTSGMVKALDTVHGV 343

Query: 214 MIGR 217
            +GR
Sbjct: 344 GLGR 347


>gi|313617256|gb|EFR89728.1| NADPH dehydrogenase [Listeria innocua FSL S4-378]
 gi|313622445|gb|EFR92893.1| NADPH dehydrogenase [Listeria innocua FSL J1-023]
          Length = 338

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P +   E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPISNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D ++IGR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIIGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               E     +   
Sbjct: 317 KEAAETLGETIEAP 330


>gi|308806710|ref|XP_003080666.1| CG3645-PB, isoform B (ISS) [Ostreococcus tauri]
 gi|116059127|emb|CAL54834.1| CG3645-PB, isoform B (ISS) [Ostreococcus tauri]
          Length = 110

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 1/32 (3%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMIVADAI 32
           MVD ++  +R   +      L YT MI A   
Sbjct: 71  MVDQSELAFRELCKRY-GATLGYTPMIHARLF 101


>gi|330446547|ref|ZP_08310199.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328490738|dbj|GAA04696.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 670

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 35/227 (15%), Positives = 74/227 (32%), Gaps = 28/227 (12%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
           LL       +   V+ + +R            E+ +   I         ++A++  + GY
Sbjct: 105 LLHAGRYAMSPFAVSASAIRSPISKFTPSKMSERQILKTI-----DAFAKSAELAREAGY 159

Query: 75  NEINL---------NVGC-PSARVHEGSFGACLMLNPDIV-GDCIAAMCKALSIPVTVKC 123
           + + L            C  S   ++   G+    N      + + A+   +     +  
Sbjct: 160 DGVELMGSEGYLINQFICQRSNCRYDDWGGSY--ENRIRFPLEIVKAVRARVGRDFIIIF 217

Query: 124 RIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           R+     V+       +  L K+++K+GV    ++      +   P    ++P   +  V
Sbjct: 218 RLSMLDLVEQGSTHEEVVILAKALEKAGVT--ILNTGIGWHEARIPTIATQVPRAAFAWV 275

Query: 180 YE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            E +K E     +  N  +     A  IL     D V + R    + 
Sbjct: 276 TEKLKSEVSIPLVTCNR-INTPQVADDILSSGQADMVSMARPFLADP 321


>gi|226305290|ref|YP_002765248.1| oxidoreductase [Rhodococcus erythropolis PR4]
 gi|226184405|dbj|BAH32509.1| putative oxidoreductase [Rhodococcus erythropolis PR4]
          Length = 643

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 66/177 (37%), Gaps = 17/177 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD---------IVGDCIAAMC 112
             EA+ +    G + + L+ G    R     F + L              +V + I+A+ 
Sbjct: 143 FREASAMAIASGMDGVELDAG---PRSILRQFLSGLTNTRHDRYGTDRVALVREIISAVR 199

Query: 113 KALSIPVTVKCRIGVDDQIPAVAL-RNLVKSIKK--SGVNGIWIHARKAILKGLSPK-DN 168
           + +     V  R+  D++     L  +L     +  S +  + +  R  +      + D 
Sbjct: 200 EEVGSDHVVSLRLSCDEEASWAGLTPDLAAGFARDLSPLLDLLVVVRGGLYSSEGYRPDF 259

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
              PN + D+  EIK     + + + G + D++ A   L   + V + RA   +  +
Sbjct: 260 HCPPNFNLDLCREIK-AAVSIPVVVQGSVVDIADARAALEVAEFVEMTRAQIADPDL 315


>gi|255586410|ref|XP_002533851.1| dihydroorotate dehydrogenase, putative [Ricinus communis]
 gi|223526209|gb|EEF28534.1| dihydroorotate dehydrogenase, putative [Ricinus communis]
          Length = 429

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 7/108 (6%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 178 RVEQTGIDAIEVNFSCPHGM-PERKMGAAVGQDCGLLEEICGWVNAKATVPVWAKMTPNI 236

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            D      +    ++  +SG  GI        + G++ K  R  P ++
Sbjct: 237 TD------ITEPARAALRSGCEGISAINTIMSVMGINLKTLRPEPCVE 278


>gi|302188978|ref|ZP_07265651.1| NADH:flavin oxidoreductase/NADH oxidase:FAD-dependent pyridine
           nucleotide-disulphide oxidoreductase [Pseudomonas
           syringae pv. syringae 642]
          Length = 679

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVRRVREAVGAQFIIIFRLSMLDLVEGGSSWEEIVALAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|33599363|ref|NP_886923.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Bordetella bronchiseptica RB50]
 gi|33566959|emb|CAE30872.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Bordetella bronchiseptica RB50]
          Length = 383

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 61/167 (36%), Gaps = 10/167 (5%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG-VDDQIPAVALRN---L 139
           P +   E  +G  L        + +AA+  AL   V +  RI  VD       L +    
Sbjct: 197 PISNQREDQYGGSLENRMRFPLEVVAAVRAALPDEVPLSVRISAVDGMEHGWQLADSIVF 256

Query: 140 VKSIKKSGVNGIWIHARK---AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            + +K  GV+ +   +     +   G  P+  ++ P       + +++E   +     G 
Sbjct: 257 ARELKALGVDLVDCSSGGIQGSATAGKGPQAVKRGPGFQVPFAHAVRQEAG-IATIAVGL 315

Query: 197 LEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           + + +QA  IL     D + IGR A +N        +        S+
Sbjct: 316 IVEPAQAEAILRQEQADLIAIGREALQNPNWPLHARQALGADRDYSA 362


>gi|294498520|ref|YP_003562220.1| NADH-dependent flavin oxidoreductase [Bacillus megaterium QM B1551]
 gi|294348457|gb|ADE68786.1| NADH-dependent flavin oxidoreductase [Bacillus megaterium QM B1551]
          Length = 341

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 24/171 (14%), Positives = 59/171 (34%), Gaps = 29/171 (16%)

Query: 73  GYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMCKALSI--PV 119
           G++ + ++    +  + +             +G        ++ +   A+ +A+    PV
Sbjct: 146 GFDGVEIHGA--NGYILDQFLTDYANKRTDEYGGTTENRVRLLVEVSEAVREAVGKDYPV 203

Query: 120 TV-----KCRIGVDDQIPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
            +     K                ++   + ++G++ I +   +A     S  +      
Sbjct: 204 GIRISQGKINDYYHKWADKEKDAEIIFGQLGQAGLDFIHVTEFEAWQPAFSEGEETGA-- 261

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                +  + K+   L +  NG L D  +A +I+     D + +GR A  N
Sbjct: 262 ----TLAALAKKYSKLPVIANGSLHDPEKAKEIIEKGEADVITLGRGALAN 308


>gi|312137914|ref|YP_004005250.1| oxidoreductase [Rhodococcus equi 103S]
 gi|311887253|emb|CBH46562.1| putative oxidoreductase [Rhodococcus equi 103S]
          Length = 709

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 28/212 (13%), Positives = 61/212 (28%), Gaps = 21/212 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
              EAA  V+  G + + ++       V  G            +G  L     +  + I 
Sbjct: 177 MFAEAAGRVKAAGGDAVEIHAA--HNYVLGGFLSRYSNQRTDEYGGSLENRARLSCEVIR 234

Query: 110 AMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+   +   + V  R+        D +            +++G + I +           
Sbjct: 235 AVKAEVGDSLAVIVRLAGQEYGESDGLTPDEAARAAAMFEEAGADAIHVTGTALNAFANF 294

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                      Y     + K    + +   G +       +++     D V +GR    +
Sbjct: 295 TDGPLPNKVGYYTENAAVVKRAVSIPVITVGRML-PEVGEQMITEGHTDFVAMGRQLLAD 353

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
            A++  +    S  +         V ++FW  
Sbjct: 354 PALVDKLKAGNSEQVRPCINCYVCVQENFWDD 385


>gi|289523643|ref|ZP_06440497.1| 2-enoate reductase [Anaerobaculum hydrogeniformans ATCC BAA-1850]
 gi|289503335|gb|EFD24499.1| 2-enoate reductase [Anaerobaculum hydrogeniformans ATCC BAA-1850]
          Length = 668

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 70/207 (33%), Gaps = 43/207 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDI 103
            +  EAA+I    G++ I ++       +HEG                 +G  L      
Sbjct: 156 ERFAEAAEIAVACGFDGIEIHA------MHEGYLLDQFTMSFFNRRTDKYGGDLEGRLTF 209

Query: 104 VGDCIAAMCKALSI--PVTVKC----------RIGVDDQIPAVALRNL------VKSIKK 145
             + I A+   +    PV ++           + G+  +      R+L       K +++
Sbjct: 210 PIEIIKAIKSKVGKTFPVILRFSVKSYIKGWNKGGLPGEQFEERGRDLKEGLIAAKILEE 269

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G +G    A        +   N        D++ E+KK    + + + G +E    A +
Sbjct: 270 AGYDGFNADAGSYEAWYWAHPPNYMKHGCYIDLIRELKK-VISVPVLMAGRMELPDLAAQ 328

Query: 206 ILPS--VDGVMIGRAAYKNSAMLTTVD 230
            L     D +++GR    +      V 
Sbjct: 329 ALEEKTADVIVLGRGLLADPEWPNKVK 355


>gi|168217066|ref|ZP_02642691.1| NADH oxidase [Clostridium perfringens NCTC 8239]
 gi|182380826|gb|EDT78305.1| NADH oxidase [Clostridium perfringens NCTC 8239]
          Length = 640

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 70/188 (37%), Gaps = 19/188 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG------CPSARVHEG--SFGACLMLNPDIVGDCIAAMC 112
           K+   A   E  G + I ++        C S  +++    +G  L        + + A+ 
Sbjct: 145 KMCNCAIRAEKAGVDIIQIHGDRLVGSLC-STILNKRTDKYGGTLENRTRFALEFVRALK 203

Query: 113 KAL-SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           KA+ ++ +  K  +   ++       +      K ++++GV+ + +              
Sbjct: 204 KAVPNMTIDYKFSVVTPERGKGGVNLDEAPIFAKWLEEAGVDMLHVAQANHTGNMADTIP 263

Query: 168 NRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              +    +  DI  +IKK + ++ +   G + +   A  IL     D + IGR    ++
Sbjct: 264 PMGVQPYGFFVDIAAQIKK-SVNIPVSTVGRIFNPKMAESILESDKADIIGIGRILLADA 322

Query: 224 AMLTTVDE 231
             +  + E
Sbjct: 323 DWVNKIIE 330


>gi|299768864|ref|YP_003730890.1| NADH:flavin oxidoreductase [Acinetobacter sp. DR1]
 gi|298698952|gb|ADI89517.1| NADH:flavin oxidoreductase [Acinetobacter sp. DR1]
          Length = 369

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 55/149 (36%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----- 138
           P A      +G  L     +  + + A+  A+     V  R+   D + ++   +     
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWLESIEHWDVESTV 251

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   + + +      GL    +  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYVHVSSG-----GLHEHQSITIG-AGYQVPFAEQVKKHVSIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + +   A +IL     D + + RA   + 
Sbjct: 306 ITEPEHAEQILENQQADAIGLARAMLYDP 334


>gi|293606206|ref|ZP_06688569.1| xenobiotic reductase A [Achromobacter piechaudii ATCC 43553]
 gi|292815353|gb|EFF74471.1| xenobiotic reductase A [Achromobacter piechaudii ATCC 43553]
          Length = 370

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 69/206 (33%), Gaps = 22/206 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI- 108
            V++A+     G++ I L+            P A   + ++G  L   M  P  V   + 
Sbjct: 159 FVDSARRAIRLGFDAIELHAAHGYLLHQFLSPIANQRQDAYGGSLENRMRFPLEVFQAVR 218

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+  ++++ V V     V+              +K+ G   I + +      G+S +  
Sbjct: 219 EAVPASMALGVRVSATDWVEGGWDLEQTIVFAGQLKERGCEFIDVSSG-----GVSSQQQ 273

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
             + PN       EIK++     I + G + +  QA  IL     D V + R    +   
Sbjct: 274 IPVAPNYQVPFAAEIKRQVGMPTITV-GLITEAQQAEDILAQGQADMVALARGILYDPRW 332

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDF 251
                      +           ++F
Sbjct: 333 PWHAAAQLGGQVAAPHQYWRSQPREF 358


>gi|291559514|emb|CBL38314.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [butyrate-producing bacterium SSC/2]
          Length = 323

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 24/177 (13%), Positives = 60/177 (33%), Gaps = 18/177 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLN---------VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  + A+  ++ G++ + ++            P +      +G  +        + I  
Sbjct: 144 EQFRDCARRAKEAGFDAVEVHGAHGYLIGAFASPFSNKRSDEYGGTIRNRARFAMEIIEN 203

Query: 111 MCKALSI--PV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +      PV   +     V   +     + L + ++++G + I  H  + +       
Sbjct: 204 IKEKCGKDYPVLYRMSAVEYVPGGLEIEESKILARLVEEAGADCI--HCSQGVYASTHVI 261

Query: 167 DNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
               + P   Y       K+  D+ +   G + D+  A  +L     D V + RA+ 
Sbjct: 262 IPPSVVPRAAYVENAAEIKKVVDIPVIAVGRINDVEIAESVLQADKADLVTMARASL 318


>gi|283852112|ref|ZP_06369386.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio sp. FW1012B]
 gi|283572502|gb|EFC20488.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio sp. FW1012B]
          Length = 381

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 31/189 (16%), Positives = 67/189 (35%), Gaps = 20/189 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA +  + G + + ++            P      G++G  L     ++ + I A+ 
Sbjct: 148 FGTAAALCREAGADGVQIHAAHGYGLSQFLSPRTNRRLGAYGGSLANRARLLLEVIWAIR 207

Query: 113 KAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +    PV VK      ++  + A   R +V  +  +G + + +         LSP   
Sbjct: 208 GRVGPDYPVLVKLNSDDFIEGGLSAEESRQVVHWLAGAGADAVELSGGTFDSGRLSPIRP 267

Query: 169 RKIPNLD-----YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
            +I   D      +    +K E   + + L GG+  +  A  ++   + D V + R   +
Sbjct: 268 GRIALPDGEAYYREAARAVKAEGLPIPVLLVGGIRSLPTAEDLVASGAADMVALSRPLIR 327

Query: 222 NSAMLTTVD 230
              ++    
Sbjct: 328 EPGLVARWK 336


>gi|302928314|ref|XP_003054679.1| hypothetical protein NECHADRAFT_75659 [Nectria haematococca mpVI
           77-13-4]
 gi|256735620|gb|EEU48966.1| hypothetical protein NECHADRAFT_75659 [Nectria haematococca mpVI
           77-13-4]
          Length = 412

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 55/147 (37%), Gaps = 13/147 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS---IKKSGV 148
           ++G  +     IV D I A+  A+     V  +    D    + L+  ++    I ++G+
Sbjct: 210 AYGGSVTARAKIVVDIIKAVRAAVPPNFCVGLKFNSADHQSPIELQECLEQTAFIAEAGL 269

Query: 149 NGIWI----HARKAILKGLSPKDNRKIPNLD----YDIVYEIKKENPDLFIGLNGGLEDM 200
           + + +    +    ++ G       +          +   E++ + PD+ + + GG    
Sbjct: 270 DFLEVSGGSYENPTMIMGTEQVAKSEKTAARESFFLEFAREMRAKLPDMPLMVTGGFRTR 329

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAM 225
                 L     D + IGR +  N ++
Sbjct: 330 LGMEAALKEGACDLIGIGRPSVLNPSL 356


>gi|229543359|ref|ZP_04432419.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus coagulans 36D1]
 gi|229327779|gb|EEN93454.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus coagulans 36D1]
          Length = 343

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 28/127 (22%), Positives = 50/127 (39%), Gaps = 10/127 (7%)

Query: 105 GDCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            + IAA    +   +P+ ++   R  VD          L K+ K++GV+   I +     
Sbjct: 194 KEVIAAAKSEMPADMPLIMRISAREYVDGGYGIEESIALSKAYKEAGVDLFHISSGG--- 250

Query: 161 KGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           +G      R   +  Y + +    KE  ++ +   G LED   A  ++     D V +GR
Sbjct: 251 EGHIGAAGRPGTHAAYQVPLARQIKEALNVPVIAVGRLEDPVLANAVIGNEEADLVAVGR 310

Query: 218 AAYKNSA 224
              +N  
Sbjct: 311 GMLRNPY 317


>gi|226355907|ref|YP_002785647.1| NADPH dehydrogenase [Deinococcus deserti VCD115]
 gi|226317897|gb|ACO45893.1| putative NADPH dehydrogenase [Deinococcus deserti VCD115]
          Length = 366

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 60/181 (33%), Gaps = 23/181 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA+  E  G++ + ++            P A      +G         + + + A+
Sbjct: 165 DFASAARRAEMAGFDVVEVHAAHGYLLHQFLSPLANSRTDKYGGSFENRVRFLLEVVRAV 224

Query: 112 CKA--LSIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             +     P+ V+                 +L + ++  GV+ + I        G    +
Sbjct: 225 RASWPSHKPLFVRLSATDWAPGGWDEFQTVDLARLLRYEGVDVLDI------SSGGLTTE 278

Query: 168 NRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            R      Y       +++E PDL +   G +E   +A  +L +   D + +GR    + 
Sbjct: 279 QRITVGSAYQTPFAAMVRREVPDLIVMTVGQIETPERAEGLLLNGDADLIALGRPLLGDP 338

Query: 224 A 224
            
Sbjct: 339 H 339


>gi|317498156|ref|ZP_07956457.1| NADH flavin oxidoreductase/NADH oxidase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894511|gb|EFV16692.1| NADH flavin oxidoreductase/NADH oxidase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 331

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 24/177 (13%), Positives = 60/177 (33%), Gaps = 18/177 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLN---------VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  + A+  ++ G++ + ++            P +      +G  +        + I  
Sbjct: 152 EQFGDCARRAKEAGFDAVEVHGAHGYLIGAFASPFSNKRSDEYGGTIRNRARFAMEIIEN 211

Query: 111 MCKALSI--PV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +      PV   +     V   +     + L + ++++G + I  H  + +       
Sbjct: 212 IKEKCGKDYPVLYRMSAVEYVPGGLEIEESKILARLVEEAGADCI--HCSQGVYASTHVI 269

Query: 167 DNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
               + P   Y       K+  D+ +   G + D+  A  +L     D V + RA+ 
Sbjct: 270 IPPSVVPRAAYVENAAEIKKVVDIPVIAVGRINDVEIAESVLQADKADLVTMARASL 326


>gi|167584524|ref|ZP_02376912.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ubonensis Bu]
          Length = 369

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 63/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AA+   D G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAARRARDIGFEWLELHFAHGYLGQSFFSVHSNHRDDAYGGSADNRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            K     +P+T +  +   D      L     L + +K  G++ + +      +   +P 
Sbjct: 219 RKVWPEHLPLTARLGVIEYDGRDDETLAESIALTQRLKAEGLDLLSV-----SVGFSTPA 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQVPWGPAFLAPVAERVRREAGLPVASAWGIDTPQLAERVVADQQLDLVMVGRAHLADPH 333


>gi|163737638|ref|ZP_02145055.1| hypothetical protein RGBS107_18943 [Phaeobacter gallaeciensis
           BS107]
 gi|161389164|gb|EDQ13516.1| hypothetical protein RGBS107_18943 [Phaeobacter gallaeciensis
           BS107]
          Length = 764

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 70/209 (33%), Gaps = 24/209 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
           + V AA++ E  G++ I L+            P + +   ++G  L   +  P  V D +
Sbjct: 550 EFVAAAQMAERAGFDMIELHAAHGYLISSFISPKSNIRTDAYGGSLENRLRYPLEVFDAM 609

Query: 109 AAMCKALSIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A+  A   P++V+        D+ +       + ++   +G + I + A +   +   P
Sbjct: 610 RAVWPA-DKPMSVRISANDWVGDEGVTPEEAVEIARAFTAAGADIIDVSAGQTSTE-AQP 667

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R       D +         +     G + +   A  IL +   D V +GR    + 
Sbjct: 668 VYGRMFQTPFSDRIRNDA----GIATMAVGNIYEADHANSILMAGRADLVCVGRPHLADP 723

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
              L               P     D+ +
Sbjct: 724 YWTLHEASRIGDRHADWPLPYLAGRDQAW 752


>gi|325123352|gb|ADY82875.1| putative FMN oxidoreductase [Acinetobacter calcoaceticus PHEA-2]
          Length = 369

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 55/149 (36%), Gaps = 15/149 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----- 138
           P A      +G  L     +  + + A+  A+     V  R+   D + ++   +     
Sbjct: 192 PIANQRTDEYGGSLENRMRMTLEVLQAIKLAVPEGYPVGVRLSATDWLESIEHWDVESTV 251

Query: 139 -LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
            L K++++ G   + + +      GL    +  I    Y +   E  K++  + +   G 
Sbjct: 252 GLSKALEQLGAAYVHVSSG-----GLHEHQSITIG-AGYQVPFAEQVKKHVSIPVIAVGL 305

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNS 223
           + +   A +IL     D + + RA   + 
Sbjct: 306 ITEPEHAEQILENQQADAIGLARAMLYDP 334


>gi|255320374|ref|ZP_05361558.1| 2,4-dienoyl coenzyme A reductase [Acinetobacter radioresistens
           SK82]
 gi|262379344|ref|ZP_06072500.1| 2,4-dienoyl-CoA reductase [Acinetobacter radioresistens SH164]
 gi|255302569|gb|EET81802.1| 2,4-dienoyl coenzyme A reductase [Acinetobacter radioresistens
           SK82]
 gi|262298801|gb|EEY86714.1| 2,4-dienoyl-CoA reductase [Acinetobacter radioresistens SH164]
          Length = 676

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 21/126 (16%), Positives = 46/126 (36%), Gaps = 10/126 (7%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     VD+      +  + ++++K+GV  +  +      +
Sbjct: 198 EIVKAIREAVGEKFIICFRLSMLDLVDNGNTMDEVIQIAQALEKAGVTLL--NTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   + D   E+K+      I  N  +     A  IL     D V + R 
Sbjct: 256 ARIPTIVTSVPRAAFVDYTAEVKQYVNIPVIASNR-INMPETAETILAEGKADMVQMARP 314

Query: 219 AYKNSA 224
              +  
Sbjct: 315 FLADPF 320


>gi|16801676|ref|NP_471944.1| NADPH dehydrogenase NamA [Listeria innocua Clip11262]
 gi|68052785|sp|Q928C2|NAMA_LISIN RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|16415151|emb|CAC97841.1| lin2614 [Listeria innocua Clip11262]
          Length = 338

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P +   E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPISNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVEPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D ++IGR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIIGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               E     +   
Sbjct: 317 KEAAETLGETIEAP 330


>gi|307102243|gb|EFN50585.1| hypothetical protein CHLNCDRAFT_55724 [Chlorella variabilis]
          Length = 349

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 7/86 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +  ++ G +   +N  CP     E   G  +  + +++ +    +    +IPV  K    
Sbjct: 6   ERCQEAGVDAFEINFSCPHGM-PERRMGMAMGQDCELLHEVCGWINAKSTIPVWAKMTPN 64

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIW 152
           V D           ++   +G  GI 
Sbjct: 65  VTDISMP------ARTALAAGCEGIA 84


>gi|193076782|gb|ABO11501.2| 24-dienoyl-CoA reductase [Acinetobacter baumannii ATCC 17978]
          Length = 676

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 70/236 (29%), Gaps = 42/236 (17%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+ + ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSSAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINL------------------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            GY+ + +                     C    +         M  P    + + A+  
Sbjct: 155 AGYDGVEIMGSEGYLINQFLSRHVNQRTDCWGGEIENR------MRFP---VEIVKAIRA 205

Query: 114 ALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +  R+     V D      +  + K+++K+GV  +  +      +   P    
Sbjct: 206 KVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARVPTIVT 263

Query: 170 KIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            +P   + D    +K+      I  N  +     A +IL     D + + R    +
Sbjct: 264 SVPRAAFVDYTAHVKQHISIPVIASNR-INMPETAEEILATGKADMIQMARPLLAD 318


>gi|317033813|ref|XP_001395504.2| FMN binding oxidoreductase [Aspergillus niger CBS 513.88]
          Length = 418

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 60/188 (31%), Gaps = 25/188 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V  A+I+   G++ I ++            P + + +  +G        IV + I  +
Sbjct: 169 QFVTCARILARCGFSGIEIHAAHGYLLSQFLSPRSNIRQDEYGGSAERRARIVLEIIQQI 228

Query: 112 CKALSIPVTVKCRIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSPK 166
              +     +  ++   D            ++    +G++ + I         + G   +
Sbjct: 229 RDTVPATFCIGIKLNSADLNTSECEDTMTQIRLFADAGIDFLEISGGSYEDPTMMGRGVR 288

Query: 167 DNRKIPNLD---------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMI 215
           D                  D   + +K+ PDL + L GG          L   + D V I
Sbjct: 289 DETSPGKSQSTESREAFFLDFARQTRKQFPDLILLLTGGFRTRKGIEGALNSGACDLVGI 348

Query: 216 GRAAYKNS 223
           GR A    
Sbjct: 349 GRPAVLKP 356


>gi|284166624|ref|YP_003404903.1| NADH:flavin oxidoreductase/NADH oxidase [Haloterrigena turkmenica
           DSM 5511]
 gi|284016279|gb|ADB62230.1| NADH:flavin oxidoreductase/NADH oxidase [Haloterrigena turkmenica
           DSM 5511]
          Length = 369

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 33/262 (12%), Positives = 73/262 (27%), Gaps = 70/262 (26%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQE-KPLALQI---------------GGADISK- 61
           +A ++ +++ A A+ +G++      +    +P   Q+                  DI   
Sbjct: 99  DAPIFAQLMHAGALSQGNRYTDERLAPSAIRPTGEQLEMYGGSGEFPEPRAATTDDIEDV 158

Query: 62  ---LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------- 98
                 AA+   D  ++ + +                 L+                    
Sbjct: 159 IENFATAAERAVDANFDGVEV-----------HGANGYLLDQFLTTYTNERDDEYGGNVE 207

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP--------AVALRNLVKSIKKSGVNG 150
               +  + + A+  A      V  RI                     + + +  +G + 
Sbjct: 208 NRIRLTAEVLEAVQAATPDEFVVGVRISQSKVNDPDYRWPGGEDDAEVIFERLTDAGADY 267

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS 209
           + +       + ++       P L      E+     D+ +  NG LED   A   +   
Sbjct: 268 LHV-----TEEDVTTPAFESGPTL-----TELADRYGDVPVIANGALEDPDAARATVEEG 317

Query: 210 VDGVMIGRAAYKNSAMLTTVDE 231
            D + + + A  N      V E
Sbjct: 318 ADLITLAKGALANPDWPRRVAE 339


>gi|123492285|ref|XP_001326031.1| Dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
 gi|121908939|gb|EAY13808.1| Dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
          Length = 372

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 18/99 (18%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSF-----------GACLMLNPDIVGDCIAAMCKA 114
            K V   G + + LN+ CP   VH               G  L  +P  V      + +A
Sbjct: 42  VKDVIAAGADALELNLSCP-NEVHGEGGCKGGFDTENKIGMALGTHPVSVKRISQYVKEA 100

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
            ++P  VK    + D I      ++ ++  + G +G+ +
Sbjct: 101 TTVPFFVKLTPNITDPI------DIAQAALEGGADGVAM 133


>gi|86133319|ref|ZP_01051901.1| Dihydroorotate dehydrogenase [Polaribacter sp. MED152]
 gi|85820182|gb|EAQ41329.1| Dihydroorotate dehydrogenase [Polaribacter sp. MED152]
          Length = 344

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 68/180 (37%), Gaps = 30/180 (16%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAM-----CKALSIPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I A       K +  P+ +K    ++
Sbjct: 171 VDYFVLNVSCPNVGSHAK------LNDKDYLIELITACQKLNNTKEVQKPILLKIAPDLN 224

Query: 129 DQIPAVALRNLVKSIKKSGVNGIW----------IHARKAILK--GLSPKDNRKIPNLDY 176
           D    + L  ++  + ++ ++G+           + A +  LK  G      + I N   
Sbjct: 225 D----IQLDEIIALVAETKIDGVIASNTSTTRANLKASEERLKEIGNGGVSGQPIKNQST 280

Query: 177 DIVYEIKK-ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA-AYKNSAMLTTVDEYF 233
            ++  + +  N    I   GG+     AL+ +    D V I     Y+  +++  +++  
Sbjct: 281 KVIRYLAENSNKSFPIIGVGGIHSAEDALEKIEAGADLVQIYTGFIYEGPSLIKKINKAI 340


>gi|94985071|ref|YP_604435.1| NADH:flavin oxidoreductase/NADH oxidase [Deinococcus geothermalis
           DSM 11300]
 gi|94555352|gb|ABF45266.1| NADH:flavin oxidoreductase/NADH oxidase [Deinococcus geothermalis
           DSM 11300]
          Length = 369

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 28/156 (17%), Positives = 53/156 (33%), Gaps = 12/156 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G         + + + A+       +P  V V      +    A     L   ++  GV
Sbjct: 212 YGGSFENRVRFLLEVVRAVRATWPTHLPLLVRVSATDWAEGGWDADQTVQLAGLLRFEGV 271

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + + + +      GL+P        L        +K+E PDL +   G ++  +QA ++L
Sbjct: 272 DVLDVSSG-----GLTPMQQITAGPLYQVPFAARVKQEVPDLRVMAVGMIDTPAQAEQVL 326

Query: 208 PS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
                D V + RA  ++          F    T   
Sbjct: 327 AEGSADLVALARAFLRDPHWPQRAAREFGLRPTLPD 362


>gi|237800377|ref|ZP_04588838.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. oryzae str.
           1_6]
 gi|331023234|gb|EGI03291.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. oryzae str.
           1_6]
          Length = 679

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+I+++G   I  +    
Sbjct: 197 LAVEIVTRVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAIERAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTARLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|134080221|emb|CAK46200.1| unnamed protein product [Aspergillus niger]
          Length = 436

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 60/188 (31%), Gaps = 25/188 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V  A+I+   G++ I ++            P + + +  +G        IV + I  +
Sbjct: 193 QFVTCARILARCGFSGIEIHAAHGYLLSQFLSPRSNIRQDEYGGSAERRARIVLEIIQQI 252

Query: 112 CKALSIPVTVKCRIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSPK 166
              +     +  ++   D            ++    +G++ + I         + G   +
Sbjct: 253 RDTVPATFCIGIKLNSADLNTSECEDTMTQIRLFADAGIDFLEISGGSYEDPTMMGRGVR 312

Query: 167 DNRKIPNLD---------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMI 215
           D                  D   + +K+ PDL + L GG          L   + D V I
Sbjct: 313 DETSPGKSQSTESREAFFLDFARQTRKQFPDLILLLTGGFRTRKGIEGALNSGACDLVGI 372

Query: 216 GRAAYKNS 223
           GR A    
Sbjct: 373 GRPAVLKP 380


>gi|331086106|ref|ZP_08335189.1| hypothetical protein HMPREF0987_01492 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330407029|gb|EGG86534.1| hypothetical protein HMPREF0987_01492 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 641

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 61/178 (34%), Gaps = 15/178 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLN----VGCPSARVHEG---SFGACLMLNPDIVGDCIAAMCK 113
           K+ E AK  +  G + I ++    VG  S+ +       +G  L        + + A+ K
Sbjct: 145 KMCECAKRAQTAGIDAIQVHGDRLVGALSSTILNHRTDKYGGSLENRTRFAIELVTALRK 204

Query: 114 AL-----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           A+        + V         + A       K ++++GV+ + +               
Sbjct: 205 AVPDMIIDYKLAVVTPQRGKGGVIAEEAVIFAKWLEEAGVDMLHVAQANHTGNMADTIPP 264

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             + P   +  +    KE  ++ +   G +   + A  IL     D + +GR    + 
Sbjct: 265 MGVQPYAFFADIAGKVKEQVNIPVSTVGRIVSPALAESILESGKADIIGLGRPLLADP 322


>gi|217979114|ref|YP_002363261.1| dihydroorotate dehydrogenase [Methylocella silvestris BL2]
 gi|217504490|gb|ACK51899.1| dihydroorotate dehydrogenase [Methylocella silvestris BL2]
          Length = 337

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 72/208 (34%), Gaps = 22/208 (10%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP 101
             +  + P+   + G  ++  V+ A+++E  G   + LN+     R+  G          
Sbjct: 96  ARAAVDIPVIASLNGTTVAGWVDYARLIEQAGATALELNI----YRIASGPGVTGGQAEA 151

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----- 156
           D V   + A+   + +PV VK            A  +  + +  +G +G+ +  R     
Sbjct: 152 DCVA-LLEAVRSRVKLPVAVKLHPYFS------AFGDFAQQLDHAGADGLVLFNRLYQPD 204

Query: 157 ----KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVD 211
               +   K  +         L    +  +    P   +    G++   + +K IL   +
Sbjct: 205 IDLLRLAWKNDATLSGAGEIRLGLLWLSVLSGRLPHASLAAGTGVDTAEEVIKYILAGAN 264

Query: 212 GVMIGRAAYKN-SAMLTTVDEYFSNPLT 238
            VM   +  ++    L T+       L+
Sbjct: 265 AVMTASSLLRHGPGHLRTLVSGLETWLS 292


>gi|46124301|ref|XP_386704.1| hypothetical protein FG06528.1 [Gibberella zeae PH-1]
          Length = 452

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 34/215 (15%), Positives = 67/215 (31%), Gaps = 40/215 (18%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGS 92
                 + +++Q         V+AA      G++ I L+            PS       
Sbjct: 209 EHHPTPRSMSIQEINQLKKDFVKAANRAVTAGFDVIELHFAHGYLVSSFLTPSVNKRTDQ 268

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCR---------IGVDDQIPAVALRNLVK 141
           +G        +  + +  +   +   +P+ V+               +         L +
Sbjct: 269 YGGSFENRTRLALELVEEVRAVIPETMPLFVRISATDWLDTNSEYNGESWTVDQAARLTQ 328

Query: 142 SIKKSGVNGIWI-----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNG 195
              + GV+ I +     H  + +  G       +     Y     IKKE  D + +   G
Sbjct: 329 LFAERGVDVIDVSSGGNHPMQKVQGGPG----YQAKFAKY-----IKKEVGDKILVSTVG 379

Query: 196 GLEDMSQALKILPSVDG-----VMIGRAAYKNSAM 225
            ++  + A +I+   DG     V  GR   KN  +
Sbjct: 380 SIKTGTLAEEIISGEDGVPLDLVAAGRMFQKNPGL 414


>gi|300854681|ref|YP_003779665.1| putative NADH:flavin oxidoreductase [Clostridium ljungdahlii DSM
           13528]
 gi|300434796|gb|ADK14563.1| predicted NADH:flavin oxidoreductase [Clostridium ljungdahlii DSM
           13528]
          Length = 658

 Score = 45.2 bits (106), Expect = 0.015,   Method: Composition-based stats.
 Identities = 21/145 (14%), Positives = 47/145 (32%), Gaps = 15/145 (10%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSI--PVTVKC----------RIGVDDQIPAVALRNLV 140
           +G        I+ + I  + + +    PV ++               +D +       + 
Sbjct: 191 YGGSTENRARIIKEIIQGIRQRVGREYPVIMRISADEFLRDSVFPIKEDGLLLDEAVEIC 250

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           K +   G++ I + A        + +           +   +KK   D+ +   G + + 
Sbjct: 251 KYLVPFGLDAINVSAGIYETMNKAWEPTSYPEGWKIYLAEAVKKAV-DVPVFGVGTIRNP 309

Query: 201 SQALKILPS--VDGVMIGRAAYKNS 223
             A K++    VD V I R    + 
Sbjct: 310 DFAEKVISEGKVDCVTIARGLLADP 334


>gi|332285552|ref|YP_004417463.1| putative FMN oxidoreductase [Pusillimonas sp. T7-7]
 gi|330429505|gb|AEC20839.1| putative FMN oxidoreductase [Pusillimonas sp. T7-7]
          Length = 413

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 36/217 (16%), Positives = 77/217 (35%), Gaps = 31/217 (14%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGS 92
             + +E  + +Q          +AAK V+  G++ ++++            P +   E  
Sbjct: 178 ALTPEEIKILVQKY-------AQAAKRVQLAGFDVLDIHAAHGYLLHSFLSPISNTREDE 230

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKC-----RIGVDDQIPAVALRN---LVKS 142
           +G  +      + + I A+        P+ V+      R  +D +    ++ +   L + 
Sbjct: 231 YGGDIQGRMRFLLEAIEAIRSEWPTDKPLFVRISCVDRRKDIDTEQDGWSIEDSFILARE 290

Query: 143 IKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVY-EIKKENPDLFIGLNGGLED 199
           +   GV+ I   +   +A   G+     R+     + + Y E  +   ++     G + D
Sbjct: 291 LAARGVDLIDCSSGGIRAENSGMDYVKKRQSVRKGHQVPYAEAIRAETNIPTMAVGAIID 350

Query: 200 MSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             QA  I+     D V IGR A ++            
Sbjct: 351 GPQAEHIIANGQADLVAIGRQALRDPHWALNAAHSLG 387


>gi|237801385|ref|ZP_04589846.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Pseudomonas syringae pv. oryzae str. 1_6]
 gi|331024244|gb|EGI04301.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Pseudomonas syringae pv. oryzae str. 1_6]
          Length = 370

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 24/135 (17%), Positives = 50/135 (37%), Gaps = 16/135 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  + IA + K A   PV V+   G  +              ++  ++  +GV+ I
Sbjct: 209 QRLRLTFEVIAEVKKVAGQAPVGVRLSQGKVNDFEHKWAGGERDAEIIFGALADAGVDYI 268

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SV 210
            +                  P  +  +V   ++  P + +  NGGL +  +A ++L    
Sbjct: 269 HV--------TEHEACQPAFPQGEASLVKLARRYAPGVALIANGGLHEPDKAQQVLQDGA 320

Query: 211 DGVMIGRAAYKNSAM 225
           D + +G+ A  N  +
Sbjct: 321 DIIAVGKGALANPDL 335


>gi|320450383|ref|YP_004202479.1| dihydroorotate dehydrogenase [Thermus scotoductus SA-01]
 gi|320150552|gb|ADW21930.1| dihydroorotate dehydrogenase [Thermus scotoductus SA-01]
          Length = 332

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 68/205 (33%), Gaps = 25/205 (12%)

Query: 63  VEAAKIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           VE AK++E+ G + I LN    P+     G+    + L+       I A+ +++ IPV V
Sbjct: 117 VEYAKLLEEAGADAIELNLYYIPTDPALSGAEVEAMYLDT------IRAVVESVRIPVAV 170

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---------KAILKGLSPKDNRKIP 172
           K            A  +  K ++ +G   + +  R            +            
Sbjct: 171 KVGHAF------TAFAHFAKQVEATGARALVLFNRFYQPDLDLETLSVVPTLSLSRPYEA 224

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKN-SAMLTTVD 230
            L    +  +      L + L GG+    +A+K +L     VM+  A  +       TV 
Sbjct: 225 LLRIHWIALLYGRVG-LELALTGGVHSGKEAIKGLLSGAQVVMMTSAVLEKGPGHFRTVL 283

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKI 255
           E     +           +     +
Sbjct: 284 EELKAFMEEKEYASVEEMRGVMSYL 308


>gi|150019919|ref|YP_001305273.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosipho melanesiensis
           BI429]
 gi|149792440|gb|ABR29888.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosipho melanesiensis
           BI429]
          Length = 622

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 33/192 (17%), Positives = 70/192 (36%), Gaps = 20/192 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI--------VGDCIAAM 111
               E A   ++ G + I +  G     +    +   +    D           + ++A+
Sbjct: 138 HAFKENALRAQEAGADAIEIQFG--HGYIVHQFYSERMNKRKDEYGKDKLKFAKELLSAI 195

Query: 112 CKALSIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
              + IP+ ++      VD  I    L  +    ++ GV+ I +    A        ++ 
Sbjct: 196 TSEIKIPLFLRISGSEFVDGGITLEELSRIFLLAQEFGVSVIHVGWGNACDSAPWYYNHM 255

Query: 170 KIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA-- 224
            +P  +  D + EI +    L I   G ++   +  K++    +DGV+ GR    +    
Sbjct: 256 SLPLKVMDDKLREI-RNLTSLPIIAVGRMQKDERYKKLMDDKVIDGVVFGRQLIIDPGFP 314

Query: 225 --MLTTVDEYFS 234
             +L+  D+Y  
Sbjct: 315 KKILSNSDDYIR 326


>gi|330466325|ref|YP_004404068.1| NADH:flavin oxidoreductase/NADH oxidase [Verrucosispora maris
           AB-18-032]
 gi|328809296|gb|AEB43468.1| NADH:flavin oxidoreductase/NADH oxidase [Verrucosispora maris
           AB-18-032]
          Length = 355

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 26/146 (17%), Positives = 49/146 (33%), Gaps = 11/146 (7%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKA 158
           +  +   A+  A+   V V  RI   D +      +    L   + ++GV+ +   +  A
Sbjct: 210 LTLEVARAVRAAVGEQVPVLARISATDWVEGGWTVDDSVALAVELARAGVDLVDCSSGGA 269

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
                 P        L      ++++E   +  G  G + +  QA  I+     D V++G
Sbjct: 270 SPNATVPVGRGYQVPL----AAQVRREA-QVPTGAVGLIVEPEQAEAIIADGEADLVLLG 324

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSP 242
           R   +N               T   P
Sbjct: 325 RELLRNPYWPRQAAAKLGAETTWPEP 350


>gi|325522486|gb|EGD01055.1| putative NADH:flavin oxidoreductase [Burkholderia sp. TJI49]
          Length = 411

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 28/208 (13%), Positives = 61/208 (29%), Gaps = 43/208 (20%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             +  +AA+   D G++ + +++G          P       ++G           + + 
Sbjct: 152 ADEFAQAARHARDAGFDAVEIHMGHGYLLSQFLSPLYNRRRDAYGGDAARRAAFPVEVLR 211

Query: 110 AMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHAR----KAILK 161
            +  A+   + V C+IGV + +     A     + + ++  G + + +            
Sbjct: 212 RVLDAVGRDLAVVCKIGVTEGVRGGGTADDACEIARRLEAEGAHLLVLSGGMNVESVWQL 271

Query: 162 GLSPKDNRKIPNLDYDIVYEI-------------------------KKENPDLFIGLNGG 196
             SP       N D  IV                             +    + +   GG
Sbjct: 272 FGSPLPGDARANADNAIVRAAMALQKLTEPKMGAFRELYFLEHSRKVRAAVRMPLAYLGG 331

Query: 197 LEDMSQ-ALKILPSVDGVMIGRAAYKNS 223
           +      A  +    D V + RA   + 
Sbjct: 332 VRSRENVAQAMRDGFDAVALARALVFDP 359


>gi|207108552|ref|ZP_03242714.1| transcriptional regulator, putative [Helicobacter pylori
          HPKX_438_CA4C1]
          Length = 53

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 1/38 (2%)

Query: 2  VDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKN 39
            +TD  +R   +    + +  +EM+ + +++    K 
Sbjct: 15 AGYTDLPFRSVVKKFGVD-VTTSEMVSSHSLVYAFDKT 51


>gi|291519709|emb|CBK74930.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Butyrivibrio
           fibrisolvens 16/4]
          Length = 647

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 25/152 (16%), Positives = 57/152 (37%), Gaps = 9/152 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGV 148
           +G  L     +  + + ++ +A+     ++ R+      +          + K ++   V
Sbjct: 196 YGGSLENRCRLAKEILTSIREAVGPRFPIEFRMSGSEFCEGGYGLEDGIEIAKQLEDY-V 254

Query: 149 NGIWIHARK-AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + + + A       G++     +    +  +  EIKK    + +   GGL D  Q  +I+
Sbjct: 255 DILHVSAGTYQKTFGITHPSMFEEHGRNVFLAAEIKKHV-KVPVATLGGLNDPEQMEEII 313

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
                D V +GRA   +  +   V E   + +
Sbjct: 314 ASGKADIVYMGRALLADPYLPQKVTENRDDEI 345


>gi|254519842|ref|ZP_05131898.1| NADH-dependent flavin dehydrogenase [Clostridium sp. 7_2_43FAA]
 gi|226913591|gb|EEH98792.1| NADH-dependent flavin dehydrogenase [Clostridium sp. 7_2_43FAA]
          Length = 347

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 34/186 (18%), Positives = 61/186 (32%), Gaps = 22/186 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K   A +     G++ I +             P        +G  L        + I A
Sbjct: 143 EKFRLAVRRAVKAGFDAIEIHGAHGYLIHQFHSPLTNKRSDEYGKDLTK---FGSEVIKA 199

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
               +   +P+ ++   R  V+          L K+ +K+G +   I    A  +G    
Sbjct: 200 AKNEMPEDMPLIMRISGREYVEGGYGIEKGIELAKAYQKAGADMFHI---SAGGEGPIAA 256

Query: 167 DNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
             R   +  Y + Y    KE  +  +   G L++   A  ++     D V IGRA ++N 
Sbjct: 257 AGRPGTHAAYQVPYAKAIKEALNTEVIAVGKLDEPELANAVIGNEEADLVAIGRAMFRNP 316

Query: 224 AMLTTV 229
                 
Sbjct: 317 YWALQA 322


>gi|126641119|ref|YP_001084103.1| 24-dienoyl-CoA reductase [Acinetobacter baumannii ATCC 17978]
          Length = 653

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 70/236 (29%), Gaps = 42/236 (17%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+ + ++            EK +   I         + A I + 
Sbjct: 77  LMQILHAGRYGYQPFVVSSSAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 131

Query: 72  FGYNEINL------------------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            GY+ + +                     C    +         M  P    + + A+  
Sbjct: 132 AGYDGVEIMGSEGYLINQFLSRHVNQRTDCWGGEIENR------MRFP---VEIVKAIRA 182

Query: 114 ALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +  R+     V D      +  + K+++K+GV  +  +      +   P    
Sbjct: 183 KVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARVPTIVT 240

Query: 170 KIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            +P   + D    +K+      I  N  +     A +IL     D + + R    +
Sbjct: 241 SVPRAAFVDYTAHVKQHISIPVIASNR-INMPETAEEILATGKADMIQMARPLLAD 295


>gi|303248447|ref|ZP_07334706.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio
           fructosovorans JJ]
 gi|302490158|gb|EFL50077.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio
           fructosovorans JJ]
          Length = 372

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 59/153 (38%), Gaps = 11/153 (7%)

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK--CRIGVDDQIPAVALRNLVKSIK 144
             G++G  L     ++ + I A+   +    PV  K  C   ++  + A   R +V  + 
Sbjct: 181 RSGAYGGALANRARLLLETIGAIRGRIGNDYPVLAKINCEDFIEGGMTAEEGRQVVSWLA 240

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE-----IKKENPDLFIGLNGGLED 199
            +G + + +         LSP    KI   D +  Y      IK +   + + L GG+  
Sbjct: 241 LAGADAVELSGGTLDSGKLSPVRPGKIAIPDGEAYYREQAAAIKTKGLGIPLILVGGIRS 300

Query: 200 MSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
           +  A  I+   + D V + R   +   ++   +
Sbjct: 301 LETANGIVASGTADMVALSRPLIREPGLVARWE 333


>gi|264677457|ref|YP_003277363.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           CNB-2]
 gi|262207969|gb|ACY32067.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           CNB-2]
          Length = 671

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 23/184 (12%), Positives = 56/184 (30%), Gaps = 17/184 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V  A +  + GY+ + +  G          P        +G             +  +  
Sbjct: 147 VRCACLAREAGYDGVEVMGGEGYLINQFLAPLTNFRTDEWGGDAAGRSRFALRIVQGIRA 206

Query: 114 ALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+ + D +        + +L + ++ +GVN    +      +   P    
Sbjct: 207 AVPENFVISFRLSLMDLVEHGSHWKEVLDLARQLEAAGVNLF--NTSVGWHEARIPTIAM 264

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
            +P   +    E  K+   + +  +  +     A  ++     D V + R    + A + 
Sbjct: 265 MVPRAAFSWAAEQLKQAVSVPVAASNRINTPEVADDLIAQGHADMVAMARPFLADPAFVR 324

Query: 228 TVDE 231
               
Sbjct: 325 KAQA 328


>gi|257875188|ref|ZP_05654841.1| oxidoreductase [Enterococcus casseliflavus EC20]
 gi|257809354|gb|EEV38174.1| oxidoreductase [Enterococcus casseliflavus EC20]
          Length = 370

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 33/228 (14%), Positives = 68/228 (29%), Gaps = 26/228 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A +     G++ + L             P +      +G  L      +   +  
Sbjct: 147 ENFKKATERAIKAGFDGVELHGANTYLIQQFFSPHSNRRSDEWGGSLEHRYRFIEKLVDE 206

Query: 111 MCKALS----IPVTVKCRIGVDD-QIPAVALRN---LVKSIKKSGVNGIWIHARKAILKG 162
           + + +         V  R   ++ + P +   +   LV  + + G++ + I       K 
Sbjct: 207 VLETVDQSGVKEFIVGYRFSPEEFEEPGIRFEDTLFLVDQLAEKGLDYLHISLADYTRKS 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           +S     K        VYE  K    + +   G +     A  +L   D V +GRA   +
Sbjct: 267 ISKAYQAKSMLA---YVYE--KIAQRVPLIGVGDVRTSKDAAGLLEHADFVAVGRALLID 321

Query: 223 SA----MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
                 +L   D      ++     +  +    W  +   M D     
Sbjct: 322 PHWGQKVLDGQDALIRTTVSTYEREELVLQNGVWGFMENMMPDRLNEE 369


>gi|134293525|ref|YP_001117261.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia vietnamiensis
           G4]
 gi|134136682|gb|ABO57796.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia vietnamiensis
           G4]
          Length = 369

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 64/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V +A+   D G+  + L+      G     VH       +G         + D + A+
Sbjct: 159 DFVASAQRARDLGFEWLELHFAHGYLGQSFFSVHSNQRDDEYGGSAENRGRFLVDTLKAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +     +P+T +  +   D      L     LV+ +K+ G++ + +      +   +P 
Sbjct: 219 RRVWPEHLPLTARLGVIEYDGRDEETLAESIALVQRMKQEGLDMLSV-----SVGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       + +  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPIAQRVRRETGLPVSSAWGIDTPQLANRVVAEQQLDLVMVGRAHLADPH 333


>gi|332307374|ref|YP_004435225.1| NADH:flavin oxidoreductase/NADH oxidase [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332174703|gb|AEE23957.1| NADH:flavin oxidoreductase/NADH oxidase [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 682

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 44/124 (35%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D          +  L K I+K+G     I+      +
Sbjct: 208 EVVRRVREAVGDKFIIIYRLSMLDLVEGGSTYEEVVELGKLIEKAGAT--IINTGIGWHE 265

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    +E+  + +  +  +     A ++L   D  M+   R  
Sbjct: 266 ARIPTIATKVPRAAFTWVTAKFRESLSIPVITSNRINTPEVAEQVLARGDADMVSMARPF 325

Query: 220 YKNS 223
             + 
Sbjct: 326 LADP 329


>gi|118469808|ref|YP_887645.1| oxidoreductase, FAD/FMN-binding [Mycobacterium smegmatis str. MC2
           155]
 gi|118171095|gb|ABK71991.1| oxidoreductase, FAD/FMN-binding [Mycobacterium smegmatis str. MC2
           155]
          Length = 372

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 61/181 (33%), Gaps = 20/181 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA    + GY+ + ++            P A      +G  L            A
Sbjct: 172 DRFAQAAVNAHEAGYDVVEVHAAHGYLLHQFLSPLANQRVDEYGGSLQNRLRFPLAVARA 231

Query: 111 MCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  AL    PV ++                    K +++  ++ + + +   ++    P 
Sbjct: 232 VRSALPADKPVFIRISTNDWTGGGFDFAQAVEFAKCLRELDIDLLDVTSGGLLVDAPPPP 291

Query: 167 DNRKIPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
                P L+ +    I+++   L   +G  G    + +A+     VD V +GR   ++  
Sbjct: 292 R----PALNVEPADRIRQDVGILVAPVGQIGDPNVLEEAISR-TKVDAVFLGRPLLRDPY 346

Query: 225 M 225
           +
Sbjct: 347 L 347


>gi|83584365|gb|ABC24957.1| plastid dihydroorotate dehydrogenase [Prototheca wickerhamii]
          Length = 262

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
             E+ G +   +N  CP     E   G  +  +P+++ +  + +    +IPV  K    +
Sbjct: 150 RCEEAGVDGFEINFSCPHGM-PERQMGMAMGQDPELLSEVCSWVNALATIPVWAKMTPNI 208

Query: 128 DD 129
            D
Sbjct: 209 TD 210


>gi|224826150|ref|ZP_03699253.1| NADH:flavin oxidoreductase/NADH oxidase [Lutiella nitroferrum 2002]
 gi|224601787|gb|EEG07967.1| NADH:flavin oxidoreductase/NADH oxidase [Lutiella nitroferrum 2002]
          Length = 673

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 68/236 (28%), Gaps = 37/236 (15%)

Query: 22  LYTEMIVADA------ILRGDKKNILGFSTQEKPLALQIGGADI------------SKLV 63
           L TE + A+       IL   + +         PL   I                 +   
Sbjct: 87  LVTEAVHAEGGKICLQILHSGRYSFQEQCVSASPLIAPINFYKPRELSEDDIWRTIADFA 146

Query: 64  EAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
             A++ +  GY+ + +              +       +G           + + A+  A
Sbjct: 147 RCARLAQQAGYDGVEVMGSEGYLINQFIARATNQRSDGWGGSFDNRIRFAIETVKAVRAA 206

Query: 115 LSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                 +  R+     V D      +  L K+I+K+G   I  +      +   P     
Sbjct: 207 TGPNFIIIYRLSMLDLVQDGSTWDEVVQLAKAIEKAGATLI--NTGIGWHEARVPTIATM 264

Query: 171 IPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           +P   +  V  ++  +     I  N  +     A +IL     D V + R    + 
Sbjct: 265 VPRGGFAWVTKKLMGQVGIPLITTNR-INTPEVAEEILASGCADMVSMARPFLADP 319


>gi|269218847|ref|ZP_06162701.1| xenobiotic reductase A [Actinomyces sp. oral taxon 848 str. F0332]
 gi|269211958|gb|EEZ78298.1| xenobiotic reductase A [Actinomyces sp. oral taxon 848 str. F0332]
          Length = 362

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 50/149 (33%), Gaps = 14/149 (9%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNL 139
           P + V    +G         +   + A+  A+   V    R+   D     I + A    
Sbjct: 194 PLSNVRTDEYGGSEENRRRFLIRIVDAVRSAIGDKVLC-VRLSATDWTEGGIDSEATCRT 252

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF--IGLNGGL 197
            +++   GV+ + + +      GL P      P     +  ++K+        +   G +
Sbjct: 253 AEALVAHGVDVLHVSSG-----GLLPASIPVGPGYQLPLAADVKRAVSGSQAKVVGVGLI 307

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSA 224
               QA + L     D V IGR A  +  
Sbjct: 308 SSGEQAEQALVTGRCDAVAIGRVALTDPY 336


>gi|325846512|ref|ZP_08169427.1| dihydroorotate dehydrogenase 1B [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481270|gb|EGC84311.1| dihydroorotate dehydrogenase 1B [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 153

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 27/130 (20%), Positives = 47/130 (36%), Gaps = 20/130 (15%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN---------- 149
           +P    + I  + K     + VK    V D      ++  VK  + SG +          
Sbjct: 6   DPMKACEVIEKVRKTTKKVLMVKLSPNVGD------IKEFVKIAENSGADCISLVNTFNA 59

Query: 150 -GIWIHARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
             I +  +KA+ +   +      I  +   +VYE  K    L I   GG+ +    L+ I
Sbjct: 60  MAIDVDNKKAVFENKTAGLSGPCIKPIALRMVYEASKAT-SLPIIGMGGISNYKDCLEFI 118

Query: 207 LPSVDGVMIG 216
           +     V +G
Sbjct: 119 MAGASAVQVG 128


>gi|70986758|ref|XP_748868.1| NADH-dependent flavin oxidoreductase [Aspergillus fumigatus Af293]
 gi|66846498|gb|EAL86830.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           fumigatus Af293]
 gi|159123361|gb|EDP48481.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           fumigatus A1163]
          Length = 422

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 30/203 (14%), Positives = 68/203 (33%), Gaps = 24/203 (11%)

Query: 63  VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A K     G + + + N           P+A      +G        +  +       
Sbjct: 199 VAATKRAIAAGADFVEIHNAHGYLLSSFLSPAANNRTDQYGGSFENRIRLSLEIAQLTRD 258

Query: 114 ALS--IPVTVKC-------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+   +PV ++            +    +       + + K G   +   +   +L   +
Sbjct: 259 AVGPHVPVFLRISASDWCEETLPEQSWKSEDTVRFAQELVKQGAVDLIDISSGGVL---A 315

Query: 165 PKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
            +  +  P         +KK   D L +   G + +  QA +IL    +D  ++GR   K
Sbjct: 316 QQKIKSGPAFQVPFAVAVKKAVGDKLLVAAVGAITNGKQANQILEEQDIDVALVGRGFQK 375

Query: 222 NSAMLTTVDEYFSNPLTGSSPIK 244
           +  +  T  ++    ++ ++ I+
Sbjct: 376 DPGLAWTFAQHLGVEISMANQIR 398


>gi|297830412|ref|XP_002883088.1| dihydroorotate dehydrogenase family protein [Arabidopsis lyrata
           subsp. lyrata]
 gi|297328928|gb|EFH59347.1| dihydroorotate dehydrogenase family protein [Arabidopsis lyrata
           subsp. lyrata]
          Length = 426

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 31/171 (18%), Positives = 57/171 (33%), Gaps = 24/171 (14%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 176 RVEQTGVDALEINFSCPHGM-PERRMGAAVGQDCVLLDEVCGWINAKATVPVWAKMTPNI 234

Query: 128 DD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDNRKIPN 173
            D         +     +  +   +   GV+   +     +       G S K  R I  
Sbjct: 235 TDITEPARVSLKSGCEGISAINTIMSVMGVDMKTLRPEPCVEGYSTPGGYSYKAVRPIAL 294

Query: 174 LDYDIVYE-IKKENPDLF-IGLNGGLED-MSQALKILPS------VDGVMI 215
                + + +K E  +   +   GG+E     A  IL          GVM+
Sbjct: 295 AKVMNIAKMMKSEFSENHSLSGIGGVETGYDAAEFILLGSNTVQVCTGVMM 345


>gi|225351744|ref|ZP_03742767.1| hypothetical protein BIFPSEUDO_03341 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225158088|gb|EEG71371.1| hypothetical protein BIFPSEUDO_03341 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 378

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 74/209 (35%), Gaps = 23/209 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA    D G++ + ++            P     E  +G        I+ + + A
Sbjct: 177 DQFRDAAWRAYDIGFDAVEIHAAHGYLLSQFLDPLINEREDEYGGSFDNRIRILVEVVDA 236

Query: 111 MCKALS--IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +   +PV V+                 NL K +KK GV+ + +        G+ P 
Sbjct: 237 VRSVIPDTMPVLVRVSATDWAAGGWDLDQTVNLAKVLKKHGVDLMDVSTG-----GMIPG 291

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +   DY +   E  +   ++     G +    QA KIL   + D + IGRAA ++ 
Sbjct: 292 VTIPVKP-DYQVPFAEQVRSRAEIPTTAVGLITKPKQAKKILKSGAADAIEIGRAALRDP 350

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
                       P T  +P + +  +  +
Sbjct: 351 NWPLRAAHKLGIP-TEDAPYQPQYVRGAY 378


>gi|56459187|ref|YP_154468.1| xenobiotic reductase A [Idiomarina loihiensis L2TR]
 gi|56178197|gb|AAV80919.1| Xenobiotic reductase A [Idiomarina loihiensis L2TR]
          Length = 362

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 59/177 (33%), Gaps = 15/177 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AA+   D G+  + L+              A      +G         + + + A+
Sbjct: 159 DFVAAAERARDLGFEWLELHFAHGYLGQSFFSAHANQRTDEYGGSFENRARFLVETVRAV 218

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    + P+T +  +   D      ++  VK  +     G+        +   +P  N 
Sbjct: 219 KQVWPDNFPLTARFGVIEFDGNDEQQMQESVKLTQLLKAEGLDF--LNVSISFSTPNANI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                    + E  ++  D+ +    G++    A   +    +D VM+GRA  +N  
Sbjct: 277 PWGPGFMAPIAERIRKEVDIPVASAWGIDLPQLAEHTIAQGQLDLVMVGRAHLENPH 333


>gi|311105736|ref|YP_003978589.1| NADH:flavin oxidoreductase/NADH oxidase family protein 1
           [Achromobacter xylosoxidans A8]
 gi|310760425|gb|ADP15874.1| NADH:flavin oxidoreductase/NADH oxidase family protein 1
           [Achromobacter xylosoxidans A8]
          Length = 382

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 27/202 (13%), Positives = 60/202 (29%), Gaps = 28/202 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKL------VEAAKIVEDFGYNEINL---------NVGCPS 85
           + F   E P  +    +D            AA+  ++ G++ + +               
Sbjct: 144 MTFYRGEGPYRMPEAMSDEDIAEAVEGYAHAARRAQEAGFDGVEIHGANGYLLDQFLTRY 203

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-----LRNLV 140
             + E  +G  L     +  + I A+ +++     V  R                  +  
Sbjct: 204 TNLREDRYGGSLDNRLRLTVEVIQAVRQSVGQHFVVGVRSSQGKVNDFTHKWEGGQADAA 263

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +  +  G   I        L     +  R   + +   +  + + +  + +  NG L D 
Sbjct: 264 QIYRTLGAQPID------YLHTTEFEAWRPAFDDEGPSLAALARRHVPVPVLANGSLHDP 317

Query: 201 --SQALKILPSVDGVMIGRAAY 220
             +  +      D V +GR A 
Sbjct: 318 MAAGGMMTRQEADFVSLGRGAL 339


>gi|237653151|ref|YP_002889465.1| NADH:flavin oxidoreductase/NADH oxidase [Thauera sp. MZ1T]
 gi|237624398|gb|ACR01088.1| NADH:flavin oxidoreductase/NADH oxidase [Thauera sp. MZ1T]
          Length = 365

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 26/140 (18%), Positives = 52/140 (37%), Gaps = 12/140 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKS 146
           ++G         + + + A+      ++P+TV+  +   D      L     L +S K+ 
Sbjct: 199 AYGGSFENRSRFLIETVRAVRAVWPENLPLTVRFGVIEYDGRDEETLAESIELARSFKRE 258

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM--SQAL 204
           G++ + +    + LK   P             V E  +    L +    G+++   + A 
Sbjct: 259 GLDFLNVSVGFSTLKARVP-----WGPAFLAPVAERVRREAGLPVAAAWGIDNPVIADAC 313

Query: 205 KILPSVDGVMIGRAAYKNSA 224
                +D VM+GRA   N  
Sbjct: 314 VRDGQLDLVMVGRAHLANPH 333


>gi|154496874|ref|ZP_02035570.1| hypothetical protein BACCAP_01167 [Bacteroides capillosus ATCC
           29799]
 gi|150273832|gb|EDN00945.1| hypothetical protein BACCAP_01167 [Bacteroides capillosus ATCC
           29799]
          Length = 650

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 63/164 (38%), Gaps = 12/164 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGI 151
           +G           + I A+  A+   + V+ R+  ++ IP  + +   ++ IKK+     
Sbjct: 195 YGGSFENRCRFAMEVIRAVRNAVGRDMGVEMRVSAEEVIPGGIEIDETIQFIKKAEPYVD 254

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEI-----KKENPDLFIGLNGGLEDMSQALKI 206
            +H     L G +      +P   +   + +      +   ++ I + G ++ M QA +I
Sbjct: 255 LVHV-SRGLIGEAAYSFYSMPPYYHPYCHNVPFAEKIRSQVNVPIAVVGSIKTMEQAEEI 313

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
           +     D V + R    +     T+ +  ++    + P    +D
Sbjct: 314 IAKGAADVVAMARQLLADP---DTIKKAMADQPEKTRPCLRCMD 354


>gi|307106864|gb|EFN55109.1| hypothetical protein CHLNCDRAFT_31559 [Chlorella variabilis]
          Length = 429

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 31/86 (36%), Gaps = 7/86 (8%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +  ++ G +   +N  CP     E   G  +  + +++ +    +    +IPV  K    
Sbjct: 177 ERCQEAGVDAFEINFSCPHGM-PERRMGMAMGQDCELLHEVCGWINAKSTIPVWAKMTPN 235

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIW 152
           V D           ++   +G  GI 
Sbjct: 236 VTDISMP------ARTALAAGCEGIA 255


>gi|317122852|ref|YP_004102855.1| dihydroorotate oxidase B, catalytic subunit [Thermaerobacter
           marianensis DSM 12885]
 gi|315592832|gb|ADU52128.1| dihydroorotate oxidase B, catalytic subunit [Thermaerobacter
           marianensis DSM 12885]
          Length = 336

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 62/173 (35%), Gaps = 22/173 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E P+   + G  + + VE A+ ++  G + + LN+ CP    +  + G     +P +   
Sbjct: 120 EVPVIANVVGKTVDEYVEVARRLDAAGVDALELNLSCP----NVKAGGLEFGRDPQVAAS 175

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------H 154
            + A+ +    P+ VK             L  +  ++ ++G  G+ +             
Sbjct: 176 LVRAVRRVTRRPLLVKLSPEGGR------LLEVAAAVMEAGAGGLSLINTLRGAAVDVDA 229

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            R  +           I  +    ++E+ +      +G+ G +     A  +L
Sbjct: 230 ERPVLATVGGGLSGPAIRPVAVYWIWEVYRHLRAPILGMGGVVLGRDAAELML 282


>gi|217963427|ref|YP_002349105.1| NADPH dehydrogenase (xenobiotic reductase) [Listeria monocytogenes
           HCC23]
 gi|254766774|sp|B8DBP0|NAMA_LISMH RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|217332697|gb|ACK38491.1| NADPH dehydrogenase (xenobiotic reductase) [Listeria monocytogenes
           HCC23]
 gi|307571998|emb|CAR85177.1| NADH:flavin oxidoreductase [Listeria monocytogenes L99]
          Length = 338

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               E     + G 
Sbjct: 317 KDAAEQLGETIEGP 330


>gi|302872484|ref|YP_003841120.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302575343|gb|ADL43134.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 381

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 42/111 (37%), Gaps = 17/111 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I        +E +K++E  G + I LN+ CP         G  +M   D++ + +
Sbjct: 100 PVIASINCYTDDAWLEYSKLMEQAGADAIELNLSCPH--------GVHIMSGMDVIEEMV 151

Query: 109 AA---MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                +   + IPV  K      +             + ++G +G+ +  R
Sbjct: 152 HTTKLVKSNVKIPVIPKMTPQSTNPGSD------ALRLDQAGADGLVMFNR 196


>gi|229073527|ref|ZP_04206654.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus cereus F65185]
 gi|228709601|gb|EEL61648.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus cereus F65185]
          Length = 315

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 23/161 (14%), Positives = 51/161 (31%), Gaps = 37/161 (22%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPA------VALRNLVKSI 143
            +G  ++       + + A  +A+    P+  +          A        L   ++ +
Sbjct: 139 GYGGDMVARTRFAAEIVEACRQAVGPDFPIIFRLSQWKTQDFTAKLASTPELLDEFLRPL 198

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL------ 197
             +GV+      R+  L      +  ++    +     +KK      I + G +      
Sbjct: 199 VDAGVDIFHCSTRRFWL---PEFEGSELNLAGW-----VKKLTGKPTITV-GSVGLDNEF 249

Query: 198 ------------EDMSQALKILPS--VDGVMIGRAAYKNSA 224
                        ++ + + +L    VD V IGRA   + A
Sbjct: 250 LSAFLEGKGANNTNIDKLIDMLEQEEVDLVAIGRALLADPA 290


>gi|213029658|ref|ZP_03344105.1| tRNA-dihydrouridine synthase B [Salmonella enterica subsp.
          enterica serovar Typhi str. 404ty]
          Length = 57

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 34 RGDKKNILGFSTQEKP--LALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
              K+ L     ++P    +QI G+D  ++ +AA+I  + G   I++N+G
Sbjct: 2  WESDKSRLRMVHVDEPGIRTVQIAGSDPVEMADAARINVESGAQIIDINMG 52


>gi|158319410|ref|YP_001511917.1| NADH:flavin oxidoreductase/NADH oxidase [Alkaliphilus oremlandii
           OhILAs]
 gi|158139609|gb|ABW17921.1| NADH:flavin oxidoreductase/NADH oxidase [Alkaliphilus oremlandii
           OhILAs]
          Length = 352

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 25/174 (14%), Positives = 64/174 (36%), Gaps = 15/174 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAAM 111
             ++AA   E  G++ I L+           S++V++    +G  L     +  +    +
Sbjct: 144 DFIDAAIRAEKAGFDGIELHGAHSYLLTQFFSSKVNQRTDEYGGSLENGMRMATEIFKGI 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            + +     +  R+G ++     ++  + K  +  G++ +  H            +  + 
Sbjct: 204 KEKVQDDFVIGIRMGSNENDLQTSI-EMAKKFEALGMDYL--HISTGFDNTPIETELPED 260

Query: 172 PNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              ++ +    K KE  ++ +     ++       ++    VD V IGRA   +
Sbjct: 261 FPCNWIVYGATKIKEAVNIPVVAVNSIKTAEHIQYLVDGDLVDFVAIGRAQLAD 314


>gi|239993893|ref|ZP_04714417.1| 2,4-dienoyl-CoA reductase [Alteromonas macleodii ATCC 27126]
          Length = 680

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 45/132 (34%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D          +  L K I+K+G     I+      +
Sbjct: 205 EVVRRVREAVGKNFIIIYRLSMLDLVEGGSTYDEVVQLGKEIEKAGAT--IINTGIGWHE 262

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    +E   + +  +  +     A ++L   D  M+   R  
Sbjct: 263 ARIPTIATKVPRAAFTWVTAKFREALSIPVITSNRINTPEVAEEVLSRGDADMVSMARPF 322

Query: 220 YKNSAMLTTVDE 231
             +   +    +
Sbjct: 323 LADPDFVRKAQQ 334


>gi|218778157|ref|YP_002429475.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218759541|gb|ACL02007.1| Predicted NADH:flavin oxidoreductase/NADH oxidase
           [Desulfatibacillum alkenivorans AK-01]
          Length = 640

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 25/144 (17%), Positives = 49/144 (34%), Gaps = 14/144 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G         V + +  + K +    PV   +     +        +  ++  +  +GV
Sbjct: 185 YGGDFKNRARFVIEVVEEVRKRVGDDYPVLLRISAEEYIKHGYTVDEVLTILPELIGAGV 244

Query: 149 NGIWIHARKAILKGLSPKDNRKIP---NLDYDIVYEIK-KENPDLFIGLNGGLEDMSQAL 204
           + +      ++    SP      P      ++I    K KE  D+ +   G   D  +A 
Sbjct: 245 DVLH----ASVGTHGSPGGITSAPVEYEAGWNIWRAKKIKEAVDIPVIGVGRYTDPREAD 300

Query: 205 KILPSVDGVMI--GRAAYKNSAML 226
           K + + D  MI  GR    +   L
Sbjct: 301 KAIANGDADMIAFGRQVLADPDFL 324


>gi|322831716|ref|YP_004211743.1| NADH:flavin oxidoreductase/NADH oxidase [Rahnella sp. Y9602]
 gi|321166917|gb|ADW72616.1| NADH:flavin oxidoreductase/NADH oxidase [Rahnella sp. Y9602]
          Length = 365

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 62/182 (34%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AAK   D G+  + L+       + +             +G         + +   
Sbjct: 159 DFVAAAKRARDAGFEWLELHFA--HGYLAQSFFSVHSNTRTDEYGGDFAGRSRFLIETFD 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           A+      ++P+T +  +   D      L     L + +++ G++ + +    +  +   
Sbjct: 217 AVNAVWPKNLPITARFGVIEYDGRDEETLAESIELTRILREKGLDMLNVSVGFSTWEAQI 276

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           P     +  +       ++ E   L +  + G+     A + +    +D VMIGRA   N
Sbjct: 277 PWGAGFLAPVS----RRVRAEAG-LPVASSWGVASADVAERCISEQDMDLVMIGRAMLAN 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|293401322|ref|ZP_06645466.1| NADPH dehydrogenase [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305448|gb|EFE46693.1| NADPH dehydrogenase [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 333

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 21/136 (15%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 103 IVGDCIAAMCKALSIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           ++ + I  +       V V+       +D +    ++++V++I+  G   I + +     
Sbjct: 184 LLKEIITGVRSTFEKDVIVRISAEEYEEDGLHIADMKDIVEAIESCGAAAISVSSGGLNK 243

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
             +      +IP           K+   L +   G +    +   IL     D V++GR 
Sbjct: 244 HPIQTYPMYQIPYA------RAIKQMTSLPVMGVGLITKEEEIETILAQEDCDYVLLGRK 297

Query: 219 AYKNSAMLTTVDEYFS 234
             ++   L +  + F 
Sbjct: 298 LLRDPYFLLSWQDAFG 313


>gi|3873404|gb|AAC77480.1| unknown [Rhodococcus erythropolis]
          Length = 615

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 82/227 (36%), Gaps = 30/227 (13%)

Query: 19  NALLYTEM----IVADAILRGDKKNILGFSTQ-----EKPLALQIGGADISKLVEAAKIV 69
             L +T M      + ++L G  +     + +      +P   Q+         EA+ + 
Sbjct: 67  AGLGHTGMQGSSAYSQSVLWGPSRVADPVTRELPMAMGQPEIDQLMAG----FREASAMA 122

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPD---------IVGDCIAAMCKALSIPVT 120
              G + + L+ G    R     F + L              +V + I+A+ + +     
Sbjct: 123 IASGMDGVELDAG---PRSILRQFLSGLTNTRQDRYGTDRVALVREIISAVREEVGSDHV 179

Query: 121 VKCRIGVDDQIPAVAL-RNLVKSIKK--SGVNGIWIHARKAILKGLSPK-DNRKIPNLDY 176
           V  R+  D++ P   L  +L     +  S +  + +  R  +      + D    PN + 
Sbjct: 180 VSLRLSCDEEAPWAGLTPDLAAGFARDLSPLLDLLVVVRGGLYSSEGYRPDFHCPPNFNL 239

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS 223
           D+  EIK     + + + G + D++ A   L   + V + RA   + 
Sbjct: 240 DLCREIK-AAVSIPVVVQGSVVDIADARAALGVAEFVEMTRAQIADP 285


>gi|197302391|ref|ZP_03167447.1| hypothetical protein RUMLAC_01119 [Ruminococcus lactaris ATCC
           29176]
 gi|197298512|gb|EDY33056.1| hypothetical protein RUMLAC_01119 [Ruminococcus lactaris ATCC
           29176]
          Length = 646

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 64/178 (35%), Gaps = 21/178 (11%)

Query: 65  AAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIV-GDCIAAMCKA 114
           AA +  D G++ I ++            P        +G     N      + + A+   
Sbjct: 154 AAGVASDAGFDAIEIHAHAGYLIDQFMSPVWNKRTDEYGGS-PENCARFPKEIVEAIKSV 212

Query: 115 L--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK-AILKGLSPKDNR 169
           +  S+PV  +       +          L+K ++ +GV+   I A     L  + P    
Sbjct: 213 VGDSMPVIFRISLDHRFEGGRTLEDSMKLLKVLEAAGVDAFDIDAGCYETLDYIFPPSYL 272

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
               + Y +  E +K      I  N G  +   A++++   +VD V +GRA   +  +
Sbjct: 273 GESCMSY-VCAEARKAVSVPLI--NAGSHNPDSAVELIESGNVDFVNMGRALIADPYL 327


>gi|269955127|ref|YP_003324916.1| NADH:flavin oxidoreductase/NADH oxidase [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269303808|gb|ACZ29358.1| NADH:flavin oxidoreductase/NADH oxidase [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 351

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 59/166 (35%), Gaps = 15/166 (9%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           ++G        ++ + + A+  A     P+ V+     D     +   ++  ++K   V+
Sbjct: 197 AYGGTPENRARLLAETVTAVRDAWPDGKPLLVRVSAT-DWTEGGLEPDDVAAALKGLDVD 255

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-- 207
            + +     +   +      ++P+          ++   L  G  G +    QA  IL  
Sbjct: 256 LVDVSTGGLLPAPVPAAPGYQVPHA------RRVRDVSGLPAGAVGLITSAEQAETILRD 309

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            + D V++GRAA ++              +  +     + ++  WR
Sbjct: 310 GAADAVLVGRAALRDPHWPLRAAHELGADVAWA----KQYERGAWR 351


>gi|291456178|ref|ZP_06595568.1| xenobiotic reductase A [Bifidobacterium breve DSM 20213]
 gi|291381455|gb|EFE88973.1| xenobiotic reductase A [Bifidobacterium breve DSM 20213]
          Length = 434

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 56/160 (35%), Gaps = 21/160 (13%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG------VDDQIPAVALRNLVKSIK 144
           +G  L      + + + A+   +   +PV V+           D     +      K +K
Sbjct: 275 YGGDLNGRARFLLEIVDAVRGVVPDTLPVLVRISATDWAAGGWDLDQTILVS----KMLK 330

Query: 145 KSGVNGIWIHARKAILKGLSP-KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           + GV+ + +     +     P K N ++P        E  +   D+ +   G +    QA
Sbjct: 331 EHGVDLVDVSTGGIVAGVSIPVKPNYQVPFA------EQVRAKADVPVTAVGLITKPKQA 384

Query: 204 LKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            KIL     D V IGRAA ++             P+  + 
Sbjct: 385 EKILIHGEADAVEIGRAALRDPNWPLRAAHKLGVPVAEAP 424


>gi|222081032|ref|YP_002540395.1| 2,4-dienoyl-CoA reductase (NADPH) protein [Agrobacterium
           radiobacter K84]
 gi|221725711|gb|ACM28800.1| 2,4-dienoyl-CoA reductase (NADPH) protein [Agrobacterium
           radiobacter K84]
          Length = 386

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 58/188 (30%), Gaps = 21/188 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
            + VE A   E  G++ + L+       +               +G        ++ + +
Sbjct: 154 DEFVETALSAEQAGFDGVELHAA--QGFLISSFLSPRLNRRTDQWGGSFENRIRLLMEVL 211

Query: 109 AAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIW-IHARKAILKGL 163
             +   ++    V   +  D+  P          L   ++ +G + I  + +    LK  
Sbjct: 212 RRVRAVVAPSFIVGVHLISDELAPGGWAVSEAIRLSPLLEDAGADFIMPVVSTFETLKAP 271

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
                   P   +     IKK    + +  NG ++       +L     D V + R  + 
Sbjct: 272 ENAGLMNTPFFQHSATAAIKKAVG-IPVFTNGRIDTPEAIDTVLAAGEADAVGLARPLFA 330

Query: 222 NSAMLTTV 229
           +   +  V
Sbjct: 331 DPDWVAKV 338


>gi|312879979|ref|ZP_07739779.1| dihydroorotate oxidase B, catalytic subunit [Aminomonas paucivorans
           DSM 12260]
 gi|310783270|gb|EFQ23668.1| dihydroorotate oxidase B, catalytic subunit [Aminomonas paucivorans
           DSM 12260]
          Length = 317

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 33/210 (15%), Positives = 64/210 (30%), Gaps = 30/210 (14%)

Query: 35  GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIV--EDFGYNEINLNVGCPSARVHEGS 92
             ++ + G +   K + L +   D+  L  A + +         + LN+ CP    +   
Sbjct: 81  WMRETLPGLAGTGKRIVLNLACEDLDSLGRAVEALGGASDRIAVLELNLSCP----NVDG 136

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
            GA     P+ V   +          + VK      D           ++ +  G +G+ 
Sbjct: 137 GGAAWGEAPEGVRAALGIARPGWKGILWVKLTPQAGD------FVATARAAEAGGADGVV 190

Query: 153 IH----ARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-------NPDLFIGLNGGLEDMS 201
           +          L+   P+  R +  L    V+ +             + I   GG+    
Sbjct: 191 VANTWLGAALDLQTGLPRFARSVAGLSGPAVFPLSLRLVFQTYGRVGIPIVGCGGVRSAE 250

Query: 202 QALKI-LPSVDGVMIGRAAYKNSAMLTTVD 230
            AL + L     V +G            +D
Sbjct: 251 DALCMVLAGASAVEVGT------WHFRKLD 274


>gi|323701049|gb|ADY00191.1| hypothetical protein [Streptomyces autolyticus]
          Length = 359

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 21/157 (13%), Positives = 48/157 (30%), Gaps = 12/157 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG---VDDQIPAVALRNLVKSIKKS 146
            +G           + + A+       +P+  +        ++   A     L   +K  
Sbjct: 201 GYGGSFENRARFALEVVDAVRAVWPEELPLFFRISATDWLEENGWTADDTVRLAALLKDH 260

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ + + +         P +    P         +++E   L +   G + +  QA KI
Sbjct: 261 GVDLLDVSSGGNAAGVRIPVE----PGYQVPFAARVRRETG-LPVAAVGLITEAEQAEKI 315

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +     D V++GR   ++              +    
Sbjct: 316 VTNGEADAVLLGRELLRDPYFARHAAAELGGRVHSPD 352


>gi|312135772|ref|YP_004003110.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           owensensis OL]
 gi|311775823|gb|ADQ05310.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           owensensis OL]
          Length = 381

 Score = 44.8 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 42/113 (37%), Gaps = 21/113 (18%)

Query: 49  PLALQI--GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           P+   I     D     E +K++E  G + I LN+ CP         G  +M   D++ +
Sbjct: 100 PVIASINCYTDDAWI--EYSKLMEQAGADAIELNLSCPH--------GVHIMSGMDVIEE 149

Query: 107 CIAA---MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            +     +   + IPV  K      +             + ++G +G+ +  R
Sbjct: 150 MVHTTKLVKSNVKIPVIPKMTPQSTNPGSD------ALRLDQAGADGLVMFNR 196


>gi|296333467|ref|ZP_06875920.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305675027|ref|YP_003866699.1| NADPH-dependent flavin oxidoreductase [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296149665|gb|EFG90561.1| NADPH dehydrogenase NamA [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305413271|gb|ADM38390.1| NADPH-dependent flavin oxidoreductase [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 338

 Score = 44.8 bits (105), Expect = 0.020,   Method: Composition-based stats.
 Identities = 31/193 (16%), Positives = 66/193 (34%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA   ++ G++ I ++            P +      +G         + + I  +
Sbjct: 145 EFKQAAVRAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREVIDEV 204

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P  V V      D  +         K +K+ GV+ I   +   +       D  
Sbjct: 205 KQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVQ-----ADIN 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P        +I+++  D+  G  G + + S A +IL +   D + IGR   ++     
Sbjct: 260 VFPGYQVSFAEKIREQA-DMATGAVGMITNGSMAEEILQNGRADLIFIGRELLRDPFFAR 318

Query: 228 TVDEYFSNPLTGS 240
           T  +  +  +   
Sbjct: 319 TAAKQLNTEIPAP 331


>gi|148549449|ref|YP_001269551.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
 gi|148513507|gb|ABQ80367.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
          Length = 368

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 26/158 (16%), Positives = 55/158 (34%), Gaps = 11/158 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G+C      +  + + A+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGSCFENRIRLTLEVVEAVRKAWPAELPLFVRVSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + ++  GV+ I + +      G S                E  ++  ++  G  G + +
Sbjct: 250 ARRLRSLGVDLIDVSSG-----GTSVNAEIPTGPGYQTRFAERVRKESEIATGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +QA  IL     D + + R   ++       D+    
Sbjct: 305 PAQAEHILRTGQADIIFLARELLRDPYWPLHADDDLGG 342


>gi|33595082|ref|NP_882725.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Bordetella parapertussis 12822]
 gi|33565159|emb|CAE35955.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Bordetella parapertussis]
          Length = 383

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 31/167 (18%), Positives = 59/167 (35%), Gaps = 10/167 (5%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----L 139
           P +   E  +G  L        + +AA+  AL   V +  RI   D +            
Sbjct: 197 PISNQREDLYGGSLENRMRFPLEVVAAVRAALPDEVPLSVRISAVDGVEHGWQLADSIVF 256

Query: 140 VKSIKKSGVNGIWIHARK---AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            + +K  GV+ +   +     +   G  P+  ++ P       + +++E   +     G 
Sbjct: 257 ARELKALGVDLVDCSSGGIQGSATAGKGPQAVKRGPGFQVPFAHAVRQEAG-IATIAVGL 315

Query: 197 LEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           + + +QA  IL     D + IGR A +N        +        S+
Sbjct: 316 IVEPAQAEAILRQEQADLIAIGREALQNPNWPLHARQALGADRDYSA 362


>gi|320101037|ref|YP_004176629.1| dihydroorotate dehydrogenase family protein [Desulfurococcus
           mucosus DSM 2162]
 gi|319753389|gb|ADV65147.1| dihydroorotate dehydrogenase family protein [Desulfurococcus
           mucosus DSM 2162]
          Length = 403

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 27/142 (19%), Positives = 50/142 (35%), Gaps = 22/142 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
           V +   A+ +++SIP+  K      +      +  LVK ++K GV+GI            
Sbjct: 169 VVEAAKALRESVSIPIFPKLSPFTPN------IPELVKELEKVGVDGIVATNTIGPALHI 222

Query: 153 -IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGL-EDMSQALKILP 208
            +     I+ G         P L    +  + +   N  L +   GG+   +      + 
Sbjct: 223 DVETGMPIVGGPYGYGWMSGPALKPLALAVVSQAALNTKLPVIGVGGISRGLDVIEYFMA 282

Query: 209 SVDGVMIGRAAY-KNSAMLTTV 229
               V I  AA  +   + T +
Sbjct: 283 GASAVQICTAALVEGPGVFTRI 304


>gi|255659970|ref|ZP_05405379.1| NADH:flavin oxidoreductase [Mitsuokella multacida DSM 20544]
 gi|260847721|gb|EEX67728.1| NADH:flavin oxidoreductase [Mitsuokella multacida DSM 20544]
          Length = 368

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 80/210 (38%), Gaps = 26/210 (12%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC--- 83
           +VA  + +G     L  + +E     Q         +EAAK ++  G + + L+      
Sbjct: 117 VVARPLKKGRHARAL--TVEEIHHIEQ-------CFIEAAKRLQSAGCDGVQLHAAHSYL 167

Query: 84  ------PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--PVTVKCRIGVDDQIPAVA 135
                 P+    E  +G  +     +V + I  +  A     PV +K  +    +     
Sbjct: 168 LSRFIDPTFNQREDEYGGTIENRFRMVEEIICGIHGACGKDFPVLIKVNVDTKAEDAEGY 227

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLN 194
            R++V  ++++   G+ +        G+   +  K   L Y   V  +  E PD+ + L 
Sbjct: 228 HRDMVWLLRRAKALGVELV----EFSGVDFINLPKTATLYYLPQVKRLSAEVPDMPLSLV 283

Query: 195 GGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           GG+  ++    ++   ++ V +GR+     
Sbjct: 284 GGVRSLADMEAVIKAGIECVSLGRSLIAEP 313


>gi|73670283|ref|YP_306298.1| NADH peroxidase [Methanosarcina barkeri str. Fusaro]
 gi|72397445|gb|AAZ71718.1| NADH peroxidase [Methanosarcina barkeri str. Fusaro]
          Length = 365

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 28/192 (14%), Positives = 60/192 (31%), Gaps = 28/192 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
               +A    +  G++ +   + C    +               +G  +     IV + +
Sbjct: 143 EAFTKATVRAKKAGFDGV--QLHCAHGFLLSNFISPYTNRRTDRWGGSVENRTRIVTEIV 200

Query: 109 AAMCKAL--SIPVTVK---------CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             + +    S P+ VK         C    +  +       + K ++K+GV  I +    
Sbjct: 201 RRIKEEAGDSFPILVKMNATDGFQPCCSKAELGLDIFQAVEIAKLLEKAGVCAIEVSGGI 260

Query: 158 AILKGL--SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
               G+      N       +    +  K   ++ + L GG+  +S    +L +    MI
Sbjct: 261 GEAGGVTIRTAINTPAKEAYFRDCSKAIKSAVNIPVILVGGIRSLSVINDLLENGSADMI 320

Query: 216 --GRAAYKNSAM 225
              RA      +
Sbjct: 321 SMSRAFISEPDI 332


>gi|71737925|ref|YP_274502.1| FAD/FMN-binding oxidoreductase [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71558478|gb|AAZ37689.1| oxidoreductase, FAD/FMN-binding [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 370

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 26/140 (18%), Positives = 54/140 (38%), Gaps = 16/140 (11%)

Query: 94  GACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKS 146
           G  ++    +  + IA++ K A   PV V+   G  +              ++  ++  +
Sbjct: 204 GGEVVQRLRLTLEVIASVKKVAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFATLADA 263

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ I +   +A                   +V   ++  P + +  NGGL D  +A ++
Sbjct: 264 GVDYIHVTEHEAW--------QPAFAQGKASLVELARRYAPGVALIANGGLHDPQKADQV 315

Query: 207 L-PSVDGVMIGRAAYKNSAM 225
           L    D + +G+ A  N  +
Sbjct: 316 LHQGADIIAVGKGALANPDL 335


>gi|134055669|emb|CAK44043.1| unnamed protein product [Aspergillus niger]
          Length = 440

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 64/189 (33%), Gaps = 29/189 (15%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EA K     G++ I ++            P++      +G        +  + +    + 
Sbjct: 213 EAVKRAVRAGFDAIEIHGAHGYLIHEFLSPASNKRTDEYGGSFENRIRLALELVDISRQH 272

Query: 115 L--SIPVTVKCR-------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +  ++P+  +         +  +    A     L + + + GV+ + + +      G  P
Sbjct: 273 MTPNMPLFFRVSGTDWLEHLENEPSWDASQTVRLAEVLVEHGVDVLDVSSG-----GNDP 327

Query: 166 KDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN 222
           +   K          +++K+   D L +   G +    QA  +L   +D V+IGR   KN
Sbjct: 328 RQQIKGGPAYQSPYAFQVKEALGDRLLVASVGAITSGPQANDLLNAGLDMVLIGRMFQKN 387

Query: 223 S---AMLTT 228
                    
Sbjct: 388 PGLVWTFAE 396


>gi|110003923|emb|CAK98263.1| probable trna-dihydrouridine synthase c-terminal truncated
          protein [Spiroplasma citri]
          Length = 40

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)

Query: 1  MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRG 35
          M   T+  +R     L    L+Y EM+   AIL+ 
Sbjct: 1  MAGITNEAFRIICHEL-GAGLVYAEMVSDKAILQK 34


>gi|325527792|gb|EGD05064.1| NADPH2 dehydrogenase [Burkholderia sp. TJI49]
          Length = 369

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 64/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AAK   D G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAAKRARDIGFEWLELHFAHGYLGQSFFSVHSNRRDDEYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            K     +P+T +  +   D      L     L + +K+ G++ + +      +   +P 
Sbjct: 219 RKVWPEHLPLTARFGVIEYDGRDDETLAESIALTQRLKQEGLDMLSV-----SVGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPVAERVRREAGLPVSSAWGIDTPQLADRVVAEQQLDLVMVGRAHLADPH 333


>gi|299756166|ref|XP_001829138.2| NADH:flavin oxidoreductase/NADH oxidase [Coprinopsis cinerea
           okayama7#130]
 gi|298411553|gb|EAU92773.2| NADH:flavin oxidoreductase/NADH oxidase [Coprinopsis cinerea
           okayama7#130]
          Length = 403

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 28/147 (19%), Positives = 47/147 (31%), Gaps = 19/147 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL-SIPVTVKC---------RIGVDDQIPAVALRN---L 139
           +G         +   + A  KA    P+ V+            G D +     L     L
Sbjct: 238 YGGSFENRIRFLLRVVKATRKAWPDKPLFVRVSASDWAEGPEQGDDGEWRYWGLEQSKLL 297

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + + + GV+ + + +         P     +P        EIKK  PDL +   G +  
Sbjct: 298 AQRLHEEGVDLLDVSSGGLWANQKVPA----VPGYQVPFAAEIKKAVPDLVVSAVGLITQ 353

Query: 200 MSQALKILPS--VDGVMIGRAAYKNSA 224
             QA   L     D + + R   +N  
Sbjct: 354 PEQAEGYLQEGKADVIFLARELMRNPH 380


>gi|193215112|ref|YP_001996311.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chloroherpeton
           thalassium ATCC 35110]
 gi|226700300|sp|B3QRR1|HIS4_CHLT3 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|193088589|gb|ACF13864.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Chloroherpeton thalassium ATCC 35110]
          Length = 262

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 22/98 (22%), Positives = 42/98 (42%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++    +K     I +    A L G            ++D + +I  +  D+ I + GG+
Sbjct: 34  DMAIIWRKQNAKLIHVVDLDAALTG---------KPENFDKIKQIV-DTLDIPIEIGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
                A + L   V  V+IG AA KN ++++ + E + 
Sbjct: 84  RTAEDAARYLDIGVYRVVIGSAAVKNPSLVSQLIEKYG 121


>gi|307320021|ref|ZP_07599443.1| NADH:flavin oxidoreductase/NADH oxidase [Sinorhizobium meliloti
           AK83]
 gi|306894398|gb|EFN25162.1| NADH:flavin oxidoreductase/NADH oxidase [Sinorhizobium meliloti
           AK83]
          Length = 370

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 19/126 (15%), Positives = 46/126 (36%), Gaps = 9/126 (7%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +  + + A+  A+   V +  R+               +   + G   ++    ++    
Sbjct: 216 LSLEVLKAVRAAIGPSVPLGLRLSQ--GKVNDFRHKWAER--EQGAARVFEALAESPADF 271

Query: 163 LSPKDNRKIPNL----DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
               +           +  +V   ++  P LF+  NG L D+++A +++    D + +GR
Sbjct: 272 AHVTEFEAWRPAFEGGEISLVSLARRHAPRLFLIANGSLHDLARAEQVMESGADMIALGR 331

Query: 218 AAYKNS 223
            A  N 
Sbjct: 332 GALVNP 337


>gi|295695354|ref|YP_003588592.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus tusciae DSM 2912]
 gi|295410956|gb|ADG05448.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus tusciae DSM 2912]
          Length = 342

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 21/130 (16%), Positives = 47/130 (36%), Gaps = 8/130 (6%)

Query: 106 DCIAAMCKAL--SIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + I A  + L  S+P+ ++      VD            +  +++GV+   + +      
Sbjct: 195 EVIKAARRVLPESMPIFMRISAVEYVDGGYGLEQSVEFCRRYREAGVDLFHVSSGGEGPI 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
           G       + P    +  + I++    + +   G L+D   A +++     D V +GR  
Sbjct: 255 GSGGVPGAE-PGYQVEYAHTIRRALG-VPVIAVGKLQDPRLANRVIEEEKADLVAVGRGM 312

Query: 220 YKNSAMLTTV 229
            +N       
Sbjct: 313 LRNPYWANEA 322


>gi|329937199|ref|ZP_08286798.1| oxidoreductase [Streptomyces griseoaurantiacus M045]
 gi|329303480|gb|EGG47366.1| oxidoreductase [Streptomyces griseoaurantiacus M045]
          Length = 368

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 24/157 (15%), Positives = 46/157 (29%), Gaps = 12/157 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI-----PAVALRNLVKSIKKS 146
            +G        +  +   A+  A+     +  R+   D +      A     L   +K+ 
Sbjct: 203 GYGGPFENRARLAVEVADAVRAAVPEETALFFRVSATDWVEPEGWTADDTVRLAALLKEH 262

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ + +     +     P +    P         +++E   L     G + +  QA +I
Sbjct: 263 GVDLLHVSTGGNVPHARIPAE----PGYQVPFAARVRRETG-LPSAAVGLITEPEQAERI 317

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           L     D V +GR    N                   
Sbjct: 318 LAEGEADAVALGRELLLNPYWPREAALALGEEHPFPP 354


>gi|255721889|ref|XP_002545879.1| hypothetical protein CTRG_00660 [Candida tropicalis MYA-3404]
 gi|240136368|gb|EER35921.1| hypothetical protein CTRG_00660 [Candida tropicalis MYA-3404]
          Length = 429

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 28/187 (14%), Positives = 64/187 (34%), Gaps = 22/187 (11%)

Query: 61  KLVEAAKIVED-FGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              EAA+   +  G++ I ++            P +   +  +G         + + I +
Sbjct: 204 DFGEAARRAVEISGFDVIEIHGAHGYLINEFYSPISNKRDDEYGGSFENRTRFLKEVIDS 263

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK--G 162
           +   +    PV ++     +   P          L   + + G++ + + +     +   
Sbjct: 264 VKSKIPKDTPVFLRISAAENSPDPEAWTIEDSKKLADILIEKGIDLLDVSSGGNDYRQAA 323

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE-DMSQALKILPS--VDGVMIGRA 218
            S     K   +   +   IK+   D L +   GG + D  +  + L     D V+IGR 
Sbjct: 324 RSGIAKEKTEPIHLPLSRAIKEHVGDKLLVSSVGGYDHDAEEDNRYLEEGVFDLVLIGRG 383

Query: 219 AYKNSAM 225
             ++  +
Sbjct: 384 FLRDPGL 390


>gi|226943796|ref|YP_002798869.1| Dihydroorotate dehydrogenase [Azotobacter vinelandii DJ]
 gi|226718723|gb|ACO77894.1| Dihydroorotate dehydrogenase [Azotobacter vinelandii DJ]
          Length = 332

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 69/184 (37%), Gaps = 38/184 (20%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP------- 101
           P+   + GA  +     A ++E+ G + + LN+               + ++P       
Sbjct: 101 PVIASLNGASANHWTHYAALLEEAGADALELNL-------------YFVPVDPLEPGTAV 147

Query: 102 -DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--- 157
                + +AA+ + + IPV VK            A+ N+   + + G +G+ I  R    
Sbjct: 148 EQRYLEVLAAVRRTVKIPVAVKMPPYFS------AIGNMASRLLEGGADGLVIFNRYLQP 201

Query: 158 ----AILKGLSPKDNRKIPNLDYD--IVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSV 210
                 L+ +S  +      +      +  +        +  +GG+ED+ Q +K +L   
Sbjct: 202 DIDLQRLQPISTLELSSPGEMRLPLLWIALLAGRVKG-SLAASGGVEDVEQVVKYLLAGA 260

Query: 211 DGVM 214
           D VM
Sbjct: 261 DTVM 264


>gi|78043937|ref|YP_359935.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|91206921|sp|Q3AD49|HIS4_CARHZ RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|77996052|gb|ABB14951.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 243

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 39/93 (41%), Gaps = 11/93 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L    +++G   I +        G S          +++++ EI K N  + + + GG+
Sbjct: 34  ELALKYQEAGARLIHVVDLDRAFTGESE---------NFEVIAEIIK-NVSIPVQVGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
            D+    +++   V  V++G  A  N  +L  +
Sbjct: 84  RDIESFRELIDLGVSRVIVGTIAVTNPELLEEM 116


>gi|98753|pir||B37844 probable oxidoreductase (EC 1.-.-.-) baiC - Eubacterium sp
          Length = 540

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEGS------FGACLMLNPDIVGDCIAA 110
            +    A++    G++ +  +      P   +  G       +G           + + A
Sbjct: 135 EEFGRGARMAVQAGFDAVEFHAAHSYLPHEFLSPGMNKRTDEYGGSFENRCRFCYEVVQA 194

Query: 111 MCKAL--SIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +   +   +P  +        ++  +    +   +    + GV+   +    A     S 
Sbjct: 195 IRSNIPDDMPFFMRADCIDELMEQTMTEEEIVTFINKCAELGVDVADLSRGNAT----SF 250

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
               ++P  +       + +Y IKK+  ++ +   G +     A K++     D V IGR
Sbjct: 251 ATVYEVPPFNLAHGFNIENIYNIKKQI-NIPVMGVGRINTGEMANKVIEEGKFDLVGIGR 309

Query: 218 AAYKNSAMLTTVDE 231
           A   +   +T V E
Sbjct: 310 AQLADPNWITKVRE 323


>gi|302893989|ref|XP_003045875.1| hypothetical protein NECHADRAFT_57931 [Nectria haematococca mpVI
           77-13-4]
 gi|256726802|gb|EEU40162.1| hypothetical protein NECHADRAFT_57931 [Nectria haematococca mpVI
           77-13-4]
          Length = 416

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 29/195 (14%), Positives = 57/195 (29%), Gaps = 28/195 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             A K     G++ I ++            P++      +G        ++ + +     
Sbjct: 203 AAAVKRALVVGFDAIEIHAAHGYLLNSFLSPASNQRTDEYGGSFENRTRLLIEIVQLTRT 262

Query: 114 ALSIPVTVKCRIGVDD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            +     +  R+   D         Q        L K +   GV+ + I        GL 
Sbjct: 263 IVPADFPLLVRMPGTDYLDFDPSLPQWHIEEAGKLGKILAGEGVDLLDISGG-----GLD 317

Query: 165 PKDNRKIPN-LDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            +                +KK      + +   G +    QA   L   SVD V++GR  
Sbjct: 318 SRQKITAGPGYQVPWAAAVKKAVEGTGIQVTAVGSITSGKQAQGYLSDGSVDAVLVGRGF 377

Query: 220 YKNSAMLTTVDEYFS 234
            K+  ++    +   
Sbjct: 378 LKDPNLVWHWADELD 392


>gi|154487390|ref|ZP_02028797.1| hypothetical protein BIFADO_01242 [Bifidobacterium adolescentis
           L2-32]
 gi|154083908|gb|EDN82953.1| hypothetical protein BIFADO_01242 [Bifidobacterium adolescentis
           L2-32]
          Length = 320

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 75/218 (34%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       E    ++D   + + +NV CP    +  + G  +  +P  +   I 
Sbjct: 113 VIANVAGHCDDDYAEVVSKLDDSPADMLEINVSCP----NVSAGGMSVGTDPVALSRLIT 168

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            + K     + VK    V D           ++  +SG + +            I   + 
Sbjct: 169 RLRKLTDKKMIVKLTPNVTDITVP------ARAAVESGADALSLINTLLGMRINIRTGEP 222

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           ++  +        +  +    V+ ++   P++ I   GG++    AL+ L    + V +G
Sbjct: 223 VITHVTGGVSGPAVLPVGLAAVWRVRAALPEIPIIGIGGIDSGETALEYLYAGANAVEVG 282

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA         V     + L     +  ++ K + WR
Sbjct: 283 AAALFEPTAPLRVARELDDLLDERPELADKLAKGETWR 320


>gi|294495318|ref|YP_003541811.1| NADH:flavin oxidoreductase/NADH oxidase [Methanohalophilus mahii
           DSM 5219]
 gi|292666317|gb|ADE36166.1| NADH:flavin oxidoreductase/NADH oxidase [Methanohalophilus mahii
           DSM 5219]
          Length = 361

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 63/188 (33%), Gaps = 28/188 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCI 108
              V A +  ++ G++ +   + C           P     E  +G  +     I+ + +
Sbjct: 142 DDFVNATRRAKEAGFDGV--QLHCAHGFLLSSFISPYTNRREDKWGGSVKNRTRIITEIV 199

Query: 109 AAMCKALSI--PVTVKCRIGV-------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + +S   PV VK               + A     +   ++K+GV  I +      
Sbjct: 200 RRIREDVSADYPVMVKLNATDGFDIYSGHISLDAPECVEIAALLEKAGVCAIEVSGGIVE 259

Query: 160 LKGL--SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
              +   P  + +     +    ++ K+   + + L GG+   +   ++L  V   M+  
Sbjct: 260 AGSVMSQPGVDTEEKEAYFRRYAKMIKDTVSIPVILVGGIRTRAVMDEVLR-VYADMV-- 316

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 317 -SMSRPFI 323


>gi|307313440|ref|ZP_07593062.1| NADH:flavin oxidoreductase/NADH oxidase [Sinorhizobium meliloti
           BL225C]
 gi|306899266|gb|EFN29902.1| NADH:flavin oxidoreductase/NADH oxidase [Sinorhizobium meliloti
           BL225C]
          Length = 370

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 19/126 (15%), Positives = 46/126 (36%), Gaps = 9/126 (7%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +  + + A+  A+   V +  R+               +   + G   ++    ++    
Sbjct: 216 LSLEVLKAVRAAIGPSVPLGLRLSQ--GKVNDFRHKWAER--EQGAARVFEALAESPADF 271

Query: 163 LSPKDNRKIPNL----DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
               +           +  +V   ++  P LF+  NG L D+++A +++    D + +GR
Sbjct: 272 AHVTEFEAWRPAFEGGEISLVSLARRHAPRLFLIANGSLHDLARAEQVMESGADMIALGR 331

Query: 218 AAYKNS 223
            A  N 
Sbjct: 332 GALVNP 337


>gi|322708483|gb|EFZ00061.1| NADH oxidase [Metarhizium anisopliae ARSEF 23]
          Length = 387

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 59/180 (32%), Gaps = 19/180 (10%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG 105
               I     AA+ +   GY+ I L             P+       +G  LM    I+ 
Sbjct: 170 FANVIEGFAHAAEYLHRAGYDGIELHGAHGYLLAQFLSPTTNKRTDQYGGSLMNRARIIF 229

Query: 106 DCIAAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK---- 157
           +   A+   +     V  +       D         +L  ++++SG + + +        
Sbjct: 230 EINDAIRARVPKSFIVSIKLNSVEFQDGGFSTQDCTDLCAALEESGFDFVELSGGTYEAG 289

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           A          R+   L++  +         +++   GG    S  +K L +V GV +GR
Sbjct: 290 AFYHRKESTKKREAFFLEFADIIVPGLNRTKVYVT--GGFRTTSGMVKALDTVHGVGLGR 347


>gi|288932867|ref|YP_003436927.1| radical SAM protein [Ferroglobus placidus DSM 10642]
 gi|288895115|gb|ADC66652.1| Radical SAM domain protein [Ferroglobus placidus DSM 10642]
          Length = 345

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 26/121 (21%), Positives = 47/121 (38%), Gaps = 20/121 (16%)

Query: 36  DKKNILGFSTQEKPLALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFG 94
            KK    F + E  L   I       + EAAK+  E+     + +  G     +     G
Sbjct: 118 WKKKRCKFCSIEIGLENSIVEKTPEMIAEAAKMAYEEDNSRHLTITSG----IMPGKDKG 173

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           A        + + + A+ + + IP+ V+           V  R+ ++ + +SG + I IH
Sbjct: 174 AV------KISEVVKAVKEKVDIPIHVQVD---------VVDRDFLEMLYESGADTIGIH 218

Query: 155 A 155
           A
Sbjct: 219 A 219


>gi|330842911|ref|XP_003293411.1| hypothetical protein DICPUDRAFT_158258 [Dictyostelium purpureum]
 gi|325076264|gb|EGC30065.1| hypothetical protein DICPUDRAFT_158258 [Dictyostelium purpureum]
          Length = 391

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 49/136 (36%), Gaps = 8/136 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +G        +  D I A+    + P+TV+  C   ++    +         I+K  V+ 
Sbjct: 234 YGGSFEGRFKLAKDIILAVRSVWNGPLTVRISCDEYIEGGWTSDDSVRFSLEIEKLDVDL 293

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +        S    +  P     + + IK+    L +G  G + + + A  +L   
Sbjct: 294 IECSSG----GNSSAAKIKSFPLYQVPLAHHIKRSVSKLLVGAVGLINNAADAESVLQDN 349

Query: 209 SVDGVMIGRAAYKNSA 224
             D ++ GR   +N  
Sbjct: 350 KADLILFGRGFLRNPF 365


>gi|119025782|ref|YP_909627.1| dihydroorotate dehydrogenase [Bifidobacterium adolescentis ATCC
           15703]
 gi|118765366|dbj|BAF39545.1| dihydroorotate dehydrogenase [Bifidobacterium adolescentis ATCC
           15703]
          Length = 315

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 75/218 (34%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G       E    ++D   + + +NV CP    +  + G  +  +P  +   I 
Sbjct: 108 VIANVAGHCDDDYAEVVSKLDDSPADMLEINVSCP----NVSAGGMSVGTDPVALSRLIT 163

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            + K     + VK    V D           ++  +SG + +            I   + 
Sbjct: 164 RLRKLTDKKMIVKLTPNVTDITVP------ARAAVESGADALSLINTLLGMRINIRTGEP 217

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           ++  +        +  +    V+ ++   P++ I   GG++    AL+ L    + V +G
Sbjct: 218 VITHVTGGVSGPAVLPVGLAAVWRVRAALPEIPIIGIGGIDSGETALEYLYAGANAVEVG 277

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA         V     + L     +  ++ K + WR
Sbjct: 278 AAALFEPTAPLRVARELDDLLDERPELADKLAKGETWR 315


>gi|78062586|ref|YP_372494.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia sp. 383]
 gi|77970471|gb|ABB11850.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia sp. 383]
          Length = 369

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 30/183 (16%), Positives = 64/183 (34%), Gaps = 27/183 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD------------IVGDCI 108
             V +AK   D G+  + L+    +      SF +      D             + + +
Sbjct: 159 DFVASAKRARDLGFEWLELHF---AHGYLGQSFFSVHANQRDDEYGGSAENRGRFLVETL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
           AA+ K     +P+T +  +   D      L     L + +K+ G++ + +      +   
Sbjct: 216 AAVRKVWPEHLPLTARFGVIEYDGRDEETLAESIALTQRLKQEGLDMLSV-----SVGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
           +P             + E  +    L +    G++    A +++    +D VM+GRA   
Sbjct: 271 TPDAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVAEEQLDLVMVGRAHLA 330

Query: 222 NSA 224
           +  
Sbjct: 331 DPH 333


>gi|29828051|ref|NP_822685.1| oxidoreductase [Streptomyces avermitilis MA-4680]
 gi|29605153|dbj|BAC69220.1| putative oxidoreductase [Streptomyces avermitilis MA-4680]
          Length = 359

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 20/145 (13%), Positives = 42/145 (28%), Gaps = 12/145 (8%)

Query: 104 VGDCIAAMCKA--LSIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             + + A+ +      P+  +        +    A         ++  GV+ + +     
Sbjct: 214 ALEVVDAVREVWPAGKPLFFRVSATDWLDEGGWTADDTVRFAAELQAHGVDLLDVSTG-- 271

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
                S       P         +K     L +   G + D  QA KIL     D +++G
Sbjct: 272 --GNASGVRIPTGPGYQVPFAARVK-AGTSLPVAAVGLITDAEQAEKILANGEADAILLG 328

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSS 241
           R   +N +            +   +
Sbjct: 329 RELLRNPSFARLAARELGGDVHVPA 353


>gi|68481190|ref|XP_715510.1| potential NADH-dependent flavin oxidoreductase [Candida albicans
           SC5314]
 gi|68481331|ref|XP_715440.1| potential NADH-dependent flavin oxidoreductase [Candida albicans
           SC5314]
 gi|46437062|gb|EAK96415.1| potential NADH-dependent flavin oxidoreductase [Candida albicans
           SC5314]
 gi|46437134|gb|EAK96486.1| potential NADH-dependent flavin oxidoreductase [Candida albicans
           SC5314]
          Length = 432

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 68/199 (34%), Gaps = 28/199 (14%)

Query: 61  KLVEAAKIVED---------FGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               AA+   +          G +   +N    P +      +G         + + I +
Sbjct: 204 DFGAAARRAVEISGFDAVEIHGAHGYLINEFYSPISNKRTDEYGGSFENRTRFLKEVIDS 263

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHA-----RKAI 159
           +  ++   +PV ++     +   P          L   + + G+  + + +     R+  
Sbjct: 264 VKSSIPNDVPVFLRISAAENSPDPEAWTIEDSKKLADILVEKGIALVDVSSGGNDYRQPP 323

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE-DMSQALKILPS--VDGVMI 215
             G+S K+ R+   +   +   IK+   D L +   GGLE D     K L     D  +I
Sbjct: 324 RSGIS-KELRE--PIHVPLSRAIKQHVGDKLLVSCVGGLEKDPELLNKYLEEGTFDLALI 380

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           GR   +N  ++    +   
Sbjct: 381 GRGFLRNPGLVWEFADKLG 399


>gi|323498313|ref|ZP_08103315.1| hypothetical protein VISI1226_17835 [Vibrio sinaloensis DSM 21326]
 gi|323316741|gb|EGA69750.1| hypothetical protein VISI1226_17835 [Vibrio sinaloensis DSM 21326]
          Length = 667

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 31/203 (15%), Positives = 69/203 (33%), Gaps = 25/203 (12%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHE 90
           I  F+  E  +  QI    I     +A + +  GY+ + +            C   +   
Sbjct: 123 IARFAPSEMSVR-QIK-KTIDAFANSAALAQQAGYDGVEVMGSEGYLINQFIC---KRTN 177

Query: 91  GSFGACLMLNPDIVG---DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSI 143
             +        + +    + + ++ +A+     +  R+     V++      +  L K +
Sbjct: 178 MRYDDWGGSYENRMRFPLEIVKSIRQAVGEKFIIIFRLSMLDLVEEGSTFDEVIALAKEL 237

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +K+GV    I+      +   P    ++P   +  V E  + +  + I     +    +A
Sbjct: 238 EKAGVT--IINTGIGWHEARIPTIATQVPRGAFTWVTEKVRPHVSVPIVTCNRINTPEEA 295

Query: 204 LKILP--SVDGVMIGRAAYKNSA 224
            KIL     D V + R    +  
Sbjct: 296 EKILSSGHADMVSMARPFLADPH 318


>gi|172046821|sp|P19410|BAICD_EUBSP RecName: Full=Bile acid-inducible operon protein CD; AltName:
           Full=Bile acid-inducible operon protein C; AltName:
           Full=Bile acid-inducible operon protein D
 gi|146230651|gb|AAC45411.2| BaiCD [Clostridium scindens]
          Length = 639

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEGS------FGACLMLNPDIVGDCIAA 110
            +    A++    G++ +  +      P   +  G       +G           + + A
Sbjct: 135 EEFGRGARMAVQAGFDAVEFHAAHSYLPHEFLSPGMNKRTDEYGGSFENRCRFCYEVVQA 194

Query: 111 MCKAL--SIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +   +   +P  +        ++  +    +   +    + GV+   +    A     S 
Sbjct: 195 IRSNIPDDMPFFMRADCIDELMEQTMTEEEIVTFINKCAELGVDVADLSRGNAT----SF 250

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
               ++P  +       + +Y IKK+  ++ +   G +     A K++     D V IGR
Sbjct: 251 ATVYEVPPFNLAHGFNIENIYNIKKQI-NIPVMGVGRINTGEMANKVIEEGKFDLVGIGR 309

Query: 218 AAYKNSAMLTTVDE 231
           A   +   +T V E
Sbjct: 310 AQLADPNWITKVRE 323


>gi|300693090|ref|YP_003749063.1| oxidoreductase (salicylyl-CoA 5-hydroxylase) protein (abma)
           [Ralstonia solanacearum PSI07]
 gi|299075127|emb|CBJ34409.1| putative oxidoreductase (salicylyl-CoA 5-hydroxylase) protein
           (abmA) [Ralstonia solanacearum PSI07]
          Length = 785

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 32/215 (14%), Positives = 65/215 (30%), Gaps = 29/215 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVGDC 107
            V AA++  + G++ + L   C           P   +    +G  L   +  P  V   
Sbjct: 557 FVRAARLAVEAGFDWLEL--HCAHGYLLSSFISPLTNLRSDEYGGSLENRLRYPLEVFRA 614

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A+  A   P++V+      V   I       + +  K +G + I   + +     +S 
Sbjct: 615 VRAVWPA-DKPMSVRISAHDWVQGGITPDDAVEIARIFKAAGADMIDCSSGQ-----VSK 668

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           K+      +      +  +    +     G + +      I+ +   D   + R    N 
Sbjct: 669 KEQPVYGRMFQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLANP 728

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              L          L    P + R  K    +   
Sbjct: 729 AWTLNEAARI--GYLDMPWPKQYRAGKQQLERNLE 761


>gi|239827625|ref|YP_002950249.1| NADPH dehydrogenase NamA [Geobacillus sp. WCH70]
 gi|259511219|sp|C5D427|NAMA_GEOSW RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|239807918|gb|ACS24983.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. WCH70]
          Length = 340

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 36/217 (16%), Positives = 73/217 (33%), Gaps = 29/217 (13%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSAR 87
            K +     +E   A Q G          A+  ++ G++ I ++            P + 
Sbjct: 131 PKEMTKADIEETIQAFQNG----------ARRAKEAGFDIIEIHGAHGYLINEFLSPLSN 180

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKK 145
             +  +G         +G+ I A+ +    P  V +       + +         K +K+
Sbjct: 181 RRQDEYGGSPENRYRFLGEIIDAVREVWDGPLFVRISASDYHPEGLTVKDYVPYAKRMKE 240

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            GV+ I + +   +     P   R  P         I++E  ++  G  G +    QA +
Sbjct: 241 QGVDLIDVSSGAVV-----PAKIRVYPGYQVPFAETIRREA-NIATGAVGLITSGLQAEE 294

Query: 206 ILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           IL +   D V + R   +N        +     ++ S
Sbjct: 295 ILRNGRADLVFLARELLRNPYWPYAAAKELGTTISAS 331


>gi|332290153|ref|YP_004421005.1| NADPH dehydrogenase NamA [Gallibacterium anatis UMN179]
 gi|330433049|gb|AEC18108.1| NADPH dehydrogenase NamA [Gallibacterium anatis UMN179]
          Length = 311

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 29/187 (15%), Positives = 64/187 (34%), Gaps = 31/187 (16%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              A +   + G++ I L             P +   +  +G     +  + G+ +    
Sbjct: 110 FQNAVRRAVEAGFDLIELHGAHGYLIHQFYSPKSNQRQDEYG----KDRMLFGEQVIKAA 165

Query: 113 KAL---SIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGL 163
           KA+    +P+ ++        +   +     + K    +GV+ I +    +   A  K  
Sbjct: 166 KAVMPEDMPLAIRISAQEYSANGFDSDYGVEVAKRFAAAGVDMIHVSGGGNGALAPGKHP 225

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
                 ++       +    K+   L +   G LED + A  ++ +   D V IGR   +
Sbjct: 226 EFAAGYQV------YLARKVKQATGLPVIAVGMLEDPALADFVIGNGDADLVAIGRGLLR 279

Query: 222 NS-AMLT 227
           +   +L 
Sbjct: 280 DPYWVLN 286


>gi|222530053|ref|YP_002573935.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           bescii DSM 6725]
 gi|222456900|gb|ACM61162.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 381

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 41/111 (36%), Gaps = 17/111 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I        +E +K++E  G + I LN+ CP         G  +M   D++ + +
Sbjct: 100 PVIASINCYTDDAWLEYSKLMEQAGADAIELNLSCPH--------GVHIMSGMDVIEEMV 151

Query: 109 AA---MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                +   + IPV  K      +             +  +G +G+ +  R
Sbjct: 152 NTTKLVKSNVKIPVIPKMTPQSTNPGSD------ALRLDSAGADGLVMFNR 196


>gi|50121908|ref|YP_051075.1| flavoprotein xenobiotic reductase [Pectobacterium atrosepticum
           SCRI1043]
 gi|49612434|emb|CAG75884.1| flavoprotein xenobiotic reductase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 362

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 28/183 (15%), Positives = 63/183 (34%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AA+   + G+  + L+       + +             +G         + + +
Sbjct: 158 DDFVAAARRALEAGFEWLELHFA--HGYLAQSFFSAHSNKRNDQYGGSFENRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
           AA+       +P+T +  +   D      L+    L +  K +G++ + +      +   
Sbjct: 216 AAVRDVWPQHLPLTARFGVIEFDGRDEETLQESIELTRRFKAAGLDMLSV-----SIGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
           +P+ N          + +  +E  DL +    G      A + +    +D VM+G+A   
Sbjct: 271 TPEANIPWAPAFMGPIAQQVREQADLPVSSAWGFGTPELAEQAVASDQLDLVMVGKAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|327329118|gb|EGE70878.1| dihydroorotate oxidase [Propionibacterium acnes HL103PA1]
          Length = 335

 Score = 44.4 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 65/180 (36%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +ED G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMEDAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+V  +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMVTRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  ++    +             +  +        +  + G+E  +  +K +L   D VM
Sbjct: 210 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESAADVVKYLLAGADVVM 268


>gi|91776271|ref|YP_546027.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacillus
           flagellatus KT]
 gi|91710258|gb|ABE50186.1| NADH:flavin oxidoreductase/NADH oxidase [Methylobacillus
           flagellatus KT]
          Length = 356

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 37/200 (18%), Positives = 62/200 (31%), Gaps = 24/200 (12%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDC 107
            ++   AAK   D G+  + L   C           P +   E  +G  L     +  D 
Sbjct: 155 AAQFHAAAKRALDAGFEVLEL--HCAHGYLLHEFLSPLSNRREDEYGGSLENRCRLALDI 212

Query: 108 IAAMCK--ALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
              +        PV V+      V+            K +K++G++ I   +   IL   
Sbjct: 213 ARDLRTLWPQDKPVFVRISATDWVEGGWDIDQSIQFAKWLKEAGIDLIDCSSGGLILDAK 272

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
            P      P    +    I+ E   +  G  G +    QA  IL     D VM+ R    
Sbjct: 273 IPAG----PGYQTEFAQRIRHETG-IATGAVGLITSAVQAEHILVSGQADVVMLARKLLS 327

Query: 222 NSAMLTTVDEYFSNPLTGSS 241
           +        +     +T  +
Sbjct: 328 DPHWPLHAAKELRTDVTWPA 347


>gi|301309378|ref|ZP_07215320.1| putative N-acetylmannosamine-6-phosphate epimerase superfamily
           [Bacteroides sp. 20_3]
 gi|300832467|gb|EFK63095.1| putative N-acetylmannosamine-6-phosphate epimerase superfamily
           [Bacteroides sp. 20_3]
          Length = 246

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 64/182 (35%), Gaps = 40/182 (21%)

Query: 36  DKKNILGFSTQEKPLALQIGGADI----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +KK +L        ++ Q+   D       +V+ AK  +  G   I  N           
Sbjct: 4   NKKELLDSFKGGLIVSCQVQHDDPTFSVDFVVKMAKAAQWGGAAGIRAN----------- 52

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNG 150
                   +P+     I A+ K + +PV    +I  DD    +       K++ ++G   
Sbjct: 53  --------DPEQ----IKAIKKEVDLPVIGLWKIWHDDTDVFITPTLEAAKAVWEAGAEI 100

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           I +     I     P          Y+++  +KKE P+  I     + +  +A++ +   
Sbjct: 101 IALDCTSQITHEGRPA---------YELLPIVKKEIPEAIIFA--DVSNYEEAVRAVEMG 149

Query: 210 VD 211
            D
Sbjct: 150 AD 151


>gi|256752881|ref|ZP_05493718.1| FAD-dependent pyridine nucleotide-disulphide oxidoreductase
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|256748231|gb|EEU61298.1| FAD-dependent pyridine nucleotide-disulphide oxidoreductase
           [Thermoanaerobacter ethanolicus CCSD1]
          Length = 470

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 22/142 (15%), Positives = 43/142 (30%), Gaps = 14/142 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL-SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVN 149
           +G           D +  + KAL  + V  +       D            K ++  G +
Sbjct: 26  YGGNFEGRTKFALDILRGVKKALPDMTVICRINGSDFTDGGFSIEESVRFAKLLEYHGAD 85

Query: 150 GIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQAL 204
            + I           +SP      P +    + +  KEN  + +      G + D  + L
Sbjct: 86  ALDISGGVSSTSEYHISPMGIGDKPLIG---IAKRIKENVTIPVIAVDKLGSVYDWEKIL 142

Query: 205 KILPS-VDGVMIGRAAYKNSAM 225
           +      D + I R    +  +
Sbjct: 143 E--EGIADFIGIARGLIGDPDL 162


>gi|326381904|ref|ZP_08203597.1| NADH-dependent oxidoreductase [Gordonia neofelifaecis NRRL B-59395]
 gi|326199330|gb|EGD56511.1| NADH-dependent oxidoreductase [Gordonia neofelifaecis NRRL B-59395]
          Length = 717

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 28/192 (14%), Positives = 61/192 (31%), Gaps = 31/192 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AA+ V + G + + +   C    +  G            +G  L        + IAA+
Sbjct: 178 VAAARRVREAGADAVEI--HCAHGYLLSGFLSRADNRRTDEYGGSLENRARFACEVIAAV 235

Query: 112 CKALSIPVTVKCRIGVDD-----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             A+   + V  R+   +      +         +  + +G + I +        G +P 
Sbjct: 236 KGAVGDDLAVLVRVSGREFGEAGGLSTDEAARAARMFESAGADAIDVTG-----WGRNPF 290

Query: 167 DNRKIPNLDYDI-----VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            N     L   +     +  + KE+  + +   G +         +     D V +GR  
Sbjct: 291 SNFTDGPLPDRLGAFVDLAAVVKESVSIPVITVGRVL-PEVGAAAIADGKADFVAMGRQL 349

Query: 220 YKNSAMLTTVDE 231
             +  ++  +  
Sbjct: 350 LADPDLVNKLRA 361


>gi|302388845|ref|YP_003824666.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosediminibacter
           oceani DSM 16646]
 gi|302199473|gb|ADL07043.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosediminibacter
           oceani DSM 16646]
          Length = 340

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 53/155 (34%), Gaps = 12/155 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L      + + I A+ +      P  V V      +     + L N++  +K  GV
Sbjct: 185 YGGNLQNRARFLREVIRAVREVWPEEKPLMVRVSAEDYAEGGNHDIDLANIINLVKGEGV 244

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I + +   +     P   +  P         I+K    L +   G +     A +IL 
Sbjct: 245 DIIDVSSGAVV-----PATIKAYPGYQVRFAETIRKMTG-LPVIAGGLITVPEMAEEILQ 298

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +   D V +GR   +N     +  +   + +    
Sbjct: 299 NERADMVYLGRELLRNPYWPLSAAKELGDDIKWPE 333


>gi|171742242|ref|ZP_02918049.1| hypothetical protein BIFDEN_01348 [Bifidobacterium dentium ATCC
           27678]
 gi|283456646|ref|YP_003361210.1| NADH-dependent flavin oxidoreductase [Bifidobacterium dentium Bd1]
 gi|171277856|gb|EDT45517.1| hypothetical protein BIFDEN_01348 [Bifidobacterium dentium ATCC
           27678]
 gi|283103280|gb|ADB10386.1| NADH-dependent flavin oxidoreductase [Bifidobacterium dentium Bd1]
          Length = 376

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 59/167 (35%), Gaps = 12/167 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G C      ++ + + A+   +   +PV V+                 +L K +K+ GV
Sbjct: 216 YGGCFENRIRMLVEVVDAVRTVIPDDMPVLVRISATDWAAGGWDLDQSVDLAKVLKEHGV 275

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +        GL P     +         E  +   D+ +   G +    QA K+L 
Sbjct: 276 DLVDVSTG-----GLIPDVTIPVKPGYQVPFSEQIRSRADVPVTAVGLITKPKQAEKVLK 330

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               D + IGRAA ++             P+   +P   +  +  +R
Sbjct: 331 AGQADAIEIGRAALRDPYWPLRAANKLGVPV-EEAPYPAQYVRGAFR 376


>gi|167624041|ref|YP_001674335.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella halifaxensis
           HAW-EB4]
 gi|167354063|gb|ABZ76676.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella halifaxensis
           HAW-EB4]
          Length = 706

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 29/191 (15%), Positives = 68/191 (35%), Gaps = 28/191 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AA   +  G++ + ++     + +  G            +G  L     ++ + IA
Sbjct: 172 WFASAALRAKQAGFDGVEIHAA--HSYIIAGFLSSYYNKRDDQYGGNLENRARLLLEVIA 229

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNL---VKSIKKSGVNGIWIHARKAILKG-- 162
           A+ + +    PV ++           + + +     K ++ +G+N I I A   I +G  
Sbjct: 230 AVREQVGNDYPVWLRLDAAELRTPGGITIEDCIEVAKLVEAAGLNAISISAYATINRGDA 289

Query: 163 --LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
              +P   +    LD+     +  ++  + +   G LE    A K +    +  V + R 
Sbjct: 290 FTEAPLVQKPAGFLDW---AAMVSKHVSIPVTAVGRLE-PDVANKAIGSGQIAFVAMARK 345

Query: 219 AYKNSAMLTTV 229
              +  +   +
Sbjct: 346 LLADPQLPNKI 356


>gi|23015277|ref|ZP_00055058.1| COG1902: NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Magnetospirillum magnetotacticum MS-1]
          Length = 371

 Score = 44.4 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 65/196 (33%), Gaps = 22/196 (11%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDCIA 109
            V AA+     G++ I L             P +   +  +G  L   M  P  V   + 
Sbjct: 159 FVIAAQRALRIGFDFIELHSAHGYLLHQFLSPLSNRRDDQYGGSLENRMRFPLEVITAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A+  A   P+ ++      V+    A    N  K+ K +G++ + + +   +     P  
Sbjct: 219 AVWPA-DKPLGLRISATDWVEGGWDADQAVNYAKAFKAAGIDFVCVSSGGLVSYAKVPVG 277

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
               P    ++   I++E   +     G +    QA   L     D + IGR    N   
Sbjct: 278 ----PGYQIELAARIRREAG-IPTRAVGLIATPHQAETALTEGAADLIAIGRGFLDNPRW 332

Query: 226 LTTVDEYFSNPLTGSS 241
           +    +     +T   
Sbjct: 333 VWHAAQALGAQMTYPP 348


>gi|289704916|ref|ZP_06501333.1| oxidoreductase, FAD/FMN-binding [Micrococcus luteus SK58]
 gi|289558412|gb|EFD51686.1| oxidoreductase, FAD/FMN-binding [Micrococcus luteus SK58]
          Length = 362

 Score = 44.4 bits (104), Expect = 0.026,   Method: Composition-based stats.
 Identities = 27/197 (13%), Positives = 63/197 (31%), Gaps = 24/197 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA+   + G + + ++            PS+   E ++G        +  + + A+
Sbjct: 154 EFADAARRAVEAGLDGVEVHGANGYLLHEFLAPSSNTREDAYGGSPENRARLTVEVVRAV 213

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            +A+        RI  +  +      +    +         +         +  +D    
Sbjct: 214 AQAIGAE-RTALRISPEHNVQGTIEEDRADVLATYDALLAGLADLDLAYLSVIHQDVAG- 271

Query: 172 PNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
                D+   +++      + LN   G +  + +A +I+     D V +GR    N  + 
Sbjct: 272 -----DLAAHLRESFSG-PLVLNSGFGAVTGLEEARRIVEDGLADAVAVGRELIANPDLA 325

Query: 227 TTVDEYFSNPLTGSSPI 243
               E    PL    P 
Sbjct: 326 RRWREGL--PLNEPDPT 340


>gi|325673311|ref|ZP_08153003.1| old Yellow enzyme family NADH:flavin oxidoreductase [Rhodococcus
           equi ATCC 33707]
 gi|325555901|gb|EGD25571.1| old Yellow enzyme family NADH:flavin oxidoreductase [Rhodococcus
           equi ATCC 33707]
          Length = 709

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 61/212 (28%), Gaps = 21/212 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
              EAA  V+  G + + ++       V  G            +G  L     +  + I 
Sbjct: 177 MFAEAAGRVKAAGGDAVEIHAA--HNYVLGGFLSRYSNQRTDEYGGSLENRARLSCEVIR 234

Query: 110 AMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+   +   + V  R+        + +            +++G + I +           
Sbjct: 235 AVKAEVGDSLAVIVRLAGQEYGESEGLTPDEAARAAAMFEEAGADAIHVTGTALNAFANF 294

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                      Y     + K    + +   G +       +++     D V +GR    +
Sbjct: 295 TDGPLPNKVGYYTENAAVVKRAVSIPVITVGRML-PEVGEQMITEGHTDFVAMGRQLLAD 353

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
            A++  +    S  +         V ++FW  
Sbjct: 354 PALVDKLKAGHSEQVRPCINCYVCVQENFWDD 385


>gi|295705254|ref|YP_003598329.1| FAD/FMN-binding family oxidoreductase protein [Bacillus megaterium
           DSM 319]
 gi|294802913|gb|ADF39979.1| oxidoreductase, FAD/FMN-binding family protein [Bacillus megaterium
           DSM 319]
          Length = 351

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 31/190 (16%), Positives = 62/190 (32%), Gaps = 38/190 (20%)

Query: 63  VEAAKIVEDFGYNEINL-----------NVGCPSARVHEG--SFGACLMLNPDIVGDCIA 109
            +AAK   + G++ + +           N    S   ++    +G  L      + + I+
Sbjct: 160 AQAAKNAIEAGFDGVEIHGAHGYLIDQFN----SDWSNKRTDEYGGGLAQRLTFMKEVIS 215

Query: 110 AMCKALSI-PVTVKCRIGVDDQIPA------VALRNLVKSIKKSGVNGIWIHARKAILKG 162
           A+  A+    V ++      D+          A++   ++ K++G+  I           
Sbjct: 216 AVIDAIGKERVVIRFSPHKLDKPDYRWDDTEKAIQTYTEAFKETGIEIIHPSMLDFYEDV 275

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
            + ++  +I    +D             I   G L     A K L    +D   IGR   
Sbjct: 276 QNGQNLYEITRKYWDG-----------PIIGVGDL-TPESAEKALQASWIDVAAIGRPLI 323

Query: 221 KNSAMLTTVD 230
            N   L  + 
Sbjct: 324 SNPDYLQRIK 333


>gi|218281541|ref|ZP_03487970.1| hypothetical protein EUBIFOR_00535 [Eubacterium biforme DSM 3989]
 gi|218217330|gb|EEC90868.1| hypothetical protein EUBIFOR_00535 [Eubacterium biforme DSM 3989]
          Length = 640

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 67/188 (35%), Gaps = 21/188 (11%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP------ 101
           +P  ++     + +  +AA  V+  G + + +   C  A    G F   L          
Sbjct: 135 RPATIEELHTIVDQFGQAAHRVQIAGGDGVEIQ--CAHAHGLLGGFLTPLYNKRTDEYGG 192

Query: 102 ------DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGI 151
                  +  + IA++ K       +  RI  D+        N    + K ++K+GV+ I
Sbjct: 193 NIDGRLRLCLEVIASVRKYCGDDFIIDVRISGDEYSEGGLTLNDQIYVCKQLEKAGVDFI 252

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PS 209
            +     I +G S       P        EIKK   ++ +     + +   A +++    
Sbjct: 253 HVSGGNTIKRGSSMPAPGTSPAPHAHSSEEIKKHV-NIPVATVARINEPWMAEELIANEK 311

Query: 210 VDGVMIGR 217
            D  MIGR
Sbjct: 312 CDMCMIGR 319


>gi|311894999|dbj|BAJ27407.1| putative NADPH dehydrogenase [Kitasatospora setae KM-6054]
          Length = 364

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 24/158 (15%), Positives = 47/158 (29%), Gaps = 13/158 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCR-IGVDDQIPAVALRN---LVKSIKK 145
            +G        +  +   A+       +PV  +          P+  +     L K ++ 
Sbjct: 202 GYGGDFAGRSRLAREVATAVRAVWPAELPVFFRVSATDWRPAEPSWTVEESVLLAKELQL 261

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            GV+ + +        G  P     I         E  +    + +   G + D  QA +
Sbjct: 262 IGVDLVDVSTG-----GNVPHAEITIEPGYQVPFAETIRRESGIAVNAVGLITDADQAER 316

Query: 206 ILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           I+     D VM+GR   ++             P    +
Sbjct: 317 IVADGRADAVMLGRELLRDPYWPLHAARELGVPRNWPA 354


>gi|295399066|ref|ZP_06809048.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110330|ref|YP_003988646.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y4.1MC1]
 gi|294978532|gb|EFG54128.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215431|gb|ADP74035.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacillus sp. Y4.1MC1]
          Length = 340

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 34/217 (15%), Positives = 74/217 (34%), Gaps = 29/217 (13%)

Query: 37  KKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSAR 87
            K +     +E   A Q G          A+  ++ G++ I ++            P A 
Sbjct: 131 PKEMTKADIEETIQAFQNG----------ARRAKEAGFDIIEIHAAHGYLINEFLSPLAN 180

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKK 145
             +  +G         +G+ I A+ +    P  V +       + +         K +K+
Sbjct: 181 KRKDEYGGSPENRYRFLGEVINAVKEVWDGPLFVRISASDYHPEGLTVQDYVPYAKRMKE 240

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            GV+ I + +   +   ++     ++P  +      I++E  ++  G  G +    QA +
Sbjct: 241 QGVDLIDVSSGAVVPAKINVYPGYQVPFAE-----TIRREA-EIATGAVGLITSGWQAEE 294

Query: 206 ILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           IL +   D V + R   +N        +     +   
Sbjct: 295 ILCNGRADLVFLARELLRNPYWPYAAAKELGTTIPAP 331


>gi|314922498|gb|EFS86329.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL001PA1]
 gi|314965575|gb|EFT09674.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL082PA2]
 gi|314982737|gb|EFT26829.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL110PA3]
 gi|315091391|gb|EFT63367.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL110PA4]
 gi|315094326|gb|EFT66302.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL060PA1]
 gi|315105050|gb|EFT77026.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL050PA2]
 gi|327334731|gb|EGE76442.1| dihydroorotate oxidase [Propionibacterium acnes HL097PA1]
          Length = 335

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 64/180 (35%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +ED G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMEDAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  ++    +             +  +        +  + G+E  +  +K +L   D VM
Sbjct: 210 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESAADVVKYLLAGADVVM 268


>gi|119504714|ref|ZP_01626792.1| 2,4-dienoyl-CoA reductase FadH1 [marine gamma proteobacterium
           HTCC2080]
 gi|119459319|gb|EAW40416.1| 2,4-dienoyl-CoA reductase FadH1 [marine gamma proteobacterium
           HTCC2080]
          Length = 695

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 72/235 (30%), Gaps = 38/235 (16%)

Query: 20  ALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL 79
            L Y E +VA + +R            E  +  QI           AK+ +  GY+ I +
Sbjct: 128 PLAYNEQLVAPSAVRSRIGAYTPLELDEAGIEKQIADH-----ANCAKLAQGAGYDGIEI 182

Query: 80  ----------------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
                           N          G   A  M  P    + +  + +A+     V  
Sbjct: 183 IGSAGYLLSTFLVEKTN----QRTDQWGGSYANRMRFP---LEVVRRVREAVGNEFIVIF 235

Query: 124 RIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           RI   D     +    +  L + ++ +GV  I  H      +   P     +P   +  V
Sbjct: 236 RIAAMDMLQGGMSWDEVAELSRELESAGVTMISTH--FTWHESQVPTIATMVPRAAFTGV 293

Query: 180 -YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
            + ++ E     I  N  +     A  +L     D V + R    +S  +   D 
Sbjct: 294 THRVRNEVSIPVITSNR-INTPDVAESVLEQGDADLVSMARPMLADSQFMRKADA 347


>gi|238497347|ref|XP_002379909.1| NADH oxidase, putative [Aspergillus flavus NRRL3357]
 gi|220694789|gb|EED51133.1| NADH oxidase, putative [Aspergillus flavus NRRL3357]
          Length = 456

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 27/172 (15%), Positives = 59/172 (34%), Gaps = 29/172 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            + AK     G + I ++            P +     S+G        ++ + I ++ K
Sbjct: 221 AKTAKRAVQAGADVIEIHAAHGYLIHQFLSPVSNHRTDSYGGSFENRTRLLLEIIESVRK 280

Query: 114 AL--SIPVTVKCRI----------GVDDQIPAVALRNLVKSIKKSGVNGIWI-----HAR 156
            +   +P+ ++                          L K + ++GV+ + +     H  
Sbjct: 281 EMPAGMPLFLRVSSTEWLESTEIGTKYGTWTVEDTIRLAKLLPEAGVDLLDVSSGGNHPM 340

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + +   L+     KI      I  E+K+   +L IG  G + +  QA  ++ 
Sbjct: 341 QTVNSFLTKDYQTKIAA---RIRKELKQSGVNLLIGAVGMITEAEQARDLVE 389


>gi|33302309|gb|AAQ01775.1| dihydroorotate dehydrogenase 1a [Lactococcus lactis subsp.
           hordniae]
          Length = 311

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 66/209 (31%), Gaps = 28/209 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIV 104
           QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  + +  
Sbjct: 92  QEAPIFFSIAGMSAAENIAMLKKIQESNFSGITELNLSCP--NVPGK---TQLAYDFEAT 146

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW----- 152
              +  +    + P+ VK     D     I A  L       V S+   G          
Sbjct: 147 EKLLKEVFAFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFIDSEAE 206

Query: 153 --IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
             +   K    G+     +     +    Y   K  P++ I   GG+E    A + L   
Sbjct: 207 SVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEHLL-C 263

Query: 211 DGVM--IGRAAYKN--SAMLTTVDEYFSN 235
              M  IG  A       +   + +    
Sbjct: 264 GATMLQIGT-ALHKEGPTIFDRIIKELEE 291


>gi|327179699|gb|AEA30247.1| putative oxidoreductase [Streptomyces sp. Acta 2897]
          Length = 372

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 47/147 (31%), Gaps = 22/147 (14%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA------VALRNLVKSIK 144
           +G  +     +V +  A +  A     PV V+   G  +               +  +  
Sbjct: 209 YGGGVEERLRLVREVTAEVRGATGAGFPVGVRFSQGKINDPGWRWPGGDAEAETVFTAAA 268

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +G + + +          S +D           +  + +    L +  NGGL   + A 
Sbjct: 269 TAGADYLHLAG--------SGRDWFPEGR----TLPALARTVTGLPVIANGGLHQEAVAR 316

Query: 205 KILP--SVDGVMIGRAAYKNSAMLTTV 229
           ++L     D + IG  A  N  +   V
Sbjct: 317 RVLDEGHADVLAIGTGALANPDLPRRV 343


>gi|295105157|emb|CBL02701.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Faecalibacterium prausnitzii SL3/3]
          Length = 641

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 25/209 (11%), Positives = 68/209 (32%), Gaps = 18/209 (8%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------C 83
           D + +    +++ F+ +    + ++  + I K+   A   +  G + I ++        C
Sbjct: 118 DEMRQRLHHDMMFFTDE---ASEEMLMSIIDKMCACAVRAQKAGVDVIQIHGDRLNGCLC 174

Query: 84  PSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL-----SIPVTVKCRIGVDDQIPAVALR 137
            +   H        + N       +  A+ KA+        +++         I      
Sbjct: 175 STRMNHRTDKFGGSLENRVRFARMLTRAIRKAVPDMVIDYKLSIVTPQRGKGGIDEADAV 234

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
              + + + GV+   +                 +    + + +    K+  ++ +   G 
Sbjct: 235 QFAQWLVEDGVDMFHVAQANHTGNMADTIPPMGVQPYGFFVKIAGDIKKAVNVPVSAVGR 294

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNS 223
           + D   A +++ S   D V +GR    + 
Sbjct: 295 IVDADMAARVIESGMADMVAMGRPLLADP 323


>gi|154686643|ref|YP_001421804.1| NADPH dehydrogenase NamA [Bacillus amyloliquefaciens FZB42]
 gi|171855001|sp|A7Z6E7|NAMA_BACA2 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|154352494|gb|ABS74573.1| YqjM [Bacillus amyloliquefaciens FZB42]
          Length = 338

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 67/193 (34%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA   ++ G++ I L+            P +      +G         +G+ I A+
Sbjct: 145 EFKQAAARAKEAGFDIIELHAAHGYLMHEFLSPLSNHRTDEYGGSHENRYRFLGETIEAV 204

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P+ V+       D  +         K +K+ GV+ I   +   +       D  
Sbjct: 205 KEVWDGPLFVRISASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVQ-----ADIN 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P        +I+++  ++  G  G +   + A +IL +   D + + R   ++     
Sbjct: 260 VFPGYQVSFAEKIREQA-EIATGAVGLITTGTMAEEILQNNRADLIFVARELLRDPHFAR 318

Query: 228 TVDEYFSNPLTGS 240
           +  +  +  +   
Sbjct: 319 SAAKQLNTEIPSP 331


>gi|317126479|ref|YP_004100591.1| 2,4-dienoyl-CoA reductase [Intrasporangium calvum DSM 43043]
 gi|315590567|gb|ADU49864.1| 2,4-dienoyl-CoA reductase [Intrasporangium calvum DSM 43043]
          Length = 676

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 31/225 (13%), Positives = 73/225 (32%), Gaps = 20/225 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                 A++  + GY+ + +             P       ++G        +  + + A
Sbjct: 143 EAYARCARLAREGGYDGVEIMGSEGYFLNQFLAPRTNQRTDAYGGTPENRRRLPVEVVRA 202

Query: 111 MCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A+     V  R+     V D      +  L K ++ +G     I+      +   P 
Sbjct: 203 VREAVGPDFIVIYRLSMLDLVPDGQSWEEIVALAKEVEAAGAT--IINTGIGWHEARVPT 260

Query: 167 DNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +P     ++   ++ E     I  N  +     A +++     D V + R    + 
Sbjct: 261 IVTSVPRGAFVEVTARLRPEVSIPVIASNR-ISMPDLAEQVVADGKADLVSMARPFLADP 319

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
             +L   +       T  +  +  +D  F +K ++ + +  A H 
Sbjct: 320 DWVLKAAEGRADEINTCIACNQACLDHTFAKKTASCLVNPRAGHE 364


>gi|330971426|gb|EGH71492.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 359

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 70/184 (38%), Gaps = 21/184 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCI 108
            + VEAA   E  G++ + L+     A V               +G  L      V + I
Sbjct: 143 DRFVEAAVRAERAGFDGVALHGA--FAFVLAQFLSSALNYRSDQYGGSLENRSRFVFETI 200

Query: 109 AAMCKALSIPVTVKCRIGVDDQ-IPAVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPK 166
            A+  A+     +  R+ VD   I    +R++V + +++  V+ I +        G    
Sbjct: 201 NAVRAAVGEHFQLGIRLSVDRHGIKVEEIRDVVAEIMRQQQVDYIDL---ALWDAGQRAD 257

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
           D         D+  E+ +    L  G  G +    +A ++L    D V+IGRAA  +  +
Sbjct: 258 DGPSKGRKMLDLFTELPRHGVRL--GTAGKIMGAQRAAELLEEGCDFVLIGRAACIHPDV 315

Query: 226 LTTV 229
              +
Sbjct: 316 PNRI 319


>gi|282853210|ref|ZP_06262547.1| dihydroorotate oxidase [Propionibacterium acnes J139]
 gi|282582663|gb|EFB88043.1| dihydroorotate oxidase [Propionibacterium acnes J139]
          Length = 335

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 64/180 (35%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +ED G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMEDAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  ++    +             +  +        +  + G+E  +  +K +L   D VM
Sbjct: 210 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESAADVVKYLLAGADVVM 268


>gi|47096063|ref|ZP_00233664.1| NADH:flavin oxidoreductase [Listeria monocytogenes str. 1/2a F6854]
 gi|254900391|ref|ZP_05260315.1| NADPH dehydrogenase NamA [Listeria monocytogenes J0161]
 gi|254913370|ref|ZP_05263382.1| NADH:flavin oxidoreductase [Listeria monocytogenes J2818]
 gi|254937751|ref|ZP_05269448.1| NADH:flavin oxidoreductase [Listeria monocytogenes F6900]
 gi|47015524|gb|EAL06456.1| NADH:flavin oxidoreductase [Listeria monocytogenes str. 1/2a F6854]
 gi|258610354|gb|EEW22962.1| NADH:flavin oxidoreductase [Listeria monocytogenes F6900]
 gi|293591376|gb|EFF99710.1| NADH:flavin oxidoreductase [Listeria monocytogenes J2818]
          Length = 338

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     + G 
Sbjct: 317 KDAAKQLGETIEGP 330


>gi|328470439|gb|EGF41350.1| putative NADH-dependent flavin oxidoreductase [Vibrio
           parahaemolyticus 10329]
          Length = 367

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 30/218 (13%), Positives = 68/218 (31%), Gaps = 23/218 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              A+K  ++ G++ + ++            P     E  +G  L     ++ +  +   
Sbjct: 147 FALASKRAQEAGFDGVEIHAAHTYLINQFLSPYYNRREDEYGGSLENRMRLLLEIYSETR 206

Query: 113 ----KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
                A  I V +      D  +     R + K +++ G + I     IH +   L G  
Sbjct: 207 MLVGDAFPILVKLTATEFFDGGLTFDETRIVCKKLEEVGADAIIVSGNIHGKANELVGER 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAAY 220
                      +    ++  ++  + +   GGL D+     I  + +     V   R   
Sbjct: 267 FDGYTLQEEGYFHEYGQVISQDIHIPVITVGGLRDIDAIENIAENTNIQFFAV--SRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
               ++    E    P+      K R  +  +  +  +
Sbjct: 325 AEPQLIKRWKEGNRAPVDCERCSKCRTKRGNFCVVYKN 362


>gi|221633416|ref|YP_002522641.1| inosine-5'-monophosphate dehydrogenase [Thermomicrobium roseum DSM
           5159]
 gi|221156024|gb|ACM05151.1| inosine-5'-monophosphate dehydrogenase [Thermomicrobium roseum DSM
           5159]
          Length = 511

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 32/190 (16%), Positives = 64/190 (33%), Gaps = 36/190 (18%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
               +       G     L  AA +VE+ G + +          V + + G         
Sbjct: 234 DPHGRLRVGAAVGVGPESLERAAALVEE-GVDVL----------VVDTAHGHS------- 275

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
               +  M KA      +K R  VD     +A     +++ ++G + + +      +   
Sbjct: 276 --RAVIEMVKA------IKARWDVDVIAGNIATGEAARALIEAGADAVKVGVGPGSICTT 327

Query: 164 SPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYK 221
                  +P +   + V  + +    + +  +GG++     A  I    D VM+G     
Sbjct: 328 RVVAGVGVPQITAIMDVARVARAYG-VPVIADGGIQYSGDIAKAIAAGADTVMLG----- 381

Query: 222 NSAMLTTVDE 231
             ++L  VDE
Sbjct: 382 --SLLAGVDE 389


>gi|111219681|ref|YP_710475.1| putative NADH-dependent flavin oxidoreductase [Frankia alni ACN14a]
 gi|111147213|emb|CAJ58863.1| putative NADH-dependent flavin oxidoreductase [Frankia alni ACN14a]
          Length = 382

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 36/216 (16%), Positives = 65/216 (30%), Gaps = 20/216 (9%)

Query: 65  AAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AA+     G + I L++           P +   E ++G  L          + A+  A 
Sbjct: 164 AAERAHRVGADAIELHMAHGYLLHSFLSPLSNTREDNYGGSLEGRMRFPLQVVDAVRAAW 223

Query: 116 --SIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
               P+ V+     +  D I         + ++  GV+   +        G      R  
Sbjct: 224 PDGKPLLVRVAAVDNGTDGIDIEQTVEFARRLRALGVDA--VDCSSGGYGGSYTHGIRPG 281

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
             + +      +   P + +GL   + + +QA  I+     D V +GR A  N +     
Sbjct: 282 YQVGWAGEIRARAGVPTVAVGL---VTEPAQADAIVRDGHADLVALGREALANPSWPVHA 338

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            E               +    W        D  AR
Sbjct: 339 REQLGQYDFADRFDLLPIQSRSWLAKRQRQLDRLAR 374


>gi|54309755|ref|YP_130775.1| putative 2,4-dienoyl-CoA reductase [Photobacterium profundum SS9]
 gi|46914193|emb|CAG20973.1| putative 2,4-dienoyl-CoA reductase [Photobacterium profundum SS9]
          Length = 671

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 27/189 (14%), Positives = 61/189 (32%), Gaps = 21/189 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
               ++A++  + GY+ + L            C   R +     +G        +  + +
Sbjct: 145 EAFAKSAELAREAGYDGVELMGSEGYLVNQFIC--KRSNHRYDEWGGSYENRIRLPIELV 202

Query: 109 AAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+   +     +  RI     V+       +  L K ++K GV    ++      +   
Sbjct: 203 KAVRARVGKEFIIIFRISMLDLVEQGSTQEEVVQLAKELEKVGVT--ILNTGIGWHEARV 260

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P    ++P   +  V E  K   ++ +     +     A  IL     D V + R    +
Sbjct: 261 PTIATQVPRAAFAWVTEKLKSEVNIPLVTCNRINTPQVAEDILSANQADMVSMARPFLAD 320

Query: 223 SAMLTTVDE 231
              +   ++
Sbjct: 321 PDFVAKAEQ 329


>gi|188991496|ref|YP_001903506.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           campestris pv. campestris str. B100]
 gi|226702013|sp|B0RSL9|HIS6_XANCB RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|167733256|emb|CAP51454.1| Imidazoleglycerol phosphate synthase, cyclase subunit [Xanthomonas
           campestris pv. campestris]
          Length = 258

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELAMRYRDQGADELVFYDIGASPEGRS---------VDYAWVG 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIRDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|163801949|ref|ZP_02195846.1| 2,4-dienoyl-CoA reductase [Vibrio sp. AND4]
 gi|159174457|gb|EDP59261.1| 2,4-dienoyl-CoA reductase [Vibrio sp. AND4]
          Length = 472

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 47/125 (37%), Gaps = 8/125 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ K++     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 199 EIVKAVRKSVGEDFIIIFRLSMLDLVEQGSTFEDVIELAKALEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K +  + I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVKPHVSVPIITCNRINTPGEAERILSSGHADMVSMARPF 316

Query: 220 YKNSA 224
             +  
Sbjct: 317 LADPY 321


>gi|255930171|ref|XP_002556645.1| Pc06g00300 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211581258|emb|CAP79023.1| Pc06g00300 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 413

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 62/181 (34%), Gaps = 17/181 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V++A+++ D G++ + L+            P +     ++G        IV D +    
Sbjct: 171 FVDSARLMADSGFSGVELHAAHGYLLDQFLSPKSNFRTDAYGGSAEKRAKIVLDILGGCR 230

Query: 113 KALSIPVTVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWI----HARKAILKGLSPK 166
           + +     +  ++   D   A    +   +     +G++ + I    +    +L      
Sbjct: 231 EVVPANFCIGLKLNSADHSAASFEDIMAQIGMFANAGIDFLEISGGTYENPRVLSQTKSA 290

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                     D   E +K  P+L + L GG    + A   +     D V I R A  N  
Sbjct: 291 RTAAREAFFLDFAKETRKRYPNLVLMLTGGFRSRAGAEAAIKENACDIVGIARPAAINPR 350

Query: 225 M 225
           +
Sbjct: 351 L 351


>gi|148655920|ref|YP_001276125.1| dihydroorotate dehydrogenase 2 [Roseiflexus sp. RS-1]
 gi|148568030|gb|ABQ90175.1| dihydroorotate dehydrogenase [Roseiflexus sp. RS-1]
          Length = 330

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 39/216 (18%), Positives = 69/216 (31%), Gaps = 55/216 (25%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--- 105
           P+   + G      VE A+ VE  G + + LN+               L  +PDI G   
Sbjct: 104 PIIASLNGPSDGDWVEYARKVEQAGADALELNL-------------YFLATDPDITGAAV 150

Query: 106 -----DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---- 156
                  +  +C  ++IPV VK             + N+ K   ++G  G+ +  R    
Sbjct: 151 EEQYLRLVRDVCSRVTIPVAVKMSPFFSS------IANIAKQFSEAGARGLVLFNRFYQP 204

Query: 157 ---------KAILKGLSPKDNRKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALK 205
                       LK  +  + R    L +  +    IK +          G+      LK
Sbjct: 205 DFDLEALEVVPNLKLSTSDELRL--PLRWIAILYGRIKADLALTS-----GVHTAEDVLK 257

Query: 206 -ILPSVDGVM-----IGRAAYKNSAMLTTVDEYFSN 235
            ++      M     + R   +  A+L  +  +   
Sbjct: 258 AMMAGARVAMMTSELLARGIDRIPAILQDIRTWMEE 293


>gi|317472968|ref|ZP_07932272.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
 gi|316899580|gb|EFV21590.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
          Length = 357

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 38/217 (17%), Positives = 76/217 (35%), Gaps = 29/217 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-------- 84
           LRG +      S  E  L  Q       + +EAA      GY+ + L   C         
Sbjct: 122 LRGREYTADEMSEDEILLREQ-------QFIEAAVRARAAGYDGVEL--HCAHSYFLNAF 172

Query: 85  -SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            S  V+     FG  +     +V D +  +  +      +  R+G D+     +   +  
Sbjct: 173 LSPTVNHRTDRFGGNIEGRMRVVLDIMEGIRHSCGENFLISVRLGFDEPDLESSAF-MAG 231

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-----KKENPDLFIGLNGG 196
           + +K+G++ + +        G   +   + P  ++     I      K+     +   GG
Sbjct: 232 TFEKAGMDFLHVSTGFGS-TGFMDERTMENPPDEFPFNIRIWGAMQMKQRVSCPVIAVGG 290

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +  + Q + +L     D V +GRA   +   +  + +
Sbjct: 291 IRQVQQGMFLLEQECADFVALGRALLCDPEWVIKIKQ 327


>gi|294791396|ref|ZP_06756553.1| oxidoreductase, FAD/FMN-binding [Scardovia inopinata F0304]
 gi|294457867|gb|EFG26221.1| oxidoreductase, FAD/FMN-binding [Scardovia inopinata F0304]
          Length = 397

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 31/138 (22%), Positives = 49/138 (35%), Gaps = 11/138 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G           +   A+       +PV ++       +          L K++KK G+
Sbjct: 234 YGGSFTNRIRFALEVADAVRGVWPDDLPVIMRISATDWAEGGWDIYQSVELAKALKKHGI 293

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I +     I    S       PN       EI+ +  DL +   G +    QA KIL 
Sbjct: 294 DMIDVSTGGMI----SGVTIPSRPNYQVPFAQEIRSKA-DLPVTTVGLITKPKQAEKILE 348

Query: 209 S--VDGVMIGRAAYKNSA 224
               D V IGRAA ++  
Sbjct: 349 EGRADVVEIGRAALRDPY 366


>gi|153001397|ref|YP_001367078.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS185]
 gi|151366015|gb|ABS09015.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS185]
          Length = 364

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 60/179 (33%), Gaps = 22/179 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +A+  E  G + I ++            P +      +G  L     ++     A+ 
Sbjct: 160 FVSSAQRAERLGLDAIEIHAAHGYLLHQFLSPLSNQRTDKYGGSLENRLSLLLAVFDAIK 219

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +S  + +  RI   D +           L K ++  G + I +        GLSP   
Sbjct: 220 AVISPKIALGVRISATDWVEGGWDLAQSLVLAKVLESRGCDFIHVSTG-----GLSPLQQ 274

Query: 169 RKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
             +  +        IK E  ++ +   G + D ++A  IL     D + + R    +  
Sbjct: 275 ILVAEHFQVPFAKAIKAEV-NIPVIAVGLITDANKAETILVQGQADAIALARTMLYDPH 332


>gi|154420330|ref|XP_001583180.1| oxidoreductase, FAD/FMN-binding family protein [Trichomonas
           vaginalis G3]
 gi|121917420|gb|EAY22194.1| oxidoreductase, FAD/FMN-binding family protein [Trichomonas
           vaginalis G3]
          Length = 350

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 66/173 (38%), Gaps = 23/173 (13%)

Query: 58  DISKLVEA----AKIVEDFGYNEINLNVGC----------PSARVHEGSFGACLMLNPDI 103
           DI +L+EA    A  +++ G + I ++  C          P        +G        +
Sbjct: 134 DIDELIEAYKDIALRIKNVGADGIQVH-SCHMYLLAQFLSPGENKRTDKYGGSPENRCRL 192

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKK-SGVNGIWI---HARKA 158
             + I+A+   +     V  +I  DD +       +  K++    G++ + +       A
Sbjct: 193 HNEIISAIRSVVGNDFHVSIKINGDDYKKDGTKPEDAAKTVSLLKGIDLVEVSCGRTADA 252

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILP 208
           + +    K    IP  + D    IKK NP++ I   G    + DM +AL  + 
Sbjct: 253 MARSHCFKTFPFIPTYNLDAAKTIKKANPNMPIACVGNFRKVTDMEKALDDIE 305


>gi|298376252|ref|ZP_06986208.1| N-acetylmannosamine-6-phosphate epimerase superfamily protein
           [Bacteroides sp. 3_1_19]
 gi|298267289|gb|EFI08946.1| N-acetylmannosamine-6-phosphate epimerase superfamily protein
           [Bacteroides sp. 3_1_19]
          Length = 246

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 80/234 (34%), Gaps = 49/234 (20%)

Query: 36  DKKNILGFSTQEKPLALQIGGADI----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +KK +L        ++ Q+   D       +V+ AK  +  G   I  N           
Sbjct: 4   NKKELLDSFKGGLIVSCQVQHDDPTFSVDFVVKMAKAAQWGGAVGIRAN----------- 52

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNG 150
                   +P+     I A+ K + +PV    +I  DD    +       K++ ++G   
Sbjct: 53  --------DPEQ----IKAIKKEVDLPVIGLWKIWHDDTDVFITPTLEAAKAVWEAGAEI 100

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           I +     I     P          Y+++  +KKE P+  I     + +  +A++ +   
Sbjct: 101 IALDCTSQITHEGRPA---------YELLPIVKKEIPEAIIFA--DVSNYEEAVRAVEIG 149

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYA 263
            D  ++G   Y      T   ++   P         R+ +DF  K    M  + 
Sbjct: 150 AD--IVGPTLYGY----TEATKHIEQPDLRE---FARMCRDFKDKAYVIMEGHI 194


>gi|111025846|ref|YP_708266.1| NAD(P)H-dependent reductase [Rhodococcus jostii RHA1]
 gi|110824825|gb|ABH00108.1| NAD(P)H-dependent reductase [Rhodococcus jostii RHA1]
          Length = 362

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 32/200 (16%), Positives = 67/200 (33%), Gaps = 25/200 (12%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGAC 96
           +E P+ +Q       + V A+    + G++ + L+ G          PS  V   S+G  
Sbjct: 144 EELPVVIQ-------ETVTASLNAIEAGFDGVELHAGNGFLLHEFLSPSTNVRTDSYGGT 196

Query: 97  LMLNPDIVGDCIAAMCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
              +   V + + A+  A+    V ++     +      A     ++  +   + I    
Sbjct: 197 PENHARFVVETVEAVTAAVGAHRVGIRISPENEQHDMDEANNATARATYQVLADSIA--- 253

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
               L  LS   +    +   D+          L     G +    +A+ ++     D V
Sbjct: 254 -PLKLAYLSMLHHDPSGDFVQDLRARFGGAF--LVNSGFGIVTTRDEAISLVADGHADAV 310

Query: 214 MIGRAAYKNSAMLTTVDEYF 233
           ++GR A  N  +     +  
Sbjct: 311 VVGRPAIANPDLARRWKDGL 330


>gi|89073276|ref|ZP_01159806.1| putative 2,4-dienoyl-CoA reductase [Photobacterium sp. SKA34]
 gi|89050986|gb|EAR56450.1| putative 2,4-dienoyl-CoA reductase [Photobacterium sp. SKA34]
          Length = 670

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 30/225 (13%), Positives = 73/225 (32%), Gaps = 24/225 (10%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
           LL       +   V+ + +R        F+  E      +   +     +++++  + GY
Sbjct: 105 LLHAGRYAMSPFAVSASAIRSPIS---KFTPSEMSERQILKTINA--FAKSSELAREAGY 159

Query: 75  NEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           + + L            C  + +    +G           + + A+   +     +  R+
Sbjct: 160 DGVELMGSEGYLINQFICQRSNLRYDDWGGSYENRIRFPLEVVKAVRARVGRDFIIIFRL 219

Query: 126 G----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-Y 180
                V+       +  L K+++++GV    ++      +   P    ++P   +  V  
Sbjct: 220 SMLDLVEQGSTHEEVVMLAKALEQAGVT--ILNTGIGWHEARVPTIATQVPRAAFAWVTE 277

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +K+E     +  N  +     A  IL     D V + R    + 
Sbjct: 278 RLKQEVSIPLVTCNR-INTPQVAEDILSSGQADMVSMARPFLADP 321


>gi|260776352|ref|ZP_05885247.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260607575|gb|EEX33840.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 689

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 35/200 (17%), Positives = 70/200 (35%), Gaps = 19/200 (9%)

Query: 40  ILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHE 90
           I  FS  E     QI    I     +AK+ +  GY+ + +            C    +  
Sbjct: 145 IARFSPSEMSTR-QI-HKTIDAFANSAKLAQSAGYDGVEVMGSEGYLINQFICKRTNMRY 202

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKS 146
             +G C      +  + + A+ K +     +  R+     V++      +  L K ++K+
Sbjct: 203 DEWGGCYENRMRMPLEVVRAIRKEVGEEFIIIFRLSMLDLVEEGSTFDEVITLAKELEKA 262

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV    I+      +   P    ++P   +  V E  + + ++ I     +    +A +I
Sbjct: 263 GVT--IINTGIGWHEARVPTIATQVPRGAFTWVTEKVRPHVNVPIVTCNRINTPEEAERI 320

Query: 207 LPS--VDGVMIGRAAYKNSA 224
           L     D V + R    +  
Sbjct: 321 LSGGHADMVSMARPFLADPH 340


>gi|158521466|ref|YP_001529336.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfococcus oleovorans
           Hxd3]
 gi|158510292|gb|ABW67259.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfococcus oleovorans
           Hxd3]
          Length = 635

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 23/186 (12%), Positives = 59/186 (31%), Gaps = 18/186 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA+  ++ GY+ + +             P+  +    +G  L        + + ++ 
Sbjct: 146 FGEAARRSKEAGYDCVEIIASAGYLISQFMSPATNLRTDQYGGSLENRARFGTEILQSIR 205

Query: 113 KAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +    P+ V+      +        ++   +  + +G +   + A     +   P   
Sbjct: 206 SRVGDDYPIFVRMVGDELIPGGNTIDDMKQFARIWETAGADAFNVTAG--WHESKEPMIT 263

Query: 169 RKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
             +P   +  + E IK       +  +  +     A  IL     D V + R    +  +
Sbjct: 264 MNVPRGGFVWMSEGIKSALDHAPVAASNRINSAELAEDILASGKADMVSMARPLVCDPDL 323

Query: 226 LTTVDE 231
              + +
Sbjct: 324 PNRIKQ 329


>gi|148547915|ref|YP_001268017.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
 gi|148511973|gb|ABQ78833.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
          Length = 418

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 61/185 (32%), Gaps = 17/185 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P     +  +G  L     ++ + + A+ 
Sbjct: 151 FANTARLGEQAGFTGVEIHAAHGYLLSQFLSPLTNQRKDEWGGSLENRARLLLEIVKAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSP 165
             +S+   V  ++   D           + +V+ +   GV+ + +         ++G + 
Sbjct: 211 AVVSVDFAVAVKLNSADFQRGGFTTEDAKKVVEWLNDLGVDMVELSGGSYEVPAMQGDAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+   + A  ++   VD V IG A   +  
Sbjct: 271 DGRTLAREAYFVEFARDLQTVAKMPVMVTGGIRRRAVAESVVQSGVDMVGIGTALAIDPH 330

Query: 225 MLTTV 229
           +    
Sbjct: 331 LPRDW 335


>gi|289548825|ref|YP_003473813.1| NADH:flavin oxidoreductase/NADH oxidase [Thermocrinis albus DSM
           14484]
 gi|289182442|gb|ADC89686.1| NADH:flavin oxidoreductase/NADH oxidase [Thermocrinis albus DSM
           14484]
          Length = 351

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 61/177 (34%), Gaps = 22/177 (12%)

Query: 65  AAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           A K   + G++ I ++            P +   +  +G         + + +      +
Sbjct: 159 AVKRAVEAGFDIIEIHAAHGYLIHEFLSPVSNKRKDQYGGSFENRVRFLLEVVRIARSEM 218

Query: 116 --SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIH-ARKAILKGLSPKDNRK 170
             S+P+ V+      V+          L K +KK GV+ I     R    +        +
Sbjct: 219 PDSMPLWVRISSVDYVEGGWTLEESVELAKILKKEGVDVIDCSSGRIVEDEPFGEYPGHQ 278

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
           +P  +      IK+E   L     G +     A +I+ +   D V IGR   ++  +
Sbjct: 279 VPFAE-----RIKREAGVL-TQAVGMITSYELAQEIVANGRADFVAIGREFLRDPYL 329


>gi|218262756|ref|ZP_03477114.1| hypothetical protein PRABACTJOHN_02793 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223158|gb|EEC95808.1| hypothetical protein PRABACTJOHN_02793 [Parabacteroides johnsonii
           DSM 18315]
          Length = 325

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 68/194 (35%), Gaps = 45/194 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-------- 100
           P+   I        VE A+ +E  G + + LNV               L  +        
Sbjct: 98  PVIASINCYKSDAWVEFARQIELAGADALELNV-------------FFLETDLTYNSDNM 144

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D+  + I  + + +SIPV +K    V +      +  +  ++  +G +GI +  R    
Sbjct: 145 RDLYVNIIRKVKETVSIPVMIKMSKMVGN------IPAVAHTLTVNGADGIVLFNR--FY 196

Query: 161 KGLSPKDNRKI-------------PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
           +     +N +I               L +  +  +  + P + I  + G+ D    +K  
Sbjct: 197 QPDIDINNMQIVSGNVFSNHSDLSDTLRWTAI--VSGKIPGISIASSTGVHDWEDVIKCL 254

Query: 207 LPSVDGVMIGRAAY 220
           L   D V +  A Y
Sbjct: 255 LAGADAVQMCSAVY 268


>gi|303246963|ref|ZP_07333239.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio
           fructosovorans JJ]
 gi|302491670|gb|EFL51553.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfovibrio
           fructosovorans JJ]
          Length = 364

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 35/179 (19%), Positives = 56/179 (31%), Gaps = 24/179 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            V+AAK  +      + +   C           P +   +   G  L          + A
Sbjct: 159 FVDAAKRADALDLAGVEI--HCAHGYLLHQFLSPLSNTRDDDCGGSLENRMCFPLRIVKA 216

Query: 111 MCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + KAL     +  RI   D +P            + IKK G + I + +      GLSPK
Sbjct: 217 VRKALPRNRILGIRISATDWVPGGWDIEDSVAFAREIKKLGCDYIHVSSG-----GLSPK 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
               +         E  +    L     G + D + A  I+     D V + R    + 
Sbjct: 272 QQIPLAPGYQAPFAERIRRETGLPTIAVGLITDPALAETIVVTGQADMVALARGMLYDP 330


>gi|294140057|ref|YP_003556035.1| 2,4-dienoyl-CoA reductase [Shewanella violacea DSS12]
 gi|293326526|dbj|BAJ01257.1| 2,4-dienoyl-CoA reductase, putative [Shewanella violacea DSS12]
          Length = 677

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 29/207 (14%), Positives = 63/207 (30%), Gaps = 43/207 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
           K VE+A I +  G++ + ++       VHEG                 +G          
Sbjct: 158 KFVESAAIAQKAGFDGVEIHA------VHEGYLLDQFTMKFFNKRTDEYGGSFENRYRFA 211

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPA------------------VALRNLVKSIKKS 146
            + +  +         V  R  V   + A                         K ++ +
Sbjct: 212 VEIVEGIKAVCGKHFPVSLRYSVKGNMKAYGQGILPGEEAEEVGRDMEEGLKAAKYLQDA 271

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + + + A        +   N   P +       +  E  D+ + + G +E+   A   
Sbjct: 272 GYDALNVDAGTYDSWYWNHPPNYFQPGMYKPYCKAV-SEVVDIPVLMAGRMENPDLASHA 330

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDE 231
           + +   DG+ +GR    +  ++  +  
Sbjct: 331 VENGICDGISMGRPLLADPEVVNKIRR 357


>gi|297564769|ref|YP_003683741.1| N-acylglucosamine-6-phosphate 2-epimerase [Meiothermus silvanus DSM
           9946]
 gi|296849218|gb|ADH62233.1| N-acylglucosamine-6-phosphate 2-epimerase [Meiothermus silvanus DSM
           9946]
          Length = 226

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 28/164 (17%), Positives = 54/164 (32%), Gaps = 35/164 (21%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI--VGDCIAAMCKALSIPVT 120
           +E+A+ V + G + + L+                    P +  +   I  +   L +PV 
Sbjct: 83  LESARRVVEAGADLVALSC--------------AFYQRPSLPELHTLIREIQDELGVPVM 128

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
             C    +    A A  +LV S                 L G +P         D ++V 
Sbjct: 129 ADCSTLEEGLWAAEAGADLVAS----------------TLSGYTPATQGLHQGPDLELVA 172

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           ++ ++   + +   G +    +A   L      V++G  A  N 
Sbjct: 173 DLARQA-RVPVVAEGRIWTPQEARAALEAGAYAVVVGT-AITNP 214


>gi|313500295|gb|ADR61661.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida BIRD-1]
          Length = 368

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 26/158 (16%), Positives = 55/158 (34%), Gaps = 11/158 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G+C      +  + + A+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGSCFENRIRLTLEVVDAVRKAWPAELPLFVRVSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + ++  GV+ I + +      G S                E  ++  ++  G  G + +
Sbjct: 250 ARRLRSLGVDLIDVSSG-----GTSVNAEIPTGPGYQTRFAERVRKESEIATGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +QA  IL     D + + R   ++       D+    
Sbjct: 305 PAQAEHILRTGQADIIFLARELLRDPYWPLHADDDLGG 342


>gi|270308498|ref|YP_003330556.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Dehalococcoides sp. VS]
 gi|270154390|gb|ACZ62228.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Dehalococcoides sp. VS]
          Length = 269

 Score = 44.0 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           ++++++ EI      + + + GG+  M    K+L   VD V++G AA +N  ++  +   
Sbjct: 93  VNFELIREIANSAL-IPVEVGGGIRSMDTVKKLLTAGVDRVILGTAAVENPELVREICAR 151

Query: 233 FSN 235
           +++
Sbjct: 152 YAD 154


>gi|323488578|ref|ZP_08093822.1| Probable NADH-dependent flavin oxidoreductase yqiG [Planococcus
           donghaensis MPA1U2]
 gi|323397795|gb|EGA90597.1| Probable NADH-dependent flavin oxidoreductase yqiG [Planococcus
           donghaensis MPA1U2]
          Length = 373

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 42/269 (15%), Positives = 95/269 (35%), Gaps = 37/269 (13%)

Query: 11  FFARLLTNNALLYTEM-IVADAI--LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK 67
           + A  ++N  LL  E  + A A+  LR + +     S +E    ++  G       EA +
Sbjct: 107 YHAGRMSNEKLLNGEQPVSASAVPALRPNAETPREMSHEEIKETIKAFG-------EATR 159

Query: 68  IVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNP-DIVGDCIAAMCKA 114
                G++ + +             P +      +G  +   M  P  ++     A+ + 
Sbjct: 160 RAIQAGFDGVEIHGANTYLIQQFFSPHSNTRTDQWGGDVKGRMAFPLAVIESIQQAVAEY 219

Query: 115 LSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
              P  V+ RI  +++       +     + +I   G++ + +   +     +  +D+R 
Sbjct: 220 ADKPFVVEYRISPEEREEPGITMDDTLKFLTAIADQGIDYVHVSVGRFFGGSIRVEDSRS 279

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTV- 229
              +    +         + +   GGL+ +S   + L     V +G A   +   L+ V 
Sbjct: 280 RVEVIQQHIG------TRVPVIGVGGLQTLSDVKEALEVTPLVSLGHALIMDPDWLSKVQ 333

Query: 230 ---DEYFSNPLTGSSPIKTRVDKDFWRKI 255
              DE     +  S   +  + ++ W  +
Sbjct: 334 KSRDEEIHQAIYLSKKDQLDIPENLWNMV 362


>gi|223983011|ref|ZP_03633219.1| hypothetical protein HOLDEFILI_00498 [Holdemania filiformis DSM
           12042]
 gi|223965008|gb|EEF69312.1| hypothetical protein HOLDEFILI_00498 [Holdemania filiformis DSM
           12042]
          Length = 630

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 69/184 (37%), Gaps = 27/184 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
             EAA+  +  G++ I L+ G     +               +G  L          +  
Sbjct: 132 FAEAAQQAKTLGFDAIFLHFG--HGWLAAQFLSPLFNHRTDEYGGSLPNRARFPLLILRK 189

Query: 111 MCKALS--IPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI-----LK 161
           + +A+    PV ++      V   IP       ++  +   ++G+ I A   I     + 
Sbjct: 190 IREAVGPEFPVDMRISGEECVPGSIPFEDTLAFIQMAEPY-IDGVQISAGLDINHEGNVH 248

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
             +      +PNL +     +KK  P L + + G + + S+A +IL +  VD V  GRA 
Sbjct: 249 MATTNFKEHMPNLKWA--RTVKKTCPGLVVSVVGAIMNPSEAEQILANGDVDLVAFGRAF 306

Query: 220 YKNS 223
             + 
Sbjct: 307 IADP 310


>gi|163760555|ref|ZP_02167636.1| NADH:flavin oxidoreductase/NADH oxidase [Hoeflea phototrophica
           DFL-43]
 gi|162282170|gb|EDQ32460.1| NADH:flavin oxidoreductase/NADH oxidase [Hoeflea phototrophica
           DFL-43]
          Length = 396

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 42/244 (17%), Positives = 88/244 (36%), Gaps = 24/244 (9%)

Query: 5   TDRH-YRFFARLLTNNAL-LYTEMIVADAILRGDKKNILGFSTQEKP-LALQIGGAD--- 58
           +D   +    R  T N + L+ ++  A A+      N  G S  + P LA     AD   
Sbjct: 83  SDLARFHDLTRRGTANGMHLWPQLGHAGAMAYPPISNPKGPSALDLPGLAASAMTADEIA 142

Query: 59  --ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDC 107
              ++  + AK+ +  G+  + ++            P     E  +G  +     ++ + 
Sbjct: 143 ALPAQFAQTAKLAQSAGFTGVQVHAAHGFLLSQFLSPLFNRREDGYGGSIENRMRLLLEV 202

Query: 108 IAAMCKAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           I A+  AL   +P+ VK      ++  +       +  ++  +G++ + I          
Sbjct: 203 IDAVRNALGPDMPIAVKLNATDQLEGGLGQEDALTVAAALDATGIDLLDISGGTYFPGAK 262

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           S  D+        D      ++     +   GG + ++QA   +   +VD V + RA   
Sbjct: 263 SASDSGGKGPYFLDFAKR-ARQVTRKPLMATGGFKTLAQASDAVSSGTVDMVGLARALAL 321

Query: 222 NSAM 225
              +
Sbjct: 322 EPGL 325


>gi|46908643|ref|YP_015032.1| NADPH dehydrogenase NamA [Listeria monocytogenes serotype 4b str.
           F2365]
 gi|47092757|ref|ZP_00230542.1| NADH:flavin oxidoreductase [Listeria monocytogenes str. 4b H7858]
 gi|226225019|ref|YP_002759126.1| NADH oxidase [Listeria monocytogenes Clip81459]
 gi|254825407|ref|ZP_05230408.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL J1-194]
 gi|254932288|ref|ZP_05265647.1| NADPH dehydrogenase NamA [Listeria monocytogenes HPB2262]
 gi|255521331|ref|ZP_05388568.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL J1-175]
 gi|68052638|sp|Q71WV6|NAMA_LISMF RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|259511220|sp|C1KYN8|NAMA_LISMC RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|46881915|gb|AAT05209.1| NADH:flavin oxidoreductase [Listeria monocytogenes serotype 4b str.
           F2365]
 gi|47018845|gb|EAL09593.1| NADH:flavin oxidoreductase [Listeria monocytogenes str. 4b H7858]
 gi|225877481|emb|CAS06195.1| Putative NADH oxidase [Listeria monocytogenes serotype 4b str. CLIP
           80459]
 gi|293583845|gb|EFF95877.1| NADPH dehydrogenase NamA [Listeria monocytogenes HPB2262]
 gi|293594650|gb|EFG02411.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL J1-194]
 gi|328465207|gb|EGF36470.1| NADPH dehydrogenase NamA [Listeria monocytogenes 1816]
 gi|328471280|gb|EGF42180.1| NADPH dehydrogenase NamA [Listeria monocytogenes 220]
 gi|332312901|gb|EGJ25996.1| NADPH dehydrogenase [Listeria monocytogenes str. Scott A]
          Length = 338

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     + G 
Sbjct: 317 KDAAKQLGETIEGP 330


>gi|317027898|ref|XP_001400222.2| NADH oxidase [Aspergillus niger CBS 513.88]
          Length = 339

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 42/226 (18%), Positives = 80/226 (35%), Gaps = 26/226 (11%)

Query: 38  KNILGFSTQE-KPLALQIGGAD------ISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           K I  F+  + + +A+Q+  A          L   A  V++ G     +    PSA  HE
Sbjct: 116 KRITEFAHSQSQKIAIQLAHASRKASAVAPWLSANAMAVKEVGGWPDEI--VGPSAIAHE 173

Query: 91  GSFGA---CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
               +    L  + + V + +    +A    V                L   +  +    
Sbjct: 174 EGVNSVPRAL--SEEEVKELVNDFGEAAKRAVRAGFDAIEVHSAHGYLLHQFLSPVSNHR 231

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKI 206
            +      R   +   S    R  P     + +E+K+   D L +   GG++    A ++
Sbjct: 232 TD------RSGGVHSKSAIAIRPGPAYQVHLAHEVKQAVGDRLLVTAVGGIKTGKLAEEV 285

Query: 207 LP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           +   +D V+ GR   +N  ++      F+N L     + T++D  F
Sbjct: 286 VQSGIDAVLAGRWFQQNPGLVR----AFANELGVKVRMATQIDWSF 327


>gi|146329327|ref|YP_001209578.1| dihydroorotate dehydrogenase [Dichelobacter nodosus VCS1703A]
 gi|166199349|sp|A5EV79|PYRD_DICNV RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|146232797|gb|ABQ13775.1| dihydroorotate dehydrogenase [Dichelobacter nodosus VCS1703A]
          Length = 337

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 31/159 (19%), Positives = 59/159 (37%), Gaps = 25/159 (15%)

Query: 74  YNEINLNVGCPS----ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            + + +N+  P+      +  G+    L+       D ++A+ +   +P+ VK     + 
Sbjct: 164 ADYLAINISSPNTVGLRDLQHGAALCELLQRLKTERDKLSAVYEKT-VPLLVKIAPDNER 222

Query: 130 QIPAVALRNLVKSIKKSGVNGI------------WIHARKAILKGLSPKDNRKIPNLDYD 177
           +     L  ++  I+ SG++GI              H       GLS K   +       
Sbjct: 223 E----QLDEMLSIIEDSGIDGIIATNTTLDKTAVTGHRYADEQGGLSGKPLTEKST---K 275

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMI 215
           I+  I++  PDL +  +GG+         L    D V I
Sbjct: 276 IIAHIRERLPDLPLIASGGVMSADDYYAKLEAGADLVQI 314


>gi|34809592|pdb|1JQX|A Chain A, The R57a Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
 gi|34809593|pdb|1JQX|B Chain B, The R57a Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
          Length = 311

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 68/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCP--NVPGK---PQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   K    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|34809594|pdb|1JRB|A Chain A, The P56a Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
 gi|34809595|pdb|1JRB|B Chain B, The P56a Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
          Length = 311

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 68/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCP--NVPGK---PQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   K    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|34809596|pdb|1JRC|A Chain A, The N67a Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
 gi|34809597|pdb|1JRC|B Chain B, The N67a Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
          Length = 311

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 68/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCP--NVPGK---PQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   K    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|125623791|ref|YP_001032274.1| dihydroorotate dehydrogenase 1A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|81309034|sp|Q53ZE5|PYRDA_LACLC RecName: Full=Dihydroorotate dehydrogenase A; AltName:
           Full=DHOdehase A; Short=DHOD A; Short=DHODase A;
           AltName: Full=Dihydroorotate oxidase A
 gi|146325673|sp|A2RJT9|PYRDA_LACLM RecName: Full=Dihydroorotate dehydrogenase A; AltName:
           Full=DHOdehase A; Short=DHOD A; Short=DHODase A;
           AltName: Full=Dihydroorotate oxidase A
 gi|2098351|pdb|1DOR|A Chain A, Dihydroorotate Dehydrogenase A From Lactococcus Lactis
 gi|2098352|pdb|1DOR|B Chain B, Dihydroorotate Dehydrogenase A From Lactococcus Lactis
 gi|3660331|pdb|2DOR|A Chain A, Dihydroorotate Dehydrogenase A From Lactococcus Lactis
           Complexed With Orotate
 gi|3660332|pdb|2DOR|B Chain B, Dihydroorotate Dehydrogenase A From Lactococcus Lactis
           Complexed With Orotate
 gi|34809600|pdb|1JUE|A Chain A, 1.8 A Resolution Structure Of Native Lactococcus Lactis
           Dihydroorotate Dehydrogenase A
 gi|34809601|pdb|1JUE|B Chain B, 1.8 A Resolution Structure Of Native Lactococcus Lactis
           Dihydroorotate Dehydrogenase A
 gi|114793547|pdb|2BSL|A Chain A, Crystal Structure Of L. Lactis Dihydroorotate Dehydrogense
           A In Complex With 3,4-Dihydroxybenzoate
 gi|114793548|pdb|2BSL|B Chain B, Crystal Structure Of L. Lactis Dihydroorotate Dehydrogense
           A In Complex With 3,4-Dihydroxybenzoate
 gi|114793574|pdb|2BX7|A Chain A, Crystal Structure Of L. Lactis Dihydroorotate Dehydrogense
           A In Complex With 3,5-Dihydroxybenzoate
 gi|114793575|pdb|2BX7|B Chain B, Crystal Structure Of L. Lactis Dihydroorotate Dehydrogense
           A In Complex With 3,5-Dihydroxybenzoate
 gi|511015|emb|CAA52279.1| dihydroorotate dehydrogenase A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|33302311|gb|AAQ01776.1| dihydroorotate dehydrogenase 1a [Lactococcus lactis subsp.
           cremoris]
 gi|124492599|emb|CAL97544.1| dihydroorotate dehydrogenase A [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|300070561|gb|ADJ59961.1| dihydroorotate dehydrogenase 1A [Lactococcus lactis subsp. cremoris
           NZ9000]
          Length = 311

 Score = 44.0 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 68/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCP--NVPGK---PQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   K    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|119774859|ref|YP_927599.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella amazonensis
           SB2B]
 gi|119767359|gb|ABL99929.1| 2,4-dienoyl-CoA reductase [Shewanella amazonensis SB2B]
          Length = 671

 Score = 44.0 bits (103), Expect = 0.033,   Method: Composition-based stats.
 Identities = 20/124 (16%), Positives = 44/124 (35%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+  A+     +  R+     V++      +  L K ++++GV    I+      +
Sbjct: 197 EIVRAIRAAVGSDFIIIFRLSMLDLVEEGSSWDEVVALAKGLEEAGVT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P     +P   +  V E  K+   + +     +     A +IL     D V + R  
Sbjct: 255 ARIPTIATSVPRGAFAWVTERLKQEVHIPLIATNRINTPEIAEQILASGQADMVSMARPF 314

Query: 220 YKNS 223
             + 
Sbjct: 315 LADP 318


>gi|317053823|ref|YP_004117848.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
 gi|316951818|gb|ADU71292.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
          Length = 365

 Score = 44.0 bits (103), Expect = 0.033,   Method: Composition-based stats.
 Identities = 32/206 (15%), Positives = 62/206 (30%), Gaps = 29/206 (14%)

Query: 39  NILGFSTQEKPLALQIGGADISK----LVEAAKIVEDFGYNEINLNVG---------CPS 85
           + +     E P    +  AD+ +     V +A      G+  I L+            P 
Sbjct: 133 SAIPMHEGEHPPTP-LTHADLERIKQSFVASALRAVRIGFELIELHAAHGYLLHQFLSPL 191

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVK 141
           A   +  +G  L        + + A+  A+   V V  RI   D               +
Sbjct: 192 ANQRDDEYGGSLENRMRFPLEVLEAVRAAVPAHVAVGVRISATDWVEGGWDVAQSAEFCQ 251

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLED 199
            I+  G   +       +  G      +   +  Y +    E++K    + +   G + +
Sbjct: 252 KIEALGSAYVH------VSSGGLSAQQKITVSAGYQVPFARELRK-VTRMPVIAVGLITE 304

Query: 200 MSQALKILP--SVDGVMIGRAAYKNS 223
              A  +L     D V + R    + 
Sbjct: 305 PRMAEDLLQDGDADLVALARGILYDP 330


>gi|169334204|ref|ZP_02861397.1| hypothetical protein ANASTE_00602 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258921|gb|EDS72887.1| hypothetical protein ANASTE_00602 [Anaerofustis stercorihominis DSM
           17244]
          Length = 365

 Score = 44.0 bits (103), Expect = 0.033,   Method: Composition-based stats.
 Identities = 31/190 (16%), Positives = 58/190 (30%), Gaps = 22/190 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCI 108
            K V+AA   +   Y+ + +   C           P +      +G  L     +  + +
Sbjct: 147 DKFVKAALRAKRAKYDGVEI--HCAHSYLLSDFISPLSNKRNDEYGGSLDKRMKLPLEIL 204

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             + K       +  R+G D +        + K     G + I I         +S    
Sbjct: 205 KEIRKECGNDFIISVRMGFD-EPTIDEGIKIAKMFDTCGSDIIHISTGFGSSGYMSESIM 263

Query: 169 RKIPNLDYDIVYEI-----KKENPDLFIGLNGGLEDMSQALKI-LPSV-DGVMIGRAAYK 221
            K PN D+ +   I      K      +   GG+ +   A  +      D   +GR    
Sbjct: 264 PKAPN-DFPLNIRIWASSQIKPYLSCKVIAVGGIRNAEDANTVIFEGYGDFAAVGRGLLC 322

Query: 222 NSAMLTTVDE 231
           +   +  + E
Sbjct: 323 DPEFVNKIKE 332


>gi|54303087|ref|YP_133080.1| putative NADH-dependent flavin oxidoreductase [Photobacterium
           profundum SS9]
 gi|46916515|emb|CAG23280.1| putative NADH-dependent flavin oxidoreductase [Photobacterium
           profundum SS9]
          Length = 370

 Score = 44.0 bits (103), Expect = 0.033,   Method: Composition-based stats.
 Identities = 32/223 (14%), Positives = 75/223 (33%), Gaps = 19/223 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +A++  ++ G++ + ++            P     E  +G  L     ++ +  A + 
Sbjct: 147 FAQASRRAQESGFDGVEIHAAHTYLINQFLSPYYNRREDEYGGSLDNRMRLLLEIYAEIR 206

Query: 113 KALS--IPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
           K +    P+ VK       +  +     R + + ++  GV+ I     IH +   + G S
Sbjct: 207 KLVGDEYPILVKLTASEFFEGGLTFDETRIVCQKLEAIGVDAIIISGNIHGKANSMIGES 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
                      +     +  E  ++ +   GGL D+    +I    ++    + R     
Sbjct: 267 FDGYTIQQEGYFHEYGHVISEEVNVPVITVGGLTDIDAIEEIANKTNIQYFALSRPLLSE 326

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
             ++    E    P+      K R  +  +  ++       AR
Sbjct: 327 PHLVKRWKEGNRAPVECERCSKCRTKRGNFCIVNKKRKSQLAR 369


>gi|330959324|gb|EGH59584.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. maculicola str.
           ES4326]
          Length = 679

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTRVRQAVGPQFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|209544532|ref|YP_002276761.1| NADH:flavin oxidoreductase/NADH oxidase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209532209|gb|ACI52146.1| NADH:flavin oxidoreductase/NADH oxidase [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 368

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 47/137 (34%), Gaps = 10/137 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           ++G  L        +   A+ +A    PVT++      V           L K+++  G 
Sbjct: 201 AYGGSLENRLRFPLEVFDAVREAFPDGPVTIRVSGTDWVPGGWDVEQTIALAKALESRGC 260

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I + +      GLSP+    +       +    K    + +   G +    QA  I+ 
Sbjct: 261 DAIHVSSG-----GLSPQQQIPVHPSYQVPLARAVKAETTMPVVAVGLITGFEQAEAIVA 315

Query: 209 SVDGVMI--GRAAYKNS 223
           + D  MI   R    + 
Sbjct: 316 TGDADMIALARTILYDP 332


>gi|167760750|ref|ZP_02432877.1| hypothetical protein CLOSCI_03135 [Clostridium scindens ATCC 35704]
 gi|167661637|gb|EDS05767.1| hypothetical protein CLOSCI_03135 [Clostridium scindens ATCC 35704]
          Length = 639

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEGS------FGACLMLNPDIVGDCIAA 110
            +    A++    G++ +  +      P   +  G       +G           + + A
Sbjct: 135 EEFGRGARLAVQAGFDAVEFHAAHSYLPHEFLSPGMNKRTDEYGGSFENRCRFCYEVVQA 194

Query: 111 MCKAL--SIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +   +   +P  +        ++  +    +   +    + GV+   +    A     S 
Sbjct: 195 IRSNIPDDMPFFMRADCIDELMEQTMTEEEIVTFINKCAELGVDVADLSRGNAT----SF 250

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
               ++P  +       + +Y IKK+  ++ +   G +     A K++     D V IGR
Sbjct: 251 ATVYEVPPFNLAHGFNIENIYNIKKQI-NIPVMGVGRINTGEMANKVIEEGKFDLVGIGR 309

Query: 218 AAYKNSAMLTTVDE 231
           A   +   +T V E
Sbjct: 310 AQLADPNWITKVRE 323


>gi|104784088|ref|YP_610586.1| FMN-binding oxidoreductase [Pseudomonas entomophila L48]
 gi|95113075|emb|CAK17803.1| putative oxidoreductase, FMN-binding [Pseudomonas entomophila L48]
          Length = 686

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 36/221 (16%), Positives = 76/221 (34%), Gaps = 32/221 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------- 82
           + + R   K I     +E     ++ G       +AA+  ++ G + + L+         
Sbjct: 130 EPVHRATCKTI---EPEE---IWRVIGNY----AQAARRAKEGGLDGVELSAVHQHMIDQ 179

Query: 83  CPSARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD----DQIPAVAL 136
             S RV++    +G           + + A+ K +     V  RI  D    D +    +
Sbjct: 180 FWSPRVNKRTDEWGGTFEGRMKFGLEVLKAVRKEVGDDFCVGMRICGDEFHPDGLSHEDM 239

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NRKIPNLDYDIVYEIKKENPDLFIGL 193
           + +      +G+               +  +   N   P   +  +    KE   + +  
Sbjct: 240 KQIAAYYDATGMLDFIGVVGSGCDTHNTLANVIPNMSYPPEPFLHLAAGIKEVVKVPVLH 299

Query: 194 NGGLEDMSQALKILPS--VDGVMIG--RAAYKNSAMLTTVD 230
              ++D +QA +IL    VD  M+G  RA   +  ++  + 
Sbjct: 300 AQNIKDPNQATRILEGGYVD--MVGMTRAHIADPHLIAKIK 338


>gi|332992470|gb|AEF02525.1| 2,4-dienoyl-CoA reductase [Alteromonas sp. SN2]
          Length = 680

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 43/124 (34%), Gaps = 9/124 (7%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D          +  L K I+K+G     I+      +
Sbjct: 205 EVVRRVREAVGKHFIIIYRLSMLDLVEGGSNYEEVVQLGKEIEKAGAT--IINTGIGWHE 262

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
              P    K+P   +  V    +E   + +  +  +     A ++L   D  M+   +  
Sbjct: 263 ARIPTIATKVPRAAFTWVTAKFREALSIPVITSNRINTPEVAEEVLARGDADMV---SMA 319

Query: 222 NSAM 225
              +
Sbjct: 320 RPFL 323


>gi|298717174|ref|YP_003729816.1| NADH oxidase [Pantoea vagans C9-1]
 gi|298361363|gb|ADI78144.1| NADH oxidase [Pantoea vagans C9-1]
          Length = 359

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 33/155 (21%), Positives = 59/155 (38%), Gaps = 10/155 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVK 141
           P A V E  +G        IV + IAA+ +    P+ V+       +            +
Sbjct: 177 PLANVREDQYGGSHENRYRIVREVIAAVREEWDGPLFVRISSTDYTEGGNTPEDFLTYGR 236

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +K+ GV+ I   +      G++P      PN       ++ + +  +  G  G ++   
Sbjct: 237 WMKEQGVDLIDCSSG-----GIAPAVVNVFPNYQVPA-AQLLRNSLGIKTGAVGLIQTGR 290

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           QA +IL +   D V+IGR   K+     T  +   
Sbjct: 291 QAEEILQNGRADMVLIGREMLKDPFWARTAGDDLQ 325


>gi|162146168|ref|YP_001600627.1| NADPH dehydrogenase [Gluconacetobacter diazotrophicus PAl 5]
 gi|161784743|emb|CAP54283.1| NADPH dehydrogenase [Gluconacetobacter diazotrophicus PAl 5]
          Length = 368

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 47/137 (34%), Gaps = 10/137 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL-SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           ++G  L        +   A+ +A    PVT++      V           L K+++  G 
Sbjct: 201 AYGGSLENRLRFPLEVFDAVREAFPDGPVTIRVSGTDWVPGGWDVEQTIALAKALESRGC 260

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I + +      GLSP+    +       +    K    + +   G +    QA  I+ 
Sbjct: 261 DAIHVSSG-----GLSPQQQIPVHPSYQVPLARAVKAETTMPVVAVGLITGFEQAEAIVA 315

Query: 209 SVDGVMI--GRAAYKNS 223
           + D  MI   R    + 
Sbjct: 316 TGDADMIALARTILYDP 332


>gi|319426924|gb|ADV54998.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella putrefaciens
           200]
          Length = 364

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 66/188 (35%), Gaps = 28/188 (14%)

Query: 58  DISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIV 104
           DI +L+ A    A+  E  G + I ++            P +      +G  L     ++
Sbjct: 152 DIDELIAAFVSSAQRAERLGLDGIEIHAAHGYLLHQFLSPLSNQRTDKYGGSLENRLRLL 211

Query: 105 GDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
                A+   +S    + V +     VD          L K+++  G + I +       
Sbjct: 212 LAVFDAIKAVISPKMVLGVRISATDWVDGGWDLAQSLVLAKALEARGCDFIHVSTG---- 267

Query: 161 KGLSPKDNRKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
            GLSP     IP  ++  V   +  K   ++ +   G + D ++A  IL     D + + 
Sbjct: 268 -GLSPLQQ--IPVAEHFQVPFADAIKAEVNMPVIAVGLITDANKAETILAQGQADAIALA 324

Query: 217 RAAYKNSA 224
           R    +  
Sbjct: 325 RTMLYDPH 332


>gi|260904076|ref|ZP_05912398.1| NADH:flavin oxidoreductase/NADH oxidase [Brevibacterium linens BL2]
          Length = 161

 Score = 43.7 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 53/160 (33%), Gaps = 13/160 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G  L     I+ +   A+  A+   +PV V+       +          + + + + GV
Sbjct: 6   YGGDLAGRSRILIETYQAVRAAVGEDVPVFVRLSASEWREGGFDIAEAVEVSRDLNECGV 65

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + I + +       +      ++P     +   I+ E      G  G + D  QA  IL 
Sbjct: 66  DLIDVSSGGNFPVKVPVGSGYQVP-----LSAAIRAEGVST--GTVGLITDPEQAETILA 118

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
               D + + RAA +  A                 P  TR
Sbjct: 119 SEQADAIFLARAALREPAWPQRAAHDLGVEPGPYPPQYTR 158


>gi|259502158|ref|ZP_05745060.1| dihydroorotate dehydrogenase [Lactobacillus antri DSM 16041]
 gi|259169776|gb|EEW54271.1| dihydroorotate dehydrogenase [Lactobacillus antri DSM 16041]
          Length = 292

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 29/144 (20%), Positives = 51/144 (35%), Gaps = 23/144 (15%)

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA----- 135
           + CP     +         +PD+      A+ +   +PV  K    +   +PAV      
Sbjct: 1   MSCPQTSNAKMGAEVD--EDPDLCRQLTEAVKRGSDLPVIAKISPNLSSMVPAVKGCLAG 58

Query: 136 ------LRNLVKSIKKS----GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
                 L + V+S+        V    I+ + A+  GLS K    +  +    + E++  
Sbjct: 59  GADGFSLIDTVRSVTDVDLEKNVALPNINGKSAV-SGLSGK---AVKPIALHFLQELRSA 114

Query: 186 NP--DLFIGLNGGLEDMSQALKIL 207
                L I   GG+E    A + L
Sbjct: 115 AGLEKLQIAGIGGIETWEDAAEYL 138


>gi|315283593|ref|ZP_07871742.1| NADPH dehydrogenase [Listeria marthii FSL S4-120]
 gi|313612763|gb|EFR86756.1| NADPH dehydrogenase [Listeria marthii FSL S4-120]
          Length = 205

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 33/193 (17%), Positives = 63/193 (32%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 11  DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 70

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P+ V+          +         K +K  GV  I +     +          
Sbjct: 71  KEVWDGPIIVRVSATDYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPGY 130

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N     
Sbjct: 131 QVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFAK 184

Query: 228 TVDEYFSNPLTGS 240
              +     + G 
Sbjct: 185 DAAKQLGEAIEGP 197


>gi|226362526|ref|YP_002780304.1| NADH-dependent flavin oxidoreductase [Rhodococcus opacus B4]
 gi|226241011|dbj|BAH51359.1| putative NADH-dependent flavin oxidoreductase [Rhodococcus opacus
           B4]
          Length = 367

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 61/165 (36%), Gaps = 13/165 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSG 147
            +G        ++ + IAA+       +P+ ++       +D         L++S++ SG
Sbjct: 203 GYGGDPDRRARLLREIIAAVRAVWPEELPLLLRISATDWAEDGWDVDDSVALIRSLEGSG 262

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           ++ + + +      GL+P+    +           I+ E   L +   G + D SQA ++
Sbjct: 263 IDLVDVSSG-----GLTPEQKIAVGPGYQVPFARRIRNET-SLPVAAVGLITDSSQAEQV 316

Query: 207 L--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
           L   + D V +GR   +         +      T   P   R  +
Sbjct: 317 LVDGAADAVFVGRNLLREPMWPLKAAKELGVEDTLDWPTPYRSAR 361


>gi|126175068|ref|YP_001051217.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS155]
 gi|125998273|gb|ABN62348.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS155]
          Length = 364

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 63/180 (35%), Gaps = 24/180 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +A+  E  G + I ++            P +      +G  L     ++     A+ 
Sbjct: 160 FVSSAQRAERLGLDAIEIHAAHGYLLHQFLSPLSNQRIDKYGGSLENRLSLLLAVFDAIK 219

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +S  + +  RI   D +           L K+++  G + I +        GLSP   
Sbjct: 220 AVISPKMALGVRISATDWVEGGWDLAQSLVLAKALESRGCDFIHVSTG-----GLSPLQQ 274

Query: 169 RKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             IP  ++  V   E  K   ++ +   G + D ++A  IL     D + + R    +  
Sbjct: 275 --IPVAEHFQVPFAEAIKAEVNIPVIAVGLITDANKAETILAQGQADAIALARTMLYDPH 332


>gi|209559655|ref|YP_002286127.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes NZ131]
 gi|209540856|gb|ACI61432.1| Dihydroorotate dehydrogenase [Streptococcus pyogenes NZ131]
          Length = 293

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 74/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+  + +
Sbjct: 50  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-DLV 107

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 108 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 162

Query: 136 LRN-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +          K    G+     +     +    Y  K+ 
Sbjct: 163 IFNKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 220

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 221 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 272


>gi|312880566|ref|ZP_07740366.1| NADH:flavin oxidoreductase/NADH oxidase [Aminomonas paucivorans DSM
           12260]
 gi|310783857|gb|EFQ24255.1| NADH:flavin oxidoreductase/NADH oxidase [Aminomonas paucivorans DSM
           12260]
          Length = 334

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 27/186 (14%), Positives = 58/186 (31%), Gaps = 30/186 (16%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGC----------PSARVHEGSFGACLMLNPDIVGDCI 108
               V+AA+   + GY  + ++ GC          P        +G  +     ++ D +
Sbjct: 149 PGFFVQAARRAREAGYRGVQVH-GCHGYLLGQFLSPLTNRRTDRYGGDVRGRSRLLLDVV 207

Query: 109 AAMCKA-LSIPVTVKCRI------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
            A+  A   +P+ V+              +       + + +   G + I +        
Sbjct: 208 DAVRGAFPDLPLGVRLGAADSFPGEEPRGLRVEEACAVARELAALGADWIAVSGNLC--- 264

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
                     P         I++     + +   GG+    +A ++L     D V +GR 
Sbjct: 265 ------GYDAPGGFGPYAGAIREAVGKRIPVECTGGVTSYDRARELLDRGCCDLVGVGRL 318

Query: 219 AYKNSA 224
              + A
Sbjct: 319 LLSDPA 324


>gi|83590886|ref|YP_430895.1| NADH:flavin oxidoreductase/NADH oxidase [Moorella thermoacetica
           ATCC 39073]
 gi|83573800|gb|ABC20352.1| NADH:flavin oxidoreductase/NADH oxidase [Moorella thermoacetica
           ATCC 39073]
          Length = 668

 Score = 43.7 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 31/213 (14%), Positives = 65/213 (30%), Gaps = 39/213 (18%)

Query: 53  QIGGADISKLV----EAAKIVEDFGYNEINL----------NVGCPSARVHEGS--FGAC 96
           ++  A++  LV    EAA+I  + G++ + +                A  +     +G  
Sbjct: 145 ELTTAEVETLVQRASEAAEIAVEAGFDGVEIHAMHEGYLLDQFT--IALFNRRGDKYGGA 202

Query: 97  LMLNPDIVGDCIAAMCKALSI--PVTVKCRI----------------GVDDQIPAVALRN 138
           L        + + A+   +    PV ++  I                  +          
Sbjct: 203 LEDRLTFPIEIVRAIKDRVGKDFPVVLRFSIKNYIKDWRQGGLPGENFQEKGRDVEEALA 262

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             K ++ +G +G    A        +     +       +   +K E   + + + G LE
Sbjct: 263 AAKILEGAGYDGFDADAGSYDAWYWAHPPVYQKHGCYLPLTQRLK-EVVKVPVIVAGRLE 321

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
               A + L     D + IGR    +   +  V
Sbjct: 322 IPELAEEALVKGQADMIAIGRGLLTDPYWVNKV 354


>gi|290892634|ref|ZP_06555626.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL J2-071]
 gi|290557694|gb|EFD91216.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL J2-071]
          Length = 338

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     + G 
Sbjct: 317 KDAAKQLGETIEGP 330


>gi|166711909|ref|ZP_02243116.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           oryzae pv. oryzicola BLS256]
          Length = 258

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGISDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R D   WR
Sbjct: 127 VGIDSIREDDGEWR 140


>gi|109897696|ref|YP_660951.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudoalteromonas
           atlantica T6c]
 gi|109699977|gb|ABG39897.1| 2,4-dienoyl-CoA reductase [Pseudoalteromonas atlantica T6c]
          Length = 682

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 44/124 (35%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D          +  L K I+K+G     I+      +
Sbjct: 208 EVVRRVREAVGEKFIIIYRLSMLDLVEGGSTYKEVVELGKLIEKAGAT--IINTGIGWHE 265

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    +E+  + +  +  +     A ++L   D  M+   R  
Sbjct: 266 ARIPTIATKVPRAAFTWVTAKFRESLSIPVITSNRINTPEVAEQVLARGDADMVSMARPF 325

Query: 220 YKNS 223
             + 
Sbjct: 326 LADP 329


>gi|307326552|ref|ZP_07605746.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces
           violaceusniger Tu 4113]
 gi|306887746|gb|EFN18738.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces
           violaceusniger Tu 4113]
          Length = 359

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 19/157 (12%), Positives = 46/157 (29%), Gaps = 12/157 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKSIKKS 146
            +G           + + A+       +P+  +        ++         L   +K  
Sbjct: 201 GYGGSFENRVRFALEVVDAVRAVWPEDLPLFFRISATDWLEENGWTPEDTVRLAALLKDH 260

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ + + +        +       P         +++E   L +   G + +  QA KI
Sbjct: 261 GVDLLDVSSG----GNAAGVRIPTGPGYQVRFAERVRRETG-LPVAAVGLITEAEQAEKI 315

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +     D V++GR   ++              +    
Sbjct: 316 VTNGEADAVLLGRELLRDPYFARRAATELGGQVRNPD 352


>gi|254508463|ref|ZP_05120582.1| oxidoreductase, FAD/FMN-binding family [Vibrio parahaemolyticus 16]
 gi|219548575|gb|EED25581.1| oxidoreductase, FAD/FMN-binding family [Vibrio parahaemolyticus 16]
          Length = 670

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 48/125 (38%), Gaps = 8/125 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + ++ KA+     +  R+     V++      +  L K ++K+GV    I+      +
Sbjct: 199 EIVKSIRKAVGEKFIIIFRLSMLDLVEEGSTFDEVVMLAKELEKAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  + + ++ I     +    +A +IL     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFTWVTEKVRPHVNVPIVTCNRINTPEEAERILSSGHADMVSMARPF 316

Query: 220 YKNSA 224
             +  
Sbjct: 317 LADPH 321


>gi|167565420|ref|ZP_02358336.1| xenobiotic reductase A [Burkholderia oklahomensis EO147]
 gi|167572523|ref|ZP_02365397.1| xenobiotic reductase A [Burkholderia oklahomensis C6786]
          Length = 365

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 65/180 (36%), Gaps = 25/180 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AAK   D G+  + L+       + +            ++G         + + +AA+
Sbjct: 161 VAAAKRALDAGFEWLELHFA--HGYLAQSFFSVHSNRRTDAYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +     +P+T +  +   D      L     L K  K+ G++ + +      +   +P+
Sbjct: 219 REVWPERLPLTARFGVIEYDGRDEETLAESIELAKRFKQEGLDLLSV-----TVGFSTPE 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++  + A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPVAERVRREAQLPVASAWGIDTPALAERVVKDGQLDLVMVGRAHLADPH 333


>gi|146305532|ref|YP_001185997.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas mendocina ymp]
 gi|145573733|gb|ABP83265.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas mendocina ymp]
          Length = 686

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 65/188 (34%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGSFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ +      +G+               +  +  
Sbjct: 213 EVGPDFCVGMRICGDEFHPDGLSHEDMKQIAAYYDATGMIDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE   + +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMSYPPEPFLHLAAGIKEVVKVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|186472160|ref|YP_001859502.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phymatum
           STM815]
 gi|184194492|gb|ACC72456.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phymatum
           STM815]
          Length = 687

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 68/195 (34%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRTDEWGGSLQNRLRFGVEVLQAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+     V  R+  D    D +    L+ + +++ ++G+               +  +
Sbjct: 211 REAVGKDFCVGLRMCGDEFHEDGLDHTQLKEIAQAMAETGLIDYIGVIGSGADTHNTLAN 270

Query: 168 N---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    L I     + D  QA ++L +  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKLPIMHAQSIRDAGQAERLLANGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|288941040|ref|YP_003443280.1| NADH:flavin oxidoreductase/NADH oxidase [Allochromatium vinosum DSM
           180]
 gi|288896412|gb|ADC62248.1| NADH:flavin oxidoreductase/NADH oxidase [Allochromatium vinosum DSM
           180]
          Length = 366

 Score = 43.7 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 27/177 (15%), Positives = 61/177 (34%), Gaps = 15/177 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AA    + G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAANRAREAGFEWLELHFAHGYLGQSFFSVHSNQRTDDYGGDAAGRGRFLRETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +P+T +  +   D      L   ++ ++     G+ +      +   +P    
Sbjct: 219 REVWPERLPLTARFGVIEFDGHDEETLAESIELVRDWRRGGLDL--LSVSVGFSTPTAQI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                    + E  +   +L +    G++  +   +++    +D VM+GRA   N  
Sbjct: 277 PWGPAFLAPIAERVRREAELPVASAWGIDAPATCNRVIEQQQMDLVMVGRAHLANPH 333


>gi|323435941|ref|ZP_01049138.2| Dihydroorotate dehydrogenase [Dokdonia donghaensis MED134]
 gi|321496256|gb|EAQ40372.2| Dihydroorotate dehydrogenase [Dokdonia donghaensis MED134]
          Length = 376

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 31/153 (20%), Positives = 57/153 (37%), Gaps = 28/153 (18%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I A+ KA     +  P+ +K    ++
Sbjct: 203 VDYFVLNVSCPNVSSHAK------LNDKDYLEELIQAVQKANASYEIQRPIVLKIAPDLN 256

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR------------KIPNLDY 176
           DQ     L  +V  +K +G++G+         +GL   D R             + +   
Sbjct: 257 DQ----QLDEIVALVKDTGLDGVIASNTSVNREGLKVTDARLEEIGNGGLSGKPVTDRST 312

Query: 177 DIVYEIK-KENPDLFIGLNGGLEDMSQALKILP 208
            ++  +  K N    I   GG+     AL  + 
Sbjct: 313 RVIKYLADKSNRSFPIIGVGGIHSAQDALDKIE 345


>gi|318041113|ref|ZP_07973069.1| dihydroorotate dehydrogenase 2 [Synechococcus sp. CB0101]
          Length = 332

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 22/111 (19%), Positives = 44/111 (39%), Gaps = 17/111 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLN---VGCPSARVHEGSFGACLMLNPDIVG 105
           P+   + G+      EAA+ +E  G   I LN   V C    ++            + + 
Sbjct: 106 PVIASLNGSHGGDWSEAARAIEQAGAQAIELNLYSVPC---DINRSGAEL----EAEQLA 158

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
             +  +C A+++PV VK            +L  +    +++G +G+ +  R
Sbjct: 159 -IVREVCSAVTVPVAVKLSPF------YTSLAAMAAGFQEAGASGLVLFNR 202


>gi|313606919|gb|EFR83520.1| NADPH dehydrogenase [Listeria monocytogenes FSL F2-208]
          Length = 206

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 12  DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 71

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 72  KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 130

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 131 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 184

Query: 227 TTVDEYFSNPLTGS 240
               +     + G 
Sbjct: 185 KDAAKQLGETIEGP 198


>gi|71280229|ref|YP_267674.1| 2,4-dienoyl-CoA reductase [Colwellia psychrerythraea 34H]
 gi|71145969|gb|AAZ26442.1| 2,4-dienoyl-CoA reductase [Colwellia psychrerythraea 34H]
          Length = 680

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 27/171 (15%), Positives = 56/171 (32%), Gaps = 19/171 (11%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             +AK+    GY+ + +            C         +G  +     +  + I A+  
Sbjct: 148 AYSAKLAAKAGYDGVEIMGSEGYLINQFACVRTNKRNDEWGGSIENRMRLAIETIKAVRA 207

Query: 114 ALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     I   +     V+       +  + K+++++G   I  +      +   P    
Sbjct: 208 KVGENFIIIFRLSMLDLVEGGNSWEEVVTMAKAVEQAGATLI--NTGIGWHEARVPTIVT 265

Query: 170 KIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +P   +  V E +KKE     I  N  +     A ++L     D V + R
Sbjct: 266 SVPRAAFTWVTEKMKKEVSIPLITTNR-INTPEVAEEVLATGQADMVSMAR 315


>gi|332982504|ref|YP_004463945.1| NADH:flavin oxidoreductase/NADH oxidase [Mahella australiensis 50-1
           BON]
 gi|332700182|gb|AEE97123.1| NADH:flavin oxidoreductase/NADH oxidase [Mahella australiensis 50-1
           BON]
          Length = 640

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 27/183 (14%), Positives = 60/183 (32%), Gaps = 20/183 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  + A      G++ + +             P +      +G  L+       + I+ 
Sbjct: 146 EEFGDCALRARKAGFDGVEIHGAHGYLIAQFMSPYSNKRTDEYGGSLLNRVRFPLEIISN 205

Query: 111 MCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         +  RI  D+ +P        + +   ++ +GVN I  H    +   +   
Sbjct: 206 IRAKAGNDFPIIFRISGDEFVPGGRTIEDTKTIAVLLEHAGVNAI--HVSAGVYASMQAI 263

Query: 167 DNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                    +  D   E+KK    + +   G + D   A  ++     D V +GRA+  +
Sbjct: 264 VPPAAVRHGWITDFAAEVKK-VVSIPVITVGRINDPIMAETVITSGKADFVAMGRASLAD 322

Query: 223 SAM 225
             +
Sbjct: 323 PEL 325


>gi|315304666|ref|ZP_07874879.1| NADPH dehydrogenase [Listeria ivanovii FSL F6-596]
 gi|313626960|gb|EFR95880.1| NADPH dehydrogenase [Listeria ivanovii FSL F6-596]
          Length = 338

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 62/193 (32%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P+ V+          +         K +K  GV  I +     +          
Sbjct: 204 KEVWDGPIIVRVSATDYAHGGLQLEDYIPFAKWMKADGVELIDVSTGGLVNVAPPVFPGY 263

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N     
Sbjct: 264 QVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFAK 317

Query: 228 TVDEYFSNPLTGS 240
              +     +   
Sbjct: 318 DAAQALGETIEAP 330


>gi|288940598|ref|YP_003442838.1| NADH:flavin oxidoreductase/NADH oxidase [Allochromatium vinosum DSM
           180]
 gi|288895970|gb|ADC61806.1| NADH:flavin oxidoreductase/NADH oxidase [Allochromatium vinosum DSM
           180]
          Length = 366

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 27/177 (15%), Positives = 61/177 (34%), Gaps = 15/177 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AA    + G+  + L+      G     VH       +G         + + +AA+
Sbjct: 159 DFVAAANRAREAGFEWLELHFAHGYLGQSFFSVHSNQRTDDYGGDAAGRGRFLRETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +P+T +  +   D      L   ++ ++     G+ +      +   +P    
Sbjct: 219 REVWPERLPLTARFGVIEFDGHDEETLAESIELVRDWRRGGLDL--LSVSVGFSTPTAQI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                    + E  +   +L +    G++  +   +++    +D VM+GRA   N  
Sbjct: 277 PWGPAFLAPIAERVRREAELPVASAWGIDAPATCNRVIEQQQMDLVMVGRAHLANPH 333


>gi|195970705|gb|ACG60743.1| putative dehydrogenase [Streptomyces flavoviridis]
          Length = 326

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 61/178 (34%), Gaps = 24/178 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
           +    K +  F+    P+   +      +L   AK VE  G   + L + C        +
Sbjct: 104 VNRWLKTLRSFADDRLPVIASLHADTPGELAMLAKDVETTGCRALELGISC-------LN 156

Query: 93  FGACLMLN-PDIVGDCIAAMCKALSIPVTVK----------CRIGVDDQIPAVALRNLVK 141
               L  + PD V    + +    ++P++VK           R  +     A+ L + + 
Sbjct: 157 EEDGLEDDNPDRVYAYTSEVRSKTALPMSVKLAVGEGLRDRVRAAIAGGADAITLSDTI- 215

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
               +G   +     +  L G+       +  L    +++++K    L +   GG+  
Sbjct: 216 ----AGA-AVSPTTGRLELNGVFGYSGPGLKPLVLAAIWQLRKSGIALPVMGCGGVSS 268


>gi|150008478|ref|YP_001303221.1| putative N-acetylmannosamine-6-phosphate 2-epimerase
           [Parabacteroides distasonis ATCC 8503]
 gi|255014279|ref|ZP_05286405.1| putative N-acetylmannosamine-6-phosphate 2-epimerase [Bacteroides
           sp. 2_1_7]
 gi|256841504|ref|ZP_05547011.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|149936902|gb|ABR43599.1| putative N-acetylmannosamine-6-phosphate 2-epimerase
           [Parabacteroides distasonis ATCC 8503]
 gi|256737347|gb|EEU50674.1| conserved hypothetical protein [Parabacteroides sp. D13]
          Length = 246

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 64/182 (35%), Gaps = 40/182 (21%)

Query: 36  DKKNILGFSTQEKPLALQIGGADI----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +KK +L        ++ Q+   D       +V+ AK  +  G   I  N           
Sbjct: 4   NKKELLDSFKGGLIVSCQVQHDDPTFSVDFVVKMAKAAQWGGAVGIRAN----------- 52

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNG 150
                   +P+     I A+ K + +PV    +I  DD    +       K++ ++G   
Sbjct: 53  --------DPEQ----IKAIKKEVDLPVIGLWKIWHDDTDVFITPTLEAAKAVWEAGAEI 100

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           I +     I     P          Y+++  +KKE P+  I     + +  +A++ +   
Sbjct: 101 IALDCTSQITHEGRPA---------YELLPIVKKEIPEAIIFA--DVSNYEEAVRAVEMG 149

Query: 210 VD 211
            D
Sbjct: 150 AD 151


>gi|66800821|ref|XP_629336.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
 gi|60462707|gb|EAL60909.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
          Length = 409

 Score = 43.7 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 25/155 (16%), Positives = 51/155 (32%), Gaps = 11/155 (7%)

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL------VK 141
           ++ G           ++ + + ++    S    +  RI  D+ +      +L       +
Sbjct: 240 IYGGGSFDG---RIKLLIEIVKSVRSVWSTEKPLAVRISADEWVENENGWDLNDSIKLAE 296

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            ++   V+ I +       K              ++I   I K +  L +   G +   S
Sbjct: 297 ILESLDVDLIDVSTGGNNSKQKITSKPLYQVPFSHEIKQSILKRSGKLLVSSVGLITTAS 356

Query: 202 QALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
           +A  IL S   D +M GRA  +N  +         
Sbjct: 357 EAESILESNSSDLIMFGRAFLRNPFLPIEFAHQLK 391


>gi|311109834|ref|YP_003982685.1| 2,4-dienoyl-CoA reductase [NADPH] [Achromobacter xylosoxidans A8]
 gi|310764523|gb|ADP19970.1| 2,4-dienoyl-CoA reductase [NADPH] [Achromobacter xylosoxidans A8]
          Length = 672

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 16/146 (10%), Positives = 44/146 (30%), Gaps = 8/146 (5%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSG 147
           ++G           + + A+  A      +  RI     V+D +           ++++G
Sbjct: 184 AYGGGFERRIRFPLETVQAVRAAAGRDFLLVYRISAIDLVEDGLTGAETAQFAARLQQAG 243

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ +  +      +   P     +P   +       K+   + +  +  +       ++L
Sbjct: 244 VDML--NTGIGWHESTIPTIAASVPRAGWAFAVRNIKQAVSIPVIASNRISTPQTGEQLL 301

Query: 208 PS--VDGVMIGRAAYKNSAMLTTVDE 231
                D V + R    +        +
Sbjct: 302 ADGVADFVSMARPLLADPEFAAKARQ 327


>gi|262044431|ref|ZP_06017492.1| oxidoreductase [Klebsiella pneumoniae subsp. rhinoscleromatis ATCC
           13884]
 gi|259038211|gb|EEW39421.1| oxidoreductase [Klebsiella pneumoniae subsp. rhinoscleromatis ATCC
           13884]
          Length = 300

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 27/178 (15%), Positives = 58/178 (32%), Gaps = 20/178 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNP-DIVGDCI 108
            V +A   +  G+  I L+            P +      +G  L   M  P ++     
Sbjct: 93  FVASALRAQRLGFELIELHAAHGYLLHQFLSPLSNQRRDEYGGSLENRMRYPLEVFKAIR 152

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   +++ V +     V+            + ++  G + I + +      GLSP+  
Sbjct: 153 EAVGNTMAVGVRLSATDWVEGGWDCEQSIKFSQQLETLGSDYIHVSSG-----GLSPQQA 207

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
             +            ++   + +   G + D  QA   L +   D + + RA   +  
Sbjct: 208 ITVGPGYQLPFARDIRQQVAIPVIGVGLITDPQQAEAALENGDADLIALARAVLYDPH 265


>gi|139438268|ref|ZP_01771821.1| Hypothetical protein COLAER_00810 [Collinsella aerofaciens ATCC
           25986]
 gi|133776465|gb|EBA40285.1| Hypothetical protein COLAER_00810 [Collinsella aerofaciens ATCC
           25986]
          Length = 539

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 54/134 (40%), Gaps = 7/134 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLV---KSIKKSGV 148
           +G  L      + + IA + +       +  RI  D+     + L +++   + ++K+GV
Sbjct: 82  YGGSLDARMRFLLEVIAEIRERCGKDFIIDVRISGDEYTDGGLTLNDMIYVSRRLEKAGV 141

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I +     I +G +                EIKK   ++ +   G + +   A +++ 
Sbjct: 142 DMIHVSGGTTIKRGSAIPAAGTQQASHAACSREIKKHV-NIPVATVGRINEAWIAEELIE 200

Query: 209 --SVDGVMIGRAAY 220
             + D  M+GRA  
Sbjct: 201 DSAADICMMGRANL 214


>gi|24850453|gb|AAN64920.1| putative dehydrogenase [Solanum lycopersicum]
          Length = 429

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 32/172 (18%), Positives = 55/172 (31%), Gaps = 25/172 (14%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
             E+ G +   +N  CP     E   GA +  + D++ +    +    ++PV  K    +
Sbjct: 178 RCEETGIDAFEINFSCPHGM-PERRMGAAVGQDCDLLEEVCGWINAVATVPVWAKMTPNI 236

Query: 128 DDQIPAVALR---------NLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDNRKIPN 173
            D      +           +   +   G+N   +     +       G S K    I  
Sbjct: 237 TDITKPARVALNQGCEGVSAINTIMSVMGINLDTLRPEPCVEGYSTPGGYSSKAVHPIAL 296

Query: 174 LDYDIVYE-IKKENP--DLFIGLNGGLED-MSQALKILPSVD------GVMI 215
                +   +K E    D  +   GG+E     A  IL   D      GVM+
Sbjct: 297 AKVMNIARMMKSEFGDKDYSLSAIGGVETGGDAAEFILLGADTVQVCTGVMM 348


>gi|328554115|gb|AEB24607.1| NADPH dehydrogenase NamA [Bacillus amyloliquefaciens TA208]
 gi|328912507|gb|AEB64103.1| NADPH dehydrogenase [Bacillus amyloliquefaciens LL3]
          Length = 338

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 29/193 (15%), Positives = 66/193 (34%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA   ++ G++ I L+            P +      +G         +G+ I A+
Sbjct: 145 EFKQAAARAKEAGFDIIELHAAHGYLMHEFLSPLSNHRTDEYGGSHENRYRFLGETIDAV 204

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P  V V      D  +         K +K+ GV+ I   +   +       D  
Sbjct: 205 KEVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVQ-----ADIN 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P        +I+++  ++  G  G +   + A +IL +   D + + R   ++     
Sbjct: 260 VFPGYQVSFAEKIREQA-EIATGAVGLITTGTMAEEILQNNRADLIFVARELLRDPHFAR 318

Query: 228 TVDEYFSNPLTGS 240
           +  +  +  +   
Sbjct: 319 SAAKQLNTEIPSP 331


>gi|310796559|gb|EFQ32020.1| NADH:flavin oxidoreductase/NADH oxidase [Glomerella graminicola
           M1.001]
          Length = 428

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 76/220 (34%), Gaps = 26/220 (11%)

Query: 46  QEKPLALQIGGADISKL----VEAAKIVEDFGYNEINL---------NVGCPSARVHEGS 92
           ++  +  ++   DI  L    V+A K     GY+ I +         N   P++      
Sbjct: 194 EDTYVPKEMTLEDIEILKAKWVDAVKRAVRVGYDTIEIHAAHGYLINNFLSPTSNRRTDK 253

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC----RIGVDDQIPAVAL---RNLVKSI 143
           +G        ++ +        +    PV  +      +  D  IP   +   + L K +
Sbjct: 254 YGGSFENRCRLLVELAELTRANVPDDYPVFARIPGSDYLEHDPSIPQWEISQAQELAKIL 313

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
              GV+   +       +       +   +L   +   +  E     +G  GG+     A
Sbjct: 314 AGKGVDFFDVTGGGQDARMKVAPGPKYQAHLAAAVRKAL--EGTGAVVGTVGGIATGKDA 371

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            ++L     D V++GRA  K+S ++ T  +  +  +   S
Sbjct: 372 TEVLADGQADAVLVGRAFLKDSNLVWTWADELNIDVHAPS 411


>gi|308189393|ref|YP_003933523.1| NADH oxidase [Pantoea vagans C9-1]
 gi|308056008|gb|ADO08177.1| NADH oxidase [Pantoea vagans C9-1]
          Length = 359

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 33/155 (21%), Positives = 59/155 (38%), Gaps = 10/155 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVK 141
           P A V E  +G        IV + IAA+ +    P+ V+       +            +
Sbjct: 177 PLANVREDQYGGSHENRYRIVREVIAAVREVWDGPLFVRISSTDYAEGGNTPEDFLTYGR 236

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +K+ GV+ I   +      G++P      PN       ++ + +  +  G  G ++   
Sbjct: 237 WMKEQGVDLIDCSSG-----GIAPAVVNVFPNYQVPA-AQLLRNSLGIKTGAVGLIQTGR 290

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFS 234
           QA +IL +   D V+IGR   K+     T  +   
Sbjct: 291 QAEEILQNGRADMVLIGREMLKDPFWARTAGDDLQ 325


>gi|262383327|ref|ZP_06076463.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
 gi|262294225|gb|EEY82157.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
          Length = 246

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 64/182 (35%), Gaps = 40/182 (21%)

Query: 36  DKKNILGFSTQEKPLALQIGGADI----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG 91
           +KK +L        ++ Q+   D       +V+ AK  +  G   I  N           
Sbjct: 4   NKKELLDSFKGGLIVSCQVQHDDPTFSIDFVVKMAKAAQWGGAVGIRAN----------- 52

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNG 150
                   +P+     I A+ K + +PV    +I  DD    +       K++ ++G   
Sbjct: 53  --------DPEQ----IKAIKKEVDLPVIGLWKIWHDDTDVFITPTLEAAKAVWEAGAEI 100

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           I +     I     P          Y+++  +KKE P+  I     + +  +A++ +   
Sbjct: 101 IALDCTSQITHEGRPA---------YELLPIVKKEIPEAIIFA--DVSNYEEAVRAVEMG 149

Query: 210 VD 211
            D
Sbjct: 150 AD 151


>gi|21231262|ref|NP_637179.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66768686|ref|YP_243448.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|23821707|sp|Q8P9N9|HIS6_XANCP RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|81305342|sp|Q4UU45|HIS6_XANC8 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|21112912|gb|AAM41103.1| cyclase [Xanthomonas campestris pv. campestris str. ATCC 33913]
 gi|66574018|gb|AAY49428.1| cyclase [Xanthomonas campestris pv. campestris str. 8004]
          Length = 258

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELAMRYRDQGADELVFYDIGASPEGRS---------VDYAWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIRDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|147676930|ref|YP_001211145.1| NADH:flavin oxidoreductases [Pelotomaculum thermopropionicum SI]
 gi|146273027|dbj|BAF58776.1| NADH:flavin oxidoreductases [Pelotomaculum thermopropionicum SI]
          Length = 649

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 32/187 (17%), Positives = 59/187 (31%), Gaps = 18/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA      G + + +N            P       S+G  L        + + A+ 
Sbjct: 151 FARAAGHAVAGGLDGVEINAAQFSLVRQFMSPLTNRRADSYGGSLANRLRFCIEILKAVR 210

Query: 113 KALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSGV-NGIWIHARKAILKGLSPK 166
             L     +  R+  D+  P           +   ++K  V + + + A       LS  
Sbjct: 211 AVLGEDRLLGIRLCGDELAPWGGLTPEDAAEIAVELEKLDVLDYLTVSAGSLYSLHLSAA 270

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                P    +   +IKK    L +   G +     A +I+    VDGV + RA   +  
Sbjct: 271 TFYIEPGFAVEAAAKIKKAV-RLPVFAEGRIHRPEYAARIVDEGLVDGVYMNRALICDPW 329

Query: 225 MLTTVDE 231
           +   ++ 
Sbjct: 330 LPRKLER 336


>gi|226228588|ref|YP_002762694.1| NADH-dependent flavin oxidoreductase [Gemmatimonas aurantiaca T-27]
 gi|226091779|dbj|BAH40224.1| NADH-dependent flavin oxidoreductase [Gemmatimonas aurantiaca T-27]
          Length = 356

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 29/197 (14%), Positives = 54/197 (27%), Gaps = 20/197 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V  A+   D G+    ++            P A      +G        +  +  AA
Sbjct: 157 EAFVAGARRALDAGFQVAEVHAAHGYLIHQFLSPLANQRTDQYGGSFENRIRLACEVSAA 216

Query: 111 MCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +      ++PV V+       D          L   ++  GV+ I          GL+  
Sbjct: 217 VRGVWPDNLPVIVRISATDWADGGWDIEESIQLADRLRALGVDLIDCSTG-----GLAAH 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNSA 224
               I            +    +     G + +  QA  I+ + D  M+   R   +N  
Sbjct: 272 QQITIGPGYQVPFARRIRHEGKIPTAAVGLITEAQQAEDIITNGDADMVLLAREVLRNPH 331

Query: 225 MLTTVDEYFSNPLTGSS 241
                     +  +  S
Sbjct: 332 WPLLAAHQLGDAGSWPS 348


>gi|84393630|ref|ZP_00992382.1| 2,4-dienoyl-CoA reductase [Vibrio splendidus 12B01]
 gi|84375771|gb|EAP92666.1| 2,4-dienoyl-CoA reductase [Vibrio splendidus 12B01]
          Length = 669

 Score = 43.7 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 46/124 (37%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D +   +       L + ++++GV    I+      +
Sbjct: 199 EIVKSIREAVGKDFIIIFRLSMLDLVEQGSTFEDVVLLAQKLEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K    + +     +    +A +IL     D V + R  
Sbjct: 257 ARVPTIATQVPRGAFSWVTEKVKPYVSIPVVTCNRINTPEEAERILSSGQADMVSMARPF 316

Query: 220 YKNS 223
             + 
Sbjct: 317 LADP 320


>gi|149372546|ref|ZP_01891658.1| dihydroorotate dehydrogenase [unidentified eubacterium SCB49]
 gi|149354589|gb|EDM43153.1| dihydroorotate dehydrogenase [unidentified eubacterium SCB49]
          Length = 315

 Score = 43.7 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 64/180 (35%), Gaps = 30/180 (16%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-----IPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I A+ +A        P+ +K      
Sbjct: 143 VDYFVLNVSCPNVGSHAK------LNDKDYLEELIGAVQEANKNFDKQKPILLKIAP--- 193

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR------------KIPNLDY 176
             +  V L  +V  ++ + ++G+          GL   + R             I +   
Sbjct: 194 -DLNPVQLDEIVTLVQDTKLDGVIASNTSMDRSGLKASEARLTEIGNGGLSGQPIKDKST 252

Query: 177 DIVYEIK-KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA-AYKNSAMLTTVDEYF 233
            ++  +  K N    I   GG+     AL+ L    D V I     Y+  +++  +++  
Sbjct: 253 AVIKYLADKSNKSFPIIGVGGIHSADDALEKLDAGADLVQIYTGFIYEGPSLIKKINKAI 312


>gi|5701742|dbj|BAA83084.1| LEDI-5b protein [Lithospermum erythrorhizon]
          Length = 366

 Score = 43.7 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 73/223 (32%), Gaps = 39/223 (17%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
                AA+   D G++ + L                 V++    +G  L      V + +
Sbjct: 158 DDFRIAARNAIDAGFDGVELHGAHGYLLEQFL--KDNVNDRTDKYGGSLENRCRFVLELV 215

Query: 109 AAMCKALSI-PVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            A+   +    V +K     D     D  PA     L +++ K G+  +++H  +  +K 
Sbjct: 216 EAVVNEVGADKVGIKLAPFSDFMEAGDSDPATLGTYLAEALNKFGI--LYMHVLEPRMKT 273

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
               +N  I  +        +K     F+   G   D     K L     D V+ GR   
Sbjct: 274 TGETNNESIDPM--------RKAFKGTFVVGGG--YDKELGEKALEEGRADLVVYGRPFV 323

Query: 221 KNSAMLT--TVD----EYFSNPLTGSSPIKTRVDKDFWRKISA 257
            N  +     +D    EY  N      P+    D  F  + +A
Sbjct: 324 SNPDLPKRFEIDAPLNEYDRNTFFTHDPVVGYTDYPFLEEATA 366


>gi|324516259|gb|ADY46473.1| NADH-dependent flavin oxidoreductase [Ascaris suum]
          Length = 416

 Score = 43.7 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 34/262 (12%), Positives = 84/262 (32%), Gaps = 38/262 (14%)

Query: 65  AAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AA+ ++  G++ + +NV            S       +G  LM    I+ + I  + K +
Sbjct: 167 AAEFLKTCGFHGVEINVALDFALGQLVDASTNSRSDEYGGSLMNRTRILFEIIKGIRKHI 226

Query: 116 --SIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWI----HARKAILKGLSPK 166
                  V  ++   + + A          K + + G++ + +    +    +++    +
Sbjct: 227 NDDKNFIVGMKMSSTNYVSAYDEEEFAHYCKQLDRVGLDYVTLTGGEYGSIKMIESAQRE 286

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
             ++        +  ++    ++   + GGL    Q  + +     DGV     A     
Sbjct: 287 STKQRQAFFAKFITAVRMNLKNVRAFICGGLRSAEQMWEAIYEGWCDGV-----AMAKP- 340

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT--RHMIG 282
                    +     S  I     +   + +      Y A+   +G ++ QI   + +  
Sbjct: 341 --------LAAEPDLSRRILNEEVRAAKKTLIEQFDYYTAKD-AAGTQMWQIANKKPIFN 391

Query: 283 LFHGFPNSRRCRHILTVEAGAS 304
           L +   +    R  L      +
Sbjct: 392 LMN-EHHVDAFRKALKEHEAKA 412


>gi|167745478|ref|ZP_02417605.1| hypothetical protein ANACAC_00169 [Anaerostipes caccae DSM 14662]
 gi|121194492|gb|ABM47578.1| putative NADH:flavin oxidoreductase [Anaerostipes caccae]
 gi|167655199|gb|EDR99328.1| hypothetical protein ANACAC_00169 [Anaerostipes caccae DSM 14662]
          Length = 357

 Score = 43.7 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 38/217 (17%), Positives = 76/217 (35%), Gaps = 29/217 (13%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-------- 84
           LRG +      S  E  L  Q       + +EAA      GY+ + L   C         
Sbjct: 122 LRGREYTADEMSEDEILLREQ-------QFIEAAVRARAAGYDGVEL--HCAHSYFLNAF 172

Query: 85  -SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            S  V+     FG  +     +V D +  +  +      +  R+G D+     +   +  
Sbjct: 173 LSPTVNHRTDRFGGNIEGRMRVVLDIMEGIRHSCGENFLISVRLGFDEPDLESSAF-MAG 231

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-----KKENPDLFIGLNGG 196
           + +K+G++ + +        G   +   + P  ++     I      K+     +   GG
Sbjct: 232 TFEKAGMDFLHVSTGFGS-TGFMDERTMENPPDEFPFNIRIWGAMQMKQRVSCPVIAVGG 290

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +  + Q + +L     D V +GRA   +   +  + +
Sbjct: 291 IRQVQQGMFLLEQECADFVALGRALLCDPEWVIKIKQ 327


>gi|313108091|ref|ZP_07794249.1| morphinone reductase [Pseudomonas aeruginosa 39016]
 gi|310880751|gb|EFQ39345.1| morphinone reductase [Pseudomonas aeruginosa 39016]
          Length = 369

 Score = 43.7 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 61/188 (32%), Gaps = 29/188 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA+   D G++ + L              ++     ++G  L      + + + A
Sbjct: 161 DEFVRAARNALDAGFDLVELHGANGYLIDQFLASASNRRSDAYGGSLENRARFLLEIVDA 220

Query: 111 MCKALSI-PVTVKCRI-----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +  A+    V ++         + D  P      L +++++ G+  +  H  +    G  
Sbjct: 221 LVAAVGAERVGLRLSPWGTINDMHDDEPEAMTLYLAEALQRRGIAYL--HLAEWEWSGGP 278

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                    L                + + G   D  +A  IL +   D V IGR    N
Sbjct: 279 AYPQGFRERLRERFRA---------PLIVCGNY-DAERAEAILQAGLADAVAIGRPFIAN 328

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 329 PDLVERIR 336


>gi|188588987|ref|YP_001919988.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E3 str. Alaska E43]
 gi|188499268|gb|ACD52404.1| dihydroorotate dehydrogenase family protein [Clostridium botulinum
           E3 str. Alaska E43]
          Length = 362

 Score = 43.7 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 21/148 (14%), Positives = 47/148 (31%), Gaps = 23/148 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN------------GI 151
           + + + A   AL  PV +K     D       ++ + K+++++G +             I
Sbjct: 134 IVESMKAAKAALDCPVFMKMSPHTD-------IQKIAKALEEAGADGLVMINSVGPCMAI 186

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLEDMSQALKIL-P 208
            I     I+   +         +    +  I        + I   GG+     A ++L  
Sbjct: 187 DIETGYPIMGSQTGYGWLSGSAVKPVAIRNIYDASKVIKIPIIGVGGITCGKDAAEMLMA 246

Query: 209 SVDGVMIG-RAAYKNSAMLTTVDEYFSN 235
               V +   A  K   +   + +  + 
Sbjct: 247 GAQSVQVCTEAILKGPTVYGKIAKELNE 274


>gi|295696580|ref|YP_003589818.1| ferredoxin-dependent glutamate synthase [Bacillus tusciae DSM 2912]
 gi|295412182|gb|ADG06674.1| ferredoxin-dependent glutamate synthase [Bacillus tusciae DSM 2912]
          Length = 483

 Score = 43.7 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 31/155 (20%), Positives = 48/155 (30%), Gaps = 19/155 (12%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
            P+     +  +     +PV +K             L   ++   ++GV+ I I   +  
Sbjct: 233 RPEDFVALVQRLRAETGVPVGLKIAATHH-------LEEEMQIALEAGVDFITIDGAEGG 285

Query: 160 LKGLSPKDNRKIPNLDYDIVYEI------KKENPDLFIGLNGGLEDMSQALKILP-SVDG 212
             G SP     +       V         KK    + +   GGL    Q LK L    D 
Sbjct: 286 THGGSPTLQDDVGLPTLFAVSRAADVLAQKKVRGRVSLLAAGGLITPGQMLKALALGADA 345

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           V +G AA     +   V +     L    P    V
Sbjct: 346 VYVGTAA-----LFAMVSDQMVEALPFEPPTSLVV 375


>gi|218708936|ref|YP_002416557.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio splendidus LGP32]
 gi|218321955|emb|CAV17953.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio splendidus LGP32]
          Length = 670

 Score = 43.7 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 46/124 (37%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D +   +       L + ++++GV    I+      +
Sbjct: 200 EIVKSIREAVGKDFIIIFRLSMLDLVEQGSTFEDVVLLAQKLEEAGVT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K    + +     +    +A +IL     D V + R  
Sbjct: 258 ARVPTIATQVPRGAFSWVTEKVKPYVSIPVVTCNRINTPEEAERILSSGQADMVSMARPF 317

Query: 220 YKNS 223
             + 
Sbjct: 318 LADP 321


>gi|86148497|ref|ZP_01066786.1| 2,4-dienoyl-CoA reductase [Vibrio sp. MED222]
 gi|85833737|gb|EAQ51906.1| 2,4-dienoyl-CoA reductase [Vibrio sp. MED222]
          Length = 669

 Score = 43.7 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 46/124 (37%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D +   +       L + ++++GV    I+      +
Sbjct: 199 EIVKSIREAVGKDFIIIFRLSMLDLVEQGSTFEDVVLLAQKLEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K    + +     +    +A +IL     D V + R  
Sbjct: 257 ARVPTIATQVPRGAFSWVTEKVKPYVSIPVVTCNRINTPEEAERILSSGQADMVSMARPF 316

Query: 220 YKNS 223
             + 
Sbjct: 317 LADP 320


>gi|289610269|emb|CBI60288.1| unnamed protein product [Sordaria macrospora]
          Length = 53

 Score = 43.7 bits (102), Expect = 0.041,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 26 MIVADAILRGDKKNILG--FSTQEKPLALQIGGADISKLVEAAKIVEDFGY 74
          MI + A +R  +++I    +   E+P+++Q+ G    ++ EAAK+ ED G 
Sbjct: 1  MIASQAAIRETRQSIQKAMWDPVEEPVSMQLVGCTPVEMGEAAKLAEDKGA 51


>gi|330501447|ref|YP_004378316.1| putative FMN oxidoreductase [Pseudomonas mendocina NK-01]
 gi|328915732|gb|AEB56563.1| putative FMN oxidoreductase [Pseudomonas mendocina NK-01]
          Length = 686

 Score = 43.7 bits (102), Expect = 0.041,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 66/188 (35%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+ K
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHLIDQFWSPRVNKRTDEWGGTFEGRMKFGLEVLKAVRK 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ +      +G+               +  +  
Sbjct: 213 EVGDDFCVGMRITGDEFHPDGLSHEDMKQIAAYYDATGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE   + +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMSFPPEPFLHLAAGIKEVVKVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHMAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|310642020|ref|YP_003946778.1| NADH-dependent flavin oxidoreductase-like protein [Paenibacillus
           polymyxa SC2]
 gi|309246970|gb|ADO56537.1| NADH-dependent flavin oxidoreductase-like protein [Paenibacillus
           polymyxa SC2]
          Length = 340

 Score = 43.7 bits (102), Expect = 0.041,   Method: Composition-based stats.
 Identities = 30/205 (14%), Positives = 67/205 (32%), Gaps = 26/205 (12%)

Query: 54  IGGADISKLVE----AAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +   ++ ++VE    A       G + I L             P     +  +G  L   
Sbjct: 133 LSTQEVKEMVEKFRGAVARAVKAGVDAIELHGAHGYLIHQFHSPLTNQRDDEYGKDLTK- 191

Query: 101 PDIVGDCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                + I A    +   +P+ ++   +  V+         +  K  +++GV+   I + 
Sbjct: 192 --FGREIIQAAKAEMPEDMPLIMRISAKEYVEGGYDIQESISFAKEYQQAGVDIFDISSG 249

Query: 157 KAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--V 213
               +G      R   +  Y + +    ++  ++ +   G L+D   A  ++ + D   V
Sbjct: 250 G---EGPIAAWGRPGSHAAYQVTLAREIRQALEVPVIAVGRLDDPILANAVVGNEDADLV 306

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLT 238
            +GR   +N               T
Sbjct: 307 AVGRGMLRNPYWALEAATNLKKETT 331


>gi|308178928|ref|YP_003918334.1| flavin oxidoreductase [Arthrobacter arilaitensis Re117]
 gi|307746391|emb|CBT77363.1| putative flavin oxidoreductase [Arthrobacter arilaitensis Re117]
          Length = 357

 Score = 43.7 bits (102), Expect = 0.042,   Method: Composition-based stats.
 Identities = 31/220 (14%), Positives = 77/220 (35%), Gaps = 36/220 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V A++     G++ + L+            PSA     ++G         V + + A
Sbjct: 152 EEFVTASRNAIAAGFDGVELHGANGYLLHEFLAPSANTRTDNYGGSPENRASFVIEVVTA 211

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  A+      K  + +  +           +++    + +  +   A+++G++P     
Sbjct: 212 VANAIG---AGKTGLRISPEHNVQ------GAVENDRADVLATYT--ALVQGIAPLGLAN 260

Query: 171 IPNLDYD----IVYEIKKENPDLFIGLNG--GLEDMSQALKILPSV--DGVMIGRAAYKN 222
           +  L +D    +V  ++K      +   G   +    +A +++     + V++GR A  N
Sbjct: 261 LSILHHDPAGELVQSLRKAFGGPVLLNTGFAEITTYEEAARVVAEGWGEAVVVGRPAIAN 320

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
             ++    E          P+       F+ +      DY
Sbjct: 321 PDLVRRWKEQL--------PLNEPDFATFYTEGPKGYIDY 352


>gi|258621244|ref|ZP_05716278.1| 2,4-dienoyl-CoA reductase [Vibrio mimicus VM573]
 gi|258586632|gb|EEW11347.1| 2,4-dienoyl-CoA reductase [Vibrio mimicus VM573]
          Length = 547

 Score = 43.7 bits (102), Expect = 0.042,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 61/176 (34%), Gaps = 17/176 (9%)

Query: 57  ADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDC 107
             I+    +A++ +  GY+ + +            C    +    +G           + 
Sbjct: 49  NTINDFANSAELAQLAGYDGVEVMGSEGYLLNQFICKRTNMRYDEWGGSYQNRIRFSVEI 108

Query: 108 IAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +  
Sbjct: 109 VKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHEAR 166

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 167 IPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 222


>gi|91772978|ref|YP_565670.1| NADH peroxidase [Methanococcoides burtonii DSM 6242]
 gi|91711993|gb|ABE51920.1| NADH:flavin oxidoreductase/NADH oxidase [Methanococcoides burtonii
           DSM 6242]
          Length = 360

 Score = 43.7 bits (102), Expect = 0.042,   Method: Composition-based stats.
 Identities = 24/189 (12%), Positives = 60/189 (31%), Gaps = 30/189 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
               EAA+  ++ G++ +   + C    +               +G  +     IV + +
Sbjct: 142 ENFAEAARRSKEAGFDGV--QIHCAHGFLLSSFISPYTNHRTDKWGGSVENRARIVTEIV 199

Query: 109 AAMCKALSI--PVTVKCRIGV-------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + +    PV VK               + A     +   ++K+G+  I +      
Sbjct: 200 KRIQEKVGKDFPVMVKMNATDGFDVFSGKIGLDAPECVEIASLLEKAGICAIEVSGGIFE 259

Query: 160 LKGLSPKDN--RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIG 216
              +  ++    +     +    ++  +   + + L GG+   +    IL    D  MI 
Sbjct: 260 AGPVMSQNGIDSEDKEAYFRRYSKMILDTVKIPVILVGGIRTKAVMESILRGYAD--MI- 316

Query: 217 RAAYKNSAM 225
             +     +
Sbjct: 317 --SLSRPFI 323


>gi|153837573|ref|ZP_01990240.1| oxidoreductase, FAD/FMN-binding [Vibrio parahaemolyticus AQ3810]
 gi|149749070|gb|EDM59881.1| oxidoreductase, FAD/FMN-binding [Vibrio parahaemolyticus AQ3810]
          Length = 367

 Score = 43.7 bits (102), Expect = 0.042,   Method: Composition-based stats.
 Identities = 30/218 (13%), Positives = 68/218 (31%), Gaps = 23/218 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              A+K  ++ G++ + ++            P     E  +G  L     ++ +  +   
Sbjct: 147 FALASKRAQEAGFDGVEIHAAHTYLINQFLSPYYNRREDEYGGSLENRMRLLLEIYSETR 206

Query: 113 ----KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
                A  I V +      D  +     R + K +++ G + I     IH +   L G  
Sbjct: 207 MLVGDAFPILVKLTATEFFDGGLTFDETRIVCKKLEEVGADAIIVSGNIHGKANELVGER 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD----GVMIGRAAY 220
                      +    ++  ++  + +   GGL D+     I  + +     V   R   
Sbjct: 267 FDGCTLQEEGYFHEYGQVISQDIHIPVITVGGLRDIDAIENIAENTNIQFFAV--SRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
               ++    E    P+      K R  +  +  +  +
Sbjct: 325 AEPQLIKRWKEGNRAPVDCERCSKCRTKRGNFCVVYKN 362


>gi|171678437|ref|XP_001904168.1| hypothetical protein [Podospora anserina S mat+]
 gi|170937288|emb|CAP61945.1| unnamed protein product [Podospora anserina S mat+]
          Length = 495

 Score = 43.7 bits (102), Expect = 0.043,   Method: Composition-based stats.
 Identities = 23/146 (15%), Positives = 47/146 (32%), Gaps = 6/146 (4%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSG 147
           ++G  L     I+ +  A + +       +  +        D         L + ++K+G
Sbjct: 251 AYGGSLANRARIITEIAAGIREQCRKDFILAIKINSVEFQADGFTVEEASELCEILEKAG 310

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            + + +         L+ +         +  D   +I        + + GG         
Sbjct: 311 FDFVELSGGTYEEMALAHRRESTKAREAFFLDFAEKIAPRLNKTKVYVTGGFRTAKGMAD 370

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDE 231
            L SVDGV + RA   N  +   + E
Sbjct: 371 ALQSVDGVGMVRAVCNNPNLPAEILE 396


>gi|294499869|ref|YP_003563569.1| oxidoreductase, FAD/FMN-binding family protein [Bacillus megaterium
           QM B1551]
 gi|294349806|gb|ADE70135.1| oxidoreductase, FAD/FMN-binding family protein [Bacillus megaterium
           QM B1551]
          Length = 351

 Score = 43.7 bits (102), Expect = 0.043,   Method: Composition-based stats.
 Identities = 31/193 (16%), Positives = 63/193 (32%), Gaps = 38/193 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINL-----------NVGCPSARVHEG--SFGACLMLNPDIVGD 106
            +  +AAK   + G++ + +           N    S   ++    +G  L      + +
Sbjct: 157 EQYAQAAKNAIEAGFDGVEIHGAHGYLIDQFN----SDWSNKRTDEYGGDLAQRLTFMKE 212

Query: 107 CIAAMCKALSI-PVTVKCRIGVDDQIPA------VALRNLVKSIKKSGVNGIWIHARKAI 159
            I+A+  A+    V ++      D+          A++   ++ K++G+  I        
Sbjct: 213 VISAVIDAIGKERVVIRFSPHKLDKPDYRWDDTEKAIQTYTEAFKETGIEIIHPSMLDFY 272

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
               + ++  +I    +D             I   G L     A K L    +D   IGR
Sbjct: 273 EDVQNGQNLYEITRKYWDG-----------PIIGVGDL-TPESAEKALQAGWIDVAAIGR 320

Query: 218 AAYKNSAMLTTVD 230
               N   L  + 
Sbjct: 321 PLISNPDYLQRIK 333


>gi|171317802|ref|ZP_02906982.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           MEX-5]
 gi|171097026|gb|EDT41883.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           MEX-5]
          Length = 369

 Score = 43.7 bits (102), Expect = 0.043,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 62/182 (34%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V +AK   D G+  + L+       + +             +G         + D + 
Sbjct: 159 DFVASAKRARDLGFEWLELHFA--HGYLAQSFFSVHANQRDDEYGGSAENRGRFIVDTLK 216

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +     +P+T +  +   D      L     L + +K+ G++ + +      +   +
Sbjct: 217 AVRQVWPEHLPLTARLGVIEYDGRDEETLAESIALTQRMKQEGLDMLSV-----SVGFST 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P             + E  +    L +    G++    A +++    +D VM+GRA   +
Sbjct: 272 PDAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVAEQQLDLVMVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|86611475|gb|ABD14409.1| HisF [Xanthomonas oryzae pv. oryzicola]
          Length = 280

 Score = 43.7 bits (102), Expect = 0.043,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 43  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 89

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 90  RVARLI-DIPFCVAGGISDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 148

Query: 240 SSPIKTRVDKDFWR 253
                 R D   WR
Sbjct: 149 VGIDSIREDDGEWR 162


>gi|88859292|ref|ZP_01133932.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas tunicata D2]
 gi|88818309|gb|EAR28124.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudoalteromonas tunicata D2]
          Length = 653

 Score = 43.7 bits (102), Expect = 0.043,   Method: Composition-based stats.
 Identities = 16/130 (12%), Positives = 44/130 (33%), Gaps = 8/130 (6%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+   +S    +  R+ V D +        ++   K+++ +GV+    +     
Sbjct: 191 ALEIVKAVRANVSSKFIIVFRLSVHDLVENGSSGSDVQAQAKALEAAGVDIF--NTGIGW 248

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
            +   P     +P   +     + K+   + +     +     A +IL +   D + + R
Sbjct: 249 HEARVPTIASMVPQGAFQDASLLLKQTVSVPVIAVNRINTPELANQILQNGKADLISMAR 308

Query: 218 AAYKNSAMLT 227
               +     
Sbjct: 309 PLLADPDFFN 318


>gi|115358451|ref|YP_775589.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           AMMD]
 gi|170702830|ref|ZP_02893680.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           IOP40-10]
 gi|172063208|ref|YP_001810859.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           MC40-6]
 gi|115283739|gb|ABI89255.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           AMMD]
 gi|170132266|gb|EDT00744.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           IOP40-10]
 gi|171995725|gb|ACB66643.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           MC40-6]
          Length = 369

 Score = 43.7 bits (102), Expect = 0.043,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 63/183 (34%), Gaps = 27/183 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD------------IVGDCI 108
             V +AK   D G+  + L+    +      SF +      D             + D +
Sbjct: 159 DFVASAKRARDLGFEWLELHF---AHGYLGQSFFSVHANQRDDEYGGSAENRGRFIVDTL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
            A+ +     +P+T +  +   D      L     L + +K+ G++ + +      +   
Sbjct: 216 KAVRQVWPEHLPLTARLGVIEYDGRDEETLAESIALTQRMKQEGLDMLSV-----SVGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYK 221
           +P             + E  +    L +    G++    A +++    +D VM+GRA   
Sbjct: 271 TPDAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVAEQQLDLVMVGRAHLA 330

Query: 222 NSA 224
           +  
Sbjct: 331 DPH 333


>gi|332293501|ref|YP_004432110.1| dihydroorotate dehydrogenase [Krokinobacter diaphorus 4H-3-7-5]
 gi|332171587|gb|AEE20842.1| dihydroorotate dehydrogenase [Krokinobacter diaphorus 4H-3-7-5]
          Length = 355

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 30/154 (19%), Positives = 61/154 (39%), Gaps = 30/154 (19%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I A+ +A     +  P+ +K    ++
Sbjct: 182 VDYFVLNVSCPNVSSHAK------LNDKDYLEELIGAVQQANKTYAVQRPIVLKIAPDLN 235

Query: 129 DQIPAVALRNLVKSIKKSGVNG-------------IWIHARKAILKGLSPKDNRKIPNLD 175
           DQ     L  +V  +K++G++G             I   AR A + G      + + +  
Sbjct: 236 DQ----QLDEIVALVKETGLDGVIASNTSVNREGLITTEARLAEI-GNGGLSGKPVTDRS 290

Query: 176 YDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
             ++  + +++ +   I   GG+     AL  L 
Sbjct: 291 TRVIKYLSEKSSNSFPIIGVGGIHSAQDALDKLE 324


>gi|297195828|ref|ZP_06913226.1| oxidoreductase [Streptomyces pristinaespiralis ATCC 25486]
 gi|297152963|gb|EDY64678.2| oxidoreductase [Streptomyces pristinaespiralis ATCC 25486]
          Length = 354

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 47/151 (31%), Gaps = 12/151 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----VALRNLVKSIKKSG 147
           +G           + + A+       + +  RI   D +                +K+ G
Sbjct: 203 YGGSFDNRVRFALEVVDAVRAVWPEELPLFFRISATDWLEEGGWTPDDTVRFASLLKEHG 262

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ + + +     +   P      P         +K E  DL +   G + D  QA KIL
Sbjct: 263 VDLLDVSSGGNAARVRIP----TGPGYQVPFAARVKAET-DLPVAAVGLITDAEQAEKIL 317

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                D V++GR   +N +            
Sbjct: 318 ANGEADAVLLGRELLRNPSWARHAACKLGGD 348


>gi|212704058|ref|ZP_03312186.1| hypothetical protein DESPIG_02111 [Desulfovibrio piger ATCC 29098]
 gi|212672563|gb|EEB33046.1| hypothetical protein DESPIG_02111 [Desulfovibrio piger ATCC 29098]
          Length = 631

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 26/181 (14%), Positives = 58/181 (32%), Gaps = 24/181 (13%)

Query: 65  AAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AA   +  G++ + L+ G          P     +  +G  L        + I A+  A+
Sbjct: 139 AALRAQKAGFDAVELHAGNGYLPQQFLSPFTNARQDGYGGSLENRVRFTVEAIRAVRAAV 198

Query: 116 SIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWI-----HARKAILKGLSPK 166
                +  R+GV + +             + + +  ++   +          +   L+  
Sbjct: 199 GPDFPIILRLGVAEPVSGGLTLEDGVAAARILAREDIDAFDVTAGMREGGMWVTPPLALP 258

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
               I       V +  + +    +   G +   S A   +    VD V++GRA   +  
Sbjct: 259 RGTHIEKA--AAVRQAIQASR--PVIGIGRITSASLADSFITAGKVDFVVMGRALLADPE 314

Query: 225 M 225
           +
Sbjct: 315 L 315


>gi|107102482|ref|ZP_01366400.1| hypothetical protein PaerPA_01003544 [Pseudomonas aeruginosa PACS2]
 gi|116050934|ref|YP_790241.1| morphinone reductase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218890870|ref|YP_002439734.1| morphinone reductase [Pseudomonas aeruginosa LESB58]
 gi|254235910|ref|ZP_04929233.1| morphinone reductase [Pseudomonas aeruginosa C3719]
 gi|115586155|gb|ABJ12170.1| morphinone reductase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126167841|gb|EAZ53352.1| morphinone reductase [Pseudomonas aeruginosa C3719]
 gi|218771093|emb|CAW26858.1| morphinone reductase [Pseudomonas aeruginosa LESB58]
          Length = 369

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 61/188 (32%), Gaps = 29/188 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA+   D G++ + L              ++     ++G  L      + + + A
Sbjct: 161 DEFVRAARNALDAGFDLVELHGANGYLIDQFLASASNRRSDAYGGSLENRARFLLEIVDA 220

Query: 111 MCKALSI-PVTVKCRI-----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +  A+    V ++         + D  P      L +++++ G+  +  H  +    G  
Sbjct: 221 LVAAVGAERVGLRLSPWGTINDMHDDEPEAMTLYLAEALQRRGIAYL--HLAEWEWSGGP 278

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                    L                + + G   D  +A  IL +   D V IGR    N
Sbjct: 279 AYPQGFRERLRERFRA---------PLIVCGNY-DAERAEAILQAGLADAVAIGRPFIAN 328

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 329 PDLVERIR 336


>gi|15598128|ref|NP_251622.1| morphinone reductase [Pseudomonas aeruginosa PAO1]
 gi|9949027|gb|AAG06320.1|AE004719_6 morphinone reductase [Pseudomonas aeruginosa PAO1]
          Length = 369

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 61/188 (32%), Gaps = 29/188 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA+   D G++ + L              ++     ++G  L      + + + A
Sbjct: 161 DEFVRAARNALDAGFDLVELHGANGYLIDQFLASASNRRSDAYGGSLENRARFLLEIVDA 220

Query: 111 MCKALSI-PVTVKCRI-----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +  A+    V ++         + D  P      L +++++ G+  +  H  +    G  
Sbjct: 221 LVAAVGAERVGLRLSPWGTINDMHDDEPEAMTLYLAEALQRRGIAYL--HLAEWEWSGGP 278

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                    L                + + G   D  +A  IL +   D V IGR    N
Sbjct: 279 AYPQGFRERLRERFRA---------PLIVCGNY-DAERAEAILQAGLADAVAIGRPFIAN 328

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 329 PDLVERIR 336


>gi|258517346|ref|YP_003193568.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257781051|gb|ACV64945.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 661

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 23/140 (16%), Positives = 55/140 (39%), Gaps = 11/140 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ-IPAVALRNLVKSIKKSGVNGI 151
           +G  L     ++ +   A+ K +     +  R+  D+     + L + V+  +     G 
Sbjct: 190 YGGSLENRMRLLCETAEAVRKVVGKDFIMGLRLSGDEFVDGGLTLADTVEIARGIDETGF 249

Query: 152 WIHARKAILKGLSPKD------NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           + +   ++  G++ ++      N  +P      +    ++   + +   G ++D +QA +
Sbjct: 250 FDYINTSV--GIATRNLYLVEGNMCMPPGYSVYMSSAVRQAVKIPVIAVGRIKDPAQAEQ 307

Query: 206 ILPSVDGVMIG--RAAYKNS 223
           IL      MIG  RA   + 
Sbjct: 308 ILRDGHADMIGMVRAQIADP 327


>gi|152970309|ref|YP_001335418.1| putative NADH:flavin oxidoreductase/NADH oxidase [Klebsiella
           pneumoniae subsp. pneumoniae MGH 78578]
 gi|238894793|ref|YP_002919527.1| putative NADH:flavin oxidoreductase [Klebsiella pneumoniae
           NTUH-K2044]
 gi|150955158|gb|ABR77188.1| putative NADH:flavin oxidoreductase/NADH oxidase [Klebsiella
           pneumoniae subsp. pneumoniae MGH 78578]
 gi|238547109|dbj|BAH63460.1| putative NADH:flavin oxidoreductase [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 366

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 27/178 (15%), Positives = 58/178 (32%), Gaps = 20/178 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNP-DIVGDCI 108
            V +A   +  G+  I L+            P +      +G  L   M  P ++     
Sbjct: 159 FVASALRAQRLGFELIELHAAHGYLLHQFLSPLSNQRRDEYGGSLENRMRYPLEVFKAIR 218

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   +++ V +     V+            + ++  G + I + +      GLSP+  
Sbjct: 219 EAVGNTMAVGVRLSATDWVEGGWDCEQSIKFSQQLETLGSDYIHVSSG-----GLSPQQA 273

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
             +            ++   + +   G + D  QA   L +   D + + RA   +  
Sbjct: 274 ITVGPGYQLPFARDIRQQVAIPVIGVGLITDPQQAEAALENGDADLIALARAVLYDPH 331


>gi|47458903|ref|YP_015765.1| NADH:flavin oxidoreductase [Mycoplasma mobile 163K]
 gi|47458231|gb|AAT27554.1| NADH:flavin oxidoreductases [Mycoplasma mobile 163K]
          Length = 349

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 37/216 (17%), Positives = 73/216 (33%), Gaps = 34/216 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------LNPDIVG 105
              + AAK  +  G + + ++          G   + L+                  ++ 
Sbjct: 128 ENFILAAKRAKKAGVDFVEIHAA-------HGYLFSQLISPITNEINPSENIVERSRLLI 180

Query: 106 DCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           D +  + K + IP  ++  +     +   A   + L+K ++K     I+ +    IL G 
Sbjct: 181 DFVKRLKKEVDIPFGIRLSVNDYFPNGNTAKDFKPLIKELEKY---VIYFNVSSWILSGA 237

Query: 164 SPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGL---EDMSQALKILPSVDGVMIGRAA 219
              +        Y +   +  K   +  +  +G     ED+  AL     +D V IGR  
Sbjct: 238 PLLEESVKKTKLYRLEDALTIKSFTNKQVIASGNFNTKEDIDFALN--KGIDFVGIGREL 295

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
             N   L  ++ YFS     +   +      F+  I
Sbjct: 296 LFNPNFL--LNNYFSPEELKTQNFEWVKGNRFYNHI 329


>gi|11498352|ref|NP_069580.1| hypothetical protein AF0746 [Archaeoglobus fulgidus DSM 4304]
 gi|2649865|gb|AAB90493.1| conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
          Length = 249

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 34/93 (36%), Gaps = 8/93 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A++V +F    I +N  C      E   G  L+ N + + + ++   +    P  VK R 
Sbjct: 90  AELVAEFE-GIIEINAHCRQPEFVEIGCGEWLLFNHERLVEIVSKTSRIA--PTFVKIR- 145

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
                   +    + + +  +G   I + A   
Sbjct: 146 ----GGHKLDYEKIARKLFDAGCLAIHVDAMIP 174


>gi|317026403|ref|XP_001389551.2| NADH-dependent flavin oxidoreductase [Aspergillus niger CBS 513.88]
          Length = 419

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 64/189 (33%), Gaps = 29/189 (15%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EA K     G++ I ++            P++      +G        +  + +    + 
Sbjct: 213 EAVKRAVRAGFDAIEIHGAHGYLIHEFLSPASNKRTDEYGGSFENRIRLALELVDISRQH 272

Query: 115 L--SIPVTVKCR-------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +  ++P+  +         +  +    A     L + + + GV+ + + +      G  P
Sbjct: 273 MTPNMPLFFRVSGTDWLEHLENEPSWDASQTVRLAEVLVEHGVDVLDVSSG-----GNDP 327

Query: 166 KDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN 222
           +   K          +++K+   D L +   G +    QA  +L   +D V+IGR   KN
Sbjct: 328 RQQIKGGPAYQSPYAFQVKEALGDRLLVASVGAITSGPQANDLLNAGLDMVLIGRMFQKN 387

Query: 223 S---AMLTT 228
                    
Sbjct: 388 PGLVWTFAE 396


>gi|254441175|ref|ZP_05054668.1| oxidoreductase, FAD/FMN-binding superfamily [Octadecabacter
           antarcticus 307]
 gi|198251253|gb|EDY75568.1| oxidoreductase, FAD/FMN-binding superfamily [Octadecabacter
           antarcticus 307]
          Length = 407

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 32/183 (17%), Positives = 65/183 (35%), Gaps = 21/183 (11%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVG 105
            G  I K V +AK+ +D G++ I ++           S R++     +G  L     +  
Sbjct: 141 FGIIIKKFVHSAKLAQDAGFDGIEIHAAHGYLLSSALSPRINTRTDRWGGTLENRARLAL 200

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR----K 157
           D + A+  A+     V  ++   D             +   ++  GV+ I I        
Sbjct: 201 DVVRAVRAAVDPRFIVAIKLNSSDFQKGGFDHAGSVEVAIMLQDEGVDFIEISGGNFEEP 260

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
              +  S K+        Y + Y +  K   ++ + + GG    +     + +   D + 
Sbjct: 261 TAYQHTS-KNGSTKAREAYFLDYAVAIKAVLNIPLMVTGGFRSANIMNDAIENGKTDLIG 319

Query: 215 IGR 217
           +GR
Sbjct: 320 MGR 322


>gi|170723300|ref|YP_001750988.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
 gi|169761303|gb|ACA74619.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
          Length = 368

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 28/190 (14%), Positives = 59/190 (31%), Gaps = 20/190 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+A +     G+  + ++            P +      +G+C      +      A+
Sbjct: 158 EFVKATERALQAGFKVVEIHAAHGYLLHQFLSPLSNQRRDEYGSCFENRIRLTLQVTEAV 217

Query: 112 CKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            K         V V     V+D         L + ++  GV+ I + +      G S   
Sbjct: 218 RKVWPKELPLFVRVSATDWVEDGWNPDETVELARRLRALGVDLIDVSSG-----GTSMNA 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
                        E  ++  ++  G  G + + +QA  IL     D + + R   ++   
Sbjct: 273 EIPTGPGYQTRFAERVRKESEIATGTVGMITEPAQAEHILRTGQADLIFLARELLRDPYW 332

Query: 226 LTTVDEYFSN 235
               D+    
Sbjct: 333 PLHADDDLGG 342


>gi|118587871|ref|ZP_01545281.1| hypothetical protein SIAM614_09858 [Stappia aggregata IAM 12614]
 gi|118439493|gb|EAV46124.1| hypothetical protein SIAM614_09858 [Stappia aggregata IAM 12614]
          Length = 764

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 71/211 (33%), Gaps = 24/211 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
           + V AA++ E  G++ I L+            P +      +G  L   M  P  V + +
Sbjct: 549 QFVSAAEMAERAGFDMIELHAAHGYLLSSFISPVSNARTDEYGGSLDNRMRWPLEVFNAM 608

Query: 109 AAM---CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            A+    K +S+ ++  C    ++ I       + +  + +GV+ + + A +   K   P
Sbjct: 609 RAVWPEHKPMSVRISA-CDWVGEEGITPDDAVEIARRFRAAGVDLVDVSAGQTTPK-ARP 666

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R       D +    +    L     G + +   A  IL +   D V +GR    + 
Sbjct: 667 VYGRMFQTPFSDRI----RNEGGLPTMAVGNIYEADHANSILMAGRADLVAVGRPHLADP 722

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
              L    +      T             WR
Sbjct: 723 YWTLHEAAKIGDRNATDWPLPYLAGRDQMWR 753


>gi|212542479|ref|XP_002151394.1| FMN binding oxidoreductase, putative [Penicillium marneffei ATCC
           18224]
 gi|210066301|gb|EEA20394.1| FMN binding oxidoreductase, putative [Penicillium marneffei ATCC
           18224]
          Length = 417

 Score = 43.3 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 27/153 (17%), Positives = 53/153 (34%), Gaps = 16/153 (10%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVN 149
           +G        +V D I A+  A      V  ++   D     AL   +   K I ++GV+
Sbjct: 208 YGCSPEKRAKVVIDIIHAVRAATPEGFCVGVKLNSVDHQSPEALEGCISQLKMIHEAGVD 267

Query: 150 GIWIHAR-----KAILKGLSPKDNRKIPN------LDYDIVYEIKKENPDLFIGLNGGLE 198
            + I          I  G S     K  +         +    I+ + P++ + L GG  
Sbjct: 268 FVEISGGSYEDVTFITGGTSQSQQEKSAHTVAREAFFLEFADAIRSQVPEIPLLLTGGFR 327

Query: 199 DMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
                +  + +   D + + R A    ++  ++
Sbjct: 328 TRRGMVAAMQNSSCDMIGLARPAVLTPSLPKSI 360


>gi|312866045|ref|ZP_07726266.1| dihydroorotate dehydrogenase 1A [Streptococcus downei F0415]
 gi|311098449|gb|EFQ56672.1| dihydroorotate dehydrogenase 1A [Streptococcus downei F0415]
          Length = 311

 Score = 43.3 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 38/217 (17%), Positives = 70/217 (32%), Gaps = 22/217 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGY-NEINLNVGCPSARVHEG 91
              D    L  +   K   L + G    +     K V++  Y + + LN+ CP   V   
Sbjct: 80  YYLDYVTELQKAPDSKNHFLSLVGMSQEETHTILKTVQESDYEDLVELNLSCP--NVPGK 137

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIK 144
              A    + +     ++ +    + P+ +K     D      A A+ N      V  I 
Sbjct: 138 PQIAY---DFETTDQILSQVFSYFTKPLGIKLPPYFDIAHFDLAAAIFNKYPLTFVNCIN 194

Query: 145 KSG-----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             G      +   +   K    G+     +     +    Y+  + NP + I   GG++ 
Sbjct: 195 SVGNGLVIEDETVVIKPKNGFGGIGGDYVKPTALANVHAFYQ--RLNPSIQIIGTGGVKS 252

Query: 200 MSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFS 234
              A +  L     V IG A   +  A+   + +   
Sbjct: 253 GRDAFEHILCGASMVQIGTALHQEGPAVFERITKELQ 289


>gi|66807487|ref|XP_637466.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
 gi|60465889|gb|EAL63959.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
          Length = 400

 Score = 43.3 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 27/192 (14%), Positives = 55/192 (28%), Gaps = 22/192 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCP-SARVHEGSFGACLMLNPDIVGDCIA 109
                AA+  E  G++ I +             P S +  +             + D + 
Sbjct: 195 DSFRLAAERCEKAGFDFIEIHGAHGYLINQFLSPTSNKRTDQYGCGSFEDRCRFLFDIVR 254

Query: 110 AMCKALSIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+     +     V + C    +          + K ++   V+     +      G S 
Sbjct: 255 AIRSVWPVEKALGVRLSCEEWCEGGWTLDDTIRVAKILETMDVDVFDCSSG-----GNSM 309

Query: 166 KDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             +  I       + + +KK    L +   G +    +  +IL     D V + R   +N
Sbjct: 310 SQSITIGPCYQVPLAHAVKKATSKLSVACVGLINSGKEIEEILQQDRADLVFLARPFLRN 369

Query: 223 SAMLTTVDEYFS 234
                 V    +
Sbjct: 370 PHFTYQVAHELN 381


>gi|239615641|gb|EEQ92628.1| NADH-dependent flavin oxidoreductase [Ajellomyces dermatitidis
           ER-3]
 gi|327353933|gb|EGE82790.1| NADH-dependent flavin oxidoreductase [Ajellomyces dermatitidis ATCC
           18188]
          Length = 420

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 70/199 (35%), Gaps = 32/199 (16%)

Query: 64  EAAKIVEDFGYNEINL-NVG-------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            A +     G + I + N         C P +      +G        +  + I    + 
Sbjct: 201 AAVRRAVKAGVDYIEIHNAHGYLLFSFCSPISNNRTDEYGGSFENRIRLSSEIITICRQN 260

Query: 115 L--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +   +P+ ++          R  +        +R   K + + G V+ + + A      G
Sbjct: 261 MPKDMPLFLRISASEWLEQSRPDLPSWKSEDTVR-FAKILAEKGEVDLLDVSA------G 313

Query: 163 LSPKDNRKIPNLDYDI--VYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
            +  D + IP   +     + +K+   D L +G  G + +   A  +L   +D V++GR 
Sbjct: 314 GNHPDQKIIPGPCFQAHFAHAVKEAVGDKLLVGAVGSINNGIDANGLLEKGLDLVLVGRQ 373

Query: 219 AYKNSAMLTTVDEYFSNPL 237
             KN A++    E     +
Sbjct: 374 FLKNPAVVWQFAEDLGTEI 392


>gi|189347481|ref|YP_001944010.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium limicola
           DSM 245]
 gi|189341628|gb|ACD91031.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Chlorobium limicola DSM 245]
          Length = 260

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 11/94 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           R++    +K     + I    A L G           ++++ + EI +E  D+ I + GG
Sbjct: 37  RDMAIIWRKQNAKMLHIVDLDAALTGEM---------VNFERIKEIVEEL-DIPIQVGGG 86

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           +  +    + L   V  V+IG AA  N  ++  +
Sbjct: 87  IRSLEAVKRYLDIGVSRVVIGSAAVTNPELIGEL 120


>gi|326202685|ref|ZP_08192553.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium papyrosolvens
           DSM 2782]
 gi|325987269|gb|EGD48097.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium papyrosolvens
           DSM 2782]
          Length = 657

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 68/192 (35%), Gaps = 20/192 (10%)

Query: 66  AKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           AK+ +D G++ + ++            P        FG  L      +   + A+ + + 
Sbjct: 168 AKLCKDCGFDMVQVHAAHGWIFSQFLSPVLNSRTDEFGGSLENRARFLLMVLDAVREGVG 227

Query: 117 IPVTVKCRIGVDD-QIPAVALRNLVKSIK--KSGVNGIWI----HARKAILKGLSPKDNR 169
               ++ R+  DD     + L + ++  +     V+   I    H    +     P    
Sbjct: 228 PKFPIEIRLSGDDLTDIGLGLEDCIRVAQMVDDKVDLFNISCGNHEDPDVFCRTHPSAFY 287

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
               ++  +  EIKK      +   G L D +Q  +I+     D V IGRA   +  +  
Sbjct: 288 PRG-VNVYLAAEIKKHV-KTPVACVGSLNDPAQMEEIIAEGQADIVEIGRALLADPYLPK 345

Query: 228 TVDEYFSNPLTG 239
              E  ++ +T 
Sbjct: 346 KALEGNADDITP 357


>gi|330008450|ref|ZP_08306260.1| oxidoreductase, FAD/FMN-binding [Klebsiella sp. MS 92-3]
 gi|328535116|gb|EGF61627.1| oxidoreductase, FAD/FMN-binding [Klebsiella sp. MS 92-3]
          Length = 366

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 27/178 (15%), Positives = 58/178 (32%), Gaps = 20/178 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNP-DIVGDCI 108
            V +A   +  G+  I L+            P +      +G  L   M  P ++     
Sbjct: 159 FVASALRAQRLGFELIELHAAHGYLLHQFLSPLSNQRRDEYGGSLENRMRYPLEVFKAIR 218

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   +++ V +     V+            + ++  G + I + +      GLSP+  
Sbjct: 219 EAVGNTMAVGVRLSATDWVEGGWDCEQSIKFSQQLETLGSDYIHVSSG-----GLSPQQA 273

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
             +            ++   + +   G + D  QA   L +   D + + RA   +  
Sbjct: 274 ITVGPGYQLPFARDIRQQVAIPVIGVGLITDPQQAEAALENGDADLIALARAVLYDPH 331


>gi|306822185|ref|ZP_07455567.1| xenobiotic reductase A [Bifidobacterium dentium ATCC 27679]
 gi|309802239|ref|ZP_07696347.1| oxidoreductase, FAD/FMN-binding [Bifidobacterium dentium
           JCVIHMP022]
 gi|304554567|gb|EFM42472.1| xenobiotic reductase A [Bifidobacterium dentium ATCC 27679]
 gi|308221122|gb|EFO77426.1| oxidoreductase, FAD/FMN-binding [Bifidobacterium dentium
           JCVIHMP022]
          Length = 376

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 58/167 (34%), Gaps = 12/167 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G C      ++ + + A+   +   +PV V+                 +L K +K+ GV
Sbjct: 216 YGGCFENRIRMLVEVVDAVRTVIPDDMPVLVRISATDWAAGGWDLDQSVDLAKVLKEHGV 275

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + +        GL P               E  +   D+ +   G +    QA K+L 
Sbjct: 276 DLVDVSTG-----GLIPDVTIPFKPGYQVPFSEQIRSRADVPVTAVGLITKPKQAEKVLK 330

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
               D + IGRAA ++             P+   +P   +  +  +R
Sbjct: 331 AGQADAIEIGRAALRDPYWPLRAANKLGVPV-EEAPYPAQYVRGAFR 376


>gi|77918691|ref|YP_356506.1| NADH:flavin oxidoreductase [Pelobacter carbinolicus DSM 2380]
 gi|77544774|gb|ABA88336.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family [Pelobacter
           carbinolicus DSM 2380]
          Length = 365

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 33/226 (14%), Positives = 68/226 (30%), Gaps = 44/226 (19%)

Query: 24  TEMIVADA------ILRGDKKNILGFSTQEKPLAL------QIGGADISKL--------- 62
           TEM+ +        I  G  +    +  +E+ +             +  ++         
Sbjct: 87  TEMVHSHGSRIVMQIAYGGSQT--NYRPEERTIWGPSEVADLAFKVEPREMSREDIQTLK 144

Query: 63  ---VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               EAA   +  G++ + L+           CP        +G  +     IV +    
Sbjct: 145 KAYGEAANRAKAAGFDGVQLHAAHGYLLNQFLCPYYNRRTDEYGGSIENRARIVLEIYDE 204

Query: 111 MCKALSI--PVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +    PV +K       ++       R L + +   G++ I +         L P 
Sbjct: 205 VRDRVGANYPVLIKLNAEDFTENGATFEDCRYLCRELAGRGIDAIEVSCGTFASGKLGPC 264

Query: 167 DNRKIPNLDYDI----VYEIKKENPDLFIGLNGGLEDMSQALKILP 208
             R               ++ +E  D+ I + GG+       K+L 
Sbjct: 265 RTRIDAPEKEAYNAGHAAQLAEEL-DVPILVVGGIRSPEVIEKLLE 309


>gi|315502490|ref|YP_004081377.1| NADH:flavin oxidoreductase/NADH oxidase [Micromonospora sp. L5]
 gi|315409109|gb|ADU07226.1| NADH:flavin oxidoreductase/NADH oxidase [Micromonospora sp. L5]
          Length = 355

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 30/197 (15%), Positives = 58/197 (29%), Gaps = 20/197 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA    D G+  + ++            P        +G        +  +   A
Sbjct: 158 DAFATAAGRALDAGFAAVEIHAAHGYLLHEFLSPLTNRRTDGYGGDRAARMRLTLEVARA 217

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+   V V  RI   D        +    L   +  +GV+ I   +  A ++   P 
Sbjct: 218 VRAAVGESVPVLTRISATDWTDDGWTVDDSVVLAGELAAAGVDLIDTSSGGAAVQASIPV 277

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                  L       I+++   +  G  G + +  QA +I+     D V++GR   ++  
Sbjct: 278 GPGYQVPL----AARIRRDAG-VPTGAVGLIVEPEQAEQIVAGGEADLVLLGRELLRDPY 332

Query: 225 MLTTVDEYFSNPLTGSS 241
                            
Sbjct: 333 WPRRAAAKLGATPAWPD 349


>gi|297156224|gb|ADI05936.1| hypothetical protein SBI_02815 [Streptomyces bingchenggensis BCW-1]
          Length = 285

 Score = 43.3 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 31/183 (16%), Positives = 63/183 (34%), Gaps = 16/183 (8%)

Query: 26  MIVADAI----LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           MI +       +    K +   +  + P+   +     S+L + A  V+  G   + L +
Sbjct: 58  MINSTTYSKRSVDHWLKVLRSLTEDQLPIIASLHADTPSELGDLAAQVQGTGCRALELGI 117

Query: 82  GCPSARVHEGSFGACLMLN-PDIVGDCIAAMCKALSIPVTVK--CRIGVDDQIPAVALRN 138
            C        +  + L  + PD V    +      S+P++VK     G++D++ A     
Sbjct: 118 SC-------LNEESGLEDDNPDRVYAYTSETRARTSLPLSVKLAIGEGLEDRVRAAIAGG 170

Query: 139 LVKSIKKSGV--NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
                    +    +     +  L G+       I  L    ++ ++K    L I   GG
Sbjct: 171 ADAITVSDTISGAAVSPDTGELELGGVFGYSGPGIKPLVLAAIWRLRKRGFVLPIMGVGG 230

Query: 197 LED 199
           +  
Sbjct: 231 ISS 233


>gi|206901606|ref|YP_002250206.1| dihydroorotate dehydrogenase superfamily [Dictyoglomus thermophilum
           H-6-12]
 gi|206740709|gb|ACI19767.1| dihydroorotate dehydrogenase superfamily [Dictyoglomus thermophilum
           H-6-12]
          Length = 390

 Score = 43.3 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 22/109 (20%), Positives = 43/109 (39%), Gaps = 13/109 (11%)

Query: 49  PLALQI-GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I    D   L + +K+ E+ G   + LNV CP A +             D +   
Sbjct: 103 PVIPSINCITDEGWL-KYSKMAEEAGAPALELNVSCPHASISFRGQDVD-----DTILHV 156

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
              +   + IP+ VK  + +           + K+++  G++G+ +  R
Sbjct: 157 ARLVRDNVKIPIIVKLPMQLSSP------LAVAKALENIGIDGVVMFNR 199


>gi|312621650|ref|YP_004023263.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202117|gb|ADQ45444.1| dihydroorotate dehydrogenase family protein [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 381

 Score = 43.3 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 41/111 (36%), Gaps = 17/111 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   I        +E +K++E  G + I LN+ CP         G  +M   D++ + +
Sbjct: 100 PVIASINCYTDDAWLEYSKLMEQAGADAIELNLSCPH--------GVHIMSGMDVIEEMV 151

Query: 109 AA---MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                +   + IPV  K      +             +  +G +G+ +  R
Sbjct: 152 HTTKLVKSNVKIPVIPKMTPQSTNPGFD------ALRLDSAGADGLVMFNR 196


>gi|206563371|ref|YP_002234134.1| putative NADH:flavin oxidoreductase [Burkholderia cenocepacia
           J2315]
 gi|198039411|emb|CAR55377.1| putative NADH:flavin oxidoreductase [Burkholderia cenocepacia
           J2315]
          Length = 411

 Score = 43.3 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 29/208 (13%), Positives = 60/208 (28%), Gaps = 43/208 (20%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             +  +AA+   D G++ + +++G          P       ++G           D + 
Sbjct: 152 ADEFAQAARHARDAGFDAVEIHMGHGYLLSQFLSPLYNRRRDAYGGDAARRAAFPVDVLR 211

Query: 110 AMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHAR----KAILK 161
            +  A+   + V C+IGV + +     A     + + ++  G + + +            
Sbjct: 212 RVLDAVGRDLAVVCKIGVTEGVRGGGTADDACEIARRLEAEGAHLLVLSGGMNVESVWQL 271

Query: 162 GLSPKDNRKIPNLDYDIVYEI-------------------------KKENPDLFIGLNGG 196
             SP       N D  IV                             +    + +   GG
Sbjct: 272 FGSPLPGDARANADNAIVRAAMALQTLTEPKMGAFREMYFLEHSKQVRAAVRMPLAYLGG 331

Query: 197 LEDMSQ-ALKILPSVDGVMIGRAAYKNS 223
           +      A  +    D V + RA     
Sbjct: 332 VRSRDNVARAMREGFDAVALARALVFEP 359


>gi|90411633|ref|ZP_01219643.1| imidazole glycerol phosphate synthase subunit HisF [Photobacterium
           profundum 3TCK]
 gi|90327523|gb|EAS43876.1| imidazole glycerol phosphate synthase subunit HisF [Photobacterium
           profundum 3TCK]
          Length = 257

 Score = 43.3 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D V I   A  N A++T + + F 
Sbjct: 85  SVEDASRILQFGADKVSINSPALANPALITELADKFG 121


>gi|254516066|ref|ZP_05128126.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium NOR5-3]
 gi|219675788|gb|EED32154.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium NOR5-3]
          Length = 245

 Score = 43.3 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 11/134 (8%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +    +G   + +        G           ++ D V  I    PDL I + GG+  
Sbjct: 36  AQRWVDAGCRRLHLVDLNGAFAG---------APVNGDAVTAIAARFPDLPIQIGGGIRT 86

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRVDKDFWRKISA 257
           +      L   V  V+IG  A K    +      F   +  G      RV  D W ++SA
Sbjct: 87  LETIEFYLKAGVSYVIIGTQAVKQPTFVAEACAAFEGKIIVGLDARDGRVATDGWAEVSA 146

Query: 258 SMTDYAARHLHSGG 271
                 AR     G
Sbjct: 147 LQATDLARRFAGDG 160


>gi|146284546|ref|YP_001165499.1| NADH:flavin oxidoreductase/NADH oxidase [Enterobacter sp. 638]
 gi|145320679|gb|ABP62825.1| NADH:flavin oxidoreductase/NADH oxidase [Enterobacter sp. 638]
          Length = 364

 Score = 43.3 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 33/212 (15%), Positives = 68/212 (32%), Gaps = 24/212 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA+     G+  + L+            P +      +G  L      + + +A +
Sbjct: 159 DFARAAERACQAGFQWLELHFAHGFLAQSFLSPQSNTRSDEYGGSLEGRARFLLETVAEV 218

Query: 112 CK--ALSIPVTVKCRIGVDDQIPAVALRNLVKSI---KKSGVNGIWIHARKAILKGLSPK 166
            K    + P+TV+  +   D  P  +    +K I   K +GV+ + +      L   +P 
Sbjct: 219 RKFWPDNFPLTVRLGVVEFDDCPEHSFSESLKVIGWLKDAGVDFVDV-----GLSLATPG 273

Query: 167 DN-RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           +N     N        +++E  ++ +G +  +    +A + +    VD +   R    N 
Sbjct: 274 ENIPWAANFMVPWAARVRRE-KNIPVGTSWMITQAKEANEFIQDGKVDVIFFARTLLANP 332

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
                   E          P         W +
Sbjct: 333 HWPYRAARELEITDPHAVLPTPYAYWLQNWSE 364


>gi|107026444|ref|YP_623955.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia cenocepacia
           AU 1054]
 gi|116692368|ref|YP_837901.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia cenocepacia
           HI2424]
 gi|105895818|gb|ABF78982.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia cenocepacia
           AU 1054]
 gi|116650368|gb|ABK11008.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia cenocepacia
           HI2424]
          Length = 369

 Score = 43.3 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 22/128 (17%), Positives = 48/128 (37%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + D +AA+ K     +P+T +  +   D      L     L + +K+ G++ + +     
Sbjct: 211 LVDTLAAVRKVWPEHLPLTARLGVIEYDGRDEETLAESIALTQRMKREGLDMLSV----- 265

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIG 216
            +   +P             + E  +    L +    G++    A +++     D VM+G
Sbjct: 266 SVGFSTPTAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVEQAQLDLVMVG 325

Query: 217 RAAYKNSA 224
           RA   +  
Sbjct: 326 RAHLADPH 333


>gi|312888877|ref|ZP_07748439.1| NADH:flavin oxidoreductase/NADH oxidase [Mucilaginibacter paludis
           DSM 18603]
 gi|311298618|gb|EFQ75725.1| NADH:flavin oxidoreductase/NADH oxidase [Mucilaginibacter paludis
           DSM 18603]
          Length = 354

 Score = 43.3 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 38/220 (17%), Positives = 67/220 (30%), Gaps = 24/220 (10%)

Query: 39  NILGFSTQEKPLALQIGGADIS--KLVEAAKIVEDFGYNEINLNVG---------CPSAR 87
           ++     +EKPL L   G D       EA       G+  I L+            P + 
Sbjct: 133 DLAFADGEEKPLELDQEGVDKIKADFKEATYRAIKAGFKVIELHAAHGYLIHQFLSPLSN 192

Query: 88  VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSI 143
                +G        ++ +    +  A      +  RI   D  P     +    L   +
Sbjct: 193 HRTDEYGGSFENRIRLLLEITEVVRSAWPEEFPLFVRISATDWTPGGWTADDSVQLAHRL 252

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           K+ GV+ +          G  PK    +           +KKE   +  G  G + D  Q
Sbjct: 253 KEQGVDLVDCSTG-----GNVPKAKIPVGPGYQVQFAETVKKETG-ILTGAVGMITDPEQ 306

Query: 203 ALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           A +I+     D V++ R   ++            + +   
Sbjct: 307 ADQIIRNEQADMVLLARQHLRDPHFALRAAHILGHEVKWP 346


>gi|254420000|ref|ZP_05033724.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Brevundimonas sp. BAL3]
 gi|196186177|gb|EDX81153.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Brevundimonas sp. BAL3]
          Length = 255

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 11/99 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L    + +G + +  +   A  +G +         LDY  + +I +   D+   + GG
Sbjct: 33  AELAARYRDAGADELVFYDITASPEGRT---------LDYGWIRDIAR-LLDIPFCVAGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  + QA + L    D V I   A +   ++  +     
Sbjct: 83  IRSVDQAARCLDHGADKVSINSPALERPELIAEMAARLG 121


>gi|159471299|ref|XP_001693794.1| psbA translation factor [Chlamydomonas reinhardtii]
 gi|158283297|gb|EDP09048.1| psbA translation factor [Chlamydomonas reinhardtii]
          Length = 431

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 7/85 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
             E+   +   +N  CP   + E   G  +  +P+++G+    + KA ++PV  K    V
Sbjct: 183 RCEEIKVDAFEINFSCPHG-LPERRMGMAMGQDPEVLGEVCGWINKAATVPVWAKMTPNV 241

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIW 152
            D               K+G  G+ 
Sbjct: 242 TDISFP------ADVALKAGCEGVA 260


>gi|260768998|ref|ZP_05877932.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio furnissii CIP 102972]
 gi|260617028|gb|EEX42213.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio furnissii CIP 102972]
          Length = 559

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 20/132 (15%), Positives = 51/132 (38%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V++      +  L K+++ +GV    I+      +
Sbjct: 88  EVVRAIREAVGKEFIIIFRLSMLDLVEEGSTFEEVLMLAKALEAAGVT--IINTGIGWHE 145

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K + ++ +     +    +A KI+     D V + R  
Sbjct: 146 ARIPTIATQVPRAAFTWVTEKIKPHLNVPVVTCNRINTPEEAEKIVASGQADLVSMARPF 205

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 206 LADPEFVAKAEQ 217


>gi|195977769|ref|YP_002123013.1| dihydroorotate dehydrogenase 1A [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|195974474|gb|ACG62000.1| Dihydroorotate dehydrogenase [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 294

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 75/229 (32%), Gaps = 37/229 (16%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLN 80
           + TEM    A       +++G S +E              +++A   ++   Y   + LN
Sbjct: 67  IVTEMQKDQASSHHFL-SVVGMSAEET-----------ETILKA---IQASDYQGLVELN 111

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN 138
           + CP   V        L  + +     +  +    + P+ +K     D      A A+ N
Sbjct: 112 LSCP--NVPGK---PQLAYDFEATDQLLKKIFSYCTKPLGIKLPPYFDIVHFDQAAAIFN 166

Query: 139 -----LVKSIKKSGVNGIW-----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
                 V  +   G   +      +   K    G+     +     +    Y+  + NP 
Sbjct: 167 QYPLAFVNCVNSIGNGLVIDDEQVVIKPKNGFGGIGGDYIKPTALANVHAFYQ--RLNPS 224

Query: 189 LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
           + I   GG++    A +  L     V IG A   +  A+   + +   +
Sbjct: 225 IQIIGTGGVKTGRDAFEHILCGAAMVQIGTALHQEGPAIFKRITKELQD 273


>gi|15614044|ref|NP_242347.1| NADPH dehydrogenase NamA [Bacillus halodurans C-125]
 gi|68052808|sp|Q9KCT8|NAMA_BACHD RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|10174098|dbj|BAB05200.1| NADH oxidase [Bacillus halodurans C-125]
          Length = 338

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 24/154 (15%), Positives = 54/154 (35%), Gaps = 10/154 (6%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV--ALRNLVKSIKKSGVN 149
           ++G  L     ++ + I+ +      P+ V+       +          L K +KK G++
Sbjct: 184 AYGGSLENRYRLLREIISEIQTVWDGPLFVRISAAEYAEGGNELSDFITLAKWMKKQGID 243

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            I   +   +   +      ++P      + E  +   ++  G  G +    QA +IL +
Sbjct: 244 LIDCSSGAVVPAPIPVYPGYQVP------LAEAIRHEANIATGAVGLITSGIQAEEILQN 297

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
              D + + R   +N              ++G S
Sbjct: 298 ERADLIFVARELLRNPYWPREAALELGTTISGPS 331


>gi|225568703|ref|ZP_03777728.1| hypothetical protein CLOHYLEM_04782 [Clostridium hylemonae DSM
           15053]
 gi|225162202|gb|EEG74821.1| hypothetical protein CLOHYLEM_04782 [Clostridium hylemonae DSM
           15053]
          Length = 671

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 26/174 (14%), Positives = 53/174 (30%), Gaps = 15/174 (8%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            AA+   + G++ + ++ G          P+       FG C           I  +  A
Sbjct: 159 AAARRAVNAGFDLVEIHAGHSYLISQFLSPTMNDRTDEFGGCAENRARFCKMVIGEVRAA 218

Query: 115 LSIPVTVKCRIGVDDQIP-AVALRNLVKSIK--KSGVNGIWIHARKAILKGLSPKDNRKI 171
           +   V +  R+ VD+ +     L + +  ++      +     A            N   
Sbjct: 219 VGPRVPISLRLSVDELVEGGNTLEDCLAYLEYLNDEADIFDTSAALNPSIQYQIDANYLA 278

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                 +   ++++     I   G +     A  IL     D + IGR    + 
Sbjct: 279 DGWRSYMARAVREKFHKPSI-AIGNIRSPQAAEDILEKGDADLIGIGRGLIADP 331


>gi|167621801|ref|YP_001676586.1| NADH:flavin oxidoreductase/NADH oxidase [Caulobacter sp. K31]
 gi|167351542|gb|ABZ74272.1| NADH:flavin oxidoreductase/NADH oxidase [Caulobacter sp. K31]
          Length = 402

 Score = 43.3 bits (101), Expect = 0.052,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 59/178 (33%), Gaps = 17/178 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AA+   D G   +NL+            P A   +  +G         V +  AA+
Sbjct: 195 DFVAAAERARDIGVQWLNLHFAHGYLATSFLSPHANQRDDQYGGAFENRARFVLETFAAV 254

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILKGLSPKDN 168
                   P+TV+  +   D   A  L   V  + +    G+  + A  A   G S    
Sbjct: 255 RAVWPQDRPLTVRLGVVDFDGNDAQNLIESVSLLNQLKALGLDAVDASIAFASGASSPPW 314

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
              PN        +++E   L +  +  +     A  ++    VD V +GR    N  
Sbjct: 315 --GPNFMAPFAERVRRETG-LPVTASWFISQAKAADAMVADGQVDYVTLGRPLLANPH 369


>gi|332286743|ref|YP_004418654.1| salicylyl-CoA 5-hydroxylase [Pusillimonas sp. T7-7]
 gi|330430696|gb|AEC22030.1| salicylyl-CoA 5-hydroxylase [Pusillimonas sp. T7-7]
          Length = 779

 Score = 43.3 bits (101), Expect = 0.053,   Method: Composition-based stats.
 Identities = 33/185 (17%), Positives = 59/185 (31%), Gaps = 31/185 (16%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIV 104
             + VEAA+     G++ + L   C           P        +G  L   +  P  V
Sbjct: 561 CEQFVEAARRAAQAGFDWLEL--HCAHGYLLSSFISPLTNQRSDEYGGTLDNRLRYPLRV 618

Query: 105 GDCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
              +  +  + L + V +     V+  I A     + K  K++G + I   +   + K  
Sbjct: 619 FKAVREVWPQHLPMSVRISAHDWVEGGITADDAIQIAKHFKEAGADMIDCSSG-QVSKAE 677

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA---AY 220
            P   R       D    ++ E   +     G + +      I+ S      GRA   A 
Sbjct: 678 QPVYGRMYQTPFSD---RVRNEAG-IPTIAVGAIFEADHVNSIIAS------GRADLCAL 727

Query: 221 KNSAM 225
               +
Sbjct: 728 ARPHL 732


>gi|322513748|ref|ZP_08066837.1| xenobiotic reductase A [Actinobacillus ureae ATCC 25976]
 gi|322120436|gb|EFX92357.1| xenobiotic reductase A [Actinobacillus ureae ATCC 25976]
          Length = 353

 Score = 43.3 bits (101), Expect = 0.053,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 62/182 (34%), Gaps = 25/182 (13%)

Query: 64  EAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           +A K   + G++ I +             P +      +G     +  + G+ +    KA
Sbjct: 154 DAVKRAVEAGFDAIEIHGAHGYLIHQFSSPKSNQRTDEYG----QDRFLFGEQVIKAAKA 209

Query: 115 L---SIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +    +P  V +  +    D   A     + K    +G + + +    A   G+  +   
Sbjct: 210 VMPADMPLIVRISAQEFGADGFDADYGVEMAKRFAAAGADCMHV---SAGGDGVLVEGKH 266

Query: 170 KIPNLDYD-IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AM 225
              N  Y   +    K+   L     G L+D +    +L     D V +GRA  +N   +
Sbjct: 267 SPFNAGYQVYLARAVKQATSLPTIAVGMLDDANVVDHVLAIGDADLVAVGRALLRNPQWL 326

Query: 226 LT 227
           L 
Sbjct: 327 LN 328


>gi|297620581|ref|YP_003708718.1| Dihydroorotate dehydrogenase [Waddlia chondrophila WSU 86-1044]
 gi|297375882|gb|ADI37712.1| Dihydroorotate dehydrogenase [Waddlia chondrophila WSU 86-1044]
          Length = 343

 Score = 43.3 bits (101), Expect = 0.053,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 58/188 (30%), Gaps = 14/188 (7%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           L + I G    + ++ A++    G   I  N+ CP   V +      L  NP+ V +   
Sbjct: 151 LIVSIFGTTEEEYLDCARLASLCGSPVIEANLSCP--NVSKKEGN--LFANPEAVEELSR 206

Query: 110 AMCKAL-SIPVTVKCRIGVDDQI--PAVALRNLVKSIKKSGVNGI--WIHARKAILKGLS 164
            +   +   P+ +K     D +     +       +    G+N I   +H   +  +   
Sbjct: 207 KLVGVIGDTPLVIKLGAIPDQRRLQKVLTAAARAGARAVCGINTISMAVHPPLSHSRQTC 266

Query: 165 PKDNRKIPNLDYDIVYE----IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
                 I         E    I KE   L +   GG        ++L       M     
Sbjct: 267 GICGAPIFKAALAFTREAREVIDKEKLGLELMATGGATQPEHLKQMLDAGASIAMTATGM 326

Query: 220 YKNSAMLT 227
             +  + +
Sbjct: 327 MWDPYLAS 334


>gi|167771050|ref|ZP_02443103.1| hypothetical protein ANACOL_02404 [Anaerotruncus colihominis DSM
           17241]
 gi|167666720|gb|EDS10850.1| hypothetical protein ANACOL_02404 [Anaerotruncus colihominis DSM
           17241]
          Length = 799

 Score = 43.3 bits (101), Expect = 0.053,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 11/72 (15%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPS-----------ARVHEGSFGACLMLNPDIVGDCIAAM 111
           V  AK  E  G + I LN+ CP+           A       GA L     +V + + A+
Sbjct: 117 VNMAKQFEAVGADIIELNMCCPNMSYNVSLSSGGAASTSQQTGASLGRQAGVVAEIVRAI 176

Query: 112 CKALSIPVTVKC 123
            K + IP+ VK 
Sbjct: 177 KKEIHIPLFVKL 188


>gi|33603729|ref|NP_891289.1| 2,4-dienoyl-CoA reductase [NADPH] [Bordetella bronchiseptica RB50]
 gi|33577854|emb|CAE35119.1| 2,4-dienoyl-CoA reductase [NADPH] [Bordetella bronchiseptica RB50]
          Length = 672

 Score = 43.3 bits (101), Expect = 0.053,   Method: Composition-based stats.
 Identities = 17/138 (12%), Positives = 48/138 (34%), Gaps = 8/138 (5%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSG 147
           ++G        +  + + A+  A      +  RI     V+D +       L + ++++G
Sbjct: 184 AYGGSFDNRIRLPIETVRAVRAAAGPDFLLIYRISAIDLVEDGMTGAESAQLARRLQEAG 243

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ +  +      +   P     +P   ++      K+   + +  +  +       ++L
Sbjct: 244 VDML--NTGIGWHESAIPTIAASVPRAGWEFAVRNIKDAVSIPVIASNRINTPEVGERLL 301

Query: 208 P--SVDGVMIGRAAYKNS 223
              + D V + R    + 
Sbjct: 302 ADGAADFVSMARPLLADP 319


>gi|227499365|ref|ZP_03929476.1| possible NADPH dehydrogenase [Anaerococcus tetradius ATCC 35098]
 gi|227218569|gb|EEI83809.1| possible NADPH dehydrogenase [Anaerococcus tetradius ATCC 35098]
          Length = 298

 Score = 43.3 bits (101), Expect = 0.053,   Method: Composition-based stats.
 Identities = 40/186 (21%), Positives = 75/186 (40%), Gaps = 42/186 (22%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCI 108
            K +EA K VED G++ + +   C          S  V++    +G  L     ++ + +
Sbjct: 123 DKFIEAGKRVEDMGFDGLEI--HCAHGYLLNQFYSPLVNKRDDEYGGSLENRLRVLLEIL 180

Query: 109 AAMCKAL-SIPVTVKCRIGVDDQIPAVALRNLVKSIK-----------KSGVNGIWIHAR 156
             M  AL   P+ V+     D +     + + +K++K             G+NG   H+ 
Sbjct: 181 KKMRIALGDFPIMVRL-GACDYEEGGNTIDDAIKAVKVMEEYIDFIDISGGINGFMKHSD 239

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
             I  G   K+++ I            KEN  + + + GG+++  +A + +       V 
Sbjct: 240 NDI--GYFTKESKAI------------KENTKVKVLMTGGIKNKKEAEESISEGACHMVG 285

Query: 215 IGRAAY 220
           IGRA+ 
Sbjct: 286 IGRASL 291


>gi|224129636|ref|XP_002190761.1| PREDICTED: similar to dihydrouridine synthase 4-like, partial
           [Taeniopygia guttata]
          Length = 151

 Score = 43.3 bits (101), Expect = 0.054,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 52/192 (27%), Gaps = 70/192 (36%)

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALRNLVKSIKK 145
                 +GACL+  P++V D +  +   +  P  +V  +I  + +     L         
Sbjct: 1   WAISEGYGACLINKPELVKDMVRHVRNQIDNPKFSVSIKISPEKRRLQGHL--------- 51

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                         LKG+  KD  ++                                  
Sbjct: 52  ---------TAALYLKGVRKKDGDRLC--------------------------------- 69

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
                  VM+ R    N AM    +E              +  +D+        T +   
Sbjct: 70  -------VMVARGLLANPAMFAGYEE-----------TPFQCIQDWVDIALEHGTPFTCF 111

Query: 266 HLHSGGKLQQIT 277
           H H    +++IT
Sbjct: 112 HHHLMYMMERIT 123


>gi|193792426|gb|ACF20985.1| BaiCD [Clostridium hylemonae DSM 15053]
          Length = 640

 Score = 43.3 bits (101), Expect = 0.054,   Method: Composition-based stats.
 Identities = 30/194 (15%), Positives = 67/194 (34%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEGS------FGACLMLNPDIVGDCIAA 110
            +    A++    G++ +  +      P   +  G       +G           + I+A
Sbjct: 135 EEFGCGARLAVQAGFDAVEFHAAHSYLPHEFLSPGMNRRTDEYGGSFENRCRFCFEVISA 194

Query: 111 MCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +   +   +P  ++       ++  +    +   +      GV+   I    A+    S 
Sbjct: 195 IRSNIPEDMPFFMRVGSIDELMEQNMTEEEIVEFINRSADLGVDVADISRGNAM----SF 250

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
               ++P  +       + +Y IKK+     +G+ G +     A +++     D V IGR
Sbjct: 251 ATVYEVPPFNLPHGFNIENIYNIKKQIKIPVVGV-GRINTGEMANQVIEDGKFDLVAIGR 309

Query: 218 AAYKNSAMLTTVDE 231
           A   +   +T V E
Sbjct: 310 AQLADPEWVTKVRE 323


>gi|288555876|ref|YP_003427811.1| NADPH dehydrogenase NamA [Bacillus pseudofirmus OF4]
 gi|288547036|gb|ADC50919.1| NADPH dehydrogenase NamA [Bacillus pseudofirmus OF4]
          Length = 339

 Score = 43.3 bits (101), Expect = 0.055,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 60/199 (30%), Gaps = 19/199 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               E A   ++ G++ I L+            P        +G  L      +   +  
Sbjct: 144 EAFKEGAVRAKEAGFDVIELHGAHGYLINEFLSPLTNKRNDEYGGSLEARYVFLKKIVDE 203

Query: 111 MCKALSIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +    + P+ V+       D          L   +K+ GV+ I   +   +     P   
Sbjct: 204 VKTVWTGPLFVRLSACEYADGGNSMEDFIQLSAWLKEQGVDLIDTSSGAVV-----PAAI 258

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              P         I++E   +  G  G +    QA +IL     D + IGR   +N    
Sbjct: 259 PVYPGYQVKFAETIRREAG-IATGAVGMITSGLQAEEILRNERADLIFIGRELLRNPYWP 317

Query: 227 TTVDEYFSNPLTGSSPIKT 245
                  +  +   +P + 
Sbjct: 318 RQAALELNTKIEAPTPYER 336


>gi|227327481|ref|ZP_03831505.1| flavoprotein xenobiotic reductase [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 362

 Score = 43.3 bits (101), Expect = 0.055,   Method: Composition-based stats.
 Identities = 28/183 (15%), Positives = 62/183 (33%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AA+   + G+  + L+       + +             +G         + + +
Sbjct: 158 DDFVAAARRALEAGFEWLELHFA--HGYLAQSFFSVHSNKRNDQYGGSFDNRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
           AA+       +P+T +  +   D      L+    L +  K +G++ + +      +   
Sbjct: 216 AAVRDVWPQHLPLTARFGVIEFDGRDEETLQESIELTRRFKAAGLDMLSV-----SIGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           +P  N          + +  +E  DL +    G      A + +    +D VM+G+A   
Sbjct: 271 TPAANVPWAPAFMGPIAKQVREQADLPVSSAWGFGTPELAEQAVASGQLDLVMVGKAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|154504945|ref|ZP_02041683.1| hypothetical protein RUMGNA_02455 [Ruminococcus gnavus ATCC 29149]
 gi|153794828|gb|EDN77248.1| hypothetical protein RUMGNA_02455 [Ruminococcus gnavus ATCC 29149]
          Length = 344

 Score = 43.3 bits (101), Expect = 0.055,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 60/185 (32%), Gaps = 16/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLN---------VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  + AK  +  G++ + ++            P +      +G  +        + I  
Sbjct: 79  EQFGDCAKRAKAAGFDAVEVHGAHGYLAGAFASPFSNKRSDEYGGTIRNRARFGMEIIRN 138

Query: 111 MCKALSI--PV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +      PV   +     V   +     + + + ++++G + I               
Sbjct: 139 IKEKCGKDYPVLYRISSVEYVPGGLDIEESKVIARLMEEAGADCIHCSQGVYASTHTIIP 198

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
            +  +     +   E+KK    + +   G + D+  A  +L     D V + RA+  +  
Sbjct: 199 PSVFLRAGYVEHAAEMKKAV-QIPVIAVGRINDVEIAESVLQSKKADLVTMARASLADPE 257

Query: 225 MLTTV 229
           +   V
Sbjct: 258 LPNKV 262


>gi|306440723|pdb|3OIX|A Chain A, Crystal Structure Of The Putative Dihydroorotate
           Dehydrogenase From Streptococcus Mutans
 gi|306440724|pdb|3OIX|B Chain B, Crystal Structure Of The Putative Dihydroorotate
           Dehydrogenase From Streptococcus Mutans
 gi|306440725|pdb|3OIX|C Chain C, Crystal Structure Of The Putative Dihydroorotate
           Dehydrogenase From Streptococcus Mutans
 gi|306440726|pdb|3OIX|D Chain D, Crystal Structure Of The Putative Dihydroorotate
           Dehydrogenase From Streptococcus Mutans
          Length = 345

 Score = 43.3 bits (101), Expect = 0.055,   Method: Composition-based stats.
 Identities = 38/227 (16%), Positives = 70/227 (30%), Gaps = 34/227 (14%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISK------LVEAAKIVEDFGYNEINLNVGCP-S 85
              D    L      K   L + G    +      +VEA+K         + LN+ CP  
Sbjct: 114 YYLDYVTELQKQPDSKNHFLSLVGMSPEETHTILXMVEASKY-----QGLVELNLSCPNV 168

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN----- 138
               + ++      + +     ++ +    + P+ +K     D      A A+ N     
Sbjct: 169 PGXPQIAY------DFETTDQILSEVFTYFTKPLGIKLPPYFDIVHFDQAAAIFNXYPLT 222

Query: 139 LVKSIKKSG-----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            V  I   G      +   +   K    G+     +     +    Y  K+ NP + I  
Sbjct: 223 FVNCINSIGNGLVIEDETVVIXPKNGFGGIGGDYVKPTALANVHAFY--KRLNPSIQIIG 280

Query: 194 NGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSNPLT 238
            GG+     A +  L     V IG A   +   +   + +     +T
Sbjct: 281 TGGVXTGRDAFEHILCGASMVQIGTALHQEGPQIFKRITKELXAIMT 327


>gi|315180694|gb|ADT87608.1| 2,4-dienoyl-CoA reductase [Vibrio furnissii NCTC 11218]
          Length = 667

 Score = 43.3 bits (101), Expect = 0.056,   Method: Composition-based stats.
 Identities = 20/132 (15%), Positives = 51/132 (38%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V++      +  L K+++ +GV    I+      +
Sbjct: 196 EVVRAIREAVGKEFIIIFRLSMLDLVEEGSTFEEVLMLAKALEAAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K + ++ +     +    +A KI+     D V + R  
Sbjct: 254 ARIPTIATQVPRAAFTWVTEKIKPHLNVPVVTCNRINTPEEAEKIVASGQADLVSMARPF 313

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 314 LADPEFVAKAEQ 325


>gi|302417448|ref|XP_003006555.1| NADPH dehydrogenase [Verticillium albo-atrum VaMs.102]
 gi|261354157|gb|EEY16585.1| NADPH dehydrogenase [Verticillium albo-atrum VaMs.102]
          Length = 450

 Score = 43.3 bits (101), Expect = 0.056,   Method: Composition-based stats.
 Identities = 31/208 (14%), Positives = 60/208 (28%), Gaps = 37/208 (17%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               A K     G++ I L+            P++      +G        +  + +   
Sbjct: 223 DFAAAVKRALHAGFDIIELHFAHGYLVSSFLSPTSNKRTDKYGGSFENRTRLALELVEET 282

Query: 112 CKAL--SIPVTVKCR-IGVDDQIPAVALR--------NLVKSIKKSGVNGIWIHARKAIL 160
              L    P+ V+       D  P                K +   GV+ + I       
Sbjct: 283 RAILPEGTPLAVRFSATEWLDTNPEFEGESWTIKESIEFAKLLADRGVDILDI------S 336

Query: 161 KGLSPKDNRKIPNLDYDI--VYEIKKENPD-LFIGLNGGLEDMSQALKILPS-------- 209
            G +    +      Y       IKK   D  F+   G ++  + A +++          
Sbjct: 337 SGGNNAAQKVKGGPGYQAGFAKAIKKAVGDKAFVSTVGSIKTGTLAEELISGGKDEDDTP 396

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           +D V +GR   KN  ++    +     +
Sbjct: 397 LDLVAVGRMFQKNPGLVWAWADELETSI 424


>gi|256006032|ref|ZP_05430969.1| biotin carboxylase [Clostridium thermocellum DSM 2360]
 gi|255990001|gb|EEU00146.1| biotin carboxylase [Clostridium thermocellum DSM 2360]
          Length = 312

 Score = 43.3 bits (101), Expect = 0.056,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 69/199 (34%), Gaps = 43/199 (21%)

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
            R  +DD      L+ L K ++++G +G+ I+  +A+         R+    +YD +  I
Sbjct: 90  IREIIDDSNYYAHLKVLCKFVRQAGYSGLIINLDEAVNLYKITH--REAREKNYDYILTI 147

Query: 183 KKENPD-----LFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP- 236
             +        L+I  +G  E +                R  Y   A+   +     N  
Sbjct: 148 YNDILQGSVEGLYITFSGTPEFLEDER------------RGLYSYQALKRRLKPTVENEK 195

Query: 237 ----------LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                     LT  +P +T +     R I A+   Y    +       +I R+++ ++  
Sbjct: 196 YQDLKQAVIKLTPLTPEETLILLMNIRDIHAAHYGYEINVMDE-----EIRRYLLWIYK- 249

Query: 287 FPNSRR-------CRHILT 298
            P ++         R  ++
Sbjct: 250 RPGAKEHIILGDVVRQFIS 268


>gi|121534299|ref|ZP_01666123.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosinus
           carboxydivorans Nor1]
 gi|121307069|gb|EAX47987.1| NADH:flavin oxidoreductase/NADH oxidase [Thermosinus
           carboxydivorans Nor1]
          Length = 362

 Score = 43.3 bits (101), Expect = 0.056,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 62/181 (34%), Gaps = 20/181 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---C------PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V AA+  +  G + + L++    C      P     +  +G  +     I+ + +A   
Sbjct: 149 FVAAAERAKKAGCDGVQLHIAHGYCLSQFLSPYTNRRQDEWGGSIENRTRIIREIMARCR 208

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV---KSIKKSGVNGIWIHARKAILKGL--S 164
            A+     +  ++   D +     +   ++V   + +++ G   I +       KG+   
Sbjct: 209 AAVGSDFPILAKLNCTDGLSGPGYLTREDVVYTARLLERLGAAAIEVSGGIREAKGVMSR 268

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
           P    +     +       KE   + + L GGL   +    +L +    M+   A     
Sbjct: 269 PNIRSEEDEAYFAADARAIKEAVRIPVILVGGLRSTATMEGLLQNGYADMV---ALSRPF 325

Query: 225 M 225
           +
Sbjct: 326 I 326


>gi|117920872|ref|YP_870064.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. ANA-3]
 gi|117613204|gb|ABK48658.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. ANA-3]
          Length = 370

 Score = 43.3 bits (101), Expect = 0.056,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 63/182 (34%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AAK   + G+  + L+       + +             +G         + + + 
Sbjct: 157 DFVAAAKRALEAGFEWLELHFA--HGYLAQSFFSTYANQRTDEYGGDAQGRGRFLIETVE 214

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           A+       +P+T +  +   D      L     LVK  K++G++ + +      +   +
Sbjct: 215 AVRAVWPEHLPLTARFGVIEFDDKDEQTLSESIALVKQFKRAGLDMLNV-----SICFST 269

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +      +  + G+++   A + +    +D VMIG+A   N
Sbjct: 270 PTANIPWRPAFLAPIAERVRREVGFPVATSWGMDNPHHAEQAIQDQQMDLVMIGKAFLAN 329

Query: 223 SA 224
             
Sbjct: 330 PH 331


>gi|254248510|ref|ZP_04941830.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family [Burkholderia
           cenocepacia PC184]
 gi|124875011|gb|EAY65001.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family [Burkholderia
           cenocepacia PC184]
          Length = 395

 Score = 43.3 bits (101), Expect = 0.057,   Method: Composition-based stats.
 Identities = 22/128 (17%), Positives = 48/128 (37%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + D +AA+ K     +P+T +  +   D      L     L + +K+ G++ + +     
Sbjct: 237 LVDTLAAVRKVWPEHLPLTARLGVIEYDGRDEETLAESIALTQRMKREGLDMLSV----- 291

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIG 216
            +   +P             + E  +    L +    G++    A +++     D VM+G
Sbjct: 292 SVGFSTPTAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVEQAQLDLVMVG 351

Query: 217 RAAYKNSA 224
           RA   +  
Sbjct: 352 RAHLADPH 359


>gi|313817817|gb|EFS55531.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL046PA2]
          Length = 335

 Score = 42.9 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 62/180 (34%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E+ G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMENAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGL----NG-------GLEDM-SQALKILPSVDGVM 214
           +  ++    + +        P  +I       G       G+E        +L   D VM
Sbjct: 210 ETMQVEPGVW-LSPPAAARLPLTWIAALSGRIGASLAASSGVESANDVVKYLLAGADVVM 268


>gi|3402836|emb|CAA76082.1| 2-enoate reductase [Moorella thermoacetica]
          Length = 667

 Score = 42.9 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 31/213 (14%), Positives = 65/213 (30%), Gaps = 39/213 (18%)

Query: 53  QIGGADISKLV----EAAKIVEDFGYNEINL----------NVGCPSARVHEGS--FGAC 96
           ++  A++  LV    EAA+I  + G++ + +                A  +     +G  
Sbjct: 144 ELTTAEVETLVQRASEAAEIAVEAGFDGVEIHAMHEGYLLDQFT--IALFNRRGDKYGGA 201

Query: 97  LMLNPDIVGDCIAAMCKALSI--PVTVKCRI----------------GVDDQIPAVALRN 138
           L        + + A+   +    PV ++  I                  +          
Sbjct: 202 LEDRLTFPIEIVRAIKDRVGKDFPVVLRFSIKNYIKDWRQGGLPGENFQEKGRDVEEPLA 261

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             K ++ +G +G    A        +     +       +   +K E   + + + G LE
Sbjct: 262 AAKILEGAGYDGFDADAGSYDAWYWAHPPVYQKHGCYLPLTQRLK-EVVKVPVIVAGRLE 320

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSAMLTTV 229
               A + L     D + IGR    +   +  V
Sbjct: 321 IPELAEEALVKGQADMIAIGRGLLTDPYWVNKV 353


>gi|99082083|ref|YP_614237.1| salicylyl-CoA 5-hydroxylase [Ruegeria sp. TM1040]
 gi|99038363|gb|ABF64975.1| NADH:flavin oxidoreductase/NADH oxidase [Ruegeria sp. TM1040]
          Length = 764

 Score = 42.9 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 60/183 (32%), Gaps = 28/183 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA++ +  G++ I L+            P +      +G  L        +  AA
Sbjct: 548 DQFVRAAQMADRAGFDMIELHAAHGYLISSFLSPVSNQRGDDYGGSLENRLRYPLEVFAA 607

Query: 111 MCKAL--SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           M        P++V+        +D +       + ++  ++G + I + A +   +    
Sbjct: 608 MRAVWPEGKPMSVRISANDWVGEDGVTPDEAVQIARAFWEAGADLIDVSAGQTTTEAKPV 667

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA---AYKN 222
                          +I+ E     + + G + +   A  IL      M GRA   A   
Sbjct: 668 YGRMFQTP----FSDQIRNEAGICTMAV-GNIFEADHANSIL------MAGRADLVAVGR 716

Query: 223 SAM 225
             +
Sbjct: 717 PHL 719


>gi|326391046|ref|ZP_08212594.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325992914|gb|EGD51358.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 648

 Score = 42.9 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 59/188 (31%), Gaps = 16/188 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNP--DIVGDCI 108
               +AA+  ++ G++ I +             P +      +G          +     
Sbjct: 151 EAFGQAARRAKEAGFDAIEIHGAHGYLLNQFLSPYSNKRTDEYGGSFENRIRFPLEVVRR 210

Query: 109 AAMCKALSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                    P+   +     V   +     +   + + ++G++ + I         +  +
Sbjct: 211 VREEVGGDFPIIYRMSAEEYVPGGLTIEDTKIFAQKLVEAGIDALHISGGVYESSAMIIQ 270

Query: 167 DNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                     +    IKK  N  + + + G ++D   A +I+     D V IGRA   + 
Sbjct: 271 PAAIPQGCFVENAAAIKKAINSKVPVIVVGRIKDPLMAEQIIREGKADLVSIGRALLADP 330

Query: 224 AMLTTVDE 231
            +   V E
Sbjct: 331 DLPRKVSE 338


>gi|332359401|gb|EGJ37221.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK355]
          Length = 240

 Score = 42.9 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    K  K++GV  I +      L+G +          + D++  IK E   L I + G
Sbjct: 32  VLEQAKIFKEAGVTMIHVVDLDGALEGRA---------ANRDLIARIKSETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN A +    E F 
Sbjct: 82  GIRSLEQIEDYLAVGIDRVIIGSMAVKNPAFVEAALERFG 121


>gi|254425846|ref|ZP_05039563.1| Dihydroorotate dehydrogenase superfamily [Synechococcus sp. PCC
           7335]
 gi|196188269|gb|EDX83234.1| Dihydroorotate dehydrogenase superfamily [Synechococcus sp. PCC
           7335]
          Length = 341

 Score = 42.9 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 44/118 (37%), Gaps = 27/118 (22%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG- 105
           + P+   + G         A+ +E+ G + I LN+               +   P+    
Sbjct: 107 DIPIIASLNGTTPGGWTRYAEQLEEAGADAIELNI-------------YAVPTQPETTAL 153

Query: 106 -------DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                  + +  +  A++IPV VK      +      L N  +S+ ++G +G+ +  R
Sbjct: 154 QVEQTYCEIVRGVTYAVNIPVAVKLSPYFSN------LANFAESLTRAGTDGLVLFNR 205


>gi|17548253|ref|NP_521593.1| salicylyl-CoA 5-hydroxylase [Ralstonia solanacearum GMI1000]
 gi|17430499|emb|CAD17183.1| putative nadh:flavin oxidoreductases oxidoreductase protein
           [Ralstonia solanacearum GMI1000]
          Length = 785

 Score = 42.9 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 34/223 (15%), Positives = 69/223 (30%), Gaps = 29/223 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVGDC 107
            V AA++  + G++ + L   C           P   +   ++G  L   +  P  V   
Sbjct: 557 FVRAARLAVEAGFDWLEL--HCAHGYLLSSFISPLTNLRSDAYGGALENRLRYPLEVFRA 614

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A+  A   P++V+      V   I       + +  K +G + I   + +     +S 
Sbjct: 615 VRAVWPA-ERPMSVRISAHDWVQGGITPDDAVEIARLFKAAGADMIDCSSGQ-----VSK 668

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           K+      +      +  +    +     G + +      I+ +   D   + R    N 
Sbjct: 669 KEQPVYGRMYQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLANP 728

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
              L          L    P + R  K    +        AA+
Sbjct: 729 AWTLNEAARI--GYLDMPWPRQYRAGKLQLERNLERERALAAQ 769


>gi|256751541|ref|ZP_05492418.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749625|gb|EEU62652.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 648

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 59/188 (31%), Gaps = 16/188 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNP--DIVGDCI 108
               +AA+  ++ G++ I +             P +      +G          +     
Sbjct: 151 EAFGQAARRAKEAGFDAIEIHGAHGYLLNQFLSPYSNKRTDEYGGSFENRIRFPLEVVRR 210

Query: 109 AAMCKALSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                    P+   +     V   +     +   + + ++G++ + I         +  +
Sbjct: 211 VREEVGGDFPIIYRMSAEEYVPGGLTIEDTKIFAQKLVEAGIDALHISGGVYESSAMIIQ 270

Query: 167 DNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                     +    IKK  N  + + + G ++D   A +I+     D V IGRA   + 
Sbjct: 271 PAAIPQGCFVENAAAIKKAINSKVPVIVVGRIKDPLMAEQIIREGKADLVSIGRALLADP 330

Query: 224 AMLTTVDE 231
            +   V E
Sbjct: 331 DLPRKVSE 338


>gi|157963883|ref|YP_001503917.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella pealeana ATCC
           700345]
 gi|157848883|gb|ABV89382.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella pealeana ATCC
           700345]
          Length = 366

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 73/216 (33%), Gaps = 21/216 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EA++  ++ G++ + ++            P     E  +G  L      + +  A + 
Sbjct: 147 FAEASRRAQESGFDGVEIHAAHTYLINQFLSPYYNQREDEYGGSLENRMRFLLEIYAEIR 206

Query: 113 KAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
           K +    P+ VK       D  +     R++ K+++  GV+ I     IH     + G  
Sbjct: 207 KLVGDDYPILVKLTASEFFDGGLTFADTRSICKTLESIGVDAIIISGNIHGNANTVVGEQ 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAYK 221
                      +     +  +  +L I   GGL D+  A++ L    ++    + R    
Sbjct: 267 FDGYTIQSEGYFREYGAVVSQEVNLPIITVGGLADI-CAIEELANSTNIQFFALSRPLLA 325

Query: 222 NSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              ++    E  +  +      K R  +  +  +  
Sbjct: 326 EPQLIKRWKEGNAAEVDCERCSKCRTKRGNFCVVYK 361


>gi|54308279|ref|YP_129299.1| imidazole glycerol phosphate synthase subunit HisF [Photobacterium
           profundum SS9]
 gi|50402157|sp|P62452|HIS6_PHOPR RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|46912707|emb|CAG19497.1| putative imidazoleglycerol-phosphate synthase [Photobacterium
           profundum SS9]
          Length = 257

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D V I   A  N A++T + + F 
Sbjct: 85  SVEDASRILQFGADKVSINSPALANPALITELADKFG 121


>gi|254511461|ref|ZP_05123528.1| dihydroorotate oxidase [Rhodobacteraceae bacterium KLH11]
 gi|221535172|gb|EEE38160.1| dihydroorotate oxidase [Rhodobacteraceae bacterium KLH11]
          Length = 352

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 78/244 (31%), Gaps = 49/244 (20%)

Query: 35  GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC-------PSAR 87
           G+ K  L   T+++    + G  +      AA++ +      I LN+G        P   
Sbjct: 93  GNPKPRLFRLTEDRAAINRFGFNNEGMEAMAARLADRPKDAVIGLNLGANKDSDDRPGDF 152

Query: 88  VHEGSFGACLML---------NPDIVGDC------------IAAMCKALSIPVTVKCRIG 126
               +  A  +          N + + D             +     AL  P+ V  +I 
Sbjct: 153 ARVLAHCAAHLDFATVNVSSPNTEKLRDLQGKAALNALLSGVIETRNALPRPLPVFLKIA 212

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL--------DYDI 178
            D  +    L+++ +   ++GV+ +          GL   D  +   L           +
Sbjct: 213 PD--LSEAELQDIAEVATETGVDAVIATNTTLSRDGLRSADKDQAGGLSGAPLFEKSTRV 270

Query: 179 VYEIKKE-NPDLFIGLNGGLEDMSQAL-KILPSVDGV-----MIGRAAYKNSAMLTTVDE 231
           + ++ K  N D+ +   GG+    QA  KI      V     M+    Y   ++   +  
Sbjct: 271 LAQLSKLTNGDIPLIGVGGISTAEQAYAKICAGASAVQFYTAMV----YGGISLAADIAH 326

Query: 232 YFSN 235
               
Sbjct: 327 GLDE 330


>gi|258626524|ref|ZP_05721364.1| 2,4-dienoyl-CoA reductase [Vibrio mimicus VM603]
 gi|258581235|gb|EEW06144.1| 2,4-dienoyl-CoA reductase [Vibrio mimicus VM603]
          Length = 688

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 218 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 275

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 276 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 333


>gi|320327675|gb|EFW83683.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. glycinea str.
           race 4]
 gi|330882422|gb|EGH16571.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. glycinea str.
           race 4]
          Length = 679

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTRVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVKVPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|297154940|gb|ADI04652.1| 2,4-dienoyl-CoA reductase (NADPH) protein [Streptomyces
           bingchenggensis BCW-1]
          Length = 397

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 24/180 (13%), Positives = 54/180 (30%), Gaps = 21/180 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V AA++ E  G++ ++++       +  G            +G           + +  
Sbjct: 166 FVRAARLCERAGFDGVDVHAA--QGFLISGFLSSRTNRRTDEWGGDFAGRTRFALEVVRR 223

Query: 111 MCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         + V +     VD          L   ++  G   +             P 
Sbjct: 224 IVANTGPDFVVGVHLLSDERVDSGWTLDDAVRLAPLLEAEGAAFL-FAIPATFETMRLPA 282

Query: 167 DNRKIPNLDYDIVY-EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           +   +    Y +   E  +    + +  NGGL D   A+++L       V + R  + + 
Sbjct: 283 NLGMLAKPGYSLDDTEALQRAVRIPVVANGGLGDPRAAVQVLETGQASAVGLARPLFVDP 342


>gi|291003607|ref|ZP_06561580.1| dihydroorotate dehydrogenase [Saccharopolyspora erythraea NRRL
           2338]
          Length = 340

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 22/127 (17%), Positives = 38/127 (29%), Gaps = 20/127 (15%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--------- 153
           I+   +A      + PV +K     D            +   K GV+ +           
Sbjct: 185 IIESVLAEAVPRSAHPVILKLSPDYD-------YLAHARLAAKHGVSALTAINTVKGLRL 237

Query: 154 --HARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
                + +LK        R I  +   +V E++     L I   GG+       +     
Sbjct: 238 DPETGQPLLKNRFGGLSGRAIKPIGLRVVAELRDAGVKLPIIATGGIRTFDDCREYFWAG 297

Query: 210 VDGVMIG 216
            D V +G
Sbjct: 298 ADAVSLG 304


>gi|289628070|ref|ZP_06461024.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. aesculi str.
           NCPPB3681]
 gi|298486248|ref|ZP_07004311.1| 2,4-dienoyl-CoA reductase FadH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298159255|gb|EFI00313.1| 2,4-dienoyl-CoA reductase FadH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|330868393|gb|EGH03102.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. aesculi str.
           0893_23]
          Length = 679

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTRVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVKVPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|15673534|ref|NP_267708.1| dihydroorotate dehydrogenase 1A [Lactococcus lactis subsp. lactis
           Il1403]
 gi|18202789|sp|Q9CFC9|PYRDA_LACLA RecName: Full=Dihydroorotate dehydrogenase A; AltName:
           Full=DHOdehase A; Short=DHOD A; Short=DHODase A;
           AltName: Full=Dihydroorotate oxidase A
 gi|12724554|gb|AAK05650.1|AE006386_1 dihydroorotate dehydrogenase A [Lactococcus lactis subsp. lactis
           Il1403]
 gi|326407018|gb|ADZ64089.1| dihydroorotate oxidase [Lactococcus lactis subsp. lactis CV56]
          Length = 311

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 67/209 (32%), Gaps = 28/209 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIV 104
           QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  + +  
Sbjct: 92  QEAPIFFSIAGMSAAENIAMLKKIQESNFSGITELNLSCP--NVPGK---PQLAYDFEAT 146

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW----- 152
              +  +    + P+ VK     D     I A  L       V S+   G          
Sbjct: 147 EKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFIDSEAE 206

Query: 153 --IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
             +   K    G+     +     +    Y   K  P++ I   GG+E    A + L   
Sbjct: 207 SVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIKIIGTGGIETGQDAFEHLL-C 263

Query: 211 DGVM--IGRAAYKN--SAMLTTVDEYFSN 235
              M  IG  A      A+   + +    
Sbjct: 264 GATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|325273847|ref|ZP_08140028.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas sp. TJI-51]
 gi|324101013|gb|EGB98678.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas sp. TJI-51]
          Length = 289

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 25/158 (15%), Positives = 53/158 (33%), Gaps = 11/158 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G+C      +    + A+ K     +P+ V+      V+D         L
Sbjct: 111 PLSNQRRDEYGSCFENRIRLTLQVVEAVRKVWPAELPLFVRVSATDWVEDGWNPDETVEL 170

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + ++  GV+ I + +      G S                E  ++  ++  G  G + +
Sbjct: 171 ARRLRNLGVDLIDVSSG-----GTSVNAEIPTGPGYQTRFAERVRKESEIATGTVGMITE 225

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +QA  IL     D + + R   ++       D+    
Sbjct: 226 PAQAEHILRTGQADLIFLARELLRDPYWPLHADDDLGG 263


>gi|299066838|emb|CBJ38033.1| putative oxidoreductase [Ralstonia solanacearum CMR15]
          Length = 772

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 67/220 (30%), Gaps = 38/220 (17%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-- 82
            ++ A A+     ++ L        LA         + VEA +     G++ + L  G  
Sbjct: 532 PLVSASALPYLPGRSQLPREASLADLA-----RIRDQFVEATRRAAAAGFDWLELQAGHG 586

Query: 83  -------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA----LSIPVTVKCRIGVDDQI 131
                   P       ++G  L        + +AA+ +A    L I V + C        
Sbjct: 587 FLLSSFISPLTNQRTDAYGGSLENRLRFPLEVLAAVREAWPAHLPISVRISCTDWAPGGT 646

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD--IVYEIKKENPDL 189
                  + + +   G + +       +  G    D + +    Y       I+ E  ++
Sbjct: 647 TVDEAVEIARRLHLGGADLVD------VSSGEVTPDQKPVYGRLYQTPFADRIRNEA-NV 699

Query: 190 FIGLNGGLEDMSQALKILPSVDG-VMIGRA---AYKNSAM 225
                G + D          V+G V  GRA   A     +
Sbjct: 700 PTIAVGAISDAD-------QVNGIVASGRADLCALSRPHL 732


>gi|229528986|ref|ZP_04418376.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae 12129(1)]
 gi|229332760|gb|EEN98246.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae 12129(1)]
          Length = 666

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 78/233 (33%), Gaps = 26/233 (11%)

Query: 4   WTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            T+  +R  A+    LL            + + +R     I  F+  E     QI    I
Sbjct: 86  VTEAVHRHGAKIALQLLHAGRYAMHPFSQSASAIRAP---IAKFAPSEMSTR-QI-HNTI 140

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                +A++ +  GY+ + +            C    +    +G           + + A
Sbjct: 141 QDFANSAELAQLAGYDGVEVMGSEGYLINQFICKRTNMRYDEWGGSYQNRIRFPVEIVKA 200

Query: 111 MCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A+     +  R+     V+       +  L K+++++GV    I+      +   P 
Sbjct: 201 IREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHEARIPT 258

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 259 IATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|209809793|ref|YP_002265332.1| NADH oxidase [Aliivibrio salmonicida LFI1238]
 gi|208011356|emb|CAQ81811.1| NADH oxidase [Aliivibrio salmonicida LFI1238]
          Length = 370

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 29/219 (13%), Positives = 72/219 (32%), Gaps = 19/219 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +A++  ++ G++ + ++            P     E  +G  L      + D    + 
Sbjct: 147 FAQASRRAQESGFDGVEIHAAHTYLINQFLSPYYNRREDEYGGSLDNRMRFLLDIYTEIR 206

Query: 113 KAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
           K +    P+ VK       +  +     R + K +++ GV+ I     IH   + + G S
Sbjct: 207 KRVGNDFPILVKLTASEFFEGGLTFDETRLICKKLEEIGVDAIIISGNIHGNASAMIGES 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKN 222
                      +    ++  ++  + +   GGL D+   +A+    ++    + R     
Sbjct: 267 FDGYTLQEEGYFHEYGDVISKDVTVPVITVGGLTDIDAIEAMAANTNIQYFALSRPLLAE 326

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTD 261
             ++    E     +      K R  +  +  +      
Sbjct: 327 PQLIKRWKEGNRAAVDCERCSKCRTRRGNFCVVYKKRKP 365


>gi|318041623|ref|ZP_07973579.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Synechococcus sp.
           CB0101]
          Length = 331

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 67/180 (37%), Gaps = 37/180 (20%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + +Q+GG      V +A+  E+     ++        RV     G   +  P++V +   
Sbjct: 149 IPVQLGGG-----VRSAERAEELLACGLD--------RVI---LGTVAIEKPELVKEL-- 190

Query: 110 AMCKALSIPVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A      + V +  + G+       +   V   +L KS +  GV  I             
Sbjct: 191 AARHPGKVVVGIDAKDGLVATRGWIETSTVKATDLAKSFEGCGVAAII---------STD 241

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP----SVDGVMIGRAAY 220
              +  +   + + +  +  E   + +  +GG+  +   L +L      V+GV++GRA Y
Sbjct: 242 IATDGTLAGPNLEALRAMA-EASSIPVIASGGIGTLDDILSLLSIAPLGVEGVIVGRALY 300


>gi|206563260|ref|YP_002234023.1| xenobiotic reductase [Burkholderia cenocepacia J2315]
 gi|198039300|emb|CAR55265.1| xenobiotic reductase [Burkholderia cenocepacia J2315]
          Length = 369

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 64/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V +A+   D G+  + L+      G     VH       +G         + D +AA+
Sbjct: 159 DFVASAQRARDLGFEWLELHFAHGYLGQSFFSVHSNQRTDEYGGSAENRGRFLVDTLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            K     +P+T +  +   D      L     L + +K+ G++ + +      +   +P 
Sbjct: 219 RKVWPEHLPLTARLGVIEYDGRDEETLAESIALTQRMKREGLDMLSV-----SVGFSTPT 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                       + E  +    L +    G++    A +++    +D VM+GRA   +  
Sbjct: 274 AQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVAEQQLDLVMVGRAHLADPH 333


>gi|134098706|ref|YP_001104367.1| dihydroorotate dehydrogenase [Saccharopolyspora erythraea NRRL
           2338]
 gi|133911329|emb|CAM01442.1| dihydroorotate dehydrogenase [Saccharopolyspora erythraea NRRL
           2338]
          Length = 338

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 22/127 (17%), Positives = 38/127 (29%), Gaps = 20/127 (15%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--------- 153
           I+   +A      + PV +K     D            +   K GV+ +           
Sbjct: 183 IIESVLAEAVPRSAHPVILKLSPDYD-------YLAHARLAAKHGVSALTAINTVKGLRL 235

Query: 154 --HARKAILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PS 209
                + +LK        R I  +   +V E++     L I   GG+       +     
Sbjct: 236 DPETGQPLLKNRFGGLSGRAIKPIGLRVVAELRDAGVKLPIIATGGIRTFDDCREYFWAG 295

Query: 210 VDGVMIG 216
            D V +G
Sbjct: 296 ADAVSLG 302


>gi|2385388|emb|CAA04759.1| L-mandelate dehydrogenase [Rhodotorula graminis]
          Length = 491

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 28/147 (19%), Positives = 56/147 (38%), Gaps = 23/147 (15%)

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   + +PV  K    +  +  +    + + +  K+  + +     K  +  + P   
Sbjct: 269 KAIFVTVDVPVLGKRERDLKLKARSQNYEHPIAAQWKAAGSKVEETIAKRGVSDI-PDTA 327

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSVDGVMI----------G 216
               NL++D +  IK+  P + I +   G +ED+  A +     DGV++           
Sbjct: 328 HIDANLNWDDIAWIKERAPGVPIVIKGVGCVEDVELAKQY--GADGVVLSTHGARQLDGA 385

Query: 217 RAAY--------KNSAMLTTVDEYFSN 235
           RA          KN A+L  ++ Y   
Sbjct: 386 RAPLDVLIEVRRKNPALLKEIEVYVDG 412


>gi|71737111|ref|YP_273912.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. phaseolicola
           1448A]
 gi|71557664|gb|AAZ36875.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. phaseolicola
           1448A]
 gi|320325340|gb|EFW81407.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. glycinea str.
           B076]
          Length = 679

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTRVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVKVPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|21673312|ref|NP_661377.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium tepidum
           TLS]
 gi|25453035|sp|Q8KF55|HIS4_CHLTE RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|21646404|gb|AAM71719.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Chlorobium tepidum TLS]
          Length = 260

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 11/94 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++    +K     I +    A L G +         ++++ + EI     D+ I + GG
Sbjct: 33  CDMAVIWRKQNAKMIHVVDLDAALTGET---------VNFERIREIVN-VLDIPIQVGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           +  +    K L   V  V+IG AA  N  ++  +
Sbjct: 83  IRSVEAVEKYLDIGVSRVVIGSAAVTNPGLIADL 116


>gi|262171019|ref|ZP_06038697.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio mimicus MB-451]
 gi|261892095|gb|EEY38081.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio mimicus MB-451]
          Length = 688

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 218 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 275

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 276 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 333


>gi|253581631|ref|ZP_04858856.1| 2-nitropropane dioxygenase [Fusobacterium varium ATCC 27725]
 gi|251836701|gb|EES65236.1| 2-nitropropane dioxygenase [Fusobacterium varium ATCC 27725]
          Length = 312

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 9/87 (10%)

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           IP V+   L K  +K G + I +    A     + KD+       +DIV EI  EN  + 
Sbjct: 116 IPVVSSLKLAKISQKLGADAIVVEGGNAGGHLGTEKDS-------WDIVGEIA-ENISIP 167

Query: 191 IGLNGGLEDMSQALKILP-SVDGVMIG 216
           +   GG+     A ++L    DGV +G
Sbjct: 168 VFGAGGVITPEDAERMLALGADGVQMG 194


>gi|154505653|ref|ZP_02042391.1| hypothetical protein RUMGNA_03192 [Ruminococcus gnavus ATCC 29149]
 gi|153794092|gb|EDN76512.1| hypothetical protein RUMGNA_03192 [Ruminococcus gnavus ATCC 29149]
          Length = 659

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 29/185 (15%), Positives = 60/185 (32%), Gaps = 25/185 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG------CPSARVHEG--SFGACLMLNPDIVGDCIAAM 111
            K+ E  K  +  G + I ++        C S  ++    S+G             +  +
Sbjct: 162 DKIGECVKRAQSAGVDIIEVHGDRLIGSFC-STLINRRTDSYGGSFENRIRFALRVVDKI 220

Query: 112 CKAL-------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            +          +PV  +  +     +         K +++SGV+ I  H  +A   G  
Sbjct: 221 REVAPDICIDYKLPVVTENPLRGKGGLMIDEAVEFAKILERSGVDMI--HVGQANHTGNM 278

Query: 165 PKDNRKIPNLDY----DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
                 +    Y        +IK E   + +   G +     A  ++ +   D V +GR+
Sbjct: 279 NDTIPAMGTQPYCFMSKYTKQIK-EAVSIPVSSVGRIVTPENAEALIENGVCDIVGLGRS 337

Query: 219 AYKNS 223
              + 
Sbjct: 338 LLADP 342


>gi|254241597|ref|ZP_04934919.1| morphinone reductase [Pseudomonas aeruginosa 2192]
 gi|126194975|gb|EAZ59038.1| morphinone reductase [Pseudomonas aeruginosa 2192]
          Length = 369

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 60/188 (31%), Gaps = 29/188 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA+   D G++ + L              ++     ++G  L      + + + A
Sbjct: 161 DEFVRAARNALDAGFDLVELHGANGYLIDQFLASASNRRSDAYGGSLENRARFLLEIVDA 220

Query: 111 MCKALSI-PVTVKCRI-----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +  A+    V ++         + D  P      L  ++++ G+  +  H  +    G  
Sbjct: 221 LVAAVGAERVGLRLSPWGTINDMHDDEPEAMTLYLAAALQRRGIAYL--HLAEWEWSGGP 278

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                    L                + + G   D  +A  IL +   D V IGR    N
Sbjct: 279 AYPQGFRERLRERFRA---------PLIVCGNY-DAERAEAILEAGLADAVAIGRPFIAN 328

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 329 PDLVERIR 336


>gi|302385888|ref|YP_003821710.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           saccharolyticum WM1]
 gi|302196516|gb|ADL04087.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           saccharolyticum WM1]
          Length = 662

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 25/153 (16%), Positives = 51/153 (33%), Gaps = 24/153 (15%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVK---------CRIGVDDQIPAVAL----- 136
           +G  L     +  D +  +  A     PV+++          R G               
Sbjct: 198 YGGSLENRLRVATDIVKGIKAACGPDFPVSLRYSLKSCMKGIRRGGLPGEDYEEAGKDIE 257

Query: 137 --RNLVKSIKKSGVNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 K ++ +G + + + A    +      P       +  Y     + K+N D+ + 
Sbjct: 258 EGIEAAKILEAAGYDALNVDAGTYDSWYWNHPP---MYFEDGMYREFGRLVKQNVDVPVI 314

Query: 193 LNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
           L G +E+   A++ L  S D + +GR    +  
Sbjct: 315 LAGRMENPEMAIEALGDSCDIIGLGRQLLTDPY 347


>gi|299821943|ref|ZP_07053831.1| NADPH dehydrogenase [Listeria grayi DSM 20601]
 gi|299817608|gb|EFI84844.1| NADPH dehydrogenase [Listeria grayi DSM 20601]
          Length = 337

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 65/193 (33%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I L+            P +   E ++G        I+G+ I A+
Sbjct: 144 DFKRAAFRAKEAGFDVIELHAAHGYLVHQFLSPLSNRREDTYGGPAGNRYRILGEIIRAI 203

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P  V +     V   +         K +K  GV  I +        G  P    
Sbjct: 204 REVWDGPLLVRISATDYVHGGLTLEDHVPFAKWMKADGVQLIDVSTG-----GNVPVRPN 258

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
             P        +++++   +  G  G +   +QA +IL     D ++IGR   ++     
Sbjct: 259 VYPGYQTRYADDLRQKAG-IATGALGMITTGAQAEEILGNERADLIVIGRELLRDPYFAR 317

Query: 228 TVDEYFSNPLTGS 240
           T        +T  
Sbjct: 318 TAALELGEEITPP 330


>gi|213584730|ref|ZP_03366556.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 105

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 25/78 (32%), Gaps = 14/78 (17%)

Query: 201 SQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMT 260
           +QA       D VMIGR A  N   L+ V +Y                +  W ++   + 
Sbjct: 2   AQACMATSGCDAVMIGRGAL-NIPNLSRVVKYNE-------------PRMPWPEVVTLLQ 47

Query: 261 DYAARHLHSGGKLQQITR 278
            Y          L  + R
Sbjct: 48  KYTRLEKQGDTGLYHVAR 65


>gi|56418604|ref|YP_145922.1| dihydropteroate synthase [Geobacillus kaustophilus HTA426]
 gi|261417569|ref|YP_003251251.1| dihydropteroate synthase [Geobacillus sp. Y412MC61]
 gi|297528444|ref|YP_003669719.1| dihydropteroate synthase [Geobacillus sp. C56-T3]
 gi|319765226|ref|YP_004130727.1| dihydropteroate synthase [Geobacillus sp. Y412MC52]
 gi|56378446|dbj|BAD74354.1| dihydropteroate synthase [Geobacillus kaustophilus HTA426]
 gi|261374026|gb|ACX76769.1| dihydropteroate synthase [Geobacillus sp. Y412MC61]
 gi|297251696|gb|ADI25142.1| dihydropteroate synthase [Geobacillus sp. C56-T3]
 gi|317110092|gb|ADU92584.1| dihydropteroate synthase [Geobacillus sp. Y412MC52]
          Length = 283

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 87/250 (34%), Gaps = 26/250 (10%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D+   V+ AK +   G + I++           G+    L      V   + A+ KA+S+
Sbjct: 44  DVENAVKHAKRLVAEGADIIDIGGE----STRPGADPVPLDEELRRVIPAVKAIAKAVSV 99

Query: 118 PVTVKCR-------------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           P+++                  ++D   A A  ++ +     G   I +H R+ +     
Sbjct: 100 PISIDTYKAEVARQAMEAGAHIINDVWGAKADPDMARVAATYGAPIILMHNRRDMAYRDL 159

Query: 165 PKDNRKIPNLDYDIVYE--IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
             D          IV E  +K EN  +     G  + +   L+++  +D      AA   
Sbjct: 160 ISDMIADLKESIRIVKEAGVKDEN-IILDPGIGFAKTVEHNLEVMRRLDEF----AALGY 214

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             +L T  + F   + G  P++ RV+          M       +H    + ++ + M  
Sbjct: 215 PLLLGTSRKRFIGHVLG-VPVEERVEGTGATVCLGIMKGVHIVRVHDVLPIARMAKMMDA 273

Query: 283 LF-HGFPNSR 291
           +   G    R
Sbjct: 274 MLGKGESGHR 283


>gi|332521089|ref|ZP_08397547.1| dihydroorotate dehydrogenase [Lacinutrix algicola 5H-3-7-4]
 gi|332043182|gb|EGI79379.1| dihydroorotate dehydrogenase [Lacinutrix algicola 5H-3-7-4]
          Length = 341

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 66/180 (36%), Gaps = 30/180 (16%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I  + KA        P+ +K    ++
Sbjct: 171 VDYFVLNVSCPNVGSHAK------LNDKDYLLELIGTVQKANTNFTTQKPIVLKIAPDLN 224

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR------------KIPNLDY 176
           +      L  +++ ++++ ++G+          GL   D R             +     
Sbjct: 225 NG----QLDEIIELVQETSLDGVIASNTSTDRTGLKATDERLAEIGNGGLSGQPVKEKST 280

Query: 177 DIVYEI-KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA-AYKNSAMLTTVDEYF 233
            ++  + +K N    I   GG+     AL+ +    D V I     Y+  +++  +++  
Sbjct: 281 QVIKYLSQKSNKAFPIIGVGGIHSAKDALEKIEAGADLVQIYTGFIYEGPSLVKQINKAL 340


>gi|262166100|ref|ZP_06033837.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio mimicus VM223]
 gi|262025816|gb|EEY44484.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio mimicus VM223]
          Length = 666

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|149910098|ref|ZP_01898745.1| 2,4-dienoyl-CoA reductase [Moritella sp. PE36]
 gi|149806823|gb|EDM66785.1| 2,4-dienoyl-CoA reductase [Moritella sp. PE36]
          Length = 676

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 59/180 (32%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCP-SARVHEGSFGACLMLNPDIV-GDCIA 109
              + A + +  GY+ + +            C  S +  +   G+    N      + + 
Sbjct: 146 DFAKTADLAKFAGYDGVEVMGSEGYLINQFICRRSNKRTDEWGGSY--QNRMRFPIEIVK 203

Query: 110 AMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +     +  R+     V+D         L K ++K GV    I+      +   P
Sbjct: 204 AIRQRVGNDFIIIFRLSMLDLVEDGSTFEEAVELAKELEKVGVT--IINTGIGWHEARIP 261

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                +P   +  V E  K++  + +     +     A +IL     D V + R    + 
Sbjct: 262 TIVTSVPRGAFSWVTEKMKDHVSIPLVTTNRINTPEVAEQILASGQADMVSMARPMLADP 321


>gi|170289548|ref|YP_001739786.1| imidazoleglycerol phosphate synthase, cyclase subunit [Thermotoga
           sp. RQ2]
 gi|226702009|sp|B1L873|HIS6_THESQ RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|170177051|gb|ACB10103.1| imidazoleglycerol phosphate synthase, cyclase subunit [Thermotoga
           sp. RQ2]
          Length = 253

 Score = 42.9 bits (100), Expect = 0.064,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA  N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVGNPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 123 QAVVVAIDAKRVDGEFM 139


>gi|116512347|ref|YP_809563.1| dihydroorotate dehydrogenase 1A [Lactococcus lactis subsp. cremoris
           SK11]
 gi|116108001|gb|ABJ73141.1| dihydroorotate oxidase B, catalytic subunit [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 311

 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 68/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESYFSGITELNLSCP--NVPGK---PQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   K    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|317405951|gb|EFV86229.1| 2,4-dienoyl-CoA reductase [Achromobacter xylosoxidans C54]
          Length = 672

 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 25/177 (14%), Positives = 56/177 (31%), Gaps = 17/177 (9%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           +   A + +  GY+ + +             P+  +    +G C         + IAA+ 
Sbjct: 145 IAYTAMLAQAAGYDGVEVMGSEGYLLDEFTSPATNLRADVYGGCFENRIRFPLETIAAVR 204

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+     +  RI   D     +       L   ++++GV+ +  +      +   P   
Sbjct: 205 AAVGNRFLLIYRISAVDLVHGGLTGAETAQLALRLQQAGVDML--NTGVGWHESAIPTIA 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
             +P   +D      K    + +  +  +     A  +L     D V + R    + 
Sbjct: 263 ASVPKAAWDFAVRNIKGAVSIPVIASNRISTPDVAESLLAGGVADFVSMARPLLADP 319


>gi|294142024|ref|YP_003558002.1| dihydroorotate dehydrogenase [Shewanella violacea DSS12]
 gi|293328493|dbj|BAJ03224.1| dihydroorotate dehydrogenase [Shewanella violacea DSS12]
          Length = 310

 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 35/190 (18%), Positives = 63/190 (33%), Gaps = 32/190 (16%)

Query: 47  EKPLALQIGG---ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            KP+ + I G   AD   +V+A    +    + I +N  CP   +   +       + + 
Sbjct: 93  GKPIVVSISGFSLADNLTMVKA---FQTSCADLIEVNFSCP--NIEGKAQVGY---DFEQ 144

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---------- 153
               +  +C+  S P+ +K     D          +   IKK  V+ I            
Sbjct: 145 TERALEQLCELGSKPIGLKLPPYFDFSHFNT----MANIIKKFPVSFITCINSVGNTLVI 200

Query: 154 --HARKAILK---GLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALK-I 206
                 AI+K   G        I  +    V    +  P  + I   GG++  + A + +
Sbjct: 201 DPETESAIIKPKGGFGGLCGDYIKPIGLANVRAFSQLLPSSIDIIGVGGIKTGTDAFEYL 260

Query: 207 LPSVDGVMIG 216
           L     V + 
Sbjct: 261 LAGASAVQVA 270


>gi|257075641|ref|ZP_05570002.1| NADH oxidoreductase [Ferroplasma acidarmanus fer1]
          Length = 547

 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 65/176 (36%), Gaps = 18/176 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K V AA++    G++ I L+            P+       +G  +     I+ +  +A
Sbjct: 143 EKFVNAAELAYRAGFDGIELHGAHGYLLQEFISPALNKRTDEYGGSVENRIRILNEISSA 202

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +   L++P+ ++  +  DD+    A    ++   ++    + +   + +    G S    
Sbjct: 203 IKSKLNMPLGIRLSLYEDDEGGYDADYGIDVASRLENM--DYVHFSSGRFAPPGSSASFY 260

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
               ++   +  ++ K    +     G +  M    K L   D V++GR A  +  
Sbjct: 261 YDNVHIGAKLKKKLDKNTMLV-----GSIRSMEDIEKALTVSDFVVLGRQALADPY 311


>gi|78221350|ref|YP_383097.1| flavin oxidoreductase/NADH oxidase [Geobacter metallireducens
           GS-15]
 gi|78192605|gb|ABB30372.1| flavin oxidoreductase/NADH oxidase [Geobacter metallireducens
           GS-15]
          Length = 374

 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 22/149 (14%), Positives = 50/149 (33%), Gaps = 11/149 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSI--PVTVKC--RIGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L      + +   A+  A+    PV VK      ++  +       + + + + G+
Sbjct: 187 YGGSLENRCRFLLEISHAVRAAVGKDFPVMVKLNGSDNLNGGLDLEEAVLVARMLDEEGI 246

Query: 149 NGIWIHARKAILKGLSPKDN----RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           + I +        G +P       R+    +  + Y IK+      + + GG        
Sbjct: 247 DAIEVSGGTPASGGQTPVRQGIETREQEAYNLPLAYRIKQ-VVSCPVMVVGGFRTFELVE 305

Query: 205 KIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            ++     D V + R   +   +    +E
Sbjct: 306 GVIRREEADFVSLSRPLIREPNLPRRWEE 334


>gi|328753503|gb|EGF67119.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL020PA1]
          Length = 307

 Score = 42.9 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 67/197 (34%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+ + + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIVNVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G +G+ +      
Sbjct: 145 NVTAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARATADAGADGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
                      I           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAVRMIDAVTR-VVDIPVIGMGGVMTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|257483833|ref|ZP_05637874.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. tabaci ATCC
           11528]
 gi|330985623|gb|EGH83726.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. lachrymans str.
           M301315]
 gi|331012662|gb|EGH92718.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 679

 Score = 42.9 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTRVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVKVPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|237665790|ref|ZP_04525778.1| dihydroorotate dehydrogenase family protein [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|237658737|gb|EEP56289.1| dihydroorotate dehydrogenase family protein [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 362

 Score = 42.9 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 21/128 (16%), Positives = 45/128 (35%), Gaps = 11/128 (8%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR------NLVKSIKKSGVNGIW 152
            +   + + +  + +    PV +K    + D I    +        +V          I 
Sbjct: 130 KDLSNIKETLKTIRRFTQKPVFMKMSPHIPDPIGFAKMVIENKGSGIVAINSLGPTMNID 189

Query: 153 IHARKAIL---KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I  R  ++   +G        I  +   ++++IKK  P+  I   GG+      ++ +L 
Sbjct: 190 IDKRSVLIGNKEGEVWTSGPAIKPMALALIHKIKKAVPECEIIGVGGISSADDIIEFLLA 249

Query: 209 SVDGV-MI 215
               V M+
Sbjct: 250 GASAVQML 257


>gi|225570531|ref|ZP_03779556.1| hypothetical protein CLOHYLEM_06633 [Clostridium hylemonae DSM
           15053]
 gi|225160728|gb|EEG73347.1| hypothetical protein CLOHYLEM_06633 [Clostridium hylemonae DSM
           15053]
          Length = 640

 Score = 42.9 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 30/194 (15%), Positives = 66/194 (34%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEGS------FGACLMLNPDIVGDCIAA 110
            +    A++    G++ +  +      P   +  G       +G           + I+A
Sbjct: 135 EEFGCGARLAVQAGFDAVEFHAAHSYLPHEFLSPGMNRRTDEYGGSFENRCRFCFEVISA 194

Query: 111 MCKAL--SIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +   +   +P  +        ++  +    +   +      GV+   I    A+    S 
Sbjct: 195 IRSNIPEDMPFFMRVGCIDELMEQNMTEEEIVEFINRSADLGVDVADISRGNAM----SF 250

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
               ++P  +       + +Y IKK+     +G+ G +     A +++     D V IGR
Sbjct: 251 ATVYEVPPFNLPHGFNIENIYNIKKQIKIPVVGV-GRINTGEMANQVIEDGKFDLVAIGR 309

Query: 218 AAYKNSAMLTTVDE 231
           A   +   +T V E
Sbjct: 310 AQLADPEWVTKVRE 323


>gi|153826844|ref|ZP_01979511.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MZO-2]
 gi|149739365|gb|EDM53611.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MZO-2]
          Length = 666

 Score = 42.9 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 77/233 (33%), Gaps = 26/233 (11%)

Query: 4   WTDRHYRFFAR----LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            TD  +R  A+    LL            + + +R        F+  E     QI    I
Sbjct: 86  VTDAVHRHGAKIALQLLHAGRYAMHPFSQSASAIRAPIS---KFAPSEMSTR-QIR-NTI 140

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                +A++ +  GY+ + +            C    +    +G           + + A
Sbjct: 141 QDFANSAELAQLAGYDGVEVMGSEGYLINQFICKRTNMRYDEWGGSYQNRIRFPVEIVKA 200

Query: 111 MCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +A+     +  R+     V+       +  L K+++++GV    I+      +   P 
Sbjct: 201 IREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHEARIPT 258

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 259 IATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|6177796|dbj|BAA86060.1| JPR ORF1 [Pyrus pyrifolia]
          Length = 424

 Score = 42.9 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 31/172 (18%), Positives = 55/172 (31%), Gaps = 25/172 (14%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 173 RVEQTGVDALEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATVPVWAKMTPNI 231

Query: 128 DDQIPAVALR---------NLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDNRKIPN 173
            D      +           +   +   G+N   +     +       G S K    I  
Sbjct: 232 TDITQPARVALSSGCEGVSAINTIMSVMGINLTTLRPEPCVEGYSTPGGYSAKAVHPIAL 291

Query: 174 LDYDIVYEI-KKENPDL--FIGLNGGLED-MSQALKILPS------VDGVMI 215
                + ++ K E  D    +   GG+E     A  IL          GVM+
Sbjct: 292 AKVMNIAKLMKSEFGDTDYSLSGIGGVESGGDAAEFILLGANTVQVCTGVMM 343


>gi|227112273|ref|ZP_03825929.1| flavoprotein xenobiotic reductase [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 362

 Score = 42.9 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 62/183 (33%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AA+   D G+  + L+       + +             +G         + + +
Sbjct: 158 DDFVAAARRALDAGFEWLELHFA--HGYLAQSFFSVHSNKRNDQYGGSFDNRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
           AA+       +P+T +  +   D      L+    L +  K +G++ + +      +   
Sbjct: 216 AAVRDVWPQHLPLTARFGVIEFDGRDEETLQESIELTRRFKAAGLDMLSV-----SIGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           +P  N          + +  +E  DL +    G      A + +    +D VM+G+A   
Sbjct: 271 TPTANIPWAPAFMGPIAKQVREQADLPVSSAWGFGTPELAEQAVASGQLDLVMVGKAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|281212321|gb|EFA86481.1| hypothetical protein PPL_00275 [Polysphondylium pallidum PN500]
          Length = 402

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 38/199 (19%), Positives = 73/199 (36%), Gaps = 24/199 (12%)

Query: 47  EKPLALQIGGADISKLVE----AAKIVEDFGYNEINLNVG---------CPSARVHEGSF 93
           E  +  ++   +I  +V+     A  VE  G++ + ++            P +      +
Sbjct: 186 EMIVPHELSVFEIESIVQSFKDTAIRVEKAGFDALEIHGAHGYLINSFLSPLSNRRTDEY 245

Query: 94  GACLMLNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           G        I+ D + A+    S    V +     ++          L K +K+  V+ +
Sbjct: 246 GVDFEGRIKILTDIVKAIRTVWSKILMVRISAEEWIEGGWTLDDSIQLTKILKELDVDIL 305

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILPS- 209
                 A   G S         L    + E IK+E PD+     G ++ + QA+ I+   
Sbjct: 306 -----DASSGGNSADAKIPFGPLFQVPLAEGIKREVPDIITSTVGSIKTVEQAMSIIDDD 360

Query: 210 -VDGVMIGRAAYKNS-AML 226
             D VM+GR   ++   +L
Sbjct: 361 RADLVMLGRPLLRDPFWVL 379


>gi|34809598|pdb|1JUB|A Chain A, The K136e Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
 gi|34809599|pdb|1JUB|B Chain B, The K136e Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
 gi|34810495|pdb|1OVD|A Chain A, The K136e Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A In Complex With Orotate
 gi|34810496|pdb|1OVD|B Chain B, The K136e Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A In Complex With Orotate
          Length = 311

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 38/213 (17%), Positives = 67/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP            L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCP-----NVPGEPQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   K    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|329766601|ref|ZP_08258144.1| imidazoleglycerol phosphate synthase, cyclase subunit [Candidatus
           Nitrosoarchaeum limnia SFB1]
 gi|329136856|gb|EGG41149.1| imidazoleglycerol phosphate synthase, cyclase subunit [Candidatus
           Nitrosoarchaeum limnia SFB1]
          Length = 267

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K     G + +        L   +  + RK      ++V ++     D+   + GG+
Sbjct: 35  ELAKKYSDEGADELV------FLDITASDEQRKTLK---ELVRKVA-SVIDIPFTVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  A  IL    D V I   A KN  ++T + E F 
Sbjct: 85  KSLEDARNILLNGADKVGINTGAIKNPTIITELMELFG 122


>gi|229493203|ref|ZP_04386995.1| oxidoreductase, FAD/FMN-binding [Rhodococcus erythropolis SK121]
 gi|229319934|gb|EEN85763.1| oxidoreductase, FAD/FMN-binding [Rhodococcus erythropolis SK121]
          Length = 367

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 27/168 (16%), Positives = 56/168 (33%), Gaps = 24/168 (14%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKC---------RIGVDDQIPAVALRNLVK 141
           +G        ++ + ++A+ +     +P+ V+          R    D   A     L  
Sbjct: 203 YGGSFENRIRLLLEILSAVREVWPAELPLFVRVSATDWLTEERGLDVDSWTADQTVALAN 262

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            +   GV+ + +        G SP     + P         ++ E+  L     G + + 
Sbjct: 263 ILSDYGVDLVDVSTG-----GNSPAAKIPVEPGYQVPFARRLQNESL-LPAAAVGLITEP 316

Query: 201 SQALKILPSVDG----VMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
            QA KI+   DG    V++GR   ++           +  +    P +
Sbjct: 317 EQAEKIVE--DGSAVAVLLGRELLRDPYWARRAARELNTEVGPHIPSQ 362


>gi|34809590|pdb|1JQV|A Chain A, The K213e Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
 gi|34809591|pdb|1JQV|B Chain B, The K213e Mutant Of Lactococcus Lactis Dihydroorotate
           Dehydrogenase A
          Length = 311

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 38/213 (17%), Positives = 68/213 (31%), Gaps = 28/213 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLN 100
             + QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  +
Sbjct: 88  KENAQEGPIFFSIAGMSAAENIAMLKKIQESDFSGITELNLSCP--NVPGK---PQLAYD 142

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW- 152
            +     +  +    + P+ VK     D     I A  L       V S+   G      
Sbjct: 143 FEATEKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFID 202

Query: 153 ------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
                 +   +    G+     +     +    Y   K  P++ I   GG+E    A + 
Sbjct: 203 PEAESVVIKPEDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEH 260

Query: 207 LPSVDGVM--IGRAAYKN--SAMLTTVDEYFSN 235
           L      M  IG  A      A+   + +    
Sbjct: 261 LL-CGATMLQIGT-ALHKEGPAIFDRIIKELEE 291


>gi|16804509|ref|NP_465994.1| NADPH dehydrogenase NamA [Listeria monocytogenes EGD-e]
 gi|224503288|ref|ZP_03671595.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL R2-561]
 gi|254828046|ref|ZP_05232733.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL N3-165]
 gi|68052783|sp|Q8Y4H1|NAMA_LISMO RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|16411959|emb|CAD00549.1| lmo2471 [Listeria monocytogenes EGD-e]
 gi|258600430|gb|EEW13755.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL N3-165]
          Length = 338

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 65/194 (33%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     +   
Sbjct: 317 KDAAKQLGETIEAP 330


>gi|110633526|ref|YP_673734.1| NADH:flavin oxidoreductase/NADH oxidase [Mesorhizobium sp. BNC1]
 gi|110284510|gb|ABG62569.1| NADH:flavin oxidoreductase/NADH oxidase [Chelativorans sp. BNC1]
          Length = 370

 Score = 42.9 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 31/208 (14%), Positives = 60/208 (28%), Gaps = 22/208 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
               EA +     G + + ++            P +   +  +G  L   M  P  V D 
Sbjct: 159 DAFAEATRRSARLGLDAVQIHAAHGYLLHEFLSPLSNRRDDEYGGSLENRMRFPLEVFDA 218

Query: 108 IAAMCKALSIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A   A   PVTV+       +            K+++  G   I + +      GLS 
Sbjct: 219 VRAAFPA-EQPVTVRVSGTDWAEGGWTIEDTVAFAKALEARGCGAIHVSSG-----GLSA 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                I       +    K    + +   G + +  QA  I+ +   D V + R    + 
Sbjct: 273 AQRIPIGPNYQVPLARAVKAAVRMPVVAVGLITEFEQAEAIIGTGDADFVALARTILYDP 332

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
                   +    +           + +
Sbjct: 333 HWPWHAAAHLGARVKAPKQYLRSQPRRY 360


>gi|225561204|gb|EEH09485.1| NADPH dehydrogenase [Ajellomyces capsulatus G186AR]
          Length = 419

 Score = 42.9 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 69/198 (34%), Gaps = 31/198 (15%)

Query: 64  EAAKIVEDFGYNEINLNVG--------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            A +     G + I ++          C P +      +G        +  + I    + 
Sbjct: 201 AAVRRAVKAGVDYIEVHCAHGYLLFSFCSPVSNNRTDEYGGSFENRIRLTSEIITISRQN 260

Query: 115 L--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +   +P+ ++          R  +        +R   K + + G V+ + + A      G
Sbjct: 261 MPKDMPLFLRISASEWLEETRPDLPSWKSEDTVR-FAKILAEKGEVDLLDVSA------G 313

Query: 163 LSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
            +  D + IP   +     + +K+    L +G  G + +   A  +L   +D V++GR  
Sbjct: 314 GNHPDQKIIPGPCFQAHFAHAVKEAVDKLLVGAVGSINNGVDADGLLEKGLDLVLVGRLF 373

Query: 220 YKNSAMLTTVDEYFSNPL 237
            KN +++    E     L
Sbjct: 374 LKNPSVVWQFAEDLGTEL 391


>gi|254465735|ref|ZP_05079146.1| oxidoreductase, FAD/FMN-binding family [Rhodobacterales bacterium
           Y4I]
 gi|206686643|gb|EDZ47125.1| oxidoreductase, FAD/FMN-binding family [Rhodobacterales bacterium
           Y4I]
          Length = 766

 Score = 42.9 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 80/257 (31%), Gaps = 30/257 (11%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-- 82
           E + A AI   D       +   + ++     A  ++ V AA++ E  G++ I L+    
Sbjct: 522 ETVSASAIPWSDN------NPAPREISRAEMDAIKAEFVAAAQMAERAGFDMIELHAAHG 575

Query: 83  -------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV---DDQ 130
                   P + + E  +G  L        +   AM        P++V+        D+ 
Sbjct: 576 YLISSFISPKSNIREDEYGGSLENRLRYPLEVFQAMRGVWPEDKPMSVRISANDWVGDEG 635

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           +       + K+   +G + I + A +                        I+ E   + 
Sbjct: 636 VTPEEAVEIAKAFTAAGADIIDVSAGQTSTDAKPVYGRMFQTP----FSDRIRNEAG-IA 690

Query: 191 IGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIKTRV 247
               G + +   A  IL +   D V +GR    +    L            G  P+    
Sbjct: 691 TMAVGNIYEADHANSILMAGRADLVCVGRPHLADPYWSLHEAARI--GDRHGDWPLPYHA 748

Query: 248 DKDFWRKISASMTDYAA 264
            +D   +++    +   
Sbjct: 749 GRDQLWRLADREAEVIR 765


>gi|300717427|ref|YP_003742230.1| NADH-dependent flavin oxidoreductase [Erwinia billingiae Eb661]
 gi|299063263|emb|CAX60383.1| NADH-dependent flavin oxidoreductase [Erwinia billingiae Eb661]
          Length = 365

 Score = 42.9 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 28/160 (17%), Positives = 56/160 (35%), Gaps = 18/160 (11%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRI 125
           +++ F  +  NL   C          G  +     ++ + I ++ + L   IPV ++   
Sbjct: 185 LLDQFFTDYTNLRTDCW---------GGDIAGRLQLILEVIKSVRQRLGQAIPVGIRISQ 235

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD--NRKIPNLDYDIVYEIK 183
           G                   + +    +         L+  +      P     ++   +
Sbjct: 236 G----KVNDFFHKWANGEDDARIAFTLLAESGIDYLHLTEYEAWQPAFPGNLLSLIELGR 291

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           K  P+L I  NG L D  +AL+++    D + +GR A  N
Sbjct: 292 KYAPNLTIMANGSLHDECRALQVMEMGADFIALGRGALAN 331


>gi|224499828|ref|ZP_03668177.1| NADPH dehydrogenase NamA [Listeria monocytogenes Finland 1988]
 gi|254831106|ref|ZP_05235761.1| NADPH dehydrogenase NamA [Listeria monocytogenes 10403S]
 gi|255026127|ref|ZP_05298113.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL J2-003]
 gi|284802909|ref|YP_003414774.1| NADPH dehydrogenase NamA [Listeria monocytogenes 08-5578]
 gi|284996050|ref|YP_003417818.1| NADPH dehydrogenase NamA [Listeria monocytogenes 08-5923]
 gi|284058471|gb|ADB69412.1| NADPH dehydrogenase NamA [Listeria monocytogenes 08-5578]
 gi|284061517|gb|ADB72456.1| NADPH dehydrogenase NamA [Listeria monocytogenes 08-5923]
          Length = 338

 Score = 42.9 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 65/194 (33%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     +   
Sbjct: 317 KDAAKQLGETIEAP 330


>gi|304405314|ref|ZP_07386973.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus
           curdlanolyticus YK9]
 gi|304345353|gb|EFM11188.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus
           curdlanolyticus YK9]
          Length = 341

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 31/199 (15%), Positives = 61/199 (30%), Gaps = 22/199 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVG-DCIA 109
               +A       G + + L             PS       +G+    +P   G + I 
Sbjct: 144 ELFRDAVARAVQAGVDTVQLHGAHGYLIHQFHSPSINKRTDEYGS---DDPTRFGVEIIQ 200

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A    L   IP+ ++       +          L +  + +GV  + I     +    SP
Sbjct: 201 AARSVLPSHIPLQMRVSAVDYGEGGYDLAYGIELCRKYQSAGVELLDISTGGGVAT--SP 258

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                 P     +   +K+    L +   G L++   AL  + +   D V +GR   ++ 
Sbjct: 259 VMLDVYPGYQLPMARAVKEATG-LPVIAVGLLDEPKLALAAVANGDCDLVAVGRGMLRDP 317

Query: 224 AMLTTVDEYFSNPLTGSSP 242
                 ++   +      P
Sbjct: 318 YWALHAEQATGSEAKPPKP 336


>gi|297579497|ref|ZP_06941425.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae RC385]
 gi|297537091|gb|EFH75924.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae RC385]
          Length = 684

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 214 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVLLAKALEEAGVT--IINTGIGWHE 271

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 272 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 329


>gi|260427994|ref|ZP_05781973.1| NADH-flavin oxidoreductase/nadh oxidase [Citreicella sp. SE45]
 gi|260422486|gb|EEX15737.1| NADH-flavin oxidoreductase/nadh oxidase [Citreicella sp. SE45]
          Length = 444

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 22/192 (11%), Positives = 52/192 (27%), Gaps = 55/192 (28%)

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR----------N 138
            + ++G  L      + + IAA+ + +     ++ ++   D    +              
Sbjct: 189 RKDAYGGGLRNRARFLLEVIAAIRETVGREFHLQVKLSATDHNNVIPWEGRGNTVAETIK 248

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDN------------------------------ 168
           + +  +  G + + I         L+P  +                              
Sbjct: 249 VAQWCEAMGADALHISTGSLFPHPLNPPGDLPLDLLAITYDAMISSGIHGFRNFLLFRYP 308

Query: 169 --RKIPNLDYDIV-------------YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
             R I    +  +               + +E   + +   GG +  +     L  VD V
Sbjct: 309 ALRPIFRWIWFRMKAGRPVQGVGLDEARMIREAVTIPVISTGGWQSATAIRDALTKVDAV 368

Query: 214 MIGRAAYKNSAM 225
            I R+   N  +
Sbjct: 369 SIARSLVANPDL 380


>gi|152964123|ref|YP_001359907.1| NADH:flavin oxidoreductase/NADH oxidase [Kineococcus radiotolerans
           SRS30216]
 gi|151358640|gb|ABS01643.1| NADH:flavin oxidoreductase/NADH oxidase [Kineococcus radiotolerans
           SRS30216]
          Length = 359

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 37/216 (17%), Positives = 68/216 (31%), Gaps = 30/216 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V A++   D G + + ++            PS+   +  +G        +V +   A+
Sbjct: 153 DFVAASRRAVDAGLDGVEIHSANGYLLHEFLAPSSNHRDDQYGGSPENRARLVVEIATAV 212

Query: 112 CKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
              +    V V+     + Q         V++   + V G+    R   L  LS      
Sbjct: 213 AAEIGAGRVGVRISPEHNIQDALETDPADVEATYSALVEGL----RPLGLAYLSVLHADP 268

Query: 171 IPNLDYDIVYEIKKENPD--LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
              L    V  ++K+     +     G +     AL ++     D V +GR A  N  ++
Sbjct: 269 SGGL----VQGLRKQFEGHLMVNSGFGVVTSRQDALDLVAEGTADSVAVGRMAIANPDLV 324

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
               E          P        F+   +   TDY
Sbjct: 325 RRWQEDL--------PENEPNPATFYADGAEGYTDY 352


>gi|289427211|ref|ZP_06428927.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes J165]
 gi|295130562|ref|YP_003581225.1| Dihydroorotate dehydrogenase, catalytic subunit [Propionibacterium
           acnes SK137]
 gi|289159680|gb|EFD07868.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes J165]
 gi|291377036|gb|ADE00891.1| Dihydroorotate dehydrogenase, catalytic subunit [Propionibacterium
           acnes SK137]
 gi|313772129|gb|EFS38095.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL074PA1]
 gi|313807484|gb|EFS45971.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL087PA2]
 gi|313809993|gb|EFS47714.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL083PA1]
 gi|313818528|gb|EFS56242.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL046PA2]
 gi|313820295|gb|EFS58009.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL036PA1]
 gi|313822897|gb|EFS60611.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL036PA2]
 gi|313825170|gb|EFS62884.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL063PA1]
 gi|313830321|gb|EFS68035.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL007PA1]
 gi|313833696|gb|EFS71410.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL056PA1]
 gi|314925181|gb|EFS89012.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL036PA3]
 gi|314960035|gb|EFT04137.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL002PA2]
 gi|314973326|gb|EFT17422.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL053PA1]
 gi|314976004|gb|EFT20099.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL045PA1]
 gi|314978458|gb|EFT22552.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL072PA2]
 gi|314983976|gb|EFT28068.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL005PA1]
 gi|314988159|gb|EFT32250.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL005PA2]
 gi|314989963|gb|EFT34054.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL005PA3]
 gi|315080675|gb|EFT52651.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL078PA1]
 gi|315084347|gb|EFT56323.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL027PA2]
 gi|315085689|gb|EFT57665.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL002PA3]
 gi|315088890|gb|EFT60866.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL072PA1]
 gi|315096241|gb|EFT68217.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL038PA1]
 gi|327326154|gb|EGE67944.1| dihydroorotate oxidase [Propionibacterium acnes HL096PA2]
 gi|327331970|gb|EGE73707.1| dihydroorotate oxidase [Propionibacterium acnes HL096PA3]
 gi|327443172|gb|EGE89826.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL013PA2]
 gi|327445959|gb|EGE92613.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL043PA2]
 gi|327448062|gb|EGE94716.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL043PA1]
 gi|328760624|gb|EGF74191.1| dihydroorotate oxidase [Propionibacterium acnes HL099PA1]
 gi|332675402|gb|AEE72218.1| dihydroorotate dehydrogenase [Propionibacterium acnes 266]
          Length = 307

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 66/197 (33%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G +G+ +      
Sbjct: 145 NVTAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARATADAGADGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
                      I           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAVRMIDAVTR-VVDIPVIGMGGVMTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|182412430|ref|YP_001817496.1| dihydroorotate dehydrogenase [Opitutus terrae PB90-1]
 gi|177839644|gb|ACB73896.1| dihydroorotate dehydrogenase [Opitutus terrae PB90-1]
          Length = 332

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 42/261 (16%), Positives = 86/261 (32%), Gaps = 49/261 (18%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L  S  + P+   + G      ++ A+  E  G + I LN                L+ +
Sbjct: 97  LLTSELDIPIIASLNGRHPGGWLDYARKFEAAGADAIELN-------------FYQLVTD 143

Query: 101 P--------DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           P        D + + + ++  A+ IPV VK            +L +  ++++++G  G+ 
Sbjct: 144 PKVSGDEIEDELIETLRSVVTAVRIPVAVKLSPF------HTSLPHFTQALRQAGAAGLV 197

Query: 153 IHAR-------------KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           +  R             +  L+   P     +  L +  +           +  +GG+  
Sbjct: 198 LFNRLYQPDFDVDALEVQPTLRLSDP--GELLLRLRWLAILSPNHLGS---LAASGGVHS 252

Query: 200 -MSQALKILPSVDGVMIGRAAYKN-SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
               A  +L   D V I  A  +   A+L T+ + F   +           +        
Sbjct: 253 GTDVAKAVLAGADAVQIVSAVLRQGPAVLKTLLQDFETWMRTHEYTHVGEFRGGLN--LR 310

Query: 258 SMTDYAARHLHSGGKLQQITR 278
              D AA    +  ++ Q  +
Sbjct: 311 HCPDPAALERANYQRILQTWK 331


>gi|160943282|ref|ZP_02090518.1| hypothetical protein FAEPRAM212_00768 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445521|gb|EDP22524.1| hypothetical protein FAEPRAM212_00768 [Faecalibacterium prausnitzii
           M21/2]
          Length = 641

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 25/209 (11%), Positives = 68/209 (32%), Gaps = 18/209 (8%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------C 83
           D + +    +++ F+ +    + ++  + I K+   A   +  G + I ++        C
Sbjct: 118 DEMRQRLHHDMMFFTDE---ASEEMLMSIIDKMCACAVRAQKAGVDVIQIHGDRLNGCLC 174

Query: 84  PSARVHEGSFGACLMLNPDIVGDCI-AAMCKAL-----SIPVTVKCRIGVDDQIPAVALR 137
            +   H        + N       +  A+ KA+        +++         I      
Sbjct: 175 STRMNHRTDKFGGSLENRVRFARMLTRAIRKAVPDMVIDYKLSIVTPQRGKGGIDEADAV 234

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGG 196
              + + + GV+   +                 +    + + +    K+  ++ +   G 
Sbjct: 235 QFAQWLVEDGVDMFHVAQANHTGNMADTIPPMGVQPYGFFVKIAGDIKKAVNVPVSAVGR 294

Query: 197 LEDMSQALKILPS--VDGVMIGRAAYKNS 223
           + D   A +++ S   D V +GR    + 
Sbjct: 295 IVDADMAARVIESGMADIVAMGRPLLADP 323


>gi|2385386|emb|CAA04758.1| L-mandelate dehydrogenase [Rhodotorula graminis]
          Length = 565

 Score = 42.9 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 28/147 (19%), Positives = 56/147 (38%), Gaps = 23/147 (15%)

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   + +PV  K    +  +  +    + + +  K+  + +     K  +  + P   
Sbjct: 343 KAIFVTVDVPVLGKRERDLKLKARSQNYEHPIAAQWKAAGSKVEETIAKRGVSDI-PDTA 401

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKILPSVDGVMI----------G 216
               NL++D +  IK+  P + I +   G +ED+  A +     DGV++           
Sbjct: 402 HIDANLNWDDIAWIKERAPGVPIVIKGVGCVEDVELAKQY--GADGVVLSTHGARQLDGA 459

Query: 217 RAAY--------KNSAMLTTVDEYFSN 235
           RA          KN A+L  ++ Y   
Sbjct: 460 RAPLDVLIEVRRKNPALLKEIEVYVDG 486


>gi|145237054|ref|XP_001391174.1| NADH-dependent flavin oxidoreductase [Aspergillus niger CBS 513.88]
 gi|134075640|emb|CAK96532.1| unnamed protein product [Aspergillus niger]
          Length = 422

 Score = 42.9 bits (100), Expect = 0.072,   Method: Composition-based stats.
 Identities = 30/221 (13%), Positives = 69/221 (31%), Gaps = 36/221 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             A K   + G + I ++            P+A      +G        +  +       
Sbjct: 199 AAAVKRALEVGVDFIEIHGAHGYLISSFLSPAANNRTDEYGGSFENRIRLPLEIAQITRD 258

Query: 114 AL--SIPVTVKC-------RIGVDDQIPAVALRNLVKSIKKSGVNGIW------IHARKA 158
            +  ++PV ++            +            K++   G   +       +HA + 
Sbjct: 259 IVGPNVPVFLRVSASDWLEETLPEQSWGTEDTVKFAKALADQGAIDLIDISTGGVHAAQK 318

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMI 215
           +  G         P         +K+   D L +   G + +  QA  +L    +D  ++
Sbjct: 319 VKSG---------PLFQAPFAVAVKQAVGDKLLVSAVGAITNGRQANDLLEKEGLDVALV 369

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
           GR   K+  +  T  ++    ++ +S I+    +   R+  
Sbjct: 370 GRGFQKDPGLTWTFAQHLDTEISMASQIRWGFTRRGGREYI 410


>gi|110589134|gb|ABG77076.1| dihydroorotate dehydrogenase [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 104

 Score = 42.9 bits (100), Expect = 0.072,   Method: Composition-based stats.
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 4/74 (5%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
            E      + G+ + +  E  +  +D   + I +N+ CP    +    G     +P +  
Sbjct: 32  DETRFIANVSGSSVEEYYEVTRRFDDSPIDAIEINISCP----NVKEGGVAFGNDPAMSA 87

Query: 106 DCIAAMCKALSIPV 119
             + A  KA + P+
Sbjct: 88  RVVEACRKATNKPL 101


>gi|294787405|ref|ZP_06752658.1| oxidoreductase, FAD/FMN-binding [Parascardovia denticolens F0305]
 gi|315227026|ref|ZP_07868813.1| xenobiotic reductase A [Parascardovia denticolens DSM 10105]
 gi|294484761|gb|EFG32396.1| oxidoreductase, FAD/FMN-binding [Parascardovia denticolens F0305]
 gi|315119476|gb|EFT82609.1| xenobiotic reductase A [Parascardovia denticolens DSM 10105]
          Length = 410

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 34/159 (21%), Positives = 60/159 (37%), Gaps = 12/159 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGV 148
           +G   +       +   A+       +PV V+       D          L K++K+ G+
Sbjct: 247 YGGPFINRIRFALEVAEAVRGVWPDDLPVIVRLSATDWADGGWDVYQSVELGKALKERGI 306

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I + +   +L G+S       PN       EI+ +  ++ +   G +    QA KIL 
Sbjct: 307 DLIDVSSG-GMLSGVSIPAG---PNYQVPFAQEIRSKV-EIPVTTVGLITKPKQAEKILA 361

Query: 209 S--VDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIK 244
               D V IGRAA ++    L   D+   +      P +
Sbjct: 362 EGRADVVEIGRAALRDPYWPLRAADKLGLDRYQAPYPPQ 400


>gi|229524005|ref|ZP_04413410.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae bv. albensis
           VL426]
 gi|229337586|gb|EEO02603.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae bv. albensis
           VL426]
          Length = 666

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|169626359|ref|XP_001806580.1| hypothetical protein SNOG_16466 [Phaeosphaeria nodorum SN15]
 gi|111055044|gb|EAT76164.1| hypothetical protein SNOG_16466 [Phaeosphaeria nodorum SN15]
          Length = 449

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 29/185 (15%), Positives = 58/185 (31%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+ +E  GY+ I L             PS       +G  L     ++ +    
Sbjct: 175 EGFAHAAEYLEKAGYDGIQLHGAHGYLLAQFLSPSTNKRTDKYGGSLENRARLITEIGQE 234

Query: 111 MCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AILKGLS 164
           + K  S    +  +       D          L K ++ +  + + +       +  G  
Sbjct: 235 VRKRTSSNFILAIKLNSVEFQDKGFDTQEAVTLCKLLEDNTFDFVELSGGTYEQLAFGHK 294

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
            +  +K      +   +I          + GGL+  S  +  L +VDGV + R   +   
Sbjct: 295 RESTKKREAFFIEFAEKITPSLSKTRTYVTGGLKTASAMVDALQTVDGVGLARPVCQEPE 354

Query: 225 MLTTV 229
           +   +
Sbjct: 355 LPRQI 359


>gi|317500818|ref|ZP_07959031.1| NADH:flavin oxidoreductase/NADH oxidase [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331089706|ref|ZP_08338603.1| hypothetical protein HMPREF1025_02186 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316897785|gb|EFV19843.1| NADH:flavin oxidoreductase/NADH oxidase [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330404287|gb|EGG83833.1| hypothetical protein HMPREF1025_02186 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 639

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 70/182 (38%), Gaps = 27/182 (14%)

Query: 64  EAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAAMCKA 114
           +AA    + GY+ +  ++     P + +  G       +G           + I  + K 
Sbjct: 146 KAAARAVEAGYDCLEFHLAHNYLPHSFLSAGFNHREDEYGGSFENRCRFPLEVIDEIRKN 205

Query: 115 L--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +   +P+ ++     D     + + +     K  K+ GV+ + +     I    +     
Sbjct: 206 MPEGMPLFIRIDAQDDMLENGLTIEDVIRFCKIAKEHGVDVLDVSRGNII----TAASMY 261

Query: 170 KIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++P +D       D    I+KE   L +G+ G +   + A +I+    VD V++GRA   
Sbjct: 262 EVPPIDVPNGFNIDNAARIRKETGMLTVGV-GRINTAALAEEIISQDKVDMVVMGRAQLA 320

Query: 222 NS 223
           + 
Sbjct: 321 DP 322


>gi|253689092|ref|YP_003018282.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251755670|gb|ACT13746.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 362

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 63/183 (34%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AA+   D G+  + L+       + +             +G         + + +
Sbjct: 158 DDFVAAARRALDAGFEWLELHFA--HGYLAQSFFSVHSNKRNDQYGGSFDNRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
           AA+       +P+T +  +   D      L+    L +  K +G++ + +      +   
Sbjct: 216 AAVRDVWPQHLPLTARFGVIEFDGCDEETLQESIELTRRFKAAGLDMLSV-----SIGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           +P+ N          + +  +E  DL +    G      A + +    +D VM+G+A   
Sbjct: 271 TPEANIPWAPAFMGPIAKQVREQADLPVSSAWGFGTPELAEQAVASGQLDLVMVGKAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|229515372|ref|ZP_04404832.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae TMA 21]
 gi|229348077|gb|EEO13036.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae TMA 21]
          Length = 666

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|213609803|ref|ZP_03369629.1| tRNA-dihydrouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
          Length = 113

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 8/87 (9%)

Query: 1   MVDWTDRHYRFFARLLTNNALLYTEMI-VADAIL-----RGDKKNILG--FSTQEKPLAL 52
           M    D   R     + +  L  TE + V D +L           +L    +    P+ +
Sbjct: 27  MEGVLDALVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELLHASRTPSGTPVRI 86

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINL 79
           Q+ G     L E A      G   ++L
Sbjct: 87  QLLGQHPQWLAENAARATALGSYGVDL 113


>gi|154502716|ref|ZP_02039776.1| hypothetical protein RUMGNA_00529 [Ruminococcus gnavus ATCC 29149]
 gi|153796599|gb|EDN79019.1| hypothetical protein RUMGNA_00529 [Ruminococcus gnavus ATCC 29149]
          Length = 639

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 69/182 (37%), Gaps = 27/182 (14%)

Query: 64  EAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAAMCKA 114
           +AA    + GY+ +  ++     P + +  G       +G           + I  + + 
Sbjct: 146 KAAARAVEAGYDCLEFHLAHNYLPHSFLSAGFNHREDEYGGSFENRCRFPLEVIDELRRN 205

Query: 115 L--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +   +P+ ++     D     + +       KS K+ GV+ + +     I    +     
Sbjct: 206 MPEGMPLFIRIDAQDDMLENGLTIEEVIRFCKSAKEHGVDVLDVSRGNII----TAASMY 261

Query: 170 KIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++P +D       +    I+KE   L +G+ G +     A +IL    VD V++GRA   
Sbjct: 262 EVPPIDVPNGFNIENAARIRKETGMLTVGV-GRINTAELAEEILSQDKVDMVVLGRAQLA 320

Query: 222 NS 223
           + 
Sbjct: 321 DP 322


>gi|170735630|ref|YP_001776890.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia cenocepacia
           MC0-3]
 gi|169817818|gb|ACA92400.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia cenocepacia
           MC0-3]
          Length = 369

 Score = 42.9 bits (100), Expect = 0.073,   Method: Composition-based stats.
 Identities = 22/128 (17%), Positives = 49/128 (38%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + D +AA+ K     +P+T +  +   D      L     L + +K+ G++ + +     
Sbjct: 211 LVDTLAAVRKVWPEHLPLTARLGVIEYDGRDEETLAESIALTQRMKREGLDMLSV----- 265

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
            +   +P             + E  +    L +    G++    A +++    +D VM+G
Sbjct: 266 SVGFSTPTAQIPWGPAFLAPIAERVRREAGLPVSSAWGIDTPQLANRVVEQGQLDLVMVG 325

Query: 217 RAAYKNSA 224
           RA   +  
Sbjct: 326 RAHLADPH 333


>gi|313772690|gb|EFS38656.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL074PA1]
 gi|313803390|gb|EFS44572.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL110PA2]
 gi|313811171|gb|EFS48885.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL083PA1]
 gi|313832172|gb|EFS69886.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL007PA1]
 gi|313834335|gb|EFS72049.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL056PA1]
 gi|313839446|gb|EFS77160.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL086PA1]
 gi|314964100|gb|EFT08200.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL082PA1]
 gi|314974432|gb|EFT18527.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL053PA1]
 gi|314977379|gb|EFT21474.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL045PA1]
 gi|314985428|gb|EFT29520.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL005PA1]
 gi|315078794|gb|EFT50816.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL053PA2]
 gi|315081731|gb|EFT53707.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL078PA1]
 gi|315097263|gb|EFT69239.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL038PA1]
 gi|327331222|gb|EGE72961.1| dihydroorotate oxidase [Propionibacterium acnes HL096PA2]
 gi|327447405|gb|EGE94059.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL043PA1]
 gi|327450410|gb|EGE97064.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL043PA2]
 gi|327457235|gb|EGF03890.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL092PA1]
 gi|328759536|gb|EGF73142.1| dihydroorotate oxidase [Propionibacterium acnes HL099PA1]
          Length = 327

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 61/180 (33%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E+ G   I  N+      +  G          D   +
Sbjct: 95  DIPVIASLNGATNGGWVDTAKRMENAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 150 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 201

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVM 214
           +  ++    +             +  +        +  + G+E        +L   D VM
Sbjct: 202 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESANDVVKYLLAGADVVM 260


>gi|301065016|ref|ZP_07205361.1| putative NADH oxidase [delta proteobacterium NaphS2]
 gi|300440865|gb|EFK05285.1| putative NADH oxidase [delta proteobacterium NaphS2]
          Length = 647

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 63/182 (34%), Gaps = 19/182 (10%)

Query: 64  EAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAAMCKA 114
            AA      G++ I ++           S   ++    +G  L   P  +      +   
Sbjct: 156 AAALRARMAGFDAIEIHGHASYILGQFMSPFTNKRTDKYG-ELWQLPVEILQMTKQI-AG 213

Query: 115 LSIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK-- 170
              PV  +      ++          + K ++++GV+ I +       +  +        
Sbjct: 214 PDFPVIFRISGDEFLEGGRDLDGSIEICKRMEEAGVDAIDVSGGTYYFQPQTNVVFPYMT 273

Query: 171 IPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
           +P   Y D  +EIKK   ++ I + G L D   A ++L     D + IGR    +  +  
Sbjct: 274 LPRGIYVDQAWEIKKAV-NVPIIVPGRLSDPVDAERVLSEGKADFIGIGRGLIADPELPN 332

Query: 228 TV 229
            V
Sbjct: 333 KV 334


>gi|257469163|ref|ZP_05633257.1| hypothetical protein FulcA4_07445 [Fusobacterium ulcerans ATCC
           49185]
 gi|317063410|ref|ZP_07927895.1| 2-nitropropane dioxygenase [Fusobacterium ulcerans ATCC 49185]
 gi|313689086|gb|EFS25921.1| 2-nitropropane dioxygenase [Fusobacterium ulcerans ATCC 49185]
          Length = 312

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 9/87 (10%)

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           IP V+   L K  +K G + I +    A     + KD+       +DIV EI  EN  + 
Sbjct: 116 IPVVSSLKLAKISQKLGADAIVVEGGNAGGHLGTEKDS-------WDIVGEIA-ENISIP 167

Query: 191 IGLNGGLEDMSQALKILP-SVDGVMIG 216
           +   GG+     A ++L    DGV +G
Sbjct: 168 VFGAGGVITPEDAERMLALGADGVQMG 194


>gi|315497844|ref|YP_004086648.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Asticcacaulis excentricus CB 48]
 gi|315415856|gb|ADU12497.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Asticcacaulis excentricus CB 48]
          Length = 273

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 11/95 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++    +  G + + ++   A  +G +         +DY+ V +I +   D+   + GG+
Sbjct: 34  DMALRYRDEGADELVLYDITASAEGRT---------VDYNWVRDIARAL-DIPFCVAGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
               QA+K L    D V I   A +   ++  + E
Sbjct: 84  RSAEQAVKCLNSGADKVSINSPALERPDLINELAE 118


>gi|289424542|ref|ZP_06426325.1| dihydroorotate oxidase [Propionibacterium acnes SK187]
 gi|289427310|ref|ZP_06429023.1| dihydroorotate oxidase [Propionibacterium acnes J165]
 gi|295129726|ref|YP_003580389.1| dihydroorotate dehydrogenase [Propionibacterium acnes SK137]
 gi|289155239|gb|EFD03921.1| dihydroorotate oxidase [Propionibacterium acnes SK187]
 gi|289159240|gb|EFD07431.1| dihydroorotate oxidase [Propionibacterium acnes J165]
 gi|291377271|gb|ADE01126.1| dihydroorotate dehydrogenase [Propionibacterium acnes SK137]
 gi|313807032|gb|EFS45530.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL087PA2]
 gi|313814049|gb|EFS51763.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL025PA1]
 gi|313821357|gb|EFS59071.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL036PA1]
 gi|313824702|gb|EFS62416.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL036PA2]
 gi|313826366|gb|EFS64080.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL063PA1]
 gi|314926392|gb|EFS90223.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL036PA3]
 gi|314961509|gb|EFT05610.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL002PA2]
 gi|314980078|gb|EFT24172.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL072PA2]
 gi|314986932|gb|EFT31024.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL005PA2]
 gi|314990575|gb|EFT34666.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL005PA3]
 gi|315082953|gb|EFT54929.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL027PA2]
 gi|315086473|gb|EFT58449.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL002PA3]
 gi|315088187|gb|EFT60163.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL072PA1]
 gi|327333848|gb|EGE75565.1| dihydroorotate oxidase [Propionibacterium acnes HL096PA3]
 gi|327444683|gb|EGE91337.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL013PA2]
 gi|328758188|gb|EGF71804.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL020PA1]
          Length = 335

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 61/180 (33%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E+ G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMENAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVM 214
           +  ++    +             +  +        +  + G+E        +L   D VM
Sbjct: 210 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESANDVVKYLLAGADVVM 268


>gi|119960843|ref|YP_946887.1| oxidoreductase, FAD/FMN-binding family protein [Arthrobacter
           aurescens TC1]
 gi|119947702|gb|ABM06613.1| oxidoreductase, FAD/FMN-binding family protein [Arthrobacter
           aurescens TC1]
          Length = 356

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 40/231 (17%), Positives = 76/231 (32%), Gaps = 35/231 (15%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGA 95
           T E P  +Q       ++V A+    + G++ + L+            P++ V   S+G 
Sbjct: 143 TDELPGVIQ-------EIVTASTNAIEAGFDGVELHSANGYLLHEFLAPNSNVRTDSYGG 195

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                   V + + A+ +AL     V  RI  +  +  +A  +         V    I  
Sbjct: 196 SPENRARFVIETVNAVVEALGAN-RVGIRISPEHNVQGIAETDAADVRATYEVLVDTIAP 254

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG--GLEDMSQALKILPS--VD 211
                  +   D +        +V  +++     F+   G   +    +A  I+     D
Sbjct: 255 LNLAYLSILHHDPKSA------LVQGLRERFNGTFLVNTGFSEITTRDEAFAIIEDGLAD 308

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
            V++GR A  N  +     E          P+       F+   +   TDY
Sbjct: 309 AVVVGRPAIANPDLARRWRESL--------PLNEPDASTFYADGAEGYTDY 351


>gi|146313174|ref|YP_001178248.1| 2,4-dienoyl-CoA reductase [Enterobacter sp. 638]
 gi|145320050|gb|ABP62197.1| 2,4-dienoyl-CoA reductase [Enterobacter sp. 638]
          Length = 673

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 21/191 (10%), Positives = 55/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
            +    A +  + GY+ + +                 L+                     
Sbjct: 143 DEFARCAALAREAGYDGVEI-----------MGSEGYLINEFLAARTNQRDDEWGGEYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 192 RMRFAIEVVRAVRERVGTDFIIVFRLSMIDLVEGGGTFDETVQLAQAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K +     +  N  + D   A  +L + D  M
Sbjct: 250 GIGWHEARIPTIATAVPRAAFSWVTRKLKGKVSIPLVTTNR-INDPQVADDVLANGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|330890014|gb|EGH22675.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. mori str.
           301020]
          Length = 679

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTQVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    + +  + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVKVPLITTNRINTPEVAERILSEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|288962550|ref|YP_003452845.1| NADPH dehydrogenase [Azospirillum sp. B510]
 gi|288914816|dbj|BAI76301.1| NADPH dehydrogenase [Azospirillum sp. B510]
          Length = 371

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 26/137 (18%), Positives = 52/137 (37%), Gaps = 8/137 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +G  L      + + +AA+      ++P+T +  +   D      L   ++  +   V G
Sbjct: 200 YGGDLAGRSRFLLETLAAVRAVWPENLPLTARFGVIEYDGRDEETLAESIELTRNLRVGG 259

Query: 151 IWIHARKAILKGLSPKDNR-KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
           + +    ++  G S  D R          V E  +   +L +    G++    A + +  
Sbjct: 260 LDM---LSVSVGFSTPDARVPWGPAFLAPVAERVRREAELPVAAAWGIDAPRIADRTVAD 316

Query: 209 -SVDGVMIGRAAYKNSA 224
             +D VMIGRA   +  
Sbjct: 317 GQLDLVMIGRAHLADPH 333


>gi|172040637|ref|YP_001800351.1| putative oxidoreductase [Corynebacterium urealyticum DSM 7109]
 gi|171851941|emb|CAQ04917.1| putative oxidoreductase [Corynebacterium urealyticum DSM 7109]
          Length = 362

 Score = 42.9 bits (100), Expect = 0.074,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 61/186 (32%), Gaps = 16/186 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA+   D G + + +             PS+   E ++G        +  + + A
Sbjct: 153 DEFRQAARNAIDAGMDGVEIHGANGYLLQQFLSPSSNHREDAYGGTPENRYRLAQEILTA 212

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           + + +     V  R+     I  +   +        G  G+        L  +S      
Sbjct: 213 VAEEIGAD-RVALRLSPQHNIQGIEETDDADVRATYG--GLLRAVADLGLAYVSFLHAEP 269

Query: 171 IPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALKILPSVDGVMIGRAAYKNSAMLT 227
              L  ++  E  + N    + LN   G +   ++A  +    D V +GR A  N  ++ 
Sbjct: 270 TGELITELSAE-ARANGRTRVILNSGFGRVTQRAEAEDLARHGDAVAVGRLAISNPDLVR 328

Query: 228 TVDEYF 233
              E  
Sbjct: 329 RWQEKL 334


>gi|296242044|ref|YP_003649531.1| dihydroorotate dehydrogenase family protein [Thermosphaera
           aggregans DSM 11486]
 gi|296094628|gb|ADG90579.1| dihydroorotate dehydrogenase family protein [Thermosphaera
           aggregans DSM 11486]
          Length = 403

 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 56/180 (31%), Gaps = 34/180 (18%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G    +L      VE  G + I  +                +  +   V +   A+ +++
Sbjct: 134 GYKPEELALLGPKVEKAGADAIEFSTH-------------YIGKDYRPVVEAAKALRESV 180

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW------------IHARKAILKGL 163
           SIP+  K      +      + +LVK ++K  V+GI             +     I+ G 
Sbjct: 181 SIPIFAKLSPFTPN------IPDLVKDLEKVRVDGIVATNTIGPALNIDVETGMPIVGGP 234

Query: 164 SPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLED-MSQALKILPSVDGVMIGRAAY 220
                   P L    +  + +      L I   GG+   +      +     V I  AA 
Sbjct: 235 YGYGWMSGPALKPISLAVVAEAARSTKLPIIGVGGITRGVDVIEYFMAGASAVQICTAAL 294


>gi|326561701|gb|EGE12037.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis 46P47B1]
 gi|326562088|gb|EGE12416.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis 7169]
 gi|326566975|gb|EGE17107.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis BC1]
          Length = 716

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 60/175 (34%), Gaps = 21/175 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
                 AK+ +  GY+ + +              SAR ++   S+G  L        + +
Sbjct: 171 DDYAHTAKLAKKAGYDGVEIMGSEGYLINQFL--SARTNKRTDSYGGSLENRMRFAIEVV 228

Query: 109 AAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+ KA  +   +  R      V+D      +  L K+++ +GV+   I+      +   
Sbjct: 229 RAVRKAAGMDFIITFRLSMIELVEDGATMQDVITLAKALELAGVS--IINTGIGWHEARI 286

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           P     +P   +       K   ++ +     +     A +IL     D V + R
Sbjct: 287 PTIVTSVPRAAFTRYTAAVKHAINIPVIAANRINMPQTAEEILSSGQADLVQMAR 341


>gi|311068982|ref|YP_003973905.1| NADPH dehydrogenase NamA [Bacillus atrophaeus 1942]
 gi|310869499|gb|ADP32974.1| NADPH dehydrogenase NamA [Bacillus atrophaeus 1942]
          Length = 338

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 29/193 (15%), Positives = 63/193 (32%), Gaps = 19/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  +AA   ++ G++ I L+            P +      +G         + + I  +
Sbjct: 145 EFKQAAVRAKEAGFDIIELHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLRETIDEV 204

Query: 112 CKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P  V V         +         K +K+ GV+ I   +   +       D  
Sbjct: 205 KQVWDGPLFVRVSASDYTPKGLDIADHIGFAKWMKEQGVDLIDCSSGALV-----HADIN 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P        +I+++  D+  G  G + +   A +IL +   D + I R   ++     
Sbjct: 260 VFPGYQVSFADKIREQA-DIPTGAVGMITNGLAAEEILQNGRADLIFIARELLRDPFFAR 318

Query: 228 TVDEYFSNPLTGS 240
           T  +  +  +   
Sbjct: 319 TAAQQLNTNIPAP 331


>gi|284163400|ref|YP_003401679.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Haloterrigena turkmenica DSM 5511]
 gi|284013055|gb|ADB59006.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Haloterrigena turkmenica DSM 5511]
          Length = 244

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 11/96 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  +     G   + +       +G            + D + E+  E  D+   L GG+
Sbjct: 39  DAARRWLDEGAEALHLVDLDGAFEGQ---------RANGDAIDEVL-ETVDVPTQLGGGI 88

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
                A+ +L   VD V++G AA +N  ++  + E 
Sbjct: 89  RTADDAVDLLERGVDRVILGTAAVENPDIVAEISER 124


>gi|255318650|ref|ZP_05359881.1| NADPH dehydrogenase [Acinetobacter radioresistens SK82]
 gi|262379125|ref|ZP_06072281.1| NADH:flavin oxidoreductase [Acinetobacter radioresistens SH164]
 gi|255304332|gb|EET83518.1| NADPH dehydrogenase [Acinetobacter radioresistens SK82]
 gi|262298582|gb|EEY86495.1| NADH:flavin oxidoreductase [Acinetobacter radioresistens SH164]
          Length = 373

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 60/172 (34%), Gaps = 24/172 (13%)

Query: 70  EDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP 118
            + G++ I L+            P +      +G  L     +V +   A+  A+    P
Sbjct: 169 VEAGFDLIELHAAHGYLLHQFLSPLSNQRTDEYGGSLENRMRMVLEVFQAIRDAVPAGFP 228

Query: 119 VTVKCR-IGVDDQ---IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           V V+       D+           L K+++  G   I + +      GL      ++   
Sbjct: 229 VGVRLSATDWMDEQGGWNVECSAGLSKALQMLGAVYIHVSSG-----GLHEMQRIEVGP- 282

Query: 175 DYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           +Y +   E  K+   + +   G + +  QA +IL     D + + RA   + 
Sbjct: 283 NYQVPFAEKIKQRVSIPVIAVGLITEPEQAEEILQKGQADAIGLARAMLYDP 334


>gi|225570215|ref|ZP_03779240.1| hypothetical protein CLOHYLEM_06311 [Clostridium hylemonae DSM
           15053]
 gi|225161010|gb|EEG73629.1| hypothetical protein CLOHYLEM_06311 [Clostridium hylemonae DSM
           15053]
          Length = 687

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 25/148 (16%), Positives = 47/148 (31%), Gaps = 9/148 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNL 139
           P     +  +G         + + I    KAL     +  R   D+             L
Sbjct: 184 PVFNHRKDEYGGDFTNRCRFLLEIIDKCRKALGPKFPIMVRYSADEFVEGGRDLEESVTL 243

Query: 140 VKSIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            K ++K+GV+ I + A    A L    P    +   +       +++          G +
Sbjct: 244 AKVLEKNGVDAIDLSASQPSAYLMTTPPYCLPQAKGMLVPYSESVRRAVDIPVFTAIG-I 302

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNS 223
            D   A +I+     D + +GR    + 
Sbjct: 303 RDPEYAEQIIAEGKADLIALGRPQLADP 330


>gi|71000958|ref|XP_755160.1| FMN binding oxidoreductase [Aspergillus fumigatus Af293]
 gi|66852798|gb|EAL93122.1| FMN binding oxidoreductase, putative [Aspergillus fumigatus Af293]
          Length = 421

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 33/212 (15%), Positives = 72/212 (33%), Gaps = 24/212 (11%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN--------LNV 81
           D +L      +   + +E  +  Q       + V+ A+++ D G++ I         + +
Sbjct: 148 DGLLDRIISRLAFPAPRE--MTQQDIDTVTRQFVDTARLMADAGFSGIELHGAHGYLIGM 205

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
            C +  +   ++G         V D ++   K +     +  +    D   A     + +
Sbjct: 206 FCSATNLRTDAYGGSAEKRAKFVLDILSQTRKVVPATFCIGIKFNSADHSSASFEDTMTQ 265

Query: 142 S--IKKSGVNGIWIHARK--------AILKGLSPKDNRKIPNLDY--DIVYEIKKENPDL 189
              +  +G++ + +               +    K  R +    +  +   E +K  P L
Sbjct: 266 IGLLVDAGIDFLEVSGGSYEDPKMMGTNSQPQPEKSQRTLAREAFFLEFARETRKRFPTL 325

Query: 190 FIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            + L GG    + A   L     D + IGR A
Sbjct: 326 ILMLTGGFRSRAGAEHALRENACDLIGIGRPA 357


>gi|50842485|ref|YP_055712.1| dihydroorotate dehydrogenase B, catalytic subunit
           [Propionibacterium acnes KPA171202]
 gi|289425271|ref|ZP_06427048.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes SK187]
 gi|81826455|sp|Q6A912|PYRD_PROAC RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|50840087|gb|AAT82754.1| dihydroorotate dehydrogenase B, catalytic subunit
           [Propionibacterium acnes KPA171202]
 gi|289154249|gb|EFD02937.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes SK187]
 gi|313764488|gb|EFS35852.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL013PA1]
 gi|313792176|gb|EFS40277.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL110PA1]
 gi|313812975|gb|EFS50689.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL025PA1]
 gi|313816027|gb|EFS53741.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL059PA1]
 gi|313827743|gb|EFS65457.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL063PA2]
 gi|313838699|gb|EFS76413.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL086PA1]
 gi|314915481|gb|EFS79312.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL005PA4]
 gi|314918235|gb|EFS82066.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL050PA1]
 gi|314920048|gb|EFS83879.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL050PA3]
 gi|314932062|gb|EFS95893.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL067PA1]
 gi|314955933|gb|EFT00333.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL027PA1]
 gi|314958138|gb|EFT02241.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL002PA1]
 gi|314967799|gb|EFT11898.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL037PA1]
 gi|315098503|gb|EFT70479.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL059PA2]
 gi|315101140|gb|EFT73116.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL046PA1]
 gi|315105416|gb|EFT77392.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL030PA1]
 gi|315108360|gb|EFT80336.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL030PA2]
 gi|327330223|gb|EGE71972.1| dihydroorotate oxidase [Propionibacterium acnes HL097PA1]
 gi|327450815|gb|EGE97469.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL087PA3]
 gi|327453107|gb|EGE99761.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL092PA1]
 gi|327453839|gb|EGF00494.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL083PA2]
 gi|328754235|gb|EGF67851.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL087PA1]
 gi|328754515|gb|EGF68131.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL025PA2]
          Length = 307

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 66/197 (33%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G +G+ +      
Sbjct: 145 NVTAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARATADAGADGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
                      I           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAVRMIDAVTR-VVDIPVIGMGGVMTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|327484529|gb|AEA78936.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae LMA3894-4]
          Length = 666

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|229521905|ref|ZP_04411322.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae TM 11079-80]
 gi|229340830|gb|EEO05835.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae TM 11079-80]
          Length = 666

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|217966854|ref|YP_002352360.1| dihydroorotate dehydrogenase [Dictyoglomus turgidum DSM 6724]
 gi|217335953|gb|ACK41746.1| dihydroorotate dehydrogenase [Dictyoglomus turgidum DSM 6724]
          Length = 390

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           K+ E+ G   + LNV CP A +             + +      + + + IP+ VK  + 
Sbjct: 121 KMAEEVGAPALELNVSCPHASISFRGQDVD-----ETILHVARIVRENVKIPIVVKLPMQ 175

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +           + K+++  GV+G+ +  R
Sbjct: 176 LSSP------LAVAKALENIGVDGVVMFNR 199


>gi|84387914|ref|ZP_00990928.1| putative NADH-dependent flavin oxidoreductase [Vibrio splendidus
           12B01]
 gi|84377260|gb|EAP94129.1| putative NADH-dependent flavin oxidoreductase [Vibrio splendidus
           12B01]
          Length = 351

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 37/227 (16%), Positives = 79/227 (34%), Gaps = 23/227 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A+   +  G++ + ++            P     E  +G  L      + +   A
Sbjct: 126 DAFAQASLRAQKSGFDGVEIHAAHTYLINQFLSPYYNQREDEYGGSLENRMRFLLEIYTA 185

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
             K +    P+ VK       +  +     R + K +++ GV+GI     IH +   + G
Sbjct: 186 TRKLVGDDFPILVKLTASEFFEGGVTFDETRIVCKKLEQVGVDGIVVSGNIHGKADTMIG 245

Query: 163 LSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRA 218
            S  D   I    Y  +  + I ++  ++ +   GGL D    +A+     ++   + R 
Sbjct: 246 ES-HDGFTIQAEGYFHEYGHAISQDV-NIPVITVGGLTDFDAIEAIANNTGIEYFALSRP 303

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
                 ++    E   +P+      K R  +  +  ++       AR
Sbjct: 304 LLSEPHLVKRWKEGDRSPVECERCSKCRTKRGNFCVVNKDRKAQLAR 350


>gi|15641995|ref|NP_231627.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121730091|ref|ZP_01682495.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae V52]
 gi|153823322|ref|ZP_01975989.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae B33]
 gi|153829840|ref|ZP_01982507.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae 623-39]
 gi|227082120|ref|YP_002810671.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae M66-2]
 gi|229507918|ref|ZP_04397423.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae BX 330286]
 gi|229511847|ref|ZP_04401326.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae B33]
 gi|229518983|ref|ZP_04408426.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae RC9]
 gi|229607463|ref|YP_002878111.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio cholerae MJ-1236]
 gi|255745258|ref|ZP_05419207.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholera CIRS 101]
 gi|262155983|ref|ZP_06029103.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae INDRE 91/1]
 gi|262167943|ref|ZP_06035643.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae RC27]
 gi|9656535|gb|AAF95141.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae O1 biovar El Tor str.
           N16961]
 gi|121628162|gb|EAX60691.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae V52]
 gi|126519156|gb|EAZ76379.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae B33]
 gi|148874699|gb|EDL72834.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae 623-39]
 gi|227010008|gb|ACP06220.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae M66-2]
 gi|227013890|gb|ACP10100.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae O395]
 gi|229343672|gb|EEO08647.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae RC9]
 gi|229351812|gb|EEO16753.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae B33]
 gi|229355423|gb|EEO20344.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae BX 330286]
 gi|229370118|gb|ACQ60541.1| 2,4-dienoyl-CoA reductase (NADPH) [Vibrio cholerae MJ-1236]
 gi|255737088|gb|EET92484.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholera CIRS 101]
 gi|262023670|gb|EEY42371.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae RC27]
 gi|262030161|gb|EEY48805.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae INDRE 91/1]
          Length = 666

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|332674562|gb|AEE71378.1| dihydroorotate dehydrogenase [Propionibacterium acnes 266]
          Length = 335

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 61/180 (33%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E+ G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMENAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVM 214
           +  ++    +             +  +        +  + G+E        +L   D VM
Sbjct: 210 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESANDVVKYLLAGADVVM 268


>gi|147669781|ref|YP_001214599.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Dehalococcoides sp.
           BAV1]
 gi|146270729|gb|ABQ17721.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Dehalococcoides sp.
           BAV1]
          Length = 258

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++++++ EI      + + + GG+  M    K+L   VD V++G AA +N  ++  +   
Sbjct: 82  VNFELIKEIANSAL-IPVEVGGGIRSMETVKKLLVAGVDRVILGTAAVENPELVKEICAR 140

Query: 233 FSN 235
           +++
Sbjct: 141 YAD 143


>gi|153217082|ref|ZP_01950846.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae 1587]
 gi|124113884|gb|EAY32704.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae 1587]
          Length = 684

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 214 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 271

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 272 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 329


>gi|111221342|ref|YP_712136.1| putative dihydroorotate dehydrogenase A [Frankia alni ACN14a]
 gi|111148874|emb|CAJ60552.1| putative Dihydroorotate dehydrogenase A (Dihydroorotate oxidase A)
           (DHOdehase A) (DHODase A) (DHOD A) [Frankia alni ACN14a]
          Length = 318

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 13/99 (13%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML-N 100
                 KPL + + G D+ +  E A++V D G + + LN+ CP   V +G     +   +
Sbjct: 86  RAHEAGKPLIVSVAGFDVGEYQEIAEVVADAGVDLVELNLACP--NVWDGGAQKRIACFD 143

Query: 101 PDIVGDCIAAMCKAL----------SIPVTVKCRIGVDD 129
           P        A+  AL           +P  VK     D 
Sbjct: 144 PGQTAAICTAVGDALLARAGGDQAGRVPYGVKISPFSDP 182


>gi|310779428|ref|YP_003967761.1| NADH:flavin oxidoreductase/NADH oxidase [Ilyobacter polytropus DSM
           2926]
 gi|309748751|gb|ADO83413.1| NADH:flavin oxidoreductase/NADH oxidase [Ilyobacter polytropus DSM
           2926]
          Length = 649

 Score = 42.5 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 19/142 (13%), Positives = 49/142 (34%), Gaps = 5/142 (3%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVN 149
           +G  L      + + + ++  A+     ++ R+   +             +  + +S ++
Sbjct: 197 YGGSLENRVRFLQEVLDSVRNAVGYGFPIELRMSGSELFEGGYTLEDGIEIAKLVESKID 256

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
            + + A            +  IP+     +    K++  + +   GGL D     +I+  
Sbjct: 257 LLHVSAGTYQRGFGITHPSMFIPHGANVYLAAEIKKHVSVPVATIGGLNDPEMMEEIIAS 316

Query: 209 -SVDGVMIGRAAYKNSAMLTTV 229
              D V + RA   +  +   V
Sbjct: 317 GKADVVEMARALLADPELPKKV 338


>gi|229166928|ref|ZP_04294675.1| NADPH dehydrogenase [Bacillus cereus AH621]
 gi|228616556|gb|EEK73634.1| NADPH dehydrogenase [Bacillus cereus AH621]
          Length = 345

 Score = 42.5 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I A+ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDAVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ D+  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHVDIATGAVGLITTGSQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|296113738|ref|YP_003627676.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis RH4]
 gi|295921432|gb|ADG61783.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis RH4]
 gi|326563345|gb|EGE13611.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis 103P14B1]
 gi|326572949|gb|EGE22928.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis CO72]
 gi|326573762|gb|EGE23719.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis 101P30B1]
 gi|326574555|gb|EGE24495.1| 2,4-dienoyl-CoA reductase FadH [Moraxella catarrhalis O35E]
          Length = 716

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 60/175 (34%), Gaps = 21/175 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
                 AK+ +  GY+ + +              SAR ++   S+G  L        + +
Sbjct: 171 DDYAHTAKLAKKAGYDGVEIMGSEGYLINQFL--SARTNKRTDSYGGSLENRMRFAIEVV 228

Query: 109 AAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+ KA  +   +  R      V+D      +  L K+++ +GV+   I+      +   
Sbjct: 229 RAVRKAAGMDFIITFRLSMIELVEDGATMQDVITLAKALELAGVS--IINTGIGWHEARI 286

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           P     +P   +       K   ++ +     +     A +IL     D V + R
Sbjct: 287 PTIVTSVPRAAFTRYTAAVKHAINIPVIAANRINMPQTAEEILSSGQADLVQMAR 341


>gi|255037990|ref|YP_003088611.1| geranylgeranylglyceryl phosphate synthase-like protein [Dyadobacter
           fermentans DSM 18053]
 gi|254950746|gb|ACT95446.1| geranylgeranylglyceryl phosphate synthase [Dyadobacter fermentans
           DSM 18053]
          Length = 257

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTV 229
            +  + +  + +   D  I + GG++   +A   L    D +++G     N  +L  V
Sbjct: 187 PVPAETIAAV-RGTVDTPIIVGGGIDSYEKADNALRAGADVIVVGNGIEANPELLPEV 243


>gi|262189640|ref|ZP_06048024.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae CT 5369-93]
 gi|262034476|gb|EEY52832.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio cholerae CT 5369-93]
          Length = 489

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 19  EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 76

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 77  ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 134


>gi|197337489|ref|YP_002157706.1| NADH-dependent flavin oxidoreductase [Vibrio fischeri MJ11]
 gi|197314741|gb|ACH64190.1| NADH-dependent flavin oxidoreductase [Vibrio fischeri MJ11]
          Length = 370

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 32/224 (14%), Positives = 73/224 (32%), Gaps = 19/224 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A++  ++ G++ + ++            P     E  +G  L      + +  A 
Sbjct: 145 DAFAKASRRAKESGFDGVEIHAAHTYLINQFLSPYYNRREDEYGGSLDNRMRFLLEIYAE 204

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
           + K +    P+ VK       +  +     R + K +++ GV+GI     IH   + L G
Sbjct: 205 IKKQVGDDYPILVKLTASEFFEGGLTFDETRIICKKLEEIGVDGIIISGNIHGNASTLVG 264

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD--GVMIGRAAY 220
            S           +     +  ++ ++ +   GGL D++   KI    +     + R   
Sbjct: 265 ESFDGYTLQEEGYFHEYGNVISQDVNVPVITVGGLNDINAIEKIAEETNIQYFALSRPLL 324

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
               ++    E     +      K R  +  +  +         
Sbjct: 325 AEPQLIKRWKEGNRAEVDCERCSKCRTKRGNFCVVYKKRKPKKE 368


>gi|228997140|ref|ZP_04156766.1| NADPH dehydrogenase [Bacillus mycoides Rock3-17]
 gi|229004798|ref|ZP_04162530.1| NADPH dehydrogenase [Bacillus mycoides Rock1-4]
 gi|228756461|gb|EEM05774.1| NADPH dehydrogenase [Bacillus mycoides Rock1-4]
 gi|228762603|gb|EEM11524.1| NADPH dehydrogenase [Bacillus mycoides Rock3-17]
          Length = 346

 Score = 42.5 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 65/201 (32%), Gaps = 19/201 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDI 103
           Q+    IS   +AA   +  G++ I L+            P +      +G         
Sbjct: 137 QLIKKTISAFQDAACRSKQAGFDIIELHAAHGYLINEFLSPLSNKRTDEYGGSPENRYRF 196

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I A+ +  + P+ V+        + +         K +K+ GV+ I   +   I  
Sbjct: 197 LKEIIDAVNEVWNGPLFVRISANDYHPEGLTVHDYVQFAKWMKEQGVDVIDCSSGAVI-- 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P      P    +    IK +   +  G  G +    QA +IL     D + IGR  
Sbjct: 255 ---PAQIDVYPGYQVEYANHIKGQA-HIATGAVGLITSGIQAEEILANNEADLIFIGREL 310

Query: 220 YKNSAMLTTVDEYFSNPLTGS 240
            +N     T        L   
Sbjct: 311 LRNPYFPRTAANELGFELQEP 331


>gi|121591502|ref|ZP_01678770.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae 2740-80]
 gi|147675393|ref|YP_001217519.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae O395]
 gi|153820009|ref|ZP_01972676.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae NCTC 8457]
 gi|254849079|ref|ZP_05238429.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MO10]
 gi|298497975|ref|ZP_07007782.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MAK 757]
 gi|121546643|gb|EAX56830.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae 2740-80]
 gi|126509445|gb|EAZ72039.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae NCTC 8457]
 gi|146317276|gb|ABQ21815.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae O395]
 gi|254844784|gb|EET23198.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MO10]
 gi|297542308|gb|EFH78358.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MAK 757]
          Length = 684

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+     V+       +  L K+++++GV    I+      +
Sbjct: 214 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 271

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 272 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 329


>gi|254226824|ref|ZP_04920396.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae V51]
 gi|125620671|gb|EAZ49033.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae V51]
          Length = 593

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 123 EIVKAIREAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 180

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 181 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 238


>gi|325921661|ref|ZP_08183496.1| imidazole glycerol phosphate synthase subunit hisF [Xanthomonas
           gardneri ATCC 19865]
 gi|325547850|gb|EGD18869.1| imidazole glycerol phosphate synthase subunit hisF [Xanthomonas
           gardneri ATCC 19865]
          Length = 258

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIRDVDTARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGVDSIREEDGEWR 140


>gi|293394275|ref|ZP_06638575.1| 2,4-dienoyl-CoA reductase [Serratia odorifera DSM 4582]
 gi|291423253|gb|EFE96482.1| 2,4-dienoyl-CoA reductase [Serratia odorifera DSM 4582]
          Length = 677

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 63/188 (33%), Gaps = 27/188 (14%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEIN--------LNVGCPSARVHEGSF-----GAC 96
           L+ Q     I+     A + +  GY+ +         +N       V   +      G  
Sbjct: 137 LSHQQIEDTIADFAHCAALAQQAGYDGVEVMGSEGYLIN----QFLVARTNQRDDQWGGS 192

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIW 152
                    + + A+ +A+     V  R+     V+D      +  L ++I+++G   I 
Sbjct: 193 AENRMRFAVEIVRAVRQAVGREFIVIYRLSMLDLVEDGSSWQEIERLAQAIEQAGATLI- 251

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            +      +   P     +P   +  V +++  +     I  N  + D + A + L    
Sbjct: 252 -NTGIGWHEARIPTIATMVPRAGFSWVTHKLMGKVGIPLITTNR-INDPAVAEQTLAQGC 309

Query: 210 VDGVMIGR 217
            D V + R
Sbjct: 310 ADMVSMAR 317


>gi|225868930|ref|YP_002744878.1| dihydroorotate dehydrogenase [Streptococcus equi subsp.
           zooepidemicus]
 gi|259547559|sp|C0MCW6|PYRD_STRS7 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|225702206|emb|CAW99934.1| putative dihydroorotate dehydrogenase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 311

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 76/229 (33%), Gaps = 37/229 (16%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLN 80
           + TEM    A       +++G S +E              +++A   ++   Y   + LN
Sbjct: 84  IVTEMQKDQASKHHFL-SVVGMSAEET-----------ETILKA---IQASDYQGLVELN 128

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN 138
           + CP   V        L  + +     +  +    + P+ +K     D      A A+ N
Sbjct: 129 LSCP--NVPGK---PQLAYDFEATDQLLKKIFSYYTKPLGIKLPPYFDIVHFDQAAAIFN 183

Query: 139 -----LVKSIKKSGVNGIW-----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
                 V  +   G   +      +   K+   G+     +     +    Y+  + NP 
Sbjct: 184 QYPLAFVNCVNSIGNGLVIDDEQVVIKPKSGFGGIGGDYIKPTALANVHAFYQ--RLNPS 241

Query: 189 LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
           + I   GG++    A +  L     V IG A   +  A+   + +   +
Sbjct: 242 IQIIGTGGVKTGRDAFEHILCGAAMVQIGTALHQEGPAIFKRITKELQD 290


>gi|238488825|ref|XP_002375650.1| FMN binding oxidoreductase, putative [Aspergillus flavus NRRL3357]
 gi|220698038|gb|EED54378.1| FMN binding oxidoreductase, putative [Aspergillus flavus NRRL3357]
          Length = 417

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 28/188 (14%), Positives = 58/188 (30%), Gaps = 25/188 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V +A+ + + G+  + L+            P + +    +G        IV + I   
Sbjct: 168 QFVNSARFLAECGFAGVELHAAHGYLLSQFLSPKSNIRHDKYGGSPEARARIVLEIIKET 227

Query: 112 CKALSIPVTVKCRIGVDDQIPAVA--LRNLVKSIKKSGVNGIWIHARK---AILKGLSPK 166
              +     +  ++   D   +        +    +SG++ + +         + G   K
Sbjct: 228 RAVVPENFCIGLKLNSADHSASDFEDTMKQIGLFAESGIDFLEVSGGTYEDPTMMGRGLK 287

Query: 167 DNRKIPNLD---------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
           +      +          +D   E ++  P L + L GG          L     D V I
Sbjct: 288 EEIASETVQRTAAREAFFFDFAKETRRRFPGLILMLTGGFRSRQGIQAALKGGACDIVGI 347

Query: 216 GRAAYKNS 223
           GR A    
Sbjct: 348 GRPAVVCP 355


>gi|317136948|ref|XP_001727395.2| FMN binding oxidoreductase [Aspergillus oryzae RIB40]
          Length = 417

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 28/188 (14%), Positives = 58/188 (30%), Gaps = 25/188 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V +A+ + + G+  + L+            P + +    +G        IV + I   
Sbjct: 168 QFVNSARFLAECGFAGVELHAAHGYLLSQFLSPKSNIRHDKYGGSPEARARIVLEIIKET 227

Query: 112 CKALSIPVTVKCRIGVDDQIPAVA--LRNLVKSIKKSGVNGIWIHARK---AILKGLSPK 166
              +     +  ++   D   +        +    +SG++ + +         + G   K
Sbjct: 228 RAVVPENFCIGLKLNSADHSASDFEDTMKQIGLFAESGIDFLEVSGGTYEDPTMMGRGLK 287

Query: 167 DNRKIPNLD---------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
           +      +          +D   E ++  P L + L GG          L     D V I
Sbjct: 288 EEIASETVQRTAAREAFFFDFAKETRRRFPGLILMLTGGFRSRQGIQAALKGGACDIVGI 347

Query: 216 GRAAYKNS 223
           GR A    
Sbjct: 348 GRPAVVCP 355


>gi|258651938|ref|YP_003201094.1| NADH:flavin oxidoreductase/NADH oxidase [Nakamurella multipartita
           DSM 44233]
 gi|258555163|gb|ACV78105.1| NADH:flavin oxidoreductase/NADH oxidase [Nakamurella multipartita
           DSM 44233]
          Length = 359

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 32/196 (16%), Positives = 62/196 (31%), Gaps = 21/196 (10%)

Query: 73  GYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTV 121
           G++ + ++            P A      +G        ++   + A+  A     P+ V
Sbjct: 170 GFDVVEVHAAHGYLLHQFLSPLANTRTDQYGGSFDNRVRLLLAVVDAVRAAWPAGKPLLV 229

Query: 122 KCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           +      +D          L   +++ GV+ I   +      GL P     +        
Sbjct: 230 RISATDWIDGGWSVAESTELAGRLREHGVDLIDTSSG-----GLDPAQEIAVGPGYQVSF 284

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
               +    +  G  G + + +QA  IL     D V++ RAA +  A           P 
Sbjct: 285 ARDVRTKGAVATGAVGLITEPAQAQAILDEGSADVVLLARAALREPAWPLRAAHELGVP- 343

Query: 238 TGSSPIKTRVDKDFWR 253
              +P   +  +  WR
Sbjct: 344 RDEAPYPPQYVRGAWR 359


>gi|325273164|ref|ZP_08139458.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas sp. TJI-51]
 gi|324101702|gb|EGB99254.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas sp. TJI-51]
          Length = 628

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 65/188 (34%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 136 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGTFEGRMKFGLEVLKAVRA 195

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ +      +G+               +  +  
Sbjct: 196 EVGDDFCVGMRICGDEFHPDGLSHEDMKQIAAYYDATGMLDFIGVVGSGCDTHNTLANVI 255

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE   + +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 256 PNMSYPPEPFLHLAAGIKEVVKVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHMAD 313

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 314 PHLIAKIK 321


>gi|254500945|ref|ZP_05113096.1| oxidoreductase, FAD/FMN-binding family [Labrenzia alexandrii
           DFL-11]
 gi|222437016|gb|EEE43695.1| oxidoreductase, FAD/FMN-binding family [Labrenzia alexandrii
           DFL-11]
          Length = 775

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 30/184 (16%), Positives = 60/184 (32%), Gaps = 30/184 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
            + V +A++ +  G++ I L+            P + V    +G  L   M  P  V   
Sbjct: 558 DQFVASAEMADRAGFDMIELHAAHGYLLSSFISPVSNVRTDDYGGSLENRMRYPLEVLRA 617

Query: 108 IAAMCKALSIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           + A+      P++V+        +D +       + +    +G + I + A +  +    
Sbjct: 618 MRAVWPE-EKPMSVRISANDWVGEDGVTPDEAIEIARMFADAGADLIDVSAGQTTVDAKP 676

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA---AYK 221
                            I+ E     + + G + +   A  IL      M GRA   A  
Sbjct: 677 VYGRMFQTP----FSDRIRNEAGLTTMAV-GNIFEADHANSIL------MAGRADLVAVG 725

Query: 222 NSAM 225
              +
Sbjct: 726 RPHL 729


>gi|44151610|gb|AAS46743.1| putative NADH:flavin oxidoreductase 2 [Pleurotus djamor]
          Length = 396

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 35/190 (18%), Positives = 65/190 (34%), Gaps = 34/190 (17%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIV-GDCIA 109
            VEA +  E+ G++ I ++       +              S+G   + N        I 
Sbjct: 190 FVEAIERCEEVGFDFIEIHSA--HGYLFHSFLSNLSNDRTDSYGGQPLENRLRFPLRVIK 247

Query: 110 AMCKALSIPVTVKC-------RIGVDD-----QIPAVALRNLVKSIKKSGVNGIWI-HAR 156
           +  +A S P+ V+        R    D     Q      + LV  + K GV+ +      
Sbjct: 248 SCREAWSKPLFVRISASDWADRPEQGDDGLWKQWGIEQTKVLVGELLKIGVDFVDCSAGG 307

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
               + +      ++P  +      +KK  P L +G  G + D  +A   L     D ++
Sbjct: 308 NWAEQKIPLSHGYQVPFAE-----SLKKAYPGLNVGTVGLISDPEKAEGYLQEGKADVIL 362

Query: 215 IGRAAYKNSA 224
           + R   +N  
Sbjct: 363 LARELLRNPH 372


>gi|329848802|ref|ZP_08263830.1| imidazole glycerol phosphate synthase subunit hisF [Asticcacaulis
           biprosthecum C19]
 gi|328843865|gb|EGF93434.1| imidazole glycerol phosphate synthase subunit hisF [Asticcacaulis
           biprosthecum C19]
          Length = 275

 Score = 42.5 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 11/95 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++    +  G + + ++   A  +G +         +DY+ V +I +   D+   + GG+
Sbjct: 34  DMALRYRDEGADELVLYDITASSEGRT---------VDYNWVRDIARAL-DIPFCVAGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
               QA+K L    D V I   A +   ++  + E
Sbjct: 84  RSAEQAVKCLNSGADKVSINSPALERPDLINELAE 118


>gi|317484053|ref|ZP_07942986.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
 gi|316924697|gb|EFV45850.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
          Length = 644

 Score = 42.5 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 61/180 (33%), Gaps = 16/180 (8%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA+   + G++ I +             P     E ++G        +  + I    
Sbjct: 149 FCSAAERAAEAGFDVIEIHGAHGYLLSQFMSPLFNRREDAYGGNFEKRMRVPVEVIRGTR 208

Query: 113 KAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K L    P+  +C     +   I     R++ +++  +G++   +          +    
Sbjct: 209 KRLGPDFPLFFRCSVEEYLPGGITLELARDIARTVADNGIDLFNVSVGLGETNRFTGPPP 268

Query: 169 RKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                 + D    IK+   D   +G+ G + D   A  +L     D V++GRA   +  +
Sbjct: 269 CLPKGWNADRAAAIKEALGDRALVGVAGRIIDRESADAVLNSGKADLVVMGRALIADPDL 328


>gi|237738049|ref|ZP_04568530.1| 2-nitropropane dioxygenase [Fusobacterium mortiferum ATCC 9817]
 gi|229419929|gb|EEO34976.1| 2-nitropropane dioxygenase [Fusobacterium mortiferum ATCC 9817]
          Length = 312

 Score = 42.5 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 30/110 (27%), Positives = 44/110 (40%), Gaps = 20/110 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I  + K   + V           IP V+   L K  +K G + I +    A   G     
Sbjct: 104 IFEVVKGTGVKV-----------IPIVSTLKLAKISQKLGADAIVVEGGNA---GGHLGT 149

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           N       +DI+ EI K N D+ +   GG+     A ++L   VDGV +G
Sbjct: 150 NLDS----WDIMEEITK-NIDIPVFGAGGVITPEDAERMLSLGVDGVQMG 194


>gi|315078050|gb|EFT50101.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL053PA2]
          Length = 307

 Score = 42.5 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 66/197 (33%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G +G+ +      
Sbjct: 145 NVTAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARATADAGADGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
                      I           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAVRMIDAVTR-VVDIPVIGMGGVMTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|301053580|ref|YP_003791791.1| NADH oxidase [Bacillus anthracis CI]
 gi|300375749|gb|ADK04653.1| NADH oxidase [Bacillus cereus biovar anthracis str. CI]
          Length = 345

 Score = 42.5 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPEKRYRFLREIIESINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|289433010|ref|YP_003462883.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Dehalococcoides sp. GT]
 gi|288946730|gb|ADC74427.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Dehalococcoides sp. GT]
          Length = 258

 Score = 42.5 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++++++ EI      + + + GG+  M    K+L   VD V++G AA +N  ++  +   
Sbjct: 82  VNFELIKEIANSAL-IPVEVGGGIRSMETVKKLLVAGVDRVILGTAAVENPELVKEICAR 140

Query: 233 FSN 235
           +++
Sbjct: 141 YAD 143


>gi|21219623|ref|NP_625402.1| oxidoreductase [Streptomyces coelicolor A3(2)]
 gi|256789302|ref|ZP_05527733.1| oxidoreductase [Streptomyces lividans TK24]
 gi|289773190|ref|ZP_06532568.1| oxidoreductase [Streptomyces lividans TK24]
 gi|10803133|emb|CAC13061.1| putative oxidoreductase [Streptomyces coelicolor A3(2)]
 gi|289703389|gb|EFD70818.1| oxidoreductase [Streptomyces lividans TK24]
          Length = 359

 Score = 42.5 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 20/158 (12%), Positives = 45/158 (28%), Gaps = 12/158 (7%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRN 138
           P +     ++G           + + A+ +      P+  +        +          
Sbjct: 194 PHSNQRTDAYGGSYANRTRFALEVVDAVREVWPDDKPLFFRVSATDWLEEGGWTPDDTVR 253

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             + ++  G++ + +        G  P+                 K    L +   G + 
Sbjct: 254 FARDLEAHGIDLLDVSTG-----GNVPRVRIPTGPGYQVPFAARVKAGSTLPVAAVGLIT 308

Query: 199 DMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  QA KIL     D V++GR   +N +          
Sbjct: 309 EPGQAEKILANGEADAVLLGRELLRNPSWAQHAARELG 346


>gi|119963318|ref|YP_948303.1| oxidoreductase, FAD/FMN-binding family protein [Arthrobacter
           aurescens TC1]
 gi|119950177|gb|ABM09088.1| oxidoreductase, FAD/FMN-binding family protein [Arthrobacter
           aurescens TC1]
          Length = 366

 Score = 42.5 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 24/153 (15%), Positives = 60/153 (39%), Gaps = 11/153 (7%)

Query: 103 IVGDCIAAMCKAL--SIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           ++   + A+  A+  S+P+ ++       +  +   A   L ++  + GV+ + + +  A
Sbjct: 216 LMLTVVDAVRDAIPDSMPLLLRISASDWAEGGVDPDASVRLARAAAERGVDLVDVSSGGA 275

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
           +    + +  R +P       + +K +   +  G  G L   +QA  I+ +   D V + 
Sbjct: 276 V----AHQQIRAVPGYQAGFAHRVKNDAG-VPTGAVGLLTSAAQAEDIVANGRADAVFMA 330

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
           RAA ++            + +      +  V +
Sbjct: 331 RAALRDPHWWLRAAYELGHDIPWVPQYQRAVPR 363


>gi|152975320|ref|YP_001374837.1| NADPH dehydrogenase NamA [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|171769247|sp|A7GNY4|NAMA_BACCN RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|152024072|gb|ABS21842.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus cytotoxicus NVH
           391-98]
          Length = 346

 Score = 42.5 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 47/141 (33%), Gaps = 10/141 (7%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I A+ +    P+ V+        + +         K +K+ GV+ I   +   +  
Sbjct: 197 LREIIHAVKEVWEGPLFVRISADDYHPEGLTVNDYVQFAKWMKEQGVDLIDCSSGAVVPA 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
            +      ++    +       KE+  +  G  G +    QA +IL     D + +GR  
Sbjct: 257 HIDVYPGYQVKYAKH------LKEHAQIATGAVGLITSGVQAEQILVNSEADLIFVGREL 310

Query: 220 YKNSAMLTTVDEYFSNPLTGS 240
            +N     T        L   
Sbjct: 311 LRNPYFPRTAANELGFELKDP 331


>gi|113970557|ref|YP_734350.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. MR-4]
 gi|114047791|ref|YP_738341.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. MR-7]
 gi|113885241|gb|ABI39293.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. MR-4]
 gi|113889233|gb|ABI43284.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. MR-7]
          Length = 370

 Score = 42.5 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 31/182 (17%), Positives = 63/182 (34%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI-----------VGDCIA 109
             V AAK   D G+  + L+       + +  F        D            + + + 
Sbjct: 157 DFVAAAKRALDAGFEWLELHFA--HGYLAQSFFSTYANQRTDEYGGDAEGRGRFLIETVE 214

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           A+       +P+T +  +   D      L     LVK  K++G++ + +      +   +
Sbjct: 215 AVRAVWPEHLPLTARFGVIEFDDKDEQTLSESIALVKQFKRAGLDMLNV-----SICFST 269

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +      +  + G+++   A + +    +D VMIG+A   N
Sbjct: 270 PTANIPWRPAFLAPIAERVRREVGFPVATSWGMDNPHHAEQAIQDQQMDLVMIGKAFLAN 329

Query: 223 SA 224
             
Sbjct: 330 PH 331


>gi|296388578|ref|ZP_06878053.1| morphinone reductase [Pseudomonas aeruginosa PAb1]
          Length = 369

 Score = 42.5 bits (99), Expect = 0.088,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 61/188 (32%), Gaps = 29/188 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA+   D G++ + L              ++     ++G  L      + + + A
Sbjct: 161 DEFVRAARNALDAGFDLVELHGANGYLIDQFLASASNRRSDTYGGSLENRARFLLEIVDA 220

Query: 111 MCKALSI-PVTVKCRI-----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +  A+    V ++         + D  P      L +++++ G+  +  H  +    G  
Sbjct: 221 LVAAVGAERVGLRLSPWGTINDMHDDEPEAMTLYLAEALQRRGIAYL--HLAEWEWSGGP 278

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                    L                + + G   D  +A  IL +   D V IGR    N
Sbjct: 279 AYPQGFRERLRERFRA---------PLIVCGNY-DAERAEAILQAGLADAVAIGRPFIAN 328

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 329 PDLVERIR 336


>gi|116873835|ref|YP_850616.1| NADPH dehydrogenase NamA [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|123461413|sp|A0ALF5|NAMA_LISW6 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|116742713|emb|CAK21837.1| NADH:flavin oxidoreductase [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 338

 Score = 42.5 bits (99), Expect = 0.088,   Method: Composition-based stats.
 Identities = 37/195 (18%), Positives = 65/195 (33%), Gaps = 21/195 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P+ V+          +         K +K  GV  I +     +          
Sbjct: 204 KEVWDGPIIVRVSATDYAHGGLQLEDYIPFAKWMKADGVELIDVSTGGLVNVAPPVFPGY 263

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           ++P  D     EI++    +  G+ G +    QA +IL     D ++IGR   +N     
Sbjct: 264 QVPFAD-----EIRRGAG-IATGVLGLITRGEQAEEILCNERADLIIIGRELLRNPYFAK 317

Query: 228 TVDEYFSNPLTGSSP 242
             D   S   T   P
Sbjct: 318 --DAALSLGETIEGP 330


>gi|289435732|ref|YP_003465604.1| NADH:flavin oxidoreductase [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|289171976|emb|CBH28522.1| NADH:flavin oxidoreductase [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
          Length = 338

 Score = 42.5 bits (99), Expect = 0.089,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 65/194 (33%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     +   
Sbjct: 317 KDAAKELGETIEAP 330


>gi|254432195|ref|ZP_05045898.1| dihydroorotate dehydrogenase [Cyanobium sp. PCC 7001]
 gi|197626648|gb|EDY39207.1| dihydroorotate dehydrogenase [Cyanobium sp. PCC 7001]
          Length = 348

 Score = 42.5 bits (99), Expect = 0.089,   Method: Composition-based stats.
 Identities = 18/116 (15%), Positives = 43/116 (37%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI----- 103
           P+   + G+     VE A+ +E  G + + LN+               L  +P++     
Sbjct: 111 PVIASLNGSRAGSWVETARRIEAAGASALELNI-------------YVLPTDPELSSAAI 157

Query: 104 ---VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
              V + +  +   +++P+ VK             +  + + +  +G  G+ +  R
Sbjct: 158 EAEVEEIVREVRAEVALPLAVKLGPFF------TNISAMARRVAAAGAQGLVLFNR 207


>gi|70730816|ref|YP_260557.1| FMN-binding oxidoreductase [Pseudomonas fluorescens Pf-5]
 gi|68345115|gb|AAY92721.1| oxidoreductase, FMN-binding [Pseudomonas fluorescens Pf-5]
          Length = 410

 Score = 42.5 bits (99), Expect = 0.089,   Method: Composition-based stats.
 Identities = 33/228 (14%), Positives = 72/228 (31%), Gaps = 19/228 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P        +G  L     ++ + + A+ 
Sbjct: 151 FARTARLGEQAGFTGVEIHAAHGYLLSQFLSPLTNQRTDEWGGSLENRARLLLEIVKAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             +S    V  ++   D       A   R +V+ + + GV+ + +         ++G + 
Sbjct: 211 SVVSADFAVAVKLNSADFQRGGFTADDARKVVELLNELGVDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A  ++   VD V IG A   +  
Sbjct: 271 DGRTLAREAYFVEFARDIRTVARMPVMVTGGVRRRPIAEMVVQSGVDMVGIGTALAIDPH 330

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
           +            T   P  T  +K      + ++  Y  R L    K
Sbjct: 331 LPRDW--LLGKDSTPQLPPITWKNKAIAALANMAVVKYQLRKLSRAKK 376


>gi|26987052|ref|NP_742477.1| oxidoreductase, FMN-binding [Pseudomonas putida KT2440]
 gi|148545586|ref|YP_001265688.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
 gi|24981674|gb|AAN65941.1|AE016222_3 oxidoreductase, FMN-binding [Pseudomonas putida KT2440]
 gi|148509644|gb|ABQ76504.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
 gi|313496675|gb|ADR58041.1| Oxidoreductase, FMN-binding protein [Pseudomonas putida BIRD-1]
          Length = 686

 Score = 42.5 bits (99), Expect = 0.089,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 65/188 (34%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGTFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ +      +G+               +  +  
Sbjct: 213 EVGDDFCVGMRICGDEFHPDGLSHEDMKQIAAYYDATGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE   + +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMSYPPEPFLHLAAGIKEVVKVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHMAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|298490003|ref|YP_003720180.1| N-acylglucosamine-6-phosphate 2-epimerase ['Nostoc azollae' 0708]
 gi|298231921|gb|ADI63057.1| N-acylglucosamine-6-phosphate 2-epimerase ['Nostoc azollae' 0708]
          Length = 229

 Score = 42.5 bits (99), Expect = 0.090,   Method: Composition-based stats.
 Identities = 23/119 (19%), Positives = 45/119 (37%), Gaps = 19/119 (15%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + D I  + + L  PV                     K   ++GV+ +       +L 
Sbjct: 106 EKLPDIINNIHQQLGKPVMADVDTY-----------EAAKLAVEAGVDIV----GTTLLG 150

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
             S  + +      ++++ +I  EN ++F+   GG+     A K L    D V++G A 
Sbjct: 151 YTS--ETKSFAPPGWELLTQII-ENLNIFVICEGGISSPEMAKKALELGSDAVVVGTAI 206



 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 20/156 (12%), Positives = 46/156 (29%), Gaps = 37/156 (23%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +   A+   + G   + +N                    P+     I A+   + +
Sbjct: 22  DPYIIAAMAEAAVNNGAVSVRINT-------------------PNH----IKAVRAKVQV 58

Query: 118 PVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           P+    +  +      +    +   ++ ++G + I I A            NR       
Sbjct: 59  PIIGLWKQVITGSHVYITPQFHHAVAVAEAGADIIAIDATT---------RNRPGDEKLP 109

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVD 211
           DI+  I ++     +     ++    A   +   VD
Sbjct: 110 DIINNIHQQLGKPVMA---DVDTYEAAKLAVEAGVD 142


>gi|83770423|dbj|BAE60556.1| unnamed protein product [Aspergillus oryzae]
          Length = 392

 Score = 42.5 bits (99), Expect = 0.090,   Method: Composition-based stats.
 Identities = 28/188 (14%), Positives = 58/188 (30%), Gaps = 25/188 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V +A+ + + G+  + L+            P + +    +G        IV + I   
Sbjct: 143 QFVNSARFLAECGFAGVELHAAHGYLLSQFLSPKSNIRHDKYGGSPEARARIVLEIIKET 202

Query: 112 CKALSIPVTVKCRIGVDDQIPAVA--LRNLVKSIKKSGVNGIWIHARK---AILKGLSPK 166
              +     +  ++   D   +        +    +SG++ + +         + G   K
Sbjct: 203 RAVVPENFCIGLKLNSADHSASDFEDTMKQIGLFAESGIDFLEVSGGTYEDPTMMGRGLK 262

Query: 167 DNRKIPNLD---------YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
           +      +          +D   E ++  P L + L GG          L     D V I
Sbjct: 263 EEIASETVQRTAAREAFFFDFAKETRRRFPGLILMLTGGFRSRQGIQAALKGGACDIVGI 322

Query: 216 GRAAYKNS 223
           GR A    
Sbjct: 323 GRPAVVCP 330


>gi|73749015|ref|YP_308254.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Dehalococcoides sp.
           CBDB1]
 gi|91206927|sp|Q3ZYM9|HIS4_DEHSC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|73660731|emb|CAI83338.1| phosphoribosylformimino-5-aminoimidazolecarboxamide ribotide
           isomerase [Dehalococcoides sp. CBDB1]
          Length = 244

 Score = 42.5 bits (99), Expect = 0.092,   Method: Composition-based stats.
 Identities = 14/63 (22%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY 232
           ++++++ EI      + + + GG+  M    K+L   VD V++G AA +N  ++  +   
Sbjct: 68  VNFELIKEIANSAL-IPVEVGGGIRSMETVKKLLVAGVDRVILGTAAVENPELVKEICAR 126

Query: 233 FSN 235
           +++
Sbjct: 127 YAD 129


>gi|294664860|ref|ZP_06730180.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
 gi|292605382|gb|EFF48713.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
          Length = 258

 Score = 42.5 bits (99), Expect = 0.092,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|289522475|ref|ZP_06439329.1| dihydroorotate dehydrogenase(DHOdehase) [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289504311|gb|EFD25475.1| dihydroorotate dehydrogenase(DHOdehase) [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 363

 Score = 42.5 bits (99), Expect = 0.092,   Method: Composition-based stats.
 Identities = 21/144 (14%), Positives = 46/144 (31%), Gaps = 22/144 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
           V + + A  KA   P+ VK   GV D      L  L K +++ GV+ +            
Sbjct: 134 VLNTVTAARKATKKPIIVKVSPGVPD------LAELGKKLEEVGVDALAAINSVGPALRI 187

Query: 153 -IHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKI-LP 208
            +      +   +       P +    +  + +      + +   GG+      +++ + 
Sbjct: 188 DLKTGLPYMGSDTGYGWVSGPAIKGIALRHVFELSHAVSIPVIGVGGVSSGEDVIEMFMA 247

Query: 209 SVDGVMIGR-AAYKNSAMLTTVDE 231
               V I   A  +       + +
Sbjct: 248 GASAVQICTQAILEGPKAFKRIAQ 271


>gi|327470763|gb|EGF16219.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK330]
          Length = 240

 Score = 42.5 bits (99), Expect = 0.093,   Method: Composition-based stats.
 Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K++GV+ I +      L+G +          + D++ +IK E   L I + G
Sbjct: 32  VLEQARVFKEAGVSMIHVVDLDGALEGRA---------ANRDLIAQIKAETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN A +    E F 
Sbjct: 82  GIRSLEQIEDYLAVGIDRVIIGSMAVKNPAFVEAALERFG 121


>gi|212716253|ref|ZP_03324381.1| hypothetical protein BIFCAT_01169 [Bifidobacterium catenulatum DSM
           16992]
 gi|212660765|gb|EEB21340.1| hypothetical protein BIFCAT_01169 [Bifidobacterium catenulatum DSM
           16992]
          Length = 378

 Score = 42.5 bits (99), Expect = 0.093,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 71/208 (34%), Gaps = 21/208 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA    D G++ + ++            P     E  +G        ++ + + A
Sbjct: 177 DQFRDAAWRAYDIGFDAVEIHAAHGYLLSQFLDPLINEREDEYGGSFKNRIRMLVEVVDA 236

Query: 111 MCKALS--IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +   +PV V+                 +L K +K+ GV+ + +        G+ P 
Sbjct: 237 VRSVVPDTMPVLVRVSATDWAAGGWDLDQTVDLAKVLKEHGVDLVDVSTG-----GMIPG 291

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
               +         E  +    +     G +    +A KIL   + D + IGRAA ++  
Sbjct: 292 VAIPVKPGYQVPFSEQVRSRAGIPTTAVGLITKPKRAKKILKSGAADAIEIGRAALRDPN 351

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
                      P T ++P + +  +  +
Sbjct: 352 WPLRAAAKLDIP-TENAPYQPQYVRGAY 378


>gi|332293387|ref|YP_004431996.1| NADH:flavin oxidoreductase/NADH oxidase [Krokinobacter diaphorus
           4H-3-7-5]
 gi|332171473|gb|AEE20728.1| NADH:flavin oxidoreductase/NADH oxidase [Krokinobacter diaphorus
           4H-3-7-5]
          Length = 358

 Score = 42.5 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 34/179 (18%), Positives = 65/179 (36%), Gaps = 22/179 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            +EAAK     G++ I ++            P        +G        ++ +    + 
Sbjct: 158 FIEAAKRAVIAGFDVIEIHAAHGYLLNQFLSPLTNKRVDEYGGTFEKRVRLLLEVTEGIR 217

Query: 113 KALS--IPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD- 167
             +   +P+ V+       +          + + +K SGV+ I       +     P + 
Sbjct: 218 SVIPDRMPLFVRISATEWAEGGHTIEDSLKISQLLKDSGVDLIDCSTGGVVKSQEIPVEK 277

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
           N ++P  +     +IKKE  ++  G  G ++D  QA  IL     D + IGR   +N  
Sbjct: 278 NYQVPFAE-----KIKKEI-NIATGAVGLIDDAIQADDILTNDQADLIFIGREMLRNPY 330


>gi|320107926|ref|YP_004183516.1| NADH:flavin oxidoreductase/NADH oxidase [Terriglobus saanensis
           SP1PR4]
 gi|319926447|gb|ADV83522.1| NADH:flavin oxidoreductase/NADH oxidase [Terriglobus saanensis
           SP1PR4]
          Length = 392

 Score = 42.5 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 23/163 (14%), Positives = 51/163 (31%), Gaps = 22/163 (13%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKC---------RIGVDDQIPAVALRNLVK 141
           +G  L        + +  +       +PV V+          +      +         +
Sbjct: 218 YGGSLENRARFPLEIVRTVRANFPAELPVWVRLSVTDWIDPSKNIPTGGLTVEDSIAFAR 277

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY--EIKKENPDLFIGLNGGLED 199
            +K  G++ +   +      G  P+    I    Y + +   I++E   +  G  G +  
Sbjct: 278 LLKAEGIDLVDCSSG-----GNDPRQQIPIG-AGYQVAFADRIRREAG-IPTGAVGMITA 330

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
             QA +I+     D V++ R   ++        E    P +  
Sbjct: 331 PEQADQIVRTGQADVVLLARELLRDPYWPLHAAEALHKPASWP 373


>gi|288574551|ref|ZP_06392908.1| dihydroorotate dehydrogenase family protein [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570292|gb|EFC91849.1| dihydroorotate dehydrogenase family protein [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 302

 Score = 42.5 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 74/238 (31%), Gaps = 33/238 (13%)

Query: 19  NALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEI 77
           + LL  E   +D   R    + +       PL   I G     + E  K +E + G + +
Sbjct: 65  DGLLNCE-TWSDRPWRSYIDDYVKVKETGVPLICSI-GYSPEDVAELGKALEAEVGPDVV 122

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVAL 136
             +                +    D +     A+  ++S PV +K      +    A  +
Sbjct: 123 EFSTH-------------YVGKTLDPLKRVAEALRGSVSCPVWMKVSPSTPNIPEMAKVM 169

Query: 137 RNLVK---SIKKSGVNG-IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLF 190
            + V    ++   G      I   K  L           P +    +Y + +   + D  
Sbjct: 170 SDYVDGFVAVNSVGPALDFDIDKPKPRLGTEDGHGWLSGPAITGVALYAVYQISHSQDKP 229

Query: 191 IGLNGGLEDMSQALK-ILPSVDGVMI-------GRAAYKNSAMLTTVDEYFSNPLTGS 240
           +   GG+     A+K I+     V I       G   Y    + + + ++      GS
Sbjct: 230 VVGVGGIRTGEDAVKFIMAGASLVGICSEAIRRGTGIYGK--IASEISDWMDRKGYGS 285


>gi|170724054|ref|YP_001751742.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
 gi|169762057|gb|ACA75373.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
          Length = 686

 Score = 42.5 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 65/188 (34%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGTFEGRMKFGMEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ +      +G+               +  +  
Sbjct: 213 EVGDDFCVGMRICGDEFHPDGLSHEDMKQIAAYYDATGMIDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE   + +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMSYPPEPFLHLAAGIKEVVKVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|326389827|ref|ZP_08211391.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325994095|gb|EGD52523.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 606

 Score = 42.5 bits (99), Expect = 0.095,   Method: Composition-based stats.
 Identities = 22/142 (15%), Positives = 43/142 (30%), Gaps = 14/142 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL-SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVN 149
           +G           D +  + KAL  + V  +       D            K ++  G +
Sbjct: 161 YGGNFEGRTKFALDILRGVKKALPDMTVICRINGSDFTDGGFSIEESVRFAKLLEYHGAD 220

Query: 150 GIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQAL 204
            + I           +SP      P +    + +  KEN  + +      G + D  + L
Sbjct: 221 ALDISGGVSSTSEYHISPMGIGDKPLIG---IAKRIKENITIPVIAVDKLGSVYDWEKIL 277

Query: 205 KILPS-VDGVMIGRAAYKNSAM 225
           +      D + I R    +  +
Sbjct: 278 E--DGIADFIGIARGLIGDPDL 297


>gi|226360437|ref|YP_002778215.1| NADH-dependent flavin oxidoreductase [Rhodococcus opacus B4]
 gi|226238922|dbj|BAH49270.1| putative NADH-dependent flavin oxidoreductase [Rhodococcus opacus
           B4]
          Length = 366

 Score = 42.5 bits (99), Expect = 0.095,   Method: Composition-based stats.
 Identities = 25/174 (14%), Positives = 54/174 (31%), Gaps = 19/174 (10%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG---------VDDQIP 132
           P +      +G        ++ + + A+       +PV V+               D   
Sbjct: 194 PVSNHRTDGYGGSFAGRTRLLLEVVEAVRGVWPAELPVFVRVSATDWLSEEPGLDADSWT 253

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 LV+++   GV+ + + +      G++       P         I+ E   L   
Sbjct: 254 PDQTVALVQALADLGVDLVDVSSG-----GVASAQIPVGPGYQVPFARRIQSETL-LPAA 307

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
             G + +  QA +I+       V +GR   ++           +  +T   P +
Sbjct: 308 AVGLITEPEQAERIVESGEAVAVFLGRELLRDPYWPRKAARTLNAQVTPQIPAQ 361


>gi|222153391|ref|YP_002562568.1| dihydroorotate dehydrogenase 1A [Streptococcus uberis 0140J]
 gi|254788904|sp|B9DUS7|PYRD_STRU0 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|222114204|emb|CAR42755.1| putative dihydroorotate dehydrogenase [Streptococcus uberis 0140J]
          Length = 311

 Score = 42.5 bits (99), Expect = 0.096,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 56/173 (32%), Gaps = 21/173 (12%)

Query: 77  INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAV 134
           + LN+ CP   V      A    + +     +  +    + P+ VK     D      A 
Sbjct: 125 VELNLSCP--NVPGKPQIAY---DFETTEQLLTEIFSYYTKPLGVKLPPYFDIVHFDQAA 179

Query: 135 ALRN-----LVKSIKKSG-----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           A+ N      V S+   G      +   I   K    G+     +     +    Y+  +
Sbjct: 180 AIFNKFPLAFVNSVNSIGNGLVIDDETVIIKPKNGFGGIGGDYIKPTALANVHAFYQ--R 237

Query: 185 ENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
            NP + I   GG++    A +  L     V IG A  +    + T + E    
Sbjct: 238 LNPSIQIIGTGGVKSGRDAFEHILCGASMVQIGTALQEEGPEIFTRITEELKQ 290


>gi|188521010|gb|ACD58955.1| imidazoleglycerol phosphate synthase, cyclase subunit [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 247

 Score = 42.5 bits (99), Expect = 0.096,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 45/130 (34%), Gaps = 11/130 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D I    +  L    +  G + +  +   A  +G S         +DY  V  + +
Sbjct: 10  VKFHDHIDMGDIVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVERVAR 60

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              D+   + GG+ D+  A  +L    D + I   A     +++ + + F          
Sbjct: 61  LI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVVVGID 119

Query: 244 KTRVDKDFWR 253
             R D   WR
Sbjct: 120 SIREDDGQWR 129


>gi|167032099|ref|YP_001667330.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
 gi|166858587|gb|ABY96994.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
          Length = 368

 Score = 42.5 bits (99), Expect = 0.096,   Method: Composition-based stats.
 Identities = 25/158 (15%), Positives = 53/158 (33%), Gaps = 11/158 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G+C      +    + A+ K     +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDEYGSCFENRIRLTLQVVEAVRKVWPAELPLFVRVSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + ++  GV+ I + +      G S                E  ++  ++  G  G + +
Sbjct: 250 ARRLRGLGVDLIDVSSG-----GTSVNAEIPTGPGYQTRFAERVRKESEIATGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +QA  IL     D + + R   ++       D+    
Sbjct: 305 PAQAEHILRTGQADIIFLARELLRDPYWPLHADDDLGG 342


>gi|297537502|ref|YP_003673271.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylotenera sp. 301]
 gi|297256849|gb|ADI28694.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylotenera sp. 301]
          Length = 247

 Score = 42.5 bits (99), Expect = 0.097,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 172 PNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
             ++   +  I +    ++ I L GG+ D+    + L   +D V+IG AA KN   L   
Sbjct: 59  KPVNEAAIKSIVRAVGGEIPIQLGGGIRDLETIERYLDNGIDYVIIGTAAVKNPGFLHEA 118

Query: 230 -DEYFSNPLTGSSPIKTRVDKDFWRKI 255
            D +    + G    + +V  D W K+
Sbjct: 119 CDAFPGQIIVGLDAKEGKVAVDGWSKL 145


>gi|224367321|ref|YP_002601484.1| predicted NADH:flavin oxidoreductase [Desulfobacterium
           autotrophicum HRM2]
 gi|223690037|gb|ACN13320.1| predicted NADH:flavin oxidoreductase [Desulfobacterium
           autotrophicum HRM2]
          Length = 368

 Score = 42.5 bits (99), Expect = 0.097,   Method: Composition-based stats.
 Identities = 24/135 (17%), Positives = 52/135 (38%), Gaps = 11/135 (8%)

Query: 106 DCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAIL 160
           + + A+ +A+    PV +K     D Q   +AL + V   K +  +G++ I +       
Sbjct: 198 EILKAIRRAVGDDFPVLIKI-NCQDFQENGLALEDTVWVCKQLADNGMDAIELSGGMLTG 256

Query: 161 KGLSPKD---NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
             LSP     N       +       K   ++ + L GG+  +  A +++ +   D + +
Sbjct: 257 GKLSPSRVGINSPDKEAYFRQEAAAVKGAINIPLILVGGIRSLEVAQELVATKRADYLSM 316

Query: 216 GRAAYKNSAMLTTVD 230
            R   +   ++    
Sbjct: 317 CRPLIREPGLVNRWK 331


>gi|116696454|ref|YP_842030.1| NADH-dependent flavin oxidoreductase yqiG [Ralstonia eutropha H16]
 gi|113530953|emb|CAJ97300.1| NADH-dependent flavin oxidoreductase yqiG [Ralstonia eutropha H16]
          Length = 377

 Score = 42.5 bits (99), Expect = 0.097,   Method: Composition-based stats.
 Identities = 28/186 (15%), Positives = 60/186 (32%), Gaps = 34/186 (18%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
               +AA++  D G++ + ++            +                 G  +     
Sbjct: 161 EGFAQAARLARDAGFDGVEIHGA--------NGYLLDQFLTSYTNQRQDAWGGSIAQRMR 212

Query: 103 IVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           +  + + A+  A+    PV V+   G         +    +  + +      + A     
Sbjct: 213 LPLETVRAVRVAVGAGFPVGVRISQG----KVNDFVHKWPEGAEGAAAVFSALAASSVDY 268

Query: 161 KGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGR 217
             ++  +  +    D    +V   ++  P L I  NG L + S+A  +L      V +GR
Sbjct: 269 LHVTEHEAWQPAFADDGATLVQLARRAAPGLTIMANGSLHEPSRAASLLDDGATLVALGR 328

Query: 218 AAYKNS 223
            A  N 
Sbjct: 329 GALANP 334


>gi|84623781|ref|YP_451153.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
 gi|161898993|ref|YP_200900.2| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           oryzae pv. oryzae KACC10331]
 gi|229358033|ref|YP_001913487.2| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|85541727|sp|Q5H0K6|HIS6_XANOR RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|91207021|sp|Q2P3J8|HIS6_XANOM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|84367721|dbj|BAE68879.1| imidazole glycerol phosphate synthase subunit hisF [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
          Length = 258

 Score = 42.1 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 45/130 (34%), Gaps = 11/130 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D I    +  L    +  G + +  +   A  +G S         +DY  V  + +
Sbjct: 21  VKFHDHIDMGDIVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVERVAR 71

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              D+   + GG+ D+  A  +L    D + I   A     +++ + + F          
Sbjct: 72  LI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVVVGID 130

Query: 244 KTRVDKDFWR 253
             R D   WR
Sbjct: 131 SIREDDGQWR 140


>gi|21910627|ref|NP_664895.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS315]
 gi|28895686|ref|NP_802036.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes SSI-1]
 gi|81847448|sp|Q8K6X4|PYRD_STRP3 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|21904829|gb|AAM79698.1| putative dihydroorotate dehydrogenase [Streptococcus pyogenes
           MGAS315]
 gi|28810935|dbj|BAC63869.1| putative dihydroorotate dehydrogenase [Streptococcus pyogenes
           SSI-1]
          Length = 311

 Score = 42.1 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 40/230 (17%), Positives = 72/230 (31%), Gaps = 28/230 (12%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INL 79
           I +  +     +  L F      + Q KP  L + G   ++     K++    Y   + L
Sbjct: 68  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKVIMASDYEGLVEL 127

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALR 137
           N+ CP   V      A    + +     +  +    + P+ +K     D      A A+ 
Sbjct: 128 NLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAAIF 182

Query: 138 N-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           N      V  +   G   +          K    G+     +     +    Y  K+  P
Sbjct: 183 NKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRLKP 240

Query: 188 DLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 241 SIHIIGTGGIKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 290


>gi|168017088|ref|XP_001761080.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162687766|gb|EDQ74147.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 247

 Score = 42.1 bits (98), Expect = 0.099,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 52  LQIGGADISKLVEAAKIVE-DFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           +QI G++   L  AA+ +E +   +  NL +GCP   V   S+G+ L+    +V + 
Sbjct: 184 VQICGSNAGTLALAAEPIERECSVDFDNLYIGCPIDVVVNESWGSSLLTKSQLVTNF 240


>gi|269963817|ref|ZP_06178131.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269831435|gb|EEZ85580.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 252

 Score = 42.1 bits (98), Expect = 0.100,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 70/182 (38%), Gaps = 20/182 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            ++AA   +  G++ + L   C           P     +  +G  L     +V + I A
Sbjct: 67  FIDAALRADKAGFDFVEL--HCAHGYGLNQVLSPVTNQRDDQYGGSLENRTRLVVEIIEA 124

Query: 111 MCKALSIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +    +I V V+   +    + +    +  + + + K+G++ I + +         PKD 
Sbjct: 125 IKANSNIGVMVRIPGQDLYPEGLTQEDMVEVCQLLIKAGIDIIDVSSGIGGWN--RPKDR 182

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
           R    L  +  + +K+ +  + I   GG+E      + + +  +D   +GRA  K+    
Sbjct: 183 RGEGYLVSESTF-LKQADLGIPIIGVGGIESAEYIDQAVNNGWLDLAAVGRAILKDPLAF 241

Query: 227 TT 228
             
Sbjct: 242 NQ 243


>gi|317049484|ref|YP_004117132.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
 gi|316951101|gb|ADU70576.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
          Length = 367

 Score = 42.1 bits (98), Expect = 0.100,   Method: Composition-based stats.
 Identities = 26/180 (14%), Positives = 60/180 (33%), Gaps = 19/180 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AAK   D G+  + L+       + +             +G   +     + +  
Sbjct: 158 DDFVSAAKRARDAGFEWLELHFA--HGYLAQSFFSVHANQRSDEYGGDAVGRSRFLRETF 215

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            A+ +    ++P+T +  +   D      ++  +   +    NG+ +      +   +P 
Sbjct: 216 DAVREVWPENLPLTARFGVLEFDGRDEETMQEAITLTQYWRSNGLDL--LSVSMGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            N    +     +    +    + +    G++    A   +    +D VM+GRA  KN  
Sbjct: 274 ANIPWGSPFMAPIAARVRREAAIPVASAWGIDTPHIANATIEQGQLDLVMVGRAHLKNPH 333


>gi|116051720|ref|YP_789441.1| putative FMN oxidoreductase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|296387769|ref|ZP_06877244.1| putative FMN oxidoreductase [Pseudomonas aeruginosa PAb1]
 gi|115586941|gb|ABJ12956.1| putative oxidoreductase, FAD/FMN-binding [Pseudomonas aeruginosa
           UCBPP-PA14]
          Length = 368

 Score = 42.1 bits (98), Expect = 0.100,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 58/169 (34%), Gaps = 11/169 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G C      ++    AA+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGGCFENRIRLLLQVTAAVRKAWPEELPLFVRLSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +K  GV+ I + +        +  +    P    +    +KKE   +  G  G + +
Sbjct: 250 ARRLKDLGVDLIDVSSGGTA----ANAEIPVGPGYQTEFAERVKKEAG-IASGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
             QA  IL     D +++ R   ++        +   N      P   R
Sbjct: 305 PVQAEHILRTGQADLILLARELLRDPYWPLHAADELRNEQMPWPPQYLR 353


>gi|314917236|gb|EFS81067.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL050PA1]
 gi|314921611|gb|EFS85442.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL050PA3]
          Length = 269

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 63/180 (35%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E  G   I  N+      +  G          D   +
Sbjct: 37  DIPVIASLNGATNGGWVDTAKRMEGAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 91

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 92  IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 143

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  ++    +             +  +        +  + G+E  +  +K +L   D VM
Sbjct: 144 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESAADVVKYLLAGADVVM 202


>gi|240277948|gb|EER41455.1| NADPH dehydrogenase [Ajellomyces capsulatus H143]
 gi|325096010|gb|EGC49320.1| NADPH dehydrogenase [Ajellomyces capsulatus H88]
          Length = 420

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 69/199 (34%), Gaps = 32/199 (16%)

Query: 64  EAAKIVEDFGYNEINLNVG--------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            A +     G + I ++          C P +      +G        +  + I    + 
Sbjct: 201 AAVRRAVKAGVDYIEVHCAHGYLLFSFCSPVSNNRTDEYGGSFENRIRLTSEIITISRQN 260

Query: 115 L--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +   +P+ ++          R  +        +R   K + + G V+ + + A      G
Sbjct: 261 MPKDMPLFLRISASEWLEETRPDLPSWKSEDTVR-FAKILAEKGEVDLLDVSA------G 313

Query: 163 LSPKDNRKIPNLDYDI--VYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
            +  D + IP   +     + +K+   D L +G  G +     A  +L   +D V++GR 
Sbjct: 314 GNHPDQKIIPGPCFQAHFAHAVKEAVGDKLLVGAVGSINSGVDADGLLEKGLDLVLVGRL 373

Query: 219 AYKNSAMLTTVDEYFSNPL 237
             KN +++    E     L
Sbjct: 374 FLKNPSVVWQFAEDLGTEL 392


>gi|302865934|ref|YP_003834571.1| NADH:flavin oxidoreductase/NADH oxidase [Micromonospora aurantiaca
           ATCC 27029]
 gi|302568793|gb|ADL44995.1| NADH:flavin oxidoreductase/NADH oxidase [Micromonospora aurantiaca
           ATCC 27029]
          Length = 355

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 58/180 (32%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA    D G+  + ++            P        +G        +  +   A
Sbjct: 158 DAFATAAGRALDAGFAAVEIHAAHGYLLHEFLSPLTNRRTDGYGGDRAARMRLTLEVARA 217

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+   V V  RI   D        +    L   +  +GV+ I   +  A ++   P 
Sbjct: 218 VRAAVGESVPVLTRISATDWTDDGWTVDDSVVLAGELAAAGVDLIDTSSGGAAVQASIPV 277

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                  L       I+++   +  G  G + +  QA +I+     D V++GR   ++  
Sbjct: 278 GPGYQVPL----AARIRRDAG-VPTGAVGLIVEPEQAEQIVAGGEADLVLLGRELLRDPY 332


>gi|254483064|ref|ZP_05096299.1| oxidoreductase, FAD/FMN-binding family [marine gamma
           proteobacterium HTCC2148]
 gi|214036749|gb|EEB77421.1| oxidoreductase, FAD/FMN-binding family [marine gamma
           proteobacterium HTCC2148]
          Length = 692

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 26/182 (14%), Positives = 64/182 (35%), Gaps = 18/182 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + VEAA   +  G++ + L+ G          P     E ++G         +   I+A+
Sbjct: 159 EFVEAALRAKSAGFDGVELHAGHGYLLASFLSPYTNTREDNYGGSRENRARFLTQMISAI 218

Query: 112 CKA--LSIPVTVKCRIGVDDQIPAVALRNL---VKSIKKSGVNGIWIHARKAILKGLSPK 166
            +A   + P+ V+           +   +        +++G + I + A   +   ++  
Sbjct: 219 RQAAGANFPILVRLDAMEYRTKGGITPDDCAVTAALCEQAGADAIDVSAYGNVAHAIAFT 278

Query: 167 DNRKIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           +   +     +    +  K +  + +   G +E    A + L     D + +GR    + 
Sbjct: 279 EAPLVHEPGGFISFAKQVKASVGIPVIGVGRIE-AEVAERHLQAGHFDFLAMGRKLLADP 337

Query: 224 AM 225
            +
Sbjct: 338 DL 339


>gi|282854050|ref|ZP_06263387.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes J139]
 gi|282583503|gb|EFB88883.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes J139]
 gi|314923019|gb|EFS86850.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL001PA1]
 gi|314966793|gb|EFT10892.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL082PA2]
 gi|314981131|gb|EFT25225.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL110PA3]
 gi|315091955|gb|EFT63931.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL110PA4]
 gi|315093288|gb|EFT65264.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL060PA1]
 gi|315103455|gb|EFT75431.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL050PA2]
 gi|327327620|gb|EGE69396.1| dihydroorotate oxidase [Propionibacterium acnes HL103PA1]
          Length = 307

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 30/196 (15%), Positives = 61/196 (31%), Gaps = 23/196 (11%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G NG+ +      
Sbjct: 145 NATAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARATADAGANGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                      I           +  +   ++  + +      IG+ G +        ++
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAVRMIDAVTRVVDIPVIGMGGVVTSADALELMI 258

Query: 208 PSVDGVMIGRAAYKNS 223
                V +G A + + 
Sbjct: 259 AGASAVGVGTANFTDP 274


>gi|153816298|ref|ZP_01968966.1| hypothetical protein RUMTOR_02549 [Ruminococcus torques ATCC 27756]
 gi|145846351|gb|EDK23269.1| hypothetical protein RUMTOR_02549 [Ruminococcus torques ATCC 27756]
          Length = 639

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 70/182 (38%), Gaps = 27/182 (14%)

Query: 64  EAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAAMCKA 114
           +AA    + GY+ +  ++     P + +  G       +G           + I  + K 
Sbjct: 146 KAAARAVEAGYDCLEFHLAHNYLPHSFLSAGFNHREDEYGGSFENRCRFPLEVIDEIRKN 205

Query: 115 L--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +   +P+ ++     D     + + +     K  K+ GV+ + +     I    +     
Sbjct: 206 MPEGMPLCIRIDAQDDMLENGLMIEDVIRFCKIAKEHGVDVLDVSRGNII----TAASMY 261

Query: 170 KIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++P +D       D    I+KE   L +G+ G +   + A +I+    VD V++GRA   
Sbjct: 262 EVPPIDVPNGFNIDNAARIRKETGMLTVGV-GRINTAALAEEIISQDKVDMVVMGRAQLA 320

Query: 222 NS 223
           + 
Sbjct: 321 DP 322


>gi|294054684|ref|YP_003548342.1| dihydroorotate oxidase [Coraliomargarita akajimensis DSM 45221]
 gi|293614017|gb|ADE54172.1| dihydroorotate oxidase [Coraliomargarita akajimensis DSM 45221]
          Length = 332

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 33/219 (15%), Positives = 72/219 (32%), Gaps = 51/219 (23%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN--- 100
           +  + P+   + G      V  A ++++ G + + LN+               L  +   
Sbjct: 98  AACDLPVIASLNGTREGDWVNYASLIQNSGADALELNL-------------YFLATDLDE 144

Query: 101 -----PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 D     + A+ + ++IP+ VK            AL +    + ++G N + +  
Sbjct: 145 SASDLEDRCVRIVEAVKQQITIPLAVKLSPYF------TALPHFANRLSQAGANALVLFN 198

Query: 156 RKAILKGLSPKDNRKI-------------PNLDYDIVYEIKKENPDLFIGLNGGLED-MS 201
           R    +     D   I             P L +     +  +  D  + ++GG+   + 
Sbjct: 199 R--FYQPDIDADELDIEPRLQLSNSPELLPRLRW---LALLHDRIDCDLSVSGGVHTGID 253

Query: 202 QALKILPSVDGVMIGRAAYKN-SA----MLTTVDEYFSN 235
               ++   D V +  A   N  A    +L  V ++   
Sbjct: 254 AVKALMAGADSVQMVSALLMNGPAYIGTVLQEVKDWMEE 292


>gi|300774786|ref|ZP_07084649.1| dihydroorotate oxidase [Chryseobacterium gleum ATCC 35910]
 gi|300506601|gb|EFK37736.1| dihydroorotate oxidase [Chryseobacterium gleum ATCC 35910]
          Length = 345

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 26/153 (16%), Positives = 56/153 (36%), Gaps = 28/153 (18%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-----ALSIPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I  + K     A+  P+ +K    ++
Sbjct: 167 VDYFVLNVSCPNVGSHAK------LEDVDYLRELITEVKKINQSKAVQKPILLKIAPDLN 220

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWI----------HARKAILK--GLSPKDNRKIPNLDY 176
           +      L  +++ I ++ ++GI +               +L+  G      + I     
Sbjct: 221 NN----QLDEIIELIAETKIDGIVVSNTSVNREGLKTSPEVLEQIGNGGLSGKPIRERST 276

Query: 177 DIVYEI-KKENPDLFIGLNGGLEDMSQALKILP 208
            ++  +  K N    I   GG+     A++ L 
Sbjct: 277 KMIRYLSDKSNRAFPIIGVGGIHSAKDAMEKLD 309


>gi|225849071|ref|YP_002729235.1| NADPH dehydrogenase (xenobiotic reductase) [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225643326|gb|ACN98376.1| NADPH dehydrogenase (xenobiotic reductase) [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 350

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 66/181 (36%), Gaps = 24/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V AAK   + G++ I ++       +               +G  L      + + +  
Sbjct: 154 FVNAAKRAVEAGFDIIEIHAA--HGYLIHEFLSLISNHRTDEYGGSLENRERFLLEVVKK 211

Query: 111 MCKAL--SIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +  S+P  V + C   V+D        +L K +K+ G + I   +   +   +   
Sbjct: 212 VRNVIPESMPLFVRLSCVDHVEDGWTLEDSIHLAKRLKEEGCDVIDCSSGGILESEVVNA 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                P        +IK+E     + + G ++   QA +I+ +   D V IGR   K+  
Sbjct: 272 Y----PGFQVPYSEKIKREAKIKTMTV-GLIKSYYQAEEIISNNRADLVAIGREFLKDPY 326

Query: 225 M 225
           +
Sbjct: 327 L 327


>gi|223937322|ref|ZP_03629228.1| TIM-barrel protein, nifR3 family [bacterium Ellin514]
 gi|223894107|gb|EEF60562.1| TIM-barrel protein, nifR3 family [bacterium Ellin514]
          Length = 33

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 11/33 (33%), Positives = 20/33 (60%)

Query: 62 LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
          + +AA  +E  G + I++N+GCP  +V +   G
Sbjct: 1  MRDAAIYLESIGISSIDINMGCPVRKVCKVGDG 33


>gi|226307267|ref|YP_002767227.1| oxidoreductase [Rhodococcus erythropolis PR4]
 gi|226186384|dbj|BAH34488.1| putative oxidoreductase [Rhodococcus erythropolis PR4]
          Length = 367

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 54/166 (32%), Gaps = 20/166 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKC---------RIGVDDQIPAVALRNLVK 141
           +G        ++ + + A+ +     +P+ V+          R    D   A     L  
Sbjct: 203 YGGSFENRIRLLLEILTAVREVWPAELPLFVRVSATDWLTEERGLEVDSWTADQTVALAN 262

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            +   GV+ + +        G SP     + P         ++ E+  L     G + + 
Sbjct: 263 ILSDYGVDLVDVSTG-----GNSPAAQIPVEPGYQVPFARRLQNESL-LPAAAVGLITEP 316

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
            QA KI+   S   V++GR   ++           +  +    P +
Sbjct: 317 EQAEKIVEDGSAVAVLLGRELLRDPYWARRAARELNAEVGPHIPSQ 362


>gi|160876119|ref|YP_001555435.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS195]
 gi|160861641|gb|ABX50175.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS195]
 gi|315268316|gb|ADT95169.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS678]
          Length = 364

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 62/180 (34%), Gaps = 24/180 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +A+  E  G + I ++            P +      +G  L     ++     A+ 
Sbjct: 160 FVSSAQRAERLGLDAIEIHAAHGYLLHQFLSPLSNQRTDKYGGSLENRLSLLLGVFDAIK 219

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +S  + +  RI   D +           L K+++  G + I +        GLSP   
Sbjct: 220 AVISPKMALGVRISATDWVEGGWDLAQSLVLAKALESRGCDFIHVSTG-----GLSPLQQ 274

Query: 169 RKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             IP  ++  V   E  K   ++ +   G + D ++A   L     D + + R    +  
Sbjct: 275 --IPVAEHFQVPFAEAIKAEVNIPVVAVGLITDANKAETTLAQGQADAIALARTMLYDPH 332


>gi|300765030|ref|ZP_07075018.1| NADH:flavin oxidoreductase [Listeria monocytogenes FSL N1-017]
 gi|300514330|gb|EFK41389.1| NADH:flavin oxidoreductase [Listeria monocytogenes FSL N1-017]
          Length = 338

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 EEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVTPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     + G 
Sbjct: 317 KDAAKQLGETIEGP 330


>gi|84501872|ref|ZP_01000030.1| 2,4-dienoyl-CoA reductase [Oceanicola batsensis HTCC2597]
 gi|84389867|gb|EAQ02501.1| 2,4-dienoyl-CoA reductase [Oceanicola batsensis HTCC2597]
          Length = 649

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 43/132 (32%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +       V  RI   D I    PA  +  L + I+ +G +   ++      +
Sbjct: 175 EIVRAVRERCGSEFLVIYRISAADLIEGGAPADEIAALARKIEAAGAD--ILNTGIGWHE 232

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P     +P   +       K    + +  +  +     +  IL S D  MI   R  
Sbjct: 233 ARVPTIAYPVPRGAWRKAAANVKAAVSIPVVASNRINTPQLSEDILASGDADMISMARPF 292

Query: 220 YKNSAMLTTVDE 231
             +   +    E
Sbjct: 293 LADPHFVKKARE 304


>gi|319442439|ref|ZP_07991595.1| NADH-dependent flavin oxidoreductase [Corynebacterium variabile DSM
           44702]
          Length = 376

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 32/194 (16%), Positives = 65/194 (33%), Gaps = 19/194 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VEA +  +   Y+ + ++            P        +G  L     ++ + +AA+ 
Sbjct: 168 FVEATRRADAADYDVVQIHAAHGYLIHQFLSPLTNTRTDGYGGELAGRSRLLREVVAAVR 227

Query: 113 KAL--SIPVTVKCR-IGVD-DQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKD 167
                S P+ ++      D D +    + ++++ +  +G V+ I + +         P  
Sbjct: 228 AVWPDSKPLGIRVSGTDWDEDGLQVEEVASVLRDLVAAGQVSWIDVSSGGLTDGSTIPVG 287

Query: 168 NRKIPNLDYDIVYEIKKENPD---LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                 L   +   + +E        +   G +ED  QA  +L       V +GRAA  N
Sbjct: 288 PGYQVPLAVAVTEALAEEGLGEDAAVVSAVGLIEDALQAETVLATGQAHAVSVGRAALVN 347

Query: 223 SAMLTTVDEYFSNP 236
                        P
Sbjct: 348 PHWAAKAAADLRVP 361


>gi|70731328|ref|YP_261069.1| 2,4-dienoyl-CoA reductase FadH [Pseudomonas fluorescens Pf-5]
 gi|68345627|gb|AAY93233.1| 2,4-dienoyl-CoA reductase FadH [Pseudomonas fluorescens Pf-5]
          Length = 679

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 18/132 (13%), Positives = 44/132 (33%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     I   +     V+       +  L ++I+++G   I  +      +
Sbjct: 200 EIVRRVREAVGPNFIIIFRLSMLDLVEGGSTWEEIVQLAQAIEQAGATLI--NTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    + +  + +     +     A +IL   D  M+   R  
Sbjct: 258 ARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAEQILAEGDADMVSMARPF 317

Query: 220 YKNSAMLTTVDE 231
             +   +    E
Sbjct: 318 LADPDFVNKAAE 329


>gi|116754727|ref|YP_843845.1| imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta
           thermophila PT]
 gi|116666178|gb|ABK15205.1| imidazole glycerol phosphate synthase subunit hisF [Methanosaeta
           thermophila PT]
          Length = 289

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 23/140 (16%), Positives = 49/140 (35%), Gaps = 13/140 (9%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           M +   +  C+  +     +P  VK    VD +     +    +  ++ G + +      
Sbjct: 19  MRDYAKIVPCLD-VKVVDGVPSVVKGVKFVDLKHQGDPVA-FARRYQEQGADELVFLDIT 76

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           A  +G     +          V     +  D+   + GG+  +    +IL    D V I 
Sbjct: 77  ASHEGRKTMVD----------VARRVADAVDIPFTVGGGISSIQGIKEILDAGADRVGIN 126

Query: 217 RAAYKNSAMLTTVDEYFSNP 236
            AA +N  ++ +  + F + 
Sbjct: 127 TAAVRNPDLVRSAAQAFGSE 146


>gi|329926240|ref|ZP_08280804.1| NADPH dehydrogenase [Paenibacillus sp. HGF5]
 gi|328939375|gb|EGG35730.1| NADPH dehydrogenase [Paenibacillus sp. HGF5]
          Length = 345

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 31/208 (14%), Positives = 67/208 (32%), Gaps = 26/208 (12%)

Query: 54  IGGADISKLVE----AAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN 100
           +   ++ ++VE    A +     G++ I L             P        +G  L   
Sbjct: 133 LTTEEVKQMVEKFRVAVRRAVKAGFDAIELHGAHGYLIHQFHSPLTNRRTDEYGQELTK- 191

Query: 101 PDIVGDCIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                + I A    +   +P+ ++   R  V +           K  + +GV+   +   
Sbjct: 192 --FGQEVIQAAKSEMPEDMPLIMRISAREYVTNGYGIEESIAFSKIYQAAGVDMFHV--- 246

Query: 157 KAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--V 213
            A  +G    + R   ++ Y + +    KE     +   G L++ + A  ++ + D   V
Sbjct: 247 SAGGEGPIAAEGRPGTHVAYQVPLARQIKEALQAPVIAVGRLDEPALANAVIGNEDADLV 306

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +GR   +N                  +
Sbjct: 307 AVGRGMLRNPYWTLEAATLLQKEFAIPA 334


>gi|107103237|ref|ZP_01367155.1| hypothetical protein PaerPA_01004306 [Pseudomonas aeruginosa PACS2]
 gi|218890001|ref|YP_002438865.1| putative FMN oxidoreductase [Pseudomonas aeruginosa LESB58]
 gi|254236633|ref|ZP_04929956.1| hypothetical protein PACG_02636 [Pseudomonas aeruginosa C3719]
 gi|126168564|gb|EAZ54075.1| hypothetical protein PACG_02636 [Pseudomonas aeruginosa C3719]
 gi|218770224|emb|CAW25986.1| probable FMN oxidoreductase [Pseudomonas aeruginosa LESB58]
          Length = 368

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 58/169 (34%), Gaps = 11/169 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G C      ++    AA+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGGCFENRIRLLLQVTAAVRKAWPQELPLFVRLSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +K  GV+ I + +        +  +    P    +    +KKE   +  G  G + +
Sbjct: 250 ARRLKDLGVDLIDVSSGGTA----ANAEIPVGPGYQTEFAERVKKEAG-IASGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
             QA  IL     D +++ R   ++        +   N      P   R
Sbjct: 305 PVQAEHILRTGQADLILLARELLRDPYWPLHAADELRNEQMPWPPQYLR 353


>gi|322382864|ref|ZP_08056699.1| NADPH dehydrogenase NamA-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321153133|gb|EFX45588.1| NADPH dehydrogenase NamA-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 345

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 64/182 (35%), Gaps = 26/182 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K  + AK     G++ + L             P     E  +G  L        + I A
Sbjct: 150 EKFRDTAKRAVKAGFDTVELHGAHGYLIHQFHSPLTNKREDIYGQDLAR---FGIEVIQA 206

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLS-- 164
           +   L   +P+ ++      +Q       + +L +  K++GV+   + +     KG S  
Sbjct: 207 VKSELPSGMPLIMRVSAIEYEQGGYGLDHIIDLARQYKEAGVDLFDVSSGGESAKGPSNG 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKN 222
                ++P   +       K++ ++ +   G L D + A   + S D   V +GR    +
Sbjct: 267 KDPGYQVPFARH------IKDHVNIPVMSVGNLSDYNVAELTVASGDSELVAVGRGMLGD 320

Query: 223 SA 224
             
Sbjct: 321 PY 322


>gi|21242578|ref|NP_642160.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|23821709|sp|Q8PLG6|HIS6_XANAC RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|21108037|gb|AAM36696.1| cyclase [Xanthomonas axonopodis pv. citri str. 306]
          Length = 258

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|59711625|ref|YP_204401.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio fischeri
           ES114]
 gi|81310966|sp|Q5E633|HIS6_VIBF1 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|59479726|gb|AAW85513.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Vibrio fischeri ES114]
          Length = 257

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D V I   A  N  ++T + + F 
Sbjct: 85  TAEDAAKILEFGADKVSINSPALANPELITELADKFG 121


>gi|290969099|ref|ZP_06560629.1| putative L-lactate dehydrogenase [cytochrome] [Megasphaera
           genomosp. type_1 str. 28L]
 gi|290780859|gb|EFD93457.1| putative L-lactate dehydrogenase [cytochrome] [Megasphaera
           genomosp. type_1 str. 28L]
          Length = 348

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 45/115 (39%), Gaps = 22/115 (19%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--HARKAILKGL 163
           + I AM KA S+P  VK  +   +           +    +GV  I +  H  +A+    
Sbjct: 199 ESIEAMVKASSLPFIVKGIMSPQE----------AQICVDAGVAAIVVSNHGGRALDGMA 248

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
              D         +I   +K     + I ++GG+      LK+L    D V+IGR
Sbjct: 249 GTADVLP------EIAAAVK---GQIHIFVDGGVRHGEDVLKMLALGADAVLIGR 294


>gi|290560230|pdb|3IIV|A Chain A, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560231|pdb|3IIV|B Chain B, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
          Length = 263

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+ I + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPITVGGGIYDFETASELILRGADKVEINTAAVENPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                     RVD +F 
Sbjct: 123 QAVVVYIAAKRVDGEFM 139


>gi|170720754|ref|YP_001748442.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
 gi|169758757|gb|ACA72073.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
          Length = 678

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 28/231 (12%), Positives = 68/231 (29%), Gaps = 38/231 (16%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++            E  +  QI        V  A + +  GY+
Sbjct: 106 LHAGRYAYSPRQVAPSAIQAPINPFKPKELDEAGIEKQIA-----DFVNCAVLAQRAGYD 160

Query: 76  EINLNVGCPSARVHEGSFGA--CLMLNPD---------------IVGDCIAAMCKALS-- 116
            + +        +    +     L+ + +               +  + ++ +  A+   
Sbjct: 161 GVEI--------MGSEGYFINQFLVAHTNHRTDRWGGSYENRMRLAVEIVSRVRDAVGPN 212

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I   +     V+       +  L K+++++G   I  +      +   P    K+P  
Sbjct: 213 FIIIFRLSMLDLVEGGSTWDEIELLAKAVERAGATLI--NTGIGWHEARIPTIATKVPRA 270

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
            +  V    +    + +     +     A  +L   D  M+   R    + 
Sbjct: 271 AFSKVTAKLRGAVKIPLITTNRINTPEVAEAVLAEGDADMVSMARPFLADP 321


>gi|330808581|ref|YP_004353043.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|327376689|gb|AEA68039.1| putative 2,4-dienoyl-CoA reductase (NADPH) [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 679

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 42/124 (33%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     I   +     V+       +  L K+I+++G     I+      +
Sbjct: 200 EIVRRVREAVGPNFIIIFRLSMLDLVEGGSSWDEIVQLAKAIEQAGAT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    + +  + +     +     A +IL   D  M+   R  
Sbjct: 258 ARIPTIATKVPRAAFSKVTAKLRGSVSIPLITTNRINTPEVAEQILAEGDADMVSMARPF 317

Query: 220 YKNS 223
             + 
Sbjct: 318 LADP 321


>gi|284044660|ref|YP_003395000.1| dihydroorotate dehydrogenase [Conexibacter woesei DSM 14684]
 gi|283948881|gb|ADB51625.1| dihydroorotate dehydrogenase family protein [Conexibacter woesei
           DSM 14684]
          Length = 303

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 31/200 (15%), Positives = 61/200 (30%), Gaps = 26/200 (13%)

Query: 49  PLALQIGGADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           PL + + G    ++ +      E      + LNV CP         G  +  +P      
Sbjct: 101 PLIVNVMGFTREEVAQLVTAFAERDEVAALELNVSCP-----NVETGTIMGSDPTETARL 155

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVAL--------RNLVKSIKKSGVNGIWIHARKAI 159
           +  +      P+ VK      D                +L+ +I+      +    R+  
Sbjct: 156 VERVRPLTQKPIVVKLTPNASDPGAVAEAAEAAGADGLSLINTIRGM---ALDPRTREPW 212

Query: 160 L----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM 214
           L     G+S    R +       V +       + +   GG++    A  +L      V 
Sbjct: 213 LGAGTGGVSGATVRAVALAQVSDVAQ----RVSIPLIAMGGVQRGRDADDLLRAGATLVA 268

Query: 215 IGRAAYKNSAMLTTVDEYFS 234
           +G  ++++ A    V     
Sbjct: 269 VGTESFRDPAAGRRVAHELE 288


>gi|225352004|ref|ZP_03743027.1| hypothetical protein BIFPSEUDO_03609 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157251|gb|EEG70590.1| hypothetical protein BIFPSEUDO_03609 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 316

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 74/218 (33%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G      VE    + D   + + +NV CP    +  + G  +  +P  +   I 
Sbjct: 109 VIANVAGHCDDDYVEVVSKLNDSPADMLEINVSCP----NVSAGGMSVGTDPVALSRLIT 164

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            + K     + VK    V D           ++  +SG + +            I   + 
Sbjct: 165 RLRKLTDKKMIVKLTPNVTDITVP------ARAAVESGADALSMINTLLGMRINIRTGEP 218

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           I+  +        +  +    V++ +   P+  I   GG++   +AL+ L    + V +G
Sbjct: 219 IIDHVTGGVSGPAVLPMGLVAVWKTRSALPNTPIIGIGGIDSGEKALEYLYAGANAVEVG 278

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA         V       L     +  ++ K + WR
Sbjct: 279 AAALFEPTAPLRVARELDELLDARPELADKLAKGETWR 316


>gi|59712249|ref|YP_205025.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Vibrio fischeri
           ES114]
 gi|59480350|gb|AAW86137.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Vibrio fischeri
           ES114]
          Length = 667

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + I A+ + +     +  R+     V+       +  L + ++K+GV    ++      +
Sbjct: 197 EIIKAIREKVGADFIIIFRLSMLDLVEQGSTFDEVVELAQELEKAGVT--ILNTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P    ++P   +  V E +K +     +  N  +     A  IL     D V + R 
Sbjct: 255 ARIPTIATQVPRAAFSWVTEKLKNKVSIPLVTCNR-INTPEVAENILATGQADMVSMARP 313

Query: 219 AYKNS 223
              + 
Sbjct: 314 FLADP 318


>gi|313792726|gb|EFS40807.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL110PA1]
          Length = 327

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 62/180 (34%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E+ G   I  N+      +  G          D   +
Sbjct: 95  DIPVIASLNGATNGGWVDTAKRMENAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 149

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G  G+ +  R  +L+     
Sbjct: 150 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDGAGAAGLVMFNR--VLQPDINV 201

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVM 214
           +  ++    +             +  +        +  + G+E        +L   D VM
Sbjct: 202 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESANDVVKYLLAGADVVM 260


>gi|254853526|ref|ZP_05242874.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL R2-503]
 gi|258606899|gb|EEW19507.1| NADPH dehydrogenase NamA [Listeria monocytogenes FSL R2-503]
          Length = 338

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 EEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     + G 
Sbjct: 317 KDAAKQLGETIEGP 330


>gi|148974841|ref|ZP_01811821.1| putative NADH-dependent flavin oxidoreductase [Vibrionales
           bacterium SWAT-3]
 gi|145965350|gb|EDK30599.1| putative NADH-dependent flavin oxidoreductase [Vibrionales
           bacterium SWAT-3]
          Length = 370

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 74/211 (35%), Gaps = 23/211 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A+   +  G++ + ++            P     E  +G  L      + +   A
Sbjct: 145 DAFAKASLRAKQSGFDGVEIHAAHTYLINQFLSPYYNQREDEYGGSLENRMRFLLEIYTA 204

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
             K +    P+ VK       +  +     R + K +++ GV+GI     IH +   + G
Sbjct: 205 TRKLVGDDFPILVKLTASEFFEGGVTFDETRMVCKKLEEVGVDGIVVSGNIHGKADTMIG 264

Query: 163 LSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRA 218
            S  D   I    Y  +  + I ++  D+ +   GGL D    +A+     ++   + R 
Sbjct: 265 ES-YDGFTIQAEGYFHEYGHAISQDV-DIPVITVGGLTDFDAIEAIANNTGIEYFALSRP 322

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
                 ++    E   +P+      K R  +
Sbjct: 323 LLSEPHLVKRWKEGDRSPVECERCSKCRTKR 353


>gi|126731479|ref|ZP_01747285.1| probable methylamine [Sagittula stellata E-37]
 gi|126708015|gb|EBA07075.1| probable methylamine [Sagittula stellata E-37]
          Length = 689

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 64/188 (34%), Gaps = 21/188 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL----NVGCPSARVHEG------SFGACLMLNPDIVGDCIAA 110
             V AAK   + G++ INL      G     +          +G  L        + +A 
Sbjct: 152 WFVNAAKRSREAGFDLINLYGAHGFGIFQHFLSRATNQRTDEYGGSLENRSRFAREVVAD 211

Query: 111 MCKALSIPVTVKCRIGVDDQI-----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +  A+   + +  R+ +D+ I         +R+ ++  +         H       G S 
Sbjct: 212 IRDAVGDTMAIAMRVSLDESIGDLGFSNAEVRDFIEMNRDLPDIWDLAHGAWEDCSGPS- 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               K     +D+V  I  +  D  I   G        +K++   ++D +   R +  + 
Sbjct: 271 --RFKEEAAQFDLVKAIH-DFTDKPIVGVGRFTSPDVMVKMIKSGTLDMIGCARPSIADP 327

Query: 224 AMLTTVDE 231
            +   ++E
Sbjct: 328 FLPKKIEE 335


>gi|302343458|ref|YP_003807987.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfarculus baarsii DSM
           2075]
 gi|301640071|gb|ADK85393.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfarculus baarsii DSM
           2075]
          Length = 365

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 42/130 (32%), Gaps = 8/130 (6%)

Query: 109 AAMCKAL--SIPVTVKCRIGVDDQIPAVALRNL---VKSIKKSGVNGIWIHARKAILKGL 163
            A  +A+    PV +K     D     + L +     + +   GV+ I            
Sbjct: 204 QAARQAVGPDYPVFIKLSSH-DAMEGGLVLEDALHVARRLDAMGVDAIEASGGVIAAGKN 262

Query: 164 SPKDNRKIPNLDYDIVYEIK--KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
           SP    K P  +   + E K  K      +   GG     +  + L ++D V I R   +
Sbjct: 263 SPSRLVKGPEQEGYFLAEAKAIKAAVKCPVISVGGWRTRPRIEQALDAIDAVAICRPLVR 322

Query: 222 NSAMLTTVDE 231
              +     +
Sbjct: 323 QPDLPRRWAQ 332


>gi|262274574|ref|ZP_06052385.1| 2,4-dienoyl-CoA reductase [NADPH] [Grimontia hollisae CIP 101886]
 gi|262221137|gb|EEY72451.1| 2,4-dienoyl-CoA reductase [NADPH] [Grimontia hollisae CIP 101886]
          Length = 669

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 27/190 (14%), Positives = 66/190 (34%), Gaps = 17/190 (8%)

Query: 57  ADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDC 107
             I    ++A++  + GY+ + +            C  +      +G        +  D 
Sbjct: 141 NTIKDFAKSAELAREAGYDGVEIMGSEGYLINQFICARSNTRYDRWGGSYENRMRLAVDI 200

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGL 163
           + A+ +       +  R+ + D +   +  +    L K+++ +GV    I+      +  
Sbjct: 201 VKAVHERAGRDFIIIFRLSMLDLVEQGSTHDEVVMLAKALESAGVT--IINTGIGWHEAR 258

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
            P    ++P   +  V E  K   ++ +     +     A  IL     D V + R    
Sbjct: 259 IPTIATQVPRAAFAWVTERLKGEVNVPLVTCNRINTPEVAENILASGQADMVSMARPFLA 318

Query: 222 NSAMLTTVDE 231
           ++A +   ++
Sbjct: 319 DAAFVAKAEQ 328


>gi|255030195|ref|ZP_05302146.1| NADPH dehydrogenase NamA [Listeria monocytogenes LO28]
          Length = 325

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 64/189 (33%), Gaps = 21/189 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAV 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSN 235
               +    
Sbjct: 317 KDAAKQLGE 325


>gi|212715931|ref|ZP_03324059.1| hypothetical protein BIFCAT_00842 [Bifidobacterium catenulatum DSM
           16992]
 gi|212661298|gb|EEB21873.1| hypothetical protein BIFCAT_00842 [Bifidobacterium catenulatum DSM
           16992]
          Length = 316

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 74/218 (33%), Gaps = 24/218 (11%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   + G      VE    + D   + + +NV CP    +  + G  +  +P  +   I 
Sbjct: 109 VIANVAGHCDDDYVEVVSKLNDSPADMLEINVSCP----NVSAGGMSVGTDPVALSRLIT 164

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-----------IHARKA 158
            + K     + VK    V D           ++  +SG + +            I   + 
Sbjct: 165 RLRKLTDKKMIVKLTPNVTDITVP------ARAAVESGADALSMINTLLGMRINIRTGEP 218

Query: 159 ILKGL-SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           I+  +        +  +    V++ +   P   I   GG++   +AL+ L    + V +G
Sbjct: 219 IIDHVTGGVSGPAVLPMGLVAVWKTRSALPKTPIIGIGGIDSGEKALEYLYAGANAVEVG 278

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK-DFWR 253
            AA         V     + L     +  ++ K + WR
Sbjct: 279 AAALFEPTAPLRVARELDDLLDARPELADKLAKGETWR 316


>gi|294625084|ref|ZP_06703731.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
 gi|292600629|gb|EFF44719.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
          Length = 258

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDVGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|209694689|ref|YP_002262617.1| imidazole glycerol phosphate synthase subunit HisF [Aliivibrio
           salmonicida LFI1238]
 gi|226700480|sp|B6EJ93|HIS6_ALISL RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|208008640|emb|CAQ78824.1| imidazole glycerol phosphate synthase subunit HisF [Aliivibrio
           salmonicida LFI1238]
          Length = 257

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D V I   A  N  ++T + + F 
Sbjct: 85  TAEDAAKILEFGADKVSINSPALANPELITELADKFG 121


>gi|313109129|ref|ZP_07795100.1| putative FMN oxidoreductase [Pseudomonas aeruginosa 39016]
 gi|310881602|gb|EFQ40196.1| putative FMN oxidoreductase [Pseudomonas aeruginosa 39016]
          Length = 368

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 58/169 (34%), Gaps = 11/169 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G C      ++    AA+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGGCFENRIRLLLQVTAAVRKAWPEELPLFVRLSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +K  GV+ I + +        +  +    P    +    +KKE   +  G  G + +
Sbjct: 250 ARRLKDLGVDLIDVSSGGTA----ANAEIPVGPGYQTEFAERVKKEAG-IASGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
             QA  IL     D +++ R   ++        +   N      P   R
Sbjct: 305 PVQAEHILRTGQADLILLARELLRDPYWPLHAADELRNEQMPWPPQYLR 353


>gi|78047436|ref|YP_363611.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325925147|ref|ZP_08186560.1| imidazole glycerol phosphate synthase subunit hisF [Xanthomonas
           perforans 91-118]
 gi|85541726|sp|Q3BUF2|HIS6_XANC5 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|78035866|emb|CAJ23557.1| imidazoleglycerol phosphate synthase, cyclase subunit [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325544401|gb|EGD15771.1| imidazole glycerol phosphate synthase subunit hisF [Xanthomonas
           perforans 91-118]
          Length = 258

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 47/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A     +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|319901734|ref|YP_004161462.1| dihydroorotate oxidase [Bacteroides helcogenes P 36-108]
 gi|319416765|gb|ADV43876.1| dihydroorotate oxidase [Bacteroides helcogenes P 36-108]
          Length = 325

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 29/194 (14%), Positives = 59/194 (30%), Gaps = 41/194 (21%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--- 105
           P+   I     +  V+ AK +E+ G + + +N+               L  + +      
Sbjct: 98  PVIASINCYQNADWVDFAKQIEEAGADALEINI-------------LALQTDVEYTYGSF 144

Query: 106 -----DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---- 156
                D ++ + K ++IPV +K                L+  +  +G   I +  R    
Sbjct: 145 EQRHIDILSHIKKTVNIPVIMKL------GDNLTNPVALINQLYANGAAAIVLFNRFYQP 198

Query: 157 -------KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILP 208
                    +   +   +      L +  +        +L    +GG+         IL 
Sbjct: 199 DINIEKMTQVSGNVFSSEADLSKALRWIGIAS--ASVGNLDYAASGGIHSPEGVVKAILA 256

Query: 209 SVDGVMIGRAAYKN 222
               V I    Y+N
Sbjct: 257 GASAVEICSVLYQN 270


>gi|314938645|ref|ZP_07845925.1| dihydroorotate oxidase [Enterococcus faecium TX0133a04]
 gi|314944089|ref|ZP_07850752.1| dihydroorotate oxidase [Enterococcus faecium TX0133C]
 gi|314950327|ref|ZP_07853608.1| dihydroorotate oxidase [Enterococcus faecium TX0082]
 gi|314951099|ref|ZP_07854161.1| dihydroorotate oxidase [Enterococcus faecium TX0133A]
 gi|314992315|ref|ZP_07857749.1| dihydroorotate oxidase [Enterococcus faecium TX0133B]
 gi|313593131|gb|EFR71976.1| dihydroorotate oxidase [Enterococcus faecium TX0133B]
 gi|313596733|gb|EFR75578.1| dihydroorotate oxidase [Enterococcus faecium TX0133A]
 gi|313597316|gb|EFR76161.1| dihydroorotate oxidase [Enterococcus faecium TX0133C]
 gi|313642033|gb|EFS06613.1| dihydroorotate oxidase [Enterococcus faecium TX0133a04]
 gi|313643344|gb|EFS07924.1| dihydroorotate oxidase [Enterococcus faecium TX0082]
          Length = 290

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 39/211 (18%), Positives = 71/211 (33%), Gaps = 28/211 (13%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
             Q +PL   I G  + + +E  + +E  G+N I  LN+ CP   V        L  + +
Sbjct: 68  ENQNQPLFFSIAGMSVQENLEMLEKIEKSGFNGITELNLSCP--NVPGK---PQLAYDFE 122

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 123 ATYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 181

Query: 156 --------RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
                    K    G+  +  +     +    Y   K  P++ I   GG+     A +  
Sbjct: 182 EQEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLK--PEIQIIGTGGIRTGQDAFEHL 239

Query: 207 LPSVDGVMIGRAAYKN--SAMLTTVDEYFSN 235
           L     + IG          + + + +  + 
Sbjct: 240 LCGASMLQIGTE-LHKEGPEIFSRIIKELTQ 269


>gi|257878300|ref|ZP_05657953.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,230,933]
 gi|257880918|ref|ZP_05660571.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,502]
 gi|257889499|ref|ZP_05669152.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,410]
 gi|257892560|ref|ZP_05672213.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,408]
 gi|258616179|ref|ZP_05713949.1| dihydroorotate dehydrogenase 1A [Enterococcus faecium DO]
 gi|260559851|ref|ZP_05832030.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium C68]
 gi|293552751|ref|ZP_06673412.1| dihydroorotate dehydrogenase [Enterococcus faecium E1039]
 gi|293559680|ref|ZP_06676208.1| dihydroorotate dehydrogenase a [Enterococcus faecium E1162]
 gi|293569924|ref|ZP_06681011.1| dihydroorotate dehydrogenase a [Enterococcus faecium E1071]
 gi|294615209|ref|ZP_06695090.1| dihydroorotate dehydrogenase [Enterococcus faecium E1636]
 gi|294620017|ref|ZP_06699382.1| dihydroorotate dehydrogenase a [Enterococcus faecium E1679]
 gi|294620770|ref|ZP_06699976.1| dihydroorotate dehydrogenase a [Enterococcus faecium U0317]
 gi|257812528|gb|EEV41286.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,230,933]
 gi|257816576|gb|EEV43904.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,502]
 gi|257825859|gb|EEV52485.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,410]
 gi|257828939|gb|EEV55546.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,408]
 gi|260074075|gb|EEW62398.1| dihydroorotate dehydrogenase 1 [Enterococcus faecium C68]
 gi|291587672|gb|EFF19549.1| dihydroorotate dehydrogenase a [Enterococcus faecium E1071]
 gi|291591933|gb|EFF23561.1| dihydroorotate dehydrogenase [Enterococcus faecium E1636]
 gi|291593739|gb|EFF25248.1| dihydroorotate dehydrogenase a [Enterococcus faecium E1679]
 gi|291599627|gb|EFF30638.1| dihydroorotate dehydrogenase a [Enterococcus faecium U0317]
 gi|291603060|gb|EFF33251.1| dihydroorotate dehydrogenase [Enterococcus faecium E1039]
 gi|291606355|gb|EFF35761.1| dihydroorotate dehydrogenase a [Enterococcus faecium E1162]
          Length = 314

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 39/211 (18%), Positives = 71/211 (33%), Gaps = 28/211 (13%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
             Q +PL   I G  + + +E  + +E  G+N I  LN+ CP   V        L  + +
Sbjct: 92  ENQNQPLFFSIAGMSVQENLEMLEKIEKSGFNGITELNLSCP--NVPGK---PQLAYDFE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 147 ATYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 205

Query: 156 --------RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
                    K    G+  +  +     +    Y   K  P++ I   GG+     A +  
Sbjct: 206 EQEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLK--PEIQIIGTGGIRTGQDAFEHL 263

Query: 207 LPSVDGVMIGRAAYKN--SAMLTTVDEYFSN 235
           L     + IG          + + + +  + 
Sbjct: 264 LCGASMLQIGTE-LHKEGPEIFSRIIKELTQ 293


>gi|197335148|ref|YP_002156463.1| 2,4-dienoyl-coa reductase (nadph) [Vibrio fischeri MJ11]
 gi|197316638|gb|ACH66085.1| 2,4-dienoyl-coa reductase (nadph) [Vibrio fischeri MJ11]
          Length = 667

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + I A+ + +     +  R+     V+       +  L + ++K+GV    ++      +
Sbjct: 197 EIIKAIREKVGADFIIIFRLSMLDLVEQGSTFDEVVELAQELEKAGVT--ILNTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P    ++P   +  V E +K +     +  N  +     A  IL     D V + R 
Sbjct: 255 ARIPTIATQVPRAAFSWVTEKLKNKVSIPLVTCNR-INTPEVAENILATGQADMVSMARP 313

Query: 219 AYKNS 223
              + 
Sbjct: 314 FLADP 318


>gi|75812808|ref|YP_320425.1| flavin oxidoreductase/NADH oxidase [Anabaena variabilis ATCC 29413]
 gi|75705564|gb|ABA25236.1| flavin oxidoreductase/NADH oxidase [Anabaena variabilis ATCC 29413]
          Length = 357

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 61/182 (33%), Gaps = 28/182 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V AA+     G+  I ++            P +      +G  L     ++ + +  + 
Sbjct: 157 FVAAAQRALQVGFQMIEIHAAHGYLLHSFLSPLSNRRTDRYGGSLENRMRLLLEVVRRVR 216

Query: 113 KAL--SIPVTVKCRIG------VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             L   +P+ V+           D Q   +  R L    K  GV+ I +     +     
Sbjct: 217 DVLPNGMPLFVRISATDWVEGGWDLQQSIILSREL----KTLGVDLIDVSTGGLVPHARI 272

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P +             +I++E   +  G  G + +   A +I+     D V+IGR   +N
Sbjct: 273 PVEKGYQVP----FAAKIREEAGIM-TGAVGLINEAEYADQIITRGCADLVLIGRELLRN 327

Query: 223 SA 224
             
Sbjct: 328 PY 329


>gi|69248093|ref|ZP_00604622.1| Dihydroorotate dehydrogenase 1 [Enterococcus faecium DO]
 gi|68194567|gb|EAN09059.1| Dihydroorotate dehydrogenase 1 [Enterococcus faecium DO]
          Length = 315

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 39/211 (18%), Positives = 71/211 (33%), Gaps = 28/211 (13%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
             Q +PL   I G  + + +E  + +E  G+N I  LN+ CP   V        L  + +
Sbjct: 93  ENQNQPLFFSIAGMSVQENLEMLEKIEKSGFNGITELNLSCP--NVPGK---PQLAYDFE 147

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 148 ATYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 206

Query: 156 --------RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
                    K    G+  +  +     +    Y   K  P++ I   GG+     A +  
Sbjct: 207 EQEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLK--PEIQIIGTGGIRTGQDAFEHL 264

Query: 207 LPSVDGVMIGRAAYKN--SAMLTTVDEYFSN 235
           L     + IG          + + + +  + 
Sbjct: 265 LCGASMLQIGTE-LHKEGPEIFSRIIKELTQ 294


>gi|170724483|ref|YP_001758509.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella woodyi ATCC
           51908]
 gi|169809830|gb|ACA84414.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella woodyi ATCC
           51908]
          Length = 364

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 59/167 (35%), Gaps = 20/167 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +A+   +  G++ + ++            P     +  +G  L      + +  A + 
Sbjct: 147 FAQASLRAQKSGFDGVEIHAAHTYLINQFLSPYYNQRQDEYGGSLENRMRFLLEIYAEIR 206

Query: 113 KAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGLS 164
           K +    PV VK       +  +     R + K ++  GV+ I I    H     + G S
Sbjct: 207 KLVGEDYPVLVKLTASEFFEGGLTFDETRTICKKLESIGVDAIIISGNIHGNANTVVGES 266

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
             D   I N  Y      +  E  +L I   GGL D+  A++ L   
Sbjct: 267 F-DGYTIQNEGYFREFGAVVSEEVNLPIITVGGLADI-CAIEELAET 311


>gi|167762345|ref|ZP_02434472.1| hypothetical protein BACSTE_00699 [Bacteroides stercoris ATCC
           43183]
 gi|167699988|gb|EDS16567.1| hypothetical protein BACSTE_00699 [Bacteroides stercoris ATCC
           43183]
          Length = 325

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 32/210 (15%), Positives = 64/210 (30%), Gaps = 44/210 (20%)

Query: 47  EKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I    D   + E A+ +E+ G + + +N+               L  +     
Sbjct: 96  DIPVIASINCYQDADWI-EFARKIEEAGADALEVNI-------------LALQTDIQYAY 141

Query: 106 --------DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR- 156
                   D ++ + K ++IPV +K                L+  +  +G   + +  R 
Sbjct: 142 GSFEQRHIDILSHIRKTVNIPVIMKL------GDNLTNPIALIDQLYANGAAAVVMFNRF 195

Query: 157 ----------KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALK 205
                           +   D     +L +  +         L    +GG+         
Sbjct: 196 YQPDIDIEKMAQSAGSVFSTDADLSKSLRWIGIAS--AAVSKLDYAASGGIHAPEGVVKA 253

Query: 206 ILPSVDGVMIGRAAYKNSA-MLTTVDEYFS 234
           IL     V I  A Y+NS  ++     + S
Sbjct: 254 ILAGASAVEICSALYQNSYAIIEEYVRFLS 283


>gi|332980714|ref|YP_004462155.1| NADH:flavin oxidoreductase/NADH oxidase [Mahella australiensis 50-1
           BON]
 gi|332698392|gb|AEE95333.1| NADH:flavin oxidoreductase/NADH oxidase [Mahella australiensis 50-1
           BON]
          Length = 668

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 32/200 (16%), Positives = 66/200 (33%), Gaps = 44/200 (22%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
              E+A I +  G++ + ++       VHEG                 +G  LM    + 
Sbjct: 156 MAAESAAIAKMAGFDGVEIHA------VHEGYLLDQFTIAMFNRRTDKYGGDLMGRLRLP 209

Query: 105 GDCIAAMCKA------LSIPVTVKCRIG------VDDQIPAVALRN------LVKSIKKS 146
            + + A+ K       +++  ++K  I       +D +      R+      +   ++K+
Sbjct: 210 IEIVKAIKKVNGEQFPVALRFSIKSYIKDWNQGGLDGEDFVEKGRDIQEGLTIAPILEKA 269

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G +     A        +     +   L   +  ++KK      I   G ++    A K 
Sbjct: 270 GYDAFDADAGSYDAWYWAHPPIYQKHGLYLPLTEQLKKVVNAPLIIA-GRIDIPELAEKT 328

Query: 207 LPS---VDGVMIGRAAYKNS 223
           L      D + IGR    + 
Sbjct: 329 LEEGKAADMINIGRGLLADP 348


>gi|307299220|ref|ZP_07579021.1| dihydroorotate dehydrogenase family protein [Thermotogales
           bacterium mesG1.Ag.4.2]
 gi|306915016|gb|EFN45402.1| dihydroorotate dehydrogenase family protein [Thermotogales
           bacterium mesG1.Ag.4.2]
          Length = 359

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 24/151 (15%), Positives = 53/151 (35%), Gaps = 24/151 (15%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKA 158
           +P ++ + I+A+      PV +K    V D         + + +++SG +GI  I++   
Sbjct: 130 DPSLIRELISAVKAGTEKPVFLKFDPSVPDP------AEMARVVQESGGDGIVAINSLGP 183

Query: 159 ILKGLSPKDNRKIPNLD---Y---DIVYEI-------KKENPDLFIGLNGGLEDMSQALK 205
           +       +   + + D   +    ++  +        +E   L I   GG+      + 
Sbjct: 184 VYPMDRRVNRSYLGSRDGFGWISGPVIRRLSLSSVRRIREGCTLPIIGVGGIVSADDVVD 243

Query: 206 IL-PSVDGV-MIGRAAYKN-SAMLTTVDEYF 233
            L      V M+   A      +   + E  
Sbjct: 244 FLCAGASAVQMLS-GALIRGKGIFKRILESL 273


>gi|283779595|ref|YP_003370350.1| NADH:flavin oxidoreductase/NADH oxidase [Pirellula staleyi DSM
           6068]
 gi|283438048|gb|ADB16490.1| NADH:flavin oxidoreductase/NADH oxidase [Pirellula staleyi DSM
           6068]
          Length = 364

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 26/155 (16%), Positives = 50/155 (32%), Gaps = 11/155 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGV 148
           +G  L     ++    +A+ + +   + +  RI   D             L KS+ + GV
Sbjct: 206 YGGSLENRMRLLVRVASAVREVIPREMPLLTRISATDWVAGGWDIEQSIELAKSLGEVGV 265

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I + +   +     P        L       I++E   +     G +    QA  IL 
Sbjct: 266 DMIDVSSGAIVPHVKIPVAPGYQVPL----AGRIRREA-SIKTAAVGLITSPEQAQAILD 320

Query: 209 S--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           +   D ++IGR   +         E         +
Sbjct: 321 AGDADLILIGRELLREPYWAHQAYEKLGGNSAWPT 355


>gi|313126942|ref|YP_004037212.1| NADH:flavin oxidoreductase [Halogeometricum borinquense DSM 11551]
 gi|312293307|gb|ADQ67767.1| NADH:flavin oxidoreductase [Halogeometricum borinquense DSM 11551]
          Length = 362

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 30/161 (18%), Positives = 53/161 (32%), Gaps = 22/161 (13%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC--------RIGVDDQIPAVALRNLVKS 142
           +G        +V +  AA+ +      PV V+         R   D    A     L   
Sbjct: 202 YGGSFENRTRLVREITAAVREVWPEDNPVFVRLSATDWLPDRESWDLDQSA----RLAPL 257

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY-EIKKENPDLFIGLNGGLEDMS 201
           +  +G + I + A      G+ P          Y + Y E   E  +L +G  G + +  
Sbjct: 258 LADAGADLIDVSAG-----GIHPDQQVPDTGPGYQVPYAEHVNEATELAVGTVGKITEPE 312

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           QA +I+ +   D   +GR   +N              ++  
Sbjct: 313 QADQIIRNGSADIAAVGREHLRNPYFSLEAAHELDEDVSWP 353


>gi|197334847|ref|YP_002155822.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           fischeri MJ11]
 gi|226702012|sp|B5FDA4|HIS6_VIBFM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|197316337|gb|ACH65784.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           fischeri MJ11]
          Length = 257

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D V I   A  N  ++T + + F 
Sbjct: 85  TAEDAAKILEFGADKVSINSPALANPELITELADKFG 121


>gi|90410826|ref|ZP_01218841.1| putative 2,4-dienoyl-CoA reductase [Photobacterium profundum 3TCK]
 gi|90328457|gb|EAS44755.1| putative 2,4-dienoyl-CoA reductase [Photobacterium profundum 3TCK]
          Length = 674

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 30/192 (15%), Positives = 62/192 (32%), Gaps = 27/192 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG---SFGACLMLNPDIV-GD 106
               ++A++  + GY+ + L            C   R +       G+    N      +
Sbjct: 148 EAFAKSAELAREAGYDGVELMGSEGYLVNQFIC--KRSNHRYDEWGGSY--ENRIRFPIE 203

Query: 107 CIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            + A+   +     +  RI     V+       +  L K ++K GV    ++      + 
Sbjct: 204 LVKAVRARVGKEFIIIFRISMLDLVEQGSTQQEVVQLAKELEKVGVT--ILNTGIGWHEA 261

Query: 163 LSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             P    ++P   +  V E +K E     +  N  +     A  IL     D V + R  
Sbjct: 262 RVPTIATQVPRAAFAWVTEKLKTEVNIPLVTCNR-INTPQVAEDILSANQADMVSMARPF 320

Query: 220 YKNSAMLTTVDE 231
             +   +   ++
Sbjct: 321 LADPDFVAKAEQ 332


>gi|50841649|ref|YP_054876.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes KPA171202]
 gi|50839251|gb|AAT81918.1| dihydroorotate dehydrogenase [Propionibacterium acnes KPA171202]
 gi|315107547|gb|EFT79523.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL030PA1]
          Length = 335

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 63/180 (35%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E+ G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMENAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGL----NG-------GLEDM-SQALKILPSVDGVM 214
           +  ++    + +        P  +I +     G       G+E        +L   D VM
Sbjct: 210 ETMQVEPGVW-LSSPADARLPLTWIAVLSGRIGASLAASSGVESANDVVKYLLAGADVVM 268


>gi|333030145|ref|ZP_08458206.1| dihydroorotate oxidase [Bacteroides coprosuis DSM 18011]
 gi|332740742|gb|EGJ71224.1| dihydroorotate oxidase [Bacteroides coprosuis DSM 18011]
          Length = 327

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 66/187 (35%), Gaps = 35/187 (18%)

Query: 46  QEKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
            E P+   I   +D   + + AK +E  G + I +N+    + V +  +G+    + D  
Sbjct: 97  NEVPIIASINCYSDSEWI-DFAKQIEAAGADAIEINILALQSNV-KYQYGSFEQRHID-- 152

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------- 153
              +  +   + IP+ +K      + I       L++ +  +G + I +           
Sbjct: 153 --ILKHIKNTVKIPIIMKLGHNFTNPIV------LIEQLYANGADAIVLFNRFYQPDIDI 204

Query: 154 ----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
               H    +L   S   N     L +  +     E   +    +GG+ +    +K IL 
Sbjct: 205 EKMKHVAGPVLSHPSELSN----ALRWIGIAS--SEVEKIDYAASGGVHNPEDIIKTILA 258

Query: 209 SVDGVMI 215
               V I
Sbjct: 259 GATAVEI 265


>gi|58426478|gb|AAW75515.1| cyclase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|167764314|gb|ABZ91974.1| cyclase [Xanthomonas oryzae pv. oryzae]
          Length = 280

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 45/130 (34%), Gaps = 11/130 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D I    +  L    +  G + +  +   A  +G S         +DY  V  + +
Sbjct: 43  VKFHDHIDMGDIVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVERVAR 93

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              D+   + GG+ D+  A  +L    D + I   A     +++ + + F          
Sbjct: 94  LI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRPQLISELADAFGVQCVVVGID 152

Query: 244 KTRVDKDFWR 253
             R D   WR
Sbjct: 153 SIREDDGQWR 162


>gi|285018045|ref|YP_003375756.1| imidazole glycerol phosphate synthase subunit hisf protein
           [Xanthomonas albilineans GPE PC73]
 gi|283473263|emb|CBA15768.1| probable imidazole glycerol phosphate synthase subunit hisf protein
           [Xanthomonas albilineans]
          Length = 258

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 27/134 (20%), Positives = 49/134 (36%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  VD       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHVDMGD----IAELALRYRDQGADELVFYDIGASPEGRS---------VDYAWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D++ A  +L    D + I   A +  A++  + + F      
Sbjct: 68  RVAR-LLDIPFCVAGGIRDVATARLVLHAGADKISINSPALERPALIAELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R +   WR
Sbjct: 127 VGIDSIREEDGQWR 140


>gi|167463906|ref|ZP_02328995.1| NADH-dependent flavin dehydrogenase [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 338

 Score = 42.1 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 64/182 (35%), Gaps = 26/182 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K  + AK     G++ + L             P     E  +G  L        + I A
Sbjct: 143 EKFRDTAKRAVKAGFDTVELHGAHGYLIHQFHSPLTNKREDIYGQDLAR---FGIEVIQA 199

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLS-- 164
           +   L   +P+ ++      +Q       + +L +  K++GV+   + +     KG S  
Sbjct: 200 VKSELPSGMPLIMRVSAIEYEQGGYGLDHIIDLARQYKEAGVDLFDVSSGGESAKGPSNG 259

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKN 222
                ++P   +       K++ ++ +   G L D + A   + S D   V +GR    +
Sbjct: 260 KDPGYQVPFARH------IKDHVNIPVMSVGNLSDYNVAELTVASGDSELVAVGRGMLGD 313

Query: 223 SA 224
             
Sbjct: 314 PY 315


>gi|323703116|ref|ZP_08114770.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531893|gb|EGB21778.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           nigrificans DSM 574]
          Length = 338

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 29/155 (18%), Positives = 58/155 (37%), Gaps = 11/155 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDD--QIPAVALRNLVKSIKKSGV 148
           +G         +G+ + A+   L   +P+ V+      +        +  ++  +K  G+
Sbjct: 183 YGGSPENRVRFLGEVLKAVKGVLPNDMPLIVRVSAHDIEPGGNTPEDMAQMLNLVKDIGI 242

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + + + +      G++P   +  P+        IK++     IG  G + D  QA +I+ 
Sbjct: 243 DLVNVSSG-----GVTPVAPKSYPSYQIPYAITIKEKTGLPVIGG-GLVNDPLQAEQIVK 296

Query: 208 PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             VD V IGR   +N              +T   P
Sbjct: 297 SGVDLVYIGRELLRNPYWPLHAAFILREDITWPEP 331


>gi|26988211|ref|NP_743636.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida KT2440]
 gi|24982949|gb|AAN67100.1|AE016338_10 xenobiotic reductase, putative [Pseudomonas putida KT2440]
          Length = 368

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 25/158 (15%), Positives = 55/158 (34%), Gaps = 11/158 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G+C      +    + A+ K     +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDEYGSCFENRIRLTLQVVEAVRKVWPAELPLFVRVSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + ++  GV+ I + +    +      +    P         ++KE  ++  G  G + +
Sbjct: 250 ARRLRVLGVDLIDVSSGGTSVN----AEIPTGPGYQTRFAERVRKEA-EIATGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +QA  IL     D + + R   ++       D+    
Sbjct: 305 PAQAEHILRTGQADVIFLARELLRDPYWPLHADDDLGG 342


>gi|163788676|ref|ZP_02183121.1| aconitate hydratase [Flavobacteriales bacterium ALC-1]
 gi|159875913|gb|EDP69972.1| aconitate hydratase [Flavobacteriales bacterium ALC-1]
          Length = 345

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 63/180 (35%), Gaps = 30/180 (16%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-----LSIPVTVKCRIGVD 128
            +   LNV CP+   H        + + D + + I+A+ KA        P+ +K    ++
Sbjct: 171 VDYFVLNVSCPNVGSHAK------LNDKDYLLELISAVQKANRTFAAQKPILLKIAPDLN 224

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP---------NLDYDIV 179
           D      L  +V+ I ++ ++G+         + L   D R             +     
Sbjct: 225 DG----QLDEIVELIAETNLDGVIASNTSTDREDLKTSDERLSEIGNGGLSGLPIKAKST 280

Query: 180 YEIK----KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA-AYKNSAMLTTVDEYF 233
             IK    K N    I   GG+     AL  L    D V +     Y+   ++  +++  
Sbjct: 281 RVIKYLADKSNKAFPIIGVGGIHSAKDALDKLDAGADLVQVYTGFIYEGPKLIKDINKAL 340


>gi|157374804|ref|YP_001473404.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sediminis
           HAW-EB3]
 gi|157317178|gb|ABV36276.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sediminis
           HAW-EB3]
          Length = 672

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 21/137 (15%), Positives = 44/137 (32%), Gaps = 10/137 (7%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVN 149
           G        +  + +    +A+     +  R+     V+D      +  L K I+ +G  
Sbjct: 187 GGSYQNRIRLALEIVRRTREAVGKEFIIIYRLSMLDLVEDGSTWQEVVELAKGIEAAGAT 246

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
              I+      +   P     +P   + +I   +K+E        N  +     A +IL 
Sbjct: 247 --IINTGIGWHEARVPTIATSVPRGAFTEITKRMKREVTIPLCTTNR-INTPEVAEEILA 303

Query: 209 S--VDGVMIGRAAYKNS 223
               D + + R    + 
Sbjct: 304 QGNADIISMARPMLADP 320


>gi|167031351|ref|YP_001666582.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
 gi|166857839|gb|ABY96246.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
          Length = 686

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 65/188 (34%), Gaps = 22/188 (11%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+  
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGTFEGRMKFGLEVLKAVRA 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ +      +G+               +  +  
Sbjct: 213 EVGDDFCVGMRICGDEFHPDGLSHEDMKQIAAYYDSTGMLDFIGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG--RAAYKN 222
            N   P   +  +    KE   + +     ++D +QA +IL    VD  M+G  RA   +
Sbjct: 273 PNMSYPPEPFLHLAAGIKEVVKVPVLHAQNIKDPNQATRILEGGYVD--MVGMTRAHMAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHLIAKIK 338


>gi|90417355|ref|ZP_01225280.1| 2,4-dienoyl-CoA reductase [marine gamma proteobacterium HTCC2207]
 gi|90330797|gb|EAS46066.1| 2,4-dienoyl-CoA reductase [marine gamma proteobacterium HTCC2207]
          Length = 674

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 45/125 (36%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D       +  +  L K+++++G     I+      +
Sbjct: 200 EVVRRVREAVGEHFIIIFRLSMLDLVEGGSTSEEVIQLGKAVEEAGAT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRA 218
              P    K+P   +  V    +KE     I  N  +     A ++L   D  MI   R 
Sbjct: 258 AKIPTIATKVPRAAFTWVTAHFRKELSVPVITSNR-INTPELAEEVLERGDADMISMARP 316

Query: 219 AYKNS 223
              + 
Sbjct: 317 FLADP 321


>gi|88705275|ref|ZP_01102986.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Congregibacter litoralis KT71]
 gi|88700365|gb|EAQ97473.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Congregibacter litoralis KT71]
          Length = 245

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 28/134 (20%), Positives = 47/134 (35%), Gaps = 11/134 (8%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +    +G   + +        G           ++ D V  I +E P+L I + GG+ +
Sbjct: 36  AQRWVDAGCRRLHLVDLNGAFAGT---------PVNGDAVTAIAREFPELPIQIGGGIRN 86

Query: 200 MSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRVDKDFWRKISA 257
           +      L   V  V+IG  A K    +      F   +  G    + RV  D W +++A
Sbjct: 87  LETIEFYLNAGVSYVIIGTQAVKQPTFVAEACAAFPGKIIVGLDAREGRVATDGWAEVTA 146

Query: 258 SMTDYAARHLHSGG 271
                 AR     G
Sbjct: 147 LQATDLARRFADDG 160


>gi|238794359|ref|ZP_04637971.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia intermedia ATCC 29909]
 gi|238726353|gb|EEQ17895.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia intermedia ATCC 29909]
          Length = 680

 Score = 42.1 bits (98), Expect = 0.13,   Method: Composition-based stats.
 Identities = 26/206 (12%), Positives = 64/206 (31%), Gaps = 45/206 (21%)

Query: 49  PLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF---------- 93
           P   Q   +D      +     A++ +  GY+ + +        +    +          
Sbjct: 134 PFTPQALSSDEVRQTIADFANCAQLAKQAGYDGVEV--------MGSEGYLINQFLTART 185

Query: 94  -------GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKS 142
                  G           + + A+ +A      +  R+     V++      +  L ++
Sbjct: 186 NQRDDDWGGDFTRRMRFAVEIVRAVREATGTDFILIYRLSMLDLVEEGSSWQEIEQLAQA 245

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMS 201
           ++++G   I  +      +   P     +P   +  V  ++        I  N  + D +
Sbjct: 246 VEQAGATLI--NTGIGWHEARIPTIATMVPRAGFSWVTRKLMGAVAIPLITTNR-INDPA 302

Query: 202 QALKILPSVDGV--MIGRAAYKNSAM 225
            A ++L  VDG   M+   +     +
Sbjct: 303 VAEQVL--VDGCADMV---SMARPFL 323


>gi|304394558|ref|ZP_07376477.1| dihydropyrimidine dehydrogenase [NADP+] [Ahrensia sp. R2A130]
 gi|303293219|gb|EFL87600.1| dihydropyrimidine dehydrogenase [NADP+] [Ahrensia sp. R2A130]
          Length = 437

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 7/86 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            V + G + + LN GCP     E   GA +   P+ +            +PV VK    V
Sbjct: 124 RVAETGADGVELNFGCPHGMS-ERGMGAAVGQVPEYIQMVTEWCKTYGELPVIVKLTPNV 182

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWI 153
            D           ++ K  G + + +
Sbjct: 183 TDVRYP------ARAAKAGGADAVSL 202


>gi|229043818|ref|ZP_04191516.1| NADPH dehydrogenase [Bacillus cereus AH676]
 gi|228725518|gb|EEL76777.1| NADPH dehydrogenase [Bacillus cereus AH676]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTNIATGAVGLITTGSQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|237808497|ref|YP_002892937.1| imidazole glycerol phosphate synthase subunit HisF [Tolumonas
           auensis DSM 9187]
 gi|259709884|sp|C4LFI4|HIS6_TOLAT RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|237500758|gb|ACQ93351.1| imidazoleglycerol phosphate synthase, cyclase subunit [Tolumonas
           auensis DSM 9187]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +            +  D R +       V E+     D+   + GG++
Sbjct: 35  LAKRYADEGADELV------FYDITASSDARVVDKSWVSRVAEVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D V I   A +N A++T + + F 
Sbjct: 85  SVEDAKRILEFGADKVSINSPALENPALITELADRFG 121


>gi|313764839|gb|EFS36203.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL013PA1]
 gi|313815599|gb|EFS53313.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL059PA1]
 gi|313828939|gb|EFS66653.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL063PA2]
 gi|314916397|gb|EFS80228.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL005PA4]
 gi|314930740|gb|EFS94571.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL067PA1]
 gi|314955140|gb|EFS99545.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL027PA1]
 gi|314959336|gb|EFT03438.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL002PA1]
 gi|314969209|gb|EFT13307.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL037PA1]
 gi|315099591|gb|EFT71567.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL059PA2]
 gi|315102178|gb|EFT74154.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL046PA1]
 gi|315109950|gb|EFT81926.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL030PA2]
 gi|327454429|gb|EGF01084.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL087PA3]
 gi|327456496|gb|EGF03151.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL083PA2]
 gi|328756189|gb|EGF69805.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL087PA1]
 gi|328758571|gb|EGF72187.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL025PA2]
          Length = 335

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 63/180 (35%), Gaps = 26/180 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V+ AK +E  G   I  N+      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVDTAKRMEGAGAAGIECNI-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            + A+  A+S+PV VK            AL N+   +  +G + + +  R   L+     
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR--FLQPDINV 209

Query: 167 DNRKIPNLDY-----------DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           +  ++    +             +  +        +  + G+E  +  +K +L   D VM
Sbjct: 210 ETMQVEPGVWLSSPADARLPLTWIAALSGRIGA-SLAASSGVESAADVVKYLLAGADVVM 268


>gi|218283067|ref|ZP_03489162.1| hypothetical protein EUBIFOR_01748 [Eubacterium biforme DSM 3989]
 gi|218216136|gb|EEC89674.1| hypothetical protein EUBIFOR_01748 [Eubacterium biforme DSM 3989]
          Length = 643

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 37/185 (20%), Positives = 67/185 (36%), Gaps = 27/185 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----PSARVHEG------SFGACLMLNPDIVGDCI 108
            K  +AAK   + G++ +     C     P + +  G       +G           +CI
Sbjct: 146 DKFGQAAKRAVEAGFDCLE--FHCAHNYLPHSMLSGGINHRSDEWGGSFENRKKFPLECI 203

Query: 109 AAMCKALSIPVTVKCRIGVDDQI-----PAVALRNLVKSIKKSGVNGIWIHARK----AI 159
            ++   + I + +  R+   D +         +    K  K+ GV+ + I        A 
Sbjct: 204 KSIRANMPIDMPLFMRVDCHDDMLDGGLTIEEVIEFCKDAKECGVDVLNISRGNILTAAT 263

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
           L  ++P D     N+  +    I+KE   L +   G +     A KIL     D V++ R
Sbjct: 264 LYEVAPVDIENGFNV--EDAARIRKETGMLTMPC-GRINTPEFAEKILEDDKADLVVMAR 320

Query: 218 AAYKN 222
           A   +
Sbjct: 321 AQLAD 325


>gi|126666328|ref|ZP_01737307.1| NADH:flavin oxidoreductase/NADH oxidase [Marinobacter sp. ELB17]
 gi|126629129|gb|EAZ99747.1| NADH:flavin oxidoreductase/NADH oxidase [Marinobacter sp. ELB17]
          Length = 688

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 66/188 (35%), Gaps = 18/188 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAM 111
             V+AA+  +  G + + L+           S RV++    +G           + + A+
Sbjct: 151 DFVQAARRAKAGGLDGVELSAVHQHLIDQFWSPRVNKRTDKWGKTFEDRMRFGLEVVKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              + I   V  RI  D    D +    ++ +      +G+   +           S  +
Sbjct: 211 RAEVGIDFIVGLRICGDEFHPDGLSHDDMKQIAAYYDATGMVDYFGVVGSGCDTHNSLAN 270

Query: 168 ---NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              N   P   +  +    K    + +     ++D +QA +IL +  VD V + RA   +
Sbjct: 271 VIPNMSYPPEPFLHLAAGIKAVVSVPVIHAQNIKDPNQAQRILEAGYVDLVGMTRAQIAD 330

Query: 223 SAMLTTVD 230
             ++  + 
Sbjct: 331 PHIVNKIK 338


>gi|266620339|ref|ZP_06113274.1| NADH oxidase [Clostridium hathewayi DSM 13479]
 gi|288868064|gb|EFD00363.1| NADH oxidase [Clostridium hathewayi DSM 13479]
          Length = 646

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 36/216 (16%), Positives = 71/216 (32%), Gaps = 24/216 (11%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPL-ALQIGGADISKLVEAAKIVEDFGYNEINL---- 79
            M  A AI      +      +E  +  +Q+    I    +AAK   D G++ + +    
Sbjct: 118 PMKSASAIPWPMLYDQFHAIPEELTIDEIQVL---IEAFGDAAKRAVDAGFDLVEIHAAH 174

Query: 80  -----NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR--IGVDDQ 130
                N   P        +G         +G  +    + +    P+TV+        D 
Sbjct: 175 GYLITNFLSPFTNKRGDWYGGSRENRFRFLGQVVENCRRKVGPDFPLTVRLSGTDYEPDG 234

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +         K ++K G++   I       ++  +SP       N+      E  K+   
Sbjct: 235 MTIEDTIYYAKELEKLGIDAFHISGGDHHTMIHQVSPMAMPVCYNV---WAAEAVKKEVH 291

Query: 189 LFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           + +  +G +     A  IL     D + +GR  + +
Sbjct: 292 VPVMASGSITLPQYAEDILEQGKADFITLGRPMWAD 327


>gi|226359528|ref|YP_002777306.1| oxidoreductase [Rhodococcus opacus B4]
 gi|226238013|dbj|BAH48361.1| putative oxidoreductase [Rhodococcus opacus B4]
          Length = 660

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 26/184 (14%), Positives = 54/184 (29%), Gaps = 18/184 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+   D G + I +++G          P        +G  L          + A
Sbjct: 160 DAFAAAARRCSDAGVSVIEIHLGHGNLIEQFISPRTNRRTDEWGGPLENRLRFAEHVLNA 219

Query: 111 MCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGL 163
           +  A+   V V  R+       D    +    ++ ++          + +      L   
Sbjct: 220 VRNAVGPNVAVGARMTATGLEPDDPGVMDSTEIIGTVGSWDLLDYVSLTMGRYSDALNTA 279

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
               N   P   +       K   ++   + G +     A +++   S D V + RA   
Sbjct: 280 RNIPNMTFPPGLWQRYGRAIKSVLEVPTFMVGRINHPRIAEEMIESHSCDAVAMVRALIA 339

Query: 222 NSAM 225
           +  +
Sbjct: 340 DPYL 343


>gi|308186842|ref|YP_003930973.1| NADH-dependent flavin oxidoreductase [Pantoea vagans C9-1]
 gi|308057352|gb|ADO09524.1| putative NADH-dependent flavin oxidoreductase [Pantoea vagans C9-1]
          Length = 366

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 23/147 (15%), Positives = 48/147 (32%), Gaps = 13/147 (8%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G  L        +   A+ +A+  S+PV V+      V+           
Sbjct: 190 PLSNQRSDEYGGSLENRMRFPLEVFKAVREAVPASVPVGVRISATDWVEGGWEIKQSIAF 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLE 198
            + ++      I + +      GLS      +   +Y +      +E   + +   G + 
Sbjct: 250 SRELEALNCAYIHVSSG-----GLSEDQKISVGP-NYQVPFSRDIREQVSIPVIAVGLIT 303

Query: 199 DMSQALKILPS--VDGVMIGRAAYKNS 223
           +  QA  +L     D V + R    + 
Sbjct: 304 EPQQAEGVLQQGDADLVALARGILYDP 330


>gi|294955880|ref|XP_002788726.1| dihydroorotate dehydrogenase, putative [Perkinsus marinus ATCC
           50983]
 gi|239904267|gb|EER20522.1| dihydroorotate dehydrogenase, putative [Perkinsus marinus ATCC
           50983]
          Length = 471

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 63/203 (31%), Gaps = 46/203 (22%)

Query: 63  VEAAKIVEDFG-----YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
              A IV  F         I++N+ CP     EG     L     ++G  +         
Sbjct: 252 AAIADIVASFDEVAPYAAYIDVNISCP--NTAEGKTFEDLEALEKLLGALLTWRRDNYPD 309

Query: 117 IPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWI--------------------- 153
            PV VK        D      +  +V+   + GV+G  +                     
Sbjct: 310 KPVLVKLSPPPAEADDTYYEGVSRMVRKAVELGVDGFVMINTIADRGDDLNLDRSVGDSN 369

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI------L 207
           H  K  + G  P   R I  + +  VY++      + I   GG+     A ++      L
Sbjct: 370 HGEKGGISGK-PVRQRAINLVRH--VYKVT--AGKVPIIGCGGVFTAQDAYRLIRNGASL 424

Query: 208 PSVDGVMIGRAAYKNSAMLTTVD 230
             V   MI    Y+   +   ++
Sbjct: 425 IQVYTGMI----YEGPWVFRDIN 443


>gi|167746900|ref|ZP_02419027.1| hypothetical protein ANACAC_01612 [Anaerostipes caccae DSM 14662]
 gi|317471709|ref|ZP_07931050.1| N-acylglucosamine-6-phosphate 2-epimerase [Anaerostipes sp.
           3_2_56FAA]
 gi|167653860|gb|EDR97989.1| hypothetical protein ANACAC_01612 [Anaerostipes caccae DSM 14662]
 gi|316900813|gb|EFV22786.1| N-acylglucosamine-6-phosphate 2-epimerase [Anaerostipes sp.
           3_2_56FAA]
          Length = 272

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 47/107 (43%), Gaps = 15/107 (14%)

Query: 108 IAAMCKALSIPVTV--KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I A+ KA+ +PV    K R G D+++         K + ++G   I +     +      
Sbjct: 93  IRAIKKAVDLPVIGLYKIRRG-DEEVFITPTLEAAKQVWEAGAEIIAMDCTDRM-----T 146

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVD 211
           K+ R+     +++V ++K+E P+  I     + +  +A +     VD
Sbjct: 147 KEGRRA----WELVADVKREIPEAMIFA--DVSNYDEAKRAADLGVD 187


>gi|75910632|ref|YP_324928.1| flavin oxidoreductase/NADH oxidase [Anabaena variabilis ATCC 29413]
 gi|75704357|gb|ABA24033.1| flavin oxidoreductase/NADH oxidase [Anabaena variabilis ATCC 29413]
          Length = 355

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 63/178 (35%), Gaps = 20/178 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+A K     G+  I ++            P     +  +G        ++ + + A+ 
Sbjct: 159 FVQATKRSLQAGFKVIEIHAAHGYLLHQFLSPLVNQRQDDYGGSFENRTRLLREVVEAVR 218

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + L  S P+ V+      VD          +   +K  GV+ I   +      G+ P  N
Sbjct: 219 EVLPESYPLFVRLSATDWVDKGWDIEQSIAISDKLKSLGVDLIDCSSG-----GVIPGIN 273

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV-DGVMIGRAAYKNSA 224
             +         E  ++  ++  G  G +    QA +I+   V D V++GR   +N  
Sbjct: 274 IPVKPGYQAQFAERIRKEANIPTGAVGLITSPEQADQIIRSGVADIVLLGRELLRNPY 331


>gi|15598918|ref|NP_252412.1| FMN oxidoreductase [Pseudomonas aeruginosa PAO1]
 gi|9949889|gb|AAG07110.1|AE004791_7 probable FMN oxidoreductase [Pseudomonas aeruginosa PAO1]
          Length = 368

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 58/169 (34%), Gaps = 11/169 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G C      ++    AA+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGGCFENRIRLLLQVTAAVRKAWPQELPLFVRLSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +K  GV+ I + +        +  +    P    +    +KKE   +  G  G + +
Sbjct: 250 ARHLKDLGVDLIDVSSGGTA----ANAEIPVGPGYQTEFAERVKKEAG-IASGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
             QA  IL     D +++ R   ++        +   N      P   R
Sbjct: 305 PVQAEHILRTGQADLILLARELLRDPYWPLHAADELRNEQMPWPPQYLR 353


>gi|68052711|sp|Q81EF6|NAMA_BACCR RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
          Length = 345

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 186 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTNIATGAVGLITTGSQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|54293733|ref|YP_126148.1| hypothetical protein lpl0786 [Legionella pneumophila str. Lens]
 gi|53753565|emb|CAH15020.1| hypothetical protein lpl0786 [Legionella pneumophila str. Lens]
          Length = 253

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 45/135 (33%), Gaps = 15/135 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +    G + +      A L G +          +   + +   EN  + I + GG+
Sbjct: 34  EYAMAYYAQGADELIYMDTVASLYGRN----------NLSEIVKTTAENVFIPITVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A ++L    D V I  AA KN A+++ +   F +     S    R     W    
Sbjct: 84  RSVDDAKQLLRCGADKVAINTAATKNPALISDIARRFGSQCVVLSIEAKRTVNGRW---- 139

Query: 257 ASMTDYAARHLHSGG 271
             MTD    H     
Sbjct: 140 EVMTDNGREHTGMDV 154


>gi|255693918|ref|ZP_05417593.1| dihydroorotate dehydrogenase family protein [Bacteroides finegoldii
           DSM 17565]
 gi|260620283|gb|EEX43154.1| dihydroorotate dehydrogenase family protein [Bacteroides finegoldii
           DSM 17565]
          Length = 325

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 66/187 (35%), Gaps = 27/187 (14%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I   +D    V+ AK +E+ G + I +N+    + +    +G+    + D     
Sbjct: 98  PIIASINCYSDSEW-VDFAKQIEEAGADAIEINILALQSDIQYT-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           +  + K +SIPV +K                L+  +  +G   + +  R          +
Sbjct: 152 LRHIKKTVSIPVIMKL------GDNLTNPVALIDQLYANGAAAVVLFNRFYQPDINIEKM 205

Query: 161 KGLSPKDNRKIP----NLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGVMI 215
           + +S +    +      L +  +         +    +GG+ +       IL     V +
Sbjct: 206 EHISGEVFSTVADLGTPLRWIGIAS--AAVDKIDYAASGGVANAEAVVKAILAGASAVEV 263

Query: 216 GRAAYKN 222
             A Y+N
Sbjct: 264 CSAIYQN 270


>gi|229085032|ref|ZP_04217284.1| NADPH dehydrogenase [Bacillus cereus Rock3-44]
 gi|228698348|gb|EEL51081.1| NADPH dehydrogenase [Bacillus cereus Rock3-44]
          Length = 346

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 26/142 (18%), Positives = 48/142 (33%), Gaps = 10/142 (7%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I A+ +  + P+ V+        + +         K +K+ GV+ I   +   +  
Sbjct: 197 LREIIDAVHEVWNGPLFVRISANDYHPEGLTVHDYVQFAKWMKEQGVDVIDCSSGAVV-- 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P +    P         IK++  ++  G  G +    QA  IL     D + IGR  
Sbjct: 255 ---PANIDVSPGYQVTYANHIKEQA-NIATGAVGLITSGIQAEDILANHEADLIFIGREL 310

Query: 220 YKNSAMLTTVDEYFSNPLTGSS 241
            +N     T        L    
Sbjct: 311 LRNPYFPRTAANELGFELQEPR 332


>gi|331002633|ref|ZP_08326148.1| tryptophan synthase subunit alpha [Lachnospiraceae oral taxon 107
           str. F0167]
 gi|330407046|gb|EGG86550.1| tryptophan synthase subunit alpha [Lachnospiraceae oral taxon 107
           str. F0167]
          Length = 256

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 67/215 (31%), Gaps = 50/215 (23%)

Query: 54  IGGADISKLVEAAKIVE--DFGYNEINLNVGCP-----SARVHEGSFGACLML---NPDI 103
           I   D       A I+E    G + I + +  P     +  V         +      D 
Sbjct: 18  ITCGDPDVTTTKAAILEMVKNGADLIEIGI--PFSDPTAEGVVIQGANTRALEGGITTDK 75

Query: 104 VGDCIAAMCKALSIP-----------------VTVKCRIGVDD-----QIPAVALRNLVK 141
           V D +  + K +SIP                    KC     D      IP       + 
Sbjct: 76  VFDMVVELRKEISIPLVFMTYANVVFSYGTEKFFAKCSEVGIDGIILPDIPFEERNEFLD 135

Query: 142 SIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIKKE 185
             +K  ++ I + A  +                I+  L     R     D + + +I +E
Sbjct: 136 ISEKYNIDLISLIAPTSDDRIAMIAKEAKGFLYIVSSLGVTGTRSEITTDLNSIVKIVRE 195

Query: 186 NPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           N D+   +  G+    QA ++    DGV++G A  
Sbjct: 196 NTDIPCAIGFGISTPKQADEMSKIADGVIVGSAII 230


>gi|313632013|gb|EFR99126.1| NADPH dehydrogenase [Listeria seeligeri FSL N1-067]
          Length = 338

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 65/194 (33%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDVIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAI 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     +   
Sbjct: 317 KDAAKELGETIEAP 330


>gi|269103046|ref|ZP_06155743.1| imidazole glycerol phosphate synthase cyclase subunit
           [Photobacterium damselae subsp. damselae CIP 102761]
 gi|268162944|gb|EEZ41440.1| imidazole glycerol phosphate synthase cyclase subunit
           [Photobacterium damselae subsp. damselae CIP 102761]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V ++  E  D+   + GG+ 
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSQVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D V I   A  N A++T + + F 
Sbjct: 85  TVQDANQILEFGADKVSINSPALANPALITELADKFG 121


>gi|229127459|ref|ZP_04256452.1| NADPH dehydrogenase [Bacillus cereus BDRD-Cer4]
 gi|228656000|gb|EEL11845.1| NADPH dehydrogenase [Bacillus cereus BDRD-Cer4]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTNIATGAVGLITTGSQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|229529773|ref|ZP_04419163.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae 12129(1)]
 gi|229333547|gb|EEN99033.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae 12129(1)]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           LD   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------LDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|126348362|emb|CAJ90084.1| putative oxidoreductase [Streptomyces ambofaciens ATCC 23877]
          Length = 359

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 20/152 (13%), Positives = 41/152 (26%), Gaps = 12/152 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKSIKKS 146
            +G             + A+ +      P+  +        +              ++  
Sbjct: 202 GYGGSYENRTRFALQVVDAVREVWPDDKPLFFRVSATDWLEEGGWTPEDTVRFAGDLQAH 261

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           GV+ + +        G +P+                 K    L +   G + D  QA KI
Sbjct: 262 GVDLLDVSTG-----GNAPRVRIPTGPGYQVPFAARVKSGTTLPVAAVGLITDAGQAEKI 316

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           L     D V++GR   ++ +            
Sbjct: 317 LANGEADAVLLGRELLRDPSWAQHAARELGEE 348


>gi|30020160|ref|NP_831791.1| NADPH dehydrogenase NamA [Bacillus cereus ATCC 14579]
 gi|29895710|gb|AAP08992.1| NADH oxidase [Bacillus cereus ATCC 14579]
          Length = 346

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 187 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 246

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 247 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTNIATGAVGLITTGSQAEQILNNN 300

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 301 EADLIFIGRELLRNPY 316


>gi|289651308|ref|ZP_06482651.1| 2,4-dienoyl-CoA reductase [Pseudomonas syringae pv. aesculi str.
           2250]
          Length = 679

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 17/127 (13%), Positives = 44/127 (34%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     +  R+ + D          +  L K+++++G   I  +    
Sbjct: 197 LAVEIVTRVREAVGADFIIIFRLSMLDLVEGGSTWEEIVQLAKAVEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
             +   P    K+P   +  V    + +  + +     +     A +IL     D V + 
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGSVKVPLITTNRINTPEVAERILSEGDADTVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|256376343|ref|YP_003100003.1| NADH:flavin oxidoreductase/NADH oxidase [Actinosynnema mirum DSM
           43827]
 gi|255920646|gb|ACU36157.1| NADH:flavin oxidoreductase/NADH oxidase [Actinosynnema mirum DSM
           43827]
          Length = 407

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 79/238 (33%), Gaps = 26/238 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             + A   E  G++ + ++            P        +G  L     ++ + +AA+ 
Sbjct: 153 FADTAAQAERAGFDGVEVHAAHGYLIGQFLSPLVNRRADGYGGDLAARARLLLEVVAAVR 212

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARK----AILKGLS 164
            A+S    V  ++   D             ++  +  +GV+ + +        AI+   +
Sbjct: 213 GAVSPGFAVGVKLNTADFQRGGFQPQDAAEVIGMLSGAGVDLVELSGGSLESLAIMGHAA 272

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
            +          D    I  + P L + + GG+  +  A ++L      V +G A   + 
Sbjct: 273 DESTLAREAYFLDAAASILADAP-LPVMITGGVRRLPVARRVLESGASVVGVGTALAVDP 331

Query: 224 -----AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
                 +        + P+  + P K          + A M D AA    S G L+ +
Sbjct: 332 DLPHAWIAGE--HAEATPVRVNWPDKKLSSAAVQALVHARMEDLAADRDRSTGPLRAL 387


>gi|229091042|ref|ZP_04222265.1| NADPH dehydrogenase [Bacillus cereus Rock3-42]
 gi|228692173|gb|EEL45909.1| NADPH dehydrogenase [Bacillus cereus Rock3-42]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPEKRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA ++L   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQVLTNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|312897361|ref|ZP_07756787.1| pyridine nucleotide-disulfide oxidoreductase [Megasphaera
           micronuciformis F0359]
 gi|310621579|gb|EFQ05113.1| pyridine nucleotide-disulfide oxidoreductase [Megasphaera
           micronuciformis F0359]
          Length = 668

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 30/219 (13%), Positives = 67/219 (30%), Gaps = 42/219 (19%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM----- 98
           +   +PL  Q     + K  +AA+     G++ + +               + L+     
Sbjct: 135 NPAPRPLTKQEILNIVQKYADAAERAIGAGFDMVEI-----------HGGHSYLLDQFLS 183

Query: 99  --------------LNPDIVGDC-IAAMCKALSIPVTVKCRIGVDDQIP-AVALRNLVKS 142
                          N        + A+   +   V +  RI  D+ I     L + ++ 
Sbjct: 184 PLYNKRTDEFGGSYENRARFARLVVEAVRARVGKWVPISFRISADEFIEGGNTLEDTLQL 243

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDM 200
           ++        I+   A+   +  + ++      +       +KK+     + L+G + + 
Sbjct: 244 LEYIVPEVDIINVSAAVNDSIQYQIDKCDLPDAWRAYLSESVKKKFGK-PVILSGNIRNP 302

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAM-----LTTVDEY 232
             A  I+     D + IGR    +        L   D  
Sbjct: 303 QIADDIIAQGKTDFIAIGRGLIADPDWANKARLGETDHI 341


>gi|229184265|ref|ZP_04311472.1| NADPH dehydrogenase [Bacillus cereus BGSC 6E1]
 gi|228599061|gb|EEK56674.1| NADPH dehydrogenase [Bacillus cereus BGSC 6E1]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPEKRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|149191024|ref|ZP_01869285.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio shilonii
           AK1]
 gi|148835158|gb|EDL52134.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio shilonii
           AK1]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L     + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAARYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPELITELADKFG 121


>gi|118477476|ref|YP_894627.1| NADPH dehydrogenase NamA [Bacillus thuringiensis str. Al Hakam]
 gi|196046018|ref|ZP_03113246.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus 03BB108]
 gi|225864006|ref|YP_002749384.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus 03BB102]
 gi|167012457|sp|A0RD27|NAMA_BACAH RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|254766769|sp|C1ERH2|NAMA_BACC3 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|118416701|gb|ABK85120.1| NADH oxidase [Bacillus thuringiensis str. Al Hakam]
 gi|196023073|gb|EDX61752.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus 03BB108]
 gi|225788971|gb|ACO29188.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Bacillus
           cereus 03BB102]
          Length = 345

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPEKRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|40889904|pdb|1VH7|A Chain A, Crystal Structure Of A Cyclase Subunit Of
           Imidazolglycerolphosphate Synthase
          Length = 265

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 66  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGS 124

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 125 QAVVVAIDAKRVDGEFM 141


>gi|225387262|ref|ZP_03757026.1| hypothetical protein CLOSTASPAR_01014 [Clostridium asparagiforme
           DSM 15981]
 gi|225046639|gb|EEG56885.1| hypothetical protein CLOSTASPAR_01014 [Clostridium asparagiforme
           DSM 15981]
          Length = 291

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 64/208 (30%), Gaps = 27/208 (12%)

Query: 47  EKPLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHE--GSFGACLMLNPDI 103
           E PL L +   D+  LV  A           I +N+ CP +        +      +   
Sbjct: 76  ESPLILNLKAEDLEGLVRLAGTAAGCREVAGIEINMNCPYSMAATDPRQY----WRDYGW 131

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---------IH 154
           + + I  + +A    + +     +      V + ++   +K+ G +G           I 
Sbjct: 132 LREMIRGVREAAGEKLLI-----IKVPTTMVDVEDIAAIVKECGADGFTSFGALTGCAID 186

Query: 155 ARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPS 209
            R    +    G        +  L       + K   D+ I   GG+ +    ++  +  
Sbjct: 187 VRTREFRCGNSGSGGYCGPGLKPLALWSCSRVHKAV-DIPIFSAGGVTNADDVIEHIMAG 245

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              V +G A       +  + E     L
Sbjct: 246 AWMVQVGSANLTRPDFMPRLIESLDRRL 273


>gi|218233239|ref|YP_002366745.1| NADPH dehydrogenase NamA [Bacillus cereus B4264]
 gi|254766770|sp|B7HJE9|NAMA_BACC4 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|218161196|gb|ACK61188.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Bacillus
           cereus B4264]
          Length = 345

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 186 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+  +  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTKIATGAVGLITTGSQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|49481241|ref|YP_036185.1| NADPH dehydrogenase NamA [Bacillus thuringiensis serovar konkukian
           str. 97-27]
 gi|300118256|ref|ZP_07056004.1| NADPH dehydrogenase NamA [Bacillus cereus SJ1]
 gi|68052595|sp|Q6HJU1|NAMA_BACHK RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|49332797|gb|AAT63443.1| NADH oxidase [Bacillus thuringiensis serovar konkukian str. 97-27]
 gi|298724567|gb|EFI65261.1| NADPH dehydrogenase NamA [Bacillus cereus SJ1]
          Length = 345

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPEKRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYIQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|148548940|ref|YP_001269042.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
 gi|148512998|gb|ABQ79858.1| 2,4-dienoyl-CoA reductase [Pseudomonas putida F1]
          Length = 678

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 29/231 (12%), Positives = 69/231 (29%), Gaps = 38/231 (16%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++         +  E+ +  QI        V  A + +  GY+
Sbjct: 106 LHAGRYAYSPRQVAPSAIQAPINPFKPKALDEEGIEKQIA-----DFVNCAVLAQRAGYD 160

Query: 76  EINLNVGCPSARVHEGSFGA--CLMLNPD---------------IVGDCIAAMCKALS-- 116
            + +        +    +     L  + +               +  + ++ +  A+   
Sbjct: 161 GVEI--------MGSEGYFINQFLAAHTNHRTDRWGGSYENRMRLAVEIVSRVRGAVGPN 212

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I   +     V+       +  L K+I+++G   I  +      +   P    K+P  
Sbjct: 213 FIIIFRLSMLDLVEGGSTWDEIELLAKAIEQAGATLI--NTGIGWHEARIPTIATKVPRA 270

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
            +  V    +    + +     +     A  +L   D  M+   R    + 
Sbjct: 271 AFSKVTAKLRGVVSIPLITTNRINTPEVAEAVLAEGDADMVSMARPFLADP 321


>gi|309790920|ref|ZP_07685462.1| Dihydroorotate oxidase [Oscillochloris trichoides DG6]
 gi|308227034|gb|EFO80720.1| Dihydroorotate oxidase [Oscillochloris trichoides DG6]
          Length = 348

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 29/163 (17%), Positives = 58/163 (35%), Gaps = 22/163 (13%)

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
             + + +  + L+     +   I+        P+ VK        +   A+  +++ + +
Sbjct: 192 RNLQDRAHLSELLAALQEINQRISQARHTTPKPLLVKIAP----DLSEAAISEVLEVVAE 247

Query: 146 SGVNGIWI------------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIG 192
            GV+GI              H R +   GLS    R +     ++V  I++E  P L I 
Sbjct: 248 HGVSGIIATNTTIGRGGVADHPRASEAGGLS---GRPLAARALEVVRFIRREAGPTLPII 304

Query: 193 LNGGLEDMSQALKIL-PSVDGVMIGRA-AYKNSAMLTTVDEYF 233
             GG+     AL +     D + I     Y+   ++  +    
Sbjct: 305 GVGGIFTPDDALAMRNAGADLIQIYTGLIYQGPGVVRRIARAM 347


>gi|228927128|ref|ZP_04090191.1| NADPH dehydrogenase [Bacillus thuringiensis serovar pondicheriensis
           BGSC 4BA1]
 gi|229121611|ref|ZP_04250836.1| NADPH dehydrogenase [Bacillus cereus 95/8201]
 gi|228661831|gb|EEL17446.1| NADPH dehydrogenase [Bacillus cereus 95/8201]
 gi|228832454|gb|EEM78028.1| NADPH dehydrogenase [Bacillus thuringiensis serovar pondicheriensis
           BGSC 4BA1]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPEKRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYIQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|330823761|ref|YP_004387064.1| NADPH dehydrogenase [Alicycliphilus denitrificans K601]
 gi|329309133|gb|AEB83548.1| NADPH dehydrogenase [Alicycliphilus denitrificans K601]
          Length = 356

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 61/180 (33%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+     G+  I  ++G          P A      +G  L     +     AA
Sbjct: 154 DDFSAAARRANTAGFEVIECHMGHGYLLHSFLSPIANQRRDDYGGSLENRARLPLQVAAA 213

Query: 111 MCKALS--IP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + ++L   +P  V + C   V           L K +K+ GV+ I   +        +  
Sbjct: 214 VRESLPQQLPLFVRISCTDWVAGGWDLAQSIQLAKWMKEVGVDLIDCSSGAVT----ADS 269

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                P         I+++   +  G  G + + +QA +I+ +   D V +GR    N  
Sbjct: 270 PIAAAPGFHVPFATAIREQAG-IATGAVGLITEPAQAEQIVGTGLADLVFVGRGFLDNPY 328


>gi|154494906|ref|ZP_02033911.1| hypothetical protein PARMER_03950 [Parabacteroides merdae ATCC
           43184]
 gi|154085456|gb|EDN84501.1| hypothetical protein PARMER_03950 [Parabacteroides merdae ATCC
           43184]
          Length = 325

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 67/194 (34%), Gaps = 45/194 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-------- 100
           P+   I        +E A+ +E  G + + LNV               L  +        
Sbjct: 98  PVIASINCYKSDAWIEFARQIELAGADALELNV-------------FFLETDLTYNSENM 144

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            D+    I  + + +SIPV +K    V +      +  +  ++  +G +GI +  R    
Sbjct: 145 RDLYVSIIRKVKETVSIPVMIKMSKMVGN------IPAVAHTLTVNGADGIVLFNR--FY 196

Query: 161 KGLSPKDNRKI-------------PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
           +     +N +I               L +  +  +  + P + I  + G+ D    +K  
Sbjct: 197 QPDIDINNMQIVSGNVFSNHSDLSDTLRWTAI--VSGKIPGISIASSTGVHDWEDVIKCL 254

Query: 207 LPSVDGVMIGRAAY 220
           L   D + +  A Y
Sbjct: 255 LAGADAIQMCSAVY 268


>gi|229525749|ref|ZP_04415154.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae bv. albensis VL426]
 gi|229339330|gb|EEO04347.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae bv. albensis VL426]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|21228497|ref|NP_634419.1| NADH:flavin oxidoreductase [Methanosarcina mazei Go1]
 gi|20906981|gb|AAM32091.1| NADH:flavin oxidoreductases [Methanosarcina mazei Go1]
          Length = 365

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 26/197 (13%), Positives = 63/197 (31%), Gaps = 28/197 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
               +AA   +  G++ +   + C    +               +G  +     IV + +
Sbjct: 143 EAFTQAAVRAKKAGFDGV--QLHCAHGFLLSNFISPYTNRRTDRWGGSVENRARIVTEIV 200

Query: 109 AAMCKAL--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             + +    + P+ VK              +  +         K ++K+GV  I +    
Sbjct: 201 RRIKEETGSNFPIFVKMNATDGFQPGTAKAELGLTISQAMETAKLLEKAGVCAIEVSGGI 260

Query: 158 AILKGLS--PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           +   G++     N       +    +  K    + + L GG+  +S    +L +   D +
Sbjct: 261 SEAGGVTIKTAINSPSKEAYFKEYSKNIKSAVSIPVILVGGIRSLSVMEGLLENGFADLI 320

Query: 214 MIGRAAYKNSAMLTTVD 230
            + RA      ++  + 
Sbjct: 321 SMSRAFISEPDLILKLK 337


>gi|328946450|gb|EGG40590.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK1087]
          Length = 240

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K++GV  I +      L+G +          + D++  IK E   L I + G
Sbjct: 32  VLEQAQVFKEAGVTMIHVVDLDGALEGRA---------ANRDLIARIKSETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN   +    + F 
Sbjct: 82  GIRSLEQIEDYLAVGIDRVIIGSMAVKNPDFVKEALDRFG 121


>gi|313499867|gb|ADR61233.1| 2,4-dienoyl-CoA reductase [NADPH] [Pseudomonas putida BIRD-1]
          Length = 678

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 29/231 (12%), Positives = 69/231 (29%), Gaps = 38/231 (16%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++         +  E+ +  QI        V  A + +  GY+
Sbjct: 106 LHAGRYAYSPRQVAPSAIQAPINPFKPKALDEEGIEKQIA-----DFVNCAVLAQRAGYD 160

Query: 76  EINLNVGCPSARVHEGSFGA--CLMLNPD---------------IVGDCIAAMCKALS-- 116
            + +        +    +     L  + +               +  + ++ +  A+   
Sbjct: 161 GVEI--------MGSEGYFINQFLAAHTNHRTDRWGGSYENRMRLAVEIVSRVRGAVGPN 212

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I   +     V+       +  L K+I+++G   I  +      +   P    K+P  
Sbjct: 213 FIIIFRLSMLDLVEGGSTWDEIELLAKAIEQAGATLI--NTGIGWHEARIPTIATKVPRA 270

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
            +  V    +    + +     +     A  +L   D  M+   R    + 
Sbjct: 271 AFSKVTAKLRGVVSIPLITTNRINTPEVAEAVLAEGDADMVSMARPFLADP 321


>gi|296502642|ref|YP_003664342.1| NADPH dehydrogenase NamA [Bacillus thuringiensis BMB171]
 gi|296323694|gb|ADH06622.1| NADPH dehydrogenase NamA [Bacillus thuringiensis BMB171]
          Length = 345

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 186 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+  +  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTKIATGAVGLITTGSQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|229144667|ref|ZP_04273068.1| NADPH dehydrogenase [Bacillus cereus BDRD-ST24]
 gi|228638799|gb|EEK95228.1| NADPH dehydrogenase [Bacillus cereus BDRD-ST24]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+  +  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTKIATGAVGLITTGSQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|170758208|ref|YP_001786924.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169405197|gb|ACA53608.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 339

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 55/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK  ++ G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAEAAKRAKESGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V + + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCRELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +    I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASRIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|302391827|ref|YP_003827647.1| methionine synthase [Acetohalobium arabaticum DSM 5501]
 gi|302203904|gb|ADL12582.1| Methionine synthase [Acetohalobium arabaticum DSM 5501]
          Length = 265

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 87/261 (33%), Gaps = 61/261 (23%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   + E AK  E+ G + +++N             G  +   P+ +   +  + +A+ +
Sbjct: 23  DKEFIQELAKKQEEAGVDYVDVNC------------GTLIREEPEALEWLVETVQEAVDV 70

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           P+ +      D   P                 G+  H  KA++  ++ +D R    L   
Sbjct: 71  PLCI------DSPDPKAIK------------QGLEAHEGKALVNSITAEDERYDEVL--P 110

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILPSV------DGVMIGRAAYKNSAMLTTVDE 231
           ++ E       L +  NG  +D +  +++   +      DG+          A     ++
Sbjct: 111 LIKEYDANIVALVMNDNGMPDDATDRIEVATELVDNLLEDGI---------PA-----ED 156

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
            F +P+       + + +     +    + Y   H+  G         +  + HG P  +
Sbjct: 157 IFVDPIIQPIGTDSEMGEHILNAVEEISSKYEDIHITCG---------LSNISHGLPQRQ 207

Query: 292 RCRHILTVEAGASTATHHIIE 312
                  V A +      I++
Sbjct: 208 LLNQAYLVLAMSRGMDSAILD 228


>gi|260891639|ref|ZP_05902902.1| oxidoreductase, FMN-binding [Leptotrichia hofstadii F0254]
 gi|260858649|gb|EEX73149.1| oxidoreductase, FMN-binding [Leptotrichia hofstadii F0254]
          Length = 408

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 34/188 (18%), Positives = 65/188 (34%), Gaps = 22/188 (11%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA+I +  G+  + +              +  V    +G  +      + D    M 
Sbjct: 154 FGKAAEIAKKSGFTGVQIHGAHGYLISQFLSSADNVRNDEYGGSIENRMRFLVDVYNEMR 213

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARK-AILKGLSPK- 166
           + +     +  +I   D             ++K + + GV+ I I        K LS + 
Sbjct: 214 EKVGKEFPIGLKINSSDFSNNGFTEEESIVVIKKMSEIGVDLIEISGGNYENSKMLSERG 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAYKNS 223
           DN K+  +DY    +      D  I + GG   +E M +A+K    +  + I R      
Sbjct: 274 DNEKVFFIDY---AKKVLSLIDTPIVVTGGFKKVETMQKAIKK-EKISMIGIARPIVIYP 329

Query: 224 AMLTTVDE 231
            +   + E
Sbjct: 330 NLPNEIKE 337


>gi|283780885|ref|YP_003371640.1| dihydroorotate dehydrogenase family protein [Pirellula staleyi DSM
           6068]
 gi|283439338|gb|ADB17780.1| dihydroorotate dehydrogenase family protein [Pirellula staleyi DSM
           6068]
          Length = 315

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 38/189 (20%), Positives = 68/189 (35%), Gaps = 28/189 (14%)

Query: 50  LALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + + I G++ ++ V  A  + D  G   I LN+ CP    H   FGA   L   +V DC+
Sbjct: 105 IIVSIAGSNHNEFVAMAGRLSDIDGIAAIELNISCP-NVAHGIDFGADASLCEKLVSDCV 163

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLS 164
            A       P+  K    V        + ++ K     G + +     +       +   
Sbjct: 164 KATRH----PILAKLTPNVTR------IADVAKGAANGGADALSLINTVQGMAIDWRKQK 213

Query: 165 P--------KDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILPSVDGVM 214
           P             I  +    V+++++    P + IG    ++D+     I+     V 
Sbjct: 214 PLLGNVMGGLSGPAIKPIALRCVHQVRQAVSTPIIGIGGIATIDDV--MEFIVAGASAVQ 271

Query: 215 IGRAAYKNS 223
           IG A Y + 
Sbjct: 272 IGTANYYDP 280


>gi|312198476|ref|YP_004018537.1| NADH:flavin oxidoreductase/NADH oxidase [Frankia sp. EuI1c]
 gi|311229812|gb|ADP82667.1| NADH:flavin oxidoreductase/NADH oxidase [Frankia sp. EuI1c]
          Length = 663

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 60/173 (34%), Gaps = 20/173 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           + A+     G++ I L   C  + +  G            +G  L     ++ + + A+ 
Sbjct: 154 QVAEHCAAGGFDGIELQ--CSHSSIVRGFLSPATNRRTDEYGGSLANRARLLLEIVDAVR 211

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSG-VNGIWIHARKAILKGLSPKD 167
            A+   + +  RI  D+ I           +   ++ SG V+ I      A       + 
Sbjct: 212 AAIGPELALGVRICGDELIEGGTTIEDAVAIATMVEASGKVDYINTSIGVATATLYMIEA 271

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           + ++P      +    +   +L +   G  +D  QA + L     D + I R 
Sbjct: 272 SMQVPPGYAMFIPSAIRAAVNLPVVGVGRFKDPLQADRALAAGQADLIGIVRG 324


>gi|84685480|ref|ZP_01013378.1| 2,4-dienoyl-CoA reductase [Maritimibacter alkaliphilus HTCC2654]
 gi|84666637|gb|EAQ13109.1| 2,4-dienoyl-CoA reductase [Rhodobacterales bacterium HTCC2654]
          Length = 675

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 42/124 (33%), Gaps = 9/124 (7%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D +P       +  L + I+K+G     I+      +
Sbjct: 197 EIVRRVREAVGDDFIIIYRLSMIDLVPNGSTFDEVVELAQEIEKAGAT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
              P     +P   +  V +       + +  +  +     A ++L      M+   +  
Sbjct: 255 ARVPTIATSVPRAGWAWVTQKLMGKVSIPVITSNRINTPEVAEELLSQGAADMV---SMA 311

Query: 222 NSAM 225
              +
Sbjct: 312 RPFL 315


>gi|313801873|gb|EFS43107.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL110PA2]
          Length = 307

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 66/197 (33%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G +G+ +      
Sbjct: 145 NVTAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARATADAGADGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
                      I           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAMRMIDAVTR-VVDIPVIGMGGVMTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|92113118|ref|YP_573046.1| NADH:flavin oxidoreductase/NADH oxidase [Chromohalobacter
           salexigens DSM 3043]
 gi|91796208|gb|ABE58347.1| NADH:flavin oxidoreductase/NADH oxidase [Chromohalobacter
           salexigens DSM 3043]
          Length = 694

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 65/189 (34%), Gaps = 18/189 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAA 110
               + A+ V++ G + I L+           S RV++    +G           + + A
Sbjct: 150 DDFAQGARRVKEGGLDGIELSAVHQHLIDQFWSPRVNKREDQWGGSFENRMRFGLEVLKA 209

Query: 111 MCKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +   +     V  RI  D    D +    ++ +      +G+   +           +  
Sbjct: 210 VRAEVGDDFVVGLRICGDEFHPDGLTHDDMKRIAAYYDATGMVDFFGVVGSGCDTHNTLA 269

Query: 167 D---NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           +   N   P   +  +    K+   + +     ++D +QA +IL    VD V + RA   
Sbjct: 270 NVIPNMSYPPEPFLHLAAGVKDVVSVPVIHAQNIKDPNQASRILEGGYVDLVGMTRAHIA 329

Query: 222 NSAMLTTVD 230
           +  ++  + 
Sbjct: 330 DPHLIAKIQ 338


>gi|258515172|ref|YP_003191394.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257778877|gb|ACV62771.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 375

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 38/212 (17%), Positives = 70/212 (33%), Gaps = 30/212 (14%)

Query: 31  AILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-------- 82
           A      KN    S +E    +Q          EAA  V+  G++ + L+ G        
Sbjct: 124 AFESPFCKNSREISEKEINTIIQKY-------AEAAVRVKKAGFDLVELHGGRGYLMMQF 176

Query: 83  -CPSARVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN 138
             P       ++G  L   M  P  V   +  +      PV    R+  D+ IP      
Sbjct: 177 LSPYTNRRNDTYGGKLENRMRFPLEVVRAVKELV--GDFPVG--YRLTADEWIPGGFAIE 232

Query: 139 ----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGL 193
                   ++K+G+  I +         L+ +  +      Y   V E  K+  ++ + +
Sbjct: 233 EAVIFASELEKAGITYISVMTGSNESPVLNQEFQKLSAQDCYAATVSEQIKKAVNIPVIV 292

Query: 194 NGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            G +   + A  +L     D + + R    + 
Sbjct: 293 AGRIVTPTLAEGLLQKDQTDLIGLARVLLCDP 324


>gi|163939864|ref|YP_001644748.1| NADPH dehydrogenase NamA [Bacillus weihenstephanensis KBAB4]
 gi|254766773|sp|A9VRT5|NAMA_BACWK RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|163862061|gb|ABY43120.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus
           weihenstephanensis KBAB4]
          Length = 345

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I A+ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDAVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHVNIATGAVGLITTGSQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|312198230|ref|YP_004018291.1| NADH:flavin oxidoreductase/NADH oxidase [Frankia sp. EuI1c]
 gi|311229566|gb|ADP82421.1| NADH:flavin oxidoreductase/NADH oxidase [Frankia sp. EuI1c]
          Length = 671

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 27/198 (13%), Positives = 58/198 (29%), Gaps = 22/198 (11%)

Query: 48  KPLALQIGGADISKLVE----AAKIVEDFGYNEINLNVGC----------PSARVHEGSF 93
           + +  ++  A+I +LVE    AA+   D G + I ++             P+      ++
Sbjct: 138 REIPHEMTAAEIDELVEHYVLAARHAMDGGVDGIEIHGLAHGYLLGQFLSPATNHRSDAY 197

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP-----AVALRNLVKSIKKSGV 148
           G        IV   +  +  A+     +  R+  +D              + + +   GV
Sbjct: 198 GGSFENRLRIVRRIVEDVRAAVPADRVLGIRLNSNDGDGQPGLGNADWVRIAREVDGWGV 257

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKIL 207
                  +   L  +            Y++           + +   G +     A  IL
Sbjct: 258 LDYISTTQGTYLDRMQIYATSAARPAGYEVADTANLTRAVSIPVVAVGRITTPEMAEDIL 317

Query: 208 --PSVDGVMIGRAAYKNS 223
                  V + R    + 
Sbjct: 318 ASSKAQFVGMARQLMADP 335


>gi|229520432|ref|ZP_04409857.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae TM 11079-80]
 gi|229342530|gb|EEO07523.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae TM 11079-80]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|16263686|ref|NP_436479.1| dehydrogenase [Sinorhizobium meliloti 1021]
 gi|14524401|gb|AAK65891.1| dehydrogenase [Sinorhizobium meliloti 1021]
          Length = 370

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 18/126 (14%), Positives = 46/126 (36%), Gaps = 9/126 (7%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           +  + + A+  A+   V +  R+               +   + G   ++    ++    
Sbjct: 216 LSLEVLKAVRAAIGPSVPLGLRLSQ--GKVNDFRHKWAER--EQGAARVFEALAESPADF 271

Query: 163 LSPKDNRKIPNL----DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
               +           +  +V   ++  P LF+  NG L ++++A +++    D + +GR
Sbjct: 272 AHVTEFEAWRPAFEGGEISLVSLARRHAPRLFLIANGSLHELARAEQVMESGADMIALGR 331

Query: 218 AAYKNS 223
            A  N 
Sbjct: 332 GALVNP 337


>gi|313636379|gb|EFS02157.1| NADPH dehydrogenase [Listeria seeligeri FSL S4-171]
          Length = 338

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 65/194 (33%), Gaps = 21/194 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA   ++ G++ I ++            P     E ++G        I+ D I A+
Sbjct: 144 DFKRAAYRAKEAGFDAIEIHAAHGYLIHQFLSPITNRREDNYGGPAGNRYKILSDIIKAI 203

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +    P+ V+     D     + L +     K +K  GV  I +     +         
Sbjct: 204 KEVWDGPIIVRVSAT-DYAHGGLQLEDHIPFAKWMKADGVELIDVSTGGLVNVAPPVFPG 262

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
            ++P  D     EI++    +  G  G +    QA +IL     D +++GR   +N    
Sbjct: 263 YQVPFAD-----EIRRGAG-IATGALGLITRGEQAEEILCNERADLIIVGRELLRNPYFA 316

Query: 227 TTVDEYFSNPLTGS 240
               +     +   
Sbjct: 317 KDAAKELGETIEAP 330


>gi|229818147|ref|ZP_04448429.1| hypothetical protein BIFANG_03439 [Bifidobacterium angulatum DSM
           20098]
 gi|229784398|gb|EEP20512.1| hypothetical protein BIFANG_03439 [Bifidobacterium angulatum DSM
           20098]
          Length = 428

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 26/180 (14%), Positives = 55/180 (30%), Gaps = 19/180 (10%)

Query: 64  EAAKIVEDFGY---NEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP 118
           +A +I    GY     ++     P + V +  +G         + + + A+   +   +P
Sbjct: 242 QAIEIHAAHGYLISQFLD-----PLSNVRDDEYGGGFEGRIRFLVETVDAVRSMIPEDMP 296

Query: 119 --VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
             V V                 L + +K+  V+ + +     +     P   +       
Sbjct: 297 LLVRVSATDWAAGGWDLDQTVRLAQVLKEHAVDLVDVSTGGIVSGVSVPVSPKYQVPF-- 354

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  +    + +   G +    QA +I+     D V IGRAA ++            
Sbjct: 355 ---ARQVRARAQVPVTAVGLITKPKQAERIVEKGEADAVEIGRAALRDPYWPLRAAHKLG 411


>gi|194431635|ref|ZP_03063926.1| 2,4-dienoyl-CoA reductase [Shigella dysenteriae 1012]
 gi|194419991|gb|EDX36069.1| 2,4-dienoyl-CoA reductase [Shigella dysenteriae 1012]
 gi|332086748|gb|EGI91886.1| 2,4-dienoyl-CoA reductase [Shigella dysenteriae 155-74]
          Length = 672

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 79/245 (32%), Gaps = 36/245 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+     V+D         L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI-- 215
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMVSM 310

Query: 216 GRAAYKNSAMLTTVDEYFSNPL-TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            R    N+ +L+      ++ + T     +  +D+ F  K+++ + +  A H      L 
Sbjct: 311 ARPFLANAELLSKAQSGRADEINTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP 370

Query: 275 QITRH 279
            + + 
Sbjct: 371 AMQKK 375


>gi|251782877|ref|YP_002997180.1| dihydroorotate dehydrogenase 1A [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242391507|dbj|BAH81966.1| dihydroorotate dehydrogenase [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 315

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 73/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 72  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 129

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 130 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 184

Query: 136 LRN-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +          K    G+     +     +    Y  K+ 
Sbjct: 185 IFNKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 242

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 243 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 294


>gi|194291799|ref|YP_002007706.1| NADH-dependent flavin oxidoreductase [Cupriavidus taiwanensis LMG
           19424]
 gi|193225703|emb|CAQ71649.1| putative NADH-DEPENDENT FLAVIN OXIDOREDUCTASE OXIDOREDUCTASE
           PROTEIN; similar to B.subtilis namA [Cupriavidus
           taiwanensis LMG 19424]
          Length = 371

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 29/139 (20%), Positives = 46/139 (33%), Gaps = 15/139 (10%)

Query: 93  FGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSG 147
           +G  L   M  P  V D +     A   PV ++      V           L K+++  G
Sbjct: 200 YGGSLENRMRFPIEVFDAVREAFPA-QRPVWMRISATDWVPGGWDIEGTVALSKALQARG 258

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
              I +        G+SP+   K+           +K E   L     G + +  QA  I
Sbjct: 259 CAAIHVTTG-----GVSPQQAIKLGPGYQVPYAQRVKAEVG-LPTIAVGLITEPEQAEAI 312

Query: 207 L--PSVDGVMIGRAAYKNS 223
           +     D V + RA   + 
Sbjct: 313 IANQEADAVSLARAMLYDP 331


>gi|94988844|ref|YP_596945.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS9429]
 gi|94992734|ref|YP_600833.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS2096]
 gi|306827062|ref|ZP_07460360.1| dihydroorotate oxidase [Streptococcus pyogenes ATCC 10782]
 gi|94542352|gb|ABF32401.1| dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS9429]
 gi|94546242|gb|ABF36289.1| Dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS2096]
 gi|304430808|gb|EFM33819.1| dihydroorotate oxidase [Streptococcus pyogenes ATCC 10782]
          Length = 315

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 73/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 72  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 129

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 130 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 184

Query: 136 LRN-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +          K    G+     +     +    Y  K+ 
Sbjct: 185 IFNKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 242

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 243 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 294


>gi|71903821|ref|YP_280624.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS6180]
 gi|94994669|ref|YP_602767.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS10750]
 gi|71802916|gb|AAX72269.1| dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS6180]
 gi|94548177|gb|ABF38223.1| Dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS10750]
          Length = 315

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 73/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 72  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 129

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 130 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 184

Query: 136 LRN-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +          K    G+     +     +    Y  K+ 
Sbjct: 185 IFNKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 242

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 243 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 294


>gi|262402503|ref|ZP_06079064.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio sp.
           RC586]
 gi|262351285|gb|EEZ00418.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio sp.
           RC586]
          Length = 257

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|319763975|ref|YP_004127912.1| NADH:flavin oxidoreductase/NADH oxidase [Alicycliphilus
           denitrificans BC]
 gi|317118536|gb|ADV01025.1| NADH:flavin oxidoreductase/NADH oxidase [Alicycliphilus
           denitrificans BC]
          Length = 356

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 60/180 (33%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+     G+  I  ++G          P A      +G  L     +     AA
Sbjct: 154 DDFSAAARRANTAGFEVIECHMGHGYLLHSFLSPIANQRRDDYGGSLENRARLPLQVAAA 213

Query: 111 MCKALS--IP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + ++L   +P  V + C   V           L K +K+ GV+ I   +           
Sbjct: 214 VRESLPQQLPLFVRISCTDWVAGGWDLAQSIQLAKWMKEVGVDLIDCSSGAVTADSPVAA 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                P         I+++   +  G  G + + +QA +I+ +   D V +GR    N  
Sbjct: 274 ----APGFHVPFATAIREQAG-IATGAVGLITEPAQAEQIVGTGLADLVFVGRGFLDNPY 328


>gi|228958340|ref|ZP_04120065.1| NADPH dehydrogenase [Bacillus thuringiensis serovar pakistani str.
           T13001]
 gi|228801361|gb|EEM48253.1| NADPH dehydrogenase [Bacillus thuringiensis serovar pakistani str.
           T13001]
          Length = 319

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+  +  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHTKIATGAVGLITTGSQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|157961967|ref|YP_001502001.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella pealeana ATCC
           700345]
 gi|157846967|gb|ABV87466.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella pealeana ATCC
           700345]
          Length = 706

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 28/191 (14%), Positives = 66/191 (34%), Gaps = 28/191 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AA   +  G++ + ++     + +  G            +G  L     ++ + IA
Sbjct: 172 WFASAALRAKQAGFDGVEIHAA--HSYIIAGFLSAYYNKRDDKYGGSLENRARLLLEVIA 229

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNL---VKSIKKSGVNGIWIHARKAILKG-- 162
           A+ + +    PV ++           + + +     K ++ +G+N + I A     +G  
Sbjct: 230 AVRQQVGNDYPVWLRLDAAELRTPGGITIEDCIEVAKLVEAAGLNALSISAYANTNRGDA 289

Query: 163 --LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRA 218
              +P   +    L +    E+ K    + +   G LE    A K +    +  V + R 
Sbjct: 290 FTEAPLVQKPAGFLHWA--AEVSKHV-SIPVTAVGRLE-PDVADKAIGSGKIAFVAMARK 345

Query: 219 AYKNSAMLTTV 229
              +  +   +
Sbjct: 346 LLADPELPNKI 356


>gi|194333283|ref|YP_002015143.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Prosthecochloris
           aestuarii DSM 271]
 gi|226700343|sp|B4S4Z8|HIS4_PROA2 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|194311101|gb|ACF45496.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Prosthecochloris aestuarii DSM 271]
          Length = 261

 Score = 41.7 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 12/114 (10%)

Query: 123 CRIGVDDQIPAV-ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            R   D Q   +   R++    +K     + +    A L G           ++++ + E
Sbjct: 18  TRGDFDQQKIYLDNPRDMAIIWRKQNAKMLHVVDLDAALTGTM---------VNFEKIRE 68

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           I     D+ + + GG+       + L   V  V+IG AA  N  ++  +   FS
Sbjct: 69  IV-ATLDIPVQVGGGIRSFEDVERYLGIGVSRVVIGSAAVTNPQLIAELLATFS 121


>gi|77459909|ref|YP_349416.1| 2,4-dienoyl-CoA reductase [Pseudomonas fluorescens Pf0-1]
 gi|77383912|gb|ABA75425.1| putative 2,4-dienoyl-CoA reductase [Pseudomonas fluorescens Pf0-1]
          Length = 679

 Score = 41.7 bits (97), Expect = 0.17,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 45/132 (34%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     I   +     V+       +  L K+I+++G   I  +      +
Sbjct: 200 EIVRRVREAVGPNFIIIFRLSMLDLVEGGSTWEEIVTLAKAIEQAGATLI--NTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    + + ++ +     +     A +IL   D  M+   R  
Sbjct: 258 ARIPTIATKVPRAAFSKVTAKLRGSVNIPLITTNRINTPEIAEQILAEGDADMVSMARPF 317

Query: 220 YKNSAMLTTVDE 231
             +   +    E
Sbjct: 318 LADPDFVNKAAE 329


>gi|20149859|pdb|1GPW|A Chain A, Structural Evidence For Ammonia Tunneling Across The
           (BetaALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE
           Synthase Bienzyme Complex.
 gi|20149861|pdb|1GPW|C Chain C, Structural Evidence For Ammonia Tunneling Across The
           (BetaALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE
           Synthase Bienzyme Complex.
 gi|20149863|pdb|1GPW|E Chain E, Structural Evidence For Ammonia Tunneling Across The
           (BetaALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE
           Synthase Bienzyme Complex
          Length = 253

 Score = 41.7 bits (97), Expect = 0.17,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 123 QAVVVAIDAKRVDGEFM 139


>gi|86142034|ref|ZP_01060558.1| probable copper homeostasis protein [Leeuwenhoekiella blandensis
           MED217]
 gi|85831597|gb|EAQ50053.1| probable copper homeostasis protein [Leeuwenhoekiella blandensis
           MED217]
          Length = 211

 Score = 41.7 bits (97), Expect = 0.17,   Method: Composition-based stats.
 Identities = 32/157 (20%), Positives = 57/157 (36%), Gaps = 25/157 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             L +A K  E+ G + + L                 L   PD+    I+ + KA+ IPV
Sbjct: 12  ESLAQAIK-AEEKGADRLEL---------CAYLAFDGLTPAPDL----ISEVIKAVKIPV 57

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            V  R    D          +K+             +K   +G+      +   L+ + +
Sbjct: 58  RVMIRPRNGDFNYNEEELEHMKAC--------IAFCKKEGAEGVVFGVLNESKKLNIEAI 109

Query: 180 YEIKKENPDLFIGLNGGLE---DMSQALKILPSVDGV 213
             + K    L + ++  ++   D+  ALK L  V+GV
Sbjct: 110 KMLTKAAKPLKVVIHKAIDATPDIDAALKELLQVEGV 146


>gi|311695542|gb|ADP98415.1| NADH:flavin oxidoreductase/NADH oxidase [marine bacterium HP15]
          Length = 366

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 62/175 (35%), Gaps = 23/175 (13%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCR------IGVDDQIPAVA--LRNLVKSIK 144
           +G  L     +V + I A+ +A+    TV  R         D Q+P      R +V++++
Sbjct: 198 YGGSLENRLRLVVEVIRAIREAVGEDFTVGIRLSQGTVTDPDYQLPEGESGFRQIVEAVR 257

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +G + +         K     D         + + ++      + + LNG + D +   
Sbjct: 258 DAGADFVHTTDGDVNRKHFVEGD---------ESLADVAASVEGIGLILNGNI-DETNCQ 307

Query: 205 KILPSV-DGVM-IGRAAYKNSAM---LTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
            +     D ++ +G+ A  N      L    E          P  T  ++  WR+
Sbjct: 308 DVANQFPDTLLAVGKKALANPDFVQRLKDGKEIADIDFAMLQPKATISNELAWRE 362


>gi|126734054|ref|ZP_01749801.1| oxidoreductase, putative [Roseobacter sp. CCS2]
 gi|126716920|gb|EBA13784.1| oxidoreductase, putative [Roseobacter sp. CCS2]
          Length = 396

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 65/180 (36%), Gaps = 13/180 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSG 147
            +G  L     ++ + IA +C A+    PV +K      +D          ++  +  S 
Sbjct: 186 GYGGSLANRARLLLEVIATVCDAVGPAFPVILKLNATDQLDGGFTETDALAVIAMLDTSS 245

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           ++ I I          S  D+              + +   + + L GG++   QA+ +L
Sbjct: 246 LDLIDISGGTYFPGAKSASDSTGNGPYFAAFAKAARAQTT-IPLMLTGGIKTKEQAVALL 304

Query: 208 PSVDGVMIG--RAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
            +    MIG  RA   + ++ TT  +       G+ P   R        I+A  T   AR
Sbjct: 305 ETGTADMIGLARAFILDPSLPTTWHD------GGAPPPFPRFSNPPEGGITAWYTQQIAR 358


>gi|153214218|ref|ZP_01949253.1| hisF protein (cyclase) [Vibrio cholerae 1587]
 gi|262171828|ref|ZP_06039506.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           mimicus MB-451]
 gi|124115467|gb|EAY34287.1| hisF protein (cyclase) [Vibrio cholerae 1587]
 gi|261892904|gb|EEY38890.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           mimicus MB-451]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAAKILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|330800102|ref|XP_003288078.1| hypothetical protein DICPUDRAFT_33474 [Dictyostelium purpureum]
 gi|325081902|gb|EGC35402.1| hypothetical protein DICPUDRAFT_33474 [Dictyostelium purpureum]
          Length = 392

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 32/194 (16%), Positives = 60/194 (30%), Gaps = 23/194 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAA 110
               + A  +   G++ I + N           P +      +G         + + I  
Sbjct: 191 EAFKQGALRLLKAGFDMIEIHNAHGYIGNQFISPVSNQRTDEYGGSFENRIRFLLETITE 250

Query: 111 MCKALSIPVTVKCRIGVDDQ------IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +         +  R+  D+               LVK +    V+ I   +      G S
Sbjct: 251 IRSVWPTEKVLAVRLTCDEWLEDGSGWTMNDTIELVKILDTMDVDIIDCSSG-----GNS 305

Query: 165 PKDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
            K   K+  L        +KK   +LF+   G +   ++   IL     D VM+ R   +
Sbjct: 306 TKQKIKVEPLYQVPFADSVKKHTKNLFVATVGLINTGNEIEDILQQNKADIVMLARPFLR 365

Query: 222 NSAMLTTVDEYFSN 235
           N   +  V +  + 
Sbjct: 366 NPHFVYQVAKELNQ 379


>gi|254295179|ref|YP_003061202.1| NADH:flavin oxidoreductase/NADH oxidase [Hirschia baltica ATCC
           49814]
 gi|254043710|gb|ACT60505.1| NADH:flavin oxidoreductase/NADH oxidase [Hirschia baltica ATCC
           49814]
          Length = 674

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 19/128 (14%), Positives = 43/128 (33%), Gaps = 8/128 (6%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +     ++     +  R+ + D             L K+I+ +G     I+    
Sbjct: 197 LAVETVKRTRASVGENFIIIYRLSMLDLVEGGSTFEEALELGKAIEAAGAT--IINTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    KE+ ++ +  +  +     A ++L   D  MI   
Sbjct: 255 WHEARIPTIVTKVPRAAFTWVTARFKEHLNIPLITSNRINTPEVAEEVLERGDADMISMA 314

Query: 217 RAAYKNSA 224
           R    +  
Sbjct: 315 RPFLADPF 322


>gi|255930737|ref|XP_002556925.1| Pc12g00200 [Penicillium chrysogenum Wisconsin 54-1255]
 gi|211581544|emb|CAP79647.1| Pc12g00200 [Penicillium chrysogenum Wisconsin 54-1255]
          Length = 413

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 38/194 (19%), Positives = 66/194 (34%), Gaps = 26/194 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG--------CPSARVHEG--SFGACLMLNPDIVGDCIAA 110
             V AAK+  + G++ I ++          C S   ++    +G  L        + +  
Sbjct: 205 DFVNAAKLAVEAGFDVIEIHGAHGYLIHQFC-SPLTNKRTDKYGGSLENRARFALEVVQG 263

Query: 111 MCKALSIPVTVKCRIGVDDQIP------AVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +  A+     +  RI   D IP            L + ++  GV+ I + +      GL 
Sbjct: 264 IRAAIPDKTLLFYRISTTDWIPDRESWTPEQSVRLCQLLQPLGVDLIDVSSG-----GLV 318

Query: 165 PKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
           P          Y       IK   P L  G  G + D   A  I+     D V+I R   
Sbjct: 319 PDQQLPPLRPGYQAHLSQGIKDGVPGLLTGSVGMIRDGKTAEDIVASGKADVVIIAREFA 378

Query: 221 KNSAMLTTVDEYFS 234
           +N +++  +     
Sbjct: 379 RNPSLVLNIAYELG 392


>gi|167032550|ref|YP_001667781.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
 gi|166859038|gb|ABY97445.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
          Length = 678

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 29/231 (12%), Positives = 68/231 (29%), Gaps = 38/231 (16%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++            E  +  QI        V  A + +  GY+
Sbjct: 106 LHAGRYAYSPRQVAPSAIQAPINPFKPKELDEAGIEKQIA-----DFVNCAALAQRAGYD 160

Query: 76  EINLNVGCPSARVHEGSFGA--CLMLNPD---------------IVGDCIAAMCKALS-- 116
            + +        +    +     L  + +               +  + ++ +  A+   
Sbjct: 161 GVEI--------MGSEGYFINQFLAAHTNHRTDRWGGSYENRMRLAVEIVSRVRGAVGPN 212

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I   +     V+       +  L K+I+++G   I  +      +   P    K+P  
Sbjct: 213 FIIIFRLSMLDLVEGGSTWDEIELLAKAIEQAGATLI--NTGIGWHEARIPTIATKVPRA 270

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
            +  V    +   ++ +     +     A  +L   D  M+   R    + 
Sbjct: 271 AFSKVTAKLRGVVNIPLITTNRINTPEVAEAVLAEGDADMVSMARPFLADP 321


>gi|15641151|ref|NP_230783.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121587426|ref|ZP_01677195.1| hisF protein (cyclase) [Vibrio cholerae 2740-80]
 gi|121726300|ref|ZP_01679590.1| hisF protein (cyclase) [Vibrio cholerae V52]
 gi|147674704|ref|YP_001216658.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio cholerae
           O395]
 gi|153802577|ref|ZP_01957163.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           cholerae MZO-3]
 gi|153802705|ref|ZP_01957291.1| hisF protein (cyclase) [Vibrio cholerae MZO-3]
 gi|153816949|ref|ZP_01969616.1| hisF protein (cyclase) [Vibrio cholerae NCTC 8457]
 gi|153822006|ref|ZP_01974673.1| hisF protein (cyclase) [Vibrio cholerae B33]
 gi|153826054|ref|ZP_01978721.1| hisF protein (cyclase) [Vibrio cholerae MZO-2]
 gi|153828675|ref|ZP_01981342.1| hisF protein (cyclase) [Vibrio cholerae 623-39]
 gi|227081311|ref|YP_002809862.1| hisF protein [Vibrio cholerae M66-2]
 gi|229505267|ref|ZP_04394777.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae BX 330286]
 gi|229511063|ref|ZP_04400542.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae B33]
 gi|229515521|ref|ZP_04404980.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae TMA 21]
 gi|229518183|ref|ZP_04407627.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae RC9]
 gi|229608286|ref|YP_002878934.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio cholerae
           MJ-1236]
 gi|254225528|ref|ZP_04919138.1| hisF protein (cyclase) [Vibrio cholerae V51]
 gi|254291563|ref|ZP_04962353.1| hisF protein (cyclase) [Vibrio cholerae AM-19226]
 gi|254848266|ref|ZP_05237616.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio cholerae
           MO10]
 gi|255745550|ref|ZP_05419498.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholera CIRS 101]
 gi|258621696|ref|ZP_05716727.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio mimicus
           VM573]
 gi|261210701|ref|ZP_05924993.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio sp.
           RC341]
 gi|262158376|ref|ZP_06029492.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae INDRE 91/1]
 gi|262170188|ref|ZP_06037876.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae RC27]
 gi|262191470|ref|ZP_06049656.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae CT 5369-93]
 gi|297578740|ref|ZP_06940668.1| imidazole glycerol phosphate synthase subunit hisF [Vibrio cholerae
           RC385]
 gi|298498757|ref|ZP_07008564.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           cholerae MAK 757]
 gi|20455010|sp|Q9KSW8|HIS6_VIBCH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|172047398|sp|A5F289|HIS6_VIBC3 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|254801227|sp|C3LLI5|HIS6_VIBCM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|9655610|gb|AAF94297.1| imidazoleglycerol-phosphate synthase, cyclase subunit [Vibrio
           cholerae O1 biovar El Tor str. N16961]
 gi|121548346|gb|EAX58410.1| hisF protein (cyclase) [Vibrio cholerae 2740-80]
 gi|121631246|gb|EAX63619.1| hisF protein (cyclase) [Vibrio cholerae V52]
 gi|124121745|gb|EAY40488.1| hisF protein (cyclase) [Vibrio cholerae MZO-3]
 gi|124121891|gb|EAY40634.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           cholerae MZO-3]
 gi|125621998|gb|EAZ50322.1| hisF protein (cyclase) [Vibrio cholerae V51]
 gi|126512536|gb|EAZ75130.1| hisF protein (cyclase) [Vibrio cholerae NCTC 8457]
 gi|126520471|gb|EAZ77694.1| hisF protein (cyclase) [Vibrio cholerae B33]
 gi|146316587|gb|ABQ21126.1| hisF protein (cyclase) [Vibrio cholerae O395]
 gi|148875828|gb|EDL73963.1| hisF protein (cyclase) [Vibrio cholerae 623-39]
 gi|149740274|gb|EDM54421.1| hisF protein (cyclase) [Vibrio cholerae MZO-2]
 gi|150422515|gb|EDN14472.1| hisF protein (cyclase) [Vibrio cholerae AM-19226]
 gi|227009199|gb|ACP05411.1| hisF protein [Vibrio cholerae M66-2]
 gi|227013005|gb|ACP09215.1| hisF protein [Vibrio cholerae O395]
 gi|229344898|gb|EEO09872.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae RC9]
 gi|229347290|gb|EEO12250.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae TMA 21]
 gi|229351028|gb|EEO15969.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae B33]
 gi|229357490|gb|EEO22407.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae BX 330286]
 gi|229370941|gb|ACQ61364.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae MJ-1236]
 gi|254843971|gb|EET22385.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio cholerae
           MO10]
 gi|255736625|gb|EET92022.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholera CIRS 101]
 gi|258585927|gb|EEW10645.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio mimicus
           VM573]
 gi|260840186|gb|EEX66766.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio sp.
           RC341]
 gi|262021357|gb|EEY40070.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae RC27]
 gi|262029817|gb|EEY48465.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae INDRE 91/1]
 gi|262032665|gb|EEY51217.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae CT 5369-93]
 gi|297536334|gb|EFH75167.1| imidazole glycerol phosphate synthase subunit hisF [Vibrio cholerae
           RC385]
 gi|297543090|gb|EFH79140.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           cholerae MAK 757]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|311086419|gb|ADP66500.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. TLW03 (Acyrthosiphon pisum)]
 gi|311087574|gb|ADP67653.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. JF98 (Acyrthosiphon pisum)]
          Length = 247

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K G++ +  +   A  K            +D+  +  + K   ++   + GG++
Sbjct: 35  LARRYAKEGIDELVFYDITAATKN---------KLVDHSWIKNVSK-VINIPFCVAGGIK 84

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+L    D + I  +A  +  ++T + E F 
Sbjct: 85  SVEDAKKVLSSGADKISINSSALIDPNLITKISERFG 121


>gi|304409127|ref|ZP_07390748.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS183]
 gi|307303130|ref|ZP_07582885.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica BA175]
 gi|304352948|gb|EFM17345.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS183]
 gi|306913490|gb|EFN43912.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica BA175]
          Length = 368

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 51/128 (39%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + + +AA+       +P+T +  +   D      L     LVK  K++G++ + +    +
Sbjct: 211 LFETVAAVRDVWPQHLPLTARFGVIEFDHKDEETLTESIALVKQFKQAGLDMLSV----S 266

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
           I       +    P     I   +++E     +  + G+++   A   +    +D VMIG
Sbjct: 267 ICFSTPTANIPWSPAFLAPIAARVRQEVG-FPVATSWGMDNPHHANAAIEDGQMDLVMIG 325

Query: 217 RAAYKNSA 224
           +A   N  
Sbjct: 326 KAFLANPH 333


>gi|302673345|ref|XP_003026359.1| hypothetical protein SCHCODRAFT_62242 [Schizophyllum commune H4-8]
 gi|300100041|gb|EFI91456.1| hypothetical protein SCHCODRAFT_62242 [Schizophyllum commune H4-8]
          Length = 412

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 59/190 (31%), Gaps = 28/190 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG--------C-PSARVHEGSFGACLMLNPDIV-GDCIA 109
              V A    +  GY+ I ++          C P A V    +G   + N          
Sbjct: 199 DAFVAAIARAQQVGYDFIEIHAAHGYLLSTFCSPLANVRTDQWGGQPLENRLRYPLRVAK 258

Query: 110 AMCKA-LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           A  +A    P+ V+          A   ++      + G     I+A + +  G+   D 
Sbjct: 259 ACREAWADKPLFVRVTAT---DWAAGPEKDEAGMWLQWGPEQTAIYAGELMKLGVDLVDC 315

Query: 169 RKIPNLDYDIVYEI------------KKENPDLFIGLNGGLEDMSQALKILP--SVDGVM 214
               N    ++  +            KK NP L +   G + D   A   L     D ++
Sbjct: 316 SSGGNYSKQVIPPVVHGYQVPYAEIIKKANPGLVVATVGNIYDPKIAESYLQDGKADVIL 375

Query: 215 IGRAAYKNSA 224
           + R   ++  
Sbjct: 376 LARELLRHPH 385


>gi|282163379|ref|YP_003355764.1| glutamate synthase large subunit domain 2 [Methanocella paludicola
           SANAE]
 gi|282155693|dbj|BAI60781.1| glutamate synthase large subunit domain 2 [Methanocella paludicola
           SANAE]
          Length = 508

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 29/129 (22%), Positives = 48/129 (37%), Gaps = 22/129 (17%)

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   I A+ +A     PV+VK             +  +   I ++G + + I   +    
Sbjct: 297 LSQLIYALKEATEYKKPVSVKV-------AAVHNIAAICSGIVRAGADIVTIDGFRGG-T 348

Query: 162 GLSPK---DNRKIP------NLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVD 211
           G +P+   DN  IP       +D  +  E  +    + +G  GG+         I    D
Sbjct: 349 GSAPRIMRDNVGIPIELALAAVDDRLRAEGIRNQASIVVG--GGIRQSADVVKAIALGAD 406

Query: 212 GVMIGRAAY 220
            VMIG AA 
Sbjct: 407 AVMIGTAAL 415


>gi|15678077|ref|NP_275191.1| isopentenyl pyrophosphate isomerase [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|13878539|sp|O26154|IDI2_METTH RecName: Full=Isopentenyl-diphosphate delta-isomerase; Short=IPP
           isomerase; AltName: Full=Isopentenyl pyrophosphate
           isomerase
 gi|2621084|gb|AAB84555.1| conserved protein [Methanothermobacter thermautotrophicus str.
           Delta H]
          Length = 349

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 69/187 (36%), Gaps = 30/187 (16%)

Query: 43  FSTQEKPLALQIG--GADISKLVE-AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            + +E P A+ IG  G+   +  E A +++ D     ++LN   P     +         
Sbjct: 109 IAREEAPSAMLIGNIGSSHIEYAERAVEMI-DADALAVHLN---PLQESIQPGGDV---- 160

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--- 156
           +     + I+A+ +++ +PV VK       +  A         ++  GV+ I +      
Sbjct: 161 DSSGALESISAIVESVDVPVMVK-------ETGAGICSEDAIELESCGVSAIDVAGAGGT 213

Query: 157 KAILKGLSPKDNRKIPNLDYDI-VYEIKK-----ENPDLFIGLNGGLED-MSQALKILPS 209
                     D+R +  L +D  +          E+  + +  +GG+   +  A  I   
Sbjct: 214 SWAAVETYRADDRYLGELFWDWGIPTAASTVEVVESVSIPVIASGGIRSGIDAAKAISLG 273

Query: 210 VDGVMIG 216
            +  M+G
Sbjct: 274 AE--MVG 278


>gi|9955236|pdb|1THF|D Chain D, Cyclase Subunit Of Imidazoleglycerolphosphate Synthase
           From Thermotoga Maritima
          Length = 253

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 123 QAVVVAIDAKRVDGEFM 139


>gi|284993282|ref|YP_003411837.1| NADH:flavin oxidoreductase/NADH oxidase [Geodermatophilus obscurus
           DSM 43160]
 gi|284066528|gb|ADB77466.1| NADH:flavin oxidoreductase/NADH oxidase [Geodermatophilus obscurus
           DSM 43160]
          Length = 605

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 66/182 (36%), Gaps = 12/182 (6%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPS------ARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
               A+I    G + + ++ G  S      + +      A     P ++ + +AA+   L
Sbjct: 144 FAAGARIAVGAGVDGVEVDAGARSLLRQFASGLTNHRGDAYGADRPRLLREVLAAVRAEL 203

Query: 116 SIPVTVKCRIGVDDQIPAVALRN--LVKSIKKSG--VNGIWIHARKAILKGLSPKDNRKI 171
                +  R+  D++ P   +     V+ +++    V+ + +     +       D    
Sbjct: 204 GSGRVLSLRLSCDEEAPWAGITPDLAVERVRELAPLVDLLVVVRGSGLAASAYRPDGHTR 263

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           P  + D+   ++       + L G + D++ A + L     D V + RA   ++ ++   
Sbjct: 264 PGFNADLTRRVRAAAGGTPVVLQGSVVDVTAAQRALDEGVADAVEMTRAQIADADLVRKA 323

Query: 230 DE 231
             
Sbjct: 324 RA 325


>gi|256831372|ref|YP_003160099.1| NADH:flavin oxidoreductase/NADH oxidase [Jonesia denitrificans DSM
           20603]
 gi|256684903|gb|ACV07796.1| NADH:flavin oxidoreductase/NADH oxidase [Jonesia denitrificans DSM
           20603]
          Length = 367

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/154 (13%), Positives = 54/154 (35%), Gaps = 12/154 (7%)

Query: 94  GACLMLNPDIVGDCIAAMCK-ALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNG 150
           G  +     +  + +AA+ +    +P+ V+      VD            + ++ +G + 
Sbjct: 210 GGDITNRSRLAVNIVAAIRERHPEVPLFVRISATDWVDGGYTLDDATITSQLLRDAGADL 269

Query: 151 IWIHARKAILKGLSPKD-NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
           I +     + +   P     +IP+ ++         N ++ +   G + D  QA   +  
Sbjct: 270 IDVSTGGNVARAPIPAAPGYQIPHAEH------IARNANIAVSGVGMITDPHQADSYIRE 323

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
             VD +M+ R   ++        +     +   +
Sbjct: 324 GRVDAIMVARHMMRDPHFALRAADTLGQDVHWPA 357


>gi|66806937|ref|XP_637191.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
 gi|60465598|gb|EAL63680.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
          Length = 415

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 37/188 (19%), Positives = 67/188 (35%), Gaps = 21/188 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  E+A+     G++ I ++            P++      +G         + D + A+
Sbjct: 193 QFRESAERCLKIGFDMIEIHGAHGYLISSFLSPTSNKRTDQYGGDFNGRIKFLIDIVKAV 252

Query: 112 CKA--LSIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                +S P++V+  C   V D         L K ++  GV+ +   +      G S   
Sbjct: 253 RTVWPMSKPLSVRLSCEEWVKDGWHIEDTVRLAKILESLGVDILDCSSG-----GNSIDQ 307

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-A 224
             +   L      E  K N +L     G +   ++A  IL     D VM+ RA  ++   
Sbjct: 308 KIQGGPLYQVKFAEQIKRNTNLKTAAVGLINKPNEADSILETNKCDIVMMARAFLRDPFW 367

Query: 225 MLTTVDEY 232
            L   DE 
Sbjct: 368 PLHCADEL 375


>gi|154319223|ref|XP_001558929.1| hypothetical protein BC1G_02563 [Botryotinia fuckeliana B05.10]
 gi|150856994|gb|EDN32186.1| hypothetical protein BC1G_02563 [Botryotinia fuckeliana B05.10]
          Length = 432

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 61/192 (31%), Gaps = 30/192 (15%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +A +   + G++ I +             P++      +G        +V + +    
Sbjct: 224 FGDATRRAIEAGFDAIEIHGAHGYLLHQFLSPASNKRTDDYGGSFENRTRVVLEIVDRTR 283

Query: 113 KAL--SIPVTVKCR-------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + +  ++P+  +         +  +          L K +   GV+ + + +      G 
Sbjct: 284 QIMPKNMPLFFRVSGSEWLEHLAPEPSWDIQESIKLAKILATRGVDVLDVSSG-----GN 338

Query: 164 SPKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            P+   K           +IK    D L +G  G +    QA  +L    +D + IGR  
Sbjct: 339 DPRQKIKGGPAYQTPFARQIKLAVGDSLLVGTVGSITSGVQANDLLKDNGLDMIFIGRMF 398

Query: 220 YKNS---AMLTT 228
            KN         
Sbjct: 399 QKNPGLVWTFAD 410


>gi|34495624|ref|NP_899839.1| 2,4-dienoyl-CoA reductase FadH1 [Chromobacterium violaceum ATCC
           12472]
 gi|34101479|gb|AAQ57848.1| 2,4-dienoyl-CoA reductase FadH1 [Chromobacterium violaceum ATCC
           12472]
          Length = 673

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 55/181 (30%), Gaps = 23/181 (12%)

Query: 61  KLVEAAKIVEDFGYNEIN--------LNVGCPSARVHEGSF---GACLMLNPDIVGDCIA 109
                AK+ +  GY+ +         +N     AR         G           + + 
Sbjct: 144 DFANCAKLAQQAGYDGVEVMGSEGYLINQF--IARATNKRTDDWGGSFENRIRFAIETVK 201

Query: 110 AMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+  A+     +  R+     V D      + +L + I+K+G   I  +      +   P
Sbjct: 202 AVRAAVGGDFIIIYRLSMLDLVQDGSSWDEVVHLAREIEKAGATLI--NTGIGWHEARVP 259

Query: 166 KDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                +P   +  V  ++  +     I  N  +     A  IL     D V + R    +
Sbjct: 260 TIATMVPRGGFAWVTKKLMGQVKIPLITTNR-INTPEVAEDILAGGCADMVSMARPFLAD 318

Query: 223 S 223
            
Sbjct: 319 P 319


>gi|300711274|ref|YP_003737088.1| NADH-dependent flavin oxidoreductase [Halalkalicoccus jeotgali B3]
 gi|299124957|gb|ADJ15296.1| NADH-dependent flavin oxidoreductase [Halalkalicoccus jeotgali B3]
          Length = 363

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 26/199 (13%), Positives = 60/199 (30%), Gaps = 21/199 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AAK   + G+    ++            P        +G        +V     A
Sbjct: 161 EDYRAAAKRALEAGFEVAEVHAAHGYLLHEFLSPVTNDRTDEYGGDFENRTRLVRQVTEA 220

Query: 111 MCKAL--SIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +        PV V+      +   +        +L   + + G + I + +         
Sbjct: 221 VRDVWPDDNPVFVRISGTDWLPERESWTIEQSVDLADELYELGADLIDVSSGMLHPDQQL 280

Query: 165 PKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           P++          +  ++++E   D+ +G  GG+ D  QA +++     D  ++GR   +
Sbjct: 281 PQEGSAS---QLPLAAQVREERETDIAVGAVGGITDAEQADELIREGDADLAIVGREHLR 337

Query: 222 NSAMLTTVDEYFSNPLTGS 240
           +              +   
Sbjct: 338 DPYFALHAAAELGEDVEPP 356


>gi|258626358|ref|ZP_05721205.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio mimicus
           VM603]
 gi|258581410|gb|EEW06312.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio mimicus
           VM603]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|242793379|ref|XP_002482149.1| 2,4-dienoyl-CoA reductase [NADPH], putative [Talaromyces stipitatus
           ATCC 10500]
 gi|218718737|gb|EED18157.1| 2,4-dienoyl-CoA reductase [NADPH], putative [Talaromyces stipitatus
           ATCC 10500]
          Length = 412

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 26/169 (15%), Positives = 45/169 (26%), Gaps = 26/169 (15%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR------IGVDDQIPAVALRNLVKSIK 144
           +G        +  +        +   +PV ++           +            +++ 
Sbjct: 231 YGGSFENGIRLSLEIAQLTRDTVGPDVPVFLRVSASDWVQESSESTWTIDDTVKFAEALA 290

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQ 202
           K G   +          G  P       P         IKK   D L +   G L+    
Sbjct: 291 KQGAIDVI----DVSSGGAHPAQKINSFPGFQVPFAVAIKKAVGDKLAVAAVGMLDTAEL 346

Query: 203 ALKILP--SVDGVMIGRAAYKNS---AMLTT-------VDEYFSNPLTG 239
           A K+L    +D  ++GR   KN                +      P TG
Sbjct: 347 ANKVLEEDGLDFALVGRGYLKNPNLVWKFAEELGVDFSIAHQIRWPFTG 395


>gi|90412341|ref|ZP_01220345.1| putative NADH-dependent flavin oxidoreductase [Photobacterium
           profundum 3TCK]
 gi|90326603|gb|EAS43002.1| putative NADH-dependent flavin oxidoreductase [Photobacterium
           profundum 3TCK]
          Length = 370

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 30/223 (13%), Positives = 72/223 (32%), Gaps = 19/223 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              A++  ++ G++ + ++            P     E  +G  L     ++ +    + 
Sbjct: 147 FAHASRRAQESGFDGVEIHAAHTYLINQFLSPYYNRREDQYGGSLDNRMRLLLEIYVEIR 206

Query: 113 KALS--IPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLS 164
           K +    P+ VK          +     R + + ++  GV+ I     IH +   + G +
Sbjct: 207 KLVGDEYPILVKLTASEFFAGGLTFDETRIVCQKLEAIGVDAIIISGNIHGKANTMIGEA 266

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
                      +     +  E  ++ +   GGL D+    +I    ++    + R     
Sbjct: 267 FDGYTIQQEGYFHEYGHVISEEVNVPVITVGGLTDIDAIEEIANNTNIQYFALSRPLLSE 326

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
             ++    E    P+      K R  +  +  ++       AR
Sbjct: 327 PHLIKRWKEGNRTPVECERCSKCRTRRGNFCVVNKKRKSQLAR 369


>gi|15643794|ref|NP_228842.1| imidazole glycerol phosphate synthase subunit HisF [Thermotoga
           maritima MSB8]
 gi|20455028|sp|Q9X0C6|HIS6_THEMA RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|304445553|pdb|2WJZ|A Chain A, Crystal Structure Of (Hish) K181a Y138a Mutant Of
           Imidazoleglycerolphosphate Synthase (Hish Hisf) Which
           Displays Constitutive Glutaminase Activity
 gi|304445555|pdb|2WJZ|C Chain C, Crystal Structure Of (Hish) K181a Y138a Mutant Of
           Imidazoleglycerolphosphate Synthase (Hish Hisf) Which
           Displays Constitutive Glutaminase Activity
 gi|304445557|pdb|2WJZ|E Chain E, Crystal Structure Of (Hish) K181a Y138a Mutant Of
           Imidazoleglycerolphosphate Synthase (Hish Hisf) Which
           Displays Constitutive Glutaminase Activity
 gi|4981577|gb|AAD36113.1|AE001764_16 cyclase [Thermotoga maritima MSB8]
          Length = 253

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 123 QAVVVAIDAKRVDGEFM 139


>gi|226951266|ref|ZP_03821730.1| 2,4-dienoyl-CoA reductase [Acinetobacter sp. ATCC 27244]
 gi|294650783|ref|ZP_06728132.1| 2,4-dienoyl-CoA reductase [Acinetobacter haemolyticus ATCC 19194]
 gi|226838007|gb|EEH70390.1| 2,4-dienoyl-CoA reductase [Acinetobacter sp. ATCC 27244]
 gi|292823329|gb|EFF82183.1| 2,4-dienoyl-CoA reductase [Acinetobacter haemolyticus ATCC 19194]
          Length = 676

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 20/126 (15%), Positives = 44/126 (34%), Gaps = 10/126 (7%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+   +     +  R+     V D      +  + K+++K+GV  +  +      +
Sbjct: 198 EIVKAIRAKVGEKFIIAFRLSLLDLVHDGNTMQEVITVAKALEKAGVTLL--NTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   + D   E+K+      I  N  +     A +I+     D V + R 
Sbjct: 256 ARIPTIVTSVPRAAFVDYTAEVKQHLSIPVIASNR-INMPDVAEEIVASGKADMVQMARP 314

Query: 219 AYKNSA 224
              +  
Sbjct: 315 FLADPY 320


>gi|167755368|ref|ZP_02427495.1| hypothetical protein CLORAM_00882 [Clostridium ramosum DSM 1402]
 gi|167704307|gb|EDS18886.1| hypothetical protein CLORAM_00882 [Clostridium ramosum DSM 1402]
          Length = 666

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 26/205 (12%), Positives = 63/205 (30%), Gaps = 31/205 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNV-------GCPSARVHEG---SFGACLMLNPDIVGDCIA 109
            K  +AA I ++ G++ + ++         C +  +       +G  L        + + 
Sbjct: 157 EKFGDAAVIAKNSGFDGVEIHAVHEGYLLDCFTMTLFNQRTDKYGGDLKGRLRFATEIVE 216

Query: 110 AMCKALSI--PVTVKCRI----------------GVDDQIPAVALRNLVKSIKKSGVNGI 151
            +        PV ++  I                  +           VK ++++G +  
Sbjct: 217 TIKNKCGKDFPVILRFSIKSYIKQLRQGGLPGEDFKELGRDIDEAIEAVKILQEAGYDAF 276

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
              A        +         +   +V +I+       +   G ++D   A+  L    
Sbjct: 277 DADAGTYDSWYWAHPPMYFEKGMYLPLVEKIRDAAKVPLLIA-GRMDDPKMAVDALNKGT 335

Query: 210 VDGVMIGRAAYKNSAMLTTVDEYFS 234
           +DGV +GR    +   +  + +   
Sbjct: 336 IDGVGLGRPLLSDPDYVNKLKDGLE 360


>gi|254828369|ref|ZP_05233056.1| hisA [Listeria monocytogenes FSL N3-165]
 gi|258600762|gb|EEW14087.1| hisA [Listeria monocytogenes FSL N3-165]
          Length = 240

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 11/101 (10%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+ ++KK    + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEIIRKMKKAA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           M+Q    L   +D V+IG AA  +   L    + +   +  
Sbjct: 86  MAQVDYYLESGIDRVIIGSAALTDPDFLRAAVQKYGTKIAA 126


>gi|325261397|ref|ZP_08128135.1| 2-enoate reductase [Clostridium sp. D5]
 gi|324032851|gb|EGB94128.1| 2-enoate reductase [Clostridium sp. D5]
          Length = 655

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 38/258 (14%), Positives = 83/258 (32%), Gaps = 53/258 (20%)

Query: 9   YRFFARLLTNNALLYTE----MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVE 64
           +     +    A + +E    M+ A A ++         + + + ++ +     +    +
Sbjct: 76  FVQLTAMTGRAAHIESETDWKMLPAPAPIQNVW----DPAIKNRGISKEEIHKYVENFAQ 131

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVGDCI 108
           AA +V+  G + + ++       VHEG                 +G CL        + +
Sbjct: 132 AAYLVKQAGGDGVEIHA------VHEGYLLDQFAIGFYNKRTDEYGGCLENRLRFPKEIV 185

Query: 109 AAMCKALSI--PVTVK--CRIGVDD--------QIPAVALRNL------VKSIKKSGVNG 150
            A+ +      PV+V+   R  V D        +      R+L       K +++ G + 
Sbjct: 186 EAIKEKCGKDFPVSVRYSVRSYVKDFNRGALPGEEFEEKGRDLEEGVTVAKLLEEYGYDM 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS- 209
           +                       +   V  +KK      +   G  +D   A K +   
Sbjct: 246 LNCDNGSYDSWFWPHPPVYMPKACNLQDVAAVKKAVNIPVVCA-GRFDDPELAEKAIAEG 304

Query: 210 -VDGVM-IGRAAYKNSAM 225
            +D +M +GR    +  +
Sbjct: 305 RID-IMGMGRPLLADPEL 321


>gi|255527702|ref|ZP_05394559.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296185037|ref|ZP_06853447.1| 4Fe-4S binding domain protein [Clostridium carboxidivorans P7]
 gi|255508615|gb|EET84998.1| dihydroorotate dehydrogenase family protein [Clostridium
           carboxidivorans P7]
 gi|296049871|gb|EFG89295.1| 4Fe-4S binding domain protein [Clostridium carboxidivorans P7]
          Length = 360

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 22/135 (16%), Positives = 40/135 (29%), Gaps = 12/135 (8%)

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD------QIPAVALRNLVKSIKKSGVN 149
            +  + + V D +  +      PV +K   G+        ++        V         
Sbjct: 127 YMEKDLESVVDSLK-IASKSDKPVYIKISPGITKIGWYVKRLVEEGAAGFVAINSLGPCL 185

Query: 150 GIWIHARKAILKGLSPKDN---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
            I +      L G         + +  +    VY I        IG+ GG+     A+ +
Sbjct: 186 HIDVETGLPYLGGEKGYGWLSGKSLNPIALRYVYSIANSVKVPVIGV-GGISSGEDAVAM 244

Query: 207 -LPSVDGVMIGRAAY 220
            +     V I  AA 
Sbjct: 245 IMAGASAVQICTAAI 259


>gi|123496746|ref|XP_001327038.1| Bile acid-inducible operon protein C-related protein [Trichomonas
           vaginalis G3]
 gi|121909961|gb|EAY14815.1| Bile acid-inducible operon protein C-related protein [Trichomonas
           vaginalis G3]
          Length = 199

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 26/185 (14%), Positives = 65/185 (35%), Gaps = 21/185 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              +  AK V++ G + + ++            P        +G        I  + +  
Sbjct: 12  EDFIRVAKRVQNVGADGVCVHAAHGFMLSEFLSPHYNKRTDKYGGSPENRRRIFKEIVEG 71

Query: 111 MCKALSIPVTVKCRIG-VDDQIPAVALRNLVKSIKKS-GVNGIWIHARKAILKGLSPKDN 168
           +         +  +I   D     +  ++ V+++  + G++ + +        G      
Sbjct: 72  IRSTCGKDFFISTKINGADHCENGLTAKDFVQNVINTPGLDMVEVSCGFQNAAGCRTPSF 131

Query: 169 RKIPNLDYDIVYEI-----KKENPDLFIGLNGG---LEDMSQALKILPSVDGVMIGRAAY 220
           + I  + +   Y +      ++  D+ I + GG   L+DM  ALK    +  + +GR + 
Sbjct: 132 KGINGIRFKPAYNLGEALELRKVSDIPIAVVGGFRKLKDMEDALK--QGIQLISVGRPSI 189

Query: 221 KNSAM 225
            +  +
Sbjct: 190 CDPHV 194


>gi|46906809|ref|YP_013198.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|254853236|ref|ZP_05242584.1| conserved hypothetical protein [Listeria monocytogenes FSL R2-503]
 gi|254993158|ref|ZP_05275348.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes FSL J2-064]
 gi|300765371|ref|ZP_07075354.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes FSL N1-017]
 gi|60392382|sp|Q722Y6|HIS4_LISMF RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|46880075|gb|AAT03375.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes serotype 4b str.
           F2365]
 gi|258606591|gb|EEW19199.1| conserved hypothetical protein [Listeria monocytogenes FSL R2-503]
 gi|300513932|gb|EFK40996.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes FSL N1-017]
          Length = 240

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 11/99 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+  +KK    + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEIIQRMKKAA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           M+Q    L   +D V+IG AA  N   L    + +   +
Sbjct: 86  MAQVDYYLESGIDRVIIGSAALTNPDFLRAAVQKYGAKI 124


>gi|322705663|gb|EFY97247.1| NADH-dependent flavin oxidoreductase-like protein [Metarhizium
           anisopliae ARSEF 23]
          Length = 412

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 26/201 (12%), Positives = 65/201 (32%), Gaps = 22/201 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA      G++ I ++            P +     S+G         + + I  + 
Sbjct: 197 FGEAALRAVKAGFDLIEIHGAHGYLITEFLSPISNKRTDSYGGSFDNRTRFLREVIETVR 256

Query: 113 KAL--SIPVTVKCRIGV------DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             +  S+P+ ++           +      +   L K +   GV+ + + +     +   
Sbjct: 257 SVIPDSMPLWLRVSATEWMEWTGEPSWDLDSTVRLAKLLPALGVDALDVSSGGNDPRQRL 316

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-----VDGVMIGRAA 219
            ++     +L   I   ++ +  D+ +G  G ++    A  ++        D V++ R  
Sbjct: 317 LREKTYQTDLARQIRRALRADGLDMVVGAVGNIDGAEFARDVVQEGGEQSADLVLVARHF 376

Query: 220 YKNSAMLTTVDEYFSNPLTGS 240
            +    +    E    P+   
Sbjct: 377 LREPDFVLNAAERLGVPVKWP 397


>gi|299537861|ref|ZP_07051150.1| NADPH dehydrogenase [Lysinibacillus fusiformis ZC1]
 gi|298726840|gb|EFI67426.1| NADPH dehydrogenase [Lysinibacillus fusiformis ZC1]
          Length = 336

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 29/219 (13%), Positives = 66/219 (30%), Gaps = 26/219 (11%)

Query: 35  GDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPS 85
            D K     + ++    +           +AA      G++ + ++            P+
Sbjct: 124 SDYKTPTEMTEEDIHYVI-------EAFKQAAIRAAKAGFDVLEIHGAHGYLISEFLSPA 176

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSI 143
               +  +G        I+   I A+      P  V V      +D           + +
Sbjct: 177 TNKRQDQYGGSQENRYRILRQVIDAVRSVWDGPLLVRVSAEDYAEDGTTMDDFIVFSRWM 236

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           K  GV+ + +     +   ++     ++P+       E  K   D+  G  G +    QA
Sbjct: 237 KSQGVDLVDVSTGGVVPAAINVFPGYQVPHA------EAIKHGADIPTGAVGLITTAIQA 290

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +IL +   D + + R   ++        +     +   
Sbjct: 291 EEILQNNRADLIFLARVLLRDPYWALHAAKELGEDVQPP 329


>gi|73536042|pdb|2A0N|A Chain A, Crystal Structure Of Imidazole Glycerol Phosphate Synthase
           Subunit Hisf (Ec 4.1.3.-) (Tm1036) From Thermotoga
           Maritima At 1.64 A Resolution
          Length = 265

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 76  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGS 134

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 135 QAVVVAIDAKRVDGEFM 151


>gi|322377953|ref|ZP_08052441.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M334]
 gi|321281129|gb|EFX58141.1| TIM-barrel protein, NifR3 family [Streptococcus sp. M334]
          Length = 91

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 9/98 (9%), Positives = 24/98 (24%), Gaps = 10/98 (10%)

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRH 279
             N  +   ++ YF               K  +  +   +             +++    
Sbjct: 1   MGNPYLFNQINHYFETGELLPDLTFEDKMKIAYEHLKRLIN-----LKGENVAVREFRGL 55

Query: 280 MIGLFHGFPNSRRCRHILTVEAGASTATHHIIETAFNL 317
                 G   + + R  ++  +  +      IE    L
Sbjct: 56  APHYLRGTSGAAKLRGAISQASTLAE-----IEALLQL 88


>gi|296122232|ref|YP_003630010.1| NADH:flavin oxidoreductase/NADH oxidase [Planctomyces limnophilus
           DSM 3776]
 gi|296014572|gb|ADG67811.1| NADH:flavin oxidoreductase/NADH oxidase [Planctomyces limnophilus
           DSM 3776]
          Length = 477

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 35/220 (15%), Positives = 68/220 (30%), Gaps = 62/220 (28%)

Query: 65  AAKIVEDFGYNEINLNVGCP--------SARVHEGSFGACLMLNPDIVGDCIAAMCKAL- 115
           AA+     G + I++   C         +AR+  GS+G CL     +V D I A+   + 
Sbjct: 193 AARRAYQIGCDFIDIK-QCHRYLLSELLAARIRPGSYGGCLENRMRLVLDVIKAIRAEVP 251

Query: 116 --------------------------SIPVTVKCRIGV------DDQIPAVALRNLVKSI 143
                                      IPVT               QI       +V+ +
Sbjct: 252 SLILATRMNVFDGIPFKGQGEEFVGQPIPVTFPIETSFGASCTDPLQIDLTEPLEVVRRL 311

Query: 144 KKSGVNGIWIHARKAIL--KGLSPKDNRKIPN------------LDYDIVYEIKKENPDL 189
             +G++ I +           + P +   +                +++  E++K    +
Sbjct: 312 VDAGISLINVSVGNPYACPHYVRPAEQPPVDGYHAPEHPLLGVLRHFEVTKEVQKAAGAV 371

Query: 190 FIGLNG--GLEDMSQ---ALKILPS-VDGVMIGRAAYKNS 223
            +  +G   L+D +    A  +       V +GR +    
Sbjct: 372 PVVGSGYSWLQDYAFEIGAANVKQGRCQFVGLGRGSLSQP 411


>gi|121610969|ref|YP_998776.1| NADH:flavin oxidoreductase/NADH oxidase [Verminephrobacter eiseniae
           EF01-2]
 gi|121555609|gb|ABM59758.1| NADH:flavin oxidoreductase/NADH oxidase [Verminephrobacter eiseniae
           EF01-2]
          Length = 686

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 70/189 (37%), Gaps = 18/189 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG-------CPSARVHEGS--FGACLMLNPDIVGDCIAAM 111
               AA+ V+D G + I ++           S RV+  S  +G  L        + + A+
Sbjct: 150 DFGRAARRVKDAGLDGIEISAAHQHLIDQFWSPRVNHRSDEYGGSLANRLRFGIEVLQAV 209

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + +     V  R+  D    D I     + + +++ +SG+      A        +  +
Sbjct: 210 REQVGADFCVGLRVCGDEFHEDGINHEMAKEIAQAMSESGLIDFLSVAGSGADTHNTLAN 269

Query: 168 N---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +    G+ D  QA +IL +  VD V + RA   +
Sbjct: 270 CMPPMALPPEPFVHLAAGIKSVSRVPVMHAQGIRDPGQAERILAAGMVDLVGMTRAQIAD 329

Query: 223 SAMLTTVDE 231
             M+  + +
Sbjct: 330 PHMVGKIRD 338


>gi|261252589|ref|ZP_05945162.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           orientalis CIP 102891]
 gi|260935980|gb|EEX91969.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           orientalis CIP 102891]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVQRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPELITQLADKFG 121


>gi|190574123|ref|YP_001971968.1| imidazole glycerol phosphate synthase subunit HisF
           [Stenotrophomonas maltophilia K279a]
 gi|226702005|sp|B2FPM4|HIS6_STRMK RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|190012045|emb|CAQ45667.1| putative imidazole glycerol phosphate synthase subunit hisF
           [Stenotrophomonas maltophilia K279a]
          Length = 258

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 39/111 (35%), Gaps = 11/111 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D +    +  L +  +  G + +            +  + R +     + +  +  
Sbjct: 21  VRFRDHVDMGDIAELAQRYRDQGADELV------FYDIGASPEARSVDVAWIERIARLI- 73

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
              D+   + GG++ +  A ++L    D V I   A     ++T + + F 
Sbjct: 74  ---DIPFCVAGGIDSVETARRVLFAGADKVSINSPALGRPELITELADEFG 121


>gi|218897029|ref|YP_002445440.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus G9842]
 gi|254766768|sp|B7ITF9|NAMA_BACC2 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|218542665|gb|ACK95059.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus G9842]
          Length = 345

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ K    P+ V+        D +         K +K+ G++ 
Sbjct: 186 YGGSPENRYRFLREIIDSVNKVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE   +  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEYTKIATGAVGLITTGSQAEQILNDN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|327483842|gb|AEA78249.1| Imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           cholerae LMA3894-4]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|262164681|ref|ZP_06032419.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio mimicus VM223]
 gi|262027061|gb|EEY45728.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio mimicus VM223]
          Length = 363

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 26/192 (13%), Positives = 59/192 (30%), Gaps = 37/192 (19%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN----------------PDIV 104
              +AAK   + G++ + +                 L+                   +  
Sbjct: 161 DFAQAAKCAIEAGFDGVEI-----------HGGNGYLIDQFLRTNSNHRTDNYGGSRENR 209

Query: 105 GDCIAAMCKALSIPVT---VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
              +  +  A+S  +    V  R+        +   ++V +I ++      + AR     
Sbjct: 210 IRFLLEVVDAVSKAIGENRVGVRLAPFITFKDMNCPDIVPTILEASKQ---LQARDIAYL 266

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            LS  D    P +       +++   +  I    G   + +A ++L     D V  GR  
Sbjct: 267 HLSEADWDDAPTIPESFRIALREHFTNAIIVA--GRYTLERAEEVLQKGYADLVAFGRPF 324

Query: 220 YKNSAMLTTVDE 231
             N  +++ +  
Sbjct: 325 IANPDLVSRLKH 336


>gi|219681481|ref|YP_002467866.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|219682037|ref|YP_002468421.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|257471160|ref|ZP_05635159.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. LSR1 (Acyrthosiphon pisum)]
 gi|219621770|gb|ACL29926.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|219624324|gb|ACL30479.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|311085848|gb|ADP65930.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. LL01 (Acyrthosiphon pisum)]
 gi|311087001|gb|ADP67081.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. JF99 (Acyrthosiphon pisum)]
          Length = 258

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K G++ +  +   A  K            +D+  +  + K   ++   + GG++
Sbjct: 35  LARRYAKEGIDELVFYDITAATKN---------KLVDHSWIKNVSK-VINIPFCVAGGIK 84

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+L    D + I  +A  +  ++T + E F 
Sbjct: 85  SVEDAKKVLSSGADKISINSSALIDPNLITKISERFG 121


>gi|77408927|ref|ZP_00785651.1| dihydroorotate dehydrogenase A [Streptococcus agalactiae COH1]
 gi|77172469|gb|EAO75614.1| dihydroorotate dehydrogenase A [Streptococcus agalactiae COH1]
          Length = 310

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 40/208 (19%), Positives = 68/208 (32%), Gaps = 32/208 (15%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           K   L + G    +     K VE+  YN  I LN+ CP+           +   P I  D
Sbjct: 95  KNHVLSLVGLSPEETHIILKKVENSSYNGLIELNLSCPN-----------VPGKPQIAYD 143

Query: 107 ------CIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWI 153
                  ++ +      P+ +K     D      A  + N      +  +   G NG+ I
Sbjct: 144 FEMTDLILSEIFSYYQKPLGIKLPPYFDIVHFDQAATIFNKYPLAFINCVNSIG-NGLVI 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEI----KKENPDLFIGLNGGLEDMSQALKI-LP 208
                ++K  +         +    +  +    K+ NP + I   GG+++   A +  L 
Sbjct: 203 DDETVVIKPKNGFGGIGGDFIKPTALANVHAFYKRLNPSIKIIGTGGVKNGRDAFEHILC 262

Query: 209 SVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
               V IG A  K    +   V      
Sbjct: 263 GASMVQIGTALQKEGPEIFQRVSRELKE 290


>gi|22536686|ref|NP_687537.1| dihydroorotate dehydrogenase 1A [Streptococcus agalactiae 2603V/R]
 gi|25010622|ref|NP_735017.1| dihydroorotate dehydrogenase 1A [Streptococcus agalactiae NEM316]
 gi|76787324|ref|YP_329289.1| dihydroorotate dehydrogenase 1A [Streptococcus agalactiae A909]
 gi|76798116|ref|ZP_00780370.1| Dihydroorotate dehydrogenase (Dihydroorotate oxidase)(DHOdehase)
           (DHODase) (DHOD) [Streptococcus agalactiae 18RS21]
 gi|77405441|ref|ZP_00782534.1| dihydroorotate dehydrogenase A [Streptococcus agalactiae H36B]
 gi|77414012|ref|ZP_00790184.1| dihydroorotate dehydrogenase A [Streptococcus agalactiae 515]
 gi|81845475|sp|Q8E155|PYRD_STRA5 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|81845657|sp|Q8E6L0|PYRD_STRA3 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|123602204|sp|Q3K2G4|PYRD_STRA1 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|22533527|gb|AAM99409.1|AE014215_3 dihydroorotate dehydrogenase A [Streptococcus agalactiae 2603V/R]
 gi|23094976|emb|CAD46197.1| unknown [Streptococcus agalactiae NEM316]
 gi|76562381|gb|ABA44965.1| dihydroorotate dehydrogenase [Streptococcus agalactiae A909]
 gi|76586524|gb|EAO63028.1| Dihydroorotate dehydrogenase (Dihydroorotate oxidase)(DHOdehase)
           (DHODase) (DHOD) [Streptococcus agalactiae 18RS21]
 gi|77159938|gb|EAO71077.1| dihydroorotate dehydrogenase A [Streptococcus agalactiae 515]
 gi|77175934|gb|EAO78710.1| dihydroorotate dehydrogenase A [Streptococcus agalactiae H36B]
          Length = 310

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 40/208 (19%), Positives = 68/208 (32%), Gaps = 32/208 (15%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           K   L + G    +     K VE+  YN  I LN+ CP+           +   P I  D
Sbjct: 95  KNHVLSLVGLSPEETHIILKKVENSSYNGLIELNLSCPN-----------VPGKPQIAYD 143

Query: 107 ------CIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWI 153
                  ++ +      P+ +K     D      A  + N      +  +   G NG+ I
Sbjct: 144 FEMTDLILSEIFSYYQKPLGIKLPPYFDIVHFDQAATIFNKYPLAFINCVNSIG-NGLVI 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEI----KKENPDLFIGLNGGLEDMSQALKI-LP 208
                ++K  +         +    +  +    K+ NP + I   GG+++   A +  L 
Sbjct: 203 DDETVVIKPKNGFGGIGGDFIKPTALANVHAFYKRLNPSIKIIGTGGVKNGRDAFEHILC 262

Query: 209 SVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
               V IG A  K    +   V      
Sbjct: 263 GASMVQIGTALQKEGPEIFQRVSRELKE 290


>gi|262165411|ref|ZP_06033148.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           mimicus VM223]
 gi|262025127|gb|EEY43795.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           mimicus VM223]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAQDAARILEFGADKVSINSPALANPQLITDLADRFG 121


>gi|261253429|ref|ZP_05946002.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio orientalis CIP 102891]
 gi|260936820|gb|EEX92809.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio orientalis CIP 102891]
          Length = 670

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 23/125 (18%), Positives = 46/125 (36%), Gaps = 8/125 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ KA      +  R+     V++      +  L K ++K+GV    I+      +
Sbjct: 199 EVVKAIRKAAGEEFIIIFRLSMLDLVEEGSTFDEVIMLAKELEKAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  + +  + I     +    +A KIL     D V + R  
Sbjct: 257 ARIPTIATQVPRSAFTWVTEKVRPHVSVPIITCNRINTPEEAEKILASGQADMVSMARPF 316

Query: 220 YKNSA 224
             +  
Sbjct: 317 LADPH 321


>gi|296120836|ref|YP_003628614.1| NADH:flavin oxidoreductase/NADH oxidase [Planctomyces limnophilus
           DSM 3776]
 gi|296013176|gb|ADG66415.1| NADH:flavin oxidoreductase/NADH oxidase [Planctomyces limnophilus
           DSM 3776]
          Length = 360

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 27/179 (15%), Positives = 60/179 (33%), Gaps = 21/179 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V AAK   + GY  + L+            P +      +G         + + + A+ 
Sbjct: 159 FVAAAKRAIEAGYQLLELHFAHGYLAHEFWSPLSNHRTDQYGGSWENRARFLVETLDAVR 218

Query: 113 KALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLSPKD 167
                 +P+  +  +   +D  +       L   +KK G++ + + H          P  
Sbjct: 219 AVWPEHLPLIARLSVTDWIDGGVTVDESIELAAVLKKRGLDLLDVSHGFVTPDISHVPWG 278

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              +       + E  +   ++ + +   + +  QA  I+     D +M+ RA+  N  
Sbjct: 279 PGFLVP-----IAEKIRRAAEIPVAVGWMITEPQQAEAIIAHGQADFIMLARASLANPH 332


>gi|87118259|ref|ZP_01074158.1| oxidoreductase, FAD/FMN-binding [Marinomonas sp. MED121]
 gi|86165893|gb|EAQ67159.1| oxidoreductase, FAD/FMN-binding [Marinomonas sp. MED121]
          Length = 685

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 31/186 (16%), Positives = 69/186 (37%), Gaps = 18/186 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AA+  ++ G + + L+           S RV++    +G           + + A+ +
Sbjct: 153 AQAARRAKEGGLDGVELSAVHQHLIDQFWSPRVNQRDDKWGGSFENRMRFGMEVLKAVRE 212

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-- 167
            +     V  RI  D    D +    ++ + K    +G+   +           +  +  
Sbjct: 213 EVGPDFVVGLRICGDEFHPDGLNQDDMKQIAKYYNDTGLVDFFGVVGSGCDTHNTLANVI 272

Query: 168 -NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
            N   P   +  +    KE  D+ +     ++D +QA +IL +  VD V + RA   +  
Sbjct: 273 PNMSYPPEPFLHLAAGIKEIVDVPVIHAQNIKDPNQAERILDAGYVDFVGMTRAHIADPH 332

Query: 225 MLTTVD 230
           ++  + 
Sbjct: 333 LIAKIK 338


>gi|221632215|ref|YP_002521436.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Thermomicrobium roseum DSM 5159]
 gi|254801169|sp|B9KXJ4|HIS4_THERP RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|221156394|gb|ACM05521.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Thermomicrobium roseum DSM 5159]
          Length = 244

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 15/98 (15%), Positives = 36/98 (36%), Gaps = 10/98 (10%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + +    +G   + +        G           + ++++  + +  PD+ + + GG+
Sbjct: 34  EMAQRWASAGARWLHVVDLDGARLGQ---------PVQHELIERVIRAVPDVAVQVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L      V+IG AA +   ML      F 
Sbjct: 85  RTLDAVERLLVGGAARVVIGTAALERPDMLREALARFG 122


>gi|166240518|ref|XP_001732981.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
 gi|165988638|gb|EDR41088.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium discoideum AX4]
          Length = 409

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 24/158 (15%), Positives = 51/158 (32%), Gaps = 8/158 (5%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL----- 139
           S +  +   G        ++ + + ++         +  RI  D+ +      +L     
Sbjct: 234 SNKRTDSYGGGSFDGRIKLLIEIVKSVRSVWPTEKPLAVRISADEWVENENGWDLNDSIK 293

Query: 140 -VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             + ++   V+ I +       K              ++I   I K +  L +   G + 
Sbjct: 294 LAEILESLDVDLIDVSTGGNNSKQKITSKPLYQVPFSHEIKQLILKRSGKLLVSSVGLIT 353

Query: 199 DMSQALKILPSV--DGVMIGRAAYKNSAMLTTVDEYFS 234
             ++A  IL S   D +M GRA  +N  +         
Sbjct: 354 TANEAESILQSNSSDLIMFGRAFLRNPFLPIEFAHQLK 391


>gi|325962325|ref|YP_004240231.1| NADH:flavin oxidoreductase [Arthrobacter phenanthrenivorans Sphe3]
 gi|323468412|gb|ADX72097.1| NADH:flavin oxidoreductase [Arthrobacter phenanthrenivorans Sphe3]
          Length = 356

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 83/242 (34%), Gaps = 43/242 (17%)

Query: 42  GFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGS 92
             +T E P+ +Q       ++V A+    + G++ + L+            P++ V   S
Sbjct: 140 ALTTDELPMVIQ-------EIVNASLNAIEAGFDGVELHSANGYLLHEFLAPNSNVRTDS 192

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +G         V + + A+  AL     V  RI  +  +  +A  +         V    
Sbjct: 193 YGGSPENRARFVIETVNAVVAALGAN-RVGIRISPEHNVQGIAETDAADVRATYEV---- 247

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD------LFIGLNGGLEDMSQALKI 206
                 ++  ++P +   +  L +D   E+ ++         L     G +    +A  +
Sbjct: 248 ------LVDSIAPLNLAYLSILHHDPSGELVQDLRARFGGTFLVNTGFGVVTTRDEAASL 301

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +     D V++GR A  N  +     +    PL    P        F+   +   TDY A
Sbjct: 302 VADGLADAVVVGRPAIANPDLARRWKDSL--PLNEPDPS------TFYADGAKGYTDYPA 353

Query: 265 RH 266
             
Sbjct: 354 YQ 355


>gi|301060488|ref|ZP_07201333.1| putative NADH oxidase [delta proteobacterium NaphS2]
 gi|300445402|gb|EFK09322.1| putative NADH oxidase [delta proteobacterium NaphS2]
          Length = 622

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 24/157 (15%), Positives = 59/157 (37%), Gaps = 21/157 (13%)

Query: 53  QIGGADISKLVE----AAKIVEDFGYNEINLNVGC----------PSARVHEGSFGACLM 98
           Q+   +I++L +     A+   + G++ + +  GC          P   + +  +G  L 
Sbjct: 118 QLTANEIAQLAKGFGDTARRAREAGFDAVEV-CGCAGYLLSSFLSPWTNLRKDRYGGSLE 176

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIH 154
                  + I A+         +  R+  D+ +P       LRN+ K  +++G + + + 
Sbjct: 177 NRARFSLEVIEAIKAVAGKDFPLIFRMCADELMPEGNSPEDLRNVGKMFEEAGADALSLT 236

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                 +   P  + +I    +  + E  K+   + +
Sbjct: 237 VG--WHESRIPAISPEISRGHWLYLAEGMKKEVRIPV 271


>gi|193212140|ref|YP_001998093.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobaculum parvum
           NCIB 8327]
 gi|226700298|sp|B3QLK3|HIS4_CHLP8 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|193085617|gb|ACF10893.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Chlorobaculum parvum NCIB 8327]
          Length = 260

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 11/94 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++    +K     + +    A L G           ++++ + EI  E  D+ I + GG
Sbjct: 33  ADMAIIWRKQNAKMLHVVDLDAALTGEM---------VNFEKIREIV-ELLDIPIQVGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           +  +    K L   V  V+IG AA  N +++  +
Sbjct: 83  IRSVEAVEKYLSIGVSRVVIGSAAVTNPSLVADL 116


>gi|156066097|ref|XP_001598970.1| hypothetical protein SS1G_01060 [Sclerotinia sclerotiorum 1980]
 gi|154691918|gb|EDN91656.1| hypothetical protein SS1G_01060 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 443

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 30/189 (15%), Positives = 64/189 (33%), Gaps = 19/189 (10%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGAC 96
            P   +   + + K   AA+ +E  G++ I L              S   ++    +G  
Sbjct: 162 HPATQEEIDSIVDKFAHAAEYLEKAGFDGIQLHGAHGYLLAQFL--SKTTNKRTDKYGGS 219

Query: 97  LMLNPDIVGDCIAAMCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIW 152
           L     I+ +    + K +     V  ++      +D       +   ++++ +  + + 
Sbjct: 220 LENRFRIIQEVADEIHKRVKPDFIVGIKMNSVEFQEDGFTPEDAKAACQALEGARFDYVE 279

Query: 153 IHARKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
           +        G   K        ++  +   EI K        + GG + +   +  L +V
Sbjct: 280 LSGGTYQESGFVHKRESTKKRENFFLEFAEEIVKPLTKTKTYVTGGFKTVGAMVSALDTV 339

Query: 211 DGVMIGRAA 219
           DGV  GR A
Sbjct: 340 DGVGFGRPA 348


>gi|111020034|ref|YP_703006.1| NADH-dependent flavin oxidoreductase [Rhodococcus jostii RHA1]
 gi|110819564|gb|ABG94848.1| probable NADH-dependent flavin oxidoreductase [Rhodococcus jostii
           RHA1]
          Length = 389

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 27/210 (12%), Positives = 65/210 (30%), Gaps = 44/210 (20%)

Query: 65  AAKIVEDFGYNEINLNVG----CPS---ARVHEGS--FGACLMLNPDIVGDCIAAMCKAL 115
           AA+I  + G++ + ++ G      S    +++  +  +G  L     +V D    +  A+
Sbjct: 151 AARIAVESGFDAVEIHFGHNYFASSFLSPKLNRRADIYGGSLENRARVVRDVARTVRDAV 210

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIK-----------------------------KS 146
              V +  ++ +DD +P     +    +                               +
Sbjct: 211 GGRVAILAKLNMDDGVPGGFWLDEAIQVAGLLEQDGSVDALELTMGSSLLNPMYLFKGDA 270

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-----YEIKKENPDLFIGLNGGLEDMS 201
            V        + +  G+       I    Y  +         +    L + L GG+ D +
Sbjct: 271 PVREFAAAMPQPVRLGVQLAGKSMIHAYPYRDLFMLEHARQIRAAVTLPLVLLGGVTDRA 330

Query: 202 QA-LKILPSVDGVMIGRAAYKNSAMLTTVD 230
                +    + V + RA  +   ++  + 
Sbjct: 331 GMDTAMAEGFEFVAMARALLREPDLVNRIR 360


>gi|28869070|ref|NP_791689.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|28852310|gb|AAO55384.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|331017483|gb|EGH97539.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 360

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 36/226 (15%), Positives = 82/226 (36%), Gaps = 37/226 (16%)

Query: 28  VADAILRGDKKNIL--GFSTQEKPLALQI--GGADISKLVEAAKIVEDFGYNEINLNV-- 81
           VA + +R   K  +   F+   +P AL++      ++   +AA    + G++ + ++   
Sbjct: 120 VAPSAIRAQTKTFVNNAFTDVSEPRALELSELPGIVNDFRQAAANAIEAGFDGVEIHGAN 179

Query: 82  ---------GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--------PVTVKCR 124
                       SA V   ++G  +     ++ + + A+ K +          PV+    
Sbjct: 180 GYLLDQFIKD--SANVRTDAYGGSVENRARLLLEVVTAVVKEIGAHRTGVRISPVSPANG 237

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D  P      + + + + G+  + +           P+D   +   DYD    +++
Sbjct: 238 VASSDPQPQYEY--IAEQLSEQGIAFLHVVEGAT----GGPRD---VAPFDYD---ALRQ 285

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                ++  NG   D++ A       D V  GR    N  ++  + 
Sbjct: 286 RFKHTYLANNGYDLDLATARVNANKADLVAFGRPFISNPDLIERLK 331


>gi|304396884|ref|ZP_07378764.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. aB]
 gi|304355680|gb|EFM20047.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. aB]
          Length = 672

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/195 (9%), Positives = 51/195 (26%), Gaps = 33/195 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++ +  GY+ + +        +    +                 G        
Sbjct: 146 DDFARCARLAQQAGYDGVEI--------MGSEGYLINQFLVKHTNQRTDRWGGDFRQRMQ 197

Query: 103 IVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
                  A+  A      I   +     +++         L   +++ GV     +    
Sbjct: 198 FALAITRAVRAATGDAFIIIFRLSMLDLIEEGSSLEETLLLAGELEQCGVTLF--NTGIG 255

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
             +   P     +P   +  V +  + +  + +     +   + A  +L     D V + 
Sbjct: 256 WHEARIPTIATCVPRAAFAWVTQRLRAHISVPVIATNRINHPAVAEALLQSGCADMVSMA 315

Query: 217 RAAYKNSAMLTTVDE 231
           R    + A ++    
Sbjct: 316 RPFLADPAFVSKAQR 330


>gi|221069231|ref|ZP_03545336.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           KF-1]
 gi|220714254|gb|EED69622.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           KF-1]
          Length = 373

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 25/145 (17%), Positives = 50/145 (34%), Gaps = 5/145 (3%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVK 141
           P +   + ++G         + + +A + +     +P+T +  +   D      L   + 
Sbjct: 191 PHSNQRDDAYGGSFSNRARFLLETVARVREVWPEHLPLTARFGVIEYDGRDEKTLEESIA 250

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
             ++    G+ +            K     P     I   + +    L +    G++D  
Sbjct: 251 VTRQMRERGLDLLNVSVNFVIPDVKIPWGTPAFLAPIAQRVSRSAG-LPVASGWGMDDPQ 309

Query: 202 QALKILP--SVDGVMIGRAAYKNSA 224
            A +I+    VD VMIGRA   N  
Sbjct: 310 IAERIVAEHQVDLVMIGRAHLANPH 334


>gi|332991901|gb|AEF01956.1| 2,4-dienoyl-CoA reductase [Alteromonas sp. SN2]
          Length = 673

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 79/250 (31%), Gaps = 47/250 (18%)

Query: 8   HY--RFFARLLTNNALLYTEMIVADA------ILRGDKKNILGFSTQEKPLALQIGGADI 59
            +  R  A+       + TE + A+       IL   +      +    P+   I     
Sbjct: 72  PFAGRMTAKRHAKKHRVITEAVHAEGGKICMQILHSGRYGYHPLAVSASPVKSPITPFKP 131

Query: 60  SKL------------VEAAKIVEDFGYNEIN--------LNVGCPSARVHEGSF-----G 94
             L            V  A + ++ GY+ +         +N       V   +      G
Sbjct: 132 RALSSKAVTSTIKDYVSCAALAKEAGYDGVEVMGSEGYLIN----QFLVKRTNHRDDEWG 187

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNG 150
            CL     I  D +  + + +     +  R+ + D +   A  +    L K+I+K+G   
Sbjct: 188 GCLENRVKIAVDIVKGIREKVGTDFIIIYRLSMLDLVEGGAKWDEVVYLAKAIEKAGATL 247

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP- 208
           I  +      +   P  +  +P   +  +   +KKE     +  N  +     A  +L  
Sbjct: 248 I--NTGIGWHEARVPTISTSVPRAAFTWITQRMKKEVSLPLVTTNR-INTPEVAEGVLAD 304

Query: 209 -SVDGVMIGR 217
              D V + R
Sbjct: 305 GHADMVSMAR 314


>gi|284040478|ref|YP_003390408.1| geranylgeranylglyceryl phosphate synthase [Spirosoma linguale DSM
           74]
 gi|283819771|gb|ADB41609.1| geranylgeranylglyceryl phosphate synthase [Spirosoma linguale DSM
           74]
          Length = 249

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 12/85 (14%), Positives = 33/85 (38%), Gaps = 3/85 (3%)

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +    +        L  L      + P +   ++  ++K   ++ I + GG+    +A +
Sbjct: 153 AACTALAGEMLGLQLMYLDAGSGARRP-VSAAMIAAVRKAV-NVPIIVGGGITSGEKAYE 210

Query: 206 ILP-SVDGVMIGRAAYKNSAMLTTV 229
            L    D +++G    ++  +L  +
Sbjct: 211 ALKAGADMIVVGNGVEQDPDLLPQL 235


>gi|302382151|ref|YP_003817974.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Brevundimonas subvibrioides ATCC 15264]
 gi|302192779|gb|ADL00351.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Brevundimonas subvibrioides ATCC 15264]
          Length = 255

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 42/118 (35%), Gaps = 11/118 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L    +  G + +  +   A  +G +         LDY  V +I +   D+   + GG+
Sbjct: 34  ELAARYRDEGADELVFYDITASPEGRT---------LDYGWVRDIAR-LLDIPFCVAGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
             + QA   L    D V I   A +   ++T + E   +          R D ++   
Sbjct: 84  RTVDQAAACLDNGADKVSINSPALERPELITEMAERLGSQCVVVGVDSRREDGEYVVH 141


>gi|268316195|ref|YP_003289914.1| dihydroorotate dehydrogenase [Rhodothermus marinus DSM 4252]
 gi|262333729|gb|ACY47526.1| dihydroorotate dehydrogenase [Rhodothermus marinus DSM 4252]
          Length = 364

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 70/211 (33%), Gaps = 44/211 (20%)

Query: 56  GADISKLVEAAKIVEDFG---------YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
             D + L EAA  V DF           + + LN+ CP     EG        +PD +  
Sbjct: 145 THDPNILGEAA--VADFCESFRLLAPLADYVTLNISCP--NTAEGKTF----EDPDALDA 196

Query: 107 CIAAMCKA-----LSIPVTVKCRIGVDDQIPAV-ALRNLVKSIKKSGVNGIWIHARKAIL 160
            + A+        LS+PV +K       +      L  +V+  +  G+ G  +    A  
Sbjct: 197 LLRAIFAVRRELDLSVPVLLKLSPPPSSRTVFDSQLEEIVEVARAHGIAGF-VATNTASD 255

Query: 161 K----------------GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA- 203
           +                GLS +            +Y + +    L +   GG++   +A 
Sbjct: 256 REGLRTDPEALARIGPGGLSGRPLAARARCLLFYLYRLTE--GKLPLISVGGIDSAEEAY 313

Query: 204 LKILPSVDGVMIGRA-AYKNSAMLTTVDEYF 233
            +I      V +     Y+   ++  + +  
Sbjct: 314 RRIRAGASLVQLYTGLIYEGPGLVRRIKQGL 344


>gi|228900647|ref|ZP_04064867.1| NADPH dehydrogenase [Bacillus thuringiensis IBL 4222]
 gi|228858992|gb|EEN03432.1| NADPH dehydrogenase [Bacillus thuringiensis IBL 4222]
          Length = 319

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ K    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNKVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE   +  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEYTKIATGAVGLITTGSQAEQILNDN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|157150846|ref|YP_001450685.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157075640|gb|ABV10323.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Streptococcus gordonii str. Challis substr.
           CH1]
          Length = 240

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K+ GV  I +      L+G +          + D++ +IK E   L I + G
Sbjct: 32  VLEQARLFKEVGVTMIHVVDLDGALEGRA---------ANRDLIAQIKAETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN   +    E F 
Sbjct: 82  GIRSLEQIKDYLAVGIDRVIIGSMAVKNPEFVRAALERFG 121


>gi|75764190|ref|ZP_00743758.1| NADH-dependent flavin oxidoreductase [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|74488321|gb|EAO51969.1| NADH-dependent flavin oxidoreductase [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
          Length = 346

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ K    P+ V+        D +         K +K+ G++ 
Sbjct: 187 YGGSPENRYRFLREIIDSVNKVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 246

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE   +  G  G +   SQA +IL   
Sbjct: 247 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEYTKIATGAVGLITTGSQAEQILNDN 300

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 301 EADLIFIGRELLRNPY 316


>gi|121535212|ref|ZP_01667027.1| tryptophan synthase, alpha subunit [Thermosinus carboxydivorans
           Nor1]
 gi|121306203|gb|EAX47130.1| tryptophan synthase, alpha subunit [Thermosinus carboxydivorans
           Nor1]
          Length = 271

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 33/224 (14%), Positives = 70/224 (31%), Gaps = 58/224 (25%)

Query: 50  LALQIGGA-DISKLVEAAKIVEDFGYNEINLN-------VGCPSARVHEGSFGACLM--L 99
           +     G  D +  +EA + VE  G N I +           P   V + +    L    
Sbjct: 20  IVYLTAGCPDFAATLEAVQAVEAAGANIIEIGIPFSDPMADGP---VIQKAASLALQGGA 76

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
               V + +  + +  +IP+ V   +   + +    +   V+S  ++G++G+ +      
Sbjct: 77  TTGKVLELVRQIRQKSAIPLVV---MTYINTVLQFGVEKFVRSFAQAGLDGLIVPDLPVE 133

Query: 154 ---------------------------------HARKAILKGLSPKDNRKIPNLDYDIVY 180
                                            H     L  +S      +  +DY  + 
Sbjct: 134 ESALLENYCREAGLALIQFIAPTTAPERAVTICHKAAGFLYCISATGVTGVRQVDYSQIG 193

Query: 181 EI---KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
            +    ++   L + +  G+     A +     D V+IG A  +
Sbjct: 194 SLINNVRQYTSLPVAIGFGIGSPQAAREAADYADAVIIGSAIMQ 237


>gi|56460940|ref|YP_156221.1| imidazole glycerol phosphate synthase subunit HisF [Idiomarina
           loihiensis L2TR]
 gi|81821687|sp|Q5QWQ5|HIS6_IDILO RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|56179950|gb|AAV82672.1| Imidazoleglycerol-phosphate synthase [Idiomarina loihiensis L2TR]
          Length = 265

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   +SG + +  +   A   G +         +D   V  + +E    F    GG+ 
Sbjct: 35  LAKRYAESGADELVFYDITASADGRT---------VDKSWVERVAREINIPFTVA-GGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  A  +L    D + I   A  N  ++ T+ E F  
Sbjct: 85  SVEHAQTMLSMGADKISINSPALLNPNLINTLVEEFGQ 122


>gi|91791081|ref|YP_552031.1| 2,4-dienoyl-CoA reductase [Polaromonas sp. JS666]
 gi|91700962|gb|ABE47133.1| 2,4-dienoyl-CoA reductase [Polaromonas sp. JS666]
          Length = 682

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 23/183 (12%), Positives = 61/183 (33%), Gaps = 26/183 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINL--------NVGCPSARVHEGS-----FGACLMLNPDIVGD 106
              V  A++ +  G++ + +        N       V   +     FG  +     +  +
Sbjct: 148 EDYVRCAELAQRAGFDGVEIMGSEGYLLN----QFTVTRTNNRSDEFGGSMENRHRLPVE 203

Query: 107 CIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +    + L     +  R+     V+   PA  +  L ++++ +G +   ++      + 
Sbjct: 204 IVQRTRERLGPEFLLMFRVSALDLVEGGAPAAEIIQLAQAVQAAGAD--ILNTGIGWHEA 261

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
             P     +P   +       K+   + + ++  +     A +IL S D  M+   +   
Sbjct: 262 RIPTIAYVVPRAAWRFAAARIKKAVTIPVIVSNRINTPDLAEEILASGDADMV---SMAR 318

Query: 223 SAM 225
             +
Sbjct: 319 PFL 321


>gi|331006157|ref|ZP_08329483.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium IMCC1989]
 gi|330420038|gb|EGG94378.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium IMCC1989]
          Length = 242

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 49/136 (36%), Gaps = 11/136 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N  K     G   + +        G           ++ ++V EI +  P L I + GG+
Sbjct: 34  NFAKQWVDQGCRRLHLVDLNGAFAG---------EPINGEVVTEIAQAFPKLPIQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKI 255
                  K L   V+ V+IG  A K    +T +  ++  + + G       V  D W ++
Sbjct: 85  RSGEIIEKYLQAGVNYVIIGTKAVKEPEFVTEMCKQFPGHIIVGLDAKNGLVATDGWAEV 144

Query: 256 SASMTDYAARHLHSGG 271
           S       A+   + G
Sbjct: 145 SEIKATDLAKRFEADG 160


>gi|325283767|ref|YP_004256308.1| NADPH dehydrogenase [Deinococcus proteolyticus MRP]
 gi|324315576|gb|ADY26691.1| NADPH dehydrogenase [Deinococcus proteolyticus MRP]
          Length = 408

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 72/229 (31%), Gaps = 20/229 (8%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A++ +  G+  + L+            P   V    +G  L      V +   A+ 
Sbjct: 157 FARSARLAQRAGFGGVQLHAAHGYLMSQFLSPRHNVRRDEYGGSLENRMRFVLETFRAVR 216

Query: 113 KALS--IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+    PV+VK      V           +V ++ + G + I I         +     
Sbjct: 217 AAVGPHFPVSVKLNSSDFVRGGFSEEDSLAVVAALGEQGCDLIEISGGTYEKPMMLGSRE 276

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAML 226
           R     D+          P       GG  D +   + L   + D V + R    +    
Sbjct: 277 RGGFFADFAGRARAAAGVPLCVT---GGFRDAATIRQALASGAADVVGLARPLVTDP-QF 332

Query: 227 TTVDEYFSNPLTGSSPIKTRV-DKDFWRKISASMTDYAARHLHSGGKLQ 274
           +       +  +   P++T V   D    +  +  + A R L  G +++
Sbjct: 333 SARVLRGEDVSSEVRPLRTGVALLDGTGYLEIAWYEDAMRRLARGEQVR 381


>gi|322412140|gb|EFY03048.1| dihydroorotate dehydrogenase 1A [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 311

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 75/232 (32%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 68  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 125

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     + ++    + P+ +K     D      A A
Sbjct: 126 ELNLSCP--NVPGKPQIAY---DFETTDQLLESIFTYYTKPLGIKLPPYFDIVHFDQAAA 180

Query: 136 LRN-----LVKSIKKSG-----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G      +   +   K    G+     +     +    Y  K+ 
Sbjct: 181 IFNKYSLSFVNCVNSIGNGLVLEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 238

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 239 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 290


>gi|299529463|ref|ZP_07042900.1| NADH-flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           S44]
 gi|298722326|gb|EFI63246.1| NADH-flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           S44]
          Length = 372

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 24/137 (17%), Positives = 47/137 (34%), Gaps = 5/137 (3%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           ++G         + + +A + +     +P+T +  +   D      L   +   ++    
Sbjct: 199 AYGGSFSNRARFLLETVAKVREVWPEHLPLTARFGVIEYDGRDEETLEESIAVTRQMRER 258

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
           G+ +            K     P     I   + +    L +    G++D   A +I+  
Sbjct: 259 GLDLLNVSVNFVIPDVKIPWGTPAFLAPIAQRVSRSAG-LPVASGWGMDDPQIAERIVAD 317

Query: 209 -SVDGVMIGRAAYKNSA 224
             VD VMIGRA   N  
Sbjct: 318 GQVDLVMIGRAHLANPH 334


>gi|299771035|ref|YP_003733061.1| 2,4-dienoyl-CoA reductase [NADPH](2,4-dienoyl coenzymeA reductase)
           [Acinetobacter sp. DR1]
 gi|298701123|gb|ADI91688.1| 2,4-dienoyl-CoA reductase [NADPH](2,4-dienoyl coenzymeA reductase)
           [Acinetobacter sp. DR1]
          Length = 676

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 32/227 (14%), Positives = 70/227 (30%), Gaps = 24/227 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+   ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSTAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINL--------NVGCPSARVHEGSFGACLMLNPDIV-GDCIAAMCKALSIPVTVK 122
            GY+ + +        N    S            + N      + + A+   +     + 
Sbjct: 155 AGYDGVEIMGSEGYLINQFLSSHVNQRTDRWGGGIENRMRFPVEIVKAIRAKVGEKFIIC 214

Query: 123 CRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-D 177
            R+     V D      +  + K+++K+GV  +  +      +   P     +P   + D
Sbjct: 215 FRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARVPTIVTSVPRAAFVD 272

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
               +K+    + I  +  +     A +IL     D V + R    +
Sbjct: 273 YTAHVKQHI-SIPIIASNRINMPETAEEILATGKADMVQMARPLLAD 318


>gi|314962834|gb|EFT06934.1| dihydroorotate dehydrogenase 1B [Propionibacterium acnes HL082PA1]
          Length = 307

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 66/197 (33%), Gaps = 25/197 (12%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLML 99
           L     + P+   + G      V   +++        + +N+ CP   V  G        
Sbjct: 89  LAEHFPDLPIIANVAGYTTEDYVRVCEVISTAPNVAAVEINISCP--NVKRGGITFG--T 144

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------ 153
           N     D   A+  A S+PV VK    V D      +  + ++   +G +G+ +      
Sbjct: 145 NVTAAHDLTQAVVAAASVPVYVKLSPNVTD------ITEIARAPADAGADGLTLINTLTG 198

Query: 154 ------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-I 206
                      I           +  +   ++  + +   D+ +   GG+   + AL+ +
Sbjct: 199 MRINLARRTPVIANATGGLSGPAVLPIAVRMIDAVTR-VVDIPVIGMGGVMTSADALELM 257

Query: 207 LPSVDGVMIGRAAYKNS 223
           +     V +G A + + 
Sbjct: 258 MAGASAVGVGTANFTDP 274


>gi|270158982|ref|ZP_06187638.1| 2,4-dienoyl-CoA reductase [Legionella longbeachae D-4968]
 gi|289166175|ref|YP_003456313.1| 2,4-dienoyl-CoA reductase [Legionella longbeachae NSW150]
 gi|269987321|gb|EEZ93576.1| 2,4-dienoyl-CoA reductase [Legionella longbeachae D-4968]
 gi|288859348|emb|CBJ13284.1| putative 2,4-dienoyl-CoA reductase [Legionella longbeachae NSW150]
          Length = 674

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 20/193 (10%), Positives = 58/193 (30%), Gaps = 40/193 (20%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG---------------- 105
               A++ +  GY+ I +                 L+    +                  
Sbjct: 151 FARCARLAQLAGYDGIEI-----------MGSEGYLINQFIVTHTNQRQDEWGGHYSNRI 199

Query: 106 ----DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
               + + ++ +A+     +  R+     + D      +  L K+++++G   I  +   
Sbjct: 200 RFPIEIVRSVREAVGEKFIIVFRLSMLDLITDGSNWEEIVILAKALEEAGATLI--NTGI 257

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
              +   P     +P   +  + +  K    + +  +  +     A +++ S   D V +
Sbjct: 258 GWHEARVPTIATMVPEAAFTHLTQHLKPEVKIPVITSNRINTPELANQLIESGVADMVSM 317

Query: 216 GRAAYKNSAMLTT 228
            R    +  +   
Sbjct: 318 ARPFLADP-LFAE 329


>gi|184158249|ref|YP_001846588.1| NADH:flavin oxidoreductase [Acinetobacter baumannii ACICU]
 gi|183209843|gb|ACC57241.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family [Acinetobacter
           baumannii ACICU]
 gi|322508572|gb|ADX04026.1| Oxidoreductase FMN-binding protein [Acinetobacter baumannii 1656-2]
 gi|323518186|gb|ADX92567.1| NADH:flavin oxidoreductase [Acinetobacter baumannii TCDC-AB0715]
          Length = 414

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 86/230 (37%), Gaps = 23/230 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDQWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D       A   + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPQFTVAVKLNSADFQRGGFSAEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A K++   VD V I  A    
Sbjct: 270 RDGRTLAREAYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEKVIESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
             +     +     LT      T  +K      + +M  +  R+L +G K
Sbjct: 329 PNLPNAWKQ--GQNLTPELKPITWKNKTLASLANMAMVKFQLRNLSAGKK 376


>gi|160892618|ref|ZP_02073408.1| hypothetical protein CLOL250_00148 [Clostridium sp. L2-50]
 gi|156865659|gb|EDO59090.1| hypothetical protein CLOL250_00148 [Clostridium sp. L2-50]
          Length = 420

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 20/104 (19%), Positives = 37/104 (35%), Gaps = 11/104 (10%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                + K    +G + I     KA  +G            +  ++ EI K N D+ +  
Sbjct: 13  ENALEMAKFYNDAGADEIAYFDSKATKEGR---------EANIAVIKEICK-NVDIPLIA 62

Query: 194 NGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            GG+  +    K+L      V +  AA     ++T   + F + 
Sbjct: 63  CGGVRRLEDIKKMLYAGASKVCMKSAALNTPELVTEAADRFGSE 106


>gi|120598534|ref|YP_963108.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. W3-18-1]
 gi|120558627|gb|ABM24554.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sp. W3-18-1]
          Length = 368

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 66/192 (34%), Gaps = 25/192 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AAK     G+  + L+       + +             +G         + + I 
Sbjct: 159 DFVTAAKRALAAGFEWLELHFA--HGYLAQSFFSTYANQRSDQYGGSAEGRGRFLLETIK 216

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVAL---RNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +     +P+T +  +   D      L     LVK  K+ G++ + +    +I     
Sbjct: 217 AVREIWPQHLPLTARFGVIEFDDKDEQTLSESIELVKQFKQIGLDMLNV----SICFSTP 272

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
             +    P L   I   ++KE     +  + G++D  QA   +    +D VMIG+A   N
Sbjct: 273 TANIPWRPALLAPIAARVRKEVG-FPVATSWGMDDPHQANAAIENEQMDLVMIGKAFLAN 331

Query: 223 SAMLTTVDEYFS 234
                   +   
Sbjct: 332 PHWPYQAAQILK 343


>gi|296282207|ref|ZP_06860205.1| NADH:flavin oxidoreductase/NADH oxidase [Citromicrobium
           bathyomarinum JL354]
          Length = 380

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 25/177 (14%), Positives = 51/177 (28%), Gaps = 23/177 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSI-PVTVKCRIG-----VDDQIPAVALRNLVKSIKKS 146
           +G  L     ++ + +AA+ + L    V V+           D  P          +   
Sbjct: 206 YGGSLDNRLRLLDEVVAAVTEVLPAGRVGVRLSPMGGPGGSSDAKPEETYPEAAAKLAGR 265

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G+  + +             +   I       V +++K    +F+  NG       A  +
Sbjct: 266 GLAYLHVVRPNGHTGSGGSDEGNAI-------VKDMRKRFDGVFV-ANGEFSTEEAAQWV 317

Query: 207 LPS-VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                D +  GR    N  +   +            P +   +  F+   +    DY
Sbjct: 318 ADGHADAIAFGRLFIANPDLPARI--------AAGGPYEEANEDTFYGGGAEGYVDY 366


>gi|294626895|ref|ZP_06705486.1| oxidoreductase, FAD/FMN-binding [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292598755|gb|EFF42901.1| oxidoreductase, FAD/FMN-binding [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 373

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 28/169 (16%), Positives = 57/169 (33%), Gaps = 24/169 (14%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSI 143
           ++G  L     +  + + A+ +A+    PV ++                   L  L+K +
Sbjct: 197 AYGGTLEKRLRLTLEVVQAVRQAVSADFPVLLRFSQFKRSDYAARIAETPDELGRLLKPL 256

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL------ 197
            ++GV+      R+    G    D   +    +      K       IGL+G +      
Sbjct: 257 AEAGVDAFHASTRR---FGEPAFDGSPLSLAGWARQLTGKPAIAVGSIGLHGDVGEAAGA 313

Query: 198 -----EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
                 D+   ++ L     D + +GRA   +    + V +   + L G
Sbjct: 314 ESSTPADLQGVVEQLAHSEFDLIAVGRALLADPGWASKVRQGRFDELRG 362


>gi|194365539|ref|YP_002028149.1| imidazole glycerol phosphate synthase subunit HisF
           [Stenotrophomonas maltophilia R551-3]
 gi|226702004|sp|B4STP2|HIS6_STRM5 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|194348343|gb|ACF51466.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Stenotrophomonas maltophilia R551-3]
          Length = 258

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 39/111 (35%), Gaps = 11/111 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D +    +  L +  +  G + +            +  + R +     + +  +  
Sbjct: 21  VRFRDHVDMGDIAELAQRYRDQGADELV------FYDIGASPEARSVDVAWIERIARLI- 73

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
              D+   + GG++ +  A ++L    D V I   A     ++T + + F 
Sbjct: 74  ---DIPFCVAGGIDSVETARRVLFAGADKVSINSPALGRPELITELADEFG 121


>gi|328955408|ref|YP_004372741.1| NADH:flavin oxidoreductase/NADH oxidase [Coriobacterium glomerans
           PW2]
 gi|328455732|gb|AEB06926.1| NADH:flavin oxidoreductase/NADH oxidase [Coriobacterium glomerans
           PW2]
          Length = 664

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 22/210 (10%), Positives = 56/210 (26%), Gaps = 49/210 (23%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDI 103
               + A+  +  G++ + ++       VHEG                 +G  L      
Sbjct: 154 ESFGQGARNAQKAGFDGVEIHA------VHEGYLLDQFAISMFNRRSDEYGGSLENRLRF 207

Query: 104 VGDCIAAMCKAL--SIPVTVKC----------------RIGVDDQIPAVALRNLVKSIKK 145
             + +  +        PV+++                     +            + ++ 
Sbjct: 208 AREILEEIKSRCGADFPVSLRFSLKSMIKDWRDGALPEETFEERGRDTEEGIQAARLLES 267

Query: 146 SGVNGIWIHARK---AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
            G + +                    + +    Y    ++ K+   + +   G ++D   
Sbjct: 268 FGYDALSCDVGTYDSWWWNHPPMYQKKGL----YRAFCKVVKQAVSVPVICAGRMDDPDV 323

Query: 203 ALKILPSVDGVMI--GRAAYKNSAMLTTVD 230
           A   L   D  MI  GR    +  ++  + 
Sbjct: 324 AAAALSEGDCDMIGLGRPLLADPEIVNKIR 353


>gi|291613132|ref|YP_003523289.1| NADH:flavin oxidoreductase/NADH oxidase [Sideroxydans
           lithotrophicus ES-1]
 gi|291583244|gb|ADE10902.1| NADH:flavin oxidoreductase/NADH oxidase [Sideroxydans
           lithotrophicus ES-1]
          Length = 360

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 25/195 (12%), Positives = 63/195 (32%), Gaps = 20/195 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V  A+   + G+  + ++            P +   + ++G        +V + ++A+ 
Sbjct: 158 FVSGARRAREAGFQAVEIHAAHGYLLHQFLSPLSNQRKDAYGGSFENRTRLVREVVSAVR 217

Query: 113 KALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                 +P+ ++       D          L + +K  GV+ + + +       L     
Sbjct: 218 AEWPQRLPLLIRLSATDWTDGGWNVDETVELCRLLKGLGVDLVDVSSAGL----LPTASI 273

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              P    +    ++ E   +     G +   +QA  I+     D V++GR   +N    
Sbjct: 274 PAGPGFQTEFAARVRHEAG-IATAAVGLITSPAQADHIIRSGQADIVLLGREMLRNPYWP 332

Query: 227 TTVDEYFSNPLTGSS 241
               +   + +    
Sbjct: 333 LAAAQTLGHQVPWPQ 347


>gi|40062896|gb|AAR37767.1| oxidoreductase, FAD/FMN-binding [uncultured marine bacterium 442]
          Length = 409

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 31/222 (13%), Positives = 72/222 (32%), Gaps = 46/222 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA+     G++ + +++G          P     + ++G             +AA
Sbjct: 148 DDFVTAAEHCVSAGFDAVEIHMGHGYLLNQFLSPMDNKRKDAYGGSAENRARFPTRVLAA 207

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHAR---------- 156
           + + +   + V  +I V D     A         K ++ +G + + +             
Sbjct: 208 VKQRVGQDIAVLAKINVSDGRRRGANVEDAIVTAKLLEAAGADMLVLSGGRNVESGWFMF 267

Query: 157 --------------KAILKGLS-PKDNRKIPNLD------YDIVYEIKKENPDLFIGLNG 195
                         K  L G++     +  P++D      ++   +I +E   L +   G
Sbjct: 268 GSNMNLEAMYRVLGKWSLSGMAIGATAKSAPSIDFRELYFWEYSKKI-REAVSLPLTYLG 326

Query: 196 GLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           G++     A  +    + V + RA  +   ++     +   P
Sbjct: 327 GVKSADNVAQCMAAGFEAVALARALLREPDLVNKWQVHPEEP 368


>gi|304317856|ref|YP_003853001.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302779358|gb|ADL69917.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 665

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 29/163 (17%), Positives = 55/163 (33%), Gaps = 48/163 (29%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD------CIA 109
           G DI + ++AAK++ ++GY+ ++++VG         S+ A    +P +  +         
Sbjct: 254 GRDIEEGIKAAKLLVEYGYDALDVDVG---------SYDAWWWNHPPMYQEKGLYIPYAK 304

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +  A+ +PV    R+   D         L  +  + G   I    R  +          
Sbjct: 305 MVKDAVDVPVICAGRMDNPD---------LASAAVRDGACDIVSLGRPLL---------- 345

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
                D D V ++K           G    +   L       G
Sbjct: 346 ----ADPDYVNKLKA----------GDTASIRPCLSCHEGCMG 374


>gi|57233941|ref|YP_182042.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Dehalococcoides
           ethenogenes 195]
 gi|91206926|sp|Q3Z6V7|HIS4_DEHE1 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|57224389|gb|AAW39446.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Dehalococcoides ethenogenes 195]
          Length = 237

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           ++++++ EI      + + + GG+  M    K+L   VD V++G  A +N  ++  +   
Sbjct: 61  VNFELIREIANSAL-IPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICAR 119

Query: 233 FSN 235
           +++
Sbjct: 120 YAD 122


>gi|262276162|ref|ZP_06053971.1| imidazole glycerol phosphate synthase cyclase subunit [Grimontia
           hollisae CIP 101886]
 gi|262219970|gb|EEY71286.1| imidazole glycerol phosphate synthase cyclase subunit [Grimontia
           hollisae CIP 101886]
          Length = 257

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L       G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAARYATEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  N  ++T + E F 
Sbjct: 85  TAEDAKRILEFGADKISINSPALANPELITELAEKFG 121


>gi|239932734|ref|ZP_04689687.1| oxidoreductase [Streptomyces ghanaensis ATCC 14672]
 gi|291441090|ref|ZP_06580480.1| oxidoreductase [Streptomyces ghanaensis ATCC 14672]
 gi|291343985|gb|EFE70941.1| oxidoreductase [Streptomyces ghanaensis ATCC 14672]
          Length = 359

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 24/177 (13%), Positives = 52/177 (29%), Gaps = 13/177 (7%)

Query: 67  KIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC 123
           +I E  G +   +N    P +     ++G           + + A+ +      P+  + 
Sbjct: 176 EIAEIHGAHGYLINEFLSPHSNHRTDAYGGSYENRTRFALEVVDAVREEWPDGKPLFFRI 235

Query: 124 RIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
                                 +   G++ + +          S       P        
Sbjct: 236 SATDWLEGAGWTPDDTVRFATELHAHGIDLLDVSTG----GNASGARIPTGPGYQVPFAA 291

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++ E P + +   G + D +QA KIL     D V++GR   ++ +           
Sbjct: 292 RVRNETP-MPVAAVGLITDAAQAEKILANGEADAVLLGRELLRDPSWARRAARELDG 347


>gi|169825062|ref|YP_001692673.1| NADH-dependent flavin oxidoreductase [Finegoldia magna ATCC 29328]
 gi|167831867|dbj|BAG08783.1| NADH-dependent flavin oxidoreductase [Finegoldia magna ATCC 29328]
          Length = 330

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 68/187 (36%), Gaps = 22/187 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K V+AA   +  G++ + +             P        +G  +     I  + I  
Sbjct: 147 EKFVDAAVRAKKAGFDGVEIHSAHGYLLNQFLSPITNKRTDEYGGDIDGRIKIHLEIIRK 206

Query: 111 MCKAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +  + P+ ++      ++  +      +  +   K+GV+ + I     +      +
Sbjct: 207 IREKVGENYPIFIRMGAGDYLEGGLSTEDSIHAAQEFVKAGVDVLDISGGMCMFSIDDQR 266

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS- 223
                    +D + +   EN D+ + L GG++       IL     D V IGR+ +K+S 
Sbjct: 267 AGF------FDFLSKPIYENVDVPVILTGGVKTGEDVEDILNRGVCDLVGIGRSVFKDSN 320

Query: 224 AMLTTVD 230
            +   + 
Sbjct: 321 WIENEIK 327


>gi|161506216|ref|YP_001573328.1| hypothetical protein SARI_04408 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160867563|gb|ABX24186.1| hypothetical protein SARI_04408 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 676

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 27/207 (13%), Positives = 61/207 (29%), Gaps = 40/207 (19%)

Query: 42  GFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CL 97
            F+  E      LQ+    I      A++  + GY+ + +        +    +     L
Sbjct: 130 RFTPHELRHNEILQL----IDDFAHCAQLAREAGYDGVEV--------MGSEGYLINEFL 177

Query: 98  MLNPDI---------------VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRN 138
               +                  + + A+ + +     +  R+     V+D         
Sbjct: 178 TRRTNHRNDEWGGDYDNRMRFAVEVVRAVRQRVGNDFIIIYRLSMLDLVEDGGTFDETVQ 237

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L ++++ +GV  I  +      +   P     +P   +  V    K    + +     + 
Sbjct: 238 LAQAVEAAGVTLI--NTGIGWHEARIPTIATPVPRGAFSWVTRRLKGLVSVPLIATNRIN 295

Query: 199 DMSQALKILPSVDGVMIGRAAYKNSAM 225
           D   A  IL   D  M+   +     +
Sbjct: 296 DPQVAEAILARGDADMV---SMARPFL 319


>gi|149194604|ref|ZP_01871700.1| dihydroorotate dehydrogenase [Caminibacter mediatlanticus TB-2]
 gi|149135348|gb|EDM23828.1| dihydroorotate dehydrogenase [Caminibacter mediatlanticus TB-2]
          Length = 361

 Score = 41.3 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 17/117 (14%), Positives = 43/117 (36%), Gaps = 11/117 (9%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +LN + + +    +      P+ +K    ++D      +RNL      +G +GI +    
Sbjct: 191 LLNEEFIKNLFKELKNLTKKPILIKFSPDMEDD----FIRNLANISVFAGADGIIVTNTT 246

Query: 158 AILK------GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKIL 207
                            + + +  ++++  +  E    + I   GG++   +A K +
Sbjct: 247 INYDLVNSNIKKGGISGKPLASRSFEVLKIVANEVFGKIPIISVGGIDSAEEAYKRI 303


>gi|317405934|gb|EFV86212.1| NADH:flavin oxidoreductase [Achromobacter xylosoxidans C54]
          Length = 377

 Score = 41.3 bits (96), Expect = 0.22,   Method: Composition-based stats.
 Identities = 27/196 (13%), Positives = 55/196 (28%), Gaps = 18/196 (9%)

Query: 46  QEKPLALQIGGADISK----LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGS 92
           +  P+  ++   DI +      +AA+       + I +             PS+ +    
Sbjct: 147 EGWPVPREMTIRDIEEVIEAFGQAARRAHAANIDVIEIHGAHGYLIHQFLSPSSNLRTDK 206

Query: 93  FGACLMLNPDIVGDCIAAMCK--ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +G  L             + +       +  +     D          L + +   GV+ 
Sbjct: 207 YGGSLPNRMRFALQITEHIREIWPAEKALFFRISAQDDTGWGLEESFTLSRELAARGVDV 266

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +    ++  +                 I++E   +     G +    QA  I+   
Sbjct: 267 IDCSSSGTNVRSAATNAASLQLGFQVPFAEAIRRETG-IPTIAVGLIVQPQQADSIIKNG 325

Query: 209 SVDGVMIGRAAYKNSA 224
             D V IGR    N  
Sbjct: 326 QADLVAIGRELLYNPF 341


>gi|217072368|gb|ACJ84544.1| unknown [Medicago truncatula]
          Length = 424

 Score = 41.3 bits (96), Expect = 0.22,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 7/85 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + I +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 173 RVEQTGIDAIEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATVPVWAKMTPNI 231

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIW 152
            D           +    SG  GI 
Sbjct: 232 TDISQP------ARVALSSGCEGIA 250


>gi|168182431|ref|ZP_02617095.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum Bf]
 gi|237794840|ref|YP_002862392.1| FAD/FMN-binding family oxidoreductase [Clostridium botulinum Ba4
           str. 657]
 gi|182674276|gb|EDT86237.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum Bf]
 gi|229263104|gb|ACQ54137.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum Ba4 str.
           657]
          Length = 339

 Score = 41.3 bits (96), Expect = 0.22,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 56/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK  ++ G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAEAAKRAKESGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V + + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCRELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +   +I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASKIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|296130707|ref|YP_003637957.1| NADH:flavin oxidoreductase/NADH oxidase [Cellulomonas flavigena DSM
           20109]
 gi|296022522|gb|ADG75758.1| NADH:flavin oxidoreductase/NADH oxidase [Cellulomonas flavigena DSM
           20109]
          Length = 363

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 25/184 (13%), Positives = 55/184 (29%), Gaps = 21/184 (11%)

Query: 74  YNEINLNVG--------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK 122
           Y+ + ++          C P + V +  +G        +V +  +A+  A+   +PV V+
Sbjct: 176 YDVVEVHAAHGYLLHQFCSPDSNVRDDVYGGSFEARTRLVREVTSAVRAAVPDDMPVLVR 235

Query: 123 CRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
                             +L + +   GV+ + +         L        P       
Sbjct: 236 VSATDWVEPAGWTGDDTVHLARDLAPLGVDLVHVSTG----GNLPGVHVPVEPGYQVPFA 291

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
             ++ E   +     G + D +QA +++     D V + R    +              L
Sbjct: 292 ARVRAEAG-VPTVAVGAITDPAQAEEVVAGGSADAVALARPLLVDPFWPHRAALALGADL 350

Query: 238 TGSS 241
               
Sbjct: 351 PLPP 354


>gi|169796657|ref|YP_001714450.1| 2,4-dienoyl-CoA reductase [NADPH] (2,4-dienoyl coenzyme A
           reductase) [Acinetobacter baumannii AYE]
 gi|213156115|ref|YP_002318535.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii AB0057]
 gi|215484149|ref|YP_002326374.1| 2,4-dienoyl-CoA reductase [NADPH](2,4-dienoyl coenzymeA reductase)
           [Acinetobacter baumannii AB307-0294]
 gi|332854538|ref|ZP_08435416.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii 6013150]
 gi|332870167|ref|ZP_08439079.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii 6013113]
 gi|169149584|emb|CAM87473.1| 2,4-dienoyl-CoA reductase [NADPH] (2,4-dienoyl coenzyme A
           reductase) [Acinetobacter baumannii AYE]
 gi|213055275|gb|ACJ40177.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii AB0057]
 gi|213986835|gb|ACJ57134.1| 2,4-dienoyl-CoA reductase [NADPH](2,4-dienoyl coenzymeA reductase)
           [Acinetobacter baumannii AB307-0294]
 gi|332727947|gb|EGJ59342.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii 6013150]
 gi|332732434|gb|EGJ63690.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii 6013113]
          Length = 676

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 69/241 (28%), Gaps = 52/241 (21%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+ + ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSSAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINLNVGCPSARVHEGSFGACL-----------------------MLNPDIVGDCI 108
            GY+ + +                 L                       M  P    + +
Sbjct: 155 AGYDGVEI-----------MGSEGYLINQFLSRHVNQRTDRWGGEIENRMRFP---VEIV 200

Query: 109 AAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+   +     +  R+     V D      +  + K+++K+GV  +  +      +   
Sbjct: 201 KAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARV 258

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           P     +P   + D    +K+      I  N  +     A +IL     D + + R    
Sbjct: 259 PTIVTSVPRAAFVDYTAHVKQHISIPVIASNR-INMPETAEEILATGKADMIQMARPLLA 317

Query: 222 N 222
           +
Sbjct: 318 D 318


>gi|291288831|ref|YP_003505647.1| dihydroorotate oxidase [Denitrovibrio acetiphilus DSM 12809]
 gi|290885991|gb|ADD69691.1| dihydroorotate oxidase [Denitrovibrio acetiphilus DSM 12809]
          Length = 328

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 61/179 (34%), Gaps = 21/179 (11%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + + + G + + LN+      +H     A +  +       I  +     +P +VK    
Sbjct: 117 ERIANAGADALELNIN--MLSLHGAKSPADIYKD---TLQIIHTVKNTTDLPFSVKLSPY 171

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS------PKDNRKIPNLDYDIVY 180
                    +  LVK +K+ G  G+ + +R   L   +      P      P   + ++ 
Sbjct: 172 CCS------IPYLVKMLKEEGAKGVTLFSRLFELGINTNTFECEPASYYSSPEETFKVLR 225

Query: 181 EI--KKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
            +    E  D+ I  N G+         I+     V +  + YKN   ++ T  E    
Sbjct: 226 WVHLVSEQVDIEICGNTGIHTSREIIQHIIAGAGAVQMVSSIYKNGPEIIRTCLEELEQ 284


>gi|153812595|ref|ZP_01965263.1| hypothetical protein RUMOBE_02995 [Ruminococcus obeum ATCC 29174]
 gi|149831299|gb|EDM86387.1| hypothetical protein RUMOBE_02995 [Ruminococcus obeum ATCC 29174]
          Length = 257

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 30/157 (19%), Positives = 48/157 (30%), Gaps = 38/157 (24%)

Query: 102 DIVGDCIAAMCKALSIPVT----------------------VKCRIGVDDQIPAVALRNL 139
           D V D +  + K  SIP+                       V     +   +P       
Sbjct: 75  DKVFDMVEKIRKNSSIPMVFMTYANVVFSYGIERFCKRAAEVGMDGMILPDVPFEEKEEF 134

Query: 140 VKSIKKSGVNGI-----WIHARKAI-----------LKGLSPKDNRKIPNLDYDIVYEIK 183
               +K G++ I       H R ++           +  L     R     D   + E+ 
Sbjct: 135 ASVAEKYGLDLISLIAPTSHERISMIAKEAEGFVYCVSSLGVTGMRSQITTDIGAMVELV 194

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           K   D+   +  G+    QA KI    DGV++G A  
Sbjct: 195 KAQKDIPCAVGFGISTPEQAKKIAAQADGVIVGSAIV 231


>gi|71892241|ref|YP_277975.1| imidazole glycerol phosphate synthase subunit HisF [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
 gi|85541703|sp|Q494D6|HIS6_BLOPB RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|71796347|gb|AAZ41098.1| imidazole glycerol phosphate synthase [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 258

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 22/112 (19%), Positives = 42/112 (37%), Gaps = 11/112 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           I   D      +  L     KSG + +  +   A     SP D      ++   + +I K
Sbjct: 21  IQFKDHKIVGDILELANRYAKSGADELVFYDITA-----SPNDQV----VNKRWISQIAK 71

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
              ++   + GG+  + QA +IL    D + I   A  N  ++  + ++   
Sbjct: 72  -VINIPFCVAGGINTLKQAKQILASGADKISINSPALINPMLIQELADHLGT 122


>gi|152981115|ref|YP_001353337.1| xenobiotic reductase A [Janthinobacterium sp. Marseille]
 gi|151281192|gb|ABR89602.1| xenobiotic reductase A [Janthinobacterium sp. Marseille]
          Length = 362

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 27/139 (19%), Positives = 52/139 (37%), Gaps = 12/139 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSG 147
           +G         + + + A+ +     +P+TV+  +   D      L     LV+  KKSG
Sbjct: 200 YGGSAENRARFLLETLRAVREVWPEHLPLTVRFGVLEYDGRDEETLLESIGLVREFKKSG 259

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           ++ I +     I     P+ +          V E  +   D+ +    G      A +++
Sbjct: 260 MDMISVSIGFTI-----PETSIPWGPAFLGPVAERVRREADVPVSSAWGFGTPEIAQRVV 314

Query: 208 PS--VDGVMIGRAAYKNSA 224
               +D VM+GR+   N  
Sbjct: 315 EQQQLDIVMVGRSHLANPH 333


>gi|71906003|ref|YP_283590.1| NADH:flavin oxidoreductase/NADH oxidase [Dechloromonas aromatica
           RCB]
 gi|71845624|gb|AAZ45120.1| NADH:flavin oxidoreductase/NADH oxidase [Dechloromonas aromatica
           RCB]
          Length = 355

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 25/156 (16%), Positives = 51/156 (32%), Gaps = 13/156 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSG 147
           ++G        ++ + + A+      S+P+ ++      V+    A     L + +K  G
Sbjct: 197 AYGGSFENRTRLLREVVTAVRAVWPESLPLLIRLSATDWVEGGWSADETVALCRDLKTLG 256

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           V+   I        GL P     +      +    ++ E   L     G +   +QA  +
Sbjct: 257 VDLADISTA-----GLVPTAKIPVGPGFQTEFAARVRHEAG-LPTAAVGLITSAAQADHV 310

Query: 207 L--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
           L     D V++GR   +N        +         
Sbjct: 311 LRTGQADMVLLGREILRNPYWPQQAAQELRQGGAWP 346


>gi|255026427|ref|ZP_05298413.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes FSL J2-003]
          Length = 240

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 11/101 (10%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+ ++KK    + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEIIQKMKKAA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           M+Q    L   +D V+IG AA  +   L    + +   +  
Sbjct: 86  MAQVDYYLESGIDRVVIGSAALTDPDFLRAAVQKYGTKIAA 126


>gi|83950131|ref|ZP_00958864.1| oxidoreductase, FAD/FMN-binding protein [Roseovarius nubinhibens
           ISM]
 gi|83838030|gb|EAP77326.1| oxidoreductase, FAD/FMN-binding protein [Roseovarius nubinhibens
           ISM]
          Length = 404

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 37/259 (14%), Positives = 85/259 (32%), Gaps = 45/259 (17%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDC 107
              L + A++ ++ G++ + ++       +               +G  +     ++ D 
Sbjct: 144 PLDLAQTARLAQEAGFSGVQIHAA--HGFLLSQFLSPLFNKRVDDYGGSIANRMRLLLDV 201

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + A   A+     +  ++   DQ+           +V ++  S V+ I I          
Sbjct: 202 LEATRAAVGPQFPIAVKLNSSDQLEGGLGEEDALAVVAALDTSSVDAIDISGGTYFPGAK 261

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDL--FIGLNGGLEDMSQALK-ILPS-VDGVMIGRAA 219
           S  D+          +   K+        + L GG++  +QA + +L    D V + RA 
Sbjct: 262 SASDSAGGGPY---FIAFAKRARTVTSKPLMLTGGIKTRAQAQEAVLSGAADVVGLARAL 318

Query: 220 YKNSAM-------------LTTVDEYFSNPLTGSSPIK-TRVDKDF----WRKISASMTD 261
               ++                        +T    ++ T +  D     +  +  ++ +
Sbjct: 319 VLEPSLPNLWLAHQMPEPAFPRFSHAPEGGITAWYTMRLTEIGADAETGDFCDLDQALAE 378

Query: 262 YAARHLHSGGKLQQITRHM 280
           Y AR    G + +  TRH 
Sbjct: 379 YDAR---DGLRTEIWTRHF 394


>gi|257898518|ref|ZP_05678171.1| dihydroorotate dehydrogenase [Enterococcus faecium Com15]
 gi|257836430|gb|EEV61504.1| dihydroorotate dehydrogenase [Enterococcus faecium Com15]
          Length = 314

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 39/208 (18%), Positives = 69/208 (33%), Gaps = 30/208 (14%)

Query: 48  KPLALQIGG----ADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
           +PL   I G     ++  L E    +E  G+  I  LN+ CP   V        L  + +
Sbjct: 96  QPLFFSIAGMSVQENLEMLGE----IEKSGFKGITELNLSCP--NVPGK---PQLAYDFE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 147 ATYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 205

Query: 156 RKAIL-----KGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKI-LP 208
            K  +     +G        I       V     +  P++ I   GG+     A +  L 
Sbjct: 206 DKEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLKPEIQIIGTGGIRTGQDAFEHLLC 265

Query: 209 SVDGVMIGRAAYK-NSAMLTTVDEYFSN 235
               + IG   +K    + + + +  + 
Sbjct: 266 GASMLQIGTELHKERPEIFSRIIKELTQ 293


>gi|303234247|ref|ZP_07320892.1| NADH oxidase domain protein [Finegoldia magna BVS033A4]
 gi|302494611|gb|EFL54372.1| NADH oxidase domain protein [Finegoldia magna BVS033A4]
          Length = 330

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 68/187 (36%), Gaps = 22/187 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K V+AA   +  G++ + +             P        +G  +     I  + I  
Sbjct: 147 EKFVDAAVRAKKAGFDGVEIHSAHGYLLNQFLSPITNKRTDEYGGDIDGRIKIHLEIIRK 206

Query: 111 MCKAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +  + P+ ++      ++  +      +  +   K+GV+ + I     +      +
Sbjct: 207 IREKVGENYPIFIRMGAGDYLEGGLSTEDSIHAAQEFVKAGVDVLDISGGMCMFSIDDQR 266

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS- 223
                    +D + +   EN D+ + L GG++       IL     D V IGR+ +K+S 
Sbjct: 267 AGF------FDFLSKPIYENVDVPVILTGGVKTGEDVEDILNRGVCDLVGIGRSVFKDSN 320

Query: 224 AMLTTVD 230
            +   + 
Sbjct: 321 WIENEIK 327


>gi|228473712|ref|ZP_04058460.1| inosine-5'-monophosphate dehydrogenase [Capnocytophaga gingivalis
           ATCC 33624]
 gi|228274859|gb|EEK13676.1| inosine-5'-monophosphate dehydrogenase [Capnocytophaga gingivalis
           ATCC 33624]
          Length = 492

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 49/147 (33%), Gaps = 24/147 (16%)

Query: 102 DIVGDCIAAMCKALSIP---------VTV--KCR---IGVDDQIPAVALRNLVKSIKKSG 147
           +     + A   A+ I          VTV  K +     +D  +  +A       + K+G
Sbjct: 235 ERAEALVHAGVDAVVIDTAHGHTRGVVTVLKKVKEQFPQLDVVVGNIATAEAALYLAKAG 294

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLE-DMSQAL 204
            + + +      +           P L     +   +K++N  + +  +GG+        
Sbjct: 295 ADAVKVGIGPGSICTTRVVAGVGYPQLSAVMQVAAALKQQNISIPVIADGGIRYTGDIVK 354

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDE 231
            I    D VM+G       ++L  + E
Sbjct: 355 AIAAGADCVMLG-------SLLAGIKE 374


>gi|300776662|ref|ZP_07086520.1| NADPH dehydrogenase [Chryseobacterium gleum ATCC 35910]
 gi|300502172|gb|EFK33312.1| NADPH dehydrogenase [Chryseobacterium gleum ATCC 35910]
          Length = 350

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 62/182 (34%), Gaps = 26/182 (14%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA+     G++ I +             P + +    +G         + + + A+ 
Sbjct: 152 FKKAARRAVKAGFDIIEIHGAHGYLIHQFLSPLSNIRTDEYGGTFENRIRFLIEIVDAVN 211

Query: 113 KALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + L+    + V +      ++     +   L K +K+  V+ I +               
Sbjct: 212 EELNENTALFVRISGTEYAENGWDIQSSVELAKILKEHAVDLIDV-------SSGGNIHG 264

Query: 169 RKIPNLD---YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            KIP  D        +++ E   +  G  G +  + QA +IL     D + + R   +N 
Sbjct: 265 AKIPVFDGYQVPFSSQVRNEAG-VNTGAVGLITRIEQAEEILKKGDADLIFVAREILRNP 323

Query: 224 AM 225
            +
Sbjct: 324 YI 325


>gi|170695934|ref|ZP_02887073.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia graminis
           C4D1M]
 gi|170139118|gb|EDT07307.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia graminis
           C4D1M]
          Length = 521

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 16/149 (10%), Positives = 44/149 (29%), Gaps = 12/149 (8%)

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRN 138
           CP        +G  +     +  + +  + +       V  R+ + D             
Sbjct: 13  CPRTNRRTDRYGGSIENRMRLACEIVERVRETCGERFIVVYRLSLIDLVEGGNTWDETVQ 72

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + ++++ +GV     +      +   P     +P   +  +    K    + + ++  + 
Sbjct: 73  VARALEAAGVTIF--NTGIGWHEARVPTIVTSVPRAAFAALSARLKAAVTVPVIVSNRIN 130

Query: 199 DMSQALKILPSVDG----VMIGRAAYKNS 223
                  +L   DG    V + R    + 
Sbjct: 131 TPDVGEALL--ADGAGDLVSMARPLLADP 157


>gi|154274534|ref|XP_001538118.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
 gi|150414558|gb|EDN09920.1| conserved hypothetical protein [Ajellomyces capsulatus NAm1]
          Length = 420

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 70/199 (35%), Gaps = 32/199 (16%)

Query: 64  EAAKIVEDFGYNEINLNVG--------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            A +     G + I ++          C P +      +G        +  + I    + 
Sbjct: 201 AAVRRAVKAGVDYIEVHCAHGYLLFSFCSPVSNNRTDEYGGSFENRIRLTSEIITISRQN 260

Query: 115 L--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +   +P+ ++          R  +        +R   K + + G V+ + + A      G
Sbjct: 261 MPKDMPLFLRISASEWLEETRPDLPSWKSEDTVR-FAKILAEKGEVDLLDVSA------G 313

Query: 163 LSPKDNRKIPNLDYDI--VYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
            +  D + IP   +     + +K+   D L +G  G + +   A  +L   +D V++GR 
Sbjct: 314 GNHPDQKIIPGPCFQAHFAHAVKEVVGDKLLVGAVGSINNGIDADALLEKGLDLVLVGRL 373

Query: 219 AYKNSAMLTTVDEYFSNPL 237
             KN +++    E     L
Sbjct: 374 FLKNPSVVWQFAEDLGTEL 392


>gi|239503317|ref|ZP_04662627.1| 2,4-dienoyl-CoA reductase [NADPH](2,4-dienoyl coenzymeA reductase)
           [Acinetobacter baumannii AB900]
          Length = 676

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 31/241 (12%), Positives = 69/241 (28%), Gaps = 52/241 (21%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+ + ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSSAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINLNVGCPSARVHEGSFGACL-----------------------MLNPDIVGDCI 108
            GY+ + +                 L                       M  P    + +
Sbjct: 155 AGYDGVEI-----------MGSEGYLINQFLSRHVNQRTDRWGGEIENRMRFP---VEIV 200

Query: 109 AAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+   +     +  R+     V D      +  + K+++K+GV  +  +      +   
Sbjct: 201 KAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARV 258

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           P     +P   + D    +K+      I  N  +     A ++L     D + + R    
Sbjct: 259 PTIVTSVPRAAFVDYTAHVKQHISIPVIASNR-INMPETAEEVLAAGKADMIQMARPLLA 317

Query: 222 N 222
           +
Sbjct: 318 D 318


>gi|229493009|ref|ZP_04386804.1| oxidoreductase [Rhodococcus erythropolis SK121]
 gi|229320039|gb|EEN85865.1| oxidoreductase [Rhodococcus erythropolis SK121]
          Length = 391

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 26/209 (12%), Positives = 63/209 (30%), Gaps = 44/209 (21%)

Query: 65  AAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AA++  + G++ + ++ G          P     + S+G  L     +V +   ++  A+
Sbjct: 151 AARLAVEAGFDAVEIHFGHNYFASSFLSPKLNRRKDSYGGSLENRARVVLETARSVRDAV 210

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIK-----------------------------KS 146
              V +  ++ +DD +P     +    +                               +
Sbjct: 211 GDKVAILAKLNMDDGVPGGFWVDEAIQVAQWLEASGSVDALELTMGSSLLNPMYLFKGDA 270

Query: 147 GVNGIWIHARKAI-----LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +        + +     L G S         L         +    L + L GG+ D +
Sbjct: 271 PIREFAAAMPQPVRLGVQLVGKSMLHTYPYKPLFMLEQARQIRAAVKLPLVLLGGVTDKA 330

Query: 202 QA-LKILPSVDGVMIGRAAYKNSAMLTTV 229
                +    + V + RA  +   ++  +
Sbjct: 331 GMDTAMAEGFEFVAMARALLREPDLINRI 359


>gi|167578619|ref|ZP_02371493.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           TXDOH]
          Length = 687

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRADEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLANGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|124266028|ref|YP_001020032.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Methylibium
           petroleiphilum PM1]
 gi|148839502|sp|A2SE08|HIS4_METPP RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|124258803|gb|ABM93797.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Methylibium
           petroleiphilum PM1]
          Length = 248

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 11/98 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE 198
            +    +G   + +        G           ++   +  I KE  D + + L GG+ 
Sbjct: 36  ARRWLDAGARRLHLVDLNGAFAG---------KPVNEPAIKAILKEVGDEIPVQLGGGIR 86

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D+    + L   +  V+IG AA KN   L      F  
Sbjct: 87  DLDTIERYLDDGLSYVIIGTAAVKNPGFLRDACTAFGG 124


>gi|229591348|ref|YP_002873467.1| putative 2,4-dienoyl-CoA reductase [Pseudomonas fluorescens SBW25]
 gi|229363214|emb|CAY50291.1| putative 2,4-dienoyl-CoA reductase [Pseudomonas fluorescens SBW25]
          Length = 679

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 19/127 (14%), Positives = 41/127 (32%), Gaps = 8/127 (6%)

Query: 103 IVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  D +  + +A+     I   +     V+       +  L K+I+ +G   I  +    
Sbjct: 197 LAVDIVRRVREAVGPNFIIIFRLSMLDLVEGGSTWEEIVQLAKAIEGAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    +    + +     +     A +IL   D  M+   
Sbjct: 255 WHEARIPTIATKVPRGAFSKVTAKLRGAVQIPLITTNRINTPEIAEQILAEGDADMVSMA 314

Query: 217 RAAYKNS 223
           R    + 
Sbjct: 315 RPFLADP 321


>gi|153854651|ref|ZP_01995901.1| hypothetical protein DORLON_01897 [Dorea longicatena DSM 13814]
 gi|149752755|gb|EDM62686.1| hypothetical protein DORLON_01897 [Dorea longicatena DSM 13814]
          Length = 666

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 53/178 (29%), Gaps = 25/178 (14%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEG------------SFGACLMLNPDIVGD-CIAAM 111
           AAK   + G++ + ++ G   + +                 G+    N        I  +
Sbjct: 155 AAKRAVNAGFDVVEIHAG--HSYLISQFLSPTTNDRTDEFGGSA--KNRARFCRMIIDEV 210

Query: 112 CKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            KA+   V +  R+ VD+              ++ +              A ++     +
Sbjct: 211 RKAVGPRVPISLRLSVDELVEGGNTVEDCLEYLEYLNDEVDIYDTSAGLNASIQYQIDAN 270

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             +     Y +   ++ +         G + D   A  IL     D + IGR    + 
Sbjct: 271 YLEDGWRSY-MAKAVRDKFGK-PTIAIGNIRDPKIADDILARGDADLIGIGRGLIADP 326


>gi|20455018|sp|Q9RDX2|HIS6_LEGPN RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|6688606|emb|CAB65215.1| HisF protein [Legionella pneumophila]
          Length = 212

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 15/135 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +    G + +      A L G +          +   + +   EN  + I + GG+
Sbjct: 34  EYAMAYYAQGADELIYMDTVASLYGRN----------NLSEIVKTTAENVFIPITVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A ++L    D V I  AA KN  +++ +   F +     S    R     W    
Sbjct: 84  RSVDDAEQLLRCGADKVAINTAATKNPTLISDIARRFGSQCVVLSIEAKRTVNGRW---- 139

Query: 257 ASMTDYAARHLHSGG 271
             MTD    H     
Sbjct: 140 EVMTDNGREHTGMDV 154


>gi|289583104|ref|YP_003481570.1| dihydroorotate dehydrogenase [Natrialba magadii ATCC 43099]
 gi|289532657|gb|ADD07008.1| dihydroorotate dehydrogenase [Natrialba magadii ATCC 43099]
          Length = 356

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 26/143 (18%), Positives = 53/143 (37%), Gaps = 21/143 (14%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIGVDDQI 131
            + + +NV CP+       F      +P+ + +    +     L +P+ VK         
Sbjct: 173 ADYVVVNVSCPN---TPDEFDEA---SPEHLREIFETIDAENDLDVPILVKI----GPDE 222

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD--------YDIVYEIK 183
           P  ++ +LV  +++  V+GI         +GL+     +   L           ++  I 
Sbjct: 223 PEESILDLVDIVQEFDVDGIVATNTSTAREGLASAKREEWGGLSGKPVEGRSTAVIRTIA 282

Query: 184 KEN-PDLFIGLNGGLEDMSQALK 205
                DL I   GG++  + A +
Sbjct: 283 DHTDGDLPIIGVGGVDSAASAYR 305


>gi|311257422|ref|XP_003127112.1| PREDICTED: LOW QUALITY PROTEIN: HAUS augmin-like complex subunit
           5-like [Sus scrofa]
          Length = 627

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 240 SSPIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +P+  R  +   R++     A +  Y  RH+HS   +++I  +++    G  +S   R 
Sbjct: 19  EAPVAARAPESTLRRLCLGQGADIWAYVLRHVHSQRSVKKIRGNLLWY--GLQDSPEARR 76

Query: 296 ILTVEAGASTATHHIIE--TAFNLM 318
            L +EA  +     I+E   +  LM
Sbjct: 77  KLELEAAVARLQAEILELDQSLELM 101


>gi|295110520|emb|CBL24473.1| tryptophan synthase, alpha chain [Ruminococcus obeum A2-162]
          Length = 235

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 28/157 (17%), Positives = 49/157 (31%), Gaps = 38/157 (24%)

Query: 102 DIVGDCIAAMCKALSIPVT----------------------VKCRIGVDDQIPAVALRNL 139
           D V D +  + K+ SIP+                       V     +   +P       
Sbjct: 53  DKVFDMVEKIRKSTSIPMVFMTYANVVFSYGVERFCKKAAEVGMDGMILPDVPFEEKDEF 112

Query: 140 VKSIKKSGVNGI-----WIHARKAI-----------LKGLSPKDNRKIPNLDYDIVYEIK 183
               +K G++ I       H R ++           +  L     R     D   + ++ 
Sbjct: 113 ASVAEKYGLDLISLIAPTSHERISMIAKEAEGFVYCVSSLGVTGMRSQITTDIGAMVQLV 172

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           K   D+   +  G+    QA K+    DGV++G A  
Sbjct: 173 KAQKDIPCAVGFGISTPEQAKKMAAQADGVIVGSAIV 209


>gi|226365669|ref|YP_002783452.1| inosine 5-monophosphate dehydrogenase [Rhodococcus opacus B4]
 gi|226244159|dbj|BAH54507.1| IMP dehydrogenase family protein [Rhodococcus opacus B4]
          Length = 379

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 30/152 (19%), Positives = 58/152 (38%), Gaps = 21/152 (13%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+ E     E +++V  P  ++ E        L P ++   +A +  A    VT   R+
Sbjct: 91  AKLAELVALAESDVDVEAPIKKLQELHAA---PLQPGLLAAAVAQVRDAG---VTTAVRV 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
              +       R L   + ++G++ + +H    I+           P      + E+   
Sbjct: 145 SPQN------ARALTPQLLEAGIDLLVVHG--TIISAEHVAHGDSEPLNLKTFISEL--- 193

Query: 186 NPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
             D+ +   GG+ D   AL  +     GV++G
Sbjct: 194 --DVPVVA-GGVSDHRTALHLMRTGAAGVIVG 222


>gi|26988733|ref|NP_744158.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida KT2440]
 gi|24983525|gb|AAN67622.1|AE016392_3 2,4-dienoyl-CoA reductase FadH [Pseudomonas putida KT2440]
          Length = 693

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 29/231 (12%), Positives = 67/231 (29%), Gaps = 38/231 (16%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++            E  +  QI        V  A + +  GY+
Sbjct: 121 LHAGRYAYSPRQVAPSAIQAPINPFKPKELDEAGIEKQIA-----DFVNCAVLAQRAGYD 175

Query: 76  EINLNVGCPSARVHEGSFGA--CLMLNPD---------------IVGDCIAAMCKALS-- 116
            + +        +    +     L  + +               +  + ++ +  A+   
Sbjct: 176 GVEI--------MGSEGYFINQFLAAHTNHRTDRWGGSYENRMRLAVEIVSRVRGAVGPN 227

Query: 117 --IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             I   +     V+       +  L K+I+++G   I  +      +   P    K+P  
Sbjct: 228 FIIIFRLSMLDLVEGGSTWDEIELLAKAIEQAGATLI--NTGIGWHEARIPTIATKVPRA 285

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
            +  V    +    + +     +     A  +L   D  M+   R    + 
Sbjct: 286 AFSKVTAKLRGVVSIPLITTNRINTPEVAEAVLAEGDADMVSMARPFLADP 336


>gi|255524602|ref|ZP_05391556.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           carboxidivorans P7]
 gi|296185747|ref|ZP_06854154.1| 2-enoate reductase family protein [Clostridium carboxidivorans P7]
 gi|255511755|gb|EET88041.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           carboxidivorans P7]
 gi|296049575|gb|EFG89002.1| 2-enoate reductase family protein [Clostridium carboxidivorans P7]
          Length = 549

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 29/200 (14%), Positives = 61/200 (30%), Gaps = 43/200 (21%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             + A + +  G + + ++       VHEG                 +G  L     +  
Sbjct: 151 FAQGAYLAKKAGADGVEIHA------VHEGYLLDQFVIASMNYRTDEYGGSLENRLRLPI 204

Query: 106 DCIAAMCKALSI--PV----TVK--CRIGVDDQIPAVALRNL----------VKSIKKSG 147
           + + A+        PV    +VK   +      +P                  K+++ +G
Sbjct: 205 EIVQAIKAECGKDFPVLLRFSVKSYIKAFNRGALPGEEFEEFGRDIEESKIIAKALQDAG 264

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + +                       +   V EIKK   D+ +   G  +D   A K++
Sbjct: 265 YDALDCDNGSYDSWFWPHPPTYMPKACNLKDVREIKK-VVDIPVICAGRFDDPELADKVI 323

Query: 208 --PSVDGVMIGRAAYKNSAM 225
               +D + +GR    +  +
Sbjct: 324 GDGEIDMMGMGRPLLADPYI 343


>gi|228965045|ref|ZP_04126142.1| NADPH dehydrogenase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228794589|gb|EEM42098.1| NADPH dehydrogenase [Bacillus thuringiensis serovar sotto str.
           T04001]
          Length = 319

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 27/136 (19%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ K    P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNKVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGSQAEQILNDN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|217978746|ref|YP_002362893.1| NADH:flavin oxidoreductase/NADH oxidase [Methylocella silvestris
           BL2]
 gi|217504122|gb|ACK51531.1| NADH:flavin oxidoreductase/NADH oxidase [Methylocella silvestris
           BL2]
          Length = 371

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 54/168 (32%), Gaps = 22/168 (13%)

Query: 72  FGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPV 119
            G + I L+            P A      +G  L   M  P  V D + A   A   PV
Sbjct: 170 LGIDAIELHAAHGYLLHEFLSPLANQRGDQYGGSLENRMRYPLEVFDAVRAAFPA-DKPV 228

Query: 120 TVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            VK      V+  +         + I+K G + I      A   G+SP     +      
Sbjct: 229 GVKVSATDWVEGGLDLAQTIAFAREIEKRGADWIT-----ASSGGVSPLQKIPVAPNYQV 283

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
              E  K      +   G + +  QA +I+     D V + RA   + 
Sbjct: 284 PFAEGLKGAVGFPVMAVGLITEAQQAEEIIADGKADCVALARAMLYDP 331


>gi|167616760|ref|ZP_02385391.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           Bt4]
          Length = 687

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRADEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLANGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|17546545|ref|NP_519947.1| salicylyl-CoA 5-hydroxylase [Ralstonia solanacearum GMI1000]
 gi|17428843|emb|CAD15528.1| putative flavin oxidoreductase oxidoreductase protein [Ralstonia
           solanacearum GMI1000]
          Length = 772

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 30/193 (15%), Positives = 57/193 (29%), Gaps = 27/193 (13%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-- 82
            ++ A A+     ++ L        LA         + VEA +     G++ + L  G  
Sbjct: 532 PLVSASALPYLPGRSQLPREASLDDLA-----RIREQFVEATRRAAAAGFDWLELQAGHG 586

Query: 83  -------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA----LSIPVTVKCRIGVDDQI 131
                   P       ++G  L        + +AA+  A    L I V + C        
Sbjct: 587 FLLSSFISPLTNQRTDAYGGALENRLRFPLEVLAAVRAAWPAHLPISVRISCTDWAPGGT 646

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD--IVYEIKKENPDL 189
                  + + +   G + +       +  G    D + +    Y       I+ E   +
Sbjct: 647 TVDEAVEIARRLHLGGADLVD------VSSGEVTPDQKPVYGRLYQTPFADRIRNEA-RV 699

Query: 190 FIGLNGGLEDMSQ 202
                G + D  Q
Sbjct: 700 PTIAVGAISDADQ 712


>gi|332187818|ref|ZP_08389552.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Sphingomonas sp. S17]
 gi|332012168|gb|EGI54239.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Sphingomonas sp. S17]
          Length = 242

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 31/137 (22%), Positives = 54/137 (39%), Gaps = 23/137 (16%)

Query: 94  GACLMLNPDIVGDCIAA----MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
           G   + NPD V D   A    +  A+     +    G  D +  V++ +L +  + +GV 
Sbjct: 103 GTAALENPDFVRDMAKAYPGGIVVAVDAKDGMVATRGWAD-VSDVSVEDLARRFEDAGVA 161

Query: 150 G--IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG---LEDMSQ-A 203
                   R  +LKG +            D+   ++     + +  +GG   + D+   A
Sbjct: 162 ALLFTDVGRDGLLKGCN-------VPATVDLARAVR-----IPVIASGGVAGIGDIHMLA 209

Query: 204 LKILPSVDGVMIGRAAY 220
           L     V+GV+ GRA Y
Sbjct: 210 LHHQDGVEGVITGRALY 226


>gi|288962195|ref|YP_003452490.1| 2,4-dienoyl-CoA reductase (NADPH2) [Azospirillum sp. B510]
 gi|288914461|dbj|BAI75946.1| 2,4-dienoyl-CoA reductase (NADPH2) [Azospirillum sp. B510]
          Length = 718

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 17/125 (13%), Positives = 42/125 (33%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + ++ M +A+     +  R+     + D      +  L ++I+K+G     I+      +
Sbjct: 238 EIVSRMREAVGRDFIIIYRLSMLDLIPDGSTWEEVVQLAQAIEKAGAT--IINTGIGWHE 295

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P  ++  V  ++K          N  +        ++     D V + R 
Sbjct: 296 ARVPTIATSVPRANFAWVTGKLKGAVSIPLCTTNR-INTPEVGDAVIGGGLADMVSMARP 354

Query: 219 AYKNS 223
              + 
Sbjct: 355 LLADP 359


>gi|139473548|ref|YP_001128264.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes str.
           Manfredo]
 gi|229485589|sp|A2RDV3|PYRD_STRPG RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|134271795|emb|CAM30028.1| putative dihydroorotate dehydrogenase [Streptococcus pyogenes str.
           Manfredo]
          Length = 311

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 73/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 68  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 125

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 126 ELNLSCP--NVPGKPQIAY---DFETTNQLLENLFTYYTKPLGIKLPPYFDIVHFDQAAA 180

Query: 136 LRN-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +          K    G+     +     +    Y  K+ 
Sbjct: 181 IFNKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 238

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 239 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 290


>gi|83716998|ref|YP_440059.1| FAD/FMN-binding oxidoreductase [Burkholderia thailandensis E264]
 gi|257143247|ref|ZP_05591509.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           E264]
 gi|83650823|gb|ABC34887.1| oxidoreductase, FAD/FMN-binding [Burkholderia thailandensis E264]
          Length = 687

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRADEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLANGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|329769345|ref|ZP_08260761.1| hypothetical protein HMPREF0433_00525 [Gemella sanguinis M325]
 gi|328839148|gb|EGF88733.1| hypothetical protein HMPREF0433_00525 [Gemella sanguinis M325]
          Length = 409

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 32/232 (13%), Positives = 83/232 (35%), Gaps = 23/232 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           K V +AK+ ++ G++ + ++            P        +G  L      + +    M
Sbjct: 152 KFVTSAKVAKEAGFSGVQIHAAHGYLISQFLSPHDNRRTDKYGGSLENRMRFLKEIYLGM 211

Query: 112 CKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLS 164
            + L    T+  +I      +D +        +  +   G++ + I         + G +
Sbjct: 212 REELGKDFTIGIKINSTDFKEDGLTEEDSLKTIIELANLGLDFVEISGGTYERPAMMGAT 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
            K   ++   +Y    ++K++  ++ + + GG+  ++    +L   + D + I R    +
Sbjct: 272 SKSTNQVFFAEYS--KKLKQKI-EIPVVVTGGIRSINAMNTLLNDNTTDFIGIARPLTID 328

Query: 223 SAMLTTVDEYFSN--PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
             +   + +        T  S    ++DK F   +         +++  G K
Sbjct: 329 PNIPNKIKQGTYTIVETTRVSTGVKKLDKIFGSLLGIVYYQVLMQNIAKGKK 380


>gi|329955860|ref|ZP_08296663.1| dihydroorotate dehydrogenase 2 [Bacteroides clarus YIT 12056]
 gi|328525240|gb|EGF52290.1| dihydroorotate dehydrogenase 2 [Bacteroides clarus YIT 12056]
          Length = 325

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 63/207 (30%), Gaps = 45/207 (21%)

Query: 47  EKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I    D   + E AK +E+ G + + +N+               L  +     
Sbjct: 96  DIPIIASINCYQDADWI-EFAKKIEEAGADALEINI-------------LALQTDMQYAY 141

Query: 106 --------DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR- 156
                   D ++ + K ++IPV +K                L+  +  +G   + +  R 
Sbjct: 142 GSFEQRHIDILSHIKKTVNIPVIMKL------GDNLTNPIALIDQLYANGAAAVVMFNRF 195

Query: 157 ----------KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALK 205
                           +   D     +L +  +         L    +GG+         
Sbjct: 196 YQPDIDIEKMAQSAGSVFSTDADLSKSLRWIGIAS--AAVGKLDYAASGGIHAPEGVVKA 253

Query: 206 ILPSVDGVMIGRAAYKNSAMLTTVDEY 232
           IL     V I    Y+NS     +DEY
Sbjct: 254 ILAGASAVEICSVLYQNSY--AIIDEY 278


>gi|261368175|ref|ZP_05981058.1| anthraniloyl-CoA monooxygenase [Subdoligranulum variabile DSM
           15176]
 gi|282569826|gb|EFB75361.1| anthraniloyl-CoA monooxygenase [Subdoligranulum variabile DSM
           15176]
          Length = 325

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 28/178 (15%), Positives = 68/178 (38%), Gaps = 23/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFG-ACLMLNPDIVGDCIAAM 111
             EAA+   + G++ + ++            P A     ++G   +      + + + A+
Sbjct: 149 FGEAARRAREAGFDGVEIHAAHGYLLNQFYSPLANHRSDAYGPQSVENRTRFLREVLQAV 208

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +A     PV V+   G D Q     L +     + + +SG + + +            +
Sbjct: 209 RRAAGEDFPVAVRL-GGCDYQEGGSTLEDSTAACRILAESGTDLLHLTGGMNGFVRPGHQ 267

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +     ++         ++   + + L GG+  ++QA  +L     D + +GRA +++
Sbjct: 268 EPGYFQDM-----SRAARQAVQIPVLLTGGVTTLAQAQALLEEGCADLIGVGRAIFRD 320


>gi|50914537|ref|YP_060509.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS10394]
 gi|50903611|gb|AAT87326.1| Dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS10394]
          Length = 315

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 74/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 72  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 129

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 130 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 184

Query: 136 LRN-----LVKSIKKSGVNGIW-----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +      +   K    G+     +     +    Y  K+ 
Sbjct: 185 IFNKYPLSFVNCVNSIGNGLVIKDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 242

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 243 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 294


>gi|15675344|ref|NP_269518.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes M1 GAS]
 gi|71910978|ref|YP_282528.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS5005]
 gi|81856071|sp|Q99Z28|PYRD_STRP1 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|13622526|gb|AAK34239.1| putative dihydroorotate dehydrogenase [Streptococcus pyogenes M1
           GAS]
 gi|71853760|gb|AAZ51783.1| dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS5005]
          Length = 311

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 74/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 68  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 125

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 126 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 180

Query: 136 LRN-----LVKSIKKSGVNGIW-----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +      +   K    G+     +     +    Y  K+ 
Sbjct: 181 IFNKYPLSFVNCVNSIGNGLVIKDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 238

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 239 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 290


>gi|329929031|ref|ZP_08282833.1| isopentenyl-diphosphate delta-isomerase, type 2 [Paenibacillus sp.
           HGF5]
 gi|328937020|gb|EGG33449.1| isopentenyl-diphosphate delta-isomerase, type 2 [Paenibacillus sp.
           HGF5]
          Length = 370

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 46/128 (35%), Gaps = 21/128 (16%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAILKG 162
           I  +C+ LSIPV +K       ++         +++   G   I +          + K 
Sbjct: 206 IEDLCRTLSIPVGIK-------EVGWGIDGETARTLLDVGAAFIDVAGAGGTSWSQVEKF 258

Query: 163 LSPKDNRKIPN---LDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
            SP   R+        +     D + E+++  PD  +  +GGL+  +  A  +    D  
Sbjct: 259 RSPDPVRRAAAEAFAGWGNPTADCIAEVREAAPDCALIGSGGLQSGVDAAKALALGADLA 318

Query: 214 MIGRAAYK 221
             GR    
Sbjct: 319 GFGRGLLG 326


>gi|281209915|gb|EFA84083.1| hypothetical protein PPL_03156 [Polysphondylium pallidum PN500]
          Length = 378

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 11/140 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +G        I+ D + A+    S    V +     ++          L K +K+  V+ 
Sbjct: 221 YGVDFEGRIKILNDIVKAIRTVWSKILMVRISAEEWIEGGWTLNDSIRLTKILKELDVDI 280

Query: 151 IWIHARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
           +      A   G S         L    +   IK+E PD+     G ++ + QA+ I+ +
Sbjct: 281 L-----DASSGGNSANAKTPFGPLFQVPLAEAIKREIPDIITSTVGSIKTVEQAMSIIDN 335

Query: 210 --VDGVMIGRAAYKNS-AML 226
              D +M+ R   ++   +L
Sbjct: 336 DRADLIMLARPLLRDPFWVL 355


>gi|217959540|ref|YP_002338092.1| NADPH dehydrogenase NamA [Bacillus cereus AH187]
 gi|254766771|sp|B7HNI1|NAMA_BACC7 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|217063825|gb|ACJ78075.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus AH187]
          Length = 345

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 25/141 (17%), Positives = 50/141 (35%), Gaps = 11/141 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIESINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSAMLTTV 229
             D + IGR   +N    + +
Sbjct: 300 EADLIFIGRELLRNPY-FSRI 319


>gi|125718253|ref|YP_001035386.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK36]
 gi|148839531|sp|A3CNT1|HIS4_STRSV RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|125498170|gb|ABN44836.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase, putative
           [Streptococcus sanguinis SK36]
          Length = 242

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 11/102 (10%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K++GV  I +   +  L+G +          + D++ +IK E   L I + G
Sbjct: 34  VLEQARVFKEAGVTMIHVVDLEGALEGRA---------ANRDLIAQIKAETG-LAIQVGG 83

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           G+  + Q    L   +D V+IG  A KN   +    E F + 
Sbjct: 84  GIRSLEQIEDYLAVGIDRVIIGSMAVKNPEFVEAALERFGSG 125


>gi|89895408|ref|YP_518895.1| hypothetical protein DSY2662 [Desulfitobacterium hafniense Y51]
 gi|89334856|dbj|BAE84451.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 315

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 53/144 (36%), Gaps = 22/144 (15%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK-----------CRIGVDDQIPA 133
             +V    +G  +ML    V D +  + +   +PV               +      IP 
Sbjct: 59  IKKVTNKPYGVNVMLMSPFVEDVMQVIVEE-RVPVITTGAGNPGKYIPMLKEVGTKIIPV 117

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA   L + ++K+GV+ +       +  G    +   +P     +V ++  +   + +  
Sbjct: 118 VASVALARRLEKAGVDALIAEG---MESGGHIGEISTLP-----LVPQVV-DAVSIPVIA 168

Query: 194 NGGLEDMSQALKILP-SVDGVMIG 216
            GG+ D    +  L    +GV +G
Sbjct: 169 AGGIYDGRGMVAALALGAEGVQMG 192


>gi|320531779|ref|ZP_08032706.1| salicylyl-CoA 5-hydroxylase domain protein [Actinomyces sp. oral
           taxon 171 str. F0337]
 gi|320136010|gb|EFW28031.1| salicylyl-CoA 5-hydroxylase domain protein [Actinomyces sp. oral
           taxon 171 str. F0337]
          Length = 335

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 23/123 (18%), Positives = 49/123 (39%), Gaps = 13/123 (10%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+   D     +           + K+GV+ + I +      
Sbjct: 218 EVVRAVREAIGPDTLLDIRLSASDWAGGGVTGEETAAFSHELVKAGVDVLHISSG----- 272

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
           G  P +    P     +  ++K+     D+ +   G +E+ +QA + L     D + +GR
Sbjct: 273 GNVPAEIPVGPGYQLPLAEQVKQAVAGSDVPVVGVGLIEEAAQAEQALIAGQADAIAVGR 332

Query: 218 AAY 220
           AA 
Sbjct: 333 AAL 335


>gi|281492113|ref|YP_003354093.1| dihydroorotate dehydrogenase [Lactococcus lactis subsp. lactis
           KF147]
 gi|281375796|gb|ADA65293.1| Dihydroorotate dehydrogenase [Lactococcus lactis subsp. lactis
           KF147]
          Length = 311

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 66/209 (31%), Gaps = 28/209 (13%)

Query: 46  QEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIV 104
           QE P+   I G   ++ +   K +++  ++ I  LN+ CP   V        L  + +  
Sbjct: 92  QEAPIFFSIAGMSAAENIAMLKNIQESNFSGITELNLSCP--NVPGK---PQLAYDFEAT 146

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNL----VKSIKKSGVNGIW----- 152
              +  +    + P+ VK     D     I A  L       V S+   G          
Sbjct: 147 EKLLKEVFTFFTKPLGVKLPPYFDLVHFDIMAEILNQFPLTYVNSVNSIGNGLFIDSEAE 206

Query: 153 --IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
             +   K    G+     +     +    Y   K  P++ I   GG+E    A + L   
Sbjct: 207 SVVIKPKDGFGGIGGAYIKPTALANVRAFYTRLK--PEIQIIGTGGIETGQDAFEHLL-C 263

Query: 211 DGVM--IGRAAYKN--SAMLTTVDEYFSN 235
              M  IG  A       +   + +    
Sbjct: 264 GATMLQIGT-ALHKEGPTIFDRIIKELEE 291


>gi|229138766|ref|ZP_04267347.1| NADPH dehydrogenase [Bacillus cereus BDRD-ST26]
 gi|228644682|gb|EEL00933.1| NADPH dehydrogenase [Bacillus cereus BDRD-ST26]
          Length = 319

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 25/141 (17%), Positives = 50/141 (35%), Gaps = 11/141 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIESINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSAMLTTV 229
             D + IGR   +N    + +
Sbjct: 274 EADLIFIGRELLRNPY-FSRI 293


>gi|54296776|ref|YP_123145.1| hypothetical protein lpp0815 [Legionella pneumophila str. Paris]
 gi|53750561|emb|CAH11963.1| hypothetical protein lpp0815 [Legionella pneumophila str. Paris]
          Length = 253

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 15/135 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +    G + +      A L G +          +   + +   EN  + I + GG+
Sbjct: 34  EYAMAYYAQGADELIYMDTVASLYGRN----------NLSEIVKTTAENVFIPITVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A ++L    D V I  AA KN  +++ +   F +     S    R     W    
Sbjct: 84  RSVDDAKQLLRCGADKVAINTAATKNPTLISDIARRFGSQCVVLSIEAKRTVNGRW---- 139

Query: 257 ASMTDYAARHLHSGG 271
             MTD    H     
Sbjct: 140 EVMTDNGREHTGMDV 154


>gi|261820848|ref|YP_003258954.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium wasabiae
           WPP163]
 gi|261604861|gb|ACX87347.1| NADH:flavin oxidoreductase/NADH oxidase [Pectobacterium wasabiae
           WPP163]
          Length = 362

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 27/183 (14%), Positives = 62/183 (33%), Gaps = 25/183 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AA+   + G+  + L+       + +             +G         + + +
Sbjct: 158 DDFVAAARRALEAGFEWLELHFA--HGYLAQSFFSVHSNKRNDQYGGSFDNRSRFLLETL 215

Query: 109 AAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
           AA+       +P+T +  +   D      L+    L +  K +G++ + +      +   
Sbjct: 216 AAVRDVWPQHLPLTARFGVIEFDGRDEETLQESIELTRRFKAAGLDMLSV-----SIGFS 270

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           +P+            + +  +E  DL +    G      A + +    +D VM+G+A   
Sbjct: 271 TPEATIPWAPAFMGPIAQQVREQADLPVSSAWGFGTPELAEQAVASGQLDLVMVGKAHLA 330

Query: 222 NSA 224
           N  
Sbjct: 331 NPH 333


>gi|199598899|ref|ZP_03212309.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Lactobacillus rhamnosus HN001]
 gi|199590207|gb|EDY98303.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Lactobacillus rhamnosus HN001]
          Length = 381

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 21/131 (16%), Positives = 50/131 (38%), Gaps = 11/131 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
           V +    + +    P  +  RI  ++        +    L+ ++K + ++ + +      
Sbjct: 207 VHEAEKVIAETADRPFLLGYRISPEELEQPGITLDDTLALIDALKATKIDYLHVSQSDVW 266

Query: 160 LKGLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
              L   DN  I N   D++ + +    P + +   GG++   +A K + + D V IG  
Sbjct: 267 RTSLRDPDNPAIIN---DVIRDHVAGAFPIIVV---GGIKTPEEAEKAVAAFDLVAIGHE 320

Query: 219 AYKNSAMLTTV 229
             +    +  +
Sbjct: 321 MIREPHWVQKI 331


>gi|241955090|ref|XP_002420266.1| NADPH dehydrogenase, putative [Candida dubliniensis CD36]
 gi|223643607|emb|CAX42489.1| NADPH dehydrogenase, putative [Candida dubliniensis CD36]
          Length = 432

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 67/199 (33%), Gaps = 28/199 (14%)

Query: 61  KLVEAAKIVED---------FGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               AAK   +          G +   +N    P +      +G         + + I +
Sbjct: 204 DFGAAAKRAIEISGFDAVEIHGAHGYLINEFYSPISNKRTDEYGGSFENRTRFLKEVIDS 263

Query: 111 MCKALSI--PVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHA-----RKAI 159
           +  ++    PV ++     +   P          L   + + G+  + + +     R+  
Sbjct: 264 VKSSIPKDAPVFLRISAAENSPDPEAWTIEDSKKLADILIEKGIALVDVSSGGNDYRQPP 323

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE-DMSQALKILPS--VDGVMI 215
             G+S K+ R+   +   +   IK+   D L +   GGLE D     K L     D  +I
Sbjct: 324 RSGIS-KELRE--PIHVPLSRAIKQHVGDKLLVSSVGGLEKDPELLNKYLEEGAFDFALI 380

Query: 216 GRAAYKNSAMLTTVDEYFS 234
           GR   +N  ++    +   
Sbjct: 381 GRGFLRNPGLVWEFADKLG 399


>gi|183602141|ref|ZP_02963509.1| probable NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium
           animalis subsp. lactis HN019]
 gi|219683052|ref|YP_002469435.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium animalis
           subsp. lactis AD011]
 gi|241191373|ref|YP_002968767.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|241196779|ref|YP_002970334.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|183218634|gb|EDT89277.1| probable NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium
           animalis subsp. lactis HN019]
 gi|219620702|gb|ACL28859.1| probable NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium
           animalis subsp. lactis AD011]
 gi|240249765|gb|ACS46705.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240251333|gb|ACS48272.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|289177498|gb|ADC84744.1| NADH-dependent flavin oxidoreductase [Bifidobacterium animalis
           subsp. lactis BB-12]
 gi|295794366|gb|ADG33901.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 376

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 76/228 (33%), Gaps = 33/228 (14%)

Query: 49  PLALQIGGADISKLV----EAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGA 95
           P   Q+   +I  +V    +AA    + G+  I ++            P     +  +G 
Sbjct: 157 PAPRQLTVDEIHDIVNRFRDAAWRAMEAGFEVIEIHAAHGYLLSEFLDPLVNDRDDEYGG 216

Query: 96  CLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG------VDDQIPAVALRNLVKSIKKSG 147
            L     IV +   A+   +   +P+  +           D     V    L K++K+ G
Sbjct: 217 SLENRIRIVIEVADAIRSVIRGDMPLFARISATDWAEGGWDLDQSIV----LAKALKEHG 272

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ + +         L        P        +I+K+  D+ +   G +    QA +IL
Sbjct: 273 VDLVDVSTGGI----LPNVTIPTKPGYQVPFSEQIRKKA-DVPVTAVGLITKPKQAARIL 327

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
                D V IGRAA +              P T   P   +  +  WR
Sbjct: 328 AKGEADAVEIGRAALREPYWPLRAGFKLGEP-TDLLPYPPQYVRGAWR 374


>gi|83716559|ref|YP_439893.1| xenobiotic reductase A [Burkholderia thailandensis E264]
 gi|167578409|ref|ZP_02371283.1| xenobiotic reductase A [Burkholderia thailandensis TXDOH]
 gi|167616549|ref|ZP_02385180.1| xenobiotic reductase A [Burkholderia thailandensis Bt4]
 gi|257143052|ref|ZP_05591314.1| xenobiotic reductase A [Burkholderia thailandensis E264]
 gi|83650384|gb|ABC34448.1| xenobiotic reductase A [Burkholderia thailandensis E264]
          Length = 365

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 64/180 (35%), Gaps = 25/180 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AAK   D G+  + L+       + +            ++G         + + +AA+
Sbjct: 161 VAAAKRALDAGFEWLELHFA--HGYLAQSFFSVHSNRRTDAYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +     +P+T +  +   D      L     L K  K+ G++ + +      +   +P 
Sbjct: 219 REVWPERLPLTARFGVIEYDGRDEETLAESIGLAKRFKQEGLDLLSV-----TVGFSTPD 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++  + A +++    +D VM+GRA   +  
Sbjct: 274 ARIPWGPAFLAPVAERVRREAQLPVASAWGIDAPALAERVVKDGQLDLVMVGRAHLADPH 333


>gi|254282540|ref|ZP_04957508.1| NADH oxidase [gamma proteobacterium NOR51-B]
 gi|219678743|gb|EED35092.1| NADH oxidase [gamma proteobacterium NOR51-B]
          Length = 694

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 57/161 (35%), Gaps = 24/161 (14%)

Query: 93  FGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKK 145
           +G  L   M  P    + + A+  A +    V  R+  D+  P    A     + +   +
Sbjct: 198 YGGSLENRMRYP---LEILEAVRAATNKNFAVGVRLCADEMFPGGMGAEECAVMAQRFVE 254

Query: 146 SG-VNGIWIHARKAILKGLSPKDNRKIPNLD----YDIVYEIK-KENPDLFIGLNGGLED 199
           +G V+ I +        G     + ++P  D    + I    K K+  D+ + ++G +  
Sbjct: 255 TGLVDYISLAG------GSYHAYSYEVPPEDLPEGWLISRARKIKKKVDVPVIVSGAITR 308

Query: 200 MSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
                K + +   D + + R    +           ++ +T
Sbjct: 309 PEMGEKAIATGAADAIAMSRPLMADPEWAEKAKANKADEIT 349


>gi|319744550|gb|EFV96903.1| dihydroorotate oxidase [Streptococcus agalactiae ATCC 13813]
          Length = 310

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 39/208 (18%), Positives = 68/208 (32%), Gaps = 32/208 (15%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           K   L + G    +     K +E+  YN  I LN+ CP+           +   P I  D
Sbjct: 95  KNHVLSLVGLSPEETHIILKKIENSSYNGLIELNLSCPN-----------VPGKPQIAYD 143

Query: 107 ------CIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWI 153
                  ++ +      P+ +K     D      A  + N      +  +   G NG+ I
Sbjct: 144 FEMTDLILSEIFSYYQKPLGIKLPPYFDIVHFDQAATIFNKYPLAFINCVNSIG-NGLVI 202

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEI----KKENPDLFIGLNGGLEDMSQALKI-LP 208
                ++K  +         +    +  +    K+ NP + I   GG+++   A +  L 
Sbjct: 203 DDETVVIKPKNGFGGIGGDFIKPTALANVHAFYKRLNPSIKIIGTGGVKNGRDAFEHILC 262

Query: 209 SVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
               V IG A  K    +   V      
Sbjct: 263 GASMVQIGTALQKEGPEIFQRVSRELKE 290


>gi|322421348|ref|YP_004200571.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter sp. M18]
 gi|320127735|gb|ADW15295.1| NADH:flavin oxidoreductase/NADH oxidase [Geobacter sp. M18]
          Length = 348

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 61/185 (32%), Gaps = 21/185 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAA 110
              ++AA   +  G + + ++       C    PS       +G        IV   I  
Sbjct: 146 EDFIDAAYRAKLSGMDGVEIHCAHDYLLCEFLTPSFNKRTDKYGETYEGRFLIVKKIIQG 205

Query: 111 MCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +        PV VK       +++     L+ ++   K+ GV  +          G +  
Sbjct: 206 IKNKCGADYPVFVKVNSNAAEENEQYTSDLKKMIPEFKRLGVEAV-------EFSGSNFI 258

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
             +   +  +       K N D+ + + GG+ +      +L   VD + I R       +
Sbjct: 259 HMKYSDHNYFVESAMNLKGNTDIPVIVVGGIRNFEDMEAVLEAGVDMISISRPLISEPDL 318

Query: 226 LTTVD 230
           +T + 
Sbjct: 319 ITRLK 323


>gi|17228322|ref|NP_484870.1| hypothetical protein all0827 [Nostoc sp. PCC 7120]
 gi|17130172|dbj|BAB72784.1| all0827 [Nostoc sp. PCC 7120]
          Length = 355

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 61/178 (34%), Gaps = 20/178 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V+A K     G+  I ++            P     +  +G        ++ + + A+ 
Sbjct: 159 FVQATKRSLQAGFKVIEIHAAHGYLLHQFLSPLVNQRQDDYGGSFENRTRLLREVVEAVR 218

Query: 113 KAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +    S P+ V+      VD          +   +K  GV+ I   +      G+ P  N
Sbjct: 219 EVWPESYPLFVRLSATDWVDKGWDIEQSIAISDKLKSLGVDLIDCSSG-----GVIPGIN 273

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV-DGVMIGRAAYKNSA 224
             +         E  ++   +  G  G +    QA +I+   V D V++GR   +N  
Sbjct: 274 IPVKPGYQSQFAERIRKEAHIPTGAVGLITSPEQADQIIRSGVADIVLLGRELLRNPY 331


>gi|315651645|ref|ZP_07904656.1| DNA polymerase III PolC [Eubacterium saburreum DSM 3986]
 gi|315486099|gb|EFU76470.1| DNA polymerase III PolC [Eubacterium saburreum DSM 3986]
          Length = 1483

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 15/127 (11%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINLNVGCP 84
           M+V   ++       L F      +     G D   + E AK I  ++  + I+      
Sbjct: 517 MVVNAPVIEEILPKFLDFCEDYT-IVAHNAGFDTGFIRENAKRINAEYNPSIIDT----- 570

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
                  +    L+ + +     +  +CKAL+I +    R   D +  A      +K +K
Sbjct: 571 ------VAMARLLLPDLNRFK--LDTVCKALNISLEGHHRAVNDAEATAEIWVEFIKRLK 622

Query: 145 KSGVNGI 151
             G+N +
Sbjct: 623 AKGINKL 629


>gi|325676160|ref|ZP_08155841.1| oxidoreductase [Rhodococcus equi ATCC 33707]
 gi|325553070|gb|EGD22751.1| oxidoreductase [Rhodococcus equi ATCC 33707]
          Length = 399

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 26/213 (12%), Positives = 66/213 (30%), Gaps = 44/213 (20%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            +AA+   + G++ + ++ G          P     + ++G  L     IV +   A+ +
Sbjct: 151 ADAARFAIEGGFDAVEIHFGHNYFASSFLSPKLNKRKDNYGGSLENRARIVRETARAVRE 210

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIK----------------------------- 144
           A+   + V  ++ +DD +P     +    +                              
Sbjct: 211 AVGDRIAVLAKLNMDDGVPGGFWVDEAIQVAQWLEADGSLDALELTMGSSLLNPMYLFKG 270

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-----YEIKKENPDLFIGLNGGLED 199
            + V        + +  G+       I    Y+ +         +    + + L GG+ D
Sbjct: 271 DAPVRDFANAMPQPVKLGVQLVGKAFIKTYPYEPLFMLEEARQIRAAVKMPLVLLGGVTD 330

Query: 200 MSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +     +    + V + RA  +   ++  +  
Sbjct: 331 KAGMDTAMDEGFEFVAMARALLREPDLINRIQA 363


>gi|289672920|ref|ZP_06493810.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           syringae FF5]
          Length = 97

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 183 KKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAM 225
           ++  PD+ +  NGGL D  +A ++L    D + +G+ A  N  +
Sbjct: 19  RRYAPDVTLIANGGLHDPQKAEQVLRDGADIIAVGKGALANPDL 62


>gi|332142466|ref|YP_004428204.1| 2,4-dienoyl-CoA reductase [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552488|gb|AEA99206.1| 2,4-dienoyl-CoA reductase [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 680

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 20/137 (14%), Positives = 46/137 (33%), Gaps = 11/137 (8%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVN 149
           G  L     +  + +  + + +     +  R+ + D +   A  +    L K I+K+G  
Sbjct: 194 GGSLENRARLALEIVKGVREKVGTNFIIIYRLSMLDLVEGGAKWDEVVYLAKEIEKAGAT 253

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP 208
            I  +      +   P  +  +P   +  +   +KKE     +  N  +     A  +L 
Sbjct: 254 LI--NTGIGWHEARVPTISTSVPRAAFTWITQRMKKEVSIPLVTTNR-INTPEVAESVLA 310

Query: 209 SVDGVMIGRAAYKNSAM 225
                M+   +     +
Sbjct: 311 EGHADMV---SMARPFL 324


>gi|329998043|ref|ZP_08302987.1| 2,4-dienoyl-CoA reductase [Klebsiella sp. MS 92-3]
 gi|328538829|gb|EGF64899.1| 2,4-dienoyl-CoA reductase [Klebsiella sp. MS 92-3]
          Length = 532

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 2   DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 50

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L K+I+ +G     I+ 
Sbjct: 51  RMRFAVEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAKAIEAAGAT--IINT 108

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 109 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 167

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 168 V---SMARPFL 175


>gi|94967760|ref|YP_589808.1| dihydroorotate dehydrogenase 2 [Candidatus Koribacter versatilis
           Ellin345]
 gi|94549810|gb|ABF39734.1| dihydroorotate dehydrogenase [Candidatus Koribacter versatilis
           Ellin345]
          Length = 334

 Score = 41.0 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 63/191 (32%), Gaps = 56/191 (29%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV--------GDCIAAMCKALSI 117
           A+++E  G + I LN+               +  +PD+          + +  +  ++ I
Sbjct: 121 ARLMEQAGADAIELNI-------------YYVPTDPDLSGSTVEHMHAELVKVVKDSVKI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN---- 173
           PV VK            A  NL K +  +G N + I  R    +     +  ++      
Sbjct: 168 PVAVKLGPQFS------AFANLAKQLDHAGANSLVIFNR--FYQPDFDLEQLEVTPNLVL 219

Query: 174 ---------LDYDIVYEIKKENPDLF--IGLNGGLEDMSQALKILPSVDGVMIG-RAAYK 221
                    + +  +         +   I + GG+      +K       +M G R A  
Sbjct: 220 SRSNELKLRIHWAAI-----LFGKITADIAITGGVHTPEDIIK------SMMAGARVAMT 268

Query: 222 NSAMLTTVDEY 232
            SA+L    +Y
Sbjct: 269 TSALLEQGVDY 279


>gi|326429037|gb|EGD74607.1| 2,4-dienoyl-CoA reductase FadH2 [Salpingoeca sp. ATCC 50818]
          Length = 519

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  M + L     +  R+     VD       +  L K ++++GV    ++      +
Sbjct: 203 EIVRRMRQRLGEDFIIIFRLSMLDLVDKGSTWDEIVTLAKELERAGVT--ILNTGIGWHE 260

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   +  V  ++K E     + +N  +     A ++L     D V + R 
Sbjct: 261 ARIPTIAPMVPRAAFTWVTQKLKSEVSIPLVTVNR-INTPDVAERVLADGHADMVSMARP 319

Query: 219 AYKNS 223
              + 
Sbjct: 320 LLADP 324


>gi|301794382|emb|CBW36813.1| putative N-acetylmannosamine-6-phosphate 2-epimerase [Streptococcus
           pneumoniae INV104]
          Length = 228

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 9/104 (8%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K +      + A++     K   +SGV+ +        L G +P    K  N D+++V 
Sbjct: 122 IKVKYPNQLLMAAISTFEEGKVAAESGVDFV-----GTTLSGYTPYS-PKKDNPDFELVE 175

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
            + KE  D+ +   G +    QA K+L      V++G  A    
Sbjct: 176 RLVKEL-DVPVIAEGRISTPEQARKMLDLGAYAVVVG-GAITRP 217


>gi|223982644|ref|ZP_03632877.1| hypothetical protein HOLDEFILI_00151 [Holdemania filiformis DSM
           12042]
 gi|223965394|gb|EEF69673.1| hypothetical protein HOLDEFILI_00151 [Holdemania filiformis DSM
           12042]
          Length = 234

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 22/106 (20%), Positives = 45/106 (42%), Gaps = 10/106 (9%)

Query: 122 KCRIGVDDQIPAVALRNL--VKSIKKSGVNGIWIHARKAILKGLSPKD-NRKIPNLDYDI 178
           + +    DQ+    +  +   +   ++G + I        L G +    +R     D+D+
Sbjct: 122 EIKETYPDQVVMADIATINDARHSVEAGADII-----STTLSGYTEDSLDRYALGTDFDL 176

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           + +I+KE P++FI   G +    +A K      D +++G  A  N 
Sbjct: 177 IEQIRKEFPEVFINAEGRIWTREEAKKAFECGADVIVVGT-AITNP 221


>gi|52840986|ref|YP_094785.1| imidazole glycerol phosphate synthase, cyclase subunit HisF
           [Legionella pneumophila subsp. pneumophila str.
           Philadelphia 1]
 gi|52628097|gb|AAU26838.1| imidazole glycerol phosphate synthase, cyclase subunit HisF
           [Legionella pneumophila subsp. pneumophila str.
           Philadelphia 1]
          Length = 254

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 15/135 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +    G + +      A L G +          +   + +   EN  + I + GG+
Sbjct: 35  EYAMAYYAQGADELIYMDTVASLYGRN----------NLSEIVKTTAENVFIPITVGGGI 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A ++L    D V I  AA KN  +++ +   F +     S    R     W    
Sbjct: 85  RSVDDAKQLLRCGADKVAINTAATKNPTLISDIARRFGSQCVVLSIEAKRTVNGRW---- 140

Query: 257 ASMTDYAARHLHSGG 271
             MTD    H     
Sbjct: 141 EVMTDNGREHTGMDV 155


>gi|145295202|ref|YP_001138023.1| hypothetical protein cgR_1143 [Corynebacterium glutamicum R]
 gi|140845122|dbj|BAF54121.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 254

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 52/130 (40%), Gaps = 11/130 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A +VE+ G++ + +    P A     S G   M   D +   +  +  A+SIPV+V    
Sbjct: 32  AGLVEEAGFSGLTIGSH-PVADATGSSDGEN-MNFADYMA-VVKKITSAVSIPVSVDVES 88

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G       ++  +L+  I ++G  GI +     ++     +      + DY        +
Sbjct: 89  GY-----GLSPADLIAQILEAGAVGINVE---DVVHSEGKRVREAQEHADYIAAARQTAD 140

Query: 186 NPDLFIGLNG 195
              + + +NG
Sbjct: 141 VAGVDVVING 150


>gi|111020909|ref|YP_703881.1| NADPH dehydrogenase [Rhodococcus jostii RHA1]
 gi|110820439|gb|ABG95723.1| NADPH dehydrogenase [Rhodococcus jostii RHA1]
          Length = 351

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 13/78 (16%)

Query: 190 FIGLN---GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
            + +N   G +    +AL IL     D V++GR A  N  ++    E          P+ 
Sbjct: 277 PVLINSGFGAVTTRDEALAILDDGHADAVVVGRPAIANPDLVRRWQEDL--------PLN 328

Query: 245 TRVDKDFWRKISASMTDY 262
           T   + F+ + +   TDY
Sbjct: 329 TPDPETFYSEGAKGYTDY 346


>gi|84391747|ref|ZP_00991649.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           splendidus 12B01]
 gi|86147089|ref|ZP_01065406.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio sp.
           MED222]
 gi|84376460|gb|EAP93339.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           splendidus 12B01]
 gi|85835154|gb|EAQ53295.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio sp.
           MED222]
          Length = 257

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVKRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|328866121|gb|EGG14507.1| NADH:flavin oxidoreductase/NADH oxidase domain-containing protein
           [Dictyostelium fasciculatum]
          Length = 399

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 64/189 (33%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA    + G++ I ++            P++ +   S+G         + + IAA+ 
Sbjct: 197 FRDAAARALEAGFDMIEIHGAHGYLITSFLSPTSNLRTDSYGGSFENRCRFLFEIIAAIR 256

Query: 113 KA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
                  P++V+      V+D         + +  +   V+     +      G S K  
Sbjct: 257 TVWPTEKPLSVRLSAEEWVEDGWTIDDTVKICQRFQDMDVDIFDCSSG-----GNSLKQK 311

Query: 169 RKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
             + P     + +++K++   L I   G +   S+    L     D +   R   +N   
Sbjct: 312 INVYPGYQIPLAHKVKQQTTQLVIAAVGLINTGSEMESTLQQGRADLIFNARGFLRNPHF 371

Query: 226 LTTVDEYFS 234
              + E  +
Sbjct: 372 AYDLAEQLN 380


>gi|302392030|ref|YP_003827850.1| methionine synthase [Acetohalobium arabaticum DSM 5501]
 gi|302204107|gb|ADL12785.1| Methionine synthase [Acetohalobium arabaticum DSM 5501]
          Length = 265

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 85/261 (32%), Gaps = 61/261 (23%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD-CIAAMCKALS 116
           D   + + AK  E+ G + I++N G              L+       +  +  + + + 
Sbjct: 23  DTEFIQDLAKKQEEAGADYIDVNCG-------------TLIDEEQEALEWLVNTVQEVVD 69

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +P+ +      D   P    R L              H  KA++  ++ ++ R    L  
Sbjct: 70  VPLCI------DTPDPKAMDRALAA------------HDGKALVNSITAEEERFNETL-- 109

Query: 177 DIVYEIKKENPDLFIGLNG---GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           +I+ +   +   L +   G   G+ED ++  K L     D  M              +D+
Sbjct: 110 EIIQKHDAQVVALVMDDGGMPDGIEDRTRVGKKLIEDLTDAGM-------------DMDD 156

Query: 232 YFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSR 291
            + +P+         V +     I    ++Y   H+  G         +  + HG P  +
Sbjct: 157 IYVDPIIQPIGTDQEVGQHILEAIDEITSEYEDVHITCG---------LSNISHGLPQRK 207

Query: 292 RCRHILTVEAGASTATHHIIE 312
                    A A      II+
Sbjct: 208 LLNRTFVTLAMAKGMDSAIID 228


>gi|218710001|ref|YP_002417622.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           splendidus LGP32]
 gi|254801228|sp|B7VGZ7|HIS6_VIBSL RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|218323020|emb|CAV19197.1| Imidazole glycerol phosphate synthase subunit hisF1 [Vibrio
           splendidus LGP32]
          Length = 257

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVKRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|254286922|ref|ZP_04961874.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae AM-19226]
 gi|150423072|gb|EDN15021.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae AM-19226]
          Length = 666

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ + +     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIRETVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|153801831|ref|ZP_01956417.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MZO-3]
 gi|124122603|gb|EAY41346.1| 2,4-dienoyl-CoA reductase [Vibrio cholerae MZO-3]
          Length = 666

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ + +     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIRETVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|229023538|ref|ZP_04180034.1| NADPH dehydrogenase [Bacillus cereus AH1272]
 gi|228737806|gb|EEL88306.1| NADPH dehydrogenase [Bacillus cereus AH1272]
          Length = 319

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHVNIATGAVGLITTGSQAEQILKTN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|218903186|ref|YP_002451020.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus AH820]
 gi|254766767|sp|B7JKM7|NAMA_BACC0 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|218539454|gb|ACK91852.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus AH820]
          Length = 345

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|126665535|ref|ZP_01736517.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Marinobacter sp. ELB17]
 gi|126630163|gb|EBA00779.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Marinobacter sp. ELB17]
          Length = 366

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 28/178 (15%), Positives = 58/178 (32%), Gaps = 29/178 (16%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCR--------IGVDDQIPAVALRNLVKSIK 144
           +G  L     IV + I A+ +A+    T+  R                    R + ++++
Sbjct: 198 YGGNLENRLRIVVETIKAVREAVGNDFTLGIRLSQVTVTDPDYQFPEGEAGFRQIAEAVR 257

Query: 145 KSGVNGIW---IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL--ED 199
            +G + +     H R+A     +              + ++  E  +L + +NGG+   +
Sbjct: 258 DAGADFVHTTDGHVRRAPFIEGT------------KTLADVVAEVDNLELIINGGIDETN 305

Query: 200 MSQALKILPSVDGVMIGRAAYKNSAM---LTTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
                   P    + + + A  N      L    E          P  T  ++  WR+
Sbjct: 306 YQDFAADYPEAL-LAVAKKALANPDFVQRLKDGKEIDDMDFAMLQPKATIPNELAWRR 362


>gi|85703444|ref|ZP_01034548.1| FMN-dependent alpha-hydroxy acid dehydrogenase family protein
           [Roseovarius sp. 217]
 gi|85672372|gb|EAQ27229.1| FMN-dependent alpha-hydroxy acid dehydrogenase family protein
           [Roseovarius sp. 217]
          Length = 382

 Score = 41.0 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 29/130 (22%), Positives = 49/130 (37%), Gaps = 22/130 (16%)

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G  L  +PD   D +  +  A   P+ VK  +  DD            +++K+GV+
Sbjct: 227 NKHAGYLLRTSPDW--DYLRWLRDAWDGPLVVKGVLRGDD----------AAALEKAGVD 274

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILP 208
            IWI          +P     +P +         +    L + ++GG+E  +     I  
Sbjct: 275 AIWISNHAGRQFDAAPATIEALPEV---------RAATTLPVIMDGGIEGGLDVLRAIAL 325

Query: 209 SVDGVMIGRA 218
             D VM+GR 
Sbjct: 326 GADFVMLGRG 335


>gi|222481103|ref|YP_002567340.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Halorubrum lacusprofundi ATCC 49239]
 gi|222454005|gb|ACM58270.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Halorubrum lacusprofundi ATCC 49239]
          Length = 246

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 17/96 (17%), Positives = 40/96 (41%), Gaps = 11/96 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGG 196
              +   ++G   + +       +G           ++ D +  + +  PD + + L GG
Sbjct: 39  EAAERWIEAGAETLHLVDLDGAFEG---------ERVNADAIEAVVENVPDEIGLQLGGG 89

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           +     A ++L   +D V++G AA +   ++  +DE
Sbjct: 90  IRTAEGARELLDLGLDRVILGTAAVETPEIVAEIDE 125


>gi|228933362|ref|ZP_04096217.1| NADPH dehydrogenase [Bacillus thuringiensis serovar andalousiensis
           BGSC 4AW1]
 gi|228945676|ref|ZP_04108023.1| NADPH dehydrogenase [Bacillus thuringiensis serovar monterrey BGSC
           4AJ1]
 gi|228813897|gb|EEM60171.1| NADPH dehydrogenase [Bacillus thuringiensis serovar monterrey BGSC
           4AJ1]
 gi|228826318|gb|EEM72096.1| NADPH dehydrogenase [Bacillus thuringiensis serovar andalousiensis
           BGSC 4AW1]
          Length = 319

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|170727285|ref|YP_001761311.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella woodyi ATCC
           51908]
 gi|169812632|gb|ACA87216.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella woodyi ATCC
           51908]
          Length = 672

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 25/179 (13%), Positives = 51/179 (28%), Gaps = 19/179 (10%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V  A   +  GY+ + +            C         +G        +  + +   
Sbjct: 145 DFVNCALNSQAAGYDGVEIMGSEGYFINQFICKRTNHRNDRWGGSYQNRIRLALEIVRRT 204

Query: 112 CKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A+     +  R+     V+D      +  L K I+  G     I+      +   P  
Sbjct: 205 REAVGKEFIIIYRLSMLDLVEDGSTWQEVVELAKGIEAVGAT--IINTGIGWHEARVPTI 262

Query: 168 NRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +P     ++   +K+E        N  +     A  IL     D + + R    + 
Sbjct: 263 ATSVPRGAFVEVTKRMKQEVSIPLCTTNR-INTPELAEDILAQGNADIISMARPMLADP 320


>gi|92113468|ref|YP_573396.1| dihydroorotate oxidase A [Chromohalobacter salexigens DSM 3043]
 gi|91796558|gb|ABE58697.1| dihydroorotate oxidase A [Chromohalobacter salexigens DSM 3043]
          Length = 371

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 12/106 (11%)

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--------LKGLSPKDN 168
           +P+ VK    +  +  A+  R+L      + +      AR A+        L GLS +  
Sbjct: 247 VPLAVKIAPDMQAEEVALVARSLADHAVDAVIATNTTIARDAVEGLAHAEELGGLSGRPV 306

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
            +  N    ++ E+++  P L I   GG++    A        D V
Sbjct: 307 FEPSNA---VIRELRRHLPTLPIIGVGGIDSGDAAKAKREAGADLV 349


>gi|5701740|dbj|BAA83083.1| LEDI-5a protein [Lithospermum erythrorhizon]
          Length = 385

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 43/220 (19%), Positives = 73/220 (33%), Gaps = 39/220 (17%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
              V +A+   D G++ I L                 V++    +G  L      V + +
Sbjct: 160 EDFVVSARNAIDAGFDGIELHGAHGYLLEQFL--KDNVNDRTDKYGGSLENRCRFVLELV 217

Query: 109 AAMCKALSI-PVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            A+ K +    V +K     D     D  PA     LV+++ K G   +++H  +  +K 
Sbjct: 218 EAVVKEVGADKVGIKLAPFSDFMEAGDSDPAALGTYLVEALNKYG--LLYLHVLEPRMKT 275

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
               +N+ I  +        +K     F+   G   D     K L     D V+ GR   
Sbjct: 276 TGETNNQSIDPM--------RKAFKGTFMVGGG--YDKDLGEKALEEGRADLVVYGRPFV 325

Query: 221 KNSAMLT--TVDEYFSNP----LTGSSPIKTRVDKDFWRK 254
            N  +     VD   + P         P+    D  F  +
Sbjct: 326 ANPDLPKRFEVDAPLNEPDRNTFFSHDPVVGYTDYPFLEE 365


>gi|229490520|ref|ZP_04384358.1| 2,4-dienoyl-CoA reductase [Rhodococcus erythropolis SK121]
 gi|229322340|gb|EEN88123.1| 2,4-dienoyl-CoA reductase [Rhodococcus erythropolis SK121]
          Length = 643

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 58/160 (36%), Gaps = 17/160 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD---------IVGDCIAAMC 112
             EA+ +    G + + L+ G    R     F + L              +V + I+A+ 
Sbjct: 143 FREASALAVASGMDGVELDAG---PRSILRQFLSGLTNTRQDRYGSDRVALVREVISAVR 199

Query: 113 KALSIPVTVKCRIGVDDQIPAVAL-RNLVKSIKKSG---VNGIWIHARKAILKGLSPKDN 168
           + +     V  R+  D++ P   L  +L   I +     ++ + +             D 
Sbjct: 200 EEVGSDHVVSLRLSCDEEAPWAGLTPDLAIGIAREVSPFLDLLVVVRGGLYSSDRYRPDF 259

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
              PN + D+  EIK     + + + G + D++ A   L 
Sbjct: 260 HCPPNFNLDLCREIKAAL-SIPVVVQGSVVDIADAHAALE 298


>gi|228914647|ref|ZP_04078256.1| NADPH dehydrogenase [Bacillus thuringiensis serovar pulsiensis BGSC
           4CC1]
 gi|228844966|gb|EEM90008.1| NADPH dehydrogenase [Bacillus thuringiensis serovar pulsiensis BGSC
           4CC1]
          Length = 319

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|188592289|ref|YP_001796887.1| fmn oxidoreductase [Cupriavidus taiwanensis LMG 19424]
 gi|170938663|emb|CAP63650.1| putative FMN oxidoreductase [Cupriavidus taiwanensis LMG 19424]
          Length = 411

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 29/220 (13%), Positives = 76/220 (34%), Gaps = 17/220 (7%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------ 82
           A + +  +  N+       + +  Q+    I +    A++ E  G+  + ++        
Sbjct: 118 APSAVSMNLGNMSRHFNTPQAMTQQVIEDVIQRFARTAQLGEQAGFTGVEIHAAHGYLLS 177

Query: 83  ---CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVA 135
               P +     ++G  L     ++ + + A+   +S    V  ++   D       A  
Sbjct: 178 QFLSPLSNQRTDAWGGPLENRARLLFEIVKAVRAGVSPGFAVAVKLNSADFQRGGFTADD 237

Query: 136 LRNLVKSIKKSGVNGIWIHAR---KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            R +VK++ +  V+ + +         ++G +   +       +       +    + + 
Sbjct: 238 ARQVVKTLNELAVDLVELSGGSYEAPAMQGEARDGSTLAREAYFVEFARDIRAVAKMPVM 297

Query: 193 LNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
           + GG+     A +++   VD V IG A   +  +      
Sbjct: 298 VTGGIRRRPVAEQVVRSGVDMVGIGTALAIDPNLPRDWRA 337


>gi|325690495|gb|EGD32498.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK115]
          Length = 240

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K++GV  I +      L+G +          + D++ +IK E   L I + G
Sbjct: 32  VLEQARVFKEAGVTMIHVVDLDGALEGRA---------ANRDLIAQIKAETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN   +    E F 
Sbjct: 82  GIRSLEQIEDYLAVGIDRVIIGSMAVKNPDFVEAALERFG 121


>gi|312138456|ref|YP_004005792.1| oxidoreductase [Rhodococcus equi 103S]
 gi|311887795|emb|CBH47107.1| oxidoreductase [Rhodococcus equi 103S]
          Length = 399

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 26/213 (12%), Positives = 66/213 (30%), Gaps = 44/213 (20%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
            +AA+   + G++ + ++ G          P     + ++G  L     IV +   A+ +
Sbjct: 151 ADAARFAIEGGFDAVEIHFGHNYFASSFLSPKLNKRKDNYGGSLENRARIVRETARAVRE 210

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIK----------------------------- 144
           A+   + V  ++ +DD +P     +    +                              
Sbjct: 211 AVGDRIAVLAKLNMDDGVPGGFWVDEAIQVAQWLEADGSLDALELTMGSSLLNPMYLFKG 270

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-----YEIKKENPDLFIGLNGGLED 199
            + V        + +  G+       I    Y+ +         +    + + L GG+ D
Sbjct: 271 DAPVRDFANAMPQPVKLGVQLVGKAFIKAYPYEPLFMLEEARQIRAAVKMPLVLLGGVTD 330

Query: 200 MSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +     +    + V + RA  +   ++  +  
Sbjct: 331 KAGMDTAMDEGFEFVAMARALLREPDLINRIQA 363


>gi|297537385|ref|YP_003673154.1| NADH:flavin oxidoreductase/NADH oxidase [Methylotenera sp. 301]
 gi|297256732|gb|ADI28577.1| NADH:flavin oxidoreductase/NADH oxidase [Methylotenera sp. 301]
          Length = 368

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 25/181 (13%), Positives = 59/181 (32%), Gaps = 25/181 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AA   ++ G+  + ++       + +             FG           + +A
Sbjct: 159 DFVAAALRAKEAGFEWLEMHFA--HGYLAQSFTSTHSNHRTDEFGGSFQNRTRFTRETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLS 164
           A+      ++P+T +  +   D      +   ++ +K+    G++ + +     I     
Sbjct: 217 AVRNVWPDNLPLTARFGVLEFDGKDEETMSESIQLVKEWRQLGLDMLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P  N          + +  +    + +    G      A + +    +D  MIGRA  +N
Sbjct: 272 PDTNIPWGPAFMAPIAQRVRNEAQIPVSSAWGFGTPKLADQAIRNEQLDLAMIGRAHLEN 331

Query: 223 S 223
            
Sbjct: 332 P 332


>gi|189348468|ref|YP_001941664.1| Old Yellow Enzyme family NADH:flavin oxidoreductase [Burkholderia
           multivorans ATCC 17616]
 gi|189338606|dbj|BAG47674.1| Old Yellow Enzyme family NADH:flavin oxidoreductase [Burkholderia
           multivorans ATCC 17616]
          Length = 374

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 31/209 (14%), Positives = 64/209 (30%), Gaps = 42/209 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
               +AA+   D G++ + L   C +  +               +G  L      + +  
Sbjct: 163 ELYAQAARNALDAGFDGVEL--HCANGYLVNQFISAHTNQRDDEYGGSLQNRLRFLREIT 220

Query: 109 AAMCKALSI-PVTV------------KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            A+   +    V V            +  +G+ ++ P       VK +++ G+  +    
Sbjct: 221 LAVAGVVGKERVGVRFAPLFATTDEDRVYLGLVEEDPHQTYIEAVKILEEVGIAYLS--- 277

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
                  L+  D    P L       ++K      I    G     +A +++     D +
Sbjct: 278 -------LAEADWENAPELPETFREAVRKTFSGKIIYA--GKYTAERANRVIKAGWADLI 328

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             GR    N  +   +    + PL    P
Sbjct: 329 AFGRPFIANPDLPARIAN--NWPLNPVDP 355


>gi|196036683|ref|ZP_03104076.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus W]
 gi|195990752|gb|EDX54727.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus W]
          Length = 345

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|167565241|ref|ZP_02358157.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia oklahomensis
           EO147]
 gi|167572342|ref|ZP_02365216.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia oklahomensis
           C6786]
          Length = 687

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRADEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHAQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLANGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|78187544|ref|YP_375587.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium luteolum
           DSM 273]
 gi|91206937|sp|Q3B287|HIS4_PELLD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|78167446|gb|ABB24544.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium luteolum
           DSM 273]
          Length = 256

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 11/94 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++    +K     + I    A L G           ++++ + +I +E  D+ + + GG
Sbjct: 33  LDMAIIWRKQNAKMLHIVDLDAALTGEM---------VNFERIRQIVEEL-DIPVQVGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           +       + L   V  V+IG AA  N  ++  +
Sbjct: 83  IRSADDVKRYLDMGVGRVVIGSAAVTNPELVREL 116


>gi|229017362|ref|ZP_04174265.1| NADPH dehydrogenase [Bacillus cereus AH1273]
 gi|228743925|gb|EEL94024.1| NADPH dehydrogenase [Bacillus cereus AH1273]
          Length = 289

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 130 YGGSPENRYRFLREIIDSVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 189

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KE+ ++  G  G +   SQA +IL   
Sbjct: 190 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKEHVNIATGAVGLITTGSQAEQILKTN 243

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 244 EADLIFIGRELLRNPY 259


>gi|196039790|ref|ZP_03107094.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Bacillus
           cereus NVH0597-99]
 gi|196029493|gb|EDX68096.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Bacillus
           cereus NVH0597-99]
          Length = 345

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILTNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|296158433|ref|ZP_06841264.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
 gi|295891377|gb|EFG71164.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
          Length = 681

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 16/147 (10%), Positives = 44/147 (29%), Gaps = 8/147 (5%)

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRN 138
           CP       ++G  +     +  + +  +         V  RI + D             
Sbjct: 174 CPRTNRRTDAYGGSIENRMRLAREIVERVRAVCGERFIVMYRISLIDLVEGGNTWDETVQ 233

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + ++++ +GV     +      +   P     +P   +  +         + + ++  + 
Sbjct: 234 VARALETAGVTMF--NTGIGWHEARVPTIVTSVPRAAFAELSARLTAAVRVPVIVSNRIN 291

Query: 199 DMSQALKILPSVDG--VMIGRAAYKNS 223
               A ++L    G  V + R    + 
Sbjct: 292 TPEVAEELLAQGAGDLVSMARPLLADP 318


>gi|148980436|ref|ZP_01816058.1| imidazole glycerol phosphate synthase subunit HisF [Vibrionales
           bacterium SWAT-3]
 gi|145961239|gb|EDK26552.1| imidazole glycerol phosphate synthase subunit HisF [Vibrionales
           bacterium SWAT-3]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVKRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|257043984|gb|ACV33308.1| Kemp eliminase KE07 [synthetic construct]
          Length = 263

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                     RVD +F 
Sbjct: 123 QAVVVYIAAKRVDGEFM 139


>gi|254383108|ref|ZP_04998462.1| inosine 5' monophosphate dehydrogenase [Streptomyces sp. Mg1]
 gi|194342007|gb|EDX22973.1| inosine 5' monophosphate dehydrogenase [Streptomyces sp. Mg1]
          Length = 502

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 25/152 (16%), Positives = 56/152 (36%), Gaps = 26/152 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ + + G + I          V + + G     +  +VGD +A +    S+ V      
Sbjct: 242 AQALIEAGADFI----------VVDTAHG-----HSRLVGDMVAKIKSNSSVDVIGG--- 283

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
                   +A R+  +++  +G +GI +      +          +P +       +  +
Sbjct: 284 -------NIATRDGAQALIDAGCDGIKVGVGPGSICTTRVVAGIGVPQVTAIYEASLAAK 336

Query: 186 NPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
              + +  +GGL+     A  ++   D VM+G
Sbjct: 337 AAGVPVIGDGGLQYSGDIAKALVAGADTVMLG 368


>gi|149907854|ref|ZP_01896522.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Moritella sp. PE36]
 gi|149808860|gb|EDM68791.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Moritella sp. PE36]
          Length = 676

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 27/208 (12%), Positives = 68/208 (32%), Gaps = 43/208 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDI 103
            K +E+A I +  G++ + ++       VHEG                 +G         
Sbjct: 158 HKFIESAVIAQKSGFDGVEIHA------VHEGYLLDQFTMEFFNKRTDQYGGSFENRYRF 211

Query: 104 VGDCIAAMCKALSI--PVTVKCRIG----------------VDDQIPAVALRNLVKSIKK 145
             + +  +        PV+++  +                 V+            K ++ 
Sbjct: 212 AVEIVKGIKAVCGKDYPVSLRYSVKSNMKSFGEGILPGEDAVEVGRDMEEGLQAAKYLQD 271

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           +G + + + A        +   N   P +       +  E  D+ + ++G +E+   A +
Sbjct: 272 AGFDALNVDAGSYDSWYWNHPPNYFKPGMYKPYCKAV-SEVVDIPVLMSGRMENPDMASR 330

Query: 206 IL--PSVDGVMIGRAAYKNSAMLTTVDE 231
            +   + DG+ +GR    +  ++  +  
Sbjct: 331 AVIEHAADGISMGRPLLADPDVVNKIRR 358


>gi|332305812|ref|YP_004433663.1| imidazoleglycerol phosphate synthase, cyclase subunit [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332173141|gb|AEE22395.1| imidazoleglycerol phosphate synthase, cyclase subunit [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 19/116 (16%), Positives = 41/116 (35%), Gaps = 15/116 (12%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R    +      +  L +   + G + +            +  D R +       + 
Sbjct: 21  VKFR----NHETIGEIVPLAELYAQQGADELV------FYDITASSDQRVVDKSWVTRIA 70

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++     D+   + GG++ +  A +IL    D + I   A  N A++  + + F  
Sbjct: 71  QVI----DIPFCVAGGIKSVEDAGRILEMGADKISINSPALANPALIRELHDTFGQ 122


>gi|328473124|gb|EGF43972.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           parahaemolyticus 10329]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|170292384|pdb|2RKX|A Chain A, The 3d Structure Of Chain D, Cyclase Subunit Of
           Imidazoleglycerol_evolvedcerolphosphate Synthase
          Length = 255

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                     RVD +F 
Sbjct: 123 QAVVVYIAAKRVDGEFM 139


>gi|48478404|ref|YP_024110.1| histidine biosynthesis protein HisF [Picrophilus torridus DSM 9790]
 gi|48431052|gb|AAT43917.1| histidine biosynthesis protein HisF [Picrophilus torridus DSM 9790]
          Length = 249

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 35/176 (19%), Positives = 66/176 (37%), Gaps = 24/176 (13%)

Query: 103 IVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +    IAA+  +   +   VK    +D +     + N V   +  G + I        L 
Sbjct: 2   LAKRIIAALDVRNGRV---VKGVRFMDIKDAGDPVENAV-IYQDQGADEIV------FLD 51

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
             +  + R I     D+V  + +E  ++   + GG+  +  AL +L    D V +   A 
Sbjct: 52  ISATDEKRDIMI---DLVKSVSREL-NIPFTVGGGIRSVKTALNLLREGCDKVFLNTYAI 107

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           +N  ++  +        TGS+ +   VD  +            A  ++SG KL + 
Sbjct: 108 ENPWIIKEISR-----ETGSANLVIAVDAMYNNGYYVYKN---AGRINSGLKLNEW 155


>gi|28897917|ref|NP_797522.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|153838269|ref|ZP_01990936.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus AQ3810]
 gi|260364447|ref|ZP_05777072.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus K5030]
 gi|260877075|ref|ZP_05889430.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus AN-5034]
 gi|260896864|ref|ZP_05905360.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus Peru-466]
 gi|260902413|ref|ZP_05910808.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus AQ4037]
 gi|32363176|sp|Q87QK6|HIS6_VIBPA RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|28806131|dbj|BAC59406.1| imidazoleglycerol-phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149748324|gb|EDM59183.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus AQ3810]
 gi|308086995|gb|EFO36690.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus Peru-466]
 gi|308093927|gb|EFO43622.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus AN-5034]
 gi|308110653|gb|EFO48193.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus AQ4037]
 gi|308114611|gb|EFO52151.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus K5030]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|226362184|ref|YP_002779962.1| oxidoreductase [Rhodococcus opacus B4]
 gi|226240669|dbj|BAH51017.1| putative oxidoreductase [Rhodococcus opacus B4]
          Length = 389

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 28/210 (13%), Positives = 62/210 (29%), Gaps = 44/210 (20%)

Query: 65  AAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AA+I  + G++ + ++ G          P       S+G  L     +V D    +  A+
Sbjct: 151 AARIAVESGFDAVEIHFGHNYFASAFLSPKLNRRTDSYGGSLENRARVVRDVARTVRDAV 210

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIK-----------------------------KS 146
              V +  ++ +DD +P     +    +                               +
Sbjct: 211 GGRVAILAKLNMDDGVPGGFWLDEAIQVARLLERDGSVDALELTMGSSLLNPMYLFKGDA 270

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-----YEIKKENPDLFIGLNGGLEDMS 201
            V        + +  G+       I    Y  +         +    L + L GG+ D +
Sbjct: 271 PVREFAAAMPQPVRLGVQLVGKSMIHTYPYRDLFMLEHARQIRAAVTLPLVLLGGVTDRA 330

Query: 202 QA-LKILPSVDGVMIGRAAYKNSAMLTTVD 230
                +    + V + RA  +   ++  + 
Sbjct: 331 GMDTAMAEGFEFVAMARALLREPDLVNRIR 360


>gi|158319442|ref|YP_001511949.1| NADH:flavin oxidoreductase/NADH oxidase [Alkaliphilus oremlandii
           OhILAs]
 gi|158139641|gb|ABW17953.1| NADH:flavin oxidoreductase/NADH oxidase [Alkaliphilus oremlandii
           OhILAs]
          Length = 339

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 24/146 (16%), Positives = 50/146 (34%), Gaps = 13/146 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGV 148
           +G  L      + + + A+       + +  R+  +D          L  ++  +K   V
Sbjct: 185 YGGSLENRVRFLKEILEAVRTVWPKELPMILRVSAEDYVAEGNHPEDLAAMINLLKDYEV 244

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + + +   +   +      +IP        EI K   +L     G +     A +IL 
Sbjct: 245 DIVNVSSGAVVPAPIKAYPGYQIP------FSEIIKRETNLPTIGGGLVTTPLMAEEILQ 298

Query: 209 S--VDGVMIGRAAYKNS-AMLTTVDE 231
           +   D + +GR   +N    L    E
Sbjct: 299 NNRADLIFLGRELLRNPYWALHAAKE 324


>gi|78062474|ref|YP_372382.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia sp. 383]
 gi|77970359|gb|ABB11738.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia sp. 383]
          Length = 423

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 28/208 (13%), Positives = 61/208 (29%), Gaps = 43/208 (20%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             +  +AA+   D G++ + +++G          P       ++G           + + 
Sbjct: 164 ADEFAQAARHARDAGFDAVEIHMGHGYLLSQFLSPLYNRRRDAYGGDATRRATFPVEVLR 223

Query: 110 AMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHAR----KAILK 161
            +  A+   + V C+IGV + +     A     + + ++  G + + +            
Sbjct: 224 RVLDAVGRDLAVVCKIGVTEGVRGGGTADDACEIARRLEAEGAHLLVLSGGMNVESVWQL 283

Query: 162 GLSPKDNRKIPNLDYDIVYEI-------------------------KKENPDLFIGLNGG 196
             SP       N D  IV                             +    + +   GG
Sbjct: 284 FGSPLPGEARANADNAIVRTAMALQKLTEPKMGAFREMYFLEHSKKVRAAVRMPLAYLGG 343

Query: 197 LEDM-SQALKILPSVDGVMIGRAAYKNS 223
           +    +  L +    D V + RA     
Sbjct: 344 VRSRGNVELAMREGFDAVALARALVFEP 371


>gi|288817734|ref|YP_003432081.1| imidazole glycerol phosphate synthase subunit HisF [Hydrogenobacter
           thermophilus TK-6]
 gi|288787133|dbj|BAI68880.1| imidazole glycerol phosphate synthase subunit HisF [Hydrogenobacter
           thermophilus TK-6]
 gi|308751333|gb|ADO44816.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Hydrogenobacter thermophilus TK-6]
          Length = 259

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 11/92 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+ ++ G + +      A  +G S         +  D+V  + ++    F    GG+
Sbjct: 34  EVAKAYEEQGADELVFLDISASYEGRS---------IMIDVVRRVAEQVFMPFTVG-GGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTT 228
            D+    K+L    D V I  AA KN  ++  
Sbjct: 84  RDIEDIRKLLLAGADKVSINTAAVKNPGLIRE 115


>gi|217972672|ref|YP_002357423.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS223]
 gi|217497807|gb|ACK46000.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS223]
          Length = 364

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 61/180 (33%), Gaps = 24/180 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +A+  E  G + I ++            P +      +G  L     ++     A+ 
Sbjct: 160 FVSSAQRAERLGLDAIEIHAAHGYLLHQFLSPLSNQRTDKYGGSLENRLSLLLAVFDAIK 219

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +S  + +  RI   D +           L K+++  G + I +        GLS    
Sbjct: 220 AVISPKMALGVRISATDWVEGGWDLAQSLVLAKALESRGCDFIHVSTG-----GLSSLQQ 274

Query: 169 RKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             IP  ++  V   E  K   +  +   G + D ++A  IL     D + + R    +  
Sbjct: 275 --IPVAEHFQVPFAEAIKAEVNTPVIAVGLITDANKAETILAQGQADAIALARTMLYDPH 332


>gi|104780860|ref|YP_607358.1| 2,4-dienoyl-CoA reductase [Pseudomonas entomophila L48]
 gi|95109847|emb|CAK14552.1| 2,4-dienoyl-CoA reductase [Pseudomonas entomophila L48]
          Length = 678

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 18/135 (13%), Positives = 43/135 (31%), Gaps = 8/135 (5%)

Query: 103 IVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
           +  + +  + +A+     I   +     V+       +  L K+I+++G   I  +    
Sbjct: 197 LAVEIVRRVREAVGPNFIIIFRLSMLDLVEGGSTWDEIVVLAKAIEQAGATLI--NTGIG 254

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--G 216
             +   P    K+P   +  V    +    + +     +     A  +L   D  M+   
Sbjct: 255 WHEARIPTIATKVPRAAFSKVTAKLRGAVKIPLITTNRINTPEVAEAVLAEGDADMVSMA 314

Query: 217 RAAYKNSAMLTTVDE 231
           R    +   +    E
Sbjct: 315 RPFLADPDFVNKAAE 329


>gi|325510775|gb|ADZ22411.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Clostridium acetobutylicum EA 2018]
          Length = 664

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 49/150 (32%), Gaps = 19/150 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKS----- 142
           +G  L        + +  +        PVT++        D +  A+     V+      
Sbjct: 198 YGGSLENRLRFAREIVEEIKNRCGEDFPVTLRYSPKSFIKDLRDGALPGEEFVEKGRDLD 257

Query: 143 --IKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DYDIVYEIKKENPDLFIGLNG 195
             ++ + +   + +       G         P +      Y    ++ K+  D+ +   G
Sbjct: 258 EGVEAAKLLVSYGYDALDTDVGSYDSWWWSHPPMYQEKGLYRKYAKLMKDTVDVPVICAG 317

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            ++D   AL+ + +   D + +GR    + 
Sbjct: 318 RMDDPDMALEAVENGTCDVISLGRPLLADP 347


>gi|153873344|ref|ZP_02001956.1| Dihydrouridine synthase, DuS [Beggiatoa sp. PS]
 gi|152070191|gb|EDN68045.1| Dihydrouridine synthase, DuS [Beggiatoa sp. PS]
          Length = 73

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 7/46 (15%), Positives = 16/46 (34%)

Query: 253 RKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILT 298
           R I     +   +       ++   +H+     G P+S   R+ + 
Sbjct: 4   RDILLGHIENLYQFYGEYTGIRMARKHLSWYSKGQPHSATFRYTVN 49


>gi|325830246|ref|ZP_08163703.1| pyridine nucleotide-disulfide oxidoreductase [Eggerthella sp. HGA1]
 gi|325487713|gb|EGC90151.1| pyridine nucleotide-disulfide oxidoreductase [Eggerthella sp. HGA1]
          Length = 686

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 25/156 (16%), Positives = 49/156 (31%), Gaps = 25/156 (16%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCR------IGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
              IV + I  + +A      + CR            I A       ++  ++G   I I
Sbjct: 203 RTRIVREIIEGIREACGPDFVIGCRLNGREFHPTKQGITAEQAAENARAFVEAGAQYISI 262

Query: 154 HA---RKAILKG-------------LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                     +              + P  +       +  V    K+  D+ +   G +
Sbjct: 263 AGYGYGPTPFRYCPDYFPYPEPDPFMEPFMDEYRGKGLWTAVARQIKDAVDVPVITAGRM 322

Query: 198 EDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
            D + A ++L +   D + +GR  + +      VDE
Sbjct: 323 -DENLAERVLEAGDADVIALGRTLWADPWFARKVDE 357


>gi|238896607|ref|YP_002921352.1| 2,4-dieonyl-CoA reductase [Klebsiella pneumoniae NTUH-K2044]
 gi|238548934|dbj|BAH65285.1| 2,4-dieonyl-CoA reductase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
          Length = 673

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 143 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L K+I+ +G     I+ 
Sbjct: 192 RMRFAVEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAKAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|152972026|ref|YP_001337172.1| 2,4-dieonyl-CoA reductase, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|150956875|gb|ABR78905.1| 2,4-dieonyl-CoA reductase, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 673

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 143 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L K+I+ +G     I+ 
Sbjct: 192 RMRFAVEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAKAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|146293387|ref|YP_001183811.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella putrefaciens
           CN-32]
 gi|145565077|gb|ABP76012.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella putrefaciens
           CN-32]
 gi|319426690|gb|ADV54764.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella putrefaciens
           200]
          Length = 368

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 67/192 (34%), Gaps = 25/192 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AAK     G+  + L+       + +             +G         + + I 
Sbjct: 159 DFVTAAKRALAAGFEWLELHFA--HGYLAQSFFSTYANQRSDKYGGSAEGRGRFLLETIK 216

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVAL---RNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +     +P+T +  +   D      L     LVK  K+ G++ + +    +I     
Sbjct: 217 AVREIWPQHLPLTARFGVIEFDDKDEQTLSESIELVKQFKQIGLDMLNV----SICFSTP 272

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
             +    P L   I  +++KE     +  + G++D  QA   +    +D VMIG+A   N
Sbjct: 273 TANIPWRPALLAPIAAQVRKEVG-FPVATSWGMDDPHQANTAIENEQMDLVMIGKAFLAN 331

Query: 223 SAMLTTVDEYFS 234
                   +   
Sbjct: 332 PHWPYQAAQILK 343


>gi|37679540|ref|NP_934149.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           vulnificus YJ016]
 gi|48474340|sp|Q7MLS1|HIS61_VIBVY RecName: Full=Imidazole glycerol phosphate synthase subunit hisF1;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF1; AltName: Full=ImGP
           synthase subunit hisF1; Short=IGPS subunit hisF1
 gi|37198284|dbj|BAC94120.1| imidazoleglycerol-phosphate synthase [Vibrio vulnificus YJ016]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|331698024|ref|YP_004334263.1| NADPH dehydrogenase [Pseudonocardia dioxanivorans CB1190]
 gi|326952713|gb|AEA26410.1| NADPH dehydrogenase [Pseudonocardia dioxanivorans CB1190]
          Length = 748

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 40/123 (32%), Gaps = 9/123 (7%)

Query: 106 DCIAAMCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             + A+  A   P  V V          P      + +++   G + + + + + +    
Sbjct: 571 RVLDAVRAAWDGPLLVRVSAADHAPGGQPIGDAVEIGRALAAHGADAVDVSSGEVVAHER 630

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPS-VDGVMIGRAAYK 221
                     L      E  + + D+ +   GG+     A   +L    D V IGRA   
Sbjct: 631 PNYGRSYQTPL-----AERIRHDADVPVVAVGGISTADDANSIVLAGRADLVAIGRAMLH 685

Query: 222 NSA 224
           + A
Sbjct: 686 DPA 688


>gi|15896613|ref|NP_349962.1| 2-enoate reductase [Clostridium acetobutylicum ATCC 824]
 gi|15026455|gb|AAK81302.1|AE007834_2 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Clostridium acetobutylicum ATCC 824]
          Length = 664

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 20/150 (13%), Positives = 49/150 (32%), Gaps = 19/150 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKS----- 142
           +G  L        + +  +        PVT++        D +  A+     V+      
Sbjct: 198 YGGSLENRLRFAREIVEEIKNRCGEDFPVTLRYSPKSFIKDLRDGALPGEEFVEKGRDLD 257

Query: 143 --IKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DYDIVYEIKKENPDLFIGLNG 195
             ++ + +   + +       G         P +      Y    ++ K+  D+ +   G
Sbjct: 258 EGVEAAKLLVSYGYDALDTDVGSYDSWWWSHPPMYQEKGLYRKYAKLMKDTVDVPVICAG 317

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            ++D   AL+ + +   D + +GR    + 
Sbjct: 318 RMDDPDMALEAVENGTCDVISLGRPLLADP 347


>gi|148980158|ref|ZP_01815909.1| 2,4-dienoyl-CoA reductase [Vibrionales bacterium SWAT-3]
 gi|145961376|gb|EDK26683.1| 2,4-dienoyl-CoA reductase [Vibrionales bacterium SWAT-3]
          Length = 669

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 17/124 (13%), Positives = 46/124 (37%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D +   +       L + ++++GV    I+      +
Sbjct: 199 EIVKSIREAVGDDFIIIFRLSMLDLVEQGSTFEDVVLLAQKLEEAGVT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P    ++P   +  V E  K    + +     +    +A +I+     D V + R  
Sbjct: 257 ARIPTIATQVPRGAFSWVTEKVKPYVSIPVITCNRINTPEEAERIISSGQADMVSMARPF 316

Query: 220 YKNS 223
             + 
Sbjct: 317 LADP 320


>gi|295100162|emb|CBK89251.1| Putative N-acetylmannosamine-6-phosphate epimerase [Eubacterium
           cylindroides T2-87]
          Length = 255

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 21/109 (19%), Positives = 43/109 (39%), Gaps = 14/109 (12%)

Query: 108 IAAMCKALSIPVTV--KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A+ +A+ +P+    K      D++         K++ ++G   I + A   +     P
Sbjct: 56  VKAIHEAVDLPIIGLDKIYYDTMDRVIMTPTIEHAKALWEAGARIIALEATDQLNHLGVP 115

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
             N         ++ EIKKE P+  I     ++ +  A++      D V
Sbjct: 116 TRN---------LIPEIKKELPEAIIFA--DVDTVENAIEAAKLGADFV 153


>gi|188533510|ref|YP_001907307.1| Xenobiotic reductase A [Erwinia tasmaniensis Et1/99]
 gi|188028552|emb|CAO96414.1| Xenobiotic reductase A [Erwinia tasmaniensis Et1/99]
          Length = 370

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 24/138 (17%), Positives = 55/138 (39%), Gaps = 12/138 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSG 147
           +G         + + +AA+ +    ++P+T +  +   D      L     L K ++ +G
Sbjct: 204 YGGSFAGRSRFLLETLAAVREVWPENLPLTARLGVIEYDGRDEETLDESIELTKLMRNNG 263

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           ++ + +     + +   P     +       V E  +    L +  + G+E  + A +++
Sbjct: 264 LDLLNVSIGFTVAETDIPWGPGFLAP-----VSERVRRATGLPVAASWGVEAPAVAERVI 318

Query: 208 --PSVDGVMIGRAAYKNS 223
               +D VMIGRA   + 
Sbjct: 319 AEQQMDLVMIGRAHLADP 336


>gi|124515338|gb|EAY56848.1| NADH-flavin oxidoreductase/NADH oxidase [Leptospirillum rubarum]
 gi|206601640|gb|EDZ38123.1| NADH-flavin oxidoreductase/NADH oxidase [Leptospirillum sp. Group
           II '5-way CG']
          Length = 354

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 26/148 (17%), Positives = 46/148 (31%), Gaps = 10/148 (6%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
           M  P  V   +  +    S+P+ V+      V           L + +K  GV+ I    
Sbjct: 205 MRFPLEVVRSVREVW-PGSLPLWVRISSTDWVPGGWDPEMSVELCRQLKAEGVDVI---- 259

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGV 213
             A   GL+P     +       +    +   DL +   G + D  QA  +L     D V
Sbjct: 260 -DASSGGLAPDAVIPLGPGYQTGIAARIRREADLPVVAVGMITDPVQAEHVLVTGQADLV 318

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            + R   ++              +   +
Sbjct: 319 SLAREMLRDPYWPLHAAHRLGQTVDWPA 346


>gi|219669836|ref|YP_002460271.1| enoyl-(acyl-carrier-protein) reductase II [Desulfitobacterium
           hafniense DCB-2]
 gi|219540096|gb|ACL21835.1| enoyl-(acyl-carrier-protein) reductase II [Desulfitobacterium
           hafniense DCB-2]
          Length = 315

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 53/144 (36%), Gaps = 22/144 (15%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK-----------CRIGVDDQIPA 133
             +V    +G  +ML    V D +  + +   +PV               +      IP 
Sbjct: 59  IKKVTNKPYGVNVMLMSPFVEDVMQVIVEE-RVPVITTGAGNPGKYIPMLKEVGTKIIPV 117

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA   L + ++K+GV+ +       +  G    +   +P     +V ++  +   + +  
Sbjct: 118 VASVALARRLEKAGVDALIAEG---MESGGHIGEISTLP-----LVPQVV-DAVSIPVIA 168

Query: 194 NGGLEDMSQALKILP-SVDGVMIG 216
            GG+ D    +  L    +GV +G
Sbjct: 169 AGGIYDGRGMVAALALGAEGVQMG 192


>gi|313107773|ref|ZP_07793952.1| putative FMN oxidoreductase [Pseudomonas aeruginosa 39016]
 gi|310880454|gb|EFQ39048.1| putative FMN oxidoreductase [Pseudomonas aeruginosa 39016]
          Length = 411

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 24/187 (12%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAVLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   G++ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGIDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|300715115|ref|YP_003739918.1| 2,4-dieonyl-coa reductase [Erwinia billingiae Eb661]
 gi|299060951|emb|CAX58058.1| 2,4-dieonyl-coa reductase [Erwinia billingiae Eb661]
          Length = 669

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 20/189 (10%), Positives = 54/189 (28%), Gaps = 40/189 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------LN 100
                A + ++ GY+ + +                 L+                      
Sbjct: 142 DFAHCAALAKEAGYDGVEI-----------MGSEGYLINQFLAARTNQRQDDWGGDDSRR 190

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR----NLVKSIKKSGVNGIWIHAR 156
                + + A+ +A+     +  R+ + D +           L K+I+++G + I  +  
Sbjct: 191 MRFAVEIVKAVREAVGREFIIIFRLSMLDLVEQGNTLPQSIRLAKAIERAGASLI--NTG 248

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
               +   P     +P   +  V    +++  + +     +     A  +L      MI 
Sbjct: 249 IGWHEARIPTIATSVPRGAFGWVTRELRQHLSIPLIATNRINHPDVAQALLDEGCADMI- 307

Query: 217 RAAYKNSAM 225
             +     +
Sbjct: 308 --SMARPFL 314


>gi|148643689|ref|YP_001274202.1| IMP dehydrogenase/GMP reductase, GuaB [Methanobrevibacter smithii
           ATCC 35061]
 gi|222444828|ref|ZP_03607343.1| hypothetical protein METSMIALI_00441 [Methanobrevibacter smithii
           DSM 2375]
 gi|261350599|ref|ZP_05976016.1| inosine-5'-monophosphate dehydrogenase [Methanobrevibacter smithii
           DSM 2374]
 gi|148552706|gb|ABQ87834.1| IMP dehydrogenase/GMP reductase, GuaB [Methanobrevibacter smithii
           ATCC 35061]
 gi|222434393|gb|EEE41558.1| hypothetical protein METSMIALI_00441 [Methanobrevibacter smithii
           DSM 2375]
 gi|288861382|gb|EFC93680.1| inosine-5'-monophosphate dehydrogenase [Methanobrevibacter smithii
           DSM 2374]
          Length = 493

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 3/99 (3%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-DYDI 178
           T+K  I  D  +  +A     + +   GV+G+ +      +          +P L     
Sbjct: 263 TIKDNIDADLCVGNIATAEAAEDLASMGVDGLKVGIGPGSMCTTRIVAGVGVPQLTAISE 322

Query: 179 VYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           V ++ KE   + +  +GG+      A  I    D VM+G
Sbjct: 323 VADVAKEYG-IPVIADGGIRYSGDIAKAIGAGADAVMLG 360


>gi|224586475|ref|YP_002640364.1| inosine-5'-monophosphate dehydrogenase [Borrelia valaisiana VS116]
 gi|224496968|gb|ACN52604.1| inosine-5'-monophosphate dehydrogenase [Borrelia valaisiana VS116]
          Length = 404

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 31/183 (16%), Positives = 61/183 (33%), Gaps = 38/183 (20%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           +  ++ + A+  EDF     +LN             GA + ++ D        +   + +
Sbjct: 117 EAPEIYKNAEYAEDFSNVCKDLNG--------RLRVGAAVSIDVDTTERVEELVKAHVDL 168

Query: 118 PV----------------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ 154
            V                T+K +   +D     +  +     +  +G + + +       
Sbjct: 169 LVIDSAHGHSTRILELVKTIKNKYPNLDLIAGNIVTKEAALDLINAGADCLKVGIGPGSI 228

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGV 213
               I+ G+       I +     VYE+ K N ++ I  +GG+         I    D V
Sbjct: 229 CTTRIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSV 282

Query: 214 MIG 216
           MIG
Sbjct: 283 MIG 285


>gi|126174750|ref|YP_001050899.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS155]
 gi|125997955|gb|ABN62030.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS155]
          Length = 368

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 52/128 (40%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + + +AA+ +     +P+T +  +   D      L     LVK  K++G++ + +    +
Sbjct: 211 LLETVAAVREVWPQHLPLTARFGVIEFDHKDEETLTESIALVKQFKQAGLDMLNV----S 266

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
           I       +    P     I   +++E     +  + G+++   A   +    +D VMIG
Sbjct: 267 ICFSTPTANIPWSPAFLAPIAARVRQEVG-FPVATSWGMDNPHHANAAIEDEQMDLVMIG 325

Query: 217 RAAYKNSA 224
           +A   N  
Sbjct: 326 KAFLANPH 333


>gi|116050701|ref|YP_790479.1| putative FMN oxidoreductase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|115585922|gb|ABJ11937.1| putative FMN oxidoreductase [Pseudomonas aeruginosa UCBPP-PA14]
          Length = 411

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 24/187 (12%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAVLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   G++ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGIDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|94311140|ref|YP_584350.1| salicylyl-CoA 5-hydroxylase [Cupriavidus metallidurans CH34]
 gi|93354992|gb|ABF09081.1| 2-aminobenzoyl-CoA monooxygenase/reductase [Cupriavidus
           metallidurans CH34]
          Length = 791

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 61/201 (30%), Gaps = 29/201 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
              V  A+   + G++ + L   C           P       ++G  L   +  P  V 
Sbjct: 574 DDFVANARRAAEAGFDWLEL--HCAHGYLLSSFISPLTNTRTDAYGGLLANRLRYPLEVF 631

Query: 106 DCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKG 162
             + A+      P++V+      V+  I A     + ++ K +G + I     + +  + 
Sbjct: 632 AAVRAVW-PQDKPMSVRISAHDWVEGGITADDAVEIARAFKAAGADMIDCSSGQVSPDQT 690

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
                  + P  D      I+ E   +     G + +      I+ +   D   I R   
Sbjct: 691 PVYGRMYQTPFAD-----RIRNEAG-IPTIAVGAIFEADHVDSIVAAGRADLCAIARPHL 744

Query: 221 KNS-AMLTTVDEYFSNPLTGS 240
            +    L          +T  
Sbjct: 745 ADPAWTLHEAARLGYRDVTWP 765


>gi|323494983|ref|ZP_08100074.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           brasiliensis LMG 20546]
 gi|323310778|gb|EGA63951.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           brasiliensis LMG 20546]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVKRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|269124133|ref|YP_003306710.1| NADH:flavin oxidoreductase/NADH oxidase [Streptobacillus
           moniliformis DSM 12112]
 gi|268315459|gb|ACZ01833.1| NADH:flavin oxidoreductase/NADH oxidase [Streptobacillus
           moniliformis DSM 12112]
          Length = 347

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 79/208 (37%), Gaps = 33/208 (15%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMCK 113
           AAK  +  GY+ + L+       +               +G  L     ++G+ +  + K
Sbjct: 146 AAKRAQVAGYDYLELHAA--HGYLINQFLSSFSNNREDEYGGNLKNRAKLLGEILNEVRK 203

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSI--KKSGVNGIWIHARKAILKG-LSPKDNRK 170
                + ++       +   +   +L K +   K  ++ I + +   + +G LS     +
Sbjct: 204 EFKGVIGIRISAYEWAEGGYLP-EDLAKVLIDFKHNIDIIHVSSGGTVNEGILSFYPGYQ 262

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLED---MSQALKILPSVDGVMIGRAAYKNS-AML 226
           +         +  KE   L +   G ++       A++ L  +D +  GRA  +N   + 
Sbjct: 263 LSFA------KTIKEIVGLPVIAVGQIDSFDLAEFAIRDL-GIDLIAAGRALLRNPNWI- 314

Query: 227 TTVDEYFSNPLTGSSPIKTRVDKDFWRK 254
             +DE F N +  SS  +  + + ++R+
Sbjct: 315 --IDEAFKNNIDISS--RKSIKRAYYRE 338


>gi|209695597|ref|YP_002263526.1| 2,4-dienoyl-CoA reductase [NADPH] [Aliivibrio salmonicida LFI1238]
 gi|208009549|emb|CAQ79841.1| 2,4-dienoyl-CoA reductase [NADPH] [Aliivibrio salmonicida LFI1238]
          Length = 667

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 21/119 (17%), Positives = 45/119 (37%), Gaps = 10/119 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + I A+ + +     +  R+     V+       +  L ++++K+GV    ++      +
Sbjct: 197 EIIKAIREKVGADFIIIFRLSMLDLVEQGSTFEEVVELAQALEKAGVT--ILNTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P  + ++P   +  V E +K +     I  N  +     A  IL     D V + R
Sbjct: 255 TRIPTISTQVPRAAFSWVTEKLKNKVSIPLITCNR-INTPEVAENILASGQADMVSMAR 312


>gi|86144284|ref|ZP_01062616.1| putative NADH-dependent flavin oxidoreductase [Vibrio sp. MED222]
 gi|85837183|gb|EAQ55295.1| putative NADH-dependent flavin oxidoreductase [Vibrio sp. MED222]
          Length = 358

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 74/211 (35%), Gaps = 23/211 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A+   +  G++ + ++            P     E  +G  L      + +   A
Sbjct: 133 DAFAQASLRAQKSGFDGVEIHAAHTYLINQFLSPYYNQREDEYGGNLENRMRFLLEIYIA 192

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
             K +    P+ VK       +  +     R + K +++ GV+GI     IH +   + G
Sbjct: 193 TRKLVGDDFPILVKLTASEFFEGGVTFEETRIVCKKLEQVGVDGIVLSGNIHGKADTMIG 252

Query: 163 LSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRA 218
            S  D   I    Y  +  + I ++  ++ +   GGL D    +A+     ++   + R 
Sbjct: 253 ES-HDGFTIQAEGYFHEYGHAISQDV-NIPVITVGGLTDFDAIEAIANNTGIEYFALSRP 310

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
                 ++    E   +P+      K R  +
Sbjct: 311 LLSEPHLVKRWKEGDRSPVECERCSKCRTKR 341


>gi|313835284|gb|EFS72998.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL037PA2]
 gi|314928234|gb|EFS92065.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL044PA1]
 gi|314970065|gb|EFT14163.1| dihydroorotate dehydrogenase 2 [Propionibacterium acnes HL037PA3]
 gi|328905956|gb|EGG25732.1| dihydroorotate oxidase [Propionibacterium sp. P08]
          Length = 335

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 41/110 (37%), Gaps = 11/110 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           + P+   + GA     V  AK +E  G   I  NV      +  G          D   +
Sbjct: 103 DIPVIASLNGATNGGWVNTAKRMERAGAAGIECNV-----YMVPGDLEQSAEEVEDRHVE 157

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            + A+  A+S+PV VK            AL N+   +  +G + + +  R
Sbjct: 158 IVQAVKDAVSVPVAVKLSPFFS------ALGNMATRLDAAGADALVMFNR 201


>gi|224498643|ref|ZP_03666992.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes Finland 1988]
          Length = 240

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 11/101 (10%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+ ++KK    + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEIIQKMKKAA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           M+Q    L   +D V+IG AA  +   L    + +   +  
Sbjct: 86  MAQVDYYLESGIDRVIIGSAALTDPDFLRAAVQKYGTKIAA 126


>gi|169766140|ref|XP_001817541.1| NADH-dependent flavin oxidoreductase [Aspergillus oryzae RIB40]
 gi|238482811|ref|XP_002372644.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus flavus
           NRRL3357]
 gi|83765396|dbj|BAE55539.1| unnamed protein product [Aspergillus oryzae]
 gi|220700694|gb|EED57032.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus flavus
           NRRL3357]
          Length = 420

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 21/170 (12%), Positives = 56/170 (32%), Gaps = 27/170 (15%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC-------RIGVDDQIPAVALRNLVKSI 143
           +G        +  +        +   +PV ++         +  +            +++
Sbjct: 237 YGGSFENRIRLPLEIAQLTRDTVGPDVPVFLRVSASDWLEEVLPEQSFNVNETVKFAQAL 296

Query: 144 KKSGVNGIW------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGG 196
              G   +       +HA + +  G         P         +KK   D + +   G 
Sbjct: 297 VAQGAVDLIDISSGGVHAAQKVKSG---------PGFQVPFAVAVKKAVGDKMLVSAVGA 347

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           + +  QA ++L    +D  ++GR   K+  +  T  ++    ++ ++ I+
Sbjct: 348 ITNGKQANQLLEEEGIDVALVGRGFQKDPGLAWTFAQHLDTEISMANQIR 397


>gi|326794496|ref|YP_004312316.1| 2,4-dienoyl-CoA reductase (NADPH) [Marinomonas mediterranea MMB-1]
 gi|326545260|gb|ADZ90480.1| 2,4-dienoyl-CoA reductase (NADPH) [Marinomonas mediterranea MMB-1]
          Length = 681

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 34/223 (15%), Positives = 73/223 (32%), Gaps = 22/223 (9%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+  +VA + L+         S  E  +  QI     +  V AA +    GY+
Sbjct: 110 LHAGRYAYSPKLVAPSALQAPINPFKPKSLSEVEIEKQI-----NDFVHAAILAHKAGYD 164

Query: 76  EINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
            + +            C         +G        +  + ++ +  A+     +  R+ 
Sbjct: 165 GVEIMASEGYFLNQFICARTNQRLDDWGGSFDKRIKLPVEIVSRIRAAVGREFIIIFRLS 224

Query: 127 VDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           + D             L  +++K+GV+   I+      +   P    K+P   +  V + 
Sbjct: 225 MLDLVEGGSTVEETVQLGCAVEKAGVD--IINTGIGWHEARVPTIATKVPRAAFTWVTKK 282

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +E+  + +  +  +     A  +L     D V + R    + 
Sbjct: 283 FREHLSVPVVTSNRINMPDTAEGVLKRGDADLVSMARPFLADP 325


>gi|323498745|ref|ZP_08103733.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           sinaloensis DSM 21326]
 gi|323316212|gb|EGA69235.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           sinaloensis DSM 21326]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|260779085|ref|ZP_05887977.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260605249|gb|EEX31544.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|229115540|ref|ZP_04244946.1| NADPH dehydrogenase [Bacillus cereus Rock1-3]
 gi|228667953|gb|EEL23389.1| NADPH dehydrogenase [Bacillus cereus Rock1-3]
          Length = 319

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 22/125 (17%), Positives = 47/125 (37%), Gaps = 10/125 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I ++ +    P+ V+        D +         K +K+ GV+ I   +   +  
Sbjct: 171 LREIIESINEVWDGPLFVRISANDYHPDGLTVQDYVQYSKWMKEQGVDLIDCSSGAVVPT 230

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            +      ++    +       KE+ ++  G  G +   +QA +IL     D + IGR  
Sbjct: 231 HIDVYPGYQVQYAKH------IKEHANIATGAVGLITTGAQAEQILNNNEADLIFIGREL 284

Query: 220 YKNSA 224
            +N  
Sbjct: 285 LRNPY 289


>gi|89095973|ref|ZP_01168866.1| NADH-dependent flavin oxidoreductase [Bacillus sp. NRRL B-14911]
 gi|89088827|gb|EAR67935.1| NADH-dependent flavin oxidoreductase [Bacillus sp. NRRL B-14911]
          Length = 373

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 32/213 (15%), Positives = 76/213 (35%), Gaps = 29/213 (13%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLN----PDIVGDC 107
              EAA+   + GY+ + +             P +   +  +G  L         +V + 
Sbjct: 152 DFGEAARRAIEAGYDGVEIHGANGYLLQQFFSPHSNRRDDQWGGSLEKRLTFPLAVVDEV 211

Query: 108 IAAMCKALSIPVTVKCRIGVDD-QIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
              +      P  V  R   ++ + P + + +   L+  + K  ++ + +  +       
Sbjct: 212 KKTVAAHAKKPFAVGYRFSPEEPETPGITMADTLVLIDELAKKDLDYLHVSLQDFW---S 268

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN 222
           +P+   +      +I+ E  +    + +   G L    +  K     V  + +GR    +
Sbjct: 269 APRRGVEDTRSRIEIIQE--RVGSLVPVIGVGSLYTPEEVEKAFGTGVPLIALGRELIID 326

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKI 255
              +  V+E   +       IKT++DKD  +++
Sbjct: 327 PEWVQKVEEGREDE------IKTKIDKDAQQEL 353


>gi|262042668|ref|ZP_06015822.1| 2,4-dienoyl-CoA reductase [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259039893|gb|EEW41010.1| 2,4-dienoyl-CoA reductase [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 673

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 143 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L K+I+ +G     I+ 
Sbjct: 192 RMRFAVEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAKAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|254524285|ref|ZP_05136340.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Stenotrophomonas sp. SKA14]
 gi|219721876|gb|EED40401.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Stenotrophomonas sp. SKA14]
          Length = 258

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 18/115 (15%), Positives = 41/115 (35%), Gaps = 15/115 (13%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           V+ R  VD       +  L +  +  G + +            +  + R +     + + 
Sbjct: 21  VRFRDHVDMGD----IAELAQRYRDQGADELV------FYDIGASPEARSVDVAWIERIA 70

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +     D+   + GG++ +  A ++L    D V I   A     ++T + + F 
Sbjct: 71  RLI----DIPFCVAGGIDSVETARRVLFAGADKVSINSPALGRPQLITELADEFG 121


>gi|206901289|ref|YP_002250848.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dictyoglomus
           thermophilum H-6-12]
 gi|226700511|sp|B5YE90|HIS6_DICT6 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|206740392|gb|ACI19450.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dictyoglomus
           thermophilum H-6-12]
          Length = 252

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + L +  ++ G + I +    A  +G              D+V E+  E   + + + GG
Sbjct: 33  KELARRYEREGADEIVLLDITASEEGRGTF---------VDVVTEVASELF-VPLTVGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           ++++    K+L    D V I  AA +N  ++  +   F 
Sbjct: 83  IKNIEDVRKLLKAGADKVSINTAAVENPDIINQIASEFG 121


>gi|156974125|ref|YP_001445032.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio harveyi
           ATCC BAA-1116]
 gi|167012223|sp|A7MX10|HIS6_VIBHB RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|156525719|gb|ABU70805.1| hypothetical protein VIBHAR_01836 [Vibrio harveyi ATCC BAA-1116]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|32473296|ref|NP_866290.1| dihydroorotate dehydrogenase 2 [Rhodopirellula baltica SH 1]
 gi|32397976|emb|CAD78070.1| dihydroorotate dehydrogenase [Rhodopirellula baltica SH 1]
          Length = 359

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 30/202 (14%), Positives = 75/202 (37%), Gaps = 32/202 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-IVGDC 107
           P+   + G+   + ++ AK +E  G + +  N+      V +    +    + +  + D 
Sbjct: 112 PVIASMNGSSAGQWLQYAKEMESAGADALEFNL---QQAVFDSKETS---NDIEARMCDL 165

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA-RKAILKGLSPK 166
           I  + + + IPV  K             L ++   +++ GV G+ +              
Sbjct: 166 IRQVRELVVIPVAAKISQR------YTNLSSMATQLRQVGVAGLVLFTHMPQWDVSTDRM 219

Query: 167 DNRKIPNLDYDI--------VYE--IKKENPD--LFIGLNGGLEDMSQALK-ILPSVDGV 213
                  +++++        + E  ++    D  + I  +GG+ +   A+K ++   D V
Sbjct: 220 HW----TINWELSPTNSIGGILEGIVRARAGDQAISIAASGGVSNSEDAIKAMIAGADVV 275

Query: 214 MIGRAAYKN-SAMLTTVDEYFS 234
           M+  A Y+     +  + +   
Sbjct: 276 MVTSAVYRRGPDAIRDIVDGIE 297


>gi|88803275|ref|ZP_01118801.1| dihydroorotate dehydrogenase [Polaribacter irgensii 23-P]
 gi|88780841|gb|EAR12020.1| dihydroorotate dehydrogenase [Polaribacter irgensii 23-P]
          Length = 343

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 63/180 (35%), Gaps = 30/180 (16%)

Query: 74  YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK-----ALSIPVTVKCRIGVD 128
            +   LNV CP+            + + D + + I+   K      +  P+ +K      
Sbjct: 171 VDYFALNVSCPNVASDVK------LNDKDYLIELISECQKENQRFKIKKPILLKISP--- 221

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWI--------HARKAILK----GLSPKDNRKIPNLDY 176
             +  V L  ++  + ++ ++G+          H + +  +    G      + I N   
Sbjct: 222 -DLNTVQLDEIIDLVAETKIDGVIASNTSITRDHLKASEERLKEIGNGGISGQPIKNKST 280

Query: 177 DIVYEIK-KENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRA-AYKNSAMLTTVDEYF 233
            ++  +  K N    I   GG+     AL+ +    D V I     Y+   ++  +++  
Sbjct: 281 QVIKYLSEKSNKSFPIIGVGGIHSAEDALEKINAGADLVQIYTGFIYEGPGLIKKINKAI 340


>gi|218883496|ref|YP_002427878.1| dihydroorotate dehydrogenase family protein [Desulfurococcus
           kamchatkensis 1221n]
 gi|218765112|gb|ACL10511.1| dihydroorotate dehydrogenase family protein [Desulfurococcus
           kamchatkensis 1221n]
          Length = 407

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 25/132 (18%), Positives = 44/132 (33%), Gaps = 21/132 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
           V +   A+ +++ IP+  K      +      +  LVK ++K GV+GI            
Sbjct: 173 VIEAAKALRESVDIPIFPKLSPFTPN------IPELVKELEKVGVDGIVATNTIGPALHI 226

Query: 153 -IHARKAILKGLSPKDNRKIPNLDYDIVYEI--KKENPDLFIGLNGGL-EDMSQALKILP 208
            +     I+ G         P L    +  +     N  L +   GG+   +      + 
Sbjct: 227 DVETGLPIVGGPYGYGWMSGPALKPLALAVVSQVALNTKLPVIGVGGISRGVDVIEYFMA 286

Query: 209 SVDGVMIGRAAY 220
               V I  AA 
Sbjct: 287 GASAVQICTAAL 298


>gi|161522674|ref|YP_001585603.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia multivorans
           ATCC 17616]
 gi|160346227|gb|ABX19311.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia multivorans
           ATCC 17616]
          Length = 379

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 31/209 (14%), Positives = 64/209 (30%), Gaps = 42/209 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
               +AA+   D G++ + L   C +  +               +G  L      + +  
Sbjct: 168 ELYAQAARNALDAGFDGVEL--HCANGYLVNQFISAHTNQRDDEYGGSLQNRLRFLREIT 225

Query: 109 AAMCKALSI-PVTV------------KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            A+   +    V V            +  +G+ ++ P       VK +++ G+  +    
Sbjct: 226 LAVAGVVGKERVGVRFAPLFATTDEDRVYLGLVEEDPHQTYIEAVKILEEVGIAYLS--- 282

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGV 213
                  L+  D    P L       ++K      I    G     +A +++     D +
Sbjct: 283 -------LAEADWENAPELPETFREAVRKTFSGKIIYA--GKYTAERANRVIKAGWADLI 333

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             GR    N  +   +    + PL    P
Sbjct: 334 AFGRPFIANPDLPARIAN--NWPLNPVDP 360


>gi|254230158|ref|ZP_04923552.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio sp.
           Ex25]
 gi|262394614|ref|YP_003286468.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio sp.
           Ex25]
 gi|151937296|gb|EDN56160.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio sp.
           Ex25]
 gi|262338208|gb|ACY52003.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio sp.
           Ex25]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|307609545|emb|CBW99045.1| hypothetical protein LPW_08301 [Legionella pneumophila 130b]
          Length = 253

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 44/135 (32%), Gaps = 15/135 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +    G + +      A L G +          +   + +   EN  + I + GG+
Sbjct: 34  EYAMAYYAQGADELIYMDTVASLYGRN----------NLSEIVKTTAENVFIPITVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A ++L    D V I  AA KN  +++ V   F +     S    R     W    
Sbjct: 84  RSVDDAKQLLRCGADKVAINTAATKNPTLISDVARRFGSQCVVLSIEAKRTVNGRW---- 139

Query: 257 ASMTDYAARHLHSGG 271
             MTD    H     
Sbjct: 140 EVMTDNGREHTGMDV 154


>gi|295396516|ref|ZP_06806676.1| imidazole glycerol phosphate synthase subunit HisF [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294970634|gb|EFG46549.1| imidazole glycerol phosphate synthase subunit HisF [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 253

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 11/99 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              +     G + +      A   G +P          YD+V ++ +E   +   + GG+
Sbjct: 35  ECARVYATEGADELVFLDVTASSSGRAPT---------YDMVNQVAEEIF-IPFAVGGGI 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                  ++L    D V +  AA     +++ +   F N
Sbjct: 85  RSCDDVDRMLREGADKVGVNTAAIARPELISEIARRFGN 123


>gi|290560224|pdb|3IIP|A Chain A, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560225|pdb|3IIP|B Chain B, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560226|pdb|3IIP|C Chain C, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560227|pdb|3IIP|D Chain D, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560228|pdb|3IIP|E Chain E, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560229|pdb|3IIP|F Chain F, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
          Length = 256

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 65  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGS 123

Query: 236 PLTGSSPIKTRVDKDFW 252
                     RVD +F 
Sbjct: 124 QAVVVYIAAKRVDGEFM 140


>gi|261209834|ref|ZP_05924136.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio sp. RC341]
 gi|260841132|gb|EEX67652.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio sp. RC341]
          Length = 666

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+  A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIRAAVGKEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  K    + +     +    QA KI+     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIKPYLKVPVVTCNRINTPEQAEKIIASGQADMVSMAR 311


>gi|109899194|ref|YP_662449.1| imidazole glycerol phosphate synthase subunit HisF
           [Pseudoalteromonas atlantica T6c]
 gi|123360569|sp|Q15RU3|HIS6_PSEA6 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|109701475|gb|ABG41395.1| imidazole glycerol phosphate synthase subunit hisF
           [Pseudoalteromonas atlantica T6c]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 18/116 (15%), Positives = 41/116 (35%), Gaps = 15/116 (12%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R    +      +  L +   + G + +            +  D R +       + 
Sbjct: 21  VKFR----NHETIGEIVPLAELYAQQGADELV------FYDITASSDQRVVDKSWVTRIA 70

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++     D+   + GG++ +  A +IL    D + I   A  N +++  + + F  
Sbjct: 71  QVI----DIPFCVAGGIKSVEDAGRILEMGADKISINSPALANPSLIRELHDTFGQ 122


>gi|167567435|ref|ZP_02360351.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia oklahomensis
           EO147]
          Length = 416

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 80/242 (33%), Gaps = 25/242 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++  + G++ + ++            P A      +G         + + + A  
Sbjct: 165 FARTAELAVEAGFDGVQIHAAHGYLLSQFLSPVANKRTDEYGGTPANRRRFLQEVVRATR 224

Query: 113 KAL--SIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSP 165
           +A+   +PV VK      ++  +      ++   ++  G++ + I         + G+  
Sbjct: 225 RAVGSGVPVGVKLNSTDFERGGLSEAESLDVALMLQDEGIDLLEISGGNYEAPAMTGVIR 284

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            D+R           E  +    L + L GGL   +   K+L   +VD + + R      
Sbjct: 285 NDDRSREAYFLSY-AESLRAKTRLPLMLTGGLRTEAFMRKVLTDGAVDMLGLARPLALAP 343

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +          ++P       D + +++     +  R + SG       R   G 
Sbjct: 344 DLPARLLRGEDVGALPAAPKVGYAPLDSYLQLAWHAAQF--RRIGSGLAP----RPFGGA 397

Query: 284 FH 285
           F 
Sbjct: 398 FK 399


>gi|153814037|ref|ZP_01966705.1| hypothetical protein RUMTOR_00245 [Ruminococcus torques ATCC 27756]
 gi|317502380|ref|ZP_07960545.1| tryptophan synthase subunit alpha [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|145848433|gb|EDK25351.1| hypothetical protein RUMTOR_00245 [Ruminococcus torques ATCC 27756]
 gi|316896190|gb|EFV18296.1| tryptophan synthase subunit alpha [Lachnospiraceae bacterium
           8_1_57FAA]
          Length = 258

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 32/216 (14%), Positives = 59/216 (27%), Gaps = 56/216 (25%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLN-------VGCPSA-----RVHEGSFGACLMLNPD 102
           G  D+    +A +     G + I L           P       R  +G          D
Sbjct: 21  GDPDLETTKKAIRSAVKNGADLIELGIPFSDPTAEGPVIQAANLRALKGGI------TTD 74

Query: 103 IVGDCIAAMCKALSIP------------------VTVKCRIGVD----DQIPAVALRNLV 140
            +   +  + K + +P                  V+   +  +D      +P        
Sbjct: 75  KIFAFVRELRKDIDVPFVFMTYTNVVFSYGVEKFVSECQKSRIDGLILPDLPFEEKEEFH 134

Query: 141 KSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIKK 184
                 GV+ I + A  +                ++  L     R     D   +    +
Sbjct: 135 PICAGYGVDLISMVAPTSEKRIAKIAGEAEGFLYVVSSLGVTGMRSEITTDLTSIVATIR 194

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           EN  +   +  G+    QA  +    DGV++G A  
Sbjct: 195 ENTRIPCAVGFGISTPQQAAAMAEYADGVIVGSAIV 230


>gi|150400136|ref|YP_001323903.1| putative TIM-barrel protein [Methanococcus vannielii SB]
 gi|150012839|gb|ABR55291.1| putative TIM-barrel protein [Methanococcus vannielii SB]
          Length = 265

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 28/163 (17%), Positives = 57/163 (34%), Gaps = 20/163 (12%)

Query: 60  SKLVEAAKIVEDFG--YNEINLNVGCPSARVHEGSFGACLMLNPDIVGD--CIAAMCK-A 114
              + A K +       + I +N  C    +   + G  L+   + +     +  +    
Sbjct: 96  DDFLAAKKTLVQISKYADIIEINCHCRQEEITNLNLGQNLLKLENNLKLKEILTQIDNLN 155

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           L  P+ +K R      +    L + + ++K     GI I          +PK N      
Sbjct: 156 LKTPIFLKIRANF---VNFEELTDSLNNVKDY-FEGIHIDC-------FNPKKNYP---- 200

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
           D D + ++ +   +  I  N  +  +  A K++   D V + R
Sbjct: 201 DLDYLKKVWENFNEKIIIGNNSVNSIESAKKMIEYCDFVSVAR 243


>gi|91226025|ref|ZP_01260952.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           alginolyticus 12G01]
 gi|153835173|ref|ZP_01987840.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           harveyi HY01]
 gi|254506119|ref|ZP_05118263.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus 16]
 gi|269960831|ref|ZP_06175202.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio harveyi
           1DA3]
 gi|269968734|ref|ZP_06182727.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           alginolyticus 40B]
 gi|91189466|gb|EAS75743.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           alginolyticus 12G01]
 gi|148868330|gb|EDL67455.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           harveyi HY01]
 gi|219550937|gb|EED27918.1| imidazoleglycerol phosphate synthase, cyclase subunit [Vibrio
           parahaemolyticus 16]
 gi|269826661|gb|EEZ81002.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           alginolyticus 40B]
 gi|269834495|gb|EEZ88583.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio harveyi
           1DA3]
          Length = 257

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|323704878|ref|ZP_08116455.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535804|gb|EGB25578.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 665

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 30/163 (18%), Positives = 56/163 (34%), Gaps = 48/163 (29%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD------CIA 109
           G DI + +EAAK++ ++GY+ ++++VG         S+ A    +P +  +         
Sbjct: 254 GRDIEEGIEAAKLLVEYGYDALDVDVG---------SYDAWWWSHPPMYQEKGLYIPYAK 304

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            + +A+++PV    R+   D         L     + G   I    R  +          
Sbjct: 305 MVKEAVNVPVICAGRMDNPD---------LASDAVRDGACDIVSLGRPLL---------- 345

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
                D D V ++K           G    +   L       G
Sbjct: 346 ----ADPDYVNKLKA----------GDTASIRPCLSCHEGCMG 374


>gi|310830071|ref|YP_003962428.1| hypothetical protein ELI_4531 [Eubacterium limosum KIST612]
 gi|308741805|gb|ADO39465.1| hypothetical protein ELI_4531 [Eubacterium limosum KIST612]
          Length = 225

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 62/183 (33%), Gaps = 28/183 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFG---ACLMLNPDIVGD 106
            +   AK  E+ G   I  N              P   + + ++      +      V +
Sbjct: 24  IMGRMAKAAEEGGARGIRANTKADITEIKKNVDLPVIGIVKKNYADSEVYITPTMAEVKE 83

Query: 107 CIAAMCKALSIPVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGI--WIHAR------ 156
              A  + +++  TV  R G    DQ    A       +  +  + +   +HA       
Sbjct: 84  LAEARAEIIAMDATVNLRPGKITLDQFFKTAREQYPNQMFMADCSTVEEALHAAAIGFDF 143

Query: 157 --KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
               ++      +  +I N D++I+ EI ++     +   G +    +A ++L      V
Sbjct: 144 IGTTLVGYTKQSEGMRIENNDFEIIREILRK-SKTPVIAEGNINTPEKAARVLELGCYSV 202

Query: 214 MIG 216
           ++G
Sbjct: 203 VVG 205


>gi|257790129|ref|YP_003180735.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella lenta DSM
           2243]
 gi|257474026|gb|ACV54346.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella lenta DSM
           2243]
          Length = 686

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 50/161 (31%), Gaps = 35/161 (21%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCR------IGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
              IV + I  + +A      + CR            I A       ++  ++G   I I
Sbjct: 203 RTRIVREIIEGIREACGPDFVIGCRLNGREFHPTKQGITAEQAAENARAFVEAGAQYISI 262

Query: 154 HARKAILKGLSPKDNRKIPNLD---------------------YDIVYEIKKENPDLFIG 192
                   G  P   R  P+                       +  V    K+  D+ + 
Sbjct: 263 AG-----YGYGPTPFRYCPDYFPYPEPDPFMEPFMDEYRGVGLWTAVARRIKDAVDVPVI 317

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
             G + D + A ++L +   D + +GR  + +      VDE
Sbjct: 318 TAGRM-DENLAERVLEAGDADVIALGRTLWADPWFARKVDE 357


>gi|33597846|ref|NP_885489.1| tryptophan synthase subunit alpha [Bordetella parapertussis 12822]
 gi|73622000|sp|Q7W5G9|TRPA_BORPA RecName: Full=Tryptophan synthase alpha chain
 gi|33574275|emb|CAE38607.1| tryptophan synthase alpha chain [Bordetella parapertussis]
          Length = 285

 Score = 40.6 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 17/104 (16%)

Query: 130 QIPAVALRNLVKSIKKSGVNGI--------------WIHARKAILKGLSPKDNRKIPNLD 175
             P   +      + ++GV  I                   +  +  +S K      +LD
Sbjct: 134 DYPPEEVDEFAAMLAEAGVAPIFLLAPTSTEARIEAIGRVARGYVYYVSLKGVTGAGSLD 193

Query: 176 YDIVYE---IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            D V     + + +  + +G+  G+ D + A +I    D V+IG
Sbjct: 194 TDDVARKLALIRRHVHIPVGVGFGIRDAASAQRIAAHADAVVIG 237


>gi|317489580|ref|ZP_07948085.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella sp. 1_3_56FAA]
 gi|316911312|gb|EFV32916.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella sp. 1_3_56FAA]
          Length = 686

 Score = 40.6 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 50/161 (31%), Gaps = 35/161 (21%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCR------IGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
              IV + I  + +A      + CR            I A       ++  ++G   I I
Sbjct: 203 RTRIVREIIEGIREACGPDFVIGCRLNGREFHPTKQGITAEQAAENARAFVEAGAQYISI 262

Query: 154 HARKAILKGLSPKDNRKIPNLD---------------------YDIVYEIKKENPDLFIG 192
                   G  P   R  P+                       +  V    K+  D+ + 
Sbjct: 263 AG-----YGYGPTPFRYCPDYFPYPEPDPFMEPFMDEYRGVGLWTAVARRIKDAVDVPVI 317

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
             G + D + A ++L +   D + +GR  + +      VDE
Sbjct: 318 TAGRM-DENLAERVLEAGDADVIALGRTLWADPWFARKVDE 357


>gi|306836432|ref|ZP_07469408.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Corynebacterium accolens ATCC 49726]
 gi|304567683|gb|EFM43272.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Corynebacterium accolens ATCC 49726]
          Length = 256

 Score = 40.6 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 39/113 (34%), Gaps = 11/113 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L    ++ G + +      A   G S            D+V     +   + + + GG+
Sbjct: 35  ELAARYEQLGADELTFLDVSASKHGRSTM---------LDVVRR-TADQVFIPLTVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
             +    ++L    D V +  AA  N A+L  + E F +     S    R D 
Sbjct: 85  RSVDDVRELLRTGADKVSVNTAAIGNPALLRELAEVFGSQCIVLSVDARRTDA 137


>gi|293416519|ref|ZP_06659158.1| 2,4-dienoyl-CoA reductase [Escherichia coli B185]
 gi|291431875|gb|EFF04858.1| 2,4-dienoyl-CoA reductase [Escherichia coli B185]
          Length = 672

 Score = 40.6 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 23/188 (12%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+     V+D         L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|290560218|pdb|3IIO|A Chain A, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560219|pdb|3IIO|B Chain B, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560220|pdb|3IIO|C Chain C, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560221|pdb|3IIO|D Chain D, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560222|pdb|3IIO|E Chain E, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
 gi|290560223|pdb|3IIO|F Chain F, Evolutionary Optimization Of Computationally Designed
           Enzymes: Kemp Eliminases Of The Ke07 Series
          Length = 262

 Score = 40.6 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +N +++T + + F +
Sbjct: 65  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVEINTAAVENPSLITQIAQTFGS 123

Query: 236 PLTGSSPIKTRVDKDFW 252
                     RVD +F 
Sbjct: 124 QAVVVYIAAKRVDGEFM 140


>gi|256824823|ref|YP_003148783.1| imidazole glycerol phosphate synthase subunit HisF [Kytococcus
           sedentarius DSM 20547]
 gi|256688216|gb|ACV06018.1| imidazole glycerol phosphate synthase subunit hisF [Kytococcus
           sedentarius DSM 20547]
          Length = 266

 Score = 40.6 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 40/111 (36%), Gaps = 11/111 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D + A  +  L       G + +  +   A  +G +         +D D V  + +
Sbjct: 27  VRFTDHVDAGGIEELAARYAAEGADELVFYDISASPQGRA---------VDIDWVRRVAR 77

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
              D+   + GG+  + +A  +L    D V +   A +   ++  +   F 
Sbjct: 78  LI-DIPFSVAGGIRTVEEARAVLHAGADKVSVNTPALERPELVGELAGEFG 127


>gi|163750029|ref|ZP_02157273.1| dihydroorotate dehydrogenase [Shewanella benthica KT99]
 gi|161330303|gb|EDQ01284.1| dihydroorotate dehydrogenase [Shewanella benthica KT99]
          Length = 334

 Score = 40.6 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 63/193 (32%), Gaps = 40/193 (20%)

Query: 48  KPLALQIGG---ADISKLVEAAKIVEDFGYNEINLNVGCP----SARVHEGSFGACLMLN 100
           KP+ + + G   AD   +V+A    +    + I +N  CP      +V    +      +
Sbjct: 118 KPIVVSVSGFSLADNLTMVKA---FQASCADLIEVNFSCPNIEGKPQV---GY------D 165

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------- 153
            +     +  +C+  S P+ +K     D          +   IKK  V  I         
Sbjct: 166 FEQTERALEQLCQLGSKPIGLKLPPYFDFSH----FITMANIIKKFPVRFITCINSVGNT 221

Query: 154 -----HARKAILK---GLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQAL 204
                    AI+K   G        I  +    V    +  P  + I   GG++  + A 
Sbjct: 222 LVIDPETESAIIKPKGGFGGLCGDYIKPIGLANVRAFSQLLPSSIDIIGVGGIKTGTDAF 281

Query: 205 K-ILPSVDGVMIG 216
           + +L     V + 
Sbjct: 282 EYLLAGASAVQVA 294


>gi|297155462|gb|ADI05174.1| oxidoreductase [Streptomyces bingchenggensis BCW-1]
          Length = 365

 Score = 40.6 bits (94), Expect = 0.37,   Method: Composition-based stats.
 Identities = 22/162 (13%), Positives = 45/162 (27%), Gaps = 18/162 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGV----DDQI-----PAVALRNLVK 141
           +G           + + A+       +P+  +         DD        A       +
Sbjct: 203 YGGSFENRTRFALEVVDAVRAVWPDELPLFFRISATDWLTEDDSDERQGWTADDTVRFAQ 262

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +   GV+ + +       +   P      P         ++ E   L +   G + +  
Sbjct: 263 ELTAHGVDLLDVSTGGNAARVRIP----TGPGYQVPFAARVRAETG-LPVAAVGLITEPE 317

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           QA KI+     D V++GR   ++               T   
Sbjct: 318 QAEKIVAGGEADAVLLGRELLRDPYWARHAARDLGAVATVPP 359


>gi|148839476|sp|Q0A5D2|HIS4_ALHEH RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
          Length = 248

 Score = 40.6 bits (94), Expect = 0.37,   Method: Composition-based stats.
 Identities = 25/102 (24%), Positives = 42/102 (41%), Gaps = 2/102 (1%)

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVD 230
             ++ +I++ I    PDL I + GG+ D+          VD ++IG  A +    +T   
Sbjct: 59  KPVNAEIIHRIATRYPDLRIQVGGGIRDLDTIRGYREAGVDDLIIGTQAVRRPEFVTEAC 118

Query: 231 EYFSNPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           + F   +  G      RV  D W ++S       AR   + G
Sbjct: 119 QAFPGHIIVGLDARDGRVATDGWEQVSEVRAVDLARRFEAAG 160


>gi|158317038|ref|YP_001509546.1| dihydroorotate oxidase [Frankia sp. EAN1pec]
 gi|158112443|gb|ABW14640.1| Dihydroorotate oxidase [Frankia sp. EAN1pec]
          Length = 321

 Score = 40.6 bits (94), Expect = 0.37,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
               KPL + + G    +    A++  D G + I LN+GCP   V +G 
Sbjct: 90  HGYGKPLVVSVAGFAAEEYATLARVAADTGADLIELNLGCP--NVWDGG 136


>gi|319997182|gb|ADV91185.1| mitochondrial dihydroorotate dehydrogenase [Karlodinium micrum]
          Length = 351

 Score = 40.6 bits (94), Expect = 0.37,   Method: Composition-based stats.
 Identities = 41/199 (20%), Positives = 69/199 (34%), Gaps = 41/199 (20%)

Query: 40  ILGFSTQEKPLALQIG-GADISKLVEAAKIVEDFG---------YNEINLNVGCPSARVH 89
           +   S    P+ + I        L EAA  ++DF           + + LNV CP     
Sbjct: 109 LSKRSATRVPVGVNIAKTHSPEILGEAA--IDDFVTSYRTLSPLADFVVLNVSCP--NTA 164

Query: 90  EGSFGACLMLNPDIVGDCIAAM-----CKALSIPVTVKCRIGVD--DQIPAVALRNLVKS 142
           EG        +   +   + A+     C A + PV VK    VD      +  LR LV  
Sbjct: 165 EGKTF----EDSTSLRQLLDAVSRERQCSASAPPVLVKLSPPVDAASTAGSEQLRALVSI 220

Query: 143 IKKSG-VNGIWI-------------HARKAILK-GLSPKDNRKIPNLDYDIVYEIKKENP 187
            + SG V+G  +               ++A+   G      R + N     + ++ + + 
Sbjct: 221 AQASGIVDGFVVSNTAGDREVKLSPEGKEAVAAIGKGGLSGRPLCNRSTATIRKVYELSG 280

Query: 188 -DLFIGLNGGLEDMSQALK 205
             + I   GG++    A  
Sbjct: 281 GSMPIIGVGGVDSAESAYA 299


>gi|302695095|ref|XP_003037226.1| NADH:flavin oxidoreductase 1 [Schizophyllum commune H4-8]
 gi|300110923|gb|EFJ02324.1| NADH:flavin oxidoreductase 1 [Schizophyllum commune H4-8]
          Length = 402

 Score = 40.6 bits (94), Expect = 0.37,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 61/182 (33%), Gaps = 31/182 (17%)

Query: 73  GYNEINL-NVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTV 121
           G++ I + N           P +     ++G        +  + + A+  A+   +P+ +
Sbjct: 212 GFDVIEIHNAHGYLLMSFLSPISNKRTDAYGGSFENRVRLTLEVVDAVRAAIPEGMPLFL 271

Query: 122 KC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
           +          +    +         L   + + GV+ + + +      G++ K +    
Sbjct: 272 RISASDRVEAKKDEYPESWTNEDTIRLAGLLAERGVDLLDVSSG-----GVALKQDLSEQ 326

Query: 173 NLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS---AML 226
                   E+K    D + +G  GG+ +  QA  IL     D  ++G+   KN       
Sbjct: 327 GAQQRFAKEVKAALGDKILVGTVGGIVNGKQAEDILHDTGADVALVGKHFQKNPGAVWQF 386

Query: 227 TT 228
             
Sbjct: 387 AE 388


>gi|327542219|gb|EGF28709.1| dihydroorotate dehydrogenase 2 [Rhodopirellula baltica WH47]
          Length = 359

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 30/202 (14%), Positives = 75/202 (37%), Gaps = 32/202 (15%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD-IVGDC 107
           P+   + G+   + ++ AK +E  G + +  N+      V +    +    + +  + D 
Sbjct: 112 PVIASMNGSSAGQWLQYAKEMESAGADALEFNL---QQAVFDSKETS---NDIEARMCDL 165

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA-RKAILKGLSPK 166
           I  + + + IPV  K             L ++   +++ GV G+ +              
Sbjct: 166 IRQVRELVVIPVAAKISQR------YTNLSSMATQLRQVGVAGLVLFTHMPQWDVSTDRM 219

Query: 167 DNRKIPNLDYDI--------VYE--IKKENPD--LFIGLNGGLEDMSQALK-ILPSVDGV 213
                  +++++        + E  ++    D  + I  +GG+ +   A+K ++   D V
Sbjct: 220 HW----TINWELSPTNSIGGILEGIVRARAGDQAISIAASGGVSNSEDAIKAMIAGADVV 275

Query: 214 MIGRAAYKN-SAMLTTVDEYFS 234
           M+  A Y+     +  + +   
Sbjct: 276 MVTSAVYRRGPDAIRDIVDGIE 297


>gi|322706258|gb|EFY97839.1| hypothetical protein MAA_06622 [Metarhizium anisopliae ARSEF 23]
          Length = 458

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 29/206 (14%), Positives = 60/206 (29%), Gaps = 38/206 (18%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             + A +     G++ I L+            P+       +G        +  + + A 
Sbjct: 232 DFLSAVRRAVRAGFDVIELHFAHGYLVSSFLSPAVNKRTDQYGGSFENRTRLALELVEAA 291

Query: 112 CKAL--SIPVTVKCR-IGVDDQIPA---------VALRNLVKSIKKSGVNGIWIHARKAI 159
             A+   +P+  +       D  P               L K   + GV+ +       +
Sbjct: 292 RAAIPKDMPLFARISATDWLDTNPNWDGGASWTVDESVKLAKLFAERGVDVLD------V 345

Query: 160 LKGLSPKDNRKIPNLDYDI--VYEIKKENPD-LFIGLNGGLEDMSQALKILPS------- 209
             G +    + I    Y       IK    D + +   G ++    A  I+         
Sbjct: 346 SSGGNHSHQKVIGGPGYQAPFAKAIKAAVGDAMLVSSVGSIKTGEVARDIIEGGKDKDDT 405

Query: 210 -VDGVMIGRAAYKNSAMLTTVDEYFS 234
            +D +  GR   KN  ++ +  +   
Sbjct: 406 PLDLIAAGRMFLKNPGLVWSWADELG 431


>gi|296269336|ref|YP_003651968.1| dihydroorotate dehydrogenase family protein [Thermobispora bispora
           DSM 43833]
 gi|296092123|gb|ADG88075.1| dihydroorotate dehydrogenase family protein [Thermobispora bispora
           DSM 43833]
          Length = 313

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 64/175 (36%), Gaps = 25/175 (14%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK 122
           A ++ ++     + +N+ CP+A      FG     +     + ++A+       +PV  K
Sbjct: 102 ARRLADEHAIMAVEVNLSCPNAEDRGRVFG----RDGSAAAEVVSAVRAVTRYDVPVIAK 157

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWI------------HARKAILKGLSPKDNRK 170
               V D      +  + +S    G + + +              R A+  G+       
Sbjct: 158 LPPDVTD------IVAVARSCVDGGADALTLINTPLGMSIDVDAMRPALAAGVGGLSGPA 211

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSA 224
           +  L    V+++    P + I   GG+     AL+ IL     V +G A +++  
Sbjct: 212 VRPLAVRCVWQVHAALPGVPIVGVGGVATGRDALELILAGACAVGVGTAMFQDPY 266


>gi|288935418|ref|YP_003439477.1| NADH:flavin oxidoreductase/NADH oxidase [Klebsiella variicola
           At-22]
 gi|288890127|gb|ADC58445.1| NADH:flavin oxidoreductase/NADH oxidase [Klebsiella variicola
           At-22]
          Length = 366

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 63/179 (35%), Gaps = 22/179 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNP-DIVGDCI 108
            V +A   +  G+  I L+            P +      +G  L   +  P ++     
Sbjct: 159 FVASALRAQRLGFELIELHAAHGYLLHQFLSPLSNQRRDEYGGSLENRLRYPLEVFNAIR 218

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   +++ V +     V+            + ++  G + I + +      GLSP+ +
Sbjct: 219 EAVGNTMAVGVRLSATDWVEGGWDCEQSIQFSQQLEALGSDYIHVSSG-----GLSPQQS 273

Query: 169 RKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             +         ++I+++     IG+ G + D  QA   L     D + + RA   +  
Sbjct: 274 ITVGPGYQLPFAHDIRQQVAIPVIGV-GLITDPQQAEAALEDGDADLIALARAVLYDPH 331


>gi|225570498|ref|ZP_03779523.1| hypothetical protein CLOHYLEM_06599 [Clostridium hylemonae DSM
           15053]
 gi|225160695|gb|EEG73314.1| hypothetical protein CLOHYLEM_06599 [Clostridium hylemonae DSM
           15053]
          Length = 641

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 35/230 (15%), Positives = 72/230 (31%), Gaps = 27/230 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHE--------------GSFGACLMLNPDIVGDCIA 109
           EAA+     G + + +++      +                G      M  P +    I 
Sbjct: 151 EAARRAMQAGADAVEIHMA--HGYLVNSFISQRTNKRVDEFGGSFENRMRFPRL---IIE 205

Query: 110 AMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            + K +   V +  RI   D++P          +   +++ GV  + +     I      
Sbjct: 206 EVKKNVGDKVAILARINSADEVPGGVDVHDSAAIAAYLEECGVQCLHVSRAVHIKDEYMW 265

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                      ++V EIKK      I + G   +   A  ++     D V  GR +  + 
Sbjct: 266 APTTIHAGFSAELVTEIKKAVSIPVITV-GRYTEPQFAELLVKEGRTDLVAFGRQSLADP 324

Query: 224 AML-TTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK 272
            M    + E   + +   + ++  V   +  +    +T+    H   G  
Sbjct: 325 HMPEKAMQERLEDMIPCIACLQGCVANMYKGEPICCLTNPFLGHEAEGYP 374


>gi|163801185|ref|ZP_02195085.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio sp.
           AND4]
 gi|159175534|gb|EDP60331.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio sp.
           AND4]
          Length = 257

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|111023163|ref|YP_706135.1| inositol-5-monophosphate dehydrogenase [Rhodococcus jostii RHA1]
 gi|110822693|gb|ABG97977.1| possible IMP dehydrogenase/GMP reductase [Rhodococcus jostii RHA1]
          Length = 379

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 32/156 (20%), Positives = 62/156 (39%), Gaps = 29/156 (18%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK+ E     E +++V  P  ++ E        L P ++   +A +  A    VT   R+
Sbjct: 91  AKLAELVALAESDVDVEAPIKKLQELHAA---PLQPGLLAAAVAQVRDAG---VTTAVRV 144

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHA----RKAILKGLSPKDNRKIPNLDYDIVYE 181
              +       R L   + ++G++ + +H      + ++ G S   N K        + E
Sbjct: 145 SPQN------ARALTPQLLEAGIDLLVVHGTIISAEHVVHGDSEPLNLKT------FISE 192

Query: 182 IKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
           +     D+ +   GG+ D   AL  +     GV++G
Sbjct: 193 L-----DVPVVA-GGVSDHRTALHLMRTGAAGVIVG 222


>gi|47094798|ref|ZP_00232413.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes str. 1/2a F6854]
 gi|254830451|ref|ZP_05235106.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes 10403S]
 gi|254900203|ref|ZP_05260127.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes J0161]
 gi|254911243|ref|ZP_05261255.1| conserved hypothetical protein [Listeria monocytogenes J2818]
 gi|254935571|ref|ZP_05267268.1| hisA [Listeria monocytogenes F6900]
 gi|47016938|gb|EAL07856.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes str. 1/2a F6854]
 gi|258608151|gb|EEW20759.1| hisA [Listeria monocytogenes F6900]
 gi|293589174|gb|EFF97508.1| conserved hypothetical protein [Listeria monocytogenes J2818]
          Length = 240

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 11/101 (10%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+ ++KK    + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEIIQKMKKAA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           M+Q    L   +D V+IG AA  +   L    + +   +  
Sbjct: 86  MAQVDYYLESGIDRVIIGSAALTDPDFLRAAVQKYGTKIAA 126


>gi|331001986|ref|ZP_08325506.1| DNA polymerase III [Lachnospiraceae oral taxon 107 str. F0167]
 gi|330411782|gb|EGG91187.1| DNA polymerase III [Lachnospiraceae oral taxon 107 str. F0167]
          Length = 1480

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 22/131 (16%), Positives = 47/131 (35%), Gaps = 15/131 (11%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVE-DFGYNEINLNVGCP 84
           M++    +       L F  ++  +     G D   + E AK +  ++  + I+      
Sbjct: 514 MVMNAPFIEDILPKFLDFC-EDYIIVAHNAGFDTGFIRENAKKINKEYNPSIIDT----- 567

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK 144
                  +    L+   +     +  +CKAL+I +    R   D +  A      +K +K
Sbjct: 568 ------VAMARLLLPELNRFK--LDTVCKALNISLEGHHRAVNDAEATAQIWVEFIKRLK 619

Query: 145 KSGVNGIWIHA 155
             G++ +   A
Sbjct: 620 DKGISKLSEVA 630


>gi|206578227|ref|YP_002238444.1| oxidoreductase, FAD/FMN-binding [Klebsiella pneumoniae 342]
 gi|206567285|gb|ACI09061.1| oxidoreductase, FAD/FMN-binding [Klebsiella pneumoniae 342]
          Length = 366

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 63/179 (35%), Gaps = 22/179 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNP-DIVGDCI 108
            V +A   +  G+  I L+            P +      +G  L   +  P ++     
Sbjct: 159 FVASALRAQRLGFELIELHAAHGYLLHQFLSPLSNQRRDEYGGSLENRLRYPLEVFNAIR 218

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   +++ V +     V+            + ++  G + I + +      GLSP+ +
Sbjct: 219 EAVGNTMAVGVRLSATDWVEGGWDCEQSIQFSQQLEALGSDYIHVSSG-----GLSPQQS 273

Query: 169 RKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             +         ++I+++     IG+ G + D  QA   L     D + + RA   +  
Sbjct: 274 ITVGPGYQLPFAHDIRQQVAIPVIGV-GLITDPQQAEAALEDGDADLIALARAVLYDPH 331


>gi|300692281|ref|YP_003753276.1| NADPH dehydrogenase (Xenobiotic reductase) [Ralstonia solanacearum
           PSI07]
 gi|299079341|emb|CBJ52013.1| NADPH dehydrogenase (Xenobiotic reductase) [Ralstonia solanacearum
           PSI07]
          Length = 370

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 58/180 (32%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
              V  A+     G   I L+            P A     ++G      M  P  V + 
Sbjct: 157 DAFVATARRAVGLGLAAIELHAAHGYLLHEFLSPIANQRTDAYGGSRENRMRYPLEVFEA 216

Query: 108 IA-AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+  A+ + V V C   V+            ++++  G + +      A   G+SP 
Sbjct: 217 VRTAVPDAVPVGVRVSCTDWVEGGWTLEDSVAFAQALRARGCDWV-----DASSGGVSPL 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
               + +       E  + +  +     G +    +A  I+     D V +GRA   N  
Sbjct: 272 QQIPLSSGYQVPFAEAIRRDAGIPTIAVGLINAPHEAEAIIAEGRADLVAMGRAFLYNPH 331


>gi|290971106|ref|XP_002668376.1| predicted protein [Naegleria gruberi]
 gi|284081750|gb|EFC35632.1| predicted protein [Naegleria gruberi]
          Length = 371

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 70/201 (34%), Gaps = 25/201 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+AAK     G++ I ++            P++     ++G         + + +  +
Sbjct: 167 QFVDAAKRAVKAGFDVIEIHGAHGYLISSFLSPTSNQRTDAYGGSFENRIRFLIEIVQRI 226

Query: 112 CKALS--IPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
            + +   +P+ V+        ++         L K ++ SGV+ +      +  KA +  
Sbjct: 227 RENIPTEMPLFVRVSADEYVGEEGWTMKDTTELAKILRDSGVDLLDCSSGGNNAKAKISP 286

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
           +      ++P  +      +KK    L  G  G + +   A  ++     D V+IGR   
Sbjct: 287 IGIVQGYQVPFSE-----GVKKSVDGLATGAVGKIVEAKFANDLVKDGKADLVLIGRQDL 341

Query: 221 KNSAMLTTVDEYFSNPLTGSS 241
            +        +    P+    
Sbjct: 342 NDPYWPIRAAQDLDYPVAVPP 362


>gi|114321762|ref|YP_743445.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114228156|gb|ABI57955.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 252

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 25/102 (24%), Positives = 42/102 (41%), Gaps = 2/102 (1%)

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVD 230
             ++ +I++ I    PDL I + GG+ D+          VD ++IG  A +    +T   
Sbjct: 63  KPVNAEIIHRIATRYPDLRIQVGGGIRDLDTIRGYREAGVDDLIIGTQAVRRPEFVTEAC 122

Query: 231 EYFSNPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           + F   +  G      RV  D W ++S       AR   + G
Sbjct: 123 QAFPGHIIVGLDARDGRVATDGWEQVSEVRAVDLARRFEAAG 164


>gi|110640190|ref|YP_680400.1| geranylgeranylglyceryl phosphate synthase-like protein [Cytophaga
           hutchinsonii ATCC 33406]
 gi|110282871|gb|ABG61057.1| conserved hypothetical protein [Cytophaga hutchinsonii ATCC 33406]
          Length = 254

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTT 228
               +  + +  +KK      + + GG+    +A   L    D +++G A  K+  +L  
Sbjct: 182 AAKPVSAETIAAVKKAV-HCPVIVGGGVNTEEKAFAALEAGADVIVVGTAIEKDPNLLVA 240

Query: 229 V 229
           +
Sbjct: 241 I 241


>gi|323700727|ref|ZP_08112639.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfovibrio sp. ND132]
 gi|323460659|gb|EGB16524.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfovibrio desulfuricans ND132]
          Length = 242

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +S +  G   + +        G+           +++++  I  E   + + L GG+ D
Sbjct: 36  ARSWQDMGARYLHVVDLDGAFSGV---------PRNFELIKAICAELT-IPVQLGGGIRD 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ A K +   V  ++IG  A ++ A+ + + +    
Sbjct: 86  IATAQKYIEAGVHRLIIGTMALEDPALFSDLCKALPG 122


>gi|291543975|emb|CBL17084.1| tryptophan synthase, alpha chain [Ruminococcus sp. 18P13]
          Length = 258

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 34/211 (16%), Positives = 65/211 (30%), Gaps = 46/211 (21%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLN-------VGCPSARVHEGSFGACLMLNPDIVGDC 107
           G  D+       +     G + + L           P  +       A  M   D     
Sbjct: 21  GDPDLETTAAVVREAVRNGADLVELGIPFSDPTAEGPVIQGANIRALAGGMT-TDRAFAL 79

Query: 108 IAAMCKALSIPVTV------------------KCRIGVD----DQIPAVALRNLVKSIKK 145
           +  + + ++IP+                      ++G+D      +P           +K
Sbjct: 80  VENLRQDVTIPLVFMTYANVVFSYGADALFANCAKVGIDGIILPDLPFEEKDEFQSVSRK 139

Query: 146 SGVNGI-----WIHARKAI-----------LKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
            GV+ I       H R A+           +  L     R     D   + ++ +EN D+
Sbjct: 140 YGVDLISLIAPTSHQRIAMIAREAEGFLYIVSSLGVTGTRSEITTDLASIIQVVRENTDV 199

Query: 190 FIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
              +  G+   +QA ++    DGV++G A  
Sbjct: 200 PCAIGFGISTPAQARQMAELADGVIVGSAII 230


>gi|259417028|ref|ZP_05740948.1| 2-amninobenzoyl-CoA monooxygenase/reductase [Silicibacter sp.
           TrichCH4B]
 gi|259348467|gb|EEW60244.1| 2-amninobenzoyl-CoA monooxygenase/reductase [Silicibacter sp.
           TrichCH4B]
          Length = 764

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 64/187 (34%), Gaps = 24/187 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA++ +  G++ I L+            P +      +G  L        +  AA
Sbjct: 548 DQFVSAAEMADRAGFDMIELHAAHGYLISSFLSPVSNQRGDEYGGSLENRLRYPLEVFAA 607

Query: 111 MCKAL--SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGLS 164
           M        P++V+        +D +       + ++  ++G + I +   +  I     
Sbjct: 608 MRAVWPEGKPMSVRISANDWVGEDGVTPDEAVKIARAFWEAGADLIDVSAGQTTIDANPV 667

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                + P  D     +I+ E     + + G + +   A  IL +   D V +GR    +
Sbjct: 668 YGRMFQTPFSD-----QIRNEAGICTMAV-GNIFEADHANSILMAGRADLVAVGRPHLAD 721

Query: 223 S-AMLTT 228
               L  
Sbjct: 722 PYWTLRE 728


>gi|257095567|ref|YP_003169208.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
 gi|257048091|gb|ACV37279.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Candidatus Accumulibacter phosphatis clade
           IIA str. UW-1]
          Length = 247

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 4/105 (3%)

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTV 229
              +   + EI +   D + + L GG+ D+    + L   V  V+IG AA KN   L   
Sbjct: 59  KPKNERAIKEIVQAVGDDIPVQLGGGIRDLDTIERCLDDGVSYVIIGTAAVKNPGFLHDA 118

Query: 230 DEYFSNPLT-GSSPIKTRVDKDFWRKIS-ASMTDYAARHLHSGGK 272
              F   +  G      +V  D W K++   + D A ++   G +
Sbjct: 119 CGAFPGHIIVGLDARDGKVAVDGWSKMTGHDVVDLARKYEDYGVE 163


>gi|229096566|ref|ZP_04227537.1| NADPH dehydrogenase [Bacillus cereus Rock3-29]
 gi|228686772|gb|EEL40679.1| NADPH dehydrogenase [Bacillus cereus Rock3-29]
          Length = 319

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 22/125 (17%), Positives = 47/125 (37%), Gaps = 10/125 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I ++ +    P+ V+        D +         K +K+ GV+ I   +   +  
Sbjct: 171 LREIIESINEVWDGPLFVRISANDYHPDGLTVQDYVRYSKWMKEQGVDLIDCSSGAVVPT 230

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            +      ++    +       KE+ ++  G  G +   +QA +IL     D + IGR  
Sbjct: 231 HIDVYPGYQVQYAKH------IKEHANIATGAVGLITTGAQAEQILNNNEADLIFIGREL 284

Query: 220 YKNSA 224
            +N  
Sbjct: 285 LRNPY 289


>gi|302528347|ref|ZP_07280689.1| NADH-dependent flavin oxidoreductase [Streptomyces sp. AA4]
 gi|302437242|gb|EFL09058.1| NADH-dependent flavin oxidoreductase [Streptomyces sp. AA4]
          Length = 411

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 26/189 (13%), Positives = 57/189 (30%), Gaps = 37/189 (19%)

Query: 85  SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLV-- 140
           S +++     +G  L     +  D + A+  A+   + V  ++ +DD +P     +    
Sbjct: 183 SPKLNRRTDEYGGSLENRARLARDTMRAVRDAVGDRIAVIVKMNMDDGVPGGFWLDEAIP 242

Query: 141 -----------KSIK----------------KSGVNGIWIHARKAILKGLSPKDNRKIPN 173
                       +++                 + V        + +  G+     R I  
Sbjct: 243 VTQWLEADGTCDALEMTAGSSLLNPMYLFKGDAPVREFAAVLPQPLRLGVRAVGKRFIRE 302

Query: 174 LDYDIV-----YEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGVMIGRAAYKNSAMLT 227
             Y            +    L + L GG+ D +   L +      V +GRA  +   ++ 
Sbjct: 303 YPYRDAFLLEDARQIRAAVKLPMVLLGGITDRASMELAMREGFQYVAMGRALLREPDLVN 362

Query: 228 TVDEYFSNP 236
            +      P
Sbjct: 363 RIAADSRTP 371


>gi|212638822|ref|YP_002315342.1| NADPH dehydrogenase NamA [Anoxybacillus flavithermus WK1]
 gi|212560302|gb|ACJ33357.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family [Anoxybacillus
           flavithermus WK1]
          Length = 332

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 27/143 (18%), Positives = 53/143 (37%), Gaps = 10/143 (6%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I A+ +  S P+ V+        + +         K +K  GV+ I + +   +  
Sbjct: 191 LSEVIEAVKEVWSGPLFVRISASDYHPNGLTVNDYVEYAKRMKTQGVDLIDVSSGAVVPA 250

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            +      ++P  +      I++E  ++  G  G +    QA +IL +   D + IGR  
Sbjct: 251 KIDVYPGYQVPFAE-----TIRREA-NVATGAVGLITSGRQAEEILRNGRADLIFIGREL 304

Query: 220 YKNSAMLTTVDEYFSNPLTGSSP 242
            +N     T        L    P
Sbjct: 305 LRNPYWPKTAANELGIQLEAPKP 327


>gi|126665723|ref|ZP_01736704.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter sp.
           ELB17]
 gi|126629657|gb|EBA00274.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter sp.
           ELB17]
          Length = 245

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 52/136 (38%), Gaps = 11/136 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++     ++GV  + +        G           ++ +IV  I ++ PDL I + GG+
Sbjct: 34  DMATRWVEAGVRRLHLVDLNGAFAG---------EPVNGEIVKAIARKYPDLPIQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRVDKDFWRKI 255
                    L   V  V+IG  A K    +T + + F   +  G      RV  D W ++
Sbjct: 85  RSAEIIETYLQAGVQWVIIGTKAVKEPEFVTEMCKRFPGHIIVGLDAKDGRVATDGWAEV 144

Query: 256 SASMTDYAARHLHSGG 271
           S  M    A+   + G
Sbjct: 145 SEVMATDLAQRFANDG 160


>gi|160875764|ref|YP_001555080.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS195]
 gi|160861286|gb|ABX49820.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS195]
 gi|315267953|gb|ADT94806.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS678]
          Length = 368

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 51/128 (39%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + + +AA+       +P+T +  +   D      L     LVK  K++G++ + +    +
Sbjct: 211 LLETVAAVRDVWPQHLPLTARFGVIEFDHKDEETLTESIALVKQFKQAGLDMLNV----S 266

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
           I       +    P     I   +++E     +  + G+++   A   +    +D VMIG
Sbjct: 267 ICFSTPTANIPWSPAFLAPIAARVRQEVG-FPVATSWGMDNPHYANAAIEDEQMDLVMIG 325

Query: 217 RAAYKNSA 224
           +A   N  
Sbjct: 326 KAFLANPH 333


>gi|67541166|ref|XP_664357.1| hypothetical protein AN6753.2 [Aspergillus nidulans FGSC A4]
 gi|40739381|gb|EAA58571.1| hypothetical protein AN6753.2 [Aspergillus nidulans FGSC A4]
 gi|259480346|tpe|CBF71392.1| TPA: NADH-dependent flavin oxidoreductase, putative
           (AFU_orthologue; AFUA_7G06420) [Aspergillus nidulans
           FGSC A4]
          Length = 422

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 27/170 (15%), Positives = 64/170 (37%), Gaps = 27/170 (15%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG--VDDQIPAVALR-----NLVKSI 143
           +G        +  +       A+  ++PV ++      +++ +P  + +        +++
Sbjct: 239 YGGSFENRIRLSLEIAQVTRDAVGPNVPVFLRVSATDWIEETLPEESWKLSDSVRFAEAL 298

Query: 144 KKSGVNGIW------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGG 196
              G   +       +HA + I  G + +    +          IKK   D L +   G 
Sbjct: 299 AAQGAIDLIDVSSGGVHAAQKIKSGPAFQAPFAV---------AIKKAVGDKLLVATVGT 349

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           + +  QA K+L    +D  ++GR   K+  +  T  ++    +  +S I+
Sbjct: 350 ITNGKQANKLLEEEGLDVALVGRGFQKDPGLAWTFAQHLDVEIAMASQIR 399


>gi|290509468|ref|ZP_06548839.1| NADPH2 dehydrogenase [Klebsiella sp. 1_1_55]
 gi|289778862|gb|EFD86859.1| NADPH2 dehydrogenase [Klebsiella sp. 1_1_55]
          Length = 366

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 63/179 (35%), Gaps = 22/179 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNP-DIVGDCI 108
            V +A   +  G+  I L+            P +      +G  L   +  P ++     
Sbjct: 159 FVASALRAQRLGFELIELHAAHGYLLHQFLSPLSNQRRDEYGGSLDNRLRYPLEVFNAIR 218

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+   +++ V +     V+            + ++  G + I + +      GLSP+ +
Sbjct: 219 EAVGNTMAVGVRLSATDWVEGGWDCEQSIQFSQQLEALGSDYIHVSSG-----GLSPQQS 273

Query: 169 RKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
             +         ++I+++     IG+ G + D  QA   L     D + + RA   +  
Sbjct: 274 ITVGPGYQLPFAHDIRQQVAIPVIGV-GLITDPQQAEAALEDGDADLIALARAVLYDPH 331


>gi|291296487|ref|YP_003507885.1| NADH:flavin oxidoreductase/NADH oxidase [Meiothermus ruber DSM
           1279]
 gi|290471446|gb|ADD28865.1| NADH:flavin oxidoreductase/NADH oxidase [Meiothermus ruber DSM
           1279]
          Length = 775

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 32/226 (14%), Positives = 69/226 (30%), Gaps = 28/226 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLN---PDIVGDCI 108
           + V AA+   + G++ + L+           CP        +G  L      P  V   +
Sbjct: 557 EFVRAAQWGVEAGFDWLELHCAHGYLLSAFICPLTNQRTDEYGGSLENRCRYPLEVFRAL 616

Query: 109 AAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            A+  + L I V +                 + +  K++G + I       +  G + + 
Sbjct: 617 RAVWPEHLPISVRISAHDWAPGGNTPDDAVEIARLFKEAGCDLID------VSSGQTTRQ 670

Query: 168 NRKIPNLDYD--IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            R +    Y       I+ E   +     G + +      I+ +   D   I R    + 
Sbjct: 671 ARPVYGRMYQTPFADRIRNEVG-IATMAVGAIYEADHVNSIIAAGRADLCAIARPHLADP 729

Query: 224 -AMLTTVDEYFSNPLTGSSPIKT---RVDKDFWRKISASMTDYAAR 265
              L          ++      +   +++++  R       + A R
Sbjct: 730 HWTLNQAARLGYTEISWPKQYLSGKAQLERNLARASLERAEELAIR 775


>gi|33602748|ref|NP_890308.1| tryptophan synthase subunit alpha [Bordetella bronchiseptica RB50]
 gi|73621999|sp|Q7WD05|TRPA_BORBR RecName: Full=Tryptophan synthase alpha chain
 gi|33577190|emb|CAE35747.1| tryptophan synthase alpha chain [Bordetella bronchiseptica RB50]
          Length = 285

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 17/104 (16%)

Query: 130 QIPAVALRNLVKSIKKSGVNGI--------------WIHARKAILKGLSPKDNRKIPNLD 175
             P   +      + ++GV  I                   +  +  +S K      +LD
Sbjct: 134 DYPPEEVDEFAAMLAEAGVAPIFLLAPTSTEARIEAIGRVARGYVYYVSLKGVTGAGSLD 193

Query: 176 YDIVYE---IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            D V     + + +  + +G+  G+ D + A +I    D V+IG
Sbjct: 194 TDDVARKLALIRRHVHIPVGVGFGIRDAASAQRIAAHADAVVIG 237


>gi|302339228|ref|YP_003804434.1| dihydroorotate dehydrogenase [Spirochaeta smaragdinae DSM 11293]
 gi|301636413|gb|ADK81840.1| dihydroorotate dehydrogenase family protein [Spirochaeta
           smaragdinae DSM 11293]
          Length = 362

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 40/125 (32%), Gaps = 11/125 (8%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA------LRNLVKSIKKSGVNGIW 152
              + + + +    +    PV VK      D + A        +  +        V  I 
Sbjct: 126 YREETIREMVVRAKRLTDKPVFVKISPNWPDAVSAAIDTLRLGVDGITAMDSLGPVLRID 185

Query: 153 IHARKAILKGLSPKDN---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILP 208
           I   + +L G   +       I  +    V EI  +  D  I   GG+ +   A++ ++ 
Sbjct: 186 IKTGRPMLGGAHGEGWLSGAAIKPIALSYVAEIAAKT-DKPIIGLGGVMNAEDAVEMMMA 244

Query: 209 SVDGV 213
               V
Sbjct: 245 GASAV 249


>gi|167574879|ref|ZP_02367753.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia oklahomensis
           C6786]
          Length = 416

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 80/242 (33%), Gaps = 25/242 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++  + G++ + ++            P A      +G         + + + A  
Sbjct: 165 FARTAELAAEAGFDGVQIHAAHGYLLSQFLSPVANKRTDEYGGTPANRRRFLQEVVRATR 224

Query: 113 KAL--SIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSP 165
           +A+   +PV VK      ++  +      ++   ++  G++ + I         + G+  
Sbjct: 225 RAVGSGVPVGVKLNSTDFERGGLSEAESLDVALMLQDEGIDLLEISGGNYEAPAMTGVIR 284

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            D+R           E  +    L + L GGL   +   K+L   +VD + + R      
Sbjct: 285 NDDRSREAYFLSY-AESLRAKTRLPLMLTGGLRTEAFMRKVLTDGAVDMLGLARPLALAP 343

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGL 283
            +   +          ++P       D + +++     +  R + SG       R   G 
Sbjct: 344 DLPARLLRGEDVGALPAAPKVGYAPLDSYLQLAWHAAQF--RRIGSGLAP----RPFGGA 397

Query: 284 FH 285
           F 
Sbjct: 398 FK 399


>gi|163739909|ref|ZP_02147315.1| NADH oxidase [Phaeobacter gallaeciensis BS107]
 gi|161386783|gb|EDQ11146.1| putative NADH:flavin oxidoreductase / NADH oxidase [Phaeobacter
           gallaeciensis BS107]
          Length = 407

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 27/184 (14%), Positives = 62/184 (33%), Gaps = 24/184 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGS---FGACLMLNPDIVGDCIAA 110
           VE+AK+ ++ G++ + ++             S R++  S    G  L     +V   + A
Sbjct: 149 VESAKLAQEAGFDGVEIHAAHGYLLSSSL--SPRINNRSDRWGGEPLENRARLVLAVVHA 206

Query: 111 MCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKG 162
           +  A++    +  ++   D             +   ++ +GV+ I I        +    
Sbjct: 207 VRGAVNKDFILAVKLNSSDFQKGGFDHEDSVKVAVMLEAAGVDFIEISGGNFEEPSAYSH 266

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
                + +I    +       K    + + + GG    S     +     D + IGR   
Sbjct: 267 AKKSGSTQIREAYFLDYAAAIKAALSIPLMVTGGFRSASVMNDAIESGKTDLIGIGRPFI 326

Query: 221 KNSA 224
            + +
Sbjct: 327 TDPS 330


>gi|134101554|ref|YP_001107215.1| Oye family NADH-dependent flavin oxidoreductase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291008164|ref|ZP_06566137.1| Oye family NADH-dependent flavin oxidoreductase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133914177|emb|CAM04290.1| NADH-dependent flavin oxidoreductase, Oye family [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 372

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 62/202 (30%), Gaps = 49/202 (24%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
             +AA+  E  G++ + L+       + +            S+G  L+       D +AA
Sbjct: 154 FADAAQQAERIGFDGVELHGA--HGYLIDQFLWERTNRRTDSYGGDLVSRTKFAADIVAA 211

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + + +    PV ++      D   A        L  ++  +  +GV+      R+   + 
Sbjct: 212 IRERVAPDFPVVLRFSQWKADHYDARLAEDPGELETVLTPLADAGVDAFHASGRRYW-QP 270

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG-------------------LEDMSQA 203
             P     +    +      KK      I + G                    +E +   
Sbjct: 271 EFPDSGSNLNIAGWT-----KKVTGKPVITV-GSVGLDSVFEPSSLTGAAGAKVESIELL 324

Query: 204 LKILPS--VDGVMIGRAAYKNS 223
           L  L     D V +GRA   + 
Sbjct: 325 LDRLEQDEFDLVAVGRALLADP 346


>gi|307327146|ref|ZP_07606335.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces
           violaceusniger Tu 4113]
 gi|306887227|gb|EFN18224.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces
           violaceusniger Tu 4113]
          Length = 372

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 28/200 (14%), Positives = 62/200 (31%), Gaps = 46/200 (23%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
             +AA+  E  G++ + L+       + +             +G  L        D +AA
Sbjct: 155 FTKAAREAERIGFDGVELHGA--HGYLIDQFLWERTNRRTDGYGGDLASRTTFAADLVAA 212

Query: 111 MCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + + +    P+ ++      +            L  ++  + ++GV+      R+   + 
Sbjct: 213 IREQVAPGFPIVLRFSQWKSENYDARLAENPKELEAVLTPLAEAGVDAFHASGRRHW-QA 271

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFI-----------------GLNGGLEDMSQALK 205
             P    ++    +      KK      I                 G N  ++ + + L 
Sbjct: 272 EFPDTGSELNIAGWA-----KKVTGKPVITVGSVGLDTVFEPGSLSGANAAVDTIERLLD 326

Query: 206 ILP--SVDGVMIGRAAYKNS 223
            L     D V +GRA   + 
Sbjct: 327 RLERDEFDLVAVGRALLADP 346


>gi|253583384|ref|ZP_04860582.1| N-acetylmannosamine-6-phosphate 2-epimerase [Fusobacterium varium
           ATCC 27725]
 gi|251833956|gb|EES62519.1| N-acetylmannosamine-6-phosphate 2-epimerase [Fusobacterium varium
           ATCC 27725]
          Length = 242

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 24/133 (18%), Positives = 50/133 (37%), Gaps = 16/133 (12%)

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV--KCRIGVDDQIPAVALRNLVKSI 143
             V  G +G       D   + I  + K  + P+    K  +  +D     +++  V  I
Sbjct: 36  KLVACGEWGDACGYRIDTPENIIK-VRKITNKPIIGLWKINMETEDVFITPSMKE-VDEI 93

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
             +G + + + A   +                Y+++ EIK++ PDL I     + +  +A
Sbjct: 94  VNAGADIVAVDATNRVNSYGRKA---------YELIPEIKEKYPDLLILA--DIRNAEEA 142

Query: 204 LKILPSVDGVMIG 216
            + L  +   M+ 
Sbjct: 143 REALK-IGAHMVA 154


>gi|76803241|ref|YP_331336.1| NADPH dehydrogenase (OLD yellow enzyme); 2,4-dienoyl-CoA reductase
           (NADPH) [Natronomonas pharaonis DSM 2160]
 gi|76559106|emb|CAI50704.1| NADPH dehydrogenase (old yellow enzyme); 2,4-dienoyl-CoA reductase
           (NADPH) [Natronomonas pharaonis DSM 2160]
          Length = 357

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 56/177 (31%), Gaps = 26/177 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               EAA    D G++ + L+            P     E  +G         + + + +
Sbjct: 157 EAFTEAAVRAVDAGFDIVELHAAHGYLLHEFLSPVTNTREDDYGGSFENRTRFLREVVVS 216

Query: 111 MCKAL--SIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           + +A+    P+ V+          +         L   ++  GV+ I + A       + 
Sbjct: 217 VREAIPEGTPLFVRISATDWLPDRESWTVDDSTRLAAELRPLGVDLIDVSAGA-----IH 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
           P          Y + Y  +     + +G  G +     A +I+ +      GRAA  
Sbjct: 272 PDQQVPDTGPHYQVPYAEQVAESGVPVGTVGKITTPEGADEIIRN------GRAALA 322


>gi|187779767|ref|ZP_02996240.1| hypothetical protein CLOSPO_03363 [Clostridium sporogenes ATCC
           15579]
 gi|187773392|gb|EDU37194.1| hypothetical protein CLOSPO_03363 [Clostridium sporogenes ATCC
           15579]
          Length = 242

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 31/134 (23%), Positives = 60/134 (44%), Gaps = 20/134 (14%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNG 150
           G   + N ++V + +    + ++I +  K      +    I +    +  K ++K GV  
Sbjct: 103 GTAALNNRELVEEAVKKYDEKIAIGIDAKNEKVAINGWLNISSTNYIDFAKEMEKIGVRN 162

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGGLEDMSQALKILP 208
           I           +S     K PNL+     ++KK  E+    I  +GG++D+   LK++ 
Sbjct: 163 II-------FTDISKDGTLKGPNLN-----QLKKLNESVSCNIIASGGIKDIED-LKVIK 209

Query: 209 SVD--GVMIGRAAY 220
            +D  GV++G+A Y
Sbjct: 210 EMDIYGVIVGKAIY 223


>gi|329116884|ref|ZP_08245601.1| dihydroorotate dehydrogenase 1A [Streptococcus parauberis NCFD
           2020]
 gi|326907289|gb|EGE54203.1| dihydroorotate dehydrogenase 1A [Streptococcus parauberis NCFD
           2020]
          Length = 311

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 30/183 (16%), Positives = 58/183 (31%), Gaps = 22/183 (12%)

Query: 67  KIVEDFGYNE-INLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K +++  Y   + LN+ CP   V      A    + ++    +  +    + P+ VK   
Sbjct: 114 KTIQESDYQGLVELNLSCP--NVPGKPQIAY---DFEMTHSLLTEVFSYFTKPLGVKLPP 168

Query: 126 GVDD-------QIPAVALRNLVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPN 173
             D        +I        V  +   G   +          K    G+     +    
Sbjct: 169 YFDIVHFDQAAEIFNQFPLAFVNCVNSVGNGLVIEDESVVIKPKTGFGGIGGDYIKPTAL 228

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDE 231
            +    Y+  + NP + I   GG+++   A +  L     V IG A   +   +   + E
Sbjct: 229 ANVHAFYQ--RLNPSIQIVGTGGVKNGRDAFEHILCGASMVQIGTALHEEGPEIFNRITE 286

Query: 232 YFS 234
              
Sbjct: 287 ELR 289


>gi|311695901|gb|ADP98774.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [marine bacterium
           HP15]
          Length = 245

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 52/136 (38%), Gaps = 11/136 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++     ++G   + +        G           ++ +IV  I ++ PDL I + GG+
Sbjct: 34  DMATRWVEAGARRLHLVDLNGAFAG---------EPVNGEIVQAIARKYPDLPIQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKI 255
                    L   V  V+IG  A K    +T +  ++  + + G      RV  D W ++
Sbjct: 85  RSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKKFPGHIIVGLDAKDGRVATDGWAEV 144

Query: 256 SASMTDYAARHLHSGG 271
           S  M    A+   + G
Sbjct: 145 SEVMATDLAKRFANDG 160


>gi|332967994|gb|EGK07081.1| N-acylglucosamine-6-phosphate 2-epimerase [Desmospora sp. 8437]
          Length = 232

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 17/104 (16%), Positives = 41/104 (39%), Gaps = 7/104 (6%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K R+     +  V+      + ++ G + +       ++      + +KI + D+ IV 
Sbjct: 121 IKERLPDQLLMADVSTVEEAVAAERLGFDVVS----TTLVGYTRKTEGKKIYDDDFAIVK 176

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           EI + + ++ +   G +     A + L      V++G  A    
Sbjct: 177 EILQ-SVNIPVFAEGNVYTPETAKRCLELGCHAVVVG-GAITRP 218


>gi|218676284|ref|YP_002395103.1| NADH oxidase [Vibrio splendidus LGP32]
 gi|218324552|emb|CAV26054.1| NADH oxidase [Vibrio splendidus LGP32]
          Length = 370

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 74/211 (35%), Gaps = 23/211 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A+   +  G++ + ++            P     E  +G  L      + +   A
Sbjct: 145 DAFAQASLRAQKSGFDGVEIHAAHTYLINQFLSPYYNQREDEYGGNLENRMRFLLEIYIA 204

Query: 111 MCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
             K +    P+ VK       +  +     R + K +++ GV+GI     IH +   + G
Sbjct: 205 TRKLVGDDFPILVKLTASEFFEGGVTFDETRLVCKKLEQVGVDGIVVSGNIHGKADTMIG 264

Query: 163 LSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRA 218
            S  D   I    Y  +  + I ++  ++ +   GGL D    +A+     ++   + R 
Sbjct: 265 ES-HDGFTIQAEGYFHEYGHAISQDV-NIPVITVGGLTDFDAIEAIANNTGIEYFALSRP 322

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
                 ++    E   +P+      K R  +
Sbjct: 323 LLSEPHLVKRWKEGDRSPVECERCSKCRTKR 353


>gi|291548093|emb|CBL21201.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Ruminococcus
           sp. SR1/5]
          Length = 641

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 70/212 (33%), Gaps = 20/212 (9%)

Query: 47  EKPLALQIGGADISKLV----EAAKIVEDFGYNEINLNVG---------CPSARVHEGSF 93
            + +  Q+   ++ +L+    EAA+   + G + + +++           P        F
Sbjct: 130 GRDIPKQLTTEEVYELIKGYGEAARRAMEAGADAVEIHMAHGYLVSTFLSPRTNKRVDEF 189

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVN 149
           G C           I  + KA    + V  RI   D++P          +   ++  G++
Sbjct: 190 GGCFENRMRFSRLIIEEVKKATQGKIAVLARINCADEVPGGLDVHDSAAIAAYLESCGLD 249

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
           G+ +     I                   V EIK+   ++ +   G   +   A  ++  
Sbjct: 250 GLHVSRAVHIKDEFMWAPTVIHGGFSAAEVEEIKRAV-NIPVITVGRYTEPQFAELMVKE 308

Query: 210 --VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
              D V  GR +  + AM     E     +T 
Sbjct: 309 GRADLVAFGRQSLADPAMPKKAQEERLEDMTP 340


>gi|253996904|ref|YP_003048968.1| NADH:flavin oxidoreductase/NADH oxidase [Methylotenera mobilis
           JLW8]
 gi|253983583|gb|ACT48441.1| NADH:flavin oxidoreductase/NADH oxidase [Methylotenera mobilis
           JLW8]
          Length = 368

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 60/179 (33%), Gaps = 21/179 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AA+   D G+  + L++           P +      +G           + IA++
Sbjct: 159 DFALAAQRALDAGFEWLELHLAHGYMGQSFFSPHSNKRTDEYGGSYENRARFSKEMIASV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKS---GVNGIWIHARKAILKGLSPK 166
            K     +P+T +  +   D      L   ++ I +    G++ + +     I     P+
Sbjct: 219 RKIWPDHLPLTARFGVLEYDNKDEETLNESIQLINEWKQIGLDMLSVSVGFTI-----PE 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            N          + E  +    L +    G      A + +    +D VMIGRA  +N 
Sbjct: 274 TNIPWGPAFLAPIAERVRNETQLPVSSAWGFGAPKLADQAVRNEQLDLVMIGRAHLENP 332


>gi|157812545|gb|ABV80329.1| NifR3-like protein [Gluconacetobacter diazotrophicus PAl 5]
          Length = 99

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 20/64 (31%)

Query: 243 IKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEAG 302
           I    D    + I     D    H  +   L+   +H+     G P+S   R  +     
Sbjct: 2   IVPDPDLATEKAIVLDHYDMMLSHFGAHPGLRLARKHVAWYSAGLPDSAGFRAAINRVDQ 61

Query: 303 ASTA 306
           A  A
Sbjct: 62  AQEA 65


>gi|119716077|ref|YP_923042.1| NADH:flavin oxidoreductase/NADH oxidase [Nocardioides sp. JS614]
 gi|119536738|gb|ABL81355.1| NADH:flavin oxidoreductase/NADH oxidase [Nocardioides sp. JS614]
          Length = 671

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 36/209 (17%), Positives = 69/209 (33%), Gaps = 31/209 (14%)

Query: 50  LALQIGGADISKL------------VEAAKIVEDFGYNEINLNVG---------CPSARV 88
           ++  + G+    +              AAK     G + + L+VG          P    
Sbjct: 134 VSHHLWGSVPYAMSRADVRTVMEAYASAAKRAVRGGMDGVELSVGHGQMINLFLSPLTNQ 193

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            E  +G           + +  + +A+    + V V         +   A  ++ + I +
Sbjct: 194 REDEYGGSDEARFRFCREVLEGVREAVGDALLLVRVNGSDEAPGSLDQDAWLDIDQRIAE 253

Query: 146 SG-VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           SG V+ I + A        S      +    Y       K+  DL +G  G + D + A 
Sbjct: 254 SGLVDAINVSAN----FYGSVIPTMAVARGCYLHYARAVKQRVDLPVGAVGRITDPTMAA 309

Query: 205 KILPSVDGVMIG--RAAYKNSAMLTTVDE 231
           + L   D   +G  RA   +  ++  + E
Sbjct: 310 QALEDGDADFVGMTRAHIADPHLVRKIAE 338


>gi|218438248|ref|YP_002376577.1| dihydroorotate dehydrogenase 2 [Cyanothece sp. PCC 7424]
 gi|218170976|gb|ACK69709.1| dihydroorotate dehydrogenase [Cyanothece sp. PCC 7424]
          Length = 343

 Score = 40.2 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 27/118 (22%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI--- 103
           E P+   + G      +E AK +E+ G + + LNV               L  + ++   
Sbjct: 102 EIPIIASLNGVSTGGWLEYAKRIEEAGADALELNV-------------YYLPNDFEMSGA 148

Query: 104 -----VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                  + +  +   +SIPV +K      +      + N+ K +  +G +G+ +  R
Sbjct: 149 QVEQNYVEILRIIKSEISIPVAMKLSPYFSN------MANMAKQLADAGADGLVLFNR 200


>gi|167921108|ref|ZP_02508199.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           BCC215]
          Length = 370

 Score = 40.2 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 159 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 219 AAF-PDDRPVGVRVSATDWVSGGWELDDTLAFAHELKRRDCDWIDVSSG-----GVSPLQ 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 273 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 330


>gi|167721867|ref|ZP_02405103.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           DM98]
          Length = 370

 Score = 40.2 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 159 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 219 AAF-PDDRPVGVRVSATDWVSGGWELDDTLAFAHELKRRDCDWIDVSSG-----GVSPLQ 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 273 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 330


>gi|159901199|ref|YP_001547446.1| isopentenyl pyrophosphate isomerase [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159894238|gb|ABX07318.1| isopentenyl-diphosphate delta-isomerase, type 2 [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 344

 Score = 40.2 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 46/137 (33%), Gaps = 26/137 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           + A+C+AL +PV  K       ++         K + ++GV  I +              
Sbjct: 179 VEAICRALPVPVIAK-------EVGNGIGAKTAKRLVEAGVQAIDVAGAGGTSWSEVERF 231

Query: 161 KGLSPKDNRKIPN-LDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
           +  +    R       +     + + +++   P++ I  +GGL   +  A  I    D  
Sbjct: 232 RHRTQAGQRIAATFAGWGIPTTEAIKQVRAALPNIGIIGSGGLRSGLDLAKAIALGADL- 290

Query: 214 MIGRAAYKNSAMLTTVD 230
                A     +L   D
Sbjct: 291 ----GASAAPNLLAQND 303


>gi|241203628|ref|YP_002974724.1| NADH:flavin oxidoreductase/NADH oxidase [Rhizobium leguminosarum
           bv. trifolii WSM1325]
 gi|240857518|gb|ACS55185.1| NADH:flavin oxidoreductase/NADH oxidase [Rhizobium leguminosarum
           bv. trifolii WSM1325]
          Length = 365

 Score = 40.2 bits (93), Expect = 0.44,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 64/180 (35%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V AA    D G+  + L+            P +   +  +G         + + +AA+
Sbjct: 159 DFVAAAIHARDIGFRWLVLHFAHGYLGQSFFSPHSNQRDDEYGGSADNRGRFLLETLAAV 218

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSI---KKSGVNGIWIHARKAILKGLSPK 166
            +      P+T +  +   D      L++ +  +   KK+G++ I +      L   +P 
Sbjct: 219 REVWPEDRPLTARFGVIEFDGRDQETLQDAIDLVGKFKKAGLDFIDV-----SLGFSTPA 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
            N            +  ++   L    +  +    QA +++    +D VMIG+A   N  
Sbjct: 274 ANIPWGPGFIAPYADQVRKATGLPGAASWNITQPEQADELIRSGQLDLVMIGKAMLANPH 333


>gi|325675408|ref|ZP_08155092.1| 2,4-dienoyl-CoA reductase [Rhodococcus equi ATCC 33707]
 gi|325553379|gb|EGD23057.1| 2,4-dienoyl-CoA reductase [Rhodococcus equi ATCC 33707]
          Length = 652

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 24/138 (17%), Positives = 52/138 (37%), Gaps = 7/138 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGV 148
           +G  L      + + IAA+  A+   + +  R+  D+Q+P   + +    + + ++ SG 
Sbjct: 188 YGGSLENRARFLVEVIAAVRAAIGPNLVLGVRLSGDEQVPGGTVLDEAVAVARIVEASGA 247

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       + L   +        Y + + E  +    L +   G L++ ++A + L
Sbjct: 248 VDYINTTMGVATETLHLVEPSMATPRGYALHISEAIRAAVALPVIGVGRLKEPAEAERAL 307

Query: 208 PS--VDGVMIGRAAYKNS 223
                D V I R    + 
Sbjct: 308 TDGRCDLVGITRGQIADP 325


>gi|254281653|ref|ZP_04956621.1| NADH oxidase [gamma proteobacterium NOR51-B]
 gi|219677856|gb|EED34205.1| NADH oxidase [gamma proteobacterium NOR51-B]
          Length = 706

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 22/138 (15%), Positives = 49/138 (35%), Gaps = 8/138 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGV 148
           +G  L        + I A+ + +   + V  R  +++ IP          + K+I+  G+
Sbjct: 195 YGGSLENRMRFPLEVIRAVRERVGKDMVVGIRFTIEEMIPGGMEPEDWVTIAKTIEAEGL 254

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLD-YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
               +    A            +PN        ++K+E   + +    G+    +A ++L
Sbjct: 255 IDYVMTTAGAYQSPTYLMPPYDVPNAWLVPTCAKLKQEL-SIPVFAISGISTAKEAEEVL 313

Query: 208 PSVDGVMIG--RAAYKNS 223
            +    M+   RA   + 
Sbjct: 314 AAGHADMVAMTRAQIADP 331


>gi|145299083|ref|YP_001141924.1| imidazole glycerol phosphate synthase subunit HisF [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|167012126|sp|A4SMQ4|HIS6_AERS4 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|142851855|gb|ABO90176.1| imidazole glycerol phosphate synthase subunit HisF [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 257

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L +   + G + +            +  D R +       V E+     D+   + G
Sbjct: 32  IVELARRYAEEGADELV------FYDITASSDARVVDKSWVSRVAEVI----DIPFCVAG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G++ +  A +IL    D V I   A  +  ++T + E F 
Sbjct: 82  GIKSVEDARQILEFGADKVSINSPALADPGLITRLAERFG 121


>gi|254184062|ref|ZP_04890653.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1655]
 gi|184214594|gb|EDU11637.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1655]
          Length = 370

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 159 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 219 AAF-PDDRPVGVRVSATDWVSGGWELDDTLAFAHELKRRDCDWIDVSSG-----GVSPLQ 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 273 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 330


>gi|332163015|ref|YP_004299592.1| 2,4-dienoyl-CoA reductase [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|325667245|gb|ADZ43889.1| 2,4-dienoyl-CoA reductase [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
          Length = 673

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 24/197 (12%), Positives = 60/197 (30%), Gaps = 38/197 (19%)

Query: 49  PLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF---------- 93
           P A Q    D      +     A++ +  GY+ + +        +    +          
Sbjct: 127 PFAPQELSHDEVLQTIADFANCARLAKQAGYDGVEV--------MGSEGYLINQFLTART 178

Query: 94  -------GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKS 142
                  G           + + A+ +A      +  R+     V+D      +  L ++
Sbjct: 179 NHRNDEWGGDFTRRMRFAVEIVRAVREATGPDFILIYRLSMLDLVEDGSSWDEIEQLARA 238

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++++G   I  +      +   P     +P   +  V        ++ +     + + + 
Sbjct: 239 VEQAGATLI--NTGIGWHEARIPTIATMVPRAGFSWVTRKLMGKVNIPLITTNRINNPAV 296

Query: 203 ALKILP--SVDGVMIGR 217
           A ++L     D V + R
Sbjct: 297 AEQVLTDGCADMVSMAR 313


>gi|318604113|emb|CBY25611.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia enterocolitica subsp.
           palearctica Y11]
          Length = 673

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 24/197 (12%), Positives = 60/197 (30%), Gaps = 38/197 (19%)

Query: 49  PLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF---------- 93
           P A Q    D      +     A++ +  GY+ + +        +    +          
Sbjct: 127 PFAPQELSHDEVLQTIADFANCARLAKQAGYDGVEV--------MGSEGYLINQFLTART 178

Query: 94  -------GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKS 142
                  G           + + A+ +A      +  R+     V+D      +  L ++
Sbjct: 179 NHRNDEWGGDFTRRMRFAVEIVRAVREATGPDFILIYRLSMLDLVEDGSSWDEIEQLARA 238

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++++G   I  +      +   P     +P   +  V        ++ +     + + + 
Sbjct: 239 VEQAGATLI--NTGIGWHEARIPTIATMVPRAGFSWVTRKLMGKVNIPLITTNRINNPAV 296

Query: 203 ALKILP--SVDGVMIGR 217
           A ++L     D V + R
Sbjct: 297 AEQVLTDGCADMVSMAR 313


>gi|307568319|pdb|3N16|A Chain A, Xena - Y183f
          Length = 363

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGFLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|126451506|ref|YP_001068301.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106a]
 gi|134281535|ref|ZP_01768243.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 305]
 gi|167740836|ref|ZP_02413610.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           14]
 gi|167826416|ref|ZP_02457887.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           9]
 gi|167896490|ref|ZP_02483892.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           7894]
 gi|167904890|ref|ZP_02492095.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           NCTC 13177]
 gi|167913170|ref|ZP_02500261.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           112]
 gi|226193085|ref|ZP_03788695.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei Pakistan
           9]
 gi|237814387|ref|YP_002898838.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei MSHR346]
 gi|242316899|ref|ZP_04815915.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106b]
 gi|126225148|gb|ABN88688.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106a]
 gi|134247202|gb|EBA47288.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 305]
 gi|225934685|gb|EEH30662.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei Pakistan
           9]
 gi|237505892|gb|ACQ98210.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei MSHR346]
 gi|242140138|gb|EES26540.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106b]
          Length = 370

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 159 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 219 AAF-PDDRPVGVRVSATDWVSGGWELDDTLAFAHELKRRDCDWIDVSSG-----GVSPLQ 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 273 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 330


>gi|92113007|ref|YP_572935.1| 2,4-dienoyl-CoA reductase [Chromohalobacter salexigens DSM 3043]
 gi|91796097|gb|ABE58236.1| 2,4-dienoyl-CoA reductase [Chromohalobacter salexigens DSM 3043]
          Length = 670

 Score = 40.2 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 31/231 (13%), Positives = 74/231 (32%), Gaps = 22/231 (9%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+  +VA + L+         +     +  QI        V+ A+   + GY+
Sbjct: 104 LHAGRYAYSRSLVAPSPLKAPINPFTPRALSGGEVIRQI-----EDYVQCARRAREAGYD 158

Query: 76  EINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
            + +            C      +  +G           + +  + +AL     +  R+ 
Sbjct: 159 GVEVMGSEGYLINQFLCLRTNRRDDEWGGAFANRMRFAVEIVRGIRRALGDDFLIIFRLS 218

Query: 127 ----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
               V++      +  L ++I+ +G N I  +      +   P     +P   +  V   
Sbjct: 219 MIDLVEEGSSHDEVVMLGRAIEAAGANLI--NTGIGWHEARVPTIVTSVPRAAFTAVTRR 276

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            ++  D+ +     +     A ++L     D V + R    +   ++   +
Sbjct: 277 LRDELDVPLIATNRINMPDVAERVLAEGHADMVSMARPFLADPEWVSKARD 327


>gi|226948837|ref|YP_002803928.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum A2 str.
           Kyoto]
 gi|226841793|gb|ACO84459.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum A2 str.
           Kyoto]
          Length = 339

 Score = 40.2 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 56/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AAK  ++ G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAKAAKRAKESGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V + + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCRELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +   +I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASKIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|242219815|ref|XP_002475682.1| predicted protein [Postia placenta Mad-698-R]
 gi|220725112|gb|EED79115.1| predicted protein [Postia placenta Mad-698-R]
          Length = 398

 Score = 40.2 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 26/141 (18%), Positives = 42/141 (29%), Gaps = 21/141 (14%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKC---------RIGVDDQIPAVALRN---LVKSIKK 145
           M  P      IA    A   P+ V+              D       +         ++K
Sbjct: 233 MRWP---LRLIARARAAWDKPLFVRISATDWAEGPEQAPDGTWTQWGIEQSKVFAGELQK 289

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            GV+ I         +    +     P        ++KK  P+L IG  G + +  QA  
Sbjct: 290 LGVDLIDCSTGGLWAQ----QQIPLGPGYQVPFAEQLKKAYPNLPIGAVGLITEPEQAES 345

Query: 206 ILPS--VDGVMIGRAAYKNSA 224
            L     D V + R   ++  
Sbjct: 346 YLNEGKADVVFLARELMRDPH 366


>gi|168180160|ref|ZP_02614824.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum NCTC 2916]
 gi|182668930|gb|EDT80906.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum NCTC 2916]
          Length = 339

 Score = 40.2 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 56/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AAK  ++ G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAKAAKRAKESGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V + + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCRELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +   +I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASKIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|153941459|ref|YP_001390848.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum F str.
           Langeland]
 gi|152937355|gb|ABS42853.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum F str.
           Langeland]
 gi|295318917|gb|ADF99294.1| oxidoreductase, FAD/FMN-binding protein [Clostridium botulinum F
           str. 230613]
          Length = 339

 Score = 40.2 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 56/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AAK  ++ G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAKAAKRAKESGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V + + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCRELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +   +I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASKIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|157106968|ref|XP_001649565.1| (s)-2-hydroxy-acid oxidase [Aedes aegypti]
 gi|108879701|gb|EAT43926.1| (s)-2-hydroxy-acid oxidase [Aedes aegypti]
          Length = 389

 Score = 40.2 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 33/142 (23%), Positives = 53/142 (37%), Gaps = 26/142 (18%)

Query: 88  VHEGSFGACL------MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           + +G  G+ L       L+P +V D I  + K   +PV VK  +  +D           +
Sbjct: 191 IIQGKDGSGLSQYGEQQLDPSLVWDDIRWLIKISELPVLVKGILTKED----------AE 240

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDM 200
                GV+GIW+                       +++ EI     D   I ++GG+ + 
Sbjct: 241 IAVSKGVSGIWV--------SNHGGRQLDSAPATIEVLPEIVAAVGDQTTIIVDGGVRNG 292

Query: 201 SQALKILP-SVDGVMIGRAAYK 221
               K L    + VMIGR A  
Sbjct: 293 KDVFKALGLGANMVMIGRPALW 314


>gi|221232005|ref|YP_002511157.1| N-acetylmannosamine-6-phosphate 2-epimerase [Streptococcus
           pneumoniae ATCC 700669]
 gi|220674465|emb|CAR69025.1| putative N-acetylmannosamine-6-phosphate 2-epimerase [Streptococcus
           pneumoniae ATCC 700669]
          Length = 229

 Score = 40.2 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 24/114 (21%), Positives = 45/114 (39%), Gaps = 12/114 (10%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K +      +  ++     K   +SGV+ +        L G +P    K  N D+++V 
Sbjct: 122 IKVKYPNQLLMADISTFEEGKVAAESGVDFV-----GTTLSGYTPYS-PKKDNPDFELVE 175

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
            + KE  D+ +   G +    QA K+L      V++G  A         + + F
Sbjct: 176 RLVKEL-DVPVIAEGRISTPEQARKMLDLGAYAVVVG-GAITRP---KEIAQRF 224


>gi|53721586|ref|YP_110571.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia pseudomallei K96243]
 gi|134284185|ref|ZP_01770878.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 305]
 gi|167897303|ref|ZP_02484705.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia pseudomallei 7894]
 gi|167921882|ref|ZP_02508973.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia pseudomallei BCC215]
 gi|217425488|ref|ZP_03456981.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 576]
 gi|254182307|ref|ZP_04888902.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1655]
 gi|254187370|ref|ZP_04893883.1| NADH:flavin oxidoreductase/nadh oxidase family protein
           [Burkholderia pseudomallei Pasteur 52237]
 gi|254198741|ref|ZP_04905161.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei S13]
 gi|52212000|emb|CAH38007.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia pseudomallei K96243]
 gi|134244503|gb|EBA44608.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 305]
 gi|157935051|gb|EDO90721.1| NADH:flavin oxidoreductase/nadh oxidase family protein
           [Burkholderia pseudomallei Pasteur 52237]
 gi|169655480|gb|EDS88173.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei S13]
 gi|184212843|gb|EDU09886.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1655]
 gi|217391451|gb|EEC31480.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 576]
          Length = 687

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 70/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P   V    +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNVRTDEWGGSLENRLRFGVEVLTAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  +D V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLANGMIDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|332362574|gb|EGJ40374.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK1056]
          Length = 240

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K++GV  I +      L+G +          + D++ +IK E   L I + G
Sbjct: 32  VLEQARVFKEAGVTMIHVVDLDGALEGRA---------ANRDLIAQIKAETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN A +    E F 
Sbjct: 82  GIRSLDQIEDYLAVGIDRVIIGSMAVKNPAFVEAALECFG 121


>gi|225870062|ref|YP_002746009.1| dihydroorotate dehydrogenase [Streptococcus equi subsp. equi 4047]
 gi|254788903|sp|C0M8R7|PYRD_STRE4 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|225699466|emb|CAW92981.1| putative dihydroorotate dehydrogenase [Streptococcus equi subsp.
           equi 4047]
          Length = 311

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 36/229 (15%), Positives = 73/229 (31%), Gaps = 37/229 (16%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLN 80
           + TEM    A       +++G S +E              +++A   ++   Y   + LN
Sbjct: 84  IVTEMQKDQASKHHFL-SVVGMSAEET-----------ETILKA---IQASDYQGLVELN 128

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN 138
           + CP   V        L  + +     +  +    + P+ +K     D      A A+ N
Sbjct: 129 LSCP--NVPGK---PQLAYDFEATDQLLKKIFSYYTKPLGIKLPPYFDIVHFDQAAAIFN 183

Query: 139 -----LVKSIKKSGVNGIW-----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
                    +   G   +      +   K    G+     +     +    Y+  + N  
Sbjct: 184 QYPLAFANCVNSIGNGLVIDDEQVVIKPKNGFGGIGGDYIKPTALANVHAFYQ--RLNSS 241

Query: 189 LFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
           + I   GG++    A +  L     V IG A   +  A+   + +   +
Sbjct: 242 IQIIGTGGVKTGRDAFEHILCGAAMVQIGTALHQEGPAIFKRITKELQD 290


>gi|167741651|ref|ZP_02414425.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           14]
          Length = 687

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 70/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P   V    +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNVRTDEWGGSLENRLRFGVEVLTAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  +D V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVRIPVMHAQSIRDAGQAERLLANGMIDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|33240322|ref|NP_875264.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|39931404|sp|Q7VC70|HIS4_PROMA RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|33237849|gb|AAP99916.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
          Length = 256

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            L+   + +IK++   + I + GG+  + +A  ++   VD V++G  A +N  ++  + E
Sbjct: 61  PLNDSAIRKIKEKL-SIPIQIGGGIRTIQRAEDLIELGVDRVILGTIAIENPNIIEKLSE 119


>gi|330966474|gb|EGH66734.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 360

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 36/226 (15%), Positives = 80/226 (35%), Gaps = 37/226 (16%)

Query: 28  VADAILRGDKKNIL--GFSTQEKPLALQI--GGADISKLVEAAKIVEDFGYNEINLNV-- 81
           VA + +R   K  +   F+   +P AL++      ++   +AA    + G++ + ++   
Sbjct: 120 VAPSAIRAQTKTFVNNAFTDVSEPRALELSELPGIVNDFSQAAANAIEAGFDGVEIHGAN 179

Query: 82  ---------GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--------PVTVKCR 124
                       SA V   ++G  +     ++ + I A+ K +          PV+    
Sbjct: 180 GYLLDQFIKD--SANVRTDAYGGSVGNRARLLLEVITAVVKEIGAQRTGVRISPVSPANG 237

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D  P      + + + + G+  + +           P+D   +   DYD    +++
Sbjct: 238 VASSDPQPQYEY--IAEQLSEQGIAFLHVVEGAT----GGPRD---VAPFDYD---ALRQ 285

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                ++  NG   D+          D V  GR    N  ++  + 
Sbjct: 286 RFKHTYLANNGYDLDLETVRVNANKADLVAFGRPFISNPDLIERLK 331


>gi|312131399|ref|YP_003998739.1| dihydroorotate dehydrogenase [Leadbetterella byssophila DSM 17132]
 gi|311907945|gb|ADQ18386.1| dihydroorotate dehydrogenase [Leadbetterella byssophila DSM 17132]
          Length = 336

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 16/118 (13%), Positives = 44/118 (37%), Gaps = 18/118 (15%)

Query: 104 VGDCIAAMCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW-------- 152
           + + + A+ K       P+ +K        +    L ++++ I++SG+ GI         
Sbjct: 195 LLEILNALQKENGPNGKPIFLKIAP----DLSYEQLDDIIEIIQESGIAGIIATNTTLSR 250

Query: 153 --IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
             + ++     G      + +     +++  IK +  ++ +   GG+     A +   
Sbjct: 251 ANLKSKNVEEIGAGGLSGKPLKERSTEVIRYIKGK-SEIPVIGVGGIHTPEDAEEKFS 307


>gi|302205467|gb|ADL09809.1| Putative NAD (P)H-dependent reductase [Corynebacterium
           pseudotuberculosis C231]
          Length = 357

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 34/198 (17%), Positives = 69/198 (34%), Gaps = 28/198 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V A++   D G + + L+            PS+ V    FG      P+     +  +
Sbjct: 154 EFVAASRRAVDAGLDGVELHGANGYLLHEFLSPSSNVRTDEFGG----TPENRARFVIQV 209

Query: 112 CKALSIPVT---VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A++  +    V  RI  +  I  V   +  +++ K  V    I + +     +   D 
Sbjct: 210 VQAVAEEIGAHRVGLRISPEHNIQGVLETDREETLAKYRVLLNEIRSLELAYLSILHADY 269

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNS 223
           R       D V+++ +     F+ LN G    ++  + +        D V +GR    N 
Sbjct: 270 RS------DFVHQLAEAFGG-FVILNSGFSTYTEYAEAVGIVESGYADAVAVGRELIANP 322

Query: 224 AMLTTVDEYFSNPLTGSS 241
            ++    E     +    
Sbjct: 323 DLVRRWQEGIELNVPDPD 340


>gi|153001049|ref|YP_001366730.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS185]
 gi|151365667|gb|ABS08667.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS185]
          Length = 368

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 53/128 (41%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + + +AA+ +     +P+T +  +   D      L     LVK  K++G++ + +    +
Sbjct: 211 LLETVAAVREVWPQHLPLTARFGVIEFDHKDEETLTESIALVKQFKQAGLDMLNV----S 266

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
           I       +    P     I   +++E     +  + G+++ + A   +    +D VMIG
Sbjct: 267 ICFSTPTANIPWSPAFLAPIAARVRQEVG-FPVATSWGMDNPNHANAAIEDEQMDLVMIG 325

Query: 217 RAAYKNSA 224
           +A   N  
Sbjct: 326 KAFLANPH 333


>gi|90411799|ref|ZP_01219808.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Photobacterium profundum 3TCK]
 gi|90327361|gb|EAS43725.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Photobacterium profundum 3TCK]
          Length = 676

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 29/215 (13%), Positives = 66/215 (30%), Gaps = 43/215 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
           K +E+A I +  GY+ + ++       VHEG                 +G          
Sbjct: 159 KFIESAVIAQKSGYDGVEIHA------VHEGYLLDQFTMSFFNKRTDQYGGSFENRYRFA 212

Query: 105 GDCIAAMCKAL--SIPVTVKC----------------RIGVDDQIPAVALRNLVKSIKKS 146
            + +  +        PV+++                     +            K ++++
Sbjct: 213 VEMVEGIKAICGEDFPVSLRYSVKGNMKGFGQGILPGEQAQEVGRDMEEGLKAAKYLQEA 272

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + + + A        +   N   P +       +  E  D+ + + G +ED   A   
Sbjct: 273 GYDALNVDAGTYDAWYWNHPPNYFKPGMYQPYCKAV-SEVVDIPVLMAGRMEDPELASHA 331

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           +     DG+ +GR    +  ++  +     N +  
Sbjct: 332 INEGIADGISMGRPLLADPDVVNKIRRGRFNEVRP 366


>gi|81428060|ref|YP_395059.1| dihydroorotate dehydrogenase 1A [Lactobacillus sakei subsp. sakei
           23K]
 gi|78609701|emb|CAI54747.1| Putative dihydroorotate oxidase, catalytic subunit [Lactobacillus
           sakei subsp. sakei 23K]
          Length = 313

 Score = 40.2 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 25/175 (14%), Positives = 51/175 (29%), Gaps = 23/175 (13%)

Query: 77  INLNVGCP-SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD----DQI 131
           + LN+ CP      +  +      + + V   +  + +    P+ VK     D    DQ+
Sbjct: 125 VELNLSCPNVPGKPQTGY------DFETVEQILTRVFEVYEGPLGVKLPPYFDIVHFDQM 178

Query: 132 PAV---ALRNLVKSIKKSG----VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            A+        + S+   G    ++            G        I       V+   +
Sbjct: 179 AAILNQFPLAFINSVNSIGNGLTIDAATERVSIKPKHGFGGIGGDYIKPTALANVHTFYQ 238

Query: 185 EN-PDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKN--SAMLTTVDEYFSN 235
              P++ I   GG++      +  L     V +G  A       +   +      
Sbjct: 239 RLKPEIQIIGTGGVKSGQDVFEHLLCGASMVQVGT-ALHKEGPQIFDRLTAELQT 292


>gi|172056724|ref|YP_001813184.1| NADH:flavin oxidoreductase/NADH oxidase [Exiguobacterium sibiricum
           255-15]
 gi|171989245|gb|ACB60167.1| NADH:flavin oxidoreductase/NADH oxidase [Exiguobacterium sibiricum
           255-15]
          Length = 340

 Score = 40.2 bits (93), Expect = 0.48,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 65/193 (33%), Gaps = 18/193 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + VEAA  VE  GY+ I L+            P +   +  +G  +      + + I A+
Sbjct: 144 QFVEAALRVEQAGYDFIELHGAHGYLINTFLSPLSNKRQDQYGGSMENRMRFLLEIIDAI 203

Query: 112 CKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +   + + V+          + A     L + + K  ++ +   +   +    +     
Sbjct: 204 QEKSDLSLWVRISAADHAPGGMTAADYIPLAEELLKRNIDLLDCSSGAVV----ANAVPE 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
             P        EIK+    +  G  G +   + A +I+     D +++ R   +    + 
Sbjct: 260 VYPGYQVPYAAEIKQATG-IKTGAVGLITTATLAEEIIRSERADVILLARELLRQPYWVY 318

Query: 228 TVDEYFSNPLTGS 240
                  + ++  
Sbjct: 319 HAAAELKDEVSLP 331


>gi|315179852|gb|ADT86766.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           furnissii NCTC 11218]
          Length = 257

 Score = 40.2 bits (93), Expect = 0.48,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SADDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|254478824|ref|ZP_05092190.1| oxidoreductase, FAD/FMN-binding family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214035231|gb|EEB75939.1| oxidoreductase, FAD/FMN-binding family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 593

 Score = 40.2 bits (93), Expect = 0.48,   Method: Composition-based stats.
 Identities = 26/189 (13%), Positives = 60/189 (31%), Gaps = 18/189 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDC 107
               +AA+  ++ G++ + +             P +      +G      M  P +    
Sbjct: 96  EAFGQAARRAKEAGFDAVEIHGAHGYLINQFLSPYSNKRTDEYGGSFENRMRFP-LEVVR 154

Query: 108 IAAMCKALSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
                     P+   +     V   +     +   + + + G++ + I         +  
Sbjct: 155 RVREEVGPDFPIIYRMSAEEYVPGGLTIEDTKIFAQKLVEEGIDALHISGGVYESSAMII 214

Query: 166 KDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +          +    IKK  N  + + + G ++D   A +I+     D V +GRA   +
Sbjct: 215 QPAAIPQGCFVENAAAIKKAINSKVPVIVVGRIKDPIMAEQIIREGKADLVSMGRALLAD 274

Query: 223 SAMLTTVDE 231
             +   V E
Sbjct: 275 PELPRKVSE 283


>gi|207722665|ref|YP_002253101.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum MolK2]
 gi|206587847|emb|CAQ18429.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum MolK2]
          Length = 785

 Score = 40.2 bits (93), Expect = 0.48,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 64/217 (29%), Gaps = 29/217 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
              V AA +  + G++ + L   C           P   +    +G  L   +  P  V 
Sbjct: 555 DDFVRAAGLAVEAGFDWLEL--HCAHGYLLSSFISPLTNLRSDEYGGPLENRLRYPLEVF 612

Query: 106 DCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             + A+  A   P++V+      V   I       + +  K +G + I   + +     +
Sbjct: 613 RAVRAVWPA-DKPMSVRISAHDWVQGGITPDDAVEIARRFKAAGADMIDCSSGQ-----V 666

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           S K+      +      +  +    +     G + +      I+ +   D   + R    
Sbjct: 667 SKKEQPVYGRMFQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLA 726

Query: 222 NS-AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           N    L          L    P + R  K    +   
Sbjct: 727 NPAWALNEAARI--GYLDMPWPQQYRAGKLQLERNLE 761


>gi|240168692|ref|ZP_04747351.1| dihydroorotate dehydrogenase 2 [Mycobacterium kansasii ATCC 12478]
          Length = 337

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 23/114 (20%), Positives = 47/114 (41%), Gaps = 16/114 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV----GCPSARVHEGSFGACLMLNPD 102
           + P+   +  +        A+ ++D G   I LN+    G P  +V +G+     +    
Sbjct: 100 DIPVIASLNASTPGSWARYARSMQDAGAAAIELNIYHLPGDPGPKVSDGAA----VEQRH 155

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +  D +AA+  A ++PV VK            A  ++   +  +G +G+ +  R
Sbjct: 156 L--DVLAAVKAATAVPVAVKLSPFFS------ATADMAHRLDAAGADGLVLFNR 201


>gi|227503329|ref|ZP_03933378.1| imidazole glycerol phosphate synthase subunit HisF [Corynebacterium
           accolens ATCC 49725]
 gi|227075832|gb|EEI13795.1| imidazole glycerol phosphate synthase subunit HisF [Corynebacterium
           accolens ATCC 49725]
          Length = 256

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 21/113 (18%), Positives = 38/113 (33%), Gaps = 11/113 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L    ++ G + +      A   G S            D+V     +   + + + GG+
Sbjct: 35  ELAARYEELGADELTFLDVSASKHGRSTM---------LDVVRR-TADQVFIPLTVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
             +    ++L    D V +  AA  N  +L  + E F +     S    R D 
Sbjct: 85  RSVDNVRELLRTGADKVSVNTAAIGNPDLLRELAEVFGSQCIVLSVDARRTDA 137


>gi|104783036|ref|YP_609534.1| xenobiotic reductase A [Pseudomonas entomophila L48]
 gi|95112023|emb|CAK16750.1| xenobiotic reductase A [Pseudomonas entomophila L48]
          Length = 363

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 60/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +     +P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPEHLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P+ N          + E  +   D+ +    G      A   L    +D V +GRA   +
Sbjct: 272 PETNIPWGPAFMGPIAERVRREADIPVTSAWGFGTPELAEGALKADQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|254299811|ref|ZP_04967259.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 406e]
 gi|157809801|gb|EDO86971.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 406e]
          Length = 687

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 70/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P   V    +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNVRTDEWGGSLENRLRFGVEVLTAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  +D V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVRIPVMHAQSIRDAGQAERLLANGMIDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|260768152|ref|ZP_05877086.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           furnissii CIP 102972]
 gi|260616182|gb|EEX41367.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           furnissii CIP 102972]
          Length = 257

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SADDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|257462422|ref|ZP_05626836.1| NADH oxidase [Fusobacterium sp. D12]
 gi|317060086|ref|ZP_07924571.1| NADH oxidase [Fusobacterium sp. D12]
 gi|313685762|gb|EFS22597.1| NADH oxidase [Fusobacterium sp. D12]
          Length = 318

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 50/137 (36%), Gaps = 8/137 (5%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V   I    +       +  R+  +D      +  + K +++ G++ + +          
Sbjct: 173 VKSLIEKTRELFDDRFLLSYRMSGNDPEVEDGI-EMAKFLEQMGLDLLHVSNGVPKEVKQ 231

Query: 164 SPKDNRKIPNLDYDIV----YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
           + K +   P+  +  +     EIKK    + +    G++   QA ++L    VD V +GR
Sbjct: 232 AVKISNYPPDFPFHWITFLGIEIKKAV-SIPVIAVYGIKTEKQASRLLEEFDVDFVAVGR 290

Query: 218 AAYKNSAMLTTVDEYFS 234
           A       +    + F 
Sbjct: 291 AMIFYPNWMKKCRKDFE 307


>gi|53717123|ref|YP_105246.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 23344]
 gi|67640445|ref|ZP_00439251.1| probable N-methylproline demethylase (Stachydrineutilization
           protein StcD) [Burkholderia mallei GB8 horse 4]
 gi|76818900|ref|YP_337261.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710b]
 gi|121597276|ref|YP_990312.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei SAVP1]
 gi|124382065|ref|YP_001024811.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei NCTC 10229]
 gi|126442793|ref|YP_001061830.1| oxidoreductase [Burkholderia pseudomallei 668]
 gi|126445991|ref|YP_001079152.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei NCTC 10247]
 gi|126456967|ref|YP_001074779.1| FAD/FMN-binding oxidoreductase [Burkholderia pseudomallei 1106a]
 gi|167002650|ref|ZP_02268440.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei PRL-20]
 gi|167722683|ref|ZP_02405919.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           DM98]
 gi|167818843|ref|ZP_02450523.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           91]
 gi|167848709|ref|ZP_02474217.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           B7210]
 gi|167905664|ref|ZP_02492869.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           NCTC 13177]
 gi|167913969|ref|ZP_02501060.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           112]
 gi|237508511|ref|ZP_04521226.1| probable N-methylproline demethylase (Stachydrineutilization
           protein StcD) [Burkholderia pseudomallei MSHR346]
 gi|242313257|ref|ZP_04812274.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106b]
 gi|254175862|ref|ZP_04882521.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 10399]
 gi|254203209|ref|ZP_04909571.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei FMH]
 gi|254208544|ref|ZP_04914893.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei JHU]
 gi|254265331|ref|ZP_04956196.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710a]
 gi|254355818|ref|ZP_04972097.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei 2002721280]
 gi|52423093|gb|AAU46663.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 23344]
 gi|76583373|gb|ABA52847.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710b]
 gi|121225074|gb|ABM48605.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei SAVP1]
 gi|124290085|gb|ABM99354.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia mallei NCTC
           10229]
 gi|126222284|gb|ABN85789.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           668]
 gi|126230735|gb|ABN94148.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106a]
 gi|126238845|gb|ABO01957.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia mallei NCTC
           10247]
 gi|147746254|gb|EDK53332.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei FMH]
 gi|147751231|gb|EDK58299.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei JHU]
 gi|148024789|gb|EDK82972.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei 2002721280]
 gi|160696905|gb|EDP86875.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 10399]
 gi|235000716|gb|EEP50140.1| probable N-methylproline demethylase (Stachydrineutilization
           protein StcD) [Burkholderia pseudomallei MSHR346]
 gi|238521161|gb|EEP84615.1| probable N-methylproline demethylase (Stachydrineutilization
           protein StcD) [Burkholderia mallei GB8 horse 4]
 gi|242136496|gb|EES22899.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1106b]
 gi|243061695|gb|EES43881.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei PRL-20]
 gi|254216333|gb|EET05718.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710a]
          Length = 687

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 70/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P   V    +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNVRTDEWGGSLENRLRFGVEVLTAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  +D V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVRIPVMHAQSIRDAGQAERLLANGMIDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|322805820|emb|CBZ03385.1| putative NADH-dependent flavin oxidoreductase [Clostridium
           botulinum H04402 065]
          Length = 339

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 56/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AAK  ++ G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAKAAKRAKESGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V K + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCKELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +   +I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASKIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|284988780|ref|YP_003407334.1| NADH:flavin oxidoreductase/NADH oxidase [Geodermatophilus obscurus
           DSM 43160]
 gi|284062025|gb|ADB72963.1| NADH:flavin oxidoreductase/NADH oxidase [Geodermatophilus obscurus
           DSM 43160]
          Length = 361

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 26/150 (17%), Positives = 53/150 (35%), Gaps = 22/150 (14%)

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V ++     + Q      R+ V++   + V+ +    R   L  LS   +        +
Sbjct: 220 KVGLRISPEHNIQDAYETDRDDVRATYGALVDQL----RPLGLAYLSVLHSEPAG----E 271

Query: 178 IVYEIKKENPDLFIGLN---GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEY 232
           +V E+++      +  N   G +    +A++++     D V +GRA   N  ++      
Sbjct: 272 LVQELRERFGG-PLVANSGFGSVTTRDEAVRLIEAAHADAVAVGRAVIANPDLVERWQ-- 328

Query: 233 FSNPLTGSSPIKTRVDKDFWRKISASMTDY 262
                 G  P        F+   +   TDY
Sbjct: 329 ------GEHPENEPKAHLFYAPGAEGYTDY 352


>gi|237785967|ref|YP_002906672.1| phosphomannomutase [Corynebacterium kroppenstedtii DSM 44385]
 gi|237758879|gb|ACR18129.1| Phosphomannomutase [Corynebacterium kroppenstedtii DSM 44385]
          Length = 850

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 28/158 (17%), Positives = 55/158 (34%), Gaps = 31/158 (19%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A++  + G +EI++        V   +  A    +   V   I A+  A+  P  +K
Sbjct: 87  AEEARLAVNNGADEIDM--------VINLAAAAE--GDWATVEKDIRAVRDAVPSPTVLK 136

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
             I     +   A+     + K +G + +          G  P             +  +
Sbjct: 137 V-ILETALLSDDAIVAACNAAKNAGADFV------KTSTGFHP-----SGGASAHAIRLM 184

Query: 183 KKEN-PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
           ++   PD+ +  +GG+    +AL+        MI   A
Sbjct: 185 RETVGPDMGVKASGGIRTAEKALE--------MIAAGA 214


>gi|126740139|ref|ZP_01755829.1| hypothetical protein RSK20926_15671 [Roseobacter sp. SK209-2-6]
 gi|126718958|gb|EBA15670.1| hypothetical protein RSK20926_15671 [Roseobacter sp. SK209-2-6]
          Length = 769

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 67/208 (32%), Gaps = 22/208 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V AA++ +  G++ I L+            P + +   ++G  L        +  AAM
Sbjct: 555 EFVGAAQMADRCGFDMIELHSAHGYLISSFISPKSNIRTDAYGGSLENRLRYPLEVFAAM 614

Query: 112 CKA--LSIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
                   P++V+        D+ +       + ++  ++GV+ I + A +  +      
Sbjct: 615 RDVWPAGKPMSVRISANDWVGDEGVTPEEAVEIARAFAEAGVDIIDVSAGQTSIDAQPVY 674

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS- 223
                          I+ E   L     G + +   A  IL +   D V +GR    +  
Sbjct: 675 GRMFQTP----FSDRIRNEAG-LATMAVGNIYEADHANSILMAGRADLVCVGRPHLADPF 729

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
             L               P     D+ +
Sbjct: 730 WTLHEAARIGDRQADWPLPYLAGRDQAW 757


>gi|188492120|ref|ZP_02999390.1| 2,4-dienoyl-CoA reductase [Escherichia coli 53638]
 gi|188487319|gb|EDU62422.1| 2,4-dienoyl-CoA reductase [Escherichia coli 53638]
          Length = 672

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 32/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|169334525|ref|ZP_02861718.1| hypothetical protein ANASTE_00928 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259242|gb|EDS73208.1| hypothetical protein ANASTE_00928 [Anaerofustis stercorihominis DSM
           17244]
          Length = 352

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 62/177 (35%), Gaps = 21/177 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA   +  G+  + L+       C    P+       +G  L        + I A
Sbjct: 140 EYFVNAALRAKKAGFKAVELHGAHGYLLCEFTAPNYNKRTDEYGGSLENRFRFPIEVIKA 199

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +A+   +P+  +    V D    +      K + ++GV+ + I         L   + 
Sbjct: 200 VREAVGEDMPIYYRYGPCVPDIESGIKG---AKMLIEAGVDVLDISYANKEDVTLKTDN- 255

Query: 169 RKIPNLDYD-IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              P+ +Y     ++ KE  D+ +     +    +A  +L +   D   IGR    +
Sbjct: 256 ---PDFNYSVYSAKLIKEAVDVPVIAVNMISTPERAEYLLKNNYADFTAIGRELIAD 309


>gi|163758288|ref|ZP_02165376.1| hypothetical protein HPDFL43_01645 [Hoeflea phototrophica DFL-43]
 gi|162284577|gb|EDQ34860.1| hypothetical protein HPDFL43_01645 [Hoeflea phototrophica DFL-43]
          Length = 258

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           DIV E+ +E   + I + GG+ D+    ++L    D V I  AA K   +L  + + + +
Sbjct: 63  DIVREVAQEAF-VPITVGGGIGDLKSVKQLLDVGADKVAINTAATKRPDILREISDTYGS 121

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
             T  S    R+ +  W  ++ +  ++  R
Sbjct: 122 QATVLSIEAKRLPQGGWEAMTDNGRNHTER 151


>gi|37927614|pdb|1PS9|A Chain A, The Crystal Structure And Reaction Mechanism Of E. Coli
           2,4- Dienoyl Coa Reductase
          Length = 671

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 32/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 109 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 160

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 161 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 210

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 211 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 268

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 269 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 314


>gi|163849399|ref|YP_001637443.1| isopentenyl pyrophosphate isomerase [Chloroflexus aurantiacus
           J-10-fl]
 gi|222527397|ref|YP_002571868.1| isopentenyl pyrophosphate isomerase [Chloroflexus sp. Y-400-fl]
 gi|163670688|gb|ABY37054.1| isopentenyl-diphosphate delta-isomerase, type 2 [Chloroflexus
           aurantiacus J-10-fl]
 gi|222451276|gb|ACM55542.1| isopentenyl-diphosphate delta-isomerase, type 2 [Chloroflexus sp.
           Y-400-fl]
          Length = 346

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 24/137 (17%), Positives = 48/137 (35%), Gaps = 13/137 (9%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL-VKSIKKSGVNGIWIHARKAILK 161
           ++      +C+ L +PV VK          A+ L  + V+ I  +G  G      +   +
Sbjct: 176 LLARI-EEVCRRLEVPVIVKEVGNGIGAADAIRLYEVGVRIIDVAGAGGTSWSEVERFRQ 234

Query: 162 GLSPKDNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMI 215
                        D+     + + E++   PD+ +  +GG+   +  A  I    D    
Sbjct: 235 PNDTGRRVASAFADWGLPTTECIREVRAALPDVTLIASGGVRSGVDVAKAIALGADLAGT 294

Query: 216 GRAAYKNSAMLTTVDEY 232
            R      A+   ++E 
Sbjct: 295 AR-----PALFDAINER 306


>gi|291527594|emb|CBK93180.1| tryptophan synthase, alpha chain [Eubacterium rectale M104/1]
          Length = 255

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 73/237 (30%), Gaps = 58/237 (24%)

Query: 45  TQEKPLALQIGGADI--SKLVEAAKIVEDFGYNEINLN-------VGCPSARVHEGSFGA 95
              K     I   D       +  +     G + I L           P   V +G+   
Sbjct: 9   ENGKAFIPFITCGDPNLETTAKIVREAVANGADLIELGIPFSDPTAEGP---VIQGANIK 65

Query: 96  CLML--NPDIVGDCIAAMCKALSIP------------------VTVKCRIGVD----DQI 131
            L      D V D +  + K ++IP                  ++    IG+D      I
Sbjct: 66  ALAAGVTTDKVFDLVRDLRKDVTIPMVFMTYANVVYSYGAEKFISTCNEIGIDGLILPDI 125

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLD 175
           P       +   +K  V+ I   A  +                ++  L     R     D
Sbjct: 126 PYEEKEEFLPLCEKYDVDLISFIAPTSNDRIAMIAKEATGFIYVISSLGVTGTRSEIKTD 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
              + ++ +EN D+   +  G+    QA K+    DG ++G A      ++  +DEY
Sbjct: 186 LASIVKVIRENTDVPCAIGFGISTPKQAKKMADISDGAIVGSA------IIKIIDEY 236


>gi|152989566|ref|YP_001346782.1| putative FMN oxidoreductase [Pseudomonas aeruginosa PA7]
 gi|150964724|gb|ABR86749.1| probable FMN oxidoreductase [Pseudomonas aeruginosa PA7]
          Length = 368

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 30/169 (17%), Positives = 59/169 (34%), Gaps = 11/169 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G C      ++    AA+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGGCFENRIRLLLQVAAAVRKAWPEALPLFVRLSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +K+ GV+ I + +        +  +    P    +    ++KE   +  G  G + +
Sbjct: 250 ARRLKELGVDLIDVSSGGTA----ANAEIPVGPGYQTEFAERVRKEAG-IASGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
             QA  IL     D +++ R   ++        +   N      P   R
Sbjct: 305 PVQAEHILRTGQADLILLARELLRDPYWPLHAADELRNEQMPWPPQYLR 353


>gi|317970078|ref|ZP_07971468.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Synechococcus sp.
           CB0205]
          Length = 331

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 36/180 (20%), Positives = 65/180 (36%), Gaps = 37/180 (20%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           + +Q+GG      V +A+  E+         + C   RV     G   +  P++V +   
Sbjct: 149 IPVQLGGG-----VRSAERAEEL--------LQCGLDRVI---LGTVAIEKPELVKEL-- 190

Query: 110 AMCKALSIPVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A      + V +  + G+       +   V    L KS   SGV  I             
Sbjct: 191 ASRHPGKVVVGIDAKDGLVATRGWIETSTVQATELAKSFDGSGVAAII---------STD 241

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP----SVDGVMIGRAAY 220
              +  +   + D +  +  E   + +  +GG+  +   L +L      V GV++GRA Y
Sbjct: 242 IATDGTLAGPNIDALRAMA-EASSIPVIASGGIGTLEDILSLLSIAPLGVSGVIVGRALY 300


>gi|116328257|ref|YP_797977.1| 2,4-dienoyl-CoA reductase (NADPH) [Leptospira borgpetersenii
           serovar Hardjo-bovis L550]
 gi|116121001|gb|ABJ79044.1| 2,4-dienoyl-CoA reductase (NADPH) [Leptospira borgpetersenii
           serovar Hardjo-bovis L550]
          Length = 669

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 69/190 (36%), Gaps = 10/190 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGV 148
           FG       +   + +  + K +     V  R+   D IP          L + +K +G 
Sbjct: 183 FGGSPEKRMNFAVEVMKNVRKKVGKDFPVIYRMSGIDLIPGNPTFEEVILLAEKLKATGA 242

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKIL 207
           + + I       +   P  +  +P   +  +  EIK++  D+ I  +  +       +IL
Sbjct: 243 DALNI--GIGWHESRIPTISMLVPRGAWAKISGEIKEKIKDIPIIASNRVNMPEVMTRIL 300

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL-TGSSPIKTRVDKDFWRKISASMTDYAA 264
                D + + R    +  ++  +       + T  +  +  +D  F  ++ + + + +A
Sbjct: 301 KNHEADILSMARPFLADPDIVNKIRADQEERINTCIACNQACLDHTFKEQLVSCLVNPSA 360

Query: 265 RHLHSGGKLQ 274
                 GKL+
Sbjct: 361 NRELEIGKLK 370


>gi|220932566|ref|YP_002509474.1| glutamate synthase (NADPH) large subunit [Halothermothrix orenii H
           168]
 gi|219993876|gb|ACL70479.1| glutamate synthase (NADPH) large subunit [Halothermothrix orenii H
           168]
          Length = 437

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 25/118 (21%), Positives = 46/118 (38%), Gaps = 14/118 (11%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +  + + + +PV +K             L   +    ++GV+ I +   +A   G   
Sbjct: 233 ELVKRLKEKVDVPVGLKFAATHH-------LEKELAIAVEAGVDFITVDGAEAGTHGGPT 285

Query: 166 --KDNRKIPNLDY--DIVYEIKKENP--DLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
             +D+  +P L      V  ++KE     + +  +GGL      LK L    D V IG
Sbjct: 286 ILEDHFGLPTLHALCRTVTFLEKEGLKDKISVIASGGLLTPGHYLKALALGADAVYIG 343


>gi|325687703|gb|EGD29724.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus
           sanguinis SK72]
          Length = 240

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +    +  K++GV  I +      L+G +          + D++ +IK E   L I + G
Sbjct: 32  VLEQAQVFKEAGVTMIHVVDLDGALEGRA---------ANRDLIAQIKAETG-LAIQVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G+  + Q    L   +D V+IG  A KN A +    E F 
Sbjct: 82  GIRSLDQIEDYLAVGIDRVIIGSMAVKNPAFVEAALECFG 121


>gi|307153336|ref|YP_003888720.1| isopentenyl-diphosphate delta-isomerase, type 2 [Cyanothece sp. PCC
           7822]
 gi|306983564|gb|ADN15445.1| isopentenyl-diphosphate delta-isomerase, type 2 [Cyanothece sp. PCC
           7822]
          Length = 344

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 50/124 (40%), Gaps = 21/124 (16%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR------KAILK 161
           IA +C+ L +PV VK       ++       + K + ++GV  I +         K   +
Sbjct: 180 IAELCQKLPVPVMVK-------EVGNGISAPMAKQLIEAGVAAIDVAGAGGTSWAKVESQ 232

Query: 162 GLSPKDNRKIPN--LDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
               K  R++     D+     + +  I++  P + +  +GG+++ +  A  +    D  
Sbjct: 233 RAKDKKQRRLGQTFADWGIPTAECITSIREIAPSIPLIASGGIKNGLDAAKALALGADLA 292

Query: 214 MIGR 217
            + R
Sbjct: 293 GLAR 296


>gi|325122373|gb|ADY81896.1| NADH-flavin oxidoreductase/NADH oxidase [Acinetobacter
           calcoaceticus PHEA-2]
          Length = 412

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 33/189 (17%), Positives = 71/189 (37%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDQWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D       A   + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPTFTVAVKLNSADFQRGGFSAEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A K++   VD V I  A    
Sbjct: 270 RDGRTLAREAYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEKVVESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 329 PNLPNAWKQ 337


>gi|315617157|gb|EFU97766.1| 2,4-dienoyl-CoA reductase [NADPH] [Escherichia coli 3431]
          Length = 672

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 32/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|291302426|ref|YP_003513704.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
 gi|290571646|gb|ADD44611.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
          Length = 365

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 21/162 (12%), Positives = 46/162 (28%), Gaps = 18/162 (11%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCR---------IGVDDQIPAVALRNLV 140
           ++G           D + A+       +PV  +               +   A       
Sbjct: 203 AYGGSFEGRIRFALDVVDAVRAVWPEELPVLFRLSATDWLAEDPEDDREGWTADDTVRFA 262

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           K ++  GV+ + +        G  P               E  +    L +   G + + 
Sbjct: 263 KELQAHGVDLLDVSTG-----GNVPDAKIVTGPGYQVPFAERIRAETGLPVAAVGLITEA 317

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            QA  I+     D V++GR   ++   +    +     ++  
Sbjct: 318 HQAEDIVASGKADAVLLGRELLRDPYWVRHAAKELGAEVSAP 359


>gi|326801547|ref|YP_004319366.1| 2-nitropropane dioxygenase [Sphingobacterium sp. 21]
 gi|326552311|gb|ADZ80696.1| 2-nitropropane dioxygenase [Sphingobacterium sp. 21]
          Length = 377

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 40/108 (37%), Gaps = 7/108 (6%)

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW---IHARKAILKGLSPKDNRKIPNL 174
           P+  +C+      + A    +   +++ +GV+ I      A    +  L   ++      
Sbjct: 163 PILARCKTLGIKTVGAATTVDEAIALQHAGVDAIVATGFEAGGHRVSFLQSAEDSLTGA- 221

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYK 221
            + ++ ++  +  ++ I   GG+ D       L    D V +G A   
Sbjct: 222 -FALIPQVA-DAVNIPIIAAGGITDARGIQAALALGADAVQMGTAFLA 267


>gi|312137120|ref|YP_004004457.1| isopentenyl-diphosphate delta-isomerase [Methanothermus fervidus
           DSM 2088]
 gi|311224839|gb|ADP77695.1| isopentenyl-diphosphate delta-isomerase [Methanothermus fervidus
           DSM 2088]
          Length = 359

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 63/184 (34%), Gaps = 25/184 (13%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACL 97
             I+    ++  +   IG + +    +A ++V D     I+LN   P     +       
Sbjct: 113 YTIVREVAEDAFIIGNIGVSHVKYAKKAVEMV-DADALAIHLN---PLQEAIQPEG---- 164

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR- 156
           + +     + I  + K L +PV VK       +  A       K +K  GV  I +    
Sbjct: 165 ITHSKKTLEKIGKIVKELDVPVIVK-------ETGAGICYEDAKLLKNKGVAAIDVAGAG 217

Query: 157 ----KAILKGLSPKDNRKIPNLDYDIVYEI----KKENPDLFIGLNGGLED-MSQALKIL 207
                A+    S   +      D+ I   I     +E  D+ +  +GG+   +  A  I 
Sbjct: 218 GTSWSAVEAYRSKNSHLGKLYWDWGIPTAISTVEVREAVDIPVIASGGIRTGLDAAKAIA 277

Query: 208 PSVD 211
              D
Sbjct: 278 LGAD 281


>gi|301025133|ref|ZP_07188724.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 196-1]
 gi|299880167|gb|EFI88378.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 196-1]
          Length = 672

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 32/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|290511476|ref|ZP_06550845.1| 2,4-dienoyl-CoA reductase [Klebsiella sp. 1_1_55]
 gi|289776469|gb|EFD84468.1| 2,4-dienoyl-CoA reductase [Klebsiella sp. 1_1_55]
          Length = 673

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 143 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L K+I+ +G     I+ 
Sbjct: 192 RMRFAIEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAKAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|152996737|ref|YP_001341572.1| NADH:flavin oxidoreductase/NADH oxidase [Marinomonas sp. MWYL1]
 gi|150837661|gb|ABR71637.1| NADH:flavin oxidoreductase/NADH oxidase [Marinomonas sp. MWYL1]
          Length = 688

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 28/188 (14%), Positives = 66/188 (35%), Gaps = 18/188 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAM 111
              +AA+  ++ G + + L+           S RV++    +G           + + A+
Sbjct: 152 DFAKAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGTFEGRMKFGMEVLKAV 211

Query: 112 CKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
              +     V  RI  D+  P       ++ + +    +G+   +           +  +
Sbjct: 212 RAEVGPDFVVGMRITGDEFHPDGLGHEEMKKIAQYYDATGMVDYFGVVGSGCDTHNTLAN 271

Query: 168 ---NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              N   P   +  +    KE   + +     ++D +QA +I+ +  VD V + RA   +
Sbjct: 272 VIPNMSYPPEPFLYLAAGIKEVVKVPVIHAQNIKDPNQAKRIIEAGYVDFVGMTRAHMAD 331

Query: 223 SAMLTTVD 230
              +  + 
Sbjct: 332 PHFIAKIK 339


>gi|256556965|gb|ACU83587.1| NADH:flavin oxidoreductase [uncultured bacterium HF130_AEPn_2]
          Length = 679

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 41/124 (33%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     I   +     V+       +  L K+I+++G     I+      +
Sbjct: 200 EIVRRVREAVGPNFIIIFRLSMLDLVEGGSTWEEIVQLAKAIEQAGAT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    +    + +     +     A +IL   D  M+   R  
Sbjct: 258 ARIPTIATKVPRGAFSKVTAKLRGAVQIPLITTNRINTPEVAEQILAEGDADMVSMARPF 317

Query: 220 YKNS 223
             + 
Sbjct: 318 LADP 321


>gi|238024031|ref|YP_002908263.1| FAD/FMN-binding oxidoreductase [Burkholderia glumae BGR1]
 gi|237878696|gb|ACR31028.1| Oxidoreductase, FAD/FMN-binding [Burkholderia glumae BGR1]
          Length = 687

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGVEVLTAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    LR + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLREIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|15616726|ref|NP_239938.1| imidazole glycerol phosphate synthase subunit HisF [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|11132921|sp|P57206|HIS6_BUCAI RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|25292235|pir||H84941 hisF protein [imported] - Buchnera sp. (strain APS)
 gi|10038789|dbj|BAB12824.1| hisF protein [Buchnera aphidicola str. APS (Acyrthosiphon pisum)]
          Length = 258

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 39/97 (40%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K G++ +  +   A  K            +D   +  + K   ++   + GG++
Sbjct: 35  LARRYAKEGIDELVFYDITAATKN---------KLVDRSWIKNVSK-VINIPFCVAGGIK 84

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+L    D + I  +A  +  ++T + E F 
Sbjct: 85  SVEDAKKVLSSGADKISINSSALIDPNLITKISERFG 121


>gi|16130976|ref|NP_417552.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           str. K-12 substr. MG1655]
 gi|89109850|ref|AP_003630.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           str. K-12 substr. W3110]
 gi|170018668|ref|YP_001723622.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli ATCC
           8739]
 gi|170082623|ref|YP_001731943.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           str. K-12 substr. DH10B]
 gi|238902191|ref|YP_002927987.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           BW2952]
 gi|253772084|ref|YP_003034915.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038251|ref|ZP_04872309.1| 2,4-dienoyl-CoA reductase [Escherichia sp. 1_1_43]
 gi|254163027|ref|YP_003046135.1| 2,4-dienoyl-CoA reductase [Escherichia coli B str. REL606]
 gi|256024340|ref|ZP_05438205.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia sp.
           4_1_40B]
 gi|301644782|ref|ZP_07244757.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 146-1]
 gi|307139768|ref|ZP_07499124.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           H736]
 gi|331643779|ref|ZP_08344910.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli H736]
 gi|1176118|sp|P42593|FADH_ECOLI RecName: Full=2,4-dienoyl-CoA reductase [NADPH]; AltName:
           Full=2,4-dienoyl coenzyme A reductase
 gi|606019|gb|AAA57882.1| ORF_o672 [Escherichia coli str. K-12 substr. MG1655]
 gi|1789463|gb|AAC76116.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           str. K-12 substr. MG1655]
 gi|2584857|gb|AAB82738.1| 2,4-dienoyl-CoA reductase [Escherichia coli]
 gi|85675881|dbj|BAE77131.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           str. K12 substr. W3110]
 gi|169753596|gb|ACA76295.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli ATCC
           8739]
 gi|169890458|gb|ACB04165.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           str. K-12 substr. DH10B]
 gi|226839875|gb|EEH71896.1| 2,4-dienoyl-CoA reductase [Escherichia sp. 1_1_43]
 gi|238859748|gb|ACR61746.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           BW2952]
 gi|242378629|emb|CAQ33417.1| 2,4-dienoyl-CoA reductase [Escherichia coli BL21(DE3)]
 gi|253323128|gb|ACT27730.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974928|gb|ACT40599.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli B
           str. REL606]
 gi|253979084|gb|ACT44754.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           BL21(DE3)]
 gi|260447885|gb|ACX38307.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli DH1]
 gi|301076936|gb|EFK91742.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 146-1]
 gi|309703511|emb|CBJ02851.1| 2,4-dienoyl-CoA reductase [NADPH] [Escherichia coli ETEC H10407]
 gi|315137673|dbj|BAJ44832.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           DH1]
 gi|331037250|gb|EGI09474.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli H736]
 gi|332345037|gb|AEE58371.1| 2,4-dienoyl-CoA reductase [Escherichia coli UMNK88]
          Length = 672

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 32/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|257869966|ref|ZP_05649619.1| dihydroorotic acid dehydrogenase [Enterococcus gallinarum EG2]
 gi|257804130|gb|EEV32952.1| dihydroorotic acid dehydrogenase [Enterococcus gallinarum EG2]
          Length = 311

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 32/213 (15%), Positives = 64/213 (30%), Gaps = 30/213 (14%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCP----SARVHEGSFGACLMLNP 101
           E P    + G  + + +E  + +E   +  I  LN+ CP      +V           + 
Sbjct: 93  EAPFFFSVAGMSVEENIELLRKIEASNFRGITELNLSCPNVPGKPQVA---------YDF 143

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSG----VNG 150
            +    +  +    + P+ VK     D        +I        + SI   G    ++ 
Sbjct: 144 PLTEQILEQVFSFFTKPLGVKLPPYFDLAHFDQMAEILNKFPLTYINSINSIGNGLYIDP 203

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILPS 209
                     +G        +       V     +  P++ +   GG+     A + L  
Sbjct: 204 ETEAVVIKPKEGFGGIGGEYVKPTALANVRAFATRLKPEINVIGTGGIRSGQDAFEHLL- 262

Query: 210 VDGVM--IGRAAYKN-SAMLTTVDEYFSNPLTG 239
               M  IG    K   A+   + +  +  +T 
Sbjct: 263 CGATMLQIGTELQKEGPAIFARLKKELTEIMTA 295


>gi|302558921|ref|ZP_07311263.1| inosine-5'-monophosphate dehydrogenase [Streptomyces griseoflavus
           Tu4000]
 gi|302476539|gb|EFL39632.1| inosine-5'-monophosphate dehydrogenase [Streptomyces griseoflavus
           Tu4000]
          Length = 502

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 66/191 (34%), Gaps = 26/191 (13%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           I     ++ +K        + + L     G        A  ++E  G + I         
Sbjct: 203 ITVKDFVKAEKYPNAAKDAEGRLLVGAAVGVAGDAFERAQALIEA-GADFI--------- 252

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
            V + + G     +  +VGD +A +    S         GVD     +A R+  K++  +
Sbjct: 253 -VVDTAHG-----HSRLVGDMVAKIKSNSS---------GVDVIGGNIATRDGAKALVDA 297

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALK 205
           G +GI +      +          +P +       +  +   + +  +GGL+     A  
Sbjct: 298 GCDGIKVGVGPGSICTTRVVAGVGVPQVTAIYEAALAAKEAGVPVIGDGGLQYSGDIAKA 357

Query: 206 ILPSVDGVMIG 216
           ++   D VM+G
Sbjct: 358 LVAGADTVMLG 368


>gi|229494723|ref|ZP_04388481.1| NADH oxidase [Rhodococcus erythropolis SK121]
 gi|229318390|gb|EEN84253.1| NADH oxidase [Rhodococcus erythropolis SK121]
          Length = 705

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 54/176 (30%), Gaps = 31/176 (17%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCIA 109
              EAA  V+  G + + +   C    V               +G  +     +  + I 
Sbjct: 176 MFAEAAGRVKAAGGDAVEI--HCAHNYVLGAFLSRYTNQRSDEYGGSMENRARLACEVIR 233

Query: 110 AMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ + +   + V  R+        D +         K  +++G + I +    A+    +
Sbjct: 234 AVKEEVGGALAVIVRLAGQEYGETDGLTVDEAAAAAKMFEEAGADAIHV-TGTALNAFAN 292

Query: 165 PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
             D      + Y  D    IK+      I +           ++LP V   MI   
Sbjct: 293 FTDGPLPDKVGYYTDNATRIKQAISIPVITVG----------RMLPEVGEKMIAEG 338


>gi|197124165|ref|YP_002136116.1| NADH:flavin oxidoreductase/NADH oxidase [Anaeromyxobacter sp. K]
 gi|196174014|gb|ACG74987.1| NADH:flavin oxidoreductase/NADH oxidase [Anaeromyxobacter sp. K]
          Length = 352

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 24/139 (17%), Positives = 47/139 (33%), Gaps = 11/139 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSG 147
           ++G        +V +  AA+  A    +PV V+      V+    A     L +++K  G
Sbjct: 196 AYGGGFENRTRLVREVTAAVRAAWPEELPVLVRISATDWVEGGWDAEQSVELCRALKALG 255

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            + + +        GL P               E  +    +  G  G +    QA  ++
Sbjct: 256 ADLVDVSTG-----GLVPGAKIPAGPGYQTGFAERIRREAGVPTGSVGMITSPEQADHVI 310

Query: 208 --PSVDGVMIGRAAYKNSA 224
                D V++ R   ++  
Sbjct: 311 RSGQADLVLLARELLRDPH 329


>gi|293608822|ref|ZP_06691125.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292829395|gb|EFF87757.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 676

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 69/241 (28%), Gaps = 52/241 (21%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+   ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSTAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINLNVGCPSARVHEGSFGACL-----------------------MLNPDIVGDCI 108
            GY+ + +                 L                       M  P    + +
Sbjct: 155 AGYDGVEI-----------MGSEGYLINQFLSRHVNQRTDRWGGEIENRMRFP---VEIV 200

Query: 109 AAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+   +     +  R+     V D      +  + K+++K+GV  +  +      +   
Sbjct: 201 KAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARV 258

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           P     +P   + D    +K+    + I  +  +     A +IL     D V + R    
Sbjct: 259 PTIVTSVPRAAFVDYTAHVKQHI-SIPIIASNRINMPETAEEILATGKADMVQMARPLLA 317

Query: 222 N 222
           +
Sbjct: 318 D 318


>gi|118465531|ref|YP_883056.1| isopentenyl pyrophosphate isomerase [Mycobacterium avium 104]
 gi|118166818|gb|ABK67715.1| isopentenyl-diphosphate delta-isomerase, type 2 [Mycobacterium
           avium 104]
          Length = 344

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 25/124 (20%), Positives = 44/124 (35%), Gaps = 14/124 (11%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAILKG 162
           +     AL  PV +K    V   I   A   LV    +  V GI +          + + 
Sbjct: 179 LREAAAALDYPVLLK---EVGHGIGGAAAAELVGGEGQPPVAGIDVAGAGGTSWSRVEQF 235

Query: 163 LSPKDNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMIG 216
           +   + R     D+       + E+++  P++ +  +GG+   M  A  I    D V + 
Sbjct: 236 VRYGELRYPDLADWGVPTARAIVEVRRLLPEIPLVASGGIRTGMDAAKAIALGADVVAVA 295

Query: 217 RAAY 220
           R   
Sbjct: 296 RPLL 299


>gi|325121411|gb|ADY80934.1| 2,4-dienoyl-CoA reductase [NADPH] [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 676

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 69/241 (28%), Gaps = 52/241 (21%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+   ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSTAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINLNVGCPSARVHEGSFGACL-----------------------MLNPDIVGDCI 108
            GY+ + +                 L                       M  P    + +
Sbjct: 155 AGYDGVEI-----------MGSEGYLINQFLSRHVNQRTDRWGGEIENRMRFP---VEIV 200

Query: 109 AAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+   +     +  R+     V D      +  + K+++K+GV  +  +      +   
Sbjct: 201 KAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARV 258

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           P     +P   + D    +K+    + I  +  +     A +IL     D V + R    
Sbjct: 259 PTIVTSVPRAAFVDYTAHVKQHI-SIPIIASNRINMPETAEEILATGKADMVQMARPLLA 317

Query: 222 N 222
           +
Sbjct: 318 D 318


>gi|226304848|ref|YP_002764806.1| oxidoreductase [Rhodococcus erythropolis PR4]
 gi|226183963|dbj|BAH32067.1| putative oxidoreductase [Rhodococcus erythropolis PR4]
          Length = 390

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 25/209 (11%), Positives = 63/209 (30%), Gaps = 44/209 (21%)

Query: 65  AAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           AA++  + G++ + ++ G          P     + S+G  L     +V +   ++  A+
Sbjct: 150 AARLAVEAGFDAVEIHFGHNYFASSFLSPKLNRRKDSYGGSLENRARVVLETARSVRDAV 209

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIK-----------------------------KS 146
              + +  ++ +DD +P     +    +                               +
Sbjct: 210 GDKIAILAKLNMDDGVPGGFWVDEAIQVAQWLEASGSVDALELTMGSSLLNPMYLFKGDA 269

Query: 147 GVNGIWIHARKAI-----LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +        + +     L G S         L         +    L + L GG+ D +
Sbjct: 270 PIREFAAAMPQPVRLGVQLVGKSMLHAYPYKPLFMLEEARQIRAAVKLPLVLLGGVTDKA 329

Query: 202 QA-LKILPSVDGVMIGRAAYKNSAMLTTV 229
                +    + V + RA  +   ++  +
Sbjct: 330 GMDTAMAEGFEFVAMARALLREPDLINRI 358


>gi|213968603|ref|ZP_03396745.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato T1]
 gi|301385538|ref|ZP_07233956.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato Max13]
 gi|302060414|ref|ZP_07251955.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato K40]
 gi|302132463|ref|ZP_07258453.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|213926536|gb|EEB60089.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. tomato T1]
          Length = 360

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 36/226 (15%), Positives = 82/226 (36%), Gaps = 37/226 (16%)

Query: 28  VADAILRGDKKNIL--GFSTQEKPLALQI--GGADISKLVEAAKIVEDFGYNEINLNV-- 81
           VA + +R   K  +   F+   +P AL++      ++   +AA    + G++ + ++   
Sbjct: 120 VAPSAIRAQTKTFVNNAFTDVSEPRALELSELPGIVNDFRQAAANAIEAGFDGVEIHGAN 179

Query: 82  ---------GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--------PVTVKCR 124
                       SA V   ++G  +     ++ + + A+ K +          PV+    
Sbjct: 180 GYLLDQFIKD--SANVRTDAYGGSVENRARLLLEVVTAVVKEIGAHRTGVRISPVSPANG 237

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D  P      + + + + G+  + +           P+D   +   DYD    +++
Sbjct: 238 VASSDPQPQYEY--IAEQLSEQGIAFLHVVEGAT----GGPRD---VAPFDYD---ALRQ 285

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
                ++  NG   D++ A       D V  GR    N  ++  + 
Sbjct: 286 RFKLTYLANNGYDLDLATARVNANKADLVAFGRPFISNPDLIERLK 331


>gi|167626284|ref|YP_001676784.1| imidazole glycerol phosphate synthase subunit HisF [Francisella
           philomiragia subsp. philomiragia ATCC 25017]
 gi|189043420|sp|B0TY41|HIS6_FRAP2 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|167596285|gb|ABZ86283.1| imidazole glycerol phosphate synthase subunit HisF [Francisella
           philomiragia subsp. philomiragia ATCC 25017]
          Length = 257

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L +    +G + +  +       G SP +  K+ ++ +  + EI K+    F    G
Sbjct: 32  IIELAQKYSDAGADELVFY-----DIGASPDN--KLLSIKW--IQEIAKKINIPFCVA-G 81

Query: 196 GLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G++ +  A  IL    D + +  AA     ++  +   F 
Sbjct: 82  GIKSVENARAILNEGADKISVNSAALARPDLIDELVYEFG 121


>gi|297618217|ref|YP_003703376.1| NADH:flavin oxidoreductase/NADH oxidase [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297146054|gb|ADI02811.1| NADH:flavin oxidoreductase/NADH oxidase [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 665

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 22/178 (12%), Positives = 58/178 (32%), Gaps = 18/178 (10%)

Query: 70  EDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIP 118
            + GY+ + +             P     +  +G           + I A+  A+    P
Sbjct: 152 VEAGYDMVEVIASAGYLISQFFSPLTNQRDDEYGGDFENRCRFGVEVIKAVRTAIGSDYP 211

Query: 119 VTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           ++V+      +     ++ +      ++++G N   +       +   P+    +P   Y
Sbjct: 212 ISVRLSGNEFMQGGNGSLEMARFAARLEQAGANLFSVTGG--WHESRVPQITMNVPPGAY 269

Query: 177 DIVYE-IKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDE 231
             +   +K+   +  +     + D   A + L     D V + R    +  +   ++E
Sbjct: 270 SYLARTVKEAVNNSQVIACNRINDPVIAEQFLIEGQADLVGMARGLMADPELPRKLEE 327


>gi|238916951|ref|YP_002930468.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Eubacterium eligens ATCC 27750]
 gi|238872311|gb|ACR72021.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Eubacterium eligens ATCC 27750]
          Length = 362

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 20/117 (17%), Positives = 50/117 (42%), Gaps = 14/117 (11%)

Query: 120 TVKCRIGVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ + G+ +++   + R   + K  +++G   I        LKG           ++ +
Sbjct: 14  CVRLKKGLFNEVTVYSERPYEIAKGFEEAGAQFIHTVDLDGALKGHG---------VNAE 64

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVDEY 232
            + +I   + ++ + + GG+  +    ++L   V  V+IG  A +N   +   +D +
Sbjct: 65  TIKKIC-SSVNVPVQMGGGIRTLENIQEVLDLGVYRVIIGTKAVENPDFIKAAIDRF 120


>gi|226288127|gb|EEH43640.1| NADPH dehydrogenase [Paracoccidioides brasiliensis Pb18]
          Length = 415

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 28/192 (14%), Positives = 63/192 (32%), Gaps = 33/192 (17%)

Query: 64  EAAKIVEDFGYNEINL-NVG-------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            A +     G + I + N         C P++      +G        +  + +    + 
Sbjct: 196 AAVRRAVKAGVDYIEIHNAHGYLLFSFCSPASNNRADEYGGSFENRTRLSSEIVTITRQN 255

Query: 115 L--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +   +P+ ++          R  +        +    K + + G V+ + + +      G
Sbjct: 256 MPEDMPLFLRISASEWLEESRPDLQSWKSEDTVL-FAKILAEKGEVDLLDVSSG-----G 309

Query: 163 LSPKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
             P    K        + + +KK   D L +G  G + + + A +++   +D V +GR  
Sbjct: 310 NHPDQRIKPGPCFQAPLAFAVKKAVGDKLLVGSVGMINNGNDANRLIEEGLDIVFVGRQF 369

Query: 220 YKNS---AMLTT 228
            KN         
Sbjct: 370 QKNPGSVWQFAE 381


>gi|296536879|ref|ZP_06898925.1| NADPH dehydrogenase [Roseomonas cervicalis ATCC 49957]
 gi|296262796|gb|EFH09375.1| NADPH dehydrogenase [Roseomonas cervicalis ATCC 49957]
          Length = 375

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 58/188 (30%), Gaps = 21/188 (11%)

Query: 73  GYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           GY  I +             P +      +G        +V + + A+  A+   V +  
Sbjct: 166 GYRFIEIHGAHGYLIHQFLSPLSNQRNDGWGGDFAGRTRLVREVVRAVRAAIPDDVALGL 225

Query: 124 RIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-NRKIPNLDYDI 178
           R+   D             L   ++  G++   I +   +     P     ++P      
Sbjct: 226 RLSHTDWAEGGWTTEETVALCAELRGLGIDLADISSGGLVAHQKIPIGPGYQVPGA---- 281

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
              +++  P L +   G + +  QA  +L     D +++ RA  ++              
Sbjct: 282 -AAVRQGAPGLAVAAVGLITEPQQAQDVLSEGKADMILLARATLRDPYWPLHAAAALGRM 340

Query: 237 LTGSSPIK 244
              + P +
Sbjct: 341 DRVTVPPQ 348


>gi|291550793|emb|CBL27055.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Ruminococcus
           torques L2-14]
          Length = 643

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 63/192 (32%), Gaps = 22/192 (11%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGD 106
           +I    +AA   +  G++ + ++ G     + +             FG  +        +
Sbjct: 145 NIHMFGDAAVRAKKAGFDGVEIHAG--HGYLVQQFLSQFSNRRFDEFGGSIENRARFACE 202

Query: 107 CIAAMCKAL--SIPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIH-ARKAILK 161
               + K      PV +K      V   +     + + K ++++G + I +     A L 
Sbjct: 203 ICKDIKKKCGEDYPVIIKLSGEEKVPGGMTISDTKIIAKYLEEAGYDAIEVTICNYASLD 262

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            +S  ++  +    Y+   E  KE   + +     +     A  I+     D V I R +
Sbjct: 263 WMSAPEDEPMGFNAYN--AEKIKEGVHIPVAAIDRINTPEIAEDIIETGKADFVSISRQS 320

Query: 220 YKNSAMLTTVDE 231
                    + E
Sbjct: 321 LAEPFFPAKIKE 332


>gi|167827218|ref|ZP_02458689.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           9]
 gi|226195119|ref|ZP_03790710.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei Pakistan
           9]
 gi|225932924|gb|EEH28920.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei Pakistan
           9]
          Length = 687

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P   V    +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNVRTDEWGGSLENRLRFGVEVLTAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L    +D V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVRIPVMHAQSIRDAGQAERLLAKGMIDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|153815328|ref|ZP_01967996.1| hypothetical protein RUMTOR_01562 [Ruminococcus torques ATCC 27756]
 gi|317501684|ref|ZP_07959875.1| hypothetical protein HMPREF1026_01819 [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|145847390|gb|EDK24308.1| hypothetical protein RUMTOR_01562 [Ruminococcus torques ATCC 27756]
 gi|316896935|gb|EFV19015.1| hypothetical protein HMPREF1026_01819 [Lachnospiraceae bacterium
           8_1_57FAA]
          Length = 645

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 32/190 (16%), Positives = 76/190 (40%), Gaps = 22/190 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNV------GC-PSARVHEG--SFGACLMLNPDIV-GDCIA 109
                AA+     G + + ++       GC  + R++E    +GA  + N      + +A
Sbjct: 148 EDFALAAERAVRCGVDSLVIHGAHGQLPGCFLNKRINERTDEYGADTIENASRFTVELLA 207

Query: 110 AMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +   + ++ RI  +D I        +   VK I+   ++ + +       + L+P
Sbjct: 208 AVREKIKDRLAIEYRINANDMIEGSPSLDEVIAFVKRIEPY-IDLLHVSRGMHSEQKLAP 266

Query: 166 KDNRKI---PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
             N+ I     ++ +   +I+KE   + + + G +  + QA + +     D V + R   
Sbjct: 267 YMNQPIYYDHGINIEDAAKIRKEI-SVPVTVVGSV-TLEQAEQYIAEGKADMVSMARGLM 324

Query: 221 KNSAMLTTVD 230
            +  ++    
Sbjct: 325 ADPMVVKNAK 334


>gi|312870061|ref|ZP_07730198.1| N-acetylmannosamine-6-P epimerase [Lactobacillus oris PB013-T2-3]
 gi|311094458|gb|EFQ52765.1| N-acetylmannosamine-6-P epimerase [Lactobacillus oris PB013-T2-3]
          Length = 229

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 19/129 (14%), Positives = 43/129 (33%), Gaps = 25/129 (19%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGI--WIHA 155
           + + + + +  M            R    D +       L  V+   + G + I   +H 
Sbjct: 109 HHEELAEIVKQM------------RAEFPDTLLMADTDRLESVEIANELGFDMIGTTMHG 156

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVM 214
                +GL+  DN      D++ + E+        +   G ++  ++  + L      V+
Sbjct: 157 YTPATEGLNVADN------DFEYLKEVVDLAKA-PVIAEGKIDSPAKLKRCLELGCHAVV 209

Query: 215 IGRAAYKNS 223
           +G  A    
Sbjct: 210 VG-GAITRP 217


>gi|86137439|ref|ZP_01056016.1| NADH-dependent flavin oxidoreductase, Oye family protein
           [Roseobacter sp. MED193]
 gi|85825774|gb|EAQ45972.1| NADH-dependent flavin oxidoreductase, Oye family protein
           [Roseobacter sp. MED193]
          Length = 369

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 23/166 (13%), Positives = 42/166 (25%), Gaps = 31/166 (18%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSI 143
            +G  L        + + A+  A+    P+  +                  AL+  +  +
Sbjct: 191 GYGGDLAQRSRFALEIVRAVRAAVGDDFPIIFRFSQWKQQDYSVRLCETPEALQAFLTPL 250

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF--IGLNGGL---- 197
            ++GV+      R+         D             ++  +       +GLN       
Sbjct: 251 AEAGVDIFHCSTRRFWEPEFEGSDLNLAG-----WARKLTGKPTITVGSVGLNADFLPED 305

Query: 198 ------------EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                        D           D V +GRA   N      V E
Sbjct: 306 GTADFKAAEPASLDRLIERAERNEFDLVAVGRALIANPDWANQVAE 351


>gi|118586278|ref|ZP_01543734.1| pyridoxine biosynthesis lyase [Oenococcus oeni ATCC BAA-1163]
 gi|118433294|gb|EAV40004.1| pyridoxine biosynthesis lyase [Oenococcus oeni ATCC BAA-1163]
          Length = 294

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 67/229 (29%), Gaps = 68/229 (29%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      + A+  A+SIPV  K
Sbjct: 28  AEQAKIAEEAGATAVMALERVPSD--IRKAGGVARMADP----AIVEAVQNAVSIPVMAK 81

Query: 123 CRI---------------------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            RI                            V            V   +  G     I  
Sbjct: 82  ARIGHIVEARVLESMKVDYIDESEVLTPADDVYHIDKKAFTIPFVCGCRDLGEAARRIGE 141

Query: 156 RKAILK----------------------------GLSPKDNRKIPN---LDYDIVYEIKK 184
             A+L+                            G+SP++           YD++ EIKK
Sbjct: 142 GAAMLRTKGEPGTGNIVEAVRHMRLVNNQVNKVLGMSPEEIMVFAKELGAPYDVLLEIKK 201

Query: 185 ENPDLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAYK--NSAMLTTV 229
                 +    GG+   + A  ++    DGV +G   +K  N A     
Sbjct: 202 SGRLPVVNFAAGGVATPADAALMMELGADGVFVGSGVFKSENPAKFAKA 250


>gi|169633090|ref|YP_001706826.1| 2,4-dienoyl-CoA reductase [NADPH] (2,4-dienoyl coenzyme A
           reductase) [Acinetobacter baumannii SDF]
 gi|169151882|emb|CAP00726.1| 2,4-dienoyl-CoA reductase [NADPH] (2,4-dienoyl coenzyme A
           reductase) [Acinetobacter baumannii]
          Length = 676

 Score = 39.8 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 43/124 (34%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+   +     +  R+     V D      +  + K+++K+GV  +  +      +
Sbjct: 198 EIVKAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   + D    +K+      I  N  +     A +IL     D + + R 
Sbjct: 256 ARVPTIVTSVPRAAFVDYTAHVKQHISIPVIASNR-INMPETAEEILATGKADMIQMARP 314

Query: 219 AYKN 222
              +
Sbjct: 315 LLAD 318


>gi|53723982|ref|YP_104427.1| FAD/FMN-binding oxidoreductase [Burkholderia mallei ATCC 23344]
 gi|121599894|ref|YP_994669.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei SAVP1]
 gi|167001293|ref|ZP_02267092.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei PRL-20]
 gi|254175242|ref|ZP_04881903.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 10399]
 gi|254201501|ref|ZP_04907865.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei FMH]
 gi|52427405|gb|AAU47998.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 23344]
 gi|121228704|gb|ABM51222.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei SAVP1]
 gi|147747395|gb|EDK54471.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei FMH]
 gi|160696287|gb|EDP86257.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei ATCC 10399]
 gi|243062910|gb|EES45096.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei PRL-20]
          Length = 335

 Score = 39.8 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 124 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 183

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 184 AAF-PDDRPVGVRVSATDWVSGGWELDDTIAFAHELKRRDCDWIDVSSG-----GVSPLQ 237

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 238 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 295


>gi|291288648|ref|YP_003505464.1| dihydroorotate oxidase [Denitrovibrio acetiphilus DSM 12809]
 gi|290885808|gb|ADD69508.1| dihydroorotate oxidase [Denitrovibrio acetiphilus DSM 12809]
          Length = 326

 Score = 39.8 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 25/153 (16%), Positives = 51/153 (33%), Gaps = 33/153 (21%)

Query: 22  LYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI 77
            Y  M    A++ G  + +            P+   I         + A  +E+ G + I
Sbjct: 67  AYDYMTADAAMVYGSGEYLEYVKRAADKVTIPVIASINCEGTKWWAKFAGDIEEAGADAI 126

Query: 78  NLNVGCPSARVHEGSFGACLM---------LNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
            LN+                M            +   + +  + K +SIPV VK      
Sbjct: 127 ELNI--------------AFMPFEADITGQETEERYLEVVKEVKKTVSIPVGVKI----- 167

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
                 A+ N+++ +++ G + + +  +   LK
Sbjct: 168 -GANFSAIPNMIRKLEEVGADSVTMFNKYFQLK 199


>gi|290890547|ref|ZP_06553622.1| hypothetical protein AWRIB429_1012 [Oenococcus oeni AWRIB429]
 gi|290479943|gb|EFD88592.1| hypothetical protein AWRIB429_1012 [Oenococcus oeni AWRIB429]
          Length = 294

 Score = 39.8 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 67/229 (29%), Gaps = 68/229 (29%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      + A+  A+SIPV  K
Sbjct: 28  AEQAKIAEEAGATAVMALERVPSD--IRKAGGVARMADP----AIVEAVQNAVSIPVMAK 81

Query: 123 CRI---------------------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            RI                            V            V   +  G     I  
Sbjct: 82  ARIGHIIEARVLESMKVDYIDESEVLTPADDVYHIDKKAFTIPFVCGCRDLGEAARRIGE 141

Query: 156 RKAILK----------------------------GLSPKDNRKIPN---LDYDIVYEIKK 184
             A+L+                            G+SP++           YD++ EIKK
Sbjct: 142 GAAMLRTKGEPGTGNIVEAVRHMRLVNNQVNKVLGMSPEEIMVFAKELGAPYDVLLEIKK 201

Query: 185 ENPDLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAYK--NSAMLTTV 229
                 +    GG+   + A  ++    DGV +G   +K  N A     
Sbjct: 202 SGRLPVVNFAAGGVATPADAALMMELGADGVFVGSGVFKSENPAKFAKA 250


>gi|262404347|ref|ZP_06080902.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio sp. RC586]
 gi|262349379|gb|EEY98517.1| 2,4-dienoyl-CoA reductase [NADPH] [Vibrio sp. RC586]
          Length = 666

 Score = 39.8 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+ + D +   +       L K+++++GV    I+      +
Sbjct: 196 EIVKAIREAVGEEFIIIFRLSMLDLVEQGSTFEEVVVLAKALEEAGVT--IINTGIGWHE 253

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P    ++P   +  V E  +    + +     +    QA KIL     D V + R
Sbjct: 254 ARIPTIATQVPRAAFSWVTEKIRPYLTVPVVTCNRINTPEQAEKILASGQADMVSMAR 311


>gi|254229394|ref|ZP_04922810.1| NADH:flavin oxidoreductases, old yellow enzyme family [Vibrio sp.
           Ex25]
 gi|151938085|gb|EDN56927.1| NADH:flavin oxidoreductases, old yellow enzyme family [Vibrio sp.
           Ex25]
          Length = 173

 Score = 39.8 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 56/167 (33%), Gaps = 14/167 (8%)

Query: 104 VGDCIAAMCKALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWI----HA 155
           + +  +   K +    P+ VK       D  +     R + K +++ GV+ I +    H 
Sbjct: 4   LLEIFSETRKLVGSEFPILVKLTATEFFDGGLTFDETRVVCKKLEEVGVDAIIVSGNVHG 63

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVD---- 211
           +   L G +           +     +  ++ ++ +   GGL D+    KI  + D    
Sbjct: 64  KANELVGETFDGYTLQEEGYFHEYGHVISQDVNIPVITVGGLSDIDAIEKIAENTDIQFF 123

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISAS 258
            V   R       ++    E    P+      K R  +  +  +  +
Sbjct: 124 AV--SRPLLAEPQLIKRWKEGNRAPVDCERCSKCRTKRGNFCVVYKN 168


>gi|312887980|ref|ZP_07747564.1| NADH:flavin oxidoreductase/NADH oxidase [Mucilaginibacter paludis
           DSM 18603]
 gi|311299461|gb|EFQ76546.1| NADH:flavin oxidoreductase/NADH oxidase [Mucilaginibacter paludis
           DSM 18603]
          Length = 357

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 64/184 (34%), Gaps = 28/184 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AAK     G++ I ++ G     +               +G        ++ +   
Sbjct: 159 DFVNAAKRAVAAGFDAIEIHAG--HGYLFHQFYSNIINHRLDGYGGSFENRIRLLVETTE 216

Query: 110 AMCKALS--IPVTVKCR-IGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGL 163
            +   +   +P+ V+   +   D   A  + +   L   +K+ GV+ I   A   +    
Sbjct: 217 EIRAVIPQTMPLMVRISAVDYLDDDKAWKIEDSIVLAGILKQIGVDLITASAGGFVFLDK 276

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVD-GVMIGRAAY 220
           S    R  P+       +IK E   +  G  G + + +QA +I+     D  +M  R   
Sbjct: 277 S----RVFPSYQVPFAEKIKAETG-ILTGAVGAITEAAQADEIIASGKADLAIM-AREFL 330

Query: 221 KNSA 224
           ++  
Sbjct: 331 RDPY 334


>gi|284923109|emb|CBG36202.1| 2,4-dienoyl-CoA reductase [NADPH] [Escherichia coli 042]
          Length = 672

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 30/227 (13%), Positives = 69/227 (30%), Gaps = 45/227 (19%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSF-----------------GACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
                  +    +                 G   +       + + A+ + +     +  
Sbjct: 162 -------MGSEGYLINEFLTLRTNQRSDQWGGDYLNRMRFATEVVRAVRERVGNDFIIIY 214

Query: 124 RIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           R+ + D +           L ++I+ +G     I+      +   P     +P   +  V
Sbjct: 215 RLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAFSWV 272

Query: 180 -YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 273 TRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|116491065|ref|YP_810609.1| pyridoxine biosynthesis protein [Oenococcus oeni PSU-1]
 gi|116091790|gb|ABJ56944.1| pyridoxal phosphate synthase yaaD subunit [Oenococcus oeni PSU-1]
          Length = 294

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 67/229 (29%), Gaps = 68/229 (29%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      + A+  A+SIPV  K
Sbjct: 28  AEQAKIAEEAGATAVMALERVPSD--IRKAGGVARMADP----AIVEAVQNAVSIPVMAK 81

Query: 123 CRI---------------------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            RI                            V            V   +  G     I  
Sbjct: 82  ARIGHIIEARILESMKVDYIDESEVLTPADDVYHIDKKAFTIPFVCGCRDLGEAARRIGE 141

Query: 156 RKAILK----------------------------GLSPKDNRKIPN---LDYDIVYEIKK 184
             A+L+                            G+SP++           YD++ EIKK
Sbjct: 142 GAAMLRTKGEPGTGNIVEAVRHMRLVNNQVNKVLGMSPEEIMVFAKELGAPYDVLLEIKK 201

Query: 185 ENPDLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAYK--NSAMLTTV 229
                 +    GG+   + A  ++    DGV +G   +K  N A     
Sbjct: 202 SGRLPVVNFAAGGVATPADAALMMELGADGVFVGSGVFKSENPAKFAKA 250


>gi|224125864|ref|XP_002329736.1| predicted protein [Populus trichocarpa]
 gi|222870644|gb|EEF07775.1| predicted protein [Populus trichocarpa]
          Length = 425

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 57/172 (33%), Gaps = 25/172 (14%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 174 RVEQTGIDALEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATVPVWAKMTPNI 232

Query: 128 DD---------QIPAVALRNLVKSIKKSGVNGIWIHARKAIL-----KGLSPKDNRKIPN 173
            D         +     +  +   +   G+N   +     +       G S K    I  
Sbjct: 233 TDITQPARVSLKSGCEGVAAINTIMSVMGINLKTLRPEPCVEGYSTPGGYSSKAVHPIAL 292

Query: 174 LDYDIVYEIKKENPDLF---IGLNGGLEDMSQALK-------ILPSVDGVMI 215
                + ++ K   DL    +   GG+E  S A +        +    GVM+
Sbjct: 293 GKVMSIAKMMKSEFDLEQYSLSGIGGVETGSDAAEFILVGANTVQVCTGVMM 344


>gi|126440737|ref|YP_001061003.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 668]
 gi|126220230|gb|ABN83736.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           668]
          Length = 370

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 159 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 219 AAF-PDDRPVGVRVSATDWVSGGWELDDTIAFAHELKRRDCDWIDVSSG-----GVSPLQ 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 273 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 330


>gi|94990745|ref|YP_598845.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS10270]
 gi|94544253|gb|ABF34301.1| Dihydroorotate dehydrogenase [Streptococcus pyogenes MGAS10270]
          Length = 315

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 75/232 (32%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 72  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 129

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 130 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 184

Query: 136 LRN-----LVKSIKKSGVNGIW-----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +      +   K    G+     +     +    Y  K+ 
Sbjct: 185 IFNKYPLSFVNCVNSIGNGLVIKDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 242

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P ++I   GG++    A +  L     V IG A   +  A+   V +    
Sbjct: 243 KPSVYIIGTGGVKTGRDAFEHILCGASMVQIGTALHQEGPAIFERVTKELKT 294


>gi|56478752|ref|YP_160341.1| 2,4-dienoyl-CoA reductase [Aromatoleum aromaticum EbN1]
 gi|56314795|emb|CAI09440.1| 2,4-dienoyl-CoA reductase [Aromatoleum aromaticum EbN1]
          Length = 686

 Score = 39.8 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 24/180 (13%), Positives = 53/180 (29%), Gaps = 19/180 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                 A + +  GY+ + +             P        +G  +        + +  
Sbjct: 158 EDYARCAALAKSAGYDGVEVMGSEGYLINEFTVPHTNHRTDGWGGSVGNRHRFPVEIVRR 217

Query: 111 MCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + + +     +  R+ + D      P   +  L K+++ +G   I  +      +   P 
Sbjct: 218 VRERVGAEFIIIYRLSMLDLVEGGAPWEEIVALAKAVEAAGATLI--NTGVGWHEARIPT 275

Query: 167 DNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
               +P   +  V   +K E     I  N  +     A  +L   D  M+   R    + 
Sbjct: 276 IATMVPRGAFSWVTRRMKGEVGIPLITSNR-INTPEVAENVLTRGDADMVSMARPFLADP 334


>gi|327482514|gb|AEA85824.1| isopentenyl pyrophosphate isomerase [Pseudomonas stutzeri DSM 4166]
          Length = 346

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 27/172 (15%), Positives = 59/172 (34%), Gaps = 29/172 (16%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G  + +   A +++E      ++LN   P     +         +   V   I A+   L
Sbjct: 136 GYGVDEARRAVEMIEG-DALIVHLN---PLQEAVQTGGD----RDWRGVLQAIEALAARL 187

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------KAILKGLSPKD 167
            +PV +K       ++ A     + + +  +GV  I +           +A     + + 
Sbjct: 188 PVPVVIK-------EVGAGISAAVARRLVDAGVAAIDVAGAGGTSWAAVEAARAADASQQ 240

Query: 168 NRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
                  D+       +  +++  P+  +  +GG+ D +  A  I    D V
Sbjct: 241 AIAEAFADWGIPTAQALLAVREACPNTPLIASGGIRDGVEAAKAICLGADLV 292


>gi|319760591|ref|YP_004124529.1| imidazole glycerol phosphate synthase subunit hisF [Candidatus
           Blochmannia vafer str. BVAF]
 gi|318039305|gb|ADV33855.1| imidazole glycerol phosphate synthase subunit hisF [Candidatus
           Blochmannia vafer str. BVAF]
          Length = 258

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   KSG + +  +   A               +D   + ++ K   D+   + GG+ 
Sbjct: 35  LAQHYAKSGADELVFYDISAS---------PYNKIVDKKWILKVAK-VIDIPFCVAGGIN 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++QA +IL    D + I   A  N +++  + E+   
Sbjct: 85  TITQAKQILKFGADKISINSPALMNPSLIQDLAEHLGT 122


>gi|326776000|ref|ZP_08235265.1| NADPH dehydrogenase [Streptomyces cf. griseus XylebKG-1]
 gi|326656333|gb|EGE41179.1| NADPH dehydrogenase [Streptomyces cf. griseus XylebKG-1]
          Length = 763

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 25/203 (12%), Positives = 60/203 (29%), Gaps = 25/203 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVG 105
            +  +AA+   + G++ + L   C    +  G           ++G  L   +  P  V 
Sbjct: 545 EQFTQAARRAAESGFDLLEL--HCAHGYLLSGFLSPLTNRRTDAYGGSLEGRLRFPLDVF 602

Query: 106 DCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           D +  +  +   + V +      +    A     + ++    G + I +     ++    
Sbjct: 603 DAVRRVWPRERPMTVRISATDWAEGGTDAEDAVTIARAFADHGADAIDVSTG-QVVADER 661

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P+  R       D +    +    + +   G +        +L     D   + R    +
Sbjct: 662 PEFGRSYQTPYADRI----RNTVGVPVIAVGAISSWDDVNSLLLAGRADLCALARPHLYD 717

Query: 223 S-AMLTTVDEYFSNPLTGSSPIK 244
               L    E   +      P+ 
Sbjct: 718 PHWTLHAAAEQGYSGPAAPWPLP 740


>gi|255994518|ref|ZP_05427653.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Eubacterium saphenum ATCC 49989]
 gi|255993231|gb|EEU03320.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Eubacterium saphenum ATCC 49989]
          Length = 238

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 22/92 (23%), Positives = 43/92 (46%), Gaps = 11/92 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + K  +++G   I I       +G            +++I+  IK +  DL++ + GG+ 
Sbjct: 35  IAKGFEEAGAGHIHIVDLDGAREGT---------PANFEIIEAIKAKT-DLWVQVGGGIR 84

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTV 229
           DM +A + +   +D +++G AA KN   L   
Sbjct: 85  DMKKADRYINTGIDRIILGTAAIKNPDFLNDA 116


>gi|229161037|ref|ZP_04289025.1| NADPH dehydrogenase [Bacillus cereus R309803]
 gi|228622396|gb|EEK79234.1| NADPH dehydrogenase [Bacillus cereus R309803]
          Length = 319

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 24/125 (19%), Positives = 46/125 (36%), Gaps = 10/125 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I ++ +  S P+ V+        D +         + +K+ GV+ I   +   +  
Sbjct: 171 LREIIDSINEVWSGPLFVRISANDYHPDGLTVQDYVQYTQWMKEQGVDLIDCSSGAVV-- 228

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
              P      P         IK+   ++  G  G +   +QA +IL     D + IGR  
Sbjct: 229 ---PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNSEADLIFIGREL 284

Query: 220 YKNSA 224
            +N  
Sbjct: 285 LRNPY 289


>gi|146351243|ref|YP_001210470.1| salicylyl-CoA 5-hydroxylase [Arthrobacter nitroguajacolicus]
 gi|146218807|emb|CAL09879.1| putative flavoprotein monooxygenas /NADH:flavin oxidoreductase
           [Arthrobacter nitroguajacolicus]
          Length = 797

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 29/200 (14%), Positives = 64/200 (32%), Gaps = 20/200 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCI 108
             V+AA+   + G++ + L+            P A      +G  L   +  P  V D +
Sbjct: 549 DFVDAARRAHEAGFDLLELHAAHGYLLSSFLSPVANQRTDEYGGSLENRLRFPLEVFDAV 608

Query: 109 AAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
             +  A   P+ V+      ++    +     +  +  + G +GI +     + K   P 
Sbjct: 609 RCVWPA-DKPMVVRLSATDWIEGGNDSDDSVAIAWAFVEHGADGIDVSTG-QVAKEEKPA 666

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS- 223
             R       D + +       + +   G +        +L     D + +GR    +  
Sbjct: 667 FGRSYQTPYADRIRQEVAAPAGVAVIAVGAISTYDDVNSVLLAGRADLIALGRTHLYDPQ 726

Query: 224 A-MLTTVDEYFSNPLTGSSP 242
             +    ++ +  P     P
Sbjct: 727 WTLHAAAEQGYRGPGAAWIP 746


>gi|20808521|ref|NP_623692.1| NADH:flavin oxidoreductase [Thermoanaerobacter tengcongensis MB4]
 gi|20517143|gb|AAM25296.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Thermoanaerobacter tengcongensis MB4]
          Length = 647

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 26/189 (13%), Positives = 60/189 (31%), Gaps = 18/189 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDC 107
               +AA+  ++ G++ + +             P +      +G      M  P +    
Sbjct: 150 EAFGQAARRAKEAGFDAVEIHGAHGYLINQFLSPYSNKRTDEYGGSFENRMRFP-LEVVR 208

Query: 108 IAAMCKALSIPV--TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
                     P+   +     V   +     +   + + + G++ + I         +  
Sbjct: 209 RVREEVGPDFPIIYRMSAEEYVPGGLTIEDTKIFAQKLVEEGIDALHISGGVYESSAMII 268

Query: 166 KDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           +          +    IKK  N  + + + G ++D   A +I+     D V +GRA   +
Sbjct: 269 QPAAIPQGCFVENAAAIKKAINSKVPVIVVGRIKDPIMAEQIIREGKADLVSMGRALLAD 328

Query: 223 SAMLTTVDE 231
             +   V E
Sbjct: 329 PELPRKVSE 337


>gi|171058274|ref|YP_001790623.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Leptothrix cholodnii
           SP-6]
 gi|226700334|sp|B1XX77|HIS4_LEPCP RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|170775719|gb|ACB33858.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Leptothrix cholodnii SP-6]
          Length = 249

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 49/156 (31%), Gaps = 12/156 (7%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K     D          + +    +G   + +        G           ++   
Sbjct: 15  VRLKQGDMNDSTTFGEDPAAMARRWVDAGARRLHLVDLNGAFAG---------KPVNEGA 65

Query: 179 VYEIKKENP-DLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I      D+ I L GG+ D+    + L   +  V+IG AA KN   L      F   
Sbjct: 66  IKSIIAAVGGDIPIQLGGGIRDLDTIERYLDDGLSYVIIGTAAVKNPGFLRDACTAFGGH 125

Query: 237 LT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           +  G      +V  D W K++       AR     G
Sbjct: 126 IIVGLDARDGKVATDGWSKLTGHEVVDLARKFQDYG 161


>gi|148653907|ref|YP_001281000.1| NADH:flavin oxidoreductase/NADH oxidase [Psychrobacter sp. PRwf-1]
 gi|148572991|gb|ABQ95050.1| 2,4-dienoyl-CoA reductase [Psychrobacter sp. PRwf-1]
          Length = 725

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 20/134 (14%), Positives = 46/134 (34%), Gaps = 10/134 (7%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+ +A+     +  R+     V D      +  + K+++ +GV+    +     
Sbjct: 219 AVEVVEAIREAVGEDFIIIFRLSMIDLVKDGNVMDEVITVAKALEAAGVSIF--NTGIGW 276

Query: 160 LKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
            +   P     +P   + D   E+KK      +  N  +     A +IL     D + + 
Sbjct: 277 HEARVPTIVTSVPRAAFVDYTAEVKKHVSIPVMAANR-INMPQTAEQILANGQADLIQMA 335

Query: 217 RAAYKNSAMLTTVD 230
           R    +   +    
Sbjct: 336 RPFLADPDWVNKAK 349


>gi|259507257|ref|ZP_05750157.1| dihydroorotate oxidase [Corynebacterium efficiens YS-314]
 gi|30173310|sp|Q8FTC6|PYRD_COREF RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|259165200|gb|EEW49754.1| dihydroorotate oxidase [Corynebacterium efficiens YS-314]
          Length = 377

 Score = 39.8 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 43/112 (38%), Gaps = 11/112 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            +AA+ ++ S+PV VK    + D+    A+ +L   +  +G+          G+   A +
Sbjct: 213 ILAAVQESTSVPVLVKIAPDLSDED-VDAVADLAVELGLAGIVATNTTISREGLVTPAHE 271

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               G        +     +++  +     D L +   GG+    QA + + 
Sbjct: 272 VAEMGAGGISGPPVAERALEVLRRLHARVGDQLVLIGVGGISTPEQAWERIA 323


>gi|255588308|ref|XP_002534563.1| 2,4-dienoyl-CoA reductase [NADPH], putative [Ricinus communis]
 gi|223525019|gb|EEF27818.1| 2,4-dienoyl-CoA reductase [NADPH], putative [Ricinus communis]
          Length = 449

 Score = 39.8 bits (92), Expect = 0.60,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 62/180 (34%), Gaps = 21/180 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNV-----GCPSARVHEGS----FGACLMLNPDIVGDCIAAM 111
             V AAK   D G+  + ++      G      H       +G           + + A+
Sbjct: 240 DFVAAAKRALDAGFEWLEIHFAHGYLGQSFTSAHSNHRTDSYGGSFENRSRFTIETLEAI 299

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +    ++P+T +  +   D      L     LVK+ K+ G++ + +     I     P+
Sbjct: 300 REVWPENLPLTARFGVIEYDGKDEETLSESIQLVKAWKQRGLDMLSVSVGFTI-----PE 354

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
            N          + +  +    + +    G    + A + +    +D  MIGRA  +N  
Sbjct: 355 TNIPWGPAFLAPIAQRVRNEAGIPVSSAWGFGAPNLADQAIRKQELDLAMIGRAHLENPH 414


>gi|182435361|ref|YP_001823080.1| salicylyl-CoA 5-hydroxylase [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|178463877|dbj|BAG18397.1| putative NADH-dependent flavin oxidoreductase [Streptomyces griseus
           subsp. griseus NBRC 13350]
          Length = 763

 Score = 39.8 bits (92), Expect = 0.60,   Method: Composition-based stats.
 Identities = 25/203 (12%), Positives = 60/203 (29%), Gaps = 25/203 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVG 105
            +  +AA+   + G++ + L   C    +  G           ++G  L   +  P  V 
Sbjct: 545 EQFTQAARRAAESGFDLLEL--HCAHGYLLSGFLSPLTNRRTDAYGGSLEGRLRFPLDVF 602

Query: 106 DCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           D +  +  +   + V +      +    A     + ++    G + I +     ++    
Sbjct: 603 DAVRRVWPRERPMTVRISATDWAEGGTDAEDAVTIARAFADHGADAIDVSTG-QVVADER 661

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
           P+  R       D +    +    + +   G +        +L     D   + R    +
Sbjct: 662 PEFGRSYQTPYADRI----RNTVGVPVIAVGAISSWDDVNSLLLAGRADLCALARPHLYD 717

Query: 223 S-AMLTTVDEYFSNPLTGSSPIK 244
               L    E   +      P+ 
Sbjct: 718 PHWTLHAAAEQGYSGPAAPWPLP 740


>gi|288933473|ref|YP_003437532.1| NADH:flavin oxidoreductase/NADH oxidase [Klebsiella variicola
           At-22]
 gi|288888202|gb|ADC56520.1| NADH:flavin oxidoreductase/NADH oxidase [Klebsiella variicola
           At-22]
          Length = 673

 Score = 39.8 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 143 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L K+I+ +G     I+ 
Sbjct: 192 RMRFAIEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAKAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|167042234|gb|ABZ06965.1| putative histidine biosynthesis protein [uncultured marine
           crenarchaeote HF4000_ANIW93J19]
          Length = 267

 Score = 39.8 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +        L   + ++NR+I       V ++     ++   + GG++
Sbjct: 36  LAEKYSNEGADELV------FLDITASEENREIIKSLVSKVAQVI----NVPFTVGGGVK 85

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A  IL    D V I   A KN  ++T + E F 
Sbjct: 86  TLQHARDILLSGADKVAINTGAVKNPKIITELMELFG 122


>gi|145231593|ref|XP_001399273.1| NADH-dependent flavin oxidoreductase [Aspergillus niger CBS 513.88]
 gi|134056175|emb|CAK96350.1| unnamed protein product [Aspergillus niger]
          Length = 421

 Score = 39.8 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 31/209 (14%), Positives = 64/209 (30%), Gaps = 37/209 (17%)

Query: 63  VEAAKIVEDFGYNEINL-NVGC--------PSARVHEGSFGACL---MLNPDIVGDCIAA 110
           V AAK     G + I + N           P A      +G      M  P  +      
Sbjct: 198 VAAAKRALVAGADFIEIHNAHGYLLASFLTPYANKRTDEYGGSFENRMRLPLKIAQLTRD 257

Query: 111 MCKALSIPVTVKCR------IGVDDQIPAVALRNLVKSIKKSGVNGIW------IHARKA 158
                 +PV ++            +           +++   G   +       +H+ + 
Sbjct: 258 TVGE-HVPVFLRLSASDWLGSTSTETWDLQHAVRFAEALADQGAIDLVDVSSGGLHSSQE 316

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP--SVDGVMI 215
           +  G   +    I          +KK     + +   G + D   A ++L    +D V++
Sbjct: 317 VKSGPGFQAPFGI---------AVKKAVGERMLVATVGHIRDGKLANRLLEEEGLDVVLV 367

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           GR   K+  ++ T  ++    +     I+
Sbjct: 368 GRGFQKDPGLVWTFAQHLDVEVAMPGQIR 396


>gi|85114101|ref|XP_964639.1| NADPH dehydrogenase [Neurospora crassa OR74A]
 gi|28926428|gb|EAA35403.1| NADPH dehydrogenase [Neurospora crassa OR74A]
          Length = 434

 Score = 39.8 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 32/220 (14%), Positives = 71/220 (32%), Gaps = 25/220 (11%)

Query: 43  FSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVH 89
           ++ +  P   ++    I +LVEA    A+     G++ I ++            P +   
Sbjct: 180 YNEETFPFPKEMTVEQIHELVEAWKASAQRALKAGFDLIEIHAAHGYLISEFLSPISNQR 239

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVK------CRIGVDDQIPAVALRNLVK 141
              +G        ++ + I+A+   +   +P+ V+                      L K
Sbjct: 240 TDQYGGSFENRTRVLREIISAVRSVIPEDMPLFVRVSATEWMEYTGQPSWDLQQTIELAK 299

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            +   GV+ + + +                 ++   I   + +    L +G  G +    
Sbjct: 300 ILPDLGVDLLDVSSGGNNKDQKINVHTYYQIDMAEQIRAAVHEAGKQLLVGAVGLVTSAE 359

Query: 202 QALK-ILPSVDG-VMIGR--AAYKNSAMLTTVDEYFSNPL 237
            A + +    DG V I R   A   + M+    ++   P 
Sbjct: 360 IAKETVQEKEDGRVTIQRENGAKTRADMVLVARQFLKEPE 399


>gi|296162923|ref|ZP_06845702.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
 gi|295886834|gb|EFG66673.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
          Length = 790

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 73/218 (33%), Gaps = 34/218 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVGD 106
           + V A ++  + G++ + L   C                    +G  L   +  P  V  
Sbjct: 560 QFVRATQMSAEAGFDWLEL--HCAHGYFLSSFLSPLTNHRTDEYGGSLENHLRYPLQVFK 617

Query: 107 CIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            I A+      P++V+      V+          + ++ K +G + I + +   + K   
Sbjct: 618 AIRAVW-PQDKPISVRISANDWVEGGTTPDNAVQIARAFKAAGADMIDVSSG-QVSKDEK 675

Query: 165 PKDNR--KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           P   R  + P  D      ++ E   +     G + +      I+ +   D   I R   
Sbjct: 676 PVYGRMFQTPFAD-----RVRNEAG-IATIAVGAISEADHVNSIIAAGRADLCAIARPHL 729

Query: 221 KNS-AMLTTVDEYFSNPLTGSSP---IKTRVDKDFWRK 254
            N    L    +     +T   P    K++++++  R+
Sbjct: 730 ANPAWTLNEAAKIGYFDVTWPKPYTAAKSQLERNLERE 767


>gi|225679107|gb|EEH17391.1| NADPH dehydrogenase [Paracoccidioides brasiliensis Pb03]
          Length = 420

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 63/192 (32%), Gaps = 33/192 (17%)

Query: 64  EAAKIVEDFGYNEINL-NVG-------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
            A +     G + I + N         C P++      +G        +  + +    + 
Sbjct: 201 AAVRRAVKAGVDYIEIHNAHGYLLFSFCSPASNNRTDEYGGSFENRTRLSSEIVTITRQN 260

Query: 115 L--SIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKG 162
           +   +P+ ++          R  +        +R   K + + G V+ + + +      G
Sbjct: 261 MPEDMPLFLRISASEWLEESRPDLQSWKSEDTVR-FAKILAEKGEVDLLDVSSG-----G 314

Query: 163 LSPKDNRKIPNL-DYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
             P    K        + + +KK   D L +G  G + + + A  ++   +D V +GR  
Sbjct: 315 NHPDQRIKPGPCFQAPLAFAVKKAVGDKLLVGSVGMINNGNDANWLIEEGLDIVFVGRQF 374

Query: 220 YKNS---AMLTT 228
            KN         
Sbjct: 375 QKNPGSVWQFAE 386


>gi|172039777|ref|YP_001799491.1| 2,4-dienoyl-CoA reductase [Corynebacterium urealyticum DSM 7109]
 gi|171851081|emb|CAQ04057.1| 2,4-dienoyl-CoA reductase [Corynebacterium urealyticum DSM 7109]
          Length = 750

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 14/108 (12%), Positives = 37/108 (34%), Gaps = 6/108 (5%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+  A+     +  RI V D          +  L + ++ +GV+     +     +
Sbjct: 218 EIVKAVRAAVPEDFLIDYRISVLDLVEGGQTQEEIHELARQLQDAGVDMFS--SGIGWHE 275

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
              P     +P   +       ++  D+ + +   +     A ++L  
Sbjct: 276 AQVPTIVTSVPRGAFAWATAELRKVVDVPVVIANRINTPQVAEQLLDG 323


>gi|169831775|ref|YP_001717757.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Candidatus Desulforudis audaxviator MP104C]
 gi|226700308|sp|B1I557|HIS4_DESAP RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|169638619|gb|ACA60125.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Candidatus Desulforudis audaxviator MP104C]
          Length = 262

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 22/120 (18%), Positives = 42/120 (35%), Gaps = 12/120 (10%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++ ++ G   + +        G        +     DIV  +     ++ + + GG+ +
Sbjct: 36  ARTWEEQGARRLHVVDLDGAFTGKPQNSGVVL-----DIVKSV-----NIPVQVGGGIRN 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL-TGSSPIKTRVDKDFWRKISA 257
                  L   VD V++G AA  N   L  V   +   +  G      RV    W + +A
Sbjct: 86  PENVKCYLEHGVDRVILGTAALTNPEFLDAVVAAYGERIVVGVDCRDGRVCVQGWEQTAA 145


>gi|20090286|ref|NP_616361.1| NADH peroxidase [Methanosarcina acetivorans C2A]
 gi|19915284|gb|AAM04841.1| NADH peroxidase [Methanosarcina acetivorans C2A]
          Length = 365

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 25/174 (14%), Positives = 55/174 (31%), Gaps = 26/174 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
                AA   +  G++ I   + C    +               +G  +     IV + I
Sbjct: 143 EAFTRAAGRAKVAGFDGI--QLHCAHGFLLSNFISPYTNRRTDRWGGSVENRARIVTEII 200

Query: 109 AAMCK--ALSIPVTVKC---------RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
             + +      P+ VK                 + A     + K ++++GV  I +    
Sbjct: 201 RRIKEDAGDDFPILVKMNATDGFLPGSSKAGLGLDAPECVEIAKILERAGVCAIEVSGGI 260

Query: 158 AILKGLS--PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
               G++     N       +    ++ K   ++ + L GG+  +S    +L +
Sbjct: 261 GEAGGVTIKTAINSPAKEAYFKNYSKMIKAAVNVPVILVGGIRSLSVMECLLEN 314


>gi|314932312|gb|EFS96143.1| oxidoreductase, FAD/FMN-binding [Propionibacterium acnes HL067PA1]
          Length = 366

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 41/128 (32%), Gaps = 9/128 (7%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           DD         L +    +GV+ +      A   G S       P    D+   ++ E  
Sbjct: 246 DDGWSVEDSIELSRRFALAGVDLV-----DASSGGNSSAPIPVAPGYQADLAARVRAEA- 299

Query: 188 DLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
           D+     G +     A  +L     D VM+G AA +++            P    +P   
Sbjct: 300 DVPTATVGMIWTGELAEDLLNKGCADAVMVGLAALRDTNWPLRAAHELGVP-NEEAPWHP 358

Query: 246 RVDKDFWR 253
              +  WR
Sbjct: 359 ARFRGAWR 366


>gi|206576208|ref|YP_002236477.1| 2,4-dienoyl-CoA reductase [Klebsiella pneumoniae 342]
 gi|206565266|gb|ACI07042.1| 2,4-dienoyl-CoA reductase [Klebsiella pneumoniae 342]
          Length = 673

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 143 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDQWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+     V+D      +  L ++I+ +G     I+ 
Sbjct: 192 RMRFAIEVVKAVRQRAGHDFIIIYRLSMLDLVNDGSTLAEVTELAQAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       I  N  + D   A  IL   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRGAFSWVTRKLKGAVSIPLITTNR-INDPQVAEDILARGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|114794270|pdb|2H8Z|A Chain A, Xenobiotic Reductase A In Complex With 8-Hydroxycoumarin
 gi|114794271|pdb|2H90|A Chain A, Xenobiotic Reductase A In Complex With Coumarin
          Length = 359

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 158 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 215

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 216 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 271 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 330

Query: 223 SA 224
             
Sbjct: 331 PH 332


>gi|82545337|ref|YP_409284.1| NADPH dehydrogenase [Shigella boydii Sb227]
 gi|81246748|gb|ABB67456.1| putative NADPH dehydrogenase [Shigella boydii Sb227]
 gi|320184637|gb|EFW59434.1| 2,4-dienoyl-CoA reductase [Shigella flexneri CDC 796-83]
 gi|332092019|gb|EGI97097.1| 2,4-dienoyl-CoA reductase [Shigella boydii 3594-74]
          Length = 672

 Score = 39.8 bits (92), Expect = 0.62,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLHTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|302562002|ref|ZP_07314344.1| oxidoreductase, FAD/FMN-binding [Streptomyces griseoflavus Tu4000]
 gi|302479620|gb|EFL42713.1| oxidoreductase, FAD/FMN-binding [Streptomyces griseoflavus Tu4000]
          Length = 359

 Score = 39.8 bits (92), Expect = 0.63,   Method: Composition-based stats.
 Identities = 20/158 (12%), Positives = 44/158 (27%), Gaps = 14/158 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKSIKKS 146
           ++G           + + A+ +      P+  +        +              +   
Sbjct: 202 AYGGSYENRTRFALEVVDAVREEWPDDKPLFFRVSATDWLEEAGWTPDDTVRFASELPAH 261

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
           G++ + +        G +P                 ++ E P + +   G + D  QA K
Sbjct: 262 GIDLLDVSTG-----GNAPGVRIPTGPGYQVPFAARVRNETP-MPVAAVGLITDAGQAAK 315

Query: 206 ILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           IL     D V +GR   +N +            +    
Sbjct: 316 ILANGEADAVFLGRELLRNPSWALHAARELGGEVHIPD 353


>gi|218891123|ref|YP_002439989.1| putative FMN oxidoreductase [Pseudomonas aeruginosa LESB58]
 gi|218771348|emb|CAW27115.1| probable FMN oxidoreductase [Pseudomonas aeruginosa LESB58]
          Length = 411

 Score = 39.8 bits (92), Expect = 0.63,   Method: Composition-based stats.
 Identities = 25/187 (13%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   GV+ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|153832177|ref|ZP_01984844.1| NADH:flavin oxidoreductase [Vibrio harveyi HY01]
 gi|148871488|gb|EDL70343.1| NADH:flavin oxidoreductase [Vibrio harveyi HY01]
          Length = 363

 Score = 39.8 bits (92), Expect = 0.63,   Method: Composition-based stats.
 Identities = 27/184 (14%), Positives = 63/184 (34%), Gaps = 21/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AA+   + G++ + ++ G  +  + +            ++G         + + + 
Sbjct: 161 DFAHAAQRAIEAGFDGVEIHGG--NGYLIDQFLRTNSNHRTDNYGGTRENRLRFLLEVVD 218

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ +A+     V  R+        +   ++V +I  +      + AR      LS  D  
Sbjct: 219 AVSEAIGTN-KVGVRLAPFITFKDMNCPDIVPTILDASEQ---LQARDIAYLHLSEADWD 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P +      E+++   +  I    G     +A ++L     D V  GR    N  ++ 
Sbjct: 275 DAPVIPESFRIELREYFTNTVIVA--GSYTQDRADEVLEKGYADLVAFGRPFVSNPDLVA 332

Query: 228 TVDE 231
            +  
Sbjct: 333 RLQH 336


>gi|238561547|ref|ZP_00441808.2| oxidoreductase, FAD/FMN-binding [Burkholderia mallei GB8 horse 4]
 gi|254206840|ref|ZP_04913191.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei JHU]
 gi|147752382|gb|EDK59448.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei JHU]
 gi|238524304|gb|EEP87737.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei GB8 horse 4]
          Length = 392

 Score = 39.8 bits (92), Expect = 0.63,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 181 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 240

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 241 AAF-PDDRPVGVRVSATDWVSGGWELDDTIAFAHELKRRDCDWIDVSSG-----GVSPLQ 294

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 295 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 352


>gi|53721036|ref|YP_110022.1| putative NADH-dependent flavin oxidoreductase [Burkholderia
           pseudomallei K96243]
 gi|76809224|ref|YP_331627.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710b]
 gi|167818051|ref|ZP_02449731.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           91]
 gi|167847932|ref|ZP_02473440.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           B7210]
 gi|217424099|ref|ZP_03455599.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 576]
 gi|254186526|ref|ZP_04893043.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei Pasteur
           52237]
 gi|254258268|ref|ZP_04949322.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710a]
 gi|254298668|ref|ZP_04966119.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 406e]
 gi|52211450|emb|CAH37441.1| putative NADH-dependent flavin oxidoreductase [Burkholderia
           pseudomallei K96243]
 gi|76578677|gb|ABA48152.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710b]
 gi|157808709|gb|EDO85879.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 406e]
 gi|157934211|gb|EDO89881.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei Pasteur
           52237]
 gi|217393162|gb|EEC33184.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 576]
 gi|254216957|gb|EET06341.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei 1710a]
          Length = 370

 Score = 39.8 bits (92), Expect = 0.63,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 159 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 218

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 219 AAF-PDDRPVGVRVSATDWVSGGWELDDTIAFAHELKRRDCDWIDVSSG-----GVSPLQ 272

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 273 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 330


>gi|37520275|ref|NP_923652.1| phosphorybosilformimino-5-amino-phosphorybosil-
           4-imidazolecarboxamideisomerase [Gloeobacter violaceus
           PCC 7421]
 gi|39931347|sp|Q7NMQ9|HIS4_GLOVI RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|35211268|dbj|BAC88647.1| phosphorybosilformimino-5-amino-phosphorybosil-
           4-imidazolecarboxamideisomerase [Gloeobacter violaceus
           PCC 7421]
          Length = 255

 Score = 39.8 bits (92), Expect = 0.63,   Method: Composition-based stats.
 Identities = 29/144 (20%), Positives = 49/144 (34%), Gaps = 16/144 (11%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           + P     N  K     G   + +       +G+          +  D +  I  + P  
Sbjct: 30  EDPVAVACNWAKL----GAPRLHVVDLDGARQGM---------PVHLDALEAIVTQVP-C 75

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRV 247
            +   GGL  +     +L   VD V++G AA +N A++    E F   +  G      +V
Sbjct: 76  PVQFGGGLRSIEAVSAVLDRGVDRVILGTAAVENPALIRECCERFGGRIAVGLDARGGQV 135

Query: 248 DKDFWRKISASMTDYAARHLHSGG 271
               WR+ S       A  +   G
Sbjct: 136 AVRGWRETSEVEVTELAGEMEKLG 159


>gi|241668723|ref|ZP_04756301.1| imidazole glycerol phosphate synthase subunit HisF [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254877255|ref|ZP_05249965.1| imidazole glycerol phosphate synthase subunit hisF [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254843276|gb|EET21690.1| imidazole glycerol phosphate synthase subunit hisF [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 257

 Score = 39.4 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L +    +G + +  +       G SP +  K+ ++ +  + EI K+    F    G
Sbjct: 32  IIELAQKYSDAGADELVFY-----DIGASPDN--KLLSIKW--IQEIAKKINIPFCVA-G 81

Query: 196 GLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G++ +  A  IL    D + +  AA     ++  +   F 
Sbjct: 82  GIKSVENARAILNEGADKISVNSAALARPDLIDELVYEFG 121


>gi|260557375|ref|ZP_05829590.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii ATCC 19606]
 gi|260409001|gb|EEX02304.1| 2,4-dienoyl-CoA reductase [Acinetobacter baumannii ATCC 19606]
          Length = 676

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 43/124 (34%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+   +     +  R+     V D      +  + K+++K+GV  +  +      +
Sbjct: 198 EIVKAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   + D    +K+      I  N  +     A +IL     D + + R 
Sbjct: 256 ARVPTIVTSVPRAAFVDYTAHVKQHISIPVIASNR-INMPETAEEILAAGKADMIQMARP 314

Query: 219 AYKN 222
              +
Sbjct: 315 LLAD 318


>gi|255035945|ref|YP_003086566.1| NADH:flavin oxidoreductase/NADH oxidase [Dyadobacter fermentans DSM
           18053]
 gi|254948701|gb|ACT93401.1| NADH:flavin oxidoreductase/NADH oxidase [Dyadobacter fermentans DSM
           18053]
          Length = 354

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 30/196 (15%), Positives = 57/196 (29%), Gaps = 22/196 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              EAAK     G+  I ++            P +      +G        ++   I  +
Sbjct: 157 DFTEAAKRALQAGFKVIEIHAAHGYLLHQFLSPLSNHRTDEYGGSFENRIRLLLRVIEGI 216

Query: 112 CKA--LSIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
                  +P+  +       +          L   +K+ G++ I + +      GL+   
Sbjct: 217 QTVWPADLPLFTRISATDWAEGGWNIDESVQLAAILKEKGIDLIDVSSG-----GLAAHQ 271

Query: 168 NRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNSA 224
              +           IK+E   +  G  G + +  QA  IL + D  MI   R   +N  
Sbjct: 272 QITVGPAYQLPFASRIKRETG-ILTGTVGLITNSLQAETILVNGDADMIIMAREILRNPY 330

Query: 225 MLTTVDEYFSNPLTGS 240
                       +   
Sbjct: 331 FPLEAAHDLKENVAWP 346


>gi|226309334|ref|YP_002769294.1| NADH-dependent oxidoreductase [Rhodococcus erythropolis PR4]
 gi|226188451|dbj|BAH36555.1| putative NADH-dependent oxidoreductase [Rhodococcus erythropolis
           PR4]
          Length = 705

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 54/176 (30%), Gaps = 31/176 (17%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCIA 109
              EAA  V+  G + + +   C    V               +G  +     +  + I 
Sbjct: 176 MFAEAAGRVKAAGGDAVEI--HCAHNYVLGAFLSRYTNQRSDEYGGSMENRARLACEVIR 233

Query: 110 AMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ + +   + V  R+        D +         K  +++G + I +    A+    +
Sbjct: 234 AVKEEVGGALAVIVRLAGQEYGETDGLTVDEAAAAAKMFEEAGADAIHV-TGTALNAFAN 292

Query: 165 PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
             D      + Y  D    IK+      I +           ++LP V   MI   
Sbjct: 293 FTDGPLPDKVGYYTDNATRIKQAISIPVITVG----------RMLPEVGEKMIAEG 338


>gi|259908089|ref|YP_002648445.1| Xenobiotic reductase A [Erwinia pyrifoliae Ep1/96]
 gi|224963711|emb|CAX55209.1| Xenobiotic reductase A [Erwinia pyrifoliae Ep1/96]
 gi|283477990|emb|CAY73906.1| xenobiotic reductase A [Erwinia pyrifoliae DSM 12163]
          Length = 366

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 24/148 (16%), Positives = 56/148 (37%), Gaps = 12/148 (8%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVAL---RN 138
           P        +G         + + +AA+ +    ++P+T +  +   D      L     
Sbjct: 191 PHTNQRTDRYGGSFTGRSRFLLETLAAVREVWPENLPLTARLGVIEYDGRDEETLSESIE 250

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L + ++K+G++ + +     + +   P     +       V +  +    L +  + G+E
Sbjct: 251 LTQLMQKNGLDLLNVSIGFTVAETDIPWGPGFLAP-----VAQRVRHATGLPVATSWGME 305

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSA 224
             + A + +    +D VMIGRA   +  
Sbjct: 306 APAVAERAIAEQQMDLVMIGRALLADPH 333


>gi|222095683|ref|YP_002529740.1| nadph dehydrogenase nama [Bacillus cereus Q1]
 gi|254766772|sp|B9IY25|NAMA_BACCQ RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|221239741|gb|ACM12451.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus Q1]
          Length = 345

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIESINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|219847383|ref|YP_002461816.1| isopentenyl pyrophosphate isomerase [Chloroflexus aggregans DSM
           9485]
 gi|219541642|gb|ACL23380.1| isopentenyl-diphosphate delta-isomerase, type 2 [Chloroflexus
           aggregans DSM 9485]
          Length = 346

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 26/132 (19%), Positives = 47/132 (35%), Gaps = 12/132 (9%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNL-VKSIKKSGVNGIWIHARKAILKGLSPK 166
           I  +C+ L +PV VK          A+ L  + V+ I  +G  G      +   +     
Sbjct: 180 IEEVCRRLEVPVVVKEVGNGIGAADAIRLYEVGVRIIDVAGAGGTSWSEVERFRQPNDTG 239

Query: 167 DNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMIGRAAY 220
                   D+     + V E++   PD+ +  +GG+   +  A  I    D     R   
Sbjct: 240 RRVASAFADWGLPTTECVREVRAALPDVTLIASGGVRSGVDVAKAIALGADLAGTAR--- 296

Query: 221 KNSAMLTTVDEY 232
              A+   ++E 
Sbjct: 297 --PALFDAINER 306


>gi|147920896|ref|YP_685297.1| deoxyribose-phosphate aldolase [uncultured methanogenic archaeon
           RC-I]
 gi|121683150|sp|Q0W6M2|DEOC_UNCMA RecName: Full=Deoxyribose-phosphate aldolase; Short=DERA; AltName:
           Full=2-deoxy-D-ribose 5-phosphate aldolase; AltName:
           Full=Phosphodeoxyriboaldolase; Short=Deoxyriboaldolase
 gi|110620693|emb|CAJ35971.1| deoxyribose-phosphate aldolase [uncultured methanogenic archaeon
           RC-I]
          Length = 224

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 24/143 (16%), Positives = 45/143 (31%), Gaps = 30/143 (20%)

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS---IPVTVKCRI 125
             ++G +EI++        V    +    ML  D+    I  + K      + V ++   
Sbjct: 85  AVEYGADEIDM--------VINVGYLRSGML--DLFEKDIRTVVKVSGSAAVKVIIETCY 134

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
             D+Q          ++ KK G   +                         + V  I++ 
Sbjct: 135 LTDEQKVLA-----ARTAKKCGAAFV------------KTSTGYGPSGARLEDVRLIREA 177

Query: 186 NPDLFIGLNGGLEDMSQALKILP 208
            PD+ I  +GG+    QA     
Sbjct: 178 VPDILIKASGGIRTYEQAKAFTE 200


>gi|320547124|ref|ZP_08041420.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus equinus
           ATCC 9812]
 gi|320448250|gb|EFW88997.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Streptococcus equinus
           ATCC 9812]
          Length = 246

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 11/97 (11%)

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           K   K+G+  I +      L G +          + D++ ++KKE+  L I + GG+  +
Sbjct: 44  KIFAKAGIQFIHVVDLDGALDGRAT---------NRDLIAKLKKESG-LSIEVGGGIRTL 93

Query: 201 SQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            Q    L   +D V+IG  A KN   +    E F + 
Sbjct: 94  EQIEDYLAVGIDRVIIGSMAVKNPDFVRAALEKFGSD 130


>gi|301062508|ref|ZP_07203151.1| NADH oxidase domain protein [delta proteobacterium NaphS2]
 gi|300443365|gb|EFK07487.1| NADH oxidase domain protein [delta proteobacterium NaphS2]
          Length = 371

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 31/207 (14%), Positives = 70/207 (33%), Gaps = 18/207 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLM 98
           + L  Q       +  +AA   +  G++ + L+ G          P     +  +G  L 
Sbjct: 129 RALTSQEIDRIADRFAQAASRAKKAGFDMVELHGGTGYLLSQFVSPHTNKRDDDYGGSLE 188

Query: 99  LNPDIVGDCIAAMCKAL-SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                    ++ +  A+   PV  +      + D +         ++++K+G+  I +  
Sbjct: 189 NRIKFPLMVLSRVKSAVGDFPVGYRFLADEWLPDGLTLQESVPFAEALEKAGIAYISVMG 248

Query: 156 RKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVD 211
                    P+   K   + Y  D+   +K +     I   G +++ + A +++     D
Sbjct: 249 GT-YESFFIPEMVEKCKAVAYMADLAAAVKNKVQVPVITA-GRIKNGTVAEQVIADGKAD 306

Query: 212 GVMIGRAAYKNSAMLTTVDEYFSNPLT 238
            V + R    +      V E     +T
Sbjct: 307 LVGLARVLMCDPEWPKKVGEGREQEIT 333


>gi|260554142|ref|ZP_05826402.1| oxidoreductase FMN-binding [Acinetobacter sp. RUH2624]
 gi|260404723|gb|EEW98233.1| oxidoreductase FMN-binding [Acinetobacter sp. RUH2624]
          Length = 412

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 33/189 (17%), Positives = 71/189 (37%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDRWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D       A   + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPQFTVAVKLNSADFQRGGFSAEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A K++   VD V I  A    
Sbjct: 270 RDGRTLAREAYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEKVIESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 329 PNLPNAWKQ 337


>gi|237749015|ref|ZP_04579495.1| dihydroorotate dehydrogenase 2 [Oxalobacter formigenes OXCC13]
 gi|229380377|gb|EEO30468.1| dihydroorotate dehydrogenase 2 [Oxalobacter formigenes OXCC13]
          Length = 346

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 77/237 (32%), Gaps = 44/237 (18%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF---------GYNEINLN 80
           D ++   KK+   F  ++K +     G +    +E A  V+D+           + I +N
Sbjct: 124 DVLVENVKKS--RFHQEKKGILGLNIGKNAITPIENA--VDDYLICLEKVYPVADYIAIN 179

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS------IPVTVKCRIGVDDQIPAV 134
           +  P+ +      G       D +   + A    LS      +P+ +K    +DD     
Sbjct: 180 ISSPNTKNLRQLQGES---ELDNLLSQLKAAQSRLSDQHSRYVPLALKIAPDMDDNQVKN 236

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAI--------LKGLSPKDNRKIPNLDYDIVYEIKKEN 186
               L++      +       R A+          GLS    R +      ++  +K+E 
Sbjct: 237 IADALIRHKIDGVIATNTTITRDAVKDLPYAQEAGGLSGAPVRDVST---HVIRLLKQEL 293

Query: 187 PD-LFIGLNGGLEDMSQALKILP-SVDGV-----MIGRAAYKNSAMLTTVDEYFSNP 236
            D L I   GG+     A + +      V     MI    Y    ++    +     
Sbjct: 294 GDALPIIGVGGILSGEDAKEKMEAGASLVQVLTGMI----YSGPGLVRECVQALRRE 346


>gi|217972991|ref|YP_002357742.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS223]
 gi|217498126|gb|ACK46319.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella baltica OS223]
          Length = 368

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 51/128 (39%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + + IAA+       +P+T +  +   D      L     LVK  K++G++ + +    +
Sbjct: 211 LLETIAAVRDVWPQHLPLTARFGVIEFDHKDEETLTESIALVKQFKQAGLDMLNV----S 266

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
           I       +    P     I   +++E     +  + G+++   A   +    +D VMIG
Sbjct: 267 ICFSTPTANIPWSPAFLAPIAARVRQEVG-FPVATSWGMDNPHYANAAIEDEQMDLVMIG 325

Query: 217 RAAYKNSA 224
           +A   N  
Sbjct: 326 KAFLANPH 333


>gi|157162557|ref|YP_001459875.1| 2,4-dienoyl-CoA reductase [Escherichia coli HS]
 gi|312972654|ref|ZP_07786827.1| 2,4-dienoyl-CoA reductase [Escherichia coli 1827-70]
 gi|157068237|gb|ABV07492.1| 2,4-dienoyl-CoA reductase [Escherichia coli HS]
 gi|310332596|gb|EFP99809.1| 2,4-dienoyl-CoA reductase [Escherichia coli 1827-70]
 gi|323941822|gb|EGB38001.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli E482]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|239504208|ref|ZP_04663518.1| NADH oxidase [Acinetobacter baumannii AB900]
          Length = 412

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 33/189 (17%), Positives = 71/189 (37%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDRWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D       A   + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPQFTVAVKLNSADFQRGGFSAEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A K++   VD V I  A    
Sbjct: 270 RDGRTLAREAYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEKVIESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 329 PNLPNAWKQ 337


>gi|139439386|ref|ZP_01772827.1| Hypothetical protein COLAER_01846 [Collinsella aerofaciens ATCC
           25986]
 gi|133775165|gb|EBA38985.1| Hypothetical protein COLAER_01846 [Collinsella aerofaciens ATCC
           25986]
          Length = 678

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 19/146 (13%), Positives = 46/146 (31%), Gaps = 13/146 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL-------SIPVTVKC---RIGVDDQIPAVALRNLVKS 142
           +G           + +AA+ +A         +PV ++           +         K 
Sbjct: 219 YGGSFENRVRYALEVVAAIKEAAPQLMVEYKLPVIMENPDGTPRGKGGLQPDEACEFAKL 278

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMS 201
           ++ +G++ I +                     ++ + V E  K    + +   G +  + 
Sbjct: 279 LEGAGIDMIQVAQANHTGNMGDTIPPMGAMPYNWTLPVAERVKALVSVPVATVGRVVSVE 338

Query: 202 QALKILP--SVDGVMIGRAAYKNSAM 225
              KIL   + D +  GR+   +  +
Sbjct: 339 AGEKILEDGAADIIAYGRSLMCDPDI 364


>gi|254784649|ref|YP_003072077.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Teredinibacter
           turnerae T7901]
 gi|259709861|sp|C5BMF4|HIS4_TERTT RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|237684185|gb|ACR11449.1| 1-(5-phosphoribosyl)-5-
           ((5'-phosphoribosylamino)methylideneamino)imidazole-4-
           carboxamide isomerase [Teredinibacter turnerae T7901]
          Length = 245

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 32/156 (20%), Positives = 52/156 (33%), Gaps = 13/156 (8%)

Query: 120 TVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ R G+ D             +     G   + +        G           ++ D
Sbjct: 14  CVRLRQGLMDDSTVFGEDPVAFARQWVDKGARRLHLVDLNGAFAG---------KPVNGD 64

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +V  I K  P+L I + GG+         L   V+ V+IG  A K    +T + + F+  
Sbjct: 65  VVTAIAKAFPELPIQIGGGIRSAETIEHYLQAGVNYVIIGTKAVKEPEFVTEMCKQFAGH 124

Query: 237 LT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           +  G       V  D W ++S       A    S G
Sbjct: 125 IIVGLDAKNGFVATDGWAEVSEVKATDLAARFASDG 160


>gi|261342546|ref|ZP_05970404.1| 2,4-dienoyl-CoA reductase [Enterobacter cancerogenus ATCC 35316]
 gi|288315188|gb|EFC54126.1| 2,4-dienoyl-CoA reductase [Enterobacter cancerogenus ATCC 35316]
          Length = 673

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 23/198 (11%), Positives = 59/198 (29%), Gaps = 41/198 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A +  + GY+ + +                 L+                     
Sbjct: 143 EDFARCAALAREAGYDGVEV-----------MGSEGYLINEFLAARTNHRDDEWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 192 RMRFAIEVVRAVRERVGADFIIVYRLSMLDLVEGGGTFDETVQLAQAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K +     +  N  + D   A +++   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRAAFSWVTRKLKGKVSVPLVTTNR-INDPQVAEEVIARGDADM 308

Query: 215 I--GRAAYKNSAMLTTVD 230
           +   R    ++A+L+   
Sbjct: 309 VSMARPFLADAAILSKAQ 326


>gi|107102239|ref|ZP_01366157.1| hypothetical protein PaerPA_01003291 [Pseudomonas aeruginosa PACS2]
          Length = 411

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 25/187 (13%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   GV+ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|15597912|ref|NP_251406.1| FMN oxidoreductase [Pseudomonas aeruginosa PAO1]
 gi|9948791|gb|AAG06104.1|AE004699_9 probable FMN oxidoreductase [Pseudomonas aeruginosa PAO1]
          Length = 411

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 25/187 (13%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   GV+ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|324991616|gb|EGC23549.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK353]
          Length = 252

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    FI   GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFIVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D + +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKIAVNSSALANPQLLADCAEKFG 121


>gi|319949260|ref|ZP_08023340.1| dihydroorotate dehydrogenase 2 [Dietzia cinnamea P4]
 gi|319437050|gb|EFV92090.1| dihydroorotate dehydrogenase 2 [Dietzia cinnamea P4]
          Length = 355

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 11/113 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            +AA+    +IPV VK    +DD     A+ +LV  +  +G+         +G+   A  
Sbjct: 197 ILAAVRDVATIPVLVKIAPDLDDAD-IDAVTDLVLDLGLAGIVATNTTISRDGLRTPAAH 255

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGLEDMSQALKILPS 209
               G        +     +++  I  +    L I   GG+E        +  
Sbjct: 256 VEALGAGGISGAPVAARSREVLARIHARAGGRLVIISVGGIETPEDVWDRITH 308


>gi|254482635|ref|ZP_05095873.1| imidazoleglycerol phosphate synthase, cyclase subunit [marine gamma
           proteobacterium HTCC2148]
 gi|214036994|gb|EEB77663.1| imidazoleglycerol phosphate synthase, cyclase subunit [marine gamma
           proteobacterium HTCC2148]
          Length = 257

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 38/112 (33%), Gaps = 11/112 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +     + G + I        L   +  + R+      + +     EN  + + + GG+
Sbjct: 35  EIAIRYNEQGADEIT------FLDITASHEGRETTVHTVEQIA----ENVFIPLTVGGGI 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
             +     +L    D V I  AA  N  ++    E F +     +    RV+
Sbjct: 85  RTVEDIRTMLNAGADKVSINTAAIHNPELVREAAERFGSQCIVVAIDAKRVE 136


>gi|254468870|ref|ZP_05082276.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [beta proteobacterium KB13]
 gi|207087680|gb|EDZ64963.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [beta proteobacterium KB13]
          Length = 245

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTV 229
           ++ E+ +E  ++ I L GG+ ++     ++   +D V+IG AA  N   L   
Sbjct: 65  VIREVIQEMGEVPIQLGGGIRNLDTVESLINAGIDSVIIGTAAITNPGFLHEA 117


>gi|295835181|ref|ZP_06822114.1| oxidoreductase, FAD/FMN-binding [Streptomyces sp. SPB74]
 gi|197697891|gb|EDY44824.1| oxidoreductase, FAD/FMN-binding [Streptomyces sp. SPB74]
          Length = 367

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 53/165 (32%), Gaps = 20/165 (12%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCR-IGVDDQIP--------AVALRNLV 140
           ++G           + + A+       +P+  +       ++ P        A       
Sbjct: 204 AYGGSFENRTRFAREVVDAVRAVWPEELPLLFRISATDWFEEDPEDTRTGWTADETVAFA 263

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLED 199
           +++K+ GV+ + +        G+SP                 +KKE   L     G + +
Sbjct: 264 RTLKEHGVDLLDVSTG-----GISPTAPIATGAGYQVRFAERVKKETG-LAAAAVGLITE 317

Query: 200 MSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
             QA KIL     D V++GR   ++            +    + P
Sbjct: 318 ARQAEKILTDGQADAVLLGRELLRDPYFAAHAAAELGDRPYVAQP 362


>gi|323165035|gb|EFZ50825.1| 2,4-dienoyl-CoA reductase [Shigella sonnei 53G]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|225575128|ref|ZP_03783738.1| hypothetical protein RUMHYD_03217 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037687|gb|EEG47933.1| hypothetical protein RUMHYD_03217 [Blautia hydrogenotrophica DSM
           10507]
          Length = 259

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 22/157 (14%), Positives = 48/157 (30%), Gaps = 38/157 (24%)

Query: 102 DIVGDCIAAMCKALSIP----------------------VTVKCRIGVDDQIPAVALRNL 139
           D +   +  + +  S+P                      V V     +   +P       
Sbjct: 74  DKIFKMVDEVRQESSVPLVFMTYANVVFSYGIERFVKKAVEVGMDGLILPDVPYEEKEEF 133

Query: 140 VKSIKKSGVNGIWIHARKAILK----------------GLSPKDNRKIPNLDYDIVYEIK 183
               ++ G+  I + A  +  +                 L     R     D + + ++ 
Sbjct: 134 QAVCQRYGLAFISLIAPTSQERVSMIAREAEGFVYCVSSLGVTGVRSQITTDVEAMVKLV 193

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           K++ D+   +  G+    QA ++    DGV++G A  
Sbjct: 194 KQSRDIPCAVGFGISTPEQAREMARCADGVIVGSAIV 230


>gi|331088431|ref|ZP_08337346.1| hypothetical protein HMPREF1025_00929 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330408198|gb|EGG87686.1| hypothetical protein HMPREF1025_00929 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 606

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 32/190 (16%), Positives = 76/190 (40%), Gaps = 22/190 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNV------GC-PSARVHEG--SFGACLMLNPDIV-GDCIA 109
                AA+     G + + ++       GC  + R++E    +GA  + N      + +A
Sbjct: 109 EDFALAAERAVRCGVDSLVIHGAHGQLPGCFLNKRINERTDEYGADTIENASRFTVELLA 168

Query: 110 AMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +   + ++ RI  +D I        +   VK I+   ++ + +       + L+P
Sbjct: 169 AVREKIKDRLAIEYRINANDMIEGSPSLDEVIAFVKRIEPY-IDLLHVSRGMHSEQKLAP 227

Query: 166 KDNRKI---PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
             N+ I     ++ +   +I+KE   + + + G +  + QA + +     D V + R   
Sbjct: 228 YMNQPIYYDHGINIEDAAKIRKEI-SVPVTVVGSV-TLEQAEQYIAEGKADMVSMARGLM 285

Query: 221 KNSAMLTTVD 230
            +  ++    
Sbjct: 286 ADPMVVKNAK 295


>gi|331700762|ref|YP_004397721.1| dihydroorotate dehydrogenase family protein [Lactobacillus buchneri
           NRRL B-30929]
 gi|329128105|gb|AEB72658.1| dihydroorotate dehydrogenase family protein [Lactobacillus buchneri
           NRRL B-30929]
          Length = 314

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 84/232 (36%), Gaps = 31/232 (13%)

Query: 27  IVADAILRGDKKNILGFSTQ-----EKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLN 80
           I +  +        L F+ +      K + L I G  I + +E  K V++  ++ +  LN
Sbjct: 71  INSMGLPNHGIDYYLKFAEENQGKNGKQVILSIAGLSIDQNIEMLKKVQESSFSGLTELN 130

Query: 81  VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP---AVALR 137
           + CP+ +  +   G     + D V D + +  K    P+ +K     D       A  L 
Sbjct: 131 LSCPNVK-GKSQVG----YDFDAVRDVLTSTFKFFKKPLGLKLPPYFDFNQFNGIAEVLN 185

Query: 138 NL----VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY------DIVYEIKKE-N 186
           +     +  I   G NG+ +      +  + PK        DY        V  +++  N
Sbjct: 186 DFPITYINVINSIG-NGLVVDPETESVV-IKPKGGFGGLGGDYVKPTALANVRALRQRLN 243

Query: 187 PDLFIGLNGGLED-MSQALKILPSVDGVMIGR--AAYKNSAMLTTVDEYFSN 235
           P++ I   GG++  M     +L   + V IG          +   + +   +
Sbjct: 244 PEISIIGTGGIKSGMDVFEHVLCGANLVQIGTAFGYEGTP-IFERISKELKD 294


>gi|322372802|ref|ZP_08047338.1| dihydroorotate oxidase [Streptococcus sp. C150]
 gi|321277844|gb|EFX54913.1| dihydroorotate oxidase [Streptococcus sp. C150]
          Length = 318

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 39/193 (20%), Positives = 65/193 (33%), Gaps = 19/193 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLML 99
           L      K   L + G    +     K V++  Y   + LN+ CP   V      A    
Sbjct: 95  LQKQPNTKNHFLSLVGLSPEETHTILKKVQESDYEGLVELNLSCP--NVPGKPQIAY--- 149

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +   + +  +    + P+ VK     D      A A+ N      V  +   G NG++
Sbjct: 150 DFETTTEILTEVFSYFTKPLGVKLPPYFDIVHFDQAAAVFNQLPLVFVNCVNSIG-NGLY 208

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   +   P++ I   GG++    A +  L
Sbjct: 209 IEDESVVIKPKNGFGGIGGDYIKPTALANVHAFYQRLKPEIQIIGTGGVKSGRDAFEHIL 268

Query: 208 PSVDGVMIGRAAY 220
                V IG A  
Sbjct: 269 CGASMVQIGTALQ 281


>gi|315644544|ref|ZP_07897676.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus vortex V453]
 gi|315280051|gb|EFU43348.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus vortex V453]
          Length = 374

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 26/178 (14%), Positives = 53/178 (29%), Gaps = 37/178 (20%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSIK 144
           +G  ++       + + A+ +A+    PV ++       Q           L  L+ ++ 
Sbjct: 199 YGGDMLKRARFAIEVVKAVRQAVGPDFPVAIRLSQWKTTQYEAKLADTPEKLGQLLTALS 258

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL------- 197
            +GV+      R+         +               KK      I + G +       
Sbjct: 259 DAGVDIFHCSTRRFWEPEFEGSELNFAGWA--------KKLTGKTVITV-GSVGLDEVFT 309

Query: 198 -----------EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                      +D+ + L  L     D V +GRA   +      V +   + L   +P
Sbjct: 310 SLFTQGKGAGHKDIDELLNRLEKHEYDLVAVGRALLADPQWAAKVRDGRFDELEPFTP 367


>gi|312897989|ref|ZP_07757398.1| dehydrogenase, FMN-dependent [Megasphaera micronuciformis F0359]
 gi|310620914|gb|EFQ04465.1| dehydrogenase, FMN-dependent [Megasphaera micronuciformis F0359]
          Length = 344

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 24/113 (21%), Positives = 42/113 (37%), Gaps = 22/113 (19%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--HARKAILKGLSP 165
           I  +C+   +P  VK           +      +    +G   I +  H       G   
Sbjct: 201 IRRICQESPLPFVVK----------GIMSAKEARICADAGAGAIVVSNHG------GRIL 244

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
            D     ++  +I  EIK    ++ + ++GG+      LK+L    D V+IGR
Sbjct: 245 DDMAGTADVLPEIAAEIK---GNIPVFVDGGIRSGEDVLKMLALGADAVLIGR 294


>gi|296268371|ref|YP_003651003.1| NADH:flavin oxidoreductase/NADH oxidase [Thermobispora bispora DSM
           43833]
 gi|296091158|gb|ADG87110.1| NADH:flavin oxidoreductase/NADH oxidase [Thermobispora bispora DSM
           43833]
          Length = 362

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 23/159 (14%), Positives = 42/159 (26%), Gaps = 15/159 (9%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGV------DDQIPAVALRNLVKSI 143
           ++G           +   A+       +PV  +                      L K +
Sbjct: 202 AYGGSFENRIRFALEVADAVRAVWPDDLPVFFRVSATDWLAENGRAGWTVDDTVRLAKEL 261

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
              GV+ + + +                P         +K E  DL +   G + +  QA
Sbjct: 262 LAHGVDLLDVSSGGIT----GGVTIPAGPGYQVPFAARVKAET-DLAVSAVGLITEPRQA 316

Query: 204 LKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            +I+     D VM+GR   +N                  
Sbjct: 317 EEIVASGKADAVMLGRELLRNPYWPRYAARELGAEPGWP 355


>gi|291003498|ref|ZP_06561471.1| flavin oxidoreductase/NADH oxidase [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 370

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 29/220 (13%), Positives = 65/220 (29%), Gaps = 31/220 (14%)

Query: 48  KPLALQIGGADIS----KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFG 94
            P+  ++   +I        E+A+     G+  + L+            P +     ++G
Sbjct: 144 HPVPHELTAEEIQQLVRDFAESARRALAAGFQVVELHGAHGYLIHSFLSPVSNKRTDAYG 203

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VALRNLVKSI 143
             L        + + A+       + +  R    D +                  L K +
Sbjct: 204 GSLENRLRFPLEVVDAVRAVWPDELPLFFRTSATDWLSENPADPREGWTGEDTVRLAKEL 263

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  GV+ + +     +    +  + +  P         ++ E         G + + +QA
Sbjct: 264 QARGVDLMDVSTGGLV----ADAEIKPAPGYQVPFAARVRDEAGISA-AAVGLILEPAQA 318

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +I+ S   D VM+GR   +         E          
Sbjct: 319 EEIVSSGRADAVMLGRQLLREPYWAHRAAEELGEQPQWPD 358


>gi|226941563|ref|YP_002796637.1| NADH:flavin oxidoreductase / NADH oxidase familyprotein [Laribacter
           hongkongensis HLHK9]
 gi|226716490|gb|ACO75628.1| NADH:flavin oxidoreductase / NADH oxidase familyprotein [Laribacter
           hongkongensis HLHK9]
          Length = 371

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 27/157 (17%), Positives = 54/157 (34%), Gaps = 18/157 (11%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMC-----KALSIPVTV-KCRIGVDDQIPAVALR 137
           P +     ++G  L     +V + + A+        + I ++      G+DD        
Sbjct: 195 PHSNQRTDAYGGSLENRARLVLEVVDAVAGSWHADRVGIRLSPLGIFNGLDDTGSEDMAL 254

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L + + + G+  +           LS  D    P L  D   ++++      I   GG 
Sbjct: 255 YLAEQLSRRGMAYL----------HLSEPDWAGGPALTDDFRQQLRRHYTGTLIAA-GGY 303

Query: 198 EDMSQALKILPSV-DGVMIGRAAYKNSAMLTTVDEYF 233
           +       +   + D V  GRA   N  ++T + +  
Sbjct: 304 DTAKAERLLAAGLIDAVAFGRAFIANPDLVTRLSQGL 340


>gi|194439807|ref|ZP_03071873.1| 2,4-dienoyl-CoA reductase [Escherichia coli 101-1]
 gi|300931969|ref|ZP_07147266.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 187-1]
 gi|194421255|gb|EDX37276.1| 2,4-dienoyl-CoA reductase [Escherichia coli 101-1]
 gi|300460392|gb|EFK23885.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 187-1]
 gi|323961050|gb|EGB56666.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli H489]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|187731232|ref|YP_001881839.1| 2,4-dienoyl-CoA reductase [Shigella boydii CDC 3083-94]
 gi|187428224|gb|ACD07498.1| 2,4-dienoyl-CoA reductase [Shigella boydii CDC 3083-94]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLHTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|74313525|ref|YP_311944.1| putative NADPH dehydrogenase [Shigella sonnei Ss046]
 gi|193067445|ref|ZP_03048413.1| 2,4-dienoyl-CoA reductase [Escherichia coli E110019]
 gi|73857002|gb|AAZ89709.1| putative NADPH dehydrogenase [Shigella sonnei Ss046]
 gi|192959402|gb|EDV89837.1| 2,4-dienoyl-CoA reductase [Escherichia coli E110019]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|238585695|ref|XP_002390943.1| hypothetical protein MPER_09702 [Moniliophthora perniciosa FA553]
 gi|215454983|gb|EEB91873.1| hypothetical protein MPER_09702 [Moniliophthora perniciosa FA553]
          Length = 192

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 19/161 (11%), Positives = 44/161 (27%), Gaps = 25/161 (15%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIGVDDQIP--------AVALRNLVKS 142
           +G        +  + + A+ +   + +P+ ++       +                    
Sbjct: 2   YGGSFENRIRLSVEIVDAVREVIPVDMPLFLRVSATDFLEESLPDTPSWRVEDTIRFAHI 61

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF----------IG 192
           + + GV+ I I +               + +L  + V+        L           + 
Sbjct: 62  VAEHGVDAIDISSGGNSQHQKLGTFGSSVQHLFAEQVHSSFAAKNQLVGGKGGGARALVS 121

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNS---AMLTT 228
             G +     A ++L     D V +GR   KN         
Sbjct: 122 AVGSINTGHIAEEVLQSSKADFVTVGRHFQKNPGAVWQFAE 162


>gi|183222224|ref|YP_001840220.1| putative NADH oxidoreductase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189912277|ref|YP_001963832.1| 2,4-dienoyl-CoA reductase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167776953|gb|ABZ95254.1| 2,4-dienoyl-CoA reductase (NADPH) [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167780646|gb|ABZ98944.1| Putative NADH oxidoreductase [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 400

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 83/246 (33%), Gaps = 31/246 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V  AK+ E+ G++ + ++            P        +G  L      + + + ++ 
Sbjct: 155 FVTTAKLAENSGFDGVEIHAAHGYLISQFLSPLVNQRTDKWGGSLANRSRFLMEVVQSVR 214

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSP 165
           K++     V  ++   D             ++K I+  GV+ I +         ++G+S 
Sbjct: 215 KSVKAHFIVSVKMNSSDFQKGGFQFEDAIQVIKRIQTLGVDFIELSGGNYEAPAMQGVS- 273

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D   +    Y  D   E+ K    + I + GG+     A  +L   V  V +  A   +
Sbjct: 274 RDGSTLAREAYFLDFAREVTKMAT-VPIMVTGGIARKQIAETVLESGVSLVGVATALALH 332

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHM-I 281
             +     E  +       P+     K      + +M  Y  + L          +H  +
Sbjct: 333 PNLPNDWKE--NRNPISKLPLPNWKSKTLVGLATMAMVRYQLQRLAEK-------KHQRL 383

Query: 282 GLFHGF 287
              HGF
Sbjct: 384 QYIHGF 389


>gi|56965466|ref|YP_177198.1| NADH-dependent flavin oxidoreductase [Bacillus clausii KSM-K16]
 gi|56911710|dbj|BAD66237.1| NADH-dependent flavin oxidoreductase [Bacillus clausii KSM-K16]
          Length = 346

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 28/175 (16%), Positives = 57/175 (32%), Gaps = 31/175 (17%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSIK 144
           +G  ++       + I A  +A+    P+ ++                A  L   +  + 
Sbjct: 171 YGGDMVERTRFAVEVIEACRRAVGPDFPIVLRFSQWKSSDYTAKLATTAAELEQFLAPLT 230

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG--------- 195
            +GV+      R+         D             ++  + P + +G  G         
Sbjct: 231 DAGVDVFHCSTRRFWEPEFEGSDLNLAG-----WTKKLTGK-PTITVGSVGLDSEFTKLF 284

Query: 196 ------GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                 G+ +++  ++ L     D V IGRA   + A  + + +   N LT  SP
Sbjct: 285 AEGKGAGVSNINGLIEKLEQGEFDLVAIGRALLADPAWASKIRDGRINELTPFSP 339


>gi|88856271|ref|ZP_01130931.1| pyridoxine biosynthesis protein [marine actinobacterium PHSC20C1]
 gi|88814590|gb|EAR24452.1| pyridoxine biosynthesis protein [marine actinobacterium PHSC20C1]
          Length = 323

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 46/225 (20%), Positives = 68/225 (30%), Gaps = 70/225 (31%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K
Sbjct: 57  AEQAKIAEDAGAVAVMALERVPAD--IRSQGGVARMSDPDLIDGIIEA----VSIPVMAK 110

Query: 123 CRI--------------GVDDQIPAVALRNLVKSIKKS---------------------- 146
            RI                 D+   ++  + V  I K                       
Sbjct: 111 ARIGHFVEAQVLQALKVDYIDESEVLSPADYVNHIDKWNFDVPFVCGATNLGEALRRITE 170

Query: 147 GVNGI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK 184
           G   I                    I  +   L+  +  +           YD+V EI  
Sbjct: 171 GAAMIRSKGEAGTGDVSEATKHIRTIKGQINELRSKTADELYVAAKELQAPYDLVREIA- 229

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
           E   L + L   GG+   + A  ++    DGV +G   +   N A
Sbjct: 230 ETGKLPVVLFTAGGVATPADAALMMQLGADGVFVGSGIFKSGNPA 274


>gi|313624845|gb|EFR94773.1| 1-(5-phosphoribosyl)-5-((5-
           phosphoribosylamino)methylideneamino)imidazole-4-
           carboxamide isomerase [Listeria innocua FSL J1-023]
          Length = 240

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 32/133 (24%), Positives = 52/133 (39%), Gaps = 12/133 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            KS  K+G   + I      L+G           ++ +I+ ++KK    + + + GG+  
Sbjct: 36  AKSFAKNGATYLHIVDLDGALEGR---------PVNLEIIQQMKKAA-MVPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAML-TTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           M+Q    L   +D V+IG AA  N   L   V +Y S    G       V    W  IS 
Sbjct: 86  MAQVDYYLQSGIDRVIIGSAALTNPDFLQAAVKKYGSKIAAGIDAKNGFVATSGWLNISR 145

Query: 258 SMTDYAARHLHSG 270
                 A+ + + 
Sbjct: 146 VSFLDLAKQMEAM 158


>gi|317154150|ref|YP_004122198.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfovibrio aespoeensis Aspo-2]
 gi|316944401|gb|ADU63452.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfovibrio aespoeensis Aspo-2]
          Length = 244

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 15/99 (15%), Positives = 38/99 (38%), Gaps = 11/99 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +     G   + +        G+           +++++  I     D+ + L GG+ D
Sbjct: 36  ARRWADLGARFLHVVDLDGAFSGI---------PKNFELIRSICSSI-DIPVQLGGGIRD 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           ++ A K +   VD ++IG  A ++  + + +       +
Sbjct: 86  IATAHKYIEAGVDRLIIGTMALESPDLFSDLCRALPGKI 124


>gi|148360597|ref|YP_001251804.1| imidazole glycerol phosphate synthase cyclase subunit HisF
           [Legionella pneumophila str. Corby]
 gi|296106337|ref|YP_003618037.1| cyclase HisF [Legionella pneumophila 2300/99 Alcoy]
 gi|148282370|gb|ABQ56458.1| imidazole glycerol phosphate synthase, cyclase subunit HisF
           [Legionella pneumophila str. Corby]
 gi|295648238|gb|ADG24085.1| cyclase HisF [Legionella pneumophila 2300/99 Alcoy]
          Length = 253

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 45/135 (33%), Gaps = 15/135 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +    G + +      A L G +          +   + +   EN  + I + GG+
Sbjct: 34  EYAMAYYAQGADELIYMDTVASLYGRN----------NLSEIVKTTAENVFIPITVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A ++L    D V +  AA KN A+++ +   F +     S    R     W    
Sbjct: 84  RSVDDAKQLLRCGADKVAVNTAATKNPALISDIARRFGSQCMVLSIEAKRDINGRW---- 139

Query: 257 ASMTDYAARHLHSGG 271
             MTD    H     
Sbjct: 140 EVMTDNGREHTGMDV 154


>gi|261253501|ref|ZP_05946074.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Vibrio orientalis CIP 102891]
 gi|260936892|gb|EEX92881.1| 2-enoate reductase (Two distinct NAD(FAD)-dependent dehydrogenase
           domains) [Vibrio orientalis CIP 102891]
          Length = 673

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 31/207 (14%), Positives = 69/207 (33%), Gaps = 43/207 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
           K VE+A I +  GY+ + ++       VHEG                 +G          
Sbjct: 159 KFVESAAIAQKAGYDGVEIHA------VHEGYLLDQFSMAFFNQRTDQYGGNFENRYRFA 212

Query: 105 GDCIAAMCKAL--SIPVTVKC----------------RIGVDDQIPAVALRNLVKSIKKS 146
            + +  +      + PV+++                   GV+            K ++++
Sbjct: 213 VEIVRGIKAICGENYPVSLRYSVKSNMKGFGQGILPNEHGVEVGRDMEEGLRAAKYLQEA 272

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + + + A        +   N   P +       +  E  D+ + + G +ED   A + 
Sbjct: 273 GFDALNVDAGTYDSWYWNHPPNYFKPGMYAPYCKAV-SEVVDIPVLMAGRMEDPDLAAQA 331

Query: 207 LP-SV-DGVMIGRAAYKNSAMLTTVDE 231
           +   + DG+ +GR    +  ++  +  
Sbjct: 332 IEDGISDGISMGRPLLADPDIVNKIRR 358


>gi|169795828|ref|YP_001713621.1| putative NADH-flavin oxidoreductase/NADH oxidase [Acinetobacter
           baumannii AYE]
 gi|213157480|ref|YP_002319525.1| oxidoreductase FMN-binding [Acinetobacter baumannii AB0057]
 gi|215483313|ref|YP_002325524.1| NADH oxidase [Acinetobacter baumannii AB307-0294]
 gi|301345354|ref|ZP_07226095.1| NADH oxidase [Acinetobacter baumannii AB056]
 gi|301512439|ref|ZP_07237676.1| NADH oxidase [Acinetobacter baumannii AB058]
 gi|301596117|ref|ZP_07241125.1| NADH oxidase [Acinetobacter baumannii AB059]
 gi|332853206|ref|ZP_08434626.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013150]
 gi|332869411|ref|ZP_08438777.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013113]
 gi|169148755|emb|CAM86621.1| putative NADH-flavin oxidoreductase/NADH oxidase [Acinetobacter
           baumannii AYE]
 gi|213056640|gb|ACJ41542.1| oxidoreductase FMN-binding [Acinetobacter baumannii AB0057]
 gi|213988640|gb|ACJ58939.1| NADH oxidase [Acinetobacter baumannii AB307-0294]
 gi|332728776|gb|EGJ60136.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013150]
 gi|332732742|gb|EGJ63959.1| oxidoreductase, FAD/FMN-binding [Acinetobacter baumannii 6013113]
          Length = 412

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 33/189 (17%), Positives = 71/189 (37%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDQWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D       A   + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPQFTVAVKLNSADFQRGGFSAEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A K++   VD V I  A    
Sbjct: 270 RDGRTLAREAYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEKVIESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 329 PNLPNAWKQ 337


>gi|89896539|ref|YP_520026.1| hypothetical protein DSY3793 [Desulfitobacterium hafniense Y51]
 gi|89335987|dbj|BAE85582.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 701

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 22/137 (16%), Positives = 49/137 (35%), Gaps = 8/137 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGV 148
           +G  L      + + IA   K       +  RI  +D +P        +  V  ++++G+
Sbjct: 219 YGGSLEKRMRFIQEIIADCQKKAGEDFPIMARISAEDFMPGGCTIEDTKKYVPILERAGI 278

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
             + I       +   P  N  +P+  +  +    K+   + +     +  +  A +I+ 
Sbjct: 279 AALDIQVG--FHEAPRPLVNEFVPDGAFVGLAHEVKKVVKIPVIAGYRINTVELAEQIVA 336

Query: 209 S--VDGVMIGRAAYKNS 223
               D V + RA   + 
Sbjct: 337 QGKADMVGMARALVADP 353


>gi|254235695|ref|ZP_04929018.1| hypothetical protein PACG_01631 [Pseudomonas aeruginosa C3719]
 gi|126167626|gb|EAZ53137.1| hypothetical protein PACG_01631 [Pseudomonas aeruginosa C3719]
          Length = 411

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 24/187 (12%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   G++ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGIDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|302896220|ref|XP_003046990.1| hypothetical protein NECHADRAFT_45968 [Nectria haematococca mpVI
           77-13-4]
 gi|256727918|gb|EEU41277.1| hypothetical protein NECHADRAFT_45968 [Nectria haematococca mpVI
           77-13-4]
          Length = 408

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 84/228 (36%), Gaps = 35/228 (15%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I A+   +  PV  K       +    A +++V   + SG       ++     GL    
Sbjct: 180 IKAIFVTVDAPVPGK------READERAAQDVVIKSEMSG----SESSKDNKGSGLGRLM 229

Query: 168 NRKIPN-LDYDIVYEIKKENPDLFIGLNG--GLEDMSQALKILPSVDGVMI----GR--- 217
            + I   L+++ +  I++E   + I L G   +ED+  A++    VDGVM+    GR   
Sbjct: 230 GQYIDKSLNWEDLKWIREE-SSVPIVLKGVQTVEDVKLAVEY--GVDGVMLSNHGGRSLD 286

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQIT 277
            A  +  +L  V + F        P   +  + F        +D   + +  G     I 
Sbjct: 287 GAQASILILLEVRKRF--------PEAFQHLEIFIDGGFERGSD-ILKAIALGATAVGIA 337

Query: 278 RHMIG-LFHGFPNSRRCRHILT--VEAGASTATHHIIETAFNLMIESL 322
           R  +  L +G         IL   +E     A    ++ A   ++ +L
Sbjct: 338 RPFLYSLVYGQKGVEHLSQILKDELETSLRLAGLTSLDQATPDLVNTL 385


>gi|114794269|pdb|2H8X|A Chain A, Xenobiotic Reductase A-Oxidized
          Length = 358

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 157 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 214

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 215 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 269

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 270 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 329

Query: 223 SA 224
             
Sbjct: 330 PH 331


>gi|148839475|sp|Q0VM71|HIS4_ALCBS RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
          Length = 246

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 10/118 (8%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K     DD + +     +     + G   + +        G           ++ DI
Sbjct: 15  VRLKQGRMEDDTVFSEDPVAVASHWVERGARRLHLVDLNGAFAG---------EPVNGDI 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V  I K +PDL I + GG+         L   V  V+IG  A    A +  + E F  
Sbjct: 66  VKAIAKAHPDLPIQIGGGIRSPEIIQAYLDAGVQWVIIGTKAVNEPAFVKAMCEQFPG 123


>gi|322516642|ref|ZP_08069555.1| dihydroorotate dehydrogenase A [Streptococcus vestibularis ATCC
           49124]
 gi|322124807|gb|EFX96234.1| dihydroorotate dehydrogenase A [Streptococcus vestibularis ATCC
           49124]
          Length = 326

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 70/209 (33%), Gaps = 20/209 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLML 99
           L      K   L + G    +     K V+D  Y   + LN+ CP   V      A    
Sbjct: 103 LQKQPNTKNHFLSLVGLSPEETHTILKKVQDSDYEGLVELNLSCP--NVPGKPQIAY--- 157

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +   + +  +    + P+ VK     D      A A+ N      V  +   G NG++
Sbjct: 158 DFETTTEILTEVFSYFTKPLGVKLPPYFDIVHFDQAAAVFNQFPLVFVNCVNSIG-NGLY 216

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   +   P++ I   GG++    A +  L
Sbjct: 217 IEDESVVIKPKNGFGGIGGDYIKPTALANVHAFYQRLKPEIQIIGTGGVKSGRDAFEHIL 276

Query: 208 PSVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
                V +G A  K   A+   + +    
Sbjct: 277 CGASMVQVGTALQKEGVAIFDRITKELKE 305


>gi|312862917|ref|ZP_07723157.1| dihydroorotate dehydrogenase 1A [Streptococcus vestibularis F0396]
 gi|311101777|gb|EFQ59980.1| dihydroorotate dehydrogenase 1A [Streptococcus vestibularis F0396]
          Length = 311

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 70/209 (33%), Gaps = 20/209 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLML 99
           L      K   L + G    +     K V+D  Y   + LN+ CP   V      A    
Sbjct: 88  LQKQPNTKNHFLSLVGLSPEETHTILKKVQDSDYEGLVELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +   + +  +    + P+ VK     D      A A+ N      V  +   G NG++
Sbjct: 143 DFETTTEILTEVFSYFTKPLGVKLPPYFDIVHFDQAAAVFNQFPLVFVNCVNSIG-NGLY 201

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   +   P++ I   GG++    A +  L
Sbjct: 202 IEDESVVIKPKNGFGGIGGDYIKPTALANVHAFYQRLKPEIQIIGTGGVKSGRDAFEHIL 261

Query: 208 PSVDGVMIGRAAYKN-SAMLTTVDEYFSN 235
                V +G A  K   A+   + +    
Sbjct: 262 CGASMVQVGTALQKEGVAIFDRITKELKE 290


>gi|255021093|ref|ZP_05293146.1| NADH:flavin oxidoreductase/NADH oxidase [Acidithiobacillus caldus
           ATCC 51756]
 gi|254969507|gb|EET27016.1| NADH:flavin oxidoreductase/NADH oxidase [Acidithiobacillus caldus
           ATCC 51756]
          Length = 358

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 21/155 (13%), Positives = 43/155 (27%), Gaps = 10/155 (6%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           G   +  +  P  V   + A+     +P+ V+      V+            + ++  GV
Sbjct: 201 GGDFSGRVRFPLEVATAVRAVWPE-ELPLWVRISATDWVEGGWDLEQSIAFSRELQACGV 259

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + +   +      GL+P                  +    +     G + +  QA  IL 
Sbjct: 260 DVVHCSSG-----GLTPDAKIPAGPGFQTPFAAAIRRAVGIPTVAVGLITEAMQAEHILV 314

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
               D V + R   +N                  +
Sbjct: 315 TEQADAVALARELLRNPYWPLQAAARLGVDWPWPA 349


>gi|149908860|ref|ZP_01897520.1| 2,4-dienoyl-CoA reductase [Moritella sp. PE36]
 gi|149808134|gb|EDM68075.1| 2,4-dienoyl-CoA reductase [Moritella sp. PE36]
          Length = 680

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 43/125 (34%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + + +     +  R+     ++       +  L K+I+K+G     I+      +
Sbjct: 201 EIVRQVREKVGTDFIIIYRLSMLDLIEKGSTWQEVVTLAKAIEKAGAT--IINTGIGWHE 258

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P    K+P   +  V  ++K E     I  N  +     A  +L     D V + R 
Sbjct: 259 ARIPTIVTKVPRAAFTKVTAKLKGEVSIPLITTNR-INTPEIAESVLAQGHADMVSMARP 317

Query: 219 AYKNS 223
              + 
Sbjct: 318 FLADP 322


>gi|331087970|ref|ZP_08336893.1| tryptophan synthase subunit alpha [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330409281|gb|EGG88730.1| tryptophan synthase subunit alpha [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 258

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 31/216 (14%), Positives = 58/216 (26%), Gaps = 56/216 (25%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLN-------VGCPSA-----RVHEGSFGACLMLNPD 102
           G  D+    +A +     G + I L           P       R  +           D
Sbjct: 21  GDPDLETTKKAIRSAVKNGADLIELGIPFSDPTAEGPVIQAANLRALKSGI------TTD 74

Query: 103 IVGDCIAAMCKALSIP------------------VTVKCRIGVD----DQIPAVALRNLV 140
            +   +  + K + +P                  V+   +  +D      +P        
Sbjct: 75  KIFAFVRELRKDIDVPFVFMTYTNVVFSYGVEKFVSECQKSRIDGLILPDLPFEEKEEFH 134

Query: 141 KSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIKK 184
                 GV+ I + A  +                ++  L     R     D   +    +
Sbjct: 135 PICAGYGVDLISMVAPTSEKRIAKIAGEAEGFLYVVSSLGVTGMRSEITTDLTSIVATIR 194

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           EN  +   +  G+    QA  +    DGV++G A  
Sbjct: 195 ENTRIPCAVGFGISTPQQAAAMAEYADGVIVGSAIV 230


>gi|324326101|gb|ADY21361.1| NADPH dehydrogenase NamA [Bacillus thuringiensis serovar finitimus
           YBT-020]
          Length = 345

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         +   I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLRKIIESINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|315652874|ref|ZP_07905846.1| tryptophan synthase alpha subunit [Eubacterium saburreum DSM 3986]
 gi|315484868|gb|EFU75278.1| tryptophan synthase alpha subunit [Eubacterium saburreum DSM 3986]
          Length = 256

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 32/157 (20%), Positives = 51/157 (32%), Gaps = 38/157 (24%)

Query: 102 DIVGDCIAAMCKALSIPVTV-----------------KCRIGVDD-----QIPAVALRNL 139
           D V D +A + K +SIP+                   KC     D      IP       
Sbjct: 74  DKVFDMVADVRKEISIPLVFMTYANVIFSYGAEKFFDKCNEVGIDGIILPDIPFEEKGEF 133

Query: 140 VKSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIK 183
           +       V+ I + A  +                I+  L     R     D D + ++ 
Sbjct: 134 LDVADSHKVDLISLIAPTSDDRIAMIAKEAKGFLYIVSSLGVTGTRSEITTDLDSIVKVV 193

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           KEN  +   +  G+    QA ++    DGV++G A  
Sbjct: 194 KENTSVPCAIGFGISTPQQANEMSQIADGVIVGSAII 230


>gi|300696611|ref|YP_003747272.1| oxidoreductase (salicylyl-CoA 5-hydroxylase) protein (abmA)
           [Ralstonia solanacearum CFBP2957]
 gi|299073335|emb|CBJ52846.1| putative oxidoreductase (salicylyl-CoA 5-hydroxylase) protein
           (abmA) [Ralstonia solanacearum CFBP2957]
          Length = 785

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 34/225 (15%), Positives = 66/225 (29%), Gaps = 29/225 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
              V AA +    G++ + L   C           P   +    +G  L   +  P  V 
Sbjct: 555 DDFVRAAGLAVAAGFDWLEL--HCAHGYLLSSFISPLTNLRSDEYGGPLENRLRYPLEVF 612

Query: 106 DCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             + A+  A   P++V+      V   I       + +  K +G + I   + +     +
Sbjct: 613 RAVRAVWPA-DKPMSVRISAHDWVQGGITPDDAVEIARRFKAAGADMIDCSSGQ-----V 666

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           S K+      +      +  +    +     G + +      I+ +   D   + R    
Sbjct: 667 SKKEQPVYGRMFQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLA 726

Query: 222 NS-AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
           N    L          L    P + R  K    +        AA+
Sbjct: 727 NPAWTLNEAARI--GYLDMPWPRQYRAGKLQLERNLERERALAAQ 769


>gi|296388817|ref|ZP_06878292.1| putative FMN oxidoreductase [Pseudomonas aeruginosa PAb1]
          Length = 411

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 24/187 (12%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   G++ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGIDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRAAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|296166494|ref|ZP_06848925.1| NADH oxidase [Mycobacterium parascrofulaceum ATCC BAA-614]
 gi|295898106|gb|EFG77681.1| NADH oxidase [Mycobacterium parascrofulaceum ATCC BAA-614]
          Length = 684

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 24/134 (17%), Positives = 48/134 (35%), Gaps = 18/134 (13%)

Query: 104 VGDCIAAMCKALS--IPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--- 156
           V D +AA+   +   +P+T++      V    P      L  +   +GVN   +      
Sbjct: 204 VLDALAAIRSEIGDTLPITLRISGYERVAGGRPIFDTAQLAPAFVAAGVNAFHVSGGVID 263

Query: 157 ---KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
                ++ G    D   +            K+  D+ +   G + D ++A +IL     D
Sbjct: 264 RLVTGMVNGADDGDELNVGAA------AAVKQVVDVPVIAVGRIHDPARAERILADGRAD 317

Query: 212 GVMIGRAAYKNSAM 225
            + +GR    +  +
Sbjct: 318 FIAMGRPLLADPDL 331


>gi|237800986|ref|ZP_04589447.1| xenobiotic reductase A [Pseudomonas syringae pv. oryzae str. 1_6]
 gi|331023842|gb|EGI03899.1| xenobiotic reductase A [Pseudomonas syringae pv. oryzae str. 1_6]
          Length = 363

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +            ++G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDAYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +         D+        L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|27366192|ref|NP_761720.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           vulnificus CMCP6]
 gi|320156704|ref|YP_004189083.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           vulnificus MO6-24/O]
 gi|32363178|sp|Q8D8Q5|HIS6_VIBVU RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|27362392|gb|AAO11247.1| Imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           vulnificus CMCP6]
 gi|319932016|gb|ADV86880.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           vulnificus MO6-24/O]
          Length = 257

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  N  ++T + + F 
Sbjct: 85  SAEDAARILEFGADKVSINSPALANPQLITDLADKFG 121


>gi|193062045|ref|ZP_03043141.1| 2,4-dienoyl-CoA reductase [Escherichia coli E22]
 gi|192932265|gb|EDV84863.1| 2,4-dienoyl-CoA reductase [Escherichia coli E22]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 55/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D      +  L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAEMVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|332086555|gb|EGI91700.1| 2,4-dienoyl-CoA reductase domain protein [Shigella boydii 5216-82]
          Length = 399

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 33/246 (13%), Positives = 80/246 (32%), Gaps = 36/246 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+     V+D         L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELTQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI-- 215
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMVSM 310

Query: 216 GRAAYKNSAMLTTVDEYFSNPL-TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            R    N+ +L+      ++ + T     +  +D+ F  K+++ + +  A H      L 
Sbjct: 311 ARPFLANAELLSKAQSGRADEINTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP 370

Query: 275 QITRHM 280
            + + +
Sbjct: 371 AMQKKI 376


>gi|291463639|pdb|3L67|A Chain A, Xenobiotic Reductase A - C25s Variant
 gi|291463640|pdb|3L68|A Chain A, Xenobiotic Reductase A - C25s Variant With Coumarin
          Length = 363

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|290980795|ref|XP_002673117.1| predicted protein [Naegleria gruberi]
 gi|284086698|gb|EFC40373.1| predicted protein [Naegleria gruberi]
          Length = 371

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 70/201 (34%), Gaps = 25/201 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+AAK     G++ I ++            P++     ++G         + + +  +
Sbjct: 167 QFVDAAKRAVKAGFDVIEIHGAHGYLISSFLSPTSNQRTDAYGGSFENRIRFLIEIVQRI 226

Query: 112 CKALS--IPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKG 162
            + +   +P+ V+        ++         L K ++ SGV+ +      +  KA +  
Sbjct: 227 RENIPTEMPLFVRVSADEYVGEEGWTMKDTTELAKVLRDSGVDLLDCSSGGNNAKAKISP 286

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
           +      ++P  +      +KK    L  G  G + +   A  ++     D V+IGR   
Sbjct: 287 IGIVQGYQVPFSE-----GVKKSVDGLATGAVGKIVEAKFANDLVKDGKADLVLIGRQDL 341

Query: 221 KNSAMLTTVDEYFSNPLTGSS 241
            +        +    P+    
Sbjct: 342 NDPYWPIRAAQDLDYPVAVPP 362


>gi|291298792|ref|YP_003510070.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
 gi|290568012|gb|ADD40977.1| NADH:flavin oxidoreductase/NADH oxidase [Stackebrandtia nassauensis
           DSM 44728]
          Length = 371

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 25/176 (14%), Positives = 52/176 (29%), Gaps = 34/176 (19%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI------GVDDQIPAVALRNLVKSIK 144
           +G  +        + ++A   A+    P++ +                   L  ++  + 
Sbjct: 197 YGGDIAGRTRFAAEIVSACRAAVTPGFPISFRMSQWKMGAYQAKLAESPQELDAVLAPLA 256

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLNG------- 195
           ++GV+      R+  L         +    D ++   +KK    P + +G  G       
Sbjct: 257 RAGVDAFHCSTRRYWL--------PEFDGCDLNLAGWVKKLTGKPTITVGAVGLANEFLQ 308

Query: 196 -------GLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                      +   L  L     D V +GRA   + A          + +T   P
Sbjct: 309 SLQGDQTDATSIDGLLDRLEADEFDMVAVGRALLADPAWAAKTLAGRHDQVTPFEP 364


>gi|324993979|gb|EGC25898.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK405]
 gi|324994702|gb|EGC26615.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK678]
 gi|327463237|gb|EGF09558.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK1]
 gi|327489969|gb|EGF21758.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK1058]
          Length = 252

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELI------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|170679814|ref|YP_001745353.1| 2,4-dienoyl-CoA reductase [Escherichia coli SMS-3-5]
 gi|170517532|gb|ACB15710.1| 2,4-dienoyl-CoA reductase [Escherichia coli SMS-3-5]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 31/227 (13%), Positives = 69/227 (30%), Gaps = 45/227 (19%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSF-----------------GACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
                  +    +                 G           + ++A+ + +     +  
Sbjct: 162 -------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMRFAVEVVSAVRERVGNDFIIIY 214

Query: 124 RIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           R+     V+D         L ++I+ +G     I+      +   P     +P   +  V
Sbjct: 215 RLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAFSWV 272

Query: 180 -YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 273 TRKLKGHVSLPLVTTNR-INDPQVADDILARGDADMV---SMARPFL 315


>gi|239904672|ref|YP_002951410.1| NADH:flavin oxidoreductase [Desulfovibrio magneticus RS-1]
 gi|239794535|dbj|BAH73524.1| NADH:flavin oxidoreductase [Desulfovibrio magneticus RS-1]
          Length = 361

 Score = 39.4 bits (91), Expect = 0.75,   Method: Composition-based stats.
 Identities = 20/165 (12%), Positives = 51/165 (30%), Gaps = 11/165 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG--VDDQIPAVALRNL 139
           P + V + ++G  L     +  +  + + + +   +P+  +      +           L
Sbjct: 194 PLSNVRDDAYGGDLPGRMRLALETASTIREVIPGGMPLFTRISATDWMPGGWDLEQSVAL 253

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +   GV+ I + +   +   + P                  +E   +     G + +
Sbjct: 254 ARELAARGVDLIDVSSGGLVPDAVIPAAPGYQVPF-----AAAVRERVGVATSAVGLITE 308

Query: 200 MSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            +QA  ++     D V +GRA   +        +          P
Sbjct: 309 PAQAEAVIASGQADLVQLGRAMLHDPYWALHAAQTLGAQPDWPLP 353


>gi|117619306|ref|YP_856711.1| imidazole glycerol phosphate synthase subunit HisF [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|167012125|sp|A0KKB0|HIS6_AERHH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|117560713|gb|ABK37661.1| imidazoleglycerol phosphate synthase, cyclase subunit [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 257

 Score = 39.4 bits (91), Expect = 0.75,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L +     G + +            +  D R +       V E+     D+   + G
Sbjct: 32  IVELARRYASEGADELV------FYDITASSDERVVDKSWVSRVAEVI----DIPFCVAG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G++ +  A +IL    D V I   A  +  ++T + E F 
Sbjct: 82  GIKSVEDARQILEFGADKVSINSPALADPTLITRLAERFG 121


>gi|25028199|ref|NP_738253.1| dihydroorotate dehydrogenase 2 [Corynebacterium efficiens YS-314]
 gi|23493483|dbj|BAC18453.1| dihydroorotate dehydrogenase [Corynebacterium efficiens YS-314]
          Length = 423

 Score = 39.4 bits (91), Expect = 0.75,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 43/112 (38%), Gaps = 11/112 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            +AA+ ++ S+PV VK    + D+    A+ +L   +  +G+          G+   A +
Sbjct: 259 ILAAVQESTSVPVLVKIAPDLSDED-VDAVADLAVELGLAGIVATNTTISREGLVTPAHE 317

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               G        +     +++  +     D L +   GG+    QA + + 
Sbjct: 318 VAEMGAGGISGPPVAERALEVLRRLHARVGDQLVLIGVGGISTPEQAWERIA 369


>gi|46116340|ref|XP_384188.1| hypothetical protein FG04012.1 [Gibberella zeae PH-1]
          Length = 446

 Score = 39.4 bits (91), Expect = 0.75,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 61/178 (34%), Gaps = 16/178 (8%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA+ +E  G++ I L             P        +G        +V + IA + 
Sbjct: 177 FAHAAEFLEKAGFDGIELHGAHGYLLAQFLSPRTNNRTDEYGGSRENRMRLVLEVIAEIK 236

Query: 113 KALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           + +S    V  +    +  P        + L   ++K+ V+ + +          +    
Sbjct: 237 RRVSPKFIVGIKANAVEYTPGSVDVEDAKALAIELEKAKVDFLELSGGNYEKFAFAHVKE 296

Query: 169 RKIPNLDYDIVYE---IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS 223
                 +Y +      +K    D+ +   GG + +   +  L  +DGV +GRA+ +  
Sbjct: 297 ENRKRENYFLSQAEEIVKSLTRDMKVFSTGGFKSVKAMVDSLDIIDGVGLGRASAQEP 354


>gi|293392474|ref|ZP_06636794.1| xenobiotic reductase B [Serratia odorifera DSM 4582]
 gi|291424876|gb|EFE98085.1| xenobiotic reductase B [Serratia odorifera DSM 4582]
          Length = 340

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 44/272 (16%), Positives = 94/272 (34%), Gaps = 61/272 (22%)

Query: 28  VADAILRGDKKNILGFSTQEK-PLALQIGGADI----SKLVEAAKIVE-DFGYNEINLNV 81
           VA + ++   + +  +  + + PL  Q+  A+I         AA+      G++ + ++ 
Sbjct: 96  VAPSAVQPQGEQLTFYRGEGQYPLPRQLSDAEIRAIIDSFAGAAERAVSQAGFDGVEIHA 155

Query: 82  GCPSARVHEGSFGA--CLMLNPDIVGD---------------CIAAMCKALS----IPVT 120
                      +     L  + ++  D                I A+   L     + + 
Sbjct: 156 A--------NGYLLDQFLTKHTNLRSDKWGGDTAQRMSLNLAVIDAVRSRLGNDALVGIR 207

Query: 121 VKCRIGVDDQIPAVALRNLVKSI----KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +      D Q          +++     +SGV+ I +   +A              +   
Sbjct: 208 ISQGKVNDFQHKWENAEQDARTVFTLLAESGVDYIHLTEHQAW--------QPAFADGGL 259

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +V   +K  P++ I  NGGL ++++A  +L    D + +GR A  N          +  
Sbjct: 260 SLVALARKYAPEVTIIANGGLHEVAKAEALLQQGADLIALGRGALAN--------HDWPK 311

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
            + G  P+     ++F R+I   + D     L
Sbjct: 312 RVEGGEPL-----REFDRRILGPIADIKDSEL 338


>gi|156742187|ref|YP_001432316.1| isopentenyl pyrophosphate isomerase [Roseiflexus castenholzii DSM
           13941]
 gi|156233515|gb|ABU58298.1| isopentenyl-diphosphate delta-isomerase, type 2 [Roseiflexus
           castenholzii DSM 13941]
          Length = 345

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 24/139 (17%), Positives = 45/139 (32%), Gaps = 26/139 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------KAI 159
           I  +C  L +PV VK       ++         + +  +GV  I +           +  
Sbjct: 180 IEEVCTRLDVPVIVK-------EVGNGIGAATARRLVDAGVKVIDVAGAGGTSWSEVERF 232

Query: 160 LKGLSPKDNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
                           +     + + +++   PD+ I  +GG+   +  A  I    D  
Sbjct: 233 RHKTERGAQVAAAFAGWGIPTTEAIRQVRAALPDITIIGSGGVRSGVDVAKAIALGADL- 291

Query: 214 MIGRAAYKNSAMLTTVDEY 232
               AA    A++  VDE 
Sbjct: 292 ----AATAKPALIPAVDER 306


>gi|51038613|ref|YP_063259.1| inositol-5-monophosphate dehydrogenase [Borrelia garinii PBi]
 gi|51036286|gb|AAT93749.1| IMP dehydrogenase [Borrelia garinii PBi]
          Length = 404

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 65/198 (32%), Gaps = 45/198 (22%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           + SK+ + A+  EDF     +LN             GA + ++ D +      +   + I
Sbjct: 117 EESKIYKNAERKEDFPNACKDLNS--------RLRVGAAVSIDIDTLERVEELVKAHVDI 168

Query: 118 PV----------------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ 154
            V                T+K +   +D     +  +     +   G + + +       
Sbjct: 169 LVIDSAHGHSTRIIELVQTIKNKYPSLDLIAGNIVTKEAALDLINVGADCLKVGIGPGSI 228

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGV 213
               I+ G+       I +     VYE+ K N ++ I  +GG+         I    D V
Sbjct: 229 CTTRIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSV 282

Query: 214 MIGRAAYKNSAMLTTVDE 231
           MIG        +   V E
Sbjct: 283 MIG-------NLFAGVKE 293


>gi|291524391|emb|CBK89978.1| tryptophan synthase, alpha chain [Eubacterium rectale DSM 17629]
          Length = 255

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 73/237 (30%), Gaps = 58/237 (24%)

Query: 45  TQEKPLALQIGGADI--SKLVEAAKIVEDFGYNEINLN-------VGCPSARVHEGSFGA 95
              K     I   D       +  +     G + I L           P   V +G+   
Sbjct: 9   ENGKAFIPFITCGDPNLETTAKIVREAVANGADLIELGIPFSDPTAEGP---VIQGANIK 65

Query: 96  CLML--NPDIVGDCIAAMCKALSIP------------------VTVKCRIGVD----DQI 131
            L      D V D +  + K ++IP                  ++    IG+D      I
Sbjct: 66  ALEAGVTTDKVFDLVRDLRKDVTIPMVFMTYANVVYSYGAEKFISTCKEIGIDGLILPDI 125

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLD 175
           P       +   +K  V+ I   A  +                ++  L     R     D
Sbjct: 126 PYEEKEEFLPLCEKYDVDLISFIAPTSKDRIAMIAKEATGFIYVISSLGVTGTRSEIKTD 185

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
              + ++ +EN D+   +  G+    QA K+    DG ++G A      ++  +DEY
Sbjct: 186 LASIVKVIRENTDVPCAIGFGISTPKQAKKMADISDGAIVGSA------IIKIIDEY 236


>gi|213053183|ref|ZP_03346061.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
          Length = 597

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|149195257|ref|ZP_01872346.1| inositol-5-monophosphate dehydrogenase [Caminibacter mediatlanticus
           TB-2]
 gi|149134599|gb|EDM23086.1| inositol-5-monophosphate dehydrogenase [Caminibacter mediatlanticus
           TB-2]
          Length = 482

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 19/114 (16%), Positives = 39/114 (34%), Gaps = 15/114 (13%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           D + A+ +   + V              VA     + + K+G + + +      +     
Sbjct: 256 DLVKAVKEKFDVEVVAG----------NVATAEATRDLIKAGADAVKVGIGPGSICTTRI 305

Query: 166 KDNRKIPNLDYDIVYEIKKENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                +P +    + E  +E    D+ +  +GG++     A  I      VMIG
Sbjct: 306 VAGVGVPQI--SAIDECAREAAKYDIPVIADGGIKYSGDIAKAIAVGASSVMIG 357


>gi|16799648|ref|NP_469916.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria innocua
           Clip11262]
 gi|20454978|sp|Q92E87|HIS4_LISIN RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|16413013|emb|CAC95805.1| hisA [Listeria innocua Clip11262]
          Length = 240

 Score = 39.4 bits (91), Expect = 0.76,   Method: Composition-based stats.
 Identities = 32/133 (24%), Positives = 52/133 (39%), Gaps = 12/133 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            KS  KSG   + I      L+G           ++ +I+ ++KK    + + + GG+  
Sbjct: 36  AKSFAKSGATYLHIVDLDGALEGR---------PVNLEIIQQMKKAA-KVPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAML-TTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           M+Q    L   +D V+IG AA  +   L   V +Y S    G       V    W  IS 
Sbjct: 86  MAQIDYYLQSGIDRVIIGSAALTDPDFLQAAVKKYGSKIAAGIDAKNGFVATSGWLNISQ 145

Query: 258 SMTDYAARHLHSG 270
                 A+ + + 
Sbjct: 146 VSFLDLAKQMEAM 158


>gi|325266224|ref|ZP_08132905.1| imidazole glycerol phosphate synthase, cyclase subunit [Kingella
           denitrificans ATCC 33394]
 gi|324982319|gb|EGC17950.1| imidazole glycerol phosphate synthase, cyclase subunit [Kingella
           denitrificans ATCC 33394]
          Length = 257

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAQRYAAEGADELVFYDITASSDGRT---------VDKSWVQRVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++ A ++     D + I   A  N  ++  + E F 
Sbjct: 85  TVADAEQLFAFGADKISINSPALANPDLINQLSERFG 121


>gi|299769996|ref|YP_003732022.1| NADH oxidase [Acinetobacter sp. DR1]
 gi|298700084|gb|ADI90649.1| NADH oxidase [Acinetobacter sp. DR1]
          Length = 412

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 69/188 (36%), Gaps = 19/188 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDRWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D             +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPQFTVAVKLNSADFQRGGFSTEDAHQVVKMLNEHAVDLVELSGGSYEAPAMQGEA- 269

Query: 166 KDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           +D R +    Y + +  K ++   + + + GG+     A +++   VD V I  A     
Sbjct: 270 RDGRTLAREAYFLEFAQKIRKVAKMPVMVTGGIRRKQVAEQVVESGVDMVGIATALAIEP 329

Query: 224 AMLTTVDE 231
            +     +
Sbjct: 330 NLPNAWKQ 337


>gi|293607991|ref|ZP_06690294.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828564|gb|EFF86926.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 412

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 32/189 (16%), Positives = 70/189 (37%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDQWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D           + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPTFTVAVKLNSADFQRGGFSVEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A K++   VD V I  A    
Sbjct: 270 RDGRTLAREAYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEKVIESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 329 PNLPNAWKQ 337


>gi|262375964|ref|ZP_06069195.1| 2,4-dienoyl-CoA reductase [Acinetobacter lwoffii SH145]
 gi|262309058|gb|EEY90190.1| 2,4-dienoyl-CoA reductase [Acinetobacter lwoffii SH145]
          Length = 678

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 21/126 (16%), Positives = 43/126 (34%), Gaps = 10/126 (7%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+   +     +  R+     V D      +  + K+++K+G+  +  +     
Sbjct: 198 AVEIVKAIRAEIGEKFIICFRLSLLDLVHDGNTMQEVITVAKALEKAGITLL--NTGIGW 255

Query: 160 LKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
            +   P     +P   + D   E+KK      I  N  +     A  IL     D V + 
Sbjct: 256 HEARIPTIVTSVPRAAFVDYTSEVKKHVSVPVIASNR-INMPDTAEAILASGQADMVQMA 314

Query: 217 RAAYKN 222
           R    +
Sbjct: 315 RPLLAD 320


>gi|227506211|ref|ZP_03936260.1| NADPH dehydrogenase [Corynebacterium striatum ATCC 6940]
 gi|227197235|gb|EEI77283.1| NADPH dehydrogenase [Corynebacterium striatum ATCC 6940]
          Length = 354

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 61/188 (32%), Gaps = 32/188 (17%)

Query: 73  GYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV-- 119
           G++ I L         N   P +     S+G           + + A+   +   +P+  
Sbjct: 170 GFDTIELHGAHGYLLHNFLSPLSNQRSDSYGGSFENRVRFPLEVVDAVRAVIPQGMPLIM 229

Query: 120 ------TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
                  V  R+  D            + +++ GV+ + +        G    +    P 
Sbjct: 230 RVSATDWVTDRLAWD----VEQTIEFARLLREHGVDFVDVSTG-----GNEHAEIPVGPE 280

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
              +    +++    L +   G + +   A +IL     D + IGRAA K++       E
Sbjct: 281 YQVEYATRVREA--GLPVSTVGLITEAQHAEQILSDDRADVIEIGRAALKDAYWARHAAE 338

Query: 232 YFSNPLTG 239
               PL  
Sbjct: 339 ELGEPLEP 346


>gi|223983547|ref|ZP_03633730.1| hypothetical protein HOLDEFILI_01011 [Holdemania filiformis DSM
           12042]
 gi|223964475|gb|EEF68804.1| hypothetical protein HOLDEFILI_01011 [Holdemania filiformis DSM
           12042]
          Length = 331

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 29/176 (16%), Positives = 61/176 (34%), Gaps = 20/176 (11%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA+  +  G++ + +             P        +G  L     +    I A+ 
Sbjct: 149 FKEAARRAQAAGFDGVEIHSAHGYLLNQFYSPLTNHRTDEYGGVLENRIRLHCQIIEAIR 208

Query: 113 KALSIPVTVKCRIGVDDQIPA-VALRNLVKSI---KKSGVNGIWIHARKAILKGLSPKDN 168
             +     +  R+G  + +     + + V +    +K+GV+ I I             + 
Sbjct: 209 SQVGAEYPLALRLGACEGLENGSTMEDAVSACIQFEKAGVDLIDITGGLGGYVRPGHSEQ 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
                   D    +K+    + + L GG+ + + A  +L     D + +GRA  K+
Sbjct: 269 GYFQ----DFSTAVKQAV-SIPVLLTGGITEAAAAEALLQSGKADLIGVGRALLKD 319


>gi|167577051|ref|ZP_02369925.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           TXDOH]
          Length = 416

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 62/182 (34%), Gaps = 28/182 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++  + G++ + ++            P A      +G         + + + A  
Sbjct: 165 FARTAELAVEGGFDGVQIHAAHGYLLSQFLSPVANKRNDEYGGTPANRRRFLQEVVRATR 224

Query: 113 KAL--SIPVTVKCRIGVDDQ--IPAVALRNLVKSIKKSGVNGIWIHARK---AILKG--L 163
           +A+   +PV VK      ++  +      ++   ++  G++ + I         + G   
Sbjct: 225 RAVGDGVPVGVKLNSTDFERGGLSEAESLDVALMLQDEGIDLLEISGGNYEAPAMTGVIR 284

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIGRAAYK 221
               +R+   L Y    E  +    L + L GGL   +   K+L   DG   M+G     
Sbjct: 285 GGDRSREAYFLSY---AEALRAKTRLPLMLTGGLRTEAFMRKVLT--DGAVDMLG---LA 336

Query: 222 NS 223
             
Sbjct: 337 RP 338


>gi|119489277|ref|ZP_01622084.1| dihydroorotate dehydrogenase [Lyngbya sp. PCC 8106]
 gi|119454751|gb|EAW35896.1| dihydroorotate dehydrogenase [Lyngbya sp. PCC 8106]
          Length = 336

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 13/95 (13%)

Query: 63  VEAAKIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           VE AK+++D G + I LN    P+     G+             D +  +   ++IPVTV
Sbjct: 118 VEYAKLMQDAGADAIELNIYYVPTDFNMSGA------QVEQNYIDTLREVKAEVNIPVTV 171

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           K      +      + N+ K + ++G +G+ +  R
Sbjct: 172 KLSPFFSN------MANMAKQLDEAGADGLVLFNR 200


>gi|110645045|gb|ABG81358.1| NADH:flavin oxidoreductase-like protein [Acidithiobacillus caldus]
          Length = 337

 Score = 39.4 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 21/155 (13%), Positives = 43/155 (27%), Gaps = 10/155 (6%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGV 148
           G   +  +  P  V   + A+     +P+ V+      V+            + ++  GV
Sbjct: 180 GGDFSGRVRFPLEVATAVRAVWPE-ELPLWVRISATDWVEGGWDLEQSIAFSRELQACGV 238

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + +   +      GL+P                  +    +     G + +  QA  IL 
Sbjct: 239 DVVHCSSG-----GLTPDAKIPAGPGFQTPFAAAIRRAVGIPTVAVGLITEAMQAEHILV 293

Query: 208 -PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
               D V + R   +N                  +
Sbjct: 294 TEQADAVALARELLRNPYWPLQAAARLGVDWPWPA 328


>gi|323946849|gb|EGB42867.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli H120]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|312958442|ref|ZP_07772962.1| hypothetical protein PFWH6_0338 [Pseudomonas fluorescens WH6]
 gi|311286985|gb|EFQ65546.1| hypothetical protein PFWH6_0338 [Pseudomonas fluorescens WH6]
          Length = 245

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P+L I + GG+  +      +   V  V+IG  A K+ A +     
Sbjct: 60  PVNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACR 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W +IS       AR   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEISTVQVIDLARQFEADG 160


>gi|110835140|ref|YP_693999.1| phosphoribosylformimino-5-aminoimidazolecarboxam ide ribotide
           [Alcanivorax borkumensis SK2]
 gi|110648251|emb|CAL17727.1| phosphoribosylformimino-5-aminoimidazolecarboxam ide ribotide
           [Alcanivorax borkumensis SK2]
          Length = 258

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 10/118 (8%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K     DD + +     +     + G   + +        G           ++ DI
Sbjct: 27  VRLKQGRMEDDTVFSEDPVAVASHWVERGARRLHLVDLNGAFAG---------EPVNGDI 77

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V  I K +PDL I + GG+         L   V  V+IG  A    A +  + E F  
Sbjct: 78  VKAIAKAHPDLPIQIGGGIRSPEIIQAYLDAGVQWVIIGTKAVNEPAFVKAMCEQFPG 135


>gi|49086108|gb|AAT51328.1| PA3723 [synthetic construct]
          Length = 369

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 30/169 (17%), Positives = 58/169 (34%), Gaps = 11/169 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNL 139
           P +      +G C      ++    AA+ KA    +P+ V+      V+D         L
Sbjct: 190 PLSNQRRDQYGGCFENRIRLLLQVTAAVRKAWPQELPLFVRLSATDWVEDGWNPDETVEL 249

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            + +K  GV+ I + +        +  +    P    +    ++KE   +  G  G + +
Sbjct: 250 ARHLKDLGVDLIDVSSGGTA----ANAEIPVGPGYQTEFAERVEKEAG-IASGTVGMITE 304

Query: 200 MSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
             QA  IL     D +++ R   ++        +   N      P   R
Sbjct: 305 PVQAEHILRTGQADLILLARELLRDPYWPLHAADELRNEQMPWPPQYLR 353


>gi|6049281|gb|AAF02538.1|AF154061_1 xenobiotic reductase A [Pseudomonas putida]
          Length = 363

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 60/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P+ N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PETNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|291463635|pdb|3L5L|A Chain A, Xenobiotic Reductase A - Oxidized
 gi|291463636|pdb|3L5M|A Chain A, Xenobiotic Reductase A - Coumarin Bound
 gi|307568320|pdb|3N19|B Chain B, Xena - Reduced
 gi|307568321|pdb|3N19|D Chain D, Xena - Reduced
          Length = 363

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|242032687|ref|XP_002463738.1| hypothetical protein SORBIDRAFT_01g005150 [Sorghum bicolor]
 gi|241917592|gb|EER90736.1| hypothetical protein SORBIDRAFT_01g005150 [Sorghum bicolor]
          Length = 326

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 75/254 (29%), Gaps = 68/254 (26%)

Query: 15  LLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS--KLVEAAKIVEDF 72
            LT   L  ++ +     LR   K               I   D       EA ++++  
Sbjct: 55  RLTGAGLTVSQTMS---KLRAQGKTA---------FIPYITAGDPDLATTAEALRLLDAC 102

Query: 73  GYNEINLNV-------GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           G + I L V         P  +    +        PD V   +  +   LS PV      
Sbjct: 103 GADVIELGVPFSDPYADGPVIQA-SAARALASGTTPDAVLAMLQEVTPELSCPV---VLF 158

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGLSPKDN------------- 168
              + I    L +   ++K +GV+G+ +    +     L+  + K+N             
Sbjct: 159 SYFNPIVHWGLPDFAAAVKDAGVHGLIVPDLPYGASCALRTEAIKNNIELVLLTTPSTPA 218

Query: 169 ---RKIPNLDYDIVYEI----------------------KKENPDLFIGLNGGLEDMSQA 203
               +I       VY +                       K+  D  + +  G+      
Sbjct: 219 DRMEEITKASQGFVYLVSVNGVTGPRANVNTRVESLIQEVKQVTDKPVAVGFGISKPEHV 278

Query: 204 LKILP-SVDGVMIG 216
            +I     DGV+IG
Sbjct: 279 KQIAEWGADGVIIG 292


>gi|149915359|ref|ZP_01903886.1| dihydrodipicolinate synthase [Roseobacter sp. AzwK-3b]
 gi|149810648|gb|EDM70489.1| dihydrodipicolinate synthase [Roseobacter sp. AzwK-3b]
          Length = 652

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 18/125 (14%), Positives = 42/125 (33%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  +  A+     V  R+     V D      +  L + ++++G +   I+      +
Sbjct: 174 EVVRRVRAAVGSDFIVIYRLSMIDLVPDGSTFDEVIELAQRVEEAGAS--IINTGIGWHE 231

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   +  V  ++  +     I  N  +     A ++L     D V + R 
Sbjct: 232 ARIPTIATSVPRAAFAWVTRKLMGKVGIPVITSNR-INTPQVAEQVLAEGCADMVSMARP 290

Query: 219 AYKNS 223
              + 
Sbjct: 291 FLADP 295


>gi|145220279|ref|YP_001130988.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Prosthecochloris
           vibrioformis DSM 265]
 gi|189028229|sp|A4SG77|HIS4_PROVI RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|145206443|gb|ABP37486.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium
           phaeovibrioides DSM 265]
          Length = 256

 Score = 39.4 bits (91), Expect = 0.78,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 41/98 (41%), Gaps = 11/98 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++    +K     + I    A L G           +++DI+  I  E  D+ + + GG
Sbjct: 33  LDMAIIWRKQNAKMLHIVDLDAALTGEM---------VNFDIIANIVAEL-DIPVQIGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
           +  +    + L   V  V+IG AA  +  ++  + +++
Sbjct: 83  IRSIDAVKRYLDMGVGRVVIGSAAVTDPELVGELMKHW 120


>gi|307946920|ref|ZP_07662255.1| salicylyl-CoA 5-hydroxylase [Roseibium sp. TrichSKD4]
 gi|307770584|gb|EFO29810.1| salicylyl-CoA 5-hydroxylase [Roseibium sp. TrichSKD4]
          Length = 765

 Score = 39.4 bits (91), Expect = 0.79,   Method: Composition-based stats.
 Identities = 35/221 (15%), Positives = 73/221 (33%), Gaps = 37/221 (16%)

Query: 25  EMIVADAILRGDKKNILGFSTQEKPLALQIGGADIS----KLVEAAKIVEDFGYNEINLN 80
           E++ A AI              +  +  ++   D+     +   +A++ +  G++ I L+
Sbjct: 520 ELVSASAIPWS----------SDNAIPWELSVEDMQAIKAQFAASAEMADRAGFDMIELH 569

Query: 81  VG---------CPSARVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPVTVKCRIGV- 127
                       P +      +G  L   M  P  V + + A+  A + P++V+      
Sbjct: 570 AAHGYLISSFITPVSNTRTDDYGGSLENRMRYPLEVFEAMRAVWPA-NKPMSVRISANDW 628

Query: 128 --DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
              D +       + K  + +G + I + A +  +                     I+ E
Sbjct: 629 VGSDGVTPEEAVQIAKMFESAGADIIDVSAGQTTIDAKPVYGRMFQTP----FSDRIRNE 684

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              +     G + +   A  IL +   D V +GR    N  
Sbjct: 685 AG-IKTMAVGNIYEADHANSILMAGRADLVCVGRTHLANPY 724


>gi|146283096|ref|YP_001173249.1| FMN oxidoreductase [Pseudomonas stutzeri A1501]
 gi|145571301|gb|ABP80407.1| probable FMN oxidoreductase [Pseudomonas stutzeri A1501]
          Length = 369

 Score = 39.4 bits (91), Expect = 0.79,   Method: Composition-based stats.
 Identities = 34/190 (17%), Positives = 66/190 (34%), Gaps = 20/190 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            VEAA+     G+    ++            P +   +  +G        ++ +  AA+ 
Sbjct: 159 FVEAAERSLAAGFKIAEVHAAHGYLLHQFLSPLSNQRQDRYGGSFDNRIRLLLEVTAAVR 218

Query: 113 KALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +     +P+ V+      VDD   A     L + +K  GV+ I + +        +  D 
Sbjct: 219 QVWPEELPLFVRLSATDWVDDGWNADETVELARRLKDVGVDLIDVSSGGTA----ANADI 274

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
              P         ++KE   +  G  G + +  QA  IL     D +++ R   ++    
Sbjct: 275 PVGPGYQTQFAERVRKEAG-IATGTVGMITEAVQAEHILRTGQADLILLARELLRDPYWP 333

Query: 227 TTVDEYFSNP 236
               EY  + 
Sbjct: 334 LHAAEYLRDG 343


>gi|87303124|ref|ZP_01085922.1| dihydroorotate dehydrogenase [Synechococcus sp. WH 5701]
 gi|87282291|gb|EAQ74251.1| dihydroorotate dehydrogenase [Synechococcus sp. WH 5701]
          Length = 340

 Score = 39.4 bits (91), Expect = 0.79,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 67/184 (36%), Gaps = 37/184 (20%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGC-PSARVHEGSFGACLMLNPDIVG 105
           + P+   + G +     E A+ VE  G   I LN+   P+ R  + +             
Sbjct: 105 DIPIIASLNGTEEGHWEEIARAVEQAGAAAIELNLYAVPTDRSLDANAMEAAQ------V 158

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------- 156
           + + ++C A S+PV VK             L +L   ++ +G   + +  R         
Sbjct: 159 EIVRSVCTATSLPVAVKLSPY------YTNLSHLAHQLQAAGARALVLFNRFYQPDIDIE 212

Query: 157 ----KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
               +A L   S  D R    L +  +  +    P L    +GG+   +  +++L     
Sbjct: 213 TLEPRANLLLSSAADQRL--PLRW--IALLHGRVP-LEFAASGGISHGTDVVRML----- 262

Query: 213 VMIG 216
            M+G
Sbjct: 263 -MVG 265


>gi|47092829|ref|ZP_00230613.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes str. 4b H7858]
 gi|226223193|ref|YP_002757300.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes Clip81459]
 gi|254824163|ref|ZP_05229164.1| conserved hypothetical protein [Listeria monocytogenes FSL J1-194]
 gi|254932161|ref|ZP_05265520.1| conserved hypothetical protein [Listeria monocytogenes HPB2262]
 gi|255521468|ref|ZP_05388705.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes FSL J1-175]
 gi|259709856|sp|C1L0J3|HIS4_LISMC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|47018824|gb|EAL09573.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria monocytogenes str. 4b H7858]
 gi|225875655|emb|CAS04358.1| Putative phosphoribosylformimino-5-aminoimidazole carboxamide
           ribotide isomerase [Listeria monocytogenes serotype 4b
           str. CLIP 80459]
 gi|293583717|gb|EFF95749.1| conserved hypothetical protein [Listeria monocytogenes HPB2262]
 gi|293593395|gb|EFG01156.1| conserved hypothetical protein [Listeria monocytogenes FSL J1-194]
 gi|328467392|gb|EGF38468.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria
           monocytogenes 1816]
 gi|332310985|gb|EGJ24080.1| isomerase [Listeria monocytogenes str. Scott A]
          Length = 240

 Score = 39.4 bits (91), Expect = 0.79,   Method: Composition-based stats.
 Identities = 20/99 (20%), Positives = 39/99 (39%), Gaps = 11/99 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+  +KK    + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEIIQRMKKAA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           M+Q    L   +D V+IG AA  +   L    + +   +
Sbjct: 86  MAQVDYYLESGIDRVIIGSAALTDPDFLRAAVQKYGAKI 124


>gi|288942423|ref|YP_003444663.1| dihydroorotate dehydrogenase [Allochromatium vinosum DSM 180]
 gi|288897795|gb|ADC63631.1| dihydroorotate dehydrogenase [Allochromatium vinosum DSM 180]
          Length = 342

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 43/129 (33%), Gaps = 19/129 (14%)

Query: 98  MLNPDIVGDCIAAMCK-----ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +   D V   + A+ +     +   P+ VK    + D           ++  ++G  G+ 
Sbjct: 195 LQRVDEVARILEAIQEPNQRLSRPRPLLVKLAPDLADD----EAIECARAALEAGATGLI 250

Query: 153 IHARKAILKGLSPK--------DNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQA 203
           +       +GL             R +     +++ +++    P+  I   GG+ D   A
Sbjct: 251 LTNTTIRFEGLRSSTEGLSGGLSGRPLLARSTELLGKVRAALGPEPVIIGVGGILDPEGA 310

Query: 204 LKIL-PSVD 211
              L    D
Sbjct: 311 RAKLAAGAD 319


>gi|268590232|ref|ZP_06124453.1| imidazoleglycerol phosphate synthase, cyclase subunit [Providencia
           rettgeri DSM 1131]
 gi|291314515|gb|EFE54968.1| imidazoleglycerol phosphate synthase, cyclase subunit [Providencia
           rettgeri DSM 1131]
          Length = 258

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V ++  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVAKVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + E F 
Sbjct: 85  SVDDAAQILSFGADKISINSPALSDPTLISRLAERFG 121


>gi|170078051|ref|YP_001734689.1| dihydroorotate dehydrogenase 2 [Synechococcus sp. PCC 7002]
 gi|169885720|gb|ACA99433.1| dihydroorotate dehydrogenase [Synechococcus sp. PCC 7002]
          Length = 338

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 49/135 (36%), Gaps = 18/135 (13%)

Query: 28  VADAILRGDKKNILGF-----STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN-V 81
            A  +     +  L       S  + P+   + G+   +    AK++E  G + I LN  
Sbjct: 80  NASNVFHVGVETYLEHIRTAKSAVDMPIIASLNGSHQGEWEHTAKLMEQAGADAIELNIY 139

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
             P+     GS               +  + + L+IPV VK      +      + N+ K
Sbjct: 140 YVPTDINKNGSEVEY------EYIQIVRTVRENLNIPVAVKLSPFFSN------MANIAK 187

Query: 142 SIKKSGVNGIWIHAR 156
            +  +G +G+ +  R
Sbjct: 188 RLVDNGASGLVLFNR 202


>gi|307568318|pdb|3N14|A Chain A, Xena - W358a
          Length = 363

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|291463637|pdb|3L65|A Chain A, Xenobiotic Reductase A - C25a Mutant
 gi|291463638|pdb|3L66|A Chain A, Xenobiotic Reductase A - C25a Variant With Coumarin
          Length = 363

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|254194622|ref|ZP_04901053.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei S13]
 gi|169651372|gb|EDS84065.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei S13]
          Length = 375

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 58/178 (32%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 164 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 223

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 224 AAF-PDDRPVGVRVSATDWVSGGWELDDTIAFAHELKRRDCDWIDVSSG-----GVSPLQ 277

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              +         +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 278 KIPLSPGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 335


>gi|118602940|ref|YP_904155.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|148839525|sp|A1AXM7|HIS4_RUTMC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|118567879|gb|ABL02684.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 243

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 10/97 (10%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + +   K G   + +       +G           ++   V E+    PDL + + GG+
Sbjct: 34  EMAEQWVKQGARRVHLVDLNGAFEGR---------PVNVSSVTEVVSAFPDLPVQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
            +M  A   +   +D ++IG  A  N   ++ +   F
Sbjct: 85  RNMQIANAYIEAGIDYLIIGTMAVTNPEFVSELCREF 121


>gi|152987322|ref|YP_001349348.1| putative FMN oxidoreductase [Pseudomonas aeruginosa PA7]
 gi|150962480|gb|ABR84505.1| probable FMN oxidoreductase [Pseudomonas aeruginosa PA7]
          Length = 411

 Score = 39.4 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 67/187 (35%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V +A + E  G++ + ++            P +   E ++G  L     ++ + + A+ 
Sbjct: 151 FVRSAALAERAGFSGVQIHAAHGYLLSQFLSPLSNRREDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR--KAILKGLSPK 166
             +S    V  ++   D       A   R +V+ +   GV+ + +     +A       +
Sbjct: 211 AEVSPAFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAPAMHGEAR 270

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
           D R +    Y +      +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRTVARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALALEPG 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|260869832|ref|YP_003236234.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O111:H- str. 11128]
 gi|257766188|dbj|BAI37683.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O111:H- str. 11128]
 gi|323178787|gb|EFZ64363.1| 2,4-dienoyl-CoA reductase [Escherichia coli 1180]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|255646113|gb|ACU23543.1| unknown [Glycine max]
          Length = 424

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G +   +N  CP     E   GA +  +  ++ +    +    +IPV  K    +
Sbjct: 173 RVEQTGVDAFEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATIPVWAKMTPNI 231

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI 151
            D           +    SG  G+
Sbjct: 232 TDISQP------ARVALSSGCEGV 249


>gi|218555650|ref|YP_002388563.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           IAI1]
 gi|218362418|emb|CAR00042.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           IAI1]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|242278937|ref|YP_002991066.1| FMN-dependent alpha-hydroxy acid dehydrogenase [Desulfovibrio
           salexigens DSM 2638]
 gi|242121831|gb|ACS79527.1| FMN-dependent alpha-hydroxy acid dehydrogenase [Desulfovibrio
           salexigens DSM 2638]
          Length = 336

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 25/117 (21%), Positives = 42/117 (35%), Gaps = 21/117 (17%)

Query: 113 KALSIPVTVKCRIGVDDQIPAVA---------LRNLVKSIKKSGVNGIWI--HARKAILK 161
           K +  PVT KC   + + I +V            +  +    +G  GI +  H       
Sbjct: 182 KKMGRPVTPKCMRKLREIIESVNADFILKGIMTPDEARMAIDAGAKGIVVSNHG------ 235

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
           G           + ++I   +        + ++GG+      LK+L    D VMIGR
Sbjct: 236 GRVLDSCPGTAEVLFEISRAV---AGQCAVMVDGGVRTGIDVLKMLALGADAVMIGR 289


>gi|148990519|ref|ZP_01821657.1| Putative N-acetylmannosamine-6-phosphate epimerase [Streptococcus
           pneumoniae SP6-BS73]
 gi|149013521|ref|ZP_01834153.1| Putative N-acetylmannosamine-6-phosphate epimerase [Streptococcus
           pneumoniae SP19-BS75]
 gi|168493239|ref|ZP_02717382.1| putative N-acetylmannosamine-6-phosphate 2-epimerase (ManNAc-6-P
           epimerase) [Streptococcus pneumoniae CDC3059-06]
 gi|147762842|gb|EDK69794.1| Putative N-acetylmannosamine-6-phosphate epimerase [Streptococcus
           pneumoniae SP19-BS75]
 gi|147924235|gb|EDK75332.1| Putative N-acetylmannosamine-6-phosphate epimerase [Streptococcus
           pneumoniae SP6-BS73]
 gi|183576554|gb|EDT97082.1| putative N-acetylmannosamine-6-phosphate 2-epimerase (ManNAc-6-P
           epimerase) [Streptococcus pneumoniae CDC3059-06]
 gi|332203166|gb|EGJ17234.1| N-acetylmannosamine-6-phosphate epimerase family protein
           [Streptococcus pneumoniae GA47901]
          Length = 228

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 9/104 (8%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K +      +  ++     K   +SGV+ +        L G +P    K  N D+++V 
Sbjct: 122 IKVKYPNQLLMADISTFEEGKVAAESGVDFV-----GTTLSGYTPYS-PKKDNPDFELVE 175

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
            + KE  D+ +   G +    QA K+L      V++G  A    
Sbjct: 176 RLVKEL-DVPVIAEGRISTPEQARKMLDLGAYAVVVG-GAITRP 217


>gi|126652173|ref|ZP_01724355.1| YqjM [Bacillus sp. B14905]
 gi|126591081|gb|EAZ85192.1| YqjM [Bacillus sp. B14905]
          Length = 336

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 32/194 (16%), Positives = 57/194 (29%), Gaps = 19/194 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +AA      G++ + ++            P+    E  +G        I+   I A
Sbjct: 142 EAFKQAAIRAAKAGFDVLEIHGAHGYLISEFLSPATNKREDQYGGSQENRYRILRQIIDA 201

Query: 111 MCKALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +      P  V V      +D           + +K  GV+ + +        G+ P   
Sbjct: 202 IRSVWDGPLLVRVSAEDYAEDGTTMEDFIVFSRWMKSQGVDLVDVSTG-----GVVPAAI 256

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAML 226
              P         IK    D+  G  G +    QA +IL +   D + + R   +     
Sbjct: 257 NVFPGYQVSHAEAIKHGA-DIPTGAVGLITTAIQAEEILQNNRADLIFLARVLLREPYWP 315

Query: 227 TTVDEYFSNPLTGS 240
               +  S  L   
Sbjct: 316 LHAAKELSEELQPP 329


>gi|58258389|ref|XP_566607.1| oxidoreductase [Cryptococcus neoformans var. neoformans JEC21]
 gi|57222744|gb|AAW40788.1| oxidoreductase, putative [Cryptococcus neoformans var. neoformans
           JEC21]
          Length = 459

 Score = 39.4 bits (91), Expect = 0.81,   Method: Composition-based stats.
 Identities = 28/150 (18%), Positives = 53/150 (35%), Gaps = 27/150 (18%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------------VA 135
           +G  L     +  +    + +    P+    R+   D +                     
Sbjct: 251 YGGSLENRLRLPLEIAEIVRQKWDKPLF--YRLSATDWLEESLGKEKNANGEWVWWGIEQ 308

Query: 136 LRNLVKSIKKSGVNGIWIH-ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
               V  + + GV+ + +      + + ++P  + ++P         +KK  PDL IG  
Sbjct: 309 TTAFVGKLAELGVDLVDVSSGGNDLRQKIAPGPSYQLPFA-----AHLKKTYPDLLIGSV 363

Query: 195 GGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           G + D  QA  IL     D ++IGR   +N
Sbjct: 364 GIITDAEQANDILEQGKADVILIGRQLLRN 393


>gi|320170436|gb|EFW47335.1| vitamin B6 biosynthesis family protein [Capsaspora owczarzaki ATCC
           30864]
          Length = 325

 Score = 39.4 bits (91), Expect = 0.82,   Method: Composition-based stats.
 Identities = 28/131 (21%), Positives = 48/131 (36%), Gaps = 30/131 (22%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE A+I E+ G   +      P+        G   M +P      I  +  A++IPV  K
Sbjct: 59  VEQARIAEEAGACAVMALERVPAD--IRKHGGVARMSDPH----MIKEIKAAVTIPVMAK 112

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
           CRIG   +          + + + G++ I               ++  +   D D  + +
Sbjct: 113 CRIGHFVE---------AQILTECGIDYI--------------DESEVLTPAD-DKHHIL 148

Query: 183 KKENPDLFIGL 193
           K E P  F+  
Sbjct: 149 KSEFPIPFVCG 159


>gi|296875792|ref|ZP_06899854.1| dihydroorotate oxidase [Streptococcus parasanguinis ATCC 15912]
 gi|296433163|gb|EFH18948.1| dihydroorotate oxidase [Streptococcus parasanguinis ATCC 15912]
          Length = 311

 Score = 39.4 bits (91), Expect = 0.82,   Method: Composition-based stats.
 Identities = 37/189 (19%), Positives = 66/189 (34%), Gaps = 19/189 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  +  ++   L + G    +     K V+D  +  +  LN+ CP   V      A    
Sbjct: 88  LQETDPDRTFFLSLVGMSPEETHTILKKVQDSDFKGLTELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + D     ++ +    + P+ +K     D      A A+ N      V  +   G NG++
Sbjct: 143 DFDTTDRILSEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLY 201

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-L 207
           I     +++   G        I       V+   +  NP++ I   GG+     A +  L
Sbjct: 202 IEDESVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPEIQIVGTGGVLTGRDAFEHIL 261

Query: 208 PSVDGVMIG 216
                V IG
Sbjct: 262 CGASMVQIG 270


>gi|238063355|ref|ZP_04608064.1| FMN oxidoreductase [Micromonospora sp. ATCC 39149]
 gi|237885166|gb|EEP73994.1| FMN oxidoreductase [Micromonospora sp. ATCC 39149]
          Length = 355

 Score = 39.4 bits (91), Expect = 0.82,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 45/145 (31%), Gaps = 11/145 (7%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKA 158
           +  +   A+   +   V V  RI   D             L   +  +GV+ +   +  A
Sbjct: 210 LTLEVARAVRTTVGESVPVLTRISATDWTDGGWTIEDSVVLAGELAAAGVDLVDTSSGGA 269

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
           + +   P        L   I  E+      +  G  G + +  QA +I+     D V++G
Sbjct: 270 VPRATIPVGPGYQVPLAARIRREV-----GVPTGAVGLIVEPEQAERIVAGGEADLVLLG 324

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSS 241
           R   ++                  +
Sbjct: 325 RELLRDPYWPRRAAAKLGATPDWPA 349


>gi|194427676|ref|ZP_03060223.1| 2,4-dienoyl-CoA reductase [Escherichia coli B171]
 gi|194414184|gb|EDX30459.1| 2,4-dienoyl-CoA reductase [Escherichia coli B171]
 gi|323163131|gb|EFZ48964.1| 2,4-dienoyl-CoA reductase [Escherichia coli E128010]
          Length = 672

 Score = 39.4 bits (91), Expect = 0.82,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|329944128|ref|ZP_08292387.1| oxidoreductase, FAD/FMN-binding [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328530858|gb|EGF57714.1| oxidoreductase, FAD/FMN-binding [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 368

 Score = 39.4 bits (91), Expect = 0.82,   Method: Composition-based stats.
 Identities = 23/154 (14%), Positives = 57/154 (37%), Gaps = 9/154 (5%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A+     +  R+   D     +         + + ++GV+ + I +   +  
Sbjct: 218 EVVRAVREAVGTDTVLDIRLSASDWADGGVTGEETAAFSRELVEAGVDVLHISSGGNVPT 277

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
            +      ++P  +           P + +GL   +E+ +QA + L    VD + +GRAA
Sbjct: 278 AVPVGPGYQLPLAEQVRRAVSGTGVPVVGVGL---IEEAAQAEQALITGQVDAIAVGRAA 334

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
            ++  +               +P   +  +  W 
Sbjct: 335 LRDPYLPLRWAADLGVRSWDEAPWPIQYWRGTWH 368


>gi|14520911|ref|NP_126386.1| molybdenum cofactor biosynthesis MoaA [Pyrococcus abyssi GE5]
 gi|5458128|emb|CAB49617.1| moaA-like intein containing molybdenum cofactor biosynthesis moaA
           homolog [Pyrococcus abyssi GE5]
          Length = 1042

 Score = 39.4 bits (91), Expect = 0.82,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 17/86 (19%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q  G +      L+E  KI ++ GY+ + LN         
Sbjct: 628 QIRMMLRNAKKEHPIGANAVQFTGGEPTLRDDLIEIIKIAKEEGYDHVQLNTD------- 680

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL 115
               G  L  +P++V     A    L
Sbjct: 681 ----GIKLAFDPELVKKIRQAGVNTL 702


>gi|330012029|ref|ZP_08307246.1| putative NADH oxidase [Klebsiella sp. MS 92-3]
 gi|328534018|gb|EGF60670.1| putative NADH oxidase [Klebsiella sp. MS 92-3]
          Length = 677

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 62/185 (33%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   +  
Sbjct: 150 EKFGDAAERVRRAGFDCVEIHAGHSYLISQFLSPLFNKRTDEFGGSIENRTRILSLIVDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIK--KSGVNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++  +  V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQEKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRTPQVAEDILASGDADLIAIGRGLIAEPEW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|300857727|ref|YP_003782710.1| hypothetical protein cpfrc_00310 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300685181|gb|ADK28103.1| hypothetical protein cpfrc_00310 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302330020|gb|ADL20214.1| NADH:flavin oxidoreductase/NADH oxidase [Corynebacterium
           pseudotuberculosis 1002]
          Length = 357

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 71/198 (35%), Gaps = 28/198 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V A++   D G + + L+            PS+ V    FG      P+     +  +
Sbjct: 154 EFVAASRRAVDAGLDGVELHGANGYLLHEFLSPSSNVRTDEFGG----TPENRARFVIQV 209

Query: 112 CKALSIPVT---VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A++  +    V  RI  +  I  V   +  +++    V    I + +     +   D 
Sbjct: 210 VQAVAEEIGAHRVGLRISPEHNIQGVLETDREETLATYRVLLNEIRSLELAYLSILHADY 269

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLN---GGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           R       D V+++ +     F+ LN   G   + ++A+ I+     D V +GR    N 
Sbjct: 270 RS------DFVHQLAEAFGG-FVILNSGFGTYTEYAEAVGIVESGYADAVAVGRELIANP 322

Query: 224 AMLTTVDEYFSNPLTGSS 241
            ++    E     +    
Sbjct: 323 DLVRRWQEGIELNVPDPD 340


>gi|228991057|ref|ZP_04151018.1| NADPH dehydrogenase [Bacillus pseudomycoides DSM 12442]
 gi|228768681|gb|EEM17283.1| NADPH dehydrogenase [Bacillus pseudomycoides DSM 12442]
          Length = 346

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 36/201 (17%), Positives = 63/201 (31%), Gaps = 19/201 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDI 103
           Q+    IS   +AA   +  G++ I L+            P +      +G         
Sbjct: 137 QLIKKTISAFQDAACRSKQAGFDIIELHAAHGYLINEFLSPLSNKRTDEYGGSPENRYRF 196

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I A+ +  + P+ V+          +         K +K+  V+ I   +   I  
Sbjct: 197 LKEIIDAVNEVWNGPLFVRISANDYHPKGLTVHDYVQFAKWMKEQDVDVIDCSSGAVI-- 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P      P    +    IK +   +  G  G +    QA +IL     D + IGR  
Sbjct: 255 ---PAQIDVYPGYQVEYANHIKGQA-HIATGAVGLITSGIQAEEILANNEADLIFIGREL 310

Query: 220 YKNSAMLTTVDEYFSNPLTGS 240
            +N     T        L   
Sbjct: 311 LRNPYFPRTAANELGFELQEP 331


>gi|257126963|ref|YP_003165077.1| dihydroorotate dehydrogenase 1A [Leptotrichia buccalis C-1013-b]
 gi|257050902|gb|ACV40086.1| dihydroorotate dehydrogenase family protein [Leptotrichia buccalis
           C-1013-b]
          Length = 310

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 38/189 (20%), Positives = 62/189 (32%), Gaps = 19/189 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  +  ++     + G          K V++  +N I  LN+ CP   V      A    
Sbjct: 88  LQKTHPDRTFFFSLVGMSTEDTHALLKKVQESDFNGITELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +     +  +      P+ VK     D      A A+ N      +  +   G NG+ 
Sbjct: 143 DLETTEKLLTDIFSYFKKPLGVKLPPYFDIVHFDQAAAVFNKFPLSFINCVNSIG-NGLV 201

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   K+ NP + I   GG+     A +  L
Sbjct: 202 IEDESVVIKPKNGFGGIGGEYIKPTALANVHAFYKRLNPSIKIIGTGGVLTGQDAFEHIL 261

Query: 208 PSVDGVMIG 216
                V IG
Sbjct: 262 CGASMVQIG 270


>gi|224372556|ref|YP_002606928.1| 2-nitropropane dioxygenase, NPD [Nautilia profundicola AmH]
 gi|223588698|gb|ACM92434.1| 2-nitropropane dioxygenase, NPD [Nautilia profundicola AmH]
          Length = 361

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           K+  ++ +L  D+  E+ K +P++ +   GG+      +K +    DGV +G
Sbjct: 188 KEENQLEHLIPDVRAEVDKWDPNIPVIAAGGIWSHEDIVKFMELGADGVQLG 239


>gi|168237919|ref|ZP_02662977.1| oxidoreductase, FAD/FMN-binding family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
 gi|194735724|ref|YP_002116176.1| FAD/FMN-binding/pyridine nucleotide-disulfide oxidoreductase family
           protein [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. CVM19633]
 gi|194711226|gb|ACF90447.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197289159|gb|EDY28528.1| oxidoreductase, FAD/FMN-binding family protein [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. SL480]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|156034304|ref|XP_001585571.1| hypothetical protein SS1G_13455 [Sclerotinia sclerotiorum 1980]
 gi|154698858|gb|EDN98596.1| hypothetical protein SS1G_13455 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 435

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 27/210 (12%), Positives = 60/210 (28%), Gaps = 43/210 (20%)

Query: 63  VEAAKIVEDFGYNEINL-NVG-------C-PSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A +     G++ I + N         C P +      +G        +  + +    +
Sbjct: 211 VAALERALKAGFDVIEIHNAHGYLLHEFCSPVSNKRTDQYGGSFENRIRLTLEIVELTRQ 270

Query: 114 ALS--IPVTVKCRI--------GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            +   +P+ ++             +D         L + +   G++ + + +        
Sbjct: 271 NIPDTMPLFLRISATDWLDYEGFEEDSWKVADSARLAQILADKGIDLMDVSSGA-----N 325

Query: 164 SPKDNRKIPN-LDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS------------ 209
            P                EIK+   D + +G  G +    QA  +L              
Sbjct: 326 HPAQKITAGPGYQAPFAKEIKRAVGDRMLVGAVGIIASGKQAEALLTGKGGETGVSGEEE 385

Query: 210 -----VDGVMIGRAAYKNSAMLTTVDEYFS 234
                +D  ++ R   KN  ++    E   
Sbjct: 386 KGETELDLAIVARGFQKNPGLVWEWAEELD 415


>gi|194335645|ref|YP_002017439.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pelodictyon phaeoclathratiforme BU-1]
 gi|226700341|sp|B4SCY8|HIS4_PELPB RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|194308122|gb|ACF42822.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pelodictyon phaeoclathratiforme BU-1]
          Length = 256

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++    +K     + I    A L G           ++++ + EI   N D+ + + GG+
Sbjct: 34  DMAIIWRKQNAKMLHIVDLDAALTGEM---------VNFEKIREIVT-NLDIPVQVGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
                  + L   V  V+IG AA  N  ++  +   +
Sbjct: 84  RSADAVKRYLDIGVGRVVIGSAAVTNPKLVEELLHTY 120


>gi|26987989|ref|NP_743414.1| xenobiotic reductase A [Pseudomonas putida KT2440]
 gi|24982705|gb|AAN66878.1|AE016316_3 xenobiotic reductase A [Pseudomonas putida KT2440]
 gi|313497604|gb|ADR58970.1| XenA [Pseudomonas putida BIRD-1]
          Length = 363

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|33594459|ref|NP_882103.1| tryptophan synthase subunit alpha [Bordetella pertussis Tohama I]
 gi|73622001|sp|Q7VTF0|TRPA_BORPE RecName: Full=Tryptophan synthase alpha chain
 gi|33564534|emb|CAE43849.1| tryptophan synthase alpha chain [Bordetella pertussis Tohama I]
 gi|332383870|gb|AEE68717.1| tryptophan synthase subunit alpha [Bordetella pertussis CS]
          Length = 285

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 19/104 (18%), Positives = 37/104 (35%), Gaps = 17/104 (16%)

Query: 130 QIPAVALRNLVKSIKKSGVNGI--------------WIHARKAILKGLSPKDNRKIPNLD 175
             P   +      + ++GV  I                   +  +  +S K      +LD
Sbjct: 134 DYPPEEVDEFAVMLAEAGVAPIFLLAPTSTEARIEAIGRVARGYVYYVSLKGVTGAGSLD 193

Query: 176 YDIVYE---IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            D V     + + +  + +G+  G+ D + A +I    D V+IG
Sbjct: 194 TDDVARKLALIRRHVHIPVGVGFGIRDAASAQRIAAHADAVVIG 237


>gi|326335094|ref|ZP_08201292.1| inosine-5'-monophosphate dehydrogenase [Capnocytophaga sp. oral
           taxon 338 str. F0234]
 gi|325692732|gb|EGD34673.1| inosine-5'-monophosphate dehydrogenase [Capnocytophaga sp. oral
           taxon 338 str. F0234]
          Length = 492

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 46/147 (31%), Gaps = 24/147 (16%)

Query: 102 DIVGDCIAAMCKALSI-----------PVTVKCRIGV---DDQIPAVALRNLVKSIKKSG 147
           +     + A   A+ I            V  K +      D  +  +A       + ++G
Sbjct: 235 ERAEALVHAGVDAVVIDTAHGHTRGVVSVLKKVKEHFPSLDVVVGNIATAEAALYLAQAG 294

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLE-DMSQAL 204
            + + +      +           P L     +   +K+EN  + +  +GG+        
Sbjct: 295 ADAVKVGIGPGSICTTRVVAGVGYPQLSAVMQVAAILKRENIQIPVIADGGIRYTGDIVK 354

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDE 231
            I    D VM+G       ++L  + E
Sbjct: 355 AIAAGADCVMLG-------SLLAGIKE 374


>gi|300916713|ref|ZP_07133429.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 115-1]
 gi|300416008|gb|EFJ99318.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 115-1]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 22/188 (11%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVAEDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|260550763|ref|ZP_05824971.1| 2,4-dienoyl-CoA reductase [Acinetobacter sp. RUH2624]
 gi|260406269|gb|EEW99753.1| 2,4-dienoyl-CoA reductase [Acinetobacter sp. RUH2624]
          Length = 676

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 31/241 (12%), Positives = 69/241 (28%), Gaps = 52/241 (21%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   +V+ + ++            EK +   I         + A I + 
Sbjct: 100 LMQILHAGRYGYQPFVVSSSAIKSPISPFKPRQLSEKNILSTI-----EDYAQCADIAKK 154

Query: 72  FGYNEINLNVGCPSARVHEGSFGACL-----------------------MLNPDIVGDCI 108
            GY+ + +                 L                       M  P    + +
Sbjct: 155 AGYDGVEI-----------MGSEGYLINQFLSRHVNQRTDRWGGEIENRMRFP---VEIV 200

Query: 109 AAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+   +     +  R+     V D      +  + K+++K+GV  +  +      +   
Sbjct: 201 KAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVTVAKALEKAGVTLL--NTGIGWHEARV 258

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYK 221
           P     +P   + D    +K+    + +  +  +     A +IL      MI   R    
Sbjct: 259 PTIVTSVPRAAFVDYTAHVKQHI-SIPVIASNRINMPETAEEILAKGKADMIQMARPLLA 317

Query: 222 N 222
           +
Sbjct: 318 D 318


>gi|60682297|ref|YP_212441.1| dihydroorotate dehydrogenase 2 [Bacteroides fragilis NCTC 9343]
 gi|60493731|emb|CAH08520.1| putative dihydroorotate dehydrogenase [Bacteroides fragilis NCTC
           9343]
          Length = 324

 Score = 39.0 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 30/198 (15%), Positives = 67/198 (33%), Gaps = 24/198 (12%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I    D    V+ AK +E+ G + + +N+    + +    +G+    + D     
Sbjct: 98  PVIASINCYTDAEW-VDFAKQIEEAGADALEINILALQSDIQYK-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           ++ + K + IPV +K                L+  +  +G   + +  R          +
Sbjct: 152 LSHIKKTIRIPVIMKL------GSNFTNPVALIDQLYANGAAAVVLFNRFYQPDIDVEKM 205

Query: 161 KGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGR 217
           +  S        +L      +         +    +GG+         IL     + I  
Sbjct: 206 EHTSGDVFSNASDLSTTLRWIGISSSLVSKIDYAASGGIHKPDGIVKAILAGASAIEICS 265

Query: 218 AAYKNSAML-TTVDEYFS 234
           A Y+N+ +    ++ + S
Sbjct: 266 AIYQNTNLFVGEMNRFLS 283


>gi|308447185|ref|XP_003087356.1| hypothetical protein CRE_02791 [Caenorhabditis remanei]
 gi|308257139|gb|EFP01092.1| hypothetical protein CRE_02791 [Caenorhabditis remanei]
          Length = 243

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 42/130 (32%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I K  P+L I + GG+  +      L   V  V+IG  A +N   
Sbjct: 60  ------PIHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLDAGVSFVIIGTKAVQNPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKKFAG 123


>gi|300922293|ref|ZP_07138418.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 182-1]
 gi|301325564|ref|ZP_07219032.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 78-1]
 gi|300421355|gb|EFK04666.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 182-1]
 gi|300847615|gb|EFK75375.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 78-1]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|296117899|ref|ZP_06836482.1| dihydroorotate oxidase [Corynebacterium ammoniagenes DSM 20306]
 gi|295969130|gb|EFG82372.1| dihydroorotate oxidase [Corynebacterium ammoniagenes DSM 20306]
          Length = 380

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 43/112 (38%), Gaps = 11/112 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            ++A+ ++ S+PV VK    + D+    A+ +L   +  +G+         +G+    + 
Sbjct: 218 ILSAVQESTSVPVLVKIAPDLSDED-VDAVADLAVELGLAGIVATNTTISRDGLNSDDQF 276

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               G        +     +++  +     D L I   GG+    QA + + 
Sbjct: 277 VRELGAGGISGAPVAARSLEVLKRLYARVGDKLVIISVGGINTPQQAWERIT 328


>gi|327474844|gb|EGF20249.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK408]
          Length = 252

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELI------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|315304303|ref|ZP_07874642.1| enoyl-(acyl-carrier-protein) reductase [Listeria ivanovii FSL
           F6-596]
 gi|313627327|gb|EFR96121.1| enoyl-(acyl-carrier-protein) reductase [Listeria ivanovii FSL
           F6-596]
          Length = 309

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 19/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + K +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEEVRVVTTGAGTPKPFMGKLKAAGIKVIAVIPSVKIAKKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVV-AAVNIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|260845893|ref|YP_003223671.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O103:H2 str. 12009]
 gi|307310295|ref|ZP_07589943.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli W]
 gi|257761040|dbj|BAI32537.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O103:H2 str. 12009]
 gi|306909190|gb|EFN39685.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli W]
 gi|315062388|gb|ADT76715.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli W]
 gi|323377024|gb|ADX49292.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli KO11]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|218701854|ref|YP_002409483.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           IAI39]
 gi|218371840|emb|CAR19695.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           IAI39]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 22/188 (11%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVAEDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|56415158|ref|YP_152233.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364088|ref|YP_002143725.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129415|gb|AAV78921.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095565|emb|CAR61130.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|304385677|ref|ZP_07368021.1| possible NADPH dehydrogenase [Pediococcus acidilactici DSM 20284]
 gi|304328181|gb|EFL95403.1| possible NADPH dehydrogenase [Pediococcus acidilactici DSM 20284]
          Length = 387

 Score = 39.0 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 26/181 (14%), Positives = 65/181 (35%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EA +     G++ + +             P +      +G  +    +     + A  
Sbjct: 151 FGEATRRAIQAGFDGVEIHGANTYLIQQFFSPHSNRRTDHWGGSVEKRMNFGLAVVQAAH 210

Query: 113 KALSI----PVTVKCRIGVDD-QIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           +A++        +  RI  ++ + P + L +    +  +    ++ + +       K L+
Sbjct: 211 RAVAKYAGDHFMLGYRISPEEIEEPGIRLADTLQFIDELADQPLDYLHVSMGNVWRKSLN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN 222
               ++        +  IKK+  + L I   G +E  + A K++   +D V +GR + + 
Sbjct: 271 DDSEKR------PTILRIKKQVHNRLPIIGVGSVETPADAEKVMDEGIDFVALGRESLRE 324

Query: 223 S 223
            
Sbjct: 325 P 325


>gi|260429175|ref|ZP_05783152.1| FAD/FMN-binding/pyridine nucleotide-disulphide domain
           oxidoreductase [Citreicella sp. SE45]
 gi|260419798|gb|EEX13051.1| FAD/FMN-binding/pyridine nucleotide-disulphide domain
           oxidoreductase [Citreicella sp. SE45]
          Length = 669

 Score = 39.0 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 19/133 (14%), Positives = 46/133 (34%), Gaps = 10/133 (7%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  +  A+     V  R+ + D +P       +  L ++I+ +G +   I+      +
Sbjct: 197 EVMKRVRAAVGEDFIVIFRLSMIDLVPNGSTHEEVVQLAQAIEAAGAS--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   +  V  ++  +     I  N  +     A ++L     D V + R 
Sbjct: 255 ARVPTIATSVPRAGFAWVTKKLMGKVGIPVITSNR-INSPEVAEQVLAEGCADMVSLARP 313

Query: 219 AYKNSAMLTTVDE 231
              +   +   + 
Sbjct: 314 FLADPDFVAKAER 326


>gi|260554892|ref|ZP_05827113.1| oxidoreductase FMN-binding [Acinetobacter baumannii ATCC 19606]
 gi|260411434|gb|EEX04731.1| oxidoreductase FMN-binding [Acinetobacter baumannii ATCC 19606]
          Length = 412

 Score = 39.0 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 32/189 (16%), Positives = 71/189 (37%), Gaps = 21/189 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P +   +  +G  L     I+ + + A+ 
Sbjct: 151 FANTARLGEKAGFTGVEIHAAHGYLLSQFLSPLSNKRQDQWGGSLENRARILIEIVEAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
           K +S   TV  ++   D       A   + +VK + +  V+ + +         ++G + 
Sbjct: 211 KVVSPQFTVAVKLNSADFQRGGFSAEDAQQVVKMLNEHAVDLVELSGGSYEAPAMQGQA- 269

Query: 166 KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           +D R +    Y  +   EI+K    + + + GG+     A +++   VD V I  A    
Sbjct: 270 RDGRTLAREGYFLEFAQEIRK-VAKMPVMVTGGIRRKQVAEQVVESGVDMVGIATALAIE 328

Query: 223 SAMLTTVDE 231
             +     +
Sbjct: 329 PNLPNAWKQ 337


>gi|229029760|ref|ZP_04185832.1| NADPH dehydrogenase [Bacillus cereus AH1271]
 gi|228731575|gb|EEL82485.1| NADPH dehydrogenase [Bacillus cereus AH1271]
          Length = 345

 Score = 39.0 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 24/125 (19%), Positives = 46/125 (36%), Gaps = 10/125 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I ++ +  + P+ V+        D +         K +K+ GV+ I   +   +  
Sbjct: 197 LREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDVIDCSSGAVV-- 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P      P         IK+   ++  G  G +   +QA +IL     D + IGR  
Sbjct: 255 ---PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNNEADLIFIGREL 310

Query: 220 YKNSA 224
            +N  
Sbjct: 311 LRNPY 315


>gi|254503481|ref|ZP_05115632.1| oxidoreductase, FAD/FMN-binding superfamily [Labrenzia alexandrii
           DFL-11]
 gi|222439552|gb|EEE46231.1| oxidoreductase, FAD/FMN-binding superfamily [Labrenzia alexandrii
           DFL-11]
          Length = 386

 Score = 39.0 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 30/191 (15%), Positives = 64/191 (33%), Gaps = 30/191 (15%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSA-----------RVHEGSFGACLMLNPDIVGDCIAA 110
             +AA   E  G++ + +   C +             + +  +G  L     +  + I  
Sbjct: 159 FYQAALRAEAAGFDGVEI--HCANGYLLDQFLTAETNLRQDQYGGTLENRIRLTQEIIRE 216

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLV------KSIKKSGVNGIWIHARKAILKG 162
              A      V V+      +         L       +++  +G + I + + K   +G
Sbjct: 217 AQGATKSDFIVGVRLSQAKANIQDYFWPNGLADAKVIFQAVADAGADFIHLASEK---EG 273

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAY 220
            +     +      + +    ++   L +  NGGL  +  A +++     D V IG+ A 
Sbjct: 274 YAVHSYTEAG----ENLTTYARDLTGLPVVANGGLHVVVDANELIASRKADFVSIGKTAM 329

Query: 221 KNSAMLTTVDE 231
            N  +   V E
Sbjct: 330 LNPDLPKRVAE 340


>gi|167757725|ref|ZP_02429852.1| hypothetical protein CLOSCI_00055 [Clostridium scindens ATCC 35704]
 gi|167664607|gb|EDS08737.1| hypothetical protein CLOSCI_00055 [Clostridium scindens ATCC 35704]
          Length = 651

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 57/191 (29%), Gaps = 17/191 (8%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG-SFGACLML 99
           +PL+ +   +       AA+   + G++ I ++ G         S  +++          
Sbjct: 122 RPLSKEELKSIAKDYGAAARRAVNAGFDLIEVHAGHSYLISQFLSPTMNDRTDEFGGCAK 181

Query: 100 NPDIVGDCI-AAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIH 154
           N       +   + KA+   V +  R+ VD+              ++ +    V+     
Sbjct: 182 NRARFCRMVIDEVRKAIGPRVPISLRLSVDELVEGGNSVDDCLEYLEYLND-EVDLFDTS 240

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDG 212
           +            N         +   ++ +         G + +   A  IL     D 
Sbjct: 241 SGLNPSIQYQIDANYLEDGWRSYMAKAVRDKFGK-PTIAIGNIRNPQVAEDILARGDADL 299

Query: 213 VMIGRAAYKNS 223
           + +GR    + 
Sbjct: 300 IGMGRGLIADP 310


>gi|270290070|ref|ZP_06196296.1| NADH:flavin oxidoreductase [Pediococcus acidilactici 7_4]
 gi|270281607|gb|EFA27439.1| NADH:flavin oxidoreductase [Pediococcus acidilactici 7_4]
          Length = 387

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 26/181 (14%), Positives = 65/181 (35%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EA +     G++ + +             P +      +G  +    +     + A  
Sbjct: 151 FGEATRRAIQAGFDGVEIHGANTYLIQQFFSPHSNRRTDHWGGSVEKRMNFGLAVVQAAH 210

Query: 113 KALSI----PVTVKCRIGVDD-QIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
           +A++        +  RI  ++ + P + L +    +  +    ++ + +       K L+
Sbjct: 211 RAVAKYAGDHFMLGYRISPEEIEEPGIRLADTLQFIDELADQPLDYLHVSMGNVWRKSLN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN 222
               ++        +  IKK+  + L I   G +E  + A K++   +D V +GR + + 
Sbjct: 271 DDSEKR------PTILRIKKQVHNRLPIIGVGSVETPADAEKVMDEGIDFVALGRESLRE 324

Query: 223 S 223
            
Sbjct: 325 P 325


>gi|213410629|ref|XP_002176084.1| NADPH dehydrogenase [Schizosaccharomyces japonicus yFS275]
 gi|212004131|gb|EEB09791.1| NADPH dehydrogenase [Schizosaccharomyces japonicus yFS275]
          Length = 375

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 33/209 (15%), Positives = 68/209 (32%), Gaps = 23/209 (11%)

Query: 59  ISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
               V A K     G++ + +         ++  P++      +G           +   
Sbjct: 170 HDDFVSATKRAVTAGFDFVEIHGAHGYFLSSMSSPASNTRTDEYGGSFENRVKYPLEVTN 229

Query: 110 AMCKAL--SIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           ++ K +   +P+  +      +          L  + K +K +GV+ + +    A     
Sbjct: 230 SIRKIIPEDMPLFYRINGTDWLEPGKGWEVTDLVKMAKLLKDAGVDFLNVSTGGA----D 285

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG---GLEDMSQALKILPSVDGVMIGRAAY 220
           S +     P         +KK  P L +G  G     + +   LK     D V +GRA  
Sbjct: 286 SAQQIPVKPFFQVPFAEAVKKAVPGLAVGTVGLFCDGKSIESVLKE-ERADVVFVGRAHL 344

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
           +N A ++        P+  +      V +
Sbjct: 345 RNPAAVSAFATELDEPIVLAPQYIRSVRR 373


>gi|115360660|ref|YP_777797.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           AMMD]
 gi|115285988|gb|ABI91463.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia ambifaria
           AMMD]
          Length = 352

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 22/155 (14%), Positives = 50/155 (32%), Gaps = 11/155 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGV 148
           +G  L     ++   +AA+ +       +  R+   D +P          L + +++ GV
Sbjct: 197 YGGALENRARLLRQVVAAVREQWPRRRPLVVRLSATDWMPGGWDIEECVALCRWLREDGV 256

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I   +   +     P                I++E   +  G  G +    +  +I+ 
Sbjct: 257 DLIDTSSGGNVASAKIPVGQGYQVP----FAARIRREAG-IATGAVGMITSGRRGAEIIE 311

Query: 209 --SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
               D V++ R A ++             P+    
Sbjct: 312 RGDADLVLVAREALRDPYFPRRAAAELGVPIAVPE 346


>gi|221135194|ref|ZP_03561497.1| imidazole glycerol phosphate synthase subunit HisF [Glaciecola sp.
           HTCC2999]
          Length = 258

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K+G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQQYAKAGADELV------FYDITASSDARVVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  A KIL    D + I   A  N  ++T + + +  
Sbjct: 85  SVEDAGKILAMGADKISINSPALANPELITELHDAYGQ 122


>gi|19112660|ref|NP_595868.1| NADH-dependent flavin oxidoreductase (predicted)
           [Schizosaccharomyces pombe 972h-]
 gi|74582901|sp|O94467|OYEC_SCHPO RecName: Full=Putative NADPH dehydrogenase C23G7.10c; AltName:
           Full=Old yellow enzyme homolog 3
 gi|4106687|emb|CAA22626.1| NADH-dependent flavin oxidoreductase (predicted)
           [Schizosaccharomyces pombe]
          Length = 395

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 66/184 (35%), Gaps = 23/184 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K V AAK   + G++ I ++            P+       +G           + + +
Sbjct: 188 DKFVVAAKRAVEIGFDVIEIHGAHGYLISSTVSPATNDRNDKYGGTFEKRILFPMEVVHS 247

Query: 111 MCKAL--SIP----VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGL 163
           + KA+  S+P    VT    +             L   ++  GV+ I +        + +
Sbjct: 248 VRKAIPDSMPLFYRVTATDWLPKGQGWEIEDTVALAARLRDGGVDLIDVSSGGNHKDQRI 307

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
             KD  ++P  +     +IK +   + +G  G + D   A +IL     D   + R   +
Sbjct: 308 EVKDCYQVPFAE-----KIKDQVNGILLGAVGMIRDGLTANEILESGKADVTFVAREFLR 362

Query: 222 NSAM 225
           N ++
Sbjct: 363 NPSL 366


>gi|311696282|gb|ADP99155.1| dihydroorotate dehydrogenase 2 [marine bacterium HP15]
          Length = 330

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 25/124 (20%), Positives = 45/124 (36%), Gaps = 27/124 (21%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L   +   P+   + G         A+ +E  G + I LN+               L  +
Sbjct: 96  LLRHSLGVPVVASLNGISAGGWTRHARELEAAGAHAIELNL-------------YDLASD 142

Query: 101 PDIVGD--------CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           P+   +         + ++ + +SIPV+VK            AL   V  I++SG  G+ 
Sbjct: 143 PEETAEALEQRQLSVVRSVTEQVSIPVSVKLSPF------YSALPAFVAGIEESGARGVV 196

Query: 153 IHAR 156
           +  R
Sbjct: 197 LFNR 200


>gi|170695647|ref|ZP_02886790.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia graminis
           C4D1M]
 gi|170139446|gb|EDT07631.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia graminis
           C4D1M]
          Length = 687

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + + ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGVEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ +SG+    G+            +
Sbjct: 211 REAVGPDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSESGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|221069367|ref|ZP_03545472.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           KF-1]
 gi|220714390|gb|EED69758.1| NADH:flavin oxidoreductase/NADH oxidase [Comamonas testosteroni
           KF-1]
          Length = 774

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 59/199 (29%), Gaps = 25/199 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIA 109
           + V+AA++  D G + + L   C           P        +G  L            
Sbjct: 559 QFVQAAQMAADIGVDWLEL--HCAHGYLLSSFISPLTNHRSDEYGGSLENRLRYPLQVFK 616

Query: 110 AMCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           AM        P++V+      V   I       + K+ K +G + I   +   + K   P
Sbjct: 617 AMRAVWPQDRPMSVRISAHDWVPGGITPEDAVEIAKAFKAAGADLIDCSSG-QVSKAEKP 675

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R       D + +       +     G + +   A  I+ +   D   I R    N 
Sbjct: 676 VFGRMFQTPFADRIRQEA----GVATMAVGAISEADHANSIIAAGRADLCAIARPHLANP 731

Query: 224 -AMLTTVDEYFSNPLTGSS 241
              LT   +    P+    
Sbjct: 732 AWTLTEAAKIGYTPIVWPR 750


>gi|150016799|ref|YP_001309053.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
 gi|149903264|gb|ABR34097.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
          Length = 664

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 18/154 (11%), Positives = 44/154 (28%), Gaps = 27/154 (17%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC----------------RIGVDDQIPAV 134
           +G  L        + +  +        PVT++                    ++      
Sbjct: 198 YGGSLENRLRFAREIVEEIKDRCGEDFPVTLRYSPKSFIKDLRDGALPGEEFIEKGRDLE 257

Query: 135 ALRNLVKSIKKSGVNGIWIHAR---KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
                 K +   G + + I                  + +    Y    ++ KE  D+ +
Sbjct: 258 EGIEAAKLLVSYGYDSLDIDVGSYDSWWWSHPPMYQEKGL----YRPYAKLMKETVDVPV 313

Query: 192 GLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              G +++   A++ + +   D V +GR    + 
Sbjct: 314 ICAGRMDNPDMAIEAIENGTCDIVSLGRPLLADP 347


>gi|260857209|ref|YP_003231100.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O26:H11 str. 11368]
 gi|257755858|dbj|BAI27360.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O26:H11 str. 11368]
 gi|323154539|gb|EFZ40739.1| 2,4-dienoyl-CoA reductase [Escherichia coli EPECa14]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|217967513|ref|YP_002353019.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dictyoglomus
           turgidum DSM 6724]
 gi|226700512|sp|B8E2C8|HIS6_DICTD RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|217336612|gb|ACK42405.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dictyoglomus
           turgidum DSM 6724]
          Length = 252

 Score = 39.0 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 47/118 (39%), Gaps = 11/118 (9%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           + L +  +K G + I +    A  +G S            D+V ++  E   + + + GG
Sbjct: 33  KELARRYEKEGADEIVLLDITASEEGRSTF---------VDVVTDVASELF-VPLTVGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           ++++    ++L    D V I  +A +N  ++  +   F +     +    R  K  W 
Sbjct: 83  IKNIEDVRRLLKAGADKVSINTSAVENPDLINQIASEFGSQCLVVAIDVKRRGKKSWE 140


>gi|126731619|ref|ZP_01747424.1| hypothetical protein SSE37_00205 [Sagittula stellata E-37]
 gi|126707785|gb|EBA06846.1| hypothetical protein SSE37_00205 [Sagittula stellata E-37]
          Length = 745

 Score = 39.0 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 31/183 (16%), Positives = 57/183 (31%), Gaps = 28/183 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +  +AA++ +  G++ I L+            P +      +G  L        +  AA
Sbjct: 530 DQFAQAAQMADRAGFDMIELHAAHGYLISSFISPVSNARGDEYGGSLENRMRYPLEVFAA 589

Query: 111 MCKALSIPVTVKCRIGVDDQIPAV-----ALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           M  A  +   +  RI  +D +            + +    +G + I + A +  +    P
Sbjct: 590 MRAAWPVGKPMSVRISANDWVGEAGVTPDEAVQIARMFSDAGADLIDVSAGQTTVD-AKP 648

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA---AYKN 222
              R       D +         L     G + +   A  IL      M GRA   A   
Sbjct: 649 VYGRMFQTPFSDRIRNDA----GLKTMAVGNIYEADHANSIL------MAGRADLVAVGR 698

Query: 223 SAM 225
             +
Sbjct: 699 PHL 701


>gi|310767998|gb|ADP12948.1| Xenobiotic reductase A [Erwinia sp. Ejp617]
          Length = 366

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 24/148 (16%), Positives = 56/148 (37%), Gaps = 12/148 (8%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVAL---RN 138
           P        +G         + + +AA+ +    ++P+T +  +   D      L     
Sbjct: 191 PHTNQRTDRYGGSFAGRSRFLLETLAAVREVWPENLPLTARLGVIEYDGRDEETLSESIE 250

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L + ++K+G++ + +     + +   P     +       V +  +    L +  + G+E
Sbjct: 251 LTQLMQKNGLDLLNVSIGFTVAETDIPWGPGFLAP-----VAQRVRHATGLPVATSWGME 305

Query: 199 DMSQALKIL--PSVDGVMIGRAAYKNSA 224
             + A + +    +D VMIGRA   +  
Sbjct: 306 APAVAERAIAEQQMDLVMIGRALLADPH 333


>gi|308506869|ref|XP_003115617.1| hypothetical protein CRE_18622 [Caenorhabditis remanei]
 gi|308256152|gb|EFP00105.1| hypothetical protein CRE_18622 [Caenorhabditis remanei]
          Length = 445

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 28/186 (15%), Positives = 67/186 (36%), Gaps = 21/186 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----CP----SARVHEGSFGACLMLNP----DIVGD 106
            ++V AAK++ + G++ I +N       C     + +  +   G  L+       D++  
Sbjct: 167 DRVVYAAKLLSNCGFDGIEVNTAFGNLFCQFLGNNNKRTDEYGGDSLVKRTQFHIDLLNA 226

Query: 107 CIAAMCKALSIPVTVKC-RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
               +  A    V +K       +      +  L + ++++G + + +     + + +  
Sbjct: 227 IRKEVPAAGGFLVGLKLNSADFQNNFSNDEVSRLCEILEEAGYDFVEL-TGGQMEQCVQE 285

Query: 166 KDNRK--IPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAA 219
              R   I   +Y  + +  + K      + + GG +  S  +    L    G+   RAA
Sbjct: 286 AQQRASTIARENYFLEFIETVAKSFRKTVVYITGGWQTASGMVNAVKLNITQGIGFARAA 345

Query: 220 YKNSAM 225
                +
Sbjct: 346 AAEPDL 351


>gi|265766268|ref|ZP_06094309.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_1_16]
 gi|263253936|gb|EEZ25401.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_1_16]
          Length = 324

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 30/198 (15%), Positives = 67/198 (33%), Gaps = 24/198 (12%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I    D    V+ AK +E+ G + + +N+    + +    +G+    + D     
Sbjct: 98  PVIASINCYTDAEW-VDFAKQIEEAGADALEINILALQSDIQYK-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           ++ + K + IPV +K                L+  +  +G   + +  R          +
Sbjct: 152 LSHIKKTIRIPVIMKL------GSNFTNPVALIDQLYANGAAAVVLFNRFYQPDIDVEKM 205

Query: 161 KGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGR 217
           +  S        +L      +         +    +GG+         IL     + I  
Sbjct: 206 EHTSGDVFSNASDLSTTLRWIGISSSLVSKIDYAASGGIHKPDGIVKAILAGASAIEICS 265

Query: 218 AAYKNSAML-TTVDEYFS 234
           A Y+N+ +    ++ + S
Sbjct: 266 AIYQNTNLFVGEMNRFLS 283


>gi|218778833|ref|YP_002430151.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760217|gb|ACL02683.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfatibacillum
           alkenivorans AK-01]
          Length = 365

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 72/190 (37%), Gaps = 18/190 (9%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             K  +AA   +  G++ + ++ G          P+       +G  +     I  +   
Sbjct: 143 AEKFGQAAARAKKAGFDGVQIHSGHGYLLSQFLSPAMNRRTDEYGGPIENRCRIHLEVYR 202

Query: 110 AMCKAL--SIPVTVK--CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ +A+    PV +K  C   ++D + +       +++++ G++ + +       + LSP
Sbjct: 203 AIRQAVGSDYPVLIKLNCADFIEDGLESKDSLYAAQALEREGLDALELTGGILSSRKLSP 262

Query: 166 KD---NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
                N +     +     + KEN  + + L GG+     A +++     D V + R   
Sbjct: 263 SRANINSQDKEAYFREEARMFKENLGIPLILVGGMRSFDLAEQLVSQGCADYVSMSRPFI 322

Query: 221 KNSAMLTTVD 230
           +   ++    
Sbjct: 323 REPDLVNRWK 332


>gi|134100887|ref|YP_001106548.1| flavin oxidoreductase/NADH oxidase [Saccharopolyspora erythraea
           NRRL 2338]
 gi|133913510|emb|CAM03623.1| flavin oxidoreductase/NADH oxidase [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 352

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 29/220 (13%), Positives = 65/220 (29%), Gaps = 31/220 (14%)

Query: 48  KPLALQIGGADIS----KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFG 94
            P+  ++   +I        E+A+     G+  + L+            P +     ++G
Sbjct: 126 HPVPHELTAEEIQQLVRDFAESARRALAAGFQVVELHGAHGYLIHSFLSPVSNKRTDAYG 185

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----------VALRNLVKSI 143
             L        + + A+       + +  R    D +                  L K +
Sbjct: 186 GSLENRLRFPLEVVDAVRAVWPDELPLFFRTSATDWLSENPADPREGWTGEDTVRLAKEL 245

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +  GV+ + +     +    +  + +  P         ++ E         G + + +QA
Sbjct: 246 QARGVDLMDVSTGGLV----ADAEIKPAPGYQVPFAARVRDEAGISA-AAVGLILEPAQA 300

Query: 204 LKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +I+ S   D VM+GR   +         E          
Sbjct: 301 EEIVSSGRADAVMLGRQLLREPYWAHRAAEELGEQPQWPD 340


>gi|228920758|ref|ZP_04084098.1| NADPH dehydrogenase [Bacillus thuringiensis serovar huazhongensis
           BGSC 4BD1]
 gi|228838869|gb|EEM84170.1| NADPH dehydrogenase [Bacillus thuringiensis serovar huazhongensis
           BGSC 4BD1]
          Length = 319

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 46/136 (33%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWDGPIFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|225619197|ref|YP_002720423.1| NADH:flavin oxidoreductase/NADH oxidase [Brachyspira hyodysenteriae
           WA1]
 gi|225214016|gb|ACN82750.1| DH:flavin oxidoreductase/DH oxidase [Brachyspira hyodysenteriae
           WA1]
          Length = 344

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 47/137 (34%), Gaps = 8/137 (5%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           I+ + +    +A+     ++ RI   D +     +++    +K     G+       +  
Sbjct: 197 ILEEILRKGKEAVGKDYPIQIRISSYDWREGGNTVKDFADMLKPLEAEGL--FDSINVST 254

Query: 162 GLSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
           G    D + IP   Y I    E+K+    +     G + D   A  ++ +   D + IGR
Sbjct: 255 GAVTADGKIIPYEGYQIPFCRELKQ-YMKVPCIGGGLIYDPKMANMMVRNGAADAIYIGR 313

Query: 218 AAYKNSAMLTTVDEYFS 234
              +N            
Sbjct: 314 ELLRNPYWALQAARTLG 330


>gi|168243052|ref|ZP_02667984.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|194451080|ref|YP_002047256.1| FAD/FMN-binding/pyridine nucleotide-disulfide oxidoreductase family
           protein [Salmonella enterica subsp. enterica serovar
           Heidelberg str. SL476]
 gi|200387945|ref|ZP_03214557.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|194409384|gb|ACF69603.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|199605043|gb|EDZ03588.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|205337917|gb|EDZ24681.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHGEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|322514035|ref|ZP_08067106.1| dihydroorotate oxidase [Actinobacillus ureae ATCC 25976]
 gi|322120052|gb|EFX92023.1| dihydroorotate oxidase [Actinobacillus ureae ATCC 25976]
          Length = 325

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 33/192 (17%), Positives = 72/192 (37%), Gaps = 34/192 (17%)

Query: 65  AAKIVEDFGYNEINLNVGCPS-ARVHEGSFGACLMLNPDIVGDCIAAMCKALSI------ 117
             + V ++  + I +N+  P+   +    +G  L        + ++A+ +  SI      
Sbjct: 143 CLRKVYEY-ADYITVNISSPNTKNLRSLQYGDAL-------DELLSALKQEQSILSQKFA 194

Query: 118 ---PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI--LKGLSPKDNRKIP 172
              P+ +K    + D+  A    +LV+      + G    +R+ +  LK    +      
Sbjct: 195 KYKPLVLKIAPDLTDEEVASVADSLVRHKIDGVIAGNTTLSREPVAGLKHAEQQGGLSGK 254

Query: 173 NLDY---DIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP------SVDGVMIGRAAYKN 222
            L+     ++  + KE N  L I  +GG+  +S   + +        V   MI    Y+ 
Sbjct: 255 PLNSLSTHLIRRLAKELNGQLPIIGSGGIHSVSSGQEKIDAGASLLQVYSAMI----YQG 310

Query: 223 SAMLTTVDEYFS 234
            A++  + +   
Sbjct: 311 PALIQELAKQIK 322


>gi|261363749|ref|ZP_05976632.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Neisseria mucosa ATCC 25996]
 gi|288568324|gb|EFC89884.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Neisseria mucosa ATCC 25996]
          Length = 245

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 5/101 (4%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
               DI+  + K   D+ + L GG+ D+    K L   ++ V+IG AA KN   +    +
Sbjct: 64  PAIKDILAAVAK---DIPVQLGGGIRDLETIEKYLDLGLNDVIIGTAAVKNPDFVREACK 120

Query: 232 YFSNPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F   +  G       V  D W  ++       A+     G
Sbjct: 121 SFPGQIIVGLDAKDGMVAIDGWATVTEHHVIDLAKRFEDDG 161


>gi|26554352|ref|NP_758286.1| NADH-dependent flavin oxidoreductase [Mycoplasma penetrans HF-2]
 gi|26454362|dbj|BAC44690.1| NADH-dependent flavin oxidoreductase [Mycoplasma penetrans HF-2]
          Length = 346

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 62/179 (34%), Gaps = 24/179 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            ++AA   +  G++ + ++            P +   +  +G        ++ + +  + 
Sbjct: 150 FIDAAIRAKKAGFDMVEIHAAHGYLLSSFLTPISNQRDDVYG---QNKALLLEEILTGIK 206

Query: 113 KA--LSIPVTVKCRI---GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           KA     P+ V+        +   P   +  L   IK+S ++ I +              
Sbjct: 207 KANGSDYPIIVRISAYDWHPNGNKPQDFIEMLNPLIKQSLIDAIDVSTGGTTEDAKITAY 266

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           +        +I     K+N ++     G + D   A KI+ +   D V IGR   +N  
Sbjct: 267 DCYQIPFCLEI-----KQNVNVPCIGGGLIVDAKSANKIVENEAADAVYIGRQLLRNPY 320


>gi|323452957|gb|EGB08830.1| hypothetical protein AURANDRAFT_25630 [Aureococcus anophagefferens]
          Length = 757

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 31/232 (13%), Positives = 70/232 (30%), Gaps = 29/232 (12%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y  M VA +  +     I   +  +K +   I           A++ +  GY+
Sbjct: 148 LHAGRYAYHPMAVAPSKKKAPINVITPRALSDKDIRRTI-----DDFARCAELAKSCGYD 202

Query: 76  EINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-----VTV 121
            + +             P   V +  +G        +  + + A+  A+ +        V
Sbjct: 203 GVEIMGSEGYFINEFLAPRTNVRDDDWGGSFENRSRLALEIMKAVRAAVGVEDFAVIFRV 262

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
                V++ +       L  ++  +GV+   I+      +   P     +P   +     
Sbjct: 263 SMLELVENGLSFDESVELSAALHAAGVD--IINTGIGWHEARVPTIATCVPRGAFAFATR 320

Query: 182 IKKENPD-----LFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTT 228
             K+  D       +     + D + A +IL   D  ++   +     +   
Sbjct: 321 NVKDALDAKAAHPLLCATNRINDAATAERILARGDADLV---SLARPFLADE 369


>gi|253564756|ref|ZP_04842212.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 3_2_5]
 gi|251946221|gb|EES86598.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 3_2_5]
 gi|301163770|emb|CBW23325.1| putative dihydroorotate dehydrogenase [Bacteroides fragilis 638R]
          Length = 324

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 30/198 (15%), Positives = 67/198 (33%), Gaps = 24/198 (12%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I    D    V+ AK +E+ G + + +N+    + +    +G+    + D     
Sbjct: 98  PVIASINCYTDAEW-VDFAKQIEEAGADALEINILALQSDIQYK-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           ++ + K + IPV +K                L+  +  +G   + +  R          +
Sbjct: 152 LSHIKKTIRIPVIMKL------GSNFTNPVALIDQLYANGAAAVVLFNRFYQPDIDVEKM 205

Query: 161 KGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGR 217
           +  S        +L      +         +    +GG+         IL     + I  
Sbjct: 206 EHTSGDVFSNASDLSTTLRWIGISSSLVSKIDYAASGGIHKPDGIVKAILAGASAIEICS 265

Query: 218 AAYKNSAML-TTVDEYFS 234
           A Y+N+ +    ++ + S
Sbjct: 266 AIYQNTNLFVGEMNRFLS 283


>gi|218550362|ref|YP_002384153.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia
           fergusonii ATCC 35469]
 gi|218357903|emb|CAQ90547.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia
           fergusonii ATCC 35469]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 30/228 (13%), Positives = 65/228 (28%), Gaps = 47/228 (20%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + L+      +        L  Q     I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSALQAPINRFVPHE-----LTHQEIVQLIDSFARCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVTVK 122
                         L+                    N      + + A+ + +     + 
Sbjct: 162 --------MGSEGYLINEFLTLRTNQRNDQWGGDYRNRMRFAVEVVRAVRERVGNDFIII 213

Query: 123 CRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            R+     V++         L ++I+ +G     I+      +   P     +P   +  
Sbjct: 214 YRLSMLDLVENGSTFAETIELAQAIEAAGAT--IINTGIGWHEARIPTIATAVPRGAFSW 271

Query: 179 V-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 272 VTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|325498670|gb|EGC96529.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia
           fergusonii ECD227]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 30/228 (13%), Positives = 65/228 (28%), Gaps = 47/228 (20%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + L+      +        L  Q     I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSALQAPINRFVPHE-----LTHQEIVQLIDSFARCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVTVK 122
                         L+                    N      + + A+ + +     + 
Sbjct: 162 --------MGSEGYLINEFLTLRTNQRNDQWGGDYRNRMRFAVEVVRAVRERVGNDFIII 213

Query: 123 CRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            R+     V++         L ++I+ +G     I+      +   P     +P   +  
Sbjct: 214 YRLSMLDLVENGSTFAETIELAQAIEAAGAT--IINTGIGWHEARIPTIATAVPRGAFSW 271

Query: 179 V-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 272 VTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|325271768|ref|ZP_08138244.1| xenobiotic reductase A [Pseudomonas sp. TJI-51]
 gi|324103104|gb|EGC00475.1| xenobiotic reductase A [Pseudomonas sp. TJI-51]
          Length = 363

 Score = 39.0 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|53714240|ref|YP_100232.1| dihydroorotate dehydrogenase 2 [Bacteroides fragilis YCH46]
 gi|52217105|dbj|BAD49698.1| putative dihydropyrimidine dehydrogenase [NADP+] precursor
           [Bacteroides fragilis YCH46]
          Length = 324

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 30/198 (15%), Positives = 67/198 (33%), Gaps = 24/198 (12%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I    D    V+ AK +E+ G + + +N+    + +    +G+    + D     
Sbjct: 98  PVIASINCYTDAEW-VDFAKQIEEAGADALEINILALQSDIQYK-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           ++ + K + IPV +K                L+  +  +G   + +  R          +
Sbjct: 152 LSHIKKTIHIPVIMKL------GSNFTNPVALIDQLYANGAAAVVLFNRFYQPDIDVEKM 205

Query: 161 KGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGR 217
           +  S        +L      +         +    +GG+         IL     + I  
Sbjct: 206 EHTSGDVFSNASDLSTTLRWIGISSSLVSKIDYAASGGIHKPDGIVKAILAGASAIEICN 265

Query: 218 AAYKNSAML-TTVDEYFS 234
           A Y+N+ +    ++ + S
Sbjct: 266 AIYQNTNLFVGEMNRFLS 283


>gi|310780032|ref|YP_003968364.1| 2-nitropropane dioxygenase NPD [Ilyobacter polytropus DSM 2926]
 gi|309749355|gb|ADO84016.1| 2-nitropropane dioxygenase NPD [Ilyobacter polytropus DSM 2926]
          Length = 311

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 24/110 (21%), Positives = 44/110 (40%), Gaps = 20/110 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  + K   +P+           +P V+   L K  ++ G + I +    A     +  D
Sbjct: 105 VFELGKESGVPI-----------VPIVSSLKLAKISERLGASAIIVEGGNAGGHLGTDLD 153

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           +       +DIV EI ++      G  GG+     A ++L   VDG+ +G
Sbjct: 154 S-------WDIVGEIAEKISVPVFGA-GGVITPDDARRMLALGVDGIQMG 195


>gi|170755090|ref|YP_001781138.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum B1 str.
           Okra]
 gi|169120302|gb|ACA44138.1| oxidoreductase, FAD/FMN-binding [Clostridium botulinum B1 str.
           Okra]
          Length = 339

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 55/161 (34%), Gaps = 23/161 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AAK  +  G++ I ++            P     +  +G  +     ++ +    + 
Sbjct: 135 FAKAAKRAKQSGFDGIQIHGAHGYFLSRTLSPLFNKRKDKYGGSVEKRGALILEVYDEIR 194

Query: 113 KALSIPVTVKCRIGVDDQIP---AVALRNLV-KSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  +I   D             V + + K G++ I I     I    + K++
Sbjct: 195 KAVGKDFHISIKINCSDFEEGGATFKECEFVCRELSKKGIDSIEISGGGTIWTETNKKES 254

Query: 169 RKIPNLDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKIL 207
                   +   +I +E   P + +G+N          +IL
Sbjct: 255 IYK-----EYASKIAEEVDTPIILVGMN---RSYDNMNEIL 287


>gi|206975115|ref|ZP_03236029.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus H3081.97]
 gi|206746536|gb|EDZ57929.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus H3081.97]
          Length = 345

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|119504164|ref|ZP_01626245.1| NADH:flavin oxidoreductase/NADH oxidase [marine gamma
           proteobacterium HTCC2080]
 gi|119460167|gb|EAW41261.1| NADH:flavin oxidoreductase/NADH oxidase [marine gamma
           proteobacterium HTCC2080]
          Length = 409

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 31/222 (13%), Positives = 72/222 (32%), Gaps = 46/222 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA+     G++ + +++G          P     + ++G             +AA
Sbjct: 148 DDFVTAAEHCVSAGFDAVEIHMGHGYLLNQFLSPMDNKRKDAYGGSAENRARFPTRVLAA 207

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHA----------- 155
           + + +   + V  +I V D     A         K ++ +G + + +             
Sbjct: 208 VKQRVGQDIAVLAKINVSDGRRRGANVEDAIVTAKLLEAAGADMLVLSGGRNVESGWFMF 267

Query: 156 -------------RKAILKGLS-PKDNRKIPNLD------YDIVYEIKKENPDLFIGLNG 195
                         K  L G++     +  P++D      ++   +I +E   L +   G
Sbjct: 268 GSNMNLEAMYRVLGKWSLSGMAIGATAKSAPSIDFRELYFWEYSKKI-REAVSLPLAYLG 326

Query: 196 GLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           G++     A  +    + V + RA  +   ++     +   P
Sbjct: 327 GVKSADNVAQCMAADFEAVALARALLREPDLVNKWQVHPEEP 368


>gi|52143393|ref|YP_083438.1| NADPH dehydrogenase NamA [Bacillus cereus E33L]
 gi|68052516|sp|Q63CC9|NAMA_BACCZ RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|51976862|gb|AAU18412.1| NADH oxidase [Bacillus cereus E33L]
          Length = 345

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|329914772|ref|ZP_08276166.1| putative NADH-dependent flavin oxidoreductase [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327545052|gb|EGF30362.1| putative NADH-dependent flavin oxidoreductase [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 421

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 54/180 (30%), Gaps = 22/180 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
              V  A   E  G   + L+            P +      +G  L   M  P  V D 
Sbjct: 216 DAFVATALRAERLGIEVLELHAAHGYLLHEFLSPLSNQRTDEYGGSLENRMRFPLEVYDA 275

Query: 108 IAAMCKALSIPVTVKCRIGV--DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A   A  IP+ V+       D             ++ + G   I + +      G S 
Sbjct: 276 VRAAVPA-GIPLGVRISASDWADGGWDIEQSVVFCTALNERGCAFIDVSSG-----GTST 329

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS 223
                +            +E  ++ +   G + + + A +IL   D  MI   RA   + 
Sbjct: 330 AQKIPLSPGYQVPFAARIREETEMPVIAVGLITEAAHAEQILADGDADMIALARAMLYDP 389


>gi|312862851|ref|ZP_07723091.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus vestibularis F0396]
 gi|311101711|gb|EFQ59914.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus vestibularis F0396]
          Length = 252

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 21/119 (17%), Positives = 43/119 (36%), Gaps = 11/119 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++  ++G + +        L   +  DNR+      D+V  +  +    F    GG+  
Sbjct: 36  ARAYYEAGCDELV------FLDITATSDNRETT---VDMVRRVADQVFIPFTVG-GGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +    K+L    D V I  +A  N  ++    + F N    ++    ++    W    A
Sbjct: 86  VEDMNKMLKAGADKVAINSSALANPQLIADCAQKFGNQCVVAAIDAKKMADGSWHVFVA 144


>gi|332799899|ref|YP_004461398.1| 2,4-dienoyl-CoA reductase [Tepidanaerobacter sp. Re1]
 gi|332697634|gb|AEE92091.1| 2,4-dienoyl-CoA reductase (NADPH) [Tepidanaerobacter sp. Re1]
          Length = 637

 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 24/141 (17%), Positives = 50/141 (35%), Gaps = 12/141 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGV 148
           +G  L        +CI A+ K +    P+ VK      V+          + K ++ + +
Sbjct: 186 YGGSLKNRMRFTLECIDAIHKNVGPEFPIFVKFTPVHRVEGGRELDEGLEMAKILESANI 245

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL- 207
           + + +      +   +     +      D+V  +KK    L +   G + D  +A + L 
Sbjct: 246 DALHVDVGCYEVWHKAISTVYEPEGHQMDVVEAVKK-TVSLPVFGQGKMFDPVKAEQALV 304

Query: 208 -PSVDGV-----MIGRAAYKN 222
               D +     M+   A+ N
Sbjct: 305 EGKTDYIVLSHQMLADPAWAN 325


>gi|238782781|ref|ZP_04626810.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia bercovieri ATCC 43970]
 gi|238716204|gb|EEQ08187.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia bercovieri ATCC 43970]
          Length = 673

 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 28/206 (13%), Positives = 64/206 (31%), Gaps = 45/206 (21%)

Query: 49  PLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF---------- 93
           P A Q    D      +     A++ +  GY+ + +        +    +          
Sbjct: 127 PFAPQALSHDEVLQTIADFAHCAQLAKQAGYDGVEV--------MGSEGYLINQFLTART 178

Query: 94  -------GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKS 142
                  G           + + A+ +A      +  R+     V+D      +  L  +
Sbjct: 179 NHRDDEWGGDFTRRMRFAVEIVRAVRQATGPDFILIYRLSMLDLVEDGSSWSEIEQLALA 238

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMS 201
           ++++G   I  +      +   P     +P   +  V  ++  +     I  N  + D +
Sbjct: 239 VEQAGATLI--NTGIGWHEARIPTIATMVPRAGFSWVTRKLMGKVRIPLITTNR-INDPA 295

Query: 202 QALKILPSVDGV--MIGRAAYKNSAM 225
            A ++L  VDG   M+   +     +
Sbjct: 296 VAEQVL--VDGCADMV---SMARPFL 316


>gi|167633143|ref|ZP_02391469.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0442]
 gi|254721026|ref|ZP_05182817.1| NADPH dehydrogenase NamA [Bacillus anthracis str. A1055]
 gi|254739451|ref|ZP_05197150.1| NADPH dehydrogenase NamA [Bacillus anthracis str. Kruger B]
 gi|167531955|gb|EDR94620.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0442]
          Length = 345

 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|114570161|ref|YP_756841.1| imidazole glycerol phosphate synthase subunit HisF [Maricaulis
           maris MCS10]
 gi|122315927|sp|Q0AP84|HIS6_MARMM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|114340623|gb|ABI65903.1| imidazole glycerol phosphate synthase subunit hisF [Maricaulis
           maris MCS10]
          Length = 255

 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 17/130 (13%), Positives = 50/130 (38%), Gaps = 12/130 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D      + +L +   + G + +  +   A  +G +         ++ + V  + +
Sbjct: 21  VRFRDHEDVGDIVDLARRYAREGADELVFYDIAASARGRT---------VEPEWVSAVAR 71

Query: 185 ENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           E  D+   + GG+  +  A  ++    D + +   A ++  ++  +   F +       +
Sbjct: 72  EL-DIPFCVAGGIRSVDDARARLFAGADKISVNTPALEDPTIIDRLAAEFGSQCVVLG-V 129

Query: 244 KTRVDKDFWR 253
            +R+ +  WR
Sbjct: 130 DSRMIEGAWR 139


>gi|332289865|ref|YP_004420717.1| imidazole glycerol phosphate synthase subunit HisF [Gallibacterium
           anatis UMN179]
 gi|330432761|gb|AEC17820.1| imidazole glycerol phosphate synthase subunit HisF [Gallibacterium
           anatis UMN179]
          Length = 259

 Score = 39.0 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++ A +I     D + I   A  N  ++  + + F 
Sbjct: 85  TIADAEQIFAFGADKISINSPALANPDLINQLADRFG 121


>gi|297519813|ref|ZP_06938199.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           OP50]
          Length = 502

 Score = 39.0 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 32/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|307727868|ref|YP_003911081.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1003]
 gi|307588393|gb|ADN61790.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1003]
          Length = 687

 Score = 39.0 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + + ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGVEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ +SG+    G+            +
Sbjct: 211 REAVGPDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSESGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|229059733|ref|ZP_04197110.1| NADPH dehydrogenase [Bacillus cereus AH603]
 gi|228719562|gb|EEL71163.1| NADPH dehydrogenase [Bacillus cereus AH603]
          Length = 319

 Score = 39.0 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--P 208
           I   +   +   +      ++    +       KEN ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKENANIATGAVGLITTGLQAEQILNNS 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|26989713|ref|NP_745138.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida KT2440]
 gi|24984604|gb|AAN68602.1|AE016491_5 oxidoreductase, FMN-binding [Pseudomonas putida KT2440]
          Length = 418

 Score = 39.0 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 60/185 (32%), Gaps = 17/185 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
               A++ E  G+  + ++            P     +  +G  L     ++ + + A+ 
Sbjct: 151 FANTARLGEQAGFTGVEIHAAHGYLLSQFLSPLTNHRKDEWGGSLENRARLLLEIVKAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARK---AILKGLSP 165
             +S+   V  ++   D           + +V+ +   GV+ + +         ++G + 
Sbjct: 211 AVVSVDFAVAVKLNSADFQRGGFTTEDAKKVVEWLNDLGVDMVELSGGSYEVPAMQGDAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A  ++   VD V IG A   +  
Sbjct: 271 DGRTLAREAYFVEFARDLQTVAKMPMMVTGGIRRRPVAESVVQSGVDMVGIGTALAIDPH 330

Query: 225 MLTTV 229
           +    
Sbjct: 331 LPRDW 335


>gi|322613622|gb|EFY10563.1| hypothetical protein SEEM315_07840 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621215|gb|EFY18073.1| hypothetical protein SEEM971_20569 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624278|gb|EFY21112.1| hypothetical protein SEEM973_20685 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322627984|gb|EFY24773.1| hypothetical protein SEEM974_20605 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633102|gb|EFY29844.1| hypothetical protein SEEM201_11700 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636321|gb|EFY33029.1| hypothetical protein SEEM202_14373 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322643496|gb|EFY40058.1| hypothetical protein SEEM954_04755 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322648595|gb|EFY45042.1| hypothetical protein SEEM675_03761 [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322653647|gb|EFY49973.1| hypothetical protein SEEM965_21406 [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322657755|gb|EFY54023.1| hypothetical protein SEEM19N_17531 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322663856|gb|EFY60055.1| hypothetical protein SEEM801_03821 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322669133|gb|EFY65284.1| hypothetical protein SEEM507_10756 [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322672874|gb|EFY68981.1| hypothetical protein SEEM877_00030 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322678136|gb|EFY74199.1| hypothetical protein SEEM867_02787 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681312|gb|EFY77345.1| hypothetical protein SEEM180_21279 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322687758|gb|EFY83725.1| hypothetical protein SEEM600_15106 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195570|gb|EFZ80747.1| hypothetical protein SEEM581_10370 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199749|gb|EFZ84839.1| hypothetical protein SEEM501_16920 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202503|gb|EFZ87543.1| hypothetical protein SEEM460_17520 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323208009|gb|EFZ92955.1| hypothetical protein SEEM020_19115 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323212439|gb|EFZ97256.1| hypothetical protein SEEM6152_09423 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323215079|gb|EFZ99827.1| hypothetical protein SEEM0077_03974 [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323222809|gb|EGA07174.1| hypothetical protein SEEM0047_10230 [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323224110|gb|EGA08403.1| hypothetical protein SEEM0055_22235 [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230434|gb|EGA14552.1| hypothetical protein SEEM0052_19239 [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235214|gb|EGA19300.1| hypothetical protein SEEM3312_06748 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323239255|gb|EGA23305.1| hypothetical protein SEEM5258_06635 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323244387|gb|EGA28393.1| hypothetical protein SEEM1156_00572 [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323247004|gb|EGA30970.1| hypothetical protein SEEM9199_20640 [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323254063|gb|EGA37883.1| hypothetical protein SEEM8282_00120 [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323256180|gb|EGA39916.1| hypothetical protein SEEM8283_11286 [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262644|gb|EGA46200.1| hypothetical protein SEEM8284_02761 [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323267260|gb|EGA50744.1| hypothetical protein SEEM8285_20777 [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323269338|gb|EGA52793.1| hypothetical protein SEEM8287_11637 [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
          Length = 672

 Score = 39.0 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|255065980|ref|ZP_05317835.1| dihydroorotate oxidase [Neisseria sicca ATCC 29256]
 gi|255049891|gb|EET45355.1| dihydroorotate oxidase [Neisseria sicca ATCC 29256]
          Length = 311

 Score = 39.0 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 38/192 (19%), Positives = 62/192 (32%), Gaps = 21/192 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  S  E+   L + G    +     K V++ G+  I  LN+ CP   V      A    
Sbjct: 88  LQESQPERTFFLSLVGMSPDETHTLLKKVQNSGFKGITELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD----DQIPAVALR---NLVKSIKKSG----- 147
           + +     +         P+ +K     D    DQ   V  R     V  +   G     
Sbjct: 143 DFETTERILGEAFGYFDKPLGIKLPPYFDIVHFDQAAEVFNRHPLKFVNCVNSIGNGMYI 202

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
            +   +   K    G+  +  +     +    Y+  + NP + I   GG+     A +  
Sbjct: 203 EDESVVIRPKNGFGGIGGEYIKPTALANVHAFYQ--RLNPSIQIIGTGGVYTGRDAFEHI 260

Query: 207 LPSVDGVMIGRA 218
           L     V IG A
Sbjct: 261 LCGASMVQIGTA 272


>gi|288575894|ref|ZP_05977815.2| dihydroorotate oxidase [Neisseria mucosa ATCC 25996]
 gi|288566718|gb|EFC88278.1| dihydroorotate oxidase [Neisseria mucosa ATCC 25996]
          Length = 294

 Score = 39.0 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 38/192 (19%), Positives = 62/192 (32%), Gaps = 21/192 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  S  E+   L + G    +     K V++ G+  I  LN+ CP   V      A    
Sbjct: 71  LQESQPERTFFLSLVGMSPDETHTLLKKVQNSGFKGITELNLSCP--NVPGKPQIAY--- 125

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD----DQIPAVALR---NLVKSIKKSG----- 147
           + +     +         P+ +K     D    DQ   V  R     V  +   G     
Sbjct: 126 DFETTERILGEAFGYFDKPLGIKLPPYFDIVHFDQAAEVFNRHPLKFVNCVNSIGNGMYI 185

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI- 206
            +   +   K    G+  +  +     +    Y+  + NP + I   GG+     A +  
Sbjct: 186 EDESVVIRPKNGFGGIGGEYIKPTALANVHAFYQ--RLNPSIQIIGTGGVYTGRDAFEHI 243

Query: 207 LPSVDGVMIGRA 218
           L     V IG A
Sbjct: 244 LCGASMVQIGTA 255


>gi|194215317|ref|XP_001492288.2| PREDICTED: similar to KIAA0841 protein [Equus caballus]
          Length = 687

 Score = 39.0 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 8/85 (9%)

Query: 240 SSPIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRH 295
            +P+  RV +   R++     A +  Y  RH+HS   +Q+I  +++    G   S   R 
Sbjct: 73  EAPLAARVPESTLRRLCLGQGADIWTYILRHVHSQRSVQKIRGNLLWY--GHQGSPEARR 130

Query: 296 ILTVEAGASTATHHIIE--TAFNLM 318
            L +E   +     I+E   +  LM
Sbjct: 131 KLELETAVARLRAEILELDQSLELM 155


>gi|148359262|ref|YP_001250469.1| inosine-5'-monophosphate dehydrogenase [Legionella pneumophila str.
           Corby]
 gi|296107309|ref|YP_003619009.1| inosine 5'-monophosphate dehydrogenase [Legionella pneumophila
           2300/99 Alcoy]
 gi|148281035|gb|ABQ55123.1| inosine-5'-monophosphate dehydrogenase [Legionella pneumophila str.
           Corby]
 gi|295649210|gb|ADG25057.1| inosine 5'-monophosphate dehydrogenase [Legionella pneumophila
           2300/99 Alcoy]
          Length = 490

 Score = 39.0 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 11/86 (12%), Positives = 30/86 (34%), Gaps = 4/86 (4%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFI 191
            +A     + + ++G + + +      +          IP +    +  + +E    + +
Sbjct: 277 NIATAAAARDLYEAGADAVKVGIGPGSICTTRIVTGVGIPQI--SAIANVAQELKGIIPV 334

Query: 192 GLNGGL-EDMSQALKILPSVDGVMIG 216
             +GG+         +    D VM+G
Sbjct: 335 IADGGIRFSGDVCKALAAGADTVMLG 360


>gi|42781172|ref|NP_978419.1| NADPH dehydrogenase NamA [Bacillus cereus ATCC 10987]
 gi|68052639|sp|Q739N4|NAMA_BACC1 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|42737094|gb|AAS41027.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus ATCC 10987]
          Length = 345

 Score = 39.0 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|297526580|ref|YP_003668604.1| dihydroorotate dehydrogenase family protein [Staphylothermus
           hellenicus DSM 12710]
 gi|297255496|gb|ADI31705.1| dihydroorotate dehydrogenase family protein [Staphylothermus
           hellenicus DSM 12710]
          Length = 406

 Score = 39.0 bits (90), Expect = 1.00,   Method: Composition-based stats.
 Identities = 28/132 (21%), Positives = 44/132 (33%), Gaps = 21/132 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
           V +   A+ + + IP+  K      +      +  LVK ++K GV+GI            
Sbjct: 169 VVEAAKALREVVDIPIFAKLSPFTPN------IPELVKELEKVGVDGIVATNTIGPALHI 222

Query: 153 -IHARKAILKGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGL-EDMSQALKILP 208
            I     I+ G +       P L      V     +N  L I   GG+ +        + 
Sbjct: 223 DIETGLPIVGGPNGYGWMSGPALKPLALAVVAEAAKNTHLPIIGVGGISKGTDVIEYFMA 282

Query: 209 SVDGVMIGRAAY 220
               V I  AA 
Sbjct: 283 GASAVQICTAAL 294


>gi|54294611|ref|YP_127026.1| hypothetical protein lpl1687 [Legionella pneumophila str. Lens]
 gi|53754443|emb|CAH15927.1| hypothetical protein lpl1687 [Legionella pneumophila str. Lens]
 gi|307610419|emb|CBW99989.1| hypothetical protein LPW_17461 [Legionella pneumophila 130b]
          Length = 490

 Score = 39.0 bits (90), Expect = 1.00,   Method: Composition-based stats.
 Identities = 11/86 (12%), Positives = 30/86 (34%), Gaps = 4/86 (4%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFI 191
            +A     + + ++G + + +      +          IP +    +  + +E    + +
Sbjct: 277 NIATAAAARDLYEAGADAVKVGIGPGSICTTRIVTGVGIPQI--SAIANVAQELKGIIPV 334

Query: 192 GLNGGL-EDMSQALKILPSVDGVMIG 216
             +GG+         +    D VM+G
Sbjct: 335 IADGGIRFSGDVCKALAAGADTVMLG 360


>gi|53721749|ref|YP_110734.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia pseudomallei K96243]
 gi|76817793|ref|YP_337447.1| NADH:flavin oxidoreductase [Burkholderia pseudomallei 1710b]
 gi|126445562|ref|YP_001062062.1| oxidoreductase [Burkholderia pseudomallei 668]
 gi|126457577|ref|YP_001075014.1| FAD/FMN-binding oxidoreductase [Burkholderia pseudomallei 1106a]
 gi|167722944|ref|ZP_02406180.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           DM98]
 gi|167741928|ref|ZP_02414702.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           14]
 gi|167819108|ref|ZP_02450788.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           91]
 gi|167827489|ref|ZP_02458960.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           9]
 gi|167848963|ref|ZP_02474471.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           B7210]
 gi|167897566|ref|ZP_02484968.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           7894]
 gi|167905919|ref|ZP_02493124.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           NCTC 13177]
 gi|167914227|ref|ZP_02501318.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           112]
 gi|167922139|ref|ZP_02509230.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           BCC215]
 gi|226195018|ref|ZP_03790609.1| xenobiotic reductase A [Burkholderia pseudomallei Pakistan 9]
 gi|237509815|ref|ZP_04522530.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei MSHR346]
 gi|242312191|ref|ZP_04811208.1| xenobiotic reductase A [Burkholderia pseudomallei 1106b]
 gi|254189757|ref|ZP_04896266.1| xenobiotic reductase A [Burkholderia pseudomallei Pasteur 52237]
 gi|254192993|ref|ZP_04899428.1| xenobiotic reductase A [Burkholderia pseudomallei S13]
 gi|254262453|ref|ZP_04953318.1| xenobiotic reductase A [Burkholderia pseudomallei 1710a]
 gi|254300030|ref|ZP_04967476.1| xenobiotic reductase A [Burkholderia pseudomallei 406e]
 gi|52212163|emb|CAH38180.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia pseudomallei K96243]
 gi|76582266|gb|ABA51740.1| NADH:flavin oxidoreductase [Burkholderia pseudomallei 1710b]
 gi|126225053|gb|ABN88558.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia pseudomallei
           668]
 gi|126231345|gb|ABN94758.1| xenobiotic reductase A [Burkholderia pseudomallei 1106a]
 gi|157810145|gb|EDO87315.1| xenobiotic reductase A [Burkholderia pseudomallei 406e]
 gi|157937434|gb|EDO93104.1| xenobiotic reductase A [Burkholderia pseudomallei Pasteur 52237]
 gi|169649747|gb|EDS82440.1| xenobiotic reductase A [Burkholderia pseudomallei S13]
 gi|225932823|gb|EEH28819.1| xenobiotic reductase A [Burkholderia pseudomallei Pakistan 9]
 gi|235002020|gb|EEP51444.1| oxidoreductase, FAD/FMN-binding [Burkholderia pseudomallei MSHR346]
 gi|242135430|gb|EES21833.1| xenobiotic reductase A [Burkholderia pseudomallei 1106b]
 gi|254213455|gb|EET02840.1| xenobiotic reductase A [Burkholderia pseudomallei 1710a]
          Length = 365

 Score = 39.0 bits (90), Expect = 1.00,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 63/180 (35%), Gaps = 25/180 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AAK   D G+  + L+       + +            ++G         + + +AA+
Sbjct: 161 VAAAKRALDAGFEWLELHFA--HGYLAQSFFSVHSNRRADAYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +     +P+T +  +   D      L     L K  K  G++ + +      +   +P 
Sbjct: 219 REVWPERLPLTARFGVIEYDGRDEQTLAESIELAKRFKLEGLDLLSV-----TIGFSTPA 273

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                       V E  +    L +    G++  + A +++    +D VM+GRA   +  
Sbjct: 274 ARIPWGPAFLAPVAERVRREAQLPVASAWGIDAPALAERVVSEGQLDLVMVGRAHLADPH 333


>gi|324115304|gb|EGC09268.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia fergusonii
           B253]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 30/228 (13%), Positives = 65/228 (28%), Gaps = 47/228 (20%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + L+      +        L  Q     I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSALQAPINRFVPHE-----LTHQEIVQLIDSFARCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVTVK 122
                         L+                    N      + + A+ + +     + 
Sbjct: 162 --------MGSEGYLINEFLTLRTNQRNDQWGGDYRNRMRFAVEVVRAVRERVGNDFIII 213

Query: 123 CRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
            R+     V++         L ++I+ +G     I+      +   P     +P   +  
Sbjct: 214 YRLSMLDLVENGSTFAETIELAQAIEAAGAT--IINTGIGWHEARIPTIATAVPRGAFSW 271

Query: 179 V-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
           V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 272 VTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|296118586|ref|ZP_06837164.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Corynebacterium ammoniagenes DSM 20306]
 gi|295968485|gb|EFG81732.1| NADH:flavin oxidoreductase / NADH oxidase family protein
           [Corynebacterium ammoniagenes DSM 20306]
          Length = 384

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 9/83 (10%)

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           + +SGV+ I     KA       +D R +  L        K+  P+L +  NG ++    
Sbjct: 270 LAQSGVDYIHTTEWKAEAPAFPDEDERSLAALA-------KQAAPNLTVIANGHIDTGES 322

Query: 203 ALKIL--PSVDGVMIGRAAYKNS 223
           A  +L     D V IG+AA  N 
Sbjct: 323 ATSLLRRGDADLVAIGKAALANP 345


>gi|289616384|emb|CBI56911.1| unnamed protein product [Sordaria macrospora]
          Length = 430

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 22/150 (14%), Positives = 48/150 (32%), Gaps = 17/150 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI-----GVDDQIPAVALRNLVKSIKKSG 147
           +G        IVG+ I    + +   +             ++      +   ++  ++ G
Sbjct: 225 YGGSAEKRARIVGEIIEECRRQVKEALGEDSEEARKTGNAEETDTTEEVLRQIELFEQWG 284

Query: 148 VNGIWIHAR----KAILKGLSPKDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGL 197
           V+ + +         +  G  P+  +K            +    I+ + P L + + GG 
Sbjct: 285 VDFVEVSGGSYEDPQMANGPKPEIKQKSERTKAREAFFLEFAKIIRTKFPQLPLMVTGGF 344

Query: 198 EDMSQALKIL--PSVDGVMIGRAAYKNSAM 225
                    L     D + IGR A  N ++
Sbjct: 345 RTRQGMEAALASDDCDMIGIGRPAIINPSL 374


>gi|254461191|ref|ZP_05074607.1| 2,4-dienoyl-CoA reductase [Rhodobacterales bacterium HTCC2083]
 gi|206677780|gb|EDZ42267.1| 2,4-dienoyl-CoA reductase [Rhodobacteraceae bacterium HTCC2083]
          Length = 675

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 17/125 (13%), Positives = 45/125 (36%), Gaps = 11/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D +P  +  +    L K+++ +G     I+      +
Sbjct: 197 EIVRRVREAVGTDFIIIYRLSMIDLVPNGSTFDEVILLAKAVEDAGAT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
              P     +P   +  +  ++  E     I  N  +     A ++L S    M+   + 
Sbjct: 255 ARIPTIATSVPRAAFTWITKKLMGEVSIPVITSNR-INTPEVAEEVLSSGAANMV---SM 310

Query: 221 KNSAM 225
               +
Sbjct: 311 ARPFL 315


>gi|187927748|ref|YP_001898235.1| NADH:flavin oxidoreductase/NADH oxidase [Ralstonia pickettii 12J]
 gi|187724638|gb|ACD25803.1| NADH:flavin oxidoreductase/NADH oxidase [Ralstonia pickettii 12J]
          Length = 370

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 32/180 (17%), Positives = 59/180 (32%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
            + V+ A+     G + I L+            P A     ++G      M  P  + D 
Sbjct: 157 DQFVDTARRAVRLGLSAIELHAAHGYLLHEFLSPIANQRTDAYGGSRENRMRYPLEIFDA 216

Query: 108 IAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + A+    + + V V     V+            ++++  G + I      A   G+SP 
Sbjct: 217 VRAVVPDNIPVGVRVSATDWVEGGWAPEDSVVFAQALRARGCDWI-----DASSGGVSPL 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
               +         E  +   D+     G + +  +A  I+     D V +GRA   N  
Sbjct: 272 QQIPLSTGYQVPFAEKIRNEADIPTIAVGLINEAHEAEAIVAQGRADLVAVGRAFLYNPH 331


>gi|114766229|ref|ZP_01445220.1| NADH:flavin oxidoreductase Old Yellow Enzyme family-like protein
           [Pelagibaca bermudensis HTCC2601]
 gi|114541514|gb|EAU44558.1| NADH:flavin oxidoreductase Old Yellow Enzyme family-like protein
           [Roseovarius sp. HTCC2601]
          Length = 365

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 31/161 (19%), Positives = 58/161 (36%), Gaps = 19/161 (11%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIG-----VDDQIPAVALRNLVKSIKKSG 147
           G  L    + +   + AM +      + V+         + D+ P      ++K  ++ G
Sbjct: 200 GGSLDDRLNFMRAVLTAMMEVYPKECIGVRMSPYGTFNDIQDEDPNAKYEAMLKLCEEMG 259

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V   ++H  + ++ G       +    D +++   ++      I   G       A K L
Sbjct: 260 VG--YVHVIRPVVSGN---IQMEASGRDVEVIDTARRLYSGPLIAAAG--YTPESAEKEL 312

Query: 208 PS--VDGVMIGRAAYKNSAMLTTVDE----YFSNPLTGSSP 242
            +  VD V  GRA   N  ++  V E       NP T  +P
Sbjct: 313 EAGRVDLVAFGRAFVSNPDLVRRVAEGIPFAEGNPDTYYTP 353


>gi|16766518|ref|NP_462133.1| 2,4-dieonyl-CoA reductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167990224|ref|ZP_02571324.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|197264373|ref|ZP_03164447.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|16421776|gb|AAL22092.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|197242628|gb|EDY25248.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|205331271|gb|EDZ18035.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261248386|emb|CBG26223.1| 2,4-dienoyl-CoA reductase [NADPH] (ec 1.3.1.34) (2,4-dienoyl
           coenzyme A reductase) [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995415|gb|ACY90300.1| 2,4-dieonyl-CoA reductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159771|emb|CBW19290.1| 2,4-dienoyl-CoA reductase [NADPH] (ec 1.3.1.34) (2,4-dienoyl
           coenzyme A reductase) [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312914246|dbj|BAJ38220.1| 2,4-dieonyl-CoA reductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321225902|gb|EFX50956.1| 2,4-dienoyl-CoA reductase NADPH [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|323131579|gb|ADX19009.1| 2,4-dieonyl-CoA reductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332990084|gb|AEF09067.1| 2,4-dieonyl-CoA reductase [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|52841951|ref|YP_095750.1| inosine-5'-monophosphate dehydrogenase [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|54297637|ref|YP_124006.1| hypothetical protein lpp1688 [Legionella pneumophila str. Paris]
 gi|52629062|gb|AAU27803.1| inosine-5'-monophosphate dehydrogenase [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|53751422|emb|CAH12840.1| hypothetical protein lpp1688 [Legionella pneumophila str. Paris]
          Length = 490

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 11/86 (12%), Positives = 30/86 (34%), Gaps = 4/86 (4%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-PDLFI 191
            +A     + + ++G + + +      +          IP +    +  + +E    + +
Sbjct: 277 NIATAAAARDLYEAGADAVKVGIGPGSICTTRIVTGVGIPQI--SAIANVAQELKGIIPV 334

Query: 192 GLNGGL-EDMSQALKILPSVDGVMIG 216
             +GG+         +    D VM+G
Sbjct: 335 IADGGIRFSGDVCKALAAGADTVMLG 360


>gi|30262063|ref|NP_844440.1| NADPH dehydrogenase NamA [Bacillus anthracis str. Ames]
 gi|47527328|ref|YP_018677.1| NADPH dehydrogenase NamA [Bacillus anthracis str. 'Ames Ancestor']
 gi|49184903|ref|YP_028155.1| NADPH dehydrogenase NamA [Bacillus anthracis str. Sterne]
 gi|165870200|ref|ZP_02214856.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0488]
 gi|167638270|ref|ZP_02396547.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0193]
 gi|170706036|ref|ZP_02896498.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0389]
 gi|177650762|ref|ZP_02933659.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0174]
 gi|190567838|ref|ZP_03020749.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis Tsiankovskii-I]
 gi|227815141|ref|YP_002815150.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. CDC 684]
 gi|229602785|ref|YP_002866426.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0248]
 gi|254737073|ref|ZP_05194777.1| NADPH dehydrogenase NamA [Bacillus anthracis str. Western North
           America USA6153]
 gi|254751389|ref|ZP_05203426.1| NADPH dehydrogenase NamA [Bacillus anthracis str. Vollum]
 gi|254758261|ref|ZP_05210288.1| NADPH dehydrogenase NamA [Bacillus anthracis str. Australia 94]
 gi|68052712|sp|Q81RK6|NAMA_BACAN RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|254766765|sp|C3P7Z9|NAMA_BACAA RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|254766766|sp|C3L5F3|NAMA_BACAC RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|30256689|gb|AAP25926.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Bacillus
           anthracis str. Ames]
 gi|47502476|gb|AAT31152.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|49178830|gb|AAT54206.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. Sterne]
 gi|164714088|gb|EDR19609.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0488]
 gi|167513571|gb|EDR88940.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0193]
 gi|170129038|gb|EDS97903.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0389]
 gi|172083223|gb|EDT68284.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0174]
 gi|190560893|gb|EDV14867.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis Tsiankovskii-I]
 gi|227002573|gb|ACP12316.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Bacillus
           anthracis str. CDC 684]
 gi|229267193|gb|ACQ48830.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0248]
          Length = 345

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|253997984|ref|YP_003050047.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Methylovorus sp.
           SIP3-4]
 gi|253984663|gb|ACT49520.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylovorus sp. SIP3-4]
          Length = 246

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 172 PNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
             L+   +  I      ++ I L GG+ D+    + L   +D V+IG AA KN   L   
Sbjct: 59  KPLNEGAIKAIVDAVGGEIPIQLGGGIRDLETIERYLDDGIDYVIIGTAAVKNPGFLHEA 118

Query: 230 DEYFSNPL 237
              F   +
Sbjct: 119 CYAFPGQI 126


>gi|229132900|ref|ZP_04261744.1| NADPH dehydrogenase [Bacillus cereus BDRD-ST196]
 gi|228650570|gb|EEL06561.1| NADPH dehydrogenase [Bacillus cereus BDRD-ST196]
          Length = 319

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--P 208
           I   +   +   +      ++    +       KEN ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKENANIATGAVGLITTGLQAEQILNNS 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|229196289|ref|ZP_04323037.1| NADPH dehydrogenase [Bacillus cereus m1293]
 gi|228587143|gb|EEK45213.1| NADPH dehydrogenase [Bacillus cereus m1293]
          Length = 319

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 26/136 (19%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA KIL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEKILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|330506837|ref|YP_004383265.1| imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta
           concilii GP-6]
 gi|328927645|gb|AEB67447.1| imidazoleglycerol phosphate synthase, cyclase subunit [Methanosaeta
           concilii GP-6]
          Length = 272

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 32/100 (32%), Gaps = 11/100 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              +  +  G + +      A  +G     +          V     +  D+   + GG+
Sbjct: 39  QFARRYQDQGADELVFLDITASHEGRKTMVD----------VARRVADAVDIPFAVGGGI 88

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
             +    +IL    D V I  AA KN   +    E F + 
Sbjct: 89  GTLDGIKQILDAGADKVGINTAAVKNPDFVKEASEAFGSD 128


>gi|317970449|ref|ZP_07971839.1| inosine 5-monophosphate dehydrogenase [Synechococcus sp. CB0205]
          Length = 387

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA     K+I ++G +  ++ A     + + P+    +       +  + ++     I  
Sbjct: 140 VAALKFGKAIAEAGADLFFVQATVVSTEHIGPEGQESLD------LEALCRDFGVPVIIG 193

Query: 194 NGGLEDMSQALK-ILPSVDGVMIG 216
           N        ALK +     GVM+G
Sbjct: 194 N--CVTYDVALKLMRAGAAGVMVG 215


>gi|160932817|ref|ZP_02080206.1| hypothetical protein CLOLEP_01658 [Clostridium leptum DSM 753]
 gi|156867891|gb|EDO61263.1| hypothetical protein CLOLEP_01658 [Clostridium leptum DSM 753]
          Length = 256

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 30/214 (14%), Positives = 62/214 (28%), Gaps = 52/214 (24%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLN-------VGCPS---ARVHEGSFGACLMLNPDIV 104
           G  D+     A +   + G + I L           P    A +   + G       D +
Sbjct: 21  GDPDLETTAAAIRAAVENGADLIELGIPFSDPTAEGPVIQEANIRALNGGV----TTDKI 76

Query: 105 GDCIAAMCKALSIPV----------------------TVKCRIGVDDQIPAVALRNLVKS 142
              +  +   + +P+                       ++    +   +P       +  
Sbjct: 77  FAFVKKLRYDVKVPMVFMTYSNVVFSYGAEKFISTCKNIEIDGLILPDLPFEEKEEFLPL 136

Query: 143 IKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
             K GV+ + + A  +                I+  L     R     D   + ++ +EN
Sbjct: 137 CHKYGVDLVSLIAPTSENRIAMIAKEAEGFLYIVSSLGVTGTRSEIKTDLTSIVKVVREN 196

Query: 187 PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
             +   +  G+    QA K+    DG ++G A  
Sbjct: 197 TGIPCAIGFGISTPEQAKKMADIADGAIVGSAII 230


>gi|146284188|ref|YP_001174341.1| isopentenyl pyrophosphate isomerase [Pseudomonas stutzeri A1501]
 gi|166226202|sp|A4VR98|IDI2_PSEU5 RecName: Full=Isopentenyl-diphosphate delta-isomerase; Short=IPP
           isomerase; AltName: Full=Isopentenyl pyrophosphate
           isomerase
 gi|145572393|gb|ABP81499.1| isopentenyl-diphosphate delta-isomerase [Pseudomonas stutzeri
           A1501]
          Length = 346

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 27/172 (15%), Positives = 58/172 (33%), Gaps = 29/172 (16%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G  + +   A +++E      ++LN   P     +         +   V   I A+   L
Sbjct: 136 GYGVDEARRAVEMIEG-DALIVHLN---PLQEAVQTGGD----RDWRGVLQAIEALAARL 187

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------KAILKGLSPKD 167
            +PV +K       ++ A     + + +  +GV  I +           +A     + + 
Sbjct: 188 PVPVVIK-------EVGAGISAAVARRLVDAGVAAIDVAGAGGTSWAAVEAARAADASQQ 240

Query: 168 NRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
                  D+       +  ++   P+  +  +GG+ D +  A  I    D V
Sbjct: 241 AIAEAFADWGIPTAQALLAVRDACPNTPLIASGGIRDGVEAAKAICLGADLV 292


>gi|317484039|ref|ZP_07942972.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
 gi|316924683|gb|EFV45836.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
          Length = 645

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 26/188 (13%), Positives = 58/188 (30%), Gaps = 28/188 (14%)

Query: 64  EAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           +AA    + G++ + +             P        +G  L        +    + ++
Sbjct: 151 KAAIRAREAGFDAVEIHGAHGYLISQFLSPYTNRRTDGYGGSLENRMRFALEVCRKVRES 210

Query: 115 LSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +     V  R+   + +P          L K +   G++ +       +  GL   +   
Sbjct: 211 VGPDFPVTYRMSAVEGLPGGTTLEDSVALAKRLVADGIDALH------VSVGLRETNFMV 264

Query: 171 IPNLDYD--IVYEIKKENPD-----LFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYK 221
            P    +      + +   D     + + + G + D   A  I+   D  M+  GRA   
Sbjct: 265 SPPACVEKGWNAPLSRAVRDGIEAAVPVIVAGRVADEQTAQGIIDRGDADMVAMGRALIA 324

Query: 222 NSAMLTTV 229
           +  +   V
Sbjct: 325 DPFLPAKV 332


>gi|225847924|ref|YP_002728087.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225644666|gb|ACN99716.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 239

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 11/99 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++ K  +  G   I +      L+G            +Y +V  I K + D+ +   GGL
Sbjct: 38  DMAKYFQDCGAVHIHVVDLDGALEG---------KPKNYKVVESIVK-SVDILVEFGGGL 87

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                   +    VD V+IG  AY+N      + E F N
Sbjct: 88  RSYEAVKSMFEIGVDRVVIGSLAYENQEEFLRIVEDFKN 126


>gi|168463566|ref|ZP_02697483.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|195633582|gb|EDX51996.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|91779806|ref|YP_555014.1| salicylyl-CoA 5-hydroxylase [Burkholderia xenovorans LB400]
 gi|91692466|gb|ABE35664.1| putative 2-amninobenzoyl-CoA monooxygenase/reductase [Burkholderia
           xenovorans LB400]
          Length = 790

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 73/218 (33%), Gaps = 34/218 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVGD 106
           + V A ++  + G++ + L   C                    +G  L   +  P  V  
Sbjct: 560 QFVRATQMSAEAGFDWLEL--HCAHGYFLSSFLSPLTNHRTDEYGGSLDNRLRYPLQVFK 617

Query: 107 CIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            I A+      P++V+      V+          + ++ K +G + I + +   + K   
Sbjct: 618 AIRAVW-PQDKPISVRISANDWVEGGTTPDDAVQIARAFKAAGADMIDVSSG-QVSKDEK 675

Query: 165 PKDNR--KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           P   R  + P  D      ++ E   +     G + +      I+ +   D   I R   
Sbjct: 676 PVYGRMFQTPFAD-----RVRNEAG-IATIAVGAISEADHVNSIIAAGRADLCAIARPHL 729

Query: 221 KNS-AMLTTVDEYFSNPLTGSSP---IKTRVDKDFWRK 254
            N    L    +     +T   P    K++++++  R+
Sbjct: 730 ANPAWTLNEAAKIGYFDVTWPKPYTAAKSQLERNLERE 767


>gi|329938170|ref|ZP_08287621.1| inosine 5-monophosphate dehydrogenase [Streptomyces
           griseoaurantiacus M045]
 gi|329302659|gb|EGG46549.1| inosine 5-monophosphate dehydrogenase [Streptomyces
           griseoaurantiacus M045]
          Length = 500

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 31/191 (16%), Positives = 64/191 (33%), Gaps = 27/191 (14%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           I     ++ +K        + + L     G        A  ++E  G + I         
Sbjct: 203 ITVKDFVKAEKYPRAAKDGKGRLLVGAAVGVAGDAFERAQALIEA-GVDFI--------- 252

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
            V + + G     +  +VGD +A +     + V              +A R   +++  S
Sbjct: 253 -VVDTAHG-----HSRLVGDMVAKIKSNSHVDVIGG----------NIATREAAQALIDS 296

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALK 205
           GV+GI +      +          +P +       +  +   + +  +GGL+     A  
Sbjct: 297 GVDGIKVGVGPGSICTTRVVAGIGVPQVTAIYEAALAAKEAGVPVIGDGGLQYSGDIAKA 356

Query: 206 ILPSVDGVMIG 216
           ++   D VM+G
Sbjct: 357 LVAGADTVMLG 367


>gi|255065605|ref|ZP_05317460.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Neisseria sicca ATCC 29256]
 gi|255050430|gb|EET45894.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Neisseria sicca ATCC 29256]
          Length = 245

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 5/101 (4%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
               DI+  + K   D+ + L GG+ D+    K L   ++ V+IG AA KN   +    +
Sbjct: 64  PAIKDILAAVAK---DIPVQLGGGIRDLEAIEKYLDLGLNDVIIGTAAVKNPDFVREACK 120

Query: 232 YFSNPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F   +  G       V  D W  ++       A+     G
Sbjct: 121 TFPGQIIVGLDAKDGMVAIDGWATVTEHHVIDLAKRFEDDG 161


>gi|254821726|ref|ZP_05226727.1| isopentenyl pyrophosphate isomerase [Mycobacterium intracellulare
           ATCC 13950]
          Length = 348

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 25/124 (20%), Positives = 45/124 (36%), Gaps = 14/124 (11%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAILKG 162
           +     AL  PV +K    V   I   A+  L+ +     V GI +          + + 
Sbjct: 183 LREAADALGYPVLLK---EVGHGIGGAAVAELLGADGTLPVAGIDVAGAGGTSWSRVEQF 239

Query: 163 LSPKDNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGVMIG 216
           +   + R     D+       V E+++  P++ +  +GG+   M  A  I    D V + 
Sbjct: 240 VRYGELRHPELADWGIPTARAVVEVREALPEIPLVASGGIRTGMDAAKAIALGADVVAVA 299

Query: 217 RAAY 220
           R   
Sbjct: 300 RPLL 303


>gi|168231824|ref|ZP_02656882.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|194472956|ref|ZP_03078940.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|194459320|gb|EDX48159.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|205333864|gb|EDZ20628.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|148546524|ref|YP_001266626.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
 gi|63259215|gb|AAY40303.1| xenobiotic reductase [Pseudomonas putida]
 gi|148510582|gb|ABQ77442.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida F1]
          Length = 363

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFENRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  +          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTHIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|224585022|ref|YP_002638821.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|224469550|gb|ACN47380.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|188592346|ref|YP_001796944.1| NADH:flavin oxidoreductase/NADH oxidase [Cupriavidus taiwanensis
           LMG 19424]
 gi|170938720|emb|CAP63707.1| putative NADH:flavin oxidoreductase/NADH oxidase [Cupriavidus
           taiwanensis LMG 19424]
          Length = 413

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 20/162 (12%), Positives = 55/162 (33%), Gaps = 35/162 (21%)

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAIL 160
              +  +  A+   + V C++ V D +P            + ++  G + + +   + + 
Sbjct: 209 AAVLRQVKDAVGADLAVCCKLSVSDGVPGGNQPADSALTARLLETEGADLLTLSGGRNVE 268

Query: 161 K-------------------------GLSPKDNRKIPNLDYDIVY-----EIKKENPDLF 190
                                     G++  + R   +L +  +Y      + ++   + 
Sbjct: 269 SPWALFGSPMPTAQMKAAAPTALARLGITMLEKRTPRDLAFRELYFLEASRVVRQAVRMP 328

Query: 191 IGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           +   GG++ +   AL +    D V + RA   + A++    +
Sbjct: 329 LAYIGGVKSLDNVALLMGEGFDAVALARALIHDPALVAGWRD 370


>gi|198244260|ref|YP_002217200.1| FAD/FMN-binding/pyridine nucleotide-disulfide oxidoreductase family
           protein [Salmonella enterica subsp. enterica serovar
           Dublin str. CT_02021853]
 gi|205354133|ref|YP_002227934.1| 2,4-dienoyl-CoA reductase [NADPH] [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|207858476|ref|YP_002245127.1| 2,4-dienoyl-CoA reductase [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|197938776|gb|ACH76109.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|205273914|emb|CAR38916.1| 2,4-dienoyl-CoA reductase [NADPH] (ec 1.3.1.34) (2,4-dienoyl
           coenzyme A reductase) [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|206710279|emb|CAR34637.1| 2,4-dienoyl-CoA reductase [NADPH] (ec 1.3.1.34) (2,4-dienoyl
           coenzyme A reductase) [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|326624976|gb|EGE31321.1| 2,4-dienoyl-CoA reductase [NADPH] [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|326629253|gb|EGE35596.1| 2,4-dienoyl-CoA reductase [NADPH] [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|308275703|gb|ADO25602.1| NADH:flavin oxidoreductase/NADH oxidase [Corynebacterium
           pseudotuberculosis I19]
          Length = 357

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 33/198 (16%), Positives = 68/198 (34%), Gaps = 28/198 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V A++   D G + + L+            PS+ V    FG      P+     +  +
Sbjct: 154 EFVAASRRAVDAGLDGVELHGANGYLLHEFLSPSSNVRTDEFGG----TPENRARFVIQV 209

Query: 112 CKALSIPVT---VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            +A++  +    V  RI  +  I  V   +  +++    V    I + +     +   D 
Sbjct: 210 VQAVAEEIGAHRVGLRISPEHNIQGVLETDREETLATYRVLLNEIRSLELAYLSILHADY 269

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-----SVDGVMIGRAAYKNS 223
           R       D V+++ +     F+ LN G    ++  + +        D V +GR    N 
Sbjct: 270 RS------DFVHQLAEAFGG-FVILNSGFSTYTEYAEAVGIVESGYADAVAVGRELIANP 322

Query: 224 AMLTTVDEYFSNPLTGSS 241
            ++    E     +    
Sbjct: 323 DLVRRWQEGIELNVPDPD 340


>gi|323530113|ref|YP_004232265.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1001]
 gi|323387115|gb|ADX59205.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1001]
          Length = 687

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + + ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGVEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ +SG+    G+            +
Sbjct: 211 REAVGPDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSESGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKIPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|238893052|ref|YP_002917786.1| NADH:flavin oxidoreductase [Klebsiella pneumoniae NTUH-K2044]
 gi|238545368|dbj|BAH61719.1| NADH:flavin oxidoreductase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
          Length = 677

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 62/185 (33%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   +  
Sbjct: 150 EKFGDAAERVRRAGFDCVEIHAGHSYLISQFLSPLFNKRTDEFGGSVENRTRILSLIVDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIK--KSGVNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++  +  V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQEKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRTPQVAEDILASGDADLIAIGRGLIAEPDW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|222874561|gb|EEF11692.1| predicted protein [Populus trichocarpa]
          Length = 293

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 25/142 (17%), Positives = 48/142 (33%), Gaps = 14/142 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-----------QIPAVALRNLVK 141
            GA +   P+ +        +   +PV VK    + D              AV+L N + 
Sbjct: 1   MGAAVGQVPEYIQMVTQWCKQYSRLPVIVKLTPNITDVRFPARAAKAGGADAVSLINTIN 60

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLED 199
           S+    ++ + +H                +  +  ++V EI ++     L I   GG+  
Sbjct: 61  SLMGVNLDTLVMHPSTDGQGSHGGYCGPAVKPIAQNMVAEIARDPQTAGLPISGIGGITT 120

Query: 200 MSQALKILP-SVDGVMIGRAAY 220
              A + +      V +  AA 
Sbjct: 121 WKDAAEYIALGCGNVQVCTAAM 142


>gi|168819713|ref|ZP_02831713.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205343498|gb|EDZ30262.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|320087673|emb|CBY97437.1| putative NADPH dehydrogenase [Salmonella enterica subsp. enterica
           serovar Weltevreden str. 2007-60-3289-1]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYANRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|168262776|ref|ZP_02684749.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|205348597|gb|EDZ35228.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|161616214|ref|YP_001590179.1| hypothetical protein SPAB_04018 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|238910021|ref|ZP_04653858.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|161365578|gb|ABX69346.1| hypothetical protein SPAB_04018 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|326781361|ref|ZP_08240626.1| NADPH dehydrogenase [Streptomyces cf. griseus XylebKG-1]
 gi|326661694|gb|EGE46540.1| NADPH dehydrogenase [Streptomyces cf. griseus XylebKG-1]
          Length = 371

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 56/172 (32%), Gaps = 21/172 (12%)

Query: 67  KIVEDFGYNEINLN-VGCPSARVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPVTVK 122
           ++VE  G +   +N    P+A     ++G      +  P  V D + A+     +PV  +
Sbjct: 175 RVVEIHGAHGYLINSFLSPAANRRTDAYGGSWENRLRFPLQVVDAVRAVW-PDDLPVLFR 233

Query: 123 CR---------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
                          +         L + +   GV+ + +     +              
Sbjct: 234 TSATDWLTENPEDPREGWTGDDTVRLAQELAAHGVDLLDVSTGGLVRDAAISAHPGYQVP 293

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                  E  +    +     G + D +QA +I+ +   D VMIGR   ++ 
Sbjct: 294 F-----AEQARRTAGIPTAAVGLILDAAQAEEIVATGRADAVMIGREMLRDP 340


>gi|204928156|ref|ZP_03219356.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|204322478|gb|EDZ07675.1| oxidoreductase, FAD/FMN-binding family [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|197247696|ref|YP_002148149.1| FAD/FMN-binding/pyridine nucleotide-disulfide oxidoreductase family
           protein [Salmonella enterica subsp. enterica serovar
           Agona str. SL483]
 gi|197211399|gb|ACH48796.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
          Length = 672

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|330829575|ref|YP_004392527.1| Imidazole glycerol phosphate synthase subunit hisF [Aeromonas
           veronii B565]
 gi|328804711|gb|AEB49910.1| Imidazole glycerol phosphate synthase subunit hisF [Aeromonas
           veronii B565]
          Length = 257

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 17/100 (17%), Positives = 37/100 (37%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           +  L +   + G + +            +  D R +       V E+     D+   + G
Sbjct: 32  IVELARRYAEEGADELV------FYDITASSDARVVDKSWVSRVAEVI----DIPFCVAG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G++ +  A +IL    D + I   A  +  +++ + E F 
Sbjct: 82  GIKSVEDARQILEFGADKISINSPALADPTLISRLAERFG 121


>gi|292488682|ref|YP_003531569.1| xenobiotic reductase A [Erwinia amylovora CFBP1430]
 gi|292899839|ref|YP_003539208.1| NADH:flavin oxidoreductase [Erwinia amylovora ATCC 49946]
 gi|291199687|emb|CBJ46807.1| putative NADH:flavin oxidoreductase [Erwinia amylovora ATCC 49946]
 gi|291554116|emb|CBA21275.1| xenobiotic reductase A [Erwinia amylovora CFBP1430]
 gi|312172827|emb|CBX81083.1| xenobiotic reductase A [Erwinia amylovora ATCC BAA-2158]
          Length = 366

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/139 (15%), Positives = 51/139 (36%), Gaps = 12/139 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSG 147
           +G         + + +AA+ +    ++P+T +         D+        L + +  +G
Sbjct: 200 YGGSFAGRSRFLLETLAAVREVWPENLPLTARLGVIEYDGRDEETLTESIELTQLLHNNG 259

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           ++ + I     + +   P     +       V +  +    L +  + GLE    A + +
Sbjct: 260 LDMLNISIGFTVAETEIPWGAGFLAP-----VAQRVRHATGLPVAASWGLEAPDVAERAI 314

Query: 208 --PSVDGVMIGRAAYKNSA 224
               +D VM+GRA   +  
Sbjct: 315 AEQQMDLVMMGRALLTDPH 333


>gi|251772154|gb|EES52724.1| NADH:flavin oxidoreductase/NADH oxidase [Leptospirillum
           ferrodiazotrophum]
          Length = 353

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 67/205 (32%), Gaps = 34/205 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
              V AA+     G++ + +++           P +     S+G  L   M  P  V D 
Sbjct: 155 ESFVGAARRALSAGFDYLEIHMAHGYLLHSFLSPLSNRRTDSYGGSLDARMRFPLEVLDA 214

Query: 108 IAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN-------GIWIHARKAI 159
           +  +  +   + V +     VD      +   L + +K+ GV+       GI  HA   +
Sbjct: 215 VRKVWPEERPLGVRISAVDWVDGGWDLESSLVLARKLKERGVDLVDCSSGGIVPHAAIPV 274

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             G     +             ++KE   +     G + D +QA  IL     DGV + R
Sbjct: 275 APGYQTAFSE-----------RLRKEVG-VATLAVGMITDPAQAEHILVTGQADGVALAR 322

Query: 218 AAYKNSAMLTTVDEYFSNPLTGSSP 242
              ++                  +P
Sbjct: 323 EMLRDPYWPLHAANRLGVEFPWPAP 347


>gi|123454890|ref|XP_001315194.1| dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
 gi|121897863|gb|EAY02971.1| dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
          Length = 365

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 39/183 (21%), Positives = 63/183 (34%), Gaps = 32/183 (17%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   + G    ++ + A  V  F  + + L+                +  +P  + D I
Sbjct: 99  PMICSM-GYTADEIAQMAPKVAPF-CDGLELSTH-------------YIGDDPKPMQDAI 143

Query: 109 AAMCKALS-IPVTVKCRIGVDDQIPAVALRNLVKS----IKKSGVN-GIWIHARKAILKG 162
            A  K     PV VK     D    A A +    +    +   G    + I  + A   G
Sbjct: 144 KAAIKGSGGKPVFVKLSPFRDAPKAAKAAKEAGATGLVCVNSFGPTLALDIERKGAPFMG 203

Query: 163 LSPKDNR----KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
            S K        I  L   +VY++ KE  DL +   GG+ +   A++ L      M G  
Sbjct: 204 SSSKYGWVSGPAIKPLALRVVYDVCKEV-DLPVVGVGGISNGRDAIEFL------MAGAQ 256

Query: 219 AYK 221
           A  
Sbjct: 257 ALG 259


>gi|19746385|ref|NP_607521.1| dihydroorotate dehydrogenase 1A [Streptococcus pyogenes MGAS8232]
 gi|81847927|sp|Q8P0C0|PYRD_STRP8 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|19748584|gb|AAL98020.1| putative dihydroorotate dehydrogenase [Streptococcus pyogenes
           MGAS8232]
          Length = 311

 Score = 39.0 bits (90), Expect = 1.1,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 72/232 (31%), Gaps = 32/232 (13%)

Query: 27  IVADAILRGDKKNILGF------STQEKPLALQIGGADI---SKLVEAAKIVEDFGYNEI 77
           I +  +     +  L F      + Q KP  L + G        +++A  +  D+    +
Sbjct: 68  INSMGLPNNGFRYYLDFVSDLAKTGQHKPHFLSVVGLSPTETETILKAI-MASDYE-GLV 125

Query: 78  NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVA 135
            LN+ CP   V      A    + +     +  +    + P+ +K     D      A A
Sbjct: 126 ELNLSCP--NVPGKPQIAY---DFETTDQLLENIFTYYTKPLGIKLPPYFDIVHFDQAAA 180

Query: 136 LRN-----LVKSIKKSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           + N      V  +   G   +          K    G+     +     +    Y  K+ 
Sbjct: 181 IFNKYPLSFVNCVNSIGNGLVIEDEQVLIKPKNGFGGIGGDYIKPTALANVHAFY--KRL 238

Query: 186 NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAA-YKNSAMLTTVDEYFSN 235
            P + I   GG++    A +  L     V IG     +  A+   V +    
Sbjct: 239 KPSIHIIGTGGVKTGRDAFEHILCGASMVQIGTVLHQEGPAIFERVTKELKT 290


>gi|167553274|ref|ZP_02347024.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205322251|gb|EDZ10090.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
          Length = 672

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/221 (12%), Positives = 67/221 (30%), Gaps = 33/221 (14%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEIN---- 78
           Y   +VA + ++      +          LQ+    I      A++  + GY+ +     
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEVMGS 164

Query: 79  ----LNVGCPSARVHEG------SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
               +N       +          +G           + + A+ + +     +  R+ + 
Sbjct: 165 EGYLIN-----EFITRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRLSML 219

Query: 129 DQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           D +           L ++I+ +G + I  +      +   P     +P   +  V    K
Sbjct: 220 DLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTRKLK 277

Query: 185 ENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
            +  + +     + D   A  IL   D  M+   +     +
Sbjct: 278 GHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|66045430|ref|YP_235271.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           syringae B728a]
 gi|63256137|gb|AAY37233.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           syringae B728a]
          Length = 363

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLAESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|300704884|ref|YP_003746487.1| nadph dehydrogenasE [Ralstonia solanacearum CFBP2957]
 gi|299072548|emb|CBJ43898.1| NADPH dehydrogenase (Xenobiotic reductase) [Ralstonia solanacearum
           CFBP2957]
          Length = 370

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 54/181 (29%), Gaps = 20/181 (11%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
               V  A+     G   I L+            P A     ++G           +   
Sbjct: 156 CDAFVATARRAVRLGLAAIELHAAHGYLLHEFLSPIANQRTDAYGGSRENRMRYPLEVFE 215

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+  A+  P+ V  R+   D +             ++++  G + +      A   G+SP
Sbjct: 216 AVRAAVPDPIPVGVRMSCTDWVEGGWTLEDSVTFAQALRARGCDWV-----DASSGGVSP 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                +         E  + +  +     G +    +A  I+     D V +GRA   N 
Sbjct: 271 LQQIPLSTGYQVPFAEAIRRDAGMPTIAVGLINAPHEAEAIIAEGRADLVAMGRAFLYNP 330

Query: 224 A 224
            
Sbjct: 331 H 331


>gi|260768158|ref|ZP_05877092.1| hypothetical protein VFA_001207 [Vibrio furnissii CIP 102972]
 gi|260616188|gb|EEX41373.1| hypothetical protein VFA_001207 [Vibrio furnissii CIP 102972]
 gi|315179858|gb|ADT86772.1| Predicted enoate reductase [Vibrio furnissii NCTC 11218]
          Length = 648

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/143 (15%), Positives = 51/143 (35%), Gaps = 7/143 (4%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGV 148
           +G  +        + + ++ KA+     ++ R       +          + K I+ S +
Sbjct: 197 YGGSIENRVRFAQEVLDSVRKAVGPGFPIEFRLSGSELFEGGYDLAEGIEIAKLIE-SRI 255

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + + A            +  +P+     + E  K+   + +   GGL D +Q  +I+ 
Sbjct: 256 DLLHVSAGTYQRGFGVTHPSMFLPHGSNVYLAEAIKQQVSVPVATIGGLNDPAQMEEIIA 315

Query: 209 --SVDGVMIGRAAYKNSAMLTTV 229
               D V + RA   +  +   V
Sbjct: 316 SGKADIVEMARALLADPELPKKV 338


>gi|228985158|ref|ZP_04145325.1| NADPH dehydrogenase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|228774645|gb|EEM23044.1| NADPH dehydrogenase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 319

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|197106475|ref|YP_002131852.1| NADH:flavin oxidoreductase [Phenylobacterium zucineum HLK1]
 gi|196479895|gb|ACG79423.1| NADH:flavin oxidoreductase [Phenylobacterium zucineum HLK1]
          Length = 359

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 71/218 (32%), Gaps = 21/218 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA   E  G++ + +             P     +  +G  L     I  + I  
Sbjct: 143 EDFVAAAVRAETAGFDGVEMHGAHGYILAQFLSPEINRRDDRYGGSLENRSRIFFEIIDG 202

Query: 111 MCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDN 168
           + +       +  R+  +   +    +  + ++I + G ++ + +           P + 
Sbjct: 203 IRRRTGPDFQLGLRLSPERFGLKLAEIVEVAQAILRDGRIDYLDM---SLWDVFKEPVEE 259

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLT 227
                       E+  +  D+ +G+ G +   + A ++L    D V+IGRAA     +  
Sbjct: 260 EFKGWSLMSYFTEL--DRGDVRLGVAGKITTAAIAAEMLDKGADYVLIGRAAI----LHH 313

Query: 228 TVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
              E   +P     P+    D      +S    DY   
Sbjct: 314 DFPERARDPAFRQVPVPVSADYLQGEGVSPKFVDYLRD 351


>gi|120556081|ref|YP_960432.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter
           aquaeolei VT8]
 gi|148839498|sp|A1U5H6|HIS4_MARAV RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|120325930|gb|ABM20245.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter
           aquaeolei VT8]
          Length = 245

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 50/136 (36%), Gaps = 11/136 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++      +G   + +        G           ++ +IV  I  + P+L I + GG+
Sbjct: 34  DMATKWVDAGARRLHLVDLNGAFAG---------EPVNGEIVKAIAVKYPNLPIQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKI 255
                    L   V  V+IG  A K    +T +  E+  + + G      RV  D W ++
Sbjct: 85  RSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKEFPGHIIVGLDAKDGRVATDGWAEV 144

Query: 256 SASMTDYAARHLHSGG 271
           S  M    A+   + G
Sbjct: 145 SEVMAVDLAKRFANDG 160


>gi|319411567|emb|CBQ73611.1| related to dihydroorotate dehydrogenase, mitochondrial precursor
           [Sporisorium reilianum]
          Length = 687

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 31/167 (18%), Positives = 56/167 (33%), Gaps = 19/167 (11%)

Query: 66  AKIVEDFG--YNEINLNVGCPS----ARVHEGSFGACLMLNPDIVGD-CIAAMCKALSIP 118
            K VE  G   + I +NV  P+     R+        L+       D  + +  +     
Sbjct: 308 VKGVERLGPYADMIIVNVSSPNTPGLRRLQRRGVLEDLLTQVVKARDGMVESHLRFSDNK 367

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH----ARKAILK---GLSPKDNRKI 171
           V V   + +   +    L ++  +  KSG++G+ I     +R A L+    +        
Sbjct: 368 VAVPLLVKIAPDLSEEELHDVADAALKSGIDGLVISNTTISRPASLRSSEHVRETGGLSG 427

Query: 172 PNLDYDIVYEI----KKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
           P +    +  +    K+    L I   GG+     AL         V
Sbjct: 428 PPVKPLALKALTTVNKRLEGKLPIIGCGGIATAQDALDFAKAGASAV 474


>gi|261492819|ref|ZP_05989366.1| imidazoleglycerol-phosphate synthase [Mannheimia haemolytica
           serotype A2 str. BOVINE]
 gi|261494816|ref|ZP_05991294.1| imidazoleglycerol-phosphate synthase [Mannheimia haemolytica
           serotype A2 str. OVINE]
 gi|261309527|gb|EEY10752.1| imidazoleglycerol-phosphate synthase [Mannheimia haemolytica
           serotype A2 str. OVINE]
 gi|261311501|gb|EEY12657.1| imidazoleglycerol-phosphate synthase [Mannheimia haemolytica
           serotype A2 str. BOVINE]
          Length = 257

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/148 (14%), Positives = 48/148 (32%), Gaps = 24/148 (16%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTT-------------VDEYFSNPLTGSSPIK 244
            ++ A +I     D + I   A  N  ++T              +D +F          +
Sbjct: 85  TIADAEQIFAFGADKISINSPALANPELITELAKRFGVQAVVVGIDSWFEAETGKYWVNQ 144

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGK 272
              D+   R+    + D+       G  
Sbjct: 145 YTGDEKRTRQTEWQLLDWVEEVQKRGAG 172


>gi|54298238|ref|YP_124607.1| hypothetical protein lpp2296 [Legionella pneumophila str. Paris]
 gi|53752023|emb|CAH13449.1| hypothetical protein lpp2296 [Legionella pneumophila str. Paris]
          Length = 674

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 63/191 (32%), Gaps = 36/191 (18%)

Query: 62  LVEAAKIVEDFGYNEINL--------NVGCPSARVHE--------GSFGACLMLNPDIVG 105
               A++ +  GY+ + +        N       V          G   +  +  P    
Sbjct: 151 FARCARLAQLAGYDGVEIMGSEGYLIN----QFIVTHTNHRRDEWGGSFSNRIRFP---I 203

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D          +  L K+I+++G + I  +      +
Sbjct: 204 EIVRSVREAVGEHFIIIYRLSMLDLVAEGSNWQEVVTLAKAIEQAGASLI--NTGIGWHE 261

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MI--GR 217
              P     +P+  +  V +  K    + +  +  +     A ++L   DGV  MI   R
Sbjct: 262 ARIPTIGTMVPSAAFTQVTQHLKPEIKIPVITSNRINTPELANQLLE--DGVADMISMAR 319

Query: 218 AAYKNSAMLTT 228
               +      
Sbjct: 320 PFLADP-CFAE 329


>gi|294783432|ref|ZP_06748756.1| oxidoreductase, 2-nitropropane dioxygenase family [Fusobacterium
           sp. 1_1_41FAA]
 gi|294480310|gb|EFG28087.1| oxidoreductase, 2-nitropropane dioxygenase family [Fusobacterium
           sp. 1_1_41FAA]
          Length = 379

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 41/213 (19%), Positives = 77/213 (36%), Gaps = 40/213 (18%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
            + + N   +  E + +   +    KN       +KPLA  I  A ++   +  +   + 
Sbjct: 56  CKKVVNGRPVGAEALNSKEAMMEIFKNARKICG-DKPLACNILHA-MNDYAKVVEFAIEA 113

Query: 73  GYNEINLNVGCPS--ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           G N I    G P    ++ E         +PD+             +P+    R      
Sbjct: 114 GANIIVTGAGLPLELPKLVEN--------HPDVAI-----------VPIVSSAR------ 148

Query: 131 IPAVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKDNRKIPNLDYD-IVYEIKKEN- 186
               AL+ + K  K +G   + + +   K+     +  ++  +P    + +V E+K+E  
Sbjct: 149 ----ALKIICKKWKAAGRLPDAVIVEGPKSGGHQGAKAEDLFLPEHQLESVVPEVKEERD 204

Query: 187 --PDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
              D  I   GG+ D     KI+    D V +G
Sbjct: 205 KWGDFPIIAAGGIWDNDDIQKIMALGADAVQLG 237


>gi|182440687|ref|YP_001828406.1| putative oxidoreductase [Streptomyces griseus subsp. griseus NBRC
           13350]
 gi|178469203|dbj|BAG23723.1| putative oxidoreductase [Streptomyces griseus subsp. griseus NBRC
           13350]
          Length = 371

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/173 (16%), Positives = 56/173 (32%), Gaps = 21/173 (12%)

Query: 67  KIVEDFGYNEINLN-VGCPSARVHEGSFGACL---MLNPDIVGDCIAAMCKALSIPVTVK 122
           ++VE  G +   +N    P+A     ++G      +  P  V D + A+     +PV  +
Sbjct: 175 RVVEIHGAHGYLINSFLSPAANRRTDAYGGSWENRLRFPLQVVDAVRAVW-PDDLPVLFR 233

Query: 123 CR---------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
                          +         L + +   GV+ + +     +              
Sbjct: 234 TSATDWLTENPEDPREGWTGDDTVRLAQELAAHGVDLLDVSTGGLVRDAAISAHPGYQVP 293

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                  E  +    +     G + D +QA +I+ +   D VMIGR   ++  
Sbjct: 294 F-----AEQARRTAGIPTAAVGLILDAAQAEEIVATGRADAVMIGREMLRDPH 341


>gi|169347324|ref|ZP_02866262.1| hypothetical protein CLOSPI_00039 [Clostridium spiroforme DSM 1552]
 gi|169293941|gb|EDS76074.1| hypothetical protein CLOSPI_00039 [Clostridium spiroforme DSM 1552]
          Length = 255

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 26/157 (16%), Positives = 51/157 (32%), Gaps = 38/157 (24%)

Query: 102 DIVGDCIAAMCKALSIP------------------VTVKCRIGVD----DQIPAVALRNL 139
           D +   +  +   + IP                  ++   +I +D      +P       
Sbjct: 74  DKIFAFVKKIRNDIKIPMVFMTYANVVFSYGAKKFISTCKKIEIDGIIIPDLPFEEKEEF 133

Query: 140 VKSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIK 183
           +   ++  V  I + A  +                I+  L     R   N D   + +I 
Sbjct: 134 LSLCQEYDVALISLIAPTSKNRIAMIAKEAEGFLYIVSSLGVTGIRSEINTDLASIIKIV 193

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           +EN D+   +  G+    QA ++    DGV++G A  
Sbjct: 194 RENTDIPCAIGFGISTPKQANEMAKIADGVIVGSAII 230


>gi|164688574|ref|ZP_02212602.1| hypothetical protein CLOBAR_02219 [Clostridium bartlettii DSM
           16795]
 gi|164602987|gb|EDQ96452.1| hypothetical protein CLOBAR_02219 [Clostridium bartlettii DSM
           16795]
          Length = 670

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 58/181 (32%), Gaps = 15/181 (8%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EAAK  +  G++ + ++ G          P        FG  +          I  + K 
Sbjct: 154 EAAKRAQTAGFDAVEIHAGHSYLISQFLSPLYNNRTDEFGGSIENRTRFARLVIDEVRKN 213

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD---NRKI 171
           +     +  R+  D+ +      +      +   + + I+   A L G        N   
Sbjct: 214 VGPNFPILLRLSADEFMEGGNTIDDCLEYLEYLNDEVDIYDVSAALNGSIQYQIDANYLK 273

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
                 +   +K++     I + G + +   A  IL     D + +GR    +   +  V
Sbjct: 274 DGWRAYLSKAVKEKFGKPCITM-GNIRNPQVAEDILERGDADLIGMGRGLIADPEWVNKV 332

Query: 230 D 230
           +
Sbjct: 333 E 333


>gi|148359888|ref|YP_001251095.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella pneumophila str. Corby]
 gi|296107938|ref|YP_003619639.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella pneumophila 2300/99
           Alcoy]
 gi|148281661|gb|ABQ55749.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella pneumophila str. Corby]
 gi|295649840|gb|ADG25687.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella pneumophila 2300/99
           Alcoy]
          Length = 674

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 63/191 (32%), Gaps = 36/191 (18%)

Query: 62  LVEAAKIVEDFGYNEINL--------NVGCPSARVHE--------GSFGACLMLNPDIVG 105
               A++ +  GY+ + +        N       V          G   +  +  P    
Sbjct: 151 FARCARLAQLAGYDGVEIMGSEGYLIN----QFIVTHTNHRRDEWGGSFSNRIRFP---I 203

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D          +  L K+I+++G + I  +      +
Sbjct: 204 EIVRSVREAVGEHFIIIYRLSMLDLVAEGSNWQEVVTLAKAIEQAGASLI--NTGIGWHE 261

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MI--GR 217
              P     +P+  +  V +  K    + +  +  +     A ++L   DGV  MI   R
Sbjct: 262 ARIPTIGTMVPSAAFTQVTQHLKPEIKIPVITSNRINTPELANQLLE--DGVADMISMAR 319

Query: 218 AAYKNSAMLTT 228
               +      
Sbjct: 320 PFLADP-CFAE 329


>gi|123496953|ref|XP_001327079.1| oxidoreductase, FAD/FMN-binding family protein [Trichomonas
           vaginalis G3]
 gi|121910003|gb|EAY14856.1| oxidoreductase, FAD/FMN-binding family protein [Trichomonas
           vaginalis G3]
          Length = 335

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/130 (16%), Positives = 41/130 (31%), Gaps = 26/130 (20%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGA-----------------DISKLVEAAKIVED 71
            DA   G ++ I    ++     +QI                     I   V AAK  ++
Sbjct: 77  TDAHAEGWRETIDYIHSKGSKTIMQIADCRNIKKDGKFMTTSEISESIELFVNAAKRAQN 136

Query: 72  FGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            G + I  +            P     +  +G  L     I+ +C+ A+ +       + 
Sbjct: 137 VGADGIEFHAAHGYLLSQFLSPVTNTRDDHYGGSLKNRIRILQECVEAIRRECGKDFIIA 196

Query: 123 CRIGVDDQIP 132
            ++  DD + 
Sbjct: 197 AKMNTDDSVK 206


>gi|325696006|gb|EGD37897.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK160]
          Length = 252

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|319653849|ref|ZP_08007943.1| hypothetical protein HMPREF1013_04562 [Bacillus sp. 2_A_57_CT2]
 gi|317394385|gb|EFV75129.1| hypothetical protein HMPREF1013_04562 [Bacillus sp. 2_A_57_CT2]
          Length = 230

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 2/72 (2%)

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMI 215
             +          KI + DY ++ +I KE     +   G +     A  +L   V  V++
Sbjct: 151 PTLYGYTEETKGLKIDDHDYSVIKQIVKEVKHAKVIAEGNVSTPEIARSVLDFHVHSVVV 210

Query: 216 GRAAYKNSAMLT 227
           G  A     ++T
Sbjct: 211 G-GAITRPQIIT 221


>gi|229155641|ref|ZP_04283749.1| NADPH dehydrogenase [Bacillus cereus ATCC 4342]
 gi|228627959|gb|EEK84678.1| NADPH dehydrogenase [Bacillus cereus ATCC 4342]
          Length = 319

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|167575144|ref|ZP_02368018.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia oklahomensis
           C6786]
          Length = 376

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 32/211 (15%), Positives = 71/211 (33%), Gaps = 50/211 (23%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
              AA    + G++ I L+       + +            ++G  L     +  +  AA
Sbjct: 157 FARAACDAVETGFDAIELHGA--HGYLFDQFLWAKMNTRADAYGGSLENRLRLSTEVAAA 214

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + KA+  S+P+  +          A        L+ ++ ++  +GV+   +  R+     
Sbjct: 215 VRKAVGASVPIIFRFSQWKVQDYTAHIVESSGELKTMLDALVAAGVDIFDVSTRRFW--- 271

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFI------GLNG--------------GLEDMSQ 202
               +       D D+   ++K +    I        N               G+E++ +
Sbjct: 272 ----EPAFPSESDADLASLVRKLSGKPVIMVGSVGIDNAFSAAQVRGAEGLSVGVENLDR 327

Query: 203 ALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           A+  + +   D + +GRA   + A    V  
Sbjct: 328 AVARIEAGRADCIALGRALLADPAWPAKVRA 358


>gi|167567589|ref|ZP_02360505.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia oklahomensis
           EO147]
          Length = 376

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 32/211 (15%), Positives = 71/211 (33%), Gaps = 50/211 (23%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
              AA    + G++ I L+       + +            ++G  L     +  +  AA
Sbjct: 157 FARAACDAVETGFDAIELHGA--HGYLFDQFLWAKMNTRADAYGGSLENRLRLSTEVAAA 214

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAV------ALRNLVKSIKKSGVNGIWIHARKAILKG 162
           + KA+  S+P+  +          A        L+ ++ ++  +GV+   +  R+     
Sbjct: 215 VRKAVGASVPIIFRFSQWKVQDYTAHIVESSGELQTMLDALVAAGVDIFDVSTRRFW--- 271

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFI------GLNG--------------GLEDMSQ 202
               +       D D+   ++K +    I        N               G+E++ +
Sbjct: 272 ----EPAFPSESDADLASLVRKLSGKPVIMVGSVGIDNAFSAAQVRGAEGLSVGVENLDR 327

Query: 203 ALKILPS--VDGVMIGRAAYKNSAMLTTVDE 231
           A+  + +   D + +GRA   + A    V  
Sbjct: 328 AVARIEAGSADCIALGRALLADPAWPAKVRA 358


>gi|118589340|ref|ZP_01546746.1| dihydroorotate dehydrogenase [Stappia aggregata IAM 12614]
 gi|118438040|gb|EAV44675.1| dihydroorotate dehydrogenase [Stappia aggregata IAM 12614]
          Length = 364

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 29/128 (22%), Positives = 47/128 (36%), Gaps = 24/128 (18%)

Query: 104 VGDCIAAMCKALS---------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           + D + A+  A           +PV +K    V D+     LR++V+ +    V+G+ + 
Sbjct: 190 LADLLTAVITARDASTQKLGRKVPVLLKIAPDVADED----LRDIVEEVLAKKVDGLIVS 245

Query: 155 ARKAILKGLSPKDNRK-------IPNLDYDIV---YEIKKENPDLFIGLNGGLEDMSQAL 204
                 +GLS K   +        P      +      K   PDL I   GG++    A 
Sbjct: 246 NTTIGREGLSGKGPAQETGGLSGKPLFRKSTIMLARARKLAGPDLPIIGVGGIDSAETAW 305

Query: 205 -KILPSVD 211
            KI    D
Sbjct: 306 TKITAGAD 313


>gi|54295189|ref|YP_127604.1| hypothetical protein lpl2269 [Legionella pneumophila str. Lens]
 gi|53755021|emb|CAH16509.1| hypothetical protein lpl2269 [Legionella pneumophila str. Lens]
 gi|307611192|emb|CBX00837.1| hypothetical protein LPW_25411 [Legionella pneumophila 130b]
          Length = 674

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 63/191 (32%), Gaps = 36/191 (18%)

Query: 62  LVEAAKIVEDFGYNEINL--------NVGCPSARVHE--------GSFGACLMLNPDIVG 105
               A++ +  GY+ + +        N       V          G   +  +  P    
Sbjct: 151 FARCARLAQLAGYDGVEIMGSEGYLIN----QFIVTHTNHRRDEWGGSFSNRIRFP---I 203

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D          +  L K+I+++G + I  +      +
Sbjct: 204 EIVRSVREAVGEHFIIIYRLSMLDLVAEGSNWQEVVTLAKAIEQAGASLI--NTGIGWHE 261

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MI--GR 217
              P     +P+  +  V +  K    + +  +  +     A ++L   DGV  MI   R
Sbjct: 262 ARIPTIGTMVPSAAFTQVTQHLKPEIKIPVITSNRINTPELANQLLE--DGVADMISMAR 319

Query: 218 AAYKNSAMLTT 228
               +      
Sbjct: 320 PFLADP-CFAE 329


>gi|325687702|gb|EGD29723.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK72]
 gi|332362575|gb|EGJ40375.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK1056]
          Length = 252

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERNTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|300950702|ref|ZP_07164593.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 116-1]
 gi|300958472|ref|ZP_07170610.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 175-1]
 gi|300314868|gb|EFJ64652.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 175-1]
 gi|300449998|gb|EFK13618.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 116-1]
          Length = 672

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 34/237 (14%), Positives = 73/237 (30%), Gaps = 50/237 (21%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+     V+D         L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNSAMLTTVD 230
             V  ++K       +  N  + D   A  IL   D  M+   R+   ++ +L+   
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMVSMARSFLADAELLSKAQ 325


>gi|289704939|ref|ZP_06501355.1| putative 2,4-dienoyl-CoA reductase (NADPH) [Micrococcus luteus
           SK58]
 gi|289558329|gb|EFD51604.1| putative 2,4-dienoyl-CoA reductase (NADPH) [Micrococcus luteus
           SK58]
          Length = 701

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 77/249 (30%), Gaps = 30/249 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVEA 65
           R  A+LL       +  +V+ + +R          +  +  E+ ++             A
Sbjct: 102 RILAQLLHAGRYAPSPDLVSASAVRAPISRHTPREMTTADIERTVSA---------FARA 152

Query: 66  AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           A +  + GY+ + +             P+       +G             +AA+ +AL 
Sbjct: 153 ATLALEAGYDGVEIMASEGYLLNQFLAPATNRRADEYGGDAERRRRFPAAVVAAVREALG 212

Query: 117 ----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + V       V D      + +  ++ + +G + +         +   P     +P
Sbjct: 213 ERGVLSVRTSAADLVPDGQTRAEIADTARAFEAAGADVLM--TGIGWHESRVPTIVTSVP 270

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
              +           D+ +  +  L   ++A + L   +   V + R    +   +  + 
Sbjct: 271 RAAFLAASADLTAAVDIPVIASNRLTTPAEAEEALTSGNAALVGLARPLLADPDWMAAIS 330

Query: 231 EYFSNPLTG 239
           +  +  LT 
Sbjct: 331 DPRARTLTP 339


>gi|257884574|ref|ZP_05664227.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,501]
 gi|257887400|ref|ZP_05667053.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,141,733]
 gi|257820412|gb|EEV47560.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,231,501]
 gi|257823454|gb|EEV50386.1| dihydroorotate dehydrogenase [Enterococcus faecium 1,141,733]
          Length = 314

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 67/209 (32%), Gaps = 32/209 (15%)

Query: 48  KPLALQIGG----ADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
           +PL   I G     ++  L E    +E  G+  I  LN+ CP   V        L  + +
Sbjct: 96  QPLFFSIAGMSVQENLEMLGE----IEKSGFKGITELNLSCP--NVPGK---PQLAYDFE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 147 ATYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 205

Query: 156 RKAIL-----KGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKI-LP 208
            K  +     +G        I       V     +  P++ I   GG+     A +  L 
Sbjct: 206 DKEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLKPEIQIIGTGGIRTGQDAFEHLLC 265

Query: 209 SVDGVMIGRAAYKN--SAMLTTVDEYFSN 235
               + IG          + + + +  + 
Sbjct: 266 GASMLQIGTE-LHKEGPEIFSRIIKELTQ 293


>gi|254447184|ref|ZP_05060651.1| 2,4-dienoyl-coa reductase [gamma proteobacterium HTCC5015]
 gi|198263323|gb|EDY87601.1| 2,4-dienoyl-coa reductase [gamma proteobacterium HTCC5015]
          Length = 675

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 24/132 (18%), Positives = 47/132 (35%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+ +A      +  R+     + D      +  L K+I+ +G     I+      +
Sbjct: 199 EVVRAVREAAGDDFIIIYRLSMADLIKDGSTWEEVVTLGKAIEAAGAT--IINTGIGWHE 256

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P     +P   +  V +  KE+ DL +     + D   A  IL   D  M+   R  
Sbjct: 257 ARVPTIVTSVPRGAFTWVTQRMKEHVDLPLITTNRINDPKVAEDILARGDADMVSMARPF 316

Query: 220 YKNSAMLTTVDE 231
             +   +   +E
Sbjct: 317 LADPDFVKKAEE 328


>gi|197337042|ref|YP_002157977.1| NADH oxidase [Vibrio fischeri MJ11]
 gi|197314294|gb|ACH63743.1| NADH oxidase [Vibrio fischeri MJ11]
          Length = 676

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/215 (14%), Positives = 67/215 (31%), Gaps = 43/215 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIV 104
           K VE+A I +  GY+ + ++       VHEG                 +G          
Sbjct: 159 KFVESAMIAKKAGYDGVEIHA------VHEGYLLDQFTMEFFNQRTDQYGGSFENRYRFA 212

Query: 105 GDCIAAMCKALSIPVTVKCRIGV------------DDQIPAVALRN------LVKSIKKS 146
            + +  +         V  R  V             ++I     R+        K ++ +
Sbjct: 213 VEIVEGIKATCGRNFPVSLRYSVKGNTKGFGQGILPNEIAEEVGRDMDEGLKAAKYLQDA 272

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G + + + A        +   N   P +       +  E   + + + G +E+   A   
Sbjct: 273 GYDALNVDAGTYDAWYWNHPANYFEPGMYQPYCKAV-SEVVSIPVLMAGRMENPDLASHA 331

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
           + +   DG+ +GR    +  ++  +     N +  
Sbjct: 332 VTAGIADGISMGRPLLADPDVVNKIRRGRFNEVRP 366


>gi|157375447|ref|YP_001474047.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sediminis
           HAW-EB3]
 gi|157317821|gb|ABV36919.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella sediminis
           HAW-EB3]
          Length = 671

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 48/141 (34%), Gaps = 12/141 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + ++ K +     +  R+     VD+      +  L K ++K+GV    I+      +
Sbjct: 197 EIVRSIRKKVGDDFIIIFRLSMLDLVDNGSSWDEVVELAKWLEKAGVT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
              P     +P   +  V E  ++   + +     +     A  IL S    M+   +  
Sbjct: 255 ARVPTIATSVPRGGFAWVTERLQKEVSIPLVATNRINTPEIAEHILSSGQADMV---SMA 311

Query: 222 NSAMLTTVDEYFSNPLTGSSP 242
              +    D  F N     +P
Sbjct: 312 RPFL---ADADFVNKAAADTP 329


>gi|134278924|ref|ZP_01765637.1| xenobiotic reductase A [Burkholderia pseudomallei 305]
 gi|134249343|gb|EBA49424.1| xenobiotic reductase A [Burkholderia pseudomallei 305]
          Length = 365

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 63/177 (35%), Gaps = 19/177 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AAK   D G+  + L+       + +            ++G         + + +AA+
Sbjct: 161 VAAAKRALDAGFEWLELHFA--HGYLAQSFFSVHSNRRADAYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +P+T +  +   D      L   ++  K+  + G+ + +        +P    
Sbjct: 219 REVWPERLPLTARFGVIEYDGRDEQTLAESIELAKRFKLEGLDLLSVTIGFS--TPAARI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
                    V E  +    L +    G++  + A +++    +D VM+GRA   +  
Sbjct: 277 PWGPAFLAPVAERVRREAQLPVASAWGIDAPALAERVVSEGQLDLVMVGRAHLADPH 333


>gi|289668870|ref|ZP_06489945.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           campestris pv. musacearum NCPPB4381]
          Length = 258

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 48/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRAHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A   + +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRAQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R D   WR
Sbjct: 127 VGIDSIREDDGEWR 140


>gi|289433839|ref|YP_003463711.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|289170083|emb|CBH26623.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|313634669|gb|EFS01132.1| 1-(5-phosphoribosyl)-5-((5-
           phosphoribosylamino)methylideneamino)imidazole-4-
           carboxamide isomerase [Listeria seeligeri FSL N1-067]
 gi|313639266|gb|EFS04187.1| 1-(5-phosphoribosyl)-5-((5-
           phosphoribosylamino)methylideneamino)imidazole-4-
           carboxamide isomerase [Listeria seeligeri FSL S4-171]
          Length = 240

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 11/96 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             +  + G + + I      L+G           ++ +++ E+KK    + + + GG+  
Sbjct: 36  ATTFARDGASYLHIVDLDGALEGR---------PVNLEVIKEMKKA-SAIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           M+Q    L   +D V+IG AA  +   L T  + + 
Sbjct: 86  MAQVDYYLQSGIDRVIIGSAALTDPDFLQTAVQKYG 121


>gi|261879433|ref|ZP_06005860.1| imidazole glycerol phosphate synthase [Prevotella bergensis DSM
           17361]
 gi|270334002|gb|EFA44788.1| imidazole glycerol phosphate synthase [Prevotella bergensis DSM
           17361]
          Length = 257

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 22/117 (18%), Positives = 46/117 (39%), Gaps = 12/117 (10%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K+   +G + +      A  +      N         +V  + +E  ++   + GG+
Sbjct: 38  ELGKAYSDAGADELVFLDITASFEERKTFTN---------LVSRVAQEV-NIPFTVGGGI 87

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
             +    ++L    D V I  AA +N  ++  +   F + +   + I  R+D+D W 
Sbjct: 88  STIDDVERMLLAGADKVSINSAAIRNPQLINQIASKFGSQVCVCA-IDARLDEDGWH 143


>gi|304397408|ref|ZP_07379286.1| imidazoleglycerol phosphate synthase, cyclase subunit [Pantoea sp.
           aB]
 gi|304355026|gb|EFM19395.1| imidazoleglycerol phosphate synthase, cyclase subunit [Pantoea sp.
           aB]
          Length = 258

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAAEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  + +++T + + F 
Sbjct: 85  TPEDAARILEFGADKISINSPALADPSLITRLADRFG 121


>gi|113868429|ref|YP_726918.1| salicylyl-CoA 5-hydroxylase [Ralstonia eutropha H16]
 gi|113527205|emb|CAJ93550.1| 2-Aminobenzoyl-CoA monooxygenase/reductase [Ralstonia eutropha H16]
          Length = 784

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 29/200 (14%), Positives = 59/200 (29%), Gaps = 27/200 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
              V +A+   + G++ + L   C           P     E  +G  L   +  P  V 
Sbjct: 569 DDFVASARRAAEAGFDWLEL--HCAHGYLLSSFISPLTNTREDEYGGSLAARLRYPLEVF 626

Query: 106 DCIAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKGL 163
             +  +  +   + V +     V+  I       + ++ K +G + I     + +  +  
Sbjct: 627 AAVREVWPEHKPMSVRISAHDWVEGGITPDDAIEIARAFKAAGADMIDCSSGQVSPDQAP 686

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
                 + P  D      I+ E   +     G + +      I+ +   D   I R    
Sbjct: 687 VYGRMYQTPFAD-----RIRNEAG-IATIAVGAIFEADHVDSIIAAGRADLCAIARPHLA 740

Query: 222 NS-AMLTTVDEYFSNPLTGS 240
           N    L          +T  
Sbjct: 741 NPAWTLQEAARIGYRDITWP 760


>gi|112950051|gb|ABI26629.1| dihydroorotate dehydrogenase [Ustilago maydis]
          Length = 677

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 59/168 (35%), Gaps = 18/168 (10%)

Query: 56  GADISKLVEAAKIVEDFG--YNEINLNVGCPS----ARVHEGSFGACLMLNPDIVGD-CI 108
            ++   + +  K VE  G   + I +NV  P+     R+        L+       D  +
Sbjct: 293 TSNEESVDDYVKGVERLGPYADMIIVNVSSPNTPGLRRLQRRGVLEDLLTQVVRARDGMV 352

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH----ARKAILKG-- 162
            +  +     V V   + +   +    L ++  +  KSG++G+ I     +R A L+   
Sbjct: 353 ESHLRFSDKKVAVPLLVKIAPDLSEEELHDVADAALKSGIDGLVISNTTISRPASLRSSE 412

Query: 163 ----LSPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGLEDMSQALK 205
                       +  L    +  + K+    L I   GG+ +   AL 
Sbjct: 413 HVRETGGLSGAPVKPLALKALTTVHKRLQGKLPIIGCGGISNGQDALD 460


>gi|71018263|ref|XP_759362.1| hypothetical protein UM03215.1 [Ustilago maydis 521]
 gi|46099087|gb|EAK84320.1| hypothetical protein UM03215.1 [Ustilago maydis 521]
          Length = 799

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 59/168 (35%), Gaps = 18/168 (10%)

Query: 56  GADISKLVEAAKIVEDFG--YNEINLNVGCPS----ARVHEGSFGACLMLNPDIVGD-CI 108
            ++   + +  K VE  G   + I +NV  P+     R+        L+       D  +
Sbjct: 293 TSNEESVDDYVKGVERLGPYADMIIVNVSSPNTPGLRRLQRRGVLEDLLTQVVRARDGMV 352

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH----ARKAILKG-- 162
            +  +     V V   + +   +    L ++  +  KSG++G+ I     +R A L+   
Sbjct: 353 ESHLRFSDKKVAVPLLVKIAPDLSEEELHDVADAALKSGIDGLVISNTTISRPASLRSSE 412

Query: 163 ----LSPKDNRKIPNLDYDIVYEI-KKENPDLFIGLNGGLEDMSQALK 205
                       +  L    +  + K+    L I   GG+ +   AL 
Sbjct: 413 HVRETGGLSGAPVKPLALKALTTVHKRLQGKLPIIGCGGISNGQDALD 460


>gi|331695408|ref|YP_004331647.1| 2,4-dienoyl-CoA reductase [Pseudonocardia dioxanivorans CB1190]
 gi|326950097|gb|AEA23794.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudonocardia dioxanivorans
           CB1190]
          Length = 675

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 27/219 (12%), Positives = 63/219 (28%), Gaps = 22/219 (10%)

Query: 28  VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG----- 82
           VA + +R      +     E+ +   I           A +  + GY+ I +        
Sbjct: 119 VAPSAIRARINRFVPRPLDEEGIRELI-----DSYARCAALAREGGYDGIEIMGSEGYLI 173

Query: 83  ----CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAV 134
                P+       +G           + + A   A+     +  R+     V D     
Sbjct: 174 NTFLAPATNTRSDDWGGSPENRRRFALEVMRASRAAVGDDFVIIFRLSMADLVPDGQTWD 233

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +  L + I+ +G   +  +      +   P     +P   +  V    + +  + +  +
Sbjct: 234 EIVTLARGIEDAGATLL--NTGIGWHEAQIPTIATSVPRAAFTNVTASLRPHVGIPVITS 291

Query: 195 GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
             +     A ++L     D V + R    +   +     
Sbjct: 292 NRISMPDVAERVLAAGHADLVSMARPFLADPEWIRKARA 330


>gi|262066166|ref|ZP_06025778.1| oxidoreductase, 2-nitropropane dioxygenase family [Fusobacterium
           periodonticum ATCC 33693]
 gi|291380140|gb|EFE87658.1| oxidoreductase, 2-nitropropane dioxygenase family [Fusobacterium
           periodonticum ATCC 33693]
          Length = 379

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 37/179 (20%), Positives = 67/179 (37%), Gaps = 39/179 (21%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS--ARVHEGSFGACLMLNPDIV 104
           +KPLA  I  A ++   +  +   + G N I    G P    ++ E         +PD+ 
Sbjct: 89  DKPLACNILHA-MNDYAKVVEYAIEAGANIIVTGAGLPLELPKLVEN--------HPDVA 139

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG--VNGIWIHARKAILKG 162
                       +P+    R          AL+ + K  K +G   + + +   K+    
Sbjct: 140 I-----------VPIVSSAR----------ALKIICKKWKAAGRLPDAVIVEGPKSGGHQ 178

Query: 163 LSPKDNRKIPNLDYD-IVYEIKKEN---PDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
            +  ++  +P    + +V E+K+E     D  I   GG+ D     KI+    D V +G
Sbjct: 179 GAKAEDLFLPEHQLESVVPEVKEERDKWGDFPIIAAGGIWDNDDIQKIMTLGADAVQLG 237


>gi|238762484|ref|ZP_04623455.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia kristensenii ATCC
           33638]
 gi|238699469|gb|EEP92215.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia kristensenii ATCC
           33638]
          Length = 673

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 26/189 (13%), Positives = 60/189 (31%), Gaps = 22/189 (11%)

Query: 49  PLALQIGGADI-----SKLVEAAKIVEDFGYNEIN--------LNVGCPSARVHEG-SFG 94
           P   Q    D      +     A++ +  GY+ +         +N    +   H    +G
Sbjct: 127 PFTPQALSHDEVLQTIADFANCARLAKQAGYDGVEVMGSEGYLINQFITAKTNHRNDEWG 186

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNG 150
                      + + A+ +A      +  R+     V+D      +  L  +++++G   
Sbjct: 187 GDFTRRMRFAVEIVRAVREAAGPDFILIYRLSMLDLVEDGSSWDEIEQLALAVEQAGATL 246

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I  +      +   P     +P   +  V        ++ +     + D + A ++L   
Sbjct: 247 I--NTGIGWHEARIPTIATMVPRAGFSWVTRKLMGKVNIPLITTNRINDPAVAEQVLTDG 304

Query: 209 SVDGVMIGR 217
             D V + R
Sbjct: 305 CADMVSMAR 313


>gi|126465150|ref|YP_001040259.1| dihydroorotate dehydrogenase family protein [Staphylothermus
           marinus F1]
 gi|126013973|gb|ABN69351.1| dihydroorotate dehydrogenase family protein [Staphylothermus
           marinus F1]
          Length = 406

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 27/132 (20%), Positives = 44/132 (33%), Gaps = 21/132 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------- 152
           V +   A+ + + IP+  K      +      +  LVK ++K GV+GI            
Sbjct: 169 VVEAAKALREVVDIPIFAKLSPFTPN------IPELVKELEKVGVDGIVATNTIGPALHI 222

Query: 153 -IHARKAILKGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGL-EDMSQALKILP 208
            I     I+ G +       P L      V     +N  L +   GG+ +        + 
Sbjct: 223 DIETGLPIVGGPNGYGWMSGPALKPLALAVVAEAAKNTHLPVIGVGGISKGTDVIEYFMA 282

Query: 209 SVDGVMIGRAAY 220
               V I  AA 
Sbjct: 283 GASAVQICTAAL 294


>gi|298386605|ref|ZP_06996161.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           1_1_14]
 gi|298260982|gb|EFI03850.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           1_1_14]
          Length = 326

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 64/189 (33%), Gaps = 31/189 (16%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I   +D   + + AK +++ G + + +N+    + V    +G+    + D     
Sbjct: 98  PIIASINCYSDAEWI-DFAKQIQEAGADALEINILALQSDVQYT-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  + + +SIPV +K                L+  +  +G   + +  R    +     +
Sbjct: 152 LRHIKRTVSIPVIMKL------GDNLTNPVALIDQLYANGAAAVVLFNR--FYQPDINIE 203

Query: 168 NRK-------------IPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGV 213
           N +                L +  +     +  D     +GG+         IL     V
Sbjct: 204 NMEQISGAVFSTSADLATPLRWIGIASSVVDKIDY--AASGGVSSPEAVVKAILAGATAV 261

Query: 214 MIGRAAYKN 222
            +  A Y+N
Sbjct: 262 EVCSAVYQN 270


>gi|219722993|ref|YP_002474383.1| inosine-5'-monophosphate dehydrogenase [Borrelia garinii Far04]
 gi|219694681|gb|ACL35199.1| inosine-5'-monophosphate dehydrogenase [Borrelia garinii Far04]
          Length = 404

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 61/180 (33%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV- 119
           ++ + A++ EDF     +LN             GA + ++ D +      +   + + V 
Sbjct: 120 EIYKNAELKEDFSNACKDLNS--------RLRVGAAVSIDIDTLERVEELVKAHVDLLVI 171

Query: 120 ---------------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                          T+K +   +D     +  +     +   G + + +          
Sbjct: 172 DSAHGHSTRIIELVKTIKTKYPSLDLIAGNIVTKEAALDLINVGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|146312871|ref|YP_001177945.1| N-acetylmannosamine-6-phosphate 2-epimerase [Enterobacter sp. 638]
 gi|167012469|sp|A4WDW4|NANE_ENT38 RecName: Full=Putative N-acetylmannosamine-6-phosphate 2-epimerase;
           AltName: Full=ManNAc-6-P epimerase
 gi|145319747|gb|ABP61894.1| N-acylglucosamine-6-phosphate 2-epimerase [Enterobacter sp. 638]
          Length = 235

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 8/94 (8%), Positives = 29/94 (30%), Gaps = 4/94 (4%)

Query: 132 PAVALRNLVKSIKKSGVNGIWIHA-RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
             + + ++    +      +        +    +      +P  D + + ++      + 
Sbjct: 125 SVLLMADIATLAEAKEAQALGFDCVGTTLYGYTAETQGHSLPENDCEFLRDVV-AAVSIP 183

Query: 191 IGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           +   G ++   +A + L      V++G  A    
Sbjct: 184 VVAEGNVDTPERAARCLALGAHTVVVG-GAITRP 216


>gi|329890796|ref|ZP_08269139.1| imidazole glycerol phosphate synthase subunit hisF [Brevundimonas
           diminuta ATCC 11568]
 gi|328846097|gb|EGF95661.1| imidazole glycerol phosphate synthase subunit hisF [Brevundimonas
           diminuta ATCC 11568]
          Length = 255

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 11/99 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L    +  G + +  +   A  +G +         LDY  V +I +   D+   + GG
Sbjct: 33  AELAARYRDQGADELVFYDITASPEGRT---------LDYGWVQDIAR-LLDIPFCVAGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + ++ QA + L    D V I   A +   ++  +     
Sbjct: 83  IRNVEQAARCLDHGADKVSINSPALERPELIGEMAARLG 121


>gi|47566805|ref|ZP_00237523.1| xenobiotic reductase A [Bacillus cereus G9241]
 gi|47556434|gb|EAL14767.1| xenobiotic reductase A [Bacillus cereus G9241]
          Length = 345

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ G++ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|224540875|ref|ZP_03681414.1| hypothetical protein CATMIT_00018 [Catenibacterium mitsuokai DSM
           15897]
 gi|224526210|gb|EEF95315.1| hypothetical protein CATMIT_00018 [Catenibacterium mitsuokai DSM
           15897]
          Length = 311

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 32/212 (15%), Positives = 74/212 (34%), Gaps = 24/212 (11%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV-----------KCRIGVDDQIPA 133
           + R+ +  FG  LML     G+    + +  ++PV             K +      +P 
Sbjct: 56  AKRLTDKPFGVNLMLLHPQAGEMADIVVEE-NVPVVTTGAGNPGIYIKKWKEAGIIVMPV 114

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           V    L + ++K+GV+ +          G    +   +      +V ++K    ++ + +
Sbjct: 115 VPSVALARRMEKAGVDAVIAEG---TESGGHVGELTTMA-----LVPQVK-AAVNIPVIV 165

Query: 194 NGGLEDMSQALKILP-SVDGVMIGRAAYKN--SAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            GG+    Q L  +    DGV +G     +    +               + +  R+   
Sbjct: 166 AGGIASGKQLLAAVALGADGVQVGTILLASTECPIHQNYKNAIIKAKDTDTTVTGRIAGT 225

Query: 251 FWRKISASMTDYAARHLHSGGKLQQITRHMIG 282
             R +   M     +    G ++ ++ ++ +G
Sbjct: 226 PVRILKNKMARTYIKKEKEGAEMMELEKYTLG 257


>gi|121611291|ref|YP_999098.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Verminephrobacter eiseniae EF01-2]
 gi|148839534|sp|A1WR23|HIS4_VEREI RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|121555931|gb|ABM60080.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Verminephrobacter eiseniae EF01-2]
          Length = 245

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 27/120 (22%), Positives = 43/120 (35%), Gaps = 13/120 (10%)

Query: 120 TVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ R G  DQ          + +    +G   + +      L G+           +Y 
Sbjct: 14  CVRLRQGDMDQSTTFGENPAAMARQWIDAGARRLHLVDLNGALAGM---------PKNYG 64

Query: 178 IVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I KE  D + + L GG+ D+    K +   +  V+IG AA KN   L      F  
Sbjct: 65  AIKSILKEVGDDIPVQLGGGIRDLDTIEKYIDGGLRYVIIGTAAVKNPGFLKDACSAFGG 124


>gi|219723248|ref|YP_002476691.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi 156a]
 gi|219693047|gb|ACL34254.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi 156a]
          Length = 404

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 60/180 (33%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              + A+  EDF     +LN        ++   GA + ++ D +      +   + I V 
Sbjct: 120 DAYKNAEHKEDFSNACKDLN--------NKLRVGAAVSIDIDTIERVEELVKAHVDILVI 171

Query: 121 ----------------VKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                           +K +   +D     +  +     +  +G + + +          
Sbjct: 172 DSAHGHSTRIIELVKKIKTKYPNLDLIAGNIVTKEAALDLITAGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|329960819|ref|ZP_08299125.1| dihydroorotate dehydrogenase 2 [Bacteroides fluxus YIT 12057]
 gi|328532420|gb|EGF59221.1| dihydroorotate dehydrogenase 2 [Bacteroides fluxus YIT 12057]
          Length = 325

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/191 (16%), Positives = 59/191 (30%), Gaps = 31/191 (16%)

Query: 47  EKPLALQIGG---ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + P+   I     AD       AK +E+ G + + +N+      V    +G+    + D 
Sbjct: 96  DIPVIASINCYQDADWIDF---AKQIEEAGADALEVNILALQTDVQYT-YGSFEQRHID- 150

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR------- 156
               ++ + K + IPV +K                L+  +  +G   + +  R       
Sbjct: 151 ---ILSHIKKTVKIPVIMKL------GDNLTNPIALIDQLYANGAAAVVLFNRFYQPDIN 201

Query: 157 ----KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVD 211
                 I   +   +      L +  +         L    +GG+         IL    
Sbjct: 202 IEKLTQISGNIFSNEADLAKALRWIGIAS--ASVGKLDYAASGGIHSPEGVVKAILAGAS 259

Query: 212 GVMIGRAAYKN 222
            V I    Y+N
Sbjct: 260 AVEICSVLYQN 270


>gi|323351332|ref|ZP_08086988.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis VMC66]
 gi|322122556|gb|EFX94267.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis VMC66]
          Length = 252

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|315127560|ref|YP_004069563.1| N-ethylmaleimide reductase, FMN-linked [Pseudoalteromonas sp.
           SM9913]
 gi|315016074|gb|ADT69412.1| N-ethylmaleimide reductase, FMN-linked [Pseudoalteromonas sp.
           SM9913]
          Length = 393

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 25/199 (12%), Positives = 63/199 (31%), Gaps = 44/199 (22%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
            +AA+   + G++ + L   C +  +               +G  L      + + +AA+
Sbjct: 184 AQAARNALEAGFDGVEL--HCANGYLVNQFISEHTNKRDDEYGGSLTNRLRFLKEIVAAV 241

Query: 112 CKALS--------IPVT-----VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
              +          P+       +  +G+ +  P       +K ++++G+  + I     
Sbjct: 242 SDVVGPERLGVRFAPLFSSTDETRVYLGLVESDPHHTYIEAIKVLEQAGIAYLSIAEADW 301

Query: 159 ILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVM 214
                 P+   +    ++   I+Y  K                + +A+ +L     D   
Sbjct: 302 DNAPDLPEQFYQAARAEFSGRIIYAGKY--------------TVEKAVAMLAKGYGDLFA 347

Query: 215 IGRAAYKNSAMLTTVDEYF 233
            GR    N  +   +   +
Sbjct: 348 FGRPFIANPDLPARIKNQW 366


>gi|311063827|ref|YP_003970552.1| NADH-dependent flavin oxidoreductase BaiC [Bifidobacterium bifidum
           PRL2010]
 gi|310866146|gb|ADP35515.1| BaiC NADH-dependent flavin oxidoreductase [Bifidobacterium bifidum
           PRL2010]
          Length = 377

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 35/199 (17%), Positives = 64/199 (32%), Gaps = 28/199 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG------------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             +AA+     G+  I ++              C         +G  +      + +   
Sbjct: 175 FRDAAQRAVRAGFEAIEIHAAHGYLISQFLDPLC---NERADEYGGDIHGRMRFLLEVAD 231

Query: 110 AMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +   V +  RI   D            +    +K+ GV+ + +     I     P
Sbjct: 232 AIREVIPDTVPLLVRISATDWAAGGWDLDQTVDTACVLKQHGVDLMDVSTGGIIADVSIP 291

Query: 166 -KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
            K N ++P  D        +E   +     G +    QA KIL     D V IGRAA ++
Sbjct: 292 VKANYQVPFSDQ------VRERAAIPTTAVGLITKPKQAEKILRAGQADAVEIGRAALRD 345

Query: 223 SAMLTTVDEYFSNPLTGSS 241
                        P++ + 
Sbjct: 346 PYWPLRAAAKLGMPVSKAP 364


>gi|228476828|ref|ZP_04061473.1| dihydroorotate dehydrogenase [Streptococcus salivarius SK126]
 gi|228251402|gb|EEK10547.1| dihydroorotate dehydrogenase [Streptococcus salivarius SK126]
          Length = 311

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 39/193 (20%), Positives = 65/193 (33%), Gaps = 19/193 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLML 99
           L      K   L + G    +     K V+D  Y   + LN+ CP   V      A    
Sbjct: 88  LQKQPNTKNHFLSLVGLSPEETHTILKKVQDSDYEGLVELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +   + +  +    + P+ VK     D      A A+ N      V  +   G NG++
Sbjct: 143 DFETTTEILTEVFSYFTKPLGVKLPPYFDIVHFDQAAAVFNQFPLVFVNCVNSIG-NGLY 201

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   +   P++ I   GG++    A +  L
Sbjct: 202 IEDESVVIKPKNGFGGIGGDYIKPTALANVHAFYQRLKPEIQIIGTGGVKSGRDAFEHIL 261

Query: 208 PSVDGVMIGRAAY 220
                V +G A  
Sbjct: 262 CGASMVQVGTALQ 274


>gi|224541536|ref|ZP_03682075.1| hypothetical protein CATMIT_00706 [Catenibacterium mitsuokai DSM
           15897]
 gi|224525573|gb|EEF94678.1| hypothetical protein CATMIT_00706 [Catenibacterium mitsuokai DSM
           15897]
          Length = 680

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 21/156 (13%), Positives = 44/156 (28%), Gaps = 31/156 (19%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVT--VKCRIGVDDQ--------------IPAV 134
           +G  L        + +  + K      PVT     +  + D                   
Sbjct: 214 YGGSLENRLRFAKEIVEEIKKTCGDDFPVTLRFSVKSMIKDWRVGALPGEDFEEKGRDTE 273

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DYDIVYEIKKENPDL 189
                 K ++  G + +          G         P +      Y    ++ KE  D+
Sbjct: 274 EGLKAAKLLESYGYDALDTD------VGTYDAWWWNHPPMYQKKGLYREYCKMVKEVVDI 327

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +   G +++   AL+ +     D + +GR    + 
Sbjct: 328 PVFCAGRMDNPDMALEAIENGECDVIDLGRPLLADP 363


>gi|169628418|ref|YP_001702067.1| NADPH dependent 2,4-dienoyl-CoA reductase FadH [Mycobacterium
           abscessus ATCC 19977]
 gi|169240385|emb|CAM61413.1| Probable NADPH dependent 2,4-dienoyl-CoA reductase FadH
           [Mycobacterium abscessus]
          Length = 687

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 58/179 (32%), Gaps = 23/179 (12%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             +AK+ +  GY+   +             P        FG        +  + + A+ K
Sbjct: 158 AHSAKMAKKAGYDGCEIMGSEGYFINQFLAPYTNDRTDEFGGNPENRRRLAVEVVKAVRK 217

Query: 114 ALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+     +  R+     V D      +  L K I+ +G     I+      +   P    
Sbjct: 218 AVGPDFIICYRLSMADYVPDGQTWDEIVALAKEIEAAGAT--IINTGIGWHEARVPTIVT 275

Query: 170 KIP-NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG----VMIGRAAYKNS 223
            +P N   D+  +I +E     +  N  +     A +IL   DG    + + R    + 
Sbjct: 276 SVPQNAFVDLSNKIAQEVRIPVMASNR-INMPQSAEQILN--DGQVQLISMARPLLADP 331


>gi|262044887|ref|ZP_06017929.1| NADH:flavin oxidoreductase [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259037614|gb|EEW38843.1| NADH:flavin oxidoreductase [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 669

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 62/185 (33%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   +  
Sbjct: 150 EKFGDAAERVRRAGFDCVEIHAGHSYLISQFLSPLFNKRTDEFGGSVENRTRILSLIVDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIK--KSGVNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++  +  V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQEKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRTPQVAEDILASGDADLIAIGRGLIAEPEW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|118468643|ref|YP_890699.1| oxidoreductase, FAD/FMN-binding [Mycobacterium smegmatis str. MC2
           155]
 gi|118169930|gb|ABK70826.1| oxidoreductase, FAD/FMN-binding [Mycobacterium smegmatis str. MC2
           155]
          Length = 343

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 33/162 (20%), Positives = 58/162 (35%), Gaps = 20/162 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI------GVDDQIPAVALRN---LVK 141
           +G  L        +   A+  A    +P+  +           DD  P   L +   L +
Sbjct: 180 YGGPLEHRMRFALEVTEAVRAAWPDGLPLFFRVSATDWLGGDTDDARPGWTLADTVELAE 239

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
            IK+ GV+ + + +      G +P     + P+        I+KE  D+     G + D 
Sbjct: 240 HIKRIGVDLVDVSSG-----GSAPDAAIPVAPSYQVPFSTRIRKEV-DVPTAAVGLITDA 293

Query: 201 SQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
            QA  I+     D V + RA  ++ A +    E   + L   
Sbjct: 294 EQADSIIAEGEADAVFLARALLRDPAWIWRAAEQLGHQLPHP 335


>gi|108801827|ref|YP_642024.1| dihydroorotate dehydrogenase 2 [Mycobacterium sp. MCS]
 gi|119870980|ref|YP_940932.1| dihydroorotate dehydrogenase 2 [Mycobacterium sp. KMS]
 gi|108772246|gb|ABG10968.1| dihydroorotate dehydrogenase [Mycobacterium sp. MCS]
 gi|119697069|gb|ABL94142.1| dihydroorotate dehydrogenase [Mycobacterium sp. KMS]
          Length = 340

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 26/128 (20%), Positives = 46/128 (35%), Gaps = 29/128 (22%)

Query: 39  NILGFS--TQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGAC 96
            +L  +    E P+   + G+     V  A+ +ED G   I LN+               
Sbjct: 91  RLLERAAAEVEVPVIGSLNGSTPGGWVRHARAMEDAGAAAIELNI-------------YQ 137

Query: 97  LMLNPDIVG--------DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           L  +  I G        D +AA+   + +PV VK            A   +   + ++G 
Sbjct: 138 LPGDSHISGREVEQRHLDILAAVKDTVDLPVAVKLSPFFS------ATAEMALRLDQAGA 191

Query: 149 NGIWIHAR 156
           +G+ +  R
Sbjct: 192 DGLVLFNR 199


>gi|299068470|emb|CBJ39693.1| putative oxidoreductase (salicylyl-CoA 5-hydroxylase) protein
           (abmA) [Ralstonia solanacearum CMR15]
          Length = 785

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 34/223 (15%), Positives = 67/223 (30%), Gaps = 29/223 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVGDC 107
            V AA +  + G++ + L   C           P   +    +G  L   +  P  V   
Sbjct: 557 FVRAAGLAVEAGFDWLEL--HCAHGYLLSSFISPLTNLRSDDYGGALENRLRYPLEVFRA 614

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + A+  A   P++V+      V   I       + +  K +G + I   + +     +S 
Sbjct: 615 VRAVWPA-DRPMSVRISAHDWVQGGITPDDAVAIARLFKAAGADMIDCSSGQ-----VSK 668

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           K+      +      +  +    +     G + +      I+ +   D   + R    N 
Sbjct: 669 KEQPVYGRMYQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLANP 728

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
              L          L    P + R  K    +        AA+
Sbjct: 729 AWTLNEAARI--GYLDMPWPRQYRAGKLQLERNLERERALAAQ 769


>gi|296138637|ref|YP_003645880.1| IMP dehydrogenase family protein [Tsukamurella paurometabola DSM
           20162]
 gi|296026771|gb|ADG77541.1| IMP dehydrogenase family protein [Tsukamurella paurometabola DSM
           20162]
          Length = 388

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 49/118 (41%), Gaps = 16/118 (13%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + +++   +  +  A    VTV  R+           R L  ++ ++G++ + IH     
Sbjct: 122 DTELLAAAVGRIRDAG---VTVAVRVSPQR------ARELTPTLLQAGIDLLVIHGTIIS 172

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
            + +S +D+   P      + ++     D+ +   GG+ D   AL  +     GV++G
Sbjct: 173 AEHVSAEDSAGEPLNLKTFIGDL-----DVPVVA-GGVSDHRTALHLMRTGAAGVIVG 224


>gi|220907903|ref|YP_002483214.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Cyanothece sp. PCC
           7425]
 gi|254801145|sp|B8HY50|HIS4_CYAP4 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|219864514|gb|ACL44853.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Cyanothece sp. PCC 7425]
          Length = 257

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 45/98 (45%), Gaps = 20/98 (20%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIW---IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +   V   +L ++++K+G  GI    IH R   L+G            + + + ++  E 
Sbjct: 142 ETSTVQATDLARTVEKAGAAGIIYTDIH-RDGTLQGP-----------NLEALRQLASEV 189

Query: 187 PDLFIGLNGGLEDMSQALKIL----PSVDGVMIGRAAY 220
            +L I  +GG+  ++  L +       V GV+IG+A Y
Sbjct: 190 -NLPIIASGGVSSIADLLNLFVLSTSGVTGVIIGKALY 226


>gi|170723074|ref|YP_001750762.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
 gi|169761077|gb|ACA74393.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida W619]
          Length = 363

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDAYGGSFENRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARMFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAGLPVTSAWGFGTPQLAEGALKANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|157867562|ref|XP_001682335.1| inosine-5'-monophosphate dehydrogenase [Leishmania major]
 gi|68125788|emb|CAJ03667.1| guanosine monophosphate reductase [Leishmania major strain
           Friedlin]
          Length = 553

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 21/119 (17%), Positives = 43/119 (36%), Gaps = 10/119 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + D+  D + A+      P+T K     D     +A     + +  +G +G+ I      
Sbjct: 326 HSDLCIDMVKALKVN---PLTNKV----DIIAGNIATAEAAQDLIDAGADGLKIGVGPGS 378

Query: 160 LKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIG 216
           +          +P L   +    + K++  +    +GG++        I    D VM+G
Sbjct: 379 ICITRLVAGSGVPQLSSVMDCARVAKKHG-VPCIADGGIKTAGDICKAIAAGADTVMLG 436


>gi|54302277|ref|YP_132270.1| putative N-ethylmaleimide reductase [Photobacterium profundum SS9]
 gi|46915699|emb|CAG22470.1| putative N-ethylmaleimide reductase [Photobacterium profundum SS9]
          Length = 369

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 28/189 (14%), Positives = 58/189 (30%), Gaps = 43/189 (22%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML------------NPDIVGDCI 108
              +AA+   + G++ I ++ G        G      +             N +     +
Sbjct: 167 DFAQAAENAIEAGFDGIEIHGG-------NGYLIDQFLRTNSNKRTDEYGGNRENRLRFL 219

Query: 109 AAMCKALSIPVTVK----------CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
             + +A+S  +  +              +D       + +  + + + G+          
Sbjct: 220 MEVVEAVSARIGAERVGVRLAPFATFKDMDCPDIVPTILDAAEHLNQCGIA--------- 270

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIG 216
               LS  D    P +  D    +++      I    G  D+ +A  IL +   D V  G
Sbjct: 271 -YMHLSEADWDDAPTIPDDFRVALRERFSGTIIVA--GRYDLKRAEYILDAGYADLVAFG 327

Query: 217 RAAYKNSAM 225
           RA   N  +
Sbjct: 328 RAFLANPDL 336


>gi|332359400|gb|EGJ37220.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK355]
          Length = 252

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 42/121 (34%), Gaps = 11/121 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEKRGTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +    ++L    D V +  +A  N  +L    E F +     +    +V    W    
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALTNPRLLADCAEKFGSQCVVLAVDAKKVAGGSWHVYL 143

Query: 257 A 257
           A
Sbjct: 144 A 144


>gi|228952434|ref|ZP_04114516.1| NADPH dehydrogenase [Bacillus thuringiensis serovar kurstaki str.
           T03a001]
 gi|228807220|gb|EEM53757.1| NADPH dehydrogenase [Bacillus thuringiensis serovar kurstaki str.
           T03a001]
          Length = 319

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 46/136 (33%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|152968657|ref|YP_001333766.1| 2,4-dieonyl-CoA reductase, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|150953506|gb|ABR75536.1| 2,4-dieonyl-CoA reductase, FMN-linked [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
          Length = 677

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 62/185 (33%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   +  
Sbjct: 150 EKFGDAAERVRRAGFDCVEIHAGHSYLISQFLSPLFNKRTDEFGGSVENRTRILSLIVDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIK--KSGVNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++  +  V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQEKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRTPQVAEDILASGDADLIAIGRGLIAEPEW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|332157688|ref|YP_004422967.1| molybdenum cofactor biosynthesis MoaA [Pyrococcus sp. NA2]
 gi|331033151|gb|AEC50963.1| molybdenum cofactor biosynthesis MoaA [Pyrococcus sp. NA2]
          Length = 966

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 17/86 (19%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + ++ P+   A+Q  G +      LVE  KI ++ GY+ I LN         
Sbjct: 552 QIRMMLRNAKKQHPIGANAVQFTGGEPTLRDDLVEIIKIAKEEGYDHIQLNTD------- 604

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL 115
               G  L   P++V     A    L
Sbjct: 605 ----GIRLAFEPELVKKIREAGVNTL 626


>gi|260892233|ref|YP_003238330.1| imidazoleglycerol phosphate synthase, cyclase subunit [Ammonifex
           degensii KC4]
 gi|260864374|gb|ACX51480.1| imidazoleglycerol phosphate synthase, cyclase subunit [Ammonifex
           degensii KC4]
          Length = 252

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 2/78 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D+V  + ++    F    GG+  +     IL    D V I  AA KN  +++   E F  
Sbjct: 64  DVVRRVAEKVFIPFTVG-GGIRTLEDIRNILTAGADKVAINTAAVKNPELISQAAEQFGR 122

Query: 236 PLTGSSPIKTRVDKDFWR 253
                +    RV    W 
Sbjct: 123 QCVVVAIDARRVGPGRWE 140


>gi|52080914|ref|YP_079705.1| NADPH dehydrogenase NamA [Bacillus licheniformis ATCC 14580]
 gi|52786289|ref|YP_092118.1| NADPH dehydrogenase NamA [Bacillus licheniformis ATCC 14580]
 gi|68052520|sp|Q65HN9|NAMA_BACLD RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|52004125|gb|AAU24067.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus licheniformis
           ATCC 14580]
 gi|52348791|gb|AAU41425.1| YqjM [Bacillus licheniformis ATCC 14580]
          Length = 339

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 27/192 (14%), Positives = 66/192 (34%), Gaps = 19/192 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             + A+  +  G++ I ++            P +   E  +G        ++ + I A+ 
Sbjct: 147 FKKGAERAKAAGFDIIEIHGAHGYLINEFLSPLSNKREDEYGGSPENRYRLLREVIDAVK 206

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  + P  V V         +         K +K+ GV+ I + +   +   ++     +
Sbjct: 207 EVWAGPLFVRVSASDYKTKGLDVADYVGFAKWMKEQGVDLIDVSSGAVVPADINVFPGYQ 266

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
           +   D   +    +    +  G  G +    QA +IL +   D + + R   ++     T
Sbjct: 267 VGFAD--TIRAQAE----IQTGAVGLITSGLQAEEILQNGRADLIFVARELLRDPYWPKT 320

Query: 229 VDEYFSNPLTGS 240
             +  +  + G 
Sbjct: 321 AAKQLNTKIEGP 332


>gi|317049677|ref|YP_004117325.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
 gi|316951294|gb|ADU70769.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
          Length = 667

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 20/180 (11%), Positives = 56/180 (31%), Gaps = 22/180 (12%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              + A++ +  GY+ + +                   + ++G  +            A+
Sbjct: 144 DFAQCARLAQQAGYDGVEIMGSEGYLINQFLVAHTNQRDDAWGGDVARRQRFALAVTRAV 203

Query: 112 CKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A+     I   +     V +        +L + +++ GV     ++     +   P  
Sbjct: 204 RAAVGNDFIIIFRISMLDLVHNGSTLQETLDLAEQLEQCGVTLF--NSGIGWHEARIPTI 261

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIGRAAYKNSAM 225
              +P   +  V +  +E   + +     +   + A  +L   DG+  M+   +     +
Sbjct: 262 ATCVPRAGFAWVTKHLRERVSVPVIATNRINHPAVAAALLH--DGIADMV---SMARPFL 316


>gi|319787412|ref|YP_004146887.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Pseudoxanthomonas suwonensis 11-1]
 gi|317465924|gb|ADV27656.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Pseudoxanthomonas suwonensis 11-1]
          Length = 257

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 43/111 (38%), Gaps = 11/111 (9%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   D +    +  L    +  G + +  +   A  +G S         +DY  V  + +
Sbjct: 21  VRFRDHVDMGDIVELALRYRDQGADELVFYDIGASPEGRS---------VDYAWVERVAR 71

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
              D+   + GG+ D+  A ++L    D + +   A +   +++ + + F 
Sbjct: 72  LI-DIPFCVAGGIRDVETARRVLHAGADKISVNSPALERPQLVSELADAFG 121


>gi|163814107|ref|ZP_02205499.1| hypothetical protein COPEUT_00260 [Coprococcus eutactus ATCC 27759]
 gi|158450556|gb|EDP27551.1| hypothetical protein COPEUT_00260 [Coprococcus eutactus ATCC 27759]
          Length = 424

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/113 (16%), Positives = 43/113 (38%), Gaps = 11/113 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K    +G + I     +A  +G  P         +  ++ +I  ++ D+ +   GG+
Sbjct: 21  EMAKYYNDAGADEIAYFDSRATKEGREP---------NVYVIRQIC-DSVDIPLIACGGV 70

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
             +    K+L      V +  AA  N  ++T   + F +     +   +  D+
Sbjct: 71  RKLEDVKKLLYAGASKVCMKSAAINNPELVTEAADRFGSERIICTIDLSECDE 123


>gi|145628854|ref|ZP_01784654.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 22.1-21]
 gi|145636258|ref|ZP_01791927.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittHH]
 gi|144979324|gb|EDJ89010.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 22.1-21]
 gi|145270423|gb|EDK10357.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittHH]
 gi|301169195|emb|CBW28792.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Haemophilus influenzae 10810]
          Length = 258

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFTFGADKISINSPALADPTLISRLADRFG 121


>gi|313200051|ref|YP_004038709.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylovorus sp. MP688]
 gi|312439367|gb|ADQ83473.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylovorus sp. MP688]
          Length = 246

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 172 PNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
             ++   +  I      ++ I L GG+ D+    + L   +D V+IG AA KN   L   
Sbjct: 59  KPVNEGAIKAIVDAVGGEIPIQLGGGIRDLETIERYLDDGIDYVIIGTAAVKNPGFLHEA 118

Query: 230 DEYFSNPL 237
              F   +
Sbjct: 119 CYAFPGQI 126


>gi|260582260|ref|ZP_05850053.1| glycosyl amidation-associated protein WbuZ [Haemophilus influenzae
           NT127]
 gi|260094628|gb|EEW78523.1| glycosyl amidation-associated protein WbuZ [Haemophilus influenzae
           NT127]
          Length = 258

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFTFGADKISINSPALADPTLISRLADRFG 121


>gi|119945359|ref|YP_943039.1| imidazole glycerol phosphate synthase subunit HisF [Psychromonas
           ingrahamii 37]
 gi|167012200|sp|A1SVC5|HIS6_PSYIN RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|119863963|gb|ABM03440.1| imidazole glycerol phosphate synthase subunit hisF [Psychromonas
           ingrahamii 37]
          Length = 257

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +            +  D R +       V E+     D+   + GG++
Sbjct: 35  LAKRYAEEGADELV------FYDITASSDARVVDKSWVSRVAEVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D V I   A  + +++  + E F 
Sbjct: 85  TIDDARRILEFGADKVSINSPALADPSLINRLSEKFG 121


>gi|72536067|gb|AAZ73134.1| isopentenyl pyrophosphate isomerase [Enterobacteriaceae bacterium
           DC404]
          Length = 349

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 24/129 (18%), Positives = 46/129 (35%), Gaps = 21/129 (16%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-- 156
            +   + + IA + + L +PV VK       ++ A    ++   +   GV  I I     
Sbjct: 171 RDWRGILNAIAQLVRDLPVPVVVK-------EVGAGISPDVACRLADVGVAMIDIAGAGG 223

Query: 157 ------KAILKGLSPKDNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQAL 204
                 +A         N  +   D+     D +  +    PD+ +  +GG+ + +  A 
Sbjct: 224 TSWAAVEAERAPTPEARNVAMAFADWGIPTADALRRVHLALPDIPLIASGGIANGIDAAK 283

Query: 205 KILPSVDGV 213
            I    D V
Sbjct: 284 AIALGADLV 292


>gi|26553769|ref|NP_757703.1| inosine-5'-monophosphate dehydrogenase [Mycoplasma penetrans HF-2]
 gi|26453776|dbj|BAC44107.1| inosine-5'-monophosphate dehydrogenase [Mycoplasma penetrans HF-2]
          Length = 483

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 26/177 (14%), Positives = 55/177 (31%), Gaps = 30/177 (16%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
             ++E+P      G     +   AK++   G + I ++                   +  
Sbjct: 214 IDSKERPKVCGAIGVTEDSIER-AKLLIAAGVDAIIIDCA---------------HGHSK 257

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            V +    +          K    +   +  V   N V  + K+G + + I      +  
Sbjct: 258 KVIELTREIK---------KLFPKLFLIVGNVVTANGVNDLYKAGADAVKIGVGPGAICT 308

Query: 163 LSPKDNRKIPNLDYDIVYEIKKEN--PDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                   IP   +  + E  +E    ++ I  +GG++        +    D VM+G
Sbjct: 309 TRTVSGVGIPQ--FSAILECYEEAKKLNIPIIADGGIKNSGDMVKALAAGADAVMLG 363


>gi|331085252|ref|ZP_08334338.1| hypothetical protein HMPREF0987_00641 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408035|gb|EGG87525.1| hypothetical protein HMPREF0987_00641 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 639

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 70/194 (36%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAA 110
                AA+     GY+ +  ++     P + +  G       +G           + I  
Sbjct: 142 ECYGAAAERAVKAGYDCLEFHLAHNYLPHSFLSAGLNHREDEYGGSFENRCRFPLEVIDE 201

Query: 111 MCKAL--SIPVTVKCRIGVD---DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + K +   +P+ ++     D   + +    +    K  K+ GV+ + +     I    + 
Sbjct: 202 LRKRMPEGMPLFIRIDAQDDLLENGMSIEEVIRFCKIAKEHGVDVLDVSRGNII----TA 257

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
               ++P +D       +    I+KE   + +G+ G +   + A +++    VD V++GR
Sbjct: 258 ASMYEVPPIDVPNAFNVENAARIRKETGMVTVGV-GRINTAALAEELIADDKVDMVVMGR 316

Query: 218 AAYKNSAMLTTVDE 231
           A   +        E
Sbjct: 317 AQLADPEFANKAKE 330


>gi|322696077|gb|EFY87875.1| hypothetical protein MAC_06123 [Metarhizium acridum CQMa 102]
          Length = 424

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 29/197 (14%), Positives = 58/197 (29%), Gaps = 38/197 (19%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             + A       G++ I L+            P+       +G        +  + + A 
Sbjct: 198 DFLSAVHRAVRAGFDVIELHFAHGYLVSSFLSPAVNKRTDQYGGSFENRSRLALELVEAT 257

Query: 112 CKAL--SIPVTVKCR-IGVDDQIPA---------VALRNLVKSIKKSGVNGIWIHARKAI 159
             A+   +P+ V+       D  P               L K + + GV+ + +      
Sbjct: 258 RAAIPKDMPLFVRISATDWLDTNPNWNGGASWTLDESVKLAKLLAERGVDVLDVST---- 313

Query: 160 LKGLSPKDNRKIPNLDYDI--VYEIKKENPD-LFIGLNGGLEDMSQALKILPS------- 209
             G +    + +    Y       IK    D + +   G ++    A  I+         
Sbjct: 314 --GGNHSHQKVVGGPGYQAPFAKAIKAAVGDAMLVSSVGSIKTGDVAQDIIQGGKDKDDT 371

Query: 210 -VDGVMIGRAAYKNSAM 225
            +D +  GR   KN  +
Sbjct: 372 PLDLIAAGRMFLKNPGL 388


>gi|257486128|ref|ZP_05640169.1| xenobiotic reductase A [Pseudomonas syringae pv. tabaci ATCC 11528]
 gi|330989363|gb|EGH87466.1| xenobiotic reductase A [Pseudomonas syringae pv. lachrymans str.
           M301315]
 gi|331010461|gb|EGH90517.1| xenobiotic reductase A [Pseudomonas syringae pv. tabaci ATCC 11528]
          Length = 363

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVLEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|229587891|ref|YP_002870010.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           fluorescens SBW25]
 gi|259709859|sp|C3K6V2|HIS4_PSEFS RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|229359757|emb|CAY46607.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) me thylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           fluorescens SBW25]
          Length = 245

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P+L I + GG+  +      +   V  V+IG  A K+ A +     
Sbjct: 60  PVNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACR 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W +IS       A+   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEISTVQVIDLAKQFEADG 160


>gi|194290089|ref|YP_002005996.1| salicylyl-CoA 5-hydroxylase [Cupriavidus taiwanensis LMG 19424]
 gi|193223924|emb|CAQ69933.1| putative OXIDOREDUCTASE PROTEIN [Cupriavidus taiwanensis LMG 19424]
          Length = 784

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 29/201 (14%), Positives = 60/201 (29%), Gaps = 29/201 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
              V +A+   + G++ + L   C           P     +  +G  L   +  P  V 
Sbjct: 569 DDFVASARRAAEAGFDWLEL--HCAHGYLLSSFISPLTNTRDDEYGGSLAARLRYPLEVF 626

Query: 106 DCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWI-HARKAILKG 162
             + A+      P++V+      V+  I       + ++ K +G + I     + +  + 
Sbjct: 627 AAVRAVW-PQDKPMSVRISAHDWVEGGITPDDAVEIARAFKAAGADMIDCSSGQVSPDQA 685

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
                  + P  D      I+ E   +     G + +      I+ +   D   I R   
Sbjct: 686 PVYGRMYQTPFAD-----RIRNEAG-IATIAVGAIFEADHVDSIIAAGRADLCAIARPHL 739

Query: 221 KNS-AMLTTVDEYFSNPLTGS 240
            N    L          +   
Sbjct: 740 ANPAWTLQEAARIGYRDIAWP 760


>gi|325661017|ref|ZP_08149644.1| hypothetical protein HMPREF0490_00376 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472524|gb|EGC75735.1| hypothetical protein HMPREF0490_00376 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 639

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 31/194 (15%), Positives = 70/194 (36%), Gaps = 27/194 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAA 110
                AA+     GY+ +  ++     P + +  G       +G           + I  
Sbjct: 142 ECYGAAAERAVKAGYDCLEFHLAHNYLPHSFLSAGLNHREDEYGGSFENRCRFPLEVIDE 201

Query: 111 MCKAL--SIPVTVKCRIGVD---DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + K +   +P+ ++     D   + +    +    K  K+ GV+ + +     I    + 
Sbjct: 202 LRKRMPEGMPLFIRIDAQDDLLENGMSIEEVIRFCKIAKEHGVDVLDVSRGNII----TA 257

Query: 166 KDNRKIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
               ++P +D       +    I+KE   + +G+ G +   + A +++    VD V++GR
Sbjct: 258 ASMYEVPPIDVPNAFNVENAARIRKETGMVTVGV-GRINTAALAEELIADDKVDMVVMGR 316

Query: 218 AAYKNSAMLTTVDE 231
           A   +        E
Sbjct: 317 AQLADPEFANKAKE 330


>gi|52842557|ref|YP_096356.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52629668|gb|AAU28409.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 674

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 63/191 (32%), Gaps = 36/191 (18%)

Query: 62  LVEAAKIVEDFGYNEINL--------NVGCPSARVHE--------GSFGACLMLNPDIVG 105
               A++ +  GY+ + +        N       V          G   +  +  P    
Sbjct: 151 FARCARLAQLAGYDGVEIMGSEGYLIN----QFIVTHTNHRRDEWGGSFSNRIRFP---I 203

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + ++ +A+     +  R+ + D          +  L K+I+++G + I  +      +
Sbjct: 204 EIVRSVREAVGEHFIIIYRLSMLDLVAEGSNWQEVVTLAKAIEQAGASLI--NTGIGWHE 261

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MI--GR 217
              P     +P+  +  V +  K    + +  +  +     A ++L   DGV  MI   R
Sbjct: 262 ARIPTIGTMVPSAAFTPVTQHLKPEIKIPVITSNRINTPELANQLLE--DGVADMISMAR 319

Query: 218 AAYKNSAMLTT 228
               +      
Sbjct: 320 PFLADP-CFAE 329


>gi|145225456|ref|YP_001136134.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium gilvum
           PYR-GCK]
 gi|145217942|gb|ABP47346.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium gilvum
           PYR-GCK]
          Length = 410

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 35/213 (16%), Positives = 71/213 (33%), Gaps = 44/213 (20%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             AA++  D G++ + +++G          P        FG  L     +    + A+ +
Sbjct: 161 ANAARLAIDSGFDAVEIHLGHNYLASSFLSPLINRRTDEFGGSLANRAKVARGAVLAVKE 220

Query: 114 ALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIK-KSGVNGIWIHARKAIL------KG 162
           A+   + V  ++ + D     I         K ++   G++ I + A  ++L      +G
Sbjct: 221 AVGDRIAVTAKLNMSDGVRGGISIEESLQTAKWLEEDGGLDAIELTAGSSLLNPMFLFRG 280

Query: 163 LSPK---DNRKIPNLDYDIVYEIKK--------------------ENPDLFIGLNGGLED 199
            +P         P L + +    KK                    +   + I L GG+ +
Sbjct: 281 GAPIKEFARNFKPPLSWGMRMTGKKFMREYPYEEAYLMRDAKKFRDELTMPIILLGGITN 340

Query: 200 MSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                  +    D V +GRA      +L  +  
Sbjct: 341 RETMDRAMAEGFDFVAMGRALLAEPDLLNRIRA 373


>gi|307069654|ref|YP_003878131.1| putative imidazole glycerol phosphate synthase, cyclase subunit
           [Candidatus Zinderia insecticola CARI]
 gi|306482914|gb|ADM89785.1| putative imidazole glycerol phosphate synthase, cyclase subunit
           [Candidatus Zinderia insecticola CARI]
          Length = 252

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           + +   K G + I      A  KG           +  DI+ +I  +   + + + GG++
Sbjct: 35  IAEKYYKEGADEITFLDINASYKG---------KKIILDIIRKISSKIF-IPLTVGGGIK 84

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           ++     IL    D V I  +A  N  ++  +   + 
Sbjct: 85  NIFDVKNILNSGADKVCINTSAILNPFLIREIKNIYG 121


>gi|255320256|ref|ZP_05361441.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter radioresistens
           SK82]
 gi|262380471|ref|ZP_06073625.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter radioresistens
           SH164]
 gi|255302695|gb|EET81927.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter radioresistens
           SK82]
 gi|262297917|gb|EEY85832.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter radioresistens
           SH164]
          Length = 246

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 22/130 (16%), Positives = 42/130 (32%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I +  P+L + + GG+  +      L   V  V+IG  A +N   
Sbjct: 60  ------PIHKPVVEAIVRAQPELPVQIGGGIRSLETIEHYLEAGVSFVIIGTKAVQNPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKKFAG 123


>gi|300777604|ref|ZP_07087462.1| NADPH dehydrogenase [Chryseobacterium gleum ATCC 35910]
 gi|300503114|gb|EFK34254.1| NADPH dehydrogenase [Chryseobacterium gleum ATCC 35910]
          Length = 352

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 67/184 (36%), Gaps = 28/184 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGS--FGACLMLNPDIVGDCIA 109
           K V+AA    + G++ I L+ G           SA +++    +G         + + + 
Sbjct: 154 KFVKAALRAVEAGFDTIELHAGHGYLFHQFY--SAVINKRQDEYGGSFENRIRFLVETVQ 211

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGL 163
            + K +   +P+ V+       +            L + +K++GV+ I          G 
Sbjct: 212 EIRKVIPAEMPLFVRISAVDYIESDKAWTLEDSIKLSEILKENGVDFITASGG-----GF 266

Query: 164 SPKDNRKI-PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           +     K+ P         IK++   +  G  G + +  QA  I+     D V+I R   
Sbjct: 267 TNVSKDKVFPGYQVPFAKAIKEQTG-ILTGAVGMITEAEQANDIIAKGDADLVIIAREHL 325

Query: 221 KNSA 224
           ++  
Sbjct: 326 RDPY 329


>gi|256374584|ref|YP_003098244.1| NADH:flavin oxidoreductase/NADH oxidase [Actinosynnema mirum DSM
           43827]
 gi|255918887|gb|ACU34398.1| NADH:flavin oxidoreductase/NADH oxidase [Actinosynnema mirum DSM
           43827]
          Length = 365

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 28/187 (14%), Positives = 60/187 (32%), Gaps = 18/187 (9%)

Query: 67  KIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC 123
           K+VE  G +   +N    P +      +G           + + A+       +PV  + 
Sbjct: 175 KVVEVHGAHGYLINSFLSPISNQRTDEYGGTTENRMRFALEVVDAVRAVWPEDLPVLFRT 234

Query: 124 R-IGVDDQIPAVALRN-----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
                  +   V         L K +++ GV+ + +        G    D        Y 
Sbjct: 235 SATDWTAEQGGVGWAEDDTVLLAKELQQRGVDLLDVST------GGMAHDAVIPVESHYQ 288

Query: 178 IVYEIK-KENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +  K +E   L  G  G + + ++A +++     D V++GR   ++        +   
Sbjct: 289 VRFAAKVREATGLPTGAVGLITEPARAEEVVATGQADAVLLGRELLRDPYWAHHAAQELG 348

Query: 235 NPLTGSS 241
                  
Sbjct: 349 VDSNWPE 355


>gi|188997566|ref|YP_001931817.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|226700367|sp|B2V6T1|HIS4_SULSY RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|188932633|gb|ACD67263.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 239

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 11/99 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++ K  + +G   I +      L+GL PK+ +         + E    + ++ I   GGL
Sbjct: 38  DMAKYFEDAGAEHIHVVDLDGALEGL-PKNIK---------ILESIVRSVNIPIEFGGGL 87

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
                   +L   V+ V+IG  AY+N      + E F N
Sbjct: 88  RSFEAVKAVLDLGVERVVIGSLAYQNPEEFYKIVESFPN 126


>gi|59714232|ref|YP_207007.1| N-ethylmaleimide reductase, FMN-linked [Vibrio fischeri ES114]
 gi|59482480|gb|AAW88119.1| N-ethylmaleimide reductase, FMN-linked [Vibrio fischeri ES114]
          Length = 373

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 28/195 (14%), Positives = 59/195 (30%), Gaps = 37/195 (18%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN----------------PDIV 104
               +AK   + G++ I +                 L+                   +  
Sbjct: 163 DFAYSAKRAIEAGFDGIEI-----------HGGNGYLIDQFLRTNSNHRTDKYGDTRENR 211

Query: 105 GDCIAAMCKALSIPVT---VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
              +  +  A+S  +    V  R+        +   ++V +I  +      + +R     
Sbjct: 212 IRFLLEVVDAVSKEIGSDKVGVRLAPFITFKDMDCPDIVPTILDA---SRELQSRNIAYL 268

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            LS  D    P +  +   E++K   +  I    G     +A +IL     D V  GR  
Sbjct: 269 HLSEADWDDAPVIPENFRIELRKLFSNTIIVA--GSYTQERANEILNKGYADLVAFGRPF 326

Query: 220 YKNSAMLTTVDEYFS 234
             N  +++ +   + 
Sbjct: 327 VSNPDLVSRLKNNYE 341


>gi|322644786|gb|EFY41321.1| FAD/FMN-binding/pyridine nucleotide-disulfide oxidoreductase family
           protein [Salmonella enterica subsp. enterica serovar
           Montevideo str. NC_MB110209-0054]
          Length = 391

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|261340472|ref|ZP_05968330.1| imidazoleglycerol phosphate synthase, cyclase subunit [Enterobacter
           cancerogenus ATCC 35316]
 gi|288317566|gb|EFC56504.1| imidazoleglycerol phosphate synthase, cyclase subunit [Enterobacter
           cancerogenus ATCC 35316]
          Length = 258

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SADDAAKILTFGADKISINSPALADPDLITRLADRFG 121


>gi|322490176|emb|CBZ25437.1| guanosine monophosphate reductase [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 492

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 21/119 (17%), Positives = 44/119 (36%), Gaps = 10/119 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + D+  D + A+  +   P+T K     D     +A     + +  +G +G+ I      
Sbjct: 265 HSDLCIDMVKALKAS---PLTSKV----DIIAGNIATAEGAQDLIDAGADGLKIGVGPGS 317

Query: 160 LKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIG 216
           +          +P L   +    + K++  +    +GG++        I    D VM+G
Sbjct: 318 ICITRLVAGSGVPQLSAVMDCARVAKKHG-VPCIADGGVKTAGDICKAIAAGADTVMLG 375


>gi|254294852|ref|YP_003060875.1| 5-dehydro-4-deoxyglucarate dehydratase [Hirschia baltica ATCC
           49814]
 gi|254043383|gb|ACT60178.1| 5-dehydro-4-deoxyglucarate dehydratase [Hirschia baltica ATCC
           49814]
          Length = 304

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/108 (17%), Positives = 33/108 (30%), Gaps = 17/108 (15%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           G  G    L P+ V   + A    +    PV   C              +L ++ +K+G 
Sbjct: 55  GGTGEFFSLRPEEVDKIVRATVDVVRGKTPVIAGC------GYGTAIATDLAQNAEKAGA 108

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
           +GI +     +  G             YD +  + +      I  N  
Sbjct: 109 DGILLLPPYLMFAGQQGL---------YDHIEAVCRSTKLGVIVYNRD 147


>gi|237801402|ref|ZP_04589863.1| hypothetical protein POR16_21446 [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331024262|gb|EGI04319.1| hypothetical protein POR16_21446 [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 325

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 13/104 (12%)

Query: 88  VHEGSFGACLMLNP--DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
             +G  G  L+     + V + + A+C A+S PV V           ++A    +  ++ 
Sbjct: 137 ARDGVHGLDLLAYRSAENVPELMRAVCAAVSKPVYVA---------GSIASPERIAIVQG 187

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           +G  G  I    A L G  P D + +P+    I+ ++   N  L
Sbjct: 188 AGAAGFTI--GTAALDGQYPADGKDVPSQLNAILRDVAALNKHL 229


>gi|218280879|ref|ZP_03487503.1| hypothetical protein EUBIFOR_00061 [Eubacterium biforme DSM 3989]
 gi|218217813|gb|EEC91351.1| hypothetical protein EUBIFOR_00061 [Eubacterium biforme DSM 3989]
          Length = 251

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D+V  + KE    F    GG+  +     +L    D V +  AA +N +++    + F N
Sbjct: 64  DVVRRVAKEIFIPFTVG-GGISTIEDVRAMLMAGADKVSLNSAAIRNPSLIEEASKRFGN 122

Query: 236 P-LTGSSPIKTRVDKDFWRKISA 257
             +  +   K R D   W     
Sbjct: 123 QCIVLAVDAKKRADNTGWNVYVE 145


>gi|315231725|ref|YP_004072161.1| hypothetical protein TERMP_01964 [Thermococcus barophilus MP]
 gi|315184753|gb|ADT84938.1| hypothetical protein TERMP_01964 [Thermococcus barophilus MP]
          Length = 583

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 17/86 (19%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q  G +      L+E  +I ++ GY+ I LN         
Sbjct: 173 QIRMMLRNAKRENPIGATAVQFTGGEPTLREDLIEIIRIAKEEGYDHIQLNTD------- 225

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL 115
               G  L   P++V     A    L
Sbjct: 226 ----GIRLAFEPELVKKIREAGVNTL 247


>gi|167839247|ref|ZP_02465974.1| xenobiotic reductase A [Burkholderia thailandensis MSMB43]
          Length = 365

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 22/128 (17%), Positives = 49/128 (38%), Gaps = 12/128 (9%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKA 158
           + + +AA+ +     +P+T +  +   D      L     L K  K+ G++ + +     
Sbjct: 211 LVETLAAVREVWPERLPLTARFGVIEYDGRDEETLAESIGLAKRFKREGLDLLSV----- 265

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIG 216
            +   +P             V E  +    L +    G++  + A +++    +D VM+G
Sbjct: 266 TIGFSTPDARIPWGPAFLAPVAERVRREAQLPVASAWGIDAPALAERVVRDGQLDLVMVG 325

Query: 217 RAAYKNSA 224
           RA   +  
Sbjct: 326 RAHLADPH 333


>gi|89092163|ref|ZP_01165118.1| 2,4-dienoyl-CoA reductase FadH [Oceanospirillum sp. MED92]
 gi|89083898|gb|EAR63115.1| 2,4-dienoyl-CoA reductase FadH [Oceanospirillum sp. MED92]
          Length = 674

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 43/124 (34%), Gaps = 8/124 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D          +  L K+I+ +G     I+      +
Sbjct: 200 EVVRRVREAVGSDFIIIYRLSMLDLVEGGSSYEEIVALGKAIEGAGAT--IINTGIGWHE 257

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    K+P   +  V    +E   + +  +  +     A ++L   D  M+   R  
Sbjct: 258 ARIPTIATKVPRAAFTWVTAKVREALSVPVITSNRINMPDVAEEVLARGDADMVSMARPF 317

Query: 220 YKNS 223
             + 
Sbjct: 318 LADP 321


>gi|330971151|gb|EGH71217.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 364

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 25/177 (14%), Positives = 61/177 (34%), Gaps = 15/177 (8%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V+AA      G+  + L+              + +    +G  L      + + + A+
Sbjct: 159 DFVDAASRALAAGFEWLELHFAHGFLGQSFLSRHSNIRNDLYGGSLENRARFILETLTAV 218

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +P+T++  +   D+  + +  + ++ ++ +   G+ +      L G +P +  
Sbjct: 219 REIWPRDLPLTMRLGVVEFDEGASESFADSLEVLRWAKAAGLDLV--DVGLAGTTPNEQV 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                      E  +    L +  +  + D  QA   +    +D VM  R    N  
Sbjct: 277 PWGPDFMVPYAERVRHETGLPVATSWMITDPKQADAFVREGRLDLVMFARTLLANPH 333


>gi|237735631|ref|ZP_04566112.1| enoate reductase [Mollicutes bacterium D7]
 gi|229381376|gb|EEO31467.1| enoate reductase [Coprobacillus sp. D7]
          Length = 647

 Score = 38.6 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 55/161 (34%), Gaps = 29/161 (18%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPA--VALRNLVKSIKKSGV 148
           +G  L        + +  +  A+    P+ +        +       +  L+K I+   V
Sbjct: 171 YGGSLENRMRFTIEHVKTIRNAVGTDFPIVILLGASDYLKGSYQFEEMLELLKRIED-DV 229

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNL----------------------DYDIVYEIKKEN 186
           + I + A   ++ G  P+D    P L                      +      +K+  
Sbjct: 230 DLINVSAGMDMIPGYFPEDQIIEPELGLEAWYSVNGKHCQSIFEPHLTNVHWAKLVKQNF 289

Query: 187 PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
           P+  +G+ G +    +A ++L    VD + +GR    +  +
Sbjct: 290 PNKLVGVIGSIMTPKEAEQLLQEGVVDIISMGRPLVADPFL 330


>gi|299782821|gb|ADJ40819.1| Transcription regulator [Lactobacillus fermentum CECT 5716]
          Length = 98

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 23/96 (23%), Gaps = 6/96 (6%)

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLF 284
           MLT    Y  N                   ++                +++         
Sbjct: 1   MLTQTVHYLENGELLPEATPEEKITTAKEHLAR-----LVDLKGEYAGVREFRGQAAYYM 55

Query: 285 HGFPNSRRCRHILTVEAGASTATHHIIETAFNLMIE 320
            G P + R +  L +EA        I +   +   E
Sbjct: 56  KGIPRAARTKVAL-MEATEQAQMDEIFDRFIDQYEE 90


>gi|262279762|ref|ZP_06057547.1| 2,4-dienoyl-CoA reductase [Acinetobacter calcoaceticus RUH2202]
 gi|262260113|gb|EEY78846.1| 2,4-dienoyl-CoA reductase [Acinetobacter calcoaceticus RUH2202]
          Length = 676

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/124 (15%), Positives = 44/124 (35%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+   +     +  R+     V D      +  + K+++K+GV  +  +      +
Sbjct: 198 EIVKAIRAKVGEKFIICFRLSLLDLVHDGNTMQEVVIVAKALEKAGVTLL--NTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   + D    +K+    + I  +  +     A +IL     D V + R 
Sbjct: 256 ARVPTIVTSVPRAAFVDYTAHVKQHI-SIPIIASNRINMPETAEEILATGKADMVQMARP 314

Query: 219 AYKN 222
              +
Sbjct: 315 LLAD 318


>gi|313110180|ref|ZP_07796079.1| LOW QUALITY PROTEIN: phosphoribosylformimino-5-aminoimidazole
           carboxamide [Pseudomonas aeruginosa 39016]
 gi|310882581|gb|EFQ41175.1| LOW QUALITY PROTEIN: phosphoribosylformimino-5-aminoimidazole
           carboxamide [Pseudomonas aeruginosa 39016]
          Length = 505

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 2/102 (1%)

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVD 230
             ++ ++V  I +  PDL I + GG+  +      +   V  V+IG  A K    +    
Sbjct: 59  KPVNGEVVTAIARRYPDLPIQIGGGIRSLETIEHYVRAGVSYVIIGTKAVKQPEFVGEAC 118

Query: 231 EYFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
             F    + G       V  D W ++S       AR   + G
Sbjct: 119 RAFPGKVIVGLDAKDGFVATDGWAEVSEVQVIDLARRFEADG 160


>gi|14591248|ref|NP_143325.1| hypothetical protein PH1458 [Pyrococcus horikoshii OT3]
 gi|3257882|dbj|BAA30565.1| 587aa long hypothetical protein [Pyrococcus horikoshii OT3]
          Length = 587

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 17/86 (19%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q  G +      L+E  KI ++ GY+ I LN         
Sbjct: 173 QIRMMLRNAKKEHPIGANAVQFTGGEPTLRDDLIEIIKIAKEEGYDHIQLNTD------- 225

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL 115
               G  L  +P++V     A    L
Sbjct: 226 ----GIKLAFDPELVKKLREAGVNTL 247


>gi|315445809|ref|YP_004078688.1| NADH:flavin oxidoreductase [Mycobacterium sp. Spyr1]
 gi|315264112|gb|ADU00854.1| NADH:flavin oxidoreductase [Mycobacterium sp. Spyr1]
          Length = 398

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 35/213 (16%), Positives = 71/213 (33%), Gaps = 44/213 (20%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             AA++  D G++ + +++G          P        FG  L     +    + A+ +
Sbjct: 149 ANAARLAIDSGFDAVEIHLGHNYLASSFLSPLINRRTDEFGGSLANRAKVARGAVLAVKE 208

Query: 114 ALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIK-KSGVNGIWIHARKAIL------KG 162
           A+   + V  ++ + D     I         K ++   G++ I + A  ++L      +G
Sbjct: 209 AVGDRIAVTAKLNMSDGVRGGISIEESLQTAKWLEEDGGLDAIELTAGSSLLNPMFLFRG 268

Query: 163 LSPK---DNRKIPNLDYDIVYEIKK--------------------ENPDLFIGLNGGLED 199
            +P         P L + +    KK                    +   + I L GG+ +
Sbjct: 269 GAPIKEFARNFKPPLSWGMRMTGKKFMREYPYEEAYLMRDAKKFRDELTMPIILLGGITN 328

Query: 200 MSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                  +    D V +GRA      +L  +  
Sbjct: 329 RETMDRAMAEGFDFVAMGRALLAEPDLLNRIRA 361


>gi|303243552|ref|ZP_07329894.1| histidine biosynthesis protein [Methanothermococcus okinawensis
           IH1]
 gi|302486113|gb|EFL49035.1| histidine biosynthesis protein [Methanothermococcus okinawensis
           IH1]
          Length = 193

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 3/48 (6%)

Query: 178 IVYEIKK--ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
            +  IK+  ++ ++ I  +GG+      LK+    V+GV+IG A YKN
Sbjct: 134 TIKPIKELVDSLNIPIIASGGITTYDDLLKLKEIGVEGVVIGSAIYKN 181


>gi|229079232|ref|ZP_04211779.1| NADPH dehydrogenase [Bacillus cereus Rock4-2]
 gi|228704079|gb|EEL56518.1| NADPH dehydrogenase [Bacillus cereus Rock4-2]
          Length = 319

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 46/136 (33%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|124385822|ref|YP_001027602.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei NCTC 10229]
 gi|126448205|ref|YP_001082499.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei NCTC 10247]
 gi|254357395|ref|ZP_04973669.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei 2002721280]
 gi|124293842|gb|ABN03111.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia mallei NCTC
           10229]
 gi|126241075|gb|ABO04168.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia mallei NCTC
           10247]
 gi|148026459|gb|EDK84544.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei 2002721280]
          Length = 335

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 59/178 (33%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIA 109
            VE+AK     G + I ++            P A   + ++G  L   M  P  V D + 
Sbjct: 124 FVESAKRAARLGIDAIEVHAAHGYLLHQFLSPLANHRDDAYGGSLENRMRFPLEVFDAVR 183

Query: 110 AMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           A       PV V+      V               +K+   + I + +      G+SP  
Sbjct: 184 AAF-PDDRPVGVRVSATDWVSGGWELDDTIAFAHELKRRDCDWIDVSSG-----GVSPLQ 237

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              + +       +  K    L     G + D + A +++ +   D V + RA   + 
Sbjct: 238 KIPLSSGYQVPFAQAVKRAVGLPTIAVGLISDPAHANRVIEAGDADFVAMARAMLYDP 295


>gi|292657096|ref|YP_003536993.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Haloferax volcanii DS2]
 gi|291370135|gb|ADE02362.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Haloferax volcanii DS2]
          Length = 238

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 11/100 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              +    +G   + +      L G    + +  P +D         +  D+ + L GG+
Sbjct: 37  EAARRWVDAGAETLHLV----DLGGAFEGERKNAPAVD------AVLDAVDVPLQLGGGI 86

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
                A  +L   VD V++G AA +N  ++  +   +   
Sbjct: 87  RTADDARDLLDRGVDRVILGTAAVENPDIVAELAADYPGG 126


>gi|229069599|ref|ZP_04202887.1| NADPH dehydrogenase [Bacillus cereus F65185]
 gi|228713509|gb|EEL65396.1| NADPH dehydrogenase [Bacillus cereus F65185]
          Length = 319

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 46/136 (33%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSVNEVWDGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|154294266|ref|XP_001547575.1| hypothetical protein BC1G_13819 [Botryotinia fuckeliana B05.10]
 gi|150844829|gb|EDN20022.1| hypothetical protein BC1G_13819 [Botryotinia fuckeliana B05.10]
          Length = 443

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 59/177 (33%), Gaps = 19/177 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCI 108
            K   AA+ +E  G++ I L              S   ++    +G  L     I+ +  
Sbjct: 174 DKFAHAAEYLEKAGFDGIQLHGAHGYLLAQFL--SKTTNKRTDKYGGSLENRFRIIQEVA 231

Query: 109 AAMCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
             + K +     V  ++       D       +   ++++ +  + + +           
Sbjct: 232 DEIHKRVKPDFIVGIKMNSVEFQQDGFTPEDAKAACQALEGARFDYVELSGGTYEESAFV 291

Query: 165 PKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAA 219
            K        ++  +   EI K        + GG + +   +  L +VDGV +GR A
Sbjct: 292 HKRESTKKRENFFIEFAEEIVKPLTKTKTYVTGGFKTVGAMVSALDTVDGVGLGRPA 348


>gi|83746203|ref|ZP_00943257.1| NADPH dehydrogenase [Ralstonia solanacearum UW551]
 gi|207744112|ref|YP_002260504.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum
           IPO1609]
 gi|83727169|gb|EAP74293.1| NADPH dehydrogenase [Ralstonia solanacearum UW551]
 gi|206595516|emb|CAQ62443.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum
           IPO1609]
          Length = 370

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 54/180 (30%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V  A+     G   I L+            P A     ++G           +   A
Sbjct: 157 DAFVATARRAVRLGLAAIELHAAHGYLLHAFLSPIANQRTDAYGGSRENRMRYPLEVFEA 216

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+  P+ V  R+   D +             ++++  G + +      A   G+SP 
Sbjct: 217 VRAAVPDPIPVGVRVSCTDWVEGGWTLEDSVAFAQALRARGCDWV-----DASSGGVSPL 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
               +         E  + +  +     G +    +A  I+     D V +GRA   N  
Sbjct: 272 QQIPLSTGYQVPFAETIRRDAGVPTIAVGLINAPHEAEAIIAEGRADLVAMGRAFLYNPH 331


>gi|332366989|gb|EGJ44729.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK1059]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|330982350|gb|EGH80453.1| tRNA-dihydrouridine synthase A [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 36

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 286 GFPNSRRCRHILTVEAGASTATHHIIETAFNLM 318
           GFP +RR R +L+V+   +     +++ A   +
Sbjct: 1   GFPGARRFRQLLSVDIHKAENPMLLLDQAAAFL 33


>gi|260772634|ref|ZP_05881550.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           metschnikovii CIP 69.14]
 gi|260611773|gb|EEX36976.1| imidazole glycerol phosphate synthase cyclase subunit [Vibrio
           metschnikovii CIP 69.14]
          Length = 257

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V ++  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKGWVAKVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  +  ++T + + F 
Sbjct: 85  TAQDAARILEFGADKVSINSPALADPNLITQLADKFG 121


>gi|254820266|ref|ZP_05225267.1| oxidoreductase, FAD/FMN-binding superfamily protein [Mycobacterium
           intracellulare ATCC 13950]
          Length = 404

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 27/216 (12%), Positives = 73/216 (33%), Gaps = 51/216 (23%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             AA++  + G++ + +++G          P     +  FG  L     +    + A+ +
Sbjct: 149 ANAARLAIEAGFDAVEIHLGHNYLASSFLSPLINRRDDEFGGSLQNRAKVARGIVMAVRR 208

Query: 114 ALSI---PVTVKCRIGVDD-------QIPAVALRNLVKSIKKSGVNGIWIHARKA----- 158
           A+     P+ V  ++ + D          ++     ++  +  G++ I + A  +     
Sbjct: 209 AVEKEGTPIAVTAKLNMADGVRGGISTDESLTTAKWLE--EDGGLDAIELTAGSSLVNPM 266

Query: 159 -ILKGLSPKDNRK---IPNLDYDIV--------------------YEIKKENPDLFIGLN 194
            + +G +P         P L + +                      ++ +    + + L 
Sbjct: 267 YLFRGDAPLKQFAGAFKPPLRWGMRMTGKKFLREYPYREAYLLRDAKLFRAELKMPLILL 326

Query: 195 GGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTV 229
           GG+ +     L +    + V + RA      ++  +
Sbjct: 327 GGITNRETMDLAMAEGFEFVAMARALLAEPDLINRI 362


>gi|289583221|ref|YP_003481687.1| imidazoleglycerol phosphate synthase, cyclase subunit [Natrialba
           magadii ATCC 43099]
 gi|289532774|gb|ADD07125.1| imidazoleglycerol phosphate synthase, cyclase subunit [Natrialba
           magadii ATCC 43099]
          Length = 271

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 44/137 (32%), Gaps = 12/137 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+  +SG +        A  +G              D+V ++  E   + + + GG+
Sbjct: 40  EMAKAYNESGADEFVFLDITASAEGRETM---------LDVVKQVADEVF-IPLTVGGGI 89

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP-LTGSSPIKTRVDKDFWRKI 255
                  + L    D V I   A +   ++      F +  +  S   K R D+D    +
Sbjct: 90  RTTEDIKETLRAGADKVSITTGALERPELINEGARAFGSQCIVISVDAKRRFDEDGEHYV 149

Query: 256 SASMTDYAARHLHSGGK 272
                         GG+
Sbjct: 150 EIDGESCWFECTKKGGR 166


>gi|193214909|ref|YP_001996108.1| inosine-5'-monophosphate dehydrogenase [Chloroherpeton thalassium
           ATCC 35110]
 gi|193088386|gb|ACF13661.1| inosine-5'-monophosphate dehydrogenase [Chloroherpeton thalassium
           ATCC 35110]
          Length = 495

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 8/44 (18%)

Query: 189 LFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + I  +GG++     A  I    DGVM+G       ++   V+E
Sbjct: 337 IPIIADGGIKYSGDIAKAIAAGADGVMVG-------SLFAGVEE 373


>gi|119719190|ref|YP_919685.1| isopentenyl pyrophosphate isomerase [Thermofilum pendens Hrk 5]
 gi|119524310|gb|ABL77682.1| isopentenyl-diphosphate delta-isomerase, type 2 [Thermofilum
           pendens Hrk 5]
          Length = 361

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 21/114 (18%), Positives = 41/114 (35%), Gaps = 10/114 (8%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNL----VKSIKKSGVNGIWIHARKAILKGL 163
           +  + K++ +PV +K       +  A+ + +     V      G +   I   +A   GL
Sbjct: 180 LREIVKSVKVPVILKQTGEGFSRESALKIADTGVKGVDVGGAGGTSFAVIEGLRARYAGL 239

Query: 164 SPKDNRKIPNLDYDI-----VYEIKKENPDLFIGLNGGLED-MSQALKILPSVD 211
              +        + I     V E++   PD+ +   GG+   +  A  I    D
Sbjct: 240 DLHEEIAFEFAGWGIPTAASVLEVRSALPDILLIATGGIRSGLDAAKVIRLGAD 293


>gi|309789908|ref|ZP_07684485.1| dihydroorotate dehydrogenase [Oscillochloris trichoides DG6]
 gi|308228040|gb|EFO81691.1| dihydroorotate dehydrogenase [Oscillochloris trichoides DG6]
          Length = 281

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 27/194 (13%), Positives = 62/194 (31%), Gaps = 26/194 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVED-FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+ + + G D +++ EAA  +E   G + I +         +  +  +      D     
Sbjct: 103 PVIVSLWGQDYTEVAEAAGQLEGVEGVSGIEI------PLSNNSATTS------DTAARL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI---HARKAILKGLS 164
           + A+  A ++P+ VK      D      +  L +++ + G + I +       A L   +
Sbjct: 151 VLAVRMATALPLLVKLPGQASD------IPGLARTVVEQGADAIALIDGIPAVAPLPDGT 204

Query: 165 PKDNRKIPNLDYDIVYEIKKENPD---LFIGLNGGLED-MSQALKILPSVDGVMIGRAAY 220
             + R        +   +     D   + +   GG+                + I     
Sbjct: 205 LVEGRLCGPAVAPVALGLVAAVSDEVNVPVIGVGGVRTAADARAMFAAGASVIGIASGLL 264

Query: 221 KNSAMLTTVDEYFS 234
            +  +   + E   
Sbjct: 265 NDLRIAAHILENLH 278


>gi|167757289|ref|ZP_02429416.1| hypothetical protein CLORAM_02839 [Clostridium ramosum DSM 1402]
 gi|167703464|gb|EDS18043.1| hypothetical protein CLORAM_02839 [Clostridium ramosum DSM 1402]
          Length = 664

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 55/161 (34%), Gaps = 29/161 (18%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPA--VALRNLVKSIKKSGV 148
           +G  L        + +  +  A+    P+ +        +       +  L+K I+   V
Sbjct: 188 YGGSLENRMRFTIEHVKTIRNAVGTDFPIVILLGASDYLKGSYQFEEMLELLKRIED-DV 246

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNL----------------------DYDIVYEIKKEN 186
           + I + A   ++ G  P+D    P L                      +      +K+  
Sbjct: 247 DLINVSAGMDMIPGYFPEDQIIEPELGLEAWYSVNGKHCQSIFEPHLTNVHWAKLVKQNF 306

Query: 187 PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
           P+  +G+ G +    +A ++L    VD + +GR    +  +
Sbjct: 307 PNKLVGVIGSIMTPKEAEQLLQEGVVDIISMGRPLVADPFL 347


>gi|167621577|ref|YP_001672085.1| NADH:flavin oxidoreductase/NADH oxidase [Caulobacter sp. K31]
 gi|167351700|gb|ABZ74426.1| NADH:flavin oxidoreductase/NADH oxidase [Caulobacter sp. K31]
          Length = 678

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/179 (10%), Positives = 54/179 (30%), Gaps = 17/179 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA + ++ GY+ + +             P        +G        +  + + A
Sbjct: 142 EDFANAAMLAKEAGYDGVEIMGSEGYLLNQFLAPRTNQRTDRWGGSAANRQRLPTEIVRA 201

Query: 111 MCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +         +  R  + D          + +  K++  +G N   ++      +   P 
Sbjct: 202 VRARCGDEFILVYRQSLLDLVEGGSTFDEVVDQAKTVAAAGANL--VNTGIGWHEARIPT 259

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
               +P   +       + + +L +  +  +     A +++   + D V + R    + 
Sbjct: 260 IAHMVPRGAFAWAAARLRSHLNLPVVASNRINTPELADRLIGDGNADMVSMARPFLSDP 318


>gi|330982424|gb|EGH80527.1| oxidoreductase, FAD/FMN-binding protein [Pseudomonas syringae pv.
           aptata str. DSM 50252]
          Length = 302

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 50/128 (39%), Gaps = 15/128 (11%)

Query: 99  LNPDIVGDCIAAMCK-ALSIPVTVKCRIGVDDQIPA-----VALRNLV-KSIKKSGVNGI 151
               +  + IAA+ K A   PV V+   G  +              ++  ++  +GV+ I
Sbjct: 182 QRLRLTLEVIAAVKKVAGQAPVGVRLSQGKVNDFQHKWAGGERDAEIIFAALADAGVDYI 241

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSV 210
            +   +A     +      +  L        ++  PD+ +  NGGL D  +A ++L    
Sbjct: 242 HVTEHEAWQPAFAQGQASSLVELA-------RRYAPDVTLIANGGLHDPQKADQVLREGA 294

Query: 211 DGVMIGRA 218
           D + +G+ 
Sbjct: 295 DIIAVGKG 302


>gi|261403130|ref|YP_003247354.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methanocaldococcus vulcanius M7]
 gi|261370123|gb|ACX72872.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methanocaldococcus vulcanius M7]
          Length = 237

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 34/157 (21%), Positives = 60/157 (38%), Gaps = 24/157 (15%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK + D G ++I +        + + +F   L+   +     I A+       V +K   
Sbjct: 88  AKRLMDIGVDKIVVGT----KAITDPTFLNELLSEIER-EKIILAVECKQGK-VAIK--- 138

Query: 126 GVDDQIPAVALRNLVKSIKK-SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           G  + I    +  + K  +K  G         + +L G+             DI+  + K
Sbjct: 139 GWKETINKNPI-EIAKKYEKKVGGILFTNVDVEGMLSGIKT-----------DIIETLVK 186

Query: 185 ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            N  + I  +GG+  +    K+    VDGV+IG A Y
Sbjct: 187 -NVRVPIIYSGGITTLEDIKKLKEIGVDGVIIGSALY 222



 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 43/103 (41%), Gaps = 9/103 (8%)

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D     + L + V   KK       +H     L  +         N + D++ +I +E  
Sbjct: 21  DPTKKHLELEDPVNVAKKW------VHDGAEYLHIVDLDAALGCGN-NVDVIEKIVEEV- 72

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           ++ + + GG+  ++ A +++   VD +++G  A  +   L  +
Sbjct: 73  NIPVEVGGGIRSLTIAKRLMDIGVDKIVVGTKAITDPTFLNEL 115


>gi|149275877|ref|ZP_01882022.1| imidazole glycerol phosphate synthase, subunit B [Pedobacter sp.
           BAL39]
 gi|149233305|gb|EDM38679.1| imidazole glycerol phosphate synthase, subunit B [Pedobacter sp.
           BAL39]
          Length = 251

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           ++V  + K+  ++   + GG+  +  A  +L    D + I  AA KN +++  +   F 
Sbjct: 64  EMVKAVAKQL-NIPFTIGGGITTIQDAEALLNAGADKISINSAAVKNPSLIEELARAFG 121


>gi|282897270|ref|ZP_06305272.1| Dihydroorotate dehydrogenase [Raphidiopsis brookii D9]
 gi|281197922|gb|EFA72816.1| Dihydroorotate dehydrogenase [Raphidiopsis brookii D9]
          Length = 343

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 46/116 (39%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--- 105
           P+   + G       E  ++++  G + + LN+               +  NPD+     
Sbjct: 103 PIIASLNGFSPGGWTEYGQLMQQAGASALELNI-------------YYVPTNPDLTSAEV 149

Query: 106 -----DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                D + ++ K+++IPV+VK               N+ K + ++G +G+ +  R
Sbjct: 150 EQNYIDILRSVKKSVTIPVSVKLSPYF------TNTANMAKRLDRAGADGLVLFNR 199


>gi|237755431|ref|ZP_04584056.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237692395|gb|EEP61378.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 239

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 11/107 (10%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           ++      ++ K  + +G   I +      L+GLS    + I  L+  IV  I     ++
Sbjct: 30  KVYNENPADMAKYFEDAGAKHIHVVDLDGALEGLS----KNIKILE-SIVRSI-----NI 79

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            I   GGL        +L   V+ V+IG  AY+N      + E F N
Sbjct: 80  PIEFGGGLRSFEAVKAVLDLGVERVVIGSLAYQNPEEFYKIVESFPN 126


>gi|254466723|ref|ZP_05080134.1| oxidoreductase, FAD/FMN-binding family [Rhodobacterales bacterium
           Y4I]
 gi|206687631|gb|EDZ48113.1| oxidoreductase, FAD/FMN-binding family [Rhodobacterales bacterium
           Y4I]
          Length = 675

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 80/247 (32%), Gaps = 44/247 (17%)

Query: 4   WTDRHY----RFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADI 59
            TDR +    R   ++L      Y    VA + ++            E  +  QI     
Sbjct: 87  VTDRVHEAGGRIAMQILHAGRYAYGPKCVAPSPVKSPISPFPPHELDEDGIEKQIA---- 142

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CLMLNPDIVGD----------- 106
             +V AA++ ++ GY+ + +        +    +     L+ + +   D           
Sbjct: 143 -DIVNAARLAQEAGYDGVEI--------MGSEGYFLNQFLVTHTNKRTDRWGGSYENRMR 193

Query: 107 ----CIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKA 158
                +    +A+     +  R+ + D +P       +  L + I+K+G     ++    
Sbjct: 194 LPIEVVRRTREAVGREFIIIYRLSMIDLVPNGSTHEEVVQLAQEIEKAGAT--ILNTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
             +   P     +P   +  V  ++  +     I  N  +     A ++L     D V +
Sbjct: 252 WHEARIPTIATSVPRAAFAWVTKKLMGKVGIPVITSNR-INTPEVAEQVLAEGCADMVSM 310

Query: 216 GRAAYKN 222
            R    +
Sbjct: 311 ARPMLAD 317


>gi|149204194|ref|ZP_01881162.1| L-lactate dehydrogenase (cytochrome) [Roseovarius sp. TM1035]
 gi|149142636|gb|EDM30681.1| L-lactate dehydrogenase (cytochrome) [Roseovarius sp. TM1035]
          Length = 382

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 28/130 (21%), Positives = 45/130 (34%), Gaps = 22/130 (16%)

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G  L  +PD   D +  +  A   P  VK  +  DD             ++K G +
Sbjct: 227 NKHAGYLLRTSPDW--DYLRWLRDAWDGPFVVKGVLRGDD----------AAMLEKEGAD 274

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILP 208
            IWI          +P     +P +         +    L + ++GG+E  +     I  
Sbjct: 275 AIWISNHAGRQFDAAPATIEALPEV---------RAATTLPVIMDGGIEGGLDVLRAIAL 325

Query: 209 SVDGVMIGRA 218
             D VM+GR 
Sbjct: 326 GADFVMMGRG 335


>gi|300937976|ref|ZP_07152758.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 21-1]
 gi|300457017|gb|EFK20510.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 21-1]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 23/189 (12%), Positives = 56/189 (29%), Gaps = 42/189 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-----------------PDIV 104
               A++  + GY+ + +                 L+                   P+ +
Sbjct: 144 FARCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYPNRM 192

Query: 105 G---DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARK 157
               + + A+ + +     +  R+ + D +           L ++I+ +G     I+   
Sbjct: 193 RFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGI 250

Query: 158 AILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
              +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+ 
Sbjct: 251 GWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV- 308

Query: 217 RAAYKNSAM 225
             +     +
Sbjct: 309 --SMARPFL 315


>gi|194431445|ref|ZP_03063737.1| imidazoleglycerol phosphate synthase, cyclase subunit [Shigella
           dysenteriae 1012]
 gi|194420270|gb|EDX36347.1| imidazoleglycerol phosphate synthase, cyclase subunit [Shigella
           dysenteriae 1012]
 gi|332091593|gb|EGI96674.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           dysenteriae 155-74]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D V I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKVSINSPALADPTLITRLADRFG 121


>gi|327461188|gb|EGF07521.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK1057]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|257053189|ref|YP_003131022.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Halorhabdus utahensis
           DSM 12940]
 gi|256691952|gb|ACV12289.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Halorhabdus utahensis DSM 12940]
          Length = 240

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 11/95 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           N  +   ++G   + +       +G            + D +  I +   D+ + L GG+
Sbjct: 37  NAAERWVEAGAETLHLIDLDGAFEG---------ERANADAIEAI-QATVDVDLQLGGGI 86

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
                A  +L   VD V++G AA ++  ++  + E
Sbjct: 87  RTAEDARALLDAGVDRVILGTAAVEDPEIVAEISE 121


>gi|229011364|ref|ZP_04168555.1| NADPH dehydrogenase [Bacillus mycoides DSM 2048]
 gi|228749881|gb|EEL99715.1| NADPH dehydrogenase [Bacillus mycoides DSM 2048]
          Length = 345

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +           +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSVNEVWNGPLFVRISANDYHPDGLTVQDYVQYTGWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +   +      ++    +       KEN ++  G  G +    QA +IL   
Sbjct: 246 IDCSSGAVVPAHIDVYPGYQVQYAKH------IKENANIATGAVGLITTGLQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D ++IGR   +N  
Sbjct: 300 EADLILIGRELLRNPY 315


>gi|92112650|ref|YP_572578.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chromohalobacter
           salexigens DSM 3043]
 gi|122420740|sp|Q1R079|HIS4_CHRSD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|91795740|gb|ABE57879.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chromohalobacter
           salexigens DSM 3043]
          Length = 249

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 38/118 (32%), Gaps = 10/118 (8%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K     D          +     ++G   + +       +G           ++ + 
Sbjct: 15  VRLKQGRMDDSTTYGDDPVAMAARWVETGARRLHLVDLNGAFEG---------KPVNAEA 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V  I +  PDL I + GG+         L   V  V+IG  A K  A +  +   F  
Sbjct: 66  VTAIARAYPDLPIQIGGGIRTAETIEAYLEAGVSYVIIGTQAVKEPAFVGEMCRRFPG 123


>gi|116627967|ref|YP_820586.1| imidazole glycerol phosphate synthase subunit HisF [Streptococcus
           thermophilus LMD-9]
 gi|116101244|gb|ABJ66390.1| imidazole glycerol phosphate synthase subunit hisF [Streptococcus
           thermophilus LMD-9]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 43/119 (36%), Gaps = 11/119 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++  ++G + +        L   +  DNR+      D+V  +  +    F    GG+  
Sbjct: 36  ARAYYEAGCDELV------FLDITATSDNRETT---VDMVRRVADQVFIPFTVG-GGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +    K+L    D V +  +A  N  ++    + F N    ++    ++    W    A
Sbjct: 86  VEDMNKMLKAGADKVAVNSSALANPQLIADCAQKFGNQCVVAAIDAKKMADGSWHVFVA 144


>gi|325830133|ref|ZP_08163590.1| pyridine nucleotide-disulfide oxidoreductase [Eggerthella sp. HGA1]
 gi|325487600|gb|EGC90038.1| pyridine nucleotide-disulfide oxidoreductase [Eggerthella sp. HGA1]
          Length = 699

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 45/161 (27%), Gaps = 36/161 (22%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWI- 153
              +V + I  + +       V  R         D I       + K    +G + I + 
Sbjct: 213 RTRLVCEIIRGVKERCGEDFIVGVRTNGQEYGHPDAITIEEGVEIAKFYDAAGADYISVT 272

Query: 154 ---HARKAIL------KGLSPKDNRK------------IPNLDYDIVYEIKKENPDLFIG 192
              +    +          SP ++ K            IP         IK+       G
Sbjct: 273 GYGYGPVPMQFALDYWMYPSPDEDMKQFLDRLDGEGLSIPPA-----AAIKQAVSAPVFG 327

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           +  G     +A   L    +D  M  RA + +  M   + E
Sbjct: 328 V--GFATPEKAEAALEKGEIDLAMFARALWADPDMPNKIAE 366


>gi|323495152|ref|ZP_08100237.1| NADH-flavin oxidoreductase [Vibrio brasiliensis LMG 20546]
 gi|323310592|gb|EGA63771.1| NADH-flavin oxidoreductase [Vibrio brasiliensis LMG 20546]
          Length = 363

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 29/184 (15%), Positives = 63/184 (34%), Gaps = 21/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AAK   + G++ + ++ G  +  + +             +G         + + + 
Sbjct: 161 DFAYAAKRAIEAGFDGVEIHGG--NGYLIDQFLRTNSNHRTDHYGGTRQNRMRFLLEVVD 218

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+  A+     V  R+        +   ++V +I ++      + AR      LS  D  
Sbjct: 219 AVSDAIGAD-KVGVRLAPFITFKDMNCPDIVPTILQA---SKELQARDIAYLHLSEADWD 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P +      E+++   +  I    G     +A +IL     D V  GR    N  +++
Sbjct: 275 DAPVIPESFRLELREYFTNTIIVA--GSYTQDRADEILEKGYADLVAFGRPFVANPDLVS 332

Query: 228 TVDE 231
            +  
Sbjct: 333 RLKH 336


>gi|312142602|ref|YP_003994048.1| ferredoxin-dependent glutamate synthase [Halanaerobium sp.
           'sapolanicus']
 gi|311903253|gb|ADQ13694.1| ferredoxin-dependent glutamate synthase [Halanaerobium sp.
           'sapolanicus']
          Length = 426

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 30/113 (26%), Positives = 47/113 (41%), Gaps = 17/113 (15%)

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP---KDNRKIP 172
            +P+ +K          A  +++ VK   K GV+GI I        G +P    D+  IP
Sbjct: 223 EVPIFMKI--------AAGRVKDDVKIAAKVGVDGIIIDG-AQGGTGAAPVMASDHLGIP 273

Query: 173 --NLDYDIVYEIKKENPD--LFIGLNGGLED-MSQALKILPSVDGVMIGRAAY 220
                   V  +++ N    + I ++GG++D    A  I    D V IG AA 
Sbjct: 274 TMPALVQAVKTLEEANLKQEIDIIISGGIKDGADLAKAIAMGADAVAIGTAAM 326


>gi|312140955|ref|YP_004008291.1| oxidoreductase [Rhodococcus equi 103S]
 gi|311890294|emb|CBH49612.1| putative oxidoreductase [Rhodococcus equi 103S]
          Length = 652

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 24/138 (17%), Positives = 51/138 (36%), Gaps = 7/138 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGV 148
           +G  L      + + IAA+  A+   + +  R+  D+Q+P   + +    + + ++ SG 
Sbjct: 188 YGGSLENRARFLVEVIAAVRAAIGPNLVLGVRLSGDEQVPGGTVLDEAVAVARIVEASGA 247

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                       + L   +        Y + + E  +    L +   G L++  +A + L
Sbjct: 248 VDYINTTMGVATETLHLVEPSMATPRGYALHISEAIRAAVALPVIGVGRLKEPVEAERAL 307

Query: 208 PS--VDGVMIGRAAYKNS 223
                D V I R    + 
Sbjct: 308 TDGRCDLVGITRGQIADP 325


>gi|257790128|ref|YP_003180734.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella lenta DSM
           2243]
 gi|257474025|gb|ACV54345.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella lenta DSM
           2243]
          Length = 699

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 45/161 (27%), Gaps = 36/161 (22%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWI- 153
              +V + I  + +       V  R         D I       + K    +G + I + 
Sbjct: 213 RTRLVCEIIRGVKERCGEDFIVGVRTNGQEYGHPDAITIEEGVEIAKFYDAAGADYISVT 272

Query: 154 ---HARKAIL------KGLSPKDNRK------------IPNLDYDIVYEIKKENPDLFIG 192
              +    +          SP ++ K            IP         IK+       G
Sbjct: 273 GYGYGPVPMQFALDYWMYPSPDEDMKQFLDRLDGEGLSIPPA-----AAIKQAVSAPVFG 327

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           +  G     +A   L    +D  M  RA + +  M   + E
Sbjct: 328 V--GFATPEKAEAALEKGEIDLAMFARALWADPDMPNKIAE 366


>gi|159463058|ref|XP_001689759.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158283747|gb|EDP09497.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 428

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 63/211 (29%), Gaps = 34/211 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDC 107
                AA+     G+  + +++           P A   +  +G  L   M  P  V + 
Sbjct: 222 DAFAAAAERSIKAGFQVVEIHMAHGYLLHQFLSPQANKRKDQYGGSLANRMRLPLAVAEA 281

Query: 108 IAAMCKALSIPVTVKCR----------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + A+     +P+ V+               D     V    L  +++  G + I + +  
Sbjct: 282 VRAVI-PPELPLAVRISATDWAGPLDGPAWDVDQSVV----LCGALRDLGCDLIDVSSGG 336

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMI 215
            + + L P            I  E +     +     G +    QA KIL     D V+I
Sbjct: 337 QLPRALIPVGPGYQVPFSERIRREARVATGTV-----GLITTGKQAEKILQEGKADVVLI 391

Query: 216 GRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           GR   ++                   P   R
Sbjct: 392 GREMLRDPNWPLRAAAELGYEGARYPPQYER 422


>gi|50842449|ref|YP_055676.1| pyridoxine biosynthesis protein [Propionibacterium acnes KPA171202]
 gi|68565722|sp|Q6A948|PDXS_PROAC RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|50840051|gb|AAT82718.1| pyridoxine biosynthesis protein [Propionibacterium acnes KPA171202]
 gi|332675362|gb|AEE72178.1| pyridoxal biosynthesis lyase PdxS [Propionibacterium acnes 266]
          Length = 304

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 41  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 94

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 95  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 154

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 155 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 214

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 215 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 254


>gi|317489579|ref|ZP_07948084.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella sp. 1_3_56FAA]
 gi|316911311|gb|EFV32915.1| NADH:flavin oxidoreductase/NADH oxidase [Eggerthella sp. 1_3_56FAA]
          Length = 699

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 45/161 (27%), Gaps = 36/161 (22%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWI- 153
              +V + I  + +       V  R         D I       + K    +G + I + 
Sbjct: 213 RTRLVCEIIRGVKERCGEDFIVGVRTNGQEYGHPDAITIEEGVEIAKFYDAAGADYISVT 272

Query: 154 ---HARKAIL------KGLSPKDNRK------------IPNLDYDIVYEIKKENPDLFIG 192
              +    +          SP ++ K            IP         IK+       G
Sbjct: 273 GYGYGPVPMQFALDYWMYPSPDEDMKQFLDRLDGEGLSIPPA-----AAIKQAVSAPVFG 327

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           +  G     +A   L    +D  M  RA + +  M   + E
Sbjct: 328 V--GFATPEKAEAALEKGEIDLAMFARALWADPDMPNKIAE 366


>gi|293570938|ref|ZP_06681983.1| dihydroorotate dehydrogenase [Enterococcus faecium E980]
 gi|291609001|gb|EFF38278.1| dihydroorotate dehydrogenase [Enterococcus faecium E980]
          Length = 314

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 65/203 (32%), Gaps = 32/203 (15%)

Query: 48  KPLALQIGG----ADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
           +PL   I G     ++  L E    +E  G+  I  LN+ CP   V        L  + +
Sbjct: 96  QPLFFSIAGMSIQENLEMLGE----IEKSGFKGITELNLSCP--NVPGK---PQLAYDFE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 147 ATYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 205

Query: 156 RKAIL-----KGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKI-LP 208
            K  +     +G        I       V     +  P++ I   GG+     A +  L 
Sbjct: 206 DKEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLKPEIQIIGTGGIRTGQDAFEHLLC 265

Query: 209 SVDGVMIGRAAYKN--SAMLTTV 229
               + IG          + + +
Sbjct: 266 GASMLQIGTE-LHKEGPEIFSRI 287


>gi|262282982|ref|ZP_06060749.1| imidazole glycerol phosphate synthase subunit hisF [Streptococcus
           sp. 2_1_36FAA]
 gi|262261234|gb|EEY79933.1| imidazole glycerol phosphate synthase subunit hisF [Streptococcus
           sp. 2_1_36FAA]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|229102660|ref|ZP_04233362.1| NADPH dehydrogenase [Bacillus cereus Rock3-28]
 gi|228680763|gb|EEL34938.1| NADPH dehydrogenase [Bacillus cereus Rock3-28]
          Length = 319

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 24/125 (19%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + I ++ +    P+ V+        D +         K +K  GV+ I   +   +  
Sbjct: 171 LREIIESINEVWDGPLFVRISANDYHPDGLTVQDYVQYSKWMKVQGVDLIDCSSGAVV-- 228

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
              P      P         IK+   ++  G  G +   +QA +IL     D + IGR  
Sbjct: 229 ---PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNNEADLIFIGREL 284

Query: 220 YKNSA 224
            +N  
Sbjct: 285 LRNPY 289


>gi|254526217|ref|ZP_05138269.1| IMP dehydrogenase family protein [Prochlorococcus marinus str. MIT
           9202]
 gi|221537641|gb|EEE40094.1| IMP dehydrogenase family protein [Prochlorococcus marinus str. MIT
           9202]
          Length = 387

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 37/118 (31%), Gaps = 21/118 (17%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I  +C+++++PV                   + K +  +GV G+ +              
Sbjct: 179 IKDLCQSMNVPVVAG----------NCVTYEVAKLLMDAGVAGLMVGIGPGAACTSRGVL 228

Query: 168 NRKIPNLDYDIVYEIKKENPD--------LFIGLNGGLEDMSQALKILP-SVDGVMIG 216
              IP      + +      D        + I  +GG+       K L    D VMIG
Sbjct: 229 GIGIPQA--TAIADCSAARNDYFKQSGCYIPIIGDGGIVTGGDICKCLACGADAVMIG 284


>gi|148251763|ref|YP_001236348.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bradyrhizobium sp.
           BTAi1]
 gi|167011508|sp|A5E8E8|HIS4_BRASB RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|146403936|gb|ABQ32442.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bradyrhizobium sp.
           BTAi1]
          Length = 247

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 51/136 (37%), Gaps = 21/136 (15%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G   + +P++V     A    +++ +     K  +    +   V   ++ K  + +GV  
Sbjct: 103 GTAAVRDPELVKTAAKAFPGRVAVGLDARDGKVAVEGWAETSEVTALDIAKRFEDAGVAA 162

Query: 151 IWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           I     AR  +LKGL+      + +               + +  +GGL  +     +L 
Sbjct: 163 IIFTDIARDGLLKGLNLDATIALGDA------------VSIPVIASGGLASIEDVKAMLT 210

Query: 209 ----SVDGVMIGRAAY 220
                ++G + GRA Y
Sbjct: 211 PRARKLEGAIAGRALY 226


>gi|330898062|gb|EGH29481.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           japonica str. M301072PT]
          Length = 363

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLAESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          V E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPVAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|323966609|gb|EGB62042.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli M863]
 gi|327251867|gb|EGE63553.1| 2,4-dienoyl-CoA reductase [Escherichia coli STEC_7v]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFARCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAIEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFTETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|254427440|ref|ZP_05041147.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Alcanivorax sp. DG881]
 gi|196193609|gb|EDX88568.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Alcanivorax sp. DG881]
          Length = 246

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 25/118 (21%), Positives = 41/118 (34%), Gaps = 10/118 (8%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K     DD + +     +     + G   + +        G           ++ +I
Sbjct: 15  VRLKQGRMEDDTVFSDDPVAVASHWVERGARRLHLVDLNGAFAG---------EPVNGEI 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V  I K +PDL I + GG+         L   V  V+IG  A    A +  + E F  
Sbjct: 66  VKAIAKAHPDLPIQIGGGIRSPEIIQAYLDAGVQWVIIGTKAVNEPAFVKAMCEQFPG 123


>gi|164661567|ref|XP_001731906.1| hypothetical protein MGL_1174 [Malassezia globosa CBS 7966]
 gi|159105807|gb|EDP44692.1| hypothetical protein MGL_1174 [Malassezia globosa CBS 7966]
          Length = 433

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 78/236 (33%), Gaps = 35/236 (14%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL------- 79
           + A A+           + +E  L+LQ         V AA+     GY+ + +       
Sbjct: 179 VSASALPFDHT----HVTPKE--LSLQQIHEVEDDFVRAAERAFRAGYDFVQIHSAHGYL 232

Query: 80  ----NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA-LSIPVTVKC-------RIGV 127
               N   P        +G        ++ + +  + +      V V+            
Sbjct: 233 VSSFNS--PLTNKRTDEYGGSFENRTRLLLNIVRRIRQQFPDRGVWVRINGTDGLPEDSK 290

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK-GLSPKDNRKIPNLDYDIVYEIKKEN 186
           D+   + + + +   ++++GV+ + + +   I    L      ++P         +++  
Sbjct: 291 DESWTSESTKAVAPLLEQAGVDMLDVSSGGTIGSIQLRASPGYQVPGAIAAKAGGLQRMR 350

Query: 187 PDLFIGLNGG-LEDMS----QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSN 235
                 LNGG  ED S     A K+L S   D + +GRA  +N   +         
Sbjct: 351 VSSVGALNGGTPEDPSREGLFAEKVLQSGDADFITLGRAFLRNPCWVEDAARNLMG 406


>gi|157413532|ref|YP_001484398.1| inosine 5-monophosphate dehydrogenase [Prochlorococcus marinus str.
           MIT 9215]
 gi|157388107|gb|ABV50812.1| putative IMP dehydrogenase [Prochlorococcus marinus str. MIT 9215]
          Length = 387

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 37/118 (31%), Gaps = 21/118 (17%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I  +C+++++PV                   + K +  +GV G+ +              
Sbjct: 179 IKDLCQSMNVPVVA----------GNCVTYEVAKLLMDAGVAGLMVGIGPGAACTSRGVL 228

Query: 168 NRKIPNLDYDIVYEIKKENPD--------LFIGLNGGLEDMSQALKILP-SVDGVMIG 216
              IP      + +      D        + I  +GG+       K L    D VMIG
Sbjct: 229 GIGIPQA--TAIADCSAARNDYFKQSGRYIPIIGDGGIVTGGDICKCLACGADAVMIG 284


>gi|125718252|ref|YP_001035385.1| imidazole glycerol phosphate synthase subunit HisF [Streptococcus
           sanguinis SK36]
 gi|167012217|sp|A3CNT0|HIS6_STRSV RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|125498169|gb|ABN44835.1| Imidazole glycerol-phosphate synthase subunit hisF, putative
           [Streptococcus sanguinis SK36]
 gi|325690496|gb|EGD32499.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK115]
 gi|328946451|gb|EGG40591.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK1087]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|71002971|ref|XP_756166.1| hypothetical protein UM00019.1 [Ustilago maydis 521]
 gi|46096171|gb|EAK81404.1| hypothetical protein UM00019.1 [Ustilago maydis 521]
          Length = 709

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 56/178 (31%), Gaps = 14/178 (7%)

Query: 85  SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRI--GVDDQIPAVALR 137
           S RV++    +G  L     IV + I ++ KA+  P   +++K       D    A    
Sbjct: 196 SPRVNKRTDQYGGNLEGRSRIVFEIIESIRKAVPDPKFIISIKINSADFADGGFDAEESF 255

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNG 195
            + K ++ +GV  I +        G   K    I    +  +    I+       + + G
Sbjct: 256 TMSKKLEAAGVGLIELSGGTYESSGFEHKKESTIARESFFIEFAERIRPHLSTARLAVTG 315

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
           G        K +     D V + R       +        S     +  +   + +  
Sbjct: 316 GFRSSKAMAKAVEERSCDIVGLARPLCGEPHL---CKHLLSGKQQKARDVHPDLPRQI 370


>gi|313898764|ref|ZP_07832298.1| N-acylglucosamine-6-phosphate 2-epimerase [Clostridium sp. HGF2]
 gi|312956346|gb|EFR37980.1| N-acylglucosamine-6-phosphate 2-epimerase [Clostridium sp. HGF2]
          Length = 249

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 28/183 (15%), Positives = 60/183 (32%), Gaps = 46/183 (25%)

Query: 38  KNILGFSTQEKPLALQIGGADISK-------LVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           + +L        ++ Q+   D          + EAAK     G   I  N          
Sbjct: 9   RALLDGLKDGLIVSCQVQKDDPIYTDDIVVKMAEAAKWA---GAVAIRANS--------- 56

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVN 149
                     P+     I A+   + +P+    +I  DD    +    +  +++ ++G  
Sbjct: 57  ----------PEQ----IKAIKDKVDLPMIGLWKIWHDDTDVFITPTMDAARAVWEAGAE 102

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
            I +     I    +           +D++  +K+E P+  I     + +M +A + +  
Sbjct: 103 IIALDCTSQITHENTQA---------WDLIKTVKQEIPEAIIFA--DVSNMEEAARAVEN 151

Query: 209 SVD 211
             D
Sbjct: 152 GAD 154


>gi|183598290|ref|ZP_02959783.1| hypothetical protein PROSTU_01677 [Providencia stuartii ATCC 25827]
 gi|188020462|gb|EDU58502.1| hypothetical protein PROSTU_01677 [Providencia stuartii ATCC 25827]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V ++  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSKVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + E F 
Sbjct: 85  SVEDAAQILSFGADKISINSPALSDPTLISRLAERFG 121


>gi|111018311|ref|YP_701283.1| oxidoreductase [Rhodococcus jostii RHA1]
 gi|110817841|gb|ABG93125.1| probable oxidoreductase [Rhodococcus jostii RHA1]
          Length = 366

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 23/165 (13%), Positives = 53/165 (32%), Gaps = 19/165 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKA--LSIPVTVKCRIGV---------DDQIPAVALRNLVK 141
           +G        ++ + + A+       +PV V+               D        +LV+
Sbjct: 203 YGGSFTGRVRLLLEVVEAVRGVWPAELPVFVRVSATDWLSEEPGLDADSWTPDQTVSLVQ 262

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           ++   GV+ + + +      G++       P         I+ E   +     G + +  
Sbjct: 263 ALADLGVDLVDVSSG-----GVASARIPIGPGYQVPFARRIQNETT-VPAAAVGLITEPE 316

Query: 202 QALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           QA +I+       V +GR   ++           +  +T   P +
Sbjct: 317 QAERIVESGEAVAVFLGRELLRDPYWPRKAALALNAQVTPQIPAQ 361


>gi|148656559|ref|YP_001276764.1| isopentenyl pyrophosphate isomerase [Roseiflexus sp. RS-1]
 gi|148568669|gb|ABQ90814.1| isopentenyl-diphosphate delta-isomerase, type 2 [Roseiflexus sp.
           RS-1]
          Length = 345

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 23/139 (16%), Positives = 47/139 (33%), Gaps = 26/139 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAIL 160
           I  +C  L +PV  K       ++         + +  +GV  I +              
Sbjct: 180 IEEVCLRLDVPVIAK-------EVGNGIGAATARRLVDAGVKIIDVAGAGGTSWSEVERY 232

Query: 161 KGLSPKDNRKIPN-LDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
           +  + +  +       +     + + +++   PD+ I  +GG+   +  A  I    D  
Sbjct: 233 RHTTGRGAQVAGAFAGWGIPTTEAIRQVRAALPDITIIGSGGVRSGVDVAKAIALGADL- 291

Query: 214 MIGRAAYKNSAMLTTVDEY 232
               AA    A++  VDE 
Sbjct: 292 ----AATARPALIPAVDER 306


>gi|330974173|gb|EGH74239.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 363

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLAESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          V E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPVAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|259501835|ref|ZP_05744737.1| N-acetylmannosamine-6-P epimerase [Lactobacillus antri DSM 16041]
 gi|259170160|gb|EEW54655.1| N-acetylmannosamine-6-P epimerase [Lactobacillus antri DSM 16041]
          Length = 196

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 42/129 (32%), Gaps = 25/129 (19%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGI--WIHA 155
           + + + D +  M            R    D +       L  V+   + G + I   +H 
Sbjct: 76  HHEELADIVEQM------------RAEFPDTLLMADTDRLESVEIANQLGFDMIGTTMHG 123

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVM 214
                +GL+  DN      D++   E+        +   G ++  ++  + L      V+
Sbjct: 124 YTPATEGLNVADN------DFEYSKEVVDLAKA-PVIAEGKIDSPAKLKRCLELGCHAVV 176

Query: 215 IGRAAYKNS 223
           +G  A    
Sbjct: 177 VG-GAITRP 184


>gi|302557044|ref|ZP_07309386.1| 2,4-dienoyl-CoA reductase [Streptomyces griseoflavus Tu4000]
 gi|302474662|gb|EFL37755.1| 2,4-dienoyl-CoA reductase [Streptomyces griseoflavus Tu4000]
          Length = 671

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     V  R+ + D +P  +  +    L K+++ +G     I+      +
Sbjct: 198 EIVRRVREAVGEDFIVIYRLSMLDLVPGGSTLDEVITLAKAVEAAGAT--IINTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   Y  V   +  E     +  N  +     A ++L     D V + R 
Sbjct: 256 ARIPTIATSVPRGAYTWVTKRLMGEVSVPLVTTNR-INTPELAERLLAEGTADMVSVARP 314

Query: 219 AYKNS 223
              + 
Sbjct: 315 MLADP 319


>gi|295130526|ref|YP_003581189.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes SK137]
 gi|291377114|gb|ADE00969.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes SK137]
          Length = 307

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 44  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 97

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 98  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 157

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 158 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 217

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 218 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 257


>gi|121698219|ref|XP_001267752.1| FMN binding oxidoreductase, putative [Aspergillus clavatus NRRL 1]
 gi|119395894|gb|EAW06326.1| FMN binding oxidoreductase, putative [Aspergillus clavatus NRRL 1]
          Length = 427

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 66/196 (33%), Gaps = 35/196 (17%)

Query: 61  KLVEAAKIVEDFGYNEINL------------NVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           + ++ A+++ D G++ + L            N   P   +   ++G         V D +
Sbjct: 171 QFIDTARLMADAGFSGVELHGAHGYLIDQFLN---PKTNLRTDAYGGSPENRAKFVLDIL 227

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNL--VKSIKKSGVNGIWIHARK--------- 157
           AA+ K +     +  +    D   +     +  +K +  +G++ + +             
Sbjct: 228 AAIRKVVPPTFCIGIKFNSADHSSSAFEDTMTQIKLLVDAGIDFLEVSGGTYEDPQMVAS 287

Query: 158 -----AILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS- 209
                A       K  R +    +  +   E +K  P L + L GG    + A   L   
Sbjct: 288 NPVAAAAAAAAPQKSQRTLAREAFFLEFARETRKRFPTLVLMLTGGFRTRAGAQSALAEN 347

Query: 210 -VDGVMIGRAAYKNSA 224
             D V IGR A    +
Sbjct: 348 ACDLVGIGRPAAVKPS 363


>gi|327470764|gb|EGF16220.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK330]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|320640154|gb|EFX09726.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. G5101]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/188 (11%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|319947834|ref|ZP_08022023.1| oxidoreductase [Dietzia cinnamea P4]
 gi|319438504|gb|EFV93435.1| oxidoreductase [Dietzia cinnamea P4]
          Length = 687

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 65/187 (34%), Gaps = 33/187 (17%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHE-----------GSFGACLMLNPDIVGDCIAAM 111
            +AA+ +   G + I ++V      +               +G  L+    +  + I+A+
Sbjct: 159 ADAAERIAKAGADAIEIHVA--HGYILGVFLNKRDNQRTDEYGGSLVNRARLACEVISAV 216

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLSPK 166
            + +  S+ V V+       Q   + L   +   +  +K+G + I +        G +P 
Sbjct: 217 KERVGDSLAVLVRVSGEEYGQEGGLELDEAILASQLFEKAGADAIHVTG-----WGRNPF 271

Query: 167 DNRKIPNLDYDIV------YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
           DN     L  D +          K+   + +   G +     A + +    VD   +GR 
Sbjct: 272 DNFTDGPL-PDTIGAYVDNAAAIKQAVSVPVIAVGRML-PEVAEQAIDDGKVDFAAMGRQ 329

Query: 219 AYKNSAM 225
              +  +
Sbjct: 330 LLADPDL 336


>gi|311068778|ref|YP_003973701.1| tryptophan synthase subunit alpha [Bacillus atrophaeus 1942]
 gi|310869295|gb|ADP32770.1| tryptophan synthase subunit alpha [Bacillus atrophaeus 1942]
          Length = 267

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 47/131 (35%), Gaps = 12/131 (9%)

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
              +   L+   + +   +        +P     ++  + +   V   +LV    +S + 
Sbjct: 104 NKEYFFALLRE-NHIDGLL-----VPDLPFEESAQLQQECKKNNVTYISLVAPTSESRLK 157

Query: 150 GIWIHARKAIL----KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            I   A   +      G++   N    +  Y  +  +K E   + + +  G+    Q +K
Sbjct: 158 KITEQAEGFVYCVSSLGVTGVRNEF-DSAVYSFIRTVK-ELSSVPVAVGFGISSREQVIK 215

Query: 206 ILPSVDGVMIG 216
           +    DGV++G
Sbjct: 216 MNEMCDGVVVG 226


>gi|209759118|gb|ACI77871.1| putative NADPH dehydrogenase [Escherichia coli]
 gi|320645451|gb|EFX14460.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H- str. 493-89]
 gi|320650762|gb|EFX19219.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H- str. H 2687]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/188 (11%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|225626482|ref|ZP_03784521.1| tryptophan synthase, alpha subunit [Brucella ceti str. Cudo]
 gi|260169514|ref|ZP_05756325.1| tryptophan synthase subunit alpha [Brucella sp. F5/99]
 gi|261759042|ref|ZP_06002751.1| tryptophan synthase subunit alpha [Brucella sp. F5/99]
 gi|225618139|gb|EEH15182.1| tryptophan synthase, alpha subunit [Brucella ceti str. Cudo]
 gi|261739026|gb|EEY27022.1| tryptophan synthase subunit alpha [Brucella sp. F5/99]
          Length = 279

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRRIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|194444842|ref|YP_002042486.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194403505|gb|ACF63727.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYASRMRFAVEVVRAVRQRVGNDFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVVNGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|15803622|ref|NP_289655.1| putative NADPH dehydrogenase [Escherichia coli O157:H7 EDL933]
 gi|15833217|ref|NP_311990.1| NADPH dehydrogenase [Escherichia coli O157:H7 str. Sakai]
 gi|168749327|ref|ZP_02774349.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4113]
 gi|168754056|ref|ZP_02779063.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4401]
 gi|168762038|ref|ZP_02787045.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4501]
 gi|168769493|ref|ZP_02794500.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4486]
 gi|168773258|ref|ZP_02798265.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4196]
 gi|168781219|ref|ZP_02806226.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4076]
 gi|168785959|ref|ZP_02810966.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC869]
 gi|168797676|ref|ZP_02822683.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC508]
 gi|195937227|ref|ZP_03082609.1| putative NADPH dehydrogenase [Escherichia coli O157:H7 str. EC4024]
 gi|208807112|ref|ZP_03249449.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4206]
 gi|208812646|ref|ZP_03253975.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4045]
 gi|208821831|ref|ZP_03262151.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4042]
 gi|209399199|ref|YP_002272554.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4115]
 gi|254795032|ref|YP_003079869.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O157:H7 str. TW14359]
 gi|261228093|ref|ZP_05942374.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O157:H7 str. FRIK2000]
 gi|261254949|ref|ZP_05947482.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O157:H7 str. FRIK966]
 gi|291284459|ref|YP_003501277.1| 2,4-dienoyl-CoA reductase [Escherichia coli O55:H7 str. CB9615]
 gi|12517668|gb|AAG58214.1|AE005538_1 putative NADPH dehydrogenase [Escherichia coli O157:H7 str. EDL933]
 gi|13363436|dbj|BAB37386.1| putative NADPH dehydrogenase [Escherichia coli O157:H7 str. Sakai]
 gi|187771008|gb|EDU34852.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4196]
 gi|188016361|gb|EDU54483.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4113]
 gi|189001019|gb|EDU70005.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4076]
 gi|189358614|gb|EDU77033.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4401]
 gi|189361417|gb|EDU79836.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4486]
 gi|189367591|gb|EDU86007.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4501]
 gi|189374009|gb|EDU92425.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC869]
 gi|189379825|gb|EDU98241.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC508]
 gi|208726913|gb|EDZ76514.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4206]
 gi|208733923|gb|EDZ82610.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4045]
 gi|208741954|gb|EDZ89636.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4042]
 gi|209160599|gb|ACI38032.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC4115]
 gi|209759120|gb|ACI77872.1| putative NADPH dehydrogenase [Escherichia coli]
 gi|209759122|gb|ACI77873.1| putative NADPH dehydrogenase [Escherichia coli]
 gi|209759124|gb|ACI77874.1| putative NADPH dehydrogenase [Escherichia coli]
 gi|209759126|gb|ACI77875.1| putative NADPH dehydrogenase [Escherichia coli]
 gi|254594432|gb|ACT73793.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O157:H7 str. TW14359]
 gi|290764332|gb|ADD58293.1| 2,4-dienoyl-CoA reductase [Escherichia coli O55:H7 str. CB9615]
 gi|320189433|gb|EFW64092.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. EC1212]
 gi|320656141|gb|EFX24053.1| 2,4-dienoyl-CoA reductase [Escherichia coli O55:H7 str. 3256-97 TW
           07815]
 gi|320661831|gb|EFX29239.1| 2,4-dienoyl-CoA reductase [Escherichia coli O55:H7 str. USDA 5905]
 gi|320666982|gb|EFX33958.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. LSU-61]
 gi|326337785|gb|EGD61619.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. 1125]
 gi|326347350|gb|EGD71075.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. 1044]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 22/188 (11%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|20089116|ref|NP_615191.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Methanosarcina
           acetivorans C2A]
 gi|22095764|sp|Q8TU55|HIS4_METAC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|19913982|gb|AAM03671.1| N-(5-phospho-D-ribosylformimino)-5-amino-1-(5-phosphoribosyl)-4-
           imidazole carboxamide isomerase [Methanosarcina
           acetivorans C2A]
          Length = 245

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 74/187 (39%), Gaps = 41/187 (21%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
           + +EK +++Q+GG  I    +AA ++E  G + I L              G   + NP++
Sbjct: 74  ACREKGVSIQVGGG-IRSFEDAASLLE-LGVSRIIL--------------GTAALQNPEL 117

Query: 104 VGD--------CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
           V          C+     A +  +++K       Q P    R   +    +G        
Sbjct: 118 VKQLSDAFGSSCVNVALDAKNGKISIKGWTEECAQTPVEMGREFEEL--GAGSLLFTNID 175

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGV 213
            + +++G++P   R++             E+  + +  +GG+  +   LK+L      GV
Sbjct: 176 TEGLMQGVNPGPTRELV------------ESVSIPVIASGGVSSLED-LKVLKQTGASGV 222

Query: 214 MIGRAAY 220
           ++G A Y
Sbjct: 223 VVGSALY 229


>gi|312136170|ref|YP_004003508.1| Radical SAM domain-containing protein [Caldicellulosiruptor
           owensensis OL]
 gi|311776221|gb|ADQ05708.1| Radical SAM domain protein [Caldicellulosiruptor owensensis OL]
          Length = 351

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 29/166 (17%), Positives = 59/166 (35%), Gaps = 34/166 (20%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++VE AK     GY+ + L              G  +    D +   I  + + + + +
Sbjct: 87  DEIVEVAKRAYQMGYHTVVLQS------------GEDMFYTKDRMCSIIKKIKENVDVAI 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+       D+          K+ K +G +   +               +  P + ++  
Sbjct: 135 TLSIGERSYDEY---------KAFKDAGADRFLMR----FETSNEKLYRQYHPGMSFEKR 181

Query: 180 YEIKKENPDL--------FIGLNG-GLEDMSQALKILPSVDGVMIG 216
            E  K   +L         IGL G  ++D++Q + ++  +D  MIG
Sbjct: 182 IECLKWFKNLGYELGTGFLIGLPGQTIDDLAQDIILVKELDADMIG 227


>gi|170686594|ref|ZP_02877815.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0465]
 gi|254684629|ref|ZP_05148489.1| NADPH dehydrogenase NamA [Bacillus anthracis str. CNEVA-9066]
 gi|170669670|gb|EDT20412.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           anthracis str. A0465]
          Length = 345

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K  GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKGQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|118467802|ref|YP_888477.1| dihydroorotate dehydrogenase 2 [Mycobacterium smegmatis str. MC2
           155]
 gi|189038432|sp|A0QZY9|PYRD_MYCS2 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|118169089|gb|ABK69985.1| dihydroorotate oxidase [Mycobacterium smegmatis str. MC2 155]
          Length = 354

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 9/109 (8%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILK---- 161
            +AA+    + PV VK    + D      + +L   +  +G+       +R  +L     
Sbjct: 198 ILAAVKAETTKPVLVKIAPDLSDSD-IDEIADLAVELGLAGIVATNTTVSRDGLLTPGVA 256

Query: 162 --GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL 207
             G      R +     +++  + +   D L +   GG+E    A + +
Sbjct: 257 DLGPGGISGRPVARRSAEVLRRLYRRVGDKLVLISVGGIETADDAWERI 305


>gi|330981706|gb|EGH79809.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           aptata str. DSM 50252]
          Length = 363

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLAESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          V E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPVAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|22126507|ref|NP_669930.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           KIM 10]
 gi|45441257|ref|NP_992796.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108806835|ref|YP_650751.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           Antiqua]
 gi|108812598|ref|YP_648365.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           Nepal516]
 gi|149366464|ref|ZP_01888498.1| histidine biosynthesic protein (cyclase) [Yersinia pestis
           CA88-4125]
 gi|153947225|ref|YP_001401403.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia
           pseudotuberculosis IP 31758]
 gi|165924716|ref|ZP_02220548.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Orientalis str. F1991016]
 gi|165939550|ref|ZP_02228095.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Orientalis str. IP275]
 gi|166009359|ref|ZP_02230257.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Antiqua str. E1979001]
 gi|166211348|ref|ZP_02237383.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Antiqua str. B42003004]
 gi|167400396|ref|ZP_02305909.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Antiqua str. UG05-0454]
 gi|167421889|ref|ZP_02313642.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Orientalis str. MG05-1020]
 gi|167423943|ref|ZP_02315696.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Mediaevalis str. K1973002]
 gi|167470867|ref|ZP_02335571.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis FV-1]
 gi|218928684|ref|YP_002346559.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           CO92]
 gi|229841525|ref|ZP_04461684.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis biovar Orientalis str. PEXU2]
 gi|229843636|ref|ZP_04463779.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis biovar Orientalis str. India 195]
 gi|229894262|ref|ZP_04509445.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis Pestoides A]
 gi|229902992|ref|ZP_04518108.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis Nepal516]
 gi|270486778|ref|ZP_06203852.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis KIM D27]
 gi|294503518|ref|YP_003567580.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           Z176003]
 gi|20454973|sp|Q8ZFY0|HIS6_YERPE RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|122979734|sp|Q1C9R6|HIS6_YERPA RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|122980070|sp|Q1CGW5|HIS6_YERPN RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|167012225|sp|A7FJH5|HIS6_YERP3 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|21959504|gb|AAM86181.1|AE013864_8 imidazole glycerol phosphate synthase subunit; imidazole glycerol
           phsphate synthase holoenzyme [Yersinia pestis KIM 10]
 gi|45436117|gb|AAS61673.1| histidine biosynthesic protein (cyclase) [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108776246|gb|ABG18765.1| imidazole glycerol phosphate synthase subunit hisF [Yersinia pestis
           Nepal516]
 gi|108778748|gb|ABG12806.1| imidazole glycerol phosphate synthase subunit hisF [Yersinia pestis
           Antiqua]
 gi|115347295|emb|CAL20189.1| histidine biosynthesic protein (cyclase) [Yersinia pestis CO92]
 gi|149290838|gb|EDM40913.1| histidine biosynthesic protein (cyclase) [Yersinia pestis
           CA88-4125]
 gi|152958720|gb|ABS46181.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pseudotuberculosis IP 31758]
 gi|165912466|gb|EDR31098.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Orientalis str. IP275]
 gi|165923776|gb|EDR40908.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Orientalis str. F1991016]
 gi|165991914|gb|EDR44215.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Antiqua str. E1979001]
 gi|166207119|gb|EDR51599.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Antiqua str. B42003004]
 gi|166960374|gb|EDR56395.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Orientalis str. MG05-1020]
 gi|167050345|gb|EDR61753.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Antiqua str. UG05-0454]
 gi|167056792|gb|EDR66555.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis biovar Mediaevalis str. K1973002]
 gi|229679902|gb|EEO76002.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis Nepal516]
 gi|229689244|gb|EEO81307.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis biovar Orientalis str. India 195]
 gi|229697891|gb|EEO87938.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis biovar Orientalis str. PEXU2]
 gi|229703660|gb|EEO90676.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis Pestoides A]
 gi|262361561|gb|ACY58282.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           D106004]
 gi|262365699|gb|ACY62256.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           D182038]
 gi|270335282|gb|EFA46059.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pestis KIM D27]
 gi|294353977|gb|ADE64318.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           Z176003]
 gi|320015589|gb|ADV99160.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Yersinia pestis biovar Medievalis str. Harbin 35]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 85  SVEDASQILTFGADKISINSPALADPTLITRLADRYG 121


>gi|314968458|gb|EFT12556.1| 2-enoate reductase family protein [Propionibacterium acnes
           HL037PA1]
          Length = 539

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|269795384|ref|YP_003314839.1| imidazole glycerol phosphate synthase subunit hisF [Sanguibacter
           keddieii DSM 10542]
 gi|269097569|gb|ACZ22005.1| imidazole glycerol phosphate synthase subunit hisF [Sanguibacter
           keddieii DSM 10542]
          Length = 257

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 11/115 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L ++   +G + +        L   +   NR+     YD+V    +E   + + + GG+
Sbjct: 35  ELARTYDAAGADELT------FLDVSASSGNRETT---YDVVRRTAEEVF-IPLTVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
             +    ++L    D V +  AA     ++  + + F + +   S    RV  D 
Sbjct: 85  RTVEDVDRLLRAGADKVGVNTAAIARPELIAEIADRFGSQVLVLSVDARRVRDDV 139


>gi|228907775|ref|ZP_04071629.1| NADPH dehydrogenase [Bacillus thuringiensis IBL 200]
 gi|228851863|gb|EEM96663.1| NADPH dehydrogenase [Bacillus thuringiensis IBL 200]
          Length = 319

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 26/136 (19%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGSQAEQILNDN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|170024756|ref|YP_001721261.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia
           pseudotuberculosis YPIII]
 gi|226702017|sp|B1JPW5|HIS6_YERPY RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|169751290|gb|ACA68808.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pseudotuberculosis YPIII]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 85  SVEDASQILTFGADKISINSPALADPTLITRLADRYG 121


>gi|39998419|ref|NP_954370.1| Oye family NADH-dependent flavin oxidoreductase [Geobacter
           sulfurreducens PCA]
 gi|39985366|gb|AAR36720.1| NADH-dependent flavin oxidoreductase, Oye family [Geobacter
           sulfurreducens PCA]
 gi|298507364|gb|ADI86087.1| NADH-dependent flavin oxidoreductase, Oye family [Geobacter
           sulfurreducens KN400]
          Length = 374

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 23/186 (12%), Positives = 60/186 (32%), Gaps = 26/186 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             + A+   ++G++ + L+            P        +G  L      + +   A+ 
Sbjct: 147 FADGARRAREWGFDAVQLHAAHGYLINQFLSPLTNHRTDHYGGNLESRALFLLETCRAVR 206

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA-------RKAILK 161
           +A+     V  ++   D +           + + + + G++ I +         R A+ +
Sbjct: 207 RAVGKEFPVMVKLNGSDNLAGGFDLDEAVQVARMLDEEGIDAIEVSGGTPASGARTAVRQ 266

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAA 219
           G+  ++       +    Y IK       + + GG         ++     D V + R  
Sbjct: 267 GIETREQEAY---NLPSAYRIKNAV-SCPVMVVGGFRSFELVEGVIRREEADYVALSRPL 322

Query: 220 YKNSAM 225
            +   +
Sbjct: 323 IREPHL 328


>gi|324505181|gb|ADY42233.1| NADH-dependent flavin oxidoreductase [Ascaris suum]
          Length = 857

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 61/188 (32%), Gaps = 25/188 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
            +   AA   ++ G++ + +   C                    +G  L     I+   I
Sbjct: 169 EQYAYAATFSQECGFDGVEI--SCAYFFALGQFLTHGENTRTDEYGGSLENRARILFRII 226

Query: 109 AAMCKALSIP----VTVKCRI-GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
            A+   +  P    + +K      +           ++S++K+G + I I      L   
Sbjct: 227 QAIRMRVRRPNNFAIGLKLFSGNFEPDYNEDEFGTFIRSVEKTGFDYITITGGHYYLL-K 285

Query: 164 SPKDNRKIPNLDYD----IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGR 217
             K+  +I N        IV  IK+      + +NGG   ++   + +      GV + R
Sbjct: 286 ELKEGEEIANKHEQFYQAIVPVIKRNLTRTKLYMNGGFVTLADMCEAIRSGWAMGVSLAR 345

Query: 218 AAYKNSAM 225
                  +
Sbjct: 346 PVAAEPGL 353


>gi|311103804|ref|YP_003976657.1| 2-amninobenzoyl-CoA monooxygenase/reductase [Achromobacter
           xylosoxidans A8]
 gi|310758493|gb|ADP13942.1| 2-amninobenzoyl-CoA monooxygenase/reductase 1 [Achromobacter
           xylosoxidans A8]
          Length = 783

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 33/184 (17%), Positives = 60/184 (32%), Gaps = 35/184 (19%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVGDC 107
            V AA+  E  G++ + L   C    +               +G  L   +  P  V   
Sbjct: 568 FVAAARRAEQAGFDWLEL--HCAHGYLLSSFISPLTNHRIDEYGGSLENRLRFPLEVFHA 625

Query: 108 IAAMC-KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + A+  +   + V +     V+  I A     + +  K +G + I   +   + K   P 
Sbjct: 626 VRAVWPETKPMSVRISASDWVEGGITADDAVAIARHFKDAGADMIDCSSG-QVSKEEKPV 684

Query: 167 DNR--KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA---AYK 221
             R  + P  D      ++ E   +     G + +   A  I+ S      GRA   A  
Sbjct: 685 YGRMFQTPFAD-----RVRNEAG-IPTIAVGAIFEADHANGIIAS------GRADLCALA 732

Query: 222 NSAM 225
              +
Sbjct: 733 RPHL 736


>gi|261493040|ref|ZP_05989581.1| flavin reductase [Mannheimia haemolytica serotype A2 str. BOVINE]
 gi|261496694|ref|ZP_05993073.1| flavin reductase [Mannheimia haemolytica serotype A2 str. OVINE]
 gi|261307663|gb|EEY08987.1| flavin reductase [Mannheimia haemolytica serotype A2 str. OVINE]
 gi|261311317|gb|EEY12479.1| flavin reductase [Mannheimia haemolytica serotype A2 str. BOVINE]
          Length = 354

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 33/218 (15%), Positives = 70/218 (32%), Gaps = 23/218 (10%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINL--- 79
           +   AI  G+    L ++ Q      ++   ++  LV+A     K   + G++ I +   
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRELTTDEVKALVQAFKDSVKRAVEAGFDTIEIHGA 172

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIP 132
                     P +      +G   ML  + V       M   + + V +  +   ++   
Sbjct: 173 HGYLIHQFYSPKSNQRSDEYGQDKMLFGEQVIQAAREVMPSEMPLIVRISAQEYGENGFG 232

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 + K    +G + + I      +                D   ++K       + 
Sbjct: 233 LDYGLQVAKRFADAGADVLDISGGGDGVLHAGNHPEFYAG-YQVDFARQVKLATGK-PVI 290

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             G L++ +    IL     D V +GRA  ++   +L 
Sbjct: 291 AVGMLDNPAVGDHILGMGDADLVAVGRALLRDPYWVLN 328


>gi|82778407|ref|YP_404756.1| putative NADPH dehydrogenase [Shigella dysenteriae Sd197]
 gi|309785395|ref|ZP_07680026.1| 2,4-dienoyl-CoA reductase [Shigella dysenteriae 1617]
 gi|81242555|gb|ABB63265.1| putative NADPH dehydrogenase [Shigella dysenteriae Sd197]
 gi|308926515|gb|EFP71991.1| 2,4-dienoyl-CoA reductase [Shigella dysenteriae 1617]
          Length = 672

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 19/127 (14%), Positives = 43/127 (33%), Gaps = 11/127 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + ++A+ + +     +  R+     V+D         L ++I+ +G     I+     
Sbjct: 195 AVEVVSAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINTGIGW 252

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
            +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+   
Sbjct: 253 HEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV--- 308

Query: 219 AYKNSAM 225
           +     +
Sbjct: 309 SMARPFL 315


>gi|154244934|ref|YP_001415892.1| NADH:flavin oxidoreductase/NADH oxidase [Xanthobacter autotrophicus
           Py2]
 gi|154159019|gb|ABS66235.1| NADH:flavin oxidoreductase/NADH oxidase [Xanthobacter autotrophicus
           Py2]
          Length = 387

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 25/140 (17%), Positives = 48/140 (34%), Gaps = 14/140 (10%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGV 148
           +G         + + + A+       + +  R GV +  P          L + +K  G+
Sbjct: 200 YGGDFTGRSRFLVEVVEAVRAEWPERLPLSMRFGVTEFAPGSQTIEDSVALARLLKPKGL 259

Query: 149 NGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           + + +         +     +   +P  +      I++E  D+    N  L D   A  I
Sbjct: 260 DLVDVSFGGNSGQAQTPWEAEGFMVPAAE-----RIRREA-DILTAANWNLADPHFADAI 313

Query: 207 LPS--VDGVMIGRAAYKNSA 224
           +    VD VM+GR    N  
Sbjct: 314 VREARVDVVMLGRPMLANPH 333


>gi|150017021|ref|YP_001309275.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
 gi|149903486|gb|ABR34319.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium beijerinckii
           NCIMB 8052]
          Length = 359

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 30/178 (16%), Positives = 62/178 (34%), Gaps = 21/178 (11%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACL 97
           E+ +++QI          AA   +  GY+ I ++            P        +G  +
Sbjct: 137 EEIVSIQI------DFANAALRAKKAGYDGIQIHAAHGYLLSKFLTPYYNRRTDEYGGSI 190

Query: 98  MLNPDIVGDCIAAMCKALSI--PVTVK--CRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
                ++ +    +   +    PV VK  C   +D  +     + + K ++  G++ + I
Sbjct: 191 DNRSRMLIETYKKIRDKVGKDYPVLVKINCEDFMDQGMTFEECKYVCKKLENLGIDAVEI 250

Query: 154 HARKAILKGLSPKDNRKIPNLD--YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
                  +       + +      Y    E  KE  ++ +   GG+ D+S   KIL  
Sbjct: 251 SGGSLSSRPNESYSRKIVKGQAPYYTFYAERIKEEVNIPVISVGGIRDISALTKILNE 308


>gi|319645129|ref|ZP_07999362.1| NADPH dehydrogenase [Bacillus sp. BT1B_CT2]
 gi|317392938|gb|EFV73732.1| NADPH dehydrogenase [Bacillus sp. BT1B_CT2]
          Length = 359

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 30/192 (15%), Positives = 66/192 (34%), Gaps = 19/192 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             + A+  +  G++ I ++            P +   E  +G        ++ + I A+ 
Sbjct: 167 FKKGAERAKAAGFDIIEIHGAHGYLINEFLSPLSNKREDEYGGSPENRYRLLREVIDAVK 226

Query: 113 KALSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  + P  V V         +         K +K+ GV+ I + +   +     P D   
Sbjct: 227 EVWAGPLFVRVSASDYKTKGLDVADYVGFAKWMKEQGVDLIDVSSGAVV-----PADINV 281

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
            P         I+ +  ++  G  G +    QA +IL +   D + + R   ++     T
Sbjct: 282 FPGYQVGFADTIRAQA-EIQTGAVGLITSGLQAEEILQNGRADLIFVARELLRDPYWPKT 340

Query: 229 VDEYFSNPLTGS 240
             +  +  + G 
Sbjct: 341 AAKQLNTKIEGP 352


>gi|239996222|ref|ZP_04716746.1| imidazole glycerol phosphate synthase subunit HisF [Alteromonas
           macleodii ATCC 27126]
          Length = 270

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 15/98 (15%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K+G + +            +  D R +       + ++     D+   + GG++
Sbjct: 35  LAEQYAKAGADELV------FYDITASSDARVVDKSWVSRIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  A +IL    D + I   A  N  ++  + + +  
Sbjct: 85  SIEDAGRILEMGADKISINSPALNNPDLINQLHDVYGQ 122


>gi|289810195|ref|ZP_06540824.1| 2,4-dieonyl-coa reductase [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 367

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 27/224 (12%), Positives = 67/224 (29%), Gaps = 39/224 (17%)

Query: 23  YTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           Y   +VA + ++      +          LQ+    I      A++  + GY+ + +   
Sbjct: 110 YQPHLVAPSAIQAPINRFMP-HELTHDEILQL----IDDFAHCAQLAREAGYDGVEV--- 161

Query: 83  CPSARVHEGSFGA--CLMLNPDI---------------VGDCIAAMCKALSIPVTVKCRI 125
                +    +     L    +                  + + A+ + +     +  R+
Sbjct: 162 -----MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMRFAVEVVRAVRQRVGNYFIIIYRL 216

Query: 126 GVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
            + D +           L ++I+ +G + I  +      +   P     +P   +  V  
Sbjct: 217 SMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIGWHEARIPTIATPVPRGAFSWVTR 274

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             K +  + +     + D   A  IL   D  M+   +     +
Sbjct: 275 KLKGHVSVPLIATNRINDPQVAETILTRGDADMV---SMARPFL 315


>gi|145598717|ref|YP_001162793.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia pestis
           Pestoides F]
 gi|167012226|sp|A4TKK8|HIS6_YERPP RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|145210413|gb|ABP39820.1| imidazole glycerol phosphate synthase subunit hisF [Yersinia pestis
           Pestoides F]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 85  SVEDASQILTFGADKISINSPALADPTLITRLADRYG 121


>gi|110639085|ref|YP_679294.1| dihydroorotate dehydrogenase 2 [Cytophaga hutchinsonii ATCC 33406]
 gi|110281766|gb|ABG59952.1| dihydroorotate dehydrogenase [Cytophaga hutchinsonii ATCC 33406]
          Length = 361

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 24/150 (16%), Positives = 54/150 (36%), Gaps = 20/150 (13%)

Query: 73  GYNEINLNVGCPS----ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD 128
             +   +NV  P+      + E      L+     V +      K++  P+ +K    + 
Sbjct: 185 CVDYFVVNVSSPNTPGLRALQEKGPLTELLNRLQEVNN-----QKSVPKPILLKIAPDLT 239

Query: 129 DQIPAVALRNLVKSIKKSGV---------NGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           ++     +  ++   K SG+         +G+     K    G+     + +     +++
Sbjct: 240 NEQL-DDIVEIITETKLSGIIATNTTISRDGLTTEKEKVEKIGMGGLSGKPLTVRSTEVI 298

Query: 180 -YEIKKENPDLFIGLNGGLEDMSQALKILP 208
            Y +KK N  + +   GG+     AL+ L 
Sbjct: 299 RYLVKKSNGSIPVIGVGGIHSPKDALEKLE 328


>gi|307824904|ref|ZP_07655126.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylobacter tundripaludum SV96]
 gi|307733951|gb|EFO04806.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methylobacter tundripaludum SV96]
          Length = 244

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 2/102 (1%)

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVD 230
              + D+++ I +  P++ + + GG+ D       L   V+ V+IG  A      +  + 
Sbjct: 59  KPRNADVIHAIVEAYPNVPVQIGGGIRDEETIQAYLNAGVEYVIIGTKAVNEPHFVRDMA 118

Query: 231 -EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            EY  + + G      +V  D W K+S       A+H    G
Sbjct: 119 LEYPRHIIVGLDAKDGKVAIDGWSKLSKHDVIDMAQHFEEYG 160


>gi|220918944|ref|YP_002494248.1| NADH:flavin oxidoreductase/NADH oxidase [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219956798|gb|ACL67182.1| NADH:flavin oxidoreductase/NADH oxidase [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 352

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 25/139 (17%), Positives = 49/139 (35%), Gaps = 11/139 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--VDDQIPAVALRNLVKSIKKSG 147
           ++G        +V +  AA+  A    +PV V+      V+    A     L +++K  G
Sbjct: 196 AYGGGFENRTRLVREVTAAVRAAWPEELPVLVRISATDWVEGGWDAEQSVELCRALKALG 255

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ + +        GL P     +         E  +    +  G  G +    QA  ++
Sbjct: 256 VDLVDVSTG-----GLVPGAKIPVGPGYQTGFAERIRREAGVATGSVGMITSPEQADHVI 310

Query: 208 --PSVDGVMIGRAAYKNSA 224
                D V++ R   ++  
Sbjct: 311 RSGQADLVLLARELLRDPH 329


>gi|51595893|ref|YP_070084.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia
           pseudotuberculosis IP 32953]
 gi|186894979|ref|YP_001872091.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia
           pseudotuberculosis PB1/+]
 gi|60392365|sp|Q66C54|HIS6_YERPS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226702016|sp|B2JZM4|HIS6_YERPB RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|51589175|emb|CAH20795.1| histidine biosynthesic protein (cyclase) [Yersinia
           pseudotuberculosis IP 32953]
 gi|186698005|gb|ACC88634.1| imidazoleglycerol phosphate synthase, cyclase subunit [Yersinia
           pseudotuberculosis PB1/+]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 85  SVEDASQILTFGADKISINSPALADPTLITRLADRYG 121


>gi|228476944|ref|ZP_04061589.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus salivarius SK126]
 gi|228251518|gb|EEK10663.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus salivarius SK126]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 43/119 (36%), Gaps = 11/119 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++  ++G + +        L   +  DNR+      D+V  +  +    F    GG+  
Sbjct: 36  ARAYYEAGCDELV------FLDITATSDNRETT---VDMVRRVADQVFIPFTVG-GGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +    K+L    D V +  +A  N  ++    + F N    ++    ++    W    A
Sbjct: 86  VEDMNKMLKAGADKVAVNSSALANPQLIADCAQKFGNQCVVAAIDAKKMADGSWHVFVA 144


>gi|226504364|ref|NP_001141081.1| hypothetical protein LOC100273163 [Zea mays]
 gi|194702554|gb|ACF85361.1| unknown [Zea mays]
          Length = 336

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 35/215 (16%), Positives = 68/215 (31%), Gaps = 58/215 (26%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNV-------GCPSARVHEGSFGACLMLNPDIVGDC 107
           G  D++   EA ++++  G + I L V         P  +    +        PD V   
Sbjct: 93  GDPDLATTAEALRLLDACGADVIELGVPFSDPYADGPVIQA-SAARALASGTTPDGVLAM 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------------- 152
           +  +   LS PV         + I    L +   ++K++GV+G+                
Sbjct: 152 LKEVTPELSCPV---VLFSYFNPIVRWGLADFAAAVKEAGVHGLIVPDLPYGNSCALTLR 208

Query: 153 -------------------------IHARKAILKGLSPKDNRKIPNLDYD-----IVYEI 182
                                    I         L+  +    P  + +     ++ E+
Sbjct: 209 TEAIKNSLELVLLTTPSTPADRMGEITRASRGFVYLATVNGVTGPRANVNTRVQSLIQEV 268

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           K+   D+ + +  G+       +I     DGV+IG
Sbjct: 269 KQ-VTDIPVAVGFGISKPEHVKQIAEWGADGVIIG 302


>gi|120402556|ref|YP_952385.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium vanbaalenii
           PYR-1]
 gi|119955374|gb|ABM12379.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium vanbaalenii
           PYR-1]
          Length = 402

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 40/213 (18%), Positives = 72/213 (33%), Gaps = 44/213 (20%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             AA++  D G++ + +++G          P        FG  L     +    + A+ +
Sbjct: 153 ANAARLAIDSGFDAVEIHLGHNYLASAFLSPLINRRTDEFGGSLENRAKVARGVVLAVRR 212

Query: 114 ALS--IPVTVK--CRIGVDDQIPAVALRNLVKSI-KKSGVNGIWIHARKAIL------KG 162
           A+   I VT K     GV   IP        K + +  G++ + + A  ++L      +G
Sbjct: 213 AVGDQIAVTAKLNMSDGVRGGIPLEESLQTAKWLEEDGGLDALELTAGSSLLNPMFLFRG 272

Query: 163 LSPK---DNRKIPNLDYDIVYEIKK--------------------ENPDLFIGLNGGLED 199
            +P         P L + I    KK                    +   L + L GG+ +
Sbjct: 273 GAPVKEFAGAFKPPLSWGIRMTGKKFMREYPYQEAYLMRDAKKFRDELKLPLILLGGITN 332

Query: 200 MSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDE 231
                  +    D V +GRA      +L  +  
Sbjct: 333 RDTMDRAMAEGFDFVAMGRALLAEPDLLNRIQA 365


>gi|73948476|ref|XP_533691.2| PREDICTED: similar to Protein KIAA0841 [Canis familiaris]
          Length = 633

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 241 SPIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
           +P+  R  +   R++     A +  Y  RH+HS   +++I  +++    G  +S   R  
Sbjct: 20  APVAARAPESTLRRLCLGQGADIWAYVLRHVHSQRSVKKIRGNLLWY--GHQDSPEARRK 77

Query: 297 LTVEAGASTATHHI--IETAFNLMIES 321
           L +EA  +     I  ++ +  L+ + 
Sbjct: 78  LELEATVARLRAEIQELDQSLELVEQE 104


>gi|77456554|ref|YP_346059.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           fluorescens Pf0-1]
 gi|91206944|sp|Q3KJI6|HIS4_PSEPF RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|77380557|gb|ABA72070.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           fluorescens Pf0-1]
          Length = 245

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P L I + GG+  +      +   V  V+IG  A K+ A +     
Sbjct: 60  PVNGEVVTAIAKRYPTLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACR 119

Query: 232 YFSNPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F   +  G       V  D W +IS       A+   + G
Sbjct: 120 AFPGKIIVGLDAKDGFVATDGWAEISTVQVIDLAKQFEADG 160


>gi|326492375|dbj|BAK01971.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326495500|dbj|BAJ85846.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326514746|dbj|BAJ99734.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 369

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 63/185 (34%), Gaps = 31/185 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
               +AA+   D G++ + ++ G  +  + E             +G  L        + +
Sbjct: 163 DDFRKAARNAIDAGFDGVEIHGG--NGYLIEQFLKDSANDRDDGYGGSLENRCRFALEVV 220

Query: 109 AAMCKALSI-PVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIW-IHARKAILK 161
           AA+ K +    V ++    +D     D  P     ++   +   G+  +  I  R A++ 
Sbjct: 221 AAVAKEVGAHRVGIRLSPFMDYMDCHDSDPHALGLHMATKLNDHGILYLHMIEPRMALVD 280

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAY 220
           G     +R +P          ++     FI  NGG +       +     D V  GR   
Sbjct: 281 GRRVVPHRLLPY---------REAFKGTFI-ANGGYDREEGDKAVSSGYADLVSFGRLFL 330

Query: 221 KNSAM 225
            N  +
Sbjct: 331 ANPDL 335


>gi|310780477|ref|YP_003968809.1| imidazole glycerol phosphate synthase subunit hisF [Ilyobacter
           polytropus DSM 2926]
 gi|309749800|gb|ADO84461.1| imidazole glycerol phosphate synthase subunit hisF [Ilyobacter
           polytropus DSM 2926]
          Length = 252

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 11/93 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           NL +   + G + +  +   A  +G           L  DIV ++  E   + + + GG+
Sbjct: 34  NLAEMYNEMGADELVFYDITATNEGR---------ELFSDIVEQVANEVF-IPLTVGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
             +    ++L    D V +   A KN  ++   
Sbjct: 84  NTLQDFDRVLKAGADKVSVNSGAIKNPELIREA 116


>gi|301166970|emb|CBW26549.1| putative 2-nitropropane dioxygenase [Bacteriovorax marinus SJ]
          Length = 315

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L    +++GV+ +     +A   G + +D     +L   +V  +     D+ I   GG
Sbjct: 125 PELALKCQQAGVDAVVAEGFEA--GGHNGRDEITTMSLIPQVVKAV-----DIPIIAAGG 177

Query: 197 LEDMSQALKILP-SVDGVMIG 216
           +      L  L    D V IG
Sbjct: 178 ISSGQSILATLALGADAVQIG 198


>gi|149185608|ref|ZP_01863924.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Erythrobacter sp. SD-21]
 gi|148830828|gb|EDL49263.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Erythrobacter sp. SD-21]
          Length = 244

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 56/137 (40%), Gaps = 21/137 (15%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVN 149
            G+  + +P+ V D        + + V  K  +   +   ++  V + +L +  + +GV 
Sbjct: 105 MGSAALKDPEFVKDMAREFEGGVVVAVDAKDGMVATEGWAEVSDVPVVDLARRFEDAGVA 164

Query: 150 G--IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA---- 203
                   R  +LKG           ++ D   ++ ++  D+ +  +GG++ +       
Sbjct: 165 ALLFTDIGRDGLLKG-----------VNLDATVDLARQV-DIPVIASGGVKGIDDIHVLS 212

Query: 204 LKILPSVDGVMIGRAAY 220
           L     ++GV+ GRA Y
Sbjct: 213 LYAKDGIEGVITGRALY 229


>gi|83747059|ref|ZP_00944104.1| protein with COG1902, NADH: flavin oxidoreductase and COG0654,
           2-polyprenyl-6-methoxyphenol hydroxylase & related
           FAD-dependent oxidoreducatse domains [Ralstonia
           solanacearum UW551]
 gi|207738497|ref|YP_002256890.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum
           IPO1609]
 gi|83726336|gb|EAP73469.1| protein with COG1902, NADH: flavin oxidoreductase and COG0654,
           2-polyprenyl-6-methoxyphenol hydroxylase & related
           FAD-dependent oxidoreducatse domains [Ralstonia
           solanacearum UW551]
 gi|206591865|emb|CAQ58771.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum
           IPO1609]
          Length = 785

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 64/217 (29%), Gaps = 29/217 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
              V AA +  + G++ + L   C           P   +    +G  L   +  P  V 
Sbjct: 555 DDFVRAAGLAVEAGFDWLEL--HCAHGYLLSSFISPLTNLRSDEYGGPLENRLRYPLEVF 612

Query: 106 DCIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
             + A+  A   P++V+      V   I       + +  K +G + I   + +     +
Sbjct: 613 CAVRAVWPA-DKPMSVRISAHDWVQGGITPDDAVEIARRFKAAGADMIDCSSGQ-----V 666

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           S K+      +      +  +    +     G + +      I+ +   D   + R    
Sbjct: 667 SKKEQPVYGRMFQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLA 726

Query: 222 NS-AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           N    L          L    P + R  K    +   
Sbjct: 727 NPAWALNEAARI--GYLDMPWPQQYRAGKLQLERNLE 761


>gi|297521368|ref|ZP_06939754.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli OP50]
          Length = 249

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 26  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 75

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + E F 
Sbjct: 76  SLEDAAKILSFGADKISINSPALADPTLITRLAERFG 112


>gi|225456230|ref|XP_002283095.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 421

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 171 RVEQTGIDALEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATVPVWAKMTPNI 229

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI 151
            D      +    +    SG  G+
Sbjct: 230 TD------ITQPARVALSSGCEGV 247


>gi|119773149|ref|YP_925889.1| oxidoreductase, FAD/FMN-binding [Shewanella amazonensis SB2B]
 gi|119765649|gb|ABL98219.1| oxidoreductase, FAD/FMN-binding [Shewanella amazonensis SB2B]
          Length = 368

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 69/202 (34%), Gaps = 30/202 (14%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEG 91
           LG +  ++    Q+ GA     V AA+     G + + L+       C    P       
Sbjct: 134 LGVTELDEDAIQQLIGA----FVTAAERAYRAGLDGVELHAAHYYLLCNFLNPVLNRRTD 189

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKKS 146
            +G  +     I+ + I  + + L     V  R+  ++    V +       +   +   
Sbjct: 190 RWGGSVENRTRILIEIIRGIRQQLPRQFLVGVRLSPENYANVVGIELQNQLAVANLLAAE 249

Query: 147 GVNGIWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
            ++ +          G S K  N K   L  +++  +        + + G + D   A +
Sbjct: 250 DIDYVH------FSMGDSFKLANGKNTALLSEVINAL---TGKTTLMMAGNIRDGEAAER 300

Query: 206 ILP-SVDGVMIGRAAYKNS-AM 225
           +L    D V IG +A  N   +
Sbjct: 301 VLSAGADLVAIGTSALGNPDWI 322


>gi|296103682|ref|YP_003613828.1| imidazole glycerol phosphate synthase subunit HisF [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058141|gb|ADF62879.1| imidazole glycerol phosphate synthase subunit HisF [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SAEDAAKILSFGADKISINSPALADPELITRLADRFG 121


>gi|289663415|ref|ZP_06484996.1| imidazole glycerol phosphate synthase subunit HisF [Xanthomonas
           campestris pv. vasculorum NCPPB702]
          Length = 258

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 48/134 (35%), Gaps = 15/134 (11%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           VK R  +D       +  L    +  G + +  +   A  +G S         +DY  V 
Sbjct: 21  VKFRDHIDMGD----IVELALRYRAQGADELVFYDIGASPEGRS---------VDYTWVE 67

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTG 239
            + +   D+   + GG+ D+  A  +L    D + I   A   + +++ + + F      
Sbjct: 68  RVARLI-DIPFCVAGGIGDVETARAVLHAGADKISINSPALGRAQLISELADAFGVQCVV 126

Query: 240 SSPIKTRVDKDFWR 253
                 R D   WR
Sbjct: 127 VGIDSIREDDGEWR 140


>gi|289427210|ref|ZP_06428926.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes J165]
 gi|289159679|gb|EFD07867.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes J165]
          Length = 307

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 44  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 97

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 98  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 157

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 158 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 217

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 218 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 257


>gi|220921385|ref|YP_002496686.1| acetylglutamate kinase [Methylobacterium nodulans ORS 2060]
 gi|254803277|sp|B8IM39|ARGB_METNO RecName: Full=Acetylglutamate kinase; AltName:
           Full=N-acetyl-L-glutamate 5-phosphotransferase; AltName:
           Full=NAG kinase; Short=AGK
 gi|219945991|gb|ACL56383.1| acetylglutamate kinase [Methylobacterium nodulans ORS 2060]
          Length = 304

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 43/209 (20%), Positives = 79/209 (37%), Gaps = 23/209 (11%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +R   R+     +   EM++A +I     K I+G+ + E   A+ + G D + +V+ A+ 
Sbjct: 89  FREGLRVTDEATVEVVEMVLAGSI----NKQIVGWISAEGGKAIGLCGKDGN-MVQ-ARR 142

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCRIGV 127
                 +  + N+        E      L+  P+ V   +  A+ KA  IPV     +G 
Sbjct: 143 ATRTVVDP-DSNI--------ERHVDLGLVGEPERVNRAVLDAVLKAELIPVLAPVAVGS 193

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D Q   V       +I  +G            + G+  KD + IP L  +    +  +  
Sbjct: 194 DGQTYNVNADTFAGAI--AGALRAKRLLLLTDVPGVLDKDKKLIPELSIEDCRRLIADGT 251

Query: 188 DLFIGLNGGLEDMSQAL-KILPSVDGVMI 215
                  G +  +   +  I   V+ V+I
Sbjct: 252 IT----GGMIPKIETCIYAIEQGVEAVVI 276


>gi|148273000|ref|YP_001222561.1| pyridoxal biosynthesis lyase PdxS [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830930|emb|CAN01874.1| conserved protein putatively involved in pyridoxine biosynthesis
           [Clavibacter michiganensis subsp. michiganensis NCPPB
           382]
          Length = 300

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 41/224 (18%), Positives = 66/224 (29%), Gaps = 70/224 (31%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I ED G   +      P+        G   M +PD++          +SIPV  K
Sbjct: 34  AEQARIAEDAGAVAVMALERVPAD--IRSQGGVARMSDPDLIDQI----KAEVSIPVMAK 87

Query: 123 CRI--------------GVDDQIPAVALRNLVKSIKKSG--------------------- 147
            RI                 D+   ++  + V  I K G                     
Sbjct: 88  ARIGHFVEAQVLQSLEVDYIDESEVLSPADYVNHIDKWGFTVPFVCGATTLGEALRRITE 147

Query: 148 ---------------VNGIWIHARK-----AILKGLSPKDNRKIPN---LDYDIVYEIKK 184
                          V+    H R        L  L+  +           YD+V E+ +
Sbjct: 148 GAAMIRSKGEAGTGDVSEATKHIRTIKSEIRTLSALTHDEIYVAAKELQAPYDLVLEVAR 207

Query: 185 --ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
             + P +     GG+   + A  ++    DGV +G   +   N 
Sbjct: 208 TGQLPVVLFTA-GGVATPADAAMMMQLGADGVFVGSGIFKSGNP 250


>gi|84687797|ref|ZP_01015667.1| FMN-dependent alpha-hydroxy acid dehydrogenase family protein
           [Maritimibacter alkaliphilus HTCC2654]
 gi|84664169|gb|EAQ10663.1| FMN-dependent alpha-hydroxy acid dehydrogenase family protein
           [Rhodobacterales bacterium HTCC2654]
          Length = 372

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 50/131 (38%), Gaps = 25/131 (19%)

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G  G  L  NPD   D +A + +    P+ VK           V    +   + ++GV+ 
Sbjct: 216 GHVGYQLRTNPDW--DYLAGLRETWDGPIIVK----------GVTDPEVAPRLAEAGVDA 263

Query: 151 IWI--HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKIL 207
           IW+  HA +      +                 I+   PD+ +  +GG+   +  A  I 
Sbjct: 264 IWLSNHAGRQFDGAPAALPALPA----------IRAALPDMPLIYDGGVNSGLDVARAIA 313

Query: 208 PSVDGVMIGRA 218
              D VM+G+A
Sbjct: 314 MGADFVMLGKA 324


>gi|325283313|ref|YP_004255854.1| NADPH dehydrogenase [Deinococcus proteolyticus MRP]
 gi|324315122|gb|ADY26237.1| NADPH dehydrogenase [Deinococcus proteolyticus MRP]
          Length = 371

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 80/238 (33%), Gaps = 28/238 (11%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLV----EAAKIVED 71
           +  +AL Y+E            + +   + +E         A   +      +  +I   
Sbjct: 145 IAPSALAYSE-------NYPQPREM---TPEEIAATPAAFAAAARRAEIAGFDTVEIHAA 194

Query: 72  FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIG--V 127
            GY  +      P +     ++G        ++ + + A+ +     +P+ V+      V
Sbjct: 195 HGY--LLHQFLSPLSNARTDAYGGTFENRIRLLLEVVRAVREVWPEHLPLLVRISATDWV 252

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-DYDIVYEIKKEN 186
           +          L + ++  GV+ + + +      GL P+    +  L        IK+  
Sbjct: 253 EGGWDLEQSAELARLLRFEGVDVLDVSSG-----GLDPRQQIAVEPLYQVPFAQAIKQAA 307

Query: 187 PDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           P+L +   G +E   QA ++L     D V +GRA  ++          F        P
Sbjct: 308 PELEVMTVGLIETPMQAEQVLQEGMADWVALGRALLRDPHWPQRAAREFGIAPALPQP 365


>gi|147918848|ref|YP_687426.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [uncultured
           methanogenic archaeon RC-I]
 gi|121685227|sp|Q0W0J3|HIS4_UNCMA RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|110622822|emb|CAJ38100.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [uncultured methanogenic archaeon RC-I]
          Length = 240

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           D+ + + GG+ D   A  +L   +D V++G AA KN  ++  + + F +  
Sbjct: 76  DVDVQVGGGIRDYETAKYLLSLGIDRVILGTAAIKNPDLVRQLADEFGSET 126


>gi|119356329|ref|YP_910973.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium
           phaeobacteroides DSM 266]
 gi|148839487|sp|A1BDS2|HIS4_CHLPD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|119353678|gb|ABL64549.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Chlorobium
           phaeobacteroides DSM 266]
          Length = 256

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 18/99 (18%), Positives = 40/99 (40%), Gaps = 11/99 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++    +K     + +    A L G           +++  + +I +E  D+ + + GG
Sbjct: 33  CDMAIIWRKQNAKMLHVVDLDAALTGEM---------VNFLKIEQIVREL-DIPLQVGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +    + L   V  V+IG AA  N  ++  V + + 
Sbjct: 83  IRSLDAVKRYLDIGVGRVVIGSAAVTNPGLIEEVLKIYR 121


>gi|310794927|gb|EFQ30388.1| NADH:flavin oxidoreductase/NADH oxidase [Glomerella graminicola
           M1.001]
          Length = 451

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 59  ISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
                 AA+ V   G++ I L             P+       +G  L     I+ +   
Sbjct: 174 ADDFAYAAEYVHRAGFDGIELHGAHGYLLAQFLSPTTNKRTDEYGGSLANRARIILEIAD 233

Query: 110 AMCKAL-----SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+   +     SI + V      +        R L  +++  G + + +       + L+
Sbjct: 234 AVRARVSDESFSIGIKVNSVEFQEGGFSTDDCRGLCAALEAHGFDFVELSGGT--YQSLA 291

Query: 165 PKDNRKIPNLD----YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
               R+          D    +  E       + GGL   +  +  L +VDGV + R
Sbjct: 292 FAHRRESTRRREAFFLDFAEAVIPELKRTKAYVTGGLRTTAAMVAALGTVDGVGLAR 348


>gi|254459996|ref|ZP_05073412.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhodobacterales bacterium HTCC2083]
 gi|206676585|gb|EDZ41072.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhodobacteraceae bacterium HTCC2083]
          Length = 239

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 23/128 (17%), Positives = 51/128 (39%), Gaps = 16/128 (12%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
            NPD+V +   A    +++ +     K       +   V L +L KS + +GV  I    
Sbjct: 108 ENPDLVREAAKAFPGHVAVGIDARGGKVATKGWAEETDVELTDLAKSFEDAGVAAII--- 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP---SVDG 212
                  ++     + PN+  +    + + +  + +  +GG+  +   + +      ++G
Sbjct: 165 ----YTDINRDGAMQGPNI--EATAALAR-SVSIPVIASGGVSSLEDLIALRECGAGLNG 217

Query: 213 VMIGRAAY 220
            + GRA Y
Sbjct: 218 AISGRALY 225


>gi|198283973|ref|YP_002220294.1| NADH:flavin oxidoreductase/NADH oxidase [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666012|ref|YP_002426610.1| oxidoreductase, FAD/FMN-binding [Acidithiobacillus ferrooxidans
           ATCC 23270]
 gi|198248494|gb|ACH84087.1| NADH:flavin oxidoreductase/NADH oxidase [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518225|gb|ACK78811.1| oxidoreductase, FAD/FMN-binding [Acidithiobacillus ferrooxidans
           ATCC 23270]
          Length = 358

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 27/142 (19%), Positives = 48/142 (33%), Gaps = 19/142 (13%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKC------RIGVDDQIPAVALRNLVKSIK 144
           +G  L     +  +  AA+       +P+ V+       R G D +   V    L K++K
Sbjct: 200 YGGSLENRMRLPLEITAAVRAVWPEDLPLWVRISATDWVRGGWDLEQSVV----LAKALK 255

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
             GV+ I   +      G++P                  ++   +     G + +  QA 
Sbjct: 256 DRGVDVIDCSSG-----GMTPDAVIPAGPGFQTPFASAIRQEVGMPTVAVGLITEAMQAE 310

Query: 205 KIL--PSVDGVMIGRAAYKNSA 224
            IL     D V + R   +N  
Sbjct: 311 HILVTEQADAVALARELLRNPY 332


>gi|170739199|ref|YP_001767854.1| acetylglutamate kinase [Methylobacterium sp. 4-46]
 gi|238688052|sp|B0UA74|ARGB_METS4 RecName: Full=Acetylglutamate kinase; AltName:
           Full=N-acetyl-L-glutamate 5-phosphotransferase; AltName:
           Full=NAG kinase; Short=AGK
 gi|168193473|gb|ACA15420.1| acetylglutamate kinase [Methylobacterium sp. 4-46]
          Length = 304

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 42/209 (20%), Positives = 79/209 (37%), Gaps = 23/209 (11%)

Query: 9   YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKI 68
           +R   R+     +   EM++A +I     K I+G+ + E   A+ + G D + +V+ A+ 
Sbjct: 89  FREGLRVTDAATVEVVEMVLAGSI----NKQIVGWISAEGGKAIGLCGKDGN-MVQ-ARR 142

Query: 69  VEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI-AAMCKALSIPVTVKCRIGV 127
                 +  + N+        E      L+  P+ V   +  A+ KA  IPV     +G 
Sbjct: 143 ATRTVVDP-DSNL--------EREVDLGLVGEPERVNRAVLDAVLKAELIPVLAPVAVGS 193

Query: 128 DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           D Q   V       +I  +G            + G+  K+ + IP L  +    +  +  
Sbjct: 194 DGQTYNVNADTFAGAI--AGALRAKRLLLLTDVPGVLDKNKKLIPELSVEDCRRLVADGT 251

Query: 188 DLFIGLNGGLEDMSQAL-KILPSVDGVMI 215
                  G +  +   +  I   V+ V+I
Sbjct: 252 IT----GGMIPKIETCIYAIEQGVEAVVI 276


>gi|281201933|gb|EFA76141.1| hydroxyacid oxidase [Polysphondylium pallidum PN500]
          Length = 366

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 18/112 (16%)

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +     +P+ VK  +   D           +     GV+ I +    A     +P     
Sbjct: 222 LKSITKLPIIVKGVMSPRD----------AEIAVTHGVDAIIVSNHGARQLDTAPSTIEV 271

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYK 221
           +P       Y +K  N    + L+GG+   +  LK L      VMIGR    
Sbjct: 272 LP-------YIVKAVNGRCPVILDGGVRRGTDILKALACGAKAVMIGRPVLW 316


>gi|159903669|ref|YP_001551013.1| inosine 5-monophosphate dehydrogenase [Prochlorococcus marinus str.
           MIT 9211]
 gi|159888845|gb|ABX09059.1| putative IMP dehydrogenase [Prochlorococcus marinus str. MIT 9211]
          Length = 387

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 32/150 (21%), Positives = 51/150 (34%), Gaps = 28/150 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI---WIHARKAILKG-L 163
           ++ +CK ++IPV V                 +   + ++G  GI            +G L
Sbjct: 179 LSKLCKTMNIPVLV----------GNCVTYEVALKLMRAGAKGILVGIGPGAACTSRGVL 228

Query: 164 SPKDNRKIPNLDYDIVYE-IKKENPD-LFIGLNGGLEDM-SQALKILPSVDGVMIG---- 216
                +     D     E  KKE  + + I  +GG+         I    DGVMIG    
Sbjct: 229 GIGTPQATAIADCSSAREDYKKETGEYVPIIADGGIVTGGDICKCIACGADGVMIGSPIA 288

Query: 217 RAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           R A +         + F   +   SP+  R
Sbjct: 289 R-AQEAPG------QGFHWGMATPSPVLPR 311


>gi|312140418|ref|YP_004007754.1| 2,4-dienoyl-CoA reductase fadh [Rhodococcus equi 103S]
 gi|311889757|emb|CBH49074.1| 2,4-dienoyl-CoA reductase FadH [Rhodococcus equi 103S]
          Length = 676

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 23/179 (12%), Positives = 57/179 (31%), Gaps = 21/179 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEG--SFGACLMLNPDIVGDCIAA 110
            V  A++    GY+ + +  G         C   R ++    +G        +  + +  
Sbjct: 146 FVRCARLARSAGYDGVEIMGGEGYFVNQFLC--ERTNKRTDEWGGTPQNRRRMAVEIVRR 203

Query: 111 MCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
              A+     +  R+ + D          +  L + ++ +G   I  +      +   P 
Sbjct: 204 TRAAVGPNFVILFRLSMADLVEGGQSWDEIVALAQEVEAAGATVI--NTDIGWHESRVPT 261

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +P   +  V E   ++  + +  +  +     A +IL    V  + + R    + 
Sbjct: 262 IVTSVPRAAFVDVTEKLAKHVSIPVVASNRINMPEIAEEILTRGEVQLISMARPMLADP 320


>gi|302186583|ref|ZP_07263256.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae pv.
           syringae 642]
          Length = 363

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 62/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLAESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          V E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPVAERVRREADIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|254361215|ref|ZP_04977359.1| flavin reductase [Mannheimia haemolytica PHL213]
 gi|153092706|gb|EDN73755.1| flavin reductase [Mannheimia haemolytica PHL213]
          Length = 354

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 33/218 (15%), Positives = 70/218 (32%), Gaps = 23/218 (10%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINL--- 79
           +   AI  G+    L ++ Q      ++   ++  LV+A     K   + G++ I +   
Sbjct: 117 VAPSAIHYGE----LDYAGQNLITPRELTTDEVKALVQAFKDSVKRAVEAGFDTIEIHGA 172

Query: 80  ------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIP 132
                     P +      +G   ML  + V       M   + + V +  +   ++   
Sbjct: 173 HGYLIHQFYSPKSNQRSDEYGQDKMLFGEQVIQAAREVMPSEMPLIVRISAQEYGENGFG 232

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 + K    +G + + I      +                D   ++K       + 
Sbjct: 233 LDYGLQVAKRFADAGADVLDISGGGDGVLHAGNHPEFYAG-YQVDFARQVKLATGK-PVI 290

Query: 193 LNGGLEDMSQALKILP--SVDGVMIGRAAYKNS-AMLT 227
             G L++ +    IL     D V +GRA  ++   +L 
Sbjct: 291 AVGMLDNPAVGDHILGMGDADLVAVGRALLRDPYWVLN 328


>gi|84499951|ref|ZP_00998217.1| hypothetical protein OB2597_08424 [Oceanicola batsensis HTCC2597]
 gi|84391885|gb|EAQ04153.1| hypothetical protein OB2597_08424 [Oceanicola batsensis HTCC2597]
          Length = 762

 Score = 38.3 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 31/214 (14%), Positives = 68/214 (31%), Gaps = 22/214 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA++ +  G++ I L+            P +      +G  L        +   A
Sbjct: 546 DQFVAAAQMADRAGFDMIELHAAHGYLLSSFISPISNHRTDDYGGSLENRMRYPLEVFRA 605

Query: 111 MCKAL--SIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           M  A     P++V+        D  +       +     ++GV+ + + A +  ++   P
Sbjct: 606 MRAAWPEDKPMSVRISATDWIGDRGVEGEEAVEIAALFHEAGVDIVDVSAGQTSVE-ARP 664

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R       D +   +     +     G + +      IL +   D V + R    + 
Sbjct: 665 VYGRMFQTPFSDRIRNER----GIPTMAVGNIYEPDHVNSILMAGRADLVCLARPHLADP 720

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
                      +  T   P+     +D  R+++ 
Sbjct: 721 YWTLHAAAALGDEET-QWPLPYLPGRDQMRRLAE 753


>gi|319651028|ref|ZP_08005163.1| hypothetical protein HMPREF1013_01772 [Bacillus sp. 2_A_57_CT2]
 gi|317397384|gb|EFV78087.1| hypothetical protein HMPREF1013_01772 [Bacillus sp. 2_A_57_CT2]
          Length = 256

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 28/78 (35%), Gaps = 2/78 (2%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            +    +++ D     I  + + + IPV+     G  + IP   +   V     +GV GI
Sbjct: 51  GYADGELIDFDRHLAIIKTIAENVKIPVSADIEAGYGEDIP--TIIEHVLMTADAGVAGI 108

Query: 152 WIHARKAILKGLSPKDNR 169
            I       KGL      
Sbjct: 109 NIEDSFKKQKGLKELSWH 126


>gi|319779419|ref|YP_004130332.1| L-lactate dehydrogenase [Taylorella equigenitalis MCE9]
 gi|317109443|gb|ADU92189.1| L-lactate dehydrogenase [Taylorella equigenitalis MCE9]
          Length = 388

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 15/100 (15%)

Query: 140 VKSIKKSGVNGIWI--HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
                 SG +   +  H  + +   LS             I+  + K + +  + L+GG+
Sbjct: 262 AIEACNSGADAFVVSNHGGRQLDGALSS------IKALLPILEAVDKISSNCEVWLDGGI 315

Query: 198 EDMSQALKILP-SVDGVMIGR------AAYKNSAMLTTVD 230
                 L+      DGVM+GR       AY    +L ++D
Sbjct: 316 RSGQDILRAYAMGADGVMVGRPYIYGLGAYGYDGVLKSLD 355


>gi|269961872|ref|ZP_06176229.1| N-ethylmaleimide reductase [Vibrio harveyi 1DA3]
 gi|269833450|gb|EEZ87552.1| N-ethylmaleimide reductase [Vibrio harveyi 1DA3]
          Length = 363

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 28/184 (15%), Positives = 63/184 (34%), Gaps = 21/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AAK   + G++ + ++ G  +  + +            ++G         + + + 
Sbjct: 161 DFAHAAKRAIEAGFDGVEIHGG--NGYLIDQFLRTNSNHRTDNYGGTRENRLRFLLEVVD 218

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ +A+     V  R+        +   ++V +I  +      + AR      LS  D  
Sbjct: 219 AVSEAIGAN-KVGVRLAPFITFKDMNCPDIVPTILDASKQ---LQARDIAYLHLSEADWD 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P +      E+++   +  I    G     +A ++L     D V  GR    N  ++ 
Sbjct: 275 DAPVIPESFRIELREYFTNTIIVA--GSYTQDRADEVLEKGYADLVAFGRPFVSNPDLVA 332

Query: 228 TVDE 231
            +  
Sbjct: 333 RLQH 336


>gi|190572985|ref|YP_001970830.1| putative 2,4-dienoyl-CoA reductase [NADPH] [Stenotrophomonas
           maltophilia K279a]
 gi|190010907|emb|CAQ44516.1| putative 2,4-dienoyl-CoA reductase [NADPH] [Stenotrophomonas
           maltophilia K279a]
          Length = 676

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 24/176 (13%), Positives = 53/176 (30%), Gaps = 17/176 (9%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             +AK+  + GY+ + +             P        +G           + +  + +
Sbjct: 151 ARSAKLAREAGYDGVEVMGSEGYLINEFIAPRTNKRSDRWGGDANQRMRFAVEIVRRIRE 210

Query: 114 ALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A      +  R+     VDD      +    ++I+ +G     I++     +   P    
Sbjct: 211 ACGPDFIIIYRLSLVDLVDDGSNWEEIVQQAQAIEAAGAT--IINSGIGWHEARIPTIAT 268

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
            +P   +  V    K +  + +     +     A  IL     D V + R    + 
Sbjct: 269 SVPRAAFAAVTAKLKPHVTVPLVATNRINMPDVAEHILASGGADMVSLARPLLADP 324


>gi|194335678|ref|YP_002017472.1| histidine biosynthesis protein [Pelodictyon phaeoclathratiforme
           BU-1]
 gi|194308155|gb|ACF42855.1| histidine biosynthesis protein [Pelodictyon phaeoclathratiforme
           BU-1]
          Length = 256

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 2/78 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           DI+    K+   + + + GG+  +  A +IL    D V +  AA  N  ++  +   F +
Sbjct: 64  DIIRSAAKDIF-VPMTVGGGIRSVEDATQILRSGADKVAVNTAAVANPKLINEISRRFGS 122

Query: 236 PLTGSSPIKTRVDKDFWR 253
                S     V KD W 
Sbjct: 123 QCMVLSIEAKEVGKDRWE 140


>gi|312973733|ref|ZP_07787905.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli 1827-70]
 gi|310332328|gb|EFP99563.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli 1827-70]
          Length = 258

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SAEDAAKILSFGADKISINSPALADPELITRLADRFG 121


>gi|159129254|gb|EDP54368.1| FMN binding oxidoreductase, putative [Aspergillus fumigatus A1163]
          Length = 421

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 35/216 (16%), Positives = 71/216 (32%), Gaps = 31/216 (14%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINL---------- 79
           D +L      +   + +E  +  Q       + V+ A+++ D G++ I L          
Sbjct: 143 DGLLDRIISRLAFPAPRE--MTQQDIDTVTRQFVDTARLMADAGFSGIELHGAHGYLIDQ 200

Query: 80  --NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR 137
             N   P   +   ++G         V D ++   K +     +  +    D   A    
Sbjct: 201 FLN---PKTNLRTDAYGGSAEKRAKFVLDILSQTRKVVPATFCIGIKFNSADHSSASFED 257

Query: 138 NLVKS--IKKSGVNGIWIHARK--------AILKGLSPKDNRKIPNLDY--DIVYEIKKE 185
            + +   +  +G++ + +               +    K  R +    +  +   E +K 
Sbjct: 258 TMTQIGLLVDAGIDFLEVSGGSYEDPKMMGTNSQPQPEKSQRTLAREAFFLEFARETRKR 317

Query: 186 NPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAA 219
            P L + L GG    + A   L     D + IGR A
Sbjct: 318 FPTLILMLTGGFRSRAGAEHALRENACDLIGIGRPA 353


>gi|149376056|ref|ZP_01893822.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter algicola
           DG893]
 gi|149359693|gb|EDM48151.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Marinobacter algicola
           DG893]
          Length = 245

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 51/136 (37%), Gaps = 11/136 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++      +G   + +        G           ++ +IV  I ++ PDL I + GG+
Sbjct: 34  DMATRWVDAGARRLHLVDLNGAFAG---------EPVNGEIVQAIARKYPDLPIQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRVDKDFWRKI 255
              S     L   V  V+IG  A K    +T + + F   +  G      RV  D W ++
Sbjct: 85  RSASTIEAYLKAGVQWVIIGTKAVKEPEFVTDMCKRFPGHIIVGLDAKDGRVATDGWAEV 144

Query: 256 SASMTDYAARHLHSGG 271
           S  M    A+   + G
Sbjct: 145 SEVMATDLAKRFANDG 160


>gi|147770516|emb|CAN75682.1| hypothetical protein VITISV_038955 [Vitis vinifera]
          Length = 401

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 151 RVEQTGIDALEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATVPVWAKMTPNI 209

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI 151
            D      +    +    SG  G+
Sbjct: 210 TD------ITQPARVALSSGCEGV 227


>gi|11993325|gb|AAG42687.1|AF271383_1 indole-3-glycerol phosphate lyase [Zea mays]
          Length = 339

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 35/215 (16%), Positives = 68/215 (31%), Gaps = 58/215 (26%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNV-------GCPSARVHEGSFGACLMLNPDIVGDC 107
           G  D++   EA ++++  G + I L V         P  +    +        PD V   
Sbjct: 96  GDPDLATTAEALRLLDACGADVIELGVPFSDPYADGPVIQA-SAARALASGTTPDGVLAM 154

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------------- 152
           +  +   LS PV         + I    L +   ++K++GV+G+                
Sbjct: 155 LKEVTPELSCPV---VLFSYFNPIVRWGLADFAAAVKEAGVHGLIVPDLPYGNSCALTLR 211

Query: 153 -------------------------IHARKAILKGLSPKDNRKIPNLDYD-----IVYEI 182
                                    I         L+  +    P  + +     ++ E+
Sbjct: 212 TEAIKNSLELVLLTTPSTPADRMEEITRASRGFVYLATVNGVTGPRANVNTRVQSLIQEV 271

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           K+   D+ + +  G+       +I     DGV+IG
Sbjct: 272 KQ-VTDIPVAVGFGISKPEHVKQIAEWGADGVIIG 305


>gi|187926027|ref|YP_001892372.1| NADH:flavin oxidoreductase/NADH oxidase [Ralstonia pickettii 12J]
 gi|241665514|ref|YP_002983873.1| salicylyl-CoA 5-hydroxylase [Ralstonia pickettii 12D]
 gi|187727781|gb|ACD28945.1| NADH:flavin oxidoreductase/NADH oxidase [Ralstonia pickettii 12J]
 gi|240867541|gb|ACS65201.1| NADH:flavin oxidoreductase/NADH oxidase [Ralstonia pickettii 12D]
          Length = 792

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 32/223 (14%), Positives = 67/223 (30%), Gaps = 29/223 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVGDC 107
            V AA++  + G++ + L   C           P        +G  L   +  P  V   
Sbjct: 564 FVHAARLAAEAGFDWLEL--HCAHGYLLSSFISPLTNQRNDEYGGTLDNRLRFPLEVFHA 621

Query: 108 IAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           +  +    + P++V+      V+  I       + +  K +G + I   + +     +S 
Sbjct: 622 VREVW-PSNKPMSVRISAHDWVEGGITPDDAVEIARVFKAAGADMIDCSSGQ-----VSK 675

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
           K+      +      +  +    +     G + +      I+ +   D   + R    N 
Sbjct: 676 KEQPVYGRMFQTPFADRVRNEAGIATIAVGAISEADHVNSIIAAGRADLCAVARPHLANP 735

Query: 224 -AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
              L          L    P + R  K    +        AA+
Sbjct: 736 AWTLNEAARI--GYLDMPWPKQYRAGKLQLERNLERERAMAAQ 776


>gi|326803094|ref|YP_004320912.1| oxidoreductase, FAD/FMN-binding protein [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651479|gb|AEA01662.1| oxidoreductase, FAD/FMN-binding protein [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 407

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 4/42 (9%)

Query: 177 DIVYEIKKE--NPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
           + V ++ K+  N  + +   GG+    +AL  L   D  M+G
Sbjct: 289 EYVNQVVKDHINGRVPVIATGGINSPDKALAALEHAD--MVG 328


>gi|326433768|gb|EGD79338.1| pyridoxine biosynthesis protein pyroA [Salpingoeca sp. ATCC 50818]
          Length = 259

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 60/177 (33%), Gaps = 22/177 (12%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            + A++ E  G   I      P+        G   M +P ++ +       A++IPV  K
Sbjct: 36  AKQAQVAEKSGACAIMALERVPAD--IRAEGGVARMSDPKLIKEI----KAAVTIPVMAK 89

Query: 123 CR--IGVDDQIPAVALRNLVKSIK-----KSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            R    V+ QI      + +   +           + +   + +   +       +    
Sbjct: 90  ARIGHFVEAQILQSLDCDFIDESEVLTPADGRCVCVCVCVCERVCVCVFVCVCVCVCYAG 149

Query: 176 YDIV--YEIK--KENPDLFIG--LNGGLEDMSQALKILP-SVDGVMIGRAAYK--NS 223
            + V    +K  ++   L +     GG+   + A  ++    DGV +G   +K  N 
Sbjct: 150 EERVPLALVKRTRDLGRLPVVNFAAGGIATPADAAMMMQLGCDGVFVGSGIFKSTNP 206


>gi|323970153|gb|EGB65426.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli TA007]
          Length = 399

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|320174518|gb|EFW49654.1| 2,4-dienoyl-CoA reductase [Shigella dysenteriae CDC 74-1112]
          Length = 399

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 24/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLHTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V+D         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|210616005|ref|ZP_03290905.1| hypothetical protein CLONEX_03124 [Clostridium nexile DSM 1787]
 gi|210150010|gb|EEA81019.1| hypothetical protein CLONEX_03124 [Clostridium nexile DSM 1787]
          Length = 256

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 65/212 (30%), Gaps = 48/212 (22%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPS------ARVHEGSFGACL--MLNPDIVGD 106
           G  D+       +   + G + I L +  P         V +G+    L   +  D +  
Sbjct: 21  GDPDLETTGAVIRAAVENGADLIELGI--PFSDPTAEGNVIQGANLRALSGGVTTDKIFA 78

Query: 107 CIAAMCKALSIP-----------------VTVKCRIGVDD-----QIPAVALRNLVKSIK 144
            +  + K + +P                     C+    D      +P       +    
Sbjct: 79  FVKELRKDVKVPMVFMTYANVVFSYGAERFLSSCKECEIDGLILPDLPFEEKEEFLPVCH 138

Query: 145 KSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           + GV+ I + A  +                I+  L     R     D   + E+ ++N D
Sbjct: 139 QYGVDLISLIAPTSANRIAMIAKEAEGFLYIVSSLGVTGARSEIKTDLASIVEVVRQNTD 198

Query: 189 LFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           +   +  G+    QA K+    DG ++G A  
Sbjct: 199 IPCAIGFGISTPEQAKKMANISDGAIVGSAIV 230


>gi|50086372|ref|YP_047882.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter sp.
           ADP1]
 gi|60392375|sp|Q6F7A5|HIS4_ACIAD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|49532348|emb|CAG70060.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter sp. ADP1]
          Length = 243

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 42/130 (32%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I K  P+L I + GG+  +      L   V  V+IG  A ++   
Sbjct: 60  ------PIHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLDAGVSFVIIGTKAVQDPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEQACKQFAG 123


>gi|110635957|ref|YP_676165.1| NADH:flavin oxidoreductase/NADH oxidase [Mesorhizobium sp. BNC1]
 gi|110286941|gb|ABG65000.1| NADH:flavin oxidoreductase/NADH oxidase [Chelativorans sp. BNC1]
          Length = 650

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 28/185 (15%), Positives = 59/185 (31%), Gaps = 20/185 (10%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA    + G + + L             P   + E  +G        +  + + A+ 
Sbjct: 152 FADAACRAREGGLDGVELSYTHGNLVQQFLSPLTNIREDEYGGSEENRLRLAREILEAVR 211

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSG----VNGIWIHARKAILKGLS 164
            AL    T+  R   D+ +P     +      + + + G    V+           + + 
Sbjct: 212 TALGDDYTLGIRFSADELVPGGYTIDDGERYARMMVEWGKLDYVSVSAGTNGSMWSRSIH 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                    +       +K+   D+ +   G + D ++A  IL     D V + RA    
Sbjct: 272 YPSISMPEKVLIPYSKRVKQAV-DVPVFCIGKITDPAEAEGILAQGEADIVGMTRAHIAE 330

Query: 223 SAMLT 227
            A++ 
Sbjct: 331 PAIIR 335


>gi|308187458|ref|YP_003931589.1| imidazole glycerol phosphate synthase subunit [Pantoea vagans C9-1]
 gi|308057968|gb|ADO10140.1| imidazole glycerol phosphate synthase subunit [Pantoea vagans C9-1]
          Length = 258

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAAEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  TPEDAARILEFGADKISINSPALADPTLITRLADRFG 121


>gi|146083468|ref|XP_001464746.1| inosine-5'-monophosphate dehydrogenase [Leishmania infantum JPCM5]
 gi|134068840|emb|CAM59774.1| putative guanosine monophosphate reductase [Leishmania infantum
           JPCM5]
 gi|322498159|emb|CBZ33234.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 492

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 21/119 (17%), Positives = 43/119 (36%), Gaps = 10/119 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + D+  D + A+      P+T K     D     +A     + +  +G +G+ I      
Sbjct: 265 HSDLCIDMVKALKVN---PLTNKV----DIIAGNIATAEAAQDLIDAGADGLKIGVGPGS 317

Query: 160 LKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIG 216
           +          +P L   +    + K++  +    +GG++        I    D VM+G
Sbjct: 318 ICITRLVAGSGVPQLSAVMDCARVAKKHG-VPCIADGGVKTAGDICKAIAAGADTVMLG 375


>gi|224586550|ref|YP_002640450.1| inosine-5'-monophosphate dehydrogenase [Borrelia spielmanii A14S]
 gi|224497612|gb|ACN53234.1| inosine-5'-monophosphate dehydrogenase [Borrelia spielmanii A14S]
          Length = 403

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 62/192 (32%), Gaps = 45/192 (23%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV---- 119
           + A+  EDF     +LN             GA + ++ D +      +   + + V    
Sbjct: 122 KNAEHKEDFPNACKDLNS--------RLRVGAAVSIDIDTIERVEELVKAHVDLLVIDSA 173

Query: 120 ------------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAIL 160
                       T+K +   +D     +  +     +  +G + + +           I+
Sbjct: 174 HGHSTRIIELVKTIKNKYPNLDLIAGNIVTKEAALDLINAGADCLKVGIGPGSICTTRIV 233

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIGRAA 219
            G+       I +     VYEI K N ++ I  +GG+         I    D VMIG   
Sbjct: 234 AGVGVPQITAICD-----VYEICK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG--- 284

Query: 220 YKNSAMLTTVDE 231
                +   V E
Sbjct: 285 ----NLFAGVKE 292


>gi|262089556|gb|ACY24655.1| FAD/FMN-binding/pyridine nucleotide-disulphide oxidoreductase
           family protein [uncultured organism]
          Length = 673

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 17/128 (13%), Positives = 42/128 (32%), Gaps = 13/128 (10%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + +      +     +  R+ + D          +  L + ++K+GV    ++     
Sbjct: 200 ALEIVRKTRARVGTNFIIIFRLSMLDLVEGGSTKEEVVQLAQELEKAGVT--ILNTGIGW 257

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIGR 217
            +   P    K+P   +  V +  K    + +     +     A +IL   DG+  M+  
Sbjct: 258 HEARIPTIATKVPRAAWAWVTQQLKGKVKIPLVATNRINTPEVAEQIL--ADGMADMV-- 313

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 314 -SMARPFL 320


>gi|288920819|ref|ZP_06415117.1| dihydroorotate dehydrogenase [Frankia sp. EUN1f]
 gi|288347778|gb|EFC82057.1| dihydroorotate dehydrogenase [Frankia sp. EUN1f]
          Length = 338

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 44  STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
               KPL + + G    +  + A++  D G + I LN+ CP   V +G 
Sbjct: 112 HNHAKPLVVSVAGFAADEYADLARVAADAGADLIELNLACP--NVWDGG 158


>gi|296125522|ref|YP_003632774.1| NADH:flavin oxidoreductase/NADH oxidase [Brachyspira murdochii DSM
           12563]
 gi|296017338|gb|ADG70575.1| NADH:flavin oxidoreductase/NADH oxidase [Brachyspira murdochii DSM
           12563]
          Length = 344

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 27/137 (19%), Positives = 48/137 (35%), Gaps = 8/137 (5%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           I+ + +    +A+     ++ RI   D +     +++ V  +K     G+       +  
Sbjct: 197 ILEEILRKGKEAVGKDYPIQIRISSYDWKEGGNTVKDFVDMLKPLEEQGL--FDSINVST 254

Query: 162 GLSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
           G    D + IP   Y I    E+K+    +     G L D   A  I+ +   D V IGR
Sbjct: 255 GAVTADGKIIPYEGYQIPFCRELKQ-YMKVPCIGGGLLTDAKMANMIVRNGAADAVYIGR 313

Query: 218 AAYKNSAMLTTVDEYFS 234
              +N            
Sbjct: 314 EILRNPYWALQAARTLG 330


>gi|209520369|ref|ZP_03269133.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. H160]
 gi|209499201|gb|EDZ99292.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. H160]
          Length = 687

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGVEVLQAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
             A+     V  R+  D    D +    L+ + +++ +SG+    G+            +
Sbjct: 211 RAAVGADFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSESGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K+   + +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKQVVKVPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|17229404|ref|NP_485952.1| dihydroorotate dehydrogenase 2 [Nostoc sp. PCC 7120]
 gi|17131002|dbj|BAB73611.1| alr1912 [Nostoc sp. PCC 7120]
          Length = 343

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 17/116 (14%), Positives = 42/116 (36%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD-- 106
           P+   + G+ +    E A+++E  G   + LN                +  +P++  +  
Sbjct: 103 PIIASLNGSSLDGWTEYARMIEQAGAAALELNT-------------YSVHTDPELTSEQI 149

Query: 107 ------CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                  +  +  ++ IPV +K             + N+ K +  +G + + +  R
Sbjct: 150 EQSYINMLKVVKASVQIPVAIKLSPYF------TNMANMAKRLDDAGADALVLFNR 199


>gi|254241141|ref|ZP_04934463.1| hypothetical protein PA2G_01830 [Pseudomonas aeruginosa 2192]
 gi|126194519|gb|EAZ58582.1| hypothetical protein PA2G_01830 [Pseudomonas aeruginosa 2192]
          Length = 411

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 25/187 (13%), Positives = 62/187 (33%), Gaps = 17/187 (9%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A + E  G++ + ++            P +     ++G  L     ++ + + A+ 
Sbjct: 151 FARSAGLAERAGFSGVEIHAAHGYLLSQFLSPLSNRRSDAWGGSLENRARLLLEIVRAVR 210

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLSP 165
             ++    V  ++   D       A   R +V+ +   GV+ + +         ++G + 
Sbjct: 211 AEVAPGFAVAVKLNSADFQRGGFSADDAREVVRMLDGLGVDLVELSGGSYEAPAMQGEAR 270

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSA 224
                     +       +    + + + GG+     A ++L   VD V IG A      
Sbjct: 271 DGRTLAREAYFVEFARDIRVAARMPVMVTGGIRRRPVAEQVLASGVDMVGIGTALAIEPN 330

Query: 225 MLTTVDE 231
           +      
Sbjct: 331 LPRDWRA 337


>gi|319939968|ref|ZP_08014323.1| dihydroorotate dehydrogenase [Streptococcus anginosus 1_2_62CV]
 gi|319810979|gb|EFW07298.1| dihydroorotate dehydrogenase [Streptococcus anginosus 1_2_62CV]
          Length = 311

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 58/163 (35%), Gaps = 19/163 (11%)

Query: 67  KIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K V+D  +  +  LN+ CP   V      A    + +     ++ +    + P+ +K   
Sbjct: 114 KKVQDSDFKGLTELNLSCP--NVPGKPQIAY---DFETTEKILSEVFDYFTKPLGIKLPP 168

Query: 126 GVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHARKAIL---KGLSPKDNRKIPNLD 175
             D      A A+ N      V  +   G NG++I+    ++   KG        I    
Sbjct: 169 YFDMAHFDQAAAIFNKFPLSFVNCVNSIG-NGLYINGETVVIRPKKGFGGIGGEYIKPTA 227

Query: 176 YDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIG 216
              V+   +  NP + I   GG+     A +  L     V +G
Sbjct: 228 LANVHAFYQRLNPSIQIIGTGGVLTGRDAFEHILCGASMVQVG 270


>gi|289425517|ref|ZP_06427294.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes SK187]
 gi|289154495|gb|EFD03183.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes SK187]
          Length = 307

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 44  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 97

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 98  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 157

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 158 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARRGE 217

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 218 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 257


>gi|254262159|emb|CAZ90488.1| Isopentenyl-diphosphate delta-isomerase fni [Enterobacter
           turicensis]
          Length = 349

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 24/129 (18%), Positives = 46/129 (35%), Gaps = 21/129 (16%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-- 156
            +   + + IA + + L +PV VK       ++ A    ++   +   GV  I I     
Sbjct: 171 RDWRGILNAIAQLVRDLPVPVVVK-------EVGAGISPDVACRLADVGVTMIDIAGAGG 223

Query: 157 ------KAILKGLSPKDNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQAL 204
                 +A         N  +   D+     D +  +    PD+ +  +GG+ + +  A 
Sbjct: 224 TSWAAVEAERAPTPEARNVAMAFADWGIPTADALRRVHLALPDIPLIASGGIANGIDAAK 283

Query: 205 KILPSVDGV 213
            I    D V
Sbjct: 284 AIALGADLV 292


>gi|327334199|gb|EGE75913.1| 2-enoate reductase [Propionibacterium acnes HL097PA1]
          Length = 670

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIIAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|300905773|ref|ZP_07123507.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 84-1]
 gi|301301873|ref|ZP_07208007.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 124-1]
 gi|300402372|gb|EFJ85910.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 84-1]
 gi|300842854|gb|EFK70614.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 124-1]
 gi|315256997|gb|EFU36965.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 85-1]
          Length = 672

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFARCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|297734363|emb|CBI15610.3| unnamed protein product [Vitis vinifera]
          Length = 366

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 7/84 (8%)

Query: 68  IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGV 127
            VE  G + + +N  CP     E   GA +  +  ++ +    +    ++PV  K    +
Sbjct: 116 RVEQTGIDALEINFSCPHGM-PERKMGAAVGQDCALLEEVCGWINAKATVPVWAKMTPNI 174

Query: 128 DDQIPAVALRNLVKSIKKSGVNGI 151
            D      +    +    SG  G+
Sbjct: 175 TD------ITQPARVALSSGCEGV 192


>gi|257467900|ref|ZP_05631996.1| putative N-acetylmannosamine-6-phosphate 2-epimerase [Fusobacterium
           ulcerans ATCC 49185]
 gi|317062189|ref|ZP_07926674.1| N-acylglucosamine-6-phosphate 2-epimerase [Fusobacterium ulcerans
           ATCC 49185]
 gi|313687865|gb|EFS24700.1| N-acylglucosamine-6-phosphate 2-epimerase [Fusobacterium ulcerans
           ATCC 49185]
          Length = 242

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 27/133 (20%), Positives = 49/133 (36%), Gaps = 16/133 (12%)

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV--KCRIGVDDQIPAVALRNLVKSI 143
             V  G +G       D   +    + K  + P+    K  I  +D      +R  V  I
Sbjct: 36  KLVMCGEWGDACGYRIDTPENIAK-IRKITNKPIIGLWKINIETEDVFITPTMRE-VDEI 93

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
            K+G + I + A   +                Y+I+ EIK++ P+L I     + +  +A
Sbjct: 94  VKAGADIIAVDATNRVNSY---------GKKTYEIISEIKEKYPELLILA--DIRNAEEA 142

Query: 204 LKILPSVDGVMIG 216
            + L  +   M+ 
Sbjct: 143 REALK-MGAHMVA 154


>gi|332362067|gb|EGJ39869.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK49]
          Length = 252

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R    L   +V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTTVL---MVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|297543525|ref|YP_003675827.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296841300|gb|ADH59816.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 341

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 63/181 (34%), Gaps = 23/181 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA+     GY+ + ++            P +   +  +G  +      + + I  + 
Sbjct: 145 FGEAARRAHLAGYDVVEIHAAHGYLIHEFLSPLSNKRKDEYGGSIENRARFLIEVIEEVR 204

Query: 113 KALS--IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K      P+ V+      ++  I    + + +  IK   V+ I + +      GL   D 
Sbjct: 205 KNWPQTKPIFVRVSADDYIEGGINIDMMVDYINMIKDK-VDLIDVSSG-----GLLSADI 258

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-AM 225
              P         IKK   ++     G +     A +IL +   D V +GR   +N   +
Sbjct: 259 NLYPGYQVKYAETIKKRC-NIKTSAVGLITTQELAEEILSNKRADLVALGRELLRNPYWV 317

Query: 226 L 226
           L
Sbjct: 318 L 318


>gi|294670847|ref|ZP_06735703.1| hypothetical protein NEIELOOT_02551 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307334|gb|EFE48577.1| hypothetical protein NEIELOOT_02551 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 246

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 3/102 (2%)

Query: 173 NLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVD 230
             ++  + EI      D+ + L GG+ D++   K L   +  V+IG AA KN A +    
Sbjct: 60  PKNFPAIREILAAVAADIPVQLGGGIRDLATIEKYLTLGLTDVIIGTAAVKNPAFVREAC 119

Query: 231 EYFSNPLTGSSPIKTRVDK-DFWRKISASMTDYAARHLHSGG 271
             F+  +      K  +   D W  ++        R     G
Sbjct: 120 REFAGHIIVGIDAKDGMAAIDGWATVTEHRAADLGRRFADDG 161


>gi|156742039|ref|YP_001432168.1| dihydroorotate dehydrogenase 2 [Roseiflexus castenholzii DSM 13941]
 gi|156233367|gb|ABU58150.1| dihydroorotate dehydrogenase [Roseiflexus castenholzii DSM 13941]
          Length = 330

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 34/216 (15%), Positives = 65/216 (30%), Gaps = 55/216 (25%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNP------- 101
           P+   + G      VE A  VE  G + + LN+               L  +P       
Sbjct: 104 PIIASLNGPSDGDWVEYANKVEQAGADALELNL-------------YFLATDPGITGAAI 150

Query: 102 -DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---- 156
            +     +  +C  ++IPV +K             + N+ K    +G  G+ +  R    
Sbjct: 151 EEQYLRLVRDVCSRVTIPVAIKMSPFFSS------IANMAKQFSDAGAKGLVLFNRFYQP 204

Query: 157 ---------KAILKGLSPKDNRKIPNLDYDIV--YEIKKENPDLFIGLNGGLEDMSQALK 205
                       LK  +  + R    L +  +    +K +          G+      LK
Sbjct: 205 DFDLETLDVVPNLKLSTSDELRL--PLRWIAILYGRVKADLALTS-----GVHTAEDVLK 257

Query: 206 -ILPSVDGVM-----IGRAAYKNSAMLTTVDEYFSN 235
            ++      M     + R   +  A+L  +  +   
Sbjct: 258 AMMAGARVAMMTSELLARGIDRIPAILNDLRAWMEE 293


>gi|116871950|ref|YP_848731.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|123458154|sp|A0AG16|HIS4_LISW6 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|116740828|emb|CAK19948.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Listeria welshimeri serovar 6b str. SLCC5334]
          Length = 240

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 50/134 (37%), Gaps = 12/134 (8%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +I+ ++K+    + + + GG+  
Sbjct: 36  AKAFATGGATYLHIVDLDGALEGR---------PVNLEIIQKMKEAAT-VPVQVGGGIRS 85

Query: 200 MSQALKIL-PSVDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           ++Q    L   +D V+IG AA  N   +   V +Y      G       V    W ++S 
Sbjct: 86  LAQVDYYLDSGIDRVIIGSAALTNPDFLHAAVQKYGPKIAVGIDAKNGYVATSGWLEVSQ 145

Query: 258 SMTDYAARHLHSGG 271
                 A+ +   G
Sbjct: 146 VNYLDLAKQMEKVG 159


>gi|325921433|ref|ZP_08183289.1| NADH:flavin oxidoreductase [Xanthomonas gardneri ATCC 19865]
 gi|325548075|gb|EGD19073.1| NADH:flavin oxidoreductase [Xanthomonas gardneri ATCC 19865]
          Length = 366

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 63/182 (34%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V AA+   D G+  + L+       + +             +G         + + + 
Sbjct: 159 DFVAAAQRARDAGFQWLELHFA--HGYLAQSFFSVHANQRQDQYGGTAENRGRFLLETLQ 216

Query: 110 AMCKALS--IPVTVKCRIGVDDQIPAVALRNLV---KSIKKSGVNGIWIHARKAILKGLS 164
           A+       +P+T +  +   D      L+  +   ++ K+SG++ + +      +   +
Sbjct: 217 AVRAVWPEHLPLTARFGVIEFDGRDEETLQEAIALTRNFKQSGLDLLNV-----SMGFST 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P               E       L +  +  ++D  +A +++    ++ VMIGRA   N
Sbjct: 272 PTAQIPWGPALLAPFAERVSREAQLPVASSWNIDDPLEADRVIAAGQMELVMIGRAHLAN 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|317491370|ref|ZP_07949806.1| imidazoleglycerol phosphate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316920917|gb|EFV42240.1| imidazoleglycerol phosphate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + + F 
Sbjct: 85  SVEDASQILTFGADKISINSPALADPDLISRLADRFG 121


>gi|326315822|ref|YP_004233494.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323372658|gb|ADX44927.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 248

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 24/120 (20%), Positives = 39/120 (32%), Gaps = 15/120 (12%)

Query: 122 KCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             R+   D   +         + +    +G   + +        G            +Y 
Sbjct: 14  CVRLKQGDMDQSTTFGEDPAAMARKWVDAGARRLHLVDLNGAFAGT---------PKNYA 64

Query: 178 IVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I KE  D L + L GG+ D+    K +   +  V+IG AA KN   L      F  
Sbjct: 65  AIKAILKEVGDDLPVQLGGGIRDLDTIEKYIDGGLRYVIIGTAAVKNPGFLKDACSAFGG 124


>gi|257386924|ref|YP_003176697.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Halomicrobium
           mukohataei DSM 12286]
 gi|257169231|gb|ACV46990.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Halomicrobium mukohataei DSM 12286]
          Length = 240

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           +       WI A    L  +      +    + D +  +  +  D  + L GG+     A
Sbjct: 34  EPVAAARRWIEAGATTLHLVDLDGAFEGERANADAIDAVL-DAVDADVQLGGGIRTAEDA 92

Query: 204 LKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           + +L   VD V++G AA +N  ++  + E
Sbjct: 93  IDLLDRGVDRVILGTAAVENPDIVAEISE 121


>gi|146312281|ref|YP_001177355.1| imidazole glycerol phosphate synthase subunit HisF [Enterobacter
           sp. 638]
 gi|167012159|sp|A4WC74|HIS6_ENT38 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|145319157|gb|ABP61304.1| imidazole glycerol phosphate synthase subunit hisF [Enterobacter
           sp. 638]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SAEDAAKILSFGADKISINSPALADPELITRLADRFG 121


>gi|49082098|gb|AAT50449.1| PA5141 [synthetic construct]
          Length = 246

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 2/102 (1%)

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVD 230
             ++ ++V  I +  PDL I + GG+  +      +   V  V+IG  A K    +    
Sbjct: 59  KPVNGEVVTAIARRYPDLPIQIGGGIRSLETIEHYVRAGVSYVIIGTKAVKQPEFVGEAC 118

Query: 231 EYFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
             F    + G       V  D W ++S       AR   + G
Sbjct: 119 RAFPGKVIVGLDAKDGFVATDGWAEVSEVQVIDLARRFEADG 160


>gi|51892068|ref|YP_074759.1| glutamate synthetase [Symbiobacterium thermophilum IAM 14863]
 gi|51855757|dbj|BAD39915.1| glutamate synthetase [Symbiobacterium thermophilum IAM 14863]
          Length = 481

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 24/123 (19%), Positives = 42/123 (34%), Gaps = 14/123 (11%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             +  +     +PV VK       +      R L  +++ +GV+ + +   +    G +P
Sbjct: 239 RLVRRLRAETGVPVGVKLAATHHLE------RELAVALE-AGVDFVTVDGAEGGTHGGAP 291

Query: 166 KDNRKIPNLDYDIVYEIK------KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
                +       V   +      K   D+ +   GGL    Q LK +    D V  G A
Sbjct: 292 TLQDDVGLPTLYAVARARDFLVRQKAAGDVSLIAAGGLITPGQMLKAMALGADAVYTGTA 351

Query: 219 AYK 221
           A  
Sbjct: 352 ALM 354


>gi|322372751|ref|ZP_08047287.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus sp. C150]
 gi|321277793|gb|EFX54862.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus sp. C150]
          Length = 252

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 43/119 (36%), Gaps = 11/119 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++  ++G + +        L   +  DNR+      D+V  +  +    F    GG+  
Sbjct: 36  ARAYYEAGCDELV------FLDITATSDNRETT---VDMVRRVADQVFIPFTVG-GGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +    K+L    D V +  +A  N  ++    + F N    ++    ++    W    A
Sbjct: 86  VEDMNKMLKAGADKVAVNSSALANPQLIADCAQKFGNQCVVAAIDAKKMADGSWHVFVA 144


>gi|313809954|gb|EFS47675.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL083PA1]
 gi|313830284|gb|EFS67998.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL007PA1]
 gi|314973289|gb|EFT17385.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL053PA1]
 gi|314975966|gb|EFT20061.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL045PA1]
 gi|314984016|gb|EFT28108.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL005PA1]
 gi|315080717|gb|EFT52693.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL078PA1]
 gi|315096203|gb|EFT68179.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL038PA1]
 gi|327326117|gb|EGE67907.1| pyridoxine biosynthesis protein [Propionibacterium acnes HL096PA2]
 gi|327445997|gb|EGE92651.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL043PA2]
 gi|327448023|gb|EGE94677.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL043PA1]
 gi|328760662|gb|EGF74229.1| pyridoxine biosynthesis protein [Propionibacterium acnes HL099PA1]
          Length = 279

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 16  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|295109161|emb|CBL23114.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Ruminococcus
           obeum A2-162]
          Length = 673

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 31/182 (17%), Positives = 54/182 (29%), Gaps = 17/182 (9%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EAAK V+  G++ I ++ G          P        FG  +          +  + K 
Sbjct: 154 EAAKRVQAIGFDAIEIHCGHSYLMSQFISPYYNKRTDEFGGSVENRLRFPRMVLEEVRKN 213

Query: 115 LS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +     I V +     V            ++ I +  ++   +              N  
Sbjct: 214 VGPWFPIIVRISAEERVPGGNTLEDTLEYLEYIDEF-IDMYDVSCGLNPSLQYQIDSNYL 272

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTT 228
                  +   +K +     I   G   D     KIL S  VD V +GR    +   +  
Sbjct: 273 PDGWRSYMARAVKDKFKKPVINA-GNYRDPEVVEKILESGDVDIVGMGRGLIADPNWVKK 331

Query: 229 VD 230
           V+
Sbjct: 332 VE 333


>gi|270263188|ref|ZP_06191458.1| NADH:flavin oxidoreductase/NADH oxidase [Serratia odorifera 4Rx13]
 gi|270042876|gb|EFA15970.1| NADH:flavin oxidoreductase/NADH oxidase [Serratia odorifera 4Rx13]
          Length = 681

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 26/185 (14%), Positives = 59/185 (31%), Gaps = 32/185 (17%)

Query: 61  KLVEAAKIVEDFGYNEIN--------LNVGCPSARVHEGSF-----GACLMLNPDIVGDC 107
                A + +  GY+ +         +N       V   +      G           + 
Sbjct: 152 DFAHCALLAQQAGYDGVEVMGSEGYLIN----QFLVSRTNQRDDSWGGSFSNRMRFAVEI 207

Query: 108 IAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           + A+ +A+     +  R+     V+D      +  L  +I+++G   I  +      +  
Sbjct: 208 VRAVRQAVGREFILIYRLSMLDLVEDGSSWQEIEQLALAIEQAGATLI--NTGIGWHEAR 265

Query: 164 SPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIGRAAY 220
            P     +P   +  V  ++  +     I  N  + D + A ++L   DG   M+   + 
Sbjct: 266 IPTIATMVPRAGFSWVTRKLMGKVRIPLITTNR-INDPAVAEQVL--ADGCADMV---SM 319

Query: 221 KNSAM 225
               +
Sbjct: 320 ARPFL 324


>gi|254497844|ref|ZP_05110610.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella drancourtii LLAP12]
 gi|254352922|gb|EET11691.1| 2,4-dienoyl-CoA reductase FadH1 [Legionella drancourtii LLAP12]
          Length = 662

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 24/192 (12%), Positives = 60/192 (31%), Gaps = 39/192 (20%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN----------------- 100
           +I      A++ +  GY+ I +                 L+                   
Sbjct: 135 NIQHFARCARLAQLAGYDGIEI-----------MGSEGYLINQFIVTHTNQRTDEWGGSY 183

Query: 101 PDIVG---DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWI 153
            + +    + + ++ +A+     +  R+     + D      +  L K I+K+G     I
Sbjct: 184 ENRIRFPLEVVRSVREAVGEKFIIVYRLSMLDLIADGSSWEEVVLLAKEIEKAGAT--II 241

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VD 211
           +      +   P     +P   +  + +  K   ++ +  +  +     A K++ S   D
Sbjct: 242 NTGIGWHEARIPTIGTMVPEAAFTTITKHLKPEVNIPLITSNRINTPEMANKLIESGVAD 301

Query: 212 GVMIGRAAYKNS 223
            V + R    + 
Sbjct: 302 MVSMARPFLADP 313


>gi|256830258|ref|YP_003158986.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfomicrobium baculatum DSM 4028]
 gi|256579434|gb|ACU90570.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfomicrobium baculatum DSM 4028]
          Length = 243

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 19/119 (15%), Positives = 46/119 (38%), Gaps = 13/119 (10%)

Query: 120 TVKCRIGVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ R GV+DQ+   +     + +   ++G   + +        G            + +
Sbjct: 14  CVRLRQGVEDQVTVFSDDPVAMARQWVEAGTRWLHVIDLDGAFSGT---------PRNME 64

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++ E+      + + L GG+  +  A K L   V  ++IG  A ++  +   + + +  
Sbjct: 65  LIRELCSAV-SIPVQLGGGIRSLDVAGKYLEAGVTRLIIGTVALEDPDLFRELCQAYPG 122


>gi|227510946|ref|ZP_03940995.1| tryptophan synthase alpha chain [Lactobacillus buchneri ATCC 11577]
 gi|227085688|gb|EEI21000.1| tryptophan synthase alpha chain [Lactobacillus buchneri ATCC 11577]
          Length = 264

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 55/157 (35%), Gaps = 42/157 (26%)

Query: 104 VGDCIAAMCKALSIP--------VTVK------CRIGVD--------DQIPAVALRNLVK 141
           V + + A  K  ++P        +  K       +   D          +P  +   +V 
Sbjct: 76  VFEIVEAARKETNVPMVFLTYLNIVFKYGYEAFLKRCADLNVSGLVIPDLPYESRDEIVP 135

Query: 142 SIKKSGVNGIWIHARKAILK------------------GLSPKDNRKIPNLDYDIVYEIK 183
             +K GV+ I +    +  +                  G++ + N     L  D+V EIK
Sbjct: 136 IAEKYGVDIIPLITPTSGHRIEKIAKSASGFIYVVSSMGITGERNEFFNGLK-DLVTEIK 194

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           K   D+   +  G+    QA ++    DGV+IG A  
Sbjct: 195 K-YTDVPTAIGFGVHTPEQAQEMAGIADGVIIGSAIV 230


>gi|323144806|ref|ZP_08079379.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Succinatimonas hippei YIT 12066]
 gi|322415426|gb|EFY06187.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Succinatimonas hippei YIT 12066]
          Length = 259

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/100 (16%), Positives = 38/100 (38%), Gaps = 11/100 (11%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           + +L K     G + +            +  D R++       + E+     ++   + G
Sbjct: 32  IVDLAKRYADEGADELV------FYDITASADRRRVDKSWVAKIAEVI----NIPFAVAG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           G++    A +IL    D + I   A  + +++T + + F 
Sbjct: 82  GIKTEEDAQQILAYGADKISINSPALADPSLITRLADRFG 121


>gi|320529351|ref|ZP_08030439.1| tryptophan synthase, alpha subunit [Selenomonas artemidis F0399]
 gi|320138317|gb|EFW30211.1| tryptophan synthase, alpha subunit [Selenomonas artemidis F0399]
          Length = 261

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 31/220 (14%), Positives = 65/220 (29%), Gaps = 59/220 (26%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLN-------VGCPS---ARVHEGSFGACLMLNPDIV 104
           G  +  + V+  +  E+ G + I L           P    A V     G  L       
Sbjct: 27  GCPNAEETVDIVRRAEEAGADVIELGLPFSDPMADGPVIQEASVMALKQGMTL----KKA 82

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAIL 160
            D +  + K   IP+     +G  + +        V     +G++G+ +    H     +
Sbjct: 83  LDIVKEIRKHSEIPL---IGMGYINMVHHYGFEKFVADFSAAGMDGVILPDVPHEESEEM 139

Query: 161 KGLSPKDN-----------------------------------RKIPNLDYDIVYEIKKE 185
           + +    +                                     +  +DY ++  +   
Sbjct: 140 RAVCAAHDFTLTEFITPGTTEERMAETCRDAAGFVYCVSNYGVTGVKEIDYSVIGRVCAA 199

Query: 186 N---PDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
                D+ + +  G+     A++     DGV++G A  K 
Sbjct: 200 ARRYTDVPLAIGFGIGTPDAAVRAARQADGVIVGSAVVKR 239


>gi|229494842|ref|ZP_04388595.1| dihydroorotate oxidase [Rhodococcus erythropolis SK121]
 gi|229318200|gb|EEN84068.1| dihydroorotate oxidase [Rhodococcus erythropolis SK121]
          Length = 356

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 42/111 (37%), Gaps = 11/111 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK----- 161
            + A+   +S+PV VK    + D+    A+ +L   +  +G+       R+  LK     
Sbjct: 197 ILQAVLDTVSVPVLVKIAPDLSDED-VDAVADLAIELGLAGIVATNTTIRRDGLKTPDAE 255

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL 207
               G        +     +++  +     D + I   GG+E   QA + +
Sbjct: 256 VAALGAGGLSGAPVAERSLEVLRRLYARVGDKMTIISVGGIETADQAWERI 306


>gi|150007198|ref|YP_001301941.1| dihydroorotate dehydrogenase 2 [Parabacteroides distasonis ATCC
           8503]
 gi|255015186|ref|ZP_05287312.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_1_7]
 gi|256840574|ref|ZP_05546082.1| dihydroorotate dehydrogenase 2 [Parabacteroides sp. D13]
 gi|262381193|ref|ZP_06074331.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_1_33B]
 gi|298377623|ref|ZP_06987575.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           3_1_19]
 gi|301311137|ref|ZP_07217065.1| dihydroorotate dehydrogenase family protein [Bacteroides sp. 20_3]
 gi|149935622|gb|ABR42319.1| dihydroorotate dehydrogenase family protein [Parabacteroides
           distasonis ATCC 8503]
 gi|256737846|gb|EEU51172.1| dihydroorotate dehydrogenase 2 [Parabacteroides sp. D13]
 gi|262296370|gb|EEY84300.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_1_33B]
 gi|298265642|gb|EFI07303.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           3_1_19]
 gi|300830711|gb|EFK61353.1| dihydroorotate dehydrogenase family protein [Bacteroides sp. 20_3]
          Length = 325

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 61/188 (32%), Gaps = 47/188 (25%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-------- 100
           P+   I        ++ A+ +E  G + + LNV                M          
Sbjct: 98  PIIASINCYKADAWIDFARQIELAGADALELNV--------------FFMETELTEDFES 143

Query: 101 -PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             D     I  + + +SIPV +K             + +LV  +K +G +G+ +  R   
Sbjct: 144 IRDTYVSIIRKVKETVSIPVIMKI------GKNYSNIPSLVNLLKVNGADGVVLFNR--F 195

Query: 160 LKGLSPKDNRKI-------------PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
            +     +N +I               + +  +  +  + P + I  + G+ D    +K 
Sbjct: 196 YQPDIDINNMQIVSGNVFSNHSDLSDTIRWTAI--VSGKIPGISIASSTGVHDWEDVVKC 253

Query: 207 -LPSVDGV 213
            L     V
Sbjct: 254 LLAGASAV 261


>gi|87312360|ref|ZP_01094452.1| dihydroorotate dehydrogenase [Blastopirellula marina DSM 3645]
 gi|87284925|gb|EAQ76867.1| dihydroorotate dehydrogenase [Blastopirellula marina DSM 3645]
          Length = 317

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 33/187 (17%), Positives = 63/187 (33%), Gaps = 22/187 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P  + I G    +  + A  +  +     I LN+ CP+     G     +   P+   D 
Sbjct: 96  PAIVSIAGRTSEEFTQMAARLSQYDEVGAIELNISCPN---VSGGVDFGI--CPETCRDL 150

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRN--------LVKSIKKSGVNGIWIHARKAI 159
           IA++    + P+  K    V       A            + ++    V+      R+  
Sbjct: 151 IASVRAQCTKPLLAKLTPNVARIADVAAAAEEGGADGISAINTLLGMAVDW----RRQKP 206

Query: 160 LKG--LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIG 216
           L G  +       I  +    VY+I +    + +   GG+  +   ++ L      V IG
Sbjct: 207 LLGNVMGGLSGPAIKPVALRCVYQIAQRV-KIPVIGIGGIGTIDDVMEFLVAGATAVQIG 265

Query: 217 RAAYKNS 223
            A + + 
Sbjct: 266 TANFNDP 272


>gi|212224671|ref|YP_002307907.1| hypothetical protein TON_1520 [Thermococcus onnurineus NA1]
 gi|212009628|gb|ACJ17010.1| hypothetical protein, conserved [Thermococcus onnurineus NA1]
          Length = 590

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 17/86 (19%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q+ G +    + L+E  +I ++ GY+ + LN         
Sbjct: 172 QIRMMLRNAKKEHPIGANAVQLTGGEPTLRNDLIEIIRIAKEEGYDHVQLNTD------- 224

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL 115
               G  L   P++V     A    L
Sbjct: 225 ----GIKLAFEPELVKKIREAGVNTL 246


>gi|108800128|ref|YP_640325.1| dihydroorotate dehydrogenase 2 [Mycobacterium sp. MCS]
 gi|119869256|ref|YP_939208.1| dihydroorotate dehydrogenase 2 [Mycobacterium sp. KMS]
 gi|126435753|ref|YP_001071444.1| dihydroorotate dehydrogenase 2 [Mycobacterium sp. JLS]
 gi|123369097|sp|Q1B765|PYRD_MYCSS RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|189038433|sp|A3Q1C6|PYRD_MYCSJ RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|189038434|sp|A1UHW0|PYRD_MYCSK RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|108770547|gb|ABG09269.1| dihydroorotate oxidase A [Mycobacterium sp. MCS]
 gi|119695345|gb|ABL92418.1| dihydroorotate oxidase A [Mycobacterium sp. KMS]
 gi|126235553|gb|ABN98953.1| dihydroorotate oxidase A [Mycobacterium sp. JLS]
          Length = 356

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 29/184 (15%), Positives = 61/184 (33%), Gaps = 23/184 (12%)

Query: 40  ILGFSTQEKPLALQIGGADI-------SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGS 92
            L   T + P+ + IG               ++A+ +       + +NV  P       +
Sbjct: 132 RLTRHTSDAPVGVNIGKTKATPADRAVEDYAQSARQLGPL-ATFLVVNVSSP------NT 184

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
            G   +   + +   + A+    S PV VK    + D      + +L   +  +G+    
Sbjct: 185 PGLRDLQAVESLRPILTAVRAQTSTPVLVKIAPDLSDAD-VDEIADLAVELGLAGIVATN 243

Query: 153 IHARKAILK-------GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQAL 204
               +A LK       G        +     +++  + +   D L +   GG+E    A 
Sbjct: 244 TTISRAGLKTPGVEELGPGGVSGAPVAARSLEVLRRLYRRAGDRLVLISVGGIETADDAW 303

Query: 205 KILP 208
           + + 
Sbjct: 304 ERIT 307


>gi|67516097|ref|XP_657934.1| hypothetical protein AN0330.2 [Aspergillus nidulans FGSC A4]
 gi|40746580|gb|EAA65736.1| hypothetical protein AN0330.2 [Aspergillus nidulans FGSC A4]
 gi|259489437|tpe|CBF89709.1| TPA: indoleamine 2,3-dioxygenase pyrrole 2,3-dioxygenase)
           (AFU_orthologue; AFUA_5G01450) [Aspergillus nidulans
           FGSC A4]
          Length = 435

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 70/208 (33%), Gaps = 43/208 (20%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             ++A+I    G + I ++            P        +G        I+ +   A+ 
Sbjct: 220 FAKSAEIAVKAGVDVIEIHAAHGYLVNEFLSPVTNRRTDQYGGSFENRTRILREIALAIR 279

Query: 113 KAL--SIPVTVKCR-IGVDDQIPAV---------ALRNLVKSIKKSGVNGIWIHARKAIL 160
           + +    P+ ++       +  PA          A   L+K + + GV+ +       + 
Sbjct: 280 EVIPEGTPLFLRISATEWIEDQPAAKDFGSWDLKASIELLKDLPEFGVDFLD------VS 333

Query: 161 KGLSPKDNRKIPNLDY--DIVYEIKKENP----DLFIGLNGGLEDMSQALKILPS----- 209
            G + KD +     DY  ++  +++KE         +G  G +     A +I+       
Sbjct: 334 SGGNHKDQKFHFFTDYQTEMAAKLRKELRASGARTLVGAVGFITQPDAAAQIVQGADEEG 393

Query: 210 ----VDGVMIGRAAYKNS-AMLTTVDEY 232
                D V+IGR   +    +L    + 
Sbjct: 394 VEAKADAVLIGRQFLREPEWVLNAAKKL 421


>gi|307293465|ref|ZP_07573309.1| NADH:flavin oxidoreductase/NADH oxidase [Sphingobium
           chlorophenolicum L-1]
 gi|306879616|gb|EFN10833.1| NADH:flavin oxidoreductase/NADH oxidase [Sphingobium
           chlorophenolicum L-1]
          Length = 361

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 29/185 (15%), Positives = 63/185 (34%), Gaps = 26/185 (14%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSI-PVTVKCRIG-----VDDQIPAVALRNLVKSIKKS 146
           +G  +     ++ +   A+  A+    V+V+         VDD  P+       +++++ 
Sbjct: 194 YGGSVENRIRLLREVAQAVVDAVGAERVSVRLSPNGDSQGVDDSDPSPLFAAAAEALQQI 253

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G+  + +               R+ P         + + +    + LN     + +A + 
Sbjct: 254 GIAFLELREPGPDGTFGRTDVPRQSP---------VIRRHFSGPLILNSDYG-LERAQQD 303

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           L S   D V  GRA   N  +           L  ++P+       F+ + +    DY A
Sbjct: 304 LDSGLADAVSFGRAFMANPDLPKR--------LLINAPLNEANMATFYTQGAEGYVDYPA 355

Query: 265 RHLHS 269
               +
Sbjct: 356 LEEAA 360


>gi|325675972|ref|ZP_08155655.1| 2,4-dienoyl-CoA reductase [Rhodococcus equi ATCC 33707]
 gi|325553210|gb|EGD22889.1| 2,4-dienoyl-CoA reductase [Rhodococcus equi ATCC 33707]
          Length = 676

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/179 (12%), Positives = 57/179 (31%), Gaps = 21/179 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEG--SFGACLMLNPDIVGDCIAA 110
            V  A++    GY+ + +  G         C   R ++    +G        +  + +  
Sbjct: 146 FVRCARLARSAGYDGVEIMGGEGYFVNQFLC--ERTNKRTDEWGGTPQNRRRMAVEIVRR 203

Query: 111 MCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
              A+     +  R+ + D          +  L + ++ +G   I  +      +   P 
Sbjct: 204 TRAAVGPNFVILFRLSMADLVEGGQSWDEIVALAQEVEAAGATVI--NTDIGWHESRVPT 261

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +P   +  V E   ++  + +  +  +     A +IL    V  + + R    + 
Sbjct: 262 IVTSVPRAAFVDVTEKLAKHVSIPVVASNRINMPEIAEEILTRGEVQLISMARPMLADP 320


>gi|229589850|ref|YP_002871969.1| putative xenobiotic reductase [Pseudomonas fluorescens SBW25]
 gi|229361716|emb|CAY48597.1| putative xenobiotic reductase [Pseudomonas fluorescens SBW25]
          Length = 363

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 59/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +         D+        L ++ K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVIEYDGRDEQTLTESIELARNFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P  N          + E  +    + +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTNIPWGPAFMGPIAERVRREAGIPVTSAWGFGTPQLAEGALQAGHLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|15600334|ref|NP_253828.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           aeruginosa PAO1]
 gi|107104237|ref|ZP_01368155.1| hypothetical protein PaerPA_01005310 [Pseudomonas aeruginosa PACS2]
 gi|116053288|ref|YP_793611.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|152989501|ref|YP_001351195.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           aeruginosa PA7]
 gi|218894240|ref|YP_002443109.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           aeruginosa LESB58]
 gi|254238157|ref|ZP_04931480.1| phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           aeruginosa C3719]
 gi|254243979|ref|ZP_04937301.1| phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           aeruginosa 2192]
 gi|296391991|ref|ZP_06881466.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           aeruginosa PAb1]
 gi|20455000|sp|Q9HU43|HIS4_PSEAE RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|122256695|sp|Q02EM5|HIS4_PSEAB RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|167012101|sp|A6VDR0|HIS4_PSEA7 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700346|sp|B7V3N4|HIS4_PSEA8 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|9951441|gb|AAG08526.1|AE004927_4 phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           aeruginosa PAO1]
 gi|115588509|gb|ABJ14524.1| phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126170088|gb|EAZ55599.1| phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           aeruginosa C3719]
 gi|126197357|gb|EAZ61420.1| phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           aeruginosa 2192]
 gi|150964659|gb|ABR86684.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudomonas aeruginosa PA7]
 gi|218774468|emb|CAW30285.1| phosphoribosylformimino-5-aminoimidazolecarboxamide [Pseudomonas
           aeruginosa LESB58]
          Length = 245

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 2/102 (1%)

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVD 230
             ++ ++V  I +  PDL I + GG+  +      +   V  V+IG  A K    +    
Sbjct: 59  KPVNGEVVTAIARRYPDLPIQIGGGIRSLETIEHYVRAGVSYVIIGTKAVKQPEFVGEAC 118

Query: 231 EYFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
             F    + G       V  D W ++S       AR   + G
Sbjct: 119 RAFPGKVIVGLDAKDGFVATDGWAEVSEVQVIDLARRFEADG 160


>gi|269928381|ref|YP_003320702.1| inosine-5'-monophosphate dehydrogenase [Sphaerobacter thermophilus
           DSM 20745]
 gi|269787738|gb|ACZ39880.1| inosine-5'-monophosphate dehydrogenase [Sphaerobacter thermophilus
           DSM 20745]
          Length = 511

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 21/130 (16%), Positives = 48/130 (36%), Gaps = 20/130 (15%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V + +AA+ +   I V              +A     +++ ++G + + +      +   
Sbjct: 278 VIEMVAAIKRRWDIDVIAG----------NIATGAAAQALIEAGADAVKVGVGPGSICTT 327

Query: 164 SPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYK 221
                  +P +   + V  + +    + +  +GG++     A  I    D VM+G     
Sbjct: 328 RVVAGIGVPQITAIMDVARVARAAG-VPVVADGGIQYSGDIAKAIAAGADTVMLG----- 381

Query: 222 NSAMLTTVDE 231
             ++L  VDE
Sbjct: 382 --SLLAGVDE 389


>gi|156977710|ref|YP_001448616.1| NADH-flavin oxidoreductase [Vibrio harveyi ATCC BAA-1116]
 gi|156529304|gb|ABU74389.1| hypothetical protein VIBHAR_06498 [Vibrio harveyi ATCC BAA-1116]
          Length = 363

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 28/184 (15%), Positives = 64/184 (34%), Gaps = 21/184 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AAK   + G++ + ++ G  +  + +            ++G         + + + 
Sbjct: 161 DFAHAAKRAIEAGFDGVEIHGG--NGYLIDQFLRTNSNHRTDNYGGTRENRLRFLLEVVD 218

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ +A+     V  R+        +   ++V +I ++      + AR      LS  D  
Sbjct: 219 AVSEAIGAN-KVGVRLAPFITFKDMNCPDIVPTILEASKQ---LQARDIAYLHLSEADWD 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P +      E+++   +  I    G     +A ++L     D V  GR    N  ++ 
Sbjct: 275 DAPVIPESFRIELREYFTNTIIVA--GSYTQDRADEVLEKGYADLVAFGRPFVSNPDLVA 332

Query: 228 TVDE 231
            +  
Sbjct: 333 RLQH 336


>gi|332141861|ref|YP_004427599.1| imidazole glycerol phosphate synthase subunit HisF [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|226700481|sp|B4RU62|HIS6_ALTMD RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|327551883|gb|AEA98601.1| imidazole glycerol phosphate synthase subunit HisF [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 270

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 15/98 (15%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K+G + +            +  D R +       + ++     D+   + GG++
Sbjct: 35  LAEQYAKAGADELV------FYDITASSDARVVDKSWVSRIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  A +IL    D + I   A  N  ++  + + +  
Sbjct: 85  SIEDAGRILEMGADKISINSPALNNPELINQLHDVYGQ 122


>gi|309774754|ref|ZP_07669776.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308917439|gb|EFP63157.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 238

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 53/123 (43%), Gaps = 18/123 (14%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNG 150
           G   + NPD + + ++   + +++ +  K  +       Q   V   +    ++  GV  
Sbjct: 103 GTAAIENPDFLREAVSMYKEKIAVGIDCKNGMVCGHGWLQESEVQYIDFAIQMEAVGVKT 162

Query: 151 IWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           I +   +R   ++G +            +++ E+KK    + I  +GG++D+S  ++ L 
Sbjct: 163 IIVTDISRDGTMRGPNT-----------EMLAELKK-TVSINIIASGGIKDISH-IRALK 209

Query: 209 SVD 211
            +D
Sbjct: 210 ELD 212



 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 12/104 (11%), Positives = 36/104 (34%), Gaps = 11/104 (10%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           + ++ ++ ++ G   + +       +G     +  +             ++  + + + G
Sbjct: 32  IADIARAFEQQGAEYVHMVDLNGAKEGKKINQDSIVKTA----------QSLSIPVEVGG 81

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
           G+  M      L   +  V++G AA +N   L      +   + 
Sbjct: 82  GIRSMEDVRFYLEQGISRVILGTAAIENPDFLREAVSMYKEKIA 125


>gi|261409700|ref|YP_003245941.1| isopentenyl pyrophosphate isomerase [Paenibacillus sp. Y412MC10]
 gi|261286163|gb|ACX68134.1| isopentenyl-diphosphate delta-isomerase, type 2 [Paenibacillus sp.
           Y412MC10]
          Length = 370

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 21/128 (16%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAILKG 162
           I  +C+ LSIPV +K       ++         +++   G   I +          + K 
Sbjct: 206 IEDLCRTLSIPVGIK-------EVGWGIDGETAQTLLDVGAAFIDVAGAGGTSWSQVEKF 258

Query: 163 LSPKDNRKIPN---LDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
            SP   R+        +     + + E+++  P   +  +GGL+  +  A  +    D  
Sbjct: 259 RSPDPVRRAAAEAFAGWGNPTAECIAEVREAAPACALIGSGGLQSGVDAAKALALGADLA 318

Query: 214 MIGRAAYK 221
             GR    
Sbjct: 319 GFGRGLLG 326


>gi|91217704|ref|ZP_01254661.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Psychroflexus torquis ATCC 700755]
 gi|91184208|gb|EAS70594.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Psychroflexus torquis ATCC 700755]
          Length = 241

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 14/96 (14%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           +   + +   +K     G++ +     ++  +L+G S            D+   I   NP
Sbjct: 143 KASNLEIEKFIKDFVAHGIDYVISTDISKDGMLQGPST-----------DLYRSILMNNP 191

Query: 188 DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN 222
           DL +  +GG+ ++     +L    +GV+IG+A Y+N
Sbjct: 192 DLKLIASGGISNLKDLEDVLEIGCEGVIIGKAIYEN 227


>gi|309797285|ref|ZP_07691680.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 145-7]
 gi|308119160|gb|EFO56422.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 145-7]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SAEDAAKILSFGADKISINSPALADPELITRLADRFG 121


>gi|294637054|ref|ZP_06715369.1| imidazoleglycerol phosphate synthase, cyclase subunit [Edwardsiella
           tarda ATCC 23685]
 gi|291089751|gb|EFE22312.1| imidazoleglycerol phosphate synthase, cyclase subunit [Edwardsiella
           tarda ATCC 23685]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +  +   A   G +         +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAQRYAAEGADELVFYDITASADGRT---------VDKRWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + +A +IL    D + I   A  +  +++ + + F 
Sbjct: 85  SVEEAGQILSYGADKISINSPALADPTLISRLADRFG 121


>gi|187919769|ref|YP_001888800.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
 gi|187718207|gb|ACD19430.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
          Length = 687

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + + ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGVEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGTEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGADFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    L +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKLPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|75909254|ref|YP_323550.1| dihydroorotate dehydrogenase 2 [Anabaena variabilis ATCC 29413]
 gi|75702979|gb|ABA22655.1| Dihydroorotate dehydrogenase [Anabaena variabilis ATCC 29413]
          Length = 343

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/116 (14%), Positives = 42/116 (36%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD-- 106
           P+   + G+ +    E A+++E  G   + LN                +  +P++  +  
Sbjct: 103 PIIASLNGSSLDGWTEYARMIEQAGATALELNT-------------YSVHTDPELTSEQI 149

Query: 107 ------CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                  +  +  ++ IPV +K             + N+ K +  +G + + +  R
Sbjct: 150 EQSYINMLKVVKASVQIPVAIKLSPYF------TNMANMAKRLDDAGADALVLFNR 199


>gi|57642080|ref|YP_184558.1| hypothetical protein TK2145 [Thermococcus kodakarensis KOD1]
 gi|57160404|dbj|BAD86334.1| hypothetical protein, conserved, radical SAM superfamily
           [Thermococcus kodakarensis KOD1]
          Length = 590

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 17/81 (20%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q  G +      L+E  +I ++ GY+ + LN         
Sbjct: 173 QIRMMLRNAKKEHPIGANAVQFTGGEPTLRDDLIEIIRIAKEEGYDHVQLNTD------- 225

Query: 90  EGSFGACLMLNPDIVGDCIAA 110
               G  L  +P++V     A
Sbjct: 226 ----GIKLAFDPELVKKIREA 242


>gi|238752854|ref|ZP_04614320.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia rohdei ATCC 43380]
 gi|238708950|gb|EEQ01202.1| 2,4-dienoyl-CoA reductase [NADPH] [Yersinia rohdei ATCC 43380]
          Length = 673

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/189 (12%), Positives = 57/189 (30%), Gaps = 40/189 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPDI 103
                A++ +  GY+ + +        +    +                 G         
Sbjct: 144 DFAHCAQLAQQAGYDGVEV--------MGSEGYLINQFLAARTNHRDDEWGGDFTQRMRF 195

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+ +A      +  R+     V++      +  L  +I+ +G   I  +     
Sbjct: 196 AVEIVRAVRQATGPDFILIYRLSMLDLVEEGSNWDEIEQLALAIEHAGATLI--NTGIGW 253

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIG 216
            +   P     +P   +  V  ++  +     I  N  + D + A ++L   DG   M+ 
Sbjct: 254 HEARIPTIATMVPRAGFSWVTRKLMGKVTIPLITTNR-INDPAVAEQVL--ADGCADMV- 309

Query: 217 RAAYKNSAM 225
             +     +
Sbjct: 310 --SMARPFL 316


>gi|229178456|ref|ZP_04305822.1| NADPH dehydrogenase [Bacillus cereus 172560W]
 gi|228604964|gb|EEK62419.1| NADPH dehydrogenase [Bacillus cereus 172560W]
          Length = 319

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 46/136 (33%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +    P+ V+        D +         K +K+ G++ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWDGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGIDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PAHIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|307545637|ref|YP_003898116.1| dihydroorotate dehydrogenase [Halomonas elongata DSM 2581]
 gi|307217661|emb|CBV42931.1| dihydroorotate dehydrogenase 2 [Halomonas elongata DSM 2581]
          Length = 342

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 24/114 (21%), Positives = 48/114 (42%), Gaps = 12/114 (10%)

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLSP 165
           A+ +A    V +  +I  D     VAL  + +S++ +GV+         +R A+      
Sbjct: 202 ALDRATGRRVPLAVKIAPDMSEAEVAL--VAQSLEANGVDAAIATNTTVSRDAVEGLPGA 259

Query: 166 KDN-----RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
           ++      R +      ++  +++  PDL I   GG++  + AL+      D V
Sbjct: 260 EEQGGLSGRPVFEPSNTVIRALRRRLPDLPIIGVGGIDSGAAALEKQEAGADLV 313


>gi|253572882|ref|ZP_04850280.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 1_1_6]
 gi|251837514|gb|EES65607.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 1_1_6]
          Length = 326

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 65/189 (34%), Gaps = 31/189 (16%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I   +D   + + AK +++ G + + +N+    + V    +G+    + D     
Sbjct: 98  PIIASINCYSDAEWI-DFAKQIQEAGADALEINILALQSDVQYT-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  + + +SIPV +K                L+  +  +G   + +  R    +     +
Sbjct: 152 LRHIKRTVSIPVIMKL------GDNLTNPVALIDQLYANGAAAVVLFNR--FYQPDINIE 203

Query: 168 NRK-------------IPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGV 213
           N +                L +  +     +  D     +GG+ +       IL     V
Sbjct: 204 NMEQISGAVFSTSADLATPLRWIGIASSVVDKIDY--AASGGVSNPEAVVKAILAGATAV 261

Query: 214 MIGRAAYKN 222
            +  A Y+N
Sbjct: 262 EVCSAVYQN 270


>gi|253773046|ref|YP_003035877.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli 'BL21-Gold(DE3)pLysS AG']
 gi|254162013|ref|YP_003045121.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli B str. REL606]
 gi|300929181|ref|ZP_07144667.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 187-1]
 gi|242377670|emb|CAQ32430.1| imidazole glycerol phosphate synthase, HisF subunit, subunit of
           imidazole glycerol phosphate synthase [Escherichia coli
           BL21(DE3)]
 gi|253324090|gb|ACT28692.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli 'BL21-Gold(DE3)pLysS AG']
 gi|253973914|gb|ACT39585.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli B str. REL606]
 gi|253978108|gb|ACT43778.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli BL21(DE3)]
 gi|300462858|gb|EFK26351.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 187-1]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + E F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLAERFG 121


>gi|299821191|ref|ZP_07053079.1| pyridoxine biosynthesis protein [Listeria grayi DSM 20601]
 gi|299816856|gb|EFI84092.1| pyridoxine biosynthesis protein [Listeria grayi DSM 20601]
          Length = 329

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 63  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 116

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 117 ARIGHITE---------ARILEAMGVDYI 136


>gi|206890008|ref|YP_002248171.1| ribulose-phosphate 3-epimerase [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741946|gb|ACI21003.1| ribulose-phosphate 3-epimerase [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 219

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 42/107 (39%), Gaps = 23/107 (21%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNV--GCPSARVHEGSFGACLMLNPDIVGDC 107
           +A  I  AD  +L E  K  E  G + I+++V  GC    +  G                
Sbjct: 4   IAPSILSADFGRLAEEVKHAEQAGADMIHIDVMDGCFVPNITIGPL-------------I 50

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           + A+ KA  +P+ V     +    P   + + VK    +G + + +H
Sbjct: 51  VEAVKKATMLPLDV----HLMIIQPEKYIEDFVK----AGADILTVH 89


>gi|262375193|ref|ZP_06068427.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter lwoffii SH145]
 gi|262310206|gb|EEY91335.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter lwoffii SH145]
          Length = 244

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I +  PDL I + GG+  +      L   V  V+IG  A ++   
Sbjct: 60  ------PIHKPVVEAIVRSQPDLPIQIGGGIRSLETIEHYLQAGVSFVIIGTKAVQDPEF 113

Query: 226 LTTVDEYFSN 235
           +      F+ 
Sbjct: 114 VEEACRKFAG 123


>gi|297560033|ref|YP_003679007.1| NADH:flavin oxidoreductase/NADH oxidase [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
 gi|296844481|gb|ADH66501.1| NADH:flavin oxidoreductase/NADH oxidase [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
          Length = 386

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 24/162 (14%), Positives = 45/162 (27%), Gaps = 18/162 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRN---------LVK 141
           +G           + + A+ +     +PV  +              R          L K
Sbjct: 215 YGGSPENRMRFALEVVEAVREVWPEHLPVFFRTSATDWLTENEADEREGWTGEDTVLLAK 274

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
            ++  GV+ + +     +   L P               E  +    L  G  G + + +
Sbjct: 275 ELQARGVDLLDVSTGGLVADALIPVGPNYQVPF-----AERVRGATGLPTGAVGAITEPA 329

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           QA +I+ S   D V +GR   +         E          
Sbjct: 330 QAEEIVASGRADAVFLGRQLLREPYWAHRAAEELGADSHWPE 371


>gi|73668839|ref|YP_304854.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Methanosarcina
           barkeri str. Fusaro]
 gi|91206930|sp|Q46CW8|HIS4_METBF RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|72396001|gb|AAZ70274.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Methanosarcina
           barkeri str. Fusaro]
          Length = 245

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 12/108 (11%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
             P     + V+     G   + +      ++G      RK   +   IV   +K+   +
Sbjct: 32  DDPVEVALDWVRK----GAKTLHLVDLDGAIEG-----ERKNAPIIEKIVSACQKKGVQI 82

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            +G  GG+     A  +L   V  V++G AA KN  ++  +   F N 
Sbjct: 83  QVG--GGIRSFEDAASLLELGVSRVILGTAALKNPELVQQLSSTFGNE 128


>gi|46136337|ref|XP_389860.1| hypothetical protein FG09684.1 [Gibberella zeae PH-1]
          Length = 426

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 28/195 (14%), Positives = 62/195 (31%), Gaps = 28/195 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V A K     G++ I ++            P++      +G        ++ + +    +
Sbjct: 213 VNAVKRALKVGFDAIEVHAAHGYLINSFLSPTSNQRTDDYGGSFENRIRLLVEIVQLTRE 272

Query: 114 ALSI--PVTVKC----RIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLS 164
            +    PV  +      +  D  +P   ++    L K +  +GV+ + +        GL 
Sbjct: 273 IVPQEYPVFARIPGTDYLDFDPSLPQWHIQEAALLAKILADNGVDLLDVTGG-----GLD 327

Query: 165 PKDNRKIPN-LDYDIVYEIKKEN--PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
            +                ++K        +   G +    QA   L   S+D V +GR  
Sbjct: 328 SRQRINSGPGYQVPWADAVRKAVKGTGTVVTSVGMITSGKQAQGYLDDGSIDAVFVGRGF 387

Query: 220 YKNSAMLTTVDEYFS 234
            K+  ++    +   
Sbjct: 388 LKDPNLVWHWADELD 402


>gi|322376459|ref|ZP_08050952.1| dihydroorotate dehydrogenase B [Streptococcus sp. M334]
 gi|321282266|gb|EFX59273.1| dihydroorotate dehydrogenase B [Streptococcus sp. M334]
          Length = 90

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 2/67 (2%)

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAML 226
                 +   ++ ++ +   DL I   GG++    AL++ L     + +G A + N    
Sbjct: 1   WSSSLPVALKLIRQVAQ-TTDLPIIGMGGVDSAEAALEMYLAGASAIGVGTANFTNPYAC 59

Query: 227 TTVDEYF 233
             + E  
Sbjct: 60  PDIIENL 66


>gi|313764526|gb|EFS35890.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL013PA1]
 gi|313807445|gb|EFS45932.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL087PA2]
 gi|313816067|gb|EFS53781.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL059PA1]
 gi|313818491|gb|EFS56205.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL046PA2]
 gi|313820256|gb|EFS57970.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL036PA1]
 gi|313822935|gb|EFS60649.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL036PA2]
 gi|313825134|gb|EFS62848.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL063PA1]
 gi|313827704|gb|EFS65418.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL063PA2]
 gi|314915521|gb|EFS79352.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL005PA4]
 gi|314918195|gb|EFS82026.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL050PA1]
 gi|314920010|gb|EFS83841.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL050PA3]
 gi|314925143|gb|EFS88974.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL036PA3]
 gi|314932024|gb|EFS95855.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL067PA1]
 gi|314955894|gb|EFT00294.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL027PA1]
 gi|314958206|gb|EFT02309.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL002PA1]
 gi|314967761|gb|EFT11860.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL037PA1]
 gi|314988199|gb|EFT32290.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL005PA2]
 gi|314990001|gb|EFT34092.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL005PA3]
 gi|315085727|gb|EFT57703.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL002PA3]
 gi|315088852|gb|EFT60828.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL072PA1]
 gi|315098463|gb|EFT70439.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL059PA2]
 gi|315101178|gb|EFT73154.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL046PA1]
 gi|315105453|gb|EFT77429.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL030PA1]
 gi|315108400|gb|EFT80376.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL030PA2]
 gi|327332009|gb|EGE73746.1| pyridoxine biosynthesis protein [Propionibacterium acnes HL096PA3]
 gi|327443212|gb|EGE89866.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL013PA2]
 gi|327450852|gb|EGE97506.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL087PA3]
 gi|327453800|gb|EGF00455.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL083PA2]
 gi|328754272|gb|EGF67888.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL087PA1]
 gi|328754475|gb|EGF68091.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL025PA2]
          Length = 279

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 16  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|224367447|ref|YP_002601610.1| FadH [Desulfobacterium autotrophicum HRM2]
 gi|223690163|gb|ACN13446.1| FadH [Desulfobacterium autotrophicum HRM2]
          Length = 678

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 20/132 (15%), Positives = 46/132 (34%), Gaps = 8/132 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +A + KA+     +  R+     VD       +  L + ++ +G   I  +      +
Sbjct: 204 EIVARVRKAVGSDFIIIYRLSMLDLVDGGSTFDEIVTLGRGVEDAGATLI--NTGIGWHE 261

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAA 219
              P    ++P   +  V    +   +L I  +  +     A  +L   D  M+   R  
Sbjct: 262 ARIPTIATRVPRAAFTWVTAKVRAELNLPIITSNRINTPGVAEAVLARGDADMVSMARPF 321

Query: 220 YKNSAMLTTVDE 231
             + A +   ++
Sbjct: 322 LADPAFVQKAEQ 333


>gi|20808781|ref|NP_623952.1| N-acetylmannosamine-6-phosphate 2-epimerase [Thermoanaerobacter
           tengcongensis MB4]
 gi|20517428|gb|AAM25556.1| putative N-acetylmannosamine-6-phosphate epimerase
           [Thermoanaerobacter tengcongensis MB4]
          Length = 207

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 18/102 (17%), Positives = 39/102 (38%), Gaps = 13/102 (12%)

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGL 163
            D + A+ K +SIPV    +   +   P +      V  + ++G + + I A KA   G 
Sbjct: 22  EDIV-AIKKEVSIPVIGLIKKRYEGYAPYITPTMEEVDKVIEAGADIVAIDATKAYKPGG 80

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                        + +  IK++ P + +     +    + ++
Sbjct: 81  LTTG---------EFLKRIKEKYPKILVMA--DISTYEEGIE 111


>gi|89075752|ref|ZP_01162140.1| imidazole glycerol phosphate synthase subunit HisF [Photobacterium
           sp. SKA34]
 gi|89048484|gb|EAR54059.1| imidazole glycerol phosphate synthase subunit HisF [Photobacterium
           sp. SKA34]
          Length = 257

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  +  +++T+ + F 
Sbjct: 85  SADDASRILQFGADKVSINSPALADPTLISTLADKFG 121


>gi|284048274|ref|YP_003398613.1| NADH:flavin oxidoreductase/NADH oxidase [Acidaminococcus fermentans
           DSM 20731]
 gi|283952495|gb|ADB47298.1| NADH:flavin oxidoreductase/NADH oxidase [Acidaminococcus fermentans
           DSM 20731]
          Length = 648

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 20/146 (13%), Positives = 46/146 (31%), Gaps = 7/146 (4%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA--VALRNLVKSIKKSG 147
           ++G  L        + + A+  A+    P+  +       +          + ++I+   
Sbjct: 196 AYGGSLENRTRFAVEVLQAVRAAVGPFFPIEFRMSGAEFTEGGYGLDEGVKIAQAIEPYA 255

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                         G++     +    +  +  EI+K      +   GGL D +   +I+
Sbjct: 256 DLLHVSAGTYQKTFGITHPSMFEDHGRNVYLAAEIRKHVSK-PVATIGGLTDPAMMEEII 314

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDE 231
                D V + R    +      +DE
Sbjct: 315 ASGKADVVYMARQLLADPETPRKIDE 340


>gi|289810743|ref|ZP_06541372.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. AG3]
          Length = 189

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|261343396|ref|ZP_05971041.1| imidazoleglycerol phosphate synthase, cyclase subunit [Providencia
           rustigianii DSM 4541]
 gi|282568538|gb|EFB74073.1| imidazoleglycerol phosphate synthase, cyclase subunit [Providencia
           rustigianii DSM 4541]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V ++  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVAKVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + + F 
Sbjct: 85  SVDDAAQILSFGADKISINSPALSDPTLISRLADRFG 121


>gi|88602326|ref|YP_502504.1| fructose-bisphosphate aldolase [Methanospirillum hungatei JF-1]
 gi|88187788|gb|ABD40785.1| 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase
           [Methanospirillum hungatei JF-1]
          Length = 257

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 28/158 (17%), Positives = 51/158 (32%), Gaps = 25/158 (15%)

Query: 24  TEMI-VADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG 82
           ++MI  A  ++R   +  +       P    I   D   +  A ++ E+ G + +  N  
Sbjct: 120 SKMIESAGMVVRDCNRWGIPLLAMIYPRGKGIDPNDPRHVGHAVRVAEELGADLVKTNYT 179

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS 142
                            +P+     +    KA SIPV +      +D      + + V  
Sbjct: 180 ----------------GDPESFAKIV----KASSIPVLIAGGEKGEDLDCYKTIYDAVHF 219

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
            K +GV       R A  +    K    I  + +  V 
Sbjct: 220 AKCAGVCM----GRNAFQRDNVAKFVSNISQVVHQGVR 253


>gi|78066422|ref|YP_369191.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia sp. 383]
 gi|77967167|gb|ABB08547.1| NADH-flavin oxidoreductase/NADH oxidase [Burkholderia sp. 383]
          Length = 372

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 32/186 (17%), Positives = 67/186 (36%), Gaps = 27/186 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINL---NVGCPSARVHEG------SFGACLMLNPDIVGDCIAA 110
            +  ++A      G++ + +   N   P   +          +G  L      + + IAA
Sbjct: 161 DEFRQSAAHARSAGFDGVEIHAANGYLPHQFLSSTLNRRDDRYGGTLANRVRFLEEIIAA 220

Query: 111 MCKALSI-PVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +   + +  V V+         V D  P      + + + ++GV   ++HA         
Sbjct: 221 VGGEIPLSRVGVRISPYAKYNNVRDTDPDATYAYVGRMLDEAGVA--YVHAADT------ 272

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNS 223
              N      D   + EI +++    + +NGG+  D++  L +    D V   RA   N 
Sbjct: 273 ---NGWSGEPDLPRIIEIVRKSFGGALIVNGGISPDVATKLIMSGDADLVAFARAYIANP 329

Query: 224 AMLTTV 229
            ++  +
Sbjct: 330 DLVERI 335


>gi|53716955|ref|YP_106013.1| xenobiotic reductase A [Burkholderia mallei ATCC 23344]
 gi|67643337|ref|ZP_00442084.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei GB8 horse 4]
 gi|121597607|ref|YP_990132.1| xenobiotic reductase A [Burkholderia mallei SAVP1]
 gi|124382582|ref|YP_001023951.1| xenobiotic reductase A [Burkholderia mallei NCTC 10229]
 gi|126445655|ref|YP_001078673.1| xenobiotic reductase A [Burkholderia mallei NCTC 10247]
 gi|167001465|ref|ZP_02267262.1| xenobiotic reductase A [Burkholderia mallei PRL-20]
 gi|254174203|ref|ZP_04880865.1| xenobiotic reductase A [Burkholderia mallei ATCC 10399]
 gi|254200866|ref|ZP_04907231.1| xenobiotic reductase A [Burkholderia mallei FMH]
 gi|254204832|ref|ZP_04911185.1| xenobiotic reductase A [Burkholderia mallei JHU]
 gi|254356598|ref|ZP_04972873.1| xenobiotic reductase A [Burkholderia mallei 2002721280]
 gi|52422925|gb|AAU46495.1| xenobiotic reductase A [Burkholderia mallei ATCC 23344]
 gi|121225405|gb|ABM48936.1| xenobiotic reductase A [Burkholderia mallei SAVP1]
 gi|124290602|gb|ABM99871.1| xenobiotic reductase A [Burkholderia mallei NCTC 10229]
 gi|126238509|gb|ABO01621.1| xenobiotic reductase A [Burkholderia mallei NCTC 10247]
 gi|147748478|gb|EDK55553.1| xenobiotic reductase A [Burkholderia mallei FMH]
 gi|147754418|gb|EDK61482.1| xenobiotic reductase A [Burkholderia mallei JHU]
 gi|148025625|gb|EDK83748.1| xenobiotic reductase A [Burkholderia mallei 2002721280]
 gi|160695249|gb|EDP85219.1| xenobiotic reductase A [Burkholderia mallei ATCC 10399]
 gi|238524660|gb|EEP88092.1| oxidoreductase, FAD/FMN-binding [Burkholderia mallei GB8 horse 4]
 gi|243062775|gb|EES44961.1| xenobiotic reductase A [Burkholderia mallei PRL-20]
          Length = 365

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 63/177 (35%), Gaps = 19/177 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AAK   D G+  + L+       + +            ++G         + + +AA+
Sbjct: 161 VAAAKRALDAGFEWLELHFA--HGYLAQSFFSVHSNRRADAYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +P+T +  +   D      L   ++  K+  + G+ + +        +P    
Sbjct: 219 REVWPERLPLTARFGVIEYDGRDEQTLAESIELAKRFKLEGLDLLSVTIGFS--TPAARI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                    V E  +    L +    G++  + A +++    +D VM+GRA   +  
Sbjct: 277 PWGPAFLAPVAERVRREAQLPVASAWGIDAPALAERVVREGQLDLVMVGRAHLADPH 333


>gi|332968806|gb|EGK07854.1| 2,4-dienoyl-coA reductase [Psychrobacter sp. 1501(2011)]
          Length = 744

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 22/131 (16%), Positives = 47/131 (35%), Gaps = 10/131 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            + A+ KA+     +  R+     V D      +  + K+++++GV+   I+      + 
Sbjct: 239 VVNAVRKAVGEDFIIVFRLSMIDLVKDGNVMDEVITVAKALEEAGVS--IINTGIGWHEA 296

Query: 163 LSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAA 219
             P     +P   + D   E+KK      +  N  +     A  IL     D + + R  
Sbjct: 297 RVPTIVTSVPRAAFVDYTAEVKKHVSIPVMAANR-INMPETAESILASGKADLIQMARPF 355

Query: 220 YKNSAMLTTVD 230
             +   +   +
Sbjct: 356 LADPHWVNKAE 366


>gi|217419312|ref|ZP_03450819.1| xenobiotic reductase A [Burkholderia pseudomallei 576]
 gi|254183090|ref|ZP_04889682.1| xenobiotic reductase A [Burkholderia pseudomallei 1655]
 gi|184213623|gb|EDU10666.1| xenobiotic reductase A [Burkholderia pseudomallei 1655]
 gi|217398616|gb|EEC38631.1| xenobiotic reductase A [Burkholderia pseudomallei 576]
          Length = 365

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 63/177 (35%), Gaps = 19/177 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
           V AAK   D G+  + L+       + +            ++G         + + +AA+
Sbjct: 161 VAAAKRALDAGFEWLELHFA--HGYLAQSFFSVHSNRRADAYGGSAENRGRFLVETLAAV 218

Query: 112 CKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     +P+T +  +   D      L   ++  K+  + G+ + +        +P    
Sbjct: 219 REVWPERLPLTARFGVIEYDGRDEQTLAESIELAKRFKLEGLDLLSVTIGFS--TPAARI 276

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSA 224
                    V E  +    L +    G++  + A +++    +D VM+GRA   +  
Sbjct: 277 PWGPAFLAPVAERVRREAQLPVASAWGIDAPALAERVVREGQLDLVMVGRAHLADPH 333


>gi|295098230|emb|CBK87320.1| imidazole glycerol phosphate synthase subunit hisF [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SADDAAKILSFGADKISINSPALADPELITRLADRFG 121


>gi|170765709|ref|ZP_02900520.1| 2,4-dienoyl-CoA reductase [Escherichia albertii TW07627]
 gi|170124855|gb|EDS93786.1| 2,4-dienoyl-CoA reductase [Escherichia albertii TW07627]
          Length = 672

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 24/195 (12%), Positives = 58/195 (29%), Gaps = 35/195 (17%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLHTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + +  + + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVRTVRERVGNDFIIIYRLSMLDLVEGGGTFSETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI-- 215
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQIADDILSRGDADMVSM 310

Query: 216 GRAAYKNSAMLTTVD 230
            RA   ++ +L+   
Sbjct: 311 ARAFLADAELLSKAR 325


>gi|296156301|ref|ZP_06839140.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
 gi|295893807|gb|EFG73586.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. Ch1-1]
          Length = 687

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + + ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGVEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGTEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGADFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    L +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKLPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|206971983|ref|ZP_03232931.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus AH1134]
 gi|206732906|gb|EDZ50080.1| NADH:flavin oxidoreductase / NADH oxidase family protein [Bacillus
           cereus AH1134]
          Length = 345

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +++ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMQEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK E+  +  G  G +    QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIK-EHTKIATGAVGLITTGPQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|167745453|ref|ZP_02417580.1| hypothetical protein ANACAC_00144 [Anaerostipes caccae DSM 14662]
 gi|167655174|gb|EDR99303.1| hypothetical protein ANACAC_00144 [Anaerostipes caccae DSM 14662]
          Length = 261

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           D+D  +++ K+N D+   +  G+    QA K+    DGV++G A  
Sbjct: 189 DFDAFFDVIKKNADIPCAVGFGISGPEQAKKMSQYCDGVIVGSAIV 234


>gi|125717357|ref|YP_001034490.1| NADH-dependent flavin oxidoreductase [Streptococcus sanguinis SK36]
 gi|125497274|gb|ABN43940.1| NADH-dependent flavin oxidoreductase, putative [Streptococcus
           sanguinis SK36]
          Length = 367

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 29/225 (12%), Positives = 74/225 (32%), Gaps = 27/225 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPD-IVGD 106
              + A +     G++ + L             P   V +  +G  L   +  P  ++  
Sbjct: 147 EDFLSAIRRAIQAGFDGVELHGANTYLIQQFVSPHPNVRQDKWGGSLNNRLRFPKTLLKR 206

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKK---SGVNGIWIHARKAILKG 162
               + +    P  +  R   ++ + P + L + ++ +++     V+ + I         
Sbjct: 207 AKQLVKEEADRPFLIGYRFSPEEIEEPGIQLYDTLQLLEQLIYHQVDYLHISTSDVWRS- 265

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAA 219
            S +D++    +   I+   KK N  + +   G ++    A ++L +  G+    +G+A 
Sbjct: 266 -SIRDSQDSEPVIQKII---KKINGRVPLIGVGQIKTKQDAQRVLDA--GIPLFALGKAL 319

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
             +      V       +  +   + + D             Y  
Sbjct: 320 LLDPDWAEKVVSGREEEVIRAYRDELQADLALPTAFVEDARSYLE 364


>gi|157369853|ref|YP_001477842.1| imidazole glycerol phosphate synthase subunit HisF [Serratia
           proteamaculans 568]
 gi|167012206|sp|A8GC74|HIS6_SERP5 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|157321617|gb|ABV40714.1| imidazoleglycerol phosphate synthase, cyclase subunit [Serratia
           proteamaculans 568]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  +  +++ + + F 
Sbjct: 85  SPEDASQILSFGADKISINSPALADPTLISRLADRFG 121


>gi|332285713|ref|YP_004417624.1| 2-oxo-4-hydroxypentanoate aldolase [Pusillimonas sp. T7-7]
 gi|330429666|gb|AEC21000.1| 2-oxo-4-hydroxypentanoate aldolase [Pusillimonas sp. T7-7]
          Length = 337

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 13/67 (19%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           G AD   L E A+ +E +G + +NL                 L+  P+ V   + A+ +A
Sbjct: 139 GMADPKTLAEEARKLESYGADYVNL--------AESQGH---LL--PEDVAARVRAVREA 185

Query: 115 LSIPVTV 121
           ++IP+  
Sbjct: 186 VNIPIGF 192


>gi|313672724|ref|YP_004050835.1| dihydroorotate oxidase [Calditerrivibrio nitroreducens DSM 19672]
 gi|312939480|gb|ADR18672.1| dihydroorotate oxidase [Calditerrivibrio nitroreducens DSM 19672]
          Length = 322

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 72/189 (38%), Gaps = 37/189 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG----DCIAAMCKALSIPVTV 121
           A+ +ED G + + LN+        +         +P  +     D + ++  A+ IP+ V
Sbjct: 114 ARQIEDAGADALELNIA-YIPFSVK--------EDPREIEKKYVDIVYSVRNAIKIPLAV 164

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD------ 175
           K            ++  +VK++K +G NGI +  +    +     +N K   L+      
Sbjct: 165 KI------GYYFTSVPLMVKNLKDAGANGITMFNK--FFRMSIDVENMKFHGLEVYSCIE 216

Query: 176 --YDIVY--EIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN-----SAM 225
             Y ++    +     ++ I  + G+ + + AL+ L        I  A YK        +
Sbjct: 217 ETYQVLRYVAVCSNQVNIDISASTGIHNANIALQHLMAGAKTFQIVSAIYKKGYGVIPEI 276

Query: 226 LTTVDEYFS 234
           +  ++ Y  
Sbjct: 277 VNDINNYLD 285


>gi|289706786|ref|ZP_06503129.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1 [Micrococcus
           luteus SK58]
 gi|289556471|gb|EFD49819.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1 [Micrococcus
           luteus SK58]
          Length = 314

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 70/225 (31%), Gaps = 70/225 (31%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I ED G   +      P+        G   M +PD++   + A    +SIPV  K
Sbjct: 48  AEQARIAEDAGAVAVMALERVPAD--IRAQGGVARMSDPDLIDGIVEA----VSIPVMAK 101

Query: 123 CRI--------------GVDDQIPAVALRNLVKSIKKS---------------------- 146
            RI                 D+   ++  + V  I K                       
Sbjct: 102 ARIGHFVEAQVLQALKVDFIDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITE 161

Query: 147 GVNGI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK 184
           G   I                    I    A L+GL+  +           Y++V E+  
Sbjct: 162 GAAMIRSKGEAGTGDVSEAVKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVA- 220

Query: 185 ENPDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
           E   L + +   GG+   + A  ++    DGV +G   +   N A
Sbjct: 221 ETGALPVVMFTAGGVATPADAALMMQMGADGVFVGSGIFKSGNPA 265


>gi|229190156|ref|ZP_04317159.1| NADPH dehydrogenase [Bacillus cereus ATCC 10876]
 gi|228593273|gb|EEK51089.1| NADPH dehydrogenase [Bacillus cereus ATCC 10876]
          Length = 319

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +++ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMQEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK E+  +  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIK-EHTKIATGAVGLITTGPQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|254392009|ref|ZP_05007200.1| inosine-5'-monophosphate dehydrogenase [Streptomyces clavuligerus
           ATCC 27064]
 gi|294814531|ref|ZP_06773174.1| Inosine-5'-monophosphate dehydrogenase [Streptomyces clavuligerus
           ATCC 27064]
 gi|326442921|ref|ZP_08217655.1| inosine-5'-monophosphate dehydrogenase [Streptomyces clavuligerus
           ATCC 27064]
 gi|197705687|gb|EDY51499.1| inosine-5'-monophosphate dehydrogenase [Streptomyces clavuligerus
           ATCC 27064]
 gi|294327130|gb|EFG08773.1| Inosine-5'-monophosphate dehydrogenase [Streptomyces clavuligerus
           ATCC 27064]
          Length = 500

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 24/118 (20%), Positives = 47/118 (39%), Gaps = 10/118 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +  +VGD +A +    S         GVD     +A R+  +++  SGV+GI +      
Sbjct: 259 HSRLVGDMVAKIKSNSS---------GVDVIGGNIATRDGAQALIDSGVDGIKVGVGPGS 309

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           +          +P +       +  +   + +  +GGL+     A  ++   D VM+G
Sbjct: 310 ICTTRVVAGIGVPQVTAIYEASLAAKAAGVPVIGDGGLQYSGDIAKALVAGADTVMLG 367


>gi|148555631|ref|YP_001263213.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Sphingomonas
           wittichii RW1]
 gi|167012111|sp|A5V9V9|HIS4_SPHWW RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|148500821|gb|ABQ69075.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Sphingomonas
           wittichii RW1]
          Length = 243

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 11/100 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            +  +   ++G   + +        G +         ++ + V  I K  P   + L GG
Sbjct: 35  ADQARRFAEAGAEWLHVVDLDGAFAGRA---------VNAEAVEAIIKAFPG-KVELGGG 84

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           + D +   + L   V+ V+IG AA +N  ++    +    
Sbjct: 85  IRDRAGIDRWLALGVERVIIGTAALQNPDLVREAAKELPG 124



 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 50/136 (36%), Gaps = 21/136 (15%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVN- 149
           G   + NPD+V +    +   + + V  +          ++  V + +L      +GV  
Sbjct: 105 GTAALQNPDLVREAAKELPGRIVVGVDARDGFVATHGWAEVSTVGITDLADRFADAGVAS 164

Query: 150 -GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
                  R  +LKG            + +    + +    + +  +GG+  ++    ++P
Sbjct: 165 LLFTDVGRDGLLKG-----------CNVEATVALARHA-SIPVIASGGVASIADIAALVP 212

Query: 209 SV----DGVMIGRAAY 220
                 +GV+ GRA Y
Sbjct: 213 HAGDGIEGVITGRALY 228


>gi|88705990|ref|ZP_01103698.1| NADH:flavin oxidoreductase/NADH oxidase [Congregibacter litoralis
           KT71]
 gi|88699704|gb|EAQ96815.1| NADH:flavin oxidoreductase/NADH oxidase [Congregibacter litoralis
           KT71]
          Length = 358

 Score = 37.9 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 58/172 (33%), Gaps = 15/172 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
              + AA   +  G+  + L             P+  + +  +G  L     ++ + I  
Sbjct: 142 DDFIAAAVRAQKAGFTGVELHGAHGYVLAQFLSPTINLRDDEYGGSLENRSRLLLEIIDG 201

Query: 111 MCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           + +       +  R+  +   I    +R+L + + + G   I             P++  
Sbjct: 202 VRERCGADFLLGVRLSAERFDIRLAEMRDLAQQLMREG--NIDFLDMSLWDSFKEPEEEG 259

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                  +   E+  +  D+ +G  G +     A + +    D  ++GR+A 
Sbjct: 260 FEGKTLLECFTEL--DRGDVLLGTAGKIRSAEDARRCIEAGADFAVVGRSAI 309


>gi|323507505|emb|CBQ67376.1| related to NADH-dependent flavin oxidoreductase [Sporisorium
           reilianum]
          Length = 420

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 50/156 (32%), Gaps = 11/156 (7%)

Query: 85  SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIP---VTVKCRI--GVDDQIPAVALR 137
           S RV+     +G  L     IV + I ++ KA+  P   +++K       D    A    
Sbjct: 196 SPRVNRRTDQYGGDLEGRSHIVFEIIESIRKAVPDPKFIISIKINSADFADGGFSAEESF 255

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNG 195
            + K ++ +GV  I +        G   K         +  +    I+       + + G
Sbjct: 256 TMSKRLEAAGVELIELSGGTYESSGFEHKKESTKARESFFIEFAERIRPHLSTAKLAVTG 315

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTV 229
           G        K +     D V + R       +   +
Sbjct: 316 GFRSSKMMAKAVEEESCDIVGMARPLCGEPYLCKDL 351


>gi|329297624|ref|ZP_08254960.1| imidazole glycerol phosphate synthase subunit HisF [Plautia stali
           symbiont]
          Length = 258

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  TPEDAARILQFGADKISINSPALADPTLITRLADRFG 121


>gi|301123101|ref|XP_002909277.1| 2,4-dienoyl-CoA reductase [Phytophthora infestans T30-4]
 gi|262100039|gb|EEY58091.1| 2,4-dienoyl-CoA reductase [Phytophthora infestans T30-4]
          Length = 703

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 45/133 (33%), Gaps = 10/133 (7%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + + A+  A+     +  R+     V+       +  L K I+ +G     I+      +
Sbjct: 197 EIVKAVRAAVGKDFIIIFRLSMLDLVEKGSTWDEIVMLAKQIEAAGAT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   +  V  ++K E     I  N  +     A +I+     D V + R 
Sbjct: 255 ARIPTIATSVPRGGFSWVTQKMKGEVSIPLITTNR-INMPDVAEQIIAEGRADMVSMARP 313

Query: 219 AYKNSAMLTTVDE 231
              +   +   +E
Sbjct: 314 FLADPEFVRKTEE 326


>gi|257463227|ref|ZP_05627626.1| hypothetical protein FuD12_05183 [Fusobacterium sp. D12]
 gi|317060813|ref|ZP_07925298.1| 2-nitropropane dioxygenase [Fusobacterium sp. D12]
 gi|313686489|gb|EFS23324.1| 2-nitropropane dioxygenase [Fusobacterium sp. D12]
          Length = 312

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 9/87 (10%)

Query: 131 IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF 190
           IP V+   L K  +K G   + +    A     S  D+       +DIV E+ + N  + 
Sbjct: 116 IPIVSSLKLAKISEKLGAPAVIVEGGNAGGHLGSELDS-------WDIVPEVAQ-NIHIP 167

Query: 191 IGLNGGLEDMSQALKILP-SVDGVMIG 216
           +   GG+       ++L     G+ +G
Sbjct: 168 VIGAGGVMTPEDGKRMLSLGAKGIQMG 194


>gi|213620873|ref|ZP_03373656.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. E98-2068]
          Length = 181

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|90419449|ref|ZP_01227359.1| putative NADH, flavin oxidoreductase/NADH oxidase [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90336386|gb|EAS50127.1| putative NADH, flavin oxidoreductase/NADH oxidase [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 792

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 30/232 (12%), Positives = 71/232 (30%), Gaps = 24/232 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIA 109
             V+A +  +  G++ + L   C           P     + ++G  +        +  A
Sbjct: 555 DFVQATERADRAGFDMLEL--HCAHGYLLASFLSPLTNHRDDAYGGSVENRLRYPLEVFA 612

Query: 110 AMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           AM  A      +  R+   D     I    +  + ++   +G + I + A + +    +P
Sbjct: 613 AMRAAWPAHKPMSVRLSATDWAEGGISEADVFAISEAFATAGCDLIDVSAGQTVAD-QAP 671

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
              R       + +  +    P + +   G + + +Q   IL +   D V +GR    N 
Sbjct: 672 VYGRMFQVQFAEAIRNV----PKMAVMAVGAITEAAQVNTILHTRRADIVALGRPHMWNP 727

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQ 275
                   ++                  +R+++            +  +   
Sbjct: 728 YFAREAAAWYDTRNQPWPKQYISGRDQAYRELTKKRAQEIELRRKARPRPHD 779


>gi|13474184|ref|NP_105752.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Mesorhizobium loti
           MAFF303099]
 gi|20454989|sp|Q98CT3|HIS4_RHILO RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|14024936|dbj|BAB51538.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Mesorhizobium loti MAFF303099]
          Length = 247

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 19/129 (14%), Positives = 51/129 (39%), Gaps = 17/129 (13%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA 155
            +PD+V     A    +++ +  K      +   +  ++ +  L +  + +GV  I    
Sbjct: 108 RDPDLVRQACKAFPGKVAVGIDAKGGKVAVEGWAEASSLGVVELARKFEGAGVAAII--- 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL----PSVD 211
                       +  +  +++D   ++  E   + +  +GGL  ++  +++       ++
Sbjct: 165 ------YTDIDRDGVLTGINWDATIDLA-EAVSIPVIASGGLASIADIVRMTMPDAQKLE 217

Query: 212 GVMIGRAAY 220
           G + GRA Y
Sbjct: 218 GAISGRALY 226


>gi|15829243|ref|NP_326603.1| NADH-dependent flavin oxidoreductase [Mycoplasma pulmonis UAB CTIP]
 gi|14090187|emb|CAC13945.1| NADH-DEPENDENT FLAVIN OXIDOREDUCTASE [Mycoplasma pulmonis]
          Length = 398

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 6/46 (13%)

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
           N+ I  + Y+ +      N  + +  NGG+  +  A++ +  VD V
Sbjct: 287 NQLINKVVYEHI------NGRVPVIANGGINSLESAIEAIEHVDLV 326


>gi|326794969|ref|YP_004312789.1| 2,4-dienoyl-CoA reductase (NADPH) [Marinomonas mediterranea MMB-1]
 gi|326545733|gb|ADZ90953.1| 2,4-dienoyl-CoA reductase (NADPH) [Marinomonas mediterranea MMB-1]
          Length = 687

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 68/188 (36%), Gaps = 18/188 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG-------CPSARVHEG--SFGACLMLNPDIVGDCIAAM 111
             V+AA+  ++ G + + L+           S RV++    +G           + + A+
Sbjct: 152 DFVQAARRAKEGGLDGVELSAVHQHMIDQFWSPRVNKRTDEWGGTFEGRMKFGMEVLKAV 211

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + +     V  RI  D    D +    ++ + +    +G+   +           +  +
Sbjct: 212 REEVGPDFAVGLRITGDEFHPDGLNHDDMKQIAQYYDATGMVDYFGVVGSGCDTHNTLAN 271

Query: 168 ---NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
              N   P   +  +    KE   + +     ++D +QA +I+ +  VD V + RA   +
Sbjct: 272 VIPNMSYPPEPFLHLAAGIKEVVSVPVIHAQNIKDPNQAKRIVEAGYVDFVGMTRAHIAD 331

Query: 223 SAMLTTVD 230
              +  + 
Sbjct: 332 PHFIAKIK 339


>gi|260912731|ref|ZP_05919217.1| imidazoleglycerol phosphate synthase [Pasteurella dagmatis ATCC
           43325]
 gi|260633109|gb|EEX51274.1| imidazoleglycerol phosphate synthase [Pasteurella dagmatis ATCC
           43325]
          Length = 257

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRT---------IDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++  + E F 
Sbjct: 85  SVEDAEKLFAFGADKISINSPALADPDLINRLAERFG 121


>gi|237739506|ref|ZP_04569987.1| 2-nitropropane dioxygenase [Fusobacterium sp. 2_1_31]
 gi|229423114|gb|EEO38161.1| 2-nitropropane dioxygenase [Fusobacterium sp. 2_1_31]
          Length = 379

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 40/213 (18%), Positives = 76/213 (35%), Gaps = 40/213 (18%)

Query: 13  ARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDF 72
            + + N   +  E + +   +    KN       +KPLA  I  A ++   +  +   + 
Sbjct: 56  CKKVVNGRPVGAEALNSKEAMMEIFKNARKICG-DKPLACNILHA-MNDYAKVVEFAIEA 113

Query: 73  GYNEINLNVGCPS--ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ 130
           G N I    G P    ++ E         +PD+             +P+    R      
Sbjct: 114 GANIIVTGAGLPLELPKLVEN--------HPDVAI-----------VPIVSSAR------ 148

Query: 131 IPAVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKDNRKIPNLDYD-IVYEIKKEN- 186
               AL+ + K  K +G   + + +   K+     +  ++  +P    + +V E+K+E  
Sbjct: 149 ----ALKIICKKWKAAGRLPDAVIVEGPKSGGHQGAKAEDLFLPEHQLESVVPEVKEERD 204

Query: 187 --PDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
              D  I   GG+ D     K +    D V +G
Sbjct: 205 KWGDFPIIAAGGIWDNDDIQKFMALGADAVQLG 237


>gi|256422655|ref|YP_003123308.1| NADH:flavin oxidoreductase/NADH oxidase [Chitinophaga pinensis DSM
           2588]
 gi|256037563|gb|ACU61107.1| NADH:flavin oxidoreductase/NADH oxidase [Chitinophaga pinensis DSM
           2588]
          Length = 377

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 31/189 (16%), Positives = 64/189 (33%), Gaps = 26/189 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V  A      G++ + ++            P   + E ++G         + +    + 
Sbjct: 167 FVATALRAVAAGFDGVEIHAANGYLLDQFITPHTNIREDAYGGNYRNRLRFLMEVYQEIK 226

Query: 113 KALSIPVTVKCRIGVDD--------QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            A+     V  R+               A A   + K +K+   + I I    A   G  
Sbjct: 227 AAVPADFIVGMRLSESKVNDLSYRWPEGAAAATAIFKVLKELEADYIHI----AAEGGNW 282

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
            +++        + +    ++     + +NGG+ DM+ A ++L     D V IG+AA  N
Sbjct: 283 GRESLYSDGRSSNGIA---RKITGRPVIVNGGMHDMTLATELLNAAQADMVSIGKAAISN 339

Query: 223 SAMLTTVDE 231
             +   +  
Sbjct: 340 PDLPNKIAR 348


>gi|193214459|ref|YP_001995658.1| dihydroorotate dehydrogenase 2 [Chloroherpeton thalassium ATCC
           35110]
 gi|193087936|gb|ACF13211.1| dihydroorotate dehydrogenase [Chloroherpeton thalassium ATCC 35110]
          Length = 332

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 20/116 (17%), Positives = 44/116 (37%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--- 105
           P+   I G+++   +  AK++E+ G + I LN+               +  NP       
Sbjct: 103 PIIASINGSEVGDWLHYAKLMEEAGADAIELNI-------------YAIPTNPSATAADI 149

Query: 106 -----DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                + +  +  ++++PV +K             L N  + +  +G N + +  R
Sbjct: 150 ENNYINILKCLKSSVTVPVAIKLSPFF------TNLGNFAERLVDAGANSLVLFNR 199


>gi|217977508|ref|YP_002361655.1| inosine-5'-monophosphate dehydrogenase [Methylocella silvestris
           BL2]
 gi|217502884|gb|ACK50293.1| inosine-5'-monophosphate dehydrogenase [Methylocella silvestris
           BL2]
          Length = 496

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 23/167 (13%), Positives = 50/167 (29%), Gaps = 32/167 (19%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+++ D G + I ++                ++     V      +              
Sbjct: 241 AEMLVDAGVDCIVID--------TAHGHSQAVLDQVLRVKRISNKVALIAG--------- 283

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
                   VA  +  K++  +G +G+ +      +          +P L   +       
Sbjct: 284 -------NVATADGCKALIDAGADGVKVGIGPGSICTTRIVAGVGVPQLTAIMDCAEAAR 336

Query: 186 NPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
             ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 337 AQNIPVIADGGIKYSGDLAKAIAAGADTVMIG-------SLFAGTDE 376


>gi|148271822|ref|YP_001221383.1| putative oxidoreductase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147829752|emb|CAN00670.1| putative oxidoreductase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
          Length = 357

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 27/196 (13%), Positives = 70/196 (35%), Gaps = 22/196 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +L  AA+   D G++ + ++            P + V   ++G        +  D   A
Sbjct: 152 DELTVAARNAVDAGFDGVEIHSANGYLLHEFLSPVSNVRTDAYGGSPENRAKLGIDVAHA 211

Query: 111 MCKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           + + +    V ++     + Q       +  ++  ++ ++GI          GL+     
Sbjct: 212 VSREIGAERVGIRISPSHNIQDVLEEDADETRATYEALLSGIAP-------LGLAYVSIL 264

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNG-GLED-MSQALKILPS--VDGVMIGRAAYKNSAM 225
                  D+V  ++K      +  +G G++    +A++++     D V +GR    N  +
Sbjct: 265 HAEPAG-DLVQGLRKTFGGPLMINSGFGVQTERDEAIQLVEEGTADVVAVGRMVIANPDL 323

Query: 226 LTTVDEYFSNPLTGSS 241
           +   ++         +
Sbjct: 324 VERWEQGLETNEPNPA 339


>gi|167035132|ref|YP_001670363.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
 gi|166861620|gb|ABZ00028.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas putida GB-1]
          Length = 363

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 60/182 (32%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +  +   D      L     L +  K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P+ N          + E  +    L +    G      A   L    +D V +GRA   +
Sbjct: 272 PETNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEGALQANQLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|90020138|ref|YP_525965.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Saccharophagus
           degradans 2-40]
 gi|123090848|sp|Q21NH6|HIS4_SACD2 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|89949738|gb|ABD79753.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Saccharophagus
           degradans 2-40]
          Length = 243

 Score = 37.9 bits (87), Expect = 2.4,   Method: Composition-based stats.
 Identities = 27/125 (21%), Positives = 47/125 (37%), Gaps = 8/125 (6%)

Query: 155 ARKAILKGLSPKDNRKI------PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           ARK + +G        +        ++ ++V  I K  P+L I + GG+  +      L 
Sbjct: 36  ARKWVEQGAKRLHLVDLNGAFAGEPVNGEVVKAIAKAYPNLPIQIGGGIRSLETIKHYLD 95

Query: 209 -SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARH 266
             V  V+IG  A K    +    D +  + + G       V  D W ++S       A+ 
Sbjct: 96  AGVTYVIIGTKAVKEPEFVKQACDAFPGHIIVGLDAKDGYVATDGWAEVSTVKATDLAKQ 155

Query: 267 LHSGG 271
             + G
Sbjct: 156 FAADG 160


>gi|256783631|ref|ZP_05522062.1| 2,4-dienoyl-CoA reductase (NADPH) [Streptomyces lividans TK24]
 gi|289767514|ref|ZP_06526892.1| 2,4-dienoyl-CoA reductase [Streptomyces lividans TK24]
 gi|289697713|gb|EFD65142.1| 2,4-dienoyl-CoA reductase [Streptomyces lividans TK24]
          Length = 671

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 43/125 (34%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     V  R+ + D +P  +  +    L K+++ +G     I+      +
Sbjct: 198 EIVRRVREAVGADFIVVYRLSMLDLVPGGSTLDEVITLAKAVEAAGAT--IINTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   Y  V   +  E     +  N  +     A  +L     D V + R 
Sbjct: 256 ARIPTIATSVPRGAYTWVTKRLMGEVSVPLVTTNR-INTPEVAEALLAEGTADMVSMARP 314

Query: 219 AYKNS 223
              + 
Sbjct: 315 MLADP 319


>gi|227551498|ref|ZP_03981547.1| dihydroorotate oxidase [Enterococcus faecium TX1330]
 gi|257895892|ref|ZP_05675545.1| dihydroorotate dehydrogenase [Enterococcus faecium Com12]
 gi|227179358|gb|EEI60330.1| dihydroorotate oxidase [Enterococcus faecium TX1330]
 gi|257832457|gb|EEV58878.1| dihydroorotate dehydrogenase [Enterococcus faecium Com12]
          Length = 314

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 66/209 (31%), Gaps = 32/209 (15%)

Query: 48  KPLALQIGG----ADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
           +PL   I G     ++  L E    +E  G   I  LN+ CP   V        L  + +
Sbjct: 96  QPLFFSIAGMSVQENLEMLGE----IEKSGLKGITELNLSCP--NVPGK---PQLAYDFE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 147 TTYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 205

Query: 156 RKAIL-----KGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKI-LP 208
            K  +     +G        I       V     +  P++ I   GG+     A +  L 
Sbjct: 206 DKEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLKPEIQIIGTGGIRTGQDAFEHLLC 265

Query: 209 SVDGVMIGRAAYKN--SAMLTTVDEYFSN 235
               + IG          + + + +  + 
Sbjct: 266 GASMLQIGTE-LHKEGPEIFSRIIKELTQ 293


>gi|207728154|ref|YP_002256548.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum MolK2]
 gi|206591399|emb|CAQ57011.1| nadh:flavin oxidoreductases protein [Ralstonia solanacearum MolK2]
          Length = 370

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 54/180 (30%), Gaps = 20/180 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V  A+     G   I L+            P A     ++G           +   A
Sbjct: 157 DAFVATARRAVRLGLAAIELHAAHGYLLHAFLSPIANQRTDAYGGSRENRMRYPLEVFEA 216

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPK 166
           +  A+  P+ V  R+   D +             ++++  G + +      A   G+SP 
Sbjct: 217 VRAAVPDPIPVGVRVSCTDWVEGGWALEDSVAFAQALRARGCDWV-----DASSGGVSPL 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
               +         E  + +  +     G +    +A  I+     D V +GRA   N  
Sbjct: 272 QQIPLSTGYQVPFAEAIRRDAGMPTIAVGLINAPHEAEAIIAEGRADLVAMGRAFLYNPH 331


>gi|157692879|ref|YP_001487341.1| NADPH dehydrogenase NamA [Bacillus pumilus SAFR-032]
 gi|167012458|sp|A8FEW4|NAMA_BACP2 RecName: Full=NADPH dehydrogenase; AltName: Full=Xenobiotic
           reductase
 gi|157681637|gb|ABV62781.1| flavin reductase [Bacillus pumilus SAFR-032]
          Length = 338

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 32/194 (16%), Positives = 66/194 (34%), Gaps = 21/194 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             +AA   +  G++ I ++            P A      +G         + + + A+ 
Sbjct: 146 FQDAAVRAKKAGFDIIEIHGAHGYLINEFLSPLANHRTDDYGGSPENRYRFLREVVNAVN 205

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKS---IKKSGVNGIWIHARKAILKGLSPKDNR 169
           +    P+ V+     D     + + + +     +K+ GV+ I + +   +   +S     
Sbjct: 206 EVWDGPLFVRVSAS-DYTTKGLDIADYIGIATWLKEQGVDLIDVSSGAVVQARISTFPGY 264

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLT 227
           ++         E  KE   +  G  G +    QA +IL     D + IGR   ++     
Sbjct: 265 QV------TFAEKIKEGAGIQTGAVGLITSGVQAEEILRNQRADLIFIGREFLRDPYFPK 318

Query: 228 TVDEYFSNPLTGSS 241
           T  E     + G  
Sbjct: 319 TAAEELRTSIEGPR 332


>gi|89896535|ref|YP_520022.1| hypothetical protein DSY3789 [Desulfitobacterium hafniense Y51]
 gi|89335983|dbj|BAE85578.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 657

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 21/141 (14%), Positives = 45/141 (31%), Gaps = 11/141 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSG- 147
           +G  L     I+ +  A + K       +  ++  D+ +           + + +  SG 
Sbjct: 184 YGGDLDNRIRIILEIAAEIKKMAGRDFNIGFKVNPDESLLGGPDLETGIEICRRLAASGD 243

Query: 148 VNGIWIHAR---KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
           V+ I I AR     +     P         +Y     +++   ++ I   G +       
Sbjct: 244 VDWIRIAARGQKPQMTHFHYPPSYMPQGTNNY-ASAAVREVVDNIPIIGGGRMTTAEFME 302

Query: 205 KILP--SVDGVMIGRAAYKNS 223
           + +     D V   RA   + 
Sbjct: 303 QSIAEGQCDAVFAARAFIVDP 323


>gi|116204409|ref|XP_001228015.1| hypothetical protein CHGG_10088 [Chaetomium globosum CBS 148.51]
 gi|88176216|gb|EAQ83684.1| hypothetical protein CHGG_10088 [Chaetomium globosum CBS 148.51]
          Length = 423

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 25/160 (15%), Positives = 58/160 (36%), Gaps = 26/160 (16%)

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIG--VDDQIPAVALR-----NLVKSIKKSGVNGIW- 152
           P  +      +     +PV ++      V++ +PA +          +++   G   +  
Sbjct: 250 PLEIAQITRDVV-GDKVPVFLRVSATDWVEETLPAESWTAKDTVRFAEALAAQGAIDLID 308

Query: 153 -----IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKI 206
                +H  + +  G + +    I          +KK   D L +   G + +  QA  +
Sbjct: 309 ISSGGVHHSQKVKSGPAFQAPFAI---------AVKKAVGDKLLVATVGSITNGKQANGL 359

Query: 207 LP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIK 244
           L    +D  ++GR   K+  +  T  ++    +  +S I+
Sbjct: 360 LEDDGLDMALVGRGFQKDPGLAWTFAQHLGTEIAMASQIR 399


>gi|301060008|ref|ZP_07200882.1| dehydrogenase, FMN-dependent [delta proteobacterium NaphS2]
 gi|300445887|gb|EFK09778.1| dehydrogenase, FMN-dependent [delta proteobacterium NaphS2]
          Length = 398

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 29/145 (20%), Positives = 51/145 (35%), Gaps = 27/145 (18%)

Query: 81  VGCPSARVHEGSFGACLMLN---PDIVGDC--IAAMCKALSIPVTVKCRIGVDDQIPAVA 135
            GCP+  V     G+ +M     P        + A+    S+P   K  +  +D      
Sbjct: 225 AGCPATGVDLDGCGSTIMERNGQPVFRKSIKDLKALVAFTSLPFIAKGIMTPED------ 278

Query: 136 LRNLVKSIKKSGVNGIWI--HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                ++  ++GV  I +  H       G        +  +   IV  + +      I  
Sbjct: 279 ----AEACVEAGVRVIAVSNHG------GRVLDHTPGVAEVLPAIVDRVGENA---LITA 325

Query: 194 NGGLEDMSQALKILP-SVDGVMIGR 217
           +GG+      +K+L    D V+IGR
Sbjct: 326 DGGVRTGYDVIKMLALGADAVLIGR 350


>gi|297197612|ref|ZP_06915009.1| 2,4-dienoyl-CoA reductase [Streptomyces sviceus ATCC 29083]
 gi|297146795|gb|EFH28346.1| 2,4-dienoyl-CoA reductase [Streptomyces sviceus ATCC 29083]
          Length = 606

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 18/125 (14%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  R+ + D +P  +  +    L ++++ +G     I+      +
Sbjct: 198 EIVRRVREAVGEDFIIVYRLSMLDLVPGGSTLDEVITLARAVEAAGAT--IINTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
              P     +P   Y  V   +  E     +  N  +     A ++L     D V + R 
Sbjct: 256 ARIPTIATSVPRGAYTWVTKRLMGEVSIPLVTTNR-INTPELAEELLADGYADMVSMARP 314

Query: 219 AYKNS 223
              + 
Sbjct: 315 MLADP 319


>gi|298293664|ref|YP_003695603.1| radical SAM protein [Starkeya novella DSM 506]
 gi|296930175|gb|ADH90984.1| Radical SAM domain protein [Starkeya novella DSM 506]
          Length = 369

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 19/97 (19%)

Query: 59  ISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
            ++L E AK   +  G   + +  G P         GA ++       +   A+  A+ +
Sbjct: 155 PAQLAEVAKAAVELDGVKHMVMTTGTP----PGKDRGAAIL------TESAQAVKAAVDL 204

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           P+ V+C    DD        +    ++ +G + + +H
Sbjct: 205 PIQVQCEPPDDD--------DWFARMRAAGADALGMH 233


>gi|91778524|ref|YP_553732.1| NADH-flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia xenovorans LB400]
 gi|91691184|gb|ABE34382.1| NADH-flavin oxidoreductase / NADH oxidase family protein
           [Burkholderia xenovorans LB400]
          Length = 687

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + + ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGVEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGTEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
            +A+     V  R+  D    D +    L+ + +++ ++G+    G+            +
Sbjct: 211 REAVGADFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSETGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    L +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVVKLPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|300871932|ref|YP_003786805.1| NADH:flavin oxidoreductase/NADH oxidase [Brachyspira pilosicoli
           95/1000]
 gi|300689633|gb|ADK32304.1| NADH:flavin oxidoreductase/NADH oxidase [Brachyspira pilosicoli
           95/1000]
          Length = 344

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 26/190 (13%), Positives = 59/190 (31%), Gaps = 22/190 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA   +  G++ I L+            P +      +G         + + +  
Sbjct: 148 DAFANAALRAKKAGFDIIELHAAHGYLISTFLSPLSNKRTDEYGK---NRAKFLEEILRK 204

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
             +A+    P+ ++     D +     +++  + +K      +       +  G    D 
Sbjct: 205 CREAVGSDYPIQIRI-SSYDWKEGGNTVKDFAEMLKPLEEAKLI--DSIDVSTGAVTADG 261

Query: 169 RKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           + IP   Y +    E+K+    +     G + D   A  ++ +   D + IGR   +N  
Sbjct: 262 KIIPYEGYQVPFCRELKQYMT-VPCIGGGLIYDPKMANMMVRNGAADAIYIGRELLRNPY 320

Query: 225 MLTTVDEYFS 234
                     
Sbjct: 321 WALQAARTLG 330


>gi|220905074|ref|YP_002480386.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|254801146|sp|B8J249|HIS4_DESDA RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|219869373|gb|ACL49708.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 250

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 20/118 (16%), Positives = 42/118 (35%), Gaps = 11/118 (9%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K     +  + A +  +  ++ +++G   + +        G +             I
Sbjct: 15  VRLKQGRAHESTVFAESPVDAARAWEEAGARWLHVVDLDGAFDGAAQSRR---------I 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           V +I      + + L GG+ DM  A   L   V  ++IG  A +   +   +   F  
Sbjct: 66  VRDICAAL-AIPVQLGGGIRDMHTAEAYLEAGVSRLIIGTLALEQPTLFADMCRAFPG 122


>gi|167747041|ref|ZP_02419168.1| hypothetical protein ANACAC_01753 [Anaerostipes caccae DSM 14662]
 gi|167654001|gb|EDR98130.1| hypothetical protein ANACAC_01753 [Anaerostipes caccae DSM 14662]
          Length = 665

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 26/182 (14%), Positives = 57/182 (31%), Gaps = 19/182 (10%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCI-AAMCK 113
           EAA   +  G++ I ++ G          P+  V    FG     N       +   + K
Sbjct: 154 EAAARAQASGFDCIEIHAGHSYLISQFLSPTTNVRTDEFGGS-PENRARFARLVLEEVRK 212

Query: 114 ALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P+ V+      ++         + ++  ++   +   + A            N 
Sbjct: 213 QVGPMFPIFVRLSADEFMEHGNTLDDTLDYLQYFQE-EADVFDVSAGLNGSIQYQIDANY 271

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNSAMLT 227
                   +   +K++     + + G + D   A  IL   D   + +GR    +   + 
Sbjct: 272 LEDGWRSYMAKAVKEKYGKPCVTM-GNIRDPRVADDILARGDADIIGMGRGLIADPCWVK 330

Query: 228 TV 229
            V
Sbjct: 331 KV 332


>gi|120403864|ref|YP_953693.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium vanbaalenii
           PYR-1]
 gi|119956682|gb|ABM13687.1| NADH:flavin oxidoreductase/NADH oxidase [Mycobacterium vanbaalenii
           PYR-1]
          Length = 410

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 26/212 (12%), Positives = 72/212 (33%), Gaps = 44/212 (20%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             AA +    G++ + L+ G          P       S+G  L     +  +   A+ +
Sbjct: 150 ARAADLAGQAGFDAVELHFGHNYLVSSFFSPLLNRRRDSYGGSLANRARLAREIAVAVRE 209

Query: 114 ALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGV-NGIWIHARKAIL------KG 162
           ++   + V  ++ +DD +P          + + ++  G  + + +    ++L      +G
Sbjct: 210 SVGDQIAVTAKLNMDDGVPGGLRLEESLQIGRWLQDDGALDALQLTVGSSLLNPMYYFRG 269

Query: 163 LSPKDNRK---IPNLDYDIV--------------------YEIKKENPDLFIGLNGGLED 199
            +P+D+        L++ ++                        +    + + L GG+  
Sbjct: 270 QAPRDDFARVFPRPLNWALLTAGRFFLRQYPFEEAYLLESARQFRHELSMPLILLGGITT 329

Query: 200 MSQA-LKILPSVDGVMIGRAAYKNSAMLTTVD 230
                  +    + V + RA  ++  ++  + 
Sbjct: 330 RDTMDQAMAEGFEYVAMARALLRDPGLVGRIR 361


>gi|317471857|ref|ZP_07931192.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
 gi|316900630|gb|EFV22609.1| NADH:flavin oxidoreductase/NADH oxidase [Anaerostipes sp.
           3_2_56FAA]
          Length = 665

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 26/182 (14%), Positives = 57/182 (31%), Gaps = 19/182 (10%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCI-AAMCK 113
           EAA   +  G++ I ++ G          P+  V    FG     N       +   + K
Sbjct: 154 EAAARAQASGFDCIEIHAGHSYLISQFLSPTTNVRTDEFGGS-PENRARFARLVLEEVRK 212

Query: 114 ALS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +    P+ V+      ++         + ++  ++   +   + A            N 
Sbjct: 213 QVGPMFPIFVRLSADEFMEHGNTLDDTLDYLQYFQE-EADVFDVSAGLNGSIQYQIDANY 271

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNSAMLT 227
                   +   +K++     + + G + D   A  IL   D   + +GR    +   + 
Sbjct: 272 LEDGWRSYMAKAVKEKYGKPCVTM-GNIRDPRVADDILARGDADIIGMGRGLIADPCWVK 330

Query: 228 TV 229
            V
Sbjct: 331 KV 332


>gi|118472910|ref|YP_885709.1| Asp/Glu racemase [Mycobacterium smegmatis str. MC2 155]
 gi|118174197|gb|ABK75093.1| Asp/Glu racemase [Mycobacterium smegmatis str. MC2 155]
          Length = 384

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 35/159 (22%), Positives = 54/159 (33%), Gaps = 20/159 (12%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D   +V AA+++ D   + I  N          G+ G+ L L  D    C  A+ +A  I
Sbjct: 51  DADTMVAAARLLADAEVDCIVWN----------GTAGSWLGLEHDR--RCCDAITEATGI 98

Query: 118 PVTVKC----RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPN 173
           P T       R  VD  I A+A         +  V+ I     +  +  +S  +     N
Sbjct: 99  PATTSTLAILRACVDFGISALA---CATPYTRDVVDAISREYARHDVGIVSHAEWELTDN 155

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
           L +      +          NG          I  +VDG
Sbjct: 156 LSFAKASSAEVAELLAAAAKNGD-PAPQGVALICTNVDG 193


>gi|320195244|gb|EFW69873.1| 2,4-dienoyl-CoA reductase [Escherichia coli WV_060327]
          Length = 672

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 55/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +        +  L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAEMVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|313114713|ref|ZP_07800215.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310622938|gb|EFQ06391.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 251

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 43/115 (37%), Gaps = 11/115 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + +    +G + +  +   A  +G +         L  DI+  +  E   + + + GG+
Sbjct: 34  EMARMYNAAGADELVFYDITASFEGRA---------LFTDILTRVASEIF-IPLTVGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
             +    ++L    D V +   A KN  ++    + + N     S    RVD  F
Sbjct: 84  NTLEDFDRVLKCGADKVSVNSGALKNPDLIPAAAQRYGNQCVVLSADVKRVDGQF 138


>gi|331648884|ref|ZP_08349972.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli M605]
 gi|281180134|dbj|BAI56464.1| putative 2,4-dieonyl-CoA reductase [Escherichia coli SE15]
 gi|330909147|gb|EGH37661.1| 2,4-dienoyl-CoA reductase [NADPH] [Escherichia coli AA86]
 gi|331042631|gb|EGI14773.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli M605]
          Length = 672

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 55/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +        +  L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAEMVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|215488411|ref|YP_002330842.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O127:H6 str. E2348/69]
 gi|312968574|ref|ZP_07782783.1| 2,4-dienoyl-CoA reductase [Escherichia coli 2362-75]
 gi|215266483|emb|CAS10922.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O127:H6 str. E2348/69]
 gi|312286792|gb|EFR14703.1| 2,4-dienoyl-CoA reductase [Escherichia coli 2362-75]
          Length = 672

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 55/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +        +  L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAEMVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|76801285|ref|YP_326293.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Natronomonas
           pharaonis DSM 2160]
 gi|91206932|sp|Q3IT10|HIS4_NATPD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|76557150|emb|CAI48725.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Natronomonas
           pharaonis DSM 2160]
          Length = 239

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 11/94 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +    +G   + +       +G            + D V  +  E  D+ + L GG+  
Sbjct: 39  AQRWVDAGAETLHLVDLDGAFEG---------ERANADAVEAVL-EATDVSVQLGGGIRT 88

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           +  A  +L   VD V++G AA +N  ++  +++ 
Sbjct: 89  VDDADSLLSMGVDRVILGTAAVENPDIVGEINDR 122


>gi|238789849|ref|ZP_04633630.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           frederiksenii ATCC 33641]
 gi|238722045|gb|EEQ13704.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           frederiksenii ATCC 33641]
          Length = 247

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 24  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 73

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 74  SVEDAGQILTFGADKISINSPALADPTLITRLADRYG 110


>gi|26249670|ref|NP_755710.1| 2,4-dienoyl-CoA reductase [Escherichia coli CFT073]
 gi|227887806|ref|ZP_04005611.1| 2,4-dienoyl-CoA reductase [Escherichia coli 83972]
 gi|300973216|ref|ZP_07172055.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 45-1]
 gi|301048078|ref|ZP_07195117.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 185-1]
 gi|26110098|gb|AAN82284.1|AE016767_44 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli CFT073]
 gi|227835202|gb|EEJ45668.1| 2,4-dienoyl-CoA reductase [Escherichia coli 83972]
 gi|300300048|gb|EFJ56433.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 185-1]
 gi|300410796|gb|EFJ94334.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 45-1]
 gi|307555187|gb|ADN47962.1| NADPH 2,4-dienoyl-CoA reductase [Escherichia coli ABU 83972]
 gi|315294992|gb|EFU54329.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 153-1]
          Length = 672

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 55/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +        +  L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAEMVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|170781144|ref|YP_001709476.1| pyridoxal biosynthesis lyase PdxS [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155712|emb|CAQ00833.1| putative pyridoxine biosynthesis protein [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 300

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 41/224 (18%), Positives = 66/224 (29%), Gaps = 70/224 (31%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I ED G   +      P+        G   M +PD++          +SIPV  K
Sbjct: 34  AEQARIAEDAGAVAVMALERVPAD--IRSQGGVARMSDPDLIDQI----KAEVSIPVMAK 87

Query: 123 CRI--------------GVDDQIPAVALRNLVKSIKKSG--------------------- 147
            RI                 D+   ++  + V  I K G                     
Sbjct: 88  ARIGHFVEAQVLQSLEVDYIDESEVLSPADYVNHIDKWGFTVPFVCGATTLGEALRRITE 147

Query: 148 ---------------VNGIWIHARK-----AILKGLSPKDNRKIPN---LDYDIVYEIKK 184
                          V+    H R        L  L+  +           YD+V E+ +
Sbjct: 148 GAAMIRSKGEAGTGDVSEATKHIRTIKSEIRALSALTHDEIYVAAKELQAPYDLVLEVAR 207

Query: 185 --ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
             + P +     GG+   + A  ++    DGV +G   +   N 
Sbjct: 208 TGQLPVVLFTA-GGVATPADAAMMMQLGADGVFVGSGIFKSGNP 250


>gi|56460757|ref|YP_156038.1| NADH:flavin oxidoreductase [Idiomarina loihiensis L2TR]
 gi|56179767|gb|AAV82489.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Idiomarina
           loihiensis L2TR]
          Length = 372

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 19/140 (13%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCR------IGVDDQIPA--VALRNLVKSIKK 145
           G  +      +   + A   A      V  R         D Q P    A+  +VK+++K
Sbjct: 199 GGDMAKRMHFLELVVKAAKSAAGDDFIVGVRLSQITVTDSDYQWPEGEDAMIKVVKAMEK 258

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL--EDMSQA 203
           +GV+ I       + K      N+ + +        I +E  D+ + +NGG+  ++    
Sbjct: 259 AGVDYIHTTDTDVMRKPFKGGSNKSLGD--------IVQEFSDIPLIVNGGISEKNYEHV 310

Query: 204 LKILPSVDGVMIGRAAYKNS 223
               P+    M  + +  N 
Sbjct: 311 AGHYPNALLAM-AKTSLANP 329


>gi|332992424|gb|AEF02479.1| imidazole glycerol phosphate synthase subunit HisF [Alteromonas sp.
           SN2]
          Length = 269

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K+G + +            +  D R +       + ++     D+   + GG++
Sbjct: 35  LAEQYAKAGADELV------FYDITASSDERVVDKSWVSRIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  A +IL    D + I   A  N A++  + + +  
Sbjct: 85  SIEDAGRILEMGADKISINSPALNNPALINAMHDVYGQ 122


>gi|319946309|ref|ZP_08020547.1| dihydroorotate dehydrogenase A [Streptococcus australis ATCC
           700641]
 gi|319747462|gb|EFV99717.1| dihydroorotate dehydrogenase A [Streptococcus australis ATCC
           700641]
          Length = 369

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 35/189 (18%), Positives = 66/189 (34%), Gaps = 19/189 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  +  ++   L + G    +     K V++  +  +  LN+ CP   V      A    
Sbjct: 146 LQETDPDRTFFLSLVGMSPEETHIILKKVQESDFKGLTELNLSCP--NVPGKPQIAY--- 200

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +     ++ +    + P+ +K     D      A A+ N      V  +   G NG++
Sbjct: 201 DFETTDRILSEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLY 259

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-L 207
           I     +++   G        I       V+   +  NP++ I   GG+     A +  L
Sbjct: 260 IEDESVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPEIQIVGTGGVLTGRDAFEHIL 319

Query: 208 PSVDGVMIG 216
                V IG
Sbjct: 320 CGASMVQIG 328


>gi|313632236|gb|EFR99298.1| NADH oxidase [Listeria seeligeri FSL N1-067]
          Length = 644

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + + +   C    +               FG C      +    I ++ 
Sbjct: 154 EAALRAKKAGADAVEI--HCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 211

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 212 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 271

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 272 VLHAGFSSDLVTQIKQAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 327


>gi|255325293|ref|ZP_05366399.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Corynebacterium tuberculostearicum SK141]
 gi|255297858|gb|EET77169.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Corynebacterium tuberculostearicum SK141]
          Length = 256

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 43/128 (33%), Gaps = 11/128 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           I  D+   A     L       G + +      A  +G S            ++V     
Sbjct: 22  INFDNLRDAGDPVELAARYDALGADELTFLDVSASKQGRSTM---------LEVVRR-TA 71

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           +   + + + GG+  +    ++L    D V I  AA KN  +L  + E F       S  
Sbjct: 72  DQVFIPLTVGGGVRSVDDVRELLRAGADKVSINTAAIKNPELLREMAEIFGAQCIVLSID 131

Query: 244 KTRVDKDF 251
             R  +++
Sbjct: 132 ARRCYEEY 139


>gi|254362269|ref|ZP_04978382.1| imidazoleglycerol-phosphate synthase [Mannheimia haemolytica
           PHL213]
 gi|153093846|gb|EDN74778.1| imidazoleglycerol-phosphate synthase [Mannheimia haemolytica
           PHL213]
          Length = 257

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 21/148 (14%), Positives = 48/148 (32%), Gaps = 24/148 (16%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D+R +     + V ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDSRTVDKSWVERVAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTT-------------VDEYFSNPLTGSSPIK 244
            ++ A +I     D + I   A  N  ++T              +D +F          +
Sbjct: 85  TIADAEQIFAFGADKISINSPALANPELITELAKRFGVQAVVVGIDSWFEAETGKYWVNQ 144

Query: 245 TRVDKDFWRKISASMTDYAARHLHSGGK 272
              D+   R+    + D+       G  
Sbjct: 145 YTGDEKRTRQTEWQLLDWVEEVQKRGAG 172


>gi|149200208|ref|ZP_01877231.1| inosine-5'-monophosphate dehydrogenase [Lentisphaera araneosa
           HTCC2155]
 gi|149136745|gb|EDM25175.1| inosine-5'-monophosphate dehydrogenase [Lentisphaera araneosa
           HTCC2155]
          Length = 500

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNGGLE 198
            K++  +G + + +      +          +P +    VYE  +  P D+ I  +GG++
Sbjct: 295 AKALADAGADAVKVGIGPGSICTTRVVCGVGVPQI--TAVYEASRAVPSDVPIIADGGIK 352

Query: 199 -DMSQALKILPSVDGVMIG 216
                   I      VM+G
Sbjct: 353 QSGDVPKAITSGASSVMMG 371


>gi|116073099|ref|ZP_01470361.1| inositol-5-monophosphate dehydrogenase [Synechococcus sp. RS9916]
 gi|116068404|gb|EAU74156.1| inositol-5-monophosphate dehydrogenase [Synechococcus sp. RS9916]
          Length = 387

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 9/84 (10%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA     K+I ++G +  ++ A       + P+    +       +  + ++     +  
Sbjct: 140 VAAMRFGKAIAEAGADLFFVQATVVSTNHIGPEGQETLD------LAALCRDMGVPVVIG 193

Query: 194 NGGLEDMSQALK-ILPSVDGVMIG 216
           N        AL+ +     GVM+G
Sbjct: 194 N--CVTYDVALELMRAGAAGVMVG 215


>gi|73538644|ref|YP_299011.1| NADH:-lavin oxidoreductase/NADH oxidase [Ralstonia eutropha JMP134]
 gi|72121981|gb|AAZ64167.1| NADH:flavin oxidoreductase/NADH oxidase:HI0933-like protein
           [Ralstonia eutropha JMP134]
          Length = 687

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 67/195 (34%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRADEWGGSLENRMRFGVEVLQAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            + +     V  R+  D    D +    L+ + +++ +SG+               +  +
Sbjct: 211 REVVGKDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSESGLVDYIGVVGSGADTHNTLAN 270

Query: 168 N---RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K    + +     + D  QA ++L +  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKSVIKVPLMHAQSIRDAGQAERLLANGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|21225349|ref|NP_631128.1| 2,4-dienoyl-CoA reductase (NADPH) [Streptomyces coelicolor A3(2)]
 gi|9716173|emb|CAC01564.1| 2,4-dienoyl-CoA reductase [NADPH] [Streptomyces coelicolor A3(2)]
          Length = 671

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 43/125 (34%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     V  R+ + D +P  +  +    L K+++ +G     I+      +
Sbjct: 198 EIVRRVREAVGADFIVVYRLSMLDLVPGGSTLDEVITLAKAVEAAGAT--IINTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   Y  V   +  E     +  N  +     A  +L     D V + R 
Sbjct: 256 ARIPTIATSVPRGAYTWVTKRLMGEVSVPLVTTNR-INTPEVAEALLAEGTADMVSMARP 314

Query: 219 AYKNS 223
              + 
Sbjct: 315 MLADP 319


>gi|239932902|ref|ZP_04689855.1| 2,4-dienoyl-CoA reductase [Streptomyces ghanaensis ATCC 14672]
 gi|291441251|ref|ZP_06580641.1| 2,4-dienoyl-CoA reductase [Streptomyces ghanaensis ATCC 14672]
 gi|291344146|gb|EFE71102.1| 2,4-dienoyl-CoA reductase [Streptomyces ghanaensis ATCC 14672]
          Length = 671

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 19/125 (15%), Positives = 44/125 (35%), Gaps = 10/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     V  R+ + D +P  +  +    L ++++ +G     I+      +
Sbjct: 198 EIVRRVREAVGEDFIVVYRLSMLDLVPGGSTLDEVITLARAVEAAGAT--IINTGIGWHE 255

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   Y  V   +  E     +  N  +     A ++L     D V + R 
Sbjct: 256 ARIPTIATSVPRGAYTWVTKRLMGEVSVPLVTTNR-INTPELAEQLLAEGYADMVSMARP 314

Query: 219 AYKNS 223
              + 
Sbjct: 315 MLADP 319


>gi|313636738|gb|EFS02398.1| NADH oxidase [Listeria seeligeri FSL S4-171]
          Length = 644

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + + +   C    +               FG C      +    I ++ 
Sbjct: 154 EAALRAKKAGADAVEI--HCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 211

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 212 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 271

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 272 VLHAGFSSDLVTQIKQAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 327


>gi|292656464|ref|YP_003536361.1| pyridoxine biosynthesis protein [Haloferax volcanii DS2]
 gi|291372428|gb|ADE04655.1| pyridoxine biosynthesis protein [Haloferax volcanii DS2]
          Length = 302

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      P+        G   M +P+ V + I     A+SIPV  K
Sbjct: 36  AEQAKIAEEAGAVAVMALEAVPAD--IRKRGGVSRMADPETVTEII----DAVSIPVMGK 89

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 90  ARIGHHTE---------AQILESIGVDMI 109


>gi|116250431|ref|YP_766269.1| hypothetical protein RL0659 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115255079|emb|CAK06153.1| conserved hypothetical protein [Rhizobium leguminosarum bv. viciae
           3841]
          Length = 372

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 19/102 (18%)

Query: 54  IGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           I      +L E AK   +  G   + +  G P         GA ++       D   A+ 
Sbjct: 153 IAHKTPEQLAEVAKAAVELDGVKHMVMTTGTPK----GDDRGAAIL------ADSARAIK 202

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
            A++IP+  +C    DD             +K++GV+ + +H
Sbjct: 203 AAVNIPIQAQCEPPEDDI--------WFTRMKEAGVDALGMH 236


>gi|289435576|ref|YP_003465448.1| NADH oxidase, putative [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
 gi|289171820|emb|CBH28366.1| NADH oxidase, putative [Listeria seeligeri serovar 1/2b str.
           SLCC3954]
          Length = 641

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + + +   C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVEI--HCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKQAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|149921432|ref|ZP_01909885.1| ribulose-phosphate 3-epimerase [Plesiocystis pacifica SIR-1]
 gi|149817752|gb|EDM77217.1| ribulose-phosphate 3-epimerase [Plesiocystis pacifica SIR-1]
          Length = 230

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 33/166 (19%), Positives = 63/166 (37%), Gaps = 28/166 (16%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +A  I  AD ++L +  + +++ G + I+++       V +G F   L + P      + 
Sbjct: 4   IAPSILSADFARLGDEVRAIDEGGADWIHVD-------VMDGRFVPNLTIGPM----VVK 52

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+      PVT K    +D  +  V     V     +G +GI +HA        + +   
Sbjct: 53  ALR-----PVTAKF---MDCHLMIVEPEKYVAEFASAGADGITVHAEACPHLHRNLQQIH 104

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
            +P+   + V      NP   +            + +L   D V+I
Sbjct: 105 ALPHHGGERVRAGVSLNPHTPV---------DVVMHVLELCDLVLI 141


>gi|104784104|ref|YP_610602.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas
           entomophila L48]
 gi|122401439|sp|Q1I3G7|HIS4_PSEE4 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|95113091|emb|CAK17819.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Pseudomonas entomophila L48]
          Length = 245

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P+L I + GG+  +      +   V  V+IG  A K    +    +
Sbjct: 60  PVNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSHVIIGTKAVKQPEFVAEACK 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++SA      A+   + G
Sbjct: 120 AFPGRVIVGLDAKDGFVATDGWAEVSAVQVIDLAKRFEADG 160


>gi|65319347|ref|ZP_00392306.1| COG1902: NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Bacillus anthracis str. A2012]
          Length = 345

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 46/136 (33%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        D +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPDGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK     +  G  G +   +QA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKXHA-XIATGAVGLITTGAQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|290889769|ref|ZP_06552857.1| hypothetical protein AWRIB429_0247 [Oenococcus oeni AWRIB429]
 gi|290480593|gb|EFD89229.1| hypothetical protein AWRIB429_0247 [Oenococcus oeni AWRIB429]
          Length = 312

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 28/230 (12%), Positives = 66/230 (28%), Gaps = 34/230 (14%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P    I G    ++++  K ++   ++ +  LN+ CP   V      A    +     + 
Sbjct: 95  PTLFSIVGLCQKEIIDNLKKLQASDFSGLTELNLSCP--NVSGKPQIAY---DFAATREI 149

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI---------------- 151
           +  +    S P+ +K     D          +   +    +  +                
Sbjct: 150 LDNVFAFYSKPLGIKLPPYFD----IAHFDQIAAILNDYPLAYVNAINSVGNGLVIDPET 205

Query: 152 --WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LP 208
              +   K    GL  K  +     +   + +  + +P + I   GG+ +        L 
Sbjct: 206 DTVMIKPKDGFGGLGGKQIKATALANVRALRQ--RLHPQIKIIATGGVTNGRDVYDHLLC 263

Query: 209 SVDGVMIGR--AAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             D V +G          +   +++              R  +   + I+
Sbjct: 264 GADLVSVGSQLGIEG-PTVFARLEKELEEIFADKGITDLRQVRGKLKLIA 312


>gi|304317890|ref|YP_003853035.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302779392|gb|ADL69951.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 605

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 29/182 (15%), Positives = 58/182 (31%), Gaps = 21/182 (11%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIA 109
               V+AAK  +  G++ I L+            P+    +  +G           + + 
Sbjct: 118 AKDFVDAAKRAKKAGFDAIELHFAHGWFVNQFLSPNVNTRDDEYGGDFDGRARFALEILK 177

Query: 110 AMCKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHA--RKAILKGL 163
            +   +   V V CRI      D          L + +++ G + + + +         +
Sbjct: 178 NVKSEVPDMVVV-CRINGSDYTDGGFDINESIKLSRLLEEHGADALNVSSGVGSTSEYHI 236

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLN--GGLEDMSQALKILPSVDGVMIGRAAYK 221
           SP      P + +  V +IK       I  +  G   D    ++     D + I R    
Sbjct: 237 SPMGIDDRPLITH--VKKIKDSVSIPVIAADKLGVAADWESIVRQ-GYADFIGIARGLIG 293

Query: 222 NS 223
           + 
Sbjct: 294 DP 295


>gi|123471862|ref|XP_001319128.1| dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
 gi|121901904|gb|EAY06905.1| dihydroorotate dehydrogenase family protein [Trichomonas vaginalis
           G3]
          Length = 365

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 44/210 (20%), Positives = 74/210 (35%), Gaps = 32/210 (15%)

Query: 22  LYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNV 81
           L+TE +  +  L  +   I     Q K   +   G    ++ + A  V  F  + + L+ 
Sbjct: 72  LWTE-LTPEQWLEHEYPKIREVCNQAKIPMICSMGYTAEEIAKMAPKVAPF-CDGLELST 129

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPVTVKCRIGVDDQIPAVALRNLV 140
                          +  +P  + D I A +  +   PV VK     D  I A A +   
Sbjct: 130 H-------------YIGDDPKPMQDAIKAAIHGSGGKPVYVKLSPFRDAPIAAKAAKAAG 176

Query: 141 KS----IKKSGVN-GIWIHARKAILKGLSPKDNR----KIPNLDYDIVYEIKKENPDLFI 191
            +    +   G    + I  + A   G + K        I  L   +VY++ KE  DL +
Sbjct: 177 ATGLVCVNSFGPTLALDIERKGAPFMGSTSKYGWVSGPAIKPLALRVVYDVCKEV-DLPV 235

Query: 192 GLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
              GG+ +   A++ L      M G  A  
Sbjct: 236 VGVGGISNGRDAIEFL------MAGAQALG 259


>gi|159042681|ref|YP_001531475.1| NADPH:2,4-dienoyl-CoA reductase [Dinoroseobacter shibae DFL 12]
 gi|157910441|gb|ABV91874.1| NADPH:2,4-dienoyl-CoA reductase [Dinoroseobacter shibae DFL 12]
          Length = 672

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 71/232 (30%), Gaps = 40/232 (17%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L      Y+   VA + ++            E  +  QI       +V AA    + GY+
Sbjct: 103 LHAGRYAYSPDCVAPSAVKSPISPFAPRELDEAGIEKQIA-----DIVTAAARAREAGYD 157

Query: 76  EINLNVGCPSARVHEGSFGA--CLMLNPDIVGD---------------CIAAMCKALSIP 118
            + +        +    +     L+ + +   D                +  +  A+   
Sbjct: 158 GVEV--------MGSEGYFLNQFLVTHTNRREDRWGGPYENRMRLPVEVVRRVRAAVGDD 209

Query: 119 VTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
             V  R+ + D IP       +  L  +I+ +G +   ++      +   P     +P  
Sbjct: 210 FIVIYRLSMIDLIPNGSTWDEVVQLAHAIEGAGAS--ILNTGIGWHEARIPTIATSVPRK 267

Query: 175 DYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            +  V  ++  E     I  N  +     A ++L     D V + R    + 
Sbjct: 268 AFAWVTRKLMGEVGIPVITSNR-INTPEIAEEVLAEGCADMVSMARPFLADP 318


>gi|300856150|ref|YP_003781134.1| enoate reductase [Clostridium ljungdahlii DSM 13528]
 gi|300436265|gb|ADK16032.1| enoate reductase [Clostridium ljungdahlii DSM 13528]
          Length = 664

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 22/150 (14%), Positives = 48/150 (32%), Gaps = 19/150 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKS----- 142
           +G  L        + +  +        PV ++        D +  A+     V+      
Sbjct: 198 YGGSLENRLRFAREIVEEIKNRCGEDFPVVLRYSPKSFIKDLRDGALPGEEFVEKGRDLD 257

Query: 143 --IKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DYDIVYEIKKENPDLFIGLNG 195
             I+ + +   + +       G         P +      Y    ++ KE  D+ I   G
Sbjct: 258 EGIEAAKLLVSYGYDSLDTDVGSYDSWWWSHPPMYQKKGLYRPYAKLMKETVDVPIICAG 317

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            ++D   AL+ + +   D + +GR    + 
Sbjct: 318 RMDDPDMALEAIENGTCDMISLGRPLLADP 347


>gi|295699482|ref|YP_003607375.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1002]
 gi|295438695|gb|ADG17864.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1002]
          Length = 687

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 69/195 (35%), Gaps = 18/195 (9%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFATAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRTDEWGGSLENRLRFGVEVLQAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVN---GIWIHARKAILKGLS 164
             A+     V  R+  D    D +    L+ + +++ +SG+    G+            +
Sbjct: 211 RAAVGADFCVGLRMCGDEFHEDGLDHEQLKEIAQAMSESGLIDYLGVIGSGADTHNTLAN 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
                 +P   +  +    K+   + +     + D  QA ++L S  VD V + RA   +
Sbjct: 271 CMPPMALPPEPFVHLAAGIKQVVKVPVMHAQSIRDAGQAERLLASGMVDLVGMTRAQIAD 330

Query: 223 SAMLTTVDEYFSNPL 237
             M+  + +   + +
Sbjct: 331 PHMVIKIRDGREDEI 345


>gi|289581403|ref|YP_003479869.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Natrialba magadii ATCC 43099]
 gi|289530956|gb|ADD05307.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Natrialba magadii ATCC 43099]
          Length = 269

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 185 ENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           E+ D+   L GG+   + A  +L   VD V++G AA ++  ++  + E
Sbjct: 91  ESVDVPTQLGGGIRTAADARDVLDRGVDRVILGTAAVEDPDIVAEISE 138


>gi|163752052|ref|ZP_02159260.1| imidazole glycerol phosphate synthase subunit HisF [Shewanella
           benthica KT99]
 gi|161328052|gb|EDP99222.1| imidazole glycerol phosphate synthase subunit HisF [Shewanella
           benthica KT99]
          Length = 257

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L     + G + +            +   NR I   D   +  + ++  D+   + GG+ 
Sbjct: 35  LAARYAEEGADELV------FYDITASAHNRVI---DKSWIRRVAEQI-DIPFCVAGGIS 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + QA + L    D + I   A  + +++  + + F 
Sbjct: 85  SIEQAREKLAFGADKISINSPALTDPSLIERLQDEFG 121


>gi|29427845|sp|Q8R7I7|NANE_THETN RecName: Full=Putative N-acetylmannosamine-6-phosphate 2-epimerase;
           AltName: Full=ManNAc-6-P epimerase
          Length = 237

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 33/211 (15%), Positives = 62/211 (29%), Gaps = 72/211 (34%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
                + + AK  E  G   I  N            +            D + A+ K +S
Sbjct: 26  HSPFIMAKMAKAAEIGGAVAIRAN-----------GY-----------EDIV-AIKKEVS 62

Query: 117 IPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSP------KDNR 169
           IPV    +   +   P +      V  + ++G + + I A KA   G         +   
Sbjct: 63  IPVIGLIKKRYEGYAPYITPTMEEVDKVIEAGADIVAIDATKAYKPGGLTTGEFLKRIKE 122

Query: 170 KIPNL----------------------------------------DYDIVYEIKKENPDL 189
           K P +                                        DY+++  + ++  ++
Sbjct: 123 KYPKILVMADISTYEEGIEAEKLGFDLISTTLSGYTEYSPELEGPDYELIERLARKV-NV 181

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAA 219
            I   G +    +A+K L      V++G A 
Sbjct: 182 PIIAEGRIWTPEEAVKALEKGAYAVVVGTAI 212


>gi|99082298|ref|YP_614452.1| 2,4-dienoyl-CoA reductase [Ruegeria sp. TM1040]
 gi|99038578|gb|ABF65190.1| 2,4-dienoyl-CoA reductase [Ruegeria sp. TM1040]
          Length = 675

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 61/185 (32%), Gaps = 33/185 (17%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CLMLNPDIVGD------------ 106
            +V AA++ ++ GY+ + +        +    +     L+ + +   D            
Sbjct: 143 DIVNAARLAQEAGYDGVEI--------MGSEGYFLNQFLVTHTNKREDRWGGSYENRMRL 194

Query: 107 ---CIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAI 159
               +  + +A+     +  R+ + D +P       +  L K+++ +G     I+     
Sbjct: 195 PVEVVRRVREAVGPEFILIYRLSMIDLVPNGSTFEEVVQLAKAVETAGAT--IINTGIGW 252

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
            +   P     +P   +  V +       + +  +  +     A  +L     D V + R
Sbjct: 253 HEARIPTIATSVPRAAFAWVTQKLMGQVSIPVITSNRINTPEVAEDVLAQGCADMVSMAR 312

Query: 218 AAYKN 222
               +
Sbjct: 313 PMLAD 317


>gi|331702555|ref|YP_004399514.1| tryptophan synthase subunit alpha [Lactobacillus buchneri NRRL
           B-30929]
 gi|329129898|gb|AEB74451.1| Tryptophan synthase alpha chain [Lactobacillus buchneri NRRL
           B-30929]
          Length = 265

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 55/157 (35%), Gaps = 42/157 (26%)

Query: 104 VGDCIAAMCKALSIPVTV-----------------KCRIG-----VDDQIPAVALRNLVK 141
           V + + A  K   +P+                   KC+       V   +P  +  ++V 
Sbjct: 76  VFEIVEAARKQTDVPIVFLTYLNIVFKYGYDAFCKKCQALGVSGLVIPDMPYESRDDIVP 135

Query: 142 SIKKSGVNGIWIHARKAILK------------------GLSPKDNRKIPNLDYDIVYEIK 183
           +  K G++ I + A  +  +                  G++ + N     L  D+V EIK
Sbjct: 136 TADKYGIDIIPLIAPTSGHRVEKIAKAASGFIYVVSSLGITGERNEFFNGLK-DLVAEIK 194

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               D+   +  G+    QA  +    DGV+IG A  
Sbjct: 195 -SYTDVPTAIGFGVHTPEQAKTMAEIADGVIIGSAIV 230


>gi|284176193|ref|YP_003406470.1| dihydroorotate dehydrogenase [Haloterrigena turkmenica DSM 5511]
 gi|284017850|gb|ADB63797.1| dihydroorotate dehydrogenase [Haloterrigena turkmenica DSM 5511]
          Length = 356

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 28/143 (19%), Positives = 55/143 (38%), Gaps = 21/143 (14%)

Query: 74  YNEINLNVGCPS--ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI 131
            + + +NV CP+     +E S        P+ +      +       V +  +IG D+  
Sbjct: 173 ADYVVVNVSCPNTPDEFNEAS--------PEHLRAIFETLEAENDGNVPMLVKIGPDE-- 222

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD--------YDIVYEIK 183
           P  A+ +LV  +++ G++GI         +GL      +   L          D++  I 
Sbjct: 223 PEDAILDLVDIVQEFGLDGIVATNTSTAREGLESPAREEWGGLSGAPIEDRSTDVIRTIA 282

Query: 184 KEN-PDLFIGLNGGLEDMSQALK 205
                +L I   GG++  + A +
Sbjct: 283 GHTDGELPIVGVGGVDSAASAYE 305


>gi|167462266|ref|ZP_02327355.1| dihydroorotate dehydrogenase 2 [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 328

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 28/153 (18%), Positives = 55/153 (35%), Gaps = 29/153 (18%)

Query: 74  YNEINLNVGCPS-ARVHEGSFGACLMLNPDIVGDCIAAMCKA------LSIPVTVKCRIG 126
            +   +N+  P+   +     G+ L+   +++      M +          PV VK    
Sbjct: 137 ADFFVVNISSPNTPDLRSLQHGSDLL---NLLHAVTDEMQRQQARYGDSGKPVLVKIAPD 193

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPKDNRKIPNLD 175
           + D+     + N + +I++SG  GI +           HA K    GLS K    +    
Sbjct: 194 LTDE----EVENTIHTIRESGAAGIIVSNTTISREGIVHAHKDQAGGLSGK---PLAECS 246

Query: 176 YDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL 207
            ++V ++       + I  +GG+     A    
Sbjct: 247 TEMVAKVYLLTGGKMPIIGSGGIFTPEDAYAKF 279


>gi|242806094|ref|XP_002484673.1| NADH-dependent flavin oxidoreductase, putative [Talaromyces
           stipitatus ATCC 10500]
 gi|218715298|gb|EED14720.1| NADH-dependent flavin oxidoreductase, putative [Talaromyces
           stipitatus ATCC 10500]
          Length = 454

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 30/139 (21%), Positives = 50/139 (35%), Gaps = 25/139 (17%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN------------LV 140
           +G        IV     A+ +A+   V +  R+   D +  + +              L 
Sbjct: 262 YGGSYENRTRIVRQIATAIREAIPPGVPLFLRVSATDWLEGIEVAKESGSWDAESTIRLA 321

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI--VYEIKKENP-----DLFIGL 193
           K +   GV+ I       +  G + KD R  P+  Y I     I+KE        L++G 
Sbjct: 322 KELPSLGVDFID------VSSGGNHKDQRIDPHTSYQINLAARIRKELHESGIHSLYVGA 375

Query: 194 NGGLEDMSQALKILPSVDG 212
            G +   S A +I+   D 
Sbjct: 376 VGSITTSSLAKEIVEGADS 394


>gi|19552014|ref|NP_600016.1| pyridoxal biosynthesis lyase PdxS [Corynebacterium glutamicum ATCC
           13032]
          Length = 319

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 35/97 (36%), Gaps = 8/97 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K RI
Sbjct: 56  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 109

Query: 126 GVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAIL 160
           G   +   +     + +   +         H  K   
Sbjct: 110 GHFVEAQVLEALGVDFIDESEVLSPADYTHHINKWKF 146


>gi|85712678|ref|ZP_01043724.1| imidazole glycerol phosphate synthase subunit HisF [Idiomarina
           baltica OS145]
 gi|85693528|gb|EAQ31480.1| imidazole glycerol phosphate synthase subunit HisF [Idiomarina
           baltica OS145]
          Length = 263

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 11/98 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +E  D+   + GG+ 
Sbjct: 35  LAKRYAEIGADELVFYDITASSDGRT---------VDKSWVERVAREI-DIPFTVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            ++   ++L    D + I   A  N  ++  + + F  
Sbjct: 85  TLAHGRELLSMGADKLSINSPALMNPELINEMVDEFGQ 122


>gi|313822109|gb|EFS59823.1| putative 2-enoate reductase [Propionibacterium acnes HL036PA1]
 gi|313823657|gb|EFS61371.1| putative 2-enoate reductase [Propionibacterium acnes HL036PA2]
 gi|314924692|gb|EFS88523.1| putative 2-enoate reductase [Propionibacterium acnes HL036PA3]
          Length = 670

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|312960338|ref|ZP_07774849.1| xenobiotic reductase A [Pseudomonas fluorescens WH6]
 gi|311285560|gb|EFQ64130.1| xenobiotic reductase A [Pseudomonas fluorescens WH6]
          Length = 363

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 58/182 (31%), Gaps = 25/182 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
             V+AA+   D G+  I L+       + +            ++G         + + +A
Sbjct: 159 DFVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDAYGGSFDNRSRFLLETLA 216

Query: 110 AMCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           A+ +    ++P+T +         D+        L ++ K  G++ + +     I     
Sbjct: 217 AVREVWPENLPLTARFGVIEYDGRDEQTLTESIELARNFKAGGLDLLSVSVGFTI----- 271

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           P             + E  +    + +    G      A   L    +D V +GRA   +
Sbjct: 272 PDTQIPWGPAFMGPIAERVRREAGIPVTSAWGFGTPQLAEGALQAGHLDLVSVGRAHLAD 331

Query: 223 SA 224
             
Sbjct: 332 PH 333


>gi|289643708|ref|ZP_06475819.1| NADH:flavin oxidoreductase/NADH oxidase [Frankia symbiont of
           Datisca glomerata]
 gi|289506486|gb|EFD27474.1| NADH:flavin oxidoreductase/NADH oxidase [Frankia symbiont of
           Datisca glomerata]
          Length = 658

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 23/190 (12%), Positives = 62/190 (32%), Gaps = 20/190 (10%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMCKA 114
           A+     G++ + L   C  + +  G           ++G  L     ++ + +  +  A
Sbjct: 156 AEHCVAGGFDGVELQ--CSHSSIVRGFLSPATNRRTDAYGGTLANRARLLLEIVDVVRVA 213

Query: 115 LS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG-VNGIWIHARKAILKGLSPKDNR 169
           L     + V +     ++          + + ++ +G V+ I      A       + + 
Sbjct: 214 LGPRRALGVRICGDELIEGGTTIEEAVAVARLVEATGKVDYINTSIGVATATLYMIEASM 273

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
           ++P      +    ++   L +   G  +D  QA + L     D + + R    +   + 
Sbjct: 274 QVPPGYAMFIPSAIRQAVSLPVVGVGRFKDPLQADRALAAGHADLIGVVRGQIADPDFVA 333

Query: 228 TVDEYFSNPL 237
                 +  +
Sbjct: 334 KARAGHATEI 343


>gi|295700539|ref|YP_003608432.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1002]
 gi|295439752|gb|ADG18921.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1002]
          Length = 794

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 31/203 (15%), Positives = 65/203 (32%), Gaps = 31/203 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVGD 106
           + V+A ++  + G++ + L   C                    +G  L   +  P  V  
Sbjct: 564 QFVKATRMSIEAGFDWLEL--HCAHGYFLSSFLSPLTNHRTDEYGGSLENRLRYPLQVFS 621

Query: 107 CIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            I A+      P++V+      V+          + +++K +G + I + +   + K   
Sbjct: 622 AIRAVW-PQDKPISVRISAHDWVEGGNTPDDAVKIAQALKAAGADMIDVSSG-QVSKEEK 679

Query: 165 PKDNR--KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           P   R  + P  D      ++ E   +     G + +      I+ +   D   I R   
Sbjct: 680 PVFGRMFQTPFAD-----RVRNEAG-IATIAVGAISEADHVNSIIAAGRADLCAIARPHL 733

Query: 221 KNS-AMLTTVDEYFSNPLTGSSP 242
            N    L    +     +    P
Sbjct: 734 ANPSWTLNEAAKIGYLDIAWPKP 756


>gi|163746743|ref|ZP_02154100.1| hypothetical protein OIHEL45_15109 [Oceanibulbus indolifex HEL-45]
 gi|161379857|gb|EDQ04269.1| hypothetical protein OIHEL45_15109 [Oceanibulbus indolifex HEL-45]
          Length = 763

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 28/185 (15%), Positives = 60/185 (32%), Gaps = 32/185 (17%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + VEA ++ E   ++ + L+            P +   +  +G  L        +   A
Sbjct: 548 DEFVEATRMAERANFDMVELHAAHGYLISSFISPLSNQRDDEYGGSLENRMRYSLEVFKA 607

Query: 111 MCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           M  A     P+ V+        +D +       + +   ++G + I + A +   +   P
Sbjct: 608 MRDAWPEGKPMAVRISANDWVEEDGVTPEEAVEIARMFSEAGADIIDVSAGQTSKQ-AKP 666

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGV-MIGRA---AY 220
              R       D +              +GG++ M+   +     V+ + M GRA     
Sbjct: 667 VYGRMFQTPFSDRIR------------NDGGIKTMAVGNIFEADHVNSILMAGRADLVCL 714

Query: 221 KNSAM 225
               +
Sbjct: 715 ARPHL 719


>gi|148975334|ref|ZP_01812258.1| N-ethylmaleimide reductase [Vibrionales bacterium SWAT-3]
 gi|145965258|gb|EDK30508.1| N-ethylmaleimide reductase [Vibrionales bacterium SWAT-3]
          Length = 362

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 64/187 (34%), Gaps = 21/187 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCIA 109
               AAK   + G+N + L+ G  +  +            + ++G         + + I 
Sbjct: 161 DFANAAKKAIEAGFNGVELHGG--NGYLIDQFLRTNSNKRKDNYGGSRENRLRFLIEVID 218

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+   +     V  R+        +   ++V +I ++      + AR      LS  D  
Sbjct: 219 AVIAEIGAD-KVGVRLAPFITFKDMNCPDIVPTILEA---SKALQARDIAYLHLSEADWD 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P +      E+++   +  I    G     +A ++L     D V  GR    N  +++
Sbjct: 275 DAPVIPESFRIELRELFSNTIIVA--GSYTPQRAEEVLSKGYADLVAFGRPFVANPDLVS 332

Query: 228 TVDEYFS 234
            +   + 
Sbjct: 333 RLQNGYE 339


>gi|46396194|sp|P82134|PDXS_CORGL RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|21323554|dbj|BAB98181.1| Pyridoxine biosynthesis enzyme [Corynebacterium glutamicum ATCC
           13032]
          Length = 317

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 35/97 (36%), Gaps = 8/97 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K RI
Sbjct: 54  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 107

Query: 126 GVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAIL 160
           G   +   +     + +   +         H  K   
Sbjct: 108 GHFVEAQVLEALGVDFIDESEVLSPADYTHHINKWKF 144


>gi|320546363|ref|ZP_08040679.1| dihydroorotate oxidase [Streptococcus equinus ATCC 9812]
 gi|320448973|gb|EFW89700.1| dihydroorotate oxidase [Streptococcus equinus ATCC 9812]
          Length = 311

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 39/197 (19%), Positives = 63/197 (31%), Gaps = 19/197 (9%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEG 91
              D    L  + + K   L + G    +     K V+   Y   + LN+ CP   V   
Sbjct: 80  YYLDYVTELQNNPESKNHFLSLVGMSEEETHTILKAVQASDYQGLVELNLSCP--NVPGK 137

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-------QIPAVALRNLVKSIK 144
              A    + +     +  +    + P+ VK     D         I    L   V  I 
Sbjct: 138 PQIAY---DFESTEKILTDIFTYFTKPLGVKLPPYFDIAHFDRAATIFNKFLLTFVNCIN 194

Query: 145 KSGVNGIWIHARKAILK---GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDM 200
             G NG+ I     ++K   G        +       V+   K+ NP + I   GG++  
Sbjct: 195 SVG-NGLVIDDETVVIKPKNGFGGIGGDYVKPTALANVHAFYKRLNPSIQIIGTGGVKSG 253

Query: 201 SQALKI-LPSVDGVMIG 216
             A +  L     V +G
Sbjct: 254 RDAFEHILCGASMVQLG 270


>gi|237744229|ref|ZP_04574710.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 7_1]
 gi|229431458|gb|EEO41670.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 7_1]
          Length = 487

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A      V+++ K+GV+ I + +     +G+             +++ EIKK  PDL + 
Sbjct: 227 AHDTIERVRALVKAGVDIITVDSAHGHSQGVI------------NMIKEIKKNFPDLDVI 274

Query: 193 LNGGLEDMSQALKILP-SVDGVMIG 216
             G +     A +++   V  V +G
Sbjct: 275 G-GNIVTAEAAKELIEAGVSAVKVG 298


>gi|227485979|ref|ZP_03916295.1| NADH:flavin oxidoreductase [Anaerococcus lactolyticus ATCC 51172]
 gi|227236024|gb|EEI86039.1| NADH:flavin oxidoreductase [Anaerococcus lactolyticus ATCC 51172]
          Length = 639

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 22/128 (17%), Positives = 48/128 (37%), Gaps = 6/128 (4%)

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVK---SIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             P+ V+       +   + L   +K   + +K+G + + I         +S        
Sbjct: 212 DTPILVRMNAEEGVEEGGLKLDEGIKVAIAYEKAGADALDISQGCNSAMAISTPPYFLKT 271

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVD 230
             + D   EIKK    + +   G +     A +++   + D V +GRA   +   +   +
Sbjct: 272 AFNEDNCREIKKHV-SIPVICPGRIISPEIAEEVISSGAADFVDVGRAQLADPDFVKKAE 330

Query: 231 EYFSNPLT 238
           E  ++ +T
Sbjct: 331 EGRADEIT 338


>gi|227875224|ref|ZP_03993366.1| NADPH dehydrogenase [Mobiluncus mulieris ATCC 35243]
 gi|227844129|gb|EEJ54296.1| NADPH dehydrogenase [Mobiluncus mulieris ATCC 35243]
          Length = 352

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 32/204 (15%), Positives = 64/204 (31%), Gaps = 27/204 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+AA+   + G++ + L+            P        +G  L        + I  +
Sbjct: 146 QFVQAARRALEAGFDFVELHGAHGYLMHEFLSPITNHRIDEYGGDLEGRFRFWKEIIVMI 205

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALR---------NLVKSIKKSGVNGIWIHARKAIL 160
              L  S P+ V+           + LR          L   + + GV+ I +       
Sbjct: 206 RAELGSSFPLLVRISATSWLPESNLELRRDVTLDDWGKLAHELSRLGVDFIDVSTG---- 261

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM-IGRA 218
            GL P     +         +  +    L +   G + + +QA +IL      V+ +GR 
Sbjct: 262 -GLVPGAQIPVAPGYQVPYAQEIQNRGPLPVSAVGLITEPAQAEQILVTGAASVVEVGRP 320

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSP 242
              + ++         +      P
Sbjct: 321 LLTDPSLPLAWAARLGDEPPVPEP 344


>gi|153808273|ref|ZP_01960941.1| hypothetical protein BACCAC_02561 [Bacteroides caccae ATCC 43185]
 gi|149129176|gb|EDM20392.1| hypothetical protein BACCAC_02561 [Bacteroides caccae ATCC 43185]
          Length = 325

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 32/201 (15%), Positives = 69/201 (34%), Gaps = 33/201 (16%)

Query: 39  NILGFSTQEKPL---ALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
            ++  S +E P+   A     +D   + + AK +E  G + + +N+    + V    +G+
Sbjct: 86  TLIKESKKECPIPIIASINCYSDSEWI-DFAKQIEAAGADALEINILALQSDVQYT-YGS 143

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
               + D     +  + K ++IPV +K                L+  +  +G   + +  
Sbjct: 144 FEQRHID----ILRHIKKTINIPVIMKL------GDNLTNPVALIDQLYANGAAAVVLFN 193

Query: 156 RKAILKGLSPKDNRK-------------IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           R    +     +N +                L +  +     +  D     +GG+ +   
Sbjct: 194 R--FYQPDINIENMEHMSGEIFSNASDLANPLRWIGIASAVVDKIDY--AASGGVANPES 249

Query: 203 -ALKILPSVDGVMIGRAAYKN 222
               IL     V +  A Y+N
Sbjct: 250 VVKAILAGASAVEVCSAIYQN 270


>gi|329115316|ref|ZP_08244070.1| Dihydroorotate Dehydrogenase [Acetobacter pomorum DM001]
 gi|326695295|gb|EGE46982.1| Dihydroorotate Dehydrogenase [Acetobacter pomorum DM001]
          Length = 348

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 69/184 (37%), Gaps = 36/184 (19%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD------ 102
           P+   + G   +  +  AK +E  G + I LN                +  NPD      
Sbjct: 116 PIIASLNGCTPAGWLRFAKDMEQAGASAIELN-------------FWHIPTNPDETGAQV 162

Query: 103 --IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--KA 158
                  +  +   + +PV+VK             L N+VK + ++G +GI +     + 
Sbjct: 163 EERCIQILRDVRAQVKVPVSVKLSPFFSS------LGNMVKRLSENGADGIVLFNSFYEP 216

Query: 159 ILKGLS-PKDNRKIPNLDYDIV-----YEIKKENPDLFIGLNGGLED-MSQALKILPSVD 211
            L+ L+   +   IP+  Y++        +  E+    + ++GG+   M  A  +L   D
Sbjct: 217 GLRSLTDSAEVDFIPSSAYELRLPLMWAVLLSEHCQADLAISGGVHSGMDVAKCLLAGAD 276

Query: 212 GVMI 215
             M+
Sbjct: 277 VAMV 280


>gi|300855600|ref|YP_003780584.1| putative NADH oxidase [Clostridium ljungdahlii DSM 13528]
 gi|300435715|gb|ADK15482.1| predicted NADH oxidase [Clostridium ljungdahlii DSM 13528]
          Length = 331

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 46/127 (36%), Gaps = 19/127 (14%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDD--------QIPAVALRNLVKSIKKSGVNGIWIHARK 157
             I A+ + +     +  R+G  D        +   VA+       +K+G++ + I    
Sbjct: 203 QIIEAVREVVGPEYPIFMRLGASDYMEGGTTLEDSKVAVCEF----EKAGLDVLDISGGF 258

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMI 215
                           L   +     K+   + + L GG+     A K+L  V  D + +
Sbjct: 259 CRFTVPGNNSQGYFSELSGSL-----KQFVSIPVILTGGITKAEAAEKLLVDVKADLIGV 313

Query: 216 GRAAYKN 222
           GRA YK+
Sbjct: 314 GRAMYKD 320


>gi|300977526|ref|ZP_07173957.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 200-1]
 gi|300308298|gb|EFJ62818.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 200-1]
 gi|324012012|gb|EGB81231.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 60-1]
          Length = 676

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 146 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 194

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 195 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 252

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 253 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 311

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 312 V---SMARPFL 319


>gi|295094820|emb|CBK83911.1| phosphoribosyl-ATP pyrophosphohydrolase [Coprococcus sp. ART55/1]
          Length = 424

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 38/100 (38%), Gaps = 11/100 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K    +G + I     KA   G  P         +  I+ +I  ++ D+ +   GG+
Sbjct: 21  EMAKYYNDAGADEIAYFDSKATKDGREP---------NVAIIRQIC-DSVDIPLIACGGV 70

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            ++    K+L      V +  AA     ++T   + F + 
Sbjct: 71  RELEDVKKLLYAGASKVCMKSAALNTPELVTEASDRFGSE 110


>gi|289428700|ref|ZP_06430383.1| putative 2-enoate reductase [Propionibacterium acnes J165]
 gi|289158098|gb|EFD06318.1| putative 2-enoate reductase [Propionibacterium acnes J165]
 gi|313819567|gb|EFS57281.1| putative 2-enoate reductase [Propionibacterium acnes HL046PA2]
 gi|313825981|gb|EFS63695.1| putative 2-enoate reductase [Propionibacterium acnes HL063PA1]
 gi|314962137|gb|EFT06238.1| putative 2-enoate reductase [Propionibacterium acnes HL002PA2]
 gi|314978983|gb|EFT23077.1| putative 2-enoate reductase [Propionibacterium acnes HL072PA2]
 gi|314986572|gb|EFT30664.1| putative 2-enoate reductase [Propionibacterium acnes HL005PA2]
 gi|314990929|gb|EFT35020.1| putative 2-enoate reductase [Propionibacterium acnes HL005PA3]
 gi|315087091|gb|EFT59067.1| putative 2-enoate reductase [Propionibacterium acnes HL002PA3]
 gi|315089265|gb|EFT61241.1| putative 2-enoate reductase [Propionibacterium acnes HL072PA1]
 gi|327329684|gb|EGE71440.1| 2-enoate reductase [Propionibacterium acnes HL096PA3]
 gi|327446369|gb|EGE93023.1| putative 2-enoate reductase [Propionibacterium acnes HL013PA2]
 gi|328752359|gb|EGF65975.1| putative 2-enoate reductase [Propionibacterium acnes HL020PA1]
 gi|332675970|gb|AEE72786.1| NADH oxidase [Propionibacterium acnes 266]
          Length = 670

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|226306698|ref|YP_002766658.1| dihydroorotate dehydrogenase [Rhodococcus erythropolis PR4]
 gi|259547552|sp|C0ZZY4|PYRD_RHOE4 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|226185815|dbj|BAH33919.1| dihydroorotate dehydrogenase [Rhodococcus erythropolis PR4]
          Length = 356

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 43/111 (38%), Gaps = 11/111 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK----- 161
            + A+   +S+PV VK    + D+    A+ +L   +  +G+       R+  LK     
Sbjct: 197 ILQAVLDTVSVPVLVKIAPDLSDED-VDAVADLAVELGLAGIVATNTTIRRDGLKTPDAE 255

Query: 162 ----GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL 207
               G        + +   +++  +     D + I   GG+E   QA + +
Sbjct: 256 VAALGAGGLSGAPVADRSLEVLRRLYARVGDKMTIISVGGIETADQAWERI 306


>gi|224583426|ref|YP_002637224.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
 gi|254801222|sp|C0Q1J7|HIS6_SALPC RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|224467953|gb|ACN45783.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Paratyphi C strain
           RKS4594]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|197106848|ref|YP_002132225.1| hypothetical protein PHZ_c3387 [Phenylobacterium zucineum HLK1]
 gi|196480268|gb|ACG79796.1| conserved hypothetical protein [Phenylobacterium zucineum HLK1]
          Length = 265

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 14/86 (16%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D V   IA + +A+ +PVT     G  D +  +A  N+ K I+   V             
Sbjct: 64  DKVCATIAEVVRAVDVPVTADIEGGYTDHLGELA-ENIAKVIEAGAV------------- 109

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENP 187
           G++ +D  + P L  + +  +K    
Sbjct: 110 GINLEDGTRDPALHAEKIAAVKAAAG 135


>gi|168236229|ref|ZP_02661287.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
 gi|194735173|ref|YP_002115164.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|226701999|sp|B4TMS0|HIS6_SALSV RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|194710675|gb|ACF89896.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|197290481|gb|EDY29836.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           SL480]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|198243359|ref|YP_002216163.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|226701993|sp|B5FM46|HIS6_SALDC RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|197937875|gb|ACH75208.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|326623909|gb|EGE30254.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Dublin str. 3246]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|16761008|ref|NP_456625.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. CT18]
 gi|16765407|ref|NP_461022.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhimurium str. LT2]
 gi|29141296|ref|NP_804638.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. Ty2]
 gi|56413024|ref|YP_150099.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Paratyphi A str. ATCC
           9150]
 gi|161613246|ref|YP_001587211.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Paratyphi B str. SPB7]
 gi|167551022|ref|ZP_02344777.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|167990991|ref|ZP_02572090.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168229396|ref|ZP_02654454.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168242149|ref|ZP_02667081.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168259622|ref|ZP_02681595.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168466268|ref|ZP_02700138.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|168818231|ref|ZP_02830231.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194446795|ref|YP_002041345.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194448693|ref|YP_002046127.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194470570|ref|ZP_03076554.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197361948|ref|YP_002141585.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Paratyphi A str.
           AKU_12601]
 gi|200387416|ref|ZP_03214028.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|204929261|ref|ZP_03220404.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205353219|ref|YP_002227020.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 287/91]
 gi|207857512|ref|YP_002244163.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Enteritidis str.
           P125109]
 gi|213161021|ref|ZP_03346731.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. E00-7866]
 gi|213420502|ref|ZP_03353568.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. E01-6750]
 gi|213425564|ref|ZP_03358314.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. E02-1180]
 gi|213584240|ref|ZP_03366066.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. E98-0664]
 gi|213648074|ref|ZP_03378127.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. J185]
 gi|213859451|ref|ZP_03385155.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. M223]
 gi|238913441|ref|ZP_04657278.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Tennessee str.
           CDC07-0191]
 gi|289826291|ref|ZP_06545403.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhi str. E98-3139]
 gi|61225725|sp|P0A1R2|HIS6_SALTY RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|61225727|sp|P0A1R3|HIS6_SALTI RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|81821364|sp|Q5PDN6|HIS6_SALPA RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|189043436|sp|A9N7S0|HIS6_SALPB RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226701994|sp|B5QZL7|HIS6_SALEP RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226701995|sp|B5RBR7|HIS6_SALG2 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226701996|sp|B4T9N9|HIS6_SALHS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226701997|sp|B4SX46|HIS6_SALNS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226701998|sp|B5BFB5|HIS6_SALPK RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|25292243|pir||AI0764 cyclase HisF [imported] - Salmonella enterica subsp. enterica
           serovar Typhi (strain CT18)
 gi|47727|emb|CAA31828.1| unnamed protein product [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|16420608|gb|AAL20981.1| imidazole glycerol phosphate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|16503306|emb|CAD02439.1| cyclase HisF [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29136922|gb|AAO68487.1| cyclase HisF [Salmonella enterica subsp. enterica serovar Typhi
           str. Ty2]
 gi|56127281|gb|AAV76787.1| cyclase HisF [Salmonella enterica subsp. enterica serovar Paratyphi
           A str. ATCC 9150]
 gi|161362610|gb|ABX66378.1| hypothetical protein SPAB_00956 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194405458|gb|ACF65680.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194406997|gb|ACF67216.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194456934|gb|EDX45773.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|195631505|gb|EDX50065.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197093425|emb|CAR58880.1| cyclase HisF [Salmonella enterica subsp. enterica serovar Paratyphi
           A str. AKU_12601]
 gi|199604514|gb|EDZ03059.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|204321805|gb|EDZ07004.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205273000|emb|CAR37948.1| Imidazole glycerol phosphate synthase subunit hisF [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 287/91]
 gi|205323970|gb|EDZ11809.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|205330556|gb|EDZ17320.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205335681|gb|EDZ22445.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205338320|gb|EDZ25084.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205344974|gb|EDZ31738.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350895|gb|EDZ37526.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|206709315|emb|CAR33655.1| Imidazole glycerol phosphate synthase subunit hisF [Salmonella
           enterica subsp. enterica serovar Enteritidis str.
           P125109]
 gi|261247292|emb|CBG25117.1| imidazole glycerol phosphate synthase subunit hisf [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           D23580]
 gi|267994131|gb|ACY89016.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           14028S]
 gi|301158638|emb|CBW18150.1| Imidazole glycerol phosphate synthase subunit hisF [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           SL1344]
 gi|312913068|dbj|BAJ37042.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           T000240]
 gi|320086511|emb|CBY96282.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Salmonella enterica subsp. enterica serovar
           Weltevreden str. 2007-60-3289-1]
 gi|321224724|gb|EFX49787.1| Imidazole glycerol phosphate synthase cyclase subunit [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322613656|gb|EFY10596.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           315996572]
 gi|322620227|gb|EFY17096.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           495297-1]
 gi|322623273|gb|EFY20114.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           495297-3]
 gi|322630478|gb|EFY27247.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           495297-4]
 gi|322632845|gb|EFY29590.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           515920-1]
 gi|322638822|gb|EFY35516.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           515920-2]
 gi|322640293|gb|EFY36955.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 531954]
 gi|322647138|gb|EFY43637.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           NC_MB110209-0054]
 gi|322652183|gb|EFY48544.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           OH_2009072675]
 gi|322653870|gb|EFY50194.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           CASC_09SCPH15965]
 gi|322660977|gb|EFY57206.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 19N]
 gi|322663082|gb|EFY59289.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           81038-01]
 gi|322668527|gb|EFY64682.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MD_MDA09249507]
 gi|322673338|gb|EFY69441.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 414877]
 gi|322679124|gb|EFY75178.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 366867]
 gi|322683219|gb|EFY79234.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 413180]
 gi|322685911|gb|EFY81901.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 446600]
 gi|323130400|gb|ADX17830.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhimurium str. 4/74]
 gi|323195198|gb|EFZ80379.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           609458-1]
 gi|323198766|gb|EFZ83866.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           556150-1]
 gi|323202410|gb|EFZ87453.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 609460]
 gi|323209205|gb|EFZ94141.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           507440-20]
 gi|323213834|gb|EFZ98611.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str. 556152]
 gi|323216138|gb|EGA00868.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB101509-0077]
 gi|323222507|gb|EGA06876.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB102109-0047]
 gi|323223743|gb|EGA08050.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB110209-0055]
 gi|323231349|gb|EGA15463.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           MB111609-0052]
 gi|323232559|gb|EGA16656.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           2009083312]
 gi|323240998|gb|EGA25038.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           2009085258]
 gi|323245583|gb|EGA29578.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           315731156]
 gi|323250162|gb|EGA34055.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2009159199]
 gi|323251056|gb|EGA34930.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008282]
 gi|323257454|gb|EGA41145.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008283]
 gi|323263347|gb|EGA46881.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008284]
 gi|323266334|gb|EGA49823.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008285]
 gi|323272294|gb|EGA55702.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Montevideo str.
           IA_2010008287]
 gi|326628306|gb|EGE34649.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Gallinarum str. 9]
 gi|332989012|gb|AEF07995.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Typhimurium str. UK-1]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|330506568|ref|YP_004382996.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methanosaeta concilii GP-6]
 gi|328927376|gb|AEB67178.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methanosaeta concilii GP-6]
          Length = 241

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 11/93 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +     G + + I      ++G            +  I+ +I KE  D++I + GG+  
Sbjct: 38  AERWIDEGADHLHIIDLDGAIQG---------KRANASILAQIVKEL-DVYIQVGGGIRS 87

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
             +A  +L   VD V++G AA K+  M+  + E
Sbjct: 88  EEEARDVLRLGVDRVILGTAALKDPDMIAQLAE 120


>gi|313763540|gb|EFS34904.1| putative 2-enoate reductase [Propionibacterium acnes HL013PA1]
 gi|313816722|gb|EFS54436.1| putative 2-enoate reductase [Propionibacterium acnes HL059PA1]
 gi|314914696|gb|EFS78527.1| putative 2-enoate reductase [Propionibacterium acnes HL005PA4]
 gi|314919344|gb|EFS83175.1| putative 2-enoate reductase [Propionibacterium acnes HL050PA1]
 gi|314920747|gb|EFS84578.1| putative 2-enoate reductase [Propionibacterium acnes HL050PA3]
 gi|314930627|gb|EFS94458.1| putative 2-enoate reductase [Propionibacterium acnes HL067PA1]
 gi|314954417|gb|EFS98823.1| putative 2-enoate reductase [Propionibacterium acnes HL027PA1]
 gi|314957499|gb|EFT01602.1| putative 2-enoate reductase [Propionibacterium acnes HL002PA1]
 gi|315099168|gb|EFT71144.1| putative 2-enoate reductase [Propionibacterium acnes HL059PA2]
 gi|315100348|gb|EFT72324.1| putative 2-enoate reductase [Propionibacterium acnes HL046PA1]
 gi|327454919|gb|EGF01574.1| putative 2-enoate reductase [Propionibacterium acnes HL087PA3]
 gi|327457795|gb|EGF04450.1| putative 2-enoate reductase [Propionibacterium acnes HL083PA2]
 gi|328755247|gb|EGF68863.1| putative 2-enoate reductase [Propionibacterium acnes HL087PA1]
 gi|328758273|gb|EGF71889.1| putative 2-enoate reductase [Propionibacterium acnes HL025PA2]
          Length = 670

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|256027893|ref|ZP_05441727.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. D11]
 gi|289765842|ref|ZP_06525220.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. D11]
 gi|289717397|gb|EFD81409.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. D11]
          Length = 487

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A      V+++ K+GV+ I + +     +G+             +++ EIKK  PDL + 
Sbjct: 227 AHDTIERVRALVKAGVDIITVDSAHGHSQGVI------------NMIKEIKKNFPDLDVI 274

Query: 193 LNGGLEDMSQALKILP-SVDGVMIG 216
             G +     A +++   V  V +G
Sbjct: 275 G-GNIVTAEAAKELIEAGVSAVKVG 298


>gi|123443882|ref|YP_001007853.1| 2,4-dienoyl-CoA reductase [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090843|emb|CAL13725.1| 2,4-dienoyl-CoA reductase [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 673

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 24/197 (12%), Positives = 57/197 (28%), Gaps = 38/197 (19%)

Query: 49  PLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF---------- 93
           P   Q    D      +     A++    GY+ + +        +    +          
Sbjct: 127 PFTPQELSHDEVLQTIADFAHCAQLARQAGYDGVEV--------MGSEGYLINQFLTART 178

Query: 94  -------GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKS 142
                  G           + + A+  A      +  R+     V+D      +  L ++
Sbjct: 179 NHRNDEWGGDFTRRMRFAVEIVRAVRAAAGPDFILIYRLSMLDLVEDGSSWDEIELLARA 238

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++++G   I  +      +   P     +P   +  V        ++ +     + D + 
Sbjct: 239 VEQAGATLI--NTGIGWHEARIPTIATMVPRAGFSWVTRKLMGKVNIPLITTNRINDPAV 296

Query: 203 ALKILP--SVDGVMIGR 217
           A ++L     D V + R
Sbjct: 297 AEQVLTDGCADMVSMAR 313


>gi|191172246|ref|ZP_03033789.1| 2,4-dienoyl-CoA reductase [Escherichia coli F11]
 gi|190907556|gb|EDV67152.1| 2,4-dienoyl-CoA reductase [Escherichia coli F11]
          Length = 672

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|330879224|gb|EGH13373.1| NADH:flavin oxidoreductase/NADH oxidase family protein [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 360

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 24/154 (15%), Positives = 54/154 (35%), Gaps = 20/154 (12%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSI--------PVTVKCRIGVDDQIPAVAL 136
           SA V   ++G  +     ++ + + A+ K +          PV+    +   D  P    
Sbjct: 190 SANVRTDAYGGSVENRARLLLEVVTAVVKEIGAQRTGVRLSPVSPANGVASSDPQPQYEY 249

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + + + + G+  + +           P+D   +   DYD    +++     ++  NG 
Sbjct: 250 --IAEQLSEQGIAFLHVVEGAT----GGPRD---VAPFDYD---ALRERFKHTYLANNGY 297

Query: 197 LEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
             D++         D V  GR    N  ++  + 
Sbjct: 298 DLDLATVRVNANKADLVAFGRPFISNPDLIERLK 331


>gi|260494187|ref|ZP_05814318.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 3_1_33]
 gi|260198333|gb|EEW95849.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 3_1_33]
          Length = 488

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
           A      V+++ K+GV+ I + +     +G+             +++ EIKK  PDL + 
Sbjct: 228 AHDTIERVRALVKAGVDIITVDSAHGHSQGVI------------NMIKEIKKNFPDLDVI 275

Query: 193 LNGGLEDMSQALKILP-SVDGVMIG 216
             G +     A +++   V  V +G
Sbjct: 276 G-GNIVTAEAAKELIEAGVSAVKVG 299


>gi|212709659|ref|ZP_03317787.1| hypothetical protein PROVALCAL_00706 [Providencia alcalifaciens DSM
           30120]
 gi|212687470|gb|EEB46998.1| hypothetical protein PROVALCAL_00706 [Providencia alcalifaciens DSM
           30120]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V ++  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVAKVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + + F 
Sbjct: 85  SVEDAAQILSFGADKLSINSPALSDPTLISRLADRFG 121


>gi|62180657|ref|YP_217074.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|81309652|sp|Q57MR8|HIS6_SALCH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|62128290|gb|AAX65993.1| imidazole glycerol phosphate synthase, subunit with HisH
           [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|322715128|gb|EFZ06699.1| imidazole glycerol phosphate synthase subunit HisF [Salmonella
           enterica subsp. enterica serovar Choleraesuis str. A50]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|51701800|sp|Q7Z892|PYRD1_SACKL RecName: Full=Dihydroorotate dehydrogenase; Short=DHOD;
           Short=DHODase; Short=DHOdehase; AltName:
           Full=Dihydroorotate oxidase
 gi|33317313|gb|AAQ04683.1|AF452109_1 cytosolic dihydroorotate dehydrogenase [Lachancea kluyveri]
 gi|33302317|gb|AAQ01779.1| dihydroorotate dehydrogenase 1a [Lachancea kluyveri]
          Length = 314

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 62/180 (34%), Gaps = 32/180 (17%)

Query: 48  KPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCP----SARVHEGSFGACLMLNPD 102
            PL   + G  + + ++  + ++D  +N I  LN+ CP      +V           + +
Sbjct: 97  TPLFFSVAGMSVEENLKMLQKIQDSDFNGITELNLSCPNVPGKPQVA---------YDFE 147

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----------- 151
           +  + +  + +    P+ VK      D      +  ++  +  S VN I           
Sbjct: 148 LTKEILTKVFEFFKKPLGVKL-PPYFDFAHFDIMAGILNQLPLSYVNCINSIGNGLYINV 206

Query: 152 ----WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
                +   K    G+  +  +     +    Y   + NP + I   GG++    A + L
Sbjct: 207 ETESVVVKPKNGFGGIGGEYVKPTALANVRAFYT--RLNPTIKIIGTGGIKTGQDAFEHL 264


>gi|320161771|ref|YP_004174996.1| imidazole glycerol phosphate synthase subunit HisF [Anaerolinea
           thermophila UNI-1]
 gi|319995625|dbj|BAJ64396.1| imidazole glycerol phosphate synthase subunit HisF [Anaerolinea
           thermophila UNI-1]
          Length = 259

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 11/96 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +   ++G + +      A  +G              ++V  +  +   L   + GG+  
Sbjct: 36  AQIYDQAGADELAFLDISATQEGRETV---------LEMVRRVA-DVVFLPFTVGGGIRT 85

Query: 200 MSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +    +IL    D V I  AA +N  +L+   E F 
Sbjct: 86  VEDVRRILLAGADKVSINSAAVRNPDLLSECAERFG 121


>gi|302035778|ref|YP_003796100.1| d-ribulose-5-phosphate 3-epimerase [Candidatus Nitrospira defluvii]
 gi|300603842|emb|CBK40174.1| D-ribulose-5-phosphate 3-epimerase [Candidatus Nitrospira defluvii]
          Length = 234

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 27/141 (19%), Positives = 53/141 (37%), Gaps = 25/141 (17%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +A  I  AD ++L E    VED G + ++++       V +G F   L + P      + 
Sbjct: 8   IAPSILSADFARLAEEVARVEDAGADWLHID-------VMDGHFVPNLTVGPP----IVE 56

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ K  ++P+ V   +   D          +    ++G + + +H          P  +R
Sbjct: 57  ALRKVTTLPLDVHLMMTNPD--------AFIGEFAEAGADYLTVHVETC------PHLHR 102

Query: 170 KIPNLDYDIVYEIKKENPDLF 190
            + ++    V      NP   
Sbjct: 103 TVQSIKERGVKAGVTLNPATP 123


>gi|288556102|ref|YP_003428037.1| tryptophan synthase subunit alpha [Bacillus pseudofirmus OF4]
 gi|288547262|gb|ADC51145.1| tryptophan synthase subunit alpha [Bacillus pseudofirmus OF4]
          Length = 266

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
           + +KI +  YD +  +K+ +P + + +  G+    Q  ++    DGV++G
Sbjct: 181 ERKKIDDRVYDFLETVKQASP-VPVAVGFGISSNEQVKEMQQHADGVIVG 229


>gi|225568483|ref|ZP_03777508.1| hypothetical protein CLOHYLEM_04560 [Clostridium hylemonae DSM
           15053]
 gi|225162711|gb|EEG75330.1| hypothetical protein CLOHYLEM_04560 [Clostridium hylemonae DSM
           15053]
          Length = 665

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 24/193 (12%), Positives = 55/193 (28%), Gaps = 22/193 (11%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                 AK +++ G + + L             P        +G         + + + A
Sbjct: 155 ELFAAGAKRLKEAGVDAVELHGAHGYLIGQFLSPYTNKRTDRYGGSFENRMRFLDEILDA 214

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALR----------NLVKSIKKSGVNGIWIHARKAIL 160
           + +       V  R   D+ +    L            + K +   GV+ + + A     
Sbjct: 215 VRRECGGDYPVIVRFSADEHMEYAGLPGEGLCLEDGVKIAKHLAGKGVDALDVSAGIYET 274

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              + +          +    +KK      I  +  + +   A ++L     D +   RA
Sbjct: 275 MNTAWEPVGFDQGWKMNGAEAVKKAVRIPVIAAS-VIREPGYAEEVLKEGKCDFIGSARA 333

Query: 219 AYKNSAMLTTVDE 231
            + +   +    E
Sbjct: 334 FFADPDWMRKARE 346


>gi|32479376|ref|NP_862229.1| dihydroorotate dehydrogenase 2 [Corynebacterium striatum]
 gi|172039958|ref|YP_001799672.1| dihydroorotate dehydrogenase 2 [Corynebacterium urealyticum DSM
           7109]
 gi|227487327|ref|ZP_03917643.1| dihydroorotate dehydrogenase 2 [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227542748|ref|ZP_03972797.1| dihydroorotate dehydrogenase 2 [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|30173373|sp|Q9FB59|PYRD_CORST RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|9945789|gb|AAG03363.1| PyrD [Corynebacterium striatum]
 gi|171851262|emb|CAQ04238.1| unnamed protein product [Corynebacterium urealyticum DSM 7109]
 gi|227092753|gb|EEI28065.1| dihydroorotate dehydrogenase 2 [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227181514|gb|EEI62486.1| dihydroorotate dehydrogenase 2 [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 359

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 20/117 (17%), Positives = 46/117 (39%), Gaps = 11/117 (9%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIW 152
           + +   +  + K+ + PV VK    + D+    A+ +L   ++ +G+         +G+ 
Sbjct: 192 EELRPILEVVKKSTTTPVLVKIAPDLSDED-IDAVADLAVELELAGIVATNTTISRSGLK 250

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
             A K    G        + N   +++  + +   D L +   GG+    QA + + 
Sbjct: 251 TPASKVEKMGAGGISGAPLENRSLEVLKRLHERVGDKLVLVSVGGISTPEQAWERIT 307


>gi|256824650|ref|YP_003148610.1| dihydroorotate oxidase A [Kytococcus sedentarius DSM 20547]
 gi|256688043|gb|ACV05845.1| dihydroorotate oxidase A [Kytococcus sedentarius DSM 20547]
          Length = 385

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 62/197 (31%), Gaps = 35/197 (17%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL---- 115
                  ++      + + +N+  P       + G   + +P+ +   +A +  A     
Sbjct: 199 EDYAACVRVAAGL-PDYLAVNISSP------NTPGLRGLADPEPLRALLAGVVAAERERA 251

Query: 116 ------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
                  +PV  K    +DD     AL   V   ++ GV GI          GL+ +D  
Sbjct: 252 DAAGTPPVPVLCKVAPDMDD----AALHAAVGIAQEEGVAGIIATNTTLRRDGLTAEDRA 307

Query: 170 KIPNLDY---------DIVYEIKKENP---DLFIGLNGGLEDMSQALK-ILPSVDGVMIG 216
            +              D   E+ +      DL +   GG+      ++ +    D V + 
Sbjct: 308 WVGPERPGGVSGAPLTDRAREVVRLVRAGCDLPVVGVGGVMTPQDGVELVRAGADLVQVY 367

Query: 217 RA-AYKNSAMLTTVDEY 232
               Y   A++  +   
Sbjct: 368 TGFIYAGPALVAGIAAR 384


>gi|254471000|ref|ZP_05084403.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudovibrio sp. JE062]
 gi|211960142|gb|EEA95339.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudovibrio sp. JE062]
          Length = 247

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 28/145 (19%), Positives = 56/145 (38%), Gaps = 21/145 (14%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVK 141
           +  V     G   + +P++V +        +++ +  K      +   +   + +  L K
Sbjct: 94  AKGVARVILGTVALRDPELVKEACKKYPDRIAVGIDAKGGKVAVEGWAETSELTVIELAK 153

Query: 142 SIKKSGVNGIWIHA--RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             + +GV  I      R  +LKGL+ +   ++ N               + I  +GGL D
Sbjct: 154 QFEDAGVAAIIYTDIDRDGVLKGLNIESTLELANA------------VSIPIIASGGLAD 201

Query: 200 MSQALKIL-PSVD---GVMIGRAAY 220
           +    +++ P  D   G + GRA Y
Sbjct: 202 IKDIERLIQPDCDILEGAISGRALY 226


>gi|50084346|ref|YP_045856.1| 2,4-dienoyl-CoA reductase [Acinetobacter sp. ADP1]
 gi|49530322|emb|CAG68034.1| 2,4-dienoyl-CoA reductase [NADPH] (2,4-dienoyl coenzyme A
           reductase) [Acinetobacter sp. ADP1]
          Length = 676

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 33/234 (14%), Positives = 73/234 (31%), Gaps = 24/234 (10%)

Query: 12  FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
             ++L      Y   IV+ + ++            EK +        I      +++ + 
Sbjct: 100 LMQILHAGRYGYQPFIVSASPIKSPISPFKPRQMSEKNIL-----DTIEDYARCSELAKK 154

Query: 72  FGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            GY+ I +                   E  +G  +        + + A+ + +     + 
Sbjct: 155 AGYDGIEIMGSEGYLLNQFLSRHVNQREDRWGGAIENRMRFAIEIVKAIREKVGEKFIIS 214

Query: 123 CRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-D 177
            R+     V D      +  + K+++K GV  +  +      +   P     +P   + D
Sbjct: 215 FRLSMLDLVHDGNTMQEVIIVAKALEKVGVTLL--NTGIGWHEARVPTIVTSVPRAAFVD 272

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               +K+      I  N  +     A  IL     D + + R    ++  +T V
Sbjct: 273 YTAYVKQHVTIPVIASNR-INMPDVAENILATGKADMIQMARPLLADAFWVTKV 325


>gi|298531043|ref|ZP_07018444.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298509066|gb|EFI32971.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 371

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 30/197 (15%), Positives = 63/197 (31%), Gaps = 18/197 (9%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
            V AA+     G++ + L             P     +  +G  L        + + A+ 
Sbjct: 143 FVRAAQRAFKAGFDMVELHGGTGYLLAQFASPRTNKRKDYYGGSLEKRMRFPLEVMQAVR 202

Query: 113 KAL-SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +A  + PV  +      + D +       L   +  +G   + +           P+  +
Sbjct: 203 EAAGNKPVGYRFLADEWLPDGLTLEESGPLASRLSDAGAAYLSVMGGT-YESFSMPEVIK 261

Query: 170 KIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                 Y  D+  EI ++   + +   G +     A ++L S   D V + R  + +   
Sbjct: 262 ATKKPGYMADLAGEI-RDQVRVPVIAAGRIALGHVAEEVLSSGRADLVGLARVLWADPEW 320

Query: 226 LTTVDEYFSNPLTGSSP 242
              V +   + L    P
Sbjct: 321 PEKVRQDREDDLVICDP 337


>gi|145638610|ref|ZP_01794219.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittII]
 gi|145272205|gb|EDK12113.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittII]
 gi|309750110|gb|ADO80094.1| Imidazole glycerol phosphate synthase, subunit HisF [Haemophilus
           influenzae R2866]
          Length = 258

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G +         +D   V  I +   D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRT---------VDKSWVERIAQAI-DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPTLISRLADRFG 121


>gi|238761100|ref|ZP_04622077.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           kristensenii ATCC 33638]
 gi|238761353|ref|ZP_04622329.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           kristensenii ATCC 33638]
 gi|238700327|gb|EEP93068.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           kristensenii ATCC 33638]
 gi|238700580|gb|EEP93320.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           kristensenii ATCC 33638]
          Length = 242

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 19  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 68

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + E + 
Sbjct: 69  SVEDAGQILTFGADKISINSPALADPTLITRLAERYG 105


>gi|254515431|ref|ZP_05127492.1| putative NADH oxidase [gamma proteobacterium NOR5-3]
 gi|219677674|gb|EED34039.1| putative NADH oxidase [gamma proteobacterium NOR5-3]
          Length = 661

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 53/141 (37%), Gaps = 9/141 (6%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI-KKSGVNGI 151
           +G  L      + + IAA+  A S    +  ++  DD +P         +I ++   +  
Sbjct: 190 YGGDLEGRTRFLRELIAAIRSACSDNFIIGLKLPADDGVPGGIDMTEAHAISQRLAADNG 249

Query: 152 WIHARKAILKGLSPKDNRKIPNLD------YDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
                       +   +  +P+         + + ++++ +PD+  G  G + D ++   
Sbjct: 250 SFDYWTWAWGTHANSLHLHLPDAHGERHPYLEAIRDLRQIDPDIPAGALGYITDPNECET 309

Query: 206 ILP--SVDGVMIGRAAYKNSA 224
            L   + D V +GR    + A
Sbjct: 310 ALTDGTADLVFLGRPLITDPA 330


>gi|194688318|gb|ACF78243.1| unknown [Zea mays]
 gi|224030037|gb|ACN34094.1| unknown [Zea mays]
          Length = 339

 Score = 37.5 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 35/215 (16%), Positives = 68/215 (31%), Gaps = 58/215 (26%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNV-------GCPSARVHEGSFGACLMLNPDIVGDC 107
           G  D++   EA ++++  G + I L V         P  +    +        PD V   
Sbjct: 96  GDPDLATTAEALRLLDACGADVIELGVPFSDPYADGPVIQA-SAARALASGTTPDGVLAM 154

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW--------------- 152
           +  +   LS PV         + I    L +   ++K++GV+G+                
Sbjct: 155 LKEVTPELSCPV---VLFSYFNPIVRWGLADFAAAVKEAGVHGLIVPDLPYGNSCALTLR 211

Query: 153 -------------------------IHARKAILKGLSPKDNRKIPNLDYD-----IVYEI 182
                                    I         L+  +    P  + +     ++ E+
Sbjct: 212 TEAIKNNLELVLLTTPSTPADRMEEITRASRGFVYLASVNGVTGPRANVNTRVQSLIQEV 271

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           K+   D+ + +  G+       +I     DGV+IG
Sbjct: 272 KQ-VTDIPVAVGFGISKPEHVKQIAEWGADGVIIG 305


>gi|270296422|ref|ZP_06202622.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270273826|gb|EFA19688.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 325

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 32/185 (17%), Positives = 58/185 (31%), Gaps = 23/185 (12%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I    +   +  AAKI E+ G + + +N+      V    +G     + D     
Sbjct: 98  PIIASINCYQNADWVEFAAKI-EEAGADALEINILALQTDVQYT-YGTFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---------KA 158
           ++ + K + IPV +K                L+  +  +G   + +  R         K 
Sbjct: 152 LSHIKKTVKIPVIMKL------GDNLTNPIALIDQLYANGAAAVVLFNRFYQPDINIEKM 205

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGVMIGR 217
           I    +   N    +     +         L    +GG+         IL     V I  
Sbjct: 206 IQVSGNVFSNEADLSKALRWIGIASAAVNKLDYAASGGIHSPEGVVKAILAGASAVEICS 265

Query: 218 AAYKN 222
             Y+N
Sbjct: 266 VLYQN 270


>gi|55379964|ref|YP_137814.1| deoxyribose-phosphate aldolase [Haloarcula marismortui ATCC 43049]
 gi|68052077|sp|Q5UX95|DEOC_HALMA RecName: Full=Deoxyribose-phosphate aldolase; Short=DERA; AltName:
           Full=2-deoxy-D-ribose 5-phosphate aldolase; AltName:
           Full=Phosphodeoxyriboaldolase; Short=Deoxyriboaldolase
 gi|55232689|gb|AAV48108.1| deoxyribose-phosphate aldolase [Haloarcula marismortui ATCC 43049]
          Length = 231

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 23/149 (15%), Positives = 53/149 (35%), Gaps = 28/149 (18%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
             + +AAK+  D G +E++  + C    +  G          D V D I  +  ++ +PV
Sbjct: 68  DSVCQAAKLAWDAGADELD--MVCNVGLLKAG--------EDDAVRDHITEVVASVPVPV 117

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            V     +        +  LV     +  +  ++       +G +              V
Sbjct: 118 KVIVEAPLLSDAELERVGQLV-----ADADAAYLKTATGFSEGGAT-------------V 159

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP 208
           ++++  +  L +  +GG+   + A  +  
Sbjct: 160 HDVEILSKYLPVKASGGVGSWADAKAMFE 188


>gi|121606505|ref|YP_983834.1| salicylyl-CoA 5-hydroxylase [Polaromonas naphthalenivorans CJ2]
 gi|120595474|gb|ABM38913.1| NADH:flavin oxidoreductase/NADH oxidase [Polaromonas
           naphthalenivorans CJ2]
          Length = 822

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 31/213 (14%), Positives = 67/213 (31%), Gaps = 29/213 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIA 109
           + V+A +   + G++ + L   C           P   +   ++G  L        +  +
Sbjct: 609 EFVQATRRAAEAGFDWLEL--HCAHGYLLSSFITPLTNLRGDAWGGSLENRCRYPLEVFS 666

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSP 165
           AM       + +  RI   D  P     +    + +  K +G + I       +  G + 
Sbjct: 667 AMRAVWPEHLPMSVRISAHDWAPGGNTGDDAVAIARLFKAAGCDFID------VSSGQTT 720

Query: 166 KDNRKIPNLDYD--IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           +  R +    Y       I+ E   +     G + ++     I+ +   D   I R    
Sbjct: 721 RAARPVYGRMYQTPFADRIRNEAG-IQTIAVGAISEVDHVNSIIAAGRADLCAIARPHLA 779

Query: 222 NS-AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +    L    +  S  +    P  +  D+ +  
Sbjct: 780 DPAWTLHEAAKLQSRHVQWPQPYLSGRDQLYRE 812


>gi|326939767|gb|AEA15663.1| NADPH dehydrogenase NamA [Bacillus thuringiensis serovar chinensis
           CT-43]
          Length = 345

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        + +         K +K+ GV+ 
Sbjct: 186 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPEGLTVQDYVQYTKWMKEQGVDL 245

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   SQA +IL   
Sbjct: 246 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGSQAEQILNNN 299

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 300 EADLIFIGRELLRNPY 315


>gi|313829449|gb|EFS67163.1| putative 2-enoate reductase [Propionibacterium acnes HL063PA2]
 gi|315108967|gb|EFT80943.1| putative 2-enoate reductase [Propionibacterium acnes HL030PA2]
          Length = 670

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|313793933|gb|EFS41957.1| putative 2-enoate reductase [Propionibacterium acnes HL110PA1]
 gi|315079563|gb|EFT51556.1| putative 2-enoate reductase [Propionibacterium acnes HL053PA2]
 gi|327452044|gb|EGE98698.1| putative 2-enoate reductase [Propionibacterium acnes HL092PA1]
          Length = 670

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|313773479|gb|EFS39445.1| putative 2-enoate reductase [Propionibacterium acnes HL074PA1]
 gi|313801320|gb|EFS42571.1| putative 2-enoate reductase [Propionibacterium acnes HL110PA2]
 gi|313811531|gb|EFS49245.1| putative 2-enoate reductase [Propionibacterium acnes HL083PA1]
 gi|313831272|gb|EFS68986.1| putative 2-enoate reductase [Propionibacterium acnes HL007PA1]
 gi|313834883|gb|EFS72597.1| putative 2-enoate reductase [Propionibacterium acnes HL056PA1]
 gi|313839957|gb|EFS77671.1| putative 2-enoate reductase [Propionibacterium acnes HL086PA1]
 gi|314963715|gb|EFT07815.1| putative 2-enoate reductase [Propionibacterium acnes HL082PA1]
 gi|314974148|gb|EFT18244.1| putative 2-enoate reductase [Propionibacterium acnes HL053PA1]
 gi|314976562|gb|EFT20657.1| putative 2-enoate reductase [Propionibacterium acnes HL045PA1]
 gi|314984381|gb|EFT28473.1| putative 2-enoate reductase [Propionibacterium acnes HL005PA1]
 gi|315081207|gb|EFT53183.1| putative 2-enoate reductase [Propionibacterium acnes HL078PA1]
 gi|315095287|gb|EFT67263.1| putative 2-enoate reductase [Propionibacterium acnes HL038PA1]
 gi|327328450|gb|EGE70212.1| 2-enoate reductase [Propionibacterium acnes HL096PA2]
 gi|327444238|gb|EGE90892.1| putative 2-enoate reductase [Propionibacterium acnes HL043PA2]
 gi|327444883|gb|EGE91537.1| putative 2-enoate reductase [Propionibacterium acnes HL043PA1]
 gi|328759979|gb|EGF73562.1| 2-enoate reductase [Propionibacterium acnes HL099PA1]
          Length = 670

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|289426418|ref|ZP_06428161.1| putative 2-enoate reductase [Propionibacterium acnes SK187]
 gi|289153146|gb|EFD01864.1| putative 2-enoate reductase [Propionibacterium acnes SK187]
          Length = 670

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|313125519|ref|YP_004035783.1| pyridoxal phosphate synthase yaad subunit [Halogeometricum
           borinquense DSM 11551]
 gi|312291884|gb|ADQ66344.1| pyridoxal phosphate synthase yaaD subunit [Halogeometricum
           borinquense DSM 11551]
          Length = 302

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      P+        G   M +P+ V + I     A+SIPV  K
Sbjct: 36  AEQARIAEEAGAVAVMALEAVPAD--IRKRGGVSRMADPETVKEII----DAVSIPVMGK 89

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 90  ARIGHHTE---------AQILESIGVDMI 109


>gi|295131091|ref|YP_003581754.1| pyridine nucleotide-disulfide oxidoreductase [Propionibacterium
           acnes SK137]
 gi|291375635|gb|ADD99489.1| pyridine nucleotide-disulfide oxidoreductase [Propionibacterium
           acnes SK137]
          Length = 663

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|150401623|ref|YP_001325389.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methanococcus aeolicus Nankai-3]
 gi|167011537|sp|A6UWA5|HIS4_META3 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|150014326|gb|ABR56777.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Methanococcus aeolicus Nankai-3]
          Length = 241

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +D + V ++  E  ++ I  +GG+      LK+    VDGV++G A Y
Sbjct: 179 IDIEPVKKLVDEL-NIPIIASGGITTYDDLLKLKEIGVDGVVVGSAIY 225


>gi|20806554|ref|NP_621725.1| NADH:flavin oxidoreductase [Thermoanaerobacter tengcongensis MB4]
 gi|254478914|ref|ZP_05092276.1| oxidoreductase, FAD/FMN-binding superfamily [Carboxydibrachium
           pacificum DSM 12653]
 gi|20514992|gb|AAM23329.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family
           [Thermoanaerobacter tengcongensis MB4]
 gi|214035136|gb|EEB75848.1| oxidoreductase, FAD/FMN-binding superfamily [Carboxydibrachium
           pacificum DSM 12653]
          Length = 337

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 61/178 (34%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK     GY+ + ++            P +   +  +G  +      + + I  + 
Sbjct: 145 FGEAAKRANLAGYDVVEIHAAHGYLIHEFLSPLSNKRKDEYGNSIENRARFLIEVIDEVR 204

Query: 113 KAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K    + P+ V+      ++  I    +   +  IK   V+ I + +      GL   D 
Sbjct: 205 KNWPQNKPIFVRVSADDYIEGGINIDMMVEYINMIKDK-VDVIDVSSG-----GLLNVDI 258

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              P         IKK   ++     G +     A +IL +   D V +GR   +N  
Sbjct: 259 NPYPGYQVKYAETIKKRC-NIKTCAVGLITTQELAEEILSNERADLVALGRELLRNPY 315


>gi|313813410|gb|EFS51124.1| putative 2-enoate reductase [Propionibacterium acnes HL025PA1]
          Length = 670

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKGLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|284167102|ref|YP_003405380.1| NADH:flavin oxidoreductase/NADH oxidase [Haloterrigena turkmenica
           DSM 5511]
 gi|284016757|gb|ADB62707.1| NADH:flavin oxidoreductase/NADH oxidase [Haloterrigena turkmenica
           DSM 5511]
          Length = 637

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/146 (15%), Positives = 47/146 (32%), Gaps = 20/146 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC---------PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA+ +E+ G++ + LN G          P   V    +G         V + IA + 
Sbjct: 145 FAAAARNLEEAGFDGVELNAGAFSVLRQFLSPRYNVRADEYGGDWESRVRFVNEAIARVS 204

Query: 113 KALSIPVTVKCRIGVDDQIPAVA--LRNLVKSIKKSGVNGIWIHARKAILK---GLSPKD 167
            A S PV +   +   +        +   +  +++       +  R    +   GLS + 
Sbjct: 205 DATSGPVGLHLSLAELEYGGYEFEDVPEFLPLLERLDYLSCTVGTRATYDRTHAGLSVQA 264

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGL 193
              +  +          +  D+ +  
Sbjct: 265 PDLLEPI------RTAADLVDVPVIG 284


>gi|172040709|ref|YP_001800423.1| dihydroorotate dehydrogenase 2 [Corynebacterium urealyticum DSM
           7109]
 gi|171852013|emb|CAQ04989.1| unnamed protein product [Corynebacterium urealyticum DSM 7109]
          Length = 375

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 80/231 (34%), Gaps = 40/231 (17%)

Query: 59  ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
            +   E+A+ V+D   + + +NV  P       + G   +   D +   +AA+ +   +P
Sbjct: 172 PNDYRESARAVKDV-ADYLVINVSSP------NTPGLRDLQAVDSLRPIVAAVQEEADLP 224

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR--------- 169
           + VK    + D+    A+ +L   +   GV G+         +GL               
Sbjct: 225 LFVKIAPDLSDED-IDAVTDLAIEL---GVTGLIATNTTISREGLKSDAQWVRSLGAGGV 280

Query: 170 ---KIPNLDYDIVYEI-KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
               +     +++  I  +    L +   GG+E   QA +         I   A    ++
Sbjct: 281 SGAPLAERSLEVLRRIAARAEGKLVLIGVGGIETPQQAWER--------IAAGA----SL 328

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQI 276
           L     +            +++ +    +I A      +  + SG + +++
Sbjct: 329 LQGYTGFIYGGPNW----ISKIHRGVAAQIRAHGLRNISEAVGSGLEWKEL 375


>gi|163732610|ref|ZP_02140055.1| 2,4-dienoyl-CoA reductase [Roseobacter litoralis Och 149]
 gi|161393970|gb|EDQ18294.1| 2,4-dienoyl-CoA reductase [Roseobacter litoralis Och 149]
          Length = 675

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 43/124 (34%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  +  A+     +  R+ + D IP       +  L ++++ +G     I+      +
Sbjct: 197 EVVRRVRAAVGADFIIIYRLSMIDLIPNGSTHDEVAQLAQAVEAAGAT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKIL-PSV-DGVMIGRA 218
              P     +P   +  V  ++  +     I  N  +     A ++L     D V + R 
Sbjct: 255 ARIPTIATSVPRAAFAWVTKKLMGKVGIPVITSNR-INTPEVAEEVLATGCADMVSMARP 313

Query: 219 AYKN 222
              +
Sbjct: 314 MLAD 317


>gi|254826941|ref|ZP_05231628.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           N3-165]
 gi|258599321|gb|EEW12646.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           N3-165]
          Length = 309

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|116873668|ref|YP_850449.1| NADH oxidase, putative [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|116742546|emb|CAK21670.1| NADH oxidase, putative [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 641

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + + +   C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVEI--HCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|16272422|ref|NP_438635.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae Rd KW20]
 gi|68249076|ref|YP_248188.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 86-028NP]
 gi|260580462|ref|ZP_05848290.1| glycosyl amidation-associated protein WbuZ [Haemophilus influenzae
           RdAW]
 gi|1170284|sp|P44436|HIS6_HAEIN RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|81336518|sp|Q4QN69|HIS6_HAEI8 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|1573453|gb|AAC22133.1| hisF cyclase (hisF) [Haemophilus influenzae Rd KW20]
 gi|68057275|gb|AAX87528.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 86-028NP]
 gi|260092804|gb|EEW76739.1| glycosyl amidation-associated protein WbuZ [Haemophilus influenzae
           RdAW]
          Length = 258

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPTLISRLADRFG 121


>gi|331654684|ref|ZP_08355684.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli M718]
 gi|331048066|gb|EGI20143.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli M718]
          Length = 672

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/188 (11%), Positives = 55/188 (29%), Gaps = 36/188 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFAHCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGR 217
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV-- 308

Query: 218 AAYKNSAM 225
            +     +
Sbjct: 309 -SMARPFL 315


>gi|226224777|ref|YP_002758884.1| hypothetical protein Lm4b_02195 [Listeria monocytogenes Clip81459]
 gi|225877239|emb|CAS05953.1| Hypothetical protein of unknown function [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
          Length = 309

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|254416537|ref|ZP_05030289.1| Putative N-acetylmannosamine-6-phosphate epimerase superfamily
           [Microcoleus chthonoplastes PCC 7420]
 gi|196176741|gb|EDX71753.1| Putative N-acetylmannosamine-6-phosphate epimerase superfamily
           [Microcoleus chthonoplastes PCC 7420]
          Length = 254

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 42/121 (34%), Gaps = 23/121 (19%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI--WIHARKAI 159
           + + + I  +   L  PV                      +  K+G + +   ++   A 
Sbjct: 134 ETLSELIPRIHAELGKPVMADI-----------DTLESATAAVKAGADVVGTTLYGYTAS 182

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
            + L P          ++++ +I ++  D+     GG+     A + L    D V++G A
Sbjct: 183 TQHLQPPG--------FELLSQIVEQL-DVPTICEGGIASPQMAQQALQLGADAVVVGTA 233

Query: 219 A 219
            
Sbjct: 234 I 234


>gi|86747534|ref|YP_484030.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhodopseudomonas
           palustris HaA2]
 gi|123293274|sp|Q2J341|HIS4_RHOP2 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|86570562|gb|ABD05119.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhodopseudomonas
           palustris HaA2]
          Length = 245

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 18/97 (18%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           +   V    + +  + +GV  I     AR  +LKG           +++D    + +   
Sbjct: 142 ESSQVTALEIAQRFEDAGVAAIIFTDIARDGLLKG-----------INWDATIALAEAI- 189

Query: 188 DLFIGLNGGLEDMSQALKILP----SVDGVMIGRAAY 220
            + +  +GGL  +     +L      ++G + GRA Y
Sbjct: 190 SIPVIASGGLASIEDVKAMLSPRAHKLEGAIAGRALY 226


>gi|15902716|ref|NP_358266.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae R6]
 gi|73621439|sp|Q8DQG9|PYRD_STRR6 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|15458260|gb|AAK99476.1| Dihydroorotate dehydrogenase [Streptococcus pneumoniae R6]
          Length = 311

 Score = 37.5 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 63/185 (34%), Gaps = 19/185 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDI 103
              +   L + G    +     K V++  +  +  LN+ CP   V      A    + + 
Sbjct: 92  ESNRTFFLSLVGMSPEETHTILKKVQESDFRGLTELNLSCP--NVPGKPQIAY---DFET 146

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHAR 156
               +A +    + P+ +K     D      A A+ N      V  +  SG NG++I   
Sbjct: 147 TDRILAEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSSG-NGLYIEDE 205

Query: 157 KAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVD 211
             +++   G        I       V+   +  NP + I   GG+     A +  L    
Sbjct: 206 SVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGAS 265

Query: 212 GVMIG 216
            V +G
Sbjct: 266 MVQVG 270


>gi|312876586|ref|ZP_07736568.1| Radical SAM domain protein [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796661|gb|EFR13008.1| Radical SAM domain protein [Caldicellulosiruptor lactoaceticus 6A]
          Length = 351

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 28/162 (17%), Positives = 61/162 (37%), Gaps = 26/162 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++VE AK     GY  + L              G  +  N D++   I  +  ++ + +
Sbjct: 87  DEIVEVAKRAYQMGYRTVVLQS------------GEDMYYNKDMLCSIIKKIKSSVDVAI 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH---ARKAILKGLSPKDNRKIPNLDY 176
           T+       D+          K+ K +G +   +    + + + +   P  + +      
Sbjct: 135 TLSIGERSYDEY---------KAFKDAGADRFLMRFETSNRQLYEKYHPGMSFENRIECL 185

Query: 177 DIVYEIKKENP-DLFIGLNG-GLEDMSQALKILPSVDGVMIG 216
             +  +  E      IGL G  ++D++Q + ++  +D  MIG
Sbjct: 186 KWIKSLGYELGTGFLIGLPGQTIDDLAQDILLVKELDADMIG 227


>gi|300855297|ref|YP_003780281.1| putative NADH:flavin oxidoreductase [Clostridium ljungdahlii DSM
           13528]
 gi|300435412|gb|ADK15179.1| putative NADH:flavin oxidoreductase [Clostridium ljungdahlii DSM
           13528]
          Length = 673

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 52/144 (36%), Gaps = 12/144 (8%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGV 148
           +G  +        +   A+ + +     ++ RI  D+     +       L+  +K   +
Sbjct: 202 YGGSIENRARFAIEVCDAIRRKVGEDFVIEFRISADEIAEEGMHFKETLELIGLLKDH-I 260

Query: 149 NGIWI----HARKAILKGLSPKDNRKIPNL-DYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           + + +    H+   +    +   N  +    +     ++KK  PDL +   G +  +  A
Sbjct: 261 DILHVSAGLHSDFNMKYYRNWCQNYMMDRCFNVHFARDVKKAYPDLLVTTVGSITSIEDA 320

Query: 204 LKILPS--VDGVMIGRAAYKNSAM 225
            KI+ +   D V + R    +  M
Sbjct: 321 EKIIANGWADFVAMCRPLMADPDM 344


>gi|259417447|ref|ZP_05741366.1| FAD/FMN-binding/pyridine nucleotide-disulphide domain
           oxidoreductase [Silicibacter sp. TrichCH4B]
 gi|259346353|gb|EEW58167.1| FAD/FMN-binding/pyridine nucleotide-disulphide domain
           oxidoreductase [Silicibacter sp. TrichCH4B]
          Length = 675

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 63/185 (34%), Gaps = 33/185 (17%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CLMLNPDIVGD------------ 106
            +V AA++ ++ GY+ + +        +    +     L+ + +   D            
Sbjct: 143 DIVNAAQLAKEAGYDGVEI--------MGSEGYFLNQFLVTHTNKREDRWGGSYENRMRL 194

Query: 107 ---CIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAI 159
               +  + +A+ +   +  R+ + D +P       +  L K+++ +G     I+     
Sbjct: 195 PVEVVRRVREAVGLEFILIYRLSMIDLVPNGSTFDEVVQLAKAVETAGAT--IINTGIGW 252

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
            +   P     +P   +  V +    +  + +  +  +     A  +L     D V + R
Sbjct: 253 HEARIPTIATSVPRAAFAWVTKKLMGHVSIPVITSNRINTPEVAEDVLAQGCADMVSMAR 312

Query: 218 AAYKN 222
               +
Sbjct: 313 PMLAD 317


>gi|171778663|ref|ZP_02919759.1| hypothetical protein STRINF_00611 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282620|gb|EDT48044.1| hypothetical protein STRINF_00611 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 311

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 40/217 (18%), Positives = 67/217 (30%), Gaps = 22/217 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEG 91
              D    L  +   K   L + G    +     K V++  Y   + LN+ CP   V   
Sbjct: 80  YYLDYVTELQNTPNSKNHFLSLVGMSEEETHTILKTVQESDYQGLVELNLSCP--NVPGK 137

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIK 144
              A    + +     +  +    + P+ VK     D      A A+ N      V  I 
Sbjct: 138 PQIAY---DFETTERILKDIFTYFTKPLGVKLPPYFDIAHFDRAAAIFNQFPLTFVNCIN 194

Query: 145 KSGVNGIWIHARKAILK---GLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDM 200
             G NG+ +     ++K   G        +       V+    + NP + I   GG++  
Sbjct: 195 SVG-NGLVVDDETVVIKPKNGFGGIGGDYVKPTALANVHAFYNRLNPSIQIIGTGGVKSG 253

Query: 201 SQALKI-LPSVDGVMIGRAAYKN--SAMLTTVDEYFS 234
             A +  L     V +G         A    + E   
Sbjct: 254 RDAFEHILCGASMVQLGT-ILHQEGPAAFARITEELK 289


>gi|297562041|ref|YP_003681015.1| dihydroorotate dehydrogenase [Nocardiopsis dassonvillei subsp.
           dassonvillei DSM 43111]
 gi|296846489|gb|ADH68509.1| dihydroorotate dehydrogenase family protein [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 316

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 30/166 (18%), Positives = 60/166 (36%), Gaps = 12/166 (7%)

Query: 51  ALQIGGADISKLVEAAKIV-EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
            + + G  +++  E A+ V    G + I +N+  P      G            V   + 
Sbjct: 101 IVSVAGTGMAEFGELARRVSAADGVSAIEVNLSSPDPSDPAGRRYVDDAAQAAAVVRTVR 160

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALR--------NLVKSIKKSGVNGIWIHARKAILK 161
           +      +PV  K    V D +   A          ++V +++   V+   +  R A+  
Sbjct: 161 S-HTRSGLPVLAKLAADVPDVVELAAACVEARADGLSMVNTVRGMAVDTRTL--RPAVAG 217

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           G+       I  L    VY + +  PD+ I   GG+   +  ++ +
Sbjct: 218 GMGGLSGPAIRPLAVGCVYRVHEALPDVPIIGMGGVRTGADVMEFM 263


>gi|46908403|ref|YP_014792.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|47091838|ref|ZP_00229633.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes str.
           4b H7858]
 gi|254825267|ref|ZP_05230268.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           J1-194]
 gi|254853296|ref|ZP_05242644.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           R2-503]
 gi|254931718|ref|ZP_05265077.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           HPB2262]
 gi|254993954|ref|ZP_05276144.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           J2-064]
 gi|255521571|ref|ZP_05388808.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           J1-175]
 gi|300764022|ref|ZP_07074018.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           N1-017]
 gi|46881674|gb|AAT04969.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|47019849|gb|EAL10587.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes str.
           4b H7858]
 gi|258606656|gb|EEW19264.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           R2-503]
 gi|293583273|gb|EFF95305.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           HPB2262]
 gi|293594513|gb|EFG02274.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           J1-194]
 gi|300515363|gb|EFK42414.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           N1-017]
 gi|328465976|gb|EGF37157.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           1816]
 gi|332312621|gb|EGJ25716.1| Putative enoyl-[acyl-carrier-protein] reductase II [Listeria
           monocytogenes str. Scott A]
          Length = 309

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|228939189|ref|ZP_04101782.1| NADPH dehydrogenase [Bacillus thuringiensis serovar berliner ATCC
           10792]
 gi|228972068|ref|ZP_04132684.1| NADPH dehydrogenase [Bacillus thuringiensis serovar thuringiensis
           str. T01001]
 gi|228978679|ref|ZP_04139050.1| NADPH dehydrogenase [Bacillus thuringiensis Bt407]
 gi|228780940|gb|EEM29147.1| NADPH dehydrogenase [Bacillus thuringiensis Bt407]
 gi|228787552|gb|EEM35515.1| NADPH dehydrogenase [Bacillus thuringiensis serovar thuringiensis
           str. T01001]
 gi|228820384|gb|EEM66416.1| NADPH dehydrogenase [Bacillus thuringiensis serovar berliner ATCC
           10792]
          Length = 319

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 48/136 (35%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        + +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPEGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +   SQA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGSQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|217963670|ref|YP_002349348.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           HCC23]
 gi|254831393|ref|ZP_05236048.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           10403S]
 gi|217332940|gb|ACK38734.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           HCC23]
 gi|307571755|emb|CAR84934.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes L99]
 gi|313607513|gb|EFR83831.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           F2-208]
          Length = 309

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|119499259|ref|XP_001266387.1| NADH-dependent flavin oxidoreductase, putative [Neosartorya
           fischeri NRRL 181]
 gi|119414551|gb|EAW24490.1| NADH-dependent flavin oxidoreductase, putative [Neosartorya
           fischeri NRRL 181]
          Length = 442

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 29/210 (13%), Positives = 64/210 (30%), Gaps = 39/210 (18%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             ++A++    G + I ++            P        +G        IV +  AA+ 
Sbjct: 219 FAKSARLAVQAGVDVIEIHGAHGYLINEFLSPVTNKRTDEYGGSFENRTRIVREVAAAIR 278

Query: 113 KAL--SIPVTVKCR-IGVDDQIPAVAL---------RNLVKSIKKSGVNGIWIHARKAIL 160
           + +   +P+ ++       +  P  A            LVK + + G++ + + +     
Sbjct: 279 EVIPEGMPLFLRISATEWLEGQPVAAESGSWDMQSSLELVKKLPEWGIDLVDVSSAANHK 338

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-------------KIL 207
                       +L   I   I+       +G  G + D  QA               +L
Sbjct: 339 DQKINLHTAYQTDLAGQIRQAIRAAGASTLVGAVGLITDSEQARGLVQGADEATTAEAML 398

Query: 208 PS----VDGVMIGRAAYKNS-AMLTTVDEY 232
                  D ++I R   +    + +T  + 
Sbjct: 399 SGPEPKADAILIARQFLREPEWVFSTARKL 428


>gi|111022784|ref|YP_705756.1| NADH-dependent flavin oxidoreductase [Rhodococcus jostii RHA1]
 gi|110822314|gb|ABG97598.1| probable NADH-dependent flavin oxidoreductase [Rhodococcus jostii
           RHA1]
          Length = 397

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 25/220 (11%), Positives = 65/220 (29%), Gaps = 48/220 (21%)

Query: 63  VEAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCIAAM 111
             AA+   + G++ + ++ G           S +V++    +G  L        +   A+
Sbjct: 156 ANAARRAVEAGFDAVEIHFG--HNYLISSFLSPKVNKRTDRYGGSLANRARFALETARAV 213

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIK--------------------------- 144
             A+   + +  ++ +DD +P     +    +                            
Sbjct: 214 RDAVGERIAILAKLNMDDGVPGGFWVDEAIQVAQWLEQDGSLDALELTAGSSLLNPMYLF 273

Query: 145 --KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-----KKENPDLFIGLNGGL 197
              + +        +    G+       +    Y   Y +      +    + + L GG+
Sbjct: 274 KGDAPLREFAAVMPQPTKLGIRLVGRHFLKEYPYRDAYLLEDARQIRAAVTMPLVLLGGI 333

Query: 198 E-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
               +  L +      V + RA  +   ++  + +   NP
Sbjct: 334 TGKATMDLAMAEGFQFVAVARALLREPDLVNRITDETHNP 373


>gi|16804140|ref|NP_465625.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes EGD-e]
 gi|224501101|ref|ZP_03669408.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL R2-561]
 gi|46396480|sp|Q8Y5G2|PDXS_LISMO RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|16411571|emb|CAD00179.1| lmo2101 [Listeria monocytogenes EGD-e]
          Length = 295

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  + KA+SIPV  K
Sbjct: 29  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMKAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|121997883|ref|YP_001002670.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Halorhodospira halophila SL1]
 gi|148839495|sp|A1WW06|HIS4_HALHL RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|121589288|gb|ABM61868.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Halorhodospira
           halophila SL1]
          Length = 246

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 17/97 (17%)

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN 186
           +Q   VA  +L +  + +GV  +      R  +++G            + +   E+ +  
Sbjct: 142 EQTSEVAAVDLARRFEDAGVAALIFTDIGRDGMMQG-----------CNVEATRELARAV 190

Query: 187 PDLFIGLNGGLEDMSQALKIL---PSVDGVMIGRAAY 220
             + +  +GG+  +     +      + G ++GRA Y
Sbjct: 191 -SIPVIASGGVSSLEDVRSLAGSPEGIAGAIVGRAIY 226


>gi|145630346|ref|ZP_01786127.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae R3021]
 gi|319775598|ref|YP_004138086.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae F3047]
 gi|329122355|ref|ZP_08250942.1| imidazole glycerol phosphate synthase, cyclase subunit [Haemophilus
           aegyptius ATCC 11116]
 gi|144984081|gb|EDJ91518.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae R3021]
 gi|309972369|gb|ADO95570.1| Imidazole glycerol phosphate synthase, subunit HisF [Haemophilus
           influenzae R2846]
 gi|317450189|emb|CBY86405.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae F3047]
 gi|327473637|gb|EGF19056.1| imidazole glycerol phosphate synthase, cyclase subunit [Haemophilus
           aegyptius ATCC 11116]
          Length = 258

 Score = 37.5 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPTLISRLADRFG 121


>gi|325280725|ref|YP_004253267.1| Pyridoxal biosynthesis lyase pdxS [Odoribacter splanchnicus DSM
           20712]
 gi|324312534|gb|ADY33087.1| Pyridoxal biosynthesis lyase pdxS [Odoribacter splanchnicus DSM
           20712]
          Length = 289

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E  G   +      P+        G   M +P      I A+ KA+SIPV  K
Sbjct: 25  AEQAKIAEAAGACAVMALERVPAD--IRRDGGVARMSDP----QMIKAIQKAVSIPVMAK 78

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  G++ I
Sbjct: 79  VRIGHFVE---------AQILEAIGIDFI 98


>gi|238795762|ref|ZP_04639276.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           mollaretii ATCC 43969]
 gi|238720488|gb|EEQ12290.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           mollaretii ATCC 43969]
          Length = 247

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 24  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 73

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 74  SVEDAAQILTFGADKISINSPALADPTLITRLADRYG 110


>gi|119475538|ref|ZP_01615891.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [marine gamma
           proteobacterium HTCC2143]
 gi|119451741|gb|EAW32974.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [marine gamma
           proteobacterium HTCC2143]
          Length = 246

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 29/156 (18%), Positives = 55/156 (35%), Gaps = 13/156 (8%)

Query: 120 TVKCRIGVDDQIPA--VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ R G+ D           + +   ++G   + +        G           ++ D
Sbjct: 14  CVRLRQGLMDDSTVYGDNPVEMARRWVEAGTRRLHLVDLNGAFDG---------KPINGD 64

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            V  I K  PDL I + GG+ ++      +   V+ ++IG  A K+   ++   + F   
Sbjct: 65  AVTSIAKAYPDLPIQIGGGIRNLETIEHYINAGVNYLIIGTRAVKDPGFVSEACKAFPGH 124

Query: 237 LT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           +  G       V  D W ++S       A+     G
Sbjct: 125 IIVGLDAKDGLVATDGWAQVSDIKATELAKRFEQDG 160


>gi|169853477|ref|XP_001833418.1| vitamin B6 biosynthesis protein [Coprinopsis cinerea okayama7#130]
 gi|116505457|gb|EAU88352.1| vitamin B6 biosynthesis protein [Coprinopsis cinerea okayama7#130]
          Length = 331

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      P+        G   M +P      I  +  A++IPV  K
Sbjct: 65  AEQARIAEEAGACAVMALERVPAD--IRKEGGVARMSDP----KMIKEIVDAVTIPVMAK 118

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 119 VRIGHFVE---------AQILQAIGVDYI 138


>gi|76802713|ref|YP_330808.1| imidazole glycerol phosphate synthase subunit HisF [Natronomonas
           pharaonis DSM 2160]
 gi|85541710|sp|Q3INY2|HIS6_NATPD RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|76558578|emb|CAI50170.1| imidazoleglycerol-phosphate synthase, cyclase subunit HisF
           [Natronomonas pharaonis DSM 2160]
          Length = 271

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 20/134 (14%), Positives = 37/134 (27%), Gaps = 11/134 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +  +D         L K   ++G +        A  +G              D V  +  
Sbjct: 27  VNFEDLEYTGDPVELAKKYNEAGADEFVFLDITASAEGRETM---------LDTVSAVAD 77

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           E   + + + GG+       + L    D V I   A +   ++    E F +     S  
Sbjct: 78  ECF-IPLTVGGGIRTRDDIKETLRAGADKVSINTGALQRPELIGEGAEAFGSQCIVISVD 136

Query: 244 KTRVDKDFWRKISA 257
             R   +       
Sbjct: 137 ARRRFDEAGEHYVE 150


>gi|328865369|gb|EGG13755.1| hydroxyacid oxidase [Dictyostelium fasciculatum]
          Length = 395

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 18/112 (16%)

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +     +PV VK  +   D               K G +GI +    A     SP     
Sbjct: 248 LKSITKLPVIVKGVMCPQD----------ALLAVKYGADGIIVSNHGARQLDTSPSTIEV 297

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYK 221
           +P       Y ++     + + ++GG+   +  LK L      VMIGR    
Sbjct: 298 LP-------YVVRAVGGRIPVIVDGGVRRGTDILKALAYGACAVMIGRPVLW 342


>gi|290512579|ref|ZP_06551945.1| NADH oxidase family NADH:flavin oxidoreductase [Klebsiella sp.
           1_1_55]
 gi|289774920|gb|EFD82922.1| NADH oxidase family NADH:flavin oxidoreductase [Klebsiella sp.
           1_1_55]
          Length = 677

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 61/185 (32%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   I  
Sbjct: 150 EKFGDAAERVRRAGFDSVEIHAGHSYLISQFLSPLFNKRTDEFGGSVENRTRILSLIIDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++     V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQDKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRSPQVAEDILASGDADLIAIGRGLIAEPEW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|269102557|ref|ZP_06155254.1| putative NADH-dependent flavin oxidoreductase [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268162455|gb|EEZ40951.1| putative NADH-dependent flavin oxidoreductase [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 367

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 65/199 (32%), Gaps = 21/199 (10%)

Query: 71  DFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPV 119
           + G++ I ++            P        +G  L      + + I    K +    P+
Sbjct: 156 ESGFDGIEIHAAHTYLINQFLSPYYNQRTDQYGGSLENRMRFLVEIIQETRKLVGNDFPI 215

Query: 120 TVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIW----IHARKAILKGLSPKDNRKIPN 173
            VK       +        R + K +++ GV+GI     IH +   + G    D   I  
Sbjct: 216 LVKLTATEFFEGGQTFEETRIICKKLEQLGVDGIIVSGNIHGKADTMVGEK-HDGYTIEA 274

Query: 174 LDYDIVY-EIKKENPDLFIGLNGGLEDMSQALKI--LPSVDGVMIGRAAYKNSAMLTTVD 230
             Y   Y ++  +   + +   GGL D S   +I    ++    + R       ++    
Sbjct: 275 EGYFHQYGQVISQEVSIPVITVGGLSDFSAIEEIANTTNIQYFALSRPLLAEPQLIKRWK 334

Query: 231 EYFSNPLTGSSPIKTRVDK 249
           +    P+      K R  +
Sbjct: 335 DGNIEPVDCERCSKCRTRR 353


>gi|225389022|ref|ZP_03758746.1| hypothetical protein CLOSTASPAR_02767 [Clostridium asparagiforme
           DSM 15981]
 gi|225044916|gb|EEG55162.1| hypothetical protein CLOSTASPAR_02767 [Clostridium asparagiforme
           DSM 15981]
          Length = 242

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 35/99 (35%), Gaps = 11/99 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            ++ +  +  G   + +      L G S         ++  ++  I  E  D+ + + GG
Sbjct: 33  ADMARMWRDQGATFLHLVDLDGALAGRS---------VNEAVIRSIV-EAVDIPVEIGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +        +L   V  V+IG  A +    +  +   F 
Sbjct: 83  IRTAEAVQNMLDLGVARVIIGTKAVERPEFMGELVAAFG 121


>gi|261404086|ref|YP_003240327.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp.
           Y412MC10]
 gi|261280549|gb|ACX62520.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp.
           Y412MC10]
          Length = 374

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 24/178 (13%), Positives = 49/178 (27%), Gaps = 37/178 (20%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSIK 144
           +G  ++       + + A+ +A+    PV ++      +Q           L  L+ ++ 
Sbjct: 199 YGGDMLKRARFAIEVVKAVRQAVGPDFPVAIRLSQWKTNQYEAKLADTPEKLGQLLTALS 258

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +GV+      R+         D               KK      I + G +       
Sbjct: 259 DAGVDIFHCSTRRFWEPEFEGSDLNFAGWA--------KKLTGKTVITV-GSVGLDEVFT 309

Query: 205 KILPS--------------------VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            +                        D V +GRA   +      V +   + L   +P
Sbjct: 310 SLFTQGKGAGQRDLEELLNRLEENEFDLVAVGRALLADPEWAAKVRDGRFDELAPFTP 367


>gi|153939296|ref|YP_001391462.1| 2-enoate reductase [Clostridium botulinum F str. Langeland]
 gi|152935192|gb|ABS40690.1| 2-enoate reductase [Clostridium botulinum F str. Langeland]
          Length = 665

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 37/206 (17%), Positives = 73/206 (35%), Gaps = 47/206 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             E+A+I +  G++ I ++       VHEG                 +G  L        
Sbjct: 158 FGESAEIAKKAGFDGIEIHA------VHEGYLLDQFAISFFNHRTDEYGGSLENRLRFAC 211

Query: 106 DCIAAMCKAL--SIPVTVK----------CRIGVDDQIPAVALRNL------VKSIKKSG 147
           + +  + K      PV+++          C+ G+ D+      R++       K +  +G
Sbjct: 212 EVVQEIKKRCGQDFPVSLRYSIKSFIKDWCKGGLPDEEFEEKGRDIPEGIEAAKILVAAG 271

Query: 148 VNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QAL 204
            + +        +      P   +K   L Y+   EI K+  D+ I   G +ED    + 
Sbjct: 272 YDALNGDVGSYDSWYWSHPPMYQKKGLYLPYN---EILKKVVDVPIITAGRMEDPELSSD 328

Query: 205 KILPS-VDGVMIGRAAYKNSAMLTTV 229
            IL    D + +GR    ++ +   +
Sbjct: 329 AILSGKTDMIALGRPLLADAEIPNKI 354


>gi|145640448|ref|ZP_01796032.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae R3021]
 gi|229844365|ref|ZP_04464505.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 6P18H1]
 gi|319898007|ref|YP_004136204.1| imidazole glycerol phosphate synthase subunit hisf [Haemophilus
           influenzae F3031]
 gi|145275034|gb|EDK14896.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 22.4-21]
 gi|229812614|gb|EEP48303.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 6P18H1]
 gi|317433513|emb|CBY81896.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae F3031]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPTLISRLADRFG 121


>gi|16801337|ref|NP_471605.1| hypothetical protein lin2273 [Listeria innocua Clip11262]
 gi|16414785|emb|CAC97501.1| lin2273 [Listeria innocua Clip11262]
          Length = 309

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|312129850|ref|YP_003997190.1| geranylgeranylglyceryl phosphate synthase family protein
           [Leadbetterella byssophila DSM 17132]
 gi|311906396|gb|ADQ16837.1| geranylgeranylglyceryl phosphate synthase family protein
           [Leadbetterella byssophila DSM 17132]
          Length = 241

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            +  +++  +K     + + + GG+       K L    D V++G A  KN   L  V E
Sbjct: 173 PVREEMIRLVKN-TVSVPVIVGGGMRTKEDVKKALSAGADIVVVGNAIEKNPEFLKEVAE 231


>gi|269978115|ref|ZP_06185065.1| NADPH dehydrogenase [Mobiluncus mulieris 28-1]
 gi|306818486|ref|ZP_07452209.1| xenobiotic reductase A [Mobiluncus mulieris ATCC 35239]
 gi|307701059|ref|ZP_07638084.1| putative NADPH dehydrogenase [Mobiluncus mulieris FB024-16]
 gi|269933624|gb|EEZ90208.1| NADPH dehydrogenase [Mobiluncus mulieris 28-1]
 gi|304648659|gb|EFM45961.1| xenobiotic reductase A [Mobiluncus mulieris ATCC 35239]
 gi|307614054|gb|EFN93298.1| putative NADPH dehydrogenase [Mobiluncus mulieris FB024-16]
          Length = 370

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 32/204 (15%), Positives = 64/204 (31%), Gaps = 27/204 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           + V+AA+   + G++ + L+            P        +G  L        + I  +
Sbjct: 164 QFVQAARRALEAGFDFVELHGAHGYLMHEFLSPITNHRIDEYGGDLEGRFRFWKEIIVMI 223

Query: 112 CKAL--SIPVTVKCRIGVDDQIPAVALR---------NLVKSIKKSGVNGIWIHARKAIL 160
              L  S P+ V+           + LR          L   + + GV+ I +       
Sbjct: 224 RAELGSSFPLLVRISATSWLPESNLELRRDVTLDDWGKLAHELSRLGVDFIDVSTG---- 279

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVM-IGRA 218
            GL P     +         +  +    L +   G + + +QA +IL      V+ +GR 
Sbjct: 280 -GLVPGAQIPVAPGYQVPYAQEIQNRGPLPVSAVGLITEPAQAEQILVTGAASVVEVGRP 338

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSP 242
              + ++         +      P
Sbjct: 339 LLTDPSLPLAWAARLGDEPPVPEP 362


>gi|116669446|ref|YP_830379.1| NADH:flavin oxidoreductase/NADH oxidase [Arthrobacter sp. FB24]
 gi|116609555|gb|ABK02279.1| NADH:flavin oxidoreductase/NADH oxidase [Arthrobacter sp. FB24]
          Length = 359

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 10/76 (13%)

Query: 189 LFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTR 246
           L     G +    +A+ ++     D V++GR A  N  ++    E          P+   
Sbjct: 284 LVNTGFGVITTREEAISLVADGHADAVVVGRPAIANPDLVRRWREDL--------PVNEP 335

Query: 247 VDKDFWRKISASMTDY 262
               F+   +   TDY
Sbjct: 336 NQATFYADGAEGYTDY 351


>gi|298370105|ref|ZP_06981421.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298281565|gb|EFI23054.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 247

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 3/102 (2%)

Query: 173 NLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV- 229
             ++  +  I  E   D+ + L GG+ D++   K L   +  V+IG AA KN   +    
Sbjct: 60  PKNFPAIKSILAEVANDIPVQLGGGIRDLATIEKYLDLGLADVIIGTAAVKNPDFVREAC 119

Query: 230 DEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            E+    + G       V  D W  ++       A+     G
Sbjct: 120 KEFPGQIIVGLDAKDGMVAIDGWATVTEHRVADLAKRFEEDG 161


>gi|269215632|ref|ZP_06159486.1| dihydroorotate oxidase [Slackia exigua ATCC 700122]
 gi|269131119|gb|EEZ62194.1| dihydroorotate oxidase [Slackia exigua ATCC 700122]
          Length = 304

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 68/190 (35%), Gaps = 17/190 (8%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFG-YNEINLNVGCPSARVHEGSFGACLMLNPDI 103
            Q  P  + + G  + + V   + +E  G  +   +N+ CP+      +FG     +   
Sbjct: 92  EQGVPSIVNVSGHSLEEYVAVLEALEADGQADAYEINISCPNVDAGGMTFGT----HVPS 147

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPA--------VALRNLVKSIKKSGVNGIWIHA 155
           V   +AA     + P+ VK    V D                +L+ ++    VN      
Sbjct: 148 VEAVVAACRAVATRPMIVKLSPNVTDIAEIARAAEASGADALSLINTLLGMAVNART--R 205

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVM 214
           R  + + +       +  +   +V++       + I   GG+     A++ +L     V 
Sbjct: 206 RPELARVVGGLSGPAVKPVALRMVWQCYNAV-KIPILGMGGIATGEDAVEFMLCGATAVA 264

Query: 215 IGRAAYKNSA 224
           +G A++ N  
Sbjct: 265 VGTASFTNPH 274


>gi|218290705|ref|ZP_03494787.1| pyridoxine biosynthesis protein [Alicyclobacillus acidocaldarius
           LAA1]
 gi|258510032|ref|YP_003183466.1| pyridoxal biosynthesis lyase PdxS [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|218239243|gb|EED06442.1| pyridoxine biosynthesis protein [Alicyclobacillus acidocaldarius
           LAA1]
 gi|257476758|gb|ACV57077.1| pyridoxine biosynthesis protein [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
          Length = 294

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 25/89 (28%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E  G   +      PS      + G   M +P      I  +  A+SIPV  K
Sbjct: 28  AEQAKIAEAAGAVAVMALERVPSD--IRKAGGVARMADP----AIIEEVMNAVSIPVMAK 81

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           CRIG   +          + ++  GV+ I
Sbjct: 82  CRIGHIVE---------ARILEAMGVDYI 101


>gi|160915849|ref|ZP_02078057.1| hypothetical protein EUBDOL_01871 [Eubacterium dolichum DSM 3991]
 gi|158432325|gb|EDP10614.1| hypothetical protein EUBDOL_01871 [Eubacterium dolichum DSM 3991]
          Length = 639

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 71/182 (39%), Gaps = 27/182 (14%)

Query: 64  EAAKIVEDFGYNEINLNVG---CPSARVHEG------SFGACLMLNPDIVGDCIAAMCKA 114
           +AA    + GY+ +  ++     P + +  G       +G           + I  + K 
Sbjct: 146 KAAARAVEAGYDCLEFHLAHNYLPHSFLSGGLNHRSDEYGGNFENRSRFPLEVIDEIRKN 205

Query: 115 L--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           +   +P+ ++     D     + + +     K  K+ GV+ + +     I    +     
Sbjct: 206 MPEGMPLFIRIDAQDDMLEGGMTIDDTIRFCKLAKEHGVDVLDVSRGNII----TAASMY 261

Query: 170 KIPNLDY------DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
           ++P +D       +   +I+KE   L IG+ G +     A +++ +  VD V++GRA   
Sbjct: 262 EVPPIDVPNGFNIENAAKIRKETGMLTIGV-GRINTAKLANELIENDRVDMVVMGRAQLA 320

Query: 222 NS 223
           + 
Sbjct: 321 DP 322


>gi|153006677|ref|YP_001381002.1| NADH:flavin oxidoreductase/NADH oxidase [Anaeromyxobacter sp.
           Fw109-5]
 gi|152030250|gb|ABS28018.1| NADH:flavin oxidoreductase/NADH oxidase [Anaeromyxobacter sp.
           Fw109-5]
          Length = 352

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 22/155 (14%), Positives = 49/155 (31%), Gaps = 11/155 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSG 147
           ++G        +V + ++A+      P+ V  RI   D             L + +   G
Sbjct: 196 AYGGSFENRTRLVREVVSAVRAEWPEPLPVIVRISATDWVEGGWDIAQSVELARGLGPLG 255

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ + + +       L+       P         I++E   +  G  G +    QA  ++
Sbjct: 256 VDLVDVSSGGL----LATAQVPAGPGYQTGFAERIRREA-HVATGAVGLITSPEQADHVI 310

Query: 208 --PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGS 240
                D V++ R   ++  +         +     
Sbjct: 311 RSGQADLVLMARELLRDPHLPLRAARVLGHEGPWP 345


>gi|320160262|ref|YP_004173486.1| inosine-5'-monophosphate dehydrogenase [Anaerolinea thermophila
           UNI-1]
 gi|319994115|dbj|BAJ62886.1| inosine-5'-monophosphate dehydrogenase [Anaerolinea thermophila
           UNI-1]
          Length = 481

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/120 (18%), Positives = 43/120 (35%), Gaps = 15/120 (12%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + D+V D +  + K LS+P+              VA    V+ + ++G + + +      
Sbjct: 256 HSDLVLDMLRTLKKKLSVPIIA----------GNVATAEGVRDLAEAGADAVKVGVGAGS 305

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKE--NPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           +          IP L    + E  +E     + I  +GG+         +      VM+G
Sbjct: 306 ICITRVVTGFGIPQL--TAILECAREGQRLGVPIIADGGVRNSGDLVKALAAGASTVMLG 363


>gi|262039266|ref|ZP_06012584.1| bifunctional enzyme NanE/nanK [Leptotrichia goodfellowii F0264]
 gi|261746760|gb|EEY34281.1| bifunctional enzyme NanE/nanK [Leptotrichia goodfellowii F0264]
          Length = 231

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
            +K+GV+ +        L G +P   +     D+ +V ++ KE  D+ +   G + +  Q
Sbjct: 145 AEKAGVDMV-----GTTLSGYTPYSEKTDGP-DFKLVEKLSKEL-DIPVIAEGKIHEPQQ 197

Query: 203 ALKILP-SVDGVMIGRAAYKNS 223
           A K++      V++G  A    
Sbjct: 198 AKKMIELGAHAVVVG-GAITRP 218


>gi|206890686|ref|YP_002248973.1| NADH oxidase [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206742624|gb|ACI21681.1| NADH oxidase [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 366

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 55/170 (32%), Gaps = 17/170 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
               +AA+  ++ G++ + +             P        +G         + +   +
Sbjct: 145 ESFGKAARRAKEAGFDGVQIHGAHGYLINQFLSPYTNRRNDYWGGDEERRFHFLEEVYNS 204

Query: 111 MCKAL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILKG 162
           +   +    PV +K      V + +       + K ++  G++ I +       K   + 
Sbjct: 205 IRDNVGYDYPVMIKLNACDFVKNGLTLEESLRIAKRLENMGIDAIEVSGGIVESKIEERP 264

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG 212
           +  K +       +    +  K+N  + I L GG+     A  IL   D 
Sbjct: 265 VRMKIDSPEKEAYFREFSKEFKKNLKVPIMLVGGIRSRQVAEDILQKNDA 314


>gi|307152880|ref|YP_003888264.1| dihydroorotate oxidase [Cyanothece sp. PCC 7822]
 gi|306983108|gb|ADN14989.1| dihydroorotate oxidase [Cyanothece sp. PCC 7822]
          Length = 346

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 44/116 (37%), Gaps = 27/116 (23%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI----- 103
           P+   + G      +E A+ +E  G + + LNV               L  + ++     
Sbjct: 104 PIIASLNGVSTGGWLEYARKIEQAGADALELNV-------------YYLPNDLEMSGAQV 150

Query: 104 ---VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
                D +  +   +SIPV +K      +      + N+ K + ++G +G+ +  R
Sbjct: 151 EQNYVDILRIIKSEISIPVAMKLSPYFSN------MANMAKQLAEAGADGLVLFNR 200


>gi|302536318|ref|ZP_07288660.1| inosine-5'-monophosphate dehydrogenase [Streptomyces sp. C]
 gi|302445213|gb|EFL17029.1| inosine-5'-monophosphate dehydrogenase [Streptomyces sp. C]
          Length = 503

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 25/152 (16%), Positives = 56/152 (36%), Gaps = 26/152 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+ + + G + I          V + + G     +  +VGD ++ +    S+ V      
Sbjct: 243 AQALIEAGADFI----------VVDTAHG-----HSRLVGDMVSKIKSNSSVDVIGG--- 284

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
                   VA R+  +++  +G +GI +      +          +P +       +  +
Sbjct: 285 -------NVATRDGAQALVDAGCDGIKVGVGPGSICTTRVVAGIGVPQVTAIYEAALAAK 337

Query: 186 NPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
              + +  +GGL+     A  ++   D VM+G
Sbjct: 338 AAGVPVIGDGGLQYSGDIAKALVAGADTVMLG 369


>gi|293401518|ref|ZP_06645661.1| N-acylglucosamine-6-phosphate 2-epimerase [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291305156|gb|EFE46402.1| N-acylglucosamine-6-phosphate 2-epimerase [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 249

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 56/180 (31%), Gaps = 45/180 (25%)

Query: 38  KNILGFSTQEKPLALQIGGADISK-------LVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           K +L        ++ Q+   D          + EAAK     G   I  N          
Sbjct: 9   KALLESFKNGLIVSCQVQKDDPIYTEDIVVKMAEAAKWA---GAVGIRANS--------- 56

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVN 149
                     P+     I A+ + + +P+    +I  +D    +       K++ ++G  
Sbjct: 57  ----------PEQ----IKAIKEKVDLPMIGLWKIWHEDTDVFITPTLEAAKAVWEAGAE 102

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS 209
            I +            K       + +D++  +KKE P+  I     +    +A   +  
Sbjct: 103 IIALDC---------TKQITHEKTIAWDLLDIVKKEIPEAIIFA--DVSSYEEAAHAIAH 151


>gi|240949781|ref|ZP_04754113.1| imidazole glycerol phosphate synthase subunit HisF [Actinobacillus
           minor NM305]
 gi|240295813|gb|EER46500.1| imidazole glycerol phosphate synthase subunit HisF [Actinobacillus
           minor NM305]
          Length = 257

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVQRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +I     D + I   A  +  +++ + + F 
Sbjct: 85  TIDDAEQIFAFGADKISINSPALADPDLISRLADRFG 121


>gi|90580087|ref|ZP_01235895.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio angustum
           S14]
 gi|90438972|gb|EAS64155.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio angustum
           S14]
          Length = 257

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  +  ++TT+ + F 
Sbjct: 85  SADDASRILQFGADKVSINSPALADPTLITTLADKFG 121


>gi|72161463|ref|YP_289120.1| dihydroorotate oxidase B, catalytic subunit [Thermobifida fusca YX]
 gi|71915195|gb|AAZ55097.1| dihydroorotate oxidase B, catalytic subunit [Thermobifida fusca YX]
          Length = 330

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 69/199 (34%), Gaps = 25/199 (12%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           GG+    +  A ++ E  G   I +N+  P      G        +P+     +AA+ + 
Sbjct: 116 GGSVDEYVTLAQRLSEAPGVTAIEVNLSSP-DLSRGGEHFTA---DPEAAAQVVAAVRET 171

Query: 115 --LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------------ARKAIL 160
               IPV  K    V D      L  L      +G +G+ +              R A+ 
Sbjct: 172 ARSDIPVFAKLSPDVAD------LVALAGKCVAAGADGLALVNTVRGMVIDVDTMRPAVA 225

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAA 219
            G+       I  +    VY++    P++ I   GG+     AL+ +L     V +G A 
Sbjct: 226 GGMGGLSGPAIRPIAVACVYQVHAAYPEVPIIGMGGIGTGRDALEFLLAGASAVAVGTAL 285

Query: 220 YKNSAMLTTVDEYFSNPLT 238
           + + +    V       L 
Sbjct: 286 FHDPSACMRVLRELERELI 304


>gi|317496062|ref|ZP_07954422.1| N-acetylmannosamine-6-phosphate 2-epimerase [Gemella moribillum
           M424]
 gi|316913637|gb|EFV35123.1| N-acetylmannosamine-6-phosphate 2-epimerase [Gemella moribillum
           M424]
          Length = 230

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 34/222 (15%), Positives = 72/222 (32%), Gaps = 39/222 (17%)

Query: 36  DKKNILGFSTQEKPLALQIGGADI---------SKLVEAAKIV----------EDFGYNE 76
           DKK +  +   E  ++ Q    +            + +AAK             D    +
Sbjct: 2   DKKELYEYLRGELIVSCQALPGEPLYREEGGVMCLMAQAAKNAGVKAIRAQGIVDIKQIK 61

Query: 77  INLNVGCPSARVHEG---SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA 133
              N+  P   + +     +   +    D V   + A    +++      R   D + P+
Sbjct: 62  EQTNL--PVIGIIKKSYPGYATYITATMDEVDKLVEAGSDIIAL--DCTNRERGDGKTPS 117

Query: 134 VALRNLVK----SIKKSGVNGI--WIHARKAILKGLSPKDNRKIP------NLDYDIVYE 181
             ++ + +     +  + ++ +   I A KA +  +    N   P        D  +V E
Sbjct: 118 EFVKEIKEKYPNIVLMADISNLEEAIEAEKAGVDFVGTTMNGYTPYTTVSKKFDPSLVKE 177

Query: 182 IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNS 223
           I K N  + +   G + +  +A   L +    M+   A    
Sbjct: 178 IVK-NVKIPVIAEGKIHEPKEAKAALEAGAHCMVVGGAITRP 218


>gi|259418616|ref|ZP_05742533.1| NADH:flavin oxidoreductase/nadh oxidase [Silicibacter sp.
           TrichCH4B]
 gi|259344838|gb|EEW56692.1| NADH:flavin oxidoreductase/nadh oxidase [Silicibacter sp.
           TrichCH4B]
          Length = 428

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 27/176 (15%), Positives = 57/176 (32%), Gaps = 20/176 (11%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           +  E A + ++ G++ I +             P     E  +G  L     I+ + + A+
Sbjct: 157 QFAETAALADEAGFDGIEIHATHGYLLSQFLSPLTNKREDQWGGSLENRARILIEIVRAI 216

Query: 112 CKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKGLS 164
              +     V  ++   D       A     +V+ +    V+ I I         + G  
Sbjct: 217 RAGVGARFGVGVKLNSADFQKGGFDAADAVAVVQMLNSEEVDLIEISGGSYESPAMHGRP 276

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL---PSVDGV-MIG 216
              + +     +            + + + GG+   + A+  L      DGV M+G
Sbjct: 277 AHASTRAREAYFVDFARDIVAVATMPVMVTGGVRRRATAMDALAPEDGRDGVAMVG 332


>gi|256824621|ref|YP_003148581.1| inosine-5'-monophosphate dehydrogenase [Kytococcus sedentarius DSM
           20547]
 gi|256688014|gb|ACV05816.1| inosine-5'-monophosphate dehydrogenase [Kytococcus sedentarius DSM
           20547]
          Length = 498

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 24/116 (20%), Positives = 43/116 (37%), Gaps = 12/116 (10%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGL 163
           V D +A +    S          VD     VA R   +++  +G +GI +      +   
Sbjct: 259 VCDMVARIKAEPSA-------AHVDVIAGNVATRAGAQALVDAGADGIKVGVGPGSICTT 311

Query: 164 SPKDNRKIPNLDYDIVYEIKKENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                  +P +    ++E  +      + I  +GGL+     A  ++   D VMIG
Sbjct: 312 RVVAGVGVPQI--SAIHEAARAAGPAGVPIIGDGGLQYSGDIAKALVAGADAVMIG 365


>gi|225574197|ref|ZP_03782807.1| hypothetical protein RUMHYD_02261 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038565|gb|EEG48811.1| hypothetical protein RUMHYD_02261 [Blautia hydrogenotrophica DSM
           10507]
          Length = 657

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 65/180 (36%), Gaps = 20/180 (11%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           +AAK+ ++ G++ + ++            P        FG             + A+ + 
Sbjct: 166 KAAKLCKETGFDMVQVHAAHGWLFSQFLSPVWNRRTDEFGGSFENRARFFLLALDAVREG 225

Query: 115 LSIPVTVKCRIGVDDQIPA-VALRNLVKSIK--KSGVNGIWI----HARKAILKGLSPKD 167
           +     ++ RI  DD     + L +  +  K     V+ I +    H   A+     P  
Sbjct: 226 VGPHFPIEARISGDDFSEIGLNLEDCTRLAKMIDGRVDLINVSCGNHEDPAMFCRTHPSA 285

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAM 225
                 ++  +  EIK+      +   G L D +Q  +IL     D V +GRA+  +  +
Sbjct: 286 FFPRG-VNVYLAAEIKRHV-KTPVACVGSLNDPAQMEEILASGQADVVELGRASLADPYL 343


>gi|218699386|ref|YP_002407015.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli IAI39]
 gi|226700515|sp|B7NQG5|HIS6_ECO7I RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|218369372|emb|CAR17130.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli IAI39]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|206581010|ref|YP_002240457.1| NADH:flavin oxidoreductase, NADH oxidase family [Klebsiella
           pneumoniae 342]
 gi|206570068|gb|ACI11844.1| NADH:flavin oxidoreductase, NADH oxidase family [Klebsiella
           pneumoniae 342]
          Length = 677

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 61/185 (32%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   I  
Sbjct: 150 EKFGDAAERVRRAGFDSVEIHAGHSYLISQFLSPLFNKRTDEFGGSVENRTRILSLIIDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++     V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQDKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRSPQVAEDILASGDADLIAIGRGLIAEPEW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|116873604|ref|YP_850385.1| dioxygenase, putative [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|116742482|emb|CAK21606.1| dioxygenase, putative [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 309

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|328472191|gb|EGF43062.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes 220]
          Length = 288

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|303251803|ref|ZP_07337974.1| hypothetical protein APP2_0124 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307249103|ref|ZP_07531110.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|302649233|gb|EFL79418.1| hypothetical protein APP2_0124 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854391|gb|EFM86587.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
          Length = 257

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++T +   F 
Sbjct: 85  TLEDAEKLFAFGADKISINSPALADPNLITELSNRFG 121


>gi|229493983|ref|ZP_04387752.1| oxidoreductase, FAD/FMN-binding family [Rhodococcus erythropolis
           SK121]
 gi|229319052|gb|EEN84904.1| oxidoreductase, FAD/FMN-binding family [Rhodococcus erythropolis
           SK121]
          Length = 676

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 63/185 (34%), Gaps = 19/185 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------C-PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           V  A++ +  GY+ + +  G         C  + +  +   G+       +  + +    
Sbjct: 148 VRCARLAKSAGYDGVEIMGGEGYFINQFLCERTNKRTDQWGGSS-ENRRRMAVEIVRRTR 206

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  R+ + D          + +L K ++ +G     I+      +   P   
Sbjct: 207 KAVGPNFIIVFRLSMADLVEGGQTWDEIVSLAKEVEAAGAT--IINTDIGWHESRVPTIV 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNSAML 226
             +P   +  +    +++ D+ +  +  +     A +IL   D   + + R    +   +
Sbjct: 265 TSVPRAAFVDITSKLEKHVDIPVAASNRINMPETAEEILNRGDAQLISMARPMLADPDWV 324

Query: 227 TTVDE 231
              + 
Sbjct: 325 NKAER 329


>gi|167839025|ref|ZP_02465802.1| oxidoreductase, FAD/FMN-binding protein [Burkholderia thailandensis
           MSMB43]
          Length = 324

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 37/100 (37%), Gaps = 13/100 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
               AAK V+D G + I ++            P        +G  L        + + A+
Sbjct: 151 DFAAAAKRVKDAGMDGIEISAAHQHLIDQFWSPRTNFRADEWGGSLENRLRFGVEVLKAV 210

Query: 112 CKALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSG 147
            +A+     V  R+  D    D +    L+ + +++ ++G
Sbjct: 211 REAVGRDFCVGLRMCGDEFHEDGLDHEQLKEIAQAMAETG 250


>gi|145632741|ref|ZP_01788475.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 3655]
 gi|145634528|ref|ZP_01790237.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittAA]
 gi|144986936|gb|EDJ93488.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 3655]
 gi|145268073|gb|EDK08068.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittAA]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQRYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPTLISRLADRFG 121


>gi|83858169|ref|ZP_00951691.1| imidazole glycerol phosphate synthase subunit HisF [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852992|gb|EAP90844.1| imidazole glycerol phosphate synthase subunit HisF [Oceanicaulis
           alexandrii HTCC2633]
          Length = 255

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/131 (12%), Positives = 44/131 (33%), Gaps = 11/131 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           +   +      +  L +     G + +  +   A   G +         ++ + V  + K
Sbjct: 21  VRFQNHEDVGGIEELAQRYAHEGADELVFYDISASPAGRT---------VEPEWVGRVAK 71

Query: 185 ENPDLFIGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
              D+   + GG+  +  A  ++    D + I   A +N  ++  + + F +        
Sbjct: 72  AI-DIPFCVAGGIRSLEHARARLFGGADKISINTPALENPDLIDAMAKEFGSQCVVVGID 130

Query: 244 KTRVDKDFWRK 254
              +D D+   
Sbjct: 131 SRVIDGDWRCH 141


>gi|295319487|gb|ADF99864.1| 2-enoate reductase [Clostridium botulinum F str. 230613]
          Length = 629

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 37/206 (17%), Positives = 73/206 (35%), Gaps = 47/206 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             E+A+I +  G++ I ++       VHEG                 +G  L        
Sbjct: 122 FGESAEIAKKAGFDGIEIHA------VHEGYLLDQFAISFFNHRTDEYGGSLENRLRFAC 175

Query: 106 DCIAAMCKAL--SIPVTVK----------CRIGVDDQIPAVALRNL------VKSIKKSG 147
           + +  + K      PV+++          C+ G+ D+      R++       K +  +G
Sbjct: 176 EVVQEIKKRCGQDFPVSLRYSIKSFIKDWCKGGLPDEEFEEKGRDIPEGIEAAKILVAAG 235

Query: 148 VNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QAL 204
            + +        +      P   +K   L Y+   EI K+  D+ I   G +ED    + 
Sbjct: 236 YDALNGDVGSYDSWYWSHPPMYQKKGLYLPYN---EILKKVVDVPIITAGRMEDPELSSD 292

Query: 205 KILPS-VDGVMIGRAAYKNSAMLTTV 229
            IL    D + +GR    ++ +   +
Sbjct: 293 AILSGKTDMIALGRPLLADAEIPNKI 318


>gi|283788331|ref|YP_003368196.1| 2,4-dienoyl-CoA reductase [NADPH] [Citrobacter rodentium ICC168]
 gi|282951785|emb|CBG91494.1| 2,4-dienoyl-CoA reductase [NADPH] [Citrobacter rodentium ICC168]
          Length = 672

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 22/191 (11%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A++  + GY+ + +                 L+                     
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLAQRTNQRDDRWGGDYAR 190

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+     V++         L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAIRQRVGDDFIIIYRLSMLDLVENGSTFEETVQLAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSVPLVTTNR-INDPQVAEAILARGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|260460974|ref|ZP_05809223.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Mesorhizobium opportunistum WSM2075]
 gi|259033008|gb|EEW34270.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Mesorhizobium opportunistum WSM2075]
          Length = 249

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 19/129 (14%), Positives = 51/129 (39%), Gaps = 17/129 (13%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA 155
            +PD+V     A    +++ +  K      +   +  ++ +  L +  + +GV  I    
Sbjct: 108 RDPDLVRQACKAFPGKVAVGIDAKGGKVAVEGWAEASSLGVIELARKFEGAGVAAII--- 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL----PSVD 211
                       +  +  +++D   ++  E   + +  +GGL  ++  +++       ++
Sbjct: 165 ------YTDIDRDGVLTGINWDATIDLA-EAVSIPVIASGGLASIADIVRMTMPDAQKLE 217

Query: 212 GVMIGRAAY 220
           G + GRA Y
Sbjct: 218 GAISGRALY 226


>gi|224367320|ref|YP_002601483.1| predicted NADH:flavin oxidoreductase/NADH oxidase [Desulfobacterium
           autotrophicum HRM2]
 gi|223690036|gb|ACN13319.1| predicted NADH:flavin oxidoreductase/NADH oxidase [Desulfobacterium
           autotrophicum HRM2]
          Length = 667

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 25/153 (16%), Positives = 59/153 (38%), Gaps = 9/153 (5%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS-----G 147
           +G  L        + +AA+   +     +  R+  +D +P    R  +++  K+     G
Sbjct: 187 YGGSLNNRMRFGLEVMAAIRAEVGPDYPIIVRMNGNDFMPQGQGRKELQAYAKALVDQAG 246

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           V+ + I+      +   P+   ++P   +  +    KE  ++ +  +  + D   A + +
Sbjct: 247 VDALCINVG--WHEARIPQITAQVPRGTFAYLARGIKEVVNVPVISSHRINDSETAREAI 304

Query: 208 PS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
                D V +GR+   +  +   V E   N + 
Sbjct: 305 SDGMCDMVAMGRSLIADPMLPMKVKEGRENQII 337


>gi|184199759|ref|YP_001853966.1| pyridoxal biosynthesis lyase PdxS [Kocuria rhizophila DC2201]
 gi|183579989|dbj|BAG28460.1| pyridoxal phosphate synthase component Pdx1 [Kocuria rhizophila
           DC2201]
          Length = 309

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 66/227 (29%), Gaps = 71/227 (31%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I ED G   +      P+        G   M +PD++   I      +SIPV  K
Sbjct: 40  AEQARIAEDAGAVAVMALERVPAD--IRSQGGVARMSDPDLIESIIDT----VSIPVMAK 93

Query: 123 CRI--------------GVDDQIPAVALRNLVKSIKKS---------------------- 146
            RI                 D+   ++  +    I K                       
Sbjct: 94  ARIGHFVEAQVLQHLKVDYIDESEVLSPADYANHIDKHRFDVPFVCGATNLGEALRRITE 153

Query: 147 GVNGI-------------------WIHARKAILKGLSPKDNRKIP------NLDYDIVYE 181
           G   I                    I A+ A L+ L       +          Y++V E
Sbjct: 154 GAAMIRSKGEAGTGDVSEATKHIRTIRAQIAELQALYTAAPDALYVKAKELQAPYELVAE 213

Query: 182 IKKENPDLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
           + +      +    GG+   + A  ++    DGV +G   +   N A
Sbjct: 214 VARTGSLPVVMFTAGGVATPADAAMMMQLGADGVFVGSGIFKSGNPA 260


>gi|169832454|ref|YP_001694191.1| NanE/NanK bifunctional enzyme [Streptococcus pneumoniae
           Hungary19A-6]
 gi|168994956|gb|ACA35568.1| NanE/NanK bifunctional enzyme [Streptococcus pneumoniae
           Hungary19A-6]
          Length = 197

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 9/104 (8%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K +      +  ++     K   +SGV+ +        L G +P    K  N D+++V 
Sbjct: 91  IKVKYPNKLLMADISTFEEGKVAVESGVDFV-----GTTLSGYTPYS-PKKDNPDFELVE 144

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
            + KE  D+ +   G +    QA K+L      V++G  A    
Sbjct: 145 RLVKEL-DVPVIAEGRISTPEQARKMLDLGAYAVVVG-GAITRP 186


>gi|320198716|gb|EFW73316.1| Imidazole glycerol phosphate synthase cyclase subunit [Escherichia
           coli EC4100B]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|315285621|gb|EFU45063.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 110-3]
 gi|323956192|gb|EGB51943.1| imidazoleglycerol phosphate synthase [Escherichia coli H263]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|269120145|ref|YP_003308322.1| NADH:flavin oxidoreductase/NADH oxidase [Sebaldella termitidis ATCC
           33386]
 gi|268614023|gb|ACZ08391.1| NADH:flavin oxidoreductase/NADH oxidase [Sebaldella termitidis ATCC
           33386]
          Length = 374

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 34/202 (16%), Positives = 66/202 (32%), Gaps = 33/202 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPDIVGDC 107
               +A K   D G++ + +             P +      +G  +   ML P  V D 
Sbjct: 151 EDFGKATKKAIDTGFDGVEIHGANTYLIQQFFSPHSNRRTDRWGGDIQKRMLFPMKVIDK 210

Query: 108 IAAMCKALSIP-VTVKCRIGVDD--------QIPAVALRNLVKSIKKS-GVNGIWIHARK 157
           +  + +        V  R   ++        +   V + NL+        ++   IHA+ 
Sbjct: 211 VKRVAEEYGKKDFIVGYRFSPEEIETPGIRIEDTLVLVENLISKELDYIHISLQDIHAKP 270

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
           ++  G        I          I K N  + +   GG+    +ALKI+    D + +G
Sbjct: 271 SMGSGYDKSMVEMI----------IDKVNGRIPVIAVGGIHTPDEALKIVEDGADMIALG 320

Query: 217 RAAYKNSAMLTTVDEYFSNPLT 238
           R        +   +E   + + 
Sbjct: 321 RELIMEPDWVKKAEEDQEDEIA 342


>gi|291283263|ref|YP_003500081.1| Imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli O55:H7 str. CB9615]
 gi|168986290|dbj|BAG11830.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli O55:H7]
 gi|290763136|gb|ADD57097.1| Imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli O55:H7 str. CB9615]
 gi|320657443|gb|EFX25241.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O55:H7 str. 3256-97 TW 07815]
 gi|320663259|gb|EFX30564.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O55:H7 str. USDA 5905]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|315283345|ref|ZP_07871556.1| NADH oxidase [Listeria marthii FSL S4-120]
 gi|313612993|gb|EFR86924.1| NADH oxidase [Listeria marthii FSL S4-120]
          Length = 644

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 154 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 211

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 212 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 271

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 272 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 327


>gi|290893117|ref|ZP_06556105.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           J2-071]
 gi|290557279|gb|EFD90805.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes FSL
           J2-071]
          Length = 309

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|119775082|ref|YP_927822.1| imidazole glycerol phosphate synthase subunit HisF [Shewanella
           amazonensis SB2B]
 gi|167012207|sp|A1S6Z6|HIS6_SHEAM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|119767582|gb|ABM00153.1| imidazole glycerol phosphate synthase subunit hisF [Shewanella
           amazonensis SB2B]
          Length = 259

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L     + G + +  +   A  KG           +D   V  I  E  D+   + GG++
Sbjct: 35  LAARYAQEGADELVFYDISASAKG---------AIVDKSWVSRIA-ERIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
              QA +IL    D + I   A  + +++  + + F 
Sbjct: 85  TAEQAREILAFGADKISINSPALSDPSLIRRLHDEFG 121


>gi|317472995|ref|ZP_07932298.1| tryptophan synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316899540|gb|EFV21551.1| tryptophan synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 261

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 13/46 (28%), Positives = 24/46 (52%)

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           D+D  +++ K+N  +   +  G+    QA K+    DGV++G A  
Sbjct: 189 DFDAFFDVIKKNTKIPCAVGFGISGPEQAKKMSQYCDGVIVGSAIV 234


>gi|306836115|ref|ZP_07469101.1| dihydroorotate oxidase [Corynebacterium accolens ATCC 49726]
 gi|304567965|gb|EFM43544.1| dihydroorotate oxidase [Corynebacterium accolens ATCC 49726]
          Length = 371

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 38/112 (33%), Gaps = 11/112 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            + A+ ++  +PV VK    + D     A+ +L   +  +G+          G+     +
Sbjct: 208 ILRAVQESTDVPVMVKIAPDLSDAD-VDAVADLAVELGLAGIVATNTTISREGLSTPRAE 266

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               G        +     +++  +       L +   GG+    QA + + 
Sbjct: 267 VEALGAGGISGPPVAERSLEVLRRLNARVGSQLVLISVGGITTPEQAWERIA 318


>gi|219718465|ref|YP_002474196.1| inosine-5'-monophosphate dehydrogenase [Borrelia garinii PBr]
 gi|219694142|gb|ACL34672.1| inosine-5'-monophosphate dehydrogenase [Borrelia garinii PBr]
          Length = 404

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 61/180 (33%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV- 119
           ++ + A++ EDF     +LN             GA + ++ D +      +   + + V 
Sbjct: 120 EIYKNAELKEDFPNACKDLNS--------RLRVGAAVSIDIDTLERVEELVKAHVDLLVI 171

Query: 120 ---------------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                          T+K +   +D     +  +     +   G + + +          
Sbjct: 172 DSAHGHSTRIIELVKTIKNKYPRLDLIAGNIVTKEAALDLINVGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|216997252|ref|YP_002333795.1| inosine-5'-monophosphate dehydrogenase [Borrelia afzelii ACA-1]
 gi|216753149|gb|ACJ73699.1| inosine-5'-monophosphate dehydrogenase [Borrelia afzelii ACA-1]
          Length = 403

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 57/171 (33%), Gaps = 38/171 (22%)

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV---------- 119
           EDF     +LN         +   GA + ++ D +      +   + + V          
Sbjct: 128 EDFSNACKDLNS--------KLRVGAAISIDIDTIERVEELVKAHVDLIVIDSAHGHSTR 179

Query: 120 ------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPK 166
                 T+K +   +D     +  +     +  +G + + +           I+ G+   
Sbjct: 180 IIELVKTIKNKYPNLDLIAGNIVTKEAALDLINAGADCLKVGIGPGSICTTRIVAGVGVP 239

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
               I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 240 QITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 284


>gi|222479102|ref|YP_002565339.1| dihydrodipicolinate synthase [Halorubrum lacusprofundi ATCC 49239]
 gi|222452004|gb|ACM56269.1| dihydrodipicolinate synthase [Halorubrum lacusprofundi ATCC 49239]
          Length = 332

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 25/138 (18%), Positives = 45/138 (32%), Gaps = 25/138 (18%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-S 116
           D  +L   A+ +E  G + +      P       +  +  M + + V D I  +  AL  
Sbjct: 43  DHEQLAANARYLERAGVDGVV-----PV----GSTGESATMSHDEHV-DVIETVRDALED 92

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +PV                  +L +    +G +G+ +         +SP  N+  P    
Sbjct: 93  VPVVAGT-----GSNNTAEALSLSERAADAGADGLLL---------ISPYYNKPEPQGFL 138

Query: 177 DIVYEIKKENPDLFIGLN 194
           +    I  E     I  N
Sbjct: 139 EHYRTIADEVDLPQIVYN 156


>gi|111074135|ref|YP_709263.1| inositol-5-monophosphate dehydrogenase [Borrelia afzelii PKo]
 gi|110891281|gb|ABH02440.1| IMP dehydrogenase [Borrelia afzelii PKo]
          Length = 403

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 57/171 (33%), Gaps = 38/171 (22%)

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV---------- 119
           EDF     +LN         +   GA + ++ D +      +   + + V          
Sbjct: 128 EDFSNACKDLNS--------KLRVGAAISIDIDTIERVEELVKAHVDLIVIDSAHGHSTR 179

Query: 120 ------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPK 166
                 T+K +   +D     +  +     +  +G + + +           I+ G+   
Sbjct: 180 IIELVKTIKNKYPNLDLIAGNIVTKEAALDLINAGADCLKVGIGPGSICTTRIVAGVGVP 239

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
               I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 240 QITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 284


>gi|330466970|ref|YP_004404713.1| dihydroorotate dehydrogenase 2 [Verrucosispora maris AB-18-032]
 gi|328809941|gb|AEB44113.1| dihydroorotate dehydrogenase 2 [Verrucosispora maris AB-18-032]
          Length = 345

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 23/127 (18%), Positives = 42/127 (33%), Gaps = 18/127 (14%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI 153
           G   + + D +   +AA+      PV VK    + +     A+  L++     G  G+  
Sbjct: 187 GLRALQDRDHLDALLAALV--GEKPVLVKIAPDLTE----PAIAELLEVCLARGAAGVIA 240

Query: 154 HARKAILKGLSPKDNRKIPNL-----------DYDIVYEIKKENP-DLFIGLNGGLEDMS 201
                   GL+P D  +                  +V  + +E    L I   GG+    
Sbjct: 241 TNTTLGRDGLAPGDRHRADEAGGLSGRPLTDRARQVVDFVHRETGGRLPIIGVGGIVHPD 300

Query: 202 QALKILP 208
            A ++  
Sbjct: 301 DAARMFD 307


>gi|330445503|ref|ZP_08309155.1| imidazole glycerol phosphate synthase, HisF subunit [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|328489694|dbj|GAA03652.1| imidazole glycerol phosphate synthase, HisF subunit [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 257

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A  +  ++TT+ + F 
Sbjct: 85  SADDASRILQFGADKVSINSPALADPTLITTLADKFG 121


>gi|298246466|ref|ZP_06970272.1| pyridoxine biosynthesis protein [Ktedonobacter racemifer DSM 44963]
 gi|297553947|gb|EFH87812.1| pyridoxine biosynthesis protein [Ktedonobacter racemifer DSM 44963]
          Length = 295

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G + +      P+        G   M +P+++        +A++IPV  K
Sbjct: 29  AEQAKIAEEAGASAVMALERVPAD--IRAHGGVARMSDPELIIKI----KEAVTIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           CRIG   +          + ++  GV+ I
Sbjct: 83  CRIGHFVE---------AEILQAIGVDCI 102


>gi|71064761|ref|YP_263488.1| 2,4-dienoyl-CoA reductase [Psychrobacter arcticus 273-4]
 gi|71037746|gb|AAZ18054.1| 2,4-dienoyl-CoA reductase [Psychrobacter arcticus 273-4]
          Length = 711

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 28/173 (16%), Positives = 64/173 (36%), Gaps = 23/173 (13%)

Query: 63  VEAAKIVEDFGYNEINL---------NVGCPSARVHEG--SFGACLMLNPDIVGDCIAAM 111
             +AK+ +  GY+ + +              S  V++    +G  +     +  D + A+
Sbjct: 161 ARSAKLAKQAGYDGVEIMGSEGYLLNQFL--SRHVNKRTDEYGGDIQGRMKLAVDVVKAV 218

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            +A      +  R+ V D +    + +    + K+++++GV    ++      +   P  
Sbjct: 219 REAAGEDFIMLFRLSVIDLVKDGNVMDEVIIVAKALEEAGVT--IMNTGIGWHEARVPTI 276

Query: 168 NRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              +P   + D   EIKK      +  N  +     A +I+     D + + R
Sbjct: 277 VTSVPRAAFVDFTAEIKKHISIPMMAANR-INMPETAEEIVASGQADLIQMAR 328


>gi|74312568|ref|YP_310987.1| imidazole glycerol phosphate synthase subunit HisF [Shigella sonnei
           Ss046]
 gi|218695651|ref|YP_002403318.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli 55989]
 gi|293415315|ref|ZP_06657958.1| imidazoleglycerol phosphate synthase [Escherichia coli B185]
 gi|85541723|sp|Q3Z0G0|HIS6_SHISS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|254801204|sp|B7L9Q2|HIS6_ECO55 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|73856045|gb|AAZ88752.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Shigella sonnei Ss046]
 gi|218352383|emb|CAU98157.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli 55989]
 gi|291432963|gb|EFF05942.1| imidazoleglycerol phosphate synthase [Escherichia coli B185]
 gi|323168840|gb|EFZ54520.1| imidazole glycerol phosphate synthase subunit hisF [Shigella sonnei
           53G]
 gi|325497763|gb|EGC95622.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           fergusonii ECD227]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|315083573|gb|EFT55549.1| putative 2-enoate reductase [Propionibacterium acnes HL027PA2]
          Length = 670

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 67/196 (34%), Gaps = 32/196 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC---------PSARVHEG--SFGACLMLNPDIVGDCIA 109
           +   AAK+  + G++ I ++  C          + + +     +G  L        + + 
Sbjct: 159 QFRIAAKVAYEAGFDGIQVHA-CHEGYLLDQFATEKFNHRTDEYGGSLENRLRFPREIVE 217

Query: 110 AMCKAL--SIPVTVKCRIG----------VDDQIPAVALRNLVKSIKKS------GVNGI 151
           A+ + +    PV ++              + D+      R++ + I+ +      G   +
Sbjct: 218 AIHETVGDDFPVQIRFSPKSMMKDWNVGALPDEDFEEVGRDMPEGIEAARLLHSYGYEAL 277

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-- 209
            I          +     +   L      E+K+  PD+ + + G ++D   A   +    
Sbjct: 278 DIDVGCYDAWFWNHPPMYQAKVLYLPYASELKEALPDIPLIVAGRMDDPDLAANAVSDGI 337

Query: 210 VDGVMIGRAAYKNSAM 225
           VD V + R    +  +
Sbjct: 338 VDMVSLARPTLADPDI 353


>gi|331677931|ref|ZP_08378606.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli H591]
 gi|331074391|gb|EGI45711.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli H591]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|145294951|ref|YP_001137772.1| pyridoxal biosynthesis lyase PdxS [Corynebacterium glutamicum R]
 gi|140844871|dbj|BAF53870.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 344

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 35/97 (36%), Gaps = 8/97 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K RI
Sbjct: 81  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 134

Query: 126 GVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAIL 160
           G   +   +     + +   +         H  K   
Sbjct: 135 GHFVEAQVLEALGVDFIDESEVLSPADYTHHINKWKF 171


>gi|29830472|ref|NP_825106.1| oxidoreductase [Streptomyces avermitilis MA-4680]
 gi|29607584|dbj|BAC71641.1| putative oxidoreductase [Streptomyces avermitilis MA-4680]
          Length = 375

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 27/159 (16%), Positives = 48/159 (30%), Gaps = 24/159 (15%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPA------VALRNLVKSI 143
           ++G   +       + +AA+  A+  S PV  +          A        L  ++  +
Sbjct: 200 AYGGDPVARTKFAAEIVAAVRSAVSPSFPVLFRYSQWKQQAYDARLAETPEELEAILAPL 259

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG------- 196
             +GV+      R+         D   +    +      K       +GLNG        
Sbjct: 260 AAAGVDAFHASTRRYWQPEFDGSD---LNLAGWTKKITGKPAISVGSVGLNGEFLKAFQG 316

Query: 197 ----LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
               +  +   L  L     D V IGRA  ++      V
Sbjct: 317 EGSTVRGIDDLLDRLESGEFDLVAIGRALLQDPEWAAKV 355


>gi|16804209|ref|NP_465694.1| hypothetical protein lmo2170 [Listeria monocytogenes EGD-e]
 gi|47095744|ref|ZP_00233350.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes str.
           1/2a F6854]
 gi|224501031|ref|ZP_03669338.1| hypothetical protein LmonFR_00680 [Listeria monocytogenes FSL
           R2-561]
 gi|254899129|ref|ZP_05259053.1| hypothetical protein LmonJ_04934 [Listeria monocytogenes J0161]
 gi|254912730|ref|ZP_05262742.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           J2818]
 gi|254937057|ref|ZP_05268754.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           F6900]
 gi|255025090|ref|ZP_05297076.1| hypothetical protein LmonocytFSL_00095 [Listeria monocytogenes FSL
           J2-003]
 gi|284802617|ref|YP_003414482.1| hypothetical protein LM5578_2373 [Listeria monocytogenes 08-5578]
 gi|284995759|ref|YP_003417527.1| hypothetical protein LM5923_2324 [Listeria monocytogenes 08-5923]
 gi|16411640|emb|CAD00248.1| lmo2170 [Listeria monocytogenes EGD-e]
 gi|47015887|gb|EAL06814.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes str.
           1/2a F6854]
 gi|258609660|gb|EEW22268.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           F6900]
 gi|284058179|gb|ADB69120.1| hypothetical protein LM5578_2373 [Listeria monocytogenes 08-5578]
 gi|284061226|gb|ADB72165.1| hypothetical protein LM5923_2324 [Listeria monocytogenes 08-5923]
 gi|293590725|gb|EFF99059.1| enoyl-(acyl-carrier-protein) reductase [Listeria monocytogenes
           J2818]
          Length = 309

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|26248400|ref|NP_754440.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli CFT073]
 gi|91211311|ref|YP_541297.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli UTI89]
 gi|110642238|ref|YP_669968.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli 536]
 gi|191169996|ref|ZP_03031550.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli F11]
 gi|300973415|ref|ZP_07172173.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 200-1]
 gi|300986920|ref|ZP_07177898.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 45-1]
 gi|331653449|ref|ZP_08354450.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli M718]
 gi|34222574|sp|Q8FG48|HIS6_ECOL6 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|122423320|sp|Q1RA48|HIS6_ECOUT RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|122958243|sp|Q0TG62|HIS6_ECOL5 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|26108804|gb|AAN81007.1|AE016762_260 Imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli CFT073]
 gi|91072885|gb|ABE07766.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli UTI89]
 gi|110343830|gb|ABG70067.1| Iimidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli 536]
 gi|190909512|gb|EDV69097.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli F11]
 gi|294489720|gb|ADE88476.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli IHE3034]
 gi|300309101|gb|EFJ63621.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 200-1]
 gi|300407849|gb|EFJ91387.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 45-1]
 gi|307626429|gb|ADN70733.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli UM146]
 gi|315295264|gb|EFU54599.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 153-1]
 gi|324015735|gb|EGB84954.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 60-1]
 gi|331048298|gb|EGI20374.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli M718]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|261407470|ref|YP_003243711.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp.
           Y412MC10]
 gi|261283933|gb|ACX65904.1| NADH:flavin oxidoreductase/NADH oxidase [Paenibacillus sp.
           Y412MC10]
          Length = 326

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 61/177 (34%), Gaps = 19/177 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            +   AA+     G++ I L+            P +     ++G  L      + + +AA
Sbjct: 144 DQFRMAARRSLQAGFDGIELHAAHGHLLHQFLSPLSNRRTDAYGGSLENRVRFIQEVLAA 203

Query: 111 MCKAL--SIPVTVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +   +    PV ++       D     A   L  +  +S ++ + + +      GL P  
Sbjct: 204 IRTEVGNDYPVQLRVSASDFADGGLTPAEVALALTYLQSELDAVHVSSG-----GLVPAA 258

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
               P         + K+  ++ +   G +   + A  IL     D V IGR   ++
Sbjct: 259 PLATPEGYQTPYAAVIKQYVNIPVIAVGNIRTQAFANFILADGMADMVAIGRPLLED 315


>gi|160902335|ref|YP_001567916.1| NADH:flavin oxidoreductase/NADH oxidase [Petrotoga mobilis SJ95]
 gi|160359979|gb|ABX31593.1| NADH:flavin oxidoreductase/NADH oxidase [Petrotoga mobilis SJ95]
          Length = 340

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 35/200 (17%), Positives = 72/200 (36%), Gaps = 30/200 (15%)

Query: 46  QEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG---------CPSARVHEGS 92
            E P+  ++   +I  ++ A    A      GY+ + ++            P +      
Sbjct: 125 DEYPIPSELTKNEIKDIIRAFGTAAARAVKVGYDTVEVHAAHGYLIHEFLSPLSNKRSDE 184

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGV 148
           +G  +      + D +  + K +   +PV ++      VD  I       +VK +K   V
Sbjct: 185 YGGKIENRVRFLRDVLIEVKKNIPDDMPVFMRISATDFVDGGIDIKETIEIVKLVKDL-V 243

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE--IKKENPDLFIGLNGGLEDMSQALKI 206
           + +   +       LSP+ +       Y I+Y   +K+E     + + G +     A +I
Sbjct: 244 DIVDCSSGGL----LSPRIDFYPG---YQIIYAEAVKRETGVPSVAV-GLITSPEMAEEI 295

Query: 207 L--PSVDGVMIGRAAYKNSA 224
           +     D V +GR   +   
Sbjct: 296 IGNERADMVALGRVLLRQPY 315


>gi|24113410|ref|NP_707920.1| imidazole glycerol phosphate synthase subunit HisF [Shigella
           flexneri 2a str. 301]
 gi|30063475|ref|NP_837646.1| imidazole glycerol phosphate synthase subunit HisF [Shigella
           flexneri 2a str. 2457T]
 gi|110805998|ref|YP_689518.1| imidazole glycerol phosphate synthase subunit HisF [Shigella
           flexneri 5 str. 8401]
 gi|48474390|sp|Q83R03|HIS6_SHIFL RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|122366482|sp|Q0T3A2|HIS6_SHIF8 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|24052432|gb|AAN43627.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH, imidazole glycerol phsphate synthase holoenzyme
           [Shigella flexneri 2a str. 301]
 gi|30041728|gb|AAP17455.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH, imidazole glycerol phsphate synthase holoenzyme
           [Shigella flexneri 2a str. 2457T]
 gi|110615546|gb|ABF04213.1| imidazole glycerol phsphate synthase holoenzyme [Shigella flexneri
           5 str. 8401]
 gi|281601477|gb|ADA74461.1| Imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri 2002017]
 gi|313649936|gb|EFS14356.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri 2a str. 2457T]
 gi|332756661|gb|EGJ87010.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri K-671]
 gi|332756873|gb|EGJ87218.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri 2747-71]
 gi|332766373|gb|EGJ96582.1| imidazole glycerol phosphate synthase, HisF subunit [Shigella
           flexneri 2930-71]
 gi|333002507|gb|EGK22069.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri K-218]
 gi|333002539|gb|EGK22100.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri VA-6]
 gi|333003527|gb|EGK23068.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri K-272]
 gi|333017070|gb|EGK36391.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri K-304]
 gi|333017197|gb|EGK36517.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           flexneri K-227]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|322384183|ref|ZP_08057893.1| dihydroorotate dehydrogenase 1B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151075|gb|EFX44392.1| dihydroorotate dehydrogenase 1B-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 365

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 28/153 (18%), Positives = 55/153 (35%), Gaps = 29/153 (18%)

Query: 74  YNEINLNVGCPS-ARVHEGSFGACLMLNPDIVGDCIAAMCKA------LSIPVTVKCRIG 126
            +   +N+  P+   +     G+ L+   +++      M +          PV VK    
Sbjct: 174 ADFFVVNISSPNTPDLRSLQHGSDLL---NLLHAVTDEMQRQQARYGDSGKPVLVKIAPD 230

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWI-----------HARKAILKGLSPKDNRKIPNLD 175
           + D+     + N + +I++SG  GI +           HA K    GLS K    +    
Sbjct: 231 LTDE----EVENTIHTIRESGAAGIIVSNTTISREGIVHAHKDQAGGLSGK---PLAECS 283

Query: 176 YDIVYEIKKENP-DLFIGLNGGLEDMSQALKIL 207
            ++V ++       + I  +GG+     A    
Sbjct: 284 TEMVAKVYLLTGGKMPIIGSGGIFTPEDAYAKF 316


>gi|320172633|gb|EFW47868.1| Imidazole glycerol phosphate synthase cyclase subunit [Shigella
           dysenteriae CDC 74-1112]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASCDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|293410380|ref|ZP_06653956.1| imidazoleglycerol phosphate synthase [Escherichia coli B354]
 gi|291470848|gb|EFF13332.1| imidazoleglycerol phosphate synthase [Escherichia coli B354]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|284802682|ref|YP_003414547.1| hypothetical protein LM5578_2438 [Listeria monocytogenes 08-5578]
 gi|284995824|ref|YP_003417592.1| hypothetical protein LM5923_2389 [Listeria monocytogenes 08-5923]
 gi|284058244|gb|ADB69185.1| hypothetical protein LM5578_2438 [Listeria monocytogenes 08-5578]
 gi|284061291|gb|ADB72230.1| hypothetical protein LM5923_2389 [Listeria monocytogenes 08-5923]
          Length = 644

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 154 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 211

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 212 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 271

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 272 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 327


>gi|320009883|gb|ADW04733.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces flavogriseus
           ATCC 33331]
          Length = 372

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 26/158 (16%), Positives = 51/158 (32%), Gaps = 34/158 (21%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPA------VALRNLVKSI 143
           ++G  ++       + +AA   A+  S P+  +      D   A        L  L+  +
Sbjct: 197 AYGGGIVARTRFAAEIVAACRAAVSDSFPLFFRMSQWKMDAYEAKLARTPEELDALLTPL 256

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLE 198
            ++GV+      R+  L         +  + D ++   +KK +         +GL+G   
Sbjct: 257 AEAGVDVFHASTRRYWL--------PEFEDSDLNLAGWVKKISGRPTVTVGSVGLDGDFF 308

Query: 199 DMSQA-------------LKILPSVDGVMIGRAAYKNS 223
              Q                     D V +GRA   + 
Sbjct: 309 SAFQGDSSSVTGIDQLLDRMERDEFDMVAVGRALIADP 346


>gi|212637918|ref|YP_002314438.1| dihydropteroate synthase [Anoxybacillus flavithermus WK1]
 gi|212559398|gb|ACJ32453.1| Dihydropteroate synthase [Anoxybacillus flavithermus WK1]
          Length = 278

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 21/113 (18%), Positives = 42/113 (37%), Gaps = 17/113 (15%)

Query: 57  ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
             + + VE AK +   G + I++           G+    L      V   + A+ KA++
Sbjct: 38  NHVEQAVERAKQLVAEGAHIIDIGGE----STRPGAEKVSLEEELRRVIPIVEAVAKAVN 93

Query: 117 IPVTVKCRI-------------GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +P+++                  ++D   A A  N+ +     GV  + +H R
Sbjct: 94  VPISIDTYKAEVAKQAIEAGATMINDVWGAKADCNMAQVAAYYGVPIVLMHNR 146


>gi|148241838|ref|YP_001226995.1| inosine 5-monophosphate dehydrogenase [Synechococcus sp. RCC307]
 gi|147850148|emb|CAK27642.1| IMP dehydrogenase/GMP reductase [Synechococcus sp. RCC307]
          Length = 387

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 9/84 (10%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA     K+I ++G +  ++ A         P+    +       +  + ++     +  
Sbjct: 140 VAALRFGKAIAEAGADLFFVQATVVSTNHTGPEGQETLD------LEALCRDMGVPVVIG 193

Query: 194 NGGLEDMSQALK-ILPSVDGVMIG 216
           N        AL+ +     GVM+G
Sbjct: 194 N--CVTYEVALQLMRAGAAGVMVG 215


>gi|16801400|ref|NP_471668.1| hypothetical protein lin2337 [Listeria innocua Clip11262]
 gi|16414860|emb|CAC97564.1| lin2337 [Listeria innocua Clip11262]
          Length = 641

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|319791945|ref|YP_004153585.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Variovorax paradoxus EPS]
 gi|315594408|gb|ADU35474.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Variovorax paradoxus EPS]
          Length = 247

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 6/68 (8%)

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPSVDG---VMIGRAAYKNSAMLT 227
              ++  +  I KE  D + + L GG+ D+    + +   DG   V+IG AA KN   L 
Sbjct: 59  KPQNHAAIKAILKEVGDDIPVQLGGGIRDLDTIERYID--DGLRYVIIGTAAVKNPGFLK 116

Query: 228 TVDEYFSN 235
                F  
Sbjct: 117 DACSAFGG 124


>gi|302390720|ref|YP_003826541.1| pyridoxal phosphate synthase yaaD subunit [Thermosediminibacter
           oceani DSM 16646]
 gi|302201348|gb|ADL08918.1| pyridoxal phosphate synthase yaaD subunit [Thermosediminibacter
           oceani DSM 16646]
          Length = 289

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 15/86 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I E+ G   +      P+        G   M +P      I A+ +A+SIPV  KCRI
Sbjct: 28  ARIAEEAGAVAVMALERVPAD--IRKQGGVARMSDP----KVIKAIKQAVSIPVMAKCRI 81

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI 151
           G   +          + ++  GV+ I
Sbjct: 82  GHFVE---------AQILEALGVDFI 98


>gi|239942889|ref|ZP_04694826.1| putative oxidoreductase [Streptomyces roseosporus NRRL 15998]
 gi|239989349|ref|ZP_04710013.1| putative oxidoreductase [Streptomyces roseosporus NRRL 11379]
 gi|291446362|ref|ZP_06585752.1| oxidoreductase [Streptomyces roseosporus NRRL 15998]
 gi|291349309|gb|EFE76213.1| oxidoreductase [Streptomyces roseosporus NRRL 15998]
          Length = 397

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 29/187 (15%), Positives = 55/187 (29%), Gaps = 37/187 (19%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA------VALRNLVKSI 143
           ++G  L+       + +AA   A+S   P+  +      D   A        L  L+  +
Sbjct: 222 AYGGDLVARTRFAAEIVAACRAAVSDAFPLFFRMSQWKADAYEAKLAETPQELDALLTPL 281

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLE 198
            ++GV+      R+  L         +  + D ++   +KK +         +GL+G   
Sbjct: 282 AEAGVDVFHASTRRYWL--------PEFEDSDLNLAGWVKKISGRPTLTVGSVGLDGDFF 333

Query: 199 DMSQA-------------LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
              Q                     D V +GRA   +                  +P   
Sbjct: 334 SAFQGNDSSVTGIEQLLDRMERDEFDMVAVGRALIADPEWAAKT---LRGRTEDITPFAA 390

Query: 246 RVDKDFW 252
            + K   
Sbjct: 391 EMLKTLH 397


>gi|224500165|ref|ZP_03668514.1| hypothetical protein LmonF1_10979 [Listeria monocytogenes Finland
           1988]
          Length = 309

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 19/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + ++K GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEKIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|312967257|ref|ZP_07781473.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli 2362-75]
 gi|168986406|dbj|BAG11944.1| imidazole glycerol phosphate synthase [Escherichia coli O55:H6]
 gi|312288065|gb|EFR15969.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli 2362-75]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|320193312|gb|EFW67950.1| Imidazole glycerol phosphate synthase cyclase subunit [Escherichia
           coli WV_060327]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|331684734|ref|ZP_08385326.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli H299]
 gi|331078349|gb|EGI49555.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli H299]
          Length = 672

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 30/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    + +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSPLQAPINRFIPHELTHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|284165070|ref|YP_003403349.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Haloterrigena turkmenica DSM 5511]
 gi|284014725|gb|ADB60676.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Haloterrigena turkmenica DSM 5511]
          Length = 270

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 22/137 (16%), Positives = 44/137 (32%), Gaps = 12/137 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+  +SG +        A  +G              D+V  +  E   + + + GG+
Sbjct: 39  EMAKAYNESGADEFVFLDITASAEGRETM---------LDVVERVADEVF-IPLTVGGGI 88

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNP-LTGSSPIKTRVDKDFWRKI 255
                  + L    D V I   A +   ++    + F N  +  S   + R D++    +
Sbjct: 89  RTTDDIKETLRAGADKVSITTGALERPELINEGAKAFGNQCIVISVDARRRFDEEGEHYV 148

Query: 256 SASMTDYAARHLHSGGK 272
                         GG+
Sbjct: 149 EIDGESCWFECTKKGGR 165


>gi|281413130|ref|YP_003347209.1| imidazoleglycerol phosphate synthase, cyclase subunit [Thermotoga
           naphthophila RKU-10]
 gi|281374233|gb|ADA67795.1| imidazoleglycerol phosphate synthase, cyclase subunit [Thermotoga
           naphthophila RKU-10]
          Length = 254

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA ++ +++T +   F +
Sbjct: 64  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVEDPSLITKIARTFGS 122

Query: 236 PLTGSSPIKTRVDKDFW 252
                +    RVD +F 
Sbjct: 123 QAVVVAIDAKRVDGEFM 139


>gi|227507902|ref|ZP_03937951.1| tryptophan synthase alpha chain [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227523137|ref|ZP_03953186.1| tryptophan synthase alpha chain [Lactobacillus hilgardii ATCC 8290]
 gi|227089685|gb|EEI24997.1| tryptophan synthase alpha chain [Lactobacillus hilgardii ATCC 8290]
 gi|227192616|gb|EEI72683.1| tryptophan synthase alpha chain [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 264

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 54/157 (34%), Gaps = 42/157 (26%)

Query: 104 VGDCIAAMCKALSIP--------VTVK------CRIGVD--------DQIPAVALRNLVK 141
           V + + A  K  ++P        +  K       +   D          +P  +   +V 
Sbjct: 76  VFEIVEAARKETNVPMVFLTYLNIVFKYGYEAFLKRCADLNVSGLVIPDLPYESRDEIVP 135

Query: 142 SIKKSGVNGIWIHARKAILK------------------GLSPKDNRKIPNLDYDIVYEIK 183
             +K GV+ I +    +  +                  G++ + N     L  D+V EIK
Sbjct: 136 IAEKYGVDIIPLITPTSGHRIEKIAKSASGFIYVVSSMGITGERNEFFNGLK-DLVTEIK 194

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           K   D+   +  G+    QA  +    DGV+IG A  
Sbjct: 195 K-YTDVPTAIGFGVHTPEQAQAMAGIADGVIIGSAIV 230


>gi|218705564|ref|YP_002413083.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli UMN026]
 gi|293405503|ref|ZP_06649495.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli FVEC1412]
 gi|298381191|ref|ZP_06990790.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli FVEC1302]
 gi|331663523|ref|ZP_08364433.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA143]
 gi|226700518|sp|B7NC65|HIS6_ECOLU RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|218432661|emb|CAR13555.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli UMN026]
 gi|284922024|emb|CBG35102.1| imidazole glycerol phosphate synthase subunit [Escherichia coli
           042]
 gi|291427711|gb|EFF00738.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli FVEC1412]
 gi|298278633|gb|EFI20147.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli FVEC1302]
 gi|331059322|gb|EGI31299.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA143]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|163841293|ref|YP_001625698.1| 2,4-dienoyl-CoA reductase (NADPH) [Renibacterium salmoninarum ATCC
           33209]
 gi|162954769|gb|ABY24284.1| 2,4-dienoyl-CoA reductase (NADPH) [Renibacterium salmoninarum ATCC
           33209]
          Length = 329

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 16/118 (13%), Positives = 39/118 (33%), Gaps = 8/118 (6%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + +A+     +  RI + D IP          L   I+ +G +    +      +
Sbjct: 107 EIVRRVREAVGTEFMISYRISLLDLIPKGQTWDETEELAHKIEAAGASFF--NTGIGWHE 164

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
              P     +P + +       +    + +  +  +     A +IL     D + + R
Sbjct: 165 ARVPTIFTSVPRVAFASWSGKLRSQVHIPVMASNRINTPETAEQILSEGNADLISMAR 222


>gi|134096220|ref|YP_001101295.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Herminiimonas
           arsenicoxydans]
 gi|167011533|sp|A4G9I7|HIS4_HERAR RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|133740123|emb|CAL63174.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase
           (Phosphoribosylformimino-5-aminoimidazole carboxamide
           ribotide isomerase) [Herminiimonas arsenicoxydans]
          Length = 265

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 30/158 (18%), Positives = 51/158 (32%), Gaps = 10/158 (6%)

Query: 122 KCRIGVDDQIPAVAL----RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             R+   D   A        ++ +   + G   + +        G     N         
Sbjct: 14  CVRLKQGDMDQATVFSEDPADMARHWLEQGARRLHLVDLNGAFAGK--PKNEPAVKAILQ 71

Query: 178 IVYEIKKENPD--LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            V E  ++N    + + L GG+ D+    + L   +  ++IG AA KN   L      F 
Sbjct: 72  AVREYAEKNGIEEIPVQLGGGIRDLDTIERYLDDGLSYIIIGTAAVKNPGFLHDACSAFP 131

Query: 235 NPLT-GSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
             +  G      +V  D W K+S       A+     G
Sbjct: 132 GQIIVGLDAKDGKVATDGWSKLSGHEVIDLAKKFEDYG 169


>gi|170019648|ref|YP_001724602.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli ATCC 8739]
 gi|189043418|sp|B1IZ49|HIS6_ECOLC RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|169754576|gb|ACA77275.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli ATCC 8739]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|313622720|gb|EFR93070.1| NADH oxidase [Listeria innocua FSL J1-023]
          Length = 644

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 154 EAALRAKKAGADAVE--VHCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 211

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 212 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 271

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 272 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 327


>gi|309791751|ref|ZP_07686241.1| isopentenyl-diphosphate delta-isomerase, type 2 [Oscillochloris
           trichoides DG6]
 gi|308226244|gb|EFO79982.1| isopentenyl-diphosphate delta-isomerase, type 2 [Oscillochloris
           trichoides DG6]
          Length = 327

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 23/113 (20%), Positives = 40/113 (35%), Gaps = 7/113 (6%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNL-VKSIKKSGVNGIWIHARKAILKGLSPK 166
           I A+CK L +PV +K          A  L    V+ I  +G  G      +   +     
Sbjct: 163 IEAVCKELPVPVVIKEVGNGIGADDARRLYECGVRVIDVAGAGGTSWSEVERFRQTSDQG 222

Query: 167 DNRKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
                   D+     + + E++   P + +  +GG+   +  A  I    D V
Sbjct: 223 RRVAGAFADWGIPTAECIREVRAALPHVTLIGSGGVRTGVDVAKAIALGADVV 275


>gi|82543402|ref|YP_407349.1| imidazole glycerol phosphate synthase subunit HisF [Shigella boydii
           Sb227]
 gi|85541721|sp|Q323I7|HIS6_SHIBS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|81244813|gb|ABB65521.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Shigella boydii Sb227]
 gi|320185794|gb|EFW60548.1| Imidazole glycerol phosphate synthase cyclase subunit [Shigella
           flexneri CDC 796-83]
 gi|332097138|gb|EGJ02121.1| imidazole glycerol phosphate synthase subunit hisF [Shigella boydii
           3594-74]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|52425937|ref|YP_089074.1| imidazole glycerol phosphate synthase subunit HisF [Mannheimia
           succiniciproducens MBEL55E]
 gi|60392363|sp|Q65RC1|HIS6_MANSM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|52307989|gb|AAU38489.1| HisF protein [Mannheimia succiniciproducens MBEL55E]
          Length = 257

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L     + G + +  +   A   G +         +D   V  +  E  D+   + GG++
Sbjct: 35  LAARYAEEGADELVFYDITASSDGRT---------VDKSWVERVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++ A +I     D + I   A  +  +++ + + F 
Sbjct: 85  TIADAEQIFTFGADKISINSPALADPDLISRLADRFG 121


>gi|19552286|ref|NP_600288.1| putative PEP phosphonomutase [Corynebacterium glutamicum ATCC
           13032]
 gi|21323827|dbj|BAB98453.1| PEP phosphonomutase and related enzymes [Corynebacterium glutamicum
           ATCC 13032]
          Length = 254

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 52/130 (40%), Gaps = 11/130 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A +VE+ G++ + +    P A     S G   M   D +   +  +  A+SIPV+V    
Sbjct: 32  AGLVEEAGFSGLTIGSH-PVADATGSSDGEN-MNFADYMA-VVKKITSAVSIPVSVDVES 88

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G       ++  +L+  I ++G  GI +     ++     +      + DY        +
Sbjct: 89  GY-----GLSPADLIAQILEAGAVGINVE---DVVHSEGKRVREAQEHADYIAAARQAAD 140

Query: 186 NPDLFIGLNG 195
              + + +NG
Sbjct: 141 VAGVDVVING 150


>gi|330951882|gb|EGH52142.1| NADH:flavin oxidoreductase/NADH oxidase [Pseudomonas syringae Cit
           7]
          Length = 363

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 63/181 (34%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +            ++G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDAYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLAESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +   D+ +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREADIAVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|324511975|gb|ADY44972.1| NADH oxidase [Ascaris suum]
          Length = 437

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 74/244 (30%), Gaps = 47/244 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCI 108
            +   AA  V+D G++ + +NVG                     +G  L     I+ + I
Sbjct: 165 ERYAYAAGFVKDCGFHGVEINVG--MDFALAQLVTATTNSRNDEYGGSLENRTRILFEVI 222

Query: 109 AAMCKAL--SIPVTVKCRI---GVDDQIPAVALRNLVKSIKKS--------GVNGIWIHA 155
            ++   +       +  ++     +D           K +  +        G N   I  
Sbjct: 223 NSIRDRVKDDKNFVLGLKLSSLNYEDGYDECEFERFCKRLDATKLDYVVITGANYEAIRQ 282

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R+ I +  S K           +   IK+        L GG     Q  + +     DG+
Sbjct: 283 REKIERDPSRKSEAFFVKFVIAVRTNIKRAKT----FLCGGFRAADQMWEAIYEGWTDGI 338

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+ R       +   +    +  +TG+            +K      DY      +G ++
Sbjct: 339 MVARPLAAEPDLPRRI---LNREVTGA------------KKSLLDEIDYGLSEYAAGTQM 383

Query: 274 QQIT 277
            Q+ 
Sbjct: 384 WQLA 387


>gi|300956255|ref|ZP_07168563.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 175-1]
 gi|307138692|ref|ZP_07498048.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli H736]
 gi|331642648|ref|ZP_08343783.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli H736]
 gi|300316906|gb|EFJ66690.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 175-1]
 gi|323940893|gb|EGB37081.1| imidazoleglycerol phosphate synthase [Escherichia coli E482]
 gi|331039446|gb|EGI11666.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli H736]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|302866820|ref|YP_003835457.1| dihydroorotate dehydrogenase [Micromonospora aurantiaca ATCC 27029]
 gi|315503235|ref|YP_004082122.1| dihydroorotate dehydrogenase [Micromonospora sp. L5]
 gi|302569679|gb|ADL45881.1| dihydroorotate dehydrogenase [Micromonospora aurantiaca ATCC 27029]
 gi|315409854|gb|ADU07971.1| dihydroorotate dehydrogenase [Micromonospora sp. L5]
          Length = 335

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/123 (16%), Positives = 41/123 (33%), Gaps = 18/123 (14%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + +   +   +AA+      PV VK    + +     A+  L++     G  G+      
Sbjct: 192 LQDRSHLDALLAALV--GEKPVLVKIAPDLTE----PAVAELLEVCLDRGAAGVIATNTT 245

Query: 158 AILKGLSPKDNRKIPNL-----------DYDIVYEIKKENP-DLFIGLNGGLEDMSQALK 205
               GL+P D  +                 ++V  + +E    L +   GG+     A +
Sbjct: 246 LARDGLAPADRERAAEAGGLSGRPLTARAREMVAFVHRETGGRLPVIGVGGILHPDDATR 305

Query: 206 ILP 208
           +  
Sbjct: 306 MFD 308


>gi|316931707|ref|YP_004106689.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhodopseudomonas palustris DX-1]
 gi|315599421|gb|ADU41956.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhodopseudomonas palustris DX-1]
          Length = 245

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 25/145 (17%), Positives = 54/145 (37%), Gaps = 21/145 (14%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV---KCRIGVDDQIPAVALRNLVK 141
           S  +     G   + +P +V +   A    +++ +     K  +    +   V    + +
Sbjct: 94  SKGIARVIIGTAAVRDPALVKEAAKAFPGRVAVGLDARDGKVAVEGWAESSQVTALEIAQ 153

Query: 142 SIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             + +GV  I     AR  +LKG           +++D    + +    + +  +GGL  
Sbjct: 154 RFEDAGVAAIIFTDIARDGLLKG-----------INWDATIALAEAI-SIPVIASGGLAS 201

Query: 200 MSQALKILP----SVDGVMIGRAAY 220
           +     +L      ++G + GRA Y
Sbjct: 202 IEDVRTLLSPRAKKLEGAIAGRALY 226


>gi|260856008|ref|YP_003229899.1| imidazole glycerol phosphate synthase, catalytic subunit
           [Escherichia coli O26:H11 str. 11368]
 gi|257754657|dbj|BAI26159.1| imidazole glycerol phosphate synthase, catalytic subunit
           [Escherichia coli O26:H11 str. 11368]
 gi|323152414|gb|EFZ38702.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli EPECa14]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|297195492|ref|ZP_06912890.1| pyridoxine biosynthesis protein [Streptomyces pristinaespiralis
           ATCC 25486]
 gi|197722107|gb|EDY66015.1| pyridoxine biosynthesis protein [Streptomyces pristinaespiralis
           ATCC 25486]
          Length = 305

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 27/101 (26%), Positives = 45/101 (44%), Gaps = 8/101 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA--AKIVEDFGYNEINLNVGCP 84
           +    + +    + +G S  ++ +A Q+ G  I  +V A  AKI ED G   +      P
Sbjct: 1   MSTSPLPQTADSSAIGTSRVKRGMAEQLKGGVIMDVVNAEQAKIAEDAGAVAVMALERVP 60

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           +        G   M +P+++ + I     A+SIPV  K RI
Sbjct: 61  AD--IRKDGGVARMSDPNMIEEII----DAVSIPVMAKSRI 95


>gi|222480563|ref|YP_002566800.1| isocitrate lyase and phosphorylmutase [Halorubrum lacusprofundi
           ATCC 49239]
 gi|222453465|gb|ACM57730.1| isocitrate lyase and phosphorylmutase [Halorubrum lacusprofundi
           ATCC 49239]
          Length = 347

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 21/102 (20%), Positives = 36/102 (35%), Gaps = 14/102 (13%)

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK--GLSPK 166
             M +A ++PV   C  G         +R  V+  +K+GV  I I  +    +   ++ K
Sbjct: 85  KRMVEATNLPVIADCDTGYGGTHN---VRRAVREYEKAGVAAIHIEDQTTPKRCGHIAGK 141

Query: 167 DNRKIPNLDYDIVYEI-KKENPDLFIG--------LNGGLED 199
           +              +  K++ D  I          NG  ED
Sbjct: 142 EVVSQEQARSRFEAAVDAKQSEDTVIIARIDSYGSANGDWED 183


>gi|110678304|ref|YP_681311.1| 2,4-dienoyl-CoA reductase [Roseobacter denitrificans OCh 114]
 gi|109454420|gb|ABG30625.1| 2,4-dienoyl-CoA reductase [Roseobacter denitrificans OCh 114]
          Length = 675

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 23/186 (12%), Positives = 60/186 (32%), Gaps = 35/186 (18%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CLMLNPDIV-------------- 104
            +V  A   ++ GY+ + +        +    +     L+ + +                
Sbjct: 143 DIVACAARAQEAGYDGVEI--------MGSEGYFLNQFLVTHTNKRTDEWGGSYENRMRL 194

Query: 105 -GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
             + +  +  A+     +  R+ + D IP  +  +    L ++++ +G     I+     
Sbjct: 195 PVEVVRRVRAAVGTDFIIIYRLSMIDLIPNGSTHDEVVQLAQAVEAAGAT--IINTGIGW 252

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKIL-PSV-DGVMIG 216
            +   P     +P   +  V  ++  +     I  N  +     A ++L     D V + 
Sbjct: 253 HEARIPTIATSVPRAAFAWVTKKLMGKVGIPVITSNR-INTPDVAEEVLATGCADMVSMA 311

Query: 217 RAAYKN 222
           R    +
Sbjct: 312 RPMLAD 317


>gi|88603870|ref|YP_504048.1| inosine-5'-monophosphate dehydrogenase [Methanospirillum hungatei
           JF-1]
 gi|88189332|gb|ABD42329.1| inosine-5'-monophosphate dehydrogenase [Methanospirillum hungatei
           JF-1]
          Length = 486

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 9/54 (16%)

Query: 179 VYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           V E+ K+  D+ I  +GG+      A  I    D VM+G        +    DE
Sbjct: 322 VAEVAKDA-DVPIIADGGIRFSGDVAKAIAAGADSVMMG-------NLFAGTDE 367


>gi|72161707|ref|YP_289364.1| NADH:flavin oxidoreductase [Thermobifida fusca YX]
 gi|71915439|gb|AAZ55341.1| NADH:flavin oxidoreductases, Old Yellow enzyme family [Thermobifida
           fusca YX]
          Length = 671

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 18/146 (12%), Positives = 45/146 (30%), Gaps = 6/146 (4%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
           ++G  L        + + A+ + +     + V    R              + + ++ +G
Sbjct: 209 AYGGSLENRARFAVEVLTAVREEIGSDMALGVRFNLREEEPGGYTLADGIEIAQYLESTG 268

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
           +         +     S           +  +    + +  L +   G +  +  A K+L
Sbjct: 269 LLDFLHAVIGSPWGDPSYIQPYFYQPAQWADLAGQLRRSVSLPVIYTGRINSVEVAEKVL 328

Query: 208 P--SVDGVMIGRAAYKNSAMLTTVDE 231
              + D V + RA   +  +L    E
Sbjct: 329 ADGNADVVGMARAFIADGDILRKARE 354


>gi|29346743|ref|NP_810246.1| dihydroorotate dehydrogenase 2 [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|29338640|gb|AAO76440.1| putative dihydropyrimidine dehydrogenase [NADP+] precursor
           [Bacteroides thetaiotaomicron VPI-5482]
          Length = 326

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 28/189 (14%), Positives = 64/189 (33%), Gaps = 31/189 (16%)

Query: 49  PLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I   +D    V+ AK +++ G + + +N+    + V    +G+    + D     
Sbjct: 98  PIIASINCYSDSEW-VDFAKQIQEAGADALEINILALQSDVQYT-YGSFEQRHID----I 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  + + ++IPV +K                L+  +  +G   + +  R    +     +
Sbjct: 152 LRHIKQTVTIPVIMKL------GDNLTNPVALIDQLYANGAAAVVLFNR--FYQPDINIE 203

Query: 168 NRK-------------IPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGV 213
           N +                L +  +         +    +GG+ +       IL     V
Sbjct: 204 NMEQVSGEVFSTSADLATPLRWIGIASSV--VNKIDYAASGGVANPEAVVKAILAGASAV 261

Query: 214 MIGRAAYKN 222
            +  A Y+N
Sbjct: 262 EVCSAIYQN 270


>gi|82777443|ref|YP_403792.1| imidazole glycerol phosphate synthase subunit HisF [Shigella
           dysenteriae Sd197]
 gi|309787884|ref|ZP_07682494.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           dysenteriae 1617]
 gi|85541722|sp|Q32EF4|HIS6_SHIDS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|81241591|gb|ABB62301.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Shigella dysenteriae Sd197]
 gi|308924283|gb|EFP69780.1| imidazole glycerol phosphate synthase subunit hisF [Shigella
           dysenteriae 1617]
 gi|324016975|gb|EGB86194.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 117-3]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|70985382|ref|XP_748197.1| NADH-dependent flavin oxidoreductase [Aspergillus fumigatus Af293]
 gi|66845825|gb|EAL86159.1| NADH-dependent flavin oxidoreductase, putative [Aspergillus
           fumigatus Af293]
          Length = 442

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 29/210 (13%), Positives = 64/210 (30%), Gaps = 39/210 (18%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             ++A++    G + I ++            P       ++G        IV +  AA+ 
Sbjct: 219 FAKSARLAVQAGVDVIEIHGAHGYLINEFLSPVTNKRTDAYGGSFENRTRIVREVAAAIR 278

Query: 113 KAL--SIPVTVKCR-IGVDDQIPAVAL---------RNLVKSIKKSGVNGIWIHARKAIL 160
             +   +P+ ++       +  P  A            LVK + + G++ + + +     
Sbjct: 279 AVIPEGMPLFLRISATEWLEGQPVAAESGSWDMQSSLELVKKLPEWGIDLVDVSSAANHK 338

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-------------KIL 207
                       +L   I   I+       +G  G + D  QA               +L
Sbjct: 339 DQKINLHTAYQTDLAGQIRQAIRAAGASTLVGAVGLITDSEQARGLVQGADEATAAEAML 398

Query: 208 PS----VDGVMIGRAAYKNS-AMLTTVDEY 232
                  D ++I R   +    + +T  + 
Sbjct: 399 SGPEPKADAILIARQFLREPEWVFSTARKL 428


>gi|15802504|ref|NP_288530.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H7 EDL933]
 gi|15832080|ref|NP_310853.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H7 str. Sakai]
 gi|16129966|ref|NP_416529.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli str. K-12 substr. MG1655]
 gi|89108846|ref|AP_002626.1| imidazole glycerol phosphate synthase, catalytic subunit with HisF
           [Escherichia coli str. K-12 substr. W3110]
 gi|168751649|ref|ZP_02776671.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4113]
 gi|168757567|ref|ZP_02782574.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4401]
 gi|168764110|ref|ZP_02789117.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4501]
 gi|168769775|ref|ZP_02794782.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4486]
 gi|168775529|ref|ZP_02800536.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4196]
 gi|168782306|ref|ZP_02807313.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4076]
 gi|168788691|ref|ZP_02813698.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC869]
 gi|168799095|ref|ZP_02824102.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC508]
 gi|170081656|ref|YP_001730976.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli str. K-12 substr. DH10B]
 gi|170679723|ref|YP_001743114.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli SMS-3-5]
 gi|193062764|ref|ZP_03043857.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli E22]
 gi|195939363|ref|ZP_03084745.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H7 str. EC4024]
 gi|208806489|ref|ZP_03248826.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4206]
 gi|208817203|ref|ZP_03258295.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4045]
 gi|208820025|ref|ZP_03260345.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4042]
 gi|209397885|ref|YP_002271266.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4115]
 gi|215487247|ref|YP_002329678.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O127:H6 str. E2348/69]
 gi|217329573|ref|ZP_03445652.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. TW14588]
 gi|238901216|ref|YP_002927012.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli BW2952]
 gi|254793807|ref|YP_003078644.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H7 str. TW14359]
 gi|256022284|ref|ZP_05436149.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia sp.
           4_1_40B]
 gi|260844636|ref|YP_003222414.1| imidazole glycerol phosphate synthase, catalytic subunit
           [Escherichia coli O103:H2 str. 12009]
 gi|261225132|ref|ZP_05939413.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli O157:H7 str. FRIK2000]
 gi|261257524|ref|ZP_05950057.1| imidazole glycerol phosphate synthase, catalytic subunit
           [Escherichia coli O157:H7 str. FRIK966]
 gi|300816654|ref|ZP_07096875.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 107-1]
 gi|300898598|ref|ZP_07116927.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 198-1]
 gi|300903896|ref|ZP_07121795.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 84-1]
 gi|300920266|ref|ZP_07136712.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 115-1]
 gi|300926487|ref|ZP_07142281.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 182-1]
 gi|301019216|ref|ZP_07183413.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 69-1]
 gi|301306507|ref|ZP_07212572.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 124-1]
 gi|301329580|ref|ZP_07222356.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 78-1]
 gi|306814853|ref|ZP_07449015.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli NC101]
 gi|331658105|ref|ZP_08359067.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA206]
 gi|331683709|ref|ZP_08384305.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli H299]
 gi|48474306|sp|P60664|HIS6_ECOLI RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|48474307|sp|P60665|HIS6_ECO57 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226700514|sp|B5YU81|HIS6_ECO5E RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226700517|sp|B1X6W2|HIS6_ECODH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226700520|sp|B1LP16|HIS6_ECOSM RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|254801203|sp|B7UT62|HIS6_ECO27 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|259709872|sp|C4ZSB4|HIS6_ECOBW RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|12516206|gb|AAG57084.1|AE005427_12 imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH = imidazole glycerol phsphate synthase holoenzyme
           [Escherichia coli O157:H7 str. EDL933]
 gi|41714|emb|CAA31817.1| unnamed protein product [Escherichia coli K-12]
 gi|1736704|dbj|BAA15857.1| imidazole glycerol phosphate synthase, catalytic subunit with HisF
           [Escherichia coli str. K12 substr. W3110]
 gi|1788336|gb|AAC75086.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli str. K-12 substr. MG1655]
 gi|4867931|dbj|BAA77740.1| cyclase [Escherichia coli]
 gi|13362294|dbj|BAB36249.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia coli O157:H7 str. Sakai]
 gi|168986349|dbj|BAG11888.1| imidazole glycerol phosphate synthase [Escherichia coli O55:H7]
 gi|169889491|gb|ACB03198.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli str. K-12 substr. DH10B]
 gi|170517441|gb|ACB15619.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli SMS-3-5]
 gi|187769016|gb|EDU32860.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4196]
 gi|188014345|gb|EDU52467.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4113]
 gi|189000198|gb|EDU69184.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4076]
 gi|189355464|gb|EDU73883.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4401]
 gi|189361282|gb|EDU79701.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4486]
 gi|189365837|gb|EDU84253.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4501]
 gi|189371559|gb|EDU89975.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC869]
 gi|189378373|gb|EDU96789.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC508]
 gi|192931407|gb|EDV84008.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli E22]
 gi|208726290|gb|EDZ75891.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4206]
 gi|208730822|gb|EDZ79512.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4045]
 gi|208740148|gb|EDZ87830.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4042]
 gi|209159285|gb|ACI36718.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. EC4115]
 gi|209748176|gb|ACI72395.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia coli]
 gi|209748178|gb|ACI72396.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia coli]
 gi|209748180|gb|ACI72397.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia coli]
 gi|215265319|emb|CAS09714.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli O127:H6 str. E2348/69]
 gi|217317341|gb|EEC25770.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli O157:H7 str. TW14588]
 gi|222033795|emb|CAP76536.1| Imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli LF82]
 gi|238861502|gb|ACR63500.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli BW2952]
 gi|254593207|gb|ACT72568.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli O157:H7 str. TW14359]
 gi|257759783|dbj|BAI31280.1| imidazole glycerol phosphate synthase, catalytic subunit
           [Escherichia coli O103:H2 str. 12009]
 gi|260448874|gb|ACX39296.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli DH1]
 gi|300357734|gb|EFJ73604.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 198-1]
 gi|300399341|gb|EFJ82879.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 69-1]
 gi|300404116|gb|EFJ87654.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 84-1]
 gi|300412768|gb|EFJ96078.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 115-1]
 gi|300417476|gb|EFK00787.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 182-1]
 gi|300530884|gb|EFK51946.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 107-1]
 gi|300838255|gb|EFK66015.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 124-1]
 gi|300844298|gb|EFK72058.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 78-1]
 gi|305852247|gb|EFM52699.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli NC101]
 gi|309702350|emb|CBJ01672.1| imidazole glycerol phosphate synthase subunit [Escherichia coli
           ETEC H10407]
 gi|312946653|gb|ADR27480.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O83:H1 str. NRG 857C]
 gi|315136658|dbj|BAJ43817.1| imidazole glycerol phosphate synthase subunit [Escherichia coli
           DH1]
 gi|315253377|gb|EFU33345.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 85-1]
 gi|315296366|gb|EFU55666.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 16-3]
 gi|315618001|gb|EFU98593.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli 3431]
 gi|320191811|gb|EFW66459.1| Imidazole glycerol phosphate synthase cyclase subunit [Escherichia
           coli O157:H7 str. EC1212]
 gi|320641404|gb|EFX10851.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H7 str. G5101]
 gi|320646774|gb|EFX15653.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H- str. 493-89]
 gi|320652053|gb|EFX20398.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H- str. H 2687]
 gi|320668131|gb|EFX35003.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli O157:H7 str. LSU-61]
 gi|323936921|gb|EGB33204.1| imidazoleglycerol phosphate synthase [Escherichia coli E1520]
 gi|323948414|gb|EGB44398.1| imidazoleglycerol phosphate synthase [Escherichia coli H120]
 gi|323961793|gb|EGB57394.1| imidazoleglycerol phosphate synthase [Escherichia coli H489]
 gi|326338381|gb|EGD62209.1| Imidazole glycerol phosphate synthase cyclase subunit [Escherichia
           coli O157:H7 str. 1044]
 gi|326347098|gb|EGD70831.1| Imidazole glycerol phosphate synthase cyclase subunit [Escherichia
           coli O157:H7 str. 1125]
 gi|331056353|gb|EGI28362.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA206]
 gi|331078661|gb|EGI49863.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli H299]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|332262174|ref|XP_003280140.1| PREDICTED: HAUS augmin-like complex subunit 5-like [Nomascus
           leucogenys]
          Length = 460

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 242 PIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P+  R  +   R++     A +  Y  +H+HS   +++I  +++    G  +S + R  L
Sbjct: 21  PVAARAPESVLRRLCLGQGADIWAYILQHVHSQRTVKKIRGNLLWY--GHQDSPQVRRKL 78

Query: 298 TVEA--GASTATHHIIETAFNLM 318
            +EA      A    ++ +  LM
Sbjct: 79  ELEAAVTRLRAEIQELDQSLELM 101


>gi|319780224|ref|YP_004139700.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Mesorhizobium ciceri biovar biserrulae
           WSM1271]
 gi|317166112|gb|ADV09650.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Mesorhizobium ciceri biovar biserrulae
           WSM1271]
          Length = 247

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 18/129 (13%), Positives = 51/129 (39%), Gaps = 17/129 (13%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIWIHA 155
            +PD+V     A    +++ +  K      +   +  ++ +  L +  + +GV  I    
Sbjct: 108 RDPDLVRQACKAFPGKVAVGIDAKGGKVAVEGWAEASSLGVVELARKFEGAGVAAII--- 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL----PSVD 211
                       +  +  +++D   ++  +   + +  +GGL  ++  +++       ++
Sbjct: 165 ------YTDIDRDGVLTGINWDATIDLA-DAVSIPVIASGGLASIADIVRMTMPDAQKLE 217

Query: 212 GVMIGRAAY 220
           G + GRA Y
Sbjct: 218 GAISGRALY 226


>gi|326777879|ref|ZP_08237144.1| NADPH dehydrogenase [Streptomyces cf. griseus XylebKG-1]
 gi|326658212|gb|EGE43058.1| NADPH dehydrogenase [Streptomyces cf. griseus XylebKG-1]
          Length = 386

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 28/186 (15%), Positives = 56/186 (30%), Gaps = 37/186 (19%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA------VALRNLVKSI 143
           ++G  L+       + +AA   A+S   P+  +      D   A        L  L+  +
Sbjct: 211 AYGGDLVARTRFAAEIVAACRAAVSDAFPLFFRMSQWKADNYEAKLARTPQELDALLTPL 270

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLE 198
            ++GV+      R+  L         +  + D ++   ++K +         +GL+G   
Sbjct: 271 AEAGVDVFHASTRRYWL--------PEFEDSDLNLAGWVRKISGRPTLTVGSVGLDGDFF 322

Query: 199 DMSQA-------------LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
              Q                     D V +GRA   +               +  +P   
Sbjct: 323 SAFQGNDSEVTGIEQLLDRMERDEFDMVAVGRALIADPEWAAKT---LRGRTSDITPFTA 379

Query: 246 RVDKDF 251
            + K  
Sbjct: 380 EMLKTL 385


>gi|281179125|dbj|BAI55455.1| imidazole glycerol phosphate synthase subunit [Escherichia coli
           SE15]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|197264407|ref|ZP_03164481.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197242662|gb|EDY25282.1| imidazoleglycerol phosphate synthase, cyclase subunit [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K L    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKTLSFGADKISINSPALADPTLITRLADRFG 121


>gi|154687236|ref|YP_001422397.1| YrpB [Bacillus amyloliquefaciens FZB42]
 gi|154353087|gb|ABS75166.1| YrpB [Bacillus amyloliquefaciens FZB42]
          Length = 343

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 38/109 (34%), Gaps = 8/109 (7%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K +                K+ ++ G++ + +   +A     S    +  P L    +  
Sbjct: 139 KLKKSGCFLFGTATTPEEAKAFEERGMDAVILQGIEAGGHRGSFLPVKGEPALGLMALIP 198

Query: 182 IKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTT 228
             K+  ++ +   GG+ D    QA + L   DGV +G        +L  
Sbjct: 199 QAKDALNIPVIAAGGIFDRRGVQAARCL-GADGVQVG-----TPFLLCE 241


>gi|149280366|ref|ZP_01886487.1| dihydroorotate dehydrogenase [Pedobacter sp. BAL39]
 gi|149228915|gb|EDM34313.1| dihydroorotate dehydrogenase [Pedobacter sp. BAL39]
          Length = 342

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 18/129 (13%), Positives = 46/129 (35%), Gaps = 21/129 (16%)

Query: 96  CLMLNPDIVGDCIAAM-----CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            L     ++   +  +        +S P+ +K        +    L ++V+ + ++G+ G
Sbjct: 191 ALQEKEPLMH-ILNTLQQRNQKDGISRPILLKIAP----DLTNEQLDDIVEIVMETGIAG 245

Query: 151 IW----------IHARKAILKGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLED 199
           +           +H ++++L        + +     ++V  +  K N    I   GG+  
Sbjct: 246 VIATNTTIDRTGLHTKESVLNEAGGLSGKPLTKRSTEVVRYLSEKSNKAFPIIGVGGIHS 305

Query: 200 MSQALKILP 208
              A + L 
Sbjct: 306 PEDAKEKLD 314


>gi|118616770|ref|YP_905102.1| NADPH dependent 2,4-dienoyl-CoA reductase FadH [Mycobacterium
           ulcerans Agy99]
 gi|118568880|gb|ABL03631.1| NADPH dependent 2,4-dienoyl-CoA reductase FadH [Mycobacterium
           ulcerans Agy99]
          Length = 674

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 23/184 (12%), Positives = 56/184 (30%), Gaps = 20/184 (10%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
                A++ ++ GY+ + +             P       S+G           + +   
Sbjct: 145 DFARCAQLAQEAGYDGVEIMGSEGYLLNQFLAPRTNQRTDSWGGTPAKRRRFPVEIVRRT 204

Query: 112 CKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A+     +  R+     V+       +  L   ++ +G     I++     +   P  
Sbjct: 205 RAAVGPDFIICYRMSMADYVEGGQSWDEIVALATELESAGAT--IINSGFGWHEARIPTI 262

Query: 168 NRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS- 223
              +P+    +I   + ++     +  N  +     A +IL   D  +I   R    +  
Sbjct: 263 VTSVPSGAFVEISNAVAEQVSIPVMTSNR-INMPQAAEQILADTDVALISMARPMLSDPE 321

Query: 224 AMLT 227
            +L 
Sbjct: 322 WVLK 325


>gi|15807324|ref|NP_296054.1| NADH oxidase-like protein [Deinococcus radiodurans R1]
 gi|6460144|gb|AAF11879.1|AE002064_10 NADH oxidase-related protein [Deinococcus radiodurans R1]
          Length = 403

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 78/233 (33%), Gaps = 27/233 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              +A++ +  G+  + L+            P   V E  +G  L      + +   A+ 
Sbjct: 151 FARSARLAQRAGFGGVQLHAAHGYLLSQFLSPRHNVREDEYGGSLENRMRFLLETFDAVR 210

Query: 113 KALS--IPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAILKGLS 164
            A+    PV+VK      V           +V ++   G + I I    + +  ++ G  
Sbjct: 211 AAVGPHFPVSVKLNSSDFVRGGFSEDDSLAVVAALGARGCDLIEISGGTYEKPMMMLGQG 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
            +        D+          P       GG  D +   + L   + D V +GR    +
Sbjct: 271 ERGGFF---ADFAGRARAAAGVPLCVT---GGFRDAATIRQTLASGAADVVGLGRPLVAD 324

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRV-DKDFWRKISASMTDYAARHLHSGGKLQ 274
            A  +       +  +   P+KT +   D    +  +  + A R L  G +++
Sbjct: 325 PA-FSARMLRGEDVSSEVRPLKTGIGLLDGSGYLEIAWYEDAMRRLARGEQVR 376


>gi|157161518|ref|YP_001458836.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli HS]
 gi|300947338|ref|ZP_07161537.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 116-1]
 gi|167012157|sp|A8A1P9|HIS6_ECOHS RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|157067198|gb|ABV06453.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli HS]
 gi|300453055|gb|EFK16675.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 116-1]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|323161942|gb|EFZ47816.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli E128010]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|312201492|gb|ADQ44792.1| Inosine-5'-monophosphate dehydrogenase (IMPdehydrogenase) (IMPDH)
           (IMPD) [Borrelia burgdorferi 297]
          Length = 404

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 59/180 (32%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              + A+  EDF     +LN        ++   GA + ++ D +      +   + I V 
Sbjct: 120 DAYKNAEHKEDFSNACKDLN--------NKLRVGAAVSIDIDTIERVEELVKAHVDILVI 171

Query: 121 ----------------VKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                           +K +   +D     +  +     +  +G + + +          
Sbjct: 172 DSAHGHSTRIIELVKKIKTKYPNLDLIAGNIVTKEAALDLITAGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE+   N ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEVCN-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|301021893|ref|ZP_07185854.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 69-1]
 gi|300397809|gb|EFJ81347.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 69-1]
          Length = 672

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 31/230 (13%), Positives = 70/230 (30%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLMLN-----------------PDIVG---DCIAAMCKALSIPVT 120
                           L+                   P+ +    + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYPNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVGLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|292490223|ref|YP_003525662.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Nitrosococcus halophilus Nc4]
 gi|291578818|gb|ADE13275.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Nitrosococcus halophilus Nc4]
          Length = 246

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 30/155 (19%), Positives = 57/155 (36%), Gaps = 11/155 (7%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++     DD + +     +     ++G+  + +        G           ++ DI
Sbjct: 15  VRLRQGRMEDDTVFSDDPVAMALHWAEAGIERLHLVDLDGAFAGQ---------PVNADI 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV-DEYFSNP 236
           +Y I +  PD+ I + GG+ D       L   V  V+IG  A      +     E+  + 
Sbjct: 66  IYNIAQALPDMDIQVGGGIRDGDTIQTYLDAGVRYVIIGTKAINTPHFVADACLEFPGHV 125

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           + G    + ++  + W K+S       ARH    G
Sbjct: 126 ILGLDAREGKIAINGWSKLSRHNVVDIARHFEKDG 160


>gi|282854089|ref|ZP_06263426.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes J139]
 gi|282583542|gb|EFB88922.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes J139]
          Length = 307

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI E+ G   +      P+        G   M +PD++   I A    +SIPV  K RI
Sbjct: 44  AKIAENAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 97

Query: 126 --------------GVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                            D+   ++  +    I K                       G  
Sbjct: 98  GHFVEAQVLESLKVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 157

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 158 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 217

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 218 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 257


>gi|281413800|ref|ZP_06245542.1| 2,4-dienoyl-CoA reductase [Micrococcus luteus NCTC 2665]
          Length = 704

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 75/249 (30%), Gaps = 30/249 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVEA 65
           R  A+LL       +  +V+ + +R          +  +  E+ ++             A
Sbjct: 105 RILAQLLHAGRYAPSPDLVSASAVRAPISRHTPREMTTADIERTVSA---------FARA 155

Query: 66  AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           A +  + GY+ + +             P+       +G             +AA+ +AL 
Sbjct: 156 ATLALEAGYDGVEIMASEGYLLNQFLAPATNRRADEYGGDAERRRRFPVAVVAAVREALG 215

Query: 117 ----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + V       V D      + +  ++ + +G + +         +   P     +P
Sbjct: 216 ERGVLSVRTSAADLVPDGQTRAEIADTARAFEAAGADVLM--TGIGWHESRVPTIVTSVP 273

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDG-VMIGRAAYKNSAMLTTVD 230
              +           D+ +  +  L   ++A   L       V + R    +   +  + 
Sbjct: 274 RAAFLAASADLTAAVDIPVIASNRLTTPAEAEAALTSGAAALVGLARPLLADPEWMAAIS 333

Query: 231 EYFSNPLTG 239
           +  +  LT 
Sbjct: 334 DPRARTLTP 342


>gi|255026390|ref|ZP_05298376.1| NADH oxidase, putative [Listeria monocytogenes FSL J2-003]
          Length = 641

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|210634494|ref|ZP_03298121.1| hypothetical protein COLSTE_02043 [Collinsella stercoris DSM 13279]
 gi|210158795|gb|EEA89766.1| hypothetical protein COLSTE_02043 [Collinsella stercoris DSM 13279]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 35/108 (32%), Gaps = 13/108 (12%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           I A+ + + +PV    +I  + +   +       +++  +G   I +          +  
Sbjct: 72  IRAIKEKVDLPVVGIWKIDRNVKDVYLTPTLEAAQAVWDAGAEIIAL---------QATN 122

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGV 213
             R    L Y  + E+K   P+  I     +     A        D V
Sbjct: 123 HKRDDGLLSYKTIEEVKAAIPEALIFA--DVATAEDARIAAECGADFV 168


>gi|123451213|ref|XP_001313802.1| oxidoreductase, FAD/FMN-binding family protein [Trichomonas
           vaginalis G3]
 gi|121895698|gb|EAY00873.1| oxidoreductase, FAD/FMN-binding family protein [Trichomonas
           vaginalis G3]
          Length = 356

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 31/189 (16%), Positives = 65/189 (34%), Gaps = 21/189 (11%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           + AK ++  G + I L+            P     E  +G        I+ + + A+ K 
Sbjct: 144 QCAKRLQQVGVDGIELHGAHGYLISSFLSPMTNHREDQYGGSPENRRRILVEIVDAIRKE 203

Query: 115 LSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGLSPKDNRK 170
                 +  +I  DD     P +   +L  ++       +W +              NR 
Sbjct: 204 CGKDFVIGIKINGDDCKAGNPGIMPNDLAATMAAIPDMDLWEVSCGFQEASTTIRSTNRI 263

Query: 171 IPNLDYDI-------VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKN 222
           +   D+ +       +  I ++     IG+ GG+      +K L    D + +GR    +
Sbjct: 264 MRRKDFPLKEGYNVPIITIVRKTTKAAIGVVGGIRKTETMIKALEEGADLISLGRPTIAD 323

Query: 223 SAMLTTVDE 231
           + ++  + E
Sbjct: 324 THVVQHIRE 332


>gi|293446384|ref|ZP_06662806.1| imidazoleglycerol phosphate synthase [Escherichia coli B088]
 gi|291323214|gb|EFE62642.1| imidazoleglycerol phosphate synthase [Escherichia coli B088]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|239833149|ref|ZP_04681478.1| tryptophan synthase, alpha subunit [Ochrobactrum intermedium LMG
           3301]
 gi|239825416|gb|EEQ96984.1| tryptophan synthase, alpha subunit [Ochrobactrum intermedium LMG
           3301]
          Length = 279

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|284991294|ref|YP_003409848.1| NADH:flavin oxidoreductase/NADH oxidase [Geodermatophilus obscurus
           DSM 43160]
 gi|284064539|gb|ADB75477.1| NADH:flavin oxidoreductase/NADH oxidase [Geodermatophilus obscurus
           DSM 43160]
          Length = 677

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 64/190 (33%), Gaps = 22/190 (11%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC--------PSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
             +AA   +D G + I L            P+    E  +G             ++A+  
Sbjct: 151 FADAAVRCKDGGLDGIELMAYGHLLDAFWTPARNRREDEYGGSFENRMRFPLQVVSAIRA 210

Query: 114 ALSIPVTVKCRIGVD----DQIPAVALRNLVKSIKKSGVNGIW-----IHARKAILKGLS 164
           A+     V  R+  D    D + A     + + +  +G++        I     + + + 
Sbjct: 211 AVGEEFVVGVRMTFDEGRSDGLQADEALRIARELTGAGIDFFSVIKGFIDTDAELAQVIP 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
           P      P+L +       KEN D+ +     + D++ A   +    VD V + RA   +
Sbjct: 271 PMGTPAAPHLAFTGW---VKENVDVPVMHAAKIGDVATARYAVTGGLVDLVGMTRALIAD 327

Query: 223 SAMLTTVDEY 232
             +   V   
Sbjct: 328 PHLPNKVAAR 337


>gi|224593656|ref|YP_002640967.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi
           CA-11.2a]
 gi|224554940|gb|ACN56313.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi
           CA-11.2a]
 gi|312150022|gb|ADQ30082.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi N40]
          Length = 404

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 59/180 (32%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              + A+  EDF     +LN        ++   GA + ++ D +      +   + I V 
Sbjct: 120 DAYKNAEHKEDFPNACKDLN--------NKLRVGAAVSIDIDTIERVEELVKAHVDILVI 171

Query: 121 ----------------VKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                           +K +   +D     +  +     +   G + + +          
Sbjct: 172 DSAHGHSTRIIELVKKIKTKYPNLDLIAGNIVTKEAALDLISVGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|224498980|ref|ZP_03667329.1| NADH oxidase, putative [Listeria monocytogenes Finland 1988]
          Length = 641

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|254448909|ref|ZP_05062364.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium HTCC5015]
 gi|198261446|gb|EDY85736.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium HTCC5015]
          Length = 244

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 28/155 (18%), Positives = 54/155 (34%), Gaps = 11/155 (7%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++     DD + +     + +    +G   + +        G            + D+
Sbjct: 15  VRLRQGRMEDDTVFSDDPVAVARRWVDAGARRLHLVDLDGAFAG---------EPRNADV 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV-DEYFSNP 236
           V+ I +  P+L + + GG+         L   V  V++G  A      ++ V   Y  + 
Sbjct: 66  VHAICEAFPELPVQIGGGIRSEKTIETYLDAGVRYVILGSKAVAEPHFVSEVCLAYQGHI 125

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           + G      +V  D W K+S       A+H    G
Sbjct: 126 IVGLDAKNGKVATDGWSKLSRHDVIDMAQHFEEDG 160


>gi|226246798|ref|YP_002776132.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi 29805]
 gi|226201693|gb|ACO38285.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi 29805]
          Length = 404

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 59/180 (32%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVT 120
              + A+  EDF     +LN        ++   GA + ++ D +      +   + I V 
Sbjct: 120 DAYKNAEHKEDFPNACKDLN--------NKLRVGAAVSIDIDTIERVEELVKAHVDILVI 171

Query: 121 ----------------VKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                           +K +   +D     +  +     +   G + + +          
Sbjct: 172 DSAHGHSTRIIELVKKIKTKYPNLDLIAGNIVTKEAALDLISVGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|167043337|gb|ABZ08041.1| putative histidine biosynthesis protein [uncultured marine
           crenarchaeote HF4000_ANIW141N1]
          Length = 267

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +        L   + ++NR+I       V ++     ++   + GG++
Sbjct: 36  LAEKYSNEGADELV------FLDITASEENREIIRSLVTKVAKVI----NIPFTVGGGVK 85

Query: 199 DMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A  I L   D V I   A K   ++T + + F 
Sbjct: 86  TLQHARDILLSGADKVAINTGAVKKPGIITDLMDLFG 122


>gi|148825246|ref|YP_001289999.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittEE]
 gi|229846561|ref|ZP_04466669.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 7P49H1]
 gi|167012164|sp|A5UA15|HIS6_HAEIE RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|148715406|gb|ABQ97616.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae PittEE]
 gi|229810654|gb|EEP46372.1| imidazole glycerol phosphate synthase subunit HisF [Haemophilus
           influenzae 7P49H1]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D R +     + + ++     D+   + GG++
Sbjct: 35  LAQHYAQEGADELV------FYDITASSDGRTVDKSWVERIAQVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  +++ + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPTLISRLADRFG 121


>gi|118577206|ref|YP_876949.1| imidazoleglycerol-phosphate synthase, cyclase subunit [Cenarchaeum
           symbiosum A]
 gi|118195727|gb|ABK78645.1| imidazoleglycerol-phosphate synthase, cyclase subunit [Cenarchaeum
           symbiosum A]
          Length = 253

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K     G + +      A  +G              ++V ++     D+   + GG+
Sbjct: 23  ELAKKYSDEGADELVFLDITASDEGRGTLR---------ELVRDVA-SVIDIPFTVGGGI 72

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +S A +IL    D V I  AA K+ ++LT + E F 
Sbjct: 73  GSISDAREILRNGADKVAINTAAVKDPSILTGLMEIFG 110


>gi|121608899|ref|YP_996706.1| dihydroorotate dehydrogenase 2 [Verminephrobacter eiseniae EF01-2]
 gi|166215967|sp|A1WJ81|PYRD_VEREI RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|121553539|gb|ABM57688.1| dihydroorotate oxidase A [Verminephrobacter eiseniae EF01-2]
          Length = 360

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 75/208 (36%), Gaps = 28/208 (13%)

Query: 30  DAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAA--KIVEDFG----YNEINLNVGC 83
            A +   +++ L  +     L L IG    + + +A+   +    G     + + LN+  
Sbjct: 124 QAFVHNLQQSRLRAAGSALRLGLNIGKNASTPMAQASSDYLACLEGVYPHADYVALNISS 183

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIA-----AMCKALSIPVTVKCRIGVDDQIPAVALRN 138
           P+ +      G   + +  ++G         A      +PV VK    +D+   ++    
Sbjct: 184 PNTQNLRTLQGDAALDH--LLGAIAERRATLAARHGRRVPVFVKIAPDLDEAQLSL---- 237

Query: 139 LVKSIKKSGVNGIWIHARK---AILKGLSPKD------NRKIPNLDYDIVYEIKKENPD- 188
           +  ++++ G++G+         A+++G              +      ++ +++      
Sbjct: 238 MAATLQRHGIDGVIATNTTIDRAVVQGQRHAQESGGLSGAPVLQASNQVIGQLRAALGKG 297

Query: 189 LFIGLNGGLEDMSQAL-KILPSVDGVMI 215
             I   GG+     A+ KI    D V I
Sbjct: 298 FPIIGVGGIMSAEDAVSKIRAGADLVQI 325


>gi|47096852|ref|ZP_00234432.1| NADH oxidase, putative [Listeria monocytogenes str. 1/2a F6854]
 gi|254826876|ref|ZP_05231563.1| conserved hypothetical protein [Listeria monocytogenes FSL N3-165]
 gi|254831328|ref|ZP_05235983.1| NADH oxidase, putative [Listeria monocytogenes 10403S]
 gi|254899063|ref|ZP_05258987.1| NADH oxidase, putative [Listeria monocytogenes J0161]
 gi|254912796|ref|ZP_05262808.1| conserved hypothetical protein [Listeria monocytogenes J2818]
 gi|254937123|ref|ZP_05268820.1| conserved hypothetical protein [Listeria monocytogenes F6900]
 gi|47014771|gb|EAL05724.1| NADH oxidase, putative [Listeria monocytogenes str. 1/2a F6854]
 gi|258599256|gb|EEW12581.1| conserved hypothetical protein [Listeria monocytogenes FSL N3-165]
 gi|258609725|gb|EEW22333.1| conserved hypothetical protein [Listeria monocytogenes F6900]
 gi|293590791|gb|EFF99125.1| conserved hypothetical protein [Listeria monocytogenes J2818]
          Length = 641

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|169631485|ref|YP_001705134.1| PEP phosphonomutase and related enzymes [Mycobacterium abscessus
           ATCC 19977]
 gi|169243452|emb|CAM64480.1| PEP phosphonomutase and related enzymes [Mycobacterium abscessus]
          Length = 251

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 21/132 (15%), Positives = 49/132 (37%), Gaps = 11/132 (8%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             +AK+  D G+  + +    P A     +     M   D+V   ++ +  A+ +PV+V 
Sbjct: 30  AWSAKLAADAGFAALTVGSH-PLADSVGKADAEG-MSFDDVVAR-VSQITAAVDLPVSVD 86

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
              G      A   + L++ + ++G  G+ I      +     +      + D      +
Sbjct: 87  IESGY-----AQTAQRLIEGLIEAGAVGLNIE---DTVHSEGGRLREPQEHADLVGALRV 138

Query: 183 KKENPDLFIGLN 194
             +   + + +N
Sbjct: 139 AADQSGVPVVIN 150


>gi|145590433|ref|YP_001152435.1| imidazoleglycerol phosphate synthase, cyclase subunit [Pyrobaculum
           arsenaticum DSM 13514]
 gi|145282201|gb|ABP49783.1| imidazole glycerol phosphate synthase subunit hisF [Pyrobaculum
           arsenaticum DSM 13514]
          Length = 251

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 11/102 (10%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +    ++ G + I I    A  +G S            + V  +  E   + + + GG+
Sbjct: 35  EMAVRYEEEGADEIAILDITATPEGRSTF---------VESVRRVA-EAVSIPVLVGGGV 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT 238
             +  A  +     D V +  AA KN  +++ +   F +  T
Sbjct: 85  RGIEDAAALFKAGADKVSVNTAAVKNPRLVSEIAREFGSQST 126


>gi|194334240|ref|YP_002016100.1| inosine-5'-monophosphate dehydrogenase [Prosthecochloris aestuarii
           DSM 271]
 gi|194312058|gb|ACF46453.1| inosine-5'-monophosphate dehydrogenase [Prosthecochloris aestuarii
           DSM 271]
          Length = 496

 Score = 37.1 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 23/135 (17%), Positives = 41/135 (30%), Gaps = 29/135 (21%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
           VGD +  + +             +      VA    V+ +  +G + + +          
Sbjct: 263 VGDMVKTIKQH---------YPDLQIVAGNVATPEAVRDLIAAGADAVKVGIGPGSICTT 313

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
            I+ G+       I N   +             I  +GG++     A  I    D VMIG
Sbjct: 314 RIVAGVGMPQLTAIMNCSEEAAK------TGTPIIADGGIKYSGDLAKAIAAGADSVMIG 367

Query: 217 RAAYKNSAMLTTVDE 231
                  ++    DE
Sbjct: 368 -------SIFAGTDE 375


>gi|319936809|ref|ZP_08011221.1| tryptophan synthase subunit alpha [Coprobacillus sp. 29_1]
 gi|319808077|gb|EFW04649.1| tryptophan synthase subunit alpha [Coprobacillus sp. 29_1]
          Length = 253

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 27/177 (15%), Positives = 59/177 (33%), Gaps = 47/177 (26%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI-------- 153
           D V D +  + +   IP+   C +   + +         +  ++ GV+GI I        
Sbjct: 74  DQVFDIVMNVRQCSQIPI---CLMTYLNPVFHYQYDKFFQKCQEVGVDGIIIPDCPYEES 130

Query: 154 --------HARKAILKGLSPKDNRKIPNLDYDI---VYEI-------------------- 182
                        ++  ++P    ++  +  +    +Y +                    
Sbjct: 131 QEVKKIAKVYGITVISMIAPTSQDRVKMIAKEAEGFIYLVSSMGVTGVRQDIHTDVSKIV 190

Query: 183 --KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
              K   D+ + +  G+    QA ++    DGV++G A  K   ++    E+  N L
Sbjct: 191 HNIKAVTDIPVAIGFGIHSPDQAQEMRKYADGVIVGSAIVK---IIAQYGEHAHNAL 244


>gi|306825014|ref|ZP_07458357.1| dihydroorotate dehydrogenase A [Streptococcus sp. oral taxon 071
           str. 73H25AP]
 gi|304432841|gb|EFM35814.1| dihydroorotate dehydrogenase A [Streptococcus sp. oral taxon 071
           str. 73H25AP]
          Length = 311

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 61/176 (34%), Gaps = 19/176 (10%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + G    +     K V++ G+  +  LN+ CP   V      A    + +     +A + 
Sbjct: 101 LVGMSPEETHTILKKVQESGFKGLTELNLSCP--NVPGKPQIAY---DFETTDRILAEVF 155

Query: 113 KALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHARKAILK---G 162
              + P+ +K     D      A A+ N      V  +   G NG++I     +++   G
Sbjct: 156 AYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDESVVIRPKNG 214

Query: 163 LSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIG 216
                   I       V+   +  NP + I   GG+     A +  L     V +G
Sbjct: 215 FGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGASMVQVG 270


>gi|255017438|ref|ZP_05289564.1| hypothetical protein LmonF_06033 [Listeria monocytogenes FSL
           F2-515]
          Length = 293

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEDVRVVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|182437258|ref|YP_001824977.1| putative oxidoreductase [Streptomyces griseus subsp. griseus NBRC
           13350]
 gi|178465774|dbj|BAG20294.1| putative oxidoreductase [Streptomyces griseus subsp. griseus NBRC
           13350]
          Length = 377

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 28/186 (15%), Positives = 56/186 (30%), Gaps = 37/186 (19%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA------VALRNLVKSI 143
           ++G  L+       + +AA   A+S   P+  +      D   A        L  L+  +
Sbjct: 202 AYGGDLVARTRFAAEIVAACRAAVSDAFPLFFRMSQWKADNYEAKLARTPQELDALLTPL 261

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF-----IGLNGGLE 198
            ++GV+      R+  L         +  + D ++   ++K +         +GL+G   
Sbjct: 262 AEAGVDVFHASTRRYWL--------PEFEDSDLNLAGWVRKISGRPTLTVGSVGLDGDFF 313

Query: 199 DMSQA-------------LKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKT 245
              Q                     D V +GRA   +               +  +P   
Sbjct: 314 SAFQGNDSKVTGIEQLLDRMERDEFDMVAVGRALIADPEWAAKT---LRGRTSDITPFTA 370

Query: 246 RVDKDF 251
            + K  
Sbjct: 371 EMLKTL 376


>gi|163844124|ref|YP_001628528.1| tryptophan synthase subunit alpha [Brucella suis ATCC 23445]
 gi|189040518|sp|B0CJK6|TRPA_BRUSI RecName: Full=Tryptophan synthase alpha chain
 gi|163674847|gb|ABY38958.1| tryptophan synthase, alpha subunit [Brucella suis ATCC 23445]
          Length = 279

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|297618893|ref|YP_003706998.1| putative phospho-2-dehydro-3-deoxyheptonate aldolase [Methanococcus
           voltae A3]
 gi|297377870|gb|ADI36025.1| predicted phospho-2-dehydro-3-deoxyheptonate aldolase
           [Methanococcus voltae A3]
          Length = 274

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 16/100 (16%), Positives = 29/100 (29%), Gaps = 16/100 (16%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNV------------GCPSARVHEGSFGACLMLNPDIVG 105
           D   +  AA++  + G + I  N             GCP   V  G          +   
Sbjct: 164 DPEYVAHAARLGAELGADIIKTNYTGDIDSFREVVRGCPVPIVIAGGPKT---NTDEEFL 220

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
             +     A +I V    R     +  +   R + + +  
Sbjct: 221 QMVKDAISAGAIGV-ASGRNVFQHRDVSGITRAICRIVHD 259


>gi|301062391|ref|ZP_07203052.1| isopentenyl-diphosphate delta-isomerase, type 2 [delta
           proteobacterium NaphS2]
 gi|300443504|gb|EFK07608.1| isopentenyl-diphosphate delta-isomerase, type 2 [delta
           proteobacterium NaphS2]
          Length = 352

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 64/167 (38%), Gaps = 29/167 (17%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           L E  ++V+  G + + L +  P  +V +G      +    +       +CK LS+PV V
Sbjct: 146 LEECERVVDMIGADALMLYLN-PMQKVFQGGGN---IKFRGLAEKI-GYICKHLSVPVIV 200

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------KAILKG------LSPKD 167
           K  +G      A  L      +KK+GV+ + +              LKG       +  D
Sbjct: 201 K-EVGFGLSDSAAML------LKKAGVSMLDVAGSGGTSWVKITRYLKGDFSAAANAHFD 253

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
              +P  D   +  + +   D+ I  +GG+ + +  A  +      V
Sbjct: 254 GWGVPTAD--ALISLCEVVKDIPIIASGGIRNGVHMAKAMALGASYV 298


>gi|148560647|ref|YP_001259908.1| tryptophan synthase subunit alpha [Brucella ovis ATCC 25840]
 gi|166200490|sp|A5VT61|TRPA_BRUO2 RecName: Full=Tryptophan synthase alpha chain
 gi|148371904|gb|ABQ61883.1| tryptophan synthase, alpha subunit [Brucella ovis ATCC 25840]
          Length = 279

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|319955624|ref|YP_004166891.1| imidazole glycerol phosphate synthase subunit hisf [Cellulophaga
           algicola DSM 14237]
 gi|319424284|gb|ADV51393.1| Imidazole glycerol phosphate synthase subunit hisF [Cellulophaga
           algicola DSM 14237]
          Length = 251

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 23/139 (16%), Positives = 51/139 (36%), Gaps = 11/139 (7%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L +    SG + +        L   + ++ RK      D+VY + ++  ++   + GG+
Sbjct: 34  ELAEIYANSGADELV------FLDISATEERRKTLA---DLVYRVAEKV-NIPFTVGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +     +L    D V I  +A KN  ++  +   F       +    R+D ++   + 
Sbjct: 84  ASIEDVDILLQNGADKVSINSSAVKNPQLINELSAKFGAQCIVVAIDAKRIDGEWIVHLV 143

Query: 257 ASMTDYAARHLHSGGKLQQ 275
                   R      +++Q
Sbjct: 144 GGKVPTEIRLFDWAKEVEQ 162


>gi|222100504|ref|YP_002535072.1| Imidazole glycerol phosphate synthase subunit hisF [Thermotoga
           neapolitana DSM 4359]
 gi|221572894|gb|ACM23706.1| Imidazole glycerol phosphate synthase subunit hisF [Thermotoga
           neapolitana DSM 4359]
          Length = 242

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V ++ ++  D+   + GG+ D   A + IL   D V I  AA +   ++T + E F +
Sbjct: 53  ELVEKVAEQI-DIPFTVGGGIHDFETASELILRGADKVSINTAAVEKPDLITRIAETFGS 111

Query: 236 PLTGSSPIKTRVDKDF 251
                +    R+D DF
Sbjct: 112 QAVVVAIDAKRMDGDF 127


>gi|70726537|ref|YP_253451.1| tryptophan synthase subunit alpha [Staphylococcus haemolyticus
           JCSC1435]
 gi|123660154|sp|Q4L680|TRPA_STAHJ RecName: Full=Tryptophan synthase alpha chain
 gi|68447261|dbj|BAE04845.1| tryptophan synthase alpha chain [Staphylococcus haemolyticus
           JCSC1435]
          Length = 243

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/116 (16%), Positives = 41/116 (35%), Gaps = 11/116 (9%)

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           PD+  +    +   +S    VK    +        ++ +VK  +   +  + ++A     
Sbjct: 110 PDLPYELTQKLKHKISK-FDVKVISLISMTANDDRIKEIVKHAEGF-IYTVTMNATTGKN 167

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
               P+   K+ +L         K + D+ +    G+        +    DGV+IG
Sbjct: 168 GTFHPQLKDKLKHL---------KAHTDIPVVAGFGIRTKEHIKDLATVADGVVIG 214


>gi|117624228|ref|YP_853141.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli APEC O1]
 gi|188492054|ref|ZP_02999324.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli 53638]
 gi|227887074|ref|ZP_04004879.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli 83972]
 gi|237704481|ref|ZP_04534962.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia sp. 3_2_53FAA]
 gi|300824741|ref|ZP_07104846.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 119-7]
 gi|300936669|ref|ZP_07151573.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 21-1]
 gi|331647674|ref|ZP_08348766.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli M605]
 gi|331673558|ref|ZP_08374321.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA280]
 gi|167012158|sp|A1ACN7|HIS6_ECOK1 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|115513352|gb|ABJ01427.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia coli APEC O1]
 gi|188487253|gb|EDU62356.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli 53638]
 gi|226900847|gb|EEH87106.1| imidazole glycerol phosphate synthase subunit in heterodimer with
           HisH [Escherichia sp. 3_2_53FAA]
 gi|227835424|gb|EEJ45890.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli 83972]
 gi|300458250|gb|EFK21743.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 21-1]
 gi|300522728|gb|EFK43797.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 119-7]
 gi|307554093|gb|ADN46868.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli ABU 83972]
 gi|323951779|gb|EGB47653.1| imidazoleglycerol phosphate synthase [Escherichia coli H252]
 gi|324008890|gb|EGB78109.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 57-2]
 gi|330911863|gb|EGH40373.1| imidazole glycerol phosphate synthase cyclase subunit [Escherichia
           coli AA86]
 gi|331043398|gb|EGI15536.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli M605]
 gi|331068831|gb|EGI40223.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA280]
          Length = 258

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|110632456|ref|YP_672664.1| dihydroorotate dehydrogenase 2 [Mesorhizobium sp. BNC1]
 gi|123354074|sp|Q11M76|PYRD_MESSB RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|110283440|gb|ABG61499.1| dihydroorotate oxidase A [Chelativorans sp. BNC1]
          Length = 363

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 24/129 (18%), Positives = 55/129 (42%), Gaps = 15/129 (11%)

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           + L+     V +  AA+ K   +PV +K    + ++    AL ++ + + + G++G+ + 
Sbjct: 190 SELLQRVMRVRNEQAALIKR-KVPVFLKIAPDLSEE----ALADIAQEVLEKGLDGLIVS 244

Query: 155 ARKAILKGLSPKDNRKIPNLDYD--------IVYEIKKEN-PDLFIGLNGGLEDMSQALK 205
                 +G+S     +   L  +        ++ ++++   P L I   GG+     AL+
Sbjct: 245 NTTLSREGVSAPAASETGGLSGEPLFERSTIVLAKMRRLVGPALPIIGVGGVHSAETALE 304

Query: 206 -ILPSVDGV 213
            +    D V
Sbjct: 305 KMRAGADLV 313


>gi|324514029|gb|ADY45738.1| NADH oxidase [Ascaris suum]
 gi|324514381|gb|ADY45849.1| NADH oxidase [Ascaris suum]
          Length = 437

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 74/244 (30%), Gaps = 47/244 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCI 108
            +   AA  V+D G++ + +NVG                     +G  L     I+ + I
Sbjct: 165 ERYAYAAGFVKDCGFHGVEINVG--MDFALAQLVTATTNSRNDEYGGSLENRTRILFEVI 222

Query: 109 AAMCKAL--SIPVTVKCRI---GVDDQIPAVALRNLVKSIKKS--------GVNGIWIHA 155
            ++   +       +  ++     +D           K +  +        G N   I  
Sbjct: 223 NSIRDRVKDDKNFVLGLKLSSLNYEDGYDECEFERFCKRLDATKLDYVVITGANYEAIRQ 282

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R+ I +  S K           +   IK+        L GG     Q  + +     DG+
Sbjct: 283 REKIERDPSRKSEAFFVKFVIAVRTNIKRAKT----FLCGGFRAADQMWEAIYEGWTDGI 338

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+ R       +   +    +  +TG+            +K      DY      +G ++
Sbjct: 339 MVARPLAAEPDLPRRI---LNREVTGA------------KKSLLDEIDYGLSEYAAGTQM 383

Query: 274 QQIT 277
            Q+ 
Sbjct: 384 WQLA 387


>gi|309365875|emb|CAP22634.2| hypothetical protein CBG_01351 [Caenorhabditis briggsae AF16]
          Length = 451

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 27/196 (13%), Positives = 65/196 (33%), Gaps = 19/196 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDI 103
           QI    + + V AAK   + G++ I L             P+       +G  L     +
Sbjct: 168 QIKTEVVDRFVYAAKYAYECGFDGIQLHGAHGYLLTQFTSPTTNNRTDKYGGSLENRNRV 227

Query: 104 VGDCIAAMCKALS------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + +   A+ + +       + +    +   +        R+L  + +K G + + +    
Sbjct: 228 IIEIYEAIRREVPESTGFLVGIKSNSKEFQEKGTTVNDARDLCAAYEKHGFDFVELTGGT 287

Query: 158 A-ILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           A        +++ KI    + +    I+    +  + L GG   +   +  +      G+
Sbjct: 288 AEKYVFAHERESTKIREAFFVEFADAIRPVFKNTVLYLTGGFRTVGAMIDAVEKNTTQGI 347

Query: 214 MIGRAAYKNSAMLTTV 229
            + R A     +   +
Sbjct: 348 GLARPATAEPDLPKKI 363


>gi|309807401|ref|ZP_07701364.1| dihydroorotate oxidase, catalytic subunit domain protein
           [Lactobacillus iners LactinV 01V1-a]
 gi|309809670|ref|ZP_07703526.1| putative dihydroorotate oxidase, catalytic subunit [Lactobacillus
           iners SPIN 2503V10-D]
 gi|308169323|gb|EFO71378.1| dihydroorotate oxidase, catalytic subunit domain protein
           [Lactobacillus iners LactinV 01V1-a]
 gi|308170030|gb|EFO72067.1| putative dihydroorotate oxidase, catalytic subunit [Lactobacillus
           iners SPIN 2503V10-D]
          Length = 114

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 7/92 (7%)

Query: 150 GIWIHARKAIL-KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
           GI I   KA L  G        I  +   +V ++ +    L I   GG+E     ++ +L
Sbjct: 9   GIDIKTHKATLGNGFGGWSGSAIKPVAVRMVAQVHQAV-KLPIIGMGGIETAEDIVEFML 67

Query: 208 PSVDGVMIGRAAYKN----SAMLTTVDEYFSN 235
                V +G A +K+      ++  ++   + 
Sbjct: 68  AGASAVAVGTAHFKDGLAIPHLVADLETLLNE 99


>gi|306842781|ref|ZP_07475422.1| tryptophan synthase, alpha subunit [Brucella sp. BO2]
 gi|306287054|gb|EFM58562.1| tryptophan synthase, alpha subunit [Brucella sp. BO2]
          Length = 279

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|257868711|ref|ZP_05648364.1| F420-dependent NADP oxidoreductase [Enterococcus gallinarum EG2]
 gi|257802875|gb|EEV31697.1| F420-dependent NADP oxidoreductase [Enterococcus gallinarum EG2]
          Length = 225

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 11/68 (16%)

Query: 34  RGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
             D ++    +      A+ I G D   + + AKIV+DFG++ + +           G  
Sbjct: 134 YHDVQDEARPAGSPDRKAMAIAGNDPESMSQTAKIVDDFGFDPVVI-----------GRL 182

Query: 94  GACLMLNP 101
              LML P
Sbjct: 183 ANGLMLEP 190


>gi|269120787|ref|YP_003308964.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Sebaldella termitidis ATCC 33386]
 gi|268614665|gb|ACZ09033.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Sebaldella termitidis ATCC 33386]
          Length = 237

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
           +++ +  +  EN DLFI + GG+ +  +  K L   V+ V++G AA +N   L  +   +
Sbjct: 62  NFETIKMLV-ENSDLFIQVGGGIRNEERIKKYLELGVNRVILGTAAIENPEFLVEMVHKY 120

Query: 234 SN 235
            +
Sbjct: 121 KD 122


>gi|225853535|ref|YP_002733768.1| tryptophan synthase subunit alpha [Brucella melitensis ATCC 23457]
 gi|256262981|ref|ZP_05465513.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 2 str.
           63/9]
 gi|254789192|sp|C0RFZ2|TRPA_BRUMB RecName: Full=Tryptophan synthase alpha chain
 gi|225641900|gb|ACO01814.1| tryptophan synthase, alpha subunit [Brucella melitensis ATCC 23457]
 gi|263092854|gb|EEZ17029.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 2 str.
           63/9]
 gi|326410104|gb|ADZ67169.1| tryptophan synthase subunit alpha [Brucella melitensis M28]
 gi|326539821|gb|ADZ88036.1| tryptophan synthase, alpha subunit [Brucella melitensis M5-90]
          Length = 279

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|218245079|ref|YP_002370450.1| dihydroorotate dehydrogenase 2 [Cyanothece sp. PCC 8801]
 gi|257058101|ref|YP_003135989.1| dihydroorotate dehydrogenase 2 [Cyanothece sp. PCC 8802]
 gi|218165557|gb|ACK64294.1| dihydroorotate dehydrogenase [Cyanothece sp. PCC 8801]
 gi|256588267|gb|ACU99153.1| dihydroorotate dehydrogenase [Cyanothece sp. PCC 8802]
          Length = 339

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 27/99 (27%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI--------VGDCIAAMCKALSI 117
           A+ ++  G + + LN+               +  + DI          D +  +  AL+I
Sbjct: 121 AQQIQQAGADALELNI-------------YYVPTDLDIPGGEVEQNYLDILKNVKAALNI 167

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           PV +K      +      + N+ K + ++G +GI +  R
Sbjct: 168 PVAIKISPYFSN------MANMAKRLAEAGADGIVLFNR 200


>gi|167757136|ref|ZP_02429263.1| hypothetical protein CLORAM_02685 [Clostridium ramosum DSM 1402]
 gi|167703311|gb|EDS17890.1| hypothetical protein CLORAM_02685 [Clostridium ramosum DSM 1402]
          Length = 332

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 29/179 (16%), Positives = 63/179 (35%), Gaps = 25/179 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEGSF------------GACLMLNPDIVGDCIA 109
             +AA+ V+  G++ + ++     A +    +            G  L     I  + I 
Sbjct: 150 FADAARRVKLAGFDGVEIHSA--HAYLLNQFYSPITNHRTDEYTGTTLEGRLRIHKEVIE 207

Query: 110 AMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+   +     +  R+G  D               + ++  GV+ + I            
Sbjct: 208 AVRSEVGEDFPIALRLGGCDYMAGGSTIEDSIKASQMLESYGVDILDITGGINRYMIPWN 267

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKN 222
           K+     ++   I+ ++      + + L GG+ +   A K+L     D + +GRA  K+
Sbjct: 268 KEPGYFSDMTEHIMEKV-----SIPVILTGGITNAMDAEKLLQLNKADLIGVGRAILKD 321


>gi|153008148|ref|YP_001369363.1| tryptophan synthase subunit alpha [Ochrobactrum anthropi ATCC
           49188]
 gi|166200570|sp|A6WX30|TRPA_OCHA4 RecName: Full=Tryptophan synthase alpha chain
 gi|151560036|gb|ABS13534.1| tryptophan synthase, alpha subunit [Ochrobactrum anthropi ATCC
           49188]
          Length = 279

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|62389677|ref|YP_225079.1| pyridoxal biosynthesis lyase PdxS [Corynebacterium glutamicum ATCC
           13032]
 gi|41325012|emb|CAF19493.1| Pyridoxine biosynthesis enzyme [Corynebacterium glutamicum ATCC
           13032]
          Length = 299

 Score = 37.1 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 35/97 (36%), Gaps = 8/97 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K RI
Sbjct: 36  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 89

Query: 126 GVDDQIPAVALR--NLVKSIKKSGVNGIWIHARKAIL 160
           G   +   +     + +   +         H  K   
Sbjct: 90  GHFVEAQVLEALGVDFIDESEVLSPADYTHHINKWKF 126


>gi|291618027|ref|YP_003520769.1| HisF [Pantoea ananatis LMG 20103]
 gi|291153057|gb|ADD77641.1| HisF [Pantoea ananatis LMG 20103]
 gi|327394429|dbj|BAK11851.1| Imidazole glycerol phosphate synthase subunit HisF [Pantoea
           ananatis AJ13355]
          Length = 258

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +            +  D+R +       V E+     D+   + GG++
Sbjct: 35  LAQRYAEEGADELV------FYDITASSDDRVVDKSWVSRVAEVI----DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  + +++T + + F 
Sbjct: 85  TPEDAARILEFGADKISINSPALADPSLITRLADRFG 121


>gi|256112431|ref|ZP_05453352.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 3 str.
           Ether]
 gi|265993869|ref|ZP_06106426.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 3 str.
           Ether]
 gi|262764850|gb|EEZ10771.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 3 str.
           Ether]
          Length = 279

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|15894331|ref|NP_347680.1| NADH:flavin oxidoreductase, NADH oxidase [Clostridium
           acetobutylicum ATCC 824]
 gi|15023957|gb|AAK79020.1|AE007620_1 NADH:flavin oxidoreductase, possible NADH oxidase [Clostridium
           acetobutylicum ATCC 824]
 gi|325508459|gb|ADZ20095.1| NADH:flavin oxidoreductase, possible NADH oxidase [Clostridium
           acetobutylicum EA 2018]
          Length = 656

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 22/142 (15%), Positives = 51/142 (35%), Gaps = 13/142 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-------QIPAVAL---RNLVKS 142
           +G       + V + +  +  A      +  R+ VD+       +   + L     + + 
Sbjct: 190 YGGSFEKRFNFVKEVVLGIKNACGQDYPISVRLTVDELLNLNGVKQEYLDLNMGIKICRE 249

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++K GV+ I +            +          + +  +K+      I +N  +++   
Sbjct: 250 LEKIGVDVINVSNGIYETFNSLSEPMTYDQGCRTERIKAVKEAVEIPVIAVN-MIKEPWF 308

Query: 203 ALKILPS--VDGVMIGRAAYKN 222
           A K+L    VD + +GRA   +
Sbjct: 309 AEKMLEDKLVDFIGLGRALVAD 330


>gi|23502956|ref|NP_699083.1| tryptophan synthase subunit alpha [Brucella suis 1330]
 gi|161620019|ref|YP_001593906.1| tryptophan synthase subunit alpha [Brucella canis ATCC 23365]
 gi|254700737|ref|ZP_05162565.1| tryptophan synthase subunit alpha [Brucella suis bv. 5 str. 513]
 gi|254705109|ref|ZP_05166937.1| tryptophan synthase subunit alpha [Brucella suis bv. 3 str. 686]
 gi|254707375|ref|ZP_05169203.1| tryptophan synthase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|254709083|ref|ZP_05170894.1| tryptophan synthase subunit alpha [Brucella pinnipedialis B2/94]
 gi|254713490|ref|ZP_05175301.1| tryptophan synthase subunit alpha [Brucella ceti M644/93/1]
 gi|254716154|ref|ZP_05177965.1| tryptophan synthase subunit alpha [Brucella ceti M13/05/1]
 gi|256030608|ref|ZP_05444222.1| tryptophan synthase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|256060070|ref|ZP_05450252.1| tryptophan synthase subunit alpha [Brucella neotomae 5K33]
 gi|256370506|ref|YP_003108017.1| tryptophan synthase subunit alpha [Brucella microti CCM 4915]
 gi|260567421|ref|ZP_05837891.1| tryptophan synthase subunit alpha [Brucella suis bv. 4 str. 40]
 gi|261217927|ref|ZP_05932208.1| tryptophan synthase subunit alpha [Brucella ceti M13/05/1]
 gi|261314858|ref|ZP_05954055.1| tryptophan synthase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|261316584|ref|ZP_05955781.1| tryptophan synthase subunit alpha [Brucella pinnipedialis B2/94]
 gi|261321223|ref|ZP_05960420.1| tryptophan synthase subunit alpha [Brucella ceti M644/93/1]
 gi|261324047|ref|ZP_05963244.1| tryptophan synthase subunit alpha [Brucella neotomae 5K33]
 gi|261751249|ref|ZP_05994958.1| tryptophan synthase subunit alpha [Brucella suis bv. 5 str. 513]
 gi|261755814|ref|ZP_05999523.1| tryptophan synthase subunit alpha [Brucella suis bv. 3 str. 686]
 gi|265987656|ref|ZP_06100213.1| tryptophan synthase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|294851334|ref|ZP_06792007.1| tryptophan synthase subunit alpha [Brucella sp. NVSL 07-0026]
 gi|306843525|ref|ZP_07476126.1| tryptophan synthase, alpha subunit [Brucella sp. BO1]
 gi|38258595|sp|Q8FXY6|TRPA_BRUSU RecName: Full=Tryptophan synthase alpha chain
 gi|189040517|sp|A9M9U0|TRPA_BRUC2 RecName: Full=Tryptophan synthase alpha chain
 gi|23348992|gb|AAN30998.1| tryptophan synthase, alpha subunit [Brucella suis 1330]
 gi|161336830|gb|ABX63135.1| tryptophan synthase, alpha subunit [Brucella canis ATCC 23365]
 gi|256000669|gb|ACU49068.1| tryptophan synthase subunit alpha [Brucella microti CCM 4915]
 gi|260156939|gb|EEW92019.1| tryptophan synthase subunit alpha [Brucella suis bv. 4 str. 40]
 gi|260923016|gb|EEX89584.1| tryptophan synthase subunit alpha [Brucella ceti M13/05/1]
 gi|261293913|gb|EEX97409.1| tryptophan synthase subunit alpha [Brucella ceti M644/93/1]
 gi|261295807|gb|EEX99303.1| tryptophan synthase subunit alpha [Brucella pinnipedialis B2/94]
 gi|261300027|gb|EEY03524.1| tryptophan synthase subunit alpha [Brucella neotomae 5K33]
 gi|261303884|gb|EEY07381.1| tryptophan synthase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|261741002|gb|EEY28928.1| tryptophan synthase subunit alpha [Brucella suis bv. 5 str. 513]
 gi|261745567|gb|EEY33493.1| tryptophan synthase subunit alpha [Brucella suis bv. 3 str. 686]
 gi|264659853|gb|EEZ30114.1| tryptophan synthase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|294819923|gb|EFG36922.1| tryptophan synthase subunit alpha [Brucella sp. NVSL 07-0026]
 gi|306276216|gb|EFM57916.1| tryptophan synthase, alpha subunit [Brucella sp. BO1]
          Length = 279

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|17988302|ref|NP_540936.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 1 str.
           16M]
 gi|17984074|gb|AAL53200.1| tryptophan synthase alpha chain [Brucella melitensis bv. 1 str.
           16M]
          Length = 303

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 220 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 271


>gi|260173861|ref|ZP_05760273.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. D2]
 gi|315922124|ref|ZP_07918364.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313695999|gb|EFS32834.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 325

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 27/169 (15%), Positives = 58/169 (34%), Gaps = 25/169 (14%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK++E+ G + + +N+    + V    +G+    + D     +  + K + IPV +K   
Sbjct: 115 AKMIEEAGADALEINILALQSEVQYT-YGSFEQRHID----ILRHIKKTIKIPVIMKL-- 167

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAILKGLSPKDNRKIP----NL 174
                        L+  +  +G   + +  R          ++ +S +           L
Sbjct: 168 ----GDNLTNPVALIDQLYANGAAAVVLFNRFYQPDINIEKMEHISGEIFSNASDLAIPL 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKN 222
            +  +     +  D     +GG+ +       IL     V +  A Y N
Sbjct: 224 RWIGIASAVVDKIDY--AASGGVANAESVVKAILAGASAVEVCSAVYLN 270


>gi|169632210|ref|YP_001705946.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii SDF]
 gi|226700273|sp|B0VPB7|HIS4_ACIBS RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|169151002|emb|CAO99635.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter baumannii]
          Length = 243

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 42/130 (32%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +  L    +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDLVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I K  P+L I + GG+  +      L   V  V+IG  A +    
Sbjct: 60  ------PIHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLEAGVTFVIIGTKAVQEPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKSFAG 123


>gi|90021106|ref|YP_526933.1| inosine-5'-monophosphate dehydrogenase [Saccharophagus degradans
           2-40]
 gi|89950706|gb|ABD80721.1| inosine-5'-monophosphate dehydrogenase [Saccharophagus degradans
           2-40]
          Length = 556

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 5/87 (5%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD--LF 190
            +A  +  K++ ++G +G+ +      +          +P +    +  +     D  + 
Sbjct: 341 NIATADAAKALVEAGADGVKVGIGPGSICTTRIVTGVGVPQI--SAIANVVDALKDTGVP 398

Query: 191 IGLNGGL-EDMSQALKILPSVDGVMIG 216
           +  +GG+      A  I+   D VM+G
Sbjct: 399 VIADGGVRFSGDVAKAIVAGADCVMMG 425


>gi|163846417|ref|YP_001634461.1| NADH:flavin oxidoreductase/NADH oxidase [Chloroflexus aurantiacus
           J-10-fl]
 gi|222524186|ref|YP_002568657.1| NADH:flavin oxidoreductase/NADH oxidase [Chloroflexus sp. Y-400-fl]
 gi|163667706|gb|ABY34072.1| NADH:flavin oxidoreductase/NADH oxidase [Chloroflexus aurantiacus
           J-10-fl]
 gi|222448065|gb|ACM52331.1| NADH:flavin oxidoreductase/NADH oxidase [Chloroflexus sp. Y-400-fl]
          Length = 354

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 22/157 (14%), Positives = 54/157 (34%), Gaps = 13/157 (8%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSG 147
           ++G  L     ++ +   A+  A    + +  R+   D  P          + + +++ G
Sbjct: 198 AYGGDLRGRARLLLEVTDAVRAAWPAQLPLAVRLSCSDWTPEGLTIADTVEVARMLRERG 257

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           V+ I   +      G++P  +  +          +I++E   +     G +     A  I
Sbjct: 258 VDLIDCSSG-----GIAPGISIPVGEGYQVPFAAQIRREA-QIATAAVGMITRPEHADAI 311

Query: 207 LPS--VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           + +   D V++GR   ++            + L    
Sbjct: 312 VRNGDADLVLLGRELLRDPHWPLRAARALGHDLAPPP 348


>gi|293412461|ref|ZP_06655184.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291469232|gb|EFF11723.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 672

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 31/230 (13%), Positives = 70/230 (30%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLMLN-----------------PDIVG---DCIAAMCKALSIPVT 120
                           L+                   P+ +    + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYPNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVGLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|268556234|ref|XP_002636106.1| Hypothetical protein CBG01351 [Caenorhabditis briggsae]
          Length = 449

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 27/196 (13%), Positives = 65/196 (33%), Gaps = 19/196 (9%)

Query: 53  QIGGADISKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDI 103
           QI    + + V AAK   + G++ I L             P+       +G  L     +
Sbjct: 166 QIKTEVVDRFVYAAKYAYECGFDGIQLHGAHGYLLTQFTSPTTNNRTDKYGGSLENRNRV 225

Query: 104 VGDCIAAMCKALS------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           + +   A+ + +       + +    +   +        R+L  + +K G + + +    
Sbjct: 226 IIEIYEAIRREVPESTGFLVGIKSNSKEFQEKGTTVNDARDLCAAYEKHGFDFVELTGGT 285

Query: 158 A-ILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           A        +++ KI    + +    I+    +  + L GG   +   +  +      G+
Sbjct: 286 AEKYVFAHERESTKIREAFFVEFADAIRPVFKNTVLYLTGGFRTVGAMIDAVEKNTTQGI 345

Query: 214 MIGRAAYKNSAMLTTV 229
            + R A     +   +
Sbjct: 346 GLARPATAEPDLPKKI 361


>gi|256045710|ref|ZP_05448588.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260563012|ref|ZP_05833498.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 1 str.
           16M]
 gi|265992131|ref|ZP_06104688.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|28380199|sp|Q8YE59|TRPA_BRUME RecName: Full=Tryptophan synthase alpha chain
 gi|260153028|gb|EEW88120.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 1 str.
           16M]
 gi|263003197|gb|EEZ15490.1| tryptophan synthase subunit alpha [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 279

 Score = 37.1 bits (85), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|327330184|gb|EGE71933.1| pyridoxine biosynthesis protein [Propionibacterium acnes HL097PA1]
          Length = 279

 Score = 37.1 bits (85), Expect = 4.1,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 16  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGAGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|295097342|emb|CBK86432.1| Putative N-acetylmannosamine-6-phosphate epimerase [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 235

 Score = 37.1 bits (85), Expect = 4.1,   Method: Composition-based stats.
 Identities = 9/90 (10%), Positives = 27/90 (30%), Gaps = 4/90 (4%)

Query: 136 LRNLVKSIKKSGVNGIWIHA-RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           + ++    +      +        +    +      +P  D   + E+      + +   
Sbjct: 129 MADIATVQEAVTAQALGFDCVGTTLYGYTAETAGHSLPENDCAFLKEVLSAVT-IPVIAE 187

Query: 195 GGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           G ++   +A + L      V++G  A    
Sbjct: 188 GNVDTPERAARCLTLGAHTVVVG-GAITRP 216


>gi|146284400|ref|YP_001174553.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas stutzeri
           A1501]
 gi|167012104|sp|A4VRW0|HIS4_PSEU5 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|145572605|gb|ABP81711.1| phosphoribosylformimino-5-aminoimidazole carboxamide [Pseudomonas
           stutzeri A1501]
 gi|327482784|gb|AEA86094.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas stutzeri
           DSM 4166]
          Length = 247

 Score = 37.1 bits (85), Expect = 4.1,   Method: Composition-based stats.
 Identities = 32/156 (20%), Positives = 57/156 (36%), Gaps = 13/156 (8%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIK--KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
            V+ R G+ D     +   +  + K  ++G   + +       +G           ++ +
Sbjct: 14  CVRLRQGLMDDATVFSDDPVAMAAKWVQAGCRRLHLVDLNGAFEGQ---------PVNGE 64

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +V  I K  PDL I + GG+  +      +   V  V+IG  A K    +T     F   
Sbjct: 65  VVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPEFVTEACRAFPGK 124

Query: 237 -LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            + G       V  D W ++S+      AR   + G
Sbjct: 125 VIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADG 160


>gi|116249809|ref|YP_765647.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|148839523|sp|Q1MNC1|HIS4_RHIL3 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|115254457|emb|CAK05531.1| putative imidazole-4-carboxamide isomerase [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 248

 Score = 37.1 bits (85), Expect = 4.1,   Method: Composition-based stats.
 Identities = 22/129 (17%), Positives = 50/129 (38%), Gaps = 17/129 (13%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKC-RIGVDDQIPAVAL--RNLVKSIKKSGVNGIWIHA 155
            NPD+V +        +++ +  K  ++ V+    A  L    L +  + +GV  I    
Sbjct: 108 RNPDLVIEACRKFPDHVAVGIDAKGGKVAVEGWAEASELGIIELARKFEGAGVAAII--- 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP----SVD 211
                       +  +  +++    E+  +   + +  +GGL  +    ++L      ++
Sbjct: 165 ------YTDIDRDGILAGINWSSTLELA-DAVSIPVIASGGLASLDDIRRMLEPDARKLE 217

Query: 212 GVMIGRAAY 220
           G + GRA Y
Sbjct: 218 GAISGRALY 226


>gi|110597879|ref|ZP_01386161.1| inosine-5'-monophosphate dehydrogenase [Chlorobium ferrooxidans DSM
           13031]
 gi|110340456|gb|EAT58942.1| inosine-5'-monophosphate dehydrogenase [Chlorobium ferrooxidans DSM
           13031]
          Length = 497

 Score = 37.1 bits (85), Expect = 4.1,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 35/100 (35%), Gaps = 8/100 (8%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            VA    V+ + ++G + + +      +          +P L   I    +    +  I 
Sbjct: 283 NVATPEAVRDLIEAGADCVKVGIGPGSICTTRIVAGVGMPQLTAIINCAEEAAKTNTPII 342

Query: 193 LNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +GG++     A  +    D VMIG       ++    DE
Sbjct: 343 ADGGVKYSGDIAKALAAGADSVMIG-------SIFAGTDE 375


>gi|16804274|ref|NP_465759.1| hypothetical protein lmo2235 [Listeria monocytogenes EGD-e]
 gi|16411705|emb|CAD00313.1| lmo2235 [Listeria monocytogenes EGD-e]
          Length = 641

 Score = 37.1 bits (85), Expect = 4.1,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|330958790|gb|EGH59050.1| xenobiotic reductase A [Pseudomonas syringae pv. maculicola str.
           ES4326]
          Length = 363

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 60/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVK---CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +         D+        L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVIEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +    + +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREAGIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|227873653|ref|ZP_03991889.1| tryptophan synthase [Oribacterium sinus F0268]
 gi|227840490|gb|EEJ50884.1| tryptophan synthase [Oribacterium sinus F0268]
          Length = 261

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 29/209 (13%), Positives = 58/209 (27%), Gaps = 53/209 (25%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSA-----RVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           +VE    + + G    +     P       R  +G          + V      + + + 
Sbjct: 35  MVENGADLIELGIPFSDPTAEGPVIMEADLRALQGG------CTTEKVFQMTKELRQEVD 88

Query: 117 IPVT----------------------VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           +P                              +   +P       ++  +  G+  I + 
Sbjct: 89  VPFVYMTYANVVFSYGSRKFMEKAKEAGVSGLILPDVPYEEREEFLQDCRDFGIALISMV 148

Query: 155 ARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           A  +                I+  L     RK    D   +  + K + D+   +  G+ 
Sbjct: 149 APTSEDRIAKIAKDAEGFLYIVSSLGVTGERKEITTDLSSLLNMVKSHTDIPCAVGFGIS 208

Query: 199 DMSQALKILPSVDGVMIGRAAYK----NS 223
              QA ++    DGV++G A  K    N 
Sbjct: 209 TKEQAKEVAKYADGVIVGSAIMKKIHENP 237


>gi|134106255|ref|XP_778138.1| hypothetical protein CNBA1380 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50260841|gb|EAL23491.1| hypothetical protein CNBA1380 [Cryptococcus neoformans var.
           neoformans B-3501A]
          Length = 467

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 8/92 (8%)

Query: 134 VALRNLVKSIKKSGVNGIWIH-ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
                 V  + + GV+ + +      + + ++P  + ++P         +KK  PDL IG
Sbjct: 315 EQTTAFVGKLAELGVDLVDVSSGGNDLRQKIAPGPSYQLPFA-----AHLKKTYPDLLIG 369

Query: 193 LNGGLEDMSQALKILPS--VDGVMIGRAAYKN 222
             G + D  QA  IL     D ++IGR   +N
Sbjct: 370 SVGIITDAEQANDILEQGKADVILIGRQLLRN 401


>gi|319442062|ref|ZP_07991218.1| dihydroorotate dehydrogenase 2 [Corynebacterium variabile DSM
           44702]
          Length = 369

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 79/243 (32%), Gaps = 33/243 (13%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAA------KIVEDFGYNEINLNVGCPSARVHEGS 92
             L    + +PL + +G   ++   +AA          D   + + +NV  P       +
Sbjct: 142 ERLRDRVEPEPLGVNLGKTKVTPAEKAADDYRISAQAVDGVADYLVINVSSP------NT 195

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG----- 147
            G   +   + +   + A+ +  + P+ VK    + D+    A+ +L   ++ +G     
Sbjct: 196 PGLRDLQAVESLRPIVEAVREVSARPLFVKIAPDLSDED-VDAVTDLAVELRVTGLIATN 254

Query: 148 --VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQAL 204
             ++   +        G        +     +++  I +   D L +   GG+E   QA 
Sbjct: 255 TTISREGLVTPGVRELGAGGVSGAPVAARALEVLQRIHRRAGDRLVLIGVGGIETPQQAW 314

Query: 205 KILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
           +         IG  A     +L     +          I   +     R   A +++   
Sbjct: 315 ER--------IGAGA----TLLQGYSAFIYGGPDWIRDIHLGLADQVRRHGLAGISEAVG 362

Query: 265 RHL 267
             L
Sbjct: 363 AEL 365


>gi|217326829|ref|ZP_03442912.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. TW14588]
 gi|217319196|gb|EEC27621.1| 2,4-dienoyl-CoA reductase [Escherichia coli O157:H7 str. TW14588]
          Length = 399

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 31/246 (12%), Positives = 80/246 (32%), Gaps = 36/246 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPD 102
                 A++  + GY+ + +        +    +                 G        
Sbjct: 142 DDFARCAQLAREAGYDGVEV--------MGSEGYLINEFLTLRTNQRSDQWGGDYHNRMR 193

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKA 158
              + ++A+ + +     +  R+ + D +           L ++I+ +G     I+    
Sbjct: 194 FAVEVVSAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIG 251

Query: 159 ILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI-- 215
             +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M+  
Sbjct: 252 WHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMVSM 310

Query: 216 GRAAYKNSAMLTTVDEYFSNPL-TGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
            R    ++ +L+      ++ + T     +  +D+ F  K+++ + +  A H      L 
Sbjct: 311 ARPFLADAELLSKAQSGRADEINTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILP 370

Query: 275 QITRHM 280
            + + +
Sbjct: 371 AMQKKI 376


>gi|315304420|ref|ZP_07874712.1| enoate reductase [Listeria ivanovii FSL F6-596]
 gi|313627210|gb|EFR96051.1| enoate reductase [Listeria ivanovii FSL F6-596]
          Length = 329

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 57/177 (32%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSGRTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI     VD  +       +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVDGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKQAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|295097603|emb|CBK86693.1| 2,4-dienoyl-CoA reductase [Enterobacter cloacae subsp. cloacae NCTC
           9394]
          Length = 673

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 20/191 (10%), Positives = 51/191 (26%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A +  + GY+ + +                 L+                     
Sbjct: 143 DDFARCAALAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDEWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 192 RMRFAVEVVRAVRERAGADFIIIFRLSMLDLVEGGGTFDETVQLAQAIEAAGAT--IINT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  ++   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRAAFSWVTRKLKGIVSVPLVTTNR-INDPQVAEDVISRGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|317054536|ref|YP_004118561.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
 gi|316952531|gb|ADU72005.1| NADH:flavin oxidoreductase/NADH oxidase [Pantoea sp. At-9b]
          Length = 648

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 20/179 (11%), Positives = 55/179 (30%), Gaps = 17/179 (9%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG-----C----PSARVHEGSFGACLMLNPDIVGDCIAA 110
               +A    +  G++ + L+       C    P        +G   +     + + ++ 
Sbjct: 151 EYYAQAVWRAKQAGFDSVELHGAHGYLICAFMSPLTNKRTDRYGGSFLGRMQFINEIMSR 210

Query: 111 MCKALS--IPVTVKC--RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
               +    P+T++       +  I       + + +++ G   I + A   +   +   
Sbjct: 211 SRALVGDEYPITIRIVGDECREGGIDPHLSVRIAQHLEQLGFAAISVSAG--MYPYIRTV 268

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK--ILPSVDGVMIGRAAYKNS 223
            N          + E  ++   + +   G L       +  +    D + +GRA   + 
Sbjct: 269 PNTYHKKGVNLYLAENIRDAVSIPVMAAGQLSSPDIQTEAIVRKKADLIALGRALIADP 327


>gi|255994517|ref|ZP_05427652.1| imidazoleglycerol phosphate synthase, cyclase subunit [Eubacterium
           saphenum ATCC 49989]
 gi|255993230|gb|EEU03319.1| imidazoleglycerol phosphate synthase, cyclase subunit [Eubacterium
           saphenum ATCC 49989]
          Length = 250

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 1/87 (1%)

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           Y+ +++  +   DL +   GGL+ +     I+    D V I   A  N  +L    E   
Sbjct: 61  YEGLFKSVRAVSDLPLVAGGGLKTIEDVDNIIKLGADMVSINTGAIDNPDLLNEAAEKIG 120

Query: 235 NPLTGSSPIKTRVDKDFWRKISASMTD 261
           +     S    +V+ ++    +A M D
Sbjct: 121 SENVILSVDAKKVNGEYHVFRNAGMMD 147


>gi|254718133|ref|ZP_05179944.1| tryptophan synthase subunit alpha [Brucella sp. 83/13]
 gi|265983086|ref|ZP_06095821.1| tryptophan synthase subunit alpha [Brucella sp. 83/13]
 gi|306837647|ref|ZP_07470516.1| tryptophan synthase, alpha subunit [Brucella sp. NF 2653]
 gi|264661678|gb|EEZ31939.1| tryptophan synthase subunit alpha [Brucella sp. 83/13]
 gi|306407205|gb|EFM63415.1| tryptophan synthase, alpha subunit [Brucella sp. NF 2653]
          Length = 279

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + DL I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STDLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|154149557|ref|YP_001403175.1| pyridoxal biosynthesis lyase PdxS [Candidatus Methanoregula boonei
           6A8]
 gi|153998109|gb|ABS54532.1| pyridoxine biosynthesis protein [Methanoregula boonei 6A8]
          Length = 298

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 6/75 (8%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E  G   +      PS      + G   M +P+ V + I A    +SIPV  K
Sbjct: 32  AEQAKIAEAAGAVAVMSLERVPSD--IRKAGGVARMADPEKVTEIIEA----VSIPVMGK 85

Query: 123 CRIGVDDQIPAVALR 137
            RIG   +   + + 
Sbjct: 86  VRIGHFVEAQVLEVL 100


>gi|15922526|ref|NP_378195.1| glutamate synthase large subunit [Sulfolobus tokodaii str. 7]
 gi|15623316|dbj|BAB67304.1| 635aa long hypothetical glutamate synthase large subunit
           [Sulfolobus tokodaii str. 7]
          Length = 635

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 30/120 (25%), Positives = 49/120 (40%), Gaps = 14/120 (11%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--HARKAILKGLSP 165
           I A+ +A   PV VK      + IP      +V  I + G +G+ I  H        +  
Sbjct: 129 IEALKEATGKPVFVKV--AATNYIPY-----IVSGIARMGADGVIIDGHGAGTGATPIVI 181

Query: 166 KDNRKIP-NLDYDIVYEIKKENP---DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +DN  IP  L      ++ +E     + +I   G + D + A K++    D V +G  A 
Sbjct: 182 RDNVGIPIELAVASADKVLREQGMRDNFYIIAAGRVADATDAAKLIALGADVVSVGTGAL 241


>gi|114562482|ref|YP_749995.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella frigidimarina
           NCIMB 400]
 gi|114333775|gb|ABI71157.1| NADH:flavin oxidoreductase/NADH oxidase [Shewanella frigidimarina
           NCIMB 400]
          Length = 334

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 61/184 (33%), Gaps = 24/184 (13%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIA 109
             V  A   +  G++ + L   C           P     +  +G  L     I+ + ++
Sbjct: 150 DFVNGAIRADKAGFDLVEL--HCAHGYGINQWLSPLTNQRQDQYGGSLENRARILLEIVS 207

Query: 110 AMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
            + +A    + V  RI   D  P       + ++ + +  +GV  + + +         P
Sbjct: 208 KIKQAAP-RLAVMTRIPGQDGYPGGLSHDDMGHVSQWLVDAGVEILNVSSGIGGWN--RP 264

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
           KD R    L  D             +   GG+E +     IL    VD V +GRA     
Sbjct: 265 KDKRGEGFLVED--AAPLTGTTTAAVIGVGGIESIDYIETILATKQVDLVAVGRAILAGP 322

Query: 224 AMLT 227
           +   
Sbjct: 323 SEFA 326


>gi|189500001|ref|YP_001959471.1| inosine-5'-monophosphate dehydrogenase [Chlorobium phaeobacteroides
           BS1]
 gi|189495442|gb|ACE03990.1| inosine-5'-monophosphate dehydrogenase [Chlorobium phaeobacteroides
           BS1]
          Length = 496

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 24/145 (16%), Positives = 47/145 (32%), Gaps = 22/145 (15%)

Query: 102 DIVGDCIAAMCKALSIP------------VTVKCRIGVDDQIPA--VALRNLVKSIKKSG 147
           D V   + A    +++             V    +   D Q+ A  VA  + V+ +  +G
Sbjct: 238 DRVTALVEAGVDVVAVDTAHGHSKAVSDMVRTIKKSFPDLQVVAGNVATADAVRDLVAAG 297

Query: 148 VNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKI 206
            + + +      +          +P L   +    +       +  +GG++     A  I
Sbjct: 298 ADAVKVGIGPGSICTTRVVAGVGMPQLTAVMKCAEEAAKTGTPLIADGGIKYSGDIAKAI 357

Query: 207 LPSVDGVMIGRAAYKNSAMLTTVDE 231
               D VMIG       ++    DE
Sbjct: 358 AAGADSVMIG-------SIFAGTDE 375


>gi|319950599|ref|ZP_08024507.1| NADH:flavin oxidoreductase/NADH oxidase [Dietzia cinnamea P4]
 gi|319435738|gb|EFV90950.1| NADH:flavin oxidoreductase/NADH oxidase [Dietzia cinnamea P4]
          Length = 397

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 69/206 (33%), Gaps = 46/206 (22%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V AA+   + G++ I ++ G          P     +  +G  L            A+  
Sbjct: 134 VRAARGAYEAGFDAIEVHFGHNYLVSEFLSPRLNRRKDEYGGSLENRARFARRIGRAIRD 193

Query: 114 ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS-----GVNGIWIHARKAIL------KG 162
           A+   + V  ++ +DD +P     +  + + +        + + +    ++L      KG
Sbjct: 194 AMGDKIAVTMKLNMDDGVPGGFWIDEARQVARWLEQDGSADALVMTVGSSLLNPIYLFKG 253

Query: 163 LSP------------------------KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
            +P                        K+        +D   +I +E  DL + L GG+ 
Sbjct: 254 DAPLEEFAATQPPVIKMGMKVVGPKMFKEYPYTDAYMFDDARQI-REAVDLPMMLLGGIV 312

Query: 199 D-MSQALKILPSVDGVMIGRAAYKNS 223
           D  S    +    + V +GRA  +  
Sbjct: 313 DRPSIDKAMNAGFEFVAMGRALLREP 338


>gi|302132185|ref|ZP_07258175.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas syringae
           pv. tomato NCPPB 1108]
          Length = 245

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ D+V  I K  P+L I + GG+  +      +   V  V+IG  A K+   +     
Sbjct: 60  PVNGDVVTAIAKRYPNLPIQIGGGIRSLETIEHYIKAGVSYVIIGTKAVKDPEFVAQACR 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++S       A+   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADG 160


>gi|289192970|ref|YP_003458911.1| pyridoxine biosynthesis protein [Methanocaldococcus sp. FS406-22]
 gi|288939420|gb|ADC70175.1| pyridoxine biosynthesis protein [Methanocaldococcus sp. FS406-22]
          Length = 330

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE A+I E+ G   +      P+      + G   M +P ++ + +     A+SIPV  K
Sbjct: 27  VEQAQIAEEAGAVAVMALERVPAD--IRAAGGVARMSDPALIEEIM----DAVSIPVMAK 80

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           CRIG   +          + ++  GV+ I
Sbjct: 81  CRIGHTKE---------AEVLEAIGVDMI 100


>gi|110643325|ref|YP_671055.1| 2,4-dienoyl-CoA reductase [Escherichia coli 536]
 gi|110344917|gb|ABG71154.1| 2,4-dienoyl-CoA reductase [Escherichia coli 536]
          Length = 672

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 31/230 (13%), Positives = 70/230 (30%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLMLN-----------------PDIVG---DCIAAMCKALSIPVT 120
                           L+                   P+ +    + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYPNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVGLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|42519875|ref|NP_965805.1| glycolate oxidase [Lactobacillus johnsonii NCC 533]
 gi|41584165|gb|AAS09771.1| glycolate oxidase [Lactobacillus johnsonii NCC 533]
          Length = 412

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 26/111 (23%), Positives = 43/111 (38%), Gaps = 15/111 (13%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I  + +   +PV VK     +D + A+           +G +GI +          +P  
Sbjct: 227 IRKIKEIADVPVIVKGVECAEDAMLAI----------GAGADGIVVSNHGGREVDGAPAT 276

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
              +P    +I   ++  N  + I L+GG+   S   K L    D V IGR
Sbjct: 277 IDVLP----EIAKAVRSSNHRVPIILDGGVRRGSHVFKALALGADLVGIGR 323


>gi|332363295|gb|EGJ41080.1| FMN reductase [Streptococcus sanguinis SK49]
          Length = 367

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 30/225 (13%), Positives = 75/225 (33%), Gaps = 27/225 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPD-IVGD 106
              + A +     G++ + L             P + V +  +G  L   +  P  ++  
Sbjct: 147 EDFLSAIRRAIQAGFDGVELHGANTYLIQQFVSPHSNVRQDKWGGSLNNRLRFPKTLLKR 206

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKK---SGVNGIWIHARKAILKG 162
               + +    P  +  R   ++ + P + L + ++ +++     V+ + I         
Sbjct: 207 AKQLVKEEADRPFLIGYRFSPEEIEEPGIQLYDTLQLLEQLIYHQVDYLHISTSDVWRS- 265

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAA 219
            S +D++    +   I+   KK N  + +   G +E    A ++L +  G+    +G+A 
Sbjct: 266 -SIRDSQDSEPVIQKII---KKINGRVPLIGVGQIETKQDAQRVLDA--GIPLFALGKAL 319

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
             +      V       +  +   + + D             Y  
Sbjct: 320 LLDPDWAEKVVSGREAEVIRAYRDELQADLALPTAFVEDARSYLE 364


>gi|324511003|gb|ADY44593.1| 12-oxophytodienoate reductase 3 [Ascaris suum]
          Length = 437

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 74/244 (30%), Gaps = 47/244 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCI 108
            +   AA  V+D G++ + +NVG                     +G  L     I+ + I
Sbjct: 165 ERYAYAAGFVKDCGFHGVEINVG--MDFALAQLVTATTNSRNDEYGGSLENRTRILFEVI 222

Query: 109 AAMCKAL--SIPVTVKCRI---GVDDQIPAVALRNLVKSIKKS--------GVNGIWIHA 155
            ++   +       +  ++     +D           K +  +        G N   I  
Sbjct: 223 NSIRDRVKDDKNFVLGLKLSSLNYEDGYDECEFERFCKRLDATKLDYVVITGANYEAIRQ 282

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R+ I +  S K           +   IK+        L GG     Q  + +     DG+
Sbjct: 283 REKIERDPSRKSEAFFVKFVIAVRTNIKRAKT----FLCGGFRAADQMWEAIYEGWTDGI 338

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+ R       +   +    +  +TG+            +K      DY      +G ++
Sbjct: 339 MVARPLAAEPDLPRRI---LNREVTGA------------KKSLLDEIDYGLSEYAAGTQM 383

Query: 274 QQIT 277
            Q+ 
Sbjct: 384 WQLA 387


>gi|324510800|gb|ADY44511.1| NADH oxidase [Ascaris suum]
          Length = 437

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 74/244 (30%), Gaps = 47/244 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCI 108
            +   AA  V+D G++ + +NVG                     +G  L     I+ + I
Sbjct: 165 ERYAYAAGFVKDCGFHGVEINVG--MDFALAQLVTATTNSRNDEYGGSLENRTRILFEVI 222

Query: 109 AAMCKAL--SIPVTVKCRI---GVDDQIPAVALRNLVKSIKKS--------GVNGIWIHA 155
            ++   +       +  ++     +D           K +  +        G N   I  
Sbjct: 223 NSIRDRVKDDKNFVLGLKLSSLNYEDGYDECEFERFCKRLDATKLDYVVITGANYEAIRQ 282

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R+ I +  S K           +   IK+        L GG     Q  + +     DG+
Sbjct: 283 REKIERDPSRKSEAFFVKFVIAVRTNIKRAKT----FLCGGFRAADQMWEAIYEGWTDGI 338

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+ R       +   +    +  +TG+            +K      DY      +G ++
Sbjct: 339 MVARPLAAEPDLPRRI---LNREVTGA------------KKSLLDEIDYGLSEYAAGTQM 383

Query: 274 QQIT 277
            Q+ 
Sbjct: 384 WQLA 387


>gi|298675323|ref|YP_003727073.1| NADH:flavin oxidoreductase/NADH oxidase [Methanohalobium
           evestigatum Z-7303]
 gi|298288311|gb|ADI74277.1| NADH:flavin oxidoreductase/NADH oxidase [Methanohalobium
           evestigatum Z-7303]
          Length = 371

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 25/143 (17%), Positives = 53/143 (37%), Gaps = 14/143 (9%)

Query: 94  GACLMLNPDIVGDCIAAMCKAL---SIPVTVKCRIG----VDDQIPAVALRN---LVKSI 143
           G  +     I+ + I  +         P+TVK         D   P + + +   + K +
Sbjct: 185 GGSVENRTRIITEIIKRIRGMTLDMDYPITVKLNSTDGFGSDSDKPGLDINDTIQIAKIL 244

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQ 202
           +++GVN I +         +S ++   +    Y     ++ K   D+ + L GG+     
Sbjct: 245 QQNGVNAIEVSGGIFETHLMSQQNIDSVEKEAYFKKNAKLIKNAVDIPVILVGGVRSKYI 304

Query: 203 ALKILPSVDGVMIGRAAYKNSAM 225
             KI+ + +  MI   +     +
Sbjct: 305 MEKIISADNADMI---SMSRPFI 324


>gi|284162156|ref|YP_003400779.1| radical SAM protein [Archaeoglobus profundus DSM 5631]
 gi|284012153|gb|ADB58106.1| Radical SAM domain protein [Archaeoglobus profundus DSM 5631]
          Length = 1034

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 16/81 (19%)

Query: 40  ILGFSTQEKP--LALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
           +L  + +E P   A+Q+ G +      LVE  +I ++ GY+ + LN             G
Sbjct: 629 MLRRAKEEIPPCNAVQLTGGEPTLRDDLVEIIRIAKEEGYDHVQLNTD-----------G 677

Query: 95  ACLMLNPDIVGDCIAAMCKAL 115
             L  + D V     A    +
Sbjct: 678 IRLAFDRDFVKAITEAGVNTI 698


>gi|189195914|ref|XP_001934295.1| NADH oxidase [Pyrenophora tritici-repentis Pt-1C-BFP]
 gi|187980174|gb|EDU46800.1| NADH oxidase [Pyrenophora tritici-repentis Pt-1C-BFP]
          Length = 449

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 26/185 (14%), Positives = 54/185 (29%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA+ +E  GY+ I L             P+      ++G  L     ++ +    
Sbjct: 175 EGFAHAAEYLEKAGYDGIQLHGAHGYLLAQFLSPTTNHRTDAYGGSLENRARLIVEIGQE 234

Query: 111 MCKALSIPVTVKCR----IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K  S    +  +       D          L K ++ +  + + +          S K
Sbjct: 235 IRKRTSPNFILSIKLNSVEFQDKGFGTAEAGTLCKMLEDNSFDFVELSGGTYEQLAFSHK 294

Query: 167 DNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSA 224
                    +  +    I          + GG +  +  +  L +VDGV + R       
Sbjct: 295 RESTKKREAFFLEFAESITPSLTKTRTYVTGGFKTAAAMVDALNTVDGVGLARPVCLEPE 354

Query: 225 MLTTV 229
           +   +
Sbjct: 355 LPRQI 359


>gi|239814421|ref|YP_002943331.1| tryptophan synthase subunit alpha [Variovorax paradoxus S110]
 gi|239800998|gb|ACS18065.1| tryptophan synthase, alpha subunit [Variovorax paradoxus S110]
          Length = 285

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 18/104 (17%), Positives = 39/104 (37%), Gaps = 17/104 (16%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWI--------------HARKAILKGLSPKDNRKIPNLD 175
             P          +K +G++ I++                    +  +S K      +LD
Sbjct: 138 DYPPEECEAFAADLKAAGIDLIFLLAPTSTSERMAQVARTASGYVYYVSLKGVTGAGHLD 197

Query: 176 YDIVYEIK---KENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            + V ++    +E+  + +G+  G+ D   A  +  + D V+IG
Sbjct: 198 TEAVGQMIPRIREHVSIPVGVGFGIRDARTAQAVGSAADAVVIG 241


>gi|39936237|ref|NP_948513.1| hypothetical protein RPA3174 [Rhodopseudomonas palustris CGA009]
 gi|81562185|sp|Q6N509|OADC_RHOPA RecName: Full=Oxaloacetate decarboxylase
 gi|39650092|emb|CAE28615.1| conserved unknown protein [Rhodopseudomonas palustris CGA009]
          Length = 288

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 52/164 (31%), Gaps = 29/164 (17%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI-------VGDCIAAMCKALSIPV 119
           +I +D G+         P            ++ +PDI       + + +  M +A ++PV
Sbjct: 32  RIADDLGF---------PFGMFGGSVASLAILGDPDIALITLTELAEQVRRMSRAAALPV 82

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            V    G      A+ +R  V+ ++ +G  G+ I            K            +
Sbjct: 83  VVDADHGY---GNALNVRRTVEELEAAGAAGLTIEDTLLPQAYGEAKPQLVSREEGLGKI 139

Query: 180 YEIKKENPDLFIGLNG-----GLEDMSQALK-----ILPSVDGV 213
                   D  + + G      +  +  A++         VD +
Sbjct: 140 KAALDARRDPNLVIIGRTGACSITSLDDAIERALAYQAAGVDAL 183


>gi|325694969|gb|EGD36874.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Streptococcus sanguinis SK150]
          Length = 121

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  K+  ++G + +        L   +  + R       ++V  + ++    F    GG+
Sbjct: 34  DAAKAYYEAGCDELV------FLDITATHEERDTT---VEMVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  +A  N  +L    E F 
Sbjct: 84  RTVDDMKRMLQAGADKVAVNSSALANPQLLADCAEKFG 121


>gi|311104727|ref|YP_003977580.1| tryptophan synthase subunit alpha 1 [Achromobacter xylosoxidans A8]
 gi|310759416|gb|ADP14865.1| tryptophan synthase, alpha subunit 1 [Achromobacter xylosoxidans
           A8]
          Length = 287

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE----IKKENPDLFIGLN 194
           L  +  ++ +  +   AR  +   +S K      +L+ D V E    I++   D+ +G+ 
Sbjct: 159 LAPTSTEARIKAVAAVARGYVY-YVSLKGVTGSGSLNTDDVAERLAVIRRHVRDIPVGVG 217

Query: 195 GGLEDMSQALKILPSVDGVMIG 216
            G+ D   A ++  + D V+IG
Sbjct: 218 FGIRDAESAQRVARAADAVVIG 239


>gi|254785436|ref|YP_003072865.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Teredinibacter turnerae T7901]
 gi|237687293|gb|ACR14557.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Teredinibacter turnerae T7901]
          Length = 259

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 189 LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV 247
           + + + GG+  +    ++L    D V I  AA  N A++  V   F +     S    R+
Sbjct: 80  IPLTVGGGIRSVEDVTELLAAGADKVAINTAAVANPALIEQVALRFGSQCMVLSIEAKRL 139

Query: 248 DKDFWRKISASMTDYAAR 265
            +D W   +    + + R
Sbjct: 140 GEDRWEVYTDCARESSGR 157


>gi|167746427|ref|ZP_02418554.1| hypothetical protein ANACAC_01137 [Anaerostipes caccae DSM 14662]
 gi|167653387|gb|EDR97516.1| hypothetical protein ANACAC_01137 [Anaerostipes caccae DSM 14662]
          Length = 644

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 19/111 (17%), Positives = 38/111 (34%), Gaps = 6/111 (5%)

Query: 111 MCKALSIPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           +      PV  +      ++            K  +K+G + I I    A   G      
Sbjct: 209 VRCGSDFPVLFRISADEFMNGGNKIEDAVVYAKLAEKAGADAIHISTGSAA-GGNIVTTY 267

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
              P  + +   ++KK    + +   G + D + A +I+     D + +GR
Sbjct: 268 YTDPGFNVENAAKVKKAV-HVPVICVGRINDPALAEEIIESGQADLISLGR 317


>gi|160882639|ref|ZP_02063642.1| hypothetical protein BACOVA_00592 [Bacteroides ovatus ATCC 8483]
 gi|237718404|ref|ZP_04548885.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_2_4]
 gi|293371407|ref|ZP_06617838.1| dihydroorotate oxidase [Bacteroides ovatus SD CMC 3f]
 gi|299149059|ref|ZP_07042121.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           3_1_23]
 gi|156111954|gb|EDO13699.1| hypothetical protein BACOVA_00592 [Bacteroides ovatus ATCC 8483]
 gi|229452337|gb|EEO58128.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 2_2_4]
 gi|292633604|gb|EFF52162.1| dihydroorotate oxidase [Bacteroides ovatus SD CMC 3f]
 gi|298513820|gb|EFI37707.1| dihydroorotate dehydrogenase family protein [Bacteroides sp.
           3_1_23]
          Length = 325

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 27/169 (15%), Positives = 58/169 (34%), Gaps = 25/169 (14%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK++E+ G + + +N+    + V    +G+    + D     +  + K + IPV +K   
Sbjct: 115 AKMIEEAGADALEINILALQSEVQYT-YGSFEQRHID----ILRHIKKTIKIPVIMKL-- 167

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAILKGLSPKDNRKIP----NL 174
                        L+  +  +G   + +  R          ++ +S +           L
Sbjct: 168 ----GDNLTNPVALIDQLYANGAAAVVLFNRFYQPDINIEKMEHISGEIFSNASDLAIPL 223

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQ-ALKILPSVDGVMIGRAAYKN 222
            +  +     +  D     +GG+ +       IL     V +  A Y N
Sbjct: 224 RWIGIASAVVDKIDY--AASGGVANAESVVKAILAGASAVEVCSAVYLN 270


>gi|114761357|ref|ZP_01441272.1| putative FMN oxidoreductase [Pelagibaca bermudensis HTCC2601]
 gi|114545605|gb|EAU48607.1| putative FMN oxidoreductase [Roseovarius sp. HTCC2601]
          Length = 369

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 72/202 (35%), Gaps = 29/202 (14%)

Query: 45  TQEKPLALQIGGADISKL----VEAAKIVEDFGYNEINL---------NVGCPSARVHEG 91
            + KP+  +I   D+ ++    V+AA+   + G++ I +             P A     
Sbjct: 125 GEGKPVPAEIASEDLPRVKQMWVDAARRSVEAGFDVIEVHSAHGYLLNQFLSPIANRRND 184

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
            +G  L        + IAA+   +     + V +    GV++           + +++ G
Sbjct: 185 DYGGELENRMRFPLEVIAAVRDVVPEDKLLFVRISAVDGVEEGWTLEESVIYGQRLREIG 244

Query: 148 VNGIWIH----ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA 203
           V+ I          A +  L+     ++P      + +  +E  +L     G +    QA
Sbjct: 245 VDVIDCSSGGIGGAATMNRLARYPGFQLP------LSQAVREGSELPTVGVGLIFKPRQA 298

Query: 204 LKILP--SVDGVMIGRAAYKNS 223
            + L     D V IGR    N 
Sbjct: 299 EEALSAGQADIVAIGRECLNNP 320


>gi|25027655|ref|NP_737709.1| putative NAD(P)H-dependent 2-cyclohexen-1-one reductase
           [Corynebacterium efficiens YS-314]
 gi|259506943|ref|ZP_05749843.1| xenobiotic reductase B [Corynebacterium efficiens YS-314]
 gi|23492937|dbj|BAC17909.1| putative NAD(P)H-dependent 2-cyclohexen-1-one reductase
           [Corynebacterium efficiens YS-314]
 gi|259165481|gb|EEW50035.1| xenobiotic reductase B [Corynebacterium efficiens YS-314]
          Length = 366

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 30/221 (13%), Positives = 72/221 (32%), Gaps = 35/221 (15%)

Query: 44  STQEKPLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVG---------CPSARVH 89
           + +  P+     G D       + V  A+     G + + ++            P+  + 
Sbjct: 138 TGKVDPVIPHELGLDELATVIDQFVAGARNAMAAGMDGVQIHGANGYLLHEFLAPTTNLR 197

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
             ++GA     P+     +A +  A++  +        +  +      N+  +I+    +
Sbjct: 198 GDAYGAS----PEKRASFVAEVVTAVAREIGAG-----NTGLRLSPQHNIQGAIETDDAD 248

Query: 150 GIWIHARKA-ILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
            +  +   A  LK L       + +  + +++  +++E     I   G         ++ 
Sbjct: 249 VLATYTALARSLKHLGLAHVELVHHEPEGELIQTLRREFGAPLIVNTG--FSRFTQREVA 306

Query: 208 PS------VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
                    D V +GR A  N  ++         PL   +P
Sbjct: 307 EELVDKQAADAVSVGRLALANPDLVRRWQ--LDGPLNEPNP 345


>gi|293396929|ref|ZP_06641203.1| imidazole glycerol phosphate synthase subunit HisF [Serratia
           odorifera DSM 4582]
 gi|291420400|gb|EFE93655.1| imidazole glycerol phosphate synthase subunit HisF [Serratia
           odorifera DSM 4582]
          Length = 258

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  + +++  + + F 
Sbjct: 85  SVDDASQILSFGADKISINSPALADPSLIGRLADRFG 121


>gi|237653288|ref|YP_002889602.1| inosine-5'-monophosphate dehydrogenase [Thauera sp. MZ1T]
 gi|237624535|gb|ACR01225.1| inosine-5'-monophosphate dehydrogenase [Thauera sp. MZ1T]
          Length = 487

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 14/82 (17%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
                + +  +GV+ I +       +G+             D V  +KK  P + +   G
Sbjct: 228 TEERAERLADAGVDMIVVDTAHGHSQGV------------LDRVGWVKKHFPHIEVVG-G 274

Query: 196 GLEDMSQALKILP-SVDGVMIG 216
            +     A  ++    DGV +G
Sbjct: 275 NIATADAARALVDAGADGVKVG 296


>gi|116873538|ref|YP_850319.1| pyridoxine biosynthesis protein [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|123464006|sp|A0AKK8|PDXS_LISW6 RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|116742416|emb|CAK21540.1| pyridoxine biosynthesis protein [Listeria welshimeri serovar 6b
           str. SLCC5334]
          Length = 295

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI ED G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 29  AEQAKIAEDAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|62389948|ref|YP_225350.1| PEP phosphonomutase or related enzyme [Corynebacterium glutamicum
           ATCC 13032]
 gi|41325284|emb|CAF19764.1| PEP phosphonomutase or related enzyme [Corynebacterium glutamicum
           ATCC 13032]
          Length = 231

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 52/130 (40%), Gaps = 11/130 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A +VE+ G++ + +    P A     S G   M   D +   +  +  A+SIPV+V    
Sbjct: 32  AGLVEEAGFSGLTIGSH-PVADATGSSDGEN-MNFADYMA-VVKKITSAVSIPVSVDVES 88

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE 185
           G       ++  +L+  I ++G  GI +     ++     +      + DY        +
Sbjct: 89  GY-----GLSPADLIAQILEAGAVGINVE---DVVHSEGKRVREAQEHADYIAAARQAAD 140

Query: 186 NPDLFIGLNG 195
              + + +NG
Sbjct: 141 VAGVDVVING 150


>gi|333022670|ref|ZP_08450734.1| putative oxidoreductase [Streptomyces sp. Tu6071]
 gi|332742522|gb|EGJ72963.1| putative oxidoreductase [Streptomyces sp. Tu6071]
          Length = 347

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 51/164 (31%), Gaps = 18/164 (10%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCR-IGVDDQIP--------AVALRNLV 140
           ++G           + + A+       +P+  +       ++ P        A       
Sbjct: 184 AYGGSYENRTRFAREVVDAVRAVWPEGLPLLFRISATDWFEEDPEDPRTGWTADETVAFA 243

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +++K+ GV+ + +        G+SP               E  K   DL     G + + 
Sbjct: 244 RTLKEHGVDLLDVSTG-----GISPTAPIAAGPGYQVRFAERVKNETDLAAAAVGLITEA 298

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            QA KIL     D +++GR   ++                 + P
Sbjct: 299 RQAEKILADGQADAILLGRELLRDPYFAAHAATELGEQPYVAQP 342


>gi|326516290|dbj|BAJ92300.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 369

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 32/183 (17%), Positives = 63/183 (34%), Gaps = 31/183 (16%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
             +AA+   D G++ + ++ G  +  + E             +G  L        + +AA
Sbjct: 165 FRKAARNAIDAGFDGVEIHGG--NGYLIEQFLKDSANDRDDGYGGSLENRCRFALEVVAA 222

Query: 111 MCKALSI-PVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIW-IHARKAILKGL 163
           + K +    V ++    +D     D  P     ++   +   G+  +  I  R A++ G 
Sbjct: 223 VAKEVGAHRVGIRLSPFMDYMDCHDSDPHALGLHMATKLNDHGILYLHMIEPRMALVDGR 282

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS-VDGVMIGRAAYKN 222
               +R +P          ++     FI  NGG +       +     D V  GR    N
Sbjct: 283 RVVPHRLLPY---------REAFKGTFI-ANGGYDREEGDKAVSSGYADLVSFGRLFLAN 332

Query: 223 SAM 225
             +
Sbjct: 333 PDL 335


>gi|325688060|gb|EGD30079.1| FMN reductase [Streptococcus sanguinis SK72]
          Length = 367

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 30/225 (13%), Positives = 75/225 (33%), Gaps = 27/225 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPD-IVGD 106
              + A +     G++ + L             P + V +  +G  L   +  P  ++  
Sbjct: 147 EDFLSAIRRAIQAGFDGVELHGANTYLIQQFVSPHSNVRQDKWGGSLNNRLRFPKTLLKR 206

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKK---SGVNGIWIHARKAILKG 162
               + +    P  +  R   ++ + P + L + ++ +++     V+ + I         
Sbjct: 207 AKQLVKEEADRPFLIGYRFSPEEIEEPGIQLYDTLQLLEQLIYHQVDYLHISTSDVWRS- 265

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAA 219
            S +D++    +   I+   KK N  + +   G +E    A ++L +  G+    +G+A 
Sbjct: 266 -SIRDSQDSEPVIQKII---KKINGRVPLIGVGQIETKQDAQRVLDA--GIPLFALGKAL 319

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
             +      V       +  +   + + D             Y  
Sbjct: 320 LLDPDWAEKVVSGREEEVIRAYRDELQADLALPTAFVEDARSYLE 364


>gi|323188473|gb|EFZ73758.1| 2,4-dienoyl-CoA reductase domain protein [Escherichia coli RN587/1]
          Length = 399

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFARCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|255523428|ref|ZP_05390397.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           carboxidivorans P7]
 gi|296184710|ref|ZP_06853121.1| 2-enoate reductase [Clostridium carboxidivorans P7]
 gi|255512886|gb|EET89157.1| NADH:flavin oxidoreductase/NADH oxidase [Clostridium
           carboxidivorans P7]
 gi|296050492|gb|EFG89915.1| 2-enoate reductase [Clostridium carboxidivorans P7]
          Length = 664

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 21/150 (14%), Positives = 48/150 (32%), Gaps = 19/150 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKS----- 142
           +G  L        + +  +        PV ++        D +  A+     V+      
Sbjct: 198 YGGSLENRLRFAREIVEEIKNRCGEDFPVALRYSPKSFIKDLRDGALPGEEFVEKGRDLE 257

Query: 143 --IKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-----DYDIVYEIKKENPDLFIGLNG 195
             I+ + +   + +       G         P +      Y    ++ K+  D+ I   G
Sbjct: 258 EGIEAAKLLVSYGYDSLDTDVGSYDSWWWSHPPMYQEKGLYRPYAKLMKDTVDVPIICAG 317

Query: 196 GLEDMSQALKILPS--VDGVMIGRAAYKNS 223
            ++D   AL+ + +   D + +GR    + 
Sbjct: 318 RMDDPDMALEAVENGTCDMISLGRPLLADP 347


>gi|320589114|gb|EFX01576.1| pyridoxine biosynthesis protein [Grosmannia clavigera kw1407]
          Length = 332

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      P+   H+G      M +PD     I A+  A++IPV  K
Sbjct: 63  AEQARIAEEAGACAVMALERVPADIRHDGGVAR--MADPD----VIRAVQAAVTIPVMAK 116

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 117 ARIGHSVE---------AQILEALGVDFI 136


>gi|312884590|ref|ZP_07744294.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309367902|gb|EFP95450.1| imidazole glycerol phosphate synthase subunit HisF [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 257

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWVRRVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D V I   A     ++T + + F 
Sbjct: 85  TKEDAARILEFGADKVSINSPALAQPTLITQLADKFG 121


>gi|223041862|ref|ZP_03612050.1| histidine biosynthesis bifunctional protein hisIE [Actinobacillus
           minor 202]
 gi|223017355|gb|EEF15778.1| histidine biosynthesis bifunctional protein hisIE [Actinobacillus
           minor 202]
          Length = 257

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +I     D + I   A  +  +++ + + F 
Sbjct: 85  TIDDAEQIFAFGADKISINSPALADPELISRLADRFG 121


>gi|163740464|ref|ZP_02147858.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Phaeobacter
           gallaeciensis 2.10]
 gi|161386322|gb|EDQ10697.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Phaeobacter
           gallaeciensis 2.10]
          Length = 669

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 43/124 (34%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +    +A+     +  R+ + D +P       +  L + I+K+G     ++      +
Sbjct: 191 EVVRRTREAVGTDFIIIYRLSMIDLVPNGSTYDEVVELAQEIEKAGAT--ILNTGIGWHE 248

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   +  V  ++  +     I  N  +     A ++L     D V + R 
Sbjct: 249 ARIPTIATSVPRAAFAWVTKKLMGKVGIPVITSNR-INTPEVAEQVLSEGCADMVSMARP 307

Query: 219 AYKN 222
              +
Sbjct: 308 MLAD 311


>gi|152971020|ref|YP_001336129.1| imidazole glycerol phosphate synthase subunit HisF [Klebsiella
           pneumoniae subsp. pneumoniae MGH 78578]
 gi|238895602|ref|YP_002920337.1| imidazole glycerol phosphate synthase subunit HisF [Klebsiella
           pneumoniae NTUH-K2044]
 gi|330002122|ref|ZP_08304202.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           sp. MS 92-3]
 gi|167012167|sp|A6TBC8|HIS6_KLEP7 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|150955869|gb|ABR77899.1| imidazole glycerol phosphate synthase subunit HisF [Klebsiella
           pneumoniae subsp. pneumoniae MGH 78578]
 gi|238547919|dbj|BAH64270.1| imidazole glycerol phosphate synthase catalytic subunit [Klebsiella
           pneumoniae subsp. pneumoniae NTUH-K2044]
 gi|328537432|gb|EGF63674.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           sp. MS 92-3]
          Length = 258

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAQILSFGADKISINSPALADPTLITRLADRFG 121


>gi|78044813|ref|YP_359561.1| glutamate synthase,-like protein [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996928|gb|ABB15827.1| glutamate synthase, homolog [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 500

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 25/128 (19%), Positives = 41/128 (32%), Gaps = 20/128 (15%)

Query: 104 VGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI--------WI 153
           +   I A+ +A     PV+VK             +  +   I ++G + I          
Sbjct: 289 LAQLIYALKEATHYEKPVSVKI-------AAVHNVAAIASGIARAGADIIYIDGFRGGTG 341

Query: 154 HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDG 212
            A   I   +       I  +D  +  E  + +  +     GG+      A  I    D 
Sbjct: 342 AAPTVIRDHIGIPIELAIAAVDDRLRAEGIRNSVSIV--AAGGIRHSGDVAKAIALGADA 399

Query: 213 VMIGRAAY 220
           V IG AA 
Sbjct: 400 VAIGTAAL 407


>gi|331017076|gb|EGH97132.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas syringae
           pv. lachrymans str. M302278PT]
          Length = 245

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ D+V  I K  P+L I + GG+  +      +   V  V+IG  A K+   +     
Sbjct: 60  PVNGDVVTAIAKRYPNLPIQIGGGIRSLETIEHYIKAGVSYVIIGTKAVKDPEFVAQACR 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++S       A+   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADG 160


>gi|311279486|ref|YP_003941717.1| NADH:flavin oxidoreductase/NADH oxidase [Enterobacter cloacae SCF1]
 gi|308748681|gb|ADO48433.1| NADH:flavin oxidoreductase/NADH oxidase [Enterobacter cloacae SCF1]
          Length = 365

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 61/187 (32%), Gaps = 26/187 (13%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              +A     + G++ + L             PSA      +G  +     +V + + A+
Sbjct: 163 DFRQAVINAREAGFDLVELHSAHGYLLHQFLSPSANHRTDQYGGSIENRARLVLEVVDAV 222

Query: 112 CKA-----LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            +A     + I V+        D  P     + +  I++ G  GI           +S  
Sbjct: 223 SEAWGADRIGIRVSPIGSFQNTDNGPNEE-ADALYLIEELGKRGIA-------YLHMSEP 274

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           D             ++++      IG   G   + +A  ++    +D V  GRA   N  
Sbjct: 275 DWAGGEPYTDAFRRKVRERFHGAIIGA--GAYTLEKAEDLIGKGLIDAVAFGRAWIANPD 332

Query: 225 MLTTVDE 231
           ++  +  
Sbjct: 333 LVARLKH 339


>gi|262040043|ref|ZP_06013305.1| imidazoleglycerol phosphate synthase [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259042620|gb|EEW43629.1| imidazoleglycerol phosphate synthase [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 258

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAQILSFGADKISINSPALADPTLITRLADRFG 121


>gi|206577737|ref|YP_002237535.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           pneumoniae 342]
 gi|288934452|ref|YP_003438511.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           variicola At-22]
 gi|290508656|ref|ZP_06548027.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           sp. 1_1_55]
 gi|226700530|sp|B5XPE2|HIS6_KLEP3 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|206566795|gb|ACI08571.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           pneumoniae 342]
 gi|288889181|gb|ADC57499.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           variicola At-22]
 gi|289778050|gb|EFD86047.1| imidazoleglycerol phosphate synthase, cyclase subunit [Klebsiella
           sp. 1_1_55]
          Length = 258

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAQILSFGADKISINSPALADPTLITRLADRFG 121


>gi|28872447|ref|NP_795066.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudomonas syringae pv. tomato str. DC3000]
 gi|213971183|ref|ZP_03399301.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudomonas syringae pv. tomato T1]
 gi|301382311|ref|ZP_07230729.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas syringae
           pv. tomato Max13]
 gi|302058518|ref|ZP_07250059.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas syringae
           pv. tomato K40]
 gi|31563079|sp|Q87UG3|HIS4_PSESM RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|28855702|gb|AAO58761.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudomonas syringae pv. tomato str. DC3000]
 gi|213924052|gb|EEB57629.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Pseudomonas syringae pv. tomato T1]
          Length = 245

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ D+V  I K  P+L I + GG+  +      +   V  V+IG  A K+   +     
Sbjct: 60  PVNGDVVTAIAKRYPNLPIQIGGGIRSLETIEHYIKAGVSYVIIGTKAVKDPEFVAQACR 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++S       A+   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADG 160


>gi|213971258|ref|ZP_03399375.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato T1]
 gi|301383892|ref|ZP_07232310.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato Max13]
 gi|302063595|ref|ZP_07255136.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato K40]
 gi|302131004|ref|ZP_07256994.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato NCPPB 1108]
 gi|213924011|gb|EEB57589.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato T1]
          Length = 363

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 61/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVLEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +    + +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREAGIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|94272494|ref|ZP_01292135.1| 2-nitropropane dioxygenase, NPD [delta proteobacterium MLMS-1]
 gi|93450110|gb|EAT01452.1| 2-nitropropane dioxygenase, NPD [delta proteobacterium MLMS-1]
          Length = 284

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +  +K G   I + A++A     + +  R+I         E++K    + +   GG+ 
Sbjct: 125 FARLAEKLGAAAIVVEAKEAGGHLGTDQALREIFP-------EVRKVVKKVPLIAAGGIT 177

Query: 199 DMSQALKILP--SVDGVMIG 216
           +  +  +++     DGV I 
Sbjct: 178 NGYEMAEMMEHYGADGVQIA 197


>gi|58696722|ref|ZP_00372267.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Drosophila simulans]
 gi|58537090|gb|EAL60210.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Drosophila simulans]
          Length = 494

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 20/117 (17%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +A +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 264 KMYPNTQLIGGNIATKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGVPQFSAIKN-- 321

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              V E  +   ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 322 ---VAEACRAR-NVRLIADGGVKYSGDVAKAIAAGADSVMIG-------SIFAGTDE 367


>gi|330876811|gb|EGH10960.1| xenobiotic reductase A [Pseudomonas syringae pv. morsprunorum str.
           M302280PT]
          Length = 363

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 61/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVLEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +    + +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREAGIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|222480633|ref|YP_002566870.1| Vitamin B6 biosynthesis protein [Halorubrum lacusprofundi ATCC
           49239]
 gi|254781606|sp|B9LRS6|PDXS_HALLT RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|222453535|gb|ACM57800.1| Vitamin B6 biosynthesis protein [Halorubrum lacusprofundi ATCC
           49239]
          Length = 302

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 36/216 (16%), Positives = 63/216 (29%), Gaps = 66/216 (30%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G   +      P+        G   M +P+ V + I      +SIPV  K RI
Sbjct: 39  ARIAEDTGAVAVMALEAVPAD--IRKRGGVARMPDPENVTEIIDE----VSIPVMGKSRI 92

Query: 126 GVDDQIPAVA-------------------------------------LRNLVKSIKKSGV 148
           G   +   +                                      L   ++ I++   
Sbjct: 93  GHRKEAEILESLGVDMIDESEVLTPADDEYHTDKRDFASPFVCGARDLPEALRRIREGAA 152

Query: 149 ------------------NGIWIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKKENP 187
                             +   I  +   L GL+ ++  K         D+V+E  +   
Sbjct: 153 MIRTKGEAGTGDVNQAVKHQRTIKTQIRTLTGLNHEEREKWAREHGAPRDLVHETAEAGR 212

Query: 188 DLFI-GLNGGLEDM-SQALKILPSVDGVMIGRAAYK 221
              +    GG+      AL +    DG+ +G   + 
Sbjct: 213 LPVVNFAAGGIATPADAALMMYHGCDGIFVGSGIFG 248


>gi|85710732|ref|ZP_01041796.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           isomerase [Erythrobacter sp. NAP1]
 gi|85687910|gb|EAQ27915.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           isomerase [Erythrobacter sp. NAP1]
          Length = 245

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 66/175 (37%), Gaps = 30/175 (17%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSF---------GACLMLNPDIVGDCIAAMCKA 114
           EA K + +     + L  G   A+  EG F         G+  + +P+ V +        
Sbjct: 67  EAVKAIVERFPGYVQLGGGIRDAKAVEGWFDLGVARVVMGSAALKDPEFVREMAREWEGG 126

Query: 115 LSIPVTVKCRIGVDD---QIPAVALRNLVKSIKKSGVN--GIWIHARKAILKGLSPKDNR 169
           + + V  K  +   +   ++  V + +L +  + +GV         R  +LKG++     
Sbjct: 127 IVVAVDAKDGMVATEGWAEVSDVPVVDLARRFEDAGVASLLFTDIGRDGLLKGVNIDATV 186

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQA----LKILPSVDGVMIGRAAY 220
            +             +  D+ +  +GG++ +       L     ++GV+ GRA Y
Sbjct: 187 DLA------------QRVDIPVIASGGVKGLDDIHVLSLNAHNGIEGVITGRALY 229


>gi|289577276|ref|YP_003475903.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           italicus Ab9]
 gi|289526989|gb|ADD01341.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           italicus Ab9]
          Length = 337

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 60/178 (33%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA+     GY+ + ++            P +   +  +G  +      + + I  + 
Sbjct: 145 FGEAARRAHLAGYDVVEIHAAHGYLIHEFLSPLSNKRKDEYGGSIENRARFLIEVIEEVR 204

Query: 113 KALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K       I V V     ++  I    + + +  IK   V+ I + +      GL   D 
Sbjct: 205 KNWPQTKLIFVRVSADDYIEGGINIDMMVDYINMIKDK-VDLIDVSSG-----GLLSADI 258

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              P         IKK   ++     G +     A +IL +   D V +GR   +N  
Sbjct: 259 NLYPGYQVKYAETIKKRC-NIKTSAVGLITTQELAEEILSNKRADLVALGRELLRNPY 315


>gi|240103669|ref|YP_002959978.1| imidazole glycerol phosphate synthase subunit HisF [Thermococcus
           gammatolerans EJ3]
 gi|259709883|sp|C5A7A2|HIS6_THEGJ RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|239911223|gb|ACS34114.1| Imidazole glycerol phosphate synthase, cyclase subunit (hisF)
           [Thermococcus gammatolerans EJ3]
          Length = 252

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 48/135 (35%), Gaps = 16/135 (11%)

Query: 103 IVGDCIAAM-CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +    IAA+  K   +   +K +   D   P      L +  +K G++ I      A  +
Sbjct: 2   LAKRIIAALDIKEGRVVKGIKFKNIRDAGDP----IELARRYEKEGIDEIVFLDITASYE 57

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
                       +  D+V  I +E    F    GG+  + +A +I+    D V I  AA 
Sbjct: 58  KRG---------ILLDLVERIAEEIYVPFTVG-GGIRTVEEAREIIKRGADKVFINTAAV 107

Query: 221 KNSAMLTTVDEYFSN 235
               ++  + +    
Sbjct: 108 DRPELVREIAQVVGT 122


>gi|304393347|ref|ZP_07375275.1| chain A, Xenobiotic Reductase A In Complex With Coumarin [Ahrensia
           sp. R2A130]
 gi|303294354|gb|EFL88726.1| chain A, Xenobiotic Reductase A In Complex With Coumarin [Ahrensia
           sp. R2A130]
          Length = 371

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 39/234 (16%), Positives = 69/234 (29%), Gaps = 34/234 (14%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           + A A+   D  +         P A  + G D+++L  A           G++ I L+  
Sbjct: 130 VSASALPYADGWH--------TPHA--LSGNDLAQLKTAFVDSTHRAVAAGFDVIELHAA 179

Query: 83  ---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC-KALSIPVTVKCRIGVDDQIP 132
                     P +     +FG  L        +   AM   A   P+ V+          
Sbjct: 180 HGYLMHQFLSPISNQRSDAFGGHLAGRMAFPLEVFEAMRIAAGDTPLGVRISASDWVADS 239

Query: 133 AVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           +  ++        +K  G + I + +      G SP+              +  +E   L
Sbjct: 240 SWTIQESNVFCTELKARGCDFIDVSSA-----GNSPQQKISTGPGYQTGFAQAVREATGL 294

Query: 190 FIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
            +   G + +  QA  IL     D V + R    +        E      T   
Sbjct: 295 PVMAVGKITNAIQAETILATGQADMVALARGMLLDPRWAWRAAEKLGEQATFPP 348


>gi|255264117|ref|ZP_05343459.1| L-lactate dehydrogenase [Thalassiobium sp. R2A62]
 gi|255106452|gb|EET49126.1| L-lactate dehydrogenase [Thalassiobium sp. R2A62]
          Length = 378

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 28/130 (21%), Positives = 48/130 (36%), Gaps = 22/130 (16%)

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVN 149
               G  L  +PD     + A+      P+ VK  +  DD           + + K G +
Sbjct: 224 NQHIGYLLRTSPDWSY--LRALRDEWDGPLIVKGVMNPDD----------CERLAKDGAD 271

Query: 150 GIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP- 208
            IWI          +P    ++P +         +   +L + ++ G+E     L+ L  
Sbjct: 272 AIWISNHAGRQFDAAPATIEQLPAI---------RAATELPVIMDSGVETGLDVLRALAL 322

Query: 209 SVDGVMIGRA 218
             D VM+GRA
Sbjct: 323 GADFVMLGRA 332


>gi|254881743|ref|ZP_05254453.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 4_3_47FAA]
 gi|294776253|ref|ZP_06741738.1| dihydroorotate oxidase [Bacteroides vulgatus PC510]
 gi|319643710|ref|ZP_07998326.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_1_40A]
 gi|254834536|gb|EET14845.1| dihydroorotate dehydrogenase 2 [Bacteroides sp. 4_3_47FAA]
 gi|294449936|gb|EFG18451.1| dihydroorotate oxidase [Bacteroides vulgatus PC510]
 gi|317384652|gb|EFV65615.1| dihydroorotate dehydrogenase [Bacteroides sp. 3_1_40A]
          Length = 324

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 15/87 (17%), Positives = 27/87 (31%), Gaps = 7/87 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
             I    K  +IPV         +        +  ++++ +G + + I      L+    
Sbjct: 85  SLIEQTKKLCTIPVIASI-----NCFSNSEWTDFARTVEAAGADALEI--NILSLQTEKE 137

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIG 192
                      DIV  IKK+     I 
Sbjct: 138 YQYGAFEQRHIDIVSSIKKQISIPVIV 164


>gi|253578131|ref|ZP_04855403.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850449|gb|EES78407.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 252

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 17/116 (14%), Positives = 40/116 (34%), Gaps = 11/116 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+   +G + +        L   +  + R       D+V  +   N  +   + GG+
Sbjct: 34  EIAKAYDAAGADELV------FLDITASCEQRDTV---VDMVRRVA-ANVFIPFTVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFW 252
             +    K+L    D + +  AA     +++   + F +     +    R +   W
Sbjct: 84  RTVDDFKKLLREGADKISVNSAAIDRPELISEAADKFGSQCVVVAIDAKRREDGGW 139


>gi|225630007|ref|YP_002726798.1| inosine monophosphate dehydrogenase [Wolbachia sp. wRi]
 gi|225591988|gb|ACN95007.1| inosine monophosphate dehydrogenase [Wolbachia sp. wRi]
          Length = 497

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 20/117 (17%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +A +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 267 KMYPNTQLIGGNIATKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGVPQFSAIKN-- 324

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              V E  +   ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 325 ---VAEACRAR-NVRLIADGGVKYSGDVAKAIAAGADSVMIG-------SIFAGTDE 370


>gi|99034743|ref|ZP_01314672.1| hypothetical protein Wendoof_01000513 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 366

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 20/117 (17%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +A +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 136 KMYPNTQLIGGNIATKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGVPQFSAIKN-- 193

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              V E  +   ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 194 ---VAEACRAR-NVRLIADGGVKYSGDVAKAIAAGADSVMIG-------SIFAGTDE 239


>gi|94266548|ref|ZP_01290234.1| 2-nitropropane dioxygenase, NPD [delta proteobacterium MLMS-1]
 gi|93452823|gb|EAT03349.1| 2-nitropropane dioxygenase, NPD [delta proteobacterium MLMS-1]
          Length = 330

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
             +  +K G   I + A++A     + +  R+I         E++K    + +   GG+ 
Sbjct: 125 FARLAEKLGAAAIVVEAKEAGGHLGTDQALREIFP-------EVRKVVKKVPLIAAGGIT 177

Query: 199 DMSQALKILP--SVDGVMIG 216
           +  +  +++     DGV I 
Sbjct: 178 NGYEMAEMMEHYGADGVQIA 197


>gi|42519998|ref|NP_965913.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Drosophila melanogaster]
 gi|42409735|gb|AAS13847.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Drosophila melanogaster]
          Length = 494

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 20/117 (17%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +A +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 264 KMYPNTQLIGGNIATKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGVPQFSAIKN-- 321

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              V E  +   ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 322 ---VAEACRAR-NVRLIADGGVKYSGDVAKAIAAGADSVMIG-------SIFAGTDE 367


>gi|34541640|ref|NP_906119.1| dihydroorotate dehydrogenase 2 [Porphyromonas gingivalis W83]
 gi|34397958|gb|AAQ67018.1| dihydroorotate dehydrogenase family protein [Porphyromonas
           gingivalis W83]
          Length = 326

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 33/169 (19%), Positives = 64/169 (37%), Gaps = 22/169 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG-DC 107
           P+   I        V+ AK  E+ G + + +N      R++   F        + +  D 
Sbjct: 98  PVIASINCFRSDSWVDFAKQFEEAGADALEIN----VMRLNTDLFFDA--NKAEQMYVDI 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK-------AIL 160
           I+++ KA+ IPV VK             + +LV  ++ +G  G+ +  R          +
Sbjct: 152 ISSLIKAIRIPVVVKLSKSF------ANIPSLVDKLRAAGAKGVVLFNRSYQPDIDIDKV 205

Query: 161 KGLSPKDNRKIPNLDYDIVYE--IKKENPDLFIGLNGGLEDMSQALKIL 207
           + ++         +   I +   +    P + I  + G+ D   ALK L
Sbjct: 206 QMVAGDVFTSAGEISDTIRHAGIVSALVPGISIASSTGIHDGEAALKCL 254


>gi|58698104|ref|ZP_00373027.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535350|gb|EAL59426.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 497

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 20/117 (17%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +A +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 267 KMYPNTQLIGGNIATKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGVPQFSAIKN-- 324

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              V E  +   ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 325 ---VAEACRAR-NVRLIADGGVKYSGDVAKAIAAGADSVMIG-------SIFAGTDE 370


>gi|290892764|ref|ZP_06555755.1| hisA protein [Listeria monocytogenes FSL J2-071]
 gi|290557576|gb|EFD91099.1| hisA protein [Listeria monocytogenes FSL J2-071]
          Length = 240

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 49/134 (36%), Gaps = 12/134 (8%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            K+    G   + I      L+G           ++ +++ ++K     + + + GG+  
Sbjct: 36  AKAFATDGATYLHIVDLDGALEGR---------PINLEVIKKMKTTA-KIPVQVGGGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLT-TVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           M+Q    L   +D V+IG AA  +   L   V +Y +    G       V    W  +S 
Sbjct: 86  MAQVDYYLESGIDRVIIGSAALTDPDFLRAAVQKYGAKIAAGIDAKNGLVATRGWLDVSQ 145

Query: 258 SMTDYAARHLHSGG 271
                 A+ +   G
Sbjct: 146 VNYLDLAKQMEEAG 159


>gi|226503259|ref|NP_001141519.1| hypothetical protein LOC100273631 [Zea mays]
 gi|194704906|gb|ACF86537.1| unknown [Zea mays]
          Length = 451

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 30/197 (15%), Positives = 60/197 (30%), Gaps = 41/197 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V+AA      G++ I L+            PS       +G        +  + +  +
Sbjct: 226 DFVKAANRAVTAGFDVIELHFAHGYLVSSFLTPSVNKRTDQYGGSFENRARLALELVEEV 285

Query: 112 CKALS--IPVTVKCRI---------GVDDQIPAVALRNLVKSIKKSGVNGIWI-----HA 155
              +   +P+ V+               +         L     + GV+ I +     H 
Sbjct: 286 RAVIPETMPLFVRISATDWLDTNPDYTGESWTVEEAAKLAGLFAERGVDVIDVSSGGNHP 345

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS----- 209
           ++ +  G         P         IKK   D + +   G ++  + A +I+       
Sbjct: 346 QQKVQGG---------PGYQAKFAKHIKKVVGDKMLVSSVGSIKTGTLAEEIISGKDDGV 396

Query: 210 -VDGVMIGRAAYKNSAM 225
            +D +  GR   KN  +
Sbjct: 397 KLDLIAAGRMFQKNPGL 413


>gi|85372672|gb|ABC70127.1| dihydroorotate dehydrogenase [Haloquadratum walsbyi]
          Length = 360

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 50/146 (34%), Gaps = 18/146 (12%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +I E  G + + +NV CP       S G   +   D +   + A+  A +  V VK    
Sbjct: 176 QIAE--GADYVAVNVSCP------NSEGMQDLQQRDSLSRIMDALTNAGAETVLVKLAPE 227

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY------ 180
           +        + +LV      G+  I  +      + L      +   L    +       
Sbjct: 228 LSLSAIEDVI-DLVDIFDLDGI--ITTNTTTERPENLESTKQTERGGLSGAPIEDHATKL 284

Query: 181 -EIKKENPDLFIGLNGGLEDMSQALK 205
            E+  +  D+ I   GG+ D + A  
Sbjct: 285 VELVAKRTDVPIIGVGGVSDAAGAYA 310


>gi|33592972|ref|NP_880616.1| NADH-dependent flavin oxidoreductase [Bordetella pertussis Tohama
           I]
 gi|33572620|emb|CAE42213.1| probable NADH-dependent flavin oxidoreductase [Bordetella pertussis
           Tohama I]
 gi|332382384|gb|AEE67231.1| NADH-dependent flavin oxidoreductase [Bordetella pertussis CS]
          Length = 342

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 21/135 (15%), Positives = 43/135 (31%), Gaps = 21/135 (15%)

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIPA------VALRNLVKSIKKSGVNGIWIHAR 156
           I    + A+ +A  +P+     I   D+           +  L+  + ++G + + I +R
Sbjct: 199 IAEAVLRAVRQACPLPIGFNYSIYKMDEYRYQPPGGGAEIAALLARLCQAGADILHISSR 258

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL-FIGLNGGLEDMSQALKIL--PSVDGV 213
                       R +    +  +            + +NGGL  +     +L     D V
Sbjct: 259 ------------RVLKPEPWGGLLAQLARAAAPKALMVNGGLATLQDCETVLAATQADLV 306

Query: 214 MIGRAAYKNSAMLTT 228
            + R    N   L  
Sbjct: 307 SLARPFLANPDWLAR 321


>gi|330722179|gb|EGH00077.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [gamma proteobacterium IMCC2047]
          Length = 245

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNS-AMLTTVD 230
            ++  IV  I +  PDL I + GG+         L   V  V+IG  A K    +     
Sbjct: 60  PVNGGIVKAIAEAYPDLPIQIGGGIRSFETIQAYLDAGVQYVIIGTKAVKEPEFVFEACK 119

Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKI 255
            +  + + G      +V  D W ++
Sbjct: 120 RFPGHIIVGLDAKDGKVAIDGWAEV 144


>gi|324998590|ref|ZP_08119702.1| 2-nitropropane dioxygenase precursor [Pseudonocardia sp. P1]
          Length = 318

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 132 PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFI 191
             VA     +    +GV+G+ +   +A   G  P        +   +V  +    PD+ +
Sbjct: 117 HVVAGAEHARKAADAGVDGLVVVGAEA---GGHPPPALVTTMV---LVRAVATAVPDIPV 170

Query: 192 GLNGGLEDMSQALKILP-SVDG 212
             +GG+ D +    +L    DG
Sbjct: 171 VASGGIADGAGLAAVLALGADG 192


>gi|315093248|gb|EFT65224.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL060PA1]
          Length = 279

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 44/221 (19%), Positives = 67/221 (30%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI E+ G   +      P+        G   M +PD++   I A    +SIPV  K RI
Sbjct: 16  AKIAENAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 126 --------------GVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                            D+   ++  +    I K                       GV 
Sbjct: 70  GHFVEAQVLESLKVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGVA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|300088233|ref|YP_003758755.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Dehalogenimonas lykanthroporepellens BL-DC-9]
 gi|299527966|gb|ADJ26434.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Dehalogenimonas lykanthroporepellens BL-DC-9]
          Length = 281

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEY 232
           ++ +++ +I +    + + + GG+ D+    ++L   +D V++G AA +N  ++      
Sbjct: 107 VNLNVISQIAQSAV-VPVQMGGGIRDLDSIRRLLKAGIDRVILGTAAVENPDLVAEACRN 165

Query: 233 FSN 235
           F  
Sbjct: 166 FGE 168


>gi|271500806|ref|YP_003333831.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dickeya
           dadantii Ech586]
 gi|270344361|gb|ACZ77126.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dickeya
           dadantii Ech586]
          Length = 258

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  + A+++ + + + 
Sbjct: 85  SVEDAGQILSFGADKISINSPALADPALISRLADRYG 121


>gi|268678703|ref|YP_003303134.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Sulfurospirillum deleyianum DSM 6946]
 gi|268616734|gb|ACZ11099.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Sulfurospirillum deleyianum DSM 6946]
          Length = 252

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 40/125 (32%), Gaps = 11/125 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K     G + +      A  +G              DIV ++ +E   + + + GG+
Sbjct: 36  EIAKRYNDEGADELTFLDITASHEGRGTI---------VDIVEKVAREVF-IPLTVGGGI 85

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +    K+L    D V I   A  N   +    + F +     +    R    +   ++
Sbjct: 86  RTLEDIYKLLHVGCDKVSINSPAIANPDFINEAAKRFGSQCIVVAIDAKRTGDSWHVYVN 145

Query: 257 ASMTD 261
               D
Sbjct: 146 GGRID 150


>gi|153953640|ref|YP_001394405.1| enoate reductase [Clostridium kluyveri DSM 555]
 gi|146346521|gb|EDK33057.1| Predicted enoate reductase [Clostridium kluyveri DSM 555]
          Length = 640

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 59/178 (33%), Gaps = 20/178 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCIAAMC 112
           +AA   +  G + +   V C          S R ++    FG C      +    I  + 
Sbjct: 151 DAALRAKKAGADAVE--VHCAHGYLINSFLSPRTNKRVDEFGGCFENRMRLPRLIIENIR 208

Query: 113 KALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D++P          +   ++  GV+ + +     +         
Sbjct: 209 KKVGHSIAIICRINSSDEMPGGLDVHDSATIAAYLEDIGVDALHVSRAVHLRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                   ++  EIK+   D+ +   G   +   A  ++     D V  GR +  +  
Sbjct: 269 VLHGGFSAELATEIKRAV-DIPVITVGRFTEPHFAELLVREGRCDLVAFGRQSLTDPH 325


>gi|325522689|gb|EGD01201.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. TJI49]
          Length = 370

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 60/186 (32%), Gaps = 27/186 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINL---NVGCPSARVHEG------SFGACLMLNPDIVGDCIAA 110
            +  +AA   +  G++ + +   N   P   +          +G  L      + + + A
Sbjct: 161 DEFRQAAVRAKAAGFDGVEIHAANGYLPHQFLSSTLNRRDDRYGGSLANRARFLAEIVDA 220

Query: 111 MCKALSI-PVTVKCRIG-----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
           +   + +  V V+         V D  P      + + + ++GV               +
Sbjct: 221 VGGVMPLSRVGVRISPYAKYNNVRDADPDATYAYVGRLLDEAGVA----------YVHAA 270

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNS 223
             +          IV   +K      +  NGG+  D +QAL      D V   RA   N 
Sbjct: 271 DTNGWSGEPDLPRIVENTRKHFGGTLVV-NGGIAPDAAQALIDAGDADLVAFARAYIANP 329

Query: 224 AMLTTV 229
            ++  +
Sbjct: 330 DLVERI 335


>gi|270261097|ref|ZP_06189370.1| imidazole glycerol phosphate synthase subunit HisF [Serratia
           odorifera 4Rx13]
 gi|270044581|gb|EFA17672.1| imidazole glycerol phosphate synthase subunit HisF [Serratia
           odorifera 4Rx13]
          Length = 258

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + + F 
Sbjct: 85  SLEDASQILSFGADKISINSPALADPTLISRLADRFG 121


>gi|118586213|ref|ZP_01543679.1| hypothetical protein OENOO_23005 [Oenococcus oeni ATCC BAA-1163]
 gi|118433353|gb|EAV40053.1| hypothetical protein OENOO_23005 [Oenococcus oeni ATCC BAA-1163]
          Length = 195

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 6/63 (9%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      + A+  A+SIPV  K
Sbjct: 28  AEQAKIAEEAGATAVMALERVPSD--IRKAGGVARMADP----AIVEAVQNAVSIPVMAK 81

Query: 123 CRI 125
            RI
Sbjct: 82  ARI 84


>gi|33574887|emb|CAE39550.1| histidine biosynthesis protein [Bordetella parapertussis]
 gi|33577956|emb|CAE35221.1| histidine biosynthesis protein [Bordetella bronchiseptica RB50]
          Length = 261

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I +   D + + + GG+ D+    + L   +  V+IG AA KN   L      F   
Sbjct: 81  IKAILQAVGDDIPVQIGGGIRDLDTIERYLDAGISYVIIGTAAVKNPGFLQDACGAFPGQ 140

Query: 237 LT-GSSPIKTRVDKDFWRKISAS 258
           +  G      +V  D W K++  
Sbjct: 141 IIVGLDARDGKVATDGWSKLTRH 163


>gi|331697963|ref|YP_004334202.1| 2,4-dienoyl-CoA reductase [Pseudonocardia dioxanivorans CB1190]
 gi|326952652|gb|AEA26349.1| 2,4-dienoyl-CoA reductase (NADPH) [Pseudonocardia dioxanivorans
           CB1190]
          Length = 673

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 19/157 (12%), Positives = 50/157 (31%), Gaps = 10/157 (6%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR--IGVDDQIPAVALRNLVK 141
           P     +  +G  L     +    +  +  A  +PV ++      +   +    +  +V 
Sbjct: 180 PVTNQRDDEYGGSLGNRMRLSRRVLETVRSATDLPVGIRISADEFLPGGLDVAQMIEIVG 239

Query: 142 SIKKSGVNGIWIHARKAILKG-----LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
            +++      ++H   +   G         D               ++  P L +     
Sbjct: 240 LLRE-EFPLAYVHVSHSAYHGSWSLSTQMADMSFGHAPFRHHAAAFRRALPGLPVIAVCR 298

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
           L+ + +A +++     D V + R    +  ++  V E
Sbjct: 299 LDTLPEAAELVADGDADLVALARPHIADPHLVRKVAE 335


>gi|313622813|gb|EFR93142.1| enoyl-(acyl-carrier-protein) reductase II [Listeria innocua FSL
           J1-023]
          Length = 309

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 18/127 (14%), Positives = 43/127 (33%), Gaps = 16/127 (12%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           +   P++V   I    + +        P   K +      I  +    + + +++ GV+ 
Sbjct: 72  MPNCPELVDVIIEEEVRIVTTGAGTPKPFMEKFKAAGIKVIAVIPSVKIAQKMEEIGVDA 131

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-S 209
           +     +A   G    +   +      +V ++     ++ +   GG+ D      +    
Sbjct: 132 VVAEGTEA---GGHVGETTTMA-----LVRQVVSAV-NIPVIAAGGIADGHGMAAVYALG 182

Query: 210 VDGVMIG 216
             GV IG
Sbjct: 183 ASGVQIG 189


>gi|311029279|ref|ZP_07707369.1| geranylgeranylglyceryl phosphate synthase-like protein [Bacillus
           sp. m3-13]
          Length = 229

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 47/128 (36%), Gaps = 23/128 (17%)

Query: 98  MLNPDIVGD---CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
           M   +IV +    + A CKA  +    + +  +D +   +A   L + +    +  +   
Sbjct: 109 MNWEEIVAEGYCILNADCKAAKL---TEAKTDLDKED-VIAYARLAEKMFNLPIFYL--- 161

Query: 155 ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                  G            D +IV   K+      +   GG+    +A ++    D V+
Sbjct: 162 ----EYSGTYG---------DVEIVQAAKQTLEKTQLFYGGGISTAERAKEMAAHADTVV 208

Query: 215 IGRAAYKN 222
           +G A Y+N
Sbjct: 209 VGNAVYEN 216


>gi|302872837|ref|YP_003841473.1| Radical SAM domain protein [Caldicellulosiruptor obsidiansis OB47]
 gi|302575696|gb|ADL43487.1| Radical SAM domain protein [Caldicellulosiruptor obsidiansis OB47]
          Length = 351

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 56/162 (34%), Gaps = 26/162 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++VE AK     GY  + L              G  +    D +   I  + + + + +
Sbjct: 87  DEIVEVAKRAYQMGYRTVVLQS------------GEDMFYTKDRMCSIIKKIKQNVDVAI 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           T+       D+          K+ K +G +   +    +  K               + +
Sbjct: 135 TLSIGERSYDEY---------KAFKDAGADRFLMRFETSNEKLYRQYHPGMSFEKRIECL 185

Query: 180 YEIK----KENPDLFIGLNG-GLEDMSQALKILPSVDGVMIG 216
             +K    +      IGL G  ++D++Q + ++  +D  MIG
Sbjct: 186 KWLKSLGYELGTGFLIGLPGQTIDDLAQDILLVKELDADMIG 227


>gi|288560179|ref|YP_003423665.1| isopentenyl diphosphate delta-isomerase Fni [Methanobrevibacter
           ruminantium M1]
 gi|288542889|gb|ADC46773.1| isopentenyl diphosphate delta-isomerase Fni [Methanobrevibacter
           ruminantium M1]
          Length = 350

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 45/119 (37%), Gaps = 18/119 (15%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR---KAILKG 162
           D I  +CK + +PV  K      +    +   + ++ ++K+GV+ I +            
Sbjct: 168 DSIKEICKTVDVPVMAK------ETGTGIRAEDAIE-LEKAGVSFIDVEGAGGTSWAAVE 220

Query: 163 LSPKDNRKIPNLDYDI-----VYEI-KKENPDLFIGLNGGL--EDMSQALKILPSVDGV 213
               ++R +  L +D      V  +    + ++ +  +GG+      +   I    D V
Sbjct: 221 TYRAEDRYLGELFWDWGIPTAVSTVEVVNSVEIPVVSSGGISFRTRCKLRAIALGADAV 279


>gi|227549270|ref|ZP_03979319.1| dihydroorotate dehydrogenase 2 [Corynebacterium lipophiloflavum DSM
           44291]
 gi|227078589|gb|EEI16552.1| dihydroorotate dehydrogenase 2 [Corynebacterium lipophiloflavum DSM
           44291]
          Length = 361

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 18/117 (15%), Positives = 42/117 (35%), Gaps = 11/117 (9%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIW 152
           + +   ++A+ +A   PV VK    + D+    A+ +L   +   G+          G+ 
Sbjct: 192 EELRPILSAVAEATDTPVLVKIAPDLSDED-VDAVADLALELALDGIVATNTTISRAGLA 250

Query: 153 IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               +    G        + +   +++  +     D L +   GG+    QA + + 
Sbjct: 251 TDPAEVEALGAGGISGVPLNDRSLEVLKRLHARVGDQLVLVSVGGISTAQQAWERIA 307


>gi|225677137|ref|ZP_03788136.1| inosine monophosphate dehydrogenase [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225590804|gb|EEH12032.1| inosine monophosphate dehydrogenase [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 497

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 20/117 (17%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +A +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 267 KMYPNTQLIGGNIATKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGVPQFSAIKN-- 324

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
              V E  +   ++ +  +GG++     A  I    D VMIG       ++    DE
Sbjct: 325 ---VAEACRAR-NVRLIADGGVKYSGDVAKAIAAGADSVMIG-------SIFAGTDE 370


>gi|224282487|ref|ZP_03645809.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium bifidum
           NCIMB 41171]
 gi|313139637|ref|ZP_07801830.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
 gi|313132147|gb|EFR49764.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
          Length = 377

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 35/199 (17%), Positives = 64/199 (32%), Gaps = 28/199 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG------------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             +AA+     G+  I ++              C         +G  +      + +   
Sbjct: 175 FRDAAQRAVRAGFEAIEIHAAHGYLISQFLDPLC---NERADEYGGDIHGRMRFLLEVAD 231

Query: 110 AMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +   V +  RI   D            +    +K+ GV+ + +     I     P
Sbjct: 232 AIREVIPDTVPLLVRISATDWAAGGWDLDQTVDTACVLKQHGVDLMDVSTGGIIADVSIP 291

Query: 166 -KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
            K N ++P  D        +E   +     G +    QA KIL     D V IGRAA ++
Sbjct: 292 VKANYQVPFSDQ------VRERAAIPTTTVGLITKPKQAEKILRAGQADAVEIGRAALRD 345

Query: 223 SAMLTTVDEYFSNPLTGSS 241
                        P++ + 
Sbjct: 346 PYWPLRAAAKLGVPVSKAP 364


>gi|254173013|ref|ZP_04879687.1| radical SAM domain protein [Thermococcus sp. AM4]
 gi|214033169|gb|EEB73997.1| radical SAM domain protein [Thermococcus sp. AM4]
          Length = 590

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 17/81 (20%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q  G +      L+E  KI ++ GY+ I LN         
Sbjct: 173 QIRMMLRNAKKEYPIGANAVQFTGGEPTLRDDLIEIIKIAKEEGYDHIQLNTD------- 225

Query: 90  EGSFGACLMLNPDIVGDCIAA 110
               G  L   P++V     A
Sbjct: 226 ----GIKLAFEPELVKKIREA 242


>gi|217963603|ref|YP_002349281.1| NADH:flavin oxidoreductase, old yellow enzyme family [Listeria
           monocytogenes HCC23]
 gi|217332873|gb|ACK38667.1| NADH:flavin oxidoreductase, old yellow enzyme family [Listeria
           monocytogenes HCC23]
 gi|307571821|emb|CAR85000.1| NADH oxidase, putative [Listeria monocytogenes L99]
          Length = 641

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|210610031|ref|ZP_03288210.1| hypothetical protein CLONEX_00396 [Clostridium nexile DSM 1787]
 gi|210152642|gb|EEA83648.1| hypothetical protein CLONEX_00396 [Clostridium nexile DSM 1787]
          Length = 667

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 26/182 (14%), Positives = 54/182 (29%), Gaps = 19/182 (10%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCI-AAMCK 113
           EAAK  +  G++ + ++ G          P        FG     N       +   +  
Sbjct: 154 EAAKRAQIAGFDAVEIHAGHSYLLSQFLSPITNKRTDEFGGS-PENRARFAKMVIEEVRA 212

Query: 114 ALS----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
            +     I V +     ++         + ++  +K  V+   +              N 
Sbjct: 213 QVGPFFPIFVRISADEFLEGGNTLEDTLDYLQYFEK-EVDVFDVSCGLNGSIQYQIDANY 271

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLT 227
                   +   +K+    + I + G + D   A  IL     D + +GR    +   + 
Sbjct: 272 LEDGWRSYMAKAVKERYGKICITM-GNIRDPQVAEDILERGDADLIGMGRGLIADPEWVN 330

Query: 228 TV 229
            V
Sbjct: 331 KV 332


>gi|118443203|ref|YP_877149.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Clostridium novyi NT]
 gi|148839488|sp|A0PXP7|HIS4_CLONN RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|118133659|gb|ABK60703.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Clostridium novyi NT]
          Length = 238

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 11/107 (10%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           +I A +  +     K+ G   I I      LKG           ++ DIV E+ K+  D+
Sbjct: 26  EIVAESAVDTALMFKECGAEYIHIVDLDGALKGKG---------INLDIVCELIKKV-DI 75

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            I   GG+ D+     ++   V  +++G AA  N  ++    + + +
Sbjct: 76  PIEFGGGIRDIETIDYLIDIGVSRIILGTAALNNEKLVREAIKRYDD 122


>gi|15603069|ref|NP_246141.1| imidazole glycerol phosphate synthase subunit HisF [Pasteurella
           multocida subsp. multocida str. Pm70]
 gi|20454995|sp|Q9CLM0|HIS6_PASMU RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|12721557|gb|AAK03288.1| HisF [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 256

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 15/97 (15%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAQRYAEEGADELVFYDITASSDGRT---------IDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++  + + F 
Sbjct: 85  SVEDAEKLFAFGADKISINSPALADPDLINRLADRFG 121


>gi|88800394|ref|ZP_01115959.1| oxidoreductase [Reinekea sp. MED297]
 gi|88776841|gb|EAR08051.1| oxidoreductase [Reinekea sp. MED297]
          Length = 358

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 80/226 (35%), Gaps = 30/226 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              + AA   +  G++ + L+       +              ++G        ++ + I
Sbjct: 142 DDFIAAAVRCQRAGFDGVELHGA--HNYILCQFLSTEYNRRTDAYGGSAENRSRLLREVI 199

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKS--IKKSGVNGIWIHARKAILKGLSPK 166
           A + +A      V  R+  +    A A    +    ++++G++ + I          SPK
Sbjct: 200 AGIRQACGNEFIVGVRLSPEGFGLAFAEMLTLSESLMREAGIDFLDI---SLWDCFGSPK 256

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGVMIGRAAYKN--- 222
           D         D   E+ +    + +G+ G L   +   + +   VD V++GRAA  +   
Sbjct: 257 DPDFQHKRLIDWYAELPRY--GVPLGVAGKLRTPADIQQAMATGVDFVLLGRAAIIHHDF 314

Query: 223 SAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLH 268
            A +   DE F      S P+      +    +S +  DY  R   
Sbjct: 315 PARM-QADELFE---PRSLPVSRATLAE--EGLSPTFVDYMGRWEG 354


>gi|290893184|ref|ZP_06556172.1| conserved hypothetical protein [Listeria monocytogenes FSL J2-071]
 gi|290557346|gb|EFD90872.1| conserved hypothetical protein [Listeria monocytogenes FSL J2-071]
          Length = 641

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|213019464|ref|ZP_03335270.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Culex quinquefasciatus JHB]
 gi|212994886|gb|EEB55528.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Culex quinquefasciatus JHB]
          Length = 492

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 18/102 (17%), Positives = 37/102 (36%), Gaps = 13/102 (12%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +  +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 264 KMYPNTQLIGGNITTKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGMPQFSAIKN-- 321

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
              + E+ K   ++ +  +GG++     A  I    D VMIG
Sbjct: 322 ---IAEVCK-TKNVRLIADGGIKYSGDVAKAIAAGADTVMIG 359


>gi|205371954|ref|ZP_03224773.1| pyridoxine biosynthesis protein [Bacillus coahuilensis m4-4]
          Length = 293

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 34/89 (38%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      P+        G   M +P      +  +  A+SIPV  K
Sbjct: 27  AEQAKIAEEAGAVAVMALERVPAD--IRKMGGVARMADP----RIVEEVMNAVSIPVMAK 80

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 81  ARIGHIVE---------ARVLEAMGVDYI 100


>gi|311741581|ref|ZP_07715405.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Corynebacterium pseudogenitalium ATCC 33035]
 gi|311303751|gb|EFQ79830.1| imidazole glycerol phosphate synthase, cyclase subunit
           [Corynebacterium pseudogenitalium ATCC 33035]
          Length = 256

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 23/128 (17%), Positives = 43/128 (33%), Gaps = 11/128 (8%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
           I  D+   A     L       G + +      A  +G S            ++V     
Sbjct: 22  INFDNLRDAGDPVELAARYDALGADELTFLDVSASKQGRSTM---------LEVVRR-TA 71

Query: 185 ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           +   + + + GG+  +    ++L    D V +  AA KN  +L  + E F       S  
Sbjct: 72  DQVFIPLTVGGGVRSVDDVRELLRAGADKVSVNTAAIKNPELLREMAEIFGAQCIVLSVD 131

Query: 244 KTRVDKDF 251
             R  +++
Sbjct: 132 ARRCREEY 139


>gi|190570948|ref|YP_001975306.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Culex quinquefasciatus Pel]
 gi|190357220|emb|CAQ54638.1| inosine-5'-monophosphate dehydrogenase [Wolbachia endosymbiont of
           Culex quinquefasciatus Pel]
          Length = 495

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 18/102 (17%), Positives = 37/102 (36%), Gaps = 13/102 (12%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAILKGLSPKDNRKIPNLD 175
           K           +  +   +++  +GV+ + +           I+ G+       I N  
Sbjct: 267 KMYPNTQLIGGNITTKEAAEALIDAGVDAVKVGIGPGSICTTRIVTGVGMPQFSAIKN-- 324

Query: 176 YDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
              + E+ K   ++ +  +GG++     A  I    D VMIG
Sbjct: 325 ---IAEVCK-TKNVRLIADGGIKYSGDVAKAIAAGADTVMIG 362


>gi|188995862|ref|YP_001930114.1| dihydroorotate dehydrogenase 2 [Porphyromonas gingivalis ATCC
           33277]
 gi|188595542|dbj|BAG34517.1| putative dihydroorotate dehydrogenase [Porphyromonas gingivalis
           ATCC 33277]
          Length = 326

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 33/169 (19%), Positives = 64/169 (37%), Gaps = 22/169 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG-DC 107
           P+   I        V+ AK  E+ G + + +N      R++   F        + +  D 
Sbjct: 98  PVIASINCFRSDSWVDFAKQFEEAGADALEIN----VMRLNTDLFFDA--NKAEQMYVDI 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK-------AIL 160
           I+++ KA+ IPV VK             + +LV  ++ +G  G+ +  R          +
Sbjct: 152 ISSLIKAIRIPVVVKLSKSF------ANIPSLVDKLRAAGAKGVVLFNRSYQPDIDIDKV 205

Query: 161 KGLSPKDNRKIPNLDYDIVYE--IKKENPDLFIGLNGGLEDMSQALKIL 207
           + ++         +   I +   +    P + I  + G+ D   ALK L
Sbjct: 206 QMVAGDVFTSAGEISDTIRHAGIVSALVPGISIASSTGIHDGEAALKCL 254


>gi|241202976|ref|YP_002974072.1| dihydroorotate dehydrogenase 2 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240856866|gb|ACS54533.1| dihydroorotate dehydrogenase [Rhizobium leguminosarum bv. trifolii
           WSM1325]
          Length = 362

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 59/185 (31%), Gaps = 37/185 (20%)

Query: 98  MLNPDIVGDCIAAMCKALS---------IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
           +   + +   ++A+  A           IPV +K    + ++     + ++       G+
Sbjct: 182 LQGRESLAVLLSAVLAARDEMAAASGRTIPVFLKIAPDLTEEG----MDDIAAEALSHGL 237

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLD-----------YDIVYEIKKEN-PDLFIGLNGG 196
           +G+ +        GL  KD R+                  ++  ++K   PDL I   GG
Sbjct: 238 DGLIVSNTTLSRDGL--KDQRQAKEAGGLSGVPLFEKSTAVLARMRKRVGPDLPIIGVGG 295

Query: 197 LEDMSQALK-ILPSVD-----GVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD 250
           +     AL+ I    D       M+    Y+   +   +    S  L        R  +D
Sbjct: 296 VSSAETALEKIRAGADLVQLYSCMV----YEGPGLAGDIVRGLSKLLDREKAASIRDLRD 351

Query: 251 FWRKI 255
                
Sbjct: 352 VRLDY 356


>gi|145220527|ref|YP_001131236.1| dihydroorotate dehydrogenase 2 [Prosthecochloris vibrioformis DSM
           265]
 gi|145206691|gb|ABP37734.1| dihydroorotate dehydrogenase [Chlorobium phaeovibrioides DSM 265]
          Length = 328

 Score = 36.7 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 77/243 (31%), Gaps = 29/243 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDC 107
           P+   I      + V+ A+ +E+ G + + +N    PS      +       N  +  D 
Sbjct: 102 PVIASINCVSPGEWVQFAREIEEAGADGLEVNIFVMPSDPSKSSA------ENEKVYFDV 155

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-KAILKGLSPK 166
           + A+ +A+ IPV  K            AL +  +++  +G+  + +  R  +    +   
Sbjct: 156 LNAVTRAVRIPVAAKVSSYFS------ALAHTAEALPSTGIGSLVMFNRFFSPDIDIDTL 209

Query: 167 DNRKIP----NLDY----DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRA 218
           + +  P      DY      +  +        +   G  +  +   ++L     V I   
Sbjct: 210 ELKPAPLFSTPADYYNSLRWIAMLSGRVGCDLVASTGVHDSDALVKQLLAGAKAVEIASV 269

Query: 219 AYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITR 278
            Y        +             +      DF  ++S   + + A    S     Q  +
Sbjct: 270 LYLK--GFEEIRTMLEGLEEYMDRLGFSSLSDFQGRMSMKHSLHPAAWERS-----QFMK 322

Query: 279 HMI 281
           H  
Sbjct: 323 HFS 325


>gi|323703740|ref|ZP_08115380.1| FMN-dependent alpha-hydroxy acid dehydrogenase [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531328|gb|EGB21227.1| FMN-dependent alpha-hydroxy acid dehydrogenase [Desulfotomaculum
           nigrificans DSM 574]
          Length = 339

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 43/119 (36%), Gaps = 22/119 (18%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  + KA  +P  +K  + VD+           +   ++GV+ I +        G    D
Sbjct: 198 LKELVKATKLPFILKGIMTVDE----------AEMAVEAGVSAIVV-----SNHGGRILD 242

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR----AAYK 221
                      +    K    + I  +GG+      LK+L    DGV++GR     A+ 
Sbjct: 243 YTPGAAEVLPAIAAAVK--GKVTIFADGGVRTGVDVLKLLALGADGVLVGRPLVVGAFG 299


>gi|310286949|ref|YP_003938207.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium bifidum
           S17]
 gi|309250885|gb|ADO52633.1| NADH-dependent flavin oxidoreductase YqjM [Bifidobacterium bifidum
           S17]
          Length = 377

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 35/199 (17%), Positives = 64/199 (32%), Gaps = 28/199 (14%)

Query: 62  LVEAAKIVEDFGYNEINLNVG------------CPSARVHEGSFGACLMLNPDIVGDCIA 109
             +AA+     G+  I ++              C         +G  +      + +   
Sbjct: 175 FRDAAQRAVRAGFEAIEIHAAHGYLISQFLDPLC---NERADEYGGDIHGRMRFLLEVAD 231

Query: 110 AMCKALSIPVTVKCRIGVDDQ----IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ + +   V +  RI   D            +    +K+ GV+ + +     I     P
Sbjct: 232 AIREVIPDTVPLLVRISATDWAAGGWDLDQTVDTACVLKQHGVDLMDVSTGGIIADVSIP 291

Query: 166 -KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN 222
            K N ++P  D        +E   +     G +    QA KIL     D V IGRAA ++
Sbjct: 292 VKANYQVPFSDQ------VRERAAIPTTTVGLITKPKQAEKILRAGQADAVEIGRAALRD 345

Query: 223 SAMLTTVDEYFSNPLTGSS 241
                        P++ + 
Sbjct: 346 PYWPLRAAAKLGVPVSKAP 364


>gi|294630970|ref|ZP_06709530.1| inosine-5'-monophosphate dehydrogenase [Streptomyces sp. e14]
 gi|292834303|gb|EFF92652.1| inosine-5'-monophosphate dehydrogenase [Streptomyces sp. e14]
          Length = 500

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 28/191 (14%), Positives = 62/191 (32%), Gaps = 27/191 (14%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSA 86
           I     ++ ++        + + L     GA    L   A+ + + G + + ++      
Sbjct: 203 ITVKDFVKAEQYPNAAKDAEGRLLVGAAVGASPEALER-AQALAEAGADFLVVDTS---- 257

Query: 87  RVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
               G     L          +A +  ++SI V              VA R+  +++  +
Sbjct: 258 ---HGHNSNALSW--------MAKIKSSVSIDVIG----------GNVATRDGAQALIDA 296

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALK 205
           GV+GI +      +          +P +       +      + +  +GGL+        
Sbjct: 297 GVDGIKVGVGPGSICTTRVVAGIGVPQVTAIYEAALAARPAGIPVIGDGGLQYSGDIGKA 356

Query: 206 ILPSVDGVMIG 216
           +    D VM+G
Sbjct: 357 LAAGADTVMLG 367


>gi|194704040|gb|ACF86104.1| unknown [Zea mays]
          Length = 371

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 30/197 (15%), Positives = 60/197 (30%), Gaps = 41/197 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
             V+AA      G++ I L+            PS       +G        +  + +  +
Sbjct: 146 DFVKAANRAVTAGFDVIELHFAHGYLVSSFLTPSVNKRTDQYGGSFENRARLALELVEEV 205

Query: 112 CKALS--IPVTVKCRI---------GVDDQIPAVALRNLVKSIKKSGVNGIWI-----HA 155
              +   +P+ V+               +         L     + GV+ I +     H 
Sbjct: 206 RAVIPETMPLFVRISATDWLDTNPDYTGESWTVEEAAKLAGLFAERGVDVIDVSSGGNHP 265

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPS----- 209
           ++ +  G         P         IKK   D + +   G ++  + A +I+       
Sbjct: 266 QQKVQGG---------PGYQAKFAKHIKKVVGDKMLVSSVGSIKTGTLAEEIISGKDDGV 316

Query: 210 -VDGVMIGRAAYKNSAM 225
            +D +  GR   KN  +
Sbjct: 317 KLDLIAAGRMFQKNPGL 333


>gi|146337382|ref|YP_001202430.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bradyrhizobium sp.
           ORS278]
 gi|167011509|sp|A4YJV4|HIS4_BRASO RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|146190188|emb|CAL74180.1| N-(5'-phospho-L-ribosyl-formimino)-5-amino-1-(5'-phosphoribosyl)-4-
           imidazolecarboxamide isomerase [Bradyrhizobium sp.
           ORS278]
          Length = 244

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 51/136 (37%), Gaps = 21/136 (15%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTV---KCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           G   + +P++V     A    +++ +     K  +    +   V   ++ K  + +GV  
Sbjct: 103 GTAAVRDPELVKMAAKAFPGRVAVGLDARDGKVAVEGWAETSEVTALDIAKRFEDAGVAA 162

Query: 151 IWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           I     AR  +LKGL+      + +               + +  +GGL  +     +L 
Sbjct: 163 IIFTDIARDGLLKGLNLDATIALGDA------------ISIPVIASGGLASIEDVKAMLT 210

Query: 209 ----SVDGVMIGRAAY 220
                ++G + GRA Y
Sbjct: 211 PRARKLEGAIAGRALY 226


>gi|319789421|ref|YP_004151054.1| predicted phospho-2-dehydro-3-deoxyheptonate aldolase [Thermovibrio
           ammonificans HB-1]
 gi|317113923|gb|ADU96413.1| predicted phospho-2-dehydro-3-deoxyheptonate aldolase [Thermovibrio
           ammonificans HB-1]
          Length = 264

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 16/100 (16%), Positives = 33/100 (33%), Gaps = 16/100 (16%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNV------------GCPSARVHEGSFGACLMLNPDIVG 105
           D   +   A++  + G + + +              GCP   V  G      M N   + 
Sbjct: 157 DPDTVAHCARVAAELGADIVKVAYTGDPQTFERVTKGCPIPVVIAGGPK---MSNDMEIL 213

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
           + +    KA +  V++  R       P   +R +   + +
Sbjct: 214 EMVEGAMKAGAKGVSIG-RNAFQHDDPEKIVRAIAAIVHE 252


>gi|261403286|ref|YP_003247510.1| pyridoxine biosynthesis protein [Methanocaldococcus vulcanius M7]
 gi|261370279|gb|ACX73028.1| pyridoxine biosynthesis protein [Methanocaldococcus vulcanius M7]
          Length = 333

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE A+I E+ G   +      P+      S G   M +P ++ + +     A+SIPV  K
Sbjct: 30  VEQAQIAEEAGAVAVMALERVPAD--IRASGGVARMSDPALIEEIM----DAVSIPVMAK 83

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           CRIG   +          + ++  GV+ I
Sbjct: 84  CRIGHTTE---------AEVLEAIGVDMI 103


>gi|224372982|ref|YP_002607354.1| dihydroorotate oxidase [Nautilia profundicola AmH]
 gi|254788896|sp|B9L9P6|PYRD_NAUPA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|223589335|gb|ACM93071.1| dihydroorotate oxidase [Nautilia profundicola AmH]
          Length = 359

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 17/118 (14%), Positives = 42/118 (35%), Gaps = 11/118 (9%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK 157
           +LN + +      +      P+ +K    ++D++    + NL      +G +GI +    
Sbjct: 191 LLNAEFISSLFGELKNLTDKPILIKFSPDMEDEL----IINLANYSVLAGADGIIVTNTT 246

Query: 158 AILK------GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKILP 208
                            + +    Y+++  +  E    + I   GG++   +A K + 
Sbjct: 247 VNYDLVNSEIKRGGISGKPLAQRSYEVLRIVAGEVFGKVPIISVGGIDSAEEAYKRIK 304


>gi|239917594|ref|YP_002957152.1| imidazole glycerol phosphate synthase subunit hisF [Micrococcus
           luteus NCTC 2665]
 gi|281413919|ref|ZP_06245661.1| imidazole glycerol phosphate synthase subunit HisF [Micrococcus
           luteus NCTC 2665]
 gi|259709878|sp|C5CBK1|HIS6_MICLC RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|239838801|gb|ACS30598.1| imidazole glycerol phosphate synthase subunit hisF [Micrococcus
           luteus NCTC 2665]
          Length = 256

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 34/98 (34%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L +    +G + I      A     +           YD+V    +E   + + + GG+
Sbjct: 35  ELARRYNAAGADEITFLDVTASTSDRATT---------YDVVTRTAEEVF-IPLTVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V +  AA     ++T +   F 
Sbjct: 85  RTVEDVDRLLRTGADKVSVNTAAVARPELITEITRRFG 122


>gi|219849645|ref|YP_002464078.1| NADH:flavin oxidoreductase/NADH oxidase [Chloroflexus aggregans DSM
           9485]
 gi|219543904|gb|ACL25642.1| NADH:flavin oxidoreductase/NADH oxidase [Chloroflexus aggregans DSM
           9485]
          Length = 354

 Score = 36.7 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 29/209 (13%), Positives = 66/209 (31%), Gaps = 32/209 (15%)

Query: 59  ISKLVEAAKIVEDF----------GYNEINL---------NVGCPSARVHEGSFGACLML 99
                  A++V DF          G+  I +         N   P        +G  L  
Sbjct: 146 PLDAAGIARVVADFATATKRARAAGFRWIEIHAAHGYLLHNFLSPLGNDRNDEYGGDLRG 205

Query: 100 NPDIVGDCIAAMCKA--LSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA 155
              ++ +  AA+       +P  V + C     + +       + + +++ GV+ I   +
Sbjct: 206 RVRLLSEVTAAVRAEWPSDLPLAVRLSCSDWTPEGLTIADTVEVARMLREQGVDLIDCSS 265

Query: 156 RKAILKGLSPKDNRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDG 212
                 G++P     +          ++++E  ++     G +     A  I+ +   D 
Sbjct: 266 G-----GIAPGITIPVGEGYQVPFAAQVRREA-NIATAAVGLITRPEHADAIVRNGDADL 319

Query: 213 VMIGRAAYKNSAMLTTVDEYFSNPLTGSS 241
           V++GR   ++            + L    
Sbjct: 320 VLLGRELLRDPHWPLRAARALGHDLAPPP 348


>gi|314923062|gb|EFS86893.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL001PA1]
 gi|314966832|gb|EFT10931.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL082PA2]
 gi|314981173|gb|EFT25267.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL110PA3]
 gi|315091994|gb|EFT63970.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL110PA4]
 gi|315103495|gb|EFT75471.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL050PA2]
 gi|327327657|gb|EGE69433.1| pyridoxine biosynthesis protein [Propionibacterium acnes HL103PA1]
          Length = 279

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI E+ G   +      P+        G   M +PD++   I A    +SIPV  K RI
Sbjct: 16  AKIAENAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 126 --------------GVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                            D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLKVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|310780553|ref|YP_003968885.1| inosine-5'-monophosphate dehydrogenase [Ilyobacter polytropus DSM
           2926]
 gi|309749876|gb|ADO84537.1| inosine-5'-monophosphate dehydrogenase [Ilyobacter polytropus DSM
           2926]
          Length = 487

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 33/100 (33%), Gaps = 6/100 (6%)

Query: 122 KCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL-DYD 177
           K R    D       +      K +  +G   + +      +          +P +   +
Sbjct: 264 KIREAFPDLDIIGGNIVTAEAAKDLADAGATAVKVGVGPGSICTTRVVAGVGVPQISAVN 323

Query: 178 IVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
            VYE  KE   + +  +GG++        I    D VMIG
Sbjct: 324 DVYEACKERG-IGVIADGGIKLSGDVVKAIAAGADCVMIG 362


>gi|291619001|ref|YP_003521743.1| FadH [Pantoea ananatis LMG 20103]
 gi|291154031|gb|ADD78615.1| FadH [Pantoea ananatis LMG 20103]
          Length = 675

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 20/180 (11%), Positives = 48/180 (26%), Gaps = 33/180 (18%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF-----------------GACLMLNPDI 103
                A++ +  GY+ + +        +    +                 G         
Sbjct: 150 DFAHCARLAQKAGYDGVEI--------MGSEGYLINQFLVQHTNQRQDRWGGDFTGRMQF 201

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAI 159
                 A+  A      +  R+ + D I           L   +++ GV     +     
Sbjct: 202 ALAITRAVRAATGERFIIIFRLSMLDLIHHGSTLEETLQLASELERCGVTLF--NTGIGW 259

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +   P     +P   +  V    +++  + +     +     A ++L     D V + R
Sbjct: 260 HEARIPTIATCVPRAAFAWVTRRLRQHVAVPVVATNRINHPQVAEQLLQDGCADMVSMAR 319


>gi|157148659|ref|YP_001455978.1| hypothetical protein CKO_04487 [Citrobacter koseri ATCC BAA-895]
 gi|157085864|gb|ABV15542.1| hypothetical protein CKO_04487 [Citrobacter koseri ATCC BAA-895]
          Length = 672

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 60/211 (28%), Gaps = 48/211 (22%)

Query: 42  GFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM- 98
            F+  E      LQ+    I      A++  + GY+ + +                 L+ 
Sbjct: 126 RFTPHELTHDEILQL----IDDFAHCAQLAREAGYDGVEV-----------MGSEGYLIN 170

Query: 99  -------------------LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VA 135
                                     + + A+ + +     +  R+ + D +        
Sbjct: 171 EFLTVRTNQRDDEWGGDYARRMRFAVEVVRAVRQRVGSDFIIIYRLSMLDLVENGGTFDE 230

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLN 194
              L ++I+ +G     I+      +   P     +P   +  V  ++K       +  N
Sbjct: 231 TVQLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAFSWVTRKLKGHVTVPLVTTN 288

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             + D   A  IL   D  M+   +     +
Sbjct: 289 R-INDPQVADDILARGDADMV---SMARPFL 315


>gi|167038818|ref|YP_001661803.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X514]
 gi|256752312|ref|ZP_05493174.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300913597|ref|ZP_07130914.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X561]
 gi|307723388|ref|YP_003903139.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X513]
 gi|166853058|gb|ABY91467.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X514]
 gi|256748799|gb|EEU61841.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300890282|gb|EFK85427.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X561]
 gi|307580449|gb|ADN53848.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X513]
          Length = 654

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 27/200 (13%), Positives = 67/200 (33%), Gaps = 38/200 (19%)

Query: 40  ILGFSTQEKPLALQ----IGGADISKLVE----AAKIVEDFGYNEINL---------NVG 82
           +   S  E  +  Q    +   ++ ++V+    AA  ++  G++ + +            
Sbjct: 119 MAAPSEVECKVVHQPVRAMSTEEVEEMVKKFVDAAVRIKKAGFDGVEVHGAHGYLINQFL 178

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN---- 138
            P        +G         + + +  + +       +  R+ VD+ +  V L N    
Sbjct: 179 SPYTNKRTDKYGGSFENRMRFLEEIVVGIREKCGKDFPLLVRLTVDEFLEKVGLPNEGLH 238

Query: 139 ------LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD-----IVYEIKKENP 187
                 + K +++ GV+ + I        G+    N       Y+      + E  K+  
Sbjct: 239 LEDGVKIAKRLEELGVDALDISC------GIYETMNVSWEPTSYEQGWKIYLAETIKKAV 292

Query: 188 DLFIGLNGGLEDMSQALKIL 207
           D+ +     + D   A +++
Sbjct: 293 DIPVIGVSVIRDPEFADRMI 312


>gi|89901066|ref|YP_523537.1| inosine-5'-monophosphate dehydrogenase [Rhodoferax ferrireducens
           T118]
 gi|89345803|gb|ABD70006.1| inosine-5'-monophosphate dehydrogenase [Rhodoferax ferrireducens
           T118]
          Length = 489

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 14/82 (17%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
               V+++ ++GV+ I +       KG+             D V  +KK  P + +   G
Sbjct: 228 TEERVEALARAGVDAIVVDTAHGHSKGVI------------DRVRWVKKNFPHIEVIG-G 274

Query: 196 GLEDMSQALKILP-SVDGVMIG 216
            +   + AL ++    D V +G
Sbjct: 275 NIATGAAALALVEAGADAVKVG 296


>gi|17227547|ref|NP_484095.1| inosine 5-monophosphate dehydrogenase [Nostoc sp. PCC 7120]
 gi|17135029|dbj|BAB77575.1| IMP dehydrogenase [Nostoc sp. PCC 7120]
          Length = 387

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 22/63 (34%), Gaps = 12/63 (19%)

Query: 189 LFIGLNGG-LEDMSQALKILPSVDGVMIG----RAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           + I  +GG +        I    DGVMIG    RAA             F   +   SP+
Sbjct: 256 IPIIADGGLITGGDICKCIACGADGVMIGSPFARAAEA-PG------RGFHWGMATPSPV 308

Query: 244 KTR 246
             R
Sbjct: 309 LPR 311


>gi|300717490|ref|YP_003742293.1| Imidazole glycerol phosphate synthase subunit [Erwinia billingiae
           Eb661]
 gi|299063326|emb|CAX60446.1| Imidazole glycerol phosphate synthase subunit [Erwinia billingiae
           Eb661]
          Length = 241

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 18  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 67

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  +  ++T + + F 
Sbjct: 68  SAEDAAQILSFGADKISINSPALADPELITRLADRFG 104


>gi|297162015|gb|ADI11727.1| putative oxidoreductase [Streptomyces bingchenggensis BCW-1]
          Length = 370

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 25/172 (14%), Positives = 53/172 (30%), Gaps = 19/172 (11%)

Query: 67  KIVEDFGYNEINLN-VGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKC 123
           ++ E  G +   +N    P++     ++G           + + A+       +PV  + 
Sbjct: 175 QVAEVHGAHGYLINSFLSPASNHRTDAYGGSFENRLRFALEVVDAVRAVWPDELPVFFRT 234

Query: 124 RIGVDDQIPAVALRN---------LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
                    A   R          L K +   GV+ + + +      G+ P         
Sbjct: 235 SATDWLTENAEDDREGWTGDDTVRLAKELHAHGVDLLDVSSG-----GMVPDARILTGPG 289

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                    +    L  G  G + D   A +I+     D +++GR   ++  
Sbjct: 290 YQVPFAAQARTETGLPTGAVGMITDPHHAEEIVAGGQADAILLGRELLRHPY 341


>gi|290894115|ref|ZP_06557087.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL J2-071]
 gi|290556304|gb|EFD89846.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL J2-071]
          Length = 295

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI ED G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 29  AEQAKIAEDAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|116627941|ref|YP_820560.1| dihydroorotate dehydrogenase 1A [Streptococcus thermophilus LMD-9]
 gi|116101218|gb|ABJ66364.1| dihydroorotate oxidase B, catalytic subunit [Streptococcus
           thermophilus LMD-9]
          Length = 312

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 39/193 (20%), Positives = 64/193 (33%), Gaps = 19/193 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLML 99
           L      K   L + G    +     K V+   Y   + LN+ CP   V      A    
Sbjct: 88  LQNQPNTKNHFLSLVGLSPEETHTILKKVQKSDYEGLVELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +   D +  +    + P+ VK     D      A A+ N      V  +   G NG++
Sbjct: 143 DFETTTDILTEVFSYFTKPLGVKLPPYFDIVHFDQAAAVFNQFPLVFVNCVNSIG-NGLY 201

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   +   P++ I   GG++    A +  L
Sbjct: 202 IEDESVVIKPKNGFGGIGGDYIKPTALANVHAFYQRLKPEIQIIGTGGVKSGRDAFEHIL 261

Query: 208 PSVDGVMIGRAAY 220
                V +G A  
Sbjct: 262 CGASMVQVGTALQ 274


>gi|55823126|ref|YP_141567.1| dihydroorotate dehydrogenase 1A [Streptococcus thermophilus
           CNRZ1066]
 gi|55739111|gb|AAV62752.1| dihydroorotate dehydrogenase A [Streptococcus thermophilus
           CNRZ1066]
          Length = 327

 Score = 36.7 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 39/193 (20%), Positives = 64/193 (33%), Gaps = 19/193 (9%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEGSFGACLML 99
           L      K   L + G    +     K V+   Y   + LN+ CP   V      A    
Sbjct: 103 LQNQPNTKNHFLSLVGLSPEETHTILKKVQKSDYEGLVELNLSCP--NVPGKPQIAY--- 157

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +   D +  +    + P+ VK     D      A A+ N      V  +   G NG++
Sbjct: 158 DFETTTDILTEVFSYFTKPLGVKLPPYFDIVHFDQAAAVFNQFPLVFVNCVNSIG-NGLY 216

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     ++K   G        I       V+   +   P++ I   GG++    A +  L
Sbjct: 217 IEDESVVIKPKNGFGGIGGDYIKPTALANVHAFYQRLKPEIQIIGTGGVKSGRDAFEHIL 276

Query: 208 PSVDGVMIGRAAY 220
                V +G A  
Sbjct: 277 CGASMVQVGTALQ 289


>gi|312623497|ref|YP_004025110.1| Radical SAM domain-containing protein [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203964|gb|ADQ47291.1| Radical SAM domain protein [Caldicellulosiruptor kronotskyensis
           2002]
          Length = 351

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 28/162 (17%), Positives = 60/162 (37%), Gaps = 26/162 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++VE AK     GY  + L              G  +    D++   I  +  ++ + +
Sbjct: 87  DEIVEVAKRAYQMGYRTVVLQS------------GEDMYYTKDMLCSIIKKIKSSVDVAI 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH---ARKAILKGLSPKDNRKIPNLDY 176
           T+       D+          K+ K +G +   +    + + + K   P  + +      
Sbjct: 135 TLSIGERSYDEY---------KAFKDAGADRFLMRFETSNEELYKKYHPGMSFEKRIECL 185

Query: 177 DIVYEIKKENP-DLFIGLNG-GLEDMSQALKILPSVDGVMIG 216
             +  +  E      IGL G  ++D++Q + ++  +D  MIG
Sbjct: 186 KWIKNLGYELGTGFLIGLPGQTIDDLAQDILLVKELDADMIG 227


>gi|291451836|ref|ZP_06591226.1| inosine-5'-monophosphate dehydrogenase [Streptomyces albus J1074]
 gi|291354785|gb|EFE81687.1| inosine-5'-monophosphate dehydrogenase [Streptomyces albus J1074]
          Length = 502

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 10/118 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +  +VGD +A +    S         GVD     +A R+  + +  SG +G+ +      
Sbjct: 260 HSRLVGDMVAKIKSNSS---------GVDVIGGNIATRDGAQMLIDSGADGVKVGVGPGS 310

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           +          +P +       +  +   + +  +GGL+     A  ++   D VM+G
Sbjct: 311 ICTTRVVAGIGVPQVTAIYEASLAAQAAGVPVIGDGGLQYSGDIAKALVAGADTVMLG 368


>gi|227503621|ref|ZP_03933670.1| dihydroorotate dehydrogenase 2 [Corynebacterium accolens ATCC
           49725]
 gi|227075657|gb|EEI13620.1| dihydroorotate dehydrogenase 2 [Corynebacterium accolens ATCC
           49725]
          Length = 371

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 38/112 (33%), Gaps = 11/112 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            + A+ ++  +PV VK    + D     A+ +L   +  +G+          G+     +
Sbjct: 208 ILRAVQESTDVPVMVKIAPDLSDAD-VDAVADLAVELGLAGIVATNTTISREGLSTPRAE 266

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               G        +     +++  +       L +   GG+    QA + + 
Sbjct: 267 VEALGAGGISGPPVAERSLEVLRRLNARVGSQLVLISVGGISTPEQAWERIS 318


>gi|51701776|sp|Q6V3X0|PYRD_SACCA RecName: Full=Dihydroorotate dehydrogenase; Short=DHOD;
           Short=DHODase; Short=DHOdehase; AltName:
           Full=Dihydroorotate oxidase
 gi|34099823|gb|AAQ57200.1| dihydroorotate dehydrogenase 1a [Naumovia castellii]
          Length = 314

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 29/199 (14%), Positives = 61/199 (30%), Gaps = 33/199 (16%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCP----SARVHEGSF 93
                   E  +   + G  I + +   + ++D  ++ I  LN+ CP      +V     
Sbjct: 88  ERQRTHPNEPAIFFSVAGMSIDENINMLRKIQDSEFHGITELNLSCPNVPGKPQVA---- 143

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-- 151
                 + D+  + +  + +    P+ +K      D      +  ++     + VN I  
Sbjct: 144 -----YDFDLTKEILDKVFQFFKKPLGIKL-PPYFDFAHFDIMAGILNQYPLAYVNSINS 197

Query: 152 -------------WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
                         +   K    G+  +  +     +    Y   + NP + I   GG+ 
Sbjct: 198 VGNGLYIDVDKESVVVKPKNGFGGIGGEYVKPTALANVRAFYT--RLNPSIKIVGTGGIR 255

Query: 199 DMSQALKI-LPSVDGVMIG 216
                 +  L     V IG
Sbjct: 256 TGKDVFEHLLCGASMVQIG 274


>gi|108805300|ref|YP_645237.1| glutamate synthase (NADPH) GltB2 subunit [Rubrobacter xylanophilus
           DSM 9941]
 gi|108766543|gb|ABG05425.1| glutamate synthase (NADPH) GltB2 subunit [Rubrobacter xylanophilus
           DSM 9941]
          Length = 460

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 44/125 (35%), Gaps = 23/125 (18%)

Query: 108 IAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           I  + +     IP+ VK          A  +++ VK   K+G + + +     +  G + 
Sbjct: 223 IEELREITDWEIPIYVKF--------GATRVKDDVKLAVKAGADVVVVDG---MQGGTAA 271

Query: 166 KDNRKIPNLDYDIVYEIKKEN---------PDLFIGLNGGLED-MSQALKILPSVDGVMI 215
             +  I +     +  I +             + + ++GG+      A  +    D V I
Sbjct: 272 TQDVFIEHAGIPTLAAITQAVEALEEMDVKGKVQLIISGGIRTGADVAKALALGADAVSI 331

Query: 216 GRAAY 220
           G+ A 
Sbjct: 332 GQGAM 336


>gi|289551626|ref|YP_003472530.1| D-arabino-3-hexulose 6-phosphate formaldehyde lyase [Staphylococcus
           lugdunensis HKU09-01]
 gi|289181157|gb|ADC88402.1| D-arabino-3-hexulose 6-phosphate formaldehyde lyase [Staphylococcus
           lugdunensis HKU09-01]
          Length = 210

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 21/101 (20%), Positives = 38/101 (37%), Gaps = 15/101 (14%)

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL-KGLSPKDNRK------------ 170
           +  + D I    L    + +   G + I +H    +  +G SP D+ +            
Sbjct: 104 KQLLVDMIAVQDLEKRAQELDDMGADYIAVHTGYDLQAEGQSPLDSLRKVKSVIKNSKVA 163

Query: 171 -IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
               +  D + EI  ENPDL I   GG+ +    +++    
Sbjct: 164 VAGGIKPDTIKEIVAENPDLVIVG-GGIANAEDPVEVAKQC 203


>gi|239917705|ref|YP_002957263.1| 2,4-dienoyl-CoA reductase [Micrococcus luteus NCTC 2665]
 gi|239838912|gb|ACS30709.1| 2,4-dienoyl-CoA reductase [Micrococcus luteus NCTC 2665]
          Length = 676

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 75/249 (30%), Gaps = 30/249 (12%)

Query: 10  RFFARLLTNNALLYTEMIVADAILRGDKKNI----LGFSTQEKPLALQIGGADISKLVEA 65
           R  A+LL       +  +V+ + +R          +  +  E+ ++             A
Sbjct: 77  RILAQLLHAGRYAPSPDLVSASAVRAPISRHTPREMTTADIERTVSA---------FARA 127

Query: 66  AKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS 116
           A +  + GY+ + +             P+       +G             +AA+ +AL 
Sbjct: 128 ATLALEAGYDGVEIMASEGYLLNQFLAPATNRRADEYGGDAERRRRFPVAVVAAVREALG 187

Query: 117 ----IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
               + V       V D      + +  ++ + +G + +         +   P     +P
Sbjct: 188 ERGVLSVRTSAADLVPDGQTRAEIADTARAFEAAGADVLM--TGIGWHESRVPTIVTSVP 245

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDG-VMIGRAAYKNSAMLTTVD 230
              +           D+ +  +  L   ++A   L       V + R    +   +  + 
Sbjct: 246 RAAFLAASADLTAAVDIPVIASNRLTTPAEAEAALTSGAAALVGLARPLLADPEWMAAIS 305

Query: 231 EYFSNPLTG 239
           +  +  LT 
Sbjct: 306 DPRARTLTP 314


>gi|309779200|ref|ZP_07673963.1| anthraniloyl-CoA monooxygenase [Ralstonia sp. 5_7_47FAA]
 gi|308922004|gb|EFP67638.1| anthraniloyl-CoA monooxygenase [Ralstonia sp. 5_7_47FAA]
          Length = 787

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 30/222 (13%), Positives = 66/222 (29%), Gaps = 27/222 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPDIVGDCIAA 110
            V +A++  + G++ + L   C           P        +G  L        +   A
Sbjct: 559 FVHSARLAAEAGFDWLEL--HCAHGYLLSSFISPLTNQRNDEYGGSLENRLRFPLEVFHA 616

Query: 111 MCKA--LSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + +    + P++V+      V+  I       + +  K +G + I   + +     +S K
Sbjct: 617 VREVWPSNKPMSVRISAHDWVEGGITPDDAVEIARVFKAAGADMIDCSSGQ-----VSKK 671

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS- 223
           +      +      +  +    +     G + +      I+ +   D   + R    N  
Sbjct: 672 EQPVYGRMFQTPFADRVRNEAGIATIAVGAISEADHVNSIIAARRADLCAVARPHLANPA 731

Query: 224 AMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAAR 265
             L          L    P + R  K    +        AA+
Sbjct: 732 WTLNEAARI--GYLDMPWPKQYRAGKLQLERNLERERAMAAQ 771


>gi|169836167|ref|ZP_02869355.1| dihydroorotate dehydrogenase 1A [candidate division TM7 single-cell
           isolate TM7a]
          Length = 284

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 64/186 (34%), Gaps = 13/186 (6%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  +  ++     + G          K V++  +N I  LN+ CP   V      A  M 
Sbjct: 60  LQKTHPDRTFFFSLVGMSTEDTHTLLKKVQESDFNGITELNLSCP--NVPGKPQIAYDME 117

Query: 100 NPD-IVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVAL---RNLVKSIKKSGVNGIWIHA 155
             + ++ D  +   K L + +     I   DQ  AV        +  +   G NG+ I  
Sbjct: 118 TTENLLADIFSYFKKPLGVKLPPYFDIVHFDQAAAVFNKFPLTFINCVNSIG-NGLVIED 176

Query: 156 RKAILK---GLSPKDNRKIPNLDYDIVYE-IKKENPDLFIGLNGGLEDMSQALKI-LPSV 210
              ++K   G        +       V+   K+ NP + I   GG+     A +  L   
Sbjct: 177 ESVVIKPKNGFGGIGGEYVKPTALANVHAFYKRLNPSIQIIGTGGVLTGQDAFEHILCGA 236

Query: 211 DGVMIG 216
             V +G
Sbjct: 237 SMVQLG 242


>gi|94676691|ref|YP_588842.1| imidazole glycerol phosphate synthase subunit HisF [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|167012136|sp|Q1LT72|HIS6_BAUCH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|94219841|gb|ABF14000.1| imidazoleglycerol phosphate synthase, cyclase subunit [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 258

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 15/96 (15%), Positives = 39/96 (40%), Gaps = 11/96 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +   K G + +  +   A  +G           +D   +  +  E  D+   + GG++ 
Sbjct: 36  AQRYAKEGADELVFYDITASSEGRV---------VDKSWIARVA-EVIDIPFCVAGGIKS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           ++QA +++    D + I   A  +  +++ + + F 
Sbjct: 86  VAQAGEVISFGADKISINSPALNDPYLISRLADRFG 121


>gi|20454954|sp|P58800|HIS6_PYRFU RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
          Length = 251

 Score = 36.7 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 50/134 (37%), Gaps = 16/134 (11%)

Query: 103 IVGDCIAAMCKALSIPV-TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +    IAA+       V  +K +   D   P      L K  +  G++ I          
Sbjct: 2   LARRIIAALDIKDGRVVKGIKFKNIRDAGDP----IELAKRYESEGIDEIVF-------- 49

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            L    + +   +  D+V  + +E    F    GG+  + +A +I+    D + I  AA 
Sbjct: 50  -LDITASYEKRKILLDLVERVAEEIYVPFTVG-GGIRTVEEAREIIRRGADKIFINTAAV 107

Query: 221 KNSAMLTTVDEYFS 234
           +N +++  + +   
Sbjct: 108 ENPSLIKEIADLIG 121


>gi|323183812|gb|EFZ69203.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli 1357]
          Length = 242

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 19  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 68

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 69  SLDDAAKILSFGADKISINSPALADPTLITRLADRFG 105


>gi|298571331|gb|ADI87675.1| NADH oxidase [uncultured Nitrospirae bacterium MY2-1F]
          Length = 388

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 19/132 (14%), Positives = 48/132 (36%), Gaps = 11/132 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALR-----NLVKSIKKSGVNGIWIHARKA 158
           + +   A+ KA+     V  ++   D +    LR      + + ++  G++ + +     
Sbjct: 211 LEEVYKAIRKAVGSDYLVFIKMNSSDHLCCGGLRPDESLRIAQRLEAIGIDAVEVSGGM- 269

Query: 159 ILKGLSPKDNRKIPNLDYDIV---YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
               L P   + +   D         + K +  + + L GG+   + A ++L     D +
Sbjct: 270 YESSLRPARTKILHPEDEAYFKGPASLFKMSLSIPVILVGGIRSRAVAEEMLDKGYADLI 329

Query: 214 MIGRAAYKNSAM 225
            + R   +   +
Sbjct: 330 SMSRPLIREPDL 341


>gi|219854262|ref|YP_002471384.1| hypothetical protein CKR_0919 [Clostridium kluyveri NBRC 12016]
 gi|219567986|dbj|BAH05970.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 644

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 59/178 (33%), Gaps = 20/178 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCP---------SARVHEG--SFGACLMLNPDIVGDCIAAMC 112
           +AA   +  G + +   V C          S R ++    FG C      +    I  + 
Sbjct: 155 DAALRAKKAGADAVE--VHCAHGYLINSFLSPRTNKRVDEFGGCFENRMRLPRLIIENIR 212

Query: 113 KALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D++P          +   ++  GV+ + +     +         
Sbjct: 213 KKVGHSIAIICRINSSDEMPGGLDVHDSATIAAYLEDIGVDALHVSRAVHLRDEYMWAPT 272

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
                   ++  EIK+   D+ +   G   +   A  ++     D V  GR +  +  
Sbjct: 273 VLHGGFSAELATEIKRAV-DIPVITVGRFTEPHFAELLVREGRCDLVAFGRQSLTDPH 329


>gi|18977826|ref|NP_579183.1| hypothetical protein PF1454 [Pyrococcus furiosus DSM 3638]
 gi|18893579|gb|AAL81578.1| hypothetical protein PF1454 [Pyrococcus furiosus DSM 3638]
          Length = 588

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 17/86 (19%)

Query: 36  DKKNILGFSTQEKPL---ALQIGGADI---SKLVEAAKIVEDFGYNEINLNVGCPSARVH 89
             + +L  + +E P+   A+Q  G +      L+E  KI ++ GY+ + LN         
Sbjct: 175 QIRMMLRNAKKENPIGANAVQFTGGEPTLRDDLIEIIKIAKEEGYDHVQLNTD------- 227

Query: 90  EGSFGACLMLNPDIVGDCIAAMCKAL 115
               G  L   P++V     A    L
Sbjct: 228 ----GIRLAFEPELVKKIREAGVNTL 249


>gi|187731617|ref|YP_001879852.1| imidazole glycerol phosphate synthase subunit HisF [Shigella boydii
           CDC 3083-94]
 gi|209919490|ref|YP_002293574.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli SE11]
 gi|218554588|ref|YP_002387501.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli IAI1]
 gi|226700516|sp|B7M404|HIS6_ECO8A RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226700519|sp|B6I896|HIS6_ECOSE RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226702002|sp|B2TYF5|HIS6_SHIB3 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|187428609|gb|ACD07883.1| imidazoleglycerol phosphate synthase, cyclase subunit [Shigella
           boydii CDC 3083-94]
 gi|209912749|dbj|BAG77823.1| imidazole glycerol phosphate synthase subunit [Escherichia coli
           SE11]
 gi|218361356|emb|CAQ98943.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli IAI1]
 gi|324119055|gb|EGC12944.1| imidazoleglycerol phosphate synthase [Escherichia coli E1167]
 gi|332092405|gb|EGI97478.1| imidazole glycerol phosphate synthase subunit hisF [Shigella boydii
           5216-82]
          Length = 258

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|294339941|emb|CAZ88304.1| N-ethylmaleimide reductase, FMN-linked [Thiomonas sp. 3As]
          Length = 372

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 23/146 (15%), Positives = 42/146 (28%), Gaps = 18/146 (12%)

Query: 93  FGACLMLNPDIVGDCIAAM-----CKALSIPVTVKC-RIGVDDQIPAVALRNLVKSIKKS 146
           +G  L     IV + I A+        + + ++    R  + D         L +   + 
Sbjct: 205 YGGSLENRARIVLEAIDALIAVAGANRVGVRISPHFNRHDIQDAQTEEIHLYLAQEFNRR 264

Query: 147 GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI 206
           G+  I I             + RK     Y            + +  N  LE      ++
Sbjct: 265 GIAYIHIAEPDWAGGPALTDEFRKKLRAAY---------AGRIIVCGNYTLESAEA--RL 313

Query: 207 LPS-VDGVMIGRAAYKNSAMLTTVDE 231
                D V  GR    N  ++    +
Sbjct: 314 ASGLADAVAFGRPFIANPDLVARFQQ 339


>gi|239979979|ref|ZP_04702503.1| inosine-5'-monophosphate dehydrogenase [Streptomyces albus J1074]
          Length = 495

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 10/118 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +  +VGD +A +    S         GVD     +A R+  + +  SG +G+ +      
Sbjct: 253 HSRLVGDMVAKIKSNSS---------GVDVIGGNIATRDGAQMLIDSGADGVKVGVGPGS 303

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           +          +P +       +  +   + +  +GGL+     A  ++   D VM+G
Sbjct: 304 ICTTRVVAGIGVPQVTAIYEASLAAQAAGVPVIGDGGLQYSGDIAKALVAGADTVMLG 361


>gi|126736812|ref|ZP_01752547.1| 2,4-dienoyl-CoA reductase [Roseobacter sp. SK209-2-6]
 gi|126721397|gb|EBA18100.1| 2,4-dienoyl-CoA reductase [Roseobacter sp. SK209-2-6]
          Length = 675

 Score = 36.7 bits (84), Expect = 5.3,   Method: Composition-based stats.
 Identities = 24/186 (12%), Positives = 62/186 (33%), Gaps = 35/186 (18%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CLMLNPDIVGD------------ 106
            +V AA++ ++ GY+ + +        +    +     L+ + +   D            
Sbjct: 143 DIVNAARLAQEAGYDGVEI--------MGSEGYFLNQFLVTHTNKREDRWGGSYENRMRL 194

Query: 107 ---CIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
               +    +A+     +  R+ + D +P  +  +    L + ++K+G     I+     
Sbjct: 195 PIEVVRRTREAVGTDFIIIYRLSMIDLVPNGSTHDEVVQLAQEVEKAGAT--IINTGIGW 252

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIG 216
            +   P     +P   +  V  ++  +     I  N  +       ++L     D V + 
Sbjct: 253 HEARIPTIATSVPRAAFAWVTKKLMGKVSIPVITSNR-INTPEVGEEVLATGCADMVSLA 311

Query: 217 RAAYKN 222
           R    +
Sbjct: 312 RPMLAD 317


>gi|332754780|gb|EGJ85145.1| hypothetical protein SF434370_2306 [Shigella flexneri 4343-70]
          Length = 272

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 23/138 (16%), Positives = 52/138 (37%), Gaps = 25/138 (18%)

Query: 89  HEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV 148
              + G+ +  +P++V     A+ +  ++P+  K    + D      +  +  + K+ G 
Sbjct: 2   TSHAMGSDVGQSPELVEKYCRAVKRGSTLPMLAKMTPNIGD------MCEVALAAKRGGA 55

Query: 149 NGIW-IHARKAIL----------------KGLSPKDNRKIPNLDYDIVYEIKK--ENPDL 189
           +GI  I+  K+I                   +S    + +  +    + +++   E  D 
Sbjct: 56  DGIAAINTVKSITNIDLNQKIGMPIVNGKSSISGYSGKAVKPIALRFIQQMRTHPELRDF 115

Query: 190 FIGLNGGLEDMSQALKIL 207
            I   GG+E    A + L
Sbjct: 116 PISGIGGIETWEDAAEFL 133


>gi|317484339|ref|ZP_07943260.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
 gi|316924417|gb|EFV45582.1| NADH flavin oxidoreductase/NADH oxidase [Bilophila wadsworthia
           3_1_6]
          Length = 647

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 25/144 (17%), Positives = 48/144 (33%), Gaps = 11/144 (7%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA------VALRNLVKSIKK 145
            +G  L        + + A+  A+     +  R    + +P            L +++  
Sbjct: 188 GYGGSLAKRLRFPAEVVRAVRAAVGGDFPILYRHTSVEDVPTGNGIDLGTTVELCRTLTD 247

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLF-IGLNGGLEDMSQAL 204
           +GVN   I A       L           +      +K+   D   + L G + D   A 
Sbjct: 248 AGVNAFDITAGMQCCFELMTPPTCMPKAWNAATSAAVKEALGDRARVMLTGRISDADTAE 307

Query: 205 KILPS--VD-GVMIGRAAYKNSAM 225
           +++     D  +M GRA   +S +
Sbjct: 308 RVVRDGLADFAIM-GRALIADSHL 330


>gi|291536409|emb|CBL09521.1| Putative N-acetylmannosamine-6-phosphate epimerase [Roseburia
           intestinalis M50/1]
 gi|291538725|emb|CBL11836.1| Putative N-acetylmannosamine-6-phosphate epimerase [Roseburia
           intestinalis XB6B4]
          Length = 232

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 42/108 (38%), Gaps = 7/108 (6%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-NRKIPNLDYDIVY 180
           K +    DQ     + +     +    + I        L G +P   N KI   D++I+ 
Sbjct: 118 KVKEKYPDQK---FMADCSTVEEALFADEIGFDFIGTTLVGYTPYSVNDKIEQNDFEIIR 174

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLT 227
           +I K+     +   G ++   +A +++      V++G  A     ++T
Sbjct: 175 KILKQVHH-PVIAEGNIDVPQKARRVVELGCYSVVVG-GAITRPQLIT 220


>gi|262370711|ref|ZP_06064036.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter johnsonii SH046]
 gi|262314511|gb|EEY95553.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter johnsonii SH046]
          Length = 243

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 22/130 (16%), Positives = 42/130 (32%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I +  P+L I + GG+  +      L   V  V+IG  A ++   
Sbjct: 60  ------PIHKPVVEAITRAQPELPIQIGGGIRSLETIEHYLEAGVSFVIIGTKAVQDPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKKFAG 123


>gi|157159234|ref|YP_001463376.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli E24377A]
 gi|167012156|sp|A7ZNJ7|HIS6_ECO24 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|157081264|gb|ABV20972.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli E24377A]
          Length = 258

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|330963615|gb|EGH63875.1| xenobiotic reductase A [Pseudomonas syringae pv. actinidiae str.
           M302091]
          Length = 363

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 61/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVLEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +    + +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREAGIPVTSAWGFGEPKLAEEAVKAGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|322367909|ref|ZP_08042478.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Haladaptatus
           paucihalophilus DX253]
 gi|320551925|gb|EFW93570.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Haladaptatus
           paucihalophilus DX253]
          Length = 240

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
             D+ + L GG+   + A  +L   VD V++G AA +N  ++  + E +  
Sbjct: 75  AVDVEVQLGGGIRTATDATDLLSRGVDRVILGTAAIENPDIVAEISEEYPG 125


>gi|283783638|ref|YP_003374392.1| MaoC-like protein [Gardnerella vaginalis 409-05]
 gi|283441582|gb|ADB14048.1| MaoC-like protein [Gardnerella vaginalis 409-05]
          Length = 3192

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 29/154 (18%), Positives = 50/154 (32%), Gaps = 28/154 (18%)

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALRN 138
             G P   V   +     +   D   + +A++ +A   P VT K             +R 
Sbjct: 484 QSGAPIDGVVISAG----IPELDEAKELVASL-QADGFPYVTFK-------PGTVDQIRQ 531

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +V+  K      I +        G        + +L      ++ +E  +L +   GG+ 
Sbjct: 532 VVRIAKAVAPATIIVQVEGGAAGGHHS--WESLDDLLMTTYAQV-RECENLVLVAGGGIG 588

Query: 199 DMSQALKILPS------------VDGVMIGRAAY 220
              +A   +              VD VMIG AA 
Sbjct: 589 TPERAADYISGEWANEYGLPNMPVDAVMIGTAAM 622


>gi|222530603|ref|YP_002574485.1| biotin synthase [Caldicellulosiruptor bescii DSM 6725]
 gi|222457450|gb|ACM61712.1| Radical SAM domain protein [Caldicellulosiruptor bescii DSM 6725]
          Length = 351

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 28/162 (17%), Positives = 60/162 (37%), Gaps = 26/162 (16%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV 119
            ++VE AK     GY  + L              G  +    D++   I  +  ++ + +
Sbjct: 87  DEIVEVAKRAYQMGYRTVVLQS------------GEDMYYTKDMLCSIIKKIKSSVDVAI 134

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH---ARKAILKGLSPKDNRKIPNLDY 176
           T+       D+          K+ K +G +   +    + K + +   P  + +      
Sbjct: 135 TLSIGERSYDEY---------KAFKDAGADRFLMRFETSNKKLYRKYHPGMSFENRIECL 185

Query: 177 DIVYEIKKENP-DLFIGLNG-GLEDMSQALKILPSVDGVMIG 216
             +  +  E      IGL G  ++D++Q + ++  +D  MIG
Sbjct: 186 KWIKNLGYELGTGFLIGLPGQTIDDLAQDILLVKELDADMIG 227


>gi|157151110|ref|YP_001450684.1| imidazole glycerol phosphate synthase subunit HisF [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|189043446|sp|A8AY24|HIS6_STRGC RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|157075904|gb|ABV10587.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Streptococcus gordonii str. Challis substr. CH1]
          Length = 252

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 2/92 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           ++V  + ++    F    GG+  +    ++L    D V +  +A  N  +L    E F +
Sbjct: 64  EMVRRVAEQVFIPFTVG-GGIRTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKFGS 122

Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHL 267
                +    +     W    A     + R L
Sbjct: 123 QCVVLAVDAKKEADGSWHVYLAGGRKDSGREL 154


>gi|37525478|ref|NP_928822.1| hypothetical protein plu1530 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784906|emb|CAE13823.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 297

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 17/120 (14%), Positives = 44/120 (36%), Gaps = 18/120 (15%)

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
           +++      +L++++ ++GV+ I           L+  +   +  L       ++  N  
Sbjct: 16  NKVDEKTFISLIENLVEAGVDSIGALGSTGSYAYLTLSERAHVARL------AVEHANSI 69

Query: 189 LFIGLNG-----GLEDMSQALKILPSVDGVMIGRAAYKNS------AMLTTVDEYFSNPL 237
             +   G      +  +++  +    V  VM+   +Y+        ++   V  Y S PL
Sbjct: 70  PVMVSIGALRVADILSLAEDAQH-AGVSAVMLAPVSYQRPTPDEVYSLYEEVSRYLSVPL 128


>gi|154248055|ref|YP_001419013.1| isopentenyl pyrophosphate isomerase [Xanthobacter autotrophicus
           Py2]
 gi|226707324|sp|A7IMW3|IDI2_XANP2 RecName: Full=Isopentenyl-diphosphate delta-isomerase; Short=IPP
           isomerase; AltName: Full=Isopentenyl pyrophosphate
           isomerase
 gi|154162140|gb|ABS69356.1| isopentenyl-diphosphate delta-isomerase, type 2 [Xanthobacter
           autotrophicus Py2]
          Length = 343

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 58/165 (35%), Gaps = 26/165 (15%)

Query: 63  VEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           ++AA+   +  G + + +++  P     +         +   V D I ++C +LS PV V
Sbjct: 139 LDAARRAVEMIGADVLVIHLN-PLQEAIQQGGD----RDWRGVFDRIGSLCVSLSAPVVV 193

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-------KAILKGLSPKDNRKIPNL 174
           K       ++       + + +   GV  + +              +G            
Sbjct: 194 K-------EVGFGLSGAVARRLADCGVAALDVAGAGGTNWALVEGERGTGRSRAVATAFA 246

Query: 175 DY-----DIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
           D+       V E++   PDL +  +GG+   +  A  I    D V
Sbjct: 247 DWGIPTAQAVVEVRAACPDLPLIASGGVRHGVDAAKAIRLGADLV 291


>gi|88808975|ref|ZP_01124484.1| inositol-5-monophosphate dehydrogenase [Synechococcus sp. WH 7805]
 gi|88786917|gb|EAR18075.1| inositol-5-monophosphate dehydrogenase [Synechococcus sp. WH 7805]
          Length = 387

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA     K+I ++G +  ++ A     + + P+       LD ++   + ++     +  
Sbjct: 140 VAAMRFGKAIAEAGADLFFVQATVVSTQHIGPQGQ---DTLDLEV---LCRDMGVPVVIG 193

Query: 194 NGGLEDMSQALK-ILPSVDGVMIG 216
           N        AL+ +     GVM+G
Sbjct: 194 N--CVTYDVALQLMRAGAAGVMVG 215


>gi|325119121|emb|CBZ54673.1| Ethylene-inducible protein hever, related [Neospora caninum
           Liverpool]
          Length = 307

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 25/101 (24%), Positives = 40/101 (39%), Gaps = 8/101 (7%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            + A+I E  G   +      P+      S G   M +P ++ D +    KA+SIPV  K
Sbjct: 37  AQQARIAEKAGACAVMALEKIPAD--IRQSGGVARMSDPALIEDIM----KAVSIPVMAK 90

Query: 123 CR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           CR    V+ Q+ A    + +   +   V     H  K   +
Sbjct: 91  CRIGHFVEAQVLAAVGVDFIDESEVLTVADEENHINKHKFQ 131


>gi|324993551|gb|EGC25471.1| NADPH dehydrogenase [Streptococcus sanguinis SK405]
 gi|324995137|gb|EGC27049.1| NADPH dehydrogenase [Streptococcus sanguinis SK678]
 gi|327458920|gb|EGF05268.1| NADPH dehydrogenase [Streptococcus sanguinis SK1057]
 gi|327473560|gb|EGF18980.1| NADPH dehydrogenase [Streptococcus sanguinis SK408]
 gi|327489108|gb|EGF20903.1| NADPH dehydrogenase [Streptococcus sanguinis SK1058]
          Length = 367

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 31/225 (13%), Positives = 76/225 (33%), Gaps = 27/225 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPD-IVGD 106
              + A +     G++ + L             P + V +  +G  L   +  P  ++  
Sbjct: 147 EDFLSAIRRALQAGFDGVELHGANTYLIQQFVSPHSNVRQDKWGGSLNNRLRFPKTLLKR 206

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKK---SGVNGIWIHARKAILKG 162
               + +    P  +  R   ++ + P + L + ++ +++     V+ + I         
Sbjct: 207 AKQLVKEEADRPFLIGYRFSPEEIEEPGIQLYDTLQLLEQLIYHQVDYLHISTSDVWR-- 264

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV---MIGRAA 219
           LS +D++    +   I+   KK N  + +   G +E    A ++L +  G+    +G+A 
Sbjct: 265 LSIRDSQDSEPVIQKII---KKINGRVPLIGVGQIETKQDAQRVLDA--GIPLFALGKAL 319

Query: 220 YKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAA 264
             +      V       +  +   + + D             Y  
Sbjct: 320 LLDPDWAEKVVSGREAEVIRAYRDELQADLALPTAFVEDARSYLE 364


>gi|298252904|ref|ZP_06976698.1| 3-oxoacyl-[acyl-carrier protein] Fas [Gardnerella vaginalis 5-1]
 gi|297533268|gb|EFH72152.1| 3-oxoacyl-[acyl-carrier protein] Fas [Gardnerella vaginalis 5-1]
          Length = 3176

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 29/154 (18%), Positives = 50/154 (32%), Gaps = 28/154 (18%)

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALRN 138
             G P   V   +     +   D   + +A++ +A   P VT K             +R 
Sbjct: 468 QSGAPIDGVVISAG----IPELDEAKELVASL-QADGFPYVTFK-------PGTVDQIRQ 515

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +V+  K      I +        G        + +L      ++ +E  +L +   GG+ 
Sbjct: 516 VVRIAKAVAPATIIVQVEGGAAGGHHS--WESLDDLLMTTYAQV-RECENLVLVAGGGIG 572

Query: 199 DMSQALKILPS------------VDGVMIGRAAY 220
              +A   +              VD VMIG AA 
Sbjct: 573 TPERAADYISGEWANEYGLPNMPVDAVMIGTAAM 606


>gi|297243332|ref|ZP_06927266.1| 3-oxoacyl-[acyl-carrier protein] Fas [Gardnerella vaginalis AMD]
 gi|296888739|gb|EFH27477.1| 3-oxoacyl-[acyl-carrier protein] Fas [Gardnerella vaginalis AMD]
          Length = 3178

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 29/154 (18%), Positives = 50/154 (32%), Gaps = 28/154 (18%)

Query: 80  NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP-VTVKCRIGVDDQIPAVALRN 138
             G P   V   +     +   D   + +A++ +A   P VT K             +R 
Sbjct: 468 QSGAPIDGVVISAG----IPELDEAKELVASL-QADGFPYVTFK-------PGTVDQIRQ 515

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           +V+  K      I +        G        + +L      ++ +E  +L +   GG+ 
Sbjct: 516 VVRIAKAVAPATIIVQVEGGAAGGHHS--WESLDDLLMTTYAQV-RECENLVLVAGGGIG 572

Query: 199 DMSQALKILPS------------VDGVMIGRAAY 220
              +A   +              VD VMIG AA 
Sbjct: 573 TPERAADYISGEWANEYGLPNMPVDAVMIGTAAM 606


>gi|78213461|ref|YP_382240.1| inositol-5-monophosphate dehydrogenase [Synechococcus sp. CC9605]
 gi|78197920|gb|ABB35685.1| IMP dehydrogenase related 2 [Synechococcus sp. CC9605]
          Length = 387

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 9/84 (10%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA     K+I ++G +  ++ A         P     +       +  + ++     +  
Sbjct: 140 VAAMRFGKAIAEAGADLFFVQATVVSTDHTGPAGQETLD------LEALCRDMGVPVVIG 193

Query: 194 NGGLEDMSQALK-ILPSVDGVMIG 216
           N        AL+ +     GVM+G
Sbjct: 194 N--CVTYDVALQLMRAGAAGVMVG 215


>gi|1170285|sp|P45603|HIS6_KLEOX RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|530022|emb|CAA39944.1| cyclase [Klebsiella pneumoniae]
          Length = 258

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAQILSFGADKISINSPALADPTLITRLADRFG 121


>gi|296268610|ref|YP_003651242.1| inosine-5'-monophosphate dehydrogenase [Thermobispora bispora DSM
           43833]
 gi|296091397|gb|ADG87349.1| inosine-5'-monophosphate dehydrogenase [Thermobispora bispora DSM
           43833]
          Length = 492

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 9/81 (11%)

Query: 145 KSGVNGIWIHARKAILKGLSP------KDNRKIPNLDYDIVYEIKK--ENPDLFIGLNGG 196
           ++G   +      A+  G+ P      +    +       +YE+ +      + +  +GG
Sbjct: 279 RAGAQALIEAGADAVKVGVGPGSICTTRVVAGVGAPQLTAIYEVAQVCHAAGVPVIGDGG 338

Query: 197 LE-DMSQALKILPSVDGVMIG 216
           L+     A  I    D VM+G
Sbjct: 339 LQYSGDIAKAIAAGADSVMLG 359


>gi|317127161|ref|YP_004093443.1| geranylgeranylglyceryl phosphate synthase family protein [Bacillus
           cellulosilyticus DSM 2522]
 gi|315472109|gb|ADU28712.1| geranylgeranylglyceryl phosphate synthase family protein [Bacillus
           cellulosilyticus DSM 2522]
          Length = 228

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 6/61 (9%)

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
           D DIV E+K       +   GG+E   QA ++    D +++G   Y      T + E   
Sbjct: 168 DPDIVAEVKYVLEHCRLFYGGGIESFEQAKEMAQHADTIIVGNVIY------TDIKEALK 221

Query: 235 N 235
            
Sbjct: 222 T 222


>gi|126658875|ref|ZP_01730018.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Cyanothece sp.
           CCY0110]
 gi|126619825|gb|EAZ90551.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Cyanothece sp.
           CCY0110]
          Length = 257

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 52/144 (36%), Gaps = 12/144 (8%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
           QI       + +     G   + +       +G           ++ D +  I +    +
Sbjct: 26  QIYNENPVEVARQWADEGATRLHLVDLDGAKQGR---------PMNLDTIEAIVRAI-SI 75

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRV 247
            + + GGL D     +++   VD  ++G  A +N +++  + + F + +  G      +V
Sbjct: 76  PVQVGGGLRDRQSVSQLIELGVDRTIVGTVAVENPSLVQELCQAFPSKIAVGIDARNGKV 135

Query: 248 DKDFWRKISASMTDYAARHLHSGG 271
               W + S  +    A+ +   G
Sbjct: 136 ATRGWLETSEVLATDLAQQMAELG 159


>gi|187479788|ref|YP_787813.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bordetella avium
           197N]
 gi|123513593|sp|Q2KTT2|HIS4_BORA1 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|115424375|emb|CAJ50928.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bordetella avium
           197N]
          Length = 246

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I K   D + + + GG+ D+    + L   +  V+IG AA KN   L      F   
Sbjct: 66  IKAILKAVGDDIPVQIGGGIRDLDTIERYLDAGISYVIIGTAAVKNPGFLHDACGAFPGQ 125

Query: 237 LT-GSSPIKTRVDKDFWRKISAS 258
           +  G      ++  D W K++  
Sbjct: 126 IIVGLDARDGKIATDGWSKLTRH 148


>gi|302523431|ref|ZP_07275773.1| oxidoreductase [Streptomyces sp. SPB78]
 gi|318058172|ref|ZP_07976895.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces sp. SA3_actG]
 gi|318078927|ref|ZP_07986259.1| NADH:flavin oxidoreductase/NADH oxidase [Streptomyces sp. SA3_actF]
 gi|302432326|gb|EFL04142.1| oxidoreductase [Streptomyces sp. SPB78]
          Length = 367

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 51/164 (31%), Gaps = 18/164 (10%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCR-IGVDDQIP--------AVALRNLV 140
           ++G           + + A+       +P+  +       ++ P        A       
Sbjct: 204 AYGGSYENRTRFAREVVDAVRAVWPEELPLLFRISATDWFEEDPEDPRTGWTADETVAFA 263

Query: 141 KSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDM 200
           +++K+ GV+ + +        G+SP               E  K   DL     G + + 
Sbjct: 264 RTLKEHGVDLLDVSTG-----GISPTAPIAAGPGYQVRFAERVKNETDLAAAAVGLITEA 318

Query: 201 SQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            QA KIL     D +++GR   ++                 + P
Sbjct: 319 RQAEKILADGQADAILLGRELLRDPYFAAHAATELGEQPYVAQP 362


>gi|16801270|ref|NP_471538.1| pyridoxal biosynthesis lyase PdxS [Listeria innocua Clip11262]
 gi|46396492|sp|Q929R9|PDXS_LISIN RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|16414718|emb|CAC97434.1| lin2205 [Listeria innocua Clip11262]
          Length = 295

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 29  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|47091770|ref|ZP_00229565.1| pyridoxine biosynthesis protein [Listeria monocytogenes str. 4b
           H7858]
 gi|47019781|gb|EAL10519.1| pyridoxine biosynthesis protein [Listeria monocytogenes str. 4b
           H7858]
          Length = 272

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 6   AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 59

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 60  ARIGHITE---------ARVLEAMGVDYI 79


>gi|152966388|ref|YP_001362172.1| NADH:flavin oxidoreductase/NADH oxidase [Kineococcus radiotolerans
           SRS30216]
 gi|151360905|gb|ABS03908.1| NADH:flavin oxidoreductase/NADH oxidase [Kineococcus radiotolerans
           SRS30216]
          Length = 396

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 25/138 (18%), Positives = 49/138 (35%), Gaps = 9/138 (6%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGV 148
           +G  L      + + + A+ +     + +  R+G DD  P           +  +K+ G+
Sbjct: 201 YGGSLENRARFLLEALDAVREVWPERLPLTMRLGSDDFHPEGITFEESITAIGWMKEHGL 260

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL--NGGLEDMSQALKI 206
           +   I         ++P  N       +       K+  D+ +    N G+   + A   
Sbjct: 261 DLADISQGGNTDDMVNPIWN---DPSAWVARAARLKDRVDIPVTTSWNLGIPANADAAIR 317

Query: 207 LPSVDGVMIGRAAYKNSA 224
              VD V++GR A  N  
Sbjct: 318 SGDVDLVLLGRPALANPH 335


>gi|324517814|gb|ADY46926.1| NADH oxidase [Ascaris suum]
          Length = 400

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 74/244 (30%), Gaps = 47/244 (19%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARV-----------HEGSFGACLMLNPDIVGDCI 108
            +   AA  V+D G++ + +NVG                     +G  L     I+ + I
Sbjct: 128 ERYAYAAGFVKDCGFHGVEINVG--MDFALAQLVTATTNSRNDEYGGSLENRTRILFEVI 185

Query: 109 AAMCKAL--SIPVTVKCRI---GVDDQIPAVALRNLVKSIKKS--------GVNGIWIHA 155
            ++   +       +  ++     +D           K +  +        G N   I  
Sbjct: 186 NSIRDRVKDDKNFVLGLKLSSLNYEDGYDECEFERFCKRLDATKLDYVVITGANYEAIRQ 245

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGV 213
           R+ I +  S K           +   IK+        L GG     Q  + +     DG+
Sbjct: 246 REKIERDPSRKSEAFFVKFVIAVRTNIKRAKT----FLCGGFRAADQMWEAIYEGWTDGI 301

Query: 214 MIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKL 273
           M+ R       +   +    +  +TG+            +K      DY      +G ++
Sbjct: 302 MVARPLAAEPDLPRRI---LNREVTGA------------KKSLLDEIDYGLSEYAAGTQM 346

Query: 274 QQIT 277
            Q+ 
Sbjct: 347 WQLA 350


>gi|238757192|ref|ZP_04618379.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           aldovae ATCC 35236]
 gi|238704570|gb|EEP97100.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           aldovae ATCC 35236]
          Length = 247

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 24  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 73

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 74  SVEDAGQILTFGADKISINSPALADPTLITRLADRYG 110


>gi|170758753|ref|YP_001787555.1| 2-enoate reductase [Clostridium botulinum A3 str. Loch Maree]
 gi|169405742|gb|ACA54153.1| 2-enoate reductase [Clostridium botulinum A3 str. Loch Maree]
          Length = 665

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 73/206 (35%), Gaps = 47/206 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             E+A+I +  G++ + ++       VHEG                 +G  L        
Sbjct: 158 FGESAEIAKKAGFDGVEIHA------VHEGYLLDQFAISFFNHRTDEYGGSLENRLRFAC 211

Query: 106 DCIAAMCKAL--SIPVTVK----------CRIGVDDQIPAVALRNL------VKSIKKSG 147
           + +  + K      PV+++          C+ G+ D+      R++       K +  +G
Sbjct: 212 EVVQEIKKRCGQDFPVSLRYSIKSFIKDWCKGGLPDEEFEEKGRDIPEGIEAAKILVAAG 271

Query: 148 VNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QAL 204
            + +        +      P   +K   L Y+   EI K+  D+ I   G +ED    + 
Sbjct: 272 YDALNGDVGSYDSWYWSHPPMYQKKGLYLPYN---EILKKVVDVPIITAGRMEDPELSSD 328

Query: 205 KILPS-VDGVMIGRAAYKNSAMLTTV 229
            IL    D + +GR    ++ +   +
Sbjct: 329 AILSGKTDMIALGRPLLADAEIPNKI 354


>gi|115377940|ref|ZP_01465124.1| dihydroorotate oxidase [Stigmatella aurantiaca DW4/3-1]
 gi|310822299|ref|YP_003954657.1| dihydroorotate oxidase [Stigmatella aurantiaca DW4/3-1]
 gi|115365045|gb|EAU64096.1| dihydroorotate oxidase [Stigmatella aurantiaca DW4/3-1]
 gi|309395371|gb|ADO72830.1| Dihydroorotate oxidase [Stigmatella aurantiaca DW4/3-1]
          Length = 370

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 20/125 (16%), Positives = 40/125 (32%), Gaps = 21/125 (16%)

Query: 98  MLNPDIVGDCIAAMCK-----ALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
           +  P+ +   + A+       A   P+ +K    +  +    A+  +V      G++G+ 
Sbjct: 190 LQEPEQLTALLRAVKARLERVAPGKPLFLKIAPDLTPE----AVDEVVDVALACGLSGLI 245

Query: 153 I----------HARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
                      H       GLS    R+    +  I    ++    L I   GG+     
Sbjct: 246 ATNTTVARPFAHPLAQEAGGLSGAPVRE--PANAVIRRAWRRSGGTLPIIGVGGVFTAQD 303

Query: 203 ALKIL 207
             + L
Sbjct: 304 VYEKL 308


>gi|149944680|ref|NP_056117.1| HAUS augmin-like complex subunit 5 [Homo sapiens]
 gi|67460985|sp|O94927|HAUS5_HUMAN RecName: Full=HAUS augmin-like complex subunit 5
 gi|168267614|dbj|BAG09863.1| KIAA0841 protein [synthetic construct]
 gi|182888395|gb|AAI60190.1| KIAA0841 [synthetic construct]
          Length = 633

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 242 PIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P+  R  +   R++     A +  Y  +H+HS   +++I  +++    G  +S + R  L
Sbjct: 21  PVAARAPESTLRRLCLGQGADIWAYILQHVHSQRTVKKIRGNLLWY--GHQDSPQVRRKL 78

Query: 298 TVEA--GASTATHHIIETAFNLM 318
            +EA      A    ++ +  LM
Sbjct: 79  ELEAAVTRLRAEIQELDQSLELM 101


>gi|14719383|gb|AAK73169.1| NADH-dependent flavin oxidoreductase [Brevibacterium sp. HCU]
          Length = 357

 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 24/173 (13%), Positives = 59/173 (34%), Gaps = 21/173 (12%)

Query: 66  AKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL- 115
           A+   + G++ + ++            P +     S+G  L     ++ D + A    + 
Sbjct: 165 ARRAIEAGFDFVEIHAAHGYLLHEFLSPLSNNRTDSYGGSLENRARLLLDIVDATRTEVG 224

Query: 116 -SIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP 172
             +PV V+       +  +       +   +K+ GV+ I       +  G +   +  + 
Sbjct: 225 EDVPVFVRLSATDWTEGGLTLDDTVEVAGWLKEHGVDLID------VSSGGNVMASIPVG 278

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
                 +    ++   L     G + +  Q   IL     D +++GR   ++ 
Sbjct: 279 PGYQTTLAAGVRQGSGLPTAAVGLISEPFQGEHILATGQADVILVGREYLRDP 331


>gi|332284964|ref|YP_004416875.1| tryptophan synthase subunit alpha [Pusillimonas sp. T7-7]
 gi|330428917|gb|AEC20251.1| tryptophan synthase subunit alpha [Pusillimonas sp. T7-7]
          Length = 282

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 18/104 (17%), Positives = 40/104 (38%), Gaps = 17/104 (16%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARK----------AILKGL----SPKDNRKIPNLD 175
             P   + +    +  +G++ I++ A             + +G     S K      ++D
Sbjct: 132 DYPPEEIADFAVQLGAAGIDPIFLLAPTSTEARIQKVAQVARGYVYYVSLKGVTGAGHID 191

Query: 176 YDIVY---EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            + V    E  + +  + +G+  G+ D   A ++    D V+IG
Sbjct: 192 TEDVAARVEAIRRHVSVPVGVGFGIRDADSAKRLAECADAVVIG 235


>gi|315123499|ref|YP_004065505.1| imidazole glycerol phosphate synthase subunit HisF
           [Pseudoalteromonas sp. SM9913]
 gi|315017259|gb|ADT70596.1| imidazole glycerol phosphate synthase subunit HisF
           [Pseudoalteromonas sp. SM9913]
          Length = 258

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K+  ++G + +  +   A +         +   LD + V  I +   D+   + GG++
Sbjct: 35  LAKAYSEAGADELVFYEISASV---------EKRLLDVNWVENIARHI-DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            ++ A ++L    D + I   A     ++  + + F 
Sbjct: 85  SVADAARVLERGADKISINSPAIARPELIKELHDEFG 121


>gi|291278826|ref|YP_003495661.1| dihydroorotate oxidase [Deferribacter desulfuricans SSM1]
 gi|290753528|dbj|BAI79905.1| dihydroorotate oxidase [Deferribacter desulfuricans SSM1]
          Length = 325

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 22/109 (20%), Positives = 47/109 (43%), Gaps = 13/109 (11%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN-PDIVGDC 107
           P+   +   D    ++ A+ +ED G + + LN+   S +V +         +  D   + 
Sbjct: 98  PVFASVNCIDSEVWIDFARSIEDAGADGLELNISYISFQVDDN------PRDIEDKYVEI 151

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +  +   L+IP++VK            ++ N+VK +K  G + + +  R
Sbjct: 152 VEKVKNKLNIPISVKLGPYF------TSIPNMVKRLKDVGADAVVLLNR 194


>gi|187957150|gb|AAI57883.1| KIAA0841 [Homo sapiens]
          Length = 633

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 242 PIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P+  R  +   R++     A +  Y  +H+HS   +++I  +++    G  +S + R  L
Sbjct: 21  PVAARAPESTLRRLCLGQGADIWAYILQHVHSQRTVKKIRGNLLWY--GHQDSPQVRRKL 78

Query: 298 TVEA--GASTATHHIIETAFNLM 318
            +EA      A    ++ +  LM
Sbjct: 79  ELEAAVTRLRAEIQELDQSLELM 101


>gi|183984249|ref|YP_001852540.1| NADPH dependent 2,4-dienoyl-CoA reductase FadH [Mycobacterium
           marinum M]
 gi|183177575|gb|ACC42685.1| NADPH dependent 2,4-dienoyl-CoA reductase FadH [Mycobacterium
           marinum M]
          Length = 674

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 24/184 (13%), Positives = 56/184 (30%), Gaps = 20/184 (10%)

Query: 61  KLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAM 111
                A++ ++ GY+ + +             P       S+G           + +   
Sbjct: 145 DFARCAQLAQEAGYDGVEIMGSEGYLLNQFLAPRTNKRTDSWGGTPAKRRRFPVEIVRRT 204

Query: 112 CKALSIPVTVKCRI----GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
             A+     +  R+     V+       +  L   ++ +G     I++     +   P  
Sbjct: 205 RAAVGPDFIICYRMSMADYVEGGQSWDEIVALASELETAGAT--IINSGFGWHEARIPTI 262

Query: 168 NRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAYKNS- 223
              +P+    DI   + ++     +  N  +     A +IL   D  +I   R    +  
Sbjct: 263 VTSVPSGAFVDISNAVAEQVSIPVMTSNR-INMPQAAEQILADTDVALISMARPMLSDPE 321

Query: 224 AMLT 227
            +L 
Sbjct: 322 WVLK 325


>gi|170769787|ref|ZP_02904240.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           albertii TW07627]
 gi|170121401|gb|EDS90332.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           albertii TW07627]
          Length = 258

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|148245012|ref|YP_001219706.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Candidatus
           Vesicomyosocius okutanii HA]
 gi|167012117|sp|A5CVQ5|HIS4_VESOH RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|146326839|dbj|BAF61982.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Candidatus Vesicomyosocius okutanii HA]
          Length = 243

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 45/97 (46%), Gaps = 18/97 (18%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           Q   + + +L K  ++ G+N I     AR  +++G+           + + +  + K+  
Sbjct: 143 QKTNLNVVDLSKKFEQDGINSIIYTDIARDGMMQGM-----------NVEAIVNLAKQI- 190

Query: 188 DLFIGLNGGLEDMSQALKILPSVD-GVM---IGRAAY 220
            + I  +GG+ ++   +++L  V  G+M    GRA Y
Sbjct: 191 SIPIIASGGITNIGDIIRLLTEVHFGIMGVITGRAIY 227


>gi|154335212|ref|XP_001563846.1| inosine-5'-monophosphate dehydrogenase [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134060875|emb|CAM37892.1| inosine-5'-monophosphate dehydrogenase [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 492

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 18/119 (15%), Positives = 40/119 (33%), Gaps = 10/119 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + D+  D + A+               VD     +A     + +  +G +G+ +      
Sbjct: 265 HSDLCIDMVKALKANPRT-------NKVDIIAGNIATAEAAQDLIDAGADGLKVGVGPGS 317

Query: 160 LKGLSPKDNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDM-SQALKILPSVDGVMIG 216
           +          +P L   +    + K++  +    +GG++        I    D VM+G
Sbjct: 318 ICITRLVAGAGVPQLSAVMDCARVAKKHG-VPCIADGGVKTAGDICKAIAAGADTVMLG 375


>gi|148654925|ref|YP_001275130.1| dihydroorotate dehydrogenase family protein [Roseiflexus sp. RS-1]
 gi|148567035|gb|ABQ89180.1| dihydroorotate oxidase B, catalytic subunit [Roseiflexus sp. RS-1]
          Length = 264

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 16/109 (14%), Positives = 31/109 (28%), Gaps = 8/109 (7%)

Query: 133 AVALRNLVKSIKKSGVNGIWI----HARKAILKGLSPKDNRKIPNLDYDIVYEIKKEN-- 186
              L  + +SI  +G + + I    HA             R        +V     +   
Sbjct: 156 HDRLIAVARSIIDAGADALTIAFPPHACAPDPHTGELLHGRLSGPAIRPLVLAAIADVCT 215

Query: 187 -PDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYF 233
              + +   GG+  +  A   L      V +G A   +      + +  
Sbjct: 216 TTHVPVVACGGIGTVEDARAFLSAGATAVQVGSALLADPFAAVRIADAL 264


>gi|46908469|ref|YP_014858.1| NADH oxidase [Listeria monocytogenes serotype 4b str. F2365]
 gi|46881740|gb|AAT05035.1| putative NADH oxidase [Listeria monocytogenes serotype 4b str.
           F2365]
          Length = 644

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 154 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 211

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 212 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 271

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 272 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 327


>gi|75908865|ref|YP_323161.1| inosine 5-monophosphate dehydrogenase [Anabaena variabilis ATCC
           29413]
 gi|75702590|gb|ABA22266.1| IMP dehydrogenase related 2 [Anabaena variabilis ATCC 29413]
          Length = 387

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 22/63 (34%), Gaps = 12/63 (19%)

Query: 189 LFIGLNGG-LEDMSQALKILPSVDGVMIG----RAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           + I  +GG +        I    DGVMIG    RAA             F   +   SP+
Sbjct: 256 IPIIADGGLITGGDICKCIACGADGVMIGSPFARAAEA-PG------RGFHWGMATPSPV 308

Query: 244 KTR 246
             R
Sbjct: 309 LPR 311


>gi|191167715|ref|ZP_03029523.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli B7A]
 gi|194436053|ref|ZP_03068155.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli 101-1]
 gi|301018886|ref|ZP_07183119.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 196-1]
 gi|301648501|ref|ZP_07248226.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 146-1]
 gi|190902228|gb|EDV61969.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli B7A]
 gi|194424781|gb|EDX40766.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli 101-1]
 gi|299882471|gb|EFI90682.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 196-1]
 gi|301073436|gb|EFK88242.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 146-1]
 gi|323187764|gb|EFZ73064.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli RN587/1]
 gi|323968156|gb|EGB63565.1| imidazoleglycerol phosphate synthase [Escherichia coli M863]
 gi|323972825|gb|EGB68024.1| imidazoleglycerol phosphate synthase [Escherichia coli TA007]
 gi|323977809|gb|EGB72895.1| imidazoleglycerol phosphate synthase [Escherichia coli TW10509]
 gi|324114043|gb|EGC08016.1| imidazoleglycerol phosphate synthase [Escherichia fergusonii B253]
 gi|327253153|gb|EGE64807.1| imidazole glycerol phosphate synthase subunit hisF [Escherichia
           coli STEC_7v]
          Length = 258

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|296104817|ref|YP_003614963.1| 2,4-dienoyl-CoA reductase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
 gi|295059276|gb|ADF64014.1| 2,4-dienoyl-CoA reductase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
          Length = 673

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 20/191 (10%), Positives = 52/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM--------------------L 99
                 A +  + GY+ + +                 L+                     
Sbjct: 143 DDFARCAALAREAGYDGVEV-----------MGSEGYLINEFLAARTNQRDDEWGGDYAR 191

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ +       +  R+ + D +           L ++I+ +G   I  + 
Sbjct: 192 RMRFAVEVVRAVRERAGADFIIIFRLSMLDLVEGGGTFDETVQLAQAIEAAGATLI--NT 249

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K +     +  N  + D   A  ++   D  M
Sbjct: 250 GIGWHEARIPTIATPVPRAAFTWVTRKLKGKVSVPLVTTNR-INDPQVADDVISRGDADM 308

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 309 V---SMARPFL 316


>gi|33594629|ref|NP_882273.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bordetella pertussis
           Tohama I]
 gi|161609255|ref|NP_891391.2| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bordetella
           bronchiseptica RB50]
 gi|161610373|ref|NP_886400.2| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Bordetella
           parapertussis 12822]
 gi|39931427|sp|Q7VSY7|HIS4_BORPE RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|39931436|sp|Q7W2Y0|HIS4_BORPA RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|39931448|sp|Q7WDY0|HIS4_BORBR RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|33564705|emb|CAE44028.1| histidine biosynthesis protein [Bordetella pertussis Tohama I]
 gi|332384040|gb|AEE68887.1| imidazole-4-carboxamide isomerase [Bordetella pertussis CS]
          Length = 246

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP 236
           +  I +   D + + + GG+ D+    + L   +  V+IG AA KN   L      F   
Sbjct: 66  IKAILQAVGDDIPVQIGGGIRDLDTIERYLDAGISYVIIGTAAVKNPGFLQDACGAFPGQ 125

Query: 237 LT-GSSPIKTRVDKDFWRKISAS 258
           +  G      +V  D W K++  
Sbjct: 126 IIVGLDARDGKVATDGWSKLTRH 148


>gi|306830882|ref|ZP_07464044.1| dihydroorotate dehydrogenase A [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
 gi|304426905|gb|EFM30015.1| dihydroorotate dehydrogenase A [Streptococcus gallolyticus subsp.
           gallolyticus TX20005]
          Length = 311

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 39/213 (18%), Positives = 64/213 (30%), Gaps = 24/213 (11%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEG 91
              D    L  +   K   L + G    +     K V+D  Y   + LN+ CP   V   
Sbjct: 80  YYLDYVTELQNTPNSKHHFLSLVGMSEEETHTILKAVQDSDYQGLVELNLSCP--NVPGK 137

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIK 144
              A    + +     +  +    + P+ VK     D      A A+ N      V  I 
Sbjct: 138 PQIAY---DFETTETLLRDIFTYFTKPLGVKLPPYFDIAHFDRAAAIFNQFPLTFVNCIN 194

Query: 145 KSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             G   I          K    G+     +     +    Y+  + NP + I   GG++ 
Sbjct: 195 SIGNGLIIEDETVLIKPKNGFGGIGGDYVKPTALANVHAFYQ--RLNPSIQIIGTGGIKT 252

Query: 200 MSQALKI-LPSVDGVMIGRAAYKN--SAMLTTV 229
              A +  L     V +G         A+   +
Sbjct: 253 GRDAFEHILCGASMVQLGT-ILHQEGPAVFERI 284


>gi|218549439|ref|YP_002383230.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           fergusonii ATCC 35469]
 gi|218558907|ref|YP_002391820.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli S88]
 gi|226700513|sp|B7MDH9|HIS6_ECO45 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|226700522|sp|B7LUF6|HIS6_ESCF3 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|218356980|emb|CAQ89611.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia fergusonii ATCC 35469]
 gi|218365676|emb|CAR03412.1| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli S88]
 gi|332343809|gb|AEE57143.1| imidazole glycerol phosphate synthase HisF [Escherichia coli
           UMNK88]
          Length = 258

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|166366556|ref|YP_001658829.1| dihydroorotate dehydrogenase 2 [Microcystis aeruginosa NIES-843]
 gi|166088929|dbj|BAG03637.1| dihydroorotate dehydrogenase [Microcystis aeruginosa NIES-843]
          Length = 341

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 18/102 (17%), Positives = 40/102 (39%), Gaps = 27/102 (26%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--------DCIAAMCKA 114
           +E A  ++  G + + LNV               +  + ++ G        D +  +   
Sbjct: 118 LEYAIQIQQAGADALELNV-------------YYVPNDLELTGNHVEQNYIDILKIVKSE 164

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +SIPV++K      +        N+ K + ++G +G+ +  R
Sbjct: 165 VSIPVSMKLSPYFSNT------ANMAKQLAEAGADGLVLFNR 200


>gi|114707334|ref|ZP_01440231.1| 2-nitropropane dioxygenase [Fulvimarina pelagi HTCC2506]
 gi|114537215|gb|EAU40342.1| 2-nitropropane dioxygenase [Fulvimarina pelagi HTCC2506]
          Length = 357

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 20/139 (14%), Positives = 51/139 (36%), Gaps = 12/139 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-----KKENPDLFIG 192
           +  +  +++G + I   A +A       + +    N +   V  +       +     + 
Sbjct: 162 DEARQAEEAGADVIVAQASEA----GGHRGSFDPGNAELQSVGALSLLPTIVDVVCCPVV 217

Query: 193 LNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
             GG+ D   A+  L      V IG    +       ++  +++ L  +SP  T + + F
Sbjct: 218 AAGGIADARTAIAALTLGASAVQIGTGFLRTPE--AGLNPAWADALAETSPTDTALTRGF 275

Query: 252 WRKISASMTDYAARHLHSG 270
             ++  ++ +     + +G
Sbjct: 276 SGRLGRAVRNRYVAAIEAG 294


>gi|46908336|ref|YP_014725.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes serotype
           4b str. F2365]
 gi|217963741|ref|YP_002349419.1| pyridoxine biosynthesis protein [Listeria monocytogenes HCC23]
 gi|226224706|ref|YP_002758813.1| protein required for pyridoxine synthesis [Listeria monocytogenes
           Clip81459]
 gi|254826255|ref|ZP_05231256.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL J1-194]
 gi|254854068|ref|ZP_05243416.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL R2-503]
 gi|254931790|ref|ZP_05265149.1| pyridoxine biosynthesis protein [Listeria monocytogenes HPB2262]
 gi|255521113|ref|ZP_05388350.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes FSL
           J1-175]
 gi|284802547|ref|YP_003414412.1| pyridoxine biosynthesis protein [Listeria monocytogenes 08-5578]
 gi|284995689|ref|YP_003417457.1| pyridoxine biosynthesis protein [Listeria monocytogenes 08-5923]
 gi|300765552|ref|ZP_07075532.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL N1-017]
 gi|315283158|ref|ZP_07871413.1| pyridoxine biosynthesis protein [Listeria marthii FSL S4-120]
 gi|67460839|sp|Q71XR3|PDXS_LISMF RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|254781611|sp|B8DH17|PDXS_LISMH RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|259530402|sp|C1KX53|PDXS_LISMC RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|46881607|gb|AAT04902.1| pyridoxine biosynthesis protein [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|217333011|gb|ACK38805.1| pyridoxine biosynthesis protein [Listeria monocytogenes HCC23]
 gi|225877168|emb|CAS05882.1| Putative protein required for pyridoxine synthesis [Listeria
           monocytogenes serotype 4b str. CLIP 80459]
 gi|258607461|gb|EEW20069.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL R2-503]
 gi|284058109|gb|ADB69050.1| pyridoxine biosynthesis protein [Listeria monocytogenes 08-5578]
 gi|284061156|gb|ADB72095.1| pyridoxine biosynthesis protein [Listeria monocytogenes 08-5923]
 gi|293583344|gb|EFF95376.1| pyridoxine biosynthesis protein [Listeria monocytogenes HPB2262]
 gi|293595494|gb|EFG03255.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL J1-194]
 gi|300513754|gb|EFK40821.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL N1-017]
 gi|307571684|emb|CAR84863.1| pyridoxine biosynthesis lyase [Listeria monocytogenes L99]
 gi|313607631|gb|EFR83903.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL F2-208]
 gi|313613198|gb|EFR87087.1| pyridoxine biosynthesis protein [Listeria marthii FSL S4-120]
 gi|328465909|gb|EGF37090.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes 1816]
 gi|328472376|gb|EGF43244.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes 220]
          Length = 295

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 29  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|47095810|ref|ZP_00233415.1| pyridoxine biosynthesis protein [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224498454|ref|ZP_03666803.1| pyridoxine biosynthesis protein [Listeria monocytogenes Finland
           1988]
 gi|254827011|ref|ZP_05231698.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL N3-165]
 gi|254831658|ref|ZP_05236313.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes 10403S]
 gi|254899201|ref|ZP_05259125.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes J0161]
 gi|254912658|ref|ZP_05262670.1| pyridoxine biosynthesis protein [Listeria monocytogenes J2818]
 gi|254936985|ref|ZP_05268682.1| pyridoxine biosynthesis protein [Listeria monocytogenes F6900]
 gi|47015814|gb|EAL06742.1| pyridoxine biosynthesis protein [Listeria monocytogenes str. 1/2a
           F6854]
 gi|258599393|gb|EEW12718.1| pyridoxine biosynthesis protein [Listeria monocytogenes FSL N3-165]
 gi|258609588|gb|EEW22196.1| pyridoxine biosynthesis protein [Listeria monocytogenes F6900]
 gi|293590653|gb|EFF98987.1| pyridoxine biosynthesis protein [Listeria monocytogenes J2818]
          Length = 295

 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 29  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|329923248|ref|ZP_08278733.1| NADH oxidase family protein [Paenibacillus sp. HGF5]
 gi|328941483|gb|EGG37774.1| NADH oxidase family protein [Paenibacillus sp. HGF5]
          Length = 374

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 24/178 (13%), Positives = 48/178 (26%), Gaps = 37/178 (20%)

Query: 93  FGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQ------IPAVALRNLVKSIK 144
           +G  ++       + + A+ +A+    PV ++       Q           L  L+ ++ 
Sbjct: 199 YGGDMLKRARFAIEVVKAVRQAVGPDFPVAIRLSQWKTTQYEAKLADTPEKLGQLLTALS 258

Query: 145 KSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL 204
            +GV+      R+         D               KK      I + G +       
Sbjct: 259 DAGVDIFHCSTRRFWEPEFEGSDLNFAGWA--------KKLTGKTVITV-GSVGLDEVFT 309

Query: 205 KILPS--------------------VDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
            +                        D V +GRA   +      V +   + L   +P
Sbjct: 310 SLFTQGKGAGQRDLEELLNRLEEHEFDLVAVGRALLADPEWAAKVRDGRFDELAPFTP 367


>gi|300934148|ref|ZP_07149404.1| putative oxidoreductase [Corynebacterium resistens DSM 45100]
          Length = 374

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 22/142 (15%), Positives = 51/142 (35%), Gaps = 15/142 (10%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           ++G        ++ + + A+ K +     +  R+   + I  V   +  +++    V   
Sbjct: 207 NYGGSPENRARLLVEILRAVAKEIGAD-RLGVRLSPRNNIQGVVDGDDAEALASYSVLL- 264

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIK---KENPDLFIGLNGG---LEDMSQALK 205
                +    GL+          D D + +++   + N    +  N G   +     A++
Sbjct: 265 ----DEVAQLGLAYVSFLYPHPED-DFIADLRQKVRANGKTKVIFNTGFAEVTQREDAIE 319

Query: 206 IL--PSVDGVMIGRAAYKNSAM 225
            +   +VD V IGR    N  +
Sbjct: 320 QMSRENVDAVAIGRMVIANPDL 341


>gi|226224843|ref|YP_002758950.1| NADH oxidase [Listeria monocytogenes Clip81459]
 gi|225877305|emb|CAS06019.1| Putative NADH oxidase [Listeria monocytogenes serotype 4b str. CLIP
           80459]
          Length = 641

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|154252250|ref|YP_001413074.1| NADH:flavin oxidoreductase/NADH oxidase [Parvibaculum
           lavamentivorans DS-1]
 gi|154156200|gb|ABS63417.1| NADH:flavin oxidoreductase/NADH oxidase [Parvibaculum
           lavamentivorans DS-1]
          Length = 681

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 25/180 (13%), Positives = 53/180 (29%), Gaps = 19/180 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA 110
                AA +  + GY+ + +                      +G        +  + +  
Sbjct: 146 EDFGTAAALAREAGYDGVEVMGSEGYFLNQFTAARTNQRTDGWGGSAENRRRLPVEVVGR 205

Query: 111 MCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           + K       +  RI V D          +  L K ++ SG N   ++      +   P 
Sbjct: 206 VRKHCGPDFIIVYRISVLDLVEGGNSWPDVAALAKDVEVSGAN--ILNTGIGWHESRVPT 263

Query: 167 DNRKIPNLDYDI-VYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
               +P   +   +  +K E     +  N  +    QA +++     D V + R    + 
Sbjct: 264 IAHMVPRGAFTWAIKRLKAEVAIPVVASNR-INTPEQAEQLIADGQADMVSLARPLLADP 322


>gi|325517963|gb|EGC97787.1| dihydroorotate dehydrogenase 2 [Burkholderia sp. TJI49]
          Length = 307

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 8/99 (8%)

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD------NRK 170
           +P+ +K    +DD+        L++   ++ +      +R A+ +GL   D       R 
Sbjct: 177 VPLALKIAPDLDDEQVKEIGDTLLRHKIEAVIATTTTLSRAAV-QGLPHADEGGGLSGRP 235

Query: 171 IPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
           + +   +++ ++  E    + I   GG+     A   L 
Sbjct: 236 VFDASNEVIRKLHAEVGSAVPIIGVGGIFSGEDARAKLA 274


>gi|213401439|ref|XP_002171492.1| dihydroorotate dehydrogenase [Schizosaccharomyces japonicus yFS275]
 gi|211999539|gb|EEB05199.1| dihydroorotate dehydrogenase [Schizosaccharomyces japonicus yFS275]
          Length = 442

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 23/177 (12%), Positives = 60/177 (33%), Gaps = 29/177 (16%)

Query: 56  GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL 115
           G +    ++  +   +F  + + +NV CP         G C + + D +   +  +    
Sbjct: 239 GDETEDFLKGVRKFGNF-ADILVVNVSCP------NISGVCNLQSKDTLVPLLNKVVAER 291

Query: 116 SI------PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----------HARKAI 159
           +       P+ VK        +    + ++  ++ ++ V+G+ +                
Sbjct: 292 NKLVSPQPPIVVKI----GPDLTEAEISDIAHALVETKVDGVIVCNSTGTRPKTLTPNKN 347

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILPSVDGVMI 215
           L+ +       +      ++  ++K+ P    I   GG+     A++        MI
Sbjct: 348 LENVGGISGPVMKPFSLRVLRLLRKDLPKEFPIIGCGGITSGKDAVE-FARAGATMI 403


>gi|160939041|ref|ZP_02086392.1| hypothetical protein CLOBOL_03935 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438004|gb|EDP15764.1| hypothetical protein CLOBOL_03935 [Clostridium bolteae ATCC
           BAA-613]
          Length = 239

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 28/160 (17%), Positives = 58/160 (36%), Gaps = 21/160 (13%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++     D  I + A   +    ++ G + + +      L G S         ++ ++
Sbjct: 15  VRLRQGAFKDITIYSDAPEKVAAHWQEKGASFLHLVDLDGALAGYS---------VNEEV 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP- 236
           +  I  +   + I + GG+       ++L   V  V+IG  A ++   L  +   F    
Sbjct: 66  IRRIA-DTVSIPIEIGGGIRSKEAVERMLDLGVRRVIIGTKAAEHPEFLRDMVRTFGEEA 124

Query: 237 -LTGSSPIKTRVDKDFWRKI--------SASMTDYAARHL 267
            + G       V  + W K+          +M +Y  RH+
Sbjct: 125 IVAGVDAKDGMVAVEGWEKVSSLTASDLCLTMKEYGVRHI 164


>gi|119094191|gb|ABL61013.1| isopentenyl-diphosphate delta isomerase isomerase Idi [uncultured
           marine bacterium HF10_25F10]
          Length = 361

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 57/153 (37%), Gaps = 22/153 (14%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR 124
           A + V D G + I +++  P     +         +   V D I  +   L +PV VK  
Sbjct: 145 ACRAVVDIGADAIFIHLN-PLQEAVQPEGET----DWRGVLDAIETLVGVLEVPVMVK-- 197

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAILKGLSPKDNRKIPNLDY--- 176
                ++ A    ++ + +  +GV+ + I          I            P LD+   
Sbjct: 198 -----EVGAGIGPDVAQRLFDAGVHAVDIAGLGGTNWTRIEAARREDAALFEPFLDWGLP 252

Query: 177 --DIVYEIKKENPDLFIGLNGGLEDMSQALKIL 207
             D +  ++   P+  +  +GG+E+   A K L
Sbjct: 253 TVDALRAVRSACPNARLIASGGVENGLDAAKAL 285


>gi|28869601|ref|NP_792220.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|28852843|gb|AAO55915.1| xenobiotic reductase A [Pseudomonas syringae pv. tomato str.
           DC3000]
          Length = 363

 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 61/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVLEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +    + +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREAAIPVTSAWGFGEPKLAEEAVKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|331674627|ref|ZP_08375386.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA280]
 gi|331068066|gb|EGI39462.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA280]
          Length = 672

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 30/230 (13%), Positives = 69/230 (30%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLMLN-----------------PDIVG---DCIAAMCKALSIPVT 120
                           L+                   P+ +    + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYPNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++        +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLTGHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|295099601|emb|CBK88690.1| Putative N-acetylmannosamine-6-phosphate epimerase [Eubacterium
           cylindroides T2-87]
          Length = 227

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 28/209 (13%), Positives = 66/209 (31%), Gaps = 32/209 (15%)

Query: 39  NILGFSTQEKPLALQIGGADI----SKLVEAAKIVEDFGYNEINLN-----------VGC 83
           N +  +  +  ++ Q    +       +   AK  ++ G   I  N           V  
Sbjct: 2   NKMETTKGQLIVSCQALPNEPLHSSFIMGRMAKAAKEGGAKGIRANTVVDIKEIKEQVDL 61

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAM-CKALSIPVTVKCRIGVD----DQIPAVALRN 138
           P   + +  +G   +     + +    M  K   I V   CR   D    D+  +     
Sbjct: 62  PVIGIIKREYGDNPVYITPTMKEIDELMEVKPEVIAVDATCRTRPDGKTLDEFVSEIRAK 121

Query: 139 LVKSIKKSGVNGI--WIHA--------RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD 188
               +  +  + +   +HA           ++         KI   D++I+  + ++   
Sbjct: 122 YPNQLLMADCSTLEEMLHADEIGFDFIGTTLVGYTEQSKGNKIEANDFEIIRSLLEKAKH 181

Query: 189 LFIGLNGGLEDMSQALKILP-SVDGVMIG 216
             +   G ++   +  ++L      V++G
Sbjct: 182 -PVIAEGNIDTPEKVRRVLDLGCYSVVVG 209


>gi|239814177|ref|YP_002943087.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Variovorax paradoxus S110]
 gi|259709863|sp|C5CQJ5|HIS4_VARPS RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|239800754|gb|ACS17821.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Variovorax paradoxus S110]
          Length = 247

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 23/121 (19%), Positives = 42/121 (34%), Gaps = 15/121 (12%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V +K        I +     + +   ++G   + +        G            ++  
Sbjct: 15  VRLKQGDMDQSTIFSEDPAAMARKWVEAGARRLHLVDLNGAFAG---------KPQNHAA 65

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILPSVDG---VMIGRAAYKNSAMLTTVDEYFS 234
           +  I +E  D + + L GG+ D+    + +   DG   V+IG AA KN   L      F 
Sbjct: 66  IKAILREVGDDIPVQLGGGIRDLDTIERYID--DGLRYVIIGTAAVKNPGFLKDACVAFG 123

Query: 235 N 235
            
Sbjct: 124 G 124


>gi|254281599|ref|ZP_04956567.1| NADH:flavin oxidoreductase/nadh oxidase family protein [gamma
           proteobacterium NOR51-B]
 gi|219677802|gb|EED34151.1| NADH:flavin oxidoreductase/nadh oxidase family protein [gamma
           proteobacterium NOR51-B]
          Length = 358

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 25/174 (14%), Positives = 60/174 (34%), Gaps = 19/174 (10%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCI 108
              V AA+     G++ + L+       +               +G  L     I+ D +
Sbjct: 142 DDFVTAARRAAKAGFDGVELHAA--HGYILGQFLSSEINQRDDHYGGSLENRARILFDLV 199

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH-ARKAILKGLSPKD 167
             +        ++  R+    +   + L  +V+  ++   +G+  +          +P D
Sbjct: 200 ERVRDVAPADFSLGVRLS--PERFGMQLDEVVEVARRLCADGLIDYIDLSLWDVFKTPAD 257

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAY 220
                    +   E+ + +  L  G  G + + + A + L   +D +++GR A 
Sbjct: 258 AESDEKTLLEFFTELDRRHVKL--GGAGKIYNAADAQRALDSGLDFIILGRGAI 309


>gi|308049595|ref|YP_003913161.1| dihydroorotate oxidase A [Ferrimonas balearica DSM 9799]
 gi|307631785|gb|ADN76087.1| dihydroorotate oxidase A [Ferrimonas balearica DSM 9799]
          Length = 341

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 45/131 (34%), Gaps = 20/131 (15%)

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVK-----------SIKKSGVNGIWIHARKAILKGLSP 165
           +PV +K    + D+       +LV+           ++ + GV  +  H     L G   
Sbjct: 213 VPVALKIAPDLSDEEIRQVAASLVRHEIDGVIATNTTLAREGVEHLPEHTEAGGLSGAPL 272

Query: 166 KDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKN- 222
            +   I      ++ ++       L I   GG++    A+  L      V I      N 
Sbjct: 273 TERSTI------VIRKLADALDGKLPILGVGGIDSAQHAMDKLDAGAKMVQIYTGFIYNG 326

Query: 223 SAMLTTVDEYF 233
             ++ T+ E F
Sbjct: 327 PELVKTITEAF 337


>gi|288937157|ref|YP_003441216.1| 2,4-dienoyl-CoA reductase (NADPH) [Klebsiella variicola At-22]
 gi|288891866|gb|ADC60184.1| 2,4-dienoyl-CoA reductase (NADPH) [Klebsiella variicola At-22]
          Length = 677

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 61/185 (32%), Gaps = 15/185 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAA 110
            K  +AA+ V   G++ + ++ G         S   ++    FG  +     I+   I  
Sbjct: 150 EKFGDAAERVRRAGFDSVEIHAGHSYLISQFLSPLFNKRTDEFGGTVENRTRILSLIIDK 209

Query: 111 MCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSG--VNGIWIHARKAILKGLSPKD 167
           +   +     V  RI  DD +     L + ++ ++     V+ I + A +     L    
Sbjct: 210 VRACVGPRFPVSLRISADDFLKGGNTLEDSLRILELCQDKVDIINVSAAQNDNLNLQIDQ 269

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAM 225
                     +   ++ +     +   G +     A  IL S   D + IGR        
Sbjct: 270 MSLEDGWKRYLSRAVRDKFHKPTVIA-GNIRSPQVAEDILASGDADLIAIGRGLIAEPEW 328

Query: 226 LTTVD 230
           +  V 
Sbjct: 329 VQKVQ 333


>gi|254825201|ref|ZP_05230202.1| conserved hypothetical protein [Listeria monocytogenes FSL J1-194]
 gi|254853358|ref|ZP_05242706.1| conserved hypothetical protein [Listeria monocytogenes FSL R2-503]
 gi|254931652|ref|ZP_05265011.1| conserved hypothetical protein [Listeria monocytogenes HPB2262]
 gi|255520410|ref|ZP_05387647.1| NADH oxidase, putative [Listeria monocytogenes FSL J1-175]
 gi|300763955|ref|ZP_07073951.1| NADH oxidase [Listeria monocytogenes FSL N1-017]
 gi|258606723|gb|EEW19331.1| conserved hypothetical protein [Listeria monocytogenes FSL R2-503]
 gi|293583207|gb|EFF95239.1| conserved hypothetical protein [Listeria monocytogenes HPB2262]
 gi|293594446|gb|EFG02207.1| conserved hypothetical protein [Listeria monocytogenes FSL J1-194]
 gi|300515296|gb|EFK42347.1| NADH oxidase [Listeria monocytogenes FSL N1-017]
 gi|328465817|gb|EGF37005.1| NADH oxidase, putative [Listeria monocytogenes 1816]
 gi|328472129|gb|EGF43004.1| NADH oxidase, putative [Listeria monocytogenes 220]
 gi|332312723|gb|EGJ25818.1| hypothetical enoate reductase [Listeria monocytogenes str. Scott A]
          Length = 641

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 151 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 208

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 209 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 269 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 324


>gi|107024221|ref|YP_622548.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           cenocepacia AU 1054]
 gi|170731764|ref|YP_001763711.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           cenocepacia MC0-3]
 gi|206558723|ref|YP_002229483.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           cenocepacia J2315]
 gi|254246524|ref|ZP_04939845.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia PC184]
 gi|122978574|sp|Q1BS30|HIS4_BURCA RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700293|sp|B1JUA4|HIS4_BURCC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700294|sp|B4E640|HIS4_BURCJ RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|105894410|gb|ABF77575.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           cenocepacia AU 1054]
 gi|124871300|gb|EAY63016.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia PC184]
 gi|158343622|gb|ABW35453.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343762|gb|ABW35579.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343772|gb|ABW35588.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343792|gb|ABW35606.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343822|gb|ABW35633.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343832|gb|ABW35642.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343852|gb|ABW35660.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343862|gb|ABW35669.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343872|gb|ABW35678.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343882|gb|ABW35687.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343902|gb|ABW35705.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343932|gb|ABW35732.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343962|gb|ABW35759.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343982|gb|ABW35777.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|169815006|gb|ACA89589.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia MC0-3]
 gi|198034760|emb|CAR50627.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia J2315]
          Length = 251

 Score = 36.3 bits (83), Expect = 5.9,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 20/93 (21%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L K  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVIDLAKKFEDYGVESIVYTDIGRDGMLQG-----------INIDATVKLAQAVGIPVIA 197

Query: 193 LNG-----GLEDMSQALKILPSVDGVMIGRAAY 220
             G      +E + +  +    V+GV+ GRA Y
Sbjct: 198 SGGLSNLTDIESLCEVEEH--GVEGVICGRAIY 228


>gi|306835362|ref|ZP_07468384.1| pyridoxal biosynthesis lyase PdxS [Corynebacterium accolens ATCC
           49726]
 gi|304568770|gb|EFM44313.1| pyridoxal biosynthesis lyase PdxS [Corynebacterium accolens ATCC
           49726]
          Length = 468

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 40/221 (18%), Positives = 67/221 (30%), Gaps = 68/221 (30%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G + +      P+        G   M +P+++   +     A+SIPV  K RI
Sbjct: 205 ARIAEDAGASAVMALERVPAD--IRAQGGVARMSDPELIEGIV----DAVSIPVMAKARI 258

Query: 126 --------------GVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                            D+   ++  + V  I K                       G  
Sbjct: 259 GHFVEAQILGELGVDFIDESEVLSPADYVNHINKWDFDVPFVCGATNLGEALRRITEGAA 318

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKKENP 187
            I                    I A  A L+ L   +           YD+V E+ +   
Sbjct: 319 MIRSKGEAGTGDVSEAVKHLRTIRAEIARLQHLDRDELYVAAKELQAPYDLVAEVAETGK 378

Query: 188 DLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
              +  + GG+   + A  +     +GV +G   +   N A
Sbjct: 379 LPVVLFVAGGVATPADAALVRQMGAEGVFVGSGIFKSGNPA 419


>gi|224591463|ref|YP_002640778.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi
           WI91-23]
 gi|224553806|gb|ACN55207.1| inosine-5'-monophosphate dehydrogenase [Borrelia burgdorferi
           WI91-23]
          Length = 404

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 2/39 (5%)

Query: 179 VYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
           VYE+ K N ++ I  +GG+         I    D VMIG
Sbjct: 248 VYEVCK-NTNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|123442987|ref|YP_001006962.1| imidazole glycerol phosphate synthase subunit HisF [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|167012224|sp|A1JTW3|HIS6_YERE8 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|122089948|emb|CAL12805.1| histidine biosynthesic protein (cyclase) [Yersinia enterocolitica
           subsp. enterocolitica 8081]
          Length = 258

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 85  SVEDAGQILTFGADKISINSPALADPTLITRLADRYG 121


>gi|86157189|ref|YP_463974.1| dihydroorotate dehydrogenase 2 [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85773700|gb|ABC80537.1| Dihydroorotate dehydrogenase [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 328

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 43/110 (39%), Gaps = 11/110 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E P+   + G+      E A+ +E  G + + LN+        E               +
Sbjct: 99  EIPVIASLNGSAAGGWTEFARDIEQAGADALELNL-----YAVEADPAVSAAEVEARYLE 153

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++A+ +A++IPV VK            AL +    +   GVNGI +  R
Sbjct: 154 AVSAVREAVTIPVAVKLSPYF------TALAHFCARLDALGVNGIVLFNR 197


>gi|33869699|gb|AAH13947.2| KIAA0841 protein [Homo sapiens]
          Length = 640

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 242 PIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P+  R  +   R++     A +  Y  +H+HS   +++I  +++    G  +S + R  L
Sbjct: 28  PVAARAPESTLRRLCLGQGADIWAYILQHVHSQRTVKKIRGNLLWY--GHQDSPQVRRKL 85

Query: 298 TVEA--GASTATHHIIETAFNLM 318
            +EA      A    ++ +  LM
Sbjct: 86  ELEAAVTRLRAEIQELDQSLELM 108


>gi|310765266|gb|ADP10216.1| 2,4-dieonyl-coa reductase [Erwinia sp. Ejp617]
          Length = 669

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 16/120 (13%), Positives = 42/120 (35%), Gaps = 8/120 (6%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
               + A+  A      +  R+ + D +   +  +    L K++++ G   +  +     
Sbjct: 194 ALAILKAVRAATGPAFIIIFRLSMLDLVEQGSTLDHTIRLAKALEQQGATLL--NTGIGW 251

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
            +   P     +P   +  V +I +++  + +     +     A  +L     D V + R
Sbjct: 252 HEARIPTIATSVPRAAFAWVTQILRQHVSIPLIATNRINHPDVAQALLDEGCADMVSMAR 311


>gi|229172749|ref|ZP_04300305.1| NADPH dehydrogenase [Bacillus cereus MM3]
 gi|228610714|gb|EEK67980.1| NADPH dehydrogenase [Bacillus cereus MM3]
          Length = 319

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 58/176 (32%), Gaps = 19/176 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAA   +  G++ I ++            P +      +G         + + I ++ 
Sbjct: 120 FQEAAIRSKQAGFDVIEIHGAHGYLINEFLSPLSNKRTDEYGGSPENRYRFLREIIDSIN 179

Query: 113 KALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  + P+ V+        D +           +K+ GV+ I   +   +     P     
Sbjct: 180 EVWNGPLFVRISANDYHPDGLTVQDYVPYTNWMKEQGVDLIDCSSGAVV-----PAHIDV 234

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSA 224
            P         IK+   ++  G  G +    QA +IL     D + IGR   +N  
Sbjct: 235 YPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNNEADLIFIGRELLRNPY 289


>gi|254479971|ref|ZP_05093219.1| oxidoreductase, FAD/FMN-binding family [marine gamma
           proteobacterium HTCC2148]
 gi|214039533|gb|EEB80192.1| oxidoreductase, FAD/FMN-binding family [marine gamma
           proteobacterium HTCC2148]
          Length = 674

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 80/237 (33%), Gaps = 22/237 (9%)

Query: 16  LTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYN 75
           L    L Y E +VA + ++      +        +  QI        V  AK+ +  GY+
Sbjct: 103 LHTGPLAYNEKLVAPSAIKSRIAPFVPNELDANGVQKQINDH-----VRCAKLAKQAGYD 157

Query: 76  EINLNVGCP-------SARVHEG--SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
            + +              + ++    +G           + +  +  A+     V  RI 
Sbjct: 158 GVEIIGSAGYLISTFLVEKTNKRTDEYGGSYENRMRFALEIVQKIRAAVGDEFIVIFRIA 217

Query: 127 VDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI 182
             D     +    +  L + ++K+GVN I  H      +   P     +P   +  V   
Sbjct: 218 AMDMLQGGMSWDEVVQLAQGLEKAGVNIISTH--FTWHESAVPTIATMVPRAAFSQVTGR 275

Query: 183 KKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
            ++N ++ +  +  +     A ++L     D V + R    ++ ++    E   + +
Sbjct: 276 IRQNVNVPMITSNRINMPHVAEEVLQRGDADLVSMARPMLADAELVNKAREGREDEI 332


>gi|159026287|emb|CAO88864.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 341

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 18/102 (17%), Positives = 40/102 (39%), Gaps = 27/102 (26%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG--------DCIAAMCKA 114
           +E A  ++  G + + LNV               +  + ++ G        D +  +   
Sbjct: 118 LEYAIQIQQAGADALELNV-------------YYVPNDLELTGNHVEQNYIDILKIVKSE 164

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +SIPV++K      +        N+ K + ++G +G+ +  R
Sbjct: 165 VSIPVSMKLSPYFSNT------ANMAKQLAEAGADGLVLFNR 200


>gi|53729144|ref|ZP_00134119.2| COG0107: Imidazoleglycerol-phosphate synthase [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
          Length = 248

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 26  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 75

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++T + + F 
Sbjct: 76  TIEDAEKLFAFGADKISINSPALADPNLITALADRFG 112


>gi|47093351|ref|ZP_00231119.1| NADH oxidase, putative [Listeria monocytogenes str. 4b H7858]
 gi|47018270|gb|EAL09035.1| NADH oxidase, putative [Listeria monocytogenes str. 4b H7858]
          Length = 616

 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 126 EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 183

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 184 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 243

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 244 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 299


>gi|329914373|ref|ZP_08276106.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Oxalobacteraceae bacterium IMCC9480]
 gi|327545135|gb|EGF30420.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Oxalobacteraceae bacterium IMCC9480]
          Length = 243

 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 44/136 (32%), Gaps = 6/136 (4%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD--LFIGLNGGL 197
            +   + G   + +        G     N          V E  + N    + I L GG+
Sbjct: 15  ARHWLEQGARRLHLVDLNGAFAGK--PKNESAVKAIIKAVREFAEANGIDQIPIQLGGGI 72

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLT-GSSPIKTRVDKDFWRKI 255
            D+    + L   +  ++IG AA KN   L      F   +  G      +V  D W K+
Sbjct: 73  RDLDTIERYLDDGLSYIIIGTAAVKNPGFLQDACSAFPGQIIVGLDARDGKVATDGWSKL 132

Query: 256 SASMTDYAARHLHSGG 271
           +       AR     G
Sbjct: 133 TGHEVIDLARKFEDYG 148


>gi|313813011|gb|EFS50725.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL025PA1]
          Length = 279

 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 42/221 (19%), Positives = 66/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 16  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           Y++V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYNLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|307256002|ref|ZP_07537790.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306865424|gb|EFM97319.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
          Length = 246

 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 24  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 73

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++T + + F 
Sbjct: 74  TIEDAEKLFAFGADKISINSPALADPNLITALADRFG 110


>gi|253578725|ref|ZP_04855996.1| NADH:flavin oxidoreductase/NADH oxidase [Ruminococcus sp.
           5_1_39B_FAA]
 gi|251849668|gb|EES77627.1| NADH:flavin oxidoreductase/NADH oxidase [Ruminococcus sp.
           5_1_39BFAA]
          Length = 897

 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 18/142 (12%), Positives = 50/142 (35%), Gaps = 13/142 (9%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD-------QIPAVALRN---LVKS 142
           +G        ++ + I  +         +  R+ V++           + +++   +  +
Sbjct: 150 YGGSFENRLRMITEIINGIRVQCGPDFPIGVRLSVEEFLDKTGVTEDYIHIQDGVKIAMA 209

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           ++K G++ I +         +  +          D++  +K       IG++  + +   
Sbjct: 210 LEKCGIDFIDVSVGLYETGSVCVEPISFPQGWRKDLIKAVKDHVSIPVIGVSC-IREPQV 268

Query: 203 ALKILPS--VDGVMIGRAAYKN 222
           A   L    VD V +GR+   +
Sbjct: 269 AESFLEGGIVDFVSMGRSWLAD 290


>gi|226307345|ref|YP_002767305.1| 2,4-dienoyl-CoA reductase [Rhodococcus erythropolis PR4]
 gi|226186462|dbj|BAH34566.1| 2,4-dienoyl-CoA reductase [Rhodococcus erythropolis PR4]
          Length = 676

 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 23/185 (12%), Positives = 63/185 (34%), Gaps = 19/185 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------C-PSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           V  A++ +  GY+ + +  G         C  + +  +   G+       +  + +    
Sbjct: 148 VRCARLAKSAGYDGVEIMGGEGYFINQFLCERTNKRTDQWGGSS-ENRRRMAVEIVRRTR 206

Query: 113 KALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA+     +  R+ + D          + +L K ++ +G     I+      +   P   
Sbjct: 207 KAVGPNFIIVFRLSMADLVEGGQTWDEIVSLAKEVEAAGAT--IINTDIGWHESRVPTIV 264

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYKNSAML 226
             +P   +  +    +++ D+ +  +  +     A +IL   D   + + R    +   +
Sbjct: 265 TSVPRAAFVDITGKLEKHVDIPVAASNRINMPETAEEILNRGDAQLISMARPMLADPDWV 324

Query: 227 TTVDE 231
              + 
Sbjct: 325 NKAER 329


>gi|332312550|gb|EGJ25645.1| Pyridoxal biosynthesis protein PDX1.3 [Listeria monocytogenes str.
           Scott A]
          Length = 300

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 34  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 87

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 88  ARIGHITE---------ARVLEAMGVDYI 107


>gi|328950986|ref|YP_004368321.1| Imidazole glycerol phosphate synthase subunit hisF [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451310|gb|AEB12211.1| Imidazole glycerol phosphate synthase subunit hisF [Marinithermus
           hydrothermalis DSM 14884]
          Length = 256

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 40/98 (40%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              ++  ++G + +        L   +  + R I     D+V  +  E   + + + GG+
Sbjct: 34  EAAQAYDRAGADELV------FLDITATHEQRAILL---DVVARVA-ETVFIPLTVGGGV 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +  A ++L    D V +  AA K   +LT +  +F 
Sbjct: 84  RTLEDARRLLLAGADKVSVNSAAVKRPELLTELAGHFG 121


>gi|291523109|emb|CBK81402.1| NADH:flavin oxidoreductases, Old Yellow Enzyme family [Coprococcus
           catus GD/7]
          Length = 650

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 25/173 (14%), Positives = 64/173 (36%), Gaps = 25/173 (14%)

Query: 58  DISKL----VEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACLMLNPD 102
           D+ ++     + A   +  G+  + +   C           P++ V    +G        
Sbjct: 145 DMDEMKAHYADCALRCKHAGFRMVMI--HCAHQNFLAQWLSPASNVRTDEYGGSPENRRR 202

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVDDQIP-AVALRNLVKSIKKSGVNGIWIHARKAILK 161
              + + A+ +A+   + ++ R+   + IP  +     +  +K++      +H  +  + 
Sbjct: 203 YPLEVLKAVREAVGEDMVIEMRVSAVEGIPGGMEFEESLAFMKEAQEYVDIVHVSQGSIF 262

Query: 162 GLSPKD------NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            LS +             L+ D   E+KK    + + + G +  + QA +I+ 
Sbjct: 263 HLSARYCIPTYFREPHKPLNVDYAAEVKKHL-HVPVAVVGMITTLEQAEEIIA 314


>gi|78044740|ref|YP_360153.1| FMN-dependent family dehydrogenase [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996855|gb|ABB15754.1| dehydrogenase, FMN-dependent family [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 340

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 26/152 (17%), Positives = 51/152 (33%), Gaps = 30/152 (19%)

Query: 118 PVTVKCRIGVDDQIPAVALR---------NLVKSIKKSGVNGIWI--HARKAILKGLSPK 166
           PV+ K    V + + +  L          +  +   ++G   I +  H       G +  
Sbjct: 189 PVSPKTLEEVMEIVNSTRLPFILKGIMTPDEAELAVQAGAKAIVVSNHG------GRTLD 242

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
           +     ++  +I   +K     + I  +GG+      LK+L    DGV+IGR        
Sbjct: 243 ETPGAADVLPEIAARVK---GKITILADGGVRSGVDVLKLLALGADGVLIGRPI------ 293

Query: 226 LTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
              +   F     G      ++ K+    +  
Sbjct: 294 ---IVAAFGGGAEGVKIYLEKIKKELREAMLL 322


>gi|116688454|ref|YP_834077.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           cenocepacia HI2424]
 gi|148839483|sp|A0K3V7|HIS4_BURCH RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|116646543|gb|ABK07184.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           cenocepacia HI2424]
          Length = 251

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 20/93 (21%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L K  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVIDLAKKFEDYGVESIVYTDIGRDGMLQG-----------INIDATVKLAQAVGIPVIA 197

Query: 193 LNG-----GLEDMSQALKILPSVDGVMIGRAAY 220
             G      +E + +  +    V+GV+ GRA Y
Sbjct: 198 SGGLSNLPDIESLCEVEEH--GVEGVICGRAIY 228


>gi|320161453|ref|YP_004174677.1| isopentenyl-diphosphate delta-isomerase [Anaerolinea thermophila
           UNI-1]
 gi|319995306|dbj|BAJ64077.1| isopentenyl-diphosphate delta-isomerase [Anaerolinea thermophila
           UNI-1]
          Length = 342

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 25/124 (20%), Positives = 46/124 (37%), Gaps = 22/124 (17%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAILKG 162
           I  +CK +S+PV  K       ++         + +  +GV+ I +          +   
Sbjct: 179 IEQVCKQVSVPVIAK-------EVGWGISERTARMLVDAGVSAIDVAGAGGTSWSQVEMY 231

Query: 163 LSPKDNRKIPNL---DYDI-----VYEIKKENPDLFIGLNGGLED-MSQALKI-LPSVDG 212
               + R        ++ I     +  +KK  P + I  +GGL+  +  A  I L +  G
Sbjct: 232 RIQDERRARIAAAFRNWGIPTAYSIQMVKKVAPHVPIIASGGLKTGVDIAKCIALGACMG 291

Query: 213 VMIG 216
            M G
Sbjct: 292 GMAG 295


>gi|302383385|ref|YP_003819208.1| isopentenyl-diphosphate delta-isomerase, type 2 [Brevundimonas
           subvibrioides ATCC 15264]
 gi|302194013|gb|ADL01585.1| isopentenyl-diphosphate delta-isomerase, type 2 [Brevundimonas
           subvibrioides ATCC 15264]
          Length = 342

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 25/129 (19%), Positives = 45/129 (34%), Gaps = 21/129 (16%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKA 158
            +   VG  + A+ + L +PV VK       +  A       + +   GV G+ +     
Sbjct: 170 RDWWGVGAALEALIRKLGVPVIVK-------ETGAGISAATARRLFAMGVAGVDVAGAGG 222

Query: 159 ILKGLSPKDN--------RKIPNLDY-----DIVYEIKKENPDLFIGLNGGLED-MSQAL 204
              GL   +           +   D+       +  +++  PD  I  +GG+ D +  A 
Sbjct: 223 ANWGLIEGERATDQADKAHALAFADWGISTARAIETVREACPDSLIIGSGGVRDGVDAAK 282

Query: 205 KILPSVDGV 213
            I    D V
Sbjct: 283 AIRLGADLV 291


>gi|238793475|ref|ZP_04637100.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           intermedia ATCC 29909]
 gi|238727248|gb|EEQ18777.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           intermedia ATCC 29909]
          Length = 247

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 24  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 73

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 74  SVEDAGQILTFGADKISINSPALADPTLITRLADRYG 110


>gi|149003383|ref|ZP_01828272.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           SP14-BS69]
 gi|147758566|gb|EDK65564.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           SP14-BS69]
          Length = 311

 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 19/185 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDI 103
              +   L + G    +     K V++  +  +  LN+ CP   V      A    + + 
Sbjct: 92  ESNRTFFLSLVGMSPEETHTILKKVQESDFCGLTELNLSCP--NVPGKPQIAY---DFET 146

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHAR 156
               +A +    + P+ +K     D      A A+ N      V  +   G NG++I   
Sbjct: 147 TDRILAEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDE 205

Query: 157 KAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVD 211
             +++   G        I       V+   +  NP + I   GG+     A +  L    
Sbjct: 206 SVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGAS 265

Query: 212 GVMIG 216
            V +G
Sbjct: 266 MVQVG 270


>gi|294811588|ref|ZP_06770231.1| Pyridoxal biosynthesis lyase pdxS [Streptomyces clavuligerus ATCC
           27064]
 gi|294324187|gb|EFG05830.1| Pyridoxal biosynthesis lyase pdxS [Streptomyces clavuligerus ATCC
           27064]
          Length = 339

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 48  KPLALQIGGADISKLVEA--AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + +A Q+ G  I  +V+A  AKI ED G   +      P+        G   M +P+++ 
Sbjct: 56  RGMAEQLKGGVIMDVVDAEQAKIAEDAGAVAVMALERVPAD--IRKDGGVARMSDPNMIE 113

Query: 106 DCIAAMCKALSIPVTVKCRI 125
           + I A    +SIPV  K RI
Sbjct: 114 EIIEA----VSIPVMAKSRI 129


>gi|255035081|ref|YP_003085702.1| NADH:flavin oxidoreductase/NADH oxidase [Dyadobacter fermentans DSM
           18053]
 gi|254947837|gb|ACT92537.1| NADH:flavin oxidoreductase/NADH oxidase [Dyadobacter fermentans DSM
           18053]
          Length = 377

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 32/186 (17%), Positives = 61/186 (32%), Gaps = 26/186 (13%)

Query: 63  VEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCK 113
           V AA + +  G++ + L+            P   +    +G         + +   A+  
Sbjct: 161 VNAALLAQQAGFDGVELHAANGYLFDQFITPHTNLRTDQYGGDERNRLRFLMEVYQAVKA 220

Query: 114 ALSIPVTVKCRIGVDDQIP--------AVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           AL     V  R+               +   R L + + +   + + I    A   G   
Sbjct: 221 ALPERFIVGIRLSESKVNDLTYRWPGGSATARRLFEVLSEINPDYVHI----AAEGGRWE 276

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
           ++      L  + +    K      +  NGG+ D++ A  +L   + D V IGRAA    
Sbjct: 277 RECLYPDGLSSNSIA---KSILRSPVIANGGMHDVALAETLLNSGAADLVSIGRAAIATP 333

Query: 224 AMLTTV 229
                +
Sbjct: 334 DWPQRI 339


>gi|158343972|gb|ABW35768.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
          Length = 251

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 20/93 (21%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L K  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVIDLAKKFEDYGVESIVYTDIGRDGMLQG-----------INIDATVKLAQAVGIPVIA 197

Query: 193 LNG-----GLEDMSQALKILPSVDGVMIGRAAY 220
             G      +E + +  +    V+GV+ GRA Y
Sbjct: 198 SGGLSNLTDIESLCEVEEH--GVEGVICGRAIY 228


>gi|169831774|ref|YP_001717756.1| imidazole glycerol phosphate synthase subunit HisF [Candidatus
           Desulforudis audaxviator MP104C]
 gi|226700508|sp|B1I556|HIS6_DESAP RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|169638618|gb|ACA60124.1| imidazoleglycerol phosphate synthase, cyclase subunit [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 252

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 44/131 (33%), Gaps = 5/131 (3%)

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIK 183
           R  V   +  V LR+    ++ + V           L   +  + R I     D+V    
Sbjct: 14  RGRVVKGVNFVNLRDAGDPVELAAVYDREGADEVVFLDITASAEGRDIVL---DMVRRTA 70

Query: 184 KENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSP 242
           ++   +   + GG+  +     IL    D V I  AA KN  ++    E F      ++ 
Sbjct: 71  EQVF-IPFAVGGGIRTVEDIRAILKAGADKVSINTAAVKNPGLIAEAAEKFGTQCIVAAI 129

Query: 243 IKTRVDKDFWR 253
              +     W 
Sbjct: 130 DAKQTGSGKWE 140


>gi|157145029|ref|YP_001452348.1| imidazole glycerol phosphate synthase subunit HisF [Citrobacter
           koseri ATCC BAA-895]
 gi|167012148|sp|A8AEJ9|HIS6_CITK8 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|157082234|gb|ABV11912.1| hypothetical protein CKO_00760 [Citrobacter koseri ATCC BAA-895]
          Length = 258

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SIDDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|76800866|ref|YP_325874.1| dihydroorotate dehydrogenase 2 [Natronomonas pharaonis DSM 2160]
 gi|121724541|sp|Q3IU78|PYRD_NATPD RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|76556731|emb|CAI48305.1| dihydroorotate oxidase [Natronomonas pharaonis DSM 2160]
          Length = 350

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 46/117 (39%), Gaps = 14/117 (11%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI----WI 153
           + + D +   +  +    + P+ VK    + D     A+ + ++ ++  G++GI      
Sbjct: 189 LQSRDRLESILGTLQDDGASPLLVKLSPDLTD----AAIEDAIEVVEDLGLDGIIATNTT 244

Query: 154 HARKAILKGLSPKD-----NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK 205
             R A L   +  +        I +   DIV  I K   D  I   GG++D   A +
Sbjct: 245 TKRPASLHSDAADEEGGLSGAPITDESTDIVRFIAKRT-DKPIVGVGGIDDAESAYE 300


>gi|4240171|dbj|BAA74864.1| KIAA0841 protein [Homo sapiens]
          Length = 641

 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 242 PIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P+  R  +   R++     A +  Y  +H+HS   +++I  +++    G  +S + R  L
Sbjct: 29  PVAARAPESTLRRLCLGQGADIWAYILQHVHSQRTVKKIRGNLLWY--GHQDSPQVRRKL 86

Query: 298 TVEA--GASTATHHIIETAFNLM 318
            +EA      A    ++ +  LM
Sbjct: 87  ELEAAVTRLRAEIQELDQSLELM 109


>gi|330888376|gb|EGH21037.1| xenobiotic reductase A [Pseudomonas syringae pv. mori str. 301020]
          Length = 363

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 60/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVVEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +   D+ +    G  +   A        +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREADIPVTSAWGFGEPKLAEDAGKSGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|289193146|ref|YP_003459087.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Methanocaldococcus sp. FS406-22]
 gi|288939596|gb|ADC70351.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Methanocaldococcus sp. FS406-22]
          Length = 272

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 177 DIVYEIKK---ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY 232
           DI+ ++ +   E   + + + GG++ +    +IL    D V I  AA KN  ++    E 
Sbjct: 60  DIIIDVVERTAEKVFIPLTVGGGIKSIEDFRRILRAGADKVSINTAAVKNPDLIKEASEI 119

Query: 233 FS 234
           F 
Sbjct: 120 FG 121


>gi|259907243|ref|YP_002647599.1| 2,4-dieonyl-coa reductase [Erwinia pyrifoliae Ep1/96]
 gi|224962865|emb|CAX54342.1| 2,4-dieonyl-coa reductase [Erwinia pyrifoliae Ep1/96]
 gi|283477054|emb|CAY72946.1| 2,4-dienoyl-CoA reductase FadH [Erwinia pyrifoliae DSM 12163]
          Length = 669

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 16/120 (13%), Positives = 42/120 (35%), Gaps = 8/120 (6%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAI 159
               + A+  A      +  R+ + D +   +  +    L K++++ G   +  +     
Sbjct: 194 ALAILKAVRAATGPAFIIIFRLSMLDLVEQGSTLDHTIRLAKALEQQGATLL--NTGIGW 251

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGR 217
            +   P     +P   +  V +I +++  + +     +     A  +L     D V + R
Sbjct: 252 HEARIPTIATSVPRAAFAWVTQILRQHVSIPLIATNRINHPDVAQALLDEGCADMVSMAR 311


>gi|171462930|ref|YP_001797043.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Polynucleobacter necessarius subsp.
           necessarius STIR1]
 gi|226700342|sp|B1XSV2|HIS4_POLNS RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|171192468|gb|ACB43429.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Polynucleobacter necessarius subsp.
           necessarius STIR1]
          Length = 253

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 4/99 (4%)

Query: 178 IVYEIKKENPD-LFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I K   D + + L GG+ D+    ++L   +  V+IG AA KN   +      F  
Sbjct: 65  AIKSILKAVGDEIPVQLGGGIRDLETIERLLDDGISTVIIGTAAVKNPGFVQDACTAFPG 124

Query: 236 P-LTGSSPIKTRVDKDFWRKISASM-TDYAARHLHSGGK 272
             + G      +V  D W KI+     D A +    G +
Sbjct: 125 HVMVGLDARDGKVATDGWSKITCHKVIDLAKKFEDWGVE 163


>gi|224007821|ref|XP_002292870.1| FADH-2,4-dienoyl-CoA reductase [Thalassiosira pseudonana CCMP1335]
 gi|220971732|gb|EED90066.1| FADH-2,4-dienoyl-CoA reductase [Thalassiosira pseudonana CCMP1335]
          Length = 800

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 26/187 (13%), Positives = 61/187 (32%), Gaps = 27/187 (14%)

Query: 60  SKLVEAAKIVEDFGYNEIN--------LNVGCPSARVHEGS-----FGACLMLNPDIVGD 106
                 A + +  GY+ +         +N       V + +     +G        I  +
Sbjct: 221 HDFANCAVLAKGAGYDGVEVMGSEGYLIN----QFLVSKTNLRTDEYGGSFANRMMIAVE 276

Query: 107 CIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +  + KA  +   +  R+     V+D      +  L ++++ +G     I+      + 
Sbjct: 277 IVKEIRKACGLDFIIIFRLSMLDLVEDGSSWEEITLLARALEDAGAT--IINTGIGWHEA 334

Query: 163 LSPKDNRKIPNLDYDIV-YEIKKEN-PDLFIGLNGGLEDMSQALKILP--SVDGVMIGRA 218
             P     +P   +  V  +++ EN   + +     +   S A  IL     D + + R 
Sbjct: 335 RIPTIATSVPRGAFSWVTKKLRDENIVSIPLCATNRINAPSTAESILASGHSDLISMARP 394

Query: 219 AYKNSAM 225
              +  +
Sbjct: 395 FLADPEI 401


>gi|254391310|ref|ZP_05006514.1| pyridoxal biosynthesis lyase pdxS [Streptomyces clavuligerus ATCC
           27064]
 gi|326440223|ref|ZP_08214957.1| pyridoxal biosynthesis lyase PdxS [Streptomyces clavuligerus ATCC
           27064]
 gi|197705001|gb|EDY50813.1| pyridoxal biosynthesis lyase pdxS [Streptomyces clavuligerus ATCC
           27064]
          Length = 307

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 48  KPLALQIGGADISKLVEA--AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + +A Q+ G  I  +V+A  AKI ED G   +      P+        G   M +P+++ 
Sbjct: 24  RGMAEQLKGGVIMDVVDAEQAKIAEDAGAVAVMALERVPAD--IRKDGGVARMSDPNMIE 81

Query: 106 DCIAAMCKALSIPVTVKCRI 125
           + I A    +SIPV  K RI
Sbjct: 82  EIIEA----VSIPVMAKSRI 97


>gi|190151383|ref|YP_001969908.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|307246965|ref|ZP_07529030.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307255947|ref|ZP_07537748.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307260400|ref|ZP_07542107.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307260432|ref|ZP_07542127.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307264740|ref|ZP_07546319.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|226700478|sp|B3GZH3|HIS6_ACTP7 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|189916514|gb|ACE62766.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|306852250|gb|EFM84490.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306861215|gb|EFM93208.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306865651|gb|EFM97532.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306869835|gb|EFN01617.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306869936|gb|EFN01701.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 257

 Score = 36.3 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++T + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPNLITALADRFG 121


>gi|305681561|ref|ZP_07404367.1| oxidoreductase, FAD/FMN-binding [Corynebacterium matruchotii ATCC
           14266]
 gi|305658721|gb|EFM48222.1| oxidoreductase, FAD/FMN-binding [Corynebacterium matruchotii ATCC
           14266]
          Length = 366

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 33/203 (16%), Positives = 67/203 (33%), Gaps = 33/203 (16%)

Query: 73  GYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           G++ + +             P +      +G        IV + I A+ + +   + +  
Sbjct: 173 GFDTVEIHGAHGYLLHQFLSPVSNHRTDDYGGSFDNRARIVIEIIDAIREVIPADMPLLL 232

Query: 124 RIGVDDQIPAV---------ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNL 174
           R+   D +  V             L    ++ GV+ I + +   +   +S     ++P  
Sbjct: 233 RLSATDWLENVPGVESWGIPETIQLATLAQEHGVDMIDVSSGGLVPAPISTGPGYQVPLA 292

Query: 175 DYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM----IGRAAYKNS-AMLTTV 229
           +        +E   + +   G L D   A ++L  VDG+     +GRAA       L   
Sbjct: 293 N------AVREAAGIPVVAVGELGDPLTAQQVL--VDGLADAIDVGRAALFEPQWPLRAA 344

Query: 230 DEYFSNPLTGSSPIKTRVDKDFW 252
            E      +   P+     +  W
Sbjct: 345 REL--GLPSEDWPVAPSYIRGVW 365


>gi|229551012|ref|ZP_04439737.1| tryptophan synthase [Lactobacillus rhamnosus LMS2-1]
 gi|258538276|ref|YP_003172775.1| tryptophan synthase subunit alpha [Lactobacillus rhamnosus Lc 705]
 gi|229315607|gb|EEN81580.1| tryptophan synthase [Lactobacillus rhamnosus LMS2-1]
 gi|257149952|emb|CAR88924.1| Tryptophan synthase alpha chain [Lactobacillus rhamnosus Lc 705]
          Length = 269

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 45/161 (27%), Gaps = 50/161 (31%)

Query: 104 VGDCIAAMCKALSIPVTV----------------------KCRIGVDDQIPAVALRNLVK 141
           V + + A  K  ++P+                        K    V   +P  +   +V 
Sbjct: 76  VFEIVEAARKKTAVPIVFLTYLNIVFKYGYDTFLKRCAELKVSGLVIPDLPYESRAEIVP 135

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI------------------- 182
             +K G++ I +          S     KI       +Y +                   
Sbjct: 136 FAEKYGIDIIPLITPT------SGHRIEKIAKSASGFIYVVSSVGITGERDEFFTGLKTL 189

Query: 183 ---KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               K   D+   +  G+    QA  +    DGV+IG A  
Sbjct: 190 VTEIKRYTDVPTAIGFGIHTPQQAQTMASIADGVIIGSAIV 230


>gi|227832310|ref|YP_002834017.1| putative inosine-5'-monophosphate dehydrogenase [Corynebacterium
           aurimucosum ATCC 700975]
 gi|262183833|ref|ZP_06043254.1| inosine 5-monophosphate dehydrogenase [Corynebacterium aurimucosum
           ATCC 700975]
 gi|227453326|gb|ACP32079.1| putative inosine-5'-monophosphate dehydrogenase [Corynebacterium
           aurimucosum ATCC 700975]
          Length = 398

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 50/131 (38%), Gaps = 27/131 (20%)

Query: 98  MLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHA-- 155
            LN +++ + IA +  +    VTV  R+           R L   + K+G   ++IH   
Sbjct: 113 PLNEELLAERIAQVRDSG---VTVAVRVSPQH------ARELAPVVIKAGAELLFIHGTL 163

Query: 156 --RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDG 212
              + +  G  P + +       + +  +     D  +   GG+ D + AL  +     G
Sbjct: 164 ISAEHVQTGGEPLNLK-------EFIGSL-----DTPVIA-GGVADYTTALHLMRAGAAG 210

Query: 213 VMIGRAAYKNS 223
           +++G     N 
Sbjct: 211 IIVGSGVNTNP 221


>gi|110667029|ref|YP_656840.1| dihydroorotate dehydrogenase 2 [Haloquadratum walsbyi DSM 16790]
 gi|109624776|emb|CAJ51182.1| dihydroorotate oxidase [Haloquadratum walsbyi DSM 16790]
          Length = 357

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 27/146 (18%), Positives = 50/146 (34%), Gaps = 18/146 (12%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           +I E  G + + +NV CP       S G   +   D +   + A+  A +  V VK    
Sbjct: 173 QIAE--GADYVAVNVSCP------NSEGMQDLQQRDSLSRIMDALTNAGAETVLVKLAPE 224

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY------ 180
           +        + +LV      G+  I  +      + L      +   L    +       
Sbjct: 225 LSLSAIEDVI-DLVDIFDLDGI--ITTNTTTERPENLESTKQTERGGLSGAPIEDHATKL 281

Query: 181 -EIKKENPDLFIGLNGGLEDMSQALK 205
            ++  +  D+ I   GG+ D + A  
Sbjct: 282 VQLVAKRTDVPIIGVGGVSDAAGAYA 307


>gi|332854977|ref|XP_003316331.1| PREDICTED: LOW QUALITY PROTEIN: HAUS augmin-like complex subunit
           5-like [Pan troglodytes]
          Length = 633

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 242 PIKTRVDKDFWRKIS----ASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHIL 297
           P+  R  +   R++     A +  Y  +H+HS   +++I  +++    G  +S + R  L
Sbjct: 21  PVAARAPESTLRRLCLGQGADIWAYILQHVHSQRTVKKIRGNLLWY--GHQDSPQVRQKL 78

Query: 298 TVEA--GASTATHHIIETAFNLM 318
            +EA      A    ++ +  LM
Sbjct: 79  ELEAAVTRLRAEIQELDQSLELM 101


>gi|226949446|ref|YP_002804537.1| 2-enoate reductase [Clostridium botulinum A2 str. Kyoto]
 gi|226841787|gb|ACO84453.1| 2-enoate reductase [Clostridium botulinum A2 str. Kyoto]
          Length = 665

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 73/206 (35%), Gaps = 47/206 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             E+A+I +  G++ + ++       VHEG                 +G  L        
Sbjct: 158 FGESAEIAKKAGFDGVEIHA------VHEGYLLDQFAISFFNHRTDEYGGSLENRLRFAC 211

Query: 106 DCIAAMCKAL--SIPVTVK----------CRIGVDDQIPAVALRNL------VKSIKKSG 147
           + +  + K      PV+++          C+ G+ D+      R++       K +  +G
Sbjct: 212 EVVQEIKKRCGQDFPVSLRYSIKSFIKDWCKGGLPDEEFEEKGRDIPEGIEAAKILVAAG 271

Query: 148 VNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QAL 204
            + +        +      P   +K   L Y+   EI K+  D+ I   G +ED    + 
Sbjct: 272 YDALNGDVGSYDSWYWSHPPMYQKKGLYLPYN---EILKKVVDVPIITAGRMEDPELSSD 328

Query: 205 KILPS-VDGVMIGRAAYKNSAMLTTV 229
            IL    D + +GR    ++ +   +
Sbjct: 329 AILSGKTDMIALGRPLLADAEIPNKI 354


>gi|218690086|ref|YP_002398298.1| imidazole glycerol phosphate synthase subunit HisF [Escherichia
           coli ED1a]
 gi|254801205|sp|B7MWU3|HIS6_ECO81 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|218427650|emb|CAR08559.2| imidazole glycerol phosphate synthase, catalytic subunit with HisH
           [Escherichia coli ED1a]
          Length = 258

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAGKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|218130109|ref|ZP_03458913.1| hypothetical protein BACEGG_01696 [Bacteroides eggerthii DSM 20697]
 gi|317476601|ref|ZP_07935846.1| dihydroorotate dehydrogenase 2 [Bacteroides eggerthii 1_2_48FAA]
 gi|217987613|gb|EEC53941.1| hypothetical protein BACEGG_01696 [Bacteroides eggerthii DSM 20697]
 gi|316907197|gb|EFV28906.1| dihydroorotate dehydrogenase 2 [Bacteroides eggerthii 1_2_48FAA]
          Length = 325

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 67/201 (33%), Gaps = 24/201 (11%)

Query: 47  EKPLALQIGG-ADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
           + P+   I    D   + E AK +E+ G + + +N+      V    +GA    + D   
Sbjct: 96  DIPIIASINCYQDADWI-EFAKKIEEAGADALEVNILALQTDVQYT-YGAFEQRHID--- 150

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR-----KAIL 160
             ++ + K ++IPV +K                L+  +  +G   + +  R       I 
Sbjct: 151 -ILSHIKKTVNIPVIMKL------GDNLTNPIALIDQLYANGAAAVVMFNRFYQPDIDIE 203

Query: 161 KGLSPKDNRKIPNLD----YDIVYEIKKENPDLFIGLNGGLEDMS-QALKILPSVDGVMI 215
           K      N    + D       +         L    +GG+         IL     V +
Sbjct: 204 KMAQSAGNVFSTDADLSKSLRWIGIASAAVNKLDYAASGGIHAPEGVVKAILAGASAVEL 263

Query: 216 GRAAYKNSA-MLTTVDEYFSN 235
             A Y NS  +++    + + 
Sbjct: 264 CSALYLNSYAVISEYTRFLNT 284


>gi|118469127|ref|YP_884835.1| transferase [Mycobacterium smegmatis str. MC2 155]
 gi|118170414|gb|ABK71310.1| transferase [Mycobacterium smegmatis str. MC2 155]
          Length = 255

 Score = 36.3 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 28/156 (17%), Positives = 58/156 (37%), Gaps = 16/156 (10%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
             +A++  D G+  + +    P A     S G   M   D++   +  +  A+ +PV+V 
Sbjct: 34  AWSARLAVDAGFAALTVGSH-PVADSIGKSDGEN-MAFEDLLTR-VRQITAAVEVPVSVD 90

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLSPKD---NRKIPNLD 175
              G  +         L++ +  +GV G      +H     L+  +       +     D
Sbjct: 91  IESGYGESP-----ERLIEGLLDAGVVGFNLEDTVHKEGKRLRTATEHAELVGQLRAAAD 145

Query: 176 YDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSV 210
              V+ +     DLF+  +G   D + +A+  +   
Sbjct: 146 AAGVHVVINARTDLFLRNDGDDADRVERAIARMSEA 181


>gi|331018966|gb|EGH99022.1| xenobiotic reductase A [Pseudomonas syringae pv. lachrymans str.
           M302278PT]
          Length = 363

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 28/181 (15%), Positives = 61/181 (33%), Gaps = 25/181 (13%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAA 110
            V+AA+   D G+  I L+       + +             +G         + + +AA
Sbjct: 160 FVDAARRARDAGFEWIELHFA--HGYLGQSFFSEHSNQRTDEYGGSFDNRSRFLLETLAA 217

Query: 111 MCKAL--SIPVTVKCRIGVDDQIPAVALR---NLVKSIKKSGVNGIWIHARKAILKGLSP 165
           + +    ++P+T +  +   D      L     L +  K  G++ + +      +   +P
Sbjct: 218 VREVWPENLPLTARFGVLEYDGRDEQTLTESIELARRFKAGGLDLLSV-----SVGFSTP 272

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNS 223
             N          + E  +    + +    G  +   A + +    +D V IGRA   + 
Sbjct: 273 DANIPWGPAFMGPIAERVRREAAIPVTSAWGFGEPKLAEEAVKAGQLDLVSIGRAHLADP 332

Query: 224 A 224
            
Sbjct: 333 H 333


>gi|313680190|ref|YP_004057929.1| imidazole glycerol phosphate synthase subunit hisf [Oceanithermus
           profundus DSM 14977]
 gi|313152905|gb|ADR36756.1| imidazole glycerol phosphate synthase subunit hisF [Oceanithermus
           profundus DSM 14977]
          Length = 255

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 21/121 (17%), Positives = 43/121 (35%), Gaps = 11/121 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
               +  +SG + +        L   +  +NR    L  ++V  +  E   +   + GG+
Sbjct: 34  EAAVAYDESGADELV------FLDITATHENR---PLVLEMVRRVA-ERVFIPFTVGGGV 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +  A  +L    D V +  AA     ++  + ++F +     +    RV    W    
Sbjct: 84  RSLEDARALLLAGADKVSVNSAAVARPELIRELADHFGSQAVVLAIDAKRVGPGRWEVYV 143

Query: 257 A 257
           A
Sbjct: 144 A 144


>gi|238753419|ref|ZP_04614782.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           ruckeri ATCC 29473]
 gi|238708372|gb|EEQ00727.1| Imidazole glycerol phosphate synthase subunit hisF [Yersinia
           ruckeri ATCC 29473]
          Length = 242

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 19  LAQRYAAEGADELVFYDITASSDGRV---------VDKSWVARVA-EVIDIPFCVAGGIK 68

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 69  SVEDAGQILTYGADKISINSPALTDPTLITRLADRYG 105


>gi|229542250|ref|ZP_04431310.1| pyridoxine biosynthesis protein [Bacillus coagulans 36D1]
 gi|229326670|gb|EEN92345.1| pyridoxine biosynthesis protein [Bacillus coagulans 36D1]
          Length = 293

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AK+ E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 27  AEQAKLAEEAGAVAVMALERVPSD--IRKAGGVARMADP----SIVEEVMNAVSIPVMAK 80

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 81  ARIGHIVE---------ARVLEAMGVDYI 100


>gi|148380120|ref|YP_001254661.1| 2-enoate reductase [Clostridium botulinum A str. ATCC 3502]
 gi|153934163|ref|YP_001384419.1| 2-enoate reductase [Clostridium botulinum A str. ATCC 19397]
 gi|153937190|ref|YP_001387955.1| 2-enoate reductase [Clostridium botulinum A str. Hall]
 gi|148289604|emb|CAL83707.1| cinnamate reductase [Clostridium botulinum A str. ATCC 3502]
 gi|152930207|gb|ABS35707.1| 2-enoate reductase [Clostridium botulinum A str. ATCC 19397]
 gi|152933104|gb|ABS38603.1| 2-enoate reductase [Clostridium botulinum A str. Hall]
          Length = 665

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 73/206 (35%), Gaps = 47/206 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             E+A+I +  G++ + ++       VHEG                 +G  L        
Sbjct: 158 FGESAEIAKKAGFDGVEIHA------VHEGYLLDQFAISFFNHRTDEYGGSLENRLRFAC 211

Query: 106 DCIAAMCKAL--SIPVTVK----------CRIGVDDQIPAVALRNL------VKSIKKSG 147
           + +  + K      PV+++          C+ G+ D+      R++       K +  +G
Sbjct: 212 EVVQEIKKRCGQDFPVSLRYSIKSFIKDWCKGGLPDEEFEEKGRDIPEGIEAAKILVAAG 271

Query: 148 VNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QAL 204
            + +        +      P   +K   L Y+   EI K+  D+ I   G +ED    + 
Sbjct: 272 YDALNGDVGSYDSWYWSHPPMYQKKGLYLPYN---EILKKVVDVPIITAGRMEDPELSSD 328

Query: 205 KILPS-VDGVMIGRAAYKNSAMLTTV 229
            IL    D + +GR    ++ +   +
Sbjct: 329 AILSGKTDMIALGRPLLADAEIPNKI 354


>gi|116491966|ref|YP_803701.1| N-acetylmannosamine-6-phosphate 2-epimerase [Pediococcus
           pentosaceus ATCC 25745]
 gi|122266570|sp|Q03HR3|NANE_PEDPA RecName: Full=Putative N-acetylmannosamine-6-phosphate 2-epimerase;
           AltName: Full=ManNAc-6-P epimerase
 gi|116102116|gb|ABJ67259.1| Putative N-acetylmannosamine-6-phosphate epimerase [Pediococcus
           pentosaceus ATCC 25745]
          Length = 229

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 11/68 (16%), Positives = 26/68 (38%), Gaps = 4/68 (5%)

Query: 158 AILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMI 215
             ++G +P      I + D++ + E++ +     I   G ++   +    L      V++
Sbjct: 152 TTMRGYTPATQGMNIADHDFEYLKELRSQVTR-PIIAEGKIDTPEKLKCCLELGCHAVVV 210

Query: 216 GRAAYKNS 223
           G  A    
Sbjct: 211 G-GAITRP 217


>gi|85091307|ref|XP_958838.1| hypothetical protein NCU08900 [Neurospora crassa OR74A]
 gi|28920225|gb|EAA29602.1| hypothetical protein NCU08900 [Neurospora crassa OR74A]
 gi|28950381|emb|CAD71223.1| related to NADH oxidase [Neurospora crassa]
          Length = 437

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 32/205 (15%), Positives = 67/205 (32%), Gaps = 42/205 (20%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCP---------SARVHEGS--FGACLMLNPDIVGDCIA 109
           K    A+I  + G+N + ++             S + +     +G        IVG+ I 
Sbjct: 178 KFAVTARITAEAGFNGVEIHAA--HGYLLAQFLSKKTNRRGDEYGGSAENRARIVGEIIK 235

Query: 110 AMCKALS--------IPVTVKCRIGVDDQ------------IPAVALRNLVKSIKKSGVN 149
              + ++            V  ++   D               A  +   ++  ++ G++
Sbjct: 236 ECRRQVTEAVGEEEAKKFVVGIKLNSADWQAGRDGKEEEETDTAEEVLKQIELFEQWGID 295

Query: 150 GIWIHAR----KAILKGLSP-KDNRKIPNLDY--DIVYEIKKENPDLFIGLNGGLEDMSQ 202
            + +         +  G  P K  R +    +  +    I+ + P L + + GG      
Sbjct: 296 FVEVSGGSYEDPQMANGPKPEKSERTMAREAFFLEFAKIIRTKFPKLPLMVTGGFRTRQG 355

Query: 203 ALKILPS--VDGVMIGRAAYKNSAM 225
               L S   D + IGR A  N ++
Sbjct: 356 MEAALESDDCDMIGIGRPAIINPSL 380


>gi|332800116|ref|YP_004461615.1| inosine-5'-monophosphate dehydrogenase [Tepidanaerobacter sp. Re1]
 gi|332697851|gb|AEE92308.1| inosine-5'-monophosphate dehydrogenase [Tepidanaerobacter sp. Re1]
          Length = 482

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 36/101 (35%), Gaps = 8/101 (7%)

Query: 122 KCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K +    D       VA  +  + +  +G + I +      +          +P +    
Sbjct: 261 KIKEMYPDLQVIAGNVATADATRDLINAGADAIKVGMGPGSICTTRVVAGIGVPQV--TA 318

Query: 179 VYEIKKENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           +YE  +E    ++ I  +GG++        I    D VM+G
Sbjct: 319 IYECSQEAAKYNIPIIADGGIKYSGDIVKAIAAGADTVMLG 359


>gi|332670545|ref|YP_004453553.1| pyridoxine biosynthesis protein [Cellulomonas fimi ATCC 484]
 gi|332339583|gb|AEE46166.1| pyridoxine biosynthesis protein [Cellulomonas fimi ATCC 484]
          Length = 310

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 66/224 (29%), Gaps = 68/224 (30%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K
Sbjct: 44  AEQAKIAEDAGAVAVMALERVPAD--IRAQGGVARMSDPDLIDGIIEA----VSIPVMAK 97

Query: 123 CRI--------------GVDDQIPAVALRNLVKSIKKS---------------------- 146
            RI                 D+   +   +    I K                       
Sbjct: 98  ARIGHFVEAQVLQSLGVDYVDESEVLTPADYAHHIDKWAFTVPFVCGATNLGEALRRITE 157

Query: 147 GVNGI--------------WIHARKAILKGLS----PKDNRKIPNLDYDIVYEIKKEN-- 186
           G   I                H R    +       P+D   +   +    YE+ KE   
Sbjct: 158 GAAMIRSKGEAGTGDVSNATTHMRTLRDEIRRLTSLPEDELYLAAKELQAPYELVKEVAT 217

Query: 187 -PDLFIGLN--GGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
              L + L   GG+   + A  ++    +GV +G   +   N A
Sbjct: 218 AGKLPVVLFTAGGIATPADAAMMMQLGAEGVFVGSGIFKSGNPA 261


>gi|188533492|ref|YP_001907289.1| Imidazole glycerol phosphate synthase subunit HisF [Erwinia
           tasmaniensis Et1/99]
 gi|188028534|emb|CAO96396.1| Imidazole glycerol phosphate synthase subunit HisF [Erwinia
           tasmaniensis Et1/99]
          Length = 247

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   +  +  E  D+   + GG++
Sbjct: 24  LAQRYAEEGADELVFYDITASSDGRV---------VDKSWISRVA-EVIDIPFCVAGGIK 73

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A  +L    D + I   A  + A++T + + F 
Sbjct: 74  SVEDAALLLSYGADKISINSPALADPALITRLADRFG 110


>gi|73668472|ref|YP_304487.1| bifunctional formaldehyde-activating enzyme/3-hexulose-6-phosphate
           synthase [Methanosarcina barkeri str. Fusaro]
 gi|97049455|sp|Q46DY5|FAEHP_METBF RecName: Full=Bifunctional enzyme fae/hps; Includes: RecName:
           Full=Formaldehyde-activating enzyme; Short=Fae;
           Includes: RecName: Full=3-hexulose-6-phosphate synthase;
           Short=HPS; AltName:
           Full=D-arabino-3-hexulose-6-phosphate formaldehyde lyase
 gi|72395634|gb|AAZ69907.1| 3-hexulose-6-phosphate synthase [Methanosarcina barkeri str.
           Fusaro]
          Length = 392

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           +  + EIKK  P + + + GG+      + +    D +++GR A  NS  +  V E F N
Sbjct: 318 WGNIAEIKKIAPKILVAVAGGVRLDKVPVALGQGADILVVGR-AITNSKDVREVAEQFIN 376

Query: 236 PLTGSSPIKTRVDKDF 251
            L      + RV  DF
Sbjct: 377 SLNKPEIDQFRVMTDF 392


>gi|50954789|ref|YP_062077.1| imidazole glycerol phosphate synthase subunit HisF [Leifsonia xyli
           subsp. xyli str. CTCB07]
 gi|60392371|sp|Q6AF73|HIS6_LEIXX RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|50951271|gb|AAT88972.1| imidazoleglycerol-phosphate synthase [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 254

 Score = 36.3 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 14/98 (14%), Positives = 32/98 (32%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
              +   + G + +      A +   S           YD+V     +   + + + GG+
Sbjct: 35  EFARRYAEQGADELTFLDVTATVDDRSTT---------YDVVRATAGQVF-IPLTVGGGV 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
                  ++L    D V +  AA     ++  + + F 
Sbjct: 85  RSTEDVARLLGSGADKVGVNSAAIARPGLVAEIADRFG 122


>gi|309800682|ref|ZP_07694823.1| dihydroorotate dehydrogenase A [Streptococcus infantis SK1302]
 gi|308115689|gb|EFO53224.1| dihydroorotate dehydrogenase A [Streptococcus infantis SK1302]
          Length = 295

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 62/176 (35%), Gaps = 19/176 (10%)

Query: 54  IGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           + G    +     K V++  +  +  LN+ CP   V      A    + +     ++ + 
Sbjct: 85  LVGMSPEETHTILKKVQESDFRGLTELNLSCP--NVPGKPQIAY---DFETTDRILSEVF 139

Query: 113 KALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHARKAILK---G 162
           +  + P+ +K     D      A A+ N      V  +   G NG++I     +++   G
Sbjct: 140 EYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDESVVIRPKNG 198

Query: 163 LSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIG 216
                   I       V+   +  NP++ I   GG+     A +  L     V +G
Sbjct: 199 FGGIGGEYIKPTALANVHAFYQRLNPEIQIIGTGGVLTGRDAFEHILCGASMVQVG 254


>gi|283785847|ref|YP_003365712.1| imidazole glycerol phosphate synthase subunit [Citrobacter
           rodentium ICC168]
 gi|282949301|emb|CBG88912.1| imidazole glycerol phosphate synthase subunit [Citrobacter
           rodentium ICC168]
          Length = 258

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K     G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYADEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
               A +IL    D + I   A  +  ++T + + F 
Sbjct: 85  SADDAAQILSFGADKISINSPALADPTLITRLADRFG 121


>gi|171780003|ref|ZP_02920907.1| hypothetical protein STRINF_01790 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281351|gb|EDT46786.1| hypothetical protein STRINF_01790 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 252

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 24/150 (16%), Positives = 50/150 (33%), Gaps = 17/150 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +  ++  ++G + +        L   +  + R       D+V  +  +    F    GG+
Sbjct: 34  DAARAYYEAGCDELV------FLDITATHEKRDTT---VDMVRRVADQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKIS 256
             +    K+L    D V +  +A  N  ++    E F N    S+    +     W    
Sbjct: 84  RSVEDMNKMLKAGADKVAVNSSAVANPQLIKECAEKFGNQCVVSAIDARKEADGTWHVYV 143

Query: 257 ASMTDYAARHLHSGGKLQQITRHMIGLFHG 286
                 A     +G  L +  + ++ L  G
Sbjct: 144 ------AGGRKDTGIDLIEWAKKVVSLGAG 167


>gi|15668587|ref|NP_247385.1| imidazole glycerol phosphate synthase subunit HisF
           [Methanocaldococcus jannaschii DSM 2661]
 gi|2498450|sp|Q57854|HIS6_METJA RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|1591117|gb|AAB98400.1| imidazoleglycerol-phosphate synthase, cyclase subunit (hisF)
           [Methanocaldococcus jannaschii DSM 2661]
          Length = 272

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 177 DIVYEIKK---ENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEY 232
           DI+ ++ +   E   + + + GG++ +    +IL    D V I  AA KN  ++    E 
Sbjct: 60  DIIIDVVERTAEKVFIPLTVGGGIKSIEDFRRILRAGADKVSINTAAVKNPNLIKEASEI 119

Query: 233 FS 234
           F 
Sbjct: 120 FG 121


>gi|300869529|ref|ZP_07114111.1| N-acetylmannosamine-6-phosphate 2-epimerase [Oscillatoria sp. PCC
           6506]
 gi|300332502|emb|CBN59309.1| N-acetylmannosamine-6-phosphate 2-epimerase [Oscillatoria sp. PCC
           6506]
          Length = 225

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 21/118 (17%), Positives = 36/118 (30%), Gaps = 23/118 (19%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI--WIHARKAI 159
           + V   IA +   L  PV                         ++G + +   ++   A 
Sbjct: 108 ETVKSLIARIHDELGKPVMAD-----------ADTLETAIKAAEAGADAVGTTLYGYTAE 156

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
            K LSP     +  +          E  D+ I   GG+     A + L      V++G
Sbjct: 157 TKHLSPPGFELLAKMV---------EKLDIPIICEGGIAGPQMAKQALDLGAFAVVVG 205


>gi|224542664|ref|ZP_03683203.1| hypothetical protein CATMIT_01848 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524374|gb|EEF93479.1| hypothetical protein CATMIT_01848 [Catenibacterium mitsuokai DSM
           15897]
          Length = 239

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 20/95 (21%), Positives = 34/95 (35%), Gaps = 12/95 (12%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             L    +K G   + +         +     +     + + +  I +    + + L GG
Sbjct: 33  EELAAGFEKMGAKYLHV---------VDLDGAKDAHATNKETIKRI-RAAISIPMELGGG 82

Query: 197 LEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
           + DM      L    VD V++G AA KN A L   
Sbjct: 83  IRDMDTVSMYLDEIGVDRVILGTAAIKNPAFLDEA 117


>gi|218706705|ref|YP_002414224.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           UMN026]
 gi|298382435|ref|ZP_06992032.1| 2,4-dienoyl-CoA reductase [Escherichia coli FVEC1302]
 gi|331664695|ref|ZP_08365600.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA143]
 gi|218433802|emb|CAR14719.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           UMN026]
 gi|298277575|gb|EFI19091.1| 2,4-dienoyl-CoA reductase [Escherichia coli FVEC1302]
 gi|331057943|gb|EGI29925.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA143]
          Length = 672

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 31/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVGLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKSHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|15893443|ref|NP_346792.1| TIM-barrel fold family protein [Clostridium acetobutylicum ATCC
           824]
 gi|15022975|gb|AAK78132.1|AE007526_11 Predicted enzyme with TIM-barrel fold [Clostridium acetobutylicum
           ATCC 824]
 gi|325507555|gb|ADZ19191.1| enzyme with TIM-barrel fold protein [Clostridium acetobutylicum EA
           2018]
          Length = 228

 Score = 36.3 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 34/111 (30%), Gaps = 32/111 (28%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           D I  + + + IP+ V      +D          V++   SG   + +   K        
Sbjct: 124 DIIREVRETIDIPIIVTVVSEYED----------VQARIDSGATILNVSGAKRTSH---- 169

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGG------LEDMSQALKILPSV 210
                       IV  I+++ P + I   GG      +E +      +   
Sbjct: 170 ------------IVRSIREKFPSIPIIATGGNNEASIIETIEAGANAITYT 208


>gi|307824905|ref|ZP_07655127.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Methylobacter tundripaludum SV96]
 gi|307733952|gb|EFO04807.1| imidazoleglycerol phosphate synthase, cyclase subunit
           [Methylobacter tundripaludum SV96]
          Length = 257

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + +   + G + I        L   +  DNR        +V ++  E   + + + GG+
Sbjct: 35  EIARRYDREGADEIT------FLDITATHDNRDTI---VHVVEQVASEVF-IPLTVGGGI 84

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D V I  AA  N   +    E F 
Sbjct: 85  RTLDDIRRMLNAGADKVGINSAAVANPEFVREAAERFG 122


>gi|300743725|ref|ZP_07072745.1| thiamine-phosphate diphosphorylase [Rothia dentocariosa M567]
 gi|300380086|gb|EFJ76649.1| thiamine-phosphate diphosphorylase [Rothia dentocariosa M567]
          Length = 219

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 4/90 (4%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
            R LV+       + I            +   NR  P L  + + E+  E  ++ +   G
Sbjct: 132 TRELVERANAV-AHLIDYIGAGPFRPSPTKASNR--PPLGIEGLRELA-ELSEVPVVAIG 187

Query: 196 GLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
            +            V GV + RA  +N  +
Sbjct: 188 DIWPQDCPSIRETGVAGVAMARAFVENPEL 217


>gi|99080004|ref|YP_612158.1| putative carboxyphosphonoenolpyruvate phosphonomutase protein
           [Ruegeria sp. TM1040]
 gi|99036284|gb|ABF62896.1| putative carboxyphosphonoenolpyruvate phosphonomutase protein
           [Ruegeria sp. TM1040]
          Length = 253

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 29/116 (25%), Positives = 43/116 (37%), Gaps = 15/116 (12%)

Query: 102 DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           D V   +A +C+ +S+PVTV    G         +   V+ + ++G  GI    R     
Sbjct: 64  DFVLRIVARICETVSVPVTVDFEGGY--ATAPSEVGENVRKVLRAGAVGINFEDRVVGGS 121

Query: 162 GLSPKDNRKIPNLDYDIVYEIK----KENPDLFIGLNGGLE---DMSQALKILPSV 210
           GL P        +  D ++ IK    +E   LFI     L    D       LP  
Sbjct: 122 GLHPVS------VQVDRIHAIKTVAAEEGVPLFINARTDLFLGRDPETHRDQLPEA 171


>gi|225026423|ref|ZP_03715615.1| hypothetical protein EUBHAL_00672 [Eubacterium hallii DSM 3353]
 gi|224956260|gb|EEG37469.1| hypothetical protein EUBHAL_00672 [Eubacterium hallii DSM 3353]
          Length = 656

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 28/196 (14%), Positives = 61/196 (31%), Gaps = 23/196 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA+   + G + + +++      +               FG             I  + 
Sbjct: 151 EAARRAMEAGADAVEIHMA--HGYLVNSFMSPRTNKRVDEFGGSFENRMRFSTLIIDEVK 208

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           KA    + V  RI   + +        +  +   ++  G++ + +     +         
Sbjct: 209 KATQGKIAVLARINSTEDMFGGLDNHDMCAIATYLESCGLDALHVSRAVHLKDEYMWAPT 268

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAML 226
                   + V  IKK    + +   G   +   A  ++   + D V  GR +  + AM 
Sbjct: 269 GIHGGFSAEYVANIKK-CVSIPVITVGRYTEPQFAEVMVRTGNADLVAFGRQSLADPAM- 326

Query: 227 TTVDEYFSNPLTGSSP 242
               + F + L   +P
Sbjct: 327 --PKKAFEDRLEDMTP 340


>gi|254487919|ref|ZP_05101124.1| oxidoreductase, FAD/FMN-binding family [Roseobacter sp. GAI101]
 gi|214044788|gb|EEB85426.1| oxidoreductase, FAD/FMN-binding family [Roseobacter sp. GAI101]
          Length = 764

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 49/323 (15%), Positives = 87/323 (26%), Gaps = 93/323 (28%)

Query: 14  RLLTNNALLYTEM--IVADAIL------------RGDKKNILGFSTQEKP--LALQIG-- 55
           R      L+YTEM  + AD  +                  +  F   E P  +  QIG  
Sbjct: 437 RAKGGAGLVYTEMTCVSADGRITPGCPGLYAPEHEAAWTRLTDFIHAETPAKICCQIGHA 496

Query: 56  -------------------GADI----------------------------SKLVEAAKI 68
                              G                               ++ V AA++
Sbjct: 497 GRKGSTQVGWEKMDAPLPSGNWPLLSASAIPWSDENATPKAMTRDDMDAVKAQFVAAAEM 556

Query: 69  VEDFGYNEINLNVG---------CPSARVHEGSFGACL---MLNPDIVGDCIAAMCKALS 116
            +  G++ I L+            P +   +  +G  L   M  P    +  AAM     
Sbjct: 557 ADRAGFDMIELHAAHGYLISSFISPLSNTRDDEYGGSLENRMRYP---LEVFAAMRDVWP 613

Query: 117 --IPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
              P+ V+        DD +       +      +G + I + A +   +   P   R  
Sbjct: 614 AAKPMAVRISANDWAGDDGVTPEEAVEIAALFDAAGADIIDVSAGQTSTQ-AKPVYGRMF 672

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS-AMLTT 228
                D +    + +  +     G + +      IL +   D V + RA   +    L  
Sbjct: 673 QTPFSDRI----RNDGGIKTMAVGNIFEADHVNSILMAGRADLVCLARAHLADPYWTLHQ 728

Query: 229 VDEYFSNPLTGSSPIKTRVDKDF 251
                        P +   D+ +
Sbjct: 729 GAALGDRQSVWPKPYEAGRDQAW 751


>gi|199599175|ref|ZP_03212578.1| Tryptophan synthase alpha chain [Lactobacillus rhamnosus HN001]
 gi|199589928|gb|EDY98031.1| Tryptophan synthase alpha chain [Lactobacillus rhamnosus HN001]
          Length = 264

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 46/161 (28%), Gaps = 50/161 (31%)

Query: 104 VGDCIAAMCKALSIPVTV----------------------KCRIGVDDQIPAVALRNLVK 141
           V + + A  K  ++P+                        K    V   +P  +   +V 
Sbjct: 76  VFEIVEAARKETTVPIVFLTYLNIVFKYGYDAFLKRCAELKVSGLVIPDLPYESRAEIVP 135

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI------------------- 182
             +K G++ I +          S     KI       +Y +                   
Sbjct: 136 FAEKYGIDIIPLITPT------SGHRIEKIAKSASGFIYVVSSVGITGERDEFFTGLKAL 189

Query: 183 ---KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               K + D+   +  G+    QA  +    DGV+IG A  
Sbjct: 190 VAEIKRSTDVPTAIGFGIHTPQQAQTMASIADGVIIGSAIV 230


>gi|50306203|ref|XP_453064.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|51701803|sp|Q7Z895|PYRD1_KLULA RecName: Full=Dihydroorotate dehydrogenase; Short=DHOD;
           Short=DHODase; Short=DHOdehase; AltName:
           Full=Dihydroorotate oxidase
 gi|33302305|gb|AAQ01773.1| dihydroorotate dehydrogenase [Kluyveromyces lactis]
 gi|49642197|emb|CAH01915.1| KLLA0C19360p [Kluyveromyces lactis]
          Length = 315

 Score = 36.3 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 29/193 (15%), Positives = 59/193 (30%), Gaps = 40/193 (20%)

Query: 39  NILGFSTQEKPLALQIGGADISKLVEAAKI---VEDFGYNEI-NLNVGCP----SARVHE 90
           +       E P  + + G  I    E  K+   ++D  +  I  LN+ CP      +V  
Sbjct: 88  DRQDRFPSENPPFMSVAGMSID---ENIKLLHRIQDSNFRGITELNLSCPNVPGKPQVA- 143

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
                    + ++    ++++ +  + P+ VK     D          +   + K  +  
Sbjct: 144 --------YDFELTDQILSSVFEFFTKPLGVKLPPYFD----FAHFDAMACILNKYPIAY 191

Query: 151 ------------IWIHARKAILK---GLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLN 194
                       I +     ++K   G        I       V     + N  + I   
Sbjct: 192 VNCINSVGNGLYIDVEKESVVIKPKDGFGGIGGEYIKPTALANVRAFYNRLNGRIRIIGT 251

Query: 195 GGLEDMSQALKIL 207
           GG++    A + L
Sbjct: 252 GGIKTGQDAFEHL 264


>gi|332800187|ref|YP_004461686.1| 2,4-dienoyl-CoA reductase [Tepidanaerobacter sp. Re1]
 gi|332697922|gb|AEE92379.1| 2,4-dienoyl-CoA reductase (NADPH) [Tepidanaerobacter sp. Re1]
          Length = 629

 Score = 36.3 bits (83), Expect = 6.9,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 68/182 (37%), Gaps = 26/182 (14%)

Query: 63  VEAAKIVEDFGYNEINLNVG---CP----SARVHEG--SFGACLMLNPDIVGDCIAAMCK 113
            +AAK   D G++ + ++ G    P    S   ++    +G             +  + +
Sbjct: 133 AQAAKDARDLGFDMVFMHFGHGWLPPQFLSPLFNKRTDEYGGSFENRARFPKMILEKVRQ 192

Query: 114 AL--SIPVTVKCRIG--VDDQIPAVALRNLVKSIK------KSGVNGIWIHARKAILKGL 163
           A+  + PV ++      V+  I        +K ++      +        H     +   
Sbjct: 193 AVGPNYPVDMRISSVEWVEGSIEFEDTLKFIKLVEPLIDTVQISCGLDINHEGNVHMVTT 252

Query: 164 SPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYK 221
           + K++   PN  Y     I K+N  + + + G + +  +A +++   +VD V  GR+   
Sbjct: 253 NFKEHM--PNAKY---ARIVKQNVSIPVSVVGAVMNPYEAEELIASGAVDLVAFGRSFIA 307

Query: 222 NS 223
           + 
Sbjct: 308 DP 309


>gi|323704494|ref|ZP_08116072.1| thiamine-phosphate pyrophosphorylase [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535956|gb|EGB25729.1| thiamine-phosphate pyrophosphorylase [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 209

 Score = 36.3 bits (83), Expect = 6.9,   Method: Composition-based stats.
 Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 6/99 (6%)

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
            +P ++  +I  D++I  ++   + ++++       +I A      G        I  LD
Sbjct: 91  DLPCSIARKIMSDNKIIGISAGCVDEAVEAERDGADYIGAGAVFYTGTKKDIGEAIGLLD 150

Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALK-ILPSVDGV 213
              +    KE   + +   GG++  S AL  +   VDG+
Sbjct: 151 LKKI----KEAVKIPVVAIGGIK-YSNALDVMRTGVDGI 184


>gi|209518947|ref|ZP_03267757.1| tryptophan synthase, alpha subunit [Burkholderia sp. H160]
 gi|209500599|gb|EEA00645.1| tryptophan synthase, alpha subunit [Burkholderia sp. H160]
          Length = 270

 Score = 36.3 bits (83), Expect = 6.9,   Method: Composition-based stats.
 Identities = 21/106 (19%), Positives = 41/106 (38%), Gaps = 21/106 (19%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAI-------------------LKGLSPKDNRK 170
             P     N  + ++ +G++ I++ A  +                    LKG++   N  
Sbjct: 130 DYPPEECANFAEQMQAAGIDPIFLLAPTSTDERIAEVGRIASGYVYYVSLKGVTGAANLD 189

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
           + ++    +  IK   P L +G+  G+ D   A  +    D V+IG
Sbjct: 190 VSSIA-SKIPAIKSRVP-LPVGVGFGIRDAQTARAVGEVADAVVIG 233


>gi|126667889|ref|ZP_01738855.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Marinobacter sp. ELB17]
 gi|126627705|gb|EAZ98336.1| NADH:flavin oxidoreductase, Old Yellow Enzyme family protein
           [Marinobacter sp. ELB17]
          Length = 697

 Score = 36.3 bits (83), Expect = 6.9,   Method: Composition-based stats.
 Identities = 21/125 (16%), Positives = 42/125 (33%), Gaps = 11/125 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +  + + +     +  R+     ++D      +  L K I+K+G   I  +      +
Sbjct: 214 EIVRRVRERVGPNFILIYRLSMLDLIEDGSTWEEVVQLAKEIEKAGATLI--NTGIGWHE 271

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
              P     +P   +  V   +K E     I  N  +     A KIL   D  M+   + 
Sbjct: 272 ARIPTIATSVPRGAFSKVTARLKSEVSIPLITTNR-INMPEVAEKILAEGDADMV---SM 327

Query: 221 KNSAM 225
               +
Sbjct: 328 ARPFL 332


>gi|83590055|ref|YP_430064.1| methyltetrahydrofolate:corrinoid/iron-sulfur protein
           methyltransferase [Moorella thermoacetica ATCC 39073]
 gi|83572969|gb|ABC19521.1| 5-methyltetrahydrofolate--homocysteine S-methyltransferase
           [Moorella thermoacetica ATCC 39073]
          Length = 267

 Score = 36.3 bits (83), Expect = 6.9,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 12/79 (15%)

Query: 43  FSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD 102
            +T  KP+   I   D + + + A    + G + I++N             G  +   P+
Sbjct: 8   INTSRKPIKEAIEREDAAYIRDIAVKQAEAGADYIDINC------------GTLIHNEPE 55

Query: 103 IVGDCIAAMCKALSIPVTV 121
           I+   +  + + + +P+ +
Sbjct: 56  IMAWLVNTVREVVDVPLCI 74


>gi|326791566|ref|YP_004309387.1| 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)
           imidazole-4-carboxamide isomerase [Clostridium
           lentocellum DSM 5427]
 gi|326542330|gb|ADZ84189.1| 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)
           imidazole-4-carboxamide isomerase [Clostridium
           lentocellum DSM 5427]
          Length = 238

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 24/99 (24%), Positives = 38/99 (38%), Gaps = 11/99 (11%)

Query: 137 RNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGG 196
             + K  +  G + + I       +G    +         DIV  +K     + I L GG
Sbjct: 33  AEMAKKWESLGGDYLHIVDLDGAKEGKGINEQ-----AVRDIVAAVK-----IPIELGGG 82

Query: 197 LEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           +  +      L   VD V++G AA KN A++    E F 
Sbjct: 83  IRTIEDINCQLDRGVDRVILGSAAIKNKALVKEAIETFG 121


>gi|330840640|ref|XP_003292320.1| hypothetical protein DICPUDRAFT_57873 [Dictyostelium purpureum]
 gi|325077442|gb|EGC31154.1| hypothetical protein DICPUDRAFT_57873 [Dictyostelium purpureum]
          Length = 398

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 66/195 (33%), Gaps = 27/195 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CP-SARVHEGSFGACLMLNPDIVGDCIA 109
               ++A+   + GY+ + ++            P S +  +   G+       ++ D I 
Sbjct: 191 EAFKQSARRSVEAGYDFLEIHSAHGYLLSSFLSPTSNKRTDEYTGSTFEGRIKLLLDIIQ 250

Query: 110 AMCKA--LSIP--VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR----KAILK 161
           A+        P  V + C   V+         NL K +    V+ +   +     K + K
Sbjct: 251 AVRTVWTTERPLAVRISCEEYVEGGWNMEDTVNLAKVLDTLDVDLLDCSSGGNNSKQVFK 310

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV--DGVMIGRAA 219
            + P              ++ K+    L IG  G + +   A  +L     D +++GRA 
Sbjct: 311 NVGPLYQVP-------FAHQAKQAVSKLLIGAVGIITNGKDAESVLQEEKSDLILVGRAF 363

Query: 220 YKNSAMLTTVDEYFS 234
            KN  +     +   
Sbjct: 364 LKNPQLTYEFAQQLG 378


>gi|323486828|ref|ZP_08092146.1| hypothetical protein HMPREF9474_03897 [Clostridium symbiosum
           WAL-14163]
 gi|323399841|gb|EGA92221.1| hypothetical protein HMPREF9474_03897 [Clostridium symbiosum
           WAL-14163]
          Length = 652

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 26/180 (14%), Positives = 56/180 (31%), Gaps = 22/180 (12%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
            +AA + E  G + +N++ G     +               +G C+          +  +
Sbjct: 152 AQAAYMAEFAGCDIVNIHGG--HGWLISQFLSDLNNHRTDKYGGCIENKARFPLMIVDRI 209

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK-- 166
            +      I   +      +  IP        K +    V+ I + A      G + +  
Sbjct: 210 RQRCPNLIIEFRLSGEEDTEGGIPIEETVEFAKLL-DGKVDIIHVSAATFHDTGTASRMF 268

Query: 167 -DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                    + +   +IK    +  + + GG+ D      +L     D V++GR    + 
Sbjct: 269 PSVFYPRGCNVENAAKIKAVVKESLVSVVGGINDPDYMESVLVDGKTDFVVVGRQFIADP 328


>gi|315659083|ref|ZP_07911949.1| 3-hexulose-6-phosphate synthase [Staphylococcus lugdunensis M23590]
 gi|315495894|gb|EFU84223.1| 3-hexulose-6-phosphate synthase [Staphylococcus lugdunensis M23590]
          Length = 213

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 21/101 (20%), Positives = 37/101 (36%), Gaps = 15/101 (14%)

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL-KGLSPKDNRK------------ 170
           +  + D I    L    + +   G + I +H    +  +G SP D+ +            
Sbjct: 107 KQLLVDMIAVQDLEKRAQELDDMGADYIAVHTGYDLQAEGQSPLDSLRKVKSVIKNSKVA 166

Query: 171 -IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSV 210
               +  D + EI  ENPDL I   GG+ +    ++     
Sbjct: 167 VAGGIKPDTIKEIVAENPDLVIVG-GGIANAEDPVEAAKQC 206


>gi|304392724|ref|ZP_07374664.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Ahrensia sp. R2A130]
 gi|303295354|gb|EFL89714.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Ahrensia sp. R2A130]
          Length = 245

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 18/129 (13%), Positives = 49/129 (37%), Gaps = 17/129 (13%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKC-RIGVDD--QIPAVALRNLVKSIKKSGVNGIWIHA 155
            +PD+V +        +++ +  K  R+ V+   +   + + ++    + +G   I    
Sbjct: 110 RDPDLVREACRKFPGKVAVGIDAKGGRVAVEGWAETSDLTVFDMAARFEDAGAAAII--- 166

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP----SVD 211
                       +  +  +++D    +  E   + +  +GGL  +    ++       ++
Sbjct: 167 ------YTDIDRDGVLAGINWDSTIALA-EATSIPVIASGGLASLDDIRRMTKPDAAKLN 219

Query: 212 GVMIGRAAY 220
           G + GRA Y
Sbjct: 220 GAITGRALY 228


>gi|291532538|emb|CBL05651.1| methionine synthase (B12-dependent) [Megamonas hypermegale ART12/1]
          Length = 790

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 28/168 (16%), Positives = 51/168 (30%), Gaps = 43/168 (25%)

Query: 40  ILGFSTQEKPLALQIG---------GADISKLVEAAKIVEDFGYNEINLNVGCPSARVHE 90
           +      + P+  Q+          G D      AA I+E  G + I  N          
Sbjct: 149 LAAKDACDLPVICQLSFSEDGRTVTGTDPQS---AAIILEAMGADIIGANCS-------- 197

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP--------AVALRNLVKS 142
                   L P+ +   I  +    S P++V+   G+                +      
Sbjct: 198 --------LGPEQLVPIIKELADNCSCPISVQANAGMPHLENGQTIFPLTPEDMAKWAPK 249

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKE-NPDL 189
           + ++G   I          G +P   + I     ++   I+K  NP+L
Sbjct: 250 LVEAGATYIGGCC------GTTPAHIKAIKEALANVSEPIRKAPNPNL 291


>gi|254994383|ref|ZP_05276573.1| NADH oxidase [Listeria monocytogenes FSL J2-064]
          Length = 550

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 20/177 (11%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAMC 112
           EAA   +  G + +   V C    +               FG C      +    I ++ 
Sbjct: 60  EAALRAKKAGADAVE--VHCAHGYLVSSFLSARTNKRVDEFGGCFENRMRLPRLIIESIR 117

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K +   + + CRI   D +           +   ++  G++G+ +     I         
Sbjct: 118 KRVGHSIAILCRINSTDGVEGGLSVQDSATVAAYLEDCGLDGLHVSRSVHIRDEYMWAPT 177

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNS 223
                   D+V +IK+      I + G   +   A  ++     D V  GR +  + 
Sbjct: 178 VLHAGFSSDLVTQIKRAVSIPVITV-GRFTEPHYAELMVREGRADLVAFGRQSLADP 233


>gi|302877744|ref|YP_003846308.1| tryptophan synthase, alpha subunit [Gallionella capsiferriformans
           ES-2]
 gi|302580533|gb|ADL54544.1| tryptophan synthase, alpha subunit [Gallionella capsiferriformans
           ES-2]
          Length = 266

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE---IKKENPDLFIGLNG 195
           L  + +++ +  +   AR  +   +S K      ++D   + +   + +++  L IG+  
Sbjct: 154 LAPTTEEARIKQVAKLARGYVY-YVSLKGVTGSGSIDLSAIEQKLPLLRQHIKLPIGVGF 212

Query: 196 GLEDMSQALKILPSVDGVMIG 216
           G+ D + A  +    DGV++G
Sbjct: 213 GIRDAATAKAVASLCDGVVVG 233


>gi|20455019|sp|Q9RPQ4|HIS6_THEP3 RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|6175608|gb|AAF05094.1|AF150930_3 cyclase [Thermoanaerobacter pseudethanolicus ATCC 33223]
          Length = 254

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +     K+G + +           L    + ++ N+  D+V  + ++    F    GG+
Sbjct: 34  EIASYYDKAGADELTF---------LDITASAELRNIMIDVVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    +IL    D V I  AA K   +++     F 
Sbjct: 84  RTVEDFREILKAGADKVSINSAAVKRPELISEAASRFG 121


>gi|148545567|ref|YP_001265669.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas putida
           F1]
 gi|167012103|sp|A5VX75|HIS4_PSEP1 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|148509625|gb|ABQ76485.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas putida
           F1]
          Length = 245

 Score = 36.3 bits (83), Expect = 7.0,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P+L I + GG+  +      +   V  V+IG  A K    +    +
Sbjct: 60  PVNGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKQPEFVAEACK 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++S+      AR   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEVSSVQVIDLARRFEADG 160


>gi|323694971|ref|ZP_08109121.1| hypothetical protein HMPREF9475_03985 [Clostridium symbiosum
           WAL-14673]
 gi|323501061|gb|EGB16973.1| hypothetical protein HMPREF9475_03985 [Clostridium symbiosum
           WAL-14673]
          Length = 652

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 26/180 (14%), Positives = 56/180 (31%), Gaps = 22/180 (12%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIAAM 111
            +AA + E  G + +N++ G     +               +G C+          +  +
Sbjct: 152 AQAAYMAEFAGCDIVNIHGG--HGWLISQFLSDLNNHRTDKYGGCIENKARFPLMIVDRI 209

Query: 112 CKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK-- 166
            +      I   +      +  IP        K +    V+ I + A      G + +  
Sbjct: 210 RQRCPNLIIEFRLSGEEDTEGGIPIEETVEFAKLL-DGKVDIIHVSAATFHDTGTASRMF 268

Query: 167 -DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
                    + +   +IK    +  + + GG+ D      +L     D V++GR    + 
Sbjct: 269 PSVFYPRGCNVENAAKIKAVVKESLVSVVGGINDPDYMESVLVDGKADFVVVGRQFIADP 328


>gi|313898743|ref|ZP_07832278.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Clostridium sp. HGF2]
 gi|312956627|gb|EFR38260.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Clostridium sp. HGF2]
          Length = 239

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 20/138 (14%), Positives = 49/138 (35%), Gaps = 13/138 (9%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           ++ K+ ++ G   + +       +G           ++ DI+ +  +    + + + GG+
Sbjct: 34  DIAKAFEQQGARYVHMVDLNGAKEG---------KKINQDIIVKTAQSL-QIPVEVGGGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRV--DKDFWRK 254
             M      L   +  V++G AA +N   L      +   +      K  +     + ++
Sbjct: 84  RSMEDVRFYLEHGIARVILGTAAIENPEFLREALAQYKEKIAVGIDCKNGMVCGHGWLQE 143

Query: 255 ISASMTDYAARHLHSGGK 272
                 D+A +    G K
Sbjct: 144 SELQYIDFAIQMEAMGVK 161


>gi|301050025|ref|ZP_07196940.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 185-1]
 gi|300298249|gb|EFJ54634.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli MS 185-1]
          Length = 258

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG+ 
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIN 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLEDAAKILSFGADKISINSPALADPTLITRLADRFG 121


>gi|284992815|ref|YP_003411369.1| inosine-5'-monophosphate dehydrogenase [Geodermatophilus obscurus
           DSM 43160]
 gi|284066060|gb|ADB76998.1| inosine-5'-monophosphate dehydrogenase [Geodermatophilus obscurus
           DSM 43160]
          Length = 501

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 17/101 (16%), Positives = 36/101 (35%), Gaps = 8/101 (7%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            VA R   +++  +GV+ + +      +          +P +       +      + + 
Sbjct: 285 NVATRAGAQALVDAGVDAVKVGVGPGSICTTRVVAGVGVPQVTAIYEAALAARPAGVPVI 344

Query: 193 LNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEY 232
            +GGL+     A  ++   D VMIG        +   V+E 
Sbjct: 345 ADGGLQYSGDIAKALVAGADTVMIG-------GLFAGVEEA 378


>gi|192361186|ref|YP_001982230.1| tryptophan synthase subunit alpha [Cellvibrio japonicus Ueda107]
 gi|190687351|gb|ACE85029.1| tryptophan synthase, alpha subunit [Cellvibrio japonicus Ueda107]
          Length = 269

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 4/91 (4%)

Query: 129 DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP- 187
           D++    +  L  +      + I  HA    L  +S K      +LD + V     E   
Sbjct: 144 DEVNLDNIFLLAPTTTVERAHKIASHA-SGFLYYVSLKGVTGAGHLDVEAVKAKLAEFGR 202

Query: 188 --DLFIGLNGGLEDMSQALKILPSVDGVMIG 216
             DL + +  G++D S A  +    DGV++G
Sbjct: 203 LTDLPVCVGFGIKDASTAKAVAQLADGVVVG 233


>gi|221134778|ref|ZP_03561081.1| 2,4-dienoyl-CoA reductase [Glaciecola sp. HTCC2999]
          Length = 680

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 20/131 (15%), Positives = 43/131 (32%), Gaps = 8/131 (6%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDD----QIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
            +  + +A+     +  R+ + D       A  +  L   I+K+G     I+      + 
Sbjct: 207 VVRRVREAVGEHFIIIYRLSMLDLVEGGSTAEEVIELGLGIEKAGAT--IINTGIGWHEA 264

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI--GRAAY 220
             P    K+P   +  V    ++  +L +  +  +     A  +L   D  M+   R   
Sbjct: 265 RIPTIATKVPRAAFTWVTAKFRQALNLPVITSNRINTPEVAESVLARGDADMVSMARPFL 324

Query: 221 KNSAMLTTVDE 231
            +   L     
Sbjct: 325 ADPQFLAKAQA 335


>gi|120609727|ref|YP_969405.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acidovorax citrulli
           AAC00-1]
 gi|148839471|sp|A1TKZ3|HIS4_ACIAC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|120588191|gb|ABM31631.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acidovorax citrulli
           AAC00-1]
          Length = 248

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 54/159 (33%), Gaps = 17/159 (10%)

Query: 122 KCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             R+   D   +         + +    +G   + +        G            ++ 
Sbjct: 14  CVRLKQGDMDQSTTFGEDPAAMARKWVDAGARRLHLVDLNGAFAG---------APKNHA 64

Query: 178 IVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSN 235
            +  I KE  D L + L GG+ D+    K +   +  V+IG AA KN   L      F  
Sbjct: 65  AIKAILKEVGDDLPVQLGGGIRDLDTIEKYIDGGLRYVIIGTAAVKNPGFLKDACSAFGG 124

Query: 236 PLT-GSSPIKTRVDKDFWRKISAS-MTDYAARHLHSGGK 272
            +  G      +V  D W K++   + D A R    G +
Sbjct: 125 HIIVGLDAKDGKVATDGWSKLTGHEVVDLAKRFEDWGVE 163


>gi|78188467|ref|YP_378805.1| IMP dehydrogenase [Chlorobium chlorochromatii CaD3]
 gi|78170666|gb|ABB27762.1| inosine-5'-monophosphate dehydrogenase [Chlorobium chlorochromatii
           CaD3]
          Length = 497

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 19/114 (16%), Positives = 38/114 (33%), Gaps = 11/114 (9%)

Query: 122 KCRIGVDDQI---PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           K +    D       VA    V+ + K+G + + +      +          +P L   +
Sbjct: 269 KIKSHYPDLQVIAGNVATPEAVRDLVKAGADCVKVGIGPGSICTTRIVAGVGMPQLTAIM 328

Query: 179 VYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
               +    +  I  +GG++     A  +    D VM+G       ++    DE
Sbjct: 329 KCAEEAAKTNTPIIADGGIKYSGDIAKALAAGADSVMMG-------SIFAGTDE 375


>gi|70608028|ref|YP_256898.1| hypothetical protein Saci_2320 [Sulfolobus acidocaldarius DSM 639]
 gi|68568676|gb|AAY81605.1| hypothetical protein Saci_2320 [Sulfolobus acidocaldarius DSM 639]
          Length = 712

 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 29/120 (24%), Positives = 47/120 (39%), Gaps = 14/120 (11%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI--HARKAILKGLSP 165
           I A+ +A   PV VK      + IP      +V  I + G +G+ I  H           
Sbjct: 206 IEALKEATGKPVFVKV--AATNYIPY-----IVSGIARMGADGVIIDGHGAGTGATPTVI 258

Query: 166 KDNRKIP-NLDYDIVYEIKKENP---DLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           +DN  IP  L   I  ++ K      +  +   G + + + A K++    D V +G  A 
Sbjct: 259 RDNLGIPIELAVAISDKVLKAQGMRDNFTVIAAGRIANATDAAKLIALGADVVSVGTGAL 318


>gi|158343712|gb|ABW35534.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343722|gb|ABW35543.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
          Length = 251

 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 35/93 (37%), Gaps = 20/93 (21%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L K  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVIDLAKKFEDYGVESIVYTDIGRDGMLQG-----------INIDATVKLAQAVGIPVIA 197

Query: 193 LNG-----GLEDMSQALKILPSVDGVMIGRAAY 220
             G      +E + +  +    V+GV+ GRA Y
Sbjct: 198 SGGLSNLTDIESLCEVEEH--GVEGVICGRAIY 228


>gi|289664230|ref|ZP_06485811.1| 2,4-dienoyl-CoA reductase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 679

 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 18/126 (14%), Positives = 42/126 (33%), Gaps = 8/126 (6%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + +  M +A      +  R+     V+D      +    ++I+ +G     I++    
Sbjct: 204 AVEIVRRMREACGPDFIIIYRLSLVDLVEDGNQWQEILAQAQAIEGAGAT--IINSGIGW 261

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGR 217
            +   P     +P   +  V    K +  + +     +     A +IL   + D V + R
Sbjct: 262 HEARIPTIATSVPRAAFAGVTAKLKPHLRIPVVATNRINMPEVAERILADGAADMVSLAR 321

Query: 218 AAYKNS 223
               + 
Sbjct: 322 PLLADP 327


>gi|255029655|ref|ZP_05301606.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes LO28]
          Length = 266

 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 35/86 (40%), Gaps = 15/86 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI E+ G   +      PS      + G   M +P      +  + KA+SIPV  K RI
Sbjct: 3   AKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMKAVSIPVMAKARI 56

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI 151
           G   +          + ++  GV+ I
Sbjct: 57  GHITE---------ARVLEAMGVDYI 73


>gi|154333749|ref|XP_001563131.1| n-ethylmaleimide reductase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
 gi|134060141|emb|CAM37455.1| n-ethylmaleimide reductase-like protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 876

 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 29/223 (13%), Positives = 69/223 (30%), Gaps = 37/223 (16%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---- 82
             AD  ++    +++  S +     +Q+        V AAK     G++ + ++ G    
Sbjct: 551 FAADGKVQSYPVDVVALSAERLKWIVQLY-------VAAAKNAMLAGFDGVEIHAGGGYL 603

Query: 83  -------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS-IPVTVKCRIG-----VDD 129
                  C + R     +G        ++ + + A+  A+    V V+         + D
Sbjct: 604 IDQFLRRCSNTR--NDDYGGSPADRCRLLDEIVDAVAAAVGRRRVGVRISPTDLSKGMKD 661

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL 189
               V    +   + +  +  I +          S  D      +   ++    +    +
Sbjct: 662 TDREVVTETVATHMGERKIAYITVA---------SGSDGYYHGPMPASLLQTALRCFGGV 712

Query: 190 FIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            +  +  +       +I   +V GV I   A  N  ++     
Sbjct: 713 VLCDD-NISLAEAEKRIATDAVQGVCITLGAIANPDIINRAIH 754


>gi|332800437|ref|YP_004461936.1| Pyridoxal biosynthesis lyase pdxS [Tepidanaerobacter sp. Re1]
 gi|332698172|gb|AEE92629.1| Pyridoxal biosynthesis lyase pdxS [Tepidanaerobacter sp. Re1]
          Length = 284

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 15/86 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I E  G   +      P+        G   M +P      I  +  A+SIPV  KCRI
Sbjct: 23  AEIAEQAGAVAVMALERVPAD--IRKQGGVARMSDP----KIIKEIKAAVSIPVMAKCRI 76

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI 151
           G   +          + ++  G++ I
Sbjct: 77  GHFVE---------AQILEALGIDYI 93


>gi|310659258|ref|YP_003936979.1| glycerol-3-phosphate responding transcription antiterminator
           [Clostridium sticklandii DSM 519]
 gi|308826036|emb|CBH22074.1| glycerol-3-phosphate responding transcription antiterminator
           [Clostridium sticklandii]
          Length = 192

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 25/60 (41%)

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + + I      +K + P     +P +   ++  IK E P++ I   G +E     + +L 
Sbjct: 117 DSLSIETNIQQIKKIRPDAVEIMPGIIPRVIKRIKSEIPEIPIIAGGLIESKEDIMDVLK 176


>gi|331668725|ref|ZP_08369573.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA271]
 gi|331063919|gb|EGI35830.1| imidazoleglycerol phosphate synthase, cyclase subunit [Escherichia
           coli TA271]
          Length = 258

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A KIL    D + I   A  +  ++T + + F 
Sbjct: 85  SLDDAAKILSFGADKISINSPALADPTLITHLADRFG 121


>gi|331659374|ref|ZP_08360316.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA206]
 gi|315297787|gb|EFU57061.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 16-3]
 gi|331053956|gb|EGI25985.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA206]
          Length = 672

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVGAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|104782188|ref|YP_608686.1| N-ethylmaleimide reductase [Pseudomonas entomophila L48]
 gi|95111175|emb|CAK15895.1| N-ethylmaleimide reductase [Pseudomonas entomophila L48]
          Length = 365

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 32/183 (17%), Positives = 62/183 (33%), Gaps = 20/183 (10%)

Query: 61  KLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
              +AA    + G++ I L+            PSA + +  +G  +     IV + + A 
Sbjct: 160 DFGQAAANARETGFDFIELHAAHGYLLHQFLTPSANIRDDRYGGSVENRARIVLEAVDAA 219

Query: 112 CKALSI-PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-WIHARKAILKGLSPKDNR 169
               S   V ++        +      +  +  + +G+  I  +  R      LS  D  
Sbjct: 220 IAQWSADRVGIRIFP-----LGGFNGVDNGEDQEAAGLYLIGELAKRNLAYLHLSEPDWA 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
               L  +    I+   P + +    G     +A  +L    +D V  GRA   N  ++ 
Sbjct: 275 GGQPLRDEFREAIRAVYPGVIVAA--GAYTAEKAEDLLSRGLIDAVAFGRAFIANPDLVE 332

Query: 228 TVD 230
            + 
Sbjct: 333 RLR 335


>gi|41407981|ref|NP_960817.1| dihydroorotate dehydrogenase 2 [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|73913688|sp|Q73YS2|PYRD_MYCPA RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|41396335|gb|AAS04200.1| PyrD [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 370

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 17/113 (15%), Positives = 36/113 (31%), Gaps = 15/113 (13%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW----------IHAR 156
            ++A+    S PV VK    + D      + ++     + G+ GI           +   
Sbjct: 211 ILSAVLAETSTPVLVKIAPDLSDSD----VDDIADLAVELGLAGIVATNTTVSRDGLRTA 266

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
                G        +     +++  +     D L +   GG+E    A + + 
Sbjct: 267 GVDQLGAGGISGPPVARRAVEVLRRLYGRVGDRLVLISVGGIETADHAWERIT 319


>gi|91974892|ref|YP_567551.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhodopseudomonas
           palustris BisB5]
 gi|123722199|sp|Q13E39|HIS4_RHOPS RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|91681348|gb|ABE37650.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhodopseudomonas
           palustris BisB5]
          Length = 245

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 18/97 (18%)

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP 187
           +   V    + +  + +GV  I     AR  +LKG           ++++    +  E  
Sbjct: 142 ESSQVTALEIAQRFEDAGVAAIIFTDIARDGLLKG-----------INWEATIALA-EAV 189

Query: 188 DLFIGLNGGLEDMSQALKILP----SVDGVMIGRAAY 220
            + +  +GGL  +     +L      ++G + GRA Y
Sbjct: 190 SIPVIASGGLASIDDVKALLSPRANKLEGAIAGRALY 226


>gi|226942619|ref|YP_002797692.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Azotobacter
           vinelandii DJ]
 gi|259709848|sp|C1DJD2|HIS4_AZOVD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226717546|gb|ACO76717.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Azotobacter vinelandii DJ]
          Length = 245

 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 53/155 (34%), Gaps = 11/155 (7%)

Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
           V ++     D  + +     +     ++G   + +       +G           ++ ++
Sbjct: 15  VRLRQGRMDDSTVFSDDPVAMAARWVEAGCRRLHLVDLNGAFEGQ---------PINGEV 65

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNP- 236
           V  I +  PDL I + GG+  +      +   V  V+IG  A K    +      F    
Sbjct: 66  VTAIARRYPDLPIQIGGGIRSLETIEHYVKAGVGYVIIGTKAVKQPEFVGEACRAFPGKV 125

Query: 237 LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
           + G       V  D W ++S+      AR   + G
Sbjct: 126 IVGLDARDGFVATDGWAEVSSVQVVDLARRFEADG 160


>gi|325266565|ref|ZP_08133242.1| L-lactate dehydrogenase [Kingella denitrificans ATCC 33394]
 gi|324982008|gb|EGC17643.1| L-lactate dehydrogenase [Kingella denitrificans ATCC 33394]
          Length = 391

 Score = 35.9 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 8/80 (10%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            +   + G + I +          +P   R +P++       ++     + + L+GG+  
Sbjct: 264 AEKAVQHGADAIVVSNHGGRQLDGAPSSIRALPDV-------VQAAGSQIEVWLDGGITT 316

Query: 200 MSQALKILP-SVDGVMIGRA 218
               L+       GVMIGRA
Sbjct: 317 GQDILRAWALGARGVMIGRA 336


>gi|260891551|ref|ZP_05902814.1| dihydroorotate oxidase [Leptotrichia hofstadii F0254]
 gi|260858934|gb|EEX73434.1| dihydroorotate oxidase [Leptotrichia hofstadii F0254]
          Length = 310

 Score = 35.9 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 36/163 (22%), Positives = 55/163 (33%), Gaps = 19/163 (11%)

Query: 67  KIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           K V++  +  I  LN+ CP   V      A    + +     +A +      P+ VK   
Sbjct: 114 KKVQESDFKGITELNLSCP--NVPGKPQIAY---DLETTEKLLADIFSYFKKPLGVKLPP 168

Query: 126 GVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHARKAILK---GLSPKDNRKIPNLD 175
             D      A A+ N      +  I   G NG+ I     ++K   G        I    
Sbjct: 169 YFDIVHFDQAAAVFNKFPLTFINCINSIG-NGLVIEDESVVIKPKNGFGGIGGEYIKPTA 227

Query: 176 YDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVDGVMIG 216
              V+   +  NP + I   GG+     A +  L     V IG
Sbjct: 228 LANVHAFYQRLNPSIKIIGTGGVLTGQDAFEHILCGASMVQIG 270


>gi|222150499|ref|YP_002559652.1| NADH:flavin oxidoreductase homolog [Macrococcus caseolyticus
           JCSC5402]
 gi|222119621|dbj|BAH16956.1| NADH:flavin oxidoreductase homolog [Macrococcus caseolyticus
           JCSC5402]
          Length = 403

 Score = 35.9 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 34/221 (15%), Positives = 67/221 (30%), Gaps = 28/221 (12%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGV 148
           +G  L      + +    M +AL     +  +I   D             ++K + + G+
Sbjct: 193 YGGTLENRMKFLVEIYTGMREALGKDFPISLKINSTDFSDKGFSLEDSITVIKKMDELGI 252

Query: 149 NGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
           + I I           PK          D   ++  E  ++ I + GG       +  + 
Sbjct: 253 DHIEISGGD----YEKPKMMGDGEVYFLDYAKKV-SEKVEVPISVIGGFRRQQSMVDAIT 307

Query: 209 SVDGVM--IGRAAYKNSAMLTTVDEYFSNPLTGS--SPIKTRVDKDFWRKISASMTDYAA 264
             +  M  IGR    N  +   + E     +T    +     +DK     +  +  +   
Sbjct: 308 ETNVSMIGIGRPLVLNPELPNQLREGTYKDITLPRLTTKVKALDKIIGGFVGLAYYEQQI 367

Query: 265 RHLHSGGK----------LQQITRHMIGLFHGFPNSRRCRH 295
           R L +  K          L ++ +      HG     + R 
Sbjct: 368 RRLGNNQKPVVHTNAWSPLFELAK-----THGAKAFSKRRR 403


>gi|120404459|ref|YP_954288.1| dihydroorotate dehydrogenase 2 [Mycobacterium vanbaalenii PYR-1]
 gi|166199369|sp|A1TAT2|PYRD_MYCVP RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|119957277|gb|ABM14282.1| dihydroorotate oxidase A [Mycobacterium vanbaalenii PYR-1]
          Length = 353

 Score = 35.9 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 28/185 (15%), Positives = 62/185 (33%), Gaps = 29/185 (15%)

Query: 41  LGFSTQEKPLALQIGGAD-------ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSF 93
           L  ++ + P+ + IG               E+A+++       + +NV  P       + 
Sbjct: 131 LTRTSSDVPIGVNIGKTKVTPPEHAAEDYAESARLLGPL-AAYLVVNVSSP------NTP 183

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW- 152
           G   + + + +   ++A+    S PV VK    + DQ     +  +     + G+ GI  
Sbjct: 184 GLRDLQSVESLRPILSAVLAETSTPVLVKIAPDLADQD----IDEIADLAVELGLAGIVA 239

Query: 153 ---------IHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQ 202
                    +        G        +     +++  +     D L +   GG+E    
Sbjct: 240 TNTTISRAGLATPGVDALGPGGISGPPVARRALEVLRRLYARVGDRLVLISVGGIETADD 299

Query: 203 ALKIL 207
           A + +
Sbjct: 300 AWERI 304


>gi|332527350|ref|ZP_08403406.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rubrivivax
           benzoatilyticus JA2]
 gi|332111759|gb|EGJ11739.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rubrivivax
           benzoatilyticus JA2]
          Length = 248

 Score = 35.9 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 11/98 (11%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLE 198
            +    +G   + +        G           ++   V  I +E  D + + L GG+ 
Sbjct: 36  ARRWLDAGARRLHLVDLNGAFAGR---------PINEAAVKAILREVGDEIPVQLGGGIR 86

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
           D+    ++L   +  V+IG AA K+   L      F  
Sbjct: 87  DLDTIERLLDDGISYVIIGTAAVKSPGFLKDACTAFGG 124


>gi|332653135|ref|ZP_08418880.1| tryptophan synthase, alpha subunit [Ruminococcaceae bacterium D16]
 gi|332518281|gb|EGJ47884.1| tryptophan synthase, alpha subunit [Ruminococcaceae bacterium D16]
          Length = 255

 Score = 35.9 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 22/157 (14%), Positives = 46/157 (29%), Gaps = 38/157 (24%)

Query: 102 DIVGDCIAAMCKALSIPVT----------------------VKCRIGVDDQIPAVALRNL 139
           D +   +  + K ++IP+                       V     +   +P       
Sbjct: 74  DKIFALVKELRKNVTIPLVFMTYANVVFSYGTDRFLARAAEVGVDGIILPDVPYEEKEEF 133

Query: 140 VKSIKKSGVNGIWIHARKA----------------ILKGLSPKDNRKIPNLDYDIVYEIK 183
               +  G++ I + A  +                ++  L     R     D   +    
Sbjct: 134 AAPCRAHGLDFISLIAPTSEHRIAAIAREAEGFLYLVSSLGVTGTRSKITTDLGSIVNAV 193

Query: 184 KENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
           +EN  +   +  G+    QA ++    DGV++G A  
Sbjct: 194 RENTQIPCAIGFGISTPEQAGQMAQLADGVIVGSAIV 230


>gi|306816566|ref|ZP_07450698.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           NC101]
 gi|305850131|gb|EFM50590.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           NC101]
          Length = 672

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVGAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|302329840|gb|ADL20034.1| Pyridoxine biosynthesis protein [Corynebacterium pseudotuberculosis
           1002]
          Length = 299

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 8/98 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR- 124
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K R 
Sbjct: 35  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 88

Query: 125 -IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
              V+ QI      + +   +         H  K   K
Sbjct: 89  GHFVEAQILESLGVDFIDESEVLSPADYTNHIDKWNFK 126


>gi|167623748|ref|YP_001674042.1| imidazole glycerol phosphate synthase subunit HisF [Shewanella
           halifaxensis HAW-EB4]
 gi|189043439|sp|B0TQY8|HIS6_SHEHH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|167353770|gb|ABZ76383.1| imidazoleglycerol phosphate synthase, cyclase subunit [Shewanella
           halifaxensis HAW-EB4]
          Length = 257

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +            +   +R I   D   +  + ++  D+   + GG+ 
Sbjct: 35  LAKRYAEEGADELV------FYDITASAHDRVI---DKSWISRVAEKI-DIPFCVAGGIR 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + QA + L    D + I   A  + +++  + + F 
Sbjct: 85  TIEQAREKLAFGADKISINSPALTDPSLIARLQDEFG 121


>gi|324008853|gb|EGB78072.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 57-2]
          Length = 672

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVGAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|320159575|ref|YP_004172799.1| pyridoxal biosynthesis lyase PdxS [Anaerolinea thermophila UNI-1]
 gi|319993428|dbj|BAJ62199.1| pyridoxal biosynthesis lyase PdxS [Anaerolinea thermophila UNI-1]
          Length = 296

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 15/88 (17%)

Query: 64  EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
           E A+I ED G   +      P+        G   M +P+++   +     A+SIPV  KC
Sbjct: 31  EHARIAEDAGAVAVMALERVPAD--IRAHGGVARMSDPELILKIM----DAVSIPVMAKC 84

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           RIG   +          + ++  GV+ I
Sbjct: 85  RIGHFVE---------AQILEAIGVDYI 103


>gi|312278554|gb|ADQ63211.1| Imidazole glycerol phosphate synthase subunit hisF [Streptococcus
           thermophilus ND03]
          Length = 252

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 45/119 (37%), Gaps = 11/119 (9%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
            ++  ++G + +        L   +  DNR+      D+V  +  +    F    GG+  
Sbjct: 36  ARAYYEAGCDELV------FLDITATSDNRETT---VDMVRRVADQVFIPFTVG-GGIRS 85

Query: 200 MSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWRKISA 257
           +    K+L    D V +  +A+ N  +++   + F N    ++    ++    W    A
Sbjct: 86  VEDMNKMLKAGADKVAVNSSAHANPQLISDCAQKFGNQCVVAAIDAKKMADGSWHVFVA 144


>gi|255026736|ref|ZP_05298722.1| pyridoxal biosynthesis lyase PdxS [Listeria monocytogenes FSL
           J2-003]
          Length = 263

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E AKI E+ G   +      PS      + G   M +P      +  +  A+SIPV  K
Sbjct: 29  AEQAKIAEEAGAVAVMALERVPSD--IRAAGGVARMADP----RIVEEVMNAVSIPVMAK 82

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 83  ARIGHITE---------ARVLEAMGVDYI 102


>gi|256810573|ref|YP_003127942.1| pyridoxine biosynthesis protein [Methanocaldococcus fervens AG86]
 gi|256793773|gb|ACV24442.1| pyridoxine biosynthesis protein [Methanocaldococcus fervens AG86]
          Length = 330

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
           VE A+I E+ G   +      P+      + G   M +P ++ + +     A+SIPV  K
Sbjct: 27  VEQAQIAEEAGAVAVMALERVPAD--IRAAGGVARMSDPALIEEIM----DAVSIPVMAK 80

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
           CRIG   +          + ++  GV+ I
Sbjct: 81  CRIGHTAE---------AEVLEAIGVDMI 100


>gi|218691385|ref|YP_002399597.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           ED1a]
 gi|218428949|emb|CAR09752.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           ED1a]
          Length = 672

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVGAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|209551547|ref|YP_002283464.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhizobium
           leguminosarum bv. trifolii WSM2304]
 gi|226700350|sp|B5ZV92|HIS4_RHILW RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|209537303|gb|ACI57238.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhizobium leguminosarum bv. trifolii WSM2304]
          Length = 248

 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 23/129 (17%), Positives = 50/129 (38%), Gaps = 17/129 (13%)

Query: 99  LNPDIVGDCIAAMCKALSIPVTVKC-RIGVDDQIPAVAL--RNLVKSIKKSGVNGIWIHA 155
            NPD+V +        +++ +  K  ++ V+    A  L    L +  + +GV  I    
Sbjct: 108 RNPDLVIEACRKFPGHVAVGIDAKGGKVAVEGWAEASELGVIELARKFEGAGVAAII--- 164

Query: 156 RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP----SVD 211
                       +  +  +++    E+  E   + +  +GGL  +    ++L      ++
Sbjct: 165 ------YTDIDRDGILAGINWTSTLELA-EAVSIPVIASGGLASLDDVRRMLEPDAQKLE 217

Query: 212 GVMIGRAAY 220
           G + GRA Y
Sbjct: 218 GAISGRALY 226


>gi|325919937|ref|ZP_08181923.1| tRNA-dihydrouridine synthase [Xanthomonas gardneri ATCC 19865]
 gi|325549585|gb|EGD20453.1| tRNA-dihydrouridine synthase [Xanthomonas gardneri ATCC 19865]
          Length = 83

 Score = 35.9 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 12/78 (15%), Positives = 22/78 (28%), Gaps = 6/78 (7%)

Query: 242 PIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHILTVEA 301
           P    V       + A    Y          ++   +H+       P S   R ++   A
Sbjct: 1   PSLALVRDTLLGHLEALHAFY-----GQPQGVRIARKHLGWYAKDHPQSADFRAVVN-RA 54

Query: 302 GASTATHHIIETAFNLMI 319
               A   +    F+ +I
Sbjct: 55  ETPEAQLALTRDYFDALI 72


>gi|307595374|ref|YP_003901691.1| triosephosphate isomerase [Vulcanisaeta distributa DSM 14429]
 gi|307550575|gb|ADN50640.1| triosephosphate isomerase [Vulcanisaeta distributa DSM 14429]
          Length = 223

 Score = 35.9 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SV 210
            +      L G     +R+ P++    V  +K+ NP + +    G+E      + +    
Sbjct: 137 AVAVEPPELIGTGKAVSREKPDVIVKTVELVKRVNPSIPVITGAGIESYEDVKRAVELGT 196

Query: 211 DGVMIGRAAY 220
            GV++  A  
Sbjct: 197 QGVLVASAIV 206


>gi|158343682|gb|ABW35507.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia multivorans]
          Length = 251

 Score = 35.9 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 16/91 (17%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L +  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVIDLAQKFEDYGVESIVYTDIGRDGMLQG-----------INIDATVKLAQAVGIPVIA 197

Query: 193 LNG--GLEDMSQALKILP-SVDGVMIGRAAY 220
             G   LED+ +  +++   V+GV+ GRA Y
Sbjct: 198 SGGLSNLEDIDKLCEVIEEGVEGVICGRAIY 228


>gi|298346785|ref|YP_003719472.1| imidazole glycerol phosphate synthase subunit hisF [Mobiluncus
           curtisii ATCC 43063]
 gi|304389511|ref|ZP_07371474.1| imidazole glycerol phosphate synthase, cyclase subunit [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
 gi|298236846|gb|ADI67978.1| imidazole glycerol phosphate synthase subunit hisF [Mobiluncus
           curtisii ATCC 43063]
 gi|304327321|gb|EFL94556.1| imidazole glycerol phosphate synthase, cyclase subunit [Mobiluncus
           curtisii subsp. curtisii ATCC 35241]
          Length = 263

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L  S   +G + I      A ++G +            ++V +  +E   + + + GG+
Sbjct: 42  ELAASYCAAGADEITFLDVSASVEGRATMA---------EVVQQCAREIF-VPLTVGGGV 91

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             ++   ++L    D V I  AA     ++T +   F 
Sbjct: 92  RSVADVERLLKSGADKVSINTAAIARPELITEIASRFG 129


>gi|222034811|emb|CAP77554.1| 2,4-dienoyl-CoA reductase [NadPH] [Escherichia coli LF82]
 gi|312947651|gb|ADR28478.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           O83:H1 str. NRG 857C]
          Length = 672

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVGAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|138893748|ref|YP_001124201.1| dihydropteroate synthase [Geobacillus thermodenitrificans NG80-2]
 gi|196250791|ref|ZP_03149478.1| dihydropteroate synthase [Geobacillus sp. G11MC16]
 gi|134265261|gb|ABO65456.1| Dihydropteroate synthase, dihydropteroatepyrophosphorylase
           [Geobacillus thermodenitrificans NG80-2]
 gi|196209741|gb|EDY04513.1| dihydropteroate synthase [Geobacillus sp. G11MC16]
          Length = 284

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 36/208 (17%), Positives = 73/208 (35%), Gaps = 29/208 (13%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC--IAAMCKAL 115
           D+ K VE AK +   G + I++                 + L+ ++      + A+   +
Sbjct: 45  DVEKAVEHAKRLVAEGADIIDIGGE------STRPGAEQVPLDEELRRVIPAVRAIASEV 98

Query: 116 SIPVTVKCR-------------IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKG 162
           ++P+++                  ++D   A A  ++       GV  I +H R  +   
Sbjct: 99  NVPISIDTYKAEVARQAIEAGAHIINDVWGAKADPDMAHVAASYGVPIILMHNRHDMAYR 158

Query: 163 LSPKDNRKIPNLDYDIVYE--IKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               D          IV +  +K EN  +     G  +     L+++  +D      AA 
Sbjct: 159 DLISDMIVDLEESICIVKQAGVKDEN-IILDPGIGFAKTFEHNLEVMRRLDEF----AAL 213

Query: 221 KNSAMLTTVDEYFSNPLTGSSPIKTRVD 248
               +L T  + F   +    P++ RV+
Sbjct: 214 GYPLLLGTSRKRFIGHVLD-VPVEERVE 240


>gi|119512336|ref|ZP_01631421.1| inositol-5-monophosphate dehydrogenase [Nodularia spumigena
           CCY9414]
 gi|119462987|gb|EAW43939.1| inositol-5-monophosphate dehydrogenase [Nodularia spumigena
           CCY9414]
          Length = 387

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 12/63 (19%)

Query: 189 LFIGLNGG-LEDMSQALKILPSVDGVMIG----RAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           + I  +GG +        I    DGVMIG    RAA             +   +   SP+
Sbjct: 256 IPIIADGGLITGGDICKCIACGADGVMIGSPFARAAEA-PG------RGYHWGMATPSPV 308

Query: 244 KTR 246
             R
Sbjct: 309 LPR 311


>gi|91212512|ref|YP_542498.1| NADPH 2,4-dienoyl-CoA reductase [Escherichia coli UTI89]
 gi|117625392|ref|YP_858715.1| NADPH 2,4-dienoyl-CoA reductase [Escherichia coli APEC O1]
 gi|218560167|ref|YP_002393080.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           S88]
 gi|91074086|gb|ABE08967.1| NADPH 2,4-dienoyl-CoA reductase [Escherichia coli UTI89]
 gi|115514516|gb|ABJ02591.1| NADPH 2,4-dienoyl-CoA reductase [Escherichia coli APEC O1]
 gi|218366936|emb|CAR04707.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           S88]
 gi|294491317|gb|ADE90073.1| 2,4-dienoyl-CoA reductase [Escherichia coli IHE3034]
 gi|307625305|gb|ADN69609.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           UM146]
 gi|315288872|gb|EFU48270.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 110-3]
 gi|323951386|gb|EGB47261.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli H252]
 gi|323957758|gb|EGB53472.1| NADH:flavin oxidoreductase/NADH oxidase [Escherichia coli H263]
          Length = 672

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 54/191 (28%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + + A+ + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVGAVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|163847638|ref|YP_001635682.1| dihydroorotate dehydrogenase [Chloroflexus aurantiacus J-10-fl]
 gi|222525496|ref|YP_002569967.1| dihydroorotate dehydrogenase [Chloroflexus sp. Y-400-fl]
 gi|163668927|gb|ABY35293.1| dihydroorotate dehydrogenase [Chloroflexus aurantiacus J-10-fl]
 gi|222449375|gb|ACM53641.1| dihydroorotate dehydrogenase [Chloroflexus sp. Y-400-fl]
          Length = 354

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 20/110 (18%), Positives = 42/110 (38%), Gaps = 15/110 (13%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVG-CPSAR-VHEGSFGACLMLNPDIVGD 106
           P+   + G      V  A+++++ G + + LN+   P    +             D   +
Sbjct: 104 PVIGSLNGVSAGGWVRYARLIQEAGADALELNIYFIPVDTNITSSEL-------EDTYVE 156

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            + A+   ++IP+ VK            AL N    + ++G N + +  R
Sbjct: 157 LVRAVRAEITIPLAVKIGPYF------TALPNFAWRLMEAGANALVLFNR 200


>gi|326390353|ref|ZP_08211912.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993630|gb|EGD52063.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 337

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 61/178 (34%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK     GY+ + ++            P +   +  +G  +      + + I  + 
Sbjct: 145 FGEAAKRANLAGYDVVEIHAAHGYLIHEFLSPLSNKRKDEYGGSIENRARFLIEVIDEVR 204

Query: 113 KAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K    + P+ V+      ++  I    +   +  IK   V+ I + +      GL   D 
Sbjct: 205 KNWPENKPIFVRVSADDYMEGGINIDMMVEYINMIKDK-VDLIDVSSG-----GLLNVDI 258

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              P         IKK   ++     G +     A +IL +   D V +GR   +N  
Sbjct: 259 NLYPGYQVKYAETIKKRC-NIKTSAVGLITTQELAEEILSNERADLVALGRELLRNPY 315


>gi|315084387|gb|EFT56363.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL027PA2]
          Length = 279

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 42/221 (19%), Positives = 65/221 (29%), Gaps = 70/221 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 16  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  + P +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMCPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNS 223
            P +     GG+   + A  ++     GV +G   +   N 
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIFKSGNP 229


>gi|293376678|ref|ZP_06622904.1| CutC family protein [Turicibacter sanguinis PC909]
 gi|325845513|ref|ZP_08168803.1| CutC family protein [Turicibacter sp. HGF1]
 gi|292644696|gb|EFF62780.1| CutC family protein [Turicibacter sanguinis PC909]
 gi|325488467|gb|EGC90886.1| CutC family protein [Turicibacter sp. HGF1]
          Length = 224

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 17/92 (18%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AK +E+ G + I L      + + EG                I ++ K++ IPV V  R 
Sbjct: 12  AKTIEECGADRIEL-----VSALTEGGLTPS--------YAIIESVVKSVKIPVNVMVRH 58

Query: 126 GVDDQIPAVALRNL----VKSIKKSGVNGIWI 153
                  +    +L    ++ IK  G NGI +
Sbjct: 59  HAKSFNYSNEEVDLMIRDIEIIKSLGANGIVL 90


>gi|262280381|ref|ZP_06058165.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter calcoaceticus RUH2202]
 gi|262258159|gb|EEY76893.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter calcoaceticus RUH2202]
          Length = 243

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 24/130 (18%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   IV  I K  P+L I + GG+  +      L   V  V+IG  A +    
Sbjct: 60  ------PIHKPIVEAIAKAQPELPIQIGGGIRSLETIEHYLEAGVTFVIIGTKAVQEPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKRFAG 123


>gi|146295548|ref|YP_001179319.1| biotin synthase [Caldicellulosiruptor saccharolyticus DSM 8903]
 gi|145409124|gb|ABP66128.1| iron-only hydrogenase maturation protein HydE [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 358

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 66/185 (35%), Gaps = 38/185 (20%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           L  S +E     Q       ++VE AK   D GY  + L  G                 +
Sbjct: 77  LRRSNKE----AQRYRMQEDEIVEVAKRAYDMGYRTVVLQSG----------------ED 116

Query: 101 P----DIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH-- 154
           P    D V   I  + + + + +T+       ++          K+ +++G +   +   
Sbjct: 117 PYYTKDKVCSIIKKIKEEVDVAITLSIGERSYEEY---------KAFREAGADRYLMRFE 167

Query: 155 -ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENP-DLFIGLNG-GLEDMSQALKILPSVD 211
            + + + +   P  + +        +  +  E      IGL G  ++D++  + ++  +D
Sbjct: 168 TSNRELYQKYHPGMSFENRIECLRWIKSLGYELGTGFLIGLPGQTIDDLANDILLVYELD 227

Query: 212 GVMIG 216
             MIG
Sbjct: 228 SDMIG 232


>gi|20090425|ref|NP_616500.1| pyridoxal biosynthesis lyase PdxS [Methanosarcina acetivorans C2A]
 gi|19915438|gb|AAM04980.1| pyridoxine biosynthesis protein [Methanosarcina acetivorans C2A]
          Length = 350

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 15/86 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I E+ G   +      P+      + G   M +P+IV   I      ++IPV  K RI
Sbjct: 87  ARIAEEAGAVAVMALQAVPAD--IRKAGGVARMADPEIVQQIIET----VTIPVMAKARI 140

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI 151
           G   +          + ++  GV+ +
Sbjct: 141 GHFVE---------AEILEALGVDMV 157


>gi|159184174|ref|NP_353168.2| 2-deoxyribose-5-phosphate aldolase [Agrobacterium tumefaciens str.
           C58]
 gi|159139507|gb|AAK85953.2| 2-deoxyribose-5-phosphate aldolase [Agrobacterium tumefaciens str.
           C58]
          Length = 257

 Score = 35.9 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 58/151 (38%), Gaps = 15/151 (9%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D++ +V   +     G +EI+L +  P  +   G        +   V + IAA+ KA + 
Sbjct: 82  DVATVVAETEAAIGDGADEIDLVI--PYRKFMAG--------DESAVAEMIAAVRKACAA 131

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV +K  +   +      +R   +     G + I     K     ++     +  ++   
Sbjct: 132 PVLLKVILETGELKDKALIRRASEIAIAEGADFIKTSTGK-----VAVNATLEAADIMLQ 186

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            + + KK+      G  G +ED +  L++  
Sbjct: 187 AIRDSKKKVGFKPAGGIGTVEDATLYLRLAE 217


>gi|332076042|gb|EGI86508.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA41301]
          Length = 311

 Score = 35.9 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 19/185 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDI 103
              +   L + G    +     K V++  +  +  LN+ CP   V      A    + + 
Sbjct: 92  ESNRTFFLSLVGMSPEETHTILKKVQESDFRGLTELNLSCP--NVPGKPQIAY---DFET 146

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHAR 156
               +A +    + P+ +K     D      A A+ N      V  +   G NG++I   
Sbjct: 147 TDRILAEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDE 205

Query: 157 KAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVD 211
             +++   G        I       V+   +  NP + I   GG+     A +  L    
Sbjct: 206 SVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGAS 265

Query: 212 GVMIG 216
            V +G
Sbjct: 266 MVQVG 270


>gi|322832479|ref|YP_004212506.1| imidazoleglycerol phosphate synthase, cyclase subunit [Rahnella sp.
           Y9602]
 gi|321167680|gb|ADW73379.1| imidazoleglycerol phosphate synthase, cyclase subunit [Rahnella sp.
           Y9602]
          Length = 257

 Score = 35.9 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   K G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAKEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  ++T + + + 
Sbjct: 85  SLEDASQILQFGADKISINSPALADPTLITRLADRYG 121


>gi|302205286|gb|ADL09628.1| Pyridoxine biosynthesis enzyme [Corynebacterium pseudotuberculosis
           C231]
 gi|308275527|gb|ADO25426.1| Pyridoxine biosynthesis protein [Corynebacterium pseudotuberculosis
           I19]
          Length = 318

 Score = 35.9 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 8/98 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR- 124
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K R 
Sbjct: 55  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 108

Query: 125 -IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
              V+ QI      + +   +         H  K   K
Sbjct: 109 GHFVEAQILESLGVDFIDESEVLSPADYTNHIDKWNFK 146


>gi|149021628|ref|ZP_01835659.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           SP23-BS72]
 gi|147930089|gb|EDK81075.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           SP23-BS72]
 gi|332077178|gb|EGI87640.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA17545]
          Length = 311

 Score = 35.9 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 19/185 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDI 103
              +   L + G    +     K V++  +  +  LN+ CP   V      A    + + 
Sbjct: 92  ESNRTFFLSLVGMSPEETHTILKKVQESDFRGLTELNLSCP--NVPGKPQIAY---DFET 146

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHAR 156
               +A +    + P+ +K     D      A A+ N      V  +   G NG++I   
Sbjct: 147 TDRILAEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDE 205

Query: 157 KAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVD 211
             +++   G        I       V+   +  NP + I   GG+     A +  L    
Sbjct: 206 SVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGAS 265

Query: 212 GVMIG 216
            V +G
Sbjct: 266 MVQVG 270


>gi|24636797|sp|Q8UJ09|DEOC_AGRT5 RecName: Full=Deoxyribose-phosphate aldolase; Short=DERA; AltName:
           Full=2-deoxy-D-ribose 5-phosphate aldolase; AltName:
           Full=Phosphodeoxyriboaldolase; Short=Deoxyriboaldolase
          Length = 259

 Score = 35.9 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 58/151 (38%), Gaps = 15/151 (9%)

Query: 58  DISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSI 117
           D++ +V   +     G +EI+L +  P  +   G        +   V + IAA+ KA + 
Sbjct: 84  DVATVVAETEAAIGDGADEIDLVI--PYRKFMAG--------DESAVAEMIAAVRKACAA 133

Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
           PV +K  +   +      +R   +     G + I     K     ++     +  ++   
Sbjct: 134 PVLLKVILETGELKDKALIRRASEIAIAEGADFIKTSTGK-----VAVNATLEAADIMLQ 188

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            + + KK+      G  G +ED +  L++  
Sbjct: 189 AIRDSKKKVGFKPAGGIGTVEDATLYLRLAE 219


>gi|15900658|ref|NP_345262.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae TIGR4]
 gi|111658346|ref|ZP_01409034.1| hypothetical protein SpneT_02000486 [Streptococcus pneumoniae
           TIGR4]
 gi|116516687|ref|YP_816159.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae D39]
 gi|148985887|ref|ZP_01818981.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae SP3-BS71]
 gi|148989845|ref|ZP_01821139.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae SP6-BS73]
 gi|148992427|ref|ZP_01822122.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae SP9-BS68]
 gi|148997160|ref|ZP_01824814.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae SP11-BS70]
 gi|149007644|ref|ZP_01831261.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           SP18-BS74]
 gi|149010610|ref|ZP_01831981.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae SP19-BS75]
 gi|168484831|ref|ZP_02709776.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC1873-00]
 gi|168486743|ref|ZP_02711251.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC1087-00]
 gi|168488433|ref|ZP_02712632.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae SP195]
 gi|168490851|ref|ZP_02714994.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC0288-04]
 gi|168492913|ref|ZP_02717056.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC3059-06]
 gi|168575423|ref|ZP_02721359.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae MLV-016]
 gi|169832400|ref|YP_001694224.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182683683|ref|YP_001835430.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae CGSP14]
 gi|194397157|ref|YP_002037410.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae G54]
 gi|221231558|ref|YP_002510710.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae ATCC 700669]
 gi|225854271|ref|YP_002735783.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae JJA]
 gi|225856438|ref|YP_002737949.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae P1031]
 gi|225858572|ref|YP_002740082.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae 70585]
 gi|225860737|ref|YP_002742246.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|237650465|ref|ZP_04524717.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae CCRI
           1974]
 gi|237821905|ref|ZP_04597750.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298229127|ref|ZP_06962808.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298255808|ref|ZP_06979394.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|298502548|ref|YP_003724488.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           TCH8431/19A]
 gi|303255823|ref|ZP_07341864.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae BS455]
 gi|303260229|ref|ZP_07346200.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP-BS293]
 gi|303261435|ref|ZP_07347383.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP14-BS292]
 gi|303264102|ref|ZP_07350023.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS397]
 gi|303266287|ref|ZP_07352178.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS457]
 gi|303268726|ref|ZP_07354516.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS458]
 gi|307067366|ref|YP_003876332.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae AP200]
 gi|307127687|ref|YP_003879718.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae 670-6B]
 gi|18285267|sp|Q9X9S0|PYRD_STRPN RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|14972239|gb|AAK74902.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae TIGR4]
 gi|116077263|gb|ABJ54983.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae D39]
 gi|147756860|gb|EDK63900.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae SP11-BS70]
 gi|147760799|gb|EDK67770.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           SP18-BS74]
 gi|147765091|gb|EDK72020.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae SP19-BS75]
 gi|147922033|gb|EDK73157.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae SP3-BS71]
 gi|147924787|gb|EDK75871.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae SP6-BS73]
 gi|147928744|gb|EDK79757.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae SP9-BS68]
 gi|168994902|gb|ACA35514.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae
           Hungary19A-6]
 gi|172041986|gb|EDT50032.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC1873-00]
 gi|182629017|gb|ACB89965.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae CGSP14]
 gi|183570267|gb|EDT90795.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC1087-00]
 gi|183573192|gb|EDT93720.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae SP195]
 gi|183574599|gb|EDT95127.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC0288-04]
 gi|183576843|gb|EDT97371.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae CDC3059-06]
 gi|183578482|gb|EDT99010.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae MLV-016]
 gi|194356824|gb|ACF55272.1| dihydroorotate dehydrogenase A [Streptococcus pneumoniae G54]
 gi|220674018|emb|CAR68531.1| putative dihydroorotate dehydrogenase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225720108|gb|ACO15962.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae 70585]
 gi|225724110|gb|ACO19963.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae JJA]
 gi|225726163|gb|ACO22015.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae P1031]
 gi|225727676|gb|ACO23527.1| dihydroorotate dehydrogenase (dihydroorotate oxidase)(dhodehase)
           (dhodase) (dhod) [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238143|gb|ADI69274.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae
           TCH8431/19A]
 gi|301793922|emb|CBW36318.1| putative dihydroorotate dehydrogenase [Streptococcus pneumoniae
           INV104]
 gi|301799779|emb|CBW32348.1| putative dihydroorotate dehydrogenase [Streptococcus pneumoniae
           OXC141]
 gi|301801610|emb|CBW34308.1| putative dihydroorotate dehydrogenase [Streptococcus pneumoniae
           INV200]
 gi|302597207|gb|EFL64312.1| dihydroorotate dehydrogenase 1A [Streptococcus pneumoniae BS455]
 gi|302637569|gb|EFL68056.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP14-BS292]
 gi|302638553|gb|EFL69017.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae SP-BS293]
 gi|302641786|gb|EFL72143.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS458]
 gi|302644217|gb|EFL74473.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS457]
 gi|302646507|gb|EFL76733.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae BS397]
 gi|306408903|gb|ADM84330.1| Dihydroorotate dehydrogenase [Streptococcus pneumoniae AP200]
 gi|306484749|gb|ADM91618.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae 670-6B]
 gi|327390120|gb|EGE88463.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA04375]
 gi|332073112|gb|EGI83591.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA17570]
 gi|332202627|gb|EGJ16696.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA41317]
 gi|332203917|gb|EGJ17984.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA47368]
 gi|332204772|gb|EGJ18837.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae GA47901]
          Length = 311

 Score = 35.9 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 19/185 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDI 103
              +   L + G    +     K V++  +  +  LN+ CP   V      A    + + 
Sbjct: 92  ESNRTFFLSLVGMSPEETHTILKKVQESDFRGLTELNLSCP--NVPGKPQIAY---DFET 146

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIWIHAR 156
               +A +    + P+ +K     D      A A+ N      V  +   G NG++I   
Sbjct: 147 TDRILAEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDE 205

Query: 157 KAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVD 211
             +++   G        I       V+   +  NP + I   GG+     A +  L    
Sbjct: 206 SVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGAS 265

Query: 212 GVMIG 216
            V +G
Sbjct: 266 MVQVG 270


>gi|308174817|ref|YP_003921522.1| anionic nitroalkane dioxygenase [Bacillus amyloliquefaciens DSM 7]
 gi|307607681|emb|CBI44052.1| putative anionic nitroalkane dioxygenase [Bacillus
           amyloliquefaciens DSM 7]
 gi|328554771|gb|AEB25263.1| anionic nitroalkane dioxygenase [Bacillus amyloliquefaciens TA208]
 gi|328913126|gb|AEB64722.1| putative anionic nitroalkane dioxygenase [Bacillus
           amyloliquefaciens LL3]
          Length = 479

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 37/109 (33%), Gaps = 8/109 (7%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K +                K+ ++ G++ + +   +A     S    +  P L    +  
Sbjct: 277 KLKKSGCFLFGTATTPEEAKAFEERGMDAVILQGIEAGGHRGSFLPVKGEPALGLMALIP 336

Query: 182 IKKENPDLFIGLNGGLEDMS--QALKILPSVDGVMIGRAAYKNSAMLTT 228
             K+   + +   GG+ D    QA + L   DGV +G        +L  
Sbjct: 337 QAKDALKIPVIAAGGIFDRRGVQAARCL-GADGVQVG-----TPFLLCE 379


>gi|168183831|ref|ZP_02618495.1| 2-enoate reductase [Clostridium botulinum Bf]
 gi|182673035|gb|EDT84996.1| 2-enoate reductase [Clostridium botulinum Bf]
          Length = 665

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 36/206 (17%), Positives = 73/206 (35%), Gaps = 47/206 (22%)

Query: 62  LVEAAKIVEDFGYNEINLNVGCPSARVHEG----------------SFGACLMLNPDIVG 105
             E+A+I +  G++ + ++       VHEG                 +G  L        
Sbjct: 158 FGESAEIAKKAGFDGVEIHA------VHEGYLLDQFAISFFNHRTDEYGGSLENRLRFAC 211

Query: 106 DCIAAMCKAL--SIPVTVK----------CRIGVDDQIPAVALRNL------VKSIKKSG 147
           + +  + K      PV+++          C+ G+ D+      R++       K +  +G
Sbjct: 212 EVVQEIKKRCGQDFPVSLRYSIKSFIKDWCKGGLPDEEFEERGRDIPEGIEAAKILVAAG 271

Query: 148 VNGIWIHARK--AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS-QAL 204
            + +        +      P   +K   L Y+   EI K+  D+ I   G +ED    + 
Sbjct: 272 YDALNGDVGSYDSWYWSHPPMYQKKGLYLPYN---EILKKVVDVPIITAGRMEDPELSSD 328

Query: 205 KILPS-VDGVMIGRAAYKNSAMLTTV 229
            IL    D + +GR    ++ +   +
Sbjct: 329 AILSGKTDMIALGRPLLADAEIPNKI 354


>gi|156339198|ref|XP_001620109.1| hypothetical protein NEMVEDRAFT_v1g223466 [Nematostella vectensis]
 gi|156204496|gb|EDO28009.1| predicted protein [Nematostella vectensis]
          Length = 802

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P L I + GG+  +      +   V  V+IG  A K    +    +
Sbjct: 352 PVNGEVVTAIAKRYPHLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKQPEFVAEACK 411

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++S       A+   + G
Sbjct: 412 AFPGKVIVGLDAKDGFVATDGWAEVSTVQVIDLAKRFEADG 452


>gi|125975369|ref|YP_001039279.1| imidazole glycerol phosphate synthase subunit HisF [Clostridium
           thermocellum ATCC 27405]
 gi|256005485|ref|ZP_05430447.1| imidazoleglycerol phosphate synthase, cyclase subunit [Clostridium
           thermocellum DSM 2360]
 gi|281419329|ref|ZP_06250344.1| imidazoleglycerol phosphate synthase, cyclase subunit [Clostridium
           thermocellum JW20]
 gi|167012152|sp|A3DJF7|HIS6_CLOTH RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|125715594|gb|ABN54086.1| imidazole glycerol phosphate synthase subunit hisF [Clostridium
           thermocellum ATCC 27405]
 gi|255990540|gb|EEU00660.1| imidazoleglycerol phosphate synthase, cyclase subunit [Clostridium
           thermocellum DSM 2360]
 gi|281406949|gb|EFB37212.1| imidazoleglycerol phosphate synthase, cyclase subunit [Clostridium
           thermocellum JW20]
 gi|316939484|gb|ADU73518.1| imidazoleglycerol phosphate synthase, cyclase subunit [Clostridium
           thermocellum DSM 1313]
          Length = 253

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            +     K+G + +           L    + +  N+  D+V  + ++    F    GG+
Sbjct: 34  EIASYYDKAGADELTF---------LDITASAEARNIMIDVVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    +IL    D V I  AA K   +++     F 
Sbjct: 84  RTVEDFREILKAGADKVSINSAAVKRPELISEAASRFG 121


>gi|325672855|ref|ZP_08152549.1| oxidoreductase [Rhodococcus equi ATCC 33707]
 gi|325556108|gb|EGD25776.1| oxidoreductase [Rhodococcus equi ATCC 33707]
          Length = 662

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 40/193 (20%), Positives = 70/193 (36%), Gaps = 27/193 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEIN-LNVGCPSARVHEGSFGACLMLNPDIVG 105
           E  + LQ  G D        +IV   GY     LN   P+  V E  +G  L     ++ 
Sbjct: 156 EGAVRLQTAGLDG------VEIVASHGYLPAQFLN---PNLNVREDRYGGSLENRMRMLR 206

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVA----LRNLVKSIKKSG-VNGIWIHARKAIL 160
           +   A+ +A+     V  R+  D+             L K++   G V+ + +    +  
Sbjct: 207 ETARAVRQAVGPDFVVGVRLSADENTYDATGESDTIALCKALDADGYVDYLNVTEGTSAS 266

Query: 161 KGLSPKDNRKIPNLDYDIVY------EIKKENPDLFIGLNGGLEDMSQALKILP--SVDG 212
            G S      +P + Y+ +Y      +IKK+     +   G +    +A  +L     D 
Sbjct: 267 TGGSTHI---VPPMHYEAMYTAPSAAKIKKQVSVPVLVA-GRINQPHEAEIVLASGQADA 322

Query: 213 VMIGRAAYKNSAM 225
             + RA   +  M
Sbjct: 323 CAMTRALICDPEM 335


>gi|86610118|ref|YP_478880.1| isopentenyl pyrophosphate isomerase [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558660|gb|ABD03617.1| isopentenyl-diphosphate delta-isomerase, type 2 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 379

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 47/128 (36%), Gaps = 21/128 (16%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR--------KAI 159
           I  +   L +PV VK       ++       + + + + GV  + +           +A 
Sbjct: 208 IEQLVAQLPVPVVVK-------EVGNGLSAKVAQRLAECGVAALDVAGAGGTSWSEVEAH 260

Query: 160 LKGLSPKDNRKIPNLDYDI-----VYEIKKENPDLFIGLNGGLED-MSQALKILPSVDGV 213
            +  + K        D+ I     + EI++  PDL +  +GG+ + +  A  I    D V
Sbjct: 261 RQPDALKKRIAHSFRDWGIPTALSLLEIRRLLPDLPLVASGGIRNGIDAAKAIRLGADVV 320

Query: 214 MIGRAAYK 221
            +   A  
Sbjct: 321 GMAAPALH 328


>gi|18978035|ref|NP_579392.1| imidazoleglycerol-phosphate synthase, cyclase subunit [Pyrococcus
           furiosus DSM 3638]
 gi|18893820|gb|AAL81787.1| imidazoleglycerol-phosphate synthase, cyclase subunit [Pyrococcus
           furiosus DSM 3638]
          Length = 266

 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 44/115 (38%), Gaps = 15/115 (13%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVY 180
           +K +   D   P      L K  +  G++ I           L    + +   +  D+V 
Sbjct: 36  IKFKNIRDAGDP----IELAKRYESEGIDEIVF---------LDITASYEKRKILLDLVE 82

Query: 181 EIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + +E    F    GG+  + +A +I+    D + I  AA +N +++  + +   
Sbjct: 83  RVAEEIYVPFTVG-GGIRTVEEAREIIRRGADKIFINTAAVENPSLIKEIADLIG 136


>gi|332360576|gb|EGJ38386.1| FMN reductase [Streptococcus sanguinis SK1056]
          Length = 367

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 23/166 (13%), Positives = 60/166 (36%), Gaps = 22/166 (13%)

Query: 60  SKLVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACL---MLNPD-IVGD 106
              + A +     G++ + L             P + V +  +G  L   +  P  ++  
Sbjct: 147 EDFLSAIRRAIQAGFDGVELHGANTYLIQQFVSPHSNVRQDKWGGSLNNRLRFPKTLLKR 206

Query: 107 CIAAMCKALSIPVTVKCRIGVDD-QIPAVALRNLVKSIKK---SGVNGIWIHARKAILKG 162
               + +    P  +  R   ++ + P + L + ++ +++     V+ + I         
Sbjct: 207 AKQLVKEEADRPFLIGYRFSPEEIEEPGIQLYDTLQLLEQLIYHQVDYLHISTSDVWRS- 265

Query: 163 LSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP 208
            S +D++    +   I+   KK N  + +   G ++    A ++L 
Sbjct: 266 -SIRDSQDSEPVIQKII---KKINGRVPLIGVGQIKTKQDAQRVLD 307


>gi|328544880|ref|YP_004304989.1| dihydroorotate dehydrogenase 2 [polymorphum gilvum SL003B-26A1]
 gi|326414622|gb|ADZ71685.1| Dihydroorotate dehydrogenase 2 [Polymorphum gilvum SL003B-26A1]
          Length = 341

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 40/102 (39%), Gaps = 14/102 (13%)

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD--------- 167
           +PV +K    VD Q    AL ++ + +  + V+G+ +        GL+ +          
Sbjct: 188 VPVLLKISPDVDQQ----ALEDIAEEVTATAVDGLIVSNTTVSRAGLTERHHAQEAGGLS 243

Query: 168 NRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKILP 208
            R +      ++  ++K   P L I   GG++    A   + 
Sbjct: 244 GRPLFRKSTIVLARMRKLVGPSLPIIGVGGIDSPQAAWTKIT 285


>gi|298675376|ref|YP_003727126.1| glutamate synthase [Methanohalobium evestigatum Z-7303]
 gi|298288364|gb|ADI74330.1| Glutamate synthase (NADPH) [Methanohalobium evestigatum Z-7303]
          Length = 503

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 26/129 (20%), Positives = 46/129 (35%), Gaps = 22/129 (17%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
           +   I A+ +A +   PV VK             +  +   + ++G + + I   +    
Sbjct: 290 LSQLIYALKEATNYEKPVGVKISA-------VHNVAAIASGVVRAGADVLTIDGYRGG-S 341

Query: 162 GLSP---KDNRKIP------NLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPSVD 211
           G SP   +DN  IP       +D  +  E  +    +     G +      A  +    D
Sbjct: 342 GASPMVIRDNVGIPIELALATVDQRLRDEGIRNRASILCA--GSIRSSADVAKAVALGAD 399

Query: 212 GVMIGRAAY 220
            V+IG AA 
Sbjct: 400 AVVIGTAAL 408


>gi|228473659|ref|ZP_04058409.1| tryptophan synthase, alpha subunit [Capnocytophaga gingivalis ATCC
           33624]
 gi|228274873|gb|EEK13688.1| tryptophan synthase, alpha subunit [Capnocytophaga gingivalis ATCC
           33624]
          Length = 253

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 20/118 (16%), Positives = 40/118 (33%), Gaps = 16/118 (13%)

Query: 115 LSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-----WIHARKAILKGLSPKDNR 169
           L   V V  R  +   +P    + LV+ ++   +  I         R A +  L      
Sbjct: 112 LEKCVVVGIRGLIIPDLPYEEAQELVEKLRAHHIAFIPLVSVTSQGRIAPIVSLGEGFVY 171

Query: 170 KIPNLDYDIVYEI-----------KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
            I +L      ++            +    L + L  G++  +   ++    DGV++G
Sbjct: 172 AIGSLGVTGSKQVDLPRLKEFITQVRAQTSLPVSLGFGIKTHADVEQMRQYADGVIVG 229


>gi|220915927|ref|YP_002491231.1| dihydroorotate dehydrogenase [Anaeromyxobacter dehalogenans 2CP-1]
 gi|219953781|gb|ACL64165.1| dihydroorotate dehydrogenase [Anaeromyxobacter dehalogenans 2CP-1]
          Length = 328

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 11/110 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E P+   + G+      E A+ +E  G + + LN+        E               +
Sbjct: 99  EIPVIASLNGSAAGGWTEFARDIEQAGADALELNL-----YAVEADPAVSAAEVEARYLE 153

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++A+  A++IPV VK            AL +    +   GVNGI +  R
Sbjct: 154 AVSAVRDAVTIPVAVKLSPYF------TALAHFCARLDALGVNGIVLFNR 197


>gi|145295651|ref|YP_001138472.1| dihydroorotate dehydrogenase 2 [Corynebacterium glutamicum R]
 gi|166199347|sp|A4QEA4|PYRD_CORGB RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|140845571|dbj|BAF54570.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 371

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 18/112 (16%), Positives = 43/112 (38%), Gaps = 11/112 (9%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGV---------NGIWIHARK 157
            +AA+ ++ ++PV VK    + D+    A+ +L   +K +G+          G+   A +
Sbjct: 210 ILAAVQESTTVPVLVKIAPDLSDED-IDAVADLAVELKLAGIVATNTTISREGLNTPAGE 268

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
               G        +     +++  +       + +   GG+    QA + + 
Sbjct: 269 VEAMGAGGISGAPVAARSLEVLKRLYARVGKEMVLISVGGISTPEQAWERIT 320


>gi|55378491|ref|YP_136341.1| pyridoxal biosynthesis lyase PdxS [Haloarcula marismortui ATCC
           43049]
 gi|68565703|sp|Q5V1G7|PDXS_HALMA RecName: Full=Pyridoxal biosynthesis lyase pdxS
 gi|55231216|gb|AAV46635.1| SOR/SNZ family [Haloarcula marismortui ATCC 43049]
          Length = 302

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 15/86 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G   +      P+        G   M +P  + + I      +SIPV  K RI
Sbjct: 39  ARIAEDAGAVAVMHLESVPAD--IRKRGGVARMADPSKLEEIIEE----VSIPVMGKARI 92

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI 151
           G   +          + ++ +G + +
Sbjct: 93  GHTAE---------AQILEAAGADMV 109


>gi|27380203|ref|NP_771732.1| oxidoreductase [Bradyrhizobium japonicum USDA 110]
 gi|27353357|dbj|BAC50357.1| bll5092 [Bradyrhizobium japonicum USDA 110]
          Length = 326

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 22/127 (17%), Positives = 43/127 (33%), Gaps = 14/127 (11%)

Query: 97  LMLNPDIVGDCIAAMCKAL------SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
           L   P+++   +AA   A+        P   K R      I  V    + +    +G + 
Sbjct: 76  LAKRPELLDIAVAAKPSAIMLSFGDPAPFVPKIRSAGARLICQVQDEAMARQALDAGADI 135

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED-MSQALKILPS 209
           +     +A   G S      +P +       +      + +   GG+ D    A  ++  
Sbjct: 136 LIAQGTEAGGHGASRTTVDLVPAV-------VDLAAGRVPVVAAGGIADGRGLAAMMMLG 188

Query: 210 VDGVMIG 216
             GV++G
Sbjct: 189 ASGVLLG 195


>gi|34762969|ref|ZP_00143947.1| Inosine-5'-monophosphate dehydrogenase [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
 gi|27887357|gb|EAA24449.1| Inosine-5'-monophosphate dehydrogenase [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
          Length = 488

 Score = 35.9 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 14/78 (17%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           V ++ K+GV+ I + +     +G+             +++ EIKK  PDL +   G +  
Sbjct: 235 VSALVKAGVDIITVDSAHGHSQGVI------------NMIKEIKKNFPDLDVIG-GNIVT 281

Query: 200 MSQALKILP-SVDGVMIG 216
              A +++   V  V +G
Sbjct: 282 AEAAKELIEAGVSAVKVG 299


>gi|300857549|ref|YP_003782532.1| pyridoxine biosynthesis protein [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300685003|gb|ADK27925.1| pyridoxine biosynthesis protein [Corynebacterium pseudotuberculosis
           FRC41]
          Length = 302

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 8/98 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCR- 124
           A+I ED G + +      P+        G   M +PD++   +     A+SIPV  K R 
Sbjct: 38  ARIAEDAGASAVMALERVPAD--IRSQGGVARMSDPDLIEGIV----NAVSIPVMAKARI 91

Query: 125 -IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK 161
              V+ QI      + +   +         H  K   K
Sbjct: 92  GHFVEAQILESLGVDFIDESEVLSPADYTNHIDKWNFK 129


>gi|300709387|ref|YP_003735201.1| dihydroorotate dehydrogenase 2 [Halalkalicoccus jeotgali B3]
 gi|299123070|gb|ADJ13409.1| dihydroorotate dehydrogenase 2 [Halalkalicoccus jeotgali B3]
          Length = 352

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 61/178 (34%), Gaps = 23/178 (12%)

Query: 67  KIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
           + + ++G +   +NV  P+        G   +         + A+ +A + P+ VK    
Sbjct: 166 RRLAEYG-DFFVVNVSSPNTPGLRDLQGEAHLR------GILTALREAGANPLLVKLSP- 217

Query: 127 VDDQIPAVALRNLVKSIKKSGVNGI----WIHARKAILKGLSPKD-----NRKIPNLDYD 177
               + + A+ + +  +    ++GI        R   L+G    +      R I     D
Sbjct: 218 ---DLSSGAIADAIGVVSDLNLDGIVATNTSAERPESLRGRHRNETGGLSGRPIEPRSTD 274

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKN-SAMLTTVDEYF 233
           ++  I     D+ I   GG+   + A  KI      V +         ++   + E  
Sbjct: 275 VIRFIATRT-DVPIVGVGGVFTAADAYRKIRAGASLVQLYTGLVYRGPSIAKEISEGL 331


>gi|291541897|emb|CBL15007.1| tryptophan synthase, alpha chain [Ruminococcus bromii L2-63]
          Length = 256

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 20/116 (17%), Positives = 37/116 (31%), Gaps = 16/116 (13%)

Query: 121 VKCRIGVDDQIPAVALRNLVKSIKKSGVNGI-----WIHARKAILKGLSPKDNRKIPNLD 175
                 +    P      L    +K G++ I       H R  ++   +      + ++ 
Sbjct: 115 CGISAVIVPDTPYEEKHELTDYSRKYGIDVISLIAPTSHERIKMIAKEAEGFVYCVSSMG 174

Query: 176 YDIVY-----------EIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
              V             + K   D+   +  G+    QA K+  S DGV++G A  
Sbjct: 175 VTGVRSEITTDVGEMVRLVKSVKDIPCAIGFGISTPEQAKKMSESADGVIVGSAIV 230


>gi|154503115|ref|ZP_02040175.1| hypothetical protein RUMGNA_00939 [Ruminococcus gnavus ATCC 29149]
 gi|153796109|gb|EDN78529.1| hypothetical protein RUMGNA_00939 [Ruminococcus gnavus ATCC 29149]
          Length = 254

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 20/117 (17%), Positives = 42/117 (35%), Gaps = 12/117 (10%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+   +G + +      A   G              D+V E+ K    +   + GG+
Sbjct: 34  EIAKAYDAAGADELVFLDITASSDGRGTVI---------DMVREVAK-CVFIPFTVGGGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTT-VDEYFSNPLTGSSPIKTRVDKDFW 252
             +     +L    D + I  +A  N  ++    D++ S  +  +   + R D+  W
Sbjct: 84  RTVEDFKALLREGADKISINSSAIANPQLIRDAADKFGSQCVVVAIDARKREDRSGW 140


>gi|296111764|ref|YP_003622146.1| cyclase [Leuconostoc kimchii IMSNU 11154]
 gi|295833296|gb|ADG41177.1| cyclase [Leuconostoc kimchii IMSNU 11154]
          Length = 254

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
           +   + + +G + +      A L+G S            D++  +      + +   GG+
Sbjct: 35  DAAIAYQNAGADELVFLDISATLEGRSTMI---------DMIERVSSAVF-IPLTAGGGV 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            D++    I+    D V +  AA  N  ++    E F 
Sbjct: 85  NDLASMRAIIKAGADKVFLNSAAVANPYLIRQGAELFG 122


>gi|256158607|ref|ZP_05456494.1| tryptophan synthase subunit alpha [Brucella ceti M490/95/1]
 gi|256254015|ref|ZP_05459551.1| tryptophan synthase subunit alpha [Brucella ceti B1/94]
 gi|261221156|ref|ZP_05935437.1| tryptophan synthase subunit alpha [Brucella ceti B1/94]
 gi|265997116|ref|ZP_06109673.1| tryptophan synthase subunit alpha [Brucella ceti M490/95/1]
 gi|260919740|gb|EEX86393.1| tryptophan synthase subunit alpha [Brucella ceti B1/94]
 gi|262551584|gb|EEZ07574.1| tryptophan synthase subunit alpha [Brucella ceti M490/95/1]
          Length = 279

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
           + V  IKK + +L I +  G++   QA  I    DGV++G A     A+   +DE
Sbjct: 196 EAVRHIKK-STNLPICVGFGVKTPEQAAAIATHADGVVVGTAIVN--AIAGELDE 247


>gi|237742231|ref|ZP_04572712.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 4_1_13]
 gi|229429879|gb|EEO40091.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 4_1_13]
          Length = 487

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 14/78 (17%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           V ++ K+GV+ I + +     +G+             +++ EIKK  PDL +   G +  
Sbjct: 234 VGALVKAGVDIITVDSAHGHSQGVI------------NMIKEIKKNFPDLDVIG-GNIVT 280

Query: 200 MSQALKILP-SVDGVMIG 216
              A +++   V  V +G
Sbjct: 281 AEAAKELIEAGVSAVKVG 298


>gi|170076894|ref|YP_001733532.1| inosine 5-monophosphate dehydrogenase [Synechococcus sp. PCC 7002]
 gi|169884563|gb|ACA98276.1| IMP dehydrogenase family protein [Synechococcus sp. PCC 7002]
          Length = 387

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 21/63 (33%), Gaps = 12/63 (19%)

Query: 189 LFIGLNGGLEDM-SQALKILPSVDGVMIG----RAAYKNSAMLTTVDEYFSNPLTGSSPI 243
           + I  +GG+         I    D VMIG    RAA             F   +   SP+
Sbjct: 256 VPIIADGGIVTGGDICKCIASGADAVMIGSPIARAAEA-PG------RGFHWGMATPSPV 308

Query: 244 KTR 246
             R
Sbjct: 309 LPR 311


>gi|187922423|ref|YP_001894065.1| CutC family protein [Burkholderia phytofirmans PsJN]
 gi|187713617|gb|ACD14841.1| CutC family protein [Burkholderia phytofirmans PsJN]
          Length = 231

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 27/114 (23%), Positives = 40/114 (35%), Gaps = 17/114 (14%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A++    G + + L        V     G    L P +    I A+  A+ IPV V  R 
Sbjct: 15  ARVAAQAGADRLEL--------VTAMGEGG---LTPSL--GLIEAVVAAVEIPVNVIVRP 61

Query: 126 G----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
                V D      +   V+++  +G NGI I    A  +       R I   D
Sbjct: 62  HSRSFVYDADDYAVMLRDVRAVTAAGANGIVIGMLNAAGEIDREGLARAIDAAD 115


>gi|5578893|emb|CAB51330.1| dihydroorotate dehydrogenase [Streptococcus pneumoniae]
          Length = 311

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 62/185 (33%), Gaps = 19/185 (10%)

Query: 45  TQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPDI 103
              +   L + G    +     K V++  +  +  LN+ CP   V      A    + + 
Sbjct: 92  ESNRTFFLSLVGMSPEETHTILKKVQESDFRGLTELNLSCP--NVPGKPQIAY---DFET 146

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVD----DQIPAVAL---RNLVKSIKKSGVNGIWIHAR 156
               +A +    + P+ +K     D    DQ  A+        V  +   G NG++I   
Sbjct: 147 TDRILAEVFAYFTKPLGIKLPPYFDIVYFDQAAAIFNKYPLKFVNCVNSIG-NGLYIEDE 205

Query: 157 KAILK---GLSPKDNRKIPNLDYDIVYEIKKE-NPDLFIGLNGGLEDMSQALKI-LPSVD 211
             +++   G        I       V+   +  NP + I   GG+     A +  L    
Sbjct: 206 SVVIRPKNGFGGIGGEYIKPTALANVHAFYQRLNPQIQIIGTGGVLTGRDAFEHILCGAS 265

Query: 212 GVMIG 216
            V +G
Sbjct: 266 MVQVG 270


>gi|150016629|ref|YP_001308883.1| tryptophan synthase, alpha subunit [Clostridium beijerinckii NCIMB
           8052]
 gi|229558002|sp|A6LU97|TRPA_CLOB8 RecName: Full=Tryptophan synthase alpha chain
 gi|149903094|gb|ABR33927.1| tryptophan synthase, alpha subunit [Clostridium beijerinckii NCIMB
           8052]
          Length = 258

 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 18/110 (16%), Positives = 45/110 (40%), Gaps = 4/110 (3%)

Query: 116 SIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL---KGLSPKDNRKIP 172
            +P+  +  +    +   + L  LV    K  +  I   A+  +       +  + + + 
Sbjct: 130 DVPLEERGDLDKICEDNCIYLIPLVARTSKDRIAAITKGAKGFVYCVSTNGTTGERKTLD 189

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKN 222
           +  ++ + E++K N D+ + +  G+       ++    DGV++G A  K 
Sbjct: 190 SGTHEYLEEVRK-NVDIPMCIGFGISSKEVVKEVKDYCDGVIVGSAIVKR 238


>gi|307251502|ref|ZP_07533409.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306860966|gb|EFM92972.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 248

 Score = 35.9 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 26  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 75

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++T + + F 
Sbjct: 76  TIEDAEKLFAFGADKISINSPALADPNLITALADRFG 112


>gi|186476422|ref|YP_001857892.1| dihydroorotate dehydrogenase 2 [Burkholderia phymatum STM815]
 gi|226710752|sp|B2JKL9|PYRD_BURP8 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|184192881|gb|ACC70846.1| Dihydroorotate oxidase [Burkholderia phymatum STM815]
          Length = 344

 Score = 35.9 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 8/99 (8%)

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD------NRK 170
           +P+ +K    +DD+        L++   +  +      +R A+ +GL   D       R 
Sbjct: 215 VPLALKIAPDLDDEQVKSIADTLLRHQFEGVIATNTTLSRTAV-QGLPHADEAGGLSGRP 273

Query: 171 IPNLDYDIVYEIKKENP-DLFIGLNGGLEDMSQALKILP 208
           + +   +++ +++ E   D+ I   GG+   + A   L 
Sbjct: 274 VFDASNEVIRKLRAEVGGDVPIIGVGGIFSGADAQAKLD 312


>gi|182678890|ref|YP_001833036.1| inosine-5'-monophosphate dehydrogenase [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182634773|gb|ACB95547.1| inosine-5'-monophosphate dehydrogenase [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 496

 Score = 35.9 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 1/85 (1%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            VA  +  K++  +G + I +      +          +P L   +         ++ + 
Sbjct: 284 NVATADGAKALIDAGADAIKVGIGPGSICTTRMVAGVGVPQLTAIMDCAEVAHAANVPVI 343

Query: 193 LNGGLE-DMSQALKILPSVDGVMIG 216
            +GG++     A  +    D VMIG
Sbjct: 344 GDGGIKYSGDLAKAVAAGADCVMIG 368


>gi|194336845|ref|YP_002018639.1| inosine-5'-monophosphate dehydrogenase [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309322|gb|ACF44022.1| inosine-5'-monophosphate dehydrogenase [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 499

 Score = 35.9 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 35/100 (35%), Gaps = 8/100 (8%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            VA    V+ + ++G + + +      +          +P L   I    +    +  I 
Sbjct: 285 NVATSEAVRDLIEAGADCVKVGIGPGSICTTRIVAGVGMPQLTAIINCAEEAAKTNTPII 344

Query: 193 LNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDE 231
            +GG++     A  +    D VMIG       ++    DE
Sbjct: 345 ADGGVKYSGDIAKALAAGADSVMIG-------SIFAGTDE 377


>gi|134294521|ref|YP_001118256.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           vietnamiensis G4]
 gi|167011516|sp|A4JAW8|HIS4_BURVG RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|134137678|gb|ABO53421.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           vietnamiensis G4]
 gi|229424439|gb|ACQ65656.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia vietnamiensis]
          Length = 251

 Score = 35.9 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 16/91 (17%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L +  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVIDLARKFEDYGVESIVYTDIGRDGMLQG-----------INIDATVKLAQAVGIPVIA 197

Query: 193 LNG--GLEDMSQALKILP-SVDGVMIGRAAY 220
             G   L D+    ++    V+GV+ GRA Y
Sbjct: 198 SGGLSNLTDIENLCEVEEHGVEGVICGRAIY 228


>gi|308049419|ref|YP_003912985.1| imidazole glycerol phosphate synthase subunit hisF [Ferrimonas
           balearica DSM 9799]
 gi|307631609|gb|ADN75911.1| imidazole glycerol phosphate synthase subunit hisF [Ferrimonas
           balearica DSM 9799]
          Length = 257

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 14/97 (14%), Positives = 36/97 (37%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L       G + +  +   A   G +         ++   V  + ++  D+   + GG++
Sbjct: 35  LAARYAAEGADELVFYDITASADGRT---------VEKSWVARVAEQL-DIPFCVAGGIK 84

Query: 199 DMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A  IL    D + +   A  +  ++  +++ F 
Sbjct: 85  TIEDAQAILADGADKISVNSPALADPNLINRLNDRFG 121


>gi|291334141|gb|ADD93811.1| hypothetical protein [uncultured marine bacterium
           MedDCM-OCT-S05-C362]
          Length = 241

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 56/175 (32%), Gaps = 21/175 (12%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EA +  E  G++ I L+            P A   E  +G  ++       +    M  A
Sbjct: 15  EAVQRCERIGFDAIELHGAHGYLVSSFLSPIANRREDEYGGDIINRMRYPLELFTKMRDA 74

Query: 115 L--SIPVTVKCR-IGVDDQ-IPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
                P+ V+      DDQ +         +++K  G +   I        G +     +
Sbjct: 75  WPDGKPMGVRFNGTDWDDQGLTTEDAITFGRALKDVGCDFFDISG------GGNSMARPQ 128

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
           +       + +  K   ++     G + D   A K++   S D + + R      
Sbjct: 129 VGPGYQAHLAKAVKHATNIPTMAVGMIRDPKLAEKLIADSSCDMIALARGLLYEP 183


>gi|302382152|ref|YP_003817975.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Brevundimonas subvibrioides ATCC 15264]
 gi|302192780|gb|ADL00352.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Brevundimonas subvibrioides ATCC 15264]
          Length = 244

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 177 DIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
           D++ E+ +  PDL +  +GG+  +           DG ++GRA Y
Sbjct: 186 DLLAEVIRRRPDLKVQASGGVSSLEDLKAARAIGCDGAIVGRAIY 230


>gi|227502773|ref|ZP_03932822.1| pyridoxine biosynthesis enzyme [Corynebacterium accolens ATCC
           49725]
 gi|227076503|gb|EEI14466.1| pyridoxine biosynthesis enzyme [Corynebacterium accolens ATCC
           49725]
          Length = 465

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 40/221 (18%), Positives = 67/221 (30%), Gaps = 68/221 (30%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I ED G + +      P+        G   M +P+++   +     A+SIPV  K RI
Sbjct: 202 ARIAEDAGASAVMALERVPAD--IRAQGGVARMSDPELIEGIV----DAVSIPVMAKARI 255

Query: 126 --------------GVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                            D+   ++  + V  I K                       G  
Sbjct: 256 GHFVEAQILGELGVDFIDESEVLSPADYVNHINKWDFDVPFVCGATNLGEALRRITEGAA 315

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKKENP 187
            I                    I A  A L+ L   +           YD+V E+ +   
Sbjct: 316 MIRSKGEAGTGDVSEAVKHLRTIRAEIARLQHLDRDELYVAAKELQAPYDLVAEVAETGK 375

Query: 188 DLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
              +  + GG+   + A  +     +GV +G   +   N A
Sbjct: 376 LPVVLFVAGGVATPADAALVRQMGAEGVFVGSGIFKSGNPA 416


>gi|306833014|ref|ZP_07466146.1| dihydroorotate dehydrogenase A [Streptococcus bovis ATCC 700338]
 gi|304424913|gb|EFM28047.1| dihydroorotate dehydrogenase A [Streptococcus bovis ATCC 700338]
          Length = 311

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 38/198 (19%), Positives = 62/198 (31%), Gaps = 21/198 (10%)

Query: 33  LRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSARVHEG 91
              D    L  +   K   L + G    +     K+V+D  Y   + LN+ CP   V   
Sbjct: 80  YYLDYVTELQNTPNSKHHFLSLVGMSEEETHTILKVVQDSDYQGLVELNLSCP--NVPGK 137

Query: 92  SFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIK 144
              A    + +     +  +    + P+ VK     D      A A+ N      V  I 
Sbjct: 138 PQIAY---DFETTETLLRDIFTYFTKPLGVKLPPYFDIAHFDRAAAIFNQFPLTFVNCIN 194

Query: 145 KSGVNGIWIHA-----RKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             G   I          K    G+     +     +    Y+  + NP + I   GG++ 
Sbjct: 195 SIGNGLIIEDETVLIKPKNGFGGIGGDYVKPTALANVHAFYQ--RLNPSIQIIGTGGVKT 252

Query: 200 MSQALKI-LPSVDGVMIG 216
              A +  L     V +G
Sbjct: 253 GRDAFEHILCGASMVQLG 270


>gi|158320486|ref|YP_001512993.1| 2-nitropropane dioxygenase NPD [Alkaliphilus oremlandii OhILAs]
 gi|158140685|gb|ABW18997.1| 2-nitropropane dioxygenase NPD [Alkaliphilus oremlandii OhILAs]
          Length = 316

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 48/144 (33%), Gaps = 22/144 (15%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV-----------KCRIGVDDQIPA 133
             +     FG  +ML    V + +  +CK  ++PV             K +      IP 
Sbjct: 59  VKKQTNKPFGVNIMLLSPFVDEVVDVVCKH-NVPVVTTGAGNPGKFMEKFKEKGIKVIPV 117

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           V    L K ++  G + + +   +A    +       +     D +         + +  
Sbjct: 118 VPSVALAKRMESLGADAVIVEGTEAG-GHVGELTTMVLTPQIVDAI--------HIPVIA 168

Query: 194 NGGLEDMSQALKILP-SVDGVMIG 216
            GG+ D    L  L    +GV +G
Sbjct: 169 AGGIADGRGFLAALSLGAEGVQMG 192


>gi|13470442|ref|NP_102010.1| oxidoreductase [Mesorhizobium loti MAFF303099]
 gi|14021183|dbj|BAB47796.1| oxidoreductase [Mesorhizobium loti MAFF303099]
          Length = 367

 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 79/246 (32%), Gaps = 28/246 (11%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG---- 82
           + A A+      N+     +E+   LQ+           A+  E  G++ I L+      
Sbjct: 133 VSASAMAYDTGWNVPRALDEEE--ILQLIERFAQA----ARRAERAGFDFIELHAAHGYL 186

Query: 83  -----CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQI----PA 133
                 P +      +G  L     +V +   A+ KA+   + +  R+ V D +      
Sbjct: 187 IFQFLSPLSNQRTDRWGGSLENRMRLVVEIARAVKKAVPK-LMLGARLSVKDWVDGGFDV 245

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
                + K++K  G+  +   +      G SP             + E  ++   +    
Sbjct: 246 EDAIEVAKALKAEGIAYLCCSSG-----GNSPLQKLPTGPGYQVHLAEAVRKGAGIPTRA 300

Query: 194 NGGLEDMSQALKILPS--VDGVMIGRAAYKNS-AMLTTVDEYFSNPLTGSSPIKTRVDKD 250
            G ++D  QA  ++     D V + RA   +          +           ++    +
Sbjct: 301 VGLIDDPQQAEAVIAEGRADMVALARAFLADPRWGWRAAATFKEKIHPAPQLARSVTTME 360

Query: 251 FWRKIS 256
            W K +
Sbjct: 361 HWMKAA 366


>gi|319941294|ref|ZP_08015625.1| imidazole glycerol phosphate synthase subunit hisF [Sutterella
           wadsworthensis 3_1_45B]
 gi|319805215|gb|EFW02038.1| imidazole glycerol phosphate synthase subunit hisF [Sutterella
           wadsworthensis 3_1_45B]
          Length = 258

 Score = 35.9 bits (82), Expect = 8.3,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 37/101 (36%), Gaps = 11/101 (10%)

Query: 135 ALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
            +  L +   + G + +  +   A   G           +D   +  + +   D+   + 
Sbjct: 31  EIVPLARRYAEEGADELVFYDITASSDGRV---------VDKSWISRVAEAI-DIPFCVA 80

Query: 195 GGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           GG+  +  A ++L    D + +   A  +  +++ + E F 
Sbjct: 81  GGIRSIEDAGRLLAFGADKISVNSPALADPTLISRLAERFG 121


>gi|258511935|ref|YP_003185369.1| NADH:flavin oxidoreductase/NADH oxidase [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478661|gb|ACV58980.1| NADH:flavin oxidoreductase/NADH oxidase [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 340

 Score = 35.9 bits (82), Expect = 8.3,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 52/167 (31%), Gaps = 15/167 (8%)

Query: 70  EDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAA-MCKALSIPV 119
              G++ I L             P     + ++G  L L    V   + A M   + + V
Sbjct: 154 VQAGFDVIELHGAHGYLIHQFHSPLTNRRKDAYGEDLALFGVEVIQAVKAEMPSGMPLFV 213

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
            V      D          + +  + +G + I + +      G     N     + Y   
Sbjct: 214 RVSAVEYADGGYDLDHAIEICRRYRDAGADVIHVSSGGEGPPGARRPGNFPGFQVPY--- 270

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
               K+   + +   G L+  + A  ++ +   D V I R   ++  
Sbjct: 271 ARRIKDALQVPVIAVGMLDHPALAESVVANGDADLVAIARGLLRDPY 317


>gi|148261864|ref|YP_001235991.1| NADH:flavin oxidoreductase/NADH oxidase [Acidiphilium cryptum JF-5]
 gi|326405369|ref|YP_004285451.1| putative oxidoreductase [Acidiphilium multivorum AIU301]
 gi|146403545|gb|ABQ32072.1| NADH:flavin oxidoreductase/NADH oxidase [Acidiphilium cryptum JF-5]
 gi|325052231|dbj|BAJ82569.1| putative oxidoreductase [Acidiphilium multivorum AIU301]
          Length = 360

 Score = 35.9 bits (82), Expect = 8.3,   Method: Composition-based stats.
 Identities = 28/157 (17%), Positives = 56/157 (35%), Gaps = 5/157 (3%)

Query: 84  PSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSI 143
           P +     ++G  L     IV + I AM       +    R+   D I      +   ++
Sbjct: 193 PVSNHRTDAYGGDLANRARIVMEAIDAMRAEWPDDLPFFVRLSCTDWIEGGFDADQAVTL 252

Query: 144 KKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI--VYEIKKENPDLFIGLNGGLEDMS 201
            +       +    +   G+SP+      +  Y +     I++E   +  G  G + +  
Sbjct: 253 CRWLAARGDVDLIDSSTGGISPQQRIPSIHPGYQVPFAERIRREAG-IATGAVGMIREPE 311

Query: 202 QALKILPS--VDGVMIGRAAYKNSAMLTTVDEYFSNP 236
            A +I+ +   D V + RA   + A      ++F  P
Sbjct: 312 LAAEIVANERADLVFLARALLADPAWPIRAAQHFGLP 348


>gi|26554017|ref|NP_757951.1| peptide deformylase [Mycoplasma penetrans HF-2]
 gi|32363151|sp|Q8EVJ8|DEF_MYCPE RecName: Full=Peptide deformylase; Short=PDF; AltName:
           Full=Polypeptide deformylase
 gi|26454025|dbj|BAC44355.1| polypeptide deformylase [Mycoplasma penetrans HF-2]
          Length = 186

 Score = 35.9 bits (82), Expect = 8.3,   Method: Composition-based stats.
 Identities = 27/174 (15%), Positives = 61/174 (35%), Gaps = 28/174 (16%)

Query: 30  DAILRGDKKNIL-GFSTQEKPLALQIGGA-DISKLVEAAKIVEDFGYNEINLNVGCPSAR 87
           + ++    ++++   + +++ +  Q+    D S   EA K     G     + +GCP   
Sbjct: 17  NPVMHKPIEDVVFPLTKEDEHVISQMLSYVDASYEGEADKYDIRAGIGIAAIQLGCPKKI 76

Query: 88  VH-----EGSFGACLMLNPDIVGDCIAAM--------------CKALSIP---VTVKCRI 125
           ++     +      LM NP I+ +  + M               K LSI    V VK   
Sbjct: 77  IYIHLDDKNGEHKYLMANPKIIKESTSKMYLKNGEGCLSVKKDHKGLSIRKSIVWVKGID 136

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
              ++   V   +L+ +  +  V+    H           + +      +++ +
Sbjct: 137 LFTNKEIEVKATDLLAACFQHEVD----HNNNKFYYNRINESDPYYVEKNWEEI 186


>gi|328771839|gb|EGF81878.1| hypothetical protein BATDEDRAFT_19038 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 313

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      P+        G   M +PD++   +AA    ++IPV  K
Sbjct: 47  AEQARIAEEAGACAVMALERVPAD--IRKDGGVARMSDPDMIKKIMAA----VTIPVMAK 100

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  G++ I
Sbjct: 101 VRIGHFVE---------AQILEHIGIDYI 120


>gi|302869933|ref|YP_003838570.1| thiamine-phosphate pyrophosphorylase [Micromonospora aurantiaca
           ATCC 27029]
 gi|302572792|gb|ADL48994.1| thiamine-phosphate pyrophosphorylase [Micromonospora aurantiaca
           ATCC 27029]
          Length = 208

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 27/174 (15%), Positives = 50/174 (28%), Gaps = 22/174 (12%)

Query: 56  GADISKLVEAAK-----------IVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIV 104
           G D   ++ AA             VED   +     + C            CL+ +   V
Sbjct: 16  GRDPLAVLRAALPVAGADLVVQVRVEDDATDREAYELACRVTEACRPYGAQCLVNDRLHV 75

Query: 105 GDCIAAM---CKALSIPVTVKCRIGVDDQIPAVALRNLV--KSIKKSGVNGIWIHARKAI 159
              + A      A  +PV    R+   D +     R  V  ++   +G + +       +
Sbjct: 76  ALAVDAAGGHVGADDLPVAAARRVLGPDAVLGATAREPVGARTAVDAGASYL-GVGPCHV 134

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
               S         +  + +  +  E   + +   GG+   S          GV
Sbjct: 135 TTTKSG----LPDPIGPEGIRAVA-EAVSVPVIAIGGVTAASVPALRAAGAYGV 183


>gi|239908116|ref|YP_002954857.1| putative oxidoreductase [Desulfovibrio magneticus RS-1]
 gi|239797982|dbj|BAH76971.1| putative oxidoreductase [Desulfovibrio magneticus RS-1]
          Length = 369

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 28/190 (14%), Positives = 62/190 (32%), Gaps = 20/190 (10%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AA +  D G + + ++            P      G++G  L     ++ + + A+ 
Sbjct: 143 FGTAAALCRDAGADGVQIHAAHGYGLSQFLSPRTNRRTGAYGGSLQNRARLLLEVLGAIR 202

Query: 113 KALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARK----AILKGLS 164
             +     V  +I  DD I     +     +V  ++ +G++ + +         +     
Sbjct: 203 GRIGREYPVLAKINSDDFIAGGFTSAECVQVVSWLEAAGLDAVELSGGVFESGRLNFSRP 262

Query: 165 PKDNRKIPNLDY-DIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDG--VMIGRAAYK 221
            +         Y D    +K     + + L GGL  +     I+ S D   V + R   +
Sbjct: 263 GRIAIPDGEAWYRDTARTVKAAGVTMPVILVGGLRSLGTCEDIIASGDAELVAMSRPFIR 322

Query: 222 NSAMLTTVDE 231
              ++     
Sbjct: 323 EPGLIARWQA 332


>gi|219670604|ref|YP_002461039.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfitobacterium
           hafniense DCB-2]
 gi|219540864|gb|ACL22603.1| NADH:flavin oxidoreductase/NADH oxidase [Desulfitobacterium
           hafniense DCB-2]
          Length = 681

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 21/147 (14%), Positives = 49/147 (33%), Gaps = 19/147 (12%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
           ++    KI++  G++ I L  G     V               +G  +        + + 
Sbjct: 150 QVANCGKILQAAGWDGIELLAG--VGGVLSRFLSKATNNRTDEYGGSVENRCRFAMEVVQ 207

Query: 110 AMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           A+ +A      V  R    D +         + +V  ++K+GV    +       +   P
Sbjct: 208 AVKEACGQEFPVLIRWSPVDYVKNGNEIEDAKQIVPYLEKAGVAWHNLAVG--WHESSVP 265

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIG 192
              ++IP+  +  +    K+   + + 
Sbjct: 266 LTTKEIPDGHWSWIAAEIKKVATIPVV 292


>gi|303250461|ref|ZP_07336658.1| hypothetical protein APP6_0031 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307251302|ref|ZP_07533221.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|302650449|gb|EFL80608.1| hypothetical protein APP6_0031 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306856668|gb|EFM88805.1| Imidazole glycerol phosphate synthase subunit hisF [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
          Length = 257

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L K   + G + +  +   A   G +         +D   V  + +   D+   + GG++
Sbjct: 35  LAKRYAEEGADELVFYDITASSDGRT---------VDKSWVERVAQ-VIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A K+     D + I   A  +  ++T + + F 
Sbjct: 85  TIEDAEKLFAFGADKISINSPALADPNLITALADRFG 121


>gi|227904847|emb|CAQ34814.1| vitamin B6 biosynthesis protein [Glomus intraradices]
          Length = 317

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      P+    +G      M +P      I  + +A++IPV  K
Sbjct: 51  AEQARIAEEAGACAVMALERVPADIRIQGGVAR--MSDP----KMIKEIKEAVTIPVMAK 104

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  G++ I
Sbjct: 105 VRIGHFVE---------AQILESIGIDYI 124


>gi|89068387|ref|ZP_01155790.1| hypothetical protein OG2516_18585 [Oceanicola granulosus HTCC2516]
 gi|89046041|gb|EAR52100.1| hypothetical protein OG2516_18585 [Oceanicola granulosus HTCC2516]
          Length = 745

 Score = 35.9 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 35/213 (16%), Positives = 69/213 (32%), Gaps = 27/213 (12%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            + V AA++    G++ I L+            P +      +G  L        +  AA
Sbjct: 530 DQFVAAAEMAGRAGFDMIELHAAHGYLVSSFLSPVSNRRTDDYGGSLDNRLRWPLEVFAA 589

Query: 111 MCKA--LSIPVTVKCRIGV---DDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
           M  A     P++V+        +D +       + ++ +++G + + + A      G + 
Sbjct: 590 MRAAWPADKPMSVRISATDWVGEDGVTPEEAVLIARAFREAGADLVDVSA------GQTT 643

Query: 166 KDNRKIPNLDYD--IVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYK 221
            D R +    +       I+ E   +     G + +   A  IL +   D V +GR    
Sbjct: 644 PDARPVYGRMFQTPFSDRIRNEAG-IRTMAVGNIYEADHANSILMAGRADLVAVGRPHLA 702

Query: 222 NS-AMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
           +                    P     D+  WR
Sbjct: 703 DPYWTFHEAARIGDRHADWPLPYLPGRDQ-LWR 734


>gi|302872730|ref|YP_003841366.1| Glutamate synthase (NADPH) [Caldicellulosiruptor obsidiansis OB47]
 gi|302575589|gb|ADL43380.1| Glutamate synthase (NADPH) [Caldicellulosiruptor obsidiansis OB47]
          Length = 502

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 28/126 (22%), Positives = 43/126 (34%), Gaps = 16/126 (12%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AI 159
           +   I A+ +A +   PV VK             +  +   I ++G + I I   +    
Sbjct: 289 LRQLIFALKEATNYTKPVGVKI-------AAVHNVAAIASGIARAGADFITIDGVRGGTG 341

Query: 160 LKGLSPKDNRKIP-NLDYDIVYEIKKENPD---LFIGLNGGLE-DMSQALKILPSVDGVM 214
              L  +DN  IP  L    V    +E      + I + G +         I    D V 
Sbjct: 342 AAPLRIRDNVGIPIELALAAVDSRLREEGIRNQVSIIVAGSIRNSADVVKAIALGADAVF 401

Query: 215 IGRAAY 220
           IG AA 
Sbjct: 402 IGTAAL 407


>gi|303245078|ref|ZP_07331397.1| geranylgeranylglyceryl phosphate synthase [Methanothermococcus
           okinawensis IH1]
 gi|302484558|gb|EFL47503.1| geranylgeranylglyceryl phosphate synthase [Methanothermococcus
           okinawensis IH1]
          Length = 260

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 181 EIKKENPDLFIGLNGGLEDMSQA-LKILPSVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + K   D+ I + GG+     A  K++   D ++ G     N  M+  + +   
Sbjct: 193 AVSKRLSDINIIVGGGIRTPEVAYKKVISGADAIVTGTLIEDNPNMVKEMRDAIK 247


>gi|297617543|ref|YP_003702702.1| NADH:flavin oxidoreductase/NADH oxidase [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297145380|gb|ADI02137.1| NADH:flavin oxidoreductase/NADH oxidase [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 643

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 35/223 (15%), Positives = 77/223 (34%), Gaps = 18/223 (8%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
            K ++AA +    G++ + ++ G          P     +  +G        ++ + +  
Sbjct: 150 DKFIKAAGLAVQAGFDGVEIHAGHGYLLGQFLSPHTNRRQDRYGRDATGRARLIMEIVDG 209

Query: 111 MCKALS---IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           +  A     + V       V   I       L + ++ +G + + +        GL+  +
Sbjct: 210 IKAACPGLVVGVRFNVADFVPGGIEPDEGVYLAQLLESAGSDYLSVTGGTH-ESGLTTVE 268

Query: 168 NRKIPN-LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
               P      +  ++KK      +G  G +     A ++L    VD V IGR    +  
Sbjct: 269 PASFPEGWRMRLAAKVKKAVSVPVVGG-GVIRHPEYAEQVLREGWVDYVFIGRGQLADGE 327

Query: 225 MLTTVDEYFSNPLTGSSPIKTRVDKDFWR-KISASMTDYAARH 266
            LT      S+ +       T + + F+   ++ ++  Y  R 
Sbjct: 328 WLTKARLQQSDRIRPCLSCNTCIAQSFYHLAVTCTVNPYIGRE 370


>gi|262373687|ref|ZP_06066965.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter junii SH205]
 gi|262311440|gb|EEY92526.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter junii SH205]
          Length = 243

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVDEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I +  P+L I + GG+  +      L   V  V+IG  A K    
Sbjct: 60  ------PIHKPVVEAIARAQPELPIQIGGGIRSLETIEHYLDAGVSFVIIGTKAVKEPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKQFAG 123


>gi|197121223|ref|YP_002133174.1| dihydroorotate dehydrogenase 2 [Anaeromyxobacter sp. K]
 gi|196171072|gb|ACG72045.1| dihydroorotate dehydrogenase [Anaeromyxobacter sp. K]
          Length = 328

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 11/110 (10%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGD 106
           E P+   + G+      E A+ +E  G + + LN+        E               +
Sbjct: 99  EIPVIASLNGSAAGGWTEFARDIEQAGADALELNL-----YAVEADPAVSAAEVEARYLE 153

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
            ++A+  A++IPV VK            AL +    +   GVNGI +  R
Sbjct: 154 AVSAVRDAVTIPVAVKLSPYF------TALAHFCARLDALGVNGIVLFNR 197


>gi|163737123|ref|ZP_02144541.1| NADH:flavin oxidoreductase/NADH oxidase [Phaeobacter gallaeciensis
           BS107]
 gi|161389727|gb|EDQ14078.1| NADH:flavin oxidoreductase/NADH oxidase [Phaeobacter gallaeciensis
           BS107]
          Length = 675

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 18/124 (14%), Positives = 43/124 (34%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIP----AVALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +    +A+     +  R+ + D +P       +  L + I+K+G     ++      +
Sbjct: 197 EVVRRTREAVGTDFIIIYRLSMIDLVPNGSTYDEVVQLAQEIEKAGAT--ILNTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
              P     +P   +  V  ++  +     I  N  +     A ++L     D V + R 
Sbjct: 255 ARIPTIATSVPRAAFAWVTKKLMGKVGIPVITSNR-INTPEVAEQVLSEGCADMVSMARP 313

Query: 219 AYKN 222
              +
Sbjct: 314 MLAD 317


>gi|91775494|ref|YP_545250.1| inosine-5'-monophosphate dehydrogenase [Methylobacillus flagellatus
           KT]
 gi|91709481|gb|ABE49409.1| inosine-5'-monophosphate dehydrogenase [Methylobacillus flagellatus
           KT]
          Length = 486

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 14/82 (17%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
               V ++ ++GV+ I +       +G+             D V  +KK  P + +   G
Sbjct: 228 TEERVAALAEAGVDVIVVDTAHGHSQGV------------LDRVNWVKKNFPHIQVIG-G 274

Query: 196 GLEDMSQALKILP-SVDGVMIG 216
            +   + A  ++    DGV +G
Sbjct: 275 NIATANAAKALVDAGADGVKVG 296


>gi|47564465|ref|ZP_00235510.1| pyruvate kinase [Bacillus cereus G9241]
 gi|47558617|gb|EAL16940.1| pyruvate kinase [Bacillus cereus G9241]
          Length = 352

 Score = 35.9 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 22/110 (20%), Positives = 42/110 (38%), Gaps = 16/110 (14%)

Query: 112 CKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKI 171
            K +++P T+     + ++         ++ + + GV+ I       + K    K+ R  
Sbjct: 148 HKGVNLPGTIVSLPAITEKDKKD-----IQFLLEEGVDFIAC---SFVRKPRHIKEIR-- 197

Query: 172 PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYK 221
                D + E K+  P+L I     +E +     I    DG+MI R    
Sbjct: 198 -----DFIKEHKETVPNL-IAKIETMEAIENFQDICKEADGIMIARGDLG 241


>gi|315655330|ref|ZP_07908230.1| imidazole glycerol phosphate synthase, cyclase subunit [Mobiluncus
           curtisii ATCC 51333]
 gi|315656757|ref|ZP_07909644.1| imidazole glycerol phosphate synthase, cyclase subunit [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
 gi|315490270|gb|EFU79895.1| imidazole glycerol phosphate synthase, cyclase subunit [Mobiluncus
           curtisii ATCC 51333]
 gi|315492712|gb|EFU82316.1| imidazole glycerol phosphate synthase, cyclase subunit [Mobiluncus
           curtisii subsp. holmesii ATCC 35242]
          Length = 263

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L      +G + I      A ++G +            ++V +  +E   + + + GG+
Sbjct: 42  ELAARYCAAGADEITFLDVSATVEGRATMA---------EVVQQCAREIF-VPLTVGGGV 91

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             ++   ++L    D V I  AA  +  ++T +   F 
Sbjct: 92  RSVADVERLLKSGADKVSINTAAIAHPELITEIASRFG 129


>gi|254499273|ref|ZP_05111949.1| inosine-5-monophosphate dehydrogenase [Legionella drancourtii
           LLAP12]
 gi|254351517|gb|EET10376.1| inosine-5-monophosphate dehydrogenase [Legionella drancourtii
           LLAP12]
          Length = 490

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 12/97 (12%), Positives = 32/97 (32%), Gaps = 4/97 (4%)

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K    V      +A     + + ++G + + +      +          +P +    +  
Sbjct: 266 KHYPDVQVIGGNIATAAAARDLYEAGADAVKVGIGPGSICTTRIVTGVGVPQI--SAIAN 323

Query: 182 IKKEN-PDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
           + +E    + +  +GG+         +    D VM+G
Sbjct: 324 VAQELKGKIPLIADGGIRFSGDVCKALAAGADTVMLG 360


>gi|271967072|ref|YP_003341268.1| morphinone reductase [Streptosporangium roseum DSM 43021]
 gi|270510247|gb|ACZ88525.1| morphinone reductase [Streptosporangium roseum DSM 43021]
          Length = 364

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 67/198 (33%), Gaps = 31/198 (15%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAA 110
              V AA+   + G++ + L+           C SA V   S+G  +        + + A
Sbjct: 163 EDFVAAARNAMEAGFDGVELHAANGYLLHQFLCGSANVRSDSYGGSVENRIRFAAEVVGA 222

Query: 111 MCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +  A+  P  V  RI   +    +   +  +                A+++ L+P +   
Sbjct: 223 VTDAIG-PERVGVRISPANPNNGIREHDPAEVY-------------PALMRALAPFEPAY 268

Query: 171 IPNLDYDI-VYEIKKEN-PDLFIGLNGGL--EDMSQALKILPS--VDGVMIGRAAYKNSA 224
           +  +++D  + E+ +   P   I   G    E +  A  +L     D V +G     N  
Sbjct: 269 VHIMEFDREITELVRAAWPGTLILNPGDTAEERIGAAAAVLREGLCDAVSLGALWLANPD 328

Query: 225 MLTTVDEYFSNPLTGSSP 242
           +   V      P     P
Sbjct: 329 LPERVKA--GGPYNEPDP 344


>gi|116694622|ref|YP_728833.1| NADH:flavin oxidoreductase [Ralstonia eutropha H16]
 gi|113529121|emb|CAJ95468.1| NADH:flavin oxidoreductase (Old Yellow Enzyme family) [Ralstonia
           eutropha H16]
          Length = 413

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 18/161 (11%), Positives = 52/161 (32%), Gaps = 35/161 (21%)

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRN----LVKSIKKSGVNGIWIHARKAIL 160
              +  +  A+   + V C++ V D +P            + ++  G + + +   + + 
Sbjct: 209 AAVLRQVKDAVGAELAVCCKLSVSDGVPGGNEPADSAVSARLLEAEGADLLTLSGGRNVE 268

Query: 161 K-------------------------GLSPKDNRKIPNLDYDIVY-----EIKKENPDLF 190
                                     G++  + R    L +  +Y      + +    + 
Sbjct: 269 SPWALFGSPMPTAQMKAAAPTAVARFGITMLEKRTPRALAFRELYFLEASRVVRRAVRMP 328

Query: 191 IGLNGGLEDM-SQALKILPSVDGVMIGRAAYKNSAMLTTVD 230
           +   GG++ + + A  +    D + + RA   + A++    
Sbjct: 329 LAYIGGVKSIGNVAQLMEEGFDCIALARALIHDPALVANWR 369


>gi|39933389|ref|NP_945665.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhodopseudomonas
           palustris CGA009]
 gi|192288745|ref|YP_001989350.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Rhodopseudomonas
           palustris TIE-1]
 gi|45476797|sp|P60582|HIS4_RHOPA RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700352|sp|B3Q950|HIS4_RHOPT RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|39653014|emb|CAE25756.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhodopseudomonas palustris CGA009]
 gi|192282494|gb|ACE98874.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Rhodopseudomonas palustris TIE-1]
          Length = 245

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 24/145 (16%), Positives = 55/145 (37%), Gaps = 21/145 (14%)

Query: 85  SARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK---CRIGVDDQIPAVALRNLVK 141
           S  +     G   + +P +V +   A    +++ +  +     +    +   V   ++ +
Sbjct: 94  SKGIARVIIGTAAVRDPALVKEAAKAFPGRVAVGLDARDGNVAVEGWAESSQVTALDIAQ 153

Query: 142 SIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
             + +GV  I     AR  +LKG           +++D    + +    + +  +GGL  
Sbjct: 154 RFEDAGVAAIIFTDIARDGLLKG-----------INWDATIALAEAI-SIPVIASGGLAS 201

Query: 200 MSQALKILP----SVDGVMIGRAAY 220
           +     +L      ++G + GRA Y
Sbjct: 202 IEDVRTLLSPRAKKLEGAIAGRALY 226


>gi|305664525|ref|YP_003860812.1| transcriptional regulator [Maribacter sp. HTCC2170]
 gi|88708542|gb|EAR00778.1| transcriptional regulator [Maribacter sp. HTCC2170]
          Length = 287

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 68/177 (38%), Gaps = 26/177 (14%)

Query: 46  QEKPLALQIGGADI-----SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           +E P+   + G D        L +    V+D G++ +N N   P+  + +G F       
Sbjct: 95  EEIPVICGVHGTDPRRRMWHFLGQ----VKDMGFSGVN-NF--PTHCIVDGHF------- 140

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
            +++ +   +  K + + V +  ++ +   I  VA       +   G + I  H    + 
Sbjct: 141 RNVLEETGMSFQKEVDM-VNLATKMDLF-SIVYVAEPEEAVQMADVGADAIISHVGTTVG 198

Query: 161 K--GLSPKDNRKIPNLDY--DIVYEIKKENPDLFIGLNGG-LEDMSQALKILPSVDG 212
              G++         +D   +I+  ++K NPD F   +GG +        IL   D 
Sbjct: 199 GSIGVTGATRSMDFAIDKTQEIIEAVRKSNPDTFFLAHGGPVNTPEDVRIILDKTDA 255


>gi|332343494|gb|AEE56828.1| conserved hypothetical protein [Escherichia coli UMNK88]
          Length = 278

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 56/146 (38%), Gaps = 19/146 (13%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLN 100
           LG    E      + G   +   +AA+ VE  G + + + +G           G      
Sbjct: 134 LGHVGNETVYEEALAGYHYTDPYQAAEFVERTGCDSLAVAIG--------NQHGVY-TSE 184

Query: 101 PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           P +  + +  +  A+S+P+ +    G+ D          +K+    G+  I IH      
Sbjct: 185 PQLNFEVVKRVRDAVSVPLVLHGASGISDAD--------IKTAISLGIAKINIHTELCQA 236

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKEN 186
             ++ K+N+  P L+ +   E++K  
Sbjct: 237 AMVAVKENQDQPFLNLE--REVRKAV 260


>gi|332286371|ref|YP_004418282.1| histidine biosynthesis protein [Pusillimonas sp. T7-7]
 gi|330430324|gb|AEC21658.1| histidine biosynthesis protein [Pusillimonas sp. T7-7]
          Length = 247

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 35/90 (38%), Gaps = 3/90 (3%)

Query: 172 PNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
              +   +  I K   D + + + GG+ D+    + L   +  V+IG AA K+   L   
Sbjct: 59  KPKNEAAIKSIIKAVADDIPVQIGGGIRDLDTIERYLDAGISYVIIGTAAVKDPGFLRDA 118

Query: 230 DEYFSNPLT-GSSPIKTRVDKDFWRKISAS 258
              F   +  G      +V  D W K++  
Sbjct: 119 CSAFPGNIIVGLDARDGKVATDGWSKLTRH 148


>gi|328856523|gb|EGG05644.1| hypothetical protein MELLADRAFT_48766 [Melampsora larici-populina
           98AG31]
          Length = 346

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 15/89 (16%)

Query: 63  VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
            E A+I E+ G   +      PS        G   M +P ++ + I     A++IPV  K
Sbjct: 80  AEQARIAEEAGACAVMALERVPSD--IRRDGGVARMSDPQMIKEII----DAVTIPVMAK 133

Query: 123 CRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
            RIG   +          + ++  GV+ I
Sbjct: 134 ARIGHFVE---------AQILQAIGVDYI 153


>gi|325969599|ref|YP_004245791.1| triosephosphate isomerase [Vulcanisaeta moutnovskia 768-28]
 gi|323708802|gb|ADY02289.1| triosephosphate isomerase [Vulcanisaeta moutnovskia 768-28]
          Length = 223

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SV 210
            +      L G     +R+ P++    V  IK+ NP + +    G+E+     K L    
Sbjct: 137 AVAVEPPELIGTGKAVSREKPDVIVKTVGLIKRVNPGIPVITGAGIENYEDVKKALELGT 196

Query: 211 DGVMIGRAAY 220
            GV++  A  
Sbjct: 197 QGVLVASAIV 206


>gi|314960073|gb|EFT04175.1| pyridoxal 5'-phosphate synthase, synthase subunit Pdx1
           [Propionibacterium acnes HL002PA2]
          Length = 279

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 42/216 (19%), Positives = 65/216 (30%), Gaps = 68/216 (31%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK--- 122
           AKI ED G   +      P+        G   M +PD++   I A    +SIPV  K   
Sbjct: 16  AKIAEDAGACAVMALERVPAD--IRAQGGVARMSDPDLIEGIIEA----VSIPVMAKARI 69

Query: 123 -----------CRIGVDDQIPAVALRNLVKSIKKS----------------------GVN 149
                       R+   D+   ++  +    I K                       G  
Sbjct: 70  GHFVEAQVLESLRVDFIDESEVLSPADYANHIDKWAFGVPFVCGATNLGEALRRITEGAA 129

Query: 150 GI-------------------WIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKK--E 185
            I                    I A  A L  +SP +           YD+V E+ +  E
Sbjct: 130 MIRSKGEAGTGDVSEAVRHLRTIRAEMARLSSMSPDELYVAAKELQAPYDLVAEVARTGE 189

Query: 186 NPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAY 220
            P +     GG+   + A  ++     GV +G   +
Sbjct: 190 LPVVLFVA-GGVATPADAALVMQMGAQGVFVGSGIF 224


>gi|292670210|ref|ZP_06603636.1| tryptophan synthase [Selenomonas noxia ATCC 43541]
 gi|292648162|gb|EFF66134.1| tryptophan synthase [Selenomonas noxia ATCC 43541]
          Length = 261

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 31/214 (14%), Positives = 62/214 (28%), Gaps = 59/214 (27%)

Query: 55  GGADISKLVEAAKIVEDFGYNEINLN-------VGCPS---ARVHEGSFGACLMLNPDIV 104
           G       V+  +  E+ G + I L           P    A V     G  +       
Sbjct: 27  GCPSAEATVDIVRRAEEAGADVIELGLPFSDPMADGPVIQEASVIALKNGMTM----KKA 82

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWI----HARKAIL 160
            + +  + K   IP+     +G  + +        V   K +G++G+      H   A +
Sbjct: 83  LEIVKEIRKHSEIPL---IGMGYINMVNHYGFEKFVADFKAAGMDGVIFPDVPHEESADM 139

Query: 161 KGLSPKDNRK-----------------------------------IPNLDYDIVYEIKKE 185
           + +    +                                     +  +DY I+  + K 
Sbjct: 140 RRICAAHDFTLTEFITPGTTEERMQETCKDARGFIYCISNYGVTGVKEIDYSIIGGVCKA 199

Query: 186 N---PDLFIGLNGGLEDMSQALKILPSVDGVMIG 216
                D+ + +  G+     A +     DGV++G
Sbjct: 200 ARRYTDVPLAIGFGIGTPEAAARAGKQADGVIVG 233


>gi|302557146|ref|ZP_07309488.1| PEP phosphonomutase [Streptomyces griseoflavus Tu4000]
 gi|302474764|gb|EFL37857.1| PEP phosphonomutase [Streptomyces griseoflavus Tu4000]
          Length = 279

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 29/148 (19%), Positives = 52/148 (35%), Gaps = 13/148 (8%)

Query: 26  MIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPS 85
           M    ++LR             +P    +   +   +  +A++VED G   +        
Sbjct: 1   MTNPSSLLREHALAFRSLHVPGRP----LLLPNAWDVA-SARLVEDAGAGAVATTGVG-V 54

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
           A     + G  L  + +     +A +  A+ +PVT     G  D    VA    V+++  
Sbjct: 55  AWALGAADGERL--DRERAPAVVAGIAGAVRVPVTADVESGWADDPAGVA--RTVRAVLA 110

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIPN 173
           +G  G+ I      L G  P   R +  
Sbjct: 111 AGAVGVNIEDA---LHGPGPAPLRPVAE 135


>gi|253732991|ref|ZP_04867156.1| possible 3-dehydro-L-gulonate-6-phosphate decarboxylase
           [Staphylococcus aureus subsp. aureus TCH130]
 gi|253729044|gb|EES97773.1| possible 3-dehydro-L-gulonate-6-phosphate decarboxylase
           [Staphylococcus aureus subsp. aureus TCH130]
          Length = 210

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 24/111 (21%), Positives = 41/111 (36%), Gaps = 21/111 (18%)

Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL-KGLSPKDNRKI----------- 171
           +  + D I    L    K + + G + I +H    +  +G SP ++ +            
Sbjct: 104 KQLLVDMIAVQDLEKRAKELDEMGADYIAVHTGYDLQAEGQSPLESLRTVKSVIKNSKVA 163

Query: 172 --PNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               +  D + EI  ENPDL I   GG+ +    ++           RAA 
Sbjct: 164 VAGGIKPDTIKEIVAENPDLVIVG-GGIANADDPVEAAKQC------RAAI 207


>gi|254166792|ref|ZP_04873646.1| tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA,
           putative [Aciduliprofundum boonei T469]
 gi|289596363|ref|YP_003483059.1| NADH:flavin oxidoreductase/NADH oxidase [Aciduliprofundum boonei
           T469]
 gi|197624402|gb|EDY36963.1| tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA,
           putative [Aciduliprofundum boonei T469]
 gi|289534150|gb|ADD08497.1| NADH:flavin oxidoreductase/NADH oxidase [Aciduliprofundum boonei
           T469]
          Length = 601

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 31/179 (17%), Positives = 57/179 (31%), Gaps = 18/179 (10%)

Query: 65  AAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--------IVGDCIAAMCKALS 116
           AA+I    G++ + +     +  +    F + L    D           +    + K   
Sbjct: 131 AAEIACKAGFDMVEVQG---AHGLLVNQFLSPLTNTRDDSWGERTKFAIEIRKEIAKRCG 187

Query: 117 IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIP---N 173
               V  R+ VDD +      +  K I +        +       GL PK+ R  P    
Sbjct: 188 WDFPVTIRLAVDDFLDGGITLDEGKRIAE---ELQNYYQMIQADIGLGPKELRLEPMPFQ 244

Query: 174 LDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDE 231
             +            + +   G + +   A +IL    D +++GR    +   L  V E
Sbjct: 245 QGWRAYLAENIRPLKVPVAAVGMIREPEVAAEILREKADMIVLGRTLIADPEWLIKVRE 303


>gi|187921793|ref|YP_001890825.1| salicylyl-CoA 5-hydroxylase [Burkholderia phytofirmans PsJN]
 gi|187720231|gb|ACD21454.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia phytofirmans
           PsJN]
          Length = 790

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 33/218 (15%), Positives = 72/218 (33%), Gaps = 34/218 (15%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVGD 106
           + V A ++  + G++ + L   C                    +G  L   +  P  V  
Sbjct: 560 QFVRATQMSAEAGFDWLEL--HCAHGYFLSSFLSPLTNHRTDEYGGSLENRLRYPLQVFK 617

Query: 107 CIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            I A+      P++V+      V+          + ++ K +G + I + +   + K   
Sbjct: 618 AIRAVW-PQEKPISVRISANDWVEGGTTPDDAVKIAQAFKAAGADMIDVSSG-QVSKEEK 675

Query: 165 PKDNR--KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           P   R  + P  D      ++ E   +     G + +      I+ +   D   I R   
Sbjct: 676 PVFGRMFQTPFAD-----RVRNEAG-IATIAVGAISEADHVNSIIAAGRADLCAIARPHL 729

Query: 221 KNS-AMLTTVDEYFSNPLTGSSP---IKTRVDKDFWRK 254
            N    L    +     +    P    K++++++  R+
Sbjct: 730 ANPSWTLNEAAKIGYFDVMWPKPYTAAKSQLERNLERE 767


>gi|119357429|ref|YP_912073.1| inosine-5'-monophosphate dehydrogenase [Chlorobium phaeobacteroides
           DSM 266]
 gi|119354778|gb|ABL65649.1| inosine-5'-monophosphate dehydrogenase [Chlorobium phaeobacteroides
           DSM 266]
          Length = 497

 Score = 35.9 bits (82), Expect = 8.6,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 42/133 (31%), Gaps = 25/133 (18%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARKAI 159
             +  M + +      K    +      VA  + V+ +  +G + + I           I
Sbjct: 261 QAVITMVETIK-----KVYPDLQVIAGNVATPDAVRDLVAAGADCVKIGIGPGSICTTRI 315

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIGRA 218
           + G+       I N   +          D  I  +GG++     A  +    D VM+G  
Sbjct: 316 VAGVGMPQFTAILNCAEEAAK------TDTPIIADGGIKYSGDIAKALAAGADTVMMG-- 367

Query: 219 AYKNSAMLTTVDE 231
                ++    DE
Sbjct: 368 -----SIFAGTDE 375


>gi|256845502|ref|ZP_05550960.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 3_1_36A2]
 gi|256719061|gb|EEU32616.1| inosine-5'-monophosphate dehydrogenase [Fusobacterium sp. 3_1_36A2]
          Length = 488

 Score = 35.9 bits (82), Expect = 8.7,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 14/78 (17%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           V ++ K+GV+ I + +     +G+             +++ EIKK  PDL +   G +  
Sbjct: 235 VSALVKAGVDIITVDSAHGHSQGVI------------NMIKEIKKNFPDLDVIG-GNIVT 281

Query: 200 MSQALKILP-SVDGVMIG 216
              A +++   V  V +G
Sbjct: 282 AEAAKELVEAGVSAVKVG 299


>gi|164686713|ref|ZP_02210741.1| hypothetical protein CLOBAR_00308 [Clostridium bartlettii DSM
           16795]
 gi|164604103|gb|EDQ97568.1| hypothetical protein CLOBAR_00308 [Clostridium bartlettii DSM
           16795]
          Length = 278

 Score = 35.9 bits (82), Expect = 8.7,   Method: Composition-based stats.
 Identities = 21/74 (28%), Positives = 29/74 (39%), Gaps = 6/74 (8%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI E+ G   +      PS        G   M +P      I  + KA+SIPV  K RI
Sbjct: 16  AKIAEEAGACAVMALERVPSD--IRKFGGVARMSDP----KMIKEIQKAVSIPVMAKARI 69

Query: 126 GVDDQIPAVALRNL 139
           G   +   +    +
Sbjct: 70  GHFVEAQILEALEI 83


>gi|146080396|ref|XP_001464008.1| n-ethylmaleimide reductase-like protein [Leishmania infantum JPCM5]
 gi|321399138|emb|CBZ08478.1| n-ethylmaleimide reductase-like protein [Leishmania infantum JPCM5]
          Length = 828

 Score = 35.9 bits (82), Expect = 8.7,   Method: Composition-based stats.
 Identities = 27/188 (14%), Positives = 64/188 (34%), Gaps = 32/188 (17%)

Query: 63  VEAAKIVEDFGYNEINLNVG-----------CPSARVHEGSFGACLMLNPDIVGDCIAAM 111
           V AAK     G++ + ++ G           C + R  +  +G        ++ + + A+
Sbjct: 581 VAAAKNAMVAGFDGVEIHAGGGYLIDQFLRKCSNTR--DDDYGGSPAGRCRLLDEIVDAV 638

Query: 112 -----CKALSIPVTVK-CRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSP 165
                 + + + V+      G+ D    V    +   + +  +  I +          S 
Sbjct: 639 AAVIGRRRVGVRVSPTDLSKGMKDTDQDVVAETVATHMAERKIAYITVA---------SG 689

Query: 166 KDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNS 223
            D      +   I+ ++ +    + +        +++A K +   +V GV I   A  N 
Sbjct: 690 SDGYYHGPVPACILKKVLQCFGGVVMCD--DNTSLAEAEKRVVADAVQGVCITLGAIANP 747

Query: 224 AMLTTVDE 231
            ++  V  
Sbjct: 748 DIMNRVIH 755


>gi|126643246|ref|YP_001086230.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii ATCC 17978]
 gi|169794443|ref|YP_001712236.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii AYE]
 gi|184159751|ref|YP_001848090.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii ACICU]
 gi|213158983|ref|YP_002320981.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Acinetobacter baumannii AB0057]
 gi|215482032|ref|YP_002324214.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Acinetobacter baumannii AB307-0294]
 gi|239502012|ref|ZP_04661322.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii AB900]
 gi|260556876|ref|ZP_05829093.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter baumannii ATCC
           19606]
 gi|301345647|ref|ZP_07226388.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii AB056]
 gi|301512344|ref|ZP_07237581.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii AB058]
 gi|301596169|ref|ZP_07241177.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii AB059]
 gi|332851918|ref|ZP_08433804.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii 6013150]
 gi|332868836|ref|ZP_08438429.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter baumannii 6013113]
 gi|332874253|ref|ZP_08442173.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter baumannii 6014059]
 gi|167011499|sp|A3M9N4|HIS4_ACIBT RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700270|sp|B7GVK1|HIS4_ACIB3 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700271|sp|B7IBD1|HIS4_ACIB5 RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700272|sp|B2I0N7|HIS4_ACIBC RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|226700274|sp|B0V8R7|HIS4_ACIBY RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|126389130|gb|ABO13628.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter baumannii ATCC 17978]
 gi|169147370|emb|CAM85231.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter baumannii AYE]
 gi|183211345|gb|ACC58743.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide
           (ProFAR) isomerase [Acinetobacter baumannii ACICU]
 gi|213058143|gb|ACJ43045.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Acinetobacter baumannii AB0057]
 gi|213988787|gb|ACJ59086.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Acinetobacter baumannii AB307-0294]
 gi|260409482|gb|EEX02783.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter baumannii ATCC
           19606]
 gi|322509664|gb|ADX05118.1| hisA [Acinetobacter baumannii 1656-2]
 gi|323519684|gb|ADX94065.1| 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii TCDC-AB0715]
 gi|332729611|gb|EGJ60948.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter
           baumannii 6013150]
 gi|332733089|gb|EGJ64288.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter baumannii 6013113]
 gi|332737537|gb|EGJ68444.1| 1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]imidazole-4-
           carboxamide isomerase [Acinetobacter baumannii 6014059]
          Length = 243

 Score = 35.9 bits (82), Expect = 8.7,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I K  P+L I + GG+  +      L   V  V+IG  A +    
Sbjct: 60  ------PIHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLEAGVTFVIIGTKAVQEPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKRFAG 123


>gi|239623579|ref|ZP_04666610.1| NADH oxidase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521610|gb|EEQ61476.1| NADH oxidase [Clostridiales bacterium 1_7_47FAA]
          Length = 640

 Score = 35.9 bits (82), Expect = 8.8,   Method: Composition-based stats.
 Identities = 29/176 (16%), Positives = 62/176 (35%), Gaps = 14/176 (7%)

Query: 27  IVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEA----AKIVEDFGYNEINLNVG 82
           I + + L  D   +L    ++    + +         +A    A+I+   GY  +  N  
Sbjct: 89  IASKSPLYPDTPKVLEI--EDIKEIVDMFAKGACIAKKAGIDGAEIIMGHGY--LANNFL 144

Query: 83  CPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA-----VALR 137
            P +      +G  L        + + A+ ++      V CRI  DD +       V  +
Sbjct: 145 TPVSNQRTDEYG-GLKGGIKFCCEIVRAVKESCGHDFAVVCRINGDDYVKEGGNSIVEAQ 203

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
            L + ++++G +G+ I A     +          P   +  + E  K   ++ +  
Sbjct: 204 LLAQELERAGADGLNISAGMRDSELSFNDHCSGQPRGAWIHLSERIKRVVNIPVIA 259


>gi|134100700|ref|YP_001106361.1| 2,4-dienoyl-CoA reductase (NADPH) [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006495|ref|ZP_06564468.1| 2,4-dienoyl-CoA reductase (NADPH) [Saccharopolyspora erythraea NRRL
           2338]
 gi|133913323|emb|CAM03436.1| 2,4-dienoyl-CoA reductase [NADPH] [Saccharopolyspora erythraea NRRL
           2338]
          Length = 675

 Score = 35.9 bits (82), Expect = 8.8,   Method: Composition-based stats.
 Identities = 21/176 (11%), Positives = 55/176 (31%), Gaps = 17/176 (9%)

Query: 71  DFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTV 121
           + GY+ + +             P   +    +G        +  + +    +A      +
Sbjct: 154 EGGYDGVEIMGSEGYLINQFLAPRTNLRTDRWGGSAENRRRLAVEIVRRCRQAAGDDFII 213

Query: 122 KCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
             R+     VD       + +L  +++++G     I+      +   P     +P   + 
Sbjct: 214 MYRLSALDLVDGGQTWQEVVDLATAVEEAGAT--IINTGIGWHEARVPTIVTSVPRAAFT 271

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
            V    + +  + +  +  +     A ++L     D V + R    + A +    E
Sbjct: 272 GVVGKLRPHVSIPVVASNRINMPQVAEEVLSRGDADLVSMARPLLADPAWVAKAGE 327


>gi|88704258|ref|ZP_01101972.1| NADH:flavin oxidoreductase/NADH oxidase [Congregibacter litoralis
           KT71]
 gi|88701309|gb|EAQ98414.1| NADH:flavin oxidoreductase/NADH oxidase [Congregibacter litoralis
           KT71]
          Length = 406

 Score = 35.9 bits (82), Expect = 8.8,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 61/188 (32%), Gaps = 30/188 (15%)

Query: 62  LVEAAKIVEDFGYNEINL---------NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
              AAK +++ G+  + +             P +   + ++G  L      + + I A+ 
Sbjct: 129 FAVAAKAMQEAGFTGVQIHGAHGYLISQFLSPRSNQRDDAYGGELAHRARFLLEIIDAVR 188

Query: 113 KAL--SIPVTVKCRIGVDDQIPAVALRN---LVKSIKKSGVNGIWIHARKAILKGLSPKD 167
            A+    PV VK     D Q    A  +   + K +++  V+ I I         L  K+
Sbjct: 189 AAVGPGFPVAVKLNSA-DFQKGGFAFEDSLQVAKWLEEHSVDVIEISGGTYEQPKLLGKE 247

Query: 168 NRKIPNLDYDIVYEIKKEN------------PDLFIGLNGGLEDMSQALKILPSVDGVMI 215
             +     +     +++E               + + + GG    +   + L      +I
Sbjct: 248 GIEPTEKQHVAETTLRREAYFVDFALAMQKQVSIPLMVTGGFRSRAAMEQALDEGGAALI 307

Query: 216 GRAAYKNS 223
           G       
Sbjct: 308 G---LGRP 312


>gi|84516407|ref|ZP_01003766.1| FMN-dependent alpha-hydroxy acid dehydrogenase family protein
           [Loktanella vestfoldensis SKA53]
 gi|84509443|gb|EAQ05901.1| FMN-dependent alpha-hydroxy acid dehydrogenase family protein
           [Loktanella vestfoldensis SKA53]
          Length = 379

 Score = 35.9 bits (82), Expect = 8.8,   Method: Composition-based stats.
 Identities = 25/111 (22%), Positives = 36/111 (32%), Gaps = 20/111 (18%)

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
            A+  A   P+ VK     DD             +   G + IW+           P   
Sbjct: 241 KALRDAWDGPLVVKGVGRADD----------AARLTDEGADAIWVSTHAGRQFDGGPASI 290

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
             +P         I+   P   I  +G +E     L+ L    D VM+GRA
Sbjct: 291 ETLP--------AIRAATPLPVIFDSG-IEGGLDVLRALALGADFVMLGRA 332


>gi|260550792|ref|ZP_05824999.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter sp. RUH2624]
 gi|299768502|ref|YP_003730528.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter sp.
           DR1]
 gi|260406102|gb|EEW99587.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter sp. RUH2624]
 gi|298698590|gb|ADI89155.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Acinetobacter sp.
           DR1]
          Length = 243

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I K  P+L I + GG+  +      L   V  V+IG  A +    
Sbjct: 60  ------PIHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLEAGVTFVIIGTKAVQEPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKRFAG 123


>gi|238794192|ref|ZP_04637807.1| N-acetylmannosamine-6-phosphate 2-epimerase [Yersinia intermedia
           ATCC 29909]
 gi|238726482|gb|EEQ18021.1| N-acetylmannosamine-6-phosphate 2-epimerase [Yersinia intermedia
           ATCC 29909]
          Length = 228

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 4/90 (4%)

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPK-DNRKIPNLDYDIVYEIKKENPDLFIGLN 194
           + ++    + +  N +        L G + +   +K+   D+  + E+     DL +   
Sbjct: 128 MADIATLEEATHANYLGFDCVGTTLHGYTKETAGQKLAQEDFRFLREVL-AAVDLPVIAE 186

Query: 195 GGLEDMSQALKILP-SVDGVMIGRAAYKNS 223
           G +E    A + L      V++G  A    
Sbjct: 187 GNVETPEMAARCLALGAHAVVVG-GAITRP 215


>gi|197301496|ref|ZP_03166575.1| hypothetical protein RUMLAC_00228 [Ruminococcus lactaris ATCC
           29176]
 gi|197299456|gb|EDY33977.1| hypothetical protein RUMLAC_00228 [Ruminococcus lactaris ATCC
           29176]
          Length = 666

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 27/182 (14%), Positives = 57/182 (31%), Gaps = 17/182 (9%)

Query: 64  EAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMCKA 114
           EAAK  +  G++ + ++ G          P        FG  L          I  + + 
Sbjct: 154 EAAKRAQIAGFDTVEIHGGHSYLLSQFLSPITNKRTDEFGGSLENRARFARLVIEEVRRQ 213

Query: 115 LS--IPVTVKCR--IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRK 170
           +    P+ ++      ++           +K ++K  V+ I +              N  
Sbjct: 214 VGPFFPIFLRISADEFMEGGNTLEDSLEYLKYLEK-EVDVIDVSCGLNGSIQYQIDANHF 272

Query: 171 IPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTT 228
                  +   +K+      + + G + D   A  IL     D + +GR    +   +  
Sbjct: 273 PDGWRSYMAKAVKERFGKPCVTM-GNIRDPHVAEDILARGDADLIGMGRGLIADPDWVNK 331

Query: 229 VD 230
           V+
Sbjct: 332 VE 333


>gi|167564326|ref|ZP_02357242.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           oklahomensis EO147]
 gi|167571475|ref|ZP_02364349.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Burkholderia
           oklahomensis C6786]
          Length = 251

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 24/135 (17%), Positives = 50/135 (37%), Gaps = 19/135 (14%)

Query: 94  GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAV---ALRNLVKSIKKSGVNG 150
           G   + +P  + D  +A    + + +  K      D    +    + +L +  +  GV  
Sbjct: 105 GTAAVKDPGFLQDACSAFAGNIIVGLDAKDGKVATDGWSKLTGHEVIDLAQKFEDYGVES 164

Query: 151 I--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG--GLEDMSQALKI 206
           I      R  +L+G           ++ +   ++ +      I   G   + D+ +  K+
Sbjct: 165 IVYTDIGRDGMLQG-----------VNIEATVKLAQAVGIPVIASGGLSNIGDIEKLCKV 213

Query: 207 L-PSVDGVMIGRAAY 220
               V+GV+ GRA Y
Sbjct: 214 EDEGVEGVICGRAIY 228


>gi|158336451|ref|YP_001517625.1| pyruvate kinase [Acaryochloris marina MBIC11017]
 gi|158306692|gb|ABW28309.1| pyruvate kinase [Acaryochloris marina MBIC11017]
          Length = 591

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 27/138 (19%), Positives = 48/138 (34%), Gaps = 16/138 (11%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIW 152
            GA ++L+   V   + ++ ++     T+ CR+ V  ++      N         V  + 
Sbjct: 123 AGATILLDDGRVEMIVESVDQSSK---TLNCRVVVGGKLSDSKGVNFPGVYLS--VKALT 177

Query: 153 IHARKAILKGL-SPKDNRKIP----NLDYDIVYEIKKENP-DLFIGLNGGLEDMS---QA 203
              R+ +  GL    D   +       D   + EI       + +     +E      Q 
Sbjct: 178 DKDREDLQFGLTHGVDWVALSFVRNPADVIEIKEIIANAGKSIPVIA--KIEKHEAITQM 235

Query: 204 LKILPSVDGVMIGRAAYK 221
            +IL   DGVMI R    
Sbjct: 236 EEILSLCDGVMIARGDLG 253


>gi|332358170|gb|EGJ36000.1| dihydroorotate dehydrogenase A [Streptococcus sanguinis SK1056]
          Length = 311

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 64/189 (33%), Gaps = 19/189 (10%)

Query: 41  LGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLML 99
           L  S   +   L + G    +     + V+   +  I  LN+ CP   V      A    
Sbjct: 88  LQESEPNRTFFLSLVGMSPEETHTILQKVQASDFKGITELNLSCP--NVPGKPQIAY--- 142

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVD--DQIPAVALRN-----LVKSIKKSGVNGIW 152
           + +     ++ +    + P+ +K     D      A A+ N      V  +   G NG++
Sbjct: 143 DFETTEKILSEVFAYFTKPLGIKLPPYFDIVHFDQAAAIFNKYPLKFVNCVNSVG-NGLY 201

Query: 153 IHARKAILK---GLSPKDNRKIPNLDYDIVYEIKKEN-PDLFIGLNGGLEDMSQALKI-L 207
           I     +++   G      + I       V+   +   P++ I   GG+     A +  L
Sbjct: 202 IEDESVVIRPKNGFGGIGGQYIKPTALANVHAFYRRLKPEIQIIGTGGVLTGRDAFEHIL 261

Query: 208 PSVDGVMIG 216
                V +G
Sbjct: 262 CGASMVQVG 270


>gi|325969130|ref|YP_004245322.1| geranylgeranylglyceryl phosphate synthase [Vulcanisaeta moutnovskia
           768-28]
 gi|323708333|gb|ADY01820.1| geranylgeranylglyceryl phosphate synthase [Vulcanisaeta moutnovskia
           768-28]
          Length = 257

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 2/65 (3%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDE 231
            +   +V  +K+      I   GG+ D  +A ++ L   D V+ G    +   ++  +  
Sbjct: 183 PVRPRMVSRVKQLVSKPLIVG-GGIRDPEKAGELALAGADAVVTGTIIEEKPELIKDIIR 241

Query: 232 YFSNP 236
                
Sbjct: 242 AVHEG 246


>gi|308235315|ref|ZP_07666052.1| MaoC-like protein [Gardnerella vaginalis ATCC 14018]
          Length = 2590

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 31/153 (20%), Positives = 54/153 (35%), Gaps = 30/153 (19%)

Query: 82  GCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVK 141
           G P   V   +     +   D   + +  + +A   P  V  + G         +R +V+
Sbjct: 487 GAPIDGVVISAG----IPELDEAKELVKTL-QADGFP-YVAFKPG-----TVEQIRQVVR 535

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV--YEIKKENPDLFIGLNGGLED 199
             K      I      A ++G S   +    +LD  ++  Y   +E  +L +   GG+  
Sbjct: 536 IAKAVKPATII-----AQVEGGSAGGHHSWESLDDLLISTYAQVRECNNLVLVAGGGIGT 590

Query: 200 MSQALKILPS------------VDGVMIGRAAY 220
            ++A   +              VD VMIG AA 
Sbjct: 591 PARAADYISGEWSNKYDLPNMPVDAVMIGTAAM 623


>gi|302390645|ref|YP_003826466.1| inosine-5'-monophosphate dehydrogenase [Thermosediminibacter oceani
           DSM 16646]
 gi|302201273|gb|ADL08843.1| inosine-5'-monophosphate dehydrogenase [Thermosediminibacter oceani
           DSM 16646]
          Length = 482

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 23/143 (16%), Positives = 45/143 (31%), Gaps = 21/143 (14%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD--LF 190
            VA     + + ++G + + +      +          +P +    +Y+  +E     + 
Sbjct: 275 NVATAEATRDLIEAGADAVKVGMGPGSICTTRVVAGIGVPQV--TAIYDCAREAEKYGVP 332

Query: 191 IGLNGGLE-DMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDK 249
           I  +GG++        I    D VMIG        +            T  SP +  + K
Sbjct: 333 IIADGGIKYSGDIVKAIAAGADSVMIG-------GLFAG---------TEESPGEIEIYK 376

Query: 250 DFWRKISASMTDYAARHLHSGGK 272
               K+   M    A    S  +
Sbjct: 377 GRSFKVYRGMGSIGAMEEGSKDR 399


>gi|257056499|ref|YP_003134331.1| dihydroorotate dehydrogenase 2 [Saccharomonospora viridis DSM
           43017]
 gi|256586371|gb|ACU97504.1| dihydroorotate oxidase A [Saccharomonospora viridis DSM 43017]
          Length = 354

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 29/151 (19%), Positives = 51/151 (33%), Gaps = 20/151 (13%)

Query: 74  YNEINLNVGCPS----ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDD 129
            + + +NV  P+     ++ +      L+         +A        P+ VK       
Sbjct: 173 ADYVAINVSSPNTPGLRKLQDRGALTELLTELSRTAHELADKAGRGPTPLLVKVAP---- 228

Query: 130 QIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD-----------NRKIPNLDYDI 178
            +   A+  L+    +  V GI          GL+P D            R +     D+
Sbjct: 229 DLSFDAIAELLDVCTEHKVAGIIATNTTLARDGLAPGDARFVEEQGGLSGRPLAARALDV 288

Query: 179 VYEIKKENPD-LFIGLNGGLEDMSQALKILP 208
           V  I ++  D L I   GG+     AL++L 
Sbjct: 289 VRFIHEQAGDSLPIIGVGGISGPDDALRMLD 319


>gi|254419613|ref|ZP_05033337.1| ribulose-phosphate 3-epimerase [Brevundimonas sp. BAL3]
 gi|196185790|gb|EDX80766.1| ribulose-phosphate 3-epimerase [Brevundimonas sp. BAL3]
          Length = 247

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 20/123 (16%), Positives = 48/123 (39%), Gaps = 19/123 (15%)

Query: 50  LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
           +   I  +D ++L E  + +E  G + I+++       V +G F   + L PD     + 
Sbjct: 33  ICPSILASDFARLGEEVRALEAAGADWIHVD-------VMDGHFVPNITLGPD----IVK 81

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+    S+P  V         +    +   +++ + +G + + +H         +    R
Sbjct: 82  AIRPHTSLPFDV--------HLMVAPVDPWLEAYRDAGADLLTVHPESGPHLHRTLARIR 133

Query: 170 KIP 172
           ++ 
Sbjct: 134 QLG 136


>gi|225576381|ref|YP_002725399.1| inosine-5'-monophosphate dehydrogenase [Borrelia sp. SV1]
 gi|225547495|gb|ACN93474.1| inosine-5'-monophosphate dehydrogenase [Borrelia sp. SV1]
          Length = 404

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 31/180 (17%), Positives = 59/180 (32%), Gaps = 38/180 (21%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPV- 119
              + A+  EDF     +LN        ++   GA + ++ D +      +   + I V 
Sbjct: 120 DAYKNAEHKEDFPNACKDLN--------NKLRVGAAVSIDIDTIERVEELVKAHVDILVI 171

Query: 120 ---------------TVKCR-IGVDDQIPAVALRNLVKSIKKSGVNGIWIH------ARK 157
                          T+K +   +D     +  +     +   G + + +          
Sbjct: 172 DSAHGHSTRIIELVKTIKTKYPNLDLIAGNIVTKEAALDLISVGADCLKVGIGPGSICTT 231

Query: 158 AILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL-EDMSQALKILPSVDGVMIG 216
            I+ G+       I +     VYE  K + ++ I  +GG+         I    D VMIG
Sbjct: 232 RIVAGVGVPQITAICD-----VYEACK-STNICIIADGGIRFSGDVVKAIAAGADSVMIG 285


>gi|83747543|ref|ZP_00944581.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Ralstonia solanacearum UW551]
 gi|83725857|gb|EAP72997.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Ralstonia solanacearum UW551]
          Length = 247

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 20/103 (19%), Positives = 37/103 (35%), Gaps = 16/103 (15%)

Query: 135 ALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L +  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 149 EVVDLARKYEDYGVEAIIYTDIGRDGMLQG-----------INIDATVKLAQSVSIPVIA 197

Query: 193 LNG--GLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEY 232
             G   L+D+     +    V+GV+ GRA Y          E+
Sbjct: 198 SGGLSNLKDIDHLCAVETEGVEGVICGRAIYSGDLNFREAQEH 240


>gi|114562889|ref|YP_750402.1| imidazole glycerol phosphate synthase subunit HisF [Shewanella
           frigidimarina NCIMB 400]
 gi|122299973|sp|Q083K1|HIS6_SHEFN RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|114334182|gb|ABI71564.1| imidazole glycerol phosphate synthase subunit hisF [Shewanella
           frigidimarina NCIMB 400]
          Length = 257

 Score = 35.9 bits (82), Expect = 8.9,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L     + G + +            +   +R I   D   V  + ++  D+   + GG++
Sbjct: 35  LAARYAEEGADELV------FYDITASAHDRVI---DKSWVSRVAEQI-DIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            + QA + L    D + I   A  + ++++ + + F 
Sbjct: 85  TIEQAREKLAFGADKISINSPALSDPSLISRLQDEFG 121


>gi|327402395|ref|YP_004343233.1| 2-nitropropane dioxygenase NPD [Fluviicola taffensis DSM 16823]
 gi|327317903|gb|AEA42395.1| 2-nitropropane dioxygenase NPD [Fluviicola taffensis DSM 16823]
          Length = 317

 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 38/98 (38%), Gaps = 8/98 (8%)

Query: 120 TVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV 179
           TV+ +      +  V+        +++GV+ +     +A   G + +D        + ++
Sbjct: 103 TVRLKEAGITVVHVVSSAKFALKAQEAGVDAVVAEGFEA--GGHNGRDETTT----FCLI 156

Query: 180 YEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIG 216
            ++K     + +   GG+      L  L    DGV IG
Sbjct: 157 PQVK-AVISIPLIAAGGIGTGRGMLAALTLGADGVQIG 193


>gi|315093772|gb|EFT65748.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL060PA1]
          Length = 504

 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            GVD     +A     K++  +GV+GI +      +          +P +    ++E  K
Sbjct: 279 QGVDVVAGNIATYEAAKALCAAGVDGIKVGIGPGSICTTRVVAGVGVPQV--TAIFEASK 336

Query: 185 ENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                D+ +  +GGL+     A  ++   D VM+G
Sbjct: 337 AARQYDVPVIGDGGLQYSGDIAKALVAGADSVMLG 371


>gi|307726837|ref|YP_003910050.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1003]
 gi|307587362|gb|ADN60759.1| NADH:flavin oxidoreductase/NADH oxidase [Burkholderia sp. CCGE1003]
          Length = 790

 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 30/193 (15%), Positives = 61/193 (31%), Gaps = 31/193 (16%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACL---MLNPDIVGD 106
           + V A ++  + G++ + L   C                    +G  L   +  P  V  
Sbjct: 560 QFVRATQMSAEAGFDWLEL--HCAHGYFLSSFLSPLTNHRTDEYGGSLENRLRYPLQVFK 617

Query: 107 CIAAMCKALSIPVTVKCRIG--VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            I A+      P++V+      V+          + ++ K +G + I + +   + K   
Sbjct: 618 AIRAVWPE-DKPISVRISANDWVEGGTTPDDAVQIARAFKAAGADMIDVSSG-QVSKEEK 675

Query: 165 PKDNR--KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAY 220
           P   R  + P  D      ++ E   +     G + +      I+ +   D   I R   
Sbjct: 676 PVYGRMFQTPFAD-----RVRNEAG-IATIAVGAISEADHVNSIIAAGRADLCAIARPHL 729

Query: 221 KNS-AMLTTVDEY 232
            N    L    + 
Sbjct: 730 ANPSWTLNEAAKI 742


>gi|288931884|ref|YP_003435944.1| imidazoleglycerol phosphate synthase, cyclase subunit [Ferroglobus
           placidus DSM 10642]
 gi|288894132|gb|ADC65669.1| imidazoleglycerol phosphate synthase, cyclase subunit [Ferroglobus
           placidus DSM 10642]
          Length = 271

 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 35/98 (35%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L K   + G + +      A  +G              D++    +E   + + + GG+
Sbjct: 38  ELAKRYDEEGADELVFLDITASAQGRKTM---------VDVIERTAEEVF-IPLTVGGGI 87

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
           + +    ++L    D V I  AA KN   +    E F 
Sbjct: 88  KSIEDINEMLSAGADKVSINTAAVKNPEFVRKAAEIFG 125


>gi|222478458|ref|YP_002564695.1| dihydroorotate dehydrogenase [Halorubrum lacusprofundi ATCC 49239]
 gi|222451360|gb|ACM55625.1| dihydroorotate dehydrogenase [Halorubrum lacusprofundi ATCC 49239]
          Length = 360

 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 69/184 (37%), Gaps = 28/184 (15%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEAAK-------IVEDFGYNEINLNVGCPSARVHE 90
           + +      E P+ + IG +  + L EA +        V D G +   +NV  P      
Sbjct: 139 ERLDREPLPEIPVGINIGKSKSTPLAEAPEDYLYTYERVADAG-DYFVVNVSSP------ 191

Query: 91  GSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG 150
            + G   + N   + + +  +  A + P+ VK        +P  A+ + +  +   G++G
Sbjct: 192 NTPGLRELQNRAALEEILGTLTDAGADPLLVKLSP----DLPEPAVEDALGVVDDLGLDG 247

Query: 151 I----WIHARKAILKGLSPKD-----NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS 201
           +       +R   LK     +      + I  +  + V  +  E  D+ +   GG+ D  
Sbjct: 248 VIATNTTTSRPNSLKSPQQAERGGLSGKPIEPIATERVRFVA-ERTDVPVIGVGGISDAK 306

Query: 202 QALK 205
            A +
Sbjct: 307 GAYE 310


>gi|55380332|ref|YP_138181.1| FMN oxidoreductase protein [Haloarcula marismortui ATCC 43049]
 gi|55233057|gb|AAV48475.1| Fmn oxidoreductase protein [Haloarcula marismortui ATCC 43049]
          Length = 407

 Score = 35.9 bits (82), Expect = 9.0,   Method: Composition-based stats.
 Identities = 22/128 (17%), Positives = 41/128 (32%), Gaps = 16/128 (12%)

Query: 105 GDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLV----KSIKKSGVNGIWIHAR 156
            + +AA+ +A      V  R+     +D+        +      + +  +G + I +   
Sbjct: 246 REVVAAVDEATPADFVVGIRVSQSTALDEDHRWPEGEDAAAVFFEELSAAGADYIHVTEP 305

Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMI 215
            A     +P      P L             +  I  NGGL     A + +    D V +
Sbjct: 306 DAT----TPAFGDDGPTLAEAAAEY---AADETVIIDNGGLGTPDAAREKIDAGADLVTL 358

Query: 216 GRAAYKNS 223
             +A  N 
Sbjct: 359 ATSALANP 366


>gi|325123766|gb|ADY83289.1| phosphoribosylformimino-5-aminoimidazole carboxamide isomerase
           [Acinetobacter calcoaceticus PHEA-2]
          Length = 243

 Score = 35.9 bits (82), Expect = 9.1,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 41/130 (31%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     DD + +       +     G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMEDDTVFSDDPVATAQHWVNEGARRLHLVDLNGAFAGT--- 59

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  +   +V  I K  P+L I + GG+  +      L   V  V+IG  A +    
Sbjct: 60  ------PIHKPVVEAIAKAQPELPIQIGGGIRSLETIEHYLEAGVTFVIIGTKAVQEPEF 113

Query: 226 LTTVDEYFSN 235
           +    + F+ 
Sbjct: 114 VEEACKRFAG 123


>gi|256019004|ref|ZP_05432869.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Shigella sp. D9]
 gi|332280101|ref|ZP_08392514.1| 2,4-dienoyl-CoA reductase [Shigella sp. D9]
 gi|332102453|gb|EGJ05799.1| 2,4-dienoyl-CoA reductase [Shigella sp. D9]
          Length = 672

 Score = 35.9 bits (82), Expect = 9.1,   Method: Composition-based stats.
 Identities = 23/191 (12%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 D +  + + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVDVVRTVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|227889188|ref|ZP_04006993.1| possible (S)-2-hydroxy-acid oxidase [Lactobacillus johnsonii ATCC
           33200]
 gi|227850417|gb|EEJ60503.1| possible (S)-2-hydroxy-acid oxidase [Lactobacillus johnsonii ATCC
           33200]
          Length = 409

 Score = 35.9 bits (82), Expect = 9.1,   Method: Composition-based stats.
 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 15/111 (13%)

Query: 108 IAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
           I  + K   +PV VK     +D                +G +GI +          +P  
Sbjct: 224 IHKIKKIADVPVIVKGVECAED----------AMLAVGAGADGIVVSNHGGREVDGAPAT 273

Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGR 217
              +P    +I   ++  N  + + L+GG+   S   K L    D V IGR
Sbjct: 274 IDVLP----EIAKAVRSSNHRVPVILDGGVRRGSHVFKALALGADLVGIGR 320


>gi|94986257|ref|YP_605621.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Deinococcus geothermalis DSM 11300]
 gi|148839490|sp|Q1IWD2|HIS4_DEIGD RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|94556538|gb|ABF46452.1| Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Deinococcus geothermalis DSM 11300]
          Length = 243

 Score = 35.9 bits (82), Expect = 9.1,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV 229
           ++ +I  E   + + + GG+ D + A  +L   V  V+IG AA KN A++  +
Sbjct: 73  VITQITAELG-VPVEVGGGIRDRAAAEALLDAGVGRVVIGTAAVKNPALVREL 124


>gi|312141877|ref|YP_004009213.1| NADH:flavin oxidoreductase/NADH oxidase [Rhodococcus equi 103S]
 gi|311891216|emb|CBH50535.1| putative NADH:flavin oxidoreductase/NADH oxidase [Rhodococcus equi
           103S]
          Length = 662

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 40/193 (20%), Positives = 70/193 (36%), Gaps = 27/193 (13%)

Query: 47  EKPLALQIGGADISKLVEAAKIVEDFGYNEIN-LNVGCPSARVHEGSFGACLMLNPDIVG 105
           E  + LQ  G D        +IV   GY     LN   P+  V E  +G  L     ++ 
Sbjct: 156 EGAIRLQTAGLDG------VEIVASHGYLPAQFLN---PNLNVREDRYGGSLENRMRMLR 206

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVA----LRNLVKSIKKSG-VNGIWIHARKAIL 160
           +   A+ +A+     V  R+  D+             L K++   G V+ + +    +  
Sbjct: 207 ETARAVRQAVGPDFVVGVRLSADENTYDATGESDTIALCKALDADGYVDYLNVTEGTSAS 266

Query: 161 KGLSPKDNRKIPNLDYDIVY------EIKKENPDLFIGLNGGLEDMSQALKILP--SVDG 212
            G S      +P + Y+ +Y      +IKK+     +   G +    +A  +L     D 
Sbjct: 267 TGGSTHI---VPPMHYEAMYTAPSAAKIKKQVSVPVLVA-GRINQPHEAEIVLASGQADA 322

Query: 213 VMIGRAAYKNSAM 225
             + RA   +  M
Sbjct: 323 CAMTRALICDPEM 335


>gi|300901469|ref|ZP_07119552.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 198-1]
 gi|300355107|gb|EFJ70977.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 198-1]
          Length = 739

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 31/230 (13%), Positives = 68/230 (29%), Gaps = 51/230 (22%)

Query: 23  YTEMIVADAILRGDKKNILGF--STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLN 80
           Y   +VA + L+      +    S +E    LQ+           A++  + GY+ + + 
Sbjct: 110 YQPHLVAPSALQAPINRFVPHELSHEE---ILQLIDN----FARCAQLAREAGYDGVEV- 161

Query: 81  VGCPSARVHEGSFGACLM-------------------LNPDIVG-DCIAAMCKALSIPVT 120
                           L+                    N      + + A+ + +     
Sbjct: 162 ----------MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRAVRERVGNDFI 211

Query: 121 VKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDY 176
           +  R+ + D +           L ++I+ +G     I+      +   P     +P   +
Sbjct: 212 IIYRLSMLDLVEGGGTFAETVGLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAF 269

Query: 177 DIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             V  ++K       +  N  + D   A  IL   D  M+   +     +
Sbjct: 270 SWVTRKLKSHVSLPLVTTNR-INDPQVADDILSRGDADMV---SMARPFL 315


>gi|154687954|ref|YP_001423115.1| thiamine-phosphate pyrophosphorylase [Bacillus amyloliquefaciens
           FZB42]
 gi|166228068|sp|A7ZA58|THIE_BACA2 RecName: Full=Thiamine-phosphate pyrophosphorylase; Short=TMP
           pyrophosphorylase; Short=TMP-PPase; AltName:
           Full=Thiamine-phosphate synthase
 gi|154353805|gb|ABS75884.1| ThiE [Bacillus amyloliquefaciens FZB42]
          Length = 224

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           VK  + +G + +       +    + KD   +  +   ++ E++++   + I   GG+  
Sbjct: 124 VKRAEAAGADYV---GMGPVYPTETKKDAEAVQGV--TLIEEVRRQGITIPIVGIGGITA 178

Query: 200 MSQALKILPSVDGV-MI 215
            + A  I    DGV MI
Sbjct: 179 DNAAPVIEAGADGVSMI 195


>gi|108762116|ref|YP_632399.1| imidazole glycerol phosphate synthase subunit HisF [Myxococcus
           xanthus DK 1622]
 gi|122980949|sp|Q1D4M4|HIS6_MYXXD RecName: Full=Imidazole glycerol phosphate synthase subunit hisF;
           AltName: Full=IGP synthase cyclase subunit; AltName:
           Full=IGP synthase subunit hisF; AltName: Full=ImGP
           synthase subunit hisF; Short=IGPS subunit hisF
 gi|108465996|gb|ABF91181.1| imidazoleglycerol phosphate synthase, cyclase subunit [Myxococcus
           xanthus DK 1622]
          Length = 253

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 44/117 (37%), Gaps = 12/117 (10%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            L +  +  G + +        L   +  + R      +++V    ++   + + + GG+
Sbjct: 34  ELARRYEAEGADELT------FLDISASAEERDTL---WELVRRTAEQLF-IPLAVGGGV 83

Query: 198 EDMSQ-ALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDFWR 253
             +      +    D V I  AA  N A+LT   E F      +S I  + D D WR
Sbjct: 84  RTVDDVGRALRAGADKVSINSAAVANPALLTACAERFGAQCVVAS-IDAKRDGDRWR 139


>gi|229109516|ref|ZP_04239107.1| NADPH dehydrogenase [Bacillus cereus Rock1-15]
 gi|228673935|gb|EEL29188.1| NADPH dehydrogenase [Bacillus cereus Rock1-15]
          Length = 319

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 47/136 (34%), Gaps = 10/136 (7%)

Query: 93  FGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNG 150
           +G         + + I ++ +  + P+ V+        + +         K +K+ GV+ 
Sbjct: 160 YGGSPENRYRFLREIIDSINEVWNGPLFVRISANDYHPEGLTVQDYVQYTKWMKEQGVDL 219

Query: 151 IWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-- 208
           I   +   +     P      P         IK+   ++  G  G +    QA +IL   
Sbjct: 220 IDCSSGAVV-----PARIDVYPGYQVQYAKHIKEHA-NIATGAVGLITTGVQAEQILNNN 273

Query: 209 SVDGVMIGRAAYKNSA 224
             D + IGR   +N  
Sbjct: 274 EADLIFIGRELLRNPY 289


>gi|209525381|ref|ZP_03273922.1| N-acylglucosamine-6-phosphate 2-epimerase [Arthrospira maxima
           CS-328]
 gi|209494232|gb|EDZ94546.1| N-acylglucosamine-6-phosphate 2-epimerase [Arthrospira maxima
           CS-328]
          Length = 223

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 18/121 (14%), Positives = 43/121 (35%), Gaps = 19/121 (15%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           + + V   IA + + L  PV               A  + V +          ++     
Sbjct: 104 DGETVASLIAQIHQKLGKPVMADIDTLAAAIAAVEAGADCVGT---------TLYGYTEA 154

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRA 218
            + LSP          ++++ ++ K+  D  +   GG+   + A + +    + +++G A
Sbjct: 155 TQHLSPPG--------FELLSQLVKQL-DCPVICEGGISSPTLAKQAIALGANAIVVGTA 205

Query: 219 A 219
            
Sbjct: 206 I 206


>gi|50843228|ref|YP_056455.1| IMP dehydrogenase / GMP reductase [Propionibacterium acnes
           KPA171202]
 gi|50840830|gb|AAT83497.1| IMP dehydrogenase / GMP reductase [Propionibacterium acnes
           KPA171202]
 gi|314924254|gb|EFS88085.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL001PA1]
 gi|314964928|gb|EFT09027.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL082PA2]
 gi|314982155|gb|EFT26248.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL110PA3]
 gi|315090386|gb|EFT62362.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL110PA4]
 gi|315103891|gb|EFT75867.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL050PA2]
 gi|315106194|gb|EFT78170.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL030PA1]
 gi|327325591|gb|EGE67390.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL103PA1]
          Length = 504

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            GVD     +A     K++  +GV+GI +      +          +P +    ++E  K
Sbjct: 279 QGVDVVAGNIATYEAAKALCAAGVDGIKVGIGPGSICTTRVVAGVGVPQV--TAIFEASK 336

Query: 185 ENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                D+ +  +GGL+     A  ++   D VM+G
Sbjct: 337 AARQYDVPVIGDGGLQYSGDIAKALVAGADSVMLG 371


>gi|191166831|ref|ZP_03028656.1| 2,4-dienoyl-CoA reductase [Escherichia coli B7A]
 gi|293449418|ref|ZP_06663839.1| 2,4-dienoyl-CoA reductase [Escherichia coli B088]
 gi|309793648|ref|ZP_07688074.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 145-7]
 gi|190903073|gb|EDV62797.1| 2,4-dienoyl-CoA reductase [Escherichia coli B7A]
 gi|291322508|gb|EFE61937.1| 2,4-dienoyl-CoA reductase [Escherichia coli B088]
 gi|308122605|gb|EFO59867.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 145-7]
 gi|320201991|gb|EFW76566.1| 2,4-dienoyl-CoA reductase [Escherichia coli EC4100B]
 gi|323183665|gb|EFZ69062.1| 2,4-dienoyl-CoA reductase [Escherichia coli 1357]
          Length = 672

 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 22/191 (11%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + +  + + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRTVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|300821678|ref|ZP_07101824.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 119-7]
 gi|300525816|gb|EFK46885.1| 2,4-dienoyl-CoA reductase [Escherichia coli MS 119-7]
          Length = 672

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 22/191 (11%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + +  + + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRTVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|302687194|ref|XP_003033277.1| hypothetical protein SCHCODRAFT_54820 [Schizophyllum commune H4-8]
 gi|300106971|gb|EFI98374.1| hypothetical protein SCHCODRAFT_54820 [Schizophyllum commune H4-8]
          Length = 477

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 16/130 (12%), Positives = 50/130 (38%), Gaps = 19/130 (14%)

Query: 94  GACLMLNPDIVGDCIAAMCKALS-------IPVTVKCRIGVDDQIPAVALRNLVKSIKKS 146
           G   +   D++   ++ + +A         +P   K  + +   +    ++ + + ++ S
Sbjct: 257 GLRGLQERDLLKKLLSGVSQARKKLPASDFVPKGPKLLLKISPDLTPEQIKEVAQVVRAS 316

Query: 147 GVNGIWIHARKAILKGLSPKD----------NRKIPNLDYDIVYEIKKENP-DLFIGLNG 195
            V+G+ + +   I +    +D             +  +    +  ++ + P ++ I   G
Sbjct: 317 HVDGVIV-SNTTIQRPKGLRDPKRDEAGGLSGPPLKPIALAALRTLRGQLPAEIPIIGCG 375

Query: 196 GLEDMSQALK 205
           G+   + AL+
Sbjct: 376 GIASGADALE 385


>gi|294677264|ref|YP_003577879.1| dihydroorotate oxidase [Rhodobacter capsulatus SB 1003]
 gi|294476084|gb|ADE85472.1| dihydroorotate oxidase-1 [Rhodobacter capsulatus SB 1003]
          Length = 335

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 35/165 (21%), Positives = 57/165 (34%), Gaps = 42/165 (25%)

Query: 70  EDFGYNEINLNVGCPSARVHEGSFGACLMLNPD--------IVGDCIAAMCKALSIPVTV 121
           E+ G   I LNV               L  +P+           D + A+C+ + IPV V
Sbjct: 124 EEAGAAAIELNV-------------YFLPTDPNVSGSDVERRTLDVVRAVCETVKIPVAV 170

Query: 122 KCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYE 181
           K               ++ K I  +G  G+ +  R      + P      P L     YE
Sbjct: 171 KIGPYFSSP------AHMAKRIVAAGAKGVVLFNRF-YQPEIDPVGLSVTPALQLSTRYE 223

Query: 182 IKKENPDLFIG-----------LNGGLEDMSQALK-ILPSVDGVM 214
           ++   P L++G            + G+E     ++ +L   D VM
Sbjct: 224 MR--LPLLWVGVLSGRLGGSLAASTGVESAEDVVRYLLAGADVVM 266


>gi|302529447|ref|ZP_07281789.1| dihydrodipicolinate synthase [Streptomyces sp. AA4]
 gi|302438342|gb|EFL10158.1| dihydrodipicolinate synthase [Streptomyces sp. AA4]
          Length = 314

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 27/89 (30%), Gaps = 12/89 (13%)

Query: 105 GDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLS 164
            + I  + KA+   V     +             L    + +G++   I         ++
Sbjct: 65  AETIRTVAKAVDDKVPF---MPGTGSAKLDETLELTAEARDAGIDAALI---------IT 112

Query: 165 PKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           P   R      Y     + KE PDL I  
Sbjct: 113 PYYARPTQEALYQWYATVAKEFPDLPIVA 141


>gi|289207313|ref|YP_003459379.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Thioalkalivibrio sp. K90mix]
 gi|288942944|gb|ADC70643.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Thioalkalivibrio sp. K90mix]
          Length = 243

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 48/136 (35%), Gaps = 11/136 (8%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K    +G   + I        G            + + V+ I +  PDL I + GG+
Sbjct: 34  EMAKRWVDAGAERLHIVDLDGAFAG---------HPRNAEAVHAIAEAFPDLPIQIGGGI 84

Query: 198 EDMSQALKILP-SVDGVMIGRAAYKNSAMLTTV-DEYFSNPLTGSSPIKTRVDKDFWRKI 255
            D       L   V+ V+IG  A      +  +  E+    + G      ++  D W K+
Sbjct: 85  RDEDTVQAYLDAGVEFVIIGTRAVSAPHFVNDLCLEFPGRIIVGLDAKDGKLAVDGWSKL 144

Query: 256 SASMTDYAARHLHSGG 271
           S       A+H  + G
Sbjct: 145 SHHDVIDLAQHFEADG 160


>gi|254469168|ref|ZP_05082573.1| oxidoreductase, FAD/FMN-binding family [Pseudovibrio sp. JE062]
 gi|211961003|gb|EEA96198.1| oxidoreductase, FAD/FMN-binding family [Pseudovibrio sp. JE062]
          Length = 765

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 33/214 (15%), Positives = 66/214 (30%), Gaps = 32/214 (14%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGC-----------PSARVHEGSFGACL---MLNPDIVG 105
            + V AAK+    G++ I   V C           P     E  +G  L   M  P    
Sbjct: 549 EEFVNAAKMANASGFDMIE--VHCAHGYLLSSFISPLTNKREDEYGGSLENRMRYP---L 603

Query: 106 DCIAAMCKAL--SIPVTVKCRIG---VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAIL 160
           + I A+ +A     P++V+        D+ +       + + +  + V+   + A +   
Sbjct: 604 EVIRAVREAWPQDKPMSVRISATDWVEDEGLTPEEAVEIARLLDAADVDICDVSAGQTST 663

Query: 161 KGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRA 218
           +                    I+ +     + + G + +      IL +   D V + R 
Sbjct: 664 R----AQPVYGRMFQVPFSDRIRNDAGMKTMAV-GNIYEPDHVNSILMAGRADLVCLARP 718

Query: 219 AYKNS-AMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
              +    L    E     +    P     D+ +
Sbjct: 719 HLSDPYWTLHAAAELGDKGVYWPEPYHAGRDQLY 752


>gi|83644201|ref|YP_432636.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Hahella chejuensis
           KCTC 2396]
 gi|123534398|sp|Q2SMB3|HIS4_HAHCH RecName: Full=1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase; AltName:
           Full=Phosphoribosylformimino-5-aminoimidazole
           carboxamide ribotide isomerase
 gi|83632244|gb|ABC28211.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Hahella chejuensis KCTC 2396]
          Length = 244

 Score = 35.6 bits (81), Expect = 9.3,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 45/130 (34%), Gaps = 10/130 (7%)

Query: 107 CIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
            I A+       V +K     D  + +    ++      +G   + +        G    
Sbjct: 3   IIPAIDLKDGKCVRLKQGRMDDSTVFSDDPVSMAAQWVDAGARRLHLVDLNGAFAG---- 58

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAM 225
                  ++ +IV  I K  PDL I + GG+ ++    + L   V  V+IG  A K  A 
Sbjct: 59  -----KPVNGEIVSAIAKAYPDLPIQIGGGIRELDIIEQYLDAGVKYVIIGTKAVKEPAF 113

Query: 226 LTTVDEYFSN 235
           +      F  
Sbjct: 114 VEEACRAFPG 123


>gi|327332310|gb|EGE74046.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           HL097PA1]
          Length = 504

 Score = 35.6 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            GVD     +A     K++  +GV+GI +      +          +P +    ++E  K
Sbjct: 279 QGVDVVAGNIATYEAAKALCAAGVDGIKVGIGPGSICTTRVVAGVGVPQV--TAIFEASK 336

Query: 185 ENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                D+ +  +GGL+     A  ++   D VM+G
Sbjct: 337 AARQYDVPVIGDGGLQYSGDIAKALVAGADSVMLG 371


>gi|295107475|emb|CBL05018.1| pyridoxal phosphate synthase yaaD subunit [Gordonibacter pamelaeae
           7-10-1-b]
          Length = 296

 Score = 35.6 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 41/221 (18%), Positives = 66/221 (29%), Gaps = 68/221 (30%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           AKI ED G   +      P+        G   M +P      I  + +A+SIPV  KCRI
Sbjct: 33  AKIAEDAGAVAVMALERVPAD--IRAHGGVARMSDP----TMIEGIVEAVSIPVMAKCRI 86

Query: 126 GV------------------------DDQIP-------------AVALRNLVKSIKKSGV 148
           G                         DD+               A  L   ++ I +   
Sbjct: 87  GHFVEAQVLQSLGVDFIDESEVLTPADDEYHVNKWDFDVPFVCGARNLGEALRRIAEGAA 146

Query: 149 ------------------NGIWIHARKAILKGLSPKDNRKIPN---LDYDIVYEIKKENP 187
                             +   +    A +KGL  +            Y++V  + +   
Sbjct: 147 MIRTKGEPGTGNVVEAVRHMRTVTTDIARIKGLRDEQLFTAAKDLQAPYELVKWVAEHGC 206

Query: 188 DLFI-GLNGGLEDMSQALKILP-SVDGVMIGRAAY--KNSA 224
              +    GG+   + A  ++    DGV +G   +   N A
Sbjct: 207 LPVVNFSAGGIATPADAALMMQLGCDGVFVGSGIFKSGNPA 247


>gi|293376887|ref|ZP_06623105.1| oxidoreductase, FAD/FMN-binding [Turicibacter sanguinis PC909]
 gi|292644497|gb|EFF62589.1| oxidoreductase, FAD/FMN-binding [Turicibacter sanguinis PC909]
          Length = 344

 Score = 35.6 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 31/217 (14%), Positives = 74/217 (34%), Gaps = 29/217 (13%)

Query: 29  ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVG------ 82
           ++  LRGD  ++       K +            ++AAK  ++ G++ + +++       
Sbjct: 116 SELWLRGDTPSLALTHEGLKSIRH--------AFIDAAKRAKEAGFDGVQVHMAHGYLLS 167

Query: 83  ---CPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL--SIPVTVKCRIGVDDQIPAVA-- 135
               P   + +  +G  +        + I  + +A   + P+ +K    V+    A    
Sbjct: 168 EFITPQHNLRQDEYGGSVENRFRFPREIILGIKQACGENYPIFIKINSNVELNDEAYESD 227

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNG 195
           L  ++  ++  GV  +        L G      +   +  Y        E   + + L G
Sbjct: 228 LLYMLNELETLGVEAV-------ELSGCDFGKKKYTDHNYYLERASRLAELTTVPLILVG 280

Query: 196 GLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
           G+  +S    +L   +D +   R       ++  +  
Sbjct: 281 GIRTLSDIEHVLQNGIDMISFCRPFICEPNLVRQLKA 317


>gi|121611761|ref|YP_999568.1| histidine biosynthesis [Verminephrobacter eiseniae EF01-2]
 gi|121556401|gb|ABM60550.1| histidine biosynthesis [Verminephrobacter eiseniae EF01-2]
          Length = 229

 Score = 35.6 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 16/85 (18%), Positives = 29/85 (34%), Gaps = 1/85 (1%)

Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFSNPL 237
           + E   +   + I + GG+  +     +L    D V I  AA     ++  V E F +  
Sbjct: 43  IIERAADQIYVPITVGGGIRSLHDVRTMLCSGADKVAINTAAVARPGLIAEVSERFGSQC 102

Query: 238 TGSSPIKTRVDKDFWRKISASMTDY 262
              S    R     W     +  ++
Sbjct: 103 MVLSVEAKRKSGGGWEAFVDNGREH 127


>gi|29831543|ref|NP_826177.1| inosine-5'-monophosphate dehydrogenase [Streptomyces avermitilis
           MA-4680]
 gi|29608659|dbj|BAC72712.1| putative inosine-5'-monophosphate dehydrogenase [Streptomyces
           avermitilis MA-4680]
          Length = 502

 Score = 35.6 bits (81), Expect = 9.4,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 46/118 (38%), Gaps = 10/118 (8%)

Query: 100 NPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
           +  +VGD +A +              GVD     +A R+  +++  SGV+GI +      
Sbjct: 260 HSRLVGDMVAKIKSNSG---------GVDVIGGNIATRDGAQALIDSGVDGIKVGVGPGS 310

Query: 160 LKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
           +          +P +       +  +   + +  +GGL+     A  ++   D VM+G
Sbjct: 311 ICTTRVVAGIGVPQVTAIYEASLAAKEAGVPVIGDGGLQYSGDIAKALVAGADTVMLG 368


>gi|328675792|gb|AEB28467.1| Inosine-5'-monophosphate dehydrogenase [Francisella cf. novicida
           3523]
          Length = 486

 Score = 35.6 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 5/87 (5%)

Query: 133 AVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPD--LF 190
            +A     K + K+G + + +      +          +P +    +  + +   +  + 
Sbjct: 277 NIATAEAAKDLVKAGADAVKVGIGPGSICTTRIVAGVGVPQI--TAIANVAEALKETGIP 334

Query: 191 IGLNGGLE-DMSQALKILPSVDGVMIG 216
           +  +GG+      A  I+     VMIG
Sbjct: 335 VIADGGIRYSGDIAKAIVAGASVVMIG 361


>gi|295695904|ref|YP_003589142.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus tusciae DSM 2912]
 gi|295411506|gb|ADG05998.1| NADH:flavin oxidoreductase/NADH oxidase [Bacillus tusciae DSM 2912]
          Length = 695

 Score = 35.6 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 23/147 (15%), Positives = 54/147 (36%), Gaps = 21/147 (14%)

Query: 38  KNILGFSTQEKPLALQIGGAD-------ISKLVEAAKIVEDFGYNEINLNVG-----CPS 85
           +++   + ++ P+  ++ G D         + V  A+++E+ G + +N+ +G      P+
Sbjct: 203 RSVRRCAGEDFPVIFRMSGLDLIPDSTTWEETVRFARLLEENGVDALNIGIGWHESAIPT 262

Query: 86  ARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKK 145
            + H                     + +A+SIPV V  RI   +    +    +   +  
Sbjct: 263 VQAHVPHAA---------FAHVAGEIKRAVSIPVVVSNRINRPELANRLLAEGVADFVSM 313

Query: 146 SGVNGIWIHARKAILKGLSPKDNRKIP 172
           +       H  + + +G     N  I 
Sbjct: 314 ARPFLADPHFVRKVEEGRPESINTCIA 340


>gi|282855112|ref|ZP_06264444.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           J139]
 gi|282581700|gb|EFB87085.1| inosine-5'-monophosphate dehydrogenase [Propionibacterium acnes
           J139]
          Length = 504

 Score = 35.6 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 125 IGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKK 184
            GVD     +A     K++  +GV+GI +      +          +P +    ++E  K
Sbjct: 279 QGVDVVAGNIATYEAAKALCAAGVDGIKVGIGPGSICTTRVVAGVGVPQV--TAIFEASK 336

Query: 185 ENP--DLFIGLNGGLE-DMSQALKILPSVDGVMIG 216
                D+ +  +GGL+     A  ++   D VM+G
Sbjct: 337 AARQYDVPVIGDGGLQYSGDIAKALVAGADSVMLG 371


>gi|242239661|ref|YP_002987842.1| imidazole glycerol phosphate synthase subunit HisF [Dickeya
           dadantii Ech703]
 gi|242131718|gb|ACS86020.1| imidazoleglycerol phosphate synthase, cyclase subunit [Dickeya
           dadantii Ech703]
          Length = 258

 Score = 35.6 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 139 LVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLE 198
           L +   + G + +  +   A   G           +D   V  +  E  D+   + GG++
Sbjct: 35  LAQRYAQEGADELVFYDITASSDGRV---------VDKSWVSRVA-EVIDIPFCVAGGIK 84

Query: 199 DMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDEYFS 234
            +  A +IL    D + I   A  +  +++ + + + 
Sbjct: 85  SIEDAGQILSFGADKISINSPALADPDLISRLADRYG 121


>gi|328765901|gb|EGF75996.1| hypothetical protein BATDEDRAFT_93141 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 193

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 143 IKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ 202
           +  S +  +       I    +  D +    L++  +  +++E PDL I   GG+  +  
Sbjct: 106 VANSPIALVDYIGAGPIFDTTTKLDAKATVGLEW--ITTLRREFPDLPIVGIGGI-TIEN 162

Query: 203 ALKILP-SVDGV 213
           A  ++    DGV
Sbjct: 163 AASVIEAGADGV 174


>gi|325273142|ref|ZP_08139438.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas sp.
           TJI-51]
 gi|324101717|gb|EGB99267.1| 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase [Pseudomonas sp.
           TJI-51]
          Length = 243

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 2/101 (1%)

Query: 173 NLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILP-SVDGVMIGRAAYKNSAMLTTVDE 231
            ++ ++V  I K  P L I + GG+  +      +   V  V+IG  A K  A +    +
Sbjct: 60  PVNGEVVTAIAKRYPTLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKQPAFVAEACK 119

Query: 232 YFSNP-LTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGG 271
            F    + G       V  D W ++S+      A+   + G
Sbjct: 120 AFPGKVIVGLDAKDGFVATDGWAEVSSVQVIDLAKRFEADG 160


>gi|323499614|ref|ZP_08104583.1| NADH:flavin oxidoreductase [Vibrio sinaloensis DSM 21326]
 gi|323315354|gb|EGA68396.1| NADH:flavin oxidoreductase [Vibrio sinaloensis DSM 21326]
          Length = 363

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 31/196 (15%), Positives = 65/196 (33%), Gaps = 23/196 (11%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
               AAK   + G++ + ++ G  +  + +             +G         +   + 
Sbjct: 161 DFAYAAKRAVEAGFDGVEIHGG--NGYLIDQFLRTNSNHREDKYGGSRENRVRFLLQVVD 218

Query: 110 AMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNR 169
           A+ + +     V  R+        +   ++V +I  +      + AR      LS  D  
Sbjct: 219 AVSEVIGAD-KVGVRLAPFITFKDMNCPDIVPTILLASQQ---LQARDIAYLHLSEADWE 274

Query: 170 KIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLT 227
             P +  D    +++   +  I   G   D  +A ++L     D V  GR    N  +++
Sbjct: 275 DAPQIPEDFRIALRERFSNTIIVAGG--YDQMRADEVLNKGYADLVAFGRPFVSNPDLVS 332

Query: 228 TVDEYFSNPLTGSSPI 243
            +      PL    P 
Sbjct: 333 RLAN--QQPLAELDPT 346


>gi|293377068|ref|ZP_06623278.1| dihydroorotate oxidase [Enterococcus faecium PC4.1]
 gi|292644284|gb|EFF62384.1| dihydroorotate oxidase [Enterococcus faecium PC4.1]
          Length = 285

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 58/178 (32%), Gaps = 28/178 (15%)

Query: 48  KPLALQIGG----ADISKLVEAAKIVEDFGYNEI-NLNVGCPSARVHEGSFGACLMLNPD 102
           +PL   I G     ++  L E    +E  G   I  LN+ CP   V        L  + +
Sbjct: 96  QPLFFSIAGMSVQENLEMLGE----IEKSGLKGITELNLSCP--NVPGK---PQLAYDFE 146

Query: 103 IVGDCIAAMCKALSIPVTVKCRIGVD-------DQIPAVALRNLVKSIKKSGVNGIWIHA 155
              + +  +    S P+ +K     D         I        V +I   G NG++I  
Sbjct: 147 TTYETLKEVFSIFSKPLGIKLPPYFDFAHFDQMADILNQFPLTYVNAINSVG-NGLYIDT 205

Query: 156 RKAIL-----KGLSPKDNRKIPNLDYDIVYEIK-KENPDLFIGLNGGLEDMSQALKIL 207
            K  +     +G        I       V     +  P++ I   GG+     A + L
Sbjct: 206 DKEAVVIKPKEGFGGIGGEYIKPTALANVRAFYTRLKPEIQIIGTGGIRTGQDAFEHL 263


>gi|328475491|gb|EGF46252.1| tryptophan synthase subunit alpha [Lactobacillus rhamnosus MTCC
           5462]
          Length = 264

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 45/161 (27%), Gaps = 50/161 (31%)

Query: 104 VGDCIAAMCKALSIPVTV----------------------KCRIGVDDQIPAVALRNLVK 141
           V + + A  K  ++P+                        K    V   +P  +   +V 
Sbjct: 76  VFEIVEAARKKTAVPIVFLTYLNIVFKYGYDAFLKRCAELKVSGLVIPDLPYESRAEIVP 135

Query: 142 SIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI------------------- 182
             +K G++ I +          S     KI       +Y +                   
Sbjct: 136 FAEKYGIDIIPLITPT------SGHRIEKIAKSASGFIYVVSSVGITGERDEFFTGLKAL 189

Query: 183 ---KKENPDLFIGLNGGLEDMSQALKILPSVDGVMIGRAAY 220
               K   D+   +  G+    QA  +    DGV+IG A  
Sbjct: 190 VAEIKRYTDVPTAIGFGIHTPQQAQTMASIADGVIIGSAIV 230


>gi|237730015|ref|ZP_04560496.1| 2,4-dienoyl-CoA reductase [Citrobacter sp. 30_2]
 gi|226908621|gb|EEH94539.1| 2,4-dienoyl-CoA reductase [Citrobacter sp. 30_2]
          Length = 672

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 27/211 (12%), Positives = 59/211 (27%), Gaps = 48/211 (22%)

Query: 42  GFSTQE--KPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLML 99
            F+  E      LQ+    I      A++  + GY+ + +                 L+ 
Sbjct: 126 RFTPHELTHDEVLQL----IEDFAHCAQLAREAGYDGVEV-----------MGSEGYLIN 170

Query: 100 N--------------------PDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VA 135
                                     + + A+ +       +  R+ + D +        
Sbjct: 171 EFLTLRTNQRDDQWGGEYANRMRFAVEVVRAVRQRAGNDFIIIFRLSMLDLVENGGTFDE 230

Query: 136 LRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLN 194
              L ++I+ +G     I+      +   P     +P   +  V  ++K       +  N
Sbjct: 231 TVQLAQAIEAAGAT--IINTGIGWHEARIPTIATPVPRGAFSWVTRKLKGHVAIPLVTTN 288

Query: 195 GGLEDMSQALKILPSVDGVMIGRAAYKNSAM 225
             + D   A  IL   D  M+   +     +
Sbjct: 289 R-INDPQVADDILARGDADMV---SMARPFL 315


>gi|157377195|ref|YP_001475795.1| N-ethylmaleimide reductase, putative [Shewanella sediminis HAW-EB3]
 gi|157319569|gb|ABV38667.1| N-ethylmaleimide reductase, putative [Shewanella sediminis HAW-EB3]
          Length = 367

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 32/181 (17%), Positives = 64/181 (35%), Gaps = 27/181 (14%)

Query: 61  KLVEAAKIVEDFGYNEINLNVGCPSARVHEG-----------SFGACLMLNPDIVGDCIA 109
              +AAK   D G++ + ++ G  +  + +            ++G         + + + 
Sbjct: 161 DFSQAAKNAIDVGFDGVEIHGG--NGYLIDQFLRTNSNHRSDAYGGSPEKRIRFLLEIVE 218

Query: 110 AMCKALSI-PVTVKCRIGVD--DQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPK 166
           A+   + +  V V+    V   D      +  ++ + K+ G  GI           LS  
Sbjct: 219 AVSAKIGVDKVGVRLAPFVTFKDMGCPEIVETILLAAKQLGELGI-------GYMHLSEA 271

Query: 167 DNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
           D    P +      E+++      I    G  D+ +A +I+     D V  GRA   N  
Sbjct: 272 DWDDAPQIPESFRIELREVFKGTIIVA--GRYDVERASEIIDQGYADLVAFGRAFIANPD 329

Query: 225 M 225
           +
Sbjct: 330 L 330


>gi|157372542|ref|YP_001480531.1| NADH:flavin oxidoreductase/NADH oxidase [Serratia proteamaculans
           568]
 gi|157324306|gb|ABV43403.1| NADH:flavin oxidoreductase/NADH oxidase [Serratia proteamaculans
           568]
          Length = 673

 Score = 35.6 bits (81), Expect = 9.6,   Method: Composition-based stats.
 Identities = 18/129 (13%), Positives = 47/129 (36%), Gaps = 15/129 (11%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIG----VDDQIPAVALRNLVKSIKKSGVNGIWIHARKAI 159
             + + A+ +A+     +  R+     V++      +  L  +++++G     I+     
Sbjct: 196 AVEIVRAVRQAVGSDFILIYRLSMLDLVEEGSSWQEIEQLALAVEQAGAT--IINTGIGW 253

Query: 160 LKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV--MIG 216
            +   P     +P   +  V  ++  +     I  N  + D + A ++L   DG   M+ 
Sbjct: 254 HEARIPTIATMVPRAGFSWVTRKLMGKVRIPLITTNR-INDPAVAEQVL--ADGCADMV- 309

Query: 217 RAAYKNSAM 225
             +     +
Sbjct: 310 --SMARPFL 316


>gi|269838240|ref|YP_003320468.1| pyridoxine biosynthesis protein [Sphaerobacter thermophilus DSM
           20745]
 gi|269787503|gb|ACZ39646.1| pyridoxine biosynthesis protein [Sphaerobacter thermophilus DSM
           20745]
          Length = 294

 Score = 35.6 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 15/86 (17%)

Query: 66  AKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
           A+I E+ G   +      P+        G   M +PD++     A+ +A+SIPV  K RI
Sbjct: 31  ARIAEEAGARAVMALERVPAD--IRREGGVARMSDPDLIL----AIKEAVSIPVMAKARI 84

Query: 126 GVDDQIPAVALRNLVKSIKKSGVNGI 151
           G   +          + ++  G++ I
Sbjct: 85  GHTAE---------AQILEALGIDFI 101


>gi|218696785|ref|YP_002404452.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           55989]
 gi|331669895|ref|ZP_08370740.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA271]
 gi|331679156|ref|ZP_08379828.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli H591]
 gi|218353517|emb|CAU99646.1| 2,4-dienoyl-CoA reductase, NADH and FMN-linked [Escherichia coli
           55989]
 gi|323173671|gb|EFZ59300.1| 2,4-dienoyl-CoA reductase [Escherichia coli LT-68]
 gi|331062808|gb|EGI34722.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli TA271]
 gi|331073221|gb|EGI44544.1| 2,4-dienoyl-CoA reductase (NADPH) [Escherichia coli H591]
          Length = 672

 Score = 35.6 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 22/191 (11%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + +  + + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRTVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|254302919|ref|ZP_04970277.1| IMP dehydrogenase [Fusobacterium nucleatum subsp. polymorphum ATCC
           10953]
 gi|148323111|gb|EDK88361.1| IMP dehydrogenase [Fusobacterium nucleatum subsp. polymorphum ATCC
           10953]
          Length = 488

 Score = 35.6 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 14/78 (17%)

Query: 140 VKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLED 199
           V ++ K+GV+ + + +     +G+             +++ EIKK  PDL I   G +  
Sbjct: 235 VSALVKAGVDIVTVDSAHGHSQGVI------------NMIKEIKKNFPDLDIIG-GNIVT 281

Query: 200 MSQALKILP-SVDGVMIG 216
              A +++   V  V +G
Sbjct: 282 AEAAKELIEAGVSAVKVG 299


>gi|56698408|ref|YP_168781.1| 2,4-dienoyl-CoA reductase [Ruegeria pomeroyi DSS-3]
 gi|56680145|gb|AAV96811.1| 2,4-dienoyl-CoA reductase [Ruegeria pomeroyi DSS-3]
          Length = 675

 Score = 35.6 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 20/124 (16%), Positives = 43/124 (34%), Gaps = 10/124 (8%)

Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKAILK 161
           + +    +A+     +  R+ + D +P       +  L K I+K+G     I+      +
Sbjct: 197 EVVRRTREAVGTDFIIIYRLSMIDLVPNGSTFDEVVQLAKEIEKAGAT--IINTGIGWHE 254

Query: 162 GLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKIL-PSV-DGVMIGRA 218
              P     +P   +  V  ++  +     I  N  +     A ++L     D V + R 
Sbjct: 255 ARIPTIATSVPRAAFAWVTKKLMGQVSIPVITSNR-INTPEVAEEVLATGCADMVSMARP 313

Query: 219 AYKN 222
              +
Sbjct: 314 MLAD 317


>gi|157159338|ref|YP_001464543.1| 2,4-dienoyl-CoA reductase [Escherichia coli E24377A]
 gi|157081368|gb|ABV21076.1| 2,4-dienoyl-CoA reductase [Escherichia coli E24377A]
          Length = 672

 Score = 35.6 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 22/191 (11%), Positives = 53/191 (27%), Gaps = 42/191 (21%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLM-------------------LN 100
                 A++  + GY+ + +                 L+                    N
Sbjct: 142 DDFAHCAQLAREAGYDGVEV-----------MGSEGYLINEFLTLRTNQRSDQWGGDYRN 190

Query: 101 PDIVG-DCIAAMCKALSIPVTVKCRIGVDDQI----PAVALRNLVKSIKKSGVNGIWIHA 155
                 + +  + + +     +  R+ + D +           L ++I+ +G     I+ 
Sbjct: 191 RMRFAVEVVRTVRERVGNDFIIIYRLSMLDLVEGGGTFAETVELAQAIEAAGAT--IINT 248

Query: 156 RKAILKGLSPKDNRKIPNLDYDIV-YEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVM 214
                +   P     +P   +  V  ++K       +  N  + D   A  IL   D  M
Sbjct: 249 GIGWHEARIPTIATPVPRGAFTWVTRKLKGHVSLPLVTTNR-INDPQVADDILSRGDADM 307

Query: 215 IGRAAYKNSAM 225
           +   +     +
Sbjct: 308 V---SMARPFL 315


>gi|158343612|gb|ABW35444.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343802|gb|ABW35615.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343892|gb|ABW35696.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343912|gb|ABW35714.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
 gi|158343922|gb|ABW35723.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase [Burkholderia cenocepacia]
          Length = 251

 Score = 35.6 bits (81), Expect = 9.9,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 20/93 (21%)

Query: 135 ALRNLVKSIKKSGVNGI--WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L K  +  GV  I      R  +L+G           ++ +   ++ +      I 
Sbjct: 149 EVIDLAKKFEDYGVESIVYTDIGRDGMLQG-----------INIEATVKLAQAVGIPVIA 197

Query: 193 LNG-----GLEDMSQALKILPSVDGVMIGRAAY 220
             G      +E + +  +    V+GV+ GRA Y
Sbjct: 198 SGGLSNLTDIESLCEVEEH--GVEGVICGRAIY 228


>gi|154482507|ref|ZP_02024955.1| hypothetical protein EUBVEN_00174 [Eubacterium ventriosum ATCC
           27560]
 gi|149736637|gb|EDM52523.1| hypothetical protein EUBVEN_00174 [Eubacterium ventriosum ATCC
           27560]
          Length = 253

 Score = 35.6 bits (81), Expect = 9.9,   Method: Composition-based stats.
 Identities = 15/98 (15%), Positives = 34/98 (34%), Gaps = 11/98 (11%)

Query: 138 NLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGL 197
            + K+  K+G + +      A                  D+V  + ++    F    GG+
Sbjct: 34  EVAKAYNKAGADELVFLDITASSDHRHTVT---------DLVRRVAEQVFIPFTVG-GGI 83

Query: 198 EDMSQALKIL-PSVDGVMIGRAAYKNSAMLTTVDEYFS 234
             +    ++L    D + I  +A  N  +++   + F 
Sbjct: 84  RTVDDFKELLREGADKISINSSAIMNPNLISEAADKFG 121


>gi|297161327|gb|ADI11039.1| oxidoreductase [Streptomyces bingchenggensis BCW-1]
          Length = 372

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 29/157 (18%), Positives = 53/157 (33%), Gaps = 20/157 (12%)

Query: 92  SFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPA------VALRNLVKSI 143
           ++G  L+       + +AA+  A+S   P+T +          A        L  L+  +
Sbjct: 197 AYGGNLVARSRFAAEVVAAVRGAVSPNFPITFRFSQWKMGAYDARLARSPQELEALLAPL 256

Query: 144 KKSGVNGIWIHARK---AILKGLS------PKDNRKIPNLDYDIVYEIKKENPDLFIGLN 194
             +GV+      R+       G         K     P +    +  +  E  D+  G  
Sbjct: 257 ADAGVDAFHCSTRRFHQPEFDGSDLNLAGWTKKLTGKPAISVGAIG-LDNEFTDVIQGRQ 315

Query: 195 GGLEDMSQALKILP--SVDGVMIGRAAYKNSAMLTTV 229
           G +  + + L  +     D   +GRA   +   LT V
Sbjct: 316 GEVTGIGELLDRMERNEFDLAAVGRALLGDPDWLTKV 352


>gi|302533408|ref|ZP_07285750.1| pyridoxine biosynthesis protein [Streptomyces sp. C]
 gi|302442303|gb|EFL14119.1| pyridoxine biosynthesis protein [Streptomyces sp. C]
          Length = 305

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 8/90 (8%)

Query: 38  KNILGFSTQEKPLALQIGGADISKLVEA--AKIVEDFGYNEINLNVGCPSARVHEGSFGA 95
           ++ +G S  ++ +A Q+ G  I  +V A  AKI ED G   +      P+        G 
Sbjct: 12  ESAIGTSRVKRGMAEQLKGGVIMDVVNAEQAKIAEDAGAVAVMALERVPAD--IRKDGGV 69

Query: 96  CLMLNPDIVGDCIAAMCKALSIPVTVKCRI 125
             M +P+++ + I A    +SIPV  K RI
Sbjct: 70  ARMSDPNMIEEIIEA----VSIPVMAKSRI 95


>gi|225573168|ref|ZP_03781923.1| hypothetical protein RUMHYD_01359 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039433|gb|EEG49679.1| hypothetical protein RUMHYD_01359 [Blautia hydrogenotrophica DSM
           10507]
          Length = 234

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 22/111 (19%), Positives = 39/111 (35%), Gaps = 16/111 (14%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVA-LRNLVKSIKKSGVNGIWIHARKAIL-K 161
           V D +AA  + + IPV    +       P +      V+++  +G     + A       
Sbjct: 48  VADILAA-RQLIDIPVIGLIKRHYAGYWPYITPTLREVEAVYLAGCEMAAVDATNQESPS 106

Query: 162 GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQAL-KILPSVD 211
           G+SP+            + EIKK  PDL +     +  + +         D
Sbjct: 107 GMSPE----------SYIREIKKRFPDLLLVA--DISTIEEGEVAEQAGAD 145


>gi|222102846|ref|YP_002539885.1| Biotin synthase-related enzyme [Agrobacterium vitis S4]
 gi|221739447|gb|ACM40180.1| Biotin synthase-related enzyme [Agrobacterium vitis S4]
          Length = 323

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 38/102 (37%), Gaps = 19/102 (18%)

Query: 54  IGGADISKLVEAAKIVEDF-GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
           +      +L E AK   +  G   + +  G P         GA ++       +   A+ 
Sbjct: 104 VAHKTPEQLAEVAKAAVELDGVKHMVMTTGTPK----GDDRGAAVL------AESARAIK 153

Query: 113 KALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
            A++IP+  +C    DD             +K +GV+ + +H
Sbjct: 154 AAVNIPIQAQCEPPEDDI--------WFSRMKDAGVDALGMH 187


>gi|213620579|ref|ZP_03373362.1| 2,4-dienoyl-CoA reductase [NADPH] (ec 1.3.1.34) (2,4-dienoyl
           coenzyme A reductase) [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 191

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 21/177 (11%), Positives = 53/177 (29%), Gaps = 31/177 (17%)

Query: 60  SKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGA--CLMLNPDI-------------- 103
                 A++  + GY+ + +        +    +     L    +               
Sbjct: 20  DDFAHCAQLAREAGYDGVEV--------MGSEGYLINEFLTRRTNHRDDEWGGDYTSRMR 71

Query: 104 -VGDCIAAMCKALSIPVTVKCRIGVDDQIPA----VALRNLVKSIKKSGVNGIWIHARKA 158
              + + A+ + +     +  R+ + D +           L ++I+ +G + I  +    
Sbjct: 72  FAVEVVRAVRQRVGNDFIIIYRLSMLDLVENGGTFDETVQLAQAIEAAGASLI--NTGIG 129

Query: 159 ILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGVMI 215
             +   P     +P   +  V    K +  + +     + D   A  IL   D  M+
Sbjct: 130 WHEARIPTIATPVPRGAFSWVTRKLKGHVSVPLIATNRINDPQVAETILTRGDADMV 186


>gi|207744504|ref|YP_002260896.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase protein [Ralstonia solanacearum IPO1609]
 gi|206595910|emb|CAQ62837.1| phosphoribosylformimino-5-aminoimidazole carboxamide ribotide
           isomerase protein [Ralstonia solanacearum IPO1609]
          Length = 233

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 20/103 (19%), Positives = 37/103 (35%), Gaps = 16/103 (15%)

Query: 135 ALRNLVKSIKKSGVNGIWIH--ARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIG 192
            + +L +  +  GV  I      R  +L+G           ++ D   ++ +      I 
Sbjct: 135 EVVDLARKYEDYGVEAIIYTDIGRDGMLQG-----------INIDATVKLAQSVSIPVIA 183

Query: 193 LNG--GLEDMSQALKI-LPSVDGVMIGRAAYKNSAMLTTVDEY 232
             G   L+D+     +    V+GV+ GRA Y          E+
Sbjct: 184 SGGLSNLKDIDHLCAVETEGVEGVICGRAIYSGDLNFREAQEH 226


>gi|189220396|ref|YP_001941036.1| dihydroorotate dehydrogenase [Methylacidiphilum infernorum V4]
 gi|189187254|gb|ACD84439.1| Dihydroorotate dehydrogenase [Methylacidiphilum infernorum V4]
          Length = 344

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 45/108 (41%), Gaps = 11/108 (10%)

Query: 49  PLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCI 108
           P+   +      + V+ AK++E+ G + + LN+   S    E      L        + +
Sbjct: 105 PIIASLNAQSPGQWVKYAKLIEEAGADALELNLY--SIPTQESLSSTEL---EQRYLEIV 159

Query: 109 AAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHAR 156
           +A  +++S+P+ VK      +     +       ++K+ V G+ +  R
Sbjct: 160 SACRQSVSLPIAVKLSPFFTNFFSFSS------RVEKTAVQGLVLFNR 201


>gi|169629190|ref|YP_001702839.1| dihydroorotate dehydrogenase 2 [Mycobacterium abscessus ATCC 19977]
 gi|226724740|sp|B1MPD4|PYRD_MYCA9 RecName: Full=Dihydroorotate dehydrogenase; AltName:
           Full=DHOdehase; Short=DHOD; Short=DHODase; AltName:
           Full=Dihydroorotate oxidase
 gi|169241157|emb|CAM62185.1| Probable dihydroorotate dehydrogenase [Mycobacterium abscessus]
          Length = 353

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 19/112 (16%), Positives = 41/112 (36%), Gaps = 9/112 (8%)

Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILK-- 161
           +   ++A+ +  + PV VK    + D      + +L   +  +G+        +A LK  
Sbjct: 195 LRKILSAVLEETTAPVLVKIAPDLSDAD-IDEIADLAVELGLAGIVATNTTISRAALKTT 253

Query: 162 -----GLSPKDNRKIPNLDYDIVYEIKKENPD-LFIGLNGGLEDMSQALKIL 207
                G        +     +++  + +   D L +   GG+ED   A   +
Sbjct: 254 GVEDLGAGGVSGPPVAARSLEVLRRLYRRVGDRLVLISVGGIEDADDAWARI 305


>gi|156742873|ref|YP_001433002.1| imidazole glycerol phosphate synthase subunit HisF [Roseiflexus
           castenholzii DSM 13941]
 gi|156234201|gb|ABU58984.1| imidazoleglycerol phosphate synthase, cyclase subunit [Roseiflexus
           castenholzii DSM 13941]
          Length = 258

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 22/132 (16%), Positives = 47/132 (35%), Gaps = 19/132 (14%)

Query: 42  GFSTQEKPLALQIG---GADIS----KLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFG 94
             +  ++P   Q+    G +        VE A+   D G  EI +N    S        G
Sbjct: 133 RVNAPDEPPRWQVFTHTGHNPRPTGLDAVEWARRGVDLGAGEIVIN----SMDADGVGSG 188

Query: 95  ACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIH 154
             L        D + A+  A+ +PV     +G  + + A  +     ++  + +     +
Sbjct: 189 YDL--------DLLRAIADAVGVPVIASGGVGSPEHMYAGLVEGCADAVLAASIFHFGAY 240

Query: 155 ARKAILKGLSPK 166
             + + + L+ +
Sbjct: 241 TIQDVKRYLAER 252


>gi|167038686|ref|YP_001661671.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X514]
 gi|300913754|ref|ZP_07131071.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X561]
 gi|307723229|ref|YP_003902980.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X513]
 gi|166852926|gb|ABY91335.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X514]
 gi|300890439|gb|EFK85584.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X561]
 gi|307580290|gb|ADN53689.1| NADH:flavin oxidoreductase/NADH oxidase [Thermoanaerobacter sp.
           X513]
          Length = 337

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 61/178 (34%), Gaps = 22/178 (12%)

Query: 62  LVEAAKIVEDFGYNEINLNVG---------CPSARVHEGSFGACLMLNPDIVGDCIAAMC 112
             EAAK     GY+ + ++            P +   +  +G  +      + + I  + 
Sbjct: 145 FGEAAKRANLAGYDIVEIHAAHGYLIHEFLSPLSNKRKDEYGNSIENRARFLIEVIDEVR 204

Query: 113 KAL--SIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDN 168
           K    + P+ V+      ++  I    +   +  IK   V+ I + +      GL   D 
Sbjct: 205 KNWPQNKPIFVRVSADDYMEGGINIDMMVEYINMIKDK-VDLIDVSSG-----GLLNVDI 258

Query: 169 RKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSA 224
              P         IKK   ++     G +     A +IL +   D V +GR   +N  
Sbjct: 259 NLYPGYQVKYAETIKKRC-NIKTSAVGLITTQELAEEILSNERADLVALGRELLRNPY 315


>gi|113954156|ref|YP_730184.1| inosine 5-monophosphate dehydrogenase [Synechococcus sp. CC9311]
 gi|113881507|gb|ABI46465.1| IMP dehydrogenase family protein [Synechococcus sp. CC9311]
          Length = 387

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 15/98 (15%), Positives = 32/98 (32%), Gaps = 18/98 (18%)

Query: 134 VALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGL 193
           VA     K+I ++G +  ++ A       + P+    +       +  + ++     +  
Sbjct: 140 VAALRFGKAIAEAGADLFFVQATVVSTDHIGPEGQETLN------LETLCRDMGVPVVIG 193

Query: 194 NGGLEDMSQALK-ILPSVDGVMIG---------RAAYK 221
           N        AL+ +     GVM+G         R    
Sbjct: 194 N--CVTYEVALQLMRAGAAGVMVGIGPGAACTSRGVLG 229


>gi|146295624|ref|YP_001179395.1| glutamate synthase (NADPH) [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409200|gb|ABP66204.1| glutamate synthase (NADPH) GltB2 subunit [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 502

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 28/126 (22%), Positives = 43/126 (34%), Gaps = 16/126 (12%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AI 159
           +   I A+ +A +   PV VK             +  +   I ++G + I I   +    
Sbjct: 289 LRQLIFALKEATNYTKPVGVKI-------AAVHNVAAIASGIARAGADFITIDGVRGGTG 341

Query: 160 LKGLSPKDNRKIP-NLDYDIVYEIKKENPD---LFIGLNGGLE-DMSQALKILPSVDGVM 214
              L  +DN  IP  L    V    +E      + I + G +         I    D V 
Sbjct: 342 AAPLRIRDNVGIPIELALAAVDSRLREEGIRNQVSIIVAGSIRNSADVVKAIALGADAVF 401

Query: 215 IGRAAY 220
           IG AA 
Sbjct: 402 IGTAAL 407


>gi|146295597|ref|YP_001179368.1| glutamate synthase (NADPH) [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409173|gb|ABP66177.1| glutamate synthase (NADPH) GltB2 subunit [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 502

 Score = 35.6 bits (81), Expect = 10.0,   Method: Composition-based stats.
 Identities = 28/126 (22%), Positives = 43/126 (34%), Gaps = 16/126 (12%)

Query: 104 VGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARK--AI 159
           +   I A+ +A +   PV VK             +  +   I ++G + I I   +    
Sbjct: 289 LRQLIFALKEATNYTKPVGVKI-------AAVHNVAAIASGIARAGADFITIDGVRGGTG 341

Query: 160 LKGLSPKDNRKIP-NLDYDIVYEIKKENPD---LFIGLNGGLE-DMSQALKILPSVDGVM 214
              L  +DN  IP  L    V    +E      + I + G +         I    D V 
Sbjct: 342 AAPLRIRDNVGIPIELALAAVDSRLREEGIRNQVSIIVAGSIRNSADVVKAIALGADAVF 401

Query: 215 IGRAAY 220
           IG AA 
Sbjct: 402 IGTAAL 407


  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
   0.316    0.159    0.475 

Lambda     K      H
   0.267   0.0484    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,402,615,246
Number of Sequences: 14124377
Number of extensions: 282229210
Number of successful extensions: 848205
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 8847
Number of HSP's successfully gapped in prelim test: 6828
Number of HSP's that attempted gapping in prelim test: 801798
Number of HSP's gapped (non-prelim): 17912
length of query: 322
length of database: 4,842,793,630
effective HSP length: 139
effective length of query: 183
effective length of database: 2,879,505,227
effective search space: 526949456541
effective search space used: 526949456541
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.3 bits)
S2: 82 (36.0 bits)